Locus 2925

Sequence ID	3L_DroMel_CAF1
Location	8,366,792 – 8,366,951
Length	159
Max. P	0.901648

overview

Window 4

Location	8,366,792 – 8,366,911
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.28
Mean single sequence MFE	-39.85
Consensus MFE	-36.41
Energy contribution	-37.23
Covariance contribution	0.81
Combinations/Pair	1.13
Mean z-score	-1.74
Structure conservation index	0.91
SVM decision value	0.95
SVM RNA-class probability	0.889076
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8366792 119 - 23771897
ACUUUGGUUCCGUCGCCGGCUGCCAGUCGGGUGCUCCCGCUGGAUUCCAGCGUGUCACCUACCACCUGGACUGGAUUCGCGACCAUACCGGCAUUGCUUACUACUAAUCGAC-UAUAUCU
...(((((...(((((.((...(((((((((((..(.((((((...)))))).).)))))..(....)))))))..)))))))...))))).....................-....... ( -37.20)
>DroSec_CAF1 3213 119 - 1
ACUUUGGUUCCGUCGCCGGCUGCCAGUCGGGUGCUCCCGCUGGCUUCCAGCGGGUCACCUACCACCUGGACUGGAUUCGCGACCAUACCGGCAUUGCUUACUACUAAACGAC-UAAAUCU
...(((((...(((((.((...(((((((((((..((((((((...)))))))).)))))..(....)))))))..)))))))...))))).....................-....... ( -44.30)
>DroYak_CAF1 3786 119 - 1
ACUUCGGUUCCUCCGCCGGCUGCCAGUCGGGUGCUCCUGCUGGCUUCCAGCGUGUGACCUACCACCUGGACUGGAUCCGCGACCACACCGGCAUCGCUUACUACUAAACGAC-UAUAUCU
.....((.((((((((.((..(((((.((((....)))))))))..)).))(.(((......)))).)))..))).))((((((.....))..))))...............-....... ( -37.70)
>DroAna_CAF1 4926 114 - 1
ACUUCGGCUCCUCUGCUGGCUGCCAGUCGGGUGCUCCUGCUGGUUUCCAGCGGGUUACCUACCACCUGGACUGGAUCCGCGACCACACCGGUAUUGCUUACU---AAACGAAAUAAA---
..(((((.(((((((((((..(((((.((((....)))))))))..))))))))...((........))...))).))((.(((.....)))...)).....---....))).....--- ( -40.20)
>consensus
ACUUCGGUUCCGCCGCCGGCUGCCAGUCGGGUGCUCCCGCUGGCUUCCAGCGGGUCACCUACCACCUGGACUGGAUCCGCGACCACACCGGCAUUGCUUACUACUAAACGAC_UAAAUCU
...(((((...(((((.((...(((((((((((..((((((((...))))))))........))))).))))))..)))))))...)))))............................. (-36.41 = -37.23 +   0.81)

