Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399108.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2384.0, 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: 8720
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.25
Warning! 2697 characters in sequence are not A, C, G, or T
Found at i:1165 original size:171 final size:171
Alignment explanation
Indices: 704--1677 Score: 505
Period size: 171 Copynumber: 5.7 Consensus size: 171
694 NNNNNNNNNN
**
704 GAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGA-TGATAAATGGA
1 GAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACT-ATAAATGGA
* * * * ** * *
768 CTTCTCTTACCTATCAATGCTTACTTCTTTATATTTCTTGAGCTAGACATTCAATTATAATGTGT
65 CTTCTCTTGCCTATGAATGCTT-CTTCTTCATGTTTCTCAAGCTAGACATTCAATTAGAATCTGT
* * *
833 TTTAACAAGAAAAGTAAAAGAACTTGAACTTAAAATCAATTTT
129 GTTAACAAGAAAAGTAAAAGAACTTCAAATTAAAATCAATTTT
* * * *
876 GAGAATATAAAACTATTTAAAGTGA-TGAATTAGGCTTTTGAAGTAAT-AAGTGACTATAAATAG
1 GAGATTATAAAACTATTTAAAGTGAGT-AATAAGGCTTTTAAAGGAATGAA-TGACTATAAAT-G
* * * * ********** * *
939 G-CTTTTCTTGCCAATGAATACTTTTTCCTTCATGTTTCTNNNNNNNNNNATTCAATTCGAGTCT
63 GACTTCTCTTGCCTATGAATGCTTCTT-CTTCATGTTTCTCAAGCTAGACATTCAATTAGAATCT
* * * ** * * *
1003 GTGTTAACCATAAATGTGCAA-AATTTCAAATTTAATTCAATTTT
127 GTGTTAACAAGAAAAGTAAAAGAACTTCAAATTAAAATCAATTTT
*
1047 GAGATTATAAAA-TAATTGAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGA
1 GAGATTATAAAACT-ATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGA
* * * *
1111 CCTCTCTTGCCTATGAATGCGTTCTTCTTCATGTTTCTCAAGCTAGGCATTCAATTATAATATGT
65 CTTCTCTTGCCTATGAATGC-TTCTTCTTCATGTTTCTCAAGCTAGACATTCAATTAGAATCTGT
* * * ******
1176 TTTAACCAGAAAAGTAAAAGAA-TTCAACTTAAAATCNNNNNN
129 GTTAACAAGAAAAGTAAAAGAACTTCAAATTAAAATCAATTTT
******** * * * * * ** **
1218 NNNNNNNNAAAACCATTTAAAGTGATTAATTAGGCTTTTGAAGCAATGGGTGACTATAAATAAAC
1 GAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGAC
* * * * * * * * * ** *
1283 TTTTTTTTCCAATGAATACTTTTTCCTTCATGTTTCTGAAGATAGACATTGAATTCTACTCTGT-
66 TTCTCTTGCCTATGAATGCTTCTT-CTTCATGTTTCTCAAGCTAGACATTCAATTAGAATCTGTG
* * * * * * *
1347 TTAACTATAAATGTGCAAAG-ATTTCAAATTTAAATCAAATTT
130 TTAACAAGAAAAGT-AAAAGAACTTCAAATTAAAATCAATTTT
* ********** *
1389 GAGATTATAAAACCATTTAAANNNNNNNNNNAGGCTTTTAAAGGAATGACTGACTATAAATGGAC
1 GAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGAC
* * * * * * *
1454 TTCTCTTACCCATGAATGCCCTCTTCTTTC-TATTTCTCAGAG-TAGACGTTCAATTATAATATG
66 TTCTCTTGCCTATGAATG-CTTCTTC-TTCATGTTTCTCA-AGCTAGACATTCAATTAGAATCTG
* * ** * * * *
1517 TTTTAACTAGAAAACCAAAACAAATTTGAACTTAAAATCAATTTT
128 TGTTAACAAGAAAAGTAAAA-GAACTTCAAATTAAAATCAATTTT
* * ** ** * *
1562 GAGATTATAAAAGC-ATTTAAAGTGACTGATAAGGCTTTTAAATCAATGGGTGACTACAAATAGA
1 GAGATTATAAAA-CTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGA
* ** * * * * * *
1626 CTTTTCTTATCAATGAATGCCTTTTTATTTATGTTTATCAAGGTAGACATTC
65 CTTCTCTTGCCTATGAATG-CTTCTTCTTCATGTTTCTCAAGCTAGACATTC
