Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold218
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: 193631
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 2 of 2
Found at i:162838 original size:52 final size:52
Alignment explanation
Indices: 162719--162839 Score: 131
Period size: 52 Copynumber: 2.3 Consensus size: 52
162709 CCCCGGTATT
* *
162719 TCTAAAATATTAATTTTTCATAATCGGGAATACTCTAACCCCGATTTTACTT
1 TCTAAAATACTAATTTTTCATAATCGGGAATACTCTAACCCCGATTTTACTC
* * * * * *
162771 TTTAGAACAC-CATTTTTCCATAATCGGGGATACTCTAGCCCCG-TTGTTA-TC
1 TCTAAAATACTAATTTTT-CATAATCGGGAATACTCTAACCCCGATT-TTACTC
162822 TCTAAAATACTAATTTTT
1 TCTAAAATACTAATTTTT
162840 TCTCGTCGAG
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
51 16 0.30
52 38 0.70
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (52 bp):
TCTAAAATACTAATTTTTCATAATCGGGAATACTCTAACCCCGATTTTACTC
Found at i:163009 original size:20 final size:20
Alignment explanation
Indices: 162984--163024 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
162974 ATCAAGTCTC
162984 AACATTTTTATCACGATTAT
1 AACATTTTTATCACGATTAT
163004 AACATTTTTATCACGATTAT
1 AACATTTTTATCACGATTAT
163024 A
1 A
163025 CATCATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (20 bp):
AACATTTTTATCACGATTAT
Found at i:164172 original size:44 final size:43
Alignment explanation
Indices: 164074--164172 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
164064 TACCGTAGAG
* * *
164074 ATTGATCATTTTATAGAGAAAATGGTTCTTCTTTTTTAAATGA
1 ATTGATCATTTTACAAAGAAAATAGTTCTTCTTTTTTAAATGA
* * *
164117 ATTAATCATTTTACAAAGAAATTAGTTCTTTTTTTCTTAAATGA
1 ATTGATCATTTTACAAAGAAAATAGTTCTTCTTTT-TTAAATGA
*
164161 ATTGATTATTTT
1 ATTGATCATTTT
164173 GTGCATTAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 29 0.62
44 18 0.38
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.49
Consensus pattern (43 bp):
ATTGATCATTTTACAAAGAAAATAGTTCTTCTTTTTTAAATGA
Found at i:168718 original size:29 final size:28
Alignment explanation
Indices: 168676--168751 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
168666 TGTACCGAAG
* *
168676 GTACCTATGACAGAGTATCTGTGCCAAAA
1 GTACCTAT-ACAGAGTACCTATGCCAAAA
*
168705 GTACCTATATCAGAGTACCTATGTCAAAA
1 GTACCTATA-CAGAGTACCTATGCCAAAA
**
168734 GTATTTATACCAGAGTAC
1 GTACCTATA-CAGAGTAC
168752 TTGTACCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (28 bp):
GTACCTATACAGAGTACCTATGCCAAAA
Found at i:169065 original size:85 final size:86
Alignment explanation
Indices: 168920--169076 Score: 291
Period size: 85 Copynumber: 1.8 Consensus size: 86
168910 AAAAGAAAAG
168920 AAAATAAATAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAATGAAA-TTTTTTTC
1 AAAATAAATAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAATGAAATTTTTTTTC
168984 TTTTTCTTTTTATGTTTCAAT
66 TTTTTCTTTTTATGTTTCAAT
169005 AAAATAAATAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAAT-AAATTTTTTTTT
1 AAAATAAATAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAATGAAA-TTTTTTTT
169069 CTTTTTCT
65 CTTTTTCT
169077 GTTTCACATA
Statistics
Matches: 70, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
84 3 0.04
85 52 0.74
86 15 0.21
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (86 bp):
AAAATAAATAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAATGAAATTTTTTTTC
TTTTTCTTTTTATGTTTCAAT
Found at i:169111 original size:85 final size:83
Alignment explanation
Indices: 168920--169099 Score: 258
Period size: 85 Copynumber: 2.2 Consensus size: 83
168910 AAAAGAAAAG
* *
168920 AAAATAAATAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAATGAAATTTTTTTCT
1 AAAAGAAAAAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAATGAAA--TTTTTCT
168985 TTTTCTTTTTATGTTTCAAT
64 TTTTCTTTTTATGTTTCAAT
* *
169005 AAAATAAATAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAAT-AAA-TTTT-TTT
1 AAAAGAAAAAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAATGAAATTTTTCTTT
*
169067 TTCTTTTTCTGTTTCACAT
66 TTCTTTTTATGTTTCA-AT
169086 AAAAAGAAAAAAAT
1 -AAAAGAAAAAAAT
169100 GTAGCGATAA
Statistics
Matches: 90, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
80 18 0.20
81 6 0.07
82 11 0.12
84 3 0.03
85 52 0.58
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (83 bp):
