Locus 2695

Sequence ID 3R_DroMel_CAF1
Location 7,257,116 – 7,257,300
Length 184
Max. P 0.969423
window4376 window4377 window4378 window4379 window4380

overview

Window 6

Location 7,257,116 – 7,257,232
Length 116
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.48
Mean single sequence MFE -28.35
Consensus MFE -19.24
Energy contribution -18.22
Covariance contribution -1.02
Combinations/Pair 1.44
Mean z-score -1.21
Structure conservation index 0.68
SVM decision value 0.05
SVM RNA-class probability 0.556610
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7257116 116 - 27905053
UA-UCCGUCGUAAAUUGCGAAAAUGCGCAUUCAAACGUGCUAUUUUUGCUCUAGCAAAAUAUACCCGGGCCACGGGGUGCAAUUCGUGCGAAAUGACUGCAAGGUAAGAAC-GA-UUUG
..-...(((((.....((((((((((((........)))).))))))))(((.((........((((.....)))).((((..((((.....)))).))))..)).)))))-))-)... ( -32.60)
>DroVir_CAF1 1246 114 - 1
UA-UUU-UCAUAAUUUGUAAAGAUGCGCAUUGAUACGUGCUAUUUUUGCUCUAGCAAGAUAUAUCCCGGGCACGGAGUACAUUUUGUACGCAAUGAUUGUAAGGUAAGUAUCAA-UU--
((-(..-((((.....((((((((((((........)))).))))))))....(((((((.((..(((....)))..)).))))))).....))))..))).............-..-- ( -26.40)
>DroGri_CAF1 1274 115 - 1
UA-UUU-UAAUAAUUUGUAAAAAUGCGCAUUGAAACGUGCUACUUUUGCUCCAGCAAAAUAUAUCCUGGCCACGGGGUACAAUUUGUACGCAAUGAUUGCAAAGUAAGUCU-AA-UAUA
..-...-................(((.(((((...(((((...((((((....))))))..(((((((....)))))))......))))))))))...)))..........-..-.... ( -24.80)
>DroMoj_CAF1 566 114 - 1
UA-UUU-GUAUAAUUUGUAAAAAUGCGCAUCGACACGUGCUACUUUUGCUCCAGCAAAAUAUACCCUGGGCAUGGGGUACACUUUGUACGCAAUGACUGCAAAGUAAGUAACAA-UA--
((-(((-((((((..((((.....((((........))))..((..(((.((((...........)))))))..)).))))..))))))(((.....))).)))))........-..-- ( -25.60)
>DroAna_CAF1 1211 116 - 1
UA-UUCGACGUAAUUUGCGAAAAUGCGCAUUGAAACGUGUUAUUUUUGCUCUAGCAAAAUAUACCCAGGCCACGGGGUGAAUUUUGUUCGAAAUGACUGCAAGGUAAGUUG-GC-UUUG
..-(((((........((((((((((((........))).)))))))))....(((((((.(((((.(....).))))).)))))))))))).......((((((......-))-)))) ( -31.30)
>DroPer_CAF1 1249 118 - 1
UAAAUUGUUUUAAUUUGUGAAAAUGCGUAUCGAAACGUGCUACUUUUGCUCCAGCAAAAUAUAUCCCGGCCACGGGGUUAAUUUCGUACGAAAUGAUUGCAAGGUGAGGCC-CAGUUCG
......((((((.((((..(.....((((.(((((........((((((....))))))...((((((....))))))...)))))))))......)..)))).)))))).-....... ( -29.40)
>consensus
UA_UUU_UCAUAAUUUGUAAAAAUGCGCAUUGAAACGUGCUACUUUUGCUCCAGCAAAAUAUACCCCGGCCACGGGGUACAUUUUGUACGAAAUGACUGCAAGGUAAGUAC_AA_UUUG
................(((....)))((((((...(((((...((((((....))))))..(((((((....)))))))......)))))...))).)))................... (-19.24 = -18.22 +  -1.02)