alignment

secondary structure

dotplot

Window 5

Location	8,366,831 – 8,366,951
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.83
Mean single sequence MFE	-53.85
Consensus MFE	-42.11
Energy contribution	-42.80
Covariance contribution	0.69
Combinations/Pair	1.13
Mean z-score	-2.39
Structure conservation index	0.78
SVM decision value	1.02
SVM RNA-class probability	0.901648
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8366831 120 + 23771897
GCGAAUCCAGUCCAGGUGGUAGGUGACACGCUGGAAUCCAGCGGGAGCACCCGACUGGCAGCCGGCGACGGAACCAAAGUUGGUGACCCCCACAAGCUUGGUACCGUCAUGGGUGACCAG
((....((((((..((((.(.(....).((((((...))))))..).)))).))))))..))....(((((.(((((.(((.(((.....))).)))))))).))))).(((....))). ( -53.90)
>DroSec_CAF1 3252 120 + 1
GCGAAUCCAGUCCAGGUGGUAGGUGACCCGCUGGAAGCCAGCGGGAGCACCCGACUGGCAGCCGGCGACGGAACCAAAGUUAGUGACUCCCACAAGCUUGGUACCGUCAUGGGUGACCAG
......(((.......)))..(((.(((((((((..(((((((((....)))).)))))..)))))(((((.(((((.(((.(((.....))).)))))))).)))))..)))).))).. ( -61.10)
>DroYak_CAF1 3825 120 + 1
GCGGAUCCAGUCCAGGUGGUAGGUCACACGCUGGAAGCCAGCAGGAGCACCCGACUGGCAGCCGGCGGAGGAACCGAAGUUGGUGACUCCCACAAGCUUGGUGCCGUCAUGGGUGACCAG
((((..((((.(...((((.........((((((..(((((..((.....))..)))))..))))))(((..((((....))))..)))))))..).))))..))))..(((....))). ( -52.60)
>DroAna_CAF1 4960 120 + 1
GCGGAUCCAGUCCAGGUGGUAGGUAACCCGCUGGAAACCAGCAGGAGCACCCGACUGGCAGCCAGCAGAGGAGCCGAAGUUGGUGACACCUACCAGCUUGGUACCGUCGUGUGUGACCAG
((((..((((((..((((.(.((....))(((((...)))))...).)))).))))))...)).))...((.(((.(((((((((.....)))))))))))).))((((....))))... ( -47.80)
>consensus
GCGAAUCCAGUCCAGGUGGUAGGUGACACGCUGGAAGCCAGCAGGAGCACCCGACUGGCAGCCGGCGAAGGAACCAAAGUUGGUGACUCCCACAAGCUUGGUACCGUCAUGGGUGACCAG
......(((.......)))..(((.((.((((((..(((((((((....)))).)))))..)))))(((((.(((((.(((.(((.....))).)))))))).)))))..).)).))).. (-42.11 = -42.80 +   0.69)

alignment

secondary structure

dotplot

Window 6

Location	8,366,831 – 8,366,951
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.83
Mean single sequence MFE	-49.62
Consensus MFE	-41.06
Energy contribution	-41.25
Covariance contribution	0.19
Combinations/Pair	1.19
Mean z-score	-1.71
Structure conservation index	0.83
SVM decision value	0.49
SVM RNA-class probability	0.754978
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8366831 120 - 23771897
CUGGUCACCCAUGACGGUACCAAGCUUGUGGGGGUCACCAACUUUGGUUCCGUCGCCGGCUGCCAGUCGGGUGCUCCCGCUGGAUUCCAGCGUGUCACCUACCACCUGGACUGGAUUCGC
.((((.(((......)))))))((((.((((.((..((((....)))).)).)))).)))).(((((((((((..(.((((((...)))))).).)))))..(....)))))))...... ( -47.30)
>DroSec_CAF1 3252 120 - 1
CUGGUCACCCAUGACGGUACCAAGCUUGUGGGAGUCACUAACUUUGGUUCCGUCGCCGGCUGCCAGUCGGGUGCUCCCGCUGGCUUCCAGCGGGUCACCUACCACCUGGACUGGAUUCGC
..(((.((((..(((((.((((((.(((((.....))).)).)))))).)))))((.((..(((((.((((....)))))))))..)).)))))).))).....((......))...... ( -53.50)
>DroYak_CAF1 3825 120 - 1
CUGGUCACCCAUGACGGCACCAAGCUUGUGGGAGUCACCAACUUCGGUUCCUCCGCCGGCUGCCAGUCGGGUGCUCCUGCUGGCUUCCAGCGUGUGACCUACCACCUGGACUGGAUCCGC
...((((....))))((..(((..((.((((..(((((.(((....)))....(((.((..(((((.((((....)))))))))..)).))).)))))...))))..))..)))..)).. ( -47.30)
>DroAna_CAF1 4960 120 - 1
CUGGUCACACACGACGGUACCAAGCUGGUAGGUGUCACCAACUUCGGCUCCUCUGCUGGCUGCCAGUCGGGUGCUCCUGCUGGUUUCCAGCGGGUUACCUACCACCUGGACUGGAUCCGC
..((((.(....).((((.(((.(.(((((((((...((..(....).......(((((..(((((.((((....)))))))))..)))))))..)))))))))).)))))))))))... ( -50.40)
>consensus
CUGGUCACCCAUGACGGUACCAAGCUUGUGGGAGUCACCAACUUCGGUUCCGCCGCCGGCUGCCAGUCGGGUGCUCCCGCUGGCUUCCAGCGGGUCACCUACCACCUGGACUGGAUCCGC
...(((......)))((..((((((..(((((((.((((....(((((.((......))..)))))...)))))))))))..)))(((((..(((.....)))..))))).)))..)).. (-41.06 = -41.25 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:10 2006