Locus 122

Sequence ID 3R_DroMel_CAF1
Location 680,000 – 680,127
Length 127
Max. P 0.989132
window199 window200 window201

overview

Window 9

Location 680,000 – 680,100
Length 100
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 78.13
Mean single sequence MFE -46.08
Consensus MFE -25.74
Energy contribution -27.55
Covariance contribution 1.81
Combinations/Pair 1.09
Mean z-score -2.66
Structure conservation index 0.56
SVM decision value 1.69
SVM RNA-class probability 0.972014
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 680000 100 + 27905053
CUUGC--GU------GGGCAUAACCCUUG-CCCGCCU---GGGCAAAUCCCGGACGUUGUCGAUGUGAGCGUGU-UACCGACGGCAAAAGUCGUUGCAACGCCCACUACCUGG
.....--((------(((((.......))-)))))((---(((.....)))))...........(((.((((..-...(((((((....)))))))..)))).)))....... ( -35.80)
>DroPse_CAF1 100719 99 + 1
CUUGCC-GU------GGGUUUAACCCUUU-CCGGGGC---AAGUAAAUCCCUUCGG--CUUGAGGUGGGCGUGCGUUCCGACGGCAAAAGUCGGUGCAACGCCCACC-CCUGG
(..(((-(.------(((((((.((((..-..)))).---...)))))))...)))--)..).(((((((((..((.(((((.......))))).)).)))))))))-..... ( -48.00)
>DroEre_CAF1 96278 100 + 1
CUUGU--GU------GGGCAUAUCCCUUG-CCCGACU---GGGCAAAUCCCGCACGUUGUCGAUGUGGGCGUGU-UGCCGUCGGCAAAAGUCGGUGAUACGCCCACUACCUGG
...((--((------(((.((.....(((-(((....---))))))))))))))).........((((((((((-..(((.(.......).)))..))))))))))....... ( -48.80)
>DroYak_CAF1 109311 106 + 1
CUUGU--GUAGGUAUGGGCAUAACCCUUG-CUUGACU---GGGCAAAUCCCGCACGUUGUCGAGGUGGGCGUGU-UGCCGCCGGCAAAAGUCGGUGCAACGCCCACUACCUGG
.....--.(((((((((((....(((...-(((((((---(((.....))))......))))))..)))...((-(((.((((((....)))))))))))))))).)))))). ( -46.50)
>DroAna_CAF1 99014 106 + 1
CUUGCCGGC------GGGUUUAACCCUUUGACCCUUUGACGGGUAAAUCCCGGACGUGGUCGAGGUGGGCGUGU-UGCCGACGGCAAAAGUCGGUGCAACGCCCACUACCUGG
....((((.------(((.....))).((((((......((((.....)))).....))))))(((((((((..-.((((((.......))))))...)))))))))..)))) ( -49.40)
>DroPer_CAF1 101706 99 + 1
CUUGCC-GU------GGGUUUAACCCUUU-CCGGGGC---AUGUAAAUCCCUUCGG--CUUGAGGUGGGCGUGCGUUCCGACGGCAAAAGUCGGUGCAACGCCCACC-CCUGG
(..(((-(.------(((((((.((((..-..)))).---...)))))))...)))--)..).(((((((((..((.(((((.......))))).)).)))))))))-..... ( -48.00)
>consensus
CUUGC__GU______GGGCAUAACCCUUG_CCCGACU___GGGCAAAUCCCGCACGUUGUCGAGGUGGGCGUGU_UGCCGACGGCAAAAGUCGGUGCAACGCCCACUACCUGG
...............(((.....)))..............(((.....)))............(((((((((...(((((((.......)))))))..)))))))))...... (-25.74 = -27.55 +   1.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 680,000 – 680,100
Length 100
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 78.13
Mean single sequence MFE -45.07
Consensus MFE -25.04
Energy contribution -25.24
Covariance contribution 0.20
Combinations/Pair 1.20
Mean z-score -3.12
Structure conservation index 0.56
SVM decision value 2.15
SVM RNA-class probability 0.989132
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 680000 100 - 27905053
CCAGGUAGUGGGCGUUGCAACGACUUUUGCCGUCGGUA-ACACGCUCACAUCGACAACGUCCGGGAUUUGCCC---AGGCGGG-CAAGGGUUAUGCCC------AC--GCAAG
.......((((((((......((((((((((((((((.-..........))))))..((((.(((.....)))---.))))))-))))))))))))))------))--..... ( -42.80)
>DroPse_CAF1 100719 99 - 1
CCAGG-GGUGGGCGUUGCACCGACUUUUGCCGUCGGAACGCACGCCCACCUCAAG--CCGAAGGGAUUUACUU---GCCCCGG-AAAGGGUUAAACCC------AC-GGCAAG
...((-(((((((((.((.(((((.......)))))...)))))))))))))..(--(((..(((.((((...---((((...-...)))))))))))------.)-)))... ( -49.80)
>DroEre_CAF1 96278 100 - 1
CCAGGUAGUGGGCGUAUCACCGACUUUUGCCGACGGCA-ACACGCCCACAUCGACAACGUGCGGGAUUUGCCC---AGUCGGG-CAAGGGAUAUGCCC------AC--ACAAG
