Locus 7093

Sequence ID	3R_DroMel_CAF1
Location	18,711,616 – 18,711,784
Length	168
Max. P	0.942624

overview

Window 1

Location	18,711,616 – 18,711,726
Length	110
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	68.90
Mean single sequence MFE	-28.72
Consensus MFE	-17.88
Energy contribution	-17.53
Covariance contribution	-0.36
Combinations/Pair	1.40
Mean z-score	-1.17
Structure conservation index	0.62
SVM decision value	0.30
SVM RNA-class probability	0.680112
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18711616 110 + 27905053
CUCAUUAAAAGAGAUAUUAUUUACUAUUCCCAAAAACAGCUAGAAAAAAGCUA----AGGCGCU----ACCUUCAAACCAGGAAGAGCAGCAACUGAAGGGGGCGUGGCAGGCGCCAG
(((.......)))........................((((.......)))).----.((((((----..((((.......)))).((.((..(.....)..))...)).)))))).. ( -24.60)
>DroSec_CAF1 145436 110 + 1
UUAAUUAAAAGAGGUAUCAUUCACUGUUUCCAAAAAUAGCUAGAAAAUAGCUA----GGGCGCU----ACCUUCGAAUCAGGAAGAGCAGCAACUGAGGGGGGCGUGGCAGGCGCCAG
............(((..(..((((.((..((.....((((((.....))))))----((..(((----.(((((.......)))).).)))..))...))..))))))..)..))).. ( -30.60)
>DroSim_CAF1 137088 110 + 1
UUAAUUAAAAGAGGUAUCAUUCACUGUUUCCAAAAAUAGCUAGAAAAUAGCUA----GGGCGCU----ACCUUCGAAUCAGGAAGAGCAGCAACUGAAGGGGGCGUGGCAGGCGCCAG
............(((..(..((((.((..((.....((((((.....))))))----((..(((----.(((((.......)))).).)))..))...))..))))))..)..))).. ( -30.80)
>DroEre_CAF1 142930 89 + 1
--------------------GUAAUAUUCC-AAAGAUAGCUAGAAAAGAGCUA----AGGCGCU----ACCUUCGAACCAGGAACAUAAGCAGCUGAAGGGGGCGUGGCAGGCGCCAG
--------------------..........-.....(((((.......)))))----.((((((----.(((.......))).......((.(((......)))...)).)))))).. ( -23.00)
>DroYak_CAF1 141036 114 + 1
CUAAAUGAAUGUGAUGCCAUCGAAUAUUCCUAAAAAUAGCUAGAAAAUAGCUA----AGGCGCUUUGAGCCUUUGAACCAGGAACAGAAGCAGCUAAAGGGGGCGUGGCAGGCGCCAG
..........(((.(((((.((....(((((.....((((((.....))))))----.((((((((...(((.......)))....))))).)))..))))).)))))))..)))... ( -33.70)
>DroAna_CAF1 129791 109 + 1
CUAAACGAAUUGUGUGGCACAGAA--CUCGGGUACUUGGCUUGCAACAAGCCAAAUGAGAAGCUCU--AAUUUUGGGUAACGAACGG----GGAU-GAGGAGGCGUGGCAGGCGCCAG
...........((.((.(((....--((((.....((((((((...)))))))).))))...((((--.(((((.(........).)----))))-..))))..))).)).))..... ( -29.60)
>consensus
CUAAUUAAAAGAGGUAUCAUUCAAUAUUCCCAAAAAUAGCUAGAAAAUAGCUA____AGGCGCU____ACCUUCGAACCAGGAACAGCAGCAACUGAAGGGGGCGUGGCAGGCGCCAG
....................................((((((.....))))))......(((((.....((((((...................)))))).)))))(((....))).. (-17.88 = -17.53 +  -0.36)

