Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403035.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_702.0, 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: 21694
ACGTcount: A:0.21, C:0.07, G:0.08, T:0.21
Warning! 9378 characters in sequence are not A, C, G, or T
Found at i:1548 original size:171 final size:169
Alignment explanation
Indices: 1155--1550 Score: 412
Period size: 171 Copynumber: 2.3 Consensus size: 169
1145 NNNNNNNNNN
* *
1155 AATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTAAAGTAAGTAATAACTCTTCTGAAG
1 AATTC-AATTTAAATCAATTTTGAGATTATAAAAC-ATTTAAAGTGAGTAATAACGCTTCTGAAG
* ** **
1220 GAATAAGTGACTATAAATAGACTTTTCTTACTAATGAATGCTGTTTTCTTTGTGTTTCTTGAGGT
64 GAATAAGTGACTATAAATAGACTTTTCTTACCAATGAATGCTGTTTTCTTCATGTTTCTCAAGGT
*
1285 CGACATTCAATTATAGTCTGTTTTAACTAAAAATGTGAAAA
129 AGACATTCAATTATAGTCTGTTTTAACTAAAAATGTGAAAA
* * * * * * * *
1326 AATCCAACTTAAAATCAATTATG-GCACTATAAAATCATTTAGAGCGAGTAATAAGGCTTTTGAA
1 AATTCAA-TTTAAATCAATTTTGAG-ATTATAAAA-CATTTAAAGTGAGTAATAACGCTTCTGAA
* ** *
1390 GGTATGGGCT-ACTATAAATGGA-TTTTCCTTACCAATGAATGCAT-TTGTT-TTCATGTTTCTC
63 GGAATAAG-TGACTATAAATAGACTTTT-CTTACCAATGAATGC-TGTT-TTCTTCATGTTTCTC
*
1451 AAGGTAGACATTCAATTCTAGT-TAGTTTTAACT-AAAATGT-ACAAA
124 AAGGTAGACATTCAATTATAGTCT-GTTTTAACTAAAAATGTGA-AAA
*
1496 GAATTCAGATTTAAATCAATTTTGAGATTATAAGACAATTTAAAGTGAGTAATAA
1 -AATTCA-ATTTAAATCAATTTTGAGATTATAAAAC-ATTTAAAGTGAGTAATAA
1551 ANNNNNNNNN
Statistics
Matches: 184, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
169 1 0.01
170 19 0.10
171 157 0.85
172 7 0.04
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (169 bp):
AATTCAATTTAAATCAATTTTGAGATTATAAAACATTTAAAGTGAGTAATAACGCTTCTGAAGGA
ATAAGTGACTATAAATAGACTTTTCTTACCAATGAATGCTGTTTTCTTCATGTTTCTCAAGGTAG
ACATTCAATTATAGTCTGTTTTAACTAAAAATGTGAAAA
Found at i:5487 original size:22 final size:22
Alignment explanation
Indices: 5457--5500 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
5447 AAATCAATTT
5457 TGAGATTATCAAACCATTTAAAG
1 TGAGATTAT-AAACCATTTAAAG
* *
5480 TGAG-TTATAAAGCTTTTAAAG
1 TGAGATTATAAACCATTTAAAG
5501 GAATGGGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 4 0.21
23 4 0.21
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
TGAGATTATAAACCATTTAAAG
Found at i:7531 original size:171 final size:171
Alignment explanation
Indices: 7241--7589 Score: 397
Period size: 171 Copynumber: 2.0 Consensus size: 171
7231 NNNNNNNAGT
* * *
7241 GAGTAATAAGGCTTCTGAAGGAATGAGTGACTATAAATAGACTTTTCTTACTAATGAATGTTGTT
1 GAGTAATAAGGCTTCTGAAGGAATGAGTGACTATAAATAGACTTTTCTCACCAATGAATGCTGTT
** * * *
7306 TTCTTTGTGTTTCTTGAGGTCGACATTCAGTTATAGTCTGTTTTAACCAAAAATATGA-AAAAAT
66 TTCTTCATATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATAT-ACAAAAAT
* *
7370 TCA-ACTTAAAATCAATTATG-GCATTATAAAACTATTTAGAGC
130 TCATA-TTAAAATCAATTATGAG-ATTATAAAACCATTTAAAGC
* * * *
7412 GAGTAATGAGGCTTTTGAAGGTATGAGCT-ACTATAAATGGA-TTTTCCTCACCAATGAATGCTG
