Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398585.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1875.0, 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: 13142
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.23
Warning! 4481 characters in sequence are not A, C, G, or T
Found at i:10056 original size:170 final size:170
Alignment explanation
Indices: 9760--10743 Score: 644
Period size: 170 Copynumber: 5.9 Consensus size: 170
9750 AAAAGGCTAC
* * * ** * * * *
9760 AATTGAATGTCTGCCTTGGGAAACATGAA-GCAAAAGCTAACTATTGGCACGAAAAGTCAATTTG
1 AATTGAATGTCTACCTCGAGAAACATGAATAAAAAAGC-ATC-ATTGGCAAGAAAAGTCCATTTA
* ** * * *** * * ** *
9824 CAGTCACTTA-AGCCTTCGAAAGCCTTATTACTTGGTTTAAACGGTTTTATAAACTAATAATTGT
64 TAGTCACCCATA-CCTTCAAAAGCCTTATTGCTCACTTTAAATGGTTTTATGATGTCATAATTGT
* * * * * *
9888 TTTTATGTTCAATATTTTTACATTTTTTGTTAAAA-AGACTA-
128 TTTTAAGTTGAATCTTTTCACATTTTTGGTTAAAACAGATTAT
* * * *
9929 GATCTGAATGTGTACCTCAAGAAAAATGAATAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTA
1 AAT-TGAATGTCTACCTCGAGAAACATGAATAAAAAAGCA-TCATTGGCAAGAAAAGTCCATTTA
*
9994 TAGTCACCCATACCTTCAAAAGCCTTATTGCTCACTTTAAATGGTTTTATGATGTCATAATTGAT
64 TAGTCACCCATACCTTCAAAAGCCTTATTGCTCACTTTAAATGGTTTTATGATGTCATAATTGTT
* **
10059 TTGAAGTTGGCTCTTTTCACATTTTTGGTTAAAACAGATTAT
129 TTTAAGTTGAATCTTTTCACATTTTTGGTTAAAACAGATTAT
* * * * * * * *
10101 AATTGATTGTCTACCTTGACAAACATGAA-GACAAGGTACTCATTGGTAAGAAAAGTCCATTTAT
1 AATTGAATGTCTACCTCGAGAAACATGAATAAAAAAGCA-TCATTGGCAAGAAAAGTCCATTTAT
* *
10165 AGTCACCCATAACTTCAAAAGCCTTATTGCTCGCTTTAAATGGTTTTATGATGTCATAATT-TAT
65 AGTCACCCATACCTTCAAAAGCCTTATTGCTCACTTTAAATGGTTTTATGATGTCATAATTGT-T
*
10229 TTTAAGTTGTATCTTTTCACATTTTTGGTTAAAACAGATTAT
129 TTTAAGTTGAATCTTTTCACATTTTTGGTTAAAACAGATTAT
* *** ** * *
10271 AATTGAATGTCTATCTCGAGAAACATGAAGTAAAGGTGC-TCACCGACAAGAAAAGTCCATTTGT
1 AATTGAATGTCTACCTCGAGAAACATGAA-TAAAAAAGCATCATTGGCAAGAAAAGTCCATTTAT
* * * * * *
10335 AGTCACCCATTCCTTTAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCCA-AATTGAT
65 AGTCACCCATACCTTCAAAAGCCTTATTGCTCACTTTAAATGGTTTTATGATGT-CATAATTGTT
* ** * *
10399 TTGAAGTTGAATCTTTTTGCATTTTTGGTTTAAA-AG-TCTAC
129 TTTAAGTTGAATCTTTTCACATTTTTGGTTAAAACAGAT-TAT
* * *** * * * **
10440 AATTGAA-----A----GTGAAGCA--AA-AGCCAA-C--CATTGACACGAATAGTCCATTTGCA
1 AATTGAATGTCTACCTCGAGAAACATGAATAAAAAAGCATCATTGGCAAGAAAAGTCCATTTATA
** * * * * *** *
10490 GTCACTTA-AGCCTTCGAAAGCGTTATTACATC-GTTTAAATGGTTTTAT-AAACCAATAACTGT
66 GTCACCCATA-CCTTCAAAAGCCTTATTGC-TCACTTTAAATGGTTTTATGATGTC-ATAATTGT
* * * * * * *
