Locus 2403

Sequence ID	3R_DroMel_CAF1
Location	6,753,125 – 6,753,313
Length	188
Max. P	0.995152

overview

Window 6

Location	6,753,125 – 6,753,245
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.33
Mean single sequence MFE	-27.66
Consensus MFE	-27.24
Energy contribution	-27.44
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.98
SVM decision value	2.55
SVM RNA-class probability	0.995152
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6753125 120 + 27905053
AAGCCCAACACCCGUCAGCAGAAUCAGCAACAACUGGCGGGCAGCUACUUACUUAAAAAGCAUUGAGCCGAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAG
.............((((((....((((......)))).((((.(((............)))((((.((.((((....))))...)))))).......))))..))))))........... ( -27.50)
>DroSec_CAF1 17293 119 + 1
AAGCCCAACACCCGUCAGCAGAAUCAGCAACAACUGGCGGGCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCC-CCACGCCCACGCUGACUGCACUUAAAG
.............((((((....((((......)))).((((.(((............)))((((.((.((((......)))).))))))..-....))))..))))))........... ( -27.70)
>DroSim_CAF1 21693 120 + 1
AAGCCCAACACCCGUCAGCAGAAUCAGCAACAACUGGCGGGCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAG
.............((((((....((((......)))).((((.(((............)))((((.((.((((......)))).)))))).......))))..))))))........... ( -27.70)
>DroEre_CAF1 1652 120 + 1
AAGCCCAACACCCGUCAGCAGAAUCAGCAACAACUGGCGGGCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAG
.............((((((....((((......)))).((((.(((............)))((((.((.((((......)))).)))))).......))))..))))))........... ( -27.70)
>DroYak_CAF1 13563 120 + 1
AAGCCCAACACCCGUCAGCAGAAUCAGCAACAACUGGCGGGCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAG
.............((((((....((((......)))).((((.(((............)))((((.((.((((......)))).)))))).......))))..))))))........... ( -27.70)
>consensus
AAGCCCAACACCCGUCAGCAGAAUCAGCAACAACUGGCGGGCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAG
.............((((((....((((......)))).((((.(((............)))((((.((.((((......)))).)))))).......))))..))))))........... (-27.24 = -27.44 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	6,753,165 – 6,753,279
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.07
Mean single sequence MFE	-33.82
Consensus MFE	-30.12
Energy contribution	-30.92
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.35
Structure conservation index	0.89
SVM decision value	0.62
SVM RNA-class probability	0.803477
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6753165 114 + 27905053
GCAGCUACUUACUUAAAAAGCAUUGAGCCGAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGUG------
...(((............)))((((.((.((((....))))...))))))((((((((..(((((.....)).......(((((.......)))))..).))..))))))))..------ ( -34.40)
>DroSec_CAF1 17333 113 + 1
GCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCC-CCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGUG------
.....(((((((((((......)))))..)))))).............((((-(((((..(((((.....)).......(((((.......)))))..).))..))))))))).------ ( -33.60)
>DroSim_CAF1 21733 114 + 1
GCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGUG------
...(((............)))((((.((.((((......)))).))))))((((((((..(((((.....)).......(((((.......)))))..).))..))))))))..------ ( -34.60)
>DroEre_CAF1 1692 120 + 1
GCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCAUGGUGGUGAAAGUG
.....(((((((((((......)))))..)))))).((((((((((((...............((.....)).......(((((.......)))))..........)))).)))))))). ( -29.40)
>DroYak_CAF1 13603 118 + 1
GCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGGCAGUG--
((.(((............)))((((.((.((((......)))).))))))((((((((..(((((.....)).......(((((.......)))))..).))..))))))))))....-- ( -37.10)
>consensus
GCAGCUACUUACUUAAAAAGCAUUGAGCCUAAGUAAACUUUUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGUG______
...(((............)))((((.((.((((......)))).))))))((((((((..(((((.....)).......(((((.......)))))..).))..))))))))........ (-30.12 = -30.92 +   0.80)

