Locus 9389

Sequence ID	3R_DroMel_CAF1
Location	24,910,841 – 24,910,978
Length	137
Max. P	0.999992

overview

Window 2

Location	24,910,841 – 24,910,940
Length	99
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	95.48
Mean single sequence MFE	-29.24
Consensus MFE	-28.12
Energy contribution	-28.32
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.96
SVM decision value	3.39
SVM RNA-class probability	0.999128
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24910841 99 + 27905053
UCUCAUUGCGCUUAAAGCACACUUCACUGCUCUGAUGUAUGUCAAUUAGUCGACAAAUUGAUUGCGGCGCAUUCAACGCCGCCCAGCAGAUGAAGAAGU----
......((.((.....)).))((((((((((.........(((((((.(....).))))))).((((((.......))))))..))))).)))))....---- ( -29.40)
>DroSec_CAF1 22495 103 + 1
UCUCAUUGCGCUUAAAGCACACUUCACUGCUCUGAUGUAUGUCAAUUAGUCGACAAAUUGAUUGCGGCGCAUUCAACGCCGCCCAGCAGAUGAAGAAGUAGGU
.....((((((.....))...((((((((((.........(((((((.(....).))))))).((((((.......))))))..))))).)))))..)))).. ( -30.70)
>DroSim_CAF1 22137 103 + 1
UCUCAUUGCGCUUAAAGCACACUUCACUGCUCUGAUGUAUGUCAAUUAGUCGACAAAUUGAUUGCGGCGCAUUCAACGCCGCCCAGCAGAUGAAGAAGUAGGU
.....((((((.....))...((((((((((.........(((((((.(....).))))))).((((((.......))))))..))))).)))))..)))).. ( -30.70)
>DroEre_CAF1 22570 99 + 1
UCCCAUUGCGCUUUAAGCACACUUCAGUGCUCUGAUGUAUGUCAAUUAGUCGACAAAUUGAUUGCGGCGCAUUCAACGCCGCCCAGCAAAUGAAGAAGU----
...((((((((.((((((((......))))).))).))..(((((((.(....).))))))).((((((.......))))))...)).)))).......---- ( -26.00)
>DroYak_CAF1 22860 98 + 1
UCUCAUUGCGCUUUAAGCACACUUCACUGCUCUGAUGUAUGUCAAUUAGUCGACAAAUUGAUUGCGGCGCAUUCAACGCCGCCCAGCAGAUGAAG-AGU----
......((.((.....)).))((((((((((.........(((((((.(....).))))))).((((((.......))))))..))))).)))))-...---- ( -29.40)
>consensus
UCUCAUUGCGCUUAAAGCACACUUCACUGCUCUGAUGUAUGUCAAUUAGUCGACAAAUUGAUUGCGGCGCAUUCAACGCCGCCCAGCAGAUGAAGAAGU____
......((.((.....)).))((((((((((.........(((((((.(....).))))))).((((((.......))))))..))))).)))))........ (-28.12 = -28.32 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	24,910,841 – 24,910,940
Length	99
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	95.48
Mean single sequence MFE	-36.24
Consensus MFE	-35.72
Energy contribution	-35.92
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.38
Structure conservation index	0.99
SVM decision value	5.71
SVM RNA-class probability	0.999992
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24910841 99 - 27905053
----ACUUCUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGCAGUGAAGUGUGCUUUAAGCGCAAUGAGA
----.((((((((.(((((..(((((((.....)))))))........((((((....))))))........))))))))))(((((.....)))))..))). ( -37.00)
>DroSec_CAF1 22495 103 - 1
ACCUACUUCUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGCAGUGAAGUGUGCUUUAAGCGCAAUGAGA
.....((((((((.(((((..(((((((.....)))))))........((((((....))))))........))))))))))(((((.....)))))..))). ( -37.00)
>DroSim_CAF1 22137 103 - 1
ACCUACUUCUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGCAGUGAAGUGUGCUUUAAGCGCAAUGAGA
.....((((((((.(((((..(((((((.....)))))))........((((((....))))))........))))))))))(((((.....)))))..))). ( -37.00)
>DroEre_CAF1 22570 99 - 1
----ACUUCUUCAUUUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGCACUGAAGUGUGCUUAAAGCGCAAUGGGA
----.....((((((((((..(((((((.....)))))))........((((((....)))))).......((((((......))))))..)))).)))))). ( -33.10)
>DroYak_CAF1 22860 98 - 1
----ACU-CUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGCAGUGAAGUGUGCUUAAAGCGCAAUGAGA
----.((-(((((.(((((..(((((((.....)))))))........((((((....))))))........))))))))).(((((.....)))))..))). ( -37.10)
>consensus
____ACUUCUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGCAGUGAAGUGUGCUUUAAGCGCAAUGAGA
........(((((.(((((..(((((((.....)))))))........((((((....))))))........))))))))))(((((.....)))))...... (-35.72 = -35.92 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	24,910,869 – 24,910,978
Length	109
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	94.43
Mean single sequence MFE	-26.84
Consensus MFE	-24.58
Energy contribution	-24.98
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.08
Structure conservation index	0.92
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24910869 109 - 27905053
GCUCAGACAGCC--UCGUUAUUGCCCUCCAGAACCACCCU----ACUUCUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGC
((((.((..((.--........((((..((((........----.........))))..))))(((((.....)))))))..))....((((((....)))))).......)))) ( -31.83)
>DroSec_CAF1 22523 115 - 1
GCCCAGACAGCCCCUCGUUAUUGCCCUCCAGAACCACCCUACCUACUUCUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGC
((.(.((..((...........((((..((((.....................))))..))))(((((.....)))))))..))....((((((....)))))).......).)) ( -26.80)
>DroSim_CAF1 22165 115 - 1
GCCCAGACAGCCCAUCGUUAUUGCCCUCCAGAACCACCCUACCUACUUCUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGC
((.(.((..((...........((((..((((.....................))))..))))(((((.....)))))))..))....((((((....)))))).......).)) ( -26.80)
>DroEre_CAF1 22598 109 - 1
GCCCAGACAGCC--UCGUUAUUGCCCUCCACAACCACCCU----ACUUCUUCAUUUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGC
((((((.(((..--..........................----..........)))))))))(((((.....)))))..........((((((....))))))........... ( -23.46)
>DroYak_CAF1 22888 108 - 1
GCCCAGACAGCC--UCUUUAUUGCCCUACACAACCACCCU----ACU-CUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGC
((((((.(((..--..........................----...-......)))))))))(((((.....)))))..........((((((....))))))........... ( -25.29)
>consensus
GCCCAGACAGCC__UCGUUAUUGCCCUCCAGAACCACCCU____ACUUCUUCAUCUGCUGGGCGGCGUUGAAUGCGCCGCAAUCAAUUUGUCGACUAAUUGACAUACAUCAGAGC
((.(.((..((...........((((..((((.....................))))..))))(((((.....)))))))..))....((((((....)))))).......).)) (-24.58 = -24.98 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:33:26 2006