Locus 4500

Sequence ID 2R_DroMel_CAF1
Location 14,783,763 – 14,783,893
Length 130
Max. P 0.982696
window7203 window7204 window7205

overview

Window 3

Location 14,783,763 – 14,783,866
Length 103
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 83.36
Mean single sequence MFE -32.62
Consensus MFE -22.12
Energy contribution -23.60
Covariance contribution 1.48
Combinations/Pair 1.21
Mean z-score -1.82
Structure conservation index 0.68
SVM decision value 0.27
SVM RNA-class probability 0.661121
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14783763 103 + 20766785
--------GCGAAAAGCUUUCGUUUUGCUCUUUUUGUUGUGUGCAAAAAUGC-UCUCUGAUUGGUCGGCUUGCGAAUUUCGGGGGAAUUCGCGAGUCGC-AAAAGCGAAUCGA
--------((.....)).((((((((((..(((((((.....))))))).))-..........(.((((((((((((((.....)))))))))))))))-.)))))))).... ( -34.50)
>DroSec_CAF1 18643 103 + 1
--------GCGAAAAGCUUUUGUUUUGCUCGUUUUGUUGUGUGCAAAAAUGC-UCUCUGAUUGGUCGGCUUGCGAAUUUCGGGGGAAUUCGCGAGUCGC-AAAAGCGAAUCGA
--------.(((...((((((((...((...((((((.....))))))..))-.............(((((((((((((.....)))))))))))))))-))))))...))). ( -37.80)
>DroEre_CAF1 17839 103 + 1
--------GCGAAAAGCUUUCGUUUUGCUCGUUUUGUUGUGUGCAAAAAUGC-UCUCUGAUUGGUCGGCUUGCGAAUUUCGGAGGAAUUCGCGAGUCGC-AGAAGCGAAUCGA
--------((.....)).((((((((((...((((((.....))))))..))-..........(.((((((((((((((.....)))))))))))))))-.)))))))).... ( -35.30)
>DroWil_CAF1 25763 113 + 1
AGCUUCAUGGUCAAAGCUUUCGUUUUGCUCUUUUUGUUAUUUGCCAAUUUGCCUCUCUGAUUGGUCGGAUUGCGAAUUUCGUGUAUUUUCGCGAAUGCCGAUGAGCGAAUCCA
.(((.((((((((((((....)))))).....(((((.(((((((((((.........)))))).))))).))))).((((((......)))))).))).))))))....... ( -29.10)
>DroAna_CAF1 14624 103 + 1
--------GAGAAAAGCUCUUGUUUUGCUCGUUUUGUUGUGUGCAAAAAUGC-UCUCUGAUUGGUCGGAUUGCGAAUUUCGGAGCAUUUCGCGAACCUC-UCAGGCGAAUGGA
--------(((.(((((....))))).))).((((((.....))))))((((-(((..((((.((......)).))))..)))))))(((((.......-....))))).... ( -26.40)
>consensus
________GCGAAAAGCUUUCGUUUUGCUCGUUUUGUUGUGUGCAAAAAUGC_UCUCUGAUUGGUCGGCUUGCGAAUUUCGGGGGAAUUCGCGAGUCGC_AAAAGCGAAUCGA
..................((((((((((...((((((.....))))))..))..............(((((((((((((.....)))))))))))))....)))))))).... (-22.12 = -23.60 +   1.48)

