Locus 7060

Sequence ID	X_DroMel_CAF1
Location	17,700,102 – 17,700,236
Length	134
Max. P	0.999937

overview

Window 2

Location	17,700,102 – 17,700,196
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-26.30
Consensus MFE	-26.50
Energy contribution	-26.34
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.23
Structure conservation index	1.01
SVM decision value	4.01
SVM RNA-class probability	0.999756
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17700102 94 - 22224390
UUGGGAAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGCAAAGCAAGCGAUAGCCGCUUUCUUUUGUGAUAAAAACAA
......(((((.(((.(((((.....))))).)))......(((((((((((.((...(....)....))))))))))))))))))........ ( -26.20)
>DroSec_CAF1 4263 93 - 1
UUGGGAAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGCA-AGCAAGCGAUAGCCGCUUUCUUUUGUGAUAAAAACAA
......(((((.(((.(((((.....))))).)))......(((((((((((.((.-..(....)...))))))))))))))))))........ ( -26.00)
>DroSim_CAF1 5327 93 - 1
UUGGGAAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGCA-AGCAAGCGAUAGCCGCUUUCUUUUGUGAUAAAAACAA
......(((((.(((.(((((.....))))).)))......(((((((((((.((.-..(....)...))))))))))))))))))........ ( -26.00)
>DroEre_CAF1 5137 93 - 1
UUGGGGAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGUG-AGCAAGCGGUAGCCGCUUUCUUUUGUGAUAAAAACAA
.((...(((((.(((.(((((.....))))).)))......(((((((((((.((.-.((.....)).)))))))))))))))))).....)). ( -26.20)
>DroYak_CAF1 5156 93 - 1
UUGGGAAUUACAGGGAUUUCGUGUGACGAAACCUCAGCGAAGAAGGAGAGCGAGCG-AGCAAGCGAUAGCCGCUUUCUUUUGUGAUAAAAACAA
......(((((.(((.(((((.....))))).)))......(((((((((((.((.-..(....)...))))))))))))))))))........ ( -27.10)
>consensus
UUGGGAAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGCA_AGCAAGCGAUAGCCGCUUUCUUUUGUGAUAAAAACAA
......(((((.(((.(((((.....))))).)))......(((((((((((.((...(....)....))))))))))))))))))........ (-26.50 = -26.34 +  -0.16)

