Locus 7130

Sequence ID	X_DroMel_CAF1
Location	17,893,012 – 17,893,150
Length	138
Max. P	0.957439

overview

Window 6

Location	17,893,012 – 17,893,130
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	86.75
Mean single sequence MFE	-31.64
Consensus MFE	-24.30
Energy contribution	-24.93
Covariance contribution	0.63
Combinations/Pair	1.08
Mean z-score	-1.83
Structure conservation index	0.77
SVM decision value	0.59
SVM RNA-class probability	0.791196
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17893012 118 + 22224390
CAUAUGUGUUUAUAUAUUAUAUUAUUCCCAGUGUAGCGCCACAUGCAAGAUGUUGUCCCCUUUUAUUUAUUUGUGGAAAAGGGCAUCCCGGGGGCAGUGGCUAAACUGGACACAAAAU
....(((((....(((......)))..(((((.....(((((..((.....))(((((((((((((......))))))..(((...)))))))))))))))...)))))))))).... ( -34.60)
>DroSec_CAF1 157070 111 + 1
CAUAUGU------AUAUAAUAUUAUUCCCAGUGUAGCGCCACAUGCAAGAUGUUGUCC-CUUUUAUUUAUUUGUGGAAAAGGGCAUCCCGGGAGCAGUGGCUAAACUGGACACAAAAU
.......------..............(((((.....(((((.(((.......((.((-(((((............)))))))))((....))))))))))...)))))......... ( -27.90)
>DroEre_CAF1 152526 108 + 1
----UA-----AUGUAUAAUAUUAUUCCCAGUGUAGCGCCACAUGCAAGAUGUCGUCC-CUUUAAUUUAUUUGGGAAAAGGGGCAUCCCGGGGGCAGUGGCUAAACUGGACACAAAAU
----..-----................(((((.....(((((.(((..((((((.(((-(............)))).....))))))(....)))))))))...)))))......... ( -30.30)
>DroYak_CAF1 153410 107 + 1
----UA------AAUACGACAUUAUUCCCAGUGUAGUGCCACAUGCAAGAUGUUGUCC-CUUUUAUUUAUUGGGCGAAAGGGGCAUCCCGGGGGCAGUGGCUAAACUGGACACAAAAU
----..------...............(((((.....(((((.(((.......(((((-((((..((.....))..)))))))))........))))))))...)))))......... ( -33.76)
>consensus
____UA______UAUAUAAUAUUAUUCCCAGUGUAGCGCCACAUGCAAGAUGUUGUCC_CUUUUAUUUAUUUGGGGAAAAGGGCAUCCCGGGGGCAGUGGCUAAACUGGACACAAAAU
...........................(((((.....(((((.(((........((((..((((((......))))))..)))).((....))))))))))...)))))......... (-24.30 = -24.93 +   0.63)

