Locus 5870

Sequence ID X_DroMel_CAF1
Location 15,133,970 – 15,134,246
Length 276
Max. P 0.999452
window9524 window9525 window9526 window9527 window9528 window9529 window9530

overview

Window 4

Location 15,133,970 – 15,134,089
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.52
Mean single sequence MFE -37.30
Consensus MFE -32.96
Energy contribution -33.56
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.88
SVM decision value 3.08
SVM RNA-class probability 0.998371
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15133970 119 + 22224390
CUACGAGUACGAGCAUAUGUGCUGAAAUCAGCGGCGCGUGCGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCAGUUUUUUGUUGAGUUGGGAAAAGUUUCGAUUUACGAAAA-AC
...((.(((((.((.....(((((....))))))).)))))(((((....)))))(((((((((.......((((((((.......))))))))......)))))))))..))....-.. ( -39.52)
>DroSec_CAF1 45418 119 + 1
CUGCGAGUACGAGCAUAUGUGCUGAUAUCAGCGGCGCGUGCGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCAGUUUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA-AC
.((((.(((((.((.....(((((....))))))).))))).))))((((((...(((((((((((((((((((.........)))))..)))))).....))))))))..))))))-.. ( -39.30)
>DroSim_CAF1 36158 119 + 1
CUACGAGUACGAGCAUAUGUGCUGAAAUCAGCGGCGCGUGCGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCAGUUUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA-AC
...((.(((((.((.....(((((....))))))).)))))(((((....)))))(((((((((((((((((((.........)))))..)))))).....))))))))..))....-.. ( -39.30)
>DroEre_CAF1 52345 108 + 1
AU------------UUAUGUGCUGAAAUCAGCGGCGCGUGCGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCACUUUUUUGUCGACUUGGGAAAAGUUUCGAUUUACGAAAAAAA
..------------.(((((((((.......)))))))))((((((....))))))(((((((((((((..((((..........)))).)))))).....)))))))............ ( -35.80)
>DroYak_CAF1 53073 107 + 1
AU------------AUAUGUGCUGAAAUCAGCGGCGCGUGCGCGCAUUUUUGCGCGAUCGAAACCCGAGAAGGAUUCAGUUUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA-AC
..------------.(((((((((.......)))))))))((((((....))))))(((((((((((((.......(((....)))....)))))).....))))))).........-.. ( -32.60)
>consensus
CU_CGAGUACGAGCAUAUGUGCUGAAAUCAGCGGCGCGUGCGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCAGUUUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA_AC
...............(((((((((.......)))))))))((((((....))))))((((((((((((((((((.........)))))..)))))).....)))))))............ (-32.96 = -33.56 +   0.60)

alignment

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secondary structure

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Window 5

Location 15,134,010 – 15,134,129
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.65
Mean single sequence MFE -30.83
Consensus MFE -28.34
Energy contribution -28.74
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.92
SVM decision value 0.78
SVM RNA-class probability 0.849776
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15134010 119 + 22224390
CGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCAGUUUUUUGUUGAGUUGGGAAAAGUUUCGAUUUACGAAAA-ACAUUCCCACUGUCUGUGUUUGUCAUCCUUCGAAAAUCUGCU
((((((....)))))).(((((....((..((((....(((((((((.((((((..(....)..)))))))))))))-)).....(((.....))).))))..)).)))))......... ( -32.50)
>DroSec_CAF1 45458 119 + 1
CGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCAGUUUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA-ACAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCU
((((((....)))))).(((.(((..((((((......)))))).)))(((.((((((...(((((.....))))).-...))))))..)))................)))......... ( -31.00)
>DroSim_CAF1 36198 119 + 1
CGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCAGUUUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA-ACAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCU
((((((....)))))).(((.(((..((((((......)))))).)))(((.((((((...(((((.....))))).-...))))))..)))................)))......... ( -31.00)
>DroEre_CAF1 52373 120 + 1
CGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCACUUUUUUGUCGACUUGGGAAAAGUUUCGAUUUACGAAAAAAAAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCU
((((((....)))))).(((........(((((((..........)))(((.((((((...(((((.....))))).....))))))..)))...)))).........)))......... ( -28.63)
>DroYak_CAF1 53101 119 + 1
CGCGCAUUUUUGCGCGAUCGAAACCCGAGAAGGAUUCAGUUUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA-ACAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCU
((((((....)))))).(((.....)))........(((.((((((..(((.((((((...(((((.....))))).-...))))))..))).(((.....)))....)))))).))).. ( -31.00)
>consensus
CGCGCAUUUUUGCGCGAUCGAAACCCGAGAACGAUUCAGUUUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA_ACAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCU
((((((....)))))).(((.....)))........(((.((((((..(((.((((((...(((((.....))))).....))))))..))).(((.....)))....)))))).))).. (-28.34 = -28.74 +   0.40)

