Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398963.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2245.0, 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: 10020
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.29
Warning! 2464 characters in sequence are not A, C, G, or T
Found at i:849 original size:169 final size:168
Alignment explanation
Indices: 176--924 Score: 529
Period size: 171 Copynumber: 4.4 Consensus size: 168
166 NNNNNNNNNN
* * * * *
176 TAACCTCATAATTGATTTGAATTTGAATTTTTT-TAAGATTTTTATTAAATCAAATTATAATTGA
1 TAACCTCATAATT-ATTTTAACTTGAATTTTTTAT-A-TTTTTTATTAAAACAGATTATAATTGA
* * * * * * * * * * * * *
240 ATGTTTTTCTCGAGAAACGTGAAGAAAAAGATATCCATTAGTAAGAAAAGTTCATTTATAGTAAC
63 ATGTCTGTC-CAAAAAATGTAAAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATTGTCAC
* ** * * *
305 TCATCCCTTCGAAAGCCTTATTACTCGCTTTAAATAATTTTT
127 CCAAGCCTTCGAAAGCCTTATTACTCGATTTAAATGATTTTA
* * ********* *
347 TAATCTCATGATTAGTTTTANNNNNNNNNNTTTTATA-TTTTTATTAAAACAGATTTTAATTGAA
1 TAACCTCATAATTA-TTTTA-ACTTGAATTTTTTATATTTTTTATTAAAACAGATTATAATTGAA
** * *
411 TGTCTACCTCAAAAAATGTAAAAAAAAATTATATCCATTGGCAAGAGAAGTCCATTTATTGTCA-
64 TGTCTGTC-CAAAAAATGT-AAAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATTGTCAC
* * * *
475 CAAAGCCTTCAAAAGTCTTATTACTCGGTTTAAATGATTTTA
127 CCAAGCCTTCGAAAGCCTTATTACTCGATTTAAATGATTTTA
** * *
517 TAACCTCATAATTCATTTTAACTTGAATTTTTTAATAACTTTTATTAAAACAAATCATAATTGAA
1 TAACCTCATAATT-ATTTTAACTTGAATTTTTT-ATATTTTTTATTAAAACAGATTATAATTGAA
* * * * * *
582 TGTCTGTCCAGAGAAACGTGAAGAAAATGGTATCCATTGGCAAGAAAAGTCCATTTATAGTCACC
64 TGTCTGTCCA-AAAAATGTAAAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATTGTCACC
* ********** *
647 CATGCCTT-GAAAAGNNNNNNNNNNCGCTTTAAATGATTTTA
128 CAAGCCTTCG-AAAGCCTTATTACTCGATTTAAATGATTTTA
* *
688 TAACCCCATAATTGATTTTAATTTGAATTTTTTAT-TTTTTTATTAAAACAGATTATAATTGAAN
1 TAACCTCATAATT-ATTTTAACTTGAATTTTTTATATTTTTTATTAAAACAGATTATAATTGAA-
********* * *
752 NNNNNNNNNAAAAAATATAAAGAAAATGATATCCATTGACAAGAGAAGTCCATTTATTGTCACCC
64 TGTCTGTCCAAAAAATGTAAAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATTGTCACCC
* *
817 ACGCCTTCGAAAGCCTTATTACTCGATTTAAAT-AGTTTTG
129 AAGCCTTCGAAAGCCTTATTACTCGATTTAAATGA-TTTTA
* * ** *
857 TAATCTAATAATTAGTTTTAAGATGAACTTTTTTATATTTTTTATTAAAATAGATTATAATTGAA
1 TAACCTCATAATTA-TTTTAACTTGAA-TTTTTTATATTTTTTATTAAAACAGATTATAATTGAA
922 TGT
64 TGT
925 TTGNNNNNNN
Statistics
Matches: 437, Mismatches: 125, Indels: 33
0.73 0.21 0.06
Matches are distributed among these distances:
