Locus 1564

Sequence ID 3L_DroMel_CAF1
Location 4,561,415 – 4,561,535
Length 120
Max. P 0.997554
window2425 window2426 window2427

overview

Window 5

Location 4,561,415 – 4,561,512
Length 97
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 87.07
Mean single sequence MFE -47.62
Consensus MFE -42.03
Energy contribution -43.00
Covariance contribution 0.97
Combinations/Pair 1.12
Mean z-score -5.12
Structure conservation index 0.88
SVM decision value 2.88
SVM RNA-class probability 0.997554
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4561415 97 + 23771897
------------------GAUU-UUGGGCACUGUUGGCGGAAUCCGCAAGAGAAGCUUGGCUGAGCACAGCCGGAACCUGAGUUGUUUUGUGGAUUCUGCUGACAGGACACCCACA
------------------....-.((((..((((..(((((((((((((((..((((((((((....)))))(....).))))).)))))))))))))))..))))....)))).. ( -49.60)
>DroSec_CAF1 138402 97 + 1
------------------GAUU-UUGGGCCCUGUUGGCGGAAUCCGCAAGAGAAGCUUGGCUGAACACAGCCGGAAUCUGAGUUGUUUUGUGGAUUCUGCUGACAGGACACCCACA
------------------....-.((((.(((((..(((((((((((((((..((((((((((....))))).......))))).)))))))))))))))..)))))...)))).. ( -50.71)
>DroSim_CAF1 138632 97 + 1
------------------GAUU-UUGGGCCCUGUUGGCGGAAUCCGCAAGAGAAGCUUGGCUGAACACAGCCGGAAUCUGAGUUGUUUUGUGGAUUCUGCUGACAGGACACCCACA
------------------....-.((((.(((((..(((((((((((((((..((((((((((....))))).......))))).)))))))))))))))..)))))...)))).. ( -50.71)
>DroEre_CAF1 146461 97 + 1
------------------GAAU-UUGAGCCCGGUUGGCGGAAUCCGCAAGAGAAGCUUGGCUGAGCACAGCCGGAAUCUGAGUUGUUUUGUGGAUUCUGCUGACAGGACACCCACA
------------------....-....(.((.((..(((((((((((((((..((((((((((....))))).......))))).)))))))))))))))..)).)).)....... ( -41.41)
>DroYak_CAF1 142932 98 + 1
------------------GAUUUUUGGGCCCUGUUGGCGGAAUCCGCAAGAGAAGCUUGGCUGAGCACAGCCGGAAUCUGAGUUGUUUUGUGGAUACUGCUGACAGGACACCCACA
------------------......((((.(((((..((((.((((((((((..((((((((((....))))).......))))).)))))))))).))))..)))))...)))).. ( -46.31)
>DroAna_CAF1 140008 116 + 1
AAGACACGGCCACACCGAGUUUUUGGGGCUAUGUUGGCGGAAUCCGCAAGUGAAGUUCGGCUGAACAUUGCCGGAAUCAGAGUUGUUGUGUUGAUUCUGCUGACAGGGCACCCACA
(((((.(((.....))).)))))(((((((.(((..((((((((.(((((..(..((((((........)))))).......)..)).))).))))))))..))).))).)))).. ( -47.00)
>consensus
__________________GAUU_UUGGGCCCUGUUGGCGGAAUCCGCAAGAGAAGCUUGGCUGAACACAGCCGGAAUCUGAGUUGUUUUGUGGAUUCUGCUGACAGGACACCCACA
.........................(((.(((((..(((((((((((((((..((((((((((....)))))(....).))))).)))))))))))))))..)))))...)))... (-42.03 = -43.00 +   0.97)

