Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398535.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1828.0, 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: 5577
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.20
Warning! 2400 characters in sequence are not A, C, G, or T
Found at i:563 original size:171 final size:170
Alignment explanation
Indices: 1--1483 Score: 1390
Period size: 171 Copynumber: 8.7 Consensus size: 170
* * *
1 TAAAGCGAGTAATAAAGCTTTTGAAGGAAGGGGTGACTATAAATGGACTTTTCTTGTCAATGAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * ********
66 AT-GTTTTTCTTCACGTTTCTCAAAGTACACATTCAATTATAGTNNNNNNNNNNA-AAAAATGTA
66 -TCCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGT--CTGTTTTAACAAAAATGT-
* * * * *
129 AAAAAAAATTCAACTTAAAATCAAATATAAGATTATAAAACCACT
127 -AAAACAATTCAACTTAAAATCAATTATGAGATTATAAAATCATT
* * * * *
174 AAAAGTGAGTAATACGACTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAA-
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * * * * *
238 TGCTATTTTATTCATGTTTCTCAAGGAAGACATTTAATTATAGTTTGTTTTAACTGAAAATGTAA
66 TCCT-TTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAAC-AAAAATGT--
* **
303 AAAAAAATTCAACTTACGATCAATTATGAGATTATAAAATCATT
127 AAAACAATTCAACTTAAAATCAATTATGAGATTATAAAATCATT
* ** * * * *
347 TAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTGACTATAAATGGGCTTCTCTTGTCAATAAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * ** * *
412 TCCTTCTTCTTCACGTTTTTTTAGGAAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAAA
66 TCCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTT-AACAAAAATGTAAA
* ** * *
477 ACAATTCGACTTAAAATTGATTATTAGATTATAAAATAATT
130 ACAATTCAACTTAAAATCAATTATGAGATTATAAAATCATT
* * * * * *
518 TAAAGCAAGCAATAAGGCTTTTGAAGGAATGGGTGACCATAAATGGTCATTTCTTGCCAATAAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * **
583 GCCTTTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTATTGCAA-AAAAATGTAAAA
66 TCCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAA
*
647 CAATTTC-ACTTAAAATCAATTATGAGATTGTAAAATCATT
131 CAA-TTCAACTTAAAATCAATTATGAGATTATAAAATCATT
* * * * *
687 TAAAGCGAGTAATAAAGTTTTTGAAGGAATGGGTGACTACAAAAGGACTTTTCTTCCCAATGAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * *
752 GT-CTTTTT-TTACACGTTTCTCAAAGTAGACATTCAATCATAGTATGTTTTAACCAAATATGTA
66 -TCCTTTTTCTT-CACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAATGTA
* * *
815 AAAAAATTCAACTTATAATCAATTATGAGATTATAAAACCATT
128 AAACAATTCAACTTAAAATCAATTATGAGATTATAAAATCATT
********** * *
858 TAAANNNNNNNNNNAGGCTTTTGAAGGAATGGGTGACTATAAAAGGACTTTTCTTGTCAATGAA-
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
** * * * * * * * *
922 TCCTTGTTTCTTTTCATTTCTCGAGGTTGACATTCCATTGTAGTCTATTTTAACCAAAAATCTTA
66 TCCTT-TTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAA-CAAAAAT-GTA
* * * *
987 AAA-AATTTAACTTAAAATCAATTACGATATTATAAAACCATT
128 AAACAATTCAACTTAAAATCAATTATGAGATTATAAAATCATT
* * ********** *
1029 CAGAGCGAGTAATAAGGCTTTTGAAGGAATGNNNNNNNNNNAATGAACTTTTCTTGCCAATGAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * *
1094 GCCTTTTTCTTAATGTTTCTCAAAGTAGACATTCAATTATAGTCTATTTTAACTAAAAATATAAA
