Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold109
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1855911
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.34
Warning! 69956 characters in sequence are not A, C, G, or T
File 4 of 13
Found at i:453573 original size:240 final size:240
Alignment explanation
Indices: 453137--453649 Score: 686
Period size: 240 Copynumber: 2.1 Consensus size: 240
453127 AAAAATTATG
* * * * * * *
453137 TTTAGGTTCGAATTAGGCTTGATCCAAAATATTTGGGGATGCAAGTGACTTATTATAATTAGAAA
1 TTTAGGTTCGAATTAAGCTTGATCTAAAAGATTTGGGAATACAAGTGACTTATTACAATTAAAAA
* * * * *
453202 TGTTTATTGATCGAGTTGAATCATATCATAATTTTAAAAATTTAAAAAATTTTTGTTTAGGTTCG
66 TATTTATTGATCGAGTTGAATCATAGCACAATTTTAAAAATTTAAAAAATTTCTGTTTAGGTTCA
* *
453267 AATTAGGCTTGATACAAAAGATTTGGAGACGTAAGTGATTTATTACACTTAAAAATGTTAATTGA
131 AATTAGGCTTGATACAAAAGATTTGGAGACGTAAGTGACTTATTACACTTAAAAATATTAATTGA
* * *
453332 TCGAGTTGAATTAGATTACAATTCTAAAAATTTTAAAAATTTCTA
196 TCAAGTTGAATCAGATCACAATTCTAAAAATTTTAAAAATTTCTA
* * * *
453377 TTTAGGTTTGAATTAAGCTTGATCTAATAGATTTGGGAATACAAGTGATTTATTACACTTAAAAA
1 TTTAGGTTCGAATTAAGCTTGATCTAAAAGATTTGGGAATACAAGTGACTTATTACAATTAAAAA
* *
453442 TATTTATTGATCGAGTTGAATTATAGCACAATTTTAAAAATTTTAAAAATTTCTGTTTAGGTTCA
66 TATTTATTGATCGAGTTGAATCATAGCACAATTTTAAAAATTTAAAAAATTTCTGTTTAGGTTCA
* * * * ** *
453507 AATTGGGCTTGATCCAAAAGATTT-GAGGATGTAAGTGACTTATTATACTTGGAAATATTTATTG
131 AATTAGGCTTGATACAAAAGATTTGGA-GACGTAAGTGACTTATTACACTTAAAAATATTAATTG
* * * * *
453571 ATCAAGTTGAATCAGATCATAATTTTAAAAATTTTAAGAATTTTTG
195 ATCAAGTTGAATCAGATCACAATTCTAAAAATTTTAAAAATTTCTA
*
453617 TTTAGGTTCGAATTAAACTTGATCTAAAAGATT
1 TTTAGGTTCGAATTAAGCTTGATCTAAAAGATT
453650 GAATTTTATG
Statistics
Matches: 234, Mismatches: 38, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
239 2 0.01
240 232 0.99
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.40
Consensus pattern (240 bp):
TTTAGGTTCGAATTAAGCTTGATCTAAAAGATTTGGGAATACAAGTGACTTATTACAATTAAAAA
TATTTATTGATCGAGTTGAATCATAGCACAATTTTAAAAATTTAAAAAATTTCTGTTTAGGTTCA
AATTAGGCTTGATACAAAAGATTTGGAGACGTAAGTGACTTATTACACTTAAAAATATTAATTGA
TCAAGTTGAATCAGATCACAATTCTAAAAATTTTAAAAATTTCTA
Found at i:454143 original size:23 final size:23
Alignment explanation
Indices: 454105--454148 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
454095 TAATTTTAAA
454105 ATATATAATATAAAATTATTTTT
1 ATATATAATATAAAATTATTTTT
454128 ATATAATAATAT-AAATTATTT
1 ATAT-ATAATATAAAATTATTT
454149 ATGTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATATAATATAAAATTATTTTT
Found at i:454818 original size:32 final size:32
Alignment explanation
Indices: 454780--454867 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 32
454770 AATTTAATGA
*
454780 ATTAAATATAATTATTTGTAAATTTGATAAAT
1 ATTAAATATAATTATTTATAAATTTGATAAAT
* * *
454812 ATTAAATA-AAATA-ATACTAAATTTGATGAAT
1 ATTAAATATAATTATTTA-TAAATTTGATAAAT
* * *
454843 ATTAGACATAGTTATTTATAAATTT
1 ATTAAATATAATTATTTATAAATTT
454868 AATAGTCATT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
30 1 0.02
31 23 0.52
32 18 0.41
33 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (32 bp):
ATTAAATATAATTATTTATAAATTTGATAAAT
Found at i:455567 original size:16 final size:16
Alignment explanation
Indices: 455546--455576 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
455536 TTACTTAAAA
455546 ATATTAATTAATTATT
1 ATATTAATTAATTATT
*
455562 ATATTATTTAATTAT
1 ATATTAATTAATTAT
455577 ATAATTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTAATTAATTATT
Found at i:455586 original size:20 final size:20
Alignment explanation
Indices: 455549--455586 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
455539 CTTAAAAATA
*
455549 TTAATTAATTATTATATTAT
1 TTAATTAATAATTATATTAT
455569 TTAATTATATAATT-TATT
1 TTAATTA-ATAATTATATT
455587 TAATCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATTAATAATTATATTAT
Found at i:455642 original size:23 final size:23
Alignment explanation
Indices: 455616--455671 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
455606 TTAATTAAGT
*
455616 TAATGTCA-CATAAGTCGTAATAC
1 TAAT-TCATCATAAGTCGCAATAC
* *
455639 TAATTTATCATAAGTTGCAATAC
1 TAATTCATCATAAGTCGCAATAC
*
455662 TAATTTATCA
1 TAATTCATCA
455672 CATTATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (23 bp):
TAATTCATCATAAGTCGCAATAC
Found at i:456243 original size:10 final size:10
Alignment explanation
Indices: 456228--456258 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
456218 ATTTAAATTA
456228 ATAAATAAAC
1 ATAAATAAAC
456238 ATAAATAAAC
1 ATAAATAAAC
456248 ATAAATCAAAC
1 ATAAAT-AAAC
456259 CATTTATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (10 bp):
ATAAATAAAC
Found at i:456327 original size:18 final size:18
Alignment explanation
Indices: 456304--456338 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
456294 GCTTAATTTT
456304 TTTTACTTCAAAAAAAAC
1 TTTTACTTCAAAAAAAAC
*
456322 TTTTACTTTAAAAAAAA
1 TTTTACTTCAAAAAAAA
456339 ACCACTACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTTACTTCAAAAAAAAC
Found at i:456335 original size:19 final size:18
Alignment explanation
Indices: 456304--456340 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
456294 GCTTAATTTT
*
456304 TTTTACTTCAAAAAAAAC
1 TTTTACTTAAAAAAAAAC
456322 TTTTACTTTAAAAAAAAAC
1 TTTTAC-TTAAAAAAAAAC
456341 CACTACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTTACTTAAAAAAAAAC
Found at i:456815 original size:2 final size:2
Alignment explanation
Indices: 456808--456837 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
456798 CCAATAATAC
456808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
456838 TTGTTTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:457003 original size:15 final size:15
Alignment explanation
Indices: 456965--457052 Score: 58
Period size: 15 Copynumber: 5.9 Consensus size: 15
456955 AAAGTTCTAT
*
456965 AAATTTAATTAAA-A
1 AAATTTAATTAAATT
* *
456979 AAAATTAATTTAATT
1 AAATTTAATTAAATT
*
456994 AAATTAAATTTAAATTT
1 AAATTTAA-TTAAA-TT
* *
457011 AAATTTAAATAATTT
1 AAATTTAATTAAATT
457026 AAA--TAATTAAA-T
1 AAATTTAATTAAATT
*
457038 AAATTATATTTAAAT
1 AAATT-TAATTAAAT
457053 ATCTTAATAT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
12 4 0.07
13 6 0.11
14 11 0.20
15 18 0.33
16 7 0.13
17 9 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTTAATTAAATT
Found at i:457008 original size:6 final size:6
Alignment explanation
Indices: 456992--457020 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
456982 ATTAATTTAA
456992 TTAAA- TTAAAT TTAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
457021 AATTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:457037 original size:8 final size:9
Alignment explanation
Indices: 457012--457076 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
457002 TTTAAATTTA
457012 AATTTAAAT
1 AATTTAAAT
457021 AATTTAAAT
1 AATTTAAAT
457030 AA-TTAAAT
1 AATTTAAAT
*
457038 AAATT--AT
1 AATTTAAAT
457045 -ATTTAAAT
1 AATTTAAAT
457053 -ATCTT-AAT
1 AAT-TTAAAT
457061 -ATTTAAAT
1 AATTTAAAT
*
457069 AATATAAA
1 AATTTAAA
457077 CTTTATATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
6 3 0.06
7 4 0.08
8 20 0.42
9 21 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTTAAAT
Found at i:457040 original size:27 final size:25
Alignment explanation
Indices: 456980--457042 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
456970 TAATTAAAAA
* *
456980 AAATTAATTTAATTAAATTAAATTT
1 AAATAAATTTAAATAAATTAAATTT
*
457005 AAATTTAAATTTAAATAATTTAAATAATT
1 AAA--TAAATTTAAATAAATTAAAT--TT
457034 AAATAAATT
1 AAATAAATT
457043 ATATTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 3 0.10
27 23 0.74
29 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATAAATTTAAATAAATTAAATTT
Found at i:457049 original size:32 final size:33
Alignment explanation
Indices: 456984--457070 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 33
456974 TAAAAAAAAT
*
456984 TAATTTAATTAAATTAAATTTAAATTTAAATTTAAA
1 TAATTTAAAT-AATTAAA--TAAATTTAAATTTAAA
*
457020 TAATTTAAATAATTAAATAAA-TTATATTTAAA
