Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402879.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_593.0, 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: 5357
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.23
Warning! 1954 characters in sequence are not A, C, G, or T
Found at i:1078 original size:171 final size:170
Alignment explanation
Indices: 787--1586 Score: 907
Period size: 170 Copynumber: 4.7 Consensus size: 170
777 NNNNNNNNNN
** * *
787 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGGAATGGGTGACTAGAAATGGACTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTT
* * * * ** * *
852 TTCTTGC-CAATGAAT-GCTTTTTTCTTCATGTTTCTC-GATGAAGAAATTGAATTATTCTCTGT
66 TTCTT-CTCAATGAATAGC-TTTTTCTACATGTTTCCCAG-GGTAGGCATTCAATTATTGTCTGT
* *
914 TTTAATAAAAAATGTAAACAAATTCAACTTAAAATTAATTATGA
128 TTTAATGAAAAATGTAAA-AAATTCAACTTAAAATCAATTATGA
* * *
958 GATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTGAAGCAATAGGTGACTATAAATGAACTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTT
* * *
1023 TTGTTCTCAATGAATAGCTTTTTCTACACGTTTCCCAGGGTAGGCATTCAATTATTGTCCGTTTT
66 TTCTTCTCAATGAATAGCTTTTTCTACATGTTTCCCAGGGTAGGCATTCAATTATTGTCTGTTTT
1088 AATGAAAAATGTAAAAAATTCAACTTAAAATCAATTATGA
131 AATGAAAAATGTAAAAAATTCAACTTAAAATCAATTATGA
* * * * * *
1128 GATTATAAAACCATTTAAAACGAGTAATGAGACTTTT-CATGAAAAGGTTGACTATAAATGGACT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGG-TGACTATAAATGGACT
* * * * * * * *
1192 TTTCTTCTCAATGAATGGCTTTTTTTTCATGTTTTCTAAGGTAGGCATTCAATTCTTGTTTGTTT
65 TTTCTTCTCAATGAATAGCTTTTTCTACATGTTTCCCAGGGTAGGCATTCAATTATTGTCTGTTT
*
1257 TAATGAAAAATGTAAAAAATTCAACTTAAAATCAGTTATGA
130 TAATGAAAAATGTAAAAAATTCAACTTAAAATCAATTATGA
* * * * *
1298 GATTATAAAACCATTTAAAGTGAGTAATGAGGCTTTTGACGAAATAGGTGACTATAAATAGACTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTT
* *** * *
1363 TTCTTAC-CAATGAATACCTTTTTCCT-CATGCTTTTTGA-GGTAGACAATCAATTATTGTCTGT
66 TTCTT-CTCAATGAATAGCTTTTT-CTACATG-TTTCCCAGGGTAGGCATTCAATTATTGTCTGT
* * * *
1425 TTTAATCAAAAATATAAAAAAAATCAACTTAAAAAT-AAATATGA
128 TTTAATGAAAAATGT-AAAAAATTCAACTT-AAAATCAATTATGA
** * *
1469 GATTATAAAACCATTTAAAGCGAGTAATAATACTTTTGAAGGAATAGGTGACAATAAATGGATTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTT
* * * * *
1534 TTTTTCTTAATGAATAGTTTTTTCTACATGTTTCAC-GAGGTAAGCATTCAATT
66 TTCTTCTCAATGAATAGCTTTTTCTACATGTTTCCCAG-GGTAGGCATTCAATT
1587 CTTGCTAATA
Statistics
Matches: 532, Mismatches: 83, Indels: 28
0.83 0.13 0.04
Matches are distributed among these distances:
169 6 0.01
170 279 0.52
171 239 0.45
172 8 0.02
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (170 bp):
GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTT
TTCTTCTCAATGAATAGCTTTTTCTACATGTTTCCCAGGGTAGGCATTCAATTATTGTCTGTTTT
AATGAAAAATGTAAAAAATTCAACTTAAAATCAATTATGA
Found at i:1484 original size:341 final size:339
Alignment explanation
