Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2689
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: 31060
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:402 original size:20 final size:19
Alignment explanation
Indices: 365--404 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
355 CGTGACTTAA
* *
365 TGATATATTTTGATATTAT
1 TGATATATGTTGAGATTAT
384 TGATATTATGTTGAGATTAT
1 TGATA-TATGTTGAGATTAT
404 T
1 T
405 TGGAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (19 bp):
TGATATATGTTGAGATTAT
Found at i:882 original size:179 final size:184
Alignment explanation
Indices: 602--949 Score: 477
Period size: 179 Copynumber: 1.9 Consensus size: 184
592 TTTGAAAATG
* * *
602 TGAAAGGGGGTTGCTATGTGCTGATTCCCCCGATGGGGTGCTACAGTGCTGATTCCCCGGTTCAT
1 TGAAAAGGGGTTGCTATGTACTCATTCCCCCGATGGGGTGCTACAGTGCTGATTCCCCGGTTCAT
667 TGGTGGTGCTAAAGTGCGATATCCCACCATTATC-TTTGAAATGAT-GAAAGGGGTTGCTA-TGT
66 TGGTGGTGCTAAAGTGCGATATCCCACCATTATCTTTTGAAATG-TCGAAA-GGGTTGCTATTGT
*
729 GCTGATT-TC-CCGA-G-GGTTGCTAAGTGCGATATCCATTTGTATTATTTTGAAA
129 GCTGATTCCCGCCGAGGCGGTTGCTAAGTGCGATATCCATTTGTATTATTTTGAAA
* *
781 TGAAAAGGGGTTGCTATGTACTCATTCCCCCGA-GGGTTGCTA-AGTGCTCGATTCCCGCGTTTC
1 TGAAAAGGGGTTGCTATGTACTCATTCCCCCGATGGGGTGCTACAGTGCT-GATTCCC-CGGTTC
*
844 ATTTGGTTAGGTGCT-AAGTG-GATATTCCACCA-TATCTTTTGAAATGTCGAAAGGGTTGCTAT
64 A-TTGG-T-GGTGCTAAAGTGCGATATCCCACCATTATCTTTTGAAATGTCGAAAGGGTTGCTAT
*
906 TGTGTTGATTCCCGCCGAGGCGGTTGCTAAGTGCGATATCCATT
126 TGTGCTGATTCCCGCCGAGGCGGTTGCTAAGTGCGATATCCATT
950 GTGATATTGA
Statistics
Matches: 149, Mismatches: 8, Indels: 19
0.85 0.05 0.11
Matches are distributed among these distances:
177 6 0.04
178 15 0.10
179 50 0.34
180 37 0.25
181 7 0.05
182 10 0.07
183 1 0.01
184 23 0.15
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (184 bp):
TGAAAAGGGGTTGCTATGTACTCATTCCCCCGATGGGGTGCTACAGTGCTGATTCCCCGGTTCAT
TGGTGGTGCTAAAGTGCGATATCCCACCATTATCTTTTGAAATGTCGAAAGGGTTGCTATTGTGC
TGATTCCCGCCGAGGCGGTTGCTAAGTGCGATATCCATTTGTATTATTTTGAAA
Found at i:8507 original size:27 final size:27
Alignment explanation
Indices: 8465--8516 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
8455 GAAATGTGAA
*
8465 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
8492 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
8517 GGTTCATTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:8529 original size:103 final size:103
Alignment explanation
Indices: 8389--8610 Score: 374
Period size: 103 Copynumber: 2.2 Consensus size: 103
8379 TGTATATAAA
** * *
8389 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
8453 TTGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
* *
8492 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
8557 TGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
8595 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
8611 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 111 0.99
104 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:8631 original size:71 final size:71
Alignment explanation
Indices: 8530--8681 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 71
8520 TCATTGGTGG
* *
8530 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA-GGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
8594 GAGGGGT
65 GAGGGGT
***
8601 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
8666 AGGGGT
66 AGGGGT
8672 TGCTAAGTGC
1 TGCTAAGTGC
8682 TGATTCCCCG
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 3 0.04
71 72 0.96
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:8682 original size:174 final size:175
Alignment explanation
Indices: 8452--8899 Score: 828
Period size: 175 Copynumber: 2.6 Consensus size: 175
8442 CCACCATATC
*
8452 TTTGAAATGTGAAA-GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCC
1 TTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCC
8516 CGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAA-GGGGTTGCTAT
65 CGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTAT
8580 GTGCTGATTCCCCCGAGGGGTTGCTAAGTGCGATATCCATTGTATA
130 GTGCTGATTCCCCCGAGGGGTTGCTAAGTGCGATATCCATTGTATA
8626 TTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
1 TTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
8691 GGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATG
66 GGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATG
8756 TGCTGATTCCCCCGAGGGGTTGCTAAGTGCGATATCCATTGTATA
131 TGCTGATTCCCCCGAGGGGTTGCTAAGTGCGATATCCATTGTATA
*
8801 TTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGATGATTCCCC
1 TTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
* * *
8866 GATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
66 GGTTCATTGGTGGTGCTAAGTGCGATATCCACCA
8900 ATAACGGTTA
Statistics
Matches: 267, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
173 3 0.01
174 112 0.42
175 152 0.57
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (175 bp):
TTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
GGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATG
TGCTGATTCCCCCGAGGGGTTGCTAAGTGCGATATCCATTGTATA
Found at i:8837 original size:71 final size:72
Alignment explanation
Indices: 8704--8855 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
8694 TCATTGGTGG
* *
8704 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