1 TAATTTAAATAATTAAATAAATTTAAATTTAAA
*
457052 T-ATCTT-AATATTTAAATAA
1 TAAT-TTAAATAATTAAATAA
457071 TATAAACTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
31 14 0.30
32 13 0.28
33 4 0.09
35 7 0.15
36 9 0.19
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
TAATTTAAATAATTAAATAAATTTAAATTTAAA
Found at i:457052 original size:44 final size:48
Alignment explanation
Indices: 456988--457076 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 48
456978 AAAAATTAAT
* *
456988 TTAATTAAATTAAATTT-AA-AT-TTAA-ATTTAAATAATTTAAATAA
1 TTAAATAAATTAAATTTAAATATCTTAATATTTAAATAATATAAATAA
*
457032 TTAAATAAATTATATTTAAATATCTTAATATTTAAATAATATAAA
1 TTAAATAAATTAAATTTAAATATCTTAATATTTAAATAATATAAA
457077 CTTTATATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 15 0.39
45 2 0.05
46 2 0.05
47 4 0.11
48 15 0.39
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (48 bp):
TTAAATAAATTAAATTTAAATATCTTAATATTTAAATAATATAAATAA
Found at i:457395 original size:15 final size:14
Alignment explanation
Indices: 457375--457413 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
457365 TTATTATTTT
457375 TAATTAATATTAAAA
1 TAATTAA-ATTAAAA
457390 TAATT-AATTAAAA
1 TAATTAAATTAAAA
457403 -AATTAAATTAA
1 TAATTAAATTAA
457414 TTTTAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.17
13 13 0.57
14 1 0.04
15 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATTAAATTAAAA
Found at i:457431 original size:22 final size:23
Alignment explanation
Indices: 457393--457446 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
457383 ATTAAAATAA
457393 TTAATTAAA-AAATTAAA-TTAATT
1 TTAA-TAAATAAATTAAATTTAA-T
457416 TTAATAAATAAA-TAAATTTAAT
1 TTAATAAATAAATTAAATTTAAT
457438 TTAATAAAT
1 TTAATAAAT
457447 TGAGCTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAATAAATAAATTAAATTTAAT
Found at i:457968 original size:14 final size:13
Alignment explanation
Indices: 457952--458000 Score: 64
Period size: 14 Copynumber: 3.8 Consensus size: 13
457942 TATTTACTTT
457952 TATATAATATAAA
1 TATATAATATAAA
*
457965 TTATAAAATATAAA
1 -TATATAATATAAA
*
457979 TATA-AATATATA
1 TATATAATATAAA
457991 TATATAATAT
1 TATATAATAT
458001 TATTATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
12 11 0.34
13 9 0.28
14 12 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATAATATAAA
Found at i:457981 original size:6 final size:6
Alignment explanation
Indices: 457952--458000 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
457942 TATTTACTTT
*
457952 TATATAA TATAAA TTATAAAA TATAAA TATAAA TATATA TATATAA TAT
1 TATA-AA TATAAA -TAT-AAA TATAAA TATAAA TATAAA TATA-AA TAT
458001 TATTATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 20 0.54
7 14 0.38
8 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
TATAAA
Found at i:458071 original size:12 final size:13
Alignment explanation
Indices: 458054--458082 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
458044 GATTTTTTTA
458054 ATTTAAACTT-AT
1 ATTTAAACTTAAT
458066 ATTTAAACTTAAT
1 ATTTAAACTTAAT
458079 ATTT
1 ATTT
458083 TTATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAAACTTAAT
Found at i:458323 original size:16 final size:15
Alignment explanation
Indices: 458287--458337 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
458277 ATTTAAACTA
458287 TTAAATTAAA-TTAT
1 TTAAATTAAATTTAT
*
458301 ATAAAATTTAAATTTAT
1 -TTAAA-TTAAATTTAT
458318 TTAAATTATAATTTAAT
1 TTAAATTA-AATTT-AT
458335 TTA
1 TTA
458338 TAAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 7 0.23
16 14 0.47
17 9 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAATTAAATTTAT
Found at i:458336 original size:17 final size:18
Alignment explanation
Indices: 458311--458351 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
458301 ATAAAATTTA
*
458311 AATTT-ATTTA-AATTAT
1 AATTTAATTTATAAATAT
458327 AATTTAATTTATAAATAT
1 AATTTAATTTATAAATAT
458345 -ATTTAAT
1 AATTTAAT
458352 AACATAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTAATTTATAAATAT
Found at i:459953 original size:26 final size:26
Alignment explanation
Indices: 459898--459959 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
459888 AAACATTAAG
* *
459898 TTTTTTTTTAAGTAAAAAAGTTTATA
1 TTTTTTTTTAAGAAAAAAAGTTGATA
*
459924 TTTTTTTTTAAGAAAAAGAAG-TGAGTT
1 TTTTTTTTTAAGAAAAA-AAGTTGA-TA
459951 TTTTTTTTT
1 TTTTTTTTT
459960 TAAAATGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.56
Consensus pattern (26 bp):
TTTTTTTTTAAGAAAAAAAGTTGATA
Found at i:459955 original size:28 final size:28
Alignment explanation
Indices: 459924--459992 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
459914 AAAGTTTATA
459924 TTTTTTTTTAAGAA-AAAGAAGTGAGT-TT
1 TTTTTTTTTAA-AAGAAA-AAGTGAGTATT
459952 TTTTTTTTTAAAATGAAAAAGTGAGTAGTT
1 TTTTTTTTTAAAA-GAAAAAGTGAGTA-TT
*
459982 TTTTTATTTAA
1 TTTTTTTTTAA
459993 TGAATGGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 2 0.06
28 19 0.53
29 3 0.08
30 12 0.33
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (28 bp):
TTTTTTTTTAAAAGAAAAAGTGAGTATT
Found at i:459970 original size:31 final size:28
Alignment explanation
Indices: 459924--459986 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 28
459914 AAAGTTTATA
459924 TTTTTTTTTAAGAAAAAG-AAGTGAGTTT
1 TTTTTTTTTAAGAAAAAGTAAGT-AGTTT
*
459952 TTTTTTTTTAAAATGAAAAAGTGAGTAGTTT
1 TTTTTTTTT--AA-GAAAAAGTAAGTAGTTT
459983 TTTT
1 TTTT
459987 ATTTAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 9 0.30
30 2 0.07
31 16 0.53
32 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (28 bp):
TTTTTTTTTAAGAAAAAGTAAGTAGTTT
Found at i:460308 original size:8 final size:8
Alignment explanation
Indices: 460295--460425 Score: 51
Period size: 8 Copynumber: 15.9 Consensus size: 8
460285 ACCTCAAATA
460295 ATTTATAT
1 ATTTATAT
460303 ATTTATAT
1 ATTTATAT
*
460311 TTTTATTAT
1 ATTTA-TAT
460320 ATTATAATCAT
1 ATT-T-AT-AT
*
460331 ATTTAAAAT
1 ATTT-ATAT
460340 ATTTA-AT
1 ATTTATAT
*
460347 ATGTATATAAA
1 AT-T-TAT-AT
*
460358 ATTTAATAA
1 ATTT-ATAT
*
460367 ATTAATA-
1 ATTTATAT
460374 ATTTATAT
1 ATTTATAT
* *
460382 -TGTA-AA
1 ATTTATAT
460388 ATTT-TA-
1 ATTTATAT
460394 ATTTATAT
1 ATTTATAT
460402 ATTTATATT
1 ATTTATA-T
460411 ATATTATAT
1 AT-TTATAT
460420 -TTTATA
1 ATTTATA
460426 ATAACTTTTT
Statistics
Matches: 98, Mismatches: 9, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
6 5 0.05
7 23 0.23
8 25 0.26
9 23 0.23
10 13 0.13
11 9 0.09
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (8 bp):
ATTTATAT
Found at i:461705 original size:2 final size:2
Alignment explanation
Indices: 461698--461725 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
461688 TTGATGTGTT
461698 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
461726 AGACAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:461880 original size:9 final size:9
Alignment explanation
Indices: 461855--461884 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
461845 AAGGGTGAGT
461855 TTTAATCGA
1 TTTAATCGA
461864 TTTAAATCGA
1 TTT-AATCGA
461874 TTTAATCGA
1 TTTAATCGA
461883 TT
1 TT
461885 AAATTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (9 bp):
TTTAATCGA
Found at i:462050 original size:12 final size:12
Alignment explanation
Indices: 462035--462074 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
462025 TAATTTTTAA
462035 AATATATATTAT
1 AATATATATTAT
462047 AATATATATTATTT
1 AATATATATTA--T
*
462061 AATATATAATAT
1 AATATATATTAT
462073 AA
1 AA
462075 AATTGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 14 0.56
14 11 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATATATTAT
Found at i:462055 original size:14 final size:14
Alignment explanation
Indices: 462035--462068 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
462025 TAATTTTTAA
462035 AATATATATTA--T
1 AATATATATTATTT
462047 AATATATATTATTT
1 AATATATATTATTT
462061 AATATATA
1 AATATATA
462069 ATATAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATATATTATTT
Found at i:462085 original size:24 final size:26
Alignment explanation
Indices: 462035--462099 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
