Locus 8318

Sequence ID	3L_DroMel_CAF1
Location	21,787,877 – 21,788,015
Length	138
Max. P	0.883462

overview

Window 3

Location	21,787,877 – 21,787,975
Length	98
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.73
Mean single sequence MFE	-26.58
Consensus MFE	-16.37
Energy contribution	-16.32
Covariance contribution	-0.05
Combinations/Pair	1.23
Mean z-score	-1.78
Structure conservation index	0.62
SVM decision value	0.93
SVM RNA-class probability	0.883462
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21787877 98 + 23771897
--CACAAA---AUUUCGCUAGUGGGC----AAGCAA-----AAUAACGAGUAUUGGUUAAAAA-A-------AAAGUGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCA
--(((...---.....(((.(....)----.)))..-----..((((........))))....-.-------...)))..(((((..(((((.......)))))..)))))......... ( -23.90)
>DroSec_CAF1 7378 99 + 1
--CACAAU---AUUUCGCUGGUGGGC----AAAGAA-----AAUAACGAGUAUUGCUCAAAAAAA-------AAAAAGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCA
--......---.....((.(((((((----((....-----...........)))))).......-------........(((((..(((((.......)))))..)))))..))).)). ( -26.16)
>DroSim_CAF1 12644 97 + 1
--CACAAU---AUUUCGCUGGUGGGC----AAACAA-----AAUAACGAGUAUUGCUCAAAAA---------AAAAAGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCA
--......---.....((.(((((((----((((..-----........)).)))))).....---------........(((((..(((((.......)))))..)))))..))).)). ( -27.10)
>DroEre_CAF1 13478 92 + 1
--UACAGA---AUU-CGCUGGUGGGC----AAGCAA-----AAUAACGAGUAUCCCCUAAAAA-------------AGAAAGGGGCACCCGGAUUCGAACCGGGGACCUCUCGAUCUGUG
--((((((---...-.(((.......----.)))..-----.....((((...(((((.....-------------....)))))..(((((.......))))).....)))).)))))) ( -29.10)
>DroYak_CAF1 13381 90 + 1
--CACAAA---AUUUCGC---UGGGC----AAACAA-----AAAAACGAGUAUCCCUUAAAAA-------------AGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCA
--......---.....((---((...----...)).-----.....((((...(((((.....-------------..)))))((..(((((.......)))))..)).))))....)). ( -24.60)
>DroAna_CAF1 17840 120 + 1
CUGGCAGUAUAUUUUCGUUUAUGAGCGGGAAAGUAAUGGUUUAUAAAGAAUACCAUUAAAGGAAAAAAAGCCAAAAAAAAGGGGGCACCCGGAUUUGAACCAGGGACCUCUCGAUCUGCA
.((((......((..((((....))))..))..(((((((...........)))))))...........)))).......(((((..((.((.......)).))..)))))......... ( -28.60)
>consensus
__CACAAA___AUUUCGCUGGUGGGC____AAACAA_____AAUAACGAGUAUCGCUUAAAAA_________AAAAAGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCA
................(((....)))......................................................(((((..(((((.......)))))..)))))......... (-16.37 = -16.32 +  -0.05)

