Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397795.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1094.0, 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: 28838
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.21
Warning! 12314 characters in sequence are not A, C, G, or T
Found at i:317 original size:173 final size:171
Alignment explanation
Indices: 1--362 Score: 476
Period size: 172 Copynumber: 2.1 Consensus size: 171
* * * * *
1 TTTTTTT-TTCATATTTCTTAAGGTAGACATTCAATCATAGTCTATTTTAATAAAAAATGTAAAA
1 TTTTTTTCTTCATATTTCTCAAAGTAGAAATTCAATCATAATCTATTTTAACAAAAAATGTAAAA
* * * * *
65 CAAATTGAGCTTAAAATCAATTATGAGATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA
66 AAAATTAAACTTAAAATCAATTATGAGATTACAAAACCATTTAAACCGAGTAATAAAGCTTTTGA
* * *
130 AGGAACGGGAGACTATAAATGGACTTTTCTTGCTAATGAATG
131 AGGAACGGGAGACTATAAATGGAC-TTCCTTGCCAATGAAAG
* * * *
172 TTTTTTTCTTCATGTTTCTCAAAGTAGAAATTCAATTATAATCTGTTTTAACCAAAAATGTAAAA
1 TTTTTTTCTTCATATTTCTCAAAGTAGAAATTCAATCATAATCTATTTTAACAAAAAATGTAAAA
* * *
237 AAAATTTAAACTTAAAATTAA-TATTGAGATTATAAAATCATTTAAACCGAGTAATAAAGCTTTT
66 AAAA-TTAAACTTAAAATCAATTA-TGAGATTACAAAACCATTTAAACCGAGTAATAAAGCTTTT
*
301 GAAGGAATGGGAGACTATAAATGGACTTCCTTGCCAATGAAAG
129 GAAGGAACGGGAGACTATAAATGGACTTCCTTGCCAATGAAAG
* *
344 CTTTTTTCTTCACATTTCT
1 TTTTTTTCTTCATATTTCT
363 AGAGGCCGAC
Statistics
Matches: 164, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
171 7 0.04
172 83 0.51
173 74 0.45
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (171 bp):
TTTTTTTCTTCATATTTCTCAAAGTAGAAATTCAATCATAATCTATTTTAACAAAAAATGTAAAA
AAAATTAAACTTAAAATCAATTATGAGATTACAAAACCATTTAAACCGAGTAATAAAGCTTTTGA
AGGAACGGGAGACTATAAATGGACTTCCTTGCCAATGAAAG
Found at i:934 original size:173 final size:169
Alignment explanation
Indices: 541--1043 Score: 642
Period size: 171 Copynumber: 2.9 Consensus size: 169
531 NNNNNNNNNN
* * * *
541 TAAAATGAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTT-AATAGAATGGTT
1 TAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAA-GGAATGGTT
*
605 GACTATAAATGGACTTTTCTTAT-CAATAAATACCTTTTTTTTCACGTTTCTCATG-G-TAGACA
65 -ACTATAAATAGACTTTT-TT-TGCAATAAATACCTTTTTTTTCACG-TT-TCATGAGATAGACA
* *
667 TTCAATTATAATCTGTTGTAACTAAAAATGTAAAAATATTTAACT
125 TTCAATTATAATCTGTTTTAACTAAAAATGTAAAAATATTGAACT
* *
712 TAAAATCAATTTTGAGACTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTT
1 TAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATG-GTT
* * *
777 ACTATAAATAGACTTTTTTTGCTAATAAA-AGCCTTCTTCTTCATGTTTCATGAGATAGACATTC
65 ACTATAAATAGACTTTTTTTGC-AATAAATA-CCTTTTTTTTCACGTTTCATGAGATAGACATTC
* *
841 AATTATAATCTGTTTTAACTACAAATTTAAAAAAATATTGAACT
128 AATTATAATCTGTTTTAACTAAAAATGT--AAAAATATTGAACT
* *
885 TAAAATCAATTTTGAGATTATAAAACCATTAAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
1 TAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGTT
* * * * *
950 ACTATAAATAGACCTTTCTTGCCAATAAATA-CTTTTTTTTTACGTTTCTTGAGATAAACATTCA
65 ACTATAAATAGACTTTTTTTG-CAATAAATACCTTTTTTTTCACGTTTCATGAGATAGACATTCA
1014 ATTATAATCTGTTTTAA-TCAAAAATGTAAA
129 ATTATAATCTGTTTTAACT-AAAAATGTAAA
1044 NNNNNNNNNN
Statistics
Matches: 291, Mismatches: 28, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
169 6 0.02
170 10 0.03
171 120 0.41
172 55 0.19
173 97 0.33
174 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (169 bp):
TAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGTTA
