Locus 4779

Sequence ID 3L_DroMel_CAF1
Location 13,399,004 – 13,399,164
Length 160
Max. P 0.999859
window7524 window7525 window7526 window7527

overview

Window 4

Location 13,399,004 – 13,399,124
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.00
Mean single sequence MFE -41.86
Consensus MFE -39.24
Energy contribution -39.00
Covariance contribution -0.24
Combinations/Pair 1.09
Mean z-score -1.19
Structure conservation index 0.94
SVM decision value 0.48
SVM RNA-class probability 0.753549
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13399004 120 + 23771897
CAUCCUGUUUUCGGCUGGAAGAGACACAAUUGUCCAGGUAAUUUAAACCGCCGGGCAAAAUGCCGAACGUGUUAGCUAACGGCCGGUGCAUUGUGCAUUGCCCCGGCUGAUAGCCAUCGC
......((((.((((((((.((.......)).))))(((.......)))))))(((.....)))))))(((...((((.(((((((.(((........))).))))))).))))...))) ( -43.40)
>DroSec_CAF1 14575 120 + 1
CAUCUUGUUUUCGACUGGAGGAGAAACAGUUGUCCAGGUAAUUUAAACCGCCGGGCAAAAUGCCGAACGUGUUAGCUAACGGCCGGUGCAUUGUGUAUUGCCCCGGCUGAUAGCCAUCGC
.........((((.((((.(((.((....)).))).(((.......))).))))((.....)))))).(((...((((.(((((((.(((........))).))))))).))))...))) ( -39.00)
>DroSim_CAF1 11566 120 + 1
CAUCCUGUUUUCGACUGGAGGAGAAACAGUUGUCCAGGUAAUUUAAACCGCCGGGCAAAAUGCCGAACGUGUUAGCUAACGGCCGGUGCAUUGUGUAUUGCCCCGGCUGAUAGCCAUCGC
...((((....((((((.........))))))..))))...............(((.....)))....(((...((((.(((((((.(((........))).))))))).))))...))) ( -40.60)
>DroEre_CAF1 12152 120 + 1
CAUCCUGUUUUCGGUUGGAAGAGAAACAGUUGUCCAGGUAAUUCAAACCGCCGGGCAAAAUGCCGAACGCGUUAGCUAACGGCCGGUGCAUUAUGUACUGCCCCGGCUGAUAGCCAUCGC
......((((.((((((((...((.....)).))))(((.......)))))))(((.....)))))))(((...((((.(((((((.(((........))).))))))).))))...))) ( -41.40)
>DroYak_CAF1 11789 120 + 1
CAUCCUGCUUUCGGUUGGUGGGGAAACAGUUGUCCAGGUAAUUCAAGCCGCCGGGCAAGAUGCCGAACGCGUUAGCUAACGGCCGGUGCAAUGUGUACUGCCCCGGCUGGUAGCCAUCGC
((((.((((..(((((((...(....)......)))(((.......))))))))))).))))......(((...((((.(((((((.(((........))).))))))).))))...))) ( -44.90)
>consensus
CAUCCUGUUUUCGGCUGGAGGAGAAACAGUUGUCCAGGUAAUUUAAACCGCCGGGCAAAAUGCCGAACGUGUUAGCUAACGGCCGGUGCAUUGUGUAUUGCCCCGGCUGAUAGCCAUCGC
.........((((((((.........)).((((((.(((.......)))...))))))...)))))).(((...((((.(((((((.(((........))).))))))).))))...))) (-39.24 = -39.00 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,399,004 – 13,399,124
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.00
Mean single sequence MFE -40.67
Consensus MFE -34.18
Energy contribution -34.94
Covariance contribution 0.76
Combinations/Pair 1.03
Mean z-score -1.33
Structure conservation index 0.84
SVM decision value 0.19
SVM RNA-class probability 0.627461
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13399004 120 - 23771897
GCGAUGGCUAUCAGCCGGGGCAAUGCACAAUGCACCGGCCGUUAGCUAACACGUUCGGCAUUUUGCCCGGCGGUUUAAAUUACCUGGACAAUUGUGUCUCUUCCAGCCGAAAACAGGAUG