168 2 0.00
169 118 0.27
170 142 0.32
171 169 0.39
172 5 0.01
173 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.38
Consensus pattern (168 bp):
TAACCTCATAATTATTTTAACTTGAATTTTTTATATTTTTTATTAAAACAGATTATAATTGAATG
TCTGTCCAAAAAATGTAAAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATTGTCACCCAA
GCCTTCGAAAGCCTTATTACTCGATTTAAATGATTTTA
Found at i:3021 original size:170 final size:171
Alignment explanation
Indices: 2788--3213 Score: 597
Period size: 170 Copynumber: 2.5 Consensus size: 171
2778 AAGGAACGTG
* * *
2788 AAGAAAAAGATATCCATTGCCAAGA-ATAGTCCATTTATAGTCATCCATACCTTCGAAAGCCTTA
1 AAGAAAATGATATCCATTGGCAAGAGA-AGTCCATTTATAGTCACCCATACCTTCGAAAGCCTTA
* ********** *
2852 TGACTCGCTTTAAATGGTTTTTTAATCTCATAATTNNNNNNNNNNTGAACTTTTTTATATTTTTT
65 TGACTCGCTTTAAATGATTTTTTAATCTCATAATTTGGTTTAAGTTGAACTTTTTTACATTTTTT
* *
2917 ATTAAAACAGATTATAATTGAATGTCTACCTCAAAAAA-ATA
130 ATTAAAACAGAATATAATTGAACGTCTACCTCAAAAAATATA
* * *
2958 AAGAAAATGATATCCATCGGCAAGAGAAGTCTATTTATTGTCACCCATACCTTCGAAAGCCTTAT
1 AAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATAGTCACCCATACCTTCGAAAGCCTTAT
*
3023 GACTTGCTTTAAATGATTTTTTAATCTCATAATTTGGTTTAAGTTGAACTTTTTTACATTTTTTA
66 GACTCGCTTTAAATGATTTTTTAATCTCATAATTTGGTTTAAGTTGAACTTTTTTACATTTTTTA
3088 TTAAAACAGAATATAATTGAACGTCTACCTCAAAAAATATA
131 TTAAAACAGAATATAATTGAACGTCTACCTCAAAAAATATA
* *
3129 AAGAAAATAATATCCATTGGCAAGAGAAGTCCATTTATGGTCACCCATACCTTCGAAAGCCTTAT
1 AAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATAGTCACCCATACCTTCGAAAGCCTTAT
* *
3194 TACTCGCCTTAAAT-ATTTTT
66 GACTCGCTTTAAATGATTTTT
3214 ATAACCTCNN
Statistics
Matches: 226, Mismatches: 28, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
170 150 0.66
171 76 0.34
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.35
Consensus pattern (171 bp):
AAGAAAATGATATCCATTGGCAAGAGAAGTCCATTTATAGTCACCCATACCTTCGAAAGCCTTAT
GACTCGCTTTAAATGATTTTTTAATCTCATAATTTGGTTTAAGTTGAACTTTTTTACATTTTTTA
TTAAAACAGAATATAATTGAACGTCTACCTCAAAAAATATA
Found at i:3740 original size:171 final size:168
Alignment explanation
Indices: 3441--3985 Score: 430
Period size: 171 Copynumber: 3.2 Consensus size: 168
3431 NNNNTTTAAT
* ** * *
3441 CTCATAATTAGTTTTAAGTTGGACTTTTTTATATTTTTTGTTGAAACAAATTATAATTGAATATT
1 CTCATAATTAATTTTAA-TTAAATTTTTTTATA-TTTTT-TTAAAACAAATTATAATTGAATATT
* * ********** *
3506 TACCATGAGAAACATGAAGAAAAAGATATCCATTAG-CAAGAANNNNNNNNNNATAGCCACCCAT
63 TACCTTGAGAAACATGAAGAAAAAGATATCCATTGGAC-AGAAAAGTCCATTTATAGTCACCCAT
* *
