Locus 4693

Sequence ID	3R_DroMel_CAF1
Location	12,343,883 – 12,344,129
Length	246
Max. P	0.999507

overview

Window 9

Location	12,343,883 – 12,343,998
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	99.65
Mean single sequence MFE	-33.86
Consensus MFE	-33.00
Energy contribution	-33.20
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.92
Structure conservation index	0.97
SVM decision value	3.67
SVM RNA-class probability	0.999507
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12343883 115 - 27905053
UUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGCUGGUUUCGUUUGCCGCUGUGUUGCUGAUAUCUUUUGUGCAGCGAAAUGGUUUAUUGGCCUAUUAGCGCAGCAUUU
...................(((((((((.((((.(((.((..((.((((((..(((((..(....(....)....)..)))))))))))...))..))))).))))))))))))) ( -33.70)
>DroSec_CAF1 12630 115 - 1
UUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGCUGGUUUCGGUUGCCGCUGUGUUGCUGAUAUCUUUUGUGCAGCGAAAUGGUUUAUUGGCCUAUUAGCGCAGCAUUU
...................(((((((((.((((.(((.((..((..(.(((..(((((..(....(....)....)..))))).))).)...))..))))).))))))))))))) ( -33.90)
>DroSim_CAF1 11763 115 - 1
UUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGCUGGUUUCGGUUGCCGCUGUGUUGCUGAUAUCUUUUGUGCAGCGAAAUGGUUUAUUGGCCUAUUAGCGCAGCAUUU
...................(((((((((.((((.(((.((..((..(.(((..(((((..(....(....)....)..))))).))).)...))..))))).))))))))))))) ( -33.90)
>DroEre_CAF1 12594 115 - 1
UUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGCUGGUUUCGGUUGCCGCUGUGUUGCUGAUAUCUUUUGUGCAGCGAAAUGGUUUAUUGGCCUAUUAGCGCAGCAUUU
...................(((((((((.((((.(((.((..((..(.(((..(((((..(....(....)....)..))))).))).)...))..))))).))))))))))))) ( -33.90)
>DroYak_CAF1 8573 115 - 1
UUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGCUGGUUUCGGUUGCCGCUGUGUUGCUGAUAUCUUUUGUGCAGCGAAAUGGUUUAUUGGCCUAUUAGCGCAGCAUUU
...................(((((((((.((((.(((.((..((..(.(((..(((((..(....(....)....)..))))).))).)...))..))))).))))))))))))) ( -33.90)
>consensus
UUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGCUGGUUUCGGUUGCCGCUGUGUUGCUGAUAUCUUUUGUGCAGCGAAAUGGUUUAUUGGCCUAUUAGCGCAGCAUUU
...................(((((((((.((((.(((.((..((..(.(((..(((((..(....(....)....)..))))).))).)...))..))))).))))))))))))) (-33.00 = -33.20 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	12,343,958 – 12,344,068
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	98.73
Mean single sequence MFE	-28.29
Consensus MFE	-26.65
Energy contribution	-27.05
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.94
SVM decision value	0.78
SVM RNA-class probability	0.850073
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12343958 110 + 27905053
GCGCCAACAACAGCAACAUUUAUUAAUUAGUGAGAAAAAAUUAAUGCGCAACUGUCAUCAUUACUCGUGCCCCAUCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUAGU
((((............((((........)))).............)))).(((((.(((........((((((((((((((...)))))))...))).)))))))))))) ( -25.81)
>DroSec_CAF1 12705 110 + 1
GCGCCAACAACAGCAACAUUUAUUAAUUAGUGAGAAAAAAUUAAUGCGCAACUGUCAUCAUUACUCCUGCCCCAUCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUGGU
((((............((((........)))).............)))).......(((((...(((.(((((((((((((...)))))))...))).)))))).))))) ( -28.91)
>DroSim_CAF1 11838 110 + 1
GCGCCAACAACAGCAACAUUUAUUAAUUAGUGAGAAAAAAUUAAUGCGCAACUGUCAUCAUUACUCCUGCCCCAUCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUGGU
((((............((((........)))).............)))).......(((((...(((.(((((((((((((...)))))))...))).)))))).))))) ( -28.91)
>DroEre_CAF1 12669 110 + 1
GCGCCAACAACAGCAACAUUUAUUAAUUAGUGAGAAAAAAUUAAUGCGCAACUGUCAUCAUUACUCCUGCCCCAUCCACAGGAUCUGUGGACAUUGGCGGCGGAUAUGGU
((((............((((........)))).............)))).......(((((...(((.(((((((((((((...)))))))...))).)))))).))))) ( -28.91)
>DroYak_CAF1 8648 110 + 1
