Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397807.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1108.0, 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: 13249
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.23
Warning! 5025 characters in sequence are not A, C, G, or T
Found at i:4204 original size:169 final size:168
Alignment explanation
Indices: 3912--4457 Score: 545
Period size: 171 Copynumber: 3.2 Consensus size: 168
3902 NNNNNNNNNN
* ** *
3912 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATGTTTT-ACATTTTTCCTTAAAACAA
1 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTCACATTTTTGGTTAAAACAG
* * * * * ** * * *
3976 ATTATAATTTAATGCCTGCCTCAAGAAACATGTTGAAAAAAATATTTATTCGGAAGAAAAGTCCA
66 ACTATAAATAAATGTCTACCTCAAGAAACATGAAGAAAAAAGTATTAATT-GGAAGAAAAGTCTA
* *
4041 TTTATAGTCGCATTCCTTCAAAAGCCTTTTTACTCACTT
130 TTTATAGTCGCATTCCTTCAAAAGCCTTATTACTCGCTT
**********
4080 TAAATGGTTTTATAATCTCATANNNNNNNNNNAGTTGAATTTTTTCACATTTTTGGTTAAAACAG
1 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTCACATTTTTGGTTAAAACAG
* * * *
4145 ACTATAAATCAATGTCTACCTCGAGAAACATGCAGAAAAAAGTATTCATTGGAAAGAAAAGTCTA
66 ACTATAAATAAATGTCTACCTCAAGAAACATGAAGAAAAAAGTATTAATTGG-AAGAAAAGTCTA
********* *
4210 TTTATAGTCTNNNNNNNNNNCAAAAGCCTTATTAGTCGCTT
130 TTTATAGTC--GCATTCCTTCAAAAGCCTTATTACTCGCTT
* * * * * *
4251 TAAATAGTTTTATAATCCCACAATTGATTTTAAGTTTAATTTTTTCATATTTTCGGTTAAAACAG
1 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTCACATTTTTGGTTAAAACAG
* * *
4316 ACTATAAATAAATGTATACCTCAAGAAACATGAAGCAAAAAGCATTAATTGGCAAGAAAAGTCTA
66 ACTATAAATAAATGTCTACCTCAAGAAACATGAAGAAAAAAGTATTAATTGG-AAGAAAAGTCTA
* * *
4381 TTTATAGTAACTCATTCCTTCAGAAGGCTTATTACTCGCTT
130 TTTATAGT--CGCATTCCTTCAAAAGCCTTATTACTCGCTT
*
4422 TAAATGGTTTTATAATTTCATAATTGATTTTAAGTT
1 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTT
4458 NNNNNNNNNN
Statistics
Matches: 295, Mismatches: 77, Indels: 9
0.77 0.20 0.02
Matches are distributed among these distances:
168 36 0.12
169 76 0.26
171 182 0.62
173 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.36
Consensus pattern (168 bp):
TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTCACATTTTTGGTTAAAACAG
ACTATAAATAAATGTCTACCTCAAGAAACATGAAGAAAAAAGTATTAATTGGAAGAAAAGTCTAT
TTATAGTCGCATTCCTTCAAAAGCCTTATTACTCGCTT
Found at i:6023 original size:170 final size:169
Alignment explanation
Indices: 5511--6087 Score: 446
Period size: 171 Copynumber: 3.4 Consensus size: 169
5501 NNNNNNNNNN
* * * **
5511 ATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTCTTGGTTAAAACAAACTCTAATTGAATG
1 ATCTCATAATTGATTTTAAATTGAATTTTTTTACATTTTTGGTTAAAACAGACAATAATTGAATG
* * ** * * **
5576 TATACCTTGAGAAACATGAAAAAAAAGAGATTCATTGGCAAGAAAACTCCATTTATAGT-TGCTC
66 TCTATCTCAAGAAACATGAAAAAAAAGAGATTCATTGGCAA-AAAAGTCTATTTATAGTCACCT-
* * * **********
5640 ATTTCTTCAGAAGCCTTATTACTCACTTTAAANNNNNNNNNN
129 ATTCCTTCAAAAGCCTTATTACT-ACTCTAAATAGTTTTATA
* * * *
5682 NTCTCATAATTAATTTTAAGTTGAATTTTTTTATATTTTTGGTTAAAACAGACTAA-AATTGAAT
1 ATCTCATAATTGATTTTAAATTGAATTTTTTTACATTTTTGGTTAAAACAGAC-AATAATTGAAT
* * * ** * * ** * * * *
