Locus 7237

Sequence ID	2L_DroMel_CAF1
Location	20,273,424 – 20,273,567
Length	143
Max. P	0.978270

overview

Window 3

Location	20,273,424 – 20,273,535
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.46
Mean single sequence MFE	-24.30
Consensus MFE	-22.98
Energy contribution	-23.18
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.95
SVM decision value	1.81
SVM RNA-class probability	0.978270
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20273424 111 - 22407834
GAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCC------CGUCCGGCAACAGCAUUUGCACAUGACCAUAGA---
..((((((.....((((((............))))))......................((((((.....))))))..------..))))))....((....)).............--- ( -23.40)
>DroSec_CAF1 24275 114 - 1
GAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCC------CGUCCGGCAACAGCAUUUGCACAUGACCGUAGAACA
..((((((.....((((((............))))))......................((((((.....))))))..------..)))))).......(((((........)))))... ( -23.80)
>DroSim_CAF1 23153 114 - 1
GAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCC------CGUCCGGCAGCAGCAUUUGCACAUGACCGUAGAACA
..((((((.....((((((............))))))......................((((((.....))))))..------..)))))).......(((((........)))))... ( -23.80)
>DroEre_CAF1 4399 117 - 1
GAGCUGGAAAAAAGGGUAACAUAAAGCUCUCCUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUUUCGUUCCCGUCCGGCAACAGCAUUUGCACAUGACCGUAGA---
..((((((.....(((.(((.....((......))......................((((((((.....)))))))).)))))).))))))....((....)).............--- ( -27.10)
>DroYak_CAF1 4876 111 - 1
GAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCU------CGUCCGGCAACAGCAUUUGCACAUGACCGUAGA---
..((((((.....((((((............))))))......................((((((.....))))))..------..))))))....((....)).............--- ( -23.40)
>consensus
GAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCC______CGUCCGGCAACAGCAUUUGCACAUGACCGUAGA___
..((((((.....((((((............))))))......................((((((.....))))))..........))))))....((....))................ (-22.98 = -23.18 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	20,273,457 – 20,273,567
Length	110
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	92.43
Mean single sequence MFE	-17.01
Consensus MFE	-15.32
Energy contribution	-15.16
Covariance contribution	-0.16
Combinations/Pair	1.06
Mean z-score	-1.51
Structure conservation index	0.90
SVM decision value	1.27
SVM RNA-class probability	0.937926
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20273457 110 - 22407834
UAAACGGCACAGAAACAAAAAAAAAAAAUGGUGAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCC--
...((((..(((..((..............))...))).......((((((............)))))).......))))...........((((((.....))))))..-- ( -15.74)
>DroSec_CAF1 24311 109 - 1
UAAACGGCACAGAAACAAAAAA-AAACAUGGUGAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCC--
...((((..(((..((......-.......))...))).......((((((............)))))).......))))...........((((((.....))))))..-- ( -15.82)
>DroSim_CAF1 23189 109 - 1
UAAACGGCACAGAAACAAAAAA-AAACAUGGUGAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCC--
...((((..(((..((......-.......))...))).......((((((............)))))).......))))...........((((((.....))))))..-- ( -15.82)
>DroEre_CAF1 4436 106 - 1
UAAACGGCACAGAAAAA------AAUAAUGGUGAGCUGGAAAAAAGGGUAACAUAAAGCUCUCCUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUUUCG
.....((((........------......((.(((((...................))))).)))))).....................((((((((.....)))))))).. ( -18.84)
>DroYak_CAF1 4909 102 - 1
UAAACGGCACAGAAAAA------A--AAUGGGGAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCU--
.....((((........------.--...((((((((...................)))))))))))).......................((((((.....))))))..-- ( -18.81)
>consensus
UAAACGGCACAGAAACAAAAAA_AAAAAUGGUGAGCUGGAAAAAAGGGUAACAUAAAGCUCUCUUGCCCACAAAAAUCGUAAAAAAUUAAAAGUAUCUCGCAGAUACUCC__
.....((((....................((.(((((...................))))).)))))).......................((((((.....)))))).... (-15.32 = -15.16 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:12 2006