Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400801.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3976.0, 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: 2241
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.27
Warning! 567 characters in sequence are not A, C, G, or T
Found at i:1520 original size:172 final size:170
Alignment explanation
Indices: 1008--2239 Score: 1046
Period size: 172 Copynumber: 7.2 Consensus size: 170
998 NNNNNNNNNN
* * * * * *
1008 GACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCATGGTAAACATTCGATTCTATTCT
1 GACTTTTCTTGCCAATGAAT-CCTTTTTCTTCATGATTCTTAAGGTAAACATTCAATTCTAGTCT
* *
1073 ATTTTAATAAAAAATGTACAA-AACATTCAAATTTAAATCAATTTTGAGATTATAAAACT-ATTT
65 GTTTTAACAAAAAATGTACAAGAA-A-TCAAATTTAAATCAATTTTGAGATTATAAAA-TAATTT
* * *
1136 AAATTGAGTAATAAGGCTCTTGAAGGAATGGGTGACTATAAATG
127 AAAGTGAGTTATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
* * * * * *
1180 GACTTTTATTGCCAATGAATGCCTTTTTCTTTAAAT-TTTTTTAAGTTAAACATTCAATTATAGT
1 GACTTTTCTTGCCAATGAAT-CCTTTTTC-TT-CATGATTCTTAAGGTAAACATTCAATTCTAGT
* * * * ** * **
1244 CTG-TTTAATC-AAAAATATA-AAAAAATTCAACTTAAAATCAATTACG-GTATTACAAAACCAT
63 CTGTTTTAA-CAAAAAATGTACAAGAAA-TCAAATTTAAATCAATTTTGAG-ATTATAAAATAAT
* * * *
1305 TTAAAGCGAGTTATAATGCTTTTGAAGGTATGGTTGACTATAAATG
125 TTAAAGTGAGTTATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
* * * * *
1351 GACTTTTCTTGGCAATAAATCCATTTTTCTTCATGATTCTTAAGGTAGATATTCAATTCTAGCCT
1 GACTTTTCTTGCCAATGAATCC-TTTTTCTTCATGATTCTTAAGGTAAACATTCAATTCTAGTCT
* * * *
1416 ATTTTAACGAAAAATGTACAATGAAATCAAATTTAAACCAATTTTGAGATTAGAAAATAATTTAA
65 GTTTTAACAAAAAATGTACAA-GAAATCAAATTTAAATCAATTTTGAGATTATAAAATAATTTAA
*
1481 AGTGAGTTATAAGGC-TTTGAAAGGAATGGGTGACTATAAATT
129 AGTGAGTTATAAGGCTTTTG-AAGGAATGGGTGACTATAAATG
* * *
1523 GACTTTTATTGCCAATGAATGCCTTTTTCTTTATG--TCTCTAGAGGTAAACATTCAATTATAGT
1 GACTTTTCTTGCCAATGAAT-CCTTTTTCTTCATGATTCT-TA-AGGTAAACATTCAATTCTAGT
* * * *** ** * *
1586 CTG-TTTAACCAAAAATGTAAAAAAAAATTTTATTTAAAATCAA-TTACAGCATTACAAAATCAT
63 CTGTTTTAACAAAAAATGT-ACAAGAAATCAAATTT-AAATCAATTTTGAG-ATTATAAAATAAT
* * ** * *
1649 TTAAAGCT-AGTAAAAATACTTTTGAAGGTATGAGTGACTATAAATG
125 TTAAAG-TGAGTTATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
* ** * * *
1695 GACATTTCTTATCAATGAATGCATTTTTCTTCATGATTCTTAAGGTAGACATTCAATCCTAGTCT
1 GACTTTTCTTGCCAATGAAT-CCTTTTTCTTCATGATTCTTAAGGTAAACATTCAATTCTAGTCT
* * *
1760 GTTTTAACTAAAAATGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAATAATTTAA
65 GTTTTAACAAAAAATGTAC-AAGAAATCAAATTTAAATCAATTTTGAGATTATAAAATAATTTAA
* *
1825 AGTGAGTAATAAGGCTTTTGAA-CAAGTGGGTGACTATAAATG
