Locus 452

Sequence ID	2R_DroMel_CAF1
Location	2,595,455 – 2,595,588
Length	133
Max. P	0.977412

overview

Window 3

Location	2,595,455 – 2,595,565
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	87.18
Mean single sequence MFE	-20.90
Consensus MFE	-16.94
Energy contribution	-17.54
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.81
SVM decision value	0.91
SVM RNA-class probability	0.879159
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2595455 110 + 20766785
UAAUUGCCAGAGAAUUUACGAUAAUGUUUUAAAUUAAAAAGGAUGUUGGACCGGGCAUCCCAAGCCCAUCCACAUCCACAACUGUAUCCCUGUCCCCAUGCCCAUUCCCA
.......(((.((...((((.((((.......))))....((((((.(((..((((.......)))).))))))))).....)))))).))).................. ( -23.20)
>DroSec_CAF1 29628 110 + 1
UAAUUGCCAGAGAAUUUACGAUAAUGUUUUAAAUUAAAAAGGAUGUUGGACCGGGCAUCCCAAGCCCAUCCACAUCCACAACUGUAUCCCUGUCCCCAUGCCCAUCCCCA
.......(((.((...((((.((((.......))))....((((((.(((..((((.......)))).))))))))).....)))))).))).................. ( -23.20)
>DroSim_CAF1 29154 110 + 1
UAAUUGCCAGAGAAUUUACGAUAAUGUUUUAAAUUAAAAAGGAUGUUGGACCGGGCAUCCCAAGCCCAUCCACAUCCACAACUGUAUCCCUGUCCCCAUGCCCAUCCCCA
.......(((.((...((((.((((.......))))....((((((.(((..((((.......)))).))))))))).....)))))).))).................. ( -23.20)
>DroEre_CAF1 29469 109 + 1
UAAUUGCCAGAGAAUUUACGAUAAUGUUUUAAAUUAAAAAGGAUGUUGGACCA-GCAACCCAAGCCCAUCCACAUCCACAUCCACAUCCACAUCAACAUCCACAUCCGUA
................((((.((((.......))))....((((((.(((...-((.......))...))))))))).............................)))) ( -15.10)
>DroYak_CAF1 28377 94 + 1
UAAUUGCCAGAGAAUUUACGAUAAUGUUUUAAAUUAAAAAGGAUGUUGGACCGGGCAUCCCAAGCCCAUCCACAUCAACAACCGUAACCAUGCC----------------
...............(((((.((((.......)))).....(((((.(((..((((.......)))).))))))))......))))).......---------------- ( -19.80)
>consensus
UAAUUGCCAGAGAAUUUACGAUAAUGUUUUAAAUUAAAAAGGAUGUUGGACCGGGCAUCCCAAGCCCAUCCACAUCCACAACUGUAUCCCUGUCCCCAUGCCCAUCCCCA
............((((((.(((...))).)))))).....((((((.(((..((((.......)))).)))))))))................................. (-16.94 = -17.54 +   0.60)

