Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold878
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: 29831
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:434 original size:51 final size:52
Alignment explanation
Indices: 350--468 Score: 170
Period size: 51 Copynumber: 2.3 Consensus size: 52
340 CTTTGTATGA
* *
350 ACATGCAGGAAAATTTGCCCAGATGTATCGATACATTA-TAAAAGTA-CGAT
1 ACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAAAGTATCGAT
* * *
400 ACATGCGGGCAAATTTGGCCCAGATGTATCGATACACTATTCAATGTATCGAT
1 ACATGCAGGCAAATTT-GCCCAGATGTATCGATACACTATTAAAAGTATCGAT
453 ACATGCAGGCAAATTT
1 ACATGCAGGCAAATTT
469 TCATATTTCG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 14 0.23
51 21 0.35
52 6 0.10
53 19 0.32
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (52 bp):
ACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAAAGTATCGAT
Found at i:8132 original size:13 final size:13
Alignment explanation
Indices: 8114--8139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8104 CAATTTTTGG
8114 TGTATCGATACAT
1 TGTATCGATACAT
8127 TGTATCGATACAT
1 TGTATCGATACAT
8140 ACTTGGTGTG
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13498 original size:13 final size:13
Alignment explanation
Indices: 13480--13518 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
13470 ACATCATTCC
*
13480 TTGTATTGATACA
1 TTGTATCGATACA
13493 TTGTATCGATACA
1 TTGTATCGATACA
*
13506 CTGTATCGATACA
1 TTGTATCGATACA
13519 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:13686 original size:20 final size:20
Alignment explanation
Indices: 13641--13687 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
13631 AAATCTTTTG
*
13641 CAAAATTCTTGTTTTTCACTT
1 CAAAATTCTCGTTTTTCAC-T
13662 CAAAATTCATCGTTTTTCA-T
1 CAAAATTC-TCGTTTTTCACT
13682 CAAAAT
1 CAAAAT
13688 CAGCTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 8 0.33
22 9 0.38
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATTCTCGTTTTTCACT
Found at i:19061 original size:2 final size:2
Alignment explanation
Indices: 19049--19089 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
19039 AATCAAAATC
* * *
19049 AT AT TT AT AT AT AT AT AT AT AT AT AC AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19090 GATGACCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19947 original size:18 final size:20
Alignment explanation
Indices: 19904--19948 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
19894 TAGAAATATT
19904 TTTAATTTTATATTTATTAA
1 TTTAATTTTATATTTATTAA
**
19924 AATAATTTTAT-TTT-TTAA
1 TTTAATTTTATATTTATTAA
19942 TTTAATT
1 TTTAATT
19949 GATGTAACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 9 0.43
19 3 0.14
20 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAATTTTATATTTATTAA
Found at i:20849 original size:21 final size:21
Alignment explanation
Indices: 20837--20878 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20827 TTTAGTGAGG
20837 AAGAAGCTATTTTAAGTCAAC
1 AAGAAGCTATTTTAAGTCAAC
*
20858 AAGAAGCTATTGTAAGTCAAC
1 AAGAAGCTATTTTAAGTCAAC
20879 CCCACAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (21 bp):
AAGAAGCTATTTTAAGTCAAC
Found at i:21029 original size:25 final size:24
Alignment explanation
Indices: 20991--21042 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 24
20981 AAGTCTCTGG
20991 ATCTTGGTTATATTAACTGCTGTA
1 ATCTTGGTTATATTAACTGCTGTA
21015 ATCTTGGATTATATTAACTGCTGTA
1 ATCTTGG-TTATATTAACTGCTGTA
21040 ATC
1 ATC
21043 AGAGTTTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.44
Consensus pattern (24 bp):
ATCTTGGTTATATTAACTGCTGTA
Found at i:23565 original size:16 final size:16
Alignment explanation
Indices: 23546--23618 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 16
23536 AAAATTATCA
*
23546 GAACTCGAAATAGCCC
1 GAACTCGAAAAAGCCC
**
23562 GAACTCGAAAAAGTTC
1 GAACTCGAAAAAGCCC
* **
23578 GAACTCAAAAAAGCTG
1 GAACTCGAAAAAGCCC
23594 GAACTCGAAAGAA-CCC
1 GAACTCGAAA-AAGCCC
*
23610 GAACCCGAA
1 GAACTCGAA
23619 TTTAATACTA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
16 44 0.96
17 2 0.04
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (16 bp):
GAACTCGAAAAAGCCC
Found at i:24591 original size:23 final size:20
Alignment explanation
Indices: 24561--24602 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 20
24551 TTAAATGGGT
24561 TTTTAAATATTATATTAAATATA
1 TTTTAAAT-TT-T-TTAAATATA
