Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold33
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: 69280
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1929 original size:20 final size:20
Alignment explanation
Indices: 1904--1948 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1894 TAAATACACA
1904 TAATTAAAATT-AGACACAAT
1 TAATT-AAATTAAGACACAAT
*
1924 TAATTAAGTTAAGACACAAT
1 TAATTAAATTAAGACACAAT
1944 TAATT
1 TAATT
1949 CGGTTAGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (20 bp):
TAATTAAATTAAGACACAAT
Found at i:1954 original size:20 final size:19
Alignment explanation
Indices: 1913--1958 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
1903 ATAATTAAAA
1913 TTAGACACAATTAATTAAG
1 TTAGACACAATTAATTAAG
**
1932 TTAAGACACAATTAATTCGG
1 TT-AGACACAATTAATTAAG
1952 TTAGACA
1 TTAGACA
1959 AGACATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (19 bp):
TTAGACACAATTAATTAAG
Found at i:7744 original size:11 final size:11
Alignment explanation
Indices: 7728--7756 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
7718 TAGGTTTGTG
7728 AAATTCAAAAA
1 AAATTCAAAAA
7739 AAATTC-AAAA
1 AAATTCAAAAA
7749 AAATTCAA
1 AAATTCAA
7757 GTTGTATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:11297 original size:7 final size:6
Alignment explanation
Indices: 11236--11351 Score: 74
Period size: 6 Copynumber: 19.0 Consensus size: 6
11226 AATGAAAAAG
** *
11236 AAGAAA AAGAAA AAGAAA GTGAAG AAGAAA AAGAAA AAGAAA AA-AAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** * * ** * *
11283 TTGCAA AAGAAA AA-AAA ATCGAAA AAGTGA GAGAAA AAGAAA ATGAAGAA
1 AAGAAA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA AAGAAA AAG-A-AA
*
11333 AAGAAA ATTGAAA AAGAAA
1 AAGAAA A-AGAAA AAGAAA
11352 TTGAGATTGA
Statistics
Matches: 80, Mismatches: 24, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
5 7 0.09
6 58 0.73
7 11 0.14
8 4 0.05
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (6 bp):
AAGAAA
Found at i:11360 original size:18 final size:18
Alignment explanation
Indices: 11339--11373 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11329 AGAAAAGAAA
11339 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
11357 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
11374 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:17566 original size:34 final size:34
Alignment explanation
Indices: 17528--17603 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
17518 AAATTTAAAT
*
17528 AAATTAATTATTAACACTTATTTGAACTGAACTA
1 AAATTAATTACTAACACTTATTTGAACTGAACTA
* *
17562 AAATTAATTGCTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTGAACTGAACTA
*
17596 AAGTTAAT
1 AAATTAAT
17604 AAACTAACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTGAACTGAACTA
Found at i:19492 original size:18 final size:18
Alignment explanation
Indices: 19471--19521 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
19461 TCGCTTGCAA
* *
19471 TTTCTTTTTCTTTTT-TC
1 TTTCTATTTCTTTTTAAC
19488 TTTTCTATTTCTTTTTAAC
1 -TTTCTATTTCTTTTTAAC
19507 TTTCTATTTCTTTTT
1 TTTCTATTTCTTTTT
19522 CTTCCTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 29 0.97
19 1 0.03
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTATTTCTTTTTAAC
Found at i:24681 original size:47 final size:47
Alignment explanation
Indices: 24554--24856 Score: 489
Period size: 47 Copynumber: 6.4 Consensus size: 47
24544 CAGCCAAGAC
24554 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
24601 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
24650 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
24697 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
24744 AGTGTATATATGTGATAAGGCCTAATGGCCGATATGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * *
24791 AGTGTATATATGTGACAAGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
24838 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
24857 TCCCGAAGGG
Statistics
