Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2140
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: 31081
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:2546 original size:13 final size:13
Alignment explanation
Indices: 2528--2554 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2518 ACATTATGCT
2528 TTGTATCGATACA
1 TTGTATCGATACA
2541 TTGTATCGATACA
1 TTGTATCGATACA
2554 T
1 T
2555 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2563 original size:19 final size:19
Alignment explanation
Indices: 2539--2594 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
2529 TGTATCGATA
*
2539 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGAT
2558 CATTGTATCGAT-CATGGAT
1 CATTGTATCGATACAT-GAT
*
2577 AATTGTATCGATACATGA
1 CATTGTATCGATACATGA
2595 GATTGGCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.09
19 27 0.82
20 3 0.09
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:2779 original size:125 final size:125
Alignment explanation
Indices: 2622--2884 Score: 526
Period size: 125 Copynumber: 2.1 Consensus size: 125
2612 CTACCACTGT
2622 TTGTATCGATACATGGTACAATGTATCGGTACATTGTATCAATACATGATGAACTGTATCGATAC
1 TTGTATCGATACATGGTACAATGTATCGGTACATTGTATCAATACATGATGAACTGTATCGATAC
2687 ATTACTTGTAACGGCTATAAACGGCTATAATTTCAAATCAATGTATCAATACATTATGAA
66 ATTACTTGTAACGGCTATAAACGGCTATAATTTCAAATCAATGTATCAATACATTATGAA
2747 TTGTATCGATACATGGTACAATGTATCGGTACATTGTATCAATACATGATGAACTGTATCGATAC
1 TTGTATCGATACATGGTACAATGTATCGGTACATTGTATCAATACATGATGAACTGTATCGATAC
2812 ATTACTTGTAACGGCTATAAACGGCTATAATTTCAAATCAATGTATCAATACATTATGAA
66 ATTACTTGTAACGGCTATAAACGGCTATAATTTCAAATCAATGTATCAATACATTATGAA
2872 TTGTATCGATACA
1 TTGTATCGATACA
2885 GGAAAGCATT
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 138 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (125 bp):
TTGTATCGATACATGGTACAATGTATCGGTACATTGTATCAATACATGATGAACTGTATCGATAC
ATTACTTGTAACGGCTATAAACGGCTATAATTTCAAATCAATGTATCAATACATTATGAA
Found at i:2805 original size:33 final size:33
Alignment explanation
Indices: 2746--2814 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2736 TACATTATGA
* * *
2746 ATTGTATCGATACATGGTACAATGTATCGGTAC
1 ATTGTATCAATACATGATACAATGTATCGATAC
*
2779 ATTGTATCAATACATGATGA-ACTGTATCGATAC
1 ATTGTATCAATACATGAT-ACAATGTATCGATAC
2812 ATT
1 ATT
2815 ACTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (33 bp):
ATTGTATCAATACATGATACAATGTATCGATAC
Found at i:7946 original size:13 final size:13
Alignment explanation
Indices: 7928--7953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7918 CAATTTTTTG
7928 TGTATCGATACAT
1 TGTATCGATACAT
7941 TGTATCGATACAT
1 TGTATCGATACAT
7954 ACTTGGTGTA
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:7968 original size:32 final size:33
Alignment explanation
Indices: 7908--7971 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
7898 TACAAGCCAA
** *
7908 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
7941 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
7972 AGTTTGTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:8713 original size:49 final size:50
Alignment explanation
Indices: 8641--8742 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 50
8631 TTTAGCAAAT
*
8641 TTACGCATTCTTCCCTTTTAT-AAAAAAAATCTCCCCCTTAATAAAGTAA
1 TTACGCATTCTCCCCTTTTATAAAAAAAAATCTCCCCCTTAATAAAGTAA
8690 TTACGCATTCTCCCCTTTTATAAAAAAAAAATCTCCCCCTTAATAAAGTAA
1 TTACGCATTCTCCCCTTTTAT-AAAAAAAAATCTCCCCCTTAATAAAGTAA
8741 TT
1 TT
8743 CACACATATC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 20 0.40
51 30 0.60
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (50 bp):
TTACGCATTCTCCCCTTTTATAAAAAAAAATCTCCCCCTTAATAAAGTAA
Found at i:8761 original size:51 final size:51
Alignment explanation
Indices: 8662--8762 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
8652 TCCCTTTTAT
* * ****
8662 AAAAAAAATCTCCCCCTTAATAAAGTAATTACGCATTCTCCCCTTTTATAA
1 AAAAAAAATCTCCCCCTTAATAAAGTAATTACACATTATCAAAATTTATAA
8713 AAAAAAAATCTCCCCCTTAATAAAGTAATTCACACA-TATCAAAATTTATA
1 AAAAAAAATCTCCCCCTTAATAAAGTAATT-ACACATTATCAAAATTTATA
8763 TCAAAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 39 0.91
52 4 0.09
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.30
Consensus pattern (51 bp):
AAAAAAAATCTCCCCCTTAATAAAGTAATTACACATTATCAAAATTTATAA
Found at i:8765 original size:12 final size:12
Alignment explanation
Indices: 8748--8773 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8738 TAATTCACAC
8748 ATATCAAAATTT
1 ATATCAAAATTT
8760 ATATCAAAATTT
1 ATATCAAAATTT
8772 AT
1 AT
8774 TTGCATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATCAAAATTT
Found at i:10962 original size:82 final size:84
Alignment explanation
Indices: 10831--10993 Score: 192
Period size: 82 Copynumber: 2.0 Consensus size: 84
10821 CATTTTCTAC
* * *
10831 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTTTTTAAAAGAAT-T-ATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCATTTATTTCTTTTAAAAGAATATCATTCTCTAAAC
10894 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
10913 TTGCAACTC-TTTCATATTCTTCTCTAATTC-TCTTAATTTCTTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCAT-TT-ATTTCTTTTAAAAGAATATCATTCTCTA
