Locus 1041

Sequence ID 3L_DroMel_CAF1
Location 3,079,229 – 3,079,397
Length 168
Max. P 0.904297
window1606 window1607 window1608 window1609 window1610

overview

Window 6

Location 3,079,229 – 3,079,342
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.36
Mean single sequence MFE -36.80
Consensus MFE -28.90
Energy contribution -28.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.18
Structure conservation index 0.79
SVM decision value 0.00
SVM RNA-class probability 0.535915
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3079229 113 - 23771897
CAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGGGAUUCGAGUGACCAAGCAGCAACUAA---UUCCUCG----
...((((((((.(((((((.(((.(((((....(((((.....)))))..((((.......))))....))))).))).))))))).)))....((......))..---.))))).---- ( -38.20)
>DroVir_CAF1 29204 115 - 1
CUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUGCAAACCGAGCGACUUAGCUGGCACUAG---AGCCACAAG--
...(((....))).((((((..(.(((((....(((((.....)))))..((((.......))))....))))).)...)))))).(((......)))(((.....---.))).....-- ( -39.00)
>DroGri_CAF1 24108 116 - 1
CUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUACAACUGCGACGACUUAACCAGCACUAG---AACAGCG-CAA
...((((...(((((.......)))))..))))(((.((.(((((.(...((((.......))))..((((....))))).))))))))))........((.((..---...)).)-).. ( -34.10)
>DroWil_CAF1 19736 113 - 1
CAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAAUUGGAAGUUGCCUGACCAAAUAGCCAUUUA---AGACACA----
...(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))...(((...(((......)))....)))....---.......---- ( -31.70)
>DroMoj_CAF1 25438 117 - 1
CUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUACGUUGCCAGCGACUUAACUGCCACUAG---AACCACUAGAA
...(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))((.((.((((....)))).)).))....((((---.....)))).. ( -34.90)
>DroAna_CAF1 11611 116 - 1
CAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGGAGCAAGCGCGGCUAAACAGCCACUUGAGGCGCGUUG----
...(((....)))..((((.(((.(((((....(((((.....)))))..((((.......))))....))))).))).))))..((((((((....)))).(....)))))....---- ( -42.90)
>consensus
CAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUGCAACUCGAGCGACUAAACAGCCACUAG___AGCCACG____
...(((((..(((((.......)))))......(((((.....)))))..((((.......))))....))))).............................................. (-28.90 = -28.90 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 7

Location 3,079,262 – 3,079,374
Length 112
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 82.00
Mean single sequence MFE -35.25
Consensus MFE -29.80
Energy contribution -29.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.85
SVM decision value 0.75
SVM RNA-class probability 0.841254
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3079262 112 + 23771897
CCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGU---UGCUCCCCCCAGUCCGAA
...(((((((....(((.(((.(((...(((......)))..((((((.((.((((((.......))))).).)).))))))..)))...))).---.)))..)))))))..... ( -40.10)
>DroVir_CAF1 29239 97 + 1
GCAUCUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUAAACUUUUU-------A-----------UUAUA
..((((((((.....((((.......))))....(((....((((....))))(((((.......))))).))))))))))).........-------.-----------..... ( -32.90)
>DroGri_CAF1 24144 109 + 1
GUAUCUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUAAACUUUUUUGUACACAAUG---CUU---UUUU
.(((((((((.....((((.......))))....(((....((((....))))(((((.......))))).))))))))))))...................---...---.... ( -34.20)
>DroWil_CAF1 19769 109 + 1
CCAAUUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGAGAUAACUUUUUUG---UUCUU--UGCAGU-CAAA
((....)).......((((.......))))....((((((((((((((.((.((((((.......))))).).)).)))))...(((......)---)).))--))))))-)... ( -37.90)
>DroMoj_CAF1 25475 109 + 1
GUAUCUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUAAACUUUUUU---CACAUUA---UUUGUUUAUU
.(((((((((.....((((.......))))....(((....((((....))))(((((.......))))).)))))))))))).........---.......---.......... ( -34.20)
>DroAna_CAF1 11647 102 + 1
CCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACUUUUUUGU---UCUUU-------UU---C
((((..(((((((..((((.......))))...........((((....))))(((((.......)))))))))))))))).............---.....-------..---. ( -32.20)
>consensus
CCAACUGGGGAUAUAGCUCAGUGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUAGGUAAACUUUUUUGU___UACUU_______UUUAUA
......(((((((..((((.......))))...........((((....))))(((((.......))))))))))))...................................... (-29.80 = -29.80 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 8

Location 3,079,262 – 3,079,374
Length 112
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 82.00
Mean single sequence MFE -33.25
Consensus MFE -28.90
Energy contribution -28.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.87
SVM decision value 1.04
SVM RNA-class probability 0.904297
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3079262 112 - 23771897
UUCGGACUGGGGGGAGCA---ACAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGG
..(.(((((((((.(((.---.......((((((((..(((....))).)))..)))))(((((.(..(((((.....)))))..).))).)).....)))...))))))))).) ( -42.70)
>DroVir_CAF1 29239 97 - 1
UAUAA-----------U-------AAAAAGUUUACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUGC
.....-----------.-------.....((((((((.(((....)))))))..)))).(((((....(((((.....)))))..((((.......))))....)))))...... ( -29.00)
>DroGri_CAF1 24144 109 - 1
AAAA---AAG---CAUUGUGUACAAAAAAGUUUACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUAC
....---...---....((((........((((((((.(((....)))))))..)))).(((((....(((((.....)))))..((((.......))))....)))))..)))) ( -29.60)
>DroWil_CAF1 19769 109 - 1
UUUG-ACUGCA--AAGAA---CAAAAAAGUUAUCUCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAAUUGG
((((-((((((--...((---(......)))...((.(((((...(((((.......)))))..))))).))..)))))))))).((((.......))))............... ( -36.90)
>DroMoj_CAF1 25475 109 - 1
AAUAAACAAA---UAAUGUG---AAAAAAGUUUACCUAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUAC
..........---....(((---((.....)))))...(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))...... ( -29.80)
>DroAna_CAF1 11647 102 - 1
G---AA-------AAAGA---ACAAAAAAGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGUUGG
.---..-------...((---((......)))).(((((((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))..)))) ( -31.50)
>consensus
UAUAAA_______AAAUA___ACAAAAAAGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCACUGAGCUAUAUCCCCAGAUGC
......................................(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))...... (-28.90 = -28.90 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 9

