Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399830.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3068.0, 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: 4271
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.25
Warning! 1241 characters in sequence are not A, C, G, or T
Found at i:506 original size:172 final size:171
Alignment explanation
Indices: 1--1249 Score: 1146
Period size: 172 Copynumber: 7.3 Consensus size: 171
* * * ** * * * * ***
1 AAGGAATGGGTGACTAAAAATGGACATTTCTTGTTAATGAATGCCTTCTTCTTCGTATTTCTCAA
1 AAGGAATGGGAGACTATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTACACGTTTCTCAA
* * * ** * *
66 GGA-AGACATTCATTTTTAATCTTTTTTAACCAAAAAATTTAAAAAAAACT-ATATTTAAAATCA
66 -GATAGACATTCAATTATAATCTGTTTTAA-CAAAAAATAGAAAAAAAATTCA-ACTTAAAATCA
* * *
129 ATTTTGAGATTATAAAACCTTTTAAAGCGAGTAATAAAGTTTTTG
128 A-TTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * ** *
174 AAGGAATGGGAGGCTATAAATGGACATTTCTTTCAAAGGAATGGCTTTTT-TATACGTTTCTCAA
1 AAGGAATGGGAGACTATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTACACGTTTCTCAA
* * * *
238 GGTAGACATTCAATTATAGTCTGTTTTAACAAAAAAT--ATAAAAAATTCAACTTAAAATCAGTT
66 GATAGACATTCAATTATAATCTGTTTTAACAAAAAATAGAAAAAAAATTCAACTTAAAATCAATT
* * *
301 ATAAGATTATAAAAGCATTCAAAGCGAGTAATAAGGCTTTTG
131 -TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * *
343 AAAGAATGAGAGACCATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTACATGTTTCTCAA
1 AAGGAATGGGAGACTATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTACACGTTTCTCAA
* * *
408 GATAGACATTTAATTATAATCTGTTTTAACTAAAAATAGAAAAAAAATTAAACTTAAAATCAATG
66 GATAGACATTCAATTATAATCTGTTTTAACAAAAAATAGAAAAAAAATTCAACTTAAAATCAAT-
* * * * * *
473 TCGACATAATAAAAGCATTTATAGCGAGTAATAAGGATTTTG
130 TTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * *
515 AAGGAATGGGAGAAC-ATAAATGTACTTTTCTTCCTAATTAATGGTTTTTTGTACACGTTT-TCT
1 AAGGAATGGGAG-ACTATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTACACGTTTCTC-
* * * * * * * *
578 ATGAAATACATTCAATTATAATTTTTTTTAACTAAAAATAGAAAAAAAATTGAACTTCAAATCAA
64 AAGATAGACATTCAATTATAATCTGTTTTAACAAAAAATAGAAAAAAAATTCAACTTAAAATCAA
* * * *
643 TTTTGACATAATAAAACCATCTAAAGTGAGTAATAAGGCTTTTG
129 -TTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * * * *
687 AAGGAATGGAAGACTATAAATGAACTTTTCTTTCAAATGAATGGCTTTTTCTGCACGGTTCCCAA
1 AAGGAATGGGAGACTATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTACACGTTTCTCAA
* * * * ** *
752 GGA-AGACATTAAATTATAGTCTATTTTGAGGAAAAAT-GCAAAAAAA-TCAACTTAAAATCAAT
66 -GATAGACATTCAATTATAATCTGTTTTAACAAAAAATAGAAAAAAAATTCAACTTAAAATCAAT
** * *
814 TATGAGATTATAAAACCATTTAAAATGAGTAATAAGGTTTTTA
130 T-TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * * * * * *
857 AAGCAATGGGTA-ACTATAAATTGATTTTTCTT-GTCAATAAAAAGCCTTTTTCTTCGCCTTTCT
1 AAGGAATGGG-AGACTATAAATGGACTTTTCTTCCT-AAT-TAATGGCTTTTTCTACACGTTTCT
** * * * * * *
920 TGAGGTAGACATTTAATTATAATCTGTTTTAACCAAAACTATATAAAAAATTCAACTTAAAATCA
63 CAAGATAGACATTCAATTATAATCTGTTTTAACAAAAAATAGAAAAAAAATTCAACTTAAAATCA
*
985 ATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTTTTTG
128 A-TTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * * * * *
1030 AAGGAATGGTAGGCTATAAATGGAC--TT-TTCCAAAATAATGGTTTTTTCTATATGTTTCTCAA
1 AAGGAATGGGAGACTATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTACACGTTTCTCAA
* ** * * *
1092 GGTAGACATTCAATTATAGGCTGCTTTAACAAAAAATA-TAAAAGAATTCAACTTAAAATCAATT
66 GATAGACATTCAATTATAATCTGTTTTAACAAAAAATAGAAAAAAAATTCAACTTAAAATCAATT
* * * * * *
1156 ATAAAATTATAAAAGCATTCAAAGCGAGTAATAAAGCTTTTA
131 -TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
1198 AAGGAATGGGAGAC-ATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTA
1 AAGGAATGGGAGACTATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTA
1250 TATGTTTCCC
Statistics
Matches: 876, Mismatches: 173, Indels: 57
0.79 0.16 0.05
Matches are distributed among these distances:
167 12 0.01
168 69 0.08
169 146 0.17
170 147 0.17
171 68 0.08
172 313 0.36
173 119 0.14
174 2 0.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
AAGGAATGGGAGACTATAAATGGACTTTTCTTCCTAATTAATGGCTTTTTCTACACGTTTCTCAA
GATAGACATTCAATTATAATCTGTTTTAACAAAAAATAGAAAAAAAATTCAACTTAAAATCAATT
TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
Found at i:1031 original size:343 final size:336
Alignment explanation
Indices: 58--1246 Score: 1141
Period size: 341 Copynumber: 3.5 Consensus size: 336
48 CTTCTTCGTA
* * * * * * *
58 TTTCTCAAGGAAGACATTCATTTTTAATCTTTTTTAACCAAAAAATTTAAAAAAAA-CTATATTT
1 TTTCTCAAGGAAGACATTAAATTATAGTCTGTTTTAA-CAAAAAA-TGAAAAAAAATC-A-ACTT
* * * *
122 AAAATCAATTTTGAGATTATAAAACCTTTTAAAGCGAGTAATAAAGTTTTTGAAGGAATGGGAGG
62 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGTTTTTAAAGGAATGGGAGA
* * **
187 CTATAAATGGACATTTCTTTCAA-AGGAATGGCTTTTTTATACG-TTTCTCAAGGTAGACATTCA
127 C-ATAAATGGACTTTTCTTTCAATA-AAATGGCTTTTTT-T-CGCTTTCTTGAGGTAGACATTCA
* * * * *
250 ATTATAGTCTGTTTTAA-CAAAAAATATAAAAAATTCAACTTAAAATCAGTTATAAGATTATAAA
188 ATTATAATCTGTTTTAACCAAAATATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAA
* * * *
314 AGCATTCAAAGCGAGTAATAAGGCTTTTGAAAGAAT-GAGAGACCATAAATGGACTTTTCTTCCT
253 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGA-AGACTATAAATGGACTTTTCTT-C-
*
378 AATTAATGGCTTTTTCTACATG
315 AAATAATGGCTTTTTCTACATG
* * * *
400 TTTCTCAA-GATAGACATTTAATTATAATCTGTTTTAACTAAAAATAGAAAAAAAATTAAACTTA
1 TTTCTCAAGGA-AGACATTAAATTATAGTCTGTTTTAACAAAAAAT-GAAAAAAAA-TCAACTTA
* * * * * * * *
464 AAATCAATGT-CGACATAATAAAAGCATTTATAGCGAGTAATAAGGATTTTGAAGGAATGGGAGA
63 AAATCAAT-TATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGTTTTTAAAGGAATGGGAG-
* * * * * *
528 ACATAAATGTACTTTTCTTCCTAAT-TAATGG-TTTTTTGTACACGTTTTCTATGA--AATACAT
126 ACATAAATGGACTTTTCTTTC-AATAAAATGGCTTTTTT-T---CGCTTTCT-TGAGGTAGACAT
* * * * * * * * *
589 TCAATTATAATTTTTTTTAACTAAAAATAGAAAAAAAATTGAACTTCAAATCAATTTTGACATAA
185 TCAATTATAATCTGTTTTAAC-CAAAATATATAAAAAATTCAACTTAAAATCAATTTTGAGATTA
* * *
654 TAAAACCATCTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATAAATGAACTTTTCTT
249 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATAAATGGACTTTTC-T
* *
719 TCAAATGAATGGCTTTTTCTGCACG
