Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397505.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3665.0, 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: 11387
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.23
Warning! 4634 characters in sequence are not A, C, G, or T
Found at i:1180 original size:168 final size:170
Alignment explanation
Indices: 876--1189 Score: 422
Period size: 168 Copynumber: 1.9 Consensus size: 170
866 NNNNNNNGCC
* *
876 TTATTACTCTCTTTAAAAGGTTTTATAATCTCATAATTGATTTTAAGTTGATTTTTTTTAAAGTT
1 TTATTACTCGCTTTAAAAGGTTTTATAATATCATAATTGATTTTAAGTT-ATTTTTTTTAAAGTT
* ** * * *
941 TTGGTTAAACAAGACTATAATTGAATGTCTACCTTGAGGAACGTGAAGAAAAAGACATTTATTGG
65 TTGGTAAAACAAGACTATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGACATTCATTGA
*
1006 CAAGAAAAGTTCATTTATAGGCACCTATTCATTTAAAAGGT
130 CAAGAAAAGTCCATTTATAGGCACCTATTCATTTAAAAGGT
* * *
1047 TTATTACTCGCTTTAAAGGGTTTTATAATATCATAATTGATTTTAAGTT-TTTTTTTT-CATTTT
1 TTATTACTCGCTTTAAAAGGTTTTATAATATCATAATTGATTTTAAGTTATTTTTTTTAAAGTTT
* * *
1110 TTGTCAAAAC-AGATTATAATTGAAAT-TCTACCTCAAGAAACGTGAAGAAAAA-AGTATTCATT
66 TGGT-AAAACAAGACTATAATTG-AATGTCTACCTCAAGAAACGTGAAGAAAAAGA-CATTCATT
1172 GACAAGAAAAGTCCATTT
128 GACAAGAAAAGTCCATTT
1190 NNNNNNNNNN
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
167 1 0.01
168 63 0.50
169 15 0.12
171 46 0.37
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (170 bp):
TTATTACTCGCTTTAAAAGGTTTTATAATATCATAATTGATTTTAAGTTATTTTTTTTAAAGTTT
TGGTAAAACAAGACTATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGACATTCATTGAC
AAGAAAAGTCCATTTATAGGCACCTATTCATTTAAAAGGT
Found at i:2886 original size:171 final size:170
Alignment explanation
Indices: 2612--3064 Score: 516
Period size: 172 Copynumber: 2.6 Consensus size: 170
2602 TATTTTCATG
* * * * * * * *
2612 TAAAATAAATTATAATTGACTGTCTACCTTCAGAAATGTAAAGAAAAAGACAATCATTGGTAAAA
1 TAAAACAAATTATAATTAACTGTCTACCATAAGAAACGTAAAGAAAAAGGCATTCATTGGCAAAA
*
2677 AAAGTCCATTTATAGTCACACATTCCTTTAACAGTCTTATTACTCGCTTTAAATAGTATTATAAT
66 AAAGTCTATTTATAGTCAC-CATTCCTTTAA-AGTCTTATTACTCGCTTTAAATAGTATTATAAT
*
2742 C-TCAAATTAATTTTAATTTAAATTCTTTGCATATT-TTTAGT
129 CTTAAAATTAATTTTAATTTAAATTCTTTGCATATTGTTT-GT
* * * * *
2783 TAAAACAAATTATAATTAACTGTCTACCATGAGAAACGTGATGAAAAAGGCATTCATAGGCAAGA
1 TAAAACAAATTATAATTAACTGTCTACCATAAGAAACGTAAAGAAAAAGGCATTCATTGGCAAAA
* * *
2848 AAAGTCTATTTATAGTCACCTATTCCTTTATAAGTCTTATTACTAGTTTTAAATAGTTTTATAAT
66 AAAGTCTATTTATAGTCACC-ATTCCTTTA-AAGTCTTATTACTCGCTTTAAATAGTATTATAAT
