Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1902
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: 29877
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:30 original size:22 final size:23
Alignment explanation
Indices: 2--45 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
1 A
2 TAAATTATTATT-ATATTAAATT
1 TAAATTATTATTAATATTAAATT
24 TAAATTATTATTAAATATTAAA
1 TAAATTATTATT-AATATTAAA
46 ATCATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.60
24 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAATTATTATTAATATTAAATT
Found at i:37 original size:17 final size:17
Alignment explanation
Indices: 11--45 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1 ATAAATTATT
11 ATTATATTAAAT-TTAA
1 ATTATATTAAATATTAA
27 ATTATTATTAAATATTAA
1 ATTA-TATTAAATATTAA
45 A
1 A
46 ATCATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATATTAAATATTAA
Found at i:698 original size:35 final size:33
Alignment explanation
Indices: 641--761 Score: 93
Period size: 36 Copynumber: 3.4 Consensus size: 33
631 ATGTAATTTA
*
641 TTTTTTAAAAATATTATTTTTATTTAATATTATAAAT
1 TTTTTTTAAAA-ATTA--TTTATTTAATATTAT-AAT
*
678 TTTTTTTAATAAATTATTTATATTAGATAATT-T-TT
1 TTTTTTTAA-AAATTATTTAT-TTA-AT-ATTATAAT
*
713 TTATTTTTAAAAATTATTAACATTTAATATTATTAAT
1 TT-TTTTTAAAAATTATT--TATTTAATATTA-TAAT
750 TTTTTTTAAAAA
1 TTTTTTTAAAAA
762 AATTTAAATT
Statistics
Matches: 70, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
34 3 0.04
35 18 0.26
36 24 0.34
37 20 0.29
38 5 0.07
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.59
Consensus pattern (33 bp):
TTTTTTTAAAAATTATTTATTTAATATTATAAT
Found at i:701 original size:72 final size:72
Alignment explanation
Indices: 625--774 Score: 166
Period size: 72 Copynumber: 2.1 Consensus size: 72
615 GTAATTATAA
***
625 ATATTTATG-TAA-TTTATT-TTTTAAAAATATTATTTTTATTTAATATTATAAATTTTTTTTAA
1 ATATTTATGATAATTTTATTATTTTAAAAA-ATTATTAACATTTAATATTATAAATTTTTTTTAA
*
687 TAAATTATTT
65 -AAA-AATTT
* * *
697 ATA-TTA-GATAATTTTTTTATTTTTAAAAATTATTAACATTTAATATTATTAATTTTTTTTAAA
1 ATATTTATGATAATTTTATTATTTTAAAAAATTATTAACATTTAATATTATAAATTTTTTTTAAA
760 AAAATTT
66 AAAATTT
*
767 AAATTTAT
1 ATATTTAT
775 TATTTTTATA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
70 7 0.11
71 12 0.18
72 38 0.58
73 8 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (72 bp):
ATATTTATGATAATTTTATTATTTTAAAAAATTATTAACATTTAATATTATAAATTTTTTTTAAA
AAAATTT
Found at i:773 original size:35 final size:35
Alignment explanation
Indices: 662--793 Score: 94
Period size: 36 Copynumber: 3.7 Consensus size: 35
652 TATTATTTTT
* * *
662 ATTTAATATTATAAATTTTTTTTAATAAATTATTTAT
1 ATTTAATATTATTAATTTTTTTTAA-AAA-AATTTAA
*
699 A-TTAGATAATT-TT--TTTATTTTT-AAAAATTATTAA
1 ATTTA-AT-ATTATTAATTT-TTTTTAAAAAAAT-TTAA
733 CATTTAATATTATTAATTTTTTTTAAAAAAATTTAA
1 -ATTTAATATTATTAATTTTTTTTAAAAAAATTTAA
* * *
769 ATTTATTATTTTTATAATTTTTTTA
1 ATTTAATATTATTA-ATTTTTTTTA
794 CATTTAGAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
33 1 0.01
34 9 0.12
35 21 0.28
36 29 0.38
37 13 0.17
38 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (35 bp):
ATTTAATATTATTAATTTTTTTTAAAAAAATTTAA
Found at i:939 original size:53 final size:52
Alignment explanation
Indices: 827--941 Score: 133
Period size: 53 Copynumber: 2.2 Consensus size: 52
817 ATTTTTATTA
* * * * **
827 TTATATAAATATAAATTTAATATTTTAATCATATCAATATTAATATATTTTAT
1 TTAT-TAAATATAAATTTAATATCTTAATCATATAAATATCAATATAATAAAT
880 TATATTAAATATAAATTTAATATCTTAATCATATAAATAACTCAAT-TAATAAAT
1 T-TATTAAATATAAATTTAATATCTTAATCATATAAAT-A-TCAATATAATAAAT
934 TTATTAAA
1 TTATTAAA
942 ACATAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
53 39 0.74
54 10 0.19
55 4 0.08
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (52 bp):
TTATTAAATATAAATTTAATATCTTAATCATATAAATATCAATATAATAAAT
Found at i:10685 original size:13 final size:13
Alignment explanation
Indices: 10667--10691 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10657 CTAACCAGGT
10667 CTTTTTTTTTTTC
1 CTTTTTTTTTTTC
10680 CTTTTTTTTTTT
1 CTTTTTTTTTTT
10692 TCTGAATAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
CTTTTTTTTTTTC
Found at i:12087 original size:2 final size:2
