Locus 6261

Sequence ID 2L_DroMel_CAF1
Location 17,394,416 – 17,394,596
Length 180
Max. P 0.972771
window10004 window10005 window10006 window10007

overview

Window 4

Location 17,394,416 – 17,394,524
Length 108
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 74.59
Mean single sequence MFE -22.47
Consensus MFE -9.94
Energy contribution -10.67
Covariance contribution 0.73
Combinations/Pair 1.28
Mean z-score -1.90
Structure conservation index 0.44
SVM decision value 0.18
SVM RNA-class probability 0.622266
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17394416 108 + 22407834
CGAA--AUGCUAAACAAUUGC-AAUGCAUUUUAUGGA----AAUUCGGGGCGACUUCGUGUAAAGAUGUAUAUGUAUGUACAUUUUUGUAUAUCUACAAA-CCCGUCCUG---UCUAUA
.(((--((((...........-...)))))))(((((----....(((((((....))).((((((((((((....))))))))))))............-)))).....---))))). ( -27.54)
>DroSec_CAF1 16394 85 + 1
CGAA--CUGCUAAAAAAUUGC-AAUGCAUUUUAUGGA----AAUUCGGGGCGACU--------------------GUAUACA---UUGUAUAUCUACAAA-CCCGUCCUG---UCUAUA
....--.(((.........))-)........((((((----....(((((((..(--------------------(....))---(((((....))))).-..)))))))---)))))) ( -15.40)
>DroSim_CAF1 15920 101 + 1
CGAA--AUGCUAAACAAUUGC-AAUGCAUUUUAUGGA----AAUUCGGGGCGACUUCGUGUAUA----UAUAUAUAUAUGCA---UUGUAUAUCUACAAA-CCCGUCCUG---UCUAUA
.(((--((((...........-...)))))))(((((----....(((((((......((((((----((....))))))))---(((((....))))).-..)))))))---))))). ( -25.44)
>DroEre_CAF1 18390 104 + 1
CGAA--AUGCUAAGCAAUUGCCAAUGCAUUUUAUGGACUCACAUUUGGGGCGACU-CGUGUAUA----UAU--GUAUGUACAU--UUGUAUAUCAACAAA-CCCGUCCUG---UCUAUA
.(((--((((...((....))....)))))))((((((........((((((...-.(((((((----(..--..))))))))--((((......)))).-..)))))))---))))). ( -26.50)
>DroYak_CAF1 15916 97 + 1
CGAA--AUGCUAAACAAUUGCAAAUGCAUUUAAUGGA----AAUUCGGGGCGACUUCGUGUAUA----UAU------GUACAU--CUGUAUAUCUACAAA-CCCGUCCUG---UCUAUA
..((--((((...............)))))).(((((----....(((((((......((((..----.((------((((..--..)))))).))))..-..)))))))---))))). ( -21.86)
>DroAna_CAF1 11422 97 + 1
CCAAAAACGCCAA--AA-UGCGAAUGCAUUUUAUGGA----AAUUCGUCUCGAGUUCUCAUCU----------GUAUGUACAC-----UAUAUAUACAAUAUCUGUGAAAUACGCUAUA
.......(((...--..-.)))...((((((((((((----((((((...))))))......(----------(((((((...-----..))))))))...))))))))))..)).... ( -18.10)
>consensus
CGAA__AUGCUAAACAAUUGC_AAUGCAUUUUAUGGA____AAUUCGGGGCGACUUCGUGUAUA____UAU__GUAUGUACAU__UUGUAUAUCUACAAA_CCCGUCCUG___UCUAUA
..................(((....)))...((((((........(((((((((.....))..............(((((((....)))))))..........)))))))...)))))) ( -9.94 = -10.67 +   0.73)