* * * *
2913 CTTAAAATTAGTTTTAATTTGAATTTTTTGTATATTGTTTGT
129 CTTAAAATTAATTTTAATTTAAATTCTTTGCATATTGTTTGT
* * * * * * * * *
2955 TAAAACAGATTATAATTAAATGTTTACCACAAGTAACATTAAGAAAAATGCATTTC-TTGACAAA
1 TAAAACAAATTATAATTAACTGTCTACCATAAGAAACGTAAAGAAAAAGGCA-TTCATTGGCAAA
* *
3019 AAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
65 AAAAGTCTATTTATAGTCA-CCATTCCTT-TAAAGTCTTATTACTC
3065 NNNNNNNNNN
Statistics
Matches: 238, Mismatches: 37, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
170 1 0.00
171 111 0.47
172 117 0.49
173 9 0.04
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (170 bp):
TAAAACAAATTATAATTAACTGTCTACCATAAGAAACGTAAAGAAAAAGGCATTCATTGGCAAAA
AAAGTCTATTTATAGTCACCATTCCTTTAAAGTCTTATTACTCGCTTTAAATAGTATTATAATCT
TAAAATTAATTTTAATTTAAATTCTTTGCATATTGTTTGT
Found at i:3585 original size:172 final size:172
Alignment explanation
Indices: 3290--3602 Score: 419
Period size: 172 Copynumber: 1.8 Consensus size: 172
3280 NNNNNNNNNN
* * *
3290 TTTTAAGTTAAATTTGTTTTACATTTTCATTTAAAACAAATTATAATTGACTGTCTACCTTGAGA
1 TTTTAAGTTAAATTTGTTTTACATTTTCATGTAAAACAAATTATAATTGACTGTCTACCATAAGA
* * * * * * ** *
3355 AACCTGAATAAAAATACATTTATTTGCAAGAAAAGTCCATTTATAGTTGCCGATTCCTTTAAAAA
66 AACCTAAAGAAAAAGACAGTCATTGGCAAGAAAAGTCCATTTATAGTCACCGATTCCTTCAAAAA
3420 CCTTATTACTCTCTGTAAAAGGTTTTATATTCTCAAAATTAA
131 CCTTATTACTCTCTGTAAAAGGTTTTATATTCTCAAAATTAA
* * * *
3462 TTTTAAGTTATATTTTTTTTATATTTTCATGTAAAACAAATTATAATTGACTTTCTACCATAAGA
1 TTTTAAGTTAAATTTGTTTTACATTTTCATGTAAAACAAATTATAATTGACTGTCTACCATAAGA
* * * * * * *
3527 AACGTAAAGAAAAAGATAGTCATTGGTAAGAGAAGTCCATTTATAGTCATCTATTCCTTCAAAAG
66 AACCTAAAGAAAAAGACAGTCATTGGCAAGAAAAGTCCATTTATAGTCACCGATTCCTTCAAAAA
3592 CCTTATTACTC
131 CCTTATTACTC
3603 GCTTTNNNNN
Statistics
Matches: 118, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
172 118 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (172 bp):
TTTTAAGTTAAATTTGTTTTACATTTTCATGTAAAACAAATTATAATTGACTGTCTACCATAAGA
AACCTAAAGAAAAAGACAGTCATTGGCAAGAAAAGTCCATTTATAGTCACCGATTCCTTCAAAAA
CCTTATTACTCTCTGTAAAAGGTTTTATATTCTCAAAATTAA
Found at i:8858 original size:174 final size:171
Alignment explanation
Indices: 8546--9469 Score: 693
Period size: 172 Copynumber: 5.4 Consensus size: 171
8536 NNNNNNNNNN
* *
8546 TTTATATTCTCAAAATTGATTTTAAGTTTAA-TTTTTTTAAATTTTCATTTAAAACAAATTATAA
1 TTTATATTCTCAAAATTGATTTTAAG-TTAATTTTTTTTACATTTTTA-TTAAAACAAATTATAA
* * *
8610 TTGACTGTT-TACCTGGAGAAACGT-AAAAAAAAATACATTTATTGATAAGGAAAGTCCATTTAT
64 TTGAAT-TTCTACCTAGAGAAACGTGAAAAAAAAATACATTTATTGATAAGAAAAGTCCATTTAT
