Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399148.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2422.0, 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: 8364
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.22
Warning! 3501 characters in sequence are not A, C, G, or T
Found at i:1393 original size:170 final size:170
Alignment explanation
Indices: 1030--1672 Score: 442
Period size: 170 Copynumber: 3.8 Consensus size: 170
1020 NNNNNNNNNN
* * ** *
1030 AATAGACTTTTCTTGCCAATGAATGCTTTTTACTTCACTTTTCTCAAGGCAGACATTCAATTATA
1 AATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACTATTCTCAAACCAAACATTCAATTATA
** ** * * *
1095 GTATGTTTTAATTAAAAATATAAAAAATTGAACTTAAATTTAATTATGAGATTATAAAATCATTT
66 GTATGTTTTAACAAAAAATATAAAAAATCCAACTTAAAATCAATTATGAGATTATAAAACCATTT
*
1160 ATAACTAATAAAAAGGCTTTTAAAGGAATAGGAGGCTATA
131 ATAACGAATAAAAAGGCTTTTAAAGGAATAGGAGGCTATA
* *** * *
1200 AATAGAATTTTCTTATTAATGAATGCTTTTTTCTTCA-TGATTGTCAAACCAAACATTGAATTAT
1 AATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACT-ATTCTCAAACCAAACATTCAATTAT
*
1264 AGTATGTTTTAACAAAAAATATAAAAAAATCCAACTTAAAATCAATTATTAGATTAT-AAACCAT
65 AGTATGTTTTAACAAAAAATAT-AAAAAATCCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * **********
1328 TTA-AAGCGAGTAATAAGGNNNNNNNNNNAAT-GAGAGGCTATA
129 TTATAA-CGAATAAAAAGGCTTTTAAAGGAATAG-GAGGCTATA
* ***
1370 AATAGACTTTTCTTGCCAATGAATGCTTTTTTCTACA-TATTTCTCAAGGTAAACATTCAATTAT
1 AATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACTA-TTCTCAAACCAAACATTCAATTAT
** * * * ******** * *
1434 AGCCTCTTTTAACGAAAAATGT-AAAAATNNNNNNNNNNAAATTAATTATGAGATTATAAAAGCA
65 AGTATGTTTTAACAAAAAATATAAAAAAT--CCAACTTAAAATCAATTATGAGATTATAAAACCA
** * * * * * * * *
1498 TTTGA-AGTGAGTAATATGGCTTTTGAAGCAAAAGGTGACTATA
128 TTT-ATAACGAATAAAAAGGCTTTTAAAGGAATAGGAGGCTATA
* * * * ** *
1541 AAT-GAACTTTTCTTCCCAATGAATGCTTTTTGCTTCA-TGTTTCTCGAGGCAAATATTCAATTA
1 AATAG-ACTTTTCTTGCCAATGAATGCTTTTTTCTTCACT-ATTCTCAAACCAAACATTCAATTA
* * * * * *
1604 TGGTCTGTTTTAATCAAAAAAGTA-AAAAAATTCTACCTAAAATCAATTATGAGATTAGAAAACC
64 TAGTATGTTTTAA-CAAAAAA-TATAAAAAATCCAACTTAAAATCAATTATGAGATTATAAAACC
1668 ATTTA
127 ATTTA
1673 AAGCAAGTAA
Statistics
Matches: 361, Mismatches: 97, Indels: 30
0.74 0.20 0.06
Matches are distributed among these distances:
168 6 0.02
169 5 0.01
170 189 0.52
171 145 0.40
172 9 0.02
173 7 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.35
Consensus pattern (170 bp):
AATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACTATTCTCAAACCAAACATTCAATTATA
GTATGTTTTAACAAAAAATATAAAAAATCCAACTTAAAATCAATTATGAGATTATAAAACCATTT
ATAACGAATAAAAAGGCTTTTAAAGGAATAGGAGGCTATA
Found at i:1481 original size:341 final size:331
Alignment explanation
Indices: 1030--1687 Score: 682
Period size: 341 Copynumber: 2.0 Consensus size: 331
1020 NNNNNNNNNN
* *
