Locus 7875

Sequence ID	3L_DroMel_CAF1
Location	21,028,605 – 21,028,765
Length	160
Max. P	0.773624

overview

Window 6

Location	21,028,605 – 21,028,725
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-22.63
Consensus MFE	-22.43
Energy contribution	-22.43
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.99
SVM decision value	0.53
SVM RNA-class probability	0.770308
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21028605 120 + 23771897
CAAGCGAUCUCUAUUCAAUGUUUGUCAAUCAAAUUAGUCGCCGAUGAUUGCAAUCUAAAUUAAUGAAAUGCAAUCAUAAGGCGCACGCCAACCAAUUAAACCCACUGACGACAAAAAGUA
....................((((((..........((((((.(((((((((.((.........))..)))))))))..)))).))......((...........))..))))))..... ( -22.40)
>DroSec_CAF1 83640 119 + 1
CAAGCGAUCUCUAUUCAAUGUUUGUCAAUCAAAUUAGUCGCCGAUGAUUGCAAUCUAAAUUAAUGAAAUGCAAUCAUAAGGCGCACGCCAACCAAUUAAACCCACUGACGACAA-AAGUA
....................((((((..........((((((.(((((((((.((.........))..)))))))))..)))).))......((...........))..)))))-).... ( -22.40)
>DroEre_CAF1 5254 120 + 1
CAAGCGAUCUCCAUUCAAUGUUUGUCAAUCAAAUUAGUCGCCGAUGAUUGCAGUCUAAAUUAAUGAAAUGCAAUCAUAAGGCGCACGCCAACCAAUUAAACCCACUGACGACAAAAAGUA
....................((((((..........((((((.(((((((((.((.........))..)))))))))..)))).))......((...........))..))))))..... ( -23.10)
>consensus
CAAGCGAUCUCUAUUCAAUGUUUGUCAAUCAAAUUAGUCGCCGAUGAUUGCAAUCUAAAUUAAUGAAAUGCAAUCAUAAGGCGCACGCCAACCAAUUAAACCCACUGACGACAAAAAGUA
...(((.............(((((.....)))))..(.((((.(((((((((.((.........))..)))))))))..))))).)))................................ (-22.43 = -22.43 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	21,028,605 – 21,028,725
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-31.57
Consensus MFE	-30.70
Energy contribution	-30.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.97
SVM decision value	0.36
SVM RNA-class probability	0.704926
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21028605 120 - 23771897
UACUUUUUGUCGUCAGUGGGUUUAAUUGGUUGGCGUGCGCCUUAUGAUUGCAUUUCAUUAAUUUAGAUUGCAAUCAUCGGCGACUAAUUUGAUUGACAAACAUUGAAUAGAGAUCGCUUG
...(((((((..((((((..((((((..(((((....((((..(((((((((..((.........)).))))))))).)))).)))).)..))))).)..)))))))))))))....... ( -32.10)
>DroSec_CAF1 83640 119 - 1
UACUU-UUGUCGUCAGUGGGUUUAAUUGGUUGGCGUGCGCCUUAUGAUUGCAUUUCAUUAAUUUAGAUUGCAAUCAUCGGCGACUAAUUUGAUUGACAAACAUUGAAUAGAGAUCGCUUG
..(((-(.....((((((..((((((..(((((....((((..(((((((((..((.........)).))))))))).)))).)))).)..))))).)..))))))..))))........ ( -31.80)
>DroEre_CAF1 5254 120 - 1
UACUUUUUGUCGUCAGUGGGUUUAAUUGGUUGGCGUGCGCCUUAUGAUUGCAUUUCAUUAAUUUAGACUGCAAUCAUCGGCGACUAAUUUGAUUGACAAACAUUGAAUGGAGAUCGCUUG
...((((..(..((((((..((((((..(((((....((((..(((((((((.(..(......)..).))))))))).)))).)))).)..))))).)..)))))))..))))....... ( -30.80)
>consensus
UACUUUUUGUCGUCAGUGGGUUUAAUUGGUUGGCGUGCGCCUUAUGAUUGCAUUUCAUUAAUUUAGAUUGCAAUCAUCGGCGACUAAUUUGAUUGACAAACAUUGAAUAGAGAUCGCUUG
.......(.((.((((((..((((((..(((((....((((..(((((((((..((.........)).))))))))).)))).)))).)..))))).)..))))))...)).)....... (-30.70 = -30.70 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	21,028,645 – 21,028,765
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-22.76
Consensus MFE	-22.85
Energy contribution	-22.19
Covariance contribution	-0.66
Combinations/Pair	1.10
Mean z-score	-1.64
Structure conservation index	1.00
SVM decision value	0.54
SVM RNA-class probability	0.773624
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21028645 120 + 23771897
CCGAUGAUUGCAAUCUAAAUUAAUGAAAUGCAAUCAUAAGGCGCACGCCAACCAAUUAAACCCACUGACGACAAAAAGUAAAUUUGCGCUUAAACGAUUGCGCCAUCGAUUCAAUUUCAU
.(((((..(((((((.......((((.......)))).(((((((((.((...............)).))((.....)).....)))))))....))))))).)))))............ ( -23.16)
>DroSec_CAF1 83680 119 + 1
CCGAUGAUUGCAAUCUAAAUUAAUGAAAUGCAAUCAUAAGGCGCACGCCAACCAAUUAAACCCACUGACGACAA-AAGUAAAUUUGCGCUUAAACGAUUGCGCCAUCGAUUCAAUUUCAU
.(((((..(((((((.......((((.......)))).(((((((((.((...............)).))((..-..)).....)))))))....))))))).)))))............ ( -23.16)
>DroEre_CAF1 5294 120 + 1
CCGAUGAUUGCAGUCUAAAUUAAUGAAAUGCAAUCAUAAGGCGCACGCCAACCAAUUAAACCCACUGACGACAAAAAGUAAAUUUGCGCUUAAACGGUUGCACCAUCGAUUCAAUUUCAU
((((((((((((.((.........))..))))))))).(((((((((.((...............)).))((.....)).....)))))))...)))....................... ( -21.96)
>consensus
CCGAUGAUUGCAAUCUAAAUUAAUGAAAUGCAAUCAUAAGGCGCACGCCAACCAAUUAAACCCACUGACGACAAAAAGUAAAUUUGCGCUUAAACGAUUGCGCCAUCGAUUCAAUUUCAU
.(((((..(((((((.......((((.......)))).(((((((((.((...............)).))((.....)).....)))))))....))))))).)))))............ (-22.85 = -22.19 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:14 2006