Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008637.1 Hibiscus syriacus cultivar Beakdansim tig00111610_pilon, whole genome shotgun sequence
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: 80779
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15142 original size:11 final size:11
Alignment explanation
Indices: 15126--15150 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15116 TAAAAAAATA
15126 CCCCTTAGCAG
1 CCCCTTAGCAG
15137 CCCCTTAGCAG
1 CCCCTTAGCAG
15148 CCC
1 CCC
15151 ATGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (11 bp):
CCCCTTAGCAG
Found at i:18471 original size:15 final size:16
Alignment explanation
Indices: 18443--18474 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
18433 AAAATCTTTC
18443 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
18459 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
18474 T
1 T
18475 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:19249 original size:16 final size:16
Alignment explanation
Indices: 19225--19257 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19215 TATCGCCGAC
*
19225 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
19241 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
19257 C
1 C
19258 TTGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:26286 original size:65 final size:65
Alignment explanation
Indices: 26122--26310 Score: 319
Period size: 65 Copynumber: 2.9 Consensus size: 65
26112 TAACACAGAT
* *
26122 AACCACATT-TATTTAGGCCTTACTATTCCTAGTCCTTAATATTTTCTAACAATTTC-AAAGCAA
1 AACCACATTCTATTTAGGCCTTACTATTCCTAGTCCTTAATATTTTATAACAATTTCAAAAACAA
*
26185 AACCACATTCTATTTATGCCTTACTATTCCTAGTCCTTAATATTTTATAACAATTTCAAAAACAA
1 AACCACATTCTATTTAGGCCTTACTATTCCTAGTCCTTAATATTTTATAACAATTTCAAAAACAA
* *
26250 AACCAAATTCTATTTAGGCCTTACTATTCCTAGTCCTTAATATTTTGTAACAATTTCAAAA
1 AACCACATTCTATTTAGGCCTTACTATTCCTAGTCCTTAATATTTTATAACAATTTCAAAA
26311 GCTGGGGTGC
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
63 9 0.08
64 45 0.38
65 64 0.54
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (65 bp):
AACCACATTCTATTTAGGCCTTACTATTCCTAGTCCTTAATATTTTATAACAATTTCAAAAACAA
Found at i:26564 original size:36 final size:36
Alignment explanation
Indices: 26524--26600 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
26514 CACTCCCAGC
* *
26524 GAGATGACTGGTATTGGAAGGCTTAAGCACAATATA
1 GAGATGACTGGTATCGGAAGGCTGAAGCACAATATA
* *
26560 GAGATGACTGGTATCGGAAGGCTGAAGGACAATATG
1 GAGATGACTGGTATCGGAAGGCTGAAGCACAATATA
26596 GAGAT
1 GAGAT
26601 CAAAGAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.22
Consensus pattern (36 bp):
GAGATGACTGGTATCGGAAGGCTGAAGCACAATATA
Found at i:28154 original size:23 final size:23
Alignment explanation
Indices: 28128--28176 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
28118 TTGCCTGACA
*
28128 AAATTTTAA-ATATTAATATAATT
1 AAATTATAATATATTAAT-TAATT
*
28151 AAATTATAATATATTAATTATTT
1 AAATTATAATATATTAATTAATT
28174 AAA
1 AAA
28177 ACAACTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATTATAATATATTAATTAATT
Found at i:30539 original size:22 final size:22
Alignment explanation
Indices: 30514--30555 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30504 ATTCAATGGT
*
30514 TAATA-TTTATATATGTTACAAA
1 TAATAGTTTAAATAT-TTACAAA
30536 TAATAGTTTAAATATTTACA
1 TAATAGTTTAAATATTTACA
30556 TCGTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
TAATAGTTTAAATATTTACAAA
Found at i:34519 original size:23 final size:23
Alignment explanation
Indices: 34491--34548 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
34481 AAATTAATAA
34491 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
34514 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
34537 TATA--ATGTAAAA
1 TATATTATGTAAAA
