Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3756
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: 17355
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Found at i:3320 original size:11 final size:12
Alignment explanation
Indices: 3306--3340 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
3296 AGAAAAAAAA
3306 AAGAGAG-AGGG
1 AAGAGAGAAGGG
3317 AAGAGAGAAGGG
1 AAGAGAGAAGGG
3329 -AGAGAGAAGGG
1 AAGAGAGAAGGG
3340 A
1 A
3341 GGGGAATCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AAGAGAGAAGGG
Found at i:4695 original size:132 final size:131
Alignment explanation
Indices: 4477--5324 Score: 1338
Period size: 132 Copynumber: 6.6 Consensus size: 131
4467 GATCTGTAAT
*
4477 CTTCGATCTACTTCACGCCAAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACC
1 CTTCGATCTACTTCACGCC-AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
* * *
4542 AGTATGGGAAGACAAGATCTGCATCGTCAATCCACTTCCTACCAATATAGGAAGACCA-GATCTG
65 AATATGGGAAGACAAGATCTGCATC-TCGATCCACTTCCTACCAATATAGGAAGA-TAGGATCTG
4606 CTAC
128 CTAC
* * *
4610 CTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
4675 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATC-TCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
4740 AC
130 AC
4742 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
4807 ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTA
66 ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTA
4872 C
131 C
4873 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
4938 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATC-TCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
5003 AC
130 AC
5005 CTTCGATCTA-TTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
* *
5069 ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTA
66 ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTA
*
5134 T
131 C
5135 C-TCGATCTACTTCACG-CAA-ACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
*
5197 ATAT-GGAAGACAAGATCTGCATCTCGAT-CACTT-CTACC-A-ATAGG-AGACAGGA-CTGCTA
66 ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTA
*
5255 T
131 C
*** * * * *
5256 CTTCGAT-TAC--CACG-CAATATGGGAAGACAAGAT-TG-TATCTTTGATCCACTTC-CTACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
*
5314 ATATAGGAAGA
66 ATATGGGAAGA
5325 TAGGACCTAT
Statistics
Matches: 688, Mismatches: 21, Indels: 27
0.93 0.03 0.04
Matches are distributed among these distances:
117 9 0.01
118 20 0.03
119 9 0.01
120 12 0.02
121 11 0.02
122 13 0.02
123 5 0.01
124 1 0.00
125 5 0.01
126 5 0.01
127 24 0.03
128 47 0.07
129 11 0.02
130 46 0.07
131 210 0.31
132 242 0.35
133 18 0.03
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (131 bp):
CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTA
C
Found at i:4965 original size:263 final size:263
Alignment explanation
Indices: 4477--5324 Score: 1358
Period size: 263 Copynumber: 3.3 Consensus size: 263
4467 GATCTGTAAT
*
4477 CTTCGATCTACTTCACGCCAAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACC
1 CTTCGATCTACTTCACGCC-AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
* *
4542 AGTATGGGAAGACAAGATCTGCATCGTCAATCCACTTCCTACCAATATAGGAAGACCA-GATCTG
65 AATATGGGAAGACAAGATCTGCATC-TCGATCCACTTCCTACCAATATAGGAAGA-CAGGATCTG
* * *
4606 CTACCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCAATCTACTTCGCC
128 CTACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
4671 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATC
193 ACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATC
4736 TGCTAC
258 TGCTAC
4742 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
*
4807 ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTA
66 ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTA
4872 CCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
131 CCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
4937 AATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGC
196 AATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGC
5002 TAC
261 TAC
5005 CTTCGATCTA-TTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
*
5069 ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTA
66 ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTA
*
5134 TC-TCGATCTACTTCACG-CAA-ACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
131 CCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
*
5196 AATAT-GGAAGACAAGATCTGCATC-TCGAT-CACTT-CTACC-A-ATAGG-AGACAGGA-CTGC
196 AATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGC
*
5253 TAT
261 TAC
*** * * * *
5256 CTTCGAT-TAC--CACG-CAATATGGGAAGACAAGAT-TG-TATCTTTGATCCACTTC-CTACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
*
5314 ATATAGGAAGA
66 ATATGGGAAGA
5325 TAGGACCTAT
Statistics
Matches: 561, Mismatches: 20, Indels: 24
0.93 0.03 0.04
Matches are distributed among these distances:
245 15 0.03
246 14 0.02
247 2 0.00
248 16 0.03
249 4 0.01
250 2 0.00
251 13 0.02
252 7 0.01
253 5 0.01
254 1 0.00
255 5 0.01
256 5 0.01
257 5 0.01
258 19 0.03
259 47 0.08
260 3 0.01
261 15 0.03
262 119 0.21
263 177 0.32
264 68 0.12
265 19 0.03
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (263 bp):
CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
ATATGGGAAGACAAGATCTGCATCTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTA
CCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
AATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGC
TAC
Found at i:15818 original size:16 final size:15
Alignment explanation
Indices: 15794--15842 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
15784 GCATGAAGTG
15794 CAGAAAAAAAACAAAA
1 CAGAAAAAAAA-AAAA
15810 CAGATAAAAAAAAAAA
1 CAGA-AAAAAAAAAAA
* *
15826 AAAAAAAAAAAAAAA
1 CAGAAAAAAAAAAAA
15841 CA
1 CA
15843 ATTTATCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 12 0.41
16 10 0.34
17 7 0.24
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (15 bp):
CAGAAAAAAAAAAAA
Found at i:15819 original size:1 final size:1
Alignment explanation
Indices: 15815--15840 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
15805 CAAAACAGAT
15815 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
15841 CAATTTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.