Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398542.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1834.0, 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: 2574
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.33
Warning! 328 characters in sequence are not A, C, G, or T
Found at i:489 original size:170 final size:172
Alignment explanation
Indices: 222--554 Score: 463
Period size: 170 Copynumber: 1.9 Consensus size: 172
212 TTCATTGGTA
* * * *
222 AGAAAAGTCCATTTATAGTCACCCATACCTTCGGAGGCCTTATTACTCACATTAAATGATTTTAT
1 AGAAAAGTCCATTTATAGCCACCCATACCTTCGAAAGCCTTATTACTCACATTAAACGATTTTAT
* * * *
287 AAGCTTATAACTGATTTTATATTAAGTTTTTTATAT-TTTTTTATTAAAACAGATTATAATTGAA
66 AACCTCATAACTGATTTTAGATTAAATTTTTTATATATTTTTTATTAAAACAGATTATAATTGAA
* * *
351 TGTCTACCTCGAG-AACGTGAAGAAAAAGATATCCATTAACT
131 CGTCTACCTCGAGAAACATAAAGAAAAAGATATCCATTAACT
* ** * ***
392 AGAAAAGTCTATTTATAGCCACTTATACCTTCGAAAGCTTTATTACTCGTTTTAAACGATTTTAT
1 AGAAAAGTCCATTTATAGCCACCCATACCTTCGAAAGCCTTATTACTCACATTAAACGATTTTAT
*
457 AACCTCATAATTGATTTTAGATTAAATTTTTTATATATTTTTTATTAAAACAGATTATAATTGAA
66 AACCTCATAACTGATTTTAGATTAAATTTTTTATATATTTTTTATTAAAACAGATTATAATTGAA
* *
522 CGTCTACCTCTAGAAATATAAAGAAAAAGATAT
131 CGTCTACCTCGAGAAACATAAAGAAAAAGATAT
555 TCGTTGGTGA
Statistics
Matches: 140, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
170 85 0.61
171 39 0.28
172 16 0.11
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (172 bp):
AGAAAAGTCCATTTATAGCCACCCATACCTTCGAAAGCCTTATTACTCACATTAAACGATTTTAT
AACCTCATAACTGATTTTAGATTAAATTTTTTATATATTTTTTATTAAAACAGATTATAATTGAA
CGTCTACCTCGAGAAACATAAAGAAAAAGATATCCATTAACT
Found at i:609 original size:172 final size:169
Alignment explanation
Indices: 201--779 Score: 567
Period size: 172 Copynumber: 3.4 Consensus size: 169
191 NNNNNNNNNN
* * *
201 AGAAAAAGATATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATACCTTCGGAGGCCTTATT
1 AGAAAAAGATATTCATTGGT-AGAAAAGTCTATTTATAGTCA-CCATACCTTCGAAAGCCTTATT
* * * * *
266 ACTCACATTAAATGATTTTATAAGCTTATAACTGATTTTATATTAAGTTTTTTATAT-TTTTTTA
64 ACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTA-ATTAAGTTTTTTATATATTTTTTA
* * *
330 TTAAAACAGATTATAATTGAATGTCTACCTCGAG-AACGTGA
128 TTAAAACAGATTATAATTGAATGTCTACCTCTAGAAATGTAA
* ** * * *
371 AGAAAAAGATATCCATTAACTAGAAAAGTCTATTTATAGCCACTTATACCTTCGAAAGCTTTATT
1 AGAAAAAGATATTCATT-GGTAGAAAAGTCTATTTATAGTCAC-CATACCTTCGAAAGCCTTATT
* * *
436 ACTCGTTTTAAACGATTTTATAACCTCATAATTGATTTTAGATTAAATTTTTTATATATTTTTTA
64 ACTCGCTTTAAATGATTTTATAACCTCATAATTGATTTTA-ATTAAGTTTTTTATATATTTTTTA
* *
501 TTAAAACAGATTATAATTGAACGTCTACCTCTAGAAATATAA
128 TTAAAACAGATTATAATTGAATGTCTACCTCTAGAAATGTAA
* * * * * * *
543 AGAAAAAGATATTCGTTGGTGAGAATAGTTTATTTATTGTTAGCCACACCTTCTAAAGCCTTATT
1 AGAAAAAGATATTCATTGGT-AGAAAAGTCTATTTATAGTCA-CCATACCTTCGAAAGCCTTATT
* * ** * * *
608 ACACGCTTT-AATTATTTTTATATTCTCATAATTGACTTTAAGTAGAGTTTTTT-TACATTTTTT
64 ACTCGCTTTAAATGA-TTTTATAACCTCATAATTGATTTTAATTA-AGTTTTTTATATATTTTTT
* * ** * *
671 ATTAAAAACAGATTAAAATTAAATACCTTCCCCTAGAAATGTAA
127 ATT-AAAACAGATTATAATTGAATGTCTACCTCTAGAAATGTAA
* ** * *
715 AGAAAAAG-TCATTAATTGACAAGAAAAGTCTATTTATAATCATCCATGCCTTC-AAAGCCTTAT
1 AGAAAAAGAT-ATTCATTG-GTAGAAAAGTCTATTTATAGTCA-CCATACCTTCGAAAGCCTTAT
778 TA
63 TA
780 TGTGCCTAAA
Statistics
Matches: 332, Mismatches: 66, Indels: 21
0.79 0.16 0.05
Matches are distributed among these distances:
169 1 0.00
170 100 0.30
171 72 0.22
172 158 0.48
