Locus 2123

Sequence ID	X_DroMel_CAF1
Location	5,751,291 – 5,751,476
Length	185
Max. P	0.960917

overview

Window 7

Location	5,751,291 – 5,751,396
Length	105
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	81.13
Mean single sequence MFE	-36.62
Consensus MFE	-25.16
Energy contribution	-27.60
Covariance contribution	2.45
Combinations/Pair	1.17
Mean z-score	-1.49
Structure conservation index	0.69
SVM decision value	0.21
SVM RNA-class probability	0.633745
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5751291 105 + 22224390
AUGUAUUGGUAUCUCUGUGCAGGAUUCGUGGGCAAAGCACUGAUCGAAAAGCUGCUGCGCUCCUGUCCAAAACUGGGCCGCAUCUAUGUGCUGAUGCGGCCCAAG
.(((((.((....)).)))))((((..(.((((..((((((........)).))))..))))).)))).....(((((((((((........))))))))))).. ( -41.90)
>DroGri_CAF1 29291 89 + 1
----------------AAAUAGGUUUCGUUGGCAAGGCACUCAUUGAGAAACUGUUGCGUUCGUGUCCAACGCUAAGCAGAAUCUAUGUGCUGCUGCGGCCCAAG
----------------.....((..((((.((((..((((......(((..((((((((((.......)))))..)))))..)))..)))))))))))).))... ( -22.80)
>DroSec_CAF1 24241 105 + 1
GUAUAUUGGUAUCUCUGUGCAGGCUUCGUGGGCAAGGCACUGAUCGAAAAGCUGCUGCGCUCCUGUCCAAAACUGGGCCGCAUCUACGUGCUCAUGCGGCCCAAG
.....((((.......((((((((((..((..((......))..))..))))..))))))......))))...((((((((((..........)))))))))).. ( -36.92)
>DroSim_CAF1 24830 105 + 1
GUAUAUUGGUAUCUCUGUGCAGGCUUCGUGGGCAAGGCACUGAUCGAAAAGCUGCUGCGCUCCUGUCCAAAACUGGGCCGCAUCUACGUGCUCAUGCGGCCCAAG
.....((((.......((((((((((..((..((......))..))..))))..))))))......))))...((((((((((..........)))))))))).. ( -36.92)
>DroEre_CAF1 24743 103 + 1
--UAAUUGGUAUUUUCGCGCAGGCUUCGUGGGCAAGGCUCUGAUCGAGAAGCUGCUGCGCUCGUGUCCAAAAGUGGGCCGCAUCUACGUGCUGAUGCGGCCCAAA
--...((((.((....(((((((((((.((..((......))..)).)))))..))))))....))))))...(((((((((((........))))))))))).. ( -46.10)
>DroYak_CAF1 26071 103 + 1
--AUCUUGAUAUCUUUGCGCAGGAUUCGUGGGCAAGGCUCUGAUCGAGAAGCUGCUGCGCUCGUGUCCCAAACUGGGCCGCAUCUAUGUGCUGAUGCGACCCAAA
--.....(((((....((((((.(((((.((((...))))....))))....).))))))..)))))......((((.((((((........)))))).)))).. ( -35.10)
>consensus
__AUAUUGGUAUCUCUGUGCAGGCUUCGUGGGCAAGGCACUGAUCGAAAAGCUGCUGCGCUCCUGUCCAAAACUGGGCCGCAUCUACGUGCUGAUGCGGCCCAAG
.....((((.......((((((((((..((..((......))..))..))))..))))))......))))...(((((((((((........))))))))))).. (-25.16 = -27.60 +   2.45)

