Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400932.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4094.0, 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: 2675
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.29
Warning! 589 characters in sequence are not A, C, G, or T
Found at i:897 original size:170 final size:155
Alignment explanation
Indices: 610--925 Score: 400
Period size: 170 Copynumber: 1.9 Consensus size: 155
600 NNNNNAGTGG
*
610 AATTTTTTTACATTTTTCTTTAAAACAGACAATAATTGAATGTCTAACTCCAGAAACGTGTAGAA
1 AATTTTTTTACATTTTTCTTTAAAACAGACAATAATTGAATGTCTAACTCCAGAAACATGTAGAA
* * *
675 AAAGAGATTGATTGAGAAAAAAAGTCTATTTATAGTCACTTATTCCTTTAAAAGGCTTATTACTC
66 AAAGACATTAATTGAGAAAAAAAGTCTATTTATAGTCACTCATTCCTTTAAAAGGCTTATTACTC
*
740 GTTTTAAATAATTTTATAATCTCAT
131 GCTTTAAATAATTTTATAATCTCAT
*
765 AATTNNNNNNNNNNNNNNNNTTTTTACATTTTTCTTTAAAACAGACAATAATTGAATTTCTAACT
1 AATT----------------TTTTTACATTTTTCTTTAAAACAGACAATAATTGAATGTCTAACT
* *
830 CCA-AAACATGTAGAAAAAGCCATTAATTGAGAAAAAAAGTCTATTTATAGTCACTCATTCTTTT
50 CCAGAAACATGTAGAAAAAGACATTAATTGAGAAAAAAAGTCTATTTATAGTCACTCATTCCTTT
*
894 AAAAGGCTTATTACTCGCTTTAAATAGTTTTA
115 AAAAGGCTTATTACTCGCTTTAAATAATTTTA
926 NNNNNNNNNN
Statistics
Matches: 136, Mismatches: 9, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
155 4 0.03
170 85 0.62
171 47 0.35
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.37
Consensus pattern (155 bp):
AATTTTTTTACATTTTTCTTTAAAACAGACAATAATTGAATGTCTAACTCCAGAAACATGTAGAA
AAAGACATTAATTGAGAAAAAAAGTCTATTTATAGTCACTCATTCCTTTAAAAGGCTTATTACTC
GCTTTAAATAATTTTATAATCTCAT
Found at i:1284 original size:171 final size:169
Alignment explanation
Indices: 973--1835 Score: 515
Period size: 170 Copynumber: 5.0 Consensus size: 169
963 NNNNNNNNNN
* *
973 TTAAAACATACTATAATTGAATGTCTACCTT-GAGACATGTGA-AGAAACAAGC-ATTCATTAAG
1 TTAAAACATACTATAATTG-ATGTCTA-CTTAG-GAAATGT-ATAGAAA-AAACTATTCATTAAG
* * ** * *
1035 AAGAAAAGT-TCAATTAGAGTCACCCATTTTTTGAAAAG-CTTATTACTAGCTTTAAA-CAGTTT
61 AAGAAAAGTCT-ATTTACAGTCACCCATTCCTTCAAAAGACTTATTACTAGCTTTAAATGA-TTT
* *
1097 TATAATCTCGTAATTGATTTTAAGTTGAATCATTTTTCAT-TTTTT-G
124 TATAATCTCATAATTGATTTAAAGTTGAAT--TTTTTCATATTTTTCG
* * *
1143 TTAAAACATACTATAAGTGATGGTCTACTTTAGGAAATGTTTAGAAAAAATTATTCATTAAGAAG
1 TTAAAACATACTATAATTGAT-GTCTAC-TTAGGAAATGTATAGAAAAAACTATTCATTAAGAAG
* * *
1208 AAAAGTCTATTTATAATCACTCATTCCTTCAAAAGACTTATTACCT-GCTTTAAATGATTTTATA
64 AAAAGTCTATTTACAGTCACCCATTCCTTCAAAAGACTTATTA-CTAGCTTTAAATGATTTTATA
* * *
1272 ATCTCATAATTGATTTAAAGTTGAGTTTTTTTATATTTTTCT
128 ATCTCATAATTGATTTAAAGTTGAATTTTTTCATATTTTTCG
* * * * * * ** * *
1314 TTAAAACAGACTATAATTGAAAGCCTAGCTCAAGAAATATATAGAAGAAGCCTGTTCATTGAGAA
1 TTAAAACATACTATAATTG-ATGTCTA-CTTAGGAAATGTATAGAA-AAAACTATTCATTAAGAA
* * * * *
1379 GAAAAGCCTATTCACAGTTACCCATTCCTTCAAAA-ATCTTATTACTCGATTTAAATGATTTTAT
63 GAAAAGTCTATTTACAGTCACCCATTCCTTCAAAAGA-CTTATTACTAGCTTTAAATGATTTTAT
********** * *
1443 AATCTCATAATTGATNNNNNNNNNNATTTTTTTATATTTTTGG
127 AATCTCATAATTGATTTAAAGTTGAATTTTTTCATATTTTTCG
* * * * * * * *
1486 TTAAAACAGACTATAATTAAATGTTTGCCTCAAGAAA--CAT-GCAACAAAAGCTATTCATTGAG
1 TTAAAACATACTATAATT-GATGTCT-ACTTAGGAAATGTATAG-AA-AAAA-CTATTCATTAAG
* * * * * * * *
1548 AAGAAAAGTCCATTTATAGTGACCCATTCCTTCAAAAGGCTTACTACTCGTTTTAAATGGTTTTA
