Locus 6693

Sequence ID	2L_DroMel_CAF1
Location	18,725,804 – 18,726,044
Length	240
Max. P	0.983063

overview

Window 2

Location	18,725,804 – 18,725,924
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.63
Mean single sequence MFE	-40.82
Consensus MFE	-37.97
Energy contribution	-38.61
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.25
Structure conservation index	0.93
SVM decision value	0.45
SVM RNA-class probability	0.741226
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18725804 120 - 22407834
GCAUUGGGGCGAUUAGUAGCGCCUUUCGAUUUUUUUUUUCGCCCCUCGUUUUGGAGUGAAUGUUUUGGGCGCGUCCAUCGCAGAGGAGGAGUAACGAGGGGUGGGGGCAAAUUAAGCAGG
((...((((((........))))))..(((((...((..(((((((((((..........(((..((((....))))..)))..........)))))))))))..)).)))))..))... ( -40.85)
>DroSec_CAF1 18390 118 - 1
GCAUUGGGGCGAUUAGUAGCGCCUUUCGAUUUU--UUUUCGCCCCUCGUUUUGGAGUGAAUGUUUUGGGCGCGUCCAUCGCAGAGGAGGAGUAACGAGGGGUGGGGGCAAAUUAAGCAGG
((...((((((........))))))..(((((.--((..(((((((((((..........(((..((((....))))..)))..........)))))))))))..)).)))))..))... ( -43.25)
>DroSim_CAF1 16854 118 - 1
GCAUUGGGGCGAUUAGUAGCGCCUUUCGAUUUU--UUUUCGCCCCUCGUUUUGGAGUGAAUGUUUUGGGCGCGUCCAUCGCAGAGGAGGAGUAACGAGGGGUGGGGGCAAAUUAAGCAGG
((...((((((........))))))..(((((.--((..(((((((((((..........(((..((((....))))..)))..........)))))))))))..)).)))))..))... ( -43.25)
>DroEre_CAF1 18512 117 - 1
GCAUUGGGGCGAUUAGUAGCGCCUUUCGAUUUU---UUUCGCCCCGCGUUUUGGAGUGAAUGUUUUGGGCGCGUCCAGUGCAGAGGAGGAGUAACGAGGGGUGGGGGCAAAUUAAGCAGG
((...((((((........))))))..((((((---(..((((((.((((..........(((.(((((....))))).)))..........)))).))))))..)).)))))..))... ( -38.65)
>DroYak_CAF1 18546 117 - 1
GCAUUGGGGCGAUUAGUAGCGCCUUUCGAUUUU---UUUCGCCCCGUGUUUUGGAGUGAAUGUUUUGGGCGCGUCCAGUGCAGAGGCGGAGUAACGAGGGGUGGGGGCAAAUUAAGCAGG
((...((((((........))))))..((((((---(..((((((.((((.....((...(((.(((((....))))).)))...)).....)))).))))))..)).)))))..))... ( -38.10)
>consensus
GCAUUGGGGCGAUUAGUAGCGCCUUUCGAUUUU__UUUUCGCCCCUCGUUUUGGAGUGAAUGUUUUGGGCGCGUCCAUCGCAGAGGAGGAGUAACGAGGGGUGGGGGCAAAUUAAGCAGG
((...((((((........))))))..(((((...((..(((((((((((..........(((..((((....))))..)))..........)))))))))))..)).)))))..))... (-37.97 = -38.61 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	18,725,844 – 18,725,964
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.84
Mean single sequence MFE	-31.48
Consensus MFE	-26.67
Energy contribution	-26.71
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.06
Structure conservation index	0.85
SVM decision value	1.93
SVM RNA-class probability	0.983063
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18725844 120 + 22407834
CGAUGGACGCGCCCAAAACAUUCACUCCAAAACGAGGGGCGAAAAAAAAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUAUGGAUUCAAUGUAUGUAUCUGCAUCUGACGGAUACAU
...(((......)))..(((((.(.((((......(((((((.........((....)).........)))))))........)))).).)))))((((((((((....).))))))))) ( -32.61)
