Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403300.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_972.0, 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: 6251
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.30
Warning! 1023 characters in sequence are not A, C, G, or T
Found at i:486 original size:29 final size:29
Alignment explanation
Indices: 444--503 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
434 TAAGTATAAA
*
444 AAATTAATTTTATT-AAAAAATAAATATTT
1 AAATTAATATTATTCAAAAAA-AAATATTT
* * *
473 AAATTTATATTATTCAAATAAAAGTATTT
1 AAATTAATATTATTCAAAAAAAAATATTT
502 AA
1 AA
504 CAATATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
AAATTAATATTATTCAAAAAAAAATATTT
Found at i:2126 original size:239 final size:242
Alignment explanation
Indices: 1838--2332 Score: 680
Period size: 244 Copynumber: 2.0 Consensus size: 242
1828 NNNNNNNNNN
1838 ATTAAGTAAAAAAAAATCTAATTTTAGTAAAAAATAAATATTTAAATATATATTC-TAAGACTAA
1 ATTAAGTAAAAAAAAATCTAATTTTAGTAAAAAATAAATATTTAAATATATATTCTTAAG-CTAA
* * * * *
1902 A-AGTGTTTAATGATATATAAA-TT-TTTTTAAA-TAATAATAAAAATAATTATAAATCAAAATT
65 ATA-TGTTTAACGACATATAAATTTATTTTTAAACAAATAATAAAAAAAATTACAAATCAAAATT
* * *
1963 AG-CATAGATAAATTTTGACGTAAACCTATAACAATTTACGTAAAAACTTATAAAGGT-GAAATA
129 -GTCATAGATAAATTTTGACGTAAAACTATAACAATTGACGTAAAAACTTATAAAAGTAG-AATA
* *
2026 ATTAAATTTTAAATGTTGACGTAAATATATGAGAGTTAACGTAACAAGTCA
192 ACTAAATTTTAAATGTTAACGTAAATATATGAGAGTTAACGTAACAAGTCA
* * * **
2077 ATTGAGTAAAAAAAATTTTAATTTTAGTAAAAAATAAATATTTAAATATATATTCTTCTGCTAAA
1 ATTAAGTAAAAAAAAATCTAATTTTAGTAAAAAATAAATATTTAAATATATATTCTTAAGCTAAA
*
2142 TATGTTTAACGACATATAAATTTTAATTTTTAAACAAATAATAAAAAAAATTACAACTCAAAATT
66 TATGTTTAACGACATATAAA-TTT-ATTTTTAAACAAATAATAAAAAAAATTACAAATCAAAATT
* * *
2207 GTCATAGATAAATTTTGATGTAAAACTATAACAATTGATGTAAAAATTTATAAAAGTAGAATAAC
129 GTCATAGATAAATTTTGACGTAAAACTATAACAATTGACGTAAAAACTTATAAAAGTAGAATAAC
* * * *
2272 TAAATTTTAAATTTTAACGTAAATATATTAGAGTTAACGTAATAAGTTA
194 TAAATTTTAAATGTTAACGTAAATATATGAGAGTTAACGTAACAAGTCA
2321 ATTAAGTAAAAA
1 ATTAAGTAAAAA
2333 CGTCACATTT
Statistics
Matches: 223, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
239 73 0.33
240 3 0.01
241 2 0.01
243 9 0.04
244 135 0.61
245 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.35
Consensus pattern (242 bp):
ATTAAGTAAAAAAAAATCTAATTTTAGTAAAAAATAAATATTTAAATATATATTCTTAAGCTAAA
TATGTTTAACGACATATAAATTTATTTTTAAACAAATAATAAAAAAAATTACAAATCAAAATTGT
CATAGATAAATTTTGACGTAAAACTATAACAATTGACGTAAAAACTTATAAAAGTAGAATAACTA
AATTTTAAATGTTAACGTAAATATATGAGAGTTAACGTAACAAGTCA
Found at i:2428 original size:244 final size:243
Alignment explanation
Indices: 1838--2568 Score: 582
Period size: 244 Copynumber: 3.0 Consensus size: 243
1828 NNNNNNNNNN
** * * *
1838 ATTAAGTAAAAAAAAATCTAATTTTAGTAAAAAATAAATATTTAAATATATATTC-TAAGACTAA
1 ATTAAGT-AAAAAACGTC-AATTTTAATAAAAAATAAACATTTAAATATATATTCATCAG-CTAA
* * * * *
1902 A-AGTGTTTAATGATATATAAATTTT--T-TTAAAT---AATAATAAAAATAATTATAAATCAAA
63 ATA-TGTGTAACGACATATAAATTTTAATGTTAAATAAAAATAATAAAAAAAATTACAAATCAAA
* * *
1960 ATTAGCATAGATAAATTTTGACGTAAACCTATAACAATTTACGTAAAAACTTATAAAGGTGAAAT
127 ATTAGCATAGATAAATTTTGACGTAAAACTATAACAATTGACGTAAAAACTTATAAAAGTGAAAT
* *
2025 AATTAAATTTTAAATGTTGACGTAAATATATGAGAGTTAACGTAACAAGTCA
192 AACTAAATTTTAAATGTTAACGTAAATATATGAGAGTTAACGTAACAAGTCA
* ** * * * * *
2077 ATTGAGTAAAAAAAATTTTAATTTTAGTAAAAAATAAATATTTAAATATATATTCTTCTGCTAAA
1 ATTAAGT--AAAAAACGTCAATTTTAATAAAAAATAAACATTTAAATATATATTCATCAGCTAAA
* * * * *
2142 TATGTTTAACGACATATAAATTTTAATTTTTAA-ACAAATAATAAAAAAAATTACAACTCAAAAT
64 TATGTGTAACGACATATAAATTTTAATGTTAAATAAAAATAATAAAAAAAATTACAAATCAAAAT
