Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398691.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1977.0, 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: 5427
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.18
Warning! 2900 characters in sequence are not A, C, G, or T
Found at i:1141 original size:171 final size:170
Alignment explanation
Indices: 611--1508 Score: 726
Period size: 171 Copynumber: 5.2 Consensus size: 170
601 NNNNNNNNNN
* * * *
611 CTTAAAATCAATTATGAGTTTATAAAACAATTTAAAGCGAGTAATAAAGCTTTTGAAGGAATAGG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGG
* * *
676 TGACCATAAATAGACTTTTCTTGCCAATGAATGTGTTTTTCTTCATG-TTTCTTAAGGCAACCAT
66 TGACTATAAATAGACTTTTCTTGCCAATGAATGAGTTTTTCTTCATGTTTTC-T-AGGCAAGCAT
*
740 TCAATTATAGTCTGTTTTATCTAAAAATGTAAAAATATTTAA
129 TCAATTATAGTCTGTTTTATCTAAAAATGTAAAAAAATTTAA
************ * * *
782 CTTAAAATCNNNNNNNNNNNNATAAAACAACTTAAAACGAGTAATAAGGTTTTTGAAGAAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGG
** * * * * * * *
847 TGACTATAAAGGGACTTTTCTTACCAACGAAAGCA-TTTTTCTTCACGTTTTTATAAGCAAACAT
66 TGACTATAAATAGACTTTTCTTGCCAATGAATG-AGTTTTTCTTCATG-TTTTCTAGGCAAGCAT
* * * *
911 TCAATTATAGTCTGTTTTAACTAAAAATATAAAATAATTCAA
129 TCAATTATAGTCTGTTTTATCTAAAAATGTAAAAAAATTTAA
********** * **
953 CNNNNNNNNNNTTATGAGATTATAAAACATTTTAAAGCGAGTAATAAGAATTTTGAAGAAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGG
*
1018 TGACTATAAATAGACTTTTCTTGCAAATGAATGAGTTTTTCTTCATGTTTTGCTAGGCAAGCATT
66 TGACTATAAATAGACTTTTCTTGCCAATGAATGAGTTTTTCTTCATGTTTT-CTAGGCAAGCATT
* * *
1083 CAATTATACTCTGTTATATCCAAAAATGTAAAAAAATTTAA
130 CAATTATAGTCTGTTTTATCTAAAAATGTAAAAAAATTTAA
* * ********** *
1124 CTTAAAATCAATTATGAGTTTATAAAATANNNNNNNNNNAGTAATAAGGCTTTTGAAGGAATGGG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGG
* * * * * *
1189 TAACTATAAATGGACTTTTCTTGTCAACGAATGCA-TTTTTCTTCATGTTTATCTAAGTCGA-CA
66 TGACTATAAATAGACTTTTCTTGCCAATGAATG-AGTTTTTCTTCATGTTT-TCT-AGGCAAGCA
* * * * * *
1252 TTGAATTATAGTCTGTTTTAACTAAGAATATAAAAATATTCAA
128 TTCAATTATAGTCTGTTTTATCTAAAAATGTAAAAAAATTTAA
* ********** * * * *
1295 CTTAAAATTAATTATGAGATTNNNNNNNNNNTTAAAGCGACTAATAAGGCTTTTGACGGAACTAG
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGA-AGAAATGG
* * * * * *
1360 GTGACAATAAATAGACTTTTCTTGCCCATGAAT-ATGCTTTTCTTCATGTTTCTCGAGGTAAGAA
65 GTGACTATAAATAGACTTTTCTTGCCAATGAATGA-GTTTTTCTTCATGTTT-TCTAGGCAAGCA
* * * *
1424 TTCAATTATACTCTATTTTATCCAAAAATGTAAAACAATTTAA
128 TTCAATTATAGTCTGTTTTATCTAAAAATGTAAAAAAATTTAA
*
1467 CTTAAAATCAATTATGAGATCATAAAACAATTTAAAGCGAGT
1 CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGT
1509 NNNNNNNNNN
Statistics
