Locus 944

Sequence ID	2R_DroMel_CAF1
Location	4,076,315 – 4,076,595
Length	280
Max. P	0.999867

overview

Window 5

Location	4,076,315 – 4,076,435
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-44.92
Consensus MFE	-40.78
Energy contribution	-40.98
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-1.14
Structure conservation index	0.91
SVM decision value	0.04
SVM RNA-class probability	0.552426
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4076315 120 - 20766785
CCCGAGCCGGAGAAGUUCGAUCCCAGUCGCUUCGACCCGGAGGAAGUCAAGAACCGCCAUCCGAUGGCCUAUUUGCCCUUUGGCGAUGGACCAAGGAACUGCAUUGGUCUGCGGUUCGGU
.((((((((.(((.((((..(((..((((...))))..))).(....)..)))).((..(((..(((((...(((((....))))).)).))).)))...)).....))).)))))))). ( -44.60)
>DroSec_CAF1 59078 120 - 1
CCCGAGCCGGAAAAGUUCGAUCCCAGUCGCUUCGAUCCGGAGGAAGUCAAGAACCGCCAUCCGAUGGCCUACUUGCCCUUUGGCGAUGGACCAAGGAACUGCAUUGGACUGCGGUUCGGA
.((((((((....((((((((..((((..((......((((((..((.....))..)).)))).(((((...(((((....))))).)).)))))..)))).)))))))).)))))))). ( -43.50)
>DroSim_CAF1 67284 120 - 1
CCCGAGCCGGAAAAGUUCGAUCCCAGUCGCUUCGAUCCGGAGGAAGUCAAGAACCGCCAUCCGAUGGCCUACUUGCCCUUUGGCGAUGGACCAAGGAACUGCAUUGGACUGCGGUUCGGA
.((((((((....((((((((..((((..((......((((((..((.....))..)).)))).(((((...(((((....))))).)).)))))..)))).)))))))).)))))))). ( -43.50)
>DroEre_CAF1 60399 120 - 1
CCCGAUCCGGAAAGGUUCGAUCCCAGUCGCUUUGAUCCGGAGGAAGUCAAGAACCGCCAUCCGAUGGCCUACUUGCCCUUUGGCGAUGGACCGCGGAACUGCAUUGGACUGCGGUUCGGA
.((..((((((..((..((((....))))..))..)))))).........(((((((..((((((((((...(((((....))))).)).))(((....)))))))))..))))))))). ( -47.50)
>DroYak_CAF1 63363 120 - 1
CCCGAACCGGAAAAGUUCGAUCCCAGUCGCUUUGAUCCGGAGGAAGUCAAAAACCGCCAUCCGAUGGCCUACUUGCCCUUUGGCGAUGGACCUCGGAACUGCAUUGGACUGCGGUUCGGA
.((((((((....((((((((..((((...........((.((..........)).)).(((((.((((...(((((....))))).)).))))))))))).)))))))).)))))))). ( -45.50)
>consensus
CCCGAGCCGGAAAAGUUCGAUCCCAGUCGCUUCGAUCCGGAGGAAGUCAAGAACCGCCAUCCGAUGGCCUACUUGCCCUUUGGCGAUGGACCAAGGAACUGCAUUGGACUGCGGUUCGGA
.((((((((....((((((((..(((((.........((((((..((.....))..)).)))).(((((...(((((....))))).)).)))..).)))).)))))))).)))))))). (-40.78 = -40.98 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	4,076,395 – 4,076,515
