Locus 97

Sequence ID	4_DroMel_CAF1
Location	724,364 – 724,574
Length	210
Max. P	0.778934

overview

Window 1

Location	724,364 – 724,457
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	91.89
Mean single sequence MFE	-14.18
Consensus MFE	-12.92
Energy contribution	-12.20
Covariance contribution	-0.72
Combinations/Pair	1.29
Mean z-score	-1.20
Structure conservation index	0.91
SVM decision value	0.25
SVM RNA-class probability	0.654044
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 724364 93 - 1281640
CACACCCCCCCCCCCCCCAGCAAUUACACACAUGUUGCAUUCCAUUUGAAUUCAAGCUGGCCAGACAAGUUGCCAGCAGCACACUCGUCCAAU
................(((((.....((....))(((.((((.....)))).))))))))...(((.((((((.....))).))).))).... ( -15.40)
>DroSec_CAF1 12606 86 - 1
CACACUC-------CUCCAGCAAUUACACACAUGUUGCAUUCCAUUUGAAUUCAAGCUGGCCUGACAAGUUGCCAGCAGCACACUCGUCCAAU
.......-------.....((.............(((.((((.....)))).)))((((((((....))..)))))).))............. ( -15.90)
>DroSim_CAF1 962 86 - 1
CACACUC-------CUCCAGCAAUUACACACAUGUUGCAUUCCAUUUGAAUUCAAGCUGGCCAGACAAGUUGCCAGCAGCACACUCGUCCAAU
.......-------..(((((.....((....))(((.((((.....)))).))))))))...(((.((((((.....))).))).))).... ( -15.20)
>DroEre_CAF1 13712 86 - 1
CACACUC-------UUCCAGCAAUUACACACAUGUUGCAUUCCAUUUGAAUUUAAGCUGGCCAAACAAGUUGCCGGCAGCACACUCGUCCAAU
.......-------.....(((((.........))))).................((((((..........))))))................ ( -13.90)
>DroYak_CAF1 18311 86 - 1
CACACUC-------CUCCAUCAAUUACACACAUGUUGCAUUCCAUUUGAAUUCAAGCUGGCCAAACAAGUUGCUGGUAGCACACUCGUCCAAU
.......-------(((((.(((((.......((((.....(((((((....)))).)))...))))))))).))).)).............. ( -10.51)
>consensus
CACACUC_______CUCCAGCAAUUACACACAUGUUGCAUUCCAUUUGAAUUCAAGCUGGCCAGACAAGUUGCCAGCAGCACACUCGUCCAAU
................................(((.((.......(((....)))((((((..........)))))).))))).......... (-12.92 = -12.20 +  -0.72)

alignment

secondary structure

dotplot

Window 2

Location	724,457 – 724,574
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.42
Mean single sequence MFE	-42.94
Consensus MFE	-30.98
Energy contribution	-31.86
Covariance contribution	0.88
Combinations/Pair	1.14
Mean z-score	-1.90
Structure conservation index	0.72
SVM decision value	0.55
SVM RNA-class probability	0.778934
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 724457 117 + 1281640
GCACUGGGCGACUUCUCGAAAGGCGGUGAAAGCGGCAGGCGCUGCACCGUUUACACACAGUUUCUUGCUGGAAGGAACAACAUCCAGUUCCAGACCAGCACUUUCAUGU---CUGUUCAG
...(((((((((.....(((((((((((..((((.....)))).))))))...............((((((..(((((........)))))...)))))))))))..))---).)))))) ( -42.20)
>DroSec_CAF1 12692 120 + 1
GCACUGGGCGCCUUCUCGGAAGGCGGUAAAAGCGGUAGCUACUGCACCGUUUACACACAGCUUCUUGCUGGAAGGAACAACAUCCAGUUCCAGACCAGCAGUUUCAUGUAGACAGUUCAG
...((((((((((((...))))))(((....(((((....))))))))(((((((...((((....(((((..(((((........)))))...)))))))))...))))))).)))))) ( -44.60)
>DroSim_CAF1 1048 120 + 1
GCACUGGGCGCCUUCUCGGAAGGCGGUGAAAGCGGUAGCUACUGCACCGUUUACACACAGCUUCUUGCUGGAAGGAACAACAUCCAGUUCCAGACCAGCAGUUUCAUGUAGACAGUUCAG
...((((((((((((...)))))).(((.(((((((.((....))))))))).)))(((.....(((((((..(((((........)))))...))))))).....))).....)))))) ( -47.40)
>DroEre_CAF1 13798 120 + 1
AUGCCGGGCGCCUUUUCGGGAGGCGGUGAGAGCGGCAGCCGCUGCACCGUUUACAAGCAGCAUCUUACUGGAAGGAAUAGCAUUCAGUUCCAGACCAAAUUUUCCAUGUAGACUGUUCAG
.....(((((((((.....)))))((((..(((((...))))).))))(((((((............((((((.((((...))))..)))))).............))))))).)))).. ( -37.71)
>DroYak_CAF1 18397 120 + 1
AGGCCGGGCGCCUUCUGGAGACGCGGUGAGCGCGGCAACCGCUGCACCGUUUAUAAACAGCAUCUCACGGGAAGGAACAACAUUCAGUUCCAGAACAGGAGUUCCUUGUAGACAGUUCAG
.(((.....)))(((((((((.((((((((((.(....))))).))))(((....))).)).)))).))))).(((((........))))).(((((((....)))((....)))))).. ( -42.80)
>consensus
GCACUGGGCGCCUUCUCGGAAGGCGGUGAAAGCGGCAGCCGCUGCACCGUUUACACACAGCUUCUUGCUGGAAGGAACAACAUCCAGUUCCAGACCAGCAGUUUCAUGUAGACAGUUCAG
...(((((((((((.....)))))(((....(((((....))))))))(((((((..((((.....))))...(((((........)))))...............))))))).)))))) (-30.98 = -31.86 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:32 2006