Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402942.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_603.0, 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: 11830
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.25
Warning! 3893 characters in sequence are not A, C, G, or T
Found at i:5160 original size:169 final size:171
Alignment explanation
Indices: 4852--5189 Score: 448
Period size: 169 Copynumber: 2.0 Consensus size: 171
4842 NNNNNNNNNN
* * **
4852 CATAATTGATTTTAAGTTAAATTTTTTTACATTTTTCATTAAAACAGACTATAAATGAATGTTTG
1 CATAATTGATTTTAAGTTAAATTTTTTTACATTTTTCACTAAAACAAACTATAAATGAATGCATG
** * * * *
4917 CCTTGAGAAATATGTAGAAAAAGTCATTCACTGAGAAGAAAAGTCTATTTATAGTCACCCATTCC
66 CCTCAAGAAATAGGTAGAAAAAGTCATTCACTAAGAAGAAAAGTCCATTCATAGTCACCCATTCC
* * *
4982 TTGAAAAGCTTTATTGCTCGCTTTAAATTGTATTATAATAT
131 TTCAAAAGCTTTATTACTCACTTTAAATTGTATTATAATAT
* * *
5023 CATAATT-ATTTTAAG-TAGATGTTTTTTACATTTTTCACTAAAATAAACTATAATTGAATGCAT
1 CATAATTGATTTTAAGTTAAAT-TTTTTTACATTTTTCACTAAAACAAACTATAAATGAATGCAT
* * * * *
5086 GCCTCAAGAAAT-GGTAGAAAATGTCATTTATTAAGAAGAAAATTCCATTCATATTCACCCATTC
65 GCCTCAAGAAATAGGTAGAAAAAGTCATTCACTAAGAAGAAAAGTCCATTCATAGTCACCCATTC
*
5150 CTTCAAAAGCTTTATTACTCACTTTAAATTGTTTTATAAT
130 CTTCAAAAGCTTTATTACTCACTTTAAATTGTATTATAAT
5190 TTCANNNNNN
Statistics
Matches: 144, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
169 83 0.58
170 54 0.38
171 7 0.05
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (171 bp):
CATAATTGATTTTAAGTTAAATTTTTTTACATTTTTCACTAAAACAAACTATAAATGAATGCATG
CCTCAAGAAATAGGTAGAAAAAGTCATTCACTAAGAAGAAAAGTCCATTCATAGTCACCCATTCC
TTCAAAAGCTTTATTACTCACTTTAAATTGTATTATAATAT
Found at i:5751 original size:171 final size:170
Alignment explanation
Indices: 5435--6054 Score: 468
Period size: 171 Copynumber: 3.6 Consensus size: 170
5425 NNNNNNNNTC
* ** * * *
5435 TTTTAACATTTTTGGTTAAAAAAGACTATAATTGAATG-TGTACCTC-AAAAAATATGATGAAAA
1 TTTTTACATTTTTCATTAAAATAGACTATAATTGAATGCT-TACCTCGAGAAAATGT-A-GAAAA
* * * * * * *
5498 AGGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTTCTTGAAAAGCCTTATTACACGC
63 AGTCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTGCTCGC
* * * *********
5563 TTGAAATAGTTTTATAATCCCATAATTGATTNNNNNNNNNNT-T
128 TTTAAATAGTATTATAATACCATAATTGATT-TTAAACAGATGT
5606 TTTTTACATTTTTCATTAAAATAGACTATAATTGAATGCTTACCTCGAGAAACATGTAGAAAAAG
1 TTTTTACATTTTTCATTAAAATAGACTATAATTGAATGCTTACCTCGAGAAA-ATGTAGAAAAAG
* * * * *
5671 TCATTCACTGATAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTAATTGCTCACTT
65 TCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTGCTCGCTT
* * *
5736 TAAATTGTATTATAATATCATAATTTATTTTAAACAGATGT
130 TAAATAGTATTATAATACCATAATTGATTTTAAACAGATGT
* * * * * *
