Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2190
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: 35512
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:42 original size:27 final size:27
Alignment explanation
Indices: 1--573 Score: 916
Period size: 27 Copynumber: 21.1 Consensus size: 27
1 AGGGTGCCACGGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
* *
28 AGGGTGCCACAGAGTTGTGGACTAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
*
55 AGGGTGCCACGGAATTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
*
82 AGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
109 AGGGTGCCACGGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
136 AGGGTGCCACGGAGTTGTGGACTTTAAA
1 AGGGTGCCACGGAGTTGTGGAC-TTAAA
164 AGGGTGCCACGGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
191 AGGGTGCCACGGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
218 AGGGTGCCACGGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
*
245 AGGGTGCCACGGAGTTGTGGACTAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
272 AGGGTGCCACGGAGTTGTGGACTTTAAA
1 AGGGTGCCACGGAGTTGTGGAC-TTAAA
*
300 AGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
*
327 A-GATGCCACGGAGTT-TGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
* *
352 AGGGTGCCACAGAGTTGTGGACTAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
* *
379 AGGGTACCACGGAGTTGTGGATTTTAAA
1 AGGGTGCCACGGAGTTGTGGA-CTTAAA
*
407 AGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
*
434 AGGGTGCCACGGAGTTGTGGATTTTAAA
1 AGGGTGCCACGGAGTTGTGGA-CTTAAA
*
462 AGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
*
489 AGGGTACCACGGAGTTGTGGACTTTAAA
1 AGGGTGCCACGGAGTTGTGGAC-TTAAA
*
517 AGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAA
* *
544 AGGATGCCACAGAGTTGTGGACTTTAAA
1 AGGGTGCCACGGAGTTGTGGAC-TTAAA
572 AG
1 AG
574 AAAATGCCAC
Statistics
Matches: 506, Mismatches: 32, Indels: 15
0.92 0.06 0.03
Matches are distributed among these distances:
25 11 0.02
26 24 0.05
27 339 0.67
28 132 0.26
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
AGGGTGCCACGGAGTTGTGGACTTAAA
Found at i:188 original size:55 final size:54
Alignment explanation
Indices: 1--573 Score: 952
Period size: 55 Copynumber: 10.5 Consensus size: 54
*
1 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
*
55 AGGGTGCCACGGAATTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
*
109 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAA
*
164 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
* *
218 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
272 AGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
* *
327 A-GATGCCACGGAGTT-TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
* *
379 AGGGTACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
*
434 AGGGTGCCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
*
489 AGGGTACCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
1 AGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
* *
544 AGGATGCCACAGAGTTGTGGACTTTAAAAG
1 AGGGTGCCACGGAGTTGTGGAC-TTAAAAG
574 AAAATGCCAC
Statistics
Matches: 494, Mismatches: 19, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
52 32 0.06
53 17 0.03
54 196 0.40
55 249 0.50
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (54 bp):
AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
Found at i:1641 original size:13 final size:13
Alignment explanation
Indices: 1623--1648 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1613 AGGGTGAAAA
1623 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
1636 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
1649 TAGGATTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
GGTTTTTTTTTTT
Found at i:7788 original size:22 final size:23
Alignment explanation
Indices: 7740--7789 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
7730 AATATTTTTT
* *
7740 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAACAAATAAACATA
7763 ATTTTTTAAAA-AAA-AAACATA
1 ATTTTTTAAAACAAATAAACATA
*
7784 AATTTT
1 ATTTTT
7790 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 11 0.46
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTTTTTAAAACAAATAAACATA
Found at i:8338 original size:14 final size:14
Alignment explanation
Indices: 8321--8357 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
8311 TCCTTTCATA
*
8321 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTCT
8335 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
*
8349 TTCTTTCTT
1 TTTTTTCTT
8358 CTTCATCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:16945 original size:3 final size:3
Alignment explanation
Indices: 16937--16969 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
16927 TTTGATGCCA
16937 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
16970 CTTTTTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:21893 original size:18 final size:19
Alignment explanation
