Locus 182

Sequence ID 2R_DroMel_CAF1
Location 1,438,237 – 1,438,676
Length 439
Max. P 0.984905
window408 window409 window410 window411 window412 window413 window414 window415 window416 window417

overview

Window 8

Location 1,438,237 – 1,438,357
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.75
Mean single sequence MFE -32.88
Consensus MFE -29.44
Energy contribution -29.88
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.53
Structure conservation index 0.90
SVM decision value 0.29
SVM RNA-class probability 0.669613
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438237 120 - 20766785
CGUUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCAUCAAAUUCGGGACGCGGGAUUAAGGCACAGCAAGCAGGGUUCAUUACAGAUAAAAUUAUCAUUAUGCGUACGGUAUAAAUUCA
.((((((((..(...(((((((..(((((....))).((......))))..)))))))...)..)))))))).((((........((((....)))).((((((.....)))))))))). ( -30.10)
>DroSec_CAF1 55610 120 - 1
CGCUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCAUAAAAUUGGGGACGCGGGAUUAAGGCACAGCAAGCAGGGUUCAUUACAGAUAAGAUUAUCAUUAUGCGUACGGUAUAAAUUCA
.((((((((..(...(((((((..((...(((((.......))))).))..)))))))...)..)))))))).((((........((((....)))).((((((.....)))))))))). ( -35.10)
>DroEre_CAF1 54780 120 - 1
CGUUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCAUAGGAUUCGGGACGCGGGAUUAAGGCACAGCAAGCAGGGUUCAUUAGAGAUACAAUUAUCAUUAUGAGUACGGUAUAAAUUCA
.((((((((..(...(((((((...((..(((((((...))))).))..)))))))))...)..)))))))).(..(((((....((((....))))...)))))..)............ ( -34.20)
>DroYak_CAF1 59798 120 - 1
CGUUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCGUGGGAUUCGGGACGCGGGAUUAAGGCUCAGCAAGCAGGGUUCGUUAGAGAUAAAAUUAUUAUUAUGAGUACGGUAUAAAUUCA
.((((((((..(...(((((((...((..(((((((...))))).))..)))))))))...)..)))))))).(..(((((....((((....))))...)))))..)............ ( -32.10)
>consensus
CGUUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCAUAAAAUUCGGGACGCGGGAUUAAGGCACAGCAAGCAGGGUUCAUUACAGAUAAAAUUAUCAUUAUGAGUACGGUAUAAAUUCA
.((((((((..(...(((((((...((..((((((.....)))).))..)))))))))...)..)))))))).(..(((((....((((....))))...)))))..)............ (-29.44 = -29.88 +   0.44) 

