Locus 1991

Sequence ID	3R_DroMel_CAF1
Location	5,633,335 – 5,633,446
Length	111
Max. P	0.617245

overview

Window 2

Location	5,633,335 – 5,633,446
Length	111
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	82.16
Mean single sequence MFE	-44.43
Consensus MFE	-29.28
Energy contribution	-29.42
Covariance contribution	0.14
Combinations/Pair	1.25
Mean z-score	-1.79
Structure conservation index	0.66
SVM decision value	0.17
SVM RNA-class probability	0.617245
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5633335 111 + 27905053
CUCCGCCGGACGCAGCUGUUCCAGCUCCGGCUGCUUCACCUGUGGCACCUGCAGACGGUCCCAUCUCUCCGCCUUGUGUGUAGAGGCGUCGAGAUCUUUUCCUAGCCGGCA
....(((((.((((((((.........))))))).....(((..(...)..)))..((....(((((..((((((.......))))))..))))).....))..)))))). ( -42.90)
>DroSec_CAF1 6963 111 + 1
CACCGCCGGACGCUGCUGUUCCAGAUCCGGCUGCUUCACCUGUGGCACCCGCAGACGGUCCCAUCUCUCCGCCUUGUGUGUAGAGGCGUCGAGACCUUUUCCUCGCCGGCA
....(((((.(((.((((.........)))).)).....((((((...))))))..((.....((((..((((((.......))))))..))))......))..)))))). ( -39.90)
>DroSim_CAF1 7650 111 + 1
CGCCGCCGGACGCUGCUGUUCCAGAUCCGGCUGCUUCACCUGUCGCACCCGCAGACGGUCCCAUCUCUCCGCCUUGUGUGUAGAGGCGUCGAGACCUUUUCCUCGCCGGCA
.(((((((((..(((......))).)))))).((.....(((((((....)).))))).....((((..((((((.......))))))..))))..........)).))). ( -41.90)
>DroEre_CAF1 8124 111 + 1
CACCGCCGGACGCUGCUGUUCCAGCUCCGGCUGCUUCACCUGUGGAUCCCGCAGCCGGUCCCAUCUCUCCACCUUGUGUGUAGAGGCGUCGAGAUCUUUUCCUCGCCGGCA
....(((((((((.((((...)))).((((((((((((....))))....))))))))......((((.(((.....))).)))))))))(((........)))..)))). ( -45.70)
>DroYak_CAF1 7699 111 + 1
CACCGCCGGACGCUGCUGUUCCAGCUCCGACUGCUUCUCCAGUGGCUCCAGCAGUCGGUCCCAUCUCUCCGCCUUGUGUGUAAAGGCGUCGGGAUCUUUUCCUCGCCGGCA
....(((((.(((((......)))).(((((((((...((...))....)))))))))....(((((..((((((.......))))))..))))).........)))))). ( -44.70)
>DroMoj_CAF1 7001 108 + 1
CACCGCUGGCCGC---ACUGCCUCCACUGCCCGCAUCCAUGCUGGGCACUGCCGCCGUGUCCGUCUCCCCGCUCUGCGUGUAAAGGCGGCGUGAGCGCUUGCGUGCCGGCA
....(((((((((---(..(((((.((((((((((....))).)))))..((((((.((..(((...........)))..))..))))))))))).)).)))).)))))). ( -51.50)
>consensus
CACCGCCGGACGCUGCUGUUCCAGCUCCGGCUGCUUCACCUGUGGCACCCGCAGACGGUCCCAUCUCUCCGCCUUGUGUGUAGAGGCGUCGAGAUCUUUUCCUCGCCGGCA
....(((((.((..............(((.((((................)))).))).....((((..((((((.......))))))..)))).........))))))). (-29.28 = -29.42 +   0.14)

alignment

secondary structure

dotplot

Window 3

Location	5,633,335 – 5,633,446
Length	111
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	82.16
Mean single sequence MFE	-47.00
Consensus MFE	-32.52
Energy contribution	-33.97
Covariance contribution	1.45
Combinations/Pair	1.27
Mean z-score	-1.36
Structure conservation index	0.69
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5633335 111 - 27905053
UGCCGGCUAGGAAAAGAUCUCGACGCCUCUACACACAAGGCGGAGAGAUGGGACCGUCUGCAGGUGCCACAGGUGAAGCAGCCGGAGCUGGAACAGCUGCGUCCGGCGGAG
..((((((........(((((..(((((.........)))))..)))))((.(((.......))).))...........)))))).((((((.(......))))))).... ( -43.80)
>DroSec_CAF1 6963 111 - 1
UGCCGGCGAGGAAAAGGUCUCGACGCCUCUACACACAAGGCGGAGAGAUGGGACCGUCUGCGGGUGCCACAGGUGAAGCAGCCGGAUCUGGAACAGCAGCGUCCGGCGGUG
.(((((((........(((((..(((((.........)))))..)))))....(((....))).))))............((((((((((......))).)))))))))). ( -45.30)
>DroSim_CAF1 7650 111 - 1
UGCCGGCGAGGAAAAGGUCUCGACGCCUCUACACACAAGGCGGAGAGAUGGGACCGUCUGCGGGUGCGACAGGUGAAGCAGCCGGAUCUGGAACAGCAGCGUCCGGCGGCG
.(((.((.........(((((..(((((.........)))))..)))))...((((((.((....))))).)))...)).((((((((((......))).)))))))))). ( -46.60)
>DroEre_CAF1 8124 111 - 1
UGCCGGCGAGGAAAAGAUCUCGACGCCUCUACACACAAGGUGGAGAGAUGGGACCGGCUGCGGGAUCCACAGGUGAAGCAGCCGGAGCUGGAACAGCAGCGUCCGGCGGUG
.((((.(.........(((((..(((((.........)))))..))))).(((((((((((...(((....)))...)))))))).((((......)))).)))).)))). ( -48.30)
>DroYak_CAF1 7699 111 - 1
UGCCGGCGAGGAAAAGAUCCCGACGCCUUUACACACAAGGCGGAGAGAUGGGACCGACUGCUGGAGCCACUGGAGAAGCAGUCGGAGCUGGAACAGCAGCGUCCGGCGGUG
.(((((((.........(((((.((((((.......))))))......)))))(((((((((....((...))...))))))))).((((...))))..)).))))).... ( -46.90)
>DroMoj_CAF1 7001 108 - 1
UGCCGGCACGCAAGCGCUCACGCCGCCUUUACACGCAGAGCGGGGAGACGGACACGGCGGCAGUGCCCAGCAUGGAUGCGGGCAGUGGAGGCAGU---GCGGCCAGCGGUG
.((.(((.((((.((.(((((((((((......(((...))).(....)......))))))..(((((.(((....)))))))))).)))))..)---)))))).)).... ( -51.10)
>consensus
UGCCGGCGAGGAAAAGAUCUCGACGCCUCUACACACAAGGCGGAGAGAUGGGACCGUCUGCGGGUGCCACAGGUGAAGCAGCCGGAGCUGGAACAGCAGCGUCCGGCGGUG
.(((.((.........(((((..(((((.........)))))..)))))((.(((.......))).)).........)).((((((((((......)))).))))))))). (-32.52 = -33.97 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:29 2006