Locus 398

Sequence ID X_DroMel_CAF1
Location 1,173,876 – 1,174,269
Length 393
Max. P 0.999668
window604 window605 window606 window607 window608 window609

overview

Window 4

Location 1,173,876 – 1,173,969
Length 93
Sequences 3
Columns 93
Reading direction forward
Mean pairwise identity 98.57
Mean single sequence MFE -37.67
Consensus MFE -37.53
Energy contribution -37.53
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 1.00
SVM decision value -0.03
SVM RNA-class probability 0.519933
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1173876 93 + 22224390
ACCCCUCGAAAUGGGGAACGCAGCCGUGCAACCGAGCGGCUGGUUGGCUGCUGAAAGGUCAUUGGGCUUGUUCAGACGCCCGUUCAGCUCAGA
..(((.......)))((((((((((((........)))))))...(((..((((((((((....))))).)))))..))))))))........ ( -36.60)
>DroSec_CAF1 9893 93 + 1
ACCCCUCGAAAUGGGGAACGCAGCCGUGCAACGGGGCGGCUGGUUGGCUGCUGAAAGGUCAUUGGGCUUGUUCAGACGCCCGUUCAGCUCAGA
..(((.......)))((((((((((((.(....).)))))))...(((..((((((((((....))))).)))))..))))))))........ ( -38.20)
>DroSim_CAF1 24981 93 + 1
ACCCCUCGAAAUGGGGAACGCAGCCGUGCAACGGGGCGGCUGGUUGGCUGCUGAAAGGUCAUUGGGCUUGUUCAGACGCCCGUUCAGCUCAGA
..(((.......)))((((((((((((.(....).)))))))...(((..((((((((((....))))).)))))..))))))))........ ( -38.20)
>consensus
ACCCCUCGAAAUGGGGAACGCAGCCGUGCAACGGGGCGGCUGGUUGGCUGCUGAAAGGUCAUUGGGCUUGUUCAGACGCCCGUUCAGCUCAGA
..(((.......)))((((((((((((.(....).)))))))...(((..((((((((((....))))).)))))..))))))))........ (-37.53 = -37.53 +   0.00)

alignment

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secondary structure

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Window 5

Location 1,173,929 – 1,174,041
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.55
Mean single sequence MFE -45.14
Consensus MFE -39.18
Energy contribution -38.86
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -3.11
Structure conservation index 0.87
SVM decision value 3.86
SVM RNA-class probability 0.999668
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1173929 112 + 22224390
AAAGGUCAUUGGGCUUGUUCAGACGCCCGUUCAGCUCAGACGGAGUUCGAAGCUGCAUCCUGCUUGAGCCCUUGCUGC--------UCCGUGUCAAUGACACGCCCUUUGGCCAAUACCC
...(((((..((((.((((..(((((..(..((((......((.((((.((((........))))))))))..)))).--------.).)))))...)))).))))..)))))....... ( -41.80)
>DroSec_CAF1 9946 112 + 1
AAAGGUCAUUGGGCUUGUUCAGACGCCCGUUCAGCUCAGACGGAGUUCGGAGCUGCAUCCUGCUUGAGCCCUUGCUGC--------UCCGUGUCAAUGACACGCCCUUUGGCCAAACCCC
...(((((..((((.((((..((((((((((.......))))).....(((((.(((....((....))...))).))--------))))))))...)))).))))..)))))....... ( -47.70)
>DroSim_CAF1 25034 112 + 1
AAAGGUCAUUGGGCUUGUUCAGACGCCCGUUCAGCUCAGACGGAGUUCGGAGCUGCAUCCUGCUUGAGCCCUUGCUGC--------UCCGUGUCAAUGACACGCCCUUUGGCCAAACCCC
...(((((..((((.((((..((((((((((.......))))).....(((((.(((....((....))...))).))--------))))))))...)))).))))..)))))....... ( -47.70)
>DroEre_CAF1 9115 104 + 1
AAAGGUCAUUGGGCUUGUUCAGACGCCCGUUC-----AGACGGAGUUUGGAGCUGCAUCCUGCUUGAGCAUUUGCUGC--------UCAGUGUCAAUGACACGCCCUUUGGCC---CCUC
...(((((..((((.....(((((..((((..-----..)))).)))))((((.(((...(((....)))..))).))--------)).(((((...)))))))))..)))))---.... ( -45.00)
>DroYak_CAF1 11924 111 + 1
AAAGGUCAUUGGGCUUGUUCAGACGCCCGUUC-----AGACGGAGUUCGGAGCUGCAUCCUGCUUGAGCCUCUACUGCACUGAGGCGCAGUGUCAAUGACACGCCCUUUGGCC----CUC
...(((((..((((.((((..(((((((((..-----..))))(((..(((......))).)))((.(((((.........))))).)))))))...)))).))))..)))))----... ( -43.50)
>consensus
AAAGGUCAUUGGGCUUGUUCAGACGCCCGUUCAGCUCAGACGGAGUUCGGAGCUGCAUCCUGCUUGAGCCCUUGCUGC________UCCGUGUCAAUGACACGCCCUUUGGCCAA_CCCC
...(((((..((((.((((..((((((((((.......))))).((((.((((........))))))))....................)))))...)))).))))..)))))....... (-39.18 = -38.86 +  -0.32)

