Locus 6984

Sequence ID	X_DroMel_CAF1
Location	17,484,986 – 17,485,113
Length	127
Max. P	0.999991

overview

Window 5

Location	17,484,986 – 17,485,098
Length	112
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	91.03
Mean single sequence MFE	-38.16
Consensus MFE	-36.74
Energy contribution	-36.98
Covariance contribution	0.24
Combinations/Pair	1.08
Mean z-score	-4.13
Structure conservation index	0.96
SVM decision value	5.62
SVM RNA-class probability	0.999991
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17484986 112 + 22224390
------AGAAACGGAGAAGAAAAACGCGCAAGCGAUUUUCUUAUGCCGGCGCUGCCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAGCGAAUAAUAUACGCGAAUCGCGAUUUCACAA
------.(((((((..(((((((.(((....))).)))))))...))).(((((.((((((((.(((.....))))))))))).))))).........((((...)))).)))).... ( -42.60)
>DroSec_CAF1 2918 109 + 1
------AGAAACGGAGAAGAAAAACGCGGAAGCGAUUUUCUUAUGCCGGCGCUGCCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAGCGAA---UAUCCGCGAAACGCGAUUUCACAA
------.(((((((..(((((((.(((....))).)))))))...))).(((((.((((((((.(((.....))))))))))).)))))..---....((((...)))).)))).... ( -42.40)
>DroSim_CAF1 2679 109 + 1
------AGAAAUGGAGAAGAAAAACGCGCAAGCGAUUUUCUUAUGCCGGCGCUGCCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAGCGAA---UAUCCGCGAAACGCGAUUUCACAA
------.(((((((..(((((((.(((....))).)))))))...))..(((((.((((((((.(((.....))))))))))).)))))..---....((((...))))))))).... ( -41.30)
>DroEre_CAF1 2958 109 + 1
------AGAAACGGAGAAGAAAAACGCGAAAGCGAUUUUUUUAUGCCGGCGCUACCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAACGAA---CUUCCGCGAAUAGUGAUUUCACAA
------.(((((((..(((((((.(((....))).)))))))...))).(((((.((((((((.(((.....)))))))))))....((..---......))..))))).)))).... ( -30.10)
>DroYak_CAF1 2965 115 + 1
ACACACAGAAACGGAGAAGAAAAACGCGAAAGCGAUUUUCUUAUGCCGGCGCUACCCGAAAAAUCAUUCCAUGUGAUUUUUGGCCAACGAA---UUUCCGCGAAUUGUGAUUUCACAA
...(((((...((((((((((((.(((....))).)))))))..(((((......)).(((((((((.....)))))))))))).......---.)))))....)))))......... ( -34.40)
>consensus
______AGAAACGGAGAAGAAAAACGCGAAAGCGAUUUUCUUAUGCCGGCGCUGCCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAGCGAA___UAUCCGCGAAUCGCGAUUUCACAA
.......(((((((..(((((((.(((....))).)))))))...))).(((((.(((((((.((((.....))))))))))).))))).........(((.....))).)))).... (-36.74 = -36.98 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	17,484,986 – 17,485,098
Length	112
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	91.03
Mean single sequence MFE	-30.48
Consensus MFE	-26.24
Energy contribution	-26.16
Covariance contribution	-0.08
Combinations/Pair	1.06
Mean z-score	-1.30
Structure conservation index	0.86
SVM decision value	0.21
SVM RNA-class probability	0.637354
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17484986 112 - 22224390
UUGUGAAAUCGCGAUUCGCGUAUAUUAUUCGCUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGCAGCGCCGGCAUAAGAAAAUCGCUUGCGCGUUUUUCUUCUCCGUUUCU------
..((((.((((((...)))).)).)))).(((((.((((((.(((.......))).)))).)).))))).(((...(((((((.(((....))).)))))))..))).....------ ( -30.20)
>DroSec_CAF1 2918 109 - 1
UUGUGAAAUCGCGUUUCGCGGAUA---UUCGCUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGCAGCGCCGGCAUAAGAAAAUCGCUUCCGCGUUUUUCUUCUCCGUUUCU------
(((((((((...)))))))))...---..(((((.((((((.(((.......))).)))).)).))))).(((...(((((((.(((....))).)))))))..))).....------ ( -31.70)
>DroSim_CAF1 2679 109 - 1
UUGUGAAAUCGCGUUUCGCGGAUA---UUCGCUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGCAGCGCCGGCAUAAGAAAAUCGCUUGCGCGUUUUUCUUCUCCAUUUCU------
..(((((((...)))))))((...---..(((((.((((((.(((.......))).)))).)).)))))))((...(((((((.(((....))).)))))))..))......------ ( -30.70)
>DroEre_CAF1 2958 109 - 1
UUGUGAAAUCACUAUUCGCGGAAG---UUCGUUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGUAGCGCCGGCAUAAAAAAAUCGCUUUCGCGUUUUUCUUCUCCGUUUCU------
..(((....)))....(.((((((---(((((...(((.........))).))))))))))).)......(((.....(((((.(((....)))))))).....))).....------ ( -22.60)
>DroYak_CAF1 2965 115 - 1
UUGUGAAAUCACAAUUCGCGGAAA---UUCGUUGGCCAAAAAUCACAUGGAAUGAUUUUUCGGGUAGCGCCGGCAUAAGAAAAUCGCUUUCGCGUUUUUCUUCUCCGUUUCUGUGUGU
(((((....)))))..((((((((---..(((((.((((((((((.......)))))))).)).))))).(((...(((((((.(((....))).)))))))..)))))))))))... ( -37.20)
>consensus
UUGUGAAAUCGCGAUUCGCGGAUA___UUCGCUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGCAGCGCCGGCAUAAGAAAAUCGCUUGCGCGUUUUUCUUCUCCGUUUCU______
.((((((.......)))))).........(((((.((((((.(((.......))).)))).)).))))).(((...(((((((.(((....))).)))))))..)))........... (-26.24 = -26.16 +  -0.08)

