Locus 5570

Sequence ID 2L_DroMel_CAF1
Location 15,840,486 – 15,840,655
Length 169
Max. P 0.988460
window8837 window8838 window8839 window8840 window8841

overview

Window 7

Location 15,840,486 – 15,840,602
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.71
Mean single sequence MFE -37.36
Consensus MFE -31.50
Energy contribution -33.38
Covariance contribution 1.88
Combinations/Pair 1.06
Mean z-score -2.75
Structure conservation index 0.84
SVM decision value 2.12
SVM RNA-class probability 0.988460
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15840486 116 + 22407834
---GUGCUGUGGCUAGA-AGCCAGCGAAGCAAAAUGCUUUUAAUUAAAAGUAAACAAUAUCAAUUCGUUCGACAGUUAUCCGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGG
---.((((.((((....-.))))....))))...(((((((....)))))))..............((((((((....(((((..((((.....))))..)))))))))))))....... ( -42.30)
>DroSec_CAF1 12522 116 + 1
---GUGCUGUGGCUAGA-AGCCAGCGAAGCAAAUUGCUUUUAAUUAAAAGUAAACAAUAUCAAUUCGUUCGACAGUUAUCCGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGA
---.((((.((((....-.))))....))))..((((((((....)))))))).............((((((((....(((((..((((.....))))..)))))))))))))....... ( -43.20)
>DroSim_CAF1 12832 116 + 1
---GUGCUGUGGCUAGA-AGCCAGCGAAGCAAAAUGCUUUUAAUUAAAAGUAAACAAUAUCAAUUCGUACGACAGUUAUCCGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGG
---(((((.((((....-.))))(((((......(((((((....)))))))...........))))).(((((....(((((..((((.....))))..)))))))))))))))..... ( -38.83)
>DroPer_CAF1 21549 111 + 1
UCAGUGCUGUGGCAAGAAAGCCAGCGAAGCAAAUUGUUUUUAAUUAAAAGUAAACAAUAUCAAUUCAUUCGACAGUUAUCCUGUUAUGCUGCUGACAUUACUGGCUGGCG---------C
....(((....))).....(((((((((....(((((((............))))))).....)))......((((.....(((((......)))))..)))))))))).---------. ( -25.10)
>consensus
___GUGCUGUGGCUAGA_AGCCAGCGAAGCAAAAUGCUUUUAAUUAAAAGUAAACAAUAUCAAUUCGUUCGACAGUUAUCCGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGG
....((((.((((......))))....))))...(((((((....)))))))..............((((((((....(((((((((((.....)))))))))))))))))))....... (-31.50 = -33.38 +   1.88)

alignment

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secondary structure

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Window 8

Location 15,840,522 – 15,840,642
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.00
Mean single sequence MFE -42.17
Consensus MFE -29.55
Energy contribution -33.43
Covariance contribution 3.88
Combinations/Pair 1.06
Mean z-score -3.14
Structure conservation index 0.70
SVM decision value 1.96
SVM RNA-class probability 0.983931
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15840522 120 + 22407834
UAAUUAAAAGUAAACAAUAUCAAUUCGUUCGACAGUUAUCCGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGGCGUGGAGCCUGACGUGGCCAGGACCAAGCCAGGAUGCAUU
............................((((((....(((((..((((.....))))..)))))))))))((((((.(((.(((..((((.......)))).))).))).))))))... ( -50.10)
>DroSec_CAF1 12558 120 + 1
UAAUUAAAAGUAAACAAUAUCAAUUCGUUCGACAGUUAUCCGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGACGUGGAGCCUGACGUGGCCAGGACCAAGUCAGGAUGCAUU
............................((((((....(((((..((((.....))))..)))))))))))((((((.(((.(((..((((.......)))).))).))).))))))... ( -48.00)
>DroSim_CAF1 12868 120 + 1
UAAUUAAAAGUAAACAAUAUCAAUUCGUACGACAGUUAUCCGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGGCGUGGAGCCUGACGUGGCCAGGACCAAGCCAGGAUGCAUU
.............................(((((....(((((..((((.....))))..)))))))))).((((((.(((.(((..((((.......)))).))).))).))))))... ( -48.80)
>DroPer_CAF1 21589 110 + 1
UAAUUAAAAGUAAACAAUAUCAAUUCAUUCGACAGUUAUCCUGUUAUGCUGCUGACAUUACUGGCUGGCG---------CCAUAGACGGUGACGUGUCCAGGACCUCCUCU-AUUGCAUU
.........((((.................((((((((((...(((((.((((..(.......)..))))---------.)))))..)))))).)))).(((....)))..-.))))... ( -21.80)
>consensus
UAAUUAAAAGUAAACAAUAUCAAUUCGUUCGACAGUUAUCCGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGGCGUGGAGCCUGACGUGGCCAGGACCAAGCCAGGAUGCAUU
.............................(((((....(((((((((((.....)))))))))))))))).((((((.(((.(((..((((.......)))).))).))).))))))... (-29.55 = -33.43 +   3.88)

