Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1986
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, 702
Length: 1171
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Found at i:69 original size:46 final size:46
Alignment explanation
Indices: 2--1155 Score: 1212
Period size: 46 Copynumber: 25.6 Consensus size: 46
1 T
* *
2 CAGATCTTTTCTTCCTGTATTTGGCAGCGGAGGGGATC-AACAATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAA-GATAG
* * * *
48 CAGATCTTGCCTTCCCGTATTTGGCAGCAGAGGGGATCGAAGATAT
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * * * *
94 CAGATCTTGTCTTCCTGAATTTGGCAGCGAAAGGGATTGAAGATAT
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
*
140 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGAATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * * *
186 TAGATCTTGTCTTCCTATATCTGGCAGCGGAGGGGATCGAAGATAT
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * *
232 CAGATCTCT-TCCTCCTGTATTTGGCAACGGAGGGGATCGACGATAG
1 CAGATCT-TGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * *
278 CAGATCTTGTTTTCCTGTATCTGGCAGCGGAGGGGATCGAAGATAT
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * * *
324 CAAATCTTGTCTTCCTG-ATTTTGACAGGGGAGGGGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTA-TTTGGCAGCGGAGGGGATCGAAGATAG
* * * * *
370 CAGATCTTATCTTCCTGTTTTTGGCA-CTGGAAGAGATCGAGGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGC-GGAGGGGATCGAAGATAG
** * * *
416 CAGATCTTGTCTTCCTGTATTTGGTTGTGG-GGAGATTGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* ** *
461 CAGATCTTGTCTTCCTGTATTCGGCAGTAGAGGGGATCAAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * * * *
507 TAGACCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* *
553 CAGATCATGTTTTCCTGTATTTGGCAGC--A---GAT---A-AT--
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * *
588 -AGATCTTGTCTTCCTGTATTTGGTAG-TG-GGGGATTGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* *
631 CAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * * *
677 TAGATCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * *
723 CAGATCATGTTTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * * * *
769 TAGATCTTGTCTTCCTGAATTTGGTAG-TG-GGGGATTGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* *
813 CAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * * * * * * *
859 TAGATCTTATCTTCATGTATTTGGCTGCTGG-TGAGATTGAGGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGC-GGAGGGGATCGAAGATAG
* * *
905 CTGATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
** * * *
951 CAGATCTTGTCTTCCTGTATTTGGTTGTGG-GGAGATTGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* ** *
996 CAGATCTTGTCTTCCTGTATTCGGCAGTAGAGGGGATCAAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * * * *
1042 TAGACCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
* * *
1088 CAGATCATGTTTTCC-G----TGGCAGCGGAGGGGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
*
1129 CCGATCTTGTCTTCCTGTATTTGGCAG
1 CAGATCTTGTCTTCCTGTATTTGGCAG
1156 TGGAAGAGAT
Statistics
Matches: 908, Mismatches: 168, Indels: 64
0.80 0.15 0.06
Matches are distributed among these distances:
34 23 0.03
37 5 0.01
38 1 0.00
40 1 0.00
41 40 0.04
42 1 0.00
44 61 0.07
45 85 0.09
46 687 0.76
47 4 0.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (46 bp):
CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAG
Found at i:922 original size:182 final size:182
Alignment explanation
Indices: 13--1158 Score: 1338
Period size: 183 Copynumber: 6.4 Consensus size: 182
3 AGATCTTTTC
* * * * * *
13 TTCCTGTATTTGGCAGCGGAGGGGATC-AACAATAGCAGATCTTGCCTTCCCGTATTTGGCAGCA
