Locus 7775

Sequence ID	X_DroMel_CAF1
Location	19,338,198 – 19,338,391
Length	193
Max. P	0.995518

overview

Window 7

Location	19,338,198 – 19,338,311
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.14
Mean single sequence MFE	-27.00
Consensus MFE	-15.88
Energy contribution	-16.88
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.59
SVM decision value	0.14
SVM RNA-class probability	0.600699
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19338198 113 + 22224390
GUUACAUUUCGUGCCUAUAGCUCUAUUAGCUACAUGCUAUAUGCUAUAUGCUAUAUGCCAUAUGCCAUAUGCCAUUAGCU-------AUUUGCCAUUAGCGCCGGCGUCGACGACGCUUU
..........((((..((.((.....((((((.(((.((((((.(((((((.....).)))))).)))))).))))))))-------)...)).))..)))).((((((...)))))).. ( -32.30)
>DroSec_CAF1 10896 106 + 1
GUUACGUUUCGUGCCUAUAGCUCUAUUAGCUACAUGCUAUAUG-------CUAUAUGCCAUGUGCCAUAUGACAUUAGCU-------AUUUGCCAUUAGCGCCGGCGUCGACGACGCUUU
..........((((..((.((.....((((((.(((.((((((-------.(((((...))))).)))))).))))))))-------)...)).))..)))).((((((...)))))).. ( -28.00)
>DroEre_CAF1 10617 100 + 1
GUUACAUUUCGUGCCUAUAGCUCUAUUAGCUACAUA-----UG--------UAUAUGCUAUAUGCUAUAUGCCAUUAGCU-------UUUUGCCAUUAGCGCCGGCGUCGACGACGCUUU
..........((((..((.((...(..(((((....-----.(--------(((((((.....)).))))))...)))))-------..).)).))..)))).((((((...)))))).. ( -24.60)
>DroYak_CAF1 10667 99 + 1
GUUACAUUCCGUGCCUUUAGCUCUAUUAGCU---------------------AUAUGCUAUAUGCCAUAUGCUAUUAGCUAUUUGCCAUUUGCCAUUAGCGCCGGCGUCGACGACGCUUU
..........((((...(((((....((((.---------------------((((((.....).)))))))))..)))))...((.....)).....)))).((((((...)))))).. ( -23.10)
>consensus
GUUACAUUUCGUGCCUAUAGCUCUAUUAGCUACAUG_____UG________UAUAUGCCAUAUGCCAUAUGCCAUUAGCU_______AUUUGCCAUUAGCGCCGGCGUCGACGACGCUUU
..........((((...(((((.....)))))........................((((...((.....))...))))...................)))).((((((...)))))).. (-15.88 = -16.88 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	19,338,198 – 19,338,311
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.14
Mean single sequence MFE	-31.27
Consensus MFE	-22.64
Energy contribution	-22.45
Covariance contribution	-0.19
Combinations/Pair	1.19
Mean z-score	-2.97
Structure conservation index	0.72
SVM decision value	2.58
SVM RNA-class probability	0.995518
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19338198 113 - 22224390
AAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAU-------AGCUAAUGGCAUAUGGCAUAUGGCAUAUAGCAUAUAGCAUAUAGCAUGUAGCUAAUAGAGCUAUAGGCACGAAAUGUAAC
...((((..(((..(((.((((((.((((....-------.)))).))))(((((.(....).))))).)).((((((.((((((.....))).)))..))))))))).))).))))... ( -34.60)
>DroSec_CAF1 10896 106 - 1
AAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAU-------AGCUAAUGUCAUAUGGCACAUGGCAUAUAG-------CAUAUAGCAUGUAGCUAAUAGAGCUAUAGGCACGAAACGUAAC
...((((..(((..(((...((((.((((....-------.))))(((..(((((.(....).)))))..-------))).)))).(((((((.....)))))))))).))).))))... ( -34.40)
>DroEre_CAF1 10617 100 - 1
AAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAA-------AGCUAAUGGCAUAUAGCAUAUAGCAUAUA--------CA-----UAUGUAGCUAAUAGAGCUAUAGGCACGAAAUGUAAC
...(((((...)))))((((((((.((((....-------.)))).)))).((((((.((((((((((.--------..-----.)))).))).)))..)))))).)).))......... ( -28.80)
>DroYak_CAF1 10667 99 - 1
AAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAUGGCAAAUAGCUAAUAGCAUAUGGCAUAUAGCAUAU---------------------AGCUAAUAGAGCUAAAGGCACGGAAUGUAAC
..(((((((.......)))))))....(((..((((...(((((..(((((((((........)))))---------------------.))))....)))))...)).))...)))... ( -27.30)
>consensus
AAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAU_______AGCUAAUGGCAUAUGGCAUAUAGCAUAUA________CA_____CAUGUAGCUAAUAGAGCUAUAGGCACGAAAUGUAAC
...((((..(((..(((.((((((.((((............)))).)))).((((...))))))......................(((((((.....)))))))))).))).))))... (-22.64 = -22.45 +  -0.19)

