Locus 3648

Sequence ID 2R_DroMel_CAF1
Location 12,102,146 – 12,102,425
Length 279
Max. P 0.856369
window5939 window5940 window5941 window5942 window5943

overview

Window 9

Location 12,102,146 – 12,102,240
Length 94
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 81.82
Mean single sequence MFE -30.37
Consensus MFE -20.65
Energy contribution -21.57
Covariance contribution 0.92
Combinations/Pair 1.23
Mean z-score -1.41
Structure conservation index 0.68
SVM decision value -0.01
SVM RNA-class probability 0.529098
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12102146 94 + 20766785
UGCA--UUCUAUUUAGGCCAGGCCCACAAUGGUAUAGAAUAUCAGGGGUAGUACCAGGUUGUCCACCUGGUCGGUGAACGCCUCCACCAGAGCCGA
....--.........((((..((((....((((((...)))))).)))).(.(((((((.....))))))))((((........)))).).))).. ( -29.80)
>DroPse_CAF1 12031 96 + 1
AGGAGAUCAGAAUCAGGCCAGGCCAACGAGUAUAUAAAAGACUAGGGGCAGCACCAGAUUGUCCACCUGGUCGGUGAAGGCCUCCACCAGGGCUGA
............((((.((....................(((((((((((((....).))).)).)))))))((((........)))).)).)))) ( -29.30)
>DroEre_CAF1 6752 93 + 1
UGCA--UCC-AAUUAGGCCAGGCCCACAAUGGUAUAGAAUAUCAGGGGCAGCACCAGGUUGUCCACCUGGUCGGUGAAUGCUUCCAACAGAGCCGA
.(((--(.(-(....(((((((.......((((((...)))))).(((((((.....))))))).)))))))..)).))))............... ( -30.20)
>DroYak_CAF1 6835 93 + 1
UGGA--UAC-AAUUAGGCCAGGCCCACAAUGGUAUAGAAUAUCAGGGGCAGGACCAGGUUGUCCACCUGGUCGGUGAACGCCUCCACCAAAGCAGA
((((--...-.....((((((((((....((((((...)))))).)))).((((......))))..))))))(((....))))))).......... ( -33.00)
>DroAna_CAF1 2623 93 + 1
AUCA--ACG-CUUCAGGCUAGGCCAACGAUGAUGUAGAAUAUCAGGGGCAGCACCAGGUUGUCCACCUGGUCGGUGAAAGCCUCUACCAAAGCCGA
....--...-.....((((.(((((....((((((...)))))).(((((((.....)))))))...)))))(((....)))........)))).. ( -30.60)
>DroPer_CAF1 11777 96 + 1
AGGAGAUCAGAAUCAGGCCAGGCCAACGAGUAUAUAAAAGACUAGGGGCAGCACCAGAUUGUCCACCUGGUCGGUGAAGGCCUCCACCAGGGCUGA
............((((.((....................(((((((((((((....).))).)).)))))))((((........)))).)).)))) ( -29.30)
>consensus
AGCA__UCC_AAUCAGGCCAGGCCAACAAUGAUAUAGAAUAUCAGGGGCAGCACCAGGUUGUCCACCUGGUCGGUGAACGCCUCCACCAGAGCCGA
...............(((((((.......(((((.....))))).((((((.......)))))).)))))))((((........))))........ (-20.65 = -21.57 +   0.92)