alignment

secondary structure

dotplot

Window 2

Location	18,711,656 – 18,711,762
Length	106
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	84.43
Mean single sequence MFE	-37.80
Consensus MFE	-29.86
Energy contribution	-29.78
Covariance contribution	-0.08
Combinations/Pair	1.22
Mean z-score	-1.96
Structure conservation index	0.79
SVM decision value	0.33
SVM RNA-class probability	0.690401
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18711656 106 + 27905053
UAGAAAAAAGCUA----AGGCGCU----ACCUUCAAACCAGGAAGAGCAGCAACUGAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCUGGGA
..........((.----(((((((----.((((((..(((((.....(((...)))...((((((((((....))))..)))))).)))))....)))))).))).)))).)). ( -40.80)
>DroSec_CAF1 145476 106 + 1
UAGAAAAUAGCUA----GGGCGCU----ACCUUCGAAUCAGGAAGAGCAGCAACUGAGGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCUGGGA
..........(((----((((((.----.((((((......(.....)......))))))..))))(((....))).(((((((((((.....))))).))))))..))))).. ( -39.90)
>DroSim_CAF1 137128 106 + 1
UAGAAAAUAGCUA----GGGCGCU----ACCUUCGAAUCAGGAAGAGCAGCAACUGAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCUGGGA
..........(((----((((((.----.((((((......(.....)......))))))..))))(((....))).(((((((((((.....))))).))))))..))))).. ( -40.20)
>DroEre_CAF1 142949 106 + 1
UAGAAAAGAGCUA----AGGCGCU----ACCUUCGAACCAGGAACAUAAGCAGCUGAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCAGGGA
..........((.----.((((((----.((((((..(((((..((........))...((((((((((....))))..)))))).)))))....)))))).))).)))..)). ( -37.30)
>DroYak_CAF1 141076 110 + 1
UAGAAAAUAGCUA----AGGCGCUUUGAGCCUUUGAACCAGGAACAGAAGCAGCUAAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCAGGGA
.........(((.----.(((((((((..(((.......)))..)))).((.(((......)))...))..))))).(((((((((((.....))))).)))))))))...... ( -38.20)
>DroAna_CAF1 129829 107 + 1
UUGCAACAAGCCAAAUGAGAAGCUCU--AAUUUUGGGUAACGAACGG----GGAU-GAGGAGGCGUGGCAGGCGCCAGUUUCCCCAUUUGGGAAAUGGAGGCAGCAGCCAGGGA
..((.....))...........((((--.(((((.(........).)----))))-..)))).(.((((..(((((.(((((((.....)))))))...))).)).)))).).. ( -30.40)
>consensus
UAGAAAAUAGCUA____AGGCGCU____ACCUUCGAACCAGGAACAGCAGCAACUGAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCAGGGA
.........(((......)))........((((((...................)))))).(((.((((....))))(((((((((((.....))))).)))))).)))..... (-29.86 = -29.78 +  -0.08)

