Locus 3005

Sequence ID	3R_DroMel_CAF1
Location	8,045,189 – 8,045,331
Length	142
Max. P	0.981985

overview

Window 5

Location	8,045,189 – 8,045,309
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.00
Mean single sequence MFE	-31.99
Consensus MFE	-20.43
Energy contribution	-20.68
Covariance contribution	0.26
Combinations/Pair	1.27
Mean z-score	-1.42
Structure conservation index	0.64
SVM decision value	0.16
SVM RNA-class probability	0.614580
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8045189 120 + 27905053
CACCCGACAUGAGUGCGCAACUCCUCGCGCUUGUUCUCCACCACCGACUGGAUCUUUUUGUGCACCUCGUCUAUCUCGGACACGCUGUGCUGCUCAAACAGCGUGUCCACGUUCAGGUUU
.(((.(((((((((((((((.(((...((...((.....))...))...))).....))))))).))))).......(((((((((((.........)))))))))))..)))..))).. ( -39.90)
>DroVir_CAF1 231600 120 + 1
UACCCGACCAUCGUGCGCAACUCUUCGCGUUUGUUUUCCACCACCGUUUGGAUUUUCUUCUGCACAGCAUCGAUCUCGGACACGCCGUGCUGUUCGAACAGCGUGUCCACAUCUAAUUGC
............((((((........))........((((........)))).........)))).(((..(((...((((((((.((.........)).))))))))..)))....))) ( -28.80)
>DroGri_CAF1 160733 120 + 1
UACCCGACCAUUGUGCGAAGUUCUUCGCGCUUGUUUUCGACCACCGUUUGGAUUUUCUUCUGCACCGCAUCGAUCUCGGACACGCCGUGCUGCUCGAACAGCGUGUCCACAUCUAAUUGC
....(((..((.(((((((....)))))))..))..))).....((.((((((.......(((...)))........((((((((.((.........)).))))))))..)))))).)). ( -31.70)
>DroWil_CAF1 151494 120 + 1
CACCCAACUUGUGUUCGCAGUUCCUCCCGCUUAUUCUCCACCACUGUCUGGAUCUUUUUGUGCACGGCAUCGAUUUCCGACACAUUAUUCUGUUCGAAUAAAGUGUCCACAUUUAAGUUU
.....((((((((((((..((.((...(((......((((........)))).......)))...)).))))).....(((((.((((((.....)))))).))))).))))..))))). ( -20.92)
>DroMoj_CAF1 180251 120 + 1
UACCCGACCAUGGUGCGCAGCUCUUCUCGCUUAUUCUCCACUACUGUUUGGAUUUUCUUCUGCACAGCAUCGAUCUCGGACACGCUGUGCUGCUCAAACAGCGUGUCCACAUCUAAUUGC
.....(((.(((.((.(((((.......))......((((........))))........))).)).))).).))..(((((((((((.........)))))))))))............ ( -33.50)
>DroAna_CAF1 119332 120 + 1
UACCCAACAUGAGUGCGAAGCUCCUCCCGCUUGUUCUCAACGAGUGACUGGAUCCGCUUGUGUAUCGCAUCGAUCUCGGACACACUGUGCUGCUCGAACAGCGUGUCCACGUUCAAGUUU
......(((..((((.((...(((...(((((((.....)))))))...)))))))))..)))........((....((((((.((((.........)))).))))))....))...... ( -37.10)
>consensus
UACCCGACCAGAGUGCGCAGCUCCUCGCGCUUGUUCUCCACCACCGUCUGGAUCUUCUUCUGCACCGCAUCGAUCUCGGACACGCUGUGCUGCUCGAACAGCGUGUCCACAUCUAAGUGC
............((((..(((.......))).....((((........)))).........))))............(((((((((((.........)))))))))))............ (-20.43 = -20.68 +   0.26)

