Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402150.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5240.0, 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: 2031
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.36
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:399 original size:172 final size:171
Alignment explanation
Indices: 221--2031 Score: 1564
Period size: 172 Copynumber: 10.6 Consensus size: 171
211 NNNNNNTAAC
* * * * *
221 AAGGCTTTTAAAGGAATGGGTGACTATAATTGGACTTTTCTTGCCAATGACTGCCTTTTTTTTTA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
* * * * * * *
286 TATTTCTCAAGGTAGACATTCTATTATAATATGTTTTAACTAAAAATGAACAACAAATTGAACTT
66 TGTTTCTCAAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGAACAA-AAATTCAAATT
* * * * *
351 AAAATCAATTATGAGATTATAAGATCATTTAAAATGTGTAAT
130 TAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
*** * * *
393 AAGGCTTTTGAAGGAATTTATGATTATTAATGGACTTTTCTTGCCAATGAATGCCTTTTCCTTCA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
** * * * ** **
458 TGTTTCTTGATGTTGCCTTTCAATTATAATCT-TTCTTAATGAAAAATGTGCAAAGAATTCAAAT
66 TGTTTCTCAAGGTTGACATTCAATTATAATCTGTT-TTAACCAAAAATGAACAAA-AATTCAAAT
* * *
522 TTAAATCAATTTTGAGATTACAAAACCATTTAAAGTGAGTATT
129 TTAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
* * ** * **
565 AAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGTCAACAAATACCTTTTTCTTTG
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
* * * * ** * * *
630 CGTTTCTCGAGATTGACATTCAAGTATTGTCTGTTTTAACCAAAAATGTAA-AAAACTTCAACTA
66 TGTTTCTCAAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATG-AACAAAAATTCAAATT
* *
694 AAAATCAATTATG-GCATTATAAAACCATTTAAAGCGAGTAAT
130 TAAATCAATTATGAG-ATTATAAAACCATTTAAAGTGAGTAAT
* * * * *
736 GAGGCTTTTGAAGGAATGGGTGACTATAAATGGATTTTTCTTACCAATGTATGCCTTTTTCATCA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
**** * * *
801 TGTTTCTTGCTGTTGACATTCAATTATGATCTGTTTTAACAAAAAATGTACAAAAAATTCAAATT
66 TGTTTCTCAAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGAAC-AAAAATTCAAATT
* * *
866 TAAATCAATTTTGAGAATATAAAACCATTTAAAGTGAGTAAA
130 TAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
* * * *
908 AAGGCTTTT-AATGGAATGGGTTACTATAACTGAACTTTTCTTGTCAATGAATGCCTTTTTCATT
1 AAGGCTTTTGAA-GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTC-TT
* * * * * * * * * *
972 -ACGTTTAC-CAACGTAGAC-GTCAATTCTAGTCTTTTTTTACCAAAAATGTAA-AACAGTTCAA
64 CATGTTT-CTCAAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATG-AACAAAAATTCAA
* * ** * *
1033 CTTAAAATCAATTATG-GCATTATAAAACCACGTAAAGCGAGAAAT
127 ATTTAAATCAATTATGAG-ATTATAAAACCATTTAAAGTGAGTAAT
* * **
1078 AAGGCTTTTTGAAGGAATGGGTGACTGTAAATGGACTTTTCTTGCCAATCAATGCCTTTACCTTC
1 AAGGC-TTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTC
** ** * * * * * * *
1143 ACATTTCTTTAGGTTGACATTGAATTACAATCTTTTTTGACGAACAATGTACAAAGAATTCAAAT