Location 3,079,302 – 3,079,397
Length 95
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 81.61
Mean single sequence MFE -21.20
Consensus MFE -18.90
Energy contribution -18.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.25
Structure conservation index 0.89
SVM decision value 0.11
SVM RNA-class probability 0.587169
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3079302 95 + 23771897
AGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGUUGCU-----CCCCCCAGUCCGAAUACAAAG--UAUAUUUUUUUCUGAU
..((((((.((.((((((.......))))).).)).))))))................-----.....(((...(((((.....--..)))))....))).. ( -20.60)
>DroSec_CAF1 12050 92 + 1
AGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGCUGCU-----C---CCAGUUCAAAUAUAAAG--UAUAUUUUUUUCUGAU
..((((((.((.((((((.......))))).).)).))))))................-----.---.(((...(((((((...--)))))))....))).. ( -22.20)
>DroSim_CAF1 12063 93 + 1
AGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGCUGCU-----CC--CCAGUUCAAAUAUAAAG--UAUAUUUUUUUCUGAU
..((((((.((.((((((.......))))).).)).))))))................-----..--.(((...(((((((...--)))))))....))).. ( -22.20)
>DroEre_CAF1 16238 92 + 1
AGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUU----------GCUCCCCAGUUUUACUAAAAUUUAUAUAUUUUUGUCUGAU
..((((((.((.((((((.......))))).).)).))))))..........----------......(((....((.(((((......))))).))))).. ( -20.70)
>DroYak_CAF1 11996 99 + 1
AGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGUUGCUGCCUGCUCCCCAGUU---CUAAAAUGUAUAUAAUUUUCUCUGAU
..((((((.((.((((((.......))))).).)).))))))..((..(((((..((((.........)))).---.))))).))................. ( -22.60)
>DroAna_CAF1 11687 86 + 1
AGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACUUUUUUGUUCUU-----U-------UU---CCAACCUUUCUUUAU-UUUUCCUGAU
..((((((.((.((((((.......))))).).)).))))))................-----.-------..---...............-.......... ( -18.90)
>consensus
AGAUCGAGAGGUCCCCGGUUCAAACCCGGGUGUCCCCUUGGUAAACCUUUUUGUUGCU_____C___CCAGUUC_AAUAAAAAG__UAUAUUUUUUUCUGAU
..((((((.((.((((((.......))))).).)).))))))............................................................ (-18.90 = -18.90 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 0

Location 3,079,302 – 3,079,397
Length 95
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 81.61
Mean single sequence MFE -22.98
Consensus MFE -17.38
Energy contribution -17.55
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 0.76
SVM decision value 0.10
SVM RNA-class probability 0.582795
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3079302 95 - 23771897
AUCAGAAAAAAAUAUA--CUUUGUAUUCGGACUGGGGGG-----AGCAACAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCU
................--..........(((.(((((((-----...........((....))..(....).(((((.......)))))..))))))).))) ( -24.90)
>DroSec_CAF1 12050 92 - 1
AUCAGAAAAAAAUAUA--CUUUAUAUUUGAACUGG---G-----AGCAGCAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCU
.((((....(((((((--...)))))))...))))---.-----...........((....)).(((((...(((((.......)))))..)))))...... ( -22.40)
>DroSim_CAF1 12063 93 - 1
AUCAGAAAAAAAUAUA--CUUUAUAUUUGAACUGG--GG-----AGCAGCAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCU
..(((....(((((((--...)))))))...)))(--((-----((.........((((((((..(((....))).)))..)))))(....))))))..... ( -23.50)
>DroEre_CAF1 16238 92 - 1
AUCAGACAAAAAUAUAUAAAUUUUAGUAAAACUGGGGAGC----------AAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCU
(((..((.(((((......))))).)).....(((..(((----------......)))..)))(((((...(((((.......)))))..))))).))).. ( -23.00)
>DroYak_CAF1 11996 99 - 1
AUCAGAGAAAAUUAUAUACAUUUUAG---AACUGGGGAGCAGGCAGCAACAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCU
....((((..................---..(((.....))).............((((......(....).(((((.......)))))))))))))..... ( -22.30)
>DroAna_CAF1 11687 86 - 1
AUCAGGAAAA-AUAAAGAAAGGUUGG---AA-------A-----AAGAACAAAAAAGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCU
..........-........((((((.---..-------.-----..((((......))))....(((((...(((((.......)))))..))))))))))) ( -21.80)
>consensus
AUCAGAAAAAAAUAUA__CAUUUUAGU_GAACUGG___G_____AGCAACAAAAAGGUUUACCAAGGGGACACCCGGGUUUGAACCGGGGACCUCUCGAUCU
(((....................................................((....)).(((((...(((((.......)))))..))))).))).. (-17.38 = -17.55 +   0.17) 

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 09:57:33 2006