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAA-GATAACAGATCTTGTCTTCCTGTATTTGGTAG-T
* * * * * *
77 GAGGGGATCGAAGATATCAGATCTTGTCTTCCTGAATTTGGCAGC-GAAAGGGATTGAAGATA-T
64 G-GGGGATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCAG-AGGGGATCGAAGATAGT
* * * * *
140 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGG-GAATCGAAGATAGTAGATCTTGTC
127 -AGATCTTATCTTCATGTATTTGGCAGCGGAGGAG-ATCGAAGATAGCAGATCATGTT
* * * * *
197 TTCCTATATCTGGCAGCGGAGGGGATCGAAGATATCAGATCTCT-TCCTCCTGTATTTGGCAACG
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAACAGATCT-TGTCTTCCTGTATTTGG-TA-G
* * * * * *
261 -GAGGGGATCGACGATAGCAGATCTTGTTTTCCTGTATCTGGCAGCGGAGGGGATCGAAGATA-T
63 TG-GGGGATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAGT
* * * * * * * * * *
324 CAAATCTTGTCTTCCTG-ATTTTGACAGGGGAGGGGATCGAAGATAACAGATCTTATC
127 -AGATCTTATCTTCATGTA-TTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTT
* * * * * *
381 TTCCTGTTTTTGGCA-CTGGAAGAGATCGAGGATAGCAGATCTTGTCTTCCTGTATTTGGTTGTG
1 TTCCTGTATTTGGCAGC-GGAGGGGATCGAAGATAACAGATCTTGTCTTCCTGTATTTGGTAGTG
* * * *
445 GGGAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTCGGCAGTAGAGGGGATCAAAGATAGTAG
65 GGG-GATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAGTAG
*
510 ACCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTT
129 ATCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTT
564 TTCCTGTATTTGGCAGC--A---GAT---A-AT---AGATCTTGTCTTCCTGTATTTGGTAGTGG
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAACAGATCTTGTCTTCCTGTATTTGGTAGTGG
617 GGGATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGAT
66 GGGATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGAT
682 CTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTT
131 CTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTT
* *
734 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAATAGATCTTGTCTTCCTGAATTTGGTAGTGG
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAACAGATCTTGTCTTCCTGTATTTGGTAGTGG
799 GGGATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGAT
66 GGGATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGAT
* * * * * * *
864 CTTATCTTCATGTATTTGGCTGCTGG-TGAGATTGAGGATAGCTGATCTTGTC
131 CTTATCTTCATGTATTTGGCAGC-GGAGGAGATCGAAGATAGCAGATCATGTT
* * * *
916 TTCCTGTATTTGGCAGCGAAGGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGTTGTGG
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAACAGATCTTGTCTTCCTGTATTTGGTAGTGG
* * * *
981 GGAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTCGGCAGTAGAGGGGATCAAAGATAGTAGA
66 GG-GATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGA
*
1046 CCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTT
130 TCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTT
* *
1099 TTCC-G----TGGCAGCGGAGGGGATCGAAGATAACCGATCTTGTCTTCCTGTATTTGGCAGTGG
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAACAGATCTTGTCTTCCTGTATTTGGTAGTGG
1159 AAGAGATCGA
Statistics
Matches: 843, Mismatches: 90, Indels: 64
0.85 0.09 0.06
Matches are distributed among these distances:
170 127 0.15
171 30 0.04
172 1 0.00
174 2 0.00
175 3 0.00
178 53 0.06
179 2 0.00
181 1 0.00
182 203 0.24
183 216 0.26
184 198 0.23
185 6 0.01
186 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (182 bp):
TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAACAGATCTTGTCTTCCTGTATTTGGTAGTGG
GGGATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGAT
CTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTT
Found at i:1097 original size:535 final size:538
Alignment explanation
Indices: 49--1102 Score: 1533
