Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2019
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: 16217
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1937 original size:41 final size:42
Alignment explanation
Indices: 1764--2602 Score: 768
Period size: 42 Copynumber: 20.1 Consensus size: 42
1754 TCATTAACTT
** * * *
1764 CTGGAGACTTTTTTTTCCCTTAGTGTGCCTGTCGGTTTTAACC
1 CTGGAGAC-TTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
** * *
1807 CTAAAAACTTTCCTTCCCTTAGTCTGCCTATCGGCTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * *
1849 CTGGAGACTTTCATTTCCTTAGTCTGCTTGTCGACTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * *
1891 CTAGAGACTTTCCTTCCCTCAGTCTG-CTGTCGACTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * *
1932 TTAGAGACTTT-CTTTCCTCAGTCTGCCTGTCGGCTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * * *
1973 TTGAAGACTTT-CTATCCCTTAGTCTACTTTTTGGCTTTGACC
1 CTGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * *
2015 ATAGAGACTTTCCTACCCTTAGTTTGCCTGTCGGC-TTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
*
2056 CTGGAGAC-TTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * *
2097 CTGGAAACTTTTCTTCCCTAAGTCTG-CTATCGGCTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * *
2138 CTAGAGACTTTTCTAT-CCTCATTCTGCCTGTCGGCTTTGACC
1 CTGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACC
* * **
2180 CTCGAGACTTTTCTATCCCTTAGTCTGCCTGTCGATTTTGACC
1 CTGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCGGCTTTGACC
* * *
2223 CTGGAGGACTTT-CTTCCCTCAGTCTGCCTGTCAGTTTTGACC
1 CTGGA-GACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * * *
2265 TTGGAGACTTTTCTATCCCTCAATCTGTCTGTCGACCTTTGACC
1 CTGGAGACTTTCCT-TCCCTTAGTCTGCCTGTCG-GCTTTGACC
* * * * *
2309 CTGGAGACTTTACTTCCCTAAGTCTGTCTGTCAGCTTCGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * * *
2351 CTAGAGATTTTTCTACCCTTAGTCTGCCTGTCTGTTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* *
2393 ATGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * * *
2435 TTAGAGACTTTCTTTCCCTAAATCTACCTGTCGGCTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * **
2477 CTTGAGACTTT--TTACCCTTAGTCTGCCTATCGATTTTGA-C
1 CTGGAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACC
* *
2517 CTGGAGACTTT-CTTACCCTTAGTCTACCTGTCGGCTTTGATC
1 CTGGAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * *
2559 CTGGAGACTTTTCTACCCTCAATCTGCCTATC-GCTTTGACC
1 CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
2600 CTG
1 CTG
2603 AAGGCTGCCT
Statistics
Matches: 659, Mismatches: 121, Indels: 34
0.81 0.15 0.04
Matches are distributed among these distances:
40 49 0.07
41 168 0.25
42 348 0.53
43 69 0.10
44 25 0.04
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.38
Consensus pattern (42 bp):
CTGGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
Found at i:1965 original size:124 final size:124
Alignment explanation
Indices: 1778--2602 Score: 772
Period size: 124 Copynumber: 6.6 Consensus size: 124
1768 AGACTTTTTT
* * * * ** * * *
1778 TTCCCTTAGTGTGCCTGTCGGTTTTAACCCTAAAAACTTTCCTTCCCTTAGTCTGCCTATCGGCT
