Locus 1185

Sequence ID	X_DroMel_CAF1
Location	3,536,279 – 3,536,485
Length	206
Max. P	0.655249

overview

Window 9

Location	3,536,279 – 3,536,378
Length	99
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	93.08
Mean single sequence MFE	-29.00
Consensus MFE	-21.60
Energy contribution	-22.28
Covariance contribution	0.68
Combinations/Pair	1.04
Mean z-score	-1.94
Structure conservation index	0.74
SVM decision value	0.18
SVM RNA-class probability	0.621542
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3536279 99 - 22224390
UGUGCGGAAAUCAAAGGGAAACCUU--UGUGGGACAAAACCGGAACAGGACUCGAA-UGAGGGGUUGGUU-GUUGCGCACACAAGAGGUGAUUGAGAUUCCCC
(((((......((((((....))))--)).(.((((..(((((..(....(((...-.))))..))))))-))).)))))).....((.((.......)))). ( -27.80)
>DroSec_CAF1 44449 95 - 1
UGUGCGGAAAUCAAAGGGAAACCUU--UCUGGGACAAAACCGGAACAGGACUCGAA-AGAGGGGU----U-GUUGCACACACAAGAGGUGAUUGAGAUUCCCC
(((((((.((((.((((....))))--(((((.......)))))......(((...-.))).)))----)-.)))))))(((.....)))............. ( -30.30)
>DroSim_CAF1 45643 95 - 1
UGUGCGGAAAUCAAAGGGAAACCUU--UGUGGGACAAAACCGGAACAGGACUCGAA-AGAGGGGU----U-GUUGCACACACAAGAGGUGAUUGAGAUUCCCC
.....((.(((((((((....))))--)(((.(((((..((......)).(((...-.)))...)----)-))).))).(((.....))).....)))).)). ( -30.80)
>DroEre_CAF1 48743 99 - 1
UGUACGGAAAUCAAAGGGAAACCUCUCUGCGGGACAAAACCGGAACAGGACUCGAAAAGAGGGGU----UGGAUGCACACACGAGAGGUGAUUGAGAUUCCCC
.....((((.((((.....(((((((((.((((......((......)).))))...))))))))----).......(((.(....)))).))))..)))).. ( -27.90)
>DroYak_CAF1 44482 95 - 1
UGUGCGGAAAUCAAAGGGAAACCUU--UGUGGGACAAAACCGGAACAGGACUCGAA-AGAGGGGU----U-GAUGCACACACGAGAGGUGAUUGAGAUUCCCC
((((((..(((((((((....))))--)...........((......)).(((...-.))).)))----)-..))))))(((.....)))............. ( -28.20)
>consensus
UGUGCGGAAAUCAAAGGGAAACCUU__UGUGGGACAAAACCGGAACAGGACUCGAA_AGAGGGGU____U_GUUGCACACACAAGAGGUGAUUGAGAUUCCCC
.....((((.(((((((....)))...((((.(((....((......)).(((.....)))..........))).))))(((.....))).))))..)))).. (-21.60 = -22.28 +   0.68)

alignment

secondary structure

dotplot

Window 0

Location	3,536,345 – 3,536,452
Length	107
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	93.02
Mean single sequence MFE	-27.10
Consensus MFE	-19.85
Energy contribution	-21.60
Covariance contribution	1.75
Combinations/Pair	1.00
Mean z-score	-2.67
Structure conservation index	0.73
SVM decision value	0.23
SVM RNA-class probability	0.646439
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3536345 107 + 22224390
GUCCCACAAAGGUUUCCCUUUGAUUUCCGCACAUUCCGUUUCGAUUCUUACGCGCACAGAAGUACCUCAAUAAAGUGGACCA-ACUGGUGCUAAGAAUCGCAAUUUCC
......((((((....))))))...............(((.(((((((((.((((.(((..(..((.(......).))..).-.)))))))))))))))).))).... ( -28.60)
>DroSec_CAF1 44511 107 + 1
GUCCCAGAAAGGUUUCCCUUUGAUUUCCGCACAUUCCGUUUCGAUUCAUAAACGCACAGAAGUACCUCAAUAAAAUGGACCU-UCUGGUGCUAAGAAUCGCAAUUUCC
.......(((((....)))))(((((..((((....(((((........)))))..((((((..((..........))..))-))))))))...)))))......... ( -23.30)
>DroSim_CAF1 45705 107 + 1
GUCCCACAAAGGUUUCCCUUUGAUUUCCGCACAUUCCGUUUCGAUUCUUACGCGCACAGAAGUACCUCAAUAAAAUGGACCU-UCCGGUGCUAAGAAUCGCAAUUUCC
......((((((....))))))...............(((.(((((((((.((((.(.((((..((..........))..))-)).)))))))))))))).))).... ( -29.00)
>DroYak_CAF1 44544 108 + 1
GUCCCACAAAGGUUUCCCUUUGAUUUCCGCACAUUCCGUUUCGAUUCUUACGCGCACAGCAGAACCUCCAUAAAAUGGAUCUUUCUGAUGCUAAGAAUCGCAAUAUCC
......((((((....))))))...............(((.(((((((((.(((.....(((((..(((((...)))))...))))).)))))))))))).))).... ( -27.50)
>consensus
GUCCCACAAAGGUUUCCCUUUGAUUUCCGCACAUUCCGUUUCGAUUCUUACGCGCACAGAAGUACCUCAAUAAAAUGGACCU_UCUGGUGCUAAGAAUCGCAAUUUCC
......((((((....))))))...............(((.(((((((((.((((.((((....((..........)).....))))))))))))))))).))).... (-19.85 = -21.60 +   1.75)

