Locus 4285

Sequence ID 3L_DroMel_CAF1
Location 12,548,509 – 12,548,632
Length 123
Max. P 0.999367
window6620 window6621 window6622

overview

Window 0

Location 12,548,509 – 12,548,599
Length 90
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 98.47
Mean single sequence MFE -33.30
Consensus MFE -32.00
Energy contribution -32.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.96
SVM decision value 3.54
SVM RNA-class probability 0.999367
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12548509 90 - 23771897
G---GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUGCCAAUCCUCGCCCGCACCAAUGCCAA
(---.((((((.((...((((((((.((.....))..)))).))))(((((((.....)))))))......)).)))))).)........... ( -32.60)
>DroSec_CAF1 36650 90 - 1
G---GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUGCCAAUCCUCGCCCGCACCAAUGCCAA
(---.((((((.((...((((((((.((.....))..)))).))))(((((((.....)))))))......)).)))))).)........... ( -32.60)
>DroSim_CAF1 37884 90 - 1
G---GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUGCCAAUCCUCGCCCGCACCAAUGCCAA
(---.((((((.((...((((((((.((.....))..)))).))))(((((((.....)))))))......)).)))))).)........... ( -32.60)
>DroEre_CAF1 37621 93 - 1
GGAGGGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUGCCAAUCCUCGCCCGCACCAAUGCCAA
((.(.((((((.((...((((((((.((.....))..)))).))))(((((((.....)))))))......)).)))))).).))........ ( -35.50)
>DroYak_CAF1 37621 91 - 1
GG--GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUGCCAAUCCUCGCCCGCACCAAUGCCAA
((--(((((((.((...((((((((.((.....))..)))).))))(((((((.....)))))))......)).)))))).).))........ ( -33.20)
>consensus
G___GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUGCCAAUCCUCGCCCGCACCAAUGCCAA
.....((((((.((...((((((((.((.....))..)))).))))(((((((.....)))))))......)).))))))(((....)))... (-32.00 = -32.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,548,535 – 12,548,632
Length 97
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 91.13
Mean single sequence MFE -15.50
Consensus MFE -13.40
Energy contribution -13.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.86
SVM decision value 0.72
SVM RNA-class probability 0.831814
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12548535 97 + 23771897
CAGCAGCCAUCUUGUAGCUGCGCAUACUGACUGGUGUAUCCCUCAGAUACUUUUCAUCACCCC---CCUCAAUAUCCACUUCUUGGCU--UUU-UUUUUUCUA
..(((((.........)))))......(((.(((.(((((.....)))))...))))))....---.........(((.....)))..--...-......... ( -13.90)
>DroSec_CAF1 36676 98 + 1
CAGCAGCCAUCUUGUAGCUGCGCAUACUGACUGGUGUAUCCCUCAGAUACUUUUCAUCACCCC---CCUCAAUAUCCACUUCUUGGCU--UUUAUUUUUUUUA
..(((((.........)))))......(((.(((.(((((.....)))))...))))))....---.........(((.....)))..--............. ( -13.90)
>DroSim_CAF1 37910 98 + 1
CAGCAGCCAUCUUGUAGCUGCGCAUACUGACUGGUGUAUCCCUCAGAUACUUUUCAUCACCCC---CCUCAAUAUCCACUUCUUGGCU--UUUAUUUUUUUUA
..(((((.........)))))......(((.(((.(((((.....)))))...))))))....---.........(((.....)))..--............. ( -13.90)
>DroEre_CAF1 37647 97 + 1
CAGCAGCCAUCUUGUAGCUGCGCAUACUGACUGGUGUAUCCCUCAGAUACUUUUCAUCACCCCCUCCCUCGAUAUCCAGCUCUUAGU------AUUUUUUUUA
..(((((.........)))))..(((((((((((.(((((.....))))).....(((............)))..))))...)))))------))........ ( -18.70)
>DroYak_CAF1 37647 101 + 1
CAGCAGCCAUCUUGUAGCUGCGCAUACUGACUGGUGUAUCCCUCAGAUACUUUUCAUCACCCC--CCUUUAAAAUGCACUUCUUAGUUCGUUUUUUUUUUUUA
..(((((.........)))))......(((.(((.(((((.....)))))...))))))....--.....((((((.(((....))).))))))......... ( -17.10)
>consensus
CAGCAGCCAUCUUGUAGCUGCGCAUACUGACUGGUGUAUCCCUCAGAUACUUUUCAUCACCCC___CCUCAAUAUCCACUUCUUGGCU__UUUAUUUUUUUUA
..(((((.........)))))......(((.(((.(((((.....)))))...))))))............................................ (-13.40 = -13.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,548,535 – 12,548,632
Length 97
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 91.13
Mean single sequence MFE -24.00
Consensus MFE -19.00
Energy contribution -19.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.47
Structure conservation index 0.79
SVM decision value 1.89
SVM RNA-class probability 0.981352
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12548535 97 - 23771897
UAGAAAAAA-AAA--AGCCAAGAAGUGGAUAUUGAGG---GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUG
.........-...--...........(.(((((((..---((.....(....)(((((.....))))).))..))))))).)(((((((.....))))))).. ( -24.90)
>DroSec_CAF1 36676 98 - 1
UAAAAAAAAUAAA--AGCCAAGAAGUGGAUAUUGAGG---GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUG
.............--...........(.(((((((..---((.....(....)(((((.....))))).))..))))))).)(((((((.....))))))).. ( -24.90)
>DroSim_CAF1 37910 98 - 1
UAAAAAAAAUAAA--AGCCAAGAAGUGGAUAUUGAGG---GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUG
.............--...........(.(((((((..---((.....(....)(((((.....))))).))..))))))).)(((((((.....))))))).. ( -24.90)
>DroEre_CAF1 37647 97 - 1
UAAAAAAAAU------ACUAAGAGCUGGAUAUCGAGGGAGGGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUG
........((------(((....(((((.(((((..........)))))....(((((.....))))).))))).)))))..(((((((.....))))))).. ( -25.00)
>DroYak_CAF1 37647 101 - 1
UAAAAAAAAAAAACGAACUAAGAAGUGCAUUUUAAAGG--GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUG
...........................((((((.....--)))))).......((((((((.((.....))..)))).))))(((((((.....))))))).. ( -20.30)
>consensus
UAAAAAAAAUAAA__AGCCAAGAAGUGGAUAUUGAGG___GGGGUGAUGAAAAGUAUCUGAGGGAUACACCAGUCAGUAUGCGCAGCUACAAGAUGGCUGCUG
.....................................................((((((((.((.....))..)))).))))(((((((.....))))))).. (-19.00 = -19.00 +   0.00)

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 11:18:30 2006