Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399509.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2769.0, whole genome shotgun sequence
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: 2616
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.34
Warning! 175 characters in sequence are not A, C, G, or T
Found at i:441 original size:171 final size:169
Alignment explanation
Indices: 1--1298 Score: 785
Period size: 171 Copynumber: 7.6 Consensus size: 169
* * *
1 GGCTTTTGAAA-GAATGGGAGACTATAAATGGACTTTTCTTG-CTAATGAATGGCTCTT-TT-TG
1 GGCTTTT-AAAGGAATGAGAGACCATAAATGGACTTTTCTTGTC-AATGAAT-GCT-TTCTTCTT
** * * * *
62 CATATTT-TCTGAGGTAAACATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAAATTCAA
62 CACGTTTCT-TAAGCTAGACATTCAATTATAGTCTATTTTAAT-AAAAATGT-AAAAAAATT-AA
* * * *
126 CTT-GAATACAATTATGAGATTATAAAACCATTTAAGGCTAGTAATAA
123 CTTAAAAT-CAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAA
* * * * * *
173 GGCTTTTGACGGTATGAGAGACCATAAATGGTCTTTTCTT-TCAAATAAATAGCTTTCTT-TACA
1 GGCTTTTAAAGGAATGAGAGACCATAAATGGACTTTTCTTGTC-AATGAAT-GCTTTCTTCTTCA
* ** * *
236 CATTTCCCAAGGC-AAACATTCGATTATAGTCTATTTTAATAAAAAATGTAAAAACAATTAACTT
64 CGTTTCTTAA-GCTAGACATTCAATTATAGTCTATTTTAAT-AAAAATGTAAAAA-AATTAACTT
**********
300 AAAATCAATTANNNNNNNNNNAAACCATTTAAAGCGAGTAATAA
126 AAAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAA
* * * *
344 GGCTTTTAATGGAATGAGTGACCATAAATGGACTTTTCTTGGCAATGAATGCTTTTTTCTTCACG
1 GGCTTTTAAAGGAATGAGAGACCATAAATGGACTTTTCTTGTCAATGAATGCTTTCTTCTTCACG
* * *
409 TTTCTTAAGCTAGATATTCAATTATTGTCTATTTTAATCAAAATGT-AAAAAATTCAACTTAAAA
66 TTTCTTAAGCTAGACATTCAATTATAGTCTATTTTAATAAAAATGTAAAAAAATT-AACTTAAAA
* * *
473 TGAATCT-TGAGATAATAAAACCATTTATAGTGAGTAATAA
130 TCAAT-TATGAGATAATAAAACCATTTAAAGCGAGTAATAA
* * * *
513 GGCTTTTAAAGGAATGAGAG-CCTATAAATGAACTTTTATTGTCAATGAATGCTTTCTCCTTCAT
1 GGCTTTTAAAGGAATGAGAGACC-ATAAATGGACTTTTCTTGTCAATGAATGCTTTCTTCTTCAC
* * *
577 GTTTCTTAAAG-TAGACATTCAATTATAGTTTGTTTTAACTAAAAATGTAAAAAAATTTATCTTA
65 GTTTCTT-AAGCTAGACATTCAATTATAGTCTATTTTAA-TAAAAATGTAAAAAAA-TTAACTTA
* * * * * ****
641 AAATTAATTATGAGATTATAAAACTATTTAACGTGAGTANNNN
127 AAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAA
****** * * * * * * * * *
684 NNNNNNTGAAGGAATGGGAGACTATAAATGAACTTTTGTTCTCAATTAATGACTTT-TTCTACAT
1 GGCTTTTAAAGGAATGAGAGACCATAAATGGACTTTTCTTGTCAATGAATG-CTTTCTTCTTCAC
* * * * *
748 GTTTC-CACAGGC-AGGCATTCAATTATAGTTTGTTTTAATGAAAAATGT-AAAATATTGAACTT
65 GTTTCTTA-A-GCTAGACATTCAATTATAGTCTATTTTAAT-AAAAATGTAAAAAAATT-AACTT
* * *
810 AAAAGCAATTATGAGATTATAAAACCATTTAAAG-TATGTAATAA
126 AAAATCAATTATGAGATAATAAAACCATTTAAAGCGA-GTAATAA
* * * * ** * * * *
854 AGCTTTTAAAGGAA-CAGGTGACTATATTTAGACTTTTCTTGCCAATGAATGCTTTTTTCCTCAC
