Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400887.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4053.0, 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: 8991
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.30
Warning! 1847 characters in sequence are not A, C, G, or T
Found at i:1166 original size:171 final size:172
Alignment explanation
Indices: 592--1717 Score: 665
Period size: 171 Copynumber: 6.6 Consensus size: 172
582 NNNNNNNNNN
* * * * * *
592 ATTAAAACAGACAATAATTGATTGTTTATCTCGAGAAACATGAAGAAAAAAGCAATCATTGGCAA
1 ATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGGCATTCATTGGCAA
* * * ** ** * * *
657 GAAAAGTCTATTTATAGTCACCCGTTTATTCAAAAGCC-TTATTACTCGCTTGAAATAG-TTTTC
66 GAAAAATCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTTATTACTAGCTTTAAA-AGATTTTA
********** * *
720 TAATCTAATNNNNNNNNNNAAATTGAATTTTTTTATATTTTTC
130 TAATCTAATAATTGATTTTAAATTAAATTCTTTTATATTTTTC
* * * *
763 ATTAAAACTGACTATAATTGTATGTCTACCGCAAGAAACATGAAG-AAAAGCGCATTCATTGGCA
1 ATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAG-GCATTCATTGGCA
* * * *
827 AGAAAAATCCATTTATAGTCTCCCACTCCTTCAAAAGCCTTTATTATTAGCTTTAAATGATTTTA
65 AGAAAAATCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTTATTACTAGCTTTAAAAGATTTTA
* * *
892 TAATCTAATAATTGATTTTAAATTAAATTGTTTTATTTTTTTGG
130 TAATCTAATAATTGATTTTAAATTAAATTCTTTTATATTTTT-C
* * * *
936 GTGAAAACAGACAATAATTGAATGTCT-CTCTCGAGAAA-ATTGAAGAAAAAAGCATTCATTGGC
1 ATTAAAACAGACTATAATTGAATGTCTAC-CTCGAGAAACA-TGAAGAAAAAGGCATTCATTGGC
* * **********
999 AAGAAAAATCTATTTATAGTCACCTATTCCTTC-NNNNNNNNNNTTACTAGCTTTAAAA-AGTTT
64 AAGAAAAATCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTTATTACTAGCTTTAAAAGA-TTT
* * * *
1062 TATAATCTCATAATTGATTTTAAGTTGACTTCTTTTATATTTTTC
128 TATAATCTAATAATTGATTTTAAATTAAATTCTTTTATATTTTTC
* * * * **
1107 ATTAAAGCAGGCTATAATTGAATATCTACCTCGAGAAACATGAAGAAAAAGGAATTCATTGATAA
1 ATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGGCATTCATTGGCAA
* * * * *
1172 GAAAAGTCCATTTATAGCCTCCTATTCCTTCAACAGCCTTT-TTGCTCG-TTCTAAATAG-TTTT
66 GAAAAATCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTTATTACTAGCTT-TAAA-AGATTTT
* ********** * * * *
1234 ATAATCTCANNNNNNNNNNTAAGTTCAATTTTTTTACATTTTTC
129 ATAATCTAATAATTGATTTTAAATTAAATTCTTTTATATTTTTC
* * * * ** * **
1278 ATTAAAACATACTATAATTCAATGTTTGCCTTTAAAAACATGAAGAGAAAA-GCATTCATTGATA
1 ATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACATGAAGA-AAAAGGCATTCATTGGCA
* * * * * * *
1342 AGAAAAGTCTATTTACAGCCT-CTCATTCCTTCGAAAGTGCC-TTATTACTCGTTTTAAATA-AT
65 AGAAAAATCCATTTATAGTCTCCT-ATTCCTTC-AAA-AGCCTTTATTACTAGCTTTAAA-AGAT
* * * * * * *
