Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399714.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_296.0, 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: 8264
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.27
Warning! 1966 characters in sequence are not A, C, G, or T
Found at i:752 original size:171 final size:171
Alignment explanation
Indices: 210--1694 Score: 1648
Period size: 172 Copynumber: 8.7 Consensus size: 171
200 NNNNNNNNNN
* * * * * *
210 AAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTTTGAAGGTAGAGATTCAATCCT
1 AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCT
* * * * *
275 A-ACTTGTTTTAACCAAAAATGCACTAAGAATTCTAATTTAAATCAATTTTGAGATTATAAAACC
66 AGTC-TG-TTTAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACC
339 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-AGGTGACTAT
129 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGA-GTGACTAT
* ** * * ** *
382 AAATGGACTTCTCTTATCAATGAATGCCTTTTTCTTTACGTTTCTTGAGGTAGACATTCAATTAT
1 AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCT
* ** * * * * ** *
447 AGTCTCTTTAACAAAAAAAATAAAAAAAAAATTCAACTTAAAATCAA-TTACAGCATTACAAAAC
66 AGTCTGTTTAAC--AAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAG-ATTATAAAAC
* * *
511 CATTTAAAGTGAGTAATAATGCTTTTGAAGGTATGGGTGACTAT
128 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
* * *
555 AAATGTACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTCT
1 AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCT
* *
620 AGTATGTTGTAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACTA
66 AGTCTGTT-TAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCA
*
685 TTTAGAGTGAGTAATAA-GCTTTTGAAGGAATGAGTGACTAT
130 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
* * * * * *
726 AAATGGACTTTTCTTACCACTGAATGCCTTTTGCTTTATGTTTCTCAAGGTAGAAATTCAATTAT
1 AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCT
* * *
791 AGTTTGTTTTAACAAAAAATGTATAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAACCCA
66 AGTCTG-TTTAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCA
*
856 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
130 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
** * * * * * *
898 AAATGGACTTCCCTTGCCAATGAATGCCGTTTTCTTTATGTTTCTCAATGTACATATTCAATTAT
1 AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCT
* * * ** ** * **
963 AGTCTGTTTAACAAAAAATATA-AAAAAATTTAAATGAAAATCAATTACG-GTATTACAAATTCA
66 AGTCTGTTTAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAG-ATTATAAAACCA
** * *
1026 TTTAAAACGAGTAATAAGGCTTTTGAAGGTATGAGTAACTAT
130 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
* *
1068 AAATGGACTTTTCTTGCCAACGAATG-CTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATTCT
1 AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCT
* * *
1132 AGTCTGTTTTAACTAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGAGTATAAAAACA
66 AGTCTG-TTTAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCA
* * * *
1197 TTTAAATTGACTAATAAAGCTTTTGAAGGAATGTGTGACTAT
130 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
* * * * * * *
1239 AAATGGACTTTTTTTACCAATGAATACTTTTTTCTTCTTGTTTGTCAGGGTAGACATTCAATTCT