1 GGCTTTTAAAGGAATGA-GAGACCATAAATGGACTTTTCTTGTCAATGAATGCTTTCTTCTTCAC
* * * * * * *
918 GTTTTTCTATG-TAAACATTTAATTATAATCTATTTTAACCAAAAAGGTAAAAAAATTGAACTTA
65 GTTTCT-TAAGCTAGACATTCAATTATAGTCTATTTTAA-TAAAAATGTAAAAAAATT-AACTTA
* *********** *
982 AAATCAATTTTGAGATTNNNNNNNNNNTTAAAGTGAGTAATAA
127 AAATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAA
* * * ** * ** * *
1025 GGCTTTTAAAGGAATGGGTGACTATAAATAAAGTTTTCTTCCCAATGAATGCTTTTTTTTTCACG
1 GGCTTTTAAAGGAATGAGAGACCATAAATGGACTTTTCTTGTCAATGAATGCTTTCTTCTTCACG
* * * ** * *
1090 TTTC-TAGAGATAGACATTCAATTATAGTCTGTTCTCACCAAAAGTATAAAAAAATTCAACTTAA
66 TTTCTTA-AGCTAGACATTCAATTATAGTCTATT-TTAATAAAAATGTAAAAAAATT-AACTTAA
* * * *
1154 AATCAGTTATGAGATTATAAAACCGTTTAAAGTGAGTAATAA
128 AATCAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAA
* * * * * *
1196 GACTTTTGAA-GATAT-AGGAGACTATAAATAGACTTTTCTT-CCAAATGAATGACTTTC-TCTA
1 GGCTTTTAAAGGA-ATGA-GAGACCATAAATGGACTTTTCTTGTC-AATGAATG-CTTTCTTCTT
** *
1257 CACGTTTCCCAAGGCAAG-CATTCAATTATAGTCTATTTTAAT
62 CACGTTTCTTAA-GCTAGACATTCAATTATAGTCTATTTTAAT
1299 GAAANNNNNN
Statistics
Matches: 876, Mismatches: 206, Indels: 90
0.75 0.18 0.08
Matches are distributed among these distances:
168 6 0.01
169 131 0.15
170 149 0.17
171 476 0.54
172 113 0.13
173 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
GGCTTTTAAAGGAATGAGAGACCATAAATGGACTTTTCTTGTCAATGAATGCTTTCTTCTTCACG
TTTCTTAAGCTAGACATTCAATTATAGTCTATTTTAATAAAAATGTAAAAAAATTAACTTAAAAT
CAATTATGAGATAATAAAACCATTTAAAGCGAGTAATAA
Found at i:1110 original size:341 final size:339
Alignment explanation
Indices: 1--1297 Score: 946
Period size: 341 Copynumber: 3.8 Consensus size: 339
* * * * *
1 GGCTTTTGAAA-GAATGGGAGACTATAAATGGACTTTTCTTGCTAATGAATGGCTCTTTTTGCAT
1 GGCTTTT-AAAGGAATGGGTGACTATAAATGAACTTTTCTTCCCAATGAAT-GCT-TTTTT-CTT
* * * *
65 -A-TTTTCTGAGGTAAACATTCAATTATAGTCTGTTTTAATAAAAAATGTAAAAAAAATTCAACT
62 CACGTTTCTAAGATAGACATTCAATTATAGTCTGTTTTAAT-AAAAATGT--AAAAAATTCAACT
* * * * * * *
128 TGAATA-CAATTATGAGATTATAAAACCATTTAAGGCT-AGTAATAAGGCTTTTGACGGTATGAG
124 T-AAAAGCAATTATGAGATTATAAAACCATTTAAAG-TGAGTAATAAAGCTTTTAAAGGAAAG-G
* * * * * * * ** * *
191 AGACCATAAATGGTCTTTTCTTTCAAATAAATAGC-TTTCT--TTACACATTTCCCAAGGCAAAC
186 AGACTATAAATAGACTTTTCTTGCCAATGAAT-GCTTTTCTCCTT-CACGTTTCTTAAAGTAAAC
* * ** * ******
253 ATTCGATTATAGTCTATTTTAATAAAAAATGTAAAAACAATT-AACTTAAAATCAATTANNNNNN
249 ATTCAATTATAATCTATTTTAACCAAAAAGGTAAAAA-AATTGAACTTAAAATCAATTATGAGAT
**** * *
317 NNNNAAACCATTTAAAGCGAGTAATAA
313 TATAAAACTATTTAAAGTGAGTAATAA
* * * * **
344 GGCTTTTAATGGAATGAGTGACCATAAATGGACTTTTCTTGGCAATGAATGCTTTTTTCTTCACG
1 GGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTCCCAATGAATGCTTTTTTCTTCACG