alignment

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secondary structure

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Window 0

Location 12,102,200 – 12,102,320
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.44
Mean single sequence MFE -49.80
Consensus MFE -29.11
Energy contribution -28.59
Covariance contribution -0.52
Combinations/Pair 1.41
Mean z-score -1.73
Structure conservation index 0.58
SVM decision value 0.20
SVM RNA-class probability 0.629404
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12102200 120 - 20766785
CCGUCUGGCUCCUGGAGAUUUCCGGCCUGGUGGCCAUGAGCCAGGCCAAGUGGUUCGCCACCAUUUUCGCAGCACUGAAUUCGGCUCUGGUGGAGGCGUUCACCGACCAGGUGGACAACC
..(((((((((..((......))((((....))))..))))))))).....((((.(((.((((.....(((..(((....)))..))))))).)))(((((((.....))))))))))) ( -53.50)
>DroVir_CAF1 3184 120 - 1
CCGUUUGGCUGCUGCAGCUGGGCGGAGUUCUGGUCAUGAGCCAGGCCAAAUGGUUCGCCACGCUGUUUGCGGCGCUCAACACGGCUUUGGUGGAGGCGUCUACCGAUCAGGUGGACAAUC
(((((..((((...))))..)))))....(((((.....)))))(((......(((((((.((((....))))(((......)))..))))))))))(((((((.....))))))).... ( -51.40)
>DroPse_CAF1 12087 120 - 1
CCGUCUGGCUGCUGGAGGCGACCGGUCUGCUGGCCAUGACACAGGCCAAGUGGUUCGCAACCAUUUUCGCAGCCAUCAACUCAGCCCUGGUGGAGGCCUUCACCGACCAGGUGGACAAUC
((..((((.((.(((((((....((.((((.((((........))))(((((((.....)))))))..)))))).....(((.((....)).)))))))))).)).))))..))...... ( -51.40)
>DroMoj_CAF1 3250 120 - 1
CCGUCGGGCUGCUGCAGCUGAGCGGCGUCCUUGUCAUGACCCAGGCGAAAUGGUUCGCCACGAUUUUUGCCACACUUAAUGCAGCUCUAGUUGAGGCACUUACCGACCAGGUGGACAAUC
..(((((..((((.(((((((((((.(((........))))).((((((((((....)))....)))))))............)))).))))).))))....)))))............. ( -41.20)
>DroAna_CAF1 2676 120 - 1
CCAUUUGGCUACUGGACGCGUUCGGUCUGGUGGCGAUGACCCAGGCCAAGUGGUUCGCCUCGGUCUUUGCCGCUUUGAACUCGGCUUUGGUAGAGGCUUUCACCGACCAGGUGGACAACC
((((((((((((..((((.((((((...((((((((.((((.((((..........)))).)))).)))))))))))))).))..))..)))).((......))..))))))))...... ( -49.90)
>DroPer_CAF1 11833 120 - 1
CCGUCUGGCUGCUGGAGGCGACCGGUCUGCUGGCCAUGACACAGGCCAAGUGGUUCGCAACCAUUUUCGCAGCCAUCAACUCAGCCCUGGUGGAGGCCUUCACCGACCAGGUGGACAAUC
((..((((.((.(((((((....((.((((.((((........))))(((((((.....)))))))..)))))).....(((.((....)).)))))))))).)).))))..))...... ( -51.40)
>consensus
CCGUCUGGCUGCUGGAGGCGACCGGUCUGCUGGCCAUGACCCAGGCCAAGUGGUUCGCCACCAUUUUCGCAGCACUCAACUCAGCUCUGGUGGAGGCCUUCACCGACCAGGUGGACAAUC
((((((((..(((((......)))))....(((((........)))))..((((..(((.(((((...((.............))...))))).)))....)))).))))))))...... (-29.11 = -28.59 +  -0.52)