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.50
Mean single sequence MFE	-44.36
Consensus MFE	-36.40
Energy contribution	-37.36
Covariance contribution	0.96
Combinations/Pair	1.11
Mean z-score	-1.82
Structure conservation index	0.82
SVM decision value	1.17
SVM RNA-class probability	0.925102
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4076395 120 + 20766785
CCGGGUCGAAGCGACUGGGAUCGAACUUCUCCGGCUCGGGAUAUAUCUCCGGAUCGUGGUGGAUAUUAUGCACCGGAAUCAGGGCAAGAAUGCCCUUGUCUAGCACAAUAUCUGAGUUGG
((.(((((...))))).))...........(((((((((.((((...(((((..((((((....))))))..)))))...((((((....))))))...........))))))))))))) ( -41.60)
>DroSec_CAF1 59158 120 + 1
CCGGAUCGAAGCGACUGGGAUCGAACUUUUCCGGCUCGGGAUAUAUCUCCGGAUCGUGGUGGAUAUUGUGCACGGGUAUGAGGGCAAGAACGCCCUUGUCCAGCACAAUAUCUGUGUUGG
(((((((....(((((((((........)))))).)))(((......))).)))).))).(((((((((((...((.(..(((((......)))))..))).)))))))))))....... ( -48.80)
>DroSim_CAF1 67364 120 + 1
CCGGAUCGAAGCGACUGGGAUCGAACUUUUCCGGCUCGGGAUAUAUCUCCGGAUCGUGGUGGAUAUUGUGCACGGGUAUGAGGGCAAGAACGCCCUUGUCCAGCACAAUAUCUGUGUUGG
(((((((....(((((((((........)))))).)))(((......))).)))).))).(((((((((((...((.(..(((((......)))))..))).)))))))))))....... ( -48.80)
>DroEre_CAF1 60479 120 + 1
CCGGAUCAAAGCGACUGGGAUCGAACCUUUCCGGAUCGGGAUAUAUCUCAGGAUCGUGGUGAAUAUUGUGAACGGGAAUCAGGGCAAGGACGCCCUUGUCCAGCACAAUAUCCGAGUGGG
.(((((((..((((((((((((((.((.....)).)))......)))))))..))))..))).(((((((....(((...(((((......)))))..)))..)))))))))))...... ( -43.70)
>DroYak_CAF1 63443 120 + 1
CCGGAUCAAAGCGACUGGGAUCGAACUUUUCCGGUUCGGGAUAUAUCUCAGGGUCGUGAUGAAUAUUAUGGACGGGAAUCAGGGCAAGGACGCCCUUGUCCAGCACAAUAUCUGUGUUGG
(((..(((..((((((.((((((........))))))((((....))))..))))))..)))..........)))......((((((((....))))))))((((((.....)))))).. ( -38.90)
>consensus
CCGGAUCGAAGCGACUGGGAUCGAACUUUUCCGGCUCGGGAUAUAUCUCCGGAUCGUGGUGGAUAUUGUGCACGGGAAUCAGGGCAAGAACGCCCUUGUCCAGCACAAUAUCUGUGUUGG
(((((((.....((((((((........)))))).))((((....))))..)))).))).(((((((((((...((.(..(((((......)))))..))).)))))))))))....... (-36.40 = -37.36 +   0.96)