>DroSec_CAF1 18430 114 + 1
CGAUGGACGCGCCCAAAACAUUCACUCCAAAACGAGGGGCGAAAA--AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG----UAUCUGCAUCUGGCGGAUACAU
((.(((......)))....................(((((((...--....((....)).........)))))))........))......(((----(((((((.....)))))))))) ( -31.19)
>DroSim_CAF1 16894 114 + 1
CGAUGGACGCGCCCAAAACAUUCACUCCAAAACGAGGGGCGAAAA--AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG----UAUCUGCAUCUGGCGGAUACAU
((.(((......)))....................(((((((...--....((....)).........)))))))........))......(((----(((((((.....)))))))))) ( -31.19)
>DroEre_CAF1 18552 113 + 1
CACUGGACGCGCCCAAAACAUUCACUCCAAAACGCGGGGCGAAA---AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG----UAUCUGCAUCUGGCGGAUACAU
..(((...(((.....................)))(((((((..---....((....)).........)))))))........))).....(((----(((((((.....)))))))))) ( -31.96)
>DroYak_CAF1 18586 113 + 1
CACUGGACGCGCCCAAAACAUUCACUCCAAAACACGGGGCGAAA---AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG----UAUCUGCAUCUGGCGGAUACAU
...(((......)))..........(((.......(((((((..---....((....)).........)))))))...(....))))....(((----(((((((.....)))))))))) ( -30.46)
>consensus
CGAUGGACGCGCCCAAAACAUUCACUCCAAAACGAGGGGCGAAAA__AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG____UAUCUGCAUCUGGCGGAUACAU
...(((......)))..........(((.......(((((((.........((....)).........)))))))...(((..(((((...........))))).....))))))..... (-26.67 = -26.71 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	18,725,884 – 18,726,004
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.39
Mean single sequence MFE	-31.90
Consensus MFE	-25.20
Energy contribution	-25.44
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.85
Structure conservation index	0.79
SVM decision value	0.20
SVM RNA-class probability	0.632373
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18725884 120 + 22407834
GAAAAAAAAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUAUGGAUUCAAUGUAUGUAUCUGCAUCUGACGGAUACAUGCGGCCGAUUUCCGUGCAUUUAACGCAUAAACGCUUUUUG
............(((((((((.....((((((((((.......))).......((((((((((((....).))))))))))))).)))))...((((.......))))...))))))))) ( -34.30)
>DroSec_CAF1 18470 114 + 1
GAAAA--AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG----UAUCUGCAUCUGGCGGAUACAUGCGGCCGAUUUCCGUGCAUUUAACGCAUAAACGCUUUUUG
.....--.....(((((((((.....(((((((.(.....(....).....(((----(((((((.....))))))))))).)).)))))...((((.......))))...))))))))) ( -32.00)
>DroSim_CAF1 16934 114 + 1
GAAAA--AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG----UAUCUGCAUCUGGCGGAUACAUGCGGCCGAUUUCCGUGCAUUUAACGCAUAAACGCUUUUUG
.....--.....(((((((((.....(((((((.(.....(....).....(((----(((((((.....))))))))))).)).)))))...((((.......))))...))))))))) ( -32.00)
>DroEre_CAF1 18592 113 + 1
GAAA---AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG----UAUCUGCAUCUGGCGGAUACAUGCGGCCGAUUUCCGUGCAUUUAACGCAUAAACGCUCUUUG
