Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401807.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4914.0, 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: 2598
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.32
Warning! 400 characters in sequence are not A, C, G, or T
Found at i:2129 original size:171 final size:172
Alignment explanation
Indices: 1431--2594 Score: 789
Period size: 171 Copynumber: 6.8 Consensus size: 172
1421 NNNNNNNNNN
* ** * * * * *
1431 TTTTAGGTTGAATTTTTTTATATTTTTAGTTAAAACAAATTATAATTGAGTGTTTGCCTTGGA-A
1 TTTTAAGTTGAATTTTTTTATATTTTCGGTTAGAACAGATTATAATTGAATGTTTACCTTAGAGA
* ** **
1495 AACATAAAGAAAAAGGTATTCATTTG-CAAGAAAAGTCCATTTATAGTCACTAATTCCTTCAAAA
66 AACATGAAGAAAAAGACATTCA-TTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
********** * *
1559 GCCTTATTACTCACTNNNNNNNNNNTTATAATTTCATAATTGA
130 GCCTTATTACTCACTCTAAATAGTTTTATAATCTCAAAATTGA
* * * * * * * *
1602 TTTTAAGTTGAATTTTTTTATATTTTTGATTA-AAAAGACTATAATTCAATGTCTGCCTCAG-GA
1 TTTTAAGTTGAATTTTTTTATATTTTCGGTTAGAACAGATTATAATTGAATGTTTACCTTAGAGA
* ** ** ** *
1665 GAGGTGAAGAAAAAGGTATTCATTGGTATGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
66 AACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
****************** * *
1730 CNNNNNNNNNNNNNNNNNNTGGTTTTATAATCTCAAAATTAA
131 CCTTATTACTCACTCTAAATAGTTTTATAATCTCAAAATTGA
* ** * *
1772 TTTTAAGTTGAA-TTTTTTACATTTTTTGTTAGAACAAATTATAATCT-AATGTTTGCCTTA-AG
1 TTTTAAGTTGAATTTTTTTATATTTTCGGTTAGAACAGATTATAAT-TGAATGTTTACCTTAGAG
** * * * *
1834 AAACATGAAGAAAAAGGTATTGATT-AGCAAAAAAAGTCCATTTATAATCACTCATTCCTTCAAA
65 AAACATGAAGAAAAAGACATTCATTGA-CAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* ** **********
1898 AGCCTTAGTACTTGCGT-TAAATAGTTTTATAATCNNNNNNNNNN
129 AGCCTTATTACTCAC-TCTAAATAGTTTTATAATCTCAAAATTGA
* * * * *
1942 TTTTAAGTTAAATTTTTTTATATTTTCAGTTAAAACGGACTATAATT-AGATGTTTACCTTAGA-
1 TTTTAAGTTGAATTTTTTTATATTTTCGGTTAGAACAGATTATAATTGA-ATGTTTACCTTAGAG
* * * * * *
2005 AAACGTGAAGAAAAAGGCATTCATT-AGTATGAAAAGTCCATTTATCA-ACACCTATTCCTTCAA
65 AAACATGAAGAAAAAGACATTCATTGA-CAAGAAAAGTCCATTTAT-AGTCACCCATTCCTTCAA
* * *
2068 AAACCTTATTACTCACTCTAAATATTTTTTTAATCTCAAAATTGA
128 AAGCCTTATTACTCACTCTAAATAGTTTTATAATCTCAAAATTGA
* * ** **
2113 TTTTGAGTTGAATTTTTTTTCATTTTTTC--TTAGAACAGATTATAATCAAATGTTTACAATA-A
1 TTTTAAGTTGAA-TTTTTTT-ATATTTTCGGTTAGAACAGATTATAATTGAATGTTTACCTTAGA
* * * * * *
2175 GAAACGTGAGGAAAAAGATATTCATTGAAAAGAAAAGTTCATTTATAGTCACCCGTTCCTTCAAA
64 GAAACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
** * * ********
2240 AGCCTTATTACTTGCTTTAAAAAGTTTTATAATCTCNNNNNNNN
129 AGCCTTATTACTCACTCTAAATAGTTTTATAATCTCAAAATTGA
** * * * * * * *
2284 NNTTAGGTTGAATTATTTTATATTTTTGGTTAGAATAGATTGTAATTGAATATCTACCTTAG-GA
1 TTTTAAGTTGAATTTTTTTATATTTTCGGTTAGAACAGATTATAATTGAATGTTTACCTTAGAGA
* * * *
2348 AACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTGCATTTGTAGCCACCCATTCCTTCAAAAG
66 AACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
* *
2413 CTTTATTACTCACTGTAAATAGTTTTATAATCTCAAAATTGA
131 CCTTATTACTCACTCTAAATAGTTTTATAATCTCAAAATTGA
* * * * *
2455 TTTTAAGTTGAATTCTTTTACATTTTTGGTTAGAACAAATTATAATTGAATGTTTAGCTT-GAGA
1 TTTTAAGTTGAATTTTTTTATATTTTCGGTTAGAACAGATTATAATTGAATGTTTACCTTAGAGA
* * * * *
2519 AACATGAAAAAAAAGGCATTCTTTGACAAGAAAAGTCAATTTATAGTCACCGATTCCTTCAAAAG
