Locus 6622

Sequence ID 2R_DroMel_CAF1
Location 20,710,874 – 20,711,108
Length 234
Max. P 0.959565
window10543 window10544 window10545

overview

Window 3

Location 20,710,874 – 20,710,994
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.66
Mean single sequence MFE -29.26
Consensus MFE -25.24
Energy contribution -25.64
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.86
SVM decision value 1.50
SVM RNA-class probability 0.959565
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20710874 120 + 20766785
AACGUAUACGAAGACGCAGUUCCAAGUGCGUCCUGUAGGUGUUCCCCUGGAAGACAUCUGCCAAGCCGACUUCCUUUGGUGUAAACCAAUUUUCGUAUCAAUAAAAUUAAAAUCUACUAU
...(.(((((((((((((.(....).))))))..(((((((((((...)))..))))))))..............(((((....)))))..))))))))..................... ( -29.40)
>DroSec_CAF1 144411 119 + 1
AACGUAUACGAAGACGCAGUCCCAAGUGAGUCCUGUAGGUGUUC-CCUGCAAGACAUCUGCCAAGCCGACUUCCUUUGGUGUAAACCAAUUUUCGUAUCAAUACAAUUAAAAUCCACUAU
...(.(((((((((.((((((......))(((.((((((.....-)))))).)))..))))..............(((((....)))))))))))))))..................... ( -28.00)
>DroSim_CAF1 149402 119 + 1
AACGUAUACGAAGACGCAGUCCCAAGUGCGUCCUGUAGGUGUUC-CCUGCAAGACAUCUGCCAAGCCGACUUCCUUUGGUGUAAACCAAUUUUCGUAUCAAUACAAUUAAAAUCCACUAU
...(.(((((((((((((.(....).))))))..(((((((((.-.......)))))))))..............(((((....)))))..))))))))..................... ( -29.00)
>DroEre_CAF1 185591 120 + 1
AACGUAUACGAAGACGCAGUCCCACGUGCGUCCUGUAGGUGUUUCCCUGCAAGACAGCUGCCAAGCCGACUUCCUUUGGUGUAAACCAAUUUUCGUAUCAAUAAAAUUGAAAUCCAUUAA
...(.(((((((((.(.((((........(((.((((((......)))))).))).(((....))).)))).)..(((((....)))))))))))))))..................... ( -30.70)
>DroYak_CAF1 150486 120 + 1
AACGUAUACGAAUACGCAGUCCCACGUGCGUCCUGUAGGUGUUUCCCUGCAAGACAGCUGCCCUGCCGACUUCCUUUGGUGUAAACCAAUUUUCGUAUCAAUAAAAUUGAAAUCCAUUAA
...(.(((((((...((((...((.((..(((.((((((......)))))).))).))))..)))).........(((((....)))))..))))))))..................... ( -29.20)
>consensus
AACGUAUACGAAGACGCAGUCCCAAGUGCGUCCUGUAGGUGUUCCCCUGCAAGACAUCUGCCAAGCCGACUUCCUUUGGUGUAAACCAAUUUUCGUAUCAAUAAAAUUAAAAUCCACUAU
...(.(((((((((.((((...(....).(((.((((((......)))))).)))..))))..............(((((....)))))))))))))))..................... (-25.24 = -25.64 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,710,994 – 20,711,108
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.62
Mean single sequence MFE -32.34
Consensus MFE -25.16
Energy contribution -25.00
Covariance contribution -0.16
Combinations/Pair 1.12
Mean z-score -1.71
Structure conservation index 0.78
SVM decision value 0.47
SVM RNA-class probability 0.748585
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20710994 114 + 20766785
AGGUCUUCGUCU-UCGAACCAAAAUCGAAAUUUGGCUGUUUU----UUUAAGGGGCUCGAUAGCCUUUGUCAAAGGGCCACUAAUUGUGCUGCUAAAGAACGAA-CGAAAGAGAAAACUG
.(((.(((.(((-(((..(((((.......))))).((((((----((..((.(((.((((.((((((....)))))).....)))).))).))))))))))..-)).))))))).))). ( -29.50)
>DroSec_CAF1 144530 115 + 1
AGGUCUUCGUCUUUCGAAGCAAAAUCGAAAUUUGGCUGUUUU----UUUAAGGGGCUCGAUAGCCUUUGUCAAAGGGGCACUAAUUGUGCUGCUAAAGAACGAA-UGAAAGAGAAAACUG
.(((.(((.(((((((.(((.((((....)))).)))(((((----((..(((((((....))))))).....((.(((((.....))))).)))))))))...-)))))))))).))). ( -33.60)
>DroSim_CAF1 149521 115 + 1
