Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398466.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1763.0, 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: 3485
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.33
Warning! 572 characters in sequence are not A, C, G, or T
Found at i:398 original size:171 final size:172
Alignment explanation
Indices: 14--409 Score: 422
Period size: 172 Copynumber: 2.3 Consensus size: 172
4 ACAGTCACCC
* * * *
14 ATTCCTTCAAAAGCCTTATTACTTGCTTTAAATGGTTTTATGATAT-AAAATTTGATTTTAAGTT
1 ATTCCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAAAA-TTGAATTTAAGTT
* * * *
78 GAATTGTTTCTACATTTTTAGTTAAAACAGATTATAATTGAATGTTTATCTCGAGTAATGTGAAG
65 CAATTGTTTCTACATTTTTAGTTAAAACAGATTATAATTGAATATTTACCTCGAGAAATGTGAAG
* * *
143 AAATAAACATTCATTGGCAAGAAAAGTCTATTTATTGTGACCT
130 AAATAAACATTCATTGACAAGAAAAGTCTATTTATAGTGACCA
* ***********
186 ATTCCTTCAAAAGACTTATTACNNNNNNNNNNCGGTTTTATAATCTCAAAATTGAATTTAAGTTC
1 ATTCCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAAAATTGAATTTAAGTTC
* * * ** * * *
251 AGATT-TTTTTATATTTTTGGTTACGACATATTATAATTGATTATTTACCTTGAGAAATGTGAA-
66 A-ATTGTTTCTACATTTTTAGTTAAAACAGATTATAATTGAATATTTACCTCGAGAAATGTGAAG
* *
314 AAA-AAGGCATTCATTGACAAGAAAAGTCTATTTATAGTTACCA
130 AAATAA-ACATTCATTGACAAGAAAAGTCTATTTATAGTGACCA
* *
357 ATTCCTTCAAAAGCCTTATTACTTACTTTAAATGATTTTATAATCTCATAATT
1 ATTCCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAAAATT
410 AGTTTTAGGT
Statistics
Matches: 175, Mismatches: 46, Indels: 7
0.77 0.20 0.03
Matches are distributed among these distances:
170 2 0.01
171 74 0.42
172 92 0.53
173 7 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.40
Consensus pattern (172 bp):
ATTCCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAAAATTGAATTTAAGTTC
AATTGTTTCTACATTTTTAGTTAAAACAGATTATAATTGAATATTTACCTCGAGAAATGTGAAGA
AATAAACATTCATTGACAAGAAAAGTCTATTTATAGTGACCA
Found at i:876 original size:147 final size:149
Alignment explanation
Indices: 595--890 Score: 357
Period size: 147 Copynumber: 2.0 Consensus size: 149
585 ATTACTAATT
* * * * * *
595 TTAAATGGTTTTTTAATCTCAAAATTGATTTTAAGTTGAATTGTTTTTACATTTGTGGTTAAAAC
1 TTAAATGGTTTTATAATCTCAAAATTAATTTTAAGGTGAATTGTTTTCACATTTGTAGTGAAAAC
* * * ** *
660 AGATTATAACTAAATGTCTACATCGAGAAACATGAAGAGAAAGGTATTCATTGGTAGAAAATGTC
66 AAACTATAACTAAATGTCTACATCGAGAAACATGAAGAGAAAGGCATTCAACGGTAAAAAATGTC
* *
725 CATTTATAGTTACCTATCC
131 CATTTATAGTCACCCATCC
* *
744 TTAAATGGTTTTATAATCTCATAATTAATTTTAAGGTGAATT-TTTTCACATTTTTAGTGAAAAC
1 TTAAATGGTTTTATAATCTCAAAATTAATTTTAAGGTGAATTGTTTTCACATTTGTAGTGAAAAC
* * * *
808 AAACTATAA-TTAATGTCTACCTTGAGAAACATGAAGA-AAGAGGCATTCAACGG-AAACAAATT
