Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398038.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1346.0, 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: 5101
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.30
Warning! 701 characters in sequence are not A, C, G, or T
Found at i:647 original size:347 final size:337
Alignment explanation
Indices: 3--1335 Score: 1042
Period size: 347 Copynumber: 3.9 Consensus size: 337
1 GG
* * * * * *
3 AATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTTTTCACA-TTTCCTAAGGT
1 AATGGGTGACTATAAATGGACTTTCCTTGCCAATGAATACCTTTTTCTT-AGAGTTTCCCAAGGC
* * * * *
67 AGACATTCAAGTATAATCTGTTTTAACCAGAAAGGTCAAAATATACAACCTAAAAT-AAATTATG
65 AAACATTCAATTATAATCTGTTCTAACCA-AAAGGTCAAAA-ATTCAACTTAAAATCAAA-TATG
* * * *
131 AGGTTATAAAA--ATCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATTGGTGACGATAAGTGG
127 AGATTATAAAACCTTCA--TAAAGTGAGTAATAAGGC-TTTGAAAGAA-TGGTGACTATAAATGG
* * * * * * * *
194 AGTTTTCTTGCTAATAAATACTTTTTTATTGATATTT-TTCGAGGTAGATATTTAATTATAATCT
188 AGTTTTCTTGC-AATGAATGCCTTTTTCTTCACATTTCTT-GAGGTAGACATTTAATTATAATTT
* * * *
258 ATTTTAAACAAAAATCTATAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTCAA
251 GTTTTAAA-AAAAATCAAAAAAGAATTCAAA-TTAAATCAATTTTGAGATTATAAAACCATTTAA
* * **
323 AATGAGTACTAAGGCTTTCGAAGA
314 AGTGAGTAATAAGGCTTTTAAAGA
* *
347 AATGGATGACTATAAATGGACTTTCCTTGCCAATGAATACTTTTTTCTATAG-GTTTCCCAAGGC
1 AATGGGTGACTATAAATGGACTTTCCTTGCCAATGAATACCTTTTTCT-TAGAGTTTCCCAAGGC
* * * *
411 AGACATTCAATTACAATCTGTTCGAACGAACAAGGTCAAAAAGTTCAACTTAAAATCAAATATGA
65 AAACATTCAATTATAATCTGTTCTAACCAA-AAGGTCAAAAA-TTCAACTTAAAATCAAATATGA
* * * * *
476 GATTATAAAACCCTTCAAATAGAGTAAGTAATAACGCTTCTGAAAGAATGAGTAACTATAAATAG
128 GATTATAAAA-CCTTC--ATAAAGTGAGTAATAAGGCTT-TGAAAGAATG-GTGACTATAAATGG
* * * *
541 AGTTTTCTTGTCAATGAATGCCTTTTTCCTCACATTTCTTAAGGTTGACAATTAATTATAATTTG
188 AGTTTTCTTG-CAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAGACATTTAATTATAATTTG
* * * * *
606 TTTTAACAAAAAATCCACAAAGAATTCAAATATAAATCAATTTCGAAATTATAAAACTATTTAAA
252 TTTTAA-AAAAAATCAAAAAAGAATTCAAAT-TAAATCAATTTTGAGATTATAAAACCATTTAAA
** * *
671 GTGAGTAATGTGCCTTTTAAAGT
315 GTGAGTAATAAGGCTTTTAAAGA
* * * * * **
694 AATGGGTAAATATAAATGGAC-TTCTCTTGCCAATAAATGCCTTTTTCTTTGAGTTT--GTAGAG
1 AATGGGTGACTATAAATGGACTTTC-CTTGCCAATGAATACCTTTTTCTTAGAGTTTCCCAAG-G
* * ** * * * * * *
756 CTAAACATTCAATTATAATATGTTTTAATTAAAAATGTAAAAAAATTTGATCTGAAAATCAATTA
64 C-AAACATTCAATTATAATCTGTTCTAA-CCAAAAGGT-CAAAAA-TTCAACTTAAAATCAAATA
* *
821 TGAGATTATAAAGCCATT--TAAAGTGAGTAACAAGGCGTTT-AAAGAAAATGGGTGACTATAAA
125 TGAGATTATAAAACC-TTCATAAAGTGAGTAATAAGGC-TTTGAAAG--AAT-GGTGACTATAAA
* * * * **
883 TGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACGTTTCTCGAGCAAGACATTTAATTAT-AT
185 TGGAGTTTTCTTG-CAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAGACATTTAATTATAAT
* * * * *
947 TATGTTTTAATGAAAAATGTAAAAAAAAATTTCAACTTAAAATAAATTTTGAGATTATAAAACCA
249 T-TGTTTTAA-AAAAAAT-CAAAAAAGAA-TTCAAATT-AAATCAATTTTGAGATTATAAAACCA
*
