Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_607 ID=scaffold_607-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: 7160
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.19
Warning! 1863 characters in sequence are not A, C, G, or T
Found at i:277 original size:132 final size:132
Alignment explanation
Indices: 40--1148 Score: 1734
Period size: 132 Copynumber: 8.4 Consensus size: 132
30 TCGCTTCACC
*
40 TGTCTACCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * *
105 AGCAGATCGAAGATGGAAAATCTTATCTTACCAAGATAGTGGGAAGCAGATTTAGGCCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
170 CT
131 CT
* *
172 TGTCTCCCTGAGCAGCGGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
*
237 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCATATTTAAGCCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
302 CT
131 CT
* * *
304 TGTCTCCCTCAGCAGCAGCGGAGTGGGCTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGAGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * * * *
369 AGCAGATCGAAGA-GGTAAAATCTTATCCTTCCGACATAGTAGGAAGCAGATTTAAGTCACCAAG
66 AGCAGATCGAAGACGG-CAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAG
433 CCT
130 CCT
*
436 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAAATCTTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
*
501 AGAAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
566 CT
131 CT
* * * *
568 TGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAACTTGTAGATCTTATCTCCCCAAGCAGTAGGGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
633 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAATGGGAAGTAGATTTAAGTCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
698 CT
131 CT
* * * **
700 TGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGAAGAAG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * * *
765 AGCAGATCGAAGAGGGAAAATCTTATCTTTCCAACATAGTAGGAAGCAGATTTAAGTCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
830 CT
131 CT
* * * ** *
832 TGTTTCCCTGAGCGGCAGCGGAGTGGGTTGAAACTTGTAGATCTTATCTCCCTAAGCAGTCTTCG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * * *
897 AGCAGATCGAAGACGACAAATCTCATCTTTCCAAGATAGGGGGAAGTAGATTTATGCCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
962 CT
131 CT
* *
964 TGTCTCCCCGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* *
1029 AGCAGATCGAAGACGACAAATCTTATCTTTTCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
1094 CT
131 CT
*
1096 TGTCTCGCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCT
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCT
1149 NNNNNNNNNN
Statistics
Matches: 887, Mismatches: 88, Indels: 4
0.91 0.09 0.00
Matches are distributed among these distances:
131 2 0.00
132 883 1.00
133 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (132 bp):
TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
CT
Found at i:656 original size:44 final size:44
Alignment explanation
Indices: 474--660 Score: 110
Period size: 44 Copynumber: 4.2 Consensus size: 44
464 TGAAAATTGT
* * *
474 AAATCTTATCTCCCTAAGCAGTAGTGGAGAAGATCGAAGACGGC
1 AAATCTTATCTCCCCAAGCAGTAGGGGAGCAGATCGAAGACGGC
** ** * **
518 AAATCTTATCTTTCCAAG-A-TAGTGGGAAGCAGATTTAAGCCACC
1 AAATCTTATCTCCCCAAGCAGTAG-GGG-AGCAGATCGAAGACGGC
** * ** * * ** * * * *
562 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAA-ACTTGT
1 AAATCTTATCTCCCCAAGCAGTAGGGGAGCAGATCGAAGAC-GGC
*
606 AGATCTTATCTCCCCAAGCAGTAGGGGAGCAGATCGAAGACGGC
1 AAATCTTATCTCCCCAAGCAGTAGGGGAGCAGATCGAAGACGGC
650 AAATCTTATCT
1 AAATCTTATCT
661 TTCCAAGATA
Statistics
Matches: 95, Mismatches: 42, Indels: 12
0.64 0.28 0.08
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
44 81 0.85
45 5 0.05
46 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (44 bp):
AAATCTTATCTCCCCAAGCAGTAGGGGAGCAGATCGAAGACGGC
Found at i:778 original size:396 final size:396
Alignment explanation
Indices: 40--3459 Score: 2707
Period size: 396 Copynumber: 8.6 Consensus size: 396
30 TCGCTTCACC
*
40 TGTCTACCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * *
105 AGCAGATCGAAGATGGAAAATCTTATCTTACCAAGATAGTGGGAAGCAGATTTAGGCCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
*
170 CTTGTCTCCCTGAGCAGCGGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
131 CTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
*
235 GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCATATTTAAGCCACCAA
196 GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * *
300 GCCTTGTCTCCCTCAGCAGCAGCGGAGTGGGC-TGAAAATTGTAGATCTTATCTCCCTAAGCAGT
