Locus 5545

Sequence ID 3L_DroMel_CAF1
Location 15,227,287 – 15,227,527
Length 240
Max. P 0.999315
window8763 window8764 window8765 window8766 window8767

overview

Window 3

Location 15,227,287 – 15,227,384
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 95.88
Mean single sequence MFE -35.60
Consensus MFE -31.24
Energy contribution -31.40
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -2.31
Structure conservation index 0.88
SVM decision value 2.82
SVM RNA-class probability 0.997222
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15227287 97 + 23771897
AAGCCGAGUUUUGGGCCGGGUCAACCGCAGGUUCUGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUCCCCGAUGUUU
..(((........)))((((.....(((.((((((((((((......))))))))...)))))))...((((......)))).....))))...... ( -34.90)
>DroSec_CAF1 116565 97 + 1
AAGCCGAGUUUUGGGCCGGGUCAACCGCAGGUUCUGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUGGUGUUUAUCCCCGAUGUUU
..((((((((.((((.((((((((((...))).((((((((......))))))))..))))).)).)).)).))))))))................. ( -35.70)
>DroSim_CAF1 124389 97 + 1
AAGCCGAGUUUUGGGCCGGGUCAACCGCAGGUUCUGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUCCCCGAUGUUU
..(((........)))((((.....(((.((((((((((((......))))))))...)))))))...((((......)))).....))))...... ( -34.90)
>DroEre_CAF1 116758 96 + 1
AAGCGGAGUUUCGGGCUGGGUCAACCGCAGGUUCUGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUC-CCGACGUCU
....(((...(((((...((((....((.((((((((((((......))))))))...))))))))))((((......))))....)-))))..))) ( -34.60)
>DroYak_CAF1 122040 97 + 1
AAGCCGAGUUUCGGCUUGGGUCAACCGCAGGUUCUGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUCCCCGAUGUUU
((((((.....))))))(((.....(((.((((((((((((......))))))))...)))))))...((((......)))).....)))....... ( -37.90)
>consensus
AAGCCGAGUUUUGGGCCGGGUCAACCGCAGGUUCUGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUCCCCGAUGUUU
..........(((((...((((....((.((((((((((((......))))))))...))))))))))((((......)))).....)))))..... (-31.24 = -31.40 +   0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,227,287 – 15,227,384
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 95.88
Mean single sequence MFE -36.52
Consensus MFE -31.30
Energy contribution -32.14
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -3.34
Structure conservation index 0.86
SVM decision value 3.51
SVM RNA-class probability 0.999315
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15227287 97 - 23771897
AAACAUCGGGGAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCAGAACCUGCGGUUGACCCGGCCCAAAACUCGGCUU
.....(((((......((((....)))).(((((.((((...((((((((......))))))))((((...))))))))))))).....)))))... ( -37.00)
>DroSec_CAF1 116565 97 - 1
AAACAUCGGGGAUAAACACCAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCAGAACCUGCGGUUGACCCGGCCCAAAACUCGGCUU
.....(((((......(((......))).(((((.((((...((((((((......))))))))((((...))))))))))))).....)))))... ( -36.30)
>DroSim_CAF1 124389 97 - 1
AAACAUCGGGGAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCAGAACCUGCGGUUGACCCGGCCCAAAACUCGGCUU
.....(((((......((((....)))).(((((.((((...((((((((......))))))))((((...))))))))))))).....)))))... ( -37.00)
>DroEre_CAF1 116758 96 - 1
AGACGUCGG-GAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCAGAACCUGCGGUUGACCCAGCCCGAAACUCCGCUU
.((..((((-(.....((((....))))((..(((((.....((((((((......))))))))...)))))..))......)))))...))..... ( -33.50)
>DroYak_CAF1 122040 97 - 1
AAACAUCGGGGAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCAGAACCUGCGGUUGACCCAAGCCGAAACUCGGCUU
.......(((......((((....))))((..(((((.....((((((((......))))))))...)))))..)).)))((((((.....)))))) ( -38.80)
>consensus
AAACAUCGGGGAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCAGAACCUGCGGUUGACCCGGCCCAAAACUCGGCUU