CTATAAATAGACTTTTTTTGCAATAAATACCTTTTTTTTCACGTTTCATGAGATAGACATTCAAT
TATAATCTGTTTTAACTAAAAATGTAAAAATATTGAACT
Found at i:2039 original size:344 final size:338
Alignment explanation
Indices: 1144--2783 Score: 1608
Period size: 344 Copynumber: 4.8 Consensus size: 338
1134 NNNNNNNNNN
* * * * *
1144 CTATAAAT-GAACTTTTCCTGCTAATGAATGCTTTTTTTTTCATGTTTCTTAAG-GTAGACATTC
1 CTATAAATAG-ACTTTTCTTGCCAATAAATGCTTTTTTCTTCACGTTTC--AAGAGTAGACATTC
* * * * * *
1207 AATAATAGTCTGTTTTAATAAAAAATGAAAAAATAATTGAGCTTAAAATCAATTATGAGATTATA
63 AATTATAATCTGTTTTAATAAAAATTTAAAAAA-AATTAAACTTAAAATCAATTATGAGATTATA
* * ********** * * *
1272 AAATCATTTAAAGCGNNNNNNNNNNCTTTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTGC
127 AAACCATTAAAAGCGAGTAATAAGGCTTTTGAATGAAT-GGTGACTATAAATAGACTTTTCTTGC
* * * * * ********** *
1337 CCATGAATGCTTTTTTCTTCACGTTTCTCAAAGTAGACATTCAATNNNNNNNNNNTTTAATCAAA
191 CAATAAATAC-TTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAA
* * * * * *
1402 AATATAAAAAAAATTAAGCTTAAAATTAATATTGAGATTATAAAACTATTTAAACTGAGTAATAA
255 AATAT-AAAAAATTTAA-CTTAAAATCAATTTTGAGACTATAAAACCATTTAAAGTGAGTAATAA
1467 GGCTTTTGAAGGAATGAGAGA
318 GGCTTTTGAAGGAATGAGAGA
* * * * *
1488 CTATAAATGGAC-TTCCTTGCCAATGAAA-GCTTTTTTCTTTACGTTTCTAGATGTCGACATTCA
1 CTATAAATAGACTTTTCTTGCCAAT-AAATGCTTTTTTCTTCACGTTTCAAGA-GTAGACATTCA
* * * *
1551 ATTATAGTGTGTTTTAATTAAAAATAT-AAAAAAATTAAACTTAAAATCAATTATGAGATTTTAA
64 ATTATAATCTGTTTTAA-TAAAAATTTAAAAAAAATTAAACTTAAAATCAATTATGAGATTATAA
* * * *
1615 AACCATTTAAAGCCAGTAATAAGGCTTTT-AATAGAATGGTAGACTATAAATGGACTTTTCTTAC
128 AACCATTAAAAGCGAGTAATAAGGCTTTTGAAT-GAATGGT-GACTATAAATAGACTTTTCTTGC
* * * * * *
1679 CAATGAATACCTTTTTCTTTACGTTTCTTATGGGAGATATTCAATTATAATCTATTTTAACTAAA
191 CAATAAATA-CTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAA
*
1744 AATATAAAAACATTTAACTTCAAATCAATTTTGAGACTATAAAACCATTTAAAGTGAGTAATAAG
255 AATATAAAAA-ATTTAACTTAAAATCAATTTTGAGACTATAAAACCATTTAAAGTGAGTAATAAG
*
1809 GCTTTTGAAGGAATGAGTGA
319 GCTTTTGAAGGAATGAGAGA
* * * * * *
1829 CTATAAATAGACTTTTTTTACTAATAAATGCCTTTCTCTTCATGTTTCAAGAGATAGACATTCAA
1 CTATAAATAGACTTTTCTTGCCAATAAATGCTTTTTTCTTCACGTTTCAAGAG-TAGACATTCAA
* * *
1894 TTATAATCTGTTTTAAGTATAAATTTAAAAAAATATTGAACTTAAAATCAATTTTGAGATTATAA
65 TTATAATCTGTTTTAA-TAAAAATTTAAAAAAA-ATTAAACTTAAAATCAATTATGAGATTATAA
* *
1959 AACTATTAAAAGTGAGTAATAAGGCTTTTGAATGAATAGGTGACTATAAATAGACTTTTCTTGCC
128 AACCATTAAAAGCGAGTAATAAGGCTTTTGAATGAAT-GGTGACTATAAATAGACTTTTCTTGCC
2024 AATAAATGACTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAA
192 AATAAAT-ACTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAA
* * * *
2089 ATGTTAAAAAATTTAACTTAAAATCAATTTTGAGACTAGAAAACTATTTAAAGAGAGTAATAAGG
256 AT-ATAAAAAATTTAACTTAAAATCAATTTTGAGACTATAAAACCATTTAAAGTGAGTAATAAGG
*
2154 CTTTTGAAGGAAT-AGATTA
320 CTTTTGAAGGAATGAGA-GA
* * * * * * *
2173 CTATAAATAGACTTTTTTTGCTAATAAATG-TCATTTTCCTCACATTTGACGAGATAGACATTCA
1 CTATAAATAGACTTTTCTTGCCAATAAATGCT-TTTTTCTTCACGTTTCAAGAG-TAGACATTCA
* * * * *
2237 ATTATAATCTGTTTTAACTACAAATTTTAAAAAATATTAAACTTAAAATCAATTTTTAGAATATA
64 ATTATAATCTGTTTTAA-TA-AAAATTTAAAAAAAATTAAACTTAAAATCAATTATGAGATTATA
* * *
2302 AAACCATTAAAAGTGAGTAATAAGGCTTTTAAAGGAATGGTTGACTATAAATAGACTTTTCTTGC
127 AAACCATTAAAAGCGAGTAATAAGGCTTTTGAATGAATGG-TGACTATAAATAGACTTTTCTTGC
* * *
2367 CAATAAATACTTTTTTTTTACGTTTCTCAAGGTAGACATTTAATTATAATCTGTTTTAACCAAAA
191 CAATAAATACTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAA
