Locus 1644

Sequence ID	3R_DroMel_CAF1
Location	4,777,801 – 4,777,961
Length	160
Max. P	0.993967

overview

Window 8

Location	4,777,801 – 4,777,921
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-51.78
Consensus MFE	-48.60
Energy contribution	-48.84
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.91
Structure conservation index	0.94
SVM decision value	2.26
SVM RNA-class probability	0.991224
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4777801 120 + 27905053
GCCCAAUUCUCUUGUGUAUCUGUUGAUGUUUGAGCAGGUGCGCCUUCUGGCGAAAGGCCUUGGCGCAGACAUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAAGUGCACCUUGA
.............(((((..(((.((((((((.((((((.((((....))))....))))..)).))))))))(((((.(..((((.....))))...).))))))))..)))))..... ( -51.50)
>DroSec_CAF1 13290 120 + 1
GCCCAAUUCUCUUGUGUAUCUGUUGAUGUUUGAGCAGGUGCGCCUUCUGGCGAAAGGCCUUGGCGCAGACGUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAAGUGCACCUUGA
.............(((((..(((.((((((((.((((((.((((....))))....))))..)).))))))))(((((.(..((((.....))))...).))))))))..)))))..... ( -51.10)
>DroEre_CAF1 13448 120 + 1
GCCCAAUUCUCUUGUGUAUCUGUUGAUGUUUGAGCAGGUGCGCCUUCUGGCGAAAGGCCUUGGCGCAGACGUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAGGUGCACCUUGA
.............((((((((((.((((((((.((((((.((((....))))....))))..)).))))))))(((((.(..((((.....))))...).)))))))))))))))..... ( -56.30)
>DroYak_CAF1 13602 120 + 1
GCCCAAUUCUCUUGUGUAUCUGUUGAUGUUUGAGCAGGUGCGCCUUCUGGCGAAAGGCCUUGGCGCAGACGUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAAGUGCACCUUGA
.............(((((..(((.((((((((.((((((.((((....))))....))))..)).))))))))(((((.(..((((.....))))...).))))))))..)))))..... ( -51.10)
>DroAna_CAF1 13036 120 + 1
GCCCAAUUCUCUUGUGUAUCUGUUGAUGUUUGAGCAGGUGCGCCUUCUGGCGGAAGGCCUUGGCGCAGACGUCGCAGCGGAAGGGCUUCUCGCCCGUGUGGGUGCGAAGGUGCACCUUGA
..........((((..((((....))))..)))).((((((((((((.((((..(((((((..(((..........)))..)))))))..)))).((......))))))))))))))... ( -48.90)
>consensus
GCCCAAUUCUCUUGUGUAUCUGUUGAUGUUUGAGCAGGUGCGCCUUCUGGCGAAAGGCCUUGGCGCAGACGUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAAGUGCACCUUGA
.............((((((.(((.((((((((.((((((.((((....))))....))))..)).))))))))(((((.(..((((.....))))...).)))))))).))))))..... (-48.60 = -48.84 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	4,777,801 – 4,777,921
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-43.52
Consensus MFE	-41.02
Energy contribution	-41.50
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.94
SVM decision value	2.35
SVM RNA-class probability	0.992748
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4777801 120 - 27905053
UCAAGGUGCACUUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGAUGUCUGCGCCAAGGCCUUUCGCCAGAAGGCGCACCUGCUCAAACAUCAACAGAUACACAAGAGAAUUGGGC
...((((((.((((((((((.....((((.....))))....))))))..(....)..))))((((((.....))))))))))))((((((...((.............))...)))))) ( -42.82)
>DroSec_CAF1 13290 120 - 1
UCAAGGUGCACUUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGACGUCUGCGCCAAGGCCUUUCGCCAGAAGGCGCACCUGCUCAAACAUCAACAGAUACACAAGAGAAUUGGGC
...((((((.((((((((((.....((((.....))))....)))))).((....)).))))((((((.....))))))))))))((((((...((.............))...)))))) ( -44.42)
>DroEre_CAF1 13448 120 - 1
UCAAGGUGCACCUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGACGUCUGCGCCAAGGCCUUUCGCCAGAAGGCGCACCUGCUCAAACAUCAACAGAUACACAAGAGAAUUGGGC
...((((((.(((.((........))(((((((.(((.....((((((.....))))))..))).)))))))...))).))))))((((((...((.............))...)))))) ( -43.42)
>DroYak_CAF1 13602 120 - 1
UCAAGGUGCACUUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGACGUCUGCGCCAAGGCCUUUCGCCAGAAGGCGCACCUGCUCAAACAUCAACAGAUACACAAGAGAAUUGGGC
...((((((.((((((((((.....((((.....))))....)))))).((....)).))))((((((.....))))))))))))((((((...((.............))...)))))) ( -44.42)
>DroAna_CAF1 13036 120 - 1
UCAAGGUGCACCUUCGCACCCACACGGGCGAGAAGCCCUUCCGCUGCGACGUCUGCGCCAAGGCCUUCCGCCAGAAGGCGCACCUGCUCAAACAUCAACAGAUACACAAGAGAAUUGGGC
...((((((.((((((......)...((((.((((.((((..((.(((.....))))).)))).)))))))).))))).))))))((((((...((.............))...)))))) ( -42.52)
>consensus
UCAAGGUGCACUUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGACGUCUGCGCCAAGGCCUUUCGCCAGAAGGCGCACCUGCUCAAACAUCAACAGAUACACAAGAGAAUUGGGC
...((((((.((((((((((.....((((.....))))....)))))).((....)).))))((((((.....))))))))))))((((((...((.............))...)))))) (-41.02 = -41.50 +   0.48)

