Locus 2006

Sequence ID	3R_DroMel_CAF1
Location	5,699,804 – 5,700,029
Length	225
Max. P	0.968389

overview

Window 6

Location	5,699,804 – 5,699,918
Length	114
Sequences	3
Columns	116
Reading direction	reverse
Mean pairwise identity	93.10
Mean single sequence MFE	-30.37
Consensus MFE	-28.29
Energy contribution	-28.40
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-2.53
Structure conservation index	0.93
SVM decision value	1.50
SVM RNA-class probability	0.959581
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5699804 114 - 27905053
UUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGACGCAGCAACAAUGUUGCGAAAACAGCUGUUGAACAGCGAACAUCAGUCUCAAAACAAACGA--GAGAGAAAGAGCG
.................((..(((((((((((...(....)((((((....))))))...)))))))))))...........((..((((...........--..))))..)))). ( -29.52)
>DroSim_CAF1 2654 116 - 1
UUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGACGCAGCAACAAUGUUGCGAAAACAGCUGUUGAGCAGCGAACAUCAGUCUCACAACAAACGAGAGAGAGAAAGAGCG
.................((..(((((((((((...(....)((((((....))))))...))))))))))).)).((.....((..((((.........))))..))......)). ( -32.80)
>DroYak_CAF1 3064 113 - 1
UUAUCAAUAACAACAGAGCUAUAACAGCUGUUGGAGGCGACGCAGCAACAAUGUUGCGAAAACAGCUGUUGAACAGCGAACAUCAGCCCCAAAACAAACGAGAGAGAGAGAGA---
...((...........((((.....)))).((((.(((..(((((((....)))))))......((((.....))))........))))))).......))............--- ( -28.80)
>consensus
UUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGACGCAGCAACAAUGUUGCGAAAACAGCUGUUGAACAGCGAACAUCAGUCUCAAAACAAACGAGAGAGAGAAAGAGCG
...((.....((((((...........))))))(((((..(((((((....)))))))......((((.....))))........)))))...............))......... (-28.29 = -28.40 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	5,699,840 – 5,699,950
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.09
Mean single sequence MFE	-35.89
Consensus MFE	-17.78
Energy contribution	-19.83
Covariance contribution	2.06
Combinations/Pair	1.07
Mean z-score	-2.24
Structure conservation index	0.50
SVM decision value	0.93
SVM RNA-class probability	0.884915
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5699840 110 - 27905053
AAUGUGCGU--------GUGUGAGUGCGACUCGCUCUGGUUUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGACGCAGC-AACAAUGUUGCGAAAACAGCUG-UUGAACAGCG
.....((.(--------((...........((((((((...............))))))))(((((((((((...(....)(((((-(....))))))...))))))))-))).))))). ( -39.26)
>DroPse_CAF1 16137 100 - 1
ACUGUGCGUGUAUCAGUGUGUGUGUGCGUUUCGCUCUGUAUUAUCAAUA---ACAGAGCGGA-----------GAGGAGA-ACAGCGAACA-----GCGAACAGAGUGGAACGAGCAGCG
.((((.(((...(((.(.(((.(((.(.(((((((((((..........---))))))))))-----------)..)...-)))((.....-----))..))).).))).))).)))).. ( -30.70)
>DroSec_CAF1 3185 110 - 1
AAUGUGCGU--------GUGUGAGUGCGACUCGCUCUGGUUUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGACGCAGC-AACAAUGUUGCGAAAACAGCUG-GUGAACAGCG
..((..(..--------......)..))..((((((((...............)))))))).....((((((.(.(((..((((((-(....)))))))......))).-.).)))))). ( -37.26)
>DroSim_CAF1 2692 110 - 1
AAUGUGCGU--------GUGUGAGUGCGACUCGCUCUGGUUUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGACGCAGC-AACAAUGUUGCGAAAACAGCUG-UUGAGCAGCG
.....((.(--------((...........((((((((...............))))))))(((((((((((...(....)(((((-(....))))))...))))))))-))).))))). ( -39.56)
>DroYak_CAF1 3099 110 - 1
AAUGUGCGU--------GUGUGAGUGCGACUCGCUCUGGUUUAUCAAUAACAACAGAGCUAUAACAGCUGUUGGAGGCGACGCAGC-AACAAUGUUGCGAAAACAGCUG-UUGAACAGCG
.....((.(--------((..(((.....)))((((((...............))))))..(((((((((((...(....)(((((-(....))))))...))))))))-))).))))). ( -37.86)
>DroPer_CAF1 18514 100 - 1
ACUGUGCGUGUAUCAGUGUGUGUGUGCGUUUCGCUCUGUAUUAUCAAUA---ACAGAGCGGA-----------GAGGAGA-ACAGCGAACA-----GCGAACAGAGUGGAACGAGCAGCG
.((((.(((...(((.(.(((.(((.(.(((((((((((..........---))))))))))-----------)..)...-)))((.....-----))..))).).))).))).)))).. ( -30.70)
>consensus
AAUGUGCGU________GUGUGAGUGCGACUCGCUCUGGUUUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGACGCAGC_AACAAUGUUGCGAAAACAGCUG_UUGAACAGCG
..(((.(((.........(((...((((..((((((((...............)))))))).....(((......)))..))))....))).....)))...)))((((......)))). (-17.78 = -19.83 +   2.06)

