Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398917.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2199.0, 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: 8424
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.27
Warning! 2122 characters in sequence are not A, C, G, or T
Found at i:291 original size:172 final size:171
Alignment explanation
Indices: 3--742 Score: 662
Period size: 172 Copynumber: 4.3 Consensus size: 171
1 TC
* * * * *
3 AAAGTGAGTAATAAGGCTTTTGAAGGAGTGCGTGACTATAAATAGACTTTTCCTGCCAATGAATG
1 AAAGTGAGTAATAAGGCTTTTGAA-GAATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATA
* * * * * * * * *
68 CTCTCTTCTTTATGTTTCTCGTGGTAGAGATTCAATTACAATATGTTTTAACCAAAAAAGTAAAA
65 CTTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTATAGTATATTTTAACCAAAAATGTAAAA
* * * * *
133 AAAATTGAACTTAAAATCAATTTTGAGATTATAAATTTATTT
130 AAAATTAAAATTTAAATCAATTTTGAGATTATAAAATCATTT
* * *
175 AAAGTGATTAATAAGGCTTTTGAAGCAATGGGTGACAATAAATAGACTTTTCTTGCCAATGAATA
1 AAAGTGAGTAATAAGGCTTTTGAAG-AATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATA
* *
240 CTTTTTTCTTCATGTTTCTCATGGTAGACATTAAATTTTAGTATATTTTAACCAAAAATGTAAAA
65 CTTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTATAGTATATTTTAACCAAAAATGTAAAA
* * *
305 AACATTCAAATTTAAATCAATTTTGAGATTATAAAATCGTTT
130 AAAATTAAAATTTAAATCAATTTTGAGATTATAAAATCATTT
* * * * * * * *
347 AAACTGAGTAATAAGCCTCTAGATAGAATGAGTAACTATAAATGGACTTTTCTTGTCAATAAATA
1 AAAGTGAGTAATAAGGCTTTTGA-AGAATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATA
* * * ** * *
412 CTATTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCTAGT-TCCTTTTAACCAAAAATGTATA
65 CTTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTATAGTAT-ATTTTAACCAAAAATGTAAA
* * * *
476 AAGAATTAAAATTTAATTCAATTTTTAGATTATAAAACCATTT
129 AAAAATTAAAATTTAAATCAATTTTGAGATTATAAAATCATTT
** * * * * * *
519 AAAGTGAGTAATAACACTTTTAAAAGAATGGGTGACTATAAATGGACTTATCTTACTAATAAATG
1 AAAGTGAGTAATAAGGCTTTT-GAAGAATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATA
* * * * * * * *
584 CCTTTTTCTTTATGTTTGT--TGAGAAAGACATTCAATTATAGTCT-GTTTAACAAAAAATATAA
65 CTTTTTTCTTCATGTTTCTCATG-G-TAGACATTCAATTATAGTATATTTTAACCAAAAATGT-A
* * * * ** * *
646 AAAAAAAATCAACTTCAAATCAATTACG-GTATTACAAAACCATTT
127 AAAAAAATTAAAATTTAAATCAATTTTGAG-ATTATAAAATCATTT
** * * * * *
691 AAAACGAGTGATAAGGCTTTCGAAGGTATGGGTGACTGTAAATGGACTTTTC
1 AAAGTGAGTAATAAGGCTTTTGAA-GAATGGGTGACTATAAATAGACTTTTC
743 GAAGGTATGG
Statistics
Matches: 463, Mismatches: 95, Indels: 20
0.80 0.16 0.03
Matches are distributed among these distances:
170 1 0.00
171 19 0.04
172 439 0.95
173 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
AAAGTGAGTAATAAGGCTTTTGAAGAATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATAC
TTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTATAGTATATTTTAACCAAAAATGTAAAAA
AAATTAAAATTTAAATCAATTTTGAGATTATAAAATCATTT
Found at i:746 original size:31 final size:31
Alignment explanation
