Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2422
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: 193378
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 2
Found at i:172463 original size:197 final size:188
Alignment explanation
Indices: 172172--172721 Score: 650
Period size: 197 Copynumber: 2.9 Consensus size: 188
172162 AAAAGGATGT
* * * * * * *
172172 CAATATGCTGATTCACGGTCAGCAACAGTTAGACTTGAAGGTGACAATATGCTGATTCAAGGCCA
1 CAATATGCTAATTCAAGGCCAGCGATA-TTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCA
* * * * *
172237 ACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
65 GCGACATTGGACTTAAAGATAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
* * *
172302 GGTGAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
130 GATAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
172361 CAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCTAAAGGCGCCAATATGCTGATT
1 CAATATGCTAATTCAAGGCCAGCGATATTAGACTTAAA-G-G-T------GCCAATATGCTGATT
* * * *
172426 CAAGGCTAGCGATATTGGACTTAAAGATAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
57 CAAGGCCAGCGACATTGGACTTAAAGATAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTG
* * * * * * *
172491 GACTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGGCTTAAAGGTGAAGGT
122 GGCTTAAAGATAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGT
172556 GC
187 GC
* * * *
172558 CAATATGCTAATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCGG
1 CAATATGCTAATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAG
* * * *
172623 CTACATTGGACTTAAAGATGAAGGTACCAATGTGCTGATTCAAGGCCAACTATATTGGGTTTAAA
66 CGACATTGGACTTAAAGAT-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGGCTT-AA
* *
172688 AGATAAAGGCGCCAATGTGCTGGTTCAAGGCCAG
129 AGAT-AAGGTGCCAATGTGCTGATTCAAGGCCAG
172722 TGATATCAGA
Statistics
Matches: 305, Mismatches: 44, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
188 48 0.16
189 60 0.20
190 6 0.02
191 26 0.09
194 1 0.00
195 1 0.00
196 1 0.00
197 162 0.53
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (188 bp):
CAATATGCTAATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAG
CGACATTGGACTTAAAGATAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGGCTTAAAG
ATAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:172664 original size:92 final size:92
Alignment explanation
Indices: 172404--172680 Score: 367
Period size: 92 Copynumber: 3.0 Consensus size: 92
172394 TTAAAGGTGC
* * * *
172404 TAAAGGCGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGAT-AAAGTGCCAATGTG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTG
*
172468 CTGATTCAAGGCCAGCTACATTGGACT
66 CTGATTCAAGGCCAGCTATATTGGACT
* * *
172495 TAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGGCTTAAAGGTGAAGGTGCCA
1 T----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCA
* *
172560 ATATGCTAATTCAAGGCCAGCTATATTGGACT
61 ATGTGCTGATTCAAGGCCAGCTATATTGGACT
* * * *
172592 TAAAGGTGCCAATGTGCTGATTCAAGGCCGGCTACATTGGACTTAAAGATGAAGGTACCAATGTG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTG
*
172657 CTGATTCAAGGCCAACTATATTGG
66 CTGATTCAAGGCCAGCTATATTGG
172681 GTTTAAAAGA
Statistics
Matches: 160, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
91 1 0.01
92 77 0.48
93 1 0.01
95 1 0.01
96 42 0.26
97 38 0.24
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (92 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTG
CTGATTCAAGGCCAGCTATATTGGACT
Found at i:172814 original size:28 final size:28
Alignment explanation
Indices: 172783--172908 Score: 162
Period size: 28 Copynumber: 4.4 Consensus size: 28
172773 GTTTGCATCA
* *