* ** * ** * * *
2432 ATGTAAAAAA-AAAAATTAAAATCAATTACGAGATTATTAAACCACTTAAAGTGAGTAATAAGGC
256 ATATAAAAAATTTAACTTAAAATCAATTTTGAGACTATAAAACCATTTAAAGTGAGTAATAAGGC
* *
2496 TTTCGAAGGAATGGGAGA
321 TTTTGAAGGAATGAGAGA
* * * * * *
2514 CTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGATTCTAAAAGTAAACATTCAA
1 CTATAAATAGACTTTTCTTGCCAATAAATGCTTTTTTCTTCACGTTTC-AAGAGTAGACATTCAA
* ** * * * *
2579 TTATAGTCTAATTTAATGAAAAATGTAAAACAAATTGACCTTAAAATCAATTATGTA-ATTATAA
65 TTATAATCTGTTTTAAT-AAAAATTTAAAAAAAATTAAACTTAAAATCAATTATG-AGATTATAA
* * * * * **
2643 AACCATTTAAAGCGAGTAATAAGACTTTTGAAAGAATGAGAGACTATAAATAGACTTATTTTTAT
128 AACCATTAAAAGCGAGTAATAAGGCTTTTGAATGAATG-GTGACTATAAATAGACTT-TTCTTGC
** * * * * * * * *
2708 TTATGAATGCCTTTTTCTTCACTTTTCTCAAGGTAAACTTTCAATTGTAATCTGTTTTAACCAAA
191 CAATAAAT-ACTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAA
*
2773 AATGTAAAAAA
255 AATATAAAAAA
2784 AAAATTGAAC
Statistics
Matches: 1086, Mismatches: 180, Indels: 62
0.82 0.14 0.05
Matches are distributed among these distances:
340 84 0.08
341 213 0.20
342 254 0.23
343 122 0.11
344 388 0.36
345 25 0.02
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.36
Consensus pattern (338 bp):
CTATAAATAGACTTTTCTTGCCAATAAATGCTTTTTTCTTCACGTTTCAAGAGTAGACATTCAAT
TATAATCTGTTTTAATAAAAATTTAAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAAC
CATTAAAAGCGAGTAATAAGGCTTTTGAATGAATGGTGACTATAAATAGACTTTTCTTGCCAATA
AATACTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAAAAATATA
AAAAATTTAACTTAAAATCAATTTTGAGACTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
AAGGAATGAGAGA
Found at i:2689 original size:172 final size:171
Alignment explanation
Indices: 1144--2784 Score: 1443
Period size: 171 Copynumber: 9.6 Consensus size: 171
1134 NNNNNNNNNN
* * * * * * *
1144 CTATAAAT-GAACTTTTCCTGCTAATGAATGCTTTTTTTTTCATGTTTCTTAAGGTAGACATTCA
1 CTATAAATAG-ACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTAAAAGTAGACATTCA
* * * * * *
1208 ATAATAGTCTGTTTTAATAAAAAATGAAAAAATAATTGAGCTTAAAATCAATTATGAGATTATAA
65 ATTATAATCTGTTTTAATCAAAAATGTAAAAA-AATTAAACTTAAAATCAATTATGAGATTATAA
* ********** *
1273 AATCATTTAAAGCGNNNNNNNNNNCTTTTGAAGGAATGGGAGA
129 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGA
* * * *
1316 CTATAAATGGACTTTTCTTGCCCATGAATGCTTTTTTCTTCACGTTTCTCAAAGTAGACATTCAA
1 CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTAAAAGTAGACATTCAA
********** * * *
1381 TNNNNNNNNNNTTTAATCAAAAATATAAAAAAAATTAAGCTTAAAATTAA-TATTGAGATTATAA
66 TTATAATCTGTTTTAATCAAAAATGT-AAAAAAATTAAACTTAAAATCAATTA-TGAGATTATAA
*
1445 AACTATTTAAA-CTGAGTAATAAGGCTTTTGAAGGAATGAGAGA
129 AACCATTTAAAGC-GAGTAATAAGGCTTTTGAAGGAATGAGAGA
* * * * * *
1488 CTATAAATGGAC-TTCCTTGCCAATGAA-AGCTTTTTTCTTTACGTTTCTAGATGTCGACATTCA
1 CTATAAATAGACTTTTCTTGCCAATGAATA-CTTTTTTCTTCACGTTTCTAAAAGTAGACATTCA
* * * * *
1551 ATTATAGTGTGTTTTAATTAAAAATATAAAAAAATTAAACTTAAAATCAATTATGAGATTTTAAA
65 ATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAA
* *
1616 ACCATTTAAAGCCAGTAATAAGGCTTTT-AATAGAATG-GTAGA
130 ACCATTTAAAGCGAGTAATAAGGCTTTTGAA-GGAATGAG-AGA
* * * * * ** * *
1658 CTATAAATGGACTTTTCTTACCAATGAATACCTTTTTCTTTACGTTTCTTATGGGAGATATTCAA
1 CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTAAAAGTAGACATTCAA
* * * * * * *
1723 TTATAATCTATTTTAA-CTAAAAATATAAAAACATTTAACTTCAAATCAATTTTGAGACTATAAA
66 TTATAATCTGTTTTAATC-AAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAA
