Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_912 ID=scaffold_912-JGI_221_v2.0
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: 2682
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.28
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:68 original size:46 final size:46
Alignment explanation
Indices: 1--833 Score: 938
Period size: 46 Copynumber: 18.2 Consensus size: 46
* *
1 GATCTTGTCTTCCTGTATTTGGCAGTAGAAGGGATCGAAGATATCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
*
47 GATCTTGTCTTCTTGTATTTGGCAGCAG-AGGTGATCGAAGATAGCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGG-GATCGAAGATAGCA
* * *
93 AATCTTGTCTTCC-GGATTTGGCAGCAG-AGGAGATCGAGGATAGCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGG-GATCGAAGATAGCA
* * * *
138 TATCTTGTCTTCCTGTATTTGCCATCTAG--GGGATCGAAGATATCA
1 GATCTTGTCTTCCTGTATTTGGCAGC-AGAAGGGATCGAAGATAGCA
* * ** *
183 GATCTTGCCTTCCTGAATTTTACAGC-GAAAGGGAT-GCAAGATATCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAG-AAGGGATCG-AAGATAGCA
*
229 GATCTTGTCTTCTTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
* * * * *
275 GATCTTGTCTTCCTGTATTTGG-AGCGGAGGGGATCGAGGATATCG
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
* * **
320 GATCTTGTCTTCCTGTATTTGG-AGCGGAGGGGATCGAAGATAGTG
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
* * * * *
365 GATCTTATCTTCATATATTTGGCAGC-GGAGGAGATCGAGGATAGCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGG-GATCGAAGATAGCA
* *
411 GATCTTGTCTTCCTATATTTGGCAAC-GAATGGGATCGAAGATAGCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAA-GGGATCGAAGATAGCA
* * * *
457 GATCTTGTGTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATATCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
* ** * *
503 GATCTTTTCTTCCTGTATTTGGCAGCAGGGGGGATCGACGATAACA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
* * * *
549 GATCTTGTCTTCCTGTATTTGGCAGCAAAAGGGATTGAGGATATCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
* * *
595 GATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCAAAGATAGCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
* * * * *
641 GATCTTATCTTCCTGTATCTGGCAGCGGAGGGGATCGAAGATATCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
* * * * *
687 AATCTTGTCTTCTTGTATTTGGCAGCGGAGGGGATCGAAGATAACA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
733 GATCTTGTCTTCCTGTATTTGGCAGCAG-AGGTGATCGAAGATAGCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGG-GATCGAAGATAGCA
* * *
779 GATCTTATCTTCCAG-ATTTGGCAGCAG-AGGAGATCGAGGATAGCA
1 GATCTTGTCTTCCTGTATTTGGCAGCAGAAGG-GATCGAAGATAGCA
824 GATCTTGTCT
1 GATCTTGTCT
834 NNNNNNNNNN
Statistics
Matches: 681, Mismatches: 92, Indels: 29
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.00
45 198 0.29
46 474 0.70
47 8 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (46 bp):
GATCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATAGCA
Found at i:526 original size:138 final size:138
Alignment explanation
Indices: 1--833 Score: 1054
Period size: 138 Copynumber: 6.1 Consensus size: 138
* *
1 GATCTTGTCTTCCTGTATTTGGCAGTAGAA-GGGATCGAAGATATCAGATCTTGTCTTCTTGTAT
1 GATCTTGTCTTCCTGTATTTGGCAG-CGAAGGGGATCGAAGATATCAGATCTTGTCTTCCTGTAT
* * * * * *