Alignment explanation
Indices: 12080--12116 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
12070 CTCTATCTTT
*
12080 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12117 AAAGGGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13021 original size:17 final size:17
Alignment explanation
Indices: 12999--13032 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12989 ATATATTTGT
12999 TTTAAAGAAAAAGAACA
1 TTTAAAGAAAAAGAACA
* *
13016 TTTAAATAAAAATAACA
1 TTTAAAGAAAAAGAACA
13033 ACTTTTGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
TTTAAAGAAAAAGAACA
Found at i:15605 original size:2 final size:2
Alignment explanation
Indices: 15598--15644 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
15588 ATTTTGTATG
15598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15640 TA TA T
1 TA TA T
15645 TGGATCTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19754 original size:154 final size:155
Alignment explanation
Indices: 19507--19806 Score: 345
Period size: 154 Copynumber: 1.9 Consensus size: 155
19497 TTGAAGGAAT
*
19507 CCAAGTGTCCTCTCCAATTCCCTACATTTTTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTT
1 CCAAGTGTCCTCTCCAATTCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTT
* * * * * * *
19572 TCCTTTGCCTACCAACAAGGCTTGTTGATAGCTCCCTGTCCTAGTCATCCTTTCTGCAACCTTTA
66 TCATTAGCCTACCAACAAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTACTGCAACCTTTA
*
19637 TTTTCACTCATTTCATCGAAGGAGG
131 TTTTCACTCACTTCATCGAAGGAGG
* * * * * **
19662 CCAAGTGTCCTCTCCACA-TCCCTTCA-TTGTTTCTTTTTCTTTTTCATTTCTTTCCTTCACTCT
1 CCAAGTGTCCTCTCCA-ATTCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
* * * * * * *
19725 TTCATTAG-CTAACCAACTAGCCTTATTGATCGTTTACTATCTTGGTCATCCTTACTGTAACCTT
65 TTCATTAGCCT-ACCAACAAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTACTGCAACCTT
*
19789 TATTTTCCCTCACTTCAT
129 TATTTTCACTCACTTCAT
19807 TTCCCTTTTT
Statistics
Matches: 119, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
153 2 0.02
154 93 0.78
155 23 0.19
156 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.09, T:0.43
Consensus pattern (155 bp):
CCAAGTGTCCTCTCCAATTCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTT
TCATTAGCCTACCAACAAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTACTGCAACCTTTA
TTTTCACTCACTTCATCGAAGGAGG
Found at i:20141 original size:2 final size:2
Alignment explanation
Indices: 20134--20158 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20124 TTATTTTTAA
20134 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
20159 CGCATATAGA
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:21782 original size:10 final size:10
Alignment explanation
Indices: 21769--21807 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
21759 AATATGGGCA
*
21769 TATATGTATG
1 TATATATATG
21779 TATATATA--
1 TATATATATG
21787 TATATATATG
1 TATATATATG
21797 TATATATATG
1 TATATATATG
21807 T
1 T
21808 TTTCGATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 8 0.31
10 18 0.69
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (10 bp):
TATATATATG
Found at i:23757 original size:2 final size:2
Alignment explanation
Indices: 23750--23817 Score: 120
Period size: 2 Copynumber: 34.0 Consensus size: 2
23740 ATGTCTCACT
23750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23792 CT- TA TA TA TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA
23818 AAAGTAAAGA
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 62 0.97
3 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24080 original size:2 final size:2
Alignment explanation
Indices: 24073--24119 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
24063 GCTTCTCTAC
* * *
24073 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24115 AT AT A
1 AT AT A
24120 AATCATTAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:27048 original size:2 final size:2
Alignment explanation
Indices: 27041--27069 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27031 GTAGAAAAAC
27041 AT AT 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 AT AT A
27070 ATTTAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.