Locus 5916

Sequence ID 3L_DroMel_CAF1
Location 15,893,298 – 15,893,537
Length 239
Max. P 0.987339
window9432 window9433 window9434 window9435

overview

Window 2

Location 15,893,298 – 15,893,418
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.25
Mean single sequence MFE -34.88
Consensus MFE -26.02
Energy contribution -26.74
Covariance contribution 0.72
Combinations/Pair 1.14
Mean z-score -1.86
Structure conservation index 0.75
SVM decision value 0.21
SVM RNA-class probability 0.633140
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15893298 120 + 23771897
UACUCGGGCGUUCCACACAAUGUCCAAGUGCGAUCCCUCAGCUUUUUGGCAAAUCCAAAAUCGGUUAUCUUCAAAUGACCAUCCCGAUUGAUCAGCAGAUUCUCUGGCUUCAGAUCGCGA
.(((.(((((((......))))))).)))((((((....(((.((((((.....))))))..((((((......))))))...............(((.....))))))...)))))).. ( -32.20)
>DroSec_CAF1 1818 120 + 1
UACUCGGGCGUUCCGCACAAUGUCCAAGUGCGAUCCCUGAGCUUUUUGGCAAAGCCAAAAUCGGUUAUCUUCAAAUGGCCAUCGCGAUUGAUCAGCAGAUUCUCUGGCUUCAGAUCGCGA
..((((((.(...(((((.........)))))..)))))))..(((((((...)))))))..((((((......)))))).((((((((....(((((.....)).)))...)))))))) ( -41.20)
>DroSim_CAF1 4031 120 + 1
UACUCGGGCGUUCCGCACAAUGUCCAAGUGCGAUCCCUCAGCUUUUUGGCAAAGCCAAAAUCGGUUAUCUUCAAAUGGCCAUCGCGAUUGAUCAGCAGAUUCUCUGGCUUCAGAUCGCGA
.(((.(((((((......))))))).)))((((((.....(((....))).((((((.((((((((((......))))))...((.........)).))))...))))))..)))))).. ( -37.40)
>DroEre_CAF1 1794 120 + 1
UACUCGGGCGUUCCGCACAAUGUCCAAGUGCGAUCCCUUAGUUUUUUGGCAAAGCCAAAAUCUGUUAUUUUUAAAUGGCCAUCCCGAUUGAUCAGCAGAUUCUCUGGCUUUAAGUCGCGG
.(((.(((((((......))))))).)))(((((......(((....)))(((((((.((((((((....((((.(((.....))).))))..))))))))...)))))))..))))).. ( -34.40)
>DroYak_CAF1 1858 120 + 1
UACUCAGGUGUUCCGCACAAAGUCCAAGUGCGAUCCCUCAGCUUUUUGGCAAAGCCGAAAUCUGUUAUUUUUAAAUGGCCAUCCCUAUUGAUCAGCAGAUUCUCUGGCUUUAAGUCACGA
..((.(((.(...(((((.........)))))..)))).)).....((((((((((((((((((((.......(((((......)))))....)))))))).)).))))))..))))... ( -29.20)
>consensus
UACUCGGGCGUUCCGCACAAUGUCCAAGUGCGAUCCCUCAGCUUUUUGGCAAAGCCAAAAUCGGUUAUCUUCAAAUGGCCAUCCCGAUUGAUCAGCAGAUUCUCUGGCUUCAGAUCGCGA
.(((.(((((((......))))))).)))((((((....(((.(((((((...)))))))..((((((......))))))...............(((.....))))))...)))))).. (-26.02 = -26.74 +   0.72)

