Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399614.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2866.0, 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: 5127
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.33
Warning! 610 characters in sequence are not A, C, G, or T
Found at i:910 original size:171 final size:171
Alignment explanation
Indices: 1--1946 Score: 978
Period size: 171 Copynumber: 11.4 Consensus size: 171
* *
1 AATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGGATTCAATGGCAAGAAATGTCTATTTAT
1 AATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTTAT
* * ** * *
66 AGCCACCT-ATTCCTTAAAAAGCCTTATTACTCATTTTGAATGGTTTTATAATCTCATAATT-AT
66 AGTCA-CTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGAT
* **********
129 TTTAAGTTGAATTTTTTTAC-ATNNNNNNNNNNACAGACTAT
130 TTTAAGTTGAATTTTTTTACGTTTTTAGTTAAAACAGACTAT
* * * * * *
170 AATTGAATGTCTACCTTAAGAAACATGAAAAAAAATGTATTC-ATAGGTAAGGAAAGTCCATTTA
1 AATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGGATTCAAT-GGCAAGAAAAGTCCATTTA
* * * ********** *
234 CAGTCACTTATTCTTTCAAAAGCCTTATTACTCGNNNNNNNNNNTTTTATAATCTCATAATTGAT
65 TAGTCACTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGAT
* * * *
299 TTTGATTTAAATTTTCTTATA-TTTTTTA-TTAAAACAGACTAT
130 TTTAAGTTGAATTTT-TT-TACGTTTTTAGTTAAAACAGACTAT
* * * *** * * * *
341 AATTGAATGCCTAACTC-AGAAA-ATGTGTAGAAAAAACTATTTATTGGGAAGAAAAGTTCATTT
1 AATTGAATGTCTACCTCAAGAAACA--TGAAGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTT
* * * * **********
404 ACAGTCGCTTATTCCTTCAAAACCCTTATTACTCGCTTTAAATGGTNNNNNNNNNNCATAATTGA
64 ATAGTCACTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGA
* * * *
469 TTTTAATTTGAATTATTTTACATTTTT-GATTAAAACAGACAAT
129 TTTTAAGTTGAATTTTTTTACGTTTTTAG-TTAAAACAGACTAT
* * * * ** * * **
512 ATTTGTATATCTACCTCGAGAAACATGAAG-AAAAGATAATCATTGATAAGAAAAGTCCATTTAT
1 AATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTTAT
** ********** * * * *
576 AGTCACCCATNNNNNNNNNNGCCTTATTACTCGCTTTAAATGGTTTTACAATCTCAAAATTTATT
66 AGTCACTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGATT
* ** * * * * *
641 TTAGGTTGAATTTTTTTATATTTATAATGAATATAGACTAT
131 TTAAGTTGAATTTTTTTACGTTTTTAGTTAAAACAGACTAT
* ** * * * *
682 AATTGAATGTCGACCAT-GGGAAATATGAAGAAAAACGTATTCATTTGG-AAGAAAAGTCCATTT
1 AATTGAATGTCTACC-TCAAGAAACATGAAGAAAAAGGGATTCA-ATGGCAAGAAAAGTCCATTT
* ** ** * * * **********
745 ATAGTCTCTCGTTTTTTTAAAAGCATTATTACTCGCTTTAAATGATTTTANNNNNNNNNNATTGA
64 ATAGTCACTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGA
* * *
810 TTTTAAGTTGAATTTTTTTACGTTTTTGGGTAAAACAGACTAA
129 TTTTAAGTTGAATTTTTTTACGTTTTTAGTTAAAACAGACTAT
* * * *
853 AATTAAATGTTTACCACAAGAAACATGACA-AAAAAGGGATTCAATGGCAACAAAAGTCCATTTA
1 AATTGAATGTCTACCTCAAGAAACATGA-AGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTTA
* * **********
917 TAGTCACTAATTCTTTCGAAAGCCTTATTACTCGCTTTAAATGGTNNNNNNNNNNCATAATTGAT
65 TAGTCACTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGAT
* *
982 TTTAAGTTAAATTTTTTTACGTTTTTAATTAAAACAGACTAT
130 TTTAAGTTGAATTTTTTTACGTTTTTAGTTAAAACAGACTAT
* * * * ** *
1024 AATTGAATGTCTACCTCATGAAACGTGAAGAAAAAGAGATTCAATGGCAAGGAAAGTCTTTTTTT
1 AATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGGATTCAATGGCAAGAAAAGTC-CATTTA
* *
1089 TA-TCACTAATTCCTTCAAAAGCCTTATTAGTCACTTTAAATGGTTTTATAATTTCATAATTGAT