..(.((((((.(.(((((.(((........))).))))).).)))))).).((((((((.....)))(((((((.......))).(((((....)))))......))))......))))) ( -42.00)
>DroSec_CAF1 14575 120 - 1
GCGAUGGCUAUCAGCCGGGGCAAUACACAAUGCACCGGCCGUUAGCUAACACGUUCGGCAUUUUGCCCGGCGGUUUAAAUUACCUGGACAACUGUUUCUCCUCCAGUCGAAAACAAGAUG
.(((((((((.(.(((((.(((........))).))))).).))))))...(((..(((.....)))..)))...........(((((.............))))))))........... ( -36.12)
>DroSim_CAF1 11566 120 - 1
GCGAUGGCUAUCAGCCGGGGCAAUACACAAUGCACCGGCCGUUAGCUAACACGUUCGGCAUUUUGCCCGGCGGUUUAAAUUACCUGGACAACUGUUUCUCCUCCAGUCGAAAACAGGAUG
..(.((((((.(.(((((.(((........))).))))).).)))))).).(((..(((.....)))..)))..........((((..(.((((.........)))).)....))))... ( -37.90)
>DroEre_CAF1 12152 120 - 1
GCGAUGGCUAUCAGCCGGGGCAGUACAUAAUGCACCGGCCGUUAGCUAACGCGUUCGGCAUUUUGCCCGGCGGUUUGAAUUACCUGGACAACUGUUUCUCUUCCAACCGAAAACAGGAUG
(((.((((((.(.(((((.(((........))).))))).).)))))).)))(((((((.....)))....(((.......))).))))..((((((.((........)))))))).... ( -43.20)
>DroYak_CAF1 11789 120 - 1
GCGAUGGCUACCAGCCGGGGCAGUACACAUUGCACCGGCCGUUAGCUAACGCGUUCGGCAUCUUGCCCGGCGGCUUGAAUUACCUGGACAACUGUUUCCCCACCAACCGAAAGCAGGAUG
(((.((((((.(.(((((.(((((....))))).))))).).)))))).)))......((((((((....(((.(((........((((....))))......))))))...)))))))) ( -44.14)
>consensus
GCGAUGGCUAUCAGCCGGGGCAAUACACAAUGCACCGGCCGUUAGCUAACACGUUCGGCAUUUUGCCCGGCGGUUUAAAUUACCUGGACAACUGUUUCUCCUCCAGCCGAAAACAGGAUG
..(.((((((.(.(((((.(((........))).))))).).)))))).).((((((((.....)))(((((((.......)))((((.............))))))))......))))) (-34.18 = -34.94 +   0.76)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,399,044 – 13,399,164
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.50
Mean single sequence MFE -57.40
Consensus MFE -57.08
Energy contribution -57.08
Covariance contribution -0.00
Combinations/Pair 1.06
Mean z-score -5.22
Structure conservation index 0.99
SVM decision value 4.28
SVM RNA-class probability 0.999859
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13399044 120 + 23771897
AUUUAAACCGCCGGGCAAAAUGCCGAACGUGUUAGCUAACGGCCGGUGCAUUGUGCAUUGCCCCGGCUGAUAGCCAUCGCGUUGUUCCGGCAUUUUGCCCAACUCAAAAUUGGACGCAGU
.........((.(((((((((((((((((((...((((.(((((((.(((........))).))))))).))))...))))))....)))))))))))))...(((....)))..))... ( -55.80)
>DroSec_CAF1 14615 120 + 1
AUUUAAACCGCCGGGCAAAAUGCCGAACGUGUUAGCUAACGGCCGGUGCAUUGUGUAUUGCCCCGGCUGAUAGCCAUCGCGUUGUUCCGGCAUUUUGCCCAGCUCAAAAUUGGACGCAGU
.........((.(((((((((((((((((((...((((.(((((((.(((........))).))))))).))))...))))))....))))))))))))).))................. ( -57.70)
>DroSim_CAF1 11606 120 + 1
AUUUAAACCGCCGGGCAAAAUGCCGAACGUGUUAGCUAACGGCCGGUGCAUUGUGUAUUGCCCCGGCUGAUAGCCAUCGCGUUGUUCCGGCAUUUUGCCCAGCUCAAAAUUGGACGCAGU
.........((.(((((((((((((((((((...((((.(((((((.(((........))).))))))).))))...))))))....))))))))))))).))................. ( -57.70)
>DroEre_CAF1 12192 120 + 1
AUUCAAACCGCCGGGCAAAAUGCCGAACGCGUUAGCUAACGGCCGGUGCAUUAUGUACUGCCCCGGCUGAUAGCCAUCGCGUUGUUCCGGCAUUUUGCCCAGCUCAAAAUUGGACGCAGU
