Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2679
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: 14503
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8754 original size:19 final size:20
Alignment explanation
Indices: 8730--8782 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
8720 ATTGATACAG
**
8730 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGCACAAT
*
8749 TGTATCGATACATACACAAT
1 TGTATCGATACATGCACAAT
8769 TGTATCGATACATG
1 TGTATCGATACATG
8783 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCACAAT
Found at i:8856 original size:33 final size:32
Alignment explanation
Indices: 8814--8876 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
8804 TCACTGTTTA
8814 TATCGATACATG-GCACATTGTATCGATACAATG
1 TATCGATACATGAG-A-ATTGTATCGATACAATG
*
8847 TATCTATACATGATGAATTGTATCGATACA
1 TATCGATACATGA-GAATTGTATCGATACA
8877 TTGCTTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 25 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (32 bp):
TATCGATACATGAGAATTGTATCGATACAATG
Found at i:10475 original size:3 final size:3
Alignment explanation
Indices: 10461--10515 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
10451 ACCATAAAAC
*
10461 GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
10509 GGT GAT G
1 GAT GAT G
10516 TGGACTCAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:11399 original size:23 final size:23
Alignment explanation
Indices: 11370--11422 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
11360 TTGATTGCTA
**
11370 TTTTGCTGGTGTTTGCTTACTGT
1 TTTTGCTGGTACTTGCTTACTGT
*
11393 TTTTGCTGGTACTTGCTTATTGT
1 TTTTGCTGGTACTTGCTTACTGT
11416 TTTTGCT
1 TTTTGCT
11423 AGTTTTGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (23 bp):
TTTTGCTGGTACTTGCTTACTGT
Found at i:11812 original size:69 final size:69
Alignment explanation
Indices: 11681--12027 Score: 502
Period size: 68 Copynumber: 5.0 Consensus size: 69
11671 TCTCTTTTTT
*
11681 TTGTTTCGATTTGATTCTCTCCTTTTTTTTTCACTCTCCCTCGTTAGCTGCTGTTTCGTTTCTCT
1 TTGTTTCGATTTGATTCTCTCC-TTTTTTTT-ACTCTCCCTCGTTAGCTGTTGTTTCGTTTCTCT
11746 CCTTTC
64 CCTTTC
* *
11752 TTGTTTTC-ATTTGATTCTCTCCTTTTTTTTACACTCCCTCATTAGCTGTTGTTTCGTTTCTCTC
1 TTG-TTTCGATTTGATTCTCTCCTTTTTTTTACTCTCCCTCGTTAGCTGTTGTTTCGTTTCTCTC
11816 CTTTC
65 CTTTC
* * * * * * *
11821 TTGTTTCGATTTGATTCTCTCC-TTTTTTCACTCTCCTTCGTTAGCTGCTATTTCATTTCTTTTC
1 TTGTTTCGATTTGATTCTCTCCTTTTTTTTACTCTCCCTCGTTAGCTGTTGTTTCGTTTCTCTCC
11885 TTTC
66 TTTC
*
11889 TTGTTTCGATTTGATTCTCTCC-TTTTTTTACACTCCCTCGTTAGCTGTTGTTTCGTTTCTCTCC
1 TTGTTTCGATTTGATTCTCTCCTTTTTTTTACTCTCCCTCGTTAGCTGTTGTTTCGTTTCTCTCC
11953 TTTC
66 TTTC
* * * * *
11957 TTGTTTCGATGTGATTCTCTCATTTTTTTCACTCTCCCTCGTTAGCTATTGTTTTGTTTCTCTCC
1 TTGTTTCGATTTGATTCTCTCCTTTTTTTTACTCTCCCTCGTTAGCTGTTGTTTCGTTTCTCTCC
12022 TTTC
66 TTTC
12026 TT
1 TT
12028 CCTCCTTTTT
Statistics
Matches: 247, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
68 121 0.49
69 97 0.39
70 8 0.03
71 17 0.07
72 4 0.02
ACGTcount: A:0.08, C:0.26, G:0.10, T:0.56
Consensus pattern (69 bp):
TTGTTTCGATTTGATTCTCTCCTTTTTTTTACTCTCCCTCGTTAGCTGTTGTTTCGTTTCTCTCC
TTTC
Found at i:12061 original size:42 final size:42
Alignment explanation
Indices: 12013--12093 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
12003 TATTGTTTTG
*
12013 TTTCTCTCCTTTCTTCCTCCTTTTTTTTTGCTTTTATAGTTT
1 TTTCTCTCCTTTCTTCCTCCTTTTTGTTTGCTTTTATAGTTT
* *
12055 TTTCTCTCTTTTCTTCTTCCTTTTTGTTTGCTTTTATAG
1 TTTCTCTCCTTTCTTCCTCCTTTTTGTTTGCTTTTATAG
