Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402954.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_615.0, 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: 4887
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.24
Warning! 1745 characters in sequence are not A, C, G, or T
Found at i:618 original size:171 final size:171
Alignment explanation
Indices: 301--670 Score: 446
Period size: 171 Copynumber: 2.2 Consensus size: 171
291 NNNNNNNNNN
* * * **
301 ACTTAAAATCAATTATGAAATTATAAAATCATTTAAACTGAGTAATAAGGCTTTAGAAAGCATGG
1 ACTTAAAATCAATTATGAGATTATAAAAGCATTTAAACTGAGTAATAAGGCTTTAGAAAGAATAA
* * * ** * *
366 GTGACTAAAAATGGATATTTCTTCTCAATGAATGGCTTTTTCTATATCTTTTGTGAGGTAGGCTA
66 GTGACTAAAAATAGATATTTCTTCTCAATGAAAGGCTTTTTCTACATCTTTCCTGAGGCAAGCTA
*
431 TCAAGTATAGTCTGTTTTAA-AGAAAAATGTAAACAAATTCA
131 TCAAGTATACTCTGTTTTAATA-AAAAATGTAAACAAATTCA
* * *
472 ACTTAAAACCAATTATGAGATTATAAAAGCATTTAAAGC-GGGTAATAAGGCATTT-GAAGGAAT
1 ACTTAAAATCAATTATGAGATTATAAAAGCATTTAAA-CTGAGTAATAAGGC-TTTAGAAAGAAT
* * * *
535 AAGTTACTATAAATAGACT-TTTCTTCTCAATGAAAGGCTTTTTTTGCA-CGTTTCCTGAGGCAA
64 AAGTGACTAAAAATAGA-TATTTCTTCTCAATGAAAGGCTTTTTCTACATC-TTTCCTGAGGCAA
*
598 GC-ATTCAATTATACTCTGTTTTAATAAAAAATGTAAACAAATTCA
127 GCTA-TCAAGTATACTCTGTTTTAATAAAAAATGTAAACAAATTCA
*
643 ACTTAAAATCAATTTTGAGATTATAAAA
1 ACTTAAAATCAATTATGAGATTATAAAA
671 CTATTTNNNN
Statistics
Matches: 170, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
170 2 0.01
171 162 0.95
172 6 0.04
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (171 bp):
ACTTAAAATCAATTATGAGATTATAAAAGCATTTAAACTGAGTAATAAGGCTTTAGAAAGAATAA
GTGACTAAAAATAGATATTTCTTCTCAATGAAAGGCTTTTTCTACATCTTTCCTGAGGCAAGCTA
TCAAGTATACTCTGTTTTAATAAAAAATGTAAACAAATTCA
Found at i:1227 original size:171 final size:171
Alignment explanation
Indices: 897--1251 Score: 478
Period size: 171 Copynumber: 2.1 Consensus size: 171
887 NNNNNNNNNN
* *
897 TAAAACCATTTAAACCGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATAGGTTTTTCTT
1 TAAAACCATTTAAACCGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATAGGCTTTTCTT
* *
962 TTTAATGAATACTTGTTTCTTTACGTTTCTCAAGATAGACATTCAATTATAGTATGTTTTAATAA
66 GTCAATGAATACTTGTTTCTTTACGTTTCTCAAGATAGACATTCAATTATAGTATGTTTTAATAA
**********
1027 AAAATATANNNNNNNNNNACTTAAAATCAATTATGAGACTA
131 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGACTA
* * * * *
1068 TAAAACTATTTAAATCGAGTAATAA-GCTTTTTAAAAGAATGGGTGAGTCTAAATGGGCTTTTCT
1 TAAAACCATTTAAACCGAGTAATAAGGC-TTTTAAAAGAATGGGTGACTATAAATAGGCTTTTCT
* *
1132 TGTCAATGAATGCTTGTTTCTTTACGTTTCTCAAGATAGATATTCAATTATAGTATGTTTTAATA
65 TGTCAATGAATACTTGTTTCTTTACGTTTCTCAAGATAGACATTCAATTATAGTATGTTTTAATA
* * *
1197 CAAAATATAAAAAAATTCAACTTCAAATCAATTATGAGATTA
130 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGACTA
1239 TAAAACCATTTAA
1 TAAAACCATTTAA
1252 NNNNNNNNNN
Statistics
Matches: 158, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
170 2 0.01
171 156 0.99
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.37
Consensus pattern (171 bp):
TAAAACCATTTAAACCGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATAGGCTTTTCTT
GTCAATGAATACTTGTTTCTTTACGTTTCTCAAGATAGACATTCAATTATAGTATGTTTTAATAA
AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGACTA
Found at i:2092 original size:171 final size:170
Alignment explanation
Indices: 1807--3093 Score: 1353
Period size: 171 Copynumber: 7.5 Consensus size: 170
1797 NNNNNNNNNN
* * * * * * *
1807 AATGTCTATCTCGAGAAACGTAAAGAAACAAG-CATTCATTGACAAGAAAAGCCCTTTTGTAGTC
1 AATGTCTACCTCAAGAAACGTGAAGAAA-AAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTC
* *
