Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402992.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_659.0, 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: 3803
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.26
Warning! 1260 characters in sequence are not A, C, G, or T
Found at i:444 original size:171 final size:171
Alignment explanation
Indices: 216--1326 Score: 1314
Period size: 171 Copynumber: 6.5 Consensus size: 171
206 NNNNNNNNNN
* *
216 AAGTTGAATTTTTTTACA-TTTTT-TTAAAATAGACAATAATTGAATGTCTATCTCGAGAAACGT
1 AAGTTGAATTTTTTTACATTTTTTATTAAAATAGACTATAATTGAATGTCTACCTCGAGAAACGT
* * *
279 GCAGAAAAATCCATTGATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGGCTTA
66 GAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGGCTTA
* * *
344 TTACTCGATTTAAATAGTTTTGTAATCTCATAATTGATTTT
131 TTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
* * *
385 AAGTTGAATTTTTTTACATTTTTAATTAAAATATACTATAATTGAATGAT-TACCTCGAGAAACA
1 AAGTTGAATTTTTTTACATTTTTTATTAAAATAGACTATAATTGAATG-TCTACCTCGAGAAACG
* * * * * *
449 TGAAGAAACAA-ACATTCTTTGACAAGAAAAGTCCATTTAGAGTCACCCATTCCTTCAAAAAGCT
65 TGAAGAAA-AAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGGCT
* * *
513 TATTACTCGCTTTAAACGGTTTTATAATTTCGTAATTGATTTT
129 TATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
* * * ** *
556 AAGTTGAATTATTTTACATTTTTTATTAAAACAGACTATAAGTGTTTGTCTACTTCGAGAAACGT
1 AAGTTGAATTTTTTTACATTTTTTATTAAAATAGACTATAATTGAATGTCTACCTCGAGAAACGT
* *
621 GCAA-AAAAAGCCATTCATTGAGAAGAAAAGTCCTTTTATAGTCACTCATTCCTTCAAAAGTCTT
66 G-AAGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGGCTT
* * *
685 ATTACCCGCTTTAAATGGTTTTATAATTTCATAGTTGATTTT
130 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
* * * * * * * * *
727 AAGTTGAATTTTTGTACATTTTTTGTTAAAAAAAACTATAATTGAAAGTCTGCCT-TAGGTAAGG
1 AAGTTGAATTTTTTTACATTTTTTATTAAAATAGACTATAATTGAATGTCTACCTCGA-GAAACG
* * * *
791 TGTAGAAAAAGCCATTCATTGAGAAGAGAAA-TCCATTTTTAGTCACTCATTCTTTCAAAAGCCT
65 TGAAGAAAAAGCCATTCATTGAGAAGA-AAAGTCCATTTATAGTCACTCATTCCTTCAAAAGGCT
* * * *
855 TATTACTCG-GTTCAATGATTATATAATCTCATAATTGATTTT
129 TATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
* * * *
897 AAGTTAAATTTTTTTACATTTTTCT-TTAAATTAGA-TAATAATTGAATG-CTTATCTCAAGAAA
1 AAGTTGAATTTTTTTACATTTTT-TATTAAAATAGACT-ATAATTGAATGTC-TACCTCGAGAAA
* *
959 CGTGTAGAAAAAGCCATTGATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCCTT-AAAAGG
63 CGTGAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATT-CCTTCAAAAGG
** *
1023 CTTATTACTCGCTTTAAATAATTTTATAATCTCATAATTAATTTT
127 CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
* * * *
1068 AAGTTAAATTTTTTTATATTTTTTATTAAAATAGACTAAAATTGAATGTTTACCTCGAGAAACGT
1 AAGTTGAATTTTTTTACATTTTTTATTAAAATAGACTATAATTGAATGTCTACCTCGAGAAACGT
* * * * * *
1133 GAAGAAACAAG-CATTCAATGATAAGAAAAGTCCATTTAGAGTCACCCATTTCTTCAAAAAGCTT
66 GAAGAAA-AAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGGCTT
*
1197 ATTAATCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
130 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
