Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399982.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3209.0, 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: 5118
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.14
Warning! 2621 characters in sequence are not A, C, G, or T
Found at i:3627 original size:27 final size:27
Alignment explanation
Indices: 3544--3846 Score: 207
Period size: 27 Copynumber: 11.3 Consensus size: 27
3534 NNNNNNNGCG
* * *
3544 CTTGGAACGCCCCTGGGCACTTCTGTA
1 CTTGGAACACCCCTAGGCGCTTCTGTA
* * * *
3571 CTTAGAACA-CCCTAGGCGTTTTTGTG
1 CTTGGAACACCCCTAGGCGCTTCTGTA
* *
3597 CTTGGAACACCCCTAAGTGCTTCTGTA
1 CTTGGAACACCCCTAGGCGCTTCTGTA
* * * * **
3624 CTTGAAATACCCCTGGGTGCTTCTGCG
1 CTTGGAACACCCCTAGGCGCTTCTGTA
* *
3651 CTTGAAACTCCCCTAGGCGCTTCTGTA
1 CTTGGAACACCCCTAGGCGCTTCTGTA
* ** * * *
3678 CTTCGAA-TGCCCTCAGGTGTTTCTGTG
1 CTTGGAACACCCCT-AGGCGCTTCTGTA
* * *
3705 CTTGGAACACCCCTAAGCGTTTCTATA
1 CTTGGAACACCCCTAGGCGCTTCTGTA
* * * **
3732 CTTGGAACGCCCCTCGGTGCTTCTGCG
1 CTTGGAACACCCCTAGGCGCTTCTGTA
** *
3759 CTTGGAATGCCCCTTGGCGCTTCTGTA
1 CTTGGAACACCCCTAGGCGCTTCTGTA
** * *
3786 CTTGGAACA-TGCTAGGCGTTTCTGTG
1 CTTGGAACACCCCTAGGCGCTTCTGTA
* *
3812 CTTGGAACACCCCTAGGTGCTTTTGTA
1 CTTGGAACACCCCTAGGCGCTTCTGTA
*
3839 CTTAGAAC
1 CTTGGAAC
3847 GCACCTGGGT
Statistics
Matches: 207, Mismatches: 65, Indels: 8
0.74 0.23 0.03
Matches are distributed among these distances:
26 46 0.22
27 157 0.76
28 4 0.02
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.31
Consensus pattern (27 bp):
CTTGGAACACCCCTAGGCGCTTCTGTA
Found at i:3734 original size:108 final size:107
Alignment explanation
Indices: 3541--3826 Score: 353
Period size: 108 Copynumber: 2.7 Consensus size: 107
3531 NNNNNNNNNN
* * * ** *
3541 GCGCTTGGAACGCCCCTGGGCACTTCTGTACTTAGAACACCCTAGGCGTTTTTGTGCTTGGAACA
1 GCGCTTGGAACTCCCCTAGGCGCTTCTGTACTTAGAATGCCCTAGGCGTTTCTGTGCTTGGAACA
* * * *
3606 CCCCTAAGTGCTTCTGTACTTGAAATACCCCTGGGTGCTTCT
66 CCCCTAAGCGCTTCTATACTTGAAACACCCCTCGGTGCTTCT
* * *
3648 GCGCTTGAAACTCCCCTAGGCGCTTCTGTACTTCGAATGCCCTCAGGTGTTTCTGTGCTTGGAAC
1 GCGCTTGGAACTCCCCTAGGCGCTTCTGTACTTAGAATGCCCT-AGGCGTTTCTGTGCTTGGAAC
* * *
3713 ACCCCTAAGCGTTTCTATACTTGGAACGCCCCTCGGTGCTTCT
65 ACCCCTAAGCGCTTCTATACTTGAAACACCCCTCGGTGCTTCT
* *
3756 GCGCTTGGAA-TGCCCCTTGGCGCTTCTGTACTTGGAACATG--CTAGGCGTTTCTGTGCTTGGA
1 GCGCTTGGAACT-CCCCTAGGCGCTTCTGTACTTAG-A-ATGCCCTAGGCGTTTCTGTGCTTGGA
3818 ACACCCCTA
63 ACACCCCTA
3827 GGTGCTTTTG
Statistics
Matches: 155, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
107 64 0.41
108 87 0.56
109 1 0.01
110 3 0.02
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.30
Consensus pattern (107 bp):