alignment

secondary structure

dotplot

Window 1

Location	3,536,345 – 3,536,452
Length	107
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	93.02
Mean single sequence MFE	-31.82
Consensus MFE	-25.39
Energy contribution	-25.57
Covariance contribution	0.19
Combinations/Pair	1.08
Mean z-score	-1.82
Structure conservation index	0.80
SVM decision value	0.25
SVM RNA-class probability	0.655249
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3536345 107 - 22224390
GGAAAUUGCGAUUCUUAGCACCAGU-UGGUCCACUUUAUUGAGGUACUUCUGUGCGCGUAAGAAUCGAAACGGAAUGUGCGGAAAUCAAAGGGAAACCUUUGUGGGAC
......(((........)))(((..-...(((.(((....)))((((((((((...((.......))..)))))).)))))))...((((((....)))))))))... ( -31.10)
>DroSec_CAF1 44511 107 - 1
GGAAAUUGCGAUUCUUAGCACCAGA-AGGUCCAUUUUAUUGAGGUACUUCUGUGCGUUUAUGAAUCGAAACGGAAUGUGCGGAAAUCAAAGGGAAACCUUUCUGGGAC
........((((((...((((.(((-((..((..........))..)))))))))......))))))............(((((.....(((....)))))))).... ( -28.40)
>DroSim_CAF1 45705 107 - 1
GGAAAUUGCGAUUCUUAGCACCGGA-AGGUCCAUUUUAUUGAGGUACUUCUGUGCGCGUAAGAAUCGAAACGGAAUGUGCGGAAAUCAAAGGGAAACCUUUGUGGGAC
........(((((((((((.(((((-((..((..........))..)))))).).)).)))))))))...................((((((....))))))...... ( -33.10)
>DroYak_CAF1 44544 108 - 1
GGAUAUUGCGAUUCUUAGCAUCAGAAAGAUCCAUUUUAUGGAGGUUCUGCUGUGCGCGUAAGAAUCGAAACGGAAUGUGCGGAAAUCAAAGGGAAACCUUUGUGGGAC
(.(((((.((((((((((((((((((...(((((...)))))..)))))..))))...)))))))))......))))).)......((((((....))))))...... ( -34.70)
>consensus
GGAAAUUGCGAUUCUUAGCACCAGA_AGGUCCAUUUUAUUGAGGUACUUCUGUGCGCGUAAGAAUCGAAACGGAAUGUGCGGAAAUCAAAGGGAAACCUUUGUGGGAC
........((((((((((((((.....))).............((((....)))))).)))))))))...................((((((....))))))...... (-25.39 = -25.57 +   0.19)

