Locus 8181

Sequence ID	X_DroMel_CAF1
Location	20,344,571 – 20,344,775
Length	204
Max. P	0.952874

overview

Window 0

Location	20,344,571 – 20,344,685
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.02
Mean single sequence MFE	-34.10
Consensus MFE	-25.82
Energy contribution	-26.66
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.75
Structure conservation index	0.76
SVM decision value	0.38
SVM RNA-class probability	0.714045
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20344571 114 - 22224390
---G---GUUGUAAGGACAUGCGAGGACAUCCGCUGGGAUAAUAAUAAACAUCGGGGGACUAAAGUUGUGGACAGGCGGAGGGAGGGGGAACACCCCCAAGUCAAGUAAUUUGUCAACGA
---.---.((((...(((((((...(((.((((((.(..((......(((.(..(....)..).))).))..).))))))....(((((....)))))..)))..)))...)))).)))) ( -34.90)
>DroSec_CAF1 12317 116 - 1
CGGG---GUUGUAAGGACAUGCGAGGACAUCCGCUGGGAUAAUAAUAAACAUCGGGGGACUGAAGUGGUGGACAGGAGGAGGGAGGGGG-ACACCCCCAAGUCAAGUAAUUUGUCAACGA
....---.((((...(((((((...(((.((((((.............((.((((....)))).)))))))).....((.(((..(...-.).)))))..)))..)))...)))).)))) ( -32.71)
>DroSim_CAF1 14109 116 - 1
CGGG---GUUGUAAGGACAUGCGAGGACAUCCGCUGGGAUAAUAAUAAACAUCGGGGGACUGAAGUUGUGGACAGGAGGAGGGAGGGGG-ACACCCCCAAGUCAAGUAAUUUGUCAACGA
....---.((((...(((((((...(((.(((.(((...((......(((.((((....)))).))).))..)))..)))....(((((-...)))))..)))..)))...)))).)))) ( -33.20)
>DroEre_CAF1 8971 111 - 1
AGGGGGAGGCUGGAGGACAUGCGAGGACAUCCGCUGGGAUAAUAAUAAACAUCAGGGGACUGAAGUCGUG-ACA-----AGGGA-GGGG-AGACCCCC-AGUCAAGUAAUUUGUCAACGA
...............(((((((...(((((((....))))...........((((....)))).))).((-((.-----..((.-(((.-...)))))-.)))).)))...))))..... ( -33.70)
>DroYak_CAF1 12957 109 - 1
CGGG---GGCUGGGGGACAUGCGAGGACAUCCGCAGGGAUAAUAAUAAACAUCGGGGGACUGAAGUUGUGGACA-----AGGAA-GGGG-ACACCCCC-AGUCAAGUAAUUUGUCAACGA
....---(((((((((.(.(((.(.(((((((....))))...........((((....)))).))).).).))-----.)...-(...-.).)))))-))))................. ( -36.00)
>consensus
CGGG___GUUGUAAGGACAUGCGAGGACAUCCGCUGGGAUAAUAAUAAACAUCGGGGGACUGAAGUUGUGGACAGG_GGAGGGAGGGGG_ACACCCCCAAGUCAAGUAAUUUGUCAACGA
...............(((((((...(((((((....)))).......(((.((((....)))).))).................(((((....)))))..)))..)))...))))..... (-25.82 = -26.66 +   0.84)

