Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402452.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_553.0, 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: 12900
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.26
Warning! 3308 characters in sequence are not A, C, G, or T
Found at i:337 original size:172 final size:172
Alignment explanation
Indices: 118--481 Score: 394
Period size: 172 Copynumber: 2.1 Consensus size: 172
108 NNNNNNNNNT
* * * *
118 AAAAAAGTAAACAA-ATTTAACTTAAAATCAAATATGAGATTATAAAACCATTTAAAATGAATAA
1 AAAAATGTAAAAAACATTCAACTTAAAATCAAATATGAGATAATAAAACCATTTAAAATGAATAA
* * ** * ** *
182 TTAGGCTT-TAGAAGGCTTAAGTGACTATAAATAGACTTTTCTTATCAACGGGTGGCTTTTGCTT
66 TAAGACTTCT-GAAGGCACAAGTGACTATAAATAGACTCTTCTTATCAACGAATGGCTTTTACTT
* * * *
246 CATGTTT-TCTGAGGTAGACATTCAATTGTAATATATTTTAGCC
130 CAAGTTTCT-TGAGGCAGACATTCAATTATAATATATTTTAACC
* * * * **
289 AAAAATGTAAAAAACATTCAACTTAAAATCAATTATGAGATAATAAAACTATTTACAGTGGGTAA
1 AAAAATGTAAAAAACATTCAACTTAAAATCAAATATGAGATAATAAAACCATTTAAAATGAATAA
* * * * *
354 TAATACTTCTGAAGGCACGAGTGACTATAAATGGACTCTTCTTTTCAATGAATGGCTTTTACTTC
66 TAAGACTTCTGAAGGCACAAGTGACTATAAATAGACTCTTCTTATCAACGAATGGCTTTTACTTC
* * *
419 AAGTTTCTTGAGGCATACATTTAATTATAATCTATTTTAACC
131 AAGTTTCTTGAGGCAGACATTCAATTATAATATATTTTAACC
* *
461 AACAATAT-AAAAACATTCAAC
1 AAAAATGTAAAAAACATTCAAC
482 CTANNNNNNN
Statistics
Matches: 158, Mismatches: 32, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
171 25 0.16
172 131 0.83
173 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (172 bp):
AAAAATGTAAAAAACATTCAACTTAAAATCAAATATGAGATAATAAAACCATTTAAAATGAATAA
TAAGACTTCTGAAGGCACAAGTGACTATAAATAGACTCTTCTTATCAACGAATGGCTTTTACTTC
AAGTTTCTTGAGGCAGACATTCAATTATAATATATTTTAACC
Found at i:5122 original size:172 final size:168
Alignment explanation
Indices: 4550--5527 Score: 753
Period size: 170 Copynumber: 5.8 Consensus size: 168
4540 GTTTTAACTG
* *
4550 AAAATGTAAAAAAATTCAACGTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATA
1 AAAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * * * * * **
4615 AGGCTTTCA-AACGCTTGATTGAATATAAGTGAACTTTTTTTGCTAATGGATGGCTTTTGGTTTA
66 AGG-TTTTAGAAGGCTTGAGTGACTATAAATGGACTTTTTTT-CCAATGAATGGCTTTT-CCTT-
* * * * * **
4679 CAT-TTTCTAAGACAGATATTCAATTATAATATATTTTAATAA
127 CATGTTTTTGAGGCAAACATTCAATTATAATATATTTT-ACCA
* * * ** *
4721 AAAATGTTAAACAATTAAAATTAAAATCAATTATAAGATTATAAAACCATTT-AA---AGT--TA
1 AAAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * * * * *
4780 AAGTTTTCA-AAGGCATGGGTGACTATAGATGCACTTTTCTTACCAATGAATGGCTTTTTCTTGA
66 AGGTTTT-AGAAGGCTTGAGTGACTATAAATGGACTTTT-TTTCCAATGAATGGCTTTTCCTTCA
** * * * *** *
4844 TGTTTCTCAAAGCAAACATTCAAATATTATCCGTTTTAACTA
129 TGTTT-TTGAGGCAAACATTCAATTATAATATATTTT-ACCA
* * * * *
4886 AAAA-GTAAACAAATTGAACTTAAAATCAAATATGAGATTATAAAACCATTTAAAACGAGTAATA
1 AAAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* ** * ** *
4950 AGGTTTTAGAAGGCTTAAGTGACTATAAATGTTCTTTTTTTATCAATGGGTGGCTTTTGCTTCAT
66 AGGTTTTAGAAGGCTTGAGTGACTATAAATGGACTTTTTTT-CCAATGAATGGCTTTTCCTTCAT
* *
5015 GCTTTTTGAGGTAGACATTCAATTATAATATATTTTAGCCA
130 G-TTTTTGAGGCAAACATTCAATTATAATATATTTTA-CCA
* * ** * * *
5056 AAAATGTAAAAAAAAATCAACTTTTAATCAATTATGAGATTATAGAACCATTTACAGCGGGTAAT
1 AAAATGT-AAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* *
5121 AATGCTTTCA-AAGG-TATGAGTGACTATAAATGGACTTTTCTTTCCAATGAATGGCTTTTCCTT
65 AA-GGTTTTAGAAGGCT-TGAGTGACTATAAATGGACTTTT-TTTCCAATGAATGGCTTTTCCTT
* * *
5184 CAGGTTTCTTGAGGCAAACATTCAATTATAATCTAATTTAACCA
127 CATGTTT-TTGAGGCAAACATTCAATTATAATAT-ATTTTACCA
* * * * * *
5228 ACAATATAAAAAAATTCAACCTAAAATCAGTTATGAGATTATAAAACTATTTAAAGTGAGTAATT
1 AAAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * *** *
5293 AGGCTTTT-GAAGACGTGGGTGACTATAAATGGACTTTTCTTGGGAATGAATGGCTTTTTCTTCA
66 AGG-TTTTAGAAGGCTTGAGTGACTATAAATGGACTTTT-TTTCCAATGAATGGCTTTTCCTTCA
** * * * * *
5357 TGTTTTCCAAAGCAAATATTCAATTATAATATGTTTTAACT
129 TGTTTT-TGAGGCAAACATTCAATTATAATATATTTTACCA
* * *
5398 AAAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAGCCATTTAAATCGAGTACTA
1 AAAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * * * * * *
5463 AGGCTTTCGAATGG-ATGGGTGACTATAAATGGAC-TTTTCTCGTCAATGAATGACTTTTTCTTC
66 AGGTTTTAGAA-GGCTTGAGTGACTATAAATGGACTTTTTTTC--CAATGAATGGCTTTTCCTTC
5526 AT
128 AT
5528 ATTTCTTACA
Statistics
Matches: 639, Mismatches: 139, Indels: 59
0.76 0.17 0.07
Matches are distributed among these distances:
163 2 0.00
164 48 0.08
165 69 0.11
166 2 0.00
167 3 0.00
168 4 0.01
169 10 0.02
170 187 0.29
171 178 0.28
172 123 0.19
173 13 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (168 bp):
AAAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
AGGTTTTAGAAGGCTTGAGTGACTATAAATGGACTTTTTTTCCAATGAATGGCTTTTCCTTCATG
TTTTTGAGGCAAACATTCAATTATAATATATTTTACCA
Found at i:5564 original size:170 final size:168
Alignment explanation
Indices: 4476--5580 Score: 888
Period size: 171 Copynumber: 6.5 Consensus size: 168
4466 AAAAGATCTA
** * * * * * * *
4476 ACTTTTCTTACCAATGGATGGCTTTTTCTTTATGTTT-TTCTAGACAAACATTTAAATATTACCT
