Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398023.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_133.0, 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: 25639
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.21
Warning! 11211 characters in sequence are not A, C, G, or T
Found at i:4463 original size:20 final size:20
Alignment explanation
Indices: 4438--4487 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4428 TCGATTAAAA
4438 TGATTTTATA-ACCTCATAAT
1 TGATTTTA-AGACCTCATAAT
**
4458 TGATTTTAAGTTCTCATAAT
1 TGATTTTAAGACCTCATAAT
4478 TGATTTTAAG
1 TGATTTTAAG
4488 TTAAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (20 bp):
TGATTTTAAGACCTCATAAT
Found at i:4488 original size:20 final size:20
Alignment explanation
Indices: 4450--4489 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4440 ATTTTATAAC
4450 CTCATAATTGATTTTAAGTT
1 CTCATAATTGATTTTAAGTT
4470 CTCATAATTGATTTTAAGTT
1 CTCATAATTGATTTTAAGTT
4490 AAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
CTCATAATTGATTTTAAGTT
Found at i:5907 original size:170 final size:170
Alignment explanation
Indices: 5595--5912 Score: 401
Period size: 170 Copynumber: 1.9 Consensus size: 170
5585 NNNNNNTGTA
*
5595 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAGGTAATAAAGCTTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAGTAATAAAGCTTTT
* *
5660 GAAGGAATGAGTGACTATAAAAGGATATTTTTTCTCAATGAATGGCTTTGTTTACACGTCTCTCG
66 GAAGAAATGAGTGACTATAAAAGGATATTTCTTCTCAATGAATGGCTTTGTTTACACGTCTCTCG
* **
5725 AGGTGGACATTCAATTATAGTCTGTTTTAACAGAAAATGT
131 AGATAAACATTCAATTATAGTCTGTTTTAACAGAAAATGT
* * **
5765 AAAAAATTTAACTTAAAATCAATTATGAGATTATTAAACTATTTAAGGCAAGTAAT-AAGCCTTT
1 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAGTAATAAAG-CTTT
* * * * * * * *
5829 TGAATAAAT-AGGTGACTCTAAATGGACT-TTTCTTGTCAATTAGTGGCTTT-TTCTACATGTTT
65 TGAAGAAATGA-GTGACTATAAAAGGA-TATTTCTTCTCAATGAATGGCTTTGTT-TACACGTCT
*
5891 CTCTAGATAAACATTCAATTAT
127 CTCGAGATAAACATTCAATTAT
5913 NNNNNNNNNN
Statistics
Matches: 125, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
169 6 0.05
170 118 0.94
171 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACAAGTAATAAAGCTTTT
GAAGAAATGAGTGACTATAAAAGGATATTTCTTCTCAATGAATGGCTTTGTTTACACGTCTCTCG
AGATAAACATTCAATTATAGTCTGTTTTAACAGAAAATGT
Found at i:11363 original size:171 final size:171
Alignment explanation
Indices: 10946--11400 Score: 435
Period size: 171 Copynumber: 2.7 Consensus size: 171
10936 NNNNNNNNNN
* * *
10946 TTTTAAGTTGAATTTTTTTACATTTTT-TGTTAAAACAAACTATAATTAAATGTCCACCTCGAGA
1 TTTTAAGTTAAATTTTTTTACATTTTTCT-TTAAAACAAACTATAATTTAATGTCTACCTCGAGA
*
11010 AACATGTA-AAAAAGCCATTCATTGA-AAAAACAAGTCCATTTATAGTCACTCATTCCTTCAAAA
65 AACGTGTAGAAAAAGCCATTCATTGAGAAAAA-AAGTCCATTTATAGTCACTCATTCCTTCAAAA
11073 GCCTTAATACCCGCTTTAAATAGTTTTATAATCTCATAATTGA
