Locus 1339

Sequence ID	3R_DroMel_CAF1
Location	3,949,433 – 3,949,553
Length	120
Max. P	0.952395

overview

Window 0

Location	3,949,433 – 3,949,553
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.78
Mean single sequence MFE	-42.08
Consensus MFE	-21.47
Energy contribution	-21.28
Covariance contribution	-0.19
Combinations/Pair	1.38
Mean z-score	-1.96
Structure conservation index	0.51
SVM decision value	0.12
SVM RNA-class probability	0.594781
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3949433 120 + 27905053
AAGGAGGGGGAAACGUCACCGCCUAUUCCAAAUCCAGUUUGGACCUUCGAGCAAUGCUUUGCCGAAUAUCCAGAUAUGCUUGAGGAGAUUACCAAAAUGGGCUUCUCCAAGCCCUCGCCC
...(((((((((..((....))...)))).......(((((((..((((.((((....))))))))..)))))))........(((((...((.....))...)))))...))))).... ( -38.80)
>DroVir_CAF1 17300 120 + 1
AAGGAUGGCGAAACCCCAACGCCCAUACCCAAUCCUGUAUGGACUUUCGAGCAAUGCUUUGCCGAAUAUCCUGAUUUGCUGGGCGAAAUACAGAAGCAGGGCUUUGCGCAUCCAUCGCCC
..((((((((((.(((...(((((((((........))))(((..((((.((((....))))))))..))).........))))).....(....)..))).))))).)))))....... ( -40.00)
>DroPse_CAF1 15879 120 + 1
AAGGAGGGCGAAGAAAUCCCACCCAUACCGAAUCCGGUAUGGACAUUCGAGCAAUGCUUUGCCGAAUAUCCCGAUCUGUUGGGCGAAAUCGAGAAGCAGGGCUUCCCUAAGCCCUCGCCC
...((((((..((.........((((((((....))))))))......((((..((((((..(((....(((((....))))).....))).))))))..))))..))..)))))).... ( -47.90)
>DroGri_CAF1 15566 120 + 1
AAGGAGGGAGAAACUUUGCCAGCAAUUCCGAAUCCCGUGUGGAGUUUCGAGCAGUGCUUUGACGAGUAUCCCGAUCUGCUAGCCGAAGUGCAGAAGCAGGGUUUCGCGAAGCCCUCGCCC
...((((..(((((((..((................).)..))))))).......((((((.((((...(((..(((((..........)))))....))).)))))))))))))).... ( -38.49)
>DroMoj_CAF1 17896 120 + 1
CAGGAGGGCGAAGUGUUUGCGCCCAUACCGAAUCCUGUAUGGAAGUUCGAGCAAUGCUUUGCCGAGUACCCCGAUUUGCUGGCCGAAAUACAGAAGCAGGGAUUUACGAAGCCUUCACCC
.....(((.((((((((((.((((((((.(....).))))))..)).))))))..((((((..((((.(((.(.....(((.........)))...).))))))).)))))))))).))) ( -36.00)
>DroPer_CAF1 15868 120 + 1
AAGGAGGGCGAAGAAGUCCCACCCAUACCGAAUCCGGUAUGGACAUUCGAGCAAUGCUUUGCCGAAUAUCCCGAUCUGUUGGGUGAAAUCGAGAAGCAGGGCUUCCCUAAGCCCUCGCCC
...((((((...(((((((...((((((((....))))))))............((((((..(((....(((((....))))).....))).))))))))))))).....)))))).... ( -51.30)
>consensus
AAGGAGGGCGAAACAUUACCACCCAUACCGAAUCCGGUAUGGACAUUCGAGCAAUGCUUUGCCGAAUAUCCCGAUCUGCUGGGCGAAAUACAGAAGCAGGGCUUCCCGAAGCCCUCGCCC
...(((((..............((((((........))))))...((((.((((....))))))))........((((((...(........).))))))...........))))).... (-21.47 = -21.28 +  -0.19)

