Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398866.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2148.0, 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: 9782
ACGTcount: A:0.20, C:0.08, G:0.07, T:0.21
Warning! 4440 characters in sequence are not A, C, G, or T
Found at i:3043 original size:170 final size:170
Alignment explanation
Indices: 2489--3177 Score: 700
Period size: 171 Copynumber: 4.0 Consensus size: 170
2479 NNNNNNNNNN
* * * * *
2489 AGCCTTATTACTCACTTTAAATGGTTTTGTAATCTCCTAATTGATTTTAAGTTGAATTTTGCTT-
1 AGCCTTGTTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTT--TTC
* * * *
2553 ACATTTTTTGTTAAAACAGACTATAATTGAATGTT-TACGTTGAGAAACATG-AAGAAAAAA-AA
64 ACATTTTTTGTTAAAACAGACTATAATTGAATGTTCTGCCTCGA-AAA-ATGTAAGAAAAAAGCA
* *
2615 TTCATTGGCAAGAAAAGTCCATTTATAGTCTCTTATTCCTTTAAA
127 TTCATTGG-AAGAAAAGTCCATTTATAGTCTCTCATTCCTTCAAA
* *
2660 AGCCTTGTTACTCGTTTTAAATTGTTTTATAATCTCATTATTGATTTTAAGTTGAATTTTTTCAC
1 AGCCTTGTTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTCAC
* ** ** * * *
2725 ATTTTTAGTTTCAACAGACTATAATTGAA-CATCTGCCTTGAGAAAAAT-AAAGAAAAAGGCATT
66 ATTTTTTGTTAAAACAGACTATAATTGAATGTTCTGCC-T-CGAAAAATGTAAGAAAAAAGCATT
* * * * *
2788 CAAATGCAAGAAAAGTCAATTTATAGTCTCTTATTCCTTCTAA
129 C-ATTGGAAGAAAAGTCCATTTATAGTCTCTCATTCCTTCAAA
* * * *
2831 AGCCTTGCTACTTGCTTTAAATTGTTTTATAATCTTATAATTGATTTTAAGCTGAATTTTTTCAC
1 AGCCTTGTTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTCAC
* * * *
2896 ATTTTTTGTAAAAACAGACTATATTTGAATGTTC-GCCTCGAAAAATGTCAGAAAAAACCATTCA
66 ATTTTTTGTTAAAACAGACTATAATTGAATGTTCTGCCTCGAAAAATGTAAGAAAAAAGCATTCA
2960 TTGAGAAGAAAAGTCCATTTATAGTCATC-CATTCCTTCAAA
131 TTG-GAAGAAAAGTCCATTTATAGTC-TCTCATTCCTTCAAA
* * * * *
3001 AGCCTTTTTACTCGCTTTGAA-TGATTCTATTATCTCATAATTGATTTTAAGTTGAATTTTTTTA
1 AGCCTTGTTACTCGCTTTAAATTG-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTCA
* ** * * * *
3065 TATTTTTCATTAAAATAGACAATAATTGAATG-TCTGCCTC-AAGAAACGTATAGAAAAAGGCAT
65 CATTTTTTGTTAAAACAGACTATAATTGAATGTTCTGCCTCGAA-AAATGTA-AGAAAAAAGCAT
* * * *
3128 TCATTTGGAAGAAAAGTCTC-TTTATAATCACCCATTTCTTCAAA
128 TCA-TTGGAAGAAAAGTC-CATTTATAGTCTCTCATTCCTTCAAA
*
3172 AACCTT
1 AGCCTT
3178 ACTAGTCTCT
Statistics
Matches: 431, Mismatches: 69, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
169 19 0.04
170 171 0.40
171 230 0.53
172 11 0.03
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (170 bp):
AGCCTTGTTACTCGCTTTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTCAC
ATTTTTTGTTAAAACAGACTATAATTGAATGTTCTGCCTCGAAAAATGTAAGAAAAAAGCATTCA