462025 TAATTTTTAA
* *
462035 AATATATATTATAATATATATTATTT
1 AATATATAATATAAAATATATTATTT
*
462061 AATATATAATATAAAAT-TGTT-TTT
1 AATATATAATATAAAATATATTATTT
462085 -ATATAATAATATAAA
1 AATAT-ATAATATAAA
462100 TAATTTATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.11
24 13 0.37
25 3 0.09
26 15 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
AATATATAATATAAAATATATTATTT
Found at i:462106 original size:21 final size:21
Alignment explanation
Indices: 462015--462107 Score: 55
Period size: 21 Copynumber: 4.3 Consensus size: 21
462005 ATAAAGTTGT
* *
462015 ATTTATATAATAATTTTTAA-A
1 ATTTATATAATAA-TATAAATA
* * * *
462036 ATATATATTATAATATATATT
1 ATTTATATAATAATATAAATA
*
462057 ATTTA-ATATATAATATAAAATTGT
1 ATTTATATA-ATAATAT-AAA-T-A
*
462081 TTTTATATAATAATATAAATA
1 ATTTATATAATAATATAAATA
462102 ATTTAT
1 ATTTAT
462108 GTTTTAAAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
20 5 0.09
21 27 0.50
22 3 0.06
23 4 0.07
24 12 0.22
25 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
ATTTATATAATAATATAAATA
Found at i:462767 original size:32 final size:32
Alignment explanation
Indices: 462708--462808 Score: 145
Period size: 32 Copynumber: 3.2 Consensus size: 32
462698 ACATTGATCA
*
462708 TAAATTTAAT-GA-ATTAAATATAATTACTCG
1 TAAATTTAATAAATATTAAATATAATTACTCG
*
462738 TAAATTTAATAAATATTAAATA-AATTTACTCA
1 TAAATTTAATAAATATTAAATATAA-TTACTCG
*
462770 TAAATTTAATAAATATTAGATATAATTACTCG
1 TAAATTTAATAAATATTAAATATAATTACTCG
462802 TAAATTT
1 TAAATTT
462809 GACATTAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
30 10 0.16
31 3 0.05
32 48 0.76
33 2 0.03
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (32 bp):
TAAATTTAATAAATATTAAATATAATTACTCG
Found at i:464761 original size:2 final size:2
Alignment explanation
Indices: 464749--464779 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
464739 GCCAATGAAG
464749 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
464780 GTAATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:465009 original size:21 final size:20
Alignment explanation
Indices: 464962--465011 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
464952 ACGATAACTT
*
464962 ATTTAAAAATTTTAAAATTT
1 ATTTAAAAATTTTAAAATTA
* * *
464982 ATATAAATAATTTTTATATTA
1 ATTTAAA-AATTTTAAAATTA
465003 ATTTAAAAA
1 ATTTAAAAA
465012 AAACTTATGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAAAATTTTAAAATTA
Found at i:465383 original size:30 final size:31
Alignment explanation
Indices: 465329--465430 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
465319 AATATTGATA
* *
465329 ATAAATTTAATGAAT-TAAATATAATTATTT
1 ATAAATTTAATGAATATTAACATAATTATTT
* *
465359 ATAAATTTAATAAATATTAA-ATAATATAATGT
1 ATAAATTTAATGAATATTAACATAAT-T-ATTT
* * *
465391 -TAAATTTGATGAATATTAGACATAGTTACTT
1 ATAAATTTAATGAATATTA-ACATAATTATTT
465422 ATAAATTTA
1 ATAAATTTA
465431 TCAGACATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
30 19 0.33
31 22 0.39
32 12 0.21
33 4 0.07
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (31 bp):
ATAAATTTAATGAATATTAACATAATTATTT
Found at i:467306 original size:2 final size:2
Alignment explanation
Indices: 467294--467346 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
467284 AGATACCAAT
* * * * *
467294 TA TA CA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
467336 TA TA TA TA TA T
1 TA TA TA TA TA T
467347 TTGTTTCAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (2 bp):
TA
Found at i:467494 original size:17 final size:18
Alignment explanation
Indices: 467459--467511 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
467449 TATCTAAATT
*
467459 TAATTTAATTATTATTAAA
1 TAATTTAA-TATTAATAAA
467478 TAATTTAA-ATTAATAAA
1 TAATTTAATATTAATAAA
* *
467495 TAAATTATATTTTAATA
1 TAATTTA-ATATTAATA
467512 TTTTAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
19 14 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTTAATATTAATAAA
Found at i:468351 original size:14 final size:14
Alignment explanation
Indices: 468334--468360 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
468324 TTTTAATAAA
468334 TAAATAAATTTAAT
1 TAAATAAATTTAAT
468348 TAAATAAATTTAA
1 TAAATAAATTTAA
468361 ATAATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATAAATTTAAT
Found at i:468365 original size:18 final size:18
Alignment explanation
Indices: 468308--468371 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 18
468298 AATAATAAAA
* *
468308 TAAAAAATTAAATTAATT
1 TAAATAATTAAATAAATT
* *
468326 TTAATAAATAAATAAA-T
1 TAAATAATTAAATAAATT
468343 T---TAATTAAATAAATT
1 TAAATAATTAAATAAATT
*
468358 TAAATAATTTAATA
1 TAAATAATTAAATA
468372 TTTATTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
14 11 0.31
15 2 0.06
17 2 0.06
18 21 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATAATTAAATAAATT
Found at i:468921 original size:17 final size:18
Alignment explanation
Indices: 468899--468936 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
468889 TAACATAAAT
*
468899 TATAAAATATATAAA-AA
1 TATAAAATATAAAAATAA
468916 TAT-AAATATAAAAATAA
1 TATAAAATATAAAAATAA
468933 TATA
1 TATA
468937 TATTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TATAAAATATAAAAATAA
Found at i:469280 original size:16 final size:16
Alignment explanation
Indices: 469238--469284 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
469228 TAAATTTTAA
*
469238 ATAATAATTTAAACTAT
1 ATAA-AATTTAAATTAT
469255 -T-AAA-TTAAATTAT
1 ATAAAATTTAAATTAT
469268 ATAAAATTTAAATTAT
1 ATAAAATTTAAATTAT
469284 A
1 A
469285 ATTTAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 8 0.31
14 3 0.12
15 4 0.15
16 11 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAAATTTAAATTAT
Found at i:469599 original size:25 final size:25
Alignment explanation
Indices: 469570--469620 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
469560 AAAATTTCAC
469570 AAATATCTA-ATATTTTTTAAATTAA
1 AAATATCTATATATTTTTT-AATTAA
*
469595 AAATATTTATATATTTTTTAATTAA
1 AAATATCTATATATTTTTTAATTAA
469620 A
1 A
469621 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATATCTATATATTTTTTAATTAA
Found at i:470212 original size:157 final size:158
Alignment explanation
Indices: 469989--470464 Score: 423
Period size: 161 Copynumber: 3.0 Consensus size: 158
469979 ATATAAAGTA
* * * * *
469989 TTTTTTTATAAAAAAAATAAAATTA-TTAAAAAAGTTCATATATCGACTC-AAATAGTTAATACT
1 TTTTTTTA-AAAAAAAAAAAAATTAGTTAAATAA-TTCACATATCGACTCAAAATAGATAATATT
*
470052 TTATAA-ATAGCACAGTTTTGAAAATTCTTATATCAACGAGTTACTAGTGAGATCATGCTCAATA
64 TTATAATA-AGCACAGTTTTGAAAATTCTTATATCAACAAGTTACTAGTGAGATCATGCTCAATA
* ** *
470116 AAGATTATTTGTATTAGATTTGAGTTAT-T-
128 AAGACTATTCATATTAGATTCGAGTTATATG
*
470145 TTTTTTTAAAAAAAAAAAAAATTAGTTAGAATAATTCACATATCGCCTCAAAATAGATAATATTT
1 TTTTTTTAAAAAAAAAAAAAATTAGTTA-AATAATTCACATATCGACTCAAAATAGATAATATTT
* * * * * * * *
470210 TATAATAAGTACAGTTTCGAAAA-TCTTTACATTAATAAGTTACTAGTGGGATCATACTTAATAA
65 TATAATAAGCACAGTTTTGAAAATTC-TTATATCAACAAGTTACTAGTGAGATCATGCTCAATAA
*
470274 AGACTATTCATCTTAGATTCGAGTTATATGAGG
129 AGACTATTCATATTAGATTCGAGTTATAT---G
* * * * * * * *
470307 TATTTTCTT--ATAAAAAAAAAA-TCGTTAAAATAGTTTACATATCAACTTAAAACAAATAATAT
1 T-TTTT-TTAAAAAAAAAAAAAATTAGTT-AAATAATTCACATATCGACTCAAAATAGATAATAT
* * * * * * ***
470369 TTTATAATAAGCATAATTTTAAAAATCCTTATGTCAACAAGTTACTAATGAGATCATGCTTGGTA
63 TTTATAATAAGCACAGTTTTGAAAATTCTTATATCAACAAGTTACTAGTGAGATCATGCTCAATA
* *
470434 AAGACTATTCATCTT-GAATTTGAGTTATATG
128 AAGACTATTCATATTAG-ATTCGAGTTATATG
470465 AGGTATTTTT
Statistics
Matches: 260, Mismatches: 45, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
155 15 0.06
156 26 0.10
157 89 0.34
158 3 0.01
160 1 0.00
161 106 0.41
162 14 0.05
163 4 0.02
164 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (158 bp):
TTTTTTTAAAAAAAAAAAAAATTAGTTAAATAATTCACATATCGACTCAAAATAGATAATATTTT
ATAATAAGCACAGTTTTGAAAATTCTTATATCAACAAGTTACTAGTGAGATCATGCTCAATAAAG
ACTATTCATATTAGATTCGAGTTATATG
Found at i:470414 original size:161 final size:163
Alignment explanation
Indices: 470155--470537 Score: 396