alignment

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secondary structure

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Window 5

Location 17,394,450 – 17,394,564
Length 114
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 78.85
Mean single sequence MFE -26.95
Consensus MFE -17.69
Energy contribution -18.25
Covariance contribution 0.56
Combinations/Pair 1.23
Mean z-score -2.12
Structure conservation index 0.66
SVM decision value 1.21
SVM RNA-class probability 0.931433
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17394450 114 + 22407834
-AAUUCGGGGCGACUUCGUGUAAAGAUGUAUAUGUAUGUACAUUUUUGUAUAUCUACAAA-CCCGUCCUG---UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUUACGCGAUCUU
-......((....))((((((((((.......((((((((((....))))))..))))..-..((.((((---...((((.(((((....))))))))))))))))))))))))).... ( -32.70)
>DroSec_CAF1 16428 91 + 1
-AAUUCGGGGCGACU--------------------GUAUACA---UUGUAUAUCUACAAA-CCCGUCCUG---UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUUACGCGAUCUU
-.....((((((..(--------------------(....))---(((((....))))).-..))))))(---(((((((.(((((....))))))))).))))((.....))...... ( -22.80)
>DroSim_CAF1 15954 107 + 1
-AAUUCGGGGCGACUUCGUGUAUA----UAUAUAUAUAUGCA---UUGUAUAUCUACAAA-CCCGUCCUG---UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUUACGCGAUCUU
-.....((((((......((((((----((....))))))))---(((((....))))).-..))))))(---(((((((.(((((....))))))))).))))((.....))...... ( -29.60)
>DroEre_CAF1 18428 106 + 1
ACAUUUGGGGCGACU-CGUGUAUA----UAU--GUAUGUACAU--UUGUAUAUCAACAAA-CCCGUCCUG---UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUCACGCGAUCUU
......((((((...-.(((((((----(..--..))))))))--((((......)))).-..))))))(---(((((((.(((((....))))))))).))))((.....))...... ( -28.40)
>DroYak_CAF1 15951 102 + 1
-AAUUCGGGGCGACUUCGUGUAUA----UAU------GUACAU--CUGUAUAUCUACAAA-CCCGUCCUG---UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUUACGCGAUCUU
-.....((((((......((((..----.((------((((..--..)))))).))))..-..))))))(---(((((((.(((((....))))))))).))))((.....))...... ( -27.20)
>DroAna_CAF1 11456 103 + 1
-AAUUCGUCUCGAGUUCUCAUCU----------GUAUGUACAC-----UAUAUAUACAAUAUCUGUGAAAUACGCUAUAGAUCUCUAUCAAGAGACCGUCAGACGCUUCACGCGCUCCU
-.....((((.(((.((((...(----------(((((((...-----..))))))))..(((((((........))))))).........)))).).))))))((.....))...... ( -21.00)
>consensus
_AAUUCGGGGCGACUUCGUGUAUA____UAU__GUAUGUACAU__UUGUAUAUCUACAAA_CCCGUCCUG___UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUUACGCGAUCUU
.....(((((((((.....))..............(((((((....)))))))..........)))))))....((((((.(((((....))))))))).)).(((.....)))..... (-17.69 = -18.25 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,394,488 – 17,394,596
Length 108
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 75.80
Mean single sequence MFE -23.10
Consensus MFE -16.69
Energy contribution -17.13
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -1.90
Structure conservation index 0.72
SVM decision value 1.70
SVM RNA-class probability 0.972771
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17394488 108 + 22407834
ACAUUUUUGUAUAUCUACAAA-CCCGUCCUG---UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUUACGCGAUCUUCGCUCUCACCCACACCCGACUGGGAUCGCUUU
.....((((((....))))))-((((((..(---(((((((.(((((....))))))))).)))).......(((.....)))..............))).)))........ ( -26.10)
>DroVir_CAF1 15106 86 + 1
A------UCCG----------------A-UA---CUCAUAGAUCUCUAUCAAGAGACUGUCAAGCGCUUUACGCGCUCCUCGCUCUCGCCCUCGUCCGACUGGGAACGCUUC
.------(((.----------------.-..---.....((.(((((....)))))))(((.(((((.....)))))....((....))........)))..)))....... ( -18.70)
>DroSec_CAF1 16446 105 + 1