65 TAGTCACTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGAT
* ** * *
1153 TTTAAGTTGAGTTTTTTTAAATTTTTTGTTAAAACGGACTAT
130 TTTAAGTTGAATTTTTTTACGTTTTTAGTTAAAACAGACTAT
*
1195 AATTGAATGTCTACCTCAAGAAACATAAAGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTTAT
1 AATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTTAT
* * ******
1260 AGTCA-TCCATTCCTTCAAAA-CGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATNNNNNN
66 AGTCACT-AATTCCTTCAAAAGC-CTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGA
**** * *
1323 NNNNAAGTTGAATTTTTTTACATTTTT-GTTTAAACAGACTAT
129 TTTTAAGTTGAATTTTTTTACGTTTTTAGTTAAAACAGACTAT
* ** ** * * * * * * *
1365 AATTGAATGTCTACGTTGAGAAATGTGAAGAAAAAAGTATTTATTGGTAAGAAAAATCTATTTAT
1 AATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTTAT
* * * ********** *
1430 AGTCACCT-ATTCTTTCGAAAGCCTTATTACTCGTTTTNNNNNNNNNNATAATCTCATAATTGAT
66 AGTCA-CTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGAT
* * * * *
1494 TTTAAATTAAAGTTTTTATA--TTTTTCA-TTAAAATATACTAT
130 TTTAAGTTGAA-TTTTTTTACGTTTTT-AGTTAAAACAGACTAT
* ** * * ** * * * **
1535 AATTGAATGTCTGACTTGGA-AAATATGTAGAAAAAGCTATGCATTGGGAAGAAAAGTTTATTTA
1 AATTGAATGTCT-ACCTCAAGAAACATGAAGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTTA
* * ** * ********** *
1599 CAGTCGCCCATTCCTTCAAAAACCTTATTACTCGNNNNNNNNNNTTTTATAATCTCATAATTGAT
65 TAGTCACTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGAT
** * ** * **
1664 TTTAAGTCCAATTATTTTATATTTTT-GATTAAAATAGAAAAT
130 TTTAAGTTGAATTTTTTTACGTTTTTAG-TTAAAACAGACTAT
* * ** * * * *
1706 AATT-ATATATCTACCTCGAGAAACATGAAGAAAAAGATAGTCATTGACAAAAAAAGTCCATTTA
1 AATTGA-ATGTCTACCTCAAGAAACATGAAGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTTA
** * * * * * * *
1770 TAGTCACCCATTCCTTTAAAACCCTTAGTACTCGCTTTAAATGGTTCTATAATCTCAAAATCGAT
65 TAGTCACTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGAT
* * ** * *
1835 TTTAGGTTTGATTTTTTTTATATTTCTCAAG--AAAATAGACTAT
130 TTTAAG-TTGAATTTTTTTACGTTT-T-TAGTTAAAACAGACTAT
* * * *** * *
1878 AATTGAATGACAACCGT-AGGAAACATGAAGAAAAATATATTCATTTGG-AAGAAAAGTCTATTT
1 AATTGAATGTCTACC-TCAAGAAACATGAAGAAAAAGGGATTCA-ATGGCAAGAAAAGTCCATTT
1941 ATAGTC
64 ATAGTC
1947 TCCCATTTCT
Statistics
Matches: 1343, Mismatches: 387, Indels: 91
0.74 0.21 0.05
Matches are distributed among these distances:
168 4 0.00
169 112 0.08
170 385 0.29
171 740 0.55
172 94 0.07
173 7 0.01
175 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.36
Consensus pattern (171 bp):
AATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGGATTCAATGGCAAGAAAAGTCCATTTAT
AGTCACTAATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTCATAATTGATT
TTAAGTTGAATTTTTTTACGTTTTTAGTTAAAACAGACTAT
Found at i:3200 original size:170 final size:171
Alignment explanation
Indices: 2853--3201 Score: 407
Period size: 170 Copynumber: 2.0 Consensus size: 171
2843 NNNNNNNNNN
* * * *
2853 TTTCTTACCAATGAATACCTTTTTCTTCATGTTTCTTAAGGTAGACATTCAATTGTAGTCTGTTT
1 TTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTTAAAGTAGACATTCAATTATACTCTGTTT
* **********
2918 TAACTAAACATATAAAAAAAGTTAGCTTAAAATCAATTATGAGATTATANNNNNNNNNNAAGCGA
66 TAACAAAACATATAAAAAAAGTTAGCTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA
* * * *
2983 GTAATAAGGCTCTTGAAGGAATAGGTGACTATAAATAGACT
