Locus 1351

Sequence ID	3R_DroMel_CAF1
Location	3,994,838 – 3,995,190
Length	352
Max. P	0.921867

overview

Window 1

Location	3,994,838 – 3,994,958
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.50
Mean single sequence MFE	-24.87
Consensus MFE	-16.39
Energy contribution	-17.57
Covariance contribution	1.19
Combinations/Pair	1.15
Mean z-score	-1.59
Structure conservation index	0.66
SVM decision value	-0.02
SVM RNA-class probability	0.525246
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3994838 120 + 27905053
CAUUGUACGCCAAGAUGGAUUAGGCCAAAUCAAGACGAGAGUCGAAAGGAACAGCGUGAGGGAAACUUUAAAUAACGAUGGGUUGGAAGAAUAGGCAAUGCUCUAACAUCAAAAAAAAAA
((((((((((.....(((......)))......(((....)))..........))))((((....)))).....)))))).((((((..............))))))............. ( -25.24)
>DroSec_CAF1 636 117 + 1
CAUUGCACGCCAAGAUGGAUUAGACCAAAUCAAGACGAGAGUCGAAAGGAACAGCGUGAGGGAAACUUUAAAUAACGAUGGGUCGGAAGAAUAGGCAAUGCUCUGAAAUCAAA---AAAA
((((((...((.....))....((((..(((..(((....))).............(((((....)))))......))).))))..........)))))).............---.... ( -26.50)
>DroSim_CAF1 635 117 + 1
CAUUGCACGCCAAGAUGGAUUAGGCCAAAUCAAGACGAGAGUCGAAAGGAACAGCGUGAGGGAAACUCUAAAUAACGAUGGGUUGGAAGAAUAGGCAAUGCUCUAACAUCAAA---AAAA
((((((((((.....(((......)))......(((....)))..........)))))(((....).))......))))).((((((..............))))))......---.... ( -24.24)
>DroYak_CAF1 73 103 + 1
CAUUGCACGCCGAGAUGGAUUAGGCCAAAUCAAGACGAGAGUCGAGAGG-------------UAACUUUAAAUAGCAAGGGGUUGGAGGAAUGGGGAAUGCUCUAACAUCAAA----AAA
..((((.....((..(((......)))..))..(((....))).((((.-------------...)))).....))))(..(((((((.(........).)))))))..)...----... ( -23.50)
>consensus
CAUUGCACGCCAAGAUGGAUUAGGCCAAAUCAAGACGAGAGUCGAAAGGAACAGCGUGAGGGAAACUUUAAAUAACGAUGGGUUGGAAGAAUAGGCAAUGCUCUAACAUCAAA___AAAA
((((((...((.....))....((((.......(((....))).............(((((....)))))..........))))..........)))))).................... (-16.39 = -17.57 +   1.19)

alignment

secondary structure

dotplot

Window 2

Location	3,994,918 – 3,995,038
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.78
Mean single sequence MFE	-24.25
Consensus MFE	-17.12
Energy contribution	-17.80
Covariance contribution	0.69
Combinations/Pair	1.17
Mean z-score	-1.67
Structure conservation index	0.71
SVM decision value	0.22
SVM RNA-class probability	0.642069
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3994918 120 + 27905053
GGUUGGAAGAAUAGGCAAUGCUCUAACAUCAAAAAAAAAAUCAUAACUAAGUGAUUUUACUAUUGCAUUUUCCGCAUUGCAAUCAAAAAUCAAGAGCAGCAUAAUUAGUUGCUUAGACCC
((((..........(((((((........(((....((((((((......))))))))....)))........))))))).............(((((((.......))))))).)))). ( -27.39)
>DroSec_CAF1 716 117 + 1
GGUCGGAAGAAUAGGCAAUGCUCUGAAAUCAAA---AAAAUCAUAACUAAGUGAUUUGAUCAUUGCAUUUUCCGUAUUGCAAUCAAAGAUCAAGAUCAGCAUAAUUAGUUGCUUAGACCC
((((((((((....((((((.((((....))..---.(((((((......))))))))).)))))).))))))..............(((....)))((((........))))..)))). ( -28.10)
>DroSim_CAF1 715 117 + 1
GGUUGGAAGAAUAGGCAAUGCUCUAACAUCAAA---AAAAUCAUAACUAAGUGAUUUGAUCAUUGCAUUUUCCGUAUUGCAAUCAAAGAUCAAGAUCAGCAUAAUUAGUUGCUUAGACCC
((((((((((....((((((.((..........---.(((((((......))))))))).)))))).))))))..............(((....)))((((........))))..)))). ( -23.70)
>DroYak_CAF1 140 110 + 1
GGUUGGAGGAAUGGGGAAUGCUCUAACAUCAAA----AAAUCAUAACUAAGUGAUUUGAUCAUGCCAUUUUCUGAAUUAUAAUCAAGCAUUAAGAUCAGCAUAAUUAGUAGCUU------
((((.(..(((((((((....)))..(((....----(((((((......)))))))....)))))))))..).))))......(((((((((...........))))).))))------ ( -17.80)
>consensus
GGUUGGAAGAAUAGGCAAUGCUCUAACAUCAAA___AAAAUCAUAACUAAGUGAUUUGAUCAUUGCAUUUUCCGUAUUGCAAUCAAAGAUCAAGAUCAGCAUAAUUAGUUGCUUAGACCC
((((((((((....((((((.((..............(((((((......))))))))).)))))).))))))........................((((........))))..)))). (-17.12 = -17.80 +   0.69)