alignment

secondary structure

dotplot

Window 9

Location	19,338,238 – 19,338,351
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.87
Mean single sequence MFE	-34.85
Consensus MFE	-27.11
Energy contribution	-27.68
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.58
Structure conservation index	0.78
SVM decision value	0.25
SVM RNA-class probability	0.653619
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19338238 113 + 22224390
AUGCUAUAUGCUAUAUGCCAUAUGCCAUAUGCCAUUAGCU-------AUUUGCCAUUAGCGCCGGCGUCGACGACGCUUUUCUCUGCCCGCCGACGAUCGGGGUUCUCGGAAAUCGGCAC
..((((.(((.((((((.(....).)))))).))))))).-------...((((...(((.(((((((((.((..((........)).)).))))).)))).)))....(....))))). ( -33.70)
>DroSec_CAF1 10936 106 + 1
AUG-------CUAUAUGCCAUGUGCCAUAUGACAUUAGCU-------AUUUGCCAUUAGCGCCGGCGUCGACGACGCUUUUCUCUGCCCGCCGACGAUCGGGGUUCUCGGAAAUCGGCAC
(((-------.((((((.(....).)))))).)))..(((-------(........))))(((((((((...))))).(((((..(..(.(((.....))).)..)..))))).)))).. ( -31.40)
>DroEre_CAF1 10653 104 + 1
-UG--------UAUAUGCUAUAUGCUAUAUGCCAUUAGCU-------UUUUGCCAUUAGCGCCGGCGUCGACGACGCUUUUCUCUGCCCGCCGACGAUCGGCGUUCUCGGAAAUCGGCAC
-.(--------(((((((.....)).)))))).....(((-------..((.((...(((((((((((((.((..((........)).)).))))).))))))))...)).))..))).. ( -35.80)
>DroYak_CAF1 10698 108 + 1
------------AUAUGCUAUAUGCCAUAUGCUAUUAGCUAUUUGCCAUUUGCCAUUAGCGCCGGCGUCGACGACGCUUUUCUCUGCCCGCCGACGAUCGGCGUUCUCGGAAAUCGGCAC
------------....((((...((.....))...))))....((((((((.((...(((((((((((((.((..((........)).)).))))).))))))))...)))))).)))). ( -38.50)
>consensus
_UG________UAUAUGCCAUAUGCCAUAUGCCAUUAGCU_______AUUUGCCAUUAGCGCCGGCGUCGACGACGCUUUUCUCUGCCCGCCGACGAUCGGCGUUCUCGGAAAUCGGCAC
......................((((....((.....)).............((...(((((((((((((.((..((........)).)).))))).))))))))...)).....)))). (-27.11 = -27.68 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	19,338,238 – 19,338,351
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.87
Mean single sequence MFE	-38.35
Consensus MFE	-34.22
Energy contribution	-34.85
Covariance contribution	0.63
Combinations/Pair	1.07
Mean z-score	-2.17
Structure conservation index	0.89
SVM decision value	1.63
SVM RNA-class probability	0.968814
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19338238 113 - 22224390
GUGCCGAUUUCCGAGAACCCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAU-------AGCUAAUGGCAUAUGGCAUAUGGCAUAUAGCAUAUAGCAU
((((((....(((......(((..(((((((((((........)).))))))))).))).((((.((((....-------.)))).))))...)))....))))))...((.....)).. ( -39.00)
>DroSec_CAF1 10936 106 - 1
GUGCCGAUUUCCGAGAACCCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAU-------AGCUAAUGUCAUAUGGCACAUGGCAUAUAG-------CAU
((((((.....((.......))..(((((((((((........)).))))))))).))))))...((((....-------.))))(((..(((((.(....).)))))..-------))) ( -36.70)
>DroEre_CAF1 10653 104 - 1
GUGCCGAUUUCCGAGAACGCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAA-------AGCUAAUGGCAUAUAGCAUAUAGCAUAUA--------CA-
..((((.(((((..(..(((((.....)))))..).).)))).(((((...)))))))))((((.((((....-------.)))).))))((((.((.....)))))).--------..- ( -37.30)
>DroYak_CAF1 10698 108 - 1
GUGCCGAUUUCCGAGAACGCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAUGGCAAAUAGCUAAUAGCAUAUGGCAUAUAGCAUAU------------
.((((.(((((((..(.(((((..(((((((((((........)).))))))))).))))).)..))).))))))))....((((...((.....))...))))....------------ ( -40.40)
>consensus
GUGCCGAUUUCCGAGAACCCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAU_______AGCUAAUGGCAUAUGGCAUAUAGCAUAUA________CA_
((((((............((((..(((((((((((........)).))))))))).))))((((.((((............)))).))))...))))))..................... (-34.22 = -34.85 +   0.63)

