Locus 1698

Sequence ID	2L_DroMel_CAF1
Location	4,644,591 – 4,644,791
Length	200
Max. P	0.997711

overview

Window 9

Location	4,644,591 – 4,644,711
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	69.72
Mean single sequence MFE	-33.91
Consensus MFE	-15.10
Energy contribution	-16.10
Covariance contribution	1.00
Combinations/Pair	1.10
Mean z-score	-2.49
Structure conservation index	0.45
SVM decision value	0.65
SVM RNA-class probability	0.812307
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4644591 120 + 22407834
CCACCGGGUUCCAUUCCGCCUCUUCGACCACCAAAUCAAGGUGGACAUCCACCAGGAUCACAGAAGCCUCCUAAUGUGGGAAUAUACCCCCCAUCCACGGGCUGGAUUCCGCCAUUUGGG
(((.(((..((((..(((...((((..(((((.......)))))..((((....))))....)))).......(((.(((........))))))...)))..))))..))).....))). ( -36.30)
>DroSec_CAF1 81413 120 + 1
CCACCAGGAUCUAUGCCGCCUCUUGGAUCACCGAAUCAAAUUGGAUAUCCACCAGGAUCACUGAAGCCUCCUAAUUCCGGUAUAUAUCCCCCAUCAACGGGCUGGACUUUGCCAUCUGGU
..((((((((.((((((((((..(((((..((((......))))..)))))..)))......(((.........)))))))))).))))..........(((........)))...)))) ( -32.20)
>DroEre_CAF1 85779 102 + 1
------------------CCUCCUGGGCCACCAAACCAAGGUGGAUAUCCACCAGGAUCACAGAUGCCUCCUAAUUCUGGAUUACAUCCUCCACAACAGAAUUGGAUUCUGCCUCCUGGG
------------------.....(((((((((.......)))))...))))((((((...((((....(((.(((((((.................)))))))))).))))..)))))). ( -33.23)
>consensus
CCACC_GG_UC_AU_CCGCCUCUUGGACCACCAAAUCAAGGUGGAUAUCCACCAGGAUCACAGAAGCCUCCUAAUUCCGGAAUAUAUCCCCCAUCAACGGGCUGGAUUCUGCCAUCUGGG
..............................(((......(((((....)))))((((...........))))......((.....(((((((......)))..))))....))...))). (-15.10 = -16.10 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	4,644,631 – 4,644,751
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	79.72
Mean single sequence MFE	-40.54
Consensus MFE	-26.83
Energy contribution	-27.83
Covariance contribution	1.00
Combinations/Pair	1.07
Mean z-score	-3.29
Structure conservation index	0.66
SVM decision value	2.91
SVM RNA-class probability	0.997711
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4644631 120 + 22407834
GUGGACAUCCACCAGGAUCACAGAAGCCUCCUAAUGUGGGAAUAUACCCCCCAUCCACGGGCUGGAUUCCGCCAUUUGGGCCACUAACUCAAGGUGGACAUCCACCAGGAUCACUGUUGC
((((....))))(((((((.....(((((....(((.(((........))))))....)))))((((((((((..(((((.......))))))))))).)))).....)))).))).... ( -42.40)
>DroSec_CAF1 81453 120 + 1
UUGGAUAUCCACCAGGAUCACUGAAGCCUCCUAAUUCCGGUAUAUAUCCCCCAUCAACGGGCUGGACUUUGCCAUCUGGUCUACCAAAUCAAGGUGGAAAUCCACCAGGAUCAAUGGUGC
..((((.((((((.(((.....((....)).....)))((((....((((((......)))..)))...))))...(((....)))......)))))).))))((((.......)))).. ( -35.80)
>DroEre_CAF1 85801 120 + 1
GUGGAUAUCCACCAGGAUCACAGAUGCCUCCUAAUUCUGGAUUACAUCCUCCACAACAGAAUUGGAUUCUGCCUCCUGGGCCACCAAACCAAGGUGGAUAUCCACCAGGAUCACAGAUGC
(((((((((((((((((...((((....(((.(((((((.................)))))))))).))))..))))((....)).......)))))))))))))............... ( -43.43)
>consensus
GUGGAUAUCCACCAGGAUCACAGAAGCCUCCUAAUUCCGGAAUAUAUCCCCCAUCAACGGGCUGGAUUCUGCCAUCUGGGCCACCAAAUCAAGGUGGAAAUCCACCAGGAUCACUGAUGC
((((((.((((((((((...........))))......((.....(((((((......)))..))))....))...(((....)))......)))))).))))))............... (-26.83 = -27.83 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	4,644,631 – 4,644,751
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	79.72
Mean single sequence MFE	-45.20
Consensus MFE	-36.17
Energy contribution	-35.63
Covariance contribution	-0.54
Combinations/Pair	1.26
Mean z-score	-2.35
Structure conservation index	0.80
SVM decision value	2.06
SVM RNA-class probability	0.986857
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4644631 120 - 22407834
GCAACAGUGAUCCUGGUGGAUGUCCACCUUGAGUUAGUGGCCCAAAUGGCGGAAUCCAGCCCGUGGAUGGGGGGUAUAUUCCCACAUUAGGAGGCUUCUGUGAUCCUGGUGGAUGUCCAC
....(((.....)))(((((((((((((..((..(((.((((((...(((........)))..))((((.((((.....)))).))))....)))).)))...))..))))))))))))) ( -47.80)
>DroSec_CAF1 81453 120 - 1
GCACCAUUGAUCCUGGUGGAUUUCCACCUUGAUUUGGUAGACCAGAUGGCAAAGUCCAGCCCGUUGAUGGGGGAUAUAUACCGGAAUUAGGAGGCUUCAGUGAUCCUGGUGGAUAUCCAA
...((((..((...(((((....)))))...((((((....))))))(((........))).))..)))).((((((.((((((.((((.(......)..)))).)))))).)))))).. ( -41.40)
>DroEre_CAF1 85801 120 - 1
GCAUCUGUGAUCCUGGUGGAUAUCCACCUUGGUUUGGUGGCCCAGGAGGCAGAAUCCAAUUCUGUUGUGGAGGAUGUAAUCCAGAAUUAGGAGGCAUCUGUGAUCCUGGUGGAUAUCCAC
...............(((((((((((((..((((....)))).((((.(((((..((..(((((((.((((........)))).)).)))))))..)))))..))))))))))))))))) ( -46.40)
>consensus
GCAACAGUGAUCCUGGUGGAUAUCCACCUUGAUUUGGUGGCCCAGAUGGCAGAAUCCAGCCCGUUGAUGGGGGAUAUAUUCCAGAAUUAGGAGGCUUCUGUGAUCCUGGUGGAUAUCCAC
...............(((((((((((((....(((((..(((.....)))...((((..(((......))))))).....)))))...((((.((....))..))))))))))))))))) (-36.17 = -35.63 +  -0.54)

