Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402195.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5283.0, 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: 4868
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.31
Warning! 999 characters in sequence are not A, C, G, or T
Found at i:738 original size:171 final size:168
Alignment explanation
Indices: 424--948 Score: 545
Period size: 171 Copynumber: 3.1 Consensus size: 168
414 NNNNNNNNNN
* * ** * * *
424 CCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATTCTCTCAAAATTGATTTCATGT
1 CCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGT
* * * ** * *
489 TTATTTCTTTTACATTTTTTGTTAAAACAAATTATAATTGAATGCCTA-CCTCAAGAAATATGAA
66 TGAATT-TTTTACA-TTTTTG-TAAAACAAACTATAATTGAATGCCTACCCT-GGGAAACATGTA
* * *
553 CAAAAAGGCATTCATTG-GCAAGAAAAGTCCATTTATAAT-TAC
127 GAAAAAGCCATTCATTGAG-AAGAAAAGTCCATTTATAGTCT-C
* *
595 CCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATGGATTAATAATCTCATAATTGATTTTAAGT
1 CCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGT
* * *
660 TGAATCTTTTTACATTTTTGGCTAAAATAGACTATAGTTGAATGCCTACCCTGGGAAACATGTAG
66 TGAAT-TTTTTACATTTTT-G-TAAAACAAACTATAATTGAATGCCTACCCTGGGAAACATGTAG
* * *
725 AAAAAACCATTCATTGAGAAGGAAAGTCTATTTATAGTCTC
128 AAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCTC
* * * *
766 TCGTTCCTTT-AAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCATGATTTG-TTTTAA
1 CCATT-CTTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAT-AATTGATTTTAA
* * *
829 GTTGAA-TTTTT-GA----T-TAAAACAAACTATAATTGATTGCCTACCATGGGAAACATGTAGA
64 GTTGAATTTTTTACATTTTTGTAAAACAAACTATAATTGAATGCCTACCCTGGGAAACATGTAGA
** *
887 AAAAGTAATTCATTGAGAA-AAAAATCCATTTATAGTCTC
129 AAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCTC
926 CCATTCTTTCAAAAGCCTTATTA
1 CCATTCTTTCAAAAGCCTTATTA
949 NNNNNNNNNN
Statistics
Matches: 300, Mismatches: 46, Indels: 27
0.80 0.12 0.07
Matches are distributed among these distances:
159 4 0.01
160 33 0.11
161 55 0.18
164 1 0.00
168 1 0.00
169 5 0.02
170 5 0.02
171 182 0.61
172 14 0.05
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (168 bp):
CCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGT
TGAATTTTTTACATTTTTGTAAAACAAACTATAATTGAATGCCTACCCTGGGAAACATGTAGAAA
AAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCTC
Found at i:2038 original size:170 final size:171
Alignment explanation
Indices: 1070--2091 Score: 763
Period size: 171 Copynumber: 6.0 Consensus size: 171
1060 NNNNNNNNNN
** ** ** * * ** *
1070 AATGTCTACCTTGAGAAATGTGAAGAAAAAAACATTCATTGGTAAAAAAAGTTTATTTATAATCT
1 AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAATCA
* * **********
1135 CTCATTCCTTCAAAAGCCTTATTACTCACTTTNNNNNNNNNNATAATCTAATAATTGATTTTAAG
66 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTAATAATTGATTTTAAG
*
1200 TT-AATTTTTTT-TACATTTTTGTTTAAAATAGATTATAATTG
131 TTGAATTTTTTTATA-ATTTTAG-TTAAAATAGATTATAATTG
* * * **
1241 AATGTCTAGCTCAAGAAATATGAAGAAAAAGGCATTGATTGG-AAGGAAAAGTCCATTTATGCTC
1 AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAA-GAAAAGTCCATTTATAATC
