Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1309
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: 2068
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Found at i:70 original size:46 final size:46
Alignment explanation
Indices: 1--2068 Score: 2086
Period size: 46 Copynumber: 45.4 Consensus size: 46
* ** *
1 TCGAAGATATCAGATCTTGTCTTCCTGAATTTTACAGCGAATGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * *
47 TTGAAGATATCAGATCTAGTCTTCCTATATTTGGCAGCGGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* *
93 TCAAAGAT-TGCAGATCTTGTCTTCCTGTATCTGGCAGCGAAGGGGA
1 TCGAAGATAT-CAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * *
139 TCGAAGATAGCAGATGTTGTCTTCCTGTATCTAGG-AGCG--GCGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTAT-TTGGCAGCGAAG-GGGA
* *
184 TCGAAGATATCAAATCATGTCTTCCTGTATTTGGCAGCTG-AGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGA
* * * *
230 TCGAATATAACAGATCTTGTCTTCCTGTATTTGGCAGTGGAA-GAGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAG-CGAAGGGGA
* * * *
276 TCGAGGATAGCAGATCTTGACTTCCTGTATTTGGCAGCGGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * * *
322 TGGAAGATAGCAGATCTTGTCCTCCTGTCTTTGG-AGCGGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* **
367 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG-AGCGGCGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* *
412 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * *
458 TCGAAGATAGT-AGATCTTGTCTTTCTGTCTTTGGCAGCGGAGGGGA
1 TCGAAGATA-TCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * *
504 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGTAGTG-GGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * *
549 TTGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG-TAGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGA
* * * *
595 TC-AATGATAGT-AGATCTTATCTTCATGTATTTGGCAGCGGAGGAGA
1 TCGAA-GATA-TCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * * * *
641 TCGAGGATAGCAGATCTTTTCTTCCTGTATTGGGCAGCGAATGTGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* *
687 TCGAAGATAGCAGATCTTTTCTTCCTGTATTTGGCAGCGGAA-GGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGA
* * * * * *
733 TCGACGATAGCAGATCTTGTCTTTCTATATTTGGCAGCGGAGGGAA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* *
779 TCGAAGATAGT-AGATCTTGTCTTCCTGTATCTGGCAGCGGAGGGGA
1 TCGAAGATA-TCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
*
825 TCGAAGATATCAAATCTTGTCTTCCTGTA----GCAGCGGAA-GGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGA
* *
867 TCGAAGATAT-AAATCTTGTCTTCCTGTA----GCAGCGGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * * *
908 TCGCAGGTAGCAGATCTTGTCTTCCTGTATTTTGCAGCGGAA-GAGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGA
* * * *
954 TCGAAGATAACAGTTCTTGTCTTCCTGTATTTGGCAGCAAAAGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* *
1000 TCGAAGATATCAGATCTTGTCTTCTTGTATTTGGCAGCGGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * *
1046 TCAAAGATAGCAGATCTTGTTTTCCTG-ATTTGGCAGC-AGAGGAGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGA
* *
1091 TCGAAGATAGT-AGATCTTGTCTTCCTGTGTTTGCCAGCG-AGGGGA
1 TCGAAGATA-TCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * *
1136 TCGAAGATATCATATCTTGTCTTCCTGAATTTTGCAGCGAAAGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
*
1182 TGGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCAGAA-GGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGA
* * *
1228 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * ** *
1274 TCGAAGATAGCAGATCTTATCTTTATGTATTTGGCAGCGGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
*
1320 TCGAAGATATCAGA-CGTTGTCTTCCTGTATTTGGCAGCGGAGGGGA