Period size: 161 Copynumber: 2.3 Consensus size: 163
470145 TTTTTTTAAA
* * * * ** * * *
470155 AAAAAAAAAAATTAGTTAGAATAATTCACATATCGCCTCAAAATAGATAATATTTTATAATAAGT
1 AAAAAAAAAAA-TCGTTAAAATAGTTTACATATCAACTCAAAACAAATAATATTTTATAATAAGC
* * * * * * *
470220 ACAGTTTCGAAAATCTTTACATTAATAAGTTACTAGTGGGATCATACTTAATAAAGACTATTCAT
65 ACAATTTCAAAAATCCTTACATCAACAAGTTACTAATGAGATCATACTTAATAAAGACTATTCAT
470285 CTT-AGATTCGAGTTATATGAGGTA-TTTTCTTAT
130 CTTGA-ATTCGAGTTATATGAGGTATTTTTCTTAT
*
470318 -AAAAAAAAAATCGTTAAAATAGTTTACATATCAACTTAAAACAAATAATATTTTATAATAAGCA
1 AAAAAAAAAAATCGTTAAAATAGTTTACATATCAACTCAAAACAAATAATATTTTATAATAAGCA
* * ** * **
470382 TAATTTTAAAAATCCTTATGTCAACAAGTTACTAATGAGATCATGCTTGGTAAAGACTATTCATC
66 CAATTTCAAAAATCCTTACATCAACAAGTTACTAATGAGATCATACTTAATAAAGACTATTCATC
* *
470447 TTGAATTTGAGTTATATGAGGTATTTTTTTTAT
131 TTGAATTCGAGTTATATGAGGTATTTTTCTTAT
* * * * * * *
470480 AGAAAAAGATAAAATCATTATAATAGTTTATATATCGATTCAAAATAAAAAAT-TTTTA
1 A-AAAAA-A-AAAATCGTTAAAATAGTTTACATATCAACTCAAAACAAATAATATTTTA
470538 AATCAATGAG
Statistics
Matches: 180, Mismatches: 34, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
161 115 0.64
162 19 0.11
164 5 0.03
165 6 0.03
166 35 0.19
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (163 bp):
AAAAAAAAAAATCGTTAAAATAGTTTACATATCAACTCAAAACAAATAATATTTTATAATAAGCA
CAATTTCAAAAATCCTTACATCAACAAGTTACTAATGAGATCATACTTAATAAAGACTATTCATC
TTGAATTCGAGTTATATGAGGTATTTTTCTTAT
Found at i:470856 original size:11 final size:10
Alignment explanation
Indices: 470840--470909 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 10
470830 GATAATTCAT
470840 ATATTTATATA
1 ATATTTATA-A
470851 ATATTTATAA
1 ATATTTATAA
*
470861 AT-TTTAT-C
1 ATATTTATAA
470869 ATA-TTATAA
1 ATATTTATAA
470878 TTATATTT-TAA
1 --ATATTTATAA
470889 ATATTT-TAA
1 ATATTTATAA
470898 AT-TTATATAA
1 ATATT-TATAA
470908 AT
1 AT
470910 TTAAATATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
8 8 0.16
9 17 0.34
10 8 0.16
11 15 0.30
12 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (10 bp):
ATATTTATAA
Found at i:470920 original size:47 final size:49
Alignment explanation
Indices: 470856--470947 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
470846 ATATAATATT
* *
470856 TATAAATTTTATCATATT-ATAA-TTATATTTTA-AATATTTTAAATTTA
1 TATAAATTTAATCATATTAATAATTTATATTATATAAT-TTTTAAATTTA
470903 TATAAATTTAAAT-ATATTAATAATTTATATTATATAATTTTTAAA
1 TATAAATTT-AATCATATTAATAATTTATATTATATAATTTTTAAA
470948 ATATTTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
47 14 0.36
48 6 0.15
49 16 0.41
50 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (49 bp):
TATAAATTTAATCATATTAATAATTTATATTATATAATTTTTAAATTTA
Found at i:471326 original size:19 final size:19
Alignment explanation
Indices: 471304--471342 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
471294 AATTAAAAAA
*
471304 ATTTAAATATTTTAAATTT
1 ATTTAAATATTATAAATTT
* *
471323 ATTTTATTATTATAAATTT
1 ATTTAAATATTATAAATTT
471342 A
1 A
471343 ATTTTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTAAATATTATAAATTT
Found at i:471355 original size:18 final size:19
Alignment explanation
Indices: 471311--471355 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
471301 AAAATTTAAA
*
471311 TATTTTAAATTTATTTTAT
1 TATTATAAATTTATTTTAT
471330 TATTATAAATTTAATTTT-T
1 TATTATAAATTT-ATTTTAT
471349 T-TTATAA
1 TATTATAA
471356 CTTTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 13 0.54
20 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTATAAATTTATTTTAT
Found at i:472318 original size:27 final size:27
Alignment explanation
Indices: 472287--472372 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
472277 TTACTTTTTT
*
472287 TTAATATTATTAAAAATTATTTTTATA
1 TTAATATTAATAAAAATTATTTTTATA
**
472314 TTAATATTAATATTAA-TATTTTTATAA
1 TTAATATTAATAAAAATTATTTTTAT-A
* *
472341 TTAAATATAAATAAAAATTAATTTTTTTA
1 TT-AATATTAATAAAAATT-ATTTTTATA
472370 TTA
1 TTA
472373 TTAAATAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
26 9 0.19
27 16 0.33
28 12 0.25
29 4 0.08
30 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAATATTAATAAAAATTATTTTTATA
Found at i:472646 original size:29 final size:28
Alignment explanation
Indices: 472586--472659 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
472576 CTAATTAAAT
**
472586 TTTATATATTTTTGTAATTTTTTTTATAA
1 TTTATATATTTTT-TAATTTTCATTATAA
472615 TTTATATATTTTTTAATTTAATCATTAT-A
1 TTTATATATTTTTTAATTT--TCATTATAA
* *
472644 TTTTTATATTATTTAA
1 TTTATATATTTTTTAA
472660 ATAAATTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 6 0.15
29 28 0.72
30 5 0.13
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTATATATTTTTTAATTTTCATTATAA
Found at i:483689 original size:17 final size:17
Alignment explanation
Indices: 483667--483701 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
483657 GAAATTCGAG
* *
483667 TATATCGGATATGAATA
1 TATATCCGACATGAATA
483684 TATATCCGACATGAATA
1 TATATCCGACATGAATA
483701 T
1 T
483702 GTTTAATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (17 bp):
TATATCCGACATGAATA
Found at i:485487 original size:16 final size:16
Alignment explanation
Indices: 485449--485480 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
485439 ATGTAAAAAT
*
485449 TATTGTATTTTATATA
1 TATTATATTTTATATA
485465 TATTATATTTTATATA
1 TATTATATTTTATATA
485481 ATTTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTATATTTTATATA
Found at i:485546 original size:27 final size:26
Alignment explanation
Indices: 485508--485564 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
485498 TATATTATAT
485508 TATATCGTTTTAAATTAT-TATATAAA
1 TATATCGTTTTAAATTATGTATA-AAA
* **
485534 TATATCTTATTTATTTTATGTATAAAA
1 TATATCGT-TTTAAATTATGTATAAAA
485561 TATA
1 TATA
485565 ATTAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.27
27 15 0.58
28 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TATATCGTTTTAAATTATGTATAAAA
Found at i:486319 original size:2 final size:2
Alignment explanation
Indices: 486314--486352 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
486304 ATATATTTAT
486314 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
486353 ATCCATGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:491897 original size:3 final size:3
Alignment explanation
Indices: 491889--491925 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
491879 TGCCTCCATT
*
491889 TTC TTC TTC TTC TTC TTC TTC TTC TCC TTC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
491926 TTTTTCCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:492162 original size:6 final size:6
Alignment explanation
Indices: 492135--492196 Score: 54
Period size: 6 Copynumber: 9.7 Consensus size: 6
492125 TTAATAAAAA
* *
492135 TTAAAT TTAATT TGT-ATAT TTAATT TTAAAT TTAATTAT TTATATT TTAATT
1 TTAATT TTAATT T-TAAT-T TTAATT TTAATT TTAA-T-T TTA-ATT TTAATT
492187 TTAATT TTAA
1 TTAATT TTAA
492197 GTAAAATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
6 32 0.68
7 9 0.19
8 5 0.11
9 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (6 bp):
TTAATT
Found at i:492169 original size:12 final size:12
Alignment explanation
Indices: 492135--492196 Score: 61
Period size: 12 Copynumber: 4.8 Consensus size: 12
492125 TTAATAAAAA
492135 TTAAATTTAATT
1 TTAAATTTAATT
*
492147 TGTATATTTAATT
1 T-TAAATTTAATT
492160 TTAAATTTAATTAT
1 TTAAATTTAA-T-T
*
492174 TTATATTTTAATT
1 TTA-AATTTAATT
*
492187 TTAATTTTAA
1 TTAAATTTAA
492197 GTAAAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
12 16 0.37
13 16 0.37
14 5 0.12
15 6 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
TTAAATTTAATT
Found at i:492183 original size:21 final size:20
Alignment explanation
Indices: 492151--492192 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
492141 TTAATTTGTA
492151 TATTTAATTTTAAATTTAAT
1 TATTTAATTTTAAATTTAAT
*
492171 TATTTATATTTTAATTTTAAT
1 TATTTA-ATTTTAAATTTAAT
492192 T
1 T
492193 TTAAGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTAATTTTAAATTTAAT
Found at i:493339 original size:50 final size:50
Alignment explanation
Indices: 493227--493446 Score: 313
