Locus 1206

Sequence ID X_DroMel_CAF1
Location 3,586,989 – 3,587,130
Length 141
Max. P 0.968414
window1938 window1939 window1940

overview

Window 8

Location 3,586,989 – 3,587,099
Length 110
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 75.88
Mean single sequence MFE -31.35
Consensus MFE -13.02
Energy contribution -16.86
Covariance contribution 3.84
Combinations/Pair 1.23
Mean z-score -2.31
Structure conservation index 0.42
SVM decision value 0.80
SVM RNA-class probability 0.853486
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3586989 110 + 22224390
AAU-------UUUUUGGUAGAUAUUCGCCUGCUGUCGAUUUCUUGACACCCGGUAUUUCGCAUUUGCUCCAUACAACAAAUACCAUGGGUAUUUGCUCAUAAAUCGGGCGGAGGCAA
...-------................((((.(((((((....))))))((((((.....(((..(((.((((............)))))))..)))......)))))).).)))).. ( -29.90)
>DroVir_CAF1 76802 100 + 1
CAUU-----UGUUGCGGCA---GUUUGCCUGCUCGCCUUUUCUCAGCACCCAGCAGUUGGCAUACGCGCCAUACAACAAAAU---------UGUGCUCAUAAACCGUGUGUAGGUAA
..((-----(((((.(((.---((.((((.(((.((................))))).)))).))..)))...)))))))..---------(.(((.(((.....))).))).)... ( -24.49)
>DroSec_CAF1 45965 110 + 1
AAU-------UUUUUGGUAGAUAUUCGCCUGCUGUCGAUUUCUUGACACCCGGUAUUUCGCAUUUGCUCCAUACAACAAAUACCAUAGGUAUUUGCUCAUAAAUCGGGCGUAGGCAA
...-------................((((((((((((....))))))((((((((...((....))...))))..((((((((...)))))))).........)))).)))))).. ( -32.30)
>DroEre_CAF1 40776 110 + 1
AAU-------UUUUCGGUAGAUAUUCGCCUGCUGUCGAUUUCUUGACACCCGGUAUUUCGCAUUUGCGACAUACAACAAAUACCAUGUGCAAUCGCUCAUAAAUCGGGUGUAGGCAA
...-------................((((((.(((((....)))))(((((((((.((((....)))).))))..........(((.((....)).)))....))))))))))).. ( -35.40)
>DroYak_CAF1 41684 110 + 1
AAU-------UUUUCGGUAGAUAUUCGCCUGCUGUCAAUUUCUUGACACCCGGUAUUUCGCAUUUGCGACAUACAACAAAUACCGUGUGCAAUCGCUCAUAAAUCGGGUGUAGGCAA
...-------................((((((.(((((....)))))(((((((((.((((....)))).))))..........(((.((....)).)))....))))))))))).. ( -36.00)
>DroMoj_CAF1 80995 107 + 1
CAUUUCGUUUAUUGCGGUAGA-GUUUGCCUGCUCGCCUUUUCUCAGCACCCAGCAGUUGGCAUACGCGCCGCACAACAAAAU---------UGUGCUCAUAAACCGUGUGUAGGCAA
....((((.....))))....-..((((((((.(((.........((.....)).((((((......)))((((((.....)---------))))).....))).))).)))))))) ( -30.00)
>consensus
AAU_______UUUUCGGUAGAUAUUCGCCUGCUGUCGAUUUCUUGACACCCGGUAUUUCGCAUUUGCGCCAUACAACAAAUACCAUG_G_AUUUGCUCAUAAAUCGGGUGUAGGCAA
..........................((((((((((((....))))))((((((.....(((.(((((...................))))).)))......)))))).)))))).. (-13.02 = -16.86 +   3.84)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,586,989 – 3,587,099
Length 110
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 75.88
Mean single sequence MFE -31.77
Consensus MFE -20.06
Energy contribution -20.95
Covariance contribution 0.89
Combinations/Pair 1.25
Mean z-score -2.07
Structure conservation index 0.63
SVM decision value 1.63
SVM RNA-class probability 0.968414
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3586989 110 - 22224390
UUGCCUCCGCCCGAUUUAUGAGCAAAUACCCAUGGUAUUUGUUGUAUGGAGCAAAUGCGAAAUACCGGGUGUCAAGAAAUCGACAGCAGGCGAAUAUCUACCAAAAA-------AUU
((((((.((((((.......((((((((((...))))))))))((((...((....))...)))))))))(((.(....).))).).))))))..............-------... ( -33.80)
>DroVir_CAF1 76802 100 - 1
UUACCUACACACGGUUUAUGAGCACA---------AUUUUGUUGUAUGGCGCGUAUGCCAACUGCUGGGUGCUGAGAAAAGGCGAGCAGGCAAAC---UGCCGCAACA-----AAUG
.((((((((...(((.((((.(((((---------((...)))))...)).)))).)))...)).))))))..........(((.((((.....)---))))))....-----.... ( -27.40)
>DroSec_CAF1 45965 110 - 1
UUGCCUACGCCCGAUUUAUGAGCAAAUACCUAUGGUAUUUGUUGUAUGGAGCAAAUGCGAAAUACCGGGUGUCAAGAAAUCGACAGCAGGCGAAUAUCUACCAAAAA-------AUU
