Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400566.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3759.0, 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: 9050
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.20
Warning! 3962 characters in sequence are not A, C, G, or T
Found at i:2974 original size:171 final size:170
Alignment explanation
Indices: 2683--3606 Score: 840
Period size: 171 Copynumber: 5.4 Consensus size: 170
2673 NNNNNNNNNN
* * *
2683 AAGCGAGTAATAAGGCTTTTGAAGGCATTGGTGACTATAAATGGACTTTTCTTTCCAATGGATAT
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
* * * * *
2748 CTTTTTCTTCATGTGTC-CTGAAGCAGATAATT-AATTATAATCTGTTTTGATAAAAAATATAAA
66 CTTTTTCTTCACGTTTCTC-AAAGCAGA-CATTCAATTATAATCTGTTTTAATAAAAAATATAAA
* * *
2811 AAAGTTTTACTTAAAACTAATTATAAAATTAAAAAAGTATTTA
129 AAA-TTTAACTTAAAACTAATTATGAGATTAAAAAAGTATTTA
* * *
2854 AAGCGAGTAATAACGCTTTCGAAGGCATGGGTTACTATAAATAGACTTTTCTTGCCAATGGATAT
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
* * *
2919 CTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
66 CTTTTTCTTCACGTTTCTCAAAGCAGACATTCAATTATAATCTGTTTTAATAAAAAATAT-AAAA
* * * * *
2984 AATTCAAATTAAAA-TCAATGATGAGGTT-ATAAAGTCATTTA
130 AATTTAACTTAAAACT-AATTATGAGATTAAAAAAGT-ATTTA
* ********** *
3025 AAGCGAGTAATAAAGCNNNNNNNNNNATGGGTGACTATAAATGGACTTCGT-TTGCCAATGGATA
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTT-TTCTTGCCAATGGATA
* * * ** * * * * *
3089 TTTTTTTGTTTACGTTTCTTTAAGCAGACGTTCAATTATAATCTATTTTCATAAAAATTGTAAAA
65 TCTTTTTCTTCACGTTTCTCAAAGCAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAA
* * * *
3154 ACATTCAACTTAAAACTAATTATGAGGTTATACAA-TCATTTA
130 A-ATTTAACTTAAAACTAATTATGAGATTAAAAAAGT-ATTTA
* * * * ** * *
3196 AAGCGAGTAATAACGCTTTCGAAGGTATGTGTTACCGTAAATGGACTTTTCTTACCAATGTATAT
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
* ** *
3261 CTTTTTCTTCACGTTTCTTAAAATAGACATTCAATTATAATCTGTTTTAATTAAAAATATAAAAA
66 CTTTTTCTTCACGTTTCTCAAAGCAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
* ********** * * *
3326 AATTNNNNNNNNNNTCAATTATAAGATTACAAAAGCATTTA
131 ATTTAACTTAAAACT-AATTATGAGATTAAAAAAGTATTTA
* ** * *
3367 AAGCGAGTAATAAGGCTTTCGAACGCATGGGTGACCGTAAATGCACTTTTCTTGCCAATGAATAT
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
* *
3432 CTTTTTCTTCACGTTTC-CTAAAGCAGATAATT-AATTATAATCTATTTTAATAAAAAATATAAA
66 CTTTTTCTTCACGTTTCTC-AAAGCAGA-CATTCAATTATAATCTGTTTTAATAAAAAATAT-AA
* * * *
3495 AAAAGTTTGACTCAAAGCTAATTATGAGATTAAAAAAGCT-TTCA
128 AAAA-TTTAACTTAAAACTAATTATGAGATTAAAAAAG-TATTTA
* * * * *
3539 AAGTGATTAATAAGGCTTTCGAAAGAATGGGTGACTCTAAATGGACTTTTCTTGCCAATGGATAT
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