Matches: 239, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
47 192 0.80
49 47 0.20
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:25049 original size:37 final size:37
Alignment explanation
Indices: 24975--25049 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
24965 CCGAGCTCTA
* *
24975 AAGACCCGATGACTACGTGTGGGAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGGAATTATGTCCGGGT
* *
25012 AAGACCCGATAACTTCGTGT-GGAGATTATGTCTGGGT
1 AAGACCCGATAACTACGTGTGGGA-ATTATGTCCGGGT
25049 A
1 A
25050 TGACTTCGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 3 0.09
37 30 0.91
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGGAATTATGTCCGGGT
Found at i:28746 original size:18 final size:21
Alignment explanation
Indices: 28725--28766 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28715 TTCCATCTCA
28725 TTTTCAA-ATC-CTC-TTTCT
1 TTTTCAATATCACTCATTTCT
28743 TTTTCAATATCACTCATTTCT
1 TTTTCAATATCACTCATTTCT
28764 TTT
1 TTT
28767 GTACTCTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 3 0.14
20 3 0.14
21 8 0.38
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTCAATATCACTCATTTCT
Found at i:28805 original size:18 final size:18
Alignment explanation
Indices: 28737--28807 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
28727 TTCAAATCCT
*
28737 CTTTCTTTTTCAATATCA
1 CTTTCTTTTTCAATCTCA
*
28755 CTCATTTCTTTTGT-ACTCTCA
1 --C-TTTCTTTT-TCAATCTCA
28776 -TTTCTTTCTTCAATCTCA
1 CTTTCTTT-TTCAATCTCA
28794 CTTTCTTTTTCAAT
1 CTTTCTTTTTCAAT
28808 TTTCTTTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
17 8 0.19
18 13 0.30
19 7 0.16
20 1 0.02
21 13 0.30
22 1 0.02
ACGTcount: A:0.17, C:0.25, G:0.01, T:0.56
Consensus pattern (18 bp):
CTTTCTTTTTCAATCTCA
Found at i:33690 original size:34 final size:33
Alignment explanation
Indices: 33652--33721 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 33
33642 AGATTTAAAC
*
33652 AAATTAATTACTAACATTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTGAGCTGAAC-A
33686 AAATTAATTACTAACACTTATTTGAGCTGAACA
1 AAATTAATTACTAACACTTATTTGAGCTGAACA
33719 AAA
1 AAA
33722 GCTAATAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 4 0.11
34 31 0.89
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (33 bp):
AAATTAATTACTAACACTTATTTGAGCTGAACA
Found at i:35785 original size:11 final size:11
Alignment explanation
Indices: 35753--35811 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
35743 AGAAACAAAA
*
35753 GAATGATGAAT
1 GAATGAGGAAT
35764 G-ATGA-GAAT
1 GAATGAGGAAT
35773 GAATGAGGAAT
1 GAATGAGGAAT
*
35784 GATTGAGGGATGAT
1 GAATGA-GGA--AT
35798 GAATGAAGGAAT
1 GAATG-AGGAAT
35810 GA
1 GA
35812 GAGGGTCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 10 0.25
12 7 0.17
14 9 0.22
15 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (11 bp):
GAATGAGGAAT
Found at i:37098 original size:21 final size:21
Alignment explanation
Indices: 37072--37123 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
37062 TTGAGTTTAC
37072 ATTTATTTTGCTAGAATAATT
1 ATTTATTTTGCTAGAATAATT
* *
37093 ATTTATTTGGCTGGAATAATT
1 ATTTATTTTGCTAGAATAATT
*
37114 ATTTAATTTG
1 ATTTATTTTG
37124 TTATTAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (21 bp):
ATTTATTTTGCTAGAATAATT
Found at i:47037 original size:13 final size:12
Alignment explanation
Indices: 47011--47066 Score: 85
Period size: 12 Copynumber: 4.6 Consensus size: 12
47001 ACGGTATTGT
47011 AAAAAAATTCAA
1 AAAAAAATTCAA
* *
47023 AAAAAACTTGAA
1 AAAAAAATTCAA
47035 AAAAAAATTCAAA
1 AAAAAAATTC-AA
47048 AAAAAAATTCAA
1 AAAAAAATTCAA
47060 AAAAAAA
1 AAAAAAA
47067 GTTTGTATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
12 27 0.69
13 12 0.31
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:47041 original size:24 final size:25
Alignment explanation
Indices: 47011--47066 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
47001 ACGGTATTGT
* *
47011 AAAAAAATTC-AAAAAAAACTTGAA
1 AAAAAAATTCAAAAAAAAAATTCAA
47035 AAAAAAATTCAAAAAAAAAATTCAA
