Locus 3683

Sequence ID	3L_DroMel_CAF1
Location	10,748,229 – 10,748,411
Length	182
Max. P	0.998353

overview

Window 6

Location	10,748,229 – 10,748,331
Length	102
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	88.19
Mean single sequence MFE	-33.81
Consensus MFE	-24.41
Energy contribution	-24.63
Covariance contribution	0.22
Combinations/Pair	1.08
Mean z-score	-3.07
Structure conservation index	0.72
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10748229 102 + 23771897
GCUGCUCAA-AGUGCAGUGCGGCUCAAAACAAAGUUAUUACGGCCUAAG------------CUUUGUUUGCCUUUCUGGCUCAUGGCAAA-----AAACCCACAUGGCCAGAUCGGCCCC
(((((.(..-......).)))))...((((((((((...........))------------))))))))(((..((((((.((((.....-----.......))))))))))..)))... ( -35.50)
>DroSec_CAF1 81729 102 + 1
GCUGCUCAA-ACUGCAGUGCGGCUCAAAACAAAGUUAUUACGGCCUAAG------------CUUUGUUUGCCUUUCUGGCUCAUGGCAAA-----AAACCCACAUGACCAGAUCGGCCCC
(((((.(..-......).)))))...((((((((((...........))------------))))))))(((..(((((.(((((.....-----.......))))))))))..)))... ( -33.40)
>DroSim_CAF1 84355 102 + 1
GCUGCUCAA-ACUGCAGUGCGGCUCAAAACAAAGUUAUUACGGCCUAAG------------CUUUGUUUGCCUUUCUGGCUCAUGGCAAA-----AAACCCACAUGGCCAGAUCGGCCCC
(((((.(..-......).)))))...((((((((((...........))------------))))))))(((..((((((.((((.....-----.......))))))))))..)))... ( -35.50)
>DroEre_CAF1 86635 104 + 1
GCAGCACAAAACUGCAGUGCGGCCCAAAACAAAGUUAUUACGGCCUAAG------------CUUUGUUUGCCUUUCUGGCUCAUGGCAAAA----AAACCCACAUGGCCAGAUCGGCCCC
((.((((.........)))).))...((((((((((...........))------------))))))))(((..((((((.((((......----.......))))))))))..)))... ( -34.32)
>DroYak_CAF1 97278 107 + 1
GCUGCUCAA-AGUGCAGUGCGGCCCAAAACAAAGUUAUUACGGCCUAAG------------CUUUGUUUGCCUUUCUGGCUCAUGGCAAAAAAAAAAACCCACAUGGCCAGAUCGGCCCC
(((((....-...)))))..((((..((((((((((...........))------------)))))))).....((((((.((((.................))))))))))..)))).. ( -35.23)
>DroAna_CAF1 84136 112 + 1
GC--CUCAA-ACUGCA-----GCUCAAAACAAAGUUAUUACGGCCUAAGCUCGGGCCUAGGCUUUGUUUGCCUUUCUGGCUUAUGGCUAAAAAAAAAACCCACAUGACCAGAUCAGCACC
((--.....-...)).-----.....(((((((((..(((.(((((......)))))))))))))))))((...(((((.(((((.................))))))))))...))... ( -28.93)
>consensus
GCUGCUCAA_ACUGCAGUGCGGCUCAAAACAAAGUUAUUACGGCCUAAG____________CUUUGUUUGCCUUUCUGGCUCAUGGCAAA_____AAACCCACAUGGCCAGAUCGGCCCC
(((((.............)))))...((((((((...........................))))))))(((..(((((.(((((.................))))))))))..)))... (-24.41 = -24.63 +   0.22)