alignment

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secondary structure

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Window 6

Location 15,134,010 – 15,134,129
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.65
Mean single sequence MFE -34.60
Consensus MFE -32.34
Energy contribution -32.74
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.50
Structure conservation index 0.93
SVM decision value 3.62
SVM RNA-class probability 0.999452
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15134010 119 - 22224390
AGCAGAUUUUCGAAGGAUGACAAACACAGACAGUGGGAAUGU-UUUUCGUAAAUCGAAACUUUUCCCAACUCAACAAAAAACUGAAUCGUUCUCGGGUUUCGAUCGCGCAAAAAUGCGCG
....((..(((((.((((((........((...((((((...-.(((((.....)))))...))))))..))..((......))..)))))))))))..))...((((((....)))))) ( -32.60)
>DroSec_CAF1 45458 119 - 1
AGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUGU-UUUUCGUAAAUCGAAACUUUUCCCAAGUCAACAAAAAACUGAAUCGUUCUCGGGUUUCGAUCGCGCAAAAAUGCGCG
....((((.((.((((((((........(((..((((((...-.(((((.....)))))...)))))).)))..((......))..)))))))).))....))))(((((....))))). ( -35.80)
>DroSim_CAF1 36198 119 - 1
AGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUGU-UUUUCGUAAAUCGAAACUUUUCCCAAGUCAACAAAAAACUGAAUCGUUCUCGGGUUUCGAUCGCGCAAAAAUGCGCG
....((((.((.((((((((........(((..((((((...-.(((((.....)))))...)))))).)))..((......))..)))))))).))....))))(((((....))))). ( -35.80)
>DroEre_CAF1 52373 120 - 1
AGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUUUUUUUUCGUAAAUCGAAACUUUUCCCAAGUCGACAAAAAAGUGAAUCGUUCUCGGGUUUCGAUCGCGCAAAAAUGCGCG
....((((.((.((((((((........(((..((((((.....(((((.....)))))...)))))).))).((......))...)))))))).))....))))(((((....))))). ( -35.30)
>DroYak_CAF1 53101 119 - 1
AGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUGU-UUUUCGUAAAUCGAAACUUUUCCCAAGUCAACAAAAAACUGAAUCCUUCUCGGGUUUCGAUCGCGCAAAAAUGCGCG
....((..((((((((((..........(((..((((((...-.(((((.....)))))...)))))).)))..((......)).)))).)).))))..))...((((((....)))))) ( -33.50)
>consensus
AGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUGU_UUUUCGUAAAUCGAAACUUUUCCCAAGUCAACAAAAAACUGAAUCGUUCUCGGGUUUCGAUCGCGCAAAAAUGCGCG
....((..((((.(((((((........(((..((((((.....(((((.....)))))...)))))).)))..((......))..)))))))))))..))...((((((....)))))) (-32.34 = -32.74 +   0.40)

