Locus 5697

Sequence ID 3R_DroMel_CAF1
Location 14,927,435 – 14,927,610
Length 175
Max. P 0.709269
window9319 window9320 window9321

overview

Window 9

Location 14,927,435 – 14,927,538
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.35
Mean single sequence MFE -30.82
Consensus MFE -15.20
Energy contribution -16.68
Covariance contribution 1.48
Combinations/Pair 1.06
Mean z-score -1.89
Structure conservation index 0.49
SVM decision value 0.25
SVM RNA-class probability 0.653042
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14927435 103 + 27905053
AUCAGCUGGGGGAGCUGCACUUUUCCGACAGCCCCUGCAAUUUAUGCCCCCG-AAAAUGG-GGGA-AUAGCUC--UCAAGCACCAGAAGAUUCCCUCAAAAAAG---UGAA---------
(((..(((((((.(((((........).))))))).......(((.(((((.-.....))-))).-)))(((.--...))).))))..))).............---....--------- ( -30.10)
>DroSec_CAF1 57441 105 + 1
AUCAGCUGGGGGAGCUGCACUUUUCCGGCAGCCACAGCAAUUUAUGCCUCCGGAAAAUGGGGGGA-AAAGUUC--UCAAGCACCAGAAGAUACCCUCAAAAAAG---UGGA---------
....(((((..(((.....)))..)))))..((((.(((.....)))..........((((((..-....(((--(........))))....)))))).....)---))).--------- ( -31.60)
>DroSim_CAF1 56113 108 + 1
AUCAGCUGGGGGAGCUGCACUUUUCCGGCAGCCACAGCAAUUUAUGCCCCCGGAAAAUGGGGGGA-AAAGUUC--UCAAGCACCAGAAGAUACCCUCAAAAAAGAAAUAGA---------
(((.(((((..(((.....)))..))))).((...((.(((((.(.((((((.....)))))).)-.))))))--)...)).......)))....................--------- ( -31.80)
>DroEre_CAF1 53972 98 + 1
AUCAGCUGGGGGAGCUGCACUUUUCCGGCAC-----------UUUUCCCCCG-AAAAUGCG--UACUAAGUUCUCUCAAGUACCAGAAAAACCCCUGAAAAACA---GGCAGCGG-----
....(((((..(((.....)))..)))))..-----------.......(((-....((((--((((.((....))..)))))(((........))).......---.))).)))----- ( -26.10)
>DroYak_CAF1 60792 111 + 1
AUCAACUGGGGGAGCUGCACUUUUCCGGCAGCCCCUGCAAUUUAUGCCCCCG-AAAAUGGG--AA-AAAGUUC--UCAAGUACCAGAUGAUCCCCUGAAAAACG---GGCAUAAAAACAA
........((((.(((((.(......))))))))))....(((((((((...-....((((--((-....)))--))).....(((........)))......)---))))))))..... ( -34.50)
>consensus
AUCAGCUGGGGGAGCUGCACUUUUCCGGCAGCCACAGCAAUUUAUGCCCCCG_AAAAUGGGGGGA_AAAGUUC__UCAAGCACCAGAAGAUACCCUCAAAAAAG___UGCA_________
.((.(((((..(((.....)))..))))).................((((((.....))))))......................))................................. (-15.20 = -16.68 +   1.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,927,475 – 14,927,575
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.89
Mean single sequence MFE -19.36
Consensus MFE -3.10
Energy contribution -4.18
Covariance contribution 1.08
Combinations/Pair 1.17
Mean z-score -1.67
Structure conservation index 0.16
SVM decision value 0.31
SVM RNA-class probability 0.683777
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14927475 100 + 27905053
UUUAUGCCCCCG-AAAAUGG-GGGA-AUAGCUC--UCAAGCACCAGAAGAUUCCCUCAAAAAAG---UGAA----------CAGAGA--AAUUCCAAAUUUUUCAUUUCUAUUUUUAAAA
............-....(((-((((-((...((--(........)))..))))))))).(((((---((((----------..((((--(((.....)))))))..))).)))))).... ( -20.10)
>DroSec_CAF1 57481 101 + 1
UUUAUGCCUCCGGAAAAUGGGGGGA-AAAGUUC--UCAAGCACCAGAAGAUACCCUCAAAAAAG---UGGA----------CAGAGA--AAUUCCAAUUUUCCCAUUUCUAUUUUUA-AA
............(((((((((((((-(((.(((--((......(....)...((((......))---.)).----------..))))--).......)))))))...))))))))).-.. ( -17.50)
>DroSim_CAF1 56153 107 + 1