Period size: 535 Copynumber: 2.0 Consensus size: 538
39 CAACAATAGC
* *
49 AGATCTTGCCTTCCCGTATTTGGCAGCAGAGGGGATCGAAGATATCAGATCTTGTCTTCCTGAAT
1 AGATCTTGCCTTCCCGTATTTGGCAGCAGAGGGGATCGAAGATAGCAGATATTGTCTTCCTGAAT
* * *
114 TTGGCAGCGAAAGGGATTGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGAATCG
66 TTGGCAGCGAAAGGGATCGAAGATATCAGATCTTATCTTCATGTATTTGGCAGCGGAGGGAATCG
* *
179 AAGATAGTAGATCTTGTCTTCCTATATCTGGCAGCGGAGGGGATCGAAGATATCAGATCTCTTCC
131 AAGATAGCAGATCATGTCTTCCTATATCTGGCAGCGGAGGGGATCGAAGATATCAGATCTCTTCC
* * * * *
244 TCCTGTATTTGGCAACGGAGGGGATCGACGATAGCAGATCTTGTTTTCCTGTATCTGGCAGCGGA
196 TCCTGAATTTGGCAACGGAGGGGATCGAAGATAGCAGATATTGTCTTCCTGTATCTGGCAGCAGA
* * *
309 GGGGATCGAAGATATCAAATCTTGTCTTCCTGATTTTGACAGGGGAGGGGATCGAAGATAACAGA
261 GGGGATCGAAGATATCAAATCTTATCTTCATGATTTTGACAGGGGAGGAGATCGAAGATAACAGA
* *
374 TCTTATCTTCCTGTTTTTGGCACTGGAAGAGATCGAGGATAGCAGATCTTGTCTTCCTGTATTTG
326 TCTTATCTTCCTGTATTTGGCAC-GGAAGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTG
439 GTTGTGGGGAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTCGGCAGTAGAGGGGATCAAAGA
390 GTTGTGGGGAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTCGGCAGTAGAGGGGATCAAAGA
504 TAGTAGACCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTTTTCCT
455 TAGTAGACCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTTTTCCT
569 GTATTTGGCAGCAGATAAT
520 GTATTTGGCAGCAGATAAT
* * * * * *
588 AGATCTTGTCTTCCTGTATTTGGTAG-TG-GGGGATTGAAGATAGCAGATATTGTCTTCCTGTAT
1 AGATCTTGCCTTCCCGTATTTGGCAGCAGAGGGGATCGAAGATAGCAGATATTGTCTTCCTGAAT
*
651 TTGGCAGC-AGAGGGGATCGAAGATAGT-AGATCTTATCTTCATGTATTTGGCAGCGGA-GGAGA
66 TTGGCAGCGA-AAGGGATCGAAGATA-TCAGATCTTATCTTCATGTATTTGGCAGCGGAGGGA-A
* * *
713 TCGAAGATAGCAGATCATGTTTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAAT-AGATCT-
128 TCGAAGATAGCAGATCATGTCTTCCTATATCTGGCAGCGGAGGGGATCGAAGAT-ATCAGATCTC
* * * *
776 TGTCTTCCTGAATTTGG-TA-GTG-GGGGATTGAAGATAGCAGATATTGTCTTCCTGTATTTGGC
192 T-TCCTCCTGAATTTGGCAACG-GAGGGGATCGAAGATAGCAGATATTGTCTTCCTGTATCTGGC
* * * * * * *
838 AGCAGAGGGGATCGAAGATAGT-AGATCTTATCTTCATG-TATTTGGCTGCTGG-TGAGATTGAG
255 AGCAGAGGGGATCGAAGATA-TCAAATCTTATCTTCATGAT-TTTGACAG-GGGAGGAGATCGAA
* * *
900 GATAGCTGATCTTGTCTTCCTGTATTTGGCA-GCGAAGGAGATCGAAGATAGCAGATCTTGTCTT
317 GATAACAGATCTTATCTTCCTGTATTTGGCACG-GAA-GAGATCGAAGATAGCAGATCTTGTCTT
964 CCTGTATTTGGTTGTGGGGAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTCGGCAGTAGAGG
380 CCTGTATTTGGTTGTGGGGAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTCGGCAGTAGAGG
1029 GGATCAAAGATAGTAGACCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATC
445 GGATCAAAGATAGTAGACCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATC
1094 ATGTTTTCC
510 ATGTTTTCC
1103 GTGGCAGCGG
Statistics
Matches: 463, Mismatches: 41, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
533 1 0.00
534 4 0.01
535 272 0.59
536 10 0.02
537 149 0.32
538 4 0.01
539 23 0.05
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (538 bp):
AGATCTTGCCTTCCCGTATTTGGCAGCAGAGGGGATCGAAGATAGCAGATATTGTCTTCCTGAAT
TTGGCAGCGAAAGGGATCGAAGATATCAGATCTTATCTTCATGTATTTGGCAGCGGAGGGAATCG
AAGATAGCAGATCATGTCTTCCTATATCTGGCAGCGGAGGGGATCGAAGATATCAGATCTCTTCC
TCCTGAATTTGGCAACGGAGGGGATCGAAGATAGCAGATATTGTCTTCCTGTATCTGGCAGCAGA
GGGGATCGAAGATATCAAATCTTATCTTCATGATTTTGACAGGGGAGGAGATCGAAGATAACAGA
TCTTATCTTCCTGTATTTGGCACGGAAGAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG
TTGTGGGGAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTCGGCAGTAGAGGGGATCAAAGAT
AGTAGACCTTATCTTCATGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCATGTTTTCCTG
TATTTGGCAGCAGATAAT
Done.