Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399745.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2989.0, 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: 1967
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.33
Warning! 255 characters in sequence are not A, C, G, or T
Found at i:302 original size:171 final size:171
Alignment explanation
Indices: 4--368 Score: 534
Period size: 171 Copynumber: 2.1 Consensus size: 171
1 TTG
* * * *
4 CTTTAAATAGTTTTACAATGTCATAATTGATTTTAAGCTGCATTTTTTTATATTTTTTGTTAAAA
1 CTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTTATATTTTTAGTTAAAA
*
69 CAGATTATAATTAAATGTCCACCTTGAAAAACCTGAAGAAAAAGCCATTCATTCACAAGAAAAGT
66 CAGATTATAATTAAATGTCCACCATGAAAAACCTGAAGAAAAAGCCATTCATTCACAAGAAAAGT
*
134 CCATTTATAGTCACCCACACCTTCGAAAGCATCATTACTGA
131 CCATTTATAGTCACCCACACCTTCGAAAGCATCATTACTCA
*
175 CTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTTTTTATTTTTAGTTAAA
1 CTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGCTGAA-TTTTTTTATATTTTTAGTTAAA
* * * * * * ***
240 ATAGATTATCATTGAATGTCCACCATGAGAAACGTGAAGAAAAAG-CTTTCATTTGTAAGAAAAG
65 ACAGATTATAATTAAATGTCCACCATGAAAAACCTGAAGAAAAAGCCATTCATTCACAAGAAAAG
** *
304 TCCATTTATAGTCACCCATTCCTTCGAAAGCATTATTACTCA
130 TCCATTTATAGTCACCCACACCTTCGAAAGCATCATTACTCA
*
346 CTTTAAATAATTTTATAATCTCA
1 CTTTAAATAGTTTTATAATCTCA
369 NNNNNNNNNN
Statistics
Matches: 173, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
171 114 0.66
172 59 0.34
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (171 bp):
CTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTTATATTTTTAGTTAAAA
CAGATTATAATTAAATGTCCACCATGAAAAACCTGAAGAAAAAGCCATTCATTCACAAGAAAAGT
CCATTTATAGTCACCCACACCTTCGAAAGCATCATTACTCA
Found at i:903 original size:171 final size:171
Alignment explanation
Indices: 685--1095 Score: 498
Period size: 171 Copynumber: 2.4 Consensus size: 171
675 GAGAAATGTG
*
685 AAGAAAAGTCCATTTATAGTCACCCATGCCTTAGAAAGCATTATTACTCGCTTTAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCATTATTACTCGCTTTAAATGGTTTTA
********** * *
750 NNNNNNNNNNATTGATTTTAAGCTGAATTGTTTTACATTTTTGGCTAAAACAGATTATAATTAAA
66 TAATCTTATAATTGATTTCAAGCTGAATTGTTTTACATTTTTGACTAAAACAGATTATAATTAAA
*
815 TGTCTACCTCGAGAAACGTGAAAAAAAAGTCATTCATTGGC
131 TGTCTACCTCGAGAAACGTGAAAAAAAAGTCATTCATCGGC
* * * * * *
856 AAGAAAAGTCCAGTTATAGTCACCCATACCTTCTAAAGCATTATTACTCACTTTAAGTGATTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCATTATTACTCGCTTTAAATGGTTTTA
* ** * * * * *
921 TAATCTTATAATTGATTTCAAGTTGGGTTTTTTTACATTTTTGATTAAAATATATTATAATTGAA
66 TAATCTTATAATTGATTTCAAGCTGAATTGTTTTACATTTTTGACTAAAACAGATTATAATTAAA
* * * *
986 TGTCTACCTTGATAAACGTGAAGAAAAAGTCTTTCATCGGC
131 TGTCTACCTCGAGAAACGTGAAAAAAAAGTCATTCATCGGC
* * * *
1027 AAGGAAAGTACATTTATAGTCACCCATGCCTTCGAAAGCATTATTACTCGGTTTAAACGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCATTATTACTCGCTTTAAATGGTTTTA
1092 TAAT
66 TAAT
1096 GTCATAANNN
Statistics
Matches: 198, Mismatches: 42, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
171 198 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (171 bp):
AAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCATTATTACTCGCTTTAAATGGTTTTA
TAATCTTATAATTGATTTCAAGCTGAATTGTTTTACATTTTTGACTAAAACAGATTATAATTAAA
TGTCTACCTCGAGAAACGTGAAAAAAAAGTCATTCATCGGC
Found at i:1149 original size:171 final size:170
Alignment explanation
Indices: 760--1166 Score: 436
Period size: 171 Copynumber: 2.4 Consensus size: 170
750 NNNNNNNNNN
* * * *
760 ATTGATTTTAAGCTGAATTGTTTTACATTTTTGGCTAAAACAGATTATAATTAAATGTCTACCTC
1 ATTGATTTCAAGCTGAATTTTTTTACATTTTT-GTTAAAACATATTATAATTAAATGTCTACCTC
* * *
825 GAGAAACGTGAAAAAAAAGTCATTCATTGGCAAGAAAAGTCCAGTTATAGTCACCCATACCTTCT
65 GAGAAACGTGAAAAAAAAGTCATTCATCGGCAAGAAAAGTACAGTTATAGTCACCCATACCTTCG
** *
890 AAAGCATTATTACTCACTTTAAGTGATTTTATAATCTTATA
130 AAAGCATTATTACTCACTTTAAACGATTTTATAATCTCATA
* ** * * *
931 ATTGATTTCAAGTTGGGTTTTTTTACATTTTTGATTAAAATATATTATAATTGAATGTCTACCTT
1 ATTGATTTCAAGCTGAATTTTTTTACATTTTTG-TTAAAACATATTATAATTAAATGTCTACCTC
* * * * * *
996 GATAAACGTGAAGAAAAAGTCTTTCATCGGCAAGGAAAGTACATTTATAGTCACCCATGCCTTCG
65 GAGAAACGTGAAAAAAAAGTCATTCATCGGCAAGAAAAGTACAGTTATAGTCACCCATACCTTCG
** * *
1061 AAAGCATTATTACTCGGTTTAAACGGTTTTATAATGTCATA
130 AAAGCATTATTACTCACTTTAAACGATTTTATAATCTCATA
********** * * *
1102 ANNNNNNNNNNGCTGAATTTTTTTACATTTTTAGTTCAAACATATTATAATTAAATATCTTCCTC
1 ATTGATTTCAAGCTGAATTTTTTTACATTTTT-GTTAAAACATATTATAATTAAATGTCTACCTC
1167 AAAAAAAGTG
Statistics
Matches: 189, Mismatches: 45, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
170 1 0.01
171 187 0.99
172 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.37
Consensus pattern (170 bp):
ATTGATTTCAAGCTGAATTTTTTTACATTTTTGTTAAAACATATTATAATTAAATGTCTACCTCG
AGAAACGTGAAAAAAAAGTCATTCATCGGCAAGAAAAGTACAGTTATAGTCACCCATACCTTCGA
AAGCATTATTACTCACTTTAAACGATTTTATAATCTCATA
Found at i:1464 original size:169 final size:161
Alignment explanation
Indices: 1289--1613 Score: 350
Period size: 171 Copynumber: 2.0 Consensus size: 161
1279 NNNNNNNNNN
* * *
1289 ATTTTTTTATATTTTTAGTTAAAACATATTATAATTGAACATCTAT-CTTGAGAAATATGAA-AA
1 ATTTTTTTATATTTTTAGTTAAAACAAATTATAATTGAACAT-TATCCTTGAGAAACAAGAAGAA
* * * *
1352 AAACCCATTC-ATTGCAAGAAAAGTCCATTTATAGTAATCTATGCCTTCAAAAGTATTATCACTC
65 AAACCCATTCAATAGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTCAAAAGCATTATCACTC
1416 ACTTTAAATGGTTTTATAATCTCATAANNNNNNNNNNGTTAA
130 ACTTTAAATGGTTTTATAATCTCATAA----------GTTAA
* ** *
1458 ATTTTTTTATGTTTTTAGTTAAAACAAATTATAATTGAATGTTTTCCTTGAGAAACAAGAAGAAA
1 ATTTTTTTATATTTTTAGTTAAAACAAATTATAATTGAACATTATCCTTGAGAAACAAGAAGAAA
* ** ** * * * *
1523 AAGCCATTCAATAGTGAGAAAAGTGTATTTATAGTCACCCATGCCTTCAAAAGCATTGTTACTCG
66 AACCCATTCAATAGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTCAAAAGCATTATCACTCA
1588 CTTTAAATGGTTTTATAATCTCATAA
131 CTTTAAATGGTTTTATAATCTCATAA
1614 TTTATTTTAN
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
168 2 0.02
169 51 0.38
170 11 0.08
171 69 0.52
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.37
Consensus pattern (161 bp):
ATTTTTTTATATTTTTAGTTAAAACAAATTATAATTGAACATTATCCTTGAGAAACAAGAAGAAA
AACCCATTCAATAGCAAGAAAAGTCCATTTATAGTAACCCATGCCTTCAAAAGCATTATCACTCA
CTTTAAATGGTTTTATAATCTCATAAGTTAA
Done.