* *
1787 ACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGA
130 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGA
* * * * * * * * *
1829 CTATAAATAGACTTTTTTTACTAATAAATGCCTTTCTCTTCATGTTTC-AAGAGATAGACATTCA
1 CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTAAAAG-TAGACATTCA
* * * *
1893 ATTATAATCTGTTTTAAGT-ATAAATTTAAAAAAATATTGAACTTAAAATCAATTTTGAGATTAT
65 ATTATAATCTGTTTTAA-TCAAAAATGT-AAAAAA-ATTAAACTTAAAATCAATTATGAGATTAT
* * * * *
1957 AAAACTATTAAAAGTGAGTAATAAGGCTTTTGAATGAAT-AGGTGA
127 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGA-GAGA
* * * *
2002 CTATAAATAGACTTTTCTTGCCAATAAATGAC-TTTTTCTTTACGTTTCTCAAGGTAGACATTCA
1 CTATAAATAGACTTTTCTTGCCAATGAAT-ACTTTTTTCTTCACGTTTCTAAAAGTAGACATTCA
* * * * * * *
2066 ATTATAATCTATTTTAACCAAAAATGTTAAAAAATTTAACTTAAAATCAATTTTGAGACTAGAAA
65 ATTATAATCTGTTTTAATCAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAA
* * *
2131 ACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGAAT-AGATTA
130 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGA-GA
* * * * * * * * **
2173 CTATAAATAGACTTTTTTTGCTAATAAAT-GTCATTTTCCTCACATTT-GACGAGATAGACATTC
1 CTATAAATAGACTTTTCTTGCCAATGAATACT-TTTTTCTTCACGTTTCTAAAAG-TAGACATTC
* * * * *
2236 AATTATAATCTGTTTTAA-CTACAAATTTTAAAAAATATTAAACTTAAAATCAATTTTTAGAATA
64 AATTATAATCTGTTTTAATC-A-AAAATGTAAAAAA-ATTAAACTTAAAATCAATTATGAGATTA
* * * *
2300 TAAAACCATTAAAAGTGAGTAATAAGGCTTTTAAAGGAATG-GTTGA
126 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAG-AGA
* * * * *
2346 CTATAAATAGACTTTTCTTGCCAATAAATACTTTTTT-TTTACGTTTCTCAAGGTAGACATTTAA
1 CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTAAAAGTAGACATTCAA
* * * *
2410 TTATAATCTGTTTTAACCAAAAATGTAAAAAAA--AAAATTAAAATCAATTACGAGATTATTAAA
66 TTATAATCTGTTTTAATCAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAA
* * * *
2473 CCACTTAAAGTGAGTAATAAGGCTTTCGAAGGAATGGGAGA
131 CCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGA
* * *
2514 CTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGATTCTAAAAGTAAACATTCAA
1 CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTAAAAGTAGACATTCAA
* ** * * *
2579 TTATAGTCTAATTTAATGAAAAATGTAAAACAAATTGACCTTAAAATCAATTATGTA-ATTATAA
66 TTATAATCTGTTTTAATCAAAAATGTAAAA-AAATTAAACTTAAAATCAATTATG-AGATTATAA
* *
2643 AACCATTTAAAGCGAGTAATAAGACTTTTGAAAGAATGAGAGA
129 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGA
* **** * * * * * * *
2686 CTATAAATAGACTTATTTTTATTTATGAATGCCTTTTTCTTCACTTTTCTCAAGGTAAACTTTCA
1 CTATAAATAGACTT-TTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTAAAAGTAGACATTCA
* *
2751 ATTGTAATCTGTTTTAACCAAAAATGTAAAAAAA
65 ATTATAATCTGTTTTAATCAAAAATGTAAAAAAA
2785 AAATTGAACT
Statistics
Matches: 1202, Mismatches: 225, Indels: 84
0.80 0.15 0.06
Matches are distributed among these distances:
168 93 0.08
169 50 0.04
170 85 0.07
171 400 0.33
172 268 0.22
173 302 0.25
174 4 0.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.36
Consensus pattern (171 bp):
CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTAAAAGTAGACATTCAA
TTATAATCTGTTTTAATCAAAAATGTAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAA
CCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGAGA
Found at i:3655 original size:172 final size:172
Alignment explanation
Indices: 3193--3942 Score: 607
Period size: 172 Copynumber: 4.4 Consensus size: 172
3183 NNNNNNNNNN
* *
3193 ACATTCAATTATAGTATGTTTTAA-CTAAAAATGTAAAAACAATTGAACTTAAAATCAATTAT-A