3570 GCCTTCAAAAGCCTTATTACTCGCTCTAAATGATTTTATAAC
127 GCCTTCAAAAGCCGTATTACTCGCTTTAAATGATTTTATAAC
* * *
3612 CTTATAATTAATTTTAATCTAAATTTTTTTATATTTTTTACTAAAAGAAATTATAATTGAATTTT
1 CTCATAATTAATTTTAAT-TAAATTTTTTTATATTTTTT--TAAAACAAATTATAATTGAATATT
*
3677 TTCCTTGAGAAACATGAAGAAAAAGATATCCATTGGACAGAAAAGTCCATTTATAGTCACCCATG
63 TACCTTGAGAAACATGAAGAAAAAGATATCCATTGGACAGAAAAGTCCATTTATAGTCACCCATG
* ********** * * * *
3742 TCTTNNNNNNNNNNATTACTCACTTTAAATGCTTTTTTAAT
128 CCTTCAAAAGCCGTATTACTCGCTTTAAATGATTTTATAAC
** * * * * * * *
3783 CTCACGATTCATTTTAAGTTGAACTTTTTTATATTTTTGTTAAAATAGATTAAAATTGAA-AGTC
1 CTCATAATTAATTTTAA-TTAAATTTTTTTATATTTTT-TTAAAACAAATTATAATTGAATA-TT
* ** * * * * *
3847 TGCCTCAAAAAACGTAAAGAAAATGATATCCATTGGTA-AGAAAAGTCCATTTATAATCACCCAT
63 TACCTTGAGAAACATGAAGAAAAAGATATCCATTGG-ACAGAAAAGTCCATTTATAGTCACCCAT
* *
3911 GCCTTCAAAAGCCGTATTACTCGATTTAAATAATTTTATAAC
127 GCCTTCAAAAGCCGTATTACTCGCTTTAAATGATTTTATAAC
*
3953 CTCATAATTGATTTTAATTTAAATTTTTTTATA
1 CTCATAATTAATTTTAA-TTAAATTTTTTTATA
3986 ATTNNNNNNN
Statistics
Matches: 286, Mismatches: 80, Indels: 17
0.75 0.21 0.04
Matches are distributed among these distances:
169 1 0.00
170 130 0.45
171 152 0.53
172 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.37
Consensus pattern (168 bp):
CTCATAATTAATTTTAATTAAATTTTTTTATATTTTTTTAAAACAAATTATAATTGAATATTTAC
CTTGAGAAACATGAAGAAAAAGATATCCATTGGACAGAAAAGTCCATTTATAGTCACCCATGCCT
TCAAAAGCCGTATTACTCGCTTTAAATGATTTTATAAC
Found at i:3969 original size:170 final size:169
Alignment explanation
Indices: 3563--3985 Score: 411
Period size: 170 Copynumber: 2.5 Consensus size: 169
3553 NNNNNATAGC
* * * *
3563 CACCCATGCCTTCAAAAGCCTTATTACTCGCTCTAAATGATTTTATAACCTTATAATTAATTTTA
1 CACCCATGCCTTCAAAAGCCGTATTACTCGATTTAAATGATTTTATAACCTCATAATTAATTTTA
* ** * * ** * *
3628 ATCTAAATTTTTTTATATTTTTTACTAAAAGAAATTATAATTGAATTTTTTCCTTGAGAAACATG
66 AT-TAAATTTTTTTATATTTTTTA-TAAAAGAAATTAAAATTGAAAGTCTGCCTCAAAAAACATA
*
3693 AAGAAAAAGATATCCATTGGACAGAAAAGTCCATTTATAGT
129 AAGAAAAAGATATCCATTGGACAGAAAAGTCCATTTATAAT
* ********** * * * ** *
3734 CACCCATGTCTTNNNNNNNNNNATTACTC-ACTTTAAATGCTTTTTTAATCTCACGATTCATTTT
1 CACCCATGCCTTCAAAAGCCGTATTACTCGA-TTTAAATGATTTTATAACCTCATAATTAATTTT
* * * * *
3798 AAGTTGAACTTTTTTATATTTTTGT-TAAAATAGATTAAAATTGAAAGTCTGCCTCAAAAAACGT
65 AA-TTAAATTTTTTTATATTTTT-TATAAAAGAAATTAAAATTGAAAGTCTGCCTCAAAAAACAT
*
3862 AAAGAAAATGATATCCATTGGTA-AGAAAAGTCCATTTATAAT
128 AAAGAAAAAGATATCCATTGG-ACAGAAAAGTCCATTTATAAT
* *
3904 CACCCATGCCTTCAAAAGCCGTATTACTCGATTTAAATAATTTTATAACCTCATAATTGATTTTA
1 CACCCATGCCTTCAAAAGCCGTATTACTCGATTTAAATGATTTTATAACCTCATAATTAATTTTA
3969 ATTTAAATTTTTTTATA
66 A-TTAAATTTTTTTATA
3986 ATTNNNNNNN
Statistics
Matches: 190, Mismatches: 57, Indels: 11
0.74 0.22 0.04
Matches are distributed among these distances:
170 124 0.65
171 64 0.34
172 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.39
Consensus pattern (169 bp):
CACCCATGCCTTCAAAAGCCGTATTACTCGATTTAAATGATTTTATAACCTCATAATTAATTTTA
ATTAAATTTTTTTATATTTTTTATAAAAGAAATTAAAATTGAAAGTCTGCCTCAAAAAACATAAA
GAAAAAGATATCCATTGGACAGAAAAGTCCATTTATAAT
Found at i:4750 original size:171 final size:169
Alignment explanation
Indices: 4458--5013 Score: 589
Period size: 171 Copynumber: 3.3 Consensus size: 169
4448 NNNNNNNNNN
* * * * * *
4458 AAGAAAAAGATATTCATTGGCAAGAATAGTCCATTTATGGTCATCCACT-CCTTCGAAAGCCTTA
1 AAGAAAATGATATCCATTGGCAAGAAAAGTACATTTATAGTCACCCA-TACCTTCGAAAGCCTTA
* *
4522 TTACTCGCTTAAAATGATTTTATAATCTCATAATTAGTTTTAAGTTGAAATTTTTTATATTTTTT
65 TTACTCGCTTTAAATGATTTTATAAACTCATAATTAGTTTTAAGTTGAAATTTTTTATA-TTTTT
* *
4587 ATTGAAAA-AGATTATAATTGAATGCTTACCTCGAGAAACATA
129 ATT-AAAACAGATTATAATTGAATG-TTGCCTCAAGAAACATA
* * *********
4629 AAGAAAAAGATATCCATTAGCAAGAAAAGT-CNNNNNNNNNNCACCCATACCTTCGAAAGCCTTA
1 AAGAAAATGATATCCATTGGCAAGAAAAGTAC-ATTTATAGTCACCCATACCTTCGAAAGCCTTA
* * * ** *
4693 TTACTCGCTTTAAATGCTTTTTTAAACTCATGATTAGTTTTAAGTTGAACCTTTTTATATTTTTC
65 TTACTCGCTTTAAATGATTTTATAAACTCATAATTAGTTTTAAGTTGAAATTTTTTATATTTTTA
* * * *
4758 TTAAAATAGATTATAATCGAATGTCTGCCTCAAAAAACGTA
130 TTAAAACAGATTATAATTGAATGT-TGCCTCAAGAAACATA
* * * * *
4799 AAGAAAATGATATCCATTGGTAAGAGAAGTACATTTATAGTCACCCATGCCTTCAAAAGCTTTAT
1 AAGAAAATGATATCCATTGGCAAGAAAAGTACATTTATAGTCACCCATACCTTCGAAAGCCTTAT
* * * * *
4864 TGCTCGGTTTAAATGATTTTATAAACTCATAATTCA-TTTTTATTTGAATTTTTTTATAATTTTT
66 TACTCGCTTTAAATGATTTTATAAACTCATAATT-AGTTTTAAGTTGAAATTTTTTAT-ATTTTT
* * *
4928 ATTAAAACAGATTATAATTGAATATTTGCCTAAAGAAACATG
129 ATTAAAACAGATTATAATTGAAT-GTTGCCTCAAGAAACATA
**
4970 AAGAAAATGATATCCATTGGCAAGAAAAGTTTATTTATAGTCAC
1 AAGAAAATGATATCCATTGGCAAGAAAAGTACATTTATAGTCAC
5014 NNNNNNNNNN
Statistics
Matches: 314, Mismatches: 63, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
169 5 0.02
170 129 0.41
171 179 0.57
172 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.36
Consensus pattern (169 bp):
AAGAAAATGATATCCATTGGCAAGAAAAGTACATTTATAGTCACCCATACCTTCGAAAGCCTTAT
TACTCGCTTTAAATGATTTTATAAACTCATAATTAGTTTTAAGTTGAAATTTTTTATATTTTTAT
TAAAACAGATTATAATTGAATGTTGCCTCAAGAAACATA
Done.