Locus 7421

Sequence ID 2L_DroMel_CAF1
Location 20,604,197 – 20,604,344
Length 147
Max. P 0.999238
window11925 window11926 window11927

overview

Window 5

Location 20,604,197 – 20,604,292
Length 95
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 88.70
Mean single sequence MFE -31.15
Consensus MFE -29.20
Energy contribution -29.23
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -2.95
Structure conservation index 0.94
SVM decision value 3.45
SVM RNA-class probability 0.999238
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20604197 95 + 22407834
UCGAGAAUUUCCACCUGCAACACUGUGUGUAGCUGGUUGACAUCGGGUCAGAUCUGUU-UUUCAAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCA
..............((((.((((...))))((((((((((....((..(((((((...-.....)).)))))..))...))))))))))))))... ( -31.30)
>DroSec_CAF1 123428 94 + 1
UCGA-GAUUUGCACCUGCAACGCUGUGUGUAGCUGGUUGACAUCGGGUCAGAUCUGUU-UUUUAAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCA
....-...((((....)))).((((....(((((((((((....((..(((((((...-.....)).)))))..))...))))))))))))))).. ( -33.00)
>DroSim_CAF1 119381 95 + 1
UCAAAAAUCUGCACCUGCAACGCUGUGUGUAGCUGGUUGACAUCGGGUCAGAUCUGUU-UUUUAAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCA
.........(((....)))..((((....(((((((((((....((..(((((((...-.....)).)))))..))...))))))))))))))).. ( -32.30)
>DroEre_CAF1 109752 86 + 1
--------UUCCU-CUGCAACGCUGUGUGUAGCUGGUUGACAUCGGGUCAGAUCUGUU-UUCCUAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCA
--------.....-((((.((((...))))((((((((((....((..((((((((..-....))).)))))..))...))))))))))))))... ( -30.80)
>DroYak_CAF1 113081 96 + 1
UCCAGAAUUUCCUCCUGCAACGCUGUGUGUAGCUGGUUGACAUCGGGUCAGAUCUGUUUUUCCAAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCA
..............((((.((((...))))((((((((((....((..(((((((.........)).)))))..))...))))))))))))))... ( -30.10)
>DroAna_CAF1 116864 95 + 1
UCGUGAAUGAUUAUCUGCAACGCUGUAUGUAGCUGGUUGACAUCGGGUCAGAUCUAUCUUUUCAAGCAUUUGGUCCCCUUCAACCAGCUGUAGC-A
.....................((((....(((((((((((....((..(((((((.........)).)))))..))...)))))))))))))))-. ( -29.40)
>consensus
UCGAGAAUUUCCACCUGCAACGCUGUGUGUAGCUGGUUGACAUCGGGUCAGAUCUGUU_UUUCAAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCA
..............((((.((((...))))((((((((((....((..(((((((.........)).)))))..))...))))))))))))))... (-29.20 = -29.23 +   0.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,604,214 – 20,604,326
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.71
Mean single sequence MFE -38.63
Consensus MFE -35.52
Energy contribution -35.55
Covariance contribution 0.03
Combinations/Pair 1.03
Mean z-score -2.98
Structure conservation index 0.92
SVM decision value 2.20
SVM RNA-class probability 0.990082
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20604214 112 + 22407834
CAAC-ACUGUGUGUAGCUGGUUGACAUCGGGUCAGAUCUGUU-UUUCAAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCAGUGGUUGAUGACAACGAAAGCCUAGUGA------ACUGCG
...(-((((..(((((((((((((....((..(((((((...-.....)).)))))..))...)))))))))))))..)))))((((....))))....((..((...------.)))). ( -40.70)
>DroPse_CAF1 173378 119 + 1
CAACGGCUGUAUGUAGCUGGUUGACAUCGGGUCAGAUCUAUUUUAUCAAGUAUUUGGUCCCCUUCAACCAGCUGUAU-CAGUGGUUGAUUCCAACAAAAAACAAAAGGUGCCAACAAAUA
((((.((((.((((((((((((((....((..(((((((.........)).)))))..))...))))))))))))))-)))).))))................................. ( -38.90)
>DroEre_CAF1 109760 112 + 1
CAAC-GCUGUGUGUAGCUGGUUGACAUCGGGUCAGAUCUGUU-UUCCUAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCAGUGGUUGAUGCCAACUAAAUUCGAGUGA------ACUGUG
