Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2396
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: 25790
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Found at i:446 original size:20 final size:20
Alignment explanation
Indices: 399--472 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
389 TAAAAGACAT
*
399 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
418 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * *
439 CATGTATCGATATATTGA-A
1 AATGTATCGATACATTCATA
458 AATGTATCGATACAT
1 AATGTATCGATACAT
473 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 14 0.31
20 29 0.64
21 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:472 original size:39 final size:39
Alignment explanation
Indices: 396--472 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
386 AGGTAAAAGA
*
396 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGTAAAATATATCGATACATT
* *
435 CATACATGTATCGATATATTG-AAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGTAAAATATATCGATACAT
473 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 19 0.56
40 15 0.44
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGTAAAATATATCGATACATT
Found at i:7321 original size:13 final size:13
Alignment explanation
Indices: 7300--7347 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
7290 TACTAAAATC
*
7300 ATATTTATATTAG
1 ATATATATATTAG
*
7313 ATAAATATATTAG
1 ATATATATATTAG
* *
7326 -TATTTATATTAC
1 ATATATATATTAG
7338 ATATATATAT
1 ATATATATAT
7348 ATATCAGTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (13 bp):
ATATATATATTAG
Found at i:7321 original size:30 final size:29
Alignment explanation
Indices: 7248--7321 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
7238 ATTACTTAAA
7248 ATATTAGAT-ATATAATAAAATCATATGT
1 ATATTAGATAATATAATAAAATCATATGT
** * *
7276 ATACCA-ATATTATATACTAAAATCATATTT
1 ATATTAGATA--ATATAATAAAATCATATGT
7306 ATATTAGATAAATATA
1 ATATTAGAT-AATATA
7322 TTAGTATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
30 26 0.74
31 2 0.06
32 1 0.03
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (29 bp):
ATATTAGATAATATAATAAAATCATATGT
Found at i:7855 original size:2 final size:2
Alignment explanation
Indices: 7850--7920 Score: 61
Period size: 2 Copynumber: 35.5 Consensus size: 2
7840 ACACACACAA
* * * * * *
7850 AT AT AT AT AT AC AC AT AT AT AT GT GT AT AC AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
7892 AT AT TT AT AC AC 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
7921 AGCAGATTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:7869 original size:16 final size:16
Alignment explanation
Indices: 7844--7892 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
7834 TTACACACAC
* *
7844 ACACAAATATATATAT
1 ACACATATATATGTAT
*
7860 ACACATATATATGTGT
1 ACACATATATATGTAT
*
7876 ATACATATATATGTAT
1 ACACATATATATGTAT
7892 A
1 A
7893 TATTTATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (16 bp):
ACACATATATATGTAT
Found at i:7892 original size:24 final size:24
Alignment explanation
Indices: 7864--7919 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
7854 ATATATACAC
* *
7864 ATATATATGTGTATACATATATAT
1 ATATATATGTATACACATATATAT
* *
7888 GTATATATTTATACACATATATAT
1 ATATATATGTATACACATATATAT
7912 ATATATAT
1 ATATATAT
7920 AAGCAGATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (24 bp):
ATATATATGTATACACATATATAT
Found at i:7916 original size:22 final size:22
Alignment explanation
Indices: 7864--7917 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
7854 ATATATACAC
* *
7864 ATATATATGTGTATACATATAT
1 ATATATATATGTATACACATAT
* *
7886 ATGTATATATTTATACACATAT
1 ATATATATATGTATACACATAT