alignment

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secondary structure

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Window 9

Location 15,840,522 – 15,840,642
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.00
Mean single sequence MFE -40.00
Consensus MFE -28.41
Energy contribution -31.35
Covariance contribution 2.94
Combinations/Pair 1.08
Mean z-score -2.87
Structure conservation index 0.71
SVM decision value 1.78
SVM RNA-class probability 0.977023
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15840522 120 - 22407834
AAUGCAUCCUGGCUUGGUCCUGGCCACGUCAGGCUCCACGCCUGGAUGCUCGACACCCGGCAAUGCUGGCAGCAUCACCGGAUAACUGUCGAACGAAUUGAUAUUGUUUACUUUUAAUUA
...((((((.(((.(((.((((((...))))))..))).))).))))))((((((.((((..((((.....))))..)))).....))))))...((((((............)))))). ( -46.30)
>DroSec_CAF1 12558 120 - 1
AAUGCAUCCUGACUUGGUCCUGGCCACGUCAGGCUCCACGUCUGGAUGCUCGACACCCGGCAAUGCUGGCAGCAUCACCGGAUAACUGUCGAACGAAUUGAUAUUGUUUACUUUUAAUUA
...((((((.(((.(((.((((((...))))))..))).))).))))))((((((.((((..((((.....))))..)))).....))))))...((((((............)))))). ( -44.20)
>DroSim_CAF1 12868 120 - 1
AAUGCAUCCUGGCUUGGUCCUGGCCACGUCAGGCUCCACGCCUGGAUGCUCGACACCCGGCAAUGCUGGCAGCAUCACCGGAUAACUGUCGUACGAAUUGAUAUUGUUUACUUUUAAUUA
...((((((.(((.(((.((((((...))))))..))).))).)))))).(((((.((((..((((.....))))..)))).....)))))....((((((............)))))). ( -44.20)
>DroPer_CAF1 21589 110 - 1
AAUGCAAU-AGAGGAGGUCCUGGACACGUCACCGUCUAUGG---------CGCCAGCCAGUAAUGUCAGCAGCAUAACAGGAUAACUGUCGAAUGAAUUGAUAUUGUUUACUUUUAAUUA
.......(-(((((.((((((((((........))))).))---------.)))......(((((((((...(((.((((.....))))...)))..)))))))))....)))))).... ( -25.30)
>consensus
AAUGCAUCCUGACUUGGUCCUGGCCACGUCAGGCUCCACGCCUGGAUGCUCGACACCCGGCAAUGCUGGCAGCAUCACCGGAUAACUGUCGAACGAAUUGAUAUUGUUUACUUUUAAUUA
...((((((.(((.(((.((((((...))))))..))).))).)))))).(((((.((((..((((.....))))..)))).....)))))....((((((............)))))). (-28.41 = -31.35 +   2.94)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,840,562 – 15,840,655
Length 93
Sequences 3
Columns 93
Reading direction forward
Mean pairwise identity 98.57
Mean single sequence MFE -40.60
Consensus MFE -41.04
Energy contribution -40.60
Covariance contribution -0.44
Combinations/Pair 1.04
Mean z-score -1.42
Structure conservation index 1.01
SVM decision value 0.18
SVM RNA-class probability 0.621561
