Locus 2014

Sequence ID	2L_DroMel_CAF1
Location	5,453,966 – 5,454,072
Length	106
Max. P	0.931746

overview

Window 1

Location	5,453,966 – 5,454,072
Length	106
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	85.79
Mean single sequence MFE	-23.00
Consensus MFE	-16.18
Energy contribution	-17.26
Covariance contribution	1.08
Combinations/Pair	1.10
Mean z-score	-2.57
Structure conservation index	0.70
SVM decision value	1.22
SVM RNA-class probability	0.931746
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5453966 106 + 22407834
CAAAAA---GAAACGA------GAAAAGGGGGAAAAUUCUUGAGGGGAGUGCCGCCAAGAAAGGCGGGAAAGGAGAAAGAGCUAAGUUAUUACAUUUAGCGGGCACUAAAAUGUC
......---....(((------(((...........)))))).....(((((((((......)))...............(((((((......))))))).))))))........ ( -25.30)
>DroSec_CAF1 73375 99 + 1
---AAA---GAAACGU------GAAAAGGGGGAAAAUUCUUGAGGGGAGUGCCGCCAAGAAAGGCGGGAAAGGA----GAGCUAAGUUAUUAGAUUUAGCGGGCAAUAAAAUGUC
---...---...((((------.............(((((.....)))))((((((......))).........----..((((((((....)))))))).)))......)))). ( -20.90)
>DroSim_CAF1 84497 105 + 1
G-AAAA---GAAACGU------GAAAAGGGGGAAAAUUCUUGAGGGGAGUGCCGCCAAGAAAGGCGGGAAAGGAGAAAGAGCUAAGUUAUUACAUUUAGCGGGCACUAAAAUGUC
.-....---....(.(------...(((((......)))))..).).(((((((((......)))...............(((((((......))))))).))))))........ ( -23.70)
>DroEre_CAF1 74439 111 + 1
G-AAAAUAAACGAGGCGCAGGGGGAAAAGGGGAAAAUUCUUGAAGGGAGUGCC---ACGAAAGGCGGGAAAGGAAAAAGAGCUAAGUUAUUACAUUUAGCGGGCACUAAAAUGUC
.-...........((((((((((.............)))))).....((((((---.(....).................(((((((......))))))).))))))....)))) ( -22.02)
>DroYak_CAF1 81000 108 + 1
G-AAAAUAAGAAACGU---GAGGAAAAGGGGGAAAAUUCCUGAAGGGAGUGCC---ACGAAAGGCGGGAAAGGAAAAAGAGCUAAGUUAUUACAUUUAGCGGGCACUAAAAUGUC
.-...........(..---..)....(((((.....)))))......((((((---.(....).................(((((((......))))))).))))))........ ( -23.10)
>consensus
G_AAAA___GAAACGU______GAAAAGGGGGAAAAUUCUUGAGGGGAGUGCCGCCAAGAAAGGCGGGAAAGGAAAAAGAGCUAAGUUAUUACAUUUAGCGGGCACUAAAAUGUC
..........................(((((.....)))))......(((((((((......)))...............(((((((......))))))).))))))........ (-16.18 = -17.26 +   1.08)

alignment

secondary structure

dotplot

Window 2

Location	5,453,966 – 5,454,072
Length	106
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	85.79
Mean single sequence MFE	-15.86
Consensus MFE	-11.10
Energy contribution	-12.50
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-2.44
Structure conservation index	0.70
SVM decision value	1.01
SVM RNA-class probability	0.900088
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5453966 106 - 22407834
GACAUUUUAGUGCCCGCUAAAUGUAAUAACUUAGCUCUUUCUCCUUUCCCGCCUUUCUUGGCGGCACUCCCCUCAAGAAUUUUCCCCCUUUUC------UCGUUUC---UUUUUG
(((.....((((((.(((((.(......).)))))...............(((......))))))))).......((((...........)))------).)))..---...... ( -18.50)
>DroSec_CAF1 73375 99 - 1
GACAUUUUAUUGCCCGCUAAAUCUAAUAACUUAGCUC----UCCUUUCCCGCCUUUCUUGGCGGCACUCCCCUCAAGAAUUUUCCCCCUUUUC------ACGUUUC---UUU---
(((.......((((.(((((..........)))))..----.........(((......)))))))..........(((...........)))------..)))..---...--- ( -14.20)
>DroSim_CAF1 84497 105 - 1
GACAUUUUAGUGCCCGCUAAAUGUAAUAACUUAGCUCUUUCUCCUUUCCCGCCUUUCUUGGCGGCACUCCCCUCAAGAAUUUUCCCCCUUUUC------ACGUUUC---UUUU-C
(((.....((((((.(((((.(......).)))))...............(((......)))))))))........(((...........)))------..)))..---....-. ( -18.40)
>DroEre_CAF1 74439 111 - 1
GACAUUUUAGUGCCCGCUAAAUGUAAUAACUUAGCUCUUUUUCCUUUCCCGCCUUUCGU---GGCACUCCCUUCAAGAAUUUUCCCCUUUUCCCCCUGCGCCUCGUUUAUUUU-C
.........((((..(((((.(......).)))))...............(((......---)))................................))))............-. ( -13.30)
>DroYak_CAF1 81000 108 - 1
GACAUUUUAGUGCCCGCUAAAUGUAAUAACUUAGCUCUUUUUCCUUUCCCGCCUUUCGU---GGCACUCCCUUCAGGAAUUUUCCCCCUUUUCCUC---ACGUUUCUUAUUUU-C
.((((((.(((....)))))))))(((((...(((...............(((......---))).........(((((...........))))).---..)))..)))))..-. ( -14.90)
>consensus
GACAUUUUAGUGCCCGCUAAAUGUAAUAACUUAGCUCUUUCUCCUUUCCCGCCUUUCUUGGCGGCACUCCCCUCAAGAAUUUUCCCCCUUUUC______ACGUUUC___UUUU_C
........((((((.(((((.(......).)))))...............(((......)))))))))............................................... (-11.10 = -12.50 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:08 2006