alignment

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secondary structure

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Window 3

Location 15,893,378 – 15,893,497
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.47
Mean single sequence MFE -36.50
Consensus MFE -29.80
Energy contribution -29.80
Covariance contribution 0.00
Combinations/Pair 1.11
Mean z-score -2.38
Structure conservation index 0.82
SVM decision value 2.08
SVM RNA-class probability 0.987339
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15893378 119 + 23771897
AUCCCGAUUGAUCAGCAGAUUCUCUGGCUUCAGAUCGCGAUAAACAAUUUGCAGUGAGUGCAGGUAUUCUAG-GGCACUGACGAUCUCAGCCGCAUAGAAGUUGGCUAAAAUCGAAAUCA
....(((((....(((...((((.(((((..(((((((((........)))).((.(((((.((....))..-.))))).))))))).)))))...))))....)))..)))))...... ( -36.30)
>DroSec_CAF1 1898 120 + 1
AUCGCGAUUGAUCAGCAGAUUCUCUGGCUUCAGAUCGCGAUAAACAAUUUGCAGUGAGUGCAGGUAUUCCAGGGGCACUCACGAUCUCAGCCGCAUAGAAAUUGGCUAAAAUCGAAAUCA
....(((((....(((...((((.(((((..(((((((((........)))).((((((((.((....))....))))))))))))).)))))...))))....)))..)))))...... ( -40.50)
>DroSim_CAF1 4111 119 + 1
AUCGCGAUUGAUCAGCAGAUUCUCUGGCUUCAGAUCGCGAUAAACAAUUUGCAGUGAGUGCAGGUAUUCCAG-CGCACUCACGAUCUCAGCCGCAUAGAAAUUGGCUAAAAUCGAAAUCA
....(((((....(((...((((.(((((..(((((((((........)))).((((((((.((....))..-.))))))))))))).)))))...))))....)))..)))))...... ( -40.00)
>DroEre_CAF1 1874 118 + 1
AUCCCGAUUGAUCAGCAGAUUCUCUGGCUUUAAGUCGCGGUAAACAAUUUGCAGUGAGUGCAGGUAUUCCAG-GGCACUGACGAUCUCAGCCGCAUAGAAGUUGGCUGAAA-CAAAAUGA
.........((((.(((((((((.((((.....)))).)).....))))))).((.(((((.((....))..-.))))).))))))((((((((......).)))))))..-........ ( -35.00)
>DroYak_CAF1 1938 119 + 1
AUCCCUAUUGAUCAGCAGAUUCUCUGGCUUUAAGUCACGAUAAACAAUUUGCAGUGAGUGCAGGUAUUCCAG-GGCACUGACGAUCUCAGCCGCAUAGAAGUUGGCUAAAAUCAAAAUCA
.........((((.(((((((.((((((.....)))).)).....))))))).((.(((((.((....))..-.))))).))))))..((((((......).)))))............. ( -30.70)
>consensus
AUCCCGAUUGAUCAGCAGAUUCUCUGGCUUCAGAUCGCGAUAAACAAUUUGCAGUGAGUGCAGGUAUUCCAG_GGCACUGACGAUCUCAGCCGCAUAGAAGUUGGCUAAAAUCGAAAUCA
.......(((((.(((...((((.(((((..(((((((((........)))).((.(((((.((....))....))))).))))))).)))))...))))....)))...)))))..... (-29.80 = -29.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,893,378 – 15,893,497
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -35.32
Consensus MFE -27.64
Energy contribution -28.24
Covariance contribution 0.60
Combinations/Pair 1.11
Mean z-score -1.93
Structure conservation index 0.78
SVM decision value 0.73
SVM RNA-class probability 0.836653
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15893378 119 - 23771897
UGAUUUCGAUUUUAGCCAACUUCUAUGCGGCUGAGAUCGUCAGUGCC-CUAGAAUACCUGCACUCACUGCAAAUUGUUUAUCGCGAUCUGAAGCCAGAGAAUCUGCUGAUCAAUCGGGAU
..((..((((((((((....((((....((((.(((((((.(((((.-..((.....))))))).)).((............)))))))..))))..))))...)))))..)))))..)) ( -32.60)
>DroSec_CAF1 1898 120 - 1
UGAUUUCGAUUUUAGCCAAUUUCUAUGCGGCUGAGAUCGUGAGUGCCCCUGGAAUACCUGCACUCACUGCAAAUUGUUUAUCGCGAUCUGAAGCCAGAGAAUCUGCUGAUCAAUCGCGAU
.((((((((((((((((...........))))))))))((((((((....((....)).)))))))).).)))))....((((((((.((((((.((.....)))))..))))))))))) ( -43.00)
>DroSim_CAF1 4111 119 - 1