alignment

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secondary structure

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Window 7

Location 7,257,154 – 7,257,271
Length 117
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 79.56
Mean single sequence MFE -27.92
Consensus MFE -17.75
Energy contribution -18.03
Covariance contribution 0.28
Combinations/Pair 1.15
Mean z-score -2.26
Structure conservation index 0.64
SVM decision value 1.12
SVM RNA-class probability 0.917721
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7257154 117 + 27905053
CACCCCGUGGCCCGGGUAUAUUUUGCUAGAGCAAAAAUAGCACGUUUGAAUGCGCAUUUUCGCAAUUUACGACGGA-UAAAUUACGAAAACAAAACAAAUGCGCA-AGCUGCUAGCACG
...((((.....)))).......(((((((((..((((.....))))...((((((((((((.(((((((....).-)))))).))).........)))))))))-.))).)))))).. ( -30.60)
>DroVir_CAF1 1283 111 + 1
UACUCCGUGCCCGGGAUAUAUCUUGCUAGAGCAAAAAUAGCACGUAUCAAUGCGCAUCUUUACAAAUUAUGA-AAA-UAACUUGUAAAAAU-----AAA-ACGCAAUGCUGUCAGCACG
.....(((((.((((((((....(((((.........))))).)))))..((((.((.(((((((.((((..-..)-))).))))))).))-----...-.))))...)))...))))) ( -26.00)
>DroPse_CAF1 1297 111 + 1
AACCCCGUGGCCGGGAUAUAUUUUGCUGGAGCAAAAGUAGCACGUUUCGAUACGCAUUUUCACAAAUUAAAACAAUUUAAUUUGCGAAAA----ACAAA-GCGCA--GC-ACUAGCACG
...((((....))))........((((((.((....((.((.(((......)))..(((((.(((((((((....))))))))).)))))----.....-)))).--))-.)))))).. ( -27.90)
>DroGri_CAF1 1312 111 + 1
UACCCCGUGGCCAGGAUAUAUUUUGCUGGAGCAAAAGUAGCACGUUUCAAUGCGCAUUUUUACAAAUUAUUA-AAA-UAACUUGUAAAAAU-----AAA-ACGCAAAACAGUCAGCACA
....((.......))........((((((.((.......))..((((...((((.((((((((((.((((..-..)-))).))))))))))-----...-.))))))))..)))))).. ( -22.40)
>DroAna_CAF1 1249 115 + 1
CACCCCGUGGCCUGGGUAUAUUUUGCUAGAGCAAAAAUAACACGUUUCAAUGCGCAUUUUCGCAAAUUACGUCGAA-UAAUUUGCGAAAA-AUAACAAA-ACGCA-GGCAGCAAGCACG
......((.(((((.((...((((((....))))))......(((......)))..(((((((((((((.......-)))))))))))))-........-)).))-))).))....... ( -32.70)
>DroPer_CAF1 1288 111 + 1
AACCCCGUGGCCGGGAUAUAUUUUGCUGGAGCAAAAGUAGCACGUUUCGAUACGCAUUUUCACAAAUUAAAACAAUUUAAUUUGCGAAAA----ACAAA-GCGCA--GC-ACUAGCACG
...((((....))))........((((((.((....((.((.(((......)))..(((((.(((((((((....))))))))).)))))----.....-)))).--))-.)))))).. ( -27.90)
>consensus
AACCCCGUGGCCGGGAUAUAUUUUGCUAGAGCAAAAAUAGCACGUUUCAAUGCGCAUUUUCACAAAUUAAGACAAA_UAAUUUGCGAAAA____ACAAA_ACGCA__GC_GCUAGCACG
......(((...........((((((....))))))...((.(((......)))..(((((((((((((........)))))))))))))............))...........))). (-17.75 = -18.03 +   0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,257,154 – 7,257,271
Length 117
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.56
Mean single sequence MFE -36.58
Consensus MFE -29.93
Energy contribution -27.99
Covariance contribution -1.94
Combinations/Pair 1.42
Mean z-score -3.61
Structure conservation index 0.82
SVM decision value 1.64
SVM RNA-class probability 0.969423
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7257154 117 - 27905053
CGUGCUAGCAGCU-UGCGCAUUUGUUUUGUUUUCGUAAUUUA-UCCGUCGUAAAUUGCGAAAAUGCGCAUUCAAACGUGCUAUUUUUGCUCUAGCAAAAUAUACCCGGGCCACGGGGUG