Period size: 50 Copynumber: 4.5 Consensus size: 50
493217 TGGGTGCAAA
** *
493227 AGAGGTGGTTGTAATTGTTGACTATTCGTCACCAACC-TTGACAATCGAG
1 AGAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAG
* *
493276 AGAGGTGGTCGTAATTGTTGACTATT-TGTCACTAACCTTTGACAATCGAG
1 AGAGGTGGCCGTAATTGTTGACTATTCT-TCACCAACCTTTGACAATCGAG
* * * * *
493326 AGAGGTGACCGTAATTGTTGA--ATTCTTCACTAACTTTTGATAATAGAG
1 AGAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAG
493374 AGAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAG
1 AGAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAG
493424 AGAGGTGGCCGTAATTGTTGACT
1 AGAGGTGGCCGTAATTGTTGACT
493447 TTAAACAACT
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
48 42 0.27
49 34 0.22
50 77 0.50
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (50 bp):
AGAGGTGGCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAG
Found at i:493397 original size:98 final size:98
Alignment explanation
Indices: 493237--493445 Score: 305
Period size: 98 Copynumber: 2.1 Consensus size: 98
493227 AGAGGTGGTT
* *
493237 GTAATTGTTGACTATTCGTCACCAACCTTGACAATCGAGAGAGGTGGTCGTAATTGTTGACTATT
1 GTAATTGTTGAC-ATTCGTCACCAACCTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACTATT
*
493302 -TGTCACTAACCTTTGACAATCGAGAGAGGTGACC
65 CT-TCACCAACCTTTGACAATCGAGAGAGGTGACC
* * * *
493336 GTAATTGTTGA-ATTCTTCACTAACTTTTGATAATAGAGAGAGGTGGCCGTAATTGTTGACTATT
1 GTAATTGTTGACATTCGTCACCAAC-CTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACTATT
*
493400 CTTCACCAACCTTTGACAATCGAGAGAGGTGGCC
65 CTTCACCAACCTTTGACAATCGAGAGAGGTGACC
493434 GTAATTGTTGAC
1 GTAATTGTTGAC
493446 TTTAAACAAC
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
97 11 0.11
98 76 0.77
99 12 0.12
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (98 bp):
GTAATTGTTGACATTCGTCACCAACCTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACTATTC
TTCACCAACCTTTGACAATCGAGAGAGGTGACC
Found at i:497983 original size:50 final size:49
Alignment explanation
Indices: 497812--497979 Score: 228
Period size: 50 Copynumber: 3.4 Consensus size: 49
497802 TTGGTGCAAA
* * *
497812 AGAGGTGGCCATAATTGTTGACTATTCGTCACCAACTTTGACAATTGAG
1 AGAGGTGGCCGTAATTGTTGACTATTCTTCACCAACTTTGACAATAGAG
* * * *
497861 AGAGATGGCCGTAATTATTGACTATTCTTCACCAACCTTTGACAATCGAA
1 AGAGGTGGCCGTAATTGTTGACTATTCTTCACCAA-CTTTGACAATAGAG
*
497911 AGAGGTGGCCGTAATTGTTTACTATTCTTCACCAACTTTTGACAATAGAG
1 AGAGGTGGCCGTAATTGTTGACTATTCTTCACCAAC-TTTGACAATAGAG
**
497961 AGAGGTGATCGTAATTGTT
1 AGAGGTGGCCGTAATTGTT
497980 TACTTTAAGC
Statistics
Matches: 104, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
49 32 0.31
50 72 0.69
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (49 bp):
AGAGGTGGCCGTAATTGTTGACTATTCTTCACCAACTTTGACAATAGAG
Found at i:500656 original size:44 final size:44
Alignment explanation
Indices: 500593--500715 Score: 171
Period size: 44 Copynumber: 2.8 Consensus size: 44
500583 TCATTCTTGG
*
500593 GTTCAAGAGTCAG-ACAGGCTTAGAGCTTAAGTTTCGGACTTCGA
1 GTTCAAGAGTC-GTACAGGCTTAGAGCTTAAGTTTCGGACCTCGA
*
500637 GTTC-AGCAGTCGTACAGGCTTAGAGCATAAGTTTCGGACCTCGA
1 GTTCAAG-AGTCGTACAGGCTTAGAGCTTAAGTTTCGGACCTCGA
*
500681 GTTCAAGAGTCGT-CGAGCCTTAGAGCTTAAGTTTC
1 GTTCAAGAGTCGTAC-AGGCTTAGAGCTTAAGTTTC
500716 AACCCGTGAA
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
43 4 0.06
44 65 0.92
45 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (44 bp):
GTTCAAGAGTCGTACAGGCTTAGAGCTTAAGTTTCGGACCTCGA
Found at i:501140 original size:27 final size:26
Alignment explanation
Indices: 501079--501140 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
501069 ACAAATTATT
*
501079 AATTATTAATATATTAAAGTTTATATA
1 AATTA-TAATATATTAAACTTTATATA
*
501106 AATATATAATATTTTAAAACTTTAT-TA
1 AAT-TATAATATATT-AAACTTTATATA
501133 GAATTATA
1 -AATTATA
501141 CTTCTCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (26 bp):
AATTATAATATATTAAACTTTATATA
Found at i:501209 original size:18 final size:18
Alignment explanation
Indices: 501183--501218 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
501173 TATTAAAAAA
*
501183 ATATATTTATATTTAATT
1 ATATATTTATAATTAATT
*
501201 ATATTTTTATAATTAATT
1 ATATATTTATAATTAATT
501219 TAAATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATATTTATAATTAATT
Found at i:504247 original size:20 final size:21
Alignment explanation
Indices: 504214--504273 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
504204 GTTTTTTAAC
*
504214 ATTT-AGTAAGTATATAAA-A
1 ATTTAAGTAAATATATAAATA
504233 ATTTAAGTAAATATA-AAATA
1 ATTTAAGTAAATATATAAATA
* *
504253 TTTTAAATAAATATATAAATA
1 ATTTAAGTAAATATATAAATA
504274 TAATATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.20
20 23 0.66
21 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTAAGTAAATATATAAATA
Found at i:504321 original size:20 final size:19
Alignment explanation
Indices: 504291--504328 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
504281 AATATATTAA
504291 TTATAAAAAATATTAAAAG
1 TTATAAAAAATATTAAAAG
504310 TTATATAAAAATATTAAAA
1 TTATA-AAAAATATTAAAA
504329 TGTATTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
TTATAAAAAATATTAAAAG
Found at i:504806 original size:16 final size:16
Alignment explanation
Indices: 504785--504838 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
504775 ATCATGATAA
504785 TATATATTTTAAAATT
1 TATATATTTTAAAATT
* *
504801 TATATAATTTAAATTAT
1 TATATATTTTAAAAT-T
*
504818 TA-ATATATTAAAATT
1 TATATATTTTAAAATT
504833 TATATA
1 TATATA
504839 AATATAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 3 0.10
16 25 0.81
17 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATATTTTAAAATT
Found at i:504846 original size:17 final size:17
Alignment explanation
Indices: 504794--504848 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
504784 ATATATATTT
504794 TAAAATTTATAT-AAT-
1 TAAAATTTATATAAATA
*
504809 TTAAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
504825 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
504843 TAAAAT
1 TAAAAT
504849 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
17 10 0.31
18 7 0.22
19 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:504854 original size:20 final size:22
Alignment explanation
Indices: 504831--504894 Score: 60
Period size: 25 Copynumber: 2.9 Consensus size: 22
504821 TATATTAAAA
504831 TTTATATAAATATAA-A-ATAT
1 TTTATATAAATATAATATATAT
*
504851 TTTAAATAAAGTTATAATATTATAT
1 TTTATATAAA--TATAATA-TATAT
* *
504876 GTTATATAAATATGATATA
1 TTTATATAAATATAATATA
504895 AATATATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 9 0.26
22 7 0.20
23 7 0.20
25 12 0.34
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
TTTATATAAATATAATATATAT
Found at i:505063 original size:19 final size:19
Alignment explanation
Indices: 505041--505088 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
505031 TTTATTATAT
*
505041 TATTAAAATATTATTTTTA
1 TATTAAAACATTATTTTTA
*
505060 TATTATCATACATTATTTTTA
1 TATTA--AAACATTATTTTTA
505081 TAATTAAA
1 T-ATTAAA
505089 TTTAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
19 5 0.22
20 1 0.04
21 13 0.57
22 4 0.17
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTAAAACATTATTTTTA
Found at i:505123 original size:27 final size:29
Alignment explanation
Indices: 505069--505126 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
505059 ATATTATCAT
505069 ACATTATTTTTATAATTAAATTTAAATAAA
1 ACATTATTTTTATAATTAAA-TTAAATAAA
*
505099 ACATTATTTTTATTATTAAA-T-AATAAA
1 ACATTATTTTTATAATTAAATTAAATAAA
505126 A
1 A
505127 ATCAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.26
28 1 0.04
30 19 0.70
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
ACATTATTTTTATAATTAAATTAAATAAA
Found at i:505304 original size:22 final size:22
Alignment explanation
Indices: 505278--505319 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
505268 ACATTATAAA
*
505278 TATTAAA-ATTTTAATTTTAATT
1 TATTAAATATTAT-ATTTTAATT
505300 TATTAAATATTATATTTTAA
1 TATTAAATATTATATTTTAA
505320 ATTAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTAAATATTATATTTTAATT
