Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400126.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3342.0, 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: 6142
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.27
Warning! 1507 characters in sequence are not A, C, G, or T
Found at i:2769 original size:172 final size:159
Alignment explanation
Indices: 2567--2882 Score: 282
Period size: 172 Copynumber: 1.9 Consensus size: 159
2557 NNNNNNNNNN
* * * * *
2567 TTGAAAGAATGAGAGACTATAATGGACTTTTCTTGC-CAATGAAT-GCTTTTTGCTTCGCGTTTC
1 TTGAAAGAATGAGAGACTAAAATAGACTTTTCTT-CTCAATGAATGGCTTTTT-CTACACCTTTC
* * *
2630 GT-GTGGTAGGCATTCAATTATAGTCTGT-TTTAACT-AAAAATGTAAAAAAAATTTAACGTAAA
64 -TAG-GGCAGGCAATCAATTATAGT-TGTCTTTAA-TGAAAAATGTAAAAAAAA-TCAACGTAAA
*
2692 ATCAATTATGAGATTATANNNNNNNNNNAAGTGAGTAATAAGGATT
124 ATCAATTATAAGATTATA----------AAGTGAGTAATAAGGATT
* * *
2738 TTGAAGGAATGAGTGACTAGAAATAGACTTTTCTTCTGAATGAATGGCTTTTTCTACACCTTTCT
1 TTGAAAGAATGAGAGACTA-AAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACACCTTTCT
* **
2803 CAGGGCAGGCAATCAATTATAGTTTTCTTTAATGAAAAATGTAAAAAAAATCAATTTAAAATCAA
65 -AGGGCAGGCAATCAATTATAGTTGTCTTTAATGAAAAATGTAAAAAAAATCAACGTAAAATCAA
*
2868 TTATAAGGTTATAAA
129 TTATAAGATTATAAA
2883 ACGTTTTAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
161 2 0.02
171 45 0.37
172 67 0.55
173 8 0.07
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.34
Consensus pattern (159 bp):
TTGAAAGAATGAGAGACTAAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACACCTTTCTA
GGGCAGGCAATCAATTATAGTTGTCTTTAATGAAAAATGTAAAAAAAATCAACGTAAAATCAATT
ATAAGATTATAAAGTGAGTAATAAGGATT
Found at i:3219 original size:17 final size:17
Alignment explanation
Indices: 3194--3236 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
3184 ATAAAAAAAT
*
3194 TGAACTTAAAATCATTC
1 TGAAATTAAAATCATTC
3211 TGAAATTAAAAATCATTC
1 TGAAATT-AAAATCATTC
3229 TGAAATTA
1 TGAAATTA
3237 TAAAACCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (17 bp):
TGAAATTAAAATCATTC
Found at i:3246 original size:19 final size:19
Alignment explanation
Indices: 3200--3246 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
3190 AAATTGAACT
3200 TAAAATCATTCTGAAATTA
1 TAAAATCATTCTGAAATTA
3219 -AAAATCATTCTGAAATTA
1 TAAAATCATTCTGAAATTA
*
3237 TAAAACCATT
1 TAAAATCATT
3247 TAAAGTGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (19 bp):
TAAAATCATTCTGAAATTA
Found at i:3762 original size:171 final size:170
Alignment explanation
Indices: 3219--3785 Score: 503
Period size: 170 Copynumber: 3.3 Consensus size: 170
3209 TCTGAAATTA
* * * ***
3219 AAAATC-ATTCTGAAATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAAGANN
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGGGA
********* * * *
3283 NNNNNNNNGGACTTTTCTTGCCAATGAAT-GCTTTTTTCTTCATGTTTCGTGAGGTAGGCATTCA
66 CTAGAAACAGACTTTTCTT-CAAATGAATGGC-TTTTTCTACATGTTTCTTGAGGTAGGCATTCA
* *
3347 ATTATAGTCTATTTTAACTAAAAATGTTAAAAAAAATTTAACTT
129 ATTATAGTCTATTTTAACTAAAAAT-AT-AAAAAAATTCAACTT
********** * *
3391 AAAATCAATTATGAGATTATAAAACCNNNNNNNNNNAGTAATAAGGATTTTGAAGGAATGAGTGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGGGA
* * *** * *
3456 CTAGAAATAGACTTTTCTTCTTAATGAATGGCTTTTTCTACCCATTTCTAGAGGTAAGCATTCAA
66 CTAGAAACAGACTTTTCTTC-AAATGAATGGCTTTTTCTACATGTTTCTTGAGGTAGGCATTCAA
* **********
3521 TTATAGTCTGTTTTAA-TNNNNNNNNNNAAAAATTCAACTT
130 TTATAGTCTATTTTAACTAAAAATATAAAAAAATTCAACTT
* ** *
3561 AAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTGGTAAGGCTTTTTAAGGAATG-GGGA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGGG-
* * *
3625 ACTATAAACAGACTTTTCTTACAAATGAATGGCTTCTTCTACATGTTTCTTGAGGTAGGTATTCA
65 ACTAGAAACAGACTTTTCTT-CAAATGAATGGCTTTTTCTACATGTTTCTTGAGGTAGGCATTCA
* *
3690 ATTATATTCTATTTTAACTAAAAATATAAAAAAATTCAACTC
129 ATTATAGTCTATTTTAACTAAAAATATAAAAAAATTCAACTT
*
3732 AAAATCAATTGTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA
1 AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA
3786 NNNNNNNNNN
Statistics
Matches: 300, Mismatches: 89, Indels: 13
0.75 0.22 0.03
Matches are distributed among these distances:
169 2 0.01
170 125 0.42
171 64 0.21
172 8 0.03
173 99 0.33
174 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.34
Consensus pattern (170 bp):
AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGGGA
CTAGAAACAGACTTTTCTTCAAATGAATGGCTTTTTCTACATGTTTCTTGAGGTAGGCATTCAAT
TATAGTCTATTTTAACTAAAAATATAAAAAAATTCAACTT
Found at i:4241 original size:174 final size:171
Alignment explanation
Indices: 3933--4479 Score: 439
Period size: 174 Copynumber: 3.2 Consensus size: 171
3923 NNNNNNNNNN
* * *
3933 ATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGAGAGTAATATGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGAGAGTAATAAGGCTTTTGAAGG
* * * * *
3998 AAAGGGTGACTATAAATACACTTTTCTTGCAAGAGAATACTTTTTTCTTCATATTTCTTGAGGTA
66 AAAGGGTGACTATAAATACACTTTTCTTGCAAGAAAATACTTTTTCCTGCATATTTCTAGAGATA
* * *
4063 GACATTCAATTATAATCTGTTTTGACAAAAAATGTAAAAAAAAA
131 GACATGCAATTATAATCTATTTTAACAAAAAATGT---AAAAAA
* * * * *
4107 ATTGAACTTAAAATCAATTTTGAGATTATAAAAACATTTAGAGCGAGTTATAAGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGAGAGTAATAAGGCTTTTGAAGG
** ** ** *
4172 AATA-GGTGACTATAAATGTACTTTTCTT-CTTGATAAATGGTTTTTCCTGCATGTTTCTAGAGA
66 AA-AGGGTGACTATAAATACACTTTTCTTGCAAGA-AAATACTTTTTCCTGCATATTTCTAGAGA
* **
4235 TAGACATGCAATTATAGTCTATTTTAATGAAAAATGTAAAAAA
129 TAGACATGCAATTATAATCTATTTTAACAAAAAATGTAAAAAA
*********** *
4278 ATTCAACTTAAAATCAATT-NNNNNNNNNNNAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAAAC-ATTTAAAGAGAGTAATAAGGCTTTTGAAG
* * ** * * **
4342 GAATGAGTGACTATAAATAGTCTTTTTCTCTG-AATG--AATAGCCTTTT-CTACACCTTTCTCA
65 GAAAGGGTGACTATAAATACAC-TTTTCT-TGCAA-GAAAATA-CTTTTTCCTGCATATTTCT-A
* * * * **
4403 -AGGTAGGCAAT-CAATTATAGT-TTTTTTAATGAAAAATGTAAAAAA
125 GAGATAGAC-ATGCAATTATAATCTATTTTAACAAAAAATGTAAAAAA
*
4448 ATTCAACTTAAAATCAATTATGAGGTTATAAA
1 ATTCAACTTAAAATCAATTATGAGATTATAAA
4480 NNNNNNNNNN
Statistics
Matches: 294, Mismatches: 67, Indels: 27
0.76 0.17 0.07
Matches are distributed among these distances:
170 46 0.16
171 96 0.33
172 13 0.04
173 4 0.01
174 134 0.46
175 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
ATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGAGAGTAATAAGGCTTTTGAAGG
AAAGGGTGACTATAAATACACTTTTCTTGCAAGAAAATACTTTTTCCTGCATATTTCTAGAGATA
GACATGCAATTATAATCTATTTTAACAAAAAATGTAAAAAA
Found at i:4354 original size:171 final size:158
Alignment explanation
Indices: 4138--4467 Score: 332
Period size: 171 Copynumber: 2.0 Consensus size: 158
4128 GAGATTATAA
* *
4138 AAACATTTAGAGCGAGTTATAAGGCTTTTGAAGGAATAGGTGACTATAAAT-GTAC-TTTTCTTC
1 AAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGT-CTTTTTC-TC
** * **
4201 TTG-ATAAAT-GGTTTTTCCTGCATGTTTCT-AGAGATAGAC-ATGCAATTATAGTCTATTTTAA
64 -TGAATAAATAGCCTTTT-CTACACCTTTCTCA-AGATAGACAAT-CAATTATAGT-TATTTTAA
4262 TGAAAAATGTAAAAAAATTCAACTTAAAATCAATT
124 TGAAAAATGTAAAAAAATTCAACTTAAAATCAATT
4297 NNNNNNNNNNNAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GAGTGACTATAAATA
1 -----------AAAC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAG-GTGACTATAAATA
* * * *
4361 GTCTTTTTCTCTGAATGAATAGCCTTTTCTACACCTTTCTCAAGGTAGGCAATCAATTATAGTTT
53 GTCTTTTTCTCTGAATAAATAGCCTTTTCTACACCTTTCTCAAGATAGACAATCAATTATAGTTA
4426 TTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATT
118 TTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATT
4467 A
1 A
4468 TGAGGTTATA
Statistics
Matches: 141, Mismatches: 11, Indels: 27
0.79 0.06 0.15
Matches are distributed among these distances:
159 1 0.01
170 49 0.35
171 76 0.54
172 15 0.11
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35
Consensus pattern (158 bp):
AAACATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGTCTTTTTCTCTG
AATAAATAGCCTTTTCTACACCTTTCTCAAGATAGACAATCAATTATAGTTATTTTAATGAAAAA
TGTAAAAAAATTCAACTTAAAATCAATT
Done.