1012 TTTAAAGTGAGTAATAAGGCTTTTAAAGG
309 TTTAAAGTGAGTAATAAGGCTTTTAAAGA
* * * *
1041 AATGGGTGACTATTAATGGACCTTT-CTTGCCAATGAATACCTTTTTCTTTGCGTTTCTCAAGGC
1 AATGGGTGACTATAAATGGA-CTTTCCTTGCCAATGAATACCTTTTTCTTAGAGTTTCCCAAGGC
* ** * * * *
1105 AAACATTCAATTATAATCTGTTCAAACCAAAAAACATCAAAATATACATCTTAAAATCAATTATA
65 AAACATTCAATTATAATCTGTTCTAACC--AAAAGGTCAAAA-ATTCAACTTAAAATCAAATATG
* * * * * * * *
1170 AGGTTATGAAAA-CTAT-TTAAAATGAATAATAAGGTTTTTCAAGGAATGGGTGACTATAAATAG
127 AGATTAT-AAAACCT-TCATAAAGTGAGTAATAAGG-CTTTGAAAGAAT-GGTGACTATAAATGG
* * * * * * * *
1233 TGTTTTCTTGCTAATAAATGTCTTTTTCTTCACGTTCCTTGAGGTAGATATTCAATTATAATCTG
188 AGTTTTCTTGC-AATGAATGCCTTTTTCTTCACATTTCTTGAGGTAGACATTTAATTATAATTTG
* ** *
1298 TTTTAACCAAAAATGTATAAAGAATTCAAATTTAAATC
252 TTTTAA-AAAAAATCAAAAAAGAATTCAAA-TTAAATC
1336 NNNNNNNNNN
Statistics
Matches: 790, Mismatches: 153, Indels: 91
0.76 0.15 0.09
Matches are distributed among these distances:
343 6 0.01
344 130 0.16
345 94 0.12
346 30 0.04
347 451 0.57
348 71 0.09
349 8 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (337 bp):
AATGGGTGACTATAAATGGACTTTCCTTGCCAATGAATACCTTTTTCTTAGAGTTTCCCAAGGCA
AACATTCAATTATAATCTGTTCTAACCAAAAGGTCAAAAATTCAACTTAAAATCAAATATGAGAT
TATAAAACCTTCATAAAGTGAGTAATAAGGCTTTGAAAGAATGGTGACTATAAATGGAGTTTTCT
TGCAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAGACATTTAATTATAATTTGTTTTAAAAA
AAATCAAAAAAGAATTCAAATTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAA
GGCTTTTAAAGA
Found at i:953 original size:173 final size:171
Alignment explanation
Indices: 1--1323 Score: 863
Period size: 172 Copynumber: 7.6 Consensus size: 171
* * * * * *
1 GGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTTTTCACATTTC-CTAAG
1 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTTTTTCTTCACGTTTCTC-GA-
* * * * * * * * * * * *
65 GTAGACATTCAAGTATAATCTGTTTTAACCAGAAAGGTCAAAATA-TACAACCTAAAATAAATTA
64 GCAAACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAAATTTCATCTTAAAATCAATTA
* *
129 TGAGGTTATAAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAA
129 TGAGATTAT-AAAACCATTTAAAGTGAGTAATAAGGCTTTT-AAA
* * * * * * * * * ** *
174 -GAATTGGTGACGATAAGTGGAGTTTTCTTGCTAATAAATACTTTTTTATTGATATTTTTCGAGG
1 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTTTTTCTTCACGTTTCTCGA-G
* * * * * * * * * ** * *
238 TAGATATTTAATTATAATCTATTTTAAACAAAAATCTATAAAGAA-TTCAAATTTAAATCAATTT
65 CAAACATTCAATTATAATATGTTTTAACCAAAAATGTA-AAAAAATTTCATCTTAAAATCAATTA
* * * **
302 TGAGATTATAAAACCATTCAAAATGAGTACTAAGGCTTTCGAA
129 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * * * * * * * *
345 GAAATGGATGACTATAAATGGACTTTCCTTGCCAATGAATACTTTTTTCTAT-AGGTTTCCCAAG
1 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTTTTTCT-TCACGTTTCTCGA-
* * * ** * * * * * * *
409 GCAGACATTCAATTACAATCTGTTCGAACGAACAAGGT-CAAAAAGTTCAACTTAAAATCAAATA
64 GCAAACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAAATTTCATCTTAAAATCAATTA
* * * * *
473 TGAGATTATAAAACCCTTCAAATAGAGTAAGTAATAACGCTTCTGAAA
129 TGAGATTATAAAACCATT----TAAAGTGAGTAATAAGGCTT-TTAAA