5777 TTTTTACATTGTTCACTAAAATAGACTATAACTGAATGCTTGCCTTGAG-AAATGGTAGAAAATG
1 TTTTTACATTTTTCATTAAAATAGACTATAATTGAATGCTTACCTCGAGAAAAT-GTAGAAAAAG
* * * * * *
5841 TCATTTATTGAGAAGAACAGTCCATTCATATTGACCCATTCCTTCAAAAGCCTTATTGCTCGCTT
65 TCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTGCTCGCTT
********** ** *
5906 TANNNNNNNNNNTAAT-CTCATAATTGATTTTAAGTTAAATG-
130 TAAATAGTATTATAATAC-CATAATTGATTTTAA-ACAGATGT
* * * * * * *
5947 TTTTTA-GTTTTTTAGTTAAAACAAACTATAATTGAATG-TCTACCTCAAGAAACCTGAAGAAAA
1 TTTTTACATTTTTCA-TTAAAATAGACTATAATTGAATGCT-TACCTCGAGAAA-ATGTAGAAAA
6010 AGGT-ATTCATT-AGCAAGAAAAGTCCATTTATAGTCACCCATTCCT
63 A-GTCATTCATTGA-CAAGAAAAGTCCATTTATAGTCACCCATTCCT
6055 NNNNNNNNNN
Statistics
Matches: 353, Mismatches: 83, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
169 8 0.02
170 119 0.34
171 214 0.61
172 9 0.03
173 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.35
Consensus pattern (170 bp):
TTTTTACATTTTTCATTAAAATAGACTATAATTGAATGCTTACCTCGAGAAAATGTAGAAAAAGT
CATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTGCTCGCTTT
AAATAGTATTATAATACCATAATTGATTTTAAACAGATGT
Found at i:6514 original size:170 final size:169
Alignment explanation
Indices: 6210--6694 Score: 525
Period size: 170 Copynumber: 2.8 Consensus size: 169
6200 GAAACATGTA
* * * * * *
6210 GAAAAAGTCATTTATTGAGAAGAAAAGTGCATTTATTGTCATCCATTCTTTCAAAAGCCTTATTG
1 GAAAAAGTCATTTCTTGAGAAGAAAAGTCCATTTATAGTTACCCATTCCTTCAAAAGCCTTATTG
* * * * * * * **
6275 CTCGCTTTAAATTGTATTATAATATTATAATTGATTTTAAGTAGAGTTTTCTTATATTTATCATT
66 ATCGCTTTAAATTGTTTTATAATATAATAATTGATTTTAAGTTGAATTTTTTTACATTT-TTGTT
* * * *
6340 AAAACAGACTATAATTGAATGCCTGCC-TCTAGAAA-GGA-
130 AAAACAGACTATAATCGAAGGCCTACCAT-GAGAAACGGAG
*
6378 TAAAAATTGTCATTTCTTGAGAAGAAAAGTCCATTTATAGTTACCCATTCCTTCAAAAGCCTTAT
1 GAAAAA--GTCATTTCTTGAGAAGAAAAGTCCATTTATAGTTACCCATTCCTTCAAAAGCCTTAT
* *
6443 TGATCCCTTTAAATTGTTTTATAATATAATAATTGATTTTAAATTGAATTTTTTTACATTTTTGT
64 TGATCGCTTTAAATTGTTTTATAATATAATAATTGATTTTAAGTTGAATTTTTTTACATTTTTG-
* *
6508 TTAAAACAGACTATAATCGAAGGTCTACCATGAGAAACCTGAG
128 TTAAAACAGACTATAATCGAAGGCCTACCATGAGAAA-CGGAG
*
6551 GAAAAAGGCA-TTCATTG-GCAAGAAAAGTCCATTTATA-TT-CGCCTATTCCTTCAAAAGCCTT
1 GAAAAAGTCATTTC-TTGAG-AAGAAAAGTCCATTTATAGTTAC-CC-ATTCCTTCAAAAGCCTT
** ** * * * *
6612 ATTTTTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTCAAGTTAAATTTTTTTACATTTTT
62 ATTGATCGCTTTAAATTGTTTTATAATATAATAATTGATTTTAAGTTGAATTTTTTTACATTTTT
6677 AGTTAAAACAGACTATAA
127 -GTTAAAACAGACTATAA
6695 NNNNNNNNNN
Statistics
Matches: 269, Mismatches: 36, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
168 5 0.02
169 2 0.01
170 141 0.52
171 113 0.42
172 3 0.01
173 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (169 bp):
