Locus 1994

Sequence ID 2R_DroMel_CAF1
Location 7,517,725 – 7,517,820
Length 95
Max. P 0.884782
window3291 window3292

overview

Window 1

Location 7,517,725 – 7,517,820
Length 95
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 79.57
Mean single sequence MFE -21.42
Consensus MFE -15.37
Energy contribution -15.23
Covariance contribution -0.14
Combinations/Pair 1.18
Mean z-score -1.80
Structure conservation index 0.72
SVM decision value 0.90
SVM RNA-class probability 0.878519
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7517725 95 + 20766785
GCUUCAACUGGUUUAAAUGCA----UAUUUGUGGCAGUU------AUUAUGUACAUUUUAGCUGCAUACCU---AAAAAUAUGCAGCACCACGC---------AAUACUAUUCACGA
........((((.....((((----((((((((((((((------(..((....))..))))))).)))..---..)))))))))..))))...---------.............. ( -21.90)
>DroVir_CAF1 22400 100 + 1
GCUUCAACUGGUUUAAAUGCA--AAUGUUUGUGGCAGUU------UUUAUUUACAUUUUAGCUGCAUA--------UUCUAUGCAGCACCACGUAUGUAUGUAAAUACUU-UAGAGA
.......((((..((..((((--.((((.(((((..((.------.......))......((((((((--------...)))))))).))))).)))).))))..))..)-)))... ( -22.80)
>DroGri_CAF1 18500 112 + 1
GCUUCAACUGGUUUAAAUGCGUUAAUAUUUGUGGCAGUUUGCUUUUUUAUAUACAUUUUAGCUGCAUAGAAUAUACUACUAUGCAGCACCACGUAUG----UAAAUACUU-UAGAGA
((...(((((.(.((((((......)))))).).))))).))...(((((((((......(((((((((.........))))))))).....)))))----)))).....-...... ( -27.70)
>DroSec_CAF1 13066 95 + 1
GCUUCAACUGGUUUAAAUGCA----UAUUUGUGGCAGUU------AUUAUGUACAUUUUAUCUGCAUACCU---ACAUAUAUGCAGCACCACGC---------AAUACUAUUCUCGA
........((((.....((((----(((.((((((((.(------(..((....))..)).)))).....)---))).)))))))..))))...---------.............. ( -17.90)
>DroEre_CAF1 13855 91 + 1
GCUUCAACUGGUUCAAAUGCA----UAUUUGUGGCAGAU------AUUAUGUACAUUUUAGCUGCAUAAG-------UAUAUGCAGCACCACGC---------AAUACUUUUCUCGA
((.....(((.(.(((((...----.))))).).)))..------...............((((((((..-------..)))))))).....))---------.............. ( -19.40)
>DroYak_CAF1 13359 91 + 1
GCUUCAACUGGUUUAAAUGCA----UAUUUGUGGCAGAU------AUUAUGUACAUUUUAGCUGCAUACC-------UAUGUGCAGCACCACGC---------AAUACUAUUAUCGA
........((((.....((((----(((..(((((((.(------(..((....))..)).)))).))).-------.)))))))..))))...---------.............. ( -18.80)
>consensus
GCUUCAACUGGUUUAAAUGCA____UAUUUGUGGCAGUU______AUUAUGUACAUUUUAGCUGCAUACC_______UAUAUGCAGCACCACGC_________AAUACUAUUAUCGA
((...(((((.(.((((((......)))))).).))))).....................((((((((...........)))))))).....))....................... (-15.37 = -15.23 +  -0.14)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 7,517,725 – 7,517,820
Length 95
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 79.57
Mean single sequence MFE -21.25
Consensus MFE -15.65
Energy contribution -16.02
Covariance contribution 0.36
Combinations/Pair 1.09
Mean z-score -1.78
Structure conservation index 0.74
SVM decision value 0.93
SVM RNA-class probability 0.884782
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7517725 95 - 20766785
UCGUGAAUAGUAUU---------GCGUGGUGCUGCAUAUUUUU---AGGUAUGCAGCUAAAAUGUACAUAAU------AACUGCCACAAAUA----UGCAUUUAAACCAGUUGAAGC
...(((((.(((((---------..(((((((((((((((...---.))))))))))......((.......------.)).))))).))))----)..)))))............. ( -23.80)
>DroVir_CAF1 22400 100 - 1
UCUCUA-AAGUAUUUACAUACAUACGUGGUGCUGCAUAGAA--------UAUGCAGCUAAAAUGUAAAUAAA------AACUGCCACAAACAUU--UGCAUUUAAACCAGUUGAAGC
......-..((((....)))).....((((((((((((...--------))))))))..((((((((((...------.............)))--)))))))..))))........ ( -20.69)
>DroGri_CAF1 18500 112 - 1
UCUCUA-AAGUAUUUA----CAUACGUGGUGCUGCAUAGUAGUAUAUUCUAUGCAGCUAAAAUGUAUAUAAAAAAGCAAACUGCCACAAAUAUUAACGCAUUUAAACCAGUUGAAGC
......-.....((((----.((((((...(((((((((.........)))))))))....)))))).))))...((.(((((....((((........))))....)))))...)) ( -23.70)
>DroSec_CAF1 13066 95 - 1
UCGAGAAUAGUAUU---------GCGUGGUGCUGCAUAUAUGU---AGGUAUGCAGAUAAAAUGUACAUAAU------AACUGCCACAAAUA----UGCAUUUAAACCAGUUGAAGC
....((((.(((((---------..(((((.((((((((....---..)))))))).......((.......------.)).))))).))))----)..)))).............. ( -19.20)
>DroEre_CAF1 13855 91 - 1
UCGAGAAAAGUAUU---------GCGUGGUGCUGCAUAUA-------CUUAUGCAGCUAAAAUGUACAUAAU------AUCUGCCACAAAUA----UGCAUUUGAACCAGUUGAAGC
(((((....(((((---------..(((((((((((((..-------..))))))))....((((.....))------))..))))).))))----)...)))))............ ( -22.70)
>DroYak_CAF1 13359 91 - 1
UCGAUAAUAGUAUU---------GCGUGGUGCUGCACAUA-------GGUAUGCAGCUAAAAUGUACAUAAU------AUCUGCCACAAAUA----UGCAUUUAAACCAGUUGAAGC
((((((((.(((((---------..(((((((((((....-------....))))))....((((.....))------))..))))).))))----)..))).......)))))... ( -17.41)
>consensus
UCGAGAAAAGUAUU_________GCGUGGUGCUGCAUAUA_______GGUAUGCAGCUAAAAUGUACAUAAU______AACUGCCACAAAUA____UGCAUUUAAACCAGUUGAAGC
.........................((((((((((((((.........)))))))))....((....)).............)))))..........((.(((((.....))))))) (-15.65 = -16.02 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:15 2006