129 GCCTTAATACCCGCTTTAAATAGTTTTATAATCTCATAATTGA
* * * * * *
11116 TTTTAAG-TCAATTGTTTTTATATTTTTCTTTAAAACATACTATAA-TTAATAGCCTGCC-AGAC
1 TTTTAAGTTAAATT-TTTTTACATTTTTCTTTAAAACAAACTATAATTTAAT-GTCTACCTCGA-
* * * * * * *
11178 AAAAGGTATAGAAAAAGCGATTCATTGAGAAAAAAAATCCATTTTTAGTCACTCATTCTTTCAAA
63 GAAACGTGTAGAAAAAGCCATTCATTGAGAAAAAAAGTCCATTTATAGTCACTCATTCCTTCAAA
* * * **********
11243 A-CTCTTATTACTCGGTTTAAAT-GATTNNNNNNNNNNATAATTGA
128 AGC-CTTAATACCCGCTTTAAATAG-TTTTATAATCTCATAATTGA
* * *
11287 TTTTAAGTTAAATTTGTTTACATTTTTCTTTAAAACAGA-TAATAATTTAATGTCTATCTCGAGA
1 TTTTAAGTTAAATTTTTTTACATTTTTCTTTAAAACAAACT-ATAATTTAATGTCTACCTCGAGA
* * *
11351 AACGTGTAGAAAATA-CCATTAATTGAGAAGAAAAGTCTATTTATAGTCAC
65 AACGTGTAGAAAA-AGCCATTCATTGAGAAAAAAAGTCCATTTATAGTCAC
11401 CNNNNNNNNN
Statistics
Matches: 226, Mismatches: 46, Indels: 25
0.76 0.15 0.08
Matches are distributed among these distances:
169 11 0.05
170 47 0.21
171 150 0.66
172 18 0.08
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.37
Consensus pattern (171 bp):
TTTTAAGTTAAATTTTTTTACATTTTTCTTTAAAACAAACTATAATTTAATGTCTACCTCGAGAA
ACGTGTAGAAAAAGCCATTCATTGAGAAAAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGC
CTTAATACCCGCTTTAAATAGTTTTATAATCTCATAATTGA
Found at i:16904 original size:15 final size:16
Alignment explanation
Indices: 16879--16908 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16869 TCAATCTCAT
16879 AATTGATTTTAATTTA
1 AATTGATTTTAATTTA
16895 AATT-ATTTTAATTT
1 AATTGATTTTAATTT
16909 TTTGATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
AATTGATTTTAATTTA
Found at i:22212 original size:170 final size:170
Alignment explanation
Indices: 21680--22775 Score: 1178
Period size: 171 Copynumber: 6.4 Consensus size: 170
21670 NNNNNNNNNN
* * * *
21680 TAAATAGTTTT-TCAATCTCATAATTGATTTTAAGTT-AAATTTTTTAAAATTTTTGATTGAAAC
1 TAAATAGTTTTAT-AATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTG-TTAAAAC
* * * *
21743 ATACTATAATTGAATG--TACCTCGAGAAACTTGAAGAAACAAGCATTCATTAACAAGAAAAGTC
64 AGACTATAATTGAATGTCTACCTCGAGAAACGTGAA-AAAAAAGCATTCATTGACAAGAAAAGTC
* *
21806 CATTTAGAGTCACCCATTCCTTCAAAAAGCTTATTACTCGCTT
128 CATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
* * * * *
21849 CAAATGGTTTTACAATCTCATAATTGATTTTAAATTGAATTTTTTTACA-TTTTTGATTCAAACA
1 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTG-TTAAAACA
* * * * * * * *
21913 TACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAACAAGTATTCACTAATAAGAAAAGTCC
65 GACTATAATTGAATGTCTACCTCGAGAAACGTGAA-AAAAAAGCATTCATTGACAAGAAAAGTCC
* * * *
21978 GTTTAGAGTCACCCATTCCTTCAAAATGCTTATTACTCGTTT
129 ATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
22020 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAG
1 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAG
* * *
22085 ACTATAATTGAATGTATACCTCGAGAAACGT-AAAAAACAAGCATTCATTGACAACAAAAGTTCA
