Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397514.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1955.0, 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: 10946
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 4105 characters in sequence are not A, C, G, or T
Found at i:655 original size:21 final size:20
Alignment explanation
Indices: 617--656 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
607 TCAAAAATAG
617 TGTAAAAAATCCTATTTATT
1 TGTAAAAAATCCTATTTATT
637 TGTAAGAAACATCC-ATTTAT
1 TGTAA-AAA-ATCCTATTTAT
657 AGTCTCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (20 bp):
TGTAAAAAATCCTATTTATT
Found at i:1361 original size:171 final size:170
Alignment explanation
Indices: 3--3522 Score: 1736
Period size: 171 Copynumber: 20.7 Consensus size: 170
1 CA
* *
3 CGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTATTTACGTTTTTAGT
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTA--TA--TTTTTGGT
* * ** * * * * *
68 TAAAACAAATTATAATGGAATGTCTACCTCGAGAAATGTGAAGAATAAGGCTTTTATTGACAAGA
62 TAAAACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGA
* * * *
133 AAAGTTCATTTATAGTCTCCCATTCCTTTAAAAGCCTTAGTACT
127 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* ** ********* *
177 CTG-GTTAAA-AGGTTTTGCAATC-CAATAATTGATNNNNNNNNNNATATTTTTTCAT-TTTTCG
1 C-GCTTTAAATA-GTTTTATAATCTCAA-AATTGAT-TTTAAGTTCA-ATTTTTT-ATATTTTTG
* * * * * *
238 G-TAAAACAGATTATAATTAAATGTCTACATTAAGAAACGTAAAGAAACAAGA-ATTCATTGGCA
60 GTTAAAACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAA-AAGACATTCATTGGCA
* * * *
301 AGAAAAGTTCATTTATAGTCTCCCATTCATTCGAAAGCCTTATTACT
124 AGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
********** * * * * **
348 CGCTTTNNNNNNNNNNATAATCTCATAATTGATTTTAAGTTGAATTTTTATACATTATTATTTAA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTT-TATATTTTTGGTTAA
* * * * * ** * * ** *
413 AACAGACTATCATTGAATGT-TGACATTGGGAAATGTGAAGACAAAGGCAACCATTAGCAAGAAA
65 AACAAATTATAATTGAATGTCT-ACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAA
* * * * *
477 AGTTCATTTAGAGTCACCCATTCTTTCAAAAGCCTAATTATT
129 AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * **
519 CACTTTAAAT-GATTTTATAATCTTAAAATTGATTTTAAGTTTAATTTTTT-TATTTTTTATTAA
1 CGCTTTAAATAG-TTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTATATTTTTGGTTAA
* * * * * * * * * ** * * *
582 AATAGACTATAATTGAATGCCTATC-TCAAAAATAGTGTA-AAAAATCCTATTTATTTGTAAGAA
65 AACAAATTATAATTGAATGTCTACCTTGAGAAACA-TGAAGAAAAAGAC-ATTCATTGGCAAGAA
* ** * * *
645 ACA-TCCATTTATAGTCTCTTATTTCTTCAAAAGTCTTATTAGT
128 A-AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * ** * * *
688 CGCTTTAGAA-GGTTTTATAATCCCATAATTGATTTTGGGTTCAATTTTTTTTACATTATTGGCT
1 CGCTTTA-AATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAA--TTTTTTATATTTTTGGTT
* * * * * *
752 AAAACATATTATAATAGAATGTCCACCATGAGAAACGTGAGGAAAAAGACATTCATTGGCAAGAA
63 AAAACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAA
* *
817 AAGTCCATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACA
128 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * * *
860 CGCTTTAAATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATTTTTTATATTTTT-TTATCA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTATATTTTTGGT-T-A
*** * * * * ** ** * * *
924 AAACAGGCTATAATTGAATG-CTTGCATTAAGAAACGTCTAGAAAAACTCATTTATTTG-AAAAC
64 AAACAAATTATAATTGAATGTC-TACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGA-
* * * * * * *
987 AAATTCCATTTATAGTCTCCTATACCTTTAAAAGCTTTATTGCT
127 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * ********** * **