5746 GCCTGTCTCAAAAAATGTGTAGAAAAAGCCATTCATTGAG-AGGAAAAGCCTGTTTATATTCACC
65 GTCTATCTCAAGAAACATGAAAAAAAAGAGATTCATTG-GCA-AAAAAGTCTATTTATAGTCACC
********
5810 TATTCCTTCAAAAGCCTTATTACT-CNNNNNNNNNNGTTTTATA
128 TATTCCTTCAAAAGCCTTATTACTAC--TCTAAATAGTTTTATA
* * *
5853 ATCTCATAATTGATTTTAAATTGAATTTTCTTACATTTTTAGTTAAAATAGACAATAATTGAATG
1 ATCTCATAATTGATTTTAAATTGAATTTTTTTACATTTTTGGTTAAAACAGACAATAATTGAATG
5918 TCTATCTCAAGAAACATG-AAAAAAAGAGATTCATTGGCAAATAAAGTCTATTTATAGTCACCTA
66 TCTATCTCAAGAAACATGAAAAAAAAGAGATTCATTGGCAAA-AAAGTCTATTTATAGTCACCTA
*
5982 TTCCTTCAAAAGCCTTATGACTAGCTCTAAATAGTTTTATA
130 TTCCTTCAAAAGCCTTATTACTA-CTCTAAATAGTTTTATA
* * * * * * * *
6023 ATCTAATATTTGATTCT-AACTAAATTTTTTTTACATTTTTGATTAAAATAGACTATAATTGAAT
1 ATCTCATAATTGATTTTAAATTGAA-TTTTTTTACATTTTTGGTTAAAACAGACAATAATTGAAT
6087 G
65 G
6088 CCTCCCTCAA
Statistics
Matches: 313, Mismatches: 81, Indels: 25
0.75 0.19 0.06
Matches are distributed among these distances:
169 8 0.03
170 116 0.37
171 185 0.59
172 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (169 bp):
ATCTCATAATTGATTTTAAATTGAATTTTTTTACATTTTTGGTTAAAACAGACAATAATTGAATG
TCTATCTCAAGAAACATGAAAAAAAAGAGATTCATTGGCAAAAAAGTCTATTTATAGTCACCTAT
TCCTTCAAAAGCCTTATTACTACTCTAAATAGTTTTATA
Found at i:10367 original size:170 final size:170
Alignment explanation
Indices: 10163--10551 Score: 471
Period size: 170 Copynumber: 2.3 Consensus size: 170
10153 CTTGAGATAG
* * *
10163 GCATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATGCAACTGAAAATCAATTATGAGA
1 GCATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTGAAAATCAATTATGAGA
* * * *
10228 TTATCAAACAATTTAAAGGGAGTAATGA-GGCTTTTGAAGGAATAAGTGAATAGAAACGGACTTT
66 TTATAAAACAATTTAAAGGGAGTAAT-ACGGCTTCTGAAGCAATAAGTGAATAGAAACAGACTTT
10292 TCCT-CTCAATGAATAGCTTTTTCTACATGTTT-TCCAAGGTAA
130 TCCTGC-CAATGAATAGCTTTTTCTACATGTTTCT-CAAGGT-A
* * * *
10334 GCATTCAATTATAGTCTGTTTTAA-AAAAAATGTAAAAGAATTCAACTTAAAATTACTTATGAGA
1 GCATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTGAAAATCAATTATGAGA
* * ** * * *
10398 TTATAAAACCATTTAAAGTGAGTAATACGGCTTCTGAAGCAATGGGTGACTATAAATAGACTTTT
66 TTATAAAACAATTTAAAGGGAGTAATACGGCTTCTGAAGCAATAAGTGAATAGAAACAGACTTTT
* ** ** *
10463 CTTGCCAATGAATCTCTTTTTCTTTATGTTTCTCAATGTA
131 CCTGCCAATGAATAGCTTTTTCTACATGTTTCTCAAGGTA
* *
10503 GACATTCAATTAGAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACT
1 G-CATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACT
10552 NNNNNNNNNN
Statistics
Matches: 186, Mismatches: 27, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
169 3 0.02
170 137 0.74
171 46 0.25
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (170 bp):
GCATTCAATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTGAAAATCAATTATGAGA
TTATAAAACAATTTAAAGGGAGTAATACGGCTTCTGAAGCAATAAGTGAATAGAAACAGACTTTT
CCTGCCAATGAATAGCTTTTTCTACATGTTTCTCAAGGTA
Found at i:11525 original size:171 final size:168
Alignment explanation
Indices: 11153--11635 Score: 511
Period size: 171 Copynumber: 2.8 Consensus size: 168
11143 NNNNNNNNNN
* * * * *
11153 ATAAGGCTTTTGAAGGAATGAGTGGCTGTAAATAGACTTTTTTTGTCAATGAATCCCTTTTTCTT
1 ATAAGGCTTTTGAA-GAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAAT-GCTTTTTCTT
