Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397506.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2360.0, 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: 11365
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.24
Warning! 4049 characters in sequence are not A, C, G, or T
Found at i:2626 original size:171 final size:171
Alignment explanation
Indices: 2378--3713 Score: 1030
Period size: 171 Copynumber: 7.8 Consensus size: 171
2368 NNNNNNAAAG
* * * *
2378 AATTCAAATTGAAATCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTAAAG
1 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAG
* * * * * *******
2443 GAACGAGAGACTATAAATTGACTTTTCTTGCTAATGAATGCTTTTGTCTTCATGTTTCNNNNNNN
66 GAATGGGAGACTATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCCCAAGGT
*** * *
2508 NNNCATTCAATTACATTCTGTTTTAATCAAAAATGTAAAAA
131 AGACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAA
*
2549 AATTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAA
1 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-AAA
** * * *
2614 -GAATGGGAGACTATAAACGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACGTTTCTCAATG
65 GGAATGGGAGACTATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCCCAAGG
* ** * *
2678 TAGACACTCAATTATAATCTAATTTAACCAAAAATGTACAAAG
130 TAGACATTCAATTATAATCTGTTTTAATCAAAAATGTA-AAAA
** * * * *
2721 AATTGGA-TTGCAGAT-AATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
1 AATTCAACTT-AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAA
* * *
2784 GGAATGCGAGACTATAAATTGACTTTTCTTGCTAATGAATGCTTTTTTCTTCACCTTTCCCAAGG
65 GGAATGGGAGACTATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCCCAAGG
* * *
2849 TAGCCATTCAATTATAGTCTGTTTTAATGAAAAATGTAACAAA
130 TAGACATTCAATTATAATCTGTTTTAATCAAAAATGTAA-AAA
* * * * * *
2892 AA-TCAACTTATAATTAATTATGAGATTATAAAACAAATTTAAAACGAGTAGTAAGCCTTTTAAA
1 AATTCAACTTAAAATCAATTATGAGATTATAAAAC-CATTTAAAGCGAGTAATAAGGCTTTTAAA
* * *
2956 GGAATGGAAGACTATAAATTGACTTGTT-TTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAG
65 GGAATGGGAGACTATAAATTGACTT-TTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCCCAAG
* * * * * *
3020 GTTGATATTCAATTATAGTCTTTTTTGA-CTAAAAATGTACAAAG
129 GTAGACATTCAATTATAATCTGTTTTAATC-AAAAATGTA-AAAA
* * **********
3064 AATTCAAATTAAAATCAATTATGAGTTTATAAAACCATTTAAANNNNNNNNNNAGGCTTTTGAAA
1 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT-AAA
* ** ** * * * * * ****
3129 -GAATGAGAGACTATAAACGGACTTTTCTTAACATTAAATGCCTTTTTCTTCATGTTTCTCNNNN
65 GGAATGGGAGACTATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCCCAAGG
****** * *
3193 NNNNNNTTTAATTATAGTCTGTTTTAACTTC--AAATGTAAAAA
130 TAGACATTCAATTATAATCTGTTTTAA--TCAAAAATGTAAAAA
* ** * *********
3235 CATTTGACTTAAAATCAATTA-GTAGATTATAATACCATTTAAAGCGAGTAATAAGNNNNNNNNN
1 AATTCAACTTAAAATCAATTATG-AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAA
* * * * * * * * *
3299 NGAATGGAAAACTATAAATGGGCTTTTCTTGTCAATGAATACTTTTTTCTTCACATTTCTCAAGG