1 AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCT
* * * * *
1304 AGTCTATTTAAAAAAAAAATGTACAAA-ATTTTCAAATTTAACTAAATTTTGAGATTATAAAACC
66 AGTCTGTTT-AACAAAAAATGTACAAAGA-ATTCAAATTTAAATCAATTTTGAGATTATAAAACC
* * *
1368 ATTTAAACT-AGGTAATAAGGCTCTTGAAGGAATGGGTGACTAT
129 ATTTAAAGTGA-GTAATAAGGCTTTTGAAGGAATGAGTGACTAT
* * * * * *
1411 AAATGGACTTTTCTTGCCAATAAAT-ACTTTTTACTTCATGTTTCTGAATGTAGACATTTAATCC
1 AAATGGACTTTTCTTGCCAATGAATGCCTTTTT-CTTCATGTTTCTCAAGGTAGACATTCAATTC
* * * *
1475 TAGTATGTTTTAACTAAAAATGTACACAA-TATTCAAATTTAAATCAATTTTGAGATTACAAAAC
65 TAGTCTG-TTTAACAAAAAATGTACA-AAGAATTCAAATTTAAATCAATTTTGAGATTATAAAAC
* * *
1539 CATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATAAGTGGCTAT
128 CATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
* * * *
1583 AAA-GCGACTTCTCTTGCCAACGAATGCCTTTTTCTTTATGTTTCTCAAGCTAGAC-TCTCAATT
1 AAATG-GACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACAT-TCAATT
* * * * * *
1646 ATAGTCTATTTAACAAAAAATATA-AAAAATATTCAACTTAAAATCAATT
64 CTAGTCTGTTTAACAAAAAATGTACAAAGA-ATTCAAATTTAAATCAATT
1695 ACGGCATTAC
Statistics
Matches: 1095, Mismatches: 192, Indels: 53
0.82 0.14 0.04
Matches are distributed among these distances:
169 40 0.04
170 105 0.10
171 302 0.28
172 494 0.45
173 150 0.14
174 4 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (171 bp):
AAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCT
AGTCTGTTTAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCAT
TTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGACTAT
Found at i:1340 original size:513 final size:509
Alignment explanation
Indices: 210--1694 Score: 1836
Period size: 513 Copynumber: 2.9 Consensus size: 509
200 NNNNNNNNNN
* * * * * *
210 AAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTTTGAAGGTAGAGATTCAATCCT
1 AAATGGACTTTTCTTACCAATGAATACTTTTTTCTTCTTGTTTCTCAAGGTAGAAATTCAATTCT
* * * *
275 A-ACTTGTTTTAACCAAAAATGCACTAAGAATTCTAATTTAAATCAATTTTGAGATTATAAAACC
66 AGTC-TGTTTTAACAAAAAATGTAC-AA-AATTCAAATTTAAATCAATTTTGAGATTATAAAACC
* **
339 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTCTCTTATCAATG
128 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTCTCTTGCCAATG
* ** * *
404 AATGCCTTTTTCTTTACGTTTCTTGAGGTAGACATTCAATTATAGTCTCTTTAACAAAAAAAATA
193 AATGCCTTTTTCTTTATGTTTCTCAATGTAGACATTCAATTATAGTCTGTTTAAC--AAAAAAT-
* * * *
469 AAAAAAAAATTCAACTTAAAATCAATTACAGCATTACAAAACCATTTAAAGTGAGTAATAATGCT
255 ATAAAAAAATTCAAATTAAAATCAATTAC-GGATTACAAAACCATTTAAAGTGAGTAATAAGGCT
* * *
534 TTTGAAGGTATGGGTGACTATAAATGTACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTC
319 TTTGAAGGTATGAGTGACTATAAATGGACTTTTCTTGCCAACGAATGC-TTTTTCTTCATGTTTC
* * *
599 TCATGGTAGACATTCAATTCTAGTATGTTGTAACAAAAAATGTACAAAGAATTCAAATTTAAATC
383 TCAAGGTAGACATTCAATTCTAGTCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTTAAATC
* * *
664 AATTTTGAGATTATAAAACTATTTAGAGTGAGTAATAAGCTTTTGAAGGAATGAGTGACTAT
448 AATTTTGAGAGTATAAAACTATTTAAAGTGACTAATAAGCTTTTGAAGGAATGAGTGACTAT
* * * * *
726 AAATGGACTTTTCTTACCACTGAATGCCTTTTGCTT-TATGTTTCTCAAGGTAGAAATTCAATTA
1 AAATGGACTTTTCTTACCAATGAATACTTTTTTCTTCT-TGTTTCTCAAGGTAGAAATTCAATTC
* * *
