Locus 7179

Sequence ID 3R_DroMel_CAF1
Location 18,925,108 – 18,925,243
Length 135
Max. P 0.886304
window11610 window11611 window11612

overview

Window 0

Location 18,925,108 – 18,925,225
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 86.32
Mean single sequence MFE -30.27
Consensus MFE -20.10
Energy contribution -21.10
Covariance contribution 1.00
Combinations/Pair 1.15
Mean z-score -2.61
Structure conservation index 0.66
SVM decision value 0.94
SVM RNA-class probability 0.886304
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18925108 117 + 27905053
ACCUCGACUGCCAUCCAAAGUGACUUGCAAUAUAGUCAGAAUUGGAAGAGAUCUGCCGCCCAUUGAUAACGAUUUUCUUAUCAUAUACGCAUAAUCACUUUUGUGGCACGAUCCAAA
...(((..((((((..(((((((..(((......(((((...(((.((....)).)))....)))))...(((......)))......)))...))))))).)))))))))...... ( -26.80)
>DroSec_CAF1 36425 116 + 1
ACGUCUACUGCCAUCAAAAGUGACUUGCAAUUUAUUCAGAAUUGGAAGAGAUCUGCCGUU-UUUGAUAACGAUUUUGUUAUCAUAUACGCAUAAUCACUUUUGUGGCACGAUCCAAA
..(((...(((((.((((((((((((.((((((.....)))))).))).....(((.((.-..((((((((....))))))))...)))))...)))))))))))))).)))..... ( -36.30)
>DroSim_CAF1 36199 117 + 1
ACGUCGACUGCCAUCCAAAGUGACUUGCAAUAUAGUCAGAAUUGGAAGAGAUCUGCCGCUCUCUGAUAACGAUUUUGUUAUCAUAUACGCAUAAUCACUUUUGUGGCACGAUCCAAA
..((((..((((((..(((((((..(((......((((((..(((.((....)).)))...))))))...(((......)))......)))...))))))).))))))))))..... ( -32.20)
>DroYak_CAF1 37431 117 + 1
ACGUUGACUGUCAUCCACAGUGACGAGCAUUGUAAACAGAAUUCGAAAAGAAAUGCCGCUGUUUGAUAAUGUUUUUGUUAUCAUAUAUGCAUAAUGACUUUUGUGAUAUGAUCCAAC
.((((.(((((.....)))))))))((((((((((((((..(((.....)))......)))))).)))))))).(((..(((((((...(((((......)))))))))))).))). ( -25.80)
>consensus
ACGUCGACUGCCAUCCAAAGUGACUUGCAAUAUAGUCAGAAUUGGAAGAGAUCUGCCGCUCUUUGAUAACGAUUUUGUUAUCAUAUACGCAUAAUCACUUUUGUGGCACGAUCCAAA
..((((..(((((.(.(((((((..(((..............(((.((....)).))).....((((((((....)))))))).....)))...))))))).))))))))))..... (-20.10 = -21.10 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,925,108 – 18,925,225
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 86.32
Mean single sequence MFE -30.17
Consensus MFE -21.40
Energy contribution -23.52
Covariance contribution 2.13
Combinations/Pair 1.11
Mean z-score -2.00
Structure conservation index 0.71
SVM decision value 0.63
SVM RNA-class probability 0.803801
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18925108 117 - 27905053
UUUGGAUCGUGCCACAAAAGUGAUUAUGCGUAUAUGAUAAGAAAAUCGUUAUCAAUGGGCGGCAGAUCUCUUCCAAUUCUGACUAUAUUGCAAGUCACUUUGGAUGGCAGUCGAGGU
(((.(((..(((((..(((((((((.((((.(((((...((((....(((.......)))((.((....)).))..))))...))))))))))))))))))...)))))))).))). ( -30.70)
>DroSec_CAF1 36425 116 - 1
