Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401632.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_475.0, 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: 22774
ACGTcount: A:0.20, C:0.07, G:0.06, T:0.20
Warning! 10588 characters in sequence are not A, C, G, or T
Found at i:2693 original size:171 final size:171
Alignment explanation
Indices: 2399--2707 Score: 410
Period size: 171 Copynumber: 1.8 Consensus size: 171
2389 NNNNNNNNNN
* * * * * * *
2399 AGAAATGTGAAGAAAAACGCATTCATTGGCAGGAAAAGTCTATTTATAGTCACCCATTTCTTCTA
1 AGAAACGTGAAGAAAAACGCATACATTGGCAAGAAAAGCCCATTTATAGTCACCCATTCCTTCAA
* *
2464 AAGCTTTATTACTTGTTCAAAATTATTTTATAATCTCAAAATTGATTCTCAATTGAATTTTTTTA
66 AAGCCTTATTACTTCTTCAAAATTATTTTATAATCTCAAAATTGATTCTCAATTGAATTTTTTTA
*
2529 TATTTTTGATCAAAACAGACAATATTTGAATATTTACTTTG
131 CATTTTTGATCAAAACAGACAATATTTGAATATTTACTTTG
* * *
2570 AGAAACGTGAAGAAAAAGGGATACATTGGCAAGAAAAGCCCATTTATTGTCACCCATTCCTTCAA
1 AGAAACGTGAAGAAAAACGCATACATTGGCAAGAAAAGCCCATTTATAGTCACCCATTCCTTCAA
* * *
2635 AAGCCTTATTA-TTCACTT-TAAATT-TTTATATAATCTCATAATTGATT-TTAAGTTGAATTTT
66 AAGCCTTATTACTT--CTTCAAAATTATTT-TATAATCTCAAAATTGATTCTCAA-TTGAATTTT
2696 TTTACATTTTTG
127 TTTACATTTTTG
2708 GTTAAANNNN
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
170 8 0.07
171 108 0.92
172 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (171 bp):
AGAAACGTGAAGAAAAACGCATACATTGGCAAGAAAAGCCCATTTATAGTCACCCATTCCTTCAA
AAGCCTTATTACTTCTTCAAAATTATTTTATAATCTCAAAATTGATTCTCAATTGAATTTTTTTA
CATTTTTGATCAAAACAGACAATATTTGAATATTTACTTTG
Found at i:6273 original size:45 final size:44
Alignment explanation
Indices: 6222--6311 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
6212 NNNNNNNNNN
*
6222 TATAATCTCATAATTAATTTTAAGTT-AATTGTTTTTAAATTATTT
1 TATAATCTCATAACTAATTTTAAGTTGAATT-TTTTTAAATT-TTT
* * *
6267 TATAATCTCCTAACTGATTTTAAGTTGAATTTTTTTATATTTTT
1 TATAATCTCATAACTAATTTTAAGTTGAATTTTTTTAAATTTTT
6311 T
1 T
6312 GTCAAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 4 0.10
45 32 0.80
46 4 0.10
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.57
Consensus pattern (44 bp):
TATAATCTCATAACTAATTTTAAGTTGAATTTTTTTAAATTTTT
Found at i:7080 original size:170 final size:169
Alignment explanation
Indices: 6567--7591 Score: 738
Period size: 170 Copynumber: 6.0 Consensus size: 169
6557 NNNNNNNNNN
* * *
6567 TTAAAGCGAGTAATAAAGCTTCGAAAGAAATGGGTGACTATAAAT-GCACTTTTCTTGCCAATGA
1 TTAAAGCGAGTAATAAGGCTTTGAAAGGAATGGGTGACTATAAATAG-ACTTTTCTTGCCAATGA
* * * *
6631 ATTCGTTTTTCTTCACTTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAAT-CAAAAATAT
