Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1313
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: 20857
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Found at i:1914 original size:55 final size:58
Alignment explanation
Indices: 1827--1936 Score: 190
Period size: 55 Copynumber: 1.9 Consensus size: 58
1817 CTTGATTTCC
*
1827 AAAAATCACATAAACAAACCAATTCACACAATATCAAACATA-TTTGCATTGTGGCCA
1 AAAAATCACATAAACAAACCAATTCACACAATATCAAACATATTTTGCACTGTGGCCA
1884 AAAAATCACAT-AAC-AACCAATTCACACAATATCAAACATATTTTGCACTGTGG
1 AAAAATCACATAAACAAACCAATTCACACAATATCAAACATATTTTGCACTGTGG
1937 GTTCTAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
55 26 0.51
56 14 0.27
57 11 0.22
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (58 bp):
AAAAATCACATAAACAAACCAATTCACACAATATCAAACATATTTTGCACTGTGGCCA
Found at i:2959 original size:29 final size:28
Alignment explanation
Indices: 2922--2977 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
2912 ATTGAATTAA
* *
2922 AAATTTAATATATATTATATATCAATATT
1 AAATATAATAAATATTATATA-CAATATT
*
2951 AAATATAATAAATATTTTATACAATAT
1 AAATATAATAAATATTATATACAATAT
2978 ATATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (28 bp):
AAATATAATAAATATTATATACAATATT
Found at i:3497 original size:2 final size:2
Alignment explanation
Indices: 3490--3566 Score: 111
Period size: 2 Copynumber: 39.0 Consensus size: 2
3480 GATGAAGATC
* *
3490 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA AA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3531 TA TA TA TA AA TA TA AA 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
3567 ATTTTCTATA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:4046 original size:32 final size:30
Alignment explanation
Indices: 3980--4049 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 30
3970 TAATACGTTG
* * *
3980 ATATATTTTTAACATTTATACTATAATATT
1 ATATATTTTTAACATTTATAATATAAAATA
**
4010 ATATATTTTTATTATTATATAAATATAAAATA
1 ATATATTTTTAACATT-TAT-AATATAAAATA
4042 ATATATTT
1 ATATATTT
4050 CACAATTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 14 0.42
31 3 0.09
32 16 0.48
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATATTTTTAACATTTATAATATAAAATA
Found at i:4499 original size:18 final size:19
Alignment explanation
Indices: 4462--4500 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4452 TTATAATTTT
* *
4462 TTATTATTTTTTTTGTTAG
1 TTATTATTTTTTATGATAG
4481 TTATTA-TTTTTATGATAG
1 TTATTATTTTTTATGATAG
4499 TT
1 TT
4501 GCAAGCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (19 bp):
TTATTATTTTTTATGATAG
Found at i:7542 original size:4 final size:4
Alignment explanation
Indices: 7535--7570 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
7525 CAACAAACAA
*
7535 TAAT TAAT TAAC TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
7571 CAAGCTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:8262 original size:3 final size:3
Alignment explanation
Indices: 8254--8288 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
8244 AATTTGACAT
8254 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
8289 TCTTTTCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:8597 original size:26 final size:26
Alignment explanation
Indices: 8545--8612 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
8535 TCATTTGTAA
8545 ATAAA-AAATCAATAAATTAAATTAT
1 ATAAATAAATCAATAAATTAAATTAT
*
8570 ATAAATAAATCAAT-AATTATATTA-
1 ATAAATAAATCAATAAATTAAATTAT
* * *
8594 ATATATAATTAAATAAATT
1 ATAAATAAATCAATAAATT
8613 TAACGTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 11 0.30
25 18 0.49
26 8 0.22
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAAATAAATCAATAAATTAAATTAT
Found at i:8807 original size:15 final size:14
Alignment explanation
Indices: 8789--8825 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
8779 ATATTTTTAC
8789 TATATAATAAATAAA
1 TATATAATAAA-AAA
8804 TATATAAT--AAAA
1 TATATAATAAAAAA
8816 TATATAATAA
1 TATATAATAA
8826 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 11 0.55
13 1 0.05
15 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATATAATAAAAAA
Found at i:9415 original size:18 final size:19
Alignment explanation
Indices: 9386--9426 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
9376 AGTTTATATA
*
9386 TATTTATATTTATATTTTT
1 TATTTATATTTATATATTT
9405 TATTT-TATTTATATATTT
1 TATTTATATTTATATATTT
9423 TATT
1 TATT
9427 GCTAGGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTATATTTATATATTT
Found at i:9421 original size:13 final size:13
Alignment explanation
Indices: 9386--9426 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
9376 AGTTTATATA
*
9386 TATTTATAT-TTA
1 TATTTATATATTT
*
9398 TATTT-TTTATTT
1 TATTTATATATTT
9410 TATTTATATATTT
1 TATTTATATATTT
9423 TATT
1 TATT
9427 GCTAGGAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 2 0.08
12 12 0.50
13 10 0.42
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTTATATATTT
Found at i:9724 original size:20 final size:20
Alignment explanation
Indices: 9686--9726 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
