Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398780.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2064.0, 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: 8089
ACGTcount: A:0.19, C:0.08, G:0.07, T:0.21
Warning! 3698 characters in sequence are not A, C, G, or T
Found at i:3962 original size:46 final size:46
Alignment explanation
Indices: 3895--4039 Score: 217
Period size: 46 Copynumber: 3.2 Consensus size: 46
3885 TTATAATCTA
3895 ACAATTAATTTTAAGTTCAATTTTTTCATATTTTTGATTAAAACAG
1 ACAATTAATTTTAAGTTCAATTTTTTCATATTTTTGATTAAAACAG
*
3941 ACAATTAATTTTAAGTTCAATTTTTTCATATTTTTGATTAAAATAG
1 ACAATTAATTTTAAGTTCAATTTTTTCATATTTTTGATTAAAACAG
* * *
3987 A-AAATAA-TTGAA-TGTCTATTTTTTCATATTTTTGATTAAAACAG
1 ACAATTAATTTTAAGT-TCAATTTTTTCATATTTTTGATTAAAACAG
4031 ACAA-TAATT
1 ACAATTAATT
4040 GAATGTCTAT
Statistics
Matches: 91, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
43 1 0.01
44 36 0.40
45 8 0.09
46 46 0.51
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.47
Consensus pattern (46 bp):
ACAATTAATTTTAAGTTCAATTTTTTCATATTTTTGATTAAAACAG
Found at i:4023 original size:44 final size:44
Alignment explanation
Indices: 3914--4049 Score: 193
Period size: 44 Copynumber: 3.0 Consensus size: 44
3904 TTTAAGTTCA
* * *
3914 ATTTTTTCATATTTTTGATTAAAACAGACAATTAATTTTAA-GTTCA
1 ATTTTTTCATATTTTTGATTAAAACAGA-AAATAA-TTGAATG-TCT
*
3960 ATTTTTTCATATTTTTGATTAAAATAGAAAATAATTGAATGTCT
1 ATTTTTTCATATTTTTGATTAAAACAGAAAATAATTGAATGTCT
*
4004 ATTTTTTCATATTTTTGATTAAAACAGACAATAATTGAATGTCT
1 ATTTTTTCATATTTTTGATTAAAACAGAAAATAATTGAATGTCT
4048 AT
1 AT
4050 CTCGAGAAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
44 50 0.60
45 6 0.07
46 27 0.33
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (44 bp):
ATTTTTTCATATTTTTGATTAAAACAGAAAATAATTGAATGTCT
Found at i:5566 original size:274 final size:272
Alignment explanation
Indices: 5042--5581 Score: 629
Period size: 274 Copynumber: 2.0 Consensus size: 272
5032 ATAGACTATA
* ** *
5042 ATTGAATGTCTCCCTTGAGAAAAGCGAACAAAAAAGCTTTCATTGGCAAGAAAAGTCCATTTATA
1 ATTGAATGACTCCCTTGAGAAAAGCGAACAAAAAAGCAATCATTGGCAAAAAAAGTCCATTTATA
* *
5107 GCCTCTCATTCCCTCAAAAGCCTTATTACTCATTTTCAATAGTTTTCTAATATAATATTTGATTT
66 GCCTCTCATTCCCTCAAAAACCTTATTACTCATTTTAAATAGTTTTCTAATATAATATTTGATTT
* * *
5172 TAAGTTGAATTTTTTAAAATTTTTTATCAAAACAGACAACAATTGACTGTCTATCTTGAAAAACG
131 TAAGTTGAATTTTTTAAAATTTTTGATCAAAACAGACAACAATTGACTGTCTATCTCGAAAAACA
* **********
