Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1739
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: 15093
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Found at i:281 original size:14 final size:13
Alignment explanation
Indices: 255--304 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 13
245 TATCTTGGGT
255 TTCTTTATCTGGA
1 TTCTTTATCTGGA
268 TTCTTTATTCTGGA
1 TTCTTTA-TCTGGA
282 TT-TTCTATCTTGGA
1 TTCTT-TATC-TGGA
296 TTTCTTTAT
1 -TTCTTTAT
305 TCGGTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 11 0.34
14 14 0.44
15 5 0.16
16 2 0.06
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (13 bp):
TTCTTTATCTGGA
Found at i:312 original size:13 final size:14
Alignment explanation
Indices: 252--314 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 14
242 TCGTATCTTG
252 GGTTTCTTTA-TCT
1 GGTTTCTTTATTCT
*
265 GGATTCTTTATTCT
1 GGTTTCTTTATTCT
*
279 GGATTT-TCTA-TCTT
1 GG-TTTCTTTATTC-T
293 GGATTTCTTTATTC-
1 GG-TTTCTTTATTCT
307 GGTTTCTT
1 GGTTTCTT
315 GTTATCTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 17 0.41
14 17 0.41
15 5 0.12
16 2 0.05
ACGTcount: A:0.11, C:0.14, G:0.16, T:0.59
Consensus pattern (14 bp):
GGTTTCTTTATTCT
Found at i:2737 original size:46 final size:45
Alignment explanation
Indices: 2684--2856 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
2674 TATTTGGGCA
2684 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
2730 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGA--GATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
2775 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
2821 CCCGAGCTCGTTGAGTTGAGT-CGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2857 CGGGTTACAT
Statistics
Matches: 109, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 46 0.42
46 53 0.49
47 4 0.04
48 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:2793 original size:91 final size:90
Alignment explanation
Indices: 2680--2849 Score: 295
Period size: 91 Copynumber: 1.9 Consensus size: 90
2670 AGGATATTTG
* *
2680 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
2745 TTGAGTCCGAGTTCGAGATGTAACTA
66 TTGAGT-CGAGTTCGAGATGTAACTA
* *
2771 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
2836 TTGAGTCGAGTTCG
66 TTGAGTCGAGTTCG
2850 CTTATGGCGG
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 8 0.11
91 67 0.89
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28
Consensus pattern (90 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCGAGTTCGAGATGTAACTA
Found at i:5786 original size:15 final size:15
Alignment explanation
Indices: 5733--5793 Score: 74
Period size: 15 Copynumber: 4.2 Consensus size: 15
5723 CATAGTATCG
*
5733 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTT
5748 TATC-TGGATTT-TT
1 TATCTTGGATTTCTT
*
5761 TAT-TCTGGATTTCTC
1 TATCT-TGGATTTCTT
5776 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
5791 TAT
1 TAT
5794 TCGGTTTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 5 0.13
14 13 0.33
15 20 0.51
16 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.59
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:5802 original size:29 final size:28
Alignment explanation
Indices: 5742--5803 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
5732 GTATCTTGGG
*
5742 TTTCTTTATCTGGATTTTTTATTCTGGA
1 TTTCTCTATCTGGATTTTTTATTCTGGA
*
5770 TTTCTCTATCTTGGATTTCTTTATTC-GGT
1 TTTCTCTATC-TGGATTT-TTTATTCTGGA
5799 TTTCT
1 TTTCT
5804 TGTTATCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 9 0.30
