Locus 1091

Sequence ID 3R_DroMel_CAF1
Location 3,308,318 – 3,308,575
Length 257
Max. P 0.846011
window1775 window1776 window1777 window1778 window1779 window1780 window1781

overview

Window 5

Location 3,308,318 – 3,308,420
Length 102
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.17
Mean single sequence MFE -36.72
Consensus MFE -27.27
Energy contribution -29.40
Covariance contribution 2.13
Combinations/Pair 1.09
Mean z-score -1.42
Structure conservation index 0.74
SVM decision value -0.01
SVM RNA-class probability 0.529020
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3308318 102 - 27905053
CACCAUCCAAAAAG---------------GCUGAGUGUUUCCCAAUAUGGGCAGACGUCGAAGUUCGGCCUC---CGUUGAAGUGUGAACAUAAUUUGUCGGCAAAUUUCAGGUGAGCCU
((((........((---------------((((((((((((((.....))).)))))......)))))))).---...((((((.((.(((.....)))...)).))))))))))..... ( -28.50)
>DroSec_CAF1 12560 120 - 1
CACCCUCUAAAAAGGCCAGGGAUUCGGAGGCUGAGUGUUUGCCAAUAUGGGCAGACGUCGAAGUUCGGCCUCCGCCGUUGAAGUGUGAACAUAAUUUGUCGGCAAAUUUCAGGUGAACCU
..((((((.....))..))))....((((((((((((((((((......))))))))......))))))))))((((.(((((((....)))..)))).)))).......(((....))) ( -44.30)
>DroSim_CAF1 16754 120 - 1
CACCCUCUAAAAAGGCCAGGGAUUCGGAGGCUGAGUGUUUGCCAAUAUGGGCAGACGUCGAAGUUCGGCCUCCGCCGUUGAAGUGUGAACAUAAUUUGUCGGUAAAUUUCAGGUGAACCU
..((((((.....))..))))....((((((((((((((((((......))))))))......))))))))))((((.(((((((....)))..)))).)))).......(((....))) ( -41.90)
>DroYak_CAF1 22850 116 - 1
CACCCUCUAAAAAGGCGAGAGAUUUGGC-GCUGAAUGUUUGCCAAUAGGAGCAGACGUCGAAGUUCGGCCUU---CGUUGAAGUGUGAACAUAAUUUGUCGGCAUUUUUCAGGUGAACCU
((((.......(((((..(((.((((((-((((..((((....))))....))).))))))).))).)))))---.(..(((((((..(((.....)))..))))))).).))))..... ( -32.20)
>consensus
CACCCUCUAAAAAGGCCAGGGAUUCGGA_GCUGAGUGUUUGCCAAUAUGGGCAGACGUCGAAGUUCGGCCUC___CGUUGAAGUGUGAACAUAAUUUGUCGGCAAAUUUCAGGUGAACCU
((((....................(((((((((((((((((((......))))))))......)))))))))))....((((((.((.(((.....)))...)).))))))))))..... (-27.27 = -29.40 +   2.13) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 3,308,358 – 3,308,460
Length 102
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.31
Mean single sequence MFE -35.75
Consensus MFE -25.99
Energy contribution -27.43
Covariance contribution 1.44
Combinations/Pair 1.10
Mean z-score -1.53
Structure conservation index 0.73
SVM decision value 0.13
SVM RNA-class probability 0.596337
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3308358 102 + 27905053
CAACG---GAGGCCGAACUUCGACGUCUGCCCAUAUUGGGAAACACUCAGC---------------CUUUUUGGAUGGUGCCACAAAUCAUUCAGUGGCAUGAAUUAUAGCUGGGAAGCU
...((---(((......)))))..((...(((.....)))..)).((((((---------------.....(((.(.(((((((..........))))))).).)))..))))))..... ( -29.80)
>DroSec_CAF1 12600 120 + 1
CAACGGCGGAGGCCGAACUUCGACGUCUGCCCAUAUUGGCAAACACUCAGCCUCCGAAUCCCUGGCCUUUUUAGAGGGUGCCACAAAUCAUUUAGUGGCAUGAAUUAUAGCUGGGAAGCU
....(((((((((((.....))..((.((((......)))).)).....))))))...((((...((((....))))(((((((.((....)).)))))))...........)))).))) ( -42.30)
>DroSim_CAF1 16794 120 + 1
CAACGGCGGAGGCCGAACUUCGACGUCUGCCCAUAUUGGCAAACACUCAGCCUCCGAAUCCCUGGCCUUUUUAGAGGGUGCCACAAAUCAUUUAGUGGCAUGAAUUAUAGCUGCGAAGCU
......(((((((((.....))..((.((((......)))).)).....))))))).........((((....))))(((((((.((....)).))))))).......((((....)))) ( -38.30)