AGGUCUUCGUCUUUCGAAGCAAAAUCGAAAUUUGGCUGUUUU----UUUAAGGGGCUCGAUAGCCUUUGUCAAAGGGGCACUAAUUGUGCUGCUAAAGAACGAA-UGAAAGAGAAAACUG
.(((.(((.(((((((.(((.((((....)))).)))(((((----((..(((((((....))))))).....((.(((((.....))))).)))))))))...-)))))))))).))). ( -33.60)
>DroEre_CAF1 185711 114 + 1
AGGUCUUCGGCUUUCGAACCGAAAUCGAAAUUUGGCUGUUUUUUUUUUUAAGGGG------AGCCUUUGUCAAAAGGUCACUAAUUGUGCUGCCGAAGAACGAAAGGAAAGCGAAAACUG
...((((((((((((((.......))))))...((((.(((((......))))).------))))..........((.(((.....))))))))))))).(....).............. ( -29.80)
>DroYak_CAF1 150606 116 + 1
AGGUCUUCGGCUUUCGAACCGAAAUCGAAAUUUGGCUGUUUU----UCUAAGGGGCUCGAUAGCCUUUGUCAAAAGGCCACUAAUUGUGCUGCUGAAGAACGAAAGGAAAGCGAAAACUG
.(((.((((.(((((...(((((.......))))).((((((----((..((.(((.((((.((((((....)))))).....)))).))).))))))))))....))))))))).))). ( -35.20)
>consensus
AGGUCUUCGUCUUUCGAACCAAAAUCGAAAUUUGGCUGUUUU____UUUAAGGGGCUCGAUAGCCUUUGUCAAAGGGCCACUAAUUGUGCUGCUAAAGAACGAA_GGAAAGAGAAAACUG
.(((.(((.(((((((........(((...((((((..............((((((......)))))).......((.(((.....)))))))))))...)))..)))))))))).))). (-25.16 = -25.00 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,710,994 – 20,711,108
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.62
Mean single sequence MFE -27.07
Consensus MFE -19.80
Energy contribution -20.92
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -1.93
Structure conservation index 0.73
SVM decision value 0.28
SVM RNA-class probability 0.665257
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20710994 114 - 20766785
CAGUUUUCUCUUUCG-UUCGUUCUUUAGCAGCACAAUUAGUGGCCCUUUGACAAAGGCUAUCGAGCCCCUUAAA----AAAACAGCCAAAUUUCGAUUUUGGUUCGA-AGACGAAGACCU
..((((((((((.((-...((((..((((..(((.....)))...(((.....)))))))..))))........----.....(((((((.......))))))))))-))).)))))).. ( -25.10)
>DroSec_CAF1 144530 115 - 1
CAGUUUUCUCUUUCA-UUCGUUCUUUAGCAGCACAAUUAGUGCCCCUUUGACAAAGGCUAUCGAGCCCCUUAAA----AAAACAGCCAAAUUUCGAUUUUGCUUCGAAAGACGAAGACCU
..((((((((((((.-...((((..((((.((((.....))))..(((.....)))))))..))))........----.....(((.((((....)))).)))..)))))).)))))).. ( -28.30)
>DroSim_CAF1 149521 115 - 1
CAGUUUUCUCUUUCA-UUCGUUCUUUAGCAGCACAAUUAGUGCCCCUUUGACAAAGGCUAUCGAGCCCCUUAAA----AAAACAGCCAAAUUUCGAUUUUGCUUCGAAAGACGAAGACCU
..((((((((((((.-...((((..((((.((((.....))))..(((.....)))))))..))))........----.....(((.((((....)))).)))..)))))).)))))).. ( -28.30)
>DroEre_CAF1 185711 114 - 1
CAGUUUUCGCUUUCCUUUCGUUCUUCGGCAGCACAAUUAGUGACCUUUUGACAAAGGCU------CCCCUUAAAAAAAAAAACAGCCAAAUUUCGAUUUCGGUUCGAAAGCCGAAGACCU
...................(.((((((((..(((.....))).............((((------..................))))...((((((.......)))))))))))))).). ( -24.17)
>DroYak_CAF1 150606 116 - 1
CAGUUUUCGCUUUCCUUUCGUUCUUCAGCAGCACAAUUAGUGGCCUUUUGACAAAGGCUAUCGAGCCCCUUAGA----AAAACAGCCAAAUUUCGAUUUCGGUUCGAAAGCCGAAGACCU
..((((((((((((.........................(((((((((....))))))))).(((((.....((----((..........))))......)))))))))).))))))).. ( -29.50)
>consensus
CAGUUUUCUCUUUCA_UUCGUUCUUUAGCAGCACAAUUAGUGCCCCUUUGACAAAGGCUAUCGAGCCCCUUAAA____AAAACAGCCAAAUUUCGAUUUUGGUUCGAAAGACGAAGACCU
..((((((((((((.....((((..((((..(((.....)))...(((.....)))))))..)))).................(((((((.......))))))).)))))).)))))).. (-19.80 = -20.92 +   1.12)

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 12:15:26 2006