313 TCAAAT-AATGGCTTTTTCTACATG
* * * * ** *
744 GTTCCCAAGGAAGACATTAAATTATAGTCTATTTTGAGGAAAAATGCAAAAAAATCAACTTAAAA
1 TTTCTCAAGGAAGACATTAAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAATCAACTTAAAA
** * *
809 TCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGGTTTTTAAAGCAATGGGTA-ACTA
66 TCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGTTTTTAAAGGAATGGG-AGAC-A
* * * * *
873 TAAATTGATTTTTCTTGTCAATAAAAAGCCTTTTTCTTCGCCTTTCTTGAGGTAGACATTTAATT
129 TAAATGGACTTTTCTT-TCAATAAAATGGCTTTTT-TTCG-CTTTCTTGAGGTAGACATTCAATT
938 ATAATCTGTTTTAACCAAAACTATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAAC
191 ATAATCTGTTTTAACCAAAA-TATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAAC
* * *
1003 CATTTAAAGCGAGTAATAAGGTTTTTGAAGGAATGGTAGGCTATAAATGGACTTTTC--CAAAAT
255 CATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATAAATGGACTTTTCTTC-AAAT
* *
1066 AATGGTTTTTTCTATATG
319 AATGGCTTTTTCTACATG
* * * * *
1084 TTTCTCAAGGTAGACATTCAATTATAGGCTGCTTTAACAAAAAAT-ATAAAAGAATTCAACTTAA
1 TTTCTCAAGGAAGACATTAAATTATAGTCTGTTTTAACAAAAAATGA-AAAA-AAATCAACTTAA
* * * * *
1148 AATCAATTATAAAATTATAAAAGCATTCAAAGCGAGTAATAAAGCTTTTAAAGGAATGGGAGACA
64 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGTTTTTAAAGGAATGGGAGACA
* *
1213 TAAATGGACTTTTCTTCCTAAT-TAATGGCTTTTT
129 TAAATGGACTTTTCTTTC-AATAAAATGGCTTTTT
1247 CTATATGTTT
Statistics
Matches: 686, Mismatches: 127, Indels: 71
0.78 0.14 0.08
Matches are distributed among these distances:
339 10 0.01
340 81 0.12
341 170 0.25
342 142 0.21
343 133 0.19
344 143 0.21
345 7 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (336 bp):
TTTCTCAAGGAAGACATTAAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAATCAACTTAAAA
TCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGTTTTTAAAGGAATGGGAGACATA
AATGGACTTTTCTTTCAATAAAATGGCTTTTTTTCGCTTTCTTGAGGTAGACATTCAATTATAAT
CTGTTTTAACCAAAATATATAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTA
AAGCGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATAAATGGACTTTTCTTCAAATAATGGCT
TTTTCTACATG
Found at i:3140 original size:172 final size:169
Alignment explanation
Indices: 2554--3264 Score: 598
Period size: 172 Copynumber: 4.1 Consensus size: 169
2544 NNNNNNNNNN
* * *
2554 AAAAAAATTCAACCTAAAATCAATTTTGAGATTAT-AAACCATTTATAGCGTGTAATAAGGCTTT
1 AAAAAAATT--ACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * ** * * * ** * * * *
2618 TAAAGGTATGGGCGATTGTAAATGGACTTTGCTTGTAAATAAATGCCTTTTTCTTCAC-ATTTCT
64 TGAAGGAAAGGGAAACTATAAAT-GACTTTTCTTCCAAATGAATGACTTTTTCTACACGTTTTC-
* * * **
2682 CGAGGTAGACATTCAATTATAGTCTTTTTTAACTAAAAATTTTA
127 CAAGGTAAACATTCAATTATAGTCTGTTTTAACTAAAAA-TAGA
* * *
2726 AAAAAAACTATATTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAATGTTTT
1 AAAAAAA-T-TACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * **
2791 TGAAGGACTAAGAGG---CTGTAAATAGACCTTTCTTCCAAATGAATGGCTTTTTCTGTACG-TT
64 TGAAGGA--AAG-GGAAACTATAAAT-GACTTTTCTTCCAAATGAATGACTTTTTCTACACGTTT
** * *
2852 TCTCAAGGTAGGCATTCAATTATAGTGTGTTTTAAC-AAAAAAATGA
125 TC-CAAGGTAAACATTCAATTATAGTCTGTTTTAACTAAAAATA-GA