10552 TTTTAAGTTGAGTATTTT-ACATTTTTGGTT-CAGCATACTAG
128 TTTTAAGTTGAATCTTTTCACATTTTTGGTTAAAACAGATTAT
* * * * * * *
10593 AATTGAATGTCTATCTCAAGAAATATGAAGACAAAGGCATTCATTGGCAAGAAAAGTTCATTTAT
1 AATTGAATGTCTACCTCGAGAAACATGAATAAAAAAGCA-TCATTGGCAAGAAAAGTCCATTTAT
* ** * * *
10658 AGTCACCCATACCCTCAAATA-TTTTATTGCTCACTTTAAATAGTTTTATGATGTCATATTTGAT
65 AGTCACCCATACCTTCAAA-AGCCTTATTGCTCACTTTAAATGGTTTTATGATGTCATAATTGTT
**
10722 TTTAAGTTGGTTCTTTTCACAT
129 TTTAAGTTGAATCTTTTCACAT
10744 NNNNNNNNNN
Statistics
Matches: 627, Mismatches: 149, Indels: 77
0.74 0.17 0.09
Matches are distributed among these distances:
152 2 0.00
153 23 0.04
154 76 0.12
155 3 0.00
156 1 0.00
158 3 0.00
160 6 0.01
162 4 0.01
164 3 0.00
165 2 0.00
166 1 0.00
168 3 0.00
169 84 0.13
170 377 0.60
171 35 0.06
172 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (170 bp):
AATTGAATGTCTACCTCGAGAAACATGAATAAAAAAGCATCATTGGCAAGAAAAGTCCATTTATA
GTCACCCATACCTTCAAAAGCCTTATTGCTCACTTTAAATGGTTTTATGATGTCATAATTGTTTT
TAAGTTGAATCTTTTCACATTTTTGGTTAAAACAGATTAT
Found at i:11425 original size:170 final size:170
Alignment explanation
Indices: 10844--12157 Score: 1228
Period size: 170 Copynumber: 7.7 Consensus size: 170
10834 NNNNNNNNNN
** * *
10844 TTTCTTCATGTTTCTTGAGATAGACATGT-AATTATAATCTGTTTTAACTAAAAATGTGAAAAGA
1 TTTCTTCATGTTTCTCAAGGTAGACAT-TCAATTATAATCTGTTTTAACCAAAAATGTGAAAAGA
* * * * * *
10908 TTCAACTTAAAATCAAATATGACATCATAAAACTATTTAAAGTGAGCAATAA-GATATTTGAGGG
65 TCCAACTTAAAATCAATTATGACATCATAAAACCATTTAAAGTGAGTAATAAGGCT-TTTGAAGG
* * *
10972 TATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTT
129 TATGAGTGACTATAAATGGACTTTTCTTGCCAATGAGTACC-T
** * * * * *
11015 TTTCTTCATGTTTCTTGAGGTAGACATTCAATTCTAGTCTGTTTGAACCAAAAA--TAAAAAAAT
1 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAGAT
* ** * * *
11078 ACTCAACTTTAAAA-CAATTATTAGTTTATAAAACCATTTAAA-TGAAGTAATAACG-TTTTCAA
66 -C-CAAC-TTAAAATCAATTATGACATCATAAAACCATTTAAAGTG-AGTAATAAGGCTTTT-GA
* * * **
11140 AGGCT-TGAGTTACTACAAATGGACTTTT-GTGCCAATG-GTTGGCT
126 AGG-TATGAGTGACTATAAATGGACTTTTCTTGCCAATGAG-TACCT
** * * * * * *
11184 TTGGTTCACT-TTCCCCAAGGCAGACATTCAATTGTAACCT-TTTTAACCAAAAATGTAAAAAGA
1 TTTCTTCA-TGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAGA
* * * * *
11247 TTCAACTTAAAATCAATTTTGATATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGA
65 TCCAACTTAAAATCAATTATGACATCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGT
*
11312 ATGAGTGACTATAAATGGCCTTTTCTTGCTC-ATGAGTACCT
130 ATGAGTGACTATAAATGGACTTTTCTTGC-CAATGAGTACCT
* * *