alignment

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secondary structure

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Window 6

Location 4,561,415 – 4,561,512
Length 97
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 87.07
Mean single sequence MFE -33.97
Consensus MFE -29.59
Energy contribution -30.82
Covariance contribution 1.22
Combinations/Pair 1.08
Mean z-score -2.72
Structure conservation index 0.87
SVM decision value 1.79
SVM RNA-class probability 0.977197
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4561415 97 - 23771897
UGUGGGUGUCCUGUCAGCAGAAUCCACAAAACAACUCAGGUUCCGGCUGUGCUCAGCCAAGCUUCUCUUGCGGAUUCCGCCAACAGUGCCCAA-AAUC------------------
..(((((...((((..((.((((((...................(((((....)))))..((.......)))))))).))..)))).))))).-....------------------ ( -33.90)
>DroSec_CAF1 138402 97 - 1
UGUGGGUGUCCUGUCAGCAGAAUCCACAAAACAACUCAGAUUCCGGCUGUGUUCAGCCAAGCUUCUCUUGCGGAUUCCGCCAACAGGGCCCAA-AAUC------------------
....((.(((((((..((.((((((...................(((((....)))))..((.......)))))))).))..)))))))))..-....------------------ ( -37.40)
>DroSim_CAF1 138632 97 - 1
UGUGGGUGUCCUGUCAGCAGAAUCCACAAAACAACUCAGAUUCCGGCUGUGUUCAGCCAAGCUUCUCUUGCGGAUUCCGCCAACAGGGCCCAA-AAUC------------------
....((.(((((((..((.((((((...................(((((....)))))..((.......)))))))).))..)))))))))..-....------------------ ( -37.40)
>DroEre_CAF1 146461 97 - 1
UGUGGGUGUCCUGUCAGCAGAAUCCACAAAACAACUCAGAUUCCGGCUGUGCUCAGCCAAGCUUCUCUUGCGGAUUCCGCCAACCGGGCUCAA-AUUC------------------
(((((((...(((....))).)))))))..........((.((((((((....)))))..((.......))))).)).(((.....)))....-....------------------ ( -30.90)
>DroYak_CAF1 142932 98 - 1
UGUGGGUGUCCUGUCAGCAGUAUCCACAAAACAACUCAGAUUCCGGCUGUGCUCAGCCAAGCUUCUCUUGCGGAUUCCGCCAACAGGGCCCAAAAAUC------------------
....((.(((((((..((.(.((((...................(((((....)))))..((.......)))))).).))..))))))))).......------------------ ( -33.00)
>DroAna_CAF1 140008 116 - 1
UGUGGGUGCCCUGUCAGCAGAAUCAACACAACAACUCUGAUUCCGGCAAUGUUCAGCCGAACUUCACUUGCGGAUUCCGCCAACAUAGCCCCAAAAACUCGGUGUGGCCGUGUCUU
..((((.((..(((..((.(((((..((...((....))....((((........)))).........))..))))).))..)))..))))))...((.(((.....))).))... ( -31.20)
>consensus
UGUGGGUGUCCUGUCAGCAGAAUCCACAAAACAACUCAGAUUCCGGCUGUGCUCAGCCAAGCUUCUCUUGCGGAUUCCGCCAACAGGGCCCAA_AAUC__________________
....((.(((((((..((.((((((...................(((((....)))))..((.......)))))))).))..)))))))))......................... (-29.59 = -30.82 +   1.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,561,436 – 4,561,535
Length 99
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 97.98
Mean single sequence MFE -31.47
Consensus MFE -30.27
Energy contribution -30.27
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.96
SVM decision value 0.73
SVM RNA-class probability 0.834922
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4561436 99 + 23771897
AAUCCGCAAGAGAAGCUUGGCUGAGCACAGCCGGAACCUGAGUUGUUUUGUGGAUUCUGCUGACAGGACACCCACACACAUGGGUACCAAAAGCCACAC
(((((((((((..((((((((((....)))))(....).))))).)))))))))))..(((....((..(((((......))))).))...)))..... ( -32.90)
>DroSim_CAF1 138653 99 + 1
AAUCCGCAAGAGAAGCUUGGCUGAACACAGCCGGAAUCUGAGUUGUUUUGUGGAUUCUGCUGACAGGACACCCACACACAUGGGUACCAAAAGCCACAC
(((((((((((..((((((((((....))))).......))))).)))))))))))..(((....((..(((((......))))).))...)))..... ( -31.51)
>DroEre_CAF1 146482 99 + 1
AAUCCGCAAGAGAAGCUUGGCUGAGCACAGCCGGAAUCUGAGUUGUUUUGUGGAUUCUGCUGACAGGACACCCACACACAUGGGCACCAAAAGCCACAC
(((((((((((..((((((((((....))))).......))))).)))))))))))..(((....((...((((......))))..))...)))..... ( -30.01)
>consensus
AAUCCGCAAGAGAAGCUUGGCUGAGCACAGCCGGAAUCUGAGUUGUUUUGUGGAUUCUGCUGACAGGACACCCACACACAUGGGUACCAAAAGCCACAC
(((((((((((..((((((((((....)))))(....).))))).)))))))))))..(((....((...((((......))))..))...)))..... (-30.27 = -30.27 +   0.00)

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 10:10:46 2006