Locus 2979

Sequence ID	2L_DroMel_CAF1
Location	8,520,259 – 8,520,539
Length	280
Max. P	0.999943

overview

Window 8

Location	8,520,259 – 8,520,379
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.75
Mean single sequence MFE	-42.88
Consensus MFE	-39.56
Energy contribution	-39.76
Covariance contribution	0.20
Combinations/Pair	1.09
Mean z-score	-2.57
Structure conservation index	0.92
SVM decision value	4.36
SVM RNA-class probability	0.999881
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8520259 120 + 22407834
GGGCUUUGAACAUUAAUACGCGUGCAACGCGCCUGAUGAUUCAGCUGGCCAAGGAGAUGAAAGGCUUGGAAGCCUUCGUGCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACA
((((.((((((((((...((((.....))))..))))).)))))..((((..(((((((.((((((....))))))......)))))))..))))..........))))........... ( -43.10)
>DroSec_CAF1 29503 120 + 1
GGGCUUUGAAUAUCAAUACGCGUGCAACGCGCCUUUUGAUUCAGCUGGCCAAGGAGAUGAAAGGCUUGAAAGCCUUCGUCCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACA
((((.((((..(((((...(((((...)))))...)))))))))..((((..(((((((.((((((....))))))......)))))))..))))..........))))........... ( -41.50)
>DroSim_CAF1 28837 120 + 1
GGGCUUUGAAUAUCAAUACGCGUGCAACGCGCCUAUUGAUUCAGCUUGCCAAGGAGAUGAAAGGCUUGAAAGCCUUCGUCCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCAUA
((((.((((..(((((((.(((((...))))).)))))))))))...(((..(((((((.((((((....))))))......)))))))..)))...........))))........... ( -41.10)
>DroEre_CAF1 29121 120 + 1
GGGCUGUUAACAUUAAUACGCGGGCCACGCGCCUAUUGAUUCAGCUGGCCAAGGAGAUGAAGGGCUUAGAAGCCUUCGUGCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACA
((((((.....(((((((((((.....))))..))))))).)))).((((..(((((((.((((((....))))))......)))))))..))))....))..((((.....)))).... ( -42.60)
>DroYak_CAF1 30000 120 + 1
GGGCGCUCAACAUCAAUACGCGUGGCACGCGCCUAUUGAUUCAGCUGGCCAAGGAGAUGAAGGGCUUAGAAGCCUUCGUGCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACA
(((((((....(((((((.(((((...))))).)))))))..))).((((..(((((((.((((((....))))))......)))))))..))))..........))))........... ( -46.10)
>consensus
GGGCUUUGAACAUCAAUACGCGUGCAACGCGCCUAUUGAUUCAGCUGGCCAAGGAGAUGAAAGGCUUGGAAGCCUUCGUGCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACA
((((.......(((((((.(((((...))))).)))))))..((..((((..(((((((.((((((....))))))......)))))))..))))..))......))))........... (-39.56 = -39.76 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	8,520,259 – 8,520,379
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.75
Mean single sequence MFE	-46.78
Consensus MFE	-42.16
Energy contribution	-42.92
Covariance contribution	0.76
Combinations/Pair	1.03
Mean z-score	-1.81
Structure conservation index	0.90
SVM decision value	2.22
SVM RNA-class probability	0.990655
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8520259 120 - 22407834
UGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGCACGAAGGCUUCCAAGCCUUUCAUCUCCUUGGCCAGCUGAAUCAUCAGGCGCGUUGCACGCGUAUUAAUGUUCAAAGCCC
...........((((..(((((.(.(((((.(((((((.....(((((((....)))))))))))))).)))))..((((....))))(((((.....))))).....).))))).)))) ( -48.70)
>DroSec_CAF1 29503 120 - 1
UGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGGACGAAGGCUUUCAAGCCUUUCAUCUCCUUGGCCAGCUGAAUCAAAAGGCGCGUUGCACGCGUAUUGAUAUUCAAAGCCC
...........((((..(((((...(((((.(((((((.....(((((((....)))))))))))))).)))))......(((((...(((((.....))))).))))).))))).)))) ( -49.30)
>DroSim_CAF1 28837 120 - 1
UAUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGGACGAAGGCUUUCAAGCCUUUCAUCUCCUUGGCAAGCUGAAUCAAUAGGCGCGUUGCACGCGUAUUGAUAUUCAAAGCCC
...........((((..(((((....((((.(((((((.....(((((((....)))))))))))))).)))).......(((((((.(((.......))).))))))).))))).)))) ( -46.20)
>DroEre_CAF1 29121 120 - 1
UGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGCACGAAGGCUUCUAAGCCCUUCAUCUCCUUGGCCAGCUGAAUCAAUAGGCGCGUGGCCCGCGUAUUAAUGUUAACAGCCC
...(((((.....))))).((....(((((.(((((((.....((.((((....)))).))))))))).))))).((((...((.((((((((.....))))).))).))....)))))) ( -42.50)
>DroYak_CAF1 30000 120 - 1
UGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGCACGAAGGCUUCUAAGCCCUUCAUCUCCUUGGCCAGCUGAAUCAAUAGGCGCGUGCCACGCGUAUUGAUGUUGAGCGCCC
...........((((..........(((((.(((((((.....((.((((....)))).))))))))).))))).(((..(((((((.(((.......))).)))))))....))))))) ( -47.20)
>consensus
UGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGCACGAAGGCUUCCAAGCCUUUCAUCUCCUUGGCCAGCUGAAUCAAUAGGCGCGUUGCACGCGUAUUGAUGUUCAAAGCCC
...........((((..........(((((.(((((((.....(((((((....)))))))))))))).)))))...(((((......(((((.....)))))......)))))..)))) (-42.16 = -42.92 +   0.76)

