Locus 2297

Sequence ID 2L_DroMel_CAF1
Location 6,214,806 – 6,214,927
Length 121
Max. P 0.962131
window3686 window3687 window3688

overview

Window 6

Location 6,214,806 – 6,214,904
Length 98
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 83.05
Mean single sequence MFE -28.95
Consensus MFE -18.93
Energy contribution -20.65
Covariance contribution 1.72
Combinations/Pair 1.07
Mean z-score -2.66
Structure conservation index 0.65
SVM decision value 0.48
SVM RNA-class probability 0.754589
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6214806 98 + 22407834
------UCAU---UG-CCUGGUAUCUAGUUAAUGGGAUGCUUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUUG---
------....---((-((.(((((((........)))))))......))))..((.((((((.((((((((((.(.......).)))))))))).)))))).))....--- ( -30.20)
>DroPse_CAF1 83840 98 + 1
AGGGCUACAGAGGAGUCCU-GGAUCUAGCUAAUAGGAUGCUUAUGAUGAUACUUUGAUAAUGGCACAA---------CAGAACAGAACCAGCUGAUGUUGUGGAUUUG---
((((((.......))))))-..(((.(((.........)))...)))................(((((---------((...(((......))).)))))))......--- ( -20.50)
>DroSec_CAF1 51421 98 + 1
------UCAC---AG-CCUGGUAUCUAGUUAAUGGGAUGCUUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUUG---
------...(---((-(..(((((((........)))))))...)))).....((.((((((.((((((((((.(.......).)))))))))).)))))).))....--- ( -31.80)
>DroSim_CAF1 62749 92 + 1
------UCAC---UG-C------UCUAGUUAAUGGGAUGCUUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUUG---
------((((---..-.------....((((.(..((((((......))))))..).))))..((((((((((.(.......).)))))))))).....)))).....--- ( -26.00)
>DroEre_CAF1 50308 98 + 1
------UCCC---GG-CCUGGUAUCUAGUUAAUGGGAUGCUUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAGGAGGAACUGCUGAUAUUGUGGAUUGG---
------..((---((-(..(((((((........)))))))...)))))....((.((((((.((((((((((.(......)..)))))))))).)))))).))....--- ( -33.40)
>DroYak_CAF1 62836 101 + 1
------UCAC---AG-CCUGGUAUCUAGUUAAUGGGAUGCUUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUGGAAG
------...(---((-(..(((((((........)))))))...)))).....((.((((((.((((((((((.(.......).)))))))))).)))))).))....... ( -31.80)
>consensus
______UCAC___AG_CCUGGUAUCUAGUUAAUGGGAUGCUUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUUG___
......................((((......(((((((((......)))))))))((((((.((((((((((.(.......).)))))))))).))))))))))...... (-18.93 = -20.65 +   1.72)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,214,836 – 6,214,927
Length 91
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 70.07
Mean single sequence MFE -23.22
Consensus MFE -11.09
Energy contribution -13.53
Covariance contribution 2.45
Combinations/Pair 1.06
Mean z-score -2.07
Structure conservation index 0.48
SVM decision value 1.54
SVM RNA-class probability 0.962131
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6214836 91 + 22407834
UUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUUG-----UGAAAAAA---------------AAACCACCGAUGGAA
....((((((......((((((.((((((((((.(.......).)))))))))).))))))((.(((.-----.......)---------------)).)))))))).... ( -26.90)
>DroPse_CAF1 83879 97 + 1
UUAUGAUGAUACUUUGAUAAUGGCACAA---------CAGAACAGAACCAGCUGAUGUUGUGGAUUUG-----CGCCAGAAGGAAAAGACUUCACAGAAUGACAGAAGGCA
.......................(((((---------((...(((......))).)))))))......-----.(((.((((.......)))).(.....)......))). ( -18.50)
>DroSec_CAF1 51451 88 + 1
UUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUUG-----UGAAG------------------AAACCACCGAUGGGA
