Locus 869

Sequence ID	2L_DroMel_CAF1
Location	2,476,588 – 2,476,722
Length	134
Max. P	0.999938

overview

Window 8

Location	2,476,588 – 2,476,685
Length	97
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-36.86
Consensus MFE	-35.40
Energy contribution	-35.08
Covariance contribution	-0.32
Combinations/Pair	1.09
Mean z-score	-4.65
Structure conservation index	0.96
SVM decision value	4.68
SVM RNA-class probability	0.999938
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2476588 97 + 22407834
UUAUCUGUUUGGCUCGUUGCCGUUUUUUGUAUAAUUU----UUUAGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCGACAGCACCU
..........(((.....)))................----...((((((((..((((..((((..((((........))))..)))))))).)))))))) ( -36.50)
>DroSec_CAF1 55851 97 + 1
UUAUCUUUUUGGCUCGUUGCCGUUUUUUGUAUAAUUU----UUUAGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCGACAGCACCU
..........(((.....)))................----...((((((((..((((..((((..((((........))))..)))))))).)))))))) ( -36.50)
>DroSim_CAF1 58853 97 + 1
UUAUCUGUUUGGCUCGUUGCCGUUUUUUGUAUAAUUU----UUUAGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCGACAGCACCU
..........(((.....)))................----...((((((((..((((..((((..((((........))))..)))))))).)))))))) ( -36.50)
>DroEre_CAF1 58054 96 + 1
UUAUCUGUUUGGCUUGUUGCCGUU-UUUGUAUAAUUU----UUUAGGUGCUGCUUGCUGCUGGGUGUGACAAAUUAACGUCGUACCCAAGCGACAGCACCU
.(((..(..((((.....))))..-)..)))......----...((((((((.(((((..((((((((((........))))))))))))))))))))))) ( -37.60)
>DroYak_CAF1 58342 101 + 1
UUAUCUGUUUGGCUUGUUGCCGUUUUUUGUAUAAUUUUUUUUUUGGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCAACAGCACCU
..........(((.....))).......................((((((((..((((..((((..((((........))))..)))))))).)))))))) ( -37.20)
>consensus
UUAUCUGUUUGGCUCGUUGCCGUUUUUUGUAUAAUUU____UUUAGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCGACAGCACCU
..........(((.....))).......................((((((((..((((..((((..((((........))))..)))))))).)))))))) (-35.40 = -35.08 +  -0.32)

alignment

secondary structure

dotplot

Window 9

Location	2,476,588 – 2,476,685
Length	97
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	95.33
Mean single sequence MFE	-34.02
Consensus MFE	-32.78
Energy contribution	-33.06
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-5.44
Structure conservation index	0.96
SVM decision value	3.68
SVM RNA-class probability	0.999523
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2476588 97 - 22407834
AGGUGCUGUCGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCUAAA----AAAUUAUACAAAAAACGGCAACGAGCCAAACAGAUAA
(((((((((((((((((...((((......))))...))))..))).))))))))))...----................(((.....))).......... ( -34.80)
>DroSec_CAF1 55851 97 - 1
AGGUGCUGUCGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCUAAA----AAAUUAUACAAAAAACGGCAACGAGCCAAAAAGAUAA
(((((((((((((((((...((((......))))...))))..))).))))))))))...----................(((.....))).......... ( -34.80)
>DroSim_CAF1 58853 97 - 1
AGGUGCUGUCGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCUAAA----AAAUUAUACAAAAAACGGCAACGAGCCAAACAGAUAA
(((((((((((((((((...((((......))))...))))..))).))))))))))...----................(((.....))).......... ( -34.80)
>DroEre_CAF1 58054 96 - 1
AGGUGCUGUCGCUUGGGUACGACGUUAAUUUGUCACACCCAGCAGCAAGCAGCACCUAAA----AAAUUAUACAAA-AACGGCAACAAGCCAAACAGAUAA
(((((((((.((((((((..((((......))))..)))))..)))..)))))))))...----............-...(((.....))).......... ( -33.40)
>DroYak_CAF1 58342 101 - 1
AGGUGCUGUUGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCCAAAAAAAAAAUUAUACAAAAAACGGCAACAAGCCAAACAGAUAA
.((((((((((((((((...((((......))))...))))..)))).))))))))........................(((.....))).......... ( -32.30)
>consensus
AGGUGCUGUCGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCUAAA____AAAUUAUACAAAAAACGGCAACGAGCCAAACAGAUAA
(((((((((((((((((...((((......))))...))))..))).)))))))))).......................(((.....))).......... (-32.78 = -33.06 +   0.28)