alignment

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secondary structure

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Window 7

Location 15,134,050 – 15,134,169
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.13
Mean single sequence MFE -28.97
Consensus MFE -23.72
Energy contribution -25.56
Covariance contribution 1.84
Combinations/Pair 1.03
Mean z-score -2.81
Structure conservation index 0.82
SVM decision value 2.43
SVM RNA-class probability 0.993868
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15134050 119 + 22224390
UUUUUGUUGAGUUGGGAAAAGUUUCGAUUUACGAAAA-ACAUUCCCACUGUCUGUGUUUGUCAUCCUUCGAAAAUCUGCUUAGCCAACAUUAACGUGUUUGCCCAUCCACAAACACAUAC
....(((((.((((((.....((((((.....((.((-((((...........)))))).)).....)))))).....))))))))))).....(((((((........))))))).... ( -29.60)
>DroSec_CAF1 45498 119 + 1
UUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA-ACAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAGCCAACAUUAACGUGUUUGCCCAGCCACAAACACAUAC
........(((.((((((...(((((.....))))).-...))))))..)))(((((((((..((....))......(((..((.(((((....))))).))..))).)))))))))... ( -31.10)
>DroSim_CAF1 36238 119 + 1
UUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA-ACAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAGCCAACAUUAACGUGUUUGCCCAGCCACAAACACAUAC
........(((.((((((...(((((.....))))).-...))))))..)))(((((((((..((....))......(((..((.(((((....))))).))..))).)))))))))... ( -31.10)
>DroEre_CAF1 52413 118 + 1
UUUUUGUCGACUUGGGAAAAGUUUCGAUUUACGAAAAAAAAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAUCCAACACUAACG--AUCGCCCAGCCACAAACACAUAG
........(((.((((((...(((((.....))))).....))))))..)))(((((((((.......(((.....((......))...(....)--.))).......)))))))))... ( -23.84)
>DroYak_CAF1 53141 117 + 1
UUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA-ACAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAGCCAACAUUAACG--UUUGCCCAGCCACAAACACAUAG
........(((.((((((...(((((.....))))).-...))))))..)))(((((((((..((....))......(((..((.(((......)--)).))..))).)))))))))... ( -29.20)
>consensus
UUUUUGUUGACUUGGGAAAAGUUUCGAUUUACGAAAA_ACAUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAGCCAACAUUAACGUGUUUGCCCAGCCACAAACACAUAC
........(((.((((((...(((((.....))))).....))))))..)))(((((((((..((....))......(((..((.(((((....))))).))..))).)))))))))... (-23.72 = -25.56 +   1.84)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,134,050 – 15,134,169
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.13
Mean single sequence MFE -33.54
Consensus MFE -28.52
Energy contribution -30.12
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.85
SVM decision value 2.37
SVM RNA-class probability 0.993002
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15134050 119 - 22224390
GUAUGUGUUUGUGGAUGGGCAAACACGUUAAUGUUGGCUAAGCAGAUUUUCGAAGGAUGACAAACACAGACAGUGGGAAUGU-UUUUCGUAAAUCGAAACUUUUCCCAACUCAACAAAAA
((.(((((((((.(...(((.((((......)))).)))...)......((....))..))))))))).))..((((((...-.(((((.....)))))...))))))............ ( -31.20)
>DroSec_CAF1 45498 119 - 1
GUAUGUGUUUGUGGCUGGGCAAACACGUUAAUGUUGGCUAAGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUGU-UUUUCGUAAAUCGAAACUUUUCCCAAGUCAACAAAAA
...(((((((((.(((.(((.((((......)))).))).)))......((....))..)))))))))(((..((((((...-.(((((.....)))))...)))))).)))........ ( -35.00)
>DroSim_CAF1 36238 119 - 1
GUAUGUGUUUGUGGCUGGGCAAACACGUUAAUGUUGGCUAAGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUGU-UUUUCGUAAAUCGAAACUUUUCCCAAGUCAACAAAAA
...(((((((((.(((.(((.((((......)))).))).)))......((....))..)))))))))(((..((((((...-.(((((.....)))))...)))))).)))........ ( -35.00)
>DroEre_CAF1 52413 118 - 1
CUAUGUGUUUGUGGCUGGGCGAU--CGUUAGUGUUGGAUAAGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUUUUUUUUCGUAAAUCGAAACUUUUCCCAAGUCGACAAAAA
...(((((((((.(((...(((.--.(((..((((.....)))))))..)))..)).).)))))))))(((..((((((.....(((((.....)))))...)))))).)))........ ( -32.20)
>DroYak_CAF1 53141 117 - 1
CUAUGUGUUUGUGGCUGGGCAAA--CGUUAAUGUUGGCUAAGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUGU-UUUUCGUAAAUCGAAACUUUUCCCAAGUCAACAAAAA
...(((((((((.(((.(((.((--((....)))).))).)))......((....))..)))))))))(((..((((((...-.(((((.....)))))...)))))).)))........ ( -34.30)
>consensus
GUAUGUGUUUGUGGCUGGGCAAACACGUUAAUGUUGGCUAAGCAGAUUUUCGGAGGAUGACAAACACAGACAGUGGGAAUGU_UUUUCGUAAAUCGAAACUUUUCCCAAGUCAACAAAAA
...(((((((((.(((.(((.((((......)))).))).)))......((....))..)))))))))(((..((((((.....(((((.....)))))...)))))).)))........ (-28.52 = -30.12 +   1.60)