1030 AATAGACTTTTCTTGCCAATGAATGCTTTTTACTTCACTTTTCTCAAGGCAGACATTCAATTATA
1 AATAGACTTTTCTTGCCAATGAATGCTTTTTACTACACTTTTCTCAAGGCAAACATTCAATTATA
* * ** *
1095 GTATGTTTTAATTAAAAATATAAAAAATTGAACTTAAATTTAATTATGAGATTATAAAATCATTT
66 GCATCTTTTAACGAAAAATATAAAAAATTGAACTTAAATTTAATTATGAGATTATAAAAGCATTT
* * * * **
1160 ATAACT-AATAAAAAGGCTTTTAAAGGAATAGGAGGCTATAAATAGAA-TTTTCTTATTAATGAA
131 -GAACTGAATAAAAAGGCTTTTAAAGCAAAAGGAGACTATAAAT-GAACTTTTCTTACCAATGAA
* * *
1223 TGCTTTTTTCTTCATGATTGTCAAACCAAACATTGAATTATAGTATGTTTTAA-CAAAAAATATA
194 TGCTTTTTGCTTCATGATTCTCAAACCAAACATTCAATTATAGTATGTTTTAATCAAAAAA-ATA
* * * *
1287 AAAAAATCCAACTTAAAATCAATTATTAGATTA-TAAACCATTTAAAGCGAGTAATAAGGNNNNN
258 AAAAAATCCAACCTAAAATCAATTATGAGATTAGAAAACCATTTAAAGCAAGTAATAAGG-----
1351 NNNNNAATGAGAGGCTATA
318 -----AATGAGAGGCTATA
* *
1370 AATAGACTTTTCTTGCCAATGAATGCTTTTTTCTACA-TATTTCTCAAGGTAAACATTCAATTAT
1 AATAGACTTTTCTTGCCAATGAATGCTTTTTACTACACT-TTTCTCAAGGCAAACATTCAATTAT
* * *******
1434 AGCCTCTTTTAACGAAAAATGT-AAAAATNNNNNNNNNNAAA-TTAATTATGAGATTATAAAAGC
65 AGCATCTTTTAACGAAAAATATAAAAAAT---TGAACTTAAATTTAATTATGAGATTATAAAAGC
* * * * * * *
1497 ATTTGAAGTGAGTAATATGGCTTTTGAAGCAAAAGGTGACTATAAATGAACTTTTCTTCCCAATG
127 ATTTGAACTGAATAAAAAGGCTTTTAAAGCAAAAGGAGACTATAAATGAACTTTTCTTACCAATG
* * ** * * * *
1562 AATGCTTTTTGCTTCATGTTTCTCGAGGCAAATATTCAATTATGGTCTGTTTTAATCAAAAAAGT
192 AATGCTTTTTGCTTCATGATTCTCAAACCAAACATTCAATTATAGTATGTTTTAATCAAAAAAAT
* *
1627 AAAAAAATTCTACCTAAAATCAATTATGAGATTAGAAAACCATTTAAAGCAAGTAATAAGG
257 AAAAAAATCCAACCTAAAATCAATTATGAGATTAGAAAACCATTTAAAGCAAGTAATAAGG
1688 CTTTNNNNNN
Statistics
Matches: 262, Mismatches: 48, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
339 7 0.03
340 80 0.31
341 141 0.54
342 34 0.13
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.34
Consensus pattern (331 bp):
AATAGACTTTTCTTGCCAATGAATGCTTTTTACTACACTTTTCTCAAGGCAAACATTCAATTATA
GCATCTTTTAACGAAAAATATAAAAAATTGAACTTAAATTTAATTATGAGATTATAAAAGCATTT
GAACTGAATAAAAAGGCTTTTAAAGCAAAAGGAGACTATAAATGAACTTTTCTTACCAATGAATG
CTTTTTGCTTCATGATTCTCAAACCAAACATTCAATTATAGTATGTTTTAATCAAAAAAATAAAA
AAATCCAACCTAAAATCAATTATGAGATTAGAAAACCATTTAAAGCAAGTAATAAGGAATGAGAG
GCTATA
Found at i:1654 original size:171 final size:168
Alignment explanation
Indices: 854--2002 Score: 547
Period size: 171 Copynumber: 6.7 Consensus size: 168
844 GAATGGGTGA
* ** * * * * * ** * **
854 CTATAAATGGACTTTTCTTATCAATGAATACTTTTGTCTTTACGTTTCTTAAGATAGACAGCCAA
1 CTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGCAAACATTCAA
* * * * * *
919 TTATTA-TCTGTTTTAATAAAAAAGTTAAAAAACTTCAACTTAAAATTAATTATCAGATTAGAAA
66 TTA-TAGTATGTTTTAACAAAAAAG-TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
** * * * **
983 ACCATTTAAAATGAGTAATAAGGCTTTTGAAG-TAATGNNNNN
129 ACCATTTAAAGCGAGTAATAAGGCTTTTAAAGCAAAAG---GG
***** * *
1025 NNNNNAAT-AGACTTTTCTTGCCAATGAATGCTTTTTACTTCACT-TTTCTCAAGGCAGACATTC
