Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402554.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5627.0, 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, 939
Length: 1566
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Found at i:526 original size:170 final size:170
Alignment explanation
Indices: 3--1566 Score: 1532
Period size: 171 Copynumber: 9.2 Consensus size: 170
1 TG
** *
3 GTTTTATAATCTCATAATTGATTTTAAGTTGAATCGTTTTACATTTTTTATT-GAAACAGA-TAA
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAG-AACAGACT-A
* * * ** * * **
66 CAATTGATTCTCTGTCTTGAGAAACATGAAGAAAAAGGTATTCATTGGCAAGGAAAGTCTGTTTA
64 TAATTGAATGTCTACCTTGAGAAACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTCCATTTA
*
131 TAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
128 TAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
* * * * * *
174 GTTTTATAATTTAATAATTTATTTTAAGTTAGATTTTTTTTACATTTTTTATTAAAACAGA-TAA
1 GTTTTATAATCTCATAATTGATTTTAAGTT-GAATTTTTTTACATTTTTCATTAGAACAGACT-A
* * * * ** * * *
238 TAATTGAATCTTTACCTCT-AGAAACTTGAAGAAAAATGCATTCGTTGGTGACAAAAGACTATTT
64 TAATTGAATGTCTACCT-TGAGAAACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTCCATTT
* **
302 ATAGCCTC-CGATTCCTTCAAAAATCTTATTACTCGCTTTAAATA
127 ATAGTCTCTC-ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
* *
346 GTTCTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTTACATTTTTCATTAGAACAAACTAT
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTCATTAGAACAGACTAT
* * * *
410 AATTGAATGTCTACCTTGAGTAACATGAAGAAAAAACATTCATTGGCAAGAGAAGTCCATATATA
65 AATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATA
* * ** *
475 GTCTCTCATTCCTTCAAAAGCTTTTTTACTCATTTTAAATG
130 GTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
* * * * * * *
516 GTTCTATAATCTCATAATTAATTTTAAGTT-AAGTTTGTTACATTTTTCGTTAAAATAGACTATA
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAGAACAGACTATA
** * * *
580 ATTGAATGTCTGTCTCGAGAAACATGAAGAAGAAAGTATTCA-TGGCAAGAAAAGTCCATATATA
66 ATTGAATGTCTACCTTGAGAAACATGAAGAA-AAAGCATTCATTGGCAAGAAAAGTCCATTTATA
* ** *
644 GTCTC-CTATTCCTTCAAAAGCCTTTTTACTCATTTTAAATG
130 GTCTCTC-ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
* * * *
685 GTTTTATAATCTCATAATTGATTTTAAGCTGAATTGTTTTT-CATTTTTTATTAAAATAGACTAT
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATT-TTTTTACATTTTTCATTAGAACAGACTAT
* * * * ** * * *
749 AATTGAATATCTGCCTTAAGAAACGTGAAGTAAAAAGCATTCATTGTTAAAAAAAATCCATATAT
65 AATTGAATGTCTACCTTGAGAAACATGAAG-AAAAAGCATTCATTGGCAAGAAAAGTCCATTTAT
* * **
814 AGTCTGTCATTCCTTCAAAAGCCTTTTTACTCATTTTAAAT-
129 AGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
* ** * *
855 GATTTTATAATCTCATAATTGTTTTTAAGTTGAATCCTTTTACATTTTTCATT-GAAACTGACAA
1 G-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAG-AACAGACTA
* * * * * * *
919 CAATTGAATGT-TCATCTTAAGAAATATGAAGATAAAAGTATTCATTGGCAAGGAAAGTCCGTTT
64 TAATTGAATGTCT-ACCTTGAGAAACATGAAGA-AAAAGCATTCATTGGCAAGAAAAGTCCATTT
* * * *
983 ATA-TCTTTTATTCTTTCAAAAGCCTTATCACTCGCTTTAAATA
127 ATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
*** * * * *
1026 GTTTTATAATAGAATAATTGATTTTAAGTTGAACTTTTTTTGCATTTTT-AGTTAAAATAGACAA
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTCA-TTAGAACAGACTA
