Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397753.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_105.0, 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: 25183
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.22
Warning! 10467 characters in sequence are not A, C, G, or T
Found at i:17274 original size:171 final size:169
Alignment explanation
Indices: 16926--17297 Score: 421
Period size: 171 Copynumber: 2.2 Consensus size: 169
16916 NNNNNNNNNN
* * *
16926 CCATTCCTTTAAAAGCCTTATTACTTGCTTTAAGTGGTTTTATAATCTCATAATGGACTTTAAGT
1 CCATTCCTTCAAAAGCCTTATTACTCGCTTTAAGTAGTTTTATAATCTCATAATGGACTTTAAGT
* * **
16991 TGAATTTTTTATATTTTTGATTAAAACAGACTATAATCGAATTCTTACCTCAAGAATTGTGTAAA
66 TAAATTTTTTACATTTTTGATTAAAACAGACTATAATCGAATTCTTACCTCAAGAAACGTGTAAA
*
17056 AAGACCCAATTATTTAAAAGAAAAGTCCATTTATAGTCTA
131 AAGA-CCAATTATTGAAAAGAAAAGTCCATTTATAGTCTA
* * * *
17096 CCATTCCTTCAAAAGTCTGATTACTCGCTTT-AGATAGTTTTATAATCTCATAATTGATTTTAAG
1 CCATTCCTTCAAAAGCCTTATTACTCGCTTTAAG-TAGTTTTATAATCTCATAATGGACTTTAAG
* * * * *
17160 TTAAATCTTTTTACATTTTTGGTTATAACAGACTATAATTGAATGTC-TACTTTAAGAAACGTGA
65 TTAAAT-TTTTTACATTTTTGATTAAAACAGACTATAATCGAAT-TCTTACCTCAAGAAACGTG-
* ** * * *
17224 TGAAAAAGA-C-GTTCATTGGCAAGGAAATTCCGTTTATAGTC-A
127 T-AAAAAGACCAATT-ATTGAAAAGAAAAGTCCATTTATAGTCTA
*
17266 CTCATTCCTTCAAAAGCCTTAGTACTCGCTTT
1 C-CATTCCTTCAAAAGCCTTATTACTCGCTTT
17298 NNNNNNNNNN
Statistics
Matches: 169, Mismatches: 26, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
169 2 0.01
170 63 0.37
171 94 0.56
172 3 0.02
173 7 0.04
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (169 bp):
CCATTCCTTCAAAAGCCTTATTACTCGCTTTAAGTAGTTTTATAATCTCATAATGGACTTTAAGT
TAAATTTTTTACATTTTTGATTAAAACAGACTATAATCGAATTCTTACCTCAAGAAACGTGTAAA
AAGACCAATTATTGAAAAGAAAAGTCCATTTATAGTCTA
Found at i:23855 original size:172 final size:162
Alignment explanation
Indices: 23352--24343 Score: 478
Period size: 172 Copynumber: 5.8 Consensus size: 162
23342 NNNNNNNNNN
* * * * * *
23352 TTTTTTATATTATTGGTTAAAACCA-ATTATAATTGAATGTCTACCTCAAGAAATGTGAGGAGAA
1 TTTTTTACATTATTAGTTAAAA-CAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAA
* * * * * *
23416 AGGCATTCATTAGTAACAAAAGT-CTTGTTGTAGTCACTC-ATTCCTTCAAAAGCCTTATTACTA
65 AGGTATTCATT-GCAAGAAAAGTCCGT-TTATAGTCAC-CAATTCCTTCAAAAGCCTTATTACTC
* * * * *
23479 GCTTTAANNNNNNNNNNAATCTCATAATTGATTTTAAGGTGAA-T
127 GCTTTTA---------TAATCTCAAAATTGATTTTAAGTTCAATT
* * * * * *
23523 TTTTTTACATTTTTTA-TCAAAACAGAATATAATTGAATGTCTATCTTGAGAAACATGAAGAAGA
