Locus 3985

Sequence ID	3R_DroMel_CAF1
Location	10,816,239 – 10,816,402
Length	163
Max. P	0.999701

overview

Window 9

Location	10,816,239 – 10,816,338
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	94.07
Mean single sequence MFE	-28.92
Consensus MFE	-24.64
Energy contribution	-25.62
Covariance contribution	0.97
Combinations/Pair	1.08
Mean z-score	-1.63
Structure conservation index	0.85
SVM decision value	0.23
SVM RNA-class probability	0.646148
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10816239 99 + 27905053
GUAAAAAAUUAAUACAACGCGCAAUUAUGACCAACAACAGCGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGU
.................(((((...((((.....((.(((.(((....))).))).))(((.((((.....)))).)))..)))).)))))........ ( -31.20)
>DroSec_CAF1 85846 99 + 1
GUAAAAAAUUAAUACAACGCGCAAUUAUGACCAACAACAGCGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGU
.................(((((...((((.....((.(((.(((....))).))).))(((.((((.....)))).)))..)))).)))))........ ( -31.20)
>DroSim_CAF1 90159 99 + 1
GUAAAAAAUUAAUACAACGCGCAAUUAUGACCAACAACAGCGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGU
.................(((((...((((.....((.(((.(((....))).))).))(((.((((.....)))).)))..)))).)))))........ ( -31.20)
>DroEre_CAF1 88216 99 + 1
GUAAAAAAUUAAUACAACGCGCAAUUAUGACCAACAACGGCGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGCGCCCGAGAAUCGU
..................(((((..............(((.(((....))).)))((.(((.((((.....)))).))).)).)))))........... ( -26.90)
>DroYak_CAF1 90280 99 + 1
GUAAAAAAUUAAUACAACGCGCAAUUAUGACCAACAACAGCGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGU
.................(((((...((((.....((.(((.(((....))).))).))(((.((((.....)))).)))..)))).)))))........ ( -31.20)
>DroAna_CAF1 87552 99 + 1
GUAAAAAAUUAAUACAGCUCGCAAUUAUGGGCAACAACGGCGAAAAGUGCCUCUAGUGGCCGGAGAGACUGUCAGAAGCAACAUGGGCGCGAGAAUCGU
.................(((((..((((((....)..((((.(..((.....))..).))))...................)))))..)))))...... ( -21.80)
>consensus
GUAAAAAAUUAAUACAACGCGCAAUUAUGACCAACAACAGCGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGU
.................(((((...((((.....((.(((.(((....))).))).))(((.((((.....)))).)))..)))).)))))........ (-24.64 = -25.62 +   0.97)

alignment

secondary structure

dotplot

Window 0

Location	10,816,279 – 10,816,377
Length	98
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	89.24
Mean single sequence MFE	-45.87
Consensus MFE	-41.22
Energy contribution	-42.92
Covariance contribution	1.69
Combinations/Pair	1.04
Mean z-score	-3.28
Structure conservation index	0.90
SVM decision value	3.12
SVM RNA-class probability	0.998488
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10816279 98 + 27905053
CGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGGUGG-
...((..((((((((.(((((((.....((((((((((.......((((.......)))).....))))))))))....))))))))))))))).)).- ( -51.40)
>DroSec_CAF1 85886 98 + 1
CGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGGUGG-
...((..((((((((.(((((((.....((((((((((.......((((.......)))).....))))))))))....))))))))))))))).)).- ( -51.40)
>DroSim_CAF1 90199 98 + 1
CGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGGUGG-
...((..((((((((.(((((((.....((((((((((.......((((.......)))).....))))))))))....))))))))))))))).)).- ( -51.40)
>DroEre_CAF1 88256 91 + 1
CGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGCGCCCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGG--------
.(((....))).((.((((((((.....((((((((((......(((.........)))......))))))))))....)))))))).)).-------- ( -42.00)
>DroYak_CAF1 90320 99 + 1
CGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGGUGGU
..((.(.((((((((.(((((((.....((((((((((.......((((.......)))).....))))))))))....))))))))))))))).).)) ( -51.80)
>DroAna_CAF1 87592 92 + 1
CGAAAAGUGCCUCUAGUGGCCGGAGAGACUGUCAGAAGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGACCAAGGCCACAAAAG-------
...............((((((.......(((((((..........((((.......))))........)))))))......)))))).....------- ( -27.19)
>consensus
CGGCAAGUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGGUGG_
........((((((.((((((((.....((((((((((.......((((.......)))).....))))))))))....))))))))))))))...... (-41.22 = -42.92 +   1.69)

