Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401873.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4977.0, 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: 5127
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.23
Warning! 1961 characters in sequence are not A, C, G, or T
Found at i:3708 original size:171 final size:168
Alignment explanation
Indices: 3222--3743 Score: 502
Period size: 171 Copynumber: 3.1 Consensus size: 168
3212 CGCCTTCGAG
** * *
3222 AGCCTTATTACTCATTTTAAATAGTTTTGTAGTCTCATAATTGAGTTTAAGTTAGATATTTG--T
1 AGCCTTATTACTCGCTTTAAATAGTTTTGTAATCTCATAATTGATTTTAAGTTA-A-ATTTGTTT
* * * * * *
3285 ATATTTTTGGTTAAAACCGACTA-TAATTGAATGTTTACCTTAAAAAACAGGAAGAAAAGGGTAT
64 ACATTTTTGATTAAAA-CAACTATTAATTGAATGTTTGCCTT-AAAAACATGAAGAAAAAGG-AT
* * * *
3349 TTATTAGCAAGAAAAGTTTATTTATTGTCA-CTCATTCTTTTAAA
126 TTATT-GTAAGAAAAGTCTATTTATAGTCACCT-ATTCTTTCAAA
* * * * *
3393 AGCCTTATTACTCGCTTTTAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAC
1 AGCCTTATTACTCGCTTTAAATAGTTTTGTAATCTCATAATTGATTTTAAGTTAAATTTGTTTAC
* * * ** *
3458 ATTTTTGATTAAAACAAGT-TATAATTGATTGTCTGCCTTAAGAAATGTGAAGCAAAAATTG-TT
66 ATTTTTGATTAAAACAACTAT-TAATTGAATGTTTGCCTTAA-AAACATGAAG-AAAAA-GGATT
* * * * *
3521 CACTTATACA-AAAAGTCTACTTGTAGTCACCTATTCCTTCAAA
127 TA-TTGTA-AGAAAAGTCTATTTATAGTCACCTATTCTTTCAAA
* *
3564 AGTCTTATTACTCGCTTTAAATAGTTTTGCAATCTCATAATTGATTTTAAGTTAAATTTGTTTAC
1 AGCCTTATTACTCGCTTTAAATAGTTTTGTAATCTCATAATTGATTTTAAGTTAAATTTGTTTAC
3629 ATTTTTGATTAAAACATA-TATTAATTGAATGTTTGCCTTGAAAAACATGAAGAAAAAGGAATTT
66 ATTTTTGATTAAAACA-ACTATTAATTGAATGTTTGCCTT-AAAAACATGAAGAAAAAGG-ATTT
* * * * *
3693 GTTGGTAGGAAAAGTCCATTTATAGTTACCCATTCTTTCAAA
128 ATT-GTAAGAAAAGTCTATTTATAGTCACCTATTCTTTCAAA
3735 AGCCTTATT
1 AGCCTTATT
3744 GCTCANNNNN
Statistics
Matches: 281, Mismatches: 53, Indels: 34
0.76 0.14 0.09
Matches are distributed among these distances:
169 5 0.02
170 13 0.05
171 249 0.89
172 13 0.05
173 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (168 bp):
AGCCTTATTACTCGCTTTAAATAGTTTTGTAATCTCATAATTGATTTTAAGTTAAATTTGTTTAC
ATTTTTGATTAAAACAACTATTAATTGAATGTTTGCCTTAAAAACATGAAGAAAAAGGATTTATT
GTAAGAAAAGTCTATTTATAGTCACCTATTCTTTCAAA
Found at i:4634 original size:173 final size:170
Alignment explanation
Indices: 4135--4665 Score: 543
Period size: 171 Copynumber: 3.1 Consensus size: 170
4125 NNNNNNNNNN
* * * *
4135 TAATTGATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAAATAGGCTATAATT-AACTGTCAGC
1 TAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAAGCTATAATTGAA-TGTCTGC
* * * ** *
4199 CTTGAAAAACATGAA-AAGAAAGCCATTCATAGGCAAGAAAAGTTTATTTATAGTCACTGATTCC
65 CTTGAAAAACATGAAGAA-AAAGCCATTCATTGGCAA-AAAAGTTCATTTATAGTAACCAATTCT
* * * *
4263 TTCAATAGCTTTACTACTCACTTTAAATGGTTTTATAATATCG
128 TTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAATCTCG
* * * * *
4306 TAATTGATTTTAGGTTGAATATTTTCACATTTTTGGTTAAAAC-AGATTATAATTGAATGTTTGC
1 TAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAAG-CTATAATTGAATGTCTGC
** * * ** * * * **
4370 C-CAAAGAAACGTGAGGAAAAAGATATTCATTGACTAGAAAAGTTCATTTATAGTCACCCAAGCC