Indices: 708--817 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
698 GTGATAAGGC
*
708 TTTCGAAGGTATGGGTGACTGTAAATGGACT
1 TTTCGAAGGTATGGGTGACTATAAATGGACT
*
739 TTTCGAAGGTATGGGTGACTATAAATGAACT
1 TTTCGAAGGTATGGGTGACTATAAATGGACT
770 TTTCGAAGGTATGGGTGACTATAAATGGACT
1 TTTCGAAGGTATGGGTGACTATAAATGGACT
*
801 TTTTGAAGGTATGGGTG
1 TTTCGAAGGTATGGGTG
818 CTTTTTTCTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.27, C:0.08, G:0.31, T:0.34
Consensus pattern (31 bp):
TTTCGAAGGTATGGGTGACTATAAATGGACT
Found at i:1133 original size:406 final size:406
Alignment explanation
Indices: 415--1148 Score: 951
Period size: 406 Copynumber: 1.8 Consensus size: 406
405 ATAAATACTA
* * * *
415 TTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCTAGTTCCTTTTAACCAAAAATGTATAAAGA
1 TTTTCTTCATGTTGCTAAAGGTAAACATTCAATCCTAGTTCCTTTTAACAAAAAATGTACAAAGA
* * *
480 ATTAAAATTTAATTCAATTTTTAGATTATAAAACCATTTAAAGTGAGTAATAACACTTTTAAAAG
66 ATTAAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAATAACACTTTTAAAAG
* * * *
545 AATGGGTGACTATAAATGGACTTATCTTACTAATAAATGCCTTTTTCTTTATGTTTGTTGAGAAA
131 AATGGGTGACTATAAATGGACTTATCTTACCAATAAATGCCTTCTTCTTTATGTTTCTGGAGAAA
* * * *
610 GACATTCAATTATAGTCTGTTTAACAAAAAATATAAAAAAAAAATCAACTTCAAATCAATTACGG
196 GACATTCAATTATAATATGTTTAACAAAAAATAGAAAAAAAAAATCAACTTAAAATCAATTACGG
* ** * * *
675 TATTACAAAACCATTTAAAACGAGTGATAAGGCTTTCGAAGGTATGGGTGACTGTAAATGGACTT
261 TATTACAAAACCATTTAAAACGAGTAATAAGGCTTTCGAAGCAATAGGTGACTATAAATAGACTT
740 TTCGAAGGTATGGGTGACTATAAATGAACTTTTCGAAGGTATGGGTGACTATAAATGGACTTTTT
326 TTCGAAGGTATGGGTGACTATAAATGAACTTTTCGAAGGTATGGGTGACTATAAATGGACTTTTT
805 GAAGGTATGGGTGCTT
391 GAAGGTATGGGTGCTT
* * *
821 TTTTCTTCATGTTGCTCAAGGTAAACATTCAATTCTAG-TCCGTTTTAATAAAAAATGTACAAAG
1 TTTTCTTCATGTTGCTAAAGGTAAACATTCAATCCTAGTTCC-TTTTAACAAAAAATGTACAAAG
* * ** * *
885 AATTCAAATTTAAATCAATTTTGATATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGAAG
65 AATTAAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAATAACACTTTTAAAA
* * *
950 GAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CTCTCTTCTTTATGTTTCTCGGAG
130 GAATGGGTGACTATAAATGGACTTATCTTACCAATAAATGCCT-TCTTCTTTATGTTTCT-GGAG
* * * *
1014 -TAGACATTCAATTATAATATGTTTTAA-AAAGAAA-AGCAAAAAAAATTGAACTTAAAATCAAT
193 AAAGACATTCAATTATAATATG-TTTAACAAA-AAATAGAAAAAAAAAATCAACTTAAAATCAAT
** * ** ** *
1076 TTTGAG-ATTATAAAACTTTTTAAAGTGATTAATAAGGCTTAT-GAAGCAATAGGTGACTATAAA
256 TACG-GTATTACAAAACCATTTAAAACGAGTAATAAGGCTT-TCGAAGCAATAGGTGACTATAAA
1139 TAGACTTTTC
319 TAGACTTTTC
1149 TTAGCAATGA
Statistics
Matches: 276, Mismatches: 45, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
405 5 0.02
406 258 0.93
407 13 0.05
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (406 bp):
TTTTCTTCATGTTGCTAAAGGTAAACATTCAATCCTAGTTCCTTTTAACAAAAAATGTACAAAGA
ATTAAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAATAACACTTTTAAAAG
AATGGGTGACTATAAATGGACTTATCTTACCAATAAATGCCTTCTTCTTTATGTTTCTGGAGAAA