1 ACATTCAATTATAGTCTGTTTTAATC-AAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGA
* * * * *
3256 GGATTATGAAACCATTTAAA-ATGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAAAC
65 -GATTATAAAACTATTTAAACA-GAATAATAAGGCTTTTGAAGGGATGAGAGACTATAAATGAAC
* * * * * * ** *
3320 TTTTCTTGACAATAAATGCCTTTTTCTTT-ATGTTTCTCGAGGTAG
128 TTTTCCTGCCAATGAATG-CTTTTTTTTTCACGTTTTTTAAAGTAG
* * ** ** ******
3365 ACTTTCAATTATAATCAATTTTAGCCAAAAATGT-AAAAAAATTGAACTTAAAATCAATNNNNNN
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAG
**** ** * * *
3429 NNNNTAAAA-TCATTTAAAGTGAGTAATAAGGCTTTTG-AGGGAATGTGGGACTATAAATGAACT
66 ATTATAAAACT-ATTTAAACAGAATAATAAGGCTTTTGAAGGG-ATGAGAGACTATAAATGAACT
* *
3492 TTTCCTGCAAATGAATGCTTTTTTTTTCACGTTTTTTAAGGTAG
129 TTTCCTGCCAATGAATGCTTTTTTTTTCACGTTTTTTAAAGTAG
* *
3536 ACATTCAATAATAGTCTGTTTTAATCAAAAATGTAAAAAAAATTGAGCTTAAAATCAATTATGAG
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAG
********** *
3601 ATTATAANNNNNNNNNNAGAGAATAATAAGGCTTTTGAAGGGATGAGAGACTATAAAT-AGACTT
66 ATTATAAAACTATTTAAACAGAATAATAAGGCTTTTGAAGGGATGAGAGACTATAAATGA-ACTT
* * *
3665 TTCTTGCCAATGAATG-TTTTTCTCTTCACGTTTCTTAAAGTAG
130 TTCCTGCCAATGAATGCTTTTT-TTTTCACGTTTTTTAAAGTAG
* * * *
3708 ACATTCAATTATAATCTGTTTGAACCAAAAATGTAAAAAAAA---AACTTAAAATTAA-TATTGA
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTA-TGA
* * * ** *
3769 GATTATAAAACTATTTAAACCGAGTAATAAGGCTTTTAAAGAAATGAGAGACTATAAATGGAC--
65 GATTATAAAACTATTTAAACAGAATAATAAGGCTTTTGAAGGGATGAGAGACTATAAATGAACTT
* * * *
3832 TTCCTTGCCAATGAAAGCTTTTTTCTTT-ATG-TTTTTAGATGTCG
130 TTCC-TGCCAATGAATGCTTTTTT-TTTCACGTTTTTTA-AAGTAG
* * * * *
3876 ACATTCAATTTTAGTCTATTTTAATGAAAAATATAAAAACAATTGAACTTAAAATCAATTATGAG
1 ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAG
3941 AT
66 AT
3943 NNNNNNNNNN
Statistics
Matches: 450, Mismatches: 107, Indels: 43
0.75 0.18 0.07
Matches are distributed among these distances:
167 8 0.02
168 54 0.12
169 66 0.15
170 12 0.03
171 145 0.32
172 160 0.36
173 5 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.34
Consensus pattern (172 bp):
ACATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAAATTGAACTTAAAATCAATTATGAG
ATTATAAAACTATTTAAACAGAATAATAAGGCTTTTGAAGGGATGAGAGACTATAAATGAACTTT
TCCTGCCAATGAATGCTTTTTTTTTCACGTTTTTTAAAGTAG
Found at i:5694 original size:169 final size:168
Alignment explanation
Indices: 5161--5829 Score: 525
Period size: 171 Copynumber: 3.9 Consensus size: 168
5151 CTCGCTTTAT
* *
5161 ATGGTTTTATAATCTCATAATTGATTTTG-AGTTGAATTTTTTTATATTTTTTCTTAAAATCGAC
1 ATGGTTTTATAATCTCATAATTGA-TTTGAAGTTG-ATTTTTTTATATTTTTTATTAAAATAGAC
* * * *
5225 TATAATTGAATGCCTAGCTCAGGAAACATATAGAAAAAGCTATTCGTTGAGAAGAAAAA-ACTAT
64 TATAATTGAATGACTACCTCAGGAAACATATAGAAAAAGC-ATTCATTGAGAAGAAAAAGTCTAT
********** *
5289 TTATAGTCTCCCATTCCTTCAAAAGNNNNNNNNNNCGCTTTAA
128 TTATAGTCT-CCATTCCTTCAAAAGCCTTATTACTCGC-GTAA
* * *
5332 ATGGTTTTATAATC-CTATAATTGATTTTAATTTTAATTTTTTTATATTTTTTATTAAAATAGAC
1 ATGGTTTTATAATCTC-ATAATTGATTTGAA-GTTGATTTTTTTATATTTTTTATTAAAATAGAC
* * *************
5396 TATAATTGAATGACTGCCTCAGAAAACATATNNNNNNNNNNNNNNATTGAGAAG-AAAAGATC-A
64 TATAATTGAATGACTACCTCAGGAAACATAT-AGAAAAAGCATTCATTGAGAAGAAAAAG-TCTA
* *
5459 TTTATAGTCTCCTATTCCTTCAAAAGTCTTCTTACTCGCTGTAA
127 TTTATAGTCTCC-ATTCCTTCAAAAGCCTTATTACTCGC-GTAA
* *
5503 ATGATTTTATAATCTCATAATTGATTTGAAGTTGATTTTTTTATATTTTTTATTAAAATAGACCA
