Locus 1338

Sequence ID	3R_DroMel_CAF1
Location	3,948,705 – 3,948,835
Length	130
Max. P	0.995902

overview

Window 7

Location	3,948,705 – 3,948,816
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	75.39
Mean single sequence MFE	-38.03
Consensus MFE	-24.76
Energy contribution	-25.82
Covariance contribution	1.06
Combinations/Pair	1.23
Mean z-score	-1.57
Structure conservation index	0.65
SVM decision value	0.13
SVM RNA-class probability	0.596233
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3948705 111 + 27905053
UCGAAAUGACUACGGCGGAGAAGGACGAGGCUAUCGCGCUAAACGCAAUGAUUAUGGCGGUGGACGUCGCGACAAUCGGGAUAA---------UUACGGAGCAGGGCAUCGUGAUAGUCG
(((..(((.((((((((..((.((......)).)).))))...(((..........))))))).)))..))).......(((.(---------(((((..((...))..)))))).))). ( -27.70)
>DroSim_CAF1 17209 111 + 1
GCGAAAUGACAACGGCGGAGAAGGACGAGGCUAUCGCGGUAAACGCGAUGAUUACGGCGGUGGACGUCGCGACUAUCGUGAUAA---------UUACGGAGCAGGCUGUCGUGAUAGUCG
.......(((.(((((((.......((..(.((((((((((..(((((((.((((....)))).)))))))..)))))))))).---------)..)).......)))))))....))). ( -40.54)
>DroEre_CAF1 17161 120 + 1
UCGUGAUGACUACGGCGGAGGAAGACGAGAUUAUCGCGGUAAACGCGAUGGUUACGGCGGAGGACGCCGCGACGAUCGGGAUAACCAAGAUAAUUACGGCGCAGGGCGUCAUGAUAGUCG
((((((((.((.((.((..(.....)..(((((((..(((...(.((((.((..(((((.....)))))..)).)))).)...)))..))))))).)).)).))..))))))))...... ( -46.80)
>DroYak_CAF1 17299 103 + 1
-----------------GAGGAGGACGAGAUUAUCGCGGUAAACGCGAUGAUUAUGGCGGAGGACGUCGCGCCCAUCGGGAAAAUAGAGAUGUCUACGGCGCAGUGCGACGUGAUAGUCG
-----------------......(((..((((((((((.....))))))))))((.(((..(.((...(((((((((...........)))).....))))).)).)..))).)).))). ( -37.10)
>consensus
UCGAAAUGACUACGGCGGAGAAGGACGAGACUAUCGCGGUAAACGCGAUGAUUACGGCGGAGGACGUCGCGACAAUCGGGAUAA_________UUACGGAGCAGGGCGUCGUGAUAGUCG
............................(((((((((......(.(((((.(..(((((.....)))))..).))))).).................(((((...)))))))))))))). (-24.76 = -25.82 +   1.06)

