Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1621
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: 25035
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Found at i:66 original size:17 final size:16
Alignment explanation
Indices: 16--65 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
6 TTTTAAATTT
16 TATAAATTTTAATATA
1 TATAAATTTTAATATA
**
32 T-T-AATAATAATATTA
1 TATAAATTTTAATA-TA
47 TATAAATTTTAA-ATA
1 TATAAATTTTAATATA
62 TATA
1 TATA
66 TTTATATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
14 8 0.30
15 10 0.37
16 3 0.11
17 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAAATTTTAATATA
Found at i:88 original size:52 final size:55
Alignment explanation
Indices: 27--129 Score: 124
Period size: 52 Copynumber: 1.9 Consensus size: 55
17 ATAAATTTTA
27 ATATATTAATAATAATA-TTATATAAATTTTAA-AT-ATATATTT-ATATTATATT
1 ATATATTAATAATAATATTTATAT-AATTTTAATATAATATATTTAATATTATATT
* * ** *
79 ATATTTTAATTATTTTATTTATATTATTTTAATATAATATATTTAATATTA
1 ATATATTAATAATAATATTTATATAATTTTAATATAATATATTTAATATTA
130 AAATTTATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
52 20 0.48
53 8 0.19
54 8 0.19
55 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (55 bp):
ATATATTAATAATAATATTTATATAATTTTAATATAATATATTTAATATTATATT
Found at i:97 original size:14 final size:14
Alignment explanation
Indices: 64--109 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
54 TTTAAATATA
64 TATTTATATTATATT
1 TATTTATATTAT-TT
79 ATATTT-TAATTATTT
1 -TATTTAT-ATTATTT
94 TATTTATATTATTT
1 TATTTATATTATTT
108 TA
1 TA
110 ATATAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 14 0.50
15 4 0.14
16 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTATATTATTT
Found at i:100 original size:30 final size:28
Alignment explanation
Indices: 7--129 Score: 94
Period size: 28 Copynumber: 4.3 Consensus size: 28
1 TAAATT
* *
7 TTTAAATTTTATAAATTTTAATATATTAATA
1 TTTATATTATATAAATTTTAA-ATA-T-ATA
* *
38 ATAATATTATATAAATTTTAAATATATA
1 TTTATATTATATAAATTTTAAATATATA
*
66 TTTATATTATATTATATTTT-AAT-TAT-
1 TTTATATTATA-TAAATTTTAAATATATA
*
92 TTTAT-TTATAT-TATTTTAATATAATATA
1 TTTATATTATATAAATTTTAA-AT-ATATA
120 TTTAATATTA
1 TTT-ATATTA
130 AAATTTATAA
Statistics
Matches: 77, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
23 6 0.08
24 2 0.03
25 7 0.09
26 5 0.06
27 6 0.08
28 18 0.23
29 10 0.13
30 6 0.08
31 17 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTATATTATATAAATTTTAAATATATA
Found at i:299 original size:17 final size:16
Alignment explanation
Indices: 247--300 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
237 TTATTTAAAT
*
247 TTAAAAATTTATTATTA
1 TTAAAAATTTTTTA-TA
** *
264 TTAAAAATTTTAAAAA
1 TTAAAAATTTTTTATA
280 TTAAAAATATTTTTATA
1 TTAAAAAT-TTTTTATA
297 TTAA
1 TTAA
301 TATTTATATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAAATTTTTTATA
Found at i:327 original size:5 final size:5
Alignment explanation
Indices: 317--384 Score: 58
Period size: 5 Copynumber: 14.4 Consensus size: 5
307 TATATTTTAT
*
317 AATTA AATTA AA-TA AATTA AATT- TATTA AA-TA AA-TA TAATTA ATATT-
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA -AATTA A-ATTA
*
364 -ATTA AATTA ATTTA AATTA AA
1 AATTA AATTA AATTA AATTA AA
385 AAAATTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
3 3 0.06
4 13 0.25
5 31 0.60
6 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATTA
Found at i:332 original size:9 final size:9
Alignment explanation
Indices: 320--391 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
310 ATTTTATAAT
320 TAAATTAAA
1 TAAATTAAA
329 TAAATTAAA
1 TAAATTAAA
**
338 TTTATTAAA
1 TAAATTAAA
*
347 TAAATATAAT
1 TAAAT-TAAA
*
357 TAATATT-AT
1 TAA-ATTAAA
*
366 TAAATTAATT
1 TAAATTAA-A
376 TAAATTAAA
1 TAAATTAAA
*
385 AAAATTA
1 TAAATTA
392 TTTGAAATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
8 3 0.06
9 31 0.60
10 16 0.31
11 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAATTAAA
Found at i:336 original size:14 final size:14
Alignment explanation
Indices: 317--391 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
307 TATATTTTAT
317 AATTAAATTAAATA
1 AATTAAATTAAATA
* *
331 AATTAAATTTATTA
1 AATTAAATTAAATA
*
345 AA-TAAATATAATTA
1 AATTAAAT-TAAATA
359 ATATT--ATTAAATTA