1404 TTTATAATCTAACAATTAATTTTTAGTT-GATTTTTTTACT-TTTTTT
126 TTTATAATCTAATAATTGATTTTAAATTAAATTCTTTTA-TATTTTTC
* * * * * *
1450 ATTAAAACAGA-TGATTATTGACTGTCTATCTTGAGAAACATGAAGAGAAAGGCATTCATTGGGA
1 ATTAAAACAGACT-ATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGGCATTCATTGGCA
* * * * * ********
1514 AGAAAAGTTCATTTATAGTCACCGATTCCTTCAAAAGCC-TTATTACTCGCTTTAAANNNNNNNN
65 AGAAAAATCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTTATTACTAGCTTTAAAAGATTTTA
** * * * *
1578 NNATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTC
130 TAATCTAATAATTGATTTTAAATTAAATTCTTTTATATTTTTC
* * * * * * ** *
1621 ATTAACACA-AATAATAACTAAATGCCTATCTTAAGAAACATGAA-AAAAA-GTATTCATTGGCA
1 ATTAAAACAGACT-ATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGGCATTCATTGGCA
* *
1683 AGAAAAGTCCATTTATAGTCACCTATTCCTTCAAA
65 AGAAAAATCCATTTATAGTCTCCTATTCCTTCAAA
1718 NNNNNNNNNN
Statistics
Matches: 740, Mismatches: 186, Indels: 60
0.75 0.19 0.06
Matches are distributed among these distances:
169 44 0.06
170 50 0.07
171 334 0.45
172 198 0.27
173 108 0.15
174 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (172 bp):
ATTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGGCATTCATTGGCAA
GAAAAATCCATTTATAGTCTCCTATTCCTTCAAAAGCCTTTATTACTAGCTTTAAAAGATTTTAT
AATCTAATAATTGATTTTAAATTAAATTCTTTTATATTTTTC
Found at i:3335 original size:171 final size:160
Alignment explanation
Indices: 3028--3336 Score: 356
Period size: 170 Copynumber: 1.9 Consensus size: 160
3018 AGTCTCCTAA
* ** *
3028 TCCTTCAAAAGCCTTATTGCTCGCTTTAAATGGTTTTATAATTTCATAATTAATTTTAAGTTGAA
1 TCCTTCAAAAGCCTTATTACTCGCTTTAAATAATTTTATAATTTAATAATTAATTTTAAGTTGAA
3093 GTTTTTATATTTTTCATTAAAACAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAA
66 GTTTTTATATTTTTCATTAAAACAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAA
3158 AGCATTCACTGANNNNNNNNNNCCATTTATAGCCTCTCAT
131 AGCATTCACTGA----------CCATTTATAGCCTCTCAT
* * *
3198 TCCTTCAACAGCCTTTTTACTCG-TTCTAAATAATTTTATAATTTAATAATTAATTTTAAGTTTA
1 TCCTTCAAAAGCCTTATTACTCGCTT-TAAATAATTTTATAATTTAATAATTAATTTTAAGTTGA
* * * *
3262 ATTTTTTAATATTTTTCATT-AAACAAGACTATAATTGAATGTCTT-TCTTAA-AAAGCATGAAG
65 AGTTTTT-ATATTTTTCATTAAAACAA-ACAATAATTGAATGT-TTGCCTCAAGAAA-CATGAAG
3324 AAAAAAGCATTCA
126 AAAAAAGCATTCA
3337 TTGGCAAGAA
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
169 2 0.02
170 69 0.56
171 50 0.41
172 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.39
Consensus pattern (160 bp):
TCCTTCAAAAGCCTTATTACTCGCTTTAAATAATTTTATAATTTAATAATTAATTTTAAGTTGAA
GTTTTTATATTTTTCATTAAAACAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAA
AGCATTCACTGACCATTTATAGCCTCTCAT
