Locus 10239

Sequence ID	3R_DroMel_CAF1
Location	27,440,184 – 27,440,352
Length	168
Max. P	0.968003

overview

Window 9

Location	27,440,184 – 27,440,275
Length	91
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	76.79
Mean single sequence MFE	-25.63
Consensus MFE	-18.17
Energy contribution	-18.08
Covariance contribution	-0.08
Combinations/Pair	1.18
Mean z-score	-1.18
Structure conservation index	0.71
SVM decision value	0.45
SVM RNA-class probability	0.740801
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27440184 91 - 27905053
UUGGUCGCCAGCGAGUGCAUCUGCUGGUGGCACUGGCGCAGGUCAAACACCUGCAUG-------AGAAAAUGUAUGU-UAAGCUAUCACAUUAA------ACUCU
...(((((((((((.....)).)))))))))......((((((.....))))))..(-------((..((((((((.-.....))).)))))..------.))). ( -30.10)
>DroSec_CAF1 1565 92 - 1
UUGGUCGCCAACGAGUGCAUCUGCUGGUGGCACUGGCGCAGGUCGAACACCUGCAUG-------ACAAAUAUUAUGUUUAAGCAAUCACACUAC------ACUCU
...(((((((....(((((((....))).))))))))((((((.....))))))..)-------))........(((....)))..........------..... ( -25.20)
>DroSim_CAF1 1639 92 - 1
UUGGUCGCCAACGAGUGCAUCUGCUGGUGGCACUGGCGCAGAUCAAACACCUGCAUG-------AGAAAAUUUAUGUUUAAGCAAUCACACUAC------ACUCU
((((((((...(.((((((((....))).))))).).)).))))))......(((((-------((....))))))).................------..... ( -18.90)
>DroEre_CAF1 1561 98 - 1
UUGGUCGCCAACGAGUGCAUCUGCUGGUGGCACUGGCGCAGGUCAAACACCUGCAUG-------GCAAAUAUUGUGUUAAAGUAAUCGCAUUGAUUAGUAAUUCC
((((((((((.(.((((((((....))).))))).).((((((.....)))))).))-------))......((((..........))))..))))))....... ( -30.10)
>DroYak_CAF1 1644 90 - 1
UUGGUCGCCAACGAGUGCAUCUGCUGGUGGCACUGGCGCAGGUCAAACACCUGUGUA---------UGAUAUUGGGUUAAAGUAAUUGCAUUGA------GAUCC
..((((.((((..((((((((....))).))))).((((((((.....)))))))).---------.....)))).((((.((....)).))))------)))). ( -26.10)
>DroPer_CAF1 1565 96 - 1
UUGGUUGCCAGCGAAUGCAUCUGCUGGUGGCACUGACGCAAGUCAAACACCUGUUUAAAAAAUGGAUAAAAUUAUGA-----AAAUCAAGCUAA---GG-AAUCG
...((..((((((........))))))..))..((((....))))....((((((((.....))))).......((.-----....)).....)---))-..... ( -23.40)
>consensus
UUGGUCGCCAACGAGUGCAUCUGCUGGUGGCACUGGCGCAGGUCAAACACCUGCAUG_______ACAAAAAUUAUGUUUAAGCAAUCACACUAA______ACUCU
(..((.(((.((.(((......))).)))))))..).((((((.....))))))................................................... (-18.17 = -18.08 +  -0.08)

