Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold593
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: 19165
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Found at i:9324 original size:19 final size:19
Alignment explanation
Indices: 9302--9350 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
9292 ATATAAGTAT
* **
9302 AAAATATTAATTTTTTAAA
1 AAAATATTAAATACTTAAA
9321 AAAAT-TTAAATACTTAAA
1 AAAATATTAAATACTTAAA
9339 AAAA-ATTAAATA
1 AAAATATTAAATA
9351 TATCTATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATATTAAATACTTAAA
Found at i:9337 original size:18 final size:18
Alignment explanation
Indices: 9316--9350 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9306 TATTAATTTT
*
9316 TTAAAAAAATTTAAATAC
1 TTAAAAAAAATTAAATAC
9334 TTAAAAAAAATTAAATA
1 TTAAAAAAAATTAAATA
9351 TATCTATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAAAATTAAATAC
Found at i:11583 original size:16 final size:16
Alignment explanation
Indices: 11558--11588 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11548 TTTTATATTT
*
11558 ATTATTTTAAATTTAA
1 ATTATATTAAATTTAA
11574 ATTATATTAAATTTA
1 ATTATATTAAATTTA
11589 TTTTTTTAAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTATATTAAATTTAA
Found at i:11590 original size:30 final size:30
Alignment explanation
Indices: 11554--11650 Score: 86
Period size: 35 Copynumber: 3.0 Consensus size: 30
11544 TACGTTTTAT
11554 ATTTATTATTTTAAATTTAAATTATATTAA
1 ATTTATTATTTTAAATTTAAATTATATTAA
* *
11584 ATTTATTTTTTTAAAATTTAAAAATTTTTATTTAA
1 ATTTATTATTTT-AAATTT--AAA-TTATA-TTAA
* * * *
11619 ATTTTTTAAATTTAAGTTTAGATTATATTAA
1 ATTTATT-ATTTTAAATTTAAATTATATTAA
11650 A
1 A
11651 GATTAAGTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
30 11 0.21
31 11 0.21
32 4 0.08
33 5 0.09
34 4 0.08
35 15 0.28
36 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
ATTTATTATTTTAAATTTAAATTATATTAA
Found at i:11678 original size:22 final size:23
Alignment explanation
Indices: 11624--11692 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 23
11614 TTTAAATTTT
*
11624 TTAAA-TTTAAGTTTAGATTATA
1 TTAAAGTTTAAGTTTAGATTAAA
*
11646 TTAAAGATTAAG-TTAGATTAAA
1 TTAAAGTTTAAGTTTAGATTAAA
** * *
11668 TTTGAGTTTAAATTTTATATTAAA
1 TTAAAGTTT-AAGTTTAGATTAAA
11692 T
1 T
11693 GTAATTAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 20 0.54
23 7 0.19
24 10 0.27
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (23 bp):
TTAAAGTTTAAGTTTAGATTAAA
Found at i:12357 original size:13 final size:12
Alignment explanation
Indices: 12339--12386 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
12329 TACTTTAAGA
12339 TAAATATCAAATT
1 TAAATAT-AAATT
*
12352 TAAATAT-ATTT
1 TAAATATAAATT
12363 TAAATATAAATAT
1 TAAATATAAAT-T
*
12376 TACATATAAAT
1 TAAATATAAAT
12387 ATTTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 10 0.33
12 2 0.07
13 18 0.60
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATATAAATT
Found at i:15087 original size:16 final size:16
Alignment explanation
Indices: 15063--15166 Score: 79
Period size: 16 Copynumber: 6.4 Consensus size: 16
15053 ACTTAAGAAT
* *
15063 AATTGAATTGAAAATA
1 AATTAAATTTAAAATA
15079 AATTAAATTTAAAATA
1 AATTAAATTTAAAATA
* *
15095 ATTTAAA-ATAAAA-A
1 AATTAAATTTAAAATA
*
