Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397889.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1193.0, 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: 16540
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.18
Warning! 8892 characters in sequence are not A, C, G, or T
Found at i:3253 original size:171 final size:169
Alignment explanation
Indices: 2953--3695 Score: 766
Period size: 171 Copynumber: 4.3 Consensus size: 169
2943 CTCGAGTTAG
* * * *
2953 ACATTGAATTATTGTCTATTTTTAAAAAAATTATAAAAAAATTCAACCTAAAATCAATTATGAGA
1 ACATTCAATTATAGTCTATTTTTAAAAAAA-TACAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * *
3018 TTATAAAATCATTTAAACCGAGTAATAAAGCTTTCGAAGGAATGGGTGACTATAAATAGACTTTT
65 TTATAAAATCATTAAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT
* * * * *
3083 GTTCTCAATGAGTAAGCATTTTCTACACGTTTCTCAAGGCAG
130 GTTTTCAATGA--ATGCTTTTTCTACACGTTTCTCAAGGTAA
** * *
3125 GTATTCAATTATAGTCTATTTTTAAAAAAATACAAAAAAATTCAACTTAAAATCAATTATTAGGT
1 ACATTCAATTATAGTCTATTTTTAAAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * * *
3190 TATAAAATCGTTAAAAGCGGGTAATAAGCCTTTTGAAGGAATGAGTGATTATAAATGGACTTTT-
66 TATAAAATCATTAAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTG
* * *
3254 TTTTCAAT-AACTGGCTTTTTTTACATGTTTCTCAAGATAA
131 TTTTCAATGAA-T-GCTTTTTCTACACGTTTCTCAAGGTAA
* * * *
3294 ACAATCAATTTTAGTCTA-TTTTAACCAAAAATGTA-AAAAAAATTCAATTTAAAATCAGTTATG
1 ACATTCAATTATAGTCTATTTTTAA--AAAAA--TACAAAAAAATTCAACTTAAAATCAATTATG
* *
3357 AGATTATAAAA-CTATTTAAAA-CGAGCAATAAGGCTTTTGAAGGAATGGGTGACTCTAAATGGA
62 AGATTATAAAATC-A-TTAAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGA
* * ** **
3420 CTTTTCTTTTCAATGAATGCTTTTTTCTTCATATTTCTTGAGGTAA
125 CTTTTGTTTTCAATGAATGC-TTTTTCTACACGTTTCTCAAGGTAA
* * * * *
3466 ACGTTCAATTATAGTATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGA
1 ACATTCAATTATAGTCTATTTTTA-AAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGA
* * * * * * * *
3531 TTATAAAACCAATT-AATGCGAGTACTAAGGTTTTTGAAGAAATTGGTGACTCTAAATGAACTTT
65 TTATAAAATC-ATTAAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTT
* * * *
3595 AGTTATCAATGAATGCTTGTTTCTTCACGTTTCTCAAGGTAC
129 TGTTTTCAATGAATGCTT-TTTCTACACGTTTCTCAAGGTAA
*
3637 ACATTCAATTATAGTCTA-TTTTAATAAAAATGTC-AAAAAATTCAACTTAAAATCAATTA
1 ACATTCAATTATAGTCTATTTTTAA-AAAAAT-ACAAAAAAATTCAACTTAAAATCAATTA
3696 GGAAACTATA
Statistics
Matches: 475, Mismatches: 77, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
167 1 0.00
168 6 0.01
169 37 0.08
170 54 0.11
171 288 0.61
172 82 0.17
173 6 0.01
174 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (169 bp):
ACATTCAATTATAGTCTATTTTTAAAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGAT
TATAAAATCATTAAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTG
TTTTCAATGAATGCTTTTTCTACACGTTTCTCAAGGTAA
Found at i:3668 original size:342 final size:339
Alignment explanation