1031 GGCTTTAAATAGTTTTATAATGTCATAATTGATTTNNNNNNNNNNGTTTTTACATTTTTCATTAA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTT-TAAGTTCAATTTTTTATATTTTTGGTTAA
* * * * ** * * *
1096 AATAGACTAT-ATTAGAATG-CTTGCCTTGAGAAACGGGTAGAAAAAGCCATTTATTGAG-AAGA
65 AACAAATTATAATT-GAATGTC-TACCTTGAGAAACATGAAGAAAAAGACATTCATTG-GCAAGA
*** * * * * * *
1158 GCGGTTCATTTACAGTCTCTCATTCCTTCAAAAGTCTTATTACA
127 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * * ** *
1202 CGTTTTAAATAGTTTTATAATGTTAAAATTAATTTTAAGTAGAACTTTTTTATATTTTTGGTTTA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAA-TTTTTTATATTTTTGGTTAA
* * * * * * * * *
1267 ACCAAACTATAATTCAATGTCTACCTCGAGAAACATAAAGAAAAATAAATTTATAGGCAAGAAAA
65 AACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAA
*
1332 GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTAATACT
130 GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * * *
1373 CCCTTTAAA-AGATTTTATAATCTCAAAATTGATTCTAAGTTAAATGTTTTTACATTTTTAGTTA
1 CGCTTTAAATAG-TTTTATAATCTCAAAATTGATTTTAAGTTCAAT-TTTTTATATTTTTGGTTA
* * * * ** * * * *
1437 AAATAGACTATAATTGAATATCTATGTTAAGAAACGTGAAGAAAAA-AGCATCCATTGGTAAGAA
64 AAACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGA-CATTCATTGGCAAGAA
* * * *
1501 AAATCCATTTATAGTCATCCATTTCTTCAAAAGCCTTACTACT
128 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
** * *
1544 CGCTTTAAATTCTTTTATAATCTCATAATTGA-TTTAGGTTCAATTTTTT-TACTTTATTGGTTA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTATA-TTT-TTGGTTA
* * * * ** *
1607 AAACAGATTATAATTGAATATTTACCTTGAAAAATGTGAAGAAAAAGACATTCATTGCCAA-AGA
64 AAACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGA-A
***
1671 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTNNN
128 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
******* * * * *
1714 NNNNNNNAATGGTTTAATAATCTCAAAATTGATTTTAAGTTCAATTTTTTCACATTTATGGTTAA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTT-ATATTTTTGGTTAA
* * * *
1779 AACATATTATAATTGAATGTCTACCTCGAGAAATATGAAGAAAAAGACATTAATTGGCAAGAAAA
65 AACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAA
* **********
1844 GTCTATTTATAGTCNNNNNNNNNNTCAAAAGCCTTATTACT
130 GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * *
1885 CGCTTTAAATAGTTTTACAAACTCAGAATTGATTTTAAGTTCAATTTTTTATATATTTTTAGTTA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAA-TTTTT-TATATTTTTGGTTA
* * ** * ** *
1950 AAA-AAGATTATAATTGAATGTCTATCTTGTGAAACAT-ATAGAAAAAGGTATTTATTGATAATA
64 AAACAA-ATTATAATTGAATGTCTACCTTGAGAAACATGA-AGAAAAAGACATTCATTGGCAAGA
*
2013 GAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
127 AAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* ********************* * * * *
2057 CACTTTNNNNNNNNNNNNNNNNNNNNNATTAATTTTAAGTTGAATTGTTTTACATTTTTAGTTAA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATT-TTTTATATTTTTGGTTAA
* * * * * * *
2122 AACAGACTATAATT-AATGTCTATCTTAAGAAATATGAA-AAAAATAAATTCATTGGCAAGAAAA
65 AACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAA
* * ** * **
2185 GTCTATATATAGTCACTTAATCCTTCAAAAGCCTTATTANN
130 GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
******** * * *
2226 NNNNNNNNAT-GATTTTTTAATCTCAAAATTGATTTTAAG--------TTTAAATTTCT--TTAA
1 CGCTTTAAATAG-TTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTATATTTTTGGTTAA
* * * ** ********** *
2280 AACAGACTATAATTGAATGTCTATCTCAANNNNNNNNNNGAAAAA-AGTATTCATTGGCAAGAAA
65 AACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGA-CATTCATTGGCAAGAAA
* ** * *
2344 AGTCTATTTATAGTCTGCCATTCATTCAAAAACCTTATTACT
129 AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * * * * * * **
2386 CGCTTTAAATGGTTTTATAATTTCATAATTAATTTTAGGGTTCAGTGTTTTAACATTACTGGTTA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTA-AGTTCAAT-TTTTTATATTTTTGGTTA
* * * * * ** * *
2451 AAATAGATTATAATTAAATATCTATCTCAAGAAATATGAAG-AAAAGATAGTTCATTGGCAAGAA
64 AAACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACA-TTCATTGGCAAGAA
* * * * *********
2515 AATTTCATTTATAGTCTCTCATTCGC-TCAAAAGCNNNNNNNNN
128 AAGTCCATTTATAGTCACCCATTC-CTTCAAAAGCCTTATTACT
** * * * **
2558 NACTTTAAAT-GATTTTATAATCTCATAATTGATTTTAAGCTGAATGTTTTTATATTTTTTATTA
1 CGCTTTAAATAG-TTTTATAATCTCAAAATTGATTTTAAGTTCAAT-TTTTTATATTTTTGGTTA
* ** * ** * * * * * * *
2622 AAACAGACAATAATTGAATGTTTACCTCAAGAAACGTAAAGAGAAAGGCATCCATTAGCAAGCAA
64 AAACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAA
* * * ****
2687 AGTCCATTTAGAGTCACCCATTCTTTCAAAAGTCTTATNNNN
129 AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
****** * * * * * * *
2729 NNNNNNAAATGGTTTTATAATCTCAAAATTGATTTTAAATTTAATTTTTTAACATTTATAGCTAA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTT-ATATTTTTGGTTAA
* * ** *
2794 AACAGATTATAATTGAAAGTCTACCTCAAGAAACGA-GAAGAAAACA-ACATACATTGGCAAGAA
65 AACAAATTATAATTGAATGTCTACCTTGAGAAAC-ATGAAGAAAA-AGACATTCATTGGCAAGAA
* * * *
2857 AAGTCCATTTATAGTCACCCATTCTTTTAAAAGCCGTATGACT
128 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * *
2900 CACTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTCAATTTTTCATATTTTTGGTTAAA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTATATTTTTGGTTAAA
* * **
2965 ACAGACTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAA-AGCATTCATTGGCAAGAAAA
66 ACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGA-CATTCATTGGCAAG-AAA
* * *
3029 AGTCCATTTATAGTCTCTCATTCCTTCAAAAGTCTTATTACT
129 AGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
* * * * * * *
3071 CGCTTTAAAT-GATTTTCTAATGTCATAATTGACTTT-AGTTTC-ATTTTTGTTTGCAATTATTA
1 CGCTTTAAATAG-TTTTATAATCTCAAAATTGATTTTAAG-TTCAATTTTT-TAT---ATTTTTG
* * * ** * **
3133 GTTAAAACATATTATAATTGAATGTTTACCTAGAGAAAGGTAAAGAAAAAGACATTCATTGTTAA
60 GTTAAAACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAA
*
3198 G-AAAG---------AGTCA-CCATTCCTTCAAAAGCGTTATTACT
125 GAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
3233 CGC-TTAAAT-GTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTATATTTTTGGTTAA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAA-TTTTTTATATTTTTGGTTAA
* * * * * *
3296 AACAGATTATAATTGAATGTCTACCTCATGA-AAA-GTGAAGAAAAAAATATTTATTGGTAAGAA
65 AACAAATTATAATTGAATGTCTACCT--TGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAA
* * * ******
3359 ATGTCCGTTTATAGTCACCTATTCCTTCAAAAG-CTTNNNNNNN
128 AAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTT-ATTACT
*** * * * * *
3402 NNNTTTAAATGGTTTTATAATCTCAGAATTGATTTTAAGTTCAAATTTTTATATAGTCTTAGTTA
1 CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTC-AATTTTT-TATATTTTTGGTTA
* * * * * * *
3467 AAACAGATTGTAATTAAATGTCTACCTTGTA-AAACGTGAATAAAAAGGCGTTCATT
64 AAACAAATTATAATTGAATGTCTACCTTG-AGAAACATGAAGAAAAAGACATTCATT
3523 CACAATAGAA
Statistics
Matches: 2515, Mismatches: 711, Indels: 242
0.73 0.21 0.07
Matches are distributed among these distances:
158 74 0.03
159 20 0.01
160 110 0.04
161 14 0.01
162 30 0.01
163 4 0.00
168 18 0.01
169 200 0.08
170 273 0.11
171 1231 0.49
172 431 0.17
173 17 0.01
174 81 0.03
175 4 0.00
176 7 0.00
177 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.37
Consensus pattern (170 bp):
CGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTATATTTTTGGTTAAA
ACAAATTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAG
TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACT
Done.