65 ATGTTTCTCAAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGAACAAA-AATTCAAAT
* *
1208 TTCAATCAATT-TAGAGATTACAAAACCATTTAAAGTGAGTAAT
129 TTAAATCAATTAT-GAGATTATAAAACCATTTAAAGTGAGTAAT
* * * * * * *
1251 ATGGCTTTTGGAGGAATGAGTGATTATAAATGGACTTTTCTTACCACTGAA--CCTTTTTTTTCA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
* * * **
1314 TG-TTCTGAAGGTTGACATTCAATTATAATCTATTTTAAAGC-AAAATGTGCAAAGAATTCAAAT
66 TGTTTCTCAAGGTTGACATTCAATTATAATCTGTTTT-AACCAAAAATGAACAAA-AATTCAAAT
*
1377 TTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAAT
129 TTAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
* *
1420 AACGG-TTTTGAAGGAATGGGTTACTATAAATGGACTTTTCTTGCCAATGAATGCCCTTTTTATT
1 AA-GGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CCTTTTTCTT
* * * * * * * *
1484 -ACGTTTATCAAGGTAGACATT-AATTCTAGTCTGTTTTAACTAAAAATGTAA-AAACATTCAAC
64 CATGTTTCTCAAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATG-AACAAAAATTCAAA
* * *
1546 TTAAAATCAATTATG-GCATTATAAAACCATGTAAAGCGAGTAAT
128 TTTAAATCAATTATGAG-ATTATAAAACCATTTAAAGTGAGTAAT
* * * ***
1590 AAGGCTTTTTGAAGGAATAGGTGATTACT-AATGGACTTTTCTTGTCAATGAATGCCTTGACCTT
1 AAGGC-TTTTGAAGGAATGGGTGACTA-TAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTT
* ** * * *
1654 CATGTTTTTGGAGGTTGACATTCAATTATAATCTTTTTTGACCAACAAT-ATACAAAGAATTCAA
64 CATGTTTCTCAAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGA-ACAAA-AATTCAA
* * * * *
1718 ATTTTAATCAATTTTGTGATTACAAAACCATTTAAAGTGAGTATT
127 ATTTAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
* * ** *
1763 AAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATATCTTTTTCTTTA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
* * * * * * ********** *
1828 CGTTTCTCGAGATTGATATTCAATTATAGTCTGTTTTAACCAAAAATGTTA-ANNNNNNNNNNTA
66 TGTTTCTCAAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATG-AACAAAAATTCAAATT
* * *
1892 AAAATCAATTATG-GCATTATAAAACCATTTAAAGCGAGTAAG
130 TAAATCAATTATGAG-ATTATAAAACCATTTAAAGTGAGTAAT
* * * * * * *
1934 GAGGCCTTTTTAA-GAATGGGTGACTATAAACGGATTTTTCTTACCAATGTATGCCTTTTTTTTC
1 AAGG-CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTC
* **
1998 ACGTTTCTTGAGGTTGACATTCAATTATAATCTG
65 ATGTTTCTCAAGGTTGACATTCAATTATAATCTG
Statistics
Matches: 1296, Mismatches: 297, Indels: 93
0.77 0.18 0.06
Matches are distributed among these distances:
169 133 0.10
170 121 0.09
171 411 0.32
172 534 0.41
173 95 0.07
174 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (171 bp):
AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA
TGTTTCTCAAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGAACAAAAATTCAAATTT
AAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAAT
Found at i:868 original size:343 final size:341
Alignment explanation
Indices: 221--2031 Score: 1677
Period size: 343 Copynumber: 5.3 Consensus size: 341
211 NNNNNNTAAC
* * * * *
221 AAGGCTTTTAAAGGAATGGGTGACTATAATTGGACTTTTCTTGCCAATGACTGCCTTTTTTTTTA
