Locus 6397

Sequence ID	3L_DroMel_CAF1
Location	17,138,562 – 17,138,715
Length	153
Max. P	0.980546

overview

Window 7

Location	17,138,562 – 17,138,675
Length	113
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	84.97
Mean single sequence MFE	-27.22
Consensus MFE	-22.72
Energy contribution	-21.96
Covariance contribution	-0.76
Combinations/Pair	1.17
Mean z-score	-2.03
Structure conservation index	0.83
SVM decision value	1.23
SVM RNA-class probability	0.933620
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17138562 113 + 23771897
ACAAAAAUGCAUCCUUGAACACGCACACUUAACUGGGCCUGCGUGAGUGGCAACCUCUUGCCACCCACAC-UACCCAACCCCCUCGGACGCCAUGGA-ACCACCGCCUCUCCACU
........((.(((.....((((((..(((....)))..)))))).(((((((....)))))))......-..............))).))..((((-...........)))).. ( -27.00)
>DroSec_CAF1 23002 113 + 1
ACAAAAAUGCAUCCUUGAACACGCACACUUAACUGGGCCUGCGUGAGUGGCAACCUCUUGCCACCCACAC-UACCCACCCCCCUUGGACGCCUUGGA-CCCACCGCCUCUUCACU
.......(((............)))........((((((.(((((.(((((((....))))))).)))..-...(((.......)))..))...)).-))))............. ( -26.80)
>DroEre_CAF1 24064 113 + 1
ACAAAAAUGCAUCCUUGAACACGCACACUUAACUGGGCCUGCGUGAGUGGCAACCUCUUGCCACCCACGA-AACCCACCCCCUUUGGACUCCUUGGA-CCCAACGCCUCUUCACU
...............((((...((.........((((....((((.(((((((....))))))).)))).-..))))......((((..((....))-.)))).))...)))).. ( -29.10)
>DroYak_CAF1 25253 114 + 1
ACAAAAAUGCAUCCUUGAACACGCACACUUAACUGGGCCUGCGUGAGUGGCAACCUCUUGCCACCCGCAGUUCCCCACCCCCUUUGGACUCCUUGGA-CCCACCGCCUCUCCACU
.......(((............)))........((((.(((((.(.(((((((....)))))))))))))...)))).......((((.....(((.-....)))....)))).. ( -28.20)
>DroAna_CAF1 5217 110 + 1
ACAAAAAUGCAUCCUUGAACACGCACACUUAACUGGGCCUGCGUGAGUGGCAGCCUCUUGCCUCCCUCGA-C----AGCCCGCCAGGAUCCUUUCUUCAAGACUGUCCCACCGAU
........(((..(((((................((((.((((.(.(.(((((....))))).).).)).-)----)))))...((((....)))))))))..)))......... ( -25.00)
>consensus
ACAAAAAUGCAUCCUUGAACACGCACACUUAACUGGGCCUGCGUGAGUGGCAACCUCUUGCCACCCACAA_UACCCACCCCCCUUGGACGCCUUGGA_CCCACCGCCUCUCCACU
........((.(((.....((((((..(((....)))..)))))).(((((((....))))))).....................))).....(((...)))..))......... (-22.72 = -21.96 +  -0.76)