65 GGAATGGGAGACTATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCCCAAGG
3364 TAGACATTCAATTATAGA-CTGTTTTAATCAAAAATGTAAAAA
130 TAGACATTCAATTATA-ATCTGTTTTAATCAAAAATGTAAAAA
********** * * *
3406 NNNNNNNNNNAAAATCAATTATGAGATTATGAAAA-TATTTAAA-CTGAGTATTAAGACTTTTGA
1 AATTCAACTTAAAATCAATTATGAGATTAT-AAAACCATTTAAAGC-GAGTAATAAGGCTTTT-A
* * * * *
3469 AA-GAATAGGAGACTATAAATGGACTTTTCTTTCC-ATGAATGCTTTTATCTTC-CTATTTCCCA
63 AAGGAATGGGAGACTATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTCAC-GTTTCCCA
**
3531 AGGTAGACATTCAATTATAATCTGTTTTAATGGAAAATGTAAAAA
127 AGGTAGACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAA
* ** * * * * * * *
3576 ATTTTTACTTAAAATCAATTATAAGCTTAAAAAATCATTTAAAGTGAGTAATAAGCCTTTTAAAA
1 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAG
** * * * * * *
3641 GAATAAGAGACTATAAATGGACTTTTCTTACCATTGAATGCCTTTTTCTTCACATTTCTCAAGGT
66 GAATGGGAGACTATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCCCAAGGT
3706 AGACATTC
131 AGACATTC
3714 NNNNNNNNNN
Statistics
Matches: 911, Mismatches: 221, Indels: 66
0.76 0.18 0.06
Matches are distributed among these distances:
169 11 0.01
170 142 0.16
171 502 0.55
172 221 0.24
173 34 0.04
175 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAG
GAATGGGAGACTATAAATTGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCCCAAGGT
AGACATTCAATTATAATCTGTTTTAATCAAAAATGTAAAAA
Found at i:5606 original size:171 final size:169
Alignment explanation
Indices: 5230--5613 Score: 466
Period size: 170 Copynumber: 2.3 Consensus size: 169
5220 ATTATTTATG
* * *
5230 TTAATGAAAAATGTAAAAAAATCAAC-TAAAATCAATTATGAGATTAGAAAATCATTTAAAGCAA
1 TTAATGAAAAATGTAAAAAAATTAACTTAAAATCAATTATGAGAATAGAAAACCATTTAAAGCAA
* * * * *
5294 GTGATAAGGGTTTTAAAAGAATGGGTGAATATAAATGGACTTTTCTTACCAATGAATACTTTTTT
66 GTAATAAGGCTTTTAAAAGAATGAGAGAATATAAATGGACTTTTCTTACCAATGAATACTTTTTC
** * ** *
5359 TTCATGTTTCTTGAGATAAACAATCAATTATTGTCTGTT
131 TTCACATTTCTTCAGATAAACAATCAATTATCATCAGTT
* * * * * *
5398 TTAATCAAAAATGTAAAAAAACCTAACTTAAAATCAATTTTTAGAATATAAAACCATTTAAAGCT
1 TTAATGAAAAATGTAAAAAAA-TTAACTTAAAATCAATTATGAGAATAGAAAACCATTTAAAGCA
* * * * * *
5463 AGTAATAAGGCTTTTGAAGGAGTGAGAGATTATAAATGGACTTTTCTTGCCAATGAATGCTCTTT
65 AGTAATAAGGCTTTTAAAAGAATGAGAGAATATAAATGGACTTTTCTTACCAATGAATACT-TTT
* *
5528 TCTTCACATTTCTTACAG-TAGACATTCAATTATCATCAGTT
129 TCTTCACATTTCTT-CAGATAAACAATCAATTATCATCAGTT
5569 TTAATGAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGA
1 TTAATGAAAAATGTAAAAAAA-TTAACTTAAAATCAATTATGAGA
5614 TTAGNNNNNN
Statistics
Matches: 179, Mismatches: 33, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
168 20 0.11
169 3 0.02
170 82 0.46
171 72 0.40
172 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (169 bp):
TTAATGAAAAATGTAAAAAAATTAACTTAAAATCAATTATGAGAATAGAAAACCATTTAAAGCAA
GTAATAAGGCTTTTAAAAGAATGAGAGAATATAAATGGACTTTTCTTACCAATGAATACTTTTTC
TTCACATTTCTTCAGATAAACAATCAATTATCATCAGTT
Found at i:5811 original size:342 final size:331
Alignment explanation