ACA---UUGUAUAUCUACAAA-CCCGUCCUG---UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUUACGCGAUCUUCGCUCUCACCCACAUCCGACUGGGAUCGCUUU
...---(((((....))))).-((((((..(---(((((((.(((((....))))))))).)))).......(((.....)))..............))).)))........ ( -25.60)
>DroSim_CAF1 15988 105 + 1
GCA---UUGUAUAUCUACAAA-CCCGUCCUG---UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUUACGCGAUCUUCGCUCUCACCCACAUCCGACUGGGAUCGCUUU
((.---(((((....))))).-((((((..(---(((((((.(((((....))))))))).)))).......(((.....)))..............))).)))...))... ( -27.60)
>DroWil_CAF1 19763 85 + 1
AAA---U--------UACA----------------AUUUAGAUCUCUAUCAAGAGACUGUAAAGCGCUUUACGCGAUCCUCGCUCUCACCCACAUCCGAUUGGGAUCGCUUU
...---.--------....----------------....((.(((((....)))))))(((((....)))))(((((((.((.((............)).)))))))))... ( -20.20)
>DroAna_CAF1 11484 107 + 1
ACAC-----UAUAUAUACAAUAUCUGUGAAAUACGCUAUAGAUCUCUAUCAAGAGACCGUCAGACGCUUCACGCGCUCCUCGCUCUCACCCACAUCCGAUUGGGACCGCUUC
.(((-----.((((.....))))..)))......((.((((....))))...((((.((..((.(((.....)))))...)).)))).((((........))))...))... ( -20.40)
>consensus
ACA___UUGUAUAUCUACAAA_CCCGUCCUG___UCUAUAGAUCUCUAUCAAGAGACUGUCAGGCGCUUUACGCGAUCCUCGCUCUCACCCACAUCCGACUGGGAUCGCUUU
.....................................((((.(((((....))))))))).(((((......(((.....))).....((((........))))..))))). (-16.69 = -17.13 +   0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,394,488 – 17,394,596
Length 108
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 75.80
Mean single sequence MFE -28.63
Consensus MFE -18.55
Energy contribution -18.05
Covariance contribution -0.50
Combinations/Pair 1.25
Mean z-score -1.25
Structure conservation index 0.65
SVM decision value 0.23
SVM RNA-class probability 0.644689
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17394488 108 - 22407834
AAAGCGAUCCCAGUCGGGUGUGGGUGAGAGCGAAGAUCGCGUAAAGCGCCUGACAGUCUCUUGAUAGAGAUCUAUAGA---CAGGACGGG-UUUGUAGAUAUACAAAAAUGU
...((((.(((.(((((((((...((...(((.....))).))..))))))))).((((....((((....))))...---..)))))))-.))))................ ( -35.40)
>DroVir_CAF1 15106 86 - 1
GAAGCGUUCCCAGUCGGACGAGGGCGAGAGCGAGGAGCGCGUAAAGCGCUUGACAGUCUCUUGAUAGAGAUCUAUGAG---UA-U----------------CGGA------U
.......(((..(((........((....))...((((((.....))))))))).((((((....)))))).......---..-.----------------.)))------. ( -25.10)
>DroSec_CAF1 16446 105 - 1
AAAGCGAUCCCAGUCGGAUGUGGGUGAGAGCGAAGAUCGCGUAAAGCGCCUGACAGUCUCUUGAUAGAGAUCUAUAGA---CAGGACGGG-UUUGUAGAUAUACAA---UGU
...((((.(((.(((...((((((((...(((.....)))......))))).)))((((((....)))))).......---...))))))-.))))..........---... ( -29.10)
>DroSim_CAF1 15988 105 - 1
AAAGCGAUCCCAGUCGGAUGUGGGUGAGAGCGAAGAUCGCGUAAAGCGCCUGACAGUCUCUUGAUAGAGAUCUAUAGA---CAGGACGGG-UUUGUAGAUAUACAA---UGC
...((((.(((.(((...((((((((...(((.....)))......))))).)))((((((....)))))).......---...))))))-.))))..........---... ( -29.10)
>DroWil_CAF1 19763 85 - 1
AAAGCGAUCCCAAUCGGAUGUGGGUGAGAGCGAGGAUCGCGUAAAGCGCUUUACAGUCUCUUGAUAGAGAUCUAAAU----------------UGUA--------A---UUU
...((((((((..(((....)))((....))).)))))))(((((....))))).((((((....))))))......----------------....--------.---... ( -22.30)
>DroAna_CAF1 11484 107 - 1
GAAGCGGUCCCAAUCGGAUGUGGGUGAGAGCGAGGAGCGCGUGAAGCGUCUGACGGUCUCUUGAUAGAGAUCUAUAGCGUAUUUCACAGAUAUUGUAUAUAUA-----GUGU
...(((.((((..(((....)))((....))).))).)))((((((((.(((..(((((((....)))))))..))))))..)))))..(((((((....)))-----)))) ( -30.80)
>consensus
AAAGCGAUCCCAGUCGGAUGUGGGUGAGAGCGAAGAUCGCGUAAAGCGCCUGACAGUCUCUUGAUAGAGAUCUAUAGA___CAGGACGGG_UUUGUAGAUAUACAA___UGU
...(((((((((........)))((....))...)))))).........(((...((((((....))))))...)))................................... (-18.55 = -18.05 +  -0.50)

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 12:06:41 2006