Locus 8118

Sequence ID	3L_DroMel_CAF1
Location	21,369,296 – 21,369,474
Length	178
Max. P	0.999999

overview

Window 4

Location	21,369,296 – 21,369,409
Length	113
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	74.11
Mean single sequence MFE	-51.68
Consensus MFE	-27.11
Energy contribution	-26.92
Covariance contribution	-0.19
Combinations/Pair	1.35
Mean z-score	-1.99
Structure conservation index	0.52
SVM decision value	1.13
SVM RNA-class probability	0.919114
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21369296 113 - 23771897
CAGCUGCCAUAGCCGCUGCUUGGGCGGCACUAUGCGCCUCCGCCGAGAUCCCGCUUAAGUGCAUCUGGAAGGGCAAGGGGAGUUCCGUGGGUGGCGGCGGCA-CAGAGGGUGGU---
..((..((...((((((.....)))))).((.((.(((.((((((....(((((.....(((.((.....)))))...((....))))))))))))).))).-)).))))..))--- ( -50.20)
>DroPse_CAF1 19525 113 - 1
CAGCCGCCAUUGCUGCAGCCUGAGCGGCACUAUGCGCCUCGGCCGAAAUCCCAGUCAGAUGCAUUUGGAAGGGUAAGGCAAGUUCCGCUGGAGCUGGAGGCG-CUGAUGGUGGU---
..((((((((((((((.......))))).....(((((((.(((.....(((..(((((....)))))..)))...))).((((((...)))))).))))))-).)))))))))--- ( -54.60)
>DroGri_CAF1 51358 105 - 1
CAGCUGCCAUUGCGGCCGCCUGUGCGGCACUGUGUGCCUCCGCUGAAAUUCCGCUCAAAUGCAUAUUAAAGGGUAAGGCGAUUUCUGUCGGCGCGGGCGGCUGUU------------
...........(((((((((((((((((((...)))))..(((.((((((((((......)).((((....)))).)).)))))).).)))))))))))))))).------------ ( -45.20)
>DroMoj_CAF1 34757 114 - 1
CAGCUGCCAUUGCGGCCGCUUGAGCGGCACUGUGAGCCUCCGCUGAAAUUCCGCUCAAAUGCAUG---AAGGGAAGGGAUACAUCUGUGGGCGCGGGCGGCUGUUGAUUGUGUUGUU
((((((((...(((.((((((((((((.....(.(((....))).)....)))))))).......---...(((.(.....).))))))).))).)))))))).............. ( -45.00)
>DroAna_CAF1 30637 113 - 1
CGGCUGCCAUGGCCGCUGCUUGGGCGGCACUGUGCGCCUCCGCCGAGAUCCCGGUUAGGUGCAUUUGGAAGGGCAGUGGCAGCUCCGUGGGCGGCGGCGGUG-CUGGCGGAGGU---
..((((((((.((((((((....))))).((((((((((..((((......)))).))))))))..))...))).))))))))(((((.((((.(...).))-)).)))))...--- ( -60.50)
>DroPer_CAF1 21442 113 - 1
CAGCCGCCAUUGCUGCAGCCUGAGCGGCACUAUGCGCCUCGGCCGAAAUCCCAGUCAGAUGCAUUUGGAAGGGUAAGGCAAGUUCCGCUGGAGCUGGAGGCG-CUGAUGGUGGU---
..((((((((((((((.......))))).....(((((((.(((.....(((..(((((....)))))..)))...))).((((((...)))))).))))))-).)))))))))--- ( -54.60)
>consensus
CAGCUGCCAUUGCCGCAGCCUGAGCGGCACUAUGCGCCUCCGCCGAAAUCCCGCUCAAAUGCAUUUGGAAGGGUAAGGCAAGUUCCGUGGGCGCCGGCGGCG_CUGAUGGUGGU___
..((((((......(((((....))))).......((..((((.(((..(((..................))).........))).))))..)).))))))................ (-27.11 = -26.92 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	21,369,329 – 21,369,449
