Locus 6293

Sequence ID	3R_DroMel_CAF1
Location	16,430,429 – 16,430,585
Length	156
Max. P	0.999954

overview

Window 5

Location	16,430,429 – 16,430,548
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.04
Mean single sequence MFE	-30.28
Consensus MFE	-28.80
Energy contribution	-28.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.35
Structure conservation index	0.95
SVM decision value	1.20
SVM RNA-class probability	0.929906
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16430429 119 + 27905053
ACUUAUUUAGACGCAC-UAAAGACACUGUAAAAAAAACUUUUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAA
.....(((((.....)-))))......................((((((((((((.......)))))(((((.((....))...)))))....)))))))(((...........)))... ( -30.10)
>DroSec_CAF1 26340 108 + 1
ACUUAUUUAG------------ACACUGCAAAAAAAACUUUUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAA
..........------------...(((((((((....)))))).)))(((((((.......)))))))((((....)))).(((((.......))))).(((...........)))... ( -30.40)
>DroSim_CAF1 26755 120 + 1
ACUUAUUUAGACGCACCUAAAGACACUGUAAAAAAAACUUUUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAA
.....(((((......)))))......................((((((((((((.......)))))(((((.((....))...)))))....)))))))(((...........)))... ( -30.70)
>DroEre_CAF1 26012 117 + 1
ACUUAUUUAGAAGCAC-UAAAAACACUGUAAAAAAAAAU--UUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAA
.....(((((.....)-))))..................--..((((((((((((.......)))))(((((.((....))...)))))....)))))))(((...........)))... ( -30.10)
>DroYak_CAF1 28025 117 + 1
ACUUAUUUAGAAUCAC-UAAAAACACUGUUAAAAAAACU--UUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAA
.....(((((.....)-))))..................--..((((((((((((.......)))))(((((.((....))...)))))....)))))))(((...........)))... ( -30.10)
>consensus
ACUUAUUUAGAAGCAC_UAAAAACACUGUAAAAAAAACUUUUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAA
...........................................((((((((((((.......)))))(((((.((....))...)))))....)))))))(((...........)))... (-28.80 = -28.80 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	16,430,429 – 16,430,548
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.04
Mean single sequence MFE	-37.86
Consensus MFE	-33.90
Energy contribution	-33.90
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.90
SVM decision value	1.83
SVM RNA-class probability	0.979133
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16430429 119 - 27905053
UUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAAAAGUUUUUUUUACAGUGUCUUUA-GUGCGUCUAAAUAAGU
..((((....))))..(((((((((............((((((....))))))(((((.......)))))..))))).................(..(.....-)..)))))........ ( -37.90)
>DroSec_CAF1 26340 108 - 1
UUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAAAAGUUUUUUUUGCAGUGU------------CUAAAUAAGU
..((((....))))..(((((((((............((((((....))))))(((((.......)))))..)))(((((((....))))))).))))------------))........ ( -38.70)
>DroSim_CAF1 26755 120 - 1
UUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAAAAGUUUUUUUUACAGUGUCUUUAGGUGCGUCUAAAUAAGU
..((((....))))..(((((((((............((((((....))))))(((((.......)))))..))))).................(..((....))..)))))........ ( -40.90)
>DroEre_CAF1 26012 117 - 1
UUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAA--AUUUUUUUUUACAGUGUUUUUA-GUGCUUCUAAAUAAGU
((((..(((((.(..((((((((((............((((((....))))))(((((.......)))))..)))))((--(......))).....))))).)-.)))))))))...... ( -35.40)
>DroYak_CAF1 28025 117 - 1
UUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAA--AGUUUUUUUAACAGUGUUUUUA-GUGAUUCUAAAUAAGU
..((((....)))).((.(((((((............((((((....))))))(((((.......)))))..)))))..--.(((.....))).)).))((((-(.....)))))..... ( -36.40)
>consensus
UUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAAAAGUUUUUUUUACAGUGUCUUUA_GUGCGUCUAAAUAAGU
..((((....))))......(((((............((((((....))))))(((((.......)))))..)))))........................................... (-33.90 = -33.90 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	16,430,468 – 16,430,585
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	97.43
Mean single sequence MFE	-36.72
Consensus MFE	-35.44
Energy contribution	-35.84
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.97
SVM decision value	2.81
SVM RNA-class probability	0.997192
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16430468 117 + 27905053
UUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUAUGUGUUUUCCUUAAUUCUAAGUACAAUAU
...((((((((((((.......)))))(((((.((....))...)))))....)))))))..((((((.(((..((((.....))))..)))...........))))))........ ( -37.20)
>DroSec_CAF1 26368 117 + 1
UUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUAUGUGUUUUCCUUAAUUCGAAGUACAAUAU
...((((((((((((.......)))))((((((....)))).(((((.......))))).))....(.((....)).).)))))))....(((((((........)))).))).... ( -35.40)
>DroSim_CAF1 26795 117 + 1
UUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUAUGUGUUUUCCUUAAUUCGAAGUACAAUAU
...((((((((((((.......)))))((((((....)))).(((((.......))))).))....(.((....)).).)))))))....(((((((........)))).))).... ( -35.40)
>DroEre_CAF1 26050 116 + 1
-UUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUAUGUGUUUUCCCUAAUUCUAAGUACAAUAU
-..((((((((((((.......)))))(((((.((....))...)))))....)))))))..((((((.(((..((((.....))))..)))...........))))))........ ( -37.20)
>DroYak_CAF1 28063 116 + 1
-UUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUAUGUGUUUUCACUAAUUCUAAGUACUUUAU
-..((((((((((((.......)))))(((((.((....))...)))))....)))))))..((((((......((((.....))))..(((....)))....))))))........ ( -38.40)
>consensus
UUUGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUAUGUGUUUUCCUUAAUUCUAAGUACAAUAU
...((((((((((((.......)))))(((((.((....))...)))))....)))))))..((((((.(((..((((.....))))..)))...........))))))........ (-35.44 = -35.84 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	16,430,468 – 16,430,585
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	97.43
Mean single sequence MFE	-43.00
Consensus MFE	-42.20
Energy contribution	-42.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.96
Structure conservation index	0.98
SVM decision value	4.83
SVM RNA-class probability	0.999954
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16430468 117 - 27905053
AUAUUGUACUUAGAAUUAAGGAAAACACAUAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAA
........((((....))))...........(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))... ( -42.50)
>DroSec_CAF1 26368 117 - 1
AUAUUGUACUUCGAAUUAAGGAAAACACAUAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAA
....(((..(((.......)))..)))....(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))... ( -43.20)
>DroSim_CAF1 26795 117 - 1
AUAUUGUACUUCGAAUUAAGGAAAACACAUAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAA
....(((..(((.......)))..)))....(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))... ( -43.20)
>DroEre_CAF1 26050 116 - 1
AUAUUGUACUUAGAAUUAGGGAAAACACAUAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAA-
...............................(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))..- ( -42.20)
>DroYak_CAF1 28063 116 - 1
AUAAAGUACUUAGAAUUAGUGAAAACACAUAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAA-
..................(((....)))...(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))..- ( -43.90)
>consensus
AUAUUGUACUUAGAAUUAAGGAAAACACAUAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAA
...............................(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......))))))))))))... (-42.20 = -42.20 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:57 2006