Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399008.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2288.0, 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: 8432
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.26
Warning! 2819 characters in sequence are not A, C, G, or T
Found at i:4921 original size:172 final size:169
Alignment explanation
Indices: 4620--5566 Score: 762
Period size: 171 Copynumber: 5.5 Consensus size: 169
4610 NNNNNTTGGA
* * * *
4620 AAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCTAATTATAGTCACTCATTCCTTCGAAA
1 AAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAA
* * * ** * * *
4685 GCATTACTACTCACTTTAAACGGTTTTATAATCTCATAATTGATTTTAGGTTAAATTGTTTTATA
66 GCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTATATTTTTTTACA
* *
4750 TTTTTGGGTAAATTAGATTATAATTGAGTGTCGATCTTGAG
131 TTTTTGGTTAAA-TAGATTATAATTGAATGTCG-TCTTGAG
*
4791 AAACATGGAA-AACAAAGCCATTCATTAAC-AGTAAAAGTCTATTTATAGTCACCCATGCCTTCA
1 AAACAT-GAAGAA-AAAGCCATTCATTGACAAG-AAAAGTCTATTTATAGTCACCCATGCCTTCA
* * * *
4854 AAAGCCTTGTTACTCGCTTTATATAGTTTAATAATCTCATAATTGATTTTAGGTTATTTTTTTTT
63 AAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTATATTTTTTT
* * * *
4919 ATATTTTTGGTTCAAATAGATTATAATTGACTATC-TGCTTTAAG
128 ACATTTTTGGTT-AAATAGATTATAATTGAATGTCGT-C-TTGAG
* * * *
4963 AAACGTGAAGAAAAACCCATTTAATGACAAGAAAAGTAC-ATTTATAGTCACCCATGCCTTCAAA
1 AAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGT-CTATTTATAGTCACCCATGCCTTCAAA
********** * *
5027 AGCCTTATTNNNNNNNNNNAATGGTTTTATAATCTCATAATTGATTTTAGGTT-TAATTTTATTA
65 AGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTAT-ATTTTTTTA
** * * * *
5091 CATTTTTTATTAAAATATATTATAGTTAAATGTTTGTCTT-AGG
129 CATTTTTGGTT-AAATAGATTATAATTGAATG-TCGTCTTGA-G
*** ** * * * **
5134 AAACATGAAGAAAAATTTATTCATTCCCAAGAAAAGCCTATTTATTGTCACCCAAGCCTTTGAAA
1 AAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAA
* * * *
5199 GCCTTATTACTCGTTTTAAATAGTTTTATTATCTCATAATTCATTTTAAGTTGA-ATTTTTTTAC
66 GCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTT-ATATTTTTTTAC
* * * * *
5263 ATGTTTAGTTAGAACAGATTATAATTGAATGTCTTCCTTGAA
130 ATTTTTGGTTA-AATAGATTATAATTGAATGTCGT-CTTGAG
* * * * *
5305 AAACATAAAGAAAAAGCCATTCATTGGCAAGAGAAGTCCATTTATAGTCATCCATGCCTTCAAAA
1 AAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAA
* * * * *
5370 GCCTTATTACTCGCTTTAAATTA-TTTTATAACCTTAT-ATATGCTTTCTA-GTTAAAGTTTTTT
66 GCCTTATTACTCGCTTTAAA-TAGTTTTATAATCTCATAAT-TGATTT-TAGGTTATATTTTTTT
* ********* *
5432 ACATTTTTAGTTAAAATAGATTATAATTNNNNNNNNNNCTTGGG
128 ACATTTTTGGTT-AAATAGATTATAATT-GAATGTCGTCTTGAG
* * * * ** * **
5476 AAACATGAAGAAAAAGTCATTCATTGGCTAGAAAAGTCTAATTGGAGTCACCCATTCCTTTGAAA
1 AAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAA
* * *
5541 GCCTTACTACTCACTTTAAATGGTTT
66 GCCTTATTACTCGCTTTAAATAGTTT
5567 NNNNNNNNNN
Statistics
Matches: 612, Mismatches: 138, Indels: 52
0.76 0.17 0.06
Matches are distributed among these distances:
170 11 0.02
171 448 0.73
172 149 0.24
173 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.38
Consensus pattern (169 bp):
AAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAA
GCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAGGTTATATTTTTTTACA
TTTTTGGTTAAATAGATTATAATTGAATGTCGTCTTGAG
Found at i:5079 original size:171 final size:172
Alignment explanation
Indices: 4651--5035 Score: 458
