Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403218.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_888.0, 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: 12819
ACGTcount: A:0.21, C:0.06, G:0.07, T:0.19
Warning! 5967 characters in sequence are not A, C, G, or T
Found at i:6170 original size:171 final size:161
Alignment explanation
Indices: 5856--6187 Score: 321
Period size: 171 Copynumber: 2.0 Consensus size: 161
5846 ATTATGAGAT
*
5856 TATAAAACAATTTAAAGCAAGTAATAAGGCTTGTGAAGGAATAAAAGACCATAAATTGACTTTTC
1 TATAAAACAATTTAAAGCAAGTAATAAGGCTTGTGAAGGAATAAAAGAACATAAATTGACTTTTC
* * * *
5921 TTACAAATGAATACCTTTTTCTTCACTTTTCTGAAGATAGATATTCAATTATAGTCTGTTGAAAC
66 TTACAAATGAATACCTTTTTATTCACTTTTCTGAAGACAAATATTCAATTATAGACTGTTGAAAC
* * *
5986 CAACAATGTGAAAAAATTCAACTTAAAATCA
131 CAAAAAAGTGAAAAAATTCAACTCAAAATCA
* * * *
6017 NNNNNNNNNNTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTTAAGGAATAAAAGAATATAAA
1 ----------TATAAAACAATTTAAAGCAAGTAATAAGGCTTGTGAAGGAATAAAAGAACATAAA
* * * * * * *
6082 -TGAAGTTTTCTTGCATATGAAT-GCTTGTTTATTCA-TGTTTCTTAAGGCAAACT-TTCATTTA
56 TTG-ACTTTTCTTACAAATGAATACCTT-TTTATTCACT-TTTCTGAAGACAAA-TATTCAATTA
**
6143 TAGACTGTTTTAACCAAAAAAGTGAAAAAATTCAACTCAAAATCA
117 TAGACTGTTGAAACCAAAAAAGTGAAAAAATTCAACTCAAAATCA
6188 ANNNNNNNNN
Statistics
Matches: 136, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
170 6 0.04
171 129 0.95
172 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.32
Consensus pattern (161 bp):
TATAAAACAATTTAAAGCAAGTAATAAGGCTTGTGAAGGAATAAAAGAACATAAATTGACTTTTC
TTACAAATGAATACCTTTTTATTCACTTTTCTGAAGACAAATATTCAATTATAGACTGTTGAAAC
CAAAAAAGTGAAAAAATTCAACTCAAAATCA
Found at i:7502 original size:172 final size:172
Alignment explanation
Indices: 7124--7796 Score: 698
Period size: 171 Copynumber: 3.9 Consensus size: 172
7114 NNNNNNNNNN
* * * *
7124 AAAGCCATATTACTTGCTTTAAATGGTTTTATAATATCGTAATTGATTTGAAGTTGAA-TTTTTT
1 AAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT
* * * * * *
7188 AGCATTTTT-GATTAAAACAGAATATAATTGAA-CATCTACCTTGGGAAACATGAAGAATAATGC
66 A-CATTTTTAG-TTAAAACAGACTATAATTGAATC-TTTACCTCGAGAAACATGAAGAAAAAAGC
* * * * *
7251 ATTCACT-AGCAAAAAAAGTCAATTTATAGTCACCCATCCCTTTA
128 ATTCACTGAGAAAAAAAAGTCCATTTATAGTCACTCATTCCTTCA
* * * * * * * *
7295 AAAGCCTTATTACTCGCTTTAAATGGTTCTATAATCTAATGATTTATTTTAAGTTAAATGTTTTC
1 AAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT
* * * * *
7360 ATATTTTTGGTTAAAACAGACTATAATATG-ATCTTTATCTCGAGAAACGTGAAGAAAAAGGCAT
66 ACATTTTTAGTTAAAACAGACTATAAT-TGAATCTTTACCTCGAGAAACATGAAGAAAAAAGCAT
* * *
7424 TCATTGATAAAAAAAAGTCTATTTATAGTCACTCATTCCTTCA
130 TCACTGAGAAAAAAAAGTCCATTTATAGTCACTCATTCCTTCA
* * * *
