Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398968.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2250.0, 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: 4352
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.25
Warning! 1550 characters in sequence are not A, C, G, or T
Found at i:323 original size:171 final size:160
Alignment explanation
Indices: 146--462 Score: 357
Period size: 171 Copynumber: 1.9 Consensus size: 160
136 NNNNNNNNNN
* * * *
146 TCGCTTTAAATGGTTTTATAACCTCATAATTGATTTTAAGCTGAATTGTTCT-ACATTTTTAGTT
1 TCGCTTTAAATGATTTTATAACCTCAGAATTGATTTTAAGCTCAATT-TTCTCACATTATTAGTT
* * **
210 AAAACAGACTATAATTGAATGTCTATCTTAAGAAATGTGAAGAAAAAGGCATTCATTGACAAGAA
65 AAAACAGACTATAATTGAATATCTAGCTTAA-AAACATGAAGAAAAAGGCATTCATTGACAAGAA
275 AAGTCCATTTATAGTCACTCANNNNNNNNNNAGCCTTATTAC
129 AAGTCCATTTATAGTCACTCA----------AGCCTTATTAC
* * * * *
317 TCGCTTTAAATGATTTTATAATCTCAGAATTGATTTTAGGTTCAATTTTTTCACATTATTGGTTA
1 TCGCTTTAAATGATTTTATAACCTCAGAATTGATTTTAAGCTCAATTTTCTCACATTATTAGTTA
* * * * *
382 AAACAGATTATAATTGAATATCTAGCTTTAAAACATGATGAAAAAGGCATTCATTGGCAAGGAAA
66 AAACAGACTATAATTGAATATCTAGCTTAAAAACATGAAGAAAAAGGCATTCATTGACAAGAAAA
447 GTCCATTTATAGTCAC
131 GTCCATTTATAGTCAC
463 CTATTTCTTC
Statistics
Matches: 127, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
170 49 0.39
171 78 0.61
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.36
Consensus pattern (160 bp):
TCGCTTTAAATGATTTTATAACCTCAGAATTGATTTTAAGCTCAATTTTCTCACATTATTAGTTA
AAACAGACTATAATTGAATATCTAGCTTAAAAACATGAAGAAAAAGGCATTCATTGACAAGAAAA
GTCCATTTATAGTCACTCAAGCCTTATTAC
Found at i:690 original size:170 final size:169
Alignment explanation
Indices: 1--809 Score: 683
Period size: 170 Copynumber: 4.7 Consensus size: 169
* ** * *
1 ATAATTGATTTTAAGTTGAATTTTTTACATTTTTGGTTAAAATAGACAATAATTAAATGTCTGCC
1 ATAATTGATTTTAAGTTGAATTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACC
** * * *
66 TCAAGAAAGGTGAAGAAAAAGTG-TTTCATGGGCAAGAAAAGTCCATTTATAGTCATCCATTCCT
66 T-AAGAAACATGAAGAAAAAG-GCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
********** * *
130 TCAAAANNNNNNNNNNTCGCTTTAAATGGTTTTATAACCTC
129 TCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTC
* * * *
171 ATAATTGATTTTAAGCTGAATTGTTCTACATTTTTAGTTAAAACAGACTATAATTGAATGTCTAT
1 ATAATTGATTTTAAGTTGAATT-TTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTA-
* ** * * *****