1871 ACCCATTCCTTCAAAAGCCTTATTACTCGGTTTAAATAATTTTATAATCTCATAATTGATTTTAA
65 ACCCATTCCTTCAAAAG-CTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAA
* *
1936 GTTGAATTTTTTTATATTTTTCT-TTAAAACAGACAATAATTG
129 GTTGAATTTTTTTACATTTTT-TGTTAAAACAGACTATAATTG
* ** * ** *
1978 AATGTCTAACTCAAGAAACGTGCCGCAAAAGCCATTGGTTGAGAAGAGAAGTCCATTTATAGTCA
1 AATGTCTACCTCAAGAAACGTGAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCA
*
2043 CCCATTCCTTCAAAATGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTTATTTTAAG
66 CCCATTCCTTCAAAA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAG
* * * *
2108 TTGAATTTTTTTATA-ATTTTGATTAAAACATAATATAATTG
130 TTGAATTTTTTTACATTTTTTG-TTAAAACAGACTATAATTG
* * ** *
2149 AATGTCTACCTCAAAAAACGTGAAGAAACAAG-CATTCATTGACAAGAAAAGTAGATTTAGAGTC
1 AATGTCTACCTCAAGAAACGTGAAGAAA-AAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTC
* * * *
2213 ACCCATTCCTTCAAAAAACTTATTACTCGCTTTAAATGGTTTTATAATCTCGTAATTAATTTTAA
65 ACCCATTCCTTC-AAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAA
* *
2278 ATTGAATTTTTTTACATTTTTTGTTAAAACATACTATAATTG
129 GTTGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTG
* * *
2320 ATTGTCTACCTC-AGAAA-ATGTATAGAAAAAGCCATTCATTGAGCAGAAAAGTCCATTTATAGT
1 AATGTCTACCTCAAGAAACGTG-A-AGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGT
* * * * * *
2383 TACTCATTCCTTCAAAAGTCTTATTACCCGCTTTTAAT-GATTTTGTAATCTGATAATTGATTTT
64 CACCCATTCCTTCAAAAG-CTTATTACTCGCTTTAAATAG-TTTTATAATCTCATAATTGATTTT
** ** *
2447 AAGTTGAATTTTTTTGTATTTTTTGTCGAAATAGACTATAATTG
127 AAGTTGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTG
* ** * ** * * * * *
2491 TATACCTGCCTTGAGAAACGTGTAGAAAAAGCTTATTCATTGAGAACAAAAATCTATTTATAGTC
1 AATGTCTACCTCAAGAAACGTGAAGAAAAAGC-CATTCATTGAGAAGAAAAGTCCATTTATAGTC
* * * * * * *
2556 ACCCATTCCTTTAAAAGCCTTATTACTCGGTTTAAATGGATTTATACTCTCATAATTAATTTCAA
65 ACCCATTCCTTCAAAAG-CTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAA
* * * *
2621 GTTGATTTTTTTTACATTTTTGGTTAAAACCGACTATAATTA
129 GTTGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTG
* * * *
2663 AATGCCTGCC-CTAAGAAACGTGCAA-AAAAAGCCATTCATTGAGAAGAGAAGTCCATTTACAGT
1 AATGTCTACCTC-AAGAAACGTG-AAGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGT
* * *
2726 CACCTATTCCTTCAAAAGGCTTATTACCCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTA
64 CACCCATTCCTTCAAAA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTA
* * *
2791 AGTTGAATTTTTTTACATTTTTTATTAAAATATACTATAATTG
128 AGTTGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTG
* * * * * *
2834 AATGTCTACTTCAAGGAACGTGATGAAACAAG-CATTCATTGA-AGAGAAAAGGCCATGTAGAGT
1 AATGTCTACCTCAAGAAACGTGAAGAAA-AAGCCATTCATTGAGA-AGAAAAGTCCATTTATAGT
* * * *
2897 CACCCATTCCTTCAAAAAGCTTATTATTTGCTTCAAATAGTTTTATAATCTCAAAATTGATTTTA
64 CACCCATTCCTTC-AAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTA
* *
2962 AGTTGAATTGTTTTAAATTTTTTGTTAAAACAGACTATAATTG
128 AGTTGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTG
* * * * * * *
3005 AATG-CTTACCTC-AGAAAACATGTA-AAAAAG-CATTTAATTAAGAAAAAAAATCCATTTATGG
1 AATGTC-TACCTCAAG-AAACGTGAAGAAAAAGCCA-TTCATTGAGAAGAAAAGTCCATTTATAG
* *
3066 TCACTCATTCCTTCAAAGGCCTTATTAC
63 TCACCCATTCCTTCAAAAG-CTTATTAC
3094 CCNNNNNNNN
Statistics
Matches: 925, Mismatches: 162, Indels: 59
0.81 0.14 0.05
Matches are distributed among these distances:
169 12 0.01
170 65 0.07
171 683 0.74
172 161 0.17
173 4 0.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (170 bp):
AATGTCTACCTCAAGAAACGTGAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCA
CCCATTCCTTCAAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGT
TGAATTTTTTTACATTTTTTGTTAAAACAGACTATAATTG
Done.