...(-((((..(((((((((((((....((..((((((((..-....))).)))))..))...)))))))))))))..)))))((((....))))........((...------.))... ( -38.90)
>DroYak_CAF1 113098 113 + 1
CAAC-GCUGUGUGUAGCUGGUUGACAUCGGGUCAGAUCUGUUUUUCCAAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCAGUGGUUGAUGACAACGAAGUACGAGUAA------ACUGUG
...(-((((..(((((((((((((....((..(((((((.........)).)))))..))...)))))))))))))..)))))((((....)))).............------...... ( -37.60)
>DroAna_CAF1 116881 112 + 1
CAAC-GCUGUAUGUAGCUGGUUGACAUCGGGUCAGAUCUAUCUUUUCAAGCAUUUGGUCCCCUUCAACCAGCUGUAGC-AGUGGUUGAUGACAACAAAGUACAAGUGA------AAAGUG
...(-(((((.(((((((((((((....((..(((((((.........)).)))))..))...)))))))))))))))-))))((((....)))).............------...... ( -36.80)
>DroPer_CAF1 179293 119 + 1
CAACGGCUGUAUGUAGCUGGUUGACAUCGGGUCAGAUCUAUUUUAUCAAGUAUUUGGUCCCCUUCAACCAGCUGUAU-CAGUGGUUGAUUCCAACAAAAAACAAAAGGCGCCAACAAAUA
((((.((((.((((((((((((((....((..(((((((.........)).)))))..))...))))))))))))))-)))).))))................................. ( -38.90)
>consensus
CAAC_GCUGUAUGUAGCUGGUUGACAUCGGGUCAGAUCUAUUUUUUCAAGCAUUUGGUCCCCUUCAACCAGCUGUAGCCAGUGGUUGAUGACAACAAAAUACAAGUGA______AAAGUG
((((.((((..(((((((((((((....((..(((((((.........)).)))))..))...)))))))))))))..)))).))))................................. (-35.52 = -35.55 +   0.03)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,604,253 – 20,604,344
Length 91
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 71.95
Mean single sequence MFE -24.80
Consensus MFE -13.42
Energy contribution -14.42
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.54
SVM decision value 0.74
SVM RNA-class probability 0.837371
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20604253 91 - 22407834
UG----GAAAAUGGUAAU------------------CCAUCGCAGUUCACUAGGCUUUCGUUGUCAUCAACCACUGGCUACAGCUGGUUGAAGGGGACCAAAUGCUUGAAA-AA
((----((..((((....------------------)))).....)))).((((((((.(((.((.((((((((((....))).))))))).)).))).))).)))))...-.. ( -26.50)
>DroSec_CAF1 123483 91 - 1
UG----GAAAAUAAUAAU------------------CCAUCGCAGUUCGCUAGGCUUUCGAUGUCAGCAACCACUGGCUACAGCUGGUUGAAGGGGACCAAAUGCUUAAAA-AA
((----((.........)------------------)))..(((((((.((.(((.......)))..(((((((((....))).)))))).)).))))....)))......-.. ( -22.70)
>DroSim_CAF1 119437 91 - 1
UG----GAAAAUAAUAAU------------------CCAUCGCAGUUCCCUCGGCUUUCGAUGUCAGCAACCACUGGCUACAGCUGGUUGAAGGGGACCAAAUGCUUAAAA-AA
((----((.........)------------------)))..((((((((((.(((.......)))..(((((((((....))).)))))).)))))))....)))......-.. ( -27.10)
>DroEre_CAF1 109799 105 - 1
-AGUUCACAGGUCACAGUUCACAGGUCACAGU-------GCACAGUUCACUCGAAUUUAGUUGGCAUCAACCACUGGCUACAGCUGGUUGAAGGGGACCAAAUGCUAGGAA-AA
-..........((..(((.....((((....(-------((..(((((....)))))......)))((((((((((....))).)))))))....))))....)))..)).-.. ( -24.70)
>DroYak_CAF1 113137 108 - 1
-A----AAAAAUAGUAAUUUAC-GCUUUCAGUCUGUCUAUCACAGUUUACUCGUACUUCGUUGUCAUCAACCACUGGCUACAGCUGGUUGAAGGGGACCAAAUGCUUGGAAAAA
-.----................-..((((((.((((.....)))).......(((.((.(((.((.((((((((((....))).))))))).)).))).)).)))))))))... ( -23.80)
>DroAna_CAF1 116920 80 - 1
---------------AAU------------------AAAUCACUUUUCACUUGUACUUUGUUGUCAUCAACCACU-GCUACAGCUGGUUGAAGGGGACCAAAUGCUUGAAAAGA
---------------...------------------......(((((((...(((.((.(((.((.(((((((((-(...))).))))))).)).))).)).))).))))))). ( -24.00)
>consensus
_G____GAAAAUAAUAAU__________________CCAUCACAGUUCACUCGGAUUUCGUUGUCAUCAACCACUGGCUACAGCUGGUUGAAGGGGACCAAAUGCUUGAAA_AA
...........................................................(((.((.((((((((((....))).))))))).)).)))................ (-13.42 = -14.42 +   1.00)

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 12:36:25 2006