Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398304.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1606.0, 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: 6835
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.24
Warning! 2417 characters in sequence are not A, C, G, or T
Found at i:3533 original size:171 final size:174
Alignment explanation
Indices: 3182--3557 Score: 456
Period size: 171 Copynumber: 2.2 Consensus size: 174
3172 AGCGAGTACT
* * *
3182 AAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTGCTTACCAATGAATCCCTTTTTTTTTT
1 AAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTGCTTACCAATGAATCCCATTTTTCTTC
* * *
3247 ATGTTTCTTGACATAAACATTCAATTATAATCTGTTTTAACCAAAAAAGTAAAAAAAATTTGAAC
66 ACGTTTCTTGACAGAAACATTCAATTATAATCTGTTTAAACCAAAAAAGTAAAAAAAATTTGAAC
* * *
3312 TTAAAATAAATTTTGAGATTATAAAACCATTTAAAGTGAATAAG
131 TTAAAATAAATTTTGACATTATAAAACCATTTAAAATGAATAAC
* * * *
3356 AAGGCTTTTGAAGGAAT-AGGTGACTATAAATAGACTTTTCTTGCCTATGAAT-TCATTTTTCTT
1 AAGGCTTTTGAAGGAATGA-GTGACTATAAATAGACTTTGCTTACCAATGAATCCCATTTTTCTT
** * * * * *
3419 CACGTTTCTTGAGGGAGACATTGAATTATAGTTTGTTTAAACCAAAATA-TGAAAAAAAA-TT-A
65 CACGTTTCTTGACAGAAACATTCAATTATAATCTGTTTAAACCAAAAAAGT-AAAAAAAATTTGA
* **
3481 ACTTAAAATCAATTTTGACATTATAAAACCATTTAAAATGGGTAAC
129 ACTTAAAATAAATTTTGACATTATAAAACCATTTAAAATGAATAAC
* * * *
3527 AAGGCTTTCGAAAGAATGAGAGACTGTAAAT
1 AAGGCTTTTGAAGGAATGAGTGACTATAAAT
3558 GAACCATTCT
Statistics
Matches: 172, Mismatches: 27, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
171 66 0.38
172 4 0.02
173 55 0.32
174 47 0.27
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (174 bp):
AAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTGCTTACCAATGAATCCCATTTTTCTTC
ACGTTTCTTGACAGAAACATTCAATTATAATCTGTTTAAACCAAAAAAGTAAAAAAAATTTGAAC
TTAAAATAAATTTTGACATTATAAAACCATTTAAAATGAATAAC
Found at i:3588 original size:171 final size:173
Alignment explanation
Indices: 3263--3597 Score: 387
Period size: 171 Copynumber: 1.9 Consensus size: 173
3253 CTTGACATAA
*
3263 ACATTCAATTATAATCTGTTTTAACCAAAAAAGTAAAAAAAATTTGAACTTAAAATAAATTTTGA
1 ACATTCAATTATAATCTGTTTAAACCAAAAAAGTAAAAAAAATTTGAACTTAAAATAAATTTTGA
* * * * * * **
3328 GATTATAAAACCATTTAAAGTGAATAAGAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTT
66 CATTATAAAACCATTTAAAATGAATAACAAGGCTTTCGAAAGAATAGGAGACTATAAATAGACCA
* * * *
3393 TTCTTGCCTATGAATTCATTTTTCTTCACGTTTCTTGAGGGAG
131 TTCTTGCCAATGAATGCATTTTTCTACACATTTCTTGAGGGAG
* * * * *
3436 ACATTGAATTATAGTTTGTTTAAACCAAAATA-TGAAAAAAAA-TT-AACTTAAAATCAATTTTG
1 ACATTCAATTATAATCTGTTTAAACCAAAAAAGT-AAAAAAAATTTGAACTTAAAATAAATTTTG
** *
3498 ACATTATAAAACCATTTAAAATGGGTAACAAGGCTTTCGAAAGAAT-GAGAGACTGTAAAT-GAA
