Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402050.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5145.0, 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: 2237
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.27
Warning! 645 characters in sequence are not A, C, G, or T
Found at i:314 original size:171 final size:171
Alignment explanation
Indices: 1--314 Score: 371
Period size: 171 Copynumber: 1.8 Consensus size: 171
* * *
1 AAACAGACTATAATTGAATGTCTACCTTAAGAAACGTGAAGAAACAAGCATTCAGTTAAAAGAAA
1 AAACAGACTATAATTAAATGTCAACCTCAAGAAACGTGAAGAAACAAGCATTCAGTTAAAAGAAA
* * * * ****
66 CGTCTATTTAGAGTCACCCATTCTTTCATAAAGCTTATTACTCGCTTTAAATGGTTTTATANNNN
66 AGTCCATTTAGAGTCACCCATTCTTTCATAAAGCTTATAACCCGCTTTAAATGGTTTTATAATCT
******
131 NNNNNNTGATTTTTAGTTAAATTTTTTTATATTTTTTATTA
131 CATAATTGATTTTTAGTTAAATTTTTTTATATTTTTTATTA
* * * *
172 AAACATACTATAATTAAATGTCAACCTCGAGAAACGTGAAGAAACAAGCATTGA-TTGAGAAGAA
1 AAACAGACTATAATTAAATGTCAACCTCAAGAAACGTGAAGAAACAAGCATTCAGTT-AAAAGAA
* * **
236 AAGTCCATTTATAGTTACTTATTCTTTCA-AAAGCCTTATAACCCGCTTTAAATGGTTTTATAAT
65 AAGTCCATTTAGAGTCACCCATTCTTTCATAAAG-CTTATAACCCGCTTTAAATGGTTTTATAAT
300 CTCATAATTGATTTT
129 CTCATAATTGATTTT
315 ANNNNNNNNN
Statistics
Matches: 116, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
170 6 0.05
171 110 0.95
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.36
Consensus pattern (171 bp):
AAACAGACTATAATTAAATGTCAACCTCAAGAAACGTGAAGAAACAAGCATTCAGTTAAAAGAAA
AGTCCATTTAGAGTCACCCATTCTTTCATAAAGCTTATAACCCGCTTTAAATGGTTTTATAATCT
CATAATTGATTTTTAGTTAAATTTTTTTATATTTTTTATTA
Found at i:517 original size:171 final size:161
Alignment explanation
Indices: 340--667 Score: 330
Period size: 172 Copynumber: 2.0 Consensus size: 161
330 ACATTTTTCT
*
340 TTAAAATAGACTATAATTGAA-AGCCTACCTCTT-GAAAGGTATAGAAAAAAC-CATTCATTGAG
1 TTAAAATAGACTATAATTGAATA--CT-CCTCTTGGAAACGTATAGAAAAAACTCATTCATTGA-
*
402 AAGAAAAAG-CCATTT-TTAGTCACCCATTCCTTCAAAAGGC-TTATTATCCGATTTTAA-T-AG
62 AAGAAAAAGTCCATTTGTT-GTCACCCATTCCTTCAAAA-GCATTATTATCCG-GTTTAACTGA-
*
462 TTTTATAATTTCATAATTGATTTTAAGTTGAATTGTNNNNNNNNNNTTG
123 TTTTATAATCTCATAATTGATTTTAAGTTGAATTGT----------TTG
** * * *
511 TTAAAATAGACTATAATTGAATACTTGTCTTGGGAAACGTATAGAAAAAGCTTATTCATTGACAG
1 TTAAAATAGACTATAATTGAATACTCCTCTT-GGAAACGTATAGAAAAAACTCATTCATTGAAAG
* * *
576 CAAAAGTCCATTTGTTGTCACCCGTTCCTTCAAAAGCATTATTATTCGGTTTAACTGATTTTATA
65 AAAAAGTCCATTTGTTGTCACCCATTCCTTCAAAAGCATTATTATCCGGTTTAACTGATTTTATA