5237 TGAAGACAAAAGCATTCATTGACCAGAAAAGTCCANNNNNNNNNNCCCATTCCTTCAAAAGCCTT
196 TGAAGACAAAAGCATTCATTGACCAGAAAAGCCCATTTATAGTCACCCATTCCTTCAAAAGCCTT
5302 ATTACTCATTTT
261 ATTACTCATTTT
* * *
5314 ATTGAATGACTCCCTTGAGAAAAGTTG-AGAAAAAAGCAATCATTGGCAAAAAAAAAGTCTATTT
1 ATTGAATGACTCCCTTGAGAAAAG-CGAACAAAAAAGCAATCATTGGC--AAAAAAAGTCCATTT
* * * **********
5378 ATAGCCTCTCGTTCCTTCAAAAACCTTATTACTCATTTTAAAT-GATTTTTTNNNNNNNNNNTTG
63 ATAGCCTCTCATTCCCTCAAAAACCTTATTACTCATTTTAAATAG-TTTTCTAATATAATATTTG
* * *
5442 ATTTTAAGTTGAATTTTTTTAAATTTTTGAGT-AAAACAGATAACAATTGACTGTCTATCTCGAG
127 ATTTTAAGTTGAATTTTTTAAAATTTTTGA-TCAAAACAGACAACAATTGACTGTCTATCTCGAA
* *
5506 AAACATGAAGACAAAAGCATTCATTGA-TAGGAAAAGCCCATTTATAGTCACCCCTTCCTTCAAA
191 AAACATGAAGACAAAAGCATTCATTGACCA-GAAAAGCCCATTTATAGTCACCCATTCCTTCAAA
5570 AGCCTTATTACT
255 AGCCTTATTACT
5582 AGCTTTAAAT
Statistics
Matches: 221, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
272 40 0.18
273 3 0.01
274 177 0.80
275 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.33
Consensus pattern (272 bp):
ATTGAATGACTCCCTTGAGAAAAGCGAACAAAAAAGCAATCATTGGCAAAAAAAGTCCATTTATA
GCCTCTCATTCCCTCAAAAACCTTATTACTCATTTTAAATAGTTTTCTAATATAATATTTGATTT
TAAGTTGAATTTTTTAAAATTTTTGATCAAAACAGACAACAATTGACTGTCTATCTCGAAAAACA
TGAAGACAAAAGCATTCATTGACCAGAAAAGCCCATTTATAGTCACCCATTCCTTCAAAAGCCTT
ATTACTCATTTT
Found at i:6525 original size:170 final size:171
Alignment explanation
Indices: 6333--6985 Score: 478
Period size: 171 Copynumber: 3.8 Consensus size: 171
6323 TTAAGATTAA
* * * * * *
6333 TTTTTTAATATTTTTCATTAAAATAGACTATAATTGAATGTCT-CCTTGAGAAAAGTGAACAAAA
1 TTTTTTAAAATTTTTAATTAAAACAGACTACAATTGAATGTTTACCTCGAGAAAAGTGAA-AAAA
* * * *********** *
6397 AAGCATTAACTGGCAAGAAAAGTCTATTTATAGCCTCTCATTCCTTCAAAAGNNNNNNNNNNCAT
65 AAGCATTCATTGGTAAGAAAAGTCTATTTATAGCCTCTCATTCCTTCAAAACCCTTATTACTCAC
* * *
6462 TTTAAATGGTTTTCTAATCTAATATTTGATTTTAAGTTG-AT
130 TTTAAACGGTTTTCTAATCTAATAATTGATTTTAAGTTGAAC
* * *
6503 TTTTTTAAAATTTTTAATTAAAACAGACAACAATT-AACTGTTTATCTCGAGAAATGT-AAATAC
1 TTTTTTAAAATTTTTAATTAAAACAGACTACAATTGAA-TGTTTACCTCGAGAAAAGTGAAA-A-
* * * * *
6566 AAAAGCATTCATTGATAAGAAAAGT-TCATTTATAGTCACCCATTCGTTCAAAACCCTTATTACT
63 AAAAGCATTCATTGGTAAGAAAAGTCT-ATTTATAGCCTCTCATTCCTTCAAAACCCTTATTACT
*
6630 CACTTTAAACGGTTTTCTAATCTCATAATTGATTTTAAGTTGAAC
127 CACTTTAAACGGTTTTCTAATCTAATAATTGATTTTAAGTTGAAC
* * * * * * * * *
6675 TGTTTT-ACATTTTTTATTAAAACAGATTAGAATTGAATATTTGCCTCAAGAAAAGTGAAGAAAA
