Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401277.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4420.0, 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: 2230
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:1011 original size:171 final size:171
Alignment explanation
Indices: 4--1510 Score: 1209
Period size: 170 Copynumber: 8.7 Consensus size: 171
1 AGG
* * * *
4 CTTTCAAAGGCTTGAGTGACTATAAATGG-CTTTCCT-TATCAATGGATGGCTTTT-CGTTCTTG
1 CTTTCAAAGGCTTAAGTGACTATAAATGGACTTTTCTCT-CCAATGGATGGCTTTTGC-TTCATG
* * ** * *
66 TGTCCTAAGGCAGACATTCAATTATATTAAATTTTAACCAAAAATGTGAAAAAATCTAACTTCAA
64 TTTTCTAAGGCAGACATTCAATTATAACAAATTTTAACCAAAAATGTAAAAAAATCTAACTTAAA
* * * * *
131 TTCAATTATGAGAATATAAAACCATTTTAATCAAGTAACAA-A
129 ATCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGA
* * * * * * **
173 GCTTTTAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTCCTATAGATGGCTTTTGTTTTACAT
1 -CTTTCAAAGGCTTAAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTCATGT
** * * * *
238 TTTCTAAGGTTGACAATCAATTATAACATATTTTAACCAAAAATGTAAAAAAAACATAGCTTAAA
65 TTTCTAAGGCAGACATTCAATTATAACAAATTTTAACCAAAAATGTAAAAAAATC-TAACTTAAA
********** *
303 ATCAATTATGAGAATATAAANNNNNNNNNNGCGAGTAATAAGG
129 ATCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGA
* * * *
346 CTTTCAAAGGCTTTAGTGACTATAAATGGACTTCTCTCTCTAATGGATGGCTTTTGCTTCACG-T
1 CTTTCAAAGGCTTAAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTCATGTT
* ** ** *
410 TTCTTAAGGCAGACATTCAATTATAATATTTTTTTTTTACATTTTAATGAAGCATGTAAAAATAT
66 TTC-TAAGGCAGACATTCAATTATAACA----------A-ATTTTAACCAAAAATGTAAAAAAAT
* * * * * * *
475 CCAACCTAAAATCAATTATGCGAATCTAAAACCATTGAAAGCGAGTACTAAGG
119 CTAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGA
* * *
528 CTTTCAAAGGCTTTAGTGACTATAAATGGACTTTTCTCTCTAATCGATGGCTTTTGCTTCATG-T
1 CTTTCAAAGGCTTAAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTCATGTT
* * ** * * *
592 TTCTTGAGGCAGACATTCAATTGTATTAAATTTTAACAAAAAATGTGAAAAAATCTAACTTCAAA
66 TTC-TAAGGCAGACATTCAATTATAACAAATTTTAACCAAAAATGTAAAAAAATCTAACTTAAAA
*
657 TC-AGT-TGAGAATATAAAACCATTTAAAGCGAGTAATAAGA
130 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGA
** * * * * *
697 CTTTCAAAGGCTTGCGTGACTGA-AAATAG-CTTTTTTC-CCAATGAATTGCTTTTGTTTCATGT
1 CTTTCAAAGGCTTAAGTGACT-ATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTCATGT
* * * * * *