* ** ** * * * ** *
1239 AAGTTGAATTTTTGTATGTTTTGGATTTAAACATACTATAATTGAATGTCTATATCAAGAAACGT
1 AAGTTGAATTTTTTTACATTTTTTATTAAAATAGACTATAATTGAATGTCTACCTCGAGAAACGT
1304 GAAGAAATAAG-CATTCATTGAGA
66 GAAGAAA-AAGCCATTCATTGAGA
1327 NNNNNNNNNN
Statistics
Matches: 800, Mismatches: 120, Indels: 42
0.83 0.12 0.04
Matches are distributed among these distances:
169 23 0.03
170 146 0.18
171 619 0.77
172 12 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (171 bp):
AAGTTGAATTTTTTTACATTTTTTATTAAAATAGACTATAATTGAATGTCTACCTCGAGAAACGT
GAAGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGGCTTA
TTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
Found at i:1216 original size:512 final size:511
Alignment explanation
Indices: 216--1254 Score: 1342
Period size: 512 Copynumber: 2.0 Consensus size: 511
206 NNNNNNNNNN
* * * * * *
216 AAGTTGAATTTTTTTACATTTTTTTAAAATAGACAATAATTGAATGTCTATCTCGAGAAACGTGC
1 AAGTTGAATTTTTGTACATTTTTTTAAAAAAAACAATAATTGAAAGTCTACCTAGAGAAACGTGC
* * *
281 AGAAAAATCCATTGATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGGCTTATT
66 AGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATT
* * * *
346 ACTCGATTTAAATAGTTTTGTAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAAT
131 ACTCGAGTTAAATAGTTATATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTAAT
* * *
411 TAAAATATACTATAATTGAATGATTACCTCGAGAAACATGAAGAAACAAACATTCTTTGACAAGA
196 TAAAATAGACTATAATTGAATGATTACCTCAAGAAACATGAAGAAACAAACATTCATTGACAAGA
**
476 AAAGTCCATTTAGAGTCACCCATTCCTTCAAAAAGCTTATTACTCGCTTTAAACGGTTTTATAAT
261 AAAGTCCATTTAGAGTCACCCATTCCTTCAAAAAGCTTATTACTCGCTTTAAACAATTTTATAAT
* * * * * **
541 TTCGTAATTGATTTTAAGTTGAATTATTTTACATTTTTTATTAAAACAGACTATAAGTGTTTGTC
326 CTCATAATTAATTTTAAGTTAAATTATTTTACATTTTTTATTAAAACAGACTAAAAGTGAATGTC
* * * * *
606 TACTTCGAGAAACGTGCAAAAAAAGCCATTCATTGAGAAGAAAAGTCCTTTTATAGTCACTCATT
391 TACCTCGAGAAACGTGCAAAAAAAGCCATTCAATGAGAAGAAAAGTCCATTTAGAGTCACCCATT
* * *
671 CCTTCAAAAGTCTTATTACCCGCTTTAAATGGTTTTATAATTTCATAGTTGATTTT
456 CCTTCAAAAGTCTTATTAACCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
* * * *
727 AAGTTGAATTTTTGTACATTTTTTGTTAAAAAAAACTATAATTGAAAGTCTGCCTTAG-GTAAGG
1 AAGTTGAATTTTTGTACA-TTTTT-TTAAAAAAAACAATAATTGAAAGTCTACC-TAGAGAAACG
* * *
791 TGTAGAAAAAGCCATTCATTGAGAAGAGAAA-TCCATTTTTAGTCACTCATTCTTTCAAAAGCCT
63 TGCAGAAAAAGCCATTCATTGAGAAGA-AAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCT
*
855 TATTACTCG-GTTCAAT-GATTATATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTT
127 TATTACTCGAGTTAAATAG-TTATATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTT
** * * * * * * *
918 TTCTTTAAATTAGA-TAATAATTGAATGCTTATCTCAAGAAACGTGTAGAAA-AAGCCATTGATT
191 TTAATTAAAATAGACT-ATAATTGAATGATTACCTCAAGAAACATGAAGAAACAA-ACATTCATT
* * * * *
981 GAGAAGAAAAGTCCATTTATAGTCACTCATTCCCTT-AAAAGGCTTATTACTCGCTTTAAATAAT
254 GACAAGAAAAGTCCATTTAGAGTCACCCATT-CCTTCAAAAAGCTTATTACTCGCTTTAAACAAT
* * * *
1045 TTTATAATCTCATAATTAATTTTAAGTTAAATTTTTTTATATTTTTTATTAAAATAGACTAAAAT
