Locus 37

Sequence ID	3L_DroMel_CAF1
Location	140,081 – 140,175
Length	94
Max. P	0.998595

overview

Window 4

Location	140,081 – 140,175
Length	94
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	76.10
Mean single sequence MFE	-19.80
Consensus MFE	-13.34
Energy contribution	-14.38
Covariance contribution	1.04
Combinations/Pair	1.06
Mean z-score	-2.77
Structure conservation index	0.67
SVM decision value	3.15
SVM RNA-class probability	0.998595
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 140081 94 + 23771897
---AUAAAUGCCCUAACAACAUUUAUUGAUAUAUUCUUCGAAAAAAUCGCAACACCAACAAUCGCAACGCAACUAUCGUUGUCAGGCAACG-AAUGGG
---.....(((..........(((.((((........)))).)))...((.............))...))).(((((((((.....)))))-.)))). ( -12.82)
>DroSec_CAF1 14430 78 + 1
---AUAAAUGCCCUGACAACAUUUAUUGAUAUAUUGUUCGAA-AAAUCGCAACAGCAA----------------GUUGUUGUCAGGCAACUCAAUUGG
---.....((((.((((((((....(((.....((((((((.-...))).))))))))----------------..)))))))))))).......... ( -21.50)
>DroSim_CAF1 14973 78 + 1
---AUAAAUGCCCUGACAACAUUUAUUGAUAUAUUGUUCGAA-AAAUCGCAACAGCAA----------------GUUGUUGUCAGGCAACUCAAUUGG
---.....((((.((((((((....(((.....((((((((.-...))).))))))))----------------..)))))))))))).......... ( -21.50)
>DroEre_CAF1 16028 80 + 1
UU--------CUCUGACAACAUUUAUGGAUAUAUUGCUUGAA-AAAUGGCAACAGCAAGUUU--------AAUUGUUGUUGUCAGGCAACAAAA-UGG
..--------.........(((((..................-...((((((((((((....--------..))))))))))))(....).)))-)). ( -19.70)
>DroYak_CAF1 16469 89 + 1
UCCAUAAAUGCACUGACAACAUUUAUAGAUAUAUUGCUCGAAAAAAUCGCAACAGCAAGAUU--------AAUUGUUGUUGUCAGGCAACAAAA-UGC
........(((.(((((((((...((.(((...((((((((.....)))....))))).)))--------.))...))))))))))))......-... ( -23.50)
>consensus
___AUAAAUGCCCUGACAACAUUUAUUGAUAUAUUGUUCGAA_AAAUCGCAACAGCAA___U________AA_UGUUGUUGUCAGGCAACAAAAUUGG
........(((.((((((((.....((((........)))).......((....)).....................))))))))))).......... (-13.34 = -14.38 +   1.04)

alignment

secondary structure

dotplot

Window 5

Location	140,081 – 140,175
Length	94
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	76.10
Mean single sequence MFE	-20.70
Consensus MFE	-15.20
Energy contribution	-15.64
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-2.44
Structure conservation index	0.73
SVM decision value	2.67
SVM RNA-class probability	0.996215
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 140081 94 - 23771897
CCCAUU-CGUUGCCUGACAACGAUAGUUGCGUUGCGAUUGUUGGUGUUGCGAUUUUUUCGAAGAAUAUAUCAAUAAAUGUUGUUAGGGCAUUUAU---
......-...((((((((((((((((((((...)))))))))(((((..(((.....)))......))))).......))))))).)))).....--- ( -24.90)
>DroSec_CAF1 14430 78 - 1
CCAAUUGAGUUGCCUGACAACAAC----------------UUGCUGUUGCGAUUU-UUCGAACAAUAUAUCAAUAAAUGUUGUCAGGGCAUUUAU---
.....(((((.(((((((((((..----------------....((((.(((...-.))))))).(((....)))..)))))))).)))))))).--- ( -20.30)
>DroSim_CAF1 14973 78 - 1
CCAAUUGAGUUGCCUGACAACAAC----------------UUGCUGUUGCGAUUU-UUCGAACAAUAUAUCAAUAAAUGUUGUCAGGGCAUUUAU---
.....(((((.(((((((((((..----------------....((((.(((...-.))))))).(((....)))..)))))))).)))))))).--- ( -20.30)
>DroEre_CAF1 16028 80 - 1
CCA-UUUUGUUGCCUGACAACAACAAUU--------AAACUUGCUGUUGCCAUUU-UUCAAGCAAUAUAUCCAUAAAUGUUGUCAGAG--------AA
...-.........(((((((((.(((..--------....))).((((((.....-.....))))))..........)))))))))..--------.. ( -15.80)
>DroYak_CAF1 16469 89 - 1
GCA-UUUUGUUGCCUGACAACAACAAUU--------AAUCUUGCUGUUGCGAUUUUUUCGAGCAAUAUAUCUAUAAAUGUUGUCAGUGCAUUUAUGGA
...-...((((((....(((((.(((..--------....))).)))))(((.....))).))))))..(((((((((((.......))))))))))) ( -22.20)
>consensus
CCAAUUGAGUUGCCUGACAACAACA_UU________A___UUGCUGUUGCGAUUU_UUCGAACAAUAUAUCAAUAAAUGUUGUCAGGGCAUUUAU___
..........((((((((((((......................((((.(((.....))))))).(((....)))..))))))))).)))........ (-15.20 = -15.64 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:27 2006