Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402897.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5947.0, 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: 3179
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.32
Warning! 381 characters in sequence are not A, C, G, or T
Found at i:985 original size:171 final size:169
Alignment explanation
Indices: 476--3151 Score: 2124
Period size: 171 Copynumber: 15.7 Consensus size: 169
466 NNNNNNNNNC
* * * * *
476 TAAAATCAATTATGAGATTATAAAATCATTTAAAGAGAGTAATAAGGCTTTTGGAGGCATGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGTG
* * * * * *
541 ACTATAAGTAGACTTTTCTTGTCAATGAATGGCTTTTTCTTCATGTTTCTCAAGGCAGACAGTCA
66 ACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATTCA
* *
606 ATTATAATCTATTTTAACCAAAAATAAAAAAAATTCAACT
131 ATTATAATCTGTTTTAA-CAAAAATATAAAAAATTCAACT
* * ** ** *
646 TAAAATCAATTATGAGATTATAAAACTATTTAAAACGAGTAATAAGGTTTTTGAAGGCTTGACTA
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGTG
* * * *
711 ACTATAAGTGGAC-ATT-TTATACTAATGGATGAG-TTTTGCTTCATGTTT-TTCAAGGTAGACA
66 ACTATAAATGGACTTTTCTTAT-C-AATGAATG-GCTTTTTCTTCATGTTTCTT-AAGGTAGACA
* * * *
772 TTCAATTATAATATATTGTAATCAAAATTATAAAAAAATTCAACT
127 TTCAATTATAATCTGTTTTAA-CAAAAATAT-AAAAAATTCAACT
* * ** *
817 TAAAATCAATTATGGGATTATAAAAGCGATTTAAAATGAGTAATAAGACTTTCGAAGGCTTGGGT
1 TAAAATCAATTATGAGATTATAAAA-CCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGT
* * * * * *
882 GACTATAAATGGGCTTTTCTTGTGAATGAAAGGGTTTTTCTTCATGTTTCTTAAGGTAAACATTC
65 GACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATTC
* * *
947 AATTACAATTTGTTTTAAGAAAAATATAAAACAATTCAACT
130 AATTATAATCTGTTTTAACAAAAATATAAAA-AATTCAACT
* * * * * **
988 TAAAATCATTTATGAGATTGTAAAACCATTTAAAGCGAATAATAA-AGCTTTTG-ACGATATAAG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGA-CTTTTGAAGGCT-TGGG
* * * * * *
1051 TGACTATAACTAGACTTTTCTTATCAATGAACGGCTTTTTCTTCATGTTTCTTAAGGTATATAGT
64 TGACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATT
* * *
1116 CAATTATAATCTATTTTATCAAAAATA-AAAAAATTCAACA
129 CAATTATAATCTGTTTTAACAAAAATATAAAAAATTCAACT
* * * * *
1156 TAAAATCAATTATGAGATTGTAGAACCATTTAAAGCGAGTAATAAGACTATCGAAGGCATGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGTG
* * * * * * * ** *
1221 ACTATAAATAGACTTTTCTTGTCAATGAATGGATTTGTCTTTATGTTTCTCATGACAAACATTCA
66 ACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATTCA
* * *
1286 ATTCTAATATGTTTTAACTAAAAATGTAAAAAGATTCAACT
131 ATTATAATCTGTTTTAAC-AAAAATATAAAAA-ATTCAACT
* * * * ** *
1327 TAAAATCAATTATGAGATTACAAAACCATTTAAAGTGATTAATAAGGCTTTT-AAGGGGATGAGT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAA-GGCTTGGGT
* * * * * * * *
1391 GACTATAAATAGACTTTGCTTGTCAATGAAT-GCTTTTTTTTTCATATTGTC-CAAGGTCGACAA
65 GACTATAAATGGACTTTTCTTATCAATGAATGGC-TTTTTCTTCATGTT-TCTTAAGGTAGACAT
* *
1454 TCAATTATAATCTTTTTTAACCAGAAATATAAAAAATTTCAACT
128 TCAATTATAATCTGTTTTAA-CAAAAATATAAAAAA-TTCAACT
* * *
1498 CAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTCGAAGGCTTGAGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGTG
** * * * ** ** *
1563 ACTATAGGTAGA-TTTT-TTATACCAATGGATGGCTTTTGCTTCACATTTCCCAAAGTAGACATT