65 ATGC-TTTTTCTTCACGTTTCTCGAAGTAAACATTCAATTATAGTCTG-TTT-ATCCAAAAATAT
********** * *
6695 AAAAAAANNNNNNNNNNAATCAATTATGAGATTATATAATAAT
127 AAAAAAATTTAATTCAAAATCAATTATGAGATTATAAAACAAT
* * * * * * *
6738 TTAAAGCGAGTAATAAGGCTTTCAAAGGAATGCGTGGCTATAAATGGACTTTTTTTTGCCGATGT
1 TTAAAGCGAGTAATAAGGCTTTGAAAGGAATGGGTGACTATAAATAGAC-TTTTCTTGCCAATGA
* * * * * * * *
6803 ATCCCTTTTTCTTCACGTTT-TTGCAGGCAGACAATCAAATATTA-TTTGTTT-TGACCAAAAAT
65 AT-GCTTTTTCTTCACGTTTCTCG-AAGTAAACATTCAATTA-TAGTCTGTTTAT--CCAAAAAT
* * *
6865 GT-AAAAAATTTCAATTGAAAATCAATTTTGAGATTATAAAACAAT
125 ATAAAAAAATTT-AATTCAAAATCAATTATGAGATTATAAAACAAT
* **
6910 TTAAAGCGAGCAATAAAGG-TTTGAAAAAAATGGGCT-ACTATAAATAGACTTTTCTTGCCAATG
1 TTAAAGCGAGTAAT-AAGGCTTTGAAAGGAATGGG-TGACTATAAATAGACTTTTCTTGCCAATG
*
6973 AATGCATTTTTCTTCACGTTTCTCGAAGTAAACATTCAATTATTGTCTGTTTATCCAAAAATATA
64 AATGC-TTTTTCTTCACGTTTCTCGAAGTAAACATTCAATTATAGTCTGTTTATCCAAAAATATA
* * *
7038 AAAAAATTTGATTCAAAATTAATTATGAGATTATAGAACAAT
128 AAAAAATTTAATTCAAAATCAATTATGAGATTATAAAACAAT
********** *
7080 TTAAAGCGAGTAATAAGGCTTNNNNNNNNNNGAGTGACTATAAATAGACTTTTCTTGCCAATGAA
1 TTAAAGCGAGTAATAAGGCTTTGAAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAA
* * * * * * * * *
7145 CGGCTTGTTCTAT-ACGTTTTTCGAGGTAAACATTTAATTATAGTTTTTTTAAT-GAGAAATATA
66 -TGCTTTTTCT-TCACGTTTCTCGAAGTAAACATTCAATTATAGTCTGTTT-ATCCAAAAATATA
** * *
7208 AAAAAATTTAA--CCTAATCAATTTTGAGATTATAAAATAAT
128 AAAAAATTTAATTCAAAATCAATTATGAGATTATAAAACAAT
********* * * *
7248 TTAAAGCGAGTAANNNNNNNNNNG-AAGGAATGGCTGACTATAAATGGACTTTTCATGCCAAT-A
1 TTAAAGCGAGTAA-TAAGGCTTTGAAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGA
* * * * * * **
7311 AGTGTCTTTTTCTTTACGTTTCTC-AAGGTATAGATTTAATTATAGTATATTTAAACAAAAATAT
65 A-TG-CTTTTTCTTCACGTTTCTCGAA-GTAAACATTCAATTATAGTCTGTTTATCCAAAAATAT
* *
7375 AAAAAAATTTAACTT-AAAATCAGTTATGAGATTGTAAAACAAT
127 AAAAAAATTTAA-TTCAAAATCAATTATGAGATTATAAAACAAT
* * * *
7418 TTAAAGCGAGTAATAAGGATTTTG-AATGAATGAGTGACTATAAATAGACTTTTCTTACCAATGA
1 TTAAAGCGAGTAATAAGG-CTTTGAAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGA
* * * * *
7482 ATGTGTTTTTCTTCACATTTCTCAAAGTAAACATTCAATTATTGTCTGTTTTATCCAAAAATGT-
65 ATG-CTTTTTCTTCACGTTTCTCGAAGTAAACATTCAATTATAGTCTG-TTTATCCAAAAATATA
* * * * * *
7546 AAAAAAGTCAACTT-GAAATTAGTTATGAGATTATAAAATAAT
128 AAAAAATTTAA-TTCAAAATCAATTATGAGATTATAAAACAAT
7588 TTAA
1 TTAA
7592 NNNNNNNNNN
Statistics
Matches: 664, Mismatches: 157, Indels: 67
0.75 0.18 0.08
Matches are distributed among these distances:
167 6 0.01
168 118 0.18
169 7 0.01
170 283 0.43
171 128 0.19
172 114 0.17
173 8 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (169 bp):
