Locus 615

Sequence ID 2L_DroMel_CAF1
Location 1,828,989 – 1,829,120
Length 131
Max. P 0.969076
window1006 window1007 window1008

overview

Window 6

Location 1,828,989 – 1,829,088
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.08
Mean single sequence MFE -32.06
Consensus MFE -16.89
Energy contribution -17.60
Covariance contribution 0.71
Combinations/Pair 1.20
Mean z-score -2.68
Structure conservation index 0.53
SVM decision value 0.74
SVM RNA-class probability 0.838336
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1828989 99 + 22407834
----CGGGGCGGGCCUCU----------------AGUGCCAUUUGUAAAUCAAAUUCUGACUUUGCGAAACAUCAAAAUGCUUCGAGAGCCCCCCUCA-AAAAACGAAAAUUAUUGCCAA
----.((((.(((((((.----------------..........((((((((.....))).)))))(((.(((....))).)))))).)))).)))).-..................... ( -25.00)
>DroSec_CAF1 49007 114 + 1
----CCGGGCGGGCCUCCAAUUCUGGGCCAGCCCAGUGCCAUUUGUAAAUCAAAUUCUGACUCUGCGAAACAUCAAAAUGUUUCGAGAGCCC-CCUCA-AAAAACGAAAAUUAUUGCCAA
----..((((.(((((........))))).)))).......(((((...(((.....)))((((.((((((((....))))))))))))...-.....-....)))))............ ( -32.80)
>DroSim_CAF1 29570 114 + 1
----CGGGGCGAGCCUCCAAUUCUGGGCCAGCCCAGUGCCAUUUGUAAAUCAAAUUCUGACUCUGCGAAACAUCAAAAUGUUUCGAGAGCCC-CCUCA-AAAAAUGAAAAUUAUUGCCAA
----.((((((((.........(((((....)))))....(((((.....))))).....)))..((((((((....))))))))...))))-)....-..................... ( -31.00)
>DroEre_CAF1 37564 119 + 1
GCAAUGGGGCGGGCCACCCAUUUUGGGCCAAUGCAGCGCCCUUUGUAAAUCAAAUUCUGGCCCUGCGAAACAUCAAAAUGUUUCCAGAGCGC-CCUGAGAAAAAUGAAAAUUAUUACCAA
.....(((((((((((........(((((......).))))((((.....))))...)))))(((.(((((((....))))))))))..)))-)))........................ ( -36.30)
>DroYak_CAF1 13979 109 + 1
----UGGGGCGG-----CAAUUCUGGGCCAACCCAGUGCCAUUUGUAAAUCAAAUUCUGGCCCUGCGAAACAUCAAAAUGUUUCGAGAGCGC-CCUCA-AAAAACGAAAAUUAUUGCCAA
----.(((((((-----((...(((((....)))))))))(((((.....)))))....((.((.((((((((....)))))))))).))))-)))..-..................... ( -35.20)
>consensus
____CGGGGCGGGCCUCCAAUUCUGGGCCAACCCAGUGCCAUUUGUAAAUCAAAUUCUGACUCUGCGAAACAUCAAAAUGUUUCGAGAGCCC_CCUCA_AAAAACGAAAAUUAUUGCCAA
.......(((((..........(((((....))))).....(((((...(((.....)))((((.((((((((....))))))))))))..............))))).....))))).. (-16.89 = -17.60 +   0.71)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,828,989 – 1,829,088
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.08
Mean single sequence MFE -37.06
Consensus MFE -21.35
Energy contribution -22.26
Covariance contribution 0.91
Combinations/Pair 1.18
Mean z-score -2.34
Structure conservation index 0.58
SVM decision value 0.53
SVM RNA-class probability 0.772722
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1828989 99 - 22407834
UUGGCAAUAAUUUUCGUUUUU-UGAGGGGGGCUCUCGAAGCAUUUUGAUGUUUCGCAAAGUCAGAAUUUGAUUUACAAAUGGCACU----------------AGAGGCCCGCCCCG----
..(((.....((((((.....-))))))((((.((((((((((....))))))).....((((...((((.....))))))))...----------------.))))))))))...---- ( -29.10)
>DroSec_CAF1 49007 114 - 1
UUGGCAAUAAUUUUCGUUUUU-UGAGG-GGGCUCUCGAAACAUUUUGAUGUUUCGCAGAGUCAGAAUUUGAUUUACAAAUGGCACUGGGCUGGCCCAGAAUUGGAGGCCCGCCCGG----
...((.....((((((.....-)))))-)((((((((((((((....)))))))).))))))...(((((.....))))).)).((((((.(((((.......).)))).))))))---- ( -40.70)