1 ATGGTTTTATAATCTCATAATTGATTTGAAGTTGATTTTTTTATATTTTTTATTAAAATAGACTA
* *
5568 TAATTGAATG-GTACCT-AGTGAAACAT-TAAGAAAAAAGCATTCATTG-GCAGAAAAAGTCTAT
66 TAATTGAATGACTACCTCAG-GAAACATAT-AG-AAAAAGCATTCATTGAGAAGAAAAAGTCTAT
*
5629 TTATACTCTCTCATTCCTTCAAAAGCCTTATTACTCGCGCTAA
128 TTATAGTCTC-CATTCCTTCAAAAGCCTTATTACTCGCG-TAA
* * * * * *** *
5672 ATGGTTTTATAATCTTATAATTGATTTTATGTTCAATTTGTTTTTACATTTTTGGCTAAAACAGA
1 ATGGTTTTATAATCTCATAATTGATTTGAAGTT-GA-TT-TTTTTATATTTTTTATTAAAATAGA
* * * ** * * *
5737 TTCTAATTGAATGTCTACCTCAAAAAACGT-GA-AAAAAGCCATTCATTGACAAG-AAAAGTCTA
63 CTATAATTGAATGACTACCTCAGGAAACATATAGAAAAAG-CATTCATTGAGAAGAAAAAGTCTA
*
5799 TTTATAGTCACCTATTCCTTCAAAAGCCTTA
127 TTTATAGTCTCC-ATTCCTTCAAAAGCCTTA
5830 NNNNNNNNNN
Statistics
Matches: 393, Mismatches: 83, Indels: 44
0.76 0.16 0.08
Matches are distributed among these distances:
168 9 0.02
169 86 0.22
170 61 0.16
171 189 0.48
172 37 0.09
173 10 0.03
174 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.38
Consensus pattern (168 bp):
ATGGTTTTATAATCTCATAATTGATTTGAAGTTGATTTTTTTATATTTTTTATTAAAATAGACTA
TAATTGAATGACTACCTCAGGAAACATATAGAAAAAGCATTCATTGAGAAGAAAAAGTCTATTTA
TAGTCTCCATTCCTTCAAAAGCCTTATTACTCGCGTAA
Found at i:5822 original size:171 final size:167
Alignment explanation
Indices: 5441--5829 Score: 414
Period size: 169 Copynumber: 2.3 Consensus size: 167
5431 NNNNNNNNNN
* * *
5441 ATTGAGAAGAAAAGATC-ATTTATAGTCTCCTATTCCTTCAAAAGTCTTCTTACTCGCTGTAAAT
1 ATTGACAAGAAAAG-TCTATTTATAGTC-CCTATTCCTTCAAAAGCCTTATTACTCGCTGTAAAT
* * * * *
5505 GATTTTATAATCTCATAATTGATTTGAAGTTGATTTTTTTATATTTTTTATTAAAATAGACCATA
64 GATTTTATAATCTCATAATTGATTTGAAGTTAATTTTTTTACATTTTTGACTAAAACAGACCATA
* ** *
5570 ATTGAATGGTACCTAGTGAAACATTAAGAAAAAAGCATTC
129 ATTGAATGCTACCTAGAAAAACAGT-AGAAAAAAGCATTC
* * *
5610 ATTGGC-AGAAAAAGTCTATTTATACTCTCTCATTCCTTCAAAAGCCTTATTACTCGC-GCTAAA
1 ATTGACAAG-AAAAGTCTATTTATAGTCCCT-ATTCCTTCAAAAGCCTTATTACTCGCTG-TAAA
* * * * *
5673 TGGTTTTATAATCTTATAATTGATTTTATGTTCAATTTGTTTTTACATTTTTGGCTAAAACAGAT
63 TGATTTTATAATCTCATAATTGATTTGAAGTT-AA-TT-TTTTTACATTTTTGACTAAAACAGA-
*
5738 TC-TAATTGAATGTCTACCTCA-AAAAAC-GT-GAAAAAAGCCATTC
124 CCATAATTGAATG-CTACCT-AGAAAAACAGTAGAAAAAAG-CATTC
5781 ATTGACAAGAAAAGTCTATTTATAGTCACCTATTCCTTCAAAAGCCTTA
1 ATTGACAAGAAAAGTCTATTTATAGTC-CCTATTCCTTCAAAAGCCTTA
5830 NNNNNNNNNN
Statistics
Matches: 183, Mismatches: 24, Indels: 24
0.79 0.10 0.10
Matches are distributed among these distances:
168 7 0.04
169 74 0.40
170 9 0.05
171 47 0.26
172 35 0.19
173 10 0.05
174 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (167 bp):
ATTGACAAGAAAAGTCTATTTATAGTCCCTATTCCTTCAAAAGCCTTATTACTCGCTGTAAATGA
TTTTATAATCTCATAATTGATTTGAAGTTAATTTTTTTACATTTTTGACTAAAACAGACCATAAT
TGAATGCTACCTAGAAAAACAGTAGAAAAAAGCATTC
Found at i:6545 original size:171 final size:172
Alignment explanation
Indices: 6260--6606 Score: 441
Period size: 171 Copynumber: 2.0 Consensus size: 172
6250 NNNNNNNNNN
* * * * * * **
6260 AAACTATTTAAAGTGAGTAGTAAAGTTTTTGAAAGAATGTGTGACTATAAATAGACCTTTTTTTT
1 AAACTATTTAAACTGAGTAATAAAGCTTTTGAAAGAATGAGAGACTATAAATAGAACTTTTTTGC
** * *
6325 CAATGAATGCTTTTTTTCTCACGTTTCTCAAAGTAAACATTTAATTATAATCTGTTTTAACCAAC
66 CAATGAATGCTTTTGCTCTCACGTTTCACAAAGTAAACATTCAATTATAATCTGTTTTAACCAA-
* *
6390 AA-TAT-AAAAAAATTGAACTTAAAATCAATTATGGGATTGTA
130 AAGTATAAAAAAAATTGAACTTAAAATCAATTATGAGATTATA
*
6431 AAACTATTTAAACTGAGTAATAAGGCTTTTGAAAGAATGAGAGACTATAAAT-GAACTTTTCTTG
