Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401876.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_498.0, 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: 4830
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.27
Warning! 1153 characters in sequence are not A, C, G, or T
Found at i:1857 original size:170 final size:170
Alignment explanation
Indices: 928--2227 Score: 754
Period size: 170 Copynumber: 7.6 Consensus size: 170
918 NNNNNNNNAC
* * ** * *
928 ATTTTTTGTTAAAACAGATTGCAATTGAATGTCTGCCTT-AGGAAATGTGAAGAAAAACTCATTC
1 ATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTGA-GAAACGTAAAGAAAAAC-CATTC
* * * **
992 ATTGACTAAAAAAG-CTAATTTATAGTCACCCATGCCTTCGTAAGCCTTATTACTCGCTTTAAAT
64 ATTGACTAGAAAAGTC-CATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAAT
* * ********** * * *
1056 GGTTTTGTNNNNNNNNNNTTGATTTTAAGTAGGATTTTTTTAT
128 AGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTAT
* * * * * *
1099 ATTTTTAGTTAAAACAAA-TATAAATGAATGTCTGTCTTAAAAAACATAAAGAAAAAGCCATTCA
1 ATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAA-CCATTCA
* ** * * * *
1163 TTGACTAGAAAAGTCCATTTATAGTCATCCAAGCCTTCGAAAGCATTATTTA-ACGCTTTAGAT-
65 TTGACTAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTA-TTACTCGCTTTAAATA
* * * * *
1226 GATTTTGTAATCTCATAATTGATTTTAAGTTGAAATTTTCTAC
129 G-TTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTAT
* * ** ** * ** * **
1269 ATTTTTGGTTAAAACAGA-TAGAATTGAATGTCTATCTCAAAAAATATGAAGAAAAAGGTATTCA
1 ATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAA-CCATTCA
*********** * * * * *
1333 TTGGNNNNNNNNNNCTATTTATAGTCACCAATTCCTTCAAAAGCCTTACTGCTCACTTTAAAT-G
65 TTGACTAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
* * *
1397 ATTTTATAATCTCGTAATTGATATTAAGTT-AATTTTTTTTAT
130 -TTTTATAATCTCATAATTCATTTTAAGTTGAA-TTTTTTTAT
* * * * * * ***
1439 ATTTTTTGTTAAAACATAA-TAGAAATGATTGTCTACCTT-AGAAAATGTAAAGAAAAAGTTGTT
1 ATTTTTGGTTAAAACA-AATTATAATTGAATGTCTGCCTTGAG-AAACGTAAAGAAAAA-CCATT
* * * * * * *
1502 CATTTG-CAAGAAAAGTCTATTTATAGCCACTCATTCCTTTAAAAGCCTTATTACTAGCTTTGAA
63 CA-TTGACTAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAA
* ****************** * * * *
1566 TGGTTTNNNNNNNNNNNNNNNNNNTTTAGGTTAAATTTTTTAAC
127 TAGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTAT
* *** * * * * * * *
1610 ATTTTTGGCTAAAACAGGCTATAATTAAATGTTTTCCTTGAGAAATGTGAAGAAAATGCTATTCA
1 ATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTGAGAAACGTAAAGAAAA-ACCATTCA
* * * ** ** ** *
1675 TAGGCAAGAAAAGTAGATTTATAGTCATTCATTTTTTCAAAAGCCTTATTACTCGCTTTAAATGG
65 TTGACTAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
*
1740 TTTTATAATCTTATAATTCA-TTTAAGTTGAATTTTTTTAT
130 TTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTAT
* * * *
1780 ATTTTTGCTTAAAACAAATTATAATTGAATGTCTACCTTGAGAAACGTGAAGAAAAAATCATTCA
1 ATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTGAGAAACGTAAAG-AAAAACCATTCA
* * * *
1845 TTGACTAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCTTTGTTACTCGCTTTAAATAG
65 TTGACTAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
* * * * *
1910 TTTTATAATCTCGTAATTGATTTTAAGTTAAATATTTTTAC
