Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400765.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3943.0, 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: 4847
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.30
Warning! 801 characters in sequence are not A, C, G, or T
Found at i:321 original size:171 final size:171
Alignment explanation
Indices: 5--345 Score: 414
Period size: 171 Copynumber: 2.0 Consensus size: 171
1 AGAG
* * * ** *
5 TAATAAGGCTTTTGAAGACTTGGGTGACTATAAATGGGCTTTTCTTGCCAGTGAATGTTTTTTTC
1 TAATAAGGCTTTTGAAGACTTGGGTGACAATAAATGAGCTTTTCTTGCCAATGAATGGATTTTCC
* * ** * * *****
70 TTCATGTTTCCCAAAGTAAATTTTCAATTATAATCTGTTTTAACAAACAATGTAAAAAAANNNNN
66 TTCATATTTCCCAAAGAAAACATTCAATTATAATCAGTTTTAACAAAAAATGTAAAAAAAATTCA
*****
135 NNNNNAAAGAATTTTGAGATTATAAAACCATTTAAAGAGAA
131 ACTTCAAAGAATTTTGAGATTATAAAACCATTTAAAGAGAA
**
176 TAATAAGGCTTTTGAAGGGTTGGGTGACAATAAATGAGCTTTTCTTGCCAATGAATGGATTTTCC
1 TAATAAGGCTTTTGAAGACTTGGGTGACAATAAATGAGCTTTTCTTGCCAATGAATGGATTTTCC
*
241 TTCATATTTCCCAAGGAAAACATTCAATTATAATCAGTTTTAACAAAAAATGT-AAAAAAATTCA
66 TTCATATTTCCCAAAGAAAACATTCAATTATAATCAGTTTTAACAAAAAATGTAAAAAAAATTCA
* * *
305 ACTTCAAATTAATTTTGAGGTTATAAAACTATTTAAAGAGA
131 ACTTCAAA-GAATTTTGAGATTATAAAACCATTTAAAGAGA
346 NNNNNNNNNN
Statistics
Matches: 141, Mismatches: 28, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
170 9 0.06
171 132 0.94
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.34
Consensus pattern (171 bp):
TAATAAGGCTTTTGAAGACTTGGGTGACAATAAATGAGCTTTTCTTGCCAATGAATGGATTTTCC
TTCATATTTCCCAAAGAAAACATTCAATTATAATCAGTTTTAACAAAAAATGTAAAAAAAATTCA
ACTTCAAAGAATTTTGAGATTATAAAACCATTTAAAGAGAA
Found at i:1545 original size:38 final size:38
Alignment explanation
Indices: 1494--1571 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
1484 GTAAGCATTG
*
1494 AATTATAATCTGTTTTAACCAAAAAAATAAAAAAATTC
1 AATTATAATCTGTTTTAACCAAAAAAATAAAAAAAATC
* *
1532 AATTATAATCTGTTTTAACCAAACATATAAAAAAAATC
1 AATTATAATCTGTTTTAACCAAAAAAATAAAAAAAATC
1570 AA
1 AA
1572 CCATTTAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.31
Consensus pattern (38 bp):
AATTATAATCTGTTTTAACCAAAAAAATAAAAAAAATC
Found at i:1895 original size:171 final size:171
Alignment explanation
Indices: 1570--3740 Score: 2230
Period size: 171 Copynumber: 12.8 Consensus size: 171
1560 AAAAAAAATC
* * * *
1570 AACCATTTAAAGATAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATGAATAGGC-TTTCTTACC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
* * * * *
1634 AATGAATGTG-TTTCTCTTCATGTTTTCTAAGGTAAACATTCAATTATAAAT-TGTTTTAACCAA
66 AATGAATG-GCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTAT-AATCTGTTTTAACTAA
* * * *
1697 AACTGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAA
129 AAATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
** *
1740 AATTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGAGTGACTATAAATGGGCTTTTCTTAG-
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTT-GC
* * * * * * *
1804 CAATAAATGGCTTTTTCTGT-AGGTTTCCCATGAAAAACATTCAATTATAGTCTTTTTTAACAAA
65 CAATGAATGGCTTTTTCT-TCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAA
* **
1868 AAATATAAAATAATTCAACTTAAAATCAATTTTGAGGCTATAA
129 AAATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
* * * * * * *
1911 AACCTTTTATAGAGAGCAATAAGGCTTTTGGAGGCTCGGGTGATTATAAATGAGCTTTTCTTGCC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
* * * * * *
1976 AATGAATAGCTCTTTCTTCAAGTTTGCCATGGAAAACAGTCAATTATAATCTGTTTTAACTAAAA
66 AATGAATGGCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAA
*
2041 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
131 ATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
* * * * *