1 TCGAAGATATCAGATC-TTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * *
1366 TCGAGGATATCAGATCTTATCTTCCTATATTTGG-AGCTG-AGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGA
* * * * * *
1411 TCGAAGATAGCAGATCCTGTCTTCCTGTATCTGGTAGTG-GGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * * *
1456 TTGAAGACAGT-AGATCTTCTCTTCCTGTATTTGGTAGC-ATACGGGA
1 TCGAAGATA-TCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGA
* * * * * *
1502 TCGAAGATA-GAGGATCTTATCTTCATATATTTGGCAGCGGAGGAGA
1 TCGAAGATATCA-GATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * *
1548 TCGAGGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGAAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* *
1594 TCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGAAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* *
1640 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * * **
1686 TCAAAGATAGCTGATCTTATCTTCCTGTATTTTACAGC-AGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGA
* * * * * * *
1732 TCGACGATAGCAGATCTGGTCTTCCTGTATCTGGTAGTG-GGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * * *
1777 TTGAAGACAGT-AGATCTTCTCTTCCTGTATTTGGTAGC-ATACGGGA
1 TCGAAGATA-TCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGA
** * * * * *
1823 TCGAAGATAGAAGATCTTATCTTCATATATTTGGCAGCGGAGGAGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * *
1869 TGGAGGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGAAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* *
1915 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * *
1961 TCGAAGATAGCTGATCTTGTCTTCCTGTATTTGGTAGTG-AGGGGA
1 TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
* * * * * *
2006 TTGAAGACAGT-AGACCTTCTCCTCCTATATTTGGCAGC-AGAGGGGA
1 TCGAAGATA-TCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGA
2052 TCGAAGATAGT-AGATCT
1 TCGAAGATA-TCAGATCT
Statistics
Matches: 1708, Mismatches: 252, Indels: 124
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.00
41 34 0.02
42 36 0.02
43 2 0.00
44 5 0.00
45 388 0.23
46 1226 0.72
47 15 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (46 bp):
TCGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGA
Found at i:161 original size:92 final size:92
Alignment explanation
Indices: 1--2068 Score: 2362
Period size: 92 Copynumber: 22.7 Consensus size: 92
* * ** * * * *
1 TCGAAGATATCAGATCTTGTCTTCCTGAATTTTACAGCGAATGGGATTGAAGATATCAGATCTAG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
*
66 TCTTCCTATATTTGGCAGCGGAGGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * * *
93 TCAAAGATTGCAGATCTTGTCTTCCTGTATCTGGCAGCGAAGGGGATCGAAGATAGCAGATGTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* *
158 TCTTCCTGTATCTAGG-AGCGG-CGGGA
66 TCTTCCTGTAT-TTGGCAGCGGAGGGGA
* * * * *
184 TCGAAGATATCAAATCATGTCTTCCTGTATTTGGCAGCTG-AGGGGATCGAATATAACAGATCTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGATCGAAGATAGCAGATCTT
* * *
248 GTCTTCCTGTATTTGGCAGTGGAAGAGA
65 GTCTTCCTGTATTTGGCAGCGGAGGGGA
* * * *
276 TCGAGGATAGCAGATCTTGACTTCCTGTATTTGGCAGCGGAGGGGATGGAAGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* *
341 TCCTCCTGTCTTTGG-AGCGGAGGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
**
367 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG-AGCGGCGGGGATCGAAGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* *
431 TCTTCCTGTATTTGGCAGCGAAGGAGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * * *
458 TCGAAGATAGTAGATCTTGTCTTTCTGTCTTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* *
523 TCTTCCTGTATTTGGTAGTGG-GGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * *
549 TTGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG-TAGAGGGGATC-AATGATAGTAGATCT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAA-GATAGCAGATCT