66 TCCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAAC-AAAAATGTAAA
** * * *
1159 A-AAAACAACTTCAAATCAA-TATGAGATTATAAAACCACT
130 ACAATTCAACTTAAAATCAATTATGAGATTATAAAATCATT
* * * * *
1198 TAAAGTGAGTAATGAGGCTTTTAAAGGAATGAGTGACTATAAATGCACTTTTCTTGCCAATG-AT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
** * *
1262 TGTGTTTTTCTTCACATTTCTCAAAGTAGACATTCAATTAAAGTCTGTTTTAACGAAAAATGTAA
66 T-CCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAAC-AAAAATGTAA
* *
1327 AACAATTCAACTTACAATCAATTATAAGATTATAAAA-CTATT
129 AACAATTCAACTTAAAATCAATTATGAGATTATAAAATC-ATT
* * ** * * *
1369 GAAAGCGAGTAATAAGGCTTTCGAAGGAATGGACGGCGATAAATGGACTTTTCTTGCCAAAGAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* *
1434 GCATTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTT
66 TCCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTT
1484 NNNNNNNNNN
Statistics
Matches: 1058, Mismatches: 229, Indels: 48
0.79 0.17 0.04
Matches are distributed among these distances:
168 4 0.00
169 258 0.24
170 46 0.04
171 495 0.47
172 14 0.01
173 235 0.22
174 6 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.34
Consensus pattern (170 bp):
TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
TCCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAACAAAAATGTAAAA
CAATTCAACTTAAAATCAATTATGAGATTATAAAATCATT
Found at i:802 original size:340 final size:342
Alignment explanation
Indices: 1--1483 Score: 1479
Period size: 340 Copynumber: 4.3 Consensus size: 342
* *
1 TAAAGCGAGTAATAAAGCTTTTGAAGGAAGGGGTGACTATAAATGGACTTTTCTTGTCAATGAAT
1 TAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * *********
66 ATGTTTTTCTTCACGTTTCTCAAAGTACACATTCAATTATAGTNNNNNNNNNNA-AAAAATGTAA
66 GTCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGT-CTGTTTTAAACAAAAATGT--
* * * *
130 AAAAAAATTCAACTTAAAATCAAATATAAGATTATAAAACCACTAAAAGTGAGTAATACGACTTT
128 AAAAAAATTCAACTTAAAATCAAATATGAGATTATAAAACCACTTAAAGTGAGTAATAAGGCTTT
* *
195 TGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG-CTATTTTATTCATGTTTCT
193 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCT-TTTTCTTCATGTTTCT
* * * * * * * * **
259 CAAGGAAGACATTTAATTATAGTTTGTTTTAACTGAAAATGTAAAAAAAAATTCAACTTACGATC
257 CAAAGTAGACATTCAATTATAGTCTATTTTAAC-AAAAATGT-AAAACAATTTCAACTTAAAATC
324 AATTATGAGATTATAAAATCATT
320 AATTATGAGATTATAAAATCATT
* * * * * *
347 TAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTGACTATAAATGGGCTTCTCTTGTCAATAAAT
1 TAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * ** * *
412 -TCCTTCTTCTTCACGTTTTTTTAGGAAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAA
66 GT-CTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAA
* * ** * * ** * ** *
476 AACAATTCGACTTAAAATTGATTATTAGATTATAAAATAATTTAAAGCAAGCAATAAGGCTTTTG
130 AAAAATTCAACTTAAAATCAAATATGAGATTATAAAACCACTTAAAGTGAGTAATAAGGCTTTTG
* * * *
541 AAGGAATGGGTGACCATAAATGGTCATTTCTTGCCAATAAATGCCTTTTTCTTCATGTTTCTCAA
195 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAA
**
606 AGTAGACATTCAATTATAGTCTATTGCAA-AAAAATGTAAAACAATTTC-ACTTAAAATCAATTA
260 AGTAGACATTCAATTATAGTCTATTTTAACAAAAATGTAAAACAATTTCAACTTAAAATCAATTA
*