1 AAACTATTTAAACTGAGTAATAAAGCTTTTGAAAGAATGAGAGACTATAAATAGAACTTTT-TTG
* * * *
6495 CCAGTGAATGCCTTTTGCT-TCACGTTTCACAAGGTAGACATTCAATTATAATCTGTTTTAACTA
65 CCAATGAATG-CTTTTGCTCTCACGTTTCACAAAGTAAACATTCAATTATAATCTGTTTTAACCA
* * *
6559 AAAGTGTAAAAAAAATTGAACTTAAAATTAATTTTGAGATTATA
129 AAAGTATAAAAAAAATTGAACTTAAAATCAATTATGAGATTATA
6603 AAAC
1 AAAC
6607 CATTGAAAGT
Statistics
Matches: 150, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
170 9 0.06
171 99 0.66
172 42 0.28
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (172 bp):
AAACTATTTAAACTGAGTAATAAAGCTTTTGAAAGAATGAGAGACTATAAATAGAACTTTTTTGC
CAATGAATGCTTTTGCTCTCACGTTTCACAAAGTAAACATTCAATTATAATCTGTTTTAACCAAA
AGTATAAAAAAAATTGAACTTAAAATCAATTATGAGATTATA
Found at i:7451 original size:171 final size:160
Alignment explanation
Indices: 7169--7493 Score: 302
Period size: 171 Copynumber: 2.0 Consensus size: 160
7159 NNNNNNNNNN
* * **
7169 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGGAGAATATAAATAGTTTTTTCT
1 ATAAAACCATATAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGAGAATATAAATAGACTTTTCT
* *
7234 TCTCAATGAATAGCTTTTTCTATATGTTTCCTAAGCCAAGCATTCAATTATAGTC-GATTTTAAG
66 TCTCAATGAATAGCTTTTTCTATATATTTCCTAAGCCAAGCATTCAATTATAGTCTG-TTTTAAC
*
7298 AAAAAATGTAAAAA-AATTCAACTNNNNNNNNNNNNTGAGATT
130 AAAAAATGCAAAAACAATTCAACT------------TGAGATT
* * *
7340 ATAAAACCATATAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGTGAATATAAATTGACTTTTC-
1 ATAAAACCATATAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGAGAATATAAATAGACTTTTCT
* * * **
7404 TCATCAATGAATA-CTTTTTTCT-TCTTATTTCTTGAG-GTAGACATTCAATTATAGTCTGTTTT
66 TC-TCAATGAATAGC-TTTTTCTAT-ATATTTCCTAAGCCAAG-CATTCAATTATAGTCTGTTTT
* *
7466 AACTAAAAATGCAAAAACAATTGAACTT
127 AACAAAAAATGCAAAAACAATTCAACTT
7494 AAAATCAATT
Statistics
Matches: 131, Mismatches: 17, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
160 1 0.01
170 6 0.05
171 115 0.88
172 9 0.07
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.34
Consensus pattern (160 bp):
ATAAAACCATATAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGAGAATATAAATAGACTTTTCT
TCTCAATGAATAGCTTTTTCTATATATTTCCTAAGCCAAGCATTCAATTATAGTCTGTTTTAACA
AAAAATGCAAAAACAATTCAACTTGAGATT
Found at i:12492 original size:173 final size:162
Alignment explanation
Indices: 12282--12766 Score: 379
Period size: 171 Copynumber: 2.9 Consensus size: 162
12272 GCTTAAAATC
* * * *
12282 AATTATGAGATTATAAAACTGTTTAAAGCGAGTAATAAGGTTTTTTGAAAGAATGAGAGACTATA
1 AATTATGAGAGTATAAAACTGTTTAAAGCAAGTAATAAGG-CTTTTGAAAGAATGAAAGACTATA
*
12347 AATAGACTTTTCTTGCCAATGAATATTTTTTTCTTCACGTTTCTCGAA-GTAAA-TATTCAATTA
65 AATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTC-AAGGTAAACT-TTCAATTA
* *
12410 TAGTCTATTTTAACCAAAAATGTAAAAACAATTGA
128 TAATCTATTTTAACAAAAAATGTAAAAACAATTGA
* *
12445 NNNNNNNNNNAATTATGTGAGTATAAAACCT-TTTAAGGCAAGTAATAAGGCTTTTGAAAGAATG
1 ----------AATTATGAGAGTATAAAA-CTGTTTAAAGCAAGTAATAAGGCTTTTGAAAGAATG
* * * *
12509 AAAGACTATAAATAGACTTTTTTTGCCAATGAATGCTTTTTTCTTTATGTTTCTCAAGGTAAACT
55 AAAGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTCAAGGTAAACT
* * ********
12574 TTCAATTATAATCTGTTTTAGCAAAAAATGTAAAANNNNNNNNNNNNNNNNC
120 TTCAATTATAATCTATTTTAACAAAAAATGTAAAA---------ACAATTGA
* * ** * *
12626 AATTATGAGATTATATAACCATTTAAAGCCAGTAATAAGGCTTTTG-AAGAAATGAGAGACTATA
1 AATTATGAGAGTATAAAACTGTTTAAAGCAAGTAATAAGGCTTTTGAAAG-AATGAAAGACTATA
* * * *