66 ACTATAAATGGACTTTTCTTAT--CAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATT
* * * * *
1626 CAATTATAATATATTTTAAGTAAAAATGTAAAAATATTTAACT
129 CAATTATAATCTGTTTTAA-CAAAAATATAAAAA-ATTCAACT
* * * * *
1669 TTAAATCAATTATGGGATTATAAAAGCGATTTAAAACGAGTAATAA-AGCTTTCGAAGGCTTGGG
1 TAAAATCAATTATGAGATTATAAAA-CCATTTAAAGCGAGTAATAAGA-CTTTTGAAGGCTTGGG
* * * *
1733 TGACTATAAAT-TAGCTTTTCTTGT-AGATGAAATGG-TTTTTCGTT-ATGTTTCCTAAGGTAAA
64 TGACTATAAATGGA-CTTTTCTTATCA-ATG-AATGGCTTTTTC-TTCATGTTTCTTAAGGTAGA
* **
1794 CATTCAATTACAATCTGTTTTAAGTGAAAATATAAAACAATTCAACT
125 CATTCAATTATAATCTGTTTTAA-CAAAAATATAAAA-AATTCAACT
* * * * * *
1841 TAAAATCATTTATGAGATTATAAGACCATTTAAAGCAAGCAATAAGGCTTTTGAAGG-TATGAGT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCT-TGGGT
* * * * * * *
1905 GACTATAAATGAATTTTTGTTATCAATGAATGGCTTTTTCTTCACGTTTCTCAAGGTAGATAGTC
65 GACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATTC
* * ********* *
1970 AATTATAATCTATTTTATCAAAAA-ATGNNNNNNNNNNAACA
130 AATTATAATCTGTTTTAACAAAAATAT--AAAAAATTCAACT
* * * * *
2011 TAAAATCATTTATGAGATTGTAAAACCATTTAAAGCGACTAATAAGA-TTTTCGAAGGTTTGGAT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTT-GAAGGCTTGGGT
* * * * ** ** *
2075 GACTATAAATGGAGTTTTCTTATCAATAAATGGCTTTGTCATCACATTTCCCATGGTAGACATTC
65 GACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATTC
* * * * *
2140 AATTATAATTTGCTTTAATAAAAAATATGAAATAATTCACCT
130 AATTATAATCTGTTTTAA-CAAAAATAT-AAAAAATTCAACT
* * * * * * ** * ** *
2182 AAAAATCGATTATGAGATTACAAAACCATTTCAAGTGATTAATAAGGTTTTTGAGGGGATGAGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGTG
* * * * * *
2247 ACTATAAACGGACTTTTCTTACCAATGAATGTCTTTTTCTTCATGTTT-TTCAAGGCATACAATC
66 ACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTT-AAGGTAGACATTC
* * *
2311 AATTATAATTTTTTTTAACAAAAAATATAAAAAAATTTAACT
130 AATTATAATCTGTTTTAAC-AAAAATAT-AAAAAATTCAACT
* ********* * * *
2353 TAAAATTAATTATGAGNNNNNNNNNNCAATTTAAAGCGACTAATAAGGCTTTTGAAGGCTTGGGT
1 TAAAATCAATTATGAG-ATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGT
** * ** * *
2418 GACTATTTATGGGCTTTTC-TCGCTAATGACTAGG-TTTTTCTTCATGTTTCTTAGGGTA-ACCA
65 GACTATAAATGGACTTTTCTTATC-AATGAAT-GGCTTTTTCTTCATGTTTCTTAAGGTAGA-CA
* * * * *
2480 TTCAATTACACTATGTTTTAACTAAAAATGTAAAAAAATTCAACC
127 TTCAATTATAATCTGTTTTAAC-AAAAATAT-AAAAAATTCAACT
* * * * *
2525 TAAAAACAATTAGGAGATTATAAAACTATTTAAAGTGAGTAATAA-AGCTTTTGAAGG-TAAGGG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGA-CTTTTGAAGGCT-TGGG
* ** * *
2588 TGACTATAAATGGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCTTAAGGTAAACAGT
64 TGACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATT
* * * * * * *
2653 CAATTCTAATTTGTTTTATCCAAAAATGTTAAAATATTCAGCC
129 CAATTATAATCTGTTTTA-ACAAAAAT-ATAAAAAATTCAACT
* * ** * *
2696 TAAAATTAATTATGAGATTGTAAAACCATTTAAATAGAGTAATAAGACTTTCGAAGGCATGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGTG
* * * ** *
2761 ACTATAAATAGACTTTTCTTATCAATAAATGACTTTTTCTTCACATTTCTTAA-GTCAGACAGTC
66 ACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGT-AGACATTC
*
2825 AATTATAATCTGTTTTATCCAAAAATATAAACATATATTGC--C-