GCGCCAACAACAGCAACAUUUAUUAAUUAGUGAGAAAAAAUUAAUGCGCAACUGUCAUCAUUACUCCUGCCCCAUCCACAGGAUCUGUGGACAUUGGCGGCGGAUAUGGU
((((............((((........)))).............)))).......(((((...(((.(((((((((((((...)))))))...))).)))))).))))) ( -28.91)
>consensus
GCGCCAACAACAGCAACAUUUAUUAAUUAGUGAGAAAAAAUUAAUGCGCAACUGUCAUCAUUACUCCUGCCCCAUCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUGGU
((((............((((........)))).............)))).......(((((...(((.(((((((((((((...)))))))...))).)))))).))))) (-26.65 = -27.05 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	12,343,958 – 12,344,068
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	98.73
Mean single sequence MFE	-33.90
Consensus MFE	-32.16
Energy contribution	-32.36
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.34
Structure conservation index	0.95
SVM decision value	3.10
SVM RNA-class probability	0.998428
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12343958 110 - 27905053
ACUAUAUCCGCCACCAAUGUCCACAGAUCCUGUGGAUGGGGCACGAGUAAUGAUGACAGUUGCGCAUUAAUUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGC
........((((.((...((((((((...)))))))).))...........((..(((((.(((.(((((((..........)))))))...))).)))))..)))))). ( -31.30)
>DroSec_CAF1 12705 110 - 1
ACCAUAUCCGCCACCAAUGUCCACAGAUCCUGUGGAUGGGGCAGGAGUAAUGAUGACAGUUGCGCAUUAAUUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGC
.((...((((((.(((...(((((((...))))))))))))).))).....((..(((((.(((.(((((((..........)))))))...))).)))))..))))... ( -33.80)
>DroSim_CAF1 11838 110 - 1
ACCAUAUCCGCCACCAAUGUCCACAGAUCCUGUGGAUGGGGCAGGAGUAAUGAUGACAGUUGCGCAUUAAUUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGC
.((...((((((.(((...(((((((...))))))))))))).))).....((..(((((.(((.(((((((..........)))))))...))).)))))..))))... ( -33.80)
>DroEre_CAF1 12669 110 - 1
ACCAUAUCCGCCGCCAAUGUCCACAGAUCCUGUGGAUGGGGCAGGAGUAAUGAUGACAGUUGCGCAUUAAUUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGC
........(((((((...((((((((...))))))))..))).........((..(((((.(((.(((((((..........)))))))...))).)))))..)))))). ( -35.30)
>DroYak_CAF1 8648 110 - 1
ACCAUAUCCGCCGCCAAUGUCCACAGAUCCUGUGGAUGGGGCAGGAGUAAUGAUGACAGUUGCGCAUUAAUUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGC
........(((((((...((((((((...))))))))..))).........((..(((((.(((.(((((((..........)))))))...))).)))))..)))))). ( -35.30)
>consensus
ACCAUAUCCGCCACCAAUGUCCACAGAUCCUGUGGAUGGGGCAGGAGUAAUGAUGACAGUUGCGCAUUAAUUUUUUCUCACUAAUUAAUAAAUGUUGCUGUUGUUGGCGC
......((((((.(((...(((((((...))))))))))))).)))((...((..(((((.(((.(((((((..........)))))))...))).)))))..)).)).. (-32.16 = -32.36 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	12,343,998 – 12,344,100
Length	102
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	91.05
Mean single sequence MFE	-33.23
Consensus MFE	-30.67
Energy contribution	-31.17
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.55
Structure conservation index	0.92
SVM decision value	2.36
SVM RNA-class probability	0.992961
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12343998 102 + 27905053
UUAAUGCGCAACUGUCAUCAUUACUCGUGCCCCAUCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUAGUUUGUUGUGUGUGUUCUUCCUCACACACCA-CCC----
.....(((.((((((.(((........((((((((((((((...)))))))...))).)))))))))))))))).(((((((........)))))))..-...---- ( -31.50)
>DroSec_CAF1 12745 106 + 1
UUAAUGCGCAACUGUCAUCAUUACUCCUGCCCCAUCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUGGUUUGUUGUGUGUGUUCUUCCCCACACCCCA-CCCACCG
.....(((((((....(((((...(((.(((((((((((((...)))))))...))).)))))).)))))..)))))))((((........))))....-....... ( -33.70)
>DroSim_CAF1 11878 106 + 1
UUAAUGCGCAACUGUCAUCAUUACUCCUGCCCCAUCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUGGUUUGUUGUGUGUGUUCUUCCCCACACCCCA-CCCCCCG
.....(((((((....(((((...(((.(((((((((((((...)))))))...))).)))))).)))))..)))))))((((........))))....-....... ( -33.70)