Found at i:505327 original size:23 final size:21
Alignment explanation
Indices: 505283--505327 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
505273 ATAAATATTA
* *
505283 AAATTTTAATTTTAATTTATT
1 AAATATTAATTTTAATTAATT
505304 AAATATTATATTTTAAATTAATT
1 AAATATTA-ATTTT-AATTAATT
505327 A
1 A
505328 TATAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATATTAATTTTAATTAATT
Found at i:505705 original size:29 final size:27
Alignment explanation
Indices: 505671--505733 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 27
505661 AATTATGTAA
505671 ATAAAATATAATATAAATATATGAATAT
1 ATAAAATATAATATAAATATAT-AATAT
* * *
505699 ATTAAAATTTTATATAATTATATAATAT
1 A-TAAAATATAATATAAATATATAATAT
505727 ATAAAAT
1 ATAAAAT
505734 GATTATTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 6 0.19
28 7 0.23
29 18 0.58
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
ATAAAATATAATATAAATATATAATAT
Found at i:506141 original size:24 final size:23
Alignment explanation
Indices: 506088--506146 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 23
506078 ACATAATTTA
* *
506088 TATTTTATTATATAATATATAAT
1 TATTTTATAAAATAATATATAAT
* *
506111 GATTTTTATAAAATAATGTATAATT
1 TA-TTTTATAAAATAATATATAA-T
*
506136 TATTTTTTAAA
1 TATTTTATAAA
506147 CGGTTAAAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 1 0.04
24 25 0.89
25 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (23 bp):
TATTTTATAAAATAATATATAAT
Found at i:506485 original size:6 final size:6
Alignment explanation
Indices: 506474--506506 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
506464 GCCACTCGAA
506474 TGCTCC TGCTCC TGCTCC TGCTCC TGCT-C TGCT
1 TGCTCC TGCTCC TGCTCC TGCTCC TGCTCC TGCT
506507 GACTTGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.45, G:0.18, T:0.36
Consensus pattern (6 bp):
TGCTCC
Found at i:506703 original size:2 final size:2
Alignment explanation
Indices: 506696--506730 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
506686 GTTGTATCCA
506696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
506731 CAAAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:506836 original size:14 final size:15
Alignment explanation
Indices: 506798--506839 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
506788 AATATCGATC
*
506798 ATAAATATTAATAATA
1 ATAAAAATT-ATAATA
506814 ATAAAAATTATAA-A
1 ATAAAAATTATAATA
*
506828 ATAATAATTATA
1 ATAAAAATTATA
506840 GTATCGTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 4 0.17
16 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAAAATTATAATA
Found at i:512619 original size:34 final size:34
Alignment explanation
Indices: 512580--512649 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
512570 AAAAAAATTT
**
512580 ATGATTGCATAAACATGACCAAATATTATACCAA
1 ATGATTGCATAAACACAACCAAATATTATACCAA
* *
512614 ATGATTGCATAAACACAACCAAATATTGTAGCAA
1 ATGATTGCATAAACACAACCAAATATTATACCAA
512648 AT
1 AT
512650 TTCAATCAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (34 bp):
ATGATTGCATAAACACAACCAAATATTATACCAA
Found at i:515266 original size:2 final size:2
Alignment explanation
Indices: 515259--515325 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
515249 TGTTTTCTTA
515259 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
515301 AT AT AA AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
515326 AACAACTTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:515586 original size:22 final size:23
Alignment explanation
Indices: 515559--515606 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
515549 CCACAACATG
* * *
515559 ATTTTTAAAAGAAATAAATAAAA
1 ATTTTCAAAAAAAATAAAAAAAA
515582 ATTTTCAAAAAAAATAAAAAAAA
1 ATTTTCAAAAAAAATAAAAAAAA
515605 AT
1 AT
515607 GCAGGAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
ATTTTCAAAAAAAATAAAAAAAA
Found at i:515977 original size:2 final size:2
Alignment explanation
Indices: 515970--515997 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
515960 AGAAGAATTT
515970 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
515998 AAAGAGGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:516789 original size:19 final size:19
Alignment explanation
Indices: 516767--516803 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
516757 ATATTTTCCT
* *
516767 TATATTTTTAGTGTATATA
1 TATACTTTTAGTATATATA
516786 TATACTTTTAGTATATAT
1 TATACTTTTAGTATATAT
516804 TAATATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (19 bp):
TATACTTTTAGTATATATA
Found at i:517259 original size:13 final size:13
Alignment explanation
Indices: 517241--517277 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
517231 CACATTCGTG
517241 TTTTTATATATAT
1 TTTTTATATATAT
*
517254 TTTTTAAATATAT
1 TTTTTATATATAT
*
517267 ATTTTATATAT
1 TTTTTATATAT
517278 TTCAAAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTATATATAT
Found at i:517385 original size:2 final size:2
Alignment explanation
Indices: 517378--517417 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
517368 GGTTATTATT
* *
517378 TA TA TA TA TA TA TA CA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
517418 AAAGAGAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:517954 original size:81 final size:81
Alignment explanation
Indices: 517818--517971 Score: 204
Period size: 81 Copynumber: 1.9 Consensus size: 81
517808 TTTTAATTAA
* * * *
517818 TTTAAATCGACTCAAATTAATAAAAATTTATCTTAATCCATGCTAGGTTGGAATTATTAAAATTG
1 TTTAAATCGACTCAAATTAATAAAAATTTATCTTAATCAATGCTAAGCTGAAATTATTAAAATTG
517883 -GACAAATACTCTTATC
66 AG-CAAATACTCTTATC
* * * *
517899 TTTAAATCGGCTTAAATTAATAAAAATTTATCTTAATATAATGC-AAGCTGAAATTATTAGAATT
1 TTTAAATCGACTCAAATTAATAAAAATTTATCTTAAT-CAATGCTAAGCTGAAATTATTAAAATT
517963 GAGCAAATA
65 GAGCAAATA
517972 ATCTAACCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
81 58 0.92
82 5 0.08
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.36
Consensus pattern (81 bp):
TTTAAATCGACTCAAATTAATAAAAATTTATCTTAATCAATGCTAAGCTGAAATTATTAAAATTG
AGCAAATACTCTTATC
Found at i:526539 original size:2 final size:2
Alignment explanation
Indices: 526532--526572 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
526522 AATGGAACCA
526532 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
526573 TTCCCACACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:527871 original size:20 final size:20
Alignment explanation
Indices: 527846--527951 Score: 74
Period size: 20 Copynumber: 5.3 Consensus size: 20
527836 TTTTATGAAT
*
527846 TTTATTGATAAATATTTAAA
1 TTTATTAATAAATATTTAAA
* * **
527866 TTTATTTATGAAT-TAAATAA
1 TTTATTAATAAATATTTA-AA
527886 TTTATTAATAAATATTTAAA
1 TTTATTAATAAATATTTAAA
** *
527906 TTTATT--TATTTATTTATTTA
1 TTTATTAATAAATATTTA--AA
* *
527926 TCTGTTAATAAATATTTAAA
1 TTTATTAATAAATATTTAAA
527946 TTTATT
1 TTTATT
527952 TATGAATCGA
Statistics
Matches: 62, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
18 8 0.13
19 2 0.03
20 42 0.68
21 2 0.03
22 8 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTATTAATAAATATTTAAA
Found at i:527890 original size:40 final size:40
Alignment explanation
Indices: 527846--527967 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 40
527836 TTTTATGAAT
*
527846 TTTATTGATAAATATTTAAATTTATTTATGAATTAAATAA
1 TTTATTAATAAATATTTAAATTTATTTATGAATTAAATAA
** * * *
527886 TTTATTAATAAATATTTAAATTTATTTATTTATTTATTTA
1 TTTATTAATAAATATTTAAATTTATTTATGAATTAAATAA
* * **
527926 TCTGTTAATAAATATTTAAATTTATTTATGAATCGAATAA
1 TTTATTAATAAATATTTAAATTTATTTATGAATTAAATAA
527966 TT
1 TT
527968 AATTTTATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (40 bp):
TTTATTAATAAATATTTAAATTTATTTATGAATTAAATAA
Found at i:533851 original size:30 final size:30
Alignment explanation
Indices: 533815--533872 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
533805 AACATTTAGA
* *
533815 GTAAACTCAGTCGAA-AGATCTCGGGTTATG
1 GTAAACTCAATC-AAGAGATCTCAGGTTATG
533845 GTAAACTCAATCAAGAGATCTCAGGTTA
1 GTAAACTCAATCAAGAGATCTCAGGTTA
533873 CCTTGGCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (30 bp):
