Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1117
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: 20513
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Found at i:1306 original size:24 final size:24
Alignment explanation
Indices: 1268--1314 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1258 TAATAAAAAT
1268 AAAATATTTAAAATATAA-AATTAA
1 AAAATATTTAAAATA-AATAATTAA
**
1292 AAAATATTTTTAATAAATAATTA
1 AAAATATTTAAAATAAATAATTA
1315 TAATCTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAATATTTAAAATAAATAATTAA
Found at i:2892 original size:10 final size:9
Alignment explanation
Indices: 2862--2891 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2852 CTTTAAATTC
2862 AATTTTTAA
1 AATTTTTAA
2871 AATTATTTAA
1 AATT-TTTAA
2881 AATTTTTAA
1 AATTTTTAA
2890 AA
1 AA
2892 AGATCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AATTTTTAA
Found at i:3232 original size:2 final size:2
Alignment explanation
Indices: 3225--3263 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3215 TAGATTGAAA
3225 AT AT AT AT AT 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 AT AT AT AT AT A
3264 ATGGATGGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3416 original size:15 final size:16
Alignment explanation
Indices: 3385--3417 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3375 AATATTATAG
3385 TATTCTTAAGATAATT
1 TATTCTTAAGATAATT
*
3401 TATTCTTATG-TAATT
1 TATTCTTAAGATAATT
3416 TA
1 TA
3418 GAATAAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
TATTCTTAAGATAATT
Found at i:4100 original size:15 final size:15
Alignment explanation
Indices: 4067--4111 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4057 AAATTTTTTA
* *
4067 AACTTAAATTAATCT
1 AACTTAAATTAACCC
4082 AACTTAAATTAACCC
1 AACTTAAATTAACCC
*
4097 AACTTGAAATCAACC
1 AACTT-AAATTAACC
4112 TAATTTGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (15 bp):
AACTTAAATTAACCC
Found at i:5725 original size:20 final size:19
Alignment explanation
Indices: 5697--5735 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5687 TAAATGAATT
*
5697 AAAACATAACGTAAAAAATA
1 AAAAAATAA-GTAAAAAATA
*
5717 AAAAAATAATTAAAAAATA
1 AAAAAATAAGTAAAAAATA
5736 TAAATATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAAAATAAGTAAAAAATA
Found at i:5730 original size:19 final size:19
Alignment explanation
Indices: 5708--5745 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5698 AAACATAACG
5708 TAAAAAATAAAAAAATAAT
1 TAAAAAATAAAAAAATAAT
* *
5727 TAAAAAATATAAATATAAT
1 TAAAAAATAAAAAAATAAT
5746 ATGCATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAAATAAAAAAATAAT
Found at i:6124 original size:52 final size:52
Alignment explanation
Indices: 6062--6161 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
6052 GTTATCAATA
* *
6062 ATGGTGCTCAAAGAT-AGAGTTGTTCAAGTGGAAGTGTGGGGCAACTTAGCTT
1 ATGGTGCTCAAAGATGAGAGTTG-TCAAGTGGAAATGTAGGGCAACTTAGCTT
* *
6114 ATGGTGCTCAAAGATGTGAGTTGTCAAGTGTAAATGTAGGGCAACTTA
1 ATGGTGCTCAAAGATGAGAGTTGTCAAGTGGAAATGTAGGGCAACTTA
6162 CCATAGTGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 37 0.86
53 6 0.14
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (52 bp):
ATGGTGCTCAAAGATGAGAGTTGTCAAGTGGAAATGTAGGGCAACTTAGCTT
Found at i:6763 original size:2 final size:2
Alignment explanation
Indices: 6758--6803 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6748 TTTCACCCTC
6758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6800 AT AT
1 AT AT
6804 CATTAGTACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8674 original size:25 final size:26
Alignment explanation
Indices: 8637--8693 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
8627 AATTTTTTAA
* * *
8637 AATAAATATAAATAATTTTATTT-TT
1 AATAATTAAAAATAATTTAATTTATT
*
8662 AATAATTAAAAATTATTTAATTTATT
1 AATAATTAAAAATAATTTAATTTATT
8688 AATAAT
1 AATAAT
8694 ATATAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATAATTAAAAATAATTTAATTTATT
Found at i:8700 original size:29 final size:28
Alignment explanation
Indices: 8630--8700 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 28
8620 TTATTAAAAT
* * *
8630 TTTTTAA-AATAAATATAAATAATTTTA
1 TTTTTAATAATATATAAAAATAATTTAA
*
8657 TTTTTAAT-A-AT-TAAAAATTATTTAA
1 TTTTTAATAATATATAAAAATAATTTAA