GACATTCAATTATAATATGTTTAACAAAAAATAGAAAAAAAAAATCAACTTAAAATCAATTACGG
TATTACAAAACCATTTAAAACGAGTAATAAGGCTTTCGAAGCAATAGGTGACTATAAATAGACTT
TTCGAAGGTATGGGTGACTATAAATGAACTTTTCGAAGGTATGGGTGACTATAAATGGACTTTTT
GAAGGTATGGGTGCTT
Found at i:1251 original size:172 final size:170
Alignment explanation
Indices: 818--1252 Score: 480
Period size: 172 Copynumber: 2.5 Consensus size: 170
808 GGTATGGGTG
* * *
818 CTTTTTTCTTCATGTTGCTCAAGGTAAACATTCAATTCTAGTCCGTTTTAATAAAAAATGTACAA
1 CTTTTTTCTTCATGTTTCTTAAGGTAAACATTCAATTCTAGTCTGTTTTAA-AAAAAATGTACAA
* *
883 AGAATTCAAATTTAAATCAATTTTGATATTATAAAAACATTTAAAGTGAGTAATAAGGCTTTTGA
65 A-AATTCAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTATGA
* * * *
948 AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
129 AGCAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATA
* * * ** * * * * * * *
990 CTCTCTTCTTTATGTTTC-TCGGAGTAGACATTCAATTATAATATGTTTTAAAAAGAAAAGCAAA
1 CTTTTTTCTTCATGTTTCTTAAG-GTAAACATTCAATTCTAGTCTGTTTTAAAAA-AAATG-TAC
* * * * *
1054 AAAAATTGAACTTAAAATCAATTTTGAGATTAT-AAAACTTTTTAAAGTGATTAATAAGGCTTAT
63 AAAAATTCAAATTTAAATCAATTTTGAGATTATAAAAAC-ATTTAAAGTGAGTAATAAGGCTTAT
1118 GAAGCAATAGGTGACTATAAATAGACTTTTCTTAG-CAATGAATA
127 GAAGCAATAGGTGACTATAAATAGACTTTTCTT-GCCAATGAATA
* * * * *
1162 CTTTTTTCTTCATGTTTCTTATGGTAAACATTCAGTGCTAGTCTATTTTAACCAAAAATGTACAA
1 CTTTTTTCTTCATGTTTCTTAAGGTAAACATTCAATTCTAGTCTGTTTTAA-AAAAAATGTACAA
*
1227 AACATTCAAATTTAAATTAATTTTGA
65 AA-ATTCAAATTTAAATCAATTTTGA
1253 NNNNNNNNNN
Statistics
Matches: 209, Mismatches: 46, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
171 14 0.07
172 186 0.89
173 9 0.04
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (170 bp):
CTTTTTTCTTCATGTTTCTTAAGGTAAACATTCAATTCTAGTCTGTTTTAAAAAAAATGTACAAA
AATTCAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAATAAGGCTTATGAAG
CAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATA
Found at i:4730 original size:172 final size:170
Alignment explanation
Indices: 4314--6091 Score: 1581
Period size: 172 Copynumber: 10.4 Consensus size: 170
4304 NNNNNNNNNN
* * * * *
4314 AAAA-CATTTAAAGTGAGTAATATGGCTTTTG-AGGTAATGCGTTACTATAAATGAAATTTTCTT
1 AAAACCATTTAAAGTGAGTAAAAAGG-TTTTGAAGG-AATGGGTGACTATAAATGAACTTTTCTT
* * * * *** * * *
4377 GCCAATGAATGCTCTTTTCTTTATGTTTCTCAGGGTATTTATTCAATTATAATATATTTTAACCA
64 GCCCATGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTATTTTAACCA
* * * * *
4442 GAAAA-GTAAAAAAAATAAACTTAAAATCAATTTTGTGATTAT
129 -AAAATGTACAAAAATTAAAATTTAAATCAATTTTGAGATTAT
*** * * * * *
4484 AAATTTATTTAAAGTGATTAATAAGGCTTTTGAAGTAATGGGTGACAATAAAT-AGACATTTCTT
1 AAAACCATTTAAAGTGAGTAAAAAGG-TTTTGAAGGAATGGGTGACTATAAATGA-ACTTTTCTT
* ********** *
4548 GCCAATGAATACTTTTTTCTTCATGTTNNNNNNNNNNGACATTTAATTCTAGTCTATTTTAACCA
64 GCCCATGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTATTTTAACCA
* * *
4613 AAAATGAACAAAACATTAAAATTTAAATTAATTTTGAGATTGT
129 AAAATGTACAAAA-ATTAAAATTTAAATCAATTTTGAGATTAT
* * *
4656 AAAACCATTTAAATTGAGTAAAAAGGTTGTTGAAGGAATGGGTTACTATAAATGAAGTTTTCTTG