* * * *** * *
1090 TAATTGAATGTTTAGCTCT-AGAAACTTGAAGAAAAATGCATTTGCTAGCAAGAAAAGTCTATTT
64 TAATTGAATGTCTACCT-TGAGAAACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTCCATTT
* *
1154 ATAGTCT-TCGATTCCTTCAAAAGCTTTATTACTCGCTTTAAATG
127 ATAGTCTCTC-ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
* *
1198 GTTCTATAATATCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTCATTAGAACAGACTATA
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAGAACAGACTATA
** * * * **
1262 ATTGAATGTCCGCCTTGAAAAACGTGAGGAAAAATGCATTCATTGATAAGAAAAGTCCATTTATA
66 ATTGAATGTCTACCTTGAGAAACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTCCATTTATA
* * * * *
1327 GTCTTTCATTCATTTAAAAGCCTTTTTACTCGTTTTAAATA
130 GTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
* * *
1368 GTTTTATATTCTCATAATTGATTTTAAGTTGAATATTTTTACATTTTTCATT-GTAACATACTAT
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAG-AACAGACTAT
* * * * * * *
1432 AATTGATTGTC--CGTTTAGAGAAACATGAAGAAAAAAGTAATCATTGGCAAGGAAAGCCCGTTT
65 AATTGAATGTCTAC-CTT-GAGAAACATGAAG-AAAAAGCATTCATTGGCAAGAAAAGTCCATTT
*
1495 ATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTGTAAATA
127 ATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
*
1539 GTTTTATAATCTAATAATTGATTTTAAG
1 GTTTTATAATCTCATAATTGATTTTAAG
Statistics
Matches: 1160, Mismatches: 196, Indels: 74
0.81 0.14 0.05
Matches are distributed among these distances:
168 1 0.00
169 141 0.12
170 362 0.31
171 443 0.38
172 212 0.18
173 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (170 bp):
GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTAGAACAGACTATA
ATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAG
TCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATA
Found at i:1526 original size:341 final size:340
Alignment explanation
Indices: 3--1566 Score: 1501
Period size: 341 Copynumber: 4.6 Consensus size: 340
1 TG
** * *
3 GTTTTATAATCTCATAATTGATTTTAAGTTGAATCGTTTTACATTTTTTATTGAAACAGA-TAAC
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTGAAACAGACT-AT
* * * * * **
67 AATTGATTCTCTGTCTTGAGAAACATGAAGAAAAAGGTATTCATTGGCAAGGAAAGTCTGTTTAT
65 AATTGAATGTCCGT-TTGAGAAACATGAAGAAAAAAGCATTCATTGGCAAGGAAAGTCCATTTAT
* * * * *
132 AGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATTTAATAATTTATT
129 AGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATT
* * * ** *
197 TTAAGTTAGATTTTTTTTACATTTTTTATTAAAACAGA-TAATAATTGAATCTTTACCTCTAGAA
194 TTAAGTT-GAATTTTTTTACATTTTTCATTAAAACAGACT-ATAATTGAATGTCCACCT-TAAAA
* * ** * * * * *
261 ACTTGAAGAAAAATGCATTCGTTGGTGACAAAAGACTATTTATAG-CCTCCGATTCCTTCAAAAA
256 ACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTCCATTTATAGTCTTCCGATTCCTTCAAAAG
*
325 TCTTATTACTCGCTTTAAATA
320 CCTTATTACTCGCTTTAAATA
* *
346 GTTCTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTTACATTTTTCATT-AGAACAAACTA
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTCATTGA-AACAGACTA
* * *
409 TAATTGAATGTCTAC-CTTGAGTAACATGAAGAAAAAA-CATTCATTGGCAA-GAGAAGTCCATA
64 TAATTGAATGTC--CGTTTGAGAAACATGAAGAAAAAAGCATTCATTGGCAAGGA-AAGTCCATT
* * ** * *
471 TATAGTCTCTCATTCCTTCAAAAGCTTTTTTACTCATTTTAAATGGTTCTATAATCTCATAATTA
126 TATAGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTG
* * * * *** * *
