Locus 6173

Sequence ID 2L_DroMel_CAF1
Location 17,210,295 – 17,210,420
Length 125
Max. P 0.997523
window9865 window9866 window9867 window9868

overview

Window 5

Location 17,210,295 – 17,210,390
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 76.17
Mean single sequence MFE -35.23
Consensus MFE -20.45
Energy contribution -24.40
Covariance contribution 3.95
Combinations/Pair 1.16
Mean z-score -2.87
Structure conservation index 0.58
SVM decision value 2.43
SVM RNA-class probability 0.993842
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17210295 95 + 22407834
AAUUUGGCCACGCCUAAUGACCAAAAAGGCGUGGCAUGGGCGUUGGGUGGCUGCAGGUGGUGGAUUCCCACCCCCGCAACCACAAUUAAACGCAC
......(((((((((...........)))))))))....(((((..((((.(((.((.(((((....))))))).))).)))).....))))).. ( -47.40)
>DroPse_CAF1 109604 75 + 1
AAUUCGGCCACGCUUAAUGGCCAAAACAGCAUGGCUUGGGGA------GGG-GGUGGGGGGGC-------------AAGCCACAAUUAAAUGCAC
..(((.(((.(.(((...(((((........)))))....))------).)-))).))).((.-------------...)).............. ( -19.10)
>DroSec_CAF1 53475 95 + 1
AAUUUGGCCACGCCUAAUGACCAAAAAGGCGUGGCAUGGGCGUUGGGUGGCUGCAGGUGGUGGCUUCCCACCCCCUCAACCACAAUUAAACGCAC
......(((((((((...........)))))))))....(((((..((((.((.(((.(((((....))))).))))).)))).....))))).. ( -44.30)
>DroSim_CAF1 55325 95 + 1
AAUUUGGCCACGCCUAAUGACCAAAAAGGCGUGGCAUGGGCGUUGGGUGGCUGCAGGUGGUGGAUUGCCACCCCCUCAACCACAAUUAAACGCAC
......(((((((((...........)))))))))....(((((..((((.((.(((.(((((....))))).))))).)))).....))))).. ( -44.90)
>DroYak_CAF1 53927 95 + 1
AAUUCGGCCAUGCCUAAUGACCAAAAAGGCGUGGCAUGGACGUUGGGUGGCUGCAGGUGGUGGAUGACCGCCCCCUCAACCACAAUUAAACGCAC
..(((((((((((((...........))))))))).))))((((..((((.((.(((.(((((....))))).))))).)))).....))))... ( -39.40)
>DroPer_CAF1 105683 76 + 1
AAUUCGGCCACGCUUAAUGGCCAAAACAGCAAGGCUUGGGGA------GGGGGGAGGGGGGGC-------------AAGCCACAAUUAAAUGCAC
.....(((((.......)))))..........((((((....------..............)-------------))))).............. ( -16.27)
>consensus
AAUUCGGCCACGCCUAAUGACCAAAAAGGCGUGGCAUGGGCGUUGGGUGGCUGCAGGUGGUGGAUU_CCACCCCCUCAACCACAAUUAAACGCAC
......(((((((((...........)))))))))....(((((..((((.....((.(((((....))))).))....)))).....))))).. (-20.45 = -24.40 +   3.95)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,210,295 – 17,210,390
Length 95
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 76.17
Mean single sequence MFE -37.05
Consensus MFE -21.04
Energy contribution -25.52
Covariance contribution 4.48
Combinations/Pair 1.14
Mean z-score -3.62
Structure conservation index 0.57
SVM decision value 2.88
SVM RNA-class probability 0.997523
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17210295 95 - 22407834
GUGCGUUUAAUUGUGGUUGCGGGGGUGGGAAUCCACCACCUGCAGCCACCCAACGCCCAUGCCACGCCUUUUUGGUCAUUAGGCGUGGCCAAAUU
(.(((((.....((((((((((((((((....))))).)))))))))))..))))).)..(((((((((...........)))))))))...... ( -51.90)
>DroPse_CAF1 109604 75 - 1
GUGCAUUUAAUUGUGGCUU-------------GCCCCCCCACC-CCC------UCCCCAAGCCAUGCUGUUUUGGCCAUUAAGCGUGGCCGAAUU