alignment

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secondary structure

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Window 9

Location 1,438,277 – 1,438,397
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -31.48
Consensus MFE -25.60
Energy contribution -26.60
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -1.94
Structure conservation index 0.81
SVM decision value 0.48
SVM RNA-class probability 0.751930
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438277 120 + 20766785
UGAACCCUGCUUGCUGUGCCUUAAUCCCGCGUCCCGAAUUUGAUGGAUUGGUCCGAUACGAGAUUGAUGUGCAGCAAACGAUUGCAUUUGCCAAAAUGAAAGCAAAUAUUUUAAAUACUU
.......(((((((((..(.((((((.((((..((((.((....)).))))..))...)).)))))).)..)))).........(((((....))))).)))))................ ( -29.00)
>DroSec_CAF1 55650 120 + 1
UGAACCCUGCUUGCUGUGCCUUAAUCCCGCGUCCCCAAUUUUAUGGAUUGGUCCGAUACGAGAUUGAUGUGCAGCAAGCGAUUGCAUUUGCCAAAAUGAAAUCAAAUAUUUUAAAUACUU
........((((((((..(.((((((.((..((.((((((.....))))))...))..)).)))))).)..))))))))((((.(((((....))))).))))................. ( -40.40)
>DroEre_CAF1 54820 119 + 1
UGAACCCUGCUUGCUGUGCCUUAAUCCCGCGUCCCGAAUCCUAUGGAUUGGUCCGAUACGAGAUUGAUGUGCAGCAAACG-UUGCAUUUGCCAAAACAAAAUCAAAUAUCUUAAAUACUU
(((.....(.((((((..(.((((((.((((..((.(((((...)))))))..))...)).)))))).)..)))))).)(-((((....))...)))....)))................ ( -29.40)
>DroYak_CAF1 59838 120 + 1
CGAACCCUGCUUGCUGAGCCUUAAUCCCGCGUCCCGAAUCCCACGGAUUGGUCCGAUACGAGAUUGAUGUGCAGCAAACGAUUGCAUUUGCCAAAACGAAUUCAAAUAUCUUAAAUACUU
.......((.((((((.((.((((((.((((..((.(((((...)))))))..))...)).)))))).)).)))))).)).(((.(((((......))))).)))............... ( -27.10)
>consensus
UGAACCCUGCUUGCUGUGCCUUAAUCCCGCGUCCCGAAUCCUAUGGAUUGGUCCGAUACGAGAUUGAUGUGCAGCAAACGAUUGCAUUUGCCAAAACGAAAUCAAAUAUCUUAAAUACUU
........(.((((((..(.((((((.((((..((.(((((...)))))))..))...)).)))))).)..)))))).)((((.(((((....))))).))))................. (-25.60 = -26.60 +   1.00) 

alignment

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secondary structure

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Window 0

Location 1,438,277 – 1,438,397
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -34.10
Consensus MFE -28.79
Energy contribution -28.60
Covariance contribution -0.19
Combinations/Pair 1.09
Mean z-score -1.78
Structure conservation index 0.84
SVM decision value 0.48
SVM RNA-class probability 0.751774
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438277 120 - 20766785
AAGUAUUUAAAAUAUUUGCUUUCAUUUUGGCAAAUGCAAUCGUUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCAUCAAAUUCGGGACGCGGGAUUAAGGCACAGCAAGCAGGGUUCA
............((((((((........)))))))).....((((((((..(...(((((((..(((((....))).((......))))..)))))))...)..))))))))........ ( -31.70)
>DroSec_CAF1 55650 120 - 1
AAGUAUUUAAAAUAUUUGAUUUCAUUUUGGCAAAUGCAAUCGCUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCAUAAAAUUGGGGACGCGGGAUUAAGGCACAGCAAGCAGGGUUCA
((((((.....))))))((((.(((((....))))).))))((((((((..(...(((((((..((...(((((.......))))).))..)))))))...)..))))))))........ ( -34.40)
>DroEre_CAF1 54820 119 - 1
AAGUAUUUAAGAUAUUUGAUUUUGUUUUGGCAAAUGCAA-CGUUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCAUAGGAUUCGGGACGCGGGAUUAAGGCACAGCAAGCAGGGUUCA
..((((((((((((........)))))))...)))))..-.((((((((..(...(((((((...((..(((((((...))))).))..)))))))))...)..))))))))........ ( -33.80)
>DroYak_CAF1 59838 120 - 1
AAGUAUUUAAGAUAUUUGAAUUCGUUUUGGCAAAUGCAAUCGUUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCGUGGGAUUCGGGACGCGGGAUUAAGGCUCAGCAAGCAGGGUUCG
(((((((...)))))))((((((......((....))....((((((((..(...(((((((...((..(((((((...))))).))..)))))))))...)..)))))))).)))))). ( -36.50)
>consensus
AAGUAUUUAAAAUAUUUGAUUUCAUUUUGGCAAAUGCAAUCGUUUGCUGCACAUCAAUCUCGUAUCGGACCAAUCCAUAAAAUUCGGGACGCGGGAUUAAGGCACAGCAAGCAGGGUUCA
..(((((((((((..........))))))...)))))....((((((((..(...(((((((...((..((((((.....)))).))..)))))))))...)..))))))))........ (-28.79 = -28.60 +  -0.19) 