alignment

secondary structure

dotplot

Window 8

Location	5,699,878 – 5,699,989
Length	111
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	97.31
Mean single sequence MFE	-41.81
Consensus MFE	-40.19
Energy contribution	-40.69
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-3.94
Structure conservation index	0.96
SVM decision value	1.63
SVM RNA-class probability	0.968389
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5699878 111 - 27905053
CAAAUCUACAGAGCACUUGUC-ACGCAUACGCGCAUCAUAAAUGUGCGUGUGUGAGUGCGACUCGCUCUGGUUUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGA
....(((((((.(((((....-.(((((((((((((.....))))))))))))))))))...((((((((...............))))))))......))).))))..... ( -43.26)
>DroSec_CAF1 3223 111 - 1
UA-AUCUACAGAGCACUUGUCAACGCAUACGCGCAUCAUAAAUGUGCGUGUGUGAGUGCGACUCGCUCUGGUUUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGA
..-.(((((((.(((((......(((((((((((((.....))))))))))))))))))...((((((((...............))))))))......))).))))..... ( -42.86)
>DroSim_CAF1 2730 111 - 1
CA-AUCUACAGAGCACUUGUCAACGCAUACGCGCAUCAUAAAUGUGCGUGUGUGAGUGCGACUCGCUCUGGUUUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGA
..-.(((((((.(((((......(((((((((((((.....))))))))))))))))))...((((((((...............))))))))......))).))))..... ( -42.86)
>DroYak_CAF1 3137 111 - 1
CA-AUCUACAUAGCACUUGUCAACGCAUACGCGCAUCAUAAAUGUGCGUGUGUGAGUGCGACUCGCUCUGGUUUAUCAAUAACAACAGAGCUAUAACAGCUGUUGGAGGCGA
..-.........(((((......(((((((((((((.....))))))))))))))))))..(((((((((...............))))))..((((....))))))).... ( -38.26)
>consensus
CA_AUCUACAGAGCACUUGUCAACGCAUACGCGCAUCAUAAAUGUGCGUGUGUGAGUGCGACUCGCUCUGGUUUAUCAACAACAACAGAGCGAUAACAGCUGUUGGAGGCGA
....(((((((.(((((......(((((((((((((.....))))))))))))))))))...((((((((...............))))))))......))).))))..... (-40.19 = -40.69 +   0.50)

alignment

secondary structure

dotplot

Window 9

Location	5,699,918 – 5,700,029
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.91
Mean single sequence MFE	-29.95
Consensus MFE	-13.14
Energy contribution	-15.75
Covariance contribution	2.61
Combinations/Pair	1.04
Mean z-score	-2.88
Structure conservation index	0.44
SVM decision value	1.15
SVM RNA-class probability	0.922252
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5699918 111 - 27905053
AAGAGCAGCAUAAAAUACUACGCAGUUAAAAAAACAAAACCAAAUCUACAGAGCACUUGUC-ACGCAUACGCGCAUCAUAAAUGUGCGU--------GUGUGAGUGCGACUCGCUCUGGU
.(((((.((.((......)).))((((.................((....))(((((....-.(((((((((((((.....))))))))--------)))))))))))))).)))))... ( -34.30)
>DroPse_CAF1 16197 102 - 1
-AAAAU----AAAAAUACUACGCAGUAAAAAAA--AAAACU-------CAGA-CACUUGUCAACAGAGUCCCGC---AUAACUGUGCGUGUAUCAGUGUGUGUGUGCGUUUCGCUCUGUA
-.....----.....((((....))))......--......-------..((-(....))).(((((((..(((---(((...(..(........)..)...))))))....))))))). ( -21.90)
>DroSec_CAF1 3263 111 - 1
AAGAGCAGCAUAAAAUACUACGCAGUUAAAAAAACAAAACUA-AUCUACAGAGCACUUGUCAACGCAUACGCGCAUCAUAAAUGUGCGU--------GUGUGAGUGCGACUCGCUCUGGU
.(((((.((.((......)).))((((...............-.((....))(((((......(((((((((((((.....))))))))--------)))))))))))))).)))))... ( -33.90)
>DroSim_CAF1 2770 111 - 1
AAGAGCAGCAUAAAAUACUACGCAGUUAAAAAAACAAAACCA-AUCUACAGAGCACUUGUCAACGCAUACGCGCAUCAUAAAUGUGCGU--------GUGUGAGUGCGACUCGCUCUGGU
.(((((.((.((......)).))((((...............-.((....))(((((......(((((((((((((.....))))))))--------)))))))))))))).)))))... ( -33.90)
>DroYak_CAF1 3177 111 - 1
AAGAGCAGCAUAAAAUACUACGCAGUUAUGAAAACAAAACCA-AUCUACAUAGCACUUGUCAACGCAUACGCGCAUCAUAAAUGUGCGU--------GUGUGAGUGCGACUCGCUCUGGU
.(((((((.........)).((((((((((............-.....)))))).........(((((((((((((.....))))))))--------)))))..))))....)))))... ( -33.83)
>DroPer_CAF1 18574 102 - 1
AAAAAU----AAAAAUACUACGCAGUAAAAA-A--AAAACU-------CAGA-CACUUGUCAACAGAGUCCCGC---AUAACUGUGCGUGUAUCAGUGUGUGUGUGCGUUUCGCUCUGUA
......----.....((((....))))....-.--......-------..((-(....))).(((((((..(((---(((...(..(........)..)...))))))....))))))). ( -21.90)
>consensus
AAGAGCAGCAUAAAAUACUACGCAGUUAAAAAAACAAAACCA_AUCUACAGAGCACUUGUCAACGCAUACGCGCAUCAUAAAUGUGCGU________GUGUGAGUGCGACUCGCUCUGGU
................................................((((((..((((...(((((((((((((.....))))))))........)))))...))))...)))))).. (-13.14 = -15.75 +   2.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:03 2006