alignment

secondary structure

dotplot

Window 7

Location	4,076,395 – 4,076,515
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.50
Mean single sequence MFE	-36.64
Consensus MFE	-31.84
Energy contribution	-33.08
Covariance contribution	1.24
Combinations/Pair	1.14
Mean z-score	-1.63
Structure conservation index	0.87
SVM decision value	1.24
SVM RNA-class probability	0.935327
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4076395 120 - 20766785
CCAACUCAGAUAUUGUGCUAGACAAGGGCAUUCUUGCCCUGAUUCCGGUGCAUAAUAUCCACCACGAUCCGGAGAUAUAUCCCGAGCCGGAGAAGUUCGAUCCCAGUCGCUUCGACCCGG
....(((.((((((((((..((..((((((....))))))...))....))))))))))...........(((......))).)))((((.((((..((((....))))))))...)))) ( -39.20)
>DroSec_CAF1 59158 120 - 1
CCAACACAGAUAUUGUGCUGGACAAGGGCGUUCUUGCCCUCAUACCCGUGCACAAUAUCCACCACGAUCCGGAGAUAUAUCCCGAGCCGGAAAAGUUCGAUCCCAGUCGCUUCGAUCCGG
........(((((((((((((...((((((....)))))).....))).))))))))))........((.(((......))).)).(((((......((((....))))......))))) ( -38.60)
>DroSim_CAF1 67364 120 - 1
CCAACACAGAUAUUGUGCUGGACAAGGGCGUUCUUGCCCUCAUACCCGUGCACAAUAUCCACCACGAUCCGGAGAUAUAUCCCGAGCCGGAAAAGUUCGAUCCCAGUCGCUUCGAUCCGG
........(((((((((((((...((((((....)))))).....))).))))))))))........((.(((......))).)).(((((......((((....))))......))))) ( -38.60)
>DroEre_CAF1 60479 120 - 1
CCCACUCGGAUAUUGUGCUGGACAAGGGCGUCCUUGCCCUGAUUCCCGUUCACAAUAUUCACCACGAUCCUGAGAUAUAUCCCGAUCCGGAAAGGUUCGAUCCCAGUCGCUUUGAUCCGG
.......((((((((((..(((..((((((....))))))...)))....)))))))))).....((((..((......))..))))((((..((..((((....))))..))..)))). ( -36.80)
>DroYak_CAF1 63443 120 - 1
CCAACACAGAUAUUGUGCUGGACAAGGGCGUCCUUGCCCUGAUUCCCGUCCAUAAUAUUCAUCACGACCCUGAGAUAUAUCCCGAACCGGAAAAGUUCGAUCCCAGUCGCUUUGAUCCGG
........(((((((((..(((..((((((....))))))...)))....)))))))))...........................(((((..((..((((....))))..))..))))) ( -30.00)
>consensus
CCAACACAGAUAUUGUGCUGGACAAGGGCGUUCUUGCCCUGAUUCCCGUGCACAAUAUCCACCACGAUCCGGAGAUAUAUCCCGAGCCGGAAAAGUUCGAUCCCAGUCGCUUCGAUCCGG
........((((((((((.(((..((((((....))))))...)))...))))))))))........((.(((......))).)).(((((((((..((((....))))))))..))))) (-31.84 = -33.08 +   1.24)