1 CTATAAATGA-ACTTTTCTTGCCAATGAATGCTTTTTTCTTCA-TGTTTCTCAAGGCAAACATTC
** * * *
1088 AATTATAGTATGTTTTAATTAAAAA-TATAAAAAATTGAACTTAAATTTAATTATGAGATTATAA
64 AATTATAGTATGTTTTAACAAAAAAGTA-AAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * * *
1152 AATCATTTATAA-CTAATAAAAAGGCTTTTAAAGGAATAGGAGG
128 AACCATTTA-AAGCGAGTAATAAGGCTTTTAAAGCAA-AAG-GG
*** * * ** *
1195 CTATAAATAGAA-TTTTCTTATTAATGAATGCTTTTTTCTTCATGATTGTCAAACCAAACATTGA
1 CTATAAAT-GAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGCAAACATTCA
* * *
1259 ATTATAGTATGTTTTAACAAAAAATATAAAAAAATCCAACTTAAAATCAATTATTAGATTAT-AA
65 ATTATAGTATGTTTTAACAAAAAA-GTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
********** *
1323 ACCATTTAAAGCGAGTAATAAGGNNNNNNNNNNAATGAGAGG
129 ACCATTTAAAGCGAGTAATAAGGCTTTTAAAGCAA-AAG-GG
* * *
1365 CTATAAAT-AGACTTTTCTTGCCAATGAATGCTTTTTTCTACATATTTCTCAAGGTAAACATTCA
1 CTATAAATGA-ACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGCAAACATTCA
** * * *********** *
1429 ATTATAGCCTCTTTTAACGAAAAATGTAAAAATNNNNNNNNNNAAATTAATTATGAGATTATAAA
65 ATTATAGTATGTTTTAAC-AAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * *
1494 AGCATTTGAAGTGAGTAATATGGCTTTTGAAGCAAAAGGTG
129 ACCATTTAAAGCGAGTAATAAGGCTTTTAAAGCAAAAGG-G
* * * *
1535 ACTATAAATGAACTTTTCTTCCCAATGAATGCTTTTTGCTTCATGTTTCTCGAGGCAAATATTCA
1 -CTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGCAAACATTCA
* * * * *
1600 ATTATGGTCTGTTTTAATCAAAAAAGTAAAAAAATTCTACCTAAAATCAATTATGAGATTAGAAA
65 ATTATAGTATGTTTTAA-CAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* *************
1665 ACCATTTAAAGCAAGTAATAAGGCTTTNNNNNNNNNNNNNNN
129 ACCATTTAAAGCGAGTAATAAGGCTTT--TAAAGCAAAAGGG
* * * * * *** *
1707 NTATAAATGGACTTTTCTTGTCAATGAATGCTTTTGTCTTCATGTTTCTCGAGATTAACAGTCAA
1 CTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGCAAACATTCAA
* * ********* * * * *
1772 TTATTGTCTGTTTTANNNNNNNNNNTAAAAAACTTCAACTTAAAATCAACTATTAGATTAGAAAA
66 TTATAGTATGTTTTA-ACAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* ** * * * *
1837 TCATTTAAAATGAGTAATAAAGCTTTTGAAGTAATGAGAGG
130 CCATTTAAAGCGAGTAATAAGGCTTTTAAAGCAA-AAG-GG
* * * * * * *
1878 CTATAAAT-AGACTTTTTTTGCCAATGAATACTTTTTACTTCACT-TTTCTTAAGGGAGATATTC
1 CTATAAATGA-ACTTTTCTTGCCAATGAATGCTTTTTTCTTCA-TGTTTCTCAAGGCAAACATTC
* * * * * * *
1941 AATTATAGTCTATTTTAATAAAAAATATAAAAAAATTGAACTTAAATTTAATTATGAGATTA
64 AATTATAGTATGTTTTAACAAAAAA-GTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
2003 NNNNNNNNNN
Statistics
Matches: 713, Mismatches: 236, Indels: 58
0.71 0.23 0.06
Matches are distributed among these distances:
168 1 0.00
169 7 0.01
170 237 0.33
171 460 0.65
172 8 0.01
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.35
Consensus pattern (168 bp):
CTATAAATGAACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGCAAACATTCAA
TTATAGTATGTTTTAACAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
