Locus 8417

Sequence ID	3L_DroMel_CAF1
Location	22,123,491 – 22,123,600
Length	109
Max. P	0.998531

overview

Window 4

Location	22,123,491 – 22,123,600
Length	109
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	73.52
Mean single sequence MFE	-19.30
Consensus MFE	-4.70
Energy contribution	-5.58
Covariance contribution	0.88
Combinations/Pair	1.23
Mean z-score	-2.51
Structure conservation index	0.24
SVM decision value	2.55
SVM RNA-class probability	0.995167
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22123491 109 + 23771897
CCCCUCUGGUUCUGGUUU-UGGUUCUCCUCCAGCAAUUUCUCUGCUCUCGCAUCGAAAACACC-----AAACCAAAUAAAUAAUAGUUAAAUUUU-UUCUAUUAUAUCUUUCCAGA
....(((((...((((((-(((.......)))....((((..(((....)))..)))).....-----)))))).....(((((((.........-..)))))))......))))) ( -19.70)
>DroGri_CAF1 124680 106 + 1
CCAUUCCCAUUCCCACUUCCAAAUCCCUCCCACAAAUUUCAGUGACUACGCAUUGAGUGCCC--------AGCGAAUAAAUAAUAGUUAAAUUUU--UCGUUCAUUUCCUAUAGAA
.....................................(((((((......))))))).....--------((((((.((((.........)))))--))))).............. (  -8.20)
>DroSec_CAF1 109589 113 + 1
C-CCUCUGGUUCUGGUUU-CGGUUCUCCUCCAGCAAUUUCUGUGCUCGCGCAUCGAAAGCACCAACCCAAACCAAAUAAAUAAUAGUUAAAUUUU-UUCUAUUAUAUCUUUCCAGA
.-..(((((...((((((-.((((........((..((((.((((....)))).))))))...)))).)))))).....(((((((.........-..)))))))......))))) ( -24.00)
>DroSim_CAF1 117369 114 + 1
CCCCUCUGGUUCUGGUUU-CGGUUCUCCUCCAGCAAUUUCUCUGCUCGCGCAUCGAAAGCACCAACCCAAACCAAAUAAAUAAUAGUUAAAUUUU-UUCUAUUAUAUCUUUCCAGA
....(((((...((((((-.((((.......((((.......)))).((.........))...)))).)))))).....(((((((.........-..)))))))......))))) ( -22.50)
>DroYak_CAF1 151967 99 + 1
CCCCUCUGGUUCUAGUUU-UGGUUGUCCUCCAGCCAGUUCUCUGCUCGCA-----------CC-----CAACCAAAUAAAUAAUAGUUAAAUUUCUUUCUAUUAUUGCUUUCCAGA
....(((((....(((((-((((((....(.(((.((....))))).)..-----------..-----))))))))..((((((((............)))))))))))..))))) ( -22.10)
>consensus
CCCCUCUGGUUCUGGUUU_CGGUUCUCCUCCAGCAAUUUCUCUGCUCGCGCAUCGAAAGCACC_____AAACCAAAUAAAUAAUAGUUAAAUUUU_UUCUAUUAUAUCUUUCCAGA
....(((((...(((((...((....))..(((........))).........................))))).....(((((((............)))))))......))))) ( -4.70 =  -5.58 +   0.88)

alignment

secondary structure

dotplot

Window 5

Location	22,123,491 – 22,123,600
Length	109
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	73.52
Mean single sequence MFE	-28.38
Consensus MFE	-14.86
Energy contribution	-15.74
Covariance contribution	0.88
Combinations/Pair	1.38
Mean z-score	-2.67
Structure conservation index	0.52
SVM decision value	3.13
SVM RNA-class probability	0.998531
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22123491 109 - 23771897
UCUGGAAAGAUAUAAUAGAA-AAAAUUUAACUAUUAUUUAUUUGGUUU-----GGUGUUUUCGAUGCGAGAGCAGAGAAAUUGCUGGAGGAGAACCA-AAACCAGAACCAGAGGGG
(((((......(((((((..-.........)))))))...((((((((-----(((..((((..(((....)))..))))..)))...((....)).-)))))))).))))).... ( -29.40)
>DroGri_CAF1 124680 106 - 1
UUCUAUAGGAAAUGAACGA--AAAAUUUAACUAUUAUUUAUUCGCU--------GGGCACUCAAUGCGUAGUCACUGAAAUUUGUGGGAGGGAUUUGGAAGUGGGAAUGGGAAUGG
...................--.........(((((.((((((((((--------(.(((.....))).))))((((.((((((.......))))))...)))).)))))))))))) ( -17.00)
>DroSec_CAF1 109589 113 - 1
UCUGGAAAGAUAUAAUAGAA-AAAAUUUAACUAUUAUUUAUUUGGUUUGGGUUGGUGCUUUCGAUGCGCGAGCACAGAAAUUGCUGGAGGAGAACCG-AAACCAGAACCAGAGG-G
(((((......(((((((..-.........)))))))...((((((((.(((((((..((((..(((....)))..))))..))).......)))).-)))))))).)))))..-. ( -33.71)
>DroSim_CAF1 117369 114 - 1
UCUGGAAAGAUAUAAUAGAA-AAAAUUUAACUAUUAUUUAUUUGGUUUGGGUUGGUGCUUUCGAUGCGCGAGCAGAGAAAUUGCUGGAGGAGAACCG-AAACCAGAACCAGAGGGG
(((((......(((((((..-.........)))))))...((((((((.(((((((..((((..(((....)))..))))..))).......)))).-)))))))).))))).... ( -34.71)
>DroYak_CAF1 151967 99 - 1
UCUGGAAAGCAAUAAUAGAAAGAAAUUUAACUAUUAUUUAUUUGGUUG-----GG-----------UGCGAGCAGAGAACUGGCUGGAGGACAACCA-AAACUAGAACCAGAGGGG
(((((.....(((((((((((....)))..))))))))..((((((((-----..-----------..(.(((((....)).))).)....))))))-)).......))))).... ( -27.10)
>consensus
UCUGGAAAGAUAUAAUAGAA_AAAAUUUAACUAUUAUUUAUUUGGUUU_____GGUGCUUUCGAUGCGCGAGCAGAGAAAUUGCUGGAGGAGAACCG_AAACCAGAACCAGAGGGG
(((((......(((((((............)))))))...(((((((......((((.((((..(((....)))..)))).))))...((....))...))))))).))))).... (-14.86 = -15.74 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:49 2006