7908 ATATATATAT
1 ATATATATAT
7918 ATAAGCAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (22 bp):
ATATATATATGTATACACATAT
Found at i:9736 original size:20 final size:20
Alignment explanation
Indices: 9713--9754 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
9703 TTTGATTATT
* *
9713 AAAAATATATTTTTTCATCC
1 AAAAATACATTCTTTCATCC
*
9733 AAAAATGCATTCTTTCATCC
1 AAAAATACATTCTTTCATCC
9753 AA
1 AA
9755 CCAACGCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAATACATTCTTTCATCC
Found at i:10034 original size:16 final size:15
Alignment explanation
Indices: 10012--10070 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
10002 TTGAAATTAG
10012 TAAATTTTAATTTTT
1 TAAATTTTAATTTTT
* *
10027 TAAAATTTAAATATTT
1 T-AAATTTTAATTTTT
10043 T--ATTTTAAATTTTTT
1 TAAATTTT-AA-TTTTT
*
10058 TAAATTTCAATTT
1 TAAATTTTAATTT
10071 ATTTTTAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 9 0.26
16 15 0.44
17 4 0.12
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TAAATTTTAATTTTT
Found at i:10749 original size:43 final size:41
Alignment explanation
Indices: 10667--10808 Score: 130
Period size: 42 Copynumber: 3.4 Consensus size: 41
10657 AATTAAAATG
* * * *
10667 AAATTATAAAAAT-ACTTTAATTT-TTTTTTCAACACGTTATT
1 AAATTATAAAATTAACTAT-ATTTATTTTTT-AAAATGTTATT
10708 AAAATTAGTAAAATTAA-TAATATTTATTTTTTAAAATGTTATTT
1 -AAATTA-TAAAATTAACT-ATATTTATTTTTTAAAATGTTA-TT
* *
10752 AAA-TATAAAAATTAACTGTATTTATTTTTTAAAATATTATT
1 AAATTAT-AAAATTAACTATATTTATTTTTTAAAATGTTATT
10793 AAATTATTAAAATTAA
1 AAATTA-TAAAATTAA
10809 AGGTATTTGA
Statistics
Matches: 85, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
41 6 0.07
42 46 0.54
43 23 0.27
44 10 0.12
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (41 bp):
AAATTATAAAATTAACTATATTTATTTTTTAAAATGTTATT
Found at i:10815 original size:42 final size:41
Alignment explanation
Indices: 10703--10816 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 41
10693 TTTCAACACG
* * *
10703 TTATTAAAATTAGTAAAATTAATAATATTTATTTTTTAAAATG
1 TTATT-AAATTATTAAAATTAA-AGTATTTATTTTTTAAAATA
* *
10746 TTATTTAAA-TATAAAAATTAACTGTATTTATTTTTTAAAATA
1 TTA-TTAAATTATTAAAATTAA-AGTATTTATTTTTTAAAATA
10788 TTATTAAATTATTAAAATTAAAGGTATTT
1 TTATTAAATTATTAAAATTAAA-GTATTT
10817 GAAAAATAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 5 0.08
42 47 0.78
43 6 0.10
44 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (41 bp):
TTATTAAATTATTAAAATTAAAGTATTTATTTTTTAAAATA
Found at i:11318 original size:21 final size:20
Alignment explanation
Indices: 11281--11319 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11271 AAGTTTTAGA
*
11281 TTTTTCAATTTATTTTACGT
1 TTTTTCAATTTACTTTACGT
*
11301 TTTTTCATTTTACCTTTAC
1 TTTTTCAATTTA-CTTTAC
11320 CCAATTTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTTCAATTTACTTTACGT
Found at i:11762 original size:24 final size:24
Alignment explanation
Indices: 11735--11783 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
11725 TTAATTCATT
*
11735 AATTTTCCTCAAATTTTGCAGTAA
1 AATTTTCCTCAAATTCTGCAGTAA
*
11759 AATTTTGCTCAAATTCTGCAGTAA
1 AATTTTCCTCAAATTCTGCAGTAA
11783 A
1 A
11784 TTCAGCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (24 bp):
AATTTTCCTCAAATTCTGCAGTAA
Found at i:11791 original size:23 final size:24
Alignment explanation
Indices: 11742--11796 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
11732 ATTAATTTTC
* **
11742 CTCAAATTTTGCAGTAAAATTTTG
1 CTCAAATTCTGCAGTAAAATTCAG
11766 CTCAAATTCTGCAGT-AAATTCAG
1 CTCAAATTCTGCAGTAAAATTCAG
11789 CTCAAATT
1 CTCAAATT
11797 AATTCACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (24 bp):
CTCAAATTCTGCAGTAAAATTCAG
Found at i:12662 original size:26 final size:26