GAAAAAGTCATTTCTTGAGAAGAAAAGTCCATTTATAGTTACCCATTCCTTCAAAAGCCTTATTG
ATCGCTTTAAATTGTTTTATAATATAATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGTTA
AAACAGACTATAATCGAAGGCCTACCATGAGAAACGGAG
Found at i:6715 original size:171 final size:169
Alignment explanation
Indices: 6198--7645 Score: 631
Period size: 171 Copynumber: 8.5 Consensus size: 169
6188 TGCTTGCCTC
* * * * *
6198 GAGAAACATGTAGAAAAAGTCATTTATTGAG-AAGAAAAGTGCATTTAT-TGTCATCCATTCTTT
1 GAGAAACATGAAGAAAAAGACATTAATTG-GCAAGAAAAGTCCATTTATAT-TC--CCATTCCTT
** * * * * * * * *
6261 CAAAAGCCTTATTGCTCGCTTTAAATTGTATTATAATATTATAATTGATTTTAAGTAGAGTTTTC
62 CAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
* * * * * *
6326 TTATATTTATCA-TTAAAACAGACTATAATTGAATGCCTGCC-T
127 TTACATTT-TTAGTTAAAACAGACTATAATCGAAGGTCTACCAT
* * ** * **
6368 CTAGAAAGGAT-AA-AAATTGTCATTTCTTGAG-AAGAAAAGTCCATTTATAGTTACCCATTCCT
1 -GAGAAA-CATGAAGAAAAAGACATTAATTG-GCAAGAAAAGTCCATTTATA-TT-CCCATTCCT
* * * * * *
6430 TCAAAAGCCTTATTGATCCCTTTAAATTGTTTTATAATATAATAATTGATTTTAAATTGAATTTT
61 TCAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTT
6495 TTTACATTTTT-GTTTAAAACAGACTATAATCGAAGGTCTACCAT
126 TTTACATTTTTAG-TTAAAACAGACTATAATCGAAGGTCTACCAT
* * * *
6539 GAGAAACCTGAGGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATATTCGCCTATTCCTTCA
1 GAGAAACATGAAGAAAAAGACATTAATTGGCAAGAAAAGTCCATTTATATTC-CC-ATTCCTTCA
** * * * *
6604 AAAGCCTTATTTTTCGCTTTAAAAGGTTTTATAATCTCATAATTGATTTCAAGTTAAATTTTTTT
64 AAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT
********** *
6669 ACATTTTTAGTTAAAACAGACTATAANNNNNNNNNNACCTT
129 ACATTTTTAGTTAAAACAGACTATAATCGAAGGTCTACCAT
** *
6710 GAGAAACATGAAGAAAAAGACATTAATTGGCAAGAAAAGTCTC-TTTATAGGCACCCATTCCTTT
1 GAGAAACATGAAGAAAAAGACATTAATTGGCAAGAAAAGTC-CATTTATA--TTCCCATTCCTTC
* * * *
6774 TAAAGCCCTATTACTCATTTTAAATGGTTTTACT-ATCTCATAATTGATTTTAAGTTGAATTTTT
63 AAAAGCCTTATTAATCACTTTAAATGGTTTTA-TAATCTCATAATTGATTTTAAGTTGAATTTTT
* ********** * * *
6838 TTATATTTTTTA-TTAAAANNNNNNNNNNTTGAATG-CTTGCC-T
127 TTACA-TTTTTAGTTAAAACAGACTATAATCGAAGGTC-TACCAT
* * ** * * * * * *
6880 CTAAAAACATTTAGAAAAAGCCATTCATTAAG-AAGAACAGTCAATTTATATTTACTCATTCCTT
1 -GAGAAACATGAAGAAAAAGACATTAATT-GGCAAGAAAAGTCCATTTATA-TT-CCCATTCCTT
* ** *** * ********** *
6944 GAAAAGCCTTATTGCTTGTTTTAAATTGTTTTATAATCTCATNNNNNNNNNNAAGTTGAATTATT
62 CAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
* * * * *
7009 TTACAATTTTAGTTAAAACAGACTATAATTGAATGTCTATCTT
127 TTACATTTTTAGTTAAAACAGACTATAATCGAAGGTCTACCAT
* ** ** * * * * * *
7052 AAGAAATGTGAAGAAAATCATATTCATTTGCAAGAAAAGCCCA-TTATAGTCACCTATTCTTTCA
1 GAGAAACATGAAGAAAAAGACATTAATTGGCAAGAAAAGTCCATTTATATTC-CC-ATTCCTTCA
** * * * ** *********
7116 AAAATCTTGTTACTCACTTGAAATACTTTTATAATCTCATAATTGATTTTAAGTTGNNNNNNNNN