....((.(((((((((((.((.....((((((((((((-(....(((.((.((....)))).)))..))))).---.))).))-))))))))))))))------))--))... ( -45.00)
>DroYak_CAF1 109311 106 - 1
CCAGGUAGUGGGCGUUGCACCGACUUUUGCCGGCGGCA-ACACGCCCACCUCGACAACGUGCGGGAUUUGCCC---AGUCAAG-CAAGGGUUAUGCCCAUACCUAC--ACAAG
..(((((.(((((((......(((((((((.(((((((-(....(((.(..((....)).).)))..))))).---.)))..)-))))))))))))))))))))..--..... ( -39.00)
>DroAna_CAF1 99014 106 - 1
CCAGGUAGUGGGCGUUGCACCGACUUUUGCCGUCGGCA-ACACGCCCACCUCGACCACGUCCGGGAUUUACCCGUCAAAGGGUCAAAGGGUUAAACCC------GCCGGCAAG
...(((.((((((((....(((((.......)))))..-..))))))))....)))..(.((((..(((((((......)))).)))(((.....)))------.)))))... ( -44.00)
>DroPer_CAF1 101706 99 - 1
CCAGG-GGUGGGCGUUGCACCGACUUUUGCCGUCGGAACGCACGCCCACCUCAAG--CCGAAGGGAUUUACAU---GCCCCGG-AAAGGGUUAAACCC------AC-GGCAAG
...((-(((((((((.((.(((((.......)))))...)))))))))))))..(--(((..(((.((((...---((((...-...)))))))))))------.)-)))... ( -49.80)
>consensus
CCAGGUAGUGGGCGUUGCACCGACUUUUGCCGUCGGCA_ACACGCCCACCUCGACAACGUACGGGAUUUACCC___AGCCGGG_AAAGGGUUAAACCC______AC__GCAAG
.......((((((((....(((((.......))))).....)))))))).............(((....((((..............))))....)))............... (-25.04 = -25.24 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 680,028 – 680,127
Length 99
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 80.29
Mean single sequence MFE -42.68
Consensus MFE -27.43
Energy contribution -29.23
Covariance contribution 1.81
Combinations/Pair 1.09
Mean z-score -1.67
Structure conservation index 0.64
SVM decision value 0.35
SVM RNA-class probability 0.699569
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 680028 99 + 27905053
GGGCAAAUCCCGGACGUUGUCGAUGUGAGCGUGU-UACCGACGGCAAAAGUCGUUGCAACGCCCACUACCUGGCUUAACCCGCCACUG---GCCGG-GCGGGUC
(((.....))).......((((..(((.((((..-...(((((((....)))))))..)))).)))....))))...(((((((....---....)-)))))). ( -36.30)
>DroPse_CAF1 100748 100 + 1
AAGUAAAUCCCUUCGG--CUUGAGGUGGGCGUGCGUUCCGACGGCAAAAGUCGGUGCAACGCCCACC-CCUGGCUUAACCCGCCACCAUCCUACGC-GCGGGCC
..............((--((.(.(((((((((..((.(((((.......))))).)).)))))))))-.).))))...((((((..........).-))))).. ( -42.70)
>DroEre_CAF1 96306 102 + 1
GGGCAAAUCCCGCACGUUGUCGAUGUGGGCGUGU-UGCCGUCGGCAAAAGUCGGUGAUACGCCCACUACCUGGCUUAACCCGCCACUGGCCAUCGG-UCGGGCC
(((.....)))((...........((((((((((-..(((.(.......).)))..))))))))))....((((.......))))((((((...))-)))))). ( -44.80)
>DroYak_CAF1 109345 93 + 1
GGGCAAAUCCCGCACGUUGUCGAGGUGGGCGUGU-UGCCGCCGGCAAAAGUCGGUGCAACGCCCACUACCUGGCUUAACCCG---------GUCGG-UCGGGCC
((((....(((((.((....))..)))))...((-(((.((((((....))))))))))))))).......((((..(((..---------...))-)..)))) ( -43.40)
>DroAna_CAF1 99048 100 + 1
GGGUAAAUCCCGGACGUGGUCGAGGUGGGCGUGU-UGCCGACGGCAAAAGUCGGUGCAACGCCCACUACCUGGCUUAACCCGCCACCG---GACGCUGCGAGCC
(((.....)))((.((..(.((.(((((((((..-.((((((.......))))))...))))))))).((((((.......))))..)---).)))..))..)) ( -46.20)
>DroPer_CAF1 101735 100 + 1
AUGUAAAUCCCUUCGG--CUUGAGGUGGGCGUGCGUUCCGACGGCAAAAGUCGGUGCAACGCCCACC-CCUGGCUUAACCCGCCACCAUCCUACGC-GCGGGCC
..............((--((.(.(((((((((..((.(((((.......))))).)).)))))))))-.).))))...((((((..........).-))))).. ( -42.70)
>consensus
GGGCAAAUCCCGCACGUUGUCGAGGUGGGCGUGU_UGCCGACGGCAAAAGUCGGUGCAACGCCCACUACCUGGCUUAACCCGCCACCG___GACGC_GCGGGCC
........(((............(((((((((...(((((((.......)))))))..)))))))))...((((.......))))..............))).. (-27.43 = -29.23 +   1.81)

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 09:33:47 2006