alignment

secondary structure

dotplot

Window 4

Location	21,787,877 – 21,787,975
Length	98
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.73
Mean single sequence MFE	-25.57
Consensus MFE	-17.92
Energy contribution	-16.82
Covariance contribution	-1.11
Combinations/Pair	1.42
Mean z-score	-1.47
Structure conservation index	0.70
SVM decision value	0.92
SVM RNA-class probability	0.881014
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21787877 98 - 23771897
UGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCACUUU-------U-UUUUUAACCAAUACUCGUUAUU-----UUGCUU----GCCCACUAGCGAAAU---UUUGUG--
.(((((.((((.((..(((((.......)))))..)).........((-------.-.....))......))))..(((-----(((((.----.......))))))))---))))).-- ( -23.90)
>DroSec_CAF1 7378 99 - 1
UGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCUUUUU-------UUUUUUUGAGCAAUACUCGUUAUU-----UUCUUU----GCCCACCAGCGAAAU---AUUGUG--
.((((...((((((..(((((.......)))))..))...........-------.......(((.....))).....)-----)))(((----((......)))))..---.)))).-- ( -22.10)
>DroSim_CAF1 12644 97 - 1
UGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCUUUUU---------UUUUUGAGCAAUACUCGUUAUU-----UUGUUU----GCCCACCAGCGAAAU---AUUGUG--
.((((..((((.((..(((((.......)))))..)).....(((...---------.....))).....)))).((((-----(((((.----.......))))))))---))))).-- ( -24.20)
>DroEre_CAF1 13478 92 - 1
CACAGAUCGAGAGGUCCCCGGUUCGAAUCCGGGUGCCCCUUUCU-------------UUUUUAGGGGAUACUCGUUAUU-----UUGCUU----GCCCACCAGCG-AAU---UCUGUA--
.(((((.((((.((..(((((.......)))))..))((((...-------------.....))))....))))....(-----(((((.----.......))))-)).---))))).-- ( -30.40)
>DroYak_CAF1 13381 90 - 1
UGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCU-------------UUUUUAAGGGAUACUCGUUUUU-----UUGUUU----GCCCA---GCGAAAU---UUUGUG--
.(((((.((((.((..(((((.......)))))..))(((((..-------------.....)))))...))))...((-----(((((.----....)---)))))).---))))).-- ( -28.80)
>DroAna_CAF1 17840 120 - 1
UGCAGAUCGAGAGGUCCCUGGUUCAAAUCCGGGUGCCCCCUUUUUUUUGGCUUUUUUUCCUUUAAUGGUAUUCUUUAUAAACCAUUACUUUCCCGCUCAUAAACGAAAAUAUACUGCCAG
.((((...((((((..(((((.......)))))..)).((........)).....))))...(((((((...........)))))))..........................))))... ( -24.00)
>consensus
UGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCUUUUU_________UUUUUAAGCAAUACUCGUUAUU_____UUGCUU____GCCCACCAGCGAAAU___AUUGUG__
.((((..((((.((..(((((.......)))))..)).....................((......))..))))....................((......)).........))))... (-17.92 = -16.82 +  -1.11)