alignment

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secondary structure

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Window 4

Location 14,783,788 – 14,783,893
Length 105
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 79.22
Mean single sequence MFE -37.94
Consensus MFE -21.86
Energy contribution -24.06
Covariance contribution 2.20
Combinations/Pair 1.13
Mean z-score -2.59
Structure conservation index 0.58
SVM decision value 1.92
SVM RNA-class probability 0.982696
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14783788 105 + 20766785
UUGUUGUGUGCAAAAAUGC-UCUCUGAUUGGUCGGCUUGCGAAUUUCGGGGGAAUUCGCGAGUCGC-AAAAGCGAAUCGAAAGCUUGCACAA------UUUGCCGAGCGG-----CAA
......(((((((....((-(.((.((((.((((((((((((((((.....)))))))))))))).-....)).)))))).)))))))))).------.(((((....))-----))) ( -42.90)
>DroSec_CAF1 18668 105 + 1
UUGUUGUGUGCAAAAAUGC-UCUCUGAUUGGUCGGCUUGCGAAUUUCGGGGGAAUUCGCGAGUCGC-AAAAGCGAAUCGAAAGCUUGCACAA------UUUGCCGAGCGG-----CAA
......(((((((....((-(.((.((((.((((((((((((((((.....)))))))))))))).-....)).)))))).)))))))))).------.(((((....))-----))) ( -42.90)
>DroEre_CAF1 17864 105 + 1
UUGUUGUGUGCAAAAAUGC-UCUCUGAUUGGUCGGCUUGCGAAUUUCGGAGGAAUUCGCGAGUCGC-AGAAGCGAAUCGAAAGCUUGCACAA------UCUGCCGAGCGG-----CAG
......(((((((....((-(.((.((((.((((((((((((((((.....)))))))))))))).-....)).)))))).)))))))))).------.(((((....))-----))) ( -44.50)
>DroWil_CAF1 25796 118 + 1
UUGUUAUUUGCCAAUUUGCCUCUCUGAUUGGUCGGAUUGCGAAUUUCGUGUAUUUUCGCGAAUGCCGAUGAGCGAAUCCAAAGUUUGCACAUAAGAGCUUCGUCUAGCCGACACACAA
..(..((((((.((((((((.........)).))))))))))))..)((((......(((((.((..(((.((((((.....)))))).)))....))))))).......)))).... ( -29.52)
>DroAna_CAF1 14649 104 + 1
UUGUUGUGUGCAAAAAUGC-UCUCUGAUUGGUCGGAUUGCGAAUUUCGGAGCAUUUCGCGAACCUC-UCAGGCGAAUGGAAAGCUUGCAAGA------A-AGCGUCUCGG-----GAG
.....((.(((..((((((-(((..((((.((......)).))))..))))))))).))).))(((-((((((...(....)((((......------)-))))))).))-----))) ( -29.90)
>consensus
UUGUUGUGUGCAAAAAUGC_UCUCUGAUUGGUCGGCUUGCGAAUUUCGGGGGAAUUCGCGAGUCGC_AAAAGCGAAUCGAAAGCUUGCACAA______UUUGCCGAGCGG_____CAA
......(((((((....((.....(((((.((((((((((((((((.....))))))))))))))......)).)))))...)))))))))........................... (-21.86 = -24.06 +   2.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,783,788 – 14,783,893
Length 105
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 79.22
Mean single sequence MFE -31.76
Consensus MFE -14.60
Energy contribution -17.04
Covariance contribution 2.44
Combinations/Pair 1.04
Mean z-score -2.56
Structure conservation index 0.46
SVM decision value 1.50
SVM RNA-class probability 0.959709
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14783788 105 - 20766785
UUG-----CCGCUCGGCAAA------UUGUGCAAGCUUUCGAUUCGCUUUU-GCGACUCGCGAAUUCCCCCGAAAUUCGCAAGCCGACCAAUCAGAGA-GCAUUUUUGCACACAACAA
(((-----((....))))).------.(((((((((((((((.((((....-)))).))(((((((.......)))))))..............))))-))....)))))))...... ( -37.10)
>DroSec_CAF1 18668 105 - 1
UUG-----CCGCUCGGCAAA------UUGUGCAAGCUUUCGAUUCGCUUUU-GCGACUCGCGAAUUCCCCCGAAAUUCGCAAGCCGACCAAUCAGAGA-GCAUUUUUGCACACAACAA
(((-----((....))))).------.(((((((((((((((.((((....-)))).))(((((((.......)))))))..............))))-))....)))))))...... ( -37.10)
>DroEre_CAF1 17864 105 - 1
CUG-----CCGCUCGGCAGA------UUGUGCAAGCUUUCGAUUCGCUUCU-GCGACUCGCGAAUUCCUCCGAAAUUCGCAAGCCGACCAAUCAGAGA-GCAUUUUUGCACACAACAA
(((-----((....))))).------.(((((((((((((((.((((....-)))).))(((((((.......)))))))..............))))-))....)))))))...... ( -39.10)
>DroWil_CAF1 25796 118 - 1
UUGUGUGUCGGCUAGACGAAGCUCUUAUGUGCAAACUUUGGAUUCGCUCAUCGGCAUUCGCGAAAAUACACGAAAUUCGCAAUCCGACCAAUCAGAGAGGCAAAUUGGCAAAUAACAA
.(((.((((((((......))))......(((...(((((((.....)).((((.(((.(((((...........)))))))))))).....)))))..)))....))))....))). ( -24.70)
>DroAna_CAF1 14649 104 - 1
CUC-----CCGAGACGCU-U------UCUUGCAAGCUUUCCAUUCGCCUGA-GAGGUUCGCGAAAUGCUCCGAAAUUCGCAAUCCGACCAAUCAGAGA-GCAUUUUUGCACACAACAA
...-----..((((.(((-(------......))))))))...((..((((-..((((.(((((.(.......).))))).....))))..)))).))-(((....)))......... ( -20.80)
>consensus
UUG_____CCGCUCGGCAAA______UUGUGCAAGCUUUCGAUUCGCUUUU_GCGACUCGCGAAUUCCCCCGAAAUUCGCAAGCCGACCAAUCAGAGA_GCAUUUUUGCACACAACAA
...........................(((((((((((((((.((((.....)))).))(((((((.......)))))))..............)))).))....)))))))...... (-14.60 = -17.04 +   2.44)

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 11:21:24 2006