>DroYak_CAF1 22890 116 + 1
CAACG---AAGGCCGAACUUCGACGUCUGCUCCUAUUGGCAAACAUUCAGC-GCCAAAUCUCUCGCCUUUUUAGAGGGUGCCACAAAUCAUUAAGUGGCAUGAAUUAUAGCUGGGAAGCA
...((---(((......)))))......((((((((((((...........-))))).....((.((((....))))(((((((..........)))))))))........)))).))). ( -32.60)
>consensus
CAACG___GAGGCCGAACUUCGACGUCUGCCCAUAUUGGCAAACACUCAGC_UCCGAAUCCCUGGCCUUUUUAGAGGGUGCCACAAAUCAUUUAGUGGCAUGAAUUAUAGCUGGGAAGCU
..(((.(((((......))))).))).((((......))))....((((((..............((((....))))(((((((..........)))))))........))))))..... (-25.99 = -27.43 +   1.44) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 3,308,358 – 3,308,460
Length 102
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.31
Mean single sequence MFE -38.85
Consensus MFE -28.91
Energy contribution -30.97
Covariance contribution 2.06
Combinations/Pair 1.07
Mean z-score -1.92
Structure conservation index 0.74
SVM decision value 0.66
SVM RNA-class probability 0.813383
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3308358 102 - 27905053
AGCUUCCCAGCUAUAAUUCAUGCCACUGAAUGAUUUGUGGCACCAUCCAAAAAG---------------GCUGAGUGUUUCCCAAUAUGGGCAGACGUCGAAGUUCGGCCUC---CGUUG
.........(((((((.((((........)))).)))))))......(((..((---------------((((((((((((((.....))).)))))......)))))))).---..))) ( -29.40)
>DroSec_CAF1 12600 120 - 1
AGCUUCCCAGCUAUAAUUCAUGCCACUAAAUGAUUUGUGGCACCCUCUAAAAAGGCCAGGGAUUCGGAGGCUGAGUGUUUGCCAAUAUGGGCAGACGUCGAAGUUCGGCCUCCGCCGUUG
.((.((((.(((((((.((((........)))).)))))))..(((......)))...))))...((((((((((((((((((......))))))))......))))))))))))..... ( -48.60)
>DroSim_CAF1 16794 120 - 1
AGCUUCGCAGCUAUAAUUCAUGCCACUAAAUGAUUUGUGGCACCCUCUAAAAAGGCCAGGGAUUCGGAGGCUGAGUGUUUGCCAAUAUGGGCAGACGUCGAAGUUCGGCCUCCGCCGUUG
......((.(((((((.((((........)))).))))))).((((((.....))..))))....((((((((((((((((((......))))))))......))))))))))))..... ( -45.30)
>DroYak_CAF1 22890 116 - 1
UGCUUCCCAGCUAUAAUUCAUGCCACUUAAUGAUUUGUGGCACCCUCUAAAAAGGCGAGAGAUUUGGC-GCUGAAUGUUUGCCAAUAGGAGCAGACGUCGAAGUUCGGCCUU---CGUUG
.........(((((((.((((........)))).)))))))..........(((((..(((.((((((-((((..((((....))))....))).))))))).))).)))))---..... ( -32.10)
>consensus
AGCUUCCCAGCUAUAAUUCAUGCCACUAAAUGAUUUGUGGCACCCUCUAAAAAGGCCAGGGAUUCGGA_GCUGAGUGUUUGCCAAUAUGGGCAGACGUCGAAGUUCGGCCUC___CGUUG
.........(((((((.((((........)))).))))))).......................(((((((((((((((((((......))))))))......)))))))))))...... (-28.91 = -30.97 +   2.06) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 3,308,395 – 3,308,500
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.04
Mean single sequence MFE -33.92
Consensus MFE -27.84
Energy contribution -28.15
Covariance contribution 0.31
Combinations/Pair 1.08
Mean z-score -1.60
Structure conservation index 0.82
SVM decision value 0.36
SVM RNA-class probability 0.702427
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3308395 105 + 27905053
AAACACUCAGC---------------CUUUUUGGAUGGUGCCACAAAUCAUUCAGUGGCAUGAAUUAUAGCUGGGAAGCUCAGAACGUGCUUCCAGCGUUAAAGUGUCAUUACUGGGCUA
........(((---------------((....(((((((.......)))))))((((((((........(((((.((((.(.....).)))))))))......))))))))...))))). ( -34.54)
>DroSec_CAF1 12640 120 + 1
AAACACUCAGCCUCCGAAUCCCUGGCCUUUUUAGAGGGUGCCACAAAUCAUUUAGUGGCAUGAAUUAUAGCUGGGAAGCUUAGAACGUGCUCCCAGCGUUAAAGUGUCAUUACUGGGCUU