Indices: 787--1590 Score: 964
Period size: 341 Copynumber: 2.4 Consensus size: 339
777 NNNNNNNNNN
* ** *
787 GATTATAAAACCATTTAAAGCGAGTAATAAGGC-TTTCAAAGGAATGGGTGACTAGAAATGGACT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTC-AA-GAAAAGGTGACTATAAATGGACT
* * * ** * * *
851 TTTCTTGC-CAATGAATGCTTTTTTCTTCATGTTTCTCGATGAAGAAATTGAATTATTCTCTGTT
64 TTTCTT-CTCAATGAATGCTTTTTTCTTCATGTTTCT-AAGGTAGGCATTCAATTCTTGTCTGTT
*
915 TTAATAAAAAATGTAAACAAATTCAACTTAAAATTAATTATGAGATTATAAAACCATTTAAAGCA
127 TTAATAAAAAATGTAAACAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCA
* * *
980 AGTAATAAGGCTTTTGAAGCAATAGGTGACTATAAATGAACTTTTGTTCTCAATGAATAGCTTTT
192 AGTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGAACTTTTCTTCTCAATGAATACCTTTT
* * * * *
1045 TCTACACGTTTCCCAGGGTAGGCATTCAATTATTGTCCGTTTTAATGAAAAATGTAAAAAATTCA
257 TCTACACGTTTCCCAGGGTAGACAATCAATTATTGTCCGTTTTAATCAAAAATATAAAAAAATCA
*
1110 ACTTAAAATCAATTATGA
322 ACTTAAAATCAAATATGA
* * *
1128 GATTATAAAACCATTTAAAACGAGTAATGAGACTTTTCATGAAAAGGTTGACTATAAATGGACTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTCAAGAAAAGG-TGACTATAAATGGACTT
*
1193 TTCTTCTCAATGAATGGCTTTTTT-TTCATGTTTTCTAAGGTAGGCATTCAATTCTTGTTTGTTT
65 TTCTTCTCAATGAAT-GCTTTTTTCTTCATG-TTTCTAAGGTAGGCATTCAATTCTTGTCTGTTT
* * **
1257 TAATGAAAAATGTAAA-AAATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTTAAAGTGA
128 TAATAAAAAATGTAAACAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAA
* *
1321 GTAATGAGGCTTTTGACGAAATAGGTGACTATAAAT-AGACTTTTCTTAC-CAATGAATACCTTT
193 GTAATAAGGCTTTTGAAGAAATAGGTGACTATAAATGA-ACTTTTCTT-CTCAATGAATACCTTT
* *** *
1384 TTCCT-CATGCTTTTTGA-GGTAGACAATCAATTATTGTCTGTTTTAATCAAAAATATAAAAAAA
256 TT-CTACACG-TTTCCCAGGGTAGACAATCAATTATTGTCCGTTTTAATCAAAAATAT-AAAAAA
1447 ATCAACTTAAAAAT-AAATATGA
318 ATCAACTT-AAAATCAAATATGA
* * * * *
1469 GATTATAAAACCATTTAAAGCGAGTAATAATACTTTTGAAGGAATAGGTGACAATAAATGGATTT
1 GATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTCAA-GAAAAGGTGACTATAAATGGACTT
* * * *
1534 TTTTTCTTAATGAATAG-TTTTTTCTACATGTTTC-ACGAGGTAAGCATTCAATTCTTG
65 TTCTTCTCAATGAAT-GCTTTTTTCTTCATGTTTCTA--AGGTAGGCATTCAATTCTTG
1591 CTAATAGGTA
Statistics
Matches: 398, Mismatches: 50, Indels: 30
0.83 0.10 0.06
Matches are distributed among these distances:
339 2 0.01
340 153 0.38
341 215 0.54
342 28 0.07
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (339 bp):
GATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTCAAGAAAAGGTGACTATAAATGGACTTT
TCTTCTCAATGAATGCTTTTTTCTTCATGTTTCTAAGGTAGGCATTCAATTCTTGTCTGTTTTAA
TAAAAAATGTAAACAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTA
ATAAGGCTTTTGAAGAAATAGGTGACTATAAATGAACTTTTCTTCTCAATGAATACCTTTTTCTA
CACGTTTCCCAGGGTAGACAATCAATTATTGTCCGTTTTAATCAAAAATATAAAAAAATCAACTT
AAAATCAAATATGA
Found at i:2060 original size:258 final size:258
Alignment explanation
Indices: 1599--2071 Score: 613
Period size: 258 Copynumber: 1.8 Consensus size: 258
