Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1997
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: 4509
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Found at i:1719 original size:13 final size:13
Alignment explanation
Indices: 1701--1726 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1691 CAAAAGATCC
1701 ATGTATCGATACA
1 ATGTATCGATACA
1714 ATGTATCGATACA
1 ATGTATCGATACA
1727 CAGAAAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2445 original size:54 final size:53
Alignment explanation
Indices: 2334--3162 Score: 1308
Period size: 54 Copynumber: 15.3 Consensus size: 53
2324 ATAAATTGTA
* * * * *
2334 TCCTGCTCATTGAGGAGTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
2388 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAA-GTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
2442 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2497 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
2552 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
2606 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
2661 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
2716 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
2770 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
2825 TCCTGCTCTTTG-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
2879 TCCTGCTCTTTGAGGACTGAAA-TGCCACCAACTTGTGTGGGCTTTAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTG
*
2931 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTG
*
2985 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTG
*
3039 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTG
3093 TCCTGCTCTTTGAGGACTGAAA--GCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
3145 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
3163 AAAAAGCGGA
Statistics
Matches: 746, Mismatches: 15, Indels: 30
0.94 0.02 0.04
Matches are distributed among these distances:
51 24 0.03
52 46 0.06
53 35 0.05
54 388 0.52
55 247 0.33
56 6 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (53 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTG
Found at i:2539 original size:164 final size:163
Alignment explanation
Indices: 2334--3162 Score: 1371
Period size: 164 Copynumber: 5.1 Consensus size: 163
2324 ATAAATTGTA
* * * *
2334 TCCTGCTCATTGAGGA--GTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCT
* * * *
2397 TTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAA-GTGTCCTGCTCTTTGGGGAATG
64 TTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
2461 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
128 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2497 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTT
2562 TGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAA
65 TGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAA
2627 AGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
130 AGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2661 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCT
2725 TTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGA
64 TTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGA
2790 AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
129 AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2825 TCCTGCTCTTTG-GGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCT
2888 TTGAGGACTG-AAATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTGG
64 TTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-G
*
2951 AAA-ATGCCACCAACTTGTGTGGGCTTTAA-AGGTG
128 AAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2985 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTT
3050 GAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTGAA
66 GAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAA
3114 A---GCCACCAACTTGTGTGGGCTTTAAGAGGTG
130 AGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
3145 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
3163 AAAAAGCGGA
Statistics
Matches: 644, Mismatches: 11, Indels: 25
0.95 0.02 0.04
Matches are distributed among these distances:
159 24 0.04
160 63 0.10
161 85 0.13
162 85 0.13
163 108 0.17
164 274 0.43
165 5 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (163 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTT
GAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAA
GGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:2547 original size:109 final size:106
Alignment explanation
Indices: 2334--3167 Score: 1318
Period size: 109 Copynumber: 7.7 Consensus size: 106
2324 ATAAATTGTA
* * * * *
2334 TCCTGCTCATTGAGGAGTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTT
* *
2399 GAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAA-GTG
65 GAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
2442 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTT
2507 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
64 TGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
2552 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTT
*
2617 GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
65 GAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAA-AGGTG
2661 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTT
2726 TGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
64 TGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGGTG
2770 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTT
*
2835 TG-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
64 TGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAA-AGGTG
2879 TCCTGCTCTTTGAGGACTGAAA-TGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTG
2943 AGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTG
66 AGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTG
*
2985 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTT
3050 GAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTG
65 GAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTG
3093 TCCTGCTCTTTGAGGACTGAAA--GCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTT
*
3156 GAGGACTAAAAA
65 GAGGACTGAAAA
3168 GCGGAAGGAG
Statistics
Matches: 692, Mismatches: 17, Indels: 37
0.93 0.02 0.05
Matches are distributed among these distances:
105 28 0.04
106 63 0.09
107 63 0.09
108 143 0.21
109 314 0.45
110 81 0.12
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (106 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTG
AGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAGGTG
Found at i:4152 original size:10 final size:9
Alignment explanation
Indices: 4123--4182 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
4113 CTTAAGTAGG
4123 TTTTTTCTT
1 TTTTTTCTT
* *
4132 TTCTCTCTT
1 TTTTTTCTT
*
4141 TTTCTTTGTT
1 TTT-TTTCTT
4151 TTGTTTT-TT
1 TT-TTTTCTT
*
4160 TTTGTT-TT
1 TTTTTTCTT
4168 TTTTTTCTT
1 TTTTTTCTT
4177 TTTTTT
1 TTTTTT
4183 TGAAGAGAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 10 0.24
9 21 0.51
10 9 0.22
11 1 0.02
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:4170 original size:11 final size:11
Alignment explanation
Indices: 4149--4183 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
4139 TTTTTCTTTG
4149 TTTTG-TTTTT
1 TTTTGTTTTTT
4159 TTTTGTTTTTT
1 TTTTGTTTTTT
*
4170 TTTTCTTTTTT
1 TTTTGTTTTTT
4181 TTT
1 TTT
4184 GAAGAGAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:4182 original size:15 final size:15
Alignment explanation
Indices: 4123--4183 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
4113 CTTAAGTAGG
* *
4123 TTTTTTCTTTTCTCT
1 TTTTTTCTTTTTTTT
* *
4138 CTTTTTCTTTGTTTTG
1 TTTTTTCTTT-TTTTT
*
4154 TTTTTT-TTTGTTTT
1 TTTTTTCTTTTTTTT
4168 TTTTTTCTTTTTTTT
1 TTTTTTCTTTTTTTT
4183 T
1 T
4184 GAAGAGAAGG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 9 0.25
15 20 0.56
16 7 0.19
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:4183 original size:10 final size:10
Alignment explanation
Indices: 4124--4183 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
4114 TTAAGTAGGT
4124 TTTTTCTTTTC
1 TTTTT-TTTTC
* *
4135 TCTCTTTTTC
1 TTTTTTTTTC
4145 TTTGTTTTGTT-
1 TTT-TTTT-TTC
*
4156 TTTTTTTGT-
1 TTTTTTTTTC
4165 TTTTTTTTTC
1 TTTTTTTTTC
4175 TTTTTTTTT
1 TTTTTTTTT
4184 GAAGAGAAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 9 0.22
10 20 0.50
11 9 0.22
12 2 0.05
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Done.