* * *
1305 ACCCATTCCATCAAAAGCCTTGTTACTCACTTT-AATGGTTTTATAATCTCAA-AATTGATTTTA
65 ACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCT-AATAATTGATTTTA
* * **
1368 ACG-TGAATTCTTTGTA-CATTTTTTTCTAAAATAGATTATAATTG
129 A-GTTGAATT-TTTTTATAATTTTAGT-TAAAATAGATTATAATTG
*********** * * *
1412 AATGTCTACCTTNNNNNNNNNNAAGAAAAAGGCATTCATTGACAAGAAAAGTTCTTTTA-AAGTC
1 AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAA-TC
* * * * * ** * *
1476 ACTCGTTCCTTAAAAAGCCGTATTACTCGCATTAAATAATTTTATAATCTCATAATTGATTTTAG
65 ACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTAATAATTGATTTTAA
* **********
1541 GTTGAATTTTTTTATATTTTTAGNNNNNNNNNNTTATAATTG
130 GTTGAATTTTTTTATAATTTTAGTTAAAATAGATTATAATTG
* * * * * *
1583 AATGTTTACCTTAGGAAACATGAAGAAAAAGGCATTCATTAGCAAGACAAGTCCATTTATAATTA
1 AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAATCA
* * * * * *
1648 CCCATTCTTTCAAAAGTCTTATTACTCGCTTTAAACGCTTTTATAATCTCATAATTGGTTTTAAG
66 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTAATAATTGATTTTAAG
* * *
1713 TTGAAGTTTTTTATATTTTTAGTTAAAATAGACTATAATTG
131 TTGAATTTTTTTATAATTTTAGTTAAAATAGATTATAATTG
* * * * * ** * *
1754 AATGTCTACCTCAAGAACCATAAAGAAAAAAGAATTCATCGATAAGAAAAGTCTATTTATAGTCA
1 AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAATCA
* ********** *
1819 CCCATT--TATCAAAAGCCTTATTACTCACTTTNNNNNNNNNNATAATCTAAAAATTGATTTTAA
66 CCCATTCCT-TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTAATAATTGATTTTAA
* * * *
1882 TTTGAA-TTCTTTATACATTTTGGTTAAAATAGATTATAATTA
130 GTTGAATTTTTTTATA-ATTTTAGTTAAAATAGATTATAATTG
* * * * *
1924 AATATCTGCCTCAAGAAACGTGAA-AAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAATCT
1 AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAATCA
* * * * *
1988 TCCATTCGTTCAAAAGTCTTATTACTCGCTTTAAATGGTTTTACAATCTAATAATTAATTTTAAG
66 CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTAATAATTGATTTTAAG
* * *
2053 TTTAATTTTTTTATATTTTTAGTTAAAACAGATTATAAT
131 TTGAATTTTTTTATAATTTTAGTTAAAATAGATTATAAT
2092 NNNNNNNNNN
Statistics
Matches: 648, Mismatches: 184, Indels: 39
0.74 0.21 0.04
Matches are distributed among these distances:
169 47 0.07
170 174 0.27
171 384 0.59
172 43 0.07
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (171 bp):
AATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAATCA
CCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTAATAATTGATTTTAAG
TTGAATTTTTTTATAATTTTAGTTAAAATAGATTATAATTG
Found at i:3662 original size:171 final size:169
Alignment explanation
Indices: 3240--4075 Score: 643
Period size: 171 Copynumber: 4.9 Consensus size: 169
3230 NNNNNNNNNT
* *
3240 AATCTCATAATTGATTTTAAGTTGAAGTTTTTTACATTTTTGC-TTAAAATAGATTATAATTGAA
1 AATCTCATAATTGATTTTAAGTTGAAATTTTTTACATTTTT-CATTAAAACAGATTATAATTGAA
* * * * *
3304 TGTCTACCTCGAGAAACATAAAGAAAAAGGTATTCATTGGCGAGAAAAGTGCA--TATAGTCACC
65 TGTCTGCCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGT-CATTTATAGTCA-C
* * * *
3367 CATTCCTTTAAAAGCTTTATT-CTCGCTTTAAATGGTTTTAT
128 CATTCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTAC
* * * * * * * *
3408 TATCCCAAAATTGATTATATGTTCAATTTTTTTTACATTTTT-AGTTAGAACAGATTATAATTGA
1 AATCTCATAATTGATTTTAAGTTGAA-ATTTTTTACATTTTTCA-TTAAAACAGATTATAATTGA
* * **
3472 ATCTCTGTCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCTCGAAAAGTCTATTTATAGTCAC
64 ATGTCTGCCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTC-ATTTATAGTCAC
*
3537 CAAATCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTAC
128 C-ATTCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTAC
* * * *
3580 AATCTCATAATGGATTTTAAGTTGAAATTTTTTACATTTTTCATCAAAACATACTATAATTGAAT
1 AATCTCATAATTGATTTTAAGTTGAAATTTTTTACATTTTTCATTAAAACAGATTATAATTGAAT
* * * * * * * *
3645 GTCTGCCTTGGGAAACATGTAGAGAAAGCCAATAATTGAG-AAGAAAGGTCCATTTATAGTCTCT
66 GTCTGCCTTGAGAAACATGAAGAAAAAGGCATTCATTG-GCAAGAAAAGT-CATTTATAGTCAC-
* * *
3709 CATTCTTTCAAAAGCCTTATTACTCAT-TTTAAATAGTTTTAT
128 CATTCCTTCAAAAGCCTTATTACTC-TCTTTAAATGGTTTTAC
*********** **
3751 NNNNNNNNNNNTGATTTTAAGTTG-AATGTTTTTACATTTTTGGTTAAAACAGATTATAATTGAA
1 AATCTCATAATTGATTTTAAGTTGAAAT-TTTTTACATTTTTCATTAAAACAGATTATAATTGAA
* * ** * * *********
3815 TCTCTACCTTGAGAAAGGTAAAGAAAAAGACATTCATTGGCAAGAAANNNNNNNNNNTAGTCACC
65 TGTCTGCCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAA-AGTCATTTATAGTCA-C
* * * *
3880 CATTCTTTCGAAAGCCTTATTTCT-TGCTTTAAATGGTTTTAT
128 CATTCCTTCAAAAGCCTTATTACTCT-CTTTAAATGGTTTTAC
* * * * ***
3922 AATCTCATAATTCATTTTAAG-TCAAATTGTTTTATATTTTTTATTTGGACAGATTATAATTGAA
1 AATCTCATAATTGATTTTAAGTTGAAATT-TTTTACATTTTTCATTAAAACAGATTATAATTGAA
*** * * *
3986 TGTGAACCTGGAGAAACATGAAGAAAAAGCCATAT-ATTGAG-AAGAAAAGTCCATTTATAGTCT
65 TGTCTGCCTTGAGAAACATGAAGAAAAAGGCAT-TCATTG-GCAAGAAAAGT-CATTTATAGTCA
*
4049 CTCATTTCTTCAAAAGCCTTATTACTC
127 C-CATTCCTTCAAAAGCCTTATTACTC
4076 GCTTNNNNNN
Statistics
Matches: 510, Mismatches: 132, Indels: 48
0.74 0.19 0.07
Matches are distributed among these distances:
168 21 0.04
169 77 0.15
170 9 0.02
171 358 0.70
172 45 0.09
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.37
Consensus pattern (169 bp):
AATCTCATAATTGATTTTAAGTTGAAATTTTTTACATTTTTCATTAAAACAGATTATAATTGAAT
GTCTGCCTTGAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCATTTATAGTCACCAT
TCCTTCAAAAGCCTTATTACTCTCTTTAAATGGTTTTAC
Found at i:3878 original size:342 final size:331
Alignment explanation
Indices: 3437--4075 Score: 712
Period size: 342 Copynumber: 1.9 Consensus size: 331
3427 TGTTCAATTT
* ** *
3437 TTTTTACATTTTTAGTTAGAACAGATTATAATTGAATCTCTGTCTTGAGAAACATGAAGAAAAAG
1 TTTTTACATTTTTAGTTAAAACAGATTATAATTGAATCTCTACCTTGAGAAACATAAAGAAAAAG
* **
3502 GCATTCATTGGCTCGAAAAGTCTATTTATAGTCACCAAATCCTTCAAAAGCCTTATTACTCT-CT
66 ACATTCATTGGCAAGAAAAGTCTATTTATAGTCACCAAATCCTTCAAAAGCCTTATTACT-TGCT
* *
3566 TTAAATGGTTTTACAATCTCATAATGGATTTTAAGTTGAAATT-TTTTACATTTTTCATCAAAAC
130 TTAAATGGTTTTACAATCTCATAATGCATTTTAAG-TCAAATTGTTTTACATTTTTCATCAAAAC
* ** * * *
3630 ATACTATAATTGAATGTCTGCCTTGG-GAAACATGTAGAGAAAGCCA-ATAATTGAGAAGAAAGG
194 AGACTATAATTGAATGTCAACC-TGGAGAAACATGAAGAAAAAGCCATAT-ATTGAGAAGAAAAG
3693 TCCATTTATAGTCTCTCA-TTCTTTCAAAAGCCTTATTACTCATTTTAAATAGTTTTATNNNNNN