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.22
Mean single sequence MFE	-51.73
Consensus MFE	-30.29
Energy contribution	-31.07
Covariance contribution	0.78
Combinations/Pair	1.15
Mean z-score	-1.66
Structure conservation index	0.59
SVM decision value	0.42
SVM RNA-class probability	0.727415
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21369329 120 + 23771897
CCCCUUGCCCUUCCAGAUGCACUUAAGCGGGAUCUCGGCGGAGGCGCAUAGUGCCGCCCAAGCAGCGGCUAUGGCAGCUGCCCAAGCUGCAGCAGCCCAAGCUGCUGCGGCGGAACAACA
......(((((.((((((.(.(......)).)))).)).)).))).....((.(((((...(((((((((..(((.(((((.......))))).)))..)))))))))))))).)).... ( -53.60)
>DroPse_CAF1 19558 120 + 1
UGCCUUACCCUUCCAAAUGCAUCUGACUGGGAUUUCGGCCGAGGCGCAUAGUGCCGCUCAGGCUGCAGCAAUGGCGGCUGCCCAGGCCGCGGCGGCUCAGGCGGCAGCGGCAGACCAGCA
.................(((......(((((....(((((..(((((...)))))(((...((....))...)))))))))))))(((((.((.((....)).)).)))))......))) ( -49.60)
>DroWil_CAF1 18874 120 + 1
UACGUUACCCUUCAAUAUGCAUCUAGCUGGUAUUUCACCAGGUGCCCAUAGUGCCGCCCAAGCGGCAGCCAUGGCCGCUGCCCAAGCAGCCGCCGCUCAGGCUGCUGCAGCUGAACAGCA
.................(((...((((((((.....))).((..(.....)..))......(((((((((.((((.(((((....))))).))))....))))))))))))))....))) ( -46.60)
>DroMoj_CAF1 34794 117 + 1
AUCCCUUCCCUU---CAUGCAUUUGAGCGGAAUUUCAGCGGAGGCUCACAGUGCCGCUCAAGCGGCCGCAAUGGCAGCUGCGCAGGCCGCGGCAGCGCAAGCCGCCGCUGCGGAUCAACA
((((........---..(((..((((((((.(((..(((....)))...))).))))))))(((((.((....)).)))))))).((.(((((.((....)).))))).))))))..... ( -53.00)
>DroAna_CAF1 30670 118 + 1
GCCACUGCCCUUCCAAAUGCACCUAACCGGGAUCUCGGCGGAGGCGCACAGUGCCGCCCAAGCAGCGGCCAUGGCAGCCGCCCAAGCUGCAGCGGCACAGGCAGCGGCGGCCGAACAG--
(((.(((((........(((.(((..((((....))))...))).)))..(((((((...(((.(((((.......)))))....)))...))))))).))))).)))..........-- ( -55.40)
>DroPer_CAF1 21475 120 + 1
UGCCUUACCCUUCCAAAUGCAUCUGACUGGGAUUUCGGCCGAGGCGCAUAGUGCCGCUCAGGCUGCAGCAAUGGCGGCUGCCCAGGCCGCGGCGGCUCAGGCGGCAGCGGCCGACCAGCA
.((....(((...((........))...)))...(((((((..((((...(.((((((..(((((((((.......)))))...))))..)))))).)..)).))..)))))))...)). ( -52.20)
>consensus
UCCCUUACCCUUCCAAAUGCAUCUAACCGGGAUUUCGGCGGAGGCGCAUAGUGCCGCCCAAGCAGCAGCAAUGGCAGCUGCCCAAGCCGCGGCGGCUCAGGCGGCAGCGGCCGAACAGCA
............................(((....((((...(((((...)))))(((...((....))...))).)))))))..(((((.((.((....)).)).)))))......... (-30.29 = -31.07 +   0.78)

