Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2106
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: 47175
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:457 original size:27 final size:28
Alignment explanation
Indices: 421--484 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
411 AAAATAATTT
*
421 TATTTAATTAAATATAAT-TTTTATTAAA
1 TATTTAATTAAATATAATATTTAATT-AA
* *
449 TATTT-ATTATATTTAATATTTAATTAA
1 TATTTAATTAAATATAATATTTAATTAA
*
476 TATTAAATT
1 TATTTAATT
485 TATTTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TATTTAATTAAATATAATATTTAATTAA
Found at i:475 original size:11 final size:11
Alignment explanation
Indices: 461--502 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
451 TTTATTATAT
461 TTAATATTTAA
1 TTAATATTTAA
*
472 TTAATATTAAA
1 TTAATATTTAA
*
483 TT--TATTTAT
1 TTAATATTTAA
492 TTAATATTTAA
1 TTAATATTTAA
503 AATTTTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 7 0.28
11 18 0.72
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTAATATTTAA
Found at i:490 original size:20 final size:21
Alignment explanation
Indices: 465--513 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
455 TTATATTTAA
*
465 TATTTAATTAATA-TTAAATT
1 TATTTAATTAATATTTAAAAT
*
485 TATTTATTTAATATTTAAAAT
1 TATTTAATTAATATTTAAAAT
506 T-TTTAATT
1 TATTTAATT
514 GCACTACTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTAATTAATATTTAAAAT
Found at i:2163 original size:3 final size:3
Alignment explanation
Indices: 2155--2184 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2145 GGCTTATTAA
2155 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2185 TAAAGCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:15387 original size:1 final size:1
Alignment explanation
Indices: 15381--15405 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
15371 TTTAGAATAC
15381 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
15406 GGAGCTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25286 original size:18 final size:19
Alignment explanation
Indices: 25254--25289 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
25244 CTTCTTTTGC
25254 AAGCATTTGACTGTTGTAG
1 AAGCATTTGACTGTTGTAG
*
25273 AAGC-TTTGATTGTTGTA
1 AAGCATTTGACTGTTGTA
25290 TGTATTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (19 bp):
AAGCATTTGACTGTTGTAG
Found at i:25699 original size:14 final size:15
Alignment explanation
Indices: 25676--25709 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
25666 ATTTATGTGA
*
25676 TATTTTAATTAT-TT
1 TATTTGAATTATATT
25690 TATTTGAATTATATT
1 TATTTGAATTATATT
25705 TATTT
1 TATTT
25710 AATCTAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTTGAATTATATT
Found at i:27224 original size:10 final size:10
Alignment explanation
Indices: 27205--27235 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
27195 GTATCGATAT
27205 ATAAACAGTG
1 ATAAACAGTG
*
27215 ATAAATAGTG
1 ATAAACAGTG
27225 ATAAACAGTG
1 ATAAACAGTG
27235 A
1 A
27236 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (10 bp):
ATAAACAGTG
Found at i:27989 original size:20 final size:20
Alignment explanation
Indices: 27947--27988 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27937 TGGTGCCATA
*
27947 TTTCTTTTTTCCTTTTCTCT
1 TTTCTTTTTTCCTTTTATCT
*
27967 TTTCTTTTTTTCTTTTAT-T
1 TTTCTTTTTTCCTTTTATCT
27986 TTT
1 TTT
27989 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTCTTTTTTCCTTTTATCT
Found at i:28341 original size:18 final size:18
Alignment explanation
Indices: 28305--28350 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28295 TTATCCTTTC
28305 TTAATAATTA-AAAATAA
1 TTAATAATTATAAAATAA
**
28322 TTAATAATTATATTATAA
1 TTAATAATTATAAAATAA
*
28340 TTTATAATTAT
1 TTAATAATTAT
28351 TTTTATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAATAATTATAAAATAA
Found at i:31810 original size:10 final size:10
Alignment explanation
Indices: 31791--31821 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
31781 GTATCGATAC
31791 ATGAACAGTG
1 ATGAACAGTG
*
31801 ATGAATAGTG
1 ATGAACAGTG
31811 ATGAACAGTG
1 ATGAACAGTG
31821 A
1 A
31822 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:31925 original size:53 final size:53
Alignment explanation
Indices: 31845--31981 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
31835 CTACTACCAA
* * *
31845 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGTTACTGCCAGTGACC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
31898 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
31951 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATA-TTGTGTGTATCGATAC
31982 TATGCAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 63 0.80
54 16 0.20
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:39181 original size:13 final size:14
Alignment explanation
Indices: 39161--39197 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
39151 AAAAAATAAA
39161 AGAAGGGAAGAGGG
