Locus 6977

Sequence ID X_DroMel_CAF1
Location 17,470,284 – 17,470,437
Length 153
Max. P 0.999519
window11394 window11395 window11396 window11397 window11398

overview

Window 4

Location 17,470,284 – 17,470,376
Length 92
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 69.20
Mean single sequence MFE -34.20
Consensus MFE -22.35
Energy contribution -22.18
Covariance contribution -0.16
Combinations/Pair 1.44
Mean z-score -2.82
Structure conservation index 0.65
SVM decision value 2.61
SVM RNA-class probability 0.995731
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17470284 92 + 22224390
UUGGU-----CAAU---AA-----ACAGAGGGUAUGCAGCGCCAGAAACCCAAGGGACCCGGCAAACCGGGUUCGCGU------UUCAAGCCGGGAUCCGGCACGUUC--AAA
.....-----....---..-----...(((.((.((.(((((..(.....)...((((((((....))))))))))))------).)).(((((...))))))).)))--... ( -31.90)
>DroSec_CAF1 428 93 + 1
UUGGU-----CAAAA--AA-----ACAGAGGGUAUGCAGCGCCAGAAACCCAAGGGACCCGGCAAACCGGGUCCGCGU------UUCAAGCCGGGUUCCGGCACGUUC--AAA
.....-----.....--..-----...(((.((.((.(((((..(.....)...((((((((....))))))))))))------).)).(((((...))))))).)))--... ( -34.80)
>DroSim_CAF1 53 95 + 1
UUGGU-----CAAAAAAAA-----ACAGAGGGUAUGCAGCGCCAGAAACCCAAGGGACCCGGCAAACCGGGUCCGCGU------UUCAAGCCGGGUUCCGGCACGUUC--AAA
.....-----.........-----...(((.((.((.(((((..(.....)...((((((((....))))))))))))------).)).(((((...))))))).)))--... ( -34.80)
>DroEre_CAF1 27 92 + 1
UCGAC-----CAAU---AA-----ACAAAGGGUAUGCAGCGCCAGAAACCCAAGGGACCCGGCAAAUCGGGUCCGCGU------UUCAAGCCGGGAUCUGGCAAGAGC--AAA
...((-----(...---..-----......))).(((...((((((..(((...((((((((....))))))))((..------.....)).))).))))))....))--).. ( -33.80)
>DroMoj_CAF1 2085 106 + 1
UUGCUUUUAACAAUUACAAAUAAAGUACGCGGUAUGCAAAAACAGAAGCCUCGAGGUCCUGGAAAACCAGGAUCGCGUGCGCCAUCCAAGCCGGGCGGCAGCC---AA--A--
..(((...................(((((((((.((......))...)))....((((((((....))))))))))))))(((..((.....))..)))))).---..--.-- ( -36.50)
>DroAna_CAF1 678 88 + 1
UUGAA-----CCGC---AU-----UAACAGGAUAUGCAGCGCCAGAAACCAAGGGGGCCGGGCAAACCCGGUCCAAGG------UUCAAA------UCCGGCAAGGGCUUCAA
.((((-----((((---((-----.........))))...(((.((((((....((((((((....))))))))..))------))....------)).)))...)).)))). ( -33.40)
>consensus
UUGGU_____CAAU___AA_____ACAGAGGGUAUGCAGCGCCAGAAACCCAAGGGACCCGGCAAACCGGGUCCGCGU______UUCAAGCCGGGAUCCGGCACGUUC__AAA
.............................((((.((......))...))))...((((((((....))))))))...............((((.....))))........... (-22.35 = -22.18 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,470,284 – 17,470,376
Length 92
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 69.20
Mean single sequence MFE -34.70
