Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401573.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4697.0, 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, 612
Length: 1021
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:363 original size:173 final size:171
Alignment explanation
Indices: 8--428 Score: 460
Period size: 173 Copynumber: 2.5 Consensus size: 171
1 TTAAATG
**
8 GTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTTA-CTTTTGTGATTAAAAC-ATGTT
1 GTTTTATAATCTCAAAATTGATTTTAAGTTCAA-TTTTTTTACCTTTT-TGATT-AAACTAAATT
* * *
71 ATAATTAAATGTCTACATTGAGAAACATGAAGAAAAAGACATTCATTGACAAGAAAAGTCCATTT
63 ATAATTGAATGTCTACATTAAGAAACATGAAGAAAAAGACATTCATTGACAAGAAAAGACCATTT
* ******
136 ATTATCACTTATTCCTTCAAAAGCCTTATTACTCGCTTNNNNNN
128 ATTATCACTCATTCCTTCAAAAGCCTTATTACTCGCTTTGAATT
****
180 NNNNTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTACCTTTTTGATTAAACTAAATTATA
1 GTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTACCTTTTTGATTAAACTAAATTATA
* * *
245 ATTGAATGTTTACATTTCAAGAAACATGAAGAAAAAGGCATTCATT-AGCAAGAAAAGACTATTT
66 ATTGAATGTCTACA-TT-AAGAAACATGAAGAAAAAGACATTCATTGA-CAAGAAAAGACCATTT
309 ATTATCA-TCCATTCCTTCAAAAGCCTTATTACTCGCTTTGAATT
128 ATTATCACT-CATTCCTTCAAAAGCCTTATTACTCGCTTTGAATT
** * * * * * * *
353 GTTTTATAATC-CTGTAATTAATTTT-AGTTGAATATTTTTACATTTTT-AGTTAAAATAGAGTA
1 GTTTTATAATCTC-AAAATTGATTTTAAGTTCAATTTTTTTACCTTTTTGA-TTAAACTAAATTA
415 TAATTGAATGTCTA
64 TAATTGAATGTCTA
429 TTTATAGTTA
Statistics
Matches: 208, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
170 4 0.02
171 32 0.15
172 81 0.39
173 91 0.44
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.40
Consensus pattern (171 bp):
GTTTTATAATCTCAAAATTGATTTTAAGTTCAATTTTTTTACCTTTTTGATTAAACTAAATTATA
ATTGAATGTCTACATTAAGAAACATGAAGAAAAAGACATTCATTGACAAGAAAAGACCATTTATT
ATCACTCATTCCTTCAAAAGCCTTATTACTCGCTTTGAATT
Found at i:766 original size:170 final size:168
Alignment explanation
Indices: 440--1021 Score: 589
Period size: 170 Copynumber: 3.4 Consensus size: 168
430 TTATAGTTAC
* * * * *
440 CCATTTCTTCAAAGGCCTTATTAGTCGCTTTAAATGGTTTTATAAGCTCATAATTGACTTTAAGT
1 CCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGT
* * * * *
505 TGAAATTTTTACA-TTTTAGTTAAAACAGACTAGAATTAAATGTTTACCTAGAGAAATATGGAGA
66 TGAATTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTTTACCT-TAGAAATATGAAGA
* * * *
569 AAAAGGCATTCGTTGGTAAAAAAAAGTCCATTTATAGTCGT
130 AAAAAGCATTCCTTAG-AAAGAAAAGTCCATTTATAGTC-T
* * *
610 CCATTCCTGT-AAAAGCCTTATTACTCGCTTTATATGGTTTTATAATCTTATAATTGATTTTCAG
1 CCATTCCT-TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAG
* * * *
674 TTGAATTTTTTATATTTTTAGTTAAAACAGAGTATAATTGAATGTTGACCTCTAGAAATGTGAAG
65 TTGAATTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTTTACCT-TAGAAATATGAAG