790 TAGTTTGTTTTAACAAAAAATGTATAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAACCC
65 TAGTCTGTTTTAACAAAAAATGTA-CAA-AATTCAAATTTAAATCAATTTTGAGATTATAAAACC
*
855 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTCCCTTGCCAATG
128 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTCTCTTGCCAATG
* * *
920 AATGCCGTTTTCTTTATGTTTCTCAATGTACATATTCAATTATAGTCTGTTTAACAAAAAATATA
193 AATGCCTTTTTCTTTATGTTTCTCAATGTAGACATTCAATTATAGTCTGTTTAACAAAAAATATA
* * ** **
985 AAAAAATTTAAATGAAAATCAATTACGGTATTACAAATTCATTTAAAACGAGTAATAAGGCTTTT
258 AAAAAATTCAAATTAAAATCAATTACGG-ATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTT
* *
1050 GAAGGTATGAGTAACTATAAATGGACTTTTCTTGCCAACGAATGCTTTTTCTTCATGTTTCTGAA
322 GAAGGTATGAGTGACTATAAATGGACTTTTCTTGCCAACGAATGCTTTTTCTTCATGTTTCTCAA
*
1115 GGTAGACATTCAATTCTAGTCTGTTTTAACTAAAAATGTACAAAGAATTCAAATTTAAATCAATT
387 GGTAGACATTCAATTCTAGTCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATT
* *
1180 TTGAGAGTATAAAAAC-ATTTAAATTGACTAATAAAGCTTTTGAAGGAATGTGTGACTAT
452 TTGAGAGTAT-AAAACTATTTAAAGTGACTAAT-AAGCTTTTGAAGGAATGAGTGACTAT
* * * *
1239 AAATGGACTTTTTTTACCAATGAATACTTTTTTCTTCTTGTTTGTCAGGGTAGACATTCAATTCT
1 AAATGGACTTTTCTTACCAATGAATACTTTTTTCTTCTTGTTTCTCAAGGTAGAAATTCAATTCT
* * * * *
1304 AGTCTATTTAAAAAAAAAATGTACAAAATTTTCAAATTTAACTAAATTTTGAGATTATAAAACCA
66 AGTCTGTTTTAACAAAAAATGTACAAAA--TTCAAATTTAAATCAATTTTGAGATTATAAAACCA
* * * *
1369 TTTAAACT-AGGTAATAAGGCTCTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATA
129 TTTAAAGTGA-GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTCTCTTGCCAATG
* * * * ** * * *
1433 AAT-ACTTTTTACTTCATGTTTCTGAATGTAGACATTTAATCCTAGTATGTTTTAACTAAAAATG
193 AATGCCTTTTT-CTTTATGTTTCTCAATGTAGACATTCAATTATAGTCTG-TTTAACAAAAAATA
* * * **
1497 TACACAATATTCAAATTTAAATCAATTTTGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCT
256 TA-AAAAAATTCAAATTAAAATCAATTACG-GATTACAAAACCATTTAAAGTGAGTAATAAGGCT
* * * * * *
1562 TTTAAAGGAATAAGTGGCTATAAA-GCGACTTCTCTTGCCAACGAATGCCTTTTTCTTTATGTTT
319 TTTGAAGGTATGAGTGACTATAAATG-GACTTTTCTTGCCAACGAATG-CTTTTTCTTCATGTTT
* * * * * * *
1626 CTCAAGCTAGAC-TCTCAATTATAGTCT-ATTTAACAAAAAATATA-AAAAATATTCAACTTAAA
382 CTCAAGGTAGACAT-TCAATTCTAGTCTGTTTTAACAAAAAATGTACAAAGA-ATTCAAATTTAA
1688 ATCAATT
445 ATCAATT
1695 ACGGCATTAC
Statistics
Matches: 836, Mismatches: 115, Indels: 37
0.85 0.12 0.04
Matches are distributed among these distances:
511 2 0.00
512 111 0.13
513 322 0.39
514 27 0.03
515 120 0.14
516 254 0.30
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (509 bp):
AAATGGACTTTTCTTACCAATGAATACTTTTTTCTTCTTGTTTCTCAAGGTAGAAATTCAATTCT
AGTCTGTTTTAACAAAAAATGTACAAAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATT
TAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTCTCTTGCCAATGAAT
GCCTTTTTCTTTATGTTTCTCAATGTAGACATTCAATTATAGTCTGTTTAACAAAAAATATAAAA
AAATTCAAATTAAAATCAATTACGGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
GTATGAGTGACTATAAATGGACTTTTCTTGCCAACGAATGCTTTTTCTTCATGTTTCTCAAGGTA
GACATTCAATTCTAGTCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGA
GAGTATAAAACTATTTAAAGTGACTAATAAGCTTTTGAAGGAATGAGTGACTAT
Found at i:2468 original size:172 final size:171
Alignment explanation