CATTTAAAGCGAGTAATAAGGCTTTTAAAGCAAAAGGG
Found at i:7021 original size:171 final size:160
Alignment explanation
Indices: 6782--7106 Score: 325
Period size: 171 Copynumber: 2.0 Consensus size: 160
6772 TTGAAGTGAC
* * *
6782 TAATATGGCTTTTGAAGGAAAGGGTGACTATAAATAAACTTTTCTTGCAAATGAATGCTTTTTTC
1 TAATAAGGCTTTTGAAGGAAAGGGTGACTATAAATAAACTTTTCTTGCAAATGAATGCTGTGTTC
* * * * *
6847 TTCATGTTTCTCGAAGCA-A-ATATTCAATTATGGTCTGTTTAAAT-CAAAAATGTAAAAAAATT
66 TTCACGTTTCTCG-AG-ATAGACAGTCAATTATGATCTGTTTAAATAAAAAAAT-T-AAAAAATT
6909 CAACCTAAAATCAATTATGAGATTAGAAAACNNNNNNNNNNGAG
127 CAACCTAAAATCAATTATGAGATTAGAAAAC----------GAG
* * ** *
6953 TAATAAGGTTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTC-AGTGAATGCTGTGTT
1 TAATAAGGCTTTTGAAGGAAAGGGTGACTATAAATAAACTTTTCTTG-CAAATGAATGCTGTGTT
* * *
7017 CTTCACGTTTCTCGAGATAGACAGTCAATTATTATCTGTTTTAATAAAAAAATTAAAAAATTTAA
65 CTTCACGTTTCTCGAGATAGACAGTCAATTATGATCTGTTTAAATAAAAAAATTAAAAAATTCAA
* *
7082 CTTAAAATCAATTATTAGATTAGAA
130 CCTAAAATCAATTATGAGATTAGAA
7107 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
169 1 0.01
170 36 0.27
171 88 0.67
172 7 0.05
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.35
Consensus pattern (160 bp):
TAATAAGGCTTTTGAAGGAAAGGGTGACTATAAATAAACTTTTCTTGCAAATGAATGCTGTGTTC
TTCACGTTTCTCGAGATAGACAGTCAATTATGATCTGTTTAAATAAAAAAATTAAAAAATTCAAC
CTAAAATCAATTATGAGATTAGAAAACGAG
Found at i:7914 original size:171 final size:171
Alignment explanation
Indices: 7703--8077 Score: 420
Period size: 171 Copynumber: 2.2 Consensus size: 171
7693 NNNNNNNNNN
* * * * * * *
7703 AAAAAATT-TAACTTAAAATCAATGATTATATGATAAAACCATTTA-AATCAAGTA-ATAAGGCT
1 AAAAAATTACAACTTAAAATCAATTATGAGATTACAAAACCATTTAGAA-CAAGTACA-AAAG-T
* * *
7765 T-TTGAAGGAATGAGAGGCTATAAAAAAACTTTTCTTCCCAATGAATGCTTTTTTCTTCACT-TT
63 TATTAAAGGAATGAGAGGCTATAAAAAAACTTTTCTTACCAATGAATGCTTTCTTCTTCA-TGTT
* ** *
7828 TCTCAACCCAGACATTCAATTATAGTCTGTTTTAATGAAAAGTGTT
127 TCTCAACCCAGACATTCAATTATAATCCATTTTAATGAAAAATG-T
*
7874 AAAAAATTAC-ACTTAAAATTAATTATGAGATTACAAAACCATTTAGAACAAGTACAAAAGTTAT
1 AAAAAATTACAACTTAAAATCAATTATGAGATTACAAAACCATTTAGAACAAGTACAAAAGTTAT
* *** * * *
7938 TAAAGGAATGGGAGGCTATAAATGGACTTTTCTTATCAATGAATGCTTTCTTCTTCATGTTTGTT
66 TAAAGGAATGAGAGGCTATAAAAAAACTTTTCTTACCAATGAATGCTTTCTTCTTCATGTTTCTC
* *
8003 AAGCCAGACGTTCAATTATAATCCATTTTAATGAAAAATGT
131 AACCCAGACATTCAATTATAATCCATTTTAATGAAAAATGT
* * *
8044 CAAAAATTTCAACTTAAAATCAATTATTAGATTA
1 AAAAAATTACAACTTAAAATCAATTATGAGATTA
8078 TAANNNNNNN
Statistics
Matches: 170, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
170 12 0.07
171 155 0.91
172 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (171 bp):
AAAAAATTACAACTTAAAATCAATTATGAGATTACAAAACCATTTAGAACAAGTACAAAAGTTAT
TAAAGGAATGAGAGGCTATAAAAAAACTTTTCTTACCAATGAATGCTTTCTTCTTCATGTTTCTC
AACCCAGACATTCAATTATAATCCATTTTAATGAAAAATGT
Done.