Locus 1935

Sequence ID	3L_DroMel_CAF1
Location	5,391,420 – 5,391,703
Length	283
Max. P	0.999976

overview

Window 8

Location	5,391,420 – 5,391,530
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	90.73
Mean single sequence MFE	-26.42
Consensus MFE	-21.82
Energy contribution	-21.98
Covariance contribution	0.16
Combinations/Pair	1.17
Mean z-score	-2.49
Structure conservation index	0.83
SVM decision value	2.51
SVM RNA-class probability	0.994776
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5391420 110 - 23771897
GAAAAUACGUUUUUAAUUUCAUUGUUUACUCUGCUCCACAGGAGCUAAACAAGGAGAUUUAUGAACGUAAACUAAACUUUCGCAUAGUCUAAGGAUCAGCCUCAUAAAAA
.....(((((((..((((((.(((((((....(((((...)))))))))))).))))))...)))))))............((...(((....)))..)).......... ( -25.00)
>DroSec_CAF1 40436 110 - 1
GAAAAUAUGUUUUUAAUUUCAUUGUUUGCUCUGCCCCACAAGAGCUAAACAAGGAGAUUUAUGAACGUAAAGGAAACUUUGGCAUAGUCUAAGGAUCAUCCUCAUAAAAA
.....(((((((..((((((.(((((((((((........))))).)))))).))))))...))))))).((((..((((((......))))))....))))........ ( -28.90)
>DroSim_CAF1 40079 110 - 1
GAAAAUAUGUUUUUAAUUUCAUUGUUUGUUCUGCCCCAUAAGAGCUAAACAAAGAGAUUUAUGAACGUAAAGGAAACUUUGGCAUAGUCUAAGGAUCAUCCUCAUAAAAA
.....(((((((..((((((.(((((((((((........))))).)))))).))))))...))))))).((((..((((((......))))))....))))........ ( -26.50)
>DroEre_CAF1 40613 110 - 1
GAAAAUAUGUUUUUAAUUUCAUUGUCUGCUCCGCCCCACAAGAGCUAAACAAGGAGAUUUAUGGGCGCAAAGGAAACUUUCGCAUAUGCCAAGGAUGAGCCUCAUAAAAU
................((((.((((..((((..........))))...)))).))))(((((((((((((((....)))).)).....(....)....))).)))))).. ( -25.30)
>DroYak_CAF1 40149 110 - 1
GAAAAUAUGUUUUUAAUUUCAUUGUUUGCUCUGCCCCACAAGAGCUAAAGAAGGAGAUUUAUGAGCGUAAAGGAAACUUUCGCAUAUGCCAAGGAUGAGCCUCAUAAAAA
................((((.((.((((((((........))))).))).)).))))((((((((((.((((....)))))))....((((....)).)).))))))).. ( -26.40)
>consensus
GAAAAUAUGUUUUUAAUUUCAUUGUUUGCUCUGCCCCACAAGAGCUAAACAAGGAGAUUUAUGAACGUAAAGGAAACUUUCGCAUAGUCUAAGGAUCAGCCUCAUAAAAA
........((((..((((((.(((((((((((........))))).)))))).))))))...))))((((((....)))).))........(((.....)))........ (-21.82 = -21.98 +   0.16)

alignment

secondary structure

dotplot

Window 9

Location	5,391,460 – 5,391,558
Length	98
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	88.39
Mean single sequence MFE	-22.26
Consensus MFE	-18.96
Energy contribution	-19.12
Covariance contribution	0.16
Combinations/Pair	1.21
Mean z-score	-1.38
Structure conservation index	0.85
SVM decision value	0.10
SVM RNA-class probability	0.585006
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5391460 98 - 23771897
GAAUCUAAAUCCCGACUGUGCCCGACC---------AGAAAAUACGUUUUUAAUUUCAUUGUUUACUCUGCUCCACAGGAGCUAAACAAGGAGAUUUAUGAACGUAA
...............(((........)---------))....(((((((..((((((.(((((((....(((((...)))))))))))).))))))...))))))). ( -24.70)
>DroSec_CAF1 40476 107 - 1
GAAUCUAAAUCCCGACAGUGCCCGACCAGUAUGAGCAGAAAAUAUGUUUUUAAUUUCAUUGUUUGCUCUGCCCCACAAGAGCUAAACAAGGAGAUUUAUGAACGUAA
.............(...((((.......))))...)......(((((((..((((((.(((((((((((........))))).)))))).))))))...))))))). ( -24.60)
>DroSim_CAF1 40119 98 - 1
GAAUCUAAAUCCCGACUGUGCCCGACC---------AGAAAAUAUGUUUUUAAUUUCAUUGUUUGUUCUGCCCCAUAAGAGCUAAACAAAGAGAUUUAUGAACGUAA
...............(((........)---------))....(((((((..((((((.(((((((((((........))))).)))))).))))))...))))))). ( -21.90)
>DroEre_CAF1 40653 98 - 1
GAAUCUAAAUCCCGACUUGGGCCGUCC---------AGAAAAUAUGUUUUUAAUUUCAUUGUCUGCUCCGCCCCACAAGAGCUAAACAAGGAGAUUUAUGGGCGCAA
..........(((.....))).(((((---------((((((....)))))((((((.((((..((((..........))))...)))).))))))..))))))... ( -20.90)
>DroYak_CAF1 40189 98 - 1
GAAUCUAAAUCCCGCCAGUGCCCGUCC---------AGAAAAUAUGUUUUUAAUUUCAUUGUUUGCUCUGCCCCACAAGAGCUAAAGAAGGAGAUUUAUGAGCGUAA
...........................---------......(((((((..((((((.((.((((((((........))))).))).)).))))))...))))))). ( -19.20)
>consensus
GAAUCUAAAUCCCGACUGUGCCCGACC_________AGAAAAUAUGUUUUUAAUUUCAUUGUUUGCUCUGCCCCACAAGAGCUAAACAAGGAGAUUUAUGAACGUAA
..........................................(((((((..((((((.(((((((((((........))))).)))))).))))))...))))))). (-18.96 = -19.12 +   0.16)

