Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1254
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: 21696
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:593 original size:21 final size:21
Alignment explanation
Indices: 567--634 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 21
557 TTTATAAAAT
567 ATTTTTATTATATTTAAATAA
1 ATTTTTATTATATTTAAATAA
* *
588 ATTTTTATTTTTAATTTATATTTAA
1 ATTTTTA-TTAT-ATTTA-A-ATAA
613 ATTATTTATTAT-TTTAAATAA
1 ATT-TTTATTATATTTAAATAA
634 A
1 A
635 AATTAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 11 0.29
22 4 0.11
23 9 0.24
24 1 0.03
25 9 0.24
26 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTATTATATTTAAATAA
Found at i:610 original size:29 final size:27
Alignment explanation
Indices: 566--627 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 27
556 ATTTATAAAA
566 TATTTTTATTATATTTAAATAAATTT-T
1 TATTTTTATTATATTTAAAT-AATTTAT
*
593 TATTTTTAATTTATATTTAAATTATTTAT
1 TATTTTT-A-TTATATTTAAATAATTTAT
622 TATTTT
1 TATTTT
628 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.23
28 5 0.16
29 19 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTTTTATTATATTTAAATAATTTAT
Found at i:628 original size:28 final size:27
Alignment explanation
Indices: 566--629 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
556 ATTTATAAAA
*
566 TATTTTTATTATATTTAAATAAATTTT
1 TATTTTAATTATATTTAAATAAATTTT
*
593 TATTTTTAATTTATATTTAAAT-TATTTAT
1 TA-TTTTAA-TTATATTTAAATAAATTT-T
622 TATTTTAA
1 TATTTTAA
630 ATAAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 2 0.06
28 15 0.47
29 15 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTTTAATTATATTTAAATAAATTTT
Found at i:637 original size:23 final size:23
Alignment explanation
Indices: 560--645 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 23
550 TACTGCATTT
560 ATAAAATATT-TTTATTATATTTAA
1 ATAAAA-ATTATTTATTAT-TTTAA
** * *
584 ATAAATTTTTATTT-TTAATTTAT
1 ATAAA-AATTATTTATTATTTTAA
**
607 ATTTAAATTATTTATTATTTTAA
1 ATAAAAATTATTTATTATTTTAA
630 ATAAAAATTAATTTAT
1 ATAAAAATT-ATTTAT
646 ATTAAAAATT
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
22 6 0.13
23 21 0.46
24 16 0.35
25 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATAAAAATTATTTATTATTTTAA
Found at i:639 original size:16 final size:17
Alignment explanation
Indices: 620--662 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
610 TAAATTATTT
620 ATTATTTTA-AATAAAA
1 ATTATTTTATAATAAAA
* *
636 ATTAATTTATATTAAAA
1 ATTATTTTATAATAAAA
653 ATTTATTTTA
1 A-TTATTTTA
663 GTATAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTTTATAATAAAA
Found at i:654 original size:23 final size:23
Alignment explanation
Indices: 611--654 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
601 ATTTATATTT
**
611 AAATTATTTATTATTTTAAATAA
1 AAATTATTTATTATTAAAAATAA
634 AAATTAATTTA-TATTAAAAAT
1 AAATT-ATTTATTATTAAAAAT
655 TTATTTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATTATTTATTATTAAAAATAA
Found at i:669 original size:18 final size:16
Alignment explanation
Indices: 620--669 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
610 TAAATTATTT
*
620 ATTATTTTAAATAAAA
1 ATTATTTTATATAAAA
*
636 ATTAATTTATATTAAAA
1 ATTATTTTATA-TAAAA
653 ATTTATTTTAGTATAAA
1 A-TTATTTTA-TATAAA
670 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 9 0.32
17 6 0.21
18 11 0.39
19 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATTATTTTATATAAAA
Found at i:670 original size:39 final size:40
Alignment explanation
Indices: 598--679 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 40
588 ATTTTTATTT
*
598 TTAATTTATATTTAAATTATTTATTATTTTAAA-TAAAAA
1 TTAATTTATATTTAAATAATTTATTATTTTAAATTAAAAA
637 TTAATTTATA-TTAAA-AATTTATT-TTAGTATAAATTAAAAA
1 TTAATTTATATTTAAATAATTTATTATT--T-TAAATTAAAAA
677 TTA
1 TTA
680 TGACTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
36 2 0.05
37 7 0.18
38 6 0.16
39 14 0.37
40 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (40 bp):