* * *
612 TATCTTCATGTATTTGGCAGCGGAGGAGA
64 TGTCTTCCTGTATTTGGCAGCGGAGGGGA
* * * * * *
641 TCGAGGATAGCAGATCTTTTCTTCCTGTATTGGGCAGCGAATGTGATCGAAGATAGCAGATCTTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
*
706 TCTTCCTGTATTTGGCAGCGGAAGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * * * * *
733 TCGACGATAGCAGATCTTGTCTTTCTATATTTGGCAGCGGAGGGAATCGAAGATAGTAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
*
798 TCTTCCTGTATCTGGCAGCGGAGGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * * *
825 TCGAAGATATCAAATCTTGTCTTCCTGTA----GCAGCGGAA-GGGATCGAAGATA-TAAATCTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGATCGAAGATAGCAGATCTT
884 GTCTTCCTGTA----GCAGCGGAGGGGA
65 GTCTTCCTGTATTTGGCAGCGGAGGGGA
* * * * * *
908 TCGCAGGTAGCAGATCTTGTCTTCCTGTATTTTGCAGCGGAA-GAGATCGAAGATAACAGTTCTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGATCGAAGATAGCAGATCTT
** *
972 GTCTTCCTGTATTTGGCAGCAAAAGGGA
65 GTCTTCCTGTATTTGGCAGCGGAGGGGA
* * * *
1000 TCGAAGATATCAGATCTTGTCTTCTTGTATTTGGCAGCGGAGGGGATCAAAGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* * *
1065 TTTTCCTG-ATTTGGCAGCAGAGGAGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * * * *
1091 TCGAAGATAGTAGATCTTGTCTTCCTGTGTTTGCCAGCG-AGGGGATCGAAGATATCATATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* * * *
1155 TCTTCCTGAATTTTGCAGCGAAAGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* *
1182 TGGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGCAGAA-GGGATCGAAGATAGCAGATCTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGATCGAAGATAGCAGATCTT
*
1246 GTCTTCCTGTATTTGGCAGCGGAGGAGA
65 GTCTTCCTGTATTTGGCAGCGGAGGGGA
* ** * *
1274 TCGAAGATAGCAGATCTTATCTTTATGTATTTGGCAGCGGAGGGGATCGAAGATATCAGA-CGTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATC-TT
1338 GTCTTCCTGTATTTGGCAGCGGAGGGGA
65 GTCTTCCTGTATTTGGCAGCGGAGGGGA
* * * * *
1366 TCGAGGATATCAGATCTTATCTTCCTATATTTGG-AGCTG-AGGGGATCGAAGATAGCAGATCCT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGGGGATCGAAGATAGCAGATCTT
* * *
1429 GTCTTCCTGTATCTGGTAGTGG-GGGGA
65 GTCTTCCTGTATTTGGCAGCGGAGGGGA
* * * * * *
1456 TTGAAGACAGTAGATCTTCTCTTCCTGTATTTGGTAGC-ATACGGGATCGAAGATAG-AGGATCT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAAGATAGCA-GATCT
* * * *
1519 TATCTTCATATATTTGGCAGCGGAGGAGA
64 TGTCTTCCTGTATTTGGCAGCGGAGGGGA
* *
1548 TCGAGGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* *
1613 TCTTCCTATATTTGGCAGCGAAGGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * * *
1640 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCAAAGATAGCTGATCTTA
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
** *
1705 TCTTCCTGTATTTTACAGCAGAGGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * * * * * * * * *
1732 TCGACGATAGCAGATCTGGTCTTCCTGTATCTGGTAGTG-GGGGGATTGAAGACAGTAGATCTTC
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* ** *
1796 TCTTCCTGTATTTGGTAGCATACGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * * * * * * *
1823 TCGAAGATAGAAGATCTTATCTTCATATATTTGGCAGCGGAGGAGATGGAGGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* *
1888 TCTTCCTATATTTGGCAGCGAAGGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* *
1915 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCTGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
* *
1980 TCTTCCTGTATTTGGTAG-TGAGGGGA
66 TCTTCCTGTATTTGGCAGCGGAGGGGA
* * * * * * * *
2006 TTGAAGACAGTAGACCTTCTCCTCCTATATTTGGCAGC-AGAGGGGATCGAAGATAGTAGATCT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGGGGATCGAAGATAGCAGATCT
Statistics
Matches: 1667, Mismatches: 270, Indels: 79
0.83 0.13 0.04
Matches are distributed among these distances:
83 38 0.02
87 39 0.02
88 33 0.02
89 2 0.00
90 108 0.06