3604 CTT
66 CTT
3607 NNNNNNNNNN
Statistics
Matches: 601, Mismatches: 135, Indels: 33
0.78 0.18 0.04
Matches are distributed among these distances:
170 19 0.03
171 479 0.80
172 100 0.17
173 3 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
CTTTTTCTTCACGTTTCTCAAAGCAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
ATTTAACTTAAAACTAATTATGAGATTAAAAAAGTATTTA
Found at i:3546 original size:21 final size:22
Alignment explanation
Indices: 3522--3563 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3512 CTAATTATGA
3522 GATTAAAAAAGCTTTC-AAAGT
1 GATTAAAAAAGCTTTCGAAAGT
* *
3543 GATTAATAAGGCTTTCGAAAG
1 GATTAAAAAAGCTTTCGAAAG
3564 AATGGGTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (22 bp):
GATTAAAAAAGCTTTCGAAAGT
Found at i:8068 original size:172 final size:170
Alignment explanation
Indices: 7495--8483 Score: 679
Period size: 171 Copynumber: 5.8 Consensus size: 170
7485 NNNNNNNNNN
* * * * *
7495 TAAAGCGAGTAATAAGGC-TTTCGAAGGTATGCGTGACCATAAATGGACTTTTCTGTG-CAATGG
1 TAAAGCGAGTAATAAAGCTTTTC-AAGGCATGGGTGACTATAAATAGACTTTTCT-TGCCAATGG
* ** * * * **
7558 ATATCTTTTTCTTCACGTTTCTCAAGGTAAACATTTAATTATAATCTATTTTAATTAAAAACGTA
64 ATACCTTTTTCTTCACGTTTCTCAAGACAAACATTCAATTATAATCTGTTTTAATAAAAAATATA
* ** * * *
7623 AAAAAATTTAACTTTAAATCAATTATGAGATTACAAAAGCATT
129 AAAAAATTTAA-ATTAAAAAAATTATGAGGTTATAAAATCATT
********** * * *
7666 TAAAGCNNNNNNNNNNGC-TTTCGAAGGCATGGGTGACTATAAATGGACTCTTCCTGCCAATGGA
1 TAAAGCGAGTAATAAAGCTTTTC-AAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATGGA
* * **********
7730 TATCTTTTTCTTCACGTTTCCTGAAG-CAGATA-ATT-AANNNNNNNNNNTTTTAATAAAAAATA
65 TACCTTTTTCTTCACGTTT-CTCAAGACA-A-ACATTCAATTATAATCTGTTTTAATAAAAAATA
* * * *
7792 TAAAAAAGTTCT-ACTTAAAACTAATTAT-AGGTT-TAAAAATTTATT
127 TAAAAAAATT-TAAATTAAAA-AAATTATGAGGTTAT-AAAA-TCATT
* * **********
7837 TAAAGCGAGTAA-AAAGGC-TTTCGAAGGTATGGGTTACTATAAANNNNNNNNNNTTGCCAATGG
1 TAAAGCGAGTAATAAA-GCTTTTC-AAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATGG
* * *
7900 ATACCTTTTTCTTCACGTTTTTCAAGACAGACATTCAATTATAATCTGTCTTAATAAAAAAATAT
64 ATACCTTTTTCTTCACGTTTCTCAAGACAAACATTCAATTATAATCTGTTTTAAT-AAAAAATAT
*
7965 AAAAAAATTTAAATTAAAATAAATTATGAGGTTATAAAATTATT
128 AAAAAAATTTAAATTAAAA-AAATTATGAGGTTATAAAATCATT
* * * *
8009 TAAAGCAAGTAATAAAGCTTTTCAAGGCGTGGGTGACTATAAATTGACTTTTCTTGCCAATAGAT
1 TAAAGCGAGTAATAAAGCTTTTCAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATGGAT
* * * ** * * * * * *
8074 ACCTTTTTGTTCAGGTTTCTTAAGGGAAACGTTCAATTATGATATGTTTTTATAAAAATTGTAAA
66 ACCTTTTTCTTCACGTTTCTCAAGACAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAA
* * * *
8139 AAAATTCAACTTGAAAAAAATTATGAGATTATACAATCATT