alignment

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secondary structure

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Window 1

Location 1,438,357 – 1,438,477
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.14
Mean single sequence MFE -27.02
Consensus MFE -19.30
Energy contribution -19.42
Covariance contribution 0.13
Combinations/Pair 1.10
Mean z-score -2.03
Structure conservation index 0.71
SVM decision value 0.28
SVM RNA-class probability 0.667828
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438357 120 - 20766785
ACCACGCCGCAUCUGCGUUGUGUGCCGCACAUUAAAUGCAAUCCAGAAAAAUUGAAGAUAUAUUUACGCAAACUGCACUUAAGUAUUUAAAAUAUUUGCUUUCAUUUUGGCAAAUGCAAU
..((((((((....)))..)))))..((...((((((((.............((((......)))).((.....))......))))))))...(((((((........)))))))))... ( -23.90)
>DroSec_CAF1 55730 120 - 1
ACCACGCCGCAUCUGCGUUGUAUGCCGCACAUUAAAUGCAAGCCAGAAAAAUUGAAGAUAUAUUUACGCAAACUGCAUUUAAGUAUUUAAAAUAUUUGAUUUCAUUUUGGCAAAUGCAAU
.....((.(((((......).)))).))........((((.(((((((....(((((..........((.....))..((((((((.....))))))))))))))))))))...)))).. ( -24.80)
>DroEre_CAF1 54900 119 - 1
ACAAUGCCGCAUCCGCGUUGUGUGCGGCAAAUUAAAUGCAAGCCGGAAAAAUUGAAGAUAAAUUUACGCAAAGUGCAUUUAAGUAUUUAAGAUAUUUGAUUUUGUUUUGGCAAAUGCAA-
....(((((((..(.....)..))))))).......((((.(((((((...................((.....))..(((((((((...))))))))).....)))))))...)))).- ( -29.40)
>DroYak_CAF1 59918 120 - 1
ACCAUGCCGCAUCUACGAUGUGUGCCGCAAAUUAAAUGCAAGCCAGAAAAAUUUAAGAUGAAUUUACGCAAACUGAAUUUAAGUAUUUAAGAUAUUUGAAUUCGUUUUGGCAAAUGCAAU
.....((((((((...)))))).))...........((((.(((((((((((((.....)))))).........(((((((((((((...))))))))))))).)))))))...)))).. ( -30.00)
>consensus
ACCACGCCGCAUCUGCGUUGUGUGCCGCAAAUUAAAUGCAAGCCAGAAAAAUUGAAGAUAAAUUUACGCAAACUGCAUUUAAGUAUUUAAAAUAUUUGAUUUCAUUUUGGCAAAUGCAAU
.....((.(((((......).)))).))........((((.(((((((...................((.....))..(((((((((...))))))))).....)))))))...)))).. (-19.30 = -19.42 +   0.13) 