TTAAAGCGAGTAATAAGGCTTTGAAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAA
TGCTTTTTCTTCACGTTTCTCGAAGTAAACATTCAATTATAGTCTGTTTATCCAAAAATATAAAA
AAATTTAATTCAAAATCAATTATGAGATTATAAAACAAT
Found at i:7331 original size:168 final size:159
Alignment explanation
Indices: 7114--7436 Score: 337
Period size: 168 Copynumber: 2.0 Consensus size: 159
7104 NNNNNNNGAG
* * *
7114 TGACTATAAATAGACTTTTCTTGCCAATGAACGGCTTGTTCTATACGTTTTTCGAGGTAAACATT
1 TGACTATAAATAGACTTTTCATGCCAATGAACGGCTTGTTCTATACGTTTCTCAAGGTAAACATT
* * ** * *
7179 TAATTATAGTTTTTTTAATGAGAAATATAAAAAAATTTAACCT-AATCAATTTTGAGATTATAAA
66 TAATTATAGTATATTTAAACAAAAATATAAAAAAATTTAACCTAAATCAATTATGAGATTATAAA
*
7243 ATAATTTAAAGCGAGTAANNNNNNNNNNGAAGGAATGGC
131 ACAATTTAAAGCGAGTAA----------GAAGGAATGGC
* * * * *
7282 TGACTATAAATGGACTTTTCATGCCAAT-AA-GTGTCTTTTTCTTTACGTTTCTCAAGGTATAGA
1 TGACTATAAATAGACTTTTCATGCCAATGAACG-G-CTTGTTCTATACGTTTCTCAAGGTAAACA
* * *
7345 TTTAATTATAGTATATTTAAACAAAAATATAAAAAAATTTAACTTAAAATCAGTTATGAGATTGT
64 TTTAATTATAGTATATTTAAACAAAAATATAAAAAAATTTAACCT-AAATCAATTATGAGATTAT
*
7410 AAAACAATTTAAAGCGAGTAATAAGGA
128 AAAACAATTTAAAGCGAGTAAGAAGGA
7437 TTTTGAATGA
Statistics
Matches: 132, Mismatches: 19, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
160 5 0.04
166 1 0.01
167 3 0.02
168 88 0.67
170 35 0.27
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.35
Consensus pattern (159 bp):
TGACTATAAATAGACTTTTCATGCCAATGAACGGCTTGTTCTATACGTTTCTCAAGGTAAACATT
TAATTATAGTATATTTAAACAAAAATATAAAAAAATTTAACCTAAATCAATTATGAGATTATAAA
ACAATTTAAAGCGAGTAAGAAGGAATGGC
Found at i:8905 original size:171 final size:170
Alignment explanation
Indices: 8501--9227 Score: 447
Period size: 171 Copynumber: 4.3 Consensus size: 170
8491 CATTGGCAAG
* * * ***
8501 AAAAGTCCATTTATAGTCACCCATTTCTCCAAAACCCTTATTACTCACTTTAAATTG-TTTTNNN
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT-AATTGATTTTATA
******* * ** * *
8565 NNNNNNNAATTGATTTTAAGTTGAATTT-TTTT-CATTTTTTGTTCAAACAGACTATAATTGAAT
65 ATCTCATAATTAATTTTAAGTTGAATTTGTTTTACATTTTTCATTAAAATAGACTATAATTGAAT
* * * * **
8628 -CTCTACCTTGAGAAACGTG-AGGAAAAAGGCATTCATTGGCATG
130 GCTCT-CCTAGAGAAACATGTA-GAAAAAGTCATTCA-TAG-AAA
* * ** * ***********
8671 AAAAGTTCATTTATAGACAGTCATTTCTTCAAAAGCCTTATTACTCGNNNNNNNNNNTTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAATTGATTTTATAA
* * *
8736 TCTCAAAATTGATTTTAAGTAGAATTTG-TTTACATTTTTCATTAAAATAGACTATAATTGAATG
66 TCTCATAATTAATTTTAAGTTGAATTTGTTTTACATTTTTCATTAAAATAGACTATAATTGAATG
* *
8800 CT-TCCCTCGAGAAACATGTAGAATAAGTCATTCATTGAGAAA
131 CTCT-CCTAGAGAAACATGTAGAAAAAGTCATTCA-T-AGAAA
* * *
8842 AAAAGTCCATTTAGAGTCACGCATTCCTTCAAAAACCTTATTACTCACTTTAAATT-ATTTTATA