alignment

secondary structure

dotplot

Window 3

Location	18,711,656 – 18,711,762
Length	106
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	84.43
Mean single sequence MFE	-32.87
Consensus MFE	-22.55
Energy contribution	-22.75
Covariance contribution	0.20
Combinations/Pair	1.22
Mean z-score	-2.24
Structure conservation index	0.69
SVM decision value	-0.01
SVM RNA-class probability	0.529000
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18711656 106 - 27905053
UCCCAGGCUGCUGCCUCCAUUUCCCAAAUGGGGCAACUGGCGCCUGCCACGCCCCCUUCAGUUGCUGCUCUUCCUGGUUUGAAGGU----AGCGCCU----UAGCUUUUUUCUA
....((((.(((((((.((....(((...(((((...((((....)))).)))))....(((....))).....)))..)).))))----)))))))----............. ( -35.60)
>DroSec_CAF1 145476 106 - 1
UCCCAGGCUGCUGCCUCCAUUUCCCAAAUGGGGCAACUGGCGCCUGCCACGCCCCCCUCAGUUGCUGCUCUUCCUGAUUCGAAGGU----AGCGCCC----UAGCUAUUUUCUA
...((((..(..((..(((((.....)))))(((((((((((.......))))......))))))))).)..))))....((((((----(((....----..))))))))).. ( -33.90)
>DroSim_CAF1 137128 106 - 1
UCCCAGGCUGCUGCCUCCAUUUCCCAAAUGGGGCAACUGGCGCCUGCCACGCCCCCUUCAGUUGCUGCUCUUCCUGAUUCGAAGGU----AGCGCCC----UAGCUAUUUUCUA
...((((..(..((..(((((.....)))))(((((((((((.......))))......))))))))).)..))))....((((((----(((....----..))))))))).. ( -33.90)
>DroEre_CAF1 142949 106 - 1
UCCCUGGCUGCUGCCUCCAUUUCCCAAAUGGGGCAACUGGCGCCUGCCACGCCCCCUUCAGCUGCUUAUGUUCCUGGUUCGAAGGU----AGCGCCU----UAGCUCUUUUCUA
.....(((.(((((((.(...........(((((...((((....)))).)))))..((((..((....))..))))...).))))----)))))).----............. ( -36.10)
>DroYak_CAF1 141076 110 - 1
UCCCUGGCUGCUGCCUCCAUUUCCCAAAUGGGGCAACUGGCGCCUGCCACGCCCCCUUUAGCUGCUUCUGUUCCUGGUUCAAAGGCUCAAAGCGCCU----UAGCUAUUUUCUA
....((((((.((((.(((((.....)))))))))...(((((..(((......((...(((.......)))...))......))).....))))).----))))))....... ( -31.40)
>DroAna_CAF1 129829 107 - 1
UCCCUGGCUGCUGCCUCCAUUUCCCAAAUGGGGAAACUGGCGCCUGCCACGCCUCCUC-AUCC----CCGUUCGUUACCCAAAAUU--AGAGCUUCUCAUUUGGCUUGUUGCAA
.....(((....)))........(((((((((((....((((.......)))).....-.)))----))((((.............--.)))).....)))))).......... ( -26.34)
>consensus
UCCCAGGCUGCUGCCUCCAUUUCCCAAAUGGGGCAACUGGCGCCUGCCACGCCCCCUUCAGCUGCUGCUCUUCCUGAUUCGAAGGU____AGCGCCU____UAGCUAUUUUCUA
.....(((((.((((.(((((.....)))))))))...(((((.......(((....((((..(......)..))))......))).....))))).....)))))........ (-22.55 = -22.75 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	18,711,688 – 18,711,784
Length	96
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	90.49
Mean single sequence MFE	-35.22
Consensus MFE	-32.51
Energy contribution	-32.67
Covariance contribution	0.16
Combinations/Pair	1.07
Mean z-score	-1.62
Structure conservation index	0.92
SVM decision value	1.33
SVM RNA-class probability	0.942624
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18711688 96 + 27905053
GGAAGAGCAGCAACUGAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCUGGGAGUUUUGCCCAAAAAGUCUCGUA
....((((............((((.((((....))))(((((((((((.....))))).)))))).))))(((.......))).....).)))... ( -34.30)
>DroSec_CAF1 145508 96 + 1
GGAAGAGCAGCAACUGAGGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCUGGGAGUUUUGGCCAAAAAGUCUCGCA
.........((.........((((.((((....))))(((((((((((.....))))).)))))).))))((((.((((.....)))).)))))). ( -36.60)
>DroSim_CAF1 137160 96 + 1
GGAAGAGCAGCAACUGAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCUGGGAGUUUUGGCCAAAAAGUCUCGCA
.........((.........((((.((((....))))(((((((((((.....))))).)))))).))))((((.((((.....)))).)))))). ( -36.60)
>DroEre_CAF1 142981 96 + 1
GGAACAUAAGCAGCUGAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCAGGGAGUUUUGGCCAAAAAGUCUCGCA
.........((..........(((.((((....))))(((((((((((.....))))).)))))).))).((((.((((.....)))).)))))). ( -35.80)
>DroYak_CAF1 141112 96 + 1
GGAACAGAAGCAGCUAAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCAGGGAGUUUUGGCCAAAAAGUCUCGCA
.........((..........(((.((((....))))(((((((((((.....))))).)))))).))).((((.((((.....)))).)))))). ( -35.80)
>DroAna_CAF1 129867 89 + 1
CGAACGG----GGAU-GAGGAGGCGUGGCAGGCGCCAGUUUCCCCAUUUGGGAAAUGGAGGCAGCAGCCAGGGAGUUC-GGCCA-GAAGUCUCGCA
.......----....-......((.((((..(((((.(((((((.....)))))))...))).)).))))((((.(((-.....-))).)))))). ( -32.20)
>consensus
GGAACAGCAGCAACUGAAGGGGGCGUGGCAGGCGCCAGUUGCCCCAUUUGGGAAAUGGAGGCAGCAGCCAGGGAGUUUUGGCCAAAAAGUCUCGCA
.........((..........(((.((((....))))(((((((((((.....))))).)))))).))).((((.((((.....)))).)))))). (-32.51 = -32.67 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:12 2006