alignment

secondary structure

dotplot

Window 8

Location	17,138,562 – 17,138,675
Length	113
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	84.97
Mean single sequence MFE	-42.24
Consensus MFE	-29.36
Energy contribution	-28.80
Covariance contribution	-0.56
Combinations/Pair	1.19
Mean z-score	-2.21
Structure conservation index	0.70
SVM decision value	0.77
SVM RNA-class probability	0.845805
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17138562 113 - 23771897
AGUGGAGAGGCGGUGGU-UCCAUGGCGUCCGAGGGGGUUGGGUA-GUGUGGGUGGCAAGAGGUUGCCACUCACGCAGGCCCAGUUAAGUGUGCGUGUUCAAGGAUGCAUUUUUGU
....(.((.((.(((..-..))).)).))).......((((((.-(((((((((((((....)))))))))))))..)))))).((((.((((((.(....).)))))).)))). ( -46.10)
>DroSec_CAF1 23002 113 - 1
AGUGAAGAGGCGGUGGG-UCCAAGGCGUCCAAGGGGGGUGGGUA-GUGUGGGUGGCAAGAGGUUGCCACUCACGCAGGCCCAGUUAAGUGUGCGUGUUCAAGGAUGCAUUUUUGU
...........((((.(-(((((.(((..((....((.(((((.-(((((((((((((....)))))))))))))..))))).))...))..))).))...)))).))))..... ( -46.70)
>DroEre_CAF1 24064 113 - 1
AGUGAAGAGGCGUUGGG-UCCAAGGAGUCCAAAGGGGGUGGGUU-UCGUGGGUGGCAAGAGGUUGCCACUCACGCAGGCCCAGUUAAGUGUGCGUGUUCAAGGAUGCAUUUUUGU
..((((.(.((((((((-((....)).)))))...((.((((((-(((((((((((((....)))))))))))).))))))).)).....))).).))))............... ( -44.70)
>DroYak_CAF1 25253 114 - 1
AGUGGAGAGGCGGUGGG-UCCAAGGAGUCCAAAGGGGGUGGGGAACUGCGGGUGGCAAGAGGUUGCCACUCACGCAGGCCCAGUUAAGUGUGCGUGUUCAAGGAUGCAUUUUUGU
..((((.(.(((.((((-((....)).))))....((.((((...(((((((((((((....))))))).).))))).)))).)).....))).).))))............... ( -38.40)
>DroAna_CAF1 5217 110 - 1
AUCGGUGGGACAGUCUUGAAGAAAGGAUCCUGGCGGGCU----G-UCGAGGGAGGCAAGAGGCUGCCACUCACGCAGGCCCAGUUAAGUGUGCGUGUUCAAGGAUGCAUUUUUGU
...(.(((((...((((.....)))).))))).)(((((----.-.((.(((.((((......)))).))).))..)))))...((((.((((((.(....).)))))).)))). ( -35.30)
>consensus
AGUGGAGAGGCGGUGGG_UCCAAGGAGUCCAAGGGGGGUGGGUA_GUGUGGGUGGCAAGAGGUUGCCACUCACGCAGGCCCAGUUAAGUGUGCGUGUUCAAGGAUGCAUUUUUGU
..((((((.((..(((...)))....((((...................(((((((((....)))))))))(((((.((........)).)))))......)))))).)))))). (-29.36 = -28.80 +  -0.56)