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT-AATTGATTTTATA
**********
8906 ATCTCATNNNNNNNNNNAAGTTGAATTTGTTTTACATTTTT-AGTTAAAATAGACTATAATTGAA
65 ATCTCATAATTAATTTTAAGTTGAATTTGTTTTACATTTTTCA-TTAAAATAGACTATAATTGAA
* * * * *
8970 TG-TCTACCTTGAGAAATACGAAGAAAAGAGT-ATTCATA-AAG
129 TGCTCT-CCTAGAGAAACATGTAGAAAA-AGTCATTCATAGAAA
********** *
9011 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTNNNNNNNNNNTTTAATTGGTTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAATTGATTTTATAA
* * * * ** *
9076 ACTCATAATTAATTTTAAGTTGAA-ATGTTTTACATATTTCATTATACCAGAGTATAATTGAATG
66 TCTCATAATTAATTTTAAGTTGAATTTGTTTTACATTTTTCATTAAAATAGACTATAATTGAATG
* * * * *
9140 CATGTCTTAGA-AAACGTGTAGAAAAAGCCATTTAATAAGAAA
131 C-TCTCCTAGAGAAACATGTAGAAAAAGTCA-TTCAT-AGAAA
9182 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
9228 GNNNNNNNNN
Statistics
Matches: 414, Mismatches: 124, Indels: 37
0.72 0.22 0.06
Matches are distributed among these distances:
167 2 0.00
168 47 0.11
169 70 0.17
170 71 0.17
171 161 0.39
172 60 0.14
173 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.35
Consensus pattern (170 bp):
AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAATTGATTTTATAA
TCTCATAATTAATTTTAAGTTGAATTTGTTTTACATTTTTCATTAAAATAGACTATAATTGAATG
CTCTCCTAGAGAAACATGTAGAAAAAGTCATTCATAGAAA
Found at i:10030 original size:172 final size:161
Alignment explanation
Indices: 9820--10141 Score: 321
Period size: 172 Copynumber: 1.9 Consensus size: 161
9810 NNNNNNNNNN
* * * *
9820 ATCTCAAAATTGATTTTCAATTGAGTTTTTTCATATTTTT-AGTCAAAACAGACAATATTTGATT
1 ATCTCAAAATTGATTTTCAAATGAATTTTTTCATATTTTTGA-TCAAAACAGACAATAATTGAAT
*
9884 GTCTACCTAT-A-AAAACATGAAGAAAAAAG-AATAGATTAGCAAGAAAAGTCCATTTATAGTCA
65 GTCTA-CTATGAGAAAA-ATGAAGAAAAAAGCAAT-CATTAGCAAGAAAAGTCCATTTATAGTCA
9946 CCCATTTCTTCAAAAGCCTTATTACNNNNNNNNNNTTATTATATA
127 CCCATTTCTTCAAAAGCCTTATTAC----------TTATTATATA
* * * **
9991 ATCTCATAATTGATTTT-AAGATGAATTTGTTTTATATTTTTGATTAAAACAGACTGTAATTGAA
1 ATCTCAAAATTGATTTTCAA-ATGAATTT-TTTCATATTTTTGATCAAAACAGACAATAATTGAA
* * * * *
10055 TGTCTACTTTGAGAAAAGTGAAGAAAAATGCAATCATTGGCAAGAAAAGTCTATTTATAGTCACC
64 TGTCTACTATGAGAAAAATGAAGAAAAAAGCAATCATTAGCAAGAAAAGTCCATTTATAGTCACC
*
10120 CATTTCTTCAAAAGCTTTATTA
129 CATTTCTTCAAAAGCCTTATTA
10142 NNNNNNNNNN
Statistics
Matches: 129, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
170 2 0.02
171 25 0.19
172 94 0.73
173 8 0.06
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.36
Consensus pattern (161 bp):
ATCTCAAAATTGATTTTCAAATGAATTTTTTCATATTTTTGATCAAAACAGACAATAATTGAATG
TCTACTATGAGAAAAATGAAGAAAAAAGCAATCATTAGCAAGAAAAGTCCATTTATAGTCACCCA
