Locus 43

Sequence ID	X_DroMel_CAF1
Location	199,768 – 199,870
Length	102
Max. P	0.714526

overview

Window 3

Location	199,768 – 199,870
Length	102
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	88.19
Mean single sequence MFE	-43.02
Consensus MFE	-32.49
Energy contribution	-32.46
Covariance contribution	-0.03
Combinations/Pair	1.09
Mean z-score	-2.97
Structure conservation index	0.76
SVM decision value	0.28
SVM RNA-class probability	0.664689
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 199768 102 + 22224390
---UCGAAGUCGUAGCCUCUGCCGCUGUCACUGCUUCAGU------------CGACGGCGGCAGAAUCGCAACGGCAACGGUUUUAGAUGGCUGAAGCGUUCAUCAUUUUGCCAUUU
---(((..(((((.((.((((((((((((((((...))))------------.))))))))))))...)).)))))..)))....(((((((.(((..........))).))))))) ( -44.40)
>DroSec_CAF1 30682 102 + 1
---UCGAAGUCGCAGCCUCUGCCGCUGUCGCUGCUUCAGU------------CGACGGCGGCAGAAUCGCAACGGCAUCGGUUUUAGAUGGCUGAAGCGUUCAUCAUUUUGCCAUUU
---((((.((((..((.((((((((((((((((...))).------------)))))))))))))...))..)))).))))....(((((((.(((..........))).))))))) ( -45.50)
>DroSim_CAF1 31364 102 + 1
---UCGAAGUCGCAGCCUCUGCCGCUGUCGCUGCUUCAGU------------CGACGGCGGCAGAAUCGCAACGGCAUCGGUUUUAGAUGGCUGAAGCGUUCAUCAUUUUGCCAUUU
---((((.((((..((.((((((((((((((((...))).------------)))))))))))))...))..)))).))))....(((((((.(((..........))).))))))) ( -45.50)
>DroEre_CAF1 39255 105 + 1
GAGUCGAAGUCGCAGCCUCUGCCGCAGUCACUGCUUCAGU------------CGACGGCGGCAGAAUCGCAACGGCAACGGUUUUAGAUGGUUGAAGCGUUCAUCAUUUUGCCAUUU
((..((..((((..((.((((((((.(((((((...))))------------.))).))))))))...))..))))..))..)).(((((((.(((..........))).))))))) ( -38.20)
>DroYak_CAF1 29898 105 + 1
AAGUCGAAGUCGCAGCCUCUGCCGCAGUCACUGCUUCAGU------------CGACGGCGGCAGAAUCGCAACGGCAACGGUUUUAGAUGGCUGAAGCGUUCAUCAUUUUGCCAUUU
.....(((((..(((((((((((((.(((((((...))))------------.))).))))))))(((....((....))......))))))))..)).)))............... ( -40.40)
>DroAna_CAF1 53325 117 + 1
GGCUUGCAGUCGCUGCCUCUGCCUCAGUCGCUGUCUCAGUUGCUGCCGCAGCCGGCGUCGGCAGAGUGGCAACGGCAACGGUUUUCGAUGGUUGGAGCGUUCAUCAUUUUGCCAUUU
(((..((....)).)))((((((...((((((((..(((...)))..)))).))))...))))))(((((((((....))......(((((.........)))))...))))))).. ( -44.10)
>consensus
___UCGAAGUCGCAGCCUCUGCCGCAGUCACUGCUUCAGU____________CGACGGCGGCAGAAUCGCAACGGCAACGGUUUUAGAUGGCUGAAGCGUUCAUCAUUUUGCCAUUU
........((((..((.((((((((.(((((((...)))).............))).))))))))...))..))))...(((...((((((.((((...)))))))))).))).... (-32.49 = -32.46 +  -0.03)

alignment

secondary structure

dotplot

Window 4

Location	199,768 – 199,870
Length	102
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	88.19
Mean single sequence MFE	-39.99
Consensus MFE	-31.03
Energy contribution	-31.81
Covariance contribution	0.78
Combinations/Pair	1.06
Mean z-score	-2.76
Structure conservation index	0.78
SVM decision value	0.38
SVM RNA-class probability	0.714526
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 199768 102 - 22224390
AAAUGGCAAAAUGAUGAACGCUUCAGCCAUCUAAAACCGUUGCCGUUGCGAUUCUGCCGCCGUCG------------ACUGAAGCAGUGACAGCGGCAGAGGCUACGACUUCGA---
.((((((((...((((...((....))))))........))))))))((..(((((((((.(((.------------((((...))))))).)))))))))))..((....)).--- ( -36.50)
>DroSec_CAF1 30682 102 - 1
AAAUGGCAAAAUGAUGAACGCUUCAGCCAUCUAAAACCGAUGCCGUUGCGAUUCUGCCGCCGUCG------------ACUGAAGCAGCGACAGCGGCAGAGGCUGCGACUUCGA---
....((((....((((...((....)))))).........))))((((((.(((((((((.((((------------.(((...))))))).)))))))))..)))))).....--- ( -40.62)
>DroSim_CAF1 31364 102 - 1
AAAUGGCAAAAUGAUGAACGCUUCAGCCAUCUAAAACCGAUGCCGUUGCGAUUCUGCCGCCGUCG------------ACUGAAGCAGCGACAGCGGCAGAGGCUGCGACUUCGA---
....((((....((((...((....)))))).........))))((((((.(((((((((.((((------------.(((...))))))).)))))))))..)))))).....--- ( -40.62)
>DroEre_CAF1 39255 105 - 1
AAAUGGCAAAAUGAUGAACGCUUCAACCAUCUAAAACCGUUGCCGUUGCGAUUCUGCCGCCGUCG------------ACUGAAGCAGUGACUGCGGCAGAGGCUGCGACUUCGACUC
....(((((...((((...........))))........)))))((((((.(((((((((.(((.------------((((...))))))).)))))))))..))))))........ ( -39.90)
>DroYak_CAF1 29898 105 - 1
AAAUGGCAAAAUGAUGAACGCUUCAGCCAUCUAAAACCGUUGCCGUUGCGAUUCUGCCGCCGUCG------------ACUGAAGCAGUGACUGCGGCAGAGGCUGCGACUUCGACUU
..(((((....(((........))))))))........((((..((((((.(((((((((.(((.------------((((...))))))).)))))))))..))))))..)))).. ( -41.40)
>DroAna_CAF1 53325 117 - 1
AAAUGGCAAAAUGAUGAACGCUCCAACCAUCGAAAACCGUUGCCGUUGCCACUCUGCCGACGCCGGCUGCGGCAGCAACUGAGACAGCGACUGAGGCAGAGGCAGCGACUGCAAGCC
....(((....(((((...........))))).....(((((((((((((.(...((((....)))).).))))))..(((...(((...)))...))).))))))).......))) ( -40.90)
>consensus
AAAUGGCAAAAUGAUGAACGCUUCAGCCAUCUAAAACCGUUGCCGUUGCGAUUCUGCCGCCGUCG____________ACUGAAGCAGCGACAGCGGCAGAGGCUGCGACUUCGA___
....(((((...((((...........))))........)))))((((((.(((((((((.((((.............(((...))))))).)))))))))..))))))........ (-31.03 = -31.81 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:11 2006