Locus 5349

Sequence ID	2L_DroMel_CAF1
Location	15,145,241 – 15,145,337
Length	96
Max. P	0.748515

overview

Window 7

Location	15,145,241 – 15,145,337
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.05
Mean single sequence MFE	-31.70
Consensus MFE	-19.44
Energy contribution	-19.97
Covariance contribution	0.53
Combinations/Pair	1.05
Mean z-score	-1.60
Structure conservation index	0.61
SVM decision value	0.27
SVM RNA-class probability	0.662360
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15145241 96 + 22407834
------GCACUCACUUCCUC----------UGCAGCCUCGGCACAUGCAAUUUAUAGCCGCACGUGGUUGUUG-----CAUGUAUCACGUGACACUUGAUUUCCGGCGCAGUUG---GUU
------..........((.(----------(((.(((.....(((((((....(((((((....)))))))))-----)))))((((.(.....).))))....)))))))..)---).. ( -28.20)
>DroVir_CAF1 121309 100 + 1
----------CUGCUGUUGC----------UGCUGCCUCGGCACAUGCAAUUUAUAGCCGCACGUGGUUGUUGCAUUGCAUGUAUCACGUGACACUUGAUUUCCGGCGCAGUUCCCAGUU
----------..((((..((----------(((.(((.....(((((((((..(((((((....)))))))...)))))))))((((.(.....).))))....))))))))...)))). ( -35.70)
>DroPse_CAF1 109769 102 + 1
CUGGUUGCUGCUGCUGCUGC----------UGCAGCCUCGGCACAUGCAAUUUAUAGCCGCACGUGGUUGUUG-----CAUGUAUCACGUGACACUUGAUUUCCGGCGCAGUUG---GUU
((..((((.((.(((((...----------.)))))..(((.(((((((....(((((((....)))))))))-----)))))((((.(.....).))))..)))))))))..)---).. ( -35.40)
>DroWil_CAF1 155159 92 + 1
----------UGCCUGCCUG----------CUCAGCCUCGGCACAUGCAAUUUAUAGCCGCACGUGGUUGUUG-----CAUGUAUCACGUGACACUUGAUUUCCGGCACAGUUG---GCU
----------.....(((.(----------((..(((.....(((((((....(((((((....)))))))))-----)))))((((.(.....).))))....)))..))).)---)). ( -28.00)
>DroMoj_CAF1 128431 90 + 1
------------------------------UGCUGGCUUGGCACAUGCAAUUUAUAGCCGCACGUGGUUGUUGCAUUGCAUGUAUCACGUGACACUUGAUUUCCGGCGCAGUUGCCAGCU
------------------------------.((((((...(((((((((((..(((((((....)))))))...)))))))))((((.(.....).)))).......))....)))))). ( -34.60)
>DroAna_CAF1 96605 106 + 1
------ACAUCCACUUCCUCUUGUUGCUGCUGCAGCCUCGGCACAUGCAAUUUAUAGCCGCACGUGGUUGUUG-----CAUGUAUCACGUGACACUUGAUUUCCGGCGCAGUUG---GUU
------....................(.(((((.(((.....(((((((....(((((((....)))))))))-----)))))((((.(.....).))))....)))))))).)---... ( -28.30)
>consensus
__________CCACUGCCUC__________UGCAGCCUCGGCACAUGCAAUUUAUAGCCGCACGUGGUUGUUG_____CAUGUAUCACGUGACACUUGAUUUCCGGCGCAGUUG___GUU
..............................(((.(((.((((..............))))((((((((...((.....))...)))))))).............)))))).......... (-19.44 = -19.97 +   0.53)

alignment

secondary structure

dotplot

Window 8

Location	15,145,241 – 15,145,337
Length	96
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.05
Mean single sequence MFE	-29.25
Consensus MFE	-20.08
Energy contribution	-20.13
Covariance contribution	0.06
Combinations/Pair	1.10
Mean z-score	-1.45
Structure conservation index	0.69
SVM decision value	0.47
SVM RNA-class probability	0.748515
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15145241 96 - 22407834
AAC---CAACUGCGCCGGAAAUCAAGUGUCACGUGAUACAUG-----CAACAACCACGUGCGGCUAUAAAUUGCAUGUGCCGAGGCUGCA----------GAGGAAGUGAGUGC------
..(---(..(((((((.........(((((....)))))...-----.......(((((((((.......)))))))))....))).)))----------).))..........------ ( -27.10)
>DroVir_CAF1 121309 100 - 1
AACUGGGAACUGCGCCGGAAAUCAAGUGUCACGUGAUACAUGCAAUGCAACAACCACGUGCGGCUAUAAAUUGCAUGUGCCGAGGCAGCA----------GCAACAGCAG----------
..(((....(((((((((.......(((((....))))).(((...)))....))((((((((.......)))))))).....))).)))----------)...)))...---------- ( -28.60)
>DroPse_CAF1 109769 102 - 1
AAC---CAACUGCGCCGGAAAUCAAGUGUCACGUGAUACAUG-----CAACAACCACGUGCGGCUAUAAAUUGCAUGUGCCGAGGCUGCA----------GCAGCAGCAGCAGCAACCAG
...---...((((..(((.......(((((....)))))...-----.......(((((((((.......))))))))))))..(((((.----------...))))).))))....... ( -32.70)
>DroWil_CAF1 155159 92 - 1
AGC---CAACUGUGCCGGAAAUCAAGUGUCACGUGAUACAUG-----CAACAACCACGUGCGGCUAUAAAUUGCAUGUGCCGAGGCUGAG----------CAGGCAGGCA----------
.((---(..((((..(((...((..(((((....)))))...-----.......(((((((((.......)))))))))..))..))).)----------)))...))).---------- ( -29.70)
>DroMoj_CAF1 128431 90 - 1
AGCUGGCAACUGCGCCGGAAAUCAAGUGUCACGUGAUACAUGCAAUGCAACAACCACGUGCGGCUAUAAAUUGCAUGUGCCAAGCCAGCA------------------------------
.((((((....((((..(....)..))))....((.((((((((((((..((......))..)).....)))))))))).)).)))))).------------------------------ ( -30.10)
>DroAna_CAF1 96605 106 - 1
AAC---CAACUGCGCCGGAAAUCAAGUGUCACGUGAUACAUG-----CAACAACCACGUGCGGCUAUAAAUUGCAUGUGCCGAGGCUGCAGCAGCAACAAGAGGAAGUGGAUGU------
..(---((.((...((((.......(((((....)))))...-----.......(((((((((.......)))))))))))(..((((...))))..)....)).)))))....------ ( -27.30)
>consensus
AAC___CAACUGCGCCGGAAAUCAAGUGUCACGUGAUACAUG_____CAACAACCACGUGCGGCUAUAAAUUGCAUGUGCCGAGGCUGCA__________GAGGCAGCAG__________
..........((((((.........(((((....)))))...............(((((((((.......)))))))))....))).))).............................. (-20.08 = -20.13 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:01 2006