Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397385.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_378.0, 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: 30104
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.19
Warning! 15107 characters in sequence are not A, C, G, or T
Found at i:10040 original size:171 final size:170
Alignment explanation
Indices: 9764--10574 Score: 664
Period size: 171 Copynumber: 4.7 Consensus size: 170
9754 NNNNNNNNNN
* * * * * *
9764 TAATTGTATGTTTACCTTGAGAAACATGAAGAAAAATATATGCATTAGCAAGAAAAGTCCATTTA
1 TAATTGAATGTTTACCTTAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTA
* *********
9829 TAGTCACCCATACCTTC-ANNNNNNNNNNTACTCACTTTAAATGATTTTATAACCTCATAATTGA
66 TAGTCACCCATGCCTTCGA-AAGCCTTATTACTCACTTTAAATGATTTTATAACCTCATAATTGA
* *
9893 TTTTGAATTGAATTTTTTTATATTTTTTATTAAAATAGATTA
130 TTTT-AATTGAACTTTTTTATATTTTTTATTAAAACAGATTA
* * * * *
9935 TGATTAAATGTTTACCTTAAGACACGTGAAGAAAAATATATCCATTGGTAAGAAAAGTCCATTTA
1 TAATTGAATGTTTACCTTAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTA
********** * * * *
10000 TAGTCANNNNNNNNNNCGAAAGCCTTATTACTCGCTTTAAATTATTTTATAATCTCATAATTGGT
66 TAGTCACCCATGCCTTCGAAAGCCTTATTACTCACTTTAAATGATTTTATAACCTCATAATTGAT
* *
10065 TTTAGTTTGAA-TTGCTTTCATATTTTTTATTAAAACAGATTA
131 TTTA-ATTGAACTT--TTTTATATTTTTTATTAAAACAGATTA
* ** * * * * *
10107 TAATTGAAT-TCTACAATGAGAAACGTGAAGACAAAGATATCCATTGACAAAAAAAGTTCATTTA
1 TAATTGAATGTTTACCTTAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTA
* * * * ** * * ***
10171 TTGTAACTCATGCCTTGGAAAAACTTATTATTCACTTTAAAT-AGTTTTTTAACCTCATAANNNN
66 TAGTCACCCATGCCTTCGAAAGCCTTATTACTCACTTTAAATGA-TTTTATAACCTCATAA-TTG
******* * * *
10235 NNNNNNGTTGAACTTTTTTATATTTATTATTAAAATAGATTG
129 ATTTTAATTGAACTTTTTTATATTTTTTATTAAAACAGATTA
* * * * *
10277 TAATTGTATGTTTA-CTTCTAGAAATGTGAAGAAAAATATATCCATTAGCAAGAAAAGTCCATTT
1 TAATTGAATGTTTACCTT-AAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTT
* * *
10341 ATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGCTTTT-TAATCTCATAATT-
65 ATAGTCACCCATGCCTTCGAAAGCCTTATTACTCACTTTAAAT-GATTTTATAACCTCATAATTG
*
10404 AGTTTTAAGTTGAACTTTTTTATATTTGTTATTAAAACAGATTA
129 A-TTTTAA-TTGAACTTTTTTATATTTTTTATTAAAACAGATTA
* * * * * *
10448 TAATTGAATGTTTGCCTCAGGAAACATGAAGAAAAAGATATCCACTGGCAAGAAAAGTCCATTTG
1 TAATTGAATGTTTACCTTAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTA
* * * * * * *
10513 TACTCACCTATGCCTTCGAAAACCTTATTACTCACTTTAAATGTTTTTGTAATCTCGTAATT
66 TAGTCACCCATGCCTTCGAAAGCCTTATTACTCACTTTAAATGATTTTATAACCTCATAATT
10575 NNNNNNNNNN
Statistics
Matches: 493, Mismatches: 132, Indels: 30
0.75 0.20 0.05
Matches are distributed among these distances:
