Locus 1376

Sequence ID	2L_DroMel_CAF1
Location	3,666,340 – 3,666,574
Length	234
Max. P	0.971721

overview

Window 8

Location	3,666,340 – 3,666,434
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	87.30
Mean single sequence MFE	-18.16
Consensus MFE	-16.00
Energy contribution	-16.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.98
Structure conservation index	0.88
SVM decision value	1.68
SVM RNA-class probability	0.971721
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3666340 94 + 22407834
CUCGCUGAUUGACUUGUGUUUCCAUUUUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUCCGGAUGCUCGCGCGGGUAUUUUU
((((((((((((.(((.(((.(((.........)))..))).))).))))))).((((((.(((.......))).)).)))))))))....... ( -23.10)
>DroSec_CAF1 128774 91 + 1
CUCGCUGAUUGACUUGUGUUUCCAUUUUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUUAUUCCGGCUCCUCGUGCGU---UUUUU
..((((((((((.(((.(((.(((.........)))..))).))).))))))).((((.(((((.......)))))..))))))).---..... ( -18.80)
>DroEre_CAF1 131314 91 + 1
CUCGCUGAUUGACUUGUGUUUCCAUUUUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUCCUGCUCCUCGUGCU---AUUUUU
.(((((((((((.(((.(((.(((.........)))..))).))).)))))).)))))...............((.......)).---...... ( -16.70)
>DroYak_CAF1 138372 84 + 1
CUCGCUGAUUGACUUGUGUUUCCAUUUUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUCCUGCG-------UU---UUUUUU
.(((((((((((.(((.(((.(((.........)))..))).))).)))))).)))))(((..((....)))))..-------..---...... ( -16.20)
>DroAna_CAF1 143298 85 + 1
CUCGCUGAUUGACUUGUGUUUCCAUUUUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUUCUCCACCCC---------UUUCC
.(((((((((((.(((.(((.(((.........)))..))).))).)))))).)))))......................---------..... ( -16.00)
>consensus
CUCGCUGAUUGACUUGUGUUUCCAUUUUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUCCUGCUCCUCG_GCG____UUUUU
.(((((((((((.(((.(((.(((.........)))..))).))).)))))).))))).................................... (-16.00 = -16.00 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	3,666,340 – 3,666,434
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	87.30
Mean single sequence MFE	-16.52
Consensus MFE	-14.40
Energy contribution	-14.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.87
SVM decision value	1.42
SVM RNA-class probability	0.952021
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3666340 94 - 22407834
AAAAAUACCCGCGCGAGCAUCCGGAAUUAUCAACUGUCGCUUGAUUAAUUUGAAUUAACCAAAUUAAAAAUGGAAACACAAGUCAAUCAGCGAG
..........((....))..................(((((.((((.(((((((((.....)))).....((....))))))).))))))))). ( -18.90)
>DroSec_CAF1 128774 91 - 1
AAAAA---ACGCACGAGGAGCCGGAAUAAUCAACUGUCGCUUGAUUAAUUUGAAUUAACCAAAUUAAAAAUGGAAACACAAGUCAAUCAGCGAG
.....---.(((.((......))...............(((((.((((((((.......))))))))...((....)))))))......))).. ( -16.00)
>DroEre_CAF1 131314 91 - 1
AAAAAU---AGCACGAGGAGCAGGAAUUAUCAACUGUCGCUUGAUUAAUUUGAAUUAACCAAAUUAAAAAUGGAAACACAAGUCAAUCAGCGAG
......---....((..((((((..........)))).(((((.((((((((.......))))))))...((....)))))))...))..)).. ( -16.60)
>DroYak_CAF1 138372 84 - 1
AAAAAA---AA-------CGCAGGAAUUAUCAACUGUCGCUUGAUUAAUUUGAAUUAACCAAAUUAAAAAUGGAAACACAAGUCAAUCAGCGAG
......---..-------..(((..........)))(((((.((((.(((((((((.....)))).....((....))))))).))))))))). ( -15.30)
>DroAna_CAF1 143298 85 - 1
GGAAA---------GGGGUGGAGAAAUUAUCAACUGUCGCUUGAUUAAUUUGAAUUAACCAAAUUAAAAAUGGAAACACAAGUCAAUCAGCGAG
.....---------..(((.((.......)).))).(((((.((((.(((((((((.....)))).....((....))))))).))))))))). ( -15.80)
>consensus
AAAAA____AGC_CGAGGAGCAGGAAUUAUCAACUGUCGCUUGAUUAAUUUGAAUUAACCAAAUUAAAAAUGGAAACACAAGUCAAUCAGCGAG
....................................(((((.((((.(((((((((.....)))).....((....))))))).))))))))). (-14.40 = -14.40 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	3,666,366 – 3,666,467
Length	101
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	81.75
Mean single sequence MFE	-25.78
Consensus MFE	-14.16
Energy contribution	-15.28
Covariance contribution	1.12
Combinations/Pair	1.08
Mean z-score	-2.36
Structure conservation index	0.55
SVM decision value	0.73
SVM RNA-class probability	0.834622
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3666366 101 + 22407834
UUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUCCGGAUGCUCGCGCGGGUAUUUUU-----UUUUCGCUGGCGCAGCGAAGUGCAUUU--GUUGCA
.(((((((((.....)))))))))....(((((((.((........((((((((....))))))))..-----.((((((((...))))))))..)).))--))))). ( -30.20)
>DroSec_CAF1 128800 98 + 1
UUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUUAUUCCGGCUCCUCGUGCGU---UUUUU-----UUUUCGCUGGCGCAGCGAAGUGCAUUU--GUUGCA
.(((((((((.....)))))))))....((((((((((.......)))).....(((((.---.....-----.((((((((...))))))))))))).)--))))). ( -25.81)
>DroEre_CAF1 131340 98 + 1
UUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUCCUGCUCCUCGUGCU---AUUUUU-----UUUUUGCUGGCGCUGCGAAGUGCAUUU--GUUGCA
.(((((((((.....)))))))))....(((((((.((....((((.((.((....((.---......-----.....)).)).)).).)))...)).))--))))). ( -23.40)
>DroYak_CAF1 138398 96 + 1
UUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUCCUGCG-------UU---UUUUUUGCUCGUUUUCGCUGGCGCAGCGAAGUGCAUUU--GUUGCA
.(((((((((.....)))))))))....(((((((.((....((((((((-------((---......((........)).))))))).)))...)).))--))))). ( -28.50)
>DroAna_CAF1 143324 94 + 1
UUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUUCUCCACCCC---------UUUCC-----UGAAGCCUGGAGCUGCAAAAUGCAUUUGUGUUGCA
.(((((((((.....)))))))))....((((((...........(((((...(---------(((..-----.))))..))))).(((.....)))....)))))). ( -21.00)
>consensus
UUUAAUUUGGUUAAUUCAAAUUAAUCAAGCGACAGUUGAUAAUUCCUGCUCCUCG_GCG____UUUUU_____UUUUCGCUGGCGCAGCGAAGUGCAUUU__GUUGCA
.(((((((((.....)))))))))....(((((....((....)).............................((((((((...)))))))).........))))). (-14.16 = -15.28 +   1.12)

