Locus 2303

Sequence ID	2L_DroMel_CAF1
Location	6,228,494 – 6,228,706
Length	212
Max. P	0.969207

overview

Window 8

Location	6,228,494 – 6,228,593
Length	99
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.00
Mean single sequence MFE	-24.76
Consensus MFE	-20.83
Energy contribution	-20.79
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-2.01
Structure conservation index	0.84
SVM decision value	1.64
SVM RNA-class probability	0.969207
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6228494 99 + 22407834
CACAACAAGCUGCUUUCCCACGCAGCGGAAAACUUUGAUGAGCCUCAUUGAAAUUGAAUUUCCUACCAAGUGCCUUAC---------------------CGUGCAAUUUGUGUUUUCCCA
........(((((........)))))(((((((((..(((.....)))..))..............((((((((....---------------------.).)).))))).))))))).. ( -23.80)
>DroSec_CAF1 64999 99 + 1
CACAACAAGCUGCUUUCCCACGCAGCGGAAAACUUUGAUGAGCAUCAUUGAAAUUGAAUUUCCUACCAAGUGCCUCAC---------------------CGUGCAAUUUGUGUUUUCCCA
........(((((........)))))(((((((((..(((.....)))..))..............((((((((....---------------------.).)).))))).))))))).. ( -23.80)
>DroSim_CAF1 78182 99 + 1
CACAACAAGCUGCUUUCCCACGCAGCGGAAAACUUUGAUGAGGCUCAUUGAAAUUGAAUUUCCUACCAAGUGCCUCAC---------------------CGUGCAAUUUGUGUUUUCCCA
........(((((........)))))(((((((...(.((((((...(((................)))..)))))).---------------------)..((.....))))))))).. ( -26.29)
>DroEre_CAF1 62093 98 + 1
CACAACAAGCCGCUUUCCCACGCGGCGGAAAACUUUGAUGAGCCUCAUUGAAAUUGAAUUUCCUUCCAAGUGC-UCAC---------------------CGUGCAAUUUGUGUUUUCCCA
........(((((........)))))(((((((((..(((.....)))..))..............(((((((-....---------------------...)).))))).))))))).. ( -26.10)
>DroYak_CAF1 76653 119 + 1
CACAACAAGCCGCUUUCCCACGCAGCGGAAAACUUUGAUGAGCCUCAUUGAAAUUGAAUUUCCUUCCAAGUGC-UCACCGCUCACCGUUCUCCGUUCUCCGUGCAAUUUGUGUUUUCCCA
(((((...(((((........))((((((.(((..((((((((((....(((((...)))))......)).))-)))....)))..))).))))))....).))...)))))........ ( -23.80)
>consensus
CACAACAAGCUGCUUUCCCACGCAGCGGAAAACUUUGAUGAGCCUCAUUGAAAUUGAAUUUCCUACCAAGUGCCUCAC_____________________CGUGCAAUUUGUGUUUUCCCA
........(((((........)))))(((((((((..(((.....)))..))..............(((((((.............................)).))))).))))))).. (-20.83 = -20.79 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	6,228,593 – 6,228,706
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.54
Mean single sequence MFE	-33.32
Consensus MFE	-29.15
Energy contribution	-29.07
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-1.49
Structure conservation index	0.87
SVM decision value	0.39
SVM RNA-class probability	0.717845
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6228593 113 + 22407834
UCGUUAAAUUUCGAGCUCUGAAAGUAAUUGCAAUUGCACUCCGUUCAGGGAAUGCAACGCGGCACGUGCGGGGUGCAAAUUGCCCGGGGAACCCCGAAAAAA-------AUACUGAUUGA
(((........)))..((....((((...(((((((((((((((...(....(((...)))...)..))))))))).)))))).((((....))))......-------.))))....)) ( -34.80)
>DroSec_CAF1 65098 112 + 1
UCGUUAAAUUUCGAGCUCUGAAAGUAAUUGCAAUUGCACUCCGUUCAGGGAAUGCAACGCGGCACGUGCGGGGUGCAAAUUGCCCGGGGAACCCCGAAA-AA-------AUACUGAUUGA
(((........)))..((....((((...(((((((((((((((...(....(((...)))...)..))))))))).)))))).((((....))))...-..-------.))))....)) ( -34.80)
>DroSim_CAF1 78281 112 + 1
UCGUUAAAUUUCGAGCUCUGAAAGUAAUUGCAAUUGCACUCCGUUCAGGGAAUGCAACGCGGCACGUGCGGGGUGCAAAUUGCCCGGGGAACCCCGAAA-AA-------AUACUGAUUGA
(((........)))..((....((((...(((((((((((((((...(....(((...)))...)..))))))))).)))))).((((....))))...-..-------.))))....)) ( -34.80)
>DroEre_CAF1 62191 98 + 1
UCGUUAAACUUCGAGCUCUGAAAGUAAUUGCAAUUGCACUCAGUUCG-------------GGCACGUGCGGGGUGCAAAUUGCCCGAGGAACCCCGAAA-AA--------UGCUGAUUGA
(((.....(((((.(((.....)))....((((((((((((.((.((-------------....)).)).)))))).)))))).))))).....)))..-..--------.......... ( -25.60)
>DroYak_CAF1 76772 107 + 1
UCGUUAAAUUUCGAGCUCUGAAAGUAAUUGCAAUUGCACUCCGCUCGG------------GGCACGUGCGGGGUGCAAAUUGUCCGGGGAACCCCGAAA-AAAAAUAGUAUACUGAUUGA
(((........)))..((....((((...(((((((((((((((.((.------------....)).))))))))).)))))).((((....))))...-..........))))....)) ( -36.60)
>consensus
UCGUUAAAUUUCGAGCUCUGAAAGUAAUUGCAAUUGCACUCCGUUCAGGGAAUGCAACGCGGCACGUGCGGGGUGCAAAUUGCCCGGGGAACCCCGAAA_AA_______AUACUGAUUGA
(((........)))..((....((((...(((((((((((((((.(...................).))))))))).)))))).((((....))))..............))))....)) (-29.15 = -29.07 +  -0.08)

