Locus 942

Sequence ID	3L_DroMel_CAF1
Location	2,820,495 – 2,820,695
Length	200
Max. P	0.987366

overview

Window 7

Location	2,820,495 – 2,820,598
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.56
Mean single sequence MFE	-25.88
Consensus MFE	-12.04
Energy contribution	-14.28
Covariance contribution	2.24
Combinations/Pair	1.19
Mean z-score	-1.90
Structure conservation index	0.47
SVM decision value	0.59
SVM RNA-class probability	0.792454
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2820495 103 - 23771897
GUCA--CCCAAAAAGGGCAACAAUUGUUGCUCUUAAUUCGAACGAUAAGCUUUCGAUCGAAGGAUAUGU-----GUUUAGCCAAA------UUGUAAGAGAUCUGGAAUUUCCUUG----
....--.((...(((((((((....)))))))))..(((((.(((.......))).)))))))......-----......(((.(------((......))).)))..........---- ( -24.30)
>DroSec_CAF1 65449 100 - 1
GUCA--CCCAAAAAGGGCAACAAUUGUUGCUCUUAAUUCGCCAGAUAAGGUUUCGAUCGAAGGAUAUGU-----AAUUACCCAAA-------------AGAUCUGAGUUUUCCUUGGGAA
....--(((((.(((((((((....))))))))).....(((((((..(((..(((((....))).)).-----....)))....-------------..))))).)).....))))).. ( -28.00)
>DroSim_CAF1 56949 100 - 1
GUCA--CCCAAAAAGGGCAACAAUUGUUGCUCUUAAUUCGAACGAUAAGGUUUCGAUCGAAGGAUGUGU-----GUUUACCCAAA-------------AGAUCUGAAUUUUCAUUGGGAA
..((--(((...(((((((((....)))))))))..(((((.(((.......))).)))))))..))).-----.....((((((-------------((((....)))))..))))).. ( -28.20)
>DroEre_CAF1 68147 107 - 1
GUCA--CCCAAAA-AGGCAGCAAUUGUUACUCUUAAUUUGCCCGAUAAGGCUUCGAUCGAAAGAUAUAUGUAUUGUUUACCCAAAAGAUACAUAUAGAAGAUUUAGAUUU----------
(((.--.......-.((((..(((((.......)))))))))...((((.((((..((....))((((((((((.(((....))).)))))))))))))).)))))))..---------- ( -21.40)
>DroYak_CAF1 68036 114 - 1
GUCAUCCCCAAAA-AGGCAACAAUUGUUGCUCUUAAUUUGCCCAAUAAGGUUUCGAUCGAAAGAUGUAU-----GUUUACUUAAAAGAUAAAUGUAAAUGAUCUGGAUUUUCCUGGGGAA
....((((((..(-(((((((....))))).))).......(((...........(((....))).(((-----(((((((....)).)))))))).......))).......)))))). ( -27.50)
>consensus
GUCA__CCCAAAAAGGGCAACAAUUGUUGCUCUUAAUUCGCCCGAUAAGGUUUCGAUCGAAGGAUAUGU_____GUUUACCCAAA_______U_UA__AGAUCUGGAUUUUCCUUGGGAA
......(((((.(((((((((....)))))))))((((((..(((.......)))(((....)))......................................))))))....))))).. (-12.04 = -14.28 +   2.24)

