Locus 154

Sequence ID	2R_DroMel_CAF1
Location	1,419,876 – 1,420,140
Length	264
Max. P	0.981384

overview

Window 9

Location	1,419,876 – 1,419,996
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.08
Mean single sequence MFE	-36.58
Consensus MFE	-30.88
Energy contribution	-31.32
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.17
Structure conservation index	0.84
SVM decision value	1.89
SVM RNA-class probability	0.981384
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1419876 120 - 20766785
GCCGGCGGCCGAACUGCAAUUUCAUUUCGCAUUCAUAUGCGAAAGUUUGGCGGAUGCUUUCAGCUGGCUUUCAAACAAAGGCGGUUUAAAUCGCCAUUAAAACUCGCUCACAUCCAGGAG
((((((.((((((((..........(((((((....)))))))))))))))(((....))).))))))...........((((((....)))))).......(((.((.......))))) ( -39.70)
>DroSec_CAF1 38321 120 - 1
GCCGGCGGCCGAACUGCAAUUUCAUUUCGCAUUCAUAUGCGAAAGUUUGGCGCAUGCUUUCAGCUGGCUUUCAAACAAAGGCGGUUUAAAACGCCAUUAAAACUCGCUCACAUCCAGGAG
((((((.((((((((..........(((((((....)))))))))))))))(....).....))))))...........((((........)))).......(((.((.......))))) ( -36.90)
>DroSim_CAF1 43376 120 - 1
GCCGGCGGCCGAACUGCAAUUUCAUUUCGCAUUCAUAUGCGAAAGUUUGGCGCAUGCUUUCAGCUGGCUUUCAAACAAAGGCGGUUUAAAUCGCCAUUAAAACUCGCUCACAUCCAGGAG
((((((.((((((((..........(((((((....)))))))))))))))(....).....))))))...........((((((....)))))).......(((.((.......))))) ( -37.70)
>DroEre_CAF1 36798 120 - 1
GCCGGCGGCCGAACUGCAAUUUCAUUUCGCAUUCAUAUGCGAAAGUUUGGCGCAUGCUUUCAGCUCGCUUUCAAACAAAGGCGGUUUAAAGCGCCAUUAAAACUCGCUCACAUCCAUGAG
...(((.((((((((..........(((((((....)))))))))))))))....(((((.(((.((((((......))))))))).))))))))...........((((......)))) ( -39.60)
>DroYak_CAF1 37637 120 - 1
GCCGACGGCAGAACUGCAAUAUAAUUACGCAUUCAUAUGCGAAAGUUUGGCGCAUGCUUUCAGCUCGCUUUCAAACAAAGGCAGUUUAAAUCGCCAUUAAAACUCGCUCACAUCCAUGAG
......(((.(((((((..........(((((....)))))...((((((.((..((.....))..))..))))))....))))))).....)))...........((((......)))) ( -29.00)
>consensus
GCCGGCGGCCGAACUGCAAUUUCAUUUCGCAUUCAUAUGCGAAAGUUUGGCGCAUGCUUUCAGCUGGCUUUCAAACAAAGGCGGUUUAAAUCGCCAUUAAAACUCGCUCACAUCCAGGAG
...((((...(((((((.......((((((((....))))))))((((((.((..((.....))..))..))))))....)))))))....))))...........(((........))) (-30.88 = -31.32 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	1,419,996 – 1,420,112
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.14
Mean single sequence MFE	-37.38
Consensus MFE	-28.73
Energy contribution	-30.42
Covariance contribution	1.69
Combinations/Pair	1.14
Mean z-score	-2.03
Structure conservation index	0.77
SVM decision value	0.91
SVM RNA-class probability	0.880003
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1419996 116 + 20766785
GCGUAUAUCUCGUGCGAAAGUUUGUCCAUUCCGACAUAAAUUGGGAUGGACCCUUAAAGCUGUGCACUAACAUUGGGGAGUAAGUAUCUAUCAGAUACCUUCCCCUU----CCUGUGGAG
........((((((((..((((((((((((((((......))))))))))).....))))).)))))...(((.((((((...(((((.....))))).))))))..----...)))))) ( -39.90)
>DroSec_CAF1 38441 120 + 1
GCGUAUAUCUCGUGCGAAAGUUUGUCCAUCCCGACAUAAAUUGGGAUGGACCCUUAAAGCUGUGCACUAGCAUUGGGGAGCAAGUAUCUAUCAGAUACCUUCCCCGUCUCCCCUGUGGAG
........((((((((..((((((((((((((((......))))))))))).....))))).)))))...(((.((((((((((((((.....)))).)))....).)))))).)))))) ( -44.30)
>DroSim_CAF1 43496 120 + 1
GCGUAUAUCUCGUGCGAAAGUUUGUCCAUCCCGACAUAAAUUGGGAUGGACCCUUAAAGCUGUGCACUAGCAUUGGGGAGCAAGUAUCUAUCAGAUACCUUCCCCGUCUCCCCUGUGGAG
........((((((((..((((((((((((((((......))))))))))).....))))).)))))...(((.((((((((((((((.....)))).)))....).)))))).)))))) ( -44.30)
>DroEre_CAF1 36918 108 + 1
GCGUAUAUCUCCGGCGAAAGUUUGUCUAU-CCGACAUAAAUUGGCGUGGCCCCUUGAAGCUGUGCACUAGCAUUGG-GAACAAGUAUCUUUCGGAUACCUUC----------CUGUGGAG
........(((((((...(((.((((...-..)))).......(((..((........))..)))))).))...((-(((...(((((.....))))).)))----------)).))))) ( -27.70)
>DroYak_CAF1 37757 110 + 1
GCGUAUAACUCCGGCGAAAGCUUGUCUAUUCCGCCAUAAAUUGGGAUGGACCCUUAAAGCUCUGCACUAACAUUGGGGAACAAGUAUCUAUCAGAUACCUUG----------CUGUGGAG
........(((((((....))).((((((((((........))))))))))......((((((.((.......)).)))....(((((.....)))))...)----------))..)))) ( -30.70)
>consensus
GCGUAUAUCUCGUGCGAAAGUUUGUCCAUCCCGACAUAAAUUGGGAUGGACCCUUAAAGCUGUGCACUAGCAUUGGGGAGCAAGUAUCUAUCAGAUACCUUCCCC_U____CCUGUGGAG
........((((((((..((((((((((((((((......))))))))))).....))))).))))).......((((((...(((((.....))))).))))))............))) (-28.73 = -30.42 +   1.69)