12690 AAT-GAACTTTTTTTGCCAATGAA-AGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTA
65 AATAG-ACTTTTCTTGCCAATGAATA-CTTTTTTCTTCACGTTTCTCAAGGTAAACTTTCAATTA
* *
12753 TACTCTGTTTTAAC
128 TAATCTATTTTAAC
12767 TAAANNNNNN
Statistics
Matches: 260, Mismatches: 36, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
170 5 0.02
171 121 0.47
172 98 0.38
173 34 0.13
174 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.35
Consensus pattern (162 bp):
AATTATGAGAGTATAAAACTGTTTAAAGCAAGTAATAAGGCTTTTGAAAGAATGAAAGACTATAA
ATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACGTTTCTCAAGGTAAACTTTCAATTATAA
TCTATTTTAACAAAAAATGTAAAAACAATTGA
Found at i:12861 original size:171 final size:155
Alignment explanation
Indices: 12625--12936 Score: 263
Period size: 171 Copynumber: 1.9 Consensus size: 155
12615 NNNNNNNNNN
* * **
12625 CAATTATGAGATTATATAACCATTTAAAGCCAGTAATAAGGCTTTTGAAGAAATGAGAGACTATA
1 CAATTAGGAGATTATAAAACCATTTAAAGCCAGTAATAAGGCTTTTGAAGAAAAAAGAGACTATA
* * *
12690 AATGAACTTTTTTTGCCAATGAA-AGCT-TTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTA
66 AATGAACTTTTCTTACCAATGAATA--TATTTTTCTTCATATTTCTCAAGGTAGACATTCAATTA
* *
12753 TACTCTGTTTTAACTAAANNNNNNNNNNNNNNNNNACTTAAAAT
129 TAATCTATTTTAACTAAA-----------------ACTTAAAAT
* ** * *
12797 CAATTAGGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTTAA-AAAAAATTA-ACTAT
1 CAATTAGGAGATTATAAAACCATTTAAAGCCAGTAATAAGGCTTTTGAAGAAAAAA-GAGACTAT
* * *
12860 AAATGGACTTTTCTTATCAATGAATATATTTTTCTTCATATTTCTTAAGGTAGACATTCAATTAT
65 AAATGAACTTTTCTTACCAATGAATATATTTTTCTTCATATTTCTCAAGGTAGACATTCAATTAT
12925 AATCTATTTTAA
130 AATCTATTTTAA
12937 ACAAANNNNN
Statistics
Matches: 120, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
170 1 0.01
171 74 0.62
172 45 0.38
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.37
Consensus pattern (155 bp):
CAATTAGGAGATTATAAAACCATTTAAAGCCAGTAATAAGGCTTTTGAAGAAAAAAGAGACTATA
AATGAACTTTTCTTACCAATGAATATATTTTTCTTCATATTTCTCAAGGTAGACATTCAATTATA
ATCTATTTTAACTAAAACTTAAAAT
Found at i:18463 original size:171 final size:161
Alignment explanation
Indices: 18203--18533 Score: 355
Period size: 171 Copynumber: 2.0 Consensus size: 161
18193 GCTTTTGAAG
*
18203 GAATGGGAGACCATAAATGGATATTTCTTCCCAATGAATGATTTTTTCTTCACGTTTCTTGAAGT
1 GAATGGGAGACCATAAATGGATATTTCTTCCCAATGAATGATTTTTTCTTCACGTTTCTAGAAGT
* * * ** * *
18268 AGACATTCAAGTATAGTCTGTTTTAATGAAAAATATAAAAAAATT-GACTTTAAAATCAATTATG
66 AAACATTCAAGTATAATATGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAAAT-AATTATG
* *
18332 TGATTATAAAACAATTTAAAGAGAGTAATNNNNNNNNNNAAA
130 AGATTACAAAACAATTTAAAGAGAGTAAT----------AAA
* *
18374 GAATGGGAGACTATAAATGGACT-TTTCTTGCCAATGAATG-TATTTTTCTTCACGTTTCTCAG-
1 GAATGGGAGACCATAAATGGA-TATTTCTTCCCAATGAATGAT-TTTTTCTTCACGTTTCT-AGA
* * *
18436 GGTAAACTTTCAATTATAATATGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAAATAATTA
63 AGTAAACATTCAAGTATAATATGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAAATAATTA
* *
18501 TGAGATTACAAAACTATTTAAAGCGAGTAATAA
128 TGAGATTACAAAACAATTTAAAGAGAGTAATAA
18534 GGCTTTTGAA
Statistics
Matches: 139, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
161 2 0.01
170 1 0.01
171 125 0.90
172 11 0.08
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.34
Consensus pattern (161 bp):
GAATGGGAGACCATAAATGGATATTTCTTCCCAATGAATGATTTTTTCTTCACGTTTCTAGAAGT
AAACATTCAAGTATAATATGTTTTAACCAAAAATATAAAAAAATTAAACTTAAAAATAATTATGA
GATTACAAAACAATTTAAAGAGAGTAATAAA
Done.