1 TTCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-CTTCCCTCAGTCTGCCTGTCGGCT
* *
1843 TTGACCCTGGAGACTTTCATTTCCTTAGTCTGCTTGTCGACTTTGACCCTAGAGACTTTCC
65 TTGACCCTGGAGACTTTC-TTCCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCC
* * * *
1904 TTCCCTCAGTCTG-CTGTCGACTTTGACCTTAGAGACTTTCTTTCCTCAGTCTGCCTGTCGGCTT
1 TTCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTCCCTCAGTCTGCCTGTCGGCTT
* * * * * * * *
1968 TGACCTTGAAGACTTTCTATCCCTTAGTCTACTTTTTGGCTTTGACCATAGAGACTTTCC
66 TGACCCTGGAGACTTTCT-TCCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCC
* * * *
2028 TACCCTTAGTTTGCCTGTCGGC-TTGACCCTGGAGACTTCCTTCCCTCAGTCTGCCTGTCGGCTT
1 TTCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTCCCTCAGTCTGCCTGTCGGCTT
* * * * *
2092 TGACCCTGGAAACTTTTCTTCCCTAAGTCTG-CTATCGGCTTTGACCCTAGAGACTTTTC
66 TGACCCTGGAGAC-TTTCTTCCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCC
* * * *
2151 TAT-CCTCATTCTGCCTGTCGGCTTTGACCCTCGAGACTTTTCTATCCCTTAGTCTGCCTGTCGA
1 T-TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCT-TCCCTCAGTCTGCCTGTCGG
* * * * * *
2215 TTTTGACCCTGGAGGACTTTCTTCCCTCAGTCTGCCTGTC-AGTTTTGACCTTGGAGACTTTTC
63 CTTTGACCCTGGA-GACTTTCTTCCCTTAGTCTGCCTGTCGA-CTTTGACCCTAGAGACTTTCC
* * * * * *
2278 TATCCCTCAATCTGTCTGTCGACCTTTGACCCTGGAGACTTTACTTCCCTAAGTCTGTCTGTCAG
1 T-TCCCTCAGTCTGCCTGTCG-GCTTTGACCCTGGAGACTTT-CTTCCCTCAGTCTGCCTGTCGG
* * * * * *
2343 CTTCGACCCTAGAGATTTTTCTACCCTTAGTCTGCCTGTCTG-TTTTGACCAT-GAAGACTTTCC
63 CTTTGACCCTGGAGA-CTTTCTTCCCTTAGTCTGCCTGTC-GACTTTGACCCTAG-AGACTTTCC
* * * * * *
2406 TTCCCTTAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCTTTCCCTAAATCTACCTGTCGGCT
1 TTCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTC-TTCCCTCAGTCTGCCTGTCGGCT
* * * *
2471 TTGACCCTTGAGACTTT-TTACCCTTAGTCTGCCTATCGATTTTGA-CCTGGAGACTTT-C
65 TTGACCCTGGAGACTTTCTT-CCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCC
* * * * * *
2529 TTACCCTTAGTCTACCTGTCGGCTTTGATCCTGGAGACTTTTCTACCCTCAATCTGCCTATC-GC
1 TT-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCTTCCCTCAGTCTGCCTGTCGGC
2593 TTTGACCCTG
64 TTTGACCCTG
2603 AAGGCTGCCT
Statistics
Matches: 582, Mismatches: 94, Indels: 49
0.80 0.13 0.07
Matches are distributed among these distances:
123 55 0.09
124 210 0.36
125 67 0.12
126 104 0.18
127 46 0.08
128 83 0.14
129 17 0.03
ACGTcount: A:0.15, C:0.30, G:0.17, T:0.38
Consensus pattern (124 bp):
TTCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTCCCTCAGTCTGCCTGTCGGCTT
TGACCCTGGAGACTTTCTTCCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTTCC
Found at i:3126 original size:27 final size:27
Alignment explanation
Indices: 3095--3152 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
3085 AAAATATAAT
* *
3095 AATAAGTAGAAAT-TAAAAATTAAAAAA
1 AATAA-TAAAAATATAAAAATAAAAAAA
*
3122 AATAATAAAAATAATAGAAATAAAAAAA
1 AATAATAAAAAT-ATAAAAATAAAAAAA
3150 AAT
1 AAT
3153 CATGAAATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 6 0.23
27 5 0.19
28 15 0.58
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (27 bp):
AATAATAAAAATATAAAAATAAAAAAA
Found at i:3131 original size:9 final size:9
Alignment explanation