173 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (169 bp):
AGAAAAAGATATTCATTGGTAGAAAAGTCTATTTATAGTCACCATACCTTCGAAAGCCTTATTAC
TCGCTTTAAATGATTTTATAACCTCATAATTGATTTTAATTAAGTTTTTTATATATTTTTTATTA
AAACAGATTATAATTGAATGTCTACCTCTAGAAATGTAA
Found at i:1584 original size:170 final size:170
Alignment explanation
Indices: 1195--1598 Score: 504
Period size: 171 Copynumber: 2.4 Consensus size: 170
1185 NNNNNNNNNN
*
1195 TCTATTTATAGTCACCCATCCCTTCGAAAGCCTTATTGCCCGCTTTAAATGAATTTATAACCTAA
1 TCTATTTATAGTCACCCAT-CCTTCGAAAGCCTTATTACCCGCTTTAAATGAATTTATAACCTAA
*
1260 TAACTGATTTTAAGTTAAATTTTTTTATATTTTTTATTAAAAAAAATTATAATTGAATACCTACC
65 TAACTGATCTTAAGTTAAATTTTTTTATATTTTTTATTAAAAAAAATTATAATTGAATACCTACC
*
1325 TTAAAAAACGTGAAGAAAAAAATATCCACTGGAAAGAAAAG
130 TTAAAAAACGTGAAGAAAAAAATATCCACTAGAAAGAAAAG
* * * * * *
1366 TCTATTTATAGTCACCCATGCTTGCGAAAGCTTTATTACCCACTTTAAATGACTTTATAAGCTTA
1 TCTATTTATAGTCACCCATCCTT-CGAAAGCCTTATTACCCGCTTTAAATGAATTTATAACCTAA
* ********** **
1431 TAATTGATCTTAAGTTAAATTTTTTTATATTTTTTANNNNNNNNNNTTATAATTGAATGTCTACC
65 TAACTGATCTTAAGTTAAATTTTTTTATATTTTTTATTAAAAAAAATTATAATTGAATACCTACC
* * ** *
1496 TT-GAAAACGTGAAGAAAAAGATATCCGTTAGTAAGAAAAG
130 TTAAAAAACGTGAAGAAAAAAATATCCACTAGAAAGAAAAG
* * *
1536 TCTATTTATACTCACCCATACCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAACCT
1 TCTATTTATAGTCACCCAT-CCTTCGAAAGCCTTATTACCCGCTTTAAATGAATTTATAACCT
1599 CANNNNNNNN
Statistics
Matches: 197, Mismatches: 34, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
170 87 0.44
171 110 0.56
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.37
Consensus pattern (170 bp):
TCTATTTATAGTCACCCATCCTTCGAAAGCCTTATTACCCGCTTTAAATGAATTTATAACCTAAT
AACTGATCTTAAGTTAAATTTTTTTATATTTTTTATTAAAAAAAATTATAATTGAATACCTACCT
TAAAAAACGTGAAGAAAAAAATATCCACTAGAAAGAAAAG
Found at i:2273 original size:171 final size:161
Alignment explanation
Indices: 2114--2567 Score: 459
Period size: 171 Copynumber: 2.7 Consensus size: 161
2104 NNNNNNNNNN
* * * *
2114 TCACCCATGCCTTCGAAAGCCTTATT-GCTCGCTTTAAATGATTTTATAACCTCATAATCGCTTT
1 TCACCCATCCCTTCGAAAGCCTTATTACCT-ACTTTAAATGATTTTATAACCTCATAATCGATTT
* **
2178 TAAGTTGAATTTTTTTATAT-TTTTTATTGAAACAGATTATAATT-AAGTGTCTACCTCAAGAAA
65 TAAGTTGAATTTTTTTATATATTTTT-TTAAAACAGATTATAATTGAA-TACCTACCTCAAGAAA
2241 CATGAAGAAAAANNNNNNNNNNGGTAAGAAAAGTCCATTTATAG
128 CATGAAGAAAAA----------GGTAAGAAAAGTCCATTTATAG
* * *
2285 TCACCCATCCCTTCGAAAGTCTTATTACCTACTTTAAATGATTTTGTAACCTCATAATTGATTTT
1 TCACCCATCCCTTCGAAAGCCTTATTACCTACTTTAAATGATTTTATAACCTCATAATCGATTTT
*
2350 AAGTTGAATTTTTTTATATATTTTTTTAAAACAGATTATAATTGAATACCTACCTCAAGAAACGT
66 AAGTTGAATTTTTTTATATATTTTTTTAAAACAGATTATAATTGAATACCTACCTCAAGAAACAT
* *
2415 GAAGAAAAAGATATNNNNNNNNNNGAAAAGTCCATTTATAG
131 GAAGAAAAAGGTA----------AGAAAAGTCCATTTATAG
* * * * * **
2456 TCACCCAT-GCTTGCGAAAGCTTTATTACCCAATTTAAATGATTTTATAACCTTATAATTAATTT
1 TCACCCATCCCTT-CGAAAGCCTTATTACCTACTTTAAATGATTTTATAACCTCATAATCGATTT
*
2520 CAAGTTGAATTTTTTTATAT-TTTTTATTAAAACAGATTATAATTGAAT
65 TAAGTTGAATTTTTTTATATATTTTT-TTAAAACAGATTATAATTGAAT
2568 GTTTACC
Statistics
Matches: 246, Mismatches: 22, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
161 3 0.01
170 8 0.03
171 226 0.92
172 9 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.37
Consensus pattern (161 bp):
TCACCCATCCCTTCGAAAGCCTTATTACCTACTTTAAATGATTTTATAACCTCATAATCGATTTT
AAGTTGAATTTTTTTATATATTTTTTTAAAACAGATTATAATTGAATACCTACCTCAAGAAACAT
GAAGAAAAAGGTAAGAAAAGTCCATTTATAG
Done.