Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398745.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2029.0, 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: 2790
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.27
Warning! 705 characters in sequence are not A, C, G, or T
Found at i:1592 original size:171 final size:170
Alignment explanation
Indices: 1304--1686 Score: 500
Period size: 171 Copynumber: 2.2 Consensus size: 170
1294 NNNNNNNNNN
* * * * * **
1304 CTTTTCTTGTCAATGAATGCCTTTTTCTTTATGCTTCTTAAGATAGACATTCAATTATAATCTGT
1 CTTTTCTT-CCAATGAATGCCTTTTTCTTCATGTTTCTTGAGATAGACATTCAAGTATAATCCAT
* * * * * *
1369 TTTAATTACAAATGTAGAAAAATTTAATTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
65 TTTAACTAAAAATGTAGAAAAAATAAACTTAAAATCAATTATGAGATTATAAAACCAGTTAAAGC
* *
1434 GAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGA
130 GAGTAATAAGGCTTTTGAAAGAATGGGTGACAATAAATAGA
* * * *
1475 CTTTTCTTACCAATGAATGCCTTTTTCTTCAAGTTTCTTGATATGGACATTTAAGTATAATCCAT
1 CTTTTCTT-CCAATGAATGCCTTTTTCTTCATGTTTCTTGAGATAGACATTCAAGTATAATCCAT
*
1540 TTTAACTAAAAATGTA-AACAAAATAAACTTAAAATCAATTATGAGTTTATAAAACCAGTTAAAG
65 TTTAACTAAAAATGTAGAA-AAAATAAACTTAAAATCAATTATGAGATTATAAAACCAGTTAAAG
* *
1604 CGAGTAATAAGGCTTTTGAAGGAATGGTTGACAATAAATAGA
129 CGAGTAATAAGGCTTTTGAAAGAATGGGTGACAATAAATAGA
* *
1646 CGTTTCTTCCAATGAAT-ACTTTTTGCTTCATGTTTCTTGAG
1 CTTTTCTTCCAATGAATGCCTTTTT-CTTCATGTTTCTTGAG
1687 GCAAACATTC
Statistics
Matches: 183, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
169 6 0.03
170 25 0.14
171 152 0.83
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (170 bp):
CTTTTCTTCCAATGAATGCCTTTTTCTTCATGTTTCTTGAGATAGACATTCAAGTATAATCCATT
TTAACTAAAAATGTAGAAAAAATAAACTTAAAATCAATTATGAGATTATAAAACCAGTTAAAGCG
AGTAATAAGGCTTTTGAAAGAATGGGTGACAATAAATAGA
Found at i:2157 original size:171 final size:167
Alignment explanation
Indices: 1866--2790 Score: 932
Period size: 171 Copynumber: 5.5 Consensus size: 167
1856 CTTGAAGTAA
* * * *
1866 ACATTTAATTATAATCTGTTTTAACCAAAAATGTAAACAAACTCAACTTAAAATCAATTACGAGA
1 ACATTCAATTATAATCTGTTTTAACTAAAAATGTAAA-AAAATCAACTTAAAATCAATTATGAGA
* * * * *
1931 TAATAAAACCATTTAAAGTGAGTAATGAGGCTTTTAAAGGTACGGGTGACTATAAATAGACTTTT
65 TTATAAAA-CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTT
*
1996 CTAGGTAATGAATGGCTTTTTCTTCATATTTCTCATGGTAG
129 CTA-GTAATGAATGGCTTTTTCTTCATGTTTCTCA-GGTAG
* *
2037 ACATTCAATTATACTCAGTTTTAACTAAAAATGTAAAAAAAGTCAACTTAAAATCAATTATGAGA
1 ACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAA-TCAACTTAAAATCAATTATGAGA
* *
2102 TTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAAACTTTT
65 TTATAAAA-CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTT
** * *
2167 CTTACCAATG-ATTGCTTTTTCCTTCATGTTTCTCGAGGTAA
129 C-TAGTAATGAATGGCTTTTT-CTTCATGTTTCTC-AGGTAG
* * *
2208 ACATTCAATTATAATTTGTTTTAACCAAAAATATAAAAAAATCTAACTTAAAATCAATTATGAGA
1 ACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATC-AACTTAAAATCAATTATGAGA
* * * * * * *
2273 GTACAAAAGAATTTAAAGTGAGTAACAAGACTTTTGAAGGTATGGATGACTATAAATAGACTTTT
65 TTATAAAA-CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTT
* **
2338 CTAGTCAATGAATGGCTTTTTCTTCATGCTTTCTGAGACAG
129 CTAGT-AATGAATGGCTTTTTCTTCATG-TTTCTCAGGTAG
* * * * ** *
2379 CCATTCAATTATTATCTATTTTAA-TAAAAAATGTAAAACAATTCAACCAAAAATCAATTATGAA
1 ACATTCAATTATAATCTGTTTTAACT-AAAAATGTAAAA-AAATCAACTTAAAATCAATTATGAG
* * * * *
2443 ATTATAAAACTATTTGAAGTGAGTAATAAAGG-TTTTGAAGAAATAGGTGACTATAAACAGATTT
64 ATTATAAAAC-ATTTAAAGTGAGTAAT-AAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTT
* * *
2507 TTCTAGCCAATGAATGGTTTTTTCTTCACGTTT-TCAAGGTA-
127 TTCTAG-TAATGAATGGCTTTTTCTTCATGTTTCTC-AGGTAG
* * * * *
2548 AAAGTTCAATTATAAGT-TGTTCTAA-TAAAAA-ATATAAAAAT--A--T----TCAACTAT-AC
1 ACA-TTCAATTATAA-TCTGTTTTAACTAAAAATGTAAAAAAATCAACTTAAAATCAATTATGA-
* *
2601 GATTATACAACCATTTAAAGTGAGTAATAAGGCTTTAGAAGGAATGGGTGACTATAAAT-GAACT
63 GATTATA-AAACATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAG-ACT
* * *
2665 TTTTTTGTCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGTAG
126 TTTCTAGT-AATGAATGGCTTTTTCTTCATGTTTCTC-AGGTAG
* * * *
2709 ACATTTAATTATAATTTGTTTTAACTAAAAATGTAAAAATATTCAACTTAAAATCAACTATGAGA
1 ACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAA-AATCAACTTAAAATCAATTATGAGA
2774 TTATAAAACTATTTAAA
65 TTATAAAAC-ATTTAAA
Statistics
Matches: 619, Mismatches: 98, Indels: 74
0.78 0.12 0.09
Matches are distributed among these distances:
158 6 0.01
159 82 0.13
160 28 0.05
161 8 0.01
162 5 0.01
163 2 0.00
165 2 0.00
167 4 0.01
168 4 0.01
169 7 0.01
170 42 0.07
171 404 0.65
172 25 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (167 bp):
ACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATCAACTTAAAATCAATTATGAGAT
TATAAAACATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCT
AGTAATGAATGGCTTTTTCTTCATGTTTCTCAGGTAG
Found at i:2267 original size:342 final size:337
Alignment explanation
Indices: 1845--2790 Score: 1066
Period size: 342 Copynumber: 2.8 Consensus size: 337
1835 ACTACCTTTC
* * * * *
1845 CCTTCACGTTCCTTGAA-GTAAACATTTAATTATAATCTGTTTTAACCAAAAATGTAAACAAACT
1 CCTTCACGTT--TTCAAGGTAAACATTCAATTATAATTTGTTTTAACCAAAAATATAAAAAAACT
* *
1909 CAACTTAAAATCAATTACGAGATAATAAAACCATTTAAAGTGAGTAATGAGGCTTTTAAAGGTAC
64 -AACTTAAAATCAATTACGAGAT-ATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGTAT
1974 GGGTGACTATAAATAGACTTTTCTAGGT-AATGAATGGCTTTTTCTTCATATTTCTCATGGTAGA
