Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399672.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2919.0, 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: 1716
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.32
Warning! 283 characters in sequence are not A, C, G, or T
Found at i:428 original size:172 final size:171
Alignment explanation
Indices: 203--769 Score: 621
Period size: 172 Copynumber: 3.2 Consensus size: 171
193 TTTTTTTACG
* * * * * * *
203 TTTTAGTTAAAACATACTATAATTCAATGTTTACCTTGAGAAATGTAAAGAAAAAGGCATTCATT
1 TTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAGGAATTCATT
* * *
268 GGAAAGAAAAGTCCATTTATAGTCACCTATTCCTTTAAAAGCCTTAGTACTCACTTTAAAGGGTT
66 GGAAAGAAAAGTCCATTTATAGTCACATATTCCTTTAAAAGCCTTATTACTCACTTTAAATGGTT
* * *
333 TTATATTCTCAAAATTGATTTGAATTTGAATTCCTTGTACAT
131 TTATAATCTCAAAATTGATTT-AATTTGAATTCTTTGTATAT
* *
375 TTTTGGTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAGGAATTCATT
1 TTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAGGAATTCATT
* * * *
440 GGTAAGAAAAAGGAATTCATTGGTAAGAAAAGTCCATTTATAGTTACCCTTACGTTCAAAAGCCT
66 GGAAAG-AAAA-G--TCCATT--T----ATAGT-CA--CATA-TT--CC-T---TT-AAAAGCCT
* *
505 TATTACTTACTTTAAATGGTTTTATAATCTCAAAATTGATTTACATTTGAATTCTTTGTATAG
110 TATTACTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTA-ATTTGAATTCTTTGTATAT
* **
568 TTTTGGTTAAAATAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAAAAATTCATT
1 TTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAGGAATTCATT
* * * * * **
633 GGCAAGAAAAGTCCATTTATAGTCACTTATTCCTTCAGAAGCGTTATTACTCACTTTAAATAATT
66 GGAAAGAAAAGTCCATTTATAGTCACATATTCCTTTAAAAGCCTTATTACTCACTTTAAATGGTT
*
698 TTATAGTCTCAAAATTGATTTAAATTTGAATTCTTTGTATAT
131 TTATAATCTCAAAATTGATTT-AATTTGAATTCTTTGTATAT
*
740 TTTTGGTTAAAATAGACTAGAATTGAATGT
1 TTTTGGTTAAAACAGACTAGAATTGAATGT
770 AAAAGAAATT
Statistics
Matches: 335, Mismatches: 37, Indels: 46
0.80 0.09 0.11
Matches are distributed among these distances:
172 155 0.46
173 6 0.02
174 1 0.00
176 6 0.02
177 2 0.01
178 1 0.00
179 2 0.01
180 2 0.01
182 6 0.02
183 6 0.02
185 2 0.01
186 2 0.01
187 1 0.00
188 2 0.01
189 6 0.02
191 1 0.00
192 7 0.02
193 127 0.38
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (171 bp):
TTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAGGAATTCATT
GGAAAGAAAAGTCCATTTATAGTCACATATTCCTTTAAAAGCCTTATTACTCACTTTAAATGGTT
TTATAATCTCAAAATTGATTTAATTTGAATTCTTTGTATAT
Found at i:448 original size:21 final size:21
Alignment explanation
Indices: 422--470 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
412 GAGAAATGTG
422 AAGAAAAAGGAATTCATTGGT
1 AAGAAAAAGGAATTCATTGGT
443 AAGAAAAAGGAATTCATTGGT
1 AAGAAAAAGGAATTCATTGGT
464 AAGAAAA
1 AAGAAAA
471 GTCCATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (21 bp):
AAGAAAAAGGAATTCATTGGT
Found at i:579 original size:193 final size:193
Alignment explanation
Indices: 250--642 Score: 583
Period size: 193 Copynumber: 2.0 Consensus size: 193
240 GAGAAATGTA
* * *
250 AAGAAAAAGGCATTCATTGGAAAGAAAAGTCCATTTATAGTCACCTATTCCTTTAAAAGCCTTAG
1 AAGAAAAAGGAATTCATTGGAAAGAAAAGTCCATTTATAGTCACCTATACCTTCAAAAGCCTTAG
* *
315 TACTCACTTTAAAGGGTTTTATATTCTCAAAATTGATTTGAATTTGAATTCCTTGTACATTTTTG