9676 TGGGGTCAAT
*
9686 TAATTTATATATTTATATAA
1 TAATTTATATATCTATATAA
9706 TAATTTATATACTACTATATA
1 TAATTTATATA-T-CTATATA
9727 TTATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 1 0.06
22 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTTATATATCTATATAA
Found at i:9837 original size:12 final size:12
Alignment explanation
Indices: 9812--9844 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9802 TATATTTATT
*
9812 TTAT-TTTTATA
1 TTATATTTTACA
9823 TTATATTTTACA
1 TTATATTTTACA
9835 TTATATTTTA
1 TTATATTTTA
9845 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTTTACA
Found at i:9838 original size:17 final size:17
Alignment explanation
Indices: 9759--9853 Score: 74
Period size: 17 Copynumber: 5.8 Consensus size: 17
9749 ATATTTTTGA
*
9759 TATATTTTAAATTAT-T
1 TATATTTTATATTATAT
*
9775 AATA-TTTATATTATAT
1 TATATTTTATATTATAT
*
9791 ATAAATTTTA-A-TATAT
1 -TATATTTTATATTATAT
*
9807 T-TATTTTATTTTTATAT
1 TATATTTTA-TATTATAT
*
9824 TATATTTTACATTATAT
1 TATATTTTATATTATAT
* *
9841 TTTATTTTTTATT
1 TATATTTTATATT
9854 TTTAATCCAA
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
14 6 0.10
15 10 0.16
16 9 0.15
17 25 0.41
18 11 0.18
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTTTATATTATAT
Found at i:11846 original size:30 final size:31
Alignment explanation
Indices: 11811--11901 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
11801 AAGATTTTAT
**
11811 TTTTAA-GAGTTTATTTGGGTAAAAATT-AAA
1 TTTTAATGA-TTTATTTGAATAAAAATTAAAA
* *
11841 TTTTAATGACTTATTTGAATATAAATTAAAA
1 TTTTAATGATTTATTTGAATAAAAATTAAAA
**
11872 TTTTAATGATTTATTTGAATGTAAATTAAA
1 TTTTAATGATTTATTTGAATAAAAATTAAA
11902 GATTAAAGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 20 0.38
31 33 0.62
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (31 bp):
TTTTAATGATTTATTTGAATAAAAATTAAAA
Found at i:11873 original size:31 final size:31
Alignment explanation
Indices: 11833--11901 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
11823 ATTTGGGTAA
11833 AAATT-AAATTTTAATGACTTATTTGAATAT
1 AAATTAAAATTTTAATGACTTATTTGAATAT
* *
11863 AAATTAAAATTTTAATGATTTATTTGAATGT
1 AAATTAAAATTTTAATGACTTATTTGAATAT
11894 AAATTAAA
1 AAATTAAA
11902 GATTAAAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 5 0.14
31 31 0.86
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (31 bp):
AAATTAAAATTTTAATGACTTATTTGAATAT
Found at i:12587 original size:17 final size:17
Alignment explanation
Indices: 12548--12590 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
12538 TTTTTTACCG
12548 TTTATATAAAAATATCA
1 TTTATATAAAAATATCA
* * * *
12565 TATATATATATATATCT
1 TTTATATAAAAATATCA
12582 TTTATATAA
1 TTTATATAA
12591 TACAAACTAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATATAAAAATATCA
Found at i:13527 original size:8 final size:8
Alignment explanation
Indices: 13514--13553 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
13504 TGATGAATTT
13514 AAATTAAA
1 AAATTAAA
13522 AAATTAAA
1 AAATTAAA
13530 AAATTAATA
1 AAATTAA-A
*
13539 AAATT-AT
1 AAATTAAA
13546 AAATTAAA
1 AAATTAAA
13554 TTTAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 5 0.18
8 17 0.61
9 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAATTAAA
Found at i:14491 original size:4 final size:4
Alignment explanation
Indices: 14484--14542 Score: 52
Period size: 4 Copynumber: 15.0 Consensus size: 4
14474 AAAAATGAAA
* * *
14484 ATTT ATTT ATTTT ATAT ATTT -TTT GA-GT AATT AT-T ATTT ATTT ATTT
1 ATTT ATTT A-TTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT ATTT
14531 ATTT ATTT ATTT
1 ATTT ATTT ATTT
14543 TTCAGGTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
3 7 0.16
4 34 0.76
5 4 0.09
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:18520 original size:14 final size:16
Alignment explanation
Indices: 18486--18518 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
18476 TTTAAAATAT
18486 TTTATATTTATATAAA
1 TTTATATTTATATAAA
18502 TTTAT-TTTATATAAA
1 TTTATATTTATATAAA
18517 TT
1 TT
18519 ATAAGATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATATTTATATAAA
Found at i:18559 original size:16 final size:19
Alignment explanation
Indices: 18524--18560 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
18514 AAATTATAAG
18524 ATATTCATATATTTATATT
1 ATATTCATATATTTATATT
18543 ATATT-ATAT-TTTA-ATT
1 ATATTCATATATTTATATT
18559 AT
1 AT
18561 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 4 0.22
18 4 0.22
19 5 0.28
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTCATATATTTATATT
Found at i:20578 original size:14 final size:14
Alignment explanation
Indices: 20542--20582 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20532 ATTCAAGCTC
20542 AGCTAGTTTA-TTA
1 AGCTAGTTTATTTA
20555 A--TATGTTTATTTA
1 AGCTA-GTTTATTTA
20568 AGCTAGTTTATTTA
1 AGCTAGTTTATTTA
20582 A
1 A
20583 ATTAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 2 0.08
12 5 0.21
13 5 0.21
14 10 0.42
15 2 0.08
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (14 bp):
AGCTAGTTTATTTA
Done.