641 ATCTCATAATTGATTTTAAGTTGAATT
130 ATCTCATAATTGATTTTAAGTTGAATT
668 TTTTTACATT
Statistics
Matches: 137, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
169 4 0.03
170 2 0.01
171 51 0.37
172 77 0.56
173 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.36
Consensus pattern (161 bp):
TTAAAATAGACTATAATTGAATACTCCTCTTGGAAACGTATAGAAAAAACTCATTCATTGAAAGA
AAAAGTCCATTTGTTGTCACCCATTCCTTCAAAAGCATTATTATCCGGTTTAACTGATTTTATAA
TCTCATAATTGATTTTAAGTTGAATTGTTTG
Found at i:1785 original size:173 final size:170
Alignment explanation
Indices: 1436--2112 Score: 542
Period size: 170 Copynumber: 4.0 Consensus size: 170
1426 NNNNNNNNNN
* *
1436 TGATTTTAAGTTGAATTTTTTTATATTTTTTGTTAAAACAGTCTATAATTGAATATCTGCCTCAA
1 TGATTTTAAGTTGAATTTTTTTATA-TTTTTGTTAAAACAGACTATAATTGAATATCTACCTCAA
* * * * *
1501 GAAACATGTAAACAAAGCCATTCACTGAGAAGAAAAGTCTATTTATAGTCACCTATTCCTTCAAA
65 GAAACATGAAAAAAAAGCCATTCACTGAGAAAAAAAATCTATTTATAGTCACCCATTCCTTCAAA
* ********** * *
1566 AGGCTTATNNNNNNNNNNAAATGGTTTTATAATCTCATAAT
130 AGGCATATTACCCGCTTTAAATGCTCTTATAATCTCATAAT
* * * *
1607 TGATTTTAGGTTGAATTTTTTTATACTTTTTGTTAAAACAGACAATAATTGAATGTCTACCTCGA
1 TGATTTTAAGTTGAATTTTTTTATA-TTTTTGTTAAAACAGACTATAATTGAATATCTACCTCAA
*
1672 GAAACATGCAAAAAAAAGCCATTCACTGAGAAAAAAAAATCTATTTTTAGTCACCCATTCCTTCA
65 GAAACATG-AAAAAAAAGCCATTCACTGAG-AAAAAAAATCTATTTATAGTCACCCATTCCTTCA
* *
1737 AAAGGCATATTACCCGCTTTTAATTCTCTTATAATCTCATAAT
128 AAAGGCATATTACCCGCTTTAAATGCTCTTATAATCTCATAAT
* * *
1780 TGATTTTAAGTTGAATTTTTTTATATTTTT-TTAAAAATAGACTATAATTGAATA-CTTGCCTTA
1 TGATTTTAAGTTGAATTTTTTTATATTTTTGTT-AAAACAGACTATAATTGAATATC-TACCTCA
* * * * * * * * * * * * *
1843 GGAAACGTG-TAGAAAGGCTTATTCATTGGGAACAAAAGTCCAGTTATAGTCACACATTCCTTCA
64 AGAAACATGAAAAAAAAGC-CATTCACTGAGAAAAAAAATCTATTTATAGTCACCCATTCCTTCA
* * *********** * *
1907 AAAGCCTTATTACTNNNNNNNNNNGATTTTATAATCTCATAAT
128 AAAGGCATATTACCCGCTTTAAATGCTCTTATAATCTCATAAT
* * * *
1950 TG-TTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTAAATACCTACC-CTA
1 TGATTTTAAGTTGAATTTTTTTATATTTTT-GTTAAAACAGACTATAATTGAATATCTACCTC-A
* * * *
2013 ACAAACAT-AAAAAAAAGCCATTCATTGAGAAGAAAAGTAC-ATTTATAGTCACCCATT-CTCTC
64 AGAAACATGAAAAAAAAGCCATTCACTGAGAAAAAAAAT-CTATTTATAGTCACCCATTCCT-TC
* ** * * * *
2075 AAAAAGTTTATTACTCGATTTAAATGGTTTTATAATCT
127 AAAAGGCATATTACCCGCTTTAAATGCTCTTATAATCT
2113 NNNNNNNNNN
Statistics
Matches: 398, Mismatches: 96, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
168 2 0.01
169 84 0.21
170 97 0.24
171 80 0.20
