Locus 4574

Sequence ID	2L_DroMel_CAF1
Location	13,120,819 – 13,120,951
Length	132
Max. P	0.999912

overview

Window 8

Location	13,120,819 – 13,120,930
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.14
Mean single sequence MFE	-30.67
Consensus MFE	-16.51
Energy contribution	-16.93
Covariance contribution	0.42
Combinations/Pair	1.17
Mean z-score	-2.90
Structure conservation index	0.54
SVM decision value	2.43
SVM RNA-class probability	0.993883
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13120819 111 + 22407834
AGCUCUAUU---UUUUCCACUGUG----UACACAGACACAUAUGGAGAGCAGACAGCCUCCUGGUAUUGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACC--GAAG
.(((.....---(((((((.((((----(......)))))..))))))).....)))....((((((((((((((.((.(((((......))))).)).)))))))))..))))--)... ( -36.30)
>DroSec_CAF1 13737 111 + 1
ACCACUUUA---UUUUCCACUGUG----UACACAGCCACAUAUGGAUAGCAGACAGCCUCCUGGUAUCGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACC--GAAG
....((((.---...((((.((((----(........)))))))))................((((..(((((((.((.(((((......))))).)).)))))))....))))--)))) ( -28.80)
>DroSim_CAF1 14966 111 + 1
ACCACUUUA---UUUUCCACUGUG----UACACAGUCACAUAUGGAUAGCAGACAGCCUCCUGGUAUCGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACC--GAAG
....((((.---......(((((.----...)))))........((((.(((........))).))))(((((((.((.(((((......))))).)).)))))))........--)))) ( -29.80)
>DroEre_CAF1 15569 87 + 1
AUA------------------------------AUAUACAUAUGGAGAGCAGACAGUUUCCUGGUAUUGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACC--GA-G
...------------------------------..........(((((........)))))((((((((((((((.((.(((((......))))).)).)))))))))..))))--).-. ( -27.00)
>DroYak_CAF1 14117 111 + 1
GGAACUUUU---UUUUCCACAGUG----UACACAGACACAUAUGGAGCGCAGACAGCCUCCUGGUAUUGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACC--GAAG
((((.....---..))))...(((----(......))))....((((.((.....))))))((((((((((((((.((.(((((......))))).)).)))))))))..))))--)... ( -37.60)
>DroAna_CAF1 21911 110 + 1
AUUAUUUUGAAUUUUUUUCUUGUGCAUUUAAAAAAGCACACAUGGAAAACUUAUAGC----UGGUA---GGUUGAUGCCUUGGCCAUUUCAGCGA---UUUAAUUCAAUUUACCAAGAAG
..((..(((((((.(((((((((((..........)))))...))))))......((----(((..---(((..(....)..)))...)))))..---...)))))))..))........ ( -24.50)
>consensus
ACCACUUUA___UUUUCCACUGUG____UACACAGACACAUAUGGAGAGCAGACAGCCUCCUGGUAUUGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACC__GAAG
..............................................................((((..(((((((.((.(((((......))))).)).)))))))....))))...... (-16.51 = -16.93 +   0.42)

alignment

secondary structure

dotplot

Window 9

Location	13,120,819 – 13,120,930
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.14
Mean single sequence MFE	-31.74
Consensus MFE	-18.88
Energy contribution	-20.88
Covariance contribution	2.00
Combinations/Pair	1.16
Mean z-score	-2.44
Structure conservation index	0.59
SVM decision value	1.97
SVM RNA-class probability	0.984304
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13120819 111 - 22407834
CUUC--GGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCAAUACCAGGAGGCUGUCUGCUCUCCAUAUGUGUCUGUGUA----CACAGUGGAAAA---AAUAGAGCU
((((--((((..(((((((((.((.(.(((......))).).)).))))))))))))).)))).......(((((((((.(((((......)----)))))))))...---....)))). ( -38.71)
>DroSec_CAF1 13737 111 - 1
CUUC--GGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCGAUACCAGGAGGCUGUCUGCUAUCCAUAUGUGGCUGUGUA----CACAGUGGAAAA---UAAAGUGGU
((((--((((..(((((((((.((.(.(((......))).).)).))))))))))))).))))((.....))..(((((.((((........----)))))))))...---......... ( -36.00)
>DroSim_CAF1 14966 111 - 1
CUUC--GGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCGAUACCAGGAGGCUGUCUGCUAUCCAUAUGUGACUGUGUA----CACAGUGGAAAA---UAAAGUGGU
((((--((((..(((((((((.((.(.(((......))).).)).))))))))))))).))))((.....))..(((((.((((........----)))))))))...---......... ( -34.70)
>DroEre_CAF1 15569 87 - 1
C-UC--GGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCAAUACCAGGAAACUGUCUGCUCUCCAUAUGUAUAU------------------------------UAU
.-..--((...((((((((((.((.(.(((......))).).)).))))))))))..(((....)))........))..........------------------------------... ( -25.60)
>DroYak_CAF1 14117 111 - 1
CUUC--GGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCAAUACCAGGAGGCUGUCUGCGCUCCAUAUGUGUCUGUGUA----CACUGUGGAAAA---AAAAGUUCC
((((--((((..(((((((((.((.(.(((......))).).)).))))))))))))).))))((.....))..((((((.((((......)----)))))))))...---......... ( -37.00)
>DroAna_CAF1 21911 110 - 1
CUUCUUGGUAAAUUGAAUUAAA---UCGCUGAAAUGGCCAAGGCAUCAACC---UACCA----GCUAUAAGUUUUCCAUGUGUGCUUUUUUAAAUGCACAAGAAAAAAAUUCAAAAUAAU
............(((((((...---..(((...(((((..(((......))---)....----))))).)))((((....(((((..........))))).))))..)))))))...... ( -18.40)
>consensus
CUUC__GGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCAAUACCAGGAGGCUGUCUGCUCUCCAUAUGUGUCUGUGUA____CACAGUGGAAAA___AAAAGUGAU
......((((..(((((((((.((.(.(((......))).).)).))))))))))))).((((((.....))).)))........................................... (-18.88 = -20.88 +   2.00)