34549 ATTATAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:34591 original size:13 final size:14
Alignment explanation
Indices: 34566--34594 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34556 CTAATAATAT
34566 TAAATATTATTAAA
1 TAAATATTATTAAA
34580 TAAATA-TATTAAA
1 TAAATATTATTAAA
34593 TA
1 TA
34595 TATTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATATTATTAAA
Found at i:37600 original size:8 final size:8
Alignment explanation
Indices: 37587--37627 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
37577 CTCATTTTCA
37587 GAGAATTT
1 GAGAATTT
37595 GAGAATTT
1 GAGAATTT
*
37603 -AGAGTTT
1 GAGAATTT
*
37610 GGGAATTT
1 GAGAATTT
37618 GAGAATTT
1 GAGAATTT
37626 GA
1 GA
37628 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:37920 original size:126 final size:126
Alignment explanation
Indices: 37695--38425 Score: 1408
Period size: 126 Copynumber: 5.8 Consensus size: 126
37685 CTATAATCGG
37695 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
37760 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
37821 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
37886 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
37947 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
38012 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
38073 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
38138 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
38199 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
38264 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACATACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
38325 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
38390 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
38426 ATAACTTAAA
Statistics
Matches: 601, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 601 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
Found at i:38873 original size:33 final size:34
Alignment explanation
Indices: 38812--38911 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
38802 AAATTTAATG
*
38812 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
38846 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
38879 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
38912 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:39545 original size:21 final size:21
Alignment explanation
Indices: 39437--39542 Score: 160
Period size: 21 Copynumber: 5.0 Consensus size: 21
39427 ATAAAACCCT
*
39437 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
39458 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
39479 GCGGGCTAGGAATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
39500 GCGGGCTAGGAATGTAACCAT-
1 GCGGGCTAGGAATGTAACC-TG
*
39521 GCGGGCTCGGAATGTAATCCTG
1 GCGGGCTAGGAATGTAA-CCTG
39543 CGGAGATGGC
Statistics
Matches: 80, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
21 77 0.96
22 3 0.04
ACGTcount: A:0.22, C:0.22, G:0.37, T:0.20
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:39569 original size:63 final size:63
Alignment explanation
Indices: 39437--39569 Score: 146
Period size: 63 Copynumber: 2.1 Consensus size: 63
39427 ATAAAACCCT
* * * * *
39437 GCGGGCTAGGCATGTAACCTGGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGTAACCTG
1 GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCTGGCGGGATAGGAATATAAACTG
* *
39500 GCGGGCTAGGAATGTAACCAT-GCGGGCTCGGAATGTAATCCT-GCGGAGAT-GGCATATAAACT
1 GCGGGCTAGGAATGTAACC-TGGCGGGCTAGGAATGTAA-CCTGGCGG-GATAGGAATATAAACT
39562 G
63 G
*
39563 GTGGGCT
1 GCGGGCT
39570 TGGCATATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
63 53 0.90
64 6 0.10
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (63 bp):
GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCTGGCGGGATAGGAATATAAACTG
Found at i:39575 original size:21 final size:21
Alignment explanation
Indices: 39549--39596 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
39539 CCTGCGGAGA
*
39549 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
39570 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
39591 GGGCAT
1 TGGCAT
39597 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:41388 original size:34 final size:33
Alignment explanation
Indices: 41316--41423 Score: 110
Period size: 34 Copynumber: 3.2 Consensus size: 33
41306 TAATAATTCT
* * * *
41316 AAATAAATAATAATTATATAAATATTATTTTAA
1 AAATAAATAATATTTAAATAAATATTAATATAA
* *
41349 TAATAAAATAATATTTACATAAATATTAATATAA
1 AAAT-AAATAATATTTAAATAAATATTAATATAA
* * *
41383 AAAT-AATAACTATTTAAAAAAATACTAACATAA
1 AAATAAATAA-TATTTAAATAAATATTAATATAA
41416 AAATAAAT
1 AAATAAAT
41424 TTCTTACCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
32 5 0.08
33 26 0.42
34 31 0.50
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (33 bp):
AAATAAATAATATTTAAATAAATATTAATATAA
Found at i:41406 original size:33 final size:32
Alignment explanation
Indices: 41355--41421 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 32
41345 TTAATAATAA
* * * *
41355 AATAATATTTACATAAATATTAATATAAAAAT
1 AATAATATTTAAAAAAATACTAACATAAAAAT
41387 AATAACTATTTAAAAAAATACTAACATAAAAAT
1 AATAA-TATTTAAAAAAATACTAACATAAAAAT
41420 AA
1 AA
41422 ATTTCTTACC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 5 0.17
33 25 0.83
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (32 bp):
AATAATATTTAAAAAAATACTAACATAAAAAT
Found at i:46245 original size:2 final size:2
Alignment explanation
Indices: 46238--46264 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46228 ACATGGGGGT
46238 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
46265 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:47921 original size:13 final size:13
Alignment explanation
Indices: 47892--47926 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
47882 ATAACTAATA
*
47892 ATATTAAAT-ATT
1 ATATTAAATAAAT
47904 ATATTAAATAAAT
1 ATATTAAATAAAT
47917 ATATTAAATA
1 ATATTAAATA
47927 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:48736 original size:128 final size:128
Alignment explanation
Indices: 48508--49090 Score: 1107
Period size: 128 Copynumber: 4.6 Consensus size: 128
48498 AACAATTCAC
48508 GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCC
1 GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCC
48573 CTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGG
66 CTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGG
*
48636 GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTAATGTCC
1 GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCC
*
48701 CTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGT
66 CTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGG
*
48764 GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATATCC
1 GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCC
48829 CTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGG
66 CTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGG
*
48892 GGGCGCGCCTTCCATTATTTCGTTAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCC
1 GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCC
48957 CTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGG
66 CTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGG
*
49020 GGGCGCGCCTTCCATTATTT--TCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCC
1 GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCC
49083 CTCGGGGA
66 CTCGGGGA
49091 ATAACTTAAA
Statistics
Matches: 446, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
126 49 0.11
128 397 0.89
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (128 bp):
GGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCATTCATGTCC
CTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGG
Found at i:49539 original size:33 final size:34
Alignment explanation
Indices: 49478--49577 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
49468 AAATTTAATG
*
49478 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
49512 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
49545 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
49578 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:50027 original size:21 final size:21
Alignment explanation
Indices: 50003--50084 Score: 112
Period size: 21 Copynumber: 3.9 Consensus size: 21
49993 ATAAAACCCT
*
50003 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
50024 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
50045 GCGGGCTAGGAAGGTAACCAT-
1 GCGGGCTAGGAATGTAACC-TG
*
50066 GCGGGCTCGGAATGTAACC
1 GCGGGCTAGGAATGTAACC
50085 CTGCGGAGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
21 55 0.98
22 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.38, T:0.17
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:50089 original size:21 final size:21
Alignment explanation
Indices: 49997--50090 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
49987 TATGGTATAA
*
49997 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
50018 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
*
50039 AA-CCTGGCGGGCTAGGAAGGT
1 AACCCT-GCGGGCTAGGAATGT
* *
50060 AACCATGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
50081 AACCCTGCGG
1 AACCCTGCGG
50091 AGATGGCATA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.05
21 60 0.92
22 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.36, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:50120 original size:21 final size:21
Alignment explanation
Indices: 50094--50141 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
50084 CCTGCGGAGA
*
50094 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
50115 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
50136 GGGCAT
1 TGGCAT
50142 GTACCCCTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:51928 original size:30 final size:32
Alignment explanation
Indices: 51864--51941 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 32
51854 TTAATAATTC
*
51864 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
51898 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
51928 TATAAAAATAATAA
1 TA-AAAAATAATAA
51942 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 6 0.15
31 10 0.25
32 2 0.05
33 18 0.45
34 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:51966 original size:16 final size:18
Alignment explanation
Indices: 51925--51971 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 18
51915 ATAAATATAT
51925 TAATATAAAAATAATAAC
1 TAATATAAAAATAATAAC
*
51943 T-ATTTAAAAA-AAT-AC
1 TAATATAAAAATAATAAC
51958 TAATATAAAAATAA
1 TAATATAAAAATAA
51972 ATTTCTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 3 0.12
16 11 0.44
17 10 0.40
18 1 0.04
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATATAAAAATAATAAC
Found at i:51967 original size:33 final size:34
Alignment explanation
Indices: 51899--51971 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
51889 TTATTTTAAT
* *
51899 AAAA-AATAATATTTACATAAATATATTAATATA
1 AAAATAATAATATTTACATAAAAATACTAATATA
51932 AAAATAATAACTATTTA-A-AAAAATACTAATATA
1 AAAATAATAA-TATTTACATAAAAATACTAATATA
51965 AAAATAA
1 AAAATAA
51972 ATTTCTTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
33 24 0.67
34 6 0.17
35 6 0.17
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (34 bp):
AAAATAATAATATTTACATAAAAATACTAATATA
Found at i:53984 original size:21 final size:21
Alignment explanation
Indices: 53959--54005 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