Consensus MFE -21.83
Energy contribution -22.25
Covariance contribution 0.42
Combinations/Pair 1.37
Mean z-score -2.23
Structure conservation index 0.63
SVM decision value 2.29
SVM RNA-class probability 0.991813
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17470284 92 - 22224390
UUU--GAACGUGCCGGAUCCCGGCUUGAA------ACGCGAACCCGGUUUGCCGGGUCCCUUGGGUUUCUGGCGCUGCAUACCCUCUGU-----UU---AUUG-----ACCAA
...--....((((((((.((((((.....------..))(.((((((....)))))).)..))))..))))))))..............-----..---....-----..... ( -31.60)
>DroSec_CAF1 428 93 - 1
UUU--GAACGUGCCGGAACCCGGCUUGAA------ACGCGGACCCGGUUUGCCGGGUCCCUUGGGUUUCUGGCGCUGCAUACCCUCUGU-----UU--UUUUG-----ACCAA
...--....(((((((((((((((.....------..))((((((((....))))))))..)))).)))))))))..............-----..--.....-----..... ( -39.70)
>DroSim_CAF1 53 95 - 1
UUU--GAACGUGCCGGAACCCGGCUUGAA------ACGCGGACCCGGUUUGCCGGGUCCCUUGGGUUUCUGGCGCUGCAUACCCUCUGU-----UUUUUUUUG-----ACCAA
...--....(((((((((((((((.....------..))((((((((....))))))))..)))).)))))))))..............-----.........-----..... ( -39.70)
>DroEre_CAF1 27 92 - 1
UUU--GCUCUUGCCAGAUCCCGGCUUGAA------ACGCGGACCCGAUUUGCCGGGUCCCUUGGGUUUCUGGCGCUGCAUACCCUUUGU-----UU---AUUG-----GUCGA
..(--((...(((((((.((((((.....------..))(((((((......)))))))..))))..)))))))..)))..........-----..---....-----..... ( -34.80)
>DroMoj_CAF1 2085 106 - 1
--U--UU---GGCUGCCGCCCGGCUUGGAUGGCGCACGCGAUCCUGGUUUUCCAGGACCUCGAGGCUUCUGUUUUUGCAUACCGCGUACUUUAUUUGUAAUUGUUAAAAGCAA
--.--..---.(((((((.((.....)).))))..(((((.((((((....))))))....(((((....))))).......))))).....................))).. ( -28.90)
>DroAna_CAF1 678 88 - 1
UUGAAGCCCUUGCCGGA------UUUGAA------CCUUGGACCGGGUUUGCCCGGCCCCCUUGGUUUCUGGCGCUGCAUAUCCUGUUA-----AU---GCGG-----UUCAA
.(((.......((((((------....((------((..((.(((((....)))))...))..))))))))))(((((((.........-----))---))))-----)))). ( -33.50)
>consensus
UUU__GAACGUGCCGGAACCCGGCUUGAA______ACGCGGACCCGGUUUGCCGGGUCCCUUGGGUUUCUGGCGCUGCAUACCCUCUGU_____UU___AUUG_____ACCAA
..........(((((((..((.((.............))((((((((....))))))))....))..)))))))....................................... (-21.83 = -22.25 +   0.42)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,470,307 – 17,470,409
Length 102
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 76.94
Mean single sequence MFE -44.88
Consensus MFE -30.08
Energy contribution -32.32
Covariance contribution 2.24
Combinations/Pair 1.19
Mean z-score -3.23
Structure conservation index 0.67
SVM decision value 3.68
SVM RNA-class probability 0.999519
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17470307 102 + 22224390