8682 TTTATTAATAATATATAAA
1 TTT-TTAATAATATATAAA
8701 TTAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
25 14 0.40
26 6 0.17
27 9 0.26
28 2 0.06
29 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTTTAATAATATATAAAAATAATTTAA
Found at i:9461 original size:6 final size:6
Alignment explanation
Indices: 9446--9477 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
9436 TGTTCGACAC
9446 AAAA-A AAAACA AAAACA AAAACA AAAACA AAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAA
9478 CGAGAGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:9978 original size:4 final size:4
Alignment explanation
Indices: 9971--9996 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
9961 AGAATCTTTC
9971 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
9997 TTTTGCAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:10671 original size:22 final size:22
Alignment explanation
Indices: 10629--10671 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
10619 ACACGTCAAA
* *
10629 AAATAAAAATAATATCGAACAC
1 AAATAAAAATAATAACCAACAC
10651 AAATAAAACATAA-AACCAACA
1 AAATAAAA-ATAATAACCAACA
10672 GAATAGCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.67, C:0.16, G:0.02, T:0.14
Consensus pattern (22 bp):
AAATAAAAATAATAACCAACAC
Found at i:11208 original size:16 final size:16
Alignment explanation
Indices: 11187--11285 Score: 67
Period size: 16 Copynumber: 6.2 Consensus size: 16
11177 GTTAATGTAT
*
11187 AATTAAATTTAAATAA
1 AATTAAATTTAAATTA
* *
11203 AATTAATTTTATAATTT
1 AATTAAATTTA-AATTA
*
11220 AATAATAATTTAAATTA
1 AATTA-AATTTAAATTA
**
11237 TTTTAAATTTAAA--A
1 AATTAAATTTAAATTA
* *
11251 ATTTATATTTAAATTA
1 AATTAAATTTAAATTA
* * *
11267 AATTTAATATGAATTA
1 AATTAAATTTAAATTA
11283 AAT
1 AAT
11286 CAATCTGTCT
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
14 12 0.19
16 33 0.52
17 13 0.21
18 5 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
AATTAAATTTAAATTA
Found at i:11651 original size:24 final size:24
Alignment explanation
Indices: 11623--11697 Score: 71
Period size: 31 Copynumber: 2.9 Consensus size: 24
11613 ATTATTATTT
11623 GAAATTAAATTTTTATTTAAATAA
1 GAAATTAAATTTTTATTTAAATAA
*
11647 TAAATTATACATTTTTAATGATAATAAATAA
1 GAAATTA-A-ATTTTT-AT--T--TAAATAA
11678 GAAA-TAAATTTTTATTTAAA
1 GAAATTAAATTTTTATTTAAA
11698 ATATAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 15
0.71 0.03 0.25
Matches are distributed among these distances:
23 4 0.10
24 6 0.14
25 2 0.05
26 6 0.14
27 4 0.10
28 6 0.14
29 2 0.05
30 2 0.05
31 10 0.24
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (24 bp):
GAAATTAAATTTTTATTTAAATAA
Found at i:11700 original size:24 final size:25
Alignment explanation
Indices: 11623--11700 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 25
11613 ATTATTATTT
11623 GAAATTAAATTTTTATTT-AAATAA
1 GAAATTAAATTTTTATTTAAAATAA
* *
11647 TAAATTATACATTTTTAATGATAATAAATAA
1 GAAATTA-A-ATTTTT-AT--TTA-AAATAA
11678 GAAA-TAAATTTTTATTTAAAATA
1 GAAATTAAATTTTTATTTAAAATA
11701 TAATTTAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
24 11 0.26
25 3 0.07
26 6 0.14
27 4 0.09
28 6 0.14
29 2 0.05
30 2 0.05
31 9 0.21
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (25 bp):
GAAATTAAATTTTTATTTAAAATAA
Found at i:11700 original size:28 final size:28
Alignment explanation
Indices: 11623--11700 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 28
11613 ATTATTATTT
11623 GAAATTAAATTTTTATTT-AAAT-AATAA
1 GAAA-TAAATTTTTATTTAAAATAAATAA
* * * * *
11650 -ATTATACATTTTTAATGATAATAAATAA
1 GA-AATAAATTTTTATTTAAAATAAATAA
11678 GAAATAAATTTTTATTTAAAATA
1 GAAATAAATTTTTATTTAAAATA
11701 TAATTTAGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 7
0.69 0.19 0.13
Matches are distributed among these distances:
26 11 0.30
27 4 0.11
28 21 0.57
29 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (28 bp):
GAAATAAATTTTTATTTAAAATAAATAA
Found at i:13223 original size:16 final size:16
Alignment explanation
Indices: 13188--13225 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
13178 TGACTCGAGT
*
13188 TTGAAATAATCTAAAT
1 TTGAAATAATCTAAAC
13204 TTGAAATAAT-TCAAAC
1 TTGAAATAATCT-AAAC
13220 TTGAAA
1 TTGAAA
13226 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (16 bp):
TTGAAATAATCTAAAC
Done.