1678 NNNNNNNNNN
Statistics
Matches: 583, Mismatches: 195, Indels: 47
0.71 0.24 0.06
Matches are distributed among these distances:
170 19 0.03
171 325 0.56
172 135 0.23
173 103 0.18
174 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.35
Consensus pattern (171 bp):
GAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGAC
TTCTCTTGCCTATGAATGCTTCTTCTTCATGTTTCTCAAGCTAGACATTCAATTAGAATCTGTGT
TAACAAGAAAAGTAAAAGAACTTCAAATTAAAATCAATTTT
Found at i:1375 original size:342 final size:341
Alignment explanation
Indices: 704--1643 Score: 965
Period size: 342 Copynumber: 2.7 Consensus size: 341
694 NNNNNNNNNN
**
704 GAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGA-TGATAAATGGA
1 GAGATTATAAAA-TATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACT-ATAAATGGA
* * ** *
768 CTTCTCTTACCTATCAATGCTTACTTCTTTATATTTCTTGAGCTAGACATTCAATTATAATGTGT
64 CTTCTCTTACCTATGAATGCTT-CTTCTTCATATTTCTCAAGCTAGACATTCAATTATAATATGT
* *
833 TTTAACAAGAAAAGTAAAAGAACTTGAACTTAAAATCAATTTTGAGAATATAAAACTATTTAAAG
128 TTTAACAAGAAAAGTAAAAGAACTTCAACTTAAAATCAATTTTGAGAATATAAAACCATTTAAAG
* **
898 TGATGAATTAGGCTTTTGAAGTAATAAGTGACTATAAATAGGCTTTTCTTGCCAATGAATACTTT
193 TGATGAATTAGGCTTTTGAAGCAATAAGTGACTATAAATAAACTTTTCTTGCCAATGAATACTTT
********** *
963 TTCCTTCATGTTTCTNNNNNNNNNNATTCAATTCGAGTCTGTGTTAACCATAAATGTGCAAAATT
258 TTCCTTCATGTTTCTGAAGATAGACATTCAATTCGACTCTGTGTTAACCATAAATGTGCAAAATT
* *
1028 TCAAATTTAATTCAATTTT
323 TCAAATTTAAATCAAATTT
*
1047 GAGATTATAAAATAATTGAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGAC
1 GAGATTATAAAAT-ATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGAC
* * * *
1112 CTCTCTTGCCTATGAATGCGTTCTTCTTCATGTTTCTCAAGCTAGGCATTCAATTATAATATGTT
65 TTCTCTTACCTATGAATGC-TTCTTCTTCATATTTCTCAAGCTAGACATTCAATTATAATATGTT
* **************
1177 TTAACCAGAAAAGTAAAAGAA-TTCAACTTAAAATCNNNNNNNNNNNNNNAAAACCATTTAAAGT
129 TTAACAAGAAAAGTAAAAGAACTTCAACTTAAAATCAATTTTGAGAATATAAAACCATTTAAAGT
* ** * *
1241 GATTAATTAGGCTTTTGAAGCAATGGGTGACTATAAATAAACTTTTTTTTCCAATGAATACTTTT
194 GATGAATTAGGCTTTTGAAGCAATAAGTGACTATAAATAAACTTTTCTTGCCAATGAATACTTTT
* * *
1306 TCCTTCATGTTTCTGAAGATAGACATTGAATTCTACTCTGT-TTAACTATAAATGTGCAAAGATT
259 TCCTTCATGTTTCTGAAGATAGACATTCAATTCGACTCTGTGTTAACCATAAATGTGCAAA-ATT
1370 TCAAATTTAAATCAAATTT
323 TCAAATTTAAATCAAATTT
* ********** *
1389 GAGATTATAAAACCATTTAAANNNNNNNNNNAGGCTTTTAAAGGAATGACTGACTATAAATGGAC
1 GAGATTATAAAA-TATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGAC
* * *
1454 TTCTCTTACCCATGAATGCCCTCTTCTTTC-TATTTCTCAGAG-TAGACGTTCAATTATAATATG
65 TTCTCTTACCTATGAATG-CTTCTTC-TTCATATTTCTCA-AGCTAGACATTCAATTATAATATG
* ** * * * * *
1517 TTTTAACTAGAAAACCAAAACAAATTTGAACTTAAAATCAATTTTGAGATTATAAAAGCATTTAA
127 TTTTAACAAGAAAAGTAAAA-GAACTTCAACTTAAAATCAATTTTGAGAATATAAAACCATTTAA
* * * ** * * **
1582 AGTGACTG-ATAAGGCTTTTAAATCAATGGGTGACTACAAATAGACTTTTCTTATCAATGAAT
191 AGTGA-TGAATTAGGCTTTTGAAGCAATAAGTGACTATAAATAAACTTTTCTTGCCAATGAAT
1644 GCCTTTTTAT