129 AGTGAGTTATAAGGCTTTTGAAGGAA-TGGGTGACTATAAATG
* * * * * *** * * * * *
1867 AACTTCTCTTGCTAATGAATGCTATTTTCTTTAT-ATTTCTCGGGGTAGACGTTCAATTATAATA
1 GACTTTTCTTGCCAATGAATCCT-TTTTCTTCATGA-TTCTTAAGGTAAACATTCAATTCTAGTC
* * * * * * **
1931 TGTTTTAACCAAAAAA-CTA-AAGAATTTAAACTTAAAATCAATTTTGGGAATATAAAACCATTT
64 TGTTTTAA-CAAAAAATGTACAAGAAATCAAA-TTTAAATCAATTTTGAGATTATAAAATAATTT
* ** *
1994 AAAGTGA-TTAATAAGGCTTTTGAAGTAATAAGTGACTATAAATA
127 AAAGTGAGTT-ATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
** * * **
2038 GACTTTTCTTGCCAATGAAAACTTTTTCCTTCATGTTTCTCAAGGTCTACATTCAATTCTAGTCT
1 GACTTTTCTTGCCAATGAATCCTTTTT-CTTCATGATTCTTAAGGTAAACATTCAATTCTAGTCT
* *
2103 GTTTTAATAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAA-ACATTTA
65 GTTTTAACAAAAAATGTAC-AAGAAATCAAATTTAAATCAATTTTGAGATTATAAAATA-ATTTA
* * * *
2167 AACTGAG-TAGGAAGGCTTTTGAAGGAATAGGTGGCTATAAATG
128 AAGTGAGTTA-TAAGGCTTTTGAAGGAATGGGTGACTATAAATG
* *
2210 GACTTTTCTTGTCAATGAATGTCTTTTTCT
1 GACTTTTCTTGCCAATGAAT-CCTTTTTCT
2240 AT
Statistics
Matches: 846, Mismatches: 170, Indels: 88
0.77 0.15 0.08
Matches are distributed among these distances:
169 2 0.00
170 53 0.06
171 256 0.30
172 443 0.52
173 87 0.10
174 5 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (170 bp):
GACTTTTCTTGCCAATGAATCCTTTTTCTTCATGATTCTTAAGGTAAACATTCAATTCTAGTCTG
TTTTAACAAAAAATGTACAAGAAATCAAATTTAAATCAATTTTGAGATTATAAAATAATTTAAAG
TGAGTTATAAGGCTTTTGAAGGAATGGGTGACTATAAATG
Found at i:2130 original size:343 final size:340
Alignment explanation
Indices: 1008--2239 Score: 1430
Period size: 343 Copynumber: 3.6 Consensus size: 340
998 NNNNNNNNNN
* * * * * * *
1008 GACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCATGGTAAACATTCGATTCTATTCT
1 GACTTTTCTTGCCAATGAAAACATTTTTCTTCATGATTCTCAAGGTAGACATTCAATTCTAGTCT
1073 ATTTTAATAAAAAATGTACAAA-ACATTCAAATTTAAATCAATTTTGAGATTATAAAACT-ATTT
66 ATTTTAATAAAAAATGTACAAAGA-ATTCAAATTTAAATCAATTTTGAGATTATAAAA-TAATTT
* *
1136 AAATTGAGTAATAAGGCTCTTGAAGGAATGGGTGACTATAAATGGACTTTTATTGCCAATGAATG
129 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTATTGCCAATGAATG
* * * *
1201 CCTTTTTCTTTAAATTTTTTTA-AGTTAAACATTCAATTATAGTCTGTTTAATCAAAAATATAAA
194 CCTTTTTCTTT--ATATTTCTAGAGGTAAACATTCAATTATAGTCTGTTTAACCAAAAATAT-AA
* * *
1265 AAAATTCAACTTAAAATCAATTACGGTATTACAAAACCATTTAAAGCGAGTT-ATAATGCTTTTG
256 AAAATTTAACTTAAAATCAATTACGGCATTACAAAACCATTTAAAGTGA-TTAATAATGCTTTTG
*
1329 AAGGTATGGTTGACTATAAATG
320 AAGGTATAG-TGACTATAAATG
* * * * *
1351 GACTTTTCTTGGCAAT-AAATCCATTTTTCTTCATGATTCTTAAGGTAGATATTCAATTCTAGCC
1 GACTTTTCTTGCCAATGAAA-ACATTTTTCTTCATGATTCTCAAGGTAGACATTCAATTCTAGTC