* * *
10975 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
10994 TTCTTTGAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
81 5 0.07
82 31 0.46
83 9 0.13
84 23 0.34
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.53
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCATTTATTTCTTTTAAAAGAATATCATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:13048 original size:20 final size:20
Alignment explanation
Indices: 13023--13074 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
13013 TACAAGCCAA
** *
13023 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
13043 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
13062 TGTATCGATACAA
1 TGTATCGATACAA
13075 GTTTGTCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:13120 original size:21 final size:21
Alignment explanation
Indices: 13094--13149 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
13084 CTGCCAAGAA
13094 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
13115 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
13136 ATGTATCGATACAT
1 ATGTATCGATACAT
13150 TGCAACATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.45
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:14346 original size:13 final size:13
Alignment explanation
Indices: 14328--14353 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14318 CAATTTTTTG
14328 TGTATCGATACAT
1 TGTATCGATACAT
14341 TGTATCGATACAT
1 TGTATCGATACAT
14354 ACTTTGTGTA
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:14365 original size:32 final size:33
Alignment explanation
Indices: 14308--14371 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
14298 TACAAGCCAA
**
14308 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
14341 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
14372 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:19013 original size:15 final size:15
Alignment explanation
Indices: 18993--19023 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18983 ATTTCGTTTG
*
18993 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
19008 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
19023 G
1 G
19024 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:27401 original size:20 final size:22
Alignment explanation
Indices: 27378--27428 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
27368 TTTCACAAAC
27378 GGGGAGAAATT-TTT-ATTAAA
1 GGGGAGAAATTCTTTAATTAAA
*
27398 GGGGAGAAATTCTTTAATTAAG
1 GGGGAGAAATTCTTTAATTAAA
27420 GGGGAGAAA
1 GGGGAGAAA
27429 ACTGAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 11 0.39
21 3 0.11
22 14 0.50
ACGTcount: A:0.39, C:0.02, G:0.31, T:0.27
Consensus pattern (22 bp):
GGGGAGAAATTCTTTAATTAAA
Found at i:27992 original size:13 final size:13
Alignment explanation
Indices: 27974--28000 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27964 ACATTATGCT
27974 TTGTATCGATACA
1 TTGTATCGATACA
27987 TTGTATCGATACA
1 TTGTATCGATACA
28000 T
1 T
28001 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:28009 original size:19 final size:19
Alignment explanation
Indices: 27984--28039 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
27974 TTGTATCGAT
*
27984 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
28003 TCATTGTATCGAT-CATGG
1 ACATTGTATCGATACATGG
28021 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
28040 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.16
19 23 0.72
20 4 0.12
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:28105 original size:13 final size:13
Alignment explanation
Indices: 28084--28114 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28074 TGATACATGG
*
28084 TACAATGTATCGA
1 TACATTGTATCGA
28097 TACATTGTATCGA
1 TACATTGTATCGA
28110 TACAT
1 TACAT
28115 GATGAATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:29859 original size:102 final size:100
Alignment explanation
Indices: 29567--29897 Score: 328
Period size: 103 Copynumber: 3.2 Consensus size: 100
29557 TTTATTCATG
* * * ** * *
29567 GGGATACTCCAACCCCACCTTCCGAGGGAATACTCTGACCTTGCTCTTCAAAATATGTCAAGATT
1 GGGATACTCCAACCCCGCCTTTCGAGGGGATACTCCAACCCTGCTCTTCAAAATTTGTCAAGATT
*
29632 TGAACATTTCCTTTTGTCAAAATCATTGGTCATCCAT
66 TGAA-ATTTCC-TTTGTCAAAATCATTAGTCATCCAT
* * * * *
29669 GGGGATACTCCAACCCCGACATTCGAAGGGATATTCCAACGTCGCTGCT-TTCCAAATTTGTCAA
1 -GGGATACTCCAACCCCGCCTTTCGAGGGGATACTCCAAC--C-CTGCTCTTCAAAATTTGTCAA
* *
29733 -AATTGAAATTTTCCTTTATCAAAATCATTAGTCATCCAT
62 GATTTGAAA-TTTCCTTTGTCAAAATCATTAGTCATCCAT
* *
29772 GGGATACTCCAACCCGGCCTTTTGAGGGGATACTCCAACCCTGCTCTTCAAAATTTAGT-AAGAT
1 GGGATACTCCAACCCCGCCTTTCGAGGGGATACTCCAACCCTGCTCTTCAAAATTT-GTCAAGAT
* * *
29836 TTGAATATTTCCTTTGTCAAAAATTATTCA-TCACCCACA
65 TTGAA-ATTTCCTTTGTC-AAAATCATT-AGTCATCCA-T
* *
29875 AGGATACTCCAACCCTGCCTTTC
1 GGGATACTCCAACCCCGCCTTTC
29898 CCACTACAAC
Statistics
Matches: 187, Mismatches: 30, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
99 5 0.03
100 12 0.06
101 18 0.10
102 48 0.26
103 75 0.40
104 11 0.06
105 14 0.07
106 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (100 bp):
GGGATACTCCAACCCCGCCTTTCGAGGGGATACTCCAACCCTGCTCTTCAAAATTTGTCAAGATT
TGAAATTTCCTTTGTCAAAATCATTAGTCATCCAT
Done.