alignment

secondary structure

dotplot

Window 6

Location	8,045,189 – 8,045,309
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.00
Mean single sequence MFE	-38.90
Consensus MFE	-26.08
Energy contribution	-25.92
Covariance contribution	-0.16
Combinations/Pair	1.31
Mean z-score	-1.83
Structure conservation index	0.67
SVM decision value	0.91
SVM RNA-class probability	0.878915
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8045189 120 - 27905053
AAACCUGAACGUGGACACGCUGUUUGAGCAGCACAGCGUGUCCGAGAUAGACGAGGUGCACAAAAAGAUCCAGUCGGUGGUGGAGAACAAGCGCGAGGAGUUGCGCACUCAUGUCGGGUG
..((((((.((((((((((((((.........))))))))))).........(((.(((.(((.....(((..(((((..((.....)).)).)))))).))).))))))))))))))). ( -45.60)
>DroVir_CAF1 231600 120 - 1
GCAAUUAGAUGUGGACACGCUGUUCGAACAGCACGGCGUGUCCGAGAUCGAUGCUGUGCAGAAGAAAAUCCAAACGGUGGUGGAAAACAAACGCGAAGAGUUGCGCACGAUGGUCGGGUA
(((....(((.((((((((((((.(.....).))))))))))))..)))..)))(((((.........((((........))))........((((....)))))))))........... ( -38.70)
>DroGri_CAF1 160733 120 - 1
GCAAUUAGAUGUGGACACGCUGUUCGAGCAGCACGGCGUGUCCGAGAUCGAUGCGGUGCAGAAGAAAAUCCAAACGGUGGUCGAAAACAAGCGCGAAGAACUUCGCACAAUGGUCGGGUA
(((....(((.((((((((((((.(.....).))))))))))))..)))..))).((((.((((.....(((.....)))(((..........)))....))))))))............ ( -37.70)
>DroWil_CAF1 151494 120 - 1
AAACUUAAAUGUGGACACUUUAUUCGAACAGAAUAAUGUGUCGGAAAUCGAUGCCGUGCACAAAAAGAUCCAGACAGUGGUGGAGAAUAAGCGGGAGGAACUGCGAACACAAGUUGGGUG
...(((...(((((((((.((((((.....)))))).)))))((.........))...))))..)))((((((...(((((.....))..((((......))))...)))...)))))). ( -30.10)
>DroMoj_CAF1 180251 120 - 1
GCAAUUAGAUGUGGACACGCUGUUUGAGCAGCACAGCGUGUCCGAGAUCGAUGCUGUGCAGAAGAAAAUCCAAACAGUAGUGGAGAAUAAGCGAGAAGAGCUGCGCACCAUGGUCGGGUA
...........((((((((((((.........)))))))))))).((((.(((.(((((.........((((........)))).....(((.......)))))))).)))))))..... ( -39.50)
>DroAna_CAF1 119332 120 - 1
AAACUUGAACGUGGACACGCUGUUCGAGCAGCACAGUGUGUCCGAGAUCGAUGCGAUACACAAGCGGAUCCAGUCACUCGUUGAGAACAAGCGGGAGGAGCUUCGCACUCAUGUUGGGUA
..(((..(.((((((((((((((.(.....).)))))))))))(((((((...))))......((((((((.....((((((.......)))))).)))..))))).)))))))..))). ( -41.80)
>consensus
AAAAUUAAAUGUGGACACGCUGUUCGAGCAGCACAGCGUGUCCGAGAUCGAUGCGGUGCACAAGAAAAUCCAAACAGUGGUGGAGAACAAGCGCGAAGAGCUGCGCACAAAGGUCGGGUA
...........((((((((((((.(.....).))))))))))))...(((((...((((.........((((........)))).....(((.......)))..))))....)))))... (-26.08 = -25.92 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	8,045,229 – 8,045,331
Length	102
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	77.98
Mean single sequence MFE	-29.18
Consensus MFE	-17.92
Energy contribution	-17.32
Covariance contribution	-0.61
Combinations/Pair	1.50
Mean z-score	-2.71
Structure conservation index	0.61
SVM decision value	1.90
SVM RNA-class probability	0.981985
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8045229 102 + 27905053
CCACCGACUGGAUCUUUUUGUGCACCUCGUCUAUCUCGGACACGCUGUGCUGCUCAAACAGCGUGUCCACGUUCAGGUUUAACAAAUUGGCCGUCAUUUAG-C
.....(((.((.((..(((((..(((((((.......(((((((((((.........))))))))))))))...))))...)))))..)))))))......-. ( -34.91)
>DroVir_CAF1 231640 102 + 1
CCACCGUUUGGAUUUUCUUCUGCACAGCAUCGAUCUCGGACACGCCGUGCUGUUCGAACAGCGUGUCCACAUCUAAUUGCAGUAAAUCGGCGCUCAUUUAU-U
.....((.(.(((((....(((((.......(....)((((((((.((.........)).)))))))).........))))).))))).).))........-. ( -26.60)
>DroGri_CAF1 160773 99 + 1
CCACCGUUUGGAUUUUCUUCUGCACCGCAUCGAUCUCGGACACGCCGUGCUGCUCGAACAGCGUGUCCACAUCUAAUUGCAGUAAAUCGGCGCUCAUUU----
.....((.(.(((((....(((((.......(....)((((((((.((.........)).)))))))).........))))).))))).).))......---- ( -26.60)
>DroWil_CAF1 151534 102 + 1
CCACUGUCUGGAUCUUUUUGUGCACGGCAUCGAUUUCCGACACAUUAUUCUGUUCGAAUAAAGUGUCCACAUUUAAGUUUAACAAACUUGCCGUCAUUUUA-C
(((.....)))........(((.(((((..........(((((.((((((.....)))))).))))).......(((((.....)))))))))))))....-. ( -23.90)
>DroMoj_CAF1 180291 103 + 1
CUACUGUUUGGAUUUUCUUCUGCACAGCAUCGAUCUCGGACACGCUGUGCUGCUCAAACAGCGUGUCCACAUCUAAUUGCAAUAGAUCGGUGCUCAUUGAUUU
....(((.((((......)))).)))((((((((((.(((((((((((.........))))))))))).((......))....)))))))))).......... ( -38.40)
>DroPer_CAF1 128458 102 + 1
CCACAGUCUGUAUCUUUUUGUGCACUACAUCGAUCUCGGAUACGCUGUGCUGCUCAAACAGCGUAUCCACAUUUAAAUUCAGUAGAUUUGCCGUCAUUUAU-U
.(((((...........)))))..((((...(....)(((((((((((.........))))))))))).............))))................-. ( -24.70)
>consensus
CCACCGUCUGGAUCUUCUUCUGCACAGCAUCGAUCUCGGACACGCUGUGCUGCUCAAACAGCGUGUCCACAUCUAAUUGCAAUAAAUCGGCCCUCAUUUAU_U
...(((((((..........((.....))........(((((((((((.........)))))))))))..............)))).)))............. (-17.92 = -17.32 +  -0.61)

