Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402565.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5638.0, 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, 988
Length: 1647
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.30
Warning! 335 characters in sequence are not A, C, G, or T
Found at i:372 original size:163 final size:154
Alignment explanation
Indices: 195--563 Score: 470
Period size: 163 Copynumber: 2.3 Consensus size: 154
185 NNNNNNNNNN
* *
195 CAAAAGCTTTATTACTCGCTTTAAGTGATTTTATAATATCATATTTGATTTTAAGTTGAATTTTT
1 CAAAAGCCTTATTACTCGCTTTAAGTGATTTTATAATATCATATCTGATTTTAAGTTGAATTTTT
* *
260 TTACNNNNNNNNNNAAAACAGACTATAATTGAATGTCTATTTCGAGAAACATGAAGATTGATTGG
66 TTAC---------AAAAACAGACTATAATTGAATGTCTATTTCGAGAAACATGAAAATTGATTGG
*
325 CAACAAAAGTTCATTTATAGTTATTC-ATTCCTT
122 CAAAAAAAGTTCATTTATAGTTA-TCAATTCCTT
*
358 CAAAAGCCTTATTACTCGCTTTAAGTGATTTTATAATATCATATCTGATTTTAAGTTGAGTTTTT
1 CAAAAGCCTTATTACTCGCTTTAAGTGATTTTATAATATCATATCTGATTTTAAGTTGAATTTTT
* *
423 TTACANNNNNNNNNNAAATAGACTATAATTGAATGTCTATTTCGAGAAACATGAAAATTGATTGG
66 TTACA---------AAAACAGACTATAATTGAATGTCTATTTCGAGAAACATGAAAATTGATTGG
488 CAAAAAAAGTTCATTTATAGTTATCAATTCCTT
122 CAAAAAAAGTTCATTTATAGTTATCAATTCCTT
* *
521 CAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATATCATA
1 CAAAAGCCTTATTACTCGCTTTAAGTGATTTTATAATATCATA
564 ATTGNNNNNN
Statistics
Matches: 186, Mismatches: 10, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
162 2 0.01
163 184 0.99
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.38
Consensus pattern (154 bp):
CAAAAGCCTTATTACTCGCTTTAAGTGATTTTATAATATCATATCTGATTTTAAGTTGAATTTTT
TTACAAAAACAGACTATAATTGAATGTCTATTTCGAGAAACATGAAAATTGATTGGCAAAAAAAG
TTCATTTATAGTTATCAATTCCTT
Found at i:1130 original size:172 final size:171
Alignment explanation
Indices: 833--1647 Score: 560
Period size: 171 Copynumber: 4.8 Consensus size: 171
823 NNNNNNNNNN
* * *
833 TGATTTTAAGTTGAATTGTTTTACATTTTTCATTAAAACAGACTATAATTGAAAT-CCTACCTTG
1 TGATTTTAAGTTGAATTGTTTTACATTTTTAATTAAAACAGACTATAATTG-AATGTCTACCTTA
* * * * * * *
897 AGAAACATGTAGAAAAAGCCATTTATCGAGTAA-AAAAGTCCATTTATATTCACCTATTCCTTCA
65 AGAAACGTGAAGAAAAAGACATTCATTGAG-AAGAAAAGTCTATTTATAGTCACCTATTCCTTCA
* **
961 AAAGCCTAATTACTTGCTTTAAATTTATTTTATAATCTAATATT
129 AAAGCCTAATTACTCGCTTTAAA-TTATTTTATAATCTAATAAC
*
1005 TGATTTTAAGTT-AAATGTTTTTACATTTCTT-ATTAAAACAGACTATAATTGAATGTCTA-CTT
1 TGATTTTAAGTTGAATTG-TTTTACATTT-TTAATTAAAACAGACTATAATTGAATGTCTACCTT
* *
1067 CAAGAAACGTGAAGAAAACGACATTCATTGAGAAGAAAAGTCTATTTATAGTCACCCATTCCTTC
64 -AAGAAACGTGAAGAAAAAGACATTCATTGAGAAGAAAAGTCTATTTATAGTCACCTATTCCTTC
********** *
1132 NNNNNNNNNNTTACTCGCTTTAAATTATTTTATAATCTCATAAC
128 AAAAGCCTAATTACTCGCTTTAAATTATTTTATAATCTAATAAC
* * *
1176 TGATTTGAAGTTGAATTGCTTTACATTTTTAATTAAAACAAACTATAATTGAATGTCTACCTTAA
1 TGATTTTAAGTTGAATTGTTTTACATTTTTAATTAAAACAGACTATAATTGAATGTCTACCTTAA
* * ** * *
1241 GAAATGTGAACAAAAAGGA-ATTCATTGCCAAGAAAAGT-TCATTTATAGTCACTTATTCCTTTA
66 GAAACGTGAAGAAAAA-GACATTCATTGAGAAGAAAAGTCT-ATTTATAGTCACCTATTCCTTCA
*********** ** *
1304 AAAGCCTTNNNNNNNNNNTTAAATGGTTTTATAATCTCAA-AAT
129 AAAGCCTAATTACTCGCTTTAAATTATTTTATAATCT-AATAAC
* * ** * * * * **
1347 TGATTTTAGGTTCAATT-TTGTTACATTTTTTGTCAAAACAGATTATAATTGAATATCTACATCG
1 TGATTTTAAGTTGAATTGTT-TTACATTTTTAATTAAAACAGACTATAATTGAATGTCTACCTTA
*** * * * * * *
1411 AGATGTGAGAAGAAAAA-AGCATTCACTGACAAAAAAAGTCCATTTATAGTCACGC-ATTCTTTC
65 AGAAACGTGAAGAAAAAGA-CATTCATTGAGAAGAAAAGTCTATTTATAGTCAC-CTATTCCTTC
* * * * * *
1474 AATAGCCTTATTACTCGCTTTAAA-TAGTTTTATAGTATCATAAT
128 AAAAGCCTAATTACTCGCTTTAAATTA-TTTTATAATCTAATAAC
* ********** * *
1518 TGAATTTAAGTTGAATNNNNNNNNNNTTTTAGTTAAAACAGACTATAATTGAATGTC-AACTTAG
1 TGATTTTAAGTTGAATTGTTTTACATTTTTAATTAAAACAGACTATAATTGAATGTCTACCTTA-
* * * * *
1582 AGAAACATGGAGAAAAAGGCATTCATTG-GCAAGAAATGCCTATTTATAGTCACCTATTCCTTCA
65 AGAAACGTGAAGAAAAAGACATTCATTGAG-AAGAAAAGTCTATTTATAGTCACCTATTCCTTCA
1646 AA
129 AA
Statistics
Matches: 485, Mismatches: 135, Indels: 47
0.73 0.20 0.07
Matches are distributed among these distances:
169 1 0.00
170 8 0.02
171 355 0.73
172 119 0.25
173 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.36
Consensus pattern (171 bp):
TGATTTTAAGTTGAATTGTTTTACATTTTTAATTAAAACAGACTATAATTGAATGTCTACCTTAA
GAAACGTGAAGAAAAAGACATTCATTGAGAAGAAAAGTCTATTTATAGTCACCTATTCCTTCAAA
AGCCTAATTACTCGCTTTAAATTATTTTATAATCTAATAAC
Done.