Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1273
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: 50537
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Found at i:258 original size:15 final size:16
Alignment explanation
Indices: 231--265 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
221 AATTCTTAAG
*
231 AAAAAAAGAAAATCAT
1 AAAAAAAGAAAATAAT
247 AAAAAAAG-AAATAAT
1 AAAAAAAGAAAATAAT
262 AAAA
1 AAAA
266 GAATAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAAAAAGAAAATAAT
Found at i:14689 original size:21 final size:22
Alignment explanation
Indices: 14663--14704 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
14653 AGTTTCTCAA
*
14663 TATTTTAAT-TTCAAAATATTT
1 TATTTTAATACTCAAAATATTT
*
14684 TATTTTTATACTCAAAATATT
1 TATTTTAATACTCAAAATATT
14705 AAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAATACTCAAAATATTT
Found at i:14783 original size:22 final size:21
Alignment explanation
Indices: 14758--14836 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 21
14748 ATCTAAATTA
14758 AAAAATTTATTTAAATATAAAT
1 AAAAATTTATTT-AATATAAAT
*
14780 AAAAATTAAAAATTATTTTAATAAAAATT
1 AAAAA-T-----TTA-TTTAATATAAA-T
14809 AAAAATTTATTTAATATAAAT
1 AAAAATTTATTTAATATAAAT
*
14830 TAAAATT
1 AAAAATT
14837 ATTGACTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
21 7 0.15
22 15 0.33
23 4 0.09
28 11 0.24
29 9 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATTTATTTAATATAAAT
Found at i:14790 original size:28 final size:27
Alignment explanation
Indices: 14759--14837 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
14749 TCTAAATTAA
14759 AAAATTTATTTAAATATAAATAAAAATT
1 AAAATTTATTT-AATATAAATAAAAATT
*
14787 AAAAATTA-TT--T-T-AATAAAAATT
1 AAAATTTATTTAATATAAATAAAAATT
*
14809 AAAAATTTATTTAATATAAATTAAAATT
1 -AAAATTTATTTAATATAAATAAAAATT
14837 A
1 A
14838 TTGACTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
22 10 0.24
23 8 0.19
24 3 0.07
26 1 0.02
27 4 0.10
28 16 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAATTTATTTAATATAAATAAAAATT
Found at i:14800 original size:29 final size:30
Alignment explanation
Indices: 14752--14815 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
14742 TTTTATATCT
*
14752 AAATTAAAAAATTTATTTAAATATAAA-TAA
1 AAATTAAAAAATTTATTT-AATAAAAATTAA
14782 AAATT-AAAAA-TTATTTTAATAAAAATTAA
1 AAATTAAAAAATTTA-TTTAATAAAAATTAA
14811 AAATT
1 AAATT
14816 TATTTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 10 0.32
29 16 0.52
30 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATTAAAAAATTTATTTAATAAAAATTAA
Found at i:14806 original size:23 final size:22
Alignment explanation
Indices: 14777--14839 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
14767 TTTAAATATA
14777 AATAAAAATTAAAAATTATTTT
1 AATAAAAATTAAAAATTATTTT
14799 AATAAAAATTAAAAATT-TATTT
1 AATAAAAATTAAAAATTAT-TTT
*
14821 AATATAAATT-AAAATTATT
1 AATAAAAATTAAAAATTATT
14840 GACTTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 8 0.21
22 30 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAAAAATTAAAAATTATTTT
Found at i:15190 original size:22 final size:22