alignment

secondary structure

dotplot

Window 8

Location	8,045,229 – 8,045,331
Length	102
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	77.98
Mean single sequence MFE	-30.94
Consensus MFE	-19.64
Energy contribution	-18.28
Covariance contribution	-1.35
Combinations/Pair	1.57
Mean z-score	-2.22
Structure conservation index	0.63
SVM decision value	1.43
SVM RNA-class probability	0.953478
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8045229 102 - 27905053
G-CUAAAUGACGGCCAAUUUGUUAAACCUGAACGUGGACACGCUGUUUGAGCAGCACAGCGUGUCCGAGAUAGACGAGGUGCACAAAAAGAUCCAGUCGGUGG
.-.....((((((....(((((...((((.....((((((((((((.........)))))))))))).........))))..))))).....)).)))).... ( -30.34)
>DroVir_CAF1 231640 102 - 1
A-AUAAAUGAGCGCCGAUUUACUGCAAUUAGAUGUGGACACGCUGUUCGAACAGCACGGCGUGUCCGAGAUCGAUGCUGUGCAGAAGAAAAUCCAAACGGUGG
.-.........(((((.....(((((....(((.((((((((((((.(.....).))))))))))))..))).......)))))..(......)...))))). ( -36.60)
>DroGri_CAF1 160773 99 - 1
----AAAUGAGCGCCGAUUUACUGCAAUUAGAUGUGGACACGCUGUUCGAGCAGCACGGCGUGUCCGAGAUCGAUGCGGUGCAGAAGAAAAUCCAAACGGUGG
----.......(((((...(((((((....(((.((((((((((((.(.....).))))))))))))..)))..)))))))..((......))....))))). ( -38.00)
>DroWil_CAF1 151534 102 - 1
G-UAAAAUGACGGCAAGUUUGUUAAACUUAAAUGUGGACACUUUAUUCGAACAGAAUAAUGUGUCGGAAAUCGAUGCCGUGCACAAAAAGAUCCAGACAGUGG
.-.....((((((((((((.....))))).......(((((.((((((.....)))))).)))))..........))))).)).........(((.....))) ( -23.50)
>DroMoj_CAF1 180291 103 - 1
AAAUCAAUGAGCACCGAUCUAUUGCAAUUAGAUGUGGACACGCUGUUUGAGCAGCACAGCGUGUCCGAGAUCGAUGCUGUGCAGAAGAAAAUCCAAACAGUAG
..............((((((...(((......)))(((((((((((.........))))))))))).)))))).((((((...((......))...)))))). ( -33.70)
>DroPer_CAF1 128458 102 - 1
A-AUAAAUGACGGCAAAUCUACUGAAUUUAAAUGUGGAUACGCUGUUUGAGCAGCACAGCGUAUCCGAGAUCGAUGUAGUGCACAAAAAGAUACAGACUGUGG
.-......((((((..((((((...........))))))..)))))).......(((((((((((((....)).(((.....)))....))))).).))))). ( -23.50)
>consensus
A_AUAAAUGACCGCCAAUUUACUGAAAUUAAAUGUGGACACGCUGUUCGAGCAGCACAGCGUGUCCGAGAUCGAUGCGGUGCACAAAAAAAUCCAAACGGUGG
............(((.(((((.......))))).((((((((((((.(.....).))))))))))))...............................))).. (-19.64 = -18.28 +  -1.35)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:59 2006