alignment

secondary structure

dotplot

Window 1

Location	1,420,036 – 1,420,140
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.79
Mean single sequence MFE	-35.74
Consensus MFE	-18.49
Energy contribution	-20.38
Covariance contribution	1.89
Combinations/Pair	1.08
Mean z-score	-1.86
Structure conservation index	0.52
SVM decision value	0.19
SVM RNA-class probability	0.627338
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1420036 104 - 20766785
AGCAGCUGCAGC------------UGUUUAGUUGCGAAGGCUCCACAGG----AAGGGGAAGGUAUCUGAUAGAUACUUACUCCCCAAUGUUAGUGCACAGCUUUAAGGGUCCAUCCCAA
.(((((((....------------....))))))).((((((.(((..(----..((((((((((((.....)))))))..)))))....)..)))...))))))..(((.....))).. ( -34.70)
>DroSec_CAF1 38481 108 - 1
AGCAGCUGCAGC------------UGUUUAGUUGCGGAGGCUCCACAGGGGAGACGGGGAAGGUAUCUGAUAGAUACUUGCUCCCCAAUGCUAGUGCACAGCUUUAAGGGUCCAUCCCAA
(((..(((((((------------(....))))))))..)))......(((((((((((((((((((.....)))))))..)))))..(((....)))...........)))..)))).. ( -42.20)
>DroSim_CAF1 43536 108 - 1
AGCUGCUGCAGC------------UGUUUAGUUGCGGAGGCUCCACAGGGGAGACGGGGAAGGUAUCUGAUAGAUACUUGCUCCCCAAUGCUAGUGCACAGCUUUAAGGGUCCAUCCCAA
((((((((((((------------(....)))))))).(.((((.....)))).)((((((((((((.....)))))))..)))))..(((....))))))))....(((.....))).. ( -42.90)
>DroEre_CAF1 36957 83 - 1
AGCAGCUGCAGCU--------------------------GCUCCACAG----------GAAGGUAUCCGAAAGAUACUUGUUC-CCAAUGCUAGUGCACAGCUUCAAGGGGCCACGCCAA
((((((....)))--------------------------)))((...(----------((((((((.(....))))))..)))-)...(((....))).........))(((...))).. ( -24.40)
>DroYak_CAF1 37797 109 - 1
AGCGGCCACAGCUGGACCUGCAGCUGUUCAG-UGCGGAGGCUCCACAG----------CAAGGUAUCUGAUAGAUACUUGUUCCCCAAUGUUAGUGCAGAGCUUUAAGGGUCCAUCCCAA
.(((...(((((((......)))))))....-))).((((((((((((----------(((((((((.....))))))).........)))).)))..)))))))..(((.....))).. ( -34.50)
>consensus
AGCAGCUGCAGC____________UGUUUAGUUGCGGAGGCUCCACAGG____A_GGGGAAGGUAUCUGAUAGAUACUUGCUCCCCAAUGCUAGUGCACAGCUUUAAGGGUCCAUCCCAA
.((....))...........................((((((.............((((((((((((.....)))))))..)))))..(((....))).))))))..(((.....))).. (-18.49 = -20.38 +   1.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:16 2006