669 TGAGATTGTAAAATCATT
325 TGAGATTATAAAATCATT
* * * *
687 TAAAGCGAGTAATAAAGTTTTTGAAGGAATGGGTGACTACAAAAGGACTTTTCTTCCCAATGAAT
1 TAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * *
752 GTCTTTTT-TTACACGTTTCTCAAAGTAGACATTCAATCATAGTATGTTTTAACCAAATATGTAA
66 GTCTTTTTCTT-CACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAA
* * * **********
816 AAAAATTCAACTTATAATCAATTATGAGATTATAAAACCATTTAAANNNNNNNNNNAGGCTTTTG
130 AAAAATTCAACTTAAAATCAAATATGAGATTATAAAACCACTTAAAGTGAGTAATAAGGCTTTTG
* *
881 AAGGAATGGGTGACTATAAAAGGACTTTTCTTGTCAATGAAT-CCTTGTTTCTTTTCA--TTTCT
195 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTT-TTTC--TTCATGTTTCT
* * * * * *
943 CGAGGTTGACATTCCATTGTAGTCTATTTTAACCAAAAATCTTAAAA-AATTT-AACTTAAAATC
257 CAAAGTAGACATTCAATTATAGTCTATTTTAA-CAAAAAT-GTAAAACAATTTCAACTTAAAATC
* * *
1006 AATTACGATATTATAAAACCATT
320 AATTATGAGATTATAAAATCATT
* * * ********** *
1029 CAGAGCGAGTAATAAGGCTTTTGAAGGAATGNNNNNNNNNNAATGAACTTTTCTTGCCAATGAAT
1 TAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * *
1094 GCCTTTTTCTTAATGTTTCTCAAAGTAGACATTCAATTATAGTCTATTTT-AACTAAAAATATAA
66 GTCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAAAC-AAAAATGTAA
* * * *
1158 AAAAA-ACAACTTCAAATC-AATATGAGATTATAAAACCACTTAAAGTGAGTAATGAGGCTTTTA
130 AAAAATTCAACTTAAAATCAAATATGAGATTATAAAACCACTTAAAGTGAGTAATAAGGCTTTTG
* * * ** **
1221 AAGGAATGAGTGACTATAAATGCACTTTTCTTGCCAATGATTGTGTTTTTCTTCACATTTCTCAA
195 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAA
* * *
1286 AGTAGACATTCAATTAAAGTCTGTTTTAACGAAAAATGTAAAACAA-TTCAACTTACAATCAATT
260 AGTAGACATTCAATTATAGTCTATTTTAAC-AAAAATGTAAAACAATTTCAACTTAAAATCAATT
*
1350 ATAAGATTATAAAA-CTATT
324 ATGAGATTATAAAATC-ATT
* * * ** * * *
1369 GAAAGCGAGTAATAAGGCTTTCGAAGGAATGGACGGCGATAAATGGACTTTTCTTGCCAAAGAAT
1 TAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
1434 G-CATTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTT
66 GTC-TTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTT
1484 NNNNNNNNNN
Statistics
Matches: 923, Mismatches: 192, Indels: 50
0.79 0.16 0.04
Matches are distributed among these distances:
338 4 0.00
339 16 0.02
340 485 0.53
341 24 0.03
342 153 0.17
343 7 0.01
344 130 0.14
345 4 0.00
346 100 0.11
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.34
Consensus pattern (342 bp):
TAAAGCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT
GTCTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTTTAAACAAAAATGTAAA
AAAATTCAACTTAAAATCAAATATGAGATTATAAAACCACTTAAAGTGAGTAATAAGGCTTTTGA
AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAA
GTAGACATTCAATTATAGTCTATTTTAACAAAAATGTAAAACAATTTCAACTTAAAATCAATTAT
GAGATTATAAAATCATT
Found at i:1002 original size:511 final size:507
Alignment explanation
Indices: 1--1483 Score: 1472
Period size: 511 Copynumber: 2.9 Consensus size: 507
* * * *
1 TAAAGCGAGTAATAAAGCTTTTGAAGGAAGGGGTGACTATAAATGGACTTTTCTTGTCAATGAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACCATAAATGGACTTTTCTTGCCAAT-AA-
* * ********
66 ATG--TTTTTCTTCACGTTTCTCAAAGTACACATTCAATTATAGTNNNNNNNNNNAAAAAATGTA
64 ATGCCTTTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGT--CTATTGCAAAAAAATGT-