alignment

secondary structure

dotplot

Window 7

Location	10,748,268 – 10,748,371
Length	103
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	90.43
Mean single sequence MFE	-24.45
Consensus MFE	-22.89
Energy contribution	-23.09
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.94
SVM decision value	3.08
SVM RNA-class probability	0.998353
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10748268 103 + 23771897
CGGCCUAAGCUUUGUUUGCCUUUCUGGCUCAUGGCAAA-----AAACCCACAUGGCCAGAUCGGCCCCAGAUUUGCCCAAGCAUCAGUAUAUAUAUAUUUUUUCUUUU
.(((..(((.((((...(((..((((((.((((.....-----.......))))))))))..)))..))))))))))............................... ( -24.80)
>DroSec_CAF1 81768 98 + 1
CGGCCUAAGCUUUGUUUGCCUUUCUGGCUCAUGGCAAA-----AAACCCACAUGACCAGAUCGGCCCCAGAUUUGCCCCAGCAUAAGUAUCU----UUU-UUUUUACU
.((..((((.((((...(((..(((((.(((((.....-----.......))))))))))..)))..))))))))..)).............----...-........ ( -22.90)
>DroSim_CAF1 84394 99 + 1
CGGCCUAAGCUUUGUUUGCCUUUCUGGCUCAUGGCAAA-----AAACCCACAUGGCCAGAUCGGCCCCAGAUUUGCCCCAGCAUCAGUAUCU----UUUUUUUUUACU
.((..((((.((((...(((..((((((.((((.....-----.......))))))))))..)))..))))))))..)).............----............ ( -25.00)
>DroEre_CAF1 86675 94 + 1
CGGCCUAAGCUUUGUUUGCCUUUCUGGCUCAUGGCAAAA----AAACCCACAUGGCCAGAUCGGCCCCAGAUUUGCCCCAGCAUCAGUAUCU----UUU-UUU-----
.((..((((.((((...(((..((((((.((((......----.......))))))))))..)))..))))))))..)).............----...-...----- ( -24.92)
>DroYak_CAF1 97317 101 + 1
CGGCCUAAGCUUUGUUUGCCUUUCUGGCUCAUGGCAAAAAAAAAAACCCACAUGGCCAGAUCGGCCCCAGAUUUGCCCCAGCAUCAGUAUCU----UUU-UUU--UUU
.((..((((.((((...(((..((((((.((((.................))))))))))..)))..))))))))..)).............----...-...--... ( -24.63)
>consensus
CGGCCUAAGCUUUGUUUGCCUUUCUGGCUCAUGGCAAA_____AAACCCACAUGGCCAGAUCGGCCCCAGAUUUGCCCCAGCAUCAGUAUCU____UUU_UUU_UACU
.(((..(((.((((...(((..((((((.((((.................))))))))))..)))..))))))))))............................... (-22.89 = -23.09 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	10,748,268 – 10,748,371
Length	103
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	90.43
Mean single sequence MFE	-28.70
Consensus MFE	-27.30
Energy contribution	-27.14
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.84
Structure conservation index	0.95
SVM decision value	2.57
SVM RNA-class probability	0.995399
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10748268 103 - 23771897
AAAAGAAAAAAUAUAUAUAUACUGAUGCUUGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUU-----UUUGCCAUGAGCCAGAAAGGCAAACAAAGCUUAGGCCG
..........................((((((((.....((..(((..((((((((((.(.(...-----..).))))).))))))..)))...))..)))))))).. ( -31.30)
>DroSec_CAF1 81768 98 - 1
AGUAAAAA-AAA----AGAUACUUAUGCUGGGGCAAAUCUGGGGCCGAUCUGGUCAUGUGGGUUU-----UUUGCCAUGAGCCAGAAAGGCAAACAAAGCUUAGGCCG
........-...----..........(((..(((.....((..(((..((((((((((.(.(...-----..).)))))).)))))..)))...))..)))..))).. ( -26.40)
>DroSim_CAF1 84394 99 - 1
AGUAAAAAAAAA----AGAUACUGAUGCUGGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUU-----UUUGCCAUGAGCCAGAAAGGCAAACAAAGCUUAGGCCG
............----..........(((..(((.....((..(((..((((((((((.(.(...-----..).))))).))))))..)))...))..)))..))).. ( -28.50)