alignment

secondary structure

dotplot

Window 0

Location	8,520,299 – 8,520,419
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.33
Mean single sequence MFE	-44.00
Consensus MFE	-42.78
Energy contribution	-42.94
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-2.14
Structure conservation index	0.97
SVM decision value	3.75
SVM RNA-class probability	0.999583
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8520299 120 + 22407834
UCAGCUGGCCAAGGAGAUGAAAGGCUUGGAAGCCUUCGUGCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUAACGUGCCCGGC
..((..((((..(((((((.((((((....))))))......)))))))..))))..))......((.(((((........))))).))........((((.((((.....)))))))). ( -45.20)
>DroSec_CAF1 29543 120 + 1
UCAGCUGGCCAAGGAGAUGAAAGGCUUGAAAGCCUUCGUCCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGAC
..((..((((..(((((((.((((((....))))))......)))))))..))))..))......((.(((((........))))).)).........(((.((((.....))))))).. ( -42.80)
>DroSim_CAF1 28877 120 + 1
UCAGCUUGCCAAGGAGAUGAAAGGCUUGAAAGCCUUCGUCCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCAUAUUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGGC
...(((.(((..(((((((.((((((....))))))......)))))))..)))((((.....((((.....))))......)))))))........((((.((((.....)))))))). ( -42.20)
>DroEre_CAF1 29161 120 + 1
UCAGCUGGCCAAGGAGAUGAAGGGCUUAGAAGCCUUCGUGCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUGUCGUGCCCGGC
..((..((((..(((((((.((((((....))))))......)))))))..))))..))......((.(((((........))))).))........((((.((((.....)))))))). ( -44.90)
>DroYak_CAF1 30040 120 + 1
UCAGCUGGCCAAGGAGAUGAAGGGCUUAGAAGCCUUCGUGCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGGC
..((..((((..(((((((.((((((....))))))......)))))))..))))..))......((.(((((........))))).))........((((.((((.....)))))))). ( -44.90)
>consensus
UCAGCUGGCCAAGGAGAUGAAAGGCUUGGAAGCCUUCGUGCACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGGC
..((..((((..(((((((.((((((....))))))......)))))))..))))..))......((.(((((........))))).))........((((.((((.....)))))))). (-42.78 = -42.94 +   0.16)

