Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017970.1 Corchorus olitorius cultivar O-4 contig18003, 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: 81126
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2281 original size:19 final size:19
Alignment explanation
Indices: 2257--2293 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2247 CTGTTTGGCA
2257 ACTGTACAGATAAGATTAC
1 ACTGTACAGATAAGATTAC
*
2276 ACTGTACAGATTAGATTA
1 ACTGTACAGATAAGATTA
2294 TGTACTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATAAGATTAC
Found at i:3013 original size:17 final size:17
Alignment explanation
Indices: 2993--3031 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2983 ATTATTAGTT
2993 ATATATAATTACTAAGG
1 ATATATAATTACTAAGG
3010 ATATATAATTACTAAGG
1 ATATATAATTACTAAGG
3027 ATATA
1 ATATA
3032 ATTTGGGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (17 bp):
ATATATAATTACTAAGG
Found at i:4378 original size:104 final size:104
Alignment explanation
Indices: 4198--4398 Score: 339
Period size: 104 Copynumber: 1.9 Consensus size: 104
4188 GGATTTTTTT
* ** * *
4198 CTGACTAATCCGGATCCGATCCGTATCGCACACCTGGTTATGGTGGGTGAGTCTCCCAACAGGGC
1 CTGACTAATCCGGATCCGATCCGCATCGCACACCTAATTATGGTGAGTGAGTCTCCCAACAGAGC
4263 CTTTTGATTATTCATAAATGATCTCGTAATATTAAAACC
66 CTTTTGATTATTCATAAATGATCTCGTAATATTAAAACC
* *
4302 CTGACTAATCCGGATCCGATCCGCATCGCTCACTTAATTATGGTGAGTGAGTCTCCCAACAGAGC
1 CTGACTAATCCGGATCCGATCCGCATCGCACACCTAATTATGGTGAGTGAGTCTCCCAACAGAGC
4367 CTTTTGATTATTCATAAATGATCTCGTAATAT
66 CTTTTGATTATTCATAAATGATCTCGTAATAT
4399 GATGAAATTT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 90 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (104 bp):
CTGACTAATCCGGATCCGATCCGCATCGCACACCTAATTATGGTGAGTGAGTCTCCCAACAGAGC
CTTTTGATTATTCATAAATGATCTCGTAATATTAAAACC
Found at i:5980 original size:10 final size:10
Alignment explanation
Indices: 5959--5987 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5949 CCAATCTGAC
5959 CCTCTG-TTT
1 CCTCTGTTTT
5968 CCTCTGTTTT
1 CCTCTGTTTT
5978 CCTCTGTTTT
1 CCTCTGTTTT
5988 GTCAGGTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.00, C:0.31, G:0.10, T:0.59
Consensus pattern (10 bp):
CCTCTGTTTT
Found at i:28279 original size:28 final size:28
Alignment explanation
Indices: 28239--28300 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
28229 AACATAGAGT
28239 TCTTGCTTGGCTGGTATTCTTCTTGAGA
1 TCTTGCTTGGCTGGTATTCTTCTTGAGA
28267 TCTTGCTTGGCTGGTATTCTTCTTGAGA
1 TCTTGCTTGGCTGGTATTCTTCTTGAGA
28295 TCTTGC
1 TCTTGC
28301 ATATATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (28 bp):
TCTTGCTTGGCTGGTATTCTTCTTGAGA
Found at i:31271 original size:22 final size:22
Alignment explanation
Indices: 31246--31321 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
31236 GCTATATTAT
* * *
31246 TTTGATAACCTCCCTGTGAAAC
1 TTTGATAACCACACTATGAAAC
*
31268 TTTGATAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAC
*
31290 TTTGATAACCACACTAT-AAAA
1 TTTGATAACCACACTATGAAAC
31311 TTGTGATAACC
1 TT-TGATAACC
31322 TCTATATGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.10
22 43 0.90
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (22 bp):
TTTGATAACCACACTATGAAAC
Found at i:31318 original size:44 final size:44
Alignment explanation
Indices: 31244--31334 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
31234 TCGCTATATT
* * * *
31244 ATTTTGATAACCTCCCTGTGAAACTTTGATAACCAC-ACTATGAA
1 ATTTTGATAACCACACTATGAAAATTTGATAACCACTA-TATGAA
*
31288 ATTTTGATAACCACACTAT-AAAATTGTGATAACCTCTATATGAA
1 ATTTTGATAACCACACTATGAAAATT-TGATAACCACTATATGAA
31332 ATT
1 ATT