Indices: 2953--3717 Score: 855
Period size: 342 Copynumber: 2.2 Consensus size: 339
2943 CTCGAGTTAG
* * *
2953 ACATTGAATTATTGTCTATTTTTAAAAAAAT-TATAAAAAAATTCAACCTAAAATCAATTATGAG
1 ACATTCAATTATAGTCTA-TTTTAAAAAAATGTA-AAAAAAATTCAACTTAAAATCAATTATGAG
* *
3017 ATTATAAAA-TCATTTAAACCGAGTAATAAAGCTTTCGAAGGAATGGGTGACTATAAATAGACTT
64 ATTATAAAACT-ATTTAAAACGAGCAATAAAGCTTTCGAAGGAATGGGTGACTATAAATAGACTT
* * *** *
3081 TTGTTCTCAATGAGTAAGCATTTTCTACACGTTTCTCAAGGCAGGTATTCAATTATAGTCTATTT
128 TTCTTCTCAATGAG-AAGCATTTTCTACACATTTCTCAAGGCAAACATTCAATTATAGTATATTT
* * * * * *
3146 TTAAAAAAATACAAAAAAATTCAACTTAAAATCAATTATTAGGTTATAAAATCGTTAAAAGCGGG
192 TAAAAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTAAAAGCGAG
* * * * *
3211 TAATAAGCCTTTTGAAGGAATGAGTGATTATAAATGGACTTTTTTTTCAATAACTGGCTTTTTTT
257 TAATAAGCCTTTTGAAGAAATGAGTGACTATAAATGAACTTTGTTATCAATAACTGGCTTTTTTT
*
3276 ACATGTTTCTCAAGATAA
322 ACACGTTTCTCAAGATAA
* * * *
3294 ACAATCAATTTTAGTCTATTTTAACCAAAAATGTAAAAAAAATTCAATTTAAAATCAGTTATGAG
1 ACATTCAATTATAGTCTATTTTAA--AAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAG
* * * *
3359 ATTATAAAACTATTTAAAACGAGCAATAAGGCTTTTGAAGGAATGGGTGACTCTAAATGGACTTT
64 ATTATAAAACTATTTAAAACGAGCAATAAAGCTTTCGAAGGAATGGGTGACTATAAATAGACTTT
* * * * * ** * * *
3424 TCTTTTCAATGA-ATGCTTTTTTCTTCATATTTCTTGAGGTAAACGTTCAATTATAGTATGTTTT
129 TCTTCTCAATGAGAAGC-ATTTTCTACACATTTCTCAAGGCAAACATTCAATTATAGTATATTTT
* *
3488 AATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAATT-AATGCGA
193 AA-AAAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACC-ATTAAAAGCGA
* ** *
3552 GTACTAAGGTTTTTGAAGAAATTG-GTGACTCTAAATGAACTTTAGTTATCAATGAA-T-GCTTG
256 GTAATAAGCCTTTTGAAGAAA-TGAGTGACTATAAATGAACTTT-GTTATCAAT-AACTGGCTT-
* *
3614 TTTCTT-CACGTTTCTCAAGGTAC
317 TTT-TTACACGTTTCTCAAGATAA
* * *
3637 ACATTCAATTATAGTCTATTTTAATAAAAATGT-CAAAAAATTCAACTTAAAATCAATTAGGAAA
1 ACATTCAATTATAGTCTATTTTAA-AAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGA
*
3701 CTATAAAACTATTTAAA
65 TTATAAAACTATTTAAA
3718 GCAAATANNN
Statistics
Matches: 354, Mismatches: 58, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
340 9 0.03
341 91 0.26
342 196 0.55
343 54 0.15
344 4 0.01
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (339 bp):
ACATTCAATTATAGTCTATTTTAAAAAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGAT
TATAAAACTATTTAAAACGAGCAATAAAGCTTTCGAAGGAATGGGTGACTATAAATAGACTTTTC
TTCTCAATGAGAAGCATTTTCTACACATTTCTCAAGGCAAACATTCAATTATAGTATATTTTAAA
AAAAATACAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTAAAAGCGAGTAAT
AAGCCTTTTGAAGAAATGAGTGACTATAAATGAACTTTGTTATCAATAACTGGCTTTTTTTACAC
GTTTCTCAAGATAA
Found at i:7650 original size:171 final size:171
Alignment explanation
Indices: 7296--7668 Score: 426
Period size: 171 Copynumber: 2.2 Consensus size: 171
7286 NNNNNNNNNN
* * * * *
7296 TTTACATTTTTTGTTAAAACAGACTATAATCAATTGTCTACCTCAGGAAACGTGCAGAAACAAGC