alignment

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secondary structure

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Window 2

Location 1,438,437 – 1,438,556
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.36
Mean single sequence MFE -29.73
Consensus MFE -22.82
Energy contribution -23.63
Covariance contribution 0.81
Combinations/Pair 1.07
Mean z-score -1.88
Structure conservation index 0.77
SVM decision value 0.34
SVM RNA-class probability 0.697294
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438437 119 - 20766785
ACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUUUUUUCAGUGAACAAAAAGGGAAAUAA-AAGUGCUGUUCAUAUACCACGCCGCAUCUGCGUUGUGUGCCGCACAUUAAAUGCA
..(((((((((((........(((((.....))))).........)))))..............-..((((.((....((((.((((.......)))).)))))).))))...)))))). ( -29.43)
>DroSec_CAF1 55810 119 - 1
ACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUUGUUUCAGUGAACAAUAAGGGAAAUAA-GAGUGCAGUUCAUAUACCACGCCGCAUCUGCGUUGUAUGCCGCACAUUAAAUGCA
..(((((((((((........(((((.....))))).........)))))..............-..((((.((....((((.((((.......)))).)))))).))))...)))))). ( -29.43)
>DroEre_CAF1 54979 117 - 1
ACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUU-UUUCAGUGAACAAAAAGGGCAAUAAAAAGUGCAG--CAUAUACAAUGCCGCAUCCGCGUUGUGUGCGGCAAAUUAAAUGCA
.(.(.((((((((........(((((.....)))))..-......)))))))).).)(((........))).(--(((.((...(((((((..(.....)..)))))))...)).)))). ( -34.89)
>DroYak_CAF1 59998 119 - 1
AUGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUU-UUUCAGUGAACAAAAAGAGAAAUAAAAAGAGCAGUUCAUAUACCAUGCCGCAUCUACGAUGUGUGCCGCAAAUUAAAUGCA
.((((((((((((........(((((.....)))))..-......)))))...................((.((......))...((((((((...)))))).)).)).....))))))) ( -25.19)
>consensus
ACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUU_UUUCAGUGAACAAAAAGGGAAAUAA_AAGUGCAGUUCAUAUACCACGCCGCAUCUGCGUUGUGUGCCGCAAAUUAAAUGCA
..(((((((((((........(((((.....))))).........))))).................((((....((((((..((((.......))))))))))..))))...)))))). (-22.82 = -23.63 +   0.81) 

alignment

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secondary structure

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dotplot

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Window 3

Location 1,438,477 – 1,438,596
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.99
Mean single sequence MFE -26.73
Consensus MFE -23.99
Energy contribution -24.05
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.90
SVM decision value 0.69
SVM RNA-class probability 0.823493
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438477 119 + 20766785
AUAUGAACAGCACUU-UUAUUUCCCUUUUUGUUCACUGAAAAAAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACGUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAU
.........(((...-.....(((((.((((((((.........(((((.....)))))........)))))))).....))).))(((((((....))))))).........))).... ( -26.33)
>DroSec_CAF1 55850 119 + 1
AUAUGAACUGCACUC-UUAUUUCCCUUAUUGUUCACUGAAACAAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACGUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAU
........((((...-......(((((((((((((.........(((((.....)))))........)))))).....))))).))(((((((....))))))).........))))... ( -26.23)
>DroEre_CAF1 55019 117 + 1
AUAUG--CUGCACUUUUUAUUGCCCUUUUUGUUCACUGAAA-AAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACGUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAU
.....--.((((.......(((((...((((((((......-..(((((.....)))))........))))))))......)))))(((((((....))))))).........))))... ( -29.89)
>DroYak_CAF1 60038 119 + 1
AUAUGAACUGCUCUUUUUAUUUCUCUUUUUGUUCACUGAAA-AAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACAUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAU
.......((((.((.............((((((((......-..(((((.....)))))........)))))))).....))))))(((((((....)))))))................ ( -24.46)
>consensus
AUAUGAACUGCACUU_UUAUUUCCCUUUUUGUUCACUGAAA_AAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACGUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAU
.........((...........((((.((((((((.........(((((.....)))))........)))))))).....))).).(((((((....)))))))..........)).... (-23.99 = -24.05 +   0.06) 

