Locus 3519

Sequence ID	3R_DroMel_CAF1
Location	9,510,524 – 9,510,715
Length	191
Max. P	0.994588

overview

Window 2

Location	9,510,524 – 9,510,638
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	98.86
Mean single sequence MFE	-31.38
Consensus MFE	-30.70
Energy contribution	-30.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.98
SVM decision value	1.11
SVM RNA-class probability	0.916521
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9510524 114 - 27905053
CACAGACACAACGUCUGGCAAGUACAUCGCUUUUUGGGCCGUCUCUUUUGCGGUUCAUUCAAUAAAAUUAUUGCGAAUGGCAGGCGCAAAACAGAAUCGCAAAAAUUGCAGUGU
..(((((.....)))))......((((.((..(((..((..(((.(((((((.(((((((((((....))))..))))))..).))))))).)))...))..)))..)).)))) ( -30.70)
>DroSec_CAF1 140218 114 - 1
CACAGACACAGCGUCUGGCAAGUACAUCGCUUUUUGGGCCGUCUCUUUUGCGGUUCAUUCAAUAAAAUUAUUGCGAAUGGCAGGCGCAAAACAGAAUCGCAAAAAUUGCAGUGU
.....((((.(((((((.((......((((....((((((((.......))))))))...((((....)))))))).)).)))))))...........(((.....))).)))) ( -32.40)
>DroSim_CAF1 130354 114 - 1
CACAGACACAGCGUCUGGCAAGUACAUCGCUUUUUGGGCCGUCUCUUUUGCGGUUCAUUCAAUAAAAUUAUUGCGAAUGGCAGGCGCAAAACAGAAUCGCAAAAAUUGCAGUGU
.....((((.(((((((.((......((((....((((((((.......))))))))...((((....)))))))).)).)))))))...........(((.....))).)))) ( -32.40)
>DroEre_CAF1 148073 114 - 1
CACAGACACAUCGUCUGGCAAGUACAUCGCUUUUUGGGCCGUCUCUUUUGCGGUUCAUUCAAUAAAAUUAUUGCGAAUGGUAGGCGCAAAACAGAAUCGCAAAAAUUGCAGUGU
..(((((.....)))))......((((.((..(((..((..(((.(((((((.(((((((((((....))))..))))))..).))))))).)))...))..)))..)).)))) ( -30.70)
>DroYak_CAF1 141819 114 - 1
CACAGACACAGCGUCUGGCAAGUACAUCGCUUUUUGGGCCGUCUCUUUUGCGGUUCAUUCAAUAAAAUUAUUGCGAAUGGUAGGCGCAAAACAGAAUCGCAAAAAUUGCAGUGU
..(((((.....)))))......((((.((..(((..((..(((.(((((((.(((((((((((....))))..))))))..).))))))).)))...))..)))..)).)))) ( -30.70)
>consensus
CACAGACACAGCGUCUGGCAAGUACAUCGCUUUUUGGGCCGUCUCUUUUGCGGUUCAUUCAAUAAAAUUAUUGCGAAUGGCAGGCGCAAAACAGAAUCGCAAAAAUUGCAGUGU
..(((((.....)))))......((((.((..(((..((..(((.(((((((.(((((((((((....))))..))))))..).))))))).)))...))..)))..)).)))) (-30.70 = -30.70 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	9,510,598 – 9,510,715
Length	117
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	90.88
Mean single sequence MFE	-37.26
Consensus MFE	-32.32
Energy contribution	-34.06
Covariance contribution	1.74
Combinations/Pair	1.03
Mean z-score	-2.15
Structure conservation index	0.87
SVM decision value	2.49
SVM RNA-class probability	0.994588
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9510598 117 + 27905053
GGCCCAAAAAGCGAUGUACUUGCCAGACGUUGUGUCUGUGUGCGUCCAAGUGUCUGUAGCGCGUUGUGUGUGUAUCGCGUAUGAAAAUACAUCAACUGUUGGGCAUCAACAAAA--AAA
.((((((...((((((.....(((((((.....))))).))(((..(((((((.....)))).)))..))).))))))((((....))))........))))))..........--... ( -36.20)
>DroSec_CAF1 140292 117 + 1
GGCCCAAAAAGCGAUGUACUUGCCAGACGCUGUGUCUGUGUGCGUCCGAGUGUCUGUAGCGCGUUGUGUGUGUAUCGCGUAUGAAAAUACAUCAACUGUUGGGCAUCAACAAAA--AAA
.((((((...(((((((((....((((((((.((..((....))..))))))))))..((((...)))))))))))))((((....))))........))))))..........--... ( -38.40)
>DroSim_CAF1 130428 119 + 1
GGCCCAAAAAGCGAUGUACUUGCCAGACGCUGUGUCUGUGUGCGUCCGAGUGUCUGUAGCGCGUUGUGUGUGUAUCGCGUAUGAAAAUACAUCAACUGUUGGGCAUCAACAAAAAAAAA
.((((((...(((((((((....((((((((.((..((....))..))))))))))..((((...)))))))))))))((((....))))........))))))............... ( -38.40)
>DroEre_CAF1 148147 105 + 1
GGCCCAAAAAGCGAUGUACUUGCCAGACGAUGUGUCUGUGUGCGUUCGACGGUCUGUAGC--GUUG--UGUGUAUCGCGUAUGAAAAUACA-----UGUUGGGCAUAAAAAAAA-----
.((((((...(((((((((..(((((((.....))))).)).....(((((........)--))))--.)))))))))((((....)))).-----..))))))..........----- ( -35.70)
>DroYak_CAF1 141893 112 + 1
GGCCCAAAAAGCGAUGUACUUGCCAGACGCUGUGUCUGUGUGCGUUCGACGGUCUGUAGCGCGUUG--UGUGUAUCGCGUAUGAAAAUACAUCAACUGUUGGGCAUAAAAAAAA-----
.((((((...(((((((((..(((((((.....))))).))(((((((......)).)))))....--.)))))))))((((....))))........))))))..........----- ( -37.60)
>consensus
GGCCCAAAAAGCGAUGUACUUGCCAGACGCUGUGUCUGUGUGCGUCCGAGUGUCUGUAGCGCGUUGUGUGUGUAUCGCGUAUGAAAAUACAUCAACUGUUGGGCAUCAACAAAA__AAA
.((((((...(((((((((....(((((.....)))))(((((...((......))..)))))......)))))))))((((....))))........))))))............... (-32.32 = -34.06 +   1.74)