....---.....((((..(((.....(((((((.(.....(....).....(((----(((((((.....))))))))))).)).)))))...((((.......))))...)))..)))) ( -29.20)
>DroYak_CAF1 18626 113 + 1
GAAA---AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG----UAUCUGCAUCUGGCGGAUACAUGCGGCCGAUUUCCGUGCAUUUAACGCAUAAACGCUUUUUG
....---.....(((((((((.....(((((((.(.....(....).....(((----(((((((.....))))))))))).)).)))))...((((.......))))...))))))))) ( -32.00)
>consensus
GAAAA__AAAAUCGAAAGGCGCUACUAAUCGCCCCAAUGCCUACGGAUUCAAUG____UAUCUGCAUCUGGCGGAUACAUGCGGCCGAUUUCCGUGCAUUUAACGCAUAAACGCUUUUUG
............((((((((((........))...(((((..(((((.((..((....(((((((.....)))))))....))...))..))))))))))............)))))))) (-25.20 = -25.44 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	18,725,924 – 18,726,044
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.28
Mean single sequence MFE	-31.32
Consensus MFE	-28.14
Energy contribution	-28.14
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.48
Structure conservation index	0.90
SVM decision value	0.79
SVM RNA-class probability	0.850690
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18725924 120 - 22407834
AGCGGCGAUAAUGAUAAUCCCCGAAUGGAAUAAAAGUGUCCAAAAAGCGUUUAUGCGUUAAAUGCACGGAAAUCGGCCGCAUGUAUCCGUCAGAUGCAGAUACAUACAUUGAAUCCAUAG
.((((((((.......))).(((..((((.........))))....(((((((.....))))))).)))......)))))(((((((.((.....)).)))))))............... ( -31.00)
>DroSec_CAF1 18508 116 - 1
AGCGGCGAUAAUGAUAAUCCCCGAACGGAAUAAAAGUGUCCAAAAAGCGUUUAUGCGUUAAAUGCACGGAAAUCGGCCGCAUGUAUCCGCCAGAUGCAGAUA----CAUUGAAUCCGUAG
.((((((((.......))).(((...(((.........))).....(((((((.....))))))).)))......)))))(((((((.((.....)).))))----)))........... ( -31.40)
>DroSim_CAF1 16972 116 - 1
AGCGGCGAUAAUGAUAAUCCCCGAACGGAAUAAAAGUGUCCAAAAAGCGUUUAUGCGUUAAAUGCACGGAAAUCGGCCGCAUGUAUCCGCCAGAUGCAGAUA----CAUUGAAUCCGUAG
.((((((((.......))).(((...(((.........))).....(((((((.....))))))).)))......)))))(((((((.((.....)).))))----)))........... ( -31.40)
>DroEre_CAF1 18629 116 - 1
AGCGGCGAUAAUGAUAAUCCCCGAACGGAAUAAAAGUGUCCAAAGAGCGUUUAUGCGUUAAAUGCACGGAAAUCGGCCGCAUGUAUCCGCCAGAUGCAGAUA----CAUUGAAUCCGUAG
.((((((((.......))).(((...(((.........))).....(((((((.....))))))).)))......)))))(((((((.((.....)).))))----)))........... ( -31.40)
>DroYak_CAF1 18663 116 - 1
AGCGGCGAUAAUGAUAAUCCCCGAACGGAAUAAAAGUGUCCAAAAAGCGUUUAUGCGUUAAAUGCACGGAAAUCGGCCGCAUGUAUCCGCCAGAUGCAGAUA----CAUUGAAUCCGUAG
.((((((((.......))).(((...(((.........))).....(((((((.....))))))).)))......)))))(((((((.((.....)).))))----)))........... ( -31.40)
>consensus
AGCGGCGAUAAUGAUAAUCCCCGAACGGAAUAAAAGUGUCCAAAAAGCGUUUAUGCGUUAAAUGCACGGAAAUCGGCCGCAUGUAUCCGCCAGAUGCAGAUA____CAUUGAAUCCGUAG
.((((((((.......))).(((...(((.........))).....(((((((.....))))))).)))......))))).((((((.....))))))...................... (-28.14 = -28.14 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:39 2006