GCGCTTGGAACTCCCCTAGGCGCTTCTGTACTTAGAATGCCCTAGGCGTTTCTGTGCTTGGAACA
CCCCTAAGCGCTTCTATACTTGAAACACCCCTCGGTGCTTCT
Found at i:4170 original size:26 final size:26
Alignment explanation
Indices: 4123--4172 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4113 TATAGAAATG
* *
4123 CCTAGGGTGTTCCAAGCGCAGAAGCA
1 CCTAGGGTGCTCCAAGCACAGAAGCA
*
4149 CCTAGGGTGCTCCAAGTACAGAAG
1 CCTAGGGTGCTCCAAGCACAGAAG
4173 TNNNNNNNNN
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.16
Consensus pattern (26 bp):
CCTAGGGTGCTCCAAGCACAGAAGCA
Found at i:4240 original size:27 final size:27
Alignment explanation
Indices: 4210--4547 Score: 207
Period size: 27 Copynumber: 12.6 Consensus size: 27
4200 CCCAGGTGCA
*
4210 TTCCAAGTACAAAAGCACCTAGGGGTG
1 TTCCAAGTACAGAAGCACCTAGGGGTG
* * *
4237 TTCCAAGTACAGAAACGCCTA-GCGTG
1 TTCCAAGTACAGAAGCACCTAGGGGTG
* * **
4263 TTCCAAGTACAGAAGCGCCCAGGGGCA
1 TTCCAAGTACAGAAGCACCTAGGGGTG
** * **
4290 TTCCAAGCGCAGAAGCACCAAGGGGCA
1 TTCCAAGTACAGAAGCACCTAGGGGTG
* * * * *
4317 TTCCAAGTATAAAAACGCTTAGGGGTG
1 TTCCAAGTACAGAAGCACCTAGGGGTG
* * * **
4344 TTCCAAGCACAGAAACA-CTTGAGGGCA
1 TTCCAAGTACAGAAGCACCTAG-GGGTG
** **
4371 TTCCAAGTACAGAAGTGCCTAGGGAAG
1 TTCCAAGTACAGAAGCACCTAGGGGTG
* ** * *
4398 TTTCAAGCGCAGAAGCACCCAGGGGTA
1 TTCCAAGTACAGAAGCACCTAGGGGTG
* * *
4425 TTTCAAGTTCAGAAGCACTTAGGGGTG
1 TTCCAAGTACAGAAGCACCTAGGGGTG
* * *
4452 TTCCAAGCACAAAAACACCTA-GGGTG
1 TTCCAAGTACAGAAGCACCTAGGGGTG
* ** *
4478 TTCTAAGTACAGAAGTGCCTAGGGGCG
1 TTCCAAGTACAGAAGCACCTAGGGGTG
** * *
4505 TTCCAAGCGCAGAAGCATCC-AGAGGCG
1 TTCCAAGTACAGAAGCA-CCTAGGGGTG
*
4532 TTCCAAGTATAGAAGC
1 TTCCAAGTACAGAAGC
4548 GCCTNNNNNN
Statistics
Matches: 231, Mismatches: 75, Indels: 10
0.73 0.24 0.03
Matches are distributed among these distances:
26 45 0.19
27 181 0.78
28 5 0.02
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (27 bp):
TTCCAAGTACAGAAGCACCTAGGGGTG
Found at i:4291 original size:80 final size:81
Alignment explanation
Indices: 4200--4357 Score: 201
Period size: 80 Copynumber: 2.0 Consensus size: 81
4190 CGTAGAAGAA
* * * ** *
4200 CCCAGGTGCATTCCAAGTACAAAAGCACCTAGGGGTGTTCCAAGTACAGAAACGCCTA-GCGTGT
1 CCCAGGGGCATTCCAAGCACAAAAGCACCAAGGGGCATTCCAAGTACAAAAACGCCTAGGCGTGT
*
4264 TCCAAGTACAGAAGCG
66 TCCAAGCACAGAAGCG
* * * * *
4280 CCCAGGGGCATTCCAAGCGCAGAAGCACCAAGGGGCATTCCAAGTATAAAAACGCTTAGGGGTGT
1 CCCAGGGGCATTCCAAGCACAAAAGCACCAAGGGGCATTCCAAGTACAAAAACGCCTAGGCGTGT
4345 TCCAAGCACAGAA
66 TCCAAGCACAGAA
4358 ACACTTGAGG
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
80 48 0.74
81 17 0.26
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (81 bp):
CCCAGGGGCATTCCAAGCACAAAAGCACCAAGGGGCATTCCAAGTACAAAAACGCCTAGGCGTGT
TCCAAGCACAGAAGCG
Found at i:4341 original size:54 final size:54
