Locus 7031

Sequence ID	X_DroMel_CAF1
Location	17,594,179 – 17,594,395
Length	216
Max. P	0.999693

overview

Window 9

Location	17,594,179 – 17,594,276
Length	97
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	79.33
Mean single sequence MFE	-44.38
Consensus MFE	-24.96
Energy contribution	-25.90
Covariance contribution	0.94
Combinations/Pair	1.08
Mean z-score	-2.76
Structure conservation index	0.56
SVM decision value	1.75
SVM RNA-class probability	0.975377
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17594179 97 + 22224390
UAACCUUCCACUCCGUGGCCACGCCCACGCCCCCGAAACCUGCC----------AGCAAAAGGGA------UGG-GGGGGGGGGGGGGCAGUGGAAGUGGUGGAAUAACAGAGA
...((..((((((((..(((.(.(((.(.(((((.(..(((...----------......)))..------).)-)))).)))).))))..))).))))).))........... ( -46.50)
>DroSec_CAF1 13526 97 + 1
GAACCUUCCACUCCGUGGCCACGCCCACGCCCCCGAAACCUGCCCACUCAGGUAAGCAAAAGGGG------UG-----------GAGGCCGUGGAAGUGGUGGAAUAACAGAGA
.....((((((..(....(((((((..((((((.(..(((((......)))))...)....))))------))-----------..)).)))))..)..))))))......... ( -38.90)
>DroSim_CAF1 32167 97 + 1
GAACCUUCCACUCCGUGGCCACGCCCACGCCCCCGAAACCUGCCCACUCAGGUAAGCAAAAGGGG------UG-----------GAGGCCGUGGAAGUGGUGGAAUAACAGAGA
.....((((((..(....(((((((..((((((.(..(((((......)))))...)....))))------))-----------..)).)))))..)..))))))......... ( -38.90)
>DroEre_CAF1 20142 112 + 1
GAACCUUCCACUGCGUGGCCACGCCCACGCCCCU-GAAGCUGCCCACUCAGGUAGGCAAAAGGGGCUGCGGUGGAGGAGGGGGAGUGGCAGUGGCAGUGGUGGAAUAACCGAG-
.....((((((..(...(((((..((((.(((((-....((..(((((...((((.(......).))))))))).)).))))).))))..))))).)..))))))........- ( -53.20)
>consensus
GAACCUUCCACUCCGUGGCCACGCCCACGCCCCCGAAACCUGCCCACUCAGGUAAGCAAAAGGGG______UG___________GAGGCAGUGGAAGUGGUGGAAUAACAGAGA
...((..(((((((((((((..((....))((((.....((..((.....))..)).....)))).....................)))))))).))))).))........... (-24.96 = -25.90 +   0.94)