65 CTTGAA-AAACATGAAGAAAAAGCCATTCATTGGC-AAAAAAGTTCATTTATAGT-AACCAATTC
* ** *
4434 TTT-GAAAGCCGTATTACTTGCTTTAAATGGTTTTATAATCTCG
127 TTTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAATCTCG
* * * * *
4477 TAATTAATTTTAAGTTGAATTTTTTTTAAACTTTTTTTGCTAAAACAAGCTATACTTGAATGTCT
1 TAATTGATTTTAAGTTGAA-TTTTTTT--ACATTTTTGGTTAAAACAAGCTATAATTGAATGTCT
*
4542 GCCTTGAAAAACATGAAGAAAAA-CCATTCATTGGCAAAACAAGTCCATTTATAGTAACCAATTC
63 GCCTTGAAAAACATGAAGAAAAAGCCATTCATTGGCAAAA-AAGTTCATTTATAGTAACCAATTC
*
4606 TTTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAATCTCA
127 TTTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAATCTCG
*
4650 TAATTCATTTTAAGTT
1 TAATTGATTTTAAGTT
4666 AATCTCATAA
Statistics
Matches: 285, Mismatches: 62, Indels: 24
0.77 0.17 0.06
Matches are distributed among these distances:
170 3 0.01
171 135 0.47
172 27 0.09
173 73 0.26
174 43 0.15
175 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (170 bp):
TAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAAGCTATAATTGAATGTCTGCC
TTGAAAAACATGAAGAAAAAGCCATTCATTGGCAAAAAAGTTCATTTATAGTAACCAATTCTTTC
AAAAGCTTTATTACTCGCTTTAAATGGTTTTATAATCTCG
Found at i:4669 original size:23 final size:23
Alignment explanation
Indices: 4642--4688 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4632 AATGGTTTTA
4642 TAATCTCATAATTCATTTTAAGT
1 TAATCTCATAATTCATTTTAAGT
4665 TAATCTCATAATTCATTTTAAGT
1 TAATCTCATAATTCATTTTAAGT
4688 T
1 T
4689 GAATTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (23 bp):
TAATCTCATAATTCATTTTAAGT
Found at i:4836 original size:194 final size:195
Alignment explanation
Indices: 4469--4861 Score: 456
Period size: 194 Copynumber: 2.0 Consensus size: 195
4459 AATGGTTTTA
* * * *
4469 TAATCTCGTAATTAATTTTAAGTTGAATTTTTTTTAAACTTTTTTTGCTAAAACAAGCTATACTT
1 TAATCTCATAATTAATTTTAAGTTGAATTTTTGTTAAACTTTTTTT-CTAAAACAAGCTACAATT
* * *
4534 GAATGTCTGCCTTGAAAAACATGAAGAAAAACCATTCATTGGCAAAACAAGTCCATTTATAGTAA
65 GAATGTCTACCTTCAAAAACATGAAGAAAAACCATTCATTGACAAAACAAGTCCATTTATAGTAA
* * * * * *
4599 CCAATTCTTTCAAAAGCTTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAG
130 CCAATGCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTAATTTTAAA
4664 T
195 T
* * *
4665 TAATCTCATAATTCATTTTAAGTTGAA-TTTTGTTACA-TTTTTTAT-TAAAACATA-TTACAAT
1 TAATCTCATAATTAATTTTAAGTTGAATTTTTGTTAAACTTTTTT-TCTAAAACA-AGCTACAAT
* ** * *
4726 TGAATGTCTACC-TCAAGAAACATGAAGAAACAGCCATTTGTTGACTAGAA-AAGTTCATTTATA
64 TGAATGTCTACCTTCAA-AAACATGAAGAAA-AACCATTCATTGAC-AAAACAAGTCCATTTATA
* * * * *
4789 GTCACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATTTTATAATTAATTT
126 GTAACCAATGCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTAATTT
4854 TAAAT
191 TAAAT
4859 TAA
1 TAA
4862 ATTTTTTTTA
Statistics
Matches: 166, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
192 3 0.02
193 35 0.21
194 91 0.55
195 12 0.07
196 25 0.15
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (195 bp):
TAATCTCATAATTAATTTTAAGTTGAATTTTTGTTAAACTTTTTTTCTAAAACAAGCTACAATTG
AATGTCTACCTTCAAAAACATGAAGAAAAACCATTCATTGACAAAACAAGTCCATTTATAGTAAC
CAATGCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTAATTTTAAAT
Done.