Locus 6696

Sequence ID	2L_DroMel_CAF1
Location	18,728,214 – 18,728,374
Length	160
Max. P	0.996235

overview

Window 0

Location	18,728,214 – 18,728,334
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.77
Mean single sequence MFE	-26.03
Consensus MFE	-25.39
Energy contribution	-25.50
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.16
Structure conservation index	0.98
SVM decision value	1.16
SVM RNA-class probability	0.924228
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18728214 120 + 22407834
UUUACACAUAACAUAUAUUUUGUAUUUAGGAUGUAUCCUUAAGCGAUCCUAUCUUCACUUCACUAUAAAACGGUAGCGCUUCAUUUUGAAUGUUUUACCGUUAUCACCGAUCGCAUGGCG
......(((...((((((((((....))))))))))......((((((.(((............))).((((((((.(((((.....))).)).))))))))......)))))))))... ( -23.80)
>DroSec_CAF1 20776 119 + 1
UUAACACAUAACAUAUAUUUUGUAUUUAGGAUGUAUCCUUAAGCGAUCCUAUCUUCACUUCACUGUA-AACGGUAGCGCUUCAUUUUGAAUGUUUUACCGUUAUCACCGAUCGCAUGGCG
......(((...((((((((((....))))))))))......((((((........((......)).-((((((((.(((((.....))).)).))))))))......)))))))))... ( -27.00)
>DroSim_CAF1 19253 119 + 1
UUUACACAUAACAUAUAUUUUGUAUUUAGGAUGUAUCCUUAAGCGAUCCUAUCUUCACUUCACUGUA-AACGGUAACGCUUCAUUUUGAAUGUUUUACCGUUAUCACCGAUCGCAUGGCG
......(((...((((((((((....))))))))))......((((((........((......)).-((((((((.(((((.....))).)).))))))))......)))))))))... ( -27.30)
>consensus
UUUACACAUAACAUAUAUUUUGUAUUUAGGAUGUAUCCUUAAGCGAUCCUAUCUUCACUUCACUGUA_AACGGUAGCGCUUCAUUUUGAAUGUUUUACCGUUAUCACCGAUCGCAUGGCG
......(((...((((((((((....))))))))))......((((((........((......))..((((((((.(((((.....))).)).))))))))......)))))))))... (-25.39 = -25.50 +   0.11)