>DroSim_CAF1 29570 114 - 1
UUGGCAAUAAUUUUCAUUUUU-UGAGG-GGGCUCUCGAAACAUUUUGAUGUUUCGCAGAGUCAGAAUUUGAUUUACAAAUGGCACUGGGCUGGCCCAGAAUUGGAGGCUCGCCCCG----
............((((.....-))))(-((((...((((((((....))))))))..(((((.(.(((((.....)))))..).(((((....))))).......)))))))))).---- ( -38.50)
>DroEre_CAF1 37564 119 - 1
UUGGUAAUAAUUUUCAUUUUUCUCAGG-GCGCUCUGGAAACAUUUUGAUGUUUCGCAGGGCCAGAAUUUGAUUUACAAAGGGCGCUGCAUUGGCCCAAAAUGGGUGGCCCGCCCCAUUGC
...(((((.................((-((......(((((((....)))))))((((.(((....((((.....)))).))).))))....)))).....(((((...))))).))))) ( -37.80)
>DroYak_CAF1 13979 109 - 1
UUGGCAAUAAUUUUCGUUUUU-UGAGG-GCGCUCUCGAAACAUUUUGAUGUUUCGCAGGGCCAGAAUUUGAUUUACAAAUGGCACUGGGUUGGCCCAGAAUUG-----CCGCCCCA----
.....................-((.((-(((((((((((((((....)))))))).)))))....(((((.....)))))(((((((((....)))))...))-----))))))))---- ( -39.20)
>consensus
UUGGCAAUAAUUUUCGUUUUU_UGAGG_GGGCUCUCGAAACAUUUUGAUGUUUCGCAGAGUCAGAAUUUGAUUUACAAAUGGCACUGGGCUGGCCCAGAAUUGGAGGCCCGCCCCG____
..(((........(((..(((........((((((((((((((....)))))))).)))))).)))..))).............(((((....)))))............)))....... (-21.35 = -22.26 +   0.91)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,829,009 – 1,829,120
Length 111
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 92.96
Mean single sequence MFE -27.50
Consensus MFE -24.34
Energy contribution -24.10
Covariance contribution -0.24
Combinations/Pair 1.19
Mean z-score -1.67
Structure conservation index 0.89
SVM decision value 1.64
SVM RNA-class probability 0.969076
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1829009 111 - 22407834
CUAUGCGACAAGUCAAAUGUCAUGCAACCACUUUGGCAAUAAUUUUCGUUUUU-UGAGGGGGGCUCUCGAAGCAUUUUGAUGUUUCGCAAAGUCAGAAUUUGAUUUACAAAU
...(((((...((((((....((((..((.....))...............((-((((((...))))))))))))))))))...)))))(((((((...)))))))...... ( -24.80)
>DroSec_CAF1 49043 110 - 1
CUAUGCGACAAGUCAAAUGUCAUGCAACCACUUUGGCAAUAAUUUUCGUUUUU-UGAGG-GGGCUCUCGAAACAUUUUGAUGUUUCGCAGAGUCAGAAUUUGAUUUACAAAU
.........(((((((((.((......((.(((.(((..........)))...-.))))-)((((((((((((((....)))))))).)))))).)))))))))))...... ( -28.10)
>DroSim_CAF1 29606 110 - 1
CUAUACGACAAGUCAAAUGUCAUGCAACCACUUUGGCAAUAAUUUUCAUUUUU-UGAGG-GGGCUCUCGAAACAUUUUGAUGUUUCGCAGAGUCAGAAUUUGAUUUACAAAU
.........(((((((((((((...........)))).....((((((.....-)))))-)((((((((((((((....)))))))).))))))...)))))))))...... ( -28.60)
>DroEre_CAF1 37604 111 - 1
CUGUGCGACAAGUCAAAUGCCAUGCACCCACUUUGGUAAUAAUUUUCAUUUUUCUCAGG-GCGCUCUGGAAACAUUUUGAUGUUUCGCAGGGCCAGAAUUUGAUUUACAAAG
.........((((((((((((.((.........(((.........))).......)).)-))(((((((((((((....))))))).))))))....)))))))))...... ( -26.69)
>DroYak_CAF1 14010 110 - 1
CUAUACGACAAGUCAAAUGCCAUGCACCCACUUUGGCAAUAAUUUUCGUUUUU-UGAGG-GCGCUCUCGAAACAUUUUGAUGUUUCGCAGGGCCAGAAUUUGAUUUACAAAU
.........((((((((((((.(((..........)))......((((.....-)))))-))(((((((((((((....)))))))).)))))....)))))))))...... ( -29.30)
>consensus
CUAUGCGACAAGUCAAAUGUCAUGCAACCACUUUGGCAAUAAUUUUCGUUUUU_UGAGG_GGGCUCUCGAAACAUUUUGAUGUUUCGCAGAGUCAGAAUUUGAUUUACAAAU
.........(((((((((((((...........))))........................((((((((((((((....)))))))).))))))...)))))))))...... (-24.34 = -24.10 +  -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 09:41:03 2006