alignment

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secondary structure

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dotplot

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Window 4

Location 1,438,477 – 1,438,596
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.99
Mean single sequence MFE -32.94
Consensus MFE -29.83
Energy contribution -30.45
Covariance contribution 0.63
Combinations/Pair 1.06
Mean z-score -3.03
Structure conservation index 0.91
SVM decision value 1.99
SVM RNA-class probability 0.984905
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438477 119 - 20766785
AUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUUUUUUCAGUGAACAAAAAGGGAAAUAA-AAGUGCUGUUCAUAU
....((((((.((((((...(((((.(((.......))).)))))((((((((........(((((.....))))).........))))))))...))))))..-))))))......... ( -32.63)
>DroSec_CAF1 55850 119 - 1
AUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUUGUUUCAGUGAACAAUAAGGGAAAUAA-GAGUGCAGUUCAUAU
..((((((((.((((((...(((((.(((.......))).))))).(((((((........(((((.....))))).........)))))))....))))))..-))))))))....... ( -33.63)
>DroEre_CAF1 55019 117 - 1
AUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUU-UUUCAGUGAACAAAAAGGGCAAUAAAAAGUGCAG--CAUAU
..((((((((......(((((((....)))))))..((((.....((((((((........(((((.....)))))..-......))))))))..))))......))))))))--..... ( -36.19)
>DroYak_CAF1 60038 119 - 1
AUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUAUGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUU-UUUCAGUGAACAAAAAGAGAAAUAAAAAGAGCAGUUCAUAU
..((((.((((.(((((((((((....))))))............((((((((........(((((.....)))))..-......))))))))..))))).))))....))))....... ( -29.29)
>consensus
AUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUU_UUUCAGUGAACAAAAAGGGAAAUAA_AAGUGCAGUUCAUAU
..((((((((...((((...(((((.(((.......))).)))))((((((((........(((((.....))))).........))))))))....))))....))))))))....... (-29.83 = -30.45 +   0.63) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,438,516 – 1,438,636
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.05
Mean single sequence MFE -29.70
Consensus MFE -28.91
Energy contribution -28.98
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.61
Structure conservation index 0.97
SVM decision value 1.49
SVM RNA-class probability 0.958285
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438516 120 + 20766785
AAAAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACGUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGAAAUGCGUCAAUGUUUUGGCAACUGAACAAA
....(((((((((..(((......)))..)......((((.((((.(((((((....))))))).........(((....)))...........)))).))))))))))))......... ( -30.10)
>DroSec_CAF1 55889 120 + 1
ACAAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACGUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGGAAUGCGUCAAUGUUUUGGCAACUGAACAAA
.((.(((((((((..(((......)))..)......((((.((((.(((((((....))))))).........(((....)))...........)))).)))))))))))).))...... ( -31.80)
>DroEre_CAF1 55057 119 + 1
A-AAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACGUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGGAAUGCAUCAAUGUUUUGGCAACUGAACAAA
.-..(((((.....)))))......(((((............(((.(((((((....))))))).........)))...((((.((...)).)))))))))((((.(....).))))... ( -26.40)
>DroYak_CAF1 60078 119 + 1
A-AAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACAUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGGAAUGCGUCAAUGUUUUGGCAACUGAACAAA
.-..(((((((((..(((......)))..)......((((.((((.(((((((....))))))).........(((....)))...........)))).))))))))))))......... ( -30.50)
>consensus
A_AAUUGCCGGAUUGGCAAACAAAUGUUGAACAAAUACGUAGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGGAAUGCGUCAAUGUUUUGGCAACUGAACAAA
....(((((((((..(((......)))..)......((((.((((.(((((((....))))))).........(((....)))...........)))).))))))))))))......... (-28.91 = -28.98 +   0.06) 