24584 TTTTAAATTTTTTAAATAT
1 TTTTAAATTTTTTAAATAT
24603 TAATTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 2 0.11
23 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAATTTTTTAAATATA
Found at i:24596 original size:9 final size:10
Alignment explanation
Indices: 24560--24603 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 10
24550 ATTAAATGGG
24560 TTTTTAAATA
1 TTTTTAAATA
24570 TTATATTAAATA
1 TT-T-TTAAATA
24582 TATTTTAAAT-
1 T-TTTTAAATA
24592 TTTTTAAATA
1 TTTTTAAATA
24602 TT
1 TT
24604 AATTTACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.27
10 5 0.17
11 7 0.23
12 9 0.30
13 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:24988 original size:16 final size:15
Alignment explanation
Indices: 24963--25017 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
24953 AAACCCAAAC
*
24963 CCGAATAAGTTCGAA
1 CCGAAAAAGTTCGAA
24978 CTCGAAAAAG-TCGAA
1 C-CGAAAAAGTTCGAA
*
24993 CCCAAAAAGATTCGAA
1 CCGAAAAAG-TTCGAA
25009 CCCGAAAAA
1 -CCGAAAAA
25018 ATTTGAACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.21
15 7 0.21
16 12 0.36
17 7 0.21
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.13
Consensus pattern (15 bp):
CCGAAAAAGTTCGAA
Found at i:25025 original size:16 final size:16
Alignment explanation
Indices: 24988--25026 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
24978 CTCGAAAAAG
24988 TCGAACCCAAAAAGAT
1 TCGAACCCAAAAAGAT
25004 TCGAACCCGAAAAA-AT
1 TCGAACCC-AAAAAGAT
*
25020 TTGAACC
1 TCGAACC
25027 TAAATAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (16 bp):
TCGAACCCAAAAAGAT
Found at i:27807 original size:110 final size:113
Alignment explanation
Indices: 27676--27944 Score: 280
Period size: 114 Copynumber: 2.4 Consensus size: 113
27666 AAAGTGTTCG
* * * ** * * ** * *
27676 TACGCCAC-TTATGATTATAGATAATGATATATTTCGAGGTCAATCCCTTGGTGCT-TCGAA-TT
1 TACGTCACTTTATGACTCTAGATAATGACCTATTTCAAGGTCAATCCCTTAGTAATACCAAATTT
* *
27738 ACATAACTAATGC-AAAAAAATGAATTAT-TCTATATAAAGGGCATTCC
66 ACATAACTAATGCAAAAAAAATGAATTATCT-TATATAAAGGACATTCA
* *
27785 TACGTCACTTTATGACTCTAGATAATGACCTATTTCAAGGCCAAT-CCTTATTAATACCCAAATT
1 TACGTCACTTTATGACTCTAGATAATGACCTATTTCAAGGTCAATCCCTTAGTAATA-CCAAATT
**
27849 TACATAACTAATGCAAAAAAAAATGAATTATCTTATATAAAGGATGTTCA
65 TACATAACTAATGC-AAAAAAAATGAATTATCTTATATAAAGGACATTCA
* * * *
27899 TACGTCACTTTATTACCCTAGACAATGACCTATTCCAAGGTCAATC
1 TACGTCACTTTATGACTCTAGATAATGACCTATTTCAAGGTCAATC
27945 TTTTAGGTGC
Statistics
Matches: 130, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
109 13 0.10
110 30 0.23
111 3 0.02
112 15 0.12
114 68 0.52
115 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (113 bp):
TACGTCACTTTATGACTCTAGATAATGACCTATTTCAAGGTCAATCCCTTAGTAATACCAAATTT
ACATAACTAATGCAAAAAAAATGAATTATCTTATATAAAGGACATTCA
Found at i:27865 original size:112 final size:113
Alignment explanation
Indices: 27736--27944 Score: 305
Period size: 114 Copynumber: 1.8 Consensus size: 113
27726 GTGCTTCGAA
* *
27736 TTACATAACTAATGC-AAAAAAATGAATTAT-TCTATATAAAGGGCATTCCTACGTCACTTTATG
1 TTACATAACTAATGCAAAAAAAATGAATTATCT-TATATAAAGGACATTCATACGTCACTTTATG
* * *
27799 ACTCTAGATAATGACCTATTTCAAGGCCAATCCTTATTAATACCCAAAT
65 ACCCTAGACAATGACCTATTCCAAGGCCAATCCTTATTAATACCCAAAT
** *
27848 TTACATAACTAATGCAAAAAAAAATGAATTATCTTATATAAAGGATGTTCATACGTCACTTTATT
1 TTACATAACTAATGC-AAAAAAAATGAATTATCTTATATAAAGGACATTCATACGTCACTTTATG
*
27913 ACCCTAGACAATGACCTATTCCAAGGTCAATC
65 ACCCTAGACAATGACCTATTCCAAGGCCAATC
27945 TTTTAGGTGC
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
112 15 0.18
114 69 0.81
115 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (113 bp):
TTACATAACTAATGCAAAAAAAATGAATTATCTTATATAAAGGACATTCATACGTCACTTTATGA
CCCTAGACAATGACCTATTCCAAGGCCAATCCTTATTAATACCCAAAT
Found at i:28735 original size:25 final size:24
Alignment explanation
Indices: 28689--28774 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 24
28679 ACCCTATTTC
28689 TTTTCTTCTTTTTTTTTTTTTCCA
1 TTTTCTTCTTTTTTTTTTTTTCCA
*
28713 TTTTC--C-TTTTTTTTTTTT-CT
1 TTTTCTTCTTTTTTTTTTTTTCCA
* * * *
28733 TTCTTCTTCTTCTTTCTTTATTCCT
1 TT-TTCTTCTTTTTTTTTTTTTCCA
* *
28758 TTTTCTCCTTTTCTTTT
1 TTTTCTTCTTTTTTTTT
28775 CTGGTTTGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
20 3 0.06
21 15 0.31
22 1 0.02
23 1 0.02
24 25 0.51
25 4 0.08
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTCTTCTTTTTTTTTTTTTCCA
Done.