Locus 6577

Sequence ID 3R_DroMel_CAF1
Location 17,319,086 – 17,319,304
Length 218
Max. P 0.999149
window10700 window10701 window10702 window10703 window10704

overview

Window 0

Location 17,319,086 – 17,319,202
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.64
Mean single sequence MFE -19.70
Consensus MFE -16.37
Energy contribution -17.17
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.46
Structure conservation index 0.83
SVM decision value 2.17
SVM RNA-class probability 0.989586
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17319086 116 + 27905053
AAACUUGUUUAUGAUUUGCUUGAAGAAAUAAACACAUUUUAAUUAACAUUUAAAAUGCAUUUUAAGCAAAAAGCUUUUAAGAAA-CGGCGCCAUAACAAUAAUCAUAAC---AGCACAAA
....(((((.(((((((((((((((.........((((((((.......))))))))..)))))))))))..(((.((....))-.))).............)))))))---))...... ( -18.00)
>DroSim_CAF1 606 116 + 1
AAACUUGUUAAUGAUUUGCUUGAAGAAAUAAACACAUUUUAAUUAACAUUUAAAAUGCGUUUUAAGCAAAAAGCUUUUAAGAAA-CGGCGCCAUAACAAUAAUCAUAAC---AGCACAAA
....((((((.(((((((((((((.......((.((((((((.......)))))))).))))))))))))..(((.((....))-.))).............)))))))---))...... ( -20.71)
>DroEre_CAF1 537 120 + 1
AAACUUGUUAAUGAUCUGCUCGAAGAAAUAAACACAUUUUAAUUAACAUUUAAAAUGCGUUUUAAGCAAAAAGCUUUUAAGAAAUCGGCGCCAUAACAAUAAUCAUAACAAAAGCACAAA
....((((((.((((..((.(((......((((.((((((((.......)))))))).)))).((((.....))))........)))))(......)....))))))))))......... ( -18.70)
>DroYak_CAF1 467 120 + 1
AAACUUGUUAAUGAUUUGCUUGAAGAAAUAAACACAUUUUAAUUAACAUUUAAAAUGCGUUUUAAGCAAAAAGCUUUUAAGAAAUCGGCGCCAUAACAAUAAUCAUAACAAAAGCACAAA
....((((((.(((((((((((((.......((.((((((((.......)))))))).))))))))))))..(((...........))).............)))))))))......... ( -20.71)
>DroAna_CAF1 1290 119 + 1
AAACUUGUUAAUGAUUUGCUUUAAGAAAUAAACACAUUUUAAUUAACAUUUAAAAUGCGUUUUAAGCAAAAAGCUUUUAAGAAA-CGGCGCCAUAACAAUAAUCAUAAUAAAAGCACAAG
...(((((......(((((((........((((.((((((((.......)))))))).)))).)))))))..(((((((.....-.......................)))))))))))) ( -20.39)
>consensus
AAACUUGUUAAUGAUUUGCUUGAAGAAAUAAACACAUUUUAAUUAACAUUUAAAAUGCGUUUUAAGCAAAAAGCUUUUAAGAAA_CGGCGCCAUAACAAUAAUCAUAACAAAAGCACAAA
....(((((.(((.((((((((((.......((.((((((((.......)))))))).))))))))))))..(((...........)))..))))))))..................... (-16.37 = -17.17 +   0.80)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,319,086 – 17,319,202
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.64
Mean single sequence MFE -24.76
Consensus MFE -22.58
Energy contribution -22.46
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.28
Structure conservation index 0.91
SVM decision value 3.40
SVM RNA-class probability 0.999149
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17319086 116 - 27905053
UUUGUGCU---GUUAUGAUUAUUGUUAUGGCGCCG-UUUCUUAAAAGCUUUUUGCUUAAAAUGCAUUUUAAAUGUUAAUUAAAAUGUGUUUAUUUCUUCAAGCAAAUCAUAAACAAGUUU
.....(((---.((((((((..((((.(((.....-........((((.....)))).(((((((((((((.......)))))))))))))......)))))))))))))))...))).. ( -21.70)
>DroSim_CAF1 606 116 - 1
UUUGUGCU---GUUAUGAUUAUUGUUAUGGCGCCG-UUUCUUAAAAGCUUUUUGCUUAAAACGCAUUUUAAAUGUUAAUUAAAAUGUGUUUAUUUCUUCAAGCAAAUCAUUAACAAGUUU
(((((((.---((((((((....)))))))))).(-(((.....((((.....)))).(((((((((((((.......)))))))))))))........)))).........)))))... ( -24.10)
>DroEre_CAF1 537 120 - 1
UUUGUGCUUUUGUUAUGAUUAUUGUUAUGGCGCCGAUUUCUUAAAAGCUUUUUGCUUAAAACGCAUUUUAAAUGUUAAUUAAAAUGUGUUUAUUUCUUCGAGCAGAUCAUUAACAAGUUU
........((((((((((((...((....))(((((........((((.....)))).(((((((((((((.......)))))))))))))......))).)).))))).)))))))... ( -27.20)
>DroYak_CAF1 467 120 - 1
UUUGUGCUUUUGUUAUGAUUAUUGUUAUGGCGCCGAUUUCUUAAAAGCUUUUUGCUUAAAACGCAUUUUAAAUGUUAAUUAAAAUGUGUUUAUUUCUUCAAGCAAAUCAUUAACAAGUUU
(((((......((((((((....))))))))...((((((((..((((.....)))).(((((((((((((.......)))))))))))))........))).)))))....)))))... ( -26.50)
>DroAna_CAF1 1290 119 - 1
CUUGUGCUUUUAUUAUGAUUAUUGUUAUGGCGCCG-UUUCUUAAAAGCUUUUUGCUUAAAACGCAUUUUAAAUGUUAAUUAAAAUGUGUUUAUUUCUUAAAGCAAAUCAUUAACAAGUUU
(((((((((((((((((((....))))))).....-.....)))))))..(((((((.(((((((((((((.......)))))))))))))........)))))))......)))))... ( -24.30)
>consensus
UUUGUGCUUUUGUUAUGAUUAUUGUUAUGGCGCCG_UUUCUUAAAAGCUUUUUGCUUAAAACGCAUUUUAAAUGUUAAUUAAAAUGUGUUUAUUUCUUCAAGCAAAUCAUUAACAAGUUU
(((((......((((((((....))))))))((...........((((.....)))).(((((((((((((.......)))))))))))))..........)).........)))))... (-22.58 = -22.46 +  -0.12)

