Locus 3355

Sequence ID 3L_DroMel_CAF1
Location 9,824,162 – 9,824,361
Length 199
Max. P 0.999595
window5234 window5235 window5236 window5237 window5238

overview

Window 4

Location 9,824,162 – 9,824,282
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -33.31
Consensus MFE -30.14
Energy contribution -30.78
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.65
Structure conservation index 0.90
SVM decision value 3.10
SVM RNA-class probability 0.998442
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9824162 120 + 23771897
ACACAAAAACUCGCCUGACUGUGUGCCAUAAAAAUUUAAUAAUGAUAAAUACACUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCA
............((((.((.(((((........(((....)))......)))))...)).))))(((....(((((((((.((..(((....)))..))..))))))))).....))).. ( -34.14)
>DroSec_CAF1 118185 120 + 1
ACACAAAAACUCGCCUGACUGUGUGCCAUAAAAAUUUAAUAAUGAUAAAUAUACUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCA
............((((.((.(((((........(((....)))......)))))...)).))))(((....(((((((((.((..(((....)))..))..))))))))).....))).. ( -32.24)
>DroSim_CAF1 121427 120 + 1
ACACAAAAACUCGCCUGACUGUGUGCCAUAAAAAUUUAAUAAUGAUAAAUACAGUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCA
............((((((((((((..(((............)))....))))))))....))))(((....(((((((((.((..(((....)))..))..))))))))).....))).. ( -36.50)
>DroEre_CAF1 120973 120 + 1
ACACAAAAACUCGCCUGACUGUGUGCCAUAAAAAUUUAAUAAUGAUAAAUUCACUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCA
............((((.((...(((........(((....)))........)))...)).))))(((....(((((((((.((..(((....)))..))..))))))))).....))).. ( -33.19)
>DroYak_CAF1 131189 120 + 1
ACACAAAAACUCGCCUGACUGUGUGCCAUAAAAAUUUAAUAAUGAUAAAUACACUUUGUAUGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAUCCAAAUUGGCCUUGGCCA
............(((....((.((((((((...(((((.......)))))........)))))))).))..((((((((..((..(((....)))..))...)))))))).....))).. ( -30.50)
>consensus
ACACAAAAACUCGCCUGACUGUGUGCCAUAAAAAUUUAAUAAUGAUAAAUACACUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCA
............((((.((.(((((........(((....)))......)))))...)).))))(((....(((((((((.((..(((....)))..))..))))))))).....))).. (-30.14 = -30.78 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 9,824,162 – 9,824,282
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -36.68
Consensus MFE -34.06
Energy contribution -34.26
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.93
SVM decision value 1.69
SVM RNA-class probability 0.972347
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9824162 120 - 23771897
UGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAAGUGUAUUUAUCAUUAUUAAAUUUUUAUGGCACACAGUCAGGCGAGUUUUUGUGU
..(((...(((((((((((.(((((((...)))))))...))))))))).)).)))((((.((...(((((((((.......))))).......))))...)).))))............ ( -37.61)
>DroSec_CAF1 118185 120 - 1
UGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAAGUAUAUUUAUCAUUAUUAAAUUUUUAUGGCACACAGUCAGGCGAGUUUUUGUGU
..(((...(((((((((((.(((((((...)))))))...))))))))).)).)))(((.((.(((..(((........)))....))).)).)))((((((............)))))) ( -35.40)
>DroSim_CAF1 121427 120 - 1
UGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAACUGUAUUUAUCAUUAUUAAAUUUUUAUGGCACACAGUCAGGCGAGUUUUUGUGU
..(((...(((((((((((.(((((((...)))))))...))))))))).)).)))((((.....(((((.....((((............))))...))))).))))............ ( -35.80)
>DroEre_CAF1 120973 120 - 1
UGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAAGUGAAUUUAUCAUUAUUAAAUUUUUAUGGCACACAGUCAGGCGAGUUUUUGUGU