AAAAGAAAAAAATAAACTAACAATAATAATAACTTTGAATAAAAACATAAATGAAATTTTTCTTT
TTCTTTTTATGTTTCAAT
Found at i:169220 original size:3 final size:3
Alignment explanation
Indices: 169141--169202 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
169131 TGAATAATTG
*
169141 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AACA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
169188 AAT AAT AAAT AAT AA
1 AAT AAT -AAT AAT AA
169203 ATATACAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 44 0.83
4 5 0.09
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:169564 original size:45 final size:44
Alignment explanation
Indices: 169469--169567 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 44
169459 AACAAAATAT
* * *
169469 TATTTGATATGAGGTATTATTCGTAAGATAATATTCGGTAAGTA
1 TATTTAATACGAGATATTATTCGTAAGATAATATTCGGTAAGTA
*
169513 TCATTTAATACGAGATATTATTCGTGAA-ATAATATTC-GTGAGTTA
1 T-ATTTAATACGAGATATTATTCGT-AAGATAATATTCGGTAAG-TA
169558 CTATTTAATA
1 -TATTTAATA
169568 TAAAAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
44 5 0.11
45 39 0.83
46 3 0.06
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (44 bp):
TATTTAATACGAGATATTATTCGTAAGATAATATTCGGTAAGTA
Found at i:171651 original size:15 final size:15
Alignment explanation
Indices: 171607--171651 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
171597 TTTTAATTTT
* *
171607 TTTTAATTTTTATAA
1 TTTTAAATTTTATTA
171622 TTTTAAATTTT-TTA
1 TTTTAAATTTTATTA
171636 TTTTAAATTTTATTA
1 TTTTAAATTTTATTA
171651 T
1 T
171652 GATGTGACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTAAATTTTATTA
Found at i:173142 original size:2 final size:2
Alignment explanation
Indices: 173135--173169 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
173125 GGACATTCTA
173135 AT AT AT AT 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 AT AT AT AT A
173170 AAAGAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:174230 original size:13 final size:13
Alignment explanation
Indices: 174212--174247 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
174202 CTTTATCTCC
*
174212 TTTTTCACTTTTT
1 TTTTTCAATTTTT
174225 TTTTTCAATTTTT
1 TTTTTCAATTTTT
*
174238 TTTTTTAATT
1 TTTTTCAATT
174248 AGAAGAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTCAATTTTT
Found at i:178839 original size:45 final size:45
Alignment explanation
Indices: 178774--178908 Score: 175
Period size: 45 Copynumber: 3.0 Consensus size: 45
178764 AAAATAATTT
178774 ATTTTTTTA-TTATCTCTTAATTAATTTAATTTAATTAAAAATAA
1 ATTTTTTTATTTATCTCTTAATTAATTTAATTTAATTAAAAATAA
* *
178818 ATTTTTTTATTTATCTCTTAATTAATTTAATTTAATTAGAGATAA
1 ATTTTTTTATTTATCTCTTAATTAATTTAATTTAATTAAAAATAA
* ** * * *
178863 TATCTTTCCATTTATCTTTTGATTAATTTAATTTTATT-AAAATAA
1 -ATTTTTTTATTTATCTCTTAATTAATTTAATTTAATTAAAAATAA
178908 A
1 A
178909 GTTTGATTGG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
44 10 0.13
45 38 0.48
46 31 0.39
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (45 bp):
ATTTTTTTATTTATCTCTTAATTAATTTAATTTAATTAAAAATAA
Found at i:179488 original size:12 final size:12
Alignment explanation
Indices: 179466--179490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
179456 TATTTATTAA
179466 TTATTTTATTTT
1 TTATTTTATTTT
179478 TTATTTTATTTT
1 TTATTTTATTTT
179490 T
1 T
179491 AACTTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:179736 original size:13 final size:13
Alignment explanation
Indices: 179714--179754 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
179704 TTTAATTATT
179714 TTTA-ATATTTTA
1 TTTATATATTTTA
179726 TTTATATATTTTA
1 TTTATATATTTTA
*
179739 TATT-TTTATTTTA
1 T-TTATATATTTTA
179752 TTT
1 TTT
179755 TTAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 6 0.23
13 18 0.69
14 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATATATTTTA
Found at i:179743 original size:20 final size:19
Alignment explanation
Indices: 179709--179757 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
179699 AAATTTTTAA
179709 TTATTTTTA-ATATTTTATT
1 TTATTTTTATAT-TTTTATT
179728 TATATATTTTATATTTTTATT
1 T-TAT-TTTTATATTTTTATT
179749 TTATTTTTA
1 TTATTTTTA
179758 AAATAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.22
20 6 0.22
21 13 0.48