66 AAACTATAACTAAATGTCTACATCGAGAAACATGAAGAGAA-AGGCATTCAACGGTAAA-AAATG
*
870 TTCATTTATAGTCACCCATCC
129 TCCATTTATAGTCACCCATCC
891 CTTCAAAAGC
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
146 4 0.03
147 57 0.46
148 25 0.20
149 38 0.31
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (149 bp):
TTAAATGGTTTTATAATCTCAAAATTAATTTTAAGGTGAATTGTTTTCACATTTGTAGTGAAAAC
AAACTATAACTAAATGTCTACATCGAGAAACATGAAGAGAAAGGCATTCAACGGTAAAAAATGTC
CATTTATAGTCACCCATCC
Found at i:2263 original size:171 final size:170
Alignment explanation
Indices: 1757--2932 Score: 627
Period size: 171 Copynumber: 6.9 Consensus size: 170
1747 NNNNNNNNNN
* * * * * *
1757 TATTACTCACTTTAAACGGTTTTATAATCTCAAAATTGATTTTCAGTTGAATTTTTCTTACATTT
1 TATTACTCGCTATAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTCTTACATTT
* *
1822 TTAGTTACGACACATTATAATTGAATGTTTACCTCGAGAAATGTGAAAAAAAGACATTCATTGGC
66 TTAGTTACGACACATTATAATTGAATGTTTACCTCAAGAAACGTGAAAAAAAGACATTCATTGGC
* * *
1887 AAGAAAGTTTTACTTATAGTCACCCATTCTTTCAAAAGCCT
131 AAGAAAG-TCTATTTATAGTCACCAATTCTTTCAAAAGCCT
* * * * *
1928 TATTACTTGGTATAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTAT-TTAAATTT
1 TATTACTCGCTATAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTCTTACA-TT
** * * * * * * * *
1992 TTTA-TTAAAATAGACTATAATTGAATGTTTGCCTTAGGAAACGT-ATAGAAAAGCCATTCATTG
65 TTTAGTTACGACACATTATAATTGAATGTTTACCTCAAGAAACGTGA-AAAAAAGACATTCATTG
* * * * *
2055 AG-AAAAAAATCTATTTATAGTCTCTAATTCATTCAAAA-CTCT
129 -GCAAGAAAGTCTATTTATAGTCACCAATTCTTTCAAAAGC-CT
* ********** *
2097 TATTACTCGCTTTAAATGATTNNNNNNNNNNATAATTGATTTTAAGTTAAATTTTTCTTACATTT
1 TATTACTCGCTATAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTCTTACATTT
* * * * * *
2162 TTGGTTGCGACATATTATAATTGAATGTCTACCTCAAGAAACATGAAAAAAAGGGCATTCATTGG
66 TTAGTTACGACACATTATAATTGAATGTTTACCTCAAGAAACGTGAAAAAAA-GACATTCATTGG
*
2227 CAAGAAAGTCAATTTATAGTCACCAATTCTTTCAAAAGCCT
130 CAAGAAAGTCTATTTATAGTCACCAATTCTTTCAAAAGCCT
* ** * * * * * * * * *
2268 TATTAGTCATTTTAAATGGTTTTGTAATCTTAAAAATAATTTTAAGTTGAATTGTT-TTATATTT
1 TATTACTCGCTATAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTCTTACATTT
** * * * * * ** * * *
2332 TT-GATTAAAATAAATGATAATTGAATGTCTACCTCAAAAAATATGAAGAGAAAGGCATTTATTG
66 TTAG-TTACGACACATTATAATTGAATGTTTACCTCAAGAAACGTGAA-AAAAAGACATTCATTG
* * * * * *
2396 GTAAGAAAATTTCATTTATAGTCACCCATTCCTTCAAAAACCT
129 GCAAGAAAGTCT-ATTTATAGTCACCAATTCTTTCAAAAGCCT
* * **********
2439 TATTACTTAG-TTTAAAT-AGTTTTATAATCTCATNNNNNNNNNNAAGTTGAATTTCTT-TTACA
1 TATTAC-TCGCTATAAATGA-TTTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTCTTACA
** ** ** * * ** * * * *
2501 TTTTCGGCAAAAACATATTATACTTGAATGCCTACCTCGAGAAACATGAATAAAAAGGCATTAAT