alignment

secondary structure

dotplot

Window 2

Location	3,536,378 – 3,536,485
Length	107
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	82.95
Mean single sequence MFE	-24.52
Consensus MFE	-14.85
Energy contribution	-16.35
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.61
SVM decision value	0.11
SVM RNA-class probability	0.586198
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3536378 107 + 22224390
UUCCGUUUCGAUUCUUACGCGCACAGAAGUACCUCAAUAAAGUGGACCA-ACUGGUGCUAAGAAUCGCAAUUUCCCAGCCAAAACAGUAUGAGAUACUAUCGCAUAAA
....(((.(((((((((.((((.(((..(..((.(......).))..).-.)))))))))))))))).)))................((((.(((...))).)))).. ( -24.70)
>DroSec_CAF1 44544 107 + 1
UUCCGUUUCGAUUCAUAAACGCACAGAAGUACCUCAAUAAAAUGGACCU-UCUGGUGCUAAGAAUCGCAAUUUCCCAGCCAAGGCAGUUCGAGAUACUAUCGCAUAAA
....((((((((((.((..(((.((((((..((..........))..))-))))))).)).)))))...........((....)).....)))))............. ( -23.10)
>DroSim_CAF1 45738 107 + 1
UUCCGUUUCGAUUCUUACGCGCACAGAAGUACCUCAAUAAAAUGGACCU-UCCGGUGCUAAGAAUCGCAAUUUCCCAGCCAAGGCAGUUCGAGAUACUAUCGCAUAAA
....(((((((((((((.((((.(.((((..((..........))..))-)).)))))))))))))...........((....)).....)))))............. ( -27.40)
>DroYak_CAF1 44577 97 + 1
UUCCGUUUCGAUUCUUACGCGCACAGCAGAACCUCCAUAAAAUGGAUCUUUCUGAUGCUAAGAAUCGCAAUAUCCG--UGAAAGCA-----AAUUAUUAUUGUA----
....(((.(((((((((.(((.....(((((..(((((...)))))...))))).)))))))))))).)))....(--(....)).-----.............---- ( -22.90)
>consensus
UUCCGUUUCGAUUCUUACGCGCACAGAAGUACCUCAAUAAAAUGGACCU_UCUGGUGCUAAGAAUCGCAAUUUCCCAGCCAAAGCAGUUCGAGAUACUAUCGCAUAAA
....(((.(((((((((.((((.((((....((..........)).....))))))))))))))))).)))..................................... (-14.85 = -16.35 +   1.50)

alignment

secondary structure

dotplot

Window 3

Location	3,536,378 – 3,536,485
Length	107
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	82.95
Mean single sequence MFE	-29.28
Consensus MFE	-18.85
Energy contribution	-19.10
Covariance contribution	0.25
Combinations/Pair	1.18
Mean z-score	-1.59
Structure conservation index	0.64
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3536378 107 - 22224390
UUUAUGCGAUAGUAUCUCAUACUGUUUUGGCUGGGAAAUUGCGAUUCUUAGCACCAGU-UGGUCCACUUUAUUGAGGUACUUCUGUGCGCGUAAGAAUCGAAACGGAA
((((((((..(((((((((...((..(..(((((.....(((........))))))))-..)..))......)))))))))......))))))))............. ( -31.80)
>DroSec_CAF1 44544 107 - 1
UUUAUGCGAUAGUAUCUCGAACUGCCUUGGCUGGGAAAUUGCGAUUCUUAGCACCAGA-AGGUCCAUUUUAUUGAGGUACUUCUGUGCGUUUAUGAAUCGAAACGGAA
.....(((..((((((((((.........((((((((.......))))))))(((...-.)))........))))))))))..))).(((((........)))))... ( -26.90)
>DroSim_CAF1 45738 107 - 1
UUUAUGCGAUAGUAUCUCGAACUGCCUUGGCUGGGAAAUUGCGAUUCUUAGCACCGGA-AGGUCCAUUUUAUUGAGGUACUUCUGUGCGCGUAAGAAUCGAAACGGAA
((((((((..((((((((((.........((((((((.......))))))))(((...-.)))........))))))))))......))))))))............. ( -33.70)
>DroYak_CAF1 44577 97 - 1
----UACAAUAAUAAUU-----UGCUUUCA--CGGAUAUUGCGAUUCUUAGCAUCAGAAAGAUCCAUUUUAUGGAGGUUCUGCUGUGCGCGUAAGAAUCGAAACGGAA
----.............-----....(((.--((.......((((((((((((((((((...(((((...)))))..)))))..))))...)))))))))...))))) ( -24.70)
>consensus
UUUAUGCGAUAGUAUCUCGAACUGCCUUGGCUGGGAAAUUGCGAUUCUUAGCACCAGA_AGGUCCAUUUUAUUGAGGUACUUCUGUGCGCGUAAGAAUCGAAACGGAA
.........((((.(((((..(......)..))))).))))((((((((((((((.....))).............((((....)))))).)))))))))........ (-18.85 = -19.10 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:21 2006