Locus 5010

Sequence ID	2L_DroMel_CAF1
Location	14,393,644 – 14,393,781
Length	137
Max. P	0.961187

overview

Window 3

Location	14,393,644 – 14,393,748
Length	104
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	88.22
Mean single sequence MFE	-22.79
Consensus MFE	-18.50
Energy contribution	-18.34
Covariance contribution	-0.16
Combinations/Pair	1.22
Mean z-score	-2.13
Structure conservation index	0.81
SVM decision value	1.52
SVM RNA-class probability	0.961187
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14393644 104 + 22407834
CUACAGUUA-UGUGCACAACUAAUGUUAAUAACAUUUAAUCAGCGCUCAUCAGGUUUUAUGGCCAUUUCCAAAUGAGCAAUUAAGCUAAUGAAUUUAUUAGCCAU
..(((....-)))((......(((((.....)))))......))((((((..((..............))..))))))......(((((((....)))))))... ( -18.54)
>DroSec_CAF1 14652 104 + 1
CUACAGUUA-UGUGCACAACUAAUGUUAAUAACAUUUAAUCAGCGCUCAUCAGGUUUUAUGACCAUUUCCAAAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCAU
..(((....-)))((......(((((.....)))))......))((((((..((..............))..)))))).....((((((((....)))))))).. ( -22.74)
>DroEre_CAF1 14764 105 + 1
CUGCGCUUAUUGUGUACAACUAAUGUUAAUAACAUUUAAUCAGCGCUCAUCAGGUUUUAUGGCCAUUUCCAAAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCAU
....(((((((((((......(((((.....)))))......))))......((((....)))).......))))))).....((((((((....)))))))).. ( -26.00)
>DroYak_CAF1 14497 104 + 1
CUGCAGUUA-UGUGCACAGCUAAUGUUAAUAACAUUUAAUCAGCGCUCAUCAGGUUUUAUAGCCAUUUCCAAAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCAU
.((((....-..))))..(((...(((((......))))).)))((((((..((..............))..)))))).....((((((((....)))))))).. ( -25.14)
>DroAna_CAF1 29859 104 + 1
CUAUAAUCG-UAACCAGAACUCAUGCUAAUAGUAUUUAAUCAGCGUUCAUCGGAUUUUACGACCAUUUCUAGAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCGC
.........-......((....((((.....))))....)).((((((((((((.............))).))))))).....((((((((....)))))))))) ( -21.52)
>consensus
CUACAGUUA_UGUGCACAACUAAUGUUAAUAACAUUUAAUCAGCGCUCAUCAGGUUUUAUGGCCAUUUCCAAAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCAU
.............((......(((((.....)))))......))((((((..((..............))..)))))).....((((((((....)))))))).. (-18.50 = -18.34 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	14,393,644 – 14,393,748
Length	104
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	88.22
Mean single sequence MFE	-24.30
Consensus MFE	-17.76
Energy contribution	-17.72
Covariance contribution	-0.04
Combinations/Pair	1.16
Mean z-score	-1.93
Structure conservation index	0.73
SVM decision value	0.43
SVM RNA-class probability	0.733973
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14393644 104 - 22407834
AUGGCUAAUAAAUUCAUUAGCUUAAUUGCUCAUUUGGAAAUGGCCAUAAAACCUGAUGAGCGCUGAUUAAAUGUUAUUAACAUUAGUUGUGCACA-UAACUGUAG
(((((((.....((((..(((......)))....))))..)))))))........(((.((((.((((((.(((.....))))))))))))).))-)........ ( -21.50)
>DroSec_CAF1 14652 104 - 1
AUGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUUUGGAAAUGGUCAUAAAACCUGAUGAGCGCUGAUUAAAUGUUAUUAACAUUAGUUGUGCACA-UAACUGUAG
..(((((((......))))))).....(((((((.((..............)).)))))))(((((((((.(((.....)))))))))).))...-......... ( -23.94)
>DroEre_CAF1 14764 105 - 1
AUGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUUUGGAAAUGGCCAUAAAACCUGAUGAGCGCUGAUUAAAUGUUAUUAACAUUAGUUGUACACAAUAAGCGCAG
..(((((((......))))))).....(((((((.((..............)).)))))))(((.....(((((.....))))).((((....)))).))).... ( -24.84)
>DroYak_CAF1 14497 104 - 1
AUGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUUUGGAAAUGGCUAUAAAACCUGAUGAGCGCUGAUUAAAUGUUAUUAACAUUAGCUGUGCACA-UAACUGCAG
..(((((((......))))))).....(((((((.((..............)).)))))))(((((((((......)))..))))))..((((..-....)))). ( -25.34)
>DroAna_CAF1 29859 104 - 1
GCGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUCUAGAAAUGGUCGUAAAAUCCGAUGAACGCUGAUUAAAUACUAUUAGCAUGAGUUCUGGUUA-CGAUUAUAG
..(((((((......))))))).................((((((((((...(((..((((((((((........))))))....))))))))))-))))))).. ( -25.90)
>consensus
AUGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUUUGGAAAUGGCCAUAAAACCUGAUGAGCGCUGAUUAAAUGUUAUUAACAUUAGUUGUGCACA_UAACUGUAG
..(((((((......))))))).....(((((((.((..............)).)))))))(((((((((......)))..)))))).................. (-17.76 = -17.72 +  -0.04)

