Locus 3003

Sequence ID	2L_DroMel_CAF1
Location	8,570,849 – 8,571,019
Length	170
Max. P	0.999967

overview

Window 6

Location	8,570,849 – 8,570,964
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	85.05
Mean single sequence MFE	-36.84
Consensus MFE	-28.88
Energy contribution	-29.24
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-2.30
Structure conservation index	0.78
SVM decision value	0.47
SVM RNA-class probability	0.747670
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8570849 115 - 22407834
-UUAUUGCCGAA-ACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUC-CCAACUGAGCUAUUUCGGCACUUGAACG-GUCAGCGAUAA-AAGCUCAAGACAAACUAC
-....(((((((-((((((.......))))).....((((((.....)))))).((((..-......))))..))))))))........-((((((.....-..)))...)))....... ( -34.60)
>DroPse_CAF1 20842 114 - 1
AUGAUUGCCGAA-ACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUC-CCAACUGAGCUAUUUCGGCACUUGAGCA-ACAGGUGUCAA-AAGCUCCCUAUACGCG--
.((((.((((((-((((((.......))))).....((((((.....)))))).((((..-......))))..)))))))(((((....-.))))))))).-..((.........)).-- ( -34.60)
>DroSim_CAF1 11574 115 - 1
-GUAUUGCCGAA-ACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUC-CCAACUGAGCUAUUUCGGCACUUGACCG-UCUAACGACAA-AAGCUCAAAUCAAACUGC
-....(((((((-((((((.......))))).....((((((.....)))))).((((..-......))))..)))))))).......(-((....)))..-.................. ( -34.60)
>DroEre_CAF1 6751 114 - 1
-GGC-UGCCGAA-ACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUC-CCAACUGAGCUAUUUCGGCACUUGAGCG-AGCGGCGAUAA-AAGCUCAAUACAAGCUAC
-(((-(((((((-((((((.......))))).....((((((.....)))))).((((..-......))))..)))))))..((((((.-...........-..))))))....)))).. ( -39.74)
>DroAna_CAF1 6081 115 - 1
-AGAUUGCCGAA-ACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUC-CCAACUGAGCUAUUUCGGCACUUGGGGG-GCUGGCGCCAA-AAGCUCUUCACAGACCAU
-....(((((((-((((((.......))))).....((((((.....)))))).((((..-......))))..))))))))((((((((-(((........-.))))))))).))..... ( -41.30)
>DroPer_CAF1 22338 118 - 1
AUGACUGCCGAAAACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUCCCCAACUGAGCUAUUUCGGCACUUGAGCAAACAGGUGUCAAAAAGCUCCCUAUACUCG--
.((((.(((((((.(((((.......))))).....((((((.....)))))).((((.........))))..)))))))(((((......)))))))))..................-- ( -36.20)
>consensus
_UGAUUGCCGAA_ACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUC_CCAACUGAGCUAUUUCGGCACUUGAGCG_ACAGGCGACAA_AAGCUCAAUACAAACUAC
.....(((((((..(((((.......))))).....((((((.....)))))).((((.........))))...)))))))...((((................))))............ (-28.88 = -29.24 +   0.36)