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTA
** * * * * * * *
286 TATTTCTCAAGGTAGACATTCTATTATAATATGTTTTAACTAAAAATGAACAACAAATTGAACTT
66 CGTTTCTCGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGTA-AA-AAATTCAACTT
* * * * ***
351 AAAATCAATTATGAGATTATAAGATCATTTAAAATGTGTAATAAGGCTTTTGAAGGAATTTATGA
129 AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * * * * * *
416 TTATTAATGGACTTTTCTTGCCAATGAATGCCTTTTCCTTCATGTTTCTTGATGTTGCCTTTCAA
194 CTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTTGACATTCAA
* * *
481 TTATAATCT-TTCTTAATGAAAAATGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATTACAA
259 TTAT-ATCTGTT-TTAACGAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTACAA
*
545 AACCATTTAAAGTGAGTATT
322 AACCATTTAAAGTGAGTAAT
* ** * *
565 AAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGTCAACAAATACCTTTTTCTTTG
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTA
* * ** *
630 CGTTTCTCGAGATTGACATTCAAGTATTGTCTGTTTTAACCAAAAATGTAAAAAACTTCAACTAA
66 CGTTTCTCGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAA-TTCAACTTA
* *
695 AAATCAATTATG-GCATTATAAAACCATTTAAAGCGAGTAATGAGGCTTTTGAAGGAATGGGTGA
130 AAATCAATTATGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * * * * **
759 CTATAAATGGATTTTTCTTACCAATGTATGCCTTTTTCATCATGTTTCTTGCTGTTGACATTCAA
194 CTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTTGACATTCAA
* * *
824 TTATGATCTGTTTTAACAAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGAATATAAA
259 TTAT-ATCTGTTTTAACGAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTACAAA
*
889 ACCATTTAAAGTGAGTAAA
323 ACCATTTAAAGTGAGTAAT
* * * *
908 AAGGCTTTT-AATGGAATGGGTTACTATAACTGAACTTTTCTTGTCAATGAATGCCTTTTTCATT
1 AAGGCTTTTGAA-GGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTT
* * * * * * * * *
972 ACGTTTAC-CAACGTAGAC-GTCAATTCTAGTCTTTTTTTACCAAAAATGTAAAACAGTTCAACT
65 ACGTTT-CTCGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAA-AATTCAACT
** * *
1035 TAAAATCAATTATG-GCATTATAAAACCACGTAAAGCGAGAAATAAGGCTTTTTGAAGGAATGGG
128 TAAAATCAATTATGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGC-TTTTGAAGGAATGGG
* * ** * *
1099 TGACTGTAAATGGACTTTTCTTGCCAATCAATGCCTTTACCTTCACATTTCTTTAGGTTGACATT
191 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTTGACATT
* * * * * * * *
1164 GAATTACAATCTTTTTTGACGAACAATGTACAAAGAATTCAAATTTCAATCAATTTAGAGATTAC
256 CAATTA-TATCTGTTTTAACGAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTAC
1229 AAAACCATTTAAAGTGAGTAAT
320 AAAACCATTTAAAGTGAGTAAT
* * * * ** *
1251 ATGGCTTTTGGAGGAATGAGTGATTATAAATGGACTTTTCTTACCACTGAA--CCTTTTT-TTT-
1 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTA
* * * *
1312 CATGTTCT-GAAGGTTGACATTCAATTATAATCTATTTTAAAGC-AAAATGTGCAAAGAATTCAA
66 CGT-TTCTCG-AGGTTGACATTCAATTATAATCTGTTTT-AACCAAAAATGT--AAAAAATTCAA
* * *
1375 ATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAACGG-TTTTGAAGGAATGG