1 TTTACATTTTTTATTAAAACAGACTATAATTAATTATCTACCTCAGGAAACCTGCAAAAACAAGC
* * *
7361 ATTCATTGACAGAAAAAGTCCATTTAGAGTCACCTATTCCTTCAAAAAGTTTATTATTTGCTTTA
66 ATTCATTGACAGAAAAAGTCCATTTAGAGTCACCTACTCCTTCAAAAAGCTTATTATTTACTTTA
* * ****
7426 AATAGTTTTTTAATCTCATAATTGATTTTAAGTTGAANNNN
131 AATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTGT
****** * * * ** *
7467 NNNNNNTTTTTTATTAAAACAGTCTATAATTGATTATTTACCTCAGGAAACCTTTAAAAACAAGG
1 TTTACATTTTTTATTAAAACAGACTATAATTAATTATCTACCTCAGGAAACCTGCAAAAACAAGC
* *
7532 ATTCATTGACA-AGAAAAGTCCATTTAGAGTCA-CTCACTCTTTCAAAATGCTTATTATTTACTT
66 ATTCATTGACAGA-AAAAGTCCATTTAGAGTCACCT-ACTCCTTCAAAAAGCTTATTATTTACTT
* *
7595 TAAATAGTTTTATAATTTCTTAATTGATTTTAAGTTAAATTGT
129 TAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTGT
* *
7638 TTTACATTTTTTAATAAAATAGACTATAATT
1 TTTACATTTTTTATTAAAACAGACTATAATT
7669 NNNNNNNNNN
Statistics
Matches: 161, Mismatches: 39, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
170 3 0.02
171 158 0.98
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.39
Consensus pattern (171 bp):
TTTACATTTTTTATTAAAACAGACTATAATTAATTATCTACCTCAGGAAACCTGCAAAAACAAGC
ATTCATTGACAGAAAAAGTCCATTTAGAGTCACCTACTCCTTCAAAAAGCTTATTATTTACTTTA
AATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTGT
Found at i:8777 original size:172 final size:161
Alignment explanation
Indices: 8471--8803 Score: 387
Period size: 172 Copynumber: 2.0 Consensus size: 161
8461 NNNNNATTCC
* * *
8471 TTCAAAAGGCTTATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTGGTTTTAAGTAGAATTG
1 TTCAAAAAGCTTATTACTCGCTTTAAATAGTTTTAGAATCTCAAAATTGATTTTAAGTAGAATTG
* * ***
8536 TTTTATATTTTTTGTTAAAACAGACTATAATCGATTGTCTACCTTGGGAAACGTGCAGAAACAAG
66 TTTTATATTTTTTATTAAAACAGACTATAATCGATTATCTACCTCAAGAAACGTGCAGAAACAAG
* *
8601 CATTCATTGATAAGAAAAGTCTATTTAGAGNNNNNNNNNNT
131 CATTCATTGACAAGAAAAGTCCATTTAGAG----------T
* * * * * *
8642 TTCAAAAAGCTTATTATTTGCTTTAAATAGTTTTAGAATCTCATAATTGATTTTAAGTTGACTTT
1 TTCAAAAAGCTTATTACTCGCTTTAAATAGTTTTAGAATCTCAAAATTGATTTTAAGTAGAATTG
* * * *
8707 TTTTTTCATTTTTTATTAAAACAGTCTATAATTGATTATTTACCTCAAGAAACGTGCAGAAACAA
66 TTTTAT-ATTTTTTATTAAAACAGACTATAATCGATTATCTACCTCAAGAAACGTGCAGAAACAA
8772 GCATTCATTGACAAGAAAAGTCCATTTAGAGT
130 GCATTCATTGACAAGAAAAGTCCATTTAGAGT
8804 CACTCNNNNN
Statistics
Matches: 141, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
162 1 0.01
171 61 0.43
172 79 0.56
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.38
Consensus pattern (161 bp):
TTCAAAAAGCTTATTACTCGCTTTAAATAGTTTTAGAATCTCAAAATTGATTTTAAGTAGAATTG
TTTTATATTTTTTATTAAAACAGACTATAATCGATTATCTACCTCAAGAAACGTGCAGAAACAAG
CATTCATTGACAAGAAAAGTCCATTTAGAGT
Found at i:10535 original size:171 final size:171
Alignment explanation
Indices: 10146--10582 Score: 461
Period size: 171 Copynumber: 2.6 Consensus size: 171
10136 NNNNNNGGAG
* **
10146 TCACCTATTCCTTTGAAAAGCTTATTATTTGCTTTAAATAGTGTTT-TAATCTCATAATTGATTT
