Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402607.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5678.0, 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: 3023
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:618 original size:171 final size:170
Alignment explanation
Indices: 79--799 Score: 522
Period size: 171 Copynumber: 4.2 Consensus size: 170
69 TAAGGTAGAT
* * ** * **
79 ATTCAATTATAGTCTGTTTTAATCG-AAAATGTAAAAAAATTCAACTTAAAATCAATTATTAGTT
1 ATTCAATTATAGTTTGTTTTAAT-GAAAAATGTAAAAAAATTCATCCCAAAATCAATTATGACAT
* * * * * * ** * *
143 TATAGAATCATTTAAAACAAGTAATAAGGCTTTTGAAGGGTTGAGTGACTATAAATGAACTTTTC
65 TATAAAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGATTTTTC
* * * * * * * * *
208 ATACC-AATGGATGGCTTTTGCTTCATGTTCCCCATGATAGAC
130 -TTCCTAATGAATAGCTTTTTCTACATGTTTCCCAAG-CAGGC
* ** * ********* * *
250 ATTCAATTATAGCCTT-TTTTAACCAAAAATAT-AAAAAATNNNNNNNNNNAATCAATTTTGAGA
1 ATTCAATTATAG-TTTGTTTTAATGAAAAATGTAAAAAAAT-TCATCCCAAAATCAATTATGACA
* * * * * *
313 TTATAAAACCATTTAAAG-TA--AATAAAGCTTTCT-AAGGAATGAGTGACTACAAATGAATTTT
64 TTATAAAACCTTTTAAAGCGAGTAATAAGGCTTT-TGAAAGAATGAGTGACTATAAATGGATTTT
* * * * * * *
374 TGTTGCTAATGACTACCTTTTTATTCATGTTTCCCAAGCCAGAC
128 TCTTCCTAATGAATAGCTTTTTCTACATGTTTCCCAAG-CAGGC
* * * * * *
418 ATTAAATTATAATCTGTTCTAAGGAAAAATGTAAAAAAATTCATCCCAAAATCAATTATGAGATT
1 ATTCAATTATAGTTTGTTTTAATGAAAAATGTAAAAAAATTCATCCCAAAATCAATTATGACATT
********** * *
483 ATAAAACCNNNNNNNNNNAGTAATAAGGCTTTTGAAAGAATGTGTCACTATAAATGGATTTTTCT
66 ATAAAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGATTTTTCT
548 TCCTAATGAATAGCTTTTTCTACATGTTTCCCTAAGCAGGC
131 TCCTAATGAATAGCTTTTTCTACATGTTTCCC-AAGCAGGC
**********
589 ATTCAATTATAGTTTGTTTTAATGAAAAATGTAAAAAAATTNNNNNNNNNNTCAATTATGACATT
1 ATTCAATTATAGTTTGTTTTAATGAAAAATGTAAAAAAATTCATCCCAAAATCAATTATGACATT
* * * *
654 ATAGAACCTTTTAAAGCGAGTAATAAGGCTTTTGACAGAATGGGTGACGATAAATGGATTTTTCT
66 ATAAAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGATTTTTCT
*
719 TCCTAATGAATAGCTTTTTCTACATGTTTCTGCAAGCAGGC
131 TCCTAATGAATAGCTTTTTCTACATGTTTC-CCAAGCAGGC
760 ATTCAATTATAGTTTGTTTTAATGAAAAATGTAAAAAAAT
1 ATTCAATTATAGTTTGTTTTAATGAAAAATGTAAAAAAAT
800 NNNNNNNNNN
Statistics
Matches: 426, Mismatches: 111, Indels: 26
0.76 0.20 0.05
Matches are distributed among these distances:
167 3 0.01
168 107 0.25
169 9 0.02
170 9 0.02
171 293 0.69
172 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.34
Consensus pattern (170 bp):
ATTCAATTATAGTTTGTTTTAATGAAAAATGTAAAAAAATTCATCCCAAAATCAATTATGACATT
ATAAAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGGATTTTTCT
TCCTAATGAATAGCTTTTTCTACATGTTTCCCAAGCAGGC
Found at i:2616 original size:505 final size:500
Alignment explanation
Indices: 2081--3009 Score: 1075
Period size: 505 Copynumber: 1.8 Consensus size: 500
2071 NNNNTGTTTT
* * * *
2081 AACCAAAAATGTAAAAATATTCTACTTAAAATCAATTATGACATTATAAAACCATTTAAAG-CAA
1 AACCAAAAATATAAAAAAATTCTACTTAAAACCAACTATGACATTATAAAACCATTTAAAGTCAA
* * *
2145 GTAATAAGGGTTTTGAAGAAAT-A-TATGACTATAAATAGACTTTTCTTGCCGATGAATGCTTTT
66 -TAATAAGGCTTTTGAAGAAATGAGT-T-ACTATAAATAGACTTTTCTTACCGATGAATGCCTTT
**** *
2208 TTCTTCAAGTTTCTCAAGATAGACATTCAATTATAGTNNNNNNNNNNTAAAAATGTAAAAATATT
128 TTCTTCAAGTTTCTCAAGATAGACATTCAATTATAGT-------AACCAAAAATGTAAAAAAATT
* * ** * * *
2273 CAACTTAAAATTAATTATTAGTTTATAAAACCATTTACAGTGAGTAGA-AAGGCTTTTGAAAGGA
186 CAACTTAAAACTAATTATGACATTATAAAACCATTTAAAGCGAGTA-ATAAAGCTTTTGAAAGGA
* * * **
2337 TGGGTAGCTATAAATAGAC-TTTTCTTGTCAATGAATGTCTTTTTCTTCACGTTTCGTAAGGTAG
250 TGAGTAGCTACAAATAGACATTTT-TAG-CAATGAATACCTTTTTCTTCACGTTTCGTAAGGTAG
* * * ** *
2401 ACATTCAATTACAATATGTTTTAACCCACAATGCACAAAGAATTCAACTTAAAATC-A-A-TATA
313 ACAATAAACTACAATATGTTTTAACAAAAAATGCACAAAGAATTCAACTTAAAATCAATATTATA
2463 AAACCATTTAAAGTGAGTAATAAGGCATTTGAAAAAATGAGTGACTATAAATGGACTTTTCTTAC
378 AAACCATTTAAAGTGAGTAATAAGGCATTTGAAAAAATGAGTGACTATAAATGGACTTTTCTTAC
2528 TAATGAATGCCTTTTTCTTCACTCTCCTCGATGTAGACATTCAATTATAGTCTATTTC
443 TAATGAATGCCTTTTTCTTCACTCTCCTCGATGTAGACATTCAATTATAGTCTATTTC
*
2586 AACCAAAAATATAAAAAAATT-TAACTTAAAACCAACTATGACATTATAAAACCATTTAAAGTGA
1 AACCAAAAATATAAAAAAATTCT-ACTTAAAACCAACTATGACATTATAAAACCATTTAAAGTCA
* * *
2650 ATAATAAGGCTTTTGAAGGAATGAGTTACTATACATAGACTTTTCTTACCTATGAATGCCTTTTT
65 ATAATAAGGCTTTTGAAGAAATGAGTTACTATAAATAGACTTTTCTTACCGATGAATGCCTTTTT
* * * * *** *
2715 CTTCACGTTTCTTAAGGTAGATATTCAATTATNNNNNNNNNNAACCAAAAATGTAAAAAAATTTA
130 CTTCAAGTTTCTCAAGATAGACATTCAATTAT-------AGTAACCAAAAATGTAAAAAAATTCA
* * *
2780 ACTTAAAACTAGTTATGCCATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGGATGA
188 ACTTAAAACTAATTATGACATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAAGGATGA
* * *
2845 GTGGCTACAAATAGACAATTTTTAGCAATGAATACCTTTTTCTTCACGTTTCTTGAGGTAGACAA
253 GTAGCTACAAATAGAC-ATTTTTAGCAATGAATACCTTTTTCTTCACGTTTCGTAAGGTAGACAA
* * *
2910 TAAACTATAATATGTTTTAACAAAAAATGTACAAAGAATTTAACTTAAAATCAATTTCGTGATTA
317 TAAACTACAATATGTTTTAACAAAAAATGCACAAAGAATTCAACTTAAAATCAA-----T-ATTA
*
2975 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA
376 TAAAACCATTTAAAGTGAGTAATAAGGCATTTGAA
3010 GGAATGAATA
Statistics