8673 AGTCACCCATTCCTTTCAAAGCCTTATTACTCGCTTTAAAAGGT
128 AGTCACCCATTCCTTTCAAAGCCTTATTACTCGCTTTAAAAGGT
* * * *
8717 TTTATATTCTCAAAATTGA-TTTAGGTTAATTTTTTTTACGTTTCTTTATTAAAATAGATTATAA
1 TTTATATTCTCAAAATTGATTTTAAGTTAATTTTTTTTAC-ATT-TTTATTAAAACAAATTATAA
* * * *
8781 TTGAATATTCTACCTCGAGAAACGTGAAAAAAAAAAAATATTTATTGATAAGAAAAGTCTATTTA
64 TTGAAT-TTCTACCTAGAGAAACGTG-AAAAAAAAATACATTTATTGATAAGAAAAGTCCATTTA
* * *
8846 TAGTCACCCATTCC-TTCAAAAGCCTTATTACGCGTTTTAAATGGT
127 TAGTCACCCATTCCTTTC-AAAGCCTTATTACTCGCTTTAAAAGGT
* * *
8891 TTTATATTCAT-AAAATTAATTTTAAGTTAAATTTGTTTTACATTTTCATTTAAAACAAATTATA
1 TTTATATTC-TCAAAATTGATTTTAAGTT-AATTTTTTTTACATTTTTA-TTAAAACAAATTATA
* * * * ** *****
8955 ATTG-ATTGTCTACCTAGAAAAACATG-AAGAAAAATGCATTTATTGGCAAGAAAAGTCNNNNNN
63 ATTGAATT-TCTACCTAGAGAAACGTGAAAAAAAAATACATTTATTGATAAGAAAAGTC-CATTT
**** * * *
9018 NNNNT-GCCCATTCCTTTAAAAGCCTTATTACT-GTCTTTAAAAGAT
126 ATAGTCACCCATTCCTTTCAAAGCCTTATTACTCG-CTTTAAAAGGT
* *
9063 TTTATATTCTCGAAATTGATTTTAAGTTATATTTTTTTTACATTTTTATGTAAAACAGATTATAA
1 TTTATATTCTCAAAATTGATTTTAAGTTA-ATTTTTTTTACATTTTTAT-TAAAACAAATTATAA
* * * * * * * * * *
9128 TT-AACTGTCTACCTTAAAG-AACAT-AAAGAAAAAGATAGTCATTGGTAAGAGAAGTCCATTTA
64 TTGAA-TTTCTACC-TAGAGAAACGTGAAAAAAAAATACATTTATTGATAAGAAAAGTCCATTTA
* ********** * *
9190 TGGTCACCCANNNNNNNNNNAGCCTTATTACTCTCTTTAAAAGGC
127 TAGTCACCCATTCCTTTCAAAGCCTTATTACTCGCTTTAAAAGGT
* * ** * * ***
9235 TTTATAATCTCATAATTGATTTTAAGTTTCTTTTTTTTATATTTTTTGTTAAAGA-AGGCTATAA
1 TTTATATTCTCAAAATTGATTTTAAGTTAATTTTTTTTACA-TTTTTATTAAA-ACAAATTATAA
* * * ** * *
9299 TTGAATGTCTACCTTGGGGCACATG--AAAAAAA-ACATTTATTG-TCAAGAAAAGTCCATTCAT
64 TTGAATTTCTACCTAGAGAAACGTGAAAAAAAAATACATTTATTGAT-AAGAAAAGTCCATTTAT
* *
9360 AGTCACCTATTCC-TTCAAAAGCCTTATTACTCACTTTAATTAA--T
128 AGTCACCCATTCCTTTC-AAAGCCTTATTACTCGCTTTAA--AAGGT
* * * * * *
9404 TTTATAATCTCATAATTGATTTTAAGTTGTATTGTTTTTATATTTTTTATTAAAACAGATTATAA
1 TTTATATTCTCAAAATTGATTTTAAGTT-AATTTTTTTTACA-TTTTTATTAAAACAAATTATAA
9469 T
64 T
9470 NNNNNNNNNN
Statistics
Matches: 596, Mismatches: 122, Indels: 71
0.76 0.15 0.09
Matches are distributed among these distances:
168 1 0.00
169 81 0.14
170 51 0.09
171 84 0.14
172 222 0.37
173 11 0.02
174 108 0.18
175 27 0.05
176 11 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.40
Consensus pattern (171 bp):
TTTATATTCTCAAAATTGATTTTAAGTTAATTTTTTTTACATTTTTATTAAAACAAATTATAATT
GAATTTCTACCTAGAGAAACGTGAAAAAAAAATACATTTATTGATAAGAAAAGTCCATTTATAGT
CACCCATTCCTTTCAAAGCCTTATTACTCGCTTTAAAAGGT
Done.