Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2675
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: 63988
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4145 original size:17 final size:18
Alignment explanation
Indices: 4112--4146 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4102 CATTCTGACC
4112 ATATCTCACAAAATTTACT
1 ATATCTCAC-AAATTTACT
4131 ATATCTCAC-AATTTAC
1 ATATCTCACAAATTTAC
4147 AATTTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATCTCACAAATTTACT
Found at i:5115 original size:29 final size:30
Alignment explanation
Indices: 5058--5125 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
5048 CACCCTTAAA
* * * *
5058 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCCTCAAATTTTC
*
5088 ATATTTACACT-TTAATCCCTCAAATTTTG
1 ATATTTACACTATTAATCCCTCAAATTTTC
5117 AGTATTTAC
1 A-TATTTAC
5126 TCTTGGCCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.46
Consensus pattern (30 bp):
ATATTTACACTATTAATCCCTCAAATTTTC
Found at i:16008 original size:32 final size:32
Alignment explanation
Indices: 15967--16045 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
15957 TGATATTGAA
* * * *
15967 ATGGGCTAGGCCCAACTGATACTGGTTCTGAT
1 ATGGGCTAGGCCCAACTAATACTGATTCTAAG
*
15999 ATGGGCTAGGCCCAACTAATATTGATTCTAAG
1 ATGGGCTAGGCCCAACTAATACTGATTCTAAG
16031 ATGGGCTAGGCCCAA
1 ATGGGCTAGGCCCAA
16046 TTGCGACTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (32 bp):
ATGGGCTAGGCCCAACTAATACTGATTCTAAG
Found at i:17966 original size:21 final size:24
Alignment explanation
Indices: 17934--17989 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 24
17924 CTAATCCATT
17934 TCATACTCAATTTCATAT-C-AAAG
1 TCATAC-CAATTTCATATACTAAAG
*
17957 -CATACCAATTTCATGTACTAAAG
1 TCATACCAATTTCATATACTAAAG
17980 TCATACCAAT
1 TCATACCAAT
17990 CCATTTGGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.34
22 6 0.21
23 4 0.14
24 9 0.31
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.32
Consensus pattern (24 bp):
TCATACCAATTTCATATACTAAAG
Found at i:20686 original size:20 final size:20
Alignment explanation
Indices: 20657--20701 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20647 AACACATGTA
* *
20657 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
20677 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
20697 TTCAT
1 TTCAT
20702 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:21950 original size:27 final size:27
Alignment explanation
Indices: 21919--21972 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
21909 TGTAATGTGA
* *
21919 AATTGAATGGCAAATTATTGTTACGTG
1 AATTGAATGGCAAATTACTATTACGTG
**
21946 AATTGAATGTTAAATTACTATTACGTG
1 AATTGAATGGCAAATTACTATTACGTG
21973 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACGTG
Found at i:23719 original size:21 final size:21
Alignment explanation
Indices: 23670--23724 Score: 101
Period size: 22 Copynumber: 2.6 Consensus size: 21
23660 TTGGTCAGGC
23670 CAATTAGTACAGTTTATTAGT
1 CAATTAGTACAGTTTATTAGT
23691 CAAATTAGTACAGTTTATTAGT
1 C-AATTAGTACAGTTTATTAGT
23713 CAATTAGTACAG
1 CAATTAGTACAG
23725 GGCTTCAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 12 0.36
22 21 0.64
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (21 bp):
CAATTAGTACAGTTTATTAGT
Found at i:31236 original size:41 final size:40
Alignment explanation
Indices: 31109--31253 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
31099 CTCGCACAAG
* * * * *
31109 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
31149 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
31189 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
31230 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
31254 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:31648 original size:38 final size:38
Alignment explanation
Indices: 31606--31681 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
31596 CAAGAACTCC
*
31606 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCAGCCAAAAGAAATGAA
31644 TTCCTCCTTCCTTAGAATTTTCAGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCAGCCAAAAGAAATGAA
31682 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCAGCCAAAAGAAATGAA
Found at i:34388 original size:22 final size:24
Alignment explanation
Indices: 34345--34393 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
34335 TTTTATTTAT
* **
34345 TTTATTTTTATGGTTTTTTTTG-G
1 TTTATTTCTATGGTTTGCTTTGTG
34368 TTTATTTCT-TGGTTTGCTTTGTG
1 TTTATTTCTATGGTTTGCTTTGTG
34391 TTT
1 TTT
34394 GCATGGGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.06, C:0.04, G:0.18, T:0.71
Consensus pattern (24 bp):
TTTATTTCTATGGTTTGCTTTGTG
Found at i:41176 original size:29 final size:29
Alignment explanation
Indices: 41123--41204 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 29
41113 TGTATATAAG
* **
41123 GTGATTTGGGCTTAACAGGCCATATAAAA
1 GTGATTTGGGCCTAATGGGCCATATAAAA
* *
41152 GTGATTTGGGCCTAATGGGCGATATAAAT
1 GTGATTTGGGCCTAATGGGCCATATAAAA
*
41181 GAGA-TTGGGCC-AAGTGGGCCATAT
1 GTGATTTGGGCCTAA-TGGGCCATAT
41205 GCATGTATGT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 2 0.04
28 16 0.36
29 27 0.60
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.27
Consensus pattern (29 bp):
GTGATTTGGGCCTAATGGGCCATATAAAA
Found at i:50411 original size:46 final size:46
Alignment explanation
Indices: 50358--50626 Score: 307
Period size: 46 Copynumber: 5.8 Consensus size: 46
50348 TATTTGAGCA
*
50358 TCCGAACTCGTTGAGTTGTGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
50404 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
50449 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
50497 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
50542 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
50590 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
50627 GCGGGTTACA
Statistics
Matches: 188, Mismatches: 21, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
43 12 0.06
45 8 0.04
46 91 0.48
47 58 0.31
48 8 0.04
50 11 0.06
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:50467 original size:47 final size:47
Alignment explanation
Indices: 50404--50572 Score: 247
Period size: 47 Copynumber: 3.6 Consensus size: 47
50394 GATGCAAATG
50404 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* * * *
50451 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
50497 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
50544 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
50573 ACTCATGGAT
Statistics
Matches: 107, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 29 0.27
47 58 0.54
48 4 0.04
50 6 0.06
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:50492 original size:93 final size:93
Alignment explanation
Indices: 50355--50618 Score: 483
Period size: 93 Copynumber: 2.8 Consensus size: 93
50345 GGATATTTGA
*
50355 GCATCCGAACTCGTTGAGTTGTGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
50420 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
50448 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
50513 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
50541 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
50606 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
50619 ACTTATGGGC
Statistics
Matches: 166, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 166 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54897 original size:46 final size:46
Alignment explanation
Indices: 54847--55022 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
54837 TGGTTGAGCA
54847 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54893 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54938 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54986 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55023 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 63 0.57
47 29 0.26
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:55003 original size:93 final size:93
Alignment explanation
Indices: 54844--55015 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54834 GGATGGTTGA
* *
54844 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
54909 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
54937 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55002 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
55016 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:62452 original size:46 final size:46
Alignment explanation
Indices: 62402--62577 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
62392 TGGTTGAGCA
62402 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
62448 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
62493 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
62541 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
62578 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 63 0.57
47 29 0.26
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:62558 original size:93 final size:93
Alignment explanation
Indices: 62399--62570 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
62389 GGATGGTTGA
* *
62399 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
62464 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
62492 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
62557 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
62571 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.