66 ACTATAATTGAATGTCTACCTCGAGAAACGTGAAAAAA-AAGCATTCATTGACAAGAAAAGTCCA
*
22149 TTTAAAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
130 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
* *
22190 TAAATAGTTTTATAACCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTCTGTTAAAACAG
1 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAG
* * * * * * * *
22255 TCTATAATTGATTGTTTACCAT-GAGTAACGTGTAAAAAAAGCCATTTATTGAGAAAAAAAGTCC
66 ACTATAATTGAATGTCTACC-TCGAGAAACGTGAAAAAAAAG-CATTCATTGACAAGAAAAGTCC
** * * * *
22319 ATTT-TAGTCACTTATTTCTTCAAAAGGCTTGTTACCCACTT
129 ATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
* * * * * *
22360 TTAATAGTTTTATAATCACATAATTGATTTTAAGTTAAATTTTTTTTATATTTTTTATTAGAACA
1 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTTGTTAAAACA
* * * * *
22425 GACTATAATTGAATATCTACCT-TAGGAAACGCAT-AGAAAAATA-CTGTTCATTGAGAAGAAAA
65 GACTATAATTGAATGTCTACCTCGA-GAAACG--TGA-AAAAAAAGC-ATTCATTGACAAGAAAA
* * * *
22487 GTTCATTTATAGCCACCCATTCCTTCAAAAGCCTTATTACTCGGTT
125 GTCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
* * *
22533 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCGTTAAAA-AA
1 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAG
* * * * * *
22597 ACTATAATTGAATGTGC-ACCTCGGGAAACATG-TAACAAAGCCATTCATTGAGACGAAAAGTCC
66 ACTATAATTGAATGT-CTACCTCGAGAAACGTGAAAAAAAAG-CATTCATTGACAAGAAAAGTCC
* * * * * * *
22660 ATTTATAGCCACTCATTTCTTTAAAAGCCTTTTTACCCGCTT
129 ATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
* * ** * *
22702 TAAATAGTTTTATAAACTAATAATTGATTTTAAGTCAAATATTTTTAGATTTTTCT-TTAAAACA
1 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-TGTTAAAACA
22766 GACTATAATT
65 GACTATAATT
22776 ATAAGCCTGC
Statistics
Matches: 788, Mismatches: 116, Indels: 45
0.83 0.12 0.05
Matches are distributed among these distances:
168 4 0.01
169 171 0.22
170 238 0.30
171 258 0.33
172 47 0.06
173 70 0.09
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (170 bp):
TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAG
ACTATAATTGAATGTCTACCTCGAGAAACGTGAAAAAAAAGCATTCATTGACAAGAAAAGTCCAT
TTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTT
Found at i:22317 original size:341 final size:336
Alignment explanation
Indices: 21680--22775 Score: 1291
Period size: 341 Copynumber: 3.2 Consensus size: 336
21670 NNNNNNNNNN
* *
21680 TAAATAGTTTT-TCAATCTCATAATTGATTTTAAGTTAAA-TTTTTTAAAATTTTTGATTGAAAC
1 TAAATAGTTTTAT-AATCTCATAATTGATTTTAAGTTAAATTTTTTTAAATTTTTTG-TTAAAAC
* * * * *
21743 ATACTATAATTGAATG-TACCTCGAGAAACTTGAAGAAACAAGCATTCATTAACAAGAAAAGTCC
64 AGACTATAATTGAATGTTACCTCGAGAAACGT-AAAAAACAAGCATTCATTGACAAGAAAAGTTC
* * * *
21807 ATTTAGAGTCACCCATTCCTTCAAAAAGCTTATTACTCGCTTCAAATGGTTTTACAATCTCATAA
128 ATTTAAAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAA
* *
21872 TTGATTTTAAATTGAATTTTTTTACATTTTTGATTCAAACATACTATAATTGAATGTCTACCTTG
