Locus 5391

Sequence ID	2R_DroMel_CAF1
Location	17,411,666 – 17,411,841
Length	175
Max. P	0.878378

overview

Window 5

Location	17,411,666 – 17,411,765
Length	99
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.48
Mean single sequence MFE	-30.54
Consensus MFE	-17.14
Energy contribution	-17.67
Covariance contribution	0.53
Combinations/Pair	1.06
Mean z-score	-1.74
Structure conservation index	0.56
SVM decision value	0.03
SVM RNA-class probability	0.548799
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17411666 99 - 20766785
UGGCUUUCG-CUGAC----UUU----UUUUUUCGCCCGCGGCGCUGAUGAAUGUUGCGUGCAACAUGUUGCAGCAGGCUGUCGUCUUGCCAUCGCCAUCCGCCCUUAA
.(((....(-(....----...----...........))(((((((....((((((....))))))....)))).(((.........)))...)))....)))..... ( -28.37)
>DroSec_CAF1 127562 93 - 1
CGGCUUUCG-CUGAC----UUU-------UUUCGCCCGUGGCGCUGAUGAAUGUUGCGUGCAACAUGUUGCAGAAGGCUG---UCUUGCCAUCGCCAUCCGCUCUUAA
((((....)-)))..----...-------....((..(((((((((....((((((....))))))....)))..(((..---....)))..))))))..))...... ( -30.10)
>DroSim_CAF1 131092 93 - 1
CGGCUUUCG-CUGAC----UUU-------UUUCGCCCGUGGCGCUGAUGAAUGUUGCGUGCAACAUGUUGCAGCAGGCUG---UCUUGCCAUCGCCAUCCGCUCUUAA
((((....)-)))..----...-------....((..(((((((((....((((((....))))))....)))).(((..---....)))...)))))..))...... ( -33.30)
>DroEre_CAF1 126643 94 - 1
GGGCUUUCG-CUGGUGUUUUU----UUUUUUGCGCCCGUGGCGCUGAUGAAUGUUGCGUGCAACAUGUUGCAGCAGGCUG---UCUUGC------CAACCGCUCUUAA
((((..(((-(.(((((....----......))))).)))).((((....((((((....))))))....)))).(((..---....))------)....)))).... ( -33.10)
>DroYak_CAF1 110765 98 - 1
GGGCUUUCG-CUGGUGUAUUUUUUUUUUUAUGCGCCCGUGGCGCUGAUGAAUGUUGCGUGCAACAUGUUGCAGCAGGCUG---UCUUGC------CAGCCGCUCUUAA
((((....(-(.(((((((..........))))))).))(((((((....((((((....))))))....)))).(((..---....))------).))))))).... ( -38.70)
>DroAna_CAF1 116172 89 - 1
CUGCUUUCGGCCGAA----UAU-------CUCGCCCCAUGGCGCUGAUAAAUGUUGCAUGCAACAUGUUGCA-CAAGCUG---UCUC----CUGCCCUCCGCUCUUAA
..((....(((.(..----(((-------(.((((....))))..))))...(((...(((((....)))))-..)))..---....----).)))....))...... ( -19.70)
>consensus
CGGCUUUCG_CUGAC____UUU_______UUUCGCCCGUGGCGCUGAUGAAUGUUGCGUGCAACAUGUUGCAGCAGGCUG___UCUUGC__UCGCCAUCCGCUCUUAA
.(((((...........................(((...)))((((....((((((....))))))....)))))))))............................. (-17.14 = -17.67 +   0.53)

alignment

secondary structure

dotplot

Window 6

Location	17,411,734 – 17,411,841
Length	107
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	88.18
Mean single sequence MFE	-21.07
Consensus MFE	-14.89
Energy contribution	-15.70
Covariance contribution	0.81
Combinations/Pair	1.05
Mean z-score	-2.55
Structure conservation index	0.71
SVM decision value	0.90
SVM RNA-class probability	0.878378
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17411734 107 + 20766785
CGCGGGCGAAAAAA----AAA----GUCAGCGAAAGCCAUGGCAAAUAAAUUAAAAAUUCCAAAAAAAGAAGCAAGAAAUGAAAUAAUUAUUUUUGGGCUGCG-CAAAUUGAGGAA
(((((.(.(((((.----...----((((((....))..))))..............(((........)))...................))))).).)))))-............ ( -19.40)
>DroSec_CAF1 127627 102 + 1
CACGGGCGAAA-------AAA----GUCAGCGAAAGCCGUGGCAUAUAAAUUAAAAAUUCCAAA--AAGAAGCCAGAAAUGAAAUAAUUAUUUUUGGGCUGCG-CAAAUUGAGGAA
(((((((....-------...----))).((....))))))................((((...--......((((((((((.....))))))))))((...)-).......)))) ( -22.80)
>DroSim_CAF1 131157 102 + 1
CACGGGCGAAA-------AAA----GUCAGCGAAAGCCGUGGCAAAUAAAUUAAAAAUUCCAAA--AAGAAGCCAGAAAUGAAAUAAUUAUUUUUGGGCUGCG-CAAAUUGAGGAA
(((((((....-------...----))).((....))))))................((((...--......((((((((((.....))))))))))((...)-).......)))) ( -22.80)
>DroYak_CAF1 110824 114 + 1
CACGGGCGCAUAAAAAAAAAAAUACACCAGCGAAAGCCCAGGCAAAUAAAUUAAAAAUUCCAAA--AAGUAGCAAGAAAUGAAAUAAUUAUUUUUGGGCUGCGGCAAAUUGAGGAA
...((((............................))))..................((((...--..(((((.((((((((.....))))))))..)))))..(.....).)))) ( -19.29)
>consensus
CACGGGCGAAA_______AAA____GUCAGCGAAAGCCGUGGCAAAUAAAUUAAAAAUUCCAAA__AAGAAGCAAGAAAUGAAAUAAUUAUUUUUGGGCUGCG_CAAAUUGAGGAA
..(((((..................((((((....))..)))).............................((((((((((.....))))))))))))).))............. (-14.89 = -15.70 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:43 2006