63 TTTTTAGTTACGACACATTATAATTGAATGTTTACCTCAAGAAACGTGAA-AAAAAGACATTCAT
* * * * *
2566 TGGCAAAAAAAGTCTACTTATAGTCACCCATTCATTCAAAAGCTT
127 TGGC-AAGAAAGTCTATTTATAGTCACCAATTCTTTCAAAAGCCT
* * * * **********
2611 TATTACTCACTTTAAATGATTTTGTAATCTCAAAATTGNNNNNNNNNNGAATTTTT-TTACATTT
1 TATTACTCGCTATAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTCTTACATTT
** * * * * * *
2675 TTAGTTAAAACAGATTATAATTGAATATTTACCTCTAGAAATGTGAAGACAAAGGCATTCATTGG
66 TTAGTTACGACACATTATAATTGAATGTTTACCTCAAGAAACGTGAA-AAAAAGACATTCATTGG
* * * *
2740 TAAGAAAAGT-TCATTTATAGTCATTC-ATTCCTACAAAAGCCT
130 CAAG-AAAGTCT-ATTTATAGTCA-CCAATTCTTTCAAAAGCCT
* * * * * * *
2782 TATTACTTGCTTTAAATGGTTTTATAATCTCGTAAATGATTTTAAGCTG-ATTTTAT-TTAAATT
1 TATTACTCGCTATAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTT-TCTTACATT
** ** * * * * * * * * *
2845 TTTCCTTAAAACAGACTATAATTAAATGTTTACCTCGAGATATGTGTAGAAAAAGTCACTCATTG
65 TTTAGTTACGACACATTATAATTGAATGTTTACCTCAAGAAACGTG-AAAAAAAGACATTCATTG
* *
2910 AGAAAAAAAGTCTATTTATAGTC
129 -GCAAGAAAGTCTATTTATAGTC
2933 TCTCATTCCT
Statistics
Matches: 767, Mismatches: 211, Indels: 54
0.74 0.20 0.05
Matches are distributed among these distances:
168 1 0.00
169 72 0.09
170 163 0.21
171 394 0.51
172 128 0.17
173 9 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (170 bp):
TATTACTCGCTATAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTCTTACATTT
TTAGTTACGACACATTATAATTGAATGTTTACCTCAAGAAACGTGAAAAAAAGACATTCATTGGC
AAGAAAGTCTATTTATAGTCACCAATTCTTTCAAAAGCCT
Found at i:2755 original size:343 final size:332
Alignment explanation
Indices: 2171--2812 Score: 741
Period size: 343 Copynumber: 1.9 Consensus size: 332
2161 TTTGGTTGCG
* * *
2171 ACATATTATAATTGAATGTCTACCTCAAGAAACATGAAAAAAAGGGCATTCATTGGCAAGAAAGT
1 ACATATTATAATTGAATGCCTACCTCAAGAAACATGAAAAAAAGGGCATTAATTGGCAAAAAAGT
* * * * * *
2236 CAATTTATAGTCACCAATTCTTTCAAAAGCCTTATTAGTCATTTTAAATGGTTTTGTAATCTTAA
66 CAACTTATAGTCACCAATTCATTCAAAAGCCTTATTACTCACTTTAAATGATTTTGTAATCTCAA
* * *
2301 AAATAATTTTAAGTTGAATTGTTTTATATTTTTGATTAAAATAAATGATAATTGAATGTCTACCT
131 AAATAATTTTAAGTTGAATTGTTTTACATTTTTGATTAAAACAAATGATAATTGAATATCTACCT
* * * *
2366 CAAAAAATATGAAGAGAAAGGCATTTATTGGTAAGAAAATTTCATTTATAGTCACCCATTCCTTC
196 CAAAAAATATGAAGACAAAGGCATTCATTGGTAAGAAAAGTTCATTTATAGTCACCCATTCCTAC
2431 AAAAACCTTATTACTTAG-TTTAAATAGTTTTATAATCTCATNNNNNNNNNNAAGTTGAATTTCT
261 AAAAACCTTATTACTT-GCTTTAAATAGTTTTATAATCTCAT----------AAGTTGAATTTCT
2495 TTTACATTTTCGGCAAAA
315 TTTACATTTTCGGCAAAA
* *
2513 ACATATTATACTTGAATGCCTACCTCGAGAAACATGAATAAAAA-GGCATTAATTGGCAAAAAAA
1 ACATATTATAATTGAATGCCTACCTCAAGAAACATGAA-AAAAAGGGCATTAATTGGC-AAAAAA
* * *
2577 GTCTACTTATAGTCACCCATTCATTCAAAAGCTTTATTACTCACTTTAAATGATTTTGTAATCTC