12094 CAGCTTGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.05, C:0.22, G:0.06, T:0.67
Consensus pattern (42 bp):
TTTCTCTCCTTTCTTCCTCCTTTTTGTTTGCTTTTATAGTTT
Found at i:12444 original size:14 final size:14
Alignment explanation
Indices: 12425--12558 Score: 95
Period size: 14 Copynumber: 9.9 Consensus size: 14
12415 GAAAGAAAAC
12425 ATGCATGAAATGTA
1 ATGCATGAAATGTA
* *
12439 ATGCATGAAACGAA
1 ATGCATGAAATGTA
*
12453 ATGCATGAAATGAA
1 ATGCATGAAATGTA
* *
12467 CATTACATGAAATG-C
1 -A-TGCATGAAATGTA
12482 ATGCATGAAATGTA
1 ATGCATGAAATGTA
* *
12496 ATGTATGAAATG-C
1 ATGCATGAAATGTA
*
12509 ATGAAATGAAAAT-T-
1 ATG-CATG-AAATGTA
*
12523 ATG--TGAAATG-C
1 ATGCATGAAATGTA
12534 ATGCATGAAA-GTA
1 ATGCATGAAATGTA
12547 ATGCATGAAATG
1 ATGCATGAAATG
12559 AAAATTACGT
Statistics
Matches: 97, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
10 4 0.04
11 5 0.05
12 1 0.01
13 28 0.29
14 44 0.45
15 5 0.05
16 10 0.10
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (14 bp):
ATGCATGAAATGTA
Found at i:12492 original size:29 final size:27
Alignment explanation
Indices: 12424--12543 Score: 88
Period size: 29 Copynumber: 4.4 Consensus size: 27
12414 TGAAAGAAAA
* ** *
12424 CATGCATGAAATGTAATGCATGAAACG
1 CATGCATGAAATGAAATTAATGAAATG
*
12451 AAATGCATGAAATGAACATTACATGAAATG
1 -CATGCATGAAATGAA-ATTA-ATGAAATG
*
12481 CATGCATGAAATGTAATGT-ATG-AA--
1 CATGCATGAAATGAAAT-TAATGAAATG
*
12505 -ATGCATGAAATGAAAATTATGTGAAATG
1 CATGCATGAAATG-AAATTA-ATGAAATG
12533 CATGCATGAAA
1 CATGCATGAAA
12544 GTAATGCATG
Statistics
Matches: 73, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
23 13 0.18
24 3 0.04
25 2 0.03
26 4 0.05
27 3 0.04
28 15 0.21
29 26 0.36
30 7 0.10
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (27 bp):
CATGCATGAAATGAAATTAATGAAATG
Found at i:12495 original size:57 final size:57
Alignment explanation
Indices: 12424--12561 Score: 198
Period size: 52 Copynumber: 2.5 Consensus size: 57
12414 TGAAAGAAAA
* *
12424 CATGCATGAAATGTAATGCATGAAACGAAATGCATGAAATGAACATTACATGAAATG
1 CATGCATGAAATGTAATGCATGAAATGAAATGCATGAAATGAAAATTACATGAAATG
**
12481 CATGCATGAAATGTAATG--T---ATGAAATGCATGAAATGAAAATTATGTGAAATG
1 CATGCATGAAATGTAATGCATGAAATGAAATGCATGAAATGAAAATTACATGAAATG
12533 CATGCATGAAA-GTAATGCATGAAATGAAA
1 CATGCATGAAATGTAATGCATGAAATGAAA
12562 ATTACGTGAG
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
51 6 0.08
52 40 0.56
53 1 0.01
55 1 0.01
56 6 0.08
57 18 0.25
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (57 bp):
CATGCATGAAATGTAATGCATGAAATGAAATGCATGAAATGAAAATTACATGAAATG
Found at i:12880 original size:17 final size:17
Alignment explanation
Indices: 12833--12880 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
12823 TTTGTTATTA
*
12833 TTATTATTAATATTTTT
1 TTATTATTAATGTTTTT
* * *
12850 TTGTTTTTATTGTTTTT
1 TTATTATTAATGTTTTT
*
12867 TTATTATTCATGTT
1 TTATTATTAATGTT
12881 AAATAAACTG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (17 bp):
TTATTATTAATGTTTTT
Found at i:13451 original size:42 final size:41
Alignment explanation
Indices: 13405--13970 Score: 228
Period size: 42 Copynumber: 13.5 Consensus size: 41
13395 AAACTCTATG
* * * * *
13405 GGGTCAAAGCCAACAAGTAAACTTGAAGTGAGGCAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTT-AAGTGAGGAAGTCTCCA
* * * * **
13447 GGGTCTAAGCCGACAGGTAGAC-TAAGGGTAGGAAACTCTTTA
1 GGGTCAAAGCCGACAGGCAGACTTAAGTG-AGG-AAGTCTCCA
* *
13489 GGGTCAAAGCCGACAGGCAGACTTTAGATGAGGTAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTTAAG-TGAGGAAGTCTCCA
* *
