Locus 1812

Sequence ID	2R_DroMel_CAF1
Location	6,789,017 – 6,789,219
Length	202
Max. P	0.972047

overview

Window 3

Location	6,789,017 – 6,789,116
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	86.16
Mean single sequence MFE	-28.74
Consensus MFE	-25.16
Energy contribution	-25.52
Covariance contribution	0.36
Combinations/Pair	1.12
Mean z-score	-1.54
Structure conservation index	0.88
SVM decision value	0.36
SVM RNA-class probability	0.705204
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6789017 99 + 20766785
CGGUGUCAAGAAUCGCAUAUUGAGAAGUCUGCCCAGGCGGAUGUCAAUAAAUCUGACACCCAACACAAUCCGCCACAUUUUCAGCUCUUUCACAGGGCG
.(((((((.((......((((((...((((((....)))))).))))))..))))))))).......................(((((.....))))). ( -28.70)
>DroSec_CAF1 39165 99 + 1
CGGUGUCAAGAAUCGCAUGUUGAGAAGUCUGCCCAGGCGGAUGUCAAUAAAUCUGACACCCAACGGAAUCCGCCGCAUUUGCAGCUCUUUCACAGGGCG
.(((((((.((......((((((...((((((....)))))).))))))..)))))))))....((......))((....)).(((((.....))))). ( -31.50)
>DroSim_CAF1 48078 99 + 1
CGGUGUCAAGAAUCGCAUGUUGAGAAGUCUGCCCAGGCGGAUGUCAAUAAAUCUGACACCCAACGAAAUCCGCCACAUUUGCAGCUCUUUCACAGGGCG
.(((((((.((......((((((...((((((....)))))).))))))..)))))))))...........((.......)).(((((.....))))). ( -29.00)
>DroEre_CAF1 41759 80 + 1
CGGUGUCAAGAAUCGCAUAUUGAGAAGUCUGCCCAGGCGGAUGUCAAUAAGUCUGGCACUCAAAACAAGCC-------------------CAGAGGGCG
.(((((((.((......((((((...((((((....)))))).))))))..)))))))))........(((-------------------(...)))). ( -27.50)
>DroYak_CAF1 46946 99 + 1
CGGUGUCAAGAAUCGCAUAUUGAGAAGUCUGCCCAGGCGGAUGUCAAUAAAUCUGACACUCAACACAAUCCGCCACGAUUUGAGCUCUUUCACAGGGCG
.(((((((.((......((((((...((((((....)))))).))))))..)))))))))...((.((((......)))))).(((((.....))))). ( -27.00)
>consensus
CGGUGUCAAGAAUCGCAUAUUGAGAAGUCUGCCCAGGCGGAUGUCAAUAAAUCUGACACCCAACACAAUCCGCCACAUUUGCAGCUCUUUCACAGGGCG
.(((((((.((......((((((...((((((....)))))).))))))..))))))))).......................(((((.....))))). (-25.16 = -25.52 +   0.36)