..(((...(((((((((((.(((((((...)))))))...))))))))).)).)))((((.((..(((((.....)))))............((.....)))).))))............ ( -37.50)
>DroYak_CAF1 131189 120 - 1
UGGCCAAGGCCAAUUUGGAUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCAUACAAAGUGUAUUUAUCAUUAUUAAAUUUUUAUGGCACACAGUCAGGCGAGUUUUUGUGU
((((....))))((..(((((((((((...))))))(((((....(((((((....((((((.(((..(((........)))....))).)))))))))))))))))).)))))..)).. ( -37.10)
>consensus
UGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAAGUGUAUUUAUCAUUAUUAAAUUUUUAUGGCACACAGUCAGGCGAGUUUUUGUGU
..(((...(((((((((((.(((((((...)))))))...))))))))).)).)))(((...........(((((.......))))).....((((.....)))))))............ (-34.06 = -34.26 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 9,824,202 – 9,824,322
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.50
Mean single sequence MFE -34.28
Consensus MFE -30.30
Energy contribution -30.50
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.29
Structure conservation index 0.88
SVM decision value 0.19
SVM RNA-class probability 0.627438
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9824202 120 + 23771897
AAUGAUAAAUACACUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCAAAAGUGGUUUUCUAUGGGGCGAUAUGUUGAAUAUAUGAGC
.........(((.....)))...(((((.(((((((((((.((..(((....)))..))..))))))))(((....)))....)))..........)))))((((((...)))))).... ( -34.20)
>DroSec_CAF1 118225 120 + 1
AAUGAUAAAUAUACUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCAAAAGUGGUUUUCUAUGAGGCGAUAUGUUGAAUAUAUGAGC
.......((((((.....(((((((....).(((((((((.((..(((....)))..))..)))))))))))))))(((....((((....))))..)))..))))))............ ( -33.30)
>DroSim_CAF1 121467 120 + 1
AAUGAUAAAUACAGUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCAAAAGUGGUUUUCUAUGGGGCGAUAUGUUGAAUAUAUGAGC
.............(((..((...(((((.(((((((((((.((..(((....)))..))..))))))))(((....)))....)))..........))))).(((.....)))))..))) ( -35.30)
>DroEre_CAF1 121013 120 + 1
AAUGAUAAAUUCACUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCAAAAGUGCUUUUCCAUGCGGCGAUAUGUUGAACAUAUGAGC
.(((..(((..((((((.(((((((....).(((((((((.((..(((....)))..))..)))))))))))))))....))))))..))).)))...((.(((((.....)))))..)) ( -34.70)
>DroYak_CAF1 131229 120 + 1
AAUGAUAAAUACACUUUGUAUGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAUCCAAAUUGGCCUUGGCCAAAAGUGGUUUUCUAUGCGGCGAUAUGUUGAACAUAUGAGC
................(((((((...((((..(((((((..((..(((....)))..))...)))))))(((....)))....))))....)))))))((.(((((.....)))))..)) ( -33.90)
>consensus
AAUGAUAAAUACACUUUGUAAGGCGCCCACACAAUUUGGCAGGCGGCUGCGAAGCAACCAAGCCAAAUUGGCCUUGGCCAAAAGUGGUUUUCUAUGCGGCGAUAUGUUGAAUAUAUGAGC
..................(((((((....).(((((((((.((..(((....)))..))..)))))))))))))))(((....((((....))))..))).((((((...)))))).... (-30.30 = -30.50 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 9,824,202 – 9,824,322
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -37.01
Consensus MFE -33.16
Energy contribution -33.12
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -2.81
Structure conservation index 0.90
SVM decision value 3.76
SVM RNA-class probability 0.999595
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9824202 120 - 23771897
GCUCAUAUAUUCAACAUAUCGCCCCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAAGUGUAUUUAUCAUU
....(((((((........((((((((((..........(((((....)))))((((((.(((((((...)))))))...))))))))))).)))))........)))))))........ ( -39.19)
>DroSec_CAF1 118225 120 - 1