Indices: 5312--5959 Score: 680
Period size: 342 Copynumber: 1.9 Consensus size: 331
5302 GGTTTTAAAA
* * * *
5312 GAATGGGTGAATATAAATGGACTTTTCTTACCAATGAATACTTTTTTTTCATGTTTCTTGAGATA
1 GAATAGGTGAATATAAATGGACTTTTCCTACCAATGAATACTTTTCTTTCATGCTTCTTGAGATA
* * *
5377 AACAATCAATTATTGTCTGTTTTAATCAAAAATGTAAAAAAACCTAACTTAAAATCAATTTTTAG
66 AACAATCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAACCTAACTTAAAATCAATTATTAG
* * * * ** *
5442 AATATAAAACCATTTAAAGCTAGTAATAAGGCTTTTGAAGGAGTGAGAGATTATAAATGGACTTT
131 AATATAAAACCATTTAAAGCTAGTAATAAGACTTTTGAAAGAATGAGAGACTATAAACAGACATT
* * *
5507 TCTTGCCAATGAATGCTCTTTTCTTCACATTTCTTACA-GTAGACATTCAATTATCA-TCAGT-T
196 TCTTGCCAATGAATGCTCTTTTCTTCACACTTCTCA-AGGCAGACATTCAATTAT-AGT-A-TAT
**
5569 TTAATGAAAAATGTAAAA-AAATTTAACTTAAAATCAATTATGAGATTAGNNNNNNNNNNAAAGC
257 TTAATGAAAAATGTAAAACAAATAGAACTTAAAATCAATTATGAGATTAG----------AAAGC
5633 GAGTAATATGGCTTTTGAAG
312 GAGTAATATGGCTTTTGAAG
* *
5653 GAATAGGTGACTATAAATGGACTTTTCCTATCAATGAATGATCTTTTCTTT-ATGCTTCTTGAGA
1 GAATAGGTGAATATAAATGGACTTTTCCTACCAATGAAT-A-CTTTTCTTTCATGCTTCTTGAGA
* * * * **********
5717 TAGATATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAA-ATCAACTNNNNNNNNNNTAT
64 TAAACAATCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAACCT-AACTTAAAATCAATTAT
* * * *
5781 TAGATTATAAAACCATTTAAAG-TGAGTAATAAGACTTTTGAAAGAATGGGAGGCTCTAAACAGA
128 TAGAATATAAAACCATTTAAAGCT-AGTAATAAGACTTTTGAAAGAATGAGAGACTATAAACAGA
* * * **
5845 CATTTGTTGCCAATGAATGCTTTTTTTTTCATGCTTCTCAAGGCAGACATTCAATTATAGTATAC
192 CATTTCTTGCCAATGAATGCTCTTTTCTTCACACTTCTCAAGGCAGACATTCAATTATAGTATA-
5910 TTTAATGAAAAATGTAAAACAAATAGAACTTAAAATCAATTATGAGATTA
256 TTTAATGAAAAATGTAAAACAAATAGAACTTAAAATCAATTATGAGATTA
5960 TAAAACCGTT
Statistics
Matches: 254, Mismatches: 44, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
340 1 0.00
341 40 0.16
342 177 0.70
343 36 0.14
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (331 bp):
GAATAGGTGAATATAAATGGACTTTTCCTACCAATGAATACTTTTCTTTCATGCTTCTTGAGATA
AACAATCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAACCTAACTTAAAATCAATTATTAG
AATATAAAACCATTTAAAGCTAGTAATAAGACTTTTGAAAGAATGAGAGACTATAAACAGACATT
TCTTGCCAATGAATGCTCTTTTCTTCACACTTCTCAAGGCAGACATTCAATTATAGTATATTTAA
TGAAAAATGTAAAACAAATAGAACTTAAAATCAATTATGAGATTAGAAAGCGAGTAATATGGCTT
TTGAAG
Found at i:8602 original size:170 final size:170
Alignment explanation
Indices: 8176--9348 Score: 865
Period size: 171 Copynumber: 6.9 Consensus size: 170
8166 NNNNNNNNNN
* * ** *
8176 TAAGTTGAATTTTTTTACATTTTTTATTAAAACAGACTATAATTGAATATCTACAGCAAGAAACA
1 TAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACA
* * * * * *
8241 TGAATAAAATAGCATTCATAGGA-AAGAAAAGT-TCATGTATAGTCTCCTAATCCTTTAAAAGCC
66 TGAAGAAAAAAGCATTCAT-TGACAAGAAAAGTCT-ATTTATAGTCTCCCATTCCTTTAAAA-CC
**********
8304 TTATTACTCGCTTTAAATNNNNNNNNNNTCTCATAATTGATTT
128 TTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * * * **
8347 TAACTTGAA-TTTTTTATATTTTTAATTACAACAGACTATAATTGAATATCTATCTCGGGAAATG