318 TTTATAATCTCATAATTAATTTTAAGTTAAATTATTTTACATTTTTTATTAAAACAGACTAAAAG
* *
1110 TGAATGTTTACCTCGAGAAACGTG-AAGAAACAAG-CATTCAATGATAAGAAAAGTCCATTTAGA
383 TGAATGTCTACCTCGAGAAACGTGCAA-AAA-AAGCCATTCAATGAGAAGAAAAGTCCATTTAGA
* *
1173 GTCACCCATTTCTTCAAAAAG-CTTATTAATCGCTTTAAATGGTTTTATAATCTCATAATTGATT
446 GTCACCCATTCCTTC-AAAAGTCTTATTAACCGCTTTAAATGGTTTTATAATCTCATAATTGATT
1237 TT
510 TT
1239 AAGTTGAATTTTTGTA
1 AAGTTGAATTTTTGTA
1255 TGTTTTGGAT
Statistics
Matches: 454, Mismatches: 63, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
511 23 0.05
512 324 0.71
513 102 0.22
514 5 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (511 bp):
AAGTTGAATTTTTGTACATTTTTTTAAAAAAAACAATAATTGAAAGTCTACCTAGAGAAACGTGC
AGAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATT
ACTCGAGTTAAATAGTTATATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTAAT
TAAAATAGACTATAATTGAATGATTACCTCAAGAAACATGAAGAAACAAACATTCATTGACAAGA
AAAGTCCATTTAGAGTCACCCATTCCTTCAAAAAGCTTATTACTCGCTTTAAACAATTTTATAAT
CTCATAATTAATTTTAAGTTAAATTATTTTACATTTTTTATTAAAACAGACTAAAAGTGAATGTC
TACCTCGAGAAACGTGCAAAAAAAGCCATTCAATGAGAAGAAAAGTCCATTTAGAGTCACCCATT
CCTTCAAAAGTCTTATTAACCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
Found at i:1982 original size:170 final size:171
Alignment explanation
Indices: 1537--2033 Score: 538
Period size: 170 Copynumber: 2.9 Consensus size: 171
1527 NNNNNNNNNN
* * *
1537 CTCGGTTTAAAT-GATTTTATAATCTCATAATTGATTTTAAGTTGAACTTTTTTAACATTTTTTT
1 CTCGCTTTAAATAG-TTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACAATTTTTT
* * * * ** * *
1601 TTAAAACAGACGATAATTGATTGTCTAACTCGAGAAATATGGAGAAAAAGCCATTGATAGAGAAG
64 TTAAAATAGACAATAATTGAATGTCTAACTCAAGAAACGTGCAGAAAAAGCCATTGATTGAGAAG
*
1666 AAAAGTCTATTTATAGTCACCCATTCCCTCGAAAGGCTTATTA
129 AAAAGTCTATTTATAGTCACCCATTCCCTCGAAAGCCTTATTA
* * * *
1709 CTTGCTTTAAATAGTTTTATAATCTCACAATTGGTTTTAAGTTAAATTTTTCTT-C-ATTTTTTG
1 CTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT-TTACAATTTTTT-
* * * * *
1772 TTAAAATAGACTATAATTGAATGTCTATCTCAAGAAACGTGTATAAAAAGCCATTCATTGAGAAG
64 TTAAAATAGACAATAATTGAATGTCTAACTCAAGAAACGTGCAGAAAAAGCCATTGATTGAGAAG
* * **
1837 AAAAATCTATGTT-TAGTCACTCATTCTTTCGAAAGCCTTATTA
129 AAAAGTCTAT-TTATAGTCACCCATTCCCTCGAAAGCCTTATTA
* ********* *
1880 CTCGGTTT-AAT-GNNNNNNNNNNCTCATAATTGATTTTAAGTTGAATTTTTTTACAATTTTCTT
1 CTCGCTTTAAATAG-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACAATTTTTTT
* * *
1943 TAAATTAGGCAATAATTGAATGTCTAACTCAAGAAACGTGCAGAAAAAGCTATTGATTGAGAAGA
65 TAAAATAGACAATAATTGAATGTCTAACTCAAGAAACGTGCAGAAAAAGCCATTGATTGAGAAGA
*
2008 AAAGTCCATTTATAGTCACCCATTCC
130 AAAGTCTATTTATAGTCACCCATTCC
2034 TTCANNNNNN
Statistics
Matches: 267, Mismatches: 50, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
169 5 0.02
170 112 0.42
171 107 0.40
172 42 0.16
173 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.37
Consensus pattern (171 bp):
CTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACAATTTTTTTT
AAAATAGACAATAATTGAATGTCTAACTCAAGAAACGTGCAGAAAAAGCCATTGATTGAGAAGAA
AAGTCTATTTATAGTCACCCATTCCCTCGAAAGCCTTATTA
Done.