........(((((.........((((((((....)))).)))).........(((((((((........(((((((.((.........)))))))))......)))))))))..))))). ( -37.14)
>DroSim_CAF1 16834 120 + 1
AAACACUCAGCCUCCGAAUCCCUGGCCUUUUUAGAGGGUGCCACAAAUCAUUUAGUGGCAUGAAUUAUAGCUGCGAAGCUUAGAACGUGCUCCCAGCGUUAAAGUGUCAUUACUGGGCUU
........(((((.........((((((((....)))).)))).........(((((((((........((((.(.(((.........))).)))))......)))))))))..))))). ( -30.34)
>DroYak_CAF1 22927 119 + 1
AAACAUUCAGC-GCCAAAUCUCUCGCCUUUUUAGAGGGUGCCACAAAUCAUUAAGUGGCAUGAAUUAUAGCUGGGAAGCAGAGAACGUGCUUCCAGCGUUAAAGUGUCAUUACUGGGCUU
........(((-.(((.......(((((((...))))))).............((((((((........(((((.(((((.......))))))))))......))))))))..)))))). ( -33.64)
>consensus
AAACACUCAGC_UCCGAAUCCCUGGCCUUUUUAGAGGGUGCCACAAAUCAUUUAGUGGCAUGAAUUAUAGCUGGGAAGCUUAGAACGUGCUCCCAGCGUUAAAGUGUCAUUACUGGGCUU
.....(((((...............((((....))))(((((((..........)))))))........(((((((.((.........)))))))))...............)))))... (-27.84 = -28.15 +   0.31) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 3,308,395 – 3,308,500
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.04
Mean single sequence MFE -34.67
Consensus MFE -26.35
Energy contribution -26.35
Covariance contribution -0.00
Combinations/Pair 1.05
Mean z-score -2.03
Structure conservation index 0.76
SVM decision value 0.77
SVM RNA-class probability 0.846011
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3308395 105 - 27905053
UAGCCCAGUAAUGACACUUUAACGCUGGAAGCACGUUCUGAGCUUCCCAGCUAUAAUUCAUGCCACUGAAUGAUUUGUGGCACCAUCCAAAAAG---------------GCUGAGUGUUU
............(((((((....(((((((((.........))))))..(((((((.((((........)))).)))))))............)---------------)).))))))). ( -29.00)
>DroSec_CAF1 12640 120 - 1
AAGCCCAGUAAUGACACUUUAACGCUGGGAGCACGUUCUAAGCUUCCCAGCUAUAAUUCAUGCCACUAAAUGAUUUGUGGCACCCUCUAAAAAGGCCAGGGAUUCGGAGGCUGAGUGUUU
...((((((..(((....)))..))))))(((((......(((((((..(((((((.((((........)))).))))))).((((((.....))..))))....)))))))..))))). ( -39.60)
>DroSim_CAF1 16834 120 - 1
AAGCCCAGUAAUGACACUUUAACGCUGGGAGCACGUUCUAAGCUUCGCAGCUAUAAUUCAUGCCACUAAAUGAUUUGUGGCACCCUCUAAAAAGGCCAGGGAUUCGGAGGCUGAGUGUUU
...((((((..(((....)))..))))))(((((......((((((...(((((((.((((........)))).))))))).((((((.....))..)))).....))))))..))))). ( -36.90)
>DroYak_CAF1 22927 119 - 1
AAGCCCAGUAAUGACACUUUAACGCUGGAAGCACGUUCUCUGCUUCCCAGCUAUAAUUCAUGCCACUUAAUGAUUUGUGGCACCCUCUAAAAAGGCGAGAGAUUUGGC-GCUGAAUGUUU
.((((((((....)).((((..(((((((((((.......)))))))..(((((((.((((........)))).)))))))............))))))))...))).-)))........ ( -33.20)
>consensus
AAGCCCAGUAAUGACACUUUAACGCUGGAAGCACGUUCUAAGCUUCCCAGCUAUAAUUCAUGCCACUAAAUGAUUUGUGGCACCCUCUAAAAAGGCCAGGGAUUCGGA_GCUGAGUGUUU
............(((((((....(((((((((.........))))).)))).........((((((..........))))))..............................))))))). (-26.35 = -26.35 +  -0.00) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 3,308,460 – 3,308,575
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.73
Mean single sequence MFE -28.85
Consensus MFE -24.17
Energy contribution -25.05
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -1.46
Structure conservation index 0.84
SVM decision value 0.06
SVM RNA-class probability 0.565947
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3308460 115 + 27905053