............(((((((-------------(..........-...------....)))))))).....(((((((((.....))))))))).. ( -21.23)
>DroSec_CAF1 53475 95 - 1
GUGCGUUUAAUUGUGGUUGAGGGGGUGGGAAGCCACCACCUGCAGCCACCCAACGCCCAUGCCACGCCUUUUUGGUCAUUAGGCGUGGCCAAAUU
(.(((((.....(((((((.((((((((....))))).))).)))))))..))))).)..(((((((((...........)))))))))...... ( -47.70)
>DroSim_CAF1 55325 95 - 1
GUGCGUUUAAUUGUGGUUGAGGGGGUGGCAAUCCACCACCUGCAGCCACCCAACGCCCAUGCCACGCCUUUUUGGUCAUUAGGCGUGGCCAAAUU
(.(((((.....(((((((.((((((((....))))).))).)))))))..))))).)..(((((((((...........)))))))))...... ( -45.30)
>DroYak_CAF1 53927 95 - 1
GUGCGUUUAAUUGUGGUUGAGGGGGCGGUCAUCCACCACCUGCAGCCACCCAACGUCCAUGCCACGCCUUUUUGGUCAUUAGGCAUGGCCGAAUU
............(((((((.(((((.((....)).)).))).)))))))....((.(((((((..(((.....))).....))))))).)).... ( -37.00)
>DroPer_CAF1 105683 76 - 1
GUGCAUUUAAUUGUGGCUU-------------GCCCCCCCUCCCCCC------UCCCCAAGCCUUGCUGUUUUGGCCAUUAAGCGUGGCCGAAUU
..(((......)))(((((-------------(..............------....)))))).......(((((((((.....))))))))).. ( -19.17)
>consensus
GUGCGUUUAAUUGUGGUUGAGGGGGUGG_AAUCCACCACCUGCAGCCACCCAACGCCCAUGCCACGCCUUUUUGGUCAUUAGGCGUGGCCAAAUU
(.(((((.....(((((((.(((((.((....)).)).))).)))))))..))))).)..(((((((((...........)))))))))...... (-21.04 = -25.52 +   4.48)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,210,326 – 17,210,420
Length 94
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 78.53
Mean single sequence MFE -32.22
Consensus MFE -18.89
Energy contribution -22.23
Covariance contribution 3.35
Combinations/Pair 1.12
Mean z-score -2.21
Structure conservation index 0.59
SVM decision value 1.11
SVM RNA-class probability 0.916246
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17210326 94 + 22407834
U------------GGCAUG---GGCGUUGGGUGGCUGCAGGUGGUGGAUUCCCACCCCCGCAACCACAAUUAAACGCACGCAAAUGGCGAGCCACACACAUAAAACAAA
(------------(((...---.(((((..((((.(((.((.(((((....))))))).))).)))).....))))).(((.....))).))))............... ( -38.90)
>DroSec_CAF1 53506 94 + 1
U------------GGCAUG---GGCGUUGGGUGGCUGCAGGUGGUGGCUUCCCACCCCCUCAACCACAAUUAAACGCACGCAAAUGGCGGGCCACACACAUAAAACAAA
(------------(((...---.(((((..((((.((.(((.(((((....))))).))))).)))).....))))).(((.....))).))))............... ( -35.80)
>DroSim_CAF1 55356 94 + 1
U------------GGCAUG---GGCGUUGGGUGGCUGCAGGUGGUGGAUUGCCACCCCCUCAACCACAAUUAAACGCACGCAAAUGGCGGGCCACACACAUAAAACAAA
(------------(((...---.(((((..((((.((.(((.(((((....))))).))))).)))).....))))).(((.....))).))))............... ( -36.40)
>DroEre_CAF1 53697 92 + 1
UGGGCGUGGGCGUGGCAUG---GGCGUUGGGUGGCUGC--------------CACCCCCUGAACCACAAUUAAACGCACGCAAAUGGCGGGCCACACACAUAAAACAAA
...(.((((((.((.(((.---.((((.((((((...)--------------)))))..((.....)).........))))..))).)).))).))).).......... ( -30.90)
>DroYak_CAF1 53958 94 + 1
U------------GGCAUG---GACGUUGGGUGGCUGCAGGUGGUGGAUGACCGCCCCCUCAACCACAAUUAAACGCACGCAAAUGGCGGGCCACACACAUAAAACAAA
