Locus 4994

Sequence ID	2L_DroMel_CAF1
Location	14,375,450 – 14,375,628
Length	178
Max. P	0.983415

overview

Window 2

Location	14,375,450 – 14,375,570
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.81
Mean single sequence MFE	-24.09
Consensus MFE	-21.38
Energy contribution	-21.62
Covariance contribution	0.24
Combinations/Pair	1.10
Mean z-score	-1.79
Structure conservation index	0.89
SVM decision value	1.94
SVM RNA-class probability	0.983415
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14375450 120 - 22407834
UAUAUGUCAAACUGGUGAAUAAAUCAAUUUGACAGCUAAACGCUGCUGUUGAAAGACAGAGAGGCCAAUAGAAAGACUGUCAGAAAAAAGCGGGUAAAAAGAGAGUUGUAUAAAUCAAAG
....(((((((.((((......)))).))))))).(((...(((.(((((....)))))...)))...)))...((((.((...................)).))))............. ( -24.91)
>DroSec_CAF1 23624 119 - 1
UAUAUGUCAAACUGGUGAAUAAAUCAAUUUGACAGCUAAACGCUGCUGUUGAAAGACAGAGAGGCCAAUAGAAAGACAGCCAGGA-AAUGCGAGUAAGAAGAGAGUUGUAUAAAUCAAAG
....(((((((.((((......)))).))))))).(((...(((.(((((....)))))...)))...)))..............-.((((((.(........).))))))......... ( -24.90)
>DroSim_CAF1 25726 119 - 1
UAUAUGUCAAACUGGUGAAUAAAUCAAUUUGACAGCUAAACGCUGCUGUUGAAAGACAGAGAGGCCAAUAGAAAGACAGCCAGGA-AAUGCGAGUAAGAAGAGAGUUGUAUAAAUCAAAG
....(((((((.((((......)))).))))))).(((...(((.(((((....)))))...)))...)))..............-.((((((.(........).))))))......... ( -24.90)
>DroEre_CAF1 24364 119 - 1
UAUAUGUCAAACUGGCGAAUAAAUCAAUUUGACAGCUAAACGCUGCUGUUGAAAGACAGAGAGGCAAAUAGAAAGACAGUCAGGA-AAUGCGGGUAAGAAAAGAGUUGUAUAAAUCAAAU
...........(((((.......((.(((((.((((.....))))(((((....))))).....))))).))......)))))..-.((((((.(........).))))))......... ( -23.02)
>DroYak_CAF1 25210 119 - 1
UAUAUGUCAAACUGGCGAAUAAAUCAAUUUGACAGCUGAACGCUGCUGUUGAAAGACAGAGAGCCCAAUAGAAAGACAGUCAGGA-AAUGCGGGUAAGAAGAGAGUUGUAUAAGUCAAAG
(((.((((.....)))).)))......((((((..((((..(((.(((((....)))))..)))......(.....)..))))..-.((((((.(........).))))))..)))))). ( -22.70)
>consensus
UAUAUGUCAAACUGGUGAAUAAAUCAAUUUGACAGCUAAACGCUGCUGUUGAAAGACAGAGAGGCCAAUAGAAAGACAGUCAGGA_AAUGCGGGUAAGAAGAGAGUUGUAUAAAUCAAAG
....(((((((.((((......)))).))))))).(((...(((.(((((....)))))...)))...)))...........((...((((((.(........).))))))...)).... (-21.38 = -21.62 +   0.24)