11353 TTTCTTCATGTTTCTCGAGATAGACATTCAATTAAAATCTGTTTTAACCAAAAATGTGAAAAGAT
1 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAGAT
* * * * * * *
11418 CCAACTTAATATCAATTATCACATCATAAAACCATTTTAAGCGAGCAATAAGGCTTTCGAAGTTA
66 CCAACTTAAAATCAATTATGACATCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTA
* * *
11483 TGAGTGACTATAAATGGATTTTTCTTACCGATGAGTACCT
131 TGAGTGACTATAAATGGACTTTTCTTGCCAATGAGTACCT
* * * * *
11523 TGTCTTCATGTTTCTCAAGGTCGATATTCAATTATAATCTGTTTTAACCAGAACTGTGAAAAGAT
1 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAGAT
* * * * *
11588 TCAACTTAAAATCAATTATGACGTCATAAAACCATTTAAAGCGAGCAATAAGGCTTTTGAAGTTA
66 CCAACTTAAAATCAATTATGACATCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTA
** *
11653 TGAGTGACTATAAATTTACTTTTCTTACCAATGAGTACCT
131 TGAGTGACTATAAATGGACTTTTCTTGCCAATGAGTACCT
* * *
11693 TGTCTTCATGTTTCTCAAGGTAGACATGCAATTATAATCTGTTTTAACCAAAAAGGTGAAAAGAT
1 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAGAT
*
11758 CCAACTTAAAATCAATTATGACATCATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTA
66 CCAACTTAAAATCAATTATGACATCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTA
* * * *
11823 TGGGTGACCATAAATGGACTTTTCTTGCCAATAAATGTA-TT
131 TGAGTGACTATAAATGGACTTTTCTTGCCAAT-GA-GTACCT
** * * *
11864 TTTCTTCATGTTTCTTGAGGTAAACATTCAATTCTAGTCTGTTTTAACCAAAAATGT-AAAA-AT
1 TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAGAT
* * * * ***
11927 ACTGAACTTAAAAAT-AATTATTAGTTTATAAAACCATTTAAACCATTTAAACCAAGTAATAAGG
66 -C-CAACTT-AAAATCAATTA-T-G------ACATCA-TAAAACCATTTAAAGTGAGTAATAAGG
* * * * * *
11991 CTTTCGAAGGCT-TGAGTGATTACAAATGGACTTTTCGTACCAATG-GTAGGCT
119 CTTTTGAAGG-TATGAGTGACTATAAATGGACTTTTCTTGCCAATGAGTA-CCT
* * * * * * ** *
12043 TTTGCGTCACGTTCCTCAAGGCAGAGATTCAATTGTAGCCTTTTTTAACCAAAAATGT-AATAAG
1 TTT-CTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTGAA-AAG
* * * *
12107 ATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAAT
64 ATCCAACTTAAAATCAATTATGACATCATAAAACCATTTAAAGTGAGTAAT
12158 NNNNNNNNNN
Statistics
Matches: 946, Mismatches: 154, Indels: 86
0.80 0.13 0.07
Matches are distributed among these distances:
167 6 0.01
168 74 0.08
169 82 0.09
170 443 0.47
171 184 0.19
172 20 0.02
173 1 0.00
177 3 0.00
178 1 0.00
179 14 0.01
180 113 0.12
181 3 0.00
182 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (170 bp):
TTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAGAT
CCAACTTAAAATCAATTATGACATCATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTA
TGAGTGACTATAAATGGACTTTTCTTGCCAATGAGTACCT
Done.