759 TTTCTGAGGCA-AAATTCAATTATAACATATTTTAACTATAAATGCAAAAAAAATCTAACTTAAA
65 TTTCTAAGGCAGACATTCAATTATAACAAATTTTAACCAAAAATG-TAAAAAAATCTAACTTAAA
* * *******
823 ATCAATTATGTGAATATAAAACTATTTAAAGCGAGTNNNNNNN
129 ATCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGA
***
866 NNNTCAAAGGCTTAAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTCATGTT
1 CTTTCAAAGGCTTAAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTCATGTT
** * * * * * * *
931 TTCTAAGATAGATATCCAATTATAATAAATTTTAACCAAAAATGT-AAAAACTTTCACCATAAAA
66 TTCTAAGGCAGACATTCAATTATAACAAATTTTAACCAAAAATGTAAAAAAATCT-AACTTAAAA
** * * * *
995 TCAATTATGAGAATATAAATTCATTGAAAACGAGCAATAAGG
130 TCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGA
* * *
1037 CTTTCAAAGGCTTACGCT-ACTATAAAT-AACTTTTCT-TACCAATAGATGGCTTTTGCTTCATG
1 CTTTCAAAGGCTTAAG-TGACTATAAATGGACTTTTCTCT-CCAATGGATGGCTTTTGCTTCATG
* * * * * *
1099 TTTCCTAATGTAGACATTCAATTATAACATATTTTAACCATAAATGTAAAAAACTCTAACTTAAA
64 TTTTCTAAGGCAGACATTCAATTATAACAAATTTTAACCAAAAATGTAAAAAAATCTAACTTAAA
* * *
1164 ATTAATTATGA-AAGTATAAAACCATTTAAACCGAGTAATAAGC
129 ATCAATTATGAGAA-TATAAAACCATTTAAAGCGAGTAATAAGA
* * *
1207 CTTTCAAAGGCTTGCA-TGACTATAAATGG-CTTTCCT-TGCCAATGGATGGCTTTTTCTTCATG
1 CTTTCAAAGGCTT-AAGTGACTATAAATGGACTTTTCTCT-CCAATGGATGGCTTTTGCTTCATG
* * * * * * ** * * *
1269 TATCCTGAGGCTGACATTCAATTATAATATTTTTTTATGTTTTAATGAAACATGTAAAAATATCC
64 TTTTCTAAGGCAGACATTCAATTATAACA-------A-ATTTTAACCAAAAATGTAAAAAAATCT
* * * *
1334 AACTTAAAATCAATTATGTGAGTCTAAAACCATTTAAAGCGAGTAATAAGG
121 AACTTAAAATCAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGA
* * ** * * * *
1385 TTTTCGAAGGCTTGCGTGACTAGAAATAGACTTTTCTCTCCAATGAATGGCTTTTGCTTTATGTT
1 CTTTCAAAGGCTTAAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTCATGTT
* * * *
1450 TTCTGAGGCAGACATTCAATTATAACATATTTTAACCATAAATGAAAAAAAAAATCTAACT
66 TTCTAAGGCAGACATTCAATTATAACAAATTTTAACCAAAAATG--TAAAAAAATCTAACT
1511 GAAGAAAATC
Statistics
Matches: 1053, Mismatches: 236, Indels: 93
0.76 0.17 0.07
Matches are distributed among these distances:
166 26 0.02
167 45 0.04
168 14 0.01
169 105 0.10
170 228 0.22
171 205 0.19
172 138 0.13
173 12 0.01
178 84 0.08
179 53 0.05
180 1 0.00
182 122 0.12
183 20 0.02
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (171 bp):
CTTTCAAAGGCTTAAGTGACTATAAATGGACTTTTCTCTCCAATGGATGGCTTTTGCTTCATGTT
TTCTAAGGCAGACATTCAATTATAACAAATTTTAACCAAAAATGTAAAAAAATCTAACTTAAAAT