Matches: 541, Mismatches: 174, Indels: 23
0.73 0.24 0.03
Matches are distributed among these distances:
170 6 0.01
171 415 0.77
172 117 0.22
173 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34
Consensus pattern (170 bp):
CTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGG
TGACTATAAATAGACTTTTCTTGCCAATGAATGAGTTTTTCTTCATGTTTTCTAGGCAAGCATTC
AATTATAGTCTGTTTTATCTAAAAATGTAAAAAAATTTAA
Found at i:1261 original size:342 final size:341
Alignment explanation
Indices: 611--1508 Score: 906
Period size: 342 Copynumber: 2.6 Consensus size: 341
601 NNNNNNNNNN
* * *
611 CTTAAAATCAATTATGAGTTTATAAAACAATTTAAAGCGAGTAATAA-AGCTTTTGAAGGAATAG
1 CTTAAAATTAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGA-CTTTTGAAGAAATAG
* * *
675 GTGACCATAAATAGACTTTTCTTGCCAATGAATGTGTTTTTCTTCATG-TTTCTTAAGGCAACCA
65 GTGACAATAAATAGACTTTTCTTGCCAATGAATGAGTTTTTCTTCATGTTTTC-T-AGGCAAGCA
* * * ************
739 TTCAATTATAGTCTGTTTTATCTAAAAATGTAAAAATATTTAACTTAAAATCNNNNNNNNNNNNA
128 TTCAATTATACTCTGTTTTATCCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATCA
* *
804 TAAAACAACTTAAAACGAGTAATAAGGTTTTTGAAGAAATGGGTGACTATAAAGGGACTTTTCTT
193 TAAAACAACTTAAAACGAGTAATAAGGCTTTTGAAGAAATGGGTAACTATAAAGGGACTTTTCTT
*
869 ACCAACGAAAGCATTTTTCTTCACGTTTTTATAAGCAAACATTCAATTATAGTCTGTTTTAACTA
258 ACCAACGAAAGCATTTTTCTTCACGTTTATATAAGCAAACATTCAATTATAGTCTGTTTTAACTA
934 AAAATAT-AAAATAATTCAA
323 AAAATATAAAAAT-ATTCAA
********** * * *
953 CNNNNNNNNNNTTATGAGATTATAAAACATTTTAAAGCGAGTAATAAGAATTTTGAAGAAATGGG
1 CTTAAAATTAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGACTTTTGAAGAAATAGG
* *
1018 TGACTATAAATAGACTTTTCTTGCAAATGAATGAGTTTTTCTTCATGTTTTGCTAGGCAAGCATT
66 TGACAATAAATAGACTTTTCTTGCCAATGAATGAGTTTTTCTTCATGTTTT-CTAGGCAAGCATT
* * *
1083 CAATTATACTCTGTTATATCCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGTTTATA
130 CAATTATACTCTGTTTTATCCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATCATA
* ********** * * **
1148 AAATANNNNNNNNNNAGTAATAAGGCTTTTGAAGGAATGGGTAACTATAAATGGACTTTTCTTGT
195 AAACAACTTAAAACGAGTAATAAGGCTTTTGAAGAAATGGGTAACTATAAAGGGACTTTTCTTAC
* * * * *
1213 CAACGAATGCATTTTTCTTCATGTTTATCTAAGTC-GACATTGAATTATAGTCTGTTTTAACTAA
260 CAACGAAAGCATTTTTCTTCACGTTTATATAAG-CAAACATTCAATTATAGTCTGTTTTAACTAA
*
1277 GAATATAAAAATATTCAA
324 AAATATAAAAATATTCAA
********** * * * *
1295 CTTAAAATTAATTATGAGATTNNNNNNNNNNTTAAAGCGACTAATAAGGCTTTTGACGGAACTAG
1 CTTAAAATTAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGACTTTTGA-AGAAATAG
* * * * *
1360 GTGACAATAAATAGACTTTTCTTGCCCATGAAT-ATGCTTTTCTTCATGTTTCTCGAGGTAAGAA
65 GTGACAATAAATAGACTTTTCTTGCCAATGAATGA-GTTTTTCTTCATGTTT-TCTAGGCAAGCA
* *