TTGGAAGAAAAGTCCATTTATAGTCTCTCATTCCTTCAAA
Found at i:3192 original size:341 final size:341
Alignment explanation
Indices: 2503--3181 Score: 814
Period size: 341 Copynumber: 2.0 Consensus size: 341
2493 TTATTACTCA
* * * *
2503 CTTTAAATGGTTTTGTAATCTCCTAATTGATTTTAAGTTGAATTTTGCTTACATTTTTTGTTAAA
1 CTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTT-CTTACATTTTTTGTAAAA
* * *
2568 ACAGACTATAATTGAATGTTTACGTTGAGAAACATGAAGAAAAAAAATTCATTGGCAAGAAAAGT
65 ACAGACTATAATTGAATGTTCACCTCGAGAAACATGAAGAAAAAAAATTCATTGGCAAGAAAAGT
* * * *
2633 CCATTTATAGTCTCTTATTCCTTTAAAAGCCTTGTTACTCGTTTTAAATTGTTTTATAATCTCAT
130 CCATTTATAGTCTCTCATTCCTTCAAAAGCCTTGTTACTCGCTTTAAATTGTTCTATAATCTCAT
* ** *
2698 TATTGATTTTAAGTTGAATTTTTTCACATTTTTAGTTTCAACAGACTATAATTGAACATCTGCCT
195 AATTGATTTTAAGTTGAATTTTTTCACATTTTTAGTTAAAACAGACAATAATTGAACATCTGCCT
** * * **
2763 TGAGAAAAATAAAGAAAAAGGCATTCAAATGCAAGAAAAGTCAATTTATAGTCTCTTATTCCTTC
260 CAAGAAAAATAAAGAAAAAGGCATTCAAATGCAAGAAAAGTCAATTTATAATCACCCATTCCTTC
* * *
2828 TAAAGCCTTGCTACTTG
325 AAAAACCTTACTACTTG
* *
2845 CTTTAAATTGTTTTATAATCTTATAATTGATTTTAAGCTGAATTTT-TTCACATTTTTTGTAAAA
1 CTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTCTT-ACATTTTTTGTAAAA
* * * *
2909 ACAGACTATATTTGAATGTTCGCCTCGA-AAA-ATGTCAGAAAAAACCATTCATTGAG-AAGAAA
65 ACAGACTATAATTGAATGTTCACCTCGAGAAACATG-AAGAAAAAA-AATTCATTG-GCAAGAAA
* * *
2971 AGTCCATTTATAGTCATC-CATTCCTTCAAAAGCCTTTTTACTCGCTTTGAA-TGATTCTATTAT
127 AGTCCATTTATAGTC-TCTCATTCCTTCAAAAGCCTTGTTACTCGCTTTAAATTG-TTCTATAAT
* * * **
3034 CTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTCA-TTAAAATAGACAATAATTGAATGT
190 CTCATAATTGATTTTAAGTTGAATTTTTTCACATTTTT-AGTTAAAACAGACAATAATTGAACAT
** * ** * **
3098 CTGCCTCAAGAAACGTATAGAAAAAGGCATTCATTTGGAAGAAAAGTCTCTTTATAATCACCCAT
254 CTGCCTCAAGAAAAATAAAGAAAAAGGCATTCAAATGCAAGAAAAGTCAATTTATAATCACCCAT
*
3163 TTCTTCAAAAACCTTACTA
319 TCCTTCAAAAACCTTACTA
3182 GTCTCTTTAA
Statistics
Matches: 283, Mismatches: 47, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
339 3 0.01
340 15 0.05
341 220 0.78
342 45 0.16
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (341 bp):
CTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGCTGAATTTTCTTACATTTTTTGTAAAAA
CAGACTATAATTGAATGTTCACCTCGAGAAACATGAAGAAAAAAAATTCATTGGCAAGAAAAGTC
CATTTATAGTCTCTCATTCCTTCAAAAGCCTTGTTACTCGCTTTAAATTGTTCTATAATCTCATA
ATTGATTTTAAGTTGAATTTTTTCACATTTTTAGTTAAAACAGACAATAATTGAACATCTGCCTC
AAGAAAAATAAAGAAAAAGGCATTCAAATGCAAGAAAAGTCAATTTATAATCACCCATTCCTTCA
AAAACCTTACTACTTG
Found at i:3261 original size:71 final size:71
Alignment explanation
Indices: 3119--3263 Score: 177