65 ACATTATAAAACCATTTAAAATGAATAACAAGGCTTTCGAAAGAATAG-GAGACTATAAATAG-A
3561 CCATTCTT-CTCAATGAATGGC-TTTTTCTACACATTTC
128 CCATTCTTGC-CAATGAAT-GCATTTTTCTACACATTTC
3598 CCAAGGCAAG
Statistics
Matches: 136, Mismatches: 21, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
170 3 0.02
171 94 0.69
172 4 0.03
173 35 0.26
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (173 bp):
ACATTCAATTATAATCTGTTTAAACCAAAAAAGTAAAAAAAATTTGAACTTAAAATAAATTTTGA
CATTATAAAACCATTTAAAATGAATAACAAGGCTTTCGAAAGAATAGGAGACTATAAATAGACCA
TTCTTGCCAATGAATGCATTTTTCTACACATTTCTTGAGGGAG
Found at i:4945 original size:173 final size:169
Alignment explanation
Indices: 4587--5179 Score: 557
Period size: 171 Copynumber: 3.5 Consensus size: 169
4577 TACAGTCTCT
* * * * * * * *
4587 CATTCTTTCAAAAGTCTTGTTACCCATTTTAAATAGTTTTATAATGTCAAAATTGATTTTAAGTT
1 CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT
* * * * * * *
4652 GAATTTTTCTTA-TATTTTTGGTTTAAGCAAACTATAATTCAATGTCTACCTCAAGAAACATGAA
66 AAATTTTT-TTACT-TTTTTGGTTAAAACAAACTATAATTGAATGTCTACATCGAGAAACGTGAA
* * * *
4716 GAAAAATGAATTCATAGGTAAAAAAAGTCCATTTATAG-TCAC
129 GAAAAAAG-ATTCATTGGTAAGAAAAGTCTATTTATAGTTC-C
* * *
4758 CTATTCCCTCAAAAGCCTTTTTACTCACTTTAAATGGTTTTATAATCTCA-AATTTTATTTTAAG
1 C-ATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAA-TTGATTTTAAG
* * * * *
4822 TTCAAATGTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTCGACATCGAGAAATGTA
64 TT-AAAT-TTTTTTACTTTTTTGGTTAAAACAAACTATAATTGAATGTCTACATCGAGAAACGTG
*
4887 AAAAAAAAAGCATTCATTGGTAAGCAAAA-TCTATTTATAGTTGCC
127 AAGAAAAAAG-ATTCATTGGTAAG-AAAAGTCTATTTATAGTT-CC
* * * * ** *
4932 CATTCCTTCAAAAGCCTTAATACTCGCTTTAAAAGATTTTGCAATCTCATAATTGATTTTAGGTT
1 CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT
* * ** * ** *
4997 AAATTTTTTTACATATTTCTTTAAAACAAACTATAATTGAATGTTTATTTCGAAAAACGTGAAGA
66 AAATTTTTTTACTTTTTTGGTTAAAACAAACTATAATTGAATGTCTACATCGAGAAACGTGAAGA
* * * *
5062 AAAAAGAGTTTATTGCTAAGAAAATTCTATTTATAGTCTCT
131 AAAAAGA-TTCATTGGTAAGAAAAGTCTATTTATAGT-TCC
* * * * *
5103 CATTCGC-TCAAAAGCATTATTACTCGCTTTAAATGGTTTTATAACCTCATAATTCATTTTAAGC
1 CATTC-CTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGT
5167 TAAATTTTTTTAC
65 TAAATTTTTTTAC
5180 ATTTGTTAAG
Statistics
Matches: 345, Mismatches: 64, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
170 5 0.01
171 144 0.42
172 58 0.17
173 123 0.36
174 14 0.04
175 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (169 bp):
CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT
AAATTTTTTTACTTTTTTGGTTAAAACAAACTATAATTGAATGTCTACATCGAGAAACGTGAAGA
AAAAAGATTCATTGGTAAGAAAAGTCTATTTATAGTTCC
Found at i:6445 original size:172 final size:172
Alignment explanation
Indices: 6116--6433 Score: 381