1 TTTTTTACA-TTATTAGTTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAA-A
** ** * *
23587 AA-AAATTCATTGGCAAGAAAAGTCTATTTATAATCTCTC-ATTCCTTCAAAAG-CTCTATTACT
64 AAGGTATTCATT-GCAAGAAAAGTCCGTTTATAGTCAC-CAATTCCTTCAAAAGCCT-TATTACT
* * * *** *
23649 CTCTTTTA-AAGGTTTTATNNNNNNNNNNTTGATTTTAAGTTTAATT
126 CGCTTTTATAA--TCTCA--------AAATTGATTTTAAGTTCAATT
* * * * *
23695 TTTTTTACATAATTAGTTAAAACAAATTATAATTGAATGTCTCCCTCGAGATACGTGAATAAAAA
1 TTTTTTACATTATTAGTTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAA
*
23760 GGTATTCATTAGCAAGAAAAGTCCGTTTATAGTAACCAATTCCTTCAAAAGCCTTATTACTCGNN
66 GGTATTCATT-GCAAGAAAAGTCCGTTTATAGTCACCAATTCCTTCAAAAGCCTTATTACTCG--
*
23825 NNNNNNNNTTTTATAATCTCAAAATTGATTTTAAGTTCAATT
128 -------CTTTTATAATCTCAAAATTGATTTTAAGTTCAATT
* * * * * * *
23867 TTTTCTACATTTTTAATTAAAACAGATTATAATTGAATGCCTACCTCAAGAAATGTGAAGAGAAA
1 TTTTTTACATTATTAGTTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAA
* * * *
23932 GGCATTCATTGACAATG-AAAGTCCAG-TTATATTCTCCTATTCCTTCAAAAGCCTTATTACTCG
66 GGTATTCATTG-CAA-GAAAAGTCC-GTTTATAGTCACCAATTCCTTCAAAAGCCTTATTACTCG
* * *
23995 CNNNNNNNNNNTTTATAATCTCATAATTGATTTTAGGTTCAATT
128 C---------TTTTATAATCTCAAAATTGATTTTAAGTTCAATT
* * * * * *
24039 TGTTTTTGCATTATCT-GTTAAAACAGATAATAATTGAATGTCAACCTTGAGAAACCTAAAGAAA
1 T-TTTTTACATTAT-TAGTTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAA
** *
24103 AAGGTATTCATTTGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTANNNNNNN
64 AAGGTATTCA-TTGCAAGAAAAGTCCGTTTATAGTCACCAATTCCTTCAAAAGCCTTA-------
********** * * * * *
24168 NNNNNNNNNNNNTTATAATCTTATAATTAATTTTAAGTTGAAGT
121 --TTACTCGCTTTTATAATCTCAAAATTGATTTTAAGTTCAATT
* * * ** * * *
24212 TTTTTTACATTTTTTGTTAAAACAGAATATAATTGAATGTCTACCTTAACAAACATGAGGAAAAA
1 TTTTTTACATTATTAGTTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAA
* * * * **
24277 AGTATTCATTGGCAAGAAAAGTCCATTTATAGCCTCCCGTTCCTTCAAAAGCCTTATTACTCGCT
66 GGTATTCATT-GCAAGAAAAGTCCGTTTATAGTCACCAATTCCTTCAAAAGCCTTATTACTCGCT
24342 TT
130 TT
24344 AAATAGTTTT
Statistics
Matches: 625, Mismatches: 138, Indels: 124
0.70 0.16 0.14
Matches are distributed among these distances:
161 2 0.00
163 4 0.01
170 4 0.01
171 118 0.19
172 358 0.57
173 125 0.20
174 4 0.01
180 3 0.00
181 5 0.01
182 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.35
Consensus pattern (162 bp):
TTTTTTACATTATTAGTTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAA
GGTATTCATTGCAAGAAAAGTCCGTTTATAGTCACCAATTCCTTCAAAAGCCTTATTACTCGCTT
TTATAATCTCAAAATTGATTTTAAGTTCAATT
Done.