* * * * *
409 TTTCTTAAGCTAGATATTCAATTATTGTCTATTTTAATCAAAATGTAAAAAATTCAACTTAAAAT
66 TTTC-TAAGATAGACATTCAATTATAGTCTGTTTTAATAAAAATGTAAAAAATTCAACTTAAAA-
* * * * *
474 G-AATCT-TGAGATAATAAAACCATTTATAGTGAGTAATAAGGCTTTTAAAGGAATGAGAGCCTA
129 GCAAT-TATGAGATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTAAAGGAAAG-GAGACTA
* * * *
537 TAAAT-GAACTTTTATTGTCAATGAATGC-TTTCTCCTTCATGTTTCTTAAAGTAGACATTCAAT
192 TAAATAG-ACTTTTCTTGCCAATGAATGCTTTTCTCCTTCACGTTTCTTAAAGTAAACATTCAAT
* * * * * * * *
600 TATAGTTTGTTTTAACTAAAAATGTAAAAAAATTTATCTTAAAATTAATTATGAGATTATAAAAC
256 TATAATCTATTTTAACCAAAAAGGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAAC
* ****
665 TATTTAACGTGAGTANNNN
321 TATTTAAAGTGAGTAATAA
****** * * * * * * *
684 NNNNNNTGAAGGAATGGGAGACTATAAATGAACTTTTGTTCTCAATTAATGAC-TTTTTCTACAT
1 GGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTCCCAATGAATG-CTTTTTTCTTCAC
* ** * * * *
748 GTTTCCACAGGCAGGCATTCAATTATAGTTTGTTTTAATGAAAAATGTAAAATATTGAACTTAAA
65 GTTTCTA-AGATAGACATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAATTCAACTTAAA
*
813 AGCAATTATGAGATTATAAAACCATTTAAAGT-ATGTAATAAAGCTTTTAAAGGAACAGGTGACT
128 AGCAATTATGAGATTATAAAACCATTTAAAGTGA-GTAATAAAGCTTTTAAAGGAA-AGGAGACT
** * * * *
877 ATATTTAGACTTTTCTTGCCAATGAATGCTTTTTTCC-TCACGTTT-TTCTATGTAAACATTTAA
191 ATAAATAGACTTTTCTTGCCAATGAATGCTTTTCTCCTTCACGTTTCTT-AAAGTAAACATTCAA
* ******
940 TTATAATCTATTTTAACCAAAAAGGTAAAAAAATTGAACTTAAAATCAATTTTGAGATTNNNNNN
255 TTATAATCTATTTTAACCAAAAAGGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAA
****
1005 NNNNTTAAAGTGAGTAATAA
320 CTATTTAAAGTGAGTAATAA
* * *
1025 GGCTTTTAAAGGAATGGGTGACTATAAATAAAGTTTTCTTCCCAATGAATGCTTTTTTTTTCACG
1 GGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTCCCAATGAATGCTTTTTTCTTCACG
* ** * *
1090 TTTCTAGAGATAGACATTCAATTATAGTCTGTTCTCACCAAAAGTATAAAAAAATTCAACTTAAA
66 TTTCTA-AGATAGACATTCAATTATAGTCTGTT-TTAATAAAAATGT-AAAAAATTCAACTTAAA
* * * *
1155 ATCAGTTATGAGATTATAAAACCGTTTAAAGTGAGTAAT-AAGACTTTTGAA-GATATAGGAGAC
128 AGCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAAG-CTTTTAAAGGA-A-AGGAGAC
* ** * * *
1218 TATAAATAGACTTTTCTT-CCAAATGAATGAC-TTTCT-CTACACGTTTCCCAAGGCAAGCATTC
190 TATAAATAGACTTTTCTTGCC-AATGAATG-CTTTTCTCCTTCACGTTTCTTAAAGTAAACATTC
*
1280 AATTATAGTCTATTTTAA
253 AATTATAATCTATTTTAA
1298 TGAAANNNNN
Statistics
Matches: 745, Mismatches: 177, Indels: 65
0.75 0.18 0.07
Matches are distributed among these distances:
339 17 0.02
340 237 0.32
341 272 0.37
342 149 0.20
343 70 0.09
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (339 bp):
GGCTTTTAAAGGAATGGGTGACTATAAATGAACTTTTCTTCCCAATGAATGCTTTTTTCTTCACG
TTTCTAAGATAGACATTCAATTATAGTCTGTTTTAATAAAAATGTAAAAAATTCAACTTAAAAGC
AATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTAAAGGAAAGGAGACTATAAA
TAGACTTTTCTTGCCAATGAATGCTTTTCTCCTTCACGTTTCTTAAAGTAAACATTCAATTATAA
TCTATTTTAACCAAAAAGGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACTATTT
AAAGTGAGTAATAA
Found at i:1280 original size:512 final size:508
Alignment explanation
Indices: 1--1302 Score: 1259
Period size: 512 Copynumber: 2.5 Consensus size: 508
* * * *
1 GGCTTTTGAAA-GAATGGGAGACTATAAATGGACTTTTCTTGCTAATGAATGGC-TCTTTTTGCA
1 GGCTTTT-AAAGGAATGGGAGACTATAAATGAACTTTTCTTGCCAATGAAT-GCTTTTTTTTTCA
* * *
64 TATTTTCT-GAGGTAAACATTCAATTATAGTCTGTTTTAATAAAAAATGTA-AAAAAAATTCAAC
64 -AGTTTCTAGA-GTAGACATTCAATTATAGTCTGTTTTAA-CAAAAA-GTATAAAAAAATTCAAC
* * * * *
127 TT-GAATACAATTATGAGATTATAAAACCATTTAAGGCT-AGTAATAAGGCTTTTGACGGTATGA
125 TTAAAAT-CAATTATGAGATTATAAAACCATTTAAAG-TGAGTAATAAGACTTTTGAAGATATG-
* * * * * *
190 GAGACCATAAATGGTCTTTTCTTTCAAATAAAT-AGCTTTCTTTACACATTTCCCAAGGCAAACA
187 GAGACTATAAAT-GACTTTTCTTCCAAATAAATGA-CTTTCTCTACACGTTTCCCAAGGCAAGCA
* * * ********
254 TTCGATTATAGTCTATTTTAATAAAAAATGTAAAAACAATTAACTTAAAATCAATTANNNNNNNN
250 TTCAATTATAGTCTATTTTAATGAAAAATGTAAAAACAATTAACTTAAAAGCAATTATGAGATTA
** * * * *
319 NNAAACCATTTAAAGCGAGTAATAAGGCTTTTAATGGAATGAGTGACCATAAATGGACTTTTCTT
315 TAAAACCATTTAAAGCGAGTAATAAAGCTTTTAAAGGAAAGAGTGACCATAAATAGACTTTTCTT
* * * * ** *
384 GGCAATGAATGCTTTTTTCTTCACGTTTCTTAAGCTAGATATTCAATTATTGTCTATTTTAATCA
380 GCCAATGAATGCTTTTTTCCTCACGTTTCTTAAGCTAAACATTCAATTATAATCTATTTTAACCA
* * *
449 AAATGTAAAAAATTCAACTTAAAATGAATCTTGAGATAATAAAACCATTTATAGTGAGTAATAA
445 AAAGGTAAAAAATTCAACTTAAAATCAATCTTGAGATAATAAAACCATTTAAAGTGAGTAATAA
* * * * * ** *
513 GGCTTTTAAAGGAATGAGAGCCTATAAATGAACTTTTATTGTCAATGAATGCTTTCTCCTTCATG
1 GGCTTTTAAAGGAATGGGAGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTTTTCAAG
* * * * *
578 TTTCTTAAAGTAGACATTCAATTATAGTTTGTTTTAACTAAAAA-TGTAAAAAAATTTATCTTAA
66 TTTC-TAGAGTAGACATTCAATTATAGTCTGTTTTAAC-AAAAAGTATAAAAAAATTCAACTTAA
* * * **********
642 AATTAATTATGAGATTATAAAACTATTTAACGTGAGTANNNNNNNNNNTGAAGGA-ATGGGAGAC
129 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAA-GATAT-GGAGAC
* * * * *
706 TATAAATGAACTTTTGTTCTC-AATTAATGACTTTTTCTACATGTTT-CCACAGGCAGGCATTCA
192 TATAAATG-ACTTTTCTTC-CAAATAAATGACTTTCTCTACACGTTTCCCA-AGGCAAGCATTCA
* * *
769 ATTATAGTTTGTTTTAATGAAAAATGT-AAAA-TATTGAACTTAAAAGCAATTATGAGATTATAA
254 ATTATAGTCTATTTTAATGAAAAATGTAAAAACAATT-AACTTAAAAGCAATTATGAGATTATAA
* * **
832 AACCATTTAAAG-TATGTAATAAAGCTTTTAAAGGAACAG-GTGACTATATTTAGACTTTTCTTG
318 AACCATTTAAAGCGA-GTAATAAAGCTTTTAAAGGAA-AGAGTGACCATAAATAGACTTTTCTTG
* * *
895 CCAATGAATGCTTTTTTCCTCACGTTTTTCTATG-TAAACATTTAATTATAATCTATTTTAACCA
381 CCAATGAATGCTTTTTTCCTCACGTTTCT-TAAGCTAAACATTCAATTATAATCTATTTTAACC-