alignment

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secondary structure

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Window 2

Location 17,319,126 – 17,319,240
Length 114
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 96.08
Mean single sequence MFE -24.93
Consensus MFE -22.38
Energy contribution -22.13
Covariance contribution -0.25
Combinations/Pair 1.09
Mean z-score -1.76
Structure conservation index 0.90
SVM decision value 1.53
SVM RNA-class probability 0.961867
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17319126 114 - 27905053
GCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGUUUUGUGCU---GUUAUGAUUAUUGUUAUGGCGCCG-UUUCUUAAAAGCUUUUUGCUUAAAAUGCAUUUUAAAUGUUAAUU
(((((((..((((....))))..)))))))(((((((....((((.---((((((((....))))))))....-........((((.....)))).....))))..)))).))).... ( -27.10)
>DroPse_CAF1 2951 116 - 1
-CUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGUUUUGUGAUUUUGUUAUGAUUAUUGUUAUGGCGCCG-UUUCUUAAAAGCUUUUUGCUUAAAACGUAUUUUAAAUGCUAAUU
-((((((..((((....))))..)))))).......(((((........((((((((....))))))))....-........((((.....)))))))))((((.....))))..... ( -20.00)
>DroSim_CAF1 646 114 - 1
GCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGUUUUGUGCU---GUUAUGAUUAUUGUUAUGGCGCCG-UUUCUUAAAAGCUUUUUGCUUAAAACGCAUUUUAAAUGUUAAUU
(((((((..((((....))))..)))))))(((((((....((((.---((((((((....))))))))...(-(((.....((((.....)))).))))))))..)))).))).... ( -27.50)
>DroEre_CAF1 577 118 - 1
GCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGUUUUGUGCUUUUGUUAUGAUUAUUGUUAUGGCGCCGAUUUCUUAAAAGCUUUUUGCUUAAAACGCAUUUUAAAUGUUAAUU
(((((((..((((....))))..)))))))(((((((...((((.((((((((((((....)))))))).............((((.....))))))))))))...)))).))).... ( -27.50)
>DroYak_CAF1 507 118 - 1
GCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGUUUUGUGCUUUUGUUAUGAUUAUUGUUAUGGCGCCGAUUUCUUAAAAGCUUUUUGCUUAAAACGCAUUUUAAAUGUUAAUU
(((((((..((((....))))..)))))))(((((((...((((.((((((((((((....)))))))).............((((.....))))))))))))...)))).))).... ( -27.50)
>DroPer_CAF1 2980 116 - 1
-CUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGUUUUGUGAUUUUGUUAUGAUUAUUGUUAUGGCGCCG-UUUCUUAAAAGCUUUUUGCUUAAAACGUAUUUUAAAUGCUAAUU
-((((((..((((....))))..)))))).......(((((........((((((((....))))))))....-........((((.....)))))))))((((.....))))..... ( -20.00)
>consensus
GCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGUUUUGUGCUUUUGUUAUGAUUAUUGUUAUGGCGCCG_UUUCUUAAAAGCUUUUUGCUUAAAACGCAUUUUAAAUGUUAAUU
(((((((..((((....))))..)))))))......(((((........((((((((....)))))))).............((((.....)))))))))((((.....))))..... (-22.38 = -22.13 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,319,202 – 17,319,304
Length 102
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 82.49
Mean single sequence MFE -31.70
Consensus MFE -22.27
Energy contribution -23.02
Covariance contribution 0.75
Combinations/Pair 1.17
Mean z-score -1.62
Structure conservation index 0.70
SVM decision value 0.15
SVM RNA-class probability 0.609528