172783 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTAAAGGTTGCCACTG
*
172811 ACTTGTGGGCTTTTAAAGATTGCCACTG
1 ACTTGTGGGCTTTTAAAGGTTGCCACTG
* *
172839 ACTTATGGGTTTTTAAAGGTTGCCACTG
1 ACTTGTGGGCTTTTAAAGGTTGCCACTG
* * *
172867 ACTTGTGGACTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
172897 ACTTGTGGGCTT
1 ACTTGTGGGCTT
172909 AAAAGGAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
28 61 0.73
30 23 0.27
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (28 bp):
ACTTGTGGGCTTTTAAAGGTTGCCACTG
Found at i:172937 original size:34 final size:35
Alignment explanation
Indices: 172899--172973 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
172889 TGCCACTAAC
* *
172899 TTGTGGGCTTA-AAAGGAAAAAGAGTGCTACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
*
172933 TTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
172968 TTGTGG
1 TTGTGG
172974 ACTTTGGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.21
Consensus pattern (35 bp):
TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
Found at i:173000 original size:29 final size:29
Alignment explanation
Indices: 172949--173122 Score: 192
Period size: 29 Copynumber: 6.0 Consensus size: 29
172939 GCTTACAAAA
* * *
172949 GAAAAAGAGTGCCACGGAGTTGTGGACTTT
1 GAAAAAGA-TGCCACTGACTTGTGGGCTTT
* *
172979 GGAAAAGATGCCA-TCGACTTGTGGGCTTC
1 GAAAAAGATGCCACT-GACTTGTGGGCTTT
* *
173008 GAAAAAGGGTGCCACTGATTTGTGGGCTTT
1 GAAAAA-GATGCCACTGACTTGTGGGCTTT
* * *
173038 G--AAGGTTGCCACTGACTTGTGGACTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
173065 GAAAAAAATGCCACTAACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
173094 GAAAAAGATGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
173123 TGAAGGGTGA
Statistics
Matches: 119, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
27 21 0.18
28 2 0.02
29 69 0.58
30 26 0.22
31 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:173125 original size:86 final size:86
Alignment explanation
Indices: 172958--173128 Score: 238
Period size: 86 Copynumber: 2.0 Consensus size: 86
172948 AGAAAAAGAG
* * * * *
172958 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCATCGACTTGTGGGCTTCGAAAAAGGGTGCCAC
1 TGCCACGGACTTGTGGACTTTGAAAAAAATGCCATCAACTTGTGGGCTTCGAAAAAGGATGCCAC
*
173023 TGATTTGTGGGCTTTGAAGGT
66 TGACTTGTGGGCTTTGAAGGT
* *
173044 TGCCACTGACTTGTGGACTTTGAAAAAAATGCCA-CTAACTTGTGGGCTTTGAAAAA-GATGCCA
1 TGCCACGGACTTGTGGACTTTGAAAAAAATGCCATC-AACTTGTGGGCTTCGAAAAAGGATGCCA
173107 CTGACTTGTGGGCTTTTGAAGG
65 CTGACTTGTGGGC-TTTGAAGG
173129 GTGAGGAATG
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
85 19 0.25
86 56 0.75
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (86 bp):
TGCCACGGACTTGTGGACTTTGAAAAAAATGCCATCAACTTGTGGGCTTCGAAAAAGGATGCCAC
TGACTTGTGGGCTTTGAAGGT
Found at i:174049 original size:21 final size:21
Alignment explanation
Indices: 174023--174062 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
174013 AAATGAGTTA
174023 GTGTTTGGTCATGCTAAATAG
1 GTGTTTGGTCATGCTAAATAG
174044 GTGTTTGGTCATGCTAAAT
1 GTGTTTGGTCATGCTAAAT
174063 GCTTAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.40
Consensus pattern (21 bp):
GTGTTTGGTCATGCTAAATAG
Found at i:174110 original size:10 final size:10
Alignment explanation
Indices: 174097--174122 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
174087 TAAAAAACCA
174097 TTTATAGAGG
1 TTTATAGAGG
174107 TTTATAGAGG
1 TTTATAGAGG
174117 TTTATA
1 TTTATA
174123 AAAATCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (10 bp):
TTTATAGAGG
Found at i:174901 original size:13 final size:13
Alignment explanation
Indices: 174883--174911 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