64 GTCAACTTATAGTCACCAATTCATTCAAAAGCCTTATTACTCACTTTAAATGATTTTGTAATCTC
* *********** * * * *
2642 AAAATTGNNNNNNNNNNGAATTTTTTTACATTTTT-AGTTAAAACAGATTATAATTGAATATTTA
129 AAAAATAATTTTAAGTTGAATTGTTTTACATTTTTGA-TTAAAACAAATGATAATTGAATATCTA
* * * **
2706 CCTCTAGAAATGTGAAGACAAAGGCATTCATTGGTAAGAAAAGTTCATTTATAGTCATTCATTCC
193 CCTCAAAAAATATGAAGACAAAGGCATTCATTGGTAAGAAAAGTTCATTTATAGTCACCCATTCC
* *
2771 TACAAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTC
258 TACAAAAACCTTATTACTTGCTTTAAATAGTTTTATAATCTC
2813 GTAAATGATT
Statistics
Matches: 252, Mismatches: 44, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
342 49 0.19
343 203 0.81
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.36
Consensus pattern (332 bp):
ACATATTATAATTGAATGCCTACCTCAAGAAACATGAAAAAAAGGGCATTAATTGGCAAAAAAGT
CAACTTATAGTCACCAATTCATTCAAAAGCCTTATTACTCACTTTAAATGATTTTGTAATCTCAA
AAATAATTTTAAGTTGAATTGTTTTACATTTTTGATTAAAACAAATGATAATTGAATATCTACCT
CAAAAAATATGAAGACAAAGGCATTCATTGGTAAGAAAAGTTCATTTATAGTCACCCATTCCTAC
AAAAACCTTATTACTTGCTTTAAATAGTTTTATAATCTCATAAGTTGAATTTCTTTTACATTTTC
GGCAAAA
Found at i:3411 original size:171 final size:170
Alignment explanation
Indices: 3096--3485 Score: 446
Period size: 171 Copynumber: 2.3 Consensus size: 170
3086 NNNNNNNNNN
* ** *
3096 CTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTATTTATGTTTTTTATT
1 CTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAG-TGAATTTATTTACATTGTTTATT
* * * * *
3161 AAAACAGACTATAATTCAATATCTGCACTGAGAGAGAAGTACTAAAAGCCATTTATTGAGGAAAA
65 AAAACAGACAATAATTCAATATCTACACTGAGAAAGAAGTACAAAAAGCCATTCATTGAGGAAAA
* * *
3226 AAGTCCATTTATAGTTTCTCATTCCTTTAAAAGCCG-AATTA
130 AAGTCCAATTATAGTCTCTCATTCCTTCAAAAG-CGTAATTA
* * * * *
3267 CTCGTTTTAAATGGTTTTGTATTCTCATATTTGATTTTAAGTGAAATTTTTTTACATTGTTTATT
1 CTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTG-AATTTATTTACATTGTTTATT
* * * ** *
3332 AAAACAGACAATAATTGAATGTCTAC-CTTGAGAAACG-TGTACAAAAAGTGATTCATTG-GTAA
65 AAAACAGACAATAATTCAATATCTACAC-TGAGAAA-GAAGTACAAAAAGCCATTCATTGAGGAA
* **
3394 GAAATGTCCAATTATAGTCTCTCATTCCTTCAAAAGCGTTGTTA
128 -AAAAGTCCAATTATAGTCTCTCATTCCTTCAAAAGCGTAATTA
*
3438 CTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATT
1 CTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAG-TGAATT
Statistics
Matches: 182, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
170 8 0.04
171 171 0.94
172 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (170 bp):
CTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTGAATTTATTTACATTGTTTATTA
AAACAGACAATAATTCAATATCTACACTGAGAAAGAAGTACAAAAAGCCATTCATTGAGGAAAAA
AGTCCAATTATAGTCTCTCATTCCTTCAAAAGCGTAATTA
Done.