* * * * * * * * **
521 -GAATGAGTAACTATAAATAGAGTTTTCTTGTCAATGAATGCCTTTTTCCTCACATTTCTTAAGG
1 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTTTTTCTTCACGTTTCTCGA-G
*** * * ** * **
585 TTGACAATT-AATTATAATTTGTTTTAACAAAAAATCCACAAAGAA-TTCA-AATATAAATCAAT
65 CAAAC-ATTCAATTATAATATGTTTTAACCAAAAATGTA-AAAAAATTTCATCTTA-AAATCAAT
* * ** *
647 T-TCGAAATTATAAAACTATTTAAAGTGAGTAATGTGCCTTTTAAA
127 TAT-GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * * * * * *
692 GTAATGGGTAAATATAAATGGACTTCTCTTGCCAATAAATGCCTTTTTCTTTGA-GTTTGTAGAG
1 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTTTTTC-TTCACGTTTCTCGAG
** * *
756 CTAAACATTCAATTATAATATGTTTTAATTAAAAATGTAAAAAAATTTGATCTGAAAATCAATTA
65 C-AAACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAAATTTCATCTTAAAATCAATTA
* * *
821 TGAGATTATAAAGCCATTTAAAGTGAGTAACAAGGCGTTTAAA
129 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * *
864 GAAAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACGTTTCTCGAG
1 G-GAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTTTTTCTTCACGTTTCTCGAG
* * ** * *
929 CAAGACATTTAATTATATTATGTTTTAATGAAAAATGTAAAAAAAAATTTCAACTTAAAATAAAT
65 CAA-ACATTCAATTATAATATGTTTTAACCAAAAATGT--AAAAAAATTTCATCTTAAAATCAAT
*
994 TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
127 TATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * * * ** *
1039 GGAATGGGTGACTATTAATGGACCTTTCTTGCCAATGAATACCTTTTTCTTTGCGTTTCTCAAGG
1 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTTTTTCTTCACGTTTCTCGA-G
* ** ** ** *
1104 CAAACATTCAATTATAATCTGTTCAAACCAAAAA-ACATCAAAATATACATCTTAAAATCAATTA
65 CAAACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAAAT-TTCATCTTAAAATCAATTA
* * * * * * *
1168 TAAGGTTATGAAAACTATTTAAAATGAATAATAAGGTTTTTCAA
129 TGAGATTAT-AAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* ** * * * *
1212 GGAATGGGTGACTATAAATAGTGTTTTCTTGCTAATAAATGTCTTTTTCTTCACGTTCCTTGAGG
1 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTTTTTCTTCACGTTTCTCGA-G
* * * * *
1277 TAGATATTCAATTATAATCTGTTTTAACCAAAAATGTATAAAGAATT
65 CAAACATTCAATTATAATATGTTTTAACCAAAAATGTA-AAAAAATT
1324 CAAATTTAAA
Statistics
Matches: 888, Mismatches: 229, Indels: 65
0.75 0.19 0.05
Matches are distributed among these distances:
170 4 0.00
171 53 0.06
172 335 0.38
173 222 0.25
174 81 0.09
175 157 0.18
176 32 0.04
177 4 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGCCTTTTTCTTCACGTTTCTCGAGC
AAACATTCAATTATAATATGTTTTAACCAAAAATGTAAAAAAATTTCATCTTAAAATCAATTATG
AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
Found at i:1164 original size:519 final size:517
Alignment explanation
Indices: 1--1220 Score: 1140
Period size: 519 Copynumber: 2.4 Consensus size: 517
1 GGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTT-TTTCACATTTC-CTAA
1 GGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTT-ACATTTCTC-AA
* * ** * *
64 GGTAGACATTCAAGTATAATCTGTTTTAACC-AGAAAGGTCAAAATATACAACCTAAAATAAATT
64 GGTAGACATTCAATTATAATCTGTTTTAACCAAAAAACATCAAAATATAC-ACATAAAATCAATT