alignment

secondary structure

dotplot

Window 0

Location	17,594,179 – 17,594,276
Length	97
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	79.33
Mean single sequence MFE	-42.00
Consensus MFE	-32.67
Energy contribution	-32.80
Covariance contribution	0.13
Combinations/Pair	1.12
Mean z-score	-2.18
Structure conservation index	0.78
SVM decision value	1.75
SVM RNA-class probability	0.975669
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17594179 97 - 22224390
UCUCUGUUAUUCCACCACUUCCACUGCCCCCCCCCCCCC-CCA------UCCCUUUUGCU----------GGCAGGUUUCGGGGGCGUGGGCGUGGCCACGGAGUGGAAGGUUA
..(((.(((((((.((((.(((((.((((((....((..-(((------.(......).)----------))..))....))))))))))).))))....))))))).)))... ( -38.50)
>DroSec_CAF1 13526 97 - 1
UCUCUGUUAUUCCACCACUUCCACGGCCUC-----------CA------CCCCUUUUGCUUACCUGAGUGGGCAGGUUUCGGGGGCGUGGGCGUGGCCACGGAGUGGAAGGUUC
..(((.(((((((.((((.((((((.((((-----------(.------.....(((((((((....)))))))))....))))))))))).))))....))))))).)))... ( -40.10)
>DroSim_CAF1 32167 97 - 1
UCUCUGUUAUUCCACCACUUCCACGGCCUC-----------CA------CCCCUUUUGCUUACCUGAGUGGGCAGGUUUCGGGGGCGUGGGCGUGGCCACGGAGUGGAAGGUUC
..(((.(((((((.((((.((((((.((((-----------(.------.....(((((((((....)))))))))....))))))))))).))))....))))))).)))... ( -40.10)
>DroEre_CAF1 20142 112 - 1
-CUCGGUUAUUCCACCACUGCCACUGCCACUCCCCCUCCUCCACCGCAGCCCCUUUUGCCUACCUGAGUGGGCAGCUUC-AGGGGCGUGGGCGUGGCCACGCAGUGGAAGGUUC
-...((.....)).(((((((....(((((.(((...........((.((((((.((((((((....))))))))....-))))))))))).)))))...)))))))....... ( -49.30)
>consensus
UCUCUGUUAUUCCACCACUUCCACGGCCUC___________CA______CCCCUUUUGCUUACCUGAGUGGGCAGGUUUCGGGGGCGUGGGCGUGGCCACGGAGUGGAAGGUUC
.................(((((((.........................((((((((((((((....)))))))))....)))))(((((......)))))..))))))).... (-32.67 = -32.80 +   0.13)

