Locus 741

Sequence ID	X_DroMel_CAF1
Location	2,013,943 – 2,014,095
Length	152
Max. P	0.696314

overview

Window 0

Location	2,013,943 – 2,014,057
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-37.15
Consensus MFE	-22.53
Energy contribution	-21.22
Covariance contribution	-1.31
Combinations/Pair	1.39
Mean z-score	-1.93
Structure conservation index	0.61
SVM decision value	0.34
SVM RNA-class probability	0.696314
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2013943 114 - 22224390
GCGG-AGGGAGAGUAGGGUCUCUUUCGGGUUUUGGAUUC---CUAAUCCUUGGAUUGGUACUAGCUAU-AAAACUAGGUUUCUUGUCAU-CCGUGCCCUUAUCUGGCCCUAUCUGGGCAG
.(((-((..((((......))))..)((((..(((((..---((((((....))))))..((((....-....))))..........))-))).))))...))))((((.....)))).. ( -39.50)
>DroSec_CAF1 6863 112 - 1
GCGG-AGGAAGAGUAGGGUCUCUUUCGGGGUUCGGAUUG---CUAAUCCUUGGAUUGGUACUAGCCAU-AAAACUAGGUUUCUAGUCAU-CCGUGUCCUUAUCUA--CCUAUCUGGGCAG
((((-((((((((......)))))))((((..(((((((---((((((....))))))))........-...(((((....))))).))-)))..))))..))).--((.....)))).. ( -35.50)
>DroEre_CAF1 7438 114 - 1
GCUG-UAGGAGAAUAGAGUCCUUUCCGGGUUACGGAUGG---CCAAUCCAUGGAUUGGUACUAGCCAUAAAAACUAGGUUUCUAUUUAUGCCAUGCCUUUGUAUA--CAUAUCUGGGCAG
....-..((.((((((((.(((.((((.....))))..(---((((((....)))))))................))).))))))))...)).(((((..(((..--..)))..))))). ( -34.80)
>DroYak_CAF1 6961 116 - 1
GCGGAUAGAAGAGUGGCACCCUUU-CGGGUUCAGGAUUGUUCCGAAUCCUUGGAUUGGUACUAGCCAUUAAAACUAGGUUUCUAUUUAU-CCAUGCCCUUAUAUA--CGUAUCGGGGCAG
..(((((((..(((((((((..((-(((((((.(((....)))))))))..)))..)))....)))))).....(((....))))))))-)).((((((.(((..--..))).)))))). ( -38.80)
>consensus
GCGG_AAGAAGAGUAGGGUCCCUUUCGGGUUUCGGAUUG___CUAAUCCUUGGAUUGGUACUAGCCAU_AAAACUAGGUUUCUAGUCAU_CCAUGCCCUUAUAUA__CCUAUCUGGGCAG
.....((((((..(((...(((....)))....((.......((((((....))))))......)).......)))..)))))).........(((((..(((......)))..))))). (-22.53 = -21.22 +  -1.31)

alignment

secondary structure

dotplot

Window 1

Location	2,013,982 – 2,014,095
Length	113
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	81.29
Mean single sequence MFE	-36.13
Consensus MFE	-22.14
Energy contribution	-22.07
Covariance contribution	-0.06
Combinations/Pair	1.28
Mean z-score	-1.74
Structure conservation index	0.61
SVM decision value	-0.04
SVM RNA-class probability	0.514467
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2013982 113 + 22224390
AACCUAGUUUU-AUAGCUAGUACCAAUCCAAGGAUUAG---GAAUCCAAAACCCGAAAGAGACCCUACUCUCCCU-CCGCGGAGGCAGCGAAAAGGUGGUUGGAGGAUUCGCAGGACA
...((((((..-..))))))..((((((....))))..---((((((..(((((....)..(((...(.((.(((-(....)))).)).)....)))))))...))))))...))... ( -32.10)
>DroSec_CAF1 6900 113 + 1
AACCUAGUUUU-AUGGCUAGUACCAAUCCAAGGAUUAG---CAAUCCGAACCCCGAAAGAGACCCUACUCUUCCU-CCGCGGAGGCAUCGAAAGGGUGGUUGGAGGAUUCGCAGGACA
...((((((..-..))))))..((((((....)))).(---((((((.((((.(....)..(((((......(((-(....)))).......)))))))))...))))).)).))... ( -34.22)
>DroEre_CAF1 7476 114 + 1
AACCUAGUUUUUAUGGCUAGUACCAAUCCAUGGAUUGG---CCAUCCGUAACCCGGAAAGGACUCUAUUCUCCUA-CAGCGGUGGCAGCGGAAUGGCGGCUGUAACAUUCGCAGGACA
..((((((((((.((((((((.(((.....))))))))---)))((((.....)))))))))))...........-..((((..(((((.(.....).))))).....)))))))... ( -36.40)
>DroYak_CAF1 6998 117 + 1
AACCUAGUUUUAAUGGCUAGUACCAAUCCAAGGAUUCGGAACAAUCCUGAACCCG-AAAGGGUGCCACUCUUCUAUCCGCGGAGACAGCGGAAAGGCGGCUGUAACAUUCGCAGGACA
...((((((.....))))))..((((((....)))).)).....(((((.((((.-...))))(((.(.(((...((((((....).))))))))).)))...........))))).. ( -41.80)
>consensus
AACCUAGUUUU_AUGGCUAGUACCAAUCCAAGGAUUAG___CAAUCCGAAACCCGAAAAAGACCCUACUCUCCCA_CCGCGGAGGCAGCGAAAAGGCGGCUGGAACAUUCGCAGGACA
...((((((.....))))))......(((..(((((......)))))...........((((......))))......(((((.(((((.(.....).)))))....))))).))).. (-22.14 = -22.07 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:40 2006