alignment

secondary structure

dotplot

Window 8

Location	3,948,745 – 3,948,835
Length	90
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	70.61
Mean single sequence MFE	-31.90
Consensus MFE	-16.35
Energy contribution	-17.63
Covariance contribution	1.28
Combinations/Pair	1.06
Mean z-score	-1.89
Structure conservation index	0.51
SVM decision value	1.05
SVM RNA-class probability	0.907431
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3948745 90 + 27905053
AAACGCAAUGAUUAUGGCGGUGGACGUCGCGACAAUCGGGAUAA---------UUACGGAGCAGGGCAUCGUGAUAGUCGCGACAGUGCCGGGGGA------GGA
...(((..........))).(((((((((((((.((((.(((..---------((........))..))).)))).)))))))).)).))).....------... ( -26.70)
>DroSec_CAF1 16708 81 + 1
---------------UGCGGUGGACGUCGCGACUAUCGUGAUAA---------UUACGGAGCGGGCUGUCGUGAUAGUCGCGACAGCGGUAGUGGAGGAGGAGGA
---------------(((.((....((((((((((((((((((.---------...((...))...)))))))))))))))))).)).))).............. ( -29.80)
>DroSim_CAF1 17249 93 + 1
AAACGCGAUGAUUACGGCGGUGGACGUCGCGACUAUCGUGAUAA---------UUACGGAGCAGGCUGUCGUGAUAGUCGCGACAGCGGUGGUGGAGGA---GGA
...(((((((.((((....)))).)))))))((((((((((...---------)))).......(((((((((.....)))))))))))))))......---... ( -36.80)
>DroEre_CAF1 17201 98 + 1
AAACGCGAUGGUUACGGCGGAGGACGCCGCGACGAUCGGGAUAACCAAGAUAAUUACGGCGCAGGGCGUCAUGAUAGUCGCGACGGU------GGAGGAGGAGG-
...((((((.((..(((((.....)))))..)).)))((.....))..(((.((((.(((((...))))).)))).)))))).....------...........- ( -34.80)
>DroYak_CAF1 17322 99 + 1
AAACGCGAUGAUUAUGGCGGAGGACGUCGCGCCCAUCGGGAAAAUAGAGAUGUCUACGGCGCAGUGCGACGUGAUAGUCGCGACGGU------GGAGGAGGAGGA
...((((.(((((((.(((..(.((...(((((((((...........)))).....))))).)).)..))).))))))))).))..------............ ( -31.40)
>consensus
AAACGCGAUGAUUACGGCGGUGGACGUCGCGACUAUCGGGAUAA_________UUACGGAGCAGGGCGUCGUGAUAGUCGCGACAGUG___G_GGAGGAGGAGGA
...(((..........)))......((((((((.((((.(((.........................))).)))).))))))))..................... (-16.35 = -17.63 +   1.28)

alignment

secondary structure

dotplot

Window 9

Location	3,948,745 – 3,948,835
Length	90
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	70.61
Mean single sequence MFE	-23.58
Consensus MFE	-17.65
Energy contribution	-17.77
Covariance contribution	0.12
Combinations/Pair	1.23
Mean z-score	-1.98
Structure conservation index	0.75
SVM decision value	2.63
SVM RNA-class probability	0.995902
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3948745 90 - 27905053
UCC------UCCCCCGGCACUGUCGCGACUAUCACGAUGCCCUGCUCCGUAA---------UUAUCCCGAUUGUCGCGACGUCCACCGCCAUAAUCAUUGCGUUU
...------......((.((.((((((((.(((..((((...(((...))).---------.))))..))).))))))))))))..(((.((....)).)))... ( -22.70)
>DroSec_CAF1 16708 81 - 1
UCCUCCUCCUCCACUACCGCUGUCGCGACUAUCACGACAGCCCGCUCCGUAA---------UUAUCACGAUAGUCGCGACGUCCACCGCA---------------
..................(((((((((((((((.((......))....((..---------.....)))))))))))))))......)).--------------- ( -21.60)
>DroSim_CAF1 17249 93 - 1
UCC---UCCUCCACCACCGCUGUCGCGACUAUCACGACAGCCUGCUCCGUAA---------UUAUCACGAUAGUCGCGACGUCCACCGCCGUAAUCAUCGCGUUU
...---...............(((((((((((((((..((....)).)))..---------.......))))))))))))......(((.((....)).)))... ( -22.90)
>DroEre_CAF1 17201 98 - 1
-CCUCCUCCUCC------ACCGUCGCGACUAUCAUGACGCCCUGCGCCGUAAUUAUCUUGGUUAUCCCGAUCGUCGCGGCGUCCUCCGCCGUAACCAUCGCGUUU
-...........------..(((((((((.((((((.(((...))).))).........((.....))))).))))))))).....(((.((....)).)))... ( -25.00)
>DroYak_CAF1 17322 99 - 1
UCCUCCUCCUCC------ACCGUCGCGACUAUCACGUCGCACUGCGCCGUAGACAUCUCUAUUUUCCCGAUGGGCGCGACGUCCUCCGCCAUAAUCAUCGCGUUU
............------..(((((((((......)))))...((((((((((....)))))..........))))))))).....(((.((....)).)))... ( -25.70)
>consensus
UCCUCCUCCUCC_C___CACUGUCGCGACUAUCACGACGCCCUGCUCCGUAA_________UUAUCCCGAUAGUCGCGACGUCCACCGCCAUAAUCAUCGCGUUU
....................(((((((((((((...................................)))))))))))))........................ (-17.65 = -17.77 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:07 2006