Locus 843

Sequence ID	3L_DroMel_CAF1
Location	2,555,521 – 2,555,645
Length	124
Max. P	0.999833

overview

Window 8

Location	2,555,521 – 2,555,613
Length	92
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	68.18
Mean single sequence MFE	-13.05
Consensus MFE	-6.91
Energy contribution	-7.52
Covariance contribution	0.61
Combinations/Pair	1.07
Mean z-score	-1.40
Structure conservation index	0.53
SVM decision value	0.20
SVM RNA-class probability	0.629802
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2555521 92 - 23771897
ACGAG-----UUUUCA--GUUUUUUUUCAAAAA---AAAAAAAAAAAAACGUUGAUUACCCAAGUUAAUCAACGA--------AACU-----AACAACAAUUGCUAAUUGAUGAG
...((-----((((..--(((((((((......---.....)))))))))((((((((.......))))))))))--------))))-----..((.((((.....)))).)).. ( -15.90)
>DroVir_CAF1 22242 110 - 1
UAAAGUGCAGUUUGAAAA----UAAAACAGAAAACAAAAAAAAAAACUACUUUGAUUU-CUGGGUUAAUUAACUAACAGCAGAAGCAGCAGCAGCAACAAUUGGUAAUUGAUGCG
.....(((((((......----(((..((((((.((((............)))).)))-)))..)))...))))....((....)).)))...(((.((((.....)))).))). ( -19.00)
>DroSec_CAF1 17480 75 - 1
ACGAA-----UUUUCA----------------------AACAACAAAAACGUUGAUUACCCAAGUUAAUCAACGA--------AACU-----AACAACAAUUGCUAAUUGAUGAG
.....-----......----------------------...........(((((((((.......))))))))).--------....-----..((.((((.....)))).)).. ( -10.60)
>DroEre_CAF1 31500 77 - 1
ACGAG-----UUUUCA--------------------AGCACAACAAAAACGUUGAUUACCCGAGUUAAUCAACGA--------AACA-----AACAACAAUUGCUAAUUGAUGAG
.....-----......--------------------.............(((((((((.......))))))))).--------....-----..((.((((.....)))).)).. ( -10.60)
>DroYak_CAF1 15898 77 - 1
ACGAG-----UUUUCA--------------------AGCACAACAAAAACGUUGAUUACCCGGGUUAAUCAACGA--------AACA-----UACAACAAUUGCUAAUUGAUGAG
.....-----......--------------------.............((((((((((....).))))))))).--------....-----..((.((((.....)))).)).. ( -12.00)
>DroAna_CAF1 16390 73 - 1
---AG-----UUUUUC--------------------AGCA-AAAAAACGCUUUGAUUAUCCGGGUUAAUUAUCGA--------AACU-----AACAACAAUUGGUAAUUGAUGAG
---.(-----(((((.--------------------....-.))))))...............((((((((((((--------....-----........))))))))))))... ( -10.20)
>consensus
ACGAG_____UUUUCA____________________AGAACAAAAAAAACGUUGAUUACCCGAGUUAAUCAACGA________AACA_____AACAACAAUUGCUAAUUGAUGAG
.................................................(((((((((.......)))))))))....................((.((((.....)))).)).. ( -6.91 =  -7.52 +   0.61)

alignment

secondary structure

dotplot

Window 9

Location	2,555,548 – 2,555,645
Length	97
Sequences	3
Columns	105
Reading direction	reverse
Mean pairwise identity	73.63
Mean single sequence MFE	-15.87
Consensus MFE	-12.00
Energy contribution	-12.33
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.40
Structure conservation index	0.76
SVM decision value	4.20
SVM RNA-class probability	0.999833
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2555548 97 - 23771897
CCAUCUCAAAAUG--------UAUUGACUGUAGCACACCUACGAGUUUUCAGUUUUUUUUCAAAAAAAAAAAAAAAAAACGUUGAUUACCCAAGUUAAUCAACGA
...........((--------....((((((((.....)))).))))..))(((((((((...........)))))))))((((((((.......)))))))).. ( -16.20)
>DroSec_CAF1 17507 80 - 1
CCAUUACAAAACG--------UAUUGACUGUAGCACACCUACGAAUUUUCA-----------------AACAACAAAAACGUUGAUUACCCAAGUUAAUCAACGA
.((.(((.....)--------)).))..(((((.....)))))........-----------------...........(((((((((.......))))))))). ( -13.40)
>DroYak_CAF1 15925 90 - 1
CCAUCAACAAAUUGGGUAGAUUAUAGACUGUAGCACACCUACGAGUUUUCA---------------AGCACAACAAAAACGUUGAUUACCCGGGUUAAUCAACGA
(((.........)))((.(.....(((((((((.....)))).)))))...---------------..)))........((((((((((....).))))))))). ( -18.00)
>consensus
CCAUCACAAAAUG________UAUUGACUGUAGCACACCUACGAGUUUUCA_______________A_AACAACAAAAACGUUGAUUACCCAAGUUAAUCAACGA
.........................((((((((.....)))).))))................................((((((((((....).))))))))). (-12.00 = -12.33 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:35 2006