Indices: 2135--2474 Score: 401
Period size: 172 Copynumber: 2.0 Consensus size: 171
2125 NNNNNNNNNN
* * ** * *
2135 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATTAATACTTTTTTCCTCATGTTTGTC
1 TGAAGGAATGAGTCACTATAAATGGACTTTTCTTGCCAAAGAATACTTTTTTCCTCATGTTTCTA
* * * * * *
2200 ATGGTAGACATCAATTCTAGTCTATTCTAACCAAAAATGCATAAAACATTCAAATTTAAATCAAT
66 AAGGTAGACATCAATCCTAGTCTATTCTAACCAAAAATGCACAAAAAATTCAAAGTCAAATCAAT
********** *
2265 TTNNNNNNNNNNAAACCATTTAAACTGAGTAATAAGGCCCT
131 TTTGAGATTATAAAACCATTTAAAATGAGTAATAAGGCCCT
* * *
2306 TGAAGGAATGAGTCATTATAAATGGACTTTTCTTGCCAAAGAATACTTTTTTCTTCTTGTTTCTA
1 TGAAGGAATGAGTCACTATAAATGGACTTTTCTTGCCAAAGAATACTTTTTTCCTCATGTTTCTA
* * **
2371 AAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATTTACAAAAAATTCAAAGTCAAATCAA
66 AAGGTAGACA-TCAATCCTAGTCTATTCTAACCAAAAATGCACAAAAAATTCAAAGTCAAATCAA
2436 TTTTGAGATTATAAAACCATTTAAAATGAGTAATAAGGC
130 TTTTGAGATTATAAAACCATTTAAAATGAGTAATAAGGC
2475 TTTTGANNNN
Statistics
Matches: 138, Mismatches: 30, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
171 65 0.47
172 73 0.53
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.34
Consensus pattern (171 bp):
TGAAGGAATGAGTCACTATAAATGGACTTTTCTTGCCAAAGAATACTTTTTTCCTCATGTTTCTA
AAGGTAGACATCAATCCTAGTCTATTCTAACCAAAAATGCACAAAAAATTCAAAGTCAAATCAAT
TTTGAGATTATAAAACCATTTAAAATGAGTAATAAGGCCCT
Found at i:3248 original size:171 final size:171
Alignment explanation
Indices: 2652--4015 Score: 1172
Period size: 171 Copynumber: 8.0 Consensus size: 171
2642 NNNNNNNNNN
* * * * ** * * ** *
2652 AATTCAACTTAAAATCAATTATG-GCATTACAAAATTATTTAAAGCGAGTAATAATGCTTTCGAG
1 AATTCAAATTTAAATCAATTTTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * *
2716 GGTATGGGTGACTAT-AATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTGAAGG
65 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT-GCTTTTTTTTCATGTTTCTGAAGG
* * * * * *
2780 TAGACATTCCATCCA-AGTCTGTTTGAA-AGAAAAATGTACAAAG
129 TAGACATTCAAT-TATAGTCTGTTTTAACA-AAAAATATAAAAAA
* * *
2823 AATTCAAATTTAAATCAATTTTGAGATTATAAAACTAATTAAAGTTAGTAATAAGGCTTTTAAAG
1 AATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAG
* * * *
2888 GATTGGATGACTATAAATGGACTTTTCTTGCCAATGAATGCTCTCTTCTTTATC-TTTTTC-G-G
66 GAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCT-T-TT-TTT-TCATGTTTCTGAA
* * * *
2950 GGTAGACGTTCAATTATAATATGTTTTAACTAGAAAAACA-AAAAAA
127 GGTAGACATTCAATTATAGTCTGTTTTAAC-A-AAAAATATAAAAAA
* * * * * * *
2996 AACTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTCTTGAAG
1 AATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAG
* * * *
3061 GAATGGGT-AGCTATAAATGGACTTTTCTTGCCAATTAATACTTTTTTTTCACGTCTCTGAAGGT
66 GAATGGGTGA-CTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTTTCATGTTTCTGAAGGT
* ** * *
3125 AAACATTCAATCCTAGTCTGTTTTAACCAAAAATACAAAAAA
130 AGACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAA
* * * * * * *
3167 AATCCAAATTTAATTCAATTTTGAGAATATACAACCATTCAAAGTGAGTAATAATGCTTTTAAAC
1 AATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAG
* * * * * *
3232 GAATAGGTGACTATAAATGCACTTCTT-TTACTAAT-AATGCCTTTTTCTTT-ATATTTCTCAAG
66 GAATGGGTGACTATAAATGGACTT-TTCTTGCCAATGAATG-CTTTTT-TTTCATGTTTCTGAAG