Alignment explanation
Indices: 12633--12683 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
12623 AAAATTTTTT
12633 AATTATTA-AAATATAATTTTAATTAA
1 AATTATTATAAATATAA-TTTAATTAA
* *
12659 AATTTTTATAACTATAATTTAATTA
1 AATTATTATAAATATAATTTAATTA
12684 CAGGAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
AATTATTATAAATATAATTTAATTAA
Found at i:12983 original size:2 final size:2
Alignment explanation
Indices: 12976--13007 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12966 TTCGTAAGAC
*
12976 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13008 GGAGAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:13457 original size:12 final size:12
Alignment explanation
Indices: 13435--13570 Score: 65
Period size: 12 Copynumber: 11.5 Consensus size: 12
13425 TCCTTGATTG
13435 TAATAATATTTAA
1 TAAT-ATATTTAA
13448 TAATATATTTTAA
1 TAATATA-TTTAA
* *
13461 T-ATTTAATTTGA
1 TAATAT-ATTTAA
13473 T-A-ATATTTAA
1 TAATATATTTAA
*
13483 TGATATATTTAA
1 TAATATATTTAA
*
13495 TAGTATA-TTAA
1 TAATATATTTAA
13506 -ACATAT-TTTAA
1 TA-ATATATTTAA
*
13517 T-ATAAAATTTAA
1 TAAT-ATATTTAA
*
13529 TAATGTA-TTAA
1 TAATATATTTAA
*
13540 -AATTATTTTTAA
1 TAA-TATATTTAA
*
13552 AAATATTATTTAA
1 TAATA-TATTTAA
*
13565 TCATAT
1 TAATAT
13571 TAGATAATAT
Statistics
Matches: 94, Mismatches: 15, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
10 11 0.12
11 20 0.21
12 39 0.41
13 24 0.26
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (12 bp):
TAATATATTTAA
Found at i:13478 original size:15 final size:14
Alignment explanation
Indices: 13458--13495 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
13448 TAATATATTT
13458 TAATATTTAATTTGA
1 TAATATTTAA-TTGA
13473 TAATATTTAA-TGA
1 TAATATTTAATTGA
13486 T-ATATTTAAT
1 TAATATTTAAT
13496 AGTATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.36
13 4 0.18
15 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (14 bp):
TAATATTTAATTGA
Found at i:20522 original size:15 final size:15
Alignment explanation
Indices: 20502--20539 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
20492 AATATTTACA
*
20502 TTATTTTAG-ATTTTT
1 TTATTTT-GTATTTAT
20517 TTATTTTGTATTTAT
1 TTATTTTGTATTTAT
20532 TTATTTTG
1 TTATTTTG
20540 GGTTTTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (15 bp):
TTATTTTGTATTTAT
Found at i:22323 original size:17 final size:19
Alignment explanation
Indices: 22303--22339 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
22293 ATTAAAAATT
22303 ATTTATTTAA-A-TTAAAA
1 ATTTATTTAATATTTAAAA
22320 ATTTATTTAATATTTAAAA
1 ATTTATTTAATATTTAAAA
22339 A
1 A
22340 AATTTGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTATTTAATATTTAAAA
Found at i:22639 original size:31 final size:29
Alignment explanation
Indices: 22576--22641 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
22566 ATATTAACAA
** *
22576 AAAAATTAATAAAAATATATTTAATTATT
1 AAAAATTAATAAAAATATATTTAAAAAAT
22605 AAAAATTAAATTAAAAATATATTTAAAAAAT
1 AAAAATT-AA-TAAAAATATATTTAAAAAAT
22636 AAAAAT
1 AAAAAT
22642 GTATAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 7 0.22
30 2 0.06
31 23 0.72
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAAATTAATAAAAATATATTTAAAAAAT
Found at i:24357 original size:15 final size:16
Alignment explanation
Indices: 24331--24373 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
24321 GGTACTATTT
24331 TAATTT-TTTTAAATA
1 TAATTTATTTTAAATA
24346 T-ATTTATTTTAAATA
1 TAATTTATTTTAAATA
24361 TAATTTTATTTTA
1 TAA-TTTATTTTA
24374 TACACAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.16
15 11 0.44
16 1 0.04
17 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTATTTTAAATA
Done.