alignment

secondary structure

dotplot

Window 1

Location	19,338,278 – 19,338,391
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.45
Mean single sequence MFE	-37.86
Consensus MFE	-25.60
Energy contribution	-26.86
Covariance contribution	1.26
Combinations/Pair	1.12
Mean z-score	-1.61
Structure conservation index	0.68
SVM decision value	0.19
SVM RNA-class probability	0.626754
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19338278 113 - 22224390
AAGCAGACACUGCGCUGAACGCUCAAACACUGAAAAACUAGUGCCGAUUUCCGAGAACCCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAU-------
..((.......((((((...((((....((((......))))((((((...((.......))...))))))))))........(((((...))))))))))).....))....------- ( -35.80)
>DroSec_CAF1 10969 113 - 1
AAGCAGACACCGCGCUGAACGCUCAAACACUGAAAAACUAGUGCCGAUUUCCGAGAACCCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAU-------
..((.......((((((...((((....((((......))))((((((...((.......))...))))))))))........(((((...))))))))))).....))....------- ( -35.10)
>DroEre_CAF1 10684 113 - 1
AAGCAGACACUGCGCUGAACGCUCAAACACUGAAAAACUAGUGCCGAUUUCCGAGAACGCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAA-------
..((((...))))(((......(((.....))).....((((((((.(((((..(..(((((.....)))))..).).)))).(((((...)))))))))))))..)))....------- ( -39.40)
>DroYak_CAF1 10726 120 - 1
AAGCAGACACUGCGCUGAACGCUCAAACACUGAAAAACUAGUGCCGAUUUCCGAGAACGCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAUGGCAAAU
..((((...))))((((...(((((.....))).....((((((((.(((((..(..(((((.....)))))..).).)))).(((((...)))))))))))))...))...)))).... ( -40.60)
>DroAna_CAF1 16766 96 - 1
AAGCUGACUCGGCGAAGAACGCUCCAAUACUGAAA-GCCAGCGCCGAAA--------------CUAGCGACUGGCUUUGAGACCCGGCCGCGACGCCGGCGACGACGGCGC---------
..((((.(((((((.....))).......((.(((-((((((((.....--------------...))).)))))))).))..(((((......)))))))).).))))..--------- ( -38.40)
>consensus
AAGCAGACACUGCGCUGAACGCUCAAACACUGAAAAACUAGUGCCGAUUUCCGAGAACCCCGAUCGUCGGCGGGCAGAGAAAAGCGUCGUCGACGCCGGCGCUAAUGGCAAAU_______
..((.......(((.....)))................((((((((.....((.......))..(((((((((((........)).))))))))).))))))))...))........... (-25.60 = -26.86 +   1.26)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:18 2006