22 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTTTTATATTTTTATT
Found at i:179872 original size:15 final size:16
Alignment explanation
Indices: 179838--179872 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
179828 AAGTTTAAAA
179838 AATTATTTTATTAATT
1 AATTATTTTATTAATT
*
179854 AATTATTTT-TTACTT
1 AATTATTTTATTAATT
179869 AATT
1 AATT
179873 TTTACATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTATTTTATTAATT
Found at i:182256 original size:2 final size:2
Alignment explanation
Indices: 182249--182295 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
182239 AGTAAAAAGT
* *
182249 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TG TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
182290 TA TA TA
1 TA TA TA
182296 AATGGTTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:182707 original size:26 final size:29
Alignment explanation
Indices: 182669--182725 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
182659 AATATTATTG
* *
182669 AATATAATATATTA-ATACTTA-ATATAT
1 AATAAAATATATTATATAATTATATATAT
182696 AATAAAAT-TATTATATAATTATATATAT
1 AATAAAATATATTATATAATTATATATAT
182724 AA
1 AA
182726 ATACTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.19
27 13 0.50
28 8 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
AATAAAATATATTATATAATTATATATAT
Found at i:185607 original size:14 final size:15
Alignment explanation
Indices: 185582--185612 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
185572 AAAAAAAAAC
185582 AACAACAATAATAAT
1 AACAACAATAATAAT
185597 AACAA-AATAATAAT
1 AACAACAATAATAAT
185611 AA
1 AA
185613 TAATAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (15 bp):
AACAACAATAATAAT
Found at i:185613 original size:20 final size:19
Alignment explanation
Indices: 185588--185627 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
185578 AAACAACAAC
185588 AATAATAATAACAAAATAAT
1 AATAATAATAACAAAA-AAT
185608 AATAATAATAACAAAAAAT
1 AATAATAATAACAAAAAAT
185627 A
1 A
185628 TAGAAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (19 bp):
AATAATAATAACAAAAAAT
Found at i:188627 original size:16 final size:17
Alignment explanation
Indices: 188590--188646 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
188580 CATTTCTCAA
*
188590 TTATATAATATATATTAT
1 TTATATAATATTTA-TAT
188608 TT-TATTAATATTTATAT
1 TTATA-TAATATTTATAT
*
188625 TTATATAATATGTA-AT
1 TTATATAATATTTATAT
188641 TTATAT
1 TTATAT
188647 CATAGAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 8 0.23
17 15 0.43
18 12 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTATATAATATTTATAT
Found at i:190137 original size:21 final size:21
Alignment explanation
Indices: 190113--190180 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
190103 TTAGAACATC
190113 ATTTTTATATTAAAATAATAT
1 ATTTTTATATTAAAATAATAT
*
190134 ATTTTTAT-TTAAATTTAAT-T
1 ATTTTTATATTAAA-ATAATAT
* *
190154 ATATATTATATAAAAATAA-AT
1 AT-TTTTATATTAAAATAATAT
190175 -TTTTTA
1 ATTTTTA
190181 ATAGGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 4 0.11
20 9 0.24
21 21 0.55
22 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTATATTAAAATAATAT
Found at i:192092 original size:13 final size:13
Alignment explanation
Indices: 192074--192099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
192064 ACCAGTGATT
192074 ATAAATTCTTTAA
1 ATAAATTCTTTAA
192087 ATAAATTCTTTAA
1 ATAAATTCTTTAA
192100 TTCATAATTG
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAATTCTTTAA
Found at i:192229 original size:2 final size:2
Alignment explanation
Indices: 192222--192247 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
192212 TTTCAATCAC
192222 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
192248 CACCACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:192698 original size:1 final size:1
Alignment explanation
Indices: 192692--192848 Score: 314
Period size: 1 Copynumber: 157.0 Consensus size: 1
192682 AAACACCACA
192692 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
192757 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
192822 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
192849 AAAACAAAAA
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 156 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Done.