64 AAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT
* * * **
7181 NCATTTTTAGTT-AAATAGACTATAATTGAATATCTACC-T
129 ACATTTTTAGTTAAAACAGACTATAATCGAAGGTCTACCAT
* * * * * * ** *
7220 CGAGAATCGTAAAGAAAAAGATATTTATTGACAAGAAAAGTTAATTTATAGTCACCTATTCCTTC
1 -GAGAAACATGAAGAAAAAGACATTAATTGGCAAGAAAAGTCCATTTATATTC-CC-ATTCCTTC
** ** * ** * * *
7285 AAAAGCCTTATTGCTCGTTTTAATTTATTTTATAATCTCAAAATTGATTTTAAGTTTAACTTTTT
63 AAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTT
* * **
7350 TATATTTTTAGTTAAAACAGACTATAATCGAATGTCTACCCC
128 TACATTTTTAGTTAAAACAGACTATAATCGAAGGTCTACCAT
* * * * ********** **
7392 GAGAAACGTGAAAAAAAAG-TATTCATTGGCAAGAAAAGTCTNNNNNNNNNNACATATTCCTTCA
1 GAGAAACATGAAGAAAAAGACATTAATTGGCAAGAAAAGTC--CATTTATATTCCCATTCCTTCA
* * * * *
7456 AAAGCCTTATTACTCCCTTTAAATTGTTTTAGAATCTCATAATTGATTTTAAGTTAAATTTTTTT
64 AAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT
* * * * * *
7521 --A---TAAATTAAAACAAACTATAATTGAATGTCTGCC-T
129 ACATTTTTAGTTAAAACAGACTATAATCGAAGGTCTACCAT
* * * * * * *
7556 CGAGAAATATAAAGAAAAAGACAATCATTGGCAAGCAAAGTCCATTTATAGTCACCCATTTCTTC
1 -GAGAAACATGAAGAAAAAGACATTAATTGGCAAGAAAAGTCCATTTATA-T-TCCCATTCCTTC
* *
7621 AAAAGCCTTATTACTCGCTTTAAAT
63 AAAAGCCTTATTAATCACTTTAAAT
7646 NNNNNNNNNN
Statistics
Matches: 958, Mismatches: 279, Indels: 85
0.72 0.21 0.06
Matches are distributed among these distances:
165 43 0.04
166 51 0.05
168 3 0.00
169 59 0.06
170 362 0.38
171 420 0.44
172 19 0.02
173 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
GAGAAACATGAAGAAAAAGACATTAATTGGCAAGAAAAGTCCATTTATATTCCCATTCCTTCAAA
AGCCTTATTAATCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAC
ATTTTTAGTTAAAACAGACTATAATCGAAGGTCTACCAT
Found at i:7257 original size:169 final size:161
Alignment explanation
Indices: 7182--7636 Score: 186
Period size: 170 Copynumber: 2.7 Consensus size: 161
7172 NNNNNNNNNN
* * *
7182 CATTTTTAGTT-AAATAGACTATAATTGAATATCTACCTCGAG-AATCGTAAAGAAAAAGATATT
1 CATTTTTAGTTAAAACAGACTATAATTGAATATCTACCTCAAGAAAT-GTAAAGAAAAACATATT
* ** * * ** *
7245 TA-TTGACAAGAAAAGTTAATTTATAGTCACCTATTCCTTCAAAAGCCTTATTGCTCGTTTTAAT
65 CATTTG-CAAGAAAAGCCAATTTATAGTCACCTATTCCTTCAAAAACCTTATTACTCACTTGAAT
* *
7309 TTATTTTATAATCTCAAAATTGATTTTAAGTTTAA
129 ATATTTTATAATCTCAAAATTGATTTTAAG-TT-G
* * * * *
7344 CTTTTTTATATTTTTAGTTAAAACAGACTATAATCGAATGTCTACCCCGAGAAACGTGAAA-AAA
1 C--------ATTTTTAGTTAAAACAGACTATAATTGAATATCTACCTCAAGAAATGT-AAAGAAA
* * * *********** * * *
7408 AA-GTATTCATTGGCAAGAAAAGTCTNNNNNNNNNNACATATTCCTTCAAAAGCCTTATTACTCC
57 AACATATTCATTTGCAAGAAAAGCCAATTTATAGTCACCTATTCCTTCAAAAACCTTATTACTCA
* * * * *
7472 CTTTAA-ATTGTTTTAGAATCTCATAATTGATTTTAAGTTA
122 CTTGAATA-TATTTTATAATCTCAAAATTGATTTTAAGTTG