alignment

secondary structure

dotplot

Window 0

Location	4,777,841 – 4,777,961
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.08
Mean single sequence MFE	-52.60
Consensus MFE	-47.24
Energy contribution	-47.28
Covariance contribution	0.04
Combinations/Pair	1.08
Mean z-score	-1.59
Structure conservation index	0.90
SVM decision value	1.34
SVM RNA-class probability	0.944324
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4777841 120 + 27905053
CGCCUUCUGGCGAAAGGCCUUGGCGCAGACAUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAAGUGCACCUUGAUGUUGGACUUGUUGAGGAAUCCGCGAUUGCAGAUGCUGCA
.(((....(((.....)))..)))((((.(((((((((.(..((((.....))))...).)))))((((.(((.(((..(((.......)))..))).....))).)))).)))))))). ( -53.00)
>DroSec_CAF1 13330 120 + 1
CGCCUUCUGGCGAAAGGCCUUGGCGCAGACGUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAAGUGCACCUUGAUGUUGGACUUGUUGAGGAAUCCGCGAUUGCAGAUGCUGCA
.(((....(((.....)))..)))((((.(((((((((.(..((((.....))))...).)))))((((.(((.(((..(((.......)))..))).....))).)))).)))))))). ( -52.60)
>DroEre_CAF1 13488 120 + 1
CGCCUUCUGGCGAAAGGCCUUGGCGCAGACGUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAGGUGCACCUUGAUGUUGGACUUGUUGAGGAAUCCCCGAUUGCAGAUGCUGCA
.(((....(((.....)))..)))((((.(((((((.(((..((..(((((((((....))))..((((((.((.(.....).)).)))))).)))))..)))))..))).)))))))). ( -49.60)
>DroYak_CAF1 13642 120 + 1
CGCCUUCUGGCGAAAGGCCUUGGCGCAGACGUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAAGUGCACCUUGAUGUUGGACUUGUUGAGGAAGCCCCGAUUGCAGAUGCUGCA
.(((....(((.....)))..)))((((.(((((((.(((...((((((((((((....))))).((((((.((.(.....).)).))))))...))))))))))..))).)))))))). ( -51.90)
>DroAna_CAF1 13076 120 + 1
CGCCUUCUGGCGGAAGGCCUUGGCGCAGACGUCGCAGCGGAAGGGCUUCUCGCCCGUGUGGGUGCGAAGGUGCACCUUGAUAUUGGACUUGUUGAGGAACCCCCUGUUGCAGAUGCUGCA
.(((....(((.....)))..)))((((.(((((((((((..(((((((.(((((....))))).)))).....(((..(((.......)))..)))..))).))))))).)))))))). ( -55.90)
>consensus
CGCCUUCUGGCGAAAGGCCUUGGCGCAGACGUCGCACCGGAAGGGCUUCUCGCCCGUGUGGGUGCGCAAGUGCACCUUGAUGUUGGACUUGUUGAGGAAUCCCCGAUUGCAGAUGCUGCA
.(((....(((.....)))..)))((((.(((((((((.(..((((.....))))...).))))).....(((.(((..(((.......)))..)))((((...))))))))))))))). (-47.24 = -47.28 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	4,777,841 – 4,777,961