alignment

secondary structure

dotplot

Window 4

Location	6,789,048 – 6,789,149
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	86.44
Mean single sequence MFE	-26.42
Consensus MFE	-20.54
Energy contribution	-21.38
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.87
Structure conservation index	0.78
SVM decision value	0.66
SVM RNA-class probability	0.815912
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6789048 101 + 20766785
CCCAGGCGGAUGUCAAUAAAUCUGACACCCAACACAAUCCGCCACAUUUUCAGCUCUUUCACAGGGCGUCCAGGUCCAGUCUGUGACCUUUCACCUAAUGA
....(((((((((((.......)))))..........)))))).((((....(((((.....)))))(((((((.....)))).))).........)))). ( -26.30)
>DroSec_CAF1 39196 101 + 1
CCCAGGCGGAUGUCAAUAAAUCUGACACCCAACGGAAUCCGCCGCAUUUGCAGCUCUUUCACAGGGCGUCCAGGUCCAGUCUGUGACCUUUCACCUAAUGA
....(((((((((((.......)))).((....)).)))))))((....)).(((((.....)))))(((((((.....)))).))).............. ( -29.70)
>DroSim_CAF1 48109 101 + 1
CCCAGGCGGAUGUCAAUAAAUCUGACACCCAACGAAAUCCGCCACAUUUGCAGCUCUUUCACAGGGCGUCCAGGUCCAGUCUGUGACCUUUCACCUAAUGA
....(((((((((((.......)))))..........)))))).((((....(((((.....)))))(((((((.....)))).))).........)))). ( -26.30)
>DroEre_CAF1 41790 82 + 1
CCCAGGCGGAUGUCAAUAAGUCUGGCACUCAAAACAAGCC-------------------CAGAGGGCGUCCAGGUCCAGUCUUUGACCUUUCACCUAAUGA
...(((.(((.(((((..((.((((.(((........(((-------------------(...)))).....))))))).)))))))..))).)))..... ( -24.42)
>DroYak_CAF1 46977 101 + 1
CCCAGGCGGAUGUCAAUAAAUCUGACACUCAACACAAUCCGCCACGAUUUGAGCUCUUUCACAGGGCGUCCAGGUCCAGUCUUUGACCUUUCACCUAAUGA
....(((((((((((.......)))))..........))))))......((((((((.....)))))....(((((........))))).)))........ ( -25.40)
>consensus
CCCAGGCGGAUGUCAAUAAAUCUGACACCCAACACAAUCCGCCACAUUUGCAGCUCUUUCACAGGGCGUCCAGGUCCAGUCUGUGACCUUUCACCUAAUGA
....(((((((((((.......)))))..........))))))...............(((..(((.(...(((((........)))))..).)))..))) (-20.54 = -21.38 +   0.84)

alignment

secondary structure

dotplot

Window 5

Location	6,789,048 – 6,789,149
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	86.44
Mean single sequence MFE	-33.32
Consensus MFE	-24.53
Energy contribution	-25.45
Covariance contribution	0.92
Combinations/Pair	1.04
Mean z-score	-1.70
Structure conservation index	0.74
SVM decision value	0.19
SVM RNA-class probability	0.624237
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6789048 101 - 20766785
UCAUUAGGUGAAAGGUCACAGACUGGACCUGGACGCCCUGUGAAAGAGCUGAAAAUGUGGCGGAUUGUGUUGGGUGUCAGAUUUAUUGACAUCCGCCUGGG
...(((((((..(((((........))))).(((((((.....((..(((........)))...)).....)))))))...............))))))). ( -30.60)
>DroSec_CAF1 39196 101 - 1
UCAUUAGGUGAAAGGUCACAGACUGGACCUGGACGCCCUGUGAAAGAGCUGCAAAUGCGGCGGAUUCCGUUGGGUGUCAGAUUUAUUGACAUCCGCCUGGG
((((..((((..(((((........)))))...))))..))))....(((((....))))).....(((.((((((((((.....))))))))))..))). ( -38.20)
>DroSim_CAF1 48109 101 - 1
UCAUUAGGUGAAAGGUCACAGACUGGACCUGGACGCCCUGUGAAAGAGCUGCAAAUGUGGCGGAUUUCGUUGGGUGUCAGAUUUAUUGACAUCCGCCUGGG
...(((((((..(((((........))))).(((((((..(((((..((..(....)..))...)))))..)))))))...............))))))). ( -39.50)
>DroEre_CAF1 41790 82 - 1
UCAUUAGGUGAAAGGUCAAAGACUGGACCUGGACGCCCUCUG-------------------GGCUUGUUUUGAGUGCCAGACUUAUUGACAUCCGCCUGGG
...(((((((....(((((((.(((((((..(((((((...)-------------------)))..)))..).)).)))).))..)))))...))))))). ( -27.50)
>DroYak_CAF1 46977 101 - 1
UCAUUAGGUGAAAGGUCAAAGACUGGACCUGGACGCCCUGUGAAAGAGCUCAAAUCGUGGCGGAUUGUGUUGAGUGUCAGAUUUAUUGACAUCCGCCUGGG
((((..((((..(((((........)))))...))))..))))...........(((.(((((((.((..(((((.....)))))...)))))))))))). ( -30.80)
>consensus
UCAUUAGGUGAAAGGUCACAGACUGGACCUGGACGCCCUGUGAAAGAGCUGAAAAUGUGGCGGAUUGUGUUGGGUGUCAGAUUUAUUGACAUCCGCCUGGG
...(((((((..(((((........))))).(((((((.........((((......))))..........)))))))...............))))))). (-24.53 = -25.45 +   0.92)

