Locus 10215

Sequence ID 3R_DroMel_CAF1
Location 27,397,575 – 27,397,713
Length 138
Max. P 0.988512
window16265 window16266 window16267

overview

Window 5

Location 27,397,575 – 27,397,679
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.96
Mean single sequence MFE -21.12
Consensus MFE -13.80
Energy contribution -13.96
Covariance contribution 0.16
Combinations/Pair 1.07
Mean z-score -2.14
Structure conservation index 0.65
SVM decision value 2.12
SVM RNA-class probability 0.988512
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27397575 104 + 27905053
AGCUUAGCUAUUU-UUCCGCCCAUU--------C-AUAAUCGAUAAUCUAUCGAUAAAUACAAUCGAACCAGUAAGUGAAUCUCAACUAGUUCCU-U--UUCAAUCCAGUGAAG--AAA-
..........(((-((((.......--------.-...(((((((...)))))))..........((((.(((.((.....))..))).))))..-.--.........).))))--)).- ( -12.70)
>DroSec_CAF1 13648 116 + 1
AGCUGAAAUAUUC-GUCCGCCCAUUCAACCAUUCAACUAUCGAUACAUUAUCGAUACUAACUAUCGAACCAGUAAGUGAAUCUCAACUGGUUCCUUU--UUUAAUCCACUGCACACAAA-
.((.(........-.......................((((((((...)))))))).........((((((((.((.....))..))))))))....--.........).)).......- ( -18.50)
>DroSim_CAF1 13702 108 + 1
AGCUUAAAUAUUU-GUCCGCCCAUU--------CGACUAUCGAUACGUUAUCGAUACUAACAAUCGAACCAGUAAGUGAAUCUCAACUGGUUCCGUU--UUUAAUCCACUGCAGACAAA-
..........(((-(((.((.....--------....((((((((...)))))))).(((.(((.((((((((.((.....))..)))))))).)))--.))).......)).))))))- ( -25.10)
>DroEre_CAF1 14407 108 + 1
AGUUUAACUAUUCCAGCCGCCUACA--------C-AAAAUCGAUAAGUUAUCGACGCAUAUAAUCGAACCAGUAAGUGAAUUACCGCUGGUUCAUUUUG--UA-UUUACUACAGGCAAAA
..................((((...--------.-....((((((...))))))...((((((..((((((((..(((...))).))))))))...)))--))-).......)))).... ( -23.10)
>DroYak_CAF1 13810 107 + 1
AGCUUAACUAU---AUCCGCCUAUU--------C-AUAAUCGAUAAGUUAUCGAUAUGUAUAAUCGAACCAGUAAGUGAACCACCGCUGGUUCAUUUGGUUUA-AUUACUACAGACAAAA
...........---...........--------.-...(((((((...))))))).((((((((..((((((...((((((((....))))))))))))))..-)))).))))....... ( -26.20)
>consensus
AGCUUAACUAUUC_AUCCGCCCAUU________C_ACAAUCGAUAAGUUAUCGAUACAUACAAUCGAACCAGUAAGUGAAUCUCAACUGGUUCCUUU__UUUAAUCCACUGCAGACAAA_
......................................(((((((...)))))))..........((((((((............))))))))........................... (-13.80 = -13.96 +   0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 27,397,575 – 27,397,679
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.96
Mean single sequence MFE -28.36
Consensus MFE -17.16
Energy contribution -17.44
Covariance contribution 0.28
Combinations/Pair 1.20
Mean z-score -2.07
Structure conservation index 0.61
SVM decision value 1.71
SVM RNA-class probability 0.973607
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27397575 104 - 27905053
-UUU--CUUCACUGGAUUGAA--A-AGGAACUAGUUGAGAUUCACUUACUGGUUCGAUUGUAUUUAUCGAUAGAUUAUCGAUUAU-G--------AAUGGGCGGAA-AAAUAGCUAAGCU
-...--.((((...((((((.--.-..((((((((.(((.....)))))))))))(((.......))).........)))))).)-)--------))..(((....-.....)))..... ( -19.10)
>DroSec_CAF1 13648 116 - 1
-UUUGUGUGCAGUGGAUUAAA--AAAGGAACCAGUUGAGAUUCACUUACUGGUUCGAUAGUUAGUAUCGAUAAUGUAUCGAUAGUUGAAUGGUUGAAUGGGCGGAC-GAAUAUUUCAGCU
-(((((.(((..(.(((((..--....((((((((.(((.....))))))))))).....((((((((((((...)))))))).)))).))))).)....))).))-))).......... ( -30.00)
>DroSim_CAF1 13702 108 - 1