* *
3294 GTAGACATTCAATTATACTCTG-TTTAACATAAAAAAATAAAAAAA
128 GTAGACATTCAATTATAGTCTGTTTTAACA-AAAAATAT-AAAAAA
* ** ** * * * * * *
3339 AATTCAACTGAAAATCAATTACG-GCATTACAAATCTATTTAAAGTGAGTAATAACGCTGTTGAA
1 AATTCAAATTTAAATCAATTTTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* ** * ** * *
3403 GGTATAAGTGACTATAAATGGA-TGTTTCTTGCCAATGAATGGTTTTTTCTTTTTGTTTCTTATG
65 GGAATGGGTGACTATAAATGGACT-TTTCTTGCCAATGAATGCTTTTTT-TTCATGTTTCTGAAG
* * * * * *
3467 GTAGACAATCAATTCTAGTCTATTTTAACCAAAAATATACAAAG
128 GTAGACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAA
* *
3511 AATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGATG
1 AATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAG
* * * *
3576 GAATGGGAGACTATAAATAGACTTCTCTTACCAATGAATGCCTTTTTCTTTACA--TTTCTCG-A
66 GAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTT-TTT-CATGTTTCT-GAA
3638 GGTAGACATTCAATTATAGTCTG-TTTAACAAAAAATATAAAAAA
127 GGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAA
** * * *
3682 AATTC-AATTTAAAATCAATTACGACATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAA
1 AATTCAAATTT-AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * * * * ** *
3746 GGTATGAGTCACTATAAATTGACTTCTCTTGCCAACAAATGCTTTTTTTTCATGTTTCTTAAGGT
65 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTTTCATGTTTCTGAAGGT
* * *
3811 AGACATTCAATTATACTCCG-TTTAACAAAAAAAATAAAAAA
130 AGACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAA
* * ** * * * ** *
3852 AATTCAACTGTAAATCAATTACG-GCATTACAAAACTATTTAAAGTGAGTAATAATGCTTTCGAC
1 AATTCAAATTTAAATCAATTTTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAA
* * * * * * *
3916 GGTATGGGTGACAATAATTGGACTTTTATTGCAAATGAATGGTTTTTTCTTCATGTTT-TTAATG
65 GGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTT-TTCATGTTTCTGAA-G
* *
3980 GTAGACATTCAATTCTAGTCTGTTTTAACCAAAAAT
128 GTAGACATTCAATTATAGTCTGTTTTAACAAAAAAT
4016 GTACAAAGAA
Statistics
Matches: 958, Mismatches: 193, Indels: 83
0.78 0.16 0.07
Matches are distributed among these distances:
168 2 0.00
169 5 0.01
170 170 0.18
171 328 0.34
172 286 0.30
173 144 0.15
174 21 0.02
175 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (171 bp):
AATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAG
GAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTTTCATGTTTCTGAAGGTA
GACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAA
Found at i:3339 original size:344 final size:339
Alignment explanation
Indices: 2652--3911 Score: 1347
Period size: 344 Copynumber: 3.7 Consensus size: 339
2642 NNNNNNNNNN
* ** * *
2652 AATTCAACTTAAAATCAATTATGGCATTACAAAATTATTTAAAGCGAGTAATAATGCTTTCGAGG
1 AATTCAACTTAAAATCAATTACGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCTTT-GAAG
* *
2717 GTATGGGTGACTAT-AATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCATGTTTCTGAAGGT
65 GTATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATA-CTTTTTTTTCATGTTTCTGAAGGT
* * * ** *
2781 AGACATTCCATCCAAGTCTGTTTGAAAGAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTG
129 AGACATTCAATCCTAGTCTGTTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTTTG
* * * *
2846 AGATTATAAAACTAATTAAAGTTAGTAATAAGGCTTTTAAAGGATTGGATGACTATAAATGGACT
