Locus 5129

Sequence ID 2R_DroMel_CAF1
Location 16,692,064 – 16,692,278
Length 214
Max. P 0.990779
window8201 window8202 window8203 window8204

overview

Window 1

Location 16,692,064 – 16,692,161
Length 97
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 77.95
Mean single sequence MFE -17.00
Consensus MFE -10.86
Energy contribution -11.00
Covariance contribution 0.14
Combinations/Pair 1.13
Mean z-score -1.89
Structure conservation index 0.64
SVM decision value 1.03
SVM RNA-class probability 0.903200
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16692064 97 + 20766785
GA-ACAAUACCUU-UCUAAACAAUUUAUCCCUUUUAGUUAAUGUUCCCCAAGCAGCCCAAGCUGCUUCAGAACAUUCCCCUGCACUGCUUCCAGUACAU
..-..........-......................(..(((((((...(((((((....)))))))..)))))))..).((.((((....)))).)). ( -19.10)
>DroPse_CAF1 1702 97 + 1
AGCAGAAUAUCUAACGUGUG--UUCUUUCUUUUCCAGUUAAUGUUCCUUAAGCAGCCGAAGCUUCUUCUGAACAUCCCCAUUCUCUGCUCACAGUACAU
((((((.....((((.....--..............))))((((((...(((.(((....))).)))..))))))........)))))).......... ( -15.71)
>DroSec_CAF1 381 97 + 1
AA-ACAAUGCCUU-UCUAAACAAUAUAUCCCUUUUAGUUAAUGUUCCCCAAGCAGCCCAAGCUGCUGCAGAGUAUUCCCCUGCACUGCUUCCAGUACAU
..-..........-......................((...((.......((((((....))))))((((.(((......))).))))...))..)).. ( -16.40)
>DroSim_CAF1 378 97 + 1
AA-ACAAUGCCUU-UCUAAACAAUUUAUCCCUUUUAGUUAAUGUUCCCCAAGCAGCCCAAGCUGCUGCAGAGCAUUCCCCUGCACUGCUUCCAGUACAU
..-..........-......................(..(((((((....((((((....))))))...)))))))..).((.((((....)))).)). ( -18.90)
>DroYak_CAF1 380 98 + 1
AA-GCAAUUUCUUAUUUAUGAAAUCUAUCCUUUUUAGCUUAUGUUCCCGAAGCAACCCAAGCUGCUGCAGAACAUUCCCCUGCUCUGCUCCCAGUACAU
.(-((.(((((........)))))...........(((((..(((........)))..))))))))(((((.((......)).)))))........... ( -16.20)
>DroPer_CAF1 394 97 + 1
AGCAGAAUAUCUAACGUGUG--UUCUUUCUUUUCCAGUUAAUGUUCCUUAAGCAGCCGAAGCUUCUUCUGAACAUCCCCAUUCUCUGCUCACAGUACAU
((((((.....((((.....--..............))))((((((...(((.(((....))).)))..))))))........)))))).......... ( -15.71)
>consensus
AA_ACAAUACCUU_UCUAAACAAUCUAUCCCUUUUAGUUAAUGUUCCCCAAGCAGCCCAAGCUGCUGCAGAACAUUCCCCUGCACUGCUCCCAGUACAU
........................................((((((....((((((....))))))...)))))).........(((....)))..... (-10.86 = -11.00 +   0.14)