alignment

secondary structure

dotplot

Window 8

Location	4,076,435 – 4,076,555
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.58
Mean single sequence MFE	-41.14
Consensus MFE	-33.06
Energy contribution	-34.98
Covariance contribution	1.92
Combinations/Pair	1.12
Mean z-score	-2.45
Structure conservation index	0.80
SVM decision value	2.07
SVM RNA-class probability	0.987303
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4076435 120 + 20766785
AUAUAUCUCCGGAUCGUGGUGGAUAUUAUGCACCGGAAUCAGGGCAAGAAUGCCCUUGUCUAGCACAAUAUCUGAGUUGGGAAUUUGGUAGUCUUUAGUAGUCUCUCGAAUGAGAUGGGG
......(((((..((((...(((((((.(((...(((...((((((....))))))..))).))).)))))))...((((((..(((.(((...))).)))..))))))))))..))))) ( -35.10)
>DroSec_CAF1 59198 120 + 1
AUAUAUCUCCGGAUCGUGGUGGAUAUUGUGCACGGGUAUGAGGGCAAGAACGCCCUUGUCCAGCACAAUAUCUGUGUUGGGAAUUUGGUAGUCUUUAUUAGUCUCUCGAAUGAGAUGGGG
......(((((..((((.(..((((((((((...((.(..(((((......)))))..))).))))))))))..).((((((..(((((((...)))))))..))))))))))..))))) ( -47.40)
>DroSim_CAF1 67404 120 + 1
AUAUAUCUCCGGAUCGUGGUGGAUAUUGUGCACGGGUAUGAGGGCAAGAACGCCCUUGUCCAGCACAAUAUCUGUGUUGGGAAUUUGGUAGUCUUUAUUAGUCUCUCGAAUGAGAUGGGG
......(((((..((((.(..((((((((((...((.(..(((((......)))))..))).))))))))))..).((((((..(((((((...)))))))..))))))))))..))))) ( -47.40)
>DroEre_CAF1 60519 120 + 1
AUAUAUCUCAGGAUCGUGGUGAAUAUUGUGAACGGGAAUCAGGGCAAGGACGCCCUUGUCCAGCACAAUAUCCGAGUGGGGAAUUUUGUAGUCUCGAUUAGCCUCCCGAAUGAGAUGGGG
...(((((((...(((.((((.((((((((....(((...(((((......)))))..)))..)))))))).).(((.((((.........)))).))).)))...))).)))))))... ( -38.60)
>DroYak_CAF1 63483 120 + 1
AUAUAUCUCAGGGUCGUGAUGAAUAUUAUGGACGGGAAUCAGGGCAAGGACGCCCUUGUCCAGCACAAUAUCUGUGUUGGGAAUUUUGUAGUCUCGAUUAGCCUCUCGAACGAGAUGGGG
......((((.(((((((((....))))))..(((((..((((((......))))...(((((((((.....))))))))).....))...)))))....)))((((....)))))))). ( -37.20)
>consensus
AUAUAUCUCCGGAUCGUGGUGGAUAUUGUGCACGGGAAUCAGGGCAAGAACGCCCUUGUCCAGCACAAUAUCUGUGUUGGGAAUUUGGUAGUCUUUAUUAGUCUCUCGAAUGAGAUGGGG
......(((((..((((...(((((((((((...((.(..(((((......)))))..))).)))))))))))...((((((..(((((((...)))))))..))))))))))..))))) (-33.06 = -34.98 +   1.92)