172 53 0.13
173 82 0.21
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (170 bp):
TGATTTTAAGTTGAATTTTTTTATATTTTTGTTAAAACAGACTATAATTGAATATCTACCTCAAG
AAACATGAAAAAAAAGCCATTCACTGAGAAAAAAAATCTATTTATAGTCACCCATTCCTTCAAAA
GGCATATTACCCGCTTTAAATGCTCTTATAATCTCATAAT
Found at i:2108 original size:169 final size:172
Alignment explanation
Indices: 1436--2112 Score: 565
Period size: 171 Copynumber: 4.0 Consensus size: 172
1426 NNNNNNNNNN
** * *
1436 TGATTTTAAGTTGAATTTTTTTATATTTTTTGTTAAAACAGTCTATAATTGAATATCT-GCCTCA
1 TGATTTTAAGTTGAATTTTTTTATA-TTTTTGTTAAAACAGAATATAATTGAATACCTACCCTCA
* * *
1500 AGAAACATGTAAACAAAGCCATTCACTGAGAAGAAAAGT-CTATTTATAGTCACCTATTCCTTCA
65 AGAAACATGAAAAAAAAGCCATTCACTGAGAAGAAAAGTACTATTTATAGTCACCCATTCCTTCA
* **********
1564 AAAGGCTTATNNNNNNNNNNAAATGGTTTTATAATCTCATAAT
130 AAAAGCTTATTACTCGATTTAAATGGTTTTATAATCTCATAAT
* **
1607 TGATTTTAGGTTGAATTTTTTTATACTTTTTGTTAAAACAGACA-ATAATTGAATGTCTA-CCTC
1 TGATTTTAAGTTGAATTTTTTTATA-TTTTTGTTAAAACAGA-ATATAATTGAATACCTACCCTC
* ** *
1670 GAGAAACATGCAAAAAAAAGCCATTCACTGAGAA-AAAAAAATCTATTTTTAGTCACCCATTCCT
64 AAGAAACATG-AAAAAAAAGCCATTCACTGAGAAGAAAAGTA-CTATTTATAGTCACCCATTCCT
* * * * * ** *
1734 TCAAAAGGCATATTACCCGCTTTTAATTCTCTTATAATCTCATAAT
127 TCAAAAAGCTTATTACTCGATTTAAATGGTTTTATAATCTCATAAT
* * ** *
1780 TGATTTTAAGTTGAATTTTTTTATATTTTT-TTAAAAATAGACTATAATTGAATA-CTTGCCTTA
1 TGATTTTAAGTTGAATTTTTTTATATTTTTGTT-AAAACAGAATATAATTGAATACCTACCCTCA
* * * * * * * * * * * *
1843 GGAAACGTG-TAGAAAGGCTTATTCATTGGGAACAAAAGT-CCAGTTATAGTCACACATTCCTTC
65 AGAAACATGAAAAAAAAGC-CATTCACTGAGAAGAAAAGTACTATTTATAGTCACCCATTCCTTC
********** *
1906 -AAAAGCCTTATTACTNNNNNNNNNNGATTTTATAATCTCATAAT
129 AAAAAG-CTTATTACTCGATTTAAATGGTTTTATAATCTCATAAT
* *
1950 TG-TTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAATATAATTAAATACCTACCCT-A
1 TGATTTTAAGTTGAATTTTTTTATATTTTT-GTTAAAACAGAATATAATTGAATACCTACCCTCA
* *
2013 ACAAACAT-AAAAAAAAGCCATTCATTGAGAAGAAAAGTAC-ATTTATAGTCACCCATT-CTCTC
65 AGAAACATGAAAAAAAAGCCATTCACTGAGAAGAAAAGTACTATTTATAGTCACCCATTCCT-TC
*
2075 AAAAAGTTTATTACTCGATTTAAATGGTTTTATAATCT
129 AAAAAGCTTATTACTCGATTTAAATGGTTTTATAATCT
2113 NNNNNNNNNN
Statistics
Matches: 395, Mismatches: 93, Indels: 38
0.75 0.18 0.07
Matches are distributed among these distances:
168 2 0.01
169 84 0.21
170 87 0.22
171 90 0.23
172 57 0.14
173 75 0.19
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (172 bp):
TGATTTTAAGTTGAATTTTTTTATATTTTTGTTAAAACAGAATATAATTGAATACCTACCCTCAA