1 TTTTTTAAAATTTTTAATTAAAACAGACTACAATTGAATGTTTACCTCGAGAAAAGTGAAAAAAA
* * *
6739 AGCATTCATTGGTGAGAAAAGTCTATTTATAGCCTCTCATTCCTTC-AAAGCCTTATTACTCGCT
66 AGCATTCATTGGTAAGAAAAGTCTATTTATAGCCTCTCATTCCTTCAAAACCCTTATTACTCACT
********** *
6803 TNNNNNNNNNNTATAATCTAATAATTGATTTTAAGTT-ATAC
131 TTAAACGGTTTTCTAATCTAATAATTGATTTTAAGTTGA-AC
* * * * ** * * * * *
6844 TTTTTT-ACATTTTTTATTAAAACAGACAATAATTGACGGTTTATCTCGGGAAACGTGATGACAA
1 TTTTTTAAAATTTTTAATTAAAACAGACTACAATTGAATGTTTACCTCGAGAAAAGTGA-AAAAA
* * * * * * * * * *
6908 AAGTATTCAATGGCAAGAAAAGTCTATTTATAGTCACACATTCCTTTAAAAGCATTATTACTCGC
65 AAGCATTCATTGGTAAGAAAAGTCTATTTATAGCCTCTCATTCCTTCAAAACCCTTATTACTCAC
*
6973 TTTAAATGGTTTT
130 TTTAAACGGTTTT
6986 NNNNNNNNNN
Statistics
Matches: 372, Mismatches: 99, Indels: 23
0.75 0.20 0.05
Matches are distributed among these distances:
168 1 0.00
169 92 0.25
170 120 0.32
171 149 0.40
172 10 0.03
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (171 bp):
TTTTTTAAAATTTTTAATTAAAACAGACTACAATTGAATGTTTACCTCGAGAAAAGTGAAAAAAA
AGCATTCATTGGTAAGAAAAGTCTATTTATAGCCTCTCATTCCTTCAAAACCCTTATTACTCACT
TTAAACGGTTTTCTAATCTAATAATTGATTTTAAGTTGAAC
Found at i:6852 original size:169 final size:161
Alignment explanation
Indices: 6647--6976 Score: 333
Period size: 169 Copynumber: 2.0 Consensus size: 161
6637 AACGGTTTTC
* **
6647 TAATCTCATAATTGATTTTAAGTTGAACTGTTTTACATTTTTTATTAAAACAGATTAGAATTGAA
1 TAATCTAATAATTGATTTTAAGTTGAACTGTTTTACATTTTTTATTAAAACAGACAAGAATTGAA
* * * ** * *
6712 TATTTGCCTCAAGAAAAGTGAAGA-AAAAGCATTCATTGGTGAGAAAAGTCTATTTATAGCCTCT
66 GATTTACCTCAAGAAAAGTGAAGACAAAAGCATTCAATGGCAAGAAAAGTCTATTTATAGCCACA
* *
6776 CATTCC-TTCAAAGCCTTATTACTCGCTTNNNNNNNNNNTA
131 CATTCCTTTAAAAGCATTATTACTCGCTT----------TA
* *
6816 TAATCTAATAATTGATTTTAAGTT-ATACTTTTTTACATTTTTTATTAAAACAGACAATAATTGA
1 TAATCTAATAATTGATTTTAAGTTGA-ACTGTTTTACATTTTTTATTAAAACAGACAAGAATTGA
* * * ** * * * *
6880 CGGTTTATCTCGGGAAACGTGATGACAAAAGTATTCAATGGCAAGAAAAGTCTATTTATAGTCAC
65 AGATTTACCTCAAGAAAAGTGAAGACAAAAGCATTCAATGGCAAGAAAAGTCTATTTATAGCCAC
6945 ACATTCCTTTAAAAGCATTATTACTCGCTTTA
130 ACATTCCTTTAAAAGCATTATTACTCGCTTTA
6977 AATGGTTTTN
Statistics
Matches: 135, Mismatches: 23, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
161 2 0.01
168 1 0.01
169 73 0.54
170 39 0.29
171 20 0.15
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.37
Consensus pattern (161 bp):
TAATCTAATAATTGATTTTAAGTTGAACTGTTTTACATTTTTTATTAAAACAGACAAGAATTGAA