Indices: 3108--3149 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3098 AAGTAGAAAT
3108 TAAAAATTAA
1 TAAAAA-TAA
*
3118 AAAAAATAA
1 TAAAAATAA
3127 TAAAAATAA
1 TAAAAATAA
*
3136 TAGAAATAA
1 TAAAAATAA
3145 -AAAAA
1 TAAAAA
3150 AATCATGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 4 0.14
9 19 0.68
10 5 0.18
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (9 bp):
TAAAAATAA
Found at i:3142 original size:18 final size:17
Alignment explanation
Indices: 3086--3148 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
3076 ATTCGATATA
*
3086 AAATATAATAATAAGTAG
1 AAATATAAAAATAA-TAG
* *
3104 AAAT-TAAAAATTAAAAA
1 AAATATAAAAA-TAATAG
3121 AAATAATAAAAATAATAG
1 AAAT-ATAAAAATAATAG
3139 AAATA-AAAAA
1 AAATATAAAAA
3149 AAATCATGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
16 5 0.14
17 11 0.30
18 15 0.41
19 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (17 bp):
AAATATAAAAATAATAG
Found at i:3240 original size:31 final size:31
Alignment explanation
Indices: 3202--3265 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
3192 CATGCAAGGA
*
3202 AATGTAGCATGCAAACATGGGAGACACATGC
1 AATGTAGCATGCAAACATGGGAGACACAAGC
* *
3233 AATGTAGCATGCAATCATGGGGGACACAAGC
1 AATGTAGCATGCAAACATGGGAGACACAAGC
3264 AA
1 AA
3266 ATGGAAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.16
Consensus pattern (31 bp):
AATGTAGCATGCAAACATGGGAGACACAAGC
Found at i:3837 original size:35 final size:35
Alignment explanation
Indices: 3763--3837 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
3753 AGCCTCCGAT
* * *
3763 CCACGATCAAAGGATAGCTTCCAGCAACCTTCCAT
1 CCACGATCAAAGGATAGCTTCCAACAACCTCCCAC
*
3798 CCACGATCAAAGGATAGCTTCCAAC-AGCTCCCAGC
1 CCACGATCAAAGGATAGCTTCCAACAACCTCCCA-C
3833 CCACG
1 CCACG
3838 GTCAGTTTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 6 0.17
35 29 0.83
ACGTcount: A:0.31, C:0.37, G:0.16, T:0.16
Consensus pattern (35 bp):
CCACGATCAAAGGATAGCTTCCAACAACCTCCCAC
Found at i:4000 original size:47 final size:46
Alignment explanation
Indices: 3875--4029 Score: 175
Period size: 46 Copynumber: 3.3 Consensus size: 46
3865 CAAGAAACAA
* * ** *
3875 CTTCCAGCATCAATTCCAATAGCCTCCAATCCATGATCAGAAGCAG
1 CTTCCAGCATCCATTCTAGCAGCCTCCAATCCACGATCAGAAGCAG
* * * * *
3921 CTTCCAACATCCATTTTAGCAGCCTCCCATCCACGATCAAAAGATAG
1 CTTCCAGCATCCATTCTAGCAGCCTCCAATCCACGATCAGAAG-CAG
* ** *
3968 CTTCTAGCATCCATTCTAGTGGCCTTCAATCCACGATCAGAAGCAG
1 CTTCCAGCATCCATTCTAGCAGCCTCCAATCCACGATCAGAAGCAG
4014 CTTCCAGCATCCATTC
1 CTTCCAGCATCCATTC
4030 CAACAGCTCC
Statistics
Matches: 88, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
46 51 0.58
47 37 0.42
ACGTcount: A:0.29, C:0.34, G:0.13, T:0.25
Consensus pattern (46 bp):
CTTCCAGCATCCATTCTAGCAGCCTCCAATCCACGATCAGAAGCAG
Found at i:4130 original size:73 final size:73
Alignment explanation
Indices: 4009--4178 Score: 177
Period size: 73 Copynumber: 2.3 Consensus size: 73
3999 CACGATCAGA
* * ** * *
4009 AGCAGCTTCCAGCATCCATTCCA-ACAGCTCCTAGTCGACGGACATTTTCCAGAAGCA-TC-C-C
1 AGCAGCTTCCAGCATCCACTCCAGACAGCTCCCAACCCACGGACATTTTCCAGAAGAATTCACTC
4070 CAGCAAGC
66 CAGCAAGC
*
4078 AGCAGCTTCCAGCATCCACTCCAGTACGTAGCTCCCAACCCACGGACATTTTCCAGCAGAATTCA