1 AAAACCATTTAAAGTGAGTAAAAAGGTT-TTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
* * * *
4721 CCCATGAATACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCTAGTCTGTTTTAACCAA
65 CCCATGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTATTTTAACCAA
* * *
4786 AAATGTACAAAGAATTGAAATCTAAA-CAAATTTTTAGATTAT
130 AAATGTACAAA-AATTAAAATTTAAATC-AATTTTGAGATTAT
* *
4828 AAAACCATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
1 AAAACCATTTAAAGTGAGTAAAAAGG-TTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
* * * * * * * * * * *
4893 CCAATGAATGCTCTCTTCTTTATGTTTCTCGGGGTAGATATTCAATTATAATATGTTTTAACCAG
65 CCCATGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTATTTTAACCA-
* * * *
4958 AAAA-GTAAGAAAAATTGAACTTAAAATCAATTTTGAGATTAT
129 AAAATGT-ACAAAAATTAAAATTTAAATCAATTTTGAGATTAT
*** * * * * ** *
5000 AAATTTATTTAAAGTGATTAATAAGGCTGTCGAACCAATGGGTGACAATAAAT-AGACTTTTCTT
1 AAAACCATTTAAAGTGAGTAAAAAGG-TTTTGAAGGAATGGGTGACTATAAATGA-ACTTTTCTT
* * * *
5064 GCCGATGAATAATTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTCTACTCTATTTTAACCA
64 GCCCATGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTATTTTAACCA
* *
5129 AAAATGTACAAAACATTAAAATTTAAATAAATTTTGAGATTGT
129 AAAATGTACAAAA-ATTAAAATTTAAATCAATTTTGAGATTAT
* * * * *
5172 AAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAGGAATGGGTTACTACAAATGAAC-TTTGTTG
1 AAAACCATTTAAAGTGAGTAAAAAGG-TTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
* * * *
5236 CCCATGTATACTTTTTTCTTCATGTTTCTGAGGGTAGACATTCAA-TCTTAGTCTGTTTTAACAA
65 CCCATGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTC-TAGTCTATTTTAACCA
* * * *
5300 AAAATGTACAAAGAATTAAAATTTAAATAAATTTTTAAACTAT
129 AAAATGTACAAA-AATTAAAATTTAAATCAATTTTGAGATTAT
* * * * * *
5343 AAAACTA-TTAAAGGTGAGTAATAACGCTTTCGAAGGAATGGGTGACTATAAATGGACTGTTCTT
1 AAAACCATTTAAA-GTGAGTAA-AAAGGTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTT
* * * * * ** * * * * * *
5407 G-TCAGTGAATGCATTCTTCTTTATGTTTCTTGGGGTAGATATTCAATTATAATATGTTTGAACC
64 GCCCA-TGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTATTTTAACC
* * * *
5471 AGAAAA-GTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTAT
128 A-AAAATGT-ACAAAAATTAAAATTTAAATCAATTTTGAGATTAT
*** * * * * *
5515 AAATTTATTTAAAGTGATTAATAAGGCTTTTGAAGCAATGGGTGACAATAAA-AAGACTTTTCTT
1 AAAACCATTTAAAGTGAGTAAAAAGG-TTTTGAAGGAATGGGTGACTATAAATGA-ACTTTTCTT
* * *
5579 GCCAATGAATACTTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTCTAGTCTATTTTAATCA
64 GCCCATGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTATTTTAACCA
*
5644 AAAATGTACAAAACATTAAAATTTAAATCAATTTTGAGATTGT
129 AAAATGTACAAAA-ATTAAAATTTAAATCAATTTTGAGATTAT
* * * * * *
5687 AAAGCCATTTAAACTGAGTAATAAGGCTCTTGAAGGAATGGATGACTATAAATGAACTTTTCTTC
1 AAAACCATTTAAAGTGAGTAAAAAGG-TTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
* * * * *
5752 CCCATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACACTCAATCCTAGTCTATTTTAA-CTA