29 14 0.47
30 7 0.23
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.61
Consensus pattern (28 bp):
TTTCTCTATCTGGATTTTTTATTCTGGA
Found at i:8213 original size:46 final size:46
Alignment explanation
Indices: 8160--8335 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
8150 GTATTTGGCA
8160 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
8206 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
8251 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
8299 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
8336 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 64 0.58
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:8315 original size:93 final size:93
Alignment explanation
Indices: 8156--8328 Score: 310
Period size: 93 Copynumber: 1.9 Consensus size: 93
8146 ACTGGTATTT
* *
8156 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
8221 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
8249 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
8314 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
8329 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:10591 original size:37 final size:38
Alignment explanation
Indices: 10550--10957 Score: 358
Period size: 37 Copynumber: 11.0 Consensus size: 38
10540 AATGGAATAT
* * *
10550 TGAATAG-GCTCAAACAAGCAATGTCTACTCATTATAC
1 TGAATAGTGCTCAAACGAGCAATATCTACTAATTATAC
* *
10587 TGAAT-GTGTTCAAACGAGCAATATCTACTGAA-TCTAC
1 TGAATAGTGCTCAAACGAGCAATATCTACT-AATTATAC
* * * *
10624 TGAA-CGTACTCAAAAGAG-AATGTCTACTAATTATAC
1 TGAATAGTGCTCAAACGAGCAATATCTACTAATTATAC
*
10660 TGAA-AGTTGCTCAAACGAGCAATATCTACTAATTATAA
1 TGAATAG-TGCTCAAACGAGCAATATCTACTAATTATAC
*
10698 TGAAT-GTTCTCAAACGAGCAATATCTACTAAATT-TAC
1 TGAATAGTGCTCAAACGAGCAATATCTACT-AATTATAC
* * * *
10735 TGAAT-GTGCTCAAAAGAGCAATGTTTACTGATTATAC
1 TGAATAGTGCTCAAACGAGCAATATCTACTAATTATAC
* * * *
10772 TGAA-AGTTCCTCAAACGAGCAATATCCATTGATTATAC
1 TGAATAG-TGCTCAAACGAGCAATATCTACTAATTATAC
* *
10810 TGAAT-GGGCTCAAACGAGCAATATCTACTAAATATAC
1 TGAATAGTGCTCAAACGAGCAATATCTACTAATTATAC
* * * *
10847 TGAA-CGTGCTCAAAAGAGAAATGTCTACTAATTATAC
1 TGAATAGTGCTCAAACGAGCAATATCTACTAATTATAC
* * * *
10884 T-AAAAGTTGCTCAAACGAGCGATATCCACTGATTATAC
1 TGAATAG-TGCTCAAACGAGCAATATCTACTAATTATAC
* * ** * *
10922 TGAAT-GGGTTCAAACGAGTGATATCCACTGATTATA
1 TGAATAGTGCTCAAACGAGCAATATCTACTAATTATA
10958 TGGAATGCAT
Statistics
Matches: 305, Mismatches: 50, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
35 2 0.01
36 24 0.08
37 194 0.64
38 83 0.27
39 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (38 bp):
TGAATAGTGCTCAAACGAGCAATATCTACTAATTATAC
Found at i:10786 original size:75 final size:73
Alignment explanation
Indices: 10558--10925 Score: 398
Period size: 74 Copynumber: 5.0 Consensus size: 73
10548 ATTGAATAGG
* * * * *
10558 CTCAAACAAGCAATGTCTACTCATTATACTGAATGTGTTCAAACGAGCAATATCTACTGAATCTA
1 CTCAAACGAGCAATGTCTACTAATTATACTGAATGTGCTCAAACGAGCAATATCTACTGATTATA
10623 CTGAACGT
66 CTGAACGT
* * *
10631 ACTCAAAAGAG-AATGTCTACTAATTATACTGAAAGTTGCTCAAACGAGCAATATCTACTAATTA
1 -CTCAAACGAGCAATGTCTACTAATTATACTGAATG-TGCTCAAACGAGCAATATCTACTGATTA
* *
10695 TAATGAATGTT
64 TACTGAACG-T
* * * *
10706 CTCAAACGAGCAATATCTACTAAATT-TACTGAATGTGCTCAAAAGAGCAATGTTTACTGATTAT
1 CTCAAACGAGCAATGTCTACT-AATTATACTGAATGTGCTCAAACGAGCAATATCTACTGATTAT
*
10770 ACTGAAAGTT
65 ACTGAACG-T
* * * * * * *
10780 CCTCAAACGAGCAATATCCATTGATTATACTGAATGGGCTCAAACGAGCAATATCTACTAAATAT
1 -CTCAAACGAGCAATGTCTACTAATTATACTGAATGTGCTCAAACGAGCAATATCTACTGATTAT