170 41 0.08
171 411 0.83
172 41 0.08
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (170 bp):
TAATTGAATGTTTACCTTAAGAAACGTGAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTA
TAGTCACCCATGCCTTCGAAAGCCTTATTACTCACTTTAAATGATTTTATAACCTCATAATTGAT
TTTAATTGAACTTTTTTATATTTTTTATTAAAACAGATTA
Found at i:10208 original size:342 final size:342
Alignment explanation
Indices: 9857--10574 Score: 777
Period size: 342 Copynumber: 2.1 Consensus size: 342
9847 NNNNNNNNNN
* *
9857 TACTCACTTTAAATGATTTTATAACCTCATAATTGATTTTGAATTGAATTTTTTTATATTTTTTA
1 TACTCACTTTAAATGATTTTATAACCTCATAATTGATTTTGAATTGAACTTTTTTATATTTATTA
* * * *
9922 TTAAAATAGATTATGATTAAATGTTTACCTT-AAGACACGTGAAGAAAAATATATCCATTGGTAA
66 TTAAAATAGATTATAATTAAATGTTTA-CTTCAAGAAACGTGAAGAAAAATATATCCATTAGCAA
********** *
9986 GAAAAGTCCATTTATAGTCANNNNNNNNNNCGAAAGCCTTATTACTCGCTTTAAAT-TATTTTAT
130 GAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGATTTT-T
* *
10050 AATCTCATAATTGGTTTT-AGTTTGAA-TTGCTTTCATATTTTTTATTAAAACAGATTATAATTG
194 AATCTCATAATTAGTTTTAAG-TTGAACTT--TTTCATATTTGTTATTAAAACAGATTATAATTG
* * * * * **
10113 AAT-TCTACAATGA-GAAACGTGAAGACAAAGATATCCATTGACAAAAAAAGTTCATTTATTGTA
256 AATGTCTAC-ATCAGGAAACATGAAGAAAAAGATATCCACTGACAAAAAAAGTCCATTTATACTA
*
10176 A-CTCATGCCTTGGAAAAACTTAT
320 ACCT-ATGCCTTCGAAAAACTTAT
* * ***********
10199 TATTCACTTTAAAT-AGTTTTTTAACCTCATAANNNNNNNNNNGTTGAACTTTTTTATATTTATT
1 TACTCACTTTAAATGA-TTTTATAACCTCATAATTGATTTTGAATTGAACTTTTTTATATTTATT
* ** * *
10263 ATTAAAATAGATTGTAATTGTATGTTTACTTCTAGAAATGTGAAGAAAAATATATCCATTAGCAA
65 ATTAAAATAGATTATAATTAAATGTTTACTTCAAGAAACGTGAAGAAAAATATATCCATTAGCAA
*
10328 GAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGCTTTTTA
130 GAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGATTTTTA
*
10393 ATCTCATAATTAGTTTTAAGTTGAACTTTTTTATATTTGTTATTAAAACAGATTATAATTGAATG
195 ATCTCATAATTAGTTTTAAGTTGAACTTTTTCATATTTGTTATTAAAACAGATTATAATTGAATG
* * * * * * *
10458 TTTGCCTCAGGAAACATGAAGAAAAAGATATCCACTGGCAAGAAAAGTCCATTTGTACTCACCTA
260 TCTACATCAGGAAACATGAAGAAAAAGATATCCACTGACAAAAAAAGTCCATTTATACTAACCTA
*
10523 TGCCTTCGAAAACCTTAT
325 TGCCTTCGAAAAACTTAT
* * * *
10541 TACTCACTTTAAATGTTTTTGTAATCTCGTAATT
1 TACTCACTTTAAATGATTTTATAACCTCATAATT
10575 NNNNNNNNNN
Statistics
Matches: 305, Mismatches: 62, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
341 40 0.13
342 255 0.84
343 10 0.03
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.38
Consensus pattern (342 bp):
TACTCACTTTAAATGATTTTATAACCTCATAATTGATTTTGAATTGAACTTTTTTATATTTATTA
TTAAAATAGATTATAATTAAATGTTTACTTCAAGAAACGTGAAGAAAAATATATCCATTAGCAAG
AAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGATTTTTAA
TCTCATAATTAGTTTTAAGTTGAACTTTTTCATATTTGTTATTAAAACAGATTATAATTGAATGT
CTACATCAGGAAACATGAAGAAAAAGATATCCACTGACAAAAAAAGTCCATTTATACTAACCTAT
GCCTTCGAAAAACTTAT
Found at i:10817 original size:170 final size:154
Alignment explanation
Indices: 10607--10933 Score: 264
Period size: 170 Copynumber: 2.0 Consensus size: 154
10597 NNNNNAAAAC
* * * ** *
10607 AGATTATAATTAAATGTCTGCCTCATAAAATGTAAAGAAAATA-ATATCTATTGGGAAGAGAAGT
1 AGATTATAATTAAATATCTGCCTCAGAAAATG-AAAGAAAA-AGATATCCATTGCCAAGAAAAGT
* *
10671 CCATTTATAATCACCCATGCCTTTAAAAGCCTTATCACTCGGTTTAAAT-GATTTTATAACCTCA
64 CCATTTATAATCACCCACGCCTTTAAAAGCCTTATCACTCGCTTTAAATAG-TTTTATAACCTCA
*
10735 TAATTGATTTTAATTTCAATTTTTTANNNNNNNNNNNNNNNT
128 TAATTAATTTTAATTTCAATTTTTTA---------------T
*
10777 AGATTATAATTGAATATCTGCCTCAAGAAACATG-AAGAAAAAGATATCCATTGCCAAGAAAAGT
1 AGATTATAATTAAATATCTGCCTC-AGAAA-ATGAAAGAAAAAGATATCCATTGCCAAGAAAAGT
* ** * * * *
10841 CCATTTATACTCACCCACGCCTTTGGAAGCCTTATTACTCGCTTTAAATAGTTTTTTTATCTCAT
64 CCATTTATAATCACCCACGCCTTTAAAAGCCTTATCACTCGCTTTAAATAGTTTTATAACCTCAT
* * *
10906 AATTAATTTTGAGTTGAACTTTTTTAT
129 AATTAATTTTAATTTCAA-TTTTTTAT
10933 A
1 A
10934 TTTATTGTTA
Statistics
Matches: 132, Mismatches: 20, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
156 2 0.02
169 1 0.01
170 114 0.86
171 12 0.09
172 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.35
Consensus pattern (154 bp):
AGATTATAATTAAATATCTGCCTCAGAAAATGAAAGAAAAAGATATCCATTGCCAAGAAAAGTCC
ATTTATAATCACCCACGCCTTTAAAAGCCTTATCACTCGCTTTAAATAGTTTTATAACCTCATAA
TTAATTTTAATTTCAATTTTTTAT
Found at i:16025 original size:171 final size:167
Alignment explanation
Indices: 15700--16313 Score: 488
Period size: 171 Copynumber: 3.6 Consensus size: 167
15690 NNNNNNNNNN
* * * * * * *
15700 TTTTGAAGGCATGGGTGA-TAATAAATAGACTTCTCTTGTCAATGGATACCTTTTCTTCATGTTT
1 TTTTGAAGGCATAGGTGACT-ATAAATGGAATTTTCTTGCCAATGGATATCTTTTCTTCACGTTT
* * * * * * * *
15764 CTCGATGTAGACATTCAATTACAATCTGTTGTTATAAAAA-AATAAAAAAATCTAAATTAAAATC
65 CTTGAGGTAAACATT-AATTATAATCTGTT-TCATAAAAATTATAAAAAAATTTAACTTAAAATC
**********
15828 AATTATGAGGNNNNNNNNNNATTTAAAGCGAGTAATAAGGC
128 AATTATGA-GATTATAAAACATTTAAAGCGAGTAATAAGGC
* * *
15869 TTTTGATGGCATAGGTGACTATAAATGGAATTCTCTTGCTAATGGATATCTTTCTCTTCACGTTT
1 TTTTGAAGGCATAGGTGACTATAAATGGAATTTTCTTGCCAATGGATATCTTT-TCTTCACGTTT
* **
15934 CTTGAGGTAAACACTTAATTACAATCTGTTTCAGTAGAAAA-TATAAAAAGGTTTAACTTAAAA-
65 CTTGAGGTAAACA-TTAATTATAATCTGTTTCA-TA-AAAATTATAAAAAAATTTAACTTAAAAT
*
15997 CTAATTATGAGATTCA-AAAACCATTTAAAGCGAGTAATAAGAC
127 C-AATTATGAGATT-ATAAAA-CATTTAAAGCGAGTAATAAGGC
* * * *
16040 TTTCGAAGGCATATGTGACTATAAAT-GAACTTTTCTTGCCAATGGATATCTTTTTCATCATGTT