1 A-ATTAAATTAAA-TA
* *
373 ATTTAAATTAAAAA
1 AATTAAATTAAATA
387 AATTA
1 AATTA
392 TTTGAAATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
13 10 0.21
14 30 0.62
15 7 0.15
16 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTAAATTAAATA
Found at i:345 original size:23 final size:24
Alignment explanation
Indices: 318--384 Score: 86
Period size: 23 Copynumber: 2.8 Consensus size: 24
308 ATATTTTATA
318 ATTAAATTAAATAAATTAAAT-TT
1 ATTAAATTAAATAAATTAAATATT
341 ATTAAA-TAAATATAATT-AATATT
1 ATTAAATTAAATA-AATTAAATATT
*
364 ATTAAATTAATTTAAATTAAA
1 ATTAAATTAA-ATAAATTAAA
385 AAAATTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
22 9 0.24
23 18 0.47
24 7 0.18
25 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTAAATTAAATAAATTAAATATT
Found at i:428 original size:16 final size:17
Alignment explanation
Indices: 403--436 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
393 TTGAAATTAT
*
403 TTATTTTAAA-TTAAAC
1 TTATTATAAATTTAAAC
419 TTATTATAAATTTAAAC
1 TTATTATAAATTTAAAC
436 T
1 T
437 ATTCATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTATAAATTTAAAC
Found at i:7958 original size:14 final size:13
Alignment explanation
Indices: 7932--7974 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 13
7922 AAAATTGATA
7932 TTATTTATGATTAT
1 TTATTTAT-ATTAT
7946 TTATTGTATATTAAT
1 TTATT-TATATT-AT
7961 TTATTTATATTAT
1 TTATTTATATTAT
7974 T
1 T
7975 ATACATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.11
14 14 0.52
15 10 0.37
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (13 bp):
TTATTTATATTAT
Found at i:8038 original size:18 final size:18
Alignment explanation
Indices: 8015--8063 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
8005 CTATTTATTT
8015 TATATATAATTAATTATA
1 TATATATAATTAATTATA
8033 TATATATAATT-ATT-TA
1 TATATATAATTAATTATA
*
8049 -A-GTATAATTAATTAT
1 TATATATAATTAATTAT
8064 TAAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 7 0.25
15 4 0.14
16 3 0.11
17 3 0.11
18 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TATATATAATTAATTATA
Found at i:8064 original size:18 final size:16
Alignment explanation
Indices: 8017--8064 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 16
8007 ATTTATTTTA
*
8017 TATATAATTAATTATA
1 TATATAATTAATTATT
8033 TATAT-A-TAATTATT
1 TATATAATTAATTATT
8047 TAAGTATAATTAATTATT
1 T-A-TATAATTAATTATT
8065 AAAGAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 8 0.30
15 2 0.07
16 8 0.30
17 1 0.04
18 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TATATAATTAATTATT
Found at i:9816 original size:14 final size:15
Alignment explanation
Indices: 9797--9829 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
9787 CCCCACCTAC
9797 TTATTATAA-ATAAA
1 TTATTATAACATAAA
*
9811 TTATTATAACATAAT
1 TTATTATAACATAAA
9826 TTAT
1 TTAT
9830 AAATCAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATTATAACATAAA
Found at i:10763 original size:29 final size:29
Alignment explanation
Indices: 10719--10778 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
10709 TACATACGTC
10719 TAAGTGGATCCCTTCTAATAGCCTAATAA
1 TAAGTGGATCCCTTCTAATAGCCTAATAA
*
10748 TAAGTGGATCCTTTCTAATAGCCTAATAA
1 TAAGTGGATCCCTTCTAATAGCCTAATAA
10777 TA
1 TA
10779 TTTATAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAGTGGATCCCTTCTAATAGCCTAATAA
Found at i:11628 original size:29 final size:28
Alignment explanation
Indices: 11586--11647 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
11576 ATTAAAATTT
* *
11586 TATTGAAATATAAAAATAAATAATAACAA
1 TATTTAAAAATAAAAATAAA-AATAACAA
* * *
11615 TATTTAAAAATAAATATAAAAATGATAA
1 TATTTAAAAATAAAAATAAAAATAACAA
11643 TATTT
1 TATTT
11648 TTAGTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (28 bp):
TATTTAAAAATAAAAATAAAAATAACAA
Found at i:11645 original size:14 final size:12
Alignment explanation
Indices: 11591--11637 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
11581 AATTTTATTG
11591 AAATATAAAAAT
1 AAATATAAAAAT
*
11603 AAATAATAACAAT
1 AAAT-ATAAAAAT
*
11616 --ATTTAAAAAT
1 AAATATAAAAAT
11626 AAATATAAAAAT
1 AAATATAAAAAT
11638 GATAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
10 6 0.21
11 2 0.07
12 13 0.46
13 7 0.25
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:12403 original size:14 final size:15