alignment

secondary structure

dotplot

Window 1

Location	20,344,611 – 20,344,706
Length	95
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	85.53
Mean single sequence MFE	-33.15
Consensus MFE	-23.70
Energy contribution	-25.07
Covariance contribution	1.37
Combinations/Pair	1.04
Mean z-score	-1.76
Structure conservation index	0.71
SVM decision value	0.39
SVM RNA-class probability	0.717046
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20344611 95 - 22224390
-GGGACGCCCUCCGGAGGG-AGG----------GGUUGUAAGGACAUGCGAGGACAUCCGCUGGGAUAAUAAUAAACAUCGGGGGACUAAAGUUGUGGACAGGCGGA
-.(..(.((((((....))-)))----------).(((((......))))))..).((((((.(..((......(((.(..(....)..).))).))..).)))))) ( -28.50)
>DroSec_CAF1 12356 105 - 1
-GGGACUCCCUCCGUUGGG-AGGGGGUGUGCGGGGUUGUAAGGACAUGCGAGGACAUCCGCUGGGAUAAUAAUAAACAUCGGGGGACUGAAGUGGUGGACAGGAGGA
-.(.(((((((((....))-))))))).)(((..(((.....))).)))..(..((.(((((.(..((....))..).((((....)))))))))))..)....... ( -34.80)
>DroSim_CAF1 14148 105 - 1
-GGGACUCCCUCCGUUGGG-AGGGGGUGUGCGGGGUUGUAAGGACAUGCGAGGACAUCCGCUGGGAUAAUAAUAAACAUCGGGGGACUGAAGUUGUGGACAGGAGGA
-.(.(((((((((....))-))))))).)(((((.(((((......))))).....))))).............(((.((((....)))).)))............. ( -34.00)
>DroYak_CAF1 12994 102 - 1
AGGGACCCCCUCCGUAGGGAAGGGGGUGUGCGGGGGCUGGGGGACAUGCGAGGACAUCCGCAGGGAUAAUAAUAAACAUCGGGGGACUGAAGUUGUGGACA-----A
....(((((((((....)).))))))).((((((..((.(....)......))...))))))............(((.((((....)))).))).......-----. ( -35.30)
>consensus
_GGGACUCCCUCCGUAGGG_AGGGGGUGUGCGGGGUUGUAAGGACAUGCGAGGACAUCCGCUGGGAUAAUAAUAAACAUCGGGGGACUGAAGUUGUGGACAGGAGGA
....(((((((((....)).)))))))..............(..(((........((((....)))).......(((.((((....)))).))))))..)....... (-23.70 = -25.07 +   1.37)

alignment

secondary structure

dotplot

Window 2

Location	20,344,685 – 20,344,775
Length	90
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	81.67
Mean single sequence MFE	-21.36
Consensus MFE	-13.07
Energy contribution	-13.25
Covariance contribution	0.19
Combinations/Pair	1.12
Mean z-score	-2.61
Structure conservation index	0.61
SVM decision value	1.43
SVM RNA-class probability	0.952874
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20344685 90 + 22224390
-------CCU-CCCUCCGGAGGGCGUCCC-CCUCGGACUCAGGCUAAUAAAUAAUAAACAAACCUUGUCCCAUA--GACAGGCUUCCACUGCCUCCACCCC
-------(((-...((((..(((....))-)..))))...)))......................((((.....--))))(((.......)))........ ( -20.50)
>DroSec_CAF1 12433 99 + 1
CACACCCCCU-CCCAACGGAGGGAGUCCC-CCUCGGACUCAGGCUAAUAAAUAAUAAACAAACCUUGUCCCAUACCGACUGGCUUCCUCUACCUACCCCCC
....((((((-((....))))))((((..-....((((..(((...................))).))))......))))))................... ( -20.81)
>DroSim_CAF1 14225 99 + 1
CACACCCCCU-CCCAACGGAGGGAGUCCC-CCUCGGACUCAGGCUAAUAAAUAAUAAACAAACCUUGUCCCAUACCGACUGGCUUCCUCUACCUACCCCCC
....((((((-((....))))))((((..-....((((..(((...................))).))))......))))))................... ( -20.81)
>DroYak_CAF1 13066 88 + 1
CACACCCCCUUCCCUACGGAGGGGGUCCCUCCUCGGGCUGAGGCUAAUAAAUAAUAAACAAACCUUGUCCCAUGCCGACUGA-------------CUCCCC
...(((((((((.....)))))))))........(((.(((((...................))))).)))...........-------------...... ( -23.31)
>consensus
CACACCCCCU_CCCAACGGAGGGAGUCCC_CCUCGGACUCAGGCUAAUAAAUAAUAAACAAACCUUGUCCCAUACCGACUGGCUUCCUCUACCUACCCCCC
......((((.((....))))))((((.......((((..(((...................))).))))......))))..................... (-13.07 = -13.25 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:57:45 2006