Locus 7473

Sequence ID	3R_DroMel_CAF1
Location	19,953,097 – 19,953,195
Length	98
Max. P	0.595437

overview

Window 2

Location	19,953,097 – 19,953,195
Length	98
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	82.49
Mean single sequence MFE	-29.88
Consensus MFE	-21.53
Energy contribution	-22.06
Covariance contribution	0.53
Combinations/Pair	1.08
Mean z-score	-1.56
Structure conservation index	0.72
SVM decision value	0.12
SVM RNA-class probability	0.595437
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19953097 98 + 27905053
A---UAAGAUCUAUUUCAACUCCC-----UCACU-UUACAGAUCUCAAUGCUGCGCGAGCAGUUGGCCCAGGAGGCCAAACGGCGACAGCAGUACAUUCUACGCAGC
.---..((((((............-----.....-....))))))....(((((((..((..((((((.....))))))...))....)).(((.....)))))))) ( -27.00)
>DroVir_CAF1 16719 95 + 1
C---ACAGAACU---GCAGC-----UGAGCUCCUC-CACAGAUCUCCAUGCUGCGCGAGCAGCUGGCUCAGGAGGCCAAGCGGCGACAGCAAUAUAUACUGCGCAGC
.---......((---((.((-----((....((((-(...((...(((.(((((....)))))))).)).))))).....))))....(((........))))))). ( -36.40)
>DroSec_CAF1 12781 98 + 1
A---UAAGAUCUACAUCAAGUUCC-----UUACU-UUUCAGAUCUCUAUGCUGCGCGAGCAGUUGGCCCAGGAGGCCAAACGGCGACAGCAGUACAUUCUACGCAGC
.---..((((((.....((((...-----..)))-)...))))))....(((((((..((..((((((.....))))))...))....)).(((.....)))))))) ( -29.70)
>DroSim_CAF1 12515 98 + 1
A---UAAGAUCUACAUAAAGUUCC-----UUACU-UUUCAGAUCUCUAUGCUGCGCGAGCAGUUGGCCCAGGAGGCCAAACGGCGACAGCAGUACAUUCUACGCAGC
.---..((((((....(((((...-----..)))-))..))))))....(((((((..((..((((((.....))))))...))....)).(((.....)))))))) ( -31.60)
>DroEre_CAF1 12835 98 + 1
A---UAAUAUCUACAUGCAGUACC-----CCACU-UUUCAGAUCUCUAUGCUGCGCGAGCAGCUGGCUCAGGAGGCCAAACGGCGGCAGCAGUACAUUCUACGCAGC
.---...........(((.((.((-----((...-..............(((((....)))))(((((.....)))))...)).))..)).(((.....)))))).. ( -25.70)
>DroYak_CAF1 12700 103 + 1
AAAGUAAUAUCUACAUCAUGUACCCU---CCACU-UUUCAGAUCUCUAUGCUGCGCGAGCAGUUGGCUCAGGAGGCCAAACGGCGGCAGCAGUACAUUCUGCGCAGC
(((((......(((.....)))....---..)))-))............(((((((..((..((((((.....))))))...)).)).((((......))))))))) ( -28.90)
>consensus
A___UAAGAUCUACAUCAAGUACC_____CCACU_UUUCAGAUCUCUAUGCUGCGCGAGCAGUUGGCCCAGGAGGCCAAACGGCGACAGCAGUACAUUCUACGCAGC
......((((((...........................))))))....(((((((..((..((((((.....))))))...))....)).(((.....)))))))) (-21.53 = -22.06 +   0.53)

alignment

secondary structure

dotplot

Window 3

Location	19,953,097 – 19,953,195
Length	98
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	82.49
Mean single sequence MFE	-33.97
Consensus MFE	-25.92
Energy contribution	-25.81
Covariance contribution	-0.11
Combinations/Pair	1.19
Mean z-score	-1.46
Structure conservation index	0.76
SVM decision value	0.12
SVM RNA-class probability	0.593517
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19953097 98 - 27905053
GCUGCGUAGAAUGUACUGCUGUCGCCGUUUGGCCUCCUGGGCCAACUGCUCGCGCAGCAUUGAGAUCUGUAA-AGUGA-----GGGAGUUGAAAUAGAUCUUA---U
(((((((((......))))....((.(((.((((.....))))))).))....)))))..((((((((((..-.....-----..........))))))))))---. ( -33.53)
>DroVir_CAF1 16719 95 - 1
GCUGCGCAGUAUAUAUUGCUGUCGCCGCUUGGCCUCCUGAGCCAGCUGCUCGCGCAGCAUGGAGAUCUGUG-GAGGAGCUCA-----GCUGC---AGUUCUGU---G
(((((((((((.....))))))....(((.(((((((.((.((((((((....))))).)))...))...)-)))..))).)-----)).))---))).....---. ( -38.60)
>DroSec_CAF1 12781 98 - 1
GCUGCGUAGAAUGUACUGCUGUCGCCGUUUGGCCUCCUGGGCCAACUGCUCGCGCAGCAUAGAGAUCUGAAA-AGUAA-----GGAACUUGAUGUAGAUCUUA---U
(((((((((......))))....((.(((.((((.....))))))).))....)))))...((((((((..(-(((..-----...))))....)))))))).---. ( -35.80)
>DroSim_CAF1 12515 98 - 1
GCUGCGUAGAAUGUACUGCUGUCGCCGUUUGGCCUCCUGGGCCAACUGCUCGCGCAGCAUAGAGAUCUGAAA-AGUAA-----GGAACUUUAUGUAGAUCUUA---U
(((((((((......))))....((.(((.((((.....))))))).))....)))))...((((((((.((-(((..-----...)))))...)))))))).---. ( -35.90)
>DroEre_CAF1 12835 98 - 1
GCUGCGUAGAAUGUACUGCUGCCGCCGUUUGGCCUCCUGAGCCAGCUGCUCGCGCAGCAUAGAGAUCUGAAA-AGUGG-----GGUACUGCAUGUAGAUAUUA---U
.((((((.(...((((((((((((((....))).....((((.....))))).))))).(((....)))...-.....-----)))))..)))))))......---. ( -29.20)
>DroYak_CAF1 12700 103 - 1
GCUGCGCAGAAUGUACUGCUGCCGCCGUUUGGCCUCCUGAGCCAACUGCUCGCGCAGCAUAGAGAUCUGAAA-AGUGG---AGGGUACAUGAUGUAGAUAUUACUUU
(((((((((......)))).((.((.(((.((((....).)))))).))..)))))))......(((((...-.(((.---......)))....)))))........ ( -30.80)
>consensus
GCUGCGUAGAAUGUACUGCUGUCGCCGUUUGGCCUCCUGAGCCAACUGCUCGCGCAGCAUAGAGAUCUGAAA_AGUAA_____GGAACUUGAUGUAGAUCUUA___U
(((((((((......)))).((.((.(((.(((.......)))))).))..)))))))...((((((((.........................))))))))..... (-25.92 = -25.81 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:57 2006