Alignment explanation
Indices: 12384--12412 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12374 TAGATTATAC
12384 TTTTTTAAA-AATAT
1 TTTTTTAAATAATAT
12398 TTTTTTAAATAATAT
1 TTTTTTAAATAATAT
12413 ATACAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTTAAATAATAT
Found at i:14373 original size:30 final size:30
Alignment explanation
Indices: 14339--14400 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
14329 ATTAAAAAAT
14339 TAAAAAATTATTTTTATATTAATATTTAAA
1 TAAAAAATTATTTTTATATTAATATTTAAA
** *
14369 TAAAATCTTATTTTTATGTTAATATTTAAA
1 TAAAAAATTATTTTTATATTAATATTTAAA
14399 TA
1 TA
14401 GTAATTAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TAAAAAATTATTTTTATATTAATATTTAAA
Found at i:14518 original size:17 final size:19
Alignment explanation
Indices: 14480--14518 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
14470 CAACCCGACC
14480 ATAAACATATCTCTTATAT
1 ATAAACATATCTCTTATAT
*
14499 ATAAGCATATCTCTTATAT
1 ATAAACATATCTCTTATAT
14518 A
1 A
14519 CCAATAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (19 bp):
ATAAACATATCTCTTATAT
Found at i:15379 original size:16 final size:17
Alignment explanation
Indices: 15354--15386 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
15344 CAATTTAAAA
15354 TTTTAGATATAT-TAAT
1 TTTTAGATATATATAAT
*
15370 TTTTATATATATATAAT
1 TTTTAGATATATATAAT
15387 ATATATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTAGATATATATAAT
Found at i:19886 original size:13 final size:13
Alignment explanation
Indices: 19868--19899 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19858 CACGGTTCTA
19868 CTTGGACAAAATT
1 CTTGGACAAAATT
19881 CTTGGACAAAATT
1 CTTGGACAAAATT
*
19894 TTTGGA
1 CTTGGA
19900 ACATGGCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (13 bp):
CTTGGACAAAATT
Found at i:21901 original size:16 final size:15
Alignment explanation
Indices: 21844--21901 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
21834 TCACTTTAGG
*
21844 TTTAGATCATTTTAA
1 TTTAGATTATTTTAA
*
21859 TTTCAGATTATTTCAA
1 TTT-AGATTATTTTAA
*
21875 GTTTTAAATTATTTTGAA
1 --TTTAGATTATTTT-AA
21893 TTTAGATTA
1 TTTAGATTA
21902 ATCAAGTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.09
16 18 0.53
17 8 0.24
18 5 0.15
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (15 bp):
TTTAGATTATTTTAA
Found at i:22445 original size:16 final size:16
Alignment explanation
Indices: 22426--22459 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22416 CTCGAACCCT
*
22426 AAATAATTCAAACTTA
1 AAATAATCCAAACTTA
*
22442 AAATGATCCAAACTTA
1 AAATAATCCAAACTTA
22458 AA
1 AA
22460 TTAAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATAATCCAAACTTA
Found at i:22514 original size:19 final size:17
Alignment explanation
Indices: 22477--22515 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
22467 TTATTTTATT
*
22477 TAAAAAAATTAAGTTAA
1 TAAAAAAATTAAATTAA
22494 TAAAAATAATATAAATTAA
1 TAAAAA-AAT-TAAATTAA
22513 TAA
1 TAA
22516 TTTATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
TAAAAAAATTAAATTAA
Found at i:23277 original size:16 final size:16
Alignment explanation
Indices: 23240--23270 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23230 TCAAAATTGT
*
23240 CCGAACTCAAAATAAC
1 CCGAACTCGAAATAAC
23256 CCGAACTCGAAATAA
1 CCGAACTCGAAATAA
23271 TTCGAACCCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.29, G:0.10, T:0.13
Consensus pattern (16 bp):
CCGAACTCGAAATAAC
Found at i:23872 original size:25 final size:25
Alignment explanation
Indices: 23835--23887 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
23825 TTAAAATTTT
*
23835 TAAAAATTATAAAAAAATAAAA-AAA
1 TAAAAAATAT-AAAAAATAAAATAAA
* *
23860 TAAAAAATCTAAAAATTAAAATAAA
1 TAAAAAATATAAAAAATAAAATAAA
23885 TAA
1 TAA
23888 TACAAGCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
TAAAAAATATAAAAAATAAAATAAA
Found at i:24818 original size:15 final size:17
Alignment explanation
Indices: 24789--24822 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
24779 AAAGCAAGTA
24789 TTAATATATGTATATAT
1 TTAATATATGTATATAT
24806 TTAATATA-G-ATATAT
1 TTAATATATGTATATAT
24821 TT
1 TT
24823 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTAATATATGTATATAT
Done.