236 CTTAAGAAATGTGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACTCANNNNN
64 CCTAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
*****
301 NNNNNAGCCTTATTACTCGCTTTAAATGATTTTATAATCTC
129 TCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTC
* * * * *
342 AGAATTGATTTTAGGTTCAATTTTTTCACATTATTGGTTAAAACAGATTATAATTGAATATCTAG
1 ATAATTGATTTTAAGTTGAATTTTTT-ACATTTTTGGTTAAAACAGATTATAATTGAATGTCTA-
* * * * * *
407 CTTTA-AAACATGATGAAAAAGGCATTCATTGGCAAGGAAAGTCCATTTATAGTCACCTATTTCT
64 CCTAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
********** * *
471 TCAAAAGCCTTATTNNNNNNNNNNAATGGTTTTATAATCTA
129 TCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTC
* * * *
512 AAAATTGATTTTAAGTTGAATTTTTCTACGTTTTTAGTTAAAACAGATTATAATTGAATGCCTAC
1 ATAATTGATTTTAAGTTGAATTTTT-TACATTTTTGGTTAAAACAGATTATAATTGAATGTCTAC
* *
577 CTAGAGAAACATGAAGAAAAAGGCATTCATTGGCATGAATAG-CCATTTATAGTCACCCATTCCT
65 CTA-AGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
* * * * * *
641 TTAAAAGCGTTCTTACTCGCTTTAAATGATTTTTTAATTTT
129 TCAAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTC
* ** * *
682 ATAATTGATTTTAAGTTAAATTTTGTTTTTATGTTTGTGGTCATAACTA-ATTATAATTGAATGT
1 ATAATTGATTTTAAGTTGAA-TTT-TTTACAT-TTT-TGGTTAAAAC-AGATTATAATTGAATGT
* * * *
746 CTACCTGGAGAAATATGAAGAAAAAGGGATTCAATGGCAA-AAACAGTCCATTTATAGTCACCCA
61 CTACCT-AAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAA-AGTCCATTTATAGTCACCCA
810 ATCTNNNNNN
Statistics
Matches: 500, Mismatches: 124, Indels: 26
0.77 0.19 0.04
Matches are distributed among these distances:
169 2 0.00
170 213 0.43
171 201 0.40
172 9 0.02
173 57 0.11
174 18 0.04
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.36
Consensus pattern (169 bp):
ATAATTGATTTTAAGTTGAATTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACC
TAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTC
AAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTC
Found at i:2711 original size:171 final size:169
Alignment explanation
Indices: 2277--3265 Score: 591
Period size: 171 Copynumber: 5.8 Consensus size: 169
2267 NNNNTTGGTA
* ** * *
2277 AGAAAAGTCCATTTATAGTCATCT-ATTCCTTCAAAAGCCTTATTACTCTCTTTAATTGGTTTTA
1 AGAAAAGTCCATTTATAGTCA-CTAATTCCTTCAAAAGCCTTACTACTAGCTTTAAATAGTTTTA
* ** ** * * * * *
2341 TAA-GCTCAAAATTGATTTTGGGTTCAGTTTTTTTTTACATTTTTTGTCAAAACGGATTATAATT
65 TAATG-TCATAATTGATTTTAAGTT--G-AATTTTTTATATTTTTGGTTAAAACAGACTATAATT
* * * *
2405 GAATGTCTACCTCAAGAAACATG-AGAAAAAAAACATTCATT-GAC