130 AATTATAATCTGTTTTA-ACAAAAATATAAA-A-A-ATT-CAACT
* * * * * *
2867 TAAAATTAATTATGAGATTGTAAAACCATTTAAATCGAGTAATAAGGCTTTCGAAGGCGTGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGTG
* * * * * **
2932 ACAATAAATGGACTTTTCTTGTCAATGAATGGCTTTCTCTTCATGTTTCTCATGACAGACATTCA
66 ACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATTCA
* * **
2997 ATTATAATCCGTTTTAAGCAAAAATGTAAAAAAAATTTGACT
131 ATTATAATCTGTTTTAA-CAAAAA--TATAAAAAATTCAACT
* * * * * **
3039 TAAAATCAATTATGAGATTACAAAACTATTTAAA-CTGATTAACAAGGCTTTTG-AGGAAATGGG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGC-GAGTAATAAGACTTTTGAAGG-CTTGGG
* ** * *
3102 TGACTATAAATGGACTGTTT-TTACCAATGAATACCTTGTTGTTCATGTTT
64 TGACTATAAATGGACT-TTTCTTATCAATGAATGGCTTTTTCTTCATGTTT
3152 TCTGAGGCAA
Statistics
Matches: 2005, Mismatches: 419, Indels: 162
0.78 0.16 0.06
Matches are distributed among these distances:
168 127 0.06
169 30 0.01
170 384 0.19
171 986 0.49
172 442 0.22
173 29 0.01
174 7 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (169 bp):
TAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGGCTTGGGTG
ACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTTCATGTTTCTTAAGGTAGACATTCA
ATTATAATCTGTTTTAACAAAAATATAAAAAATTCAACT
Found at i:2710 original size:514 final size:508
Alignment explanation
Indices: 475--3133 Score: 2232
Period size: 514 Copynumber: 5.2 Consensus size: 508
465 NNNNNNNNNN
* * * * * *
475 CTAAAATCAATTATGAGATTATAAAATCATTTAAAGAGAGTAATAAGGCTTTTGGAGGCATGGGT
1 CTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGTAAGGGT
* ** ** *
540 GACTATAAGTAGACTTTTCTTGTCAATGAATGGCTTTTTCTTCATGTTTCTCAAGGCAGACAGTC
66 GACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCTCAAGGTAGACAGTC
* * * *
605 AATTATAATCTATTTTAACCAAAAATAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
131 AATTATAATCTATTTT-ATCAAAAATTAAAAATATTCAACCTAAAATCAATTATGAGATTATAAA
* * * * ** * * * * *
670 ACTATTTAAAACGAGTAATAAGGTTTTTGAAGGCTTGACTAACTATAAGTGGACATTTT-ATACT
195 ACCATTTAAAACGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATAGAC-TTTTCTTACC
* * * * * * *
734 AATGGATGAGTTTTGCTTCATGTTTTTCAAGGTAGACATTCAATTATAATATATTGTAA-TCAAA
259 AATGAATGACTTTTTCTTCATGTTTTTCAAGGCAAACATTCAATTATAATATGTTTTAACT-AAA
* * * ** *
798 ATTATAAAAAAATTCAACTTAAAATCAATTATGGGATTATAAAAGCGATTTAAAATGAGTAATAA
323 AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-CCATTTAAAGCGACTAATAA
* * * * *
863 GACTTTCGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGTGAATGAAAGGGTTTTTCTTCATG
387 GGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGTCAATG-AATGGTTTTTCTTCATG
* * * * * *
928 TTTCTTAAGGTAAACATTCAATTACAATTTGTTTTAAGAAAAATATAAAACAATTCAAC
451 TTTCTCAAGGT-AACATTCAATTATAATCTGTTTTAACAAAAATGTAAAAAAATTCAAC
* * * * * * *
987 TTAAAATCATTTATGAGATTGTAAAACCATTTAAAGCGAATAATAAAGCTTTTGACGATATA-AG
1 CTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGTA-AGGG
* * * ** * * *
1051 TGACTATAACTAGACTTTTCTTATCAATGAACGGCTTTTTCTTCATGTTTCTTAAGGTATATAGT
65 TGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCTCAAGGTAGACAGT
* * * *
1116 CAATTATAATCTATTTTATCAAAAA-TAAAAAAATTCAACATAAAATCAATTATGAGATTGTAGA
