Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399760.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3002.0, 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: 4087
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.23
Warning! 1632 characters in sequence are not A, C, G, or T
Found at i:1979 original size:171 final size:168
Alignment explanation
Indices: 904--2060 Score: 682
Period size: 171 Copynumber: 6.8 Consensus size: 168
894 NNNNNNNNNN
* * * * *
904 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATAGTTTTTATTAAAACATACTATAG
1 TTTTATAATCTCATAATTGATTTTAAG-TAAATTTTTTTCT--TTTTTGTTAAAACAGACTATAA
* * * *
969 TTGAATA-TCTACCTCAAGAAATATG-AAGAAAAATG-TATTCATTG-GTAAGAAAAGTCCATTT
63 TTGAATACT-TACCTCGAGAAATGTGCAA-AAAAA-GCCATTCATTGAG-AAGAAAAGTTCATTT
* * * *
1030 AGAGTCACCCATTCCTTCAAAAAGCCTATTACTCG-TTTTAAATGA
124 ATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTT-AATGG
********** * * *
1075 TTTTNNNNNNNNNNAATTGATTTTAGGTTGAATTTTTATATATTTTTTGTTAAAACAGACTATAA
1 TTTTATAATCTCATAATTGATTTTAAG-TAAATTTTT-T-TCTTTTTTGTTAAAACAGACTATAA
** * ********** *
1140 TTG-ATTTTTATCTCGAGAAATGTGCAAAAAAAGCCATTCANNNNNNNNNNAAGTCCATTTATAG
63 TTGAATACTTACCTCGAGAAATGTGCAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAG
** * *
1204 TCATTCATTCCTTCAGAAGGCTTATTACTCTCTTTTAATGG
128 TCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTTAATGG
* ******** *
1245 TTTTATAATCTCACAATTGATTTTNNNNNNNNNNTTTTTACTTTTTTTGTTAAAACAGACTATAA
1 TTTTATAATCTCATAATTGATTTT--AAGTAAATTTTTTTC-TTTTTTGTTAAAACAGACTATAA
* * * * * * *
1310 TTAAATACTTGCCTTGGGAAACGTGCAAAAAAGGCCTATTCATTGAGAAGAAAAG-CCTATTTAT
63 TTGAATACTTACCTCGAGAAATGTGCAAAAAAAGCC-ATTCATTGAGAAGAAAAGTTC-ATTTAT
* * * *
1374 TGTCACCCATTCCTTCAAAAGCCTTATTACTCGGTTTAAATGG
126 AGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTTAATGG
* *
1417 TTTTATAATCTCATAATTGATTTTAAGTTGAACTTTTTTACATTTTTTGTTAAAACAGACTATAA
1 TTTTATAATCTCATAATTGATTTTAAG-T-AAATTTTTTTC-TTTTTTGTTAAAACAGACTATAA
* * * ** * *
1482 TTAAATACTTGCCTCAAGAAAAATGCAAAAAAAGCCATTGAATGAGAAGAAAAGTTCATTTATAG
63 TTGAATACTTACCTCGAGAAATGTGCAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAG
********** * *
1547 TCACCCATTCCTTCAAANNNNNNNNNNCTCGCTTTAAATAG
128 TCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTTAATGG
* * * ** * * **
1588 TTTTATAATCTTATAATTGATTGTAAATTGATTTTTTTATATTTTTGATTAAAACATACTATANN
1 TTTTATAATCTCATAATTGATTTTAAGTAAATTTTTTTCT-TTTTTG-TTAAAACAGACTATAAT
******** * *
1653 NNNNNNNNTACCTCGAGAAACATGATG--AAACAAG-CATTCATTGAAAAAGAAAAG-TCAATTT
64 TGAATACTTACCTCGAG-AA-ATG-TGCAAAAAAAGCCATTCATTG-AGAAGAAAAGTTC-ATTT
* * *
1714 AAAGTCACCCATTCCTTCAAAAAGCTTATTACTCG-TTTTAAATGA
124 ATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTT-AATGG
********** * *
1759 TTNNNNNNNNNNATAATTGATTTTAGGTTAAATTTTTTTATATTTTTTGTTAAAACAGACTATAA