126 GAATGCCTAACTCAAGAAACGTGAAG-AAAAAAGCATTCATTAG-C
* ** * *
2449 AAGAAAAG-CACATTTATAGTGACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAAT-GATTT
1 -AGAAAAGTC-CATTTATAGTCACTAATTCCTTCAAAAGCCTTACTACTAGCTTTAAATAG-TTT
* ********** * *
2512 TATAATCTNNNNNNNNNNTTTAAGTTGAATTTCTTTATATTTTTGGTTAAAATAGACTATAATTA
63 TATAATGTCATAATTGATTTTAAGTTGAATTT-TTTATATTTTTGGTTAAAACAGACTATAATTG
* * ** *
2577 AATGTCTAACTCAAGAAATGTGAAGAAAAAAATATTCATTACTC
127 AATGCCTAACTCAAGAAACGTGAAGAAAAAAGCATTCATTA-GC
* * * * * **
2621 AGAAAAGTCCATTTATAGTCACTTATTCTTTCAAAAGTCTTACTACTTGCTTTAAATGGTTTTNN
1 AGAAAAGTCCATTTATAGTCACTAATTCCTTCAAAAGCCTTACTACTAGCTTTAAATAGTTTTAT
******** * *
2686 NNNNNNNNAATTGATTTTGAGTTGAATTTTTTGATATTTTTAGTTAAAACAGACTATAATTGAAT
66 AATGTCATAATTGATTTTAAGTTGAATTTTTT-ATATTTTTGGTTAAAACAGACTATAATTGAAT
* * * *
2751 GCCTACCTCAAGAAACATGAAGCAAAAGGCATTCATTAGC
130 GCCTAACTCAAGAAACGTGAAGAAAAAAGCATTCATTAGC
* * * * * *
2791 AAAAAAGACCATTTATACTCACCAATTCCTTGAAAAGCCTTATTACTAGCTTTAAATAGTTTTAT
1 AGAAAAGTCCATTTATAGTCACTAATTCCTTCAAAAGCCTTACTACTAGCTTTAAATAGTTTTAT
* *
2856 AATGTCATAATTGATTTTAAGTTGAATGTTTTTATGTTTTTGGTTAAAACAAACTATAATTGAAT
66 AATGTCATAATTGATTTTAAGTTGAAT-TTTTTATATTTTTGGTTAAAACAGACTATAATTGAAT
* *
2921 GCCT-ACTTCGAGAAACGTGAAGAAAAAAGCATTCATTGGC
130 GCCTAAC-TCAAGAAACGTGAAGAAAAAAGCATTCATTAGC
* * ************** * *
2961 ATGAAAAGTCTATTTATAGTCACTCATTCCTTNNNNNNNNNNNNNNCTCGCTTTAAATAGTTTTT
1 A-GAAAAGTCCATTTATAGTCACTAATTCCTTCAAAAGCCTTACTACTAGCTTTAAATAGTTTTA
* * ** *
3026 TAATCTCATAATTGATTTTAAGTTGAATTTTTTTTTACATTTTT-GACAATAACAGATTATAATT
65 TAATGTCATAATTGATTTTAAGTTGAA---TTTTTTATATTTTTGGTTAA-AACAGACTATAATT
* * * * * *
3090 GAATGTCTACCT-AGAGAAACAG-GAAGAAAAAGGGATTGAAT-GAC
126 GAATGCCTAACTCA-AGAAAC-GTGAAGAAAAAAGCATTCATTAG-C
* * * ** * * *
3134 AAGAGAAGTCCATTTATAGTCACCCAA-TCTTTCAAAAATCTTATTCCTTGCTTTAAAT-GTTTT
1 -AGAAAAGTCCATTTATAGTCA-CTAATTCCTTCAAAAGCCTTACTACTAGCTTTAAATAG-TTT
*** * * * *
3197 TATAAAACCATGATTGATTTTAGGTTCAACTTTTTTATATTTTTGGTTAAAACAGACAATAATTG
63 TATAATGTCATAATTGATTTTAAGTTGAA-TTTTTTATATTTTTGGTTAAAACAGACTATAATTG
3262 AATG
127 AATG
3266 TNNNNNNNNN
Statistics
Matches: 625, Mismatches: 165, Indels: 54
0.74 0.20 0.06
Matches are distributed among these distances:
169 1 0.00
170 139 0.22
171 288 0.46
172 16 0.03
173 175 0.28
174 6 0.01
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.37
Consensus pattern (169 bp):