2082 AATCATTTAAAGATAGTAATAAGGCATTTGAAGGCTTGGGTGACTATGAATAGGCTTTTC-TGCC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTG-C
* ** * * ** * *
2146 CAATGAGA-GGGTTTTTCTTCATACTTCTCAAGGCAAACATTCAAGCATAATCTGTGTTAACTTA
65 CAATGA-ATGGCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAA
* * *
2210 AAATGTAAAATAAA-TCAAGC-TCAAATCAATTATGAGATTATAA
129 AAATATAAAA-AAATTCAA-CTTAAAATCAATTTTGAGATTATAA
* *
2253 AATCATTTAAAGAGAGTAATAAGGCTTTTAAAGGCTTGGGTGACTATAAA-GGGACTTTTCTTGC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGG-CTTTTCTTGC
* * * *
2317 CAATGTATGGCTTTTTCTTCAGGTTTCCC-ATGAAAATCATTCAATTATAGTCTGTTTTAACTAA
65 CAATGAATGGCTTTTTCTTCATGTTTCCCAAGGAAAA-CATTCAATTATAATCTGTTTTAACTAA
*
2381 AAATATAAAAAAATTCAACTTAAAATCAATTTTGAGGTTATAA
129 AAATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
* * * *
2424 AACTATTTAAAAAGAGTAATAAAGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTCTTCTTGCC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
* * * * *
2489 AACGAATGGCTTTTTCATT-AGGTTTCCCATA-GAAAACATTCAGTTATAGTCTGTTTTAA-TCA
66 AATGAATGGCTTTTTC-TTCATGTTTCCCA-AGGAAAACATTCAATTATAATCTGTTTTAACTAA
*
2551 AAATATATAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
129 AAATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
* * * * *
2594 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGTCCTAGGTGACTATGAATAGGCTTTTCTTGCC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
* * *** * *
2659 AATAAATGTG-TTTCTCTTCATGTTTTTAAAGGCAAACATTCAATTATAATTTGTTTTAAC----
66 AATGAATG-GCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAA
* * * *
2719 CA-A-AAAAAAA-TCAACTTGAAATCAATTTTTAGGTTATAA
130 AATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
* * * * *
2758 AACCATTTAAAGAGAGTAATTAGGCTTTTAAAAGCTTGGGCGACTATAAATGGGCTTTTCTTTCC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
* * * * * * *
2823 AATGAATGTG-TTTTT-TTCCTGTTTCTCAAGGCAAACATTTAGTTATAATCCGTTTTAACCAAA
66 AATGAATG-GCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAA
** * * * * ** *
2886 AACGTGAAACAATTAAACTTAAAAAT-AATATAAAG-CTATAA
130 AATATAAAAAAATTCAACTT-AAAATCAATTTTGAGATTATAA
* * * * * *
2927 AATCGTTTAAAGAGAGTAACAAGGCTTTTGAAGGCTTGGGTGACTATAAATTGACTTTTCTTGTC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
* * * * * * * *
2992 AATGAATGGCTTGTTCTTTAGGTTTTCCATGGAAATCATTCAATTATAGTCTGTTTTAACCAAAA
66 AATGAATGGCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAA
* * *
3057 A-ATTAAAACAATTCAACATAAAATTAATTTTGATG-TTATAA
131 ATA-TAAAAAAATTCAACTTAAAATCAATTTTGA-GATTATAA
* *
3098 AACCATTTAAAGAAAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTTTTGCC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
** *
3163 AATGAATGTATTTTTCTTCATGTTTCTCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAA
66 AATGAATGGCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAA
* * * * * * **
3228 ATTTGAAACAATTAAATTTAAAATCAATTTTAAGGCTATAA
131 ATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
* * * * * ** * *
3269 AATCATTTAAAGATACTAATAACGCTTTTAAAGGCTTGGGTGACTATGGATGGACTTTTTTTGCC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
* * * * *
3334 AGTGAATGGATTTTTCTTCATGTTTCCTAAGGTAAACATTCAATTATAAACTGTTTTAACTAAAA
66 AATGAATGGCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAA
* * * *
3399 ATATAAAACAATTTAACTTAAAATCAATTATGAGATTACAA
131 ATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
** * * * * * *
3440 AATTATTTGAAGAGAGCAATAAGGCTTTTGAAGGCTAGGGTGACTATAATTAGGCTATTCTTGCC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
* * * ** * * *
3505 AAAGATCTAG-TTTTTCTTCATGTTTTTCAAGGCAAACATTCAATTATAAAT-TATTTTAACAAA
66 AATGA-ATGGCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTAT-AATCTGTTTTAACTAA
*
3568 AAATATAAAAAAATTCAACTTAAAAAT-AATTTTAAGATTATAA
