Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4404.0, 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: 1766
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Found at i:1002 original size:513 final size:507
Alignment explanation
Indices: 1--1762 Score: 1899
Period size: 513 Copynumber: 3.4 Consensus size: 507
** * * *
1 ATCTGTTTTAATAAAAAACGTAAAACAATTCCACTTCAAATCAAGTATGAGATTATAAAACTATT
1 ATCTGTTTTAATAAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAAC-ATT
* * * *
66 TAAAGCTG-GTAATAAGGCTTTTAAATGCATGGGTGACTATAAATGGACTTTTCTTACCAATGAA
64 TAAAG-TGAGTAATAAGGCTTTGAAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAA
* * * * * *
130 TGGCTTTTTACTCAAAT-TTTCATAGGTAGACATTCAAGTGTAATTTGTTTTAACCAAAAATATA
128 TAGCTTTTTACTC-AATGTTTCCTACGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATA
* * * * *
194 AAAAAATTTAACTTAAAATTAATTATGGGATTAGAAAATTATTTAAAGA-CAGTAATAAAGCTTT
192 AAAAAATTCAACTTAAAATCAATTATGAGATTAGAAAATCATTTAAA-ATGAGTAATAAAGCTTT
* * * * *
258 TGAAGGCATGGGTGACAATAAATGGACTTTTCTAGCTAATGAATGACTTTTTCTTCACGTTTTCA
256 TGAAGGCAT-GGTGACTATAAATGGACTTTTATTGCCAATGAATGACTTTTTCTTCACGTTTTTA
* * *
323 AGGGTAGAGATTCAATTATTATCTATTTTAACAAAAAATATAAAAACAATTCAACTCAAAATCAA
320 A-GGTAGACATTCAATTATTATCTATTTTAATAAAAAATATAAAAA-AATTCAACTTAAAATCAA
* * *
388 TTATGAGATTGTAAAACCGTTCAAAGCGAGTAATAAGACTTTTGAAGG-TATGGGTGACTAGAAA
383 TTATGAGATTGTAAAACCGTTTAAAGCCAGTAATAAGACTTTTGAAGGCTA-GGGTGACTACAAA
* *
452 TGGAGTTTTCTTGCCAATGAATAT-TTTCTTCTTCATGTTTCTCAAGTAGACATTCAATTATA
447 TGGACTTTTCTT-ACAATGAATATCTTT-TTCTTCATGTTTCTCAAGTAGACATTCAATTATA
** * * * *
514 ATCTGTTTTAATAAAAAAGGTAAACAAATTTAACTTAAAATGATTTATGAGATTAGAAAATCATT
1 ATCTGTTTTAATAAAAAATATAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAA-CATT
* * * *
579 TAAAGTGAGTAATAAGCCTTTGGAAGGCATAAGTGACTATAAATGGACCTTTCTTGCCAATGAAT
64 TAAAGTGAGTAATAAGGCTTTGAAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * * **
644 ATCTTTGTT-TTC-ATGTTTCCTAACGTACAGATTCAATTATAACCTGTTTTAATAAAAATATAT
129 AGCTTT-TTACTCAATGTTTCCT-ACGTAGACATTCAATTATAATCTGTTTTAACCAAAA-ATAT
*
707 AAAAAAATTCAACTTAAAATCAATTATGAGATTAGAAAATCATTTAAAATGAGTAATAAGGCTTT
191 AAAAAAATTCAACTTAAAATCAATTATGAGATTAGAAAATCATTTAAAATGAGTAATAAAGCTTT
* * *
772 TGAAGGCATGGATGACTATAAATGGACTTTTTTTGCCAATGAATGGCTTTTTCTTCATGTTTCTT
256 TGAAGGCATGG-TGACTATAAATGGACTTTTATTGCCAATGAATGACTTTTTCTTCACGTTT-TT
* * * * *
837 AAGGCAAACATTCAATTATTATCTATTTTAATGAAAAATATAAAAAAATTGAACTTAAAATTAAT
319 AAGGTAGACATTCAATTATTATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAAT
* * *
