Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400662.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3849.0, 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: 3819
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.19
Warning! 1727 characters in sequence are not A, C, G, or T
Found at i:444 original size:170 final size:169
Alignment explanation
Indices: 8--463 Score: 475
Period size: 172 Copynumber: 2.7 Consensus size: 169
1 GTATTTG
* * * *
8 TTGGCAAGAAAAGTCCATTTATTGTCACCCATTCTTTCAGAAGCCTTAATACTCACTTTAAATAG
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAA-AG
* * *******
73 TTTTGTAATTTCAAAATTGATTGAAATTTGAATTCTTTGTACATTTTTGGTTAAAAAAGNNNNNN
65 TTTTATAATCTCAAAATTGATTGAAATTTGAATTCTTTGTACATTTTT-GTTAAAAAAAATTATA
**** *
138 NNNNAATGTCAACATCAAGAAACATGAAGGAAAAGGTATTCA
129 ATTGAATGTCAACATCAAGAAACATGAAGAAAAAGG-ATTCA
* * * * *****
180 TTGGCAAGAAAACTCCATTAATAGTCACCCATTCCTTCAAAAACTTTATTACTCACTTTNNNNNN
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT-AAAAG
**** * *
245 NNNNATAATCTCAAGATTGATTTAAATTTGAATTCTTTGTACAATTTTTGTTAAAAAAAATTATA
65 TTTTATAATCTCAAAATTGATTGAAATTTGAATTCTTTGTAC-ATTTTTGTTAAAAAAAATTATA
* *
310 ATTGAATGTCGACCTCAAGAAACATGAAGAAAAAGG-TTCA
129 ATTGAATGTCAACATCAAGAAACATGAAGAAAAAGGATTCA
* * * *
350 TTGGTAAGAAAAGACCATTTACAGTAACCCATTCC-TCTAAAAGCCTTATTACTCACTTTAAAAG
1 TTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTC-AAAAGCCTTATTACTCACTTTAAAA-
*
414 GTTTTATAATCTCAAAATTGATTGAAATTTGAATTCTTTGTATATTTTTG
64 GTTTTATAATCTCAAAATTGATTGAAATTTGAATTCTTTGTACATTTTTG
464 NNNNNNNNNN
Statistics
Matches: 225, Mismatches: 55, Indels: 11
0.77 0.19 0.04
Matches are distributed among these distances:
169 9 0.04
170 87 0.39
172 123 0.55
173 6 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.34
Consensus pattern (169 bp):
TTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAAAGT
TTTATAATCTCAAAATTGATTGAAATTTGAATTCTTTGTACATTTTTGTTAAAAAAAATTATAAT
TGAATGTCAACATCAAGAAACATGAAGAAAAAGGATTCA
Found at i:2115 original size:171 final size:161
Alignment explanation
Indices: 1938--2246 Score: 329
Period size: 171 Copynumber: 1.9 Consensus size: 161
1928 NNNATCTCAA
* * *
1938 AATTGATTTAAATTTGAA-TCCTTTGCACATTTTTTGTTAAAACAGATTATAATTGAATGTCAA-
1 AATTGATTTAAAGTTGAAGT--TTTGCACATTTTTGGTTAAAACAGACTATAATTGAATGTCAAT
** * *
2001 CGTCAAGAAACATGAA-AAAAAGGC-ATACGTTGGCAAGAAAAATCCGTTTATAGTCACTCATTC
64 C-TCAAGAAACACAAAGAAAAAGGCAAT-CGTTGGCAAGAAAAATCCATTTATAGTCACCCATTC
2064 CTTCAAAAGCCTCATTACTTACTTTAAATGNNNNNNNNNNGCCAT
127 CTTCAAAAGCCTCATTACTTACTTTAAATG----------GCCAT
** *
2109 AATTGATTTTTAGTTGAAGTTTTTCACATTTTTGGTTAAAACAGACTATAATTGAATGTCAATCT
1 AATTGATTTAAAGTTGAAGTTTTGCACATTTTTGGTTAAAACAGACTATAATTGAATGTCAATCT
** * * *
2174 TGAGAAACACAAAGAAAAAGGTAATTGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTC
66 CAAGAAACACAAAGAAAAAGGCAATCGTTGGCAAGAAAAATCCATTTATAGTCACCCATTCCTTC