alignment

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secondary structure

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dotplot

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Window 6

Location 1,438,516 – 1,438,636
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.05
Mean single sequence MFE -28.39
Consensus MFE -26.56
Energy contribution -26.37
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -2.11
Structure conservation index 0.94
SVM decision value 0.73
SVM RNA-class probability 0.834368
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438516 120 - 20766785
UUUGUUCAGUUGCCAAAACAUUGACGCAUUUCAUGAUUGCAUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUUUU
.......(((((((.......(((......))).(((((((...(((.........(((.(((((.(((.......))).))))).))).........))).)).))))).))))))).. ( -27.87)
>DroSec_CAF1 55889 120 - 1
UUUGUUCAGUUGCCAAAACAUUGACGCAUUCCAUGAUUGCAUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUUGU
......((((((((.......((........)).(((((((...(((.........(((.(((((.(((.......))).))))).))).........))).)).))))).)))))))). ( -29.47)
>DroEre_CAF1 55057 119 - 1
UUUGUUCAGUUGCCAAAACAUUGAUGCAUUCCAUGAUUGCAUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUU-U
.......(((((((........((((((.((...)).)))))).(((..(((....(((.(((((.(((.......))).))))).)))........)))..)))......)))))))-. ( -28.70)
>DroYak_CAF1 60078 119 - 1
UUUGUUCAGUUGCCAAAACAUUGACGCAUUCCAUGAUUGCAUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUAUGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUU-U
........((((.((((((((.((((((.((..(((.(((....))).)))......)).))))))(((....)))....)))).))))..))))......(((((.....)))))..-. ( -27.50)
>consensus
UUUGUUCAGUUGCCAAAACAUUGACGCAUUCCAUGAUUGCAUUUGCAUUUAAUUUUCGAUUGCGUUGGCAAUCGCCGCCUACGUAUUUGUUCAACAUUUGUUUGCCAAUCCGGCAAUU_U
.......(((((((.......((........)).(((((((...(((.........(((.(((((.(((.......))).))))).))).........))).)).))))).))))))).. (-26.56 = -26.37 +  -0.19) 

alignment

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secondary structure

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dotplot

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Window 7

Location 1,438,556 – 1,438,676
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -26.62
Consensus MFE -25.96
Energy contribution -25.40
Covariance contribution -0.56
Combinations/Pair 1.09
Mean z-score -2.63
Structure conservation index 0.98
SVM decision value 1.42
SVM RNA-class probability 0.952140
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1438556 120 + 20766785
AGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGAAAUGCGUCAAUGUUUUGGCAACUGAACAAAUGUAAUUUAGUAAAAUAAACUUUACAAAUGCGCAAACUAA
.((((.(((((((....))))))).........(((....)))...........))))..(((((.(....).)))))..(((.((((.(((((......)))))))))..)))...... ( -26.40)
>DroSec_CAF1 55929 120 + 1
AGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGGAAUGCGUCAAUGUUUUGGCAACUGAACAAAUGUAAUUUAGUAAAAUAAACUUUACAACUGCGCAAACUAA
..(((((((((((....)))))))...((((((((((.(((((.((...)).)))))...(((((.(....).)))))..))).)))))))................))))......... ( -26.80)
>DroEre_CAF1 55096 120 + 1
AGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGGAAUGCAUCAAUGUUUUGGCAACUGAACAAAUGUAAUUUAGUAAAAUAAACUUUACAAAUGCGCAAACUAA
..(((.(((((((....)))))))...((((((((((.(((((.((...)).)))))...(((((.(....).)))))..))).)))))))...................)))....... ( -26.70)
>DroYak_CAF1 60117 120 + 1
AGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGGAAUGCGUCAAUGUUUUGGCAACUGAACAAAUGUAAUUUAGUAAAAUAAACUUUACAAAUGUGCAAACUAA
.((((.(((((((....))))))).........(((....)))...........))))..(((((.(....).)))))..((((((((.(((((......))))))))).))))...... ( -26.60)
>consensus
AGGCGGCGAUUGCCAACGCAAUCGAAAAUUAAAUGCAAAUGCAAUCAUGGAAUGCGUCAAUGUUUUGGCAACUGAACAAAUGUAAUUUAGUAAAAUAAACUUUACAAAUGCGCAAACUAA
..(((.(((((((....))))))).........(((....)))....((((.(((((...(((((.(....).))))).))))).))))(((((......))))).....)))....... (-25.96 = -25.40 +  -0.56) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:33 2006