7467 AAAGTCTTATTACTGGCTTTAAATTGTTTTATAATCTCATAATTGGTTTTAAGTTGAATTTTTTT
1 AAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT
* * * * *
7532 AGATTTTTAGTTAAAACAGACTATAATTGAATGTTTACCTCAAGAAACATAAATAAAAAAGCATT
66 ACATTTTTAGTTAAAACAGACTATAATTGAATCTTTACCTCGAGAAACATGAAGAAAAAAGCATT
* * * * *
7597 CACTG-GCAAGAAAAGTCCATTTATAGTCTCTTATTCCTGCA
131 CACTGAGAAAAAAAAGTCCATTTATAGTCACTCATTCCTTCA
* ** * * * *
7638 AAAGCCTTATTGCTTGCTTTAAATTATATTATAATCTCATGATTGATTTTAAGCTGAATTTTTTA
1 AAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT
* * * * * *
7703 ACATTTTTAGTTAAAACAAACTATAATTGAATGTTTGCCTC-AGGAAACGT-CAGAAAAAACCAT
66 ACATTTTTAGTTAAAACAGACTATAATTGAATCTTTACCTCGA-GAAACATGAAGAAAAAAGCAT
* *
7766 TCATTGAGAAGAAAAAG-CCATTTATAGTCAC
130 TCACTGAGAAAAAAAAGTCCATTTATAGTCAC
7797 CTATNNNNNN
Statistics
Matches: 417, Mismatches: 77, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
170 29 0.07
171 237 0.57
172 151 0.36
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (172 bp):
AAAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT
ACATTTTTAGTTAAAACAGACTATAATTGAATCTTTACCTCGAGAAACATGAAGAAAAAAGCATT
CACTGAGAAAAAAAAGTCCATTTATAGTCACTCATTCCTTCA
Found at i:8191 original size:171 final size:168
Alignment explanation
Indices: 7901--8916 Score: 990
Period size: 171 Copynumber: 5.9 Consensus size: 168
7891 NNNNNNNNNN
* * * *
7901 TATGAGATTATAAAACAATTTAAAGAGAGTAGTAAGGCTTTTGAAGGAATTG-GTTATTATAAAT
1 TATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TGAGTGACTATAAAT
* * * * * * * *** *
7965 GAACTTATCTTCTCAATGAATTACTTTTTCTACATGTTTCTCGAGGCGAGCATTCAATTATAGTC
65 GGACTTTTTTTC-CAATGAATGATTTTTTCTTCATGTTTCTCAAGATAAACATTCAATTATAGTC
8030 TGTTTTAATGAAAAATGTAAAAACATTCAACTTAAAATCAAT
129 TGTTTTAAT-AAAAATGTAAAAA-ATTCAACTTAAAATCAAT
* * * *
8072 CATGAGATTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTTTAAAGAAATGGGTGACTATAAAT
1 TATGAGATTATAAAA-CAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT
* * * **
8136 GGACTTTTTTTCTCAATGAATGATTTTTTCTGCACGTTTC-CACAGACAGGCATTCAATTATAGT
65 GGACTTTTTTTC-CAATGAATGATTTTTTCTTCATGTTTCTCA-AGATAAACATTCAATTATAGT
*
8200 CTGTTTTAACTAAAAATGTGAAAAAATTCAGCTTAAAATCAAT
128 CTGTTTTAA-TAAAAATGT-AAAAAATTCAACTTAAAATCAAT
* * *
8243 TATGAGATTATAAAAGAATTTAAAGC-ACGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAAT
1 TATGAGATTATAAAACAATTTAAAGCGA-GTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT
* * ** * *
8307 TGA-TTTTTCTTGCAAATGAATGCCTTTTTCTTCACT-TTTCTCAAGGTAGACATTCAATTATAG
65 GGACTTTTT-TT-CCAATGAATGATTTTTTCTTCA-TGTTTCTCAAGATAAACATTCAATTATAG
* ** * *
8370 TTTGTTGAAACAAAAAATATGAAAAAATTCAACTTAAAATCAA-
127 TCTGTTTTAA-TAAAAATGT-AAAAAATTCAACTTAAAATCAAT
* *
8413 TATTGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAAT
1 TA-TGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAAT
* * * * * * * * *
8478 GGACTTGTCTTACTAATAAATGCTTATTTCTTCATGTTTCTCAAGGTAAATATTTAATTATAGTC
65 GGACTT-TTTTTCCAATGAATGATTTTTTCTTCATGTTTCTCAAGATAAACATTCAATTATAGTC
* *
8543 AGTTTTAAATAAAAATATAAAATAATTCAACTTAAAATCAAT
129 TGTTTT-AATAAAAATGTAAAA-AATTCAACTTAAAATCAAT
* * * * * * *
8585 TATTAGATTACAAAACCATTTGAAGCGAATAATAAGTCTTTTGAAGG-ATCGGGTGACTATAAAT
1 TATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GAGTGACTATAAAT
* * * * * * * * *
8649 GCACTTTTCTTGCCAATCAAAGGTGTTTTCTTTATGTTTCTCAAGGTAAAGATTCAATTATAGTC
65 GGACTTTT-TTTCCAATGAATGATTTTTTCTTCATGTTTCTCAAGATAAACATTCAATTATAGTC
* *
8714 TGTTTTAATAAAATATCTAAAAACATTCAACTTATAA-CAAAT
129 TGTTTTAATAAAA-ATGTAAAAA-ATTCAACTTAAAATC-AAT
* * * * * * *
8756 TATGAGATTATAAAACTATTTAAATCCAATAGTAAGGCTTTTGAAGAAATGAGTGACTATAAATC
1 TATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATG
* *
8821 GACTTTTTTTACCAATAAATG-TCTTTTTCTTCATGTTTCTCAAGATAAATATTCAATTATAGTC
66 GACTTTTTTT-CCAATGAATGAT-TTTTTCTTCATGTTTCTCAAGATAAACATTCAATTATAGTC
*
8885 TATTTTAACTAAAAATGTAAAAAAATTCAACT
129 TGTTTTAA-TAAAAATGT-AAAAAATTCAACT
8917 NNNNNNNNNN
Statistics
Matches: 714, Mismatches: 102, Indels: 58
0.82 0.12 0.07
Matches are distributed among these distances:
170 31 0.04
171 651 0.91
172 30 0.04
173 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (168 bp):
TATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATG
GACTTTTTTTCCAATGAATGATTTTTTCTTCATGTTTCTCAAGATAAACATTCAATTATAGTCTG
TTTTAATAAAAATGTAAAAAATTCAACTTAAAATCAAT
Found at i:8539 original size:342 final size:336
Alignment explanation
Indices: 7901--8916 Score: 1116
Period size: 342 Copynumber: 3.0 Consensus size: 336
7891 NNNNNNNNNN
* * * * *
7901 TATGAGATTATAAAACAATTTAAAGAGAGTAGTAAGGCTTTTGAAGGAATTGGTTATTATAAATG
1 TATGAGATTATAAAACAATTTAAAG-CAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATG
* * * * *
7966 AACTTATCTT-CTCAATGAATTACTTTTTCTACATGTTTCTCGAGG-CGAGCATTCAATTATAGT
65 AACTTTTCTTGC-CAATGAA-TGCTTTTTCTTCATGTTTCTCAAGGTAGA-CATTCAATTATAGT
* *
8029 CTGTTTTAATGAAAAATGTAAAAACATTCAACTTAAAATCAATCA-TGAGATTATAAAATCATTT
127 CTGTTTTAATAAAAAATATAAAAACATTCAACTTAAAATCAAT-ATTGAGATTATAAAA-CATTT
* * * *
8093 AAAGCGAGTAATAAGGCTTTTAAAGAAATGGGTGACTATAAATGGACTTTTTTTCTCAATGAATG
190 AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTTTTTTACT-AATAAATG
* * * * ***
8158 ATTTTTTCTGCACGTTTC-CACAGACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTGAA
254 -CTTTTTCTTCATGTTTCTCA-AGATAAATATTCAATTATAGTCTGTTTTAACTAAAAATGT-AA
*
8222 AAAATTCAGCTTAAAATCAAT
316 AAAATTCAACTTAAAATCAAT
* * *
8243 TATGAGATTATAAAAGAATTTAAAGCACGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATT
1 TATGAGATTATAAAACAATTTAAAGCA-GTAATAAGGCTTTTGAAGGAATAGGTGACTATAAA-T
* *
8308 G-ATTTTTCTTGCAAATGAATGCCTTTTTCTTCACT-TTTCTCAAGGTAGACATTCAATTATAGT
64 GAACTTTTCTTGCCAATGAATG-CTTTTTCTTCA-TGTTTCTCAAGGTAGACATTCAATTATAGT
* ** *
8371 TTGTTGAAACAAAAAATATGAAAAA-ATTCAACTTAAAATCAATATTGAGATTATAAAACAATTT
127 CTGTTTTAATAAAAAATAT-AAAAACATTCAACTTAAAATCAATATTGAGATTATAAAAC-ATTT
* * * *
8435 AAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTGTCTTACTAATAAATG
190 AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTT-TTTTACTAATAAATG
* * * * *
8500 CTTATTTCTTCATGTTTCTCAAGGTAAATATTTAATTATAGTCAGTTTTAAATAAAAATATAAAA
254 CTT-TTTCTTCATGTTTCTCAAGATAAATATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAA
8565 TAATTCAACTTAAAATCAAT
318 -AATTCAACTTAAAATCAAT
* * * * * * *
8585 TATTAGATTACAAAACCATTTGAAGCGAATAATAAGTCTTTTGAAGG-ATCGGGTGACTATAAAT
1 TATGAGATTATAAAACAATTTAAAGC-AGTAATAAGGCTTTTGAAGGAAT-AGGTGACTATAAAT
* * * * * * *
8649 GCACTTTTCTTGCCAATCAAAGGTGTTTTCTTTATGTTTCTCAAGGTAAAGATTCAATTATAGTC
64 GAACTTTTCTTGCCAATGAATGCT-TTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTC
* * *
8714 TGTTTTAATAAAATATCTAAAAACATTCAACTTATAA-CAA-ATTATGAGATTATAAAACTATTT
128 TGTTTTAATAAAAAATATAAAAACATTCAACTTAAAATCAATA-T-TGAGATTATAAAAC-ATTT
* * * * * *
8777 AAATCCAATAGTAAGGCTTTTGAAGAAATGAGTGACTATAAATCGACTTTTTTTACCAATAAATG
190 AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGAC-TTTTTTACTAATAAATG
*
8842 TCTTTTTCTTCATGTTTCTCAAGATAAATATTCAATTATAGTCTATTTTAACTAAAAATGTAAAA
254 -CTTTTTCTTCATGTTTCTCAAGATAAATATTCAATTATAGTCTGTTTTAACTAAAAATGT-AAA
8907 AAATTCAACT
317 AAATTCAACT
8917 NNNNNNNNNN
Statistics
Matches: 566, Mismatches: 84, Indels: 48
0.81 0.12 0.07
Matches are distributed among these distances:
340 1 0.00
341 25 0.04
342 512 0.90
343 28 0.05
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (336 bp):
TATGAGATTATAAAACAATTTAAAGCAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGA
ACTTTTCTTGCCAATGAATGCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTCTGT
TTTAATAAAAAATATAAAAACATTCAACTTAAAATCAATATTGAGATTATAAAACATTTAAAGCG
AGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTTTTTTACTAATAAATGCTTTTTC
TTCATGTTTCTCAAGATAAATATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAATTCAAC
TTAAAATCAAT
Found at i:8877 original size:513 final size:513
Alignment explanation
Indices: 7903--8916 Score: 1203
Period size: 513 Copynumber: 2.0 Consensus size: 513
7893 NNNNNNNNTA
* ** ** *
7903 TGAGATTATAAAACAATTTAAAGAGAGTAGTAAGGCTTTTGAAGGAATTGGTTATTATAAATGAA
1 TGAGATTATAAAACAATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGAA
* * * * *
7968 CTTATCTTCTCAATGAATTACTTTTTCTACATGTTTCTCGAGGCGAGCATTCAATTATAGTCTGT