53949 CTGAAAATAT
*
53959 TAAAAATATTAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
53980 TAAAAATAATAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
54001 TAAAA
1 TAAAA
54006 TTTTACTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:56098 original size:17 final size:19
Alignment explanation
Indices: 56071--56105 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
56061 AAGTATAAGA
56071 ATTTATTT-AAAATTAATC
1 ATTTATTTAAAAATTAATC
56089 ATTT-TTTAAAAATTAAT
1 ATTTATTTAAAAATTAAT
56106 TATAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTATTTAAAAATTAATC
Found at i:57011 original size:18 final size:19
Alignment explanation
Indices: 56947--57015 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
56937 TGAATAATGA
* *
56947 TAATATTAATTTTGATACGC
1 TAATTTTAATTTTGAT-CGT
* *
56967 AAATTTTAATATTGATCGT
1 TAATTTTAATTTTGATCGT
56986 TAATTTTAATTTTGAT-GCT
1 TAATTTTAATTTTGATCG-T
57005 T-ATTTTAATTT
1 TAATTTTAATTT
57016 GATATTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
18 11 0.26
19 18 0.43
20 13 0.31
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.54
Consensus pattern (19 bp):
TAATTTTAATTTTGATCGT
Found at i:57024 original size:17 final size:17
Alignment explanation
Indices: 56969--57027 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
56959 TGATACGCAA
*
56969 ATTTTAATATTGATCGTTA
1 ATTTTAAT-TTGAT-GTTT
*
56988 ATTTTAATTTTGATGCTT
1 ATTTTAA-TTTGATGTTT
*
57006 ATTTTAATTTGATATTT
1 ATTTTAATTTGATGTTT
57023 ATTTT
1 ATTTT
57028 TATTATTGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 13 0.37
18 9 0.26
19 12 0.34
20 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.61
Consensus pattern (17 bp):
ATTTTAATTTGATGTTT
Found at i:57029 original size:18 final size:17
Alignment explanation
Indices: 56969--57027 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 17
56959 TGATACGCAA
56969 ATTTTAATATTGAT-CGTT
1 ATTTTAAT-TTGATAC-TT
*
56987 AATTTTAATTTTGATGCTT
1 -ATTTTAA-TTTGATACTT
*
57006 ATTTTAATTTGATATTT
1 ATTTTAATTTGATACTT
57023 ATTTT
1 ATTTT
57028 TATTATTGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 13 0.36
18 7 0.19
19 14 0.39
20 2 0.06
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.61
Consensus pattern (17 bp):
ATTTTAATTTGATACTT
Found at i:57046 original size:17 final size:17
Alignment explanation
Indices: 57026--57058 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57016 GATATTTATT
*
57026 TTTATTATTGCTTTTGA
1 TTTATTATTGATTTTGA
57043 TTTATTATTGATTTTG
1 TTTATTATTGATTTTG
57059 CTCAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.67
Consensus pattern (17 bp):
TTTATTATTGATTTTGA
Found at i:57618 original size:29 final size:30
Alignment explanation
Indices: 57564--57625 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
57554 AAATTTGGAC
*
57564 TAGTGACTAAAATATAAGTTTAGAAAA-TT
1 TAGTGACTAAAATATAACTTTAGAAAAGTT
* *
57593 TAGTGGCTAAAGTATAAACTTT-GAAAAGTT
1 TAGTGACTAAAATAT-AACTTTAGAAAAGTT
57623 TAG
1 TAG
57626 GACCCAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.34
Consensus pattern (30 bp):
TAGTGACTAAAATATAACTTTAGAAAAGTT
Found at i:68722 original size:15 final size:14
Alignment explanation
Indices: 68702--68753 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
68692 AATAAATCAA
68702 TAATTTATTATTTAT
1 TAATTT-TTATTTAT
*
68717 TAATTTTTATTATAC
1 TAATTTTTATT-TAT
68732 TAATTTTT-TTTAT
1 TAATTTTTATTTAT
68745 TAATTTTTA
1 TAATTTTTA
68754 CAGTTATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 10 0.30
14 7 0.21
15 16 0.48
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TAATTTTTATTTAT
Found at i:68902 original size:34 final size:33
Alignment explanation
Indices: 68839--68908 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
