Locus 6416

Sequence ID	2L_DroMel_CAF1
Location	18,026,048 – 18,026,177
Length	129
Max. P	0.896503

overview

Window 9

Location	18,026,048 – 18,026,141
Length	93
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	83.19
Mean single sequence MFE	-27.57
Consensus MFE	-17.97
Energy contribution	-18.47
Covariance contribution	0.50
Combinations/Pair	1.10
Mean z-score	-2.86
Structure conservation index	0.65
SVM decision value	0.55
SVM RNA-class probability	0.778928
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18026048 93 + 22407834
AAAGCGAA-GGGAACAGCGGAAAUGAUGCGGCUCAUUUGUGUGCUACCACAAAAUGGUGGUGGCACAGAGGAAGUGGAAUAAAUGCAGUGAUUA
...(((..-(((....(((.......)))..))).(((.(((((((((((......))))))))))).)))............)))........ ( -28.00)
>DroSec_CAF1 241963 93 + 1
AAAGCGAA-GGGAACAGCGGAAAUGAUGCGGCUCAUUUGUGUGCCACCACAAAAUGGUGGUGGCACAGGGGAAGUGGGAUAAGUGCAGUGGUUA
...((...-(....).))........((((.(((((((.(((((((((((......)))))))))))....))))))).....))))....... ( -30.80)
>DroSim_CAF1 241972 93 + 1
AAAGCGAA-GGGAACAGCGGAAAUGAUGCGGCUCAUUUGUGUGCCACCACAAAAUGGUGGUGGCACAGAGGAAGUGGGAUAAGUGCAGUGAUUA
...((...-(....).))........((((.(((((((.(((((((((((......)))))))))))....))))))).....))))....... ( -30.80)
>DroEre_CAF1 234567 94 + 1
AAAGCGAAGGGGAGAAGCGGAAGUGAUGCGGCUCAUUUGUGUGCGACCACAAAAUGGUGGUGGCACUGAGGAUGUGGCACAAAUGCAGUGAUUA
...(((....(.(...((....))..).).((((((((..((((.(((((......))))).))))...))))).))).....)))........ ( -29.20)
>DroYak_CAF1 251345 94 + 1
AAAGCCAGAGGGAGAAGCGGAAAUGAUGCGGCUCAUUUGUGUGCGACCACAACAUGGUGGUGGCACUGAGGAUGUGGCACAAAUGCAGUGAUUA
...((((....(((..(((.......)))..)))((((..((((.(((((......))))).))))...)))).))))................ ( -29.80)
>DroAna_CAF1 228847 84 + 1
AUAGAGAG-GGGGUGGCCGGAAGUGAUGCAGCUCAUUUGUGUCAGACCACAAAAUGGAGGAGAGAC--------UGCCAUA-AUGCAGGAAUUA
........-((..((((.(.((((((......)))))).)))))..)).................(--------(((....-..))))...... ( -16.80)
>consensus
AAAGCGAA_GGGAACAGCGGAAAUGAUGCGGCUCAUUUGUGUGCGACCACAAAAUGGUGGUGGCACAGAGGAAGUGGCAUAAAUGCAGUGAUUA
...(((((.(((....(((.......)))..))).)))))((((.(((((......))))).))))............................ (-17.97 = -18.47 +   0.50)

alignment

secondary structure

dotplot

Window 0

Location	18,026,048 – 18,026,141
Length	93
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	83.19
Mean single sequence MFE	-21.49
Consensus MFE	-14.63
Energy contribution	-15.35
Covariance contribution	0.72
Combinations/Pair	1.06
Mean z-score	-3.47
Structure conservation index	0.68
SVM decision value	0.99
SVM RNA-class probability	0.896503
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18026048 93 - 22407834
UAAUCACUGCAUUUAUUCCACUUCCUCUGUGCCACCACCAUUUUGUGGUAGCACACAAAUGAGCCGCAUCAUUUCCGCUGUUCCC-UUCGCUUU
........((.................(((((.(((((......))))).))))).....((((.((.........)).))))..-...))... ( -20.40)
>DroSec_CAF1 241963 93 - 1
UAACCACUGCACUUAUCCCACUUCCCCUGUGCCACCACCAUUUUGUGGUGGCACACAAAUGAGCCGCAUCAUUUCCGCUGUUCCC-UUCGCUUU
........((.................(((((((((((......))))))))))).....((((.((.........)).))))..-...))... ( -26.90)
>DroSim_CAF1 241972 93 - 1
UAAUCACUGCACUUAUCCCACUUCCUCUGUGCCACCACCAUUUUGUGGUGGCACACAAAUGAGCCGCAUCAUUUCCGCUGUUCCC-UUCGCUUU
........((.................(((((((((((......))))))))))).....((((.((.........)).))))..-...))... ( -26.90)
>DroEre_CAF1 234567 94 - 1
UAAUCACUGCAUUUGUGCCACAUCCUCAGUGCCACCACCAUUUUGUGGUCGCACACAAAUGAGCCGCAUCACUUCCGCUUCUCCCCUUCGCUUU
........((((((((............((((.(((((......))))).))))))))))(((..((.........))..)))......))... ( -18.50)
>DroYak_CAF1 251345 94 - 1
UAAUCACUGCAUUUGUGCCACAUCCUCAGUGCCACCACCAUGUUGUGGUCGCACACAAAUGAGCCGCAUCAUUUCCGCUUCUCCCUCUGGCUUU
................((((........((((.(((((......))))).))))..((((((......)))))).............))))... ( -22.20)
>DroAna_CAF1 228847 84 - 1
UAAUUCCUGCAU-UAUGGCA--------GUCUCUCCUCCAUUUUGUGGUCUGACACAAAUGAGCUGCAUCACUUCCGGCCACCCC-CUCUCUAU
......(((...-....(((--------(.(((........((((((......)))))).)))))))........))).......-........ ( -14.06)
>consensus
UAAUCACUGCAUUUAUGCCACUUCCUCUGUGCCACCACCAUUUUGUGGUCGCACACAAAUGAGCCGCAUCAUUUCCGCUGUUCCC_UUCGCUUU
........((..................((((.(((((......))))).))))..((((((......))))))..))................ (-14.63 = -15.35 +   0.72)