alignment

secondary structure

dotplot

Window 9

Location	17,138,600 – 17,138,715
Length	115
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	70.03
Mean single sequence MFE	-26.36
Consensus MFE	-14.72
Energy contribution	-14.96
Covariance contribution	0.24
Combinations/Pair	1.25
Mean z-score	-1.73
Structure conservation index	0.56
SVM decision value	0.81
SVM RNA-class probability	0.855347
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17138600 115 + 23771897
CUGCGUGAGUGGCAACCUCUUGCCACCCACAC-UACCCAACCCCCUCGGACGCCAUGGA-ACCACCGCCUCUCCACUGCAGACAGAAAAAAAUAUUGACCAAAUGGGAAAGGAUAAC
(((((((.(((((((....))))))).)))..-..............(((.((..((..-..))..))...)))...)))).............((..((....))..))....... ( -27.40)
>DroSec_CAF1 23040 114 + 1
CUGCGUGAGUGGCAACCUCUUGCCACCCACAC-UACCCACCCCCCUUGGACGCCUUGGA-CCCACCGCCUCUUCACUGCAGACAGAAAAAAA-ACUGACCAAUUUCGACAGGAUAAC
(((((((.(((((((....))))))).)))..-..............(((.((..((..-..))..)).))).....)))).(((.......-.))).................... ( -25.80)
>DroEre_CAF1 24102 101 + 1
CUGCGUGAGUGGCAACCUCUUGCCACCCACGA-AACCCACCCCCUUUGGACUCCUUGGA-CCCAACGCCUCUUCACUACAGACAGAGAAAAG-GUUGACCAA-------------AU
...((((.(((((((....))))))).)))).-...........(((((.....(((..-..))).((((.(((.((......)).))).))-))...))))-------------). ( -27.10)
>DroYak_CAF1 25291 115 + 1
CUGCGUGAGUGGCAACCUCUUGCCACCCGCAGUUCCCCACCCCCUUUGGACUCCUUGGA-CCCACCGCCUCUCCACUACACUCAGAAAAAAU-AUUUACCGAAUUGGUCAGGACAAU
(((((.(.(((((((....))))))))))))).(((..(((...(((((......((((-...........))))((......)).......-.....)))))..)))..))).... ( -28.80)
>DroAna_CAF1 5255 108 + 1
CUGCGUGAGUGGCAGCCUCUUGCCUCCCUCGA-C----AGCCCGCCAGGAUCCUUUCUUCAAGACUGUCCCACCGAUGCACUGAAGAAAAUU-AUUGAAAAUUUUUUACAUUAU---
.((((((((.(((((....)))))...)))((-(----((..(...((((.....))))...).)))))......))))).((.((((((((-......)))))))).))....--- ( -22.70)
>consensus
CUGCGUGAGUGGCAACCUCUUGCCACCCACAA_UACCCACCCCCCUUGGACGCCUUGGA_CCCACCGCCUCUCCACUGCAGACAGAAAAAAA_AUUGACCAAAUUGGACAGGAUAAC
(((((((.(((((((....))))))).))).................(((.....(((...))).......)))...)))).................................... (-14.72 = -14.96 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	17,138,600 – 17,138,715
Length	115
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	70.03
Mean single sequence MFE	-40.40
Consensus MFE	-19.80
Energy contribution	-20.16
Covariance contribution	0.36
Combinations/Pair	1.18
Mean z-score	-2.16
Structure conservation index	0.49
SVM decision value	1.86
SVM RNA-class probability	0.980546
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17138600 115 - 23771897
GUUAUCCUUUCCCAUUUGGUCAAUAUUUUUUUCUGUCUGCAGUGGAGAGGCGGUGGU-UCCAUGGCGUCCGAGGGGGUUGGGUA-GUGUGGGUGGCAAGAGGUUGCCACUCACGCAG
..(((((..((((.(((((.(....(((((..(((....)))..)))))((.(((..-..))).))).)))))))))..)))))-(((((((((((((....))))))))))))).. ( -53.30)
>DroSec_CAF1 23040 114 - 1
GUUAUCCUGUCGAAAUUGGUCAGU-UUUUUUUCUGUCUGCAGUGAAGAGGCGGUGGG-UCCAAGGCGUCCAAGGGGGGUGGGUA-GUGUGGGUGGCAAGAGGUUGCCACUCACGCAG
.....((..((....((((.(.((-((((((.(((....))).))))))))((....-.)).....).))))....))..))..-(((((((((((((....))))))))))))).. ( -43.90)
>DroEre_CAF1 24102 101 - 1
AU-------------UUGGUCAAC-CUUUUCUCUGUCUGUAGUGAAGAGGCGUUGGG-UCCAAGGAGUCCAAAGGGGGUGGGUU-UCGUGGGUGGCAAGAGGUUGCCACUCACGCAG
..-------------(((((((((-((((((.(((....))).)))))))..)))).-.))))(((..(((.......)))..)-))(((((((((((....))))))))))).... ( -38.60)
>DroYak_CAF1 25291 115 - 1
AUUGUCCUGACCAAUUCGGUAAAU-AUUUUUUCUGAGUGUAGUGGAGAGGCGGUGGG-UCCAAGGAGUCCAAAGGGGGUGGGGAACUGCGGGUGGCAAGAGGUUGCCACUCACGCAG
....((((.(((.((((((.(((.-...))).))))))............(..((((-((....)).))))..)..))).)))).(((((((((((((....))))))).).))))) ( -39.90)
>DroAna_CAF1 5255 108 - 1
---AUAAUGUAAAAAAUUUUCAAU-AAUUUUCUUCAGUGCAUCGGUGGGACAGUCUUGAAGAAAGGAUCCUGGCGGGCU----G-UCGAGGGAGGCAAGAGGCUGCCACUCACGCAG
---...(((((.((((((......-))))))......)))))..(((.((((((((...((........))...)))))----)-))(((((.(((.....))).)).))).))).. ( -26.30)
>consensus
AUUAUCCUGUCCAAAUUGGUCAAU_AUUUUUUCUGUCUGCAGUGGAGAGGCGGUGGG_UCCAAGGAGUCCAAGGGGGGUGGGUA_GUGUGGGUGGCAAGAGGUUGCCACUCACGCAG
....................................((((......(.(((..(((...)))....)))).................(((((((((((....))))))))))))))) (-19.80 = -20.16 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:29 2006