alignment

secondary structure

dotplot

Window 5

Location	14,393,682 – 14,393,781
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	88.38
Mean single sequence MFE	-23.13
Consensus MFE	-18.68
Energy contribution	-18.76
Covariance contribution	0.08
Combinations/Pair	1.11
Mean z-score	-1.91
Structure conservation index	0.81
SVM decision value	1.05
SVM RNA-class probability	0.906386
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14393682 99 + 22407834
UCAGCGCUCAUCAGGUUUUAUGGCCAUUUCCAAAUGAGCAAUUAAGCUAAUGAAUUUAUUAGCCAUUCGCGAUGUAUUGUGCAAUCAACAAAUGCCAAA
...((((.((((.((((....))))............(((((...(((((((....))))))).))).))))))....))))................. ( -20.40)
>DroSec_CAF1 14690 99 + 1
UCAGCGCUCAUCAGGUUUUAUGACCAUUUCCAAAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCAUUCGCGAUGUAUUGUGCAAUAAACAAGUGCCAAA
...((((.((((.((((....))))............((.....((((((((....))))))))....))))))....))))................. ( -24.40)
>DroEre_CAF1 14803 99 + 1
UCAGCGCUCAUCAGGUUUUAUGGCCAUUUCCAAAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCAUUCGUGAUAUAUUGUGCAAUAAACAAGUGCCAGA
...((((..((((.(.......((((((....)))).)).....((((((((....))))))))...).))))...((((.......)))))))).... ( -22.70)
>DroYak_CAF1 14535 99 + 1
UCAGCGCUCAUCAGGUUUUAUAGCCAUUUCCAAAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCAUUCGUUAUAUAUUGUGCCAUAAAAAAAUGCCAAA
..(((((((((..((..............))..)))))).....((((((((....))))))))....))).....(((.((.((......))))))). ( -21.14)
>DroAna_CAF1 29897 99 + 1
UCAGCGUUCAUCGGAUUUUACGACCAUUUCUAGAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCGCUUGUGAUAUACGGCGCAAUAAACAAGUGCUAUG
..(((((((((((((.............))).))))))).....((((((((....)))))))))))..........(((((.........)))))... ( -27.02)
>consensus
UCAGCGCUCAUCAGGUUUUAUGGCCAUUUCCAAAUGAGCAAUUAGGCUAAUGAAAUUAUUAGCCAUUCGUGAUAUAUUGUGCAAUAAACAAGUGCCAAA
...((((((((..((..............))..)))))).....((((((((....))))))))................))................. (-18.68 = -18.76 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	14,393,682 – 14,393,781
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	88.38
Mean single sequence MFE	-22.31
Consensus MFE	-20.08
Energy contribution	-19.84
Covariance contribution	-0.24
Combinations/Pair	1.20
Mean z-score	-1.37
Structure conservation index	0.90
SVM decision value	0.30
SVM RNA-class probability	0.678194
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14393682 99 - 22407834
UUUGGCAUUUGUUGAUUGCACAAUACAUCGCGAAUGGCUAAUAAAUUCAUUAGCUUAAUUGCUCAUUUGGAAAUGGCCAUAAAACCUGAUGAGCGCUGA
.(..((((((((.(((..........)))))))))(((((((......))))))).....(((((((.((..............)).)))))))))..) ( -22.14)
>DroSec_CAF1 14690 99 - 1
UUUGGCACUUGUUUAUUGCACAAUACAUCGCGAAUGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUUUGGAAAUGGUCAUAAAACCUGAUGAGCGCUGA
.(..((.........((((..........))))..(((((((......))))))).....(((((((.((..............)).)))))))))..) ( -24.04)
>DroEre_CAF1 14803 99 - 1
UCUGGCACUUGUUUAUUGCACAAUAUAUCACGAAUGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUUUGGAAAUGGCCAUAAAACCUGAUGAGCGCUGA
...(((.............................(((((((......))))))).....(((((((.((..............)).)))))))))).. ( -22.04)
>DroYak_CAF1 14535 99 - 1
UUUGGCAUUUUUUUAUGGCACAAUAUAUAACGAAUGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUUUGGAAAUGGCUAUAAAACCUGAUGAGCGCUGA
.(..((..(((.(((((........))))).))).(((((((......))))))).....(((((((.((..............)).)))))))))..) ( -22.74)
>DroAna_CAF1 29897 99 - 1
CAUAGCACUUGUUUAUUGCGCCGUAUAUCACAAGCGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUCUAGAAAUGGUCGUAAAAUCCGAUGAACGCUGA
..((((....((((((((.................(((((((......)))))))...((((....(((....)))..))))....)))))))))))). ( -20.60)
>consensus
UUUGGCACUUGUUUAUUGCACAAUAUAUCACGAAUGGCUAAUAAUUUCAUUAGCCUAAUUGCUCAUUUGGAAAUGGCCAUAAAACCUGAUGAGCGCUGA
..((((.............................(((((((......))))))).....(((((((.((..............)).))))))))))). (-20.08 = -19.84 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:26 2006