** * * * * *
128 ATGAGGTTATAAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATTGGTGACGATAAGTG
128 ATGAAATTATAAAAATCATTTAAAGTGAGTAATAAGCCTTTTGAAAGAATGGGTAAAGATAAATG
* * * * * * * * * *
193 GAGTTTTCTTGCTAATAAATACTTTTTTATTGATATTTTTCGAGGTAGATATTTAATTATAATCT
193 GACTTCTCTTGCCAATAAATACTTTTTTATTGATATTTGTAGAGCTAAACATTCAATTATAATAT
* * *
258 ATTTTAAACAAAAATCTATAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTCAA
258 ATTTTAAACAAAAATCTATAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTCAA
*
323 AATGAGTACTAAGGCTTTCGAAGAAATGGATGACTATAAATGGACTTTCCTTGCCAATGAATACT
323 AATGAGTACTAAGGCTTTCAAAGAAATGGATGACTATAAATGGACTTTCCTTGCCAATGAATACT
* * * *
388 TTTTTCTATAGGTTTCCCAAGGCAGACATTCAATTACAATCTGTTCGAACGAACAAGGTCAAAAA
388 TTTTTCTATACGTTTCCCAAGGCAGACATTCAATTACAATATGTTCGAACGAAAAAGGTAAAAAA
* *
453 GTTCAACTTAAAATCAAATATGAGATTATAAAACCCTTCAAATAGAGTAAGTAATAACGCTTCTG
453 GTTCAACTTAAAATCAAATATGAGATTATAAAACCATT---ATAAAGTAAGTAATAACGCTTCTG
518 AAA
515 AAA
* * * * * * * *
521 -GAATGAGTAACTATAAATAGAGTTTTCTTGTCAATGAATGCCTTTTTCCTCACATTTCTTAAGG
1 GGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTTACATTTCTCAAGG
* * * *
585 TTGACAATT-AATTATAATTTGTTTTAA-CAAAAAATCCA-CAAAGA-ATTCAAATATAAATCAA
66 TAGAC-ATTCAATTATAATCTGTTTTAACCAAAAAA--CATCAAA-ATATACACATA-AAATCAA
* ** *
646 TT-TCGAAATTATAAAACT-ATTTAAAGTGAGTAATGTGCCTTTT-AAAGTAATGGGTAAATATA
126 TTAT-GAAATTATAAAAATCATTTAAAGTGAGTAATAAGCCTTTTGAAAG-AATGGGTAAAGATA
* *
708 AATGGACTTCTCTTGCCAATAAATGCCTTTTTCT-TTGA-GTTTGTAGAGCTAAACATTCAATTA
189 AATGGACTTCTCTTGCCAATAAAT-ACTTTTT-TATTGATATTTGTAGAGCTAAACATTCAATTA
* ** * ** *
771 TAATATGTTTTAATTAAAAATGTA-AAAAAATT-TGATCTGAAAATCAATTATGAGATTATAAAG
252 TAATATATTTTAAACAAAAATCTATAAAAAATTCAAAT-T-AAAATCAATTATGAGATTATAAAA
* * * *
834 CCATTTAAAGTGAGTAAC-AAGGCGTTT-AAAGAAAATGGGTGACTATAAATGGACTTTTCTTGC
315 CCATTCAAAATGAGT-ACTAAGGC-TTTCAAAG-AAATGGATGACTATAAATGGACTTTCCTTGC
* * * * * * ** *
897 CAATGAAT-GTCTTTTTCT-TCACGTTTCTCGA-GCAAGACATTTAATTATATTATGTTTTAATG
377 CAATGAATACT-TTTTTCTAT-ACGTTTCCCAAGGC-AGACATTCAATTACAATATGTTCGAACG
* * * *
959 AAAAATGTAAAAAAAAATTTCAACTTAAAAT-AAATTTTGAGATTATAAAACCATT-TAAAGTGA
439 AAAAAGGT---AAAAAAGTTCAACTTAAAATCAAA-TATGAGATTATAAAACCATTATAAAGTAA
* *
1022 GTAATAAGGCTT-TTAAA
500 GTAATAACGCTTCTGAAA
* * * * *
1039 GGAATGGGTGACTATTAATGGACCTTTCTTGCCAATGAATACCTTTTTCTTTGCGTTTCTCAAGG
1 GGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTTACATTTCTCAAGG
* * ** *
1104 CAAACATTCAATTATAATCTGTTCAAACCAAAAAACATCAAAATATACATCTTAAAATCAATTAT
66 TAGACATTCAATTATAATCTGTTTTAACCAAAAAACATCAAAATATACA-CATAAAATCAATTAT
* * * * ** * *
1169 -AAGGTTATGAAAA-CTATTTAAAATGAATAATAAGGTTTTTCAAGGAATGGGT
130 GAA-ATTATAAAAATC-ATTTAAAGTGAGTAATAAGCCTTTTGAAAGAATGGGT
1221 GACTATAAAT
Statistics
Matches: 556, Mismatches: 109, Indels: 70
0.76 0.15 0.10
Matches are distributed among these distances:
517 2 0.00
518 25 0.04
519 325 0.58
520 160 0.29
521 5 0.01
522 3 0.01
523 36 0.06
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (517 bp):
GGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTTACATTTCTCAAGG
TAGACATTCAATTATAATCTGTTTTAACCAAAAAACATCAAAATATACACATAAAATCAATTATG
AAATTATAAAAATCATTTAAAGTGAGTAATAAGCCTTTTGAAAGAATGGGTAAAGATAAATGGAC
TTCTCTTGCCAATAAATACTTTTTTATTGATATTTGTAGAGCTAAACATTCAATTATAATATATT
TTAAACAAAAATCTATAAAAAATTCAAATTAAAATCAATTATGAGATTATAAAACCATTCAAAAT
GAGTACTAAGGCTTTCAAAGAAATGGATGACTATAAATGGACTTTCCTTGCCAATGAATACTTTT
TTCTATACGTTTCCCAAGGCAGACATTCAATTACAATATGTTCGAACGAAAAAGGTAAAAAAGTT
CAACTTAAAATCAAATATGAGATTATAAAACCATTATAAAGTAAGTAATAACGCTTCTGAAA
Found at i:2628 original size:172 final size:170
Alignment explanation
Indices: 2422--2952 Score: 485
Period size: 172 Copynumber: 3.1 Consensus size: 170
2412 NNNNNNNNNN
* *
2422 TAATAAGGCTTCTGAA-AGAATGGGTGACTATAAATAGAGTTTCCTTACCAATGAATGCCTTTTT
1 TAATAAGGATTTTGAAGA-AATGGGTGACTATAAAT-GA-TTTCCTTACCAATGAATGCCTTTTT
* * * * **********
2486 CTTTACGTTTCTTGAGGTTGACATTCAATTATAATCTGTTTTAGCAAAAAATNNNNNNNNNNTTC
63 CTTTACGTTTCTCGAGCTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTCAAAAAATTTC
* *
2551 AAATTTAAATCAATTTTA-AGATTATAAAACCATTTAAAGTGAG
128 AAATTAAAATCAA-TTAAGAGATTATAAAACCATTTAAAGTGAG
* * * * * *
2594 TAATATGGCTTTT-AATGTAATGGGTGAATATAAATGTACTTCTCTTACCAAGGAATGCCTTTTT
1 TAATAAGGATTTTGAA-GAAATGGGTGACTATAAATG-ATTTC-CTTACCAATGAATGCCTTTTT
* * * * * * * * * *
2658 ATTCATGTTTGTCGAGCTAAACATTCAATAATAATATGTTTTAACCAAATATGTCAAAAAATTTG
63 CTTTACGTTTCTCGAGCTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTCAAAAAATTTC
* *
2723 AACTTAAAATCAATTAAGAGATTATAAAACCGTTTAAAGTGAG
128 AAATTAAAATCAATTAAGAGATTATAAAACCATTTAAAGTGAG
* * * *
2766 TAATAAGGATTTTGAAGAAATGGGTGACTATATATGGACTTTTCTTGCCAATGAATGCCCTTTTC
1 TAATAAGGATTTTGAAGAAATGGGTGACTATAAAT-GA-TTTCCTTACCAATGAATGCCTTTTTC
* * **
2831 TTTACGTTTCTCGAGCTAGACATTCAATTACAATCTATTTTAATGAAAAATGTAAACAAAAAA-T
64 TTTACGTTTCTCGAGCTAGACATTCAATTATAATCTGTTTTAACAAAAAATGT---CAAAAAATT
* * **
2895 TCAAGTTAAAATAAATTTTGAGATTATAAAACCATTTAAAGTGAG
126 TCAAATTAAAATCAATTAAGAGATTATAAAACCATTTAAAGTGAG
*
2940 TAATAAGGCTTTT
1 TAATAAGGATTTT
2953 ANNNNNNNNN
Statistics
Matches: 285, Mismatches: 63, Indels: 20
0.77 0.17 0.05
Matches are distributed among these distances:
171 9 0.03
172 212 0.74
173 5 0.02
174 52 0.18
175 7 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
TAATAAGGATTTTGAAGAAATGGGTGACTATAAATGATTTCCTTACCAATGAATGCCTTTTTCTT
TACGTTTCTCGAGCTAGACATTCAATTATAATCTGTTTTAACAAAAAATGTCAAAAAATTTCAAA
TTAAAATCAATTAAGAGATTATAAAACCATTTAAAGTGAG
Found at i:4308 original size:172 final size:170
Alignment explanation
Indices: 4044--5101 Score: 854
Period size: 172 Copynumber: 6.2 Consensus size: 170
4034 TAAAAAAGTC
* * * * **
4044 AAAAAGTTCAACTTAAAATTAAGTTTTGAGATTATAAAACCCTTTAAAGTGACTAATGTGGCTTT
1 AAAAATTTCAACTTAAAATCAA-TTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * * * * * * * *
4109 CAATGTAATGGGTGAATGTAAATGGACTTCTCTTGCTAATGAATGCCTTTTTATTCATGTTTGTC
65 TAAAGAAATGGGTGACTATAAATGGACTT-TCTTGCCAATGAATACCTTTTTCTT-ATGTTTCTC
* *
4174 GA-GCTAAACATTCAATTATCATATGTTTTAACCAAAAATGTAA