126 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAA-GGCTTTTGAAGGAATGG
* * * ** *
1439 GTTACTATAAATGGACTTTTCTTGCCAATGAATGCCCTTTTTATT-ACGTTTATCAAGGTAGACA
190 GTGACTATAAATGGACTTTTCTTGCCAATGAATG-CCTTTTTCTTCACGTTTCTTGAGGTTGACA
* * * * * *
1503 TT-AATTCTAGTCTGTTTTAACTAAAAATGTA-AAAACATTCAACTTAAAATCAATTATG-GCAT
254 TTCAATTATA-TCTGTTTTAACGAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAG-AT
* * *
1565 TATAAAACCATGTAAAGCGAGTAAT
317 TACAAAACCATTTAAAGTGAGTAAT
* * ***
1590 AAGGCTTTTTGAAGGAATAGGTGATTACT-AATGGACTTTTCTTGTCAATGAATGCCTTGACCTT
1 AAGGC-TTTTGAAGGAATGGGTGACTA-TAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTT
* * * * * * * * *
1654 CATGTTTTTGGAGGTTGACATTCAATTATAATCTTTTTTGACCAACAATATACAAAGAATTCAAA
64 TACGTTTCTCGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGTA-AAA-AATTCAAC
** * * * *
1719 TTTTAATCAATTTTGTGATTACAAAACCATTTAAAGTGAGTATTAAGGCTTTTGAAGGAATGGGT
127 TTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
* * ** * * * *
1784 GACTATAAATAGACTTTTCTTGCCAATAAATATCTTTTTCTTTACGTTTCTCGAGATTGATATTC
192 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTTGACATTC
* * ********** ** * *
1849 AATTATAGTCTGTTTTAACCAAAAATGT-TAANNNNNNNNNNTAAAAATCAATTATG-GCATTAT
257 AATTATA-TCTGTTTTAACGAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAG-ATTAC
* *
1912 AAAACCATTTAAAGCGAGTAAG
320 AAAACCATTTAAAGTGAGTAAT
* * * * ** *
1934 GAGGCCTTTTTAA-GAATGGGTGACTATAAACGGATTTTTCTTACCAATGTATGCCTTTTT-TTT
1 AAGG-CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTT
*
1997 CACGTTTCTTGAGGTTGACATTCAATTATAATCTG
65 -ACGTTTCTCGAGGTTGACATTCAATTATAATCTG
Statistics
Matches: 1203, Mismatches: 226, Indels: 77
0.80 0.15 0.05
Matches are distributed among these distances:
338 1 0.00
339 52 0.04
340 69 0.06
341 92 0.08
342 159 0.13
343 652 0.54
344 177 0.15
345 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (341 bp):
AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTTA
CGTTTCTCGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAATGTAAAAAATTCAACTTAA
AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACT
ATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACGTTTCTTGAGGTTGACATTCAATT
ATATCTGTTTTAACGAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTACAAAACC
ATTTAAAGTGAGTAAT
Found at i:1448 original size:512 final size:513
Alignment explanation
Indices: 222--1876 Score: 1605
Period size: 512 Copynumber: 3.2 Consensus size: 513
212 NNNNNTAACA
* * * * ** *
222 AGGCTTTTAAAGGAATGGGTGACTATAATTGGACTTTTCTTGCCAATG-ACTGCCTTTTTTTTTA
1 AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGTA-TACCTTTTTCATCA
* ** * * * * * * * * *
286 TATTTCTCAAGGTAGACATTCTATTATAATATGTTTTAACTAAAAATGAACAACAAATTGAACTT
65 TGTTTCTTGAGGTTGACATTCAATTATAATCTATTTTAACAAAAAATGTACAAAAAATTCAAATT
* * * * * * * * *** *
351 AAAATCAATTATGAGATTATAAGATCATTTAAAATGTGTAATAAGGCTTTTGAA-GGAATTTATG
130 TAAATCAATTTTGAGAATATAAAACCATTTAAAGTGAGTAAAAAGGCTTTT-AATGGAATGGGTT