65 CCCATGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTATTTTAACCAA
* * *
5816 AAATGTGCAAAGAACTCAAATTTAAATCAATTTTGAGATTAT
130 AAATGTACAAA-AATTAAAATTTAAATCAATTTTGAGATTAT
* * *
5858 AAAACCATTTAAAGTGAGTAATAAGGGTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTG
1 AAAACCATTTAAAGTGAGTAA-AAAGGTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
* * * * * * * * * * *
5923 CCAATGAATGCATTTTTGTTTACGTTTCTTTA-GGTAGACATTCCATTATAGTCT-GTTTAACAA
65 CCCATGAATACTTTTTTCTTCATGTTTC-TCAGGGTAGACATTCAATTCTAGTCTATTTTAACCA
* * * * * ** * *
5986 AAAATATAAAAAAATTTAACTTAAAATCAATTACGACATTAC
129 AAAATGTACAAAAATTAAAATTTAAATCAATTTTGAGATTAT
* * * * *
6028 AAAACTATTTAAAGTGAATAATAAGGCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCTT
1 AAAACCATTTAAAGTGAGTAAAAAGG-TTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTT
6092 ACCAATGANN
Statistics
Matches: 1296, Mismatches: 274, Indels: 76
0.79 0.17 0.05
Matches are distributed among these distances:
169 3 0.00
170 96 0.07
171 394 0.30
172 773 0.60
173 30 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (170 bp):
AAAACCATTTAAAGTGAGTAAAAAGGTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTGC
CCATGAATACTTTTTTCTTCATGTTTCTCAGGGTAGACATTCAATTCTAGTCTATTTTAACCAAA
AATGTACAAAAATTAAAATTTAAATCAATTTTGAGATTAT
Found at i:5312 original size:515 final size:514
Alignment explanation
Indices: 4314--6099 Score: 2512
Period size: 515 Copynumber: 3.5 Consensus size: 514
4304 NNNNNNNNNN
* * * *
4314 AAAA-CATTTAAAGTGAGTAATATGGCTTTTG-AGGTAATGCGTTACTATAAATGAAATTTTCTT
1 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG-AATGGGTGACTATAAATGAACTTTTCTT
* * ** *
4377 GCCAATGAATGC-TCTTTTCTTTATGTTTCTCAGGGTATTTATTCAATTATAATATATTTTAACC
65 GCCAATGAATGCAT-TCTTCTTTATGTTTCTCGGGGTAGATATTCAATTATAATATGTTTTAACC
* *
4441 AGAAAAGTAAAAAAAA-TAAACTTAAAATCAATTTTGTGATTATAAATTTATTTAAAGTGATTAA
129 AGAAAAGTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAATTTATTTAAAGTGATTAA
* *
4505 TAAGGCTTTTGAAGTAATGGGTGACAATAAATAGACATTTCTTGCCAATGAATACTTTTTTCTTC
194 TAAGGCTTTTGAAGCAATGGGTGACAATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTC
********** * *
4570 ATGTTNNNNNNNNNNGACATTTAATTCTAGTCTATTTTAACCAAAAATGAACAAAACATTAAAAT
259 ATGTTTCTCATGGTAGACATTCAATTCTAGTCTATTTTAACCAAAAATGTACAAAACATTAAAAT
* * * *
4635 TTAAATTAATTTTGAGATTGTAAAACCATTTAAATTGAGTAAAAAGGTTGTTGAAGGAATGGGTT
324 TTAAATAAATTTTGAGATTGTAAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAGGAATGGGTT
* *
4700 ACTATAAATGAAGTTTTCTTGCCCATGAATACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCA
389 ACTATAAATGAA-CTTTCTTGCCCATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCA
* *
4765 ATCCTAGTCTGTTTTAACCAAAAATGTACAAAGAATTGAAATCTAAACAAATTTTTAGATTAT
453 ATCCTAGTCTGTTTTAA-CAAAAATGTACAAAGAATTAAAATTTAAACAAATTTTTAGATTAT
*
4828 AAAACCATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
1 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