>DroEre_CAF1 12709 103 + 1
UUAAUGCGCAACUGUCAUCAUUACUCCUGCCCCAUCCACAGGAUCUGUGGACAUUGGCGGCGGAUAUGGUUUGUUGUGUGUGUUU-UCCGCACCCCCCAAUA---AA
.....(((((((....(((((...(((.(((((((((((((...)))))))...))).)))))).)))))..)))))))((((..-...)))).........---.. ( -34.00)
>consensus
UUAAUGCGCAACUGUCAUCAUUACUCCUGCCCCAUCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUGGUUUGUUGUGUGUGUUCUUCCCCACACCCCA_CCC__CG
.....(((((((....(((((...(((.(((((((((((((...)))))))...))).)))))).)))))..)))))))(((........))).............. (-30.67 = -31.17 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	12,343,998 – 12,344,100
Length	102
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	91.05
Mean single sequence MFE	-34.70
Consensus MFE	-28.95
Energy contribution	-29.45
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.13
Structure conservation index	0.83
SVM decision value	1.14
SVM RNA-class probability	0.920771
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12343998 102 - 27905053
----GGG-UGGUGUGUGAGGAAGAACACACACAACAAACUAUAUCCGCCACCAAUGUCCACAGAUCCUGUGGAUGGGGCACGAGUAAUGAUGACAGUUGCGCAUUAA
----(((-(((((((((........))))))).........)))))(((.(((...(((((((...)))))))))))))..(.(((((.......))))).)..... ( -32.70)
>DroSec_CAF1 12745 106 - 1
CGGUGGG-UGGGGUGUGGGGAAGAACACACACAACAAACCAUAUCCGCCACCAAUGUCCACAGAUCCUGUGGAUGGGGCAGGAGUAAUGAUGACAGUUGCGCAUUAA
.(((..(-(...(((((........)))))...))..)))...((((((.(((...(((((((...))))))))))))).)))(((((.......)))))....... ( -38.00)
>DroSim_CAF1 11878 106 - 1
CGGGGGG-UGGGGUGUGGGGAAGAACACACACAACAAACCAUAUCCGCCACCAAUGUCCACAGAUCCUGUGGAUGGGGCAGGAGUAAUGAUGACAGUUGCGCAUUAA
...((..-((..(((((.(......).)))))..))..))...((((((.(((...(((((((...))))))))))))).)))(((((.......)))))....... ( -38.40)
>DroEre_CAF1 12709 103 - 1
UU---UAUUGGGGGGUGCGGA-AAACACACACAACAAACCAUAUCCGCCGCCAAUGUCCACAGAUCCUGUGGAUGGGGCAGGAGUAAUGAUGACAGUUGCGCAUUAA
..---..(((..(.(((.(..-...).))).)..)))......((((((.(((...(((((((...))))))))))))).)))(((((.......)))))....... ( -29.70)
>consensus
CG__GGG_UGGGGUGUGGGGAAGAACACACACAACAAACCAUAUCCGCCACCAAUGUCCACAGAUCCUGUGGAUGGGGCAGGAGUAAUGAUGACAGUUGCGCAUUAA
........((..(((((.(......).)))))..)).......((((((.(((...(((((((...))))))))))))).)))(((((.......)))))....... (-28.95 = -29.45 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	12,344,032 – 12,344,129
Length	97
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	75.90
Mean single sequence MFE	-26.87
Consensus MFE	-18.83
Energy contribution	-19.50
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.70
SVM decision value	1.41
SVM RNA-class probability	0.951229
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12344032 97 + 27905053
UCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUAGUUUGUUGUGUGUGUUCUUCCUCACACACCA-CCC----AAUAAAA-ACACCCACCCACACACACGCAC---------
(((((((...)))))))....(((((..(.........((.(((((((........))))))).)-)..----.......-.)..))))).............--------- ( -27.01)
>DroSec_CAF1 12779 108 + 1
UCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUGGUUUGUUGUGUGUGUUCUUCCCCACACCCCA-CCCACCGAAUAAAA-AUACCCACCCACA--CACACACGCACGCACA
(((((((...))))))).....((((((((((.....))))((((((((................-..............-..........)))--))))).))).)))... ( -25.30)
>DroEre_CAF1 12743 107 + 1
UCCACAGGAUCUGUGGACAUUGGCGGCGGAUAUGGUUUGUUGUGUGUGUUU-UCCGCACCCCCCAAUA---AAAACGCC-CCCACCCACCCAUCCACCCACACACACGCACA
......((((..((((....(((.((((.......(((((((.(((((...-..)))))....)))))---))..))))-.))).))))..))))................. ( -28.30)
>consensus
UCCACAGGAUCUGUGGACAUUGGUGGCGGAUAUGGUUUGUUGUGUGUGUUCUUCCCCACACCCCA_CCC____AAUAAAA_ACACCCACCCACACACACACAC_CACGCACA
(((((((...)))))))....(((((.(((((.....))))..(((((........))))).......................))))))...................... (-18.83 = -19.50 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:43 2006