-UUUGUCUGCAGUGGAUUAAA--AACGGAACCAGUUGAGAUUCACUUACUGGUUCGAUUGUUAGUAUCGAUAACGUAUCGAUAGUCG--------AAUGGGCGGAC-AAAUAUUUAAGCU
-(((((((((((((((((...--(((.......)))..))))))))...(.((((((((((..(((.((....)))))..)))))))--------))).)))))))-))).......... ( -35.10)
>DroEre_CAF1 14407 108 - 1
UUUUGCCUGUAGUAAA-UA--CAAAAUGAACCAGCGGUAAUUCACUUACUGGUUCGAUUAUAUGCGUCGAUAACUUAUCGAUUUU-G--------UGUAGGCGGCUGGAAUAGUUAAACU
.....((.((.((..(-((--((((.((((((((.(((.....)))..)))))))).........(((((((...))))))))))-)--------)))..)).)).))............ ( -26.20)
>DroYak_CAF1 13810 107 - 1
UUUUGUCUGUAGUAAU-UAAACCAAAUGAACCAGCGGUGGUUCACUUACUGGUUCGAUUAUACAUAUCGAUAACUUAUCGAUUAU-G--------AAUAGGCGGAU---AUAGUUAAGCU
.(((((((((.(((((-..(((((..(((((((....))))))).....)))))..))))).((((((((((...)))))).)))-)--------.))))))))).---........... ( -31.40)
>consensus
_UUUGUCUGCAGUGGAUUAAA__AAAGGAACCAGUUGAGAUUCACUUACUGGUUCGAUUGUAAGUAUCGAUAACUUAUCGAUUAU_G________AAUGGGCGGAC_AAAUAGUUAAGCU
....((((((.................(((((((..............)))))))..........(((((((...)))))))..................)))))).............. (-17.16 = -17.44 +   0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 27,397,605 – 27,397,713
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 71.33
Mean single sequence MFE -17.23
Consensus MFE -11.56
Energy contribution -11.52
Covariance contribution -0.04
Combinations/Pair 1.08
Mean z-score -1.39
Structure conservation index 0.67
SVM decision value 0.68
SVM RNA-class probability 0.821447
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27397605 108 + 27905053
CGAUAAUCUAUCGAUAAAUACAAUCGAACCAGUAAGUGAAUCUCAACUAGUUCCU-U--UUCAAUCCAGUGAAG--AAA-CAAGAAAUUUUAAGA-----ACAAAAAA-AACUACCAGAU
.....((((.(((((.......)))))...(((.(((........))).((((.(-(--((((......)))))--)..-.((....))....))-----))......-.)))...)))) ( -10.80)
>DroSec_CAF1 13687 107 + 1
CGAUACAUUAUCGAUACUAACUAUCGAACCAGUAAGUGAAUCUCAACUGGUUCCUUU--UUUAAUCCACUGCACACAAA-CAAGAAAUGUUAAGA-----AAAGAAAAUAA-----AUAU
(...(((((.((((((.....))))((((((((.((.....))..))))))))....--....................-...)))))))...).-----...........-----.... ( -15.40)
>DroSim_CAF1 13733 106 + 1
CGAUACGUUAUCGAUACUAACAAUCGAACCAGUAAGUGAAUCUCAACUGGUUCCGUU--UUUAAUCCACUGCAGACAAA-CAAGAAAUCUUAAGA-----AAAGAAAA-AA-----AUAU
(((((...)))))....(((.(((.((((((((.((.....))..)))))))).)))--.)))................-.......((((....-----.))))...-..-----.... ( -14.70)
>DroEre_CAF1 14438 111 + 1
CGAUAAGUUAUCGACGCAUAUAAUCGAACCAGUAAGUGAAUUACCGCUGGUUCAUUUUG--UA-UUUACUACAGGCAAAACUAAAAAG-CUAAAA----AUUAAUAAA-AACUACAUGAU
(((((...)))))..((........((((((((..(((...))).))))))))...(((--((-.....)))))))............-......----.........-........... ( -17.40)
>DroYak_CAF1 13838 117 + 1
CGAUAAGUUAUCGAUAUGUAUAAUCGAACCAGUAAGUGAACCACCGCUGGUUCAUUUGGUUUA-AUUACUACAGACAAAACUAAAAAG-CCAAGACAAUAUAUAUAAA-AACUUAAUGGU
((.((((((....((((((((..((((((((((..(((...))).))))))))..(((((((.-.....................)))-))))))..))))))))...-)))))).)).. ( -27.85)
>consensus
CGAUAAGUUAUCGAUACAUACAAUCGAACCAGUAAGUGAAUCUCAACUGGUUCCUUU__UUUAAUCCACUGCAGACAAA_CAAGAAAU_UUAAGA_____AAAAAAAA_AACU___AGAU
(((((...)))))............((((((((............))))))))................................................................... (-11.56 = -11.52 +  -0.04)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:36 2006