alignment

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secondary structure

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Window 2

Location 16,692,064 – 16,692,161
Length 97
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 77.95
Mean single sequence MFE -29.08
Consensus MFE -18.09
Energy contribution -19.78
Covariance contribution 1.70
Combinations/Pair 1.09
Mean z-score -3.20
Structure conservation index 0.62
SVM decision value 2.23
SVM RNA-class probability 0.990779
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16692064 97 - 20766785
AUGUACUGGAAGCAGUGCAGGGGAAUGUUCUGAAGCAGCUUGGGCUGCUUGGGGAACAUUAACUAAAAGGGAUAAAUUGUUUAGA-AAGGUAUUGU-UC
.(((((((....)))))))((..((((((((.(((((((....))))))).).)))))))..))...((.((((..((.......-))..)))).)-). ( -32.60)
>DroPse_CAF1 1702 97 - 1
AUGUACUGUGAGCAGAGAAUGGGGAUGUUCAGAAGAAGCUUCGGCUGCUUAAGGAACAUUAACUGGAAAAGAAAGAA--CACACGUUAGAUAUUCUGCU
..........(((((((...(..(((((((..(((.(((....))).)))...)))))))..)............((--(....))).....))))))) ( -26.10)
>DroSec_CAF1 381 97 - 1
AUGUACUGGAAGCAGUGCAGGGGAAUACUCUGCAGCAGCUUGGGCUGCUUGGGGAACAUUAACUAAAAGGGAUAUAUUGUUUAGA-AAGGCAUUGU-UU
.(((((((....)))))))((..(((..(((.(((((((....))))).)).)))..)))..)).....(((((...(((((...-.))))).)))-)) ( -27.90)
>DroSim_CAF1 378 97 - 1
AUGUACUGGAAGCAGUGCAGGGGAAUGCUCUGCAGCAGCUUGGGCUGCUUGGGGAACAUUAACUAAAAGGGAUAAAUUGUUUAGA-AAGGCAUUGU-UU
.(((((((....)))))))((..((((.(((.(((((((....))))).)).))).))))..)).....((((((..(((((...-.)))))))))-)) ( -31.30)
>DroYak_CAF1 380 98 - 1
AUGUACUGGGAGCAGAGCAGGGGAAUGUUCUGCAGCAGCUUGGGUUGCUUCGGGAACAUAAGCUAAAAAGGAUAGAUUUCAUAAAUAAGAAAUUGC-UU
...........((((((((......))))))))(((((((((.(((.(....).))).))))))..........((((((........))))))))-). ( -30.50)
>DroPer_CAF1 394 97 - 1
AUGUACUGUGAGCAGAGAAUGGGGAUGUUCAGAAGAAGCUUCGGCUGCUUAAGGAACAUUAACUGGAAAAGAAAGAA--CACACGUUAGAUAUUCUGCU
..........(((((((...(..(((((((..(((.(((....))).)))...)))))))..)............((--(....))).....))))))) ( -26.10)
>consensus
AUGUACUGGAAGCAGAGCAGGGGAAUGUUCUGAAGCAGCUUGGGCUGCUUGGGGAACAUUAACUAAAAAGGAUAGAUUGCAUAGA_AAGAUAUUGU_UU
.(((.(((....))).)))((..((((((((..((((((....))))))...))))))))..))................................... (-18.09 = -19.78 +   1.70)