194 AGATTATAAAAC-CATTAAAGTGAGTAATAAGGCTTTTAAAGAATAGG-TGACTATAAAT-GACT
* * * * * * *
2911 T-TTCTTGCCAATGAATG-CTCTCTTCTTTATCTTTTTCGGGGTAGACGTTCAATTATAATATGT
256 TCTT-TTACCAATGAATGCCT-TTTTCTTTATATTTCTCGAGGTAGACATTCAATTATAATCTG-
* *
2974 TTTAACTAGAAAAACAAAAAAA
318 TTTAACTAAAAAAATAAAAAAA
* * ** *
2996 AACTGAACTTAAAATCAATTTTGAG-ATTATAAAACCATTTAAA-CTGAGTAATAAGGCTCTTGA
1 AATTCAACTTAAAATCAATTACG-GCATTACAAAACCATTTAAAGC-GAGTAATAAGGCT-TTGA
* * * * *
3059 AGGAATGGGT-AGCTATAAATGGACTTTTCTTGCCAATTAATACTTTTTTTTCACGTCTCTGAAG
63 AGGTATGAGTGA-CTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTTTCATGTTTCTGAAG
* * * * * *
3123 GTAAACATTCAATCCTAGTCTGTTTTAACCAAAAATACAAAAAAAATCCAAATTTAATTCAATTT
127 GTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTT
* * *
3188 TGAGAATATACAACCATTCAAAGTGAGTAATAATGCTTTTAAACGAATAGGTGACTATAAATGCA
192 TGAGATTATAAAACCATT-AAAGTGAGTAATAAGGCTTTTAAA-GAATAGGTGACTATAAATG-A
* * *
3253 CTTCTTTTACTAAT-AATGCCTTTTTCTTTATATTTCTCAAGGTAGACATTCAATTATACTCTGT
254 CTTCTTTTACCAATGAATGCCTTTTTCTTTATATTTCTCGAGGTAGACATTCAATTATAATCTGT
3317 TTAACATAAAAAAATAAAAAAA
319 TTAAC-TAAAAAAATAAAAAAA
* * * * *
3339 AATTCAACTGAAAATCAATTACGGCATTACAAATCTATTTAAAGTGAGTAATAACGCTGTTGAAG
1 AATTCAACTTAAAATCAATTACGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCT-TTGAAG
* ** ** * *
3404 GTATAAGTGACTATAAATGGA-TGTTTCTTGCCAATGAATGGTTTTTTCTTTTTGTTTCTTATGG
65 GTATGAGTGACTATAAATGGACT-TTTCTTGCCAATGAATACTTTTTT-TTCATGTTTCTGAAGG
* * *
3468 TAGACAATCAATTCTAGTCTATTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTTT
128 TAGACATTCAATCCTAGTCTGTTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTTT
** * *
3533 GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGATGGAATGGGAGACTATAAATAGAC
193 GAGATTATAAAACCA-TTAAAGTGAGTAATAAGGCTTTT-AAAGAATAGGTGACTATAAAT-GAC
* * *
3598 TTCTCTTACCAATGAATGCCTTTTTCTTTACATTTCTCGAGGTAGACATTCAATTATAGTCTGTT
255 TTCTTTTACCAATGAATGCCTTTTTCTTTATATTTCTCGAGGTAGACATTCAATTATAATCTGTT
3663 TAAC--AAAAAATATAAAAAA
320 TAACTAAAAAAATA-AAAAAA
* * *
3682 AATTCAATTTAAAATCAATTACGACATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAG
1 AATTCAACTTAAAATCAATTACGGCATTACAAAACCATTTAAAGCGAGTAATAAGGC-TTTGAAG
* * * ** * *
3747 GTATGAGTCACTATAAATTGACTTCTCTTGCCAACAAATGCTTTTTTTTCATGTTTCTTAAGGTA
65 GTATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTTTCATGTTTCTGAAGGTA
** * * * * * * * * **
3812 GACATTCAATTATACTCCG-TTTAACAAAAAAAATAAAAAAAATTCAACTGTAAATCAATTACG-
130 GACATTCAATCCTAGTCTGTTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTTTGA
* * *
3875 GCATTACAAAACTATTTAAAGTGAGTAATAATGCTTT
195 G-ATTATAAAACCA-TTAAAGTGAGTAATAAGGCTTT
3912 CGACGGTATG
Statistics
Matches: 770, Mismatches: 122, Indels: 51
0.82 0.13 0.05
Matches are distributed among these distances:
340 1 0.00
341 68 0.09
342 45 0.06
343 245 0.32
344 321 0.42
345 90 0.12
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (339 bp):
AATTCAACTTAAAATCAATTACGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTGAAGG
TATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTTTCATGTTTCTGAAGGTAG
ACATTCAATCCTAGTCTGTTTTAACCAAAAATATACAAAGAATTCAAATTTAAATCAATTTTGAG