4893 CCAATGAATGC-TCTCTTCTTTATGTTTCTCGGGGTAGATATTCAATTATAATATGTTTTAACCA
66 CCAATGAATGCAT-TCTTCTTTATGTTTCTCGGGGTAGATATTCAATTATAATATGTTTTAACCA
*
4957 GAAAAGTAAGAAAAATTGAACTTAAAATCAATTTTGAGATTATAAATTTATTTAAAGTGATTAAT
130 GAAAAGTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAATTTATTTAAAGTGATTAAT
* * * * *
5022 AAGGCTGTCGAACCAATGGGTGACAATAAATAGACTTTTCTTGCCGATGAATAATTTTTTCTTCA
195 AAGGCTTTTGAAGCAATGGGTGACAATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCA
*
5087 TGTTTCTCATGGTAGACATTCAATTCTACTCTATTTTAACCAAAAATGTACAAAACATTAAAATT
260 TGTTTCTCATGGTAGACATTCAATTCTAGTCTATTTTAACCAAAAATGTACAAAACATTAAAATT
5152 TAAATAAATTTTGAGATTGTAAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAGGAATGGGTTA
325 TAAATAAATTTTGAGATTGTAAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAGGAATGGGTTA
* * * *
5217 CTACAAATGAACTTTGTTGCCCATGTATACTTTTTTCTTCATGTTTCTGAGGGTAGACATTCAAT
390 CTATAAATGAACTTTCTTGCCCATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAAT
* * * *
5282 CTTAGTCTGTTTTAACAAAAAATGTACAAAGAATTAAAATTTAAATAAATTTTTAAACTAT
455 CCTAGTCTGTTTTAAC-AAAAATGTACAAAGAATTAAAATTTAAACAAATTTTTAGATTAT
* * * * *
5343 AAAACTA-TTAAAGGTGAGTAATAACGCTTTCGAAGGAATGGGTGACTATAAATGGACTGTTCTT
1 AAAACCATTTAAA-GTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTT
* * * *
5407 GTCAGTGAATGCATTCTTCTTTATGTTTCTTGGGGTAGATATTCAATTATAATATGTTTGAACCA
65 GCCAATGAATGCATTCTTCTTTATGTTTCTCGGGGTAGATATTCAATTATAATATGTTTTAACCA
5472 GAAAAGTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAATTTATTTAAAGTGATTAAT
130 GAAAAGTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAATTTATTTAAAGTGATTAAT
*
5537 AAGGCTTTTGAAGCAATGGGTGACAATAAAAAGACTTTTCTTGCCAATGAATACTTTTTTCTTCA
195 AAGGCTTTTGAAGCAATGGGTGACAATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCA
*
5602 TGTTTCTCATGGTAGACATTCAATTCTAGTCTATTTTAATCAAAAATGTACAAAACATTAAAATT
260 TGTTTCTCATGGTAGACATTCAATTCTAGTCTATTTTAACCAAAAATGTACAAAACATTAAAATT
* * * * *
5667 TAAATCAATTTTGAGATTGTAAAGCCATTTAAACTGAGTAATAAGGCTCTTGAAGGAATGGATGA
325 TAAATAAATTTTGAGATTGTAAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAGGAATGGGTTA
* *
5732 CTATAAATGAACTTTTCTTCCCCATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACACTCAA
390 CTATAAATGAAC-TTTCTTGCCCATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAA
* * * * * *
5797 TCCTAGTCTATTTTAACTAAAATGTGCAAAGAACTCAAATTTAAATC-AATTTTGAGATTAT
454 TCCTAGTCTGTTTTAACAAAAATGTACAAAGAATTAAAATTTAAA-CAAATTTTTAGATTAT
* * *
5858 AAAACCATTTAAAGTGAGTAATAAGGGTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTG
1 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
* * * *** * * * *
5923 CCAATGAATGCATTTTTGTTTACGTTTCTTTAGGTAGACATTCCATTATAGTCTG-TTTAA-CA-
66 CCAATGAATGCATTCTTCTTTATGTTTCTCGGGGTAGATATTCAATTATAATATGTTTTAACCAG
* * ** * * ** *
5985 AAAAATATAAAAAAATTTAACTTAAAATCAATTACGACATTACAAAACTATTTAAAGTGAATAAT
131 AAAAGTA-AAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAATTTATTTAAAGTGATTAAT
* ** * *