alignment

secondary structure

dotplot

Window 3

Location	3,995,038 – 3,995,150
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	78.74
Mean single sequence MFE	-30.80
Consensus MFE	-21.50
Energy contribution	-23.12
Covariance contribution	1.62
Combinations/Pair	1.09
Mean z-score	-2.00
Structure conservation index	0.70
SVM decision value	1.14
SVM RNA-class probability	0.921867
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3995038 112 - 27905053
--------CCAACGAUCGGGUUUGGUUAUGUUUGCCAUCCACCGAUCAAUAAAUACCCUGCCUUGAGGUGGCAGCUACCACUUUGCGGGAUAAUUUCAGACAUCGAGUUGCAUAAUAAUU
--------.(((((((((((..((((.......))))..).)))))).........(((((...(((((((......)))))))))))).................)))).......... ( -34.50)
>DroSec_CAF1 833 112 - 1
--------CCAUCGAUCGGGUUUGGUUAUGUUCGCCAUUCACCGAUCACUAAAUACCCUCCCUUGAGGUGGCAGCUACCACUUUGCGGGAUAAUUCCAGACAUAGAGUUGCAUAAUAACU
--------.....(((((((..((((.......))))..).))))))...........((((.((((((((......)))))))).))))((((((........)))))).......... ( -32.30)
>DroSim_CAF1 832 112 - 1
--------CCAUCGAUCGGGUUUGGUUAUGUUUGCCAUCCACCGAUCACUAAAUACCCUGCCUUGAGGUGGCAGCUACCACUUUGCGGGAUAAUUCCAGACAUAGAGUUGCAUAAUAACU
--------.....(((((((..((((.......))))..).)))))).........(((((...(((((((......)))))))))))).((((((........)))))).......... ( -33.30)
>DroYak_CAF1 250 102 - 1
ACAACGAACCAUCGAUCGGGUUCAUGUAUGCUUGCCUUCUACCGAUCACUGAAUACCCUUUCUUGAGGUGGCAGUUACCAUUUUCUGGCAUAAUUUCAGAAA------------------
..(((...(((((((((((......(((....)))......))))))...(((......)))....)))))..))).....(((((((.......)))))))------------------ ( -23.10)
>consensus
________CCAUCGAUCGGGUUUGGUUAUGUUUGCCAUCCACCGAUCACUAAAUACCCUGCCUUGAGGUGGCAGCUACCACUUUGCGGGAUAAUUCCAGACAUAGAGUUGCAUAAUAACU
.............(((((((..((((.......))))..).)))))).........(((((...(((((((......))))))))))))............................... (-21.50 = -23.12 +   1.62)

alignment

secondary structure

dotplot

Window 4

Location	3,995,078 – 3,995,190
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.94
Mean single sequence MFE	-39.90
Consensus MFE	-28.77
Energy contribution	-29.40
Covariance contribution	0.63
Combinations/Pair	1.06
Mean z-score	-1.81
Structure conservation index	0.72
SVM decision value	0.28
SVM RNA-class probability	0.666256
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3995078 112 + 27905053
UGGUAGCUGCCACCUCAAGGCAGGGUAUUUAUUGAUCGGUGGAUGGCAAACAUAACCAAACCCGAUCGUUGG--------AUCGCUGCUUUGGCCGGAUCGCUGGCUGCGAUAAUAUCCA
..((((((((..(((((((((((.(.(((((.(((((((.(..(((.........)))..)))))))).)))--------))).)))))))))..))...)).))))))........... ( -41.30)
>DroSec_CAF1 873 112 + 1
UGGUAGCUGCCACCUCAAGGGAGGGUAUUUAGUGAUCGGUGAAUGGCGAACAUAACCAAACCCGAUCGAUGG--------AUCGCUGCUUUGGCCGGAUCGCUGGCUGCGAUAAUAUCCA
.((((((..(((((((....))))........(((((((.(..(((.........)))..)))))))).)))--------...))))))..((((((....))))))............. ( -35.60)
>DroSim_CAF1 872 112 + 1
UGGUAGCUGCCACCUCAAGGCAGGGUAUUUAGUGAUCGGUGGAUGGCAAACAUAACCAAACCCGAUCGAUGG--------AUCGCUGCUUUGGCCGGAUCGCUGGCUGCGAUAAUAUCCA
..((((((((..(((((((((((.(.(((((.(((((((.(..(((.........)))..)))))))).)))--------))).)))))))))..))...)).))))))........... ( -41.30)
>DroYak_CAF1 272 120 + 1
UGGUAACUGCCACCUCAAGAAAGGGUAUUCAGUGAUCGGUAGAAGGCAAGCAUACAUGAACCCGAUCGAUGGUUCGUUGUAUCGCUGCUUUGGUCGGAUCGCUGUCUGCGAUAAUAUCCA
((((....))))(((......)))(((..((((((((.(...((((((.(((((((((((((........)))))).))))).))))))))...).))))))))..)))........... ( -41.40)
>consensus
UGGUAGCUGCCACCUCAAGGCAGGGUAUUUAGUGAUCGGUGGAUGGCAAACAUAACCAAACCCGAUCGAUGG________AUCGCUGCUUUGGCCGGAUCGCUGGCUGCGAUAAUAUCCA
((((....))))..........(((((((((.(((((((.(..(((.........)))..)))))))).)).........(((((......((((((....)))))))))))))))))). (-28.77 = -29.40 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:34 2006