66 CTTATCTTCTCAATGAAATACTTTTTCTACATGTTTCTCAAGGCAAACATTCAATTATAGTCAGT
* * *
8033 TTTAATGAAAAATGTAAAAACATTCAACTTAAAATCAATCATGAGATTATAAAATCATTTAAAGC
131 TTTAATGAAAAATATAAAAACATTCAACTTAAAATCAATCATGAGATTACAAAACCATTTAAAGC
* * * * * *
8098 GAGTAATAAGGCTTTTAAAGAAATGGGTGACTATAAATGGACTTTTTTTCTCAATGAATGATTTT
196 GAATAATAAGGCTTTTAAAGAAATGGGTGACTATAAATGCACTTTTTTGCTCAATCAAAGATGTT
* *
8163 TTCTGCACGTTTCCACAGACAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTGAAAAAATT
261 TTCTGCACGTTTCCACAGACAAGCATTCAATTATAGTCTGTTTTAACTAAAAATCTGAAAAAATT
* * * * *
8228 CAGCTTAAAATCAATTATGAGATTATAAAAGAATTTAAAGCACGTAATAAGGCTTTTGAAGGAAT
326 CAACTTAAAATCAATTATGAGATTATAAAACAATTTAAACCACATAATAAGGCTTTTGAAGAAAT
* * * * *
8293 AAGAGACTATAAATTGATTTTTCTTGCAAATGAATGCCTTTTTCTTCACTTTTCTCAAGGTAGAC
391 AAGAGACTATAAATCGATTTTTCTTACAAATAAATGCCTTTTTCTTCACTTTTCTCAAGATAAAC
* * *
8358 ATTCAATTATAGTTTGTTGAAACAAAAAATATGAAAAAATTCAACTTAAAATCAATAT
456 ATTCAATTATAGTCTATTGAAACAAAAAATATAAAAAAATTCAACTTAAAATCAATAT
* *
8416 TGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGA
1 TGAGATTATAAAACAATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGAA
* * * * * *
8481 CTTGTCTTACT-AAT-AAATGCTTATTTCTTCATGTTTCTCAAGGTAAATATTTAATTATAGTCA
66 CTTATCTT-CTCAATGAAATACTT-TTTCTACATGTTTCTCAAGGCAAACATTCAATTATAGTCA
* * *
8544 GTTTTAAAT-AAAAATATAAAATA-ATTCAACTTAAAATCAATTATTAGATTACAAAACCATTTG
129 GTTTT-AATGAAAAATATAAAA-ACATTCAACTTAAAATCAATCATGAGATTACAAAACCATTTA
* * *
8607 AAGCGAATAATAAGTCTTTTGAAG-GATCGGGTGACTATAAATGCACTTTTCTTGC-CAATCAAA
192 AAGCGAATAATAAGGCTTTTAAAGAAAT-GGGTGACTATAAATGCACTTTT-TTGCTCAATCAAA
* ** *
8670 GGTGTTTTCTTTATGTTTCTCA-AGGTA-AAG-ATTCAATTATAGTCTGTTTTAA-TAAAATATC
255 GATGTTTTCTGCACGTTTC-CACA-G-ACAAGCATTCAATTATAGTCTGTTTTAACTAAAA-ATC
* * *
8731 T-AAAAACATTCAACTTATAA-CAAATTATGAGATTATAAAACTATTTAAATCCA-ATAGTAAGG
316 TGAAAAA-ATTCAACTTAAAATC-AATTATGAGATTATAAAACAATTTAAA-CCACATAATAAGG
* * * *
8793 CTTTTGAAGAAATGAGTGACTATAAATCGACTTTTT-TTACCAATAAATGTCTTTTTCTTCA-TG
378 CTTTTGAAGAAATAAGAGACTATAAATCGA-TTTTTCTTACAAATAAATGCCTTTTTCTTCACT-
* ** * *
8856 TTTCTCAAGATAAATATTCAATTATAGTCTATTTTAACTAAAAATGTAAAAAAATTCAACT
441 TTTCTCAAGATAAACATTCAATTATAGTCTATTGAAACAAAAAATATAAAAAAATTCAACT
8917 NNNNNNNNNN
Statistics
Matches: 421, Mismatches: 65, Indels: 30
0.82 0.13 0.06
Matches are distributed among these distances:
512 20 0.05
513 379 0.90
514 21 0.05
515 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (513 bp):
TGAGATTATAAAACAATTTAAAGAGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGAA
CTTATCTTCTCAATGAAATACTTTTTCTACATGTTTCTCAAGGCAAACATTCAATTATAGTCAGT
TTTAATGAAAAATATAAAAACATTCAACTTAAAATCAATCATGAGATTACAAAACCATTTAAAGC
GAATAATAAGGCTTTTAAAGAAATGGGTGACTATAAATGCACTTTTTTGCTCAATCAAAGATGTT