alignment

secondary structure

dotplot

Window 6

Location	6,789,116 – 6,789,219
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	95.73
Mean single sequence MFE	-32.16
Consensus MFE	-26.72
Energy contribution	-27.44
Covariance contribution	0.72
Combinations/Pair	1.09
Mean z-score	-2.17
Structure conservation index	0.83
SVM decision value	1.69
SVM RNA-class probability	0.972047
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6789116 103 - 20766785
UUCGGCCGGAGGGUGUCGAUAUUAGUGGUAUUUAUUACCGCUUCGAAUCCAGUUUUCAGUUUUUACCCAAUCAUUAGGUGAAAGGUCACAGACUGGACCUGGA
.....((((......((((....(((((((.....))))))))))).((((((((..(.((((((((.........)))))))).)...)))))))).)))). ( -32.10)
>DroSec_CAF1 39264 102 - 1
UUCG-CCGGAGGGUGUCGAUAUUAGUAAUAUUUAUUACCGCUUCAAAUCCAGUUUUCAGUUUUUACCCAAUCAUUAGGUGAAAGGUCACAGACUGGACCUGGA
....-((((((((((..(((((.....)))))...)))).))))...((((((((..(.((((((((.........)))))))).)...))))))))...)). ( -26.90)
>DroSim_CAF1 48177 103 - 1
UUCGGCCGGAGGGUGUCGAUAUUAGUGGUAUUUAUUACCGCUUCGAAUCCAGUUUUCAGUUUUUACCCAAUCAUUAGGUGAAAGGUCACAGACUGGACCUGGA
.....((((......((((....(((((((.....))))))))))).((((((((..(.((((((((.........)))))))).)...)))))))).)))). ( -32.10)
>DroEre_CAF1 41839 103 - 1
UUCGGCCGGAGGGUGUCGAUAUUAGUGGUAUUUAUUACCGCUUCGAAUCCAGUUUUCAGCUUUUAGCCAAUCAUUAGGUGAAAGGUCAAAGACUGGACCUGGA
.....((((......((((....(((((((.....))))))))))).(((((((((..((((((.(((........))).))))))..))))))))).)))). ( -36.60)
>DroYak_CAF1 47045 103 - 1
UUCGGCCGGAGGGUGUCGAUAUUAGUGGUAUUUAUUGCCGCUUCAGAGCCAGUUUUCAGUUUUUACCCAAUCAUUAGGUGAAAGGUCAAAGACUGGACCUGGA
.((((((.....).)))))....(((((((.....)))))))((((..((((((((.(.((((((((.........)))))))).)..))))))))..)))). ( -33.10)
>consensus
UUCGGCCGGAGGGUGUCGAUAUUAGUGGUAUUUAUUACCGCUUCGAAUCCAGUUUUCAGUUUUUACCCAAUCAUUAGGUGAAAGGUCACAGACUGGACCUGGA
.....((((......((((....(((((((.....))))))))))).((((((((..(.((((((((.........)))))))).)...)))))))).)))). (-26.72 = -27.44 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:42 2006