31335 AATTTTGATG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 5 0.12
44 34 0.85
45 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (44 bp):
ATTTTGATAACCACACTATGAAAATTTGATAACCACTATATGAA
Found at i:31333 original size:22 final size:21
Alignment explanation
Indices: 31246--31334 Score: 90
Period size: 22 Copynumber: 4.1 Consensus size: 21
31236 GCTATATTAT
* * *
31246 TTTGATAACCTCCCTGTGAAA
1 TTTGATAACCACACTATGAAA
31267 CTTTGATAACCACACTATGAAA
1 -TTTGATAACCACACTATGAAA
*
31289 TTTTGATAACCACACTATAAAA
1 -TTTGATAACCACACTATGAAA
*
31311 TTGTGATAACCTCTA-TATGAAA
1 TT-TGATAACCAC-ACTATGAAA
31333 TT
1 TT
31335 AATTTTGATG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.03
22 55 0.95
23 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (21 bp):
TTTGATAACCACACTATGAAA
Found at i:31425 original size:22 final size:22
Alignment explanation
Indices: 31398--31591 Score: 76
Period size: 22 Copynumber: 8.9 Consensus size: 22
31388 TAATTTGATA
31398 CACTATGGAATTTTGATAACCAT
1 CACTATGGAATTTTGATAACC-T
*
31421 -ACTAT-AAACTTTTGATAACCT
1 CACTATGGAA-TTTTGATAACCT
* * *
31442 CCCTATGGAATGTTGATAACTT
1 CACTATGGAATTTTGATAACCT
* * *
31464 C-CATATAGAA-TTTCATTAATCT
1 CAC-TATGGAATTTTGA-TAACCT
* *
31486 CACTATGAAATTTTGATTACCT
1 CACTATGGAATTTTGATAACCT
** * * *
31508 -TTTATGAAATTTTTG-TAATCA
1 CACTATGGAA-TTTTGATAACCT
* * * *
31529 CATTATGAAATTTTGACAACCA
1 CACTATGGAATTTTGATAACCT
* * * * *
31551 CATTATGAAATTTTGGTAGCCA
1 CACTATGGAATTTTGATAACCT
* *
31573 CACTATGAAATTTCGATAA
1 CACTATGGAATTTTGATAA
31592 TTTGCAAAGT
Statistics
Matches: 131, Mismatches: 30, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
21 22 0.17
22 102 0.78
23 7 0.05
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
CACTATGGAATTTTGATAACCT
Found at i:31527 original size:43 final size:44
Alignment explanation
Indices: 31480--31585 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 44
31470 AGAATTTCAT
* ** ** *
31480 TAATCTCACTATGAAATTTTGATTACC-TTTTATGAAATTTTTG
1 TAATCACACTATGAAATTTTGACAACCACATTATGAAATTTTGG
*
31523 TAATCACATTATGAAATTTTGACAACCACATTATGAAATTTTGG
1 TAATCACACTATGAAATTTTGACAACCACATTATGAAATTTTGG
**
31567 TAGCCACACTATGAAATTT
1 TAATCACACTATGAAATTT
31586 CGATAATTTG
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
43 23 0.44
44 29 0.56
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (44 bp):
TAATCACACTATGAAATTTTGACAACCACATTATGAAATTTTGG
Found at i:36916 original size:317 final size:317
Alignment explanation
Indices: 36336--36978 Score: 1232
Period size: 317 Copynumber: 2.0 Consensus size: 317
36326 TTACAAAGAT
*
36336 AGACCATCAAACTAGTAGAAAGAAGATCGACGCGAAACAGAGAAAAAGTAGGAGAGCAATTAAGG
1 AGACAATCAAACTAGTAGAAAGAAGATCGACGCGAAACAGAGAAAAAGTAGGAGAGCAATTAAGG
*
36401 GTTAGATTCAAGTTTGATGAGCCTATTACATCACATCACATACCTAATAATCCTTATCAATTTTA
66 GTTAGATTCAAGTTTGATGAGCCTATCACATCACATCACATACCTAATAATCCTTATCAATTTTA
36466 ACACAATACCTAAAGCAAAGCATACTTCCCACAGTTGAGAGACACATTAATTGACTTTCTTAATT
131 ACACAATACCTAAAGCAAAGCATACTTCCCACAGTTGAGAGACACATTAATTGACTTTCTTAATT
*
36531 AAGCTTCACCTTAATTGACTTTCTTGTATTTGGAGAAAACAAAAACAGAACAAATGTCAAAAGTG
196 AAACTTCACCTTAATTGACTTTCTTGTATTTGGAGAAAACAAAAACAGAACAAATGTCAAAAGTG
36596 TAATATACTCCCTCTATCCCATTATATAAGTCCCTTTTAATTATATCATCAAGATTA
261 TAATATACTCCCTCTATCCCATTATATAAGTCCCTTTTAATTATATCATCAAGATTA
36653 AGACAATCAAACTAGTAGAAAGAAGATCGACGCGAAACAGAGAAAAAGTAGGAGAGCAATTAAGG
1 AGACAATCAAACTAGTAGAAAGAAGATCGACGCGAAACAGAGAAAAAGTAGGAGAGCAATTAAGG
36718 GTTAGATTCAAGTTTGATGAGCCTATCACATCACATCACATACCTAATAATCCTTATCAATTTTA
66 GTTAGATTCAAGTTTGATGAGCCTATCACATCACATCACATACCTAATAATCCTTATCAATTTTA
36783 ACACAATACCTAAAGCAAAGCATACTTCCCACAGTTGAGAGACACATTAATTGACTTTCTTAATT