* * *
2206 T-GTCATAGATAAATTTTGATGTAAAACTATAACAATTGATGTAAAAATTTATAAAAGT-AGAAT
129 TAG-CATAGATAAATTTTGACGTAAAACTATAACAATTGACGTAAAAACTTATAAAAGTGA-AAT
* * * *
2269 AACTAAATTTTAAATTTTAACGTAAATATATTAGAGTTAACGTAATAAGTTA
192 AACTAAATTTTAAATGTTAACGTAAATATATGAGAGTTAACGTAACAAGTCA
* ** * *
2321 ATTAAGT-AAAAACGTCACATTTTAATAAAAATTATGCATTTATATTTATATT-ATCGAGCTAAA
1 ATTAAGTAAAAAACGTCA-ATTTTAATAAAAAATAAACATTTAAATATATATTCATC-AGCTAAA
* *
2384 -A-GCATGTAACGATAT-TCAAATTTTTATGTTAAATAAAGAATAATAAAGATAAAGAGAATTA-
64 TATG--TGTAACGACATAT-AAATTTTAATGTTAAATAAA-AATAAT--A-A-AAA-A-AATTAC
* * * * * * * * * * *
2445 TAGTTAAAAGTTA-CTATTGAAAAAGTTTGACGTAAAATTGA-AAGAATTAACGTAGAATCTTAT
119 AAATCAAAA-TTAGC-ATAGATAAATTTTGACGTAAAACT-ATAACAATTGACGTAAAAACTTAT
* ** * * * *
2508 AAAAGTGGAATAAAAAAAGTTAAAATCTTAACGTAAATGTATGAGAGTTAACGTAACAAGT
181 AAAAGTGAAATAACTAAATTTTAAATGTTAACGTAAATATATGAGAGTTAACGTAACAAGT
2569 GATAATAATA
Statistics
Matches: 397, Mismatches: 66, Indels: 47
0.78 0.13 0.09
Matches are distributed among these distances:
239 67 0.17
240 12 0.03
241 12 0.03
242 59 0.15
243 4 0.01
244 136 0.34
246 1 0.00
247 1 0.00
248 3 0.01
249 8 0.02
250 93 0.23
251 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.34
Consensus pattern (243 bp):
ATTAAGTAAAAAACGTCAATTTTAATAAAAAATAAACATTTAAATATATATTCATCAGCTAAATA
TGTGTAACGACATATAAATTTTAATGTTAAATAAAAATAATAAAAAAAATTACAAATCAAAATTA
GCATAGATAAATTTTGACGTAAAACTATAACAATTGACGTAAAAACTTATAAAAGTGAAATAACT
AAATTTTAAATGTTAACGTAAATATATGAGAGTTAACGTAACAAGTCA
Found at i:2711 original size:17 final size:17
Alignment explanation
Indices: 2643--2711 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
2633 TGTTGTAGTT
* *
2643 TAAAGTTAAAAATAAAA
1 TAAATTTAAAAATTAAA
* *
2660 TAAAATTAAAACTTAAA
1 TAAATTTAAAAATTAAA
*
2677 TAACTTTTAAATAAATTAAA
1 TAA-ATTT-AA-AAATTAAA
2697 TAAATTTAAAAATTA
1 TAAATTTAAAAATTA
2712 TCTACATTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 23 0.55
18 4 0.10
19 5 0.12
20 10 0.24
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (17 bp):
TAAATTTAAAAATTAAA
Found at i:5852 original size:2 final size:2
Alignment explanation
Indices: 5847--5900 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
5837 CCAAACTAGT
*
5847 TA TA TA TA TA TA TA TA TA TA TA TG TA T- TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5887 -A TA TT TT TA TA TA T
1 TA TA TA TA TA TA TA T
5901 GTTAAGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5931 original size:16 final size:16
Alignment explanation
Indices: 5910--5943 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5900 TGTTAAGAAA
5910 AATTAA-AAGTAAACTT
1 AATTAATAA-TAAACTT
5926 AATTAATAATAAACTT
1 AATTAATAATAAACTT
5942 AA
1 AA
5944 AATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
AATTAATAATAAACTT
Found at i:6222 original size:21 final size:22
Alignment explanation
Indices: 6198--6248 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
6188 TAAATATATC
6198 ATACAT-ACATATATT-TAATTT
1 ATACATAACAT-TATTATAATTT
6219 ATACATAAACATTATTATAATTT
1 ATACAT-AACATTATTATAATTT
6242 ATA-ATAA
1 ATACATAA
6249 ATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 8 0.30
22 6 0.22
23 13 0.48
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (22 bp):
ATACATAACATTATTATAATTT
Found at i:6248 original size:22 final size:23
Alignment explanation
Indices: 6204--6249 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
6194 TATCATACAT
6204 ACATATATTTAATTTATACATAA
1 ACATATATTTAATTTATACATAA
6227 ACAT-TATTATAATTTATA-ATAA
1 ACATATATT-TAATTTATACATAA
6249 A
1 A
6250 TT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
ACATATATTTAATTTATACATAA
Done.