TTTCTTCAAAAGCCTTATTACTTATTATATA
Found at i:10558 original size:171 final size:170
Alignment explanation
Indices: 10245--10630 Score: 492
Period size: 171 Copynumber: 2.3 Consensus size: 170
10235 NNNNNNNGCC
* *
10245 TTATTACTCGCTTTAAATTATTTTATAATCTCATAATTAATATTAAATCAATTTTTTTGTACATT
1 TTATTACTCGCTTTAAATTTTTTTATAATCTCATAATTGAT-TTAAATCAATTTTTTTGTACATT
* * * * *
10310 TTTGGATAAAACAGATAATAATTGAATGTCTACTTTGAAAAACATGAAGAAAAATGCATTCAATG
65 TTTAGATAAAACAGACAATAATTAAATGTCTACTTTG-AAAACATGAAGAAAAAGGCATACAATG
* *
10375 GCAAGAAAAGTCCATTTATAGTCACCTATTTCTTCCAAAGCT
129 GCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCT
* * *
10417 TTATTACTCGCTTTAAATTTTTTTATAATCTCAAAATTGATTCTCAATTGAA-TTTTTT-TACAT
1 TTATTACTCGCTTTAAATTTTTTTATAATCTCATAATTGATT-T-AAATCAATTTTTTTGTACAT
* * * * * *
10480 TTTTAG-TCAAAACAGACAATATTTAAATGTTTTCCTTCTG-AAACGTGAGGAAAAAGGGATACA
64 TTTTAGAT-AAAACAGACAATAATTAAATG-TCTACTT-TGAAAACATGAAGAAAAAGGCATACA
* *
10543 TTGGCAAGAAAAGTCCATTTATAGTTACCCATTTCTTCAAAAGCT
126 ATGGCAAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCT
*
10588 TTATTACTCGCTTTAAATTTTTATATAATCTCATAATTGATTT
1 TTATTACTCGCTTTAAATTTTTTTATAATCTCATAATTGATTT
10631 NNNNNNNNNN
Statistics
Matches: 187, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
170 2 0.01
171 128 0.68
172 50 0.27
173 7 0.04
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (170 bp):
TTATTACTCGCTTTAAATTTTTTTATAATCTCATAATTGATTTAAATCAATTTTTTTGTACATTT
TTAGATAAAACAGACAATAATTAAATGTCTACTTTGAAAACATGAAGAAAAAGGCATACAATGGC
AAGAAAAGTCCATTTATAGTCACCCATTTCTTCAAAAGCT
Found at i:19739 original size:171 final size:161
Alignment explanation
Indices: 19562--19884 Score: 312
Period size: 171 Copynumber: 1.9 Consensus size: 161
19552 NNNNNNNNNN
* * * * * * *
19562 TTAAATTATTATATAATCTCCTAATTGATTTTAAGA-T-CAATTGTTTTAGATTTTTGGTTAAAA
1 TTAAATTATTATATAATATCATAATTGATTCTAA-ATTGAAATT-TTTTACATTTTTGATCAAAA
* * * * *
19625 CAGACTATAATTGAATGTTTG-CTTCGAGAAACGTGAAA-AAAAACGCATTCATTGGCAAGAAAA
64 CAGACAACAATTAAATGTTTGCCTT-GAGAAACAT-AAAGAAAAACGCATGCATTGGCAAGAAAA
* * *
19688 GTCCATTTATAGTCACCCATTTCTTCCANNNNNNNNNNACTTACT
127 GTCCATTTATAATCACCAATTCCTTCCA----------ACTTACT
*
19733 TTAAATTATTTTATAATATCATAATTGATTCTAAATTGAAATTTTTTACATTTTTGATCAAAACA
1 TTAAATTATTATATAATATCATAATTGATTCTAAATTGAAATTTTTTACATTTTTGATCAAAACA
* * * *
19798 GACAACAATTAAATGTTTGCCTTGAGAAACATAAAGAAAAAGGGATGCATTGGTAAGAAAAGTCT
66 GACAACAATTAAATGTTTGCCTTGAGAAACATAAAGAAAAACGCATGCATTGGCAAGAAAAGTCC
19863 ATTTATAATCACCAATTCCTTC
131 ATTTATAATCACCAATTCCTTC
19885 AAAAACTTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
170 4 0.03