alignment

secondary structure

dotplot

Window 3

Location	17,700,116 – 17,700,236
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.82
Mean single sequence MFE	-37.40
Consensus MFE	-36.18
Energy contribution	-36.18
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.70
Structure conservation index	0.97
SVM decision value	4.26
SVM RNA-class probability	0.999854
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17700116 120 + 22224390
AAAGAAAGCGGCUAUCGCUUGCUUUGCUCGCUCUCCUUCUUCGCUGAGGUUUCGUUACACGAAAUCCCUGUAAUUCCCAAAAGUUUGAGAAAGAGAGCGAGAAAGCCACAGUUACGUUAU
.....(((((.....)))))(((((.(((((((((.(((((.(((..((....((((((.(.....).))))))..))...)))..))))).)))))))))))))).............. ( -37.80)
>DroSec_CAF1 4277 119 + 1
AAAGAAAGCGGCUAUCGCUUGCU-UGCUCGCUCUCCUUCUUCGCUGAGGUUUCGUUACACGAAAUCCCUGUAAUUCCCAAAAGUUUGAGAAAGAGAGCGAGAAAGCCACAGUUACGUUAU
.....(((((.....)))))(((-(.(((((((((.(((((.(((..((....((((((.(.....).))))))..))...)))..))))).))))))))).)))).............. ( -37.20)
>DroSim_CAF1 5341 119 + 1
AAAGAAAGCGGCUAUCGCUUGCU-UGCUCGCUCUCCUUCUUCGCUGAGGUUUCGUUACACGAAAUCCCUGUAAUUCCCAAAAGUUUGAGAAAGAGAGCGAGAAAGCCACAGUUACGUUAU
.....(((((.....)))))(((-(.(((((((((.(((((.(((..((....((((((.(.....).))))))..))...)))..))))).))))))))).)))).............. ( -37.20)
>DroEre_CAF1 5151 119 + 1
AAAGAAAGCGGCUACCGCUUGCU-CACUCGCUCUCCUUCUUCGCUGAGGUUUCGUUACACGAAAUCCCUGUAAUCCCCAAAAGUUUGAGAAAGAGAGCGAGAAAGCCACAGUUACGUUAU
.....((((((...))))))(((-..(((((((((.(((((.(((..((....((((((.(.....).))))))..))...)))..))))).)))))))))..))).............. ( -37.70)
>DroYak_CAF1 5170 119 + 1
AAAGAAAGCGGCUAUCGCUUGCU-CGCUCGCUCUCCUUCUUCGCUGAGGUUUCGUCACACGAAAUCCCUGUAAUUCCCAAAAGUUUGAGAAAGAGAGCGAGAAAGCCACAGUUACGUUAU
.....(((((.....)))))(((-..(((((((((.((((..((.(.(((((((.....))))))).).))......(((....))))))).)))))))))..))).............. ( -37.10)
>consensus
AAAGAAAGCGGCUAUCGCUUGCU_UGCUCGCUCUCCUUCUUCGCUGAGGUUUCGUUACACGAAAUCCCUGUAAUUCCCAAAAGUUUGAGAAAGAGAGCGAGAAAGCCACAGUUACGUUAU
.....(((((.....)))))(((...(((((((((.((((..((.(.(((((((.....))))))).).))......(((....))))))).)))))))))..))).............. (-36.18 = -36.18 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	17,700,116 – 17,700,236
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.82
Mean single sequence MFE	-42.04
Consensus MFE	-40.62
Energy contribution	-40.30
Covariance contribution	-0.32
Combinations/Pair	1.06
Mean z-score	-3.29
Structure conservation index	0.97
SVM decision value	4.68
SVM RNA-class probability	0.999937
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17700116 120 - 22224390
AUAACGUAACUGUGGCUUUCUCGCUCUCUUUCUCAAACUUUUGGGAAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGCAAAGCAAGCGAUAGCCGCUUUCUUU
..............((((((((((((((((((((.......((.......))(((.(((((.....))))).)))...).)))))))))))))).)))))(((((.....)))))..... ( -42.00)
>DroSec_CAF1 4277 119 - 1
AUAACGUAACUGUGGCUUUCUCGCUCUCUUUCUCAAACUUUUGGGAAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGCA-AGCAAGCGAUAGCCGCUUUCUUU
..............((((.(((((((((((((((.......((.......))(((.(((((.....))))).)))...).)))))))))))))).)-)))(((((.....)))))..... ( -41.40)
>DroSim_CAF1 5341 119 - 1
AUAACGUAACUGUGGCUUUCUCGCUCUCUUUCUCAAACUUUUGGGAAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGCA-AGCAAGCGAUAGCCGCUUUCUUU
..............((((.(((((((((((((((.......((.......))(((.(((((.....))))).)))...).)))))))))))))).)-)))(((((.....)))))..... ( -41.40)
>DroEre_CAF1 5151 119 - 1
AUAACGUAACUGUGGCUUUCUCGCUCUCUUUCUCAAACUUUUGGGGAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGUG-AGCAAGCGGUAGCCGCUUUCUUU
..............((((.(((((((((((((((.......((.......))(((.(((((.....))))).)))...).)))))))))))))).)-)))((((((...))))))..... ( -43.50)
>DroYak_CAF1 5170 119 - 1
AUAACGUAACUGUGGCUUUCUCGCUCUCUUUCUCAAACUUUUGGGAAUUACAGGGAUUUCGUGUGACGAAACCUCAGCGAAGAAGGAGAGCGAGCG-AGCAAGCGAUAGCCGCUUUCUUU
...........((((((.((((((((((((((((.......((.......))(((.(((((.....))))).)))...).)))))))))))))((.-.....)))).))))))....... ( -41.90)
>consensus
AUAACGUAACUGUGGCUUUCUCGCUCUCUUUCUCAAACUUUUGGGAAUUACAGGGAUUUCGUGUAACGAAACCUCAGCGAAGAAGGAGAGCGAGCA_AGCAAGCGAUAGCCGCUUUCUUU
...........((((((.((((((((((((((((.......((.......))(((.(((((.....))))).)))...).)))))))))))))((.......)))).))))))....... (-40.62 = -40.30 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:13 2006