alignment

secondary structure

dotplot

Window 8

Location	5,751,291 – 5,751,396
Length	105
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	81.13
Mean single sequence MFE	-34.04
Consensus MFE	-22.77
Energy contribution	-23.47
Covariance contribution	0.70
Combinations/Pair	1.26
Mean z-score	-1.53
Structure conservation index	0.67
SVM decision value	0.17
SVM RNA-class probability	0.617446
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5751291 105 - 22224390
CUUGGGCCGCAUCAGCACAUAGAUGCGGCCCAGUUUUGGACAGGAGCGCAGCAGCUUUUCGAUCAGUGCUUUGCCCACGAAUCCUGCACAGAGAUACCAAUACAU
..(((((((((((........)))))))))))((.((((...((.(((.((((.((........)))))).)))))....(((((....)).))).)))).)).. ( -40.70)
>DroGri_CAF1 29291 89 - 1
CUUGGGCCGCAGCAGCACAUAGAUUCUGCUUAGCGUUGGACACGAACGCAACAGUUUCUCAAUGAGUGCCUUGCCAACGAAACCUAUUU----------------
..((((.((..(((((((..(((..(((.((.(((((.(...).))))))))))..)))......))))..)))...))...))))...---------------- ( -19.50)
>DroSec_CAF1 24241 105 - 1
CUUGGGCCGCAUGAGCACGUAGAUGCGGCCCAGUUUUGGACAGGAGCGCAGCAGCUUUUCGAUCAGUGCCUUGCCCACGAAGCCUGCACAGAGAUACCAAUAUAC
.(((((((((((..........)))))))))))(((((..((((..((..(((((............))..)))...))...))))..)))))............ ( -33.70)
>DroSim_CAF1 24830 105 - 1
CUUGGGCCGCAUGAGCACGUAGAUGCGGCCCAGUUUUGGACAGGAGCGCAGCAGCUUUUCGAUCAGUGCCUUGCCCACGAAGCCUGCACAGAGAUACCAAUAUAC
.(((((((((((..........)))))))))))(((((..((((..((..(((((............))..)))...))...))))..)))))............ ( -33.70)
>DroEre_CAF1 24743 103 - 1
UUUGGGCCGCAUCAGCACGUAGAUGCGGCCCACUUUUGGACACGAGCGCAGCAGCUUCUCGAUCAGAGCCUUGCCCACGAAGCCUGCGCGAAAAUACCAAUUA--
..(((((((((((........)))))))))))...((((......((((((..(((((.....(((....))).....))))))))))).......))))...-- ( -41.82)
>DroYak_CAF1 26071 103 - 1
UUUGGGUCGCAUCAGCACAUAGAUGCGGCCCAGUUUGGGACACGAGCGCAGCAGCUUCUCGAUCAGAGCCUUGCCCACGAAUCCUGCGCAAAGAUAUCAAGAU--
..(((((((((((........)))))))))))((.(((((..((.(.((((..((((........)))).)))).).))..))))).))..............-- ( -34.80)
>consensus
CUUGGGCCGCAUCAGCACAUAGAUGCGGCCCAGUUUUGGACACGAGCGCAGCAGCUUCUCGAUCAGUGCCUUGCCCACGAAGCCUGCACAGAGAUACCAAUAU__
..(((((((((((........)))))))))))...............((((..(((((.....(((....))).....))))))))).................. (-22.77 = -23.47 +   0.70)

alignment

secondary structure

dotplot

Window 9

Location	5,751,356 – 5,751,476
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.39
Mean single sequence MFE	-48.15
Consensus MFE	-31.35
Energy contribution	-32.88
Covariance contribution	1.53
Combinations/Pair	1.31
Mean z-score	-2.34
Structure conservation index	0.65
SVM decision value	1.52
SVM RNA-class probability	0.960917
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5751356 120 + 22224390
UCCAAAACUGGGCCGCAUCUAUGUGCUGAUGCGGCCCAAGAAGGGCCACACAAUUGAGGAGCGCCUGCAGCUGCAGUGGGAAUCGAGGUUGUAUGAACGGCUGCGCAGAGAACAGCCCAA
........(((((((((((........)))))))))))....((((..........(((....)))(((((((.....(.(((....))).).....)))))))..........)))).. ( -46.50)
>DroVir_CAF1 3710 120 + 1
CUACACACUGGGCAAGAUCUAUGUGCUGAUACGGCCCAAGAAGGGCGUUGCCAUCGAGCAGCGCCUGGAGGCGUUGCUCAAUUGCAAGCUGUACGAGCGAUUGCGGCGCGAGCAGCCCCA
........(((((...(((........)))...)))))....(((.(((((....((((((((((....))))))))))..((((..((((((........)))))))))))))))))). ( -54.10)
>DroSim_CAF1 24895 120 + 1
UCCAAAACUGGGCCGCAUCUACGUGCUCAUGCGGCCCAAGAAGGGCCACACAAUUGAGGAGCGCCUGCAGCUGCAGUGGGAAACGAGGCUGUAUGAACGGCUGCGCAGGGAACAGCCCGA
........((((((((((..........))))))))))....((((..............((((((((....))))..(....)..((((((....)))))))))).(....).)))).. ( -46.60)
>DroEre_CAF1 24806 120 + 1
UCCAAAAGUGGGCCGCAUCUACGUGCUGAUGCGGCCCAAAAAGGGCCAAACCAUUGAGGAGCGCCUGCAGCUGCAGUGGGAAACGAGGCUGUAUGAGCGGCUGCGAAGUGAGCAGCCCGA
(((.....(((((((((((........)))))))))))....((......)).....)))((.(.(((((((...((.....))..))))))).).))((((((.......))))))... ( -55.60)
>DroYak_CAF1 26134 120 + 1
UCCCAAACUGGGCCGCAUCUAUGUGCUGAUGCGACCCAAAAAGGGCCACACCAUUGAGGAGCGCCUGCAGCAGCAGUGGGAAACGAGGCUGUACGAACGGCUGCGACGGGAGCAGCCCGA
........((((.((((((........)))))).))))....((((....((.....)).((.((((..(((((.((.(....)..(......)..)).)))))..)))).)).)))).. ( -47.30)
>DroAna_CAF1 26320 120 + 1
UCCAAAACUAAGCCGGAUUUAUGUCCUGAUGAGGCCCAAGAAGGGCAUUGAUAUCGAGGAUCGGUUGCAGCAGCAAUGGGAGACCAAGUUAUACGAUAGACUGCGUCAGGAACAGCCCGA
.............(((.....((((((((((((((((.....)))).....(((((.......(((((....)))))((....))........)))))..)).))))))).)))..))). ( -38.80)
>consensus
UCCAAAACUGGGCCGCAUCUAUGUGCUGAUGCGGCCCAAGAAGGGCCACACCAUUGAGGAGCGCCUGCAGCUGCAGUGGGAAACGAGGCUGUACGAACGGCUGCGAAGGGAACAGCCCGA
........(((((((((((........)))))))))))....((((...............((.((((....)))))).....((.((((((....)))))).)).........)))).. (-31.35 = -32.88 +   1.53)