Statistics
Matches: 484, Mismatches: 102, Indels: 21
0.80 0.17 0.03
Matches are distributed among these distances:
341 18 0.04
342 248 0.51
343 139 0.29
344 78 0.16
345 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.35
Consensus pattern (341 bp):
GAGATTATAAAATATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAATGACTATAAATGGACT
TCTCTTACCTATGAATGCTTCTTCTTCATATTTCTCAAGCTAGACATTCAATTATAATATGTTTT
AACAAGAAAAGTAAAAGAACTTCAACTTAAAATCAATTTTGAGAATATAAAACCATTTAAAGTGA
TGAATTAGGCTTTTGAAGCAATAAGTGACTATAAATAAACTTTTCTTGCCAATGAATACTTTTTC
CTTCATGTTTCTGAAGATAGACATTCAATTCGACTCTGTGTTAACCATAAATGTGCAAAATTTCA
AATTTAAATCAAATTT
Found at i:4497 original size:172 final size:170
Alignment explanation
Indices: 4083--5483 Score: 1336
Period size: 172 Copynumber: 8.2 Consensus size: 170
4073 TTTGAGCTTA
* * * * *
4083 AAATCAATTTTGAGATTATAAAATCATTTAAAGTGACTGATAAGGCTTTTCAAGCAATGGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * ** * * ** * * * *
4148 TACAAATAGACTTTTCTTATCAATGAATGCCTTTTAATTTACGTTTATCGAGGTAGACATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * *
4213 TATAGTCTGTTTTAACCAAAAGTATAAAAAAATTCAACTTT
131 TATAGTCTATTTTAA-CAAAAATGTAAAAAAATTCAACTTT
* * * * * * * *
4254 AGATCAATTATGACATTAAAAAACCATTTAAAGCGAGTAATACGACTTTTGAAGGTATGGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * *
4319 TATAAATGGACTTTTCTTGCCAATGAATACTTTTGTCCTCATGTTTCTAAAAGTAGGCAATCAAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
** * * * *
4384 CCTACTCTGTTTTAACTAAAAATTTATAAAGAATTCAGA-TTT
131 TATAGTCTATTTTAAC-AAAAATGTA-AAAAAATTCA-ACTTT
* * ** * *
4426 AAATCGATTTTGAGATTAAAAAATTATTAAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAT
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * * *
4491 TATAAATGGACTTTGCTTTCCAATAAATGCTTTTTTCTTCATGTTTCTCAAGGTGGACCTTAAAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* *
4556 TGTAGTCTATTTTAACCAAAAATGTACAAAAAATTCAAGTTT
131 TATAGTCTATTTTAA-CAAAAATGTA-AAAAAATTCAACTTT
* * * * * *
4598 GAATCAATTTTGAGATTATAAAACAATTTAAACTGAGTGATAAGGCTCTTGAAGGAATGGGTGTC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * *
4663 TATAAATGGACTTTTCTTGCCAATGATTTCTTTTTTCTTTACGTTTCTTAAGGTAGACATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * * *
4728 TATAGTCCATTTTGACAGAAAAAGTAAAAAAATTCAACTTA
131 TATAGTCTATTTTAACA-AAAATGTAAAAAAATTCAACTTT
* * * * * * *
4769 AAATTAATTATG-GCATTACAAAACTATTTACAA-CGAGTAATAAGGCTTTCGAAGGTATGGGTG
1 AAATCAATTTTGAG-ATTATAAAACCATTTA-AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * * * *
4832 GCTATAAATAGAATTTTCTTGCTAATGAATGCTTTTCTCTTCGTGTTTCTCAAAGTAGACATTCA
64 ACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCA
* * * *
4897 ATTCTAGTCTATTTTAACCAAAAATGTACAAAGATTTCAAATTT
129 ATTATAGTCTATTTTAA-CAAAAATGTA-AAAAAATTCAACTTT
* * *
4941 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGTTTTTAAAGGAATCGGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * ** * * * *