8769 GAGGGGT
66 GAGGGGT
***
8776 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
8840 GAGGGGT
66 GAGGGGT
8847 TGCTAAGTG
1 TGCTAAGTG
8856 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:13006 original size:49 final size:49
Alignment explanation
Indices: 12951--13077 Score: 211
Period size: 49 Copynumber: 2.6 Consensus size: 49
12941 TTGAATTTTA
* *
12951 AAAACTCTTTTAAATAATAATTTAAATTCTA-TTTAATTATCCTTTATTT
1 AAAACTCTTTTAAATAATAA-TTAAATTCTATTTTAATTATCATTTATCT
*
13000 AAAACTCTTGTAAATAATAATTAAATTCTATTTTAATTATCATTTATCT
1 AAAACTCTTTTAAATAATAATTAAATTCTATTTTAATTATCATTTATCT
13049 AAAACTCTTTTAAATAATAATTAAATTCT
1 AAAACTCTTTTAAATAATAATTAAATTCT
13078 CTTTCCTTAT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 10 0.14
49 63 0.86
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (49 bp):
AAAACTCTTTTAAATAATAATTAAATTCTATTTTAATTATCATTTATCT
Found at i:16208 original size:40 final size:40
Alignment explanation
Indices: 15996--16201 Score: 353
Period size: 40 Copynumber: 5.2 Consensus size: 40
15986 AACCCAAGTA
* *
15996 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
16035 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
16075 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
16115 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
16155 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
16195 CCTTCGG
1 CCTTCGG
16202 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
39 13 0.08
40 145 0.91
41 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:17243 original size:24 final size:24
Alignment explanation
Indices: 17199--17244 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
17189 ACAATTTTAG
* *
17199 AACATCTAAACAGCACTTGTTCAA
1 AACATCTAAACAACACATGTTCAA
17223 AACAT-TAAACAACTACATGTTC
1 AACATCTAAACAAC-ACATGTTC
17245 GGCTATTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (24 bp):
AACATCTAAACAACACATGTTCAA
Found at i:24247 original size:77 final size:78
Alignment explanation
Indices: 24114--24314 Score: 311
Period size: 77 Copynumber: 2.6 Consensus size: 78
24104 AACCCAAGTA
* *
24114 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTC-GGACTTAGCCGGATATAAT
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTAGCACAAATGCCTTCGGGACTTAGCCGGATATAAT
*
24177 CACTAGCACAAATG
65 AACTAGCACAAATG
*
24191 CCTTCGGGACTTAGCCCGGATATA-CA-TAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGCACTAGCACAAATGCCTTCGGGACTTAG-CCGGATATAAT
24254 AACTAGCACAAATG
65 AACTAGCACAAATG
24268 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATGCCTTCGG
24315 ATCTTAGTCC
Statistics
Matches: 114, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
75 15 0.13
76 9 0.08
77 61 0.54
78 9 0.08
79 2 0.02
80 18 0.16
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCCGGATATAGCACTAGCACAAATGCCTTCGGGACTTAGCCGGATATAATA
ACTAGCACAAATG
Found at i:24321 original size:40 final size:40
Alignment explanation
Indices: 24114--24314 Score: 308
Period size: 40 Copynumber: 5.2 Consensus size: 40
24104 AACCCAAGTA
* *
24114 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
24153 CCTTC-GGACTTAG-CCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
24191 CCTTCGGGACTTAGCCCGGATATA--CA-TAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
24228 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
24268 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
24308 CCTTCGG
1 CCTTCGG
24315 ATCTTAGTCC
Statistics
Matches: 151, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
37 35 0.23
38 35 0.23
39 15 0.10
40 66 0.44
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:25737 original size:13 final size:13
Alignment explanation
Indices: 25721--25748 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
25711 TTTATTATTT
25721 TTAACACAAAATA
1 TTAACACAAAATA
25734 TTAACACAAAATA
1 TTAACACAAAATA
25747 TT
1 TT
25749 TATAATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAACACAAAATA
Found at i:29743 original size:46 final size:46
Alignment explanation
Indices: 29687--29859 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
29677 TGGTTGAGCA
*
29687 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACG
* * * * * *
29733 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATCTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-GAA--A-ACG
* * **
29780 TCCGAACTTGTTGAGTTGAGTCCGAGTTCATTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACG
* *
29826 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29860 AGGGCGGTTA
Statistics
Matches: 100, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.60
47 28 0.28
48 2 0.02
50 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACG
Found at i:29843 original size:93 final size:93
Alignment explanation
Indices: 29684--29854 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
29674 GGATGGTTGA
* *
29684 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACGCCCGAACTCGTTGAGT
*
29749 TGAGTTCGAGTTCGTGAGATCTAACTAG
66 TGAGTCCGAGTTCGTGAGATCTAACTAG
* * ** *
29777 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCATTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACGCCCGAACTCGTTGAGT
29842 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29855 ACTTAAGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATCTAACTAG
Done.