Locus 6182

Sequence ID	3R_DroMel_CAF1
Location	16,178,640 – 16,178,782
Length	142
Max. P	0.671653

overview

Window 3

Location	16,178,640 – 16,178,742
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.40
Mean single sequence MFE	-34.58
Consensus MFE	-18.38
Energy contribution	-19.72
Covariance contribution	1.34
Combinations/Pair	1.26
Mean z-score	-1.70
Structure conservation index	0.53
SVM decision value	0.15
SVM RNA-class probability	0.605322
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16178640 102 - 27905053
AGGA--AACUUAAAUAAAAGUCGGCCAGAAGUUGUCUGCUCCUGGGAUUGCCCUCGAAAGGGGCGGCACCAGUGGGAAAACUGCGUGGG----------------GUAAACGUGGAGCUA
((..--..))............(((((((.....))))(((((((..((((((.(....)))))))..)))).)))....(..(((...----------------....)))..).))). ( -34.60)
>DroPse_CAF1 8203 113 - 1
AGGUAGAACUGAAAUAAAAGGCAAGCAAAAGUGGUCUGCUCUUGGU-----C--CCAGAGAGGCAAGGAUUGGAGGAAAACUGCGUGCGUGUGAAAUAGUUGUGGACUCACAAACGGCAC
........(((.........(((.(((...(..((...(..(..((-----(--(..(.....)..))))..)..)...))..).))).))).......(((((....))))).)))... ( -23.50)
>DroSec_CAF1 7912 102 - 1
AGGA--AACUUAAAUAAAAGUCGGCCAGAAGAUGUCUGCUCCUGGGAUUGCCCUCGAAAGGGGCGGGGCCAGUGGGAAAACUGCGUGGG----------------GAAAAUGUGCGGCUG
((..--..))........(((((..((((.....))))(((((((..((((((.(....)))))))..)))(..(.....)..)..)))----------------)........))))). ( -33.60)
>DroSim_CAF1 1319 102 - 1
AGGA--AACUUAAAUAAAAGUCGGCCAGAAGUUGUCUGCUCCUGGGAUUGCCCUUGAAAGGGGCGGGGACAGUGGGAAAACUGCGUGGG----------------GUAAACGUGCGGCUG
((..--..))...........(((((...((((.....((((((...(((((((.....)))))))...))).)))..))))(((((..----------------.....)))))))))) ( -31.60)
>DroEre_CAF1 6794 103 - 1
AGGA-AAACUUAAAUAAAAGUCGGGCAGAAGUUGCCUGCUCCUGGGAUGGCCCUCGAAAGGGGCGGGGCCAGCGGGAAAACUGCGUGGG----------------GCAAGCUACCGGCGG
....-..............(((((((....)).((.(((((((((..(.((((.(....))))).)..)))((((.....))))..)))----------------))).))..))))).. ( -40.70)
>DroYak_CAF1 8756 103 - 1
AGGA-AAACUUAAAUAAAAGUCGGGCAGAAGUUGUCUGCUCCUGGGACUGCCCUCGAAAGGGGCGGGGCCAGCGGGAAAACUGCGUGGG----------------GCGAGCUACCGGCUG
....-.............((((((((....)).(..(((((((((..((((((.(....)))))))..)))((((.....))))..)))----------------)))..)..)))))). ( -43.50)
>consensus
AGGA__AACUUAAAUAAAAGUCGGCCAGAAGUUGUCUGCUCCUGGGAUUGCCCUCGAAAGGGGCGGGGCCAGUGGGAAAACUGCGUGGG________________GCAAACGAGCGGCUG
...................((((...........((((((((((((....))).....))))))))).(((((((.....)))).)))..........................)))).. (-18.38 = -19.72 +   1.34)

