Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2153
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: 30693
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:743 original size:32 final size:35
Alignment explanation
Indices: 707--778 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 35
697 ATAAAAATAT
* *
707 TATAAAAAT-A-TAATATTTTAAAATTTATAT-AA
1 TATAAAAATCAGTAACATATTAAAATTTATATAAA
*
739 TAT--AAATCAGTAACGTATTAAAATTTATATAAA
1 TATAAAAATCAGTAACATATTAAAATTTATATAAA
772 TATAAAA
1 TATAAAA
779 TATTTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
30 4 0.12
31 1 0.03
32 20 0.62
33 5 0.16
35 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (35 bp):
TATAAAAATCAGTAACATATTAAAATTTATATAAA
Found at i:816 original size:19 final size:18
Alignment explanation
Indices: 769--816 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
759 AAATTTATAT
*
769 AAATATAAAATATTTTAA
1 AAATATATAATATTTTAA
*
787 ATATATCATAATATTTTAAA
1 AAATAT-ATAATATTTT-AA
807 AAATATATAA
1 AAATATATAA
817 ATATAAATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 5 0.20
19 13 0.52
20 7 0.28
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATATAATATTTTAA
Found at i:819 original size:20 final size:19
Alignment explanation
Indices: 769--820 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
759 AAATTTATAT
769 AAATATA-AAATATTTTAA
1 AAATATATAAATATTTTAA
*
787 ATATATCAT-AATATTTTAAA
1 AAATAT-ATAAATATTTT-AA
807 AAATATATAAATAT
1 AAATATATAAATAT
821 AAATACACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 12 0.43
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATATAAATATTTTAA
Found at i:1540 original size:8 final size:8
Alignment explanation
Indices: 1527--1560 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
1517 CCAAATTGCT
1527 AAAAAATA
1 AAAAAATA
1535 AAAAAATA
1 AAAAAATA
1543 AAAAAATA
1 AAAAAATA
*
1551 AATAAATA
1 AAAAAATA
1559 AA
1 AA
1561 GTAAATGGAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAAATA
Found at i:2788 original size:26 final size:25
Alignment explanation
Indices: 2755--2806 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 25
2745 TTTTTATAAT
2755 TAAATTTAAAAATT-ATATATTTATA
1 TAAATTTAAAAATTAATA-ATTTATA
2780 TAAATTTTAAAAATTAATAATTTATA
1 TAAA-TTTAAAAATTAATAATTTATA
2806 T
1 T
2807 TATATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 4 0.16
26 18 0.72
27 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAAATTTAAAAATTAATAATTTATA
Found at i:2814 original size:17 final size:16
Alignment explanation
Indices: 2796--2853 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 16
2786 TTAAAAATTA
2796 ATAATTTATA-T-TAT
1 ATAATTTATATTATAT
2810 ATAATTT-T-TTATAT
1 ATAATTTATATTATAT
*
2824 AT-ATTTATATTATTTT
1 ATAATTTATATTA-TAT
2840 ATAATTTATATTAT
1 ATAATTTATATTAT
2854 TTTATATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 6 0.16
14 13 0.35
15 3 0.08
16 5 0.14
17 10 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTATATTATAT
Found at i:2823 original size:12 final size:14
Alignment explanation
Indices: 2792--2853 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 14
2782 AATTTTAAAA
2792 ATTA-ATAATTTAT
1 ATTATATAATTTAT
2805 ATTATATAATTT-T
1 ATTATATAATTTAT
2818 -TTATATATATTTAT
1 ATTATATA-ATTTAT
2832 ATTATTTTATAATTTAT
1 ATTA---TATAATTTAT
2849 ATTAT
1 ATTAT
2854 TTTATATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.17
13 9 0.21
14 9 0.21
15 3 0.07
17 10 0.24
18 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTATATAATTTAT
Found at i:2830 original size:10 final size:10
Alignment explanation
Indices: 2768--2860 Score: 57
Period size: 8 Copynumber: 10.5 Consensus size: 10
2758 ATTTAAAAAT
2768 TATATATTTA
1 TATATATTTA
*
2778 TATAAATTT-
1 TATATATTTA
* *
2787 TA-AAAATTA
1 TATATATTTA
2796 -ATA-ATTTA
1 TATATATTTA
*
2804 TAT-TATATA
1 TATATATTTA
*
2813 -AT-TTTTTA
1 TATATATTTA
2821 TATATATTTA
1 TATATATTTA
2831 TAT-TATTT-
1 TATATATTTA
2839 TATA-ATTTA
1 TATATATTTA
2848 TAT-TATTT-
1 TATATATTTA
2856 TATAT
1 TATAT
2861 TTATCGTATT
Statistics
Matches: 66, Mismatches: 7, Indels: 21
0.70 0.07 0.22
Matches are distributed among these distances:
8 26 0.39
9 24 0.36
10 16 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATATATTTA
Found at i:2847 original size:27 final size:27
Alignment explanation
Indices: 2768--2861 Score: 86
Period size: 27 Copynumber: 3.5 Consensus size: 27
2758 ATTTAAAAAT
* * *
2768 TATATATTTATATAAATTTTAAAAATTA
1 TATATATTTATAT-TATTTTATAATTTA
* * **
2796 -ATA-ATTTATATTATATAATTTTTTA
1 TATATATTTATATTATTTTATAATTTA
2821 TATATATTTATATTATTTTATAATTTA
1 TATATATTTATATTATTTTATAATTTA
2848 TAT-TATTTTATATT
1 TATATA-TTTATATT
2862 TATCGTATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
25 7 0.13
26 13 0.25
27 32 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TATATATTTATATTATTTTATAATTTA
Found at i:2854 original size:17 final size:16
Alignment explanation
Indices: 2796--2864 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
2786 TTAAAAATTA
2796 ATAATTTATATTA--T
1 ATAATTTATATTATTT
*
2810 ATAATTT-T-TTATAT
1 ATAATTTATATTATTT
2824 AT-ATTTATATTATTTT
1 ATAATTTATATTA-TTT
2840 ATAATTTATATTATTT