ATTATAAAACCATTAAAGTGAGTAATAAGGCTTTTAAAGAATAGGTGACTATAAATGACTTCTTT
TACCAATGAATGCCTTTTTCTTTATATTTCTCGAGGTAGACATTCAATTATAATCTGTTTAACTA
AAAAAATAAAAAAA
Found at i:3674 original size:515 final size:513
Alignment explanation
Indices: 3007--4028 Score: 1375
Period size: 515 Copynumber: 2.0 Consensus size: 513
2997 ACTGAACTTA
3007 AAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTCTTGAAGGAATGGGTAGC
1 AAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTCTTGAAGGAATGGGTAGC
* * * *
3072 TATAAATGGACTTTTCTTGCCAATTAATACTTTTTTTTCACGTCTCTGAAGGTAAACATTCAATC
66 TATAAATAGACTTCTCTTACCAATGAATACTTTTTTTTCACGTCTCTGAAGGTAAACATTCAATC
* * * ** * * *
3137 CTAGTCTGTTTTAACCAAAAATACAAAAAAAATCCAAATTT-AATTCAATTTTGAGAATATACAA
131 ATAGTCTGTTTTAACAAAAAATACAAAAAAAATCC-AATTTAAAATCAATTACGACAATACAAAA
* * * * *
3201 CCATTCAAAGTGAGTAATAATGCTTTTAAACGAAT-AGGTGACTATAAA-TGCACTTCTTTTACT
195 CCATTCAAAGCGAGTAATAAGGCTTTTAAACGAATGA-GTCACTATAAATTG-ACTTCTCTTACC
* *
3264 AA-TAATGCCTTTTTCTTT-ATATTTCTCAAGGTAGACATTCAATTATACTCTGTTTAACATAAA
258 AACAAATG-CTTTTT-TTTCATATTTCTCAAGGTAGACATTCAATTATACTCCGTTTAACA-AAA
*
3327 AAAATAAAAAAAAATTCAACTGAAAATCAATTACGGCATTACAAATCTATTTAAAGTGAGTAATA
320 AAAAT-AAAAAAAATTCAACTGAAAATCAATTACGGCATTACAAAACTATTTAAAGTGAGTAATA
* * * *
3392 ACGCTGTT-GAAGGTATAAGTGACTATAAATGGA-TGTTTCTTGCCAATGAATGGTTTTTTCTTT
384 ACGCT-TTCGAAGGTATAAGTGACAATAAATGGACT-TTTATTGCAAATGAATGGTTTTTTCTTC
*
3455 TTGTTTCTT-ATGGTAGACAATCAATTCTAGTCTATTTTAACCAAAAATATACAAAGAATTCAAA
447 ATGTTT-TTAATGGTAGACAATCAATTCTAGTCTATTTTAACCAAAAATATACAAAGAATTCAAA
3519 TTT
511 TTT
* * *
3522 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGATGGAATGGG-AGA
1 AAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTCTTGAAGGAATGGGTAG-
* * * *
3586 CTATAAATAGACTTCTCTTACCAATGAATGCCTTTTTCTTT-ACATTTCTCG-AGGTAGACATTC
65 CTATAAATAGACTTCTCTTACCAATGAAT-ACTTTTT-TTTCACGTCTCT-GAAGGTAAACATTC
* * * *
3649 AATTATAGTCTG-TTTAACAAAAAATATAAAAAAAATTCAATTTAAAATCAATTACGACATTACA
127 AATCATAGTCTGTTTTAACAAAAAATACAAAAAAAATCCAATTTAAAATCAATTACGACAATACA
* * * *
3713 AAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGTATGAGTCACTATAAATTGACTTCTCTTGC
192 AAACCATTCAAAGCGAGTAATAAGGCTTTTAAACGAATGAGTCACTATAAATTGACTTCTCTTAC
* *
3778 CAACAAATGCTTTTTTTTCATGTTTCTTAAGGTAGACATTCAATTATACTCCGTTTAACAAAAAA
257 CAACAAATGCTTTTTTTTCATATTTCTCAAGGTAGACATTCAATTATACTCCGTTTAACAAAAAA
* *
3843 AATAAAAAAAATTCAACTGTAAATCAATTACGGCATTACAAAACTATTTAAAGTGAGTAATAATG
322 AATAAAAAAAATTCAACTGAAAATCAATTACGGCATTACAAAACTATTTAAAGTGAGTAATAACG
* ** *
3908 CTTTCGACGGTATGGGTGACAATAATTGGACTTTTATTGCAAATGAATGGTTTTTTCTTCATGTT
387 CTTTCGAAGGTATAAGTGACAATAAATGGACTTTTATTGCAAATGAATGGTTTTTTCTTCATGTT
* * *
3973 TTTAATGGTAGACATTCAATTCTAGTCTGTTTTAACCAAAAATGTACAAAGAATTC
452 TTTAATGGTAGACAATCAATTCTAGTCTATTTTAACCAAAAATATACAAAGAATTC
4029 NNNNNNNNNN
Statistics
Matches: 444, Mismatches: 51, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
512 4 0.01
513 160 0.36
514 19 0.04
515 217 0.49
516 40 0.09
517 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (513 bp):
AAATCAATTTTGAGATTATAAAACCATTTAAACTGAGTAATAAGGCTCTTGAAGGAATGGGTAGC
TATAAATAGACTTCTCTTACCAATGAATACTTTTTTTTCACGTCTCTGAAGGTAAACATTCAATC