alignment

secondary structure

dotplot

Window 1

Location	18,026,069 – 18,026,177
Length	108
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	81.60
Mean single sequence MFE	-32.85
Consensus MFE	-21.52
Energy contribution	-23.13
Covariance contribution	1.61
Combinations/Pair	1.27
Mean z-score	-2.56
Structure conservation index	0.66
SVM decision value	0.86
SVM RNA-class probability	0.868443
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18026069 108 + 22407834
AUGAUGCGGCUCAUUUGUGUGCUACCACAAAAUGGUGGUGGCACAGAGGAAGUGGAAUAAAUGCAGUGAUUAAGGGGAGGACAGUUGGUUAACGCUUCCAAUUAGAAA
......(.(((..(((.(((((((((((......))))))))))).))).))).)..............((((..(((((...(((....))).)))))..))))... ( -32.70)
>DroSec_CAF1 241984 108 + 1
AUGAUGCGGCUCAUUUGUGUGCCACCACAAAAUGGUGGUGGCACAGGGGAAGUGGGAUAAGUGCAGUGGUUAAGGGGAGGACAGUUGGUUAACGCUUCCAAUUAAAAA
....((((.(((((((.(((((((((((......)))))))))))....))))))).....))))....((((..(((((...(((....))).)))))..))))... ( -38.20)
>DroSim_CAF1 241993 108 + 1
AUGAUGCGGCUCAUUUGUGUGCCACCACAAAAUGGUGGUGGCACAGAGGAAGUGGGAUAAGUGCAGUGAUUAAGGGGAGGACAGUUGGUUAACGCUUCCAAUUAAAAA
....((((.(((((((.(((((((((((......)))))))))))....))))))).....))))....((((..(((((...(((....))).)))))..))))... ( -38.30)
>DroEre_CAF1 234589 108 + 1
GUGAUGCGGCUCAUUUGUGUGCGACCACAAAAUGGUGGUGGCACUGAGGAUGUGGCACAAAUGCAGUGAUUAAGGGGAGGACAGUUGGUAAACGCUUUCCAUUAGAAA
....((((((((((((..((((.(((((......))))).))))...))))).))).....))))....((((.((((((...(((....))).)))))).))))... ( -34.00)
>DroYak_CAF1 251367 108 + 1
AUGAUGCGGCUCAUUUGUGUGCGACCACAACAUGGUGGUGGCACUGAGGAUGUGGCACAAAUGCAGUGAUUAAGGGGAGGACAGUUGGUAAACGCUUCCAAUUAGAAA
....((((((((((((..((((.(((((......))))).))))...))))).))).....))))....((((..(((((...(((....))).)))))..))))... ( -34.90)
>DroPer_CAF1 338430 90 + 1
GCGAUG---CUCAUUUGUGUGCGACCACAAAAUGGGGGCUAAAUGGAGGCUAUGG---------AGGCGGUCAGGGGAAGA------GUAAAUGCUGGCGAUUAACUU
((....---(((((((.((((....)))))))))))((((.......))))....---------..)).(((((.(.....------.....).)))))......... ( -19.00)
>consensus
AUGAUGCGGCUCAUUUGUGUGCGACCACAAAAUGGUGGUGGCACAGAGGAAGUGGCAUAAAUGCAGUGAUUAAGGGGAGGACAGUUGGUAAACGCUUCCAAUUAAAAA
....((((..((((((.(((((((((((......))))))))))).))...))))......))))....((((..(((((...(((....))).)))))..))))... (-21.52 = -23.13 +   1.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:30 2006