171 117 0.91
172 7 0.05
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.36
Consensus pattern (161 bp):
TTAAATTATTATATAATATCATAATTGATTCTAAATTGAAATTTTTTACATTTTTGATCAAAACA
GACAACAATTAAATGTTTGCCTTGAGAAACATAAAGAAAAACGCATGCATTGGCAAGAAAAGTCC
ATTTATAATCACCAATTCCTTCCAACTTACT
Found at i:20568 original size:171 final size:167
Alignment explanation
Indices: 20260--20795 Score: 463
Period size: 171 Copynumber: 3.2 Consensus size: 167
20250 NNNNNNNNTG
* ** * * *
20260 ATTTTAAGTTTAATTTTTTTACATTTTTGGTTAAAATAGACTATAATTGAATCTCTACC-TCGAG
1 ATTTTAAGTTGAA-TTTTTTACATTTTTAATTAAACTATACTATAATTGAATGTCTACCTTC-AG
* * * * ** * *
20324 AAACGTGAGGACAAAGGCATTCATTGA-CATGAAAAGTCCATTTATAGTCA-GTCATTCCTTGAA
64 AAACATAAAGA-AAAGGC---CATTGATAAAAAAAAGTCCATTTATAGTCACG-CATACCTTCAA
* *
20387 AAGCCTTATTACTCTCTTTAAATTGTTTTATAATCTCAAAATTA
124 AAGCCTTATTACTCCCTTTAAATTGTTTTATAATCTCATAATTA
* * * *
20431 ATTTTAAGTAGAATTGTTTTACATTTTTTATTAAAAC-ATACTATAATTGAATGTTTGCCTTCAG
1 ATTTTAAGTTGAATT-TTTTACATTTTTAATT-AAACTATACTATAATTGAATGTCTACCTTCAG
** ** * * * *
20495 AAATGTGTAGAATAA-GCCATTTATTGAGAAAAAAAGTCTATTTAGAGTCACGCATCCCTTCAAA
64 AAACATAAAGAA-AAGGCCATTGA-T-A-AAAAAAAGTCCATTTATAGTCACGCATACCTTCAAA
* *****
20559 AGGCTTATTACTCCCTTTAAATTGTTTTATAATCTCATNNNNN
125 AGCCTTATTACTCCCTTTAAATTGTTTTATAATCTCATAATTA
***** *
20602 NNNNNAAGTTGAATTTTTTACATTTTTAATTAAACTATACTATGATTGAATGTCTACCTTCAGAA
1 ATTTTAAGTTGAATTTTTTACATTTTTAATTAAACTATACTATAATTGAATGTCTACCTTCAGAA
* * * *
20667 ACATAAAGAAAAGGGCATTGATAAAGAAAAGTCCATTTATAGTCACCCATACCGTCAAAAGCCTT
66 ACATAAAGAAAAGGCCATTGATAAAAAAAAGTCCATTTATAGTCACGCATACCTTCAAAAGCCTT
* * * *
20732 ATCACTCGCTTT-AATTAGTTTTATAAACTCATAATTG
131 ATTACTCCCTTTAAATT-GTTTTATAATCTCATAATTA
20769 ATTTTAAGTTGAATTTTTTTACATTTT
1 ATTTTAAGTTGAA-TTTTTTACATTTT
20796 NNNNNNNNNN
Statistics
Matches: 288, Mismatches: 64, Indels: 29
0.76 0.17 0.08
Matches are distributed among these distances:
166 4 0.01
167 72 0.25
168 14 0.05
169 7 0.02
170 58 0.20
171 127 0.44
172 6 0.02
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.38
Consensus pattern (167 bp):
ATTTTAAGTTGAATTTTTTACATTTTTAATTAAACTATACTATAATTGAATGTCTACCTTCAGAA
ACATAAAGAAAAGGCCATTGATAAAAAAAAGTCCATTTATAGTCACGCATACCTTCAAAAGCCTT
ATTACTCCCTTTAAATTGTTTTATAATCTCATAATTA
Found at i:20703 original size:18 final size:18
Alignment explanation
Indices: 20669--20703 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20659 CTTCAGAAAC
*
20669 ATAAAGAAAAGGGCATTG
1 ATAAAGAAAAGGCCATTG
*
20687 ATAAAGAAAAGTCCATT
1 ATAAAGAAAAGGCCATT
20704 TATAGTCACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (18 bp):
ATAAAGAAAAGGCCATTG
Done.