68829 AATTTTAAAT
* *
68839 TTTGTTGTAATTTTAATTATTGTTAATATTTTA
1 TTTGTTGTAATTTTAAGTATTGTTAATATTTAA
* *
68872 TTTGTT-TAATTTTTTAGTATTAGTTTATATTTAA
1 TTTGTTGTAA-TTTTAAGTATT-GTTAATATTTAA
68906 TTT
1 TTT
68909 CTATAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 3 0.10
33 15 0.48
34 13 0.42
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (33 bp):
TTTGTTGTAATTTTAAGTATTGTTAATATTTAA
Found at i:73434 original size:75 final size:75
Alignment explanation
Indices: 73347--73677 Score: 375
Period size: 75 Copynumber: 4.4 Consensus size: 75
73337 TCTTACTGGT
* * *
73347 TAAAATAAAATAGGCGCTACATATTATGTTAAACTACCTACCGGTTTGTTTGAAA-ATTACTAGT
1 TAAAATAAAATAGGCGCTACATATTACGTTAAACTACCTACCGATTTGTTT-AAAGATTACTAAT
73411 AATATAAACGG
65 AATATAAACGG
* * * * *
73422 TAAAATAAAATAGGTGCTACATATCACGTTAAATTACCTACTGGTTTGTTTAAA-AGTTACTAAT
1 TAAAATAAAATAGGCGCTACATATTACGTTAAACTACCTACCGATTTGTTTAAAGA-TTACTAAT
* *
73486 AATGTAAACGT
65 AATATAAACGG
* * * * *
73497 TAAAA-AAAA-ACGCACTACCTATTACCTTAAACTACCTACCGATTTGTTTAAAGATTATTAATA
1 TAAAATAAAATAGGCGCTACATATTACGTTAAACTACCTACCGATTTGTTTAAAGATTACTAATA
*
73560 ATATAAACGA
66 ATATAAACGG
* * * * * *
73570 TAAAATAAAATATGTGCTACCA-ATTACGTTAAACTAACTACCAATTTGTTTAAAGGTTAATAAT
1 TAAAATAAAATAGGCGCTA-CATATTACGTTAAACTACCTACCGATTTGTTTAAAGATTACTAAT
*
73634 AATATAAGCGG
65 AATATAAACGG
* *
73645 TAAAATAAAATAGGCGCTACCTATTATGTTAAA
1 TAAAATAAAATAGGCGCTACATATTACGTTAAA
73678 TAGGTGATAT
Statistics
Matches: 215, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
73 55 0.26
74 14 0.07
75 145 0.67
76 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.32
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACATATTACGTTAAACTACCTACCGATTTGTTTAAAGATTACTAATA
ATATAAACGG
Found at i:73562 original size:148 final size:150
Alignment explanation
Indices: 73347--73670 Score: 395
Period size: 148 Copynumber: 2.2 Consensus size: 150
73337 TCTTACTGGT
* * * ** * *
73347 TAAAATAAAATAGGCGCTACATATTATGTTAAACTACCTACCGGTTTGTTTGAAAATTACTAGTA
1 TAAAATAAAATACGCACTACCTATTACCTTAAACTACCTACCGATTTGTTTGAAAATTACTAATA
* * * ***
73412 ATATAAACGGTAAAATAAAATAGGTGCTA-CATATCACGTTAAATTACCTACTGGTTTGTTTAAA
66 ATATAAACGATAAAATAAAATAGGTGCTACCA-ATCACGTTAAACTAACTACCAATTTGTTTAAA
* * *
73476 AGTTACTAATAATGTAAACGT
130 AGTTAATAATAATATAAACGG
*
73497 TAAAA-AAAA-ACGCACTACCTATTACCTTAAACTACCTACCGATTTGTTT-AAAGATTATTAAT
1 TAAAATAAAATACGCACTACCTATTACCTTAAACTACCTACCGATTTGTTTGAAA-ATTACTAAT
* *
73559 AATATAAACGATAAAATAAAATATGTGCTACCAATTACGTTAAACTAACTACCAATTTGTTTAAA
65 AATATAAACGATAAAATAAAATAGGTGCTACCAATCACGTTAAACTAACTACCAATTTGTTTAAA
* *
73624 GGTTAATAATAATATAAGCGG
130 AGTTAATAATAATATAAACGG
* *
73645 TAAAATAAAATAGGCGCTACCTATTA
1 TAAAATAAAATACGCACTACCTATTA
73671 TGTTAAATAG
Statistics
Matches: 147, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
147 3 0.02
148 116 0.79
149 10 0.07
150 18 0.12
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.32
Consensus pattern (150 bp):
TAAAATAAAATACGCACTACCTATTACCTTAAACTACCTACCGATTTGTTTGAAAATTACTAATA
ATATAAACGATAAAATAAAATAGGTGCTACCAATCACGTTAAACTAACTACCAATTTGTTTAAAA
GTTAATAATAATATAAACGG
Found at i:73678 original size:23 final size:23
Alignment explanation
Indices: 73652--73723 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
73642 CGGTAAAATA
*
73652 AAATAGGCGCTACCTATTATGTT
1 AAATAGGCGCTACCTATTAAGTT
* * *
73675 AAATAGGTGATATCTATTAAGTT
1 AAATAGGCGCTACCTATTAAGTT
* *
73698 AAATAAGCGCTACCTATTACGTT
1 AAATAGGCGCTACCTATTAAGTT
73721 AAA
1 AAA
73724 CTAGCTACTA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (23 bp):
AAATAGGCGCTACCTATTAAGTT
Found at i:73936 original size:153 final size:151
Alignment explanation
Indices: 73766--74040 Score: 410
Period size: 153 Copynumber: 1.8 Consensus size: 151
73756 TTGTAAACGG
* ** * *