128 AAGGC-AAACATTCAATTATCATCTGTTTTAACCAAAAATGTAA
* * * *
4217 AAAAATTTGAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGTGAGTAATAAGGATTTT
1 AAAAATTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
* * * **
4282 GAAGAAATGAGG-GACTATAGATGGACTTTTCTTGCCAATGAATTCCTTTTTCTTTACATTTCTC
66 AAAGAAATG-GGTGACTATAAATGGAC-TTTCTTGCCAATGAATACCTTTTTC-TTATGTTTCTC
* * * * **
4346 GA-GCTAGACATTCTATTATAATCTGTTTTAATAAAAAATGTAAA
128 AAGGC-AAACATTCAATTATCATCTGTTTTAACCAAAAATGT-AA
* * * *
4390 CAAAAAATTCAACTTAAAATAAATTTTGAGATTATAAAACCATTTAAAGTGAGTAGTAAAGCTTT
1 -AAAAATTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * * *
4455 TAAAGGAGTGGGTGACTATTAATGGACGTTTCTTGCCAATGAATACCTTTTTCTTTTCGTTTCTC
65 TAAAGAAATGGGTGACTATAAATGGAC-TTTCTTGCCAATGAATACCTTTTTCTTAT-GTTTCTC
* * * * ** *
4520 AAGGCAAACGTTTAATTATAATCTGTTTAAACCAAAAA-ACAT
128 AAGGCAAACATTCAATTATCATCTGTTTTAACCAAAAATGTAA
* * * * * * * * * *
4562 CAAAATATACATCCTAAAATAAATTATGAGGTTATAAAAACTATTTAAAATGAATAATAAGGCTT
1 AAAAAT-TTCAACTTAAAATCAATTTTGAGATTAT-AAAACCATTTAAAGTGAGTAATAAGGCTT
* * * * * * *
4627 TTAAAGGAATGGGTGACTATAAATGG----TGTTGCTAATAAATACCTTTTTCTTTACGTTCCTT
64 TTAAAGAAATGGGTGACTATAAATGGACTTTCTTGCCAATGAATACCTTTTTC-TTATGTTTCTC
* * * * * *
4688 GAGGTAGACATTAAATTATAATCTGTTTTAACAAAAAATGTACA
128 AAGGCAAACATTCAATTATCATCTGTTTTAACCAAAAATGTA-A
* * ** *
4732 AAGAA-TTCAAAGTT-AAATCAATTTTGAGATTATAAAACCATTTAAAACGAGTAATAAGGATTT
1 AAAAATTTC-AACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT
* * ** * * * * * *
4795 CAAAGGAATATGTGGCTATAAATAGACTTTTCTTGACAATGAATGCCTTTTTCTTTTCGTTTCTT
65 TAAAGAAATGGGTGACTATAAATGGAC-TTTCTTGCCAATGAATACCTTTTTCTTAT-GTTTCTC
* * * **
4860 AAGGCAGACATTCAATTAT-AGCCTTTTTTAGTCAAAAATG-AA
128 AAGGCAAACATTCAATTATCA-TCTGTTTTAACCAAAAATGTAA
* *
4902 AAAAA--TCAACTTAAAATCGATTTTGAGATTATAAAGCCATTTAAAGTGAGTAATAAGGCTTTC
1 AAAAATTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTT-
* * * * *
4965 GAAA-AAATGAGTGACTATAAATGGACTCTTCTTGCCAATGAATATCTTTTTCTATAGGTTTCCC
65 TAAAGAAATGGGTGACTATAAATGGACT-TTCTTGCCAATGAATACCTTTTTCT-TATGTTTCTC
* * * *
5029 AAGGCAAACATTCAATTA-CAATCTGTTCTAACTAAAAAGGT-C
128 AAGGCAAACATTCAATTATC-ATCTGTTTTAACCAAAAATGTAA
* *
5071 AAAAAGTTCAACTTAAAATCAATTATGAGAT
1 AAAAATTTCAACTTAAAATCAATTTTGAGAT
Statistics
Matches: 701, Mismatches: 154, Indels: 62
0.76 0.17 0.07
Matches are distributed among these distances:
167 46 0.07
168 79 0.11
169 129 0.18
170 13 0.02
171 30 0.04
172 191 0.27
173 79 0.11
174 132 0.19
175 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
AAAAATTTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTT
AAAGAAATGGGTGACTATAAATGGACTTTCTTGCCAATGAATACCTTTTTCTTATGTTTCTCAAG
GCAAACATTCAATTATCATCTGTTTTAACCAAAAATGTAA
Found at i:4715 original size:168 final size:169
Alignment explanation
Indices: 4230--5055 Score: 486
Period size: 174 Copynumber: 4.8 Consensus size: 169
4220 AATTTGAACT
* * * * * * * *
4230 TAAAATCAATTATGAAATTATAAAACCATTTAAAGTGAGTAATAAGGATTTTGAAGAAATGAGG-
1 TAAAATAAATTATGAGATTATAAAACCATTTAAAATGAATAATAAAGCTTTTAAAGGAATG-GGT