CAGAACGUGCUUCCAGCGUUAAAGUGUCAUUACUGGGCUAAAUGAGUCGGCGAACUGCACAAAAAAGAAGCAGACACAUACUACGCUGGAAUAGGAUGCAAA--AAAUAUGUGCAGA---
.....(.((.(((((((((....(((((.......((((.....)))).((...((.........))..)).))))).....))))))))))).).((((..--.......))))..--- ( -29.20)
>DroSec_CAF1 12720 119 + 1
UAGAACGUGCUCCCAGCGUUAAAGUGUCAUUACUGGGCUUAAUGAGUCGACGAACUGCACAAAAAGGAAGCAGACACAUACCACGCUGGAAUAGGAUGCAAAA-AAAUAUGUGCACACAG
......((((..(((((((....(((((.......(((((...))))).......(((...........)))))))).....)))))))........(((...-.....))))))).... ( -29.20)
>DroSim_CAF1 16914 120 + 1
UAGAACGUGCUCCCAGCGUUAAAGUGUCAUUACUGGGCUUAAUGAGUCGACGAACUGCACAAAAAGGAAGCAGACACAUACCACGCUGGAAUAGGAUGCAAAAAAAAUAUGUGCACACAG
......((((..(((((((....(((((.......(((((...))))).......(((...........)))))))).....)))))))........(((.........))))))).... ( -28.40)
>DroYak_CAF1 23006 115 + 1
GAGAACGUGCUUCCAGCGUUAAAGUGUCAUUACUGGGCUUAAUGAGUCGGCGAACUGCACAAAAAAGAACCAGAUACAUACUGCGCUGGAAUAGUAUGCAAA--AAAUAUGUGCAGA---
.....((((((((((((((....(((((.......(((((...))))).((.....))..............))))).....))))))))..))))))....--.............--- ( -28.60)
>consensus
UAGAACGUGCUCCCAGCGUUAAAGUGUCAUUACUGGGCUUAAUGAGUCGACGAACUGCACAAAAAAGAAGCAGACACAUACCACGCUGGAAUAGGAUGCAAA__AAAUAUGUGCACA___
......(((((((((((((....(((((.......((((.....)))).......(((...........)))))))).....)))))))))......(((.........))))))).... (-24.17 = -25.05 +   0.88) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 3,308,460 – 3,308,575
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.73
Mean single sequence MFE -29.41
Consensus MFE -24.80
Energy contribution -25.80
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -1.58
Structure conservation index 0.84
SVM decision value 0.29
SVM RNA-class probability 0.669630
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3308460 115 - 27905053
---UCUGCACAUAUUU--UUUGCAUCCUAUUCCAGCGUAGUAUGUGUCUGCUUCUUUUUUGUGCAGUUCGCCGACUCAUUUAGCCCAGUAAUGACACUUUAACGCUGGAAGCACGUUCUG
---..((((.......--..)))).....(((((((((.....(((((((((........(((.((((....))))))).......))))..)))))....))))))))).......... ( -27.36)
>DroSec_CAF1 12720 119 - 1
CUGUGUGCACAUAUUU-UUUUGCAUCCUAUUCCAGCGUGGUAUGUGUCUGCUUCCUUUUUGUGCAGUUCGUCGACUCAUUAAGCCCAGUAAUGACACUUUAACGCUGGGAGCACGUUCUA
..(((((((.(.....-.).)))......(((((((((.....(((((((((..(((...(((.((((....))))))).)))...))))..)))))....)))))))))))))...... ( -33.40)
>DroSim_CAF1 16914 120 - 1
CUGUGUGCACAUAUUUUUUUUGCAUCCUAUUCCAGCGUGGUAUGUGUCUGCUUCCUUUUUGUGCAGUUCGUCGACUCAUUAAGCCCAGUAAUGACACUUUAACGCUGGGAGCACGUUCUA
..(((((((...........)))......(((((((((.....(((((((((..(((...(((.((((....))))))).)))...))))..)))))....)))))))))))))...... ( -33.00)
>DroYak_CAF1 23006 115 - 1
---UCUGCACAUAUUU--UUUGCAUACUAUUCCAGCGCAGUAUGUAUCUGGUUCUUUUUUGUGCAGUUCGCCGACUCAUUAAGCCCAGUAAUGACACUUUAACGCUGGAAGCACGUUCUC
---..((((.......--..)))).....((((((((.....(((..((((..(((....(((.((((....))))))).))).)))).....)))......)))))))).......... ( -23.90)
>consensus
___UCUGCACAUAUUU__UUUGCAUCCUAUUCCAGCGUAGUAUGUGUCUGCUUCCUUUUUGUGCAGUUCGCCGACUCAUUAAGCCCAGUAAUGACACUUUAACGCUGGAAGCACGUUCUA
...(((((.((.........)).......(((((((((.....(((((((((..(((...(((.((((....))))))).)))...))))..)))))....))))))))))))))..... (-24.80 = -25.80 +   1.00) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:35 2006