Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1530
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: 13435
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Found at i:4089 original size:23 final size:23
Alignment explanation
Indices: 4052--4100 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
4042 TGTATGTGGA
4052 AACATCCAAGCAGCTTTCCATGT
1 AACATCCAAGCAGCTTTCCATGT
* *
4075 AACATCTAAGTAGCTTTCCATGT
1 AACATCCAAGCAGCTTTCCATGT
4098 AAC
1 AAC
4101 CTCTTCATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (23 bp):
AACATCCAAGCAGCTTTCCATGT
Found at i:10587 original size:20 final size:20
Alignment explanation
Indices: 10562--10686 Score: 74
Period size: 20 Copynumber: 5.8 Consensus size: 20
10552 TTTTAACTAG
10562 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
10582 ATGTATCGATACATCTAGGTAAAAGATTAAA
1 ATGTATCGATACAT-T--G----A-A-T--A
* * *
10613 ATGCATCGATACATTAAAGA
1 ATGTATCGATACATTGAATA
*
10633 ATGTATCGATACATT-CATA
1 ATGTATCGATACATTGAATA
*
10652 CATGTATCGATACA-TGAAAA
1 -ATGTATCGATACATTGAATA
*
10672 ATGTATCAATACATT
1 ATGTATCGATACATT
10687 TGGGTAAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
19 15 0.18
20 45 0.55
21 1 0.01
23 2 0.02
24 1 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 14 0.17
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:11673 original size:28 final size:28
Alignment explanation
Indices: 11587--12506 Score: 516
Period size: 28 Copynumber: 32.2 Consensus size: 28
11577 TTTTTTTAAA
* *
11587 AAAAGGTGCCACTAATTTGTGTGGGCTTTG
1 AAAAGGTGCCACTGA-CT-TGTGGGCTTTG
* *
11617 AAAAGATGCCACTG--TCGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
**
11643 AAAAGGTGCCACTGACTTGTGGGCTCAG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
11671 AAAAGATGCCATTGACTTGAGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
11699 -AAAGATGCCACCGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
11726 AAAAGGATGCCA-TGGACTTGT-AGATTTG
1 AAAAGG-TGCCACT-GACTTGTGGGCTTTG
* *
11754 -AAAGGATGCCACTAAC-TGTGGGC-TTA
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* * *
11780 AAAAGATGCCACCCGACTTATGGGCTTTG
1 AAAAGGTGCCA-CTGACTTGTGGGCTTTG
**
11809 AAAAGGATGCCACCAACTTGT-GGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
*
11837 AAAAGGTGCACAATGACTTGTGGGCTTTG
1 AAAAGGTGC-CACTGACTTGTGGGCTTTG
* * *
11866 AAAAGATGCCACTGACTTATGGGCTTTT
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
11894 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * * * *
11922 AAAGGGTTTCTACTGATTTGTGAGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
** **
11951 ATATGGGTTGCCACCAACATGTGTGGGCTTTG
1 A-AAAGG-TGCCACTGAC-T-TGTGGGCTTTG
* ** *
11983 AAATGGGTTGCCACCAACTTGTGTGGGCTTTC
1 AAA-AGG-TGCCACTGAC-T-TGTGGGCTTTG
* * *
12015 AAATGAGTTTCCACTAACTTGTGTGGGCTTTG
1 AAA--AGGTGCCACTGAC-T-TGTGGGCTTTG
* *
12047 AAATGATGCCACTGACTTG-GGGCTTTGG
1 AAAAGGTGCCACTGACTTGTGGGCTTT-G
** *
12075 AATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGG-TGCCACTGAC-T-TGTGGGCTTTG
* * * * *
12106 AAACGGGTTGCAACCGACTTGTGTGCTTGG
1 AAA-AGG-TGCCACTGACTTGTGGGCTTTG
* *
12136 AAAAGATGCAACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
12164 AAAAGATGCCACCGACTTGTGGGCTTGG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
12192 AAATGGATGCCACTAACTTGTGGACTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* *
12221 -AAAGGATGCCACTGACTTGTAGGATTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* * *
12249 GAAGGGTGTCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
12277 AAAAGATGCCA-TCGACTTATGGGCTTTG
1 AAAAGGTGCCACT-GACTTGTGGGCTTTG
* * * *
12305 AAAAAGATACCACCGACTTGTGGACTTT-
1 -AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
12333 AAAAGGGTGCCACGGAGTTGTGGTCTTT-
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
* * * * * *
12361 AGAAAGATACCACGGAGTTGTAGAC-TT-
1 A-AAAGGTGCCACTGACTTGTGGGCTTTG
* * *
12388 -AAAGGATGCCACGGAGTTGT-GGATTT-
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* * *
12414 AAAAGGATGCCACGGAGTTGTGGAC-TT-