alignment

secondary structure

dotplot

Window 9

Location	4,076,435 – 4,076,555
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.58
Mean single sequence MFE	-32.55
Consensus MFE	-28.78
Energy contribution	-29.14
Covariance contribution	0.36
Combinations/Pair	1.10
Mean z-score	-3.08
Structure conservation index	0.88
SVM decision value	4.31
SVM RNA-class probability	0.999867
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4076435 120 - 20766785
CCCCAUCUCAUUCGAGAGACUACUAAAGACUACCAAAUUCCCAACUCAGAUAUUGUGCUAGACAAGGGCAUUCUUGCCCUGAUUCCGGUGCAUAAUAUCCACCACGAUCCGGAGAUAUAU
....(((((..(((.(((..........................))).((((((((((..((..((((((....))))))...))....)))))))))).....)))....))))).... ( -31.27)
>DroSec_CAF1 59198 120 - 1
CCCCAUCUCAUUCGAGAGACUAAUAAAGACUACCAAAUUCCCAACACAGAUAUUGUGCUGGACAAGGGCGUUCUUGCCCUCAUACCCGUGCACAAUAUCCACCACGAUCCGGAGAUAUAU
....(((((..(((..((.((.....)).)).................(((((((((((((...((((((....)))))).....))).)))))))))).....)))....))))).... ( -32.90)
>DroSim_CAF1 67404 120 - 1
CCCCAUCUCAUUCGAGAGACUAAUAAAGACUACCAAAUUCCCAACACAGAUAUUGUGCUGGACAAGGGCGUUCUUGCCCUCAUACCCGUGCACAAUAUCCACCACGAUCCGGAGAUAUAU
....(((((..(((..((.((.....)).)).................(((((((((((((...((((((....)))))).....))).)))))))))).....)))....))))).... ( -32.90)
>DroEre_CAF1 60519 120 - 1
CCCCAUCUCAUUCGGGAGGCUAAUCGAGACUACAAAAUUCCCCACUCGGAUAUUGUGCUGGACAAGGGCGUCCUUGCCCUGAUUCCCGUUCACAAUAUUCACCACGAUCCUGAGAUAUAU
....((((((.(((((.........(((................)))((((((((((..(((..((((((....))))))...)))....)))))))))).)).)))...)))))).... ( -37.09)
>DroYak_CAF1 63483 120 - 1
CCCCAUCUCGUUCGAGAGGCUAAUCGAGACUACAAAAUUCCCAACACAGAUAUUGUGCUGGACAAGGGCGUCCUUGCCCUGAUUCCCGUCCAUAAUAUUCAUCACGACCCUGAGAUAUAU
....(((((.(((((........)))))....................(((((((((..(((..((((((....))))))...)))....)))))))))............))))).... ( -28.60)
>consensus
CCCCAUCUCAUUCGAGAGACUAAUAAAGACUACCAAAUUCCCAACACAGAUAUUGUGCUGGACAAGGGCGUUCUUGCCCUGAUUCCCGUGCACAAUAUCCACCACGAUCCGGAGAUAUAU
....(((((..(((..((.((.....)).)).................((((((((((.(((..((((((....))))))...)))...)))))))))).....)))....))))).... (-28.78 = -29.14 +   0.36)