10845 ACTGAACGT
65 ACTGAACGT
* * * * * *
10854 GCTCAAAAGAGAAATGTCTACTAATTATACTAAAAGTTGCTCAAACGAGCGATATCCACTGATTA
1 -CTCAAACGAGCAATGTCTACTAATTATACTGAATG-TGCTCAAACGAGCAATATCTACTGATTA
10919 TACTGAA
64 TACTGAA
10926 TGGGTTCAAA
Statistics
Matches: 244, Mismatches: 43, Indels: 13
0.81 0.14 0.04
Matches are distributed among these distances:
73 22 0.09
74 112 0.46
75 106 0.43
76 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (73 bp):
CTCAAACGAGCAATGTCTACTAATTATACTGAATGTGCTCAAACGAGCAATATCTACTGATTATA
CTGAACGT
Found at i:10946 original size:112 final size:111
Alignment explanation
Indices: 10557--10939 Score: 543
Period size: 112 Copynumber: 3.4 Consensus size: 111
10547 TATTGAATAG
* * * * * * *
10557 GCTCAAACAAGCAATGTCTACTCATTATACTGAATGTGTTCAAACGAGCAATATCTACTGAATCT
1 GCTCAAACGAGCAATATCCACTGATTATACTGAATGGGTTCAAACGAGCAATATCTACTAAATAT
*
10622 ACTGAACGTACTCAAAAGAGAATGTCTACTAATTATACTGAAAGTT
66 ACTGAACGTGCTCAAAAGAGAATGTCTACTAATTATACTGAAAGTT
* * * * *
10668 GCTCAAACGAGCAATATCTACTAATTATAATGAAT-GTTCTCAAACGAGCAATATCTACTAAATT
1 GCTCAAACGAGCAATATCCACTGATTATACTGAATGGGT-TCAAACGAGCAATATCTACTAAATA
* * *
10732 TACTGAATGTGCTCAAAAGAGCAATGTTTACTGATTATACTGAAAGTT
65 TACTGAACGTGCTCAAAAGAG-AATGTCTACTAATTATACTGAAAGTT
* * *
10780 CCTCAAACGAGCAATATCCATTGATTATACTGAATGGGCTCAAACGAGCAATATCTACTAAATAT
1 GCTCAAACGAGCAATATCCACTGATTATACTGAATGGGTTCAAACGAGCAATATCTACTAAATAT
*
10845 ACTGAACGTGCTCAAAAGAGAAATGTCTACTAATTATACTAAAAGTT
66 ACTGAACGTGCTCAAAAGAG-AATGTCTACTAATTATACTGAAAGTT
*
10892 GCTCAAACGAGCGATATCCACTGATTATACTGAATGGGTTCAAACGAG
1 GCTCAAACGAGCAATATCCACTGATTATACTGAATGGGTTCAAACGAG
10940 TGATATCCAC
Statistics
Matches: 240, Mismatches: 29, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
110 1 0.00
111 73 0.30
112 165 0.69
113 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (111 bp):
GCTCAAACGAGCAATATCCACTGATTATACTGAATGGGTTCAAACGAGCAATATCTACTAAATAT
ACTGAACGTGCTCAAAAGAGAATGTCTACTAATTATACTGAAAGTT
Found at i:10956 original size:75 final size:75
Alignment explanation
Indices: 10550--10957 Score: 332
Period size: 75 Copynumber: 5.5 Consensus size: 75
10540 AATGGAATAT
* * * * * * *
10550 TGAATAGG-CTCAAACAAGCAATGTCTACTCATTATACTGAATGTGTTCAAACGAGCAATATCTA
1 TGAATGGGTCTCAAACGAGCAATATCCACTAATTATACTGAAAGTGCTCAAACGAGCAATATCTA
*
10614 CTGAA-TCTAC
66 CT-AATTATAC
* * * *
10624 TGAA--CGTACTCAAAAGAG-AATGTCTACTAATTATACTGAAAGTTGCTCAAACGAGCAATATC
1 TGAATGGGT-CTCAAACGAGCAATATCCACTAATTATACTGAAAG-TGCTCAAACGAGCAATATC
*
10686 TACTAATTATAA
64 TACTAATTATAC
* * * * * *
10698 TGAAT-GTTCTCAAACGAGCAATATCTACTAAATT-TACTGAATGTGCTCAAAAGAGCAATGTTT
1 TGAATGGGTCTCAAACGAGCAATATCCACT-AATTATACTGAAAGTGCTCAAACGAGCAATATCT
*
10761 ACTGATTATAC
65 ACTAATTATAC
* * * * * *
10772 TGAA-AGTTCCTCAAACGAGCAATATCCATTGATTATACTGAATGGGCTCAAACGAGCAATATCT
1 TGAATGGGT-CTCAAACGAGCAATATCCACTAATTATACTGAAAGTGCTCAAACGAGCAATATCT
*
10836 ACTAAATATAC
65 ACTAATTATAC
* * * * * * * * *
10847 TGAACGTG-CTCAAAAGAGAAATGTCTACTAATTATACTAAAAGTTGCTCAAACGAGCGATATCC
1 TGAATGGGTCTCAAACGAGCAATATCCACTAATTATACTGAAAG-TGCTCAAACGAGCAATATCT
*
10911 ACTGATTATAC
65 ACTAATTATAC
** *
10922 TGAATGGGT-TCAAACGAGTGATATCCACTGATTATA
1 TGAATGGGTCTCAAACGAGCAATATCCACTAATTATA
10958 TGGAATGCAT
Statistics
Matches: 270, Mismatches: 51, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
72 1 0.00
73 24 0.09
74 113 0.42
75 128 0.47
76 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (75 bp):
TGAATGGGTCTCAAACGAGCAATATCCACTAATTATACTGAAAGTGCTCAAACGAGCAATATCTA
CTAATTATAC
Done.