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.08
Mean single sequence MFE	-45.88
Consensus MFE	-42.82
Energy contribution	-43.02
Covariance contribution	0.20
Combinations/Pair	1.09
Mean z-score	-1.81
Structure conservation index	0.93
SVM decision value	2.44
SVM RNA-class probability	0.993967
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4777841 120 - 27905053
UGCAGCAUCUGCAAUCGCGGAUUCCUCAACAAGUCCAACAUCAAGGUGCACUUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGAUGUCUGCGCCAAGGCCUUUCGCCAGAAGGCG
.((((((((.((((..(((((((........))))).((......))))..))))(((((.....((((.....))))....))))))))).))))(((..(((.....)))....))). ( -45.30)
>DroSec_CAF1 13330 120 - 1
UGCAGCAUCUGCAAUCGCGGAUUCCUCAACAAGUCCAACAUCAAGGUGCACUUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGACGUCUGCGCCAAGGCCUUUCGCCAGAAGGCG
(((((...))))).....(((((........)))))........((((((..((((((((.....((((.....))))....)))))).))..))))))...((((((.....)))))). ( -47.20)
>DroEre_CAF1 13488 120 - 1
UGCAGCAUCUGCAAUCGGGGAUUCCUCAACAAGUCCAACAUCAAGGUGCACCUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGACGUCUGCGCCAAGGCCUUUCGCCAGAAGGCG
(((((...))))).....(((((........)))))........((((((..((((((((.....((((.....))))....)))))).))..))))))...((((((.....)))))). ( -46.10)
>DroYak_CAF1 13642 120 - 1
UGCAGCAUCUGCAAUCGGGGCUUCCUCAACAAGUCCAACAUCAAGGUGCACUUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGACGUCUGCGCCAAGGCCUUUCGCCAGAAGGCG
(((((...)))))....((((((.......))))))........((((((..((((((((.....((((.....))))....)))))).))..))))))...((((((.....)))))). ( -49.10)
>DroAna_CAF1 13076 120 - 1
UGCAGCAUCUGCAACAGGGGGUUCCUCAACAAGUCCAAUAUCAAGGUGCACCUUCGCACCCACACGGGCGAGAAGCCCUUCCGCUGCGACGUCUGCGCCAAGGCCUUCCGCCAGAAGGCG
.(((((.((.(((.(.(((((((.(((.....((((........(((((......))))).....))))))).)))))))..).))))).).))))......((((((.....)))))). ( -41.72)
>consensus
UGCAGCAUCUGCAAUCGGGGAUUCCUCAACAAGUCCAACAUCAAGGUGCACUUGCGCACCCACACGGGCGAGAAGCCCUUCCGGUGCGACGUCUGCGCCAAGGCCUUUCGCCAGAAGGCG
(((((...))))).....(((((........)))))........((((((..((((((((.....((((.....))))....)))))).))..))))))...((((((.....)))))). (-42.82 = -43.02 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:42 2006