Locus 7077

Sequence ID	2L_DroMel_CAF1
Location	19,807,187 – 19,807,464
Length	277
Max. P	0.999993

overview

Window 8

Location	19,807,187 – 19,807,304
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.03
Mean single sequence MFE	-26.94
Consensus MFE	-26.52
Energy contribution	-25.84
Covariance contribution	-0.68
Combinations/Pair	1.20
Mean z-score	-3.00
Structure conservation index	0.98
SVM decision value	5.75
SVM RNA-class probability	0.999993
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19807187 117 - 22407834
UAUAAAAA-CACAAAAAUCCAGAGCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCAGGAACAUUUUGGGAAUU-UUCCCGCAUUCACACACAA-CC
........-........(((.((.(((((((((....)))).((((((...........)))))).......))))))).))).......((((...-.))))..............-.. ( -28.40)
>DroSec_CAF1 73790 116 - 1
UAUAAAAA-CACAAAAAUCCA--GCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCAGGAACAUUUCGGGAAUU-UUCCCGCAUUCACACACAUCCC
........-........(((.--((((((((((....)))).((((((...........)))))).......))))))..)))......(((((...-.)))))................ ( -29.50)
>DroSim_CAF1 75573 116 - 1
UAUAAAAA-CACAAAAAUCCA--GCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCAGGAACAUUUCGGGAAUU-UUCCCGCAUUCACACACAUCCC
........-........(((.--((((((((((....)))).((((((...........)))))).......))))))..)))......(((((...-.)))))................ ( -29.50)
>DroEre_CAF1 75403 115 - 1
UAUAAAAA-CACAAAAAUCCA--GCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCAGAAGUAUUUUGGGAAUU-UUCCCGCAUUCACACACAA-CC
........-........((..--((((((((((....)))).((((((...........)))))).......))))))..))........((((...-.))))..............-.. ( -26.40)
>DroYak_CAF1 76920 117 - 1
UAUAAAAACCACAAAAAUCCA--GUCGAAGGAAAAGUUUUCAGUCGCAUAAACAUAAAUUGCGAUAGUAAUUUUCGGUCAGGAACAUUUUGGGAGUUUUUCCCGCAUUUACACACGA-CC
.....................--((((..((((((..(..((((((((...........))))))......((((.....)))).....))..)..)))))).(......)...)))-). ( -20.90)
>consensus
UAUAAAAA_CACAAAAAUCCA__GCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCAGGAACAUUUUGGGAAUU_UUCCCGCAUUCACACACAA_CC
.................(((...((((((((((....)))).((((((...........)))))).......))))))..)))......((((((...))))))................ (-26.52 = -25.84 +  -0.68)

alignment

secondary structure

dotplot

Window 9

Location	19,807,225 – 19,807,344
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.75
Mean single sequence MFE	-23.08
Consensus MFE	-19.38
Energy contribution	-18.50
Covariance contribution	-0.88
Combinations/Pair	1.20
Mean z-score	-1.49
Structure conservation index	0.84
SVM decision value	0.49
SVM RNA-class probability	0.757326
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19807225 119 - 22407834
UUUCCGUUUAUCCGAUUCUCUCCUCCUGUCGAACUUGAACUAUAAAAA-CACAAAAAUCCAGAGCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCA
.....(((((..((((...........))))....)))))........-............((.(((((((((....)))).((((((...........)))))).......))))))). ( -24.00)
>DroSec_CAF1 73829 117 - 1
CUUCCGUUUAUCUGAUUCUCUCCUCCUGUCGAACUUGAACUAUAAAAA-CACAAAAAUCCA--GCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCA
.....(((((..((((...........))))....)))))........-............--((((((((((....)))).((((((...........)))))).......)))))).. ( -22.00)
>DroSim_CAF1 75612 117 - 1
UUUCCGUUUAUCUGAUUCUCUCCUCCUGUCGAACUUGAACUAUAAAAA-CACAAAAAUCCA--GCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCA
.....(((((..((((...........))))....)))))........-............--((((((((((....)))).((((((...........)))))).......)))))).. ( -22.00)
>DroEre_CAF1 75441 117 - 1
UUUCCGUUUAUCUGGUUCUCUACUCGUGUCGAACUUGAACUAUAAAAA-CACAAAAAUCCA--GCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCA
.....((((.(.((((((.....(((...)))....)))))).).)))-)...........--((((((((((....)))).((((((...........)))))).......)))))).. ( -26.80)
>DroYak_CAF1 76959 118 - 1
UUUCAGUUUAUCUGGUUUGCUCAUCCUGUCGAACUUGAACUAUAAAAACCACAAAAAUCCA--GUCGAAGGAAAAGUUUUCAGUCGCAUAAACAUAAAUUGCGAUAGUAAUUUUCGGUCA
.....((((((((((...(((..((((.((((.((.((...................)).)--)))))))))..)))..))))....))))))..(((((((....)))))))....... ( -20.61)
>consensus
UUUCCGUUUAUCUGAUUCUCUCCUCCUGUCGAACUUGAACUAUAAAAA_CACAAAAAUCCA__GCCGAAGGAAAAGUUUCCAGUCGCAUAAACAUAAAUUGCGACAGUAAUUUUCGGUCA
.....(((((..((((...........))))....))))).......................((((((((((....)))).((((((...........)))))).......)))))).. (-19.38 = -18.50 +  -0.88)