* * * ** * ** * * * *
415 ATTATTAATGGACTTTTCTTGCCAATGAATG-CCTTTTCCTTCATGTTT-CTTGATGTTGCCTTT
194 ACTATAAATGAACTTTTCTTGCCAATGAATGCCCTTTTTATT-ACGTTTAC-CAACGTAGAC-AT
* * ** * * * *
478 CAATTATAATCT-TTCTTAATGAAAAATGTGCAAAGA-ATTCAAATTTAAATCAATTTTGAG-AT
256 CAATTCTAGTCTGTT-TTAACCAAAAATGT--AAAAACATTCAACTTAAAATCAATTATG-GCAT
* ** * * * * *
540 TACAAAACCATTTAAAGTGAGTATTAAGGC-TTTTGAAAGAATGGGTGACTATA-AATGGACTTT
317 TATAAAACCACGTAAAGCGAGAAATAAGGCTTTTTGAAGGAATAGGTGA-T-TACAATGGACTTT
* * *** ** * * * * * *** *
603 TCTTGTCAA-CAAATACCTTTTTCTTTGCGTTTCTCGAGATTGACATTCAAGTATTGTCTGTTTT
380 TCTTGCCAATC-AATGCCTTGACCTTCACATTTTTGGAGGTTGACATTCAATTACAATCTTTTTT
* * * * *** *
667 AACCAAAAATGTA-AAA-AACTTCAACTAAAAATCAA-TTATG-GCATTATAAAACCATTTAAAG
444 GACCAACAATATACAAAGAA-TTCAAATTTCAATCAATTTA-GAG-ATTACAAAACCATTTAAAG
*
728 CGAGTAAT
506 TGAGTAAT
* *
736 GAGGCTTTTGAAGGAATGGGTGACTATAAATGGATTTTTCTTACCAATGTATGCCTTTTTCATCA
1 -AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGTATACCTTTTTCATCA
** * *
801 TGTTTCTTGCTGTTGACATTCAATTATGATCTGTTTTAACAAAAAATGTACAAAAAATTCAAATT
65 TGTTTCTTGAGGTTGACATTCAATTATAATCTATTTTAACAAAAAATGTACAAAAAATTCAAATT
866 TAAATCAATTTTGAGAATATAAAACCATTTAAAGTGAGTAAAAAGGCTTTTAATGGAATGGGTTA
130 TAAATCAATTTTGAGAATATAAAACCATTTAAAGTGAGTAAAAAGGCTTTTAATGGAATGGGTTA
* * *
931 CTATAACTGAACTTTTCTTGTCAATGAATG-CCTTTTTCATTACGTTTACCAACGTAGACGTCAA
195 CTATAAATGAACTTTTCTTGCCAATGAATGCCCTTTTT-ATTACGTTTACCAACGTAGACATCAA
* *
995 TTCTAGTCTTTTTTTACCAAAAATGT-AAAACAGTTCAACTTAAAATCAATTATGGCATTATAAA
259 TTCTAGTCTGTTTTAACCAAAAATGTAAAAACA-TTCAACTTAAAATCAATTATGGCATTATAAA
*
1059 ACCACGTAAAGCGAGAAATAAGGCTTTTTGAAGGAATGGGTGACTGTA-AATGGACTTTTCTTGC
323 ACCACGTAAAGCGAGAAATAAGGCTTTTTGAAGGAATAGGTGA-T-TACAATGGACTTTTCTTGC
* * * *
1123 CAATCAATGCCTTTACCTTCACATTTCTT-TAGGTTGACATTGAATTACAATCTTTTTTGACGAA
386 CAATCAATGCCTTGACCTTCACATTT-TTGGAGGTTGACATTCAATTACAATCTTTTTTGACCAA
*
1187 CAATGTACAAAGAATTCAAATTTCAATCAATTTAGAGATTACAAAACCATTTAAAGTGAGTAAT
450 CAATATACAAAGAATTCAAATTTCAATCAATTTAGAGATTACAAAACCATTTAAAGTGAGTAAT
* * * * **
1251 ATGGCTTTTGGAGGAATGAGTGATTATAAATGGACTTTTCTTACCACTG-A-ACCTTTTTTTTCA
1 A-GGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGTATACCTTTTTCATCA
* * *
1314 TG-TTC-TGAAGGTTGACATTCAATTATAATCTATTTTAA-AGCAAAATGTGCAAAGAATTCAAA
65 TGTTTCTTG-AGGTTGACATTCAATTATAATCTATTTTAACA-AAAAATGTACAAAAAATTCAAA
* *
1376 TTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAACGG-TTTTGAA-GGAATGG
128 TTTAAATCAATTTTGAGAATATAAAACCATTTAAAGTGAGTAA-AAAGGCTTTT-AATGGAATGG
* * *
1439 GTTACTATAAATGGACTTTTCTTGCCAATGAATGCCCTTTTTATTACGTTTATCAAGGTAGACAT
191 GTTACTATAAATGAACTTTTCTTGCCAATGAATGCCCTTTTTATTACGTTTACCAACGTAGACAT
* *
1504 TAATTCTAGTCTGTTTTAACTAAAAATGTAAAAACATTCAACTTAAAATCAATTATGGCATTATA
256 CAATTCTAGTCTGTTTTAACCAAAAATGTAAAAACATTCAACTTAAAATCAATTATGGCATTATA
* *
1569 AAACCATGTAAAGCGAGTAATAAGGCTTTTTGAAGGAATAGGTGATTACTAATGGACTTTTCTTG