1 ACTTTTCTTGTCAATGAATGGCTTTTTCTTCATGTTTCTT-AAG-CAAACATTCAATTATAATCT
*
4540 GTTTTAACTGAAAATGTAAAAAAATTCAACGTAAAATCAATTATGAGATTATAAAACCATTTAAA
64 GTTTTAACT-AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * * * *
4605 GTGAGTAATAAGGCTTTCAAACGCTTGATTGAATATAAGTGA
128 -TGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGG
* * * *
4647 ACTTTTTTTG-CTAATGGATGGCTTTTGGT-TTACAT-TTTC-TAAGACAGATATTCAATTATAA
1 ACTTTTCTTGTC-AATGAATGGCTTTT--TCTT-CATGTTTCTTAAG-CAAACATTCAATTATAA
* * * * * * *
4708 TATATTTTAA-TAAAAAATGTTAAACAATTAAAATTAAAATCAATTATAAGATTATAAAACCATT
61 TCTGTTTTAACT--AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * * * *
4772 T-AA--AGT--TAAAGTTTTCAAAGGCATGGGTGACTATAGATGC
124 TAAATGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGG
** * * * * *
4812 ACTTTTCTTACCAATGAATGGCTTTTTCTTGATGTTTCTCAAAGCAAACATTCAAATATTATCCG
1 ACTTTTCTTGTCAATGAATGGCTTTTTCTTCATGTTTCT-TAAGCAAACATTCAATTATAATCTG
* * * * *
4877 TTTTAACTAAAAAGTAAACAAATTGAACTTAAAATCAAATATGAGATTATAAAACCATTTAAAAC
65 TTTTAACTAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT-AAAT
* * * * *
4942 GAGTAATAAGGTTTTAGAAGGCTTAAGTGACTATAAATGT
129 GAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGG
* * * ** * * * * *
4982 TCTTTTTTTATCAATGGGTGGCTTTTGCTTCATGCTTT-TTGAGGTAGACATTCAATTATAATAT
1 ACTTTTCTTGTCAATGAATGGCTTTTTCTTCATG-TTTCTT-AAGCAAACATTCAATTATAATCT
* * * * ** *
5046 ATTTTAGCCAAAAATGTAAAAAAAAATCAACTTTTAATCAATTATGAGATTATAGAACCATTTAC
64 GTTTTA-ACTAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA-
** * * * *
5111 AGCGGGTAATAATGCTTTCAAAGGTATGAGTGACTATAAATGG
126 AATGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGG
* * *
5154 ACTTTTCTT-TCCAATGAATGGCTTTTCCTTCAGGTTTCTTGAGGCAAACATTCAATTATAATCT
1 ACTTTTCTTGT-CAATGAATGGCTTTTTCTTCATGTTTCTT-AAGCAAACATTCAATTATAATCT
** * * * * *
5218 AATTTAACCAACAATATAAAAAAATTCAACCTAAAATCAGTTATGAGATTATAAAACTATTTAAA
64 GTTTTAACTAA-AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
* * * * *
5283 GTGAGTAATTAGGCTTTTGAAGACGTGGGTGACTATAAATGG
128 -TGAGTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGG
** ** * *
5325 ACTTTTCTTGGGAATGAATGGCTTTTTCTTCATGTTTTCCAAAGCAAATATTCAATTATAATATG
1 ACTTTTCTTGTCAATGAATGGCTTTTTCTTCATG-TTTCTTAAGCAAACATTCAATTATAATCTG
* *
5390 TTTTAACTAAAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAGCCATTTAAATC
65 TTTTAACTAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAT-
* *
5455 GAGTACTAAGGCTTTCGAATGG-ATGGGTGACTATAAATGG
129 GAGTAATAAGGCTTTCGAA-GGCATGAGTGACTATAAATGG
* * * * ** * *