alignment

secondary structure

dotplot

Window 1

Location	3,666,467 – 3,666,574
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.90
Mean single sequence MFE	-28.18
Consensus MFE	-19.86
Energy contribution	-21.10
Covariance contribution	1.24
Combinations/Pair	1.04
Mean z-score	-2.04
Structure conservation index	0.70
SVM decision value	0.44
SVM RNA-class probability	0.736675
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3666467 107 - 22407834
AAACAACAAAGUGGGAAAUGCAAUGCGUCUGGACAACGGAAAGCCCAACAA-------CAUUGGAU------GCACAUGAAUAUGGAUGAGUCUGGACGCCAAUGCCAAUGCACUUUCCA
...........((((((.((((..(((((..(((........((((((...-------..))))..------)).(((........))).)))..))))).........)))).)))))) ( -28.10)
>DroSec_CAF1 128898 107 - 1
AAACAACAAAGUGGGAAAUGCAAUGCGUCUGGACAACGGAAAGCCCAACAA-------CAUUGGAU------GCACAUGAAUAUGGAUGAGUCUGGACGCCAAUGCCAAUGCACUUUCGA
.......((((((.(....(((..(((((..(((........((((((...-------..))))..------)).(((........))).)))..)))))...)))...).))))))... ( -27.90)
>DroEre_CAF1 131438 107 - 1
AAACAACAAAGUGGGAAAUGCACUGCGUCUGGACAACGGAAAGCCCAACAA-------CAUUGGAU------GCACAUGAAUAUGGAUGAGUCUGGACGCCAAUGCCAAUGCACUCUCCA
.........((((.(....(((..(((((..(((........((((((...-------..))))..------)).(((........))).)))..)))))...)))...).))))..... ( -26.10)
>DroYak_CAF1 138494 114 - 1
AAACAACAAAGUGGGAAAUGCAAUGCGUCUGGACAACGGAAAGCCCAACAACAUUCAACAUUGGAU------GCACAUGAAUAUGGAUGAGUCUGGACGCCAAUGCCAAUGCACUUUCCA
...........((((((.((((..(((((..(((...((.....)).....((((((....((...------...))......)))))).)))..))))).........)))).)))))) ( -30.70)
>DroAna_CAF1 143418 108 - 1
AAACAACAAAGUGGGAAGU-----GCGUCUGGACAUCAGCAACGACAACGA-------CAAUGCAGAAAUAAAUAUAUGAAUAUGUAUGAGUCUGGACUCCAAUGCCAAUGCACUUUCCA
...........((((((((-----(((((..(((.((((((.((....)).-------...)))........(((((....))))).))))))..)))....((....)))))))))))) ( -28.10)
>consensus
AAACAACAAAGUGGGAAAUGCAAUGCGUCUGGACAACGGAAAGCCCAACAA_______CAUUGGAU______GCACAUGAAUAUGGAUGAGUCUGGACGCCAAUGCCAAUGCACUUUCCA
.......((((((.(....(((..(((((..(((..........((((............))))...........(((........))).)))..)))))...)))...).))))))... (-19.86 = -21.10 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:02 2006