ATAGTCTGTTTTAACAAAAAATACAAAAAAAATCCAATTTAAAATCAATTACGACAATACAAAAC
CATTCAAAGCGAGTAATAAGGCTTTTAAACGAATGAGTCACTATAAATTGACTTCTCTTACCAAC
AAATGCTTTTTTTTCATATTTCTCAAGGTAGACATTCAATTATACTCCGTTTAACAAAAAAAATA
AAAAAAATTCAACTGAAAATCAATTACGGCATTACAAAACTATTTAAAGTGAGTAATAACGCTTT
CGAAGGTATAAGTGACAATAAATGGACTTTTATTGCAAATGAATGGTTTTTTCTTCATGTTTTTA
ATGGTAGACAATCAATTCTAGTCTATTTTAACCAAAAATATACAAAGAATTCAAATTT
Found at i:6307 original size:21 final size:21
Alignment explanation
Indices: 6278--6317 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6268 NAATGGGTGA
*
6278 CAATAAATGGACTTTTCTTGC
1 CAATAAATGCACTTTTCTTGC
* *
6299 CAATGAATGCCCTTTTCTT
1 CAATAAATGCACTTTTCTT
6318 TGTGTTTGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (21 bp):
CAATAAATGCACTTTTCTTGC
Found at i:7234 original size:342 final size:333
Alignment explanation
Indices: 6596--7234 Score: 626
Period size: 342 Copynumber: 1.9 Consensus size: 333
6586 NNNNNNNNNN
* * * * * *
6596 ACAAAGAATTCAAATTTAAATCAATTTTGAGCTTATAAAACTATTTAAAGTTAGTAATAAGGGTT
1 ACAAAGAATTCAAATTTAAATCAATTTTCAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTT
* * * * * *
6661 TTAAAGGAATGGATGACTATAAATGGACTTTTTTTGCCAATTAATGCTCTTTTCTTTAAGTTTTT
66 TTAAAGGAATAGATGACTATAAATGCACTTCTCTTACCAATTAATGCTCTTTTCTTTAAGTTTCT
* * * * * ** *
6726 TAGGGTAAACGTTCAATTATAATATGTTTTAACTAGAAAAGCAAAAAAACTGAACTTAAAATCAA
131 CAAGGTAAACATTCAATTATAATATGTTTTAACAAAAAAAAAAAAAAAACTCAACTTAAAATCAA
** * * * *
6791 TTTTGAGATTATAAAACTATTTAAACTGAGTAATAAGGCTCTAGAAGGAATGGGTAGCTATAAAT
196 TTACGACATTACAAAACTATTTAAACTGAGTAATAAGGCTCTAGAAGGAATAGGTAGCAATAAAT
* * *
6856 GGACTCTTCCTGCCAATTAATACTTTTTTTTTCATGTCTCTGAAGGTAAACATTCAATCCTANNN
261 GGACTCTTACTGCCAATGAATACTTTTTTCTTCATGTCTCTGAAGGTAAACATTCAATCCTA---
6921 NNNNNNNACCAAAAATGC
323 -------ACCAAAAATGC
* * *
6939 ACAAAGACTTCAAATTTAATTCAATTTTCAGATTATAAAACCATTCAAAGTGAGTAATAATGCTT
1 ACAAAGAATTCAAATTTAAATCAATTTTCAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTT
*
7004 TTGAAGGAATA-AGTGACTATAAATGCACTTCTCTTACCAA-TAATGC-CTTTTTCTTTACA-TT
66 TTAAAGGAATAGA-TGACTATAAATGCACTTCTCTTACCAATTAATGCTC-TTTTCTTTA-AGTT
* * * * * * *
7065 TCTCAAGTTAGACATTCAATTATACTCTG-TTTAACAAAAAAATAAAAAAAAATTCTA-TTGTAA
128 TCTCAAGGTAAACATTCAATTATAATATGTTTTAACAAAAAAA-AAAAAAAAACTCAACTT-AAA
* * * * * * *
7128 ATCAATTACGTCATTACAAAACTATTTAAAGTGAGTAATAATGCTTTTGACGGTATAGGT-GACA
191 ATCAATTACGACATTACAAAACTATTTAAACTGAGTAATAAGGCTCTAGAAGGAATAGGTAG-CA
* * **
7192 ATAAATGGACTTTTATTGCCAATGAATGGTTTTTTCTTCATGT
255 ATAAATGGACTCTTACTGCCAATGAATACTTTTTTCTTCATGT
7235 TTCTCATGGT
Statistics
Matches: 239, Mismatches: 51, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
341 15 0.06
342 135 0.56
343 89 0.37
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.35
Consensus pattern (333 bp):
ACAAAGAATTCAAATTTAAATCAATTTTCAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTT
TTAAAGGAATAGATGACTATAAATGCACTTCTCTTACCAATTAATGCTCTTTTCTTTAAGTTTCT
CAAGGTAAACATTCAATTATAATATGTTTTAACAAAAAAAAAAAAAAAACTCAACTTAAAATCAA
TTACGACATTACAAAACTATTTAAACTGAGTAATAAGGCTCTAGAAGGAATAGGTAGCAATAAAT
GGACTCTTACTGCCAATGAATACTTTTTTCTTCATGTCTCTGAAGGTAAACATTCAATCCTAACC
AAAAATGC
Done.