UGAUUUCGAUUUUAGCCAAUUUCUAUGCGGCUGAGAUCGUGAGUGCG-CUGGAAUACCUGCACUCACUGCAAAUUGUUUAUCGCGAUCUGAAGCCAGAGAAUCUGCUGAUCAAUCGCGAU
.((((((((((((((((...........))))))))))(((((((((-..((....))))))))))).).)))))....((((((((.((((((.((.....)))))..))))))))))) ( -43.70)
>DroEre_CAF1 1874 118 - 1
UCAUUUUG-UUUCAGCCAACUUCUAUGCGGCUGAGAUCGUCAGUGCC-CUGGAAUACCUGCACUCACUGCAAAUUGUUUACCGCGACUUAAAGCCAGAGAAUCUGCUGAUCAAUCGGGAU
.((.((((-((((((((...........)))))))...((.(((((.-..((....)).))))).)).))))).))....((.(((.....(((.((.....)))))......))))).. ( -29.30)
>DroYak_CAF1 1938 119 - 1
UGAUUUUGAUUUUAGCCAACUUCUAUGCGGCUGAGAUCGUCAGUGCC-CUGGAAUACCUGCACUCACUGCAAAUUGUUUAUCGUGACUUAAAGCCAGAGAAUCUGCUGAUCAAUAGGGAU
((((...((((((((((...........))))))))))))))...((-((((((((..((((.....))))...)))))....(((.....(((.((.....)))))..))).))))).. ( -28.00)
>consensus
UGAUUUCGAUUUUAGCCAACUUCUAUGCGGCUGAGAUCGUCAGUGCC_CUGGAAUACCUGCACUCACUGCAAAUUGUUUAUCGCGAUCUGAAGCCAGAGAAUCUGCUGAUCAAUCGGGAU
..((((((((((((((....((((....((((.(((((((.(((((....((....)).))))).)).((............)))))))..))))..))))...)))))..))))))))) (-27.64 = -28.24 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,893,418 – 15,893,537
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.18
Mean single sequence MFE -27.82
Consensus MFE -19.94
Energy contribution -20.18
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.84
Structure conservation index 0.72
SVM decision value 1.62
SVM RNA-class probability 0.968046
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15893418 119 - 23771897
AACUAUUCUAUUAAAUCUUUUAAAUCAGAAAUCACAAAAUUGAUUUCGAUUUUAGCCAACUUCUAUGCGGCUGAGAUCGUCAGUGCC-CUAGAAUACCUGCACUCACUGCAAAUUGUUUA
...(((((((.................(((((((......)))))))((((((((((...........)))))))))).........-.)))))))..((((.....))))......... ( -27.30)
>DroSec_CAF1 1938 120 - 1
AACUAUUCUAUUAAAUCUUCUAAAUAAAAAAUCACAAAACUGAUUUCGAUUUUAGCCAAUUUCUAUGCGGCUGAGAUCGUGAGUGCCCCUGGAAUACCUGCACUCACUGCAAAUUGUUUA
....................(((((((.((((((......)))))).((((((((((...........))))))))))((((((((....((....)).))))))))......))))))) ( -31.30)
>DroSim_CAF1 4151 119 - 1
AACUAUUAAAUUAAAUCUUUUAAAUCAAAAAUCACUAAACUGAUUUCGAUUUUAGCCAAUUUCUAUGCGGCUGAGAUCGUGAGUGCG-CUGGAAUACCUGCACUCACUGCAAAUUGUUUA
.....(((((........)))))............(((((.((((((((((((((((...........))))))))))(((((((((-..((....))))))))))).).)))))))))) ( -30.80)
>DroEre_CAF1 1914 117 - 1
CACCAUUCAA-UAUAUCUUUUAUGUAUGUAUCAAUAGAAAUCAUUUUG-UUUCAGCCAACUUCUAUGCGGCUGAGAUCGUCAGUGCC-CUGGAAUACCUGCACUCACUGCAAAUUGUUUA
.........(-((((.....))))).((((.................(-((((((((...........))))))))).((.(((((.-..((....)).))))).))))))......... ( -22.50)
>DroYak_CAF1 1978 119 - 1
GGCCAUUCUAUUAAAUCGUUUAUGUAUGUAUCAAUAAUAAUGAUUUUGAUUUUAGCCAACUUCUAUGCGGCUGAGAUCGUCAGUGCC-CUGGAAUACCUGCACUCACUGCAAAUUGUUUA
.((.........((((((((....(((......)))..)))))))).((((((((((...........))))))))))((.(((((.-..((....)).))))).)).)).......... ( -27.20)
>consensus
AACUAUUCUAUUAAAUCUUUUAAAUAAGAAAUCACAAAAAUGAUUUCGAUUUUAGCCAACUUCUAUGCGGCUGAGAUCGUCAGUGCC_CUGGAAUACCUGCACUCACUGCAAAUUGUUUA
...............................................((((((((((...........))))))))))((.(((((....((....)).))))).))............. (-19.94 = -20.18 +   0.24)

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 12:03:47 2006