alignment

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secondary structure

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Window 3

Location 16,692,093 – 16,692,198
Length 105
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 78.25
Mean single sequence MFE -35.33
Consensus MFE -20.92
Energy contribution -21.73
Covariance contribution 0.81
Combinations/Pair 1.27
Mean z-score -1.92
Structure conservation index 0.59
SVM decision value 0.77
SVM RNA-class probability 0.845752
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16692093 105 - 20766785
AUCG---GUCUGAUCCCACUCGGAGCAGAUUCCCAGCACAAUGUACUGGAAGCAGUGCAGGGGAAUGUUCUGAAGCAGCUUGGGCUGCUUGGGGAACAUUAACUAAAA--
...(---((.((.((((...(((((((..(((((.......(((((((....))))))).))))))))))))(((((((....))))))).)))).))...)))....-- ( -42.50)
>DroEre_CAF1 421 105 - 1
AUCG---GUCUGAUCCCACUCGGAGCAGAUGCCCAGCACAAUGUACUGGGAGCAAAGCAGGGGAAUGUUCUGCAGCAGCUUGGGUUGCUUGGGGAACAUAAGCUAAAA--
....---(((((.(((.....))).))))).(((((.((...)).))))).....(((......(((((((.(((((((....))))).)).)))))))..)))....-- ( -34.00)
>DroWil_CAF1 2113 108 - 1
AUCACUAGCCUUCUCCCAAUCAGAGCAAAUUCCCAGUACUAUAUAUUGUGAGCAGAGGAGGGGUAUAUUCUGUAGAAGCUUCGGUUGCUUCGAGAACAUCAACUGGAA--
....(((((((((((....((((((....))).(((((.....))))))))...)))))))(((...((((...(((((.......))))).)))).)))..))))..-- ( -23.20)
>DroYak_CAF1 410 105 - 1
AUCG---GUCUGAUCCCACUCGGAGCAGAUGCCCAGCACAAUGUACUGGGAGCAGAGCAGGGGAAUGUUCUGCAGCAGCUUGGGUUGCUUCGGGAACAUAAGCUAAAA--
....---(((((.(((.....))).))))).(((((.((...)).))))).((((((((......))))))))...((((((.(((.(....).))).))))))....-- ( -41.00)
>DroMoj_CAF1 467 107 - 1
UUCA---GUUUGGUCCCAUUCCGAGCAAAUGCCCAGCACAAUGUACUGCGAACAGAGCACAGGCACAUUUUGCAGCAGCUGCGGCUGUUUCGAGAAGAGCAGCUGAAAUA
((((---(((.(.((...(((.(((((...(((((((....((..(((((((..(.((....)).)..))))))))))))).)))))))).)))..)).))))))))... ( -31.00)
>DroAna_CAF1 404 105 - 1
AUCG---GACUGAUCCCACUCGGCACAAAUGCCGAGGACUAUGUACUGCGUGCAGAGCAGUGGAAGGUUCUGUAGCAGCUUUGGCUGUUUGGGGAACAUUAACUGGGA--
....---......((((((((((((....)))))))..((.(.((((((.......)))))).)))(((((.(((((((....)))).))).)))))......)))))-- ( -40.30)
>consensus
AUCG___GUCUGAUCCCACUCGGAGCAAAUGCCCAGCACAAUGUACUGGGAGCAGAGCAGGGGAAUGUUCUGCAGCAGCUUGGGCUGCUUCGGGAACAUAAACUAAAA__
.............((((...(((((((....(((.......(((.(((....))).))).)))..))))))).((((((....))))))..))))............... (-20.92 = -21.73 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,692,161 – 16,692,278
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 76.75
Mean single sequence MFE -36.67
Consensus MFE -18.16
Energy contribution -21.11
Covariance contribution 2.95
Combinations/Pair 1.23
Mean z-score -2.02
Structure conservation index 0.50
SVM decision value 0.52
SVM RNA-class probability 0.767599
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16692161 117 - 20766785
AACUUUUGGUCACAGAUUUGUGUAGGUUCCACAGUGAUUUUAACGAUCUGGUUGACAACCAGCCGCCGAACCUCAGCCAGAUCGGUCUGAUCCCACUCGGAGCAGAUUCCCAGCACA
....((((....))))..(((((.((.................((((((((((((.................))))))))))))(((((.(((.....))).)))))..)).))))) ( -34.43)
>DroVir_CAF1 490 117 - 1
AAUUUUUGGCCACAGAUUUGUGUGCUAUCCACCUUGAUGCUGACCACAUGAUUUACCAUCAGCUGCUUCACUGCAUCCAGCUCGGACUGAUCCCAUUCCGAGCAAAUGCCGAGCACA
......(((((((......))).))))...........(((((.....((......)))))))(((((....((((...(((((((.((....)).)))))))..)))).))))).. ( -32.30)
>DroEre_CAF1 489 117 - 1
AACUUUUGGUCACAGAUAUGUGUGGGAUCAACGGUGAUUUGAACGGUCUGGUUGACAAUCAGAUCCUGAACCACAGCCAGAUCGGUCUGAUCCCACUCGGAGCAGAUGCCCAGCACA
....((((....))))...(.(((((((((.(((....)))..(((((((((((....((((...))))....)))))))))))...))))))))).)((.((....))))...... ( -41.30)
>DroYak_CAF1 478 117 - 1
AAUUUUUGGUCACAAAUAUGUGUGGGAUCAACGUUGAUUUGAACGGUCUGGUUGACAAUCAGAUCUUGAACCACAGCCAGAUCGGUCUGAUCCCACUCGGAGCAGAUGCCCAGCACA
....((((....))))...(.((((((((((((((......)))((((((((((....((((...))))....)))))))))).)).))))))))).)((.((....))))...... ( -39.00)
>DroMoj_CAF1 537 117 - 1
AACUUUUGACCACAGAUCUGUGUGGGAUCCACCUCAAUGCUGACCACAUGGUUAACCAUCAGCUGUUUCACAGUAUCCAGUUCAGUUUGGUCCCAUUCCGAGCAAAUGCCCAGCACA
...................(((((((......(((((((..(((((.((((....))))..((((.....)))).............))))).))))..)))......)))).))). ( -26.40)
>DroAna_CAF1 472 117 - 1
AACUUCUGGCCACAGAUCUGCGUCGGAUCGAUGUCGAUGUGGACGGUCUGGUUGACGAUCAGCUUCUGGACCACUGCUAGAUCGGACUGAUCCCACUCGGCACAAAUGCCGAGGACU
....((((....)))).....(((((((((...(((((.(((..((((((((((.....)))))...)))))....))).)))))..))))))..(((((((....)))))))))). ( -46.60)
>consensus
AACUUUUGGCCACAGAUAUGUGUGGGAUCCACGUUGAUGUGAACGAUCUGGUUGACAAUCAGCUGCUGAACCACAGCCAGAUCGGUCUGAUCCCACUCGGAGCAAAUGCCCAGCACA
....((((....))))...(((((((.................(((((((((((...................)))))))))))(((((.(((.....))).))))).)))).))). (-18.16 = -21.11 +   2.95)

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 11:37:18 2006