alignment

secondary structure

dotplot

Window 1

Location	10,816,279 – 10,816,377
Length	98
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	89.24
Mean single sequence MFE	-44.85
Consensus MFE	-41.45
Energy contribution	-42.03
Covariance contribution	0.58
Combinations/Pair	1.10
Mean z-score	-4.46
Structure conservation index	0.92
SVM decision value	3.91
SVM RNA-class probability	0.999701
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10816279 98 - 27905053
-CCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCACUUGCCG
-.....(((.((((((((((....((((((((((((((((.((.......))..)).)))))))))))))).....))))))).))).)))........ ( -47.40)
>DroSec_CAF1 85886 98 - 1
-CCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCACUUGCCG
-.....(((.((((((((((....((((((((((((((((.((.......))..)).)))))))))))))).....))))))).))).)))........ ( -47.40)
>DroSim_CAF1 90199 98 - 1
-CCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCACUUGCCG
-.....(((.((((((((((....((((((((((((((((.((.......))..)).)))))))))))))).....))))))).))).)))........ ( -47.40)
>DroEre_CAF1 88256 91 - 1
--------CCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGGGCGCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCACUUGCCG
--------..((((((((((....((((((((((((((((.((.....))....)).)))))))))))))).....))))))).))).(((....))). ( -46.90)
>DroYak_CAF1 90320 99 - 1
ACCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCACUUGCCG
......(((.((((((((((....((((((((((((((((.((.......))..)).)))))))))))))).....))))))).))).)))........ ( -47.40)
>DroAna_CAF1 87592 92 - 1
-------CUUUUGUGGCCUUGGUCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCUUCUGACAGUCUCUCCGGCCACUAGAGGCACUUUUCG
-------((((.((((((..((..(((((((.((((((((.((.......))..)).)))))).)))))))..))...)))))).)))).......... ( -32.60)
>consensus
_CCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCACUUGCCG
......(((.((((((((((....((((((((((((((((.((.....))....)).)))))))))))))).....)))))))).)).)))........ (-41.45 = -42.03 +   0.58)

alignment

secondary structure

dotplot

Window 2

Location	10,816,298 – 10,816,402
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.67
Mean single sequence MFE	-31.38
Consensus MFE	-25.81
Energy contribution	-26.37
Covariance contribution	0.56
Combinations/Pair	1.19
Mean z-score	-1.38
Structure conservation index	0.82
SVM decision value	1.13
SVM RNA-class probability	0.919310
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10816298 104 - 27905053
UUCCGGCUGCUCCCCCCUCUUUUUC----------------CCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGG
....(((..(...............----------------...........)..))).(((..((((((((((((((((.((.......))..)).)))))))))))))).....))). ( -32.87)
>DroSec_CAF1 85905 104 - 1
UUCCGGCUGCUGCCCCCUCCUUUUC----------------CCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGG
....(((....)))...........----------------...((((....))))((((....((((((((((((((((.((.......))..)).)))))))))))))).....)))) ( -35.30)
>DroSim_CAF1 90218 104 - 1
UUCCGGCUGCCGCCCCCUCUUUUUC----------------CCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGG
....(((....)))...........----------------...((((....))))((((....((((((((((((((((.((.......))..)).)))))))))))))).....)))) ( -34.70)
>DroEre_CAF1 88275 91 - 1
UUCCGGCGACG-CCCCCUCC----------------------------CCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGGGCGCAUGUUGCCGCUGACAGUUCCAGUGG
....(((.(((-........----------------------------...))).))).(((..((((((((((((((((.((.....))....)).)))))))))))))).....))). ( -33.90)
>DroYak_CAF1 90339 120 - 1
UUCCGACUGCGGCCCCCUCCCCUCCCCUUACCAACGUUACACCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGG
..(((....))).............................((((.(((.....))).......((((((((((((((((.((.......))..)).)))))))))))))).....)))) ( -33.20)
>DroAna_CAF1 87611 78 - 1
-----------ACCCC-------------------------------CUUUUGUGGCCUUGGUCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCUUCUGACAGUCUCUCCGG
-----------.....-------------------------------......(((....((..(((((((.((((((((.((.......))..)).)))))).)))))))..)).))). ( -18.30)
>consensus
UUCCGGCUGCGGCCCCCUCCUUUUC________________CCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGG
....((((((..........................................)))))).(((..((((((((((((((((.((.....))....)).)))))))))))))).....))). (-25.81 = -26.37 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:14 2006