..((((((.(((.-.((((.((((...(((((((((((((((-(.....)))))))))))))....)))..)))).)))).......))))))))).....(((((.(....).))))) ( -39.50)
>DroVir_CAF1 1283 111 - 1
CGUGCUGACAGCAUUGCGU-UUU-----AUUUUUACAAGUUA-UUU-UCAUAAUUUGUAAAGAUGCGCAUUGAUACGUGCUAUUUUUGCUCUAGCAAGAUAUAUCCCGGGCACGGAGUA
((((((.....((.(((((-...-----((((((((((((((-(..-..)))))))))))))))))))).))...((.(.(((((((((....)))))).))).).))))))))..... ( -35.50)
>DroPse_CAF1 1297 111 - 1
CGUGCUAGU-GC--UGCGC-UUUGU----UUUUCGCAAAUUAAAUUGUUUUAAUUUGUGAAAAUGCGUAUCGAAACGUGCUACUUUUGCUCCAGCAAAAUAUAUCCCGGCCACGGGGUU
.(..(...(-(.--(((((-.....----(((((((((((((((....))))))))))))))).))))).))....)..)...((((((....))))))...((((((....)))))). ( -36.90)
>DroGri_CAF1 1312 111 - 1
UGUGCUGACUGUUUUGCGU-UUU-----AUUUUUACAAGUUA-UUU-UAAUAAUUUGUAAAAAUGCGCAUUGAAACGUGCUACUUUUGCUCCAGCAAAAUAUAUCCUGGCCACGGGGUA
..(((((...(((((((((-...-----((((((((((((((-(..-..))))))))))))))))))))...))))(.((.......)).)))))).....(((((((....))))))) ( -34.40)
>DroAna_CAF1 1249 115 - 1
CGUGCUUGCUGCC-UGCGU-UUUGUUAU-UUUUCGCAAAUUA-UUCGACGUAAUUUGCGAAAAUGCGCAUUGAAACGUGUUAUUUUUGCUCUAGCAAAAUAUACCCAGGCCACGGGGUG
....((((..(((-((.((-(((((...-(((((((((((((-(.....))))))))))))))...)))...))))((((...((((((....)))))).)))).)))))..))))... ( -36.30)
>DroPer_CAF1 1288 111 - 1
CGUGCUAGU-GC--UGCGC-UUUGU----UUUUCGCAAAUUAAAUUGUUUUAAUUUGUGAAAAUGCGUAUCGAAACGUGCUACUUUUGCUCCAGCAAAAUAUAUCCCGGCCACGGGGUU
.(..(...(-(.--(((((-.....----(((((((((((((((....))))))))))))))).))))).))....)..)...((((((....))))))...((((((....)))))). ( -36.90)
>consensus
CGUGCUAGC_GC__UGCGC_UUUGU____UUUUCGCAAAUUA_UUUGUCAUAAUUUGUGAAAAUGCGCAUUGAAACGUGCUACUUUUGCUCCAGCAAAAUAUAUCCCGGCCACGGGGUA
.(..(.........(((((..........(((((((((((((........))))))))))))).))))).......)..)...((((((....))))))..(((((((....))))))) (-29.93 = -27.99 +  -1.94)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,257,194 – 7,257,300
Length 106
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 82.02
Mean single sequence MFE -26.87
Consensus MFE -17.54
Energy contribution -17.65
Covariance contribution 0.11
Combinations/Pair 1.12
Mean z-score -3.04
Structure conservation index 0.65
SVM decision value 1.02
SVM RNA-class probability 0.902315
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7257194 106 + 27905053
CACGUUUGAAUGCGCAUUUUCGCAAUUUACGACGGA-UAAAUUACGAAAACAAAACAAAUGCGCAAGCUGCUAGCACGUGUGCUGCUGAAGAAGAAGAAAUAUGAAA
((..(((...((((((((((((.(((((((....).-)))))).))).........)))))))))....((.((((....))))))...........)))..))... ( -21.60)
>DroPse_CAF1 1337 93 + 1
CACGUUUCGAUACGCAUUUUCACAAAUUAAAACAAUUUAAUUUGCGAAAA----ACAAA-GCGCA-GC-ACUAGCACGUGUGUGGCUGAAGAAGAAGAGA-------
....((((....(((.(((((.(((((((((....))))))))).)))))----.....-)))((-((-....(((....))).))))..))))......------- ( -20.50)
>DroEre_CAF1 1320 104 + 1
CACGUUUCAAUGCGCAUUUUCGCAAAUUACGACGAA-UAAUUUGCGAAA--AAAACAAAGGCGCAAACAGCUAGCACGUGUGCAGCUGAAGAAGAAGAAAGUUGAAA
....(((((((((((.(((((((((((((.......-))))))))))))--)........))))...(((((.(((....))))))))............))))))) ( -33.40)
>DroYak_CAF1 1292 105 + 1
CACGUUUCAAUGCGCAUUUUCGCAAAUUACGACGAA-UAAUUUGCGAAAA-AAAACAAAAGCGCAAGCAGCUAGCACGUGUGCUGCUGAAGAAGAAGAGAGAUGAAA