* *
739 AAAAAAGCATGCCTTAGCAAGAAAAGTCCATTTATAGTCT
129 AAAAAAGCATTCCTTAGAAAGAAAAGTCCATTTATAGTCT
* * * *
779 CCTATTCCTTCATAAA-CCTTATTACTCACTTTAAATGATTTTATATTCTCAAAATTGATTTTAA
1 CC-ATTCCTTCA-AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAA
* ********** * *
843 GTTCAATTTTTTTACATTTTTANNNNNNNNNNATTATAATTGAATGTTTACCTTAAGAAACATGA
64 GTTGAA-TTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTTTACCTT-AGAAATATGA
* *
908 AGAAAAAAGGCATTCAC-T-GATAAGAAAAGTTCATTTATAGTCAC
127 AGAAAAAA-GCATTC-CTTAGA-AAGAAAAGTCCATTTATAGTC-T
* * * * *
952 CCATTCTTTCAAAAACTTTATTACTTGCTTTAAATGGTTTTATACTCTCATAATTGATTTTAAGT
1 CCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGT
1017 TGAAT
66 TGAAT
Statistics
Matches: 341, Mismatches: 59, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
169 4 0.01
170 140 0.41
171 113 0.33
172 81 0.24
173 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.39
Consensus pattern (168 bp):
CCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGT
TGAATTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTTTACCTTAGAAATATGAAGAA
AAAAGCATTCCTTAGAAAGAAAAGTCCATTTATAGTCT
Found at i:995 original size:172 final size:161
Alignment explanation
Indices: 590--1017 Score: 349
Period size: 172 Copynumber: 2.5 Consensus size: 161
580 GTTGGTAAAA
** * * * *
590 AAAAGTCCATTTATAGTCGTCCATTCCTGT-AAAAGCCTTATTACTCGCTTTATATGGTTTTATA
1 AAAAGTCCATTTATAGTCACCCATTCCT-TCAAAAACCTTATTACTCACTTTAAATGATTTTATA
* * * * * ** *
654 ATCTTATAATTGATTTTCAGTTGAATTTTTTATATTTTTAGTTAAAACAGAGTATAATTGAATGT
65 CTCTCAAAATTGATTTTAAGTTCAATTTTTT-TACATTT--TT-----A-ATTATAATTGAATGT
** *
719 TGACCTCTAGAAATGTGAAGAAAAAAGCATGCCTTAGCAAG
121 TGACCTCTAGAAACATGAAGAAAAAAGCATGCCTGAGCAAG
* * * *
760 AAAAGTCCATTTATAGTCTCCTATTCCTTCATAAACCTTATTACTCACTTTAAATGATTTTATAT
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTTAAATGATTTTATAC
825 TCTCAAAATTGATTTTAAGTTCAATTTTTTTACATTTTTANNNNNNNNNNATTATAATTGAATGT
66 TCTCAAAATTGATTTTAAGTTCAATTTTTTTACATTTTTA----------ATTATAATTGAATGT
* * *
890 TTACCT-TAAGAAACATGAAGAAAAAAGGCATTCACTGA-TAAG
121 TGACCTCT-AGAAACATGAAGAAAAAA-GCATGC-CTGAGCAAG
* * * ** *
932 AAAAGTTCATTTATAGTCACCCATTCTTTCAAAAACTTTATTACTTGCTTTAAATGGTTTTATAC
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTTAAATGATTTTATAC
*
997 TCTCATAATTGATTTTAAGTT
66 TCTCAAAATTGATTTTAAGTT
1018 GAAT
Statistics
Matches: 211, Mismatches: 34, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
162 1 0.00
167 2 0.01
169 6 0.03
170 81 0.38
171 35 0.17
172 83 0.39
173 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.40
Consensus pattern (161 bp):
AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTTAAATGATTTTATAC
TCTCAAAATTGATTTTAAGTTCAATTTTTTTACATTTTTAATTATAATTGAATGTTGACCTCTAG
AAACATGAAGAAAAAAGCATGCCTGAGCAAG
Done.