alignment

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secondary structure

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Window 6

Location 1,174,041 – 1,174,132
Length 91
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 91.12
Mean single sequence MFE -36.98
Consensus MFE -31.76
Energy contribution -32.33
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.79
Structure conservation index 0.86
SVM decision value 0.77
SVM RNA-class probability 0.846566
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1174041 91 + 22224390
CGUCGCCCCACCGG-CGCUCAUUAGCGCAGCUUUAGGGCCAAUGCCAAAGGUGGGCAAAGAAAGCCCGAGGUGGGGACAAAGCCUCUGCAGC
....((((((((.(-((((....))))).(((((..(((....))).)))))((((.......))))..))))))).)...((....))... ( -37.30)
>DroSec_CAF1 10058 92 + 1
CGCCGCCCCACCUGCCGCUCAUUAGCGCAGCUUUGGGGCCAAUGCCAAAGGCGGGCAAGGAAAGCCCGAGGUGGGGACAAAGCCUCUGCAGC
.((.((((((.((((.(((....)))))))...))))))...(((...((((((((.......))))....((....))..))))..))))) ( -38.50)
>DroSim_CAF1 25146 92 + 1
CGCCGCCCCACCUGCCGCUCAUUAGCGCAGCUUUAGGGCCAAUGCCAAAGGCGGGCAAGGAAAGCCCGAGGUGGGGACAAAGCCUCUGCAGC
.((.(((((((((((.(((....))))).(((((..(((....))).)))))((((.......)))).)))))))).)...((....)).)) ( -37.00)
>DroEre_CAF1 9219 92 + 1
CGCUGCCCCACCUGCCGCUCAUUAGCGCAGCUUUAAGGCCAGCGCCAAAGGCAGGCGAACAAAGCCCCAGAUGGGGACAAAACCUCUGCAGC
.(((((..(.((((((........((((.(((....)))..))))....)))))).)......(((((....)))).).........))))) ( -35.10)
>consensus
CGCCGCCCCACCUGCCGCUCAUUAGCGCAGCUUUAGGGCCAAUGCCAAAGGCGGGCAAAGAAAGCCCGAGGUGGGGACAAAGCCUCUGCAGC
....((((((((((.((((....))))).(((((..(((....))).)))))((((.......)))).)))))))).).............. (-31.76 = -32.33 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,174,041 – 1,174,132
Length 91
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 91.12
Mean single sequence MFE -43.10
Consensus MFE -39.12
Energy contribution -38.50
Covariance contribution -0.62
Combinations/Pair 1.18
Mean z-score -2.32
Structure conservation index 0.91
SVM decision value 1.94
SVM RNA-class probability 0.983259
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1174041 91 - 22224390
GCUGCAGAGGCUUUGUCCCCACCUCGGGCUUUCUUUGCCCACCUUUGGCAUUGGCCCUAAAGCUGCGCUAAUGAGCG-CCGGUGGGGCGACG
(((.....))).(((.(((((((..(((((.....((((.......))))..))))).......(((((....))))-).)))))))))).. ( -39.50)
>DroSec_CAF1 10058 92 - 1
GCUGCAGAGGCUUUGUCCCCACCUCGGGCUUUCCUUGCCCGCCUUUGGCAUUGGCCCCAAAGCUGCGCUAAUGAGCGGCAGGUGGGGCGGCG
(((((...(((...)))(((((((.(((((.....((((.......))))..)))))....(((((........))))))))))))))))). ( -43.60)
>DroSim_CAF1 25146 92 - 1
GCUGCAGAGGCUUUGUCCCCACCUCGGGCUUUCCUUGCCCGCCUUUGGCAUUGGCCCUAAAGCUGCGCUAAUGAGCGGCAGGUGGGGCGGCG
(((((...(((...)))(((((((.(((((.....((((.......))))..)))))....(((((........))))))))))))))))). ( -44.00)
>DroEre_CAF1 9219 92 - 1
GCUGCAGAGGUUUUGUCCCCAUCUGGGGCUUUGUUCGCCUGCCUUUGGCGCUGGCCUUAAAGCUGCGCUAAUGAGCGGCAGGUGGGGCAGCG
(((((.........(((((.....)))))....((((((((((.(((((((.(((......)))))))))).....))))))))))))))). ( -45.30)
>consensus
GCUGCAGAGGCUUUGUCCCCACCUCGGGCUUUCCUUGCCCGCCUUUGGCAUUGGCCCUAAAGCUGCGCUAAUGAGCGGCAGGUGGGGCGGCG
(((((...(((...)))((((((..(((((.....((((.......))))..)))))....(((((........))))).))))))))))). (-39.12 = -38.50 +  -0.62)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,174,055 – 1,174,160
Length 105
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 71.97