129 AAATATAAAAAAATTCAACTT-AAAATCAATTTTGAGATTATAA
* * ** * *
3611 AACCATTTAAAAAGAGTAATGAGGCCCTTGAAGGCTTGGGTGACTATAAATAGGCTTTTCTTTCC
1 AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
* * * * **
3676 AATGAATGTG-TTTTT-TTCTTGTTTCTCAAGGTAAATATTCAATTATAATCCATTTTAACTAAA
66 AATGAATG-GCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAA
3739 AA
130 AA
3741 CACGAAACAA
Statistics
Matches: 1656, Mismatches: 300, Indels: 90
0.81 0.15 0.04
Matches are distributed among these distances:
163 37 0.02
164 94 0.06
165 6 0.00
166 1 0.00
167 2 0.00
168 1 0.00
169 87 0.05
170 318 0.19
171 1082 0.65
172 27 0.02
173 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (171 bp):
AACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
AATGAATGGCTTTTTCTTCATGTTTCCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAA
ATATAAAAAAATTCAACTTAAAATCAATTTTGAGATTATAA
Found at i:4364 original size:170 final size:168
Alignment explanation
Indices: 3988--4847 Score: 990
Period size: 170 Copynumber: 5.0 Consensus size: 168
3978 NNNNNNNNNN
*
3988 AGAGAGTAATAAGGCTTTTGAAGG-TATGGGTGACTATAAATGAGCTTTTCTTGCCCATGAATG-
1 AGAGAGTAATAAGGCTTTTGAAGGCT-TGGGTGACTATAAATG-GCTTTTCTTGCCAATGAATGT
* * * * *
4051 GCTCTTTCTTCAGGTTTTCCATGGAAAACATTCCATTAAAATCTGTTTTAACCAAAAATATAAAA
64 G-T-TTTCTTCATG-TTTCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAAATATAAAA
* *
4116 AAATTCAACTTAAAATCAATTTTGAGGTTATAAAACTATTTAA
126 AAATTAAACTTAAAATCAATTTTGAGGTTATAAAACCATTTAA
* * * *
4159 AGAGAGTAATAAGGCTTATGAAGTCTTGGGTGACTATGAATAGGCTTTTCTTGCCAATCAATGTG
1 AGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAAT-GGCTTTTCTTGCCAATGAATGTG
* * *
4224 TTTCTCTTCATGTTTCCAAAGGCAAACATTCAATTATAATCTATTTTAACTAAAGATA-AAAAAA
65 TTT-TCTTCATGTTTCC-AAGGAAAACATTCAATTATAATCTGTTTTAACTAAAAATATAAAAAA
* * * * *
4288 ATTTAACTTTAAATCAATTTTGAGGTTATCAAACCATCTAG
128 ATTAAACTTAAAATCAATTTTGAGGTTATAAAACCATTTAA
* ** * * * *
4329 AGAGAGTAATAAGGTTTTTGAAGGCTTCAGTGACTATAAATGACCTTTTCTTTCCAGTGAATCTG
1 AGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATG-GCTTTTCTTGCCAATGAATGTG
* * * * * *
4394 TTTTTTTCATGTTTACCAAGGCAAACATTCAATTCTAATCTGTTTTAACTAAAAACATGAAACAA
65 TTTTCTTCATGTTT-CCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAAATATAAAAAAA
* * * * *
4459 TTAAACTTAAAAACAATTTTAAGGGTATAAAATCGTTTAA
129 TTAAACTTAAAATCAATTTTGAGGTTATAAAACCATTTAA
*
4499 AGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACCATAAATGGGCTTTTCTTGCCAATGAATGGC
1 AGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAAT-GGCTTTTCTTGCCAATGAAT-G-
* * * * * * *
4564 TTTTTTTTTTAGGTTTTCCATGGAAAACATTCAATTATAGTCTGTTTTAATTAAAAATATAAAAA
63 TGTTTTCTTCATG-TTTCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAAATATAAAAA
* * * *
4629 AATTCAACATAAAATTAATTTTGATGTTATAAAACCATTTAA
127 AATTAAACTTAAAATCAATTTTGAGGTTATAAAACCATTTAA
* *
4671 AGAGTGTAATAAGGCTTTTGAAGGCTTGGGTGACTAT-AATGGGCTTTTCTTGCCAATAAATGTG
1 AGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAAT-GGCTTTTCTTGCCAATGAATGTG
* * * * * *
4735 TTTTTCTTCATGTTTCTCAAGGAAAACATTCAATCATAATATGTTTTTACTCAAAAATTTGAAAC
65 -TTTTCTTCATGTTTC-CAAGGAAAACATTCAATTATAATCTGTTTTAACT-AAAAATATAAAAA
* *
4800 AATTAAACTTAAAATCAATTTTAAGGCTATAAAACCATTTAA
127 AATTAAACTTAAAATCAATTTTGAGGTTATAAAACCATTTAA
4842 AGAGAG
1 AGAGAG
Statistics
Matches: 576, Mismatches: 98, Indels: 30
0.82 0.14 0.04
Matches are distributed among these distances:
169 52 0.09
170 230 0.40
171 170 0.30
172 121 0.21
173 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (168 bp):
AGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGCTTTTCTTGCCAATGAATGTGT
TTTCTTCATGTTTCCAAGGAAAACATTCAATTATAATCTGTTTTAACTAAAAATATAAAAAAATT
AAACTTAAAATCAATTTTGAGGTTATAAAACCATTTAA
Done.