174873 CAATTCTTCA
174883 TGTATCGATACAT
1 TGTATCGATACAT
174896 TGTATCGATACAT
1 TGTATCGATACAT
174909 TGT
1 TGT
174912 GCCATGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:175711 original size:23 final size:22
Alignment explanation
Indices: 175656--175699 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
175646 CAAAGCTCAT
*
175656 GATATAATTTAGTTTTTGATAA
1 GATATAATTTACTTTTTGATAA
175678 GATATAATTTACTTTTTGATAA
1 GATATAATTTACTTTTTGATAA
175700 ATTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
GATATAATTTACTTTTTGATAA
Found at i:175824 original size:11 final size:11
Alignment explanation
Indices: 175808--175837 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
175798 TTTATAAAAA
175808 ATTATTTAATT
1 ATTATTTAATT
175819 ATTATTTAATT
1 ATTATTTAATT
*
175830 ATTTTTTA
1 ATTATTTA
175838 TTTTTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTATTTAATT
Found at i:175964 original size:16 final size:16
Alignment explanation
Indices: 175952--175988 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
175942 GTTATTTCAG
175952 GTTCAGATCATTTCGA
1 GTTCAGATCATTTCGA
175968 GTTCAGAT--TTCTCGA
1 GTTCAGATCATT-TCGA
175983 GTTCAG
1 GTTCAG
175989 GTTTTTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 10 0.50
16 8 0.40
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (16 bp):
GTTCAGATCATTTCGA
Found at i:180704 original size:2 final size:2
Alignment explanation
Indices: 180692--180722 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
180682 ATTGGAATAC
*
180692 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
180723 TGATTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:181723 original size:15 final size:16
Alignment explanation
Indices: 181698--181734 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
181688 CTATATAAAA
181698 AAAAAACATTAATA-TG
1 AAAAAACATTAA-ACTG
181714 AAAAAA-ATTAAACTG
1 AAAAAACATTAAACTG
181729 AAAAAA
1 AAAAAA
181735 TAAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 13 0.65
16 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.19
Consensus pattern (16 bp):
AAAAAACATTAAACTG
Found at i:182499 original size:16 final size:17
Alignment explanation
Indices: 182478--182515 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
182468 TATATTAATT
182478 ATTTAAAATTAAAAT-A
1 ATTTAAAATTAAAATAA
*
182494 ATTT-AAATTTAAATAA
1 ATTTAAAATTAAAATAA
182510 ATTTAA
1 ATTTAA
182516 CTCAAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 9 0.47
17 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAAATTAAAATAA
Found at i:182507 original size:15 final size:16
Alignment explanation
Indices: 182478--182515 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
182468 TATATTAATT
182478 ATTTAAAATTAAAAT-A
1 ATTT-AAATTAAAATAA
*
182494 ATTTAAATTTAAATAA
1 ATTTAAATTAAAATAA
182510 ATTTAA
1 ATTTAA
182516 CTCAAAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTAAAATAA
Found at i:182554 original size:13 final size:14
Alignment explanation
Indices: 182536--182564 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
182526 TTTCAACTTG
182536 AATTAATTT-AAAT
1 AATTAATTTGAAAT
182549 AATTAATTTGAAAT
1 AATTAATTTGAAAT
182563 AA
1 AA
182565 CACGAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATTAATTTGAAAT
Found at i:182621 original size:22 final size:22
Alignment explanation
Indices: 182580--182621 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
182570 ATTTAAAATA
* *
182580 ATTAAATTTGATAAATTTAAGT
1 ATTAAATTTAATAAACTTAAGT
*
182602 ATTAAATTTAATTAACTTAA
1 ATTAAATTTAATAAACTTAA
182622 AATCAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTAAATTTAATAAACTTAAGT
Done.