1589 TGCTAATAGG
* * *
1599 TAAAATCAATTATGAGATTATAAAATTATTTAAAGTGAGTAATGAGGCTTTTATAGGAATGAGTG
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATGAGGCTTTTAAAGGAATGAGTG
* * * * *
1664 ACTATAAATAGACTTTTCTTGCTAATAATTATCTTTTTCTTCATGTTTCTATAGATAGACGTTCA
66 ACTATAAATAGACTTTTCTTGCTAATAATTAGCTTCTTCTACACGTTTCTATAGATAGACATTCA
* * *
1729 ATTATTGTCTGTTTAATGAAAAATATAAAAATAATTGAACATAAATCAATTTCAAGATTATAAAA
131 ATTATAGTCTGTTTAATGAAAAATATAAAAACAATTCAACATAAATCAATTTCAAGATTATAAAA
*
1794 CTATTTAAAGGGAGTAATAACAATTATAGTTTGTTTTAACTAAAAATGTAAAAAAATTCAACT
196 CTATTTAAAGCGAGTAATAACAATTATAGTTTGTTTTAACTAAAAATGTAAAAAAATTCAACT
*
1857 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAA-GAAGGCTTTTAAAGGAATGGGT
1 TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATG-AGGCTTTTAAAGGAATGAGT
* * *
1921 GAAC-ATAAATAGACTTTTC-T-CTCAATGAA-TGGCTTCTTCTACACGTTTCTCA-AGGTAGGC
65 G-ACTATAAATAGACTTTTCTTGCT-AAT-AATTAGCTTCTTCTACACGTTTCT-ATAGATAGAC
* * * * *
1981 ATTCAATTATAGTCTATTTTAGTGAAAAAT-TTAAAACAATTCAACTTAAAATCAATTAT-GAGA
126 ATTCAATTATAGTCT-GTTTAATGAAAAATATAAAAACAATTCAACAT-AAATCAATT-TCAAGA
2044 TTATAAAA-TCATTTAAAGCGAGTAATAA
188 TTATAAAACT-ATTTAAAGCGAGTAATAA
2072 GGCTTTTGAA
Statistics
Matches: 185, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
256 2 0.01
257 54 0.29
258 126 0.68
259 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (258 bp):
TAAAATCAATTATGAGATTATAAAAATATTTAAAGCGAGTAATGAGGCTTTTAAAGGAATGAGTG
ACTATAAATAGACTTTTCTTGCTAATAATTAGCTTCTTCTACACGTTTCTATAGATAGACATTCA
ATTATAGTCTGTTTAATGAAAAATATAAAAACAATTCAACATAAATCAATTTCAAGATTATAAAA
CTATTTAAAGCGAGTAATAACAATTATAGTTTGTTTTAACTAAAAATGTAAAAAAATTCAACT
Found at i:2107 original size:170 final size:170
Alignment explanation
Indices: 1813--2259 Score: 528
Period size: 170 Copynumber: 2.6 Consensus size: 170
1803 GGGAGTAATA
* * *
1813 ACAATTATAGTTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
1 ACAATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * *
1878 AAAAAT-ATTTAAAGCGAGTAAGAAGGCTTTTAAAGGAATGGGTGAACATAAATAGAC-TTTTCT
66 -AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAACATAAACAGACTTTTTCT
* * *
1941 CTCAATGAATGGCTTCTT-CTACACGTTTCTCA-AGGTAGGCAT
130 CTAAATGAAT-G-TTCTTGCTACACATTTCTCATA-GTAGACAT
* *** * *
1983 TCAATTATAGTCTATTTTAGTGAAAAATTTAAAACAATTCAACTTAAAATCAATTATGAGATTAT
1 ACAATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* *
2048 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGT-AGCTATAAACAGACTTTTTTT
66 AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAAC-ATAAACAGACTTTTTCT
* * * * *
2112 GTAAATGAATGTTTTTGTTTCACATTTCTTATAGTAGACAT
130 CTAAATGAATGTTCTTGCTACACATTTCTCATAGTAGACAT
* * * *
2153 ACAATTATAGTCTGTTTTAACCATAAATGTAAAAAAATTCAACTTAAAATTAATTTTGAGATTAT
1 ACAATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* ** *
2218 AAAA-CTGTTTAAAATGAGTAATAAGGCATTTGAAGGAATGGG