alignment

secondary structure

dotplot

Window 7

Location	17,893,012 – 17,893,130
Length	118
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	86.75
Mean single sequence MFE	-30.04
Consensus MFE	-24.80
Energy contribution	-24.55
Covariance contribution	-0.25
Combinations/Pair	1.03
Mean z-score	-2.29
Structure conservation index	0.83
SVM decision value	1.48
SVM RNA-class probability	0.957439
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17893012 118 - 22224390
AUUUUGUGUCCAGUUUAGCCACUGCCCCCGGGAUGCCCUUUUCCACAAAUAAAUAAAAGGGGACAACAUCUUGCAUGUGGCGCUACACUGGGAAUAAUAUAAUAUAUAAACACAUAUG
....((((((((((...((((((((....(((((((((((((.............)))))))....))))))))).))))).....)))))......((((...)))).))))).... ( -30.32)
>DroSec_CAF1 157070 111 - 1
AUUUUGUGUCCAGUUUAGCCACUGCUCCCGGGAUGCCCUUUUCCACAAAUAAAUAAAAG-GGACAACAUCUUGCAUGUGGCGCUACACUGGGAAUAAUAUUAUAU------ACAUAUG
...((((..(((((...((((((((....(((((((((((((............)))))-))....))))))))).))))).....)))))..))))........------....... ( -30.30)
>DroEre_CAF1 152526 108 - 1
AUUUUGUGUCCAGUUUAGCCACUGCCCCCGGGAUGCCCCUUUUCCCAAAUAAAUUAAAG-GGACGACAUCUUGCAUGUGGCGCUACACUGGGAAUAAUAUUAUACAU-----UA----
...((((..(((((...((((((((....(((((((((((((.............))))-))..).))))))))).))))).....)))))..))))..........-----..---- ( -30.52)
>DroYak_CAF1 153410 107 - 1
AUUUUGUGUCCAGUUUAGCCACUGCCCCCGGGAUGCCCCUUUCGCCCAAUAAAUAAAAG-GGACAACAUCUUGCAUGUGGCACUACACUGGGAAUAAUGUCGUAUU------UA----
...((((..(((((.((((((((((....((((((.((((((.............))))-))....))))))))).)))))..)).)))))..)))).........------..---- ( -29.02)
>consensus
AUUUUGUGUCCAGUUUAGCCACUGCCCCCGGGAUGCCCCUUUCCACAAAUAAAUAAAAG_GGACAACAUCUUGCAUGUGGCGCUACACUGGGAAUAAUAUUAUAUA______CA____
...((((..(((((...((((((((....((((((.((((((.............)))).))....))))))))).))))).....)))))..))))..................... (-24.80 = -24.55 +  -0.25)

alignment

secondary structure

dotplot

Window 8

Location	17,893,051 – 17,893,150
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	94.59
Mean single sequence MFE	-25.49
Consensus MFE	-20.37
Energy contribution	-20.12
Covariance contribution	-0.25
Combinations/Pair	1.03
Mean z-score	-1.92
Structure conservation index	0.80
SVM decision value	0.11
SVM RNA-class probability	0.586609
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17893051 99 - 22224390
CAGCUAAAGUGCUCAUAAACAUUUUGUGUCCAGUUUAGCCACUGCCCCCGGGAUGCCCUUUUCCACAAAUAAAUAAAAGGGGACAACAUCUUGCAUGUG
..((((((.((..(((((.....)))))..)).))))))((((((....(((((((((((((.............)))))))....))))))))).))) ( -25.42)
>DroSec_CAF1 157103 98 - 1
CAGCUAAAGUGCUCAUAAACAUUUUGUGUCCAGUUUAGCCACUGCUCCCGGGAUGCCCUUUUCCACAAAUAAAUAAAAG-GGACAACAUCUUGCAUGUG
..((((((.((..(((((.....)))))..)).))))))((((((....(((((((((((((............)))))-))....))))))))).))) ( -25.60)
>DroEre_CAF1 152556 98 - 1
CAGCUAAAGUGCUCAUAAAGAUUUUGUGUCCAGUUUAGCCACUGCCCCCGGGAUGCCCCUUUUCCCAAAUAAAUUAAAG-GGACGACAUCUUGCAUGUG
..((((((.((..(((((.....)))))..)).))))))((((((....(((((((((((((.............))))-))..).))))))))).))) ( -25.82)
>DroYak_CAF1 153439 98 - 1
CAGCUAAAGUGCUCAUAAACAUUUUGUGUCCAGUUUAGCCACUGCCCCCGGGAUGCCCCUUUCGCCCAAUAAAUAAAAG-GGACAACAUCUUGCAUGUG
..((((((.((..(((((.....)))))..)).))))))((((((....((((((.((((((.............))))-))....))))))))).))) ( -25.12)
>consensus
CAGCUAAAGUGCUCAUAAACAUUUUGUGUCCAGUUUAGCCACUGCCCCCGGGAUGCCCCUUUCCACAAAUAAAUAAAAG_GGACAACAUCUUGCAUGUG
..((((((.((..(((((.....)))))..)).))))))((((((....((((((.((((((.............)))).))....))))))))).))) (-20.37 = -20.12 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:55 2006