Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399858.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3091.0, 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: 2174
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.26
Warning! 666 characters in sequence are not A, C, G, or T
Found at i:1599 original size:171 final size:169
Alignment explanation
Indices: 1201--2174 Score: 929
Period size: 171 Copynumber: 5.7 Consensus size: 169
1191 NNNNNNNNNN
* * * * * * * * *
1201 ATTGATTTTAAGATGAATTTTTTGA-TTTTTTTTATAAAACAGACAATTATTGTATGTCAATCTC
1 ATTGATTTTAAGTTAAATTTTTTTACATTTTTGT-TAAAACAGACCATAATTGAATGTCTATCTC
* * * * * * * * *
1265 GAGAAACGTGCA-AAAAAGGCTTTGATTAACAAAAAAAGTCCATTTAGAGTCACCCATTCCTTCA
65 AAGAAACGTGAAGAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTAGAGTCACCCATTCCTTCA
*
1329 AAAGGCTTATTACTCGCTTTAAATAG-TTTGTAATCTCATA
130 AAA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTCATA
* * *
1369 ATTGATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACATACCATAATTGATTGTCTATCTC
1 ATTGATTTTAAGTTAAATTTTTTTACA-TTTTTGTTAAAACAGACCATAATTGAATGTCTATCTC
* ** *
1434 AAGAAACGTGAAGAAACAA-CCATTCATTGACAAGAAAAGTGAATTTAGAGTCACCCGTTCCTTC
65 AAGAAACGTGAAGAAA-AAGCCATTCATTGAGAAGAAAAGTTCATTTAGAGTCACCCATTCCTTC
* *
1498 AAAATGCTTATTATTGGCTTTAAATAGTTTTATAATCTCATA
129 AAAA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTCATA
* *
1540 ATTGATTTTAAGTTGAATTTTTTTACATCTTTTGTTAAAACAGACTATAATT-AATTGTCTA-CA
1 ATTGATTTTAAGTTAAATTTTTTTACAT-TTTTGTTAAAACAGACCATAATTGAA-TGTCTATC-
* * * * *
1603 TCGAGAAATGT-ACGTAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAGTCACTCATTCCT
63 TCAAGAAACGTGAAG-AAAAAGCCATTCATTGAGAAGAAAAGTTCATTTAGAGTCACCCATTCCT
* * * *
1667 TCAAAAGGCTTATTACCCACTTTTAATGGTTTTATAATCTCATA
127 TCAAAA-GCTTATTACTCGCTTTAAATAGTTTTATAATCTCATA
* * * * *
1711 ATTGATTTTAAGTTGAATTTTTTTTACATTTTTCTTTAAAACGGGCCATAATTGAAAG-CT-TGC
1 ATTGATTTTAAGTT-AAATTTTTTTACATTTTT-GTTAAAACAGACCATAATTGAATGTCTAT--
* * * * * * **
1774 CTCATGAAAGGT-ATAGAAAAAGTCATTTATTGAGAAGGAAAAATCCATTTTTAGTCACCCATTC
62 CTCAAGAAACGTGA-AGAAAAAGCCATTCATTGAGAA-GAAAAGTTCATTTAGAGTCACCCATTC
* * * * *
1838 TTTCAATAGCCTTATTGCTCGGTTTAAATAATTTTATAATCTCATA
125 CTTCAAAAG-CTTATTACTCGCTTTAAATAGTTTTATAATCTCATA
* * * * * *
1884 ATTAATTTTAAG-TCAATTTTGTTACATTTTTCTTTAAAACAGACAACAATTGAATGTCTATCTC
1 ATTGATTTTAAGTTAAATTTTTTTACATTTTT-GTTAAAACAGACCATAATTGAATGTCTATCTC
* * * *
1948 AAGAAACTTGCAGAAAAAG-C---CATTGACATGAAAAGTTCATTTAGAAGTCACCCATTCCTTC
65 AAGAAACGTGAAGAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTAG-AGTCACCCATTCCTTC
** * *
2009 AAAAGAAATATTACTCACTTTAAATATTTTTATAATCTCATA
129 AAAAG-CTTATTACTCGCTTTAAATAGTTTTATAATCTCATA
* * *
2051 ATTGATTTTAAGTTAAATTTTTTTACATTTTTGTTAAAACAGACTC-TAATTGAATATCCACCTC
1 ATTGATTTTAAGTTAAATTTTTTTACATTTTTGTTAAAACAGAC-CATAATTGAATGTCTATCTC
* * * *
2115 AAGAACCGTGCAA-AAAAAGTCATTCATTGAGAAGAAAAGTTCATTTATAGTCACTCATTC
65 AAGAAACGTG-AAGAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTAGAGTCACCCATTC
Statistics
Matches: 659, Mismatches: 117, Indels: 58
0.79 0.14 0.07
Matches are distributed among these distances:
166 11 0.02
167 105 0.16
168 41 0.06
169 34 0.05
170 89 0.14
171 246 0.37
172 59 0.09
173 74 0.11
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (169 bp):
ATTGATTTTAAGTTAAATTTTTTTACATTTTTGTTAAAACAGACCATAATTGAATGTCTATCTCA
AGAAACGTGAAGAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTAGAGTCACCCATTCCTTCAA
AAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATA
Found at i:1967 original size:343 final size:337
Alignment explanation
Indices: 1227--2174 Score: 962
Period size: 343 Copynumber: 2.8 Consensus size: 337
1217 ATTTTTTGAT
* * * *
1227 TTTTTTTATAAAACAGACAATTATTGTATGTCAATCTCGAGAAACGTGCA-AAAAAGGCTTTGAT
1 TTTTTTT-TAAAACAGACAATAATTGAATGTCTATCTCGAGAAAC-TGCAGAAAAA-GC-TTCAT
* * * * *
1291 TAACAAAAAAAGTCCATTTAGAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATAG-
62 TGACAAGAAAAGTTCATTTAAAGTCACCCATTCCTTCAAAAGGCTTATTACTCACTTTAAATAGT
* *
1355 TTTGTAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTATTAAAACATACCATAAT
127 TTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTT-TTAAAACAGACCATAAT
** * *
1420 TGATTGTCTATCTCAAGAAACGTGAAGAAACAACCATTCATTGACAAGAAAAGTGAATTTAGAGT
191 TGAAAGTCTATCTCAAGAAACGTGAAGAAACAACCATTCATTGACAAGAAAAATCAATTTAGAGT
* * * *
1485 CACCCGTTCCTTCAAAATGCTTATTATTGGCTTTAAATAGTTTTATAATCTCATAATTGATTTTA
256 CACCCATTCCTTCAAAATGCTTATTATCGGCTTTAAATAATTTTATAATCTCATAATTAATTTTA
* *
1550 AGTTGAATTTTTTTACA
321 AGTTCAATTTTGTTACA
* * *
1567 TCTTTTGTTAAAACAGACTATAATT-AATTGTCTA-CATCGAGAAA-TGTACGTAAAAAGCCATT
1 T-TTTTTTTAAAACAGACAATAATTGAA-TGTCTATC-TCGAGAAACTGCA-G-AAAAAG-C-TT
* * * * *
1629 CATTGAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGGCTTATTACCCACTTTTAAT
59 CATTGACAAGAAAAGTTCATTTAAAGTCACCCATTCCTTCAAAAGGCTTATTACTCACTTTAAAT
* * * *
1694 GGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTTACATTTTTCTTTAAAACGGGCCA
124 AGTTTTATAATCTCATAATTGATTTTAAGTT-AAATTTTTTTACATTTTT-TTTAAAACAGACCA
* * * * * *
1759 TAATTGAAAG-CT-TGCCTCATGAAAGGT-ATAGAAA-AAGTCATTTATTGAGAAGGAAAAATCC
187 TAATTGAAAGTCTAT--CTCAAGAAACGTGA-AGAAACAA-CCATTCATTGACAA-GAAAAATCA
** * * *
1820 ATTTTTAGTCACCCATTCTTTCAATA-GCCTTATTGCTCGG-TTTAAATAATTTTATAATCTCAT
247 ATTTAGAGTCACCCATTCCTTCAAAATG-CTTATT-ATCGGCTTTAAATAATTTTATAATCTCAT
1883 AATTAATTTTAAG-TCAATTTTGTTACA
310 AATTAATTTTAAGTTCAATTTTGTTACA
* *
1910 TTTTTCTTTAAAACAGACAACAATTGAATGTCTATCTCAAGAAACTTGCAGAAAAAGC--CATTG
1 TTTTT-TTTAAAACAGACAATAATTGAATGTCTATCTCGAGAAAC-TGCAGAAAAAGCTTCATTG
* *** *
1973 ACATGAAAAGTTCATTTAGAAGTCACCCATTCCTTCAAAAGAAATATTACTCACTTTAAATATTT
64 ACAAGAAAAGTTCATTTA-AAGTCACCCATTCCTTCAAAAGGCTTATTACTCACTTTAAATAGTT
*
2038 TTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGTTAAAACAGACTC-TAATT
128 TTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTTTAAAACAGAC-CATAATT
* * * * * * *
2102 GAATA-TCCACCTCAAGAACCGTGCAA-AAA-AAGTCATTCATTGAGAAGAAAAGTTC-ATTTAT
192 GAA-AGTCTATCTCAAGAAACGTG-AAGAAACAA-CCATTCATTGACAAGAAAA-ATCAATTTAG
*
2163 AGTCACTCATTC
253 AGTCACCCATTC
Statistics
Matches: 505, Mismatches: 73, Indels: 63
0.79 0.11 0.10
Matches are distributed among these distances:
337 21 0.04
338 50 0.10
339 44 0.09
340 95 0.19
341 70 0.14
342 37 0.07
343 110 0.22
344 72 0.14
345 6 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (337 bp):
TTTTTTTTAAAACAGACAATAATTGAATGTCTATCTCGAGAAACTGCAGAAAAAGCTTCATTGAC
AAGAAAAGTTCATTTAAAGTCACCCATTCCTTCAAAAGGCTTATTACTCACTTTAAATAGTTTTA
TAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTTTTAAAACAGACCATAATTGAAA
GTCTATCTCAAGAAACGTGAAGAAACAACCATTCATTGACAAGAAAAATCAATTTAGAGTCACCC
ATTCCTTCAAAATGCTTATTATCGGCTTTAAATAATTTTATAATCTCATAATTAATTTTAAGTTC
AATTTTGTTACA
Done.