Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401994.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5090.0, 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: 3767
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.30
Warning! 790 characters in sequence are not A, C, G, or T
Found at i:364 original size:170 final size:169
Alignment explanation
Indices: 4--392 Score: 426
Period size: 170 Copynumber: 2.3 Consensus size: 169
1 TAG
* * * * * *
4 TCACTCAA-GCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTCATAATCTTATAATTGACTT
1 TCAC-CAATGCCTTCAAAAGCCTTGTTATTCGCTTTAAATAGTTTTATAATCTCATAATTGACTT
* * * * * *
68 TATGGTGATTTTTTTTGTAGTTTTGGTTAAACATATTATAATTAAATGCCTACCTCCAGAAATGT
65 TAAGGTGAATTCTTTTGTAGTTTTAGTTAAACATATTATAATTAAATGCCTACCTCAAGAAACGT
* * * *
133 GAAAAAAGGCCATTTATTGAGAAGAAAAGTCCATTTATAG
130 GAAAAAAAGCCATTCACTGAGAAGAAAAGTCCATTTATAC
*** * * * *
173 TCATTTATTCCTTCAAAAGCCTTGTTATTCGCTTTAAACAGTTTTGTAATCTCATCATTGACTTT
1 TCACCAATGCCTTCAAAAGCCTTGTTATTCGCTTTAAATAGTTTTATAATCTCATAATTGACTTT
* * * * * *
238 AAGTTGAATTCTTTTGTATTTTTAGTTAAA-ATAAATTATAATTGAATGTCTACCTTAAGACACG
66 AAGGTGAATTCTTTTGTAGTTTTAGTTAAACAT--ATTATAATTAAATGCCTACCTCAAGAAACG
*
302 TGAAGAAAAAGCCATTCACTGA-CAGAAAAGTCCATTTATAC
129 TGAA-AAAAAGCCATTCACTGAGAAGAAAAGTCCATTTATAC
*
343 TCACCAATGCCTTTAAAAGCCTTGTTACTT-GCTTTAAATAGTTTTATAAT
1 TCACCAATGCCTTCAAAAGCCTTGTTA-TTCGCTTTAAATAGTTTTATAAT
393 NNNNNNNNNN
Statistics
Matches: 178, Mismatches: 37, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
168 3 0.02
169 74 0.42
170 85 0.48
171 16 0.09
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (169 bp):
TCACCAATGCCTTCAAAAGCCTTGTTATTCGCTTTAAATAGTTTTATAATCTCATAATTGACTTT
AAGGTGAATTCTTTTGTAGTTTTAGTTAAACATATTATAATTAAATGCCTACCTCAAGAAACGTG
AAAAAAAGCCATTCACTGAGAAGAAAAGTCCATTTATAC
Found at i:1137 original size:13 final size:12
Alignment explanation
Indices: 1112--1155 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
1102 ATAAATATAT
1112 TAAAAATAAAAAA
1 TAAAAAT-AAAAA
*
1125 TAAAAGATTAAAA
1 TAAAA-ATAAAAA
1138 TAATAAATAAAAA
1 TAA-AAATAAAAA
1151 TAAAA
1 TAAAA
1156 TATATTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.07
13 21 0.78
14 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:1381 original size:15 final size:15
Alignment explanation
Indices: 1361--1397 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1351 ATTTTCTCTA
*
1361 CAATCACATTGCTTG
1 CAATCACATTACTTG
1376 CAATCACATTACTTG
1 CAATCACATTACTTG
1391 CAATCAC
1 CAATCAC
1398 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (15 bp):
CAATCACATTACTTG
Found at i:2654 original size:171 final size:168
Alignment explanation
Indices: 1448--2685 Score: 749
Period size: 171 Copynumber: 7.3 Consensus size: 168
1438 ACCTAAATAT
** * * *
1448 TTTTATAATCTCATAATTGACTTT-AAGTT-AA-TTTTTTTTATTTTTTGTTAAAATAGATTATA
1 TTTTATAATCTCATAATTGA-TTTGAAGTTGAACTTTTTTACAATTTTTGTTAAAACAAATTATA
* * * * * * *
1510 AGTGAATGTCTACCTCGAGAAACGTGAAGAAAAAG-TCATTCATAGGCAAGAGAA-CCTATTTGT
65 ATTGAATGTATACCT-TA-AAACGTGAAGAAAAAGAT-ATTCATTGGCAAGAAAAGTCTATTTAT
** * * *
1573 AGTCACCCAAACCTTCGAAATCCTTATTACTTGCTTTAAATGA
127 AGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAA-GG
* * * * * * *
