Locus 7132

Sequence ID	3R_DroMel_CAF1
Location	18,778,996 – 18,779,130
Length	134
Max. P	0.952959

overview

Window 5

Location	18,778,996 – 18,779,091
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	75.64
Mean single sequence MFE	-12.33
Consensus MFE	-11.90
Energy contribution	-11.74
Covariance contribution	-0.16
Combinations/Pair	1.18
Mean z-score	-0.45
Structure conservation index	0.97
SVM decision value	1.43
SVM RNA-class probability	0.952959
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18778996 95 + 27905053
CACAUCAAUUAGCCACUGAUUUACUGAACUGUUACCAACGUCCACCCCUUUCUGCCUGCUUUCCACCCGCAGUUCCGCCCAGUGUACGGGCCAUC
......((((((...))))))....(((((((....................................))))))).((((.......)))).... ( -12.52)
>DroSec_CAF1 4548 92 + 1
CACA-CAAUUAGCCACUGAUUUACUGAACUGCUCCC--CCAUCUCCCUAUUCCGCCUGCUUUCCACCCGCAGUUCCGCCCAGUGUACGGGCCAUC
....-.((((((...))))))....(((((((....--..............................))))))).((((.......)))).... ( -14.78)
>DroSim_CAF1 4562 93 + 1
CACAUCAAUUAGCCACUGAUUUACUGAACUGCUCCC--CCACACCCCCUUUCCGCCUGCUUUCCACCCGCAGUUCCGCCCAGUGUACGGGCCAUC
......((((((...))))))....(((((((....--..............................))))))).((((.......)))).... ( -14.78)
>DroEre_CAF1 4383 72 + 1
CACAUCAAUUAGCCACUGAUUCACUGAACUGCCCC-----------------------CUUUCCACCCCCAGUUCCGCCCAGUGUACGGGCCAUA
......((((((...))))))....((((((....-----------------------...........)))))).((((.......)))).... ( -11.56)
>DroAna_CAF1 5811 92 + 1
UACAUCAAUUAGCAACUGAUUUACUGAAUUAUCACGAUUUUCUCUUCCUUUCUUCUCGC---CCCCACCUAGUUCCGCCCAGUGUUCGGGCCAUC
......((((((....((((..........)))).((........))............---......))))))..((((.......)))).... (  -8.00)
>consensus
CACAUCAAUUAGCCACUGAUUUACUGAACUGCUCCC__CCACCCCCCCUUUCCGCCUGCUUUCCACCCGCAGUUCCGCCCAGUGUACGGGCCAUC
......((((((...))))))....(((((((....................................))))))).((((.......)))).... (-11.90 = -11.74 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	18,779,022 – 18,779,130
Length	108
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	73.84
Mean single sequence MFE	-41.28
Consensus MFE	-21.85
Energy contribution	-22.24
Covariance contribution	0.39
Combinations/Pair	1.10
Mean z-score	-1.89
Structure conservation index	0.53
SVM decision value	0.97
SVM RNA-class probability	0.891877
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18779022 108 - 27905053
GGGUCCUCCUUUGCGGGCCUGCAGUUGUCCGGAUGUUGGGAUGGCCCGUACACUGGGCGGAACUGCGG-GUGGAAAGCAGGCAGAAAGGGGUGGACGUUGGUAACAGUU
..((((.(((((....((((((((((((((((.(((((((....)))).)))))))))..)))))).(-.(....).)))))....))))).))))............. ( -44.10)
>DroSec_CAF1 4573 106 - 1
GGGUCCUCCUUUGCGGGCCUGCAGUUGUCCGGAUGUUGGGAUGGCCCGUACACUGGGCGGAACUGCGG-GUGGAAAGCAGGCGGAAUAGGGAGAUGG--GGGAGCAGUU
.(.(((((((((((..((((((((((((((((.(((((((....)))).)))))))))..))))))))-)).....)))))(......)......))--)))).).... ( -45.00)
>DroSim_CAF1 4588 106 - 1
GGGUCCUCCUUUGCGGGCCUGCAGUUGUCCGGAUGUUGGGAUGGCCCGUACACUGGGCGGAACUGCGG-GUGGAAAGCAGGCGGAAAGGGGGUGUGG--GGGAGCAGUU
....((((((((.((.((((((((((((((((.(((((((....)))).)))))))))..))))))))-))(.....)...)).))))))))(((..--....)))... ( -45.10)
>DroEre_CAF1 4409 85 - 1
GGGUCCUCCUUUGCGGGCCUGCAGUUGUCCGGAUGUGGGUAUGGCCCGUACACUGGGCGGAACUGGGG-GUGGAAAG-----------------------GGGGCAGUU
..((((.(((((.(..((((.(((((((((((.((((((.....)))..)))))))))..))))).))-))).))))-----------------------))))).... ( -39.70)
>DroWil_CAF1 4514 83 - 1
GGGCCCCCCUUUGCGGGCCUGCAACUGUCCAGAGGUGGGAAUGGCUCGUACACUGGGCGGCACUGGGGGGCGGAGAG-----------AG---------------AGUA
..(((((((.(((((....)))))((((((((..(((.((.....)).))).))))))))....)))))))......-----------..---------------.... ( -38.00)
>DroAna_CAF1 5837 105 - 1
GGGUCCCCCCUUGCGGGCCUGCAGUUGUCCGGAUGUGGGGAUGGCCCGAACACUGGGCGGAACUAGGU-GGGG---GCGAGAAGAAAGGAAGAGAAAAUCGUGAUAAUU
..((((((((....))(((((...((((((((.(((.(((....)))..)))))))))))...)))))-))))---))............................... ( -35.80)
>consensus
GGGUCCUCCUUUGCGGGCCUGCAGUUGUCCGGAUGUGGGGAUGGCCCGUACACUGGGCGGAACUGCGG_GUGGAAAGCAGGC_GAAAGGGG__G__G__GGGAGCAGUU
((.(((.(((.((((((((.......((((........))))))))))))....))).))).))............................................. (-21.85 = -22.24 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:10 2006