91 538 0.32
92 900 0.54
93 9 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (92 bp):
TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTG
TCTTCCTGTATTTGGCAGCGGAGGGGA
Found at i:248 original size:137 final size:137
Alignment explanation
Indices: 1--2068 Score: 2374
Period size: 137 Copynumber: 15.1 Consensus size: 137
* * ** * * * *
1 TCGAAGATATCAGATCTTGTCTTCCTGAATTTTACAGCGAATGGGATTGAAGATATCAGATCTAG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTG
* * * *
66 TCTTCCTATATTTGGCAGCGGAGGGGATCAAAGATTGCAGATCTTGTCTTCCTGTATCTGGCAGC
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
131 GAAGGGGA
130 GAAGGGGA
* * * * * *
139 TCGAAGATAGCAGATGTTGTCTTCCTGTATCTAGG-AGCGGCGGGATCGAAGATATCAAATCATG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTAT-TTGGCAGCGGAGGGATCGAAGATAGCAGATCTTG
* * *
203 TCTTCCTGTATTTGGCAGCTGAGGGGATCGAATATAACAGATCTTGTCTTCCTGTATTTGGCAGT
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG-
* *
268 GGAA-GAGA
129 CGAAGGGGA
* * *
276 TCGAGGATAGCAGATCTTGACTTCCTGTATTTGGCAGCGGAGGGGATGGAAGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTG
* *
341 TCCTCCTGTCTTTGG-AGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG-AGC
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
**
404 GGCGGGGA
130 GAAGGGGA
* *
412 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATCGAAGATAGTAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGG-GATCGAAGATAGCAGATCTTG
* * * *
477 TCTTTCTGTCTTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGTAGT
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
*
542 G-GGGGGA
130 GAAGGGGA
* ** *
549 TTGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTAGAGGGGATC-AATGATAGTAGATCTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAA-GATAGCAGATCTT
* * * * * *
613 ATCTTCATGTATTTGGCAGCGGAGGAGATCGAGGATAGCAGATCTTTTCTTCCTGTATTGGGCAG
64 GTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
* *
678 CGAATGTGA
129 CGAAGGGGA
* *
687 TCGAAGATAGCAGATCTTTTCTTCCTGTATTTGGCAGCGGAAGGGATCGACGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-AGGGATCGAAGATAGCAGATCTTG
* * * * *
752 TCTTTCTATATTTGGCAGCGGAGGGAATCGAAGATAGTAGATCTTGTCTTCCTGTATCTGGCAGC
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
*
817 GGAGGGGA
130 GAAGGGGA
* * * *
825 TCGAAGATATCAAATCTTGTCTTCCTGTA----GCAGCGGAAGGGATCGAAGATA-TAAATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-AGGGATCGAAGATAGCAGATCTTG
* * *
885 TCTTCCTGTA----GCAGCGGAGGGGATCGCAGGTAGCAGATCTTGTCTTCCTGTATTTTGCAGC
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
*
946 GGAA-GAGA
130 -GAAGGGGA
* * ** *
954 TCGAAGATAACAGTTCTTGTCTTCCTGTATTTGGCAGCAAAAGGGATCGAAGATATCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GGAGGGATCGAAGATAGCAGATCTTG
* * *
1019 TCTTCTTGTATTTGGCAGCGGAGGGGATCAAAGATAGCAGATCTTGTTTTCCTG-ATTTGGCAGC
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
*
1083 -AGAGGAGA
130 GA-AGGGGA
* * * * *
1091 TCGAAGATAGTAGATCTTGTCTTCCTGTGTTTGCCAGC-GAGGGGATCGAAGATATCATATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTG
* * * * * *
1155 TCTTCCTGAATTTTGCAGCGAAAGGGATGGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGC
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
1220 AGAA-GGGA
130 -GAAGGGGA
*
1228 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAGCAGATCTTA
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGG-GATCGAAGATAGCAGATCTTG
** *
1293 TCTTTATGTATTTGGCAGCGGAGGGGATCGAAGATATCAGA-CGTTGTCTTCCTGTATTTGGCAG
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATC-TTGTCTTCCTGTATTTGGCAG
*
1357 CGGAGGGGA
129 CGAAGGGGA
* * * * * *
1366 TCGAGGATATCAGATCTTATCTTCCTATATTTGG-AGCTGAGGGGATCGAAGATAGCAGATCCTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTG
* * * * * * * *
1430 TCTTCCTGTATCTGGTAGTGG-GGGGATTGAAGACAGTAGATCTTCTCTTCCTGTATTTGGTAGC
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
*
1494 -ATACGGGA
130 GA-AGGGGA
* * * *
1502 TCGAAGATAG-AGGATCTTATCTTCATATATTTGGCAGCGGAGGAGATCGAGGATAGCAGATCTT
1 TCGAAGATAGCA-GATCTTGTCTTCCTGTATTTGGCAGCGGAGG-GATCGAAGATAGCAGATCTT
* * *
1566 GTCTTCCTATATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAG
64 GTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
1631 CGAAGGGGA
129 CGAAGGGGA
* * *
1640 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCAAAGATAGCTGATCTTA
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTG
** * * * * * *
1705 TCTTCCTGTATTTTACAGCAGAGGGGATCGACGATAGCAGATCTGGTCTTCCTGTATCTGGTAGT
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
*
1770 G-GGGGGA
130 GAAGGGGA
* * * * * ** * *
1777 TTGAAGACAGTAGATCTTCTCTTCCTGTATTTGGTAGCATACGGGATCGAAGATAGAAGATCTTA
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTG
* * * * * *
1842 TCTTCATATATTTGGCAGCGGAGGAGATGGAGGATAGCAGATCTTGTCTTCCTATATTTGGCAGC
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
1907 GAAGGGGA
130 GAAGGGGA
*
1915 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCTGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGA-GGGATCGAAGATAGCAGATCTTG
* * * * * * * * *
1980 TCTTCCTGTATTTGGTAG-TGAGGGGATTGAAGACAGTAGACCTTCTCCTCCTATATTTGGCAGC
65 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
2044 -AGAGGGGA
130 GA-AGGGGA
*
2052 TCGAAGATAGTAGATCT
1 TCGAAGATAGCAGATCT
Statistics
Matches: 1633, Mismatches: 251, Indels: 93
0.83 0.13 0.05
Matches are distributed among these distances:
129 74 0.05
130 2 0.00
133 34 0.02
134 37 0.02
135 6 0.00
136 220 0.13
137 665 0.41
138 587 0.36
139 8 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (137 bp):
TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGATCGAAGATAGCAGATCTTGT
CTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG
AAGGGGA
Found at i:313 original size:183 final size:183
Alignment explanation
Indices: 1--2068 Score: 2380
Period size: 183 Copynumber: 11.3 Consensus size: 183
* * ** * * * * *
1 TCGAAGATATCAGATCTTGTCTTCCTGAATTTTACAGCGAATGGGATTGAAGATATCAGATCTAG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
* * * *
66 TCTTCCTATATTTGGCAGCGGAGGGGATCAAAGATTGCAGATCTTGTCTTCCTGTATCTGGCAGC
66 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
* * *
131 GAAGGGGATCGAAGATAGCAGATGTTGTCTTCCTGTATCTAGG-AGCGGCGGGA
131 GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTAT-TTGGCAGCGGGGGGA
* * * * * *
184 TCGAAGATATCAAATCATGTCTTCCTGTATTTGGCAGCTGAGGGGATCGAATATAACAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
* * * * *
249 TCTTCCTGTATTTGGCAGTGGAAGAGATCGAGGATAGCAGATCTTGACTTCCTGTATTTGGCAGC
66 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
* * * *
314 GGAGGGGATGGAAGATAGCAGATCTTGTCCTCCTGTCTTTGG-AGCGGAGGGGA
131 GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-GGGGA
*
367 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGG-AGCGGCGGGGATCGAAGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
* * * * *
431 TCTTCCTGTATTTGGCAGCGAAGGAGATCGAAGATAGTAGATCTTGTCTTTCTGTCTTTGGCAGC
66 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
* * *
496 GGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGTAGTGGGGGGA
131 GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGGGGGA
* ** *
549 TTGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTAGAGGGGATC-AATGATAGTAGATCTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAA-GATAGCAGATCTT
* * * * * *
613 ATCTTCATGTATTTGGCAGCGGAGGAGATCGAGGATAGCAGATCTTTTCTTCCTGTATTGGGCAG
65 GTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
* * * *
