Locus 7909

Sequence ID X_DroMel_CAF1
Location 19,699,805 – 19,699,974
Length 169
Max. P 0.993437
window12977 window12978 window12979 window12980

overview

Window 7

Location 19,699,805 – 19,699,905
Length 100
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 79.09
Mean single sequence MFE -21.73
Consensus MFE -19.01
Energy contribution -18.57
Covariance contribution -0.44
Combinations/Pair 1.20
Mean z-score -1.48
Structure conservation index 0.87
SVM decision value 1.24
SVM RNA-class probability 0.934602
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19699805 100 - 22224390
GGAACUUAGUUCCACAAAGUAAAGUAAGUAAAUAAGUAAAGGUGGCAACUAAUGUCGUAAACAAUAUUACCGCUUGGGAAUCGAUUCUUUUCGAUUCUAA
(((((...)))))..........................((((((....((((((.(....).)))))))))))).((((((((......)))))))).. ( -22.00)
>DroSec_CAF1 6295 86 - 1
GUAACGUAGUUCCACAAAGUGGAG-------------AAAGGUGGAAGCUGAAACCGUAAGCGAUAUUACCGUUUGGGAAUCGAUUCCUUUCGAUUCUA-
..(((....((((((...))))))-------------...(((((..(((.........)))....))))))))..((((((((......)))))))).- ( -22.50)
>DroSim_CAF1 6150 87 - 1
GGAACGUAGUUCCACAAAGUGGAG-------------AAAUGUGGAAGCUAAAGCCGUAAACGAUAUUACCGUUUGGUAAUCGAUUCCUUUCGAUUCUAA
((....((((((((((........-------------...))))).)))))...))..(((((.......)))))((.((((((......)))))))).. ( -20.70)
>consensus
GGAACGUAGUUCCACAAAGUGGAG_____________AAAGGUGGAAGCUAAAGCCGUAAACGAUAUUACCGUUUGGGAAUCGAUUCCUUUCGAUUCUAA
......(((((((((..........................)))).)))))((((.((((......)))).)))).((((((((......)))))))).. (-19.01 = -18.57 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,699,840 – 19,699,945
Length 105
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 79.47
Mean single sequence MFE -28.01
Consensus MFE -21.84
Energy contribution -21.07
Covariance contribution -0.77
Combinations/Pair 1.20
Mean z-score -2.54
Structure conservation index 0.78
SVM decision value 2.40
SVM RNA-class probability 0.993437
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19699840 105 - 22224390
CAAGUACUUGCUAAGCGUGAGUGUUUGGCAUCCCAGAUGUGGAACUUAGUUCCACAAAGUAAAGUAAGUAAAUAAGUAAAGGUGGCAACUAAUGUCGUAAACAAU
....((((((((..((....))((((((....))))))(((((((...))))))).......)))))))).............((((.....))))......... ( -26.50)
>DroSec_CAF1 6329 92 - 1
CAAGUACUUGCUAAGCGCGAGUGCUUGGCAUCACAGAAGUGUAACGUAGUUCCACAAAGUGGAG-------------AAAGGUGGAAGCUGAAACCGUAAGCGAU
(((((((((((.....)))))))))))((..(((....)))..((((((((((((.........-------------....)))).)))))....)))..))... ( -27.42)
>DroSim_CAF1 6185 92 - 1
CAAGUACUUGCUAAGCGCGAGUGCUUGGCAGCACAGAUGUGGAACGUAGUUCCACAAAGUGGAG-------------AAAUGUGGAAGCUAAAGCCGUAAACGAU
.((((((((((.....))))))))))(((..(((...((((((((...))))))))..)))...-------------....((....))....)))......... ( -30.10)
>consensus
CAAGUACUUGCUAAGCGCGAGUGCUUGGCAUCACAGAUGUGGAACGUAGUUCCACAAAGUGGAG_____________AAAGGUGGAAGCUAAAGCCGUAAACGAU
(((((((((((.....)))))))))))...........((...((((((((((((..........................)))).)))))....)))..))... (-21.84 = -21.07 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,699,865 – 19,699,974
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 69.91
Mean single sequence MFE -24.40
Consensus MFE -11.69
Energy contribution -12.38
Covariance contribution 0.69
Combinations/Pair 1.16
Mean z-score -2.39
Structure conservation index 0.48
SVM decision value 1.78
SVM RNA-class probability 0.976692
