Locus 1102

Sequence ID 2L_DroMel_CAF1
Location 3,005,850 – 3,006,010
Length 160
Max. P 0.905070
window1792 window1793 window1794

overview

Window 2

Location 3,005,850 – 3,005,970
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.11
Mean single sequence MFE -31.55
Consensus MFE -25.42
Energy contribution -25.48
Covariance contribution 0.06
Combinations/Pair 1.16
Mean z-score -2.06
Structure conservation index 0.81
SVM decision value 1.04
SVM RNA-class probability 0.905070
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3005850 120 + 22407834
ACCUUUUAUAGGUAUAAAUCAAUGUGUGACUGUGAUUUAUAUUGAUUCAAUUGGGAUAAUUUGGUCUAAUUUGUGACCUUCCUAGGAUUGUUCUUUCGGAGAACCCCCUACGGAAAGAAA
.(((...((..((((((((((..(.....)..))))))))))..))......))).......((((........))))((((((((...((((((...))))))..)))).))))..... ( -28.40)
>DroSec_CAF1 13372 119 + 1
ACCUUUCAUAGGUAUAAAUCAACGUGAGACUGUGAUUUAUAUUGAUUCAAUUGGGAUAAUUUGGUCUAAUUUGUGACCUUCCUAGGAUCGUUCUCUU-AAGAACCCCCUAGUGAAAGAAG
..(((((((((((((((((((.(....)....)))))))))..(((((...(((((......((((........)))).))))))))))(((((...-.)))))..))).)))))))... ( -34.50)
>DroEre_CAF1 13327 116 + 1
ACCUUUCAUAGGUAUAAAUCAACGCGUGACU-UGAUUUAUAUUGAUUCUAUUGGGAUAAUUUGGUCUAAUUUGUGACCUUCUUAGGGCCGUUCUCUU-GAGAGC--CCUUGGGGGAGAAA
..((..(...((((((((((((........)-)))))))))))....(((..(((.......((((........))))(((((((((......))))-))))))--)).))))..))... ( -30.90)
>DroYak_CAF1 13040 116 + 1
ACCUUUCAUAGGUAUAAAUCAACGUGUGACU-UGAUUUAUAUUGGUUCUAUUGGGAUAAUUUGGUCUAAUUUGUGGCCUUCUUAGGGCUGUUCUCUG-GGGAGC--CCUAGGUAAAGAAA
.(((...(((((((((((((((........)-)))))))))).....)))).))).......((((........))))..(((((((((.((.....-)).)))--))))))........ ( -32.40)
>consensus
ACCUUUCAUAGGUAUAAAUCAACGUGUGACU_UGAUUUAUAUUGAUUCAAUUGGGAUAAUUUGGUCUAAUUUGUGACCUUCCUAGGACCGUUCUCUU_GAGAAC__CCUAGGGAAAGAAA
.(((......(((((((((((...........))))))))))).........))).......((((........))))((((((((...(((((.....)))))..))))))))...... (-25.42 = -25.48 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,005,850 – 3,005,970
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.11
Mean single sequence MFE -25.52
Consensus MFE -15.65
Energy contribution -16.65
Covariance contribution 1.00
Combinations/Pair 1.03
Mean z-score -2.33
Structure conservation index 0.61
SVM decision value 0.12
SVM RNA-class probability 0.591415
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3005850 120 - 22407834
UUUCUUUCCGUAGGGGGUUCUCCGAAAGAACAAUCCUAGGAAGGUCACAAAUUAGACCAAAUUAUCCCAAUUGAAUCAAUAUAAAUCACAGUCACACAUUGAUUUAUACCUAUAAAAGGU
.(((.((((.(((((.(((((.....)))))..)))))))))((((........))))..............)))....(((((((((..(.....)..)))))))))(((.....))). ( -26.00)
>DroSec_CAF1 13372 119 - 1
CUUCUUUCACUAGGGGGUUCUU-AAGAGAACGAUCCUAGGAAGGUCACAAAUUAGACCAAAUUAUCCCAAUUGAAUCAAUAUAAAUCACAGUCUCACGUUGAUUUAUACCUAUGAAAGGU