alignment

secondary structure

dotplot

Window 0

Location	2,476,620 – 2,476,722
Length	102
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	83.64
Mean single sequence MFE	-33.95
Consensus MFE	-25.24
Energy contribution	-25.35
Covariance contribution	0.11
Combinations/Pair	1.27
Mean z-score	-3.71
Structure conservation index	0.74
SVM decision value	1.24
SVM RNA-class probability	0.934765
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2476620 102 + 22407834
AAUUU----UUUAGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCGACAGCACCUCAGA--AAAUCAACAA-AAUCCUCAACGAAAUCGCGCGAC
.((((----(((((((((((..((((..((((..((((........))))..)))))))).)))))))).)))--))))......-....................... ( -35.10)
>DroSec_CAF1 55883 102 + 1
AAUUU----UUUAGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCGACAGCACCUCAGA--AAGUCAACAA-AAUCCUCAACGAAAUCGCGCGAC
.((((----(((((((((((..((((..((((..((((........))))..)))))))).)))))))).)))--))))......-....................... ( -35.10)
>DroSim_CAF1 58885 102 + 1
AAUUU----UUUAGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCGACAGCACCUCAGA--AAGUCAACAA-AAUCCUCAACGAAAUCGCGCGAC
.((((----(((((((((((..((((..((((..((((........))))..)))))))).)))))))).)))--))))......-....................... ( -35.10)
>DroEre_CAF1 58085 102 + 1
AAUUU----UUUAGGUGCUGCUUGCUGCUGGGUGUGACAAAUUAACGUCGUACCCAAGCGACAGCACCUCAAA--AAAUCAACAA-AAUCCUCAACGAAAUCGCGCGAC
.((((----(((((((((((.(((((..((((((((((........))))))))))))))))))))))).)))--))))......-....................... ( -35.60)
>DroYak_CAF1 58374 108 + 1
AAUUUUUUUUUUGGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCAACAGCACCUCACAGCAAAUCAACAAAAAUCCUCAGCGAAAUCGCGCGA-
............((((((((..((((..((((..((((........))))..)))))))).)))))))).........................(((....)))....- ( -36.70)
>DroAna_CAF1 66057 77 + 1
AUUUU----UUU--GUGG----UGCUGCUGGGUGUGACAAAUUAACAUCGCGCCCAACUGCCAGCAU------------CAA----------CAACAAAAGCCCGCGAC
.((((----.((--((((----(((((((((((((((..........)))))))))...).))))))------------).)----------))).))))......... ( -26.10)
>consensus
AAUUU____UUUAGGUGCUGCCUGCUGCUGGGUGUGACAAAUUAACGUCGUGCCCAAGCGACAGCACCUCAGA__AAAUCAACAA_AAUCCUCAACGAAAUCGCGCGAC
............((((((((..((((..((((((((((........)))))))))))))).))))))))........................................ (-25.24 = -25.35 +   0.11)

alignment

secondary structure

dotplot

Window 1

Location	2,476,620 – 2,476,722
Length	102
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	83.64
Mean single sequence MFE	-33.89
Consensus MFE	-23.47
Energy contribution	-25.05
Covariance contribution	1.58
Combinations/Pair	1.15
Mean z-score	-2.35
Structure conservation index	0.69
SVM decision value	0.29
SVM RNA-class probability	0.669605
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2476620 102 - 22407834
GUCGCGCGAUUUCGUUGAGGAUU-UUGUUGAUUU--UCUGAGGUGCUGUCGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCUAAA----AAAUU
.....(((....))).(((((((-.....)))))--))..(((((((((((((((((...((((......))))...))))..))).))))))))))...----..... ( -35.50)
>DroSec_CAF1 55883 102 - 1
GUCGCGCGAUUUCGUUGAGGAUU-UUGUUGACUU--UCUGAGGUGCUGUCGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCUAAA----AAAUU
((((.((((..((......))..-))))))))..--....(((((((((((((((((...((((......))))...))))..))).))))))))))...----..... ( -37.70)
>DroSim_CAF1 58885 102 - 1
GUCGCGCGAUUUCGUUGAGGAUU-UUGUUGACUU--UCUGAGGUGCUGUCGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCUAAA----AAAUU
((((.((((..((......))..-))))))))..--....(((((((((((((((((...((((......))))...))))..))).))))))))))...----..... ( -37.70)
>DroEre_CAF1 58085 102 - 1
GUCGCGCGAUUUCGUUGAGGAUU-UUGUUGAUUU--UUUGAGGUGCUGUCGCUUGGGUACGACGUUAAUUUGUCACACCCAGCAGCAAGCAGCACCUAAA----AAAUU
.....((((..((......))..-)))).(((((--(((.(((((((((.((((((((..((((......))))..)))))..)))..))))))))))))----))))) ( -35.80)
>DroYak_CAF1 58374 108 - 1
-UCGCGCGAUUUCGCUGAGGAUUUUUGUUGAUUUGCUGUGAGGUGCUGUUGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCCAAAAAAAAAAUU
-(((((((....))).(..((((......))))..).))))((((((((((((((((...((((......))))...))))..)))).))))))))............. ( -35.80)
>DroAna_CAF1 66057 77 - 1
GUCGCGGGCUUUUGUUG----------UUG------------AUGCUGGCAGUUGGGCGCGAUGUUAAUUUGUCACACCCAGCAGCA----CCAC--AAA----AAAAU
...((.(((........----------...------------..))).)).((((((.(.((((......)))).).))))))....----....--...----..... ( -20.82)
>consensus
GUCGCGCGAUUUCGUUGAGGAUU_UUGUUGAUUU__UCUGAGGUGCUGUCGCUUGGGCACGACGUUAAUUUGUCACACCCAGCAGCAGGCAGCACCUAAA____AAAUU
.(((.(((....))))))......................(((((((((((((((((...((((......))))...))))..))).))))))))))............ (-23.47 = -25.05 +   1.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:36 2006