65 TTGGCAGCAGAGGTGATCGAAGATAGCAAATCTTGTCTTCC-GGATTTGGCAGCAGAGGAGATCG
65 TTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCG
129 AGGATAGCA
130 AGGATAGCA
* * * * * *
138 TATCTTGTCTTCCTGTATTTGCCATC-TAGGGGATCGAAGATATCAGATCTTGCCTTCCTGAATT
1 GATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATATCAGATCTTGTCTTCCTGTATT
** * * * * * *
202 TTACAGCGAAAGGGAT-GCAAGATATCAGATCTTGTCTTCTTGTATTTGGCAGCAGAAGG-GATC
66 TGGCAGCGGAGGGGATCG-AAGATAGCAGATCTTATCTTCCTGTATTTGGCAGC-GGAGGAGATC
*
265 GAAGATAGCA
129 GAGGATAGCA
* * *
275 GATCTTGTCTTCCTGTATTTGG-AGCGGAGGGGATCGAGGATATCGGATCTTGTCTTCCTGTATT
1 GATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATATCAGATCTTGTCTTCCTGTATT
** * *
339 TGG-AGCGGAGGGGATCGAAGATAGTGGATCTTATCTTCATATATTTGGCAGCGGAGGAGATCGA
66 TGGCAGCGGAGGGGATCGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGA
403 GGATAGCA
131 GGATAGCA
* * * * *
411 GATCTTGTCTTCCTATATTTGGCAACGAATGGGATCGAAGATAGCAGATCTTGTGTTCCTGTATT
1 GATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATATCAGATCTTGTCTTCCTGTATT
* * *
476 TGGCAGCGGAGGGGATCGAAGATATCAGATCTTTTCTTCCTGTATTTGGCAGCAGG-GGGGATCG
66 TGGCAGCGGAGGGGATCGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGC-GGAGGAGATCG
* *
540 ACGATAACA
130 AGGATAGCA
* * * *
549 GATCTTGTCTTCCTGTATTTGGCAGCAAAAGGGATTGAGGATATCAGATCTTGTCTTCCTGTATT
1 GATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATATCAGATCTTGTCTTCCTGTATT
* * *
614 TGGCAGCGGAGGGGATCAAAGATAGCAGATCTTATCTTCCTGTATCTGGCAGCGGAGGGGATCGA
66 TGGCAGCGGAGGGGATCGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGA
* *
679 AGATATCA
131 GGATAGCA
* * * *
687 AATCTTGTCTTCTTGTATTTGGCAGCGGAGGGGATCGAAGATAACAGATCTTGTCTTCCTGTATT
1 GATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATATCAGATCTTGTCTTCCTGTATT
* * * *
752 TGGCAGCAGAGGTGATCGAAGATAGCAGATCTTATCTTCCAG-ATTTGGCAGCAGAGGAGATCGA
66 TGGCAGCGGAGGGGATCGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGA
816 GGATAGCA
131 GGATAGCA
824 GATCTTGTCT
1 GATCTTGTCT
834 NNNNNNNNNN
Statistics
Matches: 595, Mismatches: 90, Indels: 22
0.84 0.13 0.03
Matches are distributed among these distances:
135 6 0.01
136 136 0.23
137 175 0.29
138 276 0.46
139 2 0.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (138 bp):
GATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATATCAGATCTTGTCTTCCTGTATT
TGGCAGCGGAGGGGATCGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGA
GGATAGCA
Found at i:1028 original size:46 final size:46
Alignment explanation
Indices: 936--2172 Score: 1351
Period size: 46 Copynumber: 27.0 Consensus size: 46
926 NNNNNNNNAG
* * *
936 GATAGCAGATCTTGTCTTCCTGTATTTGCCATC-TAGGGGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* * * * *
981 GATATCAGATCTTGTCTTCCTGAATTTTGCAGCGAAAGGGATGGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* * * *
1027 GACAGTAGATCTTCTCTTCCTGTATTTGGCAG-TAGAGGGGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAA
* * * * * * *
1073 GATAGTAGATCTTATCTTCATATATTTGGCAGCGGAGGAGATCGAG
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* *
1119 GATAGCAGATCTTGTCTTCCTGTATTTGGCAACGGAGGGGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* *
1165 GATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGAA-GGGATCGAG