alignment

secondary structure

dotplot

Window 0

Location	4,076,475 – 4,076,595
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.50
Mean single sequence MFE	-37.38
Consensus MFE	-28.54
Energy contribution	-29.10
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.62
Structure conservation index	0.76
SVM decision value	0.05
SVM RNA-class probability	0.558087
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4076475 120 + 20766785
AGGGCAAGAAUGCCCUUGUCUAGCACAAUAUCUGAGUUGGGAAUUUGGUAGUCUUUAGUAGUCUCUCGAAUGAGAUGGGGAAGCAGUGGGUGCUUUCGAAGAGUUUCUGAAAGAGGUUUU
((((((....))))))..((((((.((.....)).))))))..((..(.(.(((((....(((((......)))))..(((((((.....)))))))))))).)..)..))......... ( -32.30)
>DroSec_CAF1 59238 120 + 1
AGGGCAAGAACGCCCUUGUCCAGCACAAUAUCUGUGUUGGGAAUUUGGUAGUCUUUAUUAGUCUCUCGAAUGAGAUGGGGAAGCAGUGGGUGCUUUCGAAGAGUUUCUGAAAGUGGUUUU
(((((......)))))..(((((((((.....)))))))))..((..(.(.(((((....(((((......)))))..(((((((.....)))))))))))).)..)..))......... ( -38.60)
>DroSim_CAF1 67444 120 + 1
AGGGCAAGAACGCCCUUGUCCAGCACAAUAUCUGUGUUGGGAAUUUGGUAGUCUUUAUUAGUCUCUCGAAUGAGAUGGGGAAGCAGUGGGUGCUUUCGAAGAGUUUCUGAAAGUUGUUUU
(((((......)))))..(((((((((.....)))))))))..((..(.(.(((((....(((((......)))))..(((((((.....)))))))))))).)..)..))......... ( -38.60)
>DroEre_CAF1 60559 120 + 1
AGGGCAAGGACGCCCUUGUCCAGCACAAUAUCCGAGUGGGGAAUUUUGUAGUCUCGAUUAGCCUCCCGAAUGAGAUGGGGAAGCAGGGGAUGCUUUCGAAGAGUUUCUGAAAGAGGUUUU
.((((((((....)))))))).((((((..(((......)))...)))).)).......((((((......(((((..(((((((.....))))))).....))))).....)))))).. ( -35.80)
>DroYak_CAF1 63523 120 + 1
AGGGCAAGGACGCCCUUGUCCAGCACAAUAUCUGUGUUGGGAAUUUUGUAGUCUCGAUUAGCCUCUCGAACGAGAUGGGGCAGCAGGGGGUGCUUUCGAAGAGUUUCUGAAAGAUGUUUU
.((((((((....)))))))).....(((((((...(..(((((((((((.((((.....(((((((......)).)))))....)))).)))......))))))))..).))))))).. ( -41.60)
>consensus
AGGGCAAGAACGCCCUUGUCCAGCACAAUAUCUGUGUUGGGAAUUUGGUAGUCUUUAUUAGUCUCUCGAAUGAGAUGGGGAAGCAGUGGGUGCUUUCGAAGAGUUUCUGAAAGAGGUUUU
(((((......)))))..(((((((((.....))))))))).......(((.(((......((((((....)))).))(((((((.....)))))))...)))...)))........... (-28.54 = -29.10 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	4,076,475 – 4,076,595
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.50
Mean single sequence MFE	-26.16
Consensus MFE	-20.54
Energy contribution	-21.02
Covariance contribution	0.48
Combinations/Pair	1.13
Mean z-score	-2.01
Structure conservation index	0.79
SVM decision value	1.00
SVM RNA-class probability	0.898099
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4076475 120 - 20766785
AAAACCUCUUUCAGAAACUCUUCGAAAGCACCCACUGCUUCCCCAUCUCAUUCGAGAGACUACUAAAGACUACCAAAUUCCCAACUCAGAUAUUGUGCUAGACAAGGGCAUUCUUGCCCU
......(((((.((...((((.((((((((.....))))...........))))))))....)))))))(((((((..((........))..))).).)))...((((((....)))))) ( -20.90)
>DroSec_CAF1 59238 120 - 1
AAAACCACUUUCAGAAACUCUUCGAAAGCACCCACUGCUUCCCCAUCUCAUUCGAGAGACUAAUAAAGACUACCAAAUUCCCAACACAGAUAUUGUGCUGGACAAGGGCGUUCUUGCCCU
.......((((......((((.((((((((.....))))...........))))))))......))))............(((.(((((...))))).)))...((((((....)))))) ( -24.50)
>DroSim_CAF1 67444 120 - 1
AAAACAACUUUCAGAAACUCUUCGAAAGCACCCACUGCUUCCCCAUCUCAUUCGAGAGACUAAUAAAGACUACCAAAUUCCCAACACAGAUAUUGUGCUGGACAAGGGCGUUCUUGCCCU
.......((((......((((.((((((((.....))))...........))))))))......))))............(((.(((((...))))).)))...((((((....)))))) ( -24.50)
>DroEre_CAF1 60559 120 - 1
AAAACCUCUUUCAGAAACUCUUCGAAAGCAUCCCCUGCUUCCCCAUCUCAUUCGGGAGGCUAAUCGAGACUACAAAAUUCCCCACUCGGAUAUUGUGCUGGACAAGGGCGUCCUUGCCCU
.........(((((...(((..(....)........(((((((.(......).))))))).....)))..(((((...(((......)))..))))))))))..((((((....)))))) ( -31.20)
>DroYak_CAF1 63523 120 - 1
AAAACAUCUUUCAGAAACUCUUCGAAAGCACCCCCUGCUGCCCCAUCUCGUUCGAGAGGCUAAUCGAGACUACAAAAUUCCCAACACAGAUAUUGUGCUGGACAAGGGCGUCCUUGCCCU
....................(((((.((((.....))))(((...((((....)))))))...)))))............(((.(((((...))))).)))...((((((....)))))) ( -29.70)
>consensus
AAAACCUCUUUCAGAAACUCUUCGAAAGCACCCACUGCUUCCCCAUCUCAUUCGAGAGACUAAUAAAGACUACCAAAUUCCCAACACAGAUAUUGUGCUGGACAAGGGCGUUCUUGCCCU
.......((((......((((.((((((((.....))))...........))))))))......))))............(((.(((((...))))).)))...((((((....)))))) (-20.54 = -21.02 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:27 2006