66 TACTCACTTTAAAGGGTTTTATAATCTCAAAATTGATTTGAATTTGAATTCCTTGTACAGTTTTG
* * ** *
380 GTTAAAACAGATTATAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAGGAATTCATTGGT
131 GTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAAAAATTCATTGGC
* * *
443 AAGAAAAAGGAATTCATTGGTAAGAAAAGTCCATTTATAGTTACCCT-TACGTTCAAAAGCCTTA
1 AAGAAAAAGGAATTCATTGGAAAGAAAAGTCCATTTATAGTCA-CCTATACCTTCAAAAGCCTTA
* * * * *
507 TTACTTACTTTAAATGGTTTTATAATCTCAAAATTGATTT-ACATTTGAATTCTTTGTATAGTTT
65 GTACTCACTTTAAAGGGTTTTATAATCTCAAAATTGATTTGA-ATTTGAATTCCTTGTACAGTTT
*
571 TGGTTAAAATAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAAAAATTCATTGGC
129 TGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAAAAATTCATTGGC
636 AAGAAAA
1 AAGAAAA
643 GTCCATTTAT
Statistics
Matches: 179, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
192 1 0.01
193 175 0.98
194 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (193 bp):
AAGAAAAAGGAATTCATTGGAAAGAAAAGTCCATTTATAGTCACCTATACCTTCAAAAGCCTTAG
TACTCACTTTAAAGGGTTTTATAATCTCAAAATTGATTTGAATTTGAATTCCTTGTACAGTTTTG
GTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAAAAATTCATTGGC
Found at i:915 original size:151 final size:151
Alignment explanation
Indices: 619--920 Score: 496
Period size: 151 Copynumber: 2.0 Consensus size: 151
609 AATGTGAAGA
** *
619 AAAAAAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACTTATTCCTTCAGAAGCGTTATTACT
1 AAAAAAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACT
* *
684 CACTTTAAATAATTTTATAGTCTCAAAATTGATTTAAATTTGAATTCTTTGTATATTTTTGGTTA
66 CACTTTAAATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTA
*
749 AAATAGACTAGAATTGAATGT
131 AAACAGACTAGAATTGAATGT
*
770 AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACT
1 AAAAAAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACT
* *
835 CACTTTAAATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTTTACATTTTTGTTTA
66 CACTTTAAATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTA
* * *
900 ACACAGATTATAATTGAATGT
131 AAACAGACTAGAATTGAATGT
921 TTGCTTTGAG
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
151 139 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (151 bp):
AAAAAAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACT
CACTTTAAATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTA
AAACAGACTAGAATTGAATGT
Found at i:1052 original size:323 final size:322
Alignment explanation
Indices: 447--1070 Score: 822
Period size: 323 Copynumber: 1.9 Consensus size: 322
437 ATTGGTAAGA
* * * *
447 AAAAGGAATTCATTGGTAAGAAAAGTCCATTTATAGTTACCCTTACGTTCAAAAGCCTTATTACT
1 AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCTTACCTTCAAAAGCCTTATTACT
* ** * *
512 TACTTTAAATGGTTTTATAATCTCAAAATTGATTTACATTTGAATTCTTTGTATAGTTTTGGTTA
66 CACTTTAAATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACAGTTTTGGTTA
* **
577 AAATAGACTAGAATTGAATGTCTACCTTGAGAAATGTGAAGAAAAAAAAATTCATTGGCAAGAAA
131 AAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAAAATTCATTGGCAAGAAA
* * * * *
642 AGTCCATTTATAGTCACTTATTCCTTCAGAAGCGTTATTACTCACTTTAAATAATTTTATAGTCT
196 ACTCCATTTATAGTCACCTATTCCTTCAAAAGCGTTATTACTCACTTTAAATAATTGTATAGACT
* *
707 CAAAATTGATTTAAATTTGAATTCTTTGTATATTTTTGGTTAAAATAGACTAGAATTGAATGT