alignment

secondary structure

dotplot

Window 8

Location	2,820,560 – 2,820,674
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.22
Mean single sequence MFE	-27.32
Consensus MFE	-8.40
Energy contribution	-9.60
Covariance contribution	1.20
Combinations/Pair	1.16
Mean z-score	-2.52
Structure conservation index	0.31
SVM decision value	0.86
SVM RNA-class probability	0.868289
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2820560 114 + 23771897
CGAAUUAAGAGCAACAAUUGUUGCCCUUUUUGGG--UGACAACAAAAGCAAUUCGAAGGAGUCUCUCCUCUGGUUUGUUUAUUUGUUUUUCGAUCGAGACCCAAA--G-UUGUUCUUUU-
......(((((((((..((((..(((.....)))--..))))...((((((..((.(((((...))))).))..)))))).((((..((((....))))..))))--)-))))))))..- ( -38.70)
>DroSec_CAF1 65511 98 + 1
CGAAUUAAGAGCAACAAUUGUUGCCCUUUUUGGG--UGACAACAAAAGCAAUUCGAA-----------------UUGUUUGUUUGCUCUUCGAUCGAGACCCAAA--G-UUGUUCUUUUG
......(((((((((..((((..(((.....)))--..))))..........(((((-----------------..((......))..)))))............--)-))))))))... ( -28.60)
>DroSim_CAF1 57011 98 + 1
CGAAUUAAGAGCAACAAUUGUUGCCCUUUUUGGG--UGACAACAAAAGCAAUUCGAA-----------------UUGUUUGUUUGCUCUUCGAUCGAGACCCAAA--G-UUGUUCUUUUG
......(((((((((..((((..(((.....)))--..))))..........(((((-----------------..((......))..)))))............--)-))))))))... ( -28.60)
>DroEre_CAF1 68217 105 + 1
CAAAUUAAGAGUAACAAUUGCUGCCU-UUUUGGG--UGACAACAAAAGCAAUUCAAAGGAGUCGC---------UCGUUUGUUGGUUUUUCGAUCAAGACCCAAA--UUUUGUUCUUUU-
......(((((.(((((.........-.((((((--(..((((((((((.((((....)))).))---------)..)))))))......(......))))))))--..))))))))))- ( -22.00)
>DroYak_CAF1 68111 106 + 1
CAAAUUAAGAGCAACAAUUGUUGCCU-UUUUGGGGAUGACAACAAAAGCAAUGCAAGGAAGUCGC---------UCGUUUGUUUGCUUUUCGAUCAAGACCCAAA--G-UUGUUCUUUU-
......(((((((((...........-.((((((..(((....((((((((.(((((((......---------)).)))))))))))))...)))...))))))--)-))))))))..- ( -26.80)
>DroAna_CAF1 54428 90 + 1
CAAUAAAAAAGCAAUAACUUUUGCCUUUUUUGGU--UGACAAAUCGAGGAAUGCAAAAGAGACCG-------------------------AAAUC-AGACCCAAAAUG-UUGUCCUUAU-
..........((((((.(((((((.(((((((((--(....)))))))))).))))))).((...-------------------------...))-..........))-))))......- ( -19.20)
>consensus
CAAAUUAAGAGCAACAAUUGUUGCCCUUUUUGGG__UGACAACAAAAGCAAUUCAAAGGAGUC_C_________UUGUUUGUUUGCUUUUCGAUCGAGACCCAAA__G_UUGUUCUUUU_
..........(((((....)))))....((((((..(((.......(((((...............................)))))......)))...))))))............... ( -8.40 =  -9.60 +   1.20)