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGATCGAA
* * * * * *
1211 GATATCGGATCTTGTCTTCCTGTATTTGGTAGTG-GGGGGATTGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* * *
1256 GACAGTAGATCTTCTCTTCCTGTATTTGGCAGC-AGAGGGGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAA
* * * * * * *
1302 GATAGTAGATCTTATCTTCATATATTTGGCAGCGGAGGAGATCGAG
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* *
1348 GATAGCAGATCTTGTCTTCCTATATTTGGCAGCGAATGGGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* *
1394 GATAGCAGATCTTGTCTTCCTGTTTTTGGCAGC-AGAGGGGATCGAG
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAA
** * *
1440 GATAGCAGATCTTACCTTCTTGTATTTGGCAGCGGAGGGGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* * * *
1486 GATATCAGATCTTGTCTTCCTGTATTTGGCAACGAAAGGGATTGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* *
1532 GATATCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
*
1578 GATAGTCGAGATCTTGTCTTCCGTGTATTTGGCAGCGAGAGGCAGA--GAA
1 GATAG-C-AGATCTTGTCTTCC-TGTATTTGGCAGCGA-AGG-GGATCGAA
* * * *
1627 GAGAGCAAATCTTATCTGCCTGTATTT-GCAGCG-A-GGGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* * * **
1670 GATAGCAGATCTTGTGTTCCTGTATTTGG-AGCGGACGCAATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* *
1715 GATAGCAGATCTCGTCTTCCTGTATTTGGCAGC-AGAGGGGATTGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAA
* * * **
1761 GATAGCAAATCTTGTCTTCCTGTATTTGGCAGCGTAGGGAAAAGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* * * *
1807 GAGAGCAAATCTTGTCTGCCTGTATTTGGCAGC-AGAGGGGATCGGA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAA
* * * *
1853 GATAGCAGATCTTGTGTTCCTGTATTTGG-AGCGGACGCGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
*
1898 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-AGAGGGGATCAAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAA
* *
1944 GATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* * *
1990 GATAGCAGATCATGTTTTCCTGTATTTGGCAGCGGAGGGGATCGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
* * *
2036 GATAGCAGATCTTGTCTTCCTGTATTTGGTAGTG--GGGGAGTTGGAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA--TCGAA
* *
2082 GATAGCAGATCTTGTCTTCCTGTATTTGGCAG-TAGAGGGGATCAAA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAA
* * * * * *
2128 GATAGTAGATCTTATCTTCATGAATTTGGCAGCGGAGGAGATCGA
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGA
2173 GGATNNNNNN
Statistics
Matches: 998, Mismatches: 160, Indels: 67
0.81 0.13 0.05
Matches are distributed among these distances:
41 2 0.00
42 1 0.00
43 30 0.03
44 7 0.01
45 143 0.14
46 754 0.76
47 15 0.02
48 20 0.02
49 21 0.02
50 3 0.00
51 2 0.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (46 bp):
GATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAA
Found at i:1434 original size:275 final size:274
Alignment explanation
Indices: 936--2172 Score: 1497
Period size: 275 Copynumber: 4.5 Consensus size: 274
926 NNNNNNNNAG
* * *
936 GATAGCAGATCTTGTCTTCCTGTATTTGCCA-TCTAGGGGATCGAAGATA-TCAGATCTTGTCTT
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGT-GAGGGGATTGAAGATAGT-AGATCTTGTCTT
* * * * * * * **
999 CCTGAATTTTGCAGC-GAAAGGGATGGAAGACAGTAGATCTTCTCTTCCTGTATTTGGCAGTAGA