257 TCCATTTATAGTCTCTCATTTC-TTCAAAAGCCTTATTACTCATTTTAAATAGTTTTAT------
3757 NNNNNTGATTTTAAGTTGAATG
315 -----TGATTTTAAGTTGAATG
* **
3779 TTTTTACATTTTTGGTTAAAACAGATTATAATTGAATCTCTACCTTGAGAAAGGTAAAGAAAAAG
1 TTTTTACATTTTTAGTTAAAACAGATTATAATTGAATCTCTACCTTGAGAAACATAAAGAAAAAG
********** * * * * *
3844 ACATTCATTGGCAAGAAANNNNNNNNNNTAGTCACCCATTCTTTCGAAAGCCTTATTTCTTGCTT
66 ACATTCATTGGCAAGAAAAGTCTATTTATAGTCACCAAATCCTTCAAAAGCCTTATTACTTGCTT
* * * * ****
3909 TAAATGGTTTTATAATCTCATAATTCATTTTAAGTCAAATTGTTTTATATTTTTTATTTGGACAG
131 TAAATGGTTTTACAATCTCATAATGCATTTTAAGTCAAATTGTTTTACATTTTTCATCAAAACAG
* *
3974 ATTATAATTGAATGTGAACCTGGAGAAACATGAAGAAAAAGCCATATATTGAGAAGAAAAGTCCA
196 ACTATAATTGAATGTCAACCTGGAGAAACATGAAGAAAAAGCCATATATTGAGAAGAAAAGTCCA
4039 TTTATAGTCTCTCATTTCTTCAAAAGCCTTATTACTC
261 TTTATAGTCTCTCATTTCTTCAAAAGCCTTATTACTC
4076 GCTTNNNNNN
Statistics
Matches: 249, Mismatches: 43, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
341 10 0.04
342 234 0.94
343 5 0.02
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.36
Consensus pattern (331 bp):
TTTTTACATTTTTAGTTAAAACAGATTATAATTGAATCTCTACCTTGAGAAACATAAAGAAAAAG
ACATTCATTGGCAAGAAAAGTCTATTTATAGTCACCAAATCCTTCAAAAGCCTTATTACTTGCTT
TAAATGGTTTTACAATCTCATAATGCATTTTAAGTCAAATTGTTTTACATTTTTCATCAAAACAG
ACTATAATTGAATGTCAACCTGGAGAAACATGAAGAAAAAGCCATATATTGAGAAGAAAAGTCCA
TTTATAGTCTCTCATTTCTTCAAAAGCCTTATTACTCATTTTAAATAGTTTTATTGATTTTAAGT
TGAATG
Found at i:4732 original size:171 final size:168
Alignment explanation
Indices: 4443--4868 Score: 429
Period size: 171 Copynumber: 2.5 Consensus size: 168
4433 NNNNNNNNNT
* * * * * * * *
4443 TTTTTTATATTTTTTG-TTAACACAGACTATATTTGAATGTTTGCCTCAACAAATGTGTAGAAAA
1 TTTTTTATA-TTTTGGATTAA-ACAGACTATAATTGAATGTCTACCTAAAGAAAGGTGAAGAAAA
* * * * * * * *
4507 AGCCATTTATTGAG-AAAAAAAATCCATTTATAGT-A-TCTTTTTCCTTCAAAAGCCTTATTACA
64 AGCCATTCACT-AGCAAGAAAAGTTCATTTATAATAACTCATTTT--TTCTAAAGCCTTATTAC-
*
4569 TAC-TTTAAATAGTTTTATAA-CTTTATAA-TTAGTTTTAAGTTGAGT
125 T-CGTTTAAATAGTTTTATAATC-TTATAATTTA-TTTTAAGTTGA-A
** * *
4614 TTTTTTATATTTTTTATTAAAACAGACTATAATTGAATGTCTATCTTGAA-AAAGGTGAAGAAAA
1 TTTTTTATATTTTGGATT-AAACAGACTATAATTGAATGTCTA-CCTAAAGAAAGGTGAAG-AAA
*
4678 AAG-TATTCACTAGCAAGAAAAGTTCATTTATAATAACTCATTTTTTCTAAAGCCTTATTACTCG
63 AAGCCATTCACTAGCAAGAAAAGTTCATTTATAATAACTCATTTTTTCTAAAGCCTTATTACTCG
4742 TTTTAAATAGTTTTATAATCTTATAATTTATTTTAAGTTGAA
128 -TTTAAATAGTTTTATAATCTTATAATTTATTTTAAGTTGAA
* * *
4784 TTTTTTATATTTTGGCTTAAACAGATTATAATTGAATGTCTACCTAAAGAAATGTGAAGAAAAAG
1 TTTTTTATATTTTGGATTAAACAGACTATAATTGAATGTCTACCTAAAGAAAGGTGAAGAAAAAG
*
4849 CCATTCACTAGGAAGAAAAG
66 CCATTCACTAGCAAGAAAAG
Statistics
Matches: 215, Mismatches: 27, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
168 10 0.05
169 50 0.23
170 23 0.11
171 109 0.51
172 17 0.08
173 6 0.03
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (168 bp):
TTTTTTATATTTTGGATTAAACAGACTATAATTGAATGTCTACCTAAAGAAAGGTGAAGAAAAAG
CCATTCACTAGCAAGAAAAGTTCATTTATAATAACTCATTTTTTCTAAAGCCTTATTACTCGTTT
AAATAGTTTTATAATCTTATAATTTATTTTAAGTTGAA
Done.