Locus 1461

Sequence ID	3R_DroMel_CAF1
Location	4,203,600 – 4,203,759
Length	159
Max. P	0.999183

overview

Window 9

Location	4,203,600 – 4,203,700
Length	100
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	78.08
Mean single sequence MFE	-24.94
Consensus MFE	-13.49
Energy contribution	-13.22
Covariance contribution	-0.28
Combinations/Pair	1.13
Mean z-score	-2.10
Structure conservation index	0.54
SVM decision value	0.77
SVM RNA-class probability	0.845953
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4203600 100 + 27905053
GCGCGCAGAGCAUUAAAAAAUUCAUAACCAAGGGGGGAGGGGGGUGA--AGGUGGUAAGAAUGAUGUCGGG-GAAAACUGAGAGCUCUGUGCUCUCAUGAAUA
..(((((((((.(((..(..(((((..((..........))..))))--)..)..)))......(.((((.-.....)))).))))))))))........... ( -30.00)
>DroSec_CAF1 14946 91 + 1
GCGCGCAGAGCAUUAAAAAAUUCAUAACGAUGGGGGGAGUGGGGAGA--G--------GAUUGCUGACG-G-GAAAACUGAGAGCUCUGCGCUCUCAUGAAUA
..(((((((((.........(((((....)))))(..((..(.....--.--------..)..))..).-.-...........)))))))))........... ( -24.40)
>DroSim_CAF1 15703 84 + 1
GCGCGCAGAGCAUUAAAAAAUUCAUAACGAGGGGGG-------GACA--G--------GAGUGCUGACG-G-GAGAACUGAGAGCUCUGCGCUCUCAUGAAUA
..(((((((((..........(((..((.....(..-------..).--.--------..))..)))((-(-.....)))...)))))))))........... ( -25.60)
>DroEre_CAF1 15663 82 + 1
CAGCACAGAGCAUUAAAAAAUUCAUAACGAUGGGG---------AGA--G--------GAGUGCUGACG-G-GAAAACUGAGAGCACUGCGCUCUCAUGAAUA
..((.....))........((((((.......(((---------((.--(--------.((((((..((-(-.....)))..)))))).).))))))))))). ( -24.11)
>DroYak_CAF1 15303 83 + 1
CUGCGCAGAGCAUUAAAAAAUUCAUAACGAUGGGG---------AGA--G--------GAGUGCUGACG-GGGAAAACUGAGAGCACUGCGCUUUCAUGAAUA
.(((.....))).......((((((.......(..---------((.--(--------.((((((..((-(......)))..)))))).).))..))))))). ( -22.91)
>DroAna_CAF1 17158 88 + 1
GCGCACUGAGCUUUAAAAAAUUCAUAACGUUUGGGCGG-----GAAAAUG--------GGGCAGUGGCG-G-GAUAACUGGGAGCGCAGAGCUCUCAUGAAUA
((.((((..((((((.....(((....(((....))).-----)))..))--------)))))))))).-.-......(((((((.....)))))))...... ( -22.60)
>consensus
GCGCGCAGAGCAUUAAAAAAUUCAUAACGAUGGGGG_______GAGA__G________GAGUGCUGACG_G_GAAAACUGAGAGCUCUGCGCUCUCAUGAAUA
..((.....))........((((((..(.....).............................................((((((.....)))))))))))). (-13.49 = -13.22 +  -0.28)

alignment

secondary structure

dotplot

Window 0

Location	4,203,637 – 4,203,727
Length	90
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	82.97
Mean single sequence MFE	-17.84
Consensus MFE	-14.37
Energy contribution	-15.01
Covariance contribution	0.64
Combinations/Pair	1.07
Mean z-score	-1.66
Structure conservation index	0.81
SVM decision value	0.35
SVM RNA-class probability	0.701708
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4203637 90 + 27905053
AGGGGGGUGAAGGUGGUAAGAAUGAUGUCGGG-GAAAACUGAGAGCUCUGUGCUCUCAUGAAUAAAUCAGAACUCAAA-AAAAUAUUGGGGG
....((((...(((.......((((..((((.-.....))))((((.....))))))))......)))...))))...-............. ( -16.62)
>DroSec_CAF1 14983 81 + 1
AGUGGGGAGAG--------GAUUGCUGACG-G-GAAAACUGAGAGCUCUGCGCUCUCAUGAAUAAAUCAGAACUCAAA-AAAAUAUGGGGGG
........(((--------.....((((..-.-......(((((((.....)))))))........))))..)))...-............. ( -16.83)
>DroSim_CAF1 15739 75 + 1
------GACAG--------GAGUGCUGACG-G-GAGAACUGAGAGCUCUGCGCUCUCAUGAAUAAAUCAGAACUCAAA-AAAAUAUGGGGGG
------.....--------((((.(((((.-.-..)...(((((((.....)))))))........)))).))))...-............. ( -19.80)
>DroEre_CAF1 15698 73 + 1
-------AGAG--------GAGUGCUGACG-G-GAAAACUGAGAGCACUGCGCUCUCAUGAAUAAAUCAGAACUCAAA-AAAAUAUGG-GGG
-------....--------((((.((((..-.-......(((((((.....)))))))........)))).))))...-.........-... ( -19.33)
>DroYak_CAF1 15338 75 + 1
-------AGAG--------GAGUGCUGACG-GGGAAAACUGAGAGCACUGCGCUUUCAUGAAUAAAUCAGAACUCAAAAAAAAUAUGG-GGG
-------....--------((((.((((.(-(......))((((((.....)))))).........)))).)))).............-... ( -16.60)
>consensus
______GAGAG________GAGUGCUGACG_G_GAAAACUGAGAGCUCUGCGCUCUCAUGAAUAAAUCAGAACUCAAA_AAAAUAUGGGGGG
...................((((.((((...........(((((((.....)))))))........)))).))))................. (-14.37 = -15.01 +   0.64)