UUUGGAUCGUGCCACAAAAGUGAUUAUGCGUAUAUGAUAACAAAAUCGUUAUCAAA-AACGGCAGAUCUCUUCCAAUUCUGAAUAAAUUGCAAGUCACUUUUGAUGGCAGUAGACGU
.........((((((((((((((((.(((((.(.(((((((......))))))).)-.))((.((....)).))...............)))))))))))))).)))))........ ( -34.80)
>DroSim_CAF1 36199 117 - 1
UUUGGAUCGUGCCACAAAAGUGAUUAUGCGUAUAUGAUAACAAAAUCGUUAUCAGAGAGCGGCAGAUCUCUUCCAAUUCUGACUAUAUUGCAAGUCACUUUGGAUGGCAGUCGACGU
......((((((((..(((((((((.(((((((((((((((......)))))))((((........)))).............)))).)))))))))))))...)))))..)))... ( -34.10)
>DroYak_CAF1 37431 117 - 1
GUUGGAUCAUAUCACAAAAGUCAUUAUGCAUAUAUGAUAACAAAAACAUUAUCAAACAGCGGCAUUUCUUUUCGAAUUCUGUUUACAAUGCUCGUCACUGUGGAUGACAGUCAACGU
(((((.((((.(((((...((.((...((((...((((((........))))))...(((((.((((......)))).)))))....))))..)).)))))))))))...))))).. ( -21.10)
>consensus
UUUGGAUCGUGCCACAAAAGUGAUUAUGCGUAUAUGAUAACAAAAUCGUUAUCAAAGAGCGGCAGAUCUCUUCCAAUUCUGACUAUAUUGCAAGUCACUUUGGAUGGCAGUCGACGU
(((((....((((((.(((((((((.((((....(((((((......)))))))........((((...........)))).......))))))))))))).).))))).))))).. (-21.40 = -23.52 +   2.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,925,148 – 18,925,243
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 88.95
Mean single sequence MFE -23.18
Consensus MFE -17.86
Energy contribution -18.55
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -2.08
Structure conservation index 0.77
SVM decision value 0.82
SVM RNA-class probability 0.859436
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18925148 95 - 27905053
CCGCUGUCUUUAUAUGCAUUUGGAUCGUGCCACAAAAGUGAUUAUGCGUAUAUGAUAAGAAAAUCGUUAUCAAUGGGCGGCAGAUCUCUUCCAAU
..(((((((.(((((((((...(((((...........))))))))))))))(((((((.....).))))))..))))))).............. ( -22.60)
>DroSec_CAF1 36465 94 - 1
CCGCUGGCUUUAUAUGCAUUUGGAUCGUGCCACAAAAGUGAUUAUGCGUAUAUGAUAACAAAAUCGUUAUCAAA-AACGGCAGAUCUCUUCCAAU
..((((....(((((((((...(((((...........))))))))))))))(((((((......)))))))..-..)))).............. ( -22.00)
>DroSim_CAF1 36239 95 - 1
CCGCUGUCUUUAUAUGCAUUUGGAUCGUGCCACAAAAGUGAUUAUGCGUAUAUGAUAACAAAAUCGUUAUCAGAGAGCGGCAGAUCUCUUCCAAU
(((((.((..(((((((((...(((((...........))))))))))))))(((((((......))))))))).)))))............... ( -27.10)
>DroYak_CAF1 37471 95 - 1
CCGCUGGCUUUAUAUGCUGUUGGAUCAUAUCACAAAAGUCAUUAUGCAUAUAUGAUAACAAAAACAUUAUCAAACAGCGGCAUUUCUUUUCGAAU
((((((....(((((((.....(((............))).....)))))))((((((........))))))..))))))............... ( -21.00)
>consensus
CCGCUGGCUUUAUAUGCAUUUGGAUCGUGCCACAAAAGUGAUUAUGCGUAUAUGAUAACAAAAUCGUUAUCAAAGAGCGGCAGAUCUCUUCCAAU
(((((.....((((((((....(((((...........))))).))))))))(((((((......)))))))...)))))............... (-17.86 = -18.55 +   0.69)

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 12:39:21 2006