** * * * *
1415 TATTTTAACGAAAAATGTACAATGAAATCAAATTTAAACCAATTTTGAGATTAGAAAATAATTTA
65 TATTTTAATAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAATAATTTA
* *
1480 AAGTGAGTTATAAGGC-TTTGAAAGGAATGGGTGACTATAAATTGACTTTTATTGCCAATGAATG
130 AAGTGAGTAATAAGGCTTTTG-AAGGAATGGGTGACTATAAATGGACTTTTATTGCCAATGAATG
* * *
1544 CCTTTTTCTTTATGTCTCTAGAGGTAAACATTCAATTATAGTCTGTTTAACCAAAAATGTAAAAA
194 CCTTTTTCTTTATATTTCTAGAGGTAAACATTCAATTATAGTCTGTTTAACCAAAAA--T-ATAA
* * * * * * *
1609 AAAATTTTATTTAAAATCAATTACAGCATTACAAAATCATTTAAAGCT-AGTAAAAATACTTTTG
256 AAAATTTAACTTAAAATCAATTACGGCATTACAAAACCATTTAAAG-TGATTAATAATGCTTTTG
1673 AAGGTATGAGTGACTATAAATG
320 AAGGTAT-AGTGACTATAAATG
* ** ** * *
1695 GACATTTCTTATCAATGAATGCATTTTTCTTCATGATTCTTAAGGTAGACATTCAATCCTAGTCT
1 GACTTTTCTTGCCAATGAAAACATTTTTCTTCATGATTCTCAAGGTAGACATTCAATTCTAGTCT
* *
1760 GTTTTAACT-AAAAATGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAATAATTTA
66 ATTTTAA-TAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAATAATTTA
* * * * *
1824 AAGTGAGTAATAAGGCTTTTGAA-CAAGTGGGTGACTATAAATGAACTTCTCTTGCTAATGAATG
130 AAGTGAGTAATAAGGCTTTTGAAGGAA-TGGGTGACTATAAATGGACTTTTATTGCCAATGAATG
* * * * * *
1888 -CTATTTTCTTTATATTTCTCGGGGTAGACGTTCAATTATAATATGTTTTAACCAAAAA-ACTAA
194 CCT-TTTTCTTTATATTTCTAGAGGTAAACATTCAATTATAGTCTG-TTTAACCAAAAATA-TAA
* ** * * * *
1951 AGAATTTAAACTTAAAATCAATTTTGGGAATATAAAACCATTTAAAGTGATTAATAAGGCTTTTG
256 AAAATTT-AACTTAAAATCAATTACGGCATTACAAAACCATTTAAAGTGATTAATAATGCTTTTG
*
2016 AA-GTAATAAGTGACTATAAATA
320 AAGGT-AT-AGTGACTATAAATG
* **
2038 GACTTTTCTTGCCAATGAAAAC-TTTTTCCTTCATGTTTCTCAAGGTCTACATTCAATTCTAGTC
1 GACTTTTCTTGCCAATGAAAACATTTTT-CTTCATGATTCTCAAGGTAGACATTCAATTCTAGTC
*
2102 TGTTTTAATAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAA-ACATTT
65 TATTTTAATAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAATA-ATTT
* ** * * * *
2166 AAACTGAGTAGGAAGGCTTTTGAAGGAATAGGTGGCTATAAATGGACTTTTCTTGTCAATGAATG
129 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTATTGCCAATGAATG
*
2231 TCTTTTTCT
194 CCTTTTTCT
2240 AT
Statistics
Matches: 756, Mismatches: 107, Indels: 52
0.83 0.12 0.06
Matches are distributed among these distances:
341 7 0.01
342 58 0.08
343 400 0.53
344 271 0.36
345 20 0.03
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (340 bp):
GACTTTTCTTGCCAATGAAAACATTTTTCTTCATGATTCTCAAGGTAGACATTCAATTCTAGTCT
ATTTTAATAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAATAATTTAA
AGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTATTGCCAATGAATGCC
TTTTTCTTTATATTTCTAGAGGTAAACATTCAATTATAGTCTGTTTAACCAAAAATATAAAAAAT
TTAACTTAAAATCAATTACGGCATTACAAAACCATTTAAAGTGATTAATAATGCTTTTGAAGGTA
TAGTGACTATAAATG
Done.