1 GAGTAATAAGGCTTCTGAAGGAATGAG-TGACTATAAATAGACTTTT-CTCACCAATGAATGCTG
* *
7475 TTTTCTTCATATTTC-TGAAGGTAGACATTCAATTCTAGT-TAGTTTTAACTAAAAATATACGAA
64 TTTTCTTCATATTTCTTG-AGGTAGACATTCAATTATAGTCT-GTTTTAACCAAAAATATAC-AA
* * * *
7538 GAATTCATATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGT
126 AAATTCATATTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
7584 GAGTAA
1 GAGTAA
7590 NNNNNNNNNN
Statistics
Matches: 150, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
170 8 0.05
171 95 0.63
172 45 0.30
173 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (171 bp):
GAGTAATAAGGCTTCTGAAGGAATGAGTGACTATAAATAGACTTTTCTCACCAATGAATGCTGTT
TTCTTCATATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATACAAAAATT
CATATTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
Found at i:15473 original size:168 final size:166
Alignment explanation
Indices: 14855--15474 Score: 534
Period size: 171 Copynumber: 3.7 Consensus size: 166
14845 NNNNNNNNNN
** *
14855 AACCATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGATTTTTCTTGCC
1 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGATTTTT-TTGCC
* * * * * * *
14920 ATTGAATGTCGTTTTCTTTACGTTTGTGAAGGTAAACATTCAATTATAGTTTGTTTTAATAAAAA
65 AATAAATGTCTTTTTCTTCACGTTTCTTAAGGTAAACATTCAATTATAG-TTATTTT-A-AAAAA
* * *
14985 ATGTGAAAAAATTCTGCTTAAAATCAATTATGGCATTATAA
127 ATATGAAAAAATTC-ACTTAAAATCAATTATGACATTATAA
* * * * * * *
15026 AACCATTTATAGCGGGTAATGAGGCTTTTGAAAGTATGAGTTACTATAAATGGACTTTTCTTGCC
1 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGA-TTTTTTTGCC
* ** * *
15091 AATAAATG-CTTTTTTCTTCATAG-TTCTTAATCTAGACATTCAATTCTAGTTAGTTTTAATAAA
65 AATAAATGTC-TTTTTCTTCA-CGTTTCTTAAGGTAAACATTCAATTATAGTTA-TTTTAA-AAA
* * * *
15154 AA-ATGTATGAAGAATTCACATTTAAATAAAATT-TGAGATTATAA
126 AATATG-A--AAAAATTCAC-TTAAAAT-CAATTATGACATTATAA
* ** * * * *
15198 AGCCATTTAAATTGAGTAATAAGGCTTTTAAAGGAAT-AG-GCAATTATAAATGGAATTTTTTGT
1 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTG--ACTATAAATGGATTTTTTTGC
* * * * * *
15261 CAATAAATGTCTTTTTTTTAACGTTTCTTGAGATAAATATTCAATTATAGTCTACTTTAAAAAAA
64 CAATAAATGTCTTTTTCTTCACGTTTCTTAAGGTAAACATTCAATTATAGT-TATTTTAAAAAAA
*
15326 TATGAAAAAAGTCAACTTAAAATCAATTATGACATTATAA
128 TATGAAAAAATTC-ACTTAAAATCAATTATGACATTATAA
* * * * *
15366 AACCATTTAGAGCGAGTAATGAGGCTTTTGAACGTATGAGTGACTATAAATGGACTTTTTTTGCT
1 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGA-TTTTTTTGCC
* * * * *
15431 AATGAATGT-TTTTTCTTCATGTCTCTCAAGGTAGACATTCAATT
65 AATAAATGTCTTTTTCTTCACGTTTCTTAAGGTAAACATTCAATT
15475 CTAATCGGTT
Statistics
Matches: 348, Mismatches: 80, Indels: 45
0.74 0.17 0.10
Matches are distributed among these distances:
167 4 0.01
168 88 0.25
169 22 0.06
170 18 0.05
171 143 0.41
172 69 0.20
173 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (166 bp):
AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGATTTTTTTGCCA
ATAAATGTCTTTTTCTTCACGTTTCTTAAGGTAAACATTCAATTATAGTTATTTTAAAAAAATAT