alignment

secondary structure

dotplot

Window 0

Location	27,440,205 – 27,440,315
Length	110
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	76.99
Mean single sequence MFE	-39.43
Consensus MFE	-30.91
Energy contribution	-30.30
Covariance contribution	-0.61
Combinations/Pair	1.28
Mean z-score	-1.06
Structure conservation index	0.78
SVM decision value	0.54
SVM RNA-class probability	0.774945
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27440205 110 + 27905053
ACAUACAUUUUCU--------CAUGCAGGUGUUUGACCUGCGCCAGUGCCACCAGCAGAUGCACUCGCUGGCGACCAAUGCGCAGGCAGCGGCCGCUGCUCAGGCGGCAGCCGUGGCC
.............--------...((((((.....))))))(((..((((..((((((.....)).))))(((.......))).))))(((((.(((((....))))).)))))))). ( -47.60)
>DroVir_CAF1 1549 110 + 1
CCGAAUCAU--------GUUUUCUGUAGGUCUUCGACUUGCGUCAAUGCCAUCAGCAGAUGCAUUCGCUGGCCACCAAUGCACAGGCCGCUGCUGCAGCGCAAGCGGCUGCCGUCGCG
.(((....(--------((.(..((..((((..(((..((((((..(((.....))))))))).)))..))))..))..).)))(((.((((((((...)).)))))).))).))).. ( -38.10)
>DroPse_CAF1 1581 115 + 1
UCAUAAUUUUCUCCAUUUUU-UA--CAGGUUUUUGACUUGCGUCAGUGCCACCAGCAGAUGCAUUCGCUGGCAACCAAUGCACAGGCAGCUGCCGCAGCACAGGCGGCCGCUGUGGCC
.............((((...-..--..(((..(((((....))))).))).(((((.((.....))))))).....))))(((((.(.((((((........)))))).))))))... ( -35.90)
>DroYak_CAF1 1666 108 + 1
ACCCAAUAUCA----------UACACAGGUGUUUGACCUGCGCCAGUGCCACCAGCAGAUGCACUCGUUGGCGACCAAUGCGCAGGCAGCGGCCGCAGCUCAGGCGGCAGCCGUGGCC
..((....(((----------.(((....))).)))(((((((...((.(.(((((((.....)).))))).)..))..)))))))..(((((.((.((....)).)).))))))).. ( -38.90)
>DroMoj_CAF1 1541 105 + 1
UUUAAC--U--------GUU---AACAGGUGUUCGACUUGCGUCAAUGCCAUCAGCAGAUGCACUCGCUGGCCACCAAUGCACAGGCUGCUGCGGCAGCACAAGCGGCCGCCGUGGCA
.....(--(--------((.---....((((..((.(.((((((..(((.....)))))))))...).))..)))).....))))((..(.(((((.((....)).))))).)..)). ( -39.80)
>DroPer_CAF1 1584 117 + 1
UCAUAAUUUUAUCCAUUUUU-UAAACAGGUGUUUGACUUGCGUCAGUGCCACCAGCAGAUGCAUUCGCUGGCAACCAAUGCACAGGCAGCUGCCGCAGCACAGGCGGCCGCUGUGGCC
............((.....(-(((((....))))))(((((((..((....(((((.((.....)))))))..))..))))).))(((((.(((((.......))))).))))))).. ( -36.30)
>consensus
UCAUAAUUUU________UU_UAAACAGGUGUUUGACUUGCGUCAGUGCCACCAGCAGAUGCACUCGCUGGCAACCAAUGCACAGGCAGCUGCCGCAGCACAGGCGGCCGCCGUGGCC
.........................(((((.....))))).((((((((..(((((.((.....)))))))........)))).(((.((((((........)))))).))).)))). (-30.91 = -30.30 +  -0.61)

alignment

secondary structure

dotplot

Window 1

Location	27,440,205 – 27,440,315
Length	110
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	76.99
Mean single sequence MFE	-45.63
Consensus MFE	-33.55
Energy contribution	-33.88
Covariance contribution	0.34
Combinations/Pair	1.15
Mean z-score	-1.99
Structure conservation index	0.74
SVM decision value	1.62
SVM RNA-class probability	0.968003
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27440205 110 - 27905053
GGCCACGGCUGCCGCCUGAGCAGCGGCCGCUGCCUGCGCAUUGGUCGCCAGCGAGUGCAUCUGCUGGUGGCACUGGCGCAGGUCAAACACCUGCAUG--------AGAAAAUGUAUGU
((...(((((((.((....)).)))))))..((((((((....(((((((((((.....)).)))))))))....))))))))......))(((((.--------.....)))))... ( -53.20)
>DroVir_CAF1 1549 110 - 1
CGCGACGGCAGCCGCUUGCGCUGCAGCAGCGGCCUGUGCAUUGGUGGCCAGCGAAUGCAUCUGCUGAUGGCAUUGACGCAAGUCGAAGACCUACAGAAAAC--------AUGAUUCGG
..((((((((((((((.((......))))))))..(((((((.((.....)).))))))).)))))..(((.(((((....))))).).))..........--------.....))). ( -41.80)
>DroPse_CAF1 1581 115 - 1
GGCCACAGCGGCCGCCUGUGCUGCGGCAGCUGCCUGUGCAUUGGUUGCCAGCGAAUGCAUCUGCUGGUGGCACUGACGCAAGUCAAAAACCUG--UA-AAAAAUGGAGAAAAUUAUGA
.(((((((((((.(((.((((.(((((....))).)))))).))).))).((....))....))).)))))..((((....))))....((..--..-......))............ ( -42.30)
>DroYak_CAF1 1666 108 - 1
GGCCACGGCUGCCGCCUGAGCUGCGGCCGCUGCCUGCGCAUUGGUCGCCAACGAGUGCAUCUGCUGGUGGCACUGGCGCAGGUCAAACACCUGUGUA----------UGAUAUUGGGU
(((..(((((((.((....)).)))))))..))).((.((...(((((((.(.(((......))).)))))....((((((((.....)))))))).----------.)))..)).)) ( -47.40)
>DroMoj_CAF1 1541 105 - 1
UGCCACGGCGGCCGCUUGUGCUGCCGCAGCAGCCUGUGCAUUGGUGGCCAGCGAGUGCAUCUGCUGAUGGCAUUGACGCAAGUCGAACACCUGUU---AAC--------A--GUUAAA
(((((((((((((....).)))))))((((((...(((((((.((.....)).))))))))))))).)))))(((((....)))))....(((..---..)--------)--)..... ( -46.60)
>DroPer_CAF1 1584 117 - 1
GGCCACAGCGGCCGCCUGUGCUGCGGCAGCUGCCUGUGCAUUGGUUGCCAGCGAAUGCAUCUGCUGGUGGCACUGACGCAAGUCAAACACCUGUUUA-AAAAAUGGAUAAAAUUAUGA
(((...(((.(((((.......))))).))))))(((.((((.((..((((((........))))))..))..((((....))))............-...)))).)))......... ( -42.50)
>consensus
GGCCACGGCGGCCGCCUGUGCUGCGGCAGCUGCCUGUGCAUUGGUCGCCAGCGAAUGCAUCUGCUGGUGGCACUGACGCAAGUCAAACACCUGUAUA_AA________AAAAUUAUGA
.(((((.((.(((((.......))))).)).((..(((((((.((.....)).)))))))..))..)))))..((((....))))................................. (-33.55 = -33.88 +   0.34)

