Locus 8044

Sequence ID	3L_DroMel_CAF1
Location	21,214,701 – 21,214,861
Length	160
Max. P	0.650847

overview

Window 2

Location	21,214,701 – 21,214,821
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.61
Mean single sequence MFE	-34.87
Consensus MFE	-31.49
Energy contribution	-31.61
Covariance contribution	0.13
Combinations/Pair	1.07
Mean z-score	-1.36
Structure conservation index	0.90
SVM decision value	-0.03
SVM RNA-class probability	0.520057
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21214701 120 + 23771897
GCAACUGCUGUUGACUAGGGCCGGUGUGUCCUCCACCUCGGCAUUCUUUUCAAUUACCUUGCCACUAACGGGUGAAUACACCUCGCUAGCCGCUUUAACGCUCUCCAGGGCCCCACAUUC
.((((....))))....((((((((((((....((((..((((................)))).(....))))).))))))).........((......)).......)))))....... ( -33.59)
>DroSim_CAF1 81763 120 + 1
GCAACUGCUGUUGACCAGGGCCGGUGUGUCCUCCACCUCGGCAUUCUUUUCGAUCACCUUGCCACUAACGGGUGAAUACACCUCGCUAGCAGCUUUCACGCUCUCCAGGGCCCCACAUUC
......(((((((.(.((((((((.(((.....))).)))))...........((((((..........)))))).....))).).)))))))......((((....))))......... ( -34.70)
>DroEre_CAF1 34341 120 + 1
GCAACUACUGUUGACCAGGGCCGGUGUGUCCUCCACCUGGGCAUUCUUUUCGAUCACCUUGCCGCUAACGGGUGAAUACACCUCGCUAGCAGCUUUUACGCUCUCCAGGGCUCCACAUUC
.((((....))))....((((((((((((((.......))))).((.....)).))))..((.((((.((((((....)))).)).)))).))...............))).))...... ( -35.80)
>DroYak_CAF1 141023 120 + 1
GCAACUACUGUUGACCAGGGCCGGUGUGUCCUCCACCAGAGCAUUCUUUUCGAUCACCUUGCCGCUAACUGGUGAAUACACCUCGCUGGCCGCUUUCACGCUCUCCAGGGCUCCACAUUC
.((((....))))....((((((((((((....(((((((((.....................)))..)))))).)))))))...((((..((......))...))))))).))...... ( -35.40)
>consensus
GCAACUACUGUUGACCAGGGCCGGUGUGUCCUCCACCUCGGCAUUCUUUUCGAUCACCUUGCCACUAACGGGUGAAUACACCUCGCUAGCAGCUUUCACGCUCUCCAGGGCCCCACAUUC
.((((....))))....((((((((((((....((((((((((................)))).....)))))).)))))))..((.....))...............)))))....... (-31.49 = -31.61 +   0.13)