130 TTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTAT
* ** * * * * * *
1951 ATTTTTGGTTAAGACAAGCTATAATTGAATTTTTGTCTTGAAAAATGTAAAGAAAAGCCATTCAT
1 ATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAACCATTCAT
* * * * * * *
2016 TGGC-AAAACAAATCCATTTGTAGTCACCCATTCCTTCCAAAGCGTTATTACTTGCTTTAAATAG
66 TGACTAGAA-AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
* *
2080 TTTTATAATCTCATAATTCATTTTTAGTTGAATTATTTTAT
130 TTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTAT
* * * * * * *
2121 ATTTTTGGTTAAAATAGATTATAATTGGATGTCTGTCTTGGGAAACATAAAGGAAAACCCATTCA
1 ATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTGAGAAACGTAAA-GAAAAACCATTCA
* * * *
2186 TTGACTAGAAAAGCCCATTTATAGCCACTCATGCCTTCAAAA
65 TTGACTAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
2228 NNNNNNNNNN
Statistics
Matches: 856, Mismatches: 252, Indels: 42
0.74 0.22 0.04
Matches are distributed among these distances:
169 7 0.01
170 520 0.61
171 318 0.37
172 11 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.38
Consensus pattern (170 bp):
ATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAACCATTCAT
TGACTAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAGT
TTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTAT
Found at i:1942 original size:341 final size:341
Alignment explanation
Indices: 1077--2227 Score: 846
Period size: 341 Copynumber: 3.4 Consensus size: 341
1067 NNNNNNNTTG
* * * * ** * *
1077 ATTTTAAGTAGGATTTTTTTATATTTTTAG-TTAAAACAAA-TATAAATGAATGTCTGTCTTAAA
1 ATTTTAAGTTGAATTATTTTATATTTTT-GCTTAAAACAAATTATAATTGAATGTCTACCTTGAG
* * * * * *
1140 AAACATAAAGAAAAAGCCATTCATTGACTAGAAAAGTCCATTTATAGTCATCCAAGCCTTCGAAA
65 AAACATAAAGAAAAAACCATTCATTGACTAGAAAAGCCCATTTATAGCCACCCATGCCTTCAAAA
* * * * *
1205 GCATTAT-TTA-ACGCTTTAGAT-GATTTTGTAATCTCATAATTGATTTTAAGTTGAAAT-TTTC
130 GC-TT-TGTTACTCGCTTTAAATAG-TTTTATAATCTCGTAATTGATTTTAAGTT-AAATATTTT
* * * * * * ** ** * * **
1266 TACATTTTTGGTTAAAAC-AGATAGAATTGAATGTCTATCTCAAAAAATATGAAGAAAAAGGTAT
191 TACATTTTTGGCTAAAACAAGCTATAATTAAATTTTTGCCTTGAAAAATGTAAAG-AAAAGCCAT
* ********** * * * *
1330 TCATTGG-NNNNNNNNNNCTATTTATAGTCACCAATTCCTTCAAAAGCCTTACTGCTCACTTTAA
255 TCATAGGCAAAACAAATAC-ATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAA
* *
1394 AT-GATTTTATAATCTCGTAATTG
319 ATAG-TTTTATAATCTCATAATTC
* * * * *
1417 ATATTAAGTT-AATTTTTTTTATATTTTTTG-TTAAAACATAA-TAGAAATGATTGTCTACCTT-
1 ATTTTAAGTTGAA-TTATTTTATA-TTTTTGCTTAAAACA-AATTATAATTGAATGTCTACCTTG
**** * * * * *
1478 AGAAA-ATGTAAAGAAAAAGTTGTTCATTTG-CAAGAAAAGTCTATTTATAGCCACTCATTCCTT
63 AGAAACA--TAAAGAAAAAACCATTCA-TTGACTAGAAAAGCCCATTTATAGCCACCCATGCCTT
* * * * * * ****************** *
1541 TAAAAGCCTTATTACTAGCTTTGAATGGTTTNNNNNNNNNNNNNNNNNNTTTAGGTTAAAT-TTT
125 CAAAAGCTTTGTTACTCGCTTTAAATAGTTTTATAATCTCGTAATTGATTTTAAGTTAAATATTT
* * *
1605 TTAACATTTTTGGCTAAAACAGGCTATAATTAAATGTTTT-CCTTGAGAAATGTGAAGAAAATGC
190 TT-ACATTTTTGGCTAAAACAAGCTATAATTAAAT-TTTTGCCTTGAAAAATGTAAAGAAAA-GC
* * * ** **
1669 TATTCATAGGCAAGAA-AAGTAGATTTATAGTCATTCATTTTTTCAAAAGCCTTATTACTCGCTT
252 CATTCATAGGCAA-AACAAATACATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTT
* *
1733 TAAATGGTTTTATAATCTTATAATTC
316 TAAATAGTTTTATAATCTCATAATTC