1 AAAAAAATTCAAAAAAAAAATTCAA
47060 AAAAAAA
1 AAAAAAA
47067 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (25 bp):
AAAAAAATTCAAAAAAAAAATTCAA
Found at i:47138 original size:16 final size:15
Alignment explanation
Indices: 47112--47162 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
47102 GTATTGAAGG
47112 AAAAAAAAGAAGAAA
1 AAAAAAAAGAAGAAA
** *
47127 AAAAATTCAGAATTAAA
1 AAAAA-AAAGAA-GAAA
47144 AAAAAAAAGAAGAAA
1 AAAAAAAAGAAGAAA
47159 AAAA
1 AAAA
47163 TATCGAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 12 0.43
16 8 0.29
17 8 0.29
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (15 bp):
AAAAAAAAGAAGAAA
Found at i:47150 original size:31 final size:32
Alignment explanation
Indices: 47112--47182 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
47102 GTATTGAAGG
47112 AAAAAAAAGAAGAAAAAAA-ATTC-AGAATTAAA
1 AAAAAAAAGAAGAAAAAAATA-TCGA-AATTAAA
*
47144 AAAAAAAAGAAGAAAAAAATATCGAAATTGAA
1 AAAAAAAAGAAGAAAAAAATATCGAAATTAAA
47176 AAAAAAA
1 AAAAAAA
47183 GAGTGATTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
32 34 0.94
33 2 0.06
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.11
Consensus pattern (32 bp):
AAAAAAAAGAAGAAAAAAATATCGAAATTAAA
Found at i:58574 original size:27 final size:27
Alignment explanation
Indices: 58544--58699 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
58534 TGCTATTCAC
* *
58544 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAATTCGCACACTTAGTGCCACATAA
* * * *
58571 TCAAATCGCACCCTTAGTGCTACATAG
1 TCAATTCGCACACTTAGTGCCACATAA
* * **
58598 TTAGATTCGCACACTTAGTGCCGCATGG
1 TCA-ATTCGCACACTTAGTGCCACATAA
*
58626 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAATTCGCACACTTAGTGCCA-CATAA
** *
58653 TCTTTTCGCACACTTAGTGCAACATAA
1 TCAATTCGCACACTTAGTGCCACATAA
58680 TCGAA-TCGCACACTTAGTGC
1 TC-AATTCGCACACTTAGTGC
58700 TGTACAATTT
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 81 0.78
28 22 0.21
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCCACATAA
Found at i:58615 original size:55 final size:55
Alignment explanation
Indices: 58549--58700 Score: 182
Period size: 54 Copynumber: 2.8 Consensus size: 55
58539 TTCACTCAAC
* *
58549 TCGCACACTTAGTGCCACGTAATCAAATCGCACCCTTAGTGCTA-CATAGTTAGAT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATA-TTAGAT
* ** * ***
58604 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCTTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTAGAT
* *
58658 TCGCACACTTAGTGCAACATAATCGAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCT
58701 GTACAATTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 40 0.50
55 40 0.50
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (55 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTAGAT
Found at i:64440 original size:12 final size:12
Alignment explanation
Indices: 64394--64440 Score: 69
Period size: 11 Copynumber: 3.9 Consensus size: 12
64384 TAATAGTTTC
64394 TCAAAAAAAAACT
1 TCAAAAAAAAA-T
*
64407 TGAAAAAAAAAT
1 TCAAAAAAAAAT
64419 TC-AAAAAAAAT
1 TCAAAAAAAAAT
64430 TCAAAAAAAAA
1 TCAAAAAAAAA
64441 ATCTAGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 11 0.35
12 10 0.32
13 10 0.32
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.15
Consensus pattern (12 bp):
TCAAAAAAAAAT
Found at i:64522 original size:14 final size:15
Alignment explanation
Indices: 64483--64522 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
64473 TATCAAGTTG
*
64483 TGAAAAAAAAATTTT
1 TGAAAAAAAAATTTA
*
64498 TGAAAGAAAAA-TTA
1 TGAAAAAAAAATTTA
64512 TGAAAAAAAAA
1 TGAAAAAAAAA
64523 GAGAGCTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (15 bp):
TGAAAAAAAAATTTA
Found at i:66116 original size:4 final size:4
Alignment explanation
Indices: 66107--66137 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
66097 AAGTTTTATT
66107 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
66138 TACTTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Done.