Alignment explanation
Indices: 15165--15209 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
15155 TAGATTTTGT
* *
15165 TTTATTTTATTAATAATTTTTA
1 TTTATTTTATAAATAATATTTA
15187 TTTATTTTATAAATAATATTTA
1 TTTATTTTATAAATAATATTTA
15209 T
1 T
15210 ATTACTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTTTATAAATAATATTTA
Found at i:18784 original size:240 final size:229
Alignment explanation
Indices: 18336--18796 Score: 663
Period size: 240 Copynumber: 2.0 Consensus size: 229
18326 CGAAAATCGA
18336 TTGCTTCATTATCTTCCACTTGGCCTATCTAACAAACTAAAAGAAGGCAAGCAGAATACAATATA
1 TTGCTTCATTATCTTCCACTTGGCCTATCTAACAAACTAAAAGAAGGCAAGCAGAATACAATATA
* *
18401 AAAAAGAAACCTTTTAAAACTAAAATAAAAAAGACTGGAACACCAAGGCCAACCCAGGACCTTGC
66 AAAAAGAAACCTTTTAAAACTAAAATAAAAAAGACTAGAACACCAAGGCCAACCCAGCACCTTGC
* * *
18466 TTAATTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTCGGAAATGGACAAATCATTCAAAA
131 CTAATTACCCTAAATCAATTGGGTTCATAAAAAGAACAGCTCGGAAATGGACAAATCATTCAAAA
18531 AAACTCTTTCACCAGTATCCTTTCTAGAGCTGGT
196 AAACTCTTTCACCAGTATCCTTTCTAGAGCTGGT
* *
18565 TTGCTTCATTGTCTTCCACTTGGCCTATCTACCAAACTACAGGAAGACAAGAAGGCAAGCAGAAT
1 TTGCTTCATTATCTTCCACTTGGCCTATCTAACAAACT------A-A-AAGAAGGCAAGCAGAAT
* * *
18630 ACATTATAAAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCTAGAACACCAAGGCCAAAT
58 ACAATATAAAAAAGAAACCTTTTAAAACTAAAATAAAAAAG--A-CTAGAACACCAAGGCC-AAC
* * *
18695 CCATCACCTTGCCTAGTTACCCTAAATCAATTGGGTTCAT-AAAAGAACAGCTTGGAAATGGACA
119 CCAGCACCTTGCCTAATTACCCTAAATCAATTGGGTTCATAAAAAGAACAGCTCGGAAATGGACA
* * *
18759 TATCATTCAAAAAACCTCTTTCACCAGTTTCCTTTCTA
184 AATCATTCAAAAAAACTCTTTCACCAGTATCCTTTCTA
18797 AAAACTGGTT
Statistics
Matches: 204, Mismatches: 16, Indels: 13
0.88 0.07 0.06
Matches are distributed among these distances:
229 36 0.18
235 1 0.00
236 1 0.00
237 56 0.27
239 1 0.00
240 72 0.35
241 37 0.18
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (229 bp):
TTGCTTCATTATCTTCCACTTGGCCTATCTAACAAACTAAAAGAAGGCAAGCAGAATACAATATA
AAAAAGAAACCTTTTAAAACTAAAATAAAAAAGACTAGAACACCAAGGCCAACCCAGCACCTTGC
CTAATTACCCTAAATCAATTGGGTTCATAAAAAGAACAGCTCGGAAATGGACAAATCATTCAAAA
AAACTCTTTCACCAGTATCCTTTCTAGAGCTGGT
Found at i:20066 original size:2 final size:2
Alignment explanation
Indices: 20053--20083 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20043 ATGGAGCCTA
*
20053 AT AT AT AC 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 AT A
20084 ACATTCTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:26304 original size:397 final size:397
Alignment explanation
Indices: 25571--26370 Score: 1593
Period size: 397 Copynumber: 2.0 Consensus size: 397
25561 AGCTAGTGAA
25571 ACATTTAAGTAGCGAAGAAAGATAGTGAAAATCACACTCCTTGCCTTAAAATTTAATATGTTTGA
1 ACATTTAAGTAGCGAAGAAAGATAGTGAAAATCACACTCCTTGCCTTAAAATTTAATATGTTTGA
25636 GGCCAATGGAATCACAGCCATCGCCAGGAACCTCTAATACACTCGGACTTTAGAAAAAAAAACTT
66 GGCCAATGGAATCACAGCCATCGCCAGGAACCTCTAATACACTCGGACTTTAGAAAAAAAAACTT
25701 GTTTAATTCTGTAGAAGTGTGCAAGGTGACTGTCAAGCCTTCAGCAGTATGTAAGAGAGTAAATG
131 GTTTAATTCTGTAGAAGTGTGCAAGGTGACTGTCAAGCCTTCAGCAGTATGTAAGAGAGTAAATG