*
1759 A-TTTAAGTTGAATTTTTTTATATTTTTGCTTAAAACAAATTATAATTGAATGTCTACCTTGAGA
1 ATTTTAAGTTGAATTATTTTATATTTTTGCTTAAAACAAATTATAATTGAATGTCTACCTTGAGA
* * * * * *
1823 AACGTGAAGAAAAAATCATTCATTGACTAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAAG
66 AACATAAAGAAAAAACCATTCATTGACTAGAAAAGCCCATTTATAGCCACCCATGCCTTCAAAAG
1888 CTTTGTTACTCGCTTTAAATAGTTTTATAATCTCGTAATTGATTTTAAGTTAAATATTTTTACAT
131 CTTTGTTACTCGCTTTAAATAGTTTTATAATCTCGTAATTGATTTTAAGTTAAATATTTTTACAT
* * * * *
1953 TTTTGGTTAAGACAAGCTATAATTGAATTTTTGTCTTGAAAAATGTAAAGAAAAGCCATTCATTG
196 TTTTGGCTAAAACAAGCTATAATTAAATTTTTGCCTTGAAAAATGTAAAGAAAAGCCATTCATAG
* * * * *
2018 GCAAAACAAATCCATTTGTAGTCACCCATTCCTTCCAAAGCGTTATTACTTGCTTTAAATAGTTT
261 GCAAAACAAATACATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTT
2083 TATAATCTCATAATTC
326 TATAATCTCATAATTC
* * * * * ** *
2099 ATTTTTAGTTGAATTATTTTATATTTTTGGTTAAAATAGATTATAATTGGATGTCTGTCTTGGGA
1 ATTTTAAGTTGAATTATTTTATATTTTTGCTTAAAACAAATTATAATTGAATGTCTACCTTGAGA
* * *
2164 AACATAAAGGAAAACCCATTCATTGACTAGAAAAGCCCATTTATAGCCACTCATGCCTTCAAAA
66 AACATAAAGAAAAAACCATTCATTGACTAGAAAAGCCCATTTATAGCCACCCATGCCTTCAAAA
2228 NNNNNNNNNN
Statistics
Matches: 627, Mismatches: 158, Indels: 51
0.75 0.19 0.06
Matches are distributed among these distances:
339 5 0.01
340 133 0.21
341 382 0.61
342 104 0.17
343 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.38
Consensus pattern (341 bp):
ATTTTAAGTTGAATTATTTTATATTTTTGCTTAAAACAAATTATAATTGAATGTCTACCTTGAGA
AACATAAAGAAAAAACCATTCATTGACTAGAAAAGCCCATTTATAGCCACCCATGCCTTCAAAAG
CTTTGTTACTCGCTTTAAATAGTTTTATAATCTCGTAATTGATTTTAAGTTAAATATTTTTACAT
TTTTGGCTAAAACAAGCTATAATTAAATTTTTGCCTTGAAAAATGTAAAGAAAAGCCATTCATAG
GCAAAACAAATACATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTT
TATAATCTCATAATTC
Found at i:2947 original size:170 final size:161
Alignment explanation
Indices: 2714--3028 Score: 294
Period size: 170 Copynumber: 1.9 Consensus size: 161
2704 TAAAACTATT
* * * * * * *
2714 TAAAGCGAGTAATAACGCTTTGGCAGGAATGGGTGACTACAAATGGATTTGTTTTGCCAATGAAT
1 TAAAGCGAGTAATAAAGCTTTGGAAGGAATGGGTGACTACAAATAGACTTCTCTAGCCAATGAAT
* * * * *
2779 GGCTTTTTCTTTACATTTTTCAA-GACAAAAATTCAATTATAGC-TTGTCTTAA-CCAAAATGTA
66 GACTTTTTCTTCACATTTCTCAAGGA-AAAAATTCAATTATA-CTTTGTCTTAAGCAAAAATATA
*
2841 AAAATATTCAACTTAAAATCAATTACGAGATTA
129 AAAAAATTCAACTTAAAATCAATTACGAGATTA
* * *
2874 TNNNNNNNNNNAAAGCGAGTAATAAAGCTTTTGAAGGCATGGGTGACTATAAATAGACTTCTCTA
1 T----------AAAGCGAGTAATAAAGCTTTGGAAGGAATGGGTGACTACAAATAGACTTCTCTA
* * * * * * *
2939 GTCAATGAATGATTTTTTCTTCACGTTTCTCAAGGAAGACATTCCATTATACTTTGTTTTAAGCA
56 GCCAATGAATGACTTTTTCTTCACATTTCTCAAGGAAAAAATTCAATTATACTTTGTCTTAAGCA
3004 AAAATATAAAAAAATTCAACTTAAA
121 AAAATATAAAAAAATTCAACTTAAA
3029 TGAATTATAA
Statistics
Matches: 119, Mismatches: 23, Indels: 15
0.76 0.15 0.10
Matches are distributed among these distances:
160 1 0.01
169 1 0.01
170 91 0.76
171 26 0.22
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.33
Consensus pattern (161 bp):
TAAAGCGAGTAATAAAGCTTTGGAAGGAATGGGTGACTACAAATAGACTTCTCTAGCCAATGAAT
GACTTTTTCTTCACATTTCTCAAGGAAAAAATTCAATTATACTTTGTCTTAAGCAAAAATATAAA
AAAATTCAACTTAAAATCAATTACGAGATTA
Done.