536 ATTTTAAGTT-AAGTTTGTTACATTTTTCGTTAAAATAGACTATAATTGAATGTCTGTCTCGAGA
191 ATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCCACCT-TAAA
* * *
600 AACATGAAGAAGAAAGTATTCA-TGGCAAGAAAAGTCCATATATAGTC-TCCTATTCCTTCAAAA
255 AACATGAAGAA-AAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCTTCCGATTCCTTCAAAA
* ** *
663 GCCTTTTTACTCATTTTAAATG
319 GCCTTATTACTCGCTTTAAATA
* * * *
685 GTTTTATAATCTCATAATTGATTTTAAGCTGAATTGTTTTT-CATTTTTTATTAAAATAGACTAT
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATT-TTTTTACATTTTTCATTGAAACAGACTAT
* * * * * * ** ** * *
749 AATTGAATATCTGCCTTAAGAAACGTGAAGTAAAAAGCATTCATTGTTAAAAAAAATCCATATAT
65 AATTGAATGTCCG-TTTGAGAAACATGAAGAAAAAAGCATTCATTGGCAAGGAAAGTCCATTTAT
* * ** * *
814 AGTCTGTCATTCCTTCAAAAGCCTTTTTACTCATTTTAAATGATTTTATAATCTCATAATTGTTT
129 AGTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATT
** * * * * * * *
879 TTAAGTTGAATCCTTTTACATTTTTCATTGAAACTGACAACAATTGAATGTTCATCTTAAGAAAT
194 TTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCCACCTTAA-AAAC
* * * ** *
944 ATGAAGATAAAAGTATTCATTGGCAAGGAAAGTCCGTTTATA-TCTT-TTATTCTTTCAAAAGCC
258 ATGAAGA-AAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCTTCCGATTCCTTCAAAAGCC
*
1007 TTATCACTCGCTTTAAATA
322 TTATTACTCGCTTTAAATA
*** * * * *
1026 GTTTTATAATAGAATAATTGATTTTAAGTTGAACTTTTTTTGCATTTTT-AGTTAAAATAGACAA
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTCA-TTGAAACAGACTA
** * * * *** * * *
1090 TAATTGAATGTTTAGCTCT-AGAAACTTGAAGAAAAATGCATTTGCTAGCAAGAAAAGTCTATTT
64 TAATTGAATG-TCCG-TTTGAGAAACATGAAGAAAAAAGCATTCATTGGCAAGGAAAGTCCATTT
* * *
1154 ATAGTCT-TCGATTCCTTCAAAAGCTTTATTACTCGCTTTAAATGGTTCTATAATATCATAATTG
127 ATAGTCTCTC-ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTG
* *
1218 ATTTTAAGTTGAATTTTTTTACA-TTTTCATTAGAACAGACTATAATTGAATGTCCGCCTTGAAA
191 ATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCCACCTT-AAA
* * ** * * *
1282 AACGTGAGGAAAAATGCATTCATTGATAAGAAAAGTCCATTTATAGTCTTTC-ATTCATTTAAAA
255 AACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTCCATTTATAGTCTTCCGATTCCTTCAAAA
* *
1346 GCCTTTTTACTCGTTTTAAATA
319 GCCTTATTACTCGCTTTAAATA
* * * *
1368 GTTTTATATTCTCATAATTGATTTTAAGTTGAATATTTTTACATTTTTCATTGTAACATACTATA
1 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTGAAACAGACTATA
* * * * *
1433 ATTGATTGTCCGTTTAGAGAAACATGAAGAAAAAAGTAATCATTGGCAAGGAAAGCCCGTTTATA
66 ATTGAATGTCCGTTT-GAGAAACATGAAGAAAAAAGCATTCATTGGCAAGGAAAGTCCATTTATA
* * *
1498 GTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTGTAAATAGTTTTATAATCTAATAATTGATTT
130 GTCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
1563 TAAG
195 TAAG
Statistics
Matches: 999, Mismatches: 188, Indels: 70
0.79 0.15 0.06
Matches are distributed among these distances:
339 126 0.13
340 160 0.16
341 319 0.32
342 310 0.31
343 83 0.08
344 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (340 bp):
GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCATTGAAACAGACTATA
ATTGAATGTCCGTTTGAGAAACATGAAGAAAAAAGCATTCATTGGCAAGGAAAGTCCATTTATAG
TCTCTCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
AAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCCACCTTAAAAACATG
AAGAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCTTCCGATTCCTTCAAAAGCCTTAT
TACTCGCTTTAAATA
Done.