alignment

secondary structure

dotplot

Window 4

Location	9,510,598 – 9,510,715
Length	117
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	90.88
Mean single sequence MFE	-31.42
Consensus MFE	-26.46
Energy contribution	-27.66
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.13
Structure conservation index	0.84
SVM decision value	2.09
SVM RNA-class probability	0.987729
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9510598 117 - 27905053
UUU--UUUUGUUGAUGCCCAACAGUUGAUGUAUUUUCAUACGCGAUACACACACAACGCGCUACAGACACUUGGACGCACACAGACACAACGUCUGGCAAGUACAUCGCUUUUUGGGCC
...--..........((((((.((.((((((((((.(....................((((((........))).)))...(((((.....)))))).)))))))))).)).)))))). ( -32.00)
>DroSec_CAF1 140292 117 - 1
UUU--UUUUGUUGAUGCCCAACAGUUGAUGUAUUUUCAUACGCGAUACACACACAACGCGCUACAGACACUCGGACGCACACAGACACAGCGUCUGGCAAGUACAUCGCUUUUUGGGCC
...--..........((((((.((.((((((((((.(...((((............))))...........(((((((...........)))))))).)))))))))).)).)))))). ( -34.10)
>DroSim_CAF1 130428 119 - 1
UUUUUUUUUGUUGAUGCCCAACAGUUGAUGUAUUUUCAUACGCGAUACACACACAACGCGCUACAGACACUCGGACGCACACAGACACAGCGUCUGGCAAGUACAUCGCUUUUUGGGCC
...............((((((.((.((((((((((.(...((((............))))...........(((((((...........)))))))).)))))))))).)).)))))). ( -34.10)
>DroEre_CAF1 148147 105 - 1
-----UUUUUUUUAUGCCCAACA-----UGUAUUUUCAUACGCGAUACACA--CAAC--GCUACAGACCGUCGAACGCACACAGACACAUCGUCUGGCAAGUACAUCGCUUUUUGGGCC
-----..........((((((..-----.((((....))))(((((..((.--....--((....(.....)....))...(((((.....)))))....))..)))))...)))))). ( -24.90)
>DroYak_CAF1 141893 112 - 1
-----UUUUUUUUAUGCCCAACAGUUGAUGUAUUUUCAUACGCGAUACACA--CAACGCGCUACAGACCGUCGAACGCACACAGACACAGCGUCUGGCAAGUACAUCGCUUUUUGGGCC
-----..........((((((.((.((((((((((.....((((.......--...)))).........((((.((((...........)))).)))))))))))))).)).)))))). ( -32.00)
>consensus
UUU__UUUUGUUGAUGCCCAACAGUUGAUGUAUUUUCAUACGCGAUACACACACAACGCGCUACAGACACUCGGACGCACACAGACACAGCGUCUGGCAAGUACAUCGCUUUUUGGGCC
...............((((((.((.((((((((((.(...((((............)))).....................(((((.....)))))).)))))))))).)).)))))). (-26.46 = -27.66 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:10 2006