Locus 8363

Sequence ID 3L_DroMel_CAF1
Location 21,953,290 – 21,953,565
Length 275
Max. P 0.893326
window13680 window13681 window13682

overview

Window 0

Location 21,953,290 – 21,953,382
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.08
Mean single sequence MFE -33.55
Consensus MFE -28.41
Energy contribution -28.63
Covariance contribution 0.23
Combinations/Pair 1.14
Mean z-score -1.62
Structure conservation index 0.85
SVM decision value 0.29
SVM RNA-class probability 0.669473
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21953290 92 - 23771897
---------------------------UCCUUUGAGGGCGGCUAAUUCGACUGCAGGUGCGGUCGCCAUUUAAUUGCAUUUGC-GCUGGAGGAGCUGCUGCAUUCGGAAUUCCUUUUACG
---------------------------(((..((..(((((((..((((..((((((((((((.........)))))))))))-).))))..))))))).))...)))............ ( -30.70)
>DroSec_CAF1 79344 92 - 1
---------------------------UCCUUUGAGGGCGGCUAAUUCGACUGCAGGUGCGGUCGCCAUUUAAUUGCAUUUGC-GCUGGAGGAGCUGCUGCAUUCGGAAUUCCUUUUACG
---------------------------(((..((..(((((((..((((..((((((((((((.........)))))))))))-).))))..))))))).))...)))............ ( -30.70)
>DroSim_CAF1 78862 92 - 1
---------------------------UCCUUUGAGGGCGGCUAAUUCGACUGCAGGUGCGGUCGCCAUUUAAUUGCAUUUGC-GCUGGAGGAGCUGCUGCAUUCGGAAUUCCUUUUACG
---------------------------(((..((..(((((((..((((..((((((((((((.........)))))))))))-).))))..))))))).))...)))............ ( -30.70)
>DroEre_CAF1 75470 92 - 1
---------------------------UCCUUUGAGGGCGGCUAAUUCGACUGCAGGUGCGGUCGCCAUUUAAUUGCAUUUGC-GCCGGAGGAGCUGCUGCAUUCGGAAUUCCUUUUACG
---------------------------(((..((..(((((((..((((..((((((((((((.........)))))))))))-).))))..))))))).))...)))............ ( -32.40)
>DroYak_CAF1 90213 92 - 1
---------------------------UCCUUUGAGGGCGGCUAAUUCGACUGCAGGUGCGGUCGCCAUUUAAUUGCAUUUGC-GCUGAAGGAGCUGCUGCAUUCGGAAUUCCUUUUAUG
---------------------------(((..((..(((((((..((((..((((((((((((.........)))))))))))-).))))..))))))).))...)))............ ( -31.20)
>DroAna_CAF1 82396 120 - 1
GGAUUCGGAGGACGUCCUGACGUUCCAUGCACUGGGGGCAGCUAAUUCGGCAGCAGGUGCGGACUUUAUUUAAUUGCAUUUGCUGCCGCAGGAUCUGCUGCAUUCUGGAAUUCUUUUACG
((((((.(.((((((....))))))).......(((((((((..((((((((((((((((((...........)))))))))))))))...)))..))))).)))).))))))....... ( -45.60)
>consensus
___________________________UCCUUUGAGGGCGGCUAAUUCGACUGCAGGUGCGGUCGCCAUUUAAUUGCAUUUGC_GCUGGAGGAGCUGCUGCAUUCGGAAUUCCUUUUACG
...........................(((..((..(((((((..((((.(.(((((((((((.........))))))))))).).))))..))))))).))...)))............ (-28.41 = -28.63 +   0.23)