127 GGGTGACTATAAATAGACTTTTCTA-GTCAATGAATGGCTTTTTCTTCATATTTCTCA-GGTAGA
*
2038 CATTCAATTATACTCAGTTTTAACTAAAAATGTAAAAAAAGTCAACTTAAAATCAATTATGAGAT
190 CATTCAATTATA-TCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * *
2103 TATAAAA-TCATTTAAAGCGAGTAAT-AAGGCTTTTGAAGGAATGGGTGACTATAAATAAACTTT
254 TATAAAACT-ATTTAAAGCGAGTAATAAAGG-TTTTGAAGAAATAGGTGACTATAAACAAACTTT
*
2166 TCTTA-CCAATGATTGCTTTTT
317 TC-TAGCCAATGAATGCTTTTT
* *
2187 CCTTCATGTTTCTCGAGGTAAACATTCAATTATAATTTGTTTTAACCAAAAATATAAAAAAATCT
1 CCTTCACGTTT-TCAAGGTAAACATTCAATTATAATTTGTTTTAACCAAAAATATAAAAAAA-CT
* * ** * * *
2252 AACTTAAAATCAATTATGAGAGTACAAAAGAATTTAAAGTGAGTAACAAGACTTTTGAAGGTATG
64 AACTTAAAATCAATTACGAGA-TATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGTATG
* * * ** *
2317 GATGACTATAAATAGACTTTTCTAGTCAATGAATGGCTTTTTCTTCATGCTTTCTGAGACAGCCA
128 GGTGACTATAAATAGACTTTTCTAGTCAATGAATGGCTTTTTCTTCAT-ATTTCTCAGGTAGACA
* ** *
2382 TTCAATTATTATCTA-TTTTAA-TAAAAAATGTAAAACAATTCAACCAAAAATCAATTATGAAAT
192 TTCAATTA-TATC-AGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * *
2445 TATAAAACTATTTGAAGTGAGTAATAAAGGTTTTGAAGAAATAGGTGACTATAAACAGATTTTTC
254 TATAAAACTATTTAAAGCGAGTAATAAAGGTTTTGAAGAAATAGGTGACTATAAACAAACTTTTC
*
2510 TAGCCAATGAATGGTTTTT
319 TAGCCAATGAATGCTTTTT
* * * * *
2529 TCTTCACGTTTTCAAGGTAAA-AGTTCAATTATAAGTTGTTCTAA-TAAAAA-ATATAAAAA-T-
1 CCTTCACGTTTTCAAGGTAAACA-TTCAATTATAATTTGTTTTAACCAAAAATATAAAAAAACTA
* * * * *
2589 A-TT-CAA-CTA-TACGA-TTATACAACCATTTAAAGTGAGTAATAAGGC-TTTAGAAGGAATGG
65 ACTTAAAATCAATTACGAGATATAAAACCATTTAAAGTGAGTAATAAGGCTTTTA-AAGGTATGG
* * **
2648 GTGACTATAAAT-GAACTTTTTTTGTCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGTAGACA
129 GTGACTATAAATAG-ACTTTTCTAGTCAATGAATGGCTTTTTCTTCATATTTCTC-AGGTAGACA
* ** * *
2712 TTTAATTATAATTTGTTTTAACTAAAAATGTAAAAATATTCAACTTAAAATCAACTATGAGATTA
192 TTCAATTAT-ATCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
2777 TAAAACTATTTAAA
256 TAAAACTATTTAAA
Statistics
Matches: 511, Mismatches: 74, Indels: 50
0.80 0.12 0.08
Matches are distributed among these distances:
329 10 0.02
330 143 0.28
331 1 0.00
332 4 0.01
333 2 0.00
334 2 0.00
335 2 0.00
336 1 0.00
337 1 0.00
339 8 0.02
340 7 0.01
341 35 0.07
342 278 0.54
343 17 0.03
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (337 bp):
CCTTCACGTTTTCAAGGTAAACATTCAATTATAATTTGTTTTAACCAAAAATATAAAAAAACTAA
CTTAAAATCAATTACGAGATATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGTATGGGT
GACTATAAATAGACTTTTCTAGTCAATGAATGGCTTTTTCTTCATATTTCTCAGGTAGACATTCA
ATTATATCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
CTATTTAAAGCGAGTAATAAAGGTTTTGAAGAAATAGGTGACTATAAACAAACTTTTCTAGCCAA
TGAATGCTTTTT
Done.