GTAAACTCAATCAAGAGATCTCAGGTTATG
Found at i:535863 original size:31 final size:31
Alignment explanation
Indices: 535828--535894 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
535818 ATATTTTATT
* *
535828 TAAATTTAATTA-TAATATCTAAATATTAATA
1 TAAATTTAATTATTAAT-TATAAATAATAATA
**
535859 TAAATTTTTTTATTAATTATAAATAATAATA
1 TAAATTTAATTATTAATTATAAATAATAATA
535890 TAAAT
1 TAAAT
535895 AATATAAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAATTTAATTATTAATTATAAATAATAATA
Found at i:536008 original size:18 final size:18
Alignment explanation
Indices: 535987--536027 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
535977 AGTTGACTTA
535987 TTTTTTAAATAAATTAAT
1 TTTTTTAAATAAATTAAT
** *
536005 TTTTTTATTTAAATTTAT
1 TTTTTTAAATAAATTAAT
536023 TTTTT
1 TTTTT
536028 AAACTGAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTAAATAAATTAAT
Found at i:537399 original size:16 final size:15
Alignment explanation
Indices: 537378--537452 Score: 53
Period size: 17 Copynumber: 4.5 Consensus size: 15
537368 ACGATATAAT
537378 TATATTTAAAATATTA
1 TATATTTAAAAT-TTA
537394 TATATTTTATAAATTT-
1 TATA-TTTA-AAATTTA
*
537410 TAACATATTAATAATTTA
1 T-ATAT-TTAA-AATTTA
*
537428 TATTATATAAAATTTAA
1 TA-TATTTAAAATTT-A
537445 TATATTTA
1 TATATTTA
537453 TTTATATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
16 17 0.36
17 23 0.49
18 7 0.15
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATTTAAAATTTA
Found at i:537437 original size:32 final size:29
Alignment explanation
Indices: 537389--537464 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 29
537379 ATATTTAAAA
* *
537389 TATTATATATTTTATAAATTTTAACATATT
1 TATT-TATATTATATAAAATTTAACATATT
*
537419 AATAATTTATATTATATAAAATTTAATATATT
1 --T-ATTTATATTATATAAAATTTAACATATT
537451 TATTTATATTATAT
1 TATTTATATTATAT
537465 TTATATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 13 0.32
30 1 0.03
32 23 0.57
33 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (29 bp):
TATTTATATTATATAAAATTTAACATATT
Found at i:537467 original size:11 final size:11
Alignment explanation
Indices: 537445--537473 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
537435 TAAAATTTAA
537445 TATATT-TATT
1 TATATTATATT
537455 TATATTATATT
1 TATATTATATT
537466 TATATTAT
1 TATATTAT
537474 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTATATT
Found at i:537982 original size:20 final size:18
Alignment explanation
Indices: 537957--538016 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 18
537947 TATAATATGA
537957 TATATAAATATCTTAAAATT
1 TATATAAA-AT-TTAAAATT
537977 TATATAAAA--T-AAA-T
1 TATATAAAATTTAAAATT
537991 TA-ATAAAATATTAAAATT
1 TATATAAAAT-TTAAAATT
538009 TATATAAA
1 TATATAAA
538017 TATATAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
13 6 0.18
14 3 0.09
15 3 0.09
16 2 0.06
17 3 0.09
18 3 0.09
19 6 0.18
20 8 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TATATAAAATTTAAAATT
Found at i:538015 original size:52 final size:53
Alignment explanation
Indices: 537918--538019 Score: 131
Period size: 52 Copynumber: 1.9 Consensus size: 53
537908 ATTTTTTTAA
*
537918 AAAATTATGATATAAAAAAATAATATAAATATAATATGATATATAAATATCTT
1 AAAATTATGATATAAAAAAATAATATAAATATAAAATGATATATAAATATCTT
*
537971 AAAATT-T-ATATAAAATAAATTAATA-AAATATTAAAAT-TTATATAAATAT
1 AAAATTATGATATAAAA-AAA-TAATATAAATA-TAAAATGATATATAAATAT
538020 ATAATATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
51 8 0.18
52 20 0.45
53 16 0.36
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (53 bp):
AAAATTATGATATAAAAAAATAATATAAATATAAAATGATATATAAATATCTT
Found at i:538017 original size:27 final size:26
Alignment explanation
Indices: 537985--538061 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 26
537975 TTTATATAAA
537985 ATAAATTAATAAAATATTAAAATTTAT
1 ATAAATT-ATAAAATATTAAAATTTAT
* *
538012 ATAAA-TATATAATATTTTAAATATTATT
1 ATAAATTATAAAATA-TTAAAAT-TTA-T
*
538040 ATAAATTATAAAATATAAAAAT
1 ATAAATTATAAAATATTAAAAT
538062 ATAAATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
25 7 0.17
26 7 0.17
27 8 0.20
28 11 0.27
29 8 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAAATTATAAAATATTAAAATTTAT
Found at i:538053 original size:54 final size:55
Alignment explanation
Indices: 537985--538091 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 55
537975 TTTATATAAA
* * * *
537985 ATAAATTAATAAAATATTAAAATTTATATA-AATATATAATATTTTAAA-TATTATT
1 ATAAATTAATAAAATATAAAAATATAAATATAATACA-AATA-TTTAAATTATTATT
538040 ATAAATT-ATAAAATATAAAAATATAAATATAATACAAATATTTAAATTATTA
1 ATAAATTAATAAAATATAAAAATATAAATATAATACAAATATTTAAATTATTA
538092 AAATGTAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
53 6 0.13
54 28 0.61
55 12 0.26
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (55 bp):
ATAAATTAATAAAATATAAAAATATAAATATAATACAAATATTTAAATTATTATT
Found at i:538093 original size:27 final size:26
Alignment explanation
Indices: 537986--538093 Score: 91
Period size: 27 Copynumber: 4.2 Consensus size: 26
537976 TTATATAAAA
537986 TAAAT-TAATAAAATATTAAAATTTAT
1 TAAATATAATAAAATATTAAAA-TTAT
* *
538012 ATAAATAT-ATAATATTTTAAATATTAT
1 -TAAATATAATAAAATATTAAA-ATTAT
* *
538039 TATAA-ATTATAAAATA-TAAAAATA-
1 TA-AATATAATAAAATATTAAAATTAT
*
538063 TAAATATAATACAAATATTTAAATTAT
1 TAAATATAATA-AAATATTAAAATTAT
538090 TAAA
1 TAAA
538094 ATGTAAGAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.03
24 7 0.11
25 8 0.12
26 14 0.22
27 32 0.49
28 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAATATAATAAAATATTAAAATTAT
Found at i:538343 original size:32 final size:33
Alignment explanation
Indices: 538307--538368 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
538297 TTTATTAATT
538307 TTTAATAT-ATTAATAATTT-ATATTATATAAAA
1 TTTAATATAATT-ATAATTTAATATTATATAAAA
*
538339 TTTAATATAATTATACTTTAATATTATATA
1 TTTAATATAATTATAATTTAATATTATATA
538369 TTTATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (33 bp):
TTTAATATAATTATAATTTAATATTATATAAAA
Found at i:538637 original size:20 final size:19
Alignment explanation
Indices: 538612--538652 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
538602 ATATTTTTAC
538612 ATATTATA-ATTATATCAAAA
1 ATATTATATATT-TAT-AAAA
538632 ATATTATATATTTATAAAA
1 ATATTATATATTTATAAAA
538651 AT
1 AT
538653 TTTGACAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 11 0.55
21 3 0.15
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTATATATTTATAAAA
Found at i:542214 original size:3 final size:3
Alignment explanation
Indices: 542206--542230 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
542196 CATTAACCAC
542206 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
542231 GAGATCATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:573429 original size:15 final size:16
Alignment explanation
Indices: 573409--573441 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
573399 AAATTTAATA
*
573409 AATTT-ATTTAAATTT
1 AATTTAATTAAAATTT
573424 AATTTAATTAAAATTT
1 AATTTAATTAAAATTT
573440 AA
1 AA
573442 AATAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTAATTAAAATTT
Found at i:573432 original size:10 final size:9
Alignment explanation
Indices: 573391--573426 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
573381 TTTTAACTCG
573391 AATTTAATA
1 AATTTAATA
573400 AATTTAATA
1 AATTTAATA
*
573409 AATTTATTTA
1 AATTTA-ATA
573419 AATTTAAT
1 AATTTAAT
573427 TTAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AATTTAATA
Found at i:573520 original size:22 final size:23
Alignment explanation
Indices: 573473--573521 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
573463 TTTATATTAA
573473 AAATATCAAATTTAATATAATTT
1 AAATATCAAATTTAATATAATTT
* *
573496 AAATATTAAATTTAAT-TGATTT
1 AAATATCAAATTTAATATAATTT
573518 AAAT
1 AAAT
573522 TAATTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATATCAAATTTAATATAATTT
Found at i:573668 original size:33 final size:35
Alignment explanation
Indices: 573630--573712 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 35
573620 ATAATTTAAA
573630 TTTAAATTTTAAAATGAGTCGAAA-TT-AAAAT-AG
1 TTTAAATTTTAAAATGA-TCGAAATTTAAAAATAAG