66 AAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGG
2260 AGAATACCTT
Statistics
Matches: 236, Mismatches: 35, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
169 12 0.05
170 210 0.89
171 14 0.06
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (170 bp):
ACAATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
AAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAACATAAACAGACTTTTTCTC
TAAATGAATGTTCTTGCTACACATTTCTCATAGTAGACAT
Found at i:4027 original size:170 final size:169
Alignment explanation
Indices: 3502--4159 Score: 732
Period size: 171 Copynumber: 3.9 Consensus size: 169
3492 NNNNNNNNNG
* * * * **
3502 AGATTATAAAACTATTTAAAACGAGTAATGAGGCTTTTGAGGGAATGAGTTACTATAAATGGACT
1 AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGGCTATAAATGGACT
* * * * * * * * * *
3567 TTTCTTGCCACTAAAT-ACCTTTTTCTTTACGTTTTTTGAGATAGTCTTTAAATTATAGTCTATT
66 TTTCTTGCCAATGAATGA--TTTTTC-TCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTT
* * *
3631 TTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATG
128 TTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATC
* *
3673 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTTAAGGAATGGGTGGCTATAAATGGACT
1 AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGGCTATAAATGGACT
* * * * *
3738 TTTCTTGCCAATGAATCCTATTTTT-TCACGTTTCTTAAGGTAGACATTCAGTTATAATCTGTTT
66 TTTCTTGCCAATGAAT--GATTTTTCTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTT
* * * * *
3802 TGACTAAAAATATAAGAAAAATTGAATTTAAAATCAATTTTC
129 TAACCAAAAATATAA-AAAAATTCAACTTAAAATCAATTATC
* * **
3844 AGATTATAAAACTATTTAATGTGAGTAATAAGGCTTTTGAAGGAATGGGTGGCT-TTGATGGA-T
1 AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGGCTATAAATGGACT
* * * * *
3907 GTTTCTTGCCTATGAATGAGTTTTTCTCCATGTTTCTCGAGGTACACATTTAATTATTGTCTGTT
66 -TTTCTTGCCAATGAATGA-TTTTTCT-CATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTT
*
3972 TTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATC
128 TTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATC
* * **
4014 A-AGTTATAAAACTATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATAGGTAACTATAAATGGAC
1 AGA-TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGGCTATAAATGGAC
* * *
4078 TTTGCTTGCCAATGAATGCATTTTTCTTCATGTCTCTTGAGGTAGACATTCAATTATTGTCTGTT
65 TTTTCTTGCCAATGAATG-ATTTTTC-TCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTT
*
4143 TTAACCAGAAATATAAA
128 TTAACCAAAAATATAAA
4160 TAGACTTTTC
Statistics
Matches: 408, Mismatches: 66, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
168 1 0.00
169 7 0.02
170 132 0.32
171 259 0.63
172 8 0.02
174 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (169 bp):
AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGGCTATAAATGGACT
TTTCTTGCCAATGAATGATTTTTCTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTA
ACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATC
Done.