1 TTTTGAAGGCATAGGTGACTATAAATGGAA-TTTTCTTGCCAATGGATATC-TTTTCTTCACGTT
* * * * *
16104 TCTCGCGGTAAACATTTAATTATAATATGTTTTTATAAAAATTATAAAAAAATTTAACTTGAAAT
64 TCTTGAGGTAAACA-TTAATTATAATCTG-TTTCATAAAAATTATAAAAAAATTTAACTTAAAAT
* * *********
16169 CAATTATGAGGTTATAAAATANNNNNNNNNNAGTAATAAGGC
127 CAATTATGAGATTATAAAACA-TTTAAAGCGAGTAATAAGGC
* * *
16211 TTTTGAAGGCAT-GTGTGACT-TAAATGGACTTTTCTTGCCAATGAATATATTTTCTTCACGTTT
1 TTTTGAAGGCATAG-GTGACTATAAATGGAATTTTCTTGCCAATGGATATCTTTTCTTCACGTTT
* *
16274 CTTGAGGTAGACATTAAATTATAATCTGTTTTAATAAAAA
65 CTTGAGGTAAACATT-AATTATAATCTG-TTTCATAAAAA
16314 NNNNNNNNNN
Statistics
Matches: 360, Mismatches: 67, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
168 2 0.01
169 90 0.25
170 71 0.20
171 189 0.52
172 8 0.02
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.36
Consensus pattern (167 bp):
TTTTGAAGGCATAGGTGACTATAAATGGAATTTTCTTGCCAATGGATATCTTTTCTTCACGTTTC
TTGAGGTAAACATTAATTATAATCTGTTTCATAAAAATTATAAAAAAATTTAACTTAAAATCAAT
TATGAGATTATAAAACATTTAAAGCGAGTAATAAGGC
Found at i:21174 original size:171 final size:169
Alignment explanation
Indices: 20742--21179 Score: 556
Period size: 171 Copynumber: 2.6 Consensus size: 169
20732 NNNNNNNNTA
* * * * *
20742 AAATAGATTATAATTGAATGTTTGCCTTGGGAAACGTGAAGAAAAAGATATCCATTCGCAAGCAA
1 AAATAGATTATAATTGATTGTCTGTCTTGAGAAACGTGAAGAAAAAGATATCCATT-GCAAGAAA
* * * * * * *
20807 TGTCCATTTATAGTATCTCATCCCTTCGGAAGCCTTATTACTTGCTTTAAATATTTTTTATAACT
65 AGTCCATTTGTAGTACCT-ATGCCTTCGAAAGCCTTATTACTCGCTTTAAATATCTTTTATAACT
* *
20872 CATAATTGATTTTAATTTGAATTTTTTTATATTTTTTATTC
129 CACAATTGATTTTAATTTGAATGTTTTTATATTTTTTATTC
* * * * *
20913 AAATGGATTATAATTGATTGTCTATCTCGAGAAACATGAATAAAAAGATATCCATTGGCAAGAAA
1 AAATAGATTATAATTGATTGTCTGTCTTGAGAAACGTGAAGAAAAAGATATCCATT-GCAAGAAA
* *
20978 AGTCCATTTAG-GGTAACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATA-CTTTTATAAC
65 AGTCCATTT-GTAGT-ACCTATGCCTTCGAAAGCCTTATTACTCGCTTTAAATATCTTTTATAA-
* *
21041 CTCACAATTGATTTTGATTTGAATGTTTTTATATTTTTTATTG
127 CTCACAATTGATTTTAATTTGAATGTTTTTATATTTTTTATTC
* *
21084 AAATAGATTATAATTGATTGTCTGTCTTGAGAAACGTGAAGGAAAAGATATCCATTGATAAGAAA
1 AAATAGATTATAATTGATTGTCTGTCTTGAGAAACGTGAAGAAAAAGATATCCATTG-CAAGAAA
*
21149 AGTCCATTTGTACTCACCTATGCCTTCGAAA
65 AGTCCATTTGTAGT-ACCTATGCCTTCGAAA
21180 NNNNNNNNNN
Statistics
Matches: 227, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
170 10 0.04
171 215 0.95
172 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (169 bp):
AAATAGATTATAATTGATTGTCTGTCTTGAGAAACGTGAAGAAAAAGATATCCATTGCAAGAAAA
GTCCATTTGTAGTACCTATGCCTTCGAAAGCCTTATTACTCGCTTTAAATATCTTTTATAACTCA
CAATTGATTTTAATTTGAATGTTTTTATATTTTTTATTC
Done.