Locus 5639

Sequence ID	2R_DroMel_CAF1
Location	17,942,323 – 17,942,449
Length	126
Max. P	0.993253

overview

Window 8

Location	17,942,323 – 17,942,413
Length	90
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	78.82
Mean single sequence MFE	-32.10
Consensus MFE	-20.62
Energy contribution	-21.18
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.13
Structure conservation index	0.64
SVM decision value	1.13
SVM RNA-class probability	0.919441
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17942323 90 - 20766785
UGAGUCAGAAGCUGACGAUCAAUUUCUGAUUACCAGUCCACUCGAAUGUGAACACCCCGUA------------------------------GCACUGGAGGGCACUGAAAUAAAGAAACA
..(((((((((.((.....)).)))))))))..((((((.(((.(.(((..((.....)).------------------------------))).).))))).))))............. ( -23.20)
>DroEre_CAF1 4237 100 - 1
UGAGUCAGAAGCUGACGAUCAAUUUCUGAUUACCAGUCCACUCGAAUGUGAGCACCCCGUGGCAAU--------------------GGCGGGCAAUGGAGGGCACUGAAAUAAAGAAACA
..(((((((((.((.....)).)))))))))..((((((.(((..((....((.((((((....))--------------------)).)))).)).))))).))))............. ( -27.90)
>DroYak_CAF1 3928 120 - 1
UGAGUCAGAAGCUGACGAUCAAUUUCUGAUUACCAGUCCACUCGAAUGUGAGCACUCCGUGCCACUGGAUGGCACUGGAGGCCACUGGUGAGCACUGGAGGGCACUGAAAUAAAGAAACA
..(((((((((.((.....)).)))))))))..((((.(((......))).((.(((((((((((..(.((((.(....))))))..))).)))).)))).))))))............. ( -45.20)
>consensus
UGAGUCAGAAGCUGACGAUCAAUUUCUGAUUACCAGUCCACUCGAAUGUGAGCACCCCGUG_CA_U____________________GG_G_GCACUGGAGGGCACUGAAAUAAAGAAACA
..(((((((((.((.....)).)))))))))..((((((.(((.(.(((..((..................................))..))).).))))).))))............. (-20.62 = -21.18 +   0.56)

alignment

secondary structure

dotplot

Window 9

Location	17,942,352 – 17,942,449
Length	97
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	83.04
Mean single sequence MFE	-42.30
Consensus MFE	-32.01
Energy contribution	-31.90
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-3.81
Structure conservation index	0.76
SVM decision value	2.38
SVM RNA-class probability	0.993253
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17942352 97 + 20766785
-------------------UACGGGGUGUUCACAUUCGAGUGGACUGGUAAUCAGAAAUUGAUCGUCAGCUUCUGACUCAC----UCCCACUGAUUGUGGGCACUGUGGCAAAAAUGGUU
-------------------..((.((((((((((.((.(((((...(((..((((((.(((.....))).))))))...))----).))))))).)))))))))).))............ ( -34.70)
>DroEre_CAF1 4271 102 + 1
--------------AUUGCCACGGGGUGCUCACAUUCGAGUGGACUGGUAAUCAGAAAUUGAUCGUCAGCUUCUGACUCAC----UCCCACUGAUUGUGGGCACUGUGGCAAAAAUGGUU
--------------.(((((((..((((((((((.((.(((((...(((..((((((.(((.....))).))))))...))----).))))))).)))))))))))))))))........ ( -44.90)
>DroYak_CAF1 3968 120 + 1
CUCCAGUGCCAUCCAGUGGCACGGAGUGCUCACAUUCGAGUGGACUGGUAAUCAGAAAUUGAUCGUCAGCUUCUGACUCACUCACUCGCUCUGAUUGUGGGCACUGUGGCAAAAAUGGUU
..((((((((((...)))))))(.((((((((((.((((((((...(((..((((((.(((.....))).))))))...)))...)))))).)).)))))))))).)........))).. ( -47.30)
>consensus
______________A_UG_CACGGGGUGCUCACAUUCGAGUGGACUGGUAAUCAGAAAUUGAUCGUCAGCUUCUGACUCAC____UCCCACUGAUUGUGGGCACUGUGGCAAAAAUGGUU
.....................((.((((((((((.((.((((((...((..((((((.(((.....))).))))))...))....)).)))))).)))))))))).))............ (-32.01 = -31.90 +  -0.11)

alignment

secondary structure

dotplot

Window 0

Location	17,942,352 – 17,942,449
Length	97
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	83.04
Mean single sequence MFE	-37.97
Consensus MFE	-26.03
Energy contribution	-27.37
Covariance contribution	1.33
Combinations/Pair	1.00
Mean z-score	-3.52
Structure conservation index	0.69
SVM decision value	2.08
SVM RNA-class probability	0.987348
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17942352 97 - 20766785
AACCAUUUUUGCCACAGUGCCCACAAUCAGUGGGA----GUGAGUCAGAAGCUGACGAUCAAUUUCUGAUUACCAGUCCACUCGAAUGUGAACACCCCGUA-------------------
................(((..((((.((((((((.----...(((((((((.((.....)).))))))))).....)))))).)).))))..)))......------------------- ( -28.30)
>DroEre_CAF1 4271 102 - 1
AACCAUUUUUGCCACAGUGCCCACAAUCAGUGGGA----GUGAGUCAGAAGCUGACGAUCAAUUUCUGAUUACCAGUCCACUCGAAUGUGAGCACCCCGUGGCAAU--------------
........(((((((.((((.((((.((((((((.----...(((((((((.((.....)).))))))))).....)))))).)).)))).))))...))))))).-------------- ( -42.90)
>DroYak_CAF1 3968 120 - 1
AACCAUUUUUGCCACAGUGCCCACAAUCAGAGCGAGUGAGUGAGUCAGAAGCUGACGAUCAAUUUCUGAUUACCAGUCCACUCGAAUGUGAGCACUCCGUGCCACUGGAUGGCACUGGAG
..(((..........(((((.((((.((.(((.((.((.((((.(((((((.((.....)).))))))))))))).))..))))).)))).)))))..((((((.....))))))))).. ( -42.70)
>consensus
AACCAUUUUUGCCACAGUGCCCACAAUCAGUGGGA____GUGAGUCAGAAGCUGACGAUCAAUUUCUGAUUACCAGUCCACUCGAAUGUGAGCACCCCGUG_CA_U______________
............(((.((((.((((.((((((((.....((((.(((((((.((.....)).)))))))))))...)))))).)).)))).))))...)))................... (-26.03 = -27.37 +   1.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:43 2006