alignment

secondary structure

dotplot

Window 5

Location	21,787,904 – 21,788,015
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.95
Mean single sequence MFE	-31.28
Consensus MFE	-27.12
Energy contribution	-27.45
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.87
SVM decision value	0.58
SVM RNA-class probability	0.788249
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21787904 111 + 23771897
-AAUAACGAGUAUUGGUUAAAAA-A-------AAAGUGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUGCCCCUGAGCUAUACCCCCACUUAUGUU
-......((((...(((......-.-------..(((...((((((((((((.......)))))((.(..(((((.....)))))..).)))))))))..)))..)))...))))..... ( -32.70)
>DroSec_CAF1 7405 112 + 1
-AAUAACGAGUAUUGCUCAAAAAAA-------AAAAAGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCCACUUAAGUU
-...((((((.....))).......-------........(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))......))) ( -32.30)
>DroSim_CAF1 12671 110 + 1
-AAUAACGAGUAUUGCUCAAAAA---------AAAAAGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCCACUUAAGUU
-...((((((.....))).....---------........(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))......))) ( -32.30)
>DroEre_CAF1 13504 106 + 1
-AAUAACGAGUAUCCCCUAAAAA-------------AGAAAGGGGCACCCGGAUUCGAACCGGGGACCUCUCGAUCUGUGGUCGAAUGCUCUACUUCUGAGCUACACCCCCACUUGUGAG
-....((((((............-------------.....((((..(((((.......)))))..))))(((((.....)))))..((((.......)))).........))))))... ( -32.10)
>DroYak_CAF1 13405 106 + 1
-AAAAACGAGUAUCCCUUAAAAA-------------AGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCCACUUGCCAC
-.....(((((....(((....)-------------))..(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))))))).... ( -32.20)
>DroAna_CAF1 17880 120 + 1
UUAUAAAGAAUACCAUUAAAGGAAAAAAAGCCAAAAAAAAGGGGGCACCCGGAUUUGAACCAGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCCGACUGAAAG
............((......))..................(((((..(((((.......)).))).....(((((.....)))))..((((.......))))....)))))......... ( -26.10)
>consensus
_AAUAACGAGUAUCGCUUAAAAA_________AAAAAGAAGGGGGCACCCGGAUUUGAACCGGGGACCUCUCGAUCUGCAGUCGAAUGCUCUACCCCUGAGCUAUACCCCCACUUAAGAU
........................................(((((..(((((.......)))))......(((((.....)))))..((((.......))))....)))))......... (-27.12 = -27.45 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	21,787,904 – 21,788,015
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.95
Mean single sequence MFE	-35.34
Consensus MFE	-31.75
Energy contribution	-31.33
Covariance contribution	-0.41
Combinations/Pair	1.15
Mean z-score	-1.34
Structure conservation index	0.90
SVM decision value	0.13
SVM RNA-class probability	0.600312
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21787904 111 - 23771897
AACAUAAGUGGGGGUAUAGCUCAGGGGCAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCACUUU-------U-UUUUUAACCAAUACUCGUUAUU-
.....(((((((((.....))).((((((..(((......))).((((....))))(((((.......)))))))))))..)))))).-------.-......................- ( -34.30)
>DroSec_CAF1 7405 112 - 1
AACUUAAGUGGGGGUAUAGCUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCUUUUU-------UUUUUUUGAGCAAUACUCGUUAUU-
...........((((((.(((((((((((..(((......))).((((....))))(((((.......))))))))))).........-------......))))).))))))......- ( -37.86)
>DroSim_CAF1 12671 110 - 1
AACUUAAGUGGGGGUAUAGCUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCUUUUU---------UUUUUGAGCAAUACUCGUUAUU-
...........((((((.(((((((((((..(((......))).((((....))))(((((.......))))))))))).........---------....))))).))))))......- ( -38.01)
>DroEre_CAF1 13504 106 - 1
CUCACAAGUGGGGGUGUAGCUCAGAAGUAGAGCAUUCGACCACAGAUCGAGAGGUCCCCGGUUCGAAUCCGGGUGCCCCUUUCU-------------UUUUUAGGGGAUACUCGUUAUU-
((((....))))......((((.......))))((((((((...((((....))))...)).)))))).(((((((((((....-------------.....))))).)))))).....- ( -36.20)
>DroYak_CAF1 13405 106 - 1
GUGGCAAGUGGGGGUAUAGCUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCU-------------UUUUUAAGGGAUACUCGUUUUU-
..(((.((((((((((..((((.......))))...........((((....))))(((((.......))))))))))))((((-------------(....)))))..))).)))...- ( -34.70)
>DroAna_CAF1 17880 120 - 1
CUUUCAGUCGGGGGUAUAGCUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCUGGUUCAAAUCCGGGUGCCCCCUUUUUUUUGGCUUUUUUUCCUUUAAUGGUAUUCUUUAUAA
.........(((((((..((((.......))))...........((((....))))(((((.......))))))))))))..................((......))............ ( -31.00)
>consensus
AACUCAAGUGGGGGUAUAGCUCAGGGGUAGAGCAUUCGACUGCAGAUCGAGAGGUCCCCGGUUCAAAUCCGGGUGCCCCCUUCUUUUU_________UUUUUAAGCAAUACUCGUUAUU_
.........(((((((..((((.......))))...........((((....))))(((((.......))))))))))))........................................ (-31.75 = -31.33 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:12:30 2006