25766 TATAAAGCAAAAGGAAAAGGACCATCACAGAAATAGCATACCTCACAGCTTATCCAAAGGGAAAG
196 TATAAAGCAAAAGGAAAAGGACCATCACAGAAATAGCATACCTCACAGCTTATCCAAAGGGAAAG
25831 GAAATTGTTGGTTACATAAAATTAGAGTCAGAACTTACATACAGACACGCACACAAAAAAAAAAA
261 GAAATTGTTGGTTACATAAAATTAGAGTCAGAACTTACATACAGACACGCACACAAAAAAAAAAA
25896 AGTAAAATGAATGAAGATAAATGACTGATTGAACCTACTTGAGGCTTATTTAGGGCTAGGTTGCC
326 AGTAAAATGAATGAAGATAAATGACTGATTGAACCTACTTGAGGCTTATTTAGGGCTAGGTTGCC
25961 GCCTGCG
391 GCCTGCG
25968 ACATTTAAGTAGCGAAGAAAGATAGTGAAAATCACACTCCTTGCCTTAAAATTTAATATGTTTGA
1 ACATTTAAGTAGCGAAGAAAGATAGTGAAAATCACACTCCTTGCCTTAAAATTTAATATGTTTGA
26033 GGCCAATGGAATCACAGCCATCGCCAGGAACCTCTAATACACTCGGACTTTAGAAAAAAAAACTT
66 GGCCAATGGAATCACAGCCATCGCCAGGAACCTCTAATACACTCGGACTTTAGAAAAAAAAACTT
26098 GTTTAATTCTGTAGAAGTGTGCAAGGTGACTGTCAAGCCTTCAGCAGTATGTAAGAGAGTAAATG
131 GTTTAATTCTGTAGAAGTGTGCAAGGTGACTGTCAAGCCTTCAGCAGTATGTAAGAGAGTAAATG
26163 TATAAAGCAAAAGGAAAAGGACCATCACAGAAATAGCATACCTCACAGCTTATCCAAAGGGAAAG
196 TATAAAGCAAAAGGAAAAGGACCATCACAGAAATAGCATACCTCACAGCTTATCCAAAGGGAAAG
26228 GAAATTGTTGGTTACATAAAATTAGAGTCAGAACTTACATACAGACACGCACACAAAAAAAAAAA
261 GAAATTGTTGGTTACATAAAATTAGAGTCAGAACTTACATACAGACACGCACACAAAAAAAAAAA
26293 AGTAAAATGAATGAAGATAAATGACTGATTGAACCTACTTGAGGCTTATTTAGGGCTAGGTTGCC
326 AGTAAAATGAATGAAGATAAATGACTGATTGAACCTACTTGAGGCTTATTTAGGGCTAGGTTGCC
26358 GCCTGCG
391 GCCTGCG
26365 AC-TTTA
1 ACATTTA
26371 TTTCCATTAC
Statistics
Matches: 403, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
396 4 0.01
397 399 0.99
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (397 bp):
ACATTTAAGTAGCGAAGAAAGATAGTGAAAATCACACTCCTTGCCTTAAAATTTAATATGTTTGA
GGCCAATGGAATCACAGCCATCGCCAGGAACCTCTAATACACTCGGACTTTAGAAAAAAAAACTT
GTTTAATTCTGTAGAAGTGTGCAAGGTGACTGTCAAGCCTTCAGCAGTATGTAAGAGAGTAAATG
TATAAAGCAAAAGGAAAAGGACCATCACAGAAATAGCATACCTCACAGCTTATCCAAAGGGAAAG
GAAATTGTTGGTTACATAAAATTAGAGTCAGAACTTACATACAGACACGCACACAAAAAAAAAAA
AGTAAAATGAATGAAGATAAATGACTGATTGAACCTACTTGAGGCTTATTTAGGGCTAGGTTGCC
GCCTGCG
Found at i:45275 original size:2 final size:2
Alignment explanation
Indices: 45268--45294 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45258 CAGTACGTAA
45268 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
45295 ATCTGAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45550 original size:29 final size:29
Alignment explanation
Indices: 45495--45550 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
45485 TTTTATATTT
*
45495 AAATAAAAAATTTATTTAAATATAAATAA
1 AAATAAAAAATTTATTTAAATAGAAATAA
**
45524 AAATAAAAAATTTATTTTGATAGAAAT
1 AAATAAAAAATTTATTTAAATAGAAAT
45551 TCAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (29 bp):
AAATAAAAAATTTATTTAAATAGAAATAA
Found at i:45979 original size:25 final size:26
Alignment explanation
Indices: 45951--46015 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
45941 TATTACATAG
*
45951 TTTTAATACATATACGTATTTT-TTA
1 TTTTAATACATATACGTATTTTATAA
* * *
45976 TTTTAATATTATTATACTTCTTTTATAA
1 TTTTAATA-CA-TATACGTATTTTATAA
46004 TTTTAATACATA
1 TTTTAATACATA
46016 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 8 0.25