61 AAGAAAAGTCTATTTACAGTCACCCATTCCTTCAAAAGACTTATTACTAGCTTTAAATGATTTTA
*********
1613 TAATCTCANNNNNNNNNNT-AAGTTGAATTTTTT-ATATTTTT-G
126 TAATCTCA-TAATTGATTTAAAGTTGAATTTTTTCATATTTTTCG
* * * * * * * *
1655 ATGAAAACATACTATAATTGAATGTTTACGTCGAGAAACGTGA-AGAAAAAAGC-ATCCATTGAC
1 -TTAAAACATACTATAATTG-ATGTCTACTTAG-GAAATGT-ATAGAAAAAA-CTATTCATTAAG
* * * * *
1718 AAGAAAAGTATATTTAGAGTCACCCATTCCTTTAAAA-AGCTTATTACTCGCTTTAAA-CAGTTT
61 AAGAAAAGTCTATTTACAGTCACCCATTCCTTCAAAAGA-CTTATTACTAGCTTTAAATGA-TTT
* * * * *
1781 TACAATCTCATAATTGATTTTAAGTTGAATTGTTTTTACATTTTTTG
124 TATAATCTCATAATTGATTTAAAGTTGAATT-TTTTCATATTTTTCG
1828 TTAAAACA
1 TTAAAACA
1836 GANNNNNNNN
Statistics
Matches: 539, Mismatches: 119, Indels: 68
0.74 0.16 0.09
Matches are distributed among these distances:
169 16 0.03
170 198 0.37
171 175 0.32
172 147 0.27
173 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.37
Consensus pattern (169 bp):
TTAAAACATACTATAATTGATGTCTACTTAGGAAATGTATAGAAAAAACTATTCATTAAGAAGAA
AAGTCTATTTACAGTCACCCATTCCTTCAAAAGACTTATTACTAGCTTTAAATGATTTTATAATC
TCATAATTGATTTAAAGTTGAATTTTTTCATATTTTTCG
Found at i:1440 original size:172 final size:169
Alignment explanation
Indices: 1194--1837 Score: 466
Period size: 172 Copynumber: 3.8 Consensus size: 169
1184 TAGAAAAAAT
* * * * *
1194 TATTCATTAAGAAGAAAAGTCTATTTATAATCACTCATTCCTTCAAAAGACTTATTAC-CTGCTT
1 TATTCATTGAGAAGAAAAGCCTATTTATAGTCACCCATTCCTTCAAAA-ACTTATTACTC-GATT
*
1258 TAAATGATTTTATAATCTCATAATTGAT-TTAAAGTTGAGTTTTTTTATATTTTTCTTTAAAACA
64 TAAATGATTTTATAATCTCATAATTGATATTAAAGTTGA-TTTTTTTATATTTTTCGTTAAAACA
* *
1322 GACTATAATTGAAA-GCCTAG-CTCAAGAAATAT-ATAGAAGAAGCC
128 GACTATAATT-AAATG-CTAGCCTCAAGAAACATCA-ACAA-AAG-C
* * * *
1366 TGTTCATTGAGAAGAAAAGCCTATTCACAGTTACCCATTCCTTCAAAAATCTTATTACTCGATTT
1 TATTCATTGAGAAGAAAAGCCTATTTATAGTCACCCATTCCTTCAAAAA-CTTATTACTCGATTT
********** *
1431 AAATGATTTTATAATCTCATAATTGATNNNNNNNNNNATTTTTTTATATTTTTGGTTAAAACAGA
65 AAATGATTTTATAATCTCATAATTGATATTAAAGTTGATTTTTTTATATTTTTCGTTAAAACAGA
* *
1496 CTATAATTAAATGTTTGCCTCAAGAAACATGCAACAAAAGC
130 CTATAATTAAATGCTAGCCTCAAGAAACAT-CAACAAAAGC
* * * *
1537 TATTCATTGAGAAGAAAAGTCC-ATTTATAGTGACCCATTCCTTCAAAAGGCTTACTACTCGTTT
1 TATTCATTGAGAAGAAAAG-CCTATTTATAGTCACCCATTCCTTCAAAA-ACTTATTACTCGATT
* ********** * *
1601 TAAATGGTTTTATAATCTCANNNNNNNNNNT-AAGTTGAATTTTTTATATTTTT-GATGAAAACA
64 TAAATGATTTTATAATCTCATAATTGATATTAAAGTTGATTTTTTTATATTTTTCG-TTAAAACA
* * * * * * * *
1664 TACTATAATTGAATGTTTA-CGTCGAGAAACGTGAAGAAAAAAGC
128 GACTATAATTAAATG-CTAGCCTCAAGAAACAT-CA-ACAAAAGC
* * ** * * *
1708 -ATCCATTGACAAGAAAAGTATATTTAGAGTCACCCATTCCTTTAAAAAGCTTATTACTCGCTTT
1 TATTCATTGAGAAGAAAAGCCTATTTATAGTCACCCATTCCTTCAAAAA-CTTATTACTCGATTT
* * * * *
1772 AAA-CAGTTTTACAATCTCATAATTGAT-TTTAAGTTGAATTGTTTTTACATTTTTTGTTAAAAC
65 AAATGA-TTTTATAATCTCATAATTGATATTAAAGTTG-ATT-TTTTTATATTTTTCGTTAAAAC
1835 AGA
127 AGA
1838 NNNNNNNNNN
Statistics
Matches: 370, Mismatches: 83, Indels: 38
0.75 0.17 0.08
Matches are distributed among these distances:
169 2 0.01
170 120 0.32
171 92 0.25
172 149 0.40
173 6 0.02
174 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
TATTCATTGAGAAGAAAAGCCTATTTATAGTCACCCATTCCTTCAAAAACTTATTACTCGATTTA
AATGATTTTATAATCTCATAATTGATATTAAAGTTGATTTTTTTATATTTTTCGTTAAAACAGAC
TATAATTAAATGCTAGCCTCAAGAAACATCAACAAAAGC
Done.