131 ACACAATACCTAAAGCAAAGCATACTTCCCACAGTTGAGAGACACATTAATTGACTTTCTTAATT
*
36848 AAACTTCACCTTAATTGATTTTCTTGTATTTGGAGAAAACAAAAACAGAACAAATGTCAAAAGTG
196 AAACTTCACCTTAATTGACTTTCTTGTATTTGGAGAAAACAAAAACAGAACAAATGTCAAAAGTG
*
36913 TAATATACTCCCTCTGTCCCATTATATAAGTCCCTTTTAATTATATCATCAAGATTA
261 TAATATACTCCCTCTATCCCATTATATAAGTCCCTTTTAATTATATCATCAAGATTA
*
36970 AGAAAATCA
1 AGACAATCA
36979 GTTATGACAT
Statistics
Matches: 320, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
317 320 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (317 bp):
AGACAATCAAACTAGTAGAAAGAAGATCGACGCGAAACAGAGAAAAAGTAGGAGAGCAATTAAGG
GTTAGATTCAAGTTTGATGAGCCTATCACATCACATCACATACCTAATAATCCTTATCAATTTTA
ACACAATACCTAAAGCAAAGCATACTTCCCACAGTTGAGAGACACATTAATTGACTTTCTTAATT
AAACTTCACCTTAATTGACTTTCTTGTATTTGGAGAAAACAAAAACAGAACAAATGTCAAAAGTG
TAATATACTCCCTCTATCCCATTATATAAGTCCCTTTTAATTATATCATCAAGATTA
Found at i:54016 original size:29 final size:30
Alignment explanation
Indices: 53983--54059 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
53973 TGGCATTTTA
*
53983 ACACGTGGCATGCCACGTGCCCTTTTT-GT
1 ACACGTGGCATGCCACGTGCCATTTTTAGT
* * *
54012 ACACGTGGCGTGCCATGTGTCATTTTTAGT
1 ACACGTGGCATGCCACGTGCCATTTTTAGT
*
54042 GCACGTGGCATGCCACGT
1 ACACGTGGCATGCCACGT
54060 CAGCCGTCGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (30 bp):
ACACGTGGCATGCCACGTGCCATTTTTAGT
Found at i:56895 original size:13 final size:13
Alignment explanation
Indices: 56877--56901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56867 CTTGTTCTTA
56877 ACATTGAAATTAG
1 ACATTGAAATTAG
56890 ACATTGAAATTA
1 ACATTGAAATTA
56902 AAATTGGTAC
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:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (13 bp):
ACATTGAAATTAG
Found at i:65346 original size:7 final size:7
Alignment explanation
Indices: 65334--65363 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
65324 TAGAAGGCAT
65334 TCTGGAC
1 TCTGGAC
65341 TCTGGAC
1 TCTGGAC
65348 TCTGGAC
1 TCTGGAC
65355 TCTGGAC
1 TCTGGAC
65362 TC
1 TC
65364 GGCATGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.30, G:0.27, T:0.30
Consensus pattern (7 bp):
TCTGGAC
Found at i:72477 original size:35 final size:35
Alignment explanation
Indices: 72431--72520 Score: 144
Period size: 35 Copynumber: 2.6 Consensus size: 35
72421 TGTATAAAAC
72431 TAGGACTAGGATTAATATTATGAGACTTGCTCGTG
1 TAGGACTAGGATTAATATTATGAGACTTGCTCGTG
*
72466 TAGGACTAGGATTAATATCATGAGACTTGCTCGTG
1 TAGGACTAGGATTAATATTATGAGACTTGCTCGTG
* * *
72501 TTGGACTAGGAATAGTATTA
1 TAGGACTAGGATTAATATTA
72521 GTTTGTAGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (35 bp):
TAGGACTAGGATTAATATTATGAGACTTGCTCGTG
Found at i:72755 original size:29 final size:29
Alignment explanation
Indices: 72720--72794 Score: 150
Period size: 29 Copynumber: 2.6 Consensus size: 29
72710 TGAAAATATG
72720 TAGACCTTTAATTCTTTATACTAGTTATA
1 TAGACCTTTAATTCTTTATACTAGTTATA
72749 TAGACCTTTAATTCTTTATACTAGTTATA
1 TAGACCTTTAATTCTTTATACTAGTTATA
72778 TAGACCTTTAATTCTTT
1 TAGACCTTTAATTCTTT
72795 TAAATTTGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (29 bp):
TAGACCTTTAATTCTTTATACTAGTTATA
Found at i:75444 original size:31 final size:29
Alignment explanation
Indices: 75406--75472 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 29
75396 GACAACTCCC
75406 ACATTTTTTTATAAGTA-ATTTAGGAATAAGA
1 ACATTTTTTT-TAAGTACA--TAGGAATAAGA
**
75437 ACATTTTTTTTGGGTACATAGGAATAAGA
1 ACATTTTTTTTAAGTACATAGGAATAAGA
75466 ACATTTT
1 ACATTTT
75473 AAAAATATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 18 0.55
30 4 0.12
31 11 0.33
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (29 bp):