73766 TAAAATATATATAACTTAACCGTTTGAAATATATTTTTTAAATTCGAAAGTAT-ATATACTTAGT
1 TAAAATATATACAACTTAACAATTTAAAATATATTTTTTAAATTCGAAAGTATGA-ATACTTACT
* *
73830 CTAAAAGTATTGATACTCTAAA-GTTTAATAATAATGTATCCATACGTACTCTAAAAGTATAAAT
65 CTAAAACTATAGATA--CTAAATG-TTAATAATAATGTATCCATACGTACTCTAAAAGTATAAAT
73894 ACTATTTCGATTGTAATATAATCGA
127 ACTATTTCGATTGTAATATAATCGA
* *
73919 TAAAATATATACAACTTAACAATTTAAAATATTTTTTTTAAATTCGAAAGTATGAATTCTTACTC
1 TAAAATATATACAACTTAACAATTTAAAATATATTTTTTAAATTCGAAAGTATGAATACTTACTC
*
73984 TAAAACTATAGATACTAAATGTTAATAATAATGTATCCATACTTACTCTAAAAGTAT
66 TAAAACTATAGATACTAAATGTTAATAATAATGTATCCATACGTACTCTAAAAGTAT
74041 TGATATTTGC
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
151 40 0.36
152 1 0.01
153 68 0.62
154 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.39
Consensus pattern (151 bp):
TAAAATATATACAACTTAACAATTTAAAATATATTTTTTAAATTCGAAAGTATGAATACTTACTC
TAAAACTATAGATACTAAATGTTAATAATAATGTATCCATACGTACTCTAAAAGTATAAATACTA
TTTCGATTGTAATATAATCGA
Found at i:74640 original size:226 final size:224
Alignment explanation
Indices: 74243--74925 Score: 743
Period size: 225 Copynumber: 3.0 Consensus size: 224
74233 CAAAATAAGA
* * * * *
74243 AATTAACATATTTTGTTGTCGTGGGATTT-TGAAGG-TCCCATCATCTTAAAC-TTGGTAATATT
1 AATTAACATATTTTGTTATCGTCGGATTTCT-AAGGCT-CTATCAACTTAAACTTTGGTAACATT
* * * ** * *
74305 TTAGGCGCTATTTAATATGTTGATAATATTAATAACAAAATAAAAAATCAACCTATTTTGTTATC
64 TTAGACGCTACTTAATATGTTGATAATATTGATAAC-AAATAAGTAATTAACATATTTTGTTATC
* * * * *
74370 GTCGAATTTCTAAGGA-CTCATCAGCTTTAAAAAGATGTTATCTATCACATTAAATAAACGCTAC
128 GTCGGATTTCTAA-GACCCCATCA-CTTTAAAAAGGTGCTATCTATTACATTAAATAAACGCTAC
* *
74434 TTGTTATGTTATTATGGATGATAATGTTTCCAAT
191 TTGTTATGTTATTATGGATGATAATATTTACAAT
* * *
74468 AATTAACATATTTTGTCATCGTCGGATTTCTAAGGCTTTATCAGCTTAAACTTTGGTAACATTTT
1 AATTAACATATTTTGTTATCGTCGGATTTCTAAGGCTCTATCAACTTAAACTTTGGTAACATTTT
* *
74533 AGACGTTACTTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATAGT
66 AGACGCTACTTAATATGTTGATAATATTGATAACAAAT-AAGTAATTAACATATTTTGTTATCGT
* * * * *
74598 CGGATTTTTAAGACCCCATCGATTTTAAAAAGGCGGTATCTATTACATTAAATAAACGCAACTTG
130 CGGATTTCTAAGACCCCATC-ACTTTAAAAAGGTGCTATCTATTACATTAAATAAACGCTACTTG
* *
74663 TTATGTTATTATGGTTGAT-ATATTTATAAT
194 TTATGTTATTATGGATGATAATATTTACAAT
* * * * *
74693 AATTAATCA-GTTATGTTATCGTCGGATTTCTAAAGCTCTATCAACTTAAATTTTGGTATCATTT
1 AATTAA-CATATTTTGTTATCGTCGGATTTCTAAGGCTCTATCAACTTAAACTTTGGTAACATTT
* * *
74757 TAGGA-GCTACCTAATATGTTGATAATATTGATAAAAAATTAAGTAATTAACTTATTTTGTTATC
65 TA-GACGCTACTTAATATGTTGATAATATTGATAACAAA-TAAGTAATTAACATATTTTGTTATC
* * * * * * * * * * *
74821 GTCGGATTTCTAAGACTCTATCAACTTTAAAAAAGTGCTACCTGTTACGTTATATGAGCTCTACA
128 GTCGGATTTCTAAGACCCCATC-ACTTTAAAAAGGTGCTATCTATTACATTAAATAAACGCTACT
*
74886 TGTTATGTTATTAT-GATTGATAATATTTTCAAT
192 TGTTATGTTATTATGGA-TGATAATATTTACAAT
74919 AATTAAC
1 AATTAAC
74926 TGATTATGTT
Statistics
Matches: 385, Mismatches: 62, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
224 1 0.00
225 229 0.59
226 154 0.40
227 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (224 bp):
AATTAACATATTTTGTTATCGTCGGATTTCTAAGGCTCTATCAACTTAAACTTTGGTAACATTTT
AGACGCTACTTAATATGTTGATAATATTGATAACAAATAAGTAATTAACATATTTTGTTATCGTC
GGATTTCTAAGACCCCATCACTTTAAAAAGGTGCTATCTATTACATTAAATAAACGCTACTTGTT
ATGTTATTATGGATGATAATATTTACAAT
Found at i:79145 original size:13 final size:13
Alignment explanation
Indices: 79123--79177 Score: 92
Period size: 13 Copynumber: 4.2 Consensus size: 13
79113 ATATTAATAT
79123 AATATATTTTTGAA
1 AATAT-TTTTTGAA
79137 AATATTTTTTGAA
1 AATATTTTTTGAA
*
79150 AATATTTTTTGGA
1 AATATTTTTTGAA
79163 AATATTTTTTGAA
1 AATATTTTTTGAA
79176 AA
1 AA
79178 CATATAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
13 34 0.87
14 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
AATATTTTTTGAA
Done.