130 CAATTATAATCTATTTTATCAAAAATTAAAAATATTCAACCTAAAATCAATTATGAGATTATAAA
* * * **
1180 ACCATTTAAAGCGAGTAATAAGACTATCGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCA
195 ACCATTTAAAACGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTACCA
* * * * * *
1245 ATGAATGGA-TTTGTCTTTATGTTTCTCATGACAAACATTCAATTCTAATATGTTTTAACTAAAA
260 ATGAAT-GACTTTTTCTTCATGTTTTTCAAGGCAAACATTCAATTATAATATGTTTTAACTAAAA
* * * * *
1309 ATGTAAAAAGATTCAACTTAAAATCAATTATGAGATTACAAAACCATTTAAAGTGATTAATAAGG
324 ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGACTAATAAGG
** * * * * * *
1374 CTTTT-AAGGGGATGAGTGACTATAAATAGACTTTGCTTGTCAATGAATGCTTTTTTTTTCATAT
389 CTTTTGAA-GGCTTGGGTGACTATAAATGGACTTTTCTTGTCAATGAATG-GTTTTTCTTCATGT
* * * * * *
1438 TGTC-CAAGGTCGACAATCAATTATAATCTTTTTTAACCAGAAATATAAAAAATTTCAA-
452 T-TCTCAAGGT-AACATTCAATTATAATCTGTTTTAA-CAAAAATGTAAAAAAATTCAAC
* *
1496 CTCAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT-AAGACTTTCGAAGGCT-TG
1 CT-AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAG-CTTTTGAAGG-TAAG
* ** * * * * *
1559 AGTGACTATAGGTAGA-TTTTTTATACCAATGGATGGCTTTTGCTTCACATTTCCCAAAGTAGAC
63 GGTGACTATAAATAGACTTTTCT-TACCAATGAATGGCTTTTTCTTCACATTTCTCAAGGTAGAC
* * * * * *
1623 ATTCAATTATAATATATTTTAAGT-AAAAATGTAAAAATATTTAACTTTAAATCAATTATGGGAT
127 AGTCAATTATAATCTATTTT-A-TCAAAAAT-TAAAAATATTCAACCTAAAATCAATTATGAGAT
* * *
1687 TATAAAAGCGATTTAAAACGAGTAATAAAGCTTTCGAAGGCTTGGGTGACTATAAATTAG-CTTT
189 TATAAAA-CCATTTAAAACGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAA-TAGACTTT
** * * * * *
1751 TCTT-GTAGATGAAATG-GTTTTTCGTT-ATG-TTTCCTAAGGTAAACATTCAATTACAATCTGT
252 TCTTACCA-ATG-AATGACTTTTTC-TTCATGTTTTTC-AAGGCAAACATTCAATTATAATATGT
* * * * *
1812 TTTAAGTGAAAATATAAAACAATTCAACTTAAAATCATTTATGAGATTATAAGACCATTTAAAGC
313 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGC
* * * * * *
1877 AAGC-AATAAGGCTTTTGAAGG-TATGAGTGACTATAAATGAATTTTTGTTATCAATGAATGGCT
378 GA-CTAATAAGGCTTTTGAAGGCT-TGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGG-T
* * * * * *******
1940 TTTTCTTCACGTTTCTCAAGGTAGATAGTCAATTATAATCTATTTTATCAAAAAATG-NNNNNNN
440 TTTTCTTCATGTTTCTCAAGGTA-ACATTCAATTATAATCTGTTTTAAC-AAAAATGTAAAAAAA
***
2004 NNNAAC
503 TTCAAC
* * * * * ** *
2010 ATAAAATCATTTATGAGATTGTAAAACCATTTAAAGCGACTAAT-AAGATTTTCGAAGGTTTGGA
1 CTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTT-GAAGGTAAGGG
* * * * * * * * *
2074 TGACTATAAATGGAGTTTTCTTATCAATAAATGGCTTTGTCATCACATTTCCCATGGTAGACATT
65 TGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCTCAAGGTAGACAGT
* * * * * *
2139 CAATTATAATTTGCTTTAAT-AAAAAATATGAAATAATTC-ACCTAAAAATCGATTATGAGATTA
130 CAATTATAATCT-ATTTTATCAAAAATTA-AAAAT-ATTCAACCT-AAAATCAATTATGAGATTA
* * ** * * * * * * **
2202 CAAAACCATTTCAAGTGATTAATAAGGTTTTTGAGGGGATGAGTGACTATAAACGGACTTTTCTT
191 TAAAACCATTTAAAACGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTT
* * * * * *
2267 ACCAATGAATGTCTTTTTCTTCATGTTTTTCAAGGCATACAATCAATTATAATTTTTTTTAACAA
256 ACCAATGAATGACTTTTTCTTCATGTTTTTCAAGGCAAACATTCAATTATAATATGTTTTAACTA
* * ********* *
2332 AAAATATAAAAAAATTTAACTTAAAATTAATTATGAGNNNNNNNNNNCAATTTAAAGCGACTAAT
321 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAG-ATTATAAAACCATTTAAAGCGACTAAT