UUUAUGCCCCCGGAAAAUGGGGGGA-AAAGUUC--UCAAGCACCAGAAGAUACCCUCAAAAAAGAAAUAGA----------CAGAGAAAAAUUUCAAAUUUCCCAUUUCUAUUUUUAAAA
....(.((((((.....)))))).)-....(((--(........))))..............(((((((((----------..(.((((.........)))).)...))))))))).... ( -17.80)
>DroEre_CAF1 54003 104 + 1
--UUUUCCCCCG-AAAAUGCG--UACUAAGUUCUCUCAAGUACCAGAAAAACCCCUGAAAAACA---GGCAGCGG------CGGAGA--AAUUCCAAAUUUUCCAUUUCUAUUUUUAAAA
--((((((.(((-....((((--((((.((....))..)))))(((........))).......---.))).)))------.)))))--).............................. ( -19.60)
>DroYak_CAF1 60832 109 + 1
UUUAUGCCCCCG-AAAAUGGG--AA-AAAGUUC--UCAAGUACCAGAUGAUCCCCUGAAAAACG---GGCAUAAAAACAAAUUUAAA--GAUUCCAAAUUUCCCAUUUCUAUUUUUAAAA
(((((((((...-....((((--((-....)))--))).....(((........)))......)---))))))))......((((((--(((...((((.....))))..))))))))). ( -21.80)
>consensus
UUUAUGCCCCCG_AAAAUGGGGGGA_AAAGUUC__UCAAGCACCAGAAGAUACCCUCAAAAAAG___UGCA__________CAGAGA__AAUUCCAAAUUUCCCAUUUCUAUUUUUAAAA
......((((((.....))))))................................................................................................. ( -3.10 =  -4.18 +   1.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,927,510 – 14,927,610
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.45
Mean single sequence MFE -20.51
Consensus MFE -1.40
Energy contribution -1.64
Covariance contribution 0.24
Combinations/Pair 1.29
Mean z-score -1.52
Structure conservation index 0.07
SVM decision value 0.37
SVM RNA-class probability 0.709269
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14927510 100 + 27905053
CACCAGAAGAUUCCCUCAAAAAAG---UGAA----------CAGAGA--AAUUCCAAAUUUUUCAUUUCUAUUUUUAAAAUGGCAGCGG-----AACAACGUUGCCUAGUUUUUCAAAUU
.....(((((.........(((((---((((----------..((((--(((.....)))))))..))).)))))).....(((((((.-----.....)))))))....)))))..... ( -21.70)
>DroSec_CAF1 57518 99 + 1
CACCAGAAGAUACCCUCAAAAAAG---UGGA----------CAGAGA--AAUUCCAAUUUUCCCAUUUCUAUUUUUA-AAUAGCAGAGG-----AGCAACAUUGCCCAGUUUUUUAAAUU
....(((((((..((((....(((---(((.----------..((((--(.......)))))))))))(((((....-)))))..))))-----.(((....)))...)))))))..... ( -15.40)
>DroSim_CAF1 56190 107 + 1
CACCAGAAGAUACCCUCAAAAAAGAAAUAGA----------CAGAGAAAAAUUUCAAAUUUCCCAUUUCUAUUUUUAAAAUAGCAGAGGA---GAGCAACGUUGCCCAGUUUUUCAAAUU
.....(((((.((((((.....(((((((((----------..(.((((.........)))).)...))))))))).........)))).---(.(((....))).).)))))))..... ( -13.64)
>DroEre_CAF1 54038 104 + 1
UACCAGAAAAACCCCUGAAAAACA---GGCAGCGG------CGGAGA--AAUUCCAAAUUUUCCAUUUCUAUUUUUAAAAGUCCAGGGGA-----GCAACGUUGCCUAGUUUUUCAAAUU
...............(((((((((---((((((((------((((((--(........)))))).................(((...)))-----))..)))))))).)))))))).... ( -29.00)
>DroYak_CAF1 60866 115 + 1
UACCAGAUGAUCCCCUGAAAAACG---GGCAUAAAAACAAAUUUAAA--GAUUCCAAAUUUCCCAUUUCUAUUUUUAAAAGUCCAGGGGAGCGGAGCGACGUUGCCUGGUUUUUCAAAUU
.(((((....(((((((......(---..........)...((((((--(((...((((.....))))..)))))))))....)))))))(((......)))...))))).......... ( -22.80)
>consensus
CACCAGAAGAUACCCUCAAAAAAG___UGCA__________CAGAGA__AAUUCCAAAUUUCCCAUUUCUAUUUUUAAAAUAGCAGAGGA____AGCAACGUUGCCUAGUUUUUCAAAUU
.....(((((................................(((((..((........))....)))))............((((.(...........).)))).....)))))..... ( -1.40 =  -1.64 +   0.24)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:08 2006