* * ***********
959 AAAAGGTAAAAAAATTGAACTTAAAATCAATTTTGAGATTNNNNNNNNNNTTAAAGTGAGTAATA
444 AAAAGGT-AAAAAATTCAACTTAAAATCAATCTTGAGATAATAAAACCATTTAAAGTGAGTAATA
1024 A
508 A
* * * * *
1025 GGCTTTTAAAGGAATGGGTGACTATAAATAAAGTTTTCTTCCCAATGAATGCTTTTTTTTTCACG
1 GGCTTTTAAAGGAATGGGAGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTTTTCAAG
* * *
1090 TTTCTAGAGATAGACATTCAATTATAGTCTGTTCTCACCAAAAGTATAAAAAAATTCAACTTAAA
66 TTTCTAGAG-TAGACATTCAATTATAGTCTGTTTTAACAAAAAGTATAAAAAAATTCAACTTAAA
* *
1155 ATCAGTTATGAGATTATAAAACCGTTTAAAGTGAGTAATAAGACTTTTGAAGATATAGGAGACTA
130 ATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAGATAT-GGAGACTA
*
1220 TAAATAGACTTTTCTTCCAAATGAATGACTTTCTCTACACGTTTCCCAAGGCAAGCATTCAATTA
194 TAAAT-GACTTTTCTTCCAAATAAATGACTTTCTCTACACGTTTCCCAAGGCAAGCATTCAATTA
1285 TAGTCTATTTTAATGAAA
258 TAGTCTATTTTAATGAAA
1303 NNNNNNNNNN
Statistics
Matches: 624, Mismatches: 140, Indels: 52
0.76 0.17 0.06
Matches are distributed among these distances:
509 4 0.01
510 126 0.20
511 148 0.24
512 341 0.55
513 5 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (508 bp):
GGCTTTTAAAGGAATGGGAGACTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTTTTCAAG
TTTCTAGAGTAGACATTCAATTATAGTCTGTTTTAACAAAAAGTATAAAAAAATTCAACTTAAAA
TCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAGATATGGAGACTATA
AATGACTTTTCTTCCAAATAAATGACTTTCTCTACACGTTTCCCAAGGCAAGCATTCAATTATAG
TCTATTTTAATGAAAAATGTAAAAACAATTAACTTAAAAGCAATTATGAGATTATAAAACCATTT
AAAGCGAGTAATAAAGCTTTTAAAGGAAAGAGTGACCATAAATAGACTTTTCTTGCCAATGAATG
CTTTTTTCCTCACGTTTCTTAAGCTAAACATTCAATTATAATCTATTTTAACCAAAAGGTAAAAA
ATTCAACTTAAAATCAATCTTGAGATAATAAAACCATTTAAAGTGAGTAATAA
Found at i:1900 original size:170 final size:170
Alignment explanation
Indices: 1422--2093 Score: 564
Period size: 171 Copynumber: 3.9 Consensus size: 170
1412 NNNNNNAAGT
* * * * * * * * *
1422 GAGTAATAAAGTTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGGCAACGAATGCTTTT
1 GAGTAAT-AAGGTCTTGAAAGAATGGGTGACTATAAATGGAATTTTCTTGCCAATGAATACCTTT
* * * * * * *
1487 TTCTTCACTTTTCTCGAGGTAGACATTCAATTATGATCTGTTTTAATCAAAAGTATAAAAAAATT
65 TTCTTCTCGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAATT
* * ****
1552 CAACTTGAAATCAATTATGAGATTATAAAACTATTTANNNN
130 AAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
****** * * ** *
1593 NNNNNNTAAGG-CTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTATCAATGAATAGCTT
1 GAGTAATAAGGTC-TTGAAA-GAATGGGTGACTATAAATGGAATTTTCTTGCCAATGAATACCTT
* * * * * * *
1657 TTTCTACAT-GTTTCTTAAGGTAGACACTCAATTATAGTCT-TTTTAATGAGAAATGTAAAAAAA
64 TTTCTTC-TCGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAA
** * *
1720 AAACAACTTAAACTCAATTATGAGATTAGAAAACTATTTAAAGC