6050 AAGGCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCTTACCAATGA
195 AAGGCTTTTGAAGCAATGGGTGACAATAAATAGACTTTTCTTGCCAATGA
6100 NNNNNNNNNN
Statistics
Matches: 1140, Mismatches: 122, Indels: 21
0.89 0.10 0.02
Matches are distributed among these distances:
512 6 0.01
513 95 0.08
514 14 0.01
515 726 0.64
516 299 0.26
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (514 bp):
AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTG
CCAATGAATGCATTCTTCTTTATGTTTCTCGGGGTAGATATTCAATTATAATATGTTTTAACCAG
AAAAGTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAATTTATTTAAAGTGATTAATA
AGGCTTTTGAAGCAATGGGTGACAATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCAT
GTTTCTCATGGTAGACATTCAATTCTAGTCTATTTTAACCAAAAATGTACAAAACATTAAAATTT
AAATAAATTTTGAGATTGTAAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAGGAATGGGTTAC
TATAAATGAACTTTCTTGCCCATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATC
CTAGTCTGTTTTAACAAAAATGTACAAAGAATTAAAATTTAAACAAATTTTTAGATTAT
Found at i:5674 original size:687 final size:686
Alignment explanation
Indices: 4585--6091 Score: 1703
Period size: 687 Copynumber: 2.2 Consensus size: 686
4575 NNNNNNNNNN
* * * * * *
4585 GACATTTAATTCTAGTCTATTTTAACCAAAAATGAACAAAACATTAAAATTTAAATTAATTTTGA
1 GACATTCAATTATAGTCTGTTTTAACAAAAAATGTACAAAA-ATTAAAATTTAAATAAATTTTGA
* * * * * * * *
4650 GATTGTAAAACCATTTAAATTGAGTAA-AAAGGTTGTTGAAGGAATGGGTTACTATAAATGAAGT
65 AATTATAAAACTATTTAAAGTGAGTAATAAAGCTT-TTGAAGGAATGGGTGACTATAAATGGACT
* * * * *
4714 TTTCTTGCCCATGAATACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCTAGTCTGTTT
129 TTTCTTGCCCATGAATACATTCTTCTTCATGTTTCTAAAGGTAGACATTCAATCATAATATGTTT
* * * *
4779 TAACCAAAAATGTACAAAGAATTGAAATCTAAACAAATTTTTAGATTATAAAACCATTTAAAGTA
194 GAACCAAAAATGTAAAAAAAATTGAAATCTAAACAAATTTTGAGATTATAAAACCATTTAAAGTA
* * * *
4844 AGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCTTGCCAATGAATGCTCTCT
259 AGTAATAAGGCTTTTGAAGCAATGGGTGACAATAAAAGAACTTTTCTTGCCAATGAATACTCTCT
* * * *
4909 TCTTTATGTTTCTCGGGGTAGATATTCAATTATAATATGTTTTAACCAGAAAAGTAAGAAAAATT
324 TCTTCATGTTTCTCAGGGTAGACATTCAATTATAATATATTTTAACCAGAAAAGTAAGAAAAATT
* * *** * * *
4974 GAACTTAAAATCAATTTTGAGATTATAAATTTATTTAAAGTGATTAATAAGGCTGTCGAACCAAT
389 AAAATTAAAATCAATTTTGAGATTATAAAGCCATTTAAACTGAGTAATAAGGCTCTCGAACCAAT
* * * *
5039 GGGTGACAATAAAT-AGACTTTTCTTGCCGATGAATAATTTTTTCTTCATGTTTCTCATGGTAGA
454 GGATGACAATAAATGA-ACTTTTCTTCCCCATGAATAATTTTTTCTTCATGTTTCTCAAGGTAGA
* * *
5103 CATTCAATTCTACTCTATTTTAACCAAAAATGTACAAA-ACATTAAAATTTAAATAAATTTTGAG
518 CACTCAATCCTACTCTATTTTAA-CAAAAATGTACAAAGA-ACTAAAATTTAAATAAATTTTGAG
* * *
5167 ATTGTAAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAGGAATGGGTTACTACAAATGAAC-TT
581 ATTATAAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAAGAATGGGTGACTACAAATGAACTTT
* * * * *
5231 TGTTGCCCATGTATACTTTTTTCTTCATGTTTC-TGAGGGTA
646 TCTTGCCAATGAATACATTTTTCTTCACGTTTCTTGA-GGTA
*
5272 GACATTCAATCT-TAGTCTGTTTTAACAAAAAATGTACAAAGAATTAAAATTTAAATAAATTTTT
