Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold368
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: 190673
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:162627 original size:19 final size:20
Alignment explanation
Indices: 162590--162627 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
162580 AAATCTAATA
162590 ATAAATTATTTTATTCTTTT
1 ATAAATTATTTTATTCTTTT
162610 ATAAATTATTTT-TTCTTT
1 ATAAATTATTTTATTCTTT
162628 GTCGTTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
ATAAATTATTTTATTCTTTT
Found at i:166385 original size:13 final size:13
Alignment explanation
Indices: 166367--166392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166357 ACATAAGTGT
166367 TGTATCGATACAA
1 TGTATCGATACAA
166380 TGTATCGATACAA
1 TGTATCGATACAA
166393 AGCTACCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:170851 original size:2 final size:2
Alignment explanation
Indices: 170844--170872 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
170834 AACAATACTA
170844 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 A
170873 AGAATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:172396 original size:6 final size:6
Alignment explanation
Indices: 172382--172526 Score: 50
Period size: 6 Copynumber: 23.0 Consensus size: 6
172372 TGAATTTAAG
* * * *
172382 TTATAT TTATTT TTATA- TTATAA TTATAT TTAAAAT TATATAA TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TT-ATAT T-TATAT TTATAT
** * *
172431 AAAT-T TTAATAT ATTAATAAT TTATAT ATTAAAAT TT-TA- ATATAT
1 TTATAT TT-ATAT -TT-AT-AT TTATAT -TT-ATAT TTATAT TTATAT
*
172476 TTATAT ATTA-AT ATTATAT TTATAT TTTTAT ATTA-AT ATTATATT TTATAT
1 TTATAT -TTATAT -TTATAT TTATAT TTATAT -TTATAT -TTATA-T TTATAT
172527 CATCTTTTAG
Statistics
Matches: 106, Mismatches: 17, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
4 1 0.01
5 9 0.08
6 55 0.52
7 27 0.25
8 12 0.11
9 2 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTATAT
Found at i:172447 original size:8 final size:8
Alignment explanation
Indices: 172436--172489 Score: 65
Period size: 8 Copynumber: 6.9 Consensus size: 8
172426 TATATAAATT
172436 TTAATATA
1 TTAATATA
172444 TTAATA-A
1 TTAATATA
*
172451 TTTATATA
1 TTAATATA
* *
172459 TTAAAATT
1 TTAATATA
172467 TTAATATA
1 TTAATATA
*
172475 TTTATATA
1 TTAATATA
172483 TTAATAT
1 TTAATAT
172490 TATATTTATA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
7 6 0.16
8 31 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTAATATA
Found at i:172505 original size:8 final size:8
Alignment explanation
Indices: 172439--172526 Score: 57
Period size: 8 Copynumber: 11.5 Consensus size: 8
172429 ATAAATTTTA
*
172439 ATATATTA
1 ATATATTT
172447 ATA-ATTT
1 ATATATTT
*
172454 ATATATTA
1 ATATATTT
*
172462 AAAT-TTT
1 ATATATTT
172469 AATATATTT
1 -ATATATTT
172478 ATATATTAAT
1 ATATATT--T
172488 ATTATATTT
1 A-TATATTT
172497 ATAT-TTT
1 ATATATTT
172504 -TATA-TT
1 ATATATTT
172510 A-ATA-TT
1 ATATATTT
172516 ATAT-TTT
1 ATATATTT
172523 ATAT
1 ATAT
172527 CATCTTTTAG
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
6 11 0.17
7 19 0.29
8 22 0.34
9 5 0.08
10 2 0.03
11 6 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATATATTT
Found at i:172520 original size:19 final size:19
Alignment explanation
Indices: 172471--172526 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
172461 AAAATTTTAA
* *
172471 TATATTTATATATTAATAT
1 TATATTTATATTTTTATAT
172490 TATATTTATATTTTTATAT
1 TATATTTATATTTTTATAT
172509 TA-ATATTATA-TTTTATAT
1 TATAT-TTATATTTTTATAT
172527 CATCTTTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 10 0.29
19 24 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTTATATTTTTATAT
Found at i:173659 original size:22 final size:22
Alignment explanation
Indices: 173629--173670 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
173619 ATCCAACTAT
* *
173629 TCACTTTTTTTAAAAAAAATAC
1 TCACATTTTATAAAAAAAATAC
173651 TCACATTTTATAAAAAAAAT
1 TCACATTTTATAAAAAAAAT
173671 TATTTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
TCACATTTTATAAAAAAAATAC
Found at i:174980 original size:20 final size:20
Alignment explanation
Indices: 174952--174990 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
174942 ATTTATAATT
* *
174952 AAAAAAAAAGAGAAAAGATG
1 AAAAAAAAAAAAAAAAGATG
*
174972 AAAAGAAAAAAAAAAAGAT
1 AAAAAAAAAAAAAAAAGAT
174991 ATCAGCCAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAGATG
Found at i:177098 original size:19 final size:18
Alignment explanation
Indices: 177073--177137 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
177063 ATTTCAACGA
177073 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
177091 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
177107 --TGTATCGATATATAAG
1 TTTGTATCGATACATAAG
177123 TTTTGTATCGATACA
1 -TTTGTATCGATACA
177138 ATGTAAGCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:177111 original size:32 final size:32
Alignment explanation
Indices: 177075--177142 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
177065 TTCAACGATT
177075 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
177107 TGTATCGATATATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
177139 TGTA
1 TGTA
177143 AGCTACTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:184784 original size:4 final size:4
Alignment explanation
Indices: 184775--184803 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
184765 TTTACATCAG
184775 AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
184804 CAAGAAATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:186575 original size:20 final size:23
Alignment explanation
Indices: 186552--186593 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
186542 AGTTAACCAA
186552 TTATTTA-TA-ATTATA-AAATT
1 TTATTTATTATATTATATAAATT
186572 TTATTTATTATATTATATAAAT
1 TTATTTATTATATTATATAAAT
186594 AAAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 6 0.32
23 4 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATTTATTATATTATATAAATT
Found at i:187406 original size:2 final size:2
Alignment explanation
Indices: 187401--187433 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
187391 CGCCTAGTTG
*
187401 CT CT CT CT CT GT CT CT CT CT CT CT CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
187434 GTCACTTGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
CT
Found at i:188529 original size:11 final size:11
Alignment explanation
Indices: 188504--188563 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
188494 AGGGATTAGT
*
188504 GGGGGG-GGGG
1 GGGGGGTGGGA
188514 GGGGGGATGGGA
1 GGGGGG-TGGGA
**
188526 GGGGGGTGAAA
1 GGGGGGTGGGA
*
188537 GGGGGGGGGGA
1 GGGGGGTGGGA
188548 -GGGGGTGGGGA
1 GGGGGGT-GGGA
188559 GGGGG
1 GGGGG
188564 TCGGGAAGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
10 11 0.28
11 15 0.38
12 13 0.33
ACGTcount: A:0.12, C:0.00, G:0.83, T:0.05
Consensus pattern (11 bp):
GGGGGGTGGGA
Found at i:188564 original size:11 final size:11
Alignment explanation
Indices: 188536--188569 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
188526 GGGGGGTGAA
*
188536 AGGGGGGGGGG
1 AGGGGGTGGGG
188547 AGGGGGTGGGG
1 AGGGGGTGGGG
*
188558 AGGGGGTCGGG
1 AGGGGGTGGGG
188569 A
1 A
188570 AGAGCGTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.12, C:0.03, G:0.79, T:0.06
Consensus pattern (11 bp):
AGGGGGTGGGG
Done.