Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4794
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: 13440
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Found at i:5365 original size:95 final size:95
Alignment explanation
Indices: 5153--5487 Score: 520
Period size: 95 Copynumber: 3.6 Consensus size: 95
5143 AATTCTAAAT
*
5153 TGTG-ATAAGGCCTAATGGCCGATGTGATG-ATGTGAAAGTGTATATATGTGATAAGGCCTAATG
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
5216 GCCGATGTGATGAAT-TG-AAGTGTATATA
66 GCCGATGTGATGAATGTGAAAGTGTATATA
*
5244 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATGTGAATAGGGCCTAAT
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-ATAAGGCCTAAT
5308 GGCCGATGTGATGAATGTGAAAGTGTATATA
65 GGCCGATGTGATGAATGTGAAAGTGTATATA
5339 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
5404 GCCGATGTGATGAATGTGAAAGTGTATATA
66 GCCGATGTGATGAATGTGAAAGTGTATATA
** * * * * * * *
5434 TGTG-ACGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGATA
1 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATA
5488 GTCCCGAAGG
Statistics
Matches: 226, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
91 4 0.02
92 39 0.17
93 32 0.14
94 43 0.19
95 93 0.41
96 15 0.07
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (95 bp):
TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
GCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:5418 original size:142 final size:140
Alignment explanation
Indices: 5153--5485 Score: 501
Period size: 142 Copynumber: 2.4 Consensus size: 140
5143 AATTCTAAAT
*
5153 TGTGATAAGGCCTAATGGCCGATGTGATGATGTGAAAGTGTATATATGTG-ATAAGGCCTAATGG
1 TGTGATAGGGCCTAATGGCCGATGTGATGATGTGAAAGTGTATATATGTGAATAAGGCCTAATGG
*
5217 CCGATGTGATGAATTGAAGTGTATATATGTGAATAGGGCCTAATGGCCGATGTGATGAATGTG-A
66 CCGATGTGATGAATTGAAGTGTATATATGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
5281 AGTGTATATA
131 AGTGTATATA
*
5291 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATAGGGCCTAAT
1 TGTG-ATAGGGCCTAATGGCCGATGTGATG-ATGTGAAAGTGTATATATGTGAATAAGGCCTAAT
5356 GGCCGATGTGATGAATGTGAAAGTGTATATATGTG-ATAAGGCCTAATGGCCGATGTGATGAATG
64 GGCCGATGTGATGAAT-TG-AAGTGTATATATGTGAATAAGGCCTAATGGCCGATGTGATGAATG
5420 TGAAAGTGTATATA
127 TGAAAGTGTATATA
** * * * * * *
5434 TGTGACGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TGTGATAGGGCCTAATGGCCGATGTGAT-GATGTGAAAGTGTATATATGTGA
5486 TAGTCCCGAA
Statistics
Matches: 177, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
138 4 0.02
139 24 0.14
140 21 0.12
141 27 0.15
142 70 0.40
143 31 0.18
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (140 bp):
TGTGATAGGGCCTAATGGCCGATGTGATGATGTGAAAGTGTATATATGTGAATAAGGCCTAATGG
CCGATGTGATGAATTGAAGTGTATATATGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGTGTATATA
Found at i:5453 original size:47 final size:47
Alignment explanation
Indices: 5153--5488 Score: 509
Period size: 47 Copynumber: 7.2 Consensus size: 47
5143 AATTCTAAAT
*
5153 TGTGATAAGGCCTAATGGCCGATGTGATG-ATGTGAAAGTGTATATA
1 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
5199 TGTGATAAGGCCTAATGGCCGATGTGATGAAT-TG-AAGTGTATATA
1 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
5244 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATA
1 TGTG-ATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
5291 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTG-ATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
5339 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTG-ATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
5387 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
** * * * * * * *
5434 TGTGACGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAA
1 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
5481 TGTGATAG
1 TGTGATAG
5489 TCCCGAAGGG
Statistics
Matches: 272, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
45 15 0.06
46 58 0.21
47 136 0.50
48 63 0.23
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (47 bp):
TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:5664 original size:38 final size:37
Alignment explanation
Indices: 5607--5682 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
5597 CTGAGCTCTA
* *
5607 AAGACCCGATGACTACGTGTGG-GAATTTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-A-TTATGTCCGGGT
*
5645 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
5682 A
1 A
5683 GATTTCGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 12 0.35
38 21 0.62
39 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:7624 original size:41 final size:42
Alignment explanation
Indices: 7562--7641 Score: 144
Period size: 41 Copynumber: 1.9 Consensus size: 42
7552 AGATTGGCTT
7562 AGTGCTCACGGTTGTGAGATT-GCACTAAGTGTGCGGGCATA
1 AGTGCTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGCATA
*
7603 AGTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGC
1 AGTGCTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGC
7642 TTGAAATGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 20 0.54
42 17 0.46
ACGTcount: A:0.20, C:0.16, G:0.36, T:0.28
Consensus pattern (42 bp):
AGTGCTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGCATA
Found at i:7658 original size:29 final size:29
Alignment explanation
Indices: 7623--7695 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
7613 GTTGTGAGAT
* *
7623 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
7652 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
7681 TGGCACT-AGTGTGCG
1 TGGCACTAAGTGTGCG
7696 TGGTTGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 13 0.32
29 27 0.68
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:8072 original size:40 final size:39
Alignment explanation
Indices: 7987--8072 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 39
7977 AATGATATCG
* * * *
7987 GGGCTAAGTCCGAAGGCAATTGAGCTAGTGATTATATCC
1 GGGCTAAGACCGAAGGCAATTGAGCGAGTGACTAAATCC
* * *
8026 GGGCTAAGACCGAAGGCATTTGGTGCGAGTTACTAAATCC
1 GGGCTAAGACCGAAGGCAATT-GAGCGAGTGACTAAATCC
8066 GGGCTAA
1 GGGCTAA
8073 ATTCCGAAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 19 0.49
40 20 0.51
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (39 bp):
GGGCTAAGACCGAAGGCAATTGAGCGAGTGACTAAATCC
Found at i:8121 original size:39 final size:40
Alignment explanation
Indices: 7980--8164 Score: 148
Period size: 39 Copynumber: 4.7 Consensus size: 40
7970 GCATTTGAAT
* *
7980 GATATCGGGGCTAAG-TCCGAAG-GCAATT-GAGCTAGTGA
1 GATATCCGGGCTAAGTTCCGAAGAGC-ATTCGTGCTAGTGA
* * * * *
8018 TTATATCCGGGCTAAG-ACCGAAG-GCATTTGGTGCGAGTTA
1 -GATATCCGGGCTAAGTTCCGAAGAGCA-TTCGTGCTAGTGA
* * *
8058 CTAAATCCGGGCTAAATTCCGAAGAGCATTCGTGCTAGTGA
1 -GATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA
* * * *
8099 GGTATCCGGACTAAGTT-CGAAGAGCATTCGTGCTGGTGT
1 GATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA
* *
8138 TATATCCGGGCTAGGTTCCGAAGAGCA
1 GATATCCGGGCTAAGTTCCGAAGAGCA
8165 ATCATGCTGG
Statistics
Matches: 117, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
38 1 0.01
39 56 0.48
40 41 0.35
41 16 0.14
42 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (40 bp):
GATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA
Found at i:8173 original size:40 final size:40
Alignment explanation
Indices: 8062--8177 Score: 144
Period size: 39 Copynumber: 2.9 Consensus size: 40
8052 GAGTTACTAA
* * *
8062 ATCCGGGCTAAATTCCGAAGAGCATTCGTGCTAGTGAGGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGAGAT
* **
8102 ATCCGGACTAAGTT-CGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGAGAT
* * *
8141 ATCCGGGCTAGGTTCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGA
8178 CATGTATTCG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 33 0.52
40 31 0.48
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGAGAT
Found at i:11564 original size:47 final size:47
Alignment explanation
Indices: 11511--11879 Score: 622
Period size: 47 Copynumber: 8.1 Consensus size: 47
11501 AATTCTAAAT
11511 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
11558 TGTGATAAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAT-AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
11606 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
11653 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
11700 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
11747 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
11794 TGTGA-ATA----TAAT-GCCGATGTGAT-AATGTGAAAGTG--TATA
1 TGTGATA-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
11833 --T-AT--GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
11875 TGTGA
1 TGTGA
11880 CCGTGTGGGT
Statistics
Matches: 308, Mismatches: 0, Indels: 30
0.91 0.00 0.09
Matches are distributed among these distances:
36 1 0.00
37 1 0.00
38 4 0.01
39 15 0.05
40 12 0.04
41 12 0.04
42 15 0.05
43 4 0.01
44 1 0.00
45 1 0.00
46 1 0.00
47 194 0.63
48 47 0.15
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:11909 original size:16 final size:17
Alignment explanation
Indices: 11888--11919 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11878 GACCGTGTGG
11888 GTGATGGA-GTGAAGTA
1 GTGATGGATGTGAAGTA
11904 GTGATGGATGTGAAGT
1 GTGATGGATGTGAAGT
11920 GCATAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28
Consensus pattern (17 bp):
GTGATGGATGTGAAGTA
Found at i:12121 original size:35 final size:37
Alignment explanation
Indices: 12054--12129 Score: 111
Period size: 35 Copynumber: 2.1 Consensus size: 37
12044 CTGAGCTCTA
* *
12054 AAGACCCGATGACTACGTGTGGGAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGGAATTATGTCCGGGT
*
12091 AAGA-CCGATAACTTCGTGT-GGAATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGGAATTATGTCCGGGT
12126 AAGA
1 AAGA
12130 TTTCGTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 19 0.53
36 13 0.36
37 4 0.11
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGGAATTATGTCCGGGT
Done.