Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399352.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_262.0, 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: 3802
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.23
Warning! 1328 characters in sequence are not A, C, G, or T
Found at i:2634 original size:171 final size:171
Alignment explanation
Indices: 2338--3419 Score: 961
Period size: 171 Copynumber: 6.3 Consensus size: 171
2328 NNNNNNNAAT
* * * *
2338 GAATGGGTGACTATAAATGGA-ATTTTTTTCCTAATGAATGCCTTTTT-TTCTACGTTTCTCGAG
1 GAATAGGTGACTATAAATGGACATTTCTTGCC-AATGAATGCCTTTTTCTT-TACGTTTCTCAAG
* * * * *
2401 GTAGACATTCAATTATAGTTTGTTTTAGCCAAAAATGTATAACAATTCAACTTAAAATCAATTAT
64 GTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATT-T
* *
2466 T-AAATTATAAAACCATTCAAAGTGAGTAATAAGGATTTTGAAG
128 TGAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
** * **
2509 TTATAGGTTACTATAAATGGACATTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTTGAGGT
1 GAATAGGTGACTATAAATGGACATTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGT
* ** * *
2574 AAACATTCAACAATAATATGTTTTAACCAAAAATGTAAAAAAATTCAACTTAACATCAATTTT-A
66 AGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGA
* ** ** *
2638 AGGTTATAAAATTATTTAAAACGAGTAATAAGCCTTTTGAAG
131 A-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * * * * * *
2680 GTATGGGTGACTATAAATGGA-TTTTGCTTGTCAATAAATACCTTTTTCTTCT-CATTTCTCAAA
1 GAATAGGTGACTATAAATGGACATTT-CTTGCCAATGAATGCCTTTTTCTT-TACGTTTCTCAAG
2743 GTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTT
64 GTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTT
* * *
2808 GAGATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTAAAG
129 GAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * * * * * * *
2851 GAATGGGTGACTCTAAATAGAC-TTTTTTGTCAATGAATGCCTTTTTCTTCACATTTCTCAAAGA
1 GAATAGGTGACTATAAATGGACATTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGT
* * * *
2915 AGACATTCAATTATAATCTTTTTTAACCAAAAATTTTAAAAAAACT-ATATTTAAAATCAATTTT
66 AGACATTCAATTATAATCTGTTTTAACCAAAAA-TGTAAAAAAATTCA-ACTTAAAATCAATTTT
* * *
2979 GAGATTATAAAACCATTTAAAGCGAGTAATTAA-GTTTTTGAAG
129 GAAATTATAAAACCATTTAAAGTGAGTAA-TAAGGCTTTTGAAG
* * * * * * * * * *
3022 GAATAAGAGGCTATAAATAGACTTTTCTT-CCAAATGAATGGCTTTTTATATATGTTTCTTAAGG
1 GAATAGGTGACTATAAATGGACATTTCTTGCC-AATGAATGCCTTTTTCTTTACGTTTCTCAAGG
* * * * * *
3086 CAGGCATTCAACTATAGTCTGTTTTAA-CAAAAGATGTAAAAAAATTGAATTTAAAATCAATTTT
65 TAGACATTCAATTATAATCTGTTTTAACCAAAA-ATGTAAAAAAATTCAACTTAAAATCAATTTT
* * * *
3150 GACATAATAAAACCATTTAAAGTAAGTAATAAGGCTTTTGACG
129 GAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * * ** ** *
3193 GAAT-GGAAGACTATAGATGAAC-TGTT-TTTCCAAATGAATGGGTTTTTCTACACGTTTCCCAA
1 GAATAGG-TGACTATAAATGGACAT-TTCTTGCC-AATGAATGCCTTTTTCTTTACGTTTCTCAA
* * * * * *** * * * *
3255 AGAAGGA-ATTAAATTATAGTCTGTTTTGAGGGAAAATGCAAAAAAAATCAACTTAACATCAATG
63 GGTA-GACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * * * ** * * *
3319 ATGAGATTACAAAACCATTAAAAACGAGTAAGAAGGTTTTTAAAG
127 TTGAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * *
3364 GAATGGGTGACTATAAATGGACATTTCTTGCCAATAAATGCCTTTTTCTTCACGTT
1 GAATAGGTGACTATAAATGGACATTTCTTGCCAATGAATGCCTTTTTCTTTACGTT
3420 AATTTTGAGA