(------------(((...---(.((((..((((.((.(((.(((((....))))).))))).)))).....))))).(((.....))).))))............... ( -32.00)
>DroAna_CAF1 128436 84 + 1
U------------GGCAGCAGAAGCAGGGGCGGGGUGGAGGUGGGGGU-------------GGCCACAAUUAAACGCACGCAAAUUGUGGGGCACACACAUAAAACAAA
.------------....((....((((..((((.((....((((....-------------..))))......)).).)))...))))...))................ ( -19.30)
>consensus
U____________GGCAUG___GGCGUUGGGUGGCUGCAGGUGGUGGAUU_CCACCCCCUCAACCACAAUUAAACGCACGCAAAUGGCGGGCCACACACAUAAAACAAA
.............(((.......(((((..((((.((..((.(((((....)))))))..)).)))).....))))).(((.....))).)))................ (-18.89 = -22.23 +   3.35)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,210,326 – 17,210,420
Length 94
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 78.53
Mean single sequence MFE -32.48
Consensus MFE -17.27
Energy contribution -20.87
Covariance contribution 3.60
Combinations/Pair 1.07
Mean z-score -1.82
Structure conservation index 0.53
SVM decision value 0.07
SVM RNA-class probability 0.568932
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17210326 94 - 22407834
UUUGUUUUAUGUGUGUGGCUCGCCAUUUGCGUGCGUUUAAUUGUGGUUGCGGGGGUGGGAAUCCACCACCUGCAGCCACCCAACGCC---CAUGCC------------A
.........((.((((((..(((.....))).(((((.....((((((((((((((((....))))).)))))))))))..))))))---))))))------------) ( -42.50)
>DroSec_CAF1 53506 94 - 1
UUUGUUUUAUGUGUGUGGCCCGCCAUUUGCGUGCGUUUAAUUGUGGUUGAGGGGGUGGGAAGCCACCACCUGCAGCCACCCAACGCC---CAUGCC------------A
.........((.((((((..(((.....))).(((((.....(((((((.((((((((....))))).))).)))))))..))))))---))))))------------) ( -38.50)
>DroSim_CAF1 55356 94 - 1
UUUGUUUUAUGUGUGUGGCCCGCCAUUUGCGUGCGUUUAAUUGUGGUUGAGGGGGUGGCAAUCCACCACCUGCAGCCACCCAACGCC---CAUGCC------------A
.........((.((((((..(((.....))).(((((.....(((((((.((((((((....))))).))).)))))))..))))))---))))))------------) ( -36.10)
>DroEre_CAF1 53697 92 - 1
UUUGUUUUAUGUGUGUGGCCCGCCAUUUGCGUGCGUUUAAUUGUGGUUCAGGGGGUG--------------GCAGCCACCCAACGCC---CAUGCCACGCCCACGCCCA
..........(((((.(((.((((......).))).......(((((...(((((((--------------(...))))))....))---...)))))))))))))... ( -32.00)
>DroYak_CAF1 53958 94 - 1
UUUGUUUUAUGUGUGUGGCCCGCCAUUUGCGUGCGUUUAAUUGUGGUUGAGGGGGCGGUCAUCCACCACCUGCAGCCACCCAACGUC---CAUGCC------------A
.........((.((((((..(((.....))).(((((.....(((((((.(((((.((....)).)).))).)))))))..))))))---))))))------------) ( -31.10)
>DroAna_CAF1 128436 84 - 1
UUUGUUUUAUGUGUGUGCCCCACAAUUUGCGUGCGUUUAAUUGUGGCC-------------ACCCCCACCUCCACCCCGCCCCUGCUUCUGCUGCC------------A
..........(((.(((..((((((((.((....))..)))))))).)-------------))...))).........((....((....)).)).------------. ( -14.70)
>consensus
UUUGUUUUAUGUGUGUGGCCCGCCAUUUGCGUGCGUUUAAUUGUGGUUGAGGGGGUGG_AAUCCACCACCUGCAGCCACCCAACGCC___CAUGCC____________A
........(((((.((((....)))).)))))(((((.....(((((((.(((((.((....)).)).))).)))))))..)))))....................... (-17.27 = -20.87 +   3.60)

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 12:04:23 2006