261 GCCTTGTCTCCCTGAGCAGCAGCGGAGT-GGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGA
* * *
364 AGAGGAGCAGATCGAAGAGGTAAAATCTTATCCTTCCGACATAGTAGGAAGCAGATTTAAGTCAC
325 AGAAGAGCAGATCGAAGAGGGAAAATCTTATCCTTCCAACATAGTAGGAAGCAGATTTAAGTCAC
429 CAAGCCT
390 CAAGCCT
*
436 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAAATCTTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
*
501 AGAAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
* * * * *
566 CTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAACTTGTAGATCTTATCTCCCCAAGCAGTAGG
131 CTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
* * *
631 GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAATGGGAAGTAGATTTAAGTCACCAA
196 GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
696 GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGAA
261 GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGAA
*
761 GAAGAGCAGATCGAAGAGGGAAAATCTTATCTTTCCAACATAGTAGGAAGCAGATTTAAGTCACC
326 GAAGAGCAGATCGAAGAGGGAAAATCTTATCCTTCCAACATAGTAGGAAGCAGATTTAAGTCACC
826 AAGCCT
391 AAGCCT
* * * ** *
832 TGTTTCCCTGAGCGGCAGCGGAGTGGGTTGAAACTTGTAGATCTTATCTCCCTAAGCAGTCTTCG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * * *
897 AGCAGATCGAAGACGACAAATCTCATCTTTCCAAGATAGGGGGAAGTAGATTTATGCCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
*
962 CTTGTCTCCCCGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
131 CTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
* *
1027 GGAGCAGATCGAAGACGACAAATCTTATCTTTTCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
196 GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * * ********
1092 GCCTTGTCTCGCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTNNNNNNNN
261 GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGAA
*****************************************************************
1157 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
326 GAAGAGCAGATCGAAGAGGGAAAATCTTATCCTTCCAACATAGTAGGAAGCAGATTTAAGTCACC
******
1222 NNNNNN
391 AAGCCT
*****************************************************************
1228 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
*****************************************************************
1293 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
***************************************************
1358 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCTAAGCAGTAGT
131 CTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
* ** * * *
1423 TGAGCAGATCGAAGACAACAAATCTTATATTCCCAAGATAGTGGGAAGCAGATTTAAGTCACCAA
196 GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * * * * *
1488 ACATTGTCTCCCTGAGCAGCAGCGGTGTAGGC-TGAAAATTATAGATCTTATCTCCCTAAGCAGT
261 GCCTTGTCTCCCTGAGCAGCAGCGGAGT-GGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGA
* * * * * * * *
1552 AG-TGCAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAATGGGAAGCAGACTTAAGTCA
325 AGAAG-AGCAGATCGAAGAGGGAAAATCTTATCCTTCCAACATAGTAGGAAGCAGATTTAAGTCA
*
1616 CCAAGCAT
389 CCAAGCCT
* *
1624 TGTCTCCTTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAATAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * * * *
1689 AGCAGATCAAAGACGGCAAATCGTATCTTTCCAACATAGGGGGAAGCAGATTGAAGTCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
* * *
1754 CTTGTCTCCCTGAGCAGCAGCGGAGTGGATTGAAAATTGTAGATCTTATATCCCTAAGCAGTAGT
131 CTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
* *
1819 GGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCTGATTTAAGCCACCAA
196 GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * * * * *
1884 GCCTTGTCTCCTTGAGTAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTCTCTCCCTAAGCAGTA
261 GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGAA
** * * * *
1949 GTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGT-GGTAAGCAGATTTAAGTCAC
326 GAAGAGCAGATCGAAGAGGGAAAATCTTATCCTTCCAACATAGTAGG-AAGCAGATTTAAGTCAC
2013 CAAGCCT
390 CAAGCCT
* *
2020 TGTCTCCCTGAGCAGCAGCGGAGTCGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * * *
2085 ACCAGATCGATGACGGTAAATCTTATCTTTCCTAA-ATAGTGGGAAGCAGATTTAAGTCACCAAA
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCC-AAGATAGTGGGAAGCAGATTTAAGCCACCAAG
* * *
2149 CATTGTCTCCCTGAGCAGCAGCGGTGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAG
130 CCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAG
* * * *
2214 TGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATATTGGGAAGCAGATTTAAGTCACCA
195 TGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