alignment

secondary structure

dotplot

Window 0

Location	5,751,356 – 5,751,476
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.39
Mean single sequence MFE	-45.24
Consensus MFE	-30.97
Energy contribution	-32.08
Covariance contribution	1.12
Combinations/Pair	1.38
Mean z-score	-1.86
Structure conservation index	0.68
SVM decision value	1.11
SVM RNA-class probability	0.916458
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5751356 120 - 22224390
UUGGGCUGUUCUCUGCGCAGCCGUUCAUACAACCUCGAUUCCCACUGCAGCUGCAGGCGCUCCUCAAUUGUGUGGCCCUUCUUGGGCCGCAUCAGCACAUAGAUGCGGCCCAGUUUUGGA
...((((((.......))))))..((((((((............((((....))))...........)))))))).((...((((((((((((........))))))))))))....)). ( -46.30)
>DroVir_CAF1 3710 120 - 1
UGGGGCUGCUCGCGCCGCAAUCGCUCGUACAGCUUGCAAUUGAGCAACGCCUCCAGGCGCUGCUCGAUGGCAACGCCCUUCUUGGGCCGUAUCAGCACAUAGAUCUUGCCCAGUGUGUAG
((((((.((....)).))....(((.((((.(.((((.((((((((.((((....)))).)))))))).)))))((((.....)))).)))).)))............))))........ ( -48.90)
>DroSim_CAF1 24895 120 - 1
UCGGGCUGUUCCCUGCGCAGCCGUUCAUACAGCCUCGUUUCCCACUGCAGCUGCAGGCGCUCCUCAAUUGUGUGGCCCUUCUUGGGCCGCAUGAGCACGUAGAUGCGGCCCAGUUUUGGA
..(((((((...((((((.((.((....)).))...........((((....))))))((((.......(((((((((.....)))))))))))))..))))..)))))))......... ( -50.11)
>DroEre_CAF1 24806 120 - 1
UCGGGCUGCUCACUUCGCAGCCGCUCAUACAGCCUCGUUUCCCACUGCAGCUGCAGGCGCUCCUCAAUGGUUUGGCCCUUUUUGGGCCGCAUCAGCACGUAGAUGCGGCCCACUUUUGGA
...((((((.......)))))).........(((..........((((....)))).....((.....))...)))((....(((((((((((........))))))))))).....)). ( -46.30)
>DroYak_CAF1 26134 120 - 1
UCGGGCUGCUCCCGUCGCAGCCGUUCGUACAGCCUCGUUUCCCACUGCUGCUGCAGGCGCUCCUCAAUGGUGUGGCCCUUUUUGGGUCGCAUCAGCACAUAGAUGCGGCCCAGUUUGGGA
...((((((.......))))))((..(((((((.............)))).)))..))((.((.....)).))..(((...((((((((((((........))))))))))))...))). ( -50.12)
>DroAna_CAF1 26320 120 - 1
UCGGGCUGUUCCUGACGCAGUCUAUCGUAUAACUUGGUCUCCCAUUGCUGCUGCAACCGAUCCUCGAUAUCAAUGCCCUUCUUGGGCCUCAUCAGGACAUAAAUCCGGCUUAGUUUUGGA
..(((((((.......))))))).(((...((((.((((.....((((....))))..(.((((.(((......((((.....))))...))))))))........)))).)))).))). ( -29.70)
>consensus
UCGGGCUGCUCCCGGCGCAGCCGUUCAUACAGCCUCGUUUCCCACUGCAGCUGCAGGCGCUCCUCAAUGGUGUGGCCCUUCUUGGGCCGCAUCAGCACAUAGAUGCGGCCCAGUUUUGGA
...((((((.......)))))).................(((.((((..((((((....((......(((((((((((.....)))))))))))......)).)))))).))))...))) (-30.97 = -32.08 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:48 2006