1 AGAAGGGAAGAGGG
39175 A-AAGGG-AGAGGG
1 AGAAGGGAAGAGGG
39187 AGAAGGAGAAG
1 AGAAGG-GAAG
39198 GGAAAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 7 0.35
13 9 0.45
14 2 0.10
15 2 0.10
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (14 bp):
AGAAGGGAAGAGGG
Found at i:39223 original size:11 final size:11
Alignment explanation
Indices: 39209--39248 Score: 53
Period size: 11 Copynumber: 3.4 Consensus size: 11
39199 GAAAAAAAGG
39209 AAAGGAAAAAA
1 AAAGGAAAAAA
39220 AAAGGAAAAAA
1 AAAGGAAAAAA
39231 AAGAGAGAAAAAA
1 AA-AG-GAAAAAA
39244 TAAAG
1 -AAAG
39249 TAAGTATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 13 0.50
12 2 0.08
13 9 0.35
14 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (11 bp):
AAAGGAAAAAA
Found at i:39226 original size:25 final size:25
Alignment explanation
Indices: 39198--39248 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
39188 GAAGGAGAAG
*
39198 GGAAAAAAAGGAAAGGAAAAAA-AAA
1 GGAAAAAAAAGAAA-GAAAAAATAAA
*
39223 GGAAAAAAAAGAGAGAAAAAATAAA
1 GGAAAAAAAAGAAAGAAAAAATAAA
39248 G
1 G
39249 TAAGTATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (25 bp):
GGAAAAAAAAGAAAGAAAAAATAAA
Found at i:39311 original size:22 final size:23
Alignment explanation
Indices: 39283--39334 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
39273 TAAAATTAAT
39283 TAAATTAAATAAAT-TTTTAAAAG
1 TAAATTAAA-AAATATTTTAAAAG
*
39306 T-AATT-AAAAATATTTTAAAAT
1 TAAATTAAAAAATATTTTAAAAG
39327 TAAATTAA
1 TAAATTAA
39335 TTGAATCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 8 0.32
23 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAATTAAAAAATATTTTAAAAG
Found at i:39853 original size:23 final size:24
Alignment explanation
Indices: 39827--39875 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
39817 TTGTATTATG
39827 TTTATATTA-TTTTCTATATTG-GT
1 TTTA-ATTACTTTTCTATATTGTGT
*
39850 TTTAATTACTTTTTTATATTGTGT
1 TTTAATTACTTTTCTATATTGTGT
39874 TT
1 TT
39876 GTATTATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.67
Consensus pattern (24 bp):
TTTAATTACTTTTCTATATTGTGT
Found at i:40041 original size:22 final size:24
Alignment explanation
Indices: 40015--40073 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
40005 CGTTCCTATA
40015 TTTATGTCATTTTAATTT-A-TTT
1 TTTATGTCATTTTAATTTAATTTT
* * *
40037 TTTATGTCATATCATTTTAATTTT
1 TTTATGTCATTTTAATTTAATTTT
*
40061 TTTATGTTATTTT
1 TTTATGTCATTTT
40074 TACTCTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 15 0.52
23 1 0.03
24 13 0.45
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (24 bp):
TTTATGTCATTTTAATTTAATTTT
Found at i:40665 original size:4 final size:4
Alignment explanation
Indices: 40656--40689 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
40646 AGTACTCTGT
40656 AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
40690 AAGTTGACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:40727 original size:4 final size:4
Alignment explanation
Indices: 40720--40744 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40710 CCATTCATTC
40720 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
40745 TAAAGCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:41629 original size:25 final size:25
Alignment explanation
Indices: 41537--41629 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 25
41527 TTTTTAATTT
41537 TTAAAAT-TTATATAAATATATAAAA
1 TTAAAATATTATATAAATATAT-AAA
* * *
41562 CTTTAAATATT-TTTATAATACA-AAA
1 -TTAAAATATTATATA-AATATATAAA
* *
41587 ATATAAATATGATATAAATATATAAA
1 TTA-AAATATTATATAAATATATAAA
*
41613 TTAAAATATTATTTAAA
1 TTAAAATATTATATAAA
41630 ACTTCATATA
Statistics
Matches: 51, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
24 1 0.02
25 26 0.51
26 17 0.33
27 7 0.14
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (25 bp):
TTAAAATATTATATAAATATATAAA
Found at i:41731 original size:4 final size:4
Alignment explanation
Indices: 41724--41749 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41714 TAATTATTTT
41724 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
41750 GTAGTTGAAC
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:43094 original size:3 final size:3
Alignment explanation
Indices: 43086--43125 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
43076 ACAGCAGTAG
* *
43086 CAA CAA CAA CAA CAA CAG CAA CAG CAA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA C
43126 GGAATAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.60, C:0.35, G:0.05, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:43712 original size:21 final size:21
Alignment explanation
Indices: 43686--43728 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
43676 ACCTGCCTTA
43686 AGTTCCTCGTCAAGAAGGAGC
1 AGTTCCTCGTCAAGAAGGAGC
43707 AGTTCCTCGTCAAGAAGGAGC
1 AGTTCCTCGTCAAGAAGGAGC
43728 A
1 A
43729 ATTTTTCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (21 bp):
AGTTCCTCGTCAAGAAGGAGC
Done.