ACATTTTTTTTAAGTACATAGGAATAAGA
Found at i:76304 original size:24 final size:26
Alignment explanation
Indices: 76254--76311 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
76244 TGTTTTTATT
**
76254 AAAAAATTATTCTCTTTTTTCCTAAA
1 AAAAAATTATTCTCTTTTAACCTAAA
76280 AAAAAATTATTCTC-TTTAACC-AAA
1 AAAAAATTATTCTCTTTTAACCTAAA
76304 AAAAAATT
1 AAAAAATT
76312 CCCTACTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 11 0.37
25 5 0.17
26 14 0.47
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAAAATTATTCTCTTTTAACCTAAA
Found at i:80577 original size:331 final size:332
Alignment explanation
Indices: 79464--81124 Score: 2512
Period size: 331 Copynumber: 5.0 Consensus size: 332
79454 GTATTTTGCA
* * * * ** * *
79464 ATTT-AAGGAGACTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCAT-CGAAATGCGTTTTT
1 ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAACTGAGCCGGAAC-TCCGAAACGAGTTTTT
* * * * *
79527 AGCCTAAAACCGTGAT-GTAACGTATACGATTTCCGCTAAAAGTTTGCAAAAAATGACCCGAAAA
65 AGCCAAAAACCGTGATGGTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAA
79591 TTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGA
129 TTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGA
* * *
79656 AGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTATTCGAATTAATTTCTATTTAACT-AA
194 AGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATTTAAATCAA
* *
79720 AAAAAGATAGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATG
259 AACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATG
79785 AATAAAGAT
324 AATAAAGAT
*
79794 ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTCCGAAACGAGTTTTTA
1 ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAACTGAGCCGGAACTCCGAAACGAGTTTTTA
**
79859 GCCAAAAACCGTGATAATTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAATT
66 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAATT
* * ** *
79924 TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATGCAAAGCCATCAAAATTAAAG
131 TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAG
** * * * *
79989 GGTTTTTCACGCTTCTCTTATCGTTTTTCCTTTTTTTTGTTCCCGAACTGATTTCTATTT-AATC
196 GGTTTTTCACGCTTCTAATATCGTTTTTCC-ATTTATT-TT--CGAATTAATTTCTATTTAAATC
* ** * * * *
80053 AAAATGAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTAGATTTGG
257 --AA--A-ACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGG
* *
80118 TT-AATTGAATATAGAT
317 TTCGA-TGAATAAAGAT
* * * * ** * * *
80134 ATTTCAAGGAGACTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCACCGAAATGCGTTTTTA
1 ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAACTGAGCCGGAACTCCGAAACGAGTTTTTA
* * *
80199 GCCGAAAACCGTGATGGTTAGTACACGATTTCCGCTAAAAGTTTGCAAAAAATGACCCGAAAATT
66 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAATT
80264 TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAG
131 TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAG
*
80329 GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTTAAATCAAAA
196 GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATTTAAATCAAAA
80394 -AAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGAA
261 CAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGAA
80458 TAAAGAT
326 TAAAGAT
*
80465 ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTCCGAAACGAGTTTTTA
1 ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAACTGAGCCGGAACTCCGAAACGAGTTTTTA
* *
80530 GCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGACCCGAAAA-T
66 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAATT
80594 TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAG
131 TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAG
80659 GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATTTAAATCAAAA
196 GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATTTAAATCAAAA
** *
80724 CAAGATTGAGATGCTCGTAAAAATTAATTTTCATATCCAATGTGGCTGACATTTGGTTCGATGAA
261 CAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGAA
80789 TAAAGAT
326 TAAAGAT
80796 ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAACTGAGCCGGAACTCCGAAACGAGTTTTTA
1 ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAACTGAGCCGGAACTCCGAAACGAGTTTTTA
* ** *
80861 GCCAAAAACCGTGATGGTTATTACATTATTTCGGCAAAAATTTTG-AAAACAATGACCCGAAAAT
66 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAA-AATGACCCGAAAAT
*
80925 CTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAA
130 TTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAA
*
80990 GGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTTGAATTAATTTCTATTTAAATCAAA
195 GGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATTTAAATCAAA
* * **
81055 ACAAGATGGAGATGCTCTTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGACTCGATGA
260 ACAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGA
81120 ATAAA
325 ATAAA
81125 CA
Statistics
Matches: 1207, Mismatches: 105, Indels: 36
0.90 0.08 0.03
Matches are distributed among these distances:
330 139 0.12
331 554 0.46
332 199 0.16
333 3 0.00
334 2 0.00
335 17 0.01
336 15 0.01
337 6 0.00
338 2 0.00
339 7 0.01
340 263 0.22
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (332 bp):
ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAACTGAGCCGGAACTCCGAAACGAGTTTTTA
GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAATT
TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAG
GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCGAATTAATTTCTATTTAAATCAAAA
CAAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGAA
TAAAGAT
Found at i:81037 original size:662 final size:668
Alignment explanation
Indices: 79464--81124 Score: 2646
Period size: 671 Copynumber: 2.5 Consensus size: 668
79454 GTATTTTGCA
79464 ATTT-AAGGAGACTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCAT-CGAAATGCGTTTTT
1 ATTTCAAGGAGACTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGC-TCCGAAATGCGTTTTT
* * *
79527 AGCCTAAAACCGTGAT-GTAACGTATACGATTTCCGCTAAAAGTTTGCAAAAAATGACCCGAAAA
65 AGCCAAAAACCGTGATGGTTA-GTACACGATTTCCGCTAAAAGTTTGCAAAAAATGACCCGAAAA
79591 TTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGA
129 TTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGA
* * *
79656 AGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTATTCGAATTAATTTCTATTTAACTAAA
194 AGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTTAAATCAA
79721 AAAAGATAGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGA
259 AAAAGATAGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGA
79786 ATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTCCGAAACG
324 ATAAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTCCGAAACG
*
79851 AGTTTTTAGCCAAAAACCGTGATAATTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACC
389 AGTTTTTAGCCAAAAACCGTGATAATTAGTACACGATTTCGGCAAAAATTTTGCAAAAAATGACC
**
79916 CGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATGCAAAGCCATCAA
454 CGAAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATGCAAAGCCAAAAA
** * * *
79981 AATTAAAGGGTTTTTCACGCTTCTCTTATCGTTTTTCCTTTTTTTTGTTCCCGAACTGATTTCTA
519 AATTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTATTTATTGTT-CCGAACTAATTTCTA
* *
80046 TTTAATCAAAATGAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTA
583 TTTAATC-AAA-GAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