CAATTATGAGAATATAAAACCATTTAAAGCGAGTAATAAGA
Found at i:1422 original size:519 final size:509
Alignment explanation
Indices: 1--1499 Score: 1246
Period size: 519 Copynumber: 2.9 Consensus size: 509
* * * * *
1 AGGCTTTCAAAGGCTTGAGTGACTATAAATG-GCTTTCCT-TATCAATGGATGGCTTTT-CGTTC
1 AGGCTTTCAAAGGCTTTAGTGACTATAAATGAACTTTTCTCT-CCAATAGATGGCTTTTGC-TTC
* * ** *
63 TTGTGTCCTAAGGCAGACATTCAATTATATTAAATTTTAACCAAAAATGTGAAAAAATCTAACTT
64 ATGTTTCCTAAGGCAGACATTCAATTATAACAAATTTTAACAAAAAATGTGAAAAAATCTAACTT
* * * * * * * *
128 CAATTCAATTATGAGAATATAAAACCATTTTAATCAAGTAACAA-AGCTTTTAAAGGCTTG-AGT
129 AAAAT-AAGT-TGAGAATATAAAACCATTTAAACCGAGTAATAAGA-CTTTCAAAGGCTTGCA-T
* * * * *
191 GACT-ATAAATGGACTTT-TCTCTCCTAT-AGATGGCTTTTGTTTTACAT-T-TTCTAAGGTTGA
190 GACTGA-AAATAG-CTTTCT-TC-CCAATGA-ATGGCTTTTG-TTT-CATGTATCCTGAGG--CA
* * * *
251 CAA-TCAATTATAACATATTTTAACCAAAAATGTAAAAAAAA--CATAGCTTAAAATCAATTATG
246 AAATTCAATTATAACATATTTTAACTATAAATGCAAAAAAAATCCA-A-CTTAAAATCAATTATG
* ********** * * * *
313 AGAATATAAANNNNNNNNNNGCGAGTAATAAGGCTTTCAAAGGCTTTAGTGACTATAAATGGACT
309 TGAATATAAAACCATTTAAAGCGAGTAATAAGGTTTTCAAAGGCTTAAGTGACTAGAAATAGACT
* * * * * * *
378 TCTCTCTCTAATGGATGGCTTTTGCTTCACG-TTTCTTAAGGCAGACATTCAATTATAATATTTT
374 TTTCTCTCCAATGAATGGCTTTTGCTTCATGTTTTC-TAAGACAGACATCCAATTATAACA----
** ** * * * *
442 TTTTTTACATTTTAATGAAGCATGTAAAAA-TATCCAACC-TAAAATCAATTATGCGAATCTAAA
434 ------A-ATTTTAACCAAAAATGAAAAAACT-TTC-ACCATAAAATCAATTATGAGAATATAAA
* * *
505 ACCATTGAAAGCGAGTACTA
490 ACCATTGAAAACGAGCAATA
* * *
525 AGGCTTTCAAAGGCTTTAGTGACTATAAATGGACTTTTCTCTCTAATCGATGGCTTTTGCTTCAT
1 AGGCTTTCAAAGGCTTTAGTGACTATAAATGAACTTTTCTCTCCAATAGATGGCTTTTGCTTCAT
* * * ** *
590 GTTTCTTGAGGCAGACATTCAATTGTATTAAATTTTAACAAAAAATGTGAAAAAATCTAACTTCA
66 GTTTCCTAAGGCAGACATTCAATTATAACAAATTTTAACAAAAAATGTGAAAAAATCTAACTTAA
* * *
655 AATCAGTTGAGAATATAAAACCATTTAAAGCGAGTAATAAGACTTTCAAAGGCTTGCGTGACTGA
131 AATAAGTTGAGAATATAAAACCATTTAAACCGAGTAATAAGACTTTCAAAGGCTTGCATGACTGA
* * * *
720 AAATAGCTTTTTTCCCAATGAATTGCTTTTGTTTCATGTTTTCTGAGGCAAAATTCAATTATAAC
196 AAATAGCTTTCTTCCCAATGAATGGCTTTTGTTTCATGTATCCTGAGGCAAAATTCAATTATAAC
* *
785 ATATTTTAACTATAAATGCAAAAAAAATCTAACTTAAAATCAATTATGTGAATATAAAACTATTT
261 ATATTTTAACTATAAATGCAAAAAAAATCCAACTTAAAATCAATTATGTGAATATAAAACCATTT
********** * * *
850 AAAGCGAGTNNNNNNNNNNTCAAAGGCTTAAGTGACTATAAATGGACTTTTCTCTCCAATGGATG