alignment

secondary structure

dotplot

Window 0

Location	19,807,344 – 19,807,464
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.74
Mean single sequence MFE	-21.40
Consensus MFE	-19.10
Energy contribution	-18.86
Covariance contribution	-0.24
Combinations/Pair	1.16
Mean z-score	-1.35
Structure conservation index	0.89
SVM decision value	0.69
SVM RNA-class probability	0.822825
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19807344 120 + 22407834
CCUUUAACUUCUAUGUAAAUUUACAACUUUGCUAGUUUUGGCUUUCGAAAAACUUCAACCGGUCCUUUUUUGGUUGCUCCUGUGGCAUAAAGCCAAUCUAGACACACACAUAAAUACCAA
.............((((....))))....((((((..(((((((((((((((..((....))...)))))))((..(....)..))..)))))))).)))).))................ ( -21.70)
>DroSec_CAF1 73946 120 + 1
CCUUUAACUUCUAUGUAAAUUUACAACUUUGCUAGUUUUGGCUUUCGAAAAACUUCAACCGGUCCUUUUUUGGUUGCUCUUGUGGCAUAAAGCCAAUCUAGACACAUACAUAAAUACAAA
...........((((((......((....))((((..(((((((((((((((..((....))...)))))))((..(....)..))..)))))))).)))).....))))))........ ( -22.30)
>DroSim_CAF1 75729 120 + 1
CCUUUAACUUCUAUGUAAAUUUACAACUUUGCUAGUUUUGGCUUUCGAAAAACUUCAACCGGUCCUUUUUUGGUUGCUCCUGUGGCAUAAAGCCAAUCUAGACACACACAUAAGUACAAA
......((((...((((....))))....((((((..(((((((((((((((..((....))...)))))))((..(....)..))..)))))))).)))).)).......))))..... ( -22.60)
>DroEre_CAF1 75558 119 + 1
CCUUUAACUUCUAUGUAAAUUUACAACUUUGCUAGUUUUGGCUUUCGAAAAACUUCACCCGAGC-UUUUUUGGUUCCUUUUGUGGCAUAAAGCCAAUUUGGACACAGACAUAAAUACAAA
.............((((..((((...((.((((((..(((((((((((((((.(((....))).-)))))))((..(....)..))..)))))))).)))).)).))...)))))))).. ( -21.10)
>DroYak_CAF1 77077 116 + 1
CCUUUAACUUCUAUGUAAAUUUACAACUUUGCUAGUUUUGGCUUUCGAAAAACUUUAACUGAGC-U---UUGGUUCCUCUUGGGGCAUAAAGCCAAUUUAGACACACACAUAAAUACAAA
.............((((..((((......((((((..((((((((((((...(((.....))).-)---)))(((((....)))))..)))))))).)))).))......)))))))).. ( -19.30)
>consensus
CCUUUAACUUCUAUGUAAAUUUACAACUUUGCUAGUUUUGGCUUUCGAAAAACUUCAACCGGUCCUUUUUUGGUUGCUCUUGUGGCAUAAAGCCAAUCUAGACACACACAUAAAUACAAA
.............((((....))))....((((((..(((((((((((((((..((....))...)))))))(((((....)))))..)))))))).)))).))................ (-19.10 = -18.86 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:48 2006