2239 AAAAGCCT
131 AAAAGCCT
2247 TAATANNNNN
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
170 49 0.41
171 67 0.56
172 3 0.03
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.32
Consensus pattern (161 bp):
AATTGATTTAAAGTTGAAGTTTTGCACATTTTTGGTTAAAACAGACTATAATTGAATGTCAATCT
CAAGAAACACAAAGAAAAAGGCAATCGTTGGCAAGAAAAATCCATTTATAGTCACCCATTCCTTC
AAAAGCCTCATTACTTACTTTAAATGGCCAT
Found at i:2220 original size:342 final size:334
Alignment explanation
Indices: 1593--2247 Score: 647
Period size: 342 Copynumber: 1.9 Consensus size: 334
1583 NNNNNNNNNN
* *
1593 AAATTGATTTAAATTTGAATTCTTTGTACATTTTTTTATTAAAACAGATTATAATTGAATGTCAA
1 AAATTGATTTAAATTTGAATCCTTTGCACATTTTTTTATTAAAACAGATTATAATTGAATGTCAA
* * *
1658 CCGTAAGAAACGTGAAGAAAAAGGCATACATTGACAAGAAAAGTCTATTAATAATCACCCATTCC
66 CCGTAAGAAACATGAAGAAAAAGGCATACATTGACAAGAAAAATCCATTAATAATCACCCATTCC
* * * **********
1723 TTCAAAAAGTCTTATTACTCACTTTACATGGTTTTATAATACCATAATNNNNNNNNNNTTGAACT
131 TTCAAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATACCATAATTGATTTTTAGTTGAACT
* * * ** ** *
1788 TTTTTACATTTTTAGTTAAAATAGAGTAGAATTGATGTCTGCCTCGAGAAACGTAATGAAAAAGG
196 TTTTCACATTTTTAGTTAAAACAGACTAGAATTGATGTCAACCTCGAGAAACACAAAGAAAAAGG
* * * *
1853 CATTCGTTGGTATGACAAGTCCATTTATAGTCACCCATTACCAT-AAAAGCCTTTTTACTCACTC
261 AATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATT-CCATCAAAAGCCTTTTTACTCACTC
1917 TAAANNNNNNNNNNATCTCA
325 TAAA----------ATCTCA
*
1937 AAATTGATTTAAATTTGAATCCTTTGCACA-TTTTTTGTTAAAACAGATTATAATTGAATGTCAA
1 AAATTGATTTAAATTTGAATCCTTTGCACATTTTTTTATTAAAACAGATTATAATTGAATGTCAA
* * * * * *
2001 -CGTCAAGAAACATGAA-AAAAAGGCATACGTTGGCAAGAAAAATCCGTTTATAGTCACTCATTC
66 CCGT-AAGAAACATGAAGAAAAAGGCATACATTGACAAGAAAAATCCATTAATAATCACCCATTC
* *********** *
2064 CTTC-AAAAGCCTCATTACTTACTTTAAATGNNNNNNNNNNGCCATAATTGATTTTTAGTTGAAG
130 CTTCAAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATACCATAATTGATTTTTAGTTGAAC
* * * *
2128 TTTTTCACATTTTTGGTTAAAACAGACTATAATTGAATGTCAATCTTGAGAAACACAAAGAAAAA
195 TTTTTCACATTTTTAGTTAAAACAGACTAGAATTG-ATGTCAACCTCGAGAAACACAAAGAAAAA
*
2193 GGTAATT-GTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTT
259 GG-AATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCATCAAAAGCCTT
2248 AATANNNNNN
Statistics
Matches: 252, Mismatches: 55, Indels: 10
0.79 0.17 0.03
Matches are distributed among these distances:
341 67 0.27
342 110 0.44
343 47 0.19
344 28 0.11
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.33
Consensus pattern (334 bp):
AAATTGATTTAAATTTGAATCCTTTGCACATTTTTTTATTAAAACAGATTATAATTGAATGTCAA
CCGTAAGAAACATGAAGAAAAAGGCATACATTGACAAGAAAAATCCATTAATAATCACCCATTCC
TTCAAAAAGCCTCATTACTCACTTTAAATGGTTTTATAATACCATAATTGATTTTTAGTTGAACT
TTTTCACATTTTTAGTTAAAACAGACTAGAATTGATGTCAACCTCGAGAAACACAAAGAAAAAGG
AATTCGTTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCATCAAAAGCCTTTTTACTCACTCT
AAAATCTCA
Done.