Locus 2480

Sequence ID 2R_DroMel_CAF1
Location 8,887,699 – 8,887,789
Length 90
Max. P 0.935775
window4094 window4095

overview

Window 4

Location 8,887,699 – 8,887,789
Length 90
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 82.96
Mean single sequence MFE -25.92
Consensus MFE -18.26
Energy contribution -18.32
Covariance contribution 0.06
Combinations/Pair 1.13
Mean z-score -3.39
Structure conservation index 0.70
SVM decision value 1.07
SVM RNA-class probability 0.910077
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8887699 90 + 20766785
ACAAAGCUGCAAAUUGGCUGGUGGUAAGUGCAGCUAUGGCUA--AGGGCAACACAGCCCCAAG----CCACCAAAAACACAACCACCCACAGCACU
.....(((((......)).((((((..(((......(((((.--.((((......))))..))----))).......))).))))))...)))... ( -30.02)
>DroSec_CAF1 132498 81 + 1
ACAAAGCUGCAAAUUGGCUGGUGGUAAGUGCAGCUAUGGCUA--AGGGCAACACAGCCCCAAG----CCACCAAAAACACAACCACC---------
....((((.......))))((((((..(((......(((((.--.((((......))))..))----))).......))).))))))--------- ( -28.22)
>DroSim_CAF1 132370 81 + 1
ACAAAGCUGCAAAUUGGCUGGUGGUAAGUGCAGCUAUGGCUA--AGGGCAACACAGCCCCAAG----CCACCAAAAACACAACCACC---------
....((((.......))))((((((..(((......(((((.--.((((......))))..))----))).......))).))))))--------- ( -28.22)
>DroEre_CAF1 135790 81 + 1
ACAAAGCUGCAAAUUGGCUGGUGGUAAGUGCAGCUAUGGCUA--AGGGCAACACAGCCCCAAA----CCACCAAAAACACAACCACC---------
....((((.......))))((((((......(((....))).--.((((......))))...)----)))))...............--------- ( -22.90)
>DroYak_CAF1 137842 90 + 1
ACAAAGCUGCAAAUUGGCUGGUGGUAAGUGCAGCUAUGGCUA--AGGGCAACACAGCCCCAAA----CCACCGAAAACACAACCACCCACAGCACU
.....((((.....(((..((((((......(((....))).--.((((......))))...)----)))))(......)..)))....))))... ( -25.30)
>DroAna_CAF1 131234 82 + 1
ACAAAGCUGCAAAUUGGCUGGCGGUAAGUGCAGCUAUAGCUUCUGGGGCAAUACUCCUUCAAUGGCCCCUUCGAUACCCCUU--------------
....(((((((.....((.....))...))))))).........(((((...............))))).............-------------- ( -20.86)
>consensus
ACAAAGCUGCAAAUUGGCUGGUGGUAAGUGCAGCUAUGGCUA__AGGGCAACACAGCCCCAAG____CCACCAAAAACACAACCACC_________
.((.(((((((.....((.....))...))))))).)).......((((......))))..................................... (-18.26 = -18.32 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,887,699 – 8,887,789
Length 90
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 82.96
Mean single sequence MFE -34.94
Consensus MFE -20.58
Energy contribution -22.17
Covariance contribution 1.58
Combinations/Pair 1.14
Mean z-score -4.07
Structure conservation index 0.59
SVM decision value 1.25
SVM RNA-class probability 0.935775
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8887699 90 - 20766785
AGUGCUGUGGGUGGUUGUGUUUUUGGUGG----CUUGGGGCUGUGUUGCCCU--UAGCCAUAGCUGCACUUACCACCAGCCAAUUUGCAGCUUUGU
...(((((.((((((.((((.....((((----((.(((((......)))))--.))))))....))))..)))))).........)))))..... ( -40.90)
>DroSec_CAF1 132498 81 - 1
---------GGUGGUUGUGUUUUUGGUGG----CUUGGGGCUGUGUUGCCCU--UAGCCAUAGCUGCACUUACCACCAGCCAAUUUGCAGCUUUGU
---------((((((.((((.....((((----((.(((((......)))))--.))))))....))))..)))))).((......))........ ( -37.10)
>DroSim_CAF1 132370 81 - 1
---------GGUGGUUGUGUUUUUGGUGG----CUUGGGGCUGUGUUGCCCU--UAGCCAUAGCUGCACUUACCACCAGCCAAUUUGCAGCUUUGU
---------((((((.((((.....((((----((.(((((......)))))--.))))))....))))..)))))).((......))........ ( -37.10)
>DroEre_CAF1 135790 81 - 1
---------GGUGGUUGUGUUUUUGGUGG----UUUGGGGCUGUGUUGCCCU--UAGCCAUAGCUGCACUUACCACCAGCCAAUUUGCAGCUUUGU
---------((((((.((((.....((((----((.(((((......)))))--.))))))....))))..)))))).((......))........ ( -34.70)
>DroYak_CAF1 137842 90 - 1
AGUGCUGUGGGUGGUUGUGUUUUCGGUGG----UUUGGGGCUGUGUUGCCCU--UAGCCAUAGCUGCACUUACCACCAGCCAAUUUGCAGCUUUGU
...(((((.((((((.((((.....((((----((.(((((......)))))--.))))))....))))..)))))).........)))))..... ( -38.50)
>DroAna_CAF1 131234 82 - 1
--------------AAGGGGUAUCGAAGGGGCCAUUGAAGGAGUAUUGCCCCAGAAGCUAUAGCUGCACUUACCGCCAGCCAAUUUGCAGCUUUGU
--------------..((((((((....)).((......)).....))))))....((...(((((((.................)))))))..)) ( -21.33)
>consensus
_________GGUGGUUGUGUUUUUGGUGG____CUUGGGGCUGUGUUGCCCU__UAGCCAUAGCUGCACUUACCACCAGCCAAUUUGCAGCUUUGU
.........((((((.((((.....((((.......(((((......))))).....))))....))))..)))))).((......))........ (-20.58 = -22.17 +   1.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:06 2006