Locus 4411

Sequence ID	2R_DroMel_CAF1
Location	14,504,807 – 14,504,972
Length	165
Max. P	0.538374

overview

Window 1

Location	14,504,807 – 14,504,910
Length	103
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	79.08
Mean single sequence MFE	-17.61
Consensus MFE	-9.27
Energy contribution	-10.85
Covariance contribution	1.58
Combinations/Pair	1.19
Mean z-score	-1.86
Structure conservation index	0.53
SVM decision value	0.01
SVM RNA-class probability	0.538374
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14504807 103 - 20766785
CCAAAAAGA-A-AAACAAAUAAAGAAAUGAAAACUGCACUGUAUUUUUGGGCUAUAAAUAAACGGAGCAGACGGGAGAAGCAGAUGCAAUCGAAACUUUUUG--AAA
.(((((((.-.-.....................((((.((((...((((.....))))...)))).))))....((...((....))..))....)))))))--... ( -17.90)
>DroSec_CAF1 136913 104 - 1
CCAAAAAGAAAAAAACAAAUCAAGAAAAGAAAACUGCACUGUAUUUUUGGGCUAUAAAUAAACGGAGCAGGCGG-CGGAGCAGAUGUAAUCGAAACUUUUUG--AUA
.(((((((..........(((............((((.((((...((((.....))))...)))).))))((..-....)).)))..........)))))))--... ( -19.15)
>DroSim_CAF1 138050 103 - 1
CCAAAAAGGAA-AAACAAAUCAAGAAAAGAAAACUGCACUGUAUUUUUGGGCUAUAAAUAAACGGAGCAGACGG-CGAAGCAGAUGCAAUCGAAACUUUUUG--AAA
.(((((((...-.....................((((.((((...((((.....))))...)))).))))....-(((.((....))..)))...)))))))--... ( -18.80)
>DroEre_CAF1 142399 92 - 1
CCAAAAGGAA------------AAAAAAGAAAACUGCACGGUAUUUUUGGGCUAUAAAUAAACGGAGCAGACAG-AGGAGCAGAUGCAAUCGAAACUUUUGG--AAA
(((((((...------------...........((((.(.((...((((.....))))...)).).))))...(-(...((....))..))....)))))))--... ( -18.30)
>DroYak_CAF1 140497 95 - 1
CCAAAAGCAAAG---------AAAAAAAGAAAACUGCACUGUAUUUUUGGGCUAUAAAUAAACGGAGCAGACAG-AGAAGCAGAUGCAAUCGAAACUUUUCG--AAA
............---------.............((((((((.((((((.(((............)))...)))-))).)))).)))).(((((....))))--).. ( -19.60)
>DroAna_CAF1 150205 85 - 1
CCAAAG---------------------AUAGAACUGCAGAAUAUUCGAGGGCUAUAAAUAAGCGAAGCAGACAA-AACAGCAGAUGCAAUCGAAACUUUUUCGGAAA
((...(---------------------((....((((.((....))....(((.......)))...))))....-....((....)).)))(((.....)))))... ( -11.90)
>consensus
CCAAAAAGAAA__________AAGAAAAGAAAACUGCACUGUAUUUUUGGGCUAUAAAUAAACGGAGCAGACAG_AGAAGCAGAUGCAAUCGAAACUUUUUG__AAA
.(((((((.........................((((.((((...((((.....))))...)))).)))).........((....))........)))))))..... ( -9.27 = -10.85 +   1.58)

alignment

secondary structure

dotplot

Window 2

Location	14,504,873 – 14,504,972
Length	99
Sequences	3
Columns	102
Reading direction	forward
Mean pairwise identity	69.86
Mean single sequence MFE	-22.48
Consensus MFE	-14.02
Energy contribution	-15.80
Covariance contribution	1.78
Combinations/Pair	1.05
Mean z-score	-1.21
Structure conservation index	0.62
SVM decision value	-0.02
SVM RNA-class probability	0.522523
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14504873 99 + 20766785
GUGCAGUUUUCAUUUCUUUAUUUGUUUU-UCUUUUUGGCCUAGGAGUGCAGACUGCAGUCUGUGAAUUCCGGGCUAGUGAGU-UCUAUUUUCGG-CAUAUUC
((((........................-.....(((((((.(((((((((((....))))))..))))))))))))((((.-......)))))-))).... ( -26.00)
>DroEre_CAF1 142464 89 + 1
GUGCAGUUUUCUUUUUU-----------UUCCUUUUGGCCUAGGAGUGCAGACUGCAGUCUGUGAAUUCCGGGCUAGUGAGU-UCUAUUUUCGG-UAUAUUC
((((.............-----------......(((((((.(((((((((((....))))))..))))))))))))((((.-......)))))-))).... ( -24.00)
>DroAna_CAF1 150272 78 + 1
CUGCAGUUCUAU--------------------CUUUGGCCUCGGGG--C--AGUGCAGUCAGUGAAUUCCGGGCAAGGGAGUUUCUAUUUUCAAUCCCACUC
............--------------------.....(((.((((.--(--(.((....)).))...)))))))..((((..............)))).... ( -17.44)
>consensus
GUGCAGUUUUCUUUU_U____________UC_UUUUGGCCUAGGAGUGCAGACUGCAGUCUGUGAAUUCCGGGCUAGUGAGU_UCUAUUUUCGG_CAUAUUC
..................................(((((((.(((((((((((....))))))..)))))))))))).(((........))).......... (-14.02 = -15.80 +   1.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:58 2006