..(((((((.((((((((((((-(.((......)).))))))((((........)))).......)))...........(((((((((..(.....)..)))))))))))))))))))). ( -32.30)
>DroEre_CAF1 13327 116 - 1
UUUCUCCCCCAAGG--GCUCUC-AAGAGAACGGCCCUAAGAAGGUCACAAAUUAGACCAAAUUAUCCCAAUAGAAUCAAUAUAAAUCA-AGUCACGCGUUGAUUUAUACCUAUGAAAGGU
.((((......(((--(((.((-....))..)))))).....((((........)))).............))))....(((((((((-((.....).))))))))))(((.....))). ( -24.50)
>DroYak_CAF1 13040 116 - 1
UUUCUUUACCUAGG--GCUCCC-CAGAGAACAGCCCUAAGAAGGCCACAAAUUAGACCAAAUUAUCCCAAUAGAACCAAUAUAAAUCA-AGUCACACGUUGAUUUAUACCUAUGAAAGGU
.((((...(.((((--(((...-........))))))).)..((.(........).)).............))))....(((((((((-(........))))))))))(((.....))). ( -19.30)
>consensus
UUUCUUUCCCUAGG__GCUCUC_AAGAGAACAACCCUAAGAAGGUCACAAAUUAGACCAAAUUAUCCCAAUAGAAUCAAUAUAAAUCA_AGUCACACGUUGAUUUAUACCUAUGAAAGGU
.((((.....((((..(((((.....)))))...))))))))((((........)))).....................(((((((((..(.....)..)))))))))(((.....))). (-15.65 = -16.65 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,005,890 – 3,006,010
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 75.10
Mean single sequence MFE -29.80
Consensus MFE -17.21
Energy contribution -17.77
Covariance contribution 0.56
Combinations/Pair 1.23
Mean z-score -1.86
Structure conservation index 0.58
SVM decision value 0.48
SVM RNA-class probability 0.751951
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3005890 120 + 22407834
AUUGAUUCAAUUGGGAUAAUUUGGUCUAAUUUGUGACCUUCCUAGGAUUGUUCUUUCGGAGAACCCCCUACGGAAAGAAAUAUGUGCAAGUGCUUGGUUAAUAUUAACAGCUAGCAUCCU
............(((((.....((((........))))((((((((...((((((...))))))..)))).))))..........((.(((..(((((....)))))..))).))))))) ( -27.20)
>DroSec_CAF1 13412 106 + 1
AUUGAUUCAAUUGGGAUAAUUUGGUCUAAUUUGUGACCUUCCUAGGAUCGUUCUCUU-AAGAACCCCCUAGUGAAAGAAGUAUUUGUAAGUUCUUGGUU-------------AGCAUCCU
...(((.((((..(((......((((........))))((((((((...(((((...-.)))))..))))).)))................)))..)))-------------.).))).. ( -24.30)
>DroEre_CAF1 13366 117 + 1
AUUGAUUCUAUUGGGAUAAUUUGGUCUAAUUUGUGACCUUCUUAGGGCCGUUCUCUU-GAGAGC--CCUUGGGGGAGAAAUAUUUUAAUGUUCGCUGUCAAUAUUAGCAGAUAGCAUCAU
..((((..((((((((((.(((((((........))))(((((((((..(((((...-.)))))--))))))))).))).))))))))))...((((((..........)))))))))). ( -31.70)
>DroYak_CAF1 13079 108 + 1
AUUGGUUCUAUUGGGAUAAUUUGGUCUAAUUUGUGGCCUUCUUAGGGCUGUUCUCUG-GGGAGC--CCUAGGUAAAGAAAUAUUUUA---------GUCCAUAUUAGCAGAUAGCAUCAU
..((((.(((((....((((.(((.((((..(((..(.(((((((((((.((.....-)).)))--)))))).)).)..)))..)))---------).))).))))...))))).)))). ( -36.00)
>consensus
AUUGAUUCAAUUGGGAUAAUUUGGUCUAAUUUGUGACCUUCCUAGGACCGUUCUCUU_GAGAAC__CCUAGGGAAAGAAAUAUUUGAAAGUUCUUGGUCAAUAUUAGCAGAUAGCAUCAU
............(((((.....((((........))))((((((((...(((((.....)))))..)))))))).........................................))))) (-17.21 = -17.77 +   0.56)

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 09:53:44 2006