* * * * * * * *
7512 AATTTTTTTATAAATTAAAACAAACTATAATTGAATGTCTGCCTCGAGAAATATAAAGAAAAAGA
1 CA---TTTT-T-AGTTAAAACAGACTATAATTGAATATCTACCTCAAGAAATGTAAAGAAAAACA
* * * * * * *
7577 CAATCATTGGCAAGCAAAGTCC-ATTTATAGTCACCCATTTCTTCAAAAGCCTTATTACTC
61 TATTCATTTGCAAGAAAAG-CCAATTTATAGTCACCTATTCCTTCAAAAACCTTATTACTC
7637 GCTTTAAATN
Statistics
Matches: 218, Mismatches: 54, Indels: 38
0.70 0.17 0.12
Matches are distributed among these distances:
160 1 0.00
162 1 0.00
163 4 0.02
164 4 0.02
165 40 0.18
166 41 0.19
167 1 0.00
168 1 0.00
169 2 0.01
170 82 0.38
171 36 0.17
172 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.35
Consensus pattern (161 bp):
CATTTTTAGTTAAAACAGACTATAATTGAATATCTACCTCAAGAAATGTAAAGAAAAACATATTC
ATTTGCAAGAAAAGCCAATTTATAGTCACCTATTCCTTCAAAAACCTTATTACTCACTTGAATAT
ATTTTATAATCTCAAAATTGATTTTAAGTTG
Found at i:11505 original size:169 final size:169
Alignment explanation
Indices: 11254--11728 Score: 487
Period size: 170 Copynumber: 2.8 Consensus size: 169
11244 TTAAAGCCAG
* * * * ** * * *
11254 CAATAAAGATTTTGAAGAAATGGGTGAGTATAAATGAACCGTTCTTCTCAATGAATGATTTTTTT
1 CAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTCTTAATAAATGA--CTTTT
* *
11319 TTA-CGTTTCACGAGGTAGACATTCAATTATAGTCTG-TTTAACT-AAAAATGTAAAAAAATTCA
64 CTACCGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAA-TGAAAAATGTAAAAAAATTCA
* *
11381 AGTTTAAATCAATTATGAGATTATAAAACAATTTAAAGAGGGA
128 AATTTAAATCAATTATGAGATTATAAAACAATTTAAAG-GGAA
*
11424 -AATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTCTTAATAAATGACAATTTC
1 CAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTCTTAATAAATGAC-TTTTC
* * * * ** * * *
11488 TACCGTTTCTTGAGGTAGGCATTCAATTGTAGTCTGTTTTAATGATAAACATAAAAAAACTCTAC
65 TACCGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTCAAA
* * ** *
11553 TTAAAATCAATTATGATATTATATTACAATTTAAAGTGAA
130 TTTAAATCAATTATGAGATTATAAAACAATTTAAAGGGAA
* * *
11593 CAATAAGGGTTTTTAAGGAATGGGTGACTATAAATGGACTTTTCTT-TTCAATAAATGACTTTGT
1 CAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTCTT-AATAAATGACTTT-T
** * * * *
11657 CTACATATTTCTCGAGGCA-AGCATTCAATTACAGTCTGTTTTAATGACAAATGTAAAGAAATT-
64 CTAC-CGTTTCTCGAGGTAGA-CATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTC
11720 AAATTTAAA
127 AAATTTAAA
11729 ATCANNNNNN
Statistics
Matches: 250, Mismatches: 46, Indels: 18
0.80 0.15 0.06
Matches are distributed among these distances:
168 5 0.02
169 85 0.34
170 115 0.46
171 45 0.18
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (169 bp):
CAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTCTTAATAAATGACTTTTCT
ACCGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAAAAATTCAAAT
TTAAATCAATTATGAGATTATAAAACAATTTAAAGGGAA
Done.