* *
11218 CATGTTTCTCT-AAGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATTAAAAAAATTCAACT
64 CATGTTTCT-TGAGGTAGACATTCATTTATAGTCTGTTTTAACCAAAAATTAAAAAAATTCAACT
* *
11282 TAAAGTAAATTATGAGATTATAAAACCATTTAAACCGAGTA
128 TAAAATAAATTATGAAATTATAAAACCATTTAAACCGAGTA
* * * *
11323 ATAAGGATTTTGAACGGATGAGTGACTATAAATAGACTTTTCTTACCAATTAATGCTTTTTGCTT
1 ATAAGGCTTTTGAA-GAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTT-CTT
* *********
11388 CATGTTTCTTGAGGTAGACATTCATTTATAGTCTGTTTTAATCAAAAANNNNNNNNNNTTCAACT
64 CATGTTTCTTGAGGTAGACATTCATTTATAGTCTGTTTTAACCAAAAA-TTAAAAAAATTCAACT
* * * *
11453 TAAAATCAATTGTGAAATTATAAAACTATTTAAAGCG-GCTA
128 TAAAATAAATTATGAAATTATAAAACCATTTAAACCGAG-TA
* * * * * *
11494 ATAAGGCTTTTGAAGAAATCAGAGACTATAAATAGAGTTTTCTTGCTAATGAAAGTTTTTTTCTT
1 ATAAGGCTTTTGAAG-AATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATG-CTTTTTCTT
* * * * *
11559 CATGTTTCTCGAGGTAGACAATGATTTATAGTCTATTTTAACCAAAAATGTGAAAAAATTCAACT
64 CATGTTTCTTGAGGTAGACATTCATTTATAGTCTGTTTTAACCAAAAAT-TAAAAAAATTCAACT
*
11624 TAAAATCAATTA
128 TAAAATAAATTA
11636 NNNNNNNNNN
Statistics
Matches: 253, Mismatches: 53, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
169 7 0.03
170 93 0.37
171 148 0.58
172 5 0.02
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.36
Consensus pattern (168 bp):
ATAAGGCTTTTGAAGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTCTTCA
TGTTTCTTGAGGTAGACATTCATTTATAGTCTGTTTTAACCAAAAATTAAAAAAATTCAACTTAA
AATAAATTATGAAATTATAAAACCATTTAAACCGAGTA
Found at i:12929 original size:171 final size:170
Alignment explanation
Indices: 12534--12931 Score: 403
Period size: 171 Copynumber: 2.3 Consensus size: 170
12524 NNNNNNNNNN
* * *
12534 TAATAAGGCTTTTGAAGGAAT-AGGTGACTATAAATGAACTTTTCTTGCCAATGATTGTCTTTTT
1 TAATAAGGCTTTTGAAGGAATGA-GTGACTATAAATG-ACTTTTCTTGTCAATGAATGACTTTTT
* * * * *
12598 CTTCACGTTTCTTGAGGTAGACATTCAATTATAATCTGTTTTATCCAAAAATGTAAAAAAATTCA
64 CTCCACGTTTCTTAAGGAAGACAATCAATTATAATCTGTTTTATCAAAAAATGTAAAAAAATTCA
* * * *
12663 TCTTAAAATCAATTATGAGATTATACAACTATTTAAAGCGAA
129 TCTTAAAAGCAATTATGAGATTATAAAACCATTTAAAGAGAA
* * ********* *
12705 TAATAAGGGTTTTGAAGGAATGGGTGACTATANNNNNNNNNNTCTTCTCAATGAATGACTTTTTC
1 TAATAAGGCTTTTGAAGGAATGAGTGACTATA-AATGACTTTTCTTGTCAATGAATGACTTTTTC
* *
12770 TCCATGTTT-TCTAAGGCAAG-CAATCAATTATAGTCTGTTTTAAT-AAAAAATGTAAAAAAATT
65 TCCACGTTTCT-TAAGG-AAGACAATCAATTATAATCTGTTTT-ATCAAAAAATGTAAAAAAA-T
* *
12832 TCA-CTTAAAAGCAATT-GGTAGATTATAAAACCATTTAAAGAGAG
126 TCATCTTAAAAGCAATTATG-AGATTATAAAACCATTTAAAGAGAA
* *
12876 TAATAAGGCTTTTGAAAGAATGAGTAACTATAAATAGACTTTTCTTGTCAATGAAT
1 TAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT-GACTTTTCTTGTCAATGAAT
12932 CCTTTTTTAT
Statistics
Matches: 177, Mismatches: 42, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
170 2 0.01
171 167 0.94
172 8 0.05
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.35
Consensus pattern (170 bp):
TAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGACTTTTCTTGTCAATGAATGACTTTTTCT
CCACGTTTCTTAAGGAAGACAATCAATTATAATCTGTTTTATCAAAAAATGTAAAAAAATTCATC
TTAAAAGCAATTATGAGATTATAAAACCATTTAAAGAGAA
Done.