Period size: 71 Copynumber: 2.0 Consensus size: 71
3109 AACGTATAGA
* * * *
3119 AAAAGGCATTCATTTGGAAGAAAAGTCTCTTTATAATCACCCATTTCTTCAAAAACCTTACTAGT
1 AAAAGGCATTCATTGGGAAGAAAAGTCTATTTATAATCACCCATTCCTTCAAAAACCTTACTACT
3184 CTCTTT
66 CTCTTT
* * * * *
3190 AAAAGGCATTCATTGGTGAA-AAAGGTCTATTTATAGTCACCCATTCCTTCATAAGCCTTATTAC
1 AAAAGGCATTCATTGG-GAAGAAAAGTCTATTTATAATCACCCATTCCTTCAAAAACCTTACTAC
3254 TGC-CTTT
65 T-CTCTTT
3261 AAA
1 AAA
3264 TAGTTTTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
71 59 0.94
72 4 0.06
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (71 bp):
AAAAGGCATTCATTGGGAAGAAAAGTCTATTTATAATCACCCATTCCTTCAAAAACCTTACTACT
CTCTTT
Found at i:3484 original size:170 final size:170
Alignment explanation
Indices: 3209--3635 Score: 587
Period size: 170 Copynumber: 2.5 Consensus size: 170
3199 TCATTGGTGA
* * *
3209 AAAAGGTCTATTTATAGTCACCCATTCCTTCATAAGCCTTATTACT-GCCTTTAAATAGTTTTAT
1 AAAA-GTCCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCG-CTTTAAATAGTTTTAT
* * *
3273 AATCTCATAATTGGTTTTAAGTTGAATTGTTTTAGATTTTTAGTTAAAACAGACTATAATTGAAT
64 AATCTCATAATTGATTTTAAGTTGAATTATTTTAGATTTTTAGTTAAAACAGACTATAATTAAAT
*
3338 GT-TACCTCGAGAAACATAAAGAAAAAAGCATTCATTGACCAG
129 GTCTACCTCGAGAAACATAAAGAAAAAA-CATTCATTGACAAG
* *
3380 AAAAGTCCATTTATAGTCATCCGTTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAA
1 AAAAGTCCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAA
* *
3445 TCTCATAACTGATTTTAAGTTGAATTATTTTATATTTTTAGTTAAAACAGACTATAATTAAATGT
66 TCTCATAATTGATTTTAAGTTGAATTATTTTAGATTTTTAGTTAAAACAGACTATAATTAAATGT
* * * *
3510 CTACCTTGAGAAACATGAAGAAACAACATTTATTGACAAG
131 CTACCTCGAGAAACATAAAGAAAAAACATTCATTGACAAG
* *
3550 -AAAGTTTCATTTATAGT-GTCCTATTCCTTCAAAAGCCTT-TCTACTCGCTTTAAATTA-TTTT
1 AAAAG-TCCATTTATAGTCATCC-ATTCCTTCAAAAGCCTTAT-TACTCGCTTTAAA-TAGTTTT
*
3611 ATAACCTCATAATTGATTTTAAGTT
62 ATAATCTCATAATTGATTTTAAGTT
3636 AGATTTTTTN
Statistics
Matches: 229, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
169 8 0.03
170 193 0.84
171 28 0.12
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (170 bp):
AAAAGTCCATTTATAGTCATCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAA
TCTCATAATTGATTTTAAGTTGAATTATTTTAGATTTTTAGTTAAAACAGACTATAATTAAATGT
CTACCTCGAGAAACATAAAGAAAAAACATTCATTGACAAG
Found at i:7356 original size:171 final size:170
Alignment explanation
Indices: 7055--7932 Score: 987
Period size: 171 Copynumber: 5.1 Consensus size: 170
7045 NNNNNNNNNN
* * * * *
7055 AAGTTGAATTGTTTTACATTTTTGGCTAAAACACACTATAATTGAATGTCTAGCATGAGAAACAT