* * * *
2279 AGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGAAGT
260 AGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGA
** * * * * * * * *
2344 AGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTACGAGATAGTGGGAAGCAGATTTAAGCCAC
325 AGAAGAGCAGATCGAAGAGGGAAAATCTTATCCTTCCAACATAGTAGGAAGCAGATTTAAGTCAC
2409 CAAGCCT
390 CAAGCCT
* *
2416 TGTCTCCTTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATATTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * * *** * *
2481 AGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGATAGTGAGAAGGTTATTTAAGTCACCAAAC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
* * *
2546 ATTGTCTCCCTGAGCAGCAGCGGTGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
131 CTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
* * * * * *
2611 GCAGCAGATCGAAGATGGCAAATCTTATCTTTCCTAGATAATGAGAAGCAGATTTAAGTCACCAA
196 GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * * *
2676 GCCTTGTCTCCCTGAGCAGCAGTGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTA
261 GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGAA
** * * * * * * * * *
2741 GTGGAGCAAATCGATGACGGTAAATCTTATCTTTCGAAAATAGTGGGAAGCAGATTTAAGTCAAC
326 GAAGAGCAGATCGAAGAGGGAAAATCTTATCCTTCCAACATAGTAGGAAGCAGATTTAAGTCACC
* *
2806 AAACAT
391 AAGCCT
* * *
2812 TGTCTCCCTGAACAGCAGCGGTGTGGGTTGAAAATTGTTGATCTTATCTCCCTAAGCAGTAGTGG
1 TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
2877 AGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGTCACCAAGC
66 AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
* * *
2942 CTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTAAAAATTGTAGATCTTATCTCCCTAAACAGTAGT
131 CTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
* * * * * * *
3007 GGAGCAGATCGAAGACGGTAAATTTTATCTTTCCAATAAAGTGGGAAACAAATTTAAGTCACCAA
196 GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
* * * *
3072 GCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTA
261 GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGAA
** * * * *
3137 GTGGTGCAGATCGAAGACGGCAAATCTTATCTTTCCCAA-ATAG-AGGGAAGCAGATTTAAGTCA
326 GAAGAGCAGATCGAAGAGGGAAAATCTTATCCTT-CCAACATAGTA-GGAAGCAGATTTAAGTCA
3200 CCAAGCCT
389 CCAAGCCT
*
3208 TGTC-CCCTTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGGAGTAGTG
1 TGTCTCCC-TGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTG
*
3272 GAGCAGATCGAAGACGGCAAATCTTATCTTTCCATGATAGTGGGAAGCAGATTTAAGCCACCAAG
65 GAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAG
* * *
3337 CCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATATTACCTCCCTAAGCAGTAG
130 CCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAG
* * *
3402 TGGAGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATAGTGAGAAGCAGATTTAA
195 TGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
3460 NNNNNNNNNN
Statistics
Matches: 2286, Mismatches: 726, Indels: 24
0.75 0.24 0.01
Matches are distributed among these distances:
395 12 0.01
396 2264 0.99
397 10 0.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.23
Consensus pattern (396 bp):
TGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGC
CTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT
GGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAA
GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGCTTGAAAATTGTAGATCTTATCTCACTAAGCAGAA
GAAGAGCAGATCGAAGAGGGAAAATCTTATCCTTCCAACATAGTAGGAAGCAGATTTAAGTCACC
AAGCCT
Found at i:1656 original size:132 final size:132
Alignment explanation
Indices: 1409--3459 Score: 3172
Period size: 132 Copynumber: 15.5 Consensus size: 132
1399 NNNNNNNNNN
* ** * *
1409 CCCTAAGCAGTAGTTGAGCAGATCGAAGACAACAAATCTTATATTCCCAAGATAGTGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* * * * * *
1474 ATTTAAGTCACCAAACATTGTCTCCCTGAGCAGCAGCGGTGTAGGCTGAAAATTATAGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
1539 CT
131 CT
* * *
1541 CCCTAAGCAGTAGTGCAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAATGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* * *
1606 ACTTAAGTCACCAAGCATTGTCTCCTTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
1671 CT
131 CT
* * * * *
1673 CCCTAAGCAATAGTGGAGCAGATCAAAGACGGCAAATCGTATCTTTCCAACATAGGGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* *
1738 ATTGAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGATTGAAAATTGTAGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
*
1803 AT
131 CT
* *
1805 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCTG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* * * *