26 3 0.09
27 11 0.34
28 10 0.31
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTTAATACATATACGTATTTTATAA
Found at i:47314 original size:22 final size:22
Alignment explanation
Indices: 47286--47329 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
47276 GGAAGGAAAA
47286 TAAAGAAGAGGAGAATTGAGAG
1 TAAAGAAGAGGAGAATTGAGAG
47308 TAAAGAAGAGGAGAATTGAGAG
1 TAAAGAAGAGGAGAATTGAGAG
47330 AGAGAACCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (22 bp):
TAAAGAAGAGGAGAATTGAGAG
Found at i:49298 original size:383 final size:382
Alignment explanation
Indices: 48585--49353 Score: 1369
Period size: 383 Copynumber: 2.0 Consensus size: 382
48575 TATAAAAACA
* * * *
48585 AAATATACCCAAGGCAGAATACACGAGTAAAAAAAGCTAAGTAGTAGATGGGTCTAATCTCCATT
1 AAATACACCCAAGGCAGAATACACAAGTAAAAAAAGCTAAGTAGTAGATGGGTCTAACCTCCATA
* **
48650 TCGGAGATGGAGTGCTGCTTCCATAGATAGAGTGGCAATCAGCTCTAAACAAAAGGGGAGGAAAT
66 TCGGAGATGGAGTGCTGCTTCCATAGATAGAGTGGCAATCAGCTCTAAAAAAAAAAGGAGGAAAT
48715 GCAAAATAAGAAAAGAAAATTGGAAATATATTTTACCTACTTGCGGAGATGGATGGAGTCACCAC
131 GCAAAATAAGAAAAGAAAATTGGAAATATATTTTACCTACTTGCGGAGATGGATGGAGTCACCAC
*
48780 ACTTGAGGTTGATCATGATGAGGAAGGGGACTTTGCTGTGCTCACACTGGCTCCACTTGAAGAAT
196 ACTTGAGGTTGATCATGATGAGGAAGGGGACTTTGCTGTGCTCACACTGGCCCCACTTGAAGAAT
*
48845 CAGCCATGACCAAGCACCTCCTTCAGCAAAAGGGATCAAGTGTAAAAGTGAAGAAAAAGAAATTT
261 CAGCCACGACCAAGCACCTCCTTCAGCAAAAGGGATCAAGTGTAAAAGTGAAGAAAAAGAAATTT
48910 TGGAAGGATAAAAGAGAAGAAGACGAGAGAAAACAAA-AAGGAAAAGAAAATAAGGTCT
326 TGGAAGGATAAAAGAGAAGAAGAC--GAGAAAACAAACAAGGAAAAGAAAATAAGGTCT
48968 AAATACACCCAAGGCAGAATACACAAGTAAAAAAAGCTAAGTAGTAGATGGGTCTAACCTCCATA
1 AAATACACCCAAGGCAGAATACACAAGTAAAAAAAGCTAAGTAGTAGATGGGTCTAACCTCCATA
** *
49033 TCGGAGATGGAGTGCTGCTTCTGTAGATAGAGTGGCGATCAGCTCTAAAAAAAAAAGGAGGAAAT
66 TCGGAGATGGAGTGCTGCTTCCATAGATAGAGTGGCAATCAGCTCTAAAAAAAAAAGGAGGAAAT
* *
49098 GCAAAATAAGAAAAGAAAATTGGACATATATTTTACGTACTTGCGGAGATGGATGGAGTCACCAC
131 GCAAAATAAGAAAAGAAAATTGGAAATATATTTTACCTACTTGCGGAGATGGATGGAGTCACCAC
*
49163 GCTTGAGGTTGATCATGATGAGGAAGGGGACTTTGCTGTGCTCACACTGGCCCCACTTGAAGAAT
196 ACTTGAGGTTGATCATGATGAGGAAGGGGACTTTGCTGTGCTCACACTGGCCCCACTTGAAGAAT
*
49228 CAGCCACGACCAAGCACCTCCTTCAGCGAAAGGGATCAAGTGTAAAAGTGAAGAAAAAGAAATTT
261 CAGCCACGACCAAGCACCTCCTTCAGCAAAAGGGATCAAGTGTAAAAGTGAAGAAAAAGAAATTT
49293 TGGAAGGATAAAAGAGAAGAAGACGAGAAAACAAACAAGGAAAAGAAAATAAGGTCT
326 TGGAAGGATAAAAGAGAAGAAGACGAGAAAACAAACAAGGAAAAGAAAATAAGGTCT
49350 AAAT
1 AAAT
49354 CCCGGACCTT
Statistics
Matches: 369, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
381 11 0.03
382 25 0.07
383 333 0.90
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.19
Consensus pattern (382 bp):
AAATACACCCAAGGCAGAATACACAAGTAAAAAAAGCTAAGTAGTAGATGGGTCTAACCTCCATA
TCGGAGATGGAGTGCTGCTTCCATAGATAGAGTGGCAATCAGCTCTAAAAAAAAAAGGAGGAAAT
GCAAAATAAGAAAAGAAAATTGGAAATATATTTTACCTACTTGCGGAGATGGATGGAGTCACCAC
ACTTGAGGTTGATCATGATGAGGAAGGGGACTTTGCTGTGCTCACACTGGCCCCACTTGAAGAAT
CAGCCACGACCAAGCACCTCCTTCAGCAAAAGGGATCAAGTGTAAAAGTGAAGAAAAAGAAATTT
TGGAAGGATAAAAGAGAAGAAGACGAGAAAACAAACAAGGAAAAGAAAATAAGGTCT
Done.