Locus 934

Sequence ID	2R_DroMel_CAF1
Location	4,069,760 – 4,069,954
Length	194
Max. P	0.999979

overview

Window 9

Location	4,069,760 – 4,069,875
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.96
Mean single sequence MFE	-34.76
Consensus MFE	-31.98
Energy contribution	-32.22
Covariance contribution	0.24
Combinations/Pair	1.10
Mean z-score	-3.38
Structure conservation index	0.92
SVM decision value	5.20
SVM RNA-class probability	0.999979
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4069760 115 + 20766785
UGGUCAACUUUUAUGGGCAGCCAAUAACGCCAGGGGAUUUGGCAAUUCUCUUCUUCUUCGCUUCUAAAUCAAUAGCAAUAAUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA-----
((((((.(.(((((((((((((((....(((((.....)))))................(((...........))).......))))))...)))))))))..).))))))....----- ( -36.00)
>DroSec_CAF1 52414 115 + 1
UGGCCAACUUUUAUGGGUAGCCAAUAACGCCAGGGGAUUUGGCAGUUCUCCUCUUCUUCGCUUCUAAAUCAAUAGCAAUAAUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA-----
((((((.(.(((((((((((((((.......((((((.........)))))).......(((...........))).......))))))...)))))))))..).))))))....----- ( -37.50)
>DroSim_CAF1 60591 115 + 1
UGGCCAACUUUUAUGGGUAGCCAAUAACGCCAGGGGAUUUGGCAAUUCUCCUCUUCUUCGCUUCUAAAUCAAUAGCAAUAAUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA-----
((((((.(.(((((((((((((((.......((((((.........)))))).......(((...........))).......))))))...)))))))))..).))))))....----- ( -37.50)
>DroEre_CAF1 53780 119 + 1
UGGCCAACUUUUAUGGUCAGCCAAUAACCCCAGGGGAUUCGGCAAUUCUCCUCUUC-CCGCUUCGAAAUCAAUAGCAAUAAUUCUGGCUAGCGCCCAUAAAUUGCUGGCCACAUAUAUAC
((((((.(.(((((((.((((((..........((((...((.......))...))-))(((...........)))........)))))...).)))))))..).))))))......... ( -31.60)
>DroYak_CAF1 56448 112 + 1
GGGCCAACUUUUAUGGUCAGCCAAUAACCCUAGGGGAUUUGGCAAUU--CCUCUUC-UCGCUUCUAAAUCAAUAGCAAUAAUUCUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA-----
.(((((.......))))).(((((...((....))...)))))....--.......-..(((...........)))........(((((((((.........)))))))))....----- ( -31.20)
>consensus
UGGCCAACUUUUAUGGGCAGCCAAUAACGCCAGGGGAUUUGGCAAUUCUCCUCUUCUUCGCUUCUAAAUCAAUAGCAAUAAUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA_____
.(((((.(.((((((((((((((........((((((.........)))))).......(((...........)))........)))))...)))))))))..).))))).......... (-31.98 = -32.22 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	4,069,760 – 4,069,875
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.96
Mean single sequence MFE	-38.02
Consensus MFE	-32.42
Energy contribution	-32.82
Covariance contribution	0.40
Combinations/Pair	1.12
Mean z-score	-2.89
Structure conservation index	0.85
SVM decision value	3.59
SVM RNA-class probability	0.999419
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4069760 115 - 20766785
-----UUUGUGGCCAGCAAUUUAUGGGCGCUAGCCAAAAUUAUUGCUAUUGAUUUAGAAGCGAAGAAGAAGAGAAUUGCCAAAUCCCCUGGCGUUAUUGGCUGCCCAUAAAAGUUGACCA
-----....(((.((((..(((((((((...((((((.....(((((...........)))))..............((((.......))))....))))))))))))))).)))).))) ( -34.90)
>DroSec_CAF1 52414 115 - 1
-----UUUGUGGCCAGCAAUUUAUGGGCGCUAGCCAAAAUUAUUGCUAUUGAUUUAGAAGCGAAGAAGAGGAGAACUGCCAAAUCCCCUGGCGUUAUUGGCUACCCAUAAAAGUUGGCCA
-----....((((((((..((((((((...(((((((.....(((((...........)))))..........(((.((((.......))))))).))))))))))))))).)))))))) ( -40.50)
>DroSim_CAF1 60591 115 - 1
-----UUUGUGGCCAGCAAUUUAUGGGCGCUAGCCAAAAUUAUUGCUAUUGAUUUAGAAGCGAAGAAGAGGAGAAUUGCCAAAUCCCCUGGCGUUAUUGGCUACCCAUAAAAGUUGGCCA
-----....((((((((..((((((((...(((((((.....(((((...........)))))..............((((.......))))....))))))))))))))).)))))))) ( -39.90)
>DroEre_CAF1 53780 119 - 1
GUAUAUAUGUGGCCAGCAAUUUAUGGGCGCUAGCCAGAAUUAUUGCUAUUGAUUUCGAAGCGG-GAAGAGGAGAAUUGCCGAAUCCCCUGGGGUUAUUGGCUGACCAUAAAAGUUGGCCA
.........((((((((..(((((((((....))).........((((.((((..(..((.((-((...((.......))...)))))))..)))).))))....)))))).)))))))) ( -40.20)
>DroYak_CAF1 56448 112 - 1
-----UUUGUGGCCAGCAAUUUAUGGGCGCUAGCCAGAAUUAUUGCUAUUGAUUUAGAAGCGA-GAAGAGG--AAUUGCCAAAUCCCCUAGGGUUAUUGGCUGACCAUAAAAGUUGGCCC
-----.....(((((((..(((((((.((((...(.((((((.......)))))).).)))).-.......--....(((((..(((...)))...)))))...))))))).))))))). ( -34.60)
>consensus
_____UUUGUGGCCAGCAAUUUAUGGGCGCUAGCCAAAAUUAUUGCUAUUGAUUUAGAAGCGAAGAAGAGGAGAAUUGCCAAAUCCCCUGGCGUUAUUGGCUGCCCAUAAAAGUUGGCCA
..........(((((((..((((((((...(((((((.....(((((...........))))).............(((((.......)))))...))))))))))))))).))))))). (-32.42 = -32.82 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	4,069,800 – 4,069,914