CAGCGCCAGAAACCCAAGGGACCCGGCAAACCGGGUUCGCGUUUCA---AGCCGGGAUCCGGCACGUUCAAAGGAGCUGGUGGUGGCCGGAAAAGCGGCGACAAC
((((.((.(((((.(...((((((((....))))))))).))))).---.(((((...))))).........)).))))...((.((((......)))).))... ( -45.60)
>DroSec_CAF1 452 102 + 1
CAGCGCCAGAAACCCAAGGGACCCGGCAAACCGGGUCCGCGUUUCA---AGCCGGGUUCCGGCACGUUCAAAGGAGCUGCUGGUGGGCGGAAAAGCGGCGACAAC
..(((((...........((((((((....))))))))((.((((.---.(((.(...((((((.((((....))))))))))).))).)))).)))))).)... ( -48.10)
>DroSim_CAF1 79 102 + 1
CAGCGCCAGAAACCCAAGGGACCCGGCAAACCGGGUCCGCGUUUCA---AGCCGGGUUCCGGCACGUUCAAAGGAGCUGCUGGUGGCCGGAAAAGCGGCGACAAC
(((((((.(((.(((...((((((((....))))))))((......---.)).)))))).)))..((((....)))).))))((.((((......)))).))... ( -51.00)
>DroEre_CAF1 50 102 + 1
CAGCGCCAGAAACCCAAGGGACCCGGCAAAUCGGGUCCGCGUUUCA---AGCCGGGAUCUGGCAAGAGCAAAGGAGCUCCUGGUGGCCGGAAGAGUGGCGACCAC
....((((((..(((...((((((((....))))))))((......---.)).))).))))))..((((......)))).((((.((((......)))).)))). ( -48.20)
>DroWil_CAF1 655 93 + 1
CAGAGGCAUAAACCAAAGCGUCCUGGU---CCUGGUGCUGGUCUUAGAAAGCCAAA---CGGCG---UAAAGGGACCGGCUGGC---AAGGACAAAUUCAACAAA
(((.(((............))))))((---(((.(((((((((((.....(((...---.))).---....)))))))))..))---.)))))............ ( -31.50)
>consensus
CAGCGCCAGAAACCCAAGGGACCCGGCAAACCGGGUCCGCGUUUCA___AGCCGGGAUCCGGCACGUUCAAAGGAGCUGCUGGUGGCCGGAAAAGCGGCGACAAC
((((.((.(((((.(...((((((((....))))))))).))))).....(((((...))))).........)).))))...((.((((......)))).))... (-30.08 = -32.32 +   2.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,470,307 – 17,470,409
Length 102
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 76.94
Mean single sequence MFE -41.13
Consensus MFE -27.20
Energy contribution -28.60
Covariance contribution 1.40
Combinations/Pair 1.21
Mean z-score -1.91
Structure conservation index 0.66
SVM decision value 1.13
SVM RNA-class probability 0.919356
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17470307 102 - 22224390
GUUGUCGCCGCUUUUCCGGCCACCACCAGCUCCUUUGAACGUGCCGGAUCCCGGCU---UGAAACGCGAACCCGGUUUGCCGGGUCCCUUGGGUUUCUGGCGCUG
((.((.((((......)))).)).))((((.((.........(((((...))))).---.(((((.(((((((((....))))))...))).))))).)).)))) ( -42.00)
>DroSec_CAF1 452 102 - 1
GUUGUCGCCGCUUUUCCGCCCACCAGCAGCUCCUUUGAACGUGCCGGAACCCGGCU---UGAAACGCGGACCCGGUUUGCCGGGUCCCUUGGGUUUCUGGCGCUG
(((((.(..((......))....).)))))..........(((((((((((((((.---......))((((((((....))))))))..)))).))))))))).. ( -43.90)
>DroSim_CAF1 79 102 - 1
GUUGUCGCCGCUUUUCCGGCCACCAGCAGCUCCUUUGAACGUGCCGGAACCCGGCU---UGAAACGCGGACCCGGUUUGCCGGGUCCCUUGGGUUUCUGGCGCUG
((((..((((......))))...)))).............(((((((((((((((.---......))((((((((....))))))))..)))).))))))))).. ( -48.70)