..((((((..(((((.(((((((((((((.......-)))))))))))))-.........)))))..((((.((((....))))))))..........))))))... ( -34.70)
>DroAna_CAF1 1289 104 + 1
CACGUUUCAAUGCGCAUUUUCGCAAAUUACGUCGAA-UAAUUUGCGAAAA-AUAACAAA-ACGCAGGCAGCAAGCACGUGUGCUGCUGAAGAAGAAGAACGAGGAAA
..(((((...((((..(((((((((((((.......-)))))))))))))-........-.))))..(((((.(((....))))))))........)))))...... ( -28.90)
>DroPer_CAF1 1328 93 + 1
CACGUUUCGAUACGCAUUUUCACAAAUUAAAACAAUUUAAUUUGCGAAAA----ACAAA-GCGCA-GC-ACUAGCACGUGUGCGGCUGAAGAAGAAGAGA-------
....((((....(((.(((((.(((((((((....))))))))).)))))----.....-)))((-((-....(((....))).))))..))))......------- ( -22.10)
>consensus
CACGUUUCAAUGCGCAUUUUCGCAAAUUACGACGAA_UAAUUUGCGAAAA_AAAACAAA_GCGCAAGCAGCUAGCACGUGUGCUGCUGAAGAAGAAGAAAGAUGAAA
....(((((..((((((((((((((((((........)))))))))))).............((.........))..))))))...)))))................ (-17.54 = -17.65 +   0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,257,194 – 7,257,300
Length 106
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 82.02
Mean single sequence MFE -29.57
Consensus MFE -22.43
Energy contribution -21.47
Covariance contribution -0.97
Combinations/Pair 1.24
Mean z-score -3.82
Structure conservation index 0.76
SVM decision value 1.49
SVM RNA-class probability 0.958079
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7257194 106 - 27905053
UUUCAUAUUUCUUCUUCUUCAGCAGCACACGUGCUAGCAGCUUGCGCAUUUGUUUUGUUUUCGUAAUUUA-UCCGUCGUAAAUUGCGAAAAUGCGCAUUCAAACGUG
.....................((((((....)))).)).(..(((((((((.........((((((((((-(.....))))))))))))))))))))..)....... ( -28.00)
>DroPse_CAF1 1337 93 - 1
-------UCUCUUCUUCUUCAGCCACACACGUGCUAGU-GC-UGCGC-UUUGU----UUUUCGCAAAUUAAAUUGUUUUAAUUUGUGAAAAUGCGUAUCGAAACGUG
-------....................(((((.....(-(.-(((((-.....----(((((((((((((((....))))))))))))))).))))).))..))))) ( -26.30)
>DroEre_CAF1 1320 104 - 1
UUUCAACUUUCUUCUUCUUCAGCUGCACACGUGCUAGCUGUUUGCGCCUUUGUUUU--UUUCGCAAAUUA-UUCGUCGUAAUUUGCGAAAAUGCGCAUUGAAACGUG
((((((.............((((((((....))).)))))..(((((........(--((((((((((((-(.....)))))))))))))).))))))))))).... ( -33.20)
>DroYak_CAF1 1292 105 - 1
UUUCAUCUCUCUUCUUCUUCAGCAGCACACGUGCUAGCUGCUUGCGCUUUUGUUUU-UUUUCGCAAAUUA-UUCGUCGUAAUUUGCGAAAAUGCGCAUUGAAACGUG
(((((..............((((((((....)))).))))..(((((.........-(((((((((((((-(.....)))))))))))))).))))).))))).... ( -32.70)
>DroAna_CAF1 1289 104 - 1
UUUCCUCGUUCUUCUUCUUCAGCAGCACACGUGCUUGCUGCCUGCGU-UUUGUUAU-UUUUCGCAAAUUA-UUCGACGUAAUUUGCGAAAAUGCGCAUUGAAACGUG
...................((((((((....))).)))))...((((-(((((...-(((((((((((((-(.....))))))))))))))...)))...)))))). ( -30.90)
>DroPer_CAF1 1328 93 - 1
-------UCUCUUCUUCUUCAGCCGCACACGUGCUAGU-GC-UGCGC-UUUGU----UUUUCGCAAAUUAAAUUGUUUUAAUUUGUGAAAAUGCGUAUCGAAACGUG
-------....................(((((.....(-(.-(((((-.....----(((((((((((((((....))))))))))))))).))))).))..))))) ( -26.30)
>consensus
UUUCAUCUCUCUUCUUCUUCAGCAGCACACGUGCUAGCUGCUUGCGC_UUUGUUUU_UUUUCGCAAAUUA_UUCGUCGUAAUUUGCGAAAAUGCGCAUUGAAACGUG
...........................(((((((.....)).(((((..........(((((((((((((........))))))))))))).))))).....))))) (-22.43 = -21.47 +  -0.97)

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 10:42:32 2006