....((((((......((((((.((((((((((.(.......).)))))))))).))))))((.(((.-----....)------------------)).)))))))).... ( -26.70)
>DroSim_CAF1 62773 88 + 1
UUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUUG-----UGAGG------------------AAACCACCGUUGGGC
.............((.((((((.((((((((((.(.......).)))))))))).)))))).))...(-----((.(.------------------...))))........ ( -25.30)
>DroYak_CAF1 62866 93 + 1
UUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUGGAAGAUUGAAA------------------GAACAACUGAUGGCA
....((((...((((.((((((.((((((((((.(.......).)))))))))).)))))).((((....))))))))------------------...))))........ ( -23.80)
>DroPer_CAF1 84499 97 + 1
UUAUGAUGAUACUUUGAUAAUGGCACAA---------CAGAACAGAACCAGCUGAUGUUGUGGAUUUG-----CGCCAGAAGGAAAAGACUUCAUAGAAUGACAGAAGGCA
((((.((((..((((.....((((((((---------((...(((......))).))))))(......-----)))))......))))...))))...))))......... ( -18.10)
>consensus
UUAUGUUGGUAUUUUGAUAAUGGCAGCAGUUCUGCGUAAUAAGAGGAACUGCUGAUAUUGUGGAUUUG_____UGAAA__________________AAACCACCGAUGGCA
.............((.((((((.((((((((((...........)))))))))).)))))).))............................................... (-11.09 = -13.53 +   2.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,214,836 – 6,214,927
Length 91
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 70.07
Mean single sequence MFE -16.55
Consensus MFE -4.29
Energy contribution -6.62
Covariance contribution 2.33
Combinations/Pair 1.00
Mean z-score -2.43
Structure conservation index 0.26
SVM decision value 0.97
SVM RNA-class probability 0.891840
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6214836 91 - 22407834
UUCCAUCGGUGGUUU---------------UUUUUUCA-----CAAAUCCACAAUAUCAGCAGUUCCUCUUAUUACGCAGAACUGCUGCCAUUAUCAAAAUACCAACAUAA
........((((.((---------------(.......-----.))).))))(((..(((((((((..(.......)..)))))))))..))).................. ( -16.90)
>DroPse_CAF1 83879 97 - 1
UGCCUUCUGUCAUUCUGUGAAGUCUUUUCCUUCUGGCG-----CAAAUCCACAACAUCAGCUGGUUCUGUUCUG---------UUGUGCCAUUAUCAAAGUAUCAUCAUAA
...............(((((.(.((((......(((((-----(((....(((..(((....)))..)))....---------)))))))).....))))...).))))). ( -18.20)
>DroSec_CAF1 51451 88 - 1
UCCCAUCGGUGGUUU------------------CUUCA-----CAAAUCCACAAUAUCAGCAGUUCCUCUUAUUACGCAGAACUGCUGCCAUUAUCAAAAUACCAACAUAA
........(((((((------------------.....-----.))).))))(((..(((((((((..(.......)..)))))))))..))).................. ( -16.50)
>DroSim_CAF1 62773 88 - 1
GCCCAACGGUGGUUU------------------CCUCA-----CAAAUCCACAAUAUCAGCAGUUCCUCUUAUUACGCAGAACUGCUGCCAUUAUCAAAAUACCAACAUAA
........(((((((------------------.....-----.))).))))(((..(((((((((..(.......)..)))))))))..))).................. ( -16.50)
>DroYak_CAF1 62866 93 - 1
UGCCAUCAGUUGUUC------------------UUUCAAUCUUCCAAUCCACAAUAUCAGCAGUUCCUCUUAUUACGCAGAACUGCUGCCAUUAUCAAAAUACCAACAUAA
........((((...------------------........................(((((((((..(.......)..)))))))))..(((.....)))..)))).... ( -13.00)
>DroPer_CAF1 84499 97 - 1
UGCCUUCUGUCAUUCUAUGAAGUCUUUUCCUUCUGGCG-----CAAAUCCACAACAUCAGCUGGUUCUGUUCUG---------UUGUGCCAUUAUCAAAGUAUCAUCAUAA
...............(((((.(.((((......(((((-----(((....(((..(((....)))..)))....---------)))))))).....))))...).))))). ( -18.20)
>consensus
UGCCAUCGGUGGUUC__________________UUUCA_____CAAAUCCACAAUAUCAGCAGUUCCUCUUAUUACGCAGAACUGCUGCCAUUAUCAAAAUACCAACAUAA
.........................................................(((((((((.............)))))))))....................... ( -4.29 =  -6.62 +   2.33)

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 10:24:21 2006