Found at i:3359 original size:171 final size:170
Alignment explanation
Indices: 2196--3410 Score: 596
Period size: 171 Copynumber: 7.1 Consensus size: 170
2186 NNNNNNACTA
** * * * * *
2196 GCTTTAAATGGTTTTATAATCTAATAATTGATTTTAAGTTAAATTGTTTTTACATTTTTGATTAA
1 GCTTTAAATAATTTTATAATTTAATAATTAATTTTAAGTTGAA--GTTTTTATATTTTTCATTAA
* * * * ** * * * * * *
2261 AACATACTATAATTGAATATATATCTTAAGAAACGTGAAGAAAAGATCATTCATTGACAAAAAAA
64 AACAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAAAGCATTCACTGACAAGAAAA
* * * *********
2326 GTCTATTTATAGTCACCCATT-CTATCAAAAGCCNNNNNNNNN
129 GTCCATTTATAGCCTCCCATTCCT-TCAAAAGCCTTATTACTC
* ** * * * * * *
2368 NCTTTAAATGGTTTTCTAATTTCATAATTGATTTTAAGTTAAATTTTTTAACATTTTTCATTAAA
1 GCTTTAAATAATTTTATAATTTAATAATTAATTTTAAGTTGAAGTTTTT-ATATTTTTCATTAAA
* ** * * * * * ** * *
2433 A-ATGATGATAATTGATTGTCTACCACAACAAATGTGAAGAAAAGAGCATTCATTGACAA-AAAC
65 ACA-AACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAAAGCATTCACTGACAAGAAA-
* * * *
2496 AGTCCATTTATAGTCTCCTAGTCCTTCAAAAGCCTTATTACTA
128 AGTCCATTTATAGCCTCCCATTCCTTCAAAAGCCTTATTACTC
********** * * * ** *
2539 GCNNNNNNNNNNTTTATAATCTAATAATTGATTTTAAGTTTATTTTTTTTATATTTTTAATTAAA
1 GCTTTAAATAATTTTATAATTTAATAATTAATTTTAAGTTGA-AGTTTTTATATTTTTCATTAAA
* * ** ** * * * *
2604 ACAGACAATAATTGATTGACTATCTCAAGAAACATGAAGAAAAAAGCTTTCATTGCCAAGAAAAA
65 ACAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAAAGCATTCACTGACAAGAAAAG
* *
2669 TCCATTTATAGTCACCCATTCCTTCACAAA-CCTTATTACTC
130 TCCATTTATAGCCTCCCATTCCTTCA-AAAGCCTTATTACTC
* * * * * * * * * *
2710 ACTTTAAATGATTTTCTAATCTCATAATTCATTTTAAGTTAAATTTTTTTACATTTTTCATTAAC
1 GCTTTAAATAATTTTATAATTTAATAATTAATTTTAAGTTGAA-GTTTTTATATTTTTCATTAAA
* * * * * ********** * *
2775 ACAAATAATAATAGAATGTCTACCTCAAGAAACGTGAANNNNNNNNNNTTCATTGGCAAGAAAAG
65 ACAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAAAGCATTCACTGACAAGAAAAG
* * * * **
2840 TCCATTTAT-GTCACCCATTCCTTTAAAAGCCTTATCACAA
130 TCCATTTATAGCCTCCCATTCCTTCAAAAGCCTTATTACTC
** * * * * ** * *
2880 GCTTTAAATGGTTTCATAATCTAATAATTGATTTTATGTTGATTTTTTTATATTTTTGATTACAA
1 GCTTTAAATAATTTTATAATTTAATAATTAATTTTAAGTTGAAGTTTTTATATTTTTCATTAAAA
* * * * * ** * * * * *******
2945 CAGACTATAATTGAATATCTACAGCAAGAAACGTGAATAAAAGAGCATTCA-TGGGCANNNNNNN
66 CAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAAAGCATTCACT-GACAAGAAAAG
*** * * * *
3009 NNNATTTATAGTCTCCTAATCCTTCAAAAGCCTTATTGCTC
130 TCCATTTATAGCCTCCCATTCCTTCAAAAGCCTTATTACTC
** *
3050 GCTTTAAATGGTTTTATAATTTCATAATTAATTTTAAGTTGAAGTTTTTATATTTTTCATTAAAA
1 GCTTTAAATAATTTTATAATTTAATAATTAATTTTAAGTTGAAGTTTTTATATTTTTCATTAAAA