alignment

secondary structure

dotplot

Window 2

Location	27,440,235 – 27,440,352
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.69
Mean single sequence MFE	-50.23
Consensus MFE	-30.64
Energy contribution	-30.12
Covariance contribution	-0.52
Combinations/Pair	1.21
Mean z-score	-1.79
Structure conservation index	0.61
SVM decision value	0.03
SVM RNA-class probability	0.547907
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27440235 117 + 27905053
UGCGCCAGUGCCACCAGCAGAUGCACUCGCUGGCGACCAAUGCGCAGGCAGCGGCCGCUGCUCAGGCGGCAGCCGUGGCCGGAGUGGCCAAUCAGC---AAAUGGGCGGCGGCGGAAGGA
..((((((((......((....))...)))))))).((....(((.....)))((((((((((((((....))).(((((.....)))))......---...)))))))))))))..... ( -55.80)
>DroVir_CAF1 1579 117 + 1
UGCGUCAAUGCCAUCAGCAGAUGCAUUCGCUGGCCACCAAUGCACAGGCCGCUGCUGCAGCGCAAGCGGCUGCCGUCGCGGGUGUCUCCAACCAAC---AAAUGGGCGGCGGCGGCAGAA
((((((..(((.....)))))))))..((((((((...........))))((((...))))...))))((((((((((((((....)))..(((..---...)))))))))))))).... ( -52.10)
>DroGri_CAF1 1697 117 + 1
UGCGACAAUGCCAUCAGCAGAUGCACUCGCUGGCCACCAACGCACAAGCCGCUGCUGCAGCGCAAGCAGCUGCCGUCGCUGGUGUCUCCAAUCAAC---AAAUGGGCGGCGGUGGCAGAA
.((((...(((.(((....)))))).))))..((((((.........((.((((((((...)).)))))).)).((((((.((.............---..)).)))))))))))).... ( -45.16)
>DroWil_CAF1 1678 120 + 1
UGCGACAAUGUCACCAACAGAUGCACUCACUGGCCACCAAUGCCCAGGCUGCCGCAGCUGCACAAGCAGCCGCCGUUGCUGGCGUCUCCAAUCAACAACAGAUGGGCGGUGGCGGUAGAA
...(((...)))(((..(((.((....)))))((((((...(((((..(((..((.(((((....))))).)).((((.(((.....)))..))))..))).)))))))))))))).... ( -45.40)
>DroMoj_CAF1 1566 117 + 1
UGCGUCAAUGCCAUCAGCAGAUGCACUCGCUGGCCACCAAUGCACAGGCUGCUGCGGCAGCACAAGCGGCCGCCGUGGCAGGCGUUUCCAAUCAAC---AAAUGGGCGGCGGUGGUAGAA
((((((..(((.....))))))))).((....((((((..(((...(.((((..((((.((.......)).))))..)))).)....(((......---...))))))..)))))).)). ( -47.80)
>DroAna_CAF1 1588 117 + 1
UGCGCCAGUGCCACCAACAAAUGCAUUCUCUAGCCACGAAUGCCCAGGCAGCGGCGGCGGCUCAGGCGGCCGCAGUGGCCGGAGUGGCCAACCAGC---AGAUGGGUGGAGGCGGAAGAA
..((((....(((((......(((...(((..(((((...(((....)))...(((((.((....)).))))).)))))..)))(((....)))))---)....))))).))))...... ( -55.10)
>consensus
UGCGACAAUGCCACCAGCAGAUGCACUCGCUGGCCACCAAUGCACAGGCAGCUGCGGCAGCACAAGCGGCCGCCGUGGCCGGAGUCUCCAAUCAAC___AAAUGGGCGGCGGCGGAAGAA
((((....(((.....)))..)))).((((((.(((..........(((.((.((.((.((....)).)).)).)).)))((.....)).............))).))))))........ (-30.64 = -30.12 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:52:25 2006