TTCTGCACGTTTCCACAGACAAGCATTCAATTATAGTCTGTTTTAACTAAAAATCTGAAAAAATT
CAACTTAAAATCAATTATGAGATTATAAAACAATTTAAACCACATAATAAGGCTTTTGAAGAAAT
AAGAGACTATAAATCGATTTTTCTTACAAATAAATGCCTTTTTCTTCACTTTTCTCAAGATAAAC
ATTCAATTATAGTCTATTGAAACAAAAAATATAAAAAAATTCAACTTAAAATCAATAT
Found at i:10099 original size:171 final size:169
Alignment explanation
Indices: 9804--10577 Score: 682
Period size: 171 Copynumber: 4.5 Consensus size: 169
9794 NNNNNNNNNN
* * * * * *
9804 GAATAAGAGACTATAAATTGACTTTTCTTGCAAATGAATGCCTTTTTCTTCACT-CTTATCAAGG
1 GAATAGGAGACTATAAATGGACTTTTCTTGCCAATAAATG-CTTTTTCTTCA-TGTTTCTCAAGG
* ** ** * *
9868 TAGACATTCAATTATAGTTTGTTGAAACAAAAAATGTGAAAAAATTCAACTTAAAATCAATAATG
64 TAAACATTCAATTATAGTCAGTTTTAACAAAAAATAT-AAAAAATTCAACTTAAAATCAATTATG
* *
9933 AGATTATAAAATAATTTAAAGCGAGTAATAGGGCTTTCGAAG
128 AGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCGAAG
* *
9975 GAATAGGAGACTATAAATGGACTTGTCTTGCCAATAAATGCTTGTTTCTTCATGTTT-TTATAGG
1 GAATAGGAGACTATAAATGGACTTTTCTTGCCAATAAATGCTT-TTTCTTCATGTTTCTCA-AGG
* * * * * *
10039 TAAATATTTAATTATAGTCACTTTTAACCAAAAATATAAAACAATTCAATTTAAAATCAATTATT
64 TAAACATTCAATTATAGTCAGTTTTAACAAAAAATATAAAA-AATTCAACTTAAAATCAATTATG
* * * *
10104 AGATTACAAAACCATTTAAAGCGACTAATAAGGCTTTTGAAG
128 AGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCGAAG
** * * * * * *
10146 GAACGGGTGACTATAAATGCACTTTTCTTACCAATGAATACTGTTTTCTTTATGTTTCTCAAGGT
1 GAATAGGAGACTATAAATGGACTTTTCTTGCCAATAAATGCT-TTTTCTTCATGTTTCTCAAGGT
* * * * *
10211 AAAGATTCAATTATAGTCTGTTTTAATAAAAAATCTAAAAATATTCGACTTAAAA-CAAATTATG
65 AAACATTCAATTATAGTCAGTTTTAACAAAAAATATAAAAA-ATTCAACTTAAAATC-AATTATG
** * * * *
10275 AGATTATAAAATTATTTAAACCCAGTACTAAGGCTTTTGAAG
128 AGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCGAAG
* * *
10317 GAATGAGG-GACTATAAATGGACTTTTTTTGCCAATGAATAT-CTTTTTCTTTACGTTTCTCAAG
1 GAAT-AGGAGACTATAAATGGACTTTTCTTGCCAAT-AA-ATGCTTTTTCTTCATGTTTCTCAAG
** * * * * * *
10380 AAAAACATTCAATTATAGTTTA-TTTTAACCAAAAATATAAAAAAATTTAATTTCAAATTAATTA
63 GTAAACATTCAATTATAG-TCAGTTTTAACAAAAAATAT-AAAAAATTCAACTTAAAATCAATTA
* * *
10444 TGAGATTATAAAGCAATTTAAAGAGAGTAGTAAGGCTTTCGAAG
126 TGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCGAAG
* * * * * * * * * * * * **
10488 GAATGGGTGATTATAAATAGATTTTTCTTTCAAATGAATGCCTTTTTCTACACGTTTTTCGAGAA
1 GAATAGGAGACTATAAATGGACTTTTCTTGCCAATAAATG-CTTTTTCTTCATGTTTCTCAAGGT
10553 AAACATT-AATTATAGTCTA-TTTTAA
65 AAACATTCAATTATAGTC-AGTTTTAA
10578 TGAAANNNNN
Statistics
Matches: 491, Mismatches: 94, Indels: 37
0.79 0.15 0.06
Matches are distributed among these distances:
169 3 0.01
170 30 0.06
171 442 0.90
172 14 0.03
173 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (169 bp):