1 ATAATTTATATTATTT
2856 -TATATTTAT
1 ATA-ATTTAT
2865 CGTATTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.06
13 5 0.11
14 11 0.23
15 5 0.11
16 13 0.28
17 10 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATATTATTT
Found at i:2861 original size:10 final size:10
Alignment explanation
Indices: 2800--2861 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 10
2790 AAATTAATAA
2800 TTTATATTA-
1 TTTATATTAT
*
2809 TATA-ATT-T
1 TTTATATTAT
2817 TTTATA-TAT
1 TTTATATTAT
2826 ATTTATATTAT
1 -TTTATATTAT
2837 TTTATA--A-
1 TTTATATTAT
2844 TTTATATTAT
1 TTTATATTAT
2854 TTTATATT
1 TTTATATT
2862 TATCGTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
7 6 0.14
8 8 0.19
9 6 0.14
10 20 0.47
11 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTATATTAT
Found at i:2871 original size:16 final size:16
Alignment explanation
Indices: 2823--2864 Score: 75
Period size: 17 Copynumber: 2.6 Consensus size: 16
2813 ATTTTTTATA
2823 TATATTTATATTATTT
1 TATATTTATATTATTT
2839 TATAATTTATATTATTT
1 TAT-ATTTATATTATTT
2856 TATATTTAT
1 TATATTTAT
2865 CGTATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTTATATTATTT
Found at i:11318 original size:2 final size:2
Alignment explanation
Indices: 11313--11349 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11303 GTGAATGTGT
11313 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
11350 GAAAAAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11849 original size:2 final size:2
Alignment explanation
Indices: 11842--11879 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
11832 CCTCCCCCAC
*
11842 GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11880 ACCTCCTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23011 original size:37 final size:39
Alignment explanation
Indices: 22932--23013 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 39
22922 TATTTGTATA
* * *
22932 ATAAAAATAATTTTATTTAAATTTAATTATAAATATTGAT
1 ATAAAAATAA-TTTATTTAAATTTAATTATAAACAATAAT
* *
22972 ATAAAAATAA-TT-TTTAAATTTTATTTTAAACAATAAT
1 ATAAAAATAATTTATTTAAATTTAATTATAAACAATAAT
23009 ATAAA
1 ATAAA
23014 TTTTAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 25 0.68
38 2 0.05
40 10 0.27
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (39 bp):
ATAAAAATAATTTATTTAAATTTAATTATAAACAATAAT
Found at i:23383 original size:15 final size:17
Alignment explanation
Indices: 23344--23389 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
23334 TTTGAATTTG
* *
23344 AATAAATATTAAATATA
1 AATATATATTTAATATA
23361 AATATATATTTAATAT-
1 AATATATATTTAATATA
23377 AAT-TATATTTAAT
1 AATATATATTTAAT
23390 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 14 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATATATTTAATATA
Found at i:23416 original size:22 final size:24
Alignment explanation
Indices: 23363--23435 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 24
23353 TAAATATAAA
*
23363 TATATATTTAATATAATTATA--TT
1 TATATATTTAA-AAAATTATATTTT
* *
23386 TA-AT-TTTTAAAAATT-TTTTTT
1 TATATATTTAAAAAATTATATTTT
23407 TATATATTTAAAAAATTATATTTT
1 TATATATTTAAAAAATTATATTTT
23431 TATAT
1 TATAT
23436 TAATATCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.03
20 5 0.12
21 8 0.20
22 4 0.10
23 12 0.30
24 10 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATATATTTAAAAAATTATATTTT
Found at i:23727 original size:2 final size:2
Alignment explanation
Indices: 23720--23744 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23710 TTGATATTAC
23720 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
23745 GGAAGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24580 original size:15 final size:14
Alignment explanation
Indices: 24545--24583 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
24535 TAAGGTAATT
24545 AATTAAATTATTTA
1 AATTAAATTATTTA
*
24559 AATTTAAAGTTATTTG
1 AA-TTAAA-TTATTTA
24575 AATTAAATT
1 AATTAAATT
24584 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.18
15 10 0.45
16 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (14 bp):
AATTAAATTATTTA
Found at i:24595 original size:22 final size:21
Alignment explanation
Indices: 24556--24600 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
24546 ATTAAATTAT
* * *
24556 TTAAATTTAAAGTTATTTGAA
1 TTAAATTTAAAATAATTTAAA
24577 TTAAATTTTAAAATAATTTAAA
1 TTAAA-TTTAAAATAATTTAAA
24599 TT
1 TT
24601 TATATCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTAAATTTAAAATAATTTAAA
Found at i:27059 original size:27 final size:27
Alignment explanation
Indices: 27021--27084 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
27011 AATCTTAAAT
27021 CAGATTGATCAAGAACGTGAGGGTGAG
1 CAGATTGATCAAGAACGTGAGGGTGAG
27048 CAGATTGATCAAGAACGTGAGGGTGAG
1 CAGATTGATCAAGAACGTGAGGGTGAG
27075 CAGATTGATC
1 CAGATTGATC
27085 GAGCTTTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (27 bp):
CAGATTGATCAAGAACGTGAGGGTGAG
Found at i:27531 original size:3 final size:3
Alignment explanation
Indices: 27523--27560 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
27513 TGTTTCTTTA
27523 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
27561 TTTATAGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.