128 TTA-AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* *
1764 GAGTAATAAGGTCTTGAAAGAATGGGTTACTATAAATGGAATTTTCTTGCCAATAAATACCTTTT
1 GAGTAATAAGGTCTTGAAAGAATGGGTGACTATAAATGGAATTTTCTTGCCAATGAATACCTTTT
* * * * * * *
1829 TCTTCTCTTTTCTCGAGATAAACATTCGATCATAATCTGTTGTAACCAAAAATGTAAAAAAATTA
66 TCTTCTCGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTA
********** *
1894 AACTTAAAATCAANNNNNNNNNNATAAAACTATTTAAAGT
131 AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
* * * ** **
1934 GAGTAATACGGCTTTTGAAAGAATGGGTGACTATAAATGG-ATTTTGCTTGCCAGTGAGCATGTT
1 GAGTAATAAGG-TCTTGAAAGAATGGGTGACTATAAATGGAATTTT-CTTGCCAATGAATACCTT
* * *
1998 TTTCTT-TACGTTTCTTAATGTAAACATTCAATTATTATCTGTTTTAATC-AAAATGTAAAAAAA
64 TTTCTTCT-CGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAA
2061 TTAAACTTAAAATCAATTATGAGATTATAAAAC
128 TTAAACTTAAAATCAATTATGAGATTATAAAAC
2094 CCTCTGAAGC
Statistics
Matches: 381, Mismatches: 110, Indels: 21
0.74 0.21 0.04
Matches are distributed among these distances:
169 1 0.00
170 172 0.45
171 207 0.54
172 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (170 bp):
GAGTAATAAGGTCTTGAAAGAATGGGTGACTATAAATGGAATTTTCTTGCCAATGAATACCTTTT
TCTTCTCGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTA
AACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGC
Found at i:2450 original size:171 final size:170
Alignment explanation
Indices: 2264--2616 Score: 396
Period size: 171 Copynumber: 2.1 Consensus size: 170
2254 NNNNNNNNNN
* *
2264 TTTAAAGCGAGTAAT-AAGCCTTTT-GAAGAAATGAGAGACTATAAATAAACTTTTT-TTATC-A
1 TTTAAAGCGAGTAATAAAG-CTTTTAAAAG-AATGAGAGACTATAAATAAA-TTTTTCTT-CCAA
* * * *
2325 ATAAATGACTTTTTCTATAC-GTTTCCTAAGGCAGGTATTCAATTAGAGTCTAG-TTTAATAAAA
62 ATAAATGAATTTTTCTACACAG-TTCCTAAGGCAAGCATTCAATTAGAGTCT-GTTTTAATAAAA
* *
2388 AATGTAAAAAAATTTAACTTC-AATACAATTATGAAATTATAAAACCA
125 AATAT-AAAAAATTCAACTTCAAAT-CAATTATGAAATTATAAAACCA
* * * **
2435 TTTAAGGCTAGTAATAAAGCTTTTAAAAGAATGAGAGATTATAAATGGATTTTTCTTCCAAATAA
1 TTTAAAGCGAGTAATAAAGCTTTTAAAAGAATGAGAGACTATAAATAAATTTTTCTTCCAAATAA
* * * * *
2500 ATGAATTTTTCTGCACAGTTCTTGAGGCAAGCATTTAATTATAGTCTGTTTTAATAAAAAATATA
66 ATGAATTTTTCTACACAGTTCCTAAGGCAAGCATTCAATTAGAGTCTGTTTTAATAAAAAATATA
* *
2565 AAAAATTCAACTTCAAATCAATTTTGAGATTATAAAACCA
131 AAAAATTCAACTTCAAATCAATTATGAAATTATAAAACCA
*
2605 TTTAAAGTGAGT
1 TTTAAAGCGAGT
Statistics
Matches: 152, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
170 50 0.33
171 95 0.62
172 7 0.05
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (170 bp):
TTTAAAGCGAGTAATAAAGCTTTTAAAAGAATGAGAGACTATAAATAAATTTTTCTTCCAAATAA
ATGAATTTTTCTACACAGTTCCTAAGGCAAGCATTCAATTAGAGTCTGTTTTAATAAAAAATATA
AAAAATTCAACTTCAAATCAATTATGAAATTATAAAACCA
Done.