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* *
12441 AAAAGGATGCCA-TGGAGTTGTGGACTTTG
1 AAAAGG-TGCCACT-GACTTGTGGGCTTTG
* * *
12470 AAAAGAAATGCCACTGAATTGTGGACTTTG
1 AAAAG--GTGCCACTGACTTGTGGGCTTTG
*
12500 AAGAGGT
1 AAAAGGT
12507 CACAATACTA
Statistics
Matches: 721, Mismatches: 126, Indels: 88
0.77 0.13 0.09
Matches are distributed among these distances:
25 5 0.01
26 48 0.07
27 108 0.15
28 271 0.38
29 123 0.17
30 72 0.10
31 9 0.01
32 84 0.12
33 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (28 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTG
Found at i:11919 original size:85 final size:85
Alignment explanation
Indices: 11606--12501 Score: 628
Period size: 85 Copynumber: 10.5 Consensus size: 85
11596 CACTAATTTG
* * * *
11606 TGTGGGCTTTGAAAAGATGCCACTG--TCGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTC
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTT
* *
11669 AGAAAA-GATGCCATTGACT
66 TGAAAAGGATGCCACTGACT
* * * ** * *
11688 TGAGGGCTTTG-AAAGATGCCACCGACTTGTGGGCTTTGAAAAGGATGCCATGGACTTGT-AGAT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACCGACTTGTGGGCT
*
11751 TTG-AAAGGATGCCACTAAC-
65 TTGAAAAGGATGCCACTGACT
* * * * *
11770 TGTGGGC-TTAAAAAGATGCCACCCGACTTATGGGCTTTGAAAAGGATGCCACCAACTTGT-GGC
1 TGTGGGCTTTGAAAAGATGCCA-CTGACTTGTGGGCTTTG-AAAGGGTGCCACCGACTTGTGGGC
*
11833 TTTGAAAAGG-TGCACAATGACT
64 TTTGAAAAGGATGC-CACTGACT
* * *
11855 TGTGGGCTTTGAAAAGATGCCACTGACTTATGGGCTTTTAAAGGGTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTT
* * * * *
11920 TGAAAGGGTTTCTACTGATT
66 TGAAAAGGATGCCACTGACT
* ** * ** *
11940 TGTGAGCTTTGATATGGGTTGCCACCAACATGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGT
1 TGTGGGCTTTGA-A-AAGATGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-TGCCACCGAC-T-T
* * * * *
12005 GTGGGCTTTCAAATGAGTTTCCACTAACTT
58 GTGGGCTTTGAAAAG-GATGCCACTGAC-T
* *
12035 GTGTGGGCTTTGAAATGATGCCACTGACTTG-GGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
1 -TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTT-GAAAGGG-TGCCACCGAC-T-TGTG
* * * *
12099 GGCTTTGAAACGGGTTGCAACCGACT
61 GGCTTTGAAA-AGGATGCCACTGACT
* * * * *
12125 TGTGTGCTTGGAAAAGATGCAACTGACTTGTGGGCTTTGAAAAGATGCCACCGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTT
* * *
12190 GGAAATGGATGCCACTAACT
66 TGAAAAGGATGCCACTGACT
* * * * * * *
12210 TGTGGACTTTGAAAGGATGCCACTGACTTGTAGGATTTGGAAGGGTGTCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTT
12275 TGAAAA-GATGCCA-TCGACT
66 TGAAAAGGATGCCACT-GACT
* * * * * * * *
12294 TATGGGCTTTGAAAAAGATACCACCGACTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGTCT
1 TGTGGGCTTTG-AAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCT
* * *
12359 TT-AGAAA-GATACCACGGAGT
65 TTGA-AAAGGATGCCACTGACT
* * * * * * * * * * *
12379 TGTAGAC-TT-AAAGGATGCCACGGAGTTGT-GGATTTAAAAGGATGCCACGGAGTTGTGGAC-T
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTT
*
12440 T-AAAAGGATGCCA-TGGAGT
66 TGAAAAGGATGCCACT-GACT
* * *
12459 TGTGGACTTTGAAAAGAAATGCCACTGAATTGTGGACTTTGAA
1 TGTGGGCTTTGAAAAG--ATGCCACTGACTTGTGGGCTTTGAA
12502 GAGGTCACAA
Statistics
Matches: 649, Mismatches: 128, Indels: 71
0.77 0.15 0.08
Matches are distributed among these distances:
79 3 0.00
80 19 0.03
81 43 0.07
82 49 0.08
83 67 0.10
84 78 0.12
85 182 0.28
86 29 0.04
87 10 0.02
88 11 0.02
89 42 0.06
90 11 0.02
91 52 0.08
92 7 0.01
93 15 0.02
94 18 0.03
95 2 0.00
96 11 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTT
TGAAAAGGATGCCACTGACT
Found at i:11981 original size:32 final size:32
Alignment explanation
Indices: 11911--12130 Score: 213
Period size: 32 Copynumber: 7.1 Consensus size: 32
11901 GCCACTGACT
* * **
11911 TGTGGGCTTTGAAA-GGGTTTCTACTGA-TT-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
11940 TGTGAGCTTTGATATGGGTTGCCACCAACATG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
11972 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * * *
12004 TGTGGGCTTTCAAATGAGTTTCCACTAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* **
12036 TGTGGGCTTTGAAAT--GATGCCACTGAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
12064 TG-GGGCTTTGGAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
12095 TGTGGGCTTTGAAACGGGTTGCAACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
12127 TGTG
1 TGTG
12131 CTTGGAAAAG
Statistics
Matches: 159, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
27 11 0.07
28 2 0.01
29 23 0.14
30 19 0.12
31 3 0.02
32 101 0.64
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (32 bp):
TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
Found at i:12344 original size:57 final size:56
Alignment explanation
Indices: 12149--12498 Score: 228
Period size: 57 Copynumber: 6.2 Consensus size: 56
12139 AGATGCAACT
* * * * ** * *
12149 GACTTGTGGGCTTTGAAAA-GATGCCACCGACTTGTGGGCTTGGAAATGGATGCCACT
1 GACTTGTGGACTTT-AAAAGGATGCCACGGAGTTGTGGGCTT-TAAAAAGATACCACG
* * * * * * ** * * ** *
12206 AACTTGTGGACTTTGAAAGGATGCCACTGACTTGTAGGATTTGGAAGGGTGTCACT
1 GACTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGGCTTTAAAAAGATACCACG
* * * *
12262 GACTTGTGGGCTTTGAAAA-GATGCCATC-GACTTATGGGCTTTGAAAAAGATACCACC
1 GACTTGTGGACTTT-AAAAGGATGCCA-CGGAGTTGTGGGCTTT-AAAAAGATACCACG
* * *
12319 GACTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGTCTTTAGAAAGATACCACG
1 GACTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGGCTTTAAAAAGATACCACG
* * * * *
12375 GAGTTGTAGAC-TT-AAAGGATGCCACGGAGTTGT-GGATTTAAAAGGATGCCACG
1 GACTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGGCTTTAAAAAGATACCACG
* * * * * *
12428 GAGTTGTGGAC-TTAAAAGGATGCCATGGAGTTGTGGACTTTGAAAAGAAATGCCACT
1 GACTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGGCTTT-AAAA-AGATACCACG
*
12485 GAATTGTGGACTTT
1 GACTTGTGGACTTT
12499 GAAGAGGTCA
Statistics
Matches: 234, Mismatches: 48, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
53 27 0.12
54 38 0.16
55 6 0.03
56 72 0.31
57 89 0.38
58 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (56 bp):
GACTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGGCTTTAAAAAGATACCACG
Found at i:12404 original size:54 final size:54
Alignment explanation
Indices: 12298--12472 Score: 212
Period size: 54 Copynumber: 3.2 Consensus size: 54
12288 TCGACTTATG
* * * *
12298 GGCTTTGAAAAAGATACCACCGACTTGTGGACTTTAAAAGGGTGCCACGGAGTTGT
1 GGCTTT-AGAAAGATACCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGT
*
12354 GGTCTTTAGAAAGATACCACGGAGTTGTAGACTT-AAAGGATGCCACGGAGTTGT
1 GG-CTTTAGAAAGATACCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
* * *
12408 GGATTTA-AAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCATGGAGTTGT
1 GGCTTTAGAAA-GATACCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
12462 GGACTTT-GAAA
1 GG-CTTTAGAAA
12473 AGAAATGCCA
Statistics
Matches: 104, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
52 3 0.03
53 24 0.23
54 42 0.40
55 8 0.08
56 23 0.22
57 4 0.04
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (54 bp):
GGCTTTAGAAAGATACCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT
Found at i:12426 original size:27 final size:27
Alignment explanation
Indices: 12322--12494 Score: 188
Period size: 27 Copynumber: 6.3 Consensus size: 27
12312 TACCACCGAC
*
12322 TTGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGA-TTTAAAAGGATGCCACGGAG
* *
12350 TTGTGGTCTTTAGAAA-GATACCACGGAG
1 TTGTGG-ATTTA-AAAGGATGCCACGGAG
* *
12378 TTGTAGACTT-AAAGGATGCCACGGAG
1 TTGTGGATTTAAAAGGATGCCACGGAG
12404 TTGTGGATTTAAAAGGATGCCACGGAG
1 TTGTGGATTTAAAAGGATGCCACGGAG
* *
12431 TTGTGGACTTAAAAGGATGCCATGGAG
1 TTGTGGATTTAAAAGGATGCCACGGAG
* * *
12458 TTGTGGACTTTGAAAAGAAATGCCACTGAA
1 TTGTGGA-TTT-AAAAG-GATGCCACGGAG
12488 TTGTGGA
1 TTGTGGA
12495 CTTTGAAGAG
Statistics
Matches: 122, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
25 3 0.02
26 19 0.16
27 50 0.41
28 27 0.22
29 8 0.07
30 15 0.12
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (27 bp):
TTGTGGATTTAAAAGGATGCCACGGAG
Done.