**********
3115 CAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAAAGCATTCACTGANNNNNNNNNN
66 CAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAAAGCATTCACTGACAAGAAAAGT
* * *
3180 CCATTTATAGCCTCTCATTCCTTCAACAGCCTTTTTACTC
131 CCATTTATAGCCTCCCATTCCTTCAAAAGCCTTATTACTC
* *
3220 G-TTCTAAATAATTTTATAATTTAATAATTAATTTTAAGTTTAATTTTTTAATATTTTTCATT-A
1 GCTT-TAAATAATTTTATAATTTAATAATTAATTTTAAGTTGAAGTTTTT-ATATTTTTCATTAA
* * * * *
3283 AACAAGACTATAATTGAATGTCTT-TCTTAA-AAAGCATGAAGAAAAAAGCATTCATTGGCAAGA
64 AACAA-ACAATAATTGAATGT-TTGCCTCAAGAAA-CATGAAGAAAAAAGCATTCACTGACAAGA
** *
3346 AAAGTGTATTTATAGCTTCCCATTCCTTCAAAAGCCTTATTACTC
126 AAAGTCCATTTATAGCCTCCCATTCCTTCAAAAGCCTTATTACTC
* **
3391 ACTTTAAATGGTTTTATAAT
1 GCTTTAAATAATTTTATAAT
3411 CTNNNNNNNN
Statistics
Matches: 809, Mismatches: 215, Indels: 39
0.76 0.20 0.04
Matches are distributed among these distances:
168 1 0.00
169 67 0.08
170 276 0.34
171 407 0.50
172 58 0.07
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.37
Consensus pattern (170 bp):
GCTTTAAATAATTTTATAATTTAATAATTAATTTTAAGTTGAAGTTTTTATATTTTTCATTAAAA
CAAACAATAATTGAATGTTTGCCTCAAGAAACATGAAGAAAAAAGCATTCACTGACAAGAAAAGT
CCATTTATAGCCTCCCATTCCTTCAAAAGCCTTATTACTC
Found at i:4739 original size:172 final size:170
Alignment explanation
Indices: 4386--4740 Score: 399
Period size: 172 Copynumber: 2.1 Consensus size: 170
4376 NNAAAGCACT
* * * * * *
4386 TTATTACTCGTTTTAAACGGTTTTATAATCTAATAATTAATTTTTAGTTGATTTTTTTATATTTT
1 TTATTACTCGCTTTAAACGATTTTATAATCTAATAAATAATTTTAAGATGATTTTTTTATAATTT
* * * * * * *
4451 TTATTAAAACAGATAATTATTGACTGTTTATCTTGAGAAACATGAAGAGAAAACCATTCATTGGC
66 TTATTAAAACAGATAATAATTAAATGTCTATCTCGAGAAACATAAAGAGAAAAACATTCATTGGC
* *****
4516 AAGAAAGGTTCATTTATAGTCACCCATTCCTTCAANNNNN
131 AAGAAAAGTTCATTTATAGTCACCCATTCCTTCAACAGCC
***** *
4556 NNNNNACTCGCTTTAAATGATTTTATAATCTAATAAATAATTTTAAGATGAATTTTTTT-TACAT
1 TTATTACTCGCTTTAAACGATTTTATAATCTAATAAATAATTTTAAGATG-ATTTTTTTATA-AT
**
4620 TTTTAGTTAAAACAGATAATAATTAAATGTCTATCTCGAGAAATGTAAAGAGAAAAACATTCATT
64 TTTTA-TTAAAACAGATAATAATTAAATGTCTATCTCGAGAAACATAAAGAGAAAAACATTCATT
* *
4685 GGCCAGAAAAGTGT-ATTTGTAGTCACCCATTCCTTCAACAGCC
128 GGCAAGAAAAGT-TCATTTATAGTCACCCATTCCTTCAACAGCC
4728 TTATTACTCGCTT
1 TTATTACTCGCTT
4741 NNNNNNNNNN
Statistics
Matches: 147, Mismatches: 34, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
170 41 0.28
171 14 0.10
172 91 0.62
173 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.39
Consensus pattern (170 bp):
TTATTACTCGCTTTAAACGATTTTATAATCTAATAAATAATTTTAAGATGATTTTTTTATAATTT
TTATTAAAACAGATAATAATTAAATGTCTATCTCGAGAAACATAAAGAGAAAAACATTCATTGGC
AAGAAAAGTTCATTTATAGTCACCCATTCCTTCAACAGCC