alignment

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secondary structure

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Window 9

Location 15,134,089 – 15,134,209
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.74
Mean single sequence MFE -17.43
Consensus MFE -13.17
Energy contribution -15.01
Covariance contribution 1.84
Combinations/Pair 1.04
Mean z-score -1.67
Structure conservation index 0.76
SVM decision value 0.10
SVM RNA-class probability 0.584770
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15134089 120 + 22224390
AUUCCCACUGUCUGUGUUUGUCAUCCUUCGAAAAUCUGCUUAGCCAACAUUAACGUGUUUGCCCAUCCACAAACACAUACAAAUGCAUACAAAAAAAAAACUAUCACAUUCGCAUCGACA
.........((((((((((((..((....))...........((.(((((....))))).))......))))))))).....((((.........................)))).))). ( -16.61)
>DroSec_CAF1 45537 117 + 1
AUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAGCCAACAUUAACGUGUUUGCCCAGCCACAAACACAUACAAAUGCAUACGAA---AAAACUAUCACAUUCUCAUCGACA
........(((.(((((((((..((....))......(((..((.(((((....))))).))..))).))))))))).)))............---........................ ( -19.10)
>DroSim_CAF1 36277 117 + 1
AUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAGCCAACAUUAACGUGUUUGCCCAGCCACAAACACAUACAAAUGCAUACGAA---AAAACUAUCACAUUCGCAUCGACA
.........((((((((((((..((....))......(((..((.(((((....))))).))..))).))))))))).....((((.......---...............)))).))). ( -20.15)
>DroEre_CAF1 52453 110 + 1
AUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAUCCAACACUAACG--AUCGCCCAGCCACAAACACAUAGAAAUGCC-----A---AAAACUAUCACAUUCGCAUCGACA
.........((((((((((((.......(((.....((......))...(....)--.))).......))))))))).....((((.-----.---...............)))).))). ( -12.87)
>DroYak_CAF1 53180 110 + 1
AUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAGCCAACAUUAACG--UUUGCCCAGCCACAAACACAUAGAAAUGCU-----A---AAAACUAUCACAUUCGCAUCGACA
.........((((((((((((..((....))......(((..((.(((......)--)).))..))).))))))))).....((((.-----.---...............)))).))). ( -18.43)
>consensus
AUUCCCACUGUCUGUGUUUGUCAUCCUCCGAAAAUCUGCUUAGCCAACAUUAACGUGUUUGCCCAGCCACAAACACAUACAAAUGCAUAC_AA___AAAACUAUCACAUUCGCAUCGACA
.........((((((((((((..((....))......(((..((.(((((....))))).))..))).))))))))).....((((.........................)))).))). (-13.17 = -15.01 +   1.84)

alignment

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secondary structure

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Window 0

Location 15,134,129 – 15,134,246
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 91.88
Mean single sequence MFE -25.84
Consensus MFE -19.17
Energy contribution -19.25
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.80
Structure conservation index 0.74
SVM decision value 0.11
SVM RNA-class probability 0.589362
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15134129 117 - 22224390
UAAUAUGUUAAUUUUAUUUGUCUUGCCUCAUUGAUUGUGUCGAUGCGAAUGUGAUAGUUUUUUUUUUGUAUGCAUUUGUAUGUGUUUGUGGAUGGGCAAACACGUUAAUGUUGGCUA
........................(((.(((((((.......(((((((((((((((........)))).)))))))))))((((((((......)))))))))))))))..))).. ( -29.50)
>DroSec_CAF1 45577 114 - 1
UAAUAUGUUAAUUUUAUUUGUCUUGCCUCAUUGAUUGUGUCGAUGAGAAUGUGAUAGUUUU---UUCGUAUGCAUUUGUAUGUGUUUGUGGCUGGGCAAACACGUUAAUGUUGGCUA
..(((((..((..(((((...(....(((((((((...)))))))))...).)))))..))---..)))))(((((...((((((((((......)))))))))).)))))...... ( -28.30)
>DroSim_CAF1 36317 114 - 1
UAAUAUGUUAAUUUUAUUUGUCUUGCCUCAUUGAUUGUGUCGAUGCGAAUGUGAUAGUUUU---UUCGUAUGCAUUUGUAUGUGUUUGUGGCUGGGCAAACACGUUAAUGUUGGCUA
........................(((.(((((((.......(((((((((((...(....---..)...)))))))))))((((((((......)))))))))))))))..))).. ( -28.00)
>DroEre_CAF1 52493 107 - 1
UAAUAUGUUAAUUUUAUUUGUCUUGCCUCAUUGAUUGUGUCGAUGCGAAUGUGAUAGUUUU---U-----GGCAUUUCUAUGUGUUUGUGGCUGGGCGAU--CGUUAGUGUUGGAUA
....(..(((((.....((((((.(((.(((.((..(((((((.((..........))..)---)-----))))).))...))).....))).)))))).--.)))))..)...... ( -20.40)
>DroYak_CAF1 53220 107 - 1
UAAUAUGUUAAUUUUAUUUGUCUUGCCUCAUUGAUUGUGUCGAUGCGAAUGUGAUAGUUUU---U-----AGCAUUUCUAUGUGUUUGUGGCUGGGCAAA--CGUUAAUGUUGGCUA
......((((((.((((((((((.(((..((((((...))))))(((((..(.((((....---.-----.......)))))..)))))))).)))))))--...))).)))))).. ( -23.00)
>consensus
UAAUAUGUUAAUUUUAUUUGUCUUGCCUCAUUGAUUGUGUCGAUGCGAAUGUGAUAGUUUU___UU_GUAUGCAUUUGUAUGUGUUUGUGGCUGGGCAAACACGUUAAUGUUGGCUA
....(..(((((....(((((((.(((.(((((((...))))))).((((((...................))))))............))).)))))))...)))))..)...... (-19.17 = -19.25 +   0.08)

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 11:58:26 2006