321 AAACCACGTAAAGCGAGAAATAAGGCTTTTTGAAGGAATAGGTGATTAC-AATGGACTTTTCTTG
* * ** *
1634 TCAATGAATGCCTTGACCTTCATGTTTTTGGAGGTTGACATTCAATTATAATCTTTTTTGACCAA
385 CCAATCAATGCCTTGACCTTCACATTTTTGGAGGTTGACATTCAATTACAATCTTTTTTGACCAA
* * * *
1699 CAATATACAAAGAATTCAAATTTTAATCAATTTTGTGATTACAAAACCATTTAAAGTGAGTATT
450 CAATATACAAAGAATTCAAATTTCAATCAATTTAGAGATTACAAAACCATTTAAAGTGAGTAAT
* * ** * * *
1763 AAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATAAATATCTTTTTCTTTA
1 -AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGTATACCTTTTTCATCA
* * * * * * *
1828 CGTTTCTCGAGATTGATATTCAATTATAGTCTGTTTTAACCAAAAATGT
65 TGTTTCTTGAGGTTGACATTCAATTATAATCTATTTTAACAAAAAATGT
1877 TAANNNNNNN
Statistics
Matches: 958, Mismatches: 151, Indels: 62
0.82 0.13 0.05
Matches are distributed among these distances:
510 2 0.00
511 9 0.01
512 417 0.44
513 77 0.08
514 122 0.13
515 320 0.33
516 11 0.01
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (513 bp):
AGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCAATGTATACCTTTTTCATCAT
GTTTCTTGAGGTTGACATTCAATTATAATCTATTTTAACAAAAAATGTACAAAAAATTCAAATTT
AAATCAATTTTGAGAATATAAAACCATTTAAAGTGAGTAAAAAGGCTTTTAATGGAATGGGTTAC
TATAAATGAACTTTTCTTGCCAATGAATGCCCTTTTTATTACGTTTACCAACGTAGACATCAATT
CTAGTCTGTTTTAACCAAAAATGTAAAAACATTCAACTTAAAATCAATTATGGCATTATAAAACC
ACGTAAAGCGAGAAATAAGGCTTTTTGAAGGAATAGGTGATTACAATGGACTTTTCTTGCCAATC
AATGCCTTGACCTTCACATTTTTGGAGGTTGACATTCAATTACAATCTTTTTTGACCAACAATAT
ACAAAGAATTCAAATTTCAATCAATTTAGAGATTACAAAACCATTTAAAGTGAGTAAT
Found at i:1953 original size:855 final size:857
Alignment explanation
Indices: 221--2030 Score: 2112
Period size: 855 Copynumber: 2.1 Consensus size: 857
211 NNNNNNTAAC
* ** * * * *** *
221 AAGGC-TTTTAAAGGAATGGGTGACTATAATTGGACTTTTCTTGCCAATGACTGCCTTTTTTTTT
1 AAGGCTTTTTGAAGGAATGGGTGACTATAAACGGACTTTTCTTACCAATCAATGCCTTTACCTTC
* ** * * * * * * * * * * *
285 ATATTTCTCAAGGTAGACATTCTATTATAATATGTTTTAACTAAAAATGAACAACA-AATTGAAC
66 ACATTTCTTGAGGTTGACATTCAATTACAATCTTTTTTGACGAACAATGTACAA-AGAATTCAAA
** * * * * *
349 TTAAAATCAATTATGAGATTATAAGATCATTTAAAATGTGTAATAAGGCTTTTGAAGGAATTTAT
130 TTTCAATCAATTATGAGATTACAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATTGAT
* * * * *
414 GATTATTAATGGACTTTTCTTGCCAATGAATGCCTTTTCCTTCATGTTTCTTGATGTTGCCTTTC
195 GATTATAAATGGACTTTTCTTACCAATGAA-GCCTTTTCCTTCATGTTTCTTGAGGTTGACATTC
*
479 AATTATAATCTTTCTTAATGAAAAATGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATTACA
259 AATTATAATCTTTCTTAAAGAAAAATGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATTACA
* *
544 AAACCATTTAAAGTGAGTATTAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGT
324 AAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGC
* * * * * *
609 CAACAAATACCTTTTTCTTTGCGTTTCTCGAGATTGACATTCAAGTATTGTCTGTTTTAACCAAA
389 CAACAAATACCTTTTTCATTACGTTTATCAAGATAGACATTCAAGTATAGTCTGTTTTAACCAAA
* *
674 AATGTAAAAAACTTCAACTAAAAATCAATTATGGCATTATAAAACCATTTAAAGCGAGTAATGAG