alignment

secondary structure

dotplot

Window 2

Location	4,644,671 – 4,644,791
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	67.19
Mean single sequence MFE	-30.78
Consensus MFE	-14.77
Energy contribution	-15.14
Covariance contribution	0.37
Combinations/Pair	1.14
Mean z-score	-2.52
Structure conservation index	0.48
SVM decision value	2.41
SVM RNA-class probability	0.993611
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4644671 120 + 22407834
AAUAUACCCCCCAUCCACGGGCUGGAUUCCGCCAUUUGGGCCACUAACUCAAGGUGGACAUCCACCAGGAUCACUGUUGCCUCCUAAUACUGGAUUGCCACCGGGCUCUAUUCCGCCGCU
............((((...((.(((((((((((..(((((.......))))))))))).))))))).))))..(.((.((.(((.......)))..)).)).)(((........)))... ( -33.10)
>DroSec_CAF1 81493 120 + 1
UAUAUAUCCCCCAUCAACGGGCUGGACUUUGCCAUCUGGUCUACCAAAUCAAGGUGGAAAUCCACCAGGAUCAAUGGUGCCUCCAAUUUCUGUAUUGCCACCGGGCUCUAUUCCGCCUCU
..................((((.(((....(((...(((..(((((.(((..(((((....)))))..)))...)))))....((((......)))))))...))).....))))))).. ( -32.20)
>DroEre_CAF1 85841 95 + 1
AUUACAUCCUCCACAACAGAAUUGGAUUCUGCCUCCUGGGCCACCAAACCAAGGUGGAUAUCCACCAGGAUCACAGAUGCCUCCUAAUUCUGGAU-------------------------
................((((((((((.((((..((((((.(((((.......))))).......))))))...))))....))).)))))))...------------------------- ( -31.50)
>DroYak_CAF1 85584 95 + 1
AUUAAACCCUCCACUACCGGGCUGGAUUCUGCCUCCUGCGCCACCAAAUCUAGGUGGACAUCCACCAGGAACACAGCUGCCUCCUAGUUCAGGAU-------------------------
.......(((..((((..(((((((....(((.....)))...)))..(((.(((((....))))).)))........))))..))))..)))..------------------------- ( -26.30)
>consensus
AAUAUACCCCCCACCAACGGGCUGGAUUCUGCCACCUGGGCCACCAAAUCAAGGUGGACAUCCACCAGGAUCACAGAUGCCUCCUAAUUCUGGAU_________________________
..................((((.........((...(((....)))......(((((....))))).)).........))))...................................... (-14.77 = -15.14 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:49 2006