GAAAAAATTCACTTAAAATCAATTATGACATTATAA
Found at i:16643 original size:172 final size:172
Alignment explanation
Indices: 15644--16940 Score: 573
Period size: 171 Copynumber: 7.6 Consensus size: 172
15634 NNCGAGGTTC
* * *
15644 ACATTCAATTATAATCTGTTATAACTAAAAAT-ATACAAAGAATTCAAATTTAAATCAATT-TCG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGA-ACAAAGAATTCAAATTTAAATCAATTAT-G
* ** * * ** *
15707 AGATTATAAAA-TCATTTAAAGTAAGTAATAAAGCTT-TCGAAGGAATGGGTGACTATAAATAGA
64 ACATTATAAAACT-ATTTAAAGCGAGTAATAAGGCTTCT-AAAGGAATAAGTGACTATAAATGGA
* * **
15770 CTTTTCCTG-CTAATGAATGT-TTTTTCTTTACGTTTCTTGAGGTAG
127 CTTTTCTTGAC-AATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
********** * * * * *
15815 ACNNNNNNNNNNAATCTGTTTTAACTAAAAATGTAA-AAA-CATT-AAGCTTAAAATCAATTATG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATG-AACAAAGAATTCAA-ATTTAAATCAATTATG
* * * * * * * * ** * *
15877 GCATTATAAAACTATTTAAAGCAAGTAGTAATGTTTTTCGAAGGTATGGGTGATTATAAATTGAC
64 ACATTATAAAACTATTTAAAGCGAGTAATAAGGCTTCT-AAAGGAATAAGTGACTATAAATGGAC
* * * *
15942 TTTTCTT-ACCAATAAATGTTTTTTTCTTCATGTCTTCT-AAGGTAA
128 TTTTCTTGA-CAATGAATGTCTTTTTCTTCACGT-TTCTCAAGGTAG
* * * * * *
15987 ACATTCAATTCTAGTCTGGTTT-ACCAAAAATGAA-AAA-ACATTCAACTTAAAATTAATTATTA
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGAACAAAGA-ATTCAAATTTAAATCAATTATGA
* ** * * ********** *
16049 -GTTCATAGGACCATTTAAAGCAAGTAATAAGGCTNNNNNNNNNNTGAGTGACTATAAATGGACT
65 CATT-ATAAAACTATTTAAAGCGAGTAATAAGGCTTCTAAAGGAATAAGTGACTATAAATGGACT
** * * * * *
16113 TTT-TCT-ACCAATGGTTGGCTTTTGCTTCACGTTCCTCAGGGCAG
129 TTTCT-TGA-CAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
* * * *********
16157 ACATTGAATTATAGTCTTTTTTAACCAAAAATGTAA-AAA-AATTC-AACTTANNNNNNNNNNTG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATG-AACAAAGAATTCAAATTTA-AATCAATTATG
* * * * * * * ** *
16219 AGATTATAAAGCCATTTAAAGTGAGTAATAAGGCCTT-TGAAGAAATAGGTGACCGTAAATAGAC
64 ACATTATAAAACTATTTAAAGCGAGTAATAAGG-CTTCTAAAGGAATAAGTGACTATAAATGGAC
* * *** * * *
16283 TTTTGTTGCCAATGAACACCTTTTTCTTCATGTTTCCCTAA-GCAG
128 TTTTCTTGACAATGAATGTCTTTTTCTTCACGTTTCTC-AAGGTAG
* * * ** * ** *
16328 ACATTCAATTATAATCTGTTCTAACCAGAAA-GGTCAAA-ACTTTCAAGCTAAAATCAATTATGA
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGAACAAAGA-ATTCAAATTTAAATCAATTATGA
** ********** * * * * * * *
16391 GGTTATANNNNNNNNNNAAGTGAGTAATAAGGCTTTTGAATGAA-AGGGTGACCATAAATGGAGT
65 CATTATAAAACTATTTAAAGCGAGTAATAAGGCTTCTAAAGGAATA-AGTGACTATAAATGGACT
* * *
16455 TTTCTT-ATCTATGAATGTCTTTTTCTTCATGTTTTTCAAGGTAG
129 TTTCTTGA-CAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
* ********** *
16499 ACATTCAATTATAGTTTGTTTTAACCAAAAATGAACAAAGAATTCAAATTTNNNNNNNNNNTGAG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGAACAAAGAATTCAAATTTAAATCAATTATGAC
* * * *
16564 ATTATAAATCTATTTAAAGTGTGTAATAAGGCTTCTAAAGGAATATGTGACTATAAATGGACTTT
66 ATTATAAAACTATTTAAAGCGAGTAATAAGGCTTCTAAAGGAATAAGTGACTATAAATGGACTTT