Mean single sequence MFE -33.93
Consensus MFE -18.50
Energy contribution -18.83
Covariance contribution 0.34
Combinations/Pair 1.10
Mean z-score -1.71
Structure conservation index 0.55
SVM decision value 0.16
SVM RNA-class probability 0.610914
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1174055 105 + 22224390
---CGCUCAUUAGCGCAGCUUUAGGGCCAAUGCCAAAGGUGGGCAAAGAAAGCCCGAGGUGGGGACAAAGCCUCUGCAGCGAAAA------------ACAUGCAAGGCUCGGACCAAAAA
---.(((..((.((.((.(((...(((....))).))).)).)).))...)))((((..((....))..((((.((((.......------------...))))))))))))........ ( -31.80)
>DroSec_CAF1 10072 106 + 1
--CCGCUCAUUAGCGCAGCUUUGGGGCCAAUGCCAAAGGCGGGCAAGGAAAGCCCGAGGUGGGGACAAAGCCUCUGCAGCGAGAA------------ACAUGCAAGGCGCGGACCAAAAA
--((((.......(((.(((((..(((....))).)))))((((.......))))...)))........((((.((((.......------------...))))))))))))........ ( -36.80)
>DroYak_CAF1 12075 106 + 1
AGCCGCUCAUUAGUGCAGCUUUGGGGCCAGCGCCAAAGGCAGCCAA----AGC----------AACACAACCUCUGCAGCGAAUGGCACGUAGAAGAAAAUGCGCAACGCGGACCAAAAA
..((((......((((((((((((.(((.........)))..))))----)))----------.......(.(((((.((.....))..))))).)....)))))...))))........ ( -33.20)
>consensus
__CCGCUCAUUAGCGCAGCUUUGGGGCCAAUGCCAAAGGCGGGCAA_GAAAGCCCGAGGUGGGGACAAAGCCUCUGCAGCGAAAA____________ACAUGCAAGGCGCGGACCAAAAA
...((((((...((...(((((..(((....))).)))))((((.......))))..............))...)).))))....................................... (-18.50 = -18.83 +   0.34)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,174,160 – 1,174,269
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.22
Mean single sequence MFE -37.02
Consensus MFE -18.83
Energy contribution -20.14
Covariance contribution 1.31
Combinations/Pair 1.07
Mean z-score -2.11
Structure conservation index 0.51
SVM decision value 0.08
SVM RNA-class probability 0.573552
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1174160 109 - 22224390
UCGCAAAUAUUUGCUCAUUUCGCAAUGUGUGGAUAGCUGCGU---GAAGGGGCUAA-AAGCCUCUUAUCGCUGCCCAAUGUUUGUGCGGCCAGC-------UACAUAUUUGAGAUUCGCA
...........(((..((((((.(((((((((...((((((.---.((.((((...-.(((........)))))))....))..))))))...)-------))))))))))))))..))) ( -37.20)
>DroSim_CAF1 25266 116 - 1
UCGCAAAUAUUUGCUCAUUUCGCAAUGUGGGGAUAGCUACGC---GAAGGGGCUGA-AAGCCUCUUAUCGCUGCCCAAUGUUUGUGCGGCCAGCAGGCCUCCACAUAUUUGAGAUUCGCA
((.((((((.((((.......))))(((((((...(((..((---.(((((((...-..)))))))...(((((.((.....)).)))))..)).)))))))))))))))).))...... ( -38.30)
>DroEre_CAF1 9350 98 - 1
UCGCAAAUAUUUCCUCAUUU--------CUGUAUUGCUGG-----AAAGGGGCUGA-AAGCCUCUUAUCGGUGGCAAAUGUUUGAGCGGGCAGAGA--------UUAUUUGAGAUUCGCA
..((....(((((...((((--------((((.(..((((-----.(((((((...-..))))))).))))..)....(((....))).)))))))--------).....)))))..)). ( -28.30)
>DroYak_CAF1 12181 116 - 1
UCGCAAAUAUUUGCCCAUUUCGUCAUGUCGGGAUUGCUGGGGGAUAAAGGGGCUAAGAAGCCUCUUAUCGCUGGCAAAUGUUUGAGCGGCCAGCGAGAAG----CUAUUUGAGCUUCGCA
..((......((.(((((..((......))..)....)))).))..((((((((....)))))))).((((((((....((....)).))))))))((((----((.....)))))))). ( -44.30)
>consensus
UCGCAAAUAUUUGCUCAUUUCGCAAUGUCGGGAUAGCUGCG____AAAGGGGCUAA_AAGCCUCUUAUCGCUGCCAAAUGUUUGAGCGGCCAGCGA________AUAUUUGAGAUUCGCA
...((((((((((((.............((((....))))......((((((((....))))))))......)))))))))))).((((..........................)))). (-18.83 = -20.14 +   1.31)

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 09:43:36 2006