902 TATGAGGTTGTAAAACCGTTTAAAGCCAGTAATAAGAATTTCGAAGGCTAGGGTGACTACAAATG
384 TATGAGATTGTAAAACCGTTTAAAGCCAGTAATAAGACTTTTGAAGGCTAGGGTGACTACAAATG
* * * *
967 GACTTTTCTTACTAATGACTATCTTTTCCTTCATGTTTGTCGAGTAGACATTCAATTATA
449 GACTTTTCTTAC-AATGAATATCTTTTTCTTCATGTTTCTCAAGTAGACATTCAATTATA
* * * * *
1027 ATATGTTTTAATAAAAAATATAAAAACATTTAACTAAAAATCAATTATGAGAATATAAAAACAAT
1 ATCTGTTTTAATAAAAAATATAAAAA-ATTCAACTTAAAATCAATTATGAGATTAT-AAAACATT
* ** * * * *
1092 TAAAGTAAAAAATTAGGCTTTCG-AAGGCATGGGTGACTATAAATGGACTTTTCTCGTCAATGAA
64 TAAAGTGAGTAATAAGGCTTT-GAAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAA
* * ** *
1156 -AGGCTTTTT-CTCAACGTTTCTCGA-GATAGATGTTCAATTATAATCTGTTTTAA-TAAAAA-A
128 TA-GCTTTTTACTCAATGTTTC-CTACG-TAGACATTCAATTATAATCTGTTTTAACCAAAAATA
** * * * *
1216 TAAAAAAATTCAACTTAAAGCCAATTATTAGATTATAAAACCATTTAAAGTGAGTAATAAAGCTT
190 TAAAAAAATTCAACTTAAAATCAATTATGAGATTAGAAAATCATTTAAAATGAGTAATAAAGCTT
* * *
1281 TTGAAAGCATAGGTGACTATAAATGGACTTTTATTGCCAATGAAT-ATATTTTTCTTTACGTTTT
255 TTGAAGGCAT-GGTGACTATAAATGGACTTTTATTGCCAATGAATGA-CTTTTTCTTCACGTTTT
* * * * * * * *
1345 TCAAGTTTGACATTCAATTATAATCTATTTTAATCAAAAATA-AATAAAATTCAATTTCAAGTCA
318 T-AAGGTAGACATTCAATTATTATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * * *
1409 ATTATTAGATTATTAAACCATTTAAAGCCAGTAATAAGGCTTTTGAAGGCATA-GGTGACTATAA
382 ATTATGAGATTGTAAAACCGTTTAAAGCCAGTAATAAGACTTTTGAAGGC-TAGGGTGACTACAA
* * *
1473 GTGGACTTTTCCTAACAATAAATATCTTTTTCTTCATGTTTC-CTAACGTAGACATTCAATTATA
446 ATGGACTTTT-CTTACAATGAATATCTTTTTCTTCATGTTTCTC-AA-GTAGACATTCAATTATA
* * ** * *
1537 ATTTATTGCAATAAAAAATATAAAAAAATTCAACTTCAAATCGATTATGAGATTATAAAACCATT
1 ATCTGTTTTAATAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CATT
* ** * *
1602 TAAAGCGAGTAATAAGGCTTTGAAAAACTTAGGTGACTATAAATAGG-CTTTTCTTGCTAATGAA
64 TAAAGTGAGTAATAAGGCTTTGAAAGGCATAGGTGACTATAAAT-GGACTTTTCTTGCCAATGAA
* * * * * *
1666 TGGCTTTTT-CTTCAA-GTTTCCTTAGGTAGACATTCAACTGTAATATGTTTTAACCAAAAATGT
128 TAGCTTTTTAC-TCAATGTTTCC-TACGTAGACATTCAATTATAATCTGTTTTAACCAAAAATAT
* *
1729 AAAAAAATTAAACTTAAAGTCAATTATGAGATTA
191 AAAAAAATTCAACTTAAAATCAATTATGAGATTA
1763 TAAA
Statistics
Matches: 1047, Mismatches: 165, Indels: 75
0.81 0.13 0.06
Matches are distributed among these distances:
508 1 0.00
509 108 0.10
510 296 0.28
511 22 0.02
512 52 0.05
513 397 0.38
514 168 0.16
515 3 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (507 bp):
ATCTGTTTTAATAAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACATTTA
AAGTGAGTAATAAGGCTTTGAAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATAG
CTTTTTACTCAATGTTTCCTACGTAGACATTCAATTATAATCTGTTTTAACCAAAAATATAAAAA
AATTCAACTTAAAATCAATTATGAGATTAGAAAATCATTTAAAATGAGTAATAAAGCTTTTGAAG
GCATGGTGACTATAAATGGACTTTTATTGCCAATGAATGACTTTTTCTTCACGTTTTTAAGGTAG
ACATTCAATTATTATCTATTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
TTGTAAAACCGTTTAAAGCCAGTAATAAGACTTTTGAAGGCTAGGGTGACTACAAATGGACTTTT
CTTACAATGAATATCTTTTTCTTCATGTTTCTCAAGTAGACATTCAATTATA
Found at i:1763 original size:171 final size:170
Alignment explanation
Indices: 1--1766 Score: 1676
Period size: 171 Copynumber: 10.3 Consensus size: 170
** * * * * *
1 ATCTGTTTTAATAAAAAACGTAAAACAATTCCACTTCAAATCAAGTATGAGATTATAAAACTATT
1 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * *
66 TAAAGCTG-GTAATAAGGCTTTTAAATGCATGGGTGACTATAAATGGACTTTTCTTACCAATGAA
66 TAAAGC-GAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAA
* * *
130 TGGCTTTTTAC-TCAAAT-TTTCATAGGTAGACATTCAAGTGTA
130 TGGCTTTTT-CTTC--ATGTTTCTTAGGTAGACATTCAATTATA
* ** * * * * **
172 ATTTGTTTTAACCAAAAATATAAAAAAATTTAACTTAAAATTAATTATGGGATTAGAAAATTATT
1 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * * *
237 TAAAGAC-AGTAATAAAGCTTTTGAAGGCATGGGTGACAATAAATGGACTTTTCTAGCTAATGAA
66 TAAAG-CGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAA
* * * * *
301 TGACTTTTTCTTCACGTTT-TCAAGGGTAGAGATTCAATTATT
130 TGGCTTTTTCTTCATGTTTCT-TA-GGTAGACATTCAATTATA
* * * * *
343 ATCTATTTTAACAAAAAATATAAAAACAATTCAACTCAAAATCAATTATGAGATTGTAAAACCGT
1 ATCTGTTTTAATAAAAAATATAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * * * *
408 TCAAAGCGAGTAATAAGACTTTTGAAGGTATGGGTGACTAGAAATGGAGTTTTCTTGCCAATGAA
65 TTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAA
** * *
473 T-ATTTTCTTCTTCATGTTTCTCAAGTAGACATTCAATTATA
130 TGGCTTT-TTCTTCATGTTTCTTAGGTAGACATTCAATTATA
** * * * * * *
514 ATCTGTTTTAATAAAAAAGGTAAACAAATTTAACTTAAAATGATTTATGAGATTAGAAAATCATT
1 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * * *
579 TAAAGTGAGTAATAAGCCTTTGGAAGGCATAAGTGACTATAAATGGACCTTTCTTGCCAATGAAT
66 TAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
** * * * *
644 ATCTTTGTT-TTCATGTTTCCTAACGTACAGATTCAATTATA
131 GGCTTT-TTCTTCATGTTT-CTTAGGTAGACATTCAATTATA
* * *
685 ACCTGTTTTAATAAAAATATATAAAAAAATTCAACTTAAAATCAATTATGAGATTAGAAAATCAT
1 ATCTGTTTTAATAAAAA-ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
** *
750 TTAAAATGAGTAATAAGGCTTTTGAAGGCAT-GGATGACTATAAATGGACTTTTTTTGCCAATGA
65 TTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGG-TGACTATAAATGGACTTTTCTTGCCAATGA
* * *
814 ATGGCTTTTTCTTCATGTTTCTTAAGGCAAACATTCAATTATT
129 ATGGCTTTTTCTTCATGTTTCTT-AGGTAGACATTCAATTATA
* * * * * * *