66 AACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
2584 CCTTATTACTC
131 CCTTATTACTC
2595 GCTT
Statistics
Matches: 760, Mismatches: 211, Indels: 44
0.75 0.21 0.04
Matches are distributed among these distances:
169 25 0.03
170 221 0.29
171 496 0.65
172 11 0.01
173 7 0.01
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.37
Consensus pattern (172 bp):
TTTTAAGTTGAATTTTTTTATATTTTCGGTTAGAACAGATTATAATTGAATGTTTACCTTAGAGA
AACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
CCTTATTACTCACTCTAAATAGTTTTATAATCTCAAAATTGA
Found at i:2269 original size:342 final size:333
Alignment explanation
Indices: 1751--2598 Score: 889
Period size: 342 Copynumber: 2.5 Consensus size: 333
1741 NNNNNNNNTG
*
1751 GTTTTATAATCTCAAAATTAATTTTAAGTTGAA-TTTTTTACATTTTTTGTTAGAACAAATTATA
1 GTTTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAGAACAAATTATA
* * * * *
1815 ATCTAATGTTTGCCTTAAGAAACATGAAGAAAAAGGTATTGATTAGCAAA-AAAAGTCCATTTAT
66 ATCAAATGTTT-ACTTAAGAAACATGAAGAAAAAGGTATTCATT-GAAAAGAAAAGTTCATTTAT
* * * * * * **
1879 AATCACTCATTCCTTCAAAAGCCTTAGTACTTGCGTTAAATAGTTTTATAATCNNNNNNNNNNTT
129 AGTCACCCGTTCCTTCAAAAGCCTTATTACTTGCTTTAAAAAGTTTTATAATC--------TCTT
* * * *
1944 TTAAGTTAAATTTTTTTATATTTTCAGTTAAAACGGACTATAATT-AGATGTTTACCTTAGAAAA
186 TTAAGTTAAATTATTTTATATTTTCAGTTAAAACAGACTATAATTGA-ATATCTACCTTAGAAAA
* * * * *
2008 CGTGAAGAAAAAGGCATTCATTAGTATGAAAAGTCCATTTATCA-ACACCTATTCCTTCAAAAAC
250 CATGAAGAAAAAGACATTCATTAGCAAGAAAAGTCCATTTAT-AGACACCCATTCCTTCAAAAAC
2072 CTTATTACTCACTCTAAATA
314 CTTATTACTCACTCTAAATA
* * * * * *
2092 TTTTTTTAATCTCAAAATTGATTTTGAGTTGAATTTTTTTTCATTTTTTCTTAGAACAGATTATA
1 GTTTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAGAACAAATTATA
* * * *
2157 ATCAAATGTTTACAATAAGAAACGTGAGGAAAAAGATATTCATTGAAAAGAAAAGTTCATTTATA
66 ATCAAATGTTTAC-TTAAGAAACATGAAGAAAAAGGTATTCATTGAAAAGAAAAGTTCATTTATA
**
2222 GTCACCCGTTCCTTCAAAAGCCTTATTACTTGCTTTAAAAAGTTTTATAATCTCNNNNNNNNNNT
130 GTCACCCGTTCCTTCAAAAGCCTTATTACTTGCTTTAAAAAGTTTTATAATCTC--------TTT
* * ** * * * * *
2287 TAGGTTGAATTATTTTATATTTTTGGTTAGAATAGATTGTAATTGAATATCTACCTTAGGAAACA
187 TAAGTTAAATTATTTTATATTTTCAGTTAAAACAGACTATAATTGAATATCTACCTTAGAAAACA
* * * * * *
2352 TGAAGAAAAAGACATTCATTGGCAAGAAAAGTGCATTTGTAGCCACCCATTCCTTCAAAAGCTTT
252 TGAAGAAAAAGACATTCATTAGCAAGAAAAGTCCATTTATAGACACCCATTCCTTCAAAAACCTT
*
2417 ATTACTCACTGTAAATA
317 ATTACTCACTCTAAATA
* *
2434 GTTTTATAATCTCAAAATTGATTTTAAGTTGAATTCTTTTACATTTTTGGTTAGAACAAATTATA
1 GTTTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAGAACAAATTATA
** * * * * *
2499 ATTGAATGTTTAGCTTGAGAAACATGAAAAAAAAGGCATTCTTTGACAAGAAAAG-TCAATTTAT
66 ATCAAATGTTTA-CTTAAGAAACATGAAGAAAAAGGTATTCATTGAAAAGAAAAGTTC-ATTTAT
*
2563 AGTCA-CCGATTCCTTCAAAAGCCTTATTACTCGCTT
129 AGTCACCCG-TTCCTTCAAAAGCCTTATTACTTGCTT
Statistics
Matches: 420, Mismatches: 71, Indels: 31
0.80 0.14 0.06
Matches are distributed among these distances:
341 40 0.10
342 378 0.90
343 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.37
Consensus pattern (333 bp):
GTTTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAGAACAAATTATA
ATCAAATGTTTACTTAAGAAACATGAAGAAAAAGGTATTCATTGAAAAGAAAAGTTCATTTATAG
TCACCCGTTCCTTCAAAAGCCTTATTACTTGCTTTAAAAAGTTTTATAATCTCTTTTAAGTTAAA
TTATTTTATATTTTCAGTTAAAACAGACTATAATTGAATATCTACCTTAGAAAACATGAAGAAAA
AGACATTCATTAGCAAGAAAAGTCCATTTATAGACACCCATTCCTTCAAAAACCTTATTACTCAC
TCTAAATA
Done.