131 AAAATTTAAATT-AAAAAAATTATGAGGTTATAAAATCATT
* * * * * **
8180 TAAAGCGAGTAATAATGC-TTTCGAAGGTATGTGTTACCATAAATAGACTTTTCTTATCAATGGA
1 TAAAGCGAGTAATAAAGCTTTTC-AAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATGGA
* * * * * ** * * *
8244 TATCTTTTTCTACATGTTTCTCGAGAAAAACATGAAATTATAATCTGTTTGAATAAAAATTAGAA
65 TACCTTTTTCTTCACGTTTCTCAAGACAAACATTCAATTATAATCTGTTTTAATAAAAAATATAA
* * *
8309 AAAAATTTAATTTAAAACCAATTATAAGGTTATAAAATCATT
130 AAAAATTTAAATTAAAA-AAATTATGAGGTTATAAAATCATT
* * * * * * * *
8351 TAAAGCGAGCAATAAGGCTTTTCAAGACATCGATGACTATAAAAAGACTTTTTTTGCTAATGGAT
1 TAAAGCGAGTAATAAAGCTTTTCAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATGGAT
* * * * * *
8416 ATCTTTTTCTTTACGTTTCTCAAGGCAGACATTCAATTATAATTTGTTTTAATAACAAATATAAA
66 ACCTTTTTCTTCACGTTTCTCAAGACAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAA
8481 AAA
131 AAA
8484 GTTCANNNNN
Statistics
Matches: 621, Mismatches: 175, Indels: 44
0.74 0.21 0.05
Matches are distributed among these distances:
169 1 0.00
170 30 0.05
171 437 0.70
172 135 0.22
173 17 0.03
174 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
TAAAGCGAGTAATAAAGCTTTTCAAGGCATGGGTGACTATAAATAGACTTTTCTTGCCAATGGAT
ACCTTTTTCTTCACGTTTCTCAAGACAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAA
AAAATTTAAATTAAAAAAATTATGAGGTTATAAAATCATT
Found at i:8811 original size:170 final size:170
Alignment explanation
Indices: 8516--8832 Score: 393
Period size: 170 Copynumber: 1.9 Consensus size: 170
8506 NNNNNNNNNN
* * * *
8516 GTAATAAGGCTTTCGAAGGCATGGGTAACTATAAATAGACTTTTCTTGCAAATGGATATCTTTTT
1 GTAATAAAGCTTTCGAAGGCATGGGTAACCATAAATAGACTTTTCTTACAAATGAATATCTTTTT
* *
8581 CTTCACGTTTCTCGAGATAAACATTCATTATAATCTATTTCCATAAAAAATATAAAAAAAATTCA
66 CTTCACGTTTCTAGAGACAAACATTCATTATAATCTATTTCCATAAAAAATATAAAAAAAATTCA
*
8646 AATTAAAAATAATTATGAGGTAATAAAATCATTCAAGCGA
131 AATTAAAAACAATTATGAGGTAATAAAATCATTCAAGCGA
* * * * * *
8686 GTAATAAAGCTTTTGAATGCGTGGGTGACCATAAATGGACTTTTCTTACCAATGAATATCTTTTT
1 GTAATAAAGCTTTCGAAGGCATGGGTAACCATAAATAGACTTTTCTTACAAATGAATATCTTTTT
* * * * * ** * * *
8751 GTTCAGGTTTCTAGAGGCAGACGTTCAATTATAATCTATTTTTATGAAAATTGT-AAAAAAATTC
66 CTTCACGTTTCTAGAGACAAACATTC-ATTATAATCTATTTCCATAAAAAATATAAAAAAAATTC
* *
8815 AACTTAAAACCAATTATG
130 AAATTAAAAACAATTATG
8833 NNNNNNNNNN
Statistics
Matches: 121, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
170 99 0.82
171 22 0.18
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (170 bp):
GTAATAAAGCTTTCGAAGGCATGGGTAACCATAAATAGACTTTTCTTACAAATGAATATCTTTTT
CTTCACGTTTCTAGAGACAAACATTCATTATAATCTATTTCCATAAAAAATATAAAAAAAATTCA
AATTAAAAACAATTATGAGGTAATAAAATCATTCAAGCGA
Done.