Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399636.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2885.0, 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: 2370
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.30
Warning! 372 characters in sequence are not A, C, G, or T
Found at i:604 original size:171 final size:166
Alignment explanation
Indices: 423--901 Score: 480
Period size: 167 Copynumber: 2.8 Consensus size: 166
413 NNNNNNNNNN
* * *
423 ATAAGGCTTTTGCAGGAATGGGTGACTATAAATAGACTTTTCTTTCTATTGTATGGCTTTTCCTA
1 ATAAGGCTTTT-CAGGAAT-GGTGACTATAAATGGACTTTTC-TTCTA-TGAATGGCTTTTTCTA
* * * *
488 CACCTTTCCTGAGATAAGCATTCAATTATAATCTATTTTAATGAAAAATGTAAAACAATTCAATT
62 CACCTTTCCTAAGACAAACATTCAATTATAATCTGTTTTAATGAAAAATGTAAAACAATTCAA-T
* ** * *
553 TAAAATCAATTATAAGGTTATAAA-ACT-ATTTCGAGTGAGTA
126 TAAAATCAATTATAAGATTA-AAACA-TAATTTAAAGCGAGAA
* * *
594 ATAAGGCTTTTAAAGGAATGGTGACTATAAATGGACTTTTCTT-TATGAATGTCTTTTTCTTCAC
1 ATAAGGCTTTT-CAGGAATGGTGACTATAAATGGACTTTTCTTCTATGAATGGCTTTTTCTACAC
* * * * ** * *
658 CTTTCTTAAGGCAAACATTCCATTATTATCTGTTTTAACCAAAAATGCAAAACAATTCAGATAAA
65 CTTTCCTAAGACAAACATTCAATTATAATCTGTTTTAATGAAAAATGTAAAACAATTCA-ATTAA
*
723 AATCAATTATGAGATTAAAACATAATTTAAAGCGAGAA
129 AATCAATTATAAGATTAAAACATAATTTAAAGCGAGAA
* * * *
761 ATAAAGCTTTTCAAGGAGTAAGTGACTCTAAATGGACTTTTCTTCTCAATGAATGG-TTTATTCT
1 ATAAGGCTTTTC-AGGAAT-GGTGACTATAAATGGACTTTTCTTCT--ATGAATGGCTTT-TTCT
* * * * * * *
825 ACACGTTTCTTAGGACAAACATTCAATTATAGTCTGTTTTAATGAAAAGTGTAAAAAAATTTAAC
61 ACACCTTTCCTAAGACAAACATTCAATTATAATCTGTTTTAATGAAAAATGTAAAACAATTCAA-
890 TTAAAATCAATT
125 TTAAAATCAATT
902 NNNNNNNNNN
Statistics
Matches: 253, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
166 4 0.02
167 107 0.42
168 25 0.10
169 3 0.01
170 25 0.10
171 89 0.35
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (166 bp):
ATAAGGCTTTTCAGGAATGGTGACTATAAATGGACTTTTCTTCTATGAATGGCTTTTTCTACACC
TTTCCTAAGACAAACATTCAATTATAATCTGTTTTAATGAAAAATGTAAAACAATTCAATTAAAA
TCAATTATAAGATTAAAACATAATTTAAAGCGAGAA
Found at i:1588 original size:171 final size:171
Alignment explanation
Indices: 1298--1619 Score: 434
Period size: 171 Copynumber: 1.9 Consensus size: 171
1288 NNNNNNNTTA
*
1298 TGAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGCATGACTATAAATGGA
1 TGAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGCATGACTATAAAAGGA
* * * * *
1363 CTTTTCTTCCCAATGAATTGCTTTTTCTATATGTTTTTTAAGGCAGGCATTCAATTATAGTCTAT
66 CTTTTCTTCCCAATGAATTGCTTTTTCTATATATTTCTCAAGGCAGACATTCAATTATAGCCTAT
*
1428 TGTAACTAAAAATGTAAAAAAATTCAACTTAAAACTAATTT
131 TGTAACCAAAAATGTAAAAAAATTCAACTTAAAACTAATTT
* * * **
1469 TGAGGTTATAAAACTA-TTAAAGGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAAGG
1 TGAGATTATAAAACAATTTAAA-GCAAGTAATAAGGCTTTTGAAGGAATGCATGACTATAAAAGG
* * * *
1533 ACTTTTTTTGCGAATGAA-TGCCTTTTTCT-TCATATTTCTCAAGGTAGACATTCAATTATAGCC
65 ACTTTTCTTCCCAATGAATTG-CTTTTTCTAT-ATATTTCTCAAGGCAGACATTCAATTATAGCC
* *
1596 TTTTTTAACCAAAAATGTAAAAAA
128 TATTGTAACCAAAAATGTAAAAAA
1620 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
170 8 0.06
171 122 0.94
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (171 bp):
TGAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGCATGACTATAAAAGGA
CTTTTCTTCCCAATGAATTGCTTTTTCTATATATTTCTCAAGGCAGACATTCAATTATAGCCTAT
TGTAACCAAAAATGTAAAAAAATTCAACTTAAAACTAATTT
Found at i:2045 original size:171 final size:170
Alignment explanation
Indices: 1750--2370 Score: 470
Period size: 171 Copynumber: 3.6 Consensus size: 170
1740 NNNNNNNNNN
* * *
1750 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCATACCAATGAATGCCTTTT
1 AGTAATAAGGC-TTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTACCAATGAATGACTTTT
* * * * * *****
1815 TCCTCATGTTTTTCGAGGTAAAGATTTAATTATAGTCTGTTTTAACCAAAAATGTAAAAANNNNN
65 TCCTCATGTTTTTCGAGGCAAAGATTCAATCATAGTCTGTTTTAACAAAAAACGTAAAAACATTC
***** *
1880 NNNNNAAAATAAATTATGAGATTATAAAATAATTTAAAGTG
130 AACTTAAAATAAATTATGAGATTATAAAACAATTTAAAGTG
** *
1921 AGTAATAAGGCTATTGAAGGAATGAGTGACTATAAATAGACTTTTCTTTTCAATTAATGACTTTT
1 AGTAATAAGGCT-TTGAAGGAATGAGTGACTATAAATAGACTTTTCTTACCAATGAATGACTTTT
1986 T-CT-ATGCATTTGTT-GAGGC-AAGAATTCAATCATAGTCTGTTTTAACAAAAAACGTAAAAAC
65 TCCTCATG--TTT-TTCGAGGCAAAG-ATTCAATCATAGTCTGTTTTAACAAAAAACGTAAAAAC
* * * *
2047 ATTCAACTTGAAATTAATTTTGAGATTATAAAACCATTTAAAGTG
126 ATTCAACTTAAAATAAATTATGAGATTATAAAACAATTTAAAGTG
* * * * *
2092 AGTATTAAGGCTTTGAAAGGAATGGGTTG-CTATAAATAGACTTTTCTTGCTAATGAATGTCTTT
1 AGTAATAAGGCTTTG-AAGGAATGAG-TGACTATAAATAGACTTTTCTTACCAATGAATGACTTT
* ** * * * * * * * *****
2156 CTCCTCACATTTCTAGAGGTAGAGATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAANNNNN
64 TTCCTCATGTTTTTCGAGGCAAAGATTCAATCATAGTCTGTTTTAACAAAAAACGTAAAAACATT
***** * **
2221 NNNNNTAAAATCAATTATGAGATTATAAAACAATTTAAACCG
129 CAACTTAAAATAAATTATGAGATTATAAAACAATTTAAAGTG
* * * *
2263 AGTAATAAAGCTTTCGAAGGAATTG-GTGACCAT-AATGGACTTTTCTT-GCAACTGAATG-CGT
1 AGTAATAAGGCTTT-GAAGGAA-TGAGTGACTATAAATAGACTTTTCTTACCAA-TGAATGAC-T
* * * * * * *
2324 TTTTCTTCACGTTTCTT-GAAGTAGACATTCAATTATAGTCTGTTTTA
62 TTTTCCTCATGTTT-TTCGAGGCAAAGATTCAATCATAGTCTGTTTTA
Statistics
Matches: 363, Mismatches: 70, Indels: 35
0.78 0.15 0.07
Matches are distributed among these distances:
169 6 0.02
170 71 0.20
171 274 0.75
172 11 0.03
173 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.35
Consensus pattern (170 bp):
AGTAATAAGGCTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTACCAATGAATGACTTTTT
CCTCATGTTTTTCGAGGCAAAGATTCAATCATAGTCTGTTTTAACAAAAAACGTAAAAACATTCA
ACTTAAAATAAATTATGAGATTATAAAACAATTTAAAGTG
Done.