* * *
129 AAAAAAAATTCAACTTAAAATCAAATATAAGATTATAAAACCACTAAAAGTGAGTAATACGACTT
126 --AAAAAATTCAACTTAAAATC-AATATGAGATTATAAAACCACTTAAAGTGAGTAATAAG-CTT
*
194 TTGAAGGAATGGGTGACTATAAATA-GACTTTTCTTGCCAATGAATG-CTATTTTATTCATGTTT
187 TTGAAGGAATGGGTGACTATAAA-AGGACTTTTCTTGCCAATGAATGTCT-TTTTATTCACGTTT
* * * * *
257 CTCAAGGAAGACATTTAATTATAGTTTGTTTTAACTGAAAATGTAAAAAAAAATTCAACTTACGA
250 CTCAAAGTAGACATTCAATTATAGTATGTTTTAAC-GAAAATGT--AAAAAAATTCAACTTACAA
*
322 TCAATTATGAGATTATAAAATCATTTAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTGACTAT
312 TCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTGACTAT
* * * * **
387 AAATGGGCTTCTCTTGTCAATAAATTCCTTCTTCTTCACGTTTTTTTAGGAAGACATTCAATTAT
377 AAAAGGACTTCTCTTGTCAATAAATTCCTTCTTCTTCACATTTCTCGAGGAAGACATTCAATTAT
* * ** ** *
452 AGTCTGTTTTAAACAAAAATGTAAAACAATTCGACTTAAAATTGATTATTAGATTATAAAATAAT
442 AGTCTATTTTAAACAAAAATGTAAAACAATTCAACTTAAAATCAATTACGAGATTATAAAACAAT
517 T
507 T
* * * *
518 TAAAGCAAGCAATAAGGCTTTTGAAGGAATGGGTGACCATAAATGGTCATTTCTTGCCAATAAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACCATAAATGGACTTTTCTTGCCAATAAAT
583 GCCTTTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTATTGCAAAAAAATGTAAAAC
66 GCCTTTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTATTGCAAAAAAATGTAAAA-
* * * * *
648 AATTTC-ACTTAAAATCAATTATGAGATTGTAAAATCATTTAAAGCGAGTAATAAAGTTTTTGAA
130 AA-TTCAACTTAAAATCAA-TATGAGATTATAAAACCACTTAAAGTGAGTAAT-AAGCTTTTGAA
* *
712 GGAATGGGTGACTACAAAAGGACTTTTCTTCCCAATGAATGTCTTTTT-TTACACGTTTCTCAAA
192 GGAATGGGTGACTATAAAAGGACTTTTCTTGCCAATGAATGTCTTTTTATT-CACGTTTCTCAAA
* * *
776 GTAGACATTCAATCATAGTATGTTTTAACCAAATATGTAAAAAAATTCAACTTATAATCAATTAT
256 GTAGACATTCAATTATAGTATGTTTTAACGAAA-ATGTAAAAAAATTCAACTTACAATCAATTAT
********** **
841 GAGATTATAAAACCATTTAAANNNNNNNNNNAGGCTTTTGAAGGAATGGGTGACTATAAAAGGAC
320 GAGATTATAAAACCATTTAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTGACTATAAAAGGAC
* * * ** ** * *
906 TTTTCTTGTCAATGAA-TCCTTGTTTCTTTTCATTTCTCGAGGTTGACATTCCATTGTAGTCTAT
385 TTCTCTTGTCAATAAATTCCTT-CTTCTTCACATTTCTCGAGGAAGACATTCAATTATAGTCTAT
* * * * *
970 TTTAACCAAAAATCTTAAAA-AATTTAACTTAAAATCAATTACGATATTATAAAACCATT
449 TTTAAACAAAAAT-GTAAAACAATTCAACTTAAAATCAATTACGAGATTATAAAACAATT
* * ********** * *
1029 CAGAGCGAGTAATAAGGCTTTTGAAGGAATGNNNNNNNNNNAATGAACTTTTCTTGCCAATGAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACCATAAATGGACTTTTCTTGCCAATAAAT
* ** *
1094 GCCTTTTTCTTAATGTTTCTCAAAGTAGACATTCAATTATAGTCTATTTTAACTAAAAATATAAA
66 GCCTTTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTATTGCAA--AAAAATGTAAA
** * * *
1159 AAAAACAACTTCAAATCAATATGAGATTATAAAACCACTTAAAGTGAGTAATGAGGCTTTTAAAG
129 AAATTCAACTTAAAATCAATATGAGATTATAAAACCACTTAAAGTGAGTAAT-AAGCTTTTGAAG
* * * * * * *
1224 GAATGAGTGACTATAAATGCACTTTTCTTGCCAATGATTGTGTTTTTCTTCACATTTCTCAAAGT
193 GAATGGGTGACTATAAAAGGACTTTTCTTGCCAATGAATGTCTTTTTATTCACGTTTCTCAAAGT
* * * *
1289 AGACATTCAATTAAAGTCTGTTTTAACGAAAAATGTAAAACAATTCAACTTACAATCAATTATAA
258 AGACATTCAATTATAGTATGTTTTAACG-AAAATGTAAAAAAATTCAACTTACAATCAATTATGA
* * * ** * ** * * *
1354 GATTATAAAACTATTGAAAGCGAGTAATAAGGCTTTCGAAGGAATGGACGGCGATAAATGGACTT
322 GATTATAAAACCATTTAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTGACTATAAAAGGACTT
* * * * * * * * * *
1419 TTCTTGCCAA-AGAATGCATTTTTCTTCACGTTTCTCAAAGTAGACATTCAATTATAGTCTGTTT
387 CTCTTGTCAATA-AATTCCTTCTTCTTCACATTTCTCGAGGAAGACATTCAATTATAGTCTATTT
1483 T
451 T
1484 NNNNNNNNNN
Statistics
Matches: 791, Mismatches: 156, Indels: 44
0.80 0.16 0.04
Matches are distributed among these distances:
510 5 0.01
511 498 0.63
512 38 0.05
513 138 0.17
514 7 0.01
515 12 0.02
516 2 0.00
517 91 0.12
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.34
Consensus pattern (507 bp):
TAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACCATAAATGGACTTTTCTTGCCAATAAAT
GCCTTTTTCTTCATGTTTCTCAAAGTAGACATTCAATTATAGTCTATTGCAAAAAAATGTAAAAA
ATTCAACTTAAAATCAATATGAGATTATAAAACCACTTAAAGTGAGTAATAAGCTTTTGAAGGAA
TGGGTGACTATAAAAGGACTTTTCTTGCCAATGAATGTCTTTTTATTCACGTTTCTCAAAGTAGA
CATTCAATTATAGTATGTTTTAACGAAAATGTAAAAAAATTCAACTTACAATCAATTATGAGATT
ATAAAACCATTTAAAGCAAGTAATAAAACTTTTGAAGGAATGGGTGACTATAAAAGGACTTCTCT
TGTCAATAAATTCCTTCTTCTTCACATTTCTCGAGGAAGACATTCAATTATAGTCTATTTTAAAC
AAAAATGTAAAACAATTCAACTTAAAATCAATTACGAGATTATAAAACAATT
Found at i:1792 original size:171 final size:169
Alignment explanation
Indices: 1503--2023 Score: 541
Period size: 171 Copynumber: 3.1 Consensus size: 169
1493 NNNNNNNNNN
* * * *
1503 TTAAAGCGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAAAGGACTTTTCCTGTCAATAAA
1 TTAAAGCGAGTTATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCCTGT-AATAAA
* * * * * * *
1568 T-TCTTGTTTATTTATATTTCTC-AAGGTTGACATTCAATTGTAGTATGTTTTAACCAAAAATGT
65 TGCCTT-TTTCTTCATGTTTCTCGAA-GTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* * *
1631 TAAAAAATTTAACTTAAAATCAATTATGATATTATAAAACCA
128 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
* * * *
1673 TTCAGAGCGAGTTATAAGGCTTTTGAAGGAATGAGTGACTATAAATGAACTTTTCTTGCTAATGA
1 TT-AAAGCGAGTTATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCCTG-TAATAA
* * *
1738 ATGCCTTTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTATTTTAACTAAAAATATA
64 ATGCCTTTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTA
* * * * *
1803 AAAAAAATCAACTTCAAATCAAATCTGAGATTATAAAATCA
129 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
** * * ********
1844 CTTAAAGTAAG-TAGTGAGGCTTTTGAAGGAATGGGTGACTATAAATGCACTTTTCNNNNNNNNN
1 -TTAAAGCGAGTTA-TAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTC-CTGTAATA
* *
1908 NATGCCTTTTTCTTCATGTTTCTTGAAGTAGACATTCAA--ATA-TCTGTTTTAACCAAAAATGT
63 AATGCCTTTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* *
1970 CAAAAAATTCAACTTACAATCAATTATGAGATTATAAAACCA
128 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
2012 TTTAAAGCGAGT
1 -TTAAAGCGAGT
2024 ANNNNNNNNN
Statistics
Matches: 288, Mismatches: 55, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
168 60 0.21
169 3 0.01
170 4 0.01
171 213 0.74
172 8 0.03
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
TTAAAGCGAGTTATAAGGCTTTTGAAGGAATGGGTGACTATAAATGAACTTTTCCTGTAATAAAT
GCCTTTTTCTTCATGTTTCTCGAAGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA
AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCA
Done.