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19699865 109 + 22224390
UUUACUUAUUUACUUACUUUACUUUGUGGAACUAAGUUCCACAUCUGGGAUGCCAAACACUCACGCUUAGCAAGUACUUGCUCCUCUGCUAACCCA---------GUGCG-CCCAUA-AA
........................((((((((...))))))))..((((.(((...............(((((....)))))...(((......))---------).)))-))))..-.. ( -22.50)
>DroSec_CAF1 6354 96 + 1
UUU-------------CUCCACUUUGUGGAACUACGUUACACUUCUGUGAUGCCAAGCACUCGCGCUUAGCAAGUACUUGCUCCUUUGCUAACCAA---------GUGCG-CCCAUA-AA
...-------------.......((((((.....(((((((....)))))))....(((((.(.(.((((((((..........)))))))))).)---------)))).-.)))))-). ( -24.50)
>DroSim_CAF1 6210 96 + 1
UUU-------------CUCCACUUUGUGGAACUACGUUCCACAUCUGUGCUGCCAAGCACUCGCGCUUAGCAAGUACUUGCUCCUUUGCUAACCAA---------GUGCG-CCCAUA-AA
...-------------........((((((((...))))))))...(((((....))))).(((((((((((((..........)))))))....)---------)))))-......-.. ( -28.50)
>DroYak_CAF1 3964 103 + 1
-----------------UCCACAAAGUGGACCUAUGUUCCACACCAGUGAUGCCAGAGUUUUCCACUUAGCGAGUACACACUCCCCUGCUAUCAAAUACGUAGCGAGGUAACUCAUAUAA
-----------------..(((...(((((.......)))))....)))......(((((..((.......((((....))))...((((((.......)))))).)).)))))...... ( -22.10)
>consensus
UUU_____________CUCCACUUUGUGGAACUACGUUCCACAUCUGUGAUGCCAAACACUCGCGCUUAGCAAGUACUUGCUCCUCUGCUAACCAA_________GUGCG_CCCAUA_AA
...................(((..((((((((...))))))))...)))..................((((((((....)))....)))))............................. (-11.69 = -12.38 +   0.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,699,865 – 19,699,974
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 69.91
Mean single sequence MFE -30.80
Consensus MFE -16.98
Energy contribution -18.10
Covariance contribution 1.12
Combinations/Pair 1.14
Mean z-score -2.14
Structure conservation index 0.55
SVM decision value 2.04
SVM RNA-class probability 0.986489
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19699865 109 - 22224390
UU-UAUGGG-CGCAC---------UGGGUUAGCAGAGGAGCAAGUACUUGCUAAGCGUGAGUGUUUGGCAUCCCAGAUGUGGAACUUAGUUCCACAAAGUAAAGUAAGUAAAUAAGUAAA
((-(((..(-(...(---------((((...((......)).......(((((((((....))))))))).))))).((((((((...)))))))).......))..)))))........ ( -32.80)
>DroSec_CAF1 6354 96 - 1
UU-UAUGGG-CGCAC---------UUGGUUAGCAAAGGAGCAAGUACUUGCUAAGCGCGAGUGCUUGGCAUCACAGAAGUGUAACGUAGUUCCACAAAGUGGAG-------------AAA
.(-((((..-.((((---------((.((..((.......(((((((((((.....)))))))))))))...))..))))))..)))))((((((...))))))-------------... ( -29.51)
>DroSim_CAF1 6210 96 - 1
UU-UAUGGG-CGCAC---------UUGGUUAGCAAAGGAGCAAGUACUUGCUAAGCGCGAGUGCUUGGCAGCACAGAUGUGGAACGUAGUUCCACAAAGUGGAG-------------AAA
..-......-..(((---------((.....((....(..(((((((((((.....))))))))))).).)).....((((((((...)))))))))))))...-------------... ( -31.90)
>DroYak_CAF1 3964 103 - 1
UUAUAUGAGUUACCUCGCUACGUAUUUGAUAGCAGGGGAGUGUGUACUCGCUAAGUGGAAAACUCUGGCAUCACUGGUGUGGAACAUAGGUCCACUUUGUGGA-----------------
.((((((.....((..((((((....)).))))..))...)))))).((((.(((((((...((.((...((((....))))..)).)).))))))).)))).----------------- ( -29.00)
>consensus
UU_UAUGGG_CGCAC_________UUGGUUAGCAAAGGAGCAAGUACUUGCUAAGCGCGAGUGCUUGGCAUCACAGAUGUGGAACGUAGUUCCACAAAGUGGAG_____________AAA
...............................((......))...(((((((((((((....)))))))).........(((((((...))))))).)))))................... (-16.98 = -18.10 +   1.12)

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 12:50:36 2006