193 TTGATTTTAAGTTGAATTTTTTTACATTTTTG-TTAAAACAT-CTATAATTGAATGTCTACC-TG
* * * * * * * *
21937 AGAAACATG-AAGAAACAAG-TATTCACTAATAAGAAAAGTCCGTTTAGAGTCACCCATTCCTTC
255 AGAAACATGTAA-AAA-AAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTTCTTC
*
22000 AAAATGCTTATTACTCGTTT
318 AAAA-GCTTATTACCCGTTT
* *
22020 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAG
1 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTAAATTTTTTGTTAAAACAG
*
22085 ACTATAATTGAATGTATACCTCGAGAAACGTAAAAAACAAGCATTCATTGACAACAAAAGTTCAT
66 ACTATAATTGAATGT-TACCTCGAGAAACGTAAAAAACAAGCATTCATTGACAAGAAAAGTTCAT
* *
22150 TTAAAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATAGTTTTATAACCTCATAATT
130 TTAAAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
* *
22215 GATTTTAAGTTGAATTTTTTTACATTTTCTGTTAAAACAGTCTATAATTGATTGTTTACCATGAG
195 GATTTTAAGTTGAATTTTTTTACATTTT-TGTTAAAACA-TCTATAATTGAATGTCTACC-TGAG
* * * * *
22280 TAACGTGTAAAAAAAGCCATTTATTGAGAAAAAAAGTCCATTT-TAGTCACTTATTTCTTCAAAA
257 AAACATGTAAAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTTCTTCAAAA
* *
22344 GGCTTGTTACCCACTTT
322 -GCTTATTACCC-GTTT
* * * *
22361 T-AATAGTTTTATAATCACATAATTGATTTTAAGTTAAATTTTTTTTATATTTTTTATTAGAACA
1 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAA-TTTTTTTAAATTTTTTGTTAAAACA
* * * * *
22425 GACTATAATTGAATATCTACCT-TAGGAAACGCATAGAAAAA-TA-CTGTTCATTGAGAAGAAAA
65 GACTATAATTGAATGT-TACCTCGA-GAAACG--TA-AAAAACAAGC-ATTCATTGACAAGAAAA
* * * *
22487 GTTCATTTATAGCCACCCATTCCTTCAAAAGCCTTATTACTCGGTTTAAATGGTTTTATAATCTC
124 GTTCATTTAAAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTATAATCTC
* *
22552 ATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCGTTAAAAAAACTATAATTGAATGTGC-AC
189 ATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-GTTAAAACATCTATAATTGAATGT-CTAC
* * * *
22616 CTCGGGAAACATGT-AACAAAGCCATTCATTGAGACGAAAAGTCCATTTATAGCCACTCATTTCT
252 CT-GAGAAACATGTAAAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTTCT
* * *
22680 TTAAAAGCCTTTTTACCCGCTT
316 TCAAAAG-CTTATTACCCGTTT
* * * * *
22702 TAAATAGTTTTATAAACTAATAATTGATTTTAAGTCAAATATTTTTAGATTTTTCT-TTAAAACA
1 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTAAATTTTT-TGTTAAAACA
22766 GACTATAATT
65 GACTATAATT
22776 ATAAGCCTGC
Statistics
Matches: 654, Mismatches: 80, Indels: 43
0.84 0.10 0.06
Matches are distributed among these distances:
340 122 0.19
341 303 0.46
342 106 0.16
343 118 0.18
344 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (336 bp):
TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTAAATTTTTTGTTAAAACAG
ACTATAATTGAATGTTACCTCGAGAAACGTAAAAAACAAGCATTCATTGACAAGAAAAGTTCATT
TAAAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTG
ATTTTAAGTTGAATTTTTTTACATTTTTGTTAAAACATCTATAATTGAATGTCTACCTGAGAAAC
ATGTAAAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTTCTTCAAAAGCTT
ATTACCCGTTT
Done.