Locus 4597

Sequence ID	3L_DroMel_CAF1
Location	13,137,486 – 13,137,685
Length	199
Max. P	0.996190

overview

Window 1

Location	13,137,486 – 13,137,606
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.33
Mean single sequence MFE	-32.26
Consensus MFE	-26.84
Energy contribution	-28.04
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.83
SVM decision value	2.06
SVM RNA-class probability	0.986890
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137486 120 + 23771897
AUAUACCCUAGCUGCGGCCAGUCCAUCAACUGCCAGUGAUUACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCACCGA
...............(((.(((......)))))).((((...(((((.((((......)))).)))))...((((((((((((....)))).......)))))))).......))))... ( -32.21)
>DroSec_CAF1 125240 120 + 1
AUAUUCCCUAGCUGCGGUCAGUCCAUCAACUGCCAGUGAUUACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUUCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCAGCGA
..........((((.((.((((......))))))........(((((.((((......)))).)))))...((((((........)))))).(((((((.....)))))))...)))).. ( -33.00)
>DroSim_CAF1 125159 120 + 1
AUAUACCCUAGCUGCGGUCAGUCCAUCAACUGCCAGUGAUUACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCAGCGA
..........((((.((.((((......)))))).(..(((.(((((.((((......)))).))))).....(((....))))))..)...(((((((.....)))))))...)))).. ( -33.90)
>DroEre_CAF1 122012 120 + 1
AUAUGCCCCAGCUGCGGUCAGUCCAUCAACUGCCAGUGAGUACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCACCGA
...............((.((((......)))))).((((((.(((((.((((......)))).)))))...((((((((((((....)))).......)))))))).....))))))... ( -34.41)
>DroYak_CAF1 126404 111 + 1
AUAUGCCCCAGCUGCGGUCAGUCCAUCAACUGCCAGUGAUUA---------CAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCACCGA
.(((((.....(((((((((((......))))..((((....---------......)))))))))))....((((....))))...)))))(((((((.....)))))))......... ( -27.80)
>consensus
AUAUACCCUAGCUGCGGUCAGUCCAUCAACUGCCAGUGAUUACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCACCGA
...........(((((((..(((........((((((....)))).)).......)))...)))))))...((((((........)))))).(((((((.....)))))))......... (-26.84 = -28.04 +   1.20)

alignment

secondary structure

dotplot

Window 2

Location	13,137,486 – 13,137,606
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.33
Mean single sequence MFE	-37.88
Consensus MFE	-32.16
Energy contribution	-33.40
Covariance contribution	1.24
Combinations/Pair	1.08
Mean z-score	-2.17
Structure conservation index	0.85
SVM decision value	2.25
SVM RNA-class probability	0.991126
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137486 120 - 23771897
UCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUAAUCACUGGCAGUUGAUGGACUGGCCGCAGCUAGGGUAUAU
.........(((((((.....)))))))(((((...((((....))))(...(((((((...((((..(((.((.((((....)))))))))....))))..)))))))...).))))). ( -38.80)
>DroSec_CAF1 125240 120 - 1
UCGCUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGAAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUAAUCACUGGCAGUUGAUGGACUGACCGCAGCUAGGGAAUAU
((.(((........((((((((.((.(((.....))).)).))))))))...(((((((...((((..(((.((.((((....)))))))))....))))..))))))).))).)).... ( -38.90)
>DroSim_CAF1 125159 120 - 1
UCGCUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUAAUCACUGGCAGUUGAUGGACUGACCGCAGCUAGGGUAUAU
.........(((((((.....)))))))(((((...((((....))))(...(((((((...((((..(((.((.((((....)))))))))....))))..)))))))...).))))). ( -38.50)
>DroEre_CAF1 122012 120 - 1
UCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUACUCACUGGCAGUUGAUGGACUGACCGCAGCUGGGGCAUAU
(((((((.......((((((((.......((((....))))))))))))((.(((.(.(((((....))))).).))).)))))))))((((((.(((.....)))))))))........ ( -40.81)
>DroYak_CAF1 126404 111 - 1
UCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUG---------UAAUCACUGGCAGUUGAUGGACUGACCGCAGCUGGGGCAUAU
(((((((..(((((((.....)))))))..(((((.(((....(((((.....)))))..)))...)))---------)).)))))))((((((.(((.....)))))))))........ ( -32.40)
>consensus
UCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUAAUCACUGGCAGUUGAUGGACUGACCGCAGCUAGGGCAUAU
.........(((((((.....)))))))(((((...((((....))))(.(.(((((((...((((..(((.((.((((....)))))))))....))))..)))))))..).)))))). (-32.16 = -33.40 +   1.24)