857 ATCTATTTTAATGAAAAATATAAAAAAATTGAACTTAAAATTAATTATGAGGTTGTAAAACCGTT
1 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* ** * * * * *
922 TAAAGCCAGTAATAAGAATTTCGAAGGC-TAGGGTGACTACAAATGGACTTTTCTTACTAATGAC
66 TAAAGCGAGTAATAAGGCTTTTGAAGGCATA-GGTGACTATAAATGGACTTTTCTTGCCAATGAA
** * * *
986 TATCTTTTCCTTCATGTTT-GTCGAGTAGACATTCAATTATA
130 TGGCTTTTTCTTCATGTTTCTTAG-GTAGACATTCAATTATA
* * * * * * *
1027 ATATGTTTTAATAAAAAATATAAAAACATTTAACTAAAAATCAATTATGAGAATATAAAAACAAT
1 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
** ** * * * * * *
1092 TAAAGTAAAAAATTAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTCGTCAATGAAA
66 TAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * **
1157 GGCTTTTTC-TCAACGTTTCTCGAGATAGATGTTCAATTATA
131 GGCTTTTTCTTC-ATGTTTCT-TAGGTAGACATTCAATTATA
** *
1198 ATCTGTTTTAAT-AAAAA-ATAAAAAAATTCAACTTAAAGCCAATTATTAGATTATAAAACCATT
1 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * *
1261 TAAAGTGAGTAATAAAGCTTTTGAAAGCATAGGTGACTATAAATGGACTTTTATTGCCAATGAAT
66 TAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
*** * * * *
1326 ATATTTTTCTTTACGTTT-TTCAAGTTTGACATTCAATTATA
131 GGCTTTTTCTTCATGTTTCTT--AGGTAGACATTCAATTATA
* * * * * * * *
1367 ATCTATTTTAATCAAAAATA-AATAAAATTCAATTTCAAGTCAATTATTAGATTATTAAACCATT
1 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * ** *
1431 TAAAGCCAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAGTGGACTTTTCCTAACAATAAAT
66 TAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
** * *
1496 ATCTTTTTCTTCATGTTTCCTAACGTAGACATTCAATTATA
131 GGCTTTTTCTTCATGTTT-CTTAGGTAGACATTCAATTATA
* * ** * *
1537 ATTTATTGCAATAAAAAATATAAAAAAATTCAACTTCAAATCGATTATGAGATTATAAAACCATT
1 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
** * *
1602 TAAAGCGAGTAATAAGGC-TTTGAAAAACTTAGGTGACTATAAATAGG-CTTTTCTTGCTAATGA
66 TAAAGCGAGTAATAAGGCTTTTG-AAGGCATAGGTGACTATAAAT-GGACTTTTCTTGCCAATGA
* * *
1665 ATGGCTTTTTCTTCAAGTTTCCTTAGGTAGACATTCAACTGTA
129 ATGGCTTTTTCTTCATGTTT-CTTAGGTAGACATTCAATTATA
* ** * * *
1708 ATATGTTTTAACCAAAAATGTAAAAAAATTAAACTTAAAGTCAATTATGAGATTATAAA
1 ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
Statistics
Matches: 1296, Mismatches: 266, Indels: 66
0.80 0.16 0.04
Matches are distributed among these distances:
168 1 0.00
169 132 0.10
170 383 0.30
171 536 0.41
172 243 0.19
173 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
ATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
TAAAGCGAGTAATAAGGCTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
GGCTTTTTCTTCATGTTTCTTAGGTAGACATTCAATTATA
Done.