Found at i:6985 original size:172 final size:171
Alignment explanation
Indices: 6684--7834 Score: 1057
Period size: 171 Copynumber: 6.7 Consensus size: 171
6674 NNNNNNNNNN
* * * * * *
6684 GGAATGAGAGGCTATAAATAGACTTTTCTT-GTTAATGAATGCTTTTTTCTTCACGTTTCTAAAC
1 GGAATGAGAGACTATAAATGGACTTTTCTTAG-CAATGAATGCTTTTTTCTTCATGTTTCTAGAG
* * * *
6748 GTAGAGATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTAAACTTCAAATTAATTAT
65 GTAGACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
* * *
6813 GAGATTATAAAACCATTTAGAA-CGAGCAAAAAGGCTGTTGAA
130 GAGATTATAAAACCATTTA-AAGCGAGTAATAAGGCTTTTGAA
* ** *
6855 GGAATGAGAGGCTATAAATAAAAC-TTTCTTAGCAATGAATGGTTTTTTCCTTCATGTTTCTAGA
1 GGAATGAGAGACTATAAAT-GGACTTTTCTTAGCAATGAATGCTTTTTT-CTTCATGTTTCTAGA
* * * * *
6919 GGTAGATATTCAATTATAGCCTGCTTTAATGGAAAAA-GTAAAAAAAGTCAACTTAAAATCAATT
64 GGTAGACATTCAATTATAGTCTGTTTTAAT-CAAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * *
6983 ATGAGAGTATAAAATCATTTAAAGAGAGTAATAAGGCTTTTGAA
128 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * *
7027 GGAATGGGTGACTATAAATGGACTTTTCTT-GCCAATGAATGCTGTTTTCATCAATTTTCTCTAG
1 GGAATGAGAGACTATAAATGGACTTTTCTTAG-CAATGAATGCTTTTTTCTTC-ATGTT-TCTAG
* * * * * * *
7091 A--TAAACATTCAATTATTGTCTATTTT-CTCAAAAATATAAAAACATTTAACTTAAAATCAATT
63 AGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * * *
7153 ATTAGATTATAAAACCATCTAAAGCTAGTAATAAGGCTTTTAAA
128 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * * * * **
7197 GGATTGAGAGACTATAAATGGACTTTTTTTACCAATAAATGCTCTTTTCTTCGTGTTTTTTTTA-
1 GGAATGAGAGACTATAAATGGACTTTTCTTAGCAATGAATGCTTTTTTCTTCATG-TTTCTAGAG
* * * * *
7261 GTAGACAATCAATTATAGTCAGTTTTAATGAAAAATATAAAAAAATTCAATTTAAAATCAATTAT
65 GTAGACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTAT
* *
7326 GAGATT-TGAAAATCATTTTAAGCGAGTAATAAGGCTTTTGAA
130 GAGATTAT-AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
* * * * *
7368 TGAATGGGTGACTATAAATGGGCTTTTCTT-GCCAATGAATGCTTTTGTT-TTCATGTTTTTTA-
1 GGAATGAGAGACTATAAATGGACTTTTCTTAG-CAATGAATGCTTTT-TTCTTCATG-TTTCTAG
* * * * *
7430 AGATAAACAATCAATTATTGTCTGTTTTGATCAAAAATGTAAAAAAAATT-AACTTAAAATCAAT
63 AGGTAGACATTCAATTATAGTCTGTTTTAATCAAAAATGT-AAAAAAATTCAACTTAAAATCAAT
* * *
7494 TATTAGATTATAAAATCATTTAAAGCTAGTAATAAGGCTTTTGAA
127 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
** * * ** *
7539 GGTCT-AGGAGACTATATATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCACATTTCTTGAG
1 GGAATGA-GAGACTATAAATGGACTTTTCTTAGCAATGAATGCTTTTTTCTTCATGTTTCTAGAG
* * * ** * * **
7603 ATACACATTTAATTATTA-TCCATTTAAATAAAAAATGTAAAAAAA-TCAA-TTAAAAATTTATT
65 GTAGACATTCAATTA-TAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTT-AAAATCAATT
