Locus 1320

Sequence ID	X_DroMel_CAF1
Location	3,932,050 – 3,932,183
Length	133
Max. P	0.996785

overview

Window 5

Location	3,932,050 – 3,932,148
Length	98
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	74.46
Mean single sequence MFE	-29.18
Consensus MFE	-12.12
Energy contribution	-13.75
Covariance contribution	1.62
Combinations/Pair	1.13
Mean z-score	-2.81
Structure conservation index	0.42
SVM decision value	0.99
SVM RNA-class probability	0.895314
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3932050 98 + 22224390
CCCGGUACAUAACAAGAAC-------CCAUUAAUAUCCAAUACCACACACACGCACAAGUGCAUCAUCAUGUGCAUGUGUGAGUGUG-------------UGAGCUACGAACAAGAGA
...(((.(.......).))-------)................(((((((.((((((.(..(((....)))..).)))))).)))))-------------))................ ( -26.80)
>DroSec_CAF1 48563 98 + 1
CCCGGUACAUAACAAGAAC-------CCAUAAAUAUCCAAUACCACACACACGCACAAGUGCAUCAUCAUGUGCAUGUGUGAGUGUG-------------UGAGCUACGAACAAGAGA
...(((.(.......).))-------)................(((((((.((((((.(..(((....)))..).)))))).)))))-------------))................ ( -26.80)
>DroYak_CAF1 53532 106 + 1
CCCGGUACAUAACAAGAAC-------CCAUUUAUAUCCAAUACCACACACACGCACAACUGCAUCAUCGUGUGCAUAUGUGAGUGUGUGUGUGUG-----UGAGCUACGAUCAAGAGA
...(((.(.......).))-------)............(((((((((((((.((((..(((((......)))))..)))).))))))))).)))-----)................. ( -29.90)
>DroPer_CAF1 53423 106 + 1
CCCGGUACAUAACAUGAACGAUCGACCCGUUGAGAUCUCUAAGCAC--GCACACACAACUGUAUCCUC---UGAAUAUCCUUGUGUGU-------GUGUGUGCCUAGAGAACAAGAGA
..............(.((((.......)))).)(.((((((.((((--(((((((((...((((....---...)))).....)))))-------)))))))).)))))).)...... ( -33.20)
>consensus
CCCGGUACAUAACAAGAAC_______CCAUUAAUAUCCAAUACCACACACACGCACAACUGCAUCAUCAUGUGCAUAUGUGAGUGUG_____________UGAGCUACGAACAAGAGA
...............................................(((((.((((.((((((......)))))).)))).)))))............................... (-12.12 = -13.75 +   1.62)

alignment

secondary structure

dotplot

Window 6

Location	3,932,082 – 3,932,183
Length	101
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	72.33
Mean single sequence MFE	-28.98
Consensus MFE	-12.12
Energy contribution	-13.75
Covariance contribution	1.62
Combinations/Pair	1.13
Mean z-score	-3.74
Structure conservation index	0.42
SVM decision value	2.75
SVM RNA-class probability	0.996785
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3932082 101 + 22224390
AUACCACACACACGCACAAGUGCAUCAUCAUGUGCAUGUGUGAGUGUG-------------UGAGCUACGAACAAGAGAAACAAUGCAAAAGUAAUAGCAACAAAGAAGCUGAU
....(((((((.((((((.(..(((....)))..).)))))).)))))-------------))((((.(......)........(((..........))).......))))... ( -29.30)
>DroSec_CAF1 48595 101 + 1
AUACCACACACACGCACAAGUGCAUCAUCAUGUGCAUGUGUGAGUGUG-------------UGAGCUACGAACAAGAGAAACAAAGCAAAAGCAAAAGCAACAAAGAAGCUGAU
....(((((((.((((((.(..(((....)))..).)))))).)))))-------------))((((.(......).........((....))..............))))... ( -29.40)
>DroYak_CAF1 53564 108 + 1
AUACCACACACACGCACAACUGCAUCAUCGUGUGCAUAUGUGAGUGUGUGUGUGUG-----UGAGCUACGAUCAAGAGAA-CAAAGCAAACGCAAAAGCAACAAAGAAGCUGAU
....(((((((((.((((..(((((......)))))..)))).)))))))))((((-----(..(((..(.((....)).-)..)))..)))))..(((.........)))... ( -34.20)
>DroPer_CAF1 53462 91 + 1
UAAGCAC--GCACACACAACUGUAUCCUC---UGAAUAUCCUUGUGUGU-------GUGUGUGCCUAGAGAACAAGAGAAACU-----------AAAGCAACCAAGAAGAUAAU
...((((--((((((((((..((((....---...))))..))))))))-------)))))).....................-----------.................... ( -23.00)
>consensus
AUACCACACACACGCACAACUGCAUCAUCAUGUGCAUAUGUGAGUGUG_____________UGAGCUACGAACAAGAGAAACAAAGCAAAAGCAAAAGCAACAAAGAAGCUGAU
........(((((.((((.((((((......)))))).)))).))))).................................................................. (-12.12 = -13.75 +   1.62)

alignment

secondary structure

dotplot

Window 7

Location	3,932,082 – 3,932,183
Length	101
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	72.33
Mean single sequence MFE	-27.30
Consensus MFE	-13.11
Energy contribution	-14.68
Covariance contribution	1.56
Combinations/Pair	1.12
Mean z-score	-2.44
Structure conservation index	0.48
SVM decision value	1.52
SVM RNA-class probability	0.960902
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3932082 101 - 22224390
AUCAGCUUCUUUGUUGCUAUUACUUUUGCAUUGUUUCUCUUGUUCGUAGCUCA-------------CACACUCACACAUGCACAUGAUGAUGCACUUGUGCGUGUGUGUGGUAU
..((((......)))).............................(((.(.((-------------(((((.((((..(((((.....).))))..)))).))))))).).))) ( -25.40)
>DroSec_CAF1 48595 101 - 1
AUCAGCUUCUUUGUUGCUUUUGCUUUUGCUUUGUUUCUCUUGUUCGUAGCUCA-------------CACACUCACACAUGCACAUGAUGAUGCACUUGUGCGUGUGUGUGGUAU
..((((......)))).....((....))................(((.(.((-------------(((((.((((..(((((.....).))))..)))).))))))).).))) ( -26.40)
>DroYak_CAF1 53564 108 - 1
AUCAGCUUCUUUGUUGCUUUUGCGUUUGCUUUG-UUCUCUUGAUCGUAGCUCA-----CACACACACACACUCACAUAUGCACACGAUGAUGCAGUUGUGCGUGUGUGUGGUAU
..((((......))))....(((((..(((.((-.((....)).)).)))..)-----)...(((((((((.((((..(((((.....).))))..)))).)))))))))))). ( -34.60)
>DroPer_CAF1 53462 91 - 1
AUUAUCUUCUUGGUUGCUUU-----------AGUUUCUCUUGUUCUCUAGGCACACAC-------ACACACAAGGAUAUUCA---GAGGAUACAGUUGUGUGUGC--GUGCUUA
...........((..((...-----------.))..)).........(((((((.(((-------(((((....(.((((..---...)))))...)))))))).--))))))) ( -22.80)
>consensus
AUCAGCUUCUUUGUUGCUUUUGCUUUUGCUUUGUUUCUCUUGUUCGUAGCUCA_____________CACACUCACACAUGCACAUGAUGAUGCACUUGUGCGUGUGUGUGGUAU
..((((......))))......................................................(.((((((((((((............)))))))))))).).... (-13.11 = -14.68 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:28 2006