* * *
573663 TTTAAATATT-AAATGATCTAAATTTAAAAATAAT
1 TTTAAATTTTAAAATGATCGAAATTTAAAAATAAG
573697 TTTAAAATTTTAAAAT
1 TTT-AAATTTTAAAAT
573713 TTAAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 5 0.12
32 8 0.20
33 14 0.34
34 4 0.10
35 6 0.15
36 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (35 bp):
TTTAAATTTTAAAATGATCGAAATTTAAAAATAAG
Found at i:573690 original size:32 final size:33
Alignment explanation
Indices: 573630--573691 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
573620 ATAATTTAAA
*
573630 TTTAAATTTTAAAATGAGTCGAAATTAAAATAG
1 TTTAAATATTAAAATGAGTCGAAATTAAAATAG
*
573663 TTTAAATATT-AAATGA-TCTAAATTTAAAA
1 TTTAAATATTAAAATGAGTCGAAA-TTAAAA
573692 ATAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 5 0.19
32 12 0.46
33 9 0.35
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (33 bp):
TTTAAATATTAAAATGAGTCGAAATTAAAATAG
Found at i:574062 original size:18 final size:18
Alignment explanation
Indices: 574035--574076 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
574025 ACAATTTAAC
574035 AATT-ATTTAAAATAAAA
1 AATTAATTTAAAATAAAA
** *
574052 AATTAATTTAATTTAAAT
1 AATTAATTTAAAATAAAA
574070 AATTAAT
1 AATTAAT
574077 ATTTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTAATTTAAAATAAAA
Found at i:579557 original size:19 final size:20
Alignment explanation
Indices: 579535--579577 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
579525 TTATTAAAAT
579535 TTAATTATAAAAA-TATATA
1 TTAATTATAAAAATTATATA
579554 TTAA-TATAAAAATTATATA
1 TTAATTATAAAAATTATATA
579573 TTAAT
1 TTAAT
579578 AATATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTATAAAAATTATATA
Found at i:580249 original size:23 final size:23
Alignment explanation
Indices: 580223--580268 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
580213 ATTTCAAATT
580223 TTATAAAATAAAATCAAA-ATTTA
1 TTATAAAATAAAAT-AAATATTTA
**
580246 TTATATTATAAAATAAATATTTA
1 TTATAAAATAAAATAAATATTTA
580269 GTAAATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TTATAAAATAAAATAAATATTTA
Found at i:582157 original size:13 final size:13
Alignment explanation
Indices: 582141--582165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
582131 TAACGATTAA
582141 ATTTAAAAAATAT
1 ATTTAAAAAATAT
582154 ATTTAAAAAATA
1 ATTTAAAAAATA
582166 AAATAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTTAAAAAATAT
Found at i:582269 original size:17 final size:16
Alignment explanation
Indices: 582233--582270 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
582223 ATAAAATTTA
582233 AAATTAATATTTTTTT
1 AAATTAATATTTTTTT
582249 AAATATAAT-TTTTTATT
1 AAAT-TAATATTTTT-TT
582266 AAATT
1 AAATT
582271 TTAACATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTAATATTTTTTT
Found at i:582978 original size:2 final size:2
Alignment explanation
Indices: 582971--582998 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
582961 AAAGTTTTCC
582971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
582999 CTGTTTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:588091 original size:79 final size:78
Alignment explanation
Indices: 587947--588193 Score: 264
Period size: 79 Copynumber: 3.1 Consensus size: 78
587937 TTTTGGAGAT
* * * * * *
587947 AATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATG-ATTAGGAAATGAAATCGGGATTG
1 AATAAC-GGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTA-GAAATAAAACCGGGGTTG
* *
588011 GAGTATCCCCTTGGA
64 GAGTATCCCCTCGAA
** * *
588026 AATAACGGGATTAAAGTATTCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGG
1 AATAACGGG-TTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGGGTTGG
588091 AGTATCCCCTCGAA
65 AGTATCCCCTCGAA
* * * *
588105 AATAACAGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTA-AGAATAAAGCCGGGGTTG
1 AATAAC-GGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGA-AATAAAACCGGGGTTG
* *
588169 GAGTACCCCCGCGAA
64 GAGTATCCCCTCGAA
*
588184 AATAATGGGT
1 AATAACGGGT
588194 GTTTTAGAAA
Statistics
Matches: 141, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
78 8 0.06
79 127 0.90
80 6 0.04
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (78 bp):
AATAACGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGA
GTATCCCCTCGAA
Found at i:588219 original size:128 final size:128
Alignment explanation
Indices: 588065--588316 Score: 380
Period size: 128 Copynumber: 2.0 Consensus size: 128
588055 GAAAAATTGA
*
588065 TGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGA
1 TGTTTTAGAAATAAAACCGGGATTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGA
*
588130 TTATGAGAAATCAATATTTTA-AGAATAAAGCCGGGGTTGGAGTACCCCCGCGAAAATAATGGG
66 TTATGAGAAATCAATATTTTAGA-AATAAAACCGGGGTTGGAGTACCCCCGCGAAAATAATGGG
* * * * *
588193 TGTTTTAGAAATAAAATCGGGATTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGA
1 TGTTTTAGAAATAAAACCGGGATTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGA
* * * * *
588258 TTATGAGAAATTAGTATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAA
66 TTATGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTACCCCCGCGAAAATAA
588317 CGGGGTTGGA
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
128 110 0.99
129 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (128 bp):
TGTTTTAGAAATAAAACCGGGATTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGA
TTATGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTACCCCCGCGAAAATAATGGG
Found at i:588298 original size:79 final size:80
Alignment explanation
Indices: 588195--588386 Score: 264
Period size: 79 Copynumber: 2.4 Consensus size: 80
588185 ATAATGGGTG
* * * * *
588195 TTTTAGAAATAAAATCGGGATTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATT
1 TTTTAGAAATAAAACCGGGGTTGGAGTATTCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATG
**
588260 ATGAG-AAATTAGTA
66 AAAAGAAAATTAGTA
*
588274 TTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATG
1 TTTTAGAAATAAAACCGGGGTTGGAGTATTCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATG
* *
588339 AAAAGAAAATTGGTG
66 AAAAGAAAATTAGTA
588354 TTTT-GAAAATAAAACCGGGGTTGGAGTA-TCCCT
1 TTTTAG-AAATAAAACCGGGGTTGGAGTATTCCCT
588387 GATTGTGAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
79 67 0.67
80 33 0.33
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (80 bp):
TTTTAGAAATAAAACCGGGGTTGGAGTATTCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATG
AAAAGAAAATTAGTA
Found at i:588417 original size:51 final size:51
Alignment explanation
Indices: 588317--588751 Score: 317
Period size: 51 Copynumber: 8.4 Consensus size: 51
588307 TCGGAAATAA
* **
588317 CGGGGTTGGAGTATCCCC-AATGAAAAGAAAATTGGTGTTTT-GAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTG--TGGAAAATTGGTGTTTTAG-AAATAAAAC
* * * *
588369 CGGGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTAGAGATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAAC
* * * * * *
588420 CGGGGTTGAAGTATCCCCGATTATGGAAAATTGATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAAC
** * ** * *
588471 CGGGGTTGGAGTATCCCC--TTG-GAGGTAA-TGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATTGTG-GAAAATTGGTGTTTTAG-A-----AAT-AAA-AC
* * * * * * *
588527 CGAGATTGGAGTATCCTCGCTTGTGAAAAATTGGTGTTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTG--TTTTAGAAATAAAAC
* * **
588580 CGGAGTTGGAGTATCCCTGATTAAAGGAAAATTGGTGTTTT-GAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-GTGGAAAATTGGTGTTTTAG-AAATAAAAC
* * *
588632 CGAGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAGATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAAC
* * * * **
588683 CGGGGTTGGAGTATCCCCGATTATGGAAAATTGATATTTTGGAAATAACGC
1 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAAC
588734 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
588752 TCGGAGGCAA
Statistics
Matches: 295, Mismatches: 68, Indels: 41
0.73 0.17 0.10
Matches are distributed among these distances:
48 6 0.02
49 6 0.02
51 163 0.55
52 50 0.17
53 20 0.07
54 16 0.05
55 5 0.02
56 15 0.05
58 5 0.02
59 5 0.02
60 1 0.00
61 3 0.01
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAAC
Done.