678 CGAATGTGATCGAAGATAGCAGATCTTTTCTTCCTGTATTTGGCAGCGGAAGGGA
130 CGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-GGGGA
* * * * *
733 TCGACGATAGCAGATCTTGTCTTTCTATATTTGGCAGCGGAGGGAATCGAAGATAGTAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
* * *
798 TCTTCCTGTATCTGGCAGCGGAGGGGATCGAAGATATCAAATCTTGTCTTCCTGTA----GCAGC
66 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
* *
859 GGAA-GGGATCGAAGATA-TAAATCTTGTCTTCCTGTA----GCAGCGGAGGGGA
131 -GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-GGGGA
* * * * * * *
908 TCGCAGGTAGCAGATCTTGTCTTCCTGTATTTTGCAGCGGAAGAGATCGAAGATAACAGTTCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
** * * *
973 TCTTCCTGTATTTGGCAGCAAAAGGGATCGAAGATATCAGATCTTGTCTTCTTGTATTTGGCAGC
66 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
* * * * *
1038 GGAGGGGATCAAAGATAGCAGATCTTGTTTTCCTG-ATTTGGCAGCAGAGGAGA
131 GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GGGGGGA
* * * * *
1091 TCGAAGATAGTAGATCTTGTCTTCCTGTGTTTGCCAGC-GAGGGGATCGAAGATATCATATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
* * * * * *
1155 TCTTCCTGAATTTTGCAGCGAAAGGGATGGAAGATATCAGATCTTGTCTTCCTGTATTTGGCAGC
66 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
*
1220 AGAA-GGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGA
131 -GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-GGGGA
* ** *
1274 TCGAAGATAGCAGATCTTATCTTTATGTATTTGGCAGCGGAGGGGATCGAAGATATCAGA-CGTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATC-TT
* * * *
1338 GTCTTCCTGTATTTGGCAGCGGAGGGGATCGAGGATATCAGATCTTATCTTCCTATATTTGG-AG
65 GTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
* * * *
1402 CTG-AGGGGATCGAAGATAGCAGATCCTGTCTTCCTGTATCTGGTAGTGGGGGGA
130 C-GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGGGGGA
* * * * * ** *
1456 TTGAAGACAGTAGATCTTCTCTTCCTGTATTTGGTAGCATACGGGATCGAAGATAG-AGGATCTT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCA-GATCTT
* * * * * *
1520 ATCTTCATATATTTGGCAGCGGAGGAGATCGAGGATAGCAGATCTTGTCTTCCTATATTTGGCAG
65 GTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
* *
1585 CGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGAAGGGGA
130 CGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCG-GGGGGA
* * *
1640 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCAAAGATAGCTGATCTTA
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
** * * * * * *
1705 TCTTCCTGTATTTTACAGCAGAGGGGATCGACGATAGCAGATCTGGTCTTCCTGTATCTGGTAGT
66 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
* * * * * * ***
1770 G-GGGGGATTGAAGACAGTAGATCTTCTCTTCCTGTATTTGGTAGCATACGGGA
131 GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GGGGGGA
* * * * * * *
1823 TCGAAGATAGAAGATCTTATCTTCATATATTTGGCAGCGGAGGAGATGGAGGATAGCAGATCTTG
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
* *
1888 TCTTCCTATATTTGGCAGCGAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
66 TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
* * * * *
1953 GGAGGGGATCGAAGATAGCTGATCTTGTCTTCCTGTATTTGGTAGTGAGGGGA
131 GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGGGGGA
* * * * * * * * *
2006 TTGAAGACAGTAGACCTTCTCCTCCTATATTTGGCAGCAGAGGGGATCGAAGATAGTAGATCT
1 TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCT
Statistics
Matches: 1604, Mismatches: 249, Indels: 64
0.84 0.13 0.03
Matches are distributed among these distances:
175 115 0.07
178 2 0.00
179 34 0.02
180 31 0.02
181 4 0.00
182 392 0.24
183 690 0.43
184 334 0.21
185 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (183 bp):
TCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTG
TCTTCCTGTATTTGGCAGCGGAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC
GAAGGGGATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGGGGGA
Done.