1616 TTTTATAATCTTATAGTTAATTTTAAGTTGAA-TTTATTTA-TATTTTTGATTCAAACAGATTAT
1 TTTTATAATCTCATAATTGATTTGAAGTTGAACTTT-TTTACAATTTTTG-TTAAAACAAATTAT
* * * * * *
1679 AATTGAATGTCTA-CATAGAGAAAGATGAAGAAAAA-CTCATTCATTGGTAAGAAGAGTCTATTT
64 AATTGAATGTATACCTTA-A-AACG-TGAAGAAAAAGAT-ATTCATTGGCAAGAAAAGTCTATTT
* ** *
1742 ATAGTCACTCATGCCTTTAAAAGCCTTATTAC-CTACTTTAAATGG
125 ATAGTCACCCATGCCTTCGAAAGCCTTATTACTC-GCTTTAAA-GG
********** * * * *
1787 TTTTATAATCTCANNNNNNNNNNGAAGTT-AATTTTTTTTA-TATTTTTGGTTAAAATAGATTAT
1 TTTTATAATCTCATAATTGATTTGAAGTTGAA-CTTTTTTACAATTTTT-GTTAAAACAAATTAT
* * * * * *
1850 AATTGAATATCTACCTTCAGAAACATGAAGAAAAAGATATTTATTGGTAAGAAAAGTCCATTTAT
64 AATTGAATGTATACCTT-A-AAACGTGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTAT
* * * ********
1915 ACTCACCCATGCCTTCAAAAGCCTTATTACTCACNNNNNNNNN
127 AGTCACCCATGCCTTCGAAAGCCTTATTACTCGC-TTTAAAGG
* * * * * ** *** *
1958 NTTTGTAATCTCATAATTGATTTTAAATTCAA-TTCTTTT-GTATTTTTGATTAAAATTGATTAC
1 TTTTATAATCTCATAATTGATTTGAAGTTGAACTT-TTTTACAATTTTTG-TTAAAACAAATTAT
* * * * ** * *
2021 AGTTGAATGTCTACAGTGAGAAACGTGAAGAAAAAGCCATTCATTTGCAAGAAAAGCCTATTTAT
64 AATTGAATGTATAC-CTTA-AAACGTGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTAT
* * * * *
2086 AGTTACCCAAGCCTTCGAAAGCCTTATTAGTTGCTTTATATGG
127 AGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTA-AAGG
* * * *
2129 TTTTATAA-CTTCATAATTGATTTGAAGTTGACCTTTTTTA-TATTTTTATTAAAATAGAA-TAT
1 TTTTATAATC-TCATAATTGATTTGAAGTTGAACTTTTTTACAATTTTTGTTAAAACA-AATTAT
* * * * * *
2191 AATTGAATATATACCTTTAGAAACATTAAGAAAAATATA-TCTATTGGTAAGAAAAGTCCATTTA
64 AATTGAATGTATACC-TTA-AAACGTGAAGAAAAAGATATTC-ATTGGCAAGAAAAGTCTATTTA
********** * *
2255 TAGTCACCNNNNNNNNNNAAAGCCTTATTACTTGCTTTAAATAG
126 TAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAA-GG
* **
2299 TTTTATGATCTCATAATTGACTTT-AAGTTG-A-TTTTTT-TTATTTTTGATTAAAACAAATTAT
1 TTTTATAATCTCATAATTGA-TTTGAAGTTGAACTTTTTTACAATTTTTG-TTAAAACAAATTAT
* * * **
2360 AATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAAATATTCATTAACAAGAAAAGTCTATTTAT
64 AATTGAATGTATACCT-TA-AAACGTGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTAT
* * * *
2425 AGTCACCTATGCCTTTGAAAGCCTTATTACTCGATTTTAACGG
127 AGTCACCCATGCCTTCGAAAGCCTTATTACTCG-CTTTAAAGG
* * * * *
2468 GTTTATAATCTCATAATTGATTTGAAGTTGAACGTTTTTACAATTTCTGTTAAAGCATATTATAA
1 TTTTATAATCTCATAATTGATTTGAAGTTGAACTTTTTTACAATTTTTGTTAAAACAAATTATAA
* * *
2533 TTGAATGTATACCTTACATAACGTGGAGAAAAAGATATTCATTGGCAAGAAAGGTCTATTAATAG
66 TTGAATGTATACCTTA-A-AACGTGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTATAG
* *
2598 TCACCCATGCCTTCAAAAACCTTATTACTCGCTTTGAAAGG
129 TCACCCATGCCTTCGAAAGCCTTATTACTCGCTTT-AAAGG
* * * *
2639 TTTTATAATCTCATAATCGATTTTATGTTGAATTTTTTTAC-ATTTTT
1 TTTTATAATCTCATAATTGATTTGAAGTTGAACTTTTTTACAATTTTT
2686 CGTTCATAAT
Statistics
Matches: 827, Mismatches: 199, Indels: 86
0.74 0.18 0.08
Matches are distributed among these distances:
167 3 0.00
168 44 0.05
169 125 0.15
170 182 0.22
171 449 0.54
172 21 0.03
173 3 0.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.38
Consensus pattern (168 bp):
TTTTATAATCTCATAATTGATTTGAAGTTGAACTTTTTTACAATTTTTGTTAAAACAAATTATAA
TTGAATGTATACCTTAAAACGTGAAGAAAAAGATATTCATTGGCAAGAAAAGTCTATTTATAGTC
ACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAAGG
Done.