64 CCTGTATTTGGCAGCAG-AGGGGATCGAAGATAGTAGATCTTATCTTCATGTATTTGGCAGCGGA
* * * * *
1063 GGGGATCGAAGATAGTAGATCTTATCTTCATATATTTGGCAGCGGAGGAGATCGAGGATAGCAGA
128 GGAGATCGAAGATAGCAGATCTTATCTTCCTATATTTGGCAGCGAAGG-GATCGAAGATAGCAGA
* *
1128 TCTTGTCTTCCTGTATTTGGCAACGGAGGGGATCGAAGATATCAGATCTTGTCTTCCTGTATTTG
192 TCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTG
* *
1193 GCAGCGGAAGGGATCGAG
257 GCAGCGGAGGGGATCGAA
* * * * * *
1211 GATATCGGATCTTGTCTTCCTGTATTTGGTAGTGGGGGGATTGAAGACAGTAGATCTTCTCTTCC
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGAGGGGATTGAAGATAGTAGATCTTGTCTTCC
*
1276 TGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGATCTTATCTTCATATATTTGGCAGCGGAGGA
66 TGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGATCTTATCTTCATGTATTTGGCAGCGGAGGA
* *
1341 GATCGAGGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGAATGGGATCGAAGATAGCAGATCT
131 GATCGAAGATAGCAGATCTTATCTTCCTATATTTGGCAGCGAA-GGGATCGAAGATAGCAGATCT
* * * ** *
1406 TGTCTTCCTGTTTTTGGCAGCAGAGGGGATCGAGGATAGCAGATCTTACCTTCTTGTATTTGGCA
195 TGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCA
1471 GCGGAGGGGATCGAA
260 GCGGAGGGGATCGAA
* ** *
1486 GATATCAGATCTTGTCTTCCTGTATTTGGCAACGAAAGGGATTGAAGATA-TCAGATCTTGTCTT
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGTG-AGGGGATTGAAGATAGT-AGATCTTGTCTT
* * *
1550 CCTGTATTTGGCAGCGGAGGGGATCGAAGATAGTCGAGATCTTGTCTTCCGTGTATTTGGCAGCG
64 CCTGTATTTGGCAGCAGAGGGGATCGAAGATAGT--AGATCTTATCTT-CATGTATTTGGCAGCG
* * * *
1615 AGAGGCAGA--GAAGAGAGCAAATCTTATCTGCCTGTATTT-GCAGCG-AGGGATCGAAGATAGC
126 -GAGG-AGATCGAAGATAGCAGATCTTATCTTCCTATATTTGGCAGCGAAGGGATCGAAGATAGC
* * ** *
1676 AGATCTTGTGTTCCTGTATTTGG-AGCGGACGCAATCGAAGATAGCAGATCTCGTCTTCCTGTAT
189 AGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTAT
* *
1740 TTGGCAGCAGAGGGGATTGAA
254 TTGGCAGCGGAGGGGATCGAA
* * * ** * * * *
1761 GATAGCAAATCTTGTCTTCCTGTATTTGGCAGCGTAGGGAAAAGAAGAGAGCAAATCTTGTCTGC
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGTG-AGGGGATTGAAGATAGTAGATCTTGTCTTC
* * * * * *
1826 CTGTATTTGGCAGCAGAGGGGATCGGAGATAGCAGATCTTGTGTTCCTGTATTTGG-AGCGGACG
65 CTGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGATCTTATCTTCATGTATTTGGCAGCGGAGG
* * * * * *
1890 CGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGGGATCAAAGATATCAGATC
130 AGATCGAAGATAGCAGATCTTATCTTCCTATATTTGGCAGC-GAAGGGATCGAAGATAGCAGATC
* * * *
1955 TTGTCTTCCTGTATTTGGCAGCGAAGGAGATCGAAGATAGCAGATCATGTTTTCCTGTATTTGGC
194 TTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGC
2020 AGCGGAGGGGATCGAA
259 AGCGGAGGGGATCGAA
* *
2036 GATAGCAGATCTTGTCTTCCTGTATTTGGTAGTG-GGGGAGTTGGAAGATAGCAGATCTTGTCTT
1 GATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGAGGGGA-TT-GAAGATAGTAGATCTTGTCTT
* * *
2100 CCTGTATTTGGCAGTAGAGGGGATCAAAGATAGTAGATCTTATCTTCATGAATTTGGCAGCGGAG
64 CCTGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGATCTTATCTTCATGTATTTGGCAGCGGAG
2165 GAGATCGA
129 GAGATCGA
2173 GGATNNNNNN
Statistics
Matches: 819, Mismatches: 122, Indels: 41
0.83 0.12 0.04
Matches are distributed among these distances:
269 2 0.00
270 3 0.00
271 30 0.04
272 15 0.02
273 16 0.02
274 35 0.04
275 545 0.67
276 110 0.13
277 1 0.00
278 17 0.02
279 38 0.05
280 4 0.00
281 3 0.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (274 bp):
GATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGAGGGGATTGAAGATAGTAGATCTTGTCTTCC
TGTATTTGGCAGCAGAGGGGATCGAAGATAGTAGATCTTATCTTCATGTATTTGGCAGCGGAGGA
GATCGAAGATAGCAGATCTTATCTTCCTATATTTGGCAGCGAAGGGATCGAAGATAGCAGATCTT
GTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
CGGAGGGGATCGAA
Found at i:2351 original size:46 final size:46
Alignment explanation
Indices: 2277--2682 Score: 497
Period size: 46 Copynumber: 9.0 Consensus size: 46
2267 NNNNNNNNNN
* *
2277 TTCCTGTATTTGGCAGCGGAAGGGATCGACGATAGCAGATCTTGTC
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
* * *
2323 TTCCTGGATTTGGCAGCGGAGGGAATCGAAGATAGTAGATCTTGTC
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
* * *
2369 TTCCTGTATCTGGCAGCGGAGGGGATCGAAGATATCAAATCTTGTC
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
* * *
2415 TTCCAGTA----GCAGCGGAGGGGATCGAAGATATCAAATCTTGTC
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
* *
2457 TTCCTGTA----GCAGCGGAGGGGATCGCAGGTAGCAGATCTTGTC
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
* * ** * *
2499 TTCCTGTATTTTGCAGCGGAAGACATCGAAGATAACAGTTCTTGTC
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
* * *
2545 TTCCTGTATTTGGCAGCAGAAGGGATCGAAGATATCAGATCTTGTC
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
* *
2591 TTCTTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTT
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
* * * *
2637 TTCCTG-ATTTGGCAGCAGAGGAGATCGAAGATAGTAGATATTGTC
1 TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
2682 T
1 T
Statistics
Matches: 315, Mismatches: 41, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
42 79 0.25
45 35 0.11
46 201 0.64
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (46 bp):
TTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTC
Found at i:2491 original size:176 final size:177
Alignment explanation
Indices: 2289--2642 Score: 489
Period size: 176 Copynumber: 2.0 Consensus size: 177
2279 CCTGTATTTG
*
2289 GCAGCGGAAGGGATCGACGATAGCAGATCTTGTCTTCCTGGATTTGGCAGCGGAGGGA-ATCGAA
1 GCAGCGGAAGGGATCGACGATAGCAGATCTTGTCTTCCTGGATTTGGCAGCGGA-AGACATCGAA
** * *
2353 GATAGTAGATCTTGTCTTCCTGTATCTGGCAGCGGAGGGGATCGAAGATATCAAATCTTGTCTTC
65 GATAACAGATCTTGTCTTCCTGTATCTGGCAGCAGAAGGGATCGAAGATATCAAATCTTGTCTTC
*
2418 CAGTA-GCAGCGGAGGGGATCGAAGATATCAAATCTTGTCTTCCTGTA
130 CAGTATGCAGCGGAGGGGATCGAAGATAGCAAATCTTGTCTTCCTGTA
* * * *
2465 GCAGCGGAGGGGATCG-CAGGTAGCAGATCTTGTCTTCCTGTATTTTGCAGCGGAAGACATCGAA
1 GCAGCGGAAGGGATCGAC-GATAGCAGATCTTGTCTTCCTGGATTTGGCAGCGGAAGACATCGAA
* * *
2529 GATAACAGTTCTTGTCTTCCTGTATTTGGCAGCAGAAGGGATCGAAGATATCAGATCTTGTCTTC
65 GATAACAGATCTTGTCTTCCTGTATCTGGCAGCAGAAGGGATCGAAGATATCAAATCTTGTCTTC
** * *
2594 TTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTTTTCCTG
130 CAGTA--T-GCAGCGGAGGGGATCGAAGATAGCAAATCTTGTCTTCCTG
2643 ATTTGGCAGC
Statistics
Matches: 155, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
175 3 0.02
176 115 0.74
180 37 0.24
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (177 bp):
GCAGCGGAAGGGATCGACGATAGCAGATCTTGTCTTCCTGGATTTGGCAGCGGAAGACATCGAAG
ATAACAGATCTTGTCTTCCTGTATCTGGCAGCAGAAGGGATCGAAGATATCAAATCTTGTCTTCC
AGTATGCAGCGGAGGGGATCGAAGATAGCAAATCTTGTCTTCCTGTA
Done.