.....(((((......(((......))).(((((.((((...((((((((......))))))))((((...))))))))))))).....)))))... (-31.30 = -32.14 +   0.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,227,305 – 15,227,420
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.91
Mean single sequence MFE -34.53
Consensus MFE -28.16
Energy contribution -29.10
Covariance contribution 0.94
Combinations/Pair 1.06
Mean z-score -1.98
Structure conservation index 0.82
SVM decision value 0.07
SVM RNA-class probability 0.570221
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15227305 115 + 23771897
GGUCAACCGCAGGUUC-UGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUCCCCGAUGUUUGUAAUUUUUUUUGUUCCGCCAUCGAUCUUGGCCGCA----
((((((.(((.(((((-(((((((......))))))))...)))))))...((((......)))).......(((((..((.(((.......))).)).)))))...))))))...---- ( -35.50)
>DroSec_CAF1 116583 115 + 1
GGUCAACCGCAGGUUC-UGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUGGUGUUUAUCCCCGAUGUUUGUAAUUUUUUUUGUUCCGCCAUCGAUCUUGGCCGCA----
((((....((.(((((-(((((((......))))))))...))))))))))((((((.((((.(.....).))))...))))...............((((.......)))).)).---- ( -36.20)
>DroSim_CAF1 124407 115 + 1
GGUCAACCGCAGGUUC-UGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUCCCCGAUGUUUGUAAUUUUUUUUGUUCCGCCAUCGAUCUUGGCCGCA----
((((((.(((.(((((-(((((((......))))))))...)))))))...((((......)))).......(((((..((.(((.......))).)).)))))...))))))...---- ( -35.50)
>DroEre_CAF1 116776 114 + 1
GGUCAACCGCAGGUUC-UGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUC-CCGACGUCUAUAAUGUUUUUUGUUCCGCCAGCGAUCUUGGCCGCA----
((((((.(((.(((((-(((((((......))))))))...))))(((...((((......)))).....-..(((((.....)))))........)))..)))...))))))...---- ( -36.80)
>DroYak_CAF1 122058 115 + 1
GGUCAACCGCAGGUUC-UGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUCCCCGAUGUUUAUAAUUUUUUUUGUUCCGCCAUCGAUCUUGGCCGCA----
((((((.(((.(((((-(((((((......))))))))...)))))))...((((......)))).......(((((...((((......)))).....)))))...))))))...---- ( -36.70)
>DroAna_CAF1 111136 108 + 1
GGUCAACCGCAGGUUCUUGGCCAUUGAUAUAUGGCCACGUUGACCGCGACCACACAAUCU------------CGACGUUUAUAAUUUUUUUUGUUCCGCCAUCGAUCUUCGCUGAACGCA
(((((((..........(((((((......))))))).)))))))(((...........(------------(((.((..((((......))))...))..))))((......)).))). ( -26.50)
>consensus
GGUCAACCGCAGGUUC_UGGCCAUUGAUAUAUGGCCAGUUUGACCGCGACCGCACAAUUUCGUGUUUAUCCCCGAUGUUUAUAAUUUUUUUUGUUCCGCCAUCGAUCUUGGCCGCA____
((((((.(((.((((..(((((((......)))))))....)))))))...((((......)))).......(((((...((((......)))).....)))))...))))))....... (-28.16 = -29.10 +   0.94)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,227,305 – 15,227,420
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.91
Mean single sequence MFE -38.98
Consensus MFE -28.82
Energy contribution -29.93
Covariance contribution 1.11
Combinations/Pair 1.03
Mean z-score -3.28
Structure conservation index 0.74
SVM decision value 0.09
SVM RNA-class probability 0.580599
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15227305 115 - 23771897
----UGCGGCCAAGAUCGAUGGCGGAACAAAAAAAAUUACAAACAUCGGGGAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCA-GAACCUGCGGUUGACC
----.((((((....((((((......................)))))).......((((....)))).))))))((((...((((((((......)))))))-)((((...)))))))) ( -39.35)
>DroSec_CAF1 116583 115 - 1
----UGCGGCCAAGAUCGAUGGCGGAACAAAAAAAAUUACAAACAUCGGGGAUAAACACCAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCA-GAACCUGCGGUUGACC
----.((((((.....(((((......................)))))((........)).........))))))((((...((((((((......)))))))-)((((...)))))))) ( -39.15)
>DroSim_CAF1 124407 115 - 1
----UGCGGCCAAGAUCGAUGGCGGAACAAAAAAAAUUACAAACAUCGGGGAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCA-GAACCUGCGGUUGACC