alignment

secondary structure

dotplot

Window 1

Location	8,520,299 – 8,520,419
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-52.10
Consensus MFE	-51.50
Energy contribution	-51.94
Covariance contribution	0.44
Combinations/Pair	1.02
Mean z-score	-2.52
Structure conservation index	0.99
SVM decision value	4.72
SVM RNA-class probability	0.999943
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8520299 120 - 22407834
GCCGGGCACGUUAGGUGCUCCGGAUAGAAACGCUCCUCAAUGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGCACGAAGGCUUCCAAGCCUUUCAUCUCCUUGGCCAGCUGA
.((((((((.....)))).)))).....((((((((((..........))))))).)))..((..(((((.(((((((.....(((((((....)))))))))))))).)))))..)).. ( -54.80)
>DroSec_CAF1 29543 120 - 1
GUCGGGCACGAUAGGUGCUCCGGAUAGAAACGCUCCUCAAUGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGGACGAAGGCUUUCAAGCCUUUCAUCUCCUUGGCCAGCUGA
.((((((((.....)))).)))).....((((((((((..........))))))).)))..((..(((((.(((((((.....(((((((....)))))))))))))).)))))..)).. ( -52.20)
>DroSim_CAF1 28877 120 - 1
GCCGGGCACGAUAGGUGCUCCGGAUAGAAACGCUCCUCAAUAUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGGACGAAGGCUUUCAAGCCUUUCAUCUCCUUGGCAAGCUGA
.((((((((.....)))).)))).....((((((((((..........))))))).)))..((...((((.(((((((.....(((((((....)))))))))))))).))))...)).. ( -52.10)
>DroEre_CAF1 29161 120 - 1
GCCGGGCACGACAGGUGCUCCGGAUAGAAACGCUCCUCAAUGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGCACGAAGGCUUCUAAGCCCUUCAUCUCCUUGGCCAGCUGA
.((((((((.....)))).)))).....((((((((((..........))))))).)))..((..(((((.(((((((.....((.((((....)))).))))))))).)))))..)).. ( -50.70)
>DroYak_CAF1 30040 120 - 1
GCCGGGCACGAUAGGUGCUCCGGAUAGAAACGCUCCUCAAUGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGCACGAAGGCUUCUAAGCCCUUCAUCUCCUUGGCCAGCUGA
.((((((((.....)))).)))).....((((((((((..........))))))).)))..((..(((((.(((((((.....((.((((....)))).))))))))).)))))..)).. ( -50.70)
>consensus
GCCGGGCACGAUAGGUGCUCCGGAUAGAAACGCUCCUCAAUGUGCUGCGAGGGGCAGUUGGAGAAGGCCGUGGAGAUGUGCACGAAGGCUUCCAAGCCUUUCAUCUCCUUGGCCAGCUGA
.((((((((.....)))).)))).(((.((((((((((..........))))))).)))......(((((.(((((((.....(((((((....)))))))))))))).)))))..))). (-51.50 = -51.94 +   0.44)

alignment

secondary structure

dotplot

Window 2

Location	8,520,339 – 8,520,459
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.00
Mean single sequence MFE	-41.98
Consensus MFE	-38.96
Energy contribution	-39.76
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.37
Structure conservation index	0.93
SVM decision value	3.52
SVM RNA-class probability	0.999328
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8520339 120 + 22407834
CACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUAACGUGCCCGGCGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCCCAGAU
...((((....((((..........((.(((((........))))).))........((((.((((.....)))))))).))))..((.(((((((.((.....)).))))))))))))) ( -43.00)
>DroSec_CAF1 29583 120 + 1
CACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGACGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCCCAGAU
...((((....((((..........((.(((((........))))).)).........(((.((((.....)))))))..))))..((.(((((((.((.....)).))))))))))))) ( -40.60)
>DroSim_CAF1 28917 120 + 1
CACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCAUAUUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGGCGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCCCAGAU
...((((....((((..........((.(((((........))))).))........((((.((((.....)))))))).))))..((.(((((((.((.....)).))))))))))))) ( -43.00)
>DroEre_CAF1 29201 120 + 1
CACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUGUCGUGCCCGGCGGCCAAGGUGCUCGAACUUAACGACACUUUGAGCCCAGAC
....(((....((((..........((.(((((........))))).))........((((.((((.....)))))))).))))..((.(((((((...........)))))))))))). ( -39.40)
>DroYak_CAF1 30080 120 + 1
CACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGGCGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCGCAGAU
...((((....((((..........((.(((((........))))).))........((((.((((.....)))))))).))))...(((((((((.((.....)).))))))))))))) ( -43.90)
>consensus
CACAUCUCCACGGCCUUCUCCAACUGCCCCUCGCAGCACAUUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGGCGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCCCAGAU
...((((....((((..........((.(((((........))))).))........((((.((((.....)))))))).))))..((.(((((((.((.....)).))))))))))))) (-38.96 = -39.76 +   0.80)