1870 ATTTAAGCCACCAAGCCTTGTCTCCTTGAGTAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTCT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
1935 CT
131 CT
*
1937 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGTAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* *
2002 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTCGGTTAAAAATTGTAGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
2067 CT
131 CT
* * *
2069 CCCTAAGCAGTAGTGGACCAGATCGATGACGGTAAATCTTATCTTTCCTAA-ATAGTGGGAAGCA
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCC-AAGATAGTGGGAAGCA
* * *
2133 GATTTAAGTCACCAAACATTGTCTCCCTGAGCAGCAGCGGTGTGGGTTGAAAATTGTAGATCTTA
65 GATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTA
2198 TCT
130 TCT
* * *
2201 CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATATTGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
2266 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
2331 CT
131 CT
* * *
2333 CCCTAAGAAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTACGAGATAGTGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* * *
2398 ATTTAAGCCACCAAGCCTTGTCTCCTTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATATTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
2463 CT
131 CT
* * * ***
2465 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGATAGTGAGAAGGTT
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* * *
2530 ATTTAAGTCACCAAACATTGTCTCCCTGAGCAGCAGCGGTGTGGGTTGAAAATTGTAGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
2595 CT
131 CT
* * * * *
2597 CCCTAAGCAGTAGTGCAGCAGATCGAAGATGGCAAATCTTATCTTTCCTAGATAATGAGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
*
2662 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTGGGTTGAAAATTGTAGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
2727 CT
131 CT
* * * * *
2729 CCCTAAGCAGTAGTGGAGCAAATCGATGACGGTAAATCTTATCTTTCGAAAATAGTGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* * * * * *
2794 ATTTAAGTCAACAAACATTGTCTCCCTGAACAGCAGCGGTGTGGGTTGAAAATTGTTGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
2859 CT
131 CT
* *
2861 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAATGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* * *
2926 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCAGAGTAGGTTAAAAATTGTAGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
2991 CT
131 CT
* * * * * * *
2993 CCCTAAACAGTAGTGGAGCAGATCGAAGACGGTAAATTTTATCTTTCCAATAAAGTGGGAAACAA
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
*
3058 ATTTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
3123 CT
131 CT
* *
3125 CCCTAAGCAGTAGTGGTGCAGATCGAAGACGGCAAATCTTATCTTTCCCAA-ATAGAGGGAAGCA
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTT-CCAAGATAGTGGGAAGCA
3189 GATTTAAGTCACCAAGCCTTGTC-CCCTTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTT
65 GATTTAAGTCACCAAGCCTTGTCTCCC-TGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTT
3253 ATCT
129 ATCT
* *
3257 CCCTAAGGAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCATGATAGTGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* * *
3322 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATATTAC
66 ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
3387 CT
131 CT
* * *
3389 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATAGTGAGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
3454 ATTTAA
66 ATTTAA
3460 NNNNNNNNNN
Statistics
Matches: 1739, Mismatches: 174, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
131 8 0.00
132 1722 0.99
133 9 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (132 bp):
CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
ATTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAT
CT
Found at i:5308 original size:132 final size:132
Alignment explanation
Indices: 5063--7160 Score: 3329
Period size: 132 Copynumber: 15.9 Consensus size: 132
5053 NNNNNNNNNN
5063 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* * * **
5128 AGATCGAAGACGGTAAATTTTATCTTTCCAACATAGAGGGAAATAGATTTAAGTCACCAAGCATT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
5193 GT
131 GT
* * * * *
5195 CTCCCTGAACAGCAGCGGAGTGGGTTGAAAATTATAGATCTTATCTCCCTAAGCAATAGTAGTGC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* * * * *
5260 AGATCGAAGACGACAAATCTTATCTTCCCAAGATAGTGAGAAGCAGATTTAAGTCACCAAACATT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
5325 GT
131 GT
*