5495 ACTTTTCTCGTCAATGAATGACTTTTTCTTCATATTTCTTACAGCAGACAACCAAATATTATCTG
1 ACTTTTCTTGTCAATGAATGGCTTTTTCTTCATGTTTCTTA-AGCAAACATTCAATTATAATCTG
* *
5560 TTTTAGTCAAAAATGTAAAAA
65 TTTTA-ACTAAAATGTAAAAA
5581 GATCTAACTT
Statistics
Matches: 740, Mismatches: 161, Indels: 66
0.77 0.17 0.07
Matches are distributed among these distances:
163 3 0.00
164 50 0.07
165 65 0.09
166 7 0.01
167 3 0.00
168 3 0.00
169 6 0.01
170 212 0.29
171 249 0.34
172 139 0.19
173 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (168 bp):
ACTTTTCTTGTCAATGAATGGCTTTTTCTTCATGTTTCTTAAGCAAACATTCAATTATAATCTGT
TTTAACTAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAATGA
GTAATAAGGCTTTCGAAGGCATGAGTGACTATAAATGG
Found at i:5573 original size:513 final size:507
Alignment explanation
Indices: 4550--5580 Score: 1110
Period size: 513 Copynumber: 2.0 Consensus size: 507
4540 GTTTTAACTG
* *
4550 AAAATGT-AAAAAAATTCAACGTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
1 AAAATGTAAAAAAAAATCAACGTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * **
4614 AAGGCTTTCAAACGCTTGATTGAATATAAGTGAACTTTTTTTGCTAATGGATGGCTTTTGGTTTA
66 AAGGCTTTCAAACGCTTGAGTGAATATAAATGAACTTTTTTTGCCAATGAATGGCTTTTGCCTTA
* * * * * * * * *
4679 CATTTTCTAAGACAGATATTCAATTATAATATATTTTAATAAAAAATGTTAAACAATTAAAATTA
131 CAGTTTCTAAGACAAACATTCAATTATAATATAATTTAACAAAAAATATAAAAAAATTAAAACTA
* *
4744 AAATCAATTATAAGATTATAAAACCATTTAAAGTTAAAGTTTTCAAAGGCATGGGTGACTATAGA
196 AAATCAATTATAAGATTATAAAACCATTTAAAGTTAAAGTTTTCAAAGACATGGGTGACTATAAA
* *
4809 TGCACTTTTCTTACCAATGAATGGCTTTTTCTTGATGTTTCTCAAAGCAAACATTCAAATATTAT
261 TGCACTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTCTCAAAGCAAACATTCAAATATAAT
* * * *
4874 CCGTTTTAACTAAAAAGTAAACAAATTGAACTTAAAATCAAATATGAGATTATAAAACCATTTAA
326 ACGTTTTAACTAAAAAGTAAAAAAATTCAACCTAAAATCAAATATGAGATTATAAAACCATTTAA
* * ** * * ** *
4939 AACGAGTAATAAGGTTTTAGAAGGCTTAAGTGACTATAAATGTTCTTTTTTTATCAATGGGTGGC
391 AACGAGTAATAAGGCTTTAGAAGGCATAAGTGACTATAAATGGACTTTTCTCATCAATGAATGAC
* * * ** *
5004 TTTTGCTTCATGCTTTTTGAGGTAGACATTCAATTATAATATATTTTAGCCA
456 TTTTGCTTCATGATTTTTGAAGCAGACAACCAAATATAATATATTTTAGCCA
* ** * * *
5056 AAAATGTAAAAAAAAATCAACTTTTAATCAATTATGAGATTATAGAACCATTTACAGCGGGTAAT
1 AAAATGTAAAAAAAAATCAACGTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * *
5121 AATGCTTTCAAA-GGTATGAGTGACTATAAATGGACTTTTCTTT-CCAATGAATGGCTTTT-CCT
66 AAGGCTTTCAAACGCT-TGAGTGAATATAAATGAACTTTT-TTTGCCAATGAATGGCTTTTGCCT
* * * * * *
5183 T-CAGGTTTCTTGAGGCAAACATTCAATTATAATCTAATTTAACCAACAATATAAAAAAATTCAA
