Locus 7230

Sequence ID	X_DroMel_CAF1
Location	18,070,318 – 18,070,514
Length	196
Max. P	0.717758

overview

Window 8

Location	18,070,318 – 18,070,434
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	90.99
Mean single sequence MFE	-42.50
Consensus MFE	-36.70
Energy contribution	-37.03
Covariance contribution	0.34
Combinations/Pair	1.06
Mean z-score	-1.83
Structure conservation index	0.86
SVM decision value	0.11
SVM RNA-class probability	0.587893
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18070318 116 + 22224390
AAUGUCGCCCCGUUUUUUUUUUGCUUGCCGUUUUUUUAAUGGGCCAUGCGCUGGCUAGCUGCUGGCCAGGUUGCAAAUCGAUG----GGUGGCGGUACUAAUAUUGGGCUGCCAGCAUGC
......((((((((.....(((((...(((((.....)))))(((.((.((..((.....))..))))))).)))))..))))----))(((((((.(((....)))))))))))).... ( -40.50)
>DroSec_CAF1 8007 115 + 1
AAUGUUGCCC-G---UUUUUUUGCUUGCCGUUU-UUUAAUGGGCCAUGUGCUGGCUAGCUGCUGGCCAGGUUGCGAAUCGAUGGAUGGGCGGCGGUACUGAUAUUGGGCUGCCAGCAUGC
.(((((((((-(---(((.(((((...(((((.-...)))))(((.((.((..((.....))..))))))).))))).....))))))))(((((..(.......)..)))))))))).. ( -45.60)
>DroSim_CAF1 12604 115 + 1
AAUGUCUCCC-G---UUUUUUUGCUUGCCGUUU-UUUAAUGGGCCAUGUGCUGGCUCGCUGCUGGCCAGGUUGCAAAUCGAUGGAUGGGCGGCGGUACUGAUAUUGGGCUGCCAGCAUGC
...((((.((-(---((..(((((...(((((.-...)))))(((.((.((..((.....))..))))))).)))))..)))))..))))(((((..(.......)..)))))....... ( -41.40)
>consensus
AAUGUCGCCC_G___UUUUUUUGCUUGCCGUUU_UUUAAUGGGCCAUGUGCUGGCUAGCUGCUGGCCAGGUUGCAAAUCGAUGGAUGGGCGGCGGUACUGAUAUUGGGCUGCCAGCAUGC
.((((.((((.....((..(((((...(((((.....)))))(((.((.((..((.....))..))))))).)))))..)).....))))(((((..(.......)..))))).)))).. (-36.70 = -37.03 +   0.34)

alignment

secondary structure

dotplot

Window 9

Location	18,070,398 – 18,070,514
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-44.17
Consensus MFE	-39.77
Energy contribution	-40.67
Covariance contribution	0.89
Combinations/Pair	1.06
Mean z-score	-1.83
Structure conservation index	0.90
SVM decision value	0.18
SVM RNA-class probability	0.619737
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18070398 116 + 22224390
AUG----GGUGGCGGUACUAAUAUUGGGCUGCCAGCAUGCAAAUGCGCCGGAAACCCUUUCGCUGCCACUCGGUAAAUAUUUCAGGCAUCGUCAGUCCGUCGCCCACGCUCAAUUUGUCC
.((----((((((((.(((..(((((((.((.((((..((....))...(....)......)))).))))))))).........(((...)))))))))))))))).............. ( -37.70)
>DroSec_CAF1 8082 120 + 1
AUGGAUGGGCGGCGGUACUGAUAUUGGGCUGCCAGCAUGCAAAUGCGCCGGAAACCCUUUCGCUGCCAGUCGGCAAAUAUUUCAGGCAUCGUCAGUCCGUCGCCCACGCUCAAUUUGUCC
.....((((((((((.((((((..(((....)))((((....))))((((....)........((((....)))).........)))...)))))))))))))))).............. ( -46.80)
>DroSim_CAF1 12679 120 + 1
AUGGAUGGGCGGCGGUACUGAUAUUGGGCUGCCAGCAUGCAAAUGCGCCGGAAACCCUUUCGCUGCCACUCGGCAAAUAUUUCAGGCAUCGGCAGUCCGUCGCCCACGCUCAAUUUGUCC
.....((((((((((((....))))((((((((.((((....))))((((....)........((((....)))).........)))...)))))))))))))))).............. ( -48.00)
>consensus
AUGGAUGGGCGGCGGUACUGAUAUUGGGCUGCCAGCAUGCAAAUGCGCCGGAAACCCUUUCGCUGCCACUCGGCAAAUAUUUCAGGCAUCGUCAGUCCGUCGCCCACGCUCAAUUUGUCC
.....((((((((((.((((((..(((....)))((((....))))((((....)........((((....)))).........)))...)))))))))))))))).............. (-39.77 = -40.67 +   0.89)

alignment

secondary structure

dotplot

Window 0

Location	18,070,398 – 18,070,514
Length	116
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-45.56
Consensus MFE	-41.72
Energy contribution	-43.16
Covariance contribution	1.45
Combinations/Pair	1.03
Mean z-score	-1.89
Structure conservation index	0.92
SVM decision value	0.39
SVM RNA-class probability	0.717758
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18070398 116 - 22224390
GGACAAAUUGAGCGUGGGCGACGGACUGACGAUGCCUGAAAUAUUUACCGAGUGGCAGCGAAAGGGUUUCCGGCGCAUUUGCAUGCUGGCAGCCCAAUAUUAGUACCGCCACC----CAU
.............(((((.(.((((((((((.((((.................)))).))...(((((.(((((((....))..))))).)))))....))))).))).).))----))) ( -40.63)
>DroSec_CAF1 8082 120 - 1
GGACAAAUUGAGCGUGGGCGACGGACUGACGAUGCCUGAAAUAUUUGCCGACUGGCAGCGAAAGGGUUUCCGGCGCAUUUGCAUGCUGGCAGCCCAAUAUCAGUACCGCCGCCCAUCCAU
...........(.(((((((.((((((((((.((((.................)))).))...(((((.(((((((....))..))))).)))))....))))).))).))))))).).. ( -49.23)
>DroSim_CAF1 12679 120 - 1
GGACAAAUUGAGCGUGGGCGACGGACUGCCGAUGCCUGAAAUAUUUGCCGAGUGGCAGCGAAAGGGUUUCCGGCGCAUUUGCAUGCUGGCAGCCCAAUAUCAGUACCGCCGCCCAUCCAU
...........(.(((((((.(((((((.((.((((.................)))).))...(((((.(((((((....))..))))).))))).....)))).))).))))))).).. ( -46.83)
>consensus
GGACAAAUUGAGCGUGGGCGACGGACUGACGAUGCCUGAAAUAUUUGCCGAGUGGCAGCGAAAGGGUUUCCGGCGCAUUUGCAUGCUGGCAGCCCAAUAUCAGUACCGCCGCCCAUCCAU
...........(.(((((((.((((((((((.((((.................)))).))...(((((.(((((((....))..))))).)))))....))))).))).))))))).).. (-41.72 = -43.16 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:37 2006