5006 TATAAATGGA-TTTCTCTTACCTATGAATTCTTACTTCTTTATGTTTCTTAAGCTAAACATTCAA
66 TATAAATGGACTTT-TCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAA
* * * * * * * *
5070 TTATAATATGTTTTGACAAGAAAAGTAAAAGAATTTGAACTTA
130 TTATAGTCTATTTTAACAA-AAATGTAAAA-AAATTCAACTTT
* * ** * * **
5113 AAATCAATTTTGAGAATATAAAACCATTTAAAGTGATTAATTTGGCGTTTGAAGTAATAAGTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* *
5178 TATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCATGGTAGACATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * *
5243 TCTAGTCTATTTTAACAAAAATGTACAAAACATTCAAATTT
131 TATAGTCTATTTTAACAAAAATGTA-AAAAAATTCAACTTT
* * *
5284 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATAGCTGAC
1 AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * ** * ** *
5349 TATAAATGGACTTCTCTTACCCATGAATGCTTACTTCTTTATGTTTCTTGAGCTAGACATTCAAT
66 TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
* * * * *
5414 TATAATATATTTTAA-ATAGAAAAGTAAAAAAATTTGAACTTA
131 TATAGTCTATTTTAACA-A-AAATGTAAAAAAA-TTCAACTTT
*
5456 AAATCAATTTTGAGAATATAAAACCATT
1 AAATCAATTTTGAGATTATAAAACCATT
5484 NNNNNNNNNN
Statistics
Matches: 986, Mismatches: 224, Indels: 39
0.79 0.18 0.03
Matches are distributed among these distances:
170 3 0.00
171 407 0.41
172 570 0.58
173 6 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (170 bp):
AAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
TATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAAT
TATAGTCTATTTTAACAAAAATGTAAAAAAATTCAACTTT
Found at i:5120 original size:515 final size:509
Alignment explanation
Indices: 4034--5483 Score: 1505
Period size: 515 Copynumber: 2.8 Consensus size: 509
4024 NNNATAGACG
* * *
4034 TTCAATTATAATATGTTTTAACTAGAAAAGCAAAAAAAGTTTGAGCTTAAAATCAATTTTGAGAT
1 TTCAATTATAATATGTTTTAACAAGAAAAG-TAAAAAA-TTTGAACTTAAAATCAATTTTGAGAT
* *
4099 TATAAAATCATTTAAAGTGACTGATAAGGCTTTTCAAGCAATGGGTGACTACAAATAGACTTTTC
64 TATAAAA-CATTTAAAGTGACTGATAAGGC-TTTGAAGCAATGGGTGACTATAAATAGACTTTTC
** * * ** * * *
4164 TTATCAATGAATGCCTTTTAATTTACGTTTATCGAGGTAGACATTCAATTATAGTCTGTTTTA-A
127 TTGCCAATGAATACTTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTACA
* * *
4228 CCAAAAGTATAAAAAAATTCAACTTTAGATCAATTATGACATTAAAAAACCATTTAAAGCGAGTA
192 -AAAAAG--TAAAAAAATTCAACTTTAAATCAATTATGGCATTAAAAAACCATTTAAAGCGAGTA
* * * * *
4293 ATACGACTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTGTCCT
254 ATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTCTCTT
* * * * * * * * *
4358 CATGTTTCTAAAAGTAGGCAATCAATCCTACTCTGTTTTAACTAAAAATTTATAAAGAATTCAGA
319 CATGTTTCT-AAAGTAGACATTCAATTCTAATCTATTTTAACTAAAAATGTAAAAAGATTTCAAA
* * ** * *
4423 TTTAAATCGATTTTGAGATTAAAAAATTATTAAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGT
383 TTTAAATCAATTTTGAGATTATAAAACCATTAAAAGTGAGTAATAAGGCTTTTAAAGGAATCGGT
* ** * ** *
4488 GATTATAAATGGACTTTGCTTTCCAATAAATGCTTTTTTCTTCATGTTTCTCAAGGTGGACC
448 GACTATAAATGGACTTTGCTTTCCAATAAATGCTTACTTCTTCATGTTTCTCAAGCTAAACA