alignment

secondary structure

dotplot

Window 3

Location	13,137,526 – 13,137,645
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.32
Mean single sequence MFE	-31.78
Consensus MFE	-27.82
Energy contribution	-29.62
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-2.20
Structure conservation index	0.88
SVM decision value	2.66
SVM RNA-class probability	0.996190
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137526 119 + 23771897
UACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCACCGAUUUGUAUCGUUCGGCGCUCGUAUGAAUGCCCAAA-AAAGC
...((((.((((......)))).))))(((((((((((.((((....)))).(((((((.....))))))).........)))))).)))))((((.((....)).))))....-..... ( -34.20)
>DroSec_CAF1 125280 120 + 1
UACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUUCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCAGCGAUUUGUAUCGUUCGGCGCUCGUAUGAAUGCCCAAAAAAAGC
..(((((.((((......)))).)))))...((((((........)))))).(((((((.....)))))))....((((((....)))))).((((.((....)).)))).......... ( -31.80)
>DroSim_CAF1 125199 120 + 1
UACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCAGCGAUUUGUAUCGUUCGGCGCUCGUAUGAAUGCCCAAAAAAAGC
...((((.((((......)))).))))(((((((((((.((((....)))).(((((((.....))))))).........)))))).)))))((((.((....)).)))).......... ( -34.20)
>DroEre_CAF1 122052 119 + 1
UACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCACCGAUUUGUAUCGCUCGGCGCUCGUAUGAAUGCCCAAA-AAAGC
..(((((.((((......)))).)))))..((((((((.((((....)))).(((((((.....))))))).........)))))).))...((((.((....)).))))....-..... ( -31.00)
>DroYak_CAF1 126444 110 + 1
UA---------CAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCACCGAUUUGUAUCGUUCGGCGCUCGUAUGAAUGCCCAAA-AAAGC
..---------.......(((......(((((((((((.((((....)))).(((((((.....))))))).........)))))).)))))((((.((....)).))))....-..))) ( -27.70)
>consensus
UACUGUGCUAGCAAAGACGCUACCGCAGAACGUGCAAAAAUGCAAUUGCAUAUUCAAGUUUUGCACUUGAAAUUCACCGAUUUGUAUCGUUCGGCGCUCGUAUGAAUGCCCAAA_AAAGC
...((((.((((......)))).))))(((((((((((.((((....)))).(((((((.....))))))).........)))))).)))))((((.((....)).)))).......... (-27.82 = -29.62 +   1.80)

alignment

secondary structure

dotplot

Window 4

Location	13,137,526 – 13,137,645
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.32
Mean single sequence MFE	-31.44
Consensus MFE	-28.96
Energy contribution	-29.60
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.19
Structure conservation index	0.92
SVM decision value	0.32
SVM RNA-class probability	0.688592
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137526 119 - 23771897
GCUUU-UUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUA
((((.-...)))).....((((((((((((..........))))).........((((((((.......((((....))))))))))))))))((.(.(((((....))))).).))))) ( -32.01)
>DroSec_CAF1 125280 120 - 1
GCUUUUUUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGCUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGAAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUA
((........(((.(((....))).)))(((((................(((((((.....)))))))..(((((........)))))))))).))(.(((((....))))).)...... ( -32.00)
>DroSim_CAF1 125199 120 - 1
GCUUUUUUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGCUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUA
((........(((.(((....))).)))(((((.........((.....(((((((.....)))))))...))...((((....))))))))).))(.(((((....))))).)...... ( -33.50)
>DroEre_CAF1 122052 119 - 1
GCUUU-UUUGGGCAUUCAUACGAGCGCCGAGCGAUACAAAUCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUA
((((.-...)))).....((((((((((((..........))))).........((((((((.......((((....))))))))))))))))((.(.(((((....))))).).))))) ( -32.81)
>DroYak_CAF1 126444 110 - 1
GCUUU-UUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUG---------UA
(((..-.((((((.(((....))).)))(((((................(((((((.....)))))))..(((((........))))))))))..))).))).......---------.. ( -26.90)
>consensus
GCUUU_UUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCAUUUUUGCACGUUCUGCGGUAGCGUCUUUGCUAGCACAGUA
((........(((.(((....))).)))(((((................(((((((.....)))))))..(((((........)))))))))).))(.(((((....))))).)...... (-28.96 = -29.60 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	13,137,566 – 13,137,685
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.41
Mean single sequence MFE	-34.99
Consensus MFE	-30.04
Energy contribution	-30.72
Covariance contribution	0.68
Combinations/Pair	1.03
Mean z-score	-1.45
Structure conservation index	0.86
SVM decision value	0.17
SVM RNA-class probability	0.618042
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137566 119 - 23771897
GUUUCGUGCCCAGGUUUUCCCAUUUUCCAGUGGGGGAGUAGCUUU-UUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCA
((...(((((((((((..(((((......)))))..)).......-)))))))))....))...((((((..........))))))...(((((((.....)))))))..(((....))) ( -36.31)
>DroSec_CAF1 125320 120 - 1
GUUUCGUGCCCAGGUUUUCCCAUUUUCCAGUGGGGGAGUAGCUUUUUUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGCUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGAA
((.(((((((((((((..(((((......)))))..))........))))))).......((.....)).)))).)).....((.....(((((((.....)))))))...))....... ( -33.00)
>DroSim_CAF1 125239 120 - 1
GUUUCGUGCCCAGGUUUUCCCAUUUUCCAGUGGGGGAGUAGCUUUUUUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGCUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCA
((.(((((((((((((..(((((......)))))..))........))))))).......((.....)).)))).)).....((.....(((((((.....)))))))...))....... ( -33.00)
>DroEre_CAF1 122092 119 - 1
GUUUCGUGCCCAGGUUUUCCUAUUUUCCAGCGGGGGAGUAGCUUU-UUUGGGCAUUCAUACGAGCGCCGAGCGAUACAAAUCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCA
((...(((((((((.....(((((..((....))..)))))....-)))))))))....))...((((((..........))))))...(((((((.....)))))))..(((....))) ( -38.40)
>DroYak_CAF1 126475 119 - 1
GUUUCGUGCCCAGGUUUUCCGAUUUUCCAGUGGGGGAGUAGCUUU-UUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCA
((...(((((((((.......(((..((....))..)))......-)))))))))....))...((((((..........))))))...(((((((.....)))))))..(((....))) ( -34.22)
>consensus
GUUUCGUGCCCAGGUUUUCCCAUUUUCCAGUGGGGGAGUAGCUUU_UUUGGGCAUUCAUACGAGCGCCGAACGAUACAAAUCGGUGAAUUUCAAGUGCAAAACUUGAAUAUGCAAUUGCA
((...(((((((((((..(((((......)))))..))........)))))))))....))..(((((((..........)))))....(((((((.....)))))))...))....... (-30.04 = -30.72 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:56 2006