Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1970
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: 38169
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:2680 original size:20 final size:21
Alignment explanation
Indices: 2657--2695 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2647 TTGAGCAATA
2657 TGTATCGATACA-TCTAGGTG
1 TGTATCGATACATTCTAGGTG
2677 TGTATCGATACATTCTAGG
1 TGTATCGATACATTCTAGG
2696 GTTTTTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAGGTG
Found at i:4131 original size:164 final size:164
Alignment explanation
Indices: 3898--4254 Score: 504
Period size: 164 Copynumber: 2.2 Consensus size: 164
3888 ATCAGTTTTG
* *
3898 AAAATTTCATTTATTTTTATGAGTTTTTCATTTTTTTCCTTGAAATTCCCTTAATTCTGAAAAAT
1 AAAATTT--TTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAATTCCCTT-ATTCTGAAAAAT
* *
3963 CGAGTTTTCTTTTCCATAAATGTTTTCAG-GGGGTTTTTCTTAGTTCAAAATTTTAAATATTCAT
63 CGAGTTTTCTATTCCATAAATGTTTTCAGCAGGG-TTTTCTTAGTTCAAAATTTTAAATATTCAT
4027 CAAATATCATCAGTTAAATCATAGTAAATCAGCTTTAA
127 CAAATATCATCAGTTAAATCATAGTAAATCAGCTTTAA
**
4065 AAAATTTTTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAATTTTTCTGT-TT-TGAAAAATC
1 AAAATTTTTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAA-TTCCCT-TATTCTGAAAAATC
* * *
4128 GAGTTTTCTATTCCATAAATGTTTTCAGCAGGGTTTTCTTGGTTCAAAATTTTTAATTTTCATCA
64 GAGTTTTCTATTCCATAAATGTTTTCAGCAGGGTTTTCTTAGTTCAAAATTTTAAATATTCATCA
* * *
4193 AATATCATCATTTAAATCATAGTAAATCAGTTTTGA
129 AATATCATCAGTTAAATCATAGTAAATCAGCTTTAA
* *
4229 AAAATTCATTAATTTTCATGAGTTTT
1 AAAATT-TTTTATTTTCATGAGTTTT
4255 GAAAATTTTT
Statistics
Matches: 172, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
164 104 0.60
165 56 0.33
166 4 0.02
167 8 0.05
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (164 bp):
AAAATTTTTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAATTCCCTTATTCTGAAAAATCGA
GTTTTCTATTCCATAAATGTTTTCAGCAGGGTTTTCTTAGTTCAAAATTTTAAATATTCATCAAA
TATCATCAGTTAAATCATAGTAAATCAGCTTTAA
Found at i:4762 original size:11 final size:11
Alignment explanation
Indices: 4746--4793 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
4736 TGGGAAATAG
4746 AAAGAAAAAAA
1 AAAGAAAAAAA
4757 AAAG-AAAAAA
1 AAAGAAAAAAA
*
4767 AAAG--AAAGA
1 AAAGAAAAAAA
4776 AAAGAAAAAGAA
1 AAAGAAAAA-AA
4788 AAAGAA
1 AAAGAA
4794 TAGAGAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 8 0.25
10 10 0.31
11 7 0.22
12 7 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:4770 original size:21 final size:22
Alignment explanation
Indices: 4746--4811 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
4736 TGGGAAATAG
4746 AAAGAAA-AAAAAAAGAAAAAA
1 AAAGAAAGAAAAAAAGAAAAAA
* *
4767 AAAGAAAGAAAAGAA-AAAGAA
1 AAAGAAAGAAAAAAAGAAAAAA
*
4788 AAAGAATAGAGAAATAAGAAAAAA
1 AAAGAA-AGA-AAAAAAGAAAAAA
4812 CAAGCTAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.49
22 9 0.24
23 5 0.14
24 5 0.14
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (22 bp):
AAAGAAAGAAAAAAAGAAAAAA
Found at i:4807 original size:31 final size:29
Alignment explanation
Indices: 4739--4809 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
4729 GGAGCTTTGG
4739 GAAAT-AG-AAAGAAAAAAAAAAGAAAAA
1 GAAATAAGAAAAGAAAAAAAAAAGAAAAA
* * *
4766 AAAAGAAAGAAAAGAAAAAGAAAAAGAATAGA
1 GAAA-TAAGAAAAGAAAAA-AAAAAGAA-AAA
4798 GAAATAAGAAAA
1 GAAATAAGAAAA
4810 AACAAGCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
27 3 0.09
29 2 0.06
30 9 0.26
31 15 0.44
32 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (29 bp):
GAAATAAGAAAAGAAAAAAAAAAGAAAAA
Found at i:5670 original size:16 final size:17
Alignment explanation
Indices: 5640--5675 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
5630 ATTTTCGAAC
5640 ATAAAAAAATGAAATAA
1 ATAAAAAAATGAAATAA
*
5657 ATAAAATAAT-AAATAA
1 ATAAAAAAATGAAATAA
5673 ATA
1 ATA
5676 TTATTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
ATAAAAAAATGAAATAA
Found at i:6604 original size:13 final size:13
Alignment explanation
Indices: 6586--6616 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
6576 ACTTTTCATT
6586 ATGTATTGATACA
1 ATGTATTGATACA
6599 ATGTATTGATACA
1 ATGTATTGATACA
6612 ATGTA
1 ATGTA
6617 CTATGTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:6706 original size:19 final size:20
Alignment explanation
Indices: 6661--6710 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
6651 CTGCCAGTTT
*
6661 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
*
6681 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
6700 CATGTATCGAT
1 CATGTATCGAT