13531 GGGTCAAAGCCGACAGGCAAACTGAAG-GTAGGAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTTAAGTG-AGG-AAGTCTCCA
* * * * * *
13573 AGGTCAAATCCAATAGGCAGACTTTAGATGAGGCAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTTAAG-TGAGGAAGTCTCCA
* **** * * * * *
13615 AGGTCAAAG-CTTTTGGTAGACTGAAAGTAAGAAAGTCTCTA
1 GGGTCAAAGCCGACAGGCAGACT-TAAGTGAGGAAGTCTCCA
* ** * *
13656 AGGTCAAAATCGACAGGCAGACTTTAGATGAGGTAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTTAAG-TGAGGAAGTCTCCA
* * * * * * *
13698 AGGTTAAACCCGACAAGCAGACTGAAGGGTAAGAAAGTC-CCTA
1 GGGTCAAAGCCGACAGGCAGACTTAA--GTGAGGAAGTCTCC-A
* * * * * *
13741 GGGTCAAAGCCAACGGGTAGATTTTAGATGAGGTAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTTAAG-TGAGGAAGTCTCCA
* * * * *
13783 AGGTCAAAAACCGACAGGCAAACTGAAAGT-AGGAAAGTCACCA
1 GGGTC-AAAGCCGACAGGCAGACT-TAAGTGAGG-AAGTCTCCA
* * * * * **
13826 GGATCAAAGCTGACGGGCAGACTTTAGATGAGGCAGTCTTTA
1 GGGTCAAAGCCGACAGGCAGACTTAAG-TGAGGAAGTCTCCA
** ** * * * *
13868 GGGTCAAAG-TTAGCAGATAGACTAAAGGGTAAGAAAGCCTCCA
1 GGGTCAAAGCCGA-CAGGCAGACTTAA--GTGAGGAAGTCTCCA
* * * * *
13911 AGGTCAAAGCCGATATGCA-ACTTTAGATGAGGCAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTTAAG-TGAGGAAGTCTCCA
13952 GGGTCAAAGCCGACAGGCA
1 GGGTCAAAGCCGACAGGCA
13971 AACTAAAAGT
Statistics
Matches: 372, Mismatches: 126, Indels: 53
0.68 0.23 0.10
Matches are distributed among these distances:
40 6 0.02
41 67 0.18
42 213 0.57
43 79 0.21
44 7 0.02
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (41 bp):
GGGTCAAAGCCGACAGGCAGACTTAAGTGAGGAAGTCTCCA
Found at i:13771 original size:85 final size:84
Alignment explanation
Indices: 13433--13970 Score: 469
Period size: 84 Copynumber: 6.4 Consensus size: 84
13423 AAACTTGAAG
* * * * **
13433 TGAGGCAGTCTCCAGGGTCTAAGCCGACAGGTAGACT-AAGGGTAGGAAACTCTTTAGGGTCAAA
1 TGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAA-GGTAGGAAAGTCCCTAGGGTCAAA
13497 GCCGACAGGCAGACTTTAGA
65 GCCGACAGGCAGACTTTAGA
* * * *
13517 TGAGGTAGTCTCCAGGGTCAAAGCCGACAGGCAAACTGAAGGTAGGAAAGTCTCC-AAGGTCAAA
1 TGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAGGAAAGTC-CCTAGGGTCAAA
* * *
13581 TCCAATAGGCAGACTTTAGA
65 GCCGACAGGCAGACTTTAGA
**** * * * * * *
13601 TGAGGCAGTCTCCAAGGTCAAAG-CTTTTGGTAGACTGAAAGTAAGAAAGTCTCTAAGGTCAAAA
1 TGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAGGAAAGTCCCTAGGGTCAAAG
*
13665 TCGACAGGCAGACTTTAGA
66 CCGACAGGCAGACTTTAGA
* * * * *
13684 TGAGGTAGTCTCCAAGGTTAAACCCGACAAGCAGACTGAAGGGTAAGAAAGTCCCTAGGGTCAAA
1 TGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAA-GGTAGGAAAGTCCCTAGGGTCAAA
* * * *
13749 GCCAACGGGTAGATTTTAGA
65 GCCGACAGGCAGACTTTAGA
* * * * *
13769 TGAGGTAGTCTCCAAGGTCAAAAACCGACAGGCAAACTGAAAGTAGGAAAGTCACC-AGGATCAA
1 TGAGGCAGTCTCCAAGGTC-AAAGCCGACAGGCAGACTGAAGGTAGGAAAGTC-CCTAGGGTCAA
* *
13833 AGCTGACGGGCAGACTTTAGA
64 AGCCGACAGGCAGACTTTAGA
** * ** ** * * * *
13854 TGAGGCAGTCTTTAGGGTCAAAG-TTAGCAGATAGACTAAAGGGTAAGAAAG-CCTCCAAGGTCA
1 TGAGGCAGTCTCCAAGGTCAAAGCCGA-CAGGCAGACTGAA-GGTAGGAAAGTCC-CTAGGGTCA
* *
13917 AAGCCGATATGCA-ACTTTAGA
63 AAGCCGACAGGCAGACTTTAGA
*
13938 TGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCA
1 TGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCA
13971 AACTAAAAGT
Statistics
Matches: 362, Mismatches: 80, Indels: 24
0.78 0.17 0.05
Matches are distributed among these distances:
82 1 0.00
83 67 0.19
84 147 0.41
85 127 0.35
86 20 0.06
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (84 bp):
TGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAGGAAAGTCCCTAGGGTCAAAG
CCGACAGGCAGACTTTAGA
Done.