Locus 1417

Sequence ID	2R_DroMel_CAF1
Location	5,475,773 – 5,475,863
Length	90
Max. P	0.977212

overview

Window 6

Location	5,475,773 – 5,475,863
Length	90
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	76.26
Mean single sequence MFE	-32.74
Consensus MFE	-17.00
Energy contribution	-18.54
Covariance contribution	1.53
Combinations/Pair	1.32
Mean z-score	-2.51
Structure conservation index	0.52
SVM decision value	1.79
SVM RNA-class probability	0.977212
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5475773 90 + 20766785
UUUAGCCCCUUUCCUCGUCCCUGGUUGCCACGAUCCC-AGAAGACCUAGGGUUUAGCUUCUGGCUGGCG--------GUCAGACAACCUGGGCGAGGAA
..........(((((((((((((..(((((.....((-((((((((...)))....))))))).)))))--------..))).......)))))))))) ( -36.31)
>DroSec_CAF1 3352 90 + 1
UUUAGCCCCUUUCCUCGUCCCCGGUUGCCACGAUCCC-AAAGGACCUAGUGUUUAGUUUCUGGCUGGCG--------GUCAGACAACCUGGGCGAGGAA
..........(((((((.(((.(((((.(((..(((.-...)))....))).......((((((.....--------))))))))))).)))))))))) ( -34.50)
>DroSim_CAF1 3704 90 + 1
UUUAGCCCCUUUCCUCGUCCCCGGUUGCCACGAUCCC-AGAAGACCUAGGGUUUAGCUUCUGGCUGGCG--------GUCAGACAACCUGGGCGAGGAA
..........(((((((.(((.(((((.(..((((((-((....((..(((.....)))..)))))).)--------))).).))))).)))))))))) ( -35.40)
>DroEre_CAF1 3396 89 + 1
-UAAACCCCCUACCUCUUCCCAGGCUGUCCCUAUCCC-AGAAGACCUAGGCUUUAGCUUCUGGCUGGCG--------GUCAGACAACCUGGGCAAGGAA
-...........(((...((((((.((((...(((((-((.(((....(((....))))))..)))).)--------))..)))).))))))..))).. ( -30.90)
>DroYak_CAF1 3455 87 + 1
--AAACCCCCUACCUCUUCCCAGGUUGUCUCUAUCCC-AGAAGAUC-AGGCUUUAGCUUCUGGCUGGCG--------GUCAGACGACCUGGGCGAGGAA
--..........((((..((((((((((((..(((((-((.(((..-.(((....))))))..)))).)--------)).)))))))))))).)))).. ( -39.80)
>DroAna_CAF1 2795 93 + 1
UCUGACCCCUU--CUUGCUUUCGAUUAUCAACAUCGUUUCAAGAUCU----UUGAGAUUCUGAUUGGCUUUGAGAGUGUCACACUACCUCGGUGAGGAA
..((((.....--...((((((((...((((((..((((((((...)----)))))))..)).))))..)))))))))))).....((((...)))).. ( -19.50)
>consensus
UUUAACCCCUUUCCUCGUCCCCGGUUGCCACGAUCCC_AGAAGACCUAGGGUUUAGCUUCUGGCUGGCG________GUCAGACAACCUGGGCGAGGAA
............((((((((..(((((........((.(((((.............)))))))(((((.........))))).))))).)))))))).. (-17.00 = -18.54 +   1.53)

alignment

secondary structure

dotplot

Window 7

Location	5,475,773 – 5,475,863
Length	90
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	76.26
Mean single sequence MFE	-32.90
Consensus MFE	-15.49
Energy contribution	-16.38
Covariance contribution	0.89
Combinations/Pair	1.33
Mean z-score	-2.06
Structure conservation index	0.47
SVM decision value	0.52
SVM RNA-class probability	0.767045
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5475773 90 - 20766785
UUCCUCGCCCAGGUUGUCUGAC--------CGCCAGCCAGAAGCUAAACCCUAGGUCUUCU-GGGAUCGUGGCAACCAGGGACGAGGAAAGGGGCUAAA
((((((((((.(((((((((((--------((....)((((((((........)).)))))-))).))).))))))).))).))))))).......... ( -38.00)
>DroSec_CAF1 3352 90 - 1
UUCCUCGCCCAGGUUGUCUGAC--------CGCCAGCCAGAAACUAAACACUAGGUCCUUU-GGGAUCGUGGCAACCGGGGACGAGGAAAGGGGCUAAA
((((((((((.(((((((((..--------...)))............(((..(((((...-.)))))))))))))).))).))))))).......... ( -34.70)
>DroSim_CAF1 3704 90 - 1
UUCCUCGCCCAGGUUGUCUGAC--------CGCCAGCCAGAAGCUAAACCCUAGGUCUUCU-GGGAUCGUGGCAACCGGGGACGAGGAAAGGGGCUAAA
((((((((((.(((((((((((--------((....)((((((((........)).)))))-))).))).))))))).))).))))))).......... ( -38.70)
>DroEre_CAF1 3396 89 - 1
UUCCUUGCCCAGGUUGUCUGAC--------CGCCAGCCAGAAGCUAAAGCCUAGGUCUUCU-GGGAUAGGGACAGCCUGGGAAGAGGUAGGGGGUUUA-
..((((.(((((((((((...(--------(.....(((((((((........)).)))))-))....)))))))))))))..))))...........- ( -36.60)
>DroYak_CAF1 3455 87 - 1
UUCCUCGCCCAGGUCGUCUGAC--------CGCCAGCCAGAAGCUAAAGCCU-GAUCUUCU-GGGAUAGAGACAACCUGGGAAGAGGUAGGGGGUUU--
..((((.(((((((.(((((..--------...)..(((((((.(.......-.).)))))-)).....)))).)))))))..))))..........-- ( -30.60)
>DroAna_CAF1 2795 93 - 1
UUCCUCACCGAGGUAGUGUGACACUCUCAAAGCCAAUCAGAAUCUCAA----AGAUCUUGAAACGAUGUUGAUAAUCGAAAGCAAG--AAGGGGUCAGA
..((((...)))).....((((.((((....((...(((..(((....----.)))..)))..((((.......))))...))...--.)))))))).. ( -18.80)
>consensus
UUCCUCGCCCAGGUUGUCUGAC________CGCCAGCCAGAAGCUAAACCCUAGGUCUUCU_GGGAUCGUGACAACCGGGGACGAGGAAAGGGGCUAAA
..((((.(((.(((((((................(((.....))).........((((.....))))...))))))).)))..))))............ (-15.49 = -16.38 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:21 2006