TTAATTTATATTTAAATAATTTATTATTTTAAATTAAAAA
Found at i:709 original size:18 final size:18
Alignment explanation
Indices: 688--736 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
678 TATGACTTAT
688 TTAAATATAATTATTTAA
1 TTAAATATAATTATTTAA
** *
706 TTAAA-ATTAAAAATTTAT
1 TTAAATA-TAATTATTTAA
724 TTAAATATAATTA
1 TTAAATATAATTA
737 AAACTTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATATAATTATTTAA
Found at i:720 original size:21 final size:20
Alignment explanation
Indices: 696--755 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 20
686 ATTTAAATAT
696 AATTATTTAATTAAAATTAAA
1 AATTATTTAA-TAAAATTAAA
*
717 AATTTATTTAAATATAATTAAA
1 AA-TTATTT-AATAAAATTAAA
*
739 ACTTATTTAGATAAAAT
1 AATTATTTA-ATAAAAT
756 AATAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 14 0.42
22 16 0.48
23 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AATTATTTAATAAAATTAAA
Found at i:1290 original size:10 final size:10
Alignment explanation
Indices: 1249--1301 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
1239 TTTGAATTTT
1249 TTAATTATTAA
1 TTAA-TATTAA
1260 TTAATAGTTAA
1 TTAATA-TTAA
* * *
1271 ATATTTTTAA
1 TTAATATTAA
1281 TTAATATTAA
1 TTAATATTAA
*
1291 TAAATATTAA
1 TTAATATTAA
1301 T
1 T
1302 ATAACTATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 23 0.68
11 11 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
TTAATATTAA
Found at i:1817 original size:3 final size:3
Alignment explanation
Indices: 1809--1850 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1799 AATAATTAGC
* *
1809 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1851 CAACACGGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2079 original size:22 final size:21
Alignment explanation
Indices: 2049--2100 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
2039 TTAATTTTTT
2049 ATTT-ATTATTCAAAAATATA
1 ATTTAATTATTCAAAAATATA
* * *
2069 TTTTAAATTATTTATAAATATA
1 ATTT-AATTATTCAAAAATATA
2091 ATTTAATTAT
1 ATTTAATTAT
2101 ATTTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 6 0.23
22 17 0.65
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTAATTATTCAAAAATATA
Found at i:2086 original size:11 final size:11
Alignment explanation
Indices: 2062--2105 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
2052 TATTATTCAA
2062 AAATATATTTT
1 AAATATATTTT
2073 AAAT-TATTTAT
1 AAATATATTT-T
*
2084 AAATATAATTT
1 AAATATATTTT
*
2095 AATTATATTTT
1 AAATATATTTT
2106 TATTTGTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 5 0.18
11 19 0.68
12 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AAATATATTTT
Found at i:11685 original size:15 final size:15
Alignment explanation
Indices: 11657--11703 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
11647 ATGTAAATAT
*
11657 AAAT-TTTAAAATTA
1 AAATATTTAATATTA
11671 AAATATTTAATATT-
1 AAATATTTAATATTA
11685 AAATATTTTAAATATTA
1 AAATA-TTT-AATATTA
11702 AA
1 AA
11704 TAAATGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 9 0.32
15 11 0.39
16 6 0.21
17 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATTTAATATTA
Found at i:11700 original size:16 final size:16
Alignment explanation
Indices: 11659--11705 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
11649 GTAAATATAA
11659 ATTTTAAA-ATTAAA-
1 ATTTTAAATATTAAAT
11673 ATATTT-AATATTAAAT
1 AT-TTTAAATATTAAAT
11689 ATTTTAAATATTAAAT
1 ATTTTAAATATTAAAT
11705 A
1 A
11706 AATGAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.14
15 12 0.41
16 13 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTTAAATATTAAAT
Found at i:11702 original size:7 final size:7
Alignment explanation
Indices: 11650--11705 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
11640 ACATTTTATG
11650 TAAATA-
1 TAAATAT
*
11656 TAAATTT
1 TAAATAT
11663 TAAA-AT
1 TAAATAT
11669 TAAAATAT
1 T-AAATAT
*
11677 TTAATAT
1 TAAATAT
11684 TAAATATTT
1 TAAATA--T
11693 TAAATAT
1 TAAATAT
11700 TAAATA
1 TAAATA
11706 AATGAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