>DroEre_CAF1 50 102 - 1
GUGGUCGCCACUCUUCCGGCCACCAGGAGCUCCUUUGCUCUUGCCAGAUCCCGGCU---UGAAACGCGGACCCGAUUUGCCGGGUCCCUUGGGUUUCUGGCGCUG
(((((((.........))))))).((((((......))))))((((((.((((((.---......))(((((((......)))))))..))))..)))))).... ( -48.40)
>DroWil_CAF1 655 93 - 1
UUUGUUGAAUUUGUCCUU---GCCAGCCGGUCCCUUUA---CGCCG---UUUGGCUUUCUAAGACCAGCACCAGG---ACCAGGACGCUUUGGUUUAUGCCUCUG
............(((((.---(((.((.((((......---.(((.---...))).......)))).))....))---.).))))).....(((....))).... ( -22.64)
>consensus
GUUGUCGCCGCUUUUCCGGCCACCAGCAGCUCCUUUGAACGUGCCGGAACCCGGCU___UGAAACGCGGACCCGGUUUGCCGGGUCCCUUGGGUUUCUGGCGCUG
...((.(((........))).))...((((.((.........((((.....)))).....(((((.(((((((((....))))))))...).))))).)).)))) (-27.20 = -28.60 +   1.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,470,347 – 17,470,437
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 90.33
Mean single sequence MFE -35.08
Consensus MFE -26.66
Energy contribution -26.74
Covariance contribution 0.08
Combinations/Pair 1.17
Mean z-score -1.99
Structure conservation index 0.76
SVM decision value 0.73
SVM RNA-class probability 0.834891
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17470347 90 + 22224390
GUUUCAAGCCGGGAUCCGGCACGUUCAAAGGAGCUGGUGGUGGCCGGAAAAGCGGCGACAACAGCCAGAAGCGUCCGCGCCAGGAGAUCA
(((((..(((((...)))))..((((....))))((((.((.((((......)))).))....))))))))).(((......)))..... ( -34.20)
>DroSec_CAF1 492 90 + 1
GUUUCAAGCCGGGUUCCGGCACGUUCAAAGGAGCUGCUGGUGGGCGGAAAAGCGGCGACAACAGCCAAAAGCGUCCGCGCCAGGAGAUCA
(((((..(((((...)))))..((((....))))..(((((..(((((...(((((.......)))....)).))))))))))))))).. ( -34.70)
>DroSim_CAF1 119 90 + 1
GUUUCAAGCCGGGUUCCGGCACGUUCAAAGGAGCUGCUGGUGGCCGGAAAAGCGGCGACAACAGCCAAAAGCGUCCGCGCCAGGAGAUCA
(((((...((((.(.((((((.((((....)))))))))).).))))......((((...((.((.....))))...))))..))))).. ( -33.60)
>DroEre_CAF1 90 90 + 1
GUUUCAAGCCGGGAUCUGGCAAGAGCAAAGGAGCUCCUGGUGGCCGGAAGAGUGGCGACCACAACCAAAAGCGUCCGCGCCAGGAGCUUA
((((...(((((...)))))..))))....((((((((((((..((((.(..(((.........)))....).)))))))))))))))). ( -37.00)
>DroYak_CAF1 116 90 + 1
GUUUCAAGCCGGGCUCCGGCAAGAACAAAGGAGCUGCUGGUGGCCGAAAAAGUGGCGACAACAACCAGAAACGUCCGCGCCAGGAGCUCA
((((...(((((...)))))..))))....(((((.((((((((((......))))(((.............)))..)))))).))))). ( -35.92)
>consensus
GUUUCAAGCCGGGAUCCGGCACGUUCAAAGGAGCUGCUGGUGGCCGGAAAAGCGGCGACAACAGCCAAAAGCGUCCGCGCCAGGAGAUCA
.......(((((...)))))..........((.((.((((((..((((...(((((.......)))....)).)))))))))).)).)). (-26.66 = -26.74 +   0.08)

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 12:27:11 2006