>DroEre_CAF1 86675 94 - 1
-----AAA-AAA----AGAUACUGAUGCUGGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUU----UUUUGCCAUGAGCCAGAAAGGCAAACAAAGCUUAGGCCG
-----...-...----..........(((..(((.....((..(((..((((((((((.(.(...----...).))))).))))))..)))...))..)))..))).. ( -28.70)
>DroYak_CAF1 97317 101 - 1
AAA--AAA-AAA----AGAUACUGAUGCUGGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUUUUUUUUUUGCCAUGAGCCAGAAAGGCAAACAAAGCUUAGGCCG
...--...-...----..........(((..(((.....((..(((..((((((((((..((........))..).))).))))))..)))...))..)))..))).. ( -28.60)
>consensus
AAAA_AAA_AAA____AGAUACUGAUGCUGGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUU_____UUUGCCAUGAGCCAGAAAGGCAAACAAAGCUUAGGCCG
..........................(((..(((.....((..(((..((((((((((..((........))..).))).))))))..)))...))..)))..))).. (-27.30 = -27.14 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	10,748,296 – 10,748,411
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.69
Mean single sequence MFE	-31.01
Consensus MFE	-26.56
Energy contribution	-26.64
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.62
Structure conservation index	0.86
SVM decision value	0.92
SVM RNA-class probability	0.882554
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10748296 115 - 23771897
CAUGUGGUUGGGGGCUAAUGCUGAGGCUAAAAACAGACAGAAAAGAAAAAAUAUAUAUAUACUGAUGCUUGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUU-----UUUGCCAUGA
((((((((..(((((....)))..((((.....(((((((.....................))).(((....)))..)))).))))..))..))))))))(((..-----...))).... ( -32.40)
>DroSec_CAF1 81796 110 - 1
CAUGUGGUUGGGGGCUAAUGCUGAGGCUAAAAACAGAAAGAGUAAAAA-AAA----AGAUACUUAUGCUGGGGCAAAUCUGGGGCCGAUCUGGUCAUGUGGGUUU-----UUUGCCAUGA
(((((((..((((((....)))..((((.....((((..(((((....-...----...))))).(((....)))..)))).))))..)))..)))))))(((..-----...))).... ( -29.80)
>DroSim_CAF1 84422 111 - 1
CAUGUGGUUGGGGGCUAAUGCUGAGGCUAAAAACAGAAAGAGUAAAAAAAAA----AGAUACUGAUGCUGGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUU-----UUUGCCAUGA
((((((((..(((((....)))..((((.....((((...((((........----...))))..(((....)))..)))).))))..))..))))))))(((..-----...))).... ( -33.00)
>DroEre_CAF1 86703 104 - 1
CAUGUGGUUGGGGGCUAAUGCUGAGGCUAAAAACCGAA-------AAA-AAA----AGAUACUGAUGCUGGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUU----UUUUGCCAUGA
((((((((..((((((..((((..(((...........-------...-...----..........)))..)))).......))))..))..))))))))(((..----....))).... ( -28.43)
>DroYak_CAF1 97345 113 - 1
CAUGUGGUUGGGGGCUAAUGCCGAGGCUAAAAACAGAAAGAAA--AAA-AAA----AGAUACUGAUGCUGGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUUUUUUUUUUGCCAUGA
((((((((..(((((....)))..((((.....((((......--...-...----((...))..(((....)))..)))).))))..))..))))))))(((..........))).... ( -31.40)
>consensus
CAUGUGGUUGGGGGCUAAUGCUGAGGCUAAAAACAGAAAGAAAA_AAA_AAA____AGAUACUGAUGCUGGGGCAAAUCUGGGGCCGAUCUGGCCAUGUGGGUUU_____UUUGCCAUGA
((((((((..(((((....)))..((((.....((((...................((...))..(((....)))..)))).))))..))..))))))))(((..........))).... (-26.56 = -26.64 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:08 2006