.........((.(((((((((((((((((((...((((.(((((((.(((........))).))))))).))))...))))))....))))))))))))).))................. ( -58.80)
>DroYak_CAF1 11829 120 + 1
AUUCAAGCCGCCGGGCAAGAUGCCGAACGCGUUAGCUAACGGCCGGUGCAAUGUGUACUGCCCCGGCUGGUAGCCAUCGCGUUGCUCCGGCAUUCUGCCCAGCUCGAAGUUGGACGUAGU
.(((.(((....(((((..((((((((((((...((((.(((((((.(((........))).))))))).))))...))))))....))))))..))))).))).)))............ ( -57.00)
>consensus
AUUUAAACCGCCGGGCAAAAUGCCGAACGUGUUAGCUAACGGCCGGUGCAUUGUGUAUUGCCCCGGCUGAUAGCCAUCGCGUUGUUCCGGCAUUUUGCCCAGCUCAAAAUUGGACGCAGU
.........((.(((((((((((((((((((...((((.(((((((.(((........))).))))))).))))...))))))....))))))))))))).))................. (-57.08 = -57.08 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,399,044 – 13,399,164
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.50
Mean single sequence MFE -59.14
Consensus MFE -56.32
Energy contribution -56.20
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -5.65
Structure conservation index 0.95
SVM decision value 3.52
SVM RNA-class probability 0.999338
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13399044 120 - 23771897
ACUGCGUCCAAUUUUGAGUUGGGCAAAAUGCCGGAACAACGCGAUGGCUAUCAGCCGGGGCAAUGCACAAUGCACCGGCCGUUAGCUAACACGUUCGGCAUUUUGCCCGGCGGUUUAAAU
.................(((((((((((((((((....(((.(.((((((.(.(((((.(((........))).))))).).)))))).).))))))))))))))))))))......... ( -54.90)
>DroSec_CAF1 14615 120 - 1
ACUGCGUCCAAUUUUGAGCUGGGCAAAAUGCCGGAACAACGCGAUGGCUAUCAGCCGGGGCAAUACACAAUGCACCGGCCGUUAGCUAACACGUUCGGCAUUUUGCCCGGCGGUUUAAAU
.................(((((((((((((((((....(((.(.((((((.(.(((((.(((........))).))))).).)))))).).))))))))))))))))))))......... ( -57.40)
>DroSim_CAF1 11606 120 - 1
ACUGCGUCCAAUUUUGAGCUGGGCAAAAUGCCGGAACAACGCGAUGGCUAUCAGCCGGGGCAAUACACAAUGCACCGGCCGUUAGCUAACACGUUCGGCAUUUUGCCCGGCGGUUUAAAU
.................(((((((((((((((((....(((.(.((((((.(.(((((.(((........))).))))).).)))))).).))))))))))))))))))))......... ( -57.40)
>DroEre_CAF1 12192 120 - 1
ACUGCGUCCAAUUUUGAGCUGGGCAAAAUGCCGGAACAACGCGAUGGCUAUCAGCCGGGGCAGUACAUAAUGCACCGGCCGUUAGCUAACGCGUUCGGCAUUUUGCCCGGCGGUUUGAAU
.................(((((((((((((((((....(((((.((((((.(.(((((.(((........))).))))).).)))))).))))))))))))))))))))))......... ( -63.60)
>DroYak_CAF1 11829 120 - 1
ACUACGUCCAACUUCGAGCUGGGCAGAAUGCCGGAGCAACGCGAUGGCUACCAGCCGGGGCAGUACACAUUGCACCGGCCGUUAGCUAACGCGUUCGGCAUCUUGCCCGGCGGCUUGAAU
............(((((((((((((..(((((((....(((((.((((((.(.(((((.(((((....))))).))))).).)))))).))))))))))))..)))))...)))))))). ( -62.40)
>consensus
ACUGCGUCCAAUUUUGAGCUGGGCAAAAUGCCGGAACAACGCGAUGGCUAUCAGCCGGGGCAAUACACAAUGCACCGGCCGUUAGCUAACACGUUCGGCAUUUUGCCCGGCGGUUUAAAU
.................(((((((((((((((((....(((.(.((((((.(.(((((.(((........))).))))).).)))))).).))))))))))))))))))))......... (-56.32 = -56.20 +  -0.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:05 2006