Matches: 349, Mismatches: 52, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
504 2 0.01
505 298 0.85
506 7 0.02
507 5 0.01
513 1 0.00
514 36 0.10
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.33
Consensus pattern (500 bp):
AACCAAAAATATAAAAAAATTCTACTTAAAACCAACTATGACATTATAAAACCATTTAAAGTCAA
TAATAAGGCTTTTGAAGAAATGAGTTACTATAAATAGACTTTTCTTACCGATGAATGCCTTTTTC
TTCAAGTTTCTCAAGATAGACATTCAATTATAGTAACCAAAAATGTAAAAAAATTCAACTTAAAA
CTAATTATGACATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAAGGATGAGTAGCTAC
AAATAGACATTTTTAGCAATGAATACCTTTTTCTTCACGTTTCGTAAGGTAGACAATAAACTACA
ATATGTTTTAACAAAAAATGCACAAAGAATTCAACTTAAAATCAATATTATAAAACCATTTAAAG
TGAGTAATAAGGCATTTGAAAAAATGAGTGACTATAAATGGACTTTTCTTACTAATGAATGCCTT
TTTCTTCACTCTCCTCGATGTAGACATTCAATTATAGTCTATTTC
Found at i:3007 original size:172 final size:168
Alignment explanation
Indices: 1659--3016 Score: 816
Period size: 171 Copynumber: 8.0 Consensus size: 168
1649 AGGAATAGAA
* * * * * * *
1659 GACTATAAAT-GAACTTTTCTTTCATATGAATGACTTTTT-TTATACATTTCTAGATGTAGGCAT
1 GACTATAAATAG-ACTTTTCTTACA-ATGAATGCCTTTTTCTT-CACGTTTCTTGAGGTAGACAT
* * * ** *
1722 TCAATTATAGTCTATTTTAATGAAAATAT-T-AAAAAATTCAACTTAAAATCAATTATGACATTA
63 TCAATTATAATATATTTCAACCAAAA-ATGTAAAAAAATTTAACTTAAAA-CAATT-TGACATTA
*** ** * *
1785 TAAAATTGTTTAAAGCAAGTAGTAAGGCTTTTGAACGAAT-AGGT
125 TAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGA-GT
** * * * *** * * * *
1829 GACTATGCATGGACTTTTCTTTCCAGTGAATATTTTTTTATTCATGTTTCTTAAGGTAAACATTC
1 GACTATAAATAGACTTTTC-TTACAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATTC
** * * * ******** *
1894 AATTATAACCT-GTTCTAACTAAAAATATAAAAAAATTTAACTTAANNNNNNNNNNGAGATTATA
65 AATTATAATATATTTC-AACCAAAAATGTAAAAAAATTTAACTTAA--AACAATTTGACATTATA
*
1958 AAACTATTTAAAGTGAGTAATAAGG-TTTGTGAAGGAATGAGT
127 AAACCATTTAAAGTGAGTAATAAGGCTTT-TGAAGGAATGAGT
* * * * * *
2000 GACTATAAATGGACTTTTCGTGT-CAATGAATGCCTTTCTCTTTACATTTCTTAAGGTAAACATT
1 GACTATAAATAGACTTTTC-T-TACAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATT
********** * * *
2064 CNNNNNNNNNNTGTTTTAACCAAAAATGTAAAAATATTCT-ACTTAAAATCAATTATGACATTAT
64 CAATTATAATATATTTCAACCAAAAATGTAAAAAAATT-TAACTTAAAA-CAATT-TGACATTAT
** * * *
2128 AAAACCATTTAAAGCAAGTAATAAGGGTTTTGAAGAAAT-ATAT
126 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGA-GT
* * * * ** *
2171 GACTATAAATAGACTTTTCTTGCCGATGAATGCTTTTTTCTTCAAGTTTCTCAAGATAGACATTC
1 GACTATAAATAGACTTTTCTT-ACAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATTC
* *********** * * * * **
2236 AATTATAGTNNNNNNNNNNTAAAAATGTAAAAATATTCAACTTAAAATTAATTATTAGTTTATAA