326 AAAGCGAGTAATAAGGTTTTCAAAGGCTTAAGTGACTAGAAATAGACTTTTCTCTCCAATGAATG
* * * *
915 GCTTTTGCTTCATGTTTTCTAAGATAGATATCCAATTATAATAAATTTTAACCAAAAATGTAAAA
391 GCTTTTGCTTCATGTTTTCTAAGACAGACATCCAATTATAACAAATTTTAACCAAAAATGAAAAA
**
980 ACTTTCACCATAAAATCAATTATGAGAATATAAATTCATTGAAAACGAGCAATA
456 ACTTTCACCATAAAATCAATTATGAGAATATAAAACCATTGAAAACGAGCAATA
1034 AGGCTTTCAAAGGC-TTACGCT-ACTATAAAT-AACTTTTCT-TACCAATAGATGGCTTTTGCTT
1 AGGCTTTCAAAGGCTTTA-G-TGACTATAAATGAACTTTTCTCT-CCAATAGATGGCTTTTGCTT
* * * * *
1095 CATGTTTCCTAATGTAGACATTCAATTATAACATATTTTAACCATAAATGT-AAAAAACTCTAAC
63 CATGTTTCCTAAGGCAGACATTCAATTATAACAAATTTTAACAAAAAATGTGAAAAAA-TCTAAC
* *
1159 TTAAAATTAATTATGA-AAGTATAAAACCATTTAAACCGAGTAATAAGCCTTTCAAAGGCTTGCA
127 TTAAAA-TAAGT-TGAGAA-TATAAAACCATTTAAACCGAGTAATAAGACTTTCAAAGGCTTGCA
* * * * *
1223 TGACT-ATAAATGGCTTTCCTTGCCAATGGATGGCTTTT-TCTTCATGTATCCTGAGGCTGACAT
189 TGACTGA-AAATAGCTTT-CTTCCCAATGAATGGCTTTTGT-TTCATGTATCCTGAGGC-AAAAT
* * ** * * *
1286 TCAATTATAATATTTTTTTATGTTTTAATGAAACATGTAAAAATATCCAACTTAAAATCAATTAT
250 TCAATTATAACA-TATTTTAACTATAAATG---CA---AAAAAAATCCAACTTAAAATCAATTAT
* * * **
1351 GTGAGTCTAAAACCATTTAAAGCGAGTAATAAGGTTTTCGAAGGCTTGCGTGACTAGAAATAGAC
308 GTGAATATAAAACCATTTAAAGCGAGTAATAAGGTTTTCAAAGGCTTAAGTGACTAGAAATAGAC
* * * * *
1416 TTTTCTCTCCAATGAATGGCTTTTGCTTTATGTTTTCTGAGGCAGACATTCAATTATAACATATT
373 TTTTCTCTCCAATGAATGGCTTTTGCTTCATGTTTTCTAAGACAGACATCCAATTATAACAAATT
*
1481 TTAACCATAAATGAAAAAA
438 TTAACCAAAAATGAAAAAA
1500 AAAATCTAAC
Statistics
Matches: 804, Mismatches: 137, Indels: 73
0.79 0.14 0.07
Matches are distributed among these distances:
507 7 0.01
508 84 0.10
509 87 0.11
510 63 0.08
511 31 0.04
512 14 0.02
513 12 0.01
516 2 0.00
519 151 0.19
520 146 0.18
521 25 0.03
522 8 0.01
523 53 0.07
524 34 0.04
525 85 0.11
526 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.34
Consensus pattern (509 bp):
AGGCTTTCAAAGGCTTTAGTGACTATAAATGAACTTTTCTCTCCAATAGATGGCTTTTGCTTCAT
GTTTCCTAAGGCAGACATTCAATTATAACAAATTTTAACAAAAAATGTGAAAAAATCTAACTTAA
AATAAGTTGAGAATATAAAACCATTTAAACCGAGTAATAAGACTTTCAAAGGCTTGCATGACTGA
AAATAGCTTTCTTCCCAATGAATGGCTTTTGTTTCATGTATCCTGAGGCAAAATTCAATTATAAC
ATATTTTAACTATAAATGCAAAAAAAATCCAACTTAAAATCAATTATGTGAATATAAAACCATTT
AAAGCGAGTAATAAGGTTTTCAAAGGCTTAAGTGACTAGAAATAGACTTTTCTCTCCAATGAATG
GCTTTTGCTTCATGTTTTCTAAGACAGACATCCAATTATAACAAATTTTAACCAAAAATGAAAAA
ACTTTCACCATAAAATCAATTATGAGAATATAAAACCATTGAAAACGAGCAATA