1 TCACCCATTCCTTCAAAAAGCTTATTATTTGCTTTAAATAGT-TTTATAATCTCATAATTGATTT
* * * *
10210 TAAGTTGAATTTTTTTACATTCTTTGTTAAAATTGACTATAATTGATTTTTCATCTCGAGAAACG
65 TAAGTTGAATTTTTTTACATTCTTTATTAAAATAGACTATAATTGATTTCTCACCTCGAGAAACG
* * * * * *
10275 TGTAGAAACAAGTATTCATTGACAGGAAAAGTCTATTTGGAG
130 TGCAGAAACAAGCATTCATTGACAAGAAAAATCTATTTAGAC
**********
10317 TCACCCATTCCTTCAAAAAGCTTATTATTTNNNNNNNNNNGTTTTATAATCTCATAATTGATTTT
1 TCACCCATTCCTTCAAAAAGCTTATTATTTGCTTTAAATAGTTTTATAATCTCATAATTGATTTT
* *
10382 AAGTTGAGCTTTTTTATA-ATT-TTTATTAAAATAGACTATTATTGATTGTCT-ACCTC-AGGAA
66 AAGTTGA-ATTTTTT-TACATTCTTTATTAAAATAGACTATAATTGATT-TCTCACCTCGA-GAA
* **
10443 ATGTGCAGAAACAAGCATTCATTGTTAAGAAAAATCTATTTAGAC
127 ACGTGCAGAAACAAGCATTCATTGACAAGAAAAATCTATTTAGAC
* * * * *
10488 TCACCGATTCTTTCAAAAATCTTATTATTTGCTTTAAATACTTTTATAATTTCATAATTGATTTT
1 TCACCCATTCCTTCAAAAAGCTTATTATTTGCTTTAAATAGTTTTATAATCTCATAATTGATTTT
* * * *
10553 AAGTTCAATTTTTTTATATTATTTGTTAAA
66 AAGTTGAATTTTTTTACATTCTTTATTAAA
10583 NNNNNNNNNN
Statistics
Matches: 213, Mismatches: 46, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
169 2 0.01
170 13 0.06
171 185 0.87
172 11 0.05
173 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.43
Consensus pattern (171 bp):
TCACCCATTCCTTCAAAAAGCTTATTATTTGCTTTAAATAGTTTTATAATCTCATAATTGATTTT
AAGTTGAATTTTTTTACATTCTTTATTAAAATAGACTATAATTGATTTCTCACCTCGAGAAACGT
GCAGAAACAAGCATTCATTGACAAGAAAAATCTATTTAGAC
Found at i:15466 original size:172 final size:161
Alignment explanation
Indices: 15262--15595 Score: 328
Period size: 172 Copynumber: 2.0 Consensus size: 161
15252 TTAAGTTCAA
* * ** * *
15262 TTTTTTTATATTTTTTGTTAAAATAGACTATAATTGAGTGTCTACTTCTGGAAACGTGAAGAAAC
1 TTTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTACCACTAGAAACGGGAAGAAAC
**********
15327 AAGCATTCATNNNNNNNNNNAGTCCATTTAGAGTCACCTATTCATTGAAAAAAGCTTATTACTAG
66 AAGCATTCATTGTTAAGAAAAGTCCATTTAGAGTCACCTATTCATT-AAAAAAGCTTATTACTAG
*
15392 CTTTAAATAGTTTTATAATCTCATAATTGATT
130 ATTTAAATAGTTTTATAATCTCATAATTGATT
*
15424 TTNNNNNNNNNNTTTTTATA-TTTTTGATTAAAACATACTATAATTGAATGTCTACCACTAGAAA
1 TT----------TTTTTATATTTTTTG-TTAAAACAGACTATAATTGAATGTCTACCACTAGAAA
* * * * * *
15488 TGGGAAGAAACAAGCATTCATTGTTAAGAAAAGTCGATTTAGAGTCACCTATTCCTTCAAAAGGT
55 CGGGAAGAAACAAGCATTCATTGTTAAGAAAAGTCCATTTAGAGTCACCTATTCATTAAAAAAGC
*
15553 TTATTACTTGATTTAAATAGTTTTATAATCTCATAATTGATT
120 TTATTACTAGATTTAAATAGTTTTATAATCTCATAATTGATT
15595 T
1 T
15596 GAAGTTGAAT
Statistics
Matches: 136, Mismatches: 25, Indels: 13
0.78 0.14 0.07
Matches are distributed among these distances:
162 2 0.01
171 52 0.38
172 82 0.60
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.38
Consensus pattern (161 bp):
TTTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTACCACTAGAAACGGGAAGAAAC
AAGCATTCATTGTTAAGAAAAGTCCATTTAGAGTCACCTATTCATTAAAAAAGCTTATTACTAGA
TTTAAATAGTTTTATAATCTCATAATTGATT
Done.