1 AAGTTGAATT-TTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACAT
* * * * ** * ** * *
7120 GATGAAACAAGCATTTATTGGTGAGAAAAGTCCATTTATAGTCACCCATTTCTTAAAAAGCCTTA
65 GAAGAAAAAAGCATTCATTTGCAAGAAAAGTCCATTTATAGTCTCATATTCCTTCAAAAGCCTTA
** * **
7185 TTACTCCCTTTAAATGGTTTCGTAATCTCATAATTGATTTT
130 TTACTTGCTTTAAATTGTTTTATAATCTCATAATTGATTTT
* *
7226 AAGTTGAATTTTCTTACATTTTTAGTTAAAACAGACGATAATTGAATGTTTACCTTGAGAAACAT
1 AAGTTGAATTTT-TTACATTTTTAGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACAT
* * *
7291 AAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCTCATATTCCTTCAAAGGCCTTA
65 GAAGAAAAAAGCATTCATTTGCAAGAAAAGTCCATTTATAGTCTCATATTCCTTCAAAAGCCTTA
* *
7356 TTACTTGCTTTGAATTATTTTATAATCTCATAATTGATTTT
130 TTACTTGCTTTAAATTGTTTTATAATCTCATAATTGATTTT
* * ** *
7397 GAGTTGAATTTTTTCACTTTTTTAGTTAAAACAGACTATAATTGAACATCTAACTTGAGAAA-AG
1 AAGTTGAATTTTTT-ACATTTTTAGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACA-
* * ** * *
7461 TGAAGAAAAAGGCATATCATTTGCAAGAAAATTGAATTTATAGTCTCTTATTCCTTCGAAAGCCT
64 TGAAGAAAAAAGCAT-TCATTTGCAAGAAAAGTCCATTTATAGTCTCATATTCCTTCAAAAGCCT
* *
7526 TATTACTTGCTTTAAATTGTTTTATAATCACATTATTGATTTT
128 TATTACTTGCTTTAAATTGTTTTATAATCTCATAATTGATTTT
** * *
7569 AAGTTGAATTGTTTTCACATTTTTAGTTTCAACAAACTATAATTGAATATCTACCTTGAGAAA-A
1 AAGTTGAATT-TTTT-ACATTTTTAGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACA
* * * * *
7633 GTGAAGCAAAAGGCATATCATTTGCAAGAAAATTCAATTTATAGTCTCCTATTCCTTCAAAAGCC
64 -TGAAGAAAAAAGCAT-TCATTTGCAAGAAAAGTCCATTTATAGTCTCATATTCCTTCAAAAGCC
*
7698 TTATTACTTGCTTTAAATTGTTTTACAATCTCATAATTGATTTT
127 TTATTACTTGCTTTAAATTGTTTTATAATCTCATAATTGATTTT
* * * ** * * * *
7742 AAGCT-AAATTTTCACATTTTGGGTTAAAACAGACTATAATTGAATGTTTGCCTTGGGAAACGTT
1 AAGTTGAATTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAAC-AT
* *
7806 G-A-AAAAAACCATTCATTATG-AAGAAAAGTCCATTTATAGTC-AACTATTCCTTCAAAAGCCT
65 GAAGAAAAAAGCATTCATT-TGCAAGAAAAGTCCATTTATAGTCTCA-TATTCCTTCAAAAGCCT
* * * *
7867 TAGTACTCGCTTTAAATTATTCTATAATCTCATAATTGATTTT
128 TATTACTTGCTTTAAATTGTTTTATAATCTCATAATTGATTTT
*
7910 AAGTTGAATTTTTTTATATTTTT
1 AAGTTGAA-TTTTTTACATTTTT
7933 CATTNNNNNN
Statistics
Matches: 606, Mismatches: 90, Indels: 23
0.84 0.13 0.03
Matches are distributed among these distances:
168 83 0.14
169 11 0.02
170 54 0.09
171 212 0.35
172 93 0.15
173 153 0.25
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (170 bp):
AAGTTGAATTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCTACCTTGAGAAACATG
AAGAAAAAAGCATTCATTTGCAAGAAAAGTCCATTTATAGTCTCATATTCCTTCAAAAGCCTTAT
TACTTGCTTTAAATTGTTTTATAATCTCATAATTGATTTT
Done.