alignment

secondary structure

dotplot

Window 7

Location	8,570,887 – 8,570,993
Length	106
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	90.42
Mean single sequence MFE	-28.41
Consensus MFE	-27.90
Energy contribution	-27.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.67
Structure conservation index	0.98
SVM decision value	5.00
SVM RNA-class probability	0.999967
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8570887 106 - 22407834
AAACA-GAAAAUGCAUUAAAAAAAAAAUUCUUAUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUCCCAACUGAGCUAUUUCGGC
.....-.............................((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -27.90)
>DroSec_CAF1 6640 103 - 1
A-ACA-GAAAAUGCAUUAAAAAAA--AGCCGUAUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUCCCAACUGAGCUAUUUCGGC
.-...-...(((((..........--....)))))((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -28.54)
>DroSim_CAF1 11612 103 - 1
A-ACA-GAAAAUGCAUUAAAAAAA--AAUCGUAUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUCCCAACUGAGCUAUUUCGGC
.-...-...((((((((.......--))).)))))((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -28.80)
>DroEre_CAF1 6789 104 - 1
AAAAAUGAAAAUACAUUAAAAAAA--UGUUGGC-UGCCGAAACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUCCCAACUGAGCUAUUUCGGC
............(((((.....))--)))....-.((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -28.90)
>DroYak_CAF1 7545 100 - 1
AAAAAU---AA--CACAAAAAAGA--AAUCGGCUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUCCCAACUGAGCUAUUUCGGC
......---..--...........--.........((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -27.90)
>consensus
AAACA_GAAAAUGCAUUAAAAAAA__AAUCGUAUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAGAUCUUCAGUCUAACGCUCUCCCAACUGAGCUAUUUCGGC
...................................((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) (-27.90 = -27.90 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	8,570,926 – 8,571,019
Length	93
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	86.04
Mean single sequence MFE	-16.96
Consensus MFE	-12.76
Energy contribution	-12.76
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.75
SVM decision value	0.00
SVM RNA-class probability	0.535992
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8570926 93 + 22407834
CUAAAGGUCCCCGGUUCAAUCCCGGGUUUCGGCAAUAAGAAUUUUUUUUUUAAUGCAUUUUC-UGUUUAUAUAUUCUUUUACUUGAAGUAAAUU
.....((..(((((.......)))))..)).(((.((((((.....)))))).)))......-..............(((((.....))))).. ( -18.70)
>DroSec_CAF1 6679 90 + 1
CUAAAGGUCCCCGGUUCAAUCCCGGGUUUCGGCAAUACGGCU--UUUUUUUAAUGCAUUUUC-UGU-UGUAUAUUCUUUUACUUAAAGUAAAUU
.....((..(((((.......)))))..))....(((((((.--..................-.))-))))).....(((((.....))))).. ( -16.95)
>DroSim_CAF1 11651 90 + 1
CUAAAGGUCCCCGGUUCAAUCCCGGGUUUCGGCAAUACGAUU--UUUUUUUAAUGCAUUUUC-UGU-UGCAUAUUCUUUUACUUGAAGUAAAUU
.....((..(((((.......)))))..)).((((((.((..--................))-)))-))).......(((((.....))))).. ( -17.87)
>DroEre_CAF1 6828 91 + 1
CUAAAGGUCCCCGGUUCAAUCCCGGGUUUCGGCA-GCCAACA--UUUUUUUAAUGUAUUUUCAUUUUUGUAUAUUCUUUUACUUCAUGUAAAUU
.....((..(((((.......)))))..))....-....(((--((.....))))).....................(((((.....))))).. ( -15.00)
>DroYak_CAF1 7584 86 + 1
CUAAAGGUCCCCGGUUCAAUCCCGGGUUUCGGCAAGCCGAUU--UCUUUUUUGUG--UU---AUUUUUUUA-AUUCUUUUACUUUAAGUAAAUU
.(((((...(((((.......)))))..((((....))))..--...........--..---.........-.........)))))........ ( -16.30)
>consensus
CUAAAGGUCCCCGGUUCAAUCCCGGGUUUCGGCAAUACGACU__UUUUUUUAAUGCAUUUUC_UGUUUGUAUAUUCUUUUACUUGAAGUAAAUU
.....((..(((((.......)))))..))...............................................(((((.....))))).. (-12.76 = -12.76 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	8,570,926 – 8,571,019
Length	93
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	86.04
Mean single sequence MFE	-15.51
Consensus MFE	-12.56
Energy contribution	-12.56
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.81
SVM decision value	-0.03
SVM RNA-class probability	0.520135
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8570926 93 - 22407834
AAUUUACUUCAAGUAAAAGAAUAUAUAAACA-GAAAAUGCAUUAAAAAAAAAAUUCUUAUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAG
..(((((.....)))))..............-......(((.(((...........))).))).....(((((.......)))))......... ( -13.80)
>DroSec_CAF1 6679 90 - 1
AAUUUACUUUAAGUAAAAGAAUAUACA-ACA-GAAAAUGCAUUAAAAAAA--AGCCGUAUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAG
..(((((.....)))))..........-...-(..(((((..........--....)))))..)....(((((.......)))))......... ( -13.84)
>DroSim_CAF1 11651 90 - 1
AAUUUACUUCAAGUAAAAGAAUAUGCA-ACA-GAAAAUGCAUUAAAAAAA--AAUCGUAUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAG
..(((((.....))))).....(((((-...-.....)))))........--..(((......)))..(((((.......)))))......... ( -16.80)
>DroEre_CAF1 6828 91 - 1
AAUUUACAUGAAGUAAAAGAAUAUACAAAAAUGAAAAUACAUUAAAAAAA--UGUUGGC-UGCCGAAACCCGGGAUUGAACCGGGGACCUUUAG
........(((((.........................(((((.....))--)))....-........(((((.......)))))...))))). ( -13.80)
>DroYak_CAF1 7584 86 - 1
AAUUUACUUAAAGUAAAAGAAU-UAAAAAAAU---AA--CACAAAAAAGA--AAUCGGCUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAG
..(((((.....))))).....-.........---..--......((((.--..((((....))))..(((((.......)))))...)))).. ( -19.30)
>consensus
AAUUUACUUCAAGUAAAAGAAUAUACAAACA_GAAAAUGCAUUAAAAAAA__AAUCGUAUUGCCGAAACCCGGGAUUGAACCGGGGACCUUUAG
..(((((.....)))))...................................................(((((.......)))))......... (-12.56 = -12.56 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:54 2006