Locus 612

Sequence ID 3L_DroMel_CAF1
Location 1,776,802 – 1,776,971
Length 169
Max. P 0.819384
window938 window939 window940 window941

overview

Window 8

Location 1,776,802 – 1,776,908
Length 106
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 85.21
Mean single sequence MFE -43.23
Consensus MFE -31.90
Energy contribution -32.23
Covariance contribution 0.34
Combinations/Pair 1.21
Mean z-score -2.85
Structure conservation index 0.74
SVM decision value 0.46
SVM RNA-class probability 0.744108
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1776802 106 + 23771897
CCUUGCCAACCUUUUUAAAAUAGGCGACGAACUUUUGCUCCAGCUGGUGGUGCGGCACCUUCUCCAGUUGCGCAAGCAGCUGCAGCAGAUGCCUCUCUUCCGGCUU--------
..(((((...............)))))..............((((((.((.(.((((.((.((.(((((((....))))))).)).)).)))).).)).)))))).-------- ( -39.66)
>DroSec_CAF1 14111 106 + 1
CCUUGCUGCCCUUUUUAAAAUAGGCGACGAACUUCUGCUGCAGCUGGUAGUGCGGCACCUUCUCCAGUUGCGCAAGUAGCUGCAGCAGAUGCCUCUCUUCCGGCUU--------
..(((.((((..((....))..)))).)))...(((((((((((((.(.(((((((..........))))))).).))))))))))))).(((........)))..-------- ( -43.20)
>DroSim_CAF1 14078 106 + 1
CCUUGCUGCCCUUUUUAAAAUAGGCGACGAACUUCUGCUGCAGCUGGUGGUGCGGCACCUUCUCCAGUUGCUCAAGCAGCUGCAGCAGAUGCCUCUCUUCCGGCUU--------
..(((.((((..((....))..)))).)))...(((((((((((((.(((.(((((..........))))))))..))))))))))))).(((........)))..-------- ( -41.40)
>DroEre_CAF1 14083 106 + 1
CCUUUCCGCCCUUUCUGAAGUGGGCGACGAACUUGUGCUGCAACUGGUGGCGUGGCACCUUCUCCAGUUGCGCAAGCAGCUGCAGCAGAUGACUCUCUUCCGGCUU--------
((....(((((..........))))).....(.(.((((((....((((......))))......((((((....)))))))))))).).)..........))...-------- ( -36.60)
>DroYak_CAF1 14004 106 + 1
CCUUCCCGCUCUUUCUGAAGUGGGCGACAAACUUCUGCUGCAGCUGGGGGCGUGGCACCUUCUCCAGUUGCGCAAGCAGCUGCAGCAGAUGGCUCUCUUCCGGCUU--------
.....(((........((((.((((.(......(((((((((((((...(((..((..........))..)))...)))))))))))))).)))).)))))))...-------- ( -45.70)
>DroAna_CAF1 13626 114 + 1
CCUUCUGGCCUUUUUUGAAGUAGGCCACGAACUUCUGCUGCAGCUGUGGGCGGGGCACCUUCUCCAGGUGCACCAGCAGCUGCUGGAGAUGCUUCUCUUCCGGCUGGGGCAUGG
..(((((((((..........)))))).)))....((((.((((((..((.((((((.((((..(((.(((....))).)))..)))).)))))).))..)))))).))))... ( -52.80)
>consensus
CCUUGCCGCCCUUUUUAAAAUAGGCGACGAACUUCUGCUGCAGCUGGUGGCGCGGCACCUUCUCCAGUUGCGCAAGCAGCUGCAGCAGAUGCCUCUCUUCCGGCUU________
......((((............))))...............((((((.((.(.((((.((.((.(((((((....))))))).)).)).)))).).)).))))))......... (-31.90 = -32.23 +   0.34) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 1,776,802 – 1,776,908
Length 106
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 85.21
Mean single sequence MFE -40.23
Consensus MFE -30.76
Energy contribution -30.77
Covariance contribution 0.00
Combinations/Pair 1.32
Mean z-score -1.98
Structure conservation index 0.76
SVM decision value 0.08