6711 GCAAAACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:11974 original size:29 final size:29
Alignment explanation
Indices: 11886--11986 Score: 114
Period size: 29 Copynumber: 3.5 Consensus size: 29
11876 ATTTTAATTG
* * *
11886 AAAAGTTTAGGGGTCAATGTGTAATTTTG
1 AAAAGTTTAAGGGTCAAAGTGTAATTTTA
* * *
11915 AAAAGTTTTAGGGTCAAAATGTGATTTTA
1 AAAAGTTTAAGGGTCAAAGTGTAATTTTA
* *
11944 AAAAGTTTAAGTGTCAAAGTGTAATTATA
1 AAAAGTTTAAGGGTCAAAGTGTAATTTTA
11973 AAAA-TTTCAAGGGT
1 AAAAGTTT-AAGGGT
11987 TAAAACCTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 56 0.95
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
AAAAGTTTAAGGGTCAAAGTGTAATTTTA
Found at i:17200 original size:18 final size:19
Alignment explanation
Indices: 17177--17217 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
17167 TAACATGAAT
17177 AATAAAAAAATAATAA-AA
1 AATAAAAAAATAATAATAA
**
17195 AATAAAAATGTAATAATAA
1 AATAAAAAAATAATAATAA
17214 AATA
1 AATA
17218 GTAATAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AATAAAAAAATAATAATAA
Found at i:17407 original size:16 final size:17
Alignment explanation
Indices: 17367--17408 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
17357 AGTGAATAAA
*
17367 CATTGCATGCATATGTT
1 CATTTCATGCATATGTT
*
17384 CATTTCATGCATATTTT
1 CATTTCATGCATATGTT
17401 C-TTTCATG
1 CATTTCATG
17409 TTTCACACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (17 bp):
CATTTCATGCATATGTT
Found at i:21098 original size:15 final size:15
Alignment explanation
Indices: 21078--21108 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21068 TTTGGTCATC
21078 ATGCTAAAATTCAAA
1 ATGCTAAAATTCAAA
*
21093 ATGCTAGAATTCAAA
1 ATGCTAAAATTCAAA
21108 A
1 A
21109 AATACAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (15 bp):
ATGCTAAAATTCAAA
Found at i:25851 original size:8 final size:8
Alignment explanation
Indices: 25834--25867 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
25824 ATTTGATTAA
*
25834 ATTTTTTG
1 ATTTTGTG
25842 ATTTTGTG
1 ATTTTGTG
25850 ATTTTGTG
1 ATTTTGTG
25858 ATTTTGTG
1 ATTTTGTG
25866 AT
1 AT
25868 GAATGATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.65
Consensus pattern (8 bp):
ATTTTGTG
Found at i:26088 original size:13 final size:13
Alignment explanation
Indices: 26070--26094 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26060 CAGCATTCCC
26070 TGTATCGATACAT
1 TGTATCGATACAT
26083 TGTATCGATACA
1 TGTATCGATACA
26095 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:26563 original size:20 final size:22
Alignment explanation
Indices: 26538--26581 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
26528 CAGCACTCAT
*
26538 CAGGTCGCGACC-GGCA-CCCC
1 CAGGTCGCAACCGGGCAGCCCC
26558 CAGGTCGCAACCGGGCAGCCCC
1 CAGGTCGCAACCGGGCAGCCCC
26580 CA
1 CA
26582 CACTCACAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.18, C:0.48, G:0.30, T:0.05
Consensus pattern (22 bp):
CAGGTCGCAACCGGGCAGCCCC
Found at i:28569 original size:13 final size:13
Alignment explanation
Indices: 28551--28575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28541 AGATTGCACA
28551 GTATCGATACATT
1 GTATCGATACATT
28564 GTATCGATACAT
1 GTATCGATACAT
28576 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:28694 original size:13 final size:13
Alignment explanation
Indices: 28676--28700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28666 ACACACAAGT
28676 TGTATCGATACAA
1 TGTATCGATACAA
28689 TGTATCGATACA
1 TGTATCGATACA
28701 TCCCAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:28718 original size:33 final size:32
Alignment explanation
Indices: 28657--28720 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
28647 CTTAACTGTT
**
28657 TGTATCGATACACACAAGTTGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
28689 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
28721 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:30450 original size:13 final size:13
Alignment explanation
Indices: 30432--30461 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30422 GATACATGGC
30432 ACATTGTATCAAT
1 ACATTGTATCAAT
*
30445 ACATTGTATCGAT
1 ACATTGTATCAAT
30458 ACAT
1 ACAT
30462 AATGAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTGTATCAAT
Found at i:35573 original size:13 final size:14
Alignment explanation
Indices: 35555--35602 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
35545 ACCATTCCTT
*
35555 GTATCGATAC-ATA
1 GTATCGAGACAATA
*
35568 GTATCGAGACAAAA
1 GTATCGAGACAATA
* *
35582 TTATCGAGACAATT
1 GTATCGAGACAATA
35596 GTATCGA
1 GTATCGA
35603 TACATGGGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (14 bp):
GTATCGAGACAATA
Done.