Found at i:1798 original size:172 final size:172
Alignment explanation
Indices: 1526--2230 Score: 744
Period size: 172 Copynumber: 4.1 Consensus size: 172
1516 AAATCGCAAC
* * *
1526 CATTGGCAAAAAAAGTCCATTTATAGTCATCCATTCCTTTAAAAGCCTTATTACTCATTTTAAAT
1 CATTGGCAAGAAAAGTCCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
* * * * *
1591 AGTTTTATAATCTCAAAACTGATTTCAATTTAAATTCTTTATACATTTTT-GGTTAAAACAAACT
66 AGTTTTATAATCTCAAAATTGATTTTAAGTTAAATTCTTTATACATTTTTAGCTT-AAACAGACT
*
1655 AGAATTGAATGTCTACCTTGAGAAACATAAAGAAAAAAGCATT
130 ATAATTGAATGTCTACCTTGAGAAACATAAAGAAAAAAGCATT
* * * * *
1698 TATTGGCAAGAAAAGTCCATTTATAGTTA-CTCATACCTTTAAAAGCCTCATTACTCACTTTAAA
1 CATTGGCAAGAAAAGTCCATTTATAGTCATC-CATTCCTTCAAAAGCCTTATTACTCACTTTAAA
* * * *
1762 TAGTTTTATAATGC-CATAATTGGTTTTAAGTTAAATTGTTTAT--ATTTTT-GGTTAAAACAGA
65 TAGTTTTATAAT-CTCAAAATTGATTTTAAGTTAAATTCTTTATACATTTTTAGCTT-AAACAGA
* * * **
1823 CTATAATTGAATGCCTA-CTTCGAGAAACGTAAAGGAAAGGGCATT
128 CTATAATTGAATGTCTACCTT-GAGAAACATAAAGAAAAAAGCATT
* *
1868 CATTAGCAAGAAAAGTCCATTTATAGTC-GCTCATTCCTTCAAAAGCCTTATTACTCACTTTAAA
1 CATTGGCAAGAAAAGTCCATTTATAGTCATC-CATTCCTTCAAAAGCCTTATTACTCACTTTAAA
* * * * * * *
1932 TGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTATATTTTTAGCTTAAACAGATT
65 TAGTTTTATAATCTCAAAATTGATTTTAAGTTAAATTCTTTATACATTTTTAGCTTAAACAGACT
* ** ** * *
1997 ATAATTGAATGTATACCTCAAGGGACATGAAGAAAAAGGCATT
130 ATAATTGAATGTCTACCTTGAGAAACATAAAGAAAAAAGCATT
* * * *
2040 TATTAGCAAGAAAACTCCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCAATTTAAAT
1 CATTGGCAAGAAAAGTCCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
* * * * ** * * * * *
2105 GGTTTCTATAACCTCATAATTGATTTTAGGTT-GTTTATTTTTACATTTTTTAGCTTGAATAGAT
66 AGTTT-TATAATCTCAAAATTGATTTTAAGTTAAATTCTTTATACA-TTTTTAGCTTAAACAGAC
* * ** *
2169 TATAATTGAATGTTTTCCTTGAGAAATGTGAAGAAAAAAGCATT
129 TATAATTGAATGTCTACCTTGAGAAACATAAAGAAAAAAGCATT
2213 CATTGGCAAGAAAAGTCC
1 CATTGGCAAGAAAAGTCC
Statistics
Matches: 448, Mismatches: 73, Indels: 23
0.82 0.13 0.04
Matches are distributed among these distances:
169 4 0.01
170 142 0.32
171 1 0.00
172 207 0.46
173 94 0.21
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (172 bp):
CATTGGCAAGAAAAGTCCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAT
AGTTTTATAATCTCAAAATTGATTTTAAGTTAAATTCTTTATACATTTTTAGCTTAAACAGACTA
TAATTGAATGTCTACCTTGAGAAACATAAAGAAAAAAGCATT
Done.