Locus 1294

Sequence ID 2L_DroMel_CAF1
Location 3,423,760 – 3,423,891
Length 131
Max. P 0.868701
window2114 window2115

overview

Window 4

Location 3,423,760 – 3,423,851
Length 91
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 83.59
Mean single sequence MFE -18.77
Consensus MFE -13.99
Energy contribution -13.59
Covariance contribution -0.40
Combinations/Pair 1.15
Mean z-score -2.04
Structure conservation index 0.75
SVM decision value 0.86
SVM RNA-class probability 0.868701
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3423760 91 - 22407834
CUGGCCCACAU----ACGCUGUUUAUAAAUAAAGCACAUCUUU-UUUACGGCAACUGCA--UGUGAGAGGGCUGAAAAAAAAAAAACAAAAAAACAAA
..(((((....----..(((............))).......(-((((((((....)).--))))))))))))......................... ( -18.20)
>DroSec_CAF1 12640 78 - 1
CUGGCCCACAU----ACGCUGUUUAUAAAUAAAGCACAUCUUU-UUUACGGCAACUGCA--UGUGAGAGGGCUAAAAA-------------AAGUAAA
.((((((....----..(((............))).......(-((((((((....)).--)))))))))))))....-------------....... ( -19.20)
>DroSim_CAF1 12817 78 - 1
CUGGCCCACAU----ACGCUGUUUAUAAAUAAAGCACAUCUUU-UUUACGGCAACUGCA--UGUGAGAGGGCUAAAAA-------------AAGUAAA
.((((((....----..(((............))).......(-((((((((....)).--)))))))))))))....-------------....... ( -19.20)
>DroEre_CAF1 12888 77 - 1
CUGGCCCACAU----ACGCUGUUUAUAAAUAAAGAACAUCUUU-UUUACGGCAACUGCA--UGUGGGAGGGCUGAAAA--------------AAUAAA
..(((((.(((----(.((.(((.......((((.....))))-........))).)).--))))...))))).....--------------...... ( -16.66)
>DroYak_CAF1 14089 81 - 1
CUGGCCCACAUCUGUGCGCUGUUUAUAAAUAC---ACAUCUUUUUUUGCGGCAAGUGCAUAUGUGAGAGGGCUGAGAA--------------AAUAAA
..(((((.(((.((((((((..(..((((...---.........))))..)..)))))))).)))...))))).....--------------...... ( -20.60)
>consensus
CUGGCCCACAU____ACGCUGUUUAUAAAUAAAGCACAUCUUU_UUUACGGCAACUGCA__UGUGAGAGGGCUGAAAA_____________AAAUAAA
.((((((..........(((((.........................)))))....((....))....))))))........................ (-13.99 = -13.59 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 3,423,779 – 3,423,891
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.20
Mean single sequence MFE -32.27
Consensus MFE -19.18
Energy contribution -20.57
Covariance contribution 1.39
Combinations/Pair 1.22
Mean z-score -1.60
Structure conservation index 0.59
SVM decision value -0.03
SVM RNA-class probability 0.517327
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3423779 112 + 22407834
UUUUUCAGCCCUCUCACA---UGCAGUUGCCGUAAA-AAAGAUGUGCUUUAUUUAUAAACAGCGU----AUGUGGGCCAGUCCAAAAAGGGAUGUCGGAUAGUGAGUGGGACGACUGGAC
...((((((((.((((((---(((.((((..(((((-((((.....)))).)))))...))))))----)))))))((.((((......))))...)).........)))....))))). ( -29.30)
>DroSec_CAF1 12647 107 + 1
-UUUUUAGCCCUCUCACA---UGCAGUUGCCGUAAA-AAAGAUGUGCUUUAUUUAUAAACAGCGU----AUGUGGGCCAGUCCGAAAAGGGAUGUCGGAUAG----UGGGACGGCUGGAC
-..(((((((..((((((---(((.((((..(((((-((((.....)))).)))))...))))))----)))))))(((((((((.........))))))..----)))...))))))). ( -34.30)
>DroAna_CAF1 15235 99 + 1
-UUUUCCGCUUUCUGAACCGCUGCAGUUGGUGUAAAAAAAUAAACGACUUAUUUAUAAAUAGCGU----AUGUGGGGCAAUCCUAAAAAGGAUAAAG----------------GAUGAGC
-......((((((((..(((((((.((((...((...((((((.....)))))).))..))))))----).))))..).(((((....)))))...)----------------)).)))) ( -19.60)
>DroSim_CAF1 12824 107 + 1
-UUUUUAGCCCUCUCACA---UGCAGUUGCCGUAAA-AAAGAUGUGCUUUAUUUAUAAACAGCGU----AUGUGGGCCAGUCCGAAAAGGGAUGUCGGAUAG----UGGGACGGCUGGAC
-..(((((((..((((((---(((.((((..(((((-((((.....)))).)))))...))))))----)))))))(((((((((.........))))))..----)))...))))))). ( -34.30)
>DroEre_CAF1 12894 107 + 1
-UUUUCAGCCCUCCCACA---UGCAGUUGCCGUAAA-AAAGAUGUUCUUUAUUUAUAAACAGCGU----AUGUGGGCCAGUCCGAAAAGGGAUGUCGGAUAG----UGGGACGGCUGGAC
-..(((((((..((((((---(((.((((..(((((-((((.....)))).)))))...))))))----)))))))(((((((((.........))))))..----)))...))))))). ( -40.20)
>DroYak_CAF1 14095 111 + 1
-UUCUCAGCCCUCUCACA-UAUGCACUUGCCGCAAAAAAAGAUGU---GUAUUUAUAAACAGCGCACAGAUGUGGGCCAGUCCGAAAAGGGAUGUCGGCUAG----UGGGAUGGCUGGAC
-.((.(((((.((((((.-..........(((((........(((---(..((.......))..))))..)))))(((.((((......))))...)))..)----))))).))))))). ( -35.90)
>consensus
_UUUUCAGCCCUCUCACA___UGCAGUUGCCGUAAA_AAAGAUGUGCUUUAUUUAUAAACAGCGU____AUGUGGGCCAGUCCGAAAAGGGAUGUCGGAUAG____UGGGACGGCUGGAC
...(((((((..((((((.......((((..(((((.((((.....)))).)))))...)))).......))))))((.((((......))))...))..............))))))). (-19.18 = -20.57 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:51 2006