alignment

secondary structure

dotplot

Window 7

Location	17,485,020 – 17,485,113
Length	93
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	91.38
Mean single sequence MFE	-23.70
Consensus MFE	-20.60
Energy contribution	-21.00
Covariance contribution	0.40
Combinations/Pair	1.09
Mean z-score	-1.38
Structure conservation index	0.87
SVM decision value	0.52
SVM RNA-class probability	0.767273
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17485020 93 + 22224390
UUAUGCCGGCGCUGCCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAGCGAAUAAUAUACGCGAAUCGCGAUUUCACAAAAAAUGCACAGGGC-U
....(((..(((((.((((((((.(((.....))))))))))).))))).........((((...))))....................)))-. ( -27.10)
>DroSec_CAF1 2952 90 + 1
UUAUGCCGGCGCUGCCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAGCGAA---UAUCCGCGAAACGCGAUUUCACAACAAACGCACAGGGC-U
....(((.((((((.((((((((.(((.....))))))))))).))))(((---....((((...))))..))).........))....)))-. ( -27.60)
>DroSim_CAF1 2713 90 + 1
UUAUGCCGGCGCUGCCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAGCGAA---UAUCCGCGAAACGCGAUUUCACAACAAACGCACAGGGC-U
....(((.((((((.((((((((.(((.....))))))))))).))))(((---....((((...))))..))).........))....)))-. ( -27.60)
>DroEre_CAF1 2992 91 + 1
UUAUGCCGGCGCUACCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAACGAA---CUUCCGCGAAUAGUGAUUUCACAACAAAUGCACAGGGUUU
.....((.((((...((((((((.(((.....))))))))))).....(..---....))).....(((....))).......))...)).... ( -15.70)
>DroYak_CAF1 3005 90 + 1
UUAUGCCGGCGCUACCCGAAAAAUCAUUCCAUGUGAUUUUUGGCCAACGAA---UUUCCGCGAAUUGUGAUUUCACAACAAAUGCACAGGGC-U
....(((((((.....).(((((((((.....))))))))).)))......---.....(((..(((((....)))))....)))....)))-. ( -20.50)
>consensus
UUAUGCCGGCGCUGCCCGAAAAUUCAUUCCAUGUGAUUUUUGGCCAGCGAA___UAUCCGCGAAUCGCGAUUUCACAACAAAUGCACAGGGC_U
....(((..(((((.(((((((.((((.....))))))))))).))))).........(((.....)))....................))).. (-20.60 = -21.00 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	17,485,020 – 17,485,113
Length	93
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	91.38
Mean single sequence MFE	-26.12
Consensus MFE	-22.26
Energy contribution	-22.62
Covariance contribution	0.36
Combinations/Pair	1.14
Mean z-score	-1.24
Structure conservation index	0.85
SVM decision value	-0.01
SVM RNA-class probability	0.527792
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17485020 93 - 22224390
A-GCCCUGUGCAUUUUUUGUGAAAUCGCGAUUCGCGUAUAUUAUUCGCUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGCAGCGCCGGCAUAA
.-(((.(((((.....(((((....))))).....))))).....(((((.((((((.(((.......))).)))).)).)))))..))).... ( -25.70)
>DroSec_CAF1 2952 90 - 1
A-GCCCUGUGCGUUUGUUGUGAAAUCGCGUUUCGCGGAUA---UUCGCUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGCAGCGCCGGCAUAA
.-(((....(((.....((((....))))...)))((...---..(((((.((((((.(((.......))).)))).)).)))))))))).... ( -26.50)
>DroSim_CAF1 2713 90 - 1
A-GCCCUGUGCGUUUGUUGUGAAAUCGCGUUUCGCGGAUA---UUCGCUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGCAGCGCCGGCAUAA
.-(((....(((.....((((....))))...)))((...---..(((((.((((((.(((.......))).)))).)).)))))))))).... ( -26.50)
>DroEre_CAF1 2992 91 - 1
AAACCCUGUGCAUUUGUUGUGAAAUCACUAUUCGCGGAAG---UUCGUUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGUAGCGCCGGCAUAA
....((.((((.......(((....)))....(.((((((---(((((...(((.........))).))))))))))).)..)))).))..... ( -23.80)
>DroYak_CAF1 3005 90 - 1
A-GCCCUGUGCAUUUGUUGUGAAAUCACAAUUCGCGGAAA---UUCGUUGGCCAAAAAUCACAUGGAAUGAUUUUUCGGGUAGCGCCGGCAUAA
.-((((((((.....((((((....)))))).)))))...---..(((((.((((((((((.......)))))))).)).)))))..))).... ( -28.10)
>consensus
A_GCCCUGUGCAUUUGUUGUGAAAUCGCGAUUCGCGGAUA___UUCGCUGGCCAAAAAUCACAUGGAAUGAAUUUUCGGGCAGCGCCGGCAUAA
..((((((((.....((((((....)))))).)))))........(((((.((((((.(((.......))).)))).)).)))))..))).... (-22.26 = -22.62 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:20 2006