129 TACA-GTTTC-TAAGACAAACATTCAATTATAATATAATTTAACAAAAAATATAAAAAAATTAAA
* * * * * *
5247 CCTAAAATCAGTTATGAGATTATAAAACTATTTAAAGTGAGTAATTAGGCTTTT-GAAGACGTGG
192 ACTAAAATCAATTATAAGATTATAAAACCATTTAAAGT---TAA--A-G-TTTTCAAAGACATGG
* *** *
5311 GTGACTATAAATGGACTTTTCTTGGGAATGAATGGCTTTTTCTTCATGTTT-TCCAAAGCAAATA
250 GTGACTATAAATGCACTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTCT-CAAAGCAAACA
* * * *
5375 TTCAATTATAATATGTTTTAACTAAAATGTAAAAAAATTCAACCTAAAATCAATTATGAGATTAT
314 TTCAAATATAATACGTTTTAACTAAAAAGTAAAAAAATTCAACCTAAAATCAAATATGAGATTAT
* * * * **
5440 AAAGCCATTTAAATCGAGTACTAAGGCTTTCGAATGG-ATGGGTGACTATAAATGGACTTTTCTC
379 AAAACCATTTAAAACGAGTAATAAGGCTTTAGAA-GGCATAAGTGACTATAAATGGACTTTTCTC
* * * * * *
5504 GTCAATGAATGACTTTTTCTTCAT-ATTTCTT-ACAGCAGACAACCAAATATTATCTGTTTTAGT
443 ATCAATGAATGACTTTTGCTTCATGATTT-TTGA-AGCAGACAACCAAATATAATATATTTTAGC
5567 CA
506 CA
5569 AAAATGTAAAAA
1 AAAATGTAAAAA
5581 GATCTAACTT
Statistics
Matches: 426, Mismatches: 83, Indels: 25
0.80 0.16 0.05
Matches are distributed among these distances:
505 2 0.00
506 15 0.04
507 167 0.39
508 3 0.01
510 3 0.01
512 6 0.01
513 224 0.53
514 6 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (507 bp):
AAAATGTAAAAAAAAATCAACGTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
AAGGCTTTCAAACGCTTGAGTGAATATAAATGAACTTTTTTTGCCAATGAATGGCTTTTGCCTTA
CAGTTTCTAAGACAAACATTCAATTATAATATAATTTAACAAAAAATATAAAAAAATTAAAACTA
AAATCAATTATAAGATTATAAAACCATTTAAAGTTAAAGTTTTCAAAGACATGGGTGACTATAAA
TGCACTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTCTCAAAGCAAACATTCAAATATAAT
ACGTTTTAACTAAAAAGTAAAAAAATTCAACCTAAAATCAAATATGAGATTATAAAACCATTTAA
AACGAGTAATAAGGCTTTAGAAGGCATAAGTGACTATAAATGGACTTTTCTCATCAATGAATGAC
TTTTGCTTCATGATTTTTGAAGCAGACAACCAAATATAATATATTTTAGCCA
Found at i:10739 original size:73 final size:73
Alignment explanation
Indices: 10585--10739 Score: 188
Period size: 73 Copynumber: 2.1 Consensus size: 73
10575 CAAGAGATAG
* *
10585 TGTTGGTCGACTAAGAGCTTACTGTCAAAAACTGGGTTCATAGATAAAAATGACTTAATCGACTA
1 TGTTAGTCGACTAAGAGCTTACTGTCAAAAACTGGGTTCAAAGATAAAAATGACTTAATCGACTA
***
10650 AGAAGTTT
66 AGAAGAAA
* * * *
10658 TGTCAGTCGACTAAGAG-TCTATTG-CGAAAAACTGGGTTCAAAGATAGAGATGACTTAATCGAC
1 TGTTAGTCGACTAAGAGCT-TACTGTC-AAAAACTGGGTTCAAAGATAAAAATGACTTAATCGAC
*
10721 TAAGTAGAAA
64 TAAGAAGAAA
10731 TGTTAGTCG
1 TGTTAGTCG
10740 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
72 2 0.03
73 67 0.97
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (73 bp):
TGTTAGTCGACTAAGAGCTTACTGTCAAAAACTGGGTTCAAAGATAAAAATGACTTAATCGACTA
AGAAGAAA
Done.