((((((.((((((.......((((((((((...))))))))))((((...((....))...)))))))))(((.(....).))).).))))))..............-------... ( -33.80)
>DroEre_CAF1 40776 110 - 1
UUGCCUACACCCGAUUUAUGAGCGAUUGCACAUGGUAUUUGUUGUAUGUCGCAAAUGCGAAAUACCGGGUGUCAAGAAAUCGACAGCAGGCGAAUAUCUACCGAAAA-------AUU
((((((.((((((.......(((((.(((.....))).)))))((((.((((....)))).)))))))))(((.(....).))).).))))))..............-------... ( -31.80)
>DroYak_CAF1 41684 110 - 1
UUGCCUACACCCGAUUUAUGAGCGAUUGCACACGGUAUUUGUUGUAUGUCGCAAAUGCGAAAUACCGGGUGUCAAGAAAUUGACAGCAGGCGAAUAUCUACCGAAAA-------AUU
((((((.((((((.......(((((.(((.....))).)))))((((.((((....)))).)))))))))(((((....))))).).))))))..............-------... ( -35.90)
>DroMoj_CAF1 80995 107 - 1
UUGCCUACACACGGUUUAUGAGCACA---------AUUUUGUUGUGCGGCGCGUAUGCCAACUGCUGGGUGCUGAGAAAAGGCGAGCAGGCAAAC-UCUACCGCAAUAAACGAAAUG
..(((.......)))...........---------((((((((.(((((.(.((.((((...((((...((((.......)))))))))))).))-.)..)))))...)))))))). ( -27.90)
>consensus
UUGCCUACACCCGAUUUAUGAGCAAAU_C_CAUGGUAUUUGUUGUAUGGCGCAAAUGCGAAAUACCGGGUGUCAAGAAAUCGACAGCAGGCGAAUAUCUACCGAAAA_______AUU
((((((.((((((.......(((((((((.....)))))))))((((...((....))...))))))))))..........(....)))))))........................ (-20.06 = -20.95 +   0.89)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,587,020 – 3,587,130
Length 110
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 78.91
Mean single sequence MFE -27.55
Consensus MFE -19.07
Energy contribution -19.45
Covariance contribution 0.38
Combinations/Pair 1.31
Mean z-score -1.76
Structure conservation index 0.69
SVM decision value 0.91
SVM RNA-class probability 0.880521
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3587020 110 - 22224390
AUUAAUCUCCAGCACGAAAAUCUGCUAAUAUUUGCCUCCGCCCGAUUUAUGAGCAAAUACCCAUGGUAUUUGUUGUAUGGAGCAAAUGCGAAAUACCGGGUGUCAAGAAA
.....(((..((((.(.....)))))............((((((.......((((((((((...))))))))))((((...((....))...))))))))))...))).. ( -28.20)
>DroSec_CAF1 45996 110 - 1
AUUAAUCUCCAGCGCGAAAAUCUGCUAAUAUUUGCCUACGCCCGAUUUAUGAGCAAAUACCUAUGGUAUUUGUUGUAUGGAGCAAAUGCGAAAUACCGGGUGUCAAGAAA
.....(((..((.(((((.((......)).)))))))(((((((.......((((((((((...))))))))))((((...((....))...)))))))))))..))).. ( -29.70)
>DroSim_CAF1 32775 110 - 1
AUUAAUCUCCAGCACGAAAAUCUGCUAAUAUUUGCCUACGCCCGAUUUAUGAGCAAAUACCCAUGGUAUUUGUUGUAUGGAACAAAUGCGAAAUACCGGGUGUCAAGAAA
..........((((.(.....)))))....((((...(((((((.......((((((((((...))))))))))((((.......)))).......)))))))))))... ( -26.90)
>DroEre_CAF1 40807 110 - 1
ACUAAUCCCUGGCACGAAAAUCAGCUAAUAUUUGCCUACACCCGAUUUAUGAGCGAUUGCACAUGGUAUUUGUUGUAUGUCGCAAAUGCGAAAUACCGGGUGUCAAGAAA
..........((((..................)))).(((((((.......(((((.(((.....))).)))))((((.((((....)))).)))))))))))....... ( -27.77)
>DroYak_CAF1 41715 105 - 1
ACUAACU-----AAUGAAAAUCAGCUAAUAUUUGCCUACACCCGAUUUAUGAGCGAUUGCACACGGUAUUUGUUGUAUGUCGCAAAUGCGAAAUACCGGGUGUCAAGAAA
.......-----........((.((........))..(((((((.......(((((.(((.....))).)))))((((.((((....)))).)))))))))))...)).. ( -25.80)
>DroMoj_CAF1 81032 97 - 1
AUAAUAAAGCAGUGCGCA----ACACAAUAUUUGCCUACACACGGUUUAUGAGCACA---------AUUUUGUUGUGCGGCGCGUAUGCCAACUGCUGGGUGCUGAGAAA
...((..(((((((((((----(((.(((...((((.((.....))....).)))..---------))).))))))))((((....)))).))))))..))......... ( -26.90)
>consensus
AUUAAUCUCCAGCACGAAAAUCAGCUAAUAUUUGCCUACACCCGAUUUAUGAGCAAAUACCCAUGGUAUUUGUUGUAUGGAGCAAAUGCGAAAUACCGGGUGUCAAGAAA
..............................((((...(((((((.......(((((((((.....)))))))))((((...((....))...)))))))))))))))... (-19.07 = -19.45 +   0.38)

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 10:03:55 2006