Locus 9812

Sequence ID	3R_DroMel_CAF1
Location	26,081,432 – 26,081,567
Length	135
Max. P	0.992161

overview

Window 4

Location	26,081,432 – 26,081,546
Length	114
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	93.50
Mean single sequence MFE	-33.18
Consensus MFE	-27.98
Energy contribution	-27.98
Covariance contribution	0.00
Combinations/Pair	1.07
Mean z-score	-1.88
Structure conservation index	0.84
SVM decision value	1.59
SVM RNA-class probability	0.966174
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26081432 114 + 27905053
UCUCAAGAUCAAGAGUGAACCACCCUGCUUUUUGUGGCAAGGGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGAGCAAAAAAA-AAAGCUGAA
.(((........))).......(((((((......))).))))((.(((...(((((..((((((((((.......))))).))))))))))))).)).......-......... ( -33.20)
>DroSec_CAF1 72908 108 + 1
CUUCAAGAUCAAGAGUGAACCACCCUGCUUUUCGAGGCAAGCGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA------AAA-AAAGCUGGA
.......................((.((((((((..(((.(((((((((...(((.....)))...(((....)))))))).))))..)))..)))------...-))))).)). ( -30.00)
>DroSim_CAF1 74568 108 + 1
UCUCAAGAUCAAGAGUGAGCCACCCUGCUUUUCGAGGCAAGCGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA------AAA-AAAGCUGGA
......(((((.(.(((.(((.(..(((((....))))).).))).))).).)).))).((((((((((.......))))).)))))...((((..------...-...)))).. ( -32.80)
>DroEre_CAF1 77873 109 + 1
UCUCAAGAUCAAGAGUGAACCACCCUGCUUUUCGUGGCAAGGGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA------AAAAAAAGCUGAA
......(((((.(.(((..((.((.((((......)))).))))..))).).)).))).((((((((((.......))))).)))))...((((..------.......)))).. ( -31.30)
>DroYak_CAF1 77574 108 + 1
UCCCAAGAGCAAGAGUGAGCCACCCUGCUUUUCGAGGCAAGGGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA------AAA-AAAGCUGGA
......(((((.(.(((.(((.((.(((((....))))).))))).))).).))).)).((((((((((.......))))).)))))...((((..------...-...)))).. ( -38.60)
>consensus
UCUCAAGAUCAAGAGUGAACCACCCUGCUUUUCGAGGCAAGGGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA______AAA_AAAGCUGGA
..(((.........(((.....(((((((......))).)))).....))).(((((..((((((((((.......))))).))))))))))...................))). (-27.98 = -27.98 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	26,081,467 – 26,081,567
Length	100
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	92.94
Mean single sequence MFE	-28.86
Consensus MFE	-25.58
Energy contribution	-25.74
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.40
Structure conservation index	0.89
SVM decision value	2.31
SVM RNA-class probability	0.992161
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26081467 100 + 27905053
GGCAAGGGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGAGCAAAAAAA-AAAGCUGAAAAUGCAUCGAAGUGGCAUCUA
....((((.(((....((((((..((((((((((.......))))).)))))...((((...........-...))))...))))))....))).).))). ( -27.54)
>DroSec_CAF1 72943 94 + 1
GGCAAGCGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA------AAA-AAAGCUGGAAAUGCAUCGAAGUGGCAUCUA
.......(.(((....((((((..((((((((((.......))))).))))).(.((((..------...-...)))).).))))))....))).)..... ( -28.70)
>DroSim_CAF1 74603 94 + 1
GGCAAGCGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA------AAA-AAAGCUGGAAAUGCAUCGAAGUGGCAUCUA
.......(.(((....((((((..((((((((((.......))))).))))).(.((((..------...-...)))).).))))))....))).)..... ( -28.70)
>DroEre_CAF1 77908 95 + 1
GGCAAGGGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA------AAAAAAAGCUGAAAAUGCAUCGGAGUGGCAUCUA
....((..((.(((.(((((((..((((((((((.......))))).)))))...((((..------.......))))...)))))).)..)))))..)). ( -28.60)
>DroYak_CAF1 77609 94 + 1
GGCAAGGGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA------AAA-AAAGCUGGAAAUGCAUCGAAGUGGCAUCUA
....((((.(((....((((((..((((((((((.......))))).))))).(.((((..------...-...)))).).))))))....))).).))). ( -29.10)
>DroAna_CAF1 82333 94 + 1
UUCAAGAGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAACGCAGCAG------AAA-AAAACUGCAUAUGCAUCGAUGUGGCAUCUA
....(((.((.(((((((((((..((((((((((.......))))).))))).....((((------...-....))))..)))))).).)))))).))). ( -30.50)
>consensus
GGCAAGGGGCACGCACAUGCAUCAUGCAACAUGCAACAGCGGCGUGAUUGCAAUGCAGCGA______AAA_AAAGCUGGAAAUGCAUCGAAGUGGCAUCUA
.......(.(((....((((((..((((((((((.......))))).)))))...((((...............))))...))))))....))).)..... (-25.58 = -25.74 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:42:48 2006