alignment

secondary structure

dotplot

Window 6

Location	21,369,369 – 21,369,474
Length	105
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	66.96
Mean single sequence MFE	-50.37
Consensus MFE	-31.54
Energy contribution	-31.77
Covariance contribution	0.23
Combinations/Pair	1.25
Mean z-score	-3.14
Structure conservation index	0.63
SVM decision value	6.90
SVM RNA-class probability	0.999999
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21369369 105 + 23771897
GAGGCGCAUAGUGCCGCCCAAGCAGCGGCUAUGGCAGCUGCCCAAGCUGCAGCAGCCCAAGCUGCUGCGGCGGAACAACAGCAACCGCCGC---------------CACCAACUUCACAU
..((((....((.(((((...(((((((((..(((.(((((.......))))).)))..)))))))))))))).))....((....)))))---------------)............. ( -48.40)
>DroGri_CAF1 51423 120 + 1
GAGGCACACAGUGCCGCACAGGCGGCCGCAAUGGCAGCUGCGCAGGCCGCGGCAGCGCAAGCCGCCGCCGCGGAUCAACAGCAGCCGGCGGCAGCGCCUCCAUCGGCAUCAUCAUCGCAU
..(((((...)))))((....((.(((((...(((.((((......(((((((.(((.....))).))))))).....)))).))).))))).))(((......))).........)).. ( -60.20)
>DroWil_CAF1 18914 99 + 1
GGUGCCCAUAGUGCCGCCCAAGCGGCAGCCAUGGCCGCUGCCCAAGCAGCCGCCGCUCAGGCUGCUGCAGCUGAACAGCA------ACCGC---------------CUCCCUCAUCACAU
((..(.....)..))((....(((((((((.((((.(((((....))))).))))....))))))))).(((....))).------...))---------------.............. ( -42.50)
>consensus
GAGGCACAUAGUGCCGCCCAAGCGGCAGCAAUGGCAGCUGCCCAAGCAGCAGCAGCCCAAGCUGCUGCAGCGGAACAACAGCA_CCGCCGC_______________CACCAUCAUCACAU
..........((.((((....(((((((((.((((.(((((.......))))).)).))))))))))).))))....))......................................... (-31.54 = -31.77 +   0.23)

alignment

secondary structure

dotplot

Window 7

Location	21,369,369 – 21,369,474
Length	105
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	66.96
Mean single sequence MFE	-59.80
Consensus MFE	-37.50
Energy contribution	-37.40
Covariance contribution	-0.10
Combinations/Pair	1.22
Mean z-score	-3.12
Structure conservation index	0.63
SVM decision value	6.88
SVM RNA-class probability	0.999999
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21369369 105 - 23771897
AUGUGAAGUUGGUG---------------GCGGCGGUUGCUGUUGUUCCGCCGCAGCAGCUUGGGCUGCUGCAGCUUGGGCAGCUGCCAUAGCCGCUGCUUGGGCGGCACUAUGCGCCUC
..(((....(((((---------------.((((((..((....)).)))))((((((((....)))))))).(((..((((((.((....)).))))))..)))).)))))..)))... ( -59.20)
>DroGri_CAF1 51423 120 - 1
AUGCGAUGAUGAUGCCGAUGGAGGCGCUGCCGCCGGCUGCUGUUGAUCCGCGGCGGCGGCUUGCGCUGCCGCGGCCUGCGCAGCUGCCAUUGCGGCCGCCUGUGCGGCACUGUGUGCCUC
..(((...((..(((((.((.(((((..(((((.(((.(((((....(((((((((((.....))))))))))).....))))).)))...)))))))))).)))))))..)).)))... ( -67.30)
>DroWil_CAF1 18914 99 - 1
AUGUGAUGAGGGAG---------------GCGGU------UGCUGUUCAGCUGCAGCAGCCUGAGCGGCGGCUGCUUGGGCAGCGGCCAUGGCUGCCGCUUGGGCGGCACUAUGGGCACC
.........((.((---------------(((((------(((((((((((((...))).))))))))))))))))).......(.((((((.((((((....)))))))))))).).)) ( -52.90)
>consensus
AUGUGAUGAUGGUG_______________GCGGCGG_UGCUGUUGUUCCGCCGCAGCAGCUUGAGCUGCCGCAGCUUGGGCAGCUGCCAUAGCCGCCGCUUGGGCGGCACUAUGCGCCUC
.........................................((((..(.((.((((((((....)))))))).))..)..)))).(((((((..(((((....))))).))))).))... (-37.50 = -37.40 +  -0.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:06:44 2006