* *
16629 TCTTGACAATGAATGTCTTTTTCTTTACGATTCTCAAGGTAG
131 TCTTGACAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
* * * ** *
16671 AAATTCAATTATAGTCTGTTTTAAGCAAAAATGTGA-AAA-AATTCACCTTAAAATCAATTATGA
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATG-AACAAAGAATTCAAATTTAAATCAATTATGA
* * * * *
16734 CATTATAAAACTATTTGAAGCGAGTAATGAGGCTTTTAAAGGTATAAGTGACTATAAATGGACAT
65 CATTATAAAACTATTTAAAGCGAGTAATAAGGCTTCTAAAGGAATAAGTGACTATAAATGGACTT
* * * *
16799 TTCTTGCCAATGAATG-CTTTTTTCTTCGCATATCTCAAGGTAG
130 TTCTTGACAATGAATGTC-TTTTTCTTCACGTTTCTCAAGGTAG
** * * * * * * *
16842 ACATTCAATCCTAGTCAGTTTTAACTAAAAATGTACAAAGAATTCAGATTTAAATCAATTTTAAG
1 ACATTCAATTATAGTCTGTTTTAACCAAAAATGAACAAAGAATTCAAATTTAAATCAATTATGAC
*
16907 ATTATAAAACTATTTAAAGTGAGTAATAAGGCTT
66 ATTATAAAACTATTTAAAGCGAGTAATAAGGCTT
16941 TTNNNNNNNN
Statistics
Matches: 827, Mismatches: 261, Indels: 75
0.71 0.22 0.06
Matches are distributed among these distances:
169 6 0.01
170 128 0.15
171 460 0.56
172 224 0.27
173 9 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.34
Consensus pattern (172 bp):
ACATTCAATTATAGTCTGTTTTAACCAAAAATGAACAAAGAATTCAAATTTAAATCAATTATGAC
ATTATAAAACTATTTAAAGCGAGTAATAAGGCTTCTAAAGGAATAAGTGACTATAAATGGACTTT
TCTTGACAATGAATGTCTTTTTCTTCACGTTTCTCAAGGTAG
Found at i:16837 original size:171 final size:172
Alignment explanation
Indices: 16408--16942 Score: 492
Period size: 172 Copynumber: 3.1 Consensus size: 172
16398 NNNNNNNNNN
* * * * ** *
16408 AAGTGAGTAATAAGGCTTTTGAATGAA-AGGGTGACCATAAATGGAGTTTTCTT-ATCTATGAAT
1 AAGTGAGTAATAAGGCTTTTAAAGGAATA-AGTGACTATAAATGGACATTTCTTGA-CAATGAAT
* * * * * * ** * *
16471 GTCTTTTTCTTCATGTTTTTCAAGGTAGACATTCAATTATAGTTTGTTTTAACCAAAAATGAACA
64 GTCTTTTTCTTTACGATTCTCAAGGTAGAAATTCAATCATAGTCAGTTTTAACTAAAAATGTACA
* *********** * * *
16536 AAGAATTCAAATTTNNNNNNNNNNTGAGATTATAAATCTATTTA
129 AAGAATTCACATTAAAATCAATTATAACATTATAAAACTATTTA
* * * *
16580 AAGTGTGTAATAAGGCTTCTAAAGGAATATGTGACTATAAATGGACTTTTCTTGACAATGAATGT
1 AAGTGAGTAATAAGGCTTTTAAAGGAATAAGTGACTATAAATGGACATTTCTTGACAATGAATGT
* *
16645 CTTTTTCTTTACGATTCTCAAGGTAGAAATTCAATTATAGTCTGTTTTAAGC-AAAAATGTGA-A
66 CTTTTTCTTTACGATTCTCAAGGTAGAAATTCAATCATAGTCAGTTTTAA-CTAAAAATGT-ACA
* * *
16708 AA-AATTCACCTTAAAATCAATTATGACATTATAAAACTATTTG
129 AAGAATTCACATTAAAATCAATTATAACATTATAAAACTATTTA
* * * *
16751 AAGCGAGTAATGAGGCTTTTAAAGGTATAAGTGACTATAAATGGACATTTCTTGCCAATGAATG-
1 AAGTGAGTAATAAGGCTTTTAAAGGAATAAGTGACTATAAATGGACATTTCTTGACAATGAATGT
* *
16815 CTTTTT-TCTT-CGCATATCTCAAGGTAGACATTCAATCCTAGTCAGTTTTAACTAAAAATGTAC
66 CTTTTTCT-TTACG-AT-TCTCAAGGTAGAAATTCAATCATAGTCAGTTTTAACTAAAAATGTAC
* * * *
16878 AAAGAATTCAGATTTAAATCAATTTTAAGATTATAAAACTATTTA
128 AAAGAATTCACATTAAAATCAATTATAACATTATAAAACTATTTA
16923 AAGTGAGTAATAAGGCTTTT
1 AAGTGAGTAATAAGGCTTTT
16943 NNNNNNNNNN
Statistics
Matches: 301, Mismatches: 52, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
169 3 0.01
170 12 0.04
171 123 0.41