alignment

secondary structure

dotplot

Window 4

Location	2,595,455 – 2,595,565
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	87.18
Mean single sequence MFE	-31.29
Consensus MFE	-22.02
Energy contribution	-22.54
Covariance contribution	0.52
Combinations/Pair	1.13
Mean z-score	-1.76
Structure conservation index	0.70
SVM decision value	0.08
SVM RNA-class probability	0.574161
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2595455 110 - 20766785
UGGGAAUGGGCAUGGGGACAGGGAUACAGUUGUGGAUGUGGAUGGGCUUGGGAUGCCCGGUCCAACAUCCUUUUUAAUUUAAAACAUUAUCGUAAAUUCUCUGGCAAUUA
.((((((..((.((....))..((((..(((..((((((((((((((.......)))).)))).))))))............)))..))))))..))))))......... ( -33.64)
>DroSec_CAF1 29628 110 - 1
UGGGGAUGGGCAUGGGGACAGGGAUACAGUUGUGGAUGUGGAUGGGCUUGGGAUGCCCGGUCCAACAUCCUUUUUAAUUUAAAACAUUAUCGUAAAUUCUCUGGCAAUUA
.((((((..((.((....))..((((..(((..((((((((((((((.......)))).)))).))))))............)))..))))))..))))))......... ( -33.14)
>DroSim_CAF1 29154 110 - 1
UGGGGAUGGGCAUGGGGACAGGGAUACAGUUGUGGAUGUGGAUGGGCUUGGGAUGCCCGGUCCAACAUCCUUUUUAAUUUAAAACAUUAUCGUAAAUUCUCUGGCAAUUA
.((((((..((.((....))..((((..(((..((((((((((((((.......)))).)))).))))))............)))..))))))..))))))......... ( -33.14)
>DroEre_CAF1 29469 109 - 1
UACGGAUGUGGAUGUUGAUGUGGAUGUGGAUGUGGAUGUGGAUGGGCUUGGGUUGC-UGGUCCAACAUCCUUUUUAAUUUAAAACAUUAUCGUAAAUUCUCUGGCAAUUA
..((((.((..(((.((((((.((..((((...((((((((((.(((.......))-).)))).))))))..))))..))...)))))).)))..))..))))....... ( -31.60)
>DroYak_CAF1 28377 94 - 1
----------------GGCAUGGUUACGGUUGUUGAUGUGGAUGGGCUUGGGAUGCCCGGUCCAACAUCCUUUUUAAUUUAAAACAUUAUCGUAAAUUCUCUGGCAAUUA
----------------(.((.((((((((((((((((((((((((((.......)))).)))).))))).............))))..)))))))...)).)).)..... ( -24.91)
>consensus
UGGGGAUGGGCAUGGGGACAGGGAUACAGUUGUGGAUGUGGAUGGGCUUGGGAUGCCCGGUCCAACAUCCUUUUUAAUUUAAAACAUUAUCGUAAAUUCUCUGGCAAUUA
................(.((((((.........((((((((((((((.......)))).)))).)))))).............((......))....)))))).)..... (-22.02 = -22.54 +   0.52)

alignment

secondary structure

dotplot

Window 5

Location	2,595,494 – 2,595,588
Length	94
Sequences	3
Columns	94
Reading direction	forward
Mean pairwise identity	97.87
Mean single sequence MFE	-21.73
Consensus MFE	-20.81
Energy contribution	-21.14
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.87
Structure conservation index	0.96
SVM decision value	1.79
SVM RNA-class probability	0.977412
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2595494 94 + 20766785
AGGAUGUUGGACCGGGCAUCCCAAGCCCAUCCACAUCCACAACUGUAUCCCUGUCCCCAUGCCCAUUCCCAUCCUCAGUUCCCCCGAUUCACUU
.((((((.(((..((((.......)))).)))))))))..(((((..............................))))).............. ( -21.11)
>DroSec_CAF1 29667 94 + 1
AGGAUGUUGGACCGGGCAUCCCAAGCCCAUCCACAUCCACAACUGUAUCCCUGUCCCCAUGCCCAUCCCCAUCCGCAGUUCCCCCGAUUCACUU
.((((((.(((..((((.......)))).)))))))))..((((((............................)))))).............. ( -22.49)
>DroSim_CAF1 29193 93 + 1
AGGAUGUUGGACCGGGCAUCCCAAGCCCAUCCACAUCCACAACUGUAUCCCUGUCCCCAUGCCCAUCCCCAUCCGCAGU-CCCCCGAUUCACUU
.((((((.(((..((((.......)))).)))))))))............((((....(((........)))..)))).-.............. ( -21.60)
>consensus
AGGAUGUUGGACCGGGCAUCCCAAGCCCAUCCACAUCCACAACUGUAUCCCUGUCCCCAUGCCCAUCCCCAUCCGCAGUUCCCCCGAUUCACUU
.((((((.(((..((((.......)))).)))))))))..(((((..............................))))).............. (-20.81 = -21.14 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:56 2006