** * * *
2397 AAGGCTTTTGAAGGCTTGGGTGACTATTTATGGGCTTTTCTCG-CTAATGACTAGGTTTTTCTTC
385 AAGGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGTC-AATGAAT-GGTTTTTCTTC
* * * * *
2461 ATGTTTCTTAGGGTAACCATTCAATTACACTATGTTTTAACTAAAAATGTAAAAAAATTCAAC
448 ATGTTTCTCAAGGTAA-CATTCAATTATAATCTGTTTTAAC-AAAAATGTAAAAAAATTCAAC
* * * *
2524 CTAAAAACAATTAGGAGATTATAAAACTATTTAAAGTGAGTAATAAAGCTTTTGAAGGTAAGGGT
1 CTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGTAAGGGT
* * *
2589 GACTATAAATGGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCTTAAGGTAAACAGTC
66 GACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCTCAAGGTAGACAGTC
* * * * * * *
2654 AATTCTAATTTGTTTTATCCAAAAATGTTAAAATATTCAGCCTAAAATTAATTATGAGATTGTAA
131 AATTATAATCTATTTTAT-CAAAAAT-TAAAAATATTCAACCTAAAATCAATTATGAGATTATAA
* *
2719 AACCATTTAAATA-GAGTAATAAGACTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTAT
194 AACCATTTAAA-ACGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTAC
* ** * * * * * *
2783 CAATAAATGACTTTTTCTTCACATTTCTT-AAGTCAGACAGTCAATTATAATCTGTTTTATCCAA
258 CAATGAATGACTTTTTCTTCATGTTT-TTCAAGGCAAACATTCAATTATAATATGTTTTAACTAA
* * * * *
2847 AAATATAAACATATATTGC--C-TAAAATTAATTATGAGATTGTAAAACCATTTAAATCGAGTAA
322 AAATATAAA-A-AAATT-CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGACTAA
* * * *
2909 TAAGGCTTTCGAAGGCGTGGGTGACAATAAATGGACTTTTCTTGTCAATGAATGGCTTTCTCTTC
384 TAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGG-TTTTTCTTC
* ** * **
2974 ATGTTTCTCATGACAGACATTCAATTATAATCCGTTTTAAGCAAAAATGTAAAAAAAATTTGAC
448 ATGTTTCTCAAGGTA-ACATTCAATTATAATCTGTTTTAA-CAAAAATGT-AAAAAAATTCAAC
* * * * * * *
3038 TTAAAATCAATTATGAGATTACAAAACTATTTAAA-CTGATTAACAAGGCTTTTG-AGGAAATGG
1 CTAAAATCAATTATGAGATTATAAAACCATTTAAAGC-GAGTAATAAAGCTTTTGAAGGTAA-GG
*
3101 GTGACTATAAATGGACTGTTT-TTACCAATGAAT
64 GTGACTATAAATAGACT-TTTCTTACCAATGAAT
3134 ACCTTGTTGT
Statistics
Matches: 1704, Mismatches: 374, Indels: 136
0.77 0.17 0.06
Matches are distributed among these distances:
508 5 0.00
509 102 0.06
510 291 0.17
511 26 0.02
512 262 0.15
513 388 0.23
514 589 0.35
515 36 0.02
516 5 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (508 bp):
CTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTTGAAGGTAAGGGT
GACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCTCAAGGTAGACAGTC
AATTATAATCTATTTTATCAAAAATTAAAAATATTCAACCTAAAATCAATTATGAGATTATAAAA
CCATTTAAAACGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATAGACTTTTCTTACCAA
TGAATGACTTTTTCTTCATGTTTTTCAAGGCAAACATTCAATTATAATATGTTTTAACTAAAAAT
ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGACTAATAAGGCT
TTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGGTTTTTCTTCATGTTTCT
CAAGGTAACATTCAATTATAATCTGTTTTAACAAAAATGTAAAAAAATTCAAC
Found at i:2962 original size:21 final size:21
Alignment explanation
Indices: 2933--2972 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2923 GCGTGGGTGA
2933 CAATAAATGGACTTT-TCTTGT
1 CAATAAATGG-CTTTCTCTTGT
*
2954 CAATGAATGGCTTTCTCTT
1 CAATAAATGGCTTTCTCTT
2973 CATGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
CAATAAATGGCTTTCTCTTGT
Done.