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17319202 102 + 27905053
ACAAAGUCGCUCACAGAUCGAUGCAUCAAAAUAUGAGCGGCGAGGGGCACGGAACGUGGCUUUUCGUUGAUUCCAGGGGAGUCUCGACCCCAAGUUCCCCGA
.....((((((((......((....))......))))))))..((((.((((((..((((.....)))).)))).((((........))))..)).)))).. ( -33.50)
>DroSim_CAF1 722 96 + 1
ACAAAGUCGCUCACAGAUCGAUGCAUCAAAAUAUGAGCGGCGAGGGGCACGGCACGAAAAGCC------CCUCCAGGGGAGUCUCGACCCCCAGUUCUGCCU
.....((((((((......((....))......))))))))(((((((............)))------))))..((((.((....)))))).......... ( -34.80)
>DroEre_CAF1 657 94 + 1
ACAAAGUCGCUCACAGAUCGAUGCAUCAAAAUAUGAGCGGUGG--GGCACGGAACGAAAAGCC------ACUCCAGGGGAAUCUCGACCCCGAGUCCCUCAA
.......((((((......((....))......))))))(.((--(((..(((..(......)------..))).((((........))))..))))).).. ( -26.30)
>DroYak_CAF1 587 96 + 1
ACAAAGUCGCUCACAGAUCGAUGCAUCAAAAUAUGAGCGGUGGGGGGCAAAGAACGAAAUGCC------ACUCCAGGGGGAUCUCGACCCCGAGCUCCUCAA
......(((((((......((....))......)))))))(((((((((..........))))------.))))).(((((.((((....)))).))))).. ( -32.20)
>consensus
ACAAAGUCGCUCACAGAUCGAUGCAUCAAAAUAUGAGCGGCGAGGGGCACGGAACGAAAAGCC______ACUCCAGGGGAAUCUCGACCCCGAGUUCCUCAA
.....((((((((......((....))......))))))))(((((((..(((..................))).((((........))))..))))))).. (-22.27 = -23.02 +   0.75)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,319,202 – 17,319,304
Length 102
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 82.49
Mean single sequence MFE -35.39
Consensus MFE -24.46
Energy contribution -25.40
Covariance contribution 0.94
Combinations/Pair 1.25
Mean z-score -1.71
Structure conservation index 0.69
SVM decision value 0.28
SVM RNA-class probability 0.665190
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17319202 102 - 27905053
UCGGGGAACUUGGGGUCGAGACUCCCCUGGAAUCAACGAAAAGCCACGUUCCGUGCCCCUCGCCGCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGU
..((((.((..((((........)))).(((((..............))))))).))))....((((((((..((((....))))..))))))))....... ( -33.94)
>DroSim_CAF1 722 96 - 1
AGGCAGAACUGGGGGUCGAGACUCCCCUGGAGG------GGCUUUUCGUGCCGUGCCCCUCGCCGCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGU
.(((......((((((....))))))...((((------(((............))))))))))(((((((..((((....))))..)))))))........ ( -42.40)
>DroEre_CAF1 657 94 - 1
UUGAGGGACUCGGGGUCGAGAUUCCCCUGGAGU------GGCUUUUCGUUCCGUGCC--CCACCGCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGU
....(((.(.(((((.(((((..((.(....).------))..)))))))))).).)--))..((((((((..((((....))))..))))))))....... ( -34.20)
>DroYak_CAF1 587 96 - 1
UUGAGGAGCUCGGGGUCGAGAUCCCCCUGGAGU------GGCAUUUCGUUCUUUGCCCCCCACCGCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGU
.((.((.((((.(((..(....)..))).))))------((((..........)))))).)).((((((((..((((....))))..))))))))....... ( -31.00)
>consensus
UUGAGGAACUCGGGGUCGAGACUCCCCUGGAGU______GGCUUUUCGUUCCGUGCCCCCCACCGCUCAUAUUUUGAUGCAUCGAUCUGUGAGCGACUUUGU
..(((((((..((((........)))).(((((.......)))))..))))))).........((((((((..((((....))))..))))))))....... (-24.46 = -25.40 +   0.94)

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 12:24:55 2006