alignment

secondary structure

dotplot

Window 9

Location	2,820,560 – 2,820,674
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.22
Mean single sequence MFE	-25.63
Consensus MFE	-11.20
Energy contribution	-12.28
Covariance contribution	1.08
Combinations/Pair	1.17
Mean z-score	-2.64
Structure conservation index	0.44
SVM decision value	2.08
SVM RNA-class probability	0.987366
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2820560 114 - 23771897
-AAAAGAACAA-C--UUUGGGUCUCGAUCGAAAAACAAAUAAACAAACCAGAGGAGAGACUCCUUCGAAUUGCUUUUGUUGUCA--CCCAAAAAGGGCAACAAUUGUUGCUCUUAAUUCG
-....(((...-.--(((((((...(((.....((((((....(((..(..(((((...)))))..)..)))..))))))))))--))))))(((((((((....)))))))))..))). ( -30.80)
>DroSec_CAF1 65511 98 - 1
CAAAAGAACAA-C--UUUGGGUCUCGAUCGAAGAGCAAACAAACAA-----------------UUCGAAUUGCUUUUGUUGUCA--CCCAAAAAGGGCAACAAUUGUUGCUCUUAAUUCG
.....(((...-.--(((((((..((((..((((((((........-----------------......))))))))))))..)--))))))(((((((((....)))))))))..))). ( -29.84)
>DroSim_CAF1 57011 98 - 1
CAAAAGAACAA-C--UUUGGGUCUCGAUCGAAGAGCAAACAAACAA-----------------UUCGAAUUGCUUUUGUUGUCA--CCCAAAAAGGGCAACAAUUGUUGCUCUUAAUUCG
.....(((...-.--(((((((..((((..((((((((........-----------------......))))))))))))..)--))))))(((((((((....)))))))))..))). ( -29.84)
>DroEre_CAF1 68217 105 - 1
-AAAAGAACAAAA--UUUGGGUCUUGAUCGAAAAACCAACAAACGA---------GCGACUCCUUUGAAUUGCUUUUGUUGUCA--CCCAAAA-AGGCAGCAAUUGUUACUCUUAAUUUG
-..((((......--....(((.((......)).)))(((((..((---------((((.((....)).))))))((((((((.--.......-.)))))))))))))..))))...... ( -19.60)
>DroYak_CAF1 68111 106 - 1
-AAAAGAACAA-C--UUUGGGUCUUGAUCGAAAAGCAAACAAACGA---------GCGACUUCCUUGCAUUGCUUUUGUUGUCAUCCCCAAAA-AGGCAACAAUUGUUGCUCUUAAUUUG
-..........-.--((((((...((((..((((((((.....(((---------(.(....)))))..))))))))...))))..))))))(-(((((((....))))).)))...... ( -26.20)
>DroAna_CAF1 54428 90 - 1
-AUAAGGACAA-CAUUUUGGGUCU-GAUUU-------------------------CGGUCUCUUUUGCAUUCCUCGAUUUGUCA--ACCAAAAAAGGCAAAAGUUAUUGCUUUUUUAUUG
-...((((...-((....(((.((-(....-------------------------))).)))...))...))))..........--....((((((((((......)))))))))).... ( -17.50)
>consensus
_AAAAGAACAA_C__UUUGGGUCUCGAUCGAAAAGCAAACAAACAA_________G_GACUCCUUCGAAUUGCUUUUGUUGUCA__CCCAAAAAAGGCAACAAUUGUUGCUCUUAAUUCG
...............((((((....((((((((........................................)))))..)))...))))))(((((((((....)))))))))...... (-11.20 = -12.28 +   1.08)

alignment

secondary structure

dotplot

Window 0

Location	2,820,598 – 2,820,695
Length	97
Sequences	3
Columns	98
Reading direction	reverse
Mean pairwise identity	83.10
Mean single sequence MFE	-19.77
Consensus MFE	-12.90
Energy contribution	-13.01
Covariance contribution	0.11
Combinations/Pair	1.05
Mean z-score	-1.94
Structure conservation index	0.65
SVM decision value	0.09
SVM RNA-class probability	0.580872
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2820598 97 - 23771897
AAUCGAAAACAAAGGCAGGCCAAAAGAACAA-CUUUGGGUCUCGAUCGAAAAACAAAUAAACAAACCAGAGGAGAGACUCCUUCGAAUUGCUUUUGUU
.......((((((((((((((.((((.....-)))).)))).........................(..(((((...)))))..)...)))))))))) ( -23.90)
>DroEre_CAF1 68254 89 - 1
AAUCGAAAACAAAGGCCAGCCAAAAGAACAAAAUUUGGGUCUUGAUCGAAAAACCAACAAACGA---------GCGACUCCUUUGAAUUGCUUUUGUU
..((((.....((((((.....(((........))).))))))..))))......(((((..((---------((((.((....)).))))))))))) ( -16.40)
>DroYak_CAF1 68150 88 - 1
AUUCGAAAACAAAGGCAAGCCAAAAGAACAA-CUUUGGGUCUUGAUCGAAAAGCAAACAAACGA---------GCGACUUCCUUGCAUUGCUUUUGUU
.......(((((((((((((..((((.....-))))(((..(((.(((.............)))---------.)))..)))..)).))))))))))) ( -19.02)
>consensus
AAUCGAAAACAAAGGCAAGCCAAAAGAACAA_CUUUGGGUCUUGAUCGAAAAACAAACAAACGA_________GCGACUCCUUUGAAUUGCUUUUGUU
.......(((((((((((.(((((.........)))))(((..................................))).........))))))))))) (-12.90 = -13.01 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:00 2006