Period size: 172 Copynumber: 1.8 Consensus size: 172
6106 NNNNNNNNNN
* * * *
6116 AAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTTATAATTGATTTTAGGTTTAATTTTTTAT
1 AAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTTAATTTTTTAT
** * * * * * *
6181 AATTTTTTTATCAAAACAGACTACAATTGAATGTTTGCCTTAGAAAACGTGTAGAGAAACCTATT
66 AATTTTGGTATCAAAACAGACTACAATTGAATGTCTACCTCAGAAAACGTGAAGAAAAACATATT
*
6246 TATTTGAAAGAAAAGTCTATTTATAGTCTCACATACCTTCAA
131 TATTGGAAAGAAAAGTCTATTTATAGTCTCACATACCTTCAA
* * *
6288 AAGCCTTATTATTGGCTTTAACTGGTTTTATAATCTCATAATTAATTTTAAGTTTAATTTTTT-T
1 AAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTTAATTTTTTAT
* * * * * *
6352 ATATTTATGGT-T-AAAACATATTATAATTGAATGTCTATCTCATAAAACGTGAAGAAAAAAGAT
66 A-ATTT-TGGTATCAAAACAGACTACAATTGAATGTCTACCTCAGAAAACGTGAAG-AAAAACAT
*
6415 ATTTATTGGCAAGAAAAGT
128 ATTTATTGGAAAGAAAAGT
6434 TCGTTTATAG
Statistics
Matches: 120, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
171 35 0.29
172 83 0.69
173 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (172 bp):
AAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTTAATTTTTTAT
AATTTTGGTATCAAAACAGACTACAATTGAATGTCTACCTCAGAAAACGTGAAGAAAAACATATT
TATTGGAAAGAAAAGTCTATTTATAGTCTCACATACCTTCAA
Found at i:6462 original size:172 final size:172
Alignment explanation
Indices: 6116--6479 Score: 378
Period size: 172 Copynumber: 2.1 Consensus size: 172
6106 NNNNNNNNNN
* * * *
6116 AAGCCTTATTACTCGCTTTAAATGGTTTTATAATTTTATAATTGATTTTAGGTTTAATTTTTTAT
1 AAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTTAATTTTTTAT
** * * * * * *
6181 AATTTTTTTATCAAAACAGACTACAATTGAATGTTTGCCTTAGAAAACGTGTAGAGAAACCTATT
66 AATTTTGGTATCAAAACAGACTACAATTGAATGTCTACCTCAGAAAACGTGAAGAAAAACATATT
* * *
6246 TATTTGAAAGAAAAGTCTATTTATAGTCTCACATACCTTCAA
131 TATTGGAAAGAAAAGTCTATTTATAGTCACACATACCGTCAA
* * *
6288 AAGCCTTATTATTGGCTTTAACTGGTTTTATAATCTCATAATTAATTTTAAGTTTAATTTTTT-T
1 AAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTTAATTTTTTAT
* * * * * *
6352 ATATTTATGGT-T-AAAACATATTATAATTGAATGTCTATCTCATAAAACGTGAAGAAAAAAGAT
66 A-ATTT-TGGTATCAAAACAGACTACAATTGAATGTCTACCTCAGAAAACGTGAAG-AAAAACAT
* * *
6415 ATTTATTGGCAAGAAAAGT-TCGTTTATAGTCAC-CTATTCCGTCAA
128 ATTTATTGGAAAGAAAAGTCT-ATTTATAGTCACAC-ATACCGTCAA
* * *
6460 AAGCCTAATAACTCGTTTTA
1 AAGCCTTATTACTCGCTTTA
6480 NNNNNNNNNN
Statistics
Matches: 155, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
171 37 0.24
172 116 0.75
173 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (172 bp):
AAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTTAATTTTTTAT
AATTTTGGTATCAAAACAGACTACAATTGAATGTCTACCTCAGAAAACGTGAAGAAAAACATATT
TATTGGAAAGAAAAGTCTATTTATAGTCACACATACCGTCAA
Done.