alignment

secondary structure

dotplot

Window 1

Location	3,949,433 – 3,949,553
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.78
Mean single sequence MFE	-47.03
Consensus MFE	-25.96
Energy contribution	-27.10
Covariance contribution	1.14
Combinations/Pair	1.38
Mean z-score	-2.61
Structure conservation index	0.55
SVM decision value	1.42
SVM RNA-class probability	0.952395
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3949433 120 - 27905053
GGGCGAGGGCUUGGAGAAGCCCAUUUUGGUAAUCUCCUCAAGCAUAUCUGGAUAUUCGGCAAAGCAUUGCUCGAAGGUCCAAACUGGAUUUGGAAUAGGCGGUGACGUUUCCCCCUCCUU
.((.(((((((((((((.(((......)))..)))))..)))).....(((((.((((((((....)))).)))).)))))..........((((...(((....))))))).)))))). ( -40.40)
>DroVir_CAF1 17300 120 - 1
GGGCGAUGGAUGCGCAAAGCCCUGCUUCUGUAUUUCGCCCAGCAAAUCAGGAUAUUCGGCAAAGCAUUGCUCGAAAGUCCAUACAGGAUUGGGUAUGGGCGUUGGGGUUUCGCCAUCCUU
.......(((((.((.(((((((((....))....((((((((.((((.((((.((((((((....)))).)))).))))......))))..)).))))))..))))))).))))))).. ( -45.50)
>DroPse_CAF1 15879 120 - 1
GGGCGAGGGCUUAGGGAAGCCCUGCUUCUCGAUUUCGCCCAACAGAUCGGGAUAUUCGGCAAAGCAUUGCUCGAAUGUCCAUACCGGAUUCGGUAUGGGUGGGAUUUCUUCGCCCUCCUU
(((((((((....(((((((...)))))))(((..(((((.........(((((((((((((....)))).)))))))))((((((....)))))))))))..))))))))))))..... ( -61.40)
>DroGri_CAF1 15566 120 - 1
GGGCGAGGGCUUCGCGAAACCCUGCUUCUGCACUUCGGCUAGCAGAUCGGGAUACUCGUCAAAGCACUGCUCGAAACUCCACACGGGAUUCGGAAUUGCUGGCAAAGUUUCUCCCUCCUU
((((((((((...(((......)))....)).)))))((((((((.((.((((.(((((...(((...))).(......)..))))))))).)).)))))))).........)))..... ( -35.80)
>DroMoj_CAF1 17896 120 - 1
GGGUGAAGGCUUCGUAAAUCCCUGCUUCUGUAUUUCGGCCAGCAAAUCGGGGUACUCGGCAAAGCAUUGCUCGAACUUCCAUACAGGAUUCGGUAUGGGCGCAAACACUUCGCCCUCCUG
((((((((((((.((..(((((((((.(((.....)))..))))....))))).....)).))))...(((((.((((((.....)))...))).))))).......))))))))..... ( -39.30)
>DroPer_CAF1 15868 120 - 1
GGGCGAGGGCUUAGGGAAGCCCUGCUUCUCGAUUUCACCCAACAGAUCGGGAUAUUCGGCAAAGCAUUGCUCGAAUGUCCAUACCGGAUUCGGUAUGGGUGGGACUUCUUCGCCCUCCUU
(((((((((....(((((((...)))))))..(..(((((.........(((((((((((((....)))).)))))))))((((((....)))))))))))..)..)))))))))..... ( -59.80)
>consensus
GGGCGAGGGCUUCGCGAAGCCCUGCUUCUGGAUUUCGCCCAGCAGAUCGGGAUAUUCGGCAAAGCAUUGCUCGAAAGUCCAUACAGGAUUCGGUAUGGGCGGGAACGCUUCGCCCUCCUU
((((((((.....(((......)))..........((((((.(.((((.((((.((((((((....)))).)))).))))......)))).)...))))))......))))))))..... (-25.96 = -27.10 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:09 2006