GAAACATGAAAAAAAAGCCATTCACTGAGAAGAAAAGTACTATTTATAGTCACCCATTCCTTCAA
AAAGCTTATTACTCGATTTAAATGGTTTTATAATCTCATAAT
Found at i:2222 original size:340 final size:331
Alignment explanation
Indices: 1590--2235 Score: 619
Period size: 339 Copynumber: 1.9 Consensus size: 331
1580 NNNNAAATGG
* *
1590 TTTTATAATCTCATAATTGATTTTAGGTTGAATTTTTTTATACTTTTTGTTAAAACAGACAATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTTGTTAAAACAGACAATAA
* ** * * *
1655 TTGAATGTCTACCTCGAGAAACATGCAAAAAAAAGCCATTCACTGAGAAAAAAAAATCTATTTTT
66 TTAAATACCTACCTCAACAAACAT-CAAAAAAAAGCCATTCACTGAGAAAAAAAAATCTATTTAT
* * * *
1720 AGTCACCCATTCCTTCAAAAGGCATATTACCCGCTTTTAATTCTCTTATAATCTCATAATTGATT
130 AGTCACCCATTCCTTCAAAAAGCATATTACCCGATTTAAATGCTCTTATAATCTCATAATTGATT
* * * *
1785 TTAAGTTGAATTTTTTTATATTTTTTTAAAAATAGACTATAATTGAATACTTGCCTTAGGAAACG
195 TTAAGTTGAATTTTTCTACATTTTTTTAAAAATA-ACTATAATTAAATACTTACCTTAGGAAACG
* **** * *
1850 TGTAGAAAGGCTTATTCATTGGGAACAAAAGTCCAGTTATAGTCACACATTCCTTCAAAAGCCTT
259 TGAAGAAACAAGTATTCATTGAGAACAAAAGTCCAGTTAGAGTCACACATTCCTTCAAAAGCCTT
1915 ATTACTNNNNNNNNNNGA
324 ATTACT----------GA
1933 TTTTATAATCTCATAATTG-TTTTAAGTTGAATTTTTTTACA-TTTTTGGTTAAAACAGA-ATAT
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTT-GTTAAAACAGACA-AT
* * *
1995 AATTAAATACCTACC-CTAACAAACAT-AAAAAAAAGCCATTCATTGAG-AAGAAAAGTAC-ATT
64 AATTAAATACCTACCTC-AACAAACATCAAAAAAAAGCCATTCACTGAGAAAAAAAAAT-CTATT
** * * * *******
2056 TATAGTCACCCATT-CTCTCAAAAAGTTTATTACTCGATTTAAATGGTTTTATAATCTNNNNNNN
127 TATAGTCACCCATTCCT-TCAAAAAGCATATTACCCGATTTAAATGCTCTTATAATCTCATAATT
*** **
2120 NNNTTTAAGTTGAATTTTTCTACATTTTTGATTAAAAGAT-ACTATAATTAAATGTTTACC-TAG
191 GATTTTAAGTTGAATTTTTCTACATTTTT--TTAAAA-ATAACTATAATTAAATACTTACCTTAG
* * *
2183 TGAAACGTGAAGAAACAAGTATTCATTGATAAGAAAAGTCCATTTAGAGTCAC
253 -GAAACGTGAAGAAACAAGTATTCATTGAGAACAAAAGTCCAGTTAGAGTCAC
2236 CC
Statistics
Matches: 248, Mismatches: 46, Indels: 21
0.79 0.15 0.07
Matches are distributed among these distances:
338 2 0.01
339 81 0.33
340 79 0.32
341 13 0.05
342 54 0.22
343 19 0.08
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.36
Consensus pattern (331 bp):
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTTGTTAAAACAGACAATAA
TTAAATACCTACCTCAACAAACATCAAAAAAAAGCCATTCACTGAGAAAAAAAAATCTATTTATA
GTCACCCATTCCTTCAAAAAGCATATTACCCGATTTAAATGCTCTTATAATCTCATAATTGATTT
TAAGTTGAATTTTTCTACATTTTTTTAAAAATAACTATAATTAAATACTTACCTTAGGAAACGTG
AAGAAACAAGTATTCATTGAGAACAAAAGTCCAGTTAGAGTCACACATTCCTTCAAAAGCCTTAT
TACTGA
Done.