15109 ATATTTAAATTTAAAATT
1 A-A-TTAAATTTAAAATA
* *
15127 ATTTAAATTTAATAT-
1 AATTAAATTTAAAATA
*
15142 AATATAAATTTAAAAAA
1 AAT-TAAATTTAAAATA
15159 TAATTAAA
1 -AATTAAA
15167 ATTCAAAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
14 2 0.03
15 7 0.10
16 47 0.68
17 9 0.13
18 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTAAATTTAAAATA
Found at i:15114 original size:26 final size:26
Alignment explanation
Indices: 15068--15117 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
15058 AGAATAATTG
*
15068 AATTGAAAATAAATTAAATTTAAAAT
1 AATTGAAAATAAATAAAATTTAAAAT
*
15094 AATTTAAAATAAA-AAATATTTAAA
1 AATTGAAAATAAATAAA-ATTTAAA
15118 TTTAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
AATTGAAAATAAATAAAATTTAAAAT
Found at i:15144 original size:48 final size:50
Alignment explanation
Indices: 15081--15176 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 50
15071 TGAAAATAAA
* * *
15081 TTAAATTTAAAATAATTTAAA-ATAAAAAAT-ATTTAAATTTAAAATTAT
1 TTAAATTTAAAATAATATAAATATAAAAAATAATTAAAATTCAAAATTAT
* *
15129 TTAAATTTAATATAATATAAATTTAAAAAATAATTAAAATTCAAAATT
1 TTAAATTTAAAATAATATAAATATAAAAAATAATTAAAATTCAAAATT
15177 TAATTTCAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
48 19 0.46
49 8 0.20
50 14 0.34
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (50 bp):
TTAAATTTAAAATAATATAAATATAAAAAATAATTAAAATTCAAAATTAT
Found at i:15150 original size:32 final size:30
Alignment explanation
Indices: 15075--15156 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 30
15065 TTGAATTGAA
15075 AATAAAT-TAAATTTAAAATAATTTAAAAT
1 AATAAATATAAATTTAAAATAATTTAAAAT
* * *
15104 AAAAAATATTTAAATTTAAAATTATTTAAATTT
1 AATAAATA--TAAATTTAAAATAATTTAAA-AT
15137 AATATAATATAAATTTAAAA
1 AATA-AATATAAATTTAAAA
15157 AATAATTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 6 0.14
32 30 0.68
33 4 0.09
34 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AATAAATATAAATTTAAAATAATTTAAAAT
Found at i:15669 original size:2 final size:2
Alignment explanation
Indices: 15664--15690 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15654 ACACACACAC
15664 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 A
15691 AATTTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17729 original size:54 final size:54
Alignment explanation
Indices: 17654--17756 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
17644 ATTCACAAAA
** **
17654 TGCATCCAAGTTCCTAAATCATGGTAAATGACCTAAATGGTATTAAAATTTAAT
1 TGCATCCAAGTTCCTAAATCATGAAAAATGACCTAAATAATATTAAAATTTAAT
* *
17708 TGCATCTAAGTCTCC-AGATCATGAAAAATGACCTAAATAATATTAAAAT
1 TGCATCCAAGT-TCCTAAATCATGAAAAATGACCTAAATAATATTAAAAT
17757 GCATGAAATG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 39 0.93
55 3 0.07
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.31
Consensus pattern (54 bp):
TGCATCCAAGTTCCTAAATCATGAAAAATGACCTAAATAATATTAAAATTTAAT
Found at i:17905 original size:25 final size:25
Alignment explanation
Indices: 17869--17916 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
17859 AAAATCCTAA
*
17869 ATCATGATAAATTACTAAAATGACT
1 ATCATGACAAATTACTAAAATGACT
*
17894 ATCATGACAAATTATTAAAATGA
1 ATCATGACAAATTACTAAAATGA
17917 TCTTAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (25 bp):
ATCATGACAAATTACTAAAATGACT
Done.