alignment

secondary structure

dotplot

Window 8

Location	6,753,165 – 6,753,279
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.07
Mean single sequence MFE	-40.21
Consensus MFE	-38.56
Energy contribution	-39.00
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.43
Structure conservation index	0.96
SVM decision value	1.55
SVM RNA-class probability	0.963271
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6753165 114 - 27905053
------CACCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAAAAGUUUACUUCGGCUCAAUGCUUUUUAAGUAAGUAGCUGC
------..((((((((..(((((((.((((((....)))))).)))).((.....)))))..))))))))...(((((..(((....)))..))....(((((.......)))))))).. ( -41.10)
>DroSec_CAF1 17333 113 - 1
------CACCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGG-GGAUUGGCGUAAAAGUUUACUUAGGCUCAAUGCUUUUUAAGUAAGUAGCUGC
------...(((((((..(((((((.((((((....)))))).)))).((.....)))))..)))))-))...(((.......(((((((((((.....)))...))))))))..))).. ( -38.80)
>DroSim_CAF1 21733 114 - 1
------CACCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAAAAGUUUACUUAGGCUCAAUGCUUUUUAAGUAAGUAGCUGC
------..((((((((..(((((((.((((((....)))))).)))).((.....)))))..))))))))...(((.......(((((((((((.....)))...))))))))..))).. ( -42.30)
>DroEre_CAF1 1692 120 - 1
CACUUUCACCACCAUGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAAAAGUUUACUUAGGCUCAAUGCUUUUUAAGUAAGUAGCUGC
..((..(((..(((((.....((((.((((((....)))))).)))).........)))))..)))..))...(((.......(((((((((((.....)))...))))))))..))).. ( -35.34)
>DroYak_CAF1 13603 118 - 1
--CACUGCCCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAAAAGUUUACUUAGGCUCAAUGCUUUUUAAGUAAGUAGCUGC
--..((((((((((((..(((((((.((((((....)))))).)))).((.....)))))..))))))))..............((((((((((.....)))...))))))))))).... ( -43.50)
>consensus
______CACCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAAAAGUUUACUUAGGCUCAAUGCUUUUUAAGUAAGUAGCUGC
........((((((((..(((((((.((((((....)))))).)))).((.....)))))..))))))))...(((.......(((((((((((.....)))...))))))))..))).. (-38.56 = -39.00 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	6,753,205 – 6,753,313
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.42
Mean single sequence MFE	-46.66
Consensus MFE	-30.77
Energy contribution	-32.57
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.66
SVM decision value	0.08
SVM RNA-class probability	0.574552
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6753205 108 + 27905053
UUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGUG------------GUGAAUGUUGGGUUGGGGUUGGGGUGCAUAUGAC
.(((.((((((((((((.(((((((.....)).......(((((.......))))).........))))).)))------------).............)))))))).)))........ ( -45.01)
>DroSec_CAF1 17373 107 + 1
UUACGCCAAUCC-CCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGUG------------GUGAAGGUUGGGCUGGGGUUGGGGUGGAGAUGAC
((((.((((.((-(((.(((((((((............))))(((...((((((.(..(.....)...).))))------------))...))))))))))))))))).))))....... ( -47.00)
>DroSim_CAF1 21773 108 + 1
UUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGUG------------GUGAAGGUUGGGCUGGGGUUGGGGUGGAGAUGAC
((((.((((((((((((.(((((((.....)).......(((((.......))))).........))))).)))------------)....((.....)))))))))).))))....... ( -47.10)
>DroEre_CAF1 1732 117 + 1
UUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCAUGGUGGUGAAAGUGGUGAUGCUGAAGGUUGG-C-GGGGUU-GGGUGGAGAUGAC
......((.(((((((.((((.(((..(((.........((.(((...(((((((...........)))))))...))).)).........)))..)-)-))))))-))).)))..)).. ( -46.07)
>DroYak_CAF1 13643 109 + 1
UUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGGCAGUG--------UGGAAGUGUGG-C-AGUGUU-GGGUGGCGAUGAC
...(((((..(((((((((((((((((.((.(((.....(((((.......)))))..(.....)))).))..)))))--------)))..))))))-.-......-))))))))..... ( -48.11)
>consensus
UUACGCCAAUCCCCCACGCCCACGCUGACUGCACUUAAAGCGGCUGAAACCGCCGCAAGAUGAUCGUGGGGGUG____________GUGAAGGUUGGGCUGGGGUUGGGGUGGAGAUGAC
.(((.((((((((.(((.(((((((.....)).......(((((.......))))).........))))).)))..........................)))))))).)))........ (-30.77 = -32.57 +   1.80)

alignment

secondary structure

dotplot

Window 0

Location	6,753,205 – 6,753,313
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.42
Mean single sequence MFE	-38.13
Consensus MFE	-30.62
Energy contribution	-30.86
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.53
Structure conservation index	0.80
SVM decision value	0.19
SVM RNA-class probability	0.627790
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6753205 108 - 27905053
GUCAUAUGCACCCCAACCCCAACCCAACAUUCAC------------CACCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAA
.........((.((((.(((.............(------------(((.((((((.....((((.((((((....)))))).)))).........)))))).))))))).)))).)).. ( -37.15)
>DroSec_CAF1 17373 107 - 1
GUCAUCUCCACCCCAACCCCAGCCCAACCUUCAC------------CACCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGG-GGAUUGGCGUAA
.........((.((((((((((((((........------------...............((((.((((((....)))))).)))).((.....)).))))).)))-)).)))).)).. ( -37.90)
>DroSim_CAF1 21773 108 - 1
GUCAUCUCCACCCCAACCCCAGCCCAACCUUCAC------------CACCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAA
.........((.((((.(((((......))...(------------(((.((((((.....((((.((((((....)))))).)))).........)))))).))))))).)))).)).. ( -38.54)
>DroEre_CAF1 1732 117 - 1
GUCAUCUCCACCC-AACCCC-G-CCAACCUUCAGCAUCACCACUUUCACCACCAUGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAA
.........((((-((.(((-(-(.........))....((((.....((((..((((...((((.((((((....)))))).))))....))))..))))..))))))).)))).)).. ( -37.70)
>DroYak_CAF1 13643 109 - 1
GUCAUCGCCACCC-AACACU-G-CCACACUUCCA--------CACUGCCCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAA
.....(((((...-......-(-(..........--------....))((((((((..(((((((.((((((....)))))).)))).((.....)))))..))))))))..)))))... ( -39.34)
>consensus
GUCAUCUCCACCCCAACCCCAGCCCAACCUUCAC____________CACCCCCACGAUCAUCUUGCGGCGGUUUCAGCCGCUUUAAGUGCAGUCAGCGUGGGCGUGGGGGAUUGGCGUAA
................................................((((((((..(((((((.((((((....)))))).)))).((.....)))))..)))))))).......... (-30.62 = -30.86 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:50 2006