alignment

secondary structure

dotplot

Window 0

Location	13,120,852 – 13,120,951
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	95.30
Mean single sequence MFE	-36.20
Consensus MFE	-33.46
Energy contribution	-34.22
Covariance contribution	0.76
Combinations/Pair	1.06
Mean z-score	-4.48
Structure conservation index	0.92
SVM decision value	4.50
SVM RNA-class probability	0.999910
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13120852 99 + 22407834
UAUGGAGAGCAGACAGCCUCCUGGUAUUGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACCGAAGGGGAUUCCUCUUCCAAAAAAA
...((((.((.....)))))).(((((((((((((.((.(((((......))))).)).)))))))))..))))(((((((...)))))))........ ( -39.00)
>DroSec_CAF1 13770 96 + 1
UAUGGAUAGCAGACAGCCUCCUGGUAUCGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACCGAAGGGGAUUCCUCUUCCAAAA---
....((((.(((........))).))))(((((((.((.(((((......))))).)).)))))))........(((((((...))))))).....--- ( -33.10)
>DroSim_CAF1 14999 97 + 1
UAUGGAUAGCAGACAGCCUCCUGGUAUCGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACCGAAGGGGAUUCCUCUUCCAAAAA--
....((((.(((........))).))))(((((((.((.(((((......))))).)).)))))))........(((((((...)))))))......-- ( -33.10)
>DroEre_CAF1 15579 96 + 1
UAUGGAGAGCAGACAGUUUCCUGGUAUUGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACCGA-GGGGAUUCCUCUUCCGAAAA--
..(((((((.....(((..((((((((((((((((.((.(((((......))))).)).)))))))))..)))).)-))..))).))).))))....-- ( -36.80)
>DroYak_CAF1 14150 97 + 1
UAUGGAGCGCAGACAGCCUCCUGGUAUUGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACCGAAGGGGAUUCCUCUUCCGAAAA--
...((((.((.....)))))).(((((((((((((.((.(((((......))))).)).)))))))))..))))(((((((...)))))))......-- ( -39.00)
>consensus
UAUGGAGAGCAGACAGCCUCCUGGUAUUGAAUUGAUGCCUUGCCCAUUCUGGCGACGCUUCAAUUCAAUUUACCGAAGGGGAUUCCUCUUCCAAAAA__
...((((.((.....)))))).((((.((((((((.((.(((((......))))).)).))))))))...))))(((((((...)))))))........ (-33.46 = -34.22 +   0.76)

alignment

secondary structure

dotplot

Window 1

Location	13,120,852 – 13,120,951
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	95.30
Mean single sequence MFE	-36.16
Consensus MFE	-32.52
Energy contribution	-33.08
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-3.86
Structure conservation index	0.90
SVM decision value	4.51
SVM RNA-class probability	0.999912
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13120852 99 - 22407834
UUUUUUUGGAAGAGGAAUCCCCUUCGGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCAAUACCAGGAGGCUGUCUGCUCUCCAUA
........((((.((....))))))((((..(((((((((.((.(.(((......))).).)).))))))))))))).((((((.....)).))))... ( -37.50)
>DroSec_CAF1 13770 96 - 1
---UUUUGGAAGAGGAAUCCCCUUCGGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCGAUACCAGGAGGCUGUCUGCUAUCCAUA
---...((((((.(((....(((((((((..(((((((((.((.(.(((......))).).)).))))))))))))).)))))...))).)).)))).. ( -35.60)
>DroSim_CAF1 14999 97 - 1
--UUUUUGGAAGAGGAAUCCCCUUCGGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCGAUACCAGGAGGCUGUCUGCUAUCCAUA
--....((((((.(((....(((((((((..(((((((((.((.(.(((......))).).)).))))))))))))).)))))...))).)).)))).. ( -35.60)
>DroEre_CAF1 15579 96 - 1
--UUUUCGGAAGAGGAAUCCCC-UCGGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCAAUACCAGGAAACUGUCUGCUCUCCAUA
--.....(((.((((.....))-))((((.((((((((((.((.(.(((......))).).)).))))))))))..(((....)))..)))).)))... ( -34.60)
>DroYak_CAF1 14150 97 - 1
--UUUUCGGAAGAGGAAUCCCCUUCGGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCAAUACCAGGAGGCUGUCUGCGCUCCAUA
--......((((.((....))))))((((..(((((((((.((.(.(((......))).).)).))))))))))))).((((((.....)).))))... ( -37.50)
>consensus
__UUUUUGGAAGAGGAAUCCCCUUCGGUAAAUUGAAUUGAAGCGUCGCCAGAAUGGGCAAGGCAUCAAUUCAAUACCAGGAGGCUGUCUGCUCUCCAUA
.......(((((.(((....(((((((((..(((((((((.((.(.(((......))).).)).))))))))))))).)))))...))).)).)))... (-32.52 = -33.08 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:26 2006