* * * * * * * *
4294 GACTATAGATGGACTTTTCTTGCCAATGAATTCCTTTTTCTTTACATTTCTCGA-GCTAGACATT
65 GACTATAAATGGA--GTTCTTGCCAATAAATACCTTTTTCTTTACGTTCCTCAAGGC-AAACATT
** * * * * * * * *
4358 CTATTATAATCTGTTTTAATAAAAAATGTAAACAAAAAATTCAACT
127 AAATTATAATCTGTTTAAACAAAAAA---CATCAAAATATACATCC
* * * * *
4404 TAAAATAAATTTTGAGATTATAAAACCATTTAAAGTGAGTAGTAAAGCTTTTAAAGGAGTGGGTG
1 TAAAATAAATTATGAGATTATAAAACCATTTAAAATGAATAATAAAGCTTTTAAAGGAATGGGTG
* * * * * *
4469 ACTATTAATGGACGTTTCTTGCCAATGAATACCTTTTTCTTTTCGTTTCTCAAGGCAAACGTTTA
66 ACTATAAATGGA-G-TTCTTGCCAATAAATACCTTTTTCTTTACGTTCCTCAAGGCAAACATTAA
4534 ATTATAATCTGTTTAAACCAAAAAACATCAAAATATACATCC
129 ATTATAATCTGTTTAAA-CAAAAAACATCAAAATATACATCC
* * *
4576 TAAAATAAATTATGAGGTTATAAAAACTATTTAAAATGAATAATAAGGCTTTTAAAGGAATGGGT
1 TAAAATAAATTATGAGATTAT-AAAACCATTTAAAATGAATAATAAAGCTTTTAAAGGAATGGGT
* * ** * *
4641 GACTATAAAT-G-G-TGTTGCTAATAAATACCTTTTTCTTTACGTTCCTTGAGGTAGACATTAAA
65 GACTATAAATGGAGTTCTTGCCAATAAATACCTTTTTCTTTACGTTCCTCAAGGCAAACATTAAA
* ** * ***
4703 TTATAATCTGTTTTAACAAAAAATGTACAAAGA-ATTCAAAG
130 TTATAATCTGTTTAAACAAAAAACAT-CAAA-ATATACATCC
* * * * * * * * **
4744 TTAAATCAATTTTGAGATTATAAAACCATTTAAAACGAGTAATAAGGATTTCAAAGGAATATGTG
1 TAAAATAAATTATGAGATTATAAAACCATTTAAAATGAATAATAAAGCTTTTAAAGGAATGGGTG
* * * * * * * * * * *
4809 GCTATAAATAGACTTTTCTTGACAATGAATGCCTTTTTCTTTTCGTTTCTTAAGGCAGACATTCA
66 ACTATAAATGGA--GTTCTTGCCAATAAATACCTTTTTCTTTACGTTCCTCAAGGCAAACATTAA
** * ** ** * * *
4874 ATTATAGCCTTTTTTAGTCAAAAATGA--AAAAAAT-CAACT
129 ATTATAATC-TGTTTAAACAAAAAACATCAAAATATACATCC
** * * * * * * * *
4913 TAAAATCGATTTTGAGATTATAAAGCCATTTAAAGTGAGTAATAAGGCTTTCGAAA-AAATGAGT
1 TAAAATAAATTATGAGATTATAAAACCATTTAAAATGAATAATAAAGCTTT-TAAAGGAATGGGT
* * * * *
4977 GACTATAAATGGACTCTTCTTGCCAATGAATATCTTTTTCTATAGGTTTCC-CAAGGCAAACATT
65 GACTATAAATGGA--GTTCTTGCCAATAAATACCTTTTTCTTTACG-TTCCTCAAGGCAAACATT
* *
5041 CAATTACAATCTGTT
127 AAATTATAATCTGTT
5056 CTAACTAAAA
Statistics
Matches: 520, Mismatches: 116, Indels: 38
0.77 0.17 0.06
Matches are distributed among these distances:
167 53 0.10
168 83 0.16
169 111 0.21
170 12 0.02
172 77 0.15
173 58 0.11
174 118 0.23
175 8 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
TAAAATAAATTATGAGATTATAAAACCATTTAAAATGAATAATAAAGCTTTTAAAGGAATGGGTG
ACTATAAATGGAGTTCTTGCCAATAAATACCTTTTTCTTTACGTTCCTCAAGGCAAACATTAAAT
TATAATCTGTTTAAACAAAAAACATCAAAATATACATCC
Found at i:5092 original size:340 final size:337
Alignment explanation
Indices: 4009--5101 Score: 1028
Period size: 340 Copynumber: 3.2 Consensus size: 337
3999 NNNNNNNNNN
* * * *
4009 ACATTCAATTACAATATTTTCTAACTAAAAAAGT-CAAAAAGTTCAACTTAAAATTAAGTTTTGA
1 ACATTCAATTACAATCTGTTCTAACTAAAAATGTACAAAAAGTTCAACTTAAAATCAA-TTTTGA
* * ** * * * *
4073 GATTATAAAACCCTTTAAAGTGACTAATGTGGCTTTCAATGTAATGGGTGAATGTAAATGGACTT
65 GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGAATGGGTGACTATAAATGGACTT
* * * * * *
4138 CTCTTGCTAATGAATGCCTTTTTATTCAT-GTTTGTCGA-GCTAAACATTCAATTAT-CATATGT
130 TTCTTGC-AATGAATGCCTTTTTCTT-TTCGTTTCTCAAGGC-AAACATTCAATTATACCT-T-T