Alignment explanation
Indices: 4184--4551 Score: 246
Period size: 54 Copynumber: 6.9 Consensus size: 54
4174 NNNNNNNNNN
* * * * * * * * *
4184 TCCAATCGTAGAAGAACCCAGGTGCATTCCAAGTACAAAAGCACCTAGGGGTGT
1 TCCAAGCGCAGAAGCACCTAGGGGCATTCCAAGTATAGAAGCGCCTAGGGGCGT
** * * * * * *
4238 TCCAAGTACAGAAACGCCTAGCGTG--TTCCAAGTACAGAAGCGCCCAGGGGCAT
1 TCCAAGCGCAGAAGCACCTAG-GGGCATTCCAAGTATAGAAGCGCCTAGGGGCGT
* * * * *
4291 TCCAAGCGCAGAAGCACCAAGGGGCATTCCAAGTATAAAAACGCTTAGGGGTGT
1 TCCAAGCGCAGAAGCACCTAGGGGCATTCCAAGTATAGAAGCGCCTAGGGGCGT
* * * * * **
4345 TCCAAGCACAGAAACA-CTTGAGGGCATTCCAAGTACAGAAGTGCCTAGGGAAGT
1 TCCAAGCGCAGAAGCACCTAG-GGGCATTCCAAGTATAGAAGCGCCTAGGGGCGT
* * * * * * *
4399 TTCAAGCGCAGAAGCACCCAGGGGTATTTCAAGT-TCAGAAGCACTTAGGGGTGT
1 TCCAAGCGCAGAAGCACCTAGGGGCATTCCAAGTAT-AGAAGCGCCTAGGGGCGT
* * * * * *
4453 TCCAAGCACAAAAACACCTAGGGTG--TTCTAAGTACAGAAGTGCCTAGGGGCGT
1 TCCAAGCGCAGAAGCACCTAGGG-GCATTCCAAGTATAGAAGCGCCTAGGGGCGT
* *
4506 TCCAAGCGCAGAAGCATCC-AGAGGCGTTCCAAGTATAGAAGCGCCT
1 TCCAAGCGCAGAAGCA-CCTAGGGGCATTCCAAGTATAGAAGCGCCT
4552 NNNNNNNNNN
Statistics
Matches: 234, Mismatches: 69, Indels: 22
0.72 0.21 0.07
Matches are distributed among these distances:
52 3 0.01
53 77 0.33
54 148 0.63
55 6 0.03
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.18
Consensus pattern (54 bp):
TCCAAGCGCAGAAGCACCTAGGGGCATTCCAAGTATAGAAGCGCCTAGGGGCGT
Found at i:4546 original size:107 final size:106
Alignment explanation
Indices: 4201--4547 Score: 417
Period size: 107 Copynumber: 3.2 Consensus size: 106
4191 GTAGAAGAAC
* * * * * *
4201 CCAGGTGCATTCCAAGTACAAAAGCACCTAGGGGTGTTCCAAGTACAGAAACGCCTAGCGTGTTC
1 CCAGGGGCATTCCAAGTATAAAAGCACTTAGGGGTGTTCCAAGCACAGAAACACCTAGGGTGTTC
* * *
4266 CAAGTACAGAAGCGCCCAGGGGCATTCCAAGCGCAGAAGCA
66 CAAGTACAGAAGTGCCTAGGGGCGTTCCAAGCGCAGAAGCA
* * * **
4307 CCAAGGGGCATTCCAAGTATAAAAACGCTTAGGGGTGTTCCAAGCACAGAAACACTTGAGGGCAT
1 CC-AGGGGCATTCCAAGTATAAAAGCACTTAGGGGTGTTCCAAGCACAGAAACACCT-AGGGTGT
** *
4372 TCCAAGTACAGAAGTGCCTAGGGAAGTTTCAAGCGCAGAAGCA
64 TCCAAGTACAGAAGTGCCTAGGGGCGTTCCAAGCGCAGAAGCA
* * * *
4415 CCCAGGGGTATTTCAAGT-TCAGAAGCACTTAGGGGTGTTCCAAGCACAAAAACACCTAGGGTGT
1 -CCAGGGGCATTCCAAGTAT-AAAAGCACTTAGGGGTGTTCCAAGCACAGAAACACCTAGGGTGT
*
4479 TCTAAGTACAGAAGTGCCTAGGGGCGTTCCAAGCGCAGAAGCA
64 TCCAAGTACAGAAGTGCCTAGGGGCGTTCCAAGCGCAGAAGCA
* * *
4522 TCCAGAGGCGTTCCAAGTATAGAAGC
1 -CCAGGGGCATTCCAAGTATAAAAGC
4548 GCCTNNNNNN
Statistics
Matches: 201, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
106 2 0.01
107 110 0.55
108 87 0.43
109 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.18
Consensus pattern (106 bp):
CCAGGGGCATTCCAAGTATAAAAGCACTTAGGGGTGTTCCAAGCACAGAAACACCTAGGGTGTTC
CAAGTACAGAAGTGCCTAGGGGCGTTCCAAGCGCAGAAGCA
Done.