* * * * *
2898 AAAAAAATCCACTTAAAATCAATTTTGAGATTATAAAAGCATTCATAGCGAGTAATAAGGCTTCT
1 AAAAAAAT-TACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * *
2963 GAAGGAAAGGGAAAAC-ATAAATGTACTTTTTTTCCTAATTAATGATTTTTTTTACACGTTTTCC
65 GAAGGAAAGGG-AAACTATAAATG-ACTTTTCTTCCAAATGAATGACTTTTTCTACACGTTTTCC
*
3027 AAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATAGA
128 AAGGTAAACATTCAATTATAGTCTGTTTTAACTAAAAATAGA
* * * *
3069 AAAAAAATTGAGCTTCAAATCAATTTTGACATAATAAAACCATTTAAAGTGAGTAATAAGGCTTT
1 AAAAAAATT-A-CTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * *
3134 TGAAGG-AATGGAAGACTATAGATGAACTTTTCTTCCAAATGAATGACTTTTCCTACACGTTTCC
64 TGAAGGAAAGGGAA-ACTATAAATG-ACTTTTCTTCCAAATGAATGACTTTTTCTACACGTTTTC
* * * ** * *
3198 CTAGG-AAGACATTAAATTATAGTCTGTTTTGAGGAAAAA-GGC
127 CAAGGTAA-ACATTCAATTATAGTCTGTTTTAACTAAAAATAGA
3240 AAAAAAATTCAACTTAAAATCAATT
1 AAAAAAATT--ACTTAAAATCAATT
3265 AAACTTATAA
Statistics
Matches: 439, Mismatches: 79, Indels: 43
0.78 0.14 0.08
Matches are distributed among these distances:
168 2 0.00
169 3 0.01
170 3 0.01
171 155 0.35
172 173 0.39
173 98 0.22
174 1 0.00
175 2 0.00
176 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (169 bp):
AAAAAAATTACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
AAGGAAAGGGAAACTATAAATGACTTTTCTTCCAAATGAATGACTTTTTCTACACGTTTTCCAAG
GTAAACATTCAATTATAGTCTGTTTTAACTAAAAATAGA
Found at i:3437 original size:227 final size:227
Alignment explanation
Indices: 3042--3492 Score: 744
Period size: 227 Copynumber: 2.0 Consensus size: 227
3032 AAACATTCAA
* * * *
3042 TTATAATCTGTTTTAACTAAAAATAGAAAAAAAATTGAGCTTCAAATCAATTTTGACATAATAAA
1 TTATAATATGGTTTAACTAAAAATAGAAAAAAAATTAAACTTCAAATCAATTTTGACATAATAAA
* *
3107 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGAAGACTATAGATGAACTTTTCTTCCAA
66 ACCATTCAAAGTGAGTAATAAGGCTTTTAAAGGAATGGAAGACTATAGATGAACTTTTCTTCCAA
* *
3172 ATGAATGACTTTTCCTACACGTTTCCCTAGGAAGACATTAAATTATAGTCTGTTTTGAGGAAAAA
131 ATGAATGACTTTTCCTACACGTTTCCCAAGGAAGACATTAAATTATAGTCTGTTTTGAGAAAAAA
3237 GGCAAAAAAATTCAACTTAAAATCAATTAAAC
196 GGCAAAAAAATTCAACTTAAAATCAATTAAAC
3269 TTATAATATGGTTTAACTAAAAATAGAAAAAAAATTAAACTT-AAATTCAATTTTGACATAATAA
1 TTATAATATGGTTTAACTAAAAATAGAAAAAAAATTAAACTTCAAA-TCAATTTTGACATAATAA
* *
3333 AAGCATTCATAGCT-AGTAATAAGGCTTTTAAAGGAATGGAAGACTATAGATGAACTTTTCTTCC
65 AACCATTCAAAG-TGAGTAATAAGGCTTTTAAAGGAATGGAAGACTATAGATGAACTTTTCTTCC
** *
3397 AAATGAATGGGTTTTTCTACACGTTTCCCAAGGAAGACATTAAATTATAGTCTGTTTTGAGAAAA
129 AAATGAATGACTTTTCCTACACGTTTCCCAAGGAAGACATTAAATTATAGTCTGTTTTGAGAAAA
*
3462 AATGCAAAAAAATTCAACTTAAAATCAATTA
194 AAGGCAAAAAAATTCAACTTAAAATCAATTA
3493 TGAGATTATA
Statistics
Matches: 208, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
226 3 0.01
227 204 0.98
228 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (227 bp):
TTATAATATGGTTTAACTAAAAATAGAAAAAAAATTAAACTTCAAATCAATTTTGACATAATAAA
ACCATTCAAAGTGAGTAATAAGGCTTTTAAAGGAATGGAAGACTATAGATGAACTTTTCTTCCAA
ATGAATGACTTTTCCTACACGTTTCCCAAGGAAGACATTAAATTATAGTCTGTTTTGAGAAAAAA
GGCAAAAAAATTCAACTTAAAATCAATTAAAC
Done.