alignment

secondary structure

dotplot

Window 0

Location	5,391,558 – 5,391,672
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.90
Mean single sequence MFE	-33.02
Consensus MFE	-27.30
Energy contribution	-27.38
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-2.36
Structure conservation index	0.83
SVM decision value	2.22
SVM RNA-class probability	0.990589
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5391558 114 + 23771897
AAUUAAACUGUCAACGGGACA------GGGUCUUCCAUUCACGGCAAACAAGCCGCCCUCCUCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGU
...(((((((.(((.(((.((------(((...........((((......))))............)))))))).((((((((((......)))).))))))....))).)).))))). ( -35.30)
>DroSec_CAF1 40583 114 + 1
AAUUAAACUGUCAACGGGACA------GGGACUCCCAUUCACCGCAAACAAGUCGCACUCCUACGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGU
.......(((((.....))))------)((....)).......(((((((....(((.......((.....))...((((((((((......)))).)))))).....)))..))))))) ( -32.50)
>DroSim_CAF1 40217 114 + 1
AAUUAAACUGUCAACGGGACA------GGGACUCCCAUUCACCGCAAACAAGCCGCACUCCUCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGU
.......(((((.....))))------)((....)).......(((((((....(((.......((.....))...((((((((((......)))).)))))).....)))..))))))) ( -32.50)
>DroEre_CAF1 40751 120 + 1
AAUUAAACUGUCAACGGGACCGGGACUGGGACUCCCAUUCACCGCAAACAAGCCGCACUCCUCCGCCUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGU
...(((((((.((((((((.(((((.((((...)))).)).)))..........((........)).)))))....((((((((((......)))).))))))....))).)).))))). ( -35.40)
>DroYak_CAF1 40287 113 + 1
AAUUAAACUGUCAACGGGACA-------GGACUCCCAUUCACCGCAAACCAGCCGCACUCCUUCGUUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGU
...(((((((.(((.(((.((-------(((............((......)).((........)).)))))))).((((((((((......)))).))))))....))).)).))))). ( -29.40)
>consensus
AAUUAAACUGUCAACGGGACA______GGGACUCCCAUUCACCGCAAACAAGCCGCACUCCUCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGU
...............((((.............)))).......(((((((....(((.......((.....))...((((((((((......)))).)))))).....)))..))))))) (-27.30 = -27.38 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	5,391,558 – 5,391,672
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.90
Mean single sequence MFE	-40.94
Consensus MFE	-35.62
Energy contribution	-36.42
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.45
Structure conservation index	0.87
SVM decision value	0.82
SVM RNA-class probability	0.857834
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5391558 114 - 23771897
ACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGAGGAGGGCGGCUUGUUUGCCGUGAAUGGAAGACCC------UGUCCCGUUGACAGUUUAAUU
.((..((((((......((((((.((((......)))))))))).(((((((..((........))..)))))))))))))..)).......(------((((.....)))))....... ( -40.80)
>DroSec_CAF1 40583 114 - 1
ACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGUAGGAGUGCGACUUGUUUGCGGUGAAUGGGAGUCCC------UGUCCCGUUGACAGUUUAAUU
..((((...((......((((((.((((......)))))))))).(((((((..(((......)))..))))))))).((.(((((((.....------..))))))).)).)))).... ( -40.80)
>DroSim_CAF1 40217 114 - 1
ACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGAGGAGUGCGGCUUGUUUGCGGUGAAUGGGAGUCCC------UGUCCCGUUGACAGUUUAAUU
..((((...((......((((((.((((......)))))))))).(((((((..(((......)))..))))))))).((.(((((((.....------..))))))).)).)))).... ( -41.00)
>DroEre_CAF1 40751 120 - 1
ACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAGGCGGAGGAGUGCGGCUUGUUUGCGGUGAAUGGGAGUCCCAGUCCCGGUCCCGUUGACAGUUUAAUU
..((((.(((((..(.....)..))))).((.(((((.(((..(..((((((..(((......)))..))))))..)((.((.((((...)))).)))).)))))))).)).)))).... ( -42.60)
>DroYak_CAF1 40287 113 - 1
ACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAACGAAGGAGUGCGGCUGGUUUGCGGUGAAUGGGAGUCC-------UGUCCCGUUGACAGUUUAAUU
.(((((.((((..((..((((((.((((......))))))))))...)).(....)...........)))))))))..((.(((((((....-------..))))))).))......... ( -39.50)
>consensus
ACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGAGGAGUGCGGCUUGUUUGCGGUGAAUGGGAGUCCC______UGUCCCGUUGACAGUUUAAUU
..((((...((......((((((.((((......)))))))))).(((((((..(((......)))..))))))))).((.(((((((.............))))))).)).)))).... (-35.62 = -36.42 +   0.80)

