Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398717.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2001.0, 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: 3487
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.31
Warning! 714 characters in sequence are not A, C, G, or T
Found at i:913 original size:171 final size:167
Alignment explanation
Indices: 672--1217 Score: 521
Period size: 171 Copynumber: 3.2 Consensus size: 167
662 NNNNNNNNNN
* * ** *
672 TTTTATAATCTCATAATTGATTTTAAGTTAAATTGTTTTACATTTTTTA-TTAAATTAGACTATC
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTAGTTAAAACAGACTATA
* * * **
736 ATTGAATGCTGGCCTCAGGAAACGTTAGGAAAAATCTATTCATTTGGACGAAAAGTCCGTTTATA
65 ATTGAATGCTGACCTCAGGAAACGTGAGGAAAAA-CTATTCATTTGGAAGAAAAGTCTATTTATA
*
801 GTCTCACATTCTTTCAAAAATATTATTACTCACTTTAAA-AGG
129 GTCAC-CATTCTTTCAAAAAT-TTATTACT-ACTTTAAATA-G
* * ** * *
843 TTTTATAACCTCATAATTGATTTTAAGCTGAATTTTTTTACATTAGTAGTTAAAACATATTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGACTATAA
* *
908 TTGAATGTCT-ACCTC-GAGAAAGGTGAAGAAAAAGCT-TTCA-TTGGCAAGAAATA-TCTATTT
66 TTGAATG-CTGACCTCAG-GAAACGTGAGGAAAAA-CTATTCATTTGG-AAGAAA-AGTCTATTT
* **
968 ATAGTCACTTATTCTTTCAAAAGCCTTATTACTAGCTTTAAATAG
126 ATAGTCAC-CATTCTTTCAAAA-ATTTATTACTA-CTTTAAATAG
* * * * * *
1013 TTTTATAAACTAATAATTGATTTTAAGTTGAGTTTTTCTACATTTTTGGTTTAAACAGACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGACTATAA
* * ** * * *
1078 TTGAATGTTGACCTCAAGAAACGTGAGGCAAAAAAAATTCATTAGTAAGAAAAGTCTATTTATTG
66 TTGAATGCTGACCTCAGGAAACGTGAGG-AAAAACTATTCATTTGGAAGAAAAGTCTATTTATAG
* * * * *
1143 TCACCTATACCTTCAAAAGCTTTATTAGTTGCTTTAAATAG
130 TCACC-ATTCTTTCAAAA-ATTTATTA-CTACTTTAAATAG
1184 TTTTATAATCTCATAATTGATTTTAAGTTGAATT
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATT
1218 NNNNNNNNNN
Statistics
Matches: 306, Mismatches: 53, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
169 6 0.02
170 130 0.42
171 165 0.54
172 5 0.02
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (167 bp):
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAACAGACTATAA
TTGAATGCTGACCTCAGGAAACGTGAGGAAAAACTATTCATTTGGAAGAAAAGTCTATTTATAGT
CACCATTCTTTCAAAAATTTATTACTACTTTAAATAG
Found at i:3246 original size:171 final size:171
Alignment explanation
Indices: 2724--3487 Score: 467
Period size: 171 Copynumber: 4.5 Consensus size: 171
2714 NNNNNNNNNN
** **
2724 AAGAAAAGT-CTATTTATAGTCACTCATTCCTTCAAAAGCCTTATTACTCACTTTGCATGGTTTT
1 AAGAAAAGTGC-ATTTATAGTCACTCATTCCTT-AAAAGCCTTATTACTTGCTTTAAATGGTTTT
* ** * * *
2788 ATTATGTCAA-AATTGATTTTATGTTCAAT-TGTTTTTACATTTTTAGTTAAAAC-GAATTATAA
64 ATAAACT-AATAATTAATTTTAGGTTCAATAT-TTTTTACATTTTTGGTTAAAACTG-ATTATAA
* * * * **
2850 TTGAATGT-TACCCA-AAGAAAGATGAAGAAAAAGACATTCATTGATA
126 TTGAATATCTA-CCATGAGAAACATGAAGAAAAAGGCATTCATTG-GC
* * * * * ********** * **
2896 AAAAAAAGTCCATTTCTAGTCACCCATTTCTTCNNNNNNNNNNTTACTCGCTTTAAATTATTTTA
1 AAGAAAAGTGCATTTATAGTCACTCATTCCTT-AAAAGCCTTATTACTTGCTTTAAATGGTTTTA
* * * * ** *
2961 TAATCTCAA-AATTGATTTTAAGTT-AGAT-TTTTTTATATTTTTGGTTAAAAAAGACTATAATT
65 TAAACT-AATAATTAATTTTAGGTTCA-ATATTTTTTACATTTTTGGTTAAAACTGATTATAATT
* * ** * * * * * * ***
3023 GAATGTCTGCTTTGGGAAACGTGATGTAAAAGCCATCCATTTAT
128 GAATATCTACCATGAGAAACATGAAGAAAAAGGCATTCATTGGC
* **
3067 ACGAAAAGTGCATTTATAGTCACTCAAGCCTTACAAAGCCTTATTACTTGCTTTAAATGGTTTTA
1 AAGAAAAGTGCATTTATAGTCACTCATTCCTTA-AAAGCCTTATTACTTGCTTTAAATGGTTTTA
* * *
3132 TAAACTAATAATTCATTTTAGGTTGAAT-TTTTTTATATTTTTGGTTAAAACAT-ATTATAATTG
65 TAAACTAATAATTAATTTTAGGTTCAATATTTTTTACATTTTTGGTTAAAAC-TGATTATAATTG
* **********
3195 AATATCTACCCTGAGNNNNNNNNNNAAAAAGGCATTCATTGGC
129 AATATCTACCATGAGAAACATGAAGAAAAAGGCATTCATTGGC
* * * *
3238 AAGAAAAGTGCATTGATAGTCAC-CTATTTCATTAATAGCCTTATTGA-TTACTTTAAATGGTTT
1 AAGAAAAGTGCATTTATAGTCACTC-A-TTCCTTAAAAGCCTTATT-ACTTGCTTTAAATGGTTT
** * *
3301 TATCATCCCAA-AATTAATTTTATGTTCAATATTTTTTACATTTTTGGTTAAAACTGATTATAAT
63 TAT-AAACTAATAATTAATTTTAGGTTCAATATTTTTTACATTTTTGGTTAAAACTGATTATAAT
* * *
3365 TGAATGTCTACTATGAGAAACATGAAGAAAAAGGCATTCATTTGC
127 TGAATATCTACCATGAGAAACATGAAGAAAAAGGCATTCATTGGC
* * * * * *
3410 AAGAAAAGTCCATTTGTAGTAACTCATTTCTTGAAAAGCCTAATTACTCGCTTTAAATGGTTTTA
1 AAGAAAAGTGCATTTATAGTCACTCATTCCTT-AAAAGCCTTATTACTTGCTTTAAATGGTTTTA
* *
3475 TAATCTCATAATT
65 TAAACTAATAATT
Statistics
Matches: 443, Mismatches: 130, Indels: 38
0.73 0.21 0.06
Matches are distributed among these distances:
170 3 0.01
171 226 0.51
172 212 0.48
173 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.38
Consensus pattern (171 bp):
AAGAAAAGTGCATTTATAGTCACTCATTCCTTAAAAGCCTTATTACTTGCTTTAAATGGTTTTAT
AAACTAATAATTAATTTTAGGTTCAATATTTTTTACATTTTTGGTTAAAACTGATTATAATTGAA
TATCTACCATGAGAAACATGAAGAAAAAGGCATTCATTGGC
Done.