261 CAAAATTAATTTAAATTTGAATTCTTTG-ATATTTTTAGTTAAAATAGACTAGAATTGAATGT
*
770 AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATT-CCTTCAGAAGCCTTATTAC
1 AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCC-TTACCTTCAAAAGCCTTATTAC
* * *
834 TCACTTTAAATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTTTACATTTTTGTTT
65 TCACTTTAAATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACAGTTTTGGTT
* * * * * * **** *
899 AACACAGATTATAATTGAATGTTTGCTTTGAGAAACATGAAGAAAAAGGCGTTCATTGGCAAGAG
130 AAAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAAAATTCATTGGCAAGAA
* * **
964 AACTCCATTTATAGTCACCTATTCTTTCAAAAGCTTTATTACTCACTTTAAATGGTTGTATA-AC
195 AACTCCATTTATAGTCACCTATTCCTTCAAAAGCGTTATTACTCACTTTAAATAATTGTATAGAC
* * *
1028 ATCAAAATTAATTTTAGA-TTGAATTTTTTGATGTTTTTAGTTA
260 -TCAAAATTAA-TTTAAATTTGAATTCTTTGATATTTTTAGTTA
1071 GAACAGTTTA
Statistics
Matches: 257, Mismatches: 41, Indels: 7
0.84 0.13 0.02
Matches are distributed among these distances:
322 12 0.05
323 238 0.93
324 7 0.03
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (322 bp):
AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCTTACCTTCAAAAGCCTTATTACT
CACTTTAAATAATTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACAGTTTTGGTTA
AAACAGACTAGAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAAAAATTCATTGGCAAGAAA
ACTCCATTTATAGTCACCTATTCCTTCAAAAGCGTTATTACTCACTTTAAATAATTGTATAGACT
CAAAATTAATTTAAATTTGAATTCTTTGATATTTTTAGTTAAAATAGACTAGAATTGAATGT
Found at i:1223 original size:171 final size:168
Alignment explanation
Indices: 770--1242 Score: 475
Period size: 171 Copynumber: 2.8 Consensus size: 168
760 AATTGAATGT
* * *
770 AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAGAAGCCTTATTACT
1 AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTTCTTCAAAAGCCTTATTACT
** * * * *
835 CACTTTAAATAATTTTATAATCTCAAAATTG-ATTTAAATTTGAATTCTTTTTACATTTTTGTTT
66 CACTTTAAAT-GGTTTATAACCT-AAAAATGAATTT-AAGTTGAATT-TTTTTATATTTTTG-TT
* * *
899 AACACAGATTATAATTGAATGTTTGCTTTGAGAAACATGAAGA
126 AACACAGATTATAATTGAATGTTTGCGTTGAGAAACATAAAAA
*** * * *
942 AAAAGGCGTTCATTGGCAAGAGAACTCCATTTATAGTCACCTA-TTCTTTCAAAAGCTTTATTAC
1 AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTTC-TTCAAAAGCCTTATTAC
* * * * * *
1006 TCACTTTAAATGGTTGTATAACATCAAAATTAATTTTAGATTGAATTTTTTGATGTTTTTAGTTA
65 TCACTTTAAATGGTT-TATAACCTAAAAATGAATTTAAG-TTGAATTTTTTTATATTTTT-GTTA
* * * * *
1071 GA-ACAGTTTATAATTGAGTGTTTTCGTTGGGAAACGTAAAAA
127 -ACACAGATTATAATTGAATGTTTGCGTTGAGAAACATAAAAA
* * * * * *
1113 AAAAGATACTCATTGGTAAGAAAAGTCCCTTTATAGTTACCTATTTCTCCAAAAGCCTTATTACT
1 AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTTCTTCAAAAGCCTTATTACT
* *
1178 TACTTTAAATGGCTTTATAACCTAAAAAATGAATATAAGTTGAATTTTTTTATATTTTTGGTTAA
66 CACTTTAAATGG-TTTATAACCT-AAAAATGAATTTAAGTTGAATTTTTTTATATTTTT-GTTAA
1243 AAAAAGGCTA
Statistics
Matches: 243, Mismatches: 49, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
170 1 0.00
171 144 0.59
172 98 0.40
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (168 bp):
AAAAGAAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTTCTTCAAAAGCCTTATTACT
CACTTTAAATGGTTTATAACCTAAAAATGAATTTAAGTTGAATTTTTTTATATTTTTGTTAACAC
AGATTATAATTGAATGTTTGCGTTGAGAAACATAAAAA
Done.