Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402274.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5357.0, 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: 2249
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.37
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:329 original size:171 final size:171
Alignment explanation
Indices: 127--2056 Score: 652
Period size: 171 Copynumber: 11.3 Consensus size: 171
117 NNNNNNNNNN
* * * *
127 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATTATTGATTTTAGGTTTATTCTTTTT-A
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGCTTGA-ACTTTTTGA
** * *
191 AGTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAGGAAATGTGAAGAAAGAGGTATTC
65 AGTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGTATTC
* * *
256 TTTGGTAA-AAAAAGACCCTTTATAGTCACACATTCCTTC-AA
130 ATTGGCAAGAAAAAGA-CATTTATAGTCACACATTCCTTCAAA
*
297 AGACCTTATTACTCATTTTAAATGGTTTTATAATCTCATAATTGATTTTAGCTTGAACTTTTTGA
1 AG-CCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGCTTGAACTTTTTGA
* ** * *
362 CGTTTTTTGTTAGAACAGATTATAATTGAATGTCTACCTTAGGAAACATGAAGAAAAAATTATTC
65 AGTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGTATTC
* * * *
427 ATTGGCAAGAAAAATATATTTATAGTCACCCATTCCTTGAAA
130 ATTGGCAAGAAAAAGACATTTATAGTCACACATTCCTTCAAA
***********
469 AGCCTTATTACTCACTTTNNNNNNNNNNGTAATCTCATAATTGATTTTAAG-TTGAACTTTTTGA
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTT-AGCTTGAACTTTTTGA
* * ** ** * *
533 CA-TTTTTGGTTAGAACAGAATATAATTGAATGTCTGTCTTGGGAAACCTAAAG-AAAAAGATAT
65 -AGTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAG-TAT
**********
596 TCATTGGCAAG-AAAAGTNNNNNNNNNNTCATC-CATTCCTTCAAA
128 TCATTGGCAAGAAAAAG-ACATTTATAGTCA-CACATTCCTTCAAA
* * * **
640 AGCCTTATTACTTATTTTAAATGGTTTTATAATCTCA-AATTTGATTTAAATTTGAA-TTCTTT-
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAA-TTGATTTTAGCTTGAACTT-TTTG
* * * * * * * * * *
702 ATACATTTTTGGTTAAAAAAAATTATAATTCATTGTCTACCT-TGAGAAACATGAAGAAAAAGGC
64 A-A-GTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAG-GAAACATGAAGAAAAAAGT
* *** * *
766 ATTCATTAGCAAGAAAACTCCATTTATAGTCACTCATTCTTTCAAA
126 ATTCATTGGCAAGAAAAAGACATTTATAGTCACACATTCCTTCAAA
* *********** * * *
812 AGTCTTATTACTNNNNNNNNNNAGTTTTATAATCTCAAAATTAATTTTAAG-TTGAA-TTTTTTA
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTT-AGCTTGAACTTTTTGA
* * * * * * * ** * * ***
875 CA-TATTT-GGTTAAAAAAGGA-AACAATTGAATGTTTGCC-CTGAGAAATGTAAAGTAAAATCC
65 -AGT-TTTGGGTTAGAACA-GATTATAATTGAATGTCTACCTCAG-GAAACATGAAGAAAAAAGT
** * * * ** * *
936 AACCATTGGC-ACAAAAAGTCCATTTATAGTCACTCAAGCCATCGCAA
126 ATTCATTGGCAAGAAAAAG-ACATTTATAGTCACACATTCCTTC-AAA
* ** * * * * * *
983 ACCCTTATTACTTGCTTTGAATGGTTTTATAAACTAATAATT-AGTTTTAAG-TTAAATTTTTTT
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGA-TTTT-AGCTTGAACTTTTTG
* * * * * * * * * * * *
1046 ATA-TTTTTGGTTAAAACAAATTAGAATTGAATGCCCACCTTC-TGAGACGTTAAGAAAAAGGCA
64 A-AGTTTTGGGTTAGAACAGATTATAATTGAATGTCTACC-TCAGGAAACATGAAGAAAAAAGTA
* * * * * * *
1109 GTCATTGGTAAG--AAAGTCTATTTACAGTTACCCATACCTTCAAA
127 TTCATTGGCAAGAAAAAGAC-ATTTATAGTCACACATTCCTTCAAA
* ********* *
1153 AGTCTTATTACTCACTTTAAATGGTTTTATAATAC-CANNNNNNNNNNTAAG-TTGAA-TATTTT
1 AGCCTTATTACTCACTTTAAATGGTTTTATAAT-CTCA-TAATTGATTTTAGCTTGAACT-TTTT
* *** * * * * * * * ** * ** *
1215 TACA-TTTTTTATTAAAACAGACTACAATTGGATCTCTATCTCAAGAAATGTAAAGAAAATGGCA
63 GA-AGTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGTA
* * * *
1279 TTCATTGGCAAG-AAAAGTCCATTTATAGTGACCCATTTCTTCAAA
127 TTCATTGGCAAGAAAAAG-ACATTTATAGTCACACATTCCTTCAAA
********** * * * **
1324 AGCCTTATTACTCACTTTAAATNNNNNNNNNNTTTCAAAATTGATTTAAATTTGAA-TTCTTTGT
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGCTTGAACTT-TTTG-
** ** * * * ** * * *
1388 ACTTTTTTAGTTAAAACATATTATAATTGAATGTCAAGTTTAAGAAACATGAA-AAAAAAGGCAT
64 AAGTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAA-GTAT
* *** * *
1452 TCATTGACAAGAAAATTCCATTTATAGTCACTCATTCCTTTAAA
128 TCATTGGCAAGAAAAAGACATTTATAGTCACACATTCCTTCAAA
********** * * *
1496 AGCNNNNNNNNNNACTTTAAATGGTTTTATAATCTCATAGTTGATTTTAGGTTGAAATTTTT-AA
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGCTTGAACTTTTTGAA
* ** * * * * * * * * *
1560 CATTTTTTGTTAGAATAGATTATAATCGAATGTTTACCTTAGAAAACCTAAATAAAAAGGTATTC
66 -GTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGTATTC
* *
1625 ATTGGCAAG-AAAAGTCCATTTATAGTCACTCATTCCTTC-AA
130 ATTGGCAAGAAAAAG-ACATTTATAGTCACACATTCCTTCAAA
* * * * **
1666 AGCCCTATTACTCACTTTAAATGGTTTTATAGTCACATAATTGATTTAAATTTGAA-TTCTTTGT
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGCTTGAACTT-TTTG-
* * * * * * ** *
1730 ACA-TTTTTGGTTAAAACATATTATGATTGAATGTCTTCCTC-GATAAATGTGAA-AAAAAAGAC
64 A-AGTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAG-GAAACATGAAGAAAAAAG-T
* ********* * *
1792 ATTCATTGACAA-AAANNNNNNNNNNATAGTTACCCATTCCTTCAAA
126 ATTCATTGGCAAGAAA-AAGACATTTATAGTCACACATTCCTTCAAA
* * * * *
1838 AGTCTTATTACTAACTTTAAATGGTTTTATAATCTCATAATTGACTTTAGGTTG-A-TTCTTTTA
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGCTTGAACTT-TTTGA
* ** * * * * * * *
1901 CGTTTTTAGTTAGAACATATTATAATTGTATGTCTGCTTTAGGAAACATCAAGAAAAAGGTATTC
65 AGTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGTATTC
** * *
1966 ATTGGCAA-AAAAAGTTTATTTATAGACACCCATTCCTTCAAA
130 ATTGGCAAGAAAAAG-ACATTTATAGTCACACATTCCTTCAAA
* * * * *
2008 GGCCTTATTACTTACTTTACATAGTTTTATAATCTCAAAATTGATTTTA
1 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTA
2057 AGTTAAATGT
Statistics
Matches: 1293, Mismatches: 402, Indels: 130
0.71 0.22 0.07
Matches are distributed among these distances:
169 10 0.01
170 360 0.28
171 576 0.45
172 328 0.25
173 18 0.01
174 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.37
Consensus pattern (171 bp):
AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAGCTTGAACTTTTTGAA
GTTTTGGGTTAGAACAGATTATAATTGAATGTCTACCTCAGGAAACATGAAGAAAAAAGTATTCA
TTGGCAAGAAAAAGACATTTATAGTCACACATTCCTTCAAA
Found at i:1232 original size:170 final size:161
Alignment explanation
Indices: 1030--1345 Score: 287
Period size: 170 Copynumber: 1.9 Consensus size: 161
1020 TAATTAGTTT
* * * * * * *
1030 TAAGTTAAATTTTTTTATATTTTTGGTTAAAACAAATTAGAATTGAATGC-CCACCTTC-TGAGA
1 TAAGTTAAATATTTTTACATTTTTGATTAAAACAAACTACAATTGAAT-CTCCACC-TCAAGAAA
* * * * *
1093 CGTTAAGAAAAAGGCAGTCATTGGTAAG-AAAGTCTATTTACAGTTACCCATACCTTCAAAAGTC
64 CGTAAAGAAAAAGGCAGTCATTGGCAAGAAAAGTCCATTTACAGTGACCCATACCTTCAAAAGCC
1157 TTATTACTCACTTTAAATGGTTTTATAATACCA
129 TTATTACTCACTTTAAATGGTTTTATAATACCA
* * * * * *
1190 NNNNNNNNNNTAAGTTGAATATTTTTACATTTTTTATTAAAACAGACTACAATTGGATCTCTATC
1 ----------TAAGTTAAATATTTTTACATTTTTGATTAAAACAAACTACAATTGAATCTCCACC
* * * * **
1255 TCAAGAAATGTAAAGAAAATGGCATTCATTGGCAAGAAAAGTCCATTTATAGTGACCCATTTCTT
56 TCAAGAAACGTAAAGAAAAAGGCAGTCATTGGCAAGAAAAGTCCATTTACAGTGACCCATACCTT
1320 CAAAAGCCTTATTACTCACTTTAAAT
121 CAAAAGCCTTATTACTCACTTTAAAT
1346 NNNNNNNNNN
Statistics
Matches: 119, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
169 3 0.03
170 68 0.57
171 48 0.40
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.35
Consensus pattern (161 bp):
TAAGTTAAATATTTTTACATTTTTGATTAAAACAAACTACAATTGAATCTCCACCTCAAGAAACG
TAAAGAAAAAGGCAGTCATTGGCAAGAAAAGTCCATTTACAGTGACCCATACCTTCAAAAGCCTT
ATTACTCACTTTAAATGGTTTTATAATACCA
Done.