Indices: 21870--21912 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
21860 ATCAGTTTGA
*
21870 GTTAAAATAAT-TTTAAAT
1 GTTAAAAAAATGTTTAAAT
*
21888 GTTAAAAAAATGTTTTAAT
1 GTTAAAAAAATGTTTAAAT
21907 GTTAAA
1 GTTAAA
21913 TAAGTAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (19 bp):
GTTAAAAAAATGTTTAAAT
Found at i:27738 original size:21 final size:21
Alignment explanation
Indices: 27714--27760 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
27704 TTTCATTTAA
*
27714 TAAAAATAAATTTTTATAAAT
1 TAAAAATAAATTTATATAAAT
* *
27735 TAAAAATTAATTTATATATAT
1 TAAAAATAAATTTATATAAAT
27756 TAAAA
1 TAAAA
27761 TATTAACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAAATAAATTTATATAAAT
Found at i:27750 original size:19 final size:22
Alignment explanation
Indices: 27714--27766 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
27704 TTTCATTTAA
* * *
27714 TAAAA-ATAAATTTTTATAAAT
1 TAAAATATTAATTTATATATAT
27735 TAAAA-ATTAATTTATATATAT
1 TAAAATATTAATTTATATATAT
27756 TAAAATATTAA
1 TAAAATATTAA
27767 CTATGTGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAATATTAATTTATATATAT
Found at i:29000 original size:15 final size:15
Alignment explanation
Indices: 28967--29010 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
28957 TTCAATTAAA
*
28967 AAAATTTT-AAATAT
1 AAAATTTTAAAATTT
*
28981 CAAATTTTAAAATTT
1 AAAATTTTAAAATTT
28996 AAAATTATTAAAATT
1 AAAATT-TTAAAATT
29011 ATTTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 7 0.28
15 10 0.40
16 8 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTTTAAAATTT
Found at i:29074 original size:84 final size:80
Alignment explanation
Indices: 28960--29150 Score: 206
Period size: 84 Copynumber: 2.4 Consensus size: 80
28950 TTATAGTTTC
** * * *
28960 AATTAAAAAAATTTTAAATATCAAATTTTAAAATTTAAAATTATTAAAATTATTTTTTAAAGAT-
1 AATTAAAAAAAAATTAAATATTAAAATTTAAAATTTAAAATTATTAAAATCATTTTTTAAAG-TG
*
29024 AAGAGCATAATTAATTGA
65 AAGA-CATAATCAATT-A
* * * * *
29042 AATTCTAAAAAAAAATTAAATGTTAAAATTTAAACTTTAAATTTATTAGACTCATTTTTTAAAGT
1 AA-T-TAAAAAAAAATTAAATATTAAAATTTAAAATTTAAAATTATTAAAATCATTTTTTAAAGT
**
29107 GATTACATAATCAATTA
64 GAAGACATAATCAATTA
29124 AATT-AAAAAAAATTAAATATTAAAATT
1 AATTAAAAAAAAATTAAATATTAAAATT
29151 CAATCTCGAA
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
79 22 0.24
80 1 0.01
81 1 0.01
82 5 0.05
83 12 0.13
84 51 0.55
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (80 bp):
AATTAAAAAAAAATTAAATATTAAAATTTAAAATTTAAAATTATTAAAATCATTTTTTAAAGTGA
AGACATAATCAATTA
Found at i:31144 original size:17 final size:17
Alignment explanation
Indices: 31110--31147 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
31100 AATTTTAAAA
**
31110 TTTAATATAAATTTAAT
1 TTTAATATAAATCGAAT
31127 TTTAATATAAATCGAAT
1 TTTAATATAAATCGAAT
31144 TTTA
1 TTTA
31148 CAAAAGCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAATATAAATCGAAT
Found at i:32405 original size:6 final size:6
Alignment explanation
Indices: 32394--32435 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
32384 GTGTATTTGA
* * *
32394 AAATTT AAATTT AAATTT AAATTT AGATTT AGATTT GAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
32436 CAAAATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:32762 original size:21 final size:21
Alignment explanation
Indices: 32738--32779 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32728 TAAAAAAGAG
* *
32738 TTAAAAATTAAATTTTAAAAT
1 TTAAAAATTAAACTTGAAAAT
*
32759 TTAAAATTTAAACTTGAAAAT
1 TTAAAAATTAAACTTGAAAAT
32780 GATGTGATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAAAAATTAAACTTGAAAAT
Found at i:33716 original size:16 final size:16
Alignment explanation
Indices: 33697--33743 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
33687 AAATTATTTT
33697 AATTATTATTAAATTA
1 AATTATTATTAAATTA
*
33713 AATTATAATTAAATTA
1 AATTATTATTAAATTA
* *
33729 TATTCTTATTTAAAT
1 AATTATTA-TTAAAT
33744 AGACACGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:34075 original size:27 final size:28
Alignment explanation
Indices: 34045--34115 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
34035 AATAATTTAT
***
34045 AAAATATTATATTTATGTCAAATAATAA
1 AAAATATTATATTTATAAAAAATAATAA
* *
34073 AAAATAATTAT-TATATAAAAAAT-ATTA
1 AAAAT-ATTATATTTATAAAAAATAATAA
34100 AAAA-ATTATATTTATA
1 AAAATATTATATTTATA
34116 TAATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 5 0.14
26 5 0.14
27 7 0.20
28 13 0.37
29 5 0.14
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (28 bp):
AAAATATTATATTTATAAAAAATAATAA
Found at i:34095 original size:28 final size:28
Alignment explanation
Indices: 34064--34118 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
34054 TATTTATGTC
34064 AAATAATAAAAAATAAT-TATTATATAAA
1 AAATAATAAAAAATAATAT-TTATATAAA
* *
34092 AAATATTAAAAAATTATATTTATATAA
1 AAATAATAAAAAATAATATTTATATAA
34119 TTTTATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AAATAATAAAAAATAATATTTATATAAA
Done.