1424 TTCAATTATACTCTATTTTATCCAAAAATGTAAAACAATTTAACTTAAAATCAATTATGAGATCA
128 TTCAATTATACTCTGTTTTATCCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATCA
* *
1489 TAAAACAATTTAAAGCGAGT
193 TAAAACAACTTAAAACGAGT
1509 NNNNNNNNNN
Statistics
Matches: 440, Mismatches: 108, Indels: 15
0.78 0.19 0.03
Matches are distributed among these distances:
342 300 0.68
343 138 0.31
344 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34
Consensus pattern (341 bp):
CTTAAAATTAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGACTTTTGAAGAAATAGG
TGACAATAAATAGACTTTTCTTGCCAATGAATGAGTTTTTCTTCATGTTTTCTAGGCAAGCATTC
AATTATACTCTGTTTTATCCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATCATAA
AACAACTTAAAACGAGTAATAAGGCTTTTGAAGAAATGGGTAACTATAAAGGGACTTTTCTTACC
AACGAAAGCATTTTTCTTCACGTTTATATAAGCAAACATTCAATTATAGTCTGTTTTAACTAAAA
ATATAAAAATATTCAA
Found at i:3241 original size:171 final size:169
Alignment explanation
Indices: 2732--3242 Score: 558
Period size: 171 Copynumber: 3.0 Consensus size: 169
2722 NNNNNNNTTA
*
2732 AATTTTTTTACATTTTTG-GATAAAACAGACTATAATTGAATGCTTGCCTCGTAAAACATGAAGA
1 AATTTTTTTACA-TTTTGAGATAAAACAGACTATAATTGAATGCTTGCCTC-AAAAACATGAAGA
* * * *
2796 GAAACTCATTCATTTGCAAGAAAAGTCTATTTATAGTCACTCATTTCTTCAAAATTCTTATTACT
64 AAAACACATTCATTGGCAAGAAAAGTCTATTTATAGTCACTCATTTCTTCAAAACT-TTATTACT
*
2861 CGCTTTAAAATGTTTCATAATCTCATAATTGATTTTAAATTG
128 CGCTTTAAAATGTTTCATAATCTCATAATTGATTTTAAGTTG
* * * * * * * * *
2903 AATTATTTTATATTTTTAGTTAAAATAGACTATAATTGAATGTTTGCTTATAAAAACGTGAAGAA
1 AATTTTTTTACATTTTGAGATAAAACAGACTATAATTGAATGCTTGCCT-CAAAAACATGAAGAA
** * ** * * *
2968 AAATGCTTTTGTTGGTAAGAAAAGTCCT-TTTATAGTCACCCATTTCTTCAAAAACCTTATTACT
65 AAACACATTCATTGGCAAGAAAAGT-CTATTTATAGTCACTCATTTCTTC-AAAACTTTATTACT
* **********
3032 CGTTTTNNNNNNNNNNATAATCTCATAATTGATTTTAAGTTG
128 CGCTTTAAAATGTTTCATAATCTCATAATTGATTTTAAGTTG
*
3074 AATTTTTTTACATTTTGAGATAAAACAGACTATAATTGAATGGTTGCCTCAAGAAACATGAAGAA
1 AATTTTTTTACATTTTGAGATAAAACAGACTATAATTGAATGCTTGCCTCAA-AAACATGAAGAA
* * * *
3139 AAACACATTCATTGGCAAGAAAAGTCTATTTATGGTCACTTATTCCTTCGAAAGCTTTATTACTC
65 AAACACATTCATTGGCAAGAAAAGTCTATTTATAGTCACTCATTTCTTC-AAAACTTTATTACTC
* * *
3204 GCTTTAAATTGTTTTATAAACTCATAATTGATTTTAAGT
129 GCTTTAAAATGTTTCATAATCTCATAATTGATTTTAAGT
3243 NNNNNNNNNN
Statistics
Matches: 267, Mismatches: 67, Indels: 12
0.77 0.19 0.03
Matches are distributed among these distances:
170 8 0.03
171 253 0.95
172 6 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (169 bp):
AATTTTTTTACATTTTGAGATAAAACAGACTATAATTGAATGCTTGCCTCAAAAACATGAAGAAA
AACACATTCATTGGCAAGAAAAGTCTATTTATAGTCACTCATTTCTTCAAAACTTTATTACTCGC
TTTAAAATGTTTCATAATCTCATAATTGATTTTAAGTTG
Done.