alignment

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secondary structure

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Window 1

Location 21,953,382 – 21,953,489
Length 107
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 90.66
Mean single sequence MFE -34.08
Consensus MFE -29.46
Energy contribution -29.38
Covariance contribution -0.08
Combinations/Pair 1.18
Mean z-score -1.57
Structure conservation index 0.86
SVM decision value 0.98
SVM RNA-class probability 0.893326
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21953382 107 + 23771897
AACAGAAUAAAGG-GGAGCA-AGAUGCGGAGCCUGAGGCGCUUUUGGUUUCGCUUAGGGUAUCUGCACUUAGGCAAAGGAAAAGCAGCAGCCGCAGAUCCGAAAAGCCU
...........((-(..((.-....))(((..(((.(((((((((..(((.(((((((((....)).))))))))))..))))))....))).))).)))......))) ( -31.20)
>DroSec_CAF1 79436 108 + 1
AACAGAAAAAAGGGGGAGCA-GGAUGCGGUGCCUGAGGCGCUUUUGUUUUCGCUUGGGGUAUCUGCACUUAGGCAAAGGAAAAGCAGCAGCCGCAGAUCCGAAAAGCUU
...............((((.-((((((((((((...)))((((((.((((.(((((((((....)).))))))))))).))))))....))))))..))).....)))) ( -35.90)
>DroSim_CAF1 78954 107 + 1
AACAGAAAAAAGG-GGAGCA-AGAUGCGGUGCCUGAGGCGCUUUUGUUUUCGCUUGGGGUAUCUGCACUUAGGCAAAGGAUAAGCAGCAGCCGCAGAUCCGAAAAGCUU
.............-.(((((-((.((((((((((.(((((..........))))).))))).)))))))).......((((..((.......))..)))).....)))) ( -31.80)
>DroEre_CAF1 75562 108 + 1
AACAGAAAAAAGG-GGAGCACGGAUGUGGUGCCUGGAGCGCUUUUGUUUCUGCUUGGGAUAUCUGCACUUGGGCGAAGGAAAAGCAGCAGCCGCAGAUCCGGAAAGCUU
.............-.((((.((((((((((((.....))((((((.((((.(((..((.........))..))))))).))))))....))))))..))))....)))) ( -35.30)
>DroYak_CAF1 90305 108 + 1
AACAGAAAAAAGA-GGAGCAAGGAUGCGGUGCCUAAGGCGCUUUUGUUGUUGCUUGGGGUAUCUGCACUUAGGCGAAGGAAAAGCAUCAGCCGCAGAUCCGGAAAGCCU
............(-((.....((((((((((((...)))((((((.((.(((((((((((....)).))))))))))).))))))....))))))..)))......))) ( -36.20)
>consensus
AACAGAAAAAAGG_GGAGCA_GGAUGCGGUGCCUGAGGCGCUUUUGUUUUCGCUUGGGGUAUCUGCACUUAGGCAAAGGAAAAGCAGCAGCCGCAGAUCCGAAAAGCUU
..............(((.......((((((((.....))((((((.((((.(((((((.........))))))))))).))))))....))))))..)))......... (-29.46 = -29.38 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,953,449 – 21,953,565
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.14
Mean single sequence MFE -36.13
Consensus MFE -18.63
Energy contribution -20.15
Covariance contribution 1.52
Combinations/Pair 1.32
Mean z-score -1.82
Structure conservation index 0.52
SVM decision value 0.17
SVM RNA-class probability 0.616021
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21953449 116 - 23771897
CACAUUUGAAAGCA-UUUGGGGCCUGGAAA---GCGGUUCGCAACUUAACCUGCCAAUUUGGUUUAUUGUUGUCCGAGAAAGGCUUUUCGGAUCUGCGGCUGCUGCUUUUCCUUUGCCUA
..((..((....))-..))((((..(((((---((((((((((((..((((.........))))....)))(((((((((....)))))))))..))))..))))).)))))...)))). ( -37.40)
>DroSec_CAF1 79504 119 - 1
CACAUUUGAAAGUU-UUUGGGGCUUGGGAAGCAGCGGUUCGCAACUUAACCUGCCAAUUUGGUUUAUUGUUGUCCGAGAAAAGCUUUUCGGAUCUGCGGCUGCUGCUUUUCCUUUGCCUA
..............-....((((..(((((((((((((.((((((..((((.........))))....)))(((((((((....)))))))))..))))))))))))..))))..)))). ( -45.50)
>DroSim_CAF1 79021 119 - 1
CACAUUUGAAAGUU-UUUGGGGCUUGGGAAGCAGCGGUUCGCAACUUAACCUGCCAAUUUGGUUUAUUGUUGUCCGAGAAAAGCUUUUCGGAUCUGCGGCUGCUGCUUAUCCUUUGCCUA
..............-....((((..(((((((((((((.((((((..((((.........))))....)))(((((((((....)))))))))..))))))))))))..))))..)))). ( -45.50)
>DroEre_CAF1 75630 117 - 1
CACAUUUGAAACGGCUUUGGGGUUUGGAAA---GCGAAUCGCAACUUAACCUGCCAAUUUGGUUUAUUGGUGUCCGAGGAAAGCUUUCCGGAUCUGCGGCUGCUGCUUUUCCUUCGCCCA
............(((...((((((((((((---((...(((..(((......(((.....))).....)))...))).....)))))))))))).((((...))))....))...))).. ( -33.60)
>DroYak_CAF1 90373 116 - 1
CACAUUUGAAACGG-UUUAGGGCUUGGAAA---GCGGUUCGCGACUUAACCUGCCAAUUUGGUUUAUUAUUGGCCGAGAAAGGCUUUCCGGAUCUGCGGCUGAUGCUUUUCCUUCGCCUA
..............-....((((..(((((---((..(((.((.........((((((..........)))))))).)))..)))))))(((...(((.....)))...)))...)))). ( -32.50)
>DroAna_CAF1 82538 92 - 1
CUGAUUUGGACUGU--------CCUGGCUA---AGAGUUCACGUCUAAGCCUGCCAAUUUGGUUUAUUG-UGUGUGAGGAAACUUUGCUCGAUUUGCGGUCAUU----------------
........((((((--------...((((.---((((....).))).)))).(((.....)))..((((-.(((.(((....)))))).))))..))))))...---------------- ( -22.30)
>consensus
CACAUUUGAAAGGU_UUUGGGGCUUGGAAA___GCGGUUCGCAACUUAACCUGCCAAUUUGGUUUAUUGUUGUCCGAGAAAAGCUUUCCGGAUCUGCGGCUGCUGCUUUUCCUUUGCCUA
...................((((..(((((...((((((((((....((((.........)))).......(((((.(((....))).))))).)))))..))))).)))))...)))). (-18.63 = -20.15 +   1.52)

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 13:13:32 2006