454 AATGTAAAAAACTTCAACTAAAAATCAATTATGGCATTATAAAACCATGTAAAGCGAGTAATAAG
* * * ***
739 GCTTTTGAAGGAATGGGTGACTATAAATGGATTTTTCTTACCAATGTATGCCTTTTTCATCATGT
519 GCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTGACCATCATGT
** * *
804 TTCTTGCTGTTGACATTCAATTATGATCTGTTTTAACAAAAAATGTACAAAAAATTCAAATTTAA
584 TTCTTGAGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATATACAAAAAATTCAAATTTAA
* *
869 ATCAATTTTGAGAATATAAAACCATTTAAAGTGAGTAAAAAGGCTTTTAATGGAATGGGTTACTA
649 ATCAATTTTGAGAATACAAAACCATTTAAAGTGAGTAAAAAGGCTTTTAATGGAATGGGTGACTA
* * * * * *
934 TAACTGAACTTTTCTTGTCAATGAATGCCTTTTTCATTACGTTTACCAACGTAGACGTCAATTCT
714 TAAATGAACTTTTCTTGCCAATAAATACCTTTTTCATTACGTTTACCAACGTAGAAGTCAATTAT
* * *
999 AGTCTTTTTTTACCAAAAATGTAAAACAGTTCAACTTAAAATCAATTATGGCATTATAAAACCAC
779 AGTCTGTTTTAACCAAAAATGTAAAACAGTTCAACTAAAAATCAATTATGGCATTATAAAACCAC
*
1064 GTAAAGCGAGAAAT
844 GTAAAGCGAGAAAG
* * *
1078 AAGGCTTTTTGAAGGAATGGGTGACTGTAAATGGACTTTTCTTGCCAATCAATGCCTTTACCTTC
1 AAGGCTTTTTGAAGGAATGGGTGACTATAAACGGACTTTTCTTACCAATCAATGCCTTTACCTTC
* *
1143 ACATTTCTTTAGGTTGACATTGAATTACAATCTTTTTTGACGAACAATGTACAAAGAATTCAAAT
66 ACATTTCTTGAGGTTGACATTCAATTACAATCTTTTTTGACGAACAATGTACAAAGAATTCAAAT
* * *
1208 TTCAATCAATT-TAGAGATTACAAAACCATTTAAAGTGAGTAATATGGCTTTTGGAGGAA-TGAG
131 TTCAATCAATTAT-GAGATTACAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATTGA-
* **
1271 TGATTATAAATGGACTTTTCTTACCACTGAA-CCTTTTTTTTCATG-TTC-TGAAGGTTGACATT
194 TGATTATAAATGGACTTTTCTTACCAATGAAGCCTTTTCCTTCATGTTTCTTG-AGGTTGACATT
*
1333 CAATTATAATCTATT-TTAAAGCAAAATGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATTA
258 CAATTATAATCT-TTCTTAAAGAAAAATGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATTA
* * *
1397 TAAAACCATTTAAAGTGAGTAATAACGG-TTTTGAAGGAATGGGTTACTATAAATGGACTTTTCT
322 CAAAACCATTTAAAGTGAGTAATAA-GGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCT
** * * * *
1461 TGCCAATGAATGCCCTTTTT-ATTACGTTTATCAAGGTAGACATT-AATTCTAGTCTGTTTTAAC
386 TGCCAACAAAT-ACCTTTTTCATTACGTTTATCAAGATAGACATTCAAGTATAGTCTGTTTTAAC
* *
1524 TAAAAATGT-AAAAACATTCAACTTAAAATCAATTATGGCATTATAAAACCATGTAAAGCGAGTA
450 CAAAAATGTAAAAAAC-TTCAACTAAAAATCAATTATGGCATTATAAAACCATGTAAAGCGAGTA
* **
1588 ATAAGGCTTTTTGAAGGAATAGGTGATTACT-AATGGACTTTTCTTGTCAATGAATGCCTTGACC
514 ATAAGGC-TTTTGAAGGAATAGGTGACTA-TAAATGGACTTTTCTTACCAATGAATGCCTTGACC
* * * * * *
1652 TTCATGTTT-TTGGAGGTTGACATTCAATTATAATCTTTTTTGACCAACAATATACAAAGAATTC
577 ATCATGTTTCTT-GAGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATATACAAAAAATTC
* * * **
1716 AAATTTTAATCAATTTTGTGATTACAAAACCATTTAAAGTGAGTATTAAGGCTTTTGAA-GGAAT
641 AAATTTAAATCAATTTTGAGAATACAAAACCATTTAAAGTGAGTAAAAAGGCTTTT-AATGGAAT
* * * *
1780 GGGTGACTATAAAT-AGACTTTTCTTGCCAATAAATATCTTTTTCTTTACGTTT-CTCGA-GATT
705 GGGTGACTATAAATGA-ACTTTTCTTGCCAATAAATACCTTTTTCATTACGTTTAC-CAACG-TA
* * **********
1842 GATATTCAATTATAGTCTGTTTTAACCAAAAATGTTAANNNNNNNNNNTAAAAATCAATTATGGC