5327 CTCCCTGAGCAGCAGCGGTGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* * *
5392 AGATCGAAGATGGCAAATCTTATCTTTCCAACATAGTAGGAAGCAGATTTAAGTCACCAAGCCTT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
5457 GT
131 GT
*
5459 CTCCCTGAGCTGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* ** * * *
5524 ATATCGAAGACAACAAATCTTATCTTCCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGCCTT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
5589 GT
131 GT
* *
5591 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTAACTCCCTAAGCAATAGTGGAGC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* *
5656 AGATCGAAGACGGCAAATCTTATCTTTCCAAAATAGTGGGAAGCAGATTTAAGTCACCAAGCCTT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
5721 GT
131 GT
* *
5723 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTCAGCAGTAGTGGATC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* * * * *
5788 AGGTCGAAGACGGTAAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGTCACCAAGCCTT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
5853 GT
131 GT
* *
5855 CTCCCTGAGCAGCAGCAGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGATC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* *
5920 AGATCGAAGACGGCAAATTTTATCTTTCCAACATAGTGGGAAACAGATTTAAGTCACCAAGCATT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
5985 GT
131 GT
* * *
5987 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCCCAAGCAATAGTGGTG
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT-CCCTAAGCAGTAGTGGAG
* *
6052 CAGATCGAAGACGGTAAATCTTATCTTTCCAAAATAGTGGGAAGCAGATTTAAGTCACCAAGCCA
65 CAGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAG-CA
6117 -TGT
129 TTGT
6120 CTCCCTGAGCAGCAGCGGA-TAGGGTTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGA
1 CTCCCTGAGCAGCAGCGGAGT-GGG-TTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGA
* * *
6184 TCAGGTCGAAGACGGCAAATCTTATCTTTTCCAAGATAGTGGGAAGCAGATTTAAGTCACCAAGC
64 GCAGATCGAAGACGGCAAATCTTATC-TTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGC
6249 ATTGT
128 ATTGT
*
6254 CTTCCTTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAG
1 C-TCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAG
* * * *
6319 CAGATCGAAGACGGTAAATTTTATCTTTCCAACATAGTGGGAAACAGATTTAAGTCACCCAGCAT
65 CAGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCAT
6384 TGT
130 TGT
* * * * *
6387 CTCCCTGAGTAGCAGTGGAGTGGGTTGAAAATTATAGATCTTATCTCCCTAAGCAATAGTAGTA-
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGT-GGAG
* *
6451 CAGATCGAAGACGGCAAATCTTATCTTTCCAAAATAGTGGGAAGCAGATTTAAGTCACCAAGCCT
65 CAGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCAT
6516 TGT
130 TGT
* *
6519 CTCCCTGAGCAGCAGCGGAATGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGATC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* * * *
6584 AGGTCGAAGACGGCAAATCTTATCTTTCCAAGATAATGGGAAGCAGATTTAAGTCACCAAGCCTT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
6649 GT
131 GT
* *
6651 CTCCCTGAGCAGCAGCAGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGT
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* * *
6716 AGACCGAAGACGACAAATCTTATCTTTCCAACATAGTGGGAAACAGATTTAAGTCACCAAGCATT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
6781 GT
131 GT
*
6783 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAATAGTGGAGC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* *
6848 AGATCGAAGACGGCAAATCTTATCTTTCCAAAATAGTGGGAAGCAGATTTAAGTCACCAAGCCTT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
6913 GT
131 GT
* * * *
6915 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCGTATGCTGTATTGGAGC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* *
6980 AGATCGAAGACGGCAAATTTTATCTTTCCAACATAGTGGGAAACAGATTTAAGTCACCAAGCATT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
7045 GT
131 GT
* * * *
7047 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTATAGATCTTATCTCCCTAAGCAATAGTAGTGC
1 CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* *
7112 AGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATT
66 AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATT
Statistics
Matches: 1808, Mismatches: 148, Indels: 20
0.91 0.07 0.01
Matches are distributed among these distances:
131 2 0.00
132 1481 0.82
133 179 0.10
134 125 0.07
135 20 0.01
136 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (132 bp):
CTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGC
AGATCGAAGACGGCAAATCTTATCTTTCCAACATAGTGGGAAGCAGATTTAAGTCACCAAGCATT
GT
Done.