1 TAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACA
********** * *
8411 TGAAGNNNNNNNNNNTCATTGAAAAGAAAAGTCTATTTATAGTCACCCATTCCTTCTAAAA-CTT
66 TGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCCCATTCCTT-TAAAACCTT
** *
8475 ATTACTCGCTTTAAATAATTTTATAATCTCATAATTCATTT
130 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * * *
8516 GAAGTTAAAGTTTTTTACATTTTTTATTAAAACAGACTATAATTAAATGTCTACCGCAAGAAACA
1 TAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACA
* * * * *
8581 TGAATAAAAGAGCATTCATTGACAAGAAAAGTTTATTTATAGTCTCCCAGTCCTTTAGAAGCCTT
66 TGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCCCATTCCTTTA-AAACCTT
* * * * *
8646 ATTACTAGCTTTAAATGGCTTTCTAATCTAATAATTAATTT
130 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * *
8687 TAAGTT-AAATTTTTTATATTTTTGATGAAAACAGA-TAATAATTGAATGTCTATCTCGAGAAA-
1 TAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACT-ATAATTGAATGTCTACCTCGAGAAAC
* * **********
8749 ATTGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCGCNNNNNNNNNNAAAAGCC
65 A-TGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCCCATTCCTTTAAAA-CC
* * *
8814 TTATTACTTGCTTTAAATGGTTGTATACTCTCATAATTGATTT
128 TTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * *
8857 TAAGTTGACTTTTTTTACATTTTTCATTAAAGCAGGCTATAATTGAATATCTACCTTGGGAAACA
1 TAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACA
********** * * * * *
8922 TGAAGAAAAAAGCATTCATTGNNNNNNNNNNTCCATTTATAGCCTCTCAATCCTTCAATAACCTT
66 TGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCCCATTCCTTTAA-AACCTT
* * *
8987 TTTGCTCG-TTCTAAATGGTTTTACAATCTCATAATTGATTT
130 ATTACTCGCTT-TAAATGGTTTTATAATCTCATAATTGATTT
** * ** * * **
9028 TAAACTCAATTTTTTTACATTTTTCATTAAATTATACTATAATTGAATGTCTGCCTTTAGAAACA
1 TAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACA
* * * * *
9093 TTAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTACAGCCTCTCATTCCATTAAAAGCACC
66 TGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCCCATTCC-TTTAAA--ACC
* * *
9158 TTATTACTCGTTTTAAATGGTTTTATAATCTAATAATTAATTT
128 TTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
** * * * * * * * *
9201 TTTGTT-TATTTTTTTACATTTTTGATTAAAACA-AATAATGATTGACTGTTTATCTTGA-AAAC
1 TAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACT-ATAATTGAATGTCTACCTCGAGAAAC
* * * * * * * *
9263 ATTAAGAGAAAAGCATTCATTGGCAAGAAAACTCAATTTATAGTCACCCATTCCTTCGAAAGCCT
65 ATGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCCCATTCCTT-TAAAACCT
9328 TATTACTCGCTTTAAATGGTT
129 TATTACTCGCTTTAAATGGTT
9349 NNNNNNNNNN
Statistics
Matches: 777, Mismatches: 205, Indels: 42
0.76 0.20 0.04
Matches are distributed among these distances:
169 70 0.09
170 301 0.39
171 318 0.41
172 46 0.06
173 40 0.05
174 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (170 bp):
TAAGTTGAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACA
TGAAGAAAAAAGCATTCATTGACAAGAAAAGTCTATTTATAGTCTCCCATTCCTTTAAAACCTTA
TTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
Done.