767 GA-AGTCAATTATAGTCTGTTTTAACCAAAAATGTAAAACAGTTCAACTAAAAATCAATTATGGC
** *
1907 ATTATAAAACCATTTAAAGCGAGTAAG
831 ATTATAAAACCACGTAAAGCGAGAAAG
* * ** ***
1934 GAGGCCTTTTT-AA-GAATGGGTGACTATAAACGGATTTTTCTTACCAATGTATGCCTTTTTTTT
1 AAGG-CTTTTTGAAGGAATGGGTGACTATAAACGGACTTTTCTTACCAATCAATGCCTTTACCTT
* *
1997 CACGTTTCTTGAGGTTGACATTCAATTATAATCT
65 CACATTTCTTGAGGTTGACATTCAATTACAATCT
2031 G
Statistics
Matches: 801, Mismatches: 134, Indels: 38
0.82 0.14 0.04
Matches are distributed among these distances:
853 6 0.01
854 83 0.10
855 424 0.53
856 99 0.12
857 15 0.02
858 174 0.22
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (857 bp):
AAGGCTTTTTGAAGGAATGGGTGACTATAAACGGACTTTTCTTACCAATCAATGCCTTTACCTTC
ACATTTCTTGAGGTTGACATTCAATTACAATCTTTTTTGACGAACAATGTACAAAGAATTCAAAT
TTCAATCAATTATGAGATTACAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATTGATG
ATTATAAATGGACTTTTCTTACCAATGAAGCCTTTTCCTTCATGTTTCTTGAGGTTGACATTCAA
TTATAATCTTTCTTAAAGAAAAATGTGCAAAGAATTCAAATTTAAATCAATTTTGAGATTACAAA
ACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCCA
ACAAATACCTTTTTCATTACGTTTATCAAGATAGACATTCAAGTATAGTCTGTTTTAACCAAAAA
TGTAAAAAACTTCAACTAAAAATCAATTATGGCATTATAAAACCATGTAAAGCGAGTAATAAGGC
TTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTACCAATGAATGCCTTGACCATCATGTTT
CTTGAGGTTGACATTCAATTATAATCTGTTTTAACAAAAAATATACAAAAAATTCAAATTTAAAT
CAATTTTGAGAATACAAAACCATTTAAAGTGAGTAAAAAGGCTTTTAATGGAATGGGTGACTATA
AATGAACTTTTCTTGCCAATAAATACCTTTTTCATTACGTTTACCAACGTAGAAGTCAATTATAG
TCTGTTTTAACCAAAAATGTAAAACAGTTCAACTAAAAATCAATTATGGCATTATAAAACCACGT
AAAGCGAGAAAG
Found at i:2022 original size:171 final size:161
Alignment explanation
Indices: 1723--2031 Score: 309
Period size: 171 Copynumber: 1.9 Consensus size: 161
1713 TTCAAATTTT
* * **
1723 AATCAATTTTGTGATTACAAAACCATTTAAAGTGAGTATTAAGGCTTTTGAAGGAATGGGTGACT
1 AATCAATTATGTGATTACAAAACCATTTAAAGCGAGTAAGAAGGCTTTTGAAGGAATGGGTGACT
* * * *
1788 ATAAATAGACTTTTCTTGCCAATAAATATCTTTTTCTTTACGTTTCTCGAGATTGATATTCAATT
66 ATAAACAGACTTTTCTTACCAATAAATACCTTTTTCTTTACGTTTCTCGAGATTGACATTCAATT
*
1853 ATAGTCTGTTTTAACCAAAAATGTTAANNNNNNNNNNTAAA
131 ATAATCTGTTTTAACCAAAAATGTTAA----------TAAA
* * *
1894 AATCAATTATG-GCATTATAAAACCATTTAAAGCGAGTAAGGAGGCCTTTTTAA-GAATGGGTGA
1 AATCAATTATGTG-ATTACAAAACCATTTAAAGCGAGTAAGAAGG-CTTTTGAAGGAATGGGTGA
* * ** * * *
1957 CTATAAACGGATTTTTCTTACCAATGTATGCCTTTTT-TTTCACGTTTCTTGAGGTTGACATTCA
64 CTATAAACAGACTTTTCTTACCAATAAATACCTTTTTCTTT-ACGTTTCTCGAGATTGACATTCA
2021 ATTATAATCTG
128 ATTATAATCTG
Statistics
Matches: 116, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
170 4 0.03
171 105 0.91
172 7 0.06
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.37
Consensus pattern (161 bp):
AATCAATTATGTGATTACAAAACCATTTAAAGCGAGTAAGAAGGCTTTTGAAGGAATGGGTGACT
ATAAACAGACTTTTCTTACCAATAAATACCTTTTTCTTTACGTTTCTCGAGATTGACATTCAATT
ATAATCTGTTTTAACCAAAAATGTTAATAAA
Done.