alignment

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secondary structure

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Window 1

Location 12,102,240 – 12,102,360
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.61
Mean single sequence MFE -48.24
Consensus MFE -25.72
Energy contribution -24.58
Covariance contribution -1.13
Combinations/Pair 1.46
Mean z-score -1.86
Structure conservation index 0.53
SVM decision value 0.32
SVM RNA-class probability 0.685884
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12102240 120 - 20766785
CUGGAGGGCACCAUUGCGUUCGUGGUGUCCAUUCUCAUGGCCGUCUGGCUCCUGGAGAUUUCCGGCCUGGUGGCCAUGAGCCAGGCCAAGUGGUUCGCCACCAUUUUCGCAGCACUGAAU
((((.(((((((((.......)))))))))...(((((((((..(.((((...((......)))))).)..)))))))))))))((.(((((((.....)))))))..)).......... ( -54.80)
>DroVir_CAF1 3224 120 - 1
CUGGAGGGCACCGUGGCCUUUGUGCUGUCCGUGCUGCUCUCCGUUUGGCUGCUGCAGCUGGGCGGAGUUCUGGUCAUGAGCCAGGCCAAAUGGUUCGCCACGCUGUUUGCGGCGCUCAAC
..(((.(((((.(......).))))).)))(((((((.(((((((..((((...))))..)))))))...((((...((((((.......))))))))))........)))))))..... ( -54.20)
>DroPse_CAF1 12127 120 - 1
CUGGAAGGCACUAUCGCCUUCGUGAUGUCCAUCCUUCUGUCCGUCUGGCUGCUGGAGGCGACCGGUCUGCUGGCCAUGACACAGGCCAAGUGGUUCGCAACCAUUUUCGCAGCCAUCAAC
...((((((......))))))..((((..((......))..))))((((((((((..(((((((.(....(((((........)))))).))).))))..))).....)))))))..... ( -46.90)
>DroMoj_CAF1 3290 120 - 1
CUGGAGGGCACUGUUGCCUUUGUGCUGUCCAUCCUGCUGUCCGUCGGGCUGCUGCAGCUGAGCGGCGUCCUUGUCAUGACCCAGGCGAAAUGGUUCGCCACGAUUUUUGCCACACUUAAU
.((((.(((((..........))))).))))....((.....(((((((.(((((......))))))))).............((((((....))))))..)))....)).......... ( -39.00)
>DroAna_CAF1 2716 120 - 1
UUGGAGGGCACCAUUGCCUUUGUGGCUUCCAUCUUGCUCUCCAUUUGGCUACUGGACGCGUUCGGUCUGGUGGCGAUGACCCAGGCCAAGUGGUUCGCCUCGGUCUUUGCCGCUUUGAAC
.(((((((((.....(((.....)))........)))))))))...(((.((..(((.(....))))..))(((((.((((.((((..........)))).)))).))))))))...... ( -47.62)
>DroPer_CAF1 11873 120 - 1
CUGGAAGGCACUAUCGCCUUCGUGAUGUCCAUCCUUCUGUCCGUCUGGCUGCUGGAGGCGACCGGUCUGCUGGCCAUGACACAGGCCAAGUGGUUCGCAACCAUUUUCGCAGCCAUCAAC
...((((((......))))))..((((..((......))..))))((((((((((..(((((((.(....(((((........)))))).))).))))..))).....)))))))..... ( -46.90)
>consensus
CUGGAGGGCACCAUUGCCUUCGUGAUGUCCAUCCUGCUGUCCGUCUGGCUGCUGGAGGCGACCGGUCUGCUGGCCAUGACCCAGGCCAAGUGGUUCGCCACCAUUUUCGCAGCACUCAAC
...((((((......))))))((((...((((..................(((((......)))))....(((((........))))).)))).))))...................... (-25.72 = -24.58 +  -1.13)