alignment

secondary structure

dotplot

Window 1

Location	4,203,637 – 4,203,727
Length	90
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	82.97
Mean single sequence MFE	-17.59
Consensus MFE	-15.29
Energy contribution	-15.97
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-3.35
Structure conservation index	0.87
SVM decision value	3.42
SVM RNA-class probability	0.999183
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4203637 90 - 27905053
CCCCCAAUAUUUU-UUUGAGUUCUGAUUUAUUCAUGAGAGCACAGAGCUCUCAGUUUUC-CCCGACAUCAUUCUUACCACCUUCACCCCCCU
.............-..((((...((((.......(((((((.....)))))))(((...-...)))))))..))))................ ( -14.30)
>DroSec_CAF1 14983 81 - 1
CCCCCCAUAUUUU-UUUGAGUUCUGAUUUAUUCAUGAGAGCGCAGAGCUCUCAGUUUUC-C-CGUCAGCAAUC--------CUCUCCCCACU
.............-...(((..(((((.......(((((((.....)))))))......-.-.))))).....--------)))........ ( -17.36)
>DroSim_CAF1 15739 75 - 1
CCCCCCAUAUUUU-UUUGAGUUCUGAUUUAUUCAUGAGAGCGCAGAGCUCUCAGUUCUC-C-CGUCAGCACUC--------CUGUC------
.............-...((((.(((((.......(((((((.....)))))))......-.-.))))).))))--------.....------ ( -21.76)
>DroEre_CAF1 15698 73 - 1
CCC-CCAUAUUUU-UUUGAGUUCUGAUUUAUUCAUGAGAGCGCAGUGCUCUCAGUUUUC-C-CGUCAGCACUC--------CUCU-------
...-.........-...((((.(((((.......(((((((.....)))))))......-.-.))))).))))--------....------- ( -20.66)
>DroYak_CAF1 15338 75 - 1
CCC-CCAUAUUUUUUUUGAGUUCUGAUUUAUUCAUGAAAGCGCAGUGCUCUCAGUUUUCCC-CGUCAGCACUC--------CUCU-------
...-.............((((.(((((.......(((.(((.....))).)))........-.))))).))))--------....------- ( -13.89)
>consensus
CCCCCCAUAUUUU_UUUGAGUUCUGAUUUAUUCAUGAGAGCGCAGAGCUCUCAGUUUUC_C_CGUCAGCACUC________CUCUC______
.................((((.(((((.......(((((((.....)))))))..........))))).))))................... (-15.29 = -15.97 +   0.68)

alignment

secondary structure

dotplot

Window 2

Location	4,203,668 – 4,203,759
Length	91
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	90.16
Mean single sequence MFE	-20.17
Consensus MFE	-17.19
Energy contribution	-17.52
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.85
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4203668 91 - 27905053
---GGAUGGAUAUGGAACAAUAAAACAUGUUU-UUCCCCCCAAUAUUUU-UUUGAGUUCUGAUUUAUUCAUGAGAGCACAGAGCUCUCAGUUUUC-C
---((((((((.((((((...((((.(((((.-........))))).))-))...)))))))))))))).(((((((.....)))))))......-. ( -22.40)
>DroSec_CAF1 15005 91 - 1
---GGAUGGAUAUGGAACAAUAAAACAUGUUU-UUCCCCCCCAUAUUUU-UUUGAGUUCUGAUUUAUUCAUGAGAGCGCAGAGCUCUCAGUUUUC-C
---(((..((((((...........)))))).-.)))............-..(((((........)))))(((((((.....)))))))......-. ( -22.20)
>DroSim_CAF1 15755 92 - 1
---GGAUGGAUAUGGAACAAUAAAACAUGUUUUUUCCCCCCCAUAUUUU-UUUGAGUUCUGAUUUAUUCAUGAGAGCGCAGAGCUCUCAGUUCUC-C
---((..(((...((((((........)))))).)))..))........-...(((..((((.....)))(((((((.....))))))))..)))-. ( -22.20)
>DroEre_CAF1 15713 90 - 1
---GGAUGGAUAUGGAACAAUAAAACAUGUUU-UUCCCC-CCAUAUUUU-UUUGAGUUCUGAUUUAUUCAUGAGAGCGCAGUGCUCUCAGUUUUC-C
---(((..((((((...........)))))).-.)))..-.........-..(((((........)))))(((((((.....)))))))......-. ( -21.10)
>DroYak_CAF1 15353 92 - 1
---GGAUGGAUAUGGAACAAUAAAACAUGUUU-UUCCCC-CCAUAUUUUUUUUGAGUUCUGAUUUAUUCAUGAAAGCGCAGUGCUCUCAGUUUUCCC
---(((..((((((...........)))))).-.)))..-.............((((.(((.(((.......)))...))).))))........... ( -15.10)
>DroAna_CAF1 17214 85 - 1
UACGGAUGGAUAUGGAACAAUAAAACAUGUUU-UUCG---------UUU-UUUCAGUUCUGAUUUAUUCAUGAGAGCUCUGCGCUCCCAGUUAUC-C
...((((((((.((((((...(((((......-...)---------)))-)....)))))))))))))).((.((((.....)))).))......-. ( -18.00)
>consensus
___GGAUGGAUAUGGAACAAUAAAACAUGUUU_UUCCCC_CCAUAUUUU_UUUGAGUUCUGAUUUAUUCAUGAGAGCGCAGAGCUCUCAGUUUUC_C
...((((((((.((((((.....................................)))))))))))))).(((((((.....)))))))........ (-17.19 = -17.52 +   0.33)

alignment

secondary structure

dotplot

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