65 AATTATAATATATTTCAACCAAAAATGTAAAAAAATTTAACTTAAAA-CAATT-TGACATTATAA
* *
2301 AACCATTTACAGTGAGTAGA-AAGGCTTTTGAAAGG-ATGGGT
128 AACCATTTAAAGTGAGTA-ATAAGGCTTTTG-AAGGAATGAGT
* * * *
2342 -AGCTATAAATAGACTTTTCTTGTCAATGAATGTCTTTTTCTTCACGTTTCGTAAGGTAGACATT
1 GA-CTATAAATAGACTTTTCTT-ACAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATT
* * * * * * * * *
2406 CAATTACAATATGTTTTAACCCACAATGCACAAAGAATTCAACTT--AA-AA--T--CAATATAA
64 CAATTATAATATATTTCAACCAAAAATGTA-AAAAAATTTAACTTAAAACAATTTGACATTATAA
* **
2464 AACCATTTAAAGTGAGTAATAAGGCATTTGAAAAAATGAGT
128 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGT
* * * *
2505 GACTATAAATGGACTTTTCTTACTAATGAATGCCTTTTTCTTCAC-TCTCCTCGATGTAGACATT
1 GACTATAAATAGACTTTTCTTAC-AATGAATGCCTTTTTCTTCACGT-TTCTTGAGGTAGACATT
* * * *
2569 CAATTATAGTCTATTTCAACCAAAAATATAAAAAAATTTAACTTAAAACCAACTATGACATTATA
64 CAATTATAATATATTTCAACCAAAAATGTAAAAAAATTTAACTTAAAA-CAA-TTTGACATTATA
*
2634 AAACCATTTAAAGTGAATAATAAGGCTTTTGAAGGAATGAGT
127 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGT
* * * * *
2676 TACTATACATAGACTTTTCTTACCTATGAATGCCTTTTTCTTCACGTTTCTTAAGGTAGATATTC
1 GACTATAAATAGACTTTTCTTA-CAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATTC
********** * *
2741 AATTATNNNNNNNNNNAACCAAAAATGTAAAAAAATTTAACTTAAAACTAGTTATGCCATTATAA
65 AATTATAATATATTTCAACCAAAAATGTAAAAAAATTTAACTTAAAAC-AATT-TGACATTATAA
* * *
2806 AACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGGATGAGT
128 AACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGT
* * * * *
2847 GGCTACAAATAGACAATTT-TTAGCAATGAATACCTTTTTCTTCACGTTTCTTGAGGTAGACAAT
1 GACTATAAATAGAC-TTTTCTTA-CAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATT
* * * * * * **
2911 AAACTATAATATGTTTTAACAAAAAATGTACAAAGAATTTAACTTAAAATCAATTTCGTGATTAT
64 CAATTATAATATATTTCAACCAAAAATGTA-AAAAAATTTAACTTAAAA-CAATTT-GACATTAT
2976 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGA
126 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGA
3017 ATAACTA
Statistics
Matches: 906, Mismatches: 235, Indels: 92
0.73 0.19 0.07
Matches are distributed among these distances:
162 17 0.02
163 107 0.12
164 3 0.00
165 1 0.00
166 2 0.00
168 2 0.00
169 6 0.01
170 66 0.07
171 608 0.67
172 93 0.10
173 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.35
Consensus pattern (168 bp):
GACTATAAATAGACTTTTCTTACAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTAGACATTCA
ATTATAATATATTTCAACCAAAAATGTAAAAAAATTTAACTTAAAACAATTTGACATTATAAAAC
CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGT
Done.