----.((((((....((((((......................)))))).......((((....)))).))))))((((...((((((((......)))))))-)((((...)))))))) ( -39.35)
>DroEre_CAF1 116776 114 - 1
----UGCGGCCAAGAUCGCUGGCGGAACAAAAAACAUUAUAGACGUCGG-GAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCA-GAACCUGCGGUUGACC
----.((((((...(((.((((((...................))))))-)))...((((....)))).))))))((((...((((((((......)))))))-)((((...)))))))) ( -42.91)
>DroYak_CAF1 122058 115 - 1
----UGCGGCCAAGAUCGAUGGCGGAACAAAAAAAAUUAUAAACAUCGGGGAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCA-GAACCUGCGGUUGACC
----.((((((....((((((......................)))))).......((((....)))).))))))((((...((((((((......)))))))-)((((...)))))))) ( -39.35)
>DroAna_CAF1 111136 108 - 1
UGCGUUCAGCGAAGAUCGAUGGCGGAACAAAAAAAAUUAUAAACGUCG------------AGAUUGUGUGGUCGCGGUCAACGUGGCCAUAUAUCAAUGGCCAAGAACCUGCGGUUGACC
.(((..((((((...((((((......................)))))------------)..)))).))..)))(((((((.(((((((......))))))).(......).))))))) ( -33.75)
>consensus
____UGCGGCCAAGAUCGAUGGCGGAACAAAAAAAAUUACAAACAUCGGGGAUAAACACGAAAUUGUGCGGUCGCGGUCAAACUGGCCAUAUAUCAAUGGCCA_GAACCUGCGGUUGACC
.....((((((....((((((......................)))))).......(((......))).))))))((((....(((((((......)))))))..((((...)))))))) (-28.82 = -29.93 +   1.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,227,420 – 15,227,527
Length 107
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 87.51
Mean single sequence MFE -29.44
Consensus MFE -24.21
Energy contribution -25.68
Covariance contribution 1.47
Combinations/Pair 1.09
Mean z-score -1.70
Structure conservation index 0.82
SVM decision value -0.03
SVM RNA-class probability 0.519619
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15227420 107 + 23771897
---AAGUCCUUU-------CUACCUGGCCCUAAAGGACACCACAAAUUUCCAAGCAAUUGGCGGUGCCUAACAAUGGCCC--AAUGGCCUUCUCGUCCCAUGGGGUCCAUCGCCCUAAG-
---.........-------.....((((((((..((((.......((..((((....))))..))..........((((.--...)))).....))))..))))).)))..........- ( -29.80)
>DroSec_CAF1 116698 107 + 1
---AAGUCCUUU-------CUACCUGGCCCUAAAGGACACCACAAAUUUCCAAGCAAUUGGCCGUGCCUAACAAUGGCCC--AAUGGCCUUCUCGUCCCAUGGGGUCCAACGCCCUAAG-
---.........-------.....((((((((..((((.............((....))(((((((((.......)))..--.)))))).....))))..))))).)))..........- ( -30.00)
>DroSim_CAF1 124522 107 + 1
---AAGUCCUUU-------CUACCUGGCCCUAAAGGACACCACAAAUUUCCAAGCAAUUGGCCGUGCCUAACAAUGGCCC--AAUGGCCUUCUCGUCCCAUGGGGUCCAACGCCCUAAG-
---.........-------.....((((((((..((((.............((....))(((((((((.......)))..--.)))))).....))))..))))).)))..........- ( -30.00)
>DroEre_CAF1 116890 104 + 1
----AGUCCUUU-------UUACCUGG-CCUAAAGGACACCACA-AUUUCCAAGCAAUUGGCCGUGCCUAACAAUGGCCC--AAUGGCCUUCGCGUCCCAUGGGGUCCAUCGCCCUGAG-
----.(((((((-------........-...)))))))......-........((....(((((((((.......)))..--.))))))...)).......(((((.....)))))...- ( -29.20)
>DroYak_CAF1 122173 113 + 1
----AGUCCUUUUACCUUCUUACCUGCCCCUAAAGGACACCACAAAUUUCCAAGCAAUUGGCCGUGCCUAACAAUGGCCC--AAUGGCCUUCUCGUCCCAUGGGGUCCAUCGCCCUAAG-
----.(((((((...................))))))).....................(((((((((.......)))..--.))))))...........((((((.....))))))..- ( -27.71)
>DroAna_CAF1 111244 120 + 1
UGUAAGUCCCUUUUACACCUUACCUGGCCCUAAAGGACACCACAAAUUUCCAGGCAAUUGGCCGUGUCUAACAAUGGCCCGCAAACGUCUUUACGUCCCAUGGGGUCUCGCCCGCAAAGA
((((((.....))))))........(((((((..((((...............((....((((((........)))))).))....((....))))))..)))))))............. ( -29.90)
>consensus
___AAGUCCUUU_______CUACCUGGCCCUAAAGGACACCACAAAUUUCCAAGCAAUUGGCCGUGCCUAACAAUGGCCC__AAUGGCCUUCUCGUCCCAUGGGGUCCAUCGCCCUAAG_
.........................(((((((..((((..(((......((((....))))..))).........((((......)))).....))))..)))))))............. (-24.21 = -25.68 +   1.47)

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 11:52:58 2006