* *
4200 TTTAACCAAAAATGTAAAAAAATTTGAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAG
190 TTTAACCAAAAATG-AAAAAAA--TCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
* * * *
4265 TGAGTAATAAGGATTTTGAAGAAATGAGGGACTATAGATGGACTTTTCTTGCCAATGAAT-TCCT
252 TGAGTAATAAGG-CTTTGAAAAAATGAGTGACTATAAATGGAC-TTTCTTGCCAATGAATAT-CT
* *
4329 TTTTCTTTACATTTCTCGA-GCTAG
314 TTTTCTTTACGTTTCCCGAGGC-AG
* * * * *
4353 ACATTCTATTATAATCTGTTTTAA-TAAAAAATGTAAACAAAAAATTCAACTTAAAATAAATTTT
1 ACATTCAATTACAATCTGTTCTAACT-AAAAATGT--ACAAAAAGTTCAACTTAAAATCAATTTT
* * * * *
4417 GAGATTATAAAACCATTTAAAGTGAGTAGTAAAGCTTTTAAAGGAGTGGGTGACTATTAATGGAC
63 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGAATGGGTGACTATAAATGGAC
* * * * * *
4482 GTTTCTTGCCAATGAATACCTTTTTCTTTTCGTTTCTCAAGGCAAACGTTTAATTATAATCTGTT
128 TTTTCTTG-CAATGAATGCCTTTTTCTTTTCGTTTCTCAAGGCAAACATTCAATTAT-ACCTTTT
* ** * * * * * * *
4547 TAAACCAAAAAACATCAAAATATACATCCTAAAATAAATTATGAGGTTATAAAAACTATTTAAAA
191 TTAACCAAAAATGA--AAAAAAT-CAACTTAAAATCAATTATGAGATTAT-AAAACCATTTAAAG
* * * * * * * *
4612 TGAATAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGG----TGTTGCTAATAAATACCTTT
252 TGAGTAATAAGGCTTTGAAA-AAATGAGTGACTATAAATGGACTTTCTTGCCAATGAATATCTTT
* *
4673 TTCTTTACG-TTCCTTGAGGTAG
316 TTCTTTACGTTTCC-CGAGGCAG
* * * * *
4695 ACATTAAATTATAATCTGTTTTAACAAAAAATGTACAAAGAA-TTCAAAGTT-AAATCAATTTTG
1 ACATTCAATTACAATCTGTTCTAACTAAAAATGTACAAA-AAGTTC-AACTTAAAATCAATTTTG
** * ** * *
4758 AGATTATAAAACCATTTAAAACGAGTAATAAGGATTTCAAAGGAATATGTGGCTATAAATAGACT
64 AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGAATGGGTGACTATAAATGGACT
* *
4823 TTTCTTGACAATGAATGCCTTTTTCTTTTCGTTTCTTAAGGCAGACATTCAATTATAGCCTTTTT
129 TTTCTTG-CAATGAATGCCTTTTTCTTTTCGTTTCTCAAGGCAAACATTCAATTATA-CCTTTTT
** * * *
4888 TAGTCAAAAATGAAAAAAATCAACTTAAAATCGATTTTGAGATTATAAAGCCATTTAAAGTGAGT
192 TAACCAAAAATGAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGT
4953 AATAAGGCTTTCGAAAAAATGAGTGACTATAAATGGACTCTTCTTGCCAATGAATATCTTTTTCT
257 AATAAGGCTTT-GAAAAAATGAGTGACTATAAATGGACT-TTCTTGCCAATGAATATCTTTTTCT
* * * *
5018 ATAGGTTTCCCAAGGCAA
320 TTACGTTTCCCGAGGCAG
* *
5036 ACATTCAATTACAATCTGTTCTAACTAAAAAGGT-CAAAAAGTTCAACTTAAAATCAATTATGAG
1 ACATTCAATTACAATCTGTTCTAACTAAAAATGTACAAAAAGTTCAACTTAAAATCAATTTTGAG
5100 AT
66 AT
Statistics
Matches: 596, Mismatches: 123, Indels: 64
0.76 0.16 0.08
Matches are distributed among these distances:
336 44 0.07
337 23 0.04
338 6 0.01
339 7 0.01
340 156 0.26
341 65 0.11
342 61 0.10
343 2 0.00
344 26 0.04
345 3 0.01
346 134 0.22
347 68 0.11
348 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (337 bp):
ACATTCAATTACAATCTGTTCTAACTAAAAATGTACAAAAAGTTCAACTTAAAATCAATTTTGAG
ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGAATGGGTGACTATAAATGGACTTT
TCTTGCAATGAATGCCTTTTTCTTTTCGTTTCTCAAGGCAAACATTCAATTATACCTTTTTTAAC
CAAAAATGAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATA
AGGCTTTGAAAAAATGAGTGACTATAAATGGACTTTCTTGCCAATGAATATCTTTTTCTTTACGT
TTCCCGAGGCAG
Done.