131 CTAATAAGGCTCTTGAAGGAATAGGTGACCAAAAATAGACC
*
3024 TTTCTTGCCATTGAAT-CCATTTTTCTTCATGTTTCTTAAAGTAGACATTCAATTATACTCTGTT
1 TTTCTTGCCAATGAATACC-TTTTTCTTCATGTTTCTTAAAGTAGACATTCAATTATACTCTGTT
* * * *
3088 TTAA-AAAATATATAAAAACATTTAGCTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTG
65 TTAACAAAACATATAAAAAAAGTTAGCTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCG
* * * *
3152 ACTAATAGGGCT-TTCGAAGTAATTGGTGACCAAAAATGGACC
130 ACTAATAAGGCTCTT-GAAGGAATAGGTGACCAAAAATAGACC
3194 TTTCTTGC
1 TTTCTTGC
3202 TNNNNNNNNN
Statistics
Matches: 148, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
169 2 0.01
170 86 0.58
171 60 0.41
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.36
Consensus pattern (171 bp):
TTTCTTGCCAATGAATACCTTTTTCTTCATGTTTCTTAAAGTAGACATTCAATTATACTCTGTTT
TAACAAAACATATAAAAAAAGTTAGCTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGA
CTAATAAGGCTCTTGAAGGAATAGGTGACCAAAAATAGACC
Found at i:5060 original size:170 final size:169
Alignment explanation
Indices: 4408--5112 Score: 635
Period size: 170 Copynumber: 4.1 Consensus size: 169
4398 NNNNNNNNNN
* * * *
4408 TGACTATAAATAGACTTTTCTTACCAATAAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATT
1 TGACTATAAATAGACTTTTCTTACCATTGAATCCTTTTTTCTTCATGTTTCTCGAGGTAGACATT
* * **********
4473 CAATTATGGTCTGTTTAAACAAAAATGTAAAAAAATTCAACTTAAAATNNNNNNNNNNATTATAA
66 CAATTATAGTCTGTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTATAA
*
4538 AACCATTTAAAGCGAGTAATAAAGG-TTTTGAAGGAATGG
131 AACCATTTAAAGCGACTAAT-AAGGCTTTTGAAGGAATGG
* * *
4577 CTGACTATAAATAGACTTTTCTTACCATTGAAT-CTTGTTTTCTTTATATTTCTTGAGGTAGACA
1 -TGACTATAAATAGACTTTTCTTACCATTGAATCCTT-TTTTCTTCATGTTTCTCGAGGTAGACA
********* *
4641 TTCAATTATAGTCTGTTTTAA-CAAAAANNNNNNNNNNATTCAACTTAAAATCAATTACGAAATT
64 TTCAATTATAGTCTG-TTTAACCAAAAA-TGTAAAAAAATTCAACTTAAAATCAATTATGAAATT
*
4705 ATAAAACCATTTAAAGTGACTAATAAGGCTTTTGAAGGAATTGG
127 ATAAAACCATTTAAAGCGACTAATAAGGCTTTTGAAGGAA-TGG
** * * * * * * *
4749 TGAGAGAAAAAAAGACTTTCCTTGCCATTGAATCCCTTTTTCTTCATGTGTCTTGAGGTAGACAT
1 TGA-CTATAAATAGACTTTTCTTACCATTGAATCCTTTTTTCTTCATGTTTCTCGAGGTAGACAT
* * * ******
4814 TCAATTATAGTCTGTTTGAGCTAAAAACGTAAAAAAATTCAACTTAAAATCAATTATGANNNNNN
65 TCAATTATAGTCTGTTT-AACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTAT
**** * * * *
4879 NNNNCTATTTAAAGCGAGTAATAAGGCTTTCGAAGGTATGAG
129 AAAACCATTTAAAGCGACTAATAAGGCTTTTGAAGGAATG-G
* * * * *
4921 TTACTATAAATGGACTTTTCTTGCCATTGAATCCTTTTTT-TGTCATGTTTCTCGTGGTAAACAT
1 TGACTATAAATAGACTTTTCTTACCATTGAATCCTTTTTTCT-TCATGTTTCTCGAGGTAGACAT
*
4985 TCAATTATAGTCTGTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATGAAATTATA
65 TCAATTATAGTCTGTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTATA
** * * **
5050 AAATTATTTAAAGCGACTAATAATGCTTTTAAAAAAATGGG
130 AAACCATTTAAAGCGACTAATAAGGCTTTTGAAGGAAT-GG
* * *
5091 AGACCATAAATGGACTTTTCTT
1 TGACTATAAATAGACTTTTCTT
5113 CCAAATGAAT
Statistics
Matches: 421, Mismatches: 102, Indels: 24
0.77 0.19 0.04
Matches are distributed among these distances:
169 3 0.01
170 162 0.38
171 129 0.31
172 120 0.29
173 7 0.02
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
TGACTATAAATAGACTTTTCTTACCATTGAATCCTTTTTTCTTCATGTTTCTCGAGGTAGACATT
CAATTATAGTCTGTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAAATTATAA
AACCATTTAAAGCGACTAATAAGGCTTTTGAAGGAATGG
Done.