GATTTACCTCAAGAAAAGTGAAGACAAAAGCATTCAATGGCAAGAAAAGTCTATTTATAGCCACA
CATTCCTTTAAAAGCATTATTACTCGCTTTA
Found at i:6970 original size:340 final size:333
Alignment explanation
Indices: 6476--7135 Score: 724
Period size: 340 Copynumber: 2.0 Consensus size: 333
6466 AATGGTTTTC
*
6476 TAATCTAATATTTGATTTTAAGTTGATTTTTTTAAAATTTTTAATTAAAACAGACAACAATTAAC
1 TAATCTAATAATTGATTTTAAGTTGATTTTTTTAAAATTTTTAATTAAAACAGACAACAATTAAC
* * * * *
6541 TGTTTATCTCGAGAAATGTAAATACAAAAGCATTCATTGATAAGAAAAGTTCATTTATAGTCACC
66 GGTTTATCTCGAGAAACGTAAATACAAAAGCATTCAATGACAAGAAAAGTTCATTTATAGTCACA
* *
6606 CATTCGTTCAAAACCCTTATTACTCACTTTAAACGGTTTTCTAATCTCATAATTGATTTTAAGTT
131 CATTCCTTCAAAACCATTATTACTCACTTTAAACGGTTTTCTAATCTCATAATTGATTTTAAGTT
* *
6671 GAACTG-TTTTACATTTTTTATT-AAAACAGATTAGAATTGAATATTTGCCTCAAGAAAAGTGAA
196 GAACTGTTTTTACATTTTTTATTAAAAAAAG-TTAGAATTGAATATCTGCCTCAAGAAAAGTGAA
* *
6734 GAAAAA-GCATTCATTGGTGAGAAAAGTCTATTTATAGCCTCTCATTCCTTCAA-AGCCTTATTA
260 GAAAAAGGCATTCATTGATGAGAAAAGTCTATTTATAGCCTCCCATTCCTTCAATAGCCTTATTA
6797 CTCGCTTNNNNNNNNNNTA
325 CTCGCTT----------TA
* * * *
6816 TAATCTAATAATTGATTTTAAGTT-ATACTTTTTT-ACATTTTTTATTAAAACAGACAATAATTG
1 TAATCTAATAATTGATTTTAAGTTGAT--TTTTTTAAAATTTTTAATTAAAACAGACAACAATTA
* * * *
6879 ACGGTTTATCTCGGGAAACGT-GATGACAAAAGTATTCAATGGCAAGAAAAG-TCTATTTATAGT
64 ACGGTTTATCTCGAGAAACGTAAAT-ACAAAAGCATTCAATGACAAGAAAAGTTC-ATTTATAGT
* * * * **********
6942 CACACATTCCTTTAAAAGCATTATTACTCGCTTTAAATGGTTTTNNNNNNNNNNAATTGATTTTA
127 CACACATTCCTTCAAAACCATTATTACTCACTTTAAACGGTTTTCTAATCTCATAATTGATTTTA
* * * * * * **
7007 AGTTGAATTGTTTTTACATTTTTTGTTAAAAAAAGTTATAATTGAATGTCTGTCTCGAGAACCGT
192 AGTTGAACTGTTTTTACATTTTTTATTAAAAAAAGTTAGAATTGAATATCTGCCTCAAGAAAAGT
* * *
7072 GAAGAAAAAGGCATTCATTGATTAGAAAAGTCTATTTATAGGCTCCCATTCCTTTAATAGCCTT
257 GAAGAAAAAGGCATTCATTGATGAGAAAAGTCTATTTATAGCCTCCCATTCCTTCAATAGCCTT
7136 TTTAATAGTT
Statistics
Matches: 267, Mismatches: 45, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
339 6 0.02
340 154 0.58
341 53 0.20
342 48 0.18
343 6 0.02
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.37
Consensus pattern (333 bp):
TAATCTAATAATTGATTTTAAGTTGATTTTTTTAAAATTTTTAATTAAAACAGACAACAATTAAC
GGTTTATCTCGAGAAACGTAAATACAAAAGCATTCAATGACAAGAAAAGTTCATTTATAGTCACA
CATTCCTTCAAAACCATTATTACTCACTTTAAACGGTTTTCTAATCTCATAATTGATTTTAAGTT
GAACTGTTTTTACATTTTTTATTAAAAAAAGTTAGAATTGAATATCTGCCTCAAGAAAAGTGAAG
AAAAAGGCATTCATTGATGAGAAAAGTCTATTTATAGCCTCCCATTCCTTCAATAGCCTTATTAC
TCGCTTTA
Done.