alignment

secondary structure

dotplot

Window 4

Location	16,178,664 – 16,178,782
Length	118
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	88.88
Mean single sequence MFE	-31.76
Consensus MFE	-23.45
Energy contribution	-23.85
Covariance contribution	0.40
Combinations/Pair	1.10
Mean z-score	-1.54
Structure conservation index	0.74
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16178664 118 + 27905053
UUUUCCCACUGGUGCCGCCCCUUUCGAGGGCAAUCCCAGGAGCAGACAACUUCUGGCCGACUUUUAUUUAAGUU-UCCUUCACCUUUCCAGAACUCAGAACUAAGGACUCGGGACUUAG
...((((...((((..(((((....).))))....(((((((.......)))))))..(((((......)))))-.....))))..(((...............)))...))))..... ( -28.76)
>DroSec_CAF1 7936 111 + 1
UUUUCCCACUGGCCCCGCCCCUUUCGAGGGCAAUCCCAGGAGCAGACAUCUUCUGGCCGACUUUUAUUUAAGUU-UCCUUCACCUUUCCAGAA-------CUCAGGACUCGGGACUUAG
...((((.((((....(((((....).))))....))))((((.......((((((..(((((......)))))-............))))))-------.....).)))))))..... ( -27.54)
>DroSim_CAF1 1343 118 + 1
UUUUCCCACUGUCCCCGCCCCUUUCAAGGGCAAUCCCAGGAGCAGACAACUUCUGGCCGACUUUUAUUUAAGUU-UCCUUCACCUUUCCAGAACUCAGAACUCAGGACUCGGGACUUAG
...((((...((((..((((.......))))....(((((((.......)))))))..(((((......)))))-.............................))))..))))..... ( -28.70)
>DroEre_CAF1 6818 119 + 1
UUUUCCCGCUGGCCCCGCCCCUUUCGAGGGCCAUCCCAGGAGCAGGCAACUUCUGCCCGACUUUUAUUUAAGUUUUCCUUCACCUUGCCGGAAUUCAGAACUGAGGACUAGGGACUUAG
...((((..((((((((.......)).))))))((((((((((.((((.....)))).).)))........(..((((..(.....)..))))..)....))).)))...))))..... ( -35.30)
>DroYak_CAF1 8780 112 + 1
UUUUCCCGCUGGCCCCGCCCCUUUCGAGGGCAGUCCCAGGAGCAGACAACUUCUGCCCGACUUUUAUUUAAGUUUUCCUUCACCUU-------UUCAGAACUGAGGACUCGGGGCUUAG
..........(((((((((((....).))))(((((((((.(((((.....))))).)(((((......)))))............-------.......))).))))).))))))... ( -38.50)
>consensus
UUUUCCCACUGGCCCCGCCCCUUUCGAGGGCAAUCCCAGGAGCAGACAACUUCUGGCCGACUUUUAUUUAAGUU_UCCUUCACCUUUCCAGAACUCAGAACUCAGGACUCGGGACUUAG
...((((.((((....((((.......))))....))))(((((((.....))))...(((((......))))).(((((......................))))))))))))..... (-23.45 = -23.85 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	16,178,664 – 16,178,782
Length	118
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	88.88
Mean single sequence MFE	-40.53
Consensus MFE	-27.56
Energy contribution	-27.72
Covariance contribution	0.16
Combinations/Pair	1.16
Mean z-score	-2.36
Structure conservation index	0.68
SVM decision value	0.29
SVM RNA-class probability	0.671653
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16178664 118 - 27905053
CUAAGUCCCGAGUCCUUAGUUCUGAGUUCUGGAAAGGUGAAGGA-AACUUAAAUAAAAGUCGGCCAGAAGUUGUCUGCUCCUGGGAUUGCCCUCGAAAGGGGCGGCACCAGUGGGAAAA
.....((((((((....(.(((((.(((((....))...(((..-..)))...........)))))))).).....))))((((..((((((.(....)))))))..)))).))))... ( -40.50)
>DroSec_CAF1 7936 111 - 1
CUAAGUCCCGAGUCCUGAG-------UUCUGGAAAGGUGAAGGA-AACUUAAAUAAAAGUCGGCCAGAAGAUGUCUGCUCCUGGGAUUGCCCUCGAAAGGGGCGGGGCCAGUGGGAAAA
.....((((((((......-------((((((...(((.(((..-..)))........)))..)))))).......))))((((..((((((.(....)))))))..)))).))))... ( -38.02)
>DroSim_CAF1 1343 118 - 1
CUAAGUCCCGAGUCCUGAGUUCUGAGUUCUGGAAAGGUGAAGGA-AACUUAAAUAAAAGUCGGCCAGAAGUUGUCUGCUCCUGGGAUUGCCCUUGAAAGGGGCGGGGACAGUGGGAAAA
(((.(((((.((((((((((..(((.((((((...(((.(((..-..)))........)))..)))))).)))...))))..))))))(((((.....))))).)))))..)))..... ( -40.70)
>DroEre_CAF1 6818 119 - 1
CUAAGUCCCUAGUCCUCAGUUCUGAAUUCCGGCAAGGUGAAGGAAAACUUAAAUAAAAGUCGGGCAGAAGUUGCCUGCUCCUGGGAUGGCCCUCGAAAGGGGCGGGGCCAGCGGGAAAA
.....((((..........(((((...((((((......(((.....)))........)))))))))))((((((((((((((((....))).....)))))))))..))))))))... ( -39.54)
>DroYak_CAF1 8780 112 - 1
CUAAGCCCCGAGUCCUCAGUUCUGAA-------AAGGUGAAGGAAAACUUAAAUAAAAGUCGGGCAGAAGUUGUCUGCUCCUGGGACUGCCCUCGAAAGGGGCGGGGCCAGCGGGAAAA
......((((..((((((..(((...-------.))))).)))).................(((((((.....)))))))((((..((((((.(....)))))))..)))))))).... ( -43.90)
>consensus
CUAAGUCCCGAGUCCUCAGUUCUGAAUUCUGGAAAGGUGAAGGA_AACUUAAAUAAAAGUCGGCCAGAAGUUGUCUGCUCCUGGGAUUGCCCUCGAAAGGGGCGGGGCCAGUGGGAAAA
....(((((.(((((...................((((........))))..............(((.(((.....))).))))))))((((.(....))))))))))........... (-27.56 = -27.72 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:45 2006