Locus 1383

Sequence ID	2L_DroMel_CAF1
Location	3,684,825 – 3,684,916
Length	91
Max. P	0.825263

overview

Window 8

Location	3,684,825 – 3,684,916
Length	91
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	74.68
Mean single sequence MFE	-27.43
Consensus MFE	-13.77
Energy contribution	-14.49
Covariance contribution	0.72
Combinations/Pair	1.25
Mean z-score	-1.87
Structure conservation index	0.50
SVM decision value	0.58
SVM RNA-class probability	0.789530
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3684825 91 + 22407834
UUCGCCC---UUAUGCCGAAGGAU---ACCAUCAGGAU--AUCCAUCUAGCAUAUCCCACAUAUGGCUGAGACAAUGGCGGGAG--------------UUCCGCCAAUGAUUA
((((((.---.(((((.((.((((---(((....)).)--)))).))..)))))..........))).))).((.((((((...--------------..)))))).)).... ( -27.40)
>DroSec_CAF1 147212 90 + 1
UUCACUC---G-CUGGCGAAGGAU---ACCAUCAGGAU--AUCCAUCUAGCAUAUCCCACAUAUGGCUGAGACAAUGGCGGGAG--------------UUCCGCCAAUGAUUA
....(((---(-((((....((((---(((....)).)--))))..))))).....(((....)))..))).((.((((((...--------------..)))))).)).... ( -29.20)
>DroSim_CAF1 156286 90 + 1
UUCACCC---G-CUGGCGAAGGAU---ACCAUCAGGAU--AUCCAUCUAGCAUAUCCCACAUAUGCCUGAGACAAUGGCGGGAG--------------UUCCGCCAAUGAUUA
(((.((.---.-..)).)))((((---(((....)).)--)))).((..((((((.....))))))..))..((.((((((...--------------..)))))).)).... ( -28.40)
>DroEre_CAF1 152217 88 + 1
UC--------G-CUGCUUUAGCAUCCUGCCAUCAGGAU--AUCCAUCCAGCAUAUCCCACAUAUGGCCGAGACAAUGGCGGCAG--------------UUCCGCCGAUGAUUA
..--------(-(((...)))).(((.(((((..((((--((.(.....).)))))).....))))).).))((.((((((...--------------..)))))).)).... ( -24.30)
>DroYak_CAF1 157655 95 + 1
UUCGCCCCCGA-CUGCUGAAGGAU---AUCAUCAGGAUAUAUCCAUCCAGCAUAUCCCACAUAUGGCUGAGACAAUGGCGGCAG--------------UUCCGCCGAUGAUUA
.......((..-(....)..))..---((((((.(((....))).((((((((((.....)))).)))).))....(((((...--------------..))))))))))).. ( -24.60)
>DroPer_CAF1 172669 100 + 1
CCCACCG---AUAGGCAGAUAGAU---ACU-----CGU--AUCCAUGCGGCAUAUCCCACAUAUGUUAAAGACAAUGGCGCGAGUCAUUCAGGCGAUGUUCCGUUGGUGAUUA
..(((((---((..(((....(((---(..-----..)--)))..)))((.(((((((.....((((...))))(((((....)))))...)).))))).))))))))).... ( -30.70)
>consensus
UUCACCC___G_CUGCCGAAGGAU___ACCAUCAGGAU__AUCCAUCCAGCAUAUCCCACAUAUGGCUGAGACAAUGGCGGGAG______________UUCCGCCAAUGAUUA
....................((((....((....))....))))...((((((((.....))))).)))...((.((((((((...............)))))))).)).... (-13.77 = -14.49 +   0.72)

alignment

secondary structure

dotplot

Window 9

Location	3,684,825 – 3,684,916
Length	91
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	74.68
Mean single sequence MFE	-31.22
Consensus MFE	-13.91
Energy contribution	-15.36
Covariance contribution	1.45
Combinations/Pair	1.18
Mean z-score	-2.08
Structure conservation index	0.45
SVM decision value	0.70
SVM RNA-class probability	0.825263
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3684825 91 - 22407834
UAAUCAUUGGCGGAA--------------CUCCCGCCAUUGUCUCAGCCAUAUGUGGGAUAUGCUAGAUGGAU--AUCCUGAUGGU---AUCCUUCGGCAUAA---GGGCGAA
.......((((((..--------------...))))))((((((...(((....)))..((((((.((.((((--(((.....)))---)))).)))))))).---)))))). ( -33.00)
>DroSec_CAF1 147212 90 - 1
UAAUCAUUGGCGGAA--------------CUCCCGCCAUUGUCUCAGCCAUAUGUGGGAUAUGCUAGAUGGAU--AUCCUGAUGGU---AUCCUUCGCCAG-C---GAGUGAA
...((((((((((..--------------...)))))..(((((((........)))))))((((.((.((((--(((.....)))---)))).))...))-)---)))))). ( -30.80)
>DroSim_CAF1 156286 90 - 1
UAAUCAUUGGCGGAA--------------CUCCCGCCAUUGUCUCAGGCAUAUGUGGGAUAUGCUAGAUGGAU--AUCCUGAUGGU---AUCCUUCGCCAG-C---GGGUGAA
....((.((((((..--------------...)))))).))..((.(((((((.....))))))).)).((((--(((.....)))---)))).(((((..-.---.))))). ( -33.00)
>DroEre_CAF1 152217 88 - 1
UAAUCAUCGGCGGAA--------------CUGCCGCCAUUGUCUCGGCCAUAUGUGGGAUAUGCUGGAUGGAU--AUCCUGAUGGCAGGAUGCUAAAGCAG-C--------GA
........(((((..--------------...)))))..(((((((........)))))))(((((..(((.(--((((((....))))))))))...)))-)--------). ( -31.00)
>DroYak_CAF1 157655 95 - 1
UAAUCAUCGGCGGAA--------------CUGCCGCCAUUGUCUCAGCCAUAUGUGGGAUAUGCUGGAUGGAUAUAUCCUGAUGAU---AUCCUUCAGCAG-UCGGGGGCGAA
........(((((..--------------...))))).(((((((..(((....)))(((.(((((((.((((((.........))---))))))))))))-)).))))))). ( -36.50)
>DroPer_CAF1 172669 100 - 1
UAAUCACCAACGGAACAUCGCCUGAAUGACUCGCGCCAUUGUCUUUAACAUAUGUGGGAUAUGCCGCAUGGAU--ACG-----AGU---AUCUAUCUGCCUAU---CGGUGGG
...(((((..(((........)))....(((((..((..(((.....))).((((((......))))))))..--.))-----)))---..............---.))))). ( -23.00)
>consensus
UAAUCAUCGGCGGAA______________CUCCCGCCAUUGUCUCAGCCAUAUGUGGGAUAUGCUAGAUGGAU__AUCCUGAUGGU___AUCCUUCGGCAG_C___GGGUGAA
........(((((...................)))))..(((((((........)))))))((((....((((....((....))....))))...))))............. (-13.91 = -15.36 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:13 2006