Locus 5171

Sequence ID	X_DroMel_CAF1
Location	13,487,553 – 13,487,669
Length	116
Max. P	0.885214

overview

Window 1

Location	13,487,553 – 13,487,669
Length	116
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	74.91
Mean single sequence MFE	-16.05
Consensus MFE	-3.14
Energy contribution	-4.82
Covariance contribution	1.68
Combinations/Pair	1.07
Mean z-score	-1.88
Structure conservation index	0.20
SVM decision value	0.94
SVM RNA-class probability	0.885214
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13487553 116 + 22224390
UUUUAAAACCACAAAUUGUGUAACCAAAGUGCAGAGAUAGAUGCACCUUAGGAGCACAUAAUAUUGGCA-AAAGCAUUGCCAAUUGAUUUACAUCUGAUUUUAAUAACCAAAUAAUU
..((((((.((.....(((((..(.((.(((((........))))).)).)..)))))....(((((((-(.....))))))))...........)).))))))............. ( -23.10)
>DroSec_CAF1 20020 104 + 1
AUUUAAAACCACAAAUUAUGUAACCAAACUGAAGAACUAGAUGC-----------ACAUAAUAUUGGCA-AAAGCAUUGCCAAUUGAUUUACAUCUAAAUUGCA-AACCAAAUAAUU
..................(((((.....(....)...((((((.-----------.......(((((((-(.....)))))))).......))))))..)))))-............ ( -14.96)
>DroSim_CAF1 13164 104 + 1
AUUUAAAACCACAAAUUGUGUAACCAAACUGCAGAACUAGAUGC-----------ACAUAAUAUUGGCA-AAAGCAUUGCCAAUUGAUUUACAUAUAAAUUGCA-AACCAAAUAAUU
................(((((((......((((........)))-----------)......(((((((-(.....))))))))....))))))).........-............ ( -16.30)
>DroEre_CAF1 3963 98 + 1
AUUUAAAACCACAAAACCUGUAACCAAACUGCAGAACUAGAUACACCUUAGGA----------------CAAAAUAAUGCCUCUUGGUUUACAUCAAAUUU-UU-AACUAAAUA-UU
.....((((((......(((((.......)))))...............(((.----------------((......)))))..))))))...........-..-.........-.. ( -11.00)
>DroYak_CAF1 4276 114 + 1
AUUUAAAACCACAAAAUGUGUAAACAAACUGCAGAACUAGUUACACCUUUGGAUCACAAAAUAUUGGUAAAAAAUAAUGCCACUUGGUUUACAACAAAAUU-UA-GACUAAAUA-UU
.....((((((((((..(((((.....((((......))))))))).)))).............(((((........)))))..))))))...........-..-.........-.. ( -14.90)
>consensus
AUUUAAAACCACAAAUUGUGUAACCAAACUGCAGAACUAGAUGCACCUU_GGA__ACAUAAUAUUGGCA_AAAGCAUUGCCAAUUGAUUUACAUCUAAAUU_CA_AACCAAAUAAUU
..................(((((.....(((......)))......................(((((((........)))))))....)))))........................ ( -3.14 =  -4.82 +   1.68)

alignment

secondary structure

dotplot

Window 2

Location	13,487,553 – 13,487,669
Length	116
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	74.91
Mean single sequence MFE	-22.90
Consensus MFE	-7.93
Energy contribution	-8.21
Covariance contribution	0.28
Combinations/Pair	1.28
Mean z-score	-1.82
Structure conservation index	0.35
SVM decision value	0.31
SVM RNA-class probability	0.681901
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13487553 116 - 22224390
AAUUAUUUGGUUAUUAAAAUCAGAUGUAAAUCAAUUGGCAAUGCUUU-UGCCAAUAUUAUGUGCUCCUAAGGUGCAUCUAUCUCUGCACUUUGGUUACACAAUUUGUGGUUUUAAAA
...(((((((((.....))))))))).((((((((((((((.....)-)))))))....((((...((((((((((........))))))))))...)))).....))))))..... ( -33.60)
>DroSec_CAF1 20020 104 - 1
AAUUAUUUGGUU-UGCAAUUUAGAUGUAAAUCAAUUGGCAAUGCUUU-UGCCAAUAUUAUGU-----------GCAUCUAGUUCUUCAGUUUGGUUACAUAAUUUGUGGUUUUAAAU
....((((((.(-..(((.(((((((((.....((((((((.....)-)))))))......)-----------)))))))).......((......)).....)))..)..)))))) ( -22.80)
>DroSim_CAF1 13164 104 - 1
AAUUAUUUGGUU-UGCAAUUUAUAUGUAAAUCAAUUGGCAAUGCUUU-UGCCAAUAUUAUGU-----------GCAUCUAGUUCUGCAGUUUGGUUACACAAUUUGUGGUUUUAAAU
.......(((((-((((.......)))))))))((((((((.....)-))))))).......-----------.....(((..(..(((.(((......))).)))..)..)))... ( -24.80)
>DroEre_CAF1 3963 98 - 1
AA-UAUUUAGUU-AA-AAAUUUGAUGUAAACCAAGAGGCAUUAUUUUG----------------UCCUAAGGUGUAUCUAGUUCUGCAGUUUGGUUACAGGUUUUGUGGUUUUAAAU
.(-((((.(((.-..-..))).)))))((((((.(((((......(((----------------(.(((((.((((........)))).)))))..))))))))).))))))..... ( -15.00)
>DroYak_CAF1 4276 114 - 1
AA-UAUUUAGUC-UA-AAUUUUGUUGUAAACCAAGUGGCAUUAUUUUUUACCAAUAUUUUGUGAUCCAAAGGUGUAACUAGUUCUGCAGUUUGUUUACACAUUUUGUGGUUUUAAAU
..-.((((((.(-((-.....(((.((((((.(((..(((..(((..((((.....(((((.....)))))..))))..)))..)))..)))))))))))).....)))..)))))) ( -18.30)
>consensus
AAUUAUUUGGUU_UA_AAUUUAGAUGUAAAUCAAUUGGCAAUGCUUU_UGCCAAUAUUAUGU__UCC_AAGGUGCAUCUAGUUCUGCAGUUUGGUUACACAAUUUGUGGUUUUAAAU
........................(((((.((((...(((..(((...(((......................)))...)))..)))...))))))))).................. ( -7.93 =  -8.21 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:33 2006