1 AGCAGCTTCCAGCATCCACTCCAG-AC--AGCTCCCAACCCACGGACATTTTCCAGAAGAATTCA
*
4143 CTCCAGCAAGT
63 CTCCAGCAAGC
* * *
4154 TGCAGCTTTCAGCATTCCACCCCAG
1 AGCAGCTTCCAGCA-TCCACTCCAG
4179 CAAGCAACAG
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
69 22 0.27
71 2 0.02
73 26 0.32
74 2 0.02
75 1 0.01
76 20 0.24
77 9 0.11
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.20
Consensus pattern (73 bp):
AGCAGCTTCCAGCATCCACTCCAGACAGCTCCCAACCCACGGACATTTTCCAGAAGAATTCACTC
CAGCAAGC
Found at i:4326 original size:26 final size:28
Alignment explanation
Indices: 4258--4326 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
4248 CAATAGCAGT
* *
4258 AGTAACTCCCAACCTTCGAGCACTCCAAC
1 AGTAGCTCCCAGCCTTCGAGCACTCC-AC
*
4287 AGCAGCTCCCAGCCTTCGAGCACT-C-C
1 AGTAGCTCCCAGCCTTCGAGCACTCCAC
4313 AGTAGCTCCCAGCC
1 AGTAGCTCCCAGCC
4327 CACGAGTACT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 14 0.39
28 1 0.03
29 21 0.58
ACGTcount: A:0.25, C:0.43, G:0.16, T:0.16
Consensus pattern (28 bp):
AGTAGCTCCCAGCCTTCGAGCACTCCAC
Found at i:10774 original size:20 final size:20
Alignment explanation
Indices: 10749--10786 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10739 AAAAAACAAA
*
10749 ATGTATCGATACATTCATAC
1 ATGTATCAATACATTCATAC
10769 ATGTATCAATACATTCAT
1 ATGTATCAATACATTCAT
10787 TGGTACATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (20 bp):
ATGTATCAATACATTCATAC
Found at i:12989 original size:12 final size:13
Alignment explanation
Indices: 12972--13007 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
12962 ATTTTTCTTT
12972 GTATCGATACA-A
1 GTATCGATACACA
*
12984 GTATCGATACACT
1 GTATCGATACACA
12997 GTATCGATACA
1 GTATCGATACA
13008 GGGGGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (13 bp):
GTATCGATACACA
Found at i:13161 original size:20 final size:19
Alignment explanation
Indices: 13119--13162 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
13109 TCAATCTTTG
13119 CAAATACTTGTTTTTCACTT
1 CAAATACTTGTTTTTCAC-T
13139 CAAATTACTTCGTTTTTCA-T
1 CAAA-TACTT-GTTTTTCACT
13159 CAAA
1 CAAA
13163 ACCAGCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
22 8 0.36
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (19 bp):
CAAATACTTGTTTTTCACT
Found at i:15510 original size:19 final size:20
Alignment explanation
Indices: 15486--15537 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
15476 TAGCCAAACT
15486 TGTATCGATACAC-AAAATA
1 TGTATCGATACACAAAAATA
15505 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC-AAAAATA
*
15526 TGTATTGATACA
1 TGTATCGATACA
15538 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACACAAAAATA
Found at i:15597 original size:22 final size:24
Alignment explanation
Indices: 15572--15615 Score: 58
Period size: 22 Copynumber: 1.9 Consensus size: 24
15562 CTATATTTTC
15572 AAATATGT-TCGAT-CA-TCACAAA
1 AAAT-TGTATCGATACATTCACAAA
15594 AAATTGTATCGATACATTCACA
1 AAATTGTATCGATACATTCACA
15616 CGGGAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.16
22 9 0.47
23 2 0.11
24 5 0.26
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (24 bp):
AAATTGTATCGATACATTCACAAA
Done.