GAATAGGAGACTATAAATGGACTTTTCTTGCCAATAAATGCTTTTTCTTCATGTTTCTCAAGGTA
AACATTCAATTATAGTCAGTTTTAACAAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGA
TTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCGAAG
Found at i:10516 original size:342 final size:342
Alignment explanation
Indices: 9812--10526 Score: 831
Period size: 342 Copynumber: 2.1 Consensus size: 342
9802 NNGAATAAGA
* * * * * *
9812 GACTATAAATTG-ACTTTTCTTGCAAATGAATGCCT-TTTTCTTCACT-CTTATCAAGGTAGACA
1 GACTATAAA-TGCACTTTTCTTACAAATGAAT-ACTGTTTTCTTTA-TGTTTCTCAAGGTAAACA
* *
9874 TTCAATTATAGTTTGTTGAAACAAAAAATGTGAAAAAATTCAACTTAAAATCAATAATGAGATTA
63 TTCAATTATAGTCTGTTGAAACAAAAAATCTGAAAAAATTCAACTTAAAATCAATAATGAGATTA
* * *
9939 TAAAATAATTTAAAGCGAGTAATAGGGCTTTCGAAGGAATAGGAGACTATAAATGGACTTGTCTT
128 TAAAATAATTTAAACCCAGTAATAAGGCTTTCGAAGGAATAGGAGACTATAAATGGACTTGTCTT
* * ** * *
10004 GCCAATAAATGCTTGTTTCTTCATGTTTTTATAGGTAAATATTTAATTATAGTCACTTTTAACCA
193 GCCAATAAATGCTTGTTTCTTCACGTTTTCATAGAAAAACATTCAATTATAGTCACTTTTAACCA
* * * *
10069 AAAATATAAAACAATTCAATTTAAAATCAATTATTAGATTACAAAACCATTTAAAGCGACTAATA
258 AAAATATAAAAAAATTCAATTTAAAATCAATTATGAGATTACAAAACAATTTAAAGAGACTAATA
*
10134 AGGCTTTTGAAGGAACGGGT
323 AGGCTTTCGAAGGAACGGGT
* *
10154 GACTATAAATGCACTTTTCTTACCAATGAATACTGTTTTCTTTATGTTTCTCAAGGTAAAGATTC
1 GACTATAAATGCACTTTTCTTACAAATGAATACTGTTTTCTTTATGTTTCTCAAGGTAAACATTC
** * * *
10219 AATTATAGTCTGTTTTAATAAAAAATCT-AAAAATATTCGACTTAAAA-CAAATTATGAGATTAT
66 AATTATAGTCTGTTGAAACAAAAAATCTGAAAAA-ATTCAACTTAAAATC-AATAATGAGATTAT
* * * * *
10282 AAAATTATTTAAACCCAGTACTAAGGCTTTTGAAGGAATGAGG-GACTATAAATGGACTTTTTTT
129 AAAATAATTTAAACCCAGTAATAAGGCTTTCGAAGGAAT-AGGAGACTATAAATGGACTTGTCTT
* *
10346 GCCAATGAATAT-CTT-TTTCTTTACGTTTCTCA-AGAAAAACATTCAATTATAGTTTA-TTTTA
193 GCCAAT-AA-ATGCTTGTTTCTTCACGTTT-TCATAGAAAAACATTCAATTATAG-TCACTTTTA
* * * * * *
10407 ACCAAAAATATAAAAAAATTTAATTTCAAATTAATTATGAGATTATAAAGCAATTTAAAGAGAGT
254 ACCAAAAATATAAAAAAATTCAATTTAAAATCAATTATGAGATTACAAAACAATTTAAAGAGACT
* *
10472 AGTAAGGCTTTCGAAGGAATGGGT
319 AATAAGGCTTTCGAAGGAACGGGT
* * *
10496 GATTATAAATAG-ATTTTTCTTTCAAATGAAT
1 GACTATAAAT-GCACTTTTCTTACAAATGAAT
10527 GCCTTTTTCT
Statistics
Matches: 314, Mismatches: 48, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
341 11 0.04
342 288 0.92
343 13 0.04
344 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (342 bp):
GACTATAAATGCACTTTTCTTACAAATGAATACTGTTTTCTTTATGTTTCTCAAGGTAAACATTC
AATTATAGTCTGTTGAAACAAAAAATCTGAAAAAATTCAACTTAAAATCAATAATGAGATTATAA
AATAATTTAAACCCAGTAATAAGGCTTTCGAAGGAATAGGAGACTATAAATGGACTTGTCTTGCC
AATAAATGCTTGTTTCTTCACGTTTTCATAGAAAAACATTCAATTATAGTCACTTTTAACCAAAA
ATATAAAAAAATTCAATTTAAAATCAATTATGAGATTACAAAACAATTTAAAGAGACTAATAAGG
CTTTCGAAGGAACGGGT
Done.