alignment

secondary structure

dotplot

Window 0

Location	6,228,593 – 6,228,706
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.54
Mean single sequence MFE	-32.32
Consensus MFE	-23.25
Energy contribution	-23.09
Covariance contribution	-0.16
Combinations/Pair	1.12
Mean z-score	-1.83
Structure conservation index	0.72
SVM decision value	0.25
SVM RNA-class probability	0.654211
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6228593 113 - 22407834
UCAAUCAGUAU-------UUUUUUCGGGGUUCCCCGGGCAAUUUGCACCCCGCACGUGCCGCGUUGCAUUCCCUGAACGGAGUGCAAUUGCAAUUACUUUCAGAGCUCGAAAUUUAACGA
....(((((..-------......((((....))))((((...(((.....)))..))))((((((((((((......))))))))).))).............))).)).......... ( -34.50)
>DroSec_CAF1 65098 112 - 1
UCAAUCAGUAU-------UU-UUUCGGGGUUCCCCGGGCAAUUUGCACCCCGCACGUGCCGCGUUGCAUUCCCUGAACGGAGUGCAAUUGCAAUUACUUUCAGAGCUCGAAAUUUAACGA
.......((..-------..-(((((((.(((....((((...(((.....)))..))))((((((((((((......))))))))).)))...........))))))))))....)).. ( -34.80)
>DroSim_CAF1 78281 112 - 1
UCAAUCAGUAU-------UU-UUUCGGGGUUCCCCGGGCAAUUUGCACCCCGCACGUGCCGCGUUGCAUUCCCUGAACGGAGUGCAAUUGCAAUUACUUUCAGAGCUCGAAAUUUAACGA
.......((..-------..-(((((((.(((....((((...(((.....)))..))))((((((((((((......))))))))).)))...........))))))))))....)).. ( -34.80)
>DroEre_CAF1 62191 98 - 1
UCAAUCAGCA--------UU-UUUCGGGGUUCCUCGGGCAAUUUGCACCCCGCACGUGCC-------------CGAACUGAGUGCAAUUGCAAUUACUUUCAGAGCUCGAAGUUUAACGA
..........--------..-(((((((.....(((((((...(((.....)))..))))-------------))).((((((((....)))......)))))..)))))))........ ( -28.30)
>DroYak_CAF1 76772 107 - 1
UCAAUCAGUAUACUAUUUUU-UUUCGGGGUUCCCCGGACAAUUUGCACCCCGCACGUGCC------------CCGAGCGGAGUGCAAUUGCAAUUACUUUCAGAGCUCGAAAUUUAACGA
....(((((...........-.((((((....))))))(((((.((((.((((.((....------------.)).)))).)))))))))..............))).)).......... ( -29.20)
>consensus
UCAAUCAGUAU_______UU_UUUCGGGGUUCCCCGGGCAAUUUGCACCCCGCACGUGCCGCGUUGCAUUCCCUGAACGGAGUGCAAUUGCAAUUACUUUCAGAGCUCGAAAUUUAACGA
....(((((..............(((((....)))))((((((.((((.(((..((.................))..))).)))))))))).............))).)).......... (-23.25 = -23.09 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:33 2006