Statistics
Matches: 749, Mismatches: 138, Indels: 48
0.80 0.15 0.05
Matches are distributed among these distances:
170 80 0.11
171 590 0.79
172 79 0.11
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
GAATAGGTGACTATAAATGGACATTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAAGGT
AGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTGA
AATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
Found at i:3308 original size:513 final size:511
Alignment explanation
Indices: 2338--3416 Score: 1154
Period size: 513 Copynumber: 2.1 Consensus size: 511
2328 NNNNNNNAAT
* * * *
2338 GAATGGGTGACTATAAATGGAATTTTTT-TCCTAATGAATGCCTTTTT-TTCTACGTTTCTCGAG
1 GAATGGGTGACTATAAATGGACTTTTTTGT-C-AATGAATGCCTTTTTCTTC-ACATTTCTCAAA
* * * * * *
2401 GTAGACATTCAATTATAGTTTGTTTTAGCCAAAAATGTATAACAATTCAACTTAAAATCAATTAT
63 GAAGACATTCAATTATAATTTGTTTTAACCAAAAATGTAAAAAAACTCAACTTAAAATCAATTAT
* ** * ** *
2466 TAAATTATAAAACCATTCAAAGTGAGTAATAAGGATTTTGAAGTTATAGGTTACTATAAATGGAC
128 TAAATTATAAAACCATTCAAAGCGAGTAATAAGGATTTTGAAGGAATAAGAGACTATAAATAGAC
* * * *
2531 ATTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTTGAGGTAAACATTCAACAATAATATGTT
193 ATTTCTTGCCAATGAATGCCTTTTTATATACGTTTCTTAAGGCAAACATTCAACAATAATATGTT
* ** * ** *
2596 TTAACCAAAAATGTAAAAAAATTCAACTTAACATCAATTTTAAGGTTATAAAATTATTTAAAACG
258 TTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTAACATAATAAAACCATTTAAAACA
* ** * *
2661 AGTAATAAGCCTTTTGAAGGTATGGGTGACTATAAATGGATTTTGCTTGTCAATAAATACCTTTT
323 AGTAATAAGCCTTTTGAAGGAATGGAAGACTATAAATGAATTTT-CTTGCCAATAAATACCTTTT
* * * * * * *
2726 TCTTCTCATTTCTCAAAGTAGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAAATTC
387 TCTACACATTTCCCAAAGAAGACATTAAATTATAATCTGTTTTAACCAAAAATGCAAAAAAAATC
** * * ** *
2791 AACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGCAATAAGGCTTTTAAAG
452 AACTTAAAATCAATGATGAGATTACAAAACCATTAAAAACGAGCAAGAAGGCTTTTAAAG
* *
2851 GAATGGGTGACTCTAAATAGACTTTTTTGTCAATGAATGCCTTTTTCTTCACATTTCTCAAAGAA
1 GAATGGGTGACTATAAATGGACTTTTTTGTCAATGAATGCCTTTTTCTTCACATTTCTCAAAGAA
* *
2916 GACATTCAATTATAATCTT-TTTTAACCAAAAATTTTAAAAAAACT-ATATTTAAAATCAATT-T
66 GACATTCAATTATAAT-TTGTTTTAACCAAAAA-TGTAAAAAAACTCA-ACTTAAAATCAATTAT
* * * *
2978 TGAGATTATAAAACCATTTAAAGCGAGTAATTAA-GTTTTTGAAGGAATAAGAGGCTATAAATAG
128 T-AAATTATAAAACCATTCAAAGCGAGTAA-TAAGGATTTTGAAGGAATAAGAGACTATAAATAG
* * * ** * * *
3042 ACTTTTCTT-CCAAATGAATGGCTTTTTATATATGTTTCTTAAGGCAGGCATTCAACTATAGTCT
191 ACATTTCTTGCC-AATGAATGCCTTTTTATATACGTTTCTTAAGGCAAACATTCAACAATAATAT
* * *
3106 GTTTTAA-CAAAAGATGTAAAAAAATTGAATTTAAAATCAATTTTGACATAATAAAACCATTTAA
255 GTTTTAACCAAAA-ATGTAAAAAAATTCAACTTAAAATCAATTTTAACATAATAAAACCATTTAA
** * * * * *
3170 AGTAAGTAATAAGGCTTTTGACGGAATGGAAGACTATAGATGAACTGTTT-TT-CCAAATGAATG
319 AACAAGTAATAAGCCTTTTGAAGGAATGGAAGACTATAAATGAA-T-TTTCTTGCC-AATAAATA
** * * * ***
3233 GGTTTTTCTACACGTTTCCCAAAGAAGGA-ATTAAATTATAGTCTGTTTTGAGGGAAAATGCAAA
381 CCTTTTTCTACACATTTCCCAAAGAA-GACATTAAATTATAATCTGTTTTAACCAAAAATGCAAA
* * *
3297 AAAAATCAACTTAACATCAATGATGAGATTACAAAACCATTAAAAACGAGTAAGAAGGTTTTTAA
445 AAAAATCAACTTAAAATCAATGATGAGATTACAAAACCATTAAAAACGAGCAAGAAGGCTTTTAA
3362 AG
510 AG
* * *
3364 GAATGGGTGACTATAAATGGACATTTCTTGCCAATAAATGCCTTTTTCTTCAC
1 GAATGGGTGACTATAAATGGAC-TTTTTTGTCAATGAATGCCTTTTTCTTCAC