alignment

secondary structure

dotplot

Window 3

Location	8,520,379 – 8,520,499
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.25
Mean single sequence MFE	-44.69
Consensus MFE	-39.58
Energy contribution	-39.30
Covariance contribution	-0.28
Combinations/Pair	1.10
Mean z-score	-1.49
Structure conservation index	0.89
SVM decision value	1.09
SVM RNA-class probability	0.912921
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8520379 120 + 22407834
UUGAGGAGCGUUUCUAUCCGGAGCACCUAACGUGCCCGGCGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCCCAGAUUUGUUGGACAAGAUGGCUCCGGCUCUUAUGGGAAAGUUUC
....(((((.((((((((((((((........((.((((((((((((((.((((.......)))))))))).))).......))))).)).....))))))).....))))))).))))) ( -42.13)
>DroSec_CAF1 29623 120 + 1
UUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGACGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCCCAGAUCUGAUGGACAAAAUGGCUCCGGCUCUGAUGGGAAAGUUUC
....(((((.(((((((((((.((((.....)))))))..((((..((.(((((((.((.....)).))))))))).........((((......).)))))))..)))))))).))))) ( -41.80)
>DroSim_CAF1 28957 120 + 1
UUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGGCGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCCCAGAUCUGAUGGACAAAAUGGCUCCGGCUCUGAUGGGAAAGUUUC
....(((((.((((((((.(((((((.....))))((((.(((((.((.(((((((.((.....)).)))))))))...((.....)).....))))))))).))))))))))).))))) ( -43.20)
>DroEre_CAF1 29241 120 + 1
UUGAGGAGCGUUUCUAUCCGGAGCACCUGUCGUGCCCGGCGGCCAAGGUGCUCGAACUUAACGACACUUUGAGCCCAGACCUGGUGGACAACAUGGCUCCGGCUCUGAUGGGAAAGUUCC
....(((((.((((((((((((((...((((.((((.(((((((((((((.(((.......)))))))))).)))..).)).)))))))).....))))))).....))))))).))))) ( -50.10)
>DroYak_CAF1 30120 120 + 1
UUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGGCGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCGCAGAUCUGGUGGACAACAUGGCUCCGGCUCUAAUGGGCAAGUUCC
....(((((........((((.((((.....))))))))(.((((..(((((((((.((.....)).))))))))).....)))).)........))))).((((....))))....... ( -46.20)
>consensus
UUGAGGAGCGUUUCUAUCCGGAGCACCUAUCGUGCCCGGCGGCCAAGGUGCUCGAAUUCAACGAGACUUUGAGCCCAGAUCUGAUGGACAAAAUGGCUCCGGCUCUGAUGGGAAAGUUUC
....(((((.((((((((((((((..((((((.(((....))))..((.(((((((.((.....)).)))))))))......))))).(.....)))))))).....))))))).))))) (-39.58 = -39.30 +  -0.28)

alignment

secondary structure

dotplot

Window 4

Location	8,520,379 – 8,520,499
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.25
Mean single sequence MFE	-40.76
Consensus MFE	-35.62
Energy contribution	-35.50
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.30
Structure conservation index	0.87
SVM decision value	0.35
SVM RNA-class probability	0.700923
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8520379 120 - 22407834
GAAACUUUCCCAUAAGAGCCGGAGCCAUCUUGUCCAACAAAUCUGGGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCCGCCGGGCACGUUAGGUGCUCCGGAUAGAAACGCUCCUCAA
....................(((((..(((.((((..(((....((((.....))))..))).....((((((((..(((....))).....)))))))).)))))))...))))).... ( -38.20)
>DroSec_CAF1 29623 120 - 1
GAAACUUUCCCAUCAGAGCCGGAGCCAUUUUGUCCAUCAGAUCUGGGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCCGUCGGGCACGAUAGGUGCUCCGGAUAGAAACGCUCCUCAA
....................(((((..((((((((.((((....((((.....))))..))))....((((((((..(((....))).....)))))))).))))))))..))))).... ( -41.60)
>DroSim_CAF1 28957 120 - 1
GAAACUUUCCCAUCAGAGCCGGAGCCAUUUUGUCCAUCAGAUCUGGGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCCGCCGGGCACGAUAGGUGCUCCGGAUAGAAACGCUCCUCAA
....................(((((..((((((((.((((....((((.....))))..))))....((((((((..(((....))).....)))))))).))))))))..))))).... ( -41.60)
>DroEre_CAF1 29241 120 - 1
GGAACUUUCCCAUCAGAGCCGGAGCCAUGUUGUCCACCAGGUCUGGGCUCAAAGUGUCGUUAAGUUCGAGCACCUUGGCCGCCGGGCACGACAGGUGCUCCGGAUAGAAACGCUCCUCAA
(((.(((((.........((((((((.((((((((....((((.((((((.((.(.......).)).)))).))..))))....)).)))))).).)))))))...)))).).))).... ( -42.50)
>DroYak_CAF1 30120 120 - 1
GGAACUUGCCCAUUAGAGCCGGAGCCAUGUUGUCCACCAGAUCUGCGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCCGCCGGGCACGAUAGGUGCUCCGGAUAGAAACGCUCCUCAA
((..((........))..))(((((....((((((.........(((..(((.((((((.......)))).)).)))..))).((((((.....)))).))))))))....))))).... ( -39.90)
>consensus
GAAACUUUCCCAUCAGAGCCGGAGCCAUGUUGUCCACCAGAUCUGGGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCCGCCGGGCACGAUAGGUGCUCCGGAUAGAAACGCUCCUCAA
...............((((..(((((...(((.....))).....)))))........(((..((((((((((((..(((....))).....))))))).)))))...)))))))..... (-35.62 = -35.50 +  -0.12)