GCUCAUAUAUUCAACAUAUCGCCUCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAAGUAUAUUUAUCAUU
....(((((((........((((.((((.((........(((((....)))))((((((.(((((((...)))))))...)))))))).))))))))........)))))))........ ( -36.59)
>DroSim_CAF1 121467 120 - 1
GCUCAUAUAUUCAACAUAUCGCCCCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAACUGUAUUUAUCAUU
....(((((..........((((((((((..........(((((....)))))((((((.(((((((...)))))))...))))))))))).)))))..........)))))........ ( -36.95)
>DroEre_CAF1 121013 120 - 1
GCUCAUAUGUUCAACAUAUCGCCGCAUGGAAAAGCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAAGUGAAUUUAUCAUU
((..(((((.....))))).))...(((((((..((((((((((....))))....(((..((((((...))))))(((..((.....).)..))))))....))))))..))).)))). ( -38.20)
>DroYak_CAF1 131229 120 - 1
GCUCAUAUGUUCAACAUAUCGCCGCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGAUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCAUACAAAGUGUAUUUAUCAUU
((..(((((.....))))).)).(.(((((....((((((.(((....)))(((((((..(((((((...)))))))....)))))))((((((...))))))))))))..))))))... ( -34.10)
>consensus
GCUCAUAUAUUCAACAUAUCGCCCCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCUGCCAAAUUGUGUGGGCGCCUUACAAAGUGUAUUUAUCAUU
(((((((((..............................(((((....)))))((((((.(((((((...)))))))...)))))).)))))))))........................ (-33.16 = -33.12 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 9,824,242 – 9,824,361
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.74
Mean single sequence MFE -32.36
Consensus MFE -24.74
Energy contribution -25.14
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.76
SVM decision value 0.89
SVM RNA-class probability 0.875942
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9824242 119 - 23771897
ACAAUAAAAA-AAAGCGUUGUCAACCGCUGAUGAUCCUUGGCUCAUAUAUUCAACAUAUCGCCCCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCU
..........-.(((.((..(((.....)))..)).)))(((...............................(((...(((((....)))))..)))...((((((...))))))))). ( -28.70)
>DroSec_CAF1 118265 119 - 1
ACAAUAAAAA-AAAGCGUUGUCAACCGCUGAUGAUCCUUGGCUCAUAUAUUCAACAUAUCGCCUCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCU
..........-.(((.((..(((.....)))..)).)))(((...............................(((...(((((....)))))..)))...((((((...))))))))). ( -28.70)
>DroSim_CAF1 121507 120 - 1
ACAAUAAAAAAAAAACGUUGUCAACCGAUGAUGAUCCUUGGCUCAUAUAUUCAACAUAUCGCCCCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCU
...............(((..((....))..)))......(((...............................(((...(((((....)))))..)))...((((((...))))))))). ( -28.20)
>DroEre_CAF1 121053 111 - 1
ACC-----AA-AAAGCGUUGUCAGCCGCUG---AUCCUUGGCUCAUAUGUUCAACAUAUCGCCGCAUGGAAAAGCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCU
...-----..-...((......(((((((.---.(((.((((..(((((.....))))).))))...)))..)))....(((((....)))))...)))).((((((...)))))))).. ( -38.90)
>DroYak_CAF1 131269 111 - 1
ACA-----AA-AAAGCGUUGUCAAGCGCUG---AUCCUUGGCUCAUAUGUUCAACAUAUCGCCGCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGAUUGGUUGCUUCGCAGCCGCCU
...-----..-...(((((((.((((((..---((((..(((..(((((.....))))).)))................(((((....)))))...))))..).))))).)))).))).. ( -37.30)
>consensus
ACAAUAAAAA_AAAGCGUUGUCAACCGCUGAUGAUCCUUGGCUCAUAUAUUCAACAUAUCGCCCCAUAGAAAACCACUUUUGGCCAAGGCCAAUUUGGCUUGGUUGCUUCGCAGCCGCCU
.............((((........))))..........(((...............................(((...(((((....)))))..)))...((((((...))))))))). (-24.74 = -25.14 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:59 2006