1 GACATTCAAT-TATAGTCTGTTTTAACAAAAAATGTACAAA-AATTAAAATTTAAATAAATTTTG
* * *
5336 AAACTATAAAACTA-TTAAAGGTGAGTAATAACGCTTTCGAAGGAATGGGTGACTATAAATGGAC
64 AAATTATAAAACTATTTAAA-GTGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGAC
* * * * *** * *
5400 TGTTCTTG-TCAGTGAATGCATTCTTCTTTATGTTTCTTGGGGTAGATATTCAATTATAATATGT
128 TTTTCTTGCCCA-TGAATACATTCTTCTTCATGTTTCTAAAGGTAGACATTCAATCATAATATGT
* ***
5464 TTGAACCAGAAAA-GTAAAAAAAATTGAACT-TAAA-ATCAATTTTGAGATTATAAATTTATTTA
192 TTGAACCA-AAAATGTAAAAAAAATTGAAATCTAAACA--AATTTTGAGATTATAAAACCATTTA
* *
5526 AAGTGATTAATAAGGCTTTTGAAGCAATGGGTGACAATAAAA-AGACTTTTCTTGCCAATGAATA
254 AAGTAAGTAATAAGGCTTTTGAAGCAATGGGTGACAATAAAAGA-ACTTTTCTTGCCAATGAATA
* * * * * * *
5590 CTTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTCTAGTCTATTTTAATCA-AAAATGTACA
318 CTCTCTTCTTCATGTTTCTCAGGGTAGACATTCAATTATAATATATTTTAACCAGAAAA-GTA-A
* * * *
5654 -AAACATTAAAATTTAAATCAATTTTGAGATTGTAAAGCCATTTAAACTGAGTAATAAGGCTCTT
381 GAAAAATTAAAATTAAAATCAATTTTGAGATTATAAAGCCATTTAAACTGAGTAATAAGGCTCTC
** * * *
5718 GAAGGAATGGATGACTATAAATGAACTTTTCTTCCCCATGAATACTTTTTTCTTCATGTTTCTGA
446 GAACCAATGGATGACAATAAATGAACTTTTCTTCCCCATGAATAATTTTTTCTTCATGTTTCTCA
* * * * *
5783 AGGTAGACACTCAATCCTAGTCTATTTTAACTAAAATGTGCAAAGAACTCAAATTTAAATCAATT
511 AGGTAGACACTCAATCCTACTCTATTTTAACAAAAATGTACAAAGAACTAAAATTTAAATAAATT
* * * * * *
5848 TTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGGTTTTGAAAGAATGGGTGACTATAAATGG
576 TTGAGATTATAAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAAGAATGGGTGACTACAAATGA
* * * *
5913 ACTTTTCTTGCCAATGAATGCATTTTTGTTTACGTTTCTTTAGGTA
641 ACTTTTCTTGCCAATGAATACATTTTTCTTCACGTTTCTTGAGGTA
* * * * * * * ** *
5959 GACATTCCATTATAGTCTG-TTTAACAAAAAATATAAAAAAATTTAACTTAAAATCAATTACGAC
1 GACATTCAATTATAGTCTGTTTTAACAAAAAATGTACAAAAATTAAAATTTAAATAAATTTTGAA
* * * *
6023 ATTACAAAACTATTTAAAGTGAATAATAAGGCTTTTGAAGGAATGGGTGACTCTAAATGGACTTT
66 ATTATAAAACTATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTT
6088 TCTT
131 TCTT
6092 ACCAATGANN
Statistics
Matches: 682, Mismatches: 121, Indels: 36
0.81 0.14 0.04
Matches are distributed among these distances:
685 74 0.11
686 126 0.18
687 467 0.68
688 15 0.02
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (686 bp):
GACATTCAATTATAGTCTGTTTTAACAAAAAATGTACAAAAATTAAAATTTAAATAAATTTTGAA
ATTATAAAACTATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTT
TCTTGCCCATGAATACATTCTTCTTCATGTTTCTAAAGGTAGACATTCAATCATAATATGTTTGA
ACCAAAAATGTAAAAAAAATTGAAATCTAAACAAATTTTGAGATTATAAAACCATTTAAAGTAAG
TAATAAGGCTTTTGAAGCAATGGGTGACAATAAAAGAACTTTTCTTGCCAATGAATACTCTCTTC
TTCATGTTTCTCAGGGTAGACATTCAATTATAATATATTTTAACCAGAAAAGTAAGAAAAATTAA
AATTAAAATCAATTTTGAGATTATAAAGCCATTTAAACTGAGTAATAAGGCTCTCGAACCAATGG
ATGACAATAAATGAACTTTTCTTCCCCATGAATAATTTTTTCTTCATGTTTCTCAAGGTAGACAC
TCAATCCTACTCTATTTTAACAAAAATGTACAAAGAACTAAAATTTAAATAAATTTTGAGATTAT
AAAACCATTTAAACTGAGTAAAAAGGCTCTTGAAAGAATGGGTGACTACAAATGAACTTTTCTTG
CCAATGAATACATTTTTCTTCACGTTTCTTGAGGTA
Done.