alignment

secondary structure

dotplot

Window 1

Location	18,728,254 – 18,728,374
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.22
Mean single sequence MFE	-28.68
Consensus MFE	-28.16
Energy contribution	-28.52
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.48
Structure conservation index	0.98
SVM decision value	1.80
SVM RNA-class probability	0.977666
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18728254 120 + 22407834
AAGCGAUCCUAUCUUCACUUCACUAUAAAACGGUAGCGCUUCAUUUUGAAUGUUUUACCGUUAUCACCGAUCGCAUGGCGUUACGUCUUACGACCGCUUUACGUAGUGGAUCUCUUCUGC
(((.(((((............(((((..((((((((.(((((.....))).)).)))))))).....((.(((...((((...))))...))).))......)))))))))).))).... ( -27.30)
>DroSec_CAF1 20816 119 + 1
AAGCGAUCCUAUCUUCACUUCACUGUA-AACGGUAGCGCUUCAUUUUGAAUGUUUUACCGUUAUCACCGAUCGCAUGGCGUUACGUCUUACGACCGCUUUACGUAGUGGAUCUCUUCUGC
..((((((........((......)).-((((((((.(((((.....))).)).))))))))......))))))..((((...))))....(((((((......))))).))........ ( -30.30)
>DroSim_CAF1 19293 119 + 1
AAGCGAUCCUAUCUUCACUUCACUGUA-AACGGUAACGCUUCAUUUUGAAUGUUUUACCGUUAUCACCGAUCGCAUGGCGUUACGUCUUACGACCGCUUUACGUAGUGGAUCUCUUCUGC
..((((((........((......)).-((((((((.(((((.....))).)).))))))))......))))))..((((...))))....(((((((......))))).))........ ( -30.60)
>DroEre_CAF1 21040 116 + 1
-AGCGAUCCUAUCUUCACUUCACUGUA-AACGGUAACGCUUCAUUUUGAAUGUUUCACCGUUAUCACCGAUCGCAUGGCGUUACGUCU--CGACCGCUUUACGUAGUGGAUCUCUUCUGC
-.((((((........((......)).-((((((((((.(((.....)))))))..))))))......))))))..((((...)))).--.(((((((......))))).))........ ( -27.60)
>DroYak_CAF1 21060 117 + 1
AAGCGAUCCUAUCUUCACUUCACUGUA-AACGGUAACGCUUCAUUUUGAAUGUUUAACCGUUAUCAUCGAUCGCAUGGCGUUACGUCU--CGACCGCUUUACGUAGUGGAUCUCUUCUGU
..((((((........((......)).-((((((((((.(((.....)))))))..))))))......))))))..((((...)))).--.(((((((......))))).))........ ( -27.60)
>consensus
AAGCGAUCCUAUCUUCACUUCACUGUA_AACGGUAACGCUUCAUUUUGAAUGUUUUACCGUUAUCACCGAUCGCAUGGCGUUACGUCUUACGACCGCUUUACGUAGUGGAUCUCUUCUGC
..((((((........((......))..((((((((.(((((.....))).)).))))))))......))))))..((((...))))....(((((((......))))).))........ (-28.16 = -28.52 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	18,728,254 – 18,728,374
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.22
Mean single sequence MFE	-32.30
Consensus MFE	-32.24
Energy contribution	-32.76
Covariance contribution	0.52
Combinations/Pair	1.06
Mean z-score	-1.70
Structure conservation index	1.00
SVM decision value	2.67
SVM RNA-class probability	0.996235
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18728254 120 - 22407834
GCAGAAGAGAUCCACUACGUAAAGCGGUCGUAAGACGUAACGCCAUGCGAUCGGUGAUAACGGUAAAACAUUCAAAAUGAAGCGCUACCGUUUUAUAGUGAAGUGAAGAUAGGAUCGCUU
....(((.(((((....((((..((((((....)))....)))..))))((((.......))))...((.((((..((((((((....))))))))..)))))).......))))).))) ( -32.30)
>DroSec_CAF1 20816 119 - 1
GCAGAAGAGAUCCACUACGUAAAGCGGUCGUAAGACGUAACGCCAUGCGAUCGGUGAUAACGGUAAAACAUUCAAAAUGAAGCGCUACCGUU-UACAGUGAAGUGAAGAUAGGAUCGCUU
....(((.(((((....((((..((((((....)))....)))..)))).(((.((..(((((((.....(((.....)))....)))))))-..)).)))..........))))).))) ( -33.70)
>DroSim_CAF1 19293 119 - 1
GCAGAAGAGAUCCACUACGUAAAGCGGUCGUAAGACGUAACGCCAUGCGAUCGGUGAUAACGGUAAAACAUUCAAAAUGAAGCGUUACCGUU-UACAGUGAAGUGAAGAUAGGAUCGCUU
....(((.(((((....((((..((((((....)))....)))..)))).(((.((..((((((((....(((.....)))...))))))))-..)).)))..........))))).))) ( -35.90)
>DroEre_CAF1 21040 116 - 1
GCAGAAGAGAUCCACUACGUAAAGCGGUCG--AGACGUAACGCCAUGCGAUCGGUGAUAACGGUGAAACAUUCAAAAUGAAGCGUUACCGUU-UACAGUGAAGUGAAGAUAGGAUCGCU-
.....((.(((((....((((..(((..((--...))...)))..)))).(((.((..((((((((....(((.....)))...))))))))-..)).)))..........))))).))- ( -31.60)
>DroYak_CAF1 21060 117 - 1
ACAGAAGAGAUCCACUACGUAAAGCGGUCG--AGACGUAACGCCAUGCGAUCGAUGAUAACGGUUAAACAUUCAAAAUGAAGCGUUACCGUU-UACAGUGAAGUGAAGAUAGGAUCGCUU
....(((.(((((....((((..(((..((--...))...)))..)))).(((.((..((((((..(((.(((.....)))..)))))))))-..)).)))..........))))).))) ( -28.00)
>consensus
GCAGAAGAGAUCCACUACGUAAAGCGGUCGUAAGACGUAACGCCAUGCGAUCGGUGAUAACGGUAAAACAUUCAAAAUGAAGCGUUACCGUU_UACAGUGAAGUGAAGAUAGGAUCGCUU
....(((.(((((....((((..((((((....)))....)))..)))).(((.((..((((((((....(((.....)))...))))))))...)).)))..........))))).))) (-32.24 = -32.76 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:46 2006