SVM RNA-class probability 0.571362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1776802 106 - 23771897
--------AAGCCGGAAGAGAGGCAUCUGCUGCAGCUGCUUGCGCAACUGGAGAAGGUGCCGCACCACCAGCUGGAGCAAAAGUUCGUCGCCUAUUUUAAAAAGGUUGGCAAGG
--------..((((((.(((.(((((((.((.(((.(((....))).))).)).)))))))((.(((.....))).)).....))).))((((.........)))))))).... ( -36.80)
>DroSec_CAF1 14111 106 - 1
--------AAGCCGGAAGAGAGGCAUCUGCUGCAGCUACUUGCGCAACUGGAGAAGGUGCCGCACUACCAGCUGCAGCAGAAGUUCGUCGCCUAUUUUAAAAAGGGCAGCAAGG
--------..(((........))).((((((((((((...((((((.((.....)).)).)))).....)))))))))))).....((.((((..........)))).)).... ( -41.00)
>DroSim_CAF1 14078 106 - 1
--------AAGCCGGAAGAGAGGCAUCUGCUGCAGCUGCUUGAGCAACUGGAGAAGGUGCCGCACCACCAGCUGCAGCAGAAGUUCGUCGCCUAUUUUAAAAAGGGCAGCAAGG
--------..(((........))).((((((((((((((((.((...)).)))..((((...))))..))))))))))))).....((.((((..........)))).)).... ( -42.80)
>DroEre_CAF1 14083 106 - 1
--------AAGCCGGAAGAGAGUCAUCUGCUGCAGCUGCUUGCGCAACUGGAGAAGGUGCCACGCCACCAGUUGCAGCACAAGUUCGUCGCCCACUUCAGAAAGGGCGGAAAGG
--------....(((((((......)))((((((((((...(((..(((......)))....)))...)))))))))).....))))((((((..........))))))..... ( -35.10)
>DroYak_CAF1 14004 106 - 1
--------AAGCCGGAAGAGAGCCAUCUGCUGCAGCUGCUUGCGCAACUGGAGAAGGUGCCACGCCCCCAGCUGCAGCAGAAGUUUGUCGCCCACUUCAGAAAGAGCGGGAAGG
--------...((.((...((((..(((((((((((((...(((..(((......)))....)))...))))))))))))).)))).)).(((.(((......))).)))..)) ( -41.30)
>DroAna_CAF1 13626 114 - 1
CCAUGCCCCAGCCGGAAGAGAAGCAUCUCCAGCAGCUGCUGGUGCACCUGGAGAAGGUGCCCCGCCCACAGCUGCAGCAGAAGUUCGUGGCCUACUUCAAAAAAGGCCAGAAGG
((.(((.......(((.((......))))).(((((((..(((((((((.....))))))...)))..))))))).)))....(((.((((((..........))))))))))) ( -44.40)
>consensus
________AAGCCGGAAGAGAGGCAUCUGCUGCAGCUGCUUGCGCAACUGGAGAAGGUGCCGCACCACCAGCUGCAGCAGAAGUUCGUCGCCUACUUCAAAAAGGGCGGCAAGG
............(....).(((.(.(((((((((((((..((.(((.((.....)).)))))......))))))))))))).)))).((((((..........))))))..... (-30.76 = -30.77 +   0.00) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 1,776,842 – 1,776,935
Length 93
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 81.13
Mean single sequence MFE -31.05
Consensus MFE -18.77
Energy contribution -18.17
Covariance contribution -0.61
Combinations/Pair 1.44
Mean z-score -1.82
Structure conservation index 0.60
SVM decision value 0.14
SVM RNA-class probability 0.602210
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1776842 93 + 23771897
CAGCUGGUGGUGCGGCACCUUCUCCAGUUGCGCAAGCAGCUGCAGCAGAUGCC---UCUCUUCCGGCUUCGUCAUUUCUGUAUCUGACGCUUUGAG
.((((((.((.(.((((.((.((.(((((((....))))))).)).)).))))---.).)).)))))).(((((..........)))))....... ( -39.00)
>DroVir_CAF1 14973 88 + 1
UAGCUGAUAAAAAUCCACAAGUUCCAGUUUUUUAAGCAACUGCUCCAGCUGCUGCUCCUGUUCCAGUU-C--CAGUU-----CCAGUUGCUUUGCG