1 TTTTATAATCTCATAATTGATTTTAAG-TAAA-TTTTTT-TCTTTTTTGTTAAAACAGACTATAA
* ** * *
1824 TTGATTTTTTATCTCGAGAAATGTACAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAG
63 TTGAATACTTACCTCGAGAAATGTGCAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAG
* * * *
1889 TCACTCACTCCTTCAGAAGGCTTATTACCCGCTTTTAATGG
128 TCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTTAATGG
* * *
1930 TTTTATAATCTCACAATCGATTTTAAGTCAATTTTTTTTGCTCTTTTTGTTAAAACAGACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGT-AAATTTTTTT-CT-TTTTTGTTAAAACAGACTATAA
* * * * * *
1995 TTGAATACTTGCCTTGGGAAATGTGCAGAAAAAGCCTGTTCATTGAGAAGAAAAGTTGATTTATA
63 TTGAATACTTACCTCGAGAAATGTGCAAAAAAAGCC-ATTCATTGAGAAGAAAAGTTCATTTATA
2060 G
127 G
2061 NNNNNNNNNN
Statistics
Matches: 731, Mismatches: 219, Indels: 71
0.72 0.21 0.07
Matches are distributed among these distances:
168 1 0.00
169 15 0.02
170 152 0.21
171 342 0.47
172 201 0.27
173 17 0.02
174 3 0.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.37
Consensus pattern (168 bp):
TTTTATAATCTCATAATTGATTTTAAGTAAATTTTTTTCTTTTTTGTTAAAACAGACTATAATTG
AATACTTACCTCGAGAAATGTGCAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAGTCA
CCCATTCCTTCAAAAGGCTTATTACTCGCTTTTAATGG
Found at i:2547 original size:171 final size:171
Alignment explanation
Indices: 2201--2590 Score: 435
Period size: 171 Copynumber: 2.3 Consensus size: 171
2191 NNNNNNNNNN
* *
2201 TTATAATCTCATAATTGATTTTAAGTTTAACTTTTTTACATTTTTCTTTAAAATAGACAATAATT
1 TTATAATCTCATAATTGATTTTAAGTTTAACTTTTTTACATTTTTCTTTAAAACAAACAATAATT
* * * * * *
2266 GAATGTCTATATAGAGAAATCTGCAGAAAAAGCCATTGATTAGGAAGAAAAGTTCATTTATAGTC
66 GAAAGCCTACATAGAGAAAGCTGCAGAAAAAGCCATTCATTAGGAAGAAAAATTCATTTATAGTC
* **********
2331 ACTCATTCCTTCAAAAGCCTTATTNNNNNNNNNNAATAGTT
131 ACCCATTCCTTCAAAAGCCTTATTACTCGGTCTAAATAGTT
* * * * * *
2372 TTATAATCTTATAATTAATTTTAAGTTGAATTTTTTTACATTGTTCTTTAAAACAAACTATAATT
1 TTATAATCTCATAATTGATTTTAAGTTTAACTTTTTTACATTTTTCTTTAAAACAAACAATAATT
* * * * *
2437 GAAAGCCTGCCTCA-AGAAAGGTGTAGAAAAAGCCATTCATTAGGAAGAAAAA-TCTATTTTTAG
66 GAAAGCCTACAT-AGAGAAAGCTGCAGAAAAAGCCATTCATTAGGAAGAAAAATTC-ATTTATAG
* *
2500 TCACCCATTCTTTCGAAAGCCTTATTACTCGGTCTAAAT-GATT
129 TCACCCATTCCTTCAAAAGCCTTATTACTCGGTCTAAATAG-TT
*
2543 TTATAGTCTCATAATTGATTTTAAGTTTAACTTTTTTACATTTTTCTT
1 TTATAATCTCATAATTGATTTTAAGTTTAACTTTTTTACATTTTTCTT
2591 NNNNNNNNNN
Statistics
Matches: 178, Mismatches: 38, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
170 3 0.02
171 174 0.98
172 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.40
Consensus pattern (171 bp):
TTATAATCTCATAATTGATTTTAAGTTTAACTTTTTTACATTTTTCTTTAAAACAAACAATAATT
GAAAGCCTACATAGAGAAAGCTGCAGAAAAAGCCATTCATTAGGAAGAAAAATTCATTTATAGTC
ACCCATTCCTTCAAAAGCCTTATTACTCGGTCTAAATAGTT
Done.