alignment

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secondary structure

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Window 2

Location 12,102,280 – 12,102,397
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 82.45
Mean single sequence MFE -45.43
Consensus MFE -33.29
Energy contribution -35.35
Covariance contribution 2.06
Combinations/Pair 1.19
Mean z-score -2.47
Structure conservation index 0.73
SVM decision value 0.81
SVM RNA-class probability 0.856369
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12102280 117 - 20766785
UAACACGCGUGCCAUACUUCUAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCGUUCGUGGUGUCCAUUCUCAUGGCCGUCUGGCUCCUGGAGAUUUCCGGCCUGGUGGCCAUGAG
..................(((((((((.....))).))))))(((((((((.......)))))))))...(((((((((..(.((((...((......)))))).)..))))))))) ( -50.80)
>DroSec_CAF1 6514 117 - 1
UAAUACAUGUGUCAUACUUCUAGGAUCUUCCCGCUCCCUGGAGGGCACCAUUGCGUUCGUGGUGUCCAUUCUCAUGGCCGUCUGGCUGCUGGCGAUUUCCGGCCUGGUGGCCAUGAG
..................((((((............))))))(((((((((.......)))))))))...((((((((((.(..(..(((((......))))))..))))))))))) ( -47.40)
>DroSim_CAF1 6479 117 - 1
UAACACAUGUGUCAUACUUCUAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCGUUCGUGGUGUCCAUUCUCAUGGCCGCCUGGCUGCUGGAGAUUUCCGGCCUGGUGGCCAUGAG
..(((....)))......(((((((((.....))).))))))(((((((((.......)))))))))...((((((((((((.((((...((......)))))).)))))))))))) ( -55.70)
>DroEre_CAF1 6885 117 - 1
UAAUACAUGUGUCAUACCCUUAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCUUUCGUCGUCUCCAUUCUAACAGCCGUCUGGCUGCUGGAGGCUACCGGCUUGGUGGCCAUGAG
.....((((.(((...(((((.(((((.....)))))...))))).((((..(((...((.(((((((......(((((....))))).))))))).)).))).))))))))))).. ( -45.30)
>DroYak_CAF1 6968 117 - 1
GAAUACAUGUGUCGUACUUUCAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCGUUCGUCGUGUCCAUUCUUAUAGCCGUCUGGCUGCUGGAGACCACCGGCUUGGUGGCCAUGAG
(((..((.(((..((.(((((((((((.....))).))))))))))..)))))..))).(((((.(((((.....((((....))))(((((......)))))..))))).))))). ( -40.20)
>DroPer_CAF1 11913 108 - 1
---------UUCAACUCUUGCAGAUUCCUCACGUUCCCUGGAAGGCACUAUCGCCUUCGUGAUGUCCAUCCUUCUGUCCGUCUGGCUGCUGGAGGCGACCGGUCUGCUGGCCAUGAC
---------.((..((((.((((...((..(((..(...(((.((.((.(((((....))))))))).)))....)..)))..)))))).))))..))..((((....))))..... ( -33.20)
>consensus
UAAUACAUGUGUCAUACUUCUAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCGUUCGUGGUGUCCAUUCUCAUGGCCGUCUGGCUGCUGGAGACUACCGGCCUGGUGGCCAUGAG
..................(((((((((.....))).))))))(((((((((.......)))))))))...((((((((((((.((((...((......)))))).)))))))))))) (-33.29 = -35.35 +   2.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,102,320 – 12,102,425
Length 105
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 78.24
Mean single sequence MFE -24.52
Consensus MFE -16.19
Energy contribution -16.88
Covariance contribution 0.70
Combinations/Pair 1.22
Mean z-score -1.34
Structure conservation index 0.66
SVM decision value 0.26
SVM RNA-class probability 0.656736
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12102320 105 - 20766785
GUUCAUUCGCAUA--UAUAAGAUUCUAUUUUAACACGCGUGCCAU-ACUUCUAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCGUUCGUGGUGUCCAUUCUCAUGG
.......(((...--..((((((...))))))....)))..((((-...(((((((((.....))).))))))(((((((((.......)))))))))......)))) ( -28.30)
>DroSec_CAF1 6554 105 - 1
GUUCAUUCGCAUA--UAUAAGAUUCUAUUUUAAUACAUGUGUCAU-ACUUCUAGGAUCUUCCCGCUCCCUGGAGGGCACCAUUGCGUUCGUGGUGUCCAUUCUCAUGG
((.....(((((.--(((.(((......))).))).)))))....-)).((((((............))))))(((((((((.......))))))))).......... ( -25.60)
>DroSim_CAF1 6519 105 - 1
GUUCAUUCGCAUU--UAUAAGUUUCUAUGUUAACACAUGUGUCAU-ACUUCUAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCGUUCGUGGUGUCCAUUCUCAUGG
.............--.....(((........))).((((.(....-...(((((((((.....))).))))))(((((((((.......)))))))))...).)))). ( -27.50)
>DroEre_CAF1 6925 105 - 1
GUUCAUCCGCAUA--UAUAAGAUUCUAUUUUAAUACAUGUGUCAU-ACCCUUAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCUUUCGUCGUCUCCAUUCUAACAG
.......(((((.--(((.(((......))).))).)))))....-.(((((.(((((.....)))))...)))))................................ ( -18.20)
>DroYak_CAF1 7008 107 - 1
GUUCAUCCGAAUAUUUAUAAGAUUCCAUUCGAAUACAUGUGUCGU-ACUUUCAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCGUUCGUCGUGUCCAUUCUUAUAG
((((....))))...(((((((...(((.((((..((.(((..((-.(((((((((((.....))).))))))))))..)))))..))))..))).....))))))). ( -27.30)
>DroAna_CAF1 2796 93 - 1
--------GCAU----UCAAGACCUUUUUUGAAUUC---UCUCUUCUCUUGCAGAAUCCUCCCGAAGUUUGGAGGGCACCAUUGCCUUUGUGGCUUCCAUCUUGCUCU
--------((((----((((((....)))))))...---........................((((((..(((((((....)))))))..)))))).....)))... ( -20.20)
>consensus
GUUCAUUCGCAUA__UAUAAGAUUCUAUUUUAAUACAUGUGUCAU_ACUUCUAGGAUCUUCCCGAUCCCUGGAGGGCACCAUUGCGUUCGUGGUGUCCAUUCUCAUGG
.................................................(((((((((.....))).))))))(((((((((.......))))))))).......... (-16.19 = -16.88 +   0.70)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:53 2006