Locus 5670

Sequence ID	3R_DroMel_CAF1
Location	14,892,417 – 14,892,549
Length	132
Max. P	0.995649

overview

Window 7

Location	14,892,417 – 14,892,516
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	95.16
Mean single sequence MFE	-23.88
Consensus MFE	-19.94
Energy contribution	-20.38
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.64
Structure conservation index	0.84
SVM decision value	2.60
SVM RNA-class probability	0.995649
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14892417 99 + 27905053
UGGCAAUUUCUUUUGCCAGUCUGUUUUUUUUUUGUAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUCAAAUUGAAAAAA
((((((......))))))..........((((..(...((((((........)))))).((((....)))))..))))((((((.....)))))).... ( -23.00)
>DroSec_CAF1 20049 96 + 1
UGGCAAUUUCUUUUGCCAGUCUGUUUU---UUUGUAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUCAAAUUGAAAAAC
((((((......))))))(((.(..((---((..(...((((((........)))))).((((....)))))..))))..))))............... ( -23.00)
>DroSim_CAF1 19921 96 + 1
UGGCAAUUUCUUUUGCCAGUCUGUUUU---UUUGCAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUCAAAUUGAAAAAC
((((((......)))))).(((((.((---((((((((((((((........)))))).)))))))).)).)))))..((((((.....)))))).... ( -27.90)
>DroEre_CAF1 19657 95 + 1
UGGCAAUUUCUUUUUCCAGUCUGUUU----UUUGUAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUGAAAUUGAAAAGC
...(((((((..((((((...((((.----((((((((((((((........)))))).)))))))).))))))))))........)))))))...... ( -23.50)
>DroYak_CAF1 22623 95 + 1
UGGCAAUUUCUUUUUCCAGUCUGUUU----UUUGUAACUACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUAAAAUUGAAAAAC
............((((((...((((.----((((((((((((((........)))).)))))))))).))))))))))((((((.....)))))).... ( -22.00)
>consensus
UGGCAAUUUCUUUUGCCAGUCUGUUUU___UUUGUAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUCAAAUUGAAAAAC
((((((......)))))).(((((........((((((((((((........)))))).))))))(....))))))..((((((.....)))))).... (-19.94 = -20.38 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	14,892,447 – 14,892,549
Length	102
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	87.84
Mean single sequence MFE	-22.06
Consensus MFE	-16.04
Energy contribution	-17.84
Covariance contribution	1.80
Combinations/Pair	1.10
Mean z-score	-1.69
Structure conservation index	0.73
SVM decision value	0.11
SVM RNA-class probability	0.588323
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14892447 102 + 27905053
UUUGUAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUCAAAUUGAAAAAACC-CGAGGGGUAA--GGAAAAGCGAAUGUUGUUUUG
....((((((((((........)))))).)))).(((((((((.....((((((.....))))))...(((-(...))))..--..........))))))))).. ( -23.20)
>DroSec_CAF1 20076 104 + 1
UUUGUAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUCAAAUUGAAAAACCCAAGAGGGGCAAGAGGAAAAGCGAAUGUUGUU-UG
....((((((((((........)))))).))))((((((((((.....((((((.....))))))...(((....)))................))))))))-)) ( -24.80)
>DroSim_CAF1 19948 104 + 1
UUUGCAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUCAAAUUGAAAAACCCAAGAGGGGCAAGAGGAAAAGCGAAUGUUGUU-UG
.(((((((((((((........)))))).)))))))(((((((.....((((((.....))))))...(((....)))................))))))).-.. ( -28.40)
>DroEre_CAF1 19683 92 + 1
UUUGUAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUGAAAUUGAAAAGCCC----GGGGUAAG-----AAGUGAAUG---UU-UG
.(((((((((((((........)))))).)))))))((..(..((...((((((.....))))))...)).----)..))...-----.........---..-.. ( -16.00)
>DroYak_CAF1 22649 92 + 1
UUUGUAACUACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUAAAAUUGAAAAACCC----GCGGUAAG-----AAGUGAGUG---UU-UG
.(((((((((((((........)))).)))))))))..(((((((...((((((.....))))))...))(----((......-----..))).)))---))-.. ( -17.90)
>consensus
UUUGUAACAACAGCAAUUAUUAGCUGUUAGUUGUAGGCAACAUGGAAAUUCGAUAUCAAAUUGAAAAACCC__GAGGGGUAAG_GGAAAAGCGAAUGUUGUU_UG
.(((((((((((((........)))))).)))))))(((((((.....((((((.....))))))..((((.....))))..............))))))).... (-16.04 = -17.84 +   1.80)

alignment

secondary structure

dotplot

Window 9

Location	14,892,447 – 14,892,549
Length	102
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	87.84
Mean single sequence MFE	-17.44
Consensus MFE	-11.64
Energy contribution	-12.04
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.37
Structure conservation index	0.67
SVM decision value	0.33
SVM RNA-class probability	0.690321
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14892447 102 - 27905053
CAAAACAACAUUCGCUUUUCC--UUACCCCUCG-GGUUUUUUCAAUUUGAUAUCGAAUUUCCAUGUUGCCUACAACUAACAGCUAAUAAUUGCUGUUGUUACAAA
.....((((((..........--..((((...)-)))......((((((....))))))...)))))).....(((.((((((........)))))))))..... ( -18.50)
>DroSec_CAF1 20076 104 - 1
CA-AACAACAUUCGCUUUUCCUCUUGCCCCUCUUGGGUUUUUCAAUUUGAUAUCGAAUUUCCAUGUUGCCUACAACUAACAGCUAAUAAUUGCUGUUGUUACAAA
..-..((((((..............((((.....)))).....((((((....))))))...)))))).....(((.((((((........)))))))))..... ( -19.70)
>DroSim_CAF1 19948 104 - 1
CA-AACAACAUUCGCUUUUCCUCUUGCCCCUCUUGGGUUUUUCAAUUUGAUAUCGAAUUUCCAUGUUGCCUACAACUAACAGCUAAUAAUUGCUGUUGUUGCAAA
..-..((((((..............((((.....)))).....((((((....))))))...))))))....((((.((((((........)))))))))).... ( -22.20)
>DroEre_CAF1 19683 92 - 1
CA-AA---CAUUCACUU-----CUUACCCC----GGGCUUUUCAAUUUCAUAUCGAAUUUCCAUGUUGCCUACAACUAACAGCUAAUAAUUGCUGUUGUUACAAA
..-..---.........-----........----((((........(((.....)))..........))))..(((.((((((........)))))))))..... ( -14.07)
>DroYak_CAF1 22649 92 - 1
CA-AA---CACUCACUU-----CUUACCGC----GGGUUUUUCAAUUUUAUAUCGAAUUUCCAUGUUGCCUACAACUAACAGCUAAUAAUUGCUGUAGUUACAAA
..-..---.........-----......(.----.(((.....(((((......)))))........)))..)(((((.((((........)))))))))..... ( -12.72)
>consensus
CA_AACAACAUUCGCUUUUCC_CUUACCCCUC__GGGUUUUUCAAUUUGAUAUCGAAUUUCCAUGUUGCCUACAACUAACAGCUAAUAAUUGCUGUUGUUACAAA
..................................(((...(((.((.....)).)))..)))..((((....))))(((((((........)))))))....... (-11.64 = -12.04 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:18 2006