alignment

secondary structure

dotplot

Window 5

Location	8,520,419 – 8,520,539
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.75
Mean single sequence MFE	-41.44
Consensus MFE	-35.88
Energy contribution	-36.56
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-1.49
Structure conservation index	0.87
SVM decision value	0.87
SVM RNA-class probability	0.870796
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8520419 120 - 22407834
ACCUGCUCGGCCAGUGCCUUGGUAUAGGUAUAGGUGUUCGGAAACUUUCCCAUAAGAGCCGGAGCCAUCUUGUCCAACAAAUCUGGGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCC
........(((((((((((......))))))(((((((((((.....)))((...(((.(.(((((...(((.....))).....)))))...).)))..)).....))))))))))))) ( -41.90)
>DroSec_CAF1 29663 120 - 1
ACCUGCUCGGCCAGUGCCUUGGUAUAGGUAUAGGUGUUCGGAAACUUUCCCAUCAGAGCCGGAGCCAUUUUGUCCAUCAGAUCUGGGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCC
........(((((((((((......))))))(((((((((((.....)))((...(((.(.(((((..((((.....))))....)))))...).)))..)).....))))))))))))) ( -43.50)
>DroSim_CAF1 28997 120 - 1
ACCUGCUCGGCCAGUGCCUUGGUAUAGGUAUAGGUGUUCGGAAACUUUCCCAUCAGAGCCGGAGCCAUUUUGUCCAUCAGAUCUGGGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCC
........(((((((((((......))))))(((((((((((.....)))((...(((.(.(((((..((((.....))))....)))))...).)))..)).....))))))))))))) ( -43.50)
>DroEre_CAF1 29281 120 - 1
ACCUGCUCGGCCAAUGCCUUGGUAUAUGUAUAGGUGUUCGGGAACUUUCCCAUCAGAGCCGGAGCCAUGUUGUCCACCAGGUCUGGGCUCAAAGUGUCGUUAAGUUCGAGCACCUUGGCC
........(((((((((....))))......((((((((((((....))))....(((((.(..((.((........))))..).))))).................))))))))))))) ( -43.20)
>DroYak_CAF1 30160 120 - 1
ACCUGCUCAGCCAGUGCCUUGGUGUAUGUAUAGGUGUUCGGGAACUUGCCCAUUAGAGCCGGAGCCAUGUUGUCCACCAGAUCUGCGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCC
.........(((((..(....)..)......(((((((((((......)))....(((.(.((((((.(((........))).)).))))...).))).........)))))))))))). ( -35.10)
>consensus
ACCUGCUCGGCCAGUGCCUUGGUAUAGGUAUAGGUGUUCGGAAACUUUCCCAUCAGAGCCGGAGCCAUGUUGUCCACCAGAUCUGGGCUCAAAGUCUCGUUGAAUUCGAGCACCUUGGCC
........(((((((((((......))))))((((((((((........))....(((.(.(((((...(((.....))).....)))))...).))).........))))))))))))) (-35.88 = -36.56 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:12 2006