172 159 0.53
173 4 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.36
Consensus pattern (172 bp):
AAGTGAGTAATAAGGCTTTTAAAGGAATAAGTGACTATAAATGGACATTTCTTGACAATGAATGT
CTTTTTCTTTACGATTCTCAAGGTAGAAATTCAATCATAGTCAGTTTTAACTAAAAATGTACAAA
GAATTCACATTAAAATCAATTATAACATTATAAAACTATTTA
Found at i:19250 original size:171 final size:170
Alignment explanation
Indices: 18504--19310 Score: 704
Period size: 172 Copynumber: 4.7 Consensus size: 170
18494 NNNNNNNNNN
* * * *
18504 ATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAAGTAGACACTCAATTCTAG
1 ATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACA-TTAATTCTAA
* * * * *
18569 TAAGTTTTAACCAAAAATGTA-AAAAGAATTCAAATTTAAATCACTTTTTAGATTATAAAACTAT
65 TATGTTTTAACCAAAAATGTACAAAA-AATTCAAATTAAAATCAATTATGAGATTATAAAACTAT
*
18633 TTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAA
129 TTAAAGCGAGTAATAAGGCTTTTAAA-GAATGAATGACTATAA
** * * * * * *
18676 ATAAACTTTT-TTAGTCAATAAATACCTTTTT-TT-ATGTTTCTCAAGCTAGACATTCAATTATA
1 ATGGACTTTTCTTA-CCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATT-AATTCTA
* * * * * *
18738 ATATGTTTTAACAAAAAATAG-ACAAAAATTTGAACTTAAAATCCATTATGAGATTAT-AAAGTA
64 ATATGTTTTAACCAAAAAT-GTACAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACT-
* *
18801 ATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGAATGACCATAA
127 ATTTAAAGCGAGTAATAAGGCTTTT-AAAGAATGAATGACTATAA
* * * *
18846 ATGGAGTTTTCTTACCAATGAATGCCTTTCTCTTC-TCAT-TTT-TCGAGGTTGACATTCAATTA
1 ATGGACTTTTCTTACCAATGAATG-CTTT-T-TTCTTCATGTTTCTCAAGGTAGACATT-AATTC
* * * * ** * * *
18908 TAATCTATTCTAACTAAATTTGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACT
62 TAATATGTTTTAACCAAAAATGTACAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACT
** **
18973 ATTTAAAGCGAGTAATAAGGCTTTCGAAGTAATGTGTGACTATAA
127 ATTTAAAGCGAGTAATAAGGCTTTTAAAG-AATGAATGACTATAA
* * * * * ** * *
19018 AAGGACTTTTCTTGCCAATAAATGCCTTTTTCTTTACATTTCTCAAGGTAGATATTTAATTCTAG
1 ATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACA-TTAATTCTAA
* ** *
19083 TCTGTTAAAACCAAAAATGTA-AAAAAATT-AAAGTTAAAATCAATTATG-GTATTATAAAACCA
65 TATGTTTTAACCAAAAATGTACAAAAAATTCAAA-TTAAAATCAATTATGAG-ATTATAAAACTA
** * * ** *
19145 TTTAGTGCGAGTAATGAGGCTTTTAAAGGTATGGGTGACTCTAA
128 TTTAAAGCGAGTAATAAGGCTTTTAAA-GAATGAATGACTATAA
* *
19189 ATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAAACACTTAATTCCAG
1 ATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACA-TTAATTCTA-
** * * * * *
19254 CCA-GTTTTAACCAAAAATATACAAAGAATTCATATTTAAATCAATTTTGAGATTATA
64 ATATGTTTTAACCAAAAATGTACAAAAAATTCAAATTAAAATCAATTATGAGATTATA
19311 NNNNNNNNNN
Statistics
Matches: 504, Mismatches: 105, Indels: 52
0.76 0.16 0.08
Matches are distributed among these distances:
169 8 0.02
170 123 0.24
171 161 0.32
172 195 0.39
173 15 0.03
174 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (170 bp):
ATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTAATTCTAAT
ATGTTTTAACCAAAAATGTACAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACTATTT
AAAGCGAGTAATAAGGCTTTTAAAGAATGAATGACTATAA
Found at i:19295 original size:343 final size:342
Alignment explanation
Indices: 18504--19310 Score: 900
Period size: 343 Copynumber: 2.4 Consensus size: 342
18494 NNNNNNNNNN
* * * *
18504 ATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAAGTAGACACTCAATTCTAG
1 ATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACACTTAATTCAAG
* * * *
18569 TAAGTTTTAACCAAAAATGTAAAAAGAATTCAAATTTAAATCACTTTTTAGATTATAAAACTATT
66 CAAGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACTATT
* * *
18634 TAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATAAACTTTTTTAGTCAATAAAT
131 TAAAGCGAGTAATAAGGCTTTCAAAGGAATGAATGACTATAAATAAACTTTTTTAGCCAATAAAT
** **
18699 ACCTTTTTTTATGTTTCTCAAGCTAGACATTCAATTATAATATGTTTTAACAAAAAATAGACAAA
196 ACCTTTTTTTACATTTCTCAAGCTAGACATTCAATTATAATATGTTAAAACAAAAAATAGACAAA
* * * ** *
18764 AATTTGAACTTAAAATCCATTATGAGATTATAAAGTAATTTAAAGTGAGTAATAAGGCTTTTGAA
261 AAATTAAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
18829 AGAATGAATGACCATAA
326 AGAATGAATGACCATAA
* * *
18846 ATGGAGTTTTCTTACCAATGAATGCCTTTCTCTTC-TCAT-TTT-TCGAGGTTGACA-TTCAATT
1 ATGGACTTTTCTTACCAATGAATG-CTTT-T-TTCTTCATGTTTCTCAAGGTAGACACTT-AATT
* * * * * **
18907 ATAATCTA-TTCTAACTAAATTTGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAA
62 -CAAGCAAGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAA
* * ** *
18971 CTATTTAAAGCGAGTAATAAGGCTTTCGAAGTAATGTGTGACTATAAA-AGGACTTTTCTT-GCC
126 CTATTTAAAGCGAGTAATAAGGCTTTCAAAGGAATGAATGACTATAAATA-AACTTTT-TTAGCC
* * * * * * * *
19034 AATAAATGCCTTTTTCTTTACATTTCTCAAGGTAGATATTTAATTCTAGTCTGTTAAAACCAAAA
189 AATAAATACC-TTTT-TTTACATTTCTCAAGCTAGACATTCAATTATAATATGTTAAAACAAAAA
* * ** *
19099 AT-GTA-AAAAAATTAAAGTTAAAATCAATTATG-GTATTATAAAACCATTTAGTGCGAGTAATG
252 ATAG-ACAAAAAATTAAACTTAAAATCAATTATGAG-ATTATAAAACAATTTAAAGCGAGTAATA
* **
19161 AGGCTTTT-AAAGGTATGGGTGACTC-TAA
315 AGGCTTTTGAAA-GAATGAATGAC-CATAA
* *
19189 ATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAAACACTTAATTCCAG
1 ATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACACTTAATTCAAG
* * *
19254 CCAGTTTTAACCAAAAATATACAAAGAATTCATATTTAAATCAATTTTGAGATTATA
66 CAAGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATA
19311 NNNNNNNNNN
Statistics
Matches: 381, Mismatches: 66, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
340 3 0.01
341 7 0.02
342 157 0.41
343 162 0.43
344 49 0.13
345 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (342 bp):
ATGGACTTTTCTTACCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACACTTAATTCAAG
CAAGTTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACTATT
TAAAGCGAGTAATAAGGCTTTCAAAGGAATGAATGACTATAAATAAACTTTTTTAGCCAATAAAT
ACCTTTTTTTACATTTCTCAAGCTAGACATTCAATTATAATATGTTAAAACAAAAAATAGACAAA
AAATTAAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAA
AGAATGAATGACCATAA
Done.