6 7 0.17
7 24 0.59
8 3 0.07
9 7 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAATAT
Found at i:12225 original size:4 final size:4
Alignment explanation
Indices: 12216--12243 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
12206 GTGAAGGAAA
12216 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
12244 TCCCAATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:13120 original size:22 final size:22
Alignment explanation
Indices: 13090--13139 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
13080 AAAATATTAT
13090 AAATATTAAATTTATA-TTTTAA
1 AAATATTAAATTT-TACTTTTAA
* *
13112 ATATATTAACTTTTACTTTTAA
1 AAATATTAAATTTTACTTTTAA
13134 AAATAT
1 AAATAT
13140 CATATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATATTAAATTTTACTTTTAA
Found at i:13510 original size:17 final size:17
Alignment explanation
Indices: 13488--13520 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13478 TATATTATAA
*
13488 TTTTTAAAAATTTTATT
1 TTTTTAAAAAATTTATT
13505 TTTTTAAAAAATTTAT
1 TTTTTAAAAAATTTAT
13521 AATATCACGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTAAAAAATTTATT
Found at i:15522 original size:20 final size:20
Alignment explanation
Indices: 15489--15529 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
15479 TAAAATTAAT
15489 TTTATTTTATTGTTCTTAAAA
1 TTTATTTTATTGTT-TTAAAA
15510 TTTATTTTA-TGTTTTAAAA
1 TTTATTTTATTGTTTTAAAA
15529 T
1 T
15530 AAAATAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 9 0.45
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTATTTTATTGTTTTAAAA
Found at i:15764 original size:21 final size:21
Alignment explanation
Indices: 15740--15794 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
15730 AATTTTAAAT
*
15740 TAATT-TTTTAATTTTTTTACA
1 TAATTATTTTAATTTTTAT-CA
*
15761 TAATTATTTTTATTTTTATCA
1 TAATTATTTTAATTTTTATCA
15782 TAATTATATTTAA
1 TAATTAT-TTTAA
15795 AATAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TAATTATTTTAATTTTTATCA
Found at i:15777 original size:23 final size:21
Alignment explanation
Indices: 15753--15793 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
15743 TTTTTTAATT
15753 TTTTTA-CATAATTATTTTTA
1 TTTTTATCATAATTATTTTTA
*
15773 TTTTTATCATAATTATATTTA
1 TTTTTATCATAATTATTTTTA
15794 AAATAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTATCATAATTATTTTTA
Found at i:15936 original size:21 final size:19
Alignment explanation
Indices: 15912--15959 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
15902 TTTTAAAATT
15912 TATATTTAT-AAATAGAATATA
1 TATATTTATGAAATA-AA-A-A
*
15933 TATATATATGAAATAAAAA
1 TATATTTATGAAATAAAAA
15952 TATATTTA
1 TATATTTA
15960 CATTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 1 0.04
21 10 0.42
22 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
TATATTTATGAAATAAAAA
Found at i:19746 original size:21 final size:21
Alignment explanation
Indices: 19722--19761 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19712 TTTATAATTA
19722 AATTTAAATAAA-AATAATTTT
1 AATTT-AATAAATAATAATTTT
*
19743 AATTTATTAAATAATAATT
1 AATTTAATAAATAATAATT
19762 CGAATCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTAATAAATAATAATTTT
Found at i:21158 original size:22 final size:22
Alignment explanation
Indices: 21098--21151 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
21088 TATTTTATTT
* *
21098 TAAATATAATTATG-ATAAAAA
1 TAAAAATAATTATGTAAAAAAA
21119 TAAAAATAATTATGTAAAAAAA
1 TAAAAATAATTATGTAAAAAAA
*
21141 TTAAAA-AATTA
1 TAAAAATAATTA
21152 ATTTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAAAATAATTATGTAAAAAAA
Found at i:21397 original size:21 final size:19
Alignment explanation
Indices: 21361--21401 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
21351 GTTTTATTTT
21361 ATTTTAAAACATAAAATAA
1 ATTTTAAAACATAAAATAA
21380 ATTTTAAGAACAATAAAATAA
1 ATTTTAA-AAC-ATAAAATAA
21401 A
1 A
21402 ATTAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (19 bp):
ATTTTAAAACATAAAATAA
Done.