**
7665 ATTG-GATTATAAAACCATTTAAAAAGAGTAATAAGGTACTTTTGAA
128 A-TGAGATTATAAAACCATTTAAAGCGAGTAATAAGG--CTTTTGAA
* * * * * * *
7711 GTAATGAGACG-CTGTAAATAGACTTTTCTCATCAATGAATGCTTTTTTCTTCACGTTTCTAAAG
1 GGAATGAGA-GACTATAAATGGACTTTTCTTAGCAATGAATGCTTTTTTCTTCATGTTTCTAGAG
* * * * *
7775 G-CGAAGATTCAATTATAGTCTATTTTAATGAAAAATGTAAAAAAATTGAACTTAAAATCA
65 GTAG-ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCA
7835 NNNNNNNNNN
Statistics
Matches: 795, Mismatches: 149, Indels: 70
0.78 0.15 0.07
Matches are distributed among these distances:
169 12 0.02
170 180 0.23
171 336 0.42
172 244 0.31
173 21 0.03
174 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (171 bp):
GGAATGAGAGACTATAAATGGACTTTTCTTAGCAATGAATGCTTTTTTCTTCATGTTTCTAGAGG
TAGACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATG
AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAA
Found at i:7011 original size:21 final size:20
Alignment explanation
Indices: 6972--7012 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6962 AAAGTCAACT
*
6972 TAAAATCAATTATGAGAGTA
1 TAAAATCAATTAAGAGAGTA
*
6992 TAAAATCATTTAAAGAGAGTA
1 TAAAATCAATT-AAGAGAGTA
7013 ATAAGGCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (20 bp):
TAAAATCAATTAAGAGAGTA
Found at i:8844 original size:171 final size:159
Alignment explanation
Indices: 8664--8976 Score: 299
Period size: 169 Copynumber: 1.9 Consensus size: 159
8654 AGCACTGAGA
* * * *
8664 GACTATAAATGAATTTCTCTTACCAATGAATACTTTTTTATTCATATTTCTTGC-TG-TAGACAT
1 GACTATAAATGAATTTCTCTTACCAACGAATAC-TTTTTATTCACATTTC-T-CAAGACAGACAT
* * * * *
8727 TCAATTAT-AGTATGTTTTAATGAAAAATGTAAAAATATTGAACTTAAAATAAATTATGAGATTA
63 TCAATTATAACT-TGTGTAAATG-AAAATGTAAAAACATTCAACTTAAAATAAATTATGAGATTA
*
8791 TAAAACCATTTAAAGCNNNNNNNNNNGCTTTTGAAGGAATGGGT
126 GAAAACCATTTAAAGC----------GCTTTTGAAGGAATGGGT
* * * * * *
8835 GACTATAAATGGATTTTTCTTGCCAACGAATACTTTTTCTTCACGTTTCTCAAGACAGACATTTA
1 GACTATAAATGAATTTCTCTTACCAACGAATACTTTTTATTCACATTTCTCAAGACAGACATTCA
* *
8900 ATTATAACTTGTGTAAATGAAAATGTAAAAACATTCAGCTTAAAATCAATTATGAGATTAGAAAA
66 ATTATAACTTGTGTAAATGAAAATGTAAAAACATTCAACTTAAAATAAATTATGAGATTAGAAAA
*
8965 TCATTTAAAGCG
131 CCATTTAAAGCG
8977 AGTAATAAGG
Statistics
Matches: 120, Mismatches: 19, Indels: 18
0.76 0.12 0.11
Matches are distributed among these distances:
159 1 0.01
168 1 0.01
169 53 0.44
170 34 0.28
171 31 0.26
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.35
Consensus pattern (159 bp):
GACTATAAATGAATTTCTCTTACCAACGAATACTTTTTATTCACATTTCTCAAGACAGACATTCA
ATTATAACTTGTGTAAATGAAAATGTAAAAACATTCAACTTAAAATAAATTATGAGATTAGAAAA
CCATTTAAAGCGCTTTTGAAGGAATGGGT
Done.