alignment

secondary structure

dotplot

Window 2

Location	5,391,592 – 5,391,703
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-36.72
Consensus MFE	-35.54
Energy contribution	-35.06
Covariance contribution	-0.48
Combinations/Pair	1.11
Mean z-score	-3.65
Structure conservation index	0.97
SVM decision value	5.14
SVM RNA-class probability	0.999976
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5391592 111 + 23771897
ACGGCAAACAAGCCGCCCUCCUCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUAAAUUCGAAUU
.((((......)))).........((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).)))).............. ( -41.00)
>DroSec_CAF1 40617 111 + 1
ACCGCAAACAAGUCGCACUCCUACGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUAAAUUCGAAUU
...((.........))........((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).)))).............. ( -35.40)
>DroSim_CAF1 40251 111 + 1
ACCGCAAACAAGCCGCACUCCUCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUAAAUUCGAAUU
...((......))...........((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).)))).............. ( -35.50)
>DroEre_CAF1 40791 111 + 1
ACCGCAAACAAGCCGCACUCCUCCGCCUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGAAGGCAUUAAAUUCGAAUU
...((......))...........((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).)))).............. ( -38.20)
>DroYak_CAF1 40320 111 + 1
ACCGCAAACCAGCCGCACUCCUUCGUUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGAAGGCAUUAAAUUCGAAUU
...........(((((........))...(((((((((((((((((......)))).))))))........((((.....)))).)))))))..))).............. ( -33.50)
>consensus
ACCGCAAACAAGCCGCACUCCUCCGCUUCCUGCUCACCUGUCGCCAUUCACCUGGCAGACAGGACACUUGCCAUGUUUGUCAUGUUGAGCAGCAGGCAUUAAAUUCGAAUU
...((......))...........((((.(((((((((((((((((......)))).))))))........((((.....)))).))))))).)))).............. (-35.54 = -35.06 +  -0.48)

alignment

secondary structure

dotplot

Window 3

Location	5,391,592 – 5,391,703
Length	111
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-42.04
Consensus MFE	-37.06
Energy contribution	-37.74
Covariance contribution	0.68
Combinations/Pair	1.03
Mean z-score	-2.75
Structure conservation index	0.88
SVM decision value	3.36
SVM RNA-class probability	0.999083
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5391592 111 - 23771897
AAUUCGAAUUUAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGAGGAGGGCGGCUUGUUUGCCGU
........(((..(((.(.(((((((.((((.....))))........((((((.((((......))))))))))))))))).).)))...))).(((((......))))) ( -42.40)
>DroSec_CAF1 40617 111 - 1
AAUUCGAAUUUAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGUAGGAGUGCGACUUGUUUGCGGU
...(((..((..((((.(.(((((((.((((.....))))........((((((.((((......))))))))))))))))).).))))..))...)))............ ( -39.20)
>DroSim_CAF1 40251 111 - 1
AAUUCGAAUUUAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGAGGAGUGCGGCUUGUUUGCGGU
..............(((..(((((((.((((.....))))........((((((.((((......)))))))))))))))))...(((((.(((.....))).)))))))) ( -41.40)
>DroEre_CAF1 40791 111 - 1
AAUUCGAAUUUAAUGCCUUCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAGGCGGAGGAGUGCGGCUUGUUUGCGGU
....((.((((..(((((((((((((.((((.....))))........((((((.((((......)))))))))))))))))))))))...)))).))((......))... ( -47.80)
>DroYak_CAF1 40320 111 - 1
AAUUCGAAUUUAAUGCCUUCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAACGAAGGAGUGCGGCUGGUUUGCGGU
....((((((...(((((((((((((.((((.....))))........((((((.((((......))))))))))))))).(....)..))))).)))...)))))).... ( -39.40)
>consensus
AAUUCGAAUUUAAUGCCUGCUGCUCAACAUGACAAACAUGGCAAGUGUCCUGUCUGCCAGGUGAAUGGCGACAGGUGAGCAGGAAGCGGAGGAGUGCGGCUUGUUUGCGGU
..............(((..(((((((.((((.....))))........((((((.((((......)))))))))))))))))...(((((.(((.....))).)))))))) (-37.06 = -37.74 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:26 2006