alignment

secondary structure

dotplot

Window 3

Location	21,214,701 – 21,214,821
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.61
Mean single sequence MFE	-43.00
Consensus MFE	-38.35
Energy contribution	-38.85
Covariance contribution	0.50
Combinations/Pair	1.14
Mean z-score	-1.51
Structure conservation index	0.89
SVM decision value	0.24
SVM RNA-class probability	0.650847
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21214701 120 - 23771897
GAAUGUGGGGCCCUGGAGAGCGUUAAAGCGGCUAGCGAGGUGUAUUCACCCGUUAGUGGCAAGGUAAUUGAAAAGAAUGCCGAGGUGGAGGACACACCGGCCCUAGUCAACAGCAGUUGC
.....(((((((...............((.(((((((.((((....))))))))))).))..((((.((.....)).))))..((((.......)))))))))))..((((....)))). ( -44.80)
>DroSim_CAF1 81763 120 - 1
GAAUGUGGGGCCCUGGAGAGCGUGAAAGCUGCUAGCGAGGUGUAUUCACCCGUUAGUGGCAAGGUGAUCGAAAAGAAUGCCGAGGUGGAGGACACACCGGCCCUGGUCAACAGCAGUUGC
......((((((...............((..((((((.((((....))))))))))..))..((((.((.....)).))))..((((.......))))))))))...((((....)))). ( -45.80)
>DroEre_CAF1 34341 120 - 1
GAAUGUGGAGCCCUGGAGAGCGUAAAAGCUGCUAGCGAGGUGUAUUCACCCGUUAGCGGCAAGGUGAUCGAAAAGAAUGCCCAGGUGGAGGACACACCGGCCCUGGUCAACAGUAGUUGC
......((.(((((((...((((....((((((((((.((((....)))))))))))))).......((.....))))))))))(((.....)))...)))))....((((....)))). ( -43.30)
>DroYak_CAF1 141023 120 - 1
GAAUGUGGAGCCCUGGAGAGCGUGAAAGCGGCCAGCGAGGUGUAUUCACCAGUUAGCGGCAAGGUGAUCGAAAAGAAUGCUCUGGUGGAGGACACACCGGCCCUGGUCAACAGUAGUUGC
......((.(((....(((((((....((.((.(((..((((....)))).))).)).)).......((.....)))))))))((((.......)))))))))....((((....)))). ( -38.10)
>consensus
GAAUGUGGAGCCCUGGAGAGCGUGAAAGCGGCUAGCGAGGUGUAUUCACCCGUUAGCGGCAAGGUGAUCGAAAAGAAUGCCCAGGUGGAGGACACACCGGCCCUGGUCAACAGCAGUUGC
.....(((((((...............((((((((((.((((....))))))))))))))..((((.((.....)).))))..((((.......)))))))))))..((((....)))). (-38.35 = -38.85 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	21,214,741 – 21,214,861
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.17
Mean single sequence MFE	-40.75
Consensus MFE	-36.47
Energy contribution	-37.97
Covariance contribution	1.50
Combinations/Pair	1.06
Mean z-score	-1.40
Structure conservation index	0.90
SVM decision value	-0.03
SVM RNA-class probability	0.519251
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21214741 120 - 23771897
CCAACUCCCAGAACCCGGCACGGAACUCAAGCAGGAUGACGAAUGUGGGGCCCUGGAGAGCGUUAAAGCGGCUAGCGAGGUGUAUUCACCCGUUAGUGGCAAGGUAAUUGAAAAGAAUGC
((..(((((((..(((.(((((..(..(.....)..)..))..))).)))..)))).))).......((.(((((((.((((....))))))))))).))..))................ ( -42.40)
>DroSim_CAF1 81803 120 - 1
CCAGCUCCCAGAACCCGGCACGGAACUCAAGCAGGAUGACGAAUGUGGGGCCCUGGAGAGCGUGAAAGCUGCUAGCGAGGUGUAUUCACCCGUUAGUGGCAAGGUGAUCGAAAAGAAUGC
((.((((((((..(((.(((((..(..(.....)..)..))..))).)))..)))).))))......((..((((((.((((....))))))))))..))..))................ ( -47.70)
>DroEre_CAF1 34381 120 - 1
UCAGCUGCCAGAACCCGGCACGGAACUCAAGCAGGAUGACGAAUGUGGAGCCCUGGAGAGCGUAAAAGCUGCUAGCGAGGUGUAUUCACCCGUUAGCGGCAAGGUGAUCGAAAAGAAUGC
((((((.((((..(.(.(((((..(..(.....)..)..))..))).).)..))))..)))......((((((((((.((((....))))))))))))))....)))............. ( -39.10)
>DroYak_CAF1 141063 120 - 1
UCAGCUCCCAGAACCCGGCACGGAACUCAAACAGGAUGACGAAUGUGGAGCCCUGGAGAGCGUGAAAGCGGCCAGCGAGGUGUAUUCACCAGUUAGCGGCAAGGUGAUCGAAAAGAAUGC
(((((((((((..(.(.(((((..(..(.....)..)..))..))).).)..)))).)))).)))..((.((.(((..((((....)))).))).)).)).................... ( -33.80)
>consensus
CCAGCUCCCAGAACCCGGCACGGAACUCAAGCAGGAUGACGAAUGUGGAGCCCUGGAGAGCGUGAAAGCGGCUAGCGAGGUGUAUUCACCCGUUAGCGGCAAGGUGAUCGAAAAGAAUGC
((.((((((((..(((.(((((..(..(.....)..)..))..))).)))..)))).))))......((((((((((.((((....))))))))))))))..))................ (-36.47 = -37.97 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:43 2006