alignment

secondary structure

dotplot

Window 3

Location	14,375,490 – 14,375,600
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	96.73
Mean single sequence MFE	-26.68
Consensus MFE	-23.78
Energy contribution	-23.82
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.77
Structure conservation index	0.89
SVM decision value	1.66
SVM RNA-class probability	0.970612
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14375490 110 + 22407834
ACAGUCUUUCUAUUGGCCUCUCUGUCUUUCAACAGCAGCGUUUAGCUGUCAAAUUGAUUUAUUCACCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAACGCGC
...(((........)))....((((......))))..(((((((..((((((((((..........))))))))))(((((((((....)))))))))...))))))).. ( -27.10)
>DroSec_CAF1 23663 110 + 1
GCUGUCUUUCUAUUGGCCUCUCUGUCUUUCAACAGCAGCGUUUAGCUGUCAAAUUGAUUUAUUCACCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAAUGCGC
(((((.........(((......))).....))))).(((((((..((((((((((..........))))))))))(((((((((....)))))))))...))))))).. ( -28.24)
>DroSim_CAF1 25765 110 + 1
GCUGUCUUUCUAUUGGCCUCUCUGUCUUUCAACAGCAGCGUUUAGCUGUCAAAUUGAUUUAUUCACCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAAUGCGC
(((((.........(((......))).....))))).(((((((..((((((((((..........))))))))))(((((((((....)))))))))...))))))).. ( -28.24)
>DroEre_CAF1 24403 110 + 1
ACUGUCUUUCUAUUUGCCUCUCUGUCUUUCAACAGCAGCGUUUAGCUGUCAAAUUGAUUUAUUCGCCAGUUUGACAUAUAUUAAUGGCCGUUGGUGUAAAAUAAAUGCGC
.....................((((......))))..(((((((..((((((((((..........))))))))))(((((((((....)))))))))...))))))).. ( -23.90)
>DroYak_CAF1 25249 110 + 1
ACUGUCUUUCUAUUGGGCUCUCUGUCUUUCAACAGCAGCGUUCAGCUGUCAAAUUGAUUUAUUCGCCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAAUGCGC
.............(((((.((((((......)))).)).)))))((((((((((((..........))))))))))(((((((((....)))))))))........)).. ( -25.90)
>consensus
ACUGUCUUUCUAUUGGCCUCUCUGUCUUUCAACAGCAGCGUUUAGCUGUCAAAUUGAUUUAUUCACCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAAUGCGC
.....................((((......))))..(((((((..((((((((((..........))))))))))(((((((((....)))))))))...))))))).. (-23.78 = -23.82 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	14,375,530 – 14,375,628
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	97.55
Mean single sequence MFE	-20.38
Consensus MFE	-18.34
Energy contribution	-19.14
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.84
Structure conservation index	0.90
SVM decision value	1.76
SVM RNA-class probability	0.975836
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14375530 98 + 22407834
UUUAGCUGUCAAAUUGAUUUAUUCACCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAACGCGCAUUAAAUUAUAAAUAUGUGAAGCUUAUU
...(((((((((((((..........)))))))))(((((((.(((((...((((((.......)))).))....))))).)))))))..)))).... ( -21.10)
>DroSec_CAF1 23703 98 + 1
UUUAGCUGUCAAAUUGAUUUAUUCACCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAAUGCGCAUUAAAUUAUAAAUAUGUGAAGCUUAUU
...(((((((((((((..........)))))))))(((((((.(((((.....(((((.......))))).....))))).)))))))..)))).... ( -21.90)
>DroSim_CAF1 25805 98 + 1
UUUAGCUGUCAAAUUGAUUUAUUCACCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAAUGCGCAUUAAAUUAUAAAUAUGUGAAGCUUAUU
...(((((((((((((..........)))))))))(((((((.(((((.....(((((.......))))).....))))).)))))))..)))).... ( -21.90)
>DroEre_CAF1 24443 98 + 1
UUUAGCUGUCAAAUUGAUUUAUUCGCCAGUUUGACAUAUAUUAAUGGCCGUUGGUGUAAAAUAAAUGCGCAUUAAAUUAUAAAUAUGUGAAUCUUAUU
......((((((((((..........))))))))))(((((((((....))))))))).(((((...(((((............)))))....))))) ( -17.90)
>DroYak_CAF1 25289 98 + 1
UUCAGCUGUCAAAUUGAUUUAUUCGCCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAAUGCGCAUUAAAUUAUAAAUAUGUGAAUCUUAUU
((((..((((((((((..........))))))))))((((((.(((((.....(((((.......))))).....))))).))))))))))....... ( -19.10)
>consensus
UUUAGCUGUCAAAUUGAUUUAUUCACCAGUUUGACAUAUAUUAAUGGUCGUUGGUGUAAAAUAAAUGCGCAUUAAAUUAUAAAUAUGUGAAGCUUAUU
...(((((((((((((..........)))))))))(((((((.(((((.....(((((.......))))).....))))).)))))))..)))).... (-18.34 = -19.14 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:05 2006