AGAAAAGTCCATTTATAGTCACTAATTCCTTCAAAAGCCTTACTACTAGCTTTAAATAGTTTTAT
AATGTCATAATTGATTTTAAGTTGAATTTTTTATATTTTTGGTTAAAACAGACTATAATTGAATG
CCTAACTCAAGAAACGTGAAGAAAAAAGCATTCATTAGC
Found at i:2914 original size:341 final size:332
Alignment explanation
Indices: 2370--2989 Score: 680
Period size: 341 Copynumber: 1.8 Consensus size: 332
2360 GGGTTCAGTT
* * * * *
2370 TTTTTTTACATTTTTTGTCAAAACGGATTATAATTGAATGTCTACCTCAAGAAACATGAGAAAAA
1 TTTTTTGACATTTTTAGTCAAAACAGACTATAATTGAATGCCTACCTCAAGAAACATGAGAAAAA
* * * *
2435 AAACATTCATTGACAAGAAAAGCACATTTATAGTGACCCATTCCTTCAAAAGCCTTATTACTCGC
66 AAACATTCATTGACAAGAAAAGCACATTTATACTCACCAATTCCTTCAAAAGCCTTATTACTAGC
********** *
2500 TTTAAATGATTTTATAATCTNNNNNNNNNNTTTAAGTTGAATTTCTTTATATTTTTGGTTAAAAT
131 TTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTCTTTATATTTTTGGTTAAAAC
* * * * *
2565 AGACTATAATTAAATGTCTAAC-TCAAGAAATGTGAAGAAAAAAATATTCATTACTCA-GAAAAG
196 AAACTATAATTAAATGCCT-ACTTCAAGAAACGTGAAGAAAAAAACATTCATT-CGCATGAAAAG
*
2628 TCCATTTATAGTCACTTATTCTTTCAAAAGTCTTACTACTTGCTTTAAATGGTTTTNNNNNNNNN
259 TCCATTTATAGTCACTCATTCTTTCAAAAGTCTTACTACTTGCTTTAAATGGTTTT---------
2693 NAATTGATTTTGAGTTGAA
315 -AATTGATTTTGAGTTGAA
* * *
2712 TTTTTTGATATTTTTAGTTAAAACAGACTATAATTGAATGCCTACCTCAAGAAACATGA-AGCAA
1 TTTTTTGACATTTTTAGTCAAAACAGACTATAATTGAATGCCTACCTCAAGAAACATGAGA-AAA
** *
2776 AAGGCATTCATT-AGCAA-AAAAG-ACCATTTATACTCACCAATTCCTTGAAAAGCCTTATTACT
65 AAAACATTCATTGA-CAAGAAAAGCA-CATTTATACTCACCAATTCCTTCAAAAGCCTTATTACT
* *
2838 AGCTTTAAAT-AGTTTTATAATGTCATAATTGATTTTAAGTTGAATGTT-TTTATGTTTTTGGTT
128 AGCTTTAAATGA-TTTTATAATCTCATAATTGATTTTAAGTTGAAT-TTCTTTATATTTTTGGTT
* * * *
2901 AAAACAAACTATAATTGAATGCCTACTTCGAGAAACGTGAAGAAAAAAGCATTCATTGGCATGAA
191 AAAACAAACTATAATTAAATGCCTACTTCAAGAAACGTGAAGAAAAAAACATTCATTCGCATGAA
*
2966 AAGTCTATTTATAGTCACTCATTC
256 AAGTCCATTTATAGTCACTCATTC
2990 CTTNNNNNNN
Statistics
Matches: 232, Mismatches: 39, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
340 6 0.03
341 157 0.68
342 69 0.30
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.36
Consensus pattern (332 bp):
TTTTTTGACATTTTTAGTCAAAACAGACTATAATTGAATGCCTACCTCAAGAAACATGAGAAAAA
AAACATTCATTGACAAGAAAAGCACATTTATACTCACCAATTCCTTCAAAAGCCTTATTACTAGC
TTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTCTTTATATTTTTGGTTAAAAC
AAACTATAATTAAATGCCTACTTCAAGAAACGTGAAGAAAAAAACATTCATTCGCATGAAAAGTC
CATTTATAGTCACTCATTCTTTCAAAAGTCTTACTACTTGCTTTAAATGGTTTTAATTGATTTTG
AGTTGAA
Done.