alignment

secondary structure

dotplot

Window 1

Location	17,594,276 – 17,594,395
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.70
Mean single sequence MFE	-35.78
Consensus MFE	-33.62
Energy contribution	-33.70
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-2.32
Structure conservation index	0.94
SVM decision value	3.90
SVM RNA-class probability	0.999693
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17594276 119 + 22224390
AAAAGGGCCGCACCAUUUGCGGCUAAUUUUGUAAAUCAUGAUAUCGUAAUUAAUUUUUGCAGCCUUCGCGCUGCAAACAGACGUGGAAUAAGGGAACCCUUUGCCGCCUACGGAUUCCC-
.....(((((((.....)))))))...................(((((.......((((((((......)))))))).....((((...((((....))))..)))).)))))......- ( -37.00)
>DroSec_CAF1 13623 118 + 1
AAAAGGGCCGCACCAUUUGCGGCUAAUUUUGUAAAUCAUGAUAUCGUAAUUAAUUUUUGCAGCCUUCGCGCUGCAAACAGACGUGGAAUAAGGUAACCCUUCGCCGCCUACGG-UUCCC-
.....(((((((.....)))))))...............((.((((((.......((((((((......)))))))).....((((...((((....))))..)))).)))))-)))..- ( -35.50)
>DroSim_CAF1 32264 118 + 1
AAAAGGGCCGCACCAUUUGCGGCUAAUUUUGUAAAUCAUGAUAUCGUAAUUAAUUUUUGCAGCCUUCGCGGUGCAAACAGACGUGGAAUAAGGUAACCCUUCGCCGCCUACGG-UUCCC-
.....(((((((.....)))))))...............((.((((((.......((((((.((.....)))))))).....((((...((((....))))..)))).)))))-)))..- ( -32.00)
>DroEre_CAF1 20254 118 + 1
AAAAAGGCCGCACCAUUUGCGGCUAAUUUUGUAAAUCAUGAUAUCGUAAUUAAUUUUUGCAGCCUUCGCGUUGCAAACAGACGUGGAA-AAGGGAACCCUUCGCCGCCUACGG-ACUCCA
.....(((((((.....)))))))...................(((((.......((((((((......)))))))).....((((..-((((....))))..)))).)))))-...... ( -35.40)
>DroYak_CAF1 25010 117 + 1
AAAAAGGCCGCACCAUUUGCGGCUAAUUUUGUAAAUCAUGAUAUCGUAAUUAAUUUUUGCAGCCUUCGCGCUGCAAACAGACGUGGAA-AAGGGAACCCUUCGCCGCCUACGG-AUCCC-
.....(((((((.....)))))))...............(((.(((((.......((((((((......)))))))).....((((..-((((....))))..)))).)))))-)))..- ( -39.00)
>consensus
AAAAGGGCCGCACCAUUUGCGGCUAAUUUUGUAAAUCAUGAUAUCGUAAUUAAUUUUUGCAGCCUUCGCGCUGCAAACAGACGUGGAAUAAGGGAACCCUUCGCCGCCUACGG_UUCCC_
.....(((((((.....)))))))...................(((((.......((((((((......)))))))).....((((...((((....))))..)))).)))))....... (-33.62 = -33.70 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	17,594,276 – 17,594,395
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.70
Mean single sequence MFE	-36.20
Consensus MFE	-31.54
Energy contribution	-31.90
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.61
Structure conservation index	0.87
SVM decision value	1.13
SVM RNA-class probability	0.919298
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17594276 119 - 22224390
-GGGAAUCCGUAGGCGGCAAAGGGUUCCCUUAUUCCACGUCUGUUUGCAGCGCGAAGGCUGCAAAAAUUAAUUACGAUAUCAUGAUUUACAAAAUUAGCCGCAAAUGGUGCGGCCCUUUU
-(((...((((..(((((.((((....))))......(((...((((((((......))))))))........))).....................)))))..)))).....))).... ( -37.20)
>DroSec_CAF1 13623 118 - 1
-GGGAA-CCGUAGGCGGCGAAGGGUUACCUUAUUCCACGUCUGUUUGCAGCGCGAAGGCUGCAAAAAUUAAUUACGAUAUCAUGAUUUACAAAAUUAGCCGCAAAUGGUGCGGCCCUUUU
-(((.(-((((..(((((.((((....))))......(((...((((((((......))))))))........))).....................)))))..)))))....))).... ( -38.70)
>DroSim_CAF1 32264 118 - 1
-GGGAA-CCGUAGGCGGCGAAGGGUUACCUUAUUCCACGUCUGUUUGCACCGCGAAGGCUGCAAAAAUUAAUUACGAUAUCAUGAUUUACAAAAUUAGCCGCAAAUGGUGCGGCCCUUUU
-(((.(-((((..(((((.((((....))))......(((...((((((..((....))))))))........))).....................)))))..)))))....))).... ( -35.60)
>DroEre_CAF1 20254 118 - 1
UGGAGU-CCGUAGGCGGCGAAGGGUUCCCUU-UUCCACGUCUGUUUGCAACGCGAAGGCUGCAAAAAUUAAUUACGAUAUCAUGAUUUACAAAAUUAGCCGCAAAUGGUGCGGCCUUUUU
..((((-(..((((((..(((((....))))-)....))))))((((((..((....))))))))..................))))).........((((((.....))))))...... ( -33.40)
>DroYak_CAF1 25010 117 - 1
-GGGAU-CCGUAGGCGGCGAAGGGUUCCCUU-UUCCACGUCUGUUUGCAGCGCGAAGGCUGCAAAAAUUAAUUACGAUAUCAUGAUUUACAAAAUUAGCCGCAAAUGGUGCGGCCUUUUU
-.((((-(..((((((..(((((....))))-)....))))))((((((((......))))))))..................))))).........((((((.....))))))...... ( -36.10)
>consensus
_GGGAA_CCGUAGGCGGCGAAGGGUUCCCUUAUUCCACGUCUGUUUGCAGCGCGAAGGCUGCAAAAAUUAAUUACGAUAUCAUGAUUUACAAAAUUAGCCGCAAAUGGUGCGGCCCUUUU
.(((...((((..(((((.((((....))))......(((...((((((((......))))))))........))).....................)))))..)))).....))).... (-31.54 = -31.90 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:35 2006