* *
80111 GATTTGGTTAATTGAATATAGAT
646 CATTTGGTTAATTGAATAAAGAT
*
80134 ATTTCAAGGAGACTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCACCGAAATGCGTTTTTA
1 ATTTCAAGGAGACTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCTCCGAAATGCGTTTTTA
*
80199 GCCGAAAACCGTGATGGTTAGTACACGATTTCCGCTAAAAGTTTGCAAAAAATGACCCGAAAATT
66 GCCAAAAACCGTGATGGTTAGTACACGATTTCCGCTAAAAGTTTGCAAAAAATGACCCGAAAATT
80264 TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAG
131 TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAG
80329 GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTTAAATCAAAA
196 GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTTAAATCAAAA
*
80394 AAGATTGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGAAT
261 AAGATAGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGAAT
80459 AAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTCCGAAACGAG
326 AAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTCCGAAACGAG
** *
80524 TTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCAAAAATTTTGCAAAAAATGACCCG
391 TTTTTAGCCAAAAACCGTGATAATTAGTACACGATTTCGGCAAAAATTTTGCAAAAAATGACCCG
* *
80589 AAAA-TTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAA
456 AAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATGCAAAGCCAAAAAAA
* *
80653 TTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-ATTTATT-TT-CGAATTAATTTCTATTT
521 TTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTATTTATTGTTCCGAACTAATTTCTATTT
* ** * *
80715 AAATC-AA-A-ACAAGATTGAGATGCTCGTAAAAATTAAT-TTTCATATCCAATGTGGCTGACAT
586 -AATCAAAGAGACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AAATCCAATGTGGCTGACAT
*
80776 TTGGTTCGA-TGAATAAAGAT
649 TTGGTT-AATTGAATAAAGAT
* * * * ** * *
80796 ATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAACTGAGCCGGAACTCCGAAACGAGTTTTTA
1 ATTTCAAGGAGACTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCTCCGAAATGCGTTTTTA
* ** * * *
80861 GCCAAAAACCGTGATGGTTATTACATTATTTCGGCAAAAATTTTG-AAAACAATGACCCGAAAAT
66 GCCAAAAACCGTGATGGTTAGTACACGATTTCCGCTAAAAGTTTGCAAAA-AATGACCCGAAAAT
*
80925 CTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAA
130 TTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAA
* *
80990 GGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTTGAATTAATTTCTATTTAAATCAAA
195 GGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTTAAATCAAA
* * **
81055 ACAAGATGGAGATGCTCTTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGACTCGATGA
260 A-AAGATAGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGA
81120 ATAAA
324 ATAAA
81125 CA
Statistics
Matches: 927, Mismatches: 56, Indels: 23
0.92 0.06 0.02
Matches are distributed among these distances:
661 6 0.01
662 294 0.32
663 66 0.07
665 2 0.00
666 15 0.02
667 4 0.00
668 2 0.00
669 5 0.01
670 93 0.10
671 437 0.47
672 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (668 bp):
ATTTCAAGGAGACTTTATGCCAAAAATCATGCAAAACTGAGTCGGGGCTCCGAAATGCGTTTTTA
GCCAAAAACCGTGATGGTTAGTACACGATTTCCGCTAAAAGTTTGCAAAAAATGACCCGAAAATT
TTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAG
GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTTCGAATTAATTTCTATTTAAATCAAAA
AAGATAGAGATGCTCGTAAAAACAAATTTTTATATCCAATGTGGCTGACATTTGGTTCGATGAAT
AAAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGAACTCCGAAACGAG
TTTTTAGCCAAAAACCGTGATAATTAGTACACGATTTCGGCAAAAATTTTGCAAAAAATGACCCG
AAAATTTTTTCCTCAAATTTTTGCCAGAATACTCAGAAAAAATATGTAATGCAAAGCCAAAAAAA
TTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTATTTATTGTTCCGAACTAATTTCTATTT
AATCAAAGAGACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGACATTT
GGTTAATTGAATAAAGAT
Done.