* * * * * * * * * **
4550 TTAAATTGTAGTCTATTTTAACCAA-AAATGTACAAAAAATTCAAGTTTGAATCAATTTTGAGAT
1 TTCAATTATAATATGTTTTAA-CAAGAAAAGTA-AAAAATTTGAACTTAAAATCAATTTTGAGAT
* * * * *
4614 TATAAAACAATTTAAACTGAGTGATAAGGCTCTTGAAGGAATGGGTGTCTATAAATGGACTTTTC
64 TATAAAAC-ATTTAAAGTGACTGATAAGGCT-TTGAAGCAATGGGTGACTATAAATAGACTTTTC
* * * *
4679 TTGCCAATGATTTCTTTTTTCTTTACGTTTCTTAAGGTAGACATTCAATTATAGTCCATTTTGAC
127 TTGCCAATGAATACTTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTT-AC
* * * *
4744 AGAAAAAGTAAAAAAATTCAACTTAAAATTAATTATGGCATTACAAAACTATTTACAA-CGAGTA
191 A-AAAAAGTAAAAAAATTCAACTTTAAATCAATTATGGCATTAAAAAACCATTTA-AAGCGAGTA
* * * * *
4808 ATAAGGCTTTCGAAGGTATGGGTGGCTATAAATAGAATTTTCTTGCTAATGAATGCTTTTCTCTT
254 ATAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTCTCTT
* * * *
4873 CGTGTTTCTCAAAGTAGACATTCAATTCTAGTCTATTTTAACCAAAAATGTACAAAGATTTCAAA
319 CATGTTTCT-AAAGTAGACATTCAATTCTAATCTATTTTAACTAAAAATGTAAAAAGATTTCAAA
* *
4938 TTTAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGTTTTTAAAGGAATCGGT
383 TTTAAATCAATTTTGAGATTATAAAACCATTAAAAGTGAGTAATAAGGCTTTTAAAGGAATCGGT
* * * * *
5003 GACTATAAATGGA-TTT-CTCTTACCTATGAATTCTTACTTCTTTATGTTTCTTAAGCTAAACA
448 GACTATAAATGGACTTTGCT-TT-CCAATAAATGCTTACTTCTTCATGTTTCTCAAGCTAAACA
* *
5065 TTCAATTATAATATGTTTTGACAAGAAAAGTAAAAGAATTTGAACTTAAAATCAATTTTGAGAAT
1 TTCAATTATAATATGTTTTAACAAGAAAAGTAAAA-AATTTGAACTTAAAATCAATTTTGAGATT
* * ** * **
5130 ATAAAACCATTTAAAGTGATTAATTTGGCGTTTGAAGTAATAAGTGACTATAAATAGACTTTTCT
65 ATAAAA-CATTTAAAGTGACTGATAAGGC-TTTGAAGCAATGGGTGACTATAAATAGACTTTTCT
* * * *
5195 TGCCAATGAATACTTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTCTAGTCTATTTTAACA
128 TGCCAATGAATACTTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTT-ACA
* * * * * *
5260 AAAATGTACAAAACATTCAAATTTAAATCAATTTTGAG-ATTATAAAACCATTTAAAGTGAGTAA
192 AAAAAGTA-AAAAAATTCAACTTTAAATCAATTATG-GCATTAAAAAACCATTTAAAGCGAGTAA
* * * * * * *
5324 TAAGGCTTTTAAAGGAATAGCTGACTATAAATGGACTTCTCTTACCCATGAATGCTTACTTCT-T
255 TAAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTT--TTCTCT
** * * * * *
5388 T-ATGTTTCTTGAGCTAGACATTCAATTATAATATATTTTAAATAGAAAA-GTAAAAAAATTTGA
318 TCATGTTTCTAAAG-TAGACATTCAATTCTAATCTATTTTAACTA-AAAATGTAAAAAGATTTCA
* * *
5451 ACTTAAAATCAATTTTGAGAATATAAAACCATT
381 AATTTAAATCAATTTTGAGATTATAAAACCATT
5484 NNNNNNNNNN
Statistics
Matches: 764, Mismatches: 150, Indels: 41
0.80 0.16 0.04
Matches are distributed among these distances:
513 2 0.00
514 24 0.03
515 689 0.90
516 37 0.05
517 12 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (509 bp):
TTCAATTATAATATGTTTTAACAAGAAAAGTAAAAAATTTGAACTTAAAATCAATTTTGAGATTA
TAAAACATTTAAAGTGACTGATAAGGCTTTGAAGCAATGGGTGACTATAAATAGACTTTTCTTGC
CAATGAATACTTTTTTCTTTACGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTACAAAAA
AGTAAAAAAATTCAACTTTAAATCAATTATGGCATTAAAAAACCATTTAAAGCGAGTAATAAGGC
TTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTCTCTTCATGTTT
CTAAAGTAGACