Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398299.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1601.0, 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: 3683
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.29
Warning! 762 characters in sequence are not A, C, G, or T
Found at i:540 original size:171 final size:170
Alignment explanation
Indices: 234--792 Score: 491
Period size: 171 Copynumber: 3.3 Consensus size: 170
224 TTTAAAGATG
* *
234 TGGGTGACTATAAATGGACTTTTCTTGCCAA-TGAATATCTTTTTCTTAACGTTTCCCATGGTAG
1 TGGGTGGCTATAAATGGACTTTTCTTGCCAATTG-ATATCTTTTTCTTAACGTTACCCATGGTAG
*
298 ACATTCAATTATAATCTGTTTTACTGAAAAATATAAAAAAATTCAACTTAAAATCAACTATAAGA
65 ACATTCAATTATAATCTATTTTACTGAAAAATATAAAAAAATTCAACTTAAAATCAACTATAAGA
* *
363 TTATAAAATCATTTAGAGCGAGTAATAAAGC-TTCTGAAGGCA
130 TTATAAAA-CATTTAAACCGAGTAATAAAGCTTTC-GAAGGCA
* *
405 TGGGTGGCTATAAATGGACCTTTT-TTGCCAATTGATATCTTTTTCTTTACGTTACGCGA-GGTA
1 TGGGTGGCTATAAATGGA-CTTTTCTTGCCAATTGATATCTTTTTCTTAACGTTAC-CCATGGTA
********** * * **
468 GACATTCAATTATAATCTATTTNNNNNNNNNNTATAAAAAAATTTAACTTAAAATCAATTATGGG
64 GACATTCAATTATAATCTATTTTACTGAAAAATATAAAAAAATTCAACTTAAAATCAACTATAAG
* * *
533 TTTATAAAACATTTAAACCGAGTAATAAGGCTTTCGAAGGTA
129 ATTATAAAACATTTAAACCGAGTAATAAAGCTTTCGAAGGCA
* * * * * * ** *
575 TGCGTGGTTATAAATGGACTTTTCTTGCCAATGGATATCTTTTCCTTCACGTTTCTTAAGGTAGA
1 TGGGTGGCTATAAATGGACTTTTCTTGCCAATTGATATCTTTTTCTTAACGTTACCCATGGTAGA
********** * * * * * * *
640 CATNNNNNNNNNNTATATTTTAATAAAAAATATAAAACAAA-TCAACTTAAAGTCGATTTTAAGC
66 CATTCAATTATAATCTATTTTACTGAAAAATATAAAA-AAATTCAACTTAAAATCAACTATAAG-
* * * *
704 A-TATAAAACCATTTAAATCGAGTAATGAGGCTTTCGAAAGCA
129 ATTATAAAA-CATTTAAACCGAGTAATAAAGCTTTCGAAGGCA
** *
746 TGGGTGGCTATAAATAAACTTTTCTTGCCAATAGATATCTTTTTCTT
1 TGGGTGGCTATAAATGGACTTTTCTTGCCAATTGATATCTTTTTCTT
793 CATGTTTCTC
Statistics
Matches: 309, Mismatches: 70, Indels: 18
0.78 0.18 0.05
Matches are distributed among these distances:
169 6 0.02
170 113 0.37
171 181 0.59
172 9 0.03
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.35
Consensus pattern (170 bp):
TGGGTGGCTATAAATGGACTTTTCTTGCCAATTGATATCTTTTTCTTAACGTTACCCATGGTAGA
CATTCAATTATAATCTATTTTACTGAAAAATATAAAAAAATTCAACTTAAAATCAACTATAAGAT
TATAAAACATTTAAACCGAGTAATAAAGCTTTCGAAGGCA
Found at i:1730 original size:171 final size:171
Alignment explanation
Indices: 1081--1860 Score: 617
Period size: 171 Copynumber: 4.6 Consensus size: 171
1071 NNNNNNNNNN
* * * * *
1081 AATTATAATCTATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTACAAAATTATAA
1 AATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGATTATAA
* * * *
1146 AAACTTTTAAAGCGAGTAATAAGGCTTTTA-AAGGCA-AGGGTGACTATAAATGGACTTTTCTAA
66 AAACATTTAAAGCAAGTAATAAGG-TTTTAGAAGGTATA-GGTGACTATAAATGGACTTTTCTTA
* * *********
1209 CTAATTGATATCTTTTTCTTCATGTTTCTTGAGGNNNNNNNNN
129 CCAATGGATATCTTTTTCTTCATGTTTCTTGAGGTAAATATTC
* * * * * * ** *
1252 NATTATTATCTGTTTTAACAAAAAACATAACAAAATTTAATTTAAAATGGATTATTAGATTATAA
1 AATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGATTATAA
* * ********** * *
1317 AAATATTTAAAGCAAGTAATAAGGCTNNNNNNNNNNTGGGTAACTATAAATGGACTTTT-TCTAC
66 AAACATTTAAAGCAAGTAATAAGGTTTTAGAAGGTATAGGTGACTATAAATGGACTTTTCT-TAC
* ** *
1381 CAATTGATATCCTTTTT-TTCATGTTTCTCAAGGTAAATATTA
130 CAATGGATAT-CTTTTTCTTCATGTTTCTTGAGGTAAATATTC
* * * * * * *
1423 AATTATTATCTATTTTAGCT-ACAAATGTAAAAAAATTTAACTTAAAATTAATTATGAGATTATA
1 AATTATTATCTGTTTTA-ATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGATTATA
* * * * * **********
1487 AAAACACTTAAAGCAAGCAATAAGGCTTTCGAAGGTATGGGTGACTATNNNNNNNNNNTTCTTAC
65 AAAACATTTAAAGCAAGTAATAAGGTTTTAGAAGGTATAGGTGACTATAAATGGACTTTTCTTAC
*
1552 CAATGGATATCTTTTTCTTTATGTTTCTTGAGGTAAATATTC
130 CAATGGATATCTTTTTCTTCATGTTTCTTGAGGTAAATATTC
* * *
1594 AATTATAATTTGTGTTAATAAAAAATATAAAACAAA-TCAACTTAAAATCAATTATAAGATTATA
1 AATTATTATCTGTTTTAATAAAAAATATAAAA-AAATTCAACTTAAAATCAATTATAAGATTATA
* * *
1658 AAAACATTTAAGGCAAGTAATAAGGTTTTAGAAGGTATAGGTGATTATAAATGGACTTTTCTTGC
65 AAAACATTTAAAGCAAGTAATAAGGTTTTAGAAGGTATAGGTGACTATAAATGGACTTTTCTTAC
* * * * * * *
1723 TAATGGATATCGTTTTCGTCATGTTTCATGAGTTACACATTC
130 CAATGGATATCTTTTTCTTCATGTTTCTTGAGGTAAATATTC
* * * * *
1765 AATTATTATCTGTTTTAAT--CAAACATAAACAAATTCAA-TTAAAAACAATTATGAGATTATAA
1 AATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGATTATAA
* *
1827 AAATATTTAAAGCGAGTAATAAGGCTTTT-GAAGG
66 AAACATTTAAAGCAAGTAATAAGG-TTTTAGAAGG
1861 CATNNNNNNN
Statistics
Matches: 470, Mismatches: 128, Indels: 25
0.75 0.21 0.04
Matches are distributed among these distances:
168 51 0.11
169 16 0.03
170 9 0.02
171 384 0.82
172 10 0.02
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.36
Consensus pattern (171 bp):
AATTATTATCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAGATTATAA
AAACATTTAAAGCAAGTAATAAGGTTTTAGAAGGTATAGGTGACTATAAATGGACTTTTCTTACC
AATGGATATCTTTTTCTTCATGTTTCTTGAGGTAAATATTC
Found at i:3408 original size:172 final size:172
Alignment explanation
Indices: 2529--3436 Score: 441
Period size: 171 Copynumber: 5.3 Consensus size: 172
2519 NNNNNNNNNN
* ** **
2529 AATTATTATCTGTTTTAG-CCAAAAATATAAAAAAATTCAACTTAAAATCAATTA-GGAGATTAT
1 AATTATAATCTGTTTTAGTAAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAAG-TTAT
* * * * * * * * *
2592 AATAACATTTAAAGCGAGTAATAAGGCGTTC-GAAGGCTTGGGTGACTATAAATAGACTTTTCTT
65 AAAAACATTCAAAGCGAGTAAAAAGGCTTTCAAAAAG-ATGAGTGACTATAAATGGACTTTTCTT
* * * * * *
2656 GCCAATGGATATCTTTTTTTTTATGTTT-CTCGAGGTAGACATTG
129 GCCAATGAATATATTTTTCTTCACGTTTCCT-GAGGTAGACATTA
* * * * * *
2700 AATTATAATTTGTTTTAAT-AAATAATA-AAAAAAATT-AACTTAAAATCAATTATCAGGTTANN
1 AATTATAATCTGTTTTAGTAAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAAGTTA-T
******** * ** *
2762 NNNNNNNNT-AAAGCGAGTAATAAGGCTTT-TGAAAGTAT-ACGTGACTATAAAAGGACTTTTCT
65 AAAAACATTCAAAGCGAGTAAAAAGGCTTTCAAAAAG-ATGA-GTGACTATAAATGGACTTTTCT
* ********* * * * *
2824 TGCCAATGGATAT-TTNNNNNNNNNNGTTTCTTGAGGCATACATTC
128 TGCCAATGAATATATT-TTTCTTCACGTTTCCTGAGGTAGACATTA
* * ** * * * * *
2869 AATTATTATCTGTTTTA--ACTAAAAACGTAACATAATTCAATTTAAAATCATTTAT-GAGATTA
1 AATTATAATCTGTTTTAGTA-AAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAAG-TTA
* * * * * ** * * * *
2931 TAAAAACATTTAAAGCAAGTGATAATGCTTT-TTAAGGCATGGGTGACTATAAATGCACTTTTCC
64 TAAAAACATTCAAAGCGAGTAAAAAGGCTTTCAAAAAG-ATGAGTGACTATAAATGGACTTTTCT
* * * * *********** *
2995 TGTCAGTGGATATCTTTTTCTTNNNNNNNNNNAAGGTAGATATTA
128 TGCCAATGAATATATTTTTCTTCACGTTTCCTGAGGTAGACATTA
* * * * ** * * *
3040 AATTATTATCTGTTTCAGT-CAAAAATGTAAATCAATTCAACTTAAATTCAATTATGAGGTTATA
1 AATTATAATCTGTTTTAGTAAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAAGTTATA
* * *
3104 AAATCATTCAAAGCGAGTAATAAGGCTTTCAAAAATATGAGTGACTATAAATGGACTTTTCTTGC
66 AAAACATTCAAAGCGAGTAAAAAGGCTTTCAAAAAGATGAGTGACTATAAATGGACTTTTCTTGC
* *
3169 CAATGAATATATTTTTCTTCACGTTTCCTGAGGCAGACATTT
131 CAATGAATATATTTTTCTTCACGTTTCCTGAGGTAGACATTA
* * * *
3211 AATTATAATATTTTTTAATAAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAATTTATA
1 AATTATAATCTGTTTTAGTAAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAAGTTATA
* ** *
3276 AAAACATTTAAAGCGAGTAAAAAGGCTTT-TGAAGGATGAGTCG-CTATAAATGGACTTTTCTTG
66 AAAACATTCAAAGCGAGTAAAAAGGCTTTCAAAAAGATGAGT-GACTATAAATGGACTTTTCTTG
* * * ********** * *
3339 CTAATGGATATCTTTTNNNNNNNNNNTCTTGAGGTAGACATTC
130 CCAATGAATATATTTTTCTTCACGTTTCCTGAGGTAGACATTA
* *
3382 AATTATAATCTGTTTTAGTAAAAAAA-ATAAAAAAAGTCAGCTTAAAATCAATTAT
1 AATTATAATCTGTTTTAGTAAAAAAATATAAAAAAATTCAACTTAAAATCAATTAT
3437 GAGATTATAN
Statistics
Matches: 546, Mismatches: 170, Indels: 43
0.72 0.22 0.06
Matches are distributed among these distances:
168 2 0.00
169 109 0.20
170 48 0.09
171 318 0.58
172 69 0.13
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35
Consensus pattern (172 bp):
AATTATAATCTGTTTTAGTAAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAAGTTATA
AAAACATTCAAAGCGAGTAAAAAGGCTTTCAAAAAGATGAGTGACTATAAATGGACTTTTCTTGC
CAATGAATATATTTTTCTTCACGTTTCCTGAGGTAGACATTA
Done.