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.92
Mean single sequence MFE	-20.84
Consensus MFE	-20.04
Energy contribution	-20.04
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.96
SVM decision value	3.45
SVM RNA-class probability	0.999233
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4069800 114 + 20766785
GGCAAUUCUCUUCUUCUUCGCUUCUAAAUCAAUAGCAAUAAUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA------ACAUAUACACAAUUUGAUAUUCCUUUUCUCGGCCACAUU
(((................(((...........)))........(((((((((.........)))))))))....------...............................)))..... ( -20.00)
>DroSec_CAF1 52454 114 + 1
GGCAGUUCUCCUCUUCUUCGCUUCUAAAUCAAUAGCAAUAAUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA------ACAUAUACACAAUUUGAUGUUCCUUUUCUCGGCCACAUU
(((................(((...........)))........(((((((((.........)))))))))....------...............................)))..... ( -20.00)
>DroSim_CAF1 60631 114 + 1
GGCAAUUCUCCUCUUCUUCGCUUCUAAAUCAAUAGCAAUAAUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA------ACAUAUACACAAUUUGAUAUUCCUUUUCUCGGCCACAUU
(((................(((...........)))........(((((((((.........)))))))))....------...............................)))..... ( -20.00)
>DroEre_CAF1 53820 119 + 1
GGCAAUUCUCCUCUUC-CCGCUUCGAAAUCAAUAGCAAUAAUUCUGGCUAGCGCCCAUAAAUUGCUGGCCACAUAUAUACCAUAUAUACAGAAUUUGAUAUUCCUUUUCUCAGCCACAUU
(((.............-..(((...........)))...((((((((((((((.........))))))))..((((((...))))))..)))))).................)))..... ( -22.90)
>DroYak_CAF1 56488 111 + 1
GGCAAUU--CCUCUUC-UCGCUUCUAAAUCAAUAGCAAUAAUUCUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA------AUAUAUACAGAAUUUGAUAUUUCUUUUCUCAGCCGCAUU
(((....--.......-..(((...........)))........(((((((((.........)))))))))....------........((((...((....))..))))..)))..... ( -21.30)
>consensus
GGCAAUUCUCCUCUUCUUCGCUUCUAAAUCAAUAGCAAUAAUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA______ACAUAUACACAAUUUGAUAUUCCUUUUCUCGGCCACAUU
(((................(((...........)))........(((((((((.........))))))))).........................................)))..... (-20.04 = -20.04 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	4,069,840 – 4,069,954
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.78
Mean single sequence MFE	-21.07
Consensus MFE	-18.71
Energy contribution	-18.59
Covariance contribution	-0.12
Combinations/Pair	1.10
Mean z-score	-1.48
Structure conservation index	0.89
SVM decision value	1.07
SVM RNA-class probability	0.909528
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4069840 114 + 20766785
AUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA------ACAUAUACACAAUUUGAUAUUCCUUUUCUCGGCCACAUUAUCAGACCGCAUACUCACACACGUGUUGGCCAUAAAUCUA
....(((((((((.........)))))))))....------..............................((((((((.....((........))......))).)))))......... ( -22.00)
>DroSec_CAF1 52494 113 + 1
AUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA------ACAUAUACACAAUUUGAUGUUCCUUUUCUCGGCCACAUUAUCAGA-CGCAUACUCACACACGUGUUGGCCAUAAAUCUA
....((((((((((........((.(((((.....------......((((.....).)))..........)))))))......((-.......))......))))))))))........ ( -22.30)
>DroSim_CAF1 60671 114 + 1
AUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA------ACAUAUACACAAUUUGAUAUUCCUUUUCUCGGCCACAUUAUCAGACCGCAUACUCACACACGUGUUGGCCAUAAAUCUA
....(((((((((.........)))))))))....------..............................((((((((.....((........))......))).)))))......... ( -22.00)
>DroEre_CAF1 53859 120 + 1
AUUCUGGCUAGCGCCCAUAAAUUGCUGGCCACAUAUAUACCAUAUAUACAGAAUUUGAUAUUCCUUUUCUCAGCCACAUUAUCAGACCGCAUACUCACACACGUGUUGGCCAUAAAUCUA
....((((((((((........(((.((....((((((...))))))......(((((((...................))))))))))))...........))))))))))........ ( -21.32)
>DroYak_CAF1 56525 114 + 1
AUUCUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA------AUAUAUACAGAAUUUGAUAUUUCUUUUCUCAGCCGCAUUAUCAGACCGCAAACUCACACACGCGUUGACCAUAAAUCAA
....(((((((((.........)))))))))(((.------............(((((((...................))))))).(((............))))))............ ( -17.71)
>consensus
AUUUUGGCUAGCGCCCAUAAAUUGCUGGCCACAAA______ACAUAUACACAAUUUGAUAUUCCUUUUCUCGGCCACAUUAUCAGACCGCAUACUCACACACGUGUUGGCCAUAAAUCUA
....(((((((((((((........))).........................(((((((...................)))))))................))))))))))........ (-18.71 = -18.59 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:50 2006