Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1517
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: 10286
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Found at i:4596 original size:27 final size:27
Alignment explanation
Indices: 4529--5076 Score: 810
Period size: 27 Copynumber: 20.0 Consensus size: 27
4519 TGGCATTTCT
* *
4529 TTTTGAAGTCCACAACTCTGTGGCATCCT
1 TTTT-AAGTCCACAACTCCGTGGCA-CCC
* *
4558 TTTTAAGTCCACAATTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
4585 TTTTAAATCCACAACTCCGTGGCACTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
4612 TTTTAAAGTCCACAACTCCGTGGCACTC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
4640 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
4668 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
** *
4695 TTCAAAGTCCACAACTCCGTGGCACTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
4722 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
4750 TTTTAAGTCCACAACTCTGTGGCA-CC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
4776 TTTCAAAGTCCACAACTCCGTGGCACCC
1 TTT-TAAGTCCACAACTCCGTGGCACCC
* * *
4804 TTTTAAGTCCACAACTCCGTAGCGCTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
4831 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
4859 TCTTTAAGTCCACAACTCCGTGGCACTC
1 T-TTTAAGTCCACAACTCCGTGGCACCC
4887 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
4914 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
4941 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
* *
4969 TTTTAAGACCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
4996 TTTTAAGTCCGCAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
5023 TTTTAAGTCCACAACTTCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
5050 TTTTAAATCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
5077 ATTTCAAAGC
Statistics
Matches: 475, Mismatches: 37, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.01
27 291 0.61
28 172 0.36
29 7 0.01
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:4721 original size:82 final size:81
Alignment explanation
Indices: 4534--5076 Score: 795
Period size: 82 Copynumber: 6.6 Consensus size: 81
4524 TTTCTTTTTG
* * * *
4534 AAGTCCACAACTCTGTGGCA-TCCTTTTTAAGTCCACAATTCTGTGGCACCCTTTTAAATCCACA
1 AAGTCCACAACTCCGTGGCACT-C-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACA
*
4598 ACTCCGTGGCACTCTTTTA
64 ACTCCGTGGCAC-CCTTTA
4617 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
1 AAGTCCACAACTCCGTGGCACTCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
*
4682 CTCCGTGGCACCCTTCA
65 CTCCGTGGCACCCTTTA
4699 AAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
1 AAGTCCACAACTCCGTGGCACTCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
*
4764 CTCTGTGGCA-CCTTTCA
65 CTCCGTGGCACCCTTT-A
* * * *
4781 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTAGCGCTCTTTTAAAGTCCACAA
1 AAGTCCACAACTCCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAA
*
4846 CTCCGTGGCACCCTCTTT
65 CTCCGTGGCACCCT-TTA
4864 AAGTCCACAACTCCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
1 AAGTCCACAACTCCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
*
4929 TCCGTGGCACCCTTTT
66 TCCGTGGCACCCTTTA
* * * *
4945 AAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCTGTGGCACCCTTTTAAGTCCGCAA
1 AAGTCCACAACTCCGTGGCA-CTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA
*
5010 CTCCGTGGCACCCTTTT
65 CTCCGTGGCACCCTTTA
* *
5027 AAGTCCACAACTTCGTGGCA-TCCTTTTAAATCCACAACTCCGTGGCACCC
1 AAGTCCACAACTCCGTGGCACT-CTTTTAAGTCCACAACTCCGTGGCACCC
5077 ATTTCAAAGC
Statistics
Matches: 425, Mismatches: 27, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
81 76 0.18
82 228 0.54
83 118 0.28
84 3 0.01
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.27
Consensus pattern (81 bp):
AAGTCCACAACTCCGTGGCACTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
TCCGTGGCACCCTTTA
Found at i:4946 original size:219 final size:218
Alignment explanation
Indices: 4529--5091 Score: 857
Period size: 219 Copynumber: 2.6 Consensus size: 218
4519 TGGCATTTCT
* * * *
4529 TTTTGAAGTCCACAACTCTGTGGCATCCTTTTTAAGTCCACAATTCTGTGGCACCCTTTTAAATC
1 TTTT-AAGTCCACAACTCTGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
4594 CACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCC
64 CACAACTCCGT-GCGCTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCC
*
4659 GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTCAAAGTCCACAACTCCGTGGCACTCTT
128 GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTCAAAGTCCACAACTCCGTGGCACCCTT
4724 TTAAAGTCCACAACTCCGTGGCA-CCC
193 TT-AAGTCCACAACTCCGTGGCATCCC
*
4750 TTTTAAGTCCACAACTCTGTGGCA-CCTTTCAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 TTTTAAGTCCACAACTCTGTGGCACCCTTT-TAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
4814 ACAACTCCGTAGCGCTCTTTTAAAGTCCACAACTCCGTGGCACCCTCTTT-AAGTCCACAACTCC
65 ACAACTCCGT-GCGCTCTTTTAAAGTCCACAACTCCGTGGCACCCT-TTTAAAGTCCACAACTCC
* **
4878 GTGGCACTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTT
128 GTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTCAAAGTCCACAACTCCGTGGCACCCTT
4943 TTAAGTCCACAACTCCGTGGCATCCC
193 TTAAGTCCACAACTCCGTGGCATCCC
* *
4969 TTTTAAGACCACAACTCTGTGGCACCCTTTTAAGTCCGCAACTCCGTGGCACCCTTTTAAGTCCA
1 TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* * *
5034 CAACTTCGTG-GCATCCTTTTAAA-TCCACAACTCCGTGGCACCCATTTCAAAGCCCACA
66 CAACTCCGTGCGC-T-CTTTTAAAGTCCACAACTCCGTGGCACCC-TTTTAAAGTCCACA
5092 CAAGTCAGTG
Statistics
Matches: 316, Mismatches: 18, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
217 2 0.01
218 48 0.15
219 234 0.74
220 28 0.09
221 4 0.01
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.27
Consensus pattern (218 bp):
TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
CAACTCCGTGCGCTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
GCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTCAAAGTCCACAACTCCGTGGCACCCTTTTA
AGTCCACAACTCCGTGGCATCCC
Found at i:5114 original size:32 final size:32
Alignment explanation
Indices: 5059--5692 Score: 1081
Period size: 32 Copynumber: 19.8 Consensus size: 32
5049 CTTTTAAATC
* *
5059 CACAACTCCGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5090 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
5122 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5154 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
5186 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5218 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5250 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
5282 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5314 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5346 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5378 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5410 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
5442 CACAAGTCGGTGGAAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
5474 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
5506 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
5538 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5570 CACAAGTCGGTGGCAATCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
5602 CACAAGTCGGCGGCAACCCATTTCAAAACCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
5634 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
5666 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
5693 TCACCATTTT
Statistics
Matches: 579, Mismatches: 23, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
31 12 0.02
32 567 0.98
ACGTcount: A:0.32, C:0.35, G:0.18, T:0.15
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:6249 original size:20 final size:20
Alignment explanation
Indices: 6221--6295 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
6211 TCATACCCTG
6221 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
6241 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
6261 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
6281 ATGTATCGATACATT
1 ATGTATCGATACATT
6296 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:6288 original size:40 final size:39
Alignment explanation
Indices: 6221--6298 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
6211 TCATACCCTG
* *
6221 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
6261 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
6299 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Done.