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15840562 93 + 22407834
CGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGGCGUGGAGCCUGACGUGGCCAGGACCAAGCCAGGAUGCAUUGUUCUCGGGGGAG
.((..((((.....))))..))(((...(((((((((.(((.(((..((((.......)))).))).))).)))))).)))..)))....... ( -41.30)
>DroSec_CAF1 12598 93 + 1
CGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGACGUGGAGCCUGACGUGGCCAGGACCAAGUCAGGAUGCAUUGUUCUCGGGGGAG
.((..((((.....))))..))(((...(((((((((.(((.(((..((((.......)))).))).))).)))))).)))..)))....... ( -39.20)
>DroSim_CAF1 12908 93 + 1
CGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGGCGUGGAGCCUGACGUGGCCAGGACCAAGCCAGGAUGCAUUGUUCUCGGGGGAG
.((..((((.....))))..))(((...(((((((((.(((.(((..((((.......)))).))).))).)))))).)))..)))....... ( -41.30)
>consensus
CGGUGAUGCUGCCAGCAUUGCCGGGUGUCGAGCAUCCAGGCGUGGAGCCUGACGUGGCCAGGACCAAGCCAGGAUGCAUUGUUCUCGGGGGAG
.((..((((.....))))..))(((...(((((((((.(((.(((..((((.......)))).))).))).)))))).)))..)))....... (-41.04 = -40.60 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,840,562 – 15,840,655
Length 93
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 98.57
Mean single sequence MFE -36.10
Consensus MFE -36.54
Energy contribution -36.10
Covariance contribution -0.44
Combinations/Pair 1.04
Mean z-score -2.35
Structure conservation index 1.01
SVM decision value 1.68
SVM RNA-class probability 0.971626
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15840562 93 - 22407834
CUCCCCCGAGAACAAUGCAUCCUGGCUUGGUCCUGGCCACGUCAGGCUCCACGCCUGGAUGCUCGACACCCGGCAAUGCUGGCAGCAUCACCG
(((....)))......((((((.(((.(((.((((((...))))))..))).))).))))))........(((..((((.....))))..))) ( -36.80)
>DroSec_CAF1 12598 93 - 1
CUCCCCCGAGAACAAUGCAUCCUGACUUGGUCCUGGCCACGUCAGGCUCCACGUCUGGAUGCUCGACACCCGGCAAUGCUGGCAGCAUCACCG
(((....)))......((((((.(((.(((.((((((...))))))..))).))).))))))........(((..((((.....))))..))) ( -34.70)
>DroSim_CAF1 12908 93 - 1
CUCCCCCGAGAACAAUGCAUCCUGGCUUGGUCCUGGCCACGUCAGGCUCCACGCCUGGAUGCUCGACACCCGGCAAUGCUGGCAGCAUCACCG
(((....)))......((((((.(((.(((.((((((...))))))..))).))).))))))........(((..((((.....))))..))) ( -36.80)
>consensus
CUCCCCCGAGAACAAUGCAUCCUGGCUUGGUCCUGGCCACGUCAGGCUCCACGCCUGGAUGCUCGACACCCGGCAAUGCUGGCAGCAUCACCG
(((....)))......((((((.(((.(((.((((((...))))))..))).))).))))))........(((..((((.....))))..))) (-36.54 = -36.10 +  -0.44)

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 11:47:28 2006