3417 GTTAATTTTG
Statistics
Matches: 463, Mismatches: 89, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
512 64 0.14
513 362 0.78
514 34 0.07
515 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (511 bp):
GAATGGGTGACTATAAATGGACTTTTTTGTCAATGAATGCCTTTTTCTTCACATTTCTCAAAGAA
GACATTCAATTATAATTTGTTTTAACCAAAAATGTAAAAAAACTCAACTTAAAATCAATTATTAA
ATTATAAAACCATTCAAAGCGAGTAATAAGGATTTTGAAGGAATAAGAGACTATAAATAGACATT
TCTTGCCAATGAATGCCTTTTTATATACGTTTCTTAAGGCAAACATTCAACAATAATATGTTTTA
ACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTTTAACATAATAAAACCATTTAAAACAAGT
AATAAGCCTTTTGAAGGAATGGAAGACTATAAATGAATTTTCTTGCCAATAAATACCTTTTTCTA
CACATTTCCCAAAGAAGACATTAAATTATAATCTGTTTTAACCAAAAATGCAAAAAAAATCAACT
TAAAATCAATGATGAGATTACAAAACCATTAAAAACGAGCAAGAAGGCTTTTAAAG
Found at i:3509 original size:105 final size:105
Alignment explanation
Indices: 3320--3524 Score: 270
Period size: 105 Copynumber: 2.0 Consensus size: 105
3310 ACATCAATGA
*
3320 TGAGATTACAAAACCATTAAAAACGAGTAAGAAGGTTTTTAAAGGAATGGGTGACTATAAATGGA
1 TGAGATTACAAAACCATTAAAAACGAGTAAGAAGGCTTTTAAAGGAATGGGTGACTATAAATGGA
*
3385 CATTTCTTGCCAATAAATGCCT-TTTTCTTCACGTTAATTT
66 AATTTCTTGCCAATAAATGCCTATTTT-TTCACGTTAATTT
* * ** * * *
3425 TGAGATTATAAAACCATTGAAAGTGATTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT-GA
1 TGAGATTACAAAACCATTAAAAACGAGTAAGAAGGCTTTTAAAGGAATGGGTGACTATAAATGGA
* * *
3489 AATTTTCTTGCTAATTAATGCCTATTTTTTTACGTT
66 AA-TTTCTTGCCAATAAATGCCTATTTTTTCACGTT
3525 TCTCGAGGTA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
104 3 0.03
105 79 0.92
106 4 0.05
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (105 bp):
TGAGATTACAAAACCATTAAAAACGAGTAAGAAGGCTTTTAAAGGAATGGGTGACTATAAATGGA
AATTTCTTGCCAATAAATGCCTATTTTTTCACGTTAATTT
Found at i:3715 original size:172 final size:171
Alignment explanation
Indices: 3420--3802 Score: 502
Period size: 172 Copynumber: 2.2 Consensus size: 171
3410 TCTTCACGTT
* * ** *
3420 AATTTTGAGATTATAAAACCA-TTGAAAGTGATTAATAAGGCTTTTGAAGGAATGGGTGACTATA
1 AATTATGAGATTATAAAACCACTT-AAAGCGAGGAATAAGGCTTTTGAAGGAATGGGTGACTAAA
* * * * * **
3484 AATGAAATTTTCTTGCTAATTAATGCCTATTTTTTTACGTTTCTCGAGGTAGCCATTCAATTATA
65 AAGGAAATTTTCTTGCCAATGAATGCCTATTTTTTTACGTTTCTCGAGGCAGACATTCAACAATA
*
3549 GTCTGTTTTAACCAAAAATGTAAACAAAATTCAACTTAAAATC
130 ATCTGTTTTAACCAAAAATGTAAA-AAAATTCAACTTAAAATC
* *
3592 AATTATGATATTATAAAACTACTTAAAGCGAGGAATAAGGCTTTTGAAGGAATGGGTGACTAAAA
1 AATTATGAGATTATAAAACCACTTAAAGCGAGGAATAAGGCTTTTGAAGGAATGGGTGACTAAAA
* *
3657 ACGGATA-TTTCTTGCCAATGAATGCCT-TTTTCTTTACGTTTCTCGATGCAGACATTCAACAAT
66 A-GGAAATTTTCTTGCCAATGAATGCCTATTTT-TTTACGTTTCTCGAGGCAGACATTCAACAAT
* *
3720 AATCTGTTTTAACCAAAAATGTAAAAAATTTTAACTTAAAATC
129 AATCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATC
* * * *
3763 AATTTTGAGATTATAGAACCATTTAAAGCGAGTAATAAGG
1 AATTATGAGATTATAAAACCACTTAAAGCGAGGAATAAGG
Statistics
Matches: 183, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
171 54 0.30
172 124 0.68
173 5 0.03
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (171 bp):
AATTATGAGATTATAAAACCACTTAAAGCGAGGAATAAGGCTTTTGAAGGAATGGGTGACTAAAA
AGGAAATTTTCTTGCCAATGAATGCCTATTTTTTTACGTTTCTCGAGGCAGACATTCAACAATAA
TCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATC
Done.