.(((((..................)))))....(((((((((....(((((..(((........))).-.--)))))-----.))))))))).... ( -18.47)
>DroSec_CAF1 14151 93 + 1
CAGCUGGUAGUGCGGCACCUUCUCCAGUUGCGCAAGUAGCUGCAGCAGAUGCC---UCUCUUCCGGCUUCGUCAUUUCUGUAUCUGCCGCUUUGAG
.(((.((((((((((((.((.((.(((((((....))))))).)).)).))))---........(((...)))......))).))))))))..... ( -33.80)
>DroSim_CAF1 14118 93 + 1
CAGCUGGUGGUGCGGCACCUUCUCCAGUUGCUCAAGCAGCUGCAGCAGAUGCC---UCUCUUCCGGCUUCGUCAUUUCUGUAUCUGCCGCUUUGAG
.((((((.((.(.((((.((.((.(((((((....))))))).)).)).))))---.).)).))))))............................ ( -32.10)
>DroEre_CAF1 14123 93 + 1
CAACUGGUGGCGUGGCACCUUCUCCAGUUGCGCAAGCAGCUGCAGCAGAUGAC---UCUCUUCCGGCUUCGUCAUUUCUGUAUCUCCCGCUUUGAG
...((.(.((((.((.........(((((((....)))))))(((.(((((((---..............)))))))))).....)))))).).)) ( -28.84)
>DroYak_CAF1 14044 93 + 1
CAGCUGGGGGCGUGGCACCUUCUCCAGUUGCGCAAGCAGCUGCAGCAGAUGGC---UCUCUUCCGGCUUCGUCAUUUCUGUAUCUGCCGCUUUGAG
.(((((((((.(.(.((.((.((.(((((((....))))))).)).)).)).)---.).)))))))))............................ ( -34.10)
>consensus
CAGCUGGUGGUGCGGCACCUUCUCCAGUUGCGCAAGCAGCUGCAGCAGAUGCC___UCUCUUCCGGCUUCGUCAUUUCUGUAUCUGCCGCUUUGAG
.((((((.((..........(((.(((((((....)))))))....)))..........)).))))))............................ (-18.77 = -18.17 +  -0.61) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 1,776,879 – 1,776,971
Length 92
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 95.29
Mean single sequence MFE -26.07
Consensus MFE -23.05
Energy contribution -23.80
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.88
SVM decision value 0.68
SVM RNA-class probability 0.819384
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1776879 92 - 23771897
GCACAGAAAAUAGAUCACCGGAACAUGACUGCAGAGCUCAAAGCGUCAGAUACAGAAAUGACGAAGCCGGAAGAGAGGCAUCUGCUGCAGCU
............................((((((.((.....))..(((((.((....)).....(((........)))))))))))))).. ( -21.30)
>DroSec_CAF1 14188 92 - 1
GCACAGAAAAUAGAUCACCGGAUCAUGGCCGCAGAGCUCAAAGCGGCAGAUACAGAAAUGACGAAGCCGGAAGAGAGGCAUCUGCUGCAGCU
((..........((((....)))).((((......)).))..(((((((((.((....)).....(((........)))))))))))).)). ( -28.50)
>DroSim_CAF1 14155 92 - 1
GCACAGAAAAUAGAUCACCGGAUCAUGACCGCAGAGCUCAAAGCGGCAGAUACAGAAAUGACGAAGCCGGAAGAGAGGCAUCUGCUGCAGCU
((..........((((....)))).(((.(.....).)))..(((((((((.((....)).....(((........)))))))))))).)). ( -27.90)
>DroYak_CAF1 14081 92 - 1
GCGCAGAAAAUAGAUCACCAGAUCAUGCCCACAGAGCUCAAAGCGGCAGAUACAGAAAUGACGAAGCCGGAAGAGAGCCAUCUGCUGCAGCU
((((((......((((....)))).......((((((((....((((.....((....)).....)))).....))))..)))))))).)). ( -26.60)
>consensus
GCACAGAAAAUAGAUCACCGGAUCAUGACCGCAGAGCUCAAAGCGGCAGAUACAGAAAUGACGAAGCCGGAAGAGAGGCAUCUGCUGCAGCU
((..........((((....))))..................(((((((((.((....)).....(((........)))))))))))).)). (-23.05 = -23.80 +   0.75) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:43 2006