Locus 2067

Sequence ID	X_DroMel_CAF1
Location	5,667,476 – 5,667,593
Length	117
Max. P	0.753543

overview

Window 9

Location	5,667,476 – 5,667,593
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.56
Mean single sequence MFE	-30.25
Consensus MFE	-23.19
Energy contribution	-25.75
Covariance contribution	2.56
Combinations/Pair	1.03
Mean z-score	-1.77
Structure conservation index	0.77
SVM decision value	0.44
SVM RNA-class probability	0.738822
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5667476 117 + 22224390
--UUUUU-UUUUUUUUACAUUUCGGUUAUAUUUGAUGAUGGCUUGGGCUGGUGCGAAAAAGUUGCGCAGUCGCCCACAUAAUUAUCGGUUUGAUUUAUGGCAGCAUUUUCGCAGCCAAUU
--.....-...............(((((...((((((((....(((((..((((((.....))))))....)))))....))))))))..)))))..((((.((......)).))))... ( -30.70)
>DroSec_CAF1 6567 119 + 1
AAUUUUU-UUUUUUUUACAUUUCGGUUAUAUUUGAUGAUGGGUUGGGCUGGUGCGAAAAAGUUGCGCAUUCGCCCACAUAAUUAUCGGUUUGAUUUAUGGCAGCAUUUUCGCAGCCAAUU
.......-...............(((((...((((((((..((.((((..(((((.........)))))..))))))...))))))))..)))))..((((.((......)).))))... ( -32.00)
>DroAna_CAF1 10674 112 + 1
AAUUUUUGUUGAUUUUUCGCCUCGGUUUUUU--------CGGUUUCGCGGGUGCGAAAAAGUUGCACAGUCGCCCACAUAAUUAUCGGUUUGAUUUAUGGCAGCAUUUUCGCAGCCAAUU
..................((.((((.....)--------)))....))((.((((((((.(((((..(((((((............)))..))))....))))).)))))))).)).... ( -27.60)
>DroSim_CAF1 6973 118 + 1
AAUUUUU-U-UUUUUUACAUUUCGGUUAUAUUUGAUGAUGGCUUGGGCUGGUGCGAAAAAGUUGCGCAGUCGCCCACAUAAUUAUCGGUUUGAUUUAUGGCAGCAUUUUCGCAGCCAAUU
.......-.-.............(((((...((((((((....(((((..((((((.....))))))....)))))....))))))))..)))))..((((.((......)).))))... ( -30.70)
>consensus
AAUUUUU_UUUUUUUUACAUUUCGGUUAUAUUUGAUGAUGGCUUGGGCUGGUGCGAAAAAGUUGCGCAGUCGCCCACAUAAUUAUCGGUUUGAUUUAUGGCAGCAUUUUCGCAGCCAAUU
.......................(((((...((((((((....(((((..((((((.....))))))....)))))....))))))))..)))))..((((.((......)).))))... (-23.19 = -25.75 +   2.56)

alignment

secondary structure

dotplot

Window 0

Location	5,667,476 – 5,667,593
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.56
Mean single sequence MFE	-22.23
Consensus MFE	-18.69
Energy contribution	-18.75
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-1.64
Structure conservation index	0.84
SVM decision value	0.48
SVM RNA-class probability	0.753543
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5667476 117 - 22224390
AAUUGGCUGCGAAAAUGCUGCCAUAAAUCAAACCGAUAAUUAUGUGGGCGACUGCGCAACUUUUUCGCACCAGCCCAAGCCAUCAUCAAAUAUAACCGAAAUGUAAAAAAAA-AAAAA--
...((((.((......)).))))...........(((.......(((((...((((.........))))...))))).......))).........................-.....-- ( -22.64)
>DroSec_CAF1 6567 119 - 1
AAUUGGCUGCGAAAAUGCUGCCAUAAAUCAAACCGAUAAUUAUGUGGGCGAAUGCGCAACUUUUUCGCACCAGCCCAACCCAUCAUCAAAUAUAACCGAAAUGUAAAAAAAA-AAAAAUU
...((((.((......)).))))...........(((.......(((((...((((.........))))...))))).......))).........................-....... ( -22.64)
>DroAna_CAF1 10674 112 - 1
AAUUGGCUGCGAAAAUGCUGCCAUAAAUCAAACCGAUAAUUAUGUGGGCGACUGUGCAACUUUUUCGCACCCGCGAAACCG--------AAAAAACCGAGGCGAAAAAUCAACAAAAAUU
..((.((((((....((((..((((((((.....)))..)))))..))))....))).....((((((....))))))...--------..........))).))............... ( -21.00)
>DroSim_CAF1 6973 118 - 1
AAUUGGCUGCGAAAAUGCUGCCAUAAAUCAAACCGAUAAUUAUGUGGGCGACUGCGCAACUUUUUCGCACCAGCCCAAGCCAUCAUCAAAUAUAACCGAAAUGUAAAAAA-A-AAAAAUU
...((((.((......)).))))...........(((.......(((((...((((.........))))...))))).......))).......................-.-....... ( -22.64)
>consensus
AAUUGGCUGCGAAAAUGCUGCCAUAAAUCAAACCGAUAAUUAUGUGGGCGACUGCGCAACUUUUUCGCACCAGCCCAACCCAUCAUCAAAUAUAACCGAAAUGUAAAAAAAA_AAAAAUU
..((((.((((((((.(.(((((((((((.....)))..)))))...((....))))).).))))))))))))............................................... (-18.69 = -18.75 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:25 2006