Period size: 172 Copynumber: 2.2 Consensus size: 172
4641 CATTGACAAG
* * * * * * * * ** *
4651 AAAAGTCTAATTATAGTCACTCATTCCTTCGAAAGCATTACTACTCACTTTAAACGGTTTTATAA
1 AAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTATATAGTTTAATAA
* *
4716 TCTCATAATTGATTTTAGGTTAAATTGTTTTATATTTTTGGGTAAATTAGATTATAATTGAGTGT
66 TCTCATAATTGATTTTAGGTTAAATTGTTTTATATTTTTGGGTAAATTAGATTATAATTGACTAT
* * *
4781 CGATCTTGAGAAACATGGAAAACAAAGCCATTCATTAACAGT
131 CGATCTTAAGAAACATGGAAAACAAACCCATTCAATAACAGT
*
4823 AAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTGTTACTCGCTTTATATAGTTTAATAA
1 AAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTATATAGTTTAATAA
** * *
4888 TCTCATAATTGATTTTAGGTTATTTTTTTTTATATTTTTGGTTCAAA-TAGATTATAATTGACTA
66 TCTCATAATTGATTTTAGGTTAAATTGTTTTATATTTTTGGGT-AAATTAGATTATAATTGACTA
* * * *
4952 TCTGCT-TTAAGAAACGT-GAAGAA-AAACCCATTTAATGACAAG-
130 TC-GATCTTAAGAAACATGGAA-AACAAACCCATTCAATAAC-AGT
4994 AAAAGTAC-ATTTATAGTCACCCATGCCTTCAAAAGCCTTATT
1 AAAAGT-CTATTTATAGTCACCCATGCCTTCAAAAGCCTTATT
5036 NNNNNNNNNN
Statistics
Matches: 182, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
171 54 0.30
172 123 0.68
173 5 0.03
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (172 bp):
AAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTATATAGTTTAATAA
TCTCATAATTGATTTTAGGTTAAATTGTTTTATATTTTTGGGTAAATTAGATTATAATTGACTAT
CGATCTTAAGAAACATGGAAAACAAACCCATTCAATAACAGT
Found at i:5399 original size:342 final size:340
Alignment explanation
Indices: 4619--5459 Score: 847
Period size: 342 Copynumber: 2.5 Consensus size: 340
4609 NNNNNNTTGG
* * * *
4619 AAAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCTAATTATAGTCACTCATTCCTTCGAA
1 AAAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGTCAC-CATGCCTTCAAA
* * * *
4684 AGCATTACTACTCACTTTAAACGGTTTTATAATCTCATAATTGATTTTAGGTTAAATTGTTTTAT
65 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGGTTAAATT-TTTTAC
*** * * *
4749 ATTTTTGGGTAAATTAGATTATAATTGAGTGTCGATCTTGAGAAACATGGAAAACAAAGCCATTC
129 ATTTTTTATTAAAATAGATTATAATTAAATGTCGATCTTGAGAAACATGGAAAACAAAGCCATTC
* * * *
4814 ATTAACAGTAAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTGTTACTCGCTTTATATA
194 ATTAACAGTAAAAGCCTATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATA
* * * * * * *
4879 GTTTAATAATCTCATAATTGATTTTAGGTTATTTTTTTTTATATTTTTGGTTCAAATAGATTATA
259 GTTTAATAATCTCATAATTCATTTTAAGTTATATTTTTTTACATGTTTAGTTCAAACAGATTATA
* * *
4944 ATTGACTATCTGCTTTA
324 ATTGAATATCTCCTTGA
* * * * *
4961 AGAAACGTGAAGAAAAACCCATTTAATGACAAGAAAAGTACATTTATAGTCACCCATGCCTTCAA
1 A-AAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGTCA-CCATGCCTTCAA
********** *
5026 AAGCCTTATTNNNNNNNNNNAATGGTTTTATAATCTCATAATTGATTTTAGGTTTAATTTTATTA
64 AAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGGTTAAATTTT-TTA
* * * ***
5091 CATTTTTTATTAAAATATATTATAGTTAAATGTTTG-TCTT-AGGAAACAT-GAAGAA-AAATTT
128 CATTTTTTATTAAAATAGATTATAATTAAATG-TCGATCTTGA-GAAACATGGAA-AACAAAGCC
** * ** *
5152 ATTCATTCCCAAG-AAAAGCCTATTTATTGTCACCCAAGCCTTTGAAAGCCTTATTACTCGTTTT
190 ATTCATTAAC-AGTAAAAGCCTATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCGCTTT
* *
5216 AAATAGTTTTATTATCTCATAATTCATTTTAAGTTGA-ATTTTTTTACATGTTTAGTT-AGAACA
254 AAATAGTTTAATAATCTCATAATTCATTTTAAGTT-ATATTTTTTTACATGTTTAGTTCA-AACA
*
5279 GATTATAATTGAATGTCTTCCTTGA
317 GATTATAATTGAATATC-TCCTTGA
* * *
5304 AAAACATAAAGAAAAAGCCATTCATTGGCAAGAGAAGTCCATTTATAGTCATCCATGCCTTCAAA
1 AAAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGTCA-CCATGCCTTCAAA
* ** * * *
5369 AGCCTTATTACTCGCTTTAAATTATTTTATAACCTTAT-ATATGCTTTCTA-GTTAAAGTTTTTT
65 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAAT-TGATTT-TAGGTTAAA-TTTTTT
5432 ACA-TTTTTAGTTAAAATAGATTATAATT
127 ACATTTTTTA-TTAAAATAGATTATAATT
5460 NNNNNNNNNN
Statistics
Matches: 399, Mismatches: 86, Indels: 28
0.78 0.17 0.05
Matches are distributed among these distances:
341 9 0.02
342 236 0.59
343 151 0.38
344 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (340 bp):
AAAACATGAAGAAAAAGCCATTCATTGACAAGAAAAGTCCATTTATAGTCACCATGCCTTCAAAA
GCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGGTTAAATTTTTTACAT
TTTTTATTAAAATAGATTATAATTAAATGTCGATCTTGAGAAACATGGAAAACAAAGCCATTCAT
TAACAGTAAAAGCCTATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATAGT
TTAATAATCTCATAATTCATTTTAAGTTATATTTTTTTACATGTTTAGTTCAAACAGATTATAAT
TGAATATCTCCTTGA
Found at i:7601 original size:171 final size:170
Alignment explanation
Indices: 7159--7858 Score: 552
Period size: 171 Copynumber: 4.1 Consensus size: 170
7149 TTTTAAGTGA
* ** *
7159 AATTATTTTACATTTTTGGTAAAACAGATTATAATTGAATGCCTGT-CA-TGAGAAACATGAAGA
1 AATTTTTTTACATTTTTATTAAAACAGATTATAATTGAATG--TTTACATTGAGAAACATGAAGA
* ** * * * *
7222 CAAAGCCATTCATTGACAAGAAAAGTTCATTTATAGTCATCCACACCTTCGAAAGCTTTATTACT
64 AAAAGCCATTCATTGACAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACT
* * * *
7287 CGCTTTAAATAGTTTTACAATCGCATAATTTATTTTAGGA-TG
129 CACTTTAAATAGTTTTATAATCTCATAATTGATTTTA-GATTG
* * * * * * ******
7329 AATTTGTTTACATTTTTTGTTAAAACAGATTATAATTGACTGTCTACCTTGAGAAACGTNNNNNN
1 AATTTTTTTACA-TTTTTATTAAAACAGATTATAATTGAATGTTTACATTGAGAAACATGAAGAA
**** * * * *
7394 NNNNCTATACATTGACAAGAAAAGCCCATATATAGTTACCCATACCTTCAAAAGCCTTATTACTC
65 AAAGCCATTCATTGACAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTC
*
7459 A-TTTGAAATAGTTTTATAACCTCATAATTGATTTTAGATTG
130 ACTTT-AAATAGTTTTATAATCTCATAATTGATTTTAGATTG
*
7500 AATTTTTTTACATGTTTTATTAAAACAGATTATAATTGAATGTTTACATTGAGAAATATGAAGAA
1 AATTTTTTTACAT-TTTTATTAAAACAGATTATAATTGAATGTTTACATTGAGAAACATGAAGAA
* * * * ** * ** ** *
7565 AAACCCATTCATTTG-CAGGTAAAGCCTATTTATAGTTTCCTA-AGTTTTGAAAGCCTTATTATT
65 AAAGCCATTCA-TTGACAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACT
********** *
7628 CACTTTAAAT-GATTTTANNNNNNNNNNATTGATTTTA-AGTTA
129 CACTTTAAATAG-TTTTATAATCTCATAATTGATTTTAGA-TTG
* * * * * * *
7670 AACTTTTTTATATTTTTAGTTAAAACAGATTATAATTGATTGTTTACCTTGAAAAATATAAAGAA
1 AATTTTTTTACATTTTTA-TTAAAACAGATTATAATTGAATGTTTACATTGAGAAACATGAAGAA
* * * * * *
7735 AGAGTCATTCATTGACAACAAAAGCCCATTTATAGTCACCTATGCCTTCAAAAACCTTATTACTC
65 AAAGCCATTCATTGACAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTC
** * *
7800 ACTTTAAACGGTTTTATAATCTCATAATCGATTTTAGGTTG
130 ACTTTAAATAGTTTTATAATCTCATAATTGATTTTAGATTG
*
7841 AATGTTTTTACATTTTTA
1 AATTTTTTTACATTTTTA
7859 GTTANNNNNN
Statistics
Matches: 403, Mismatches: 112, Indels: 29
0.74 0.21 0.05
Matches are distributed among these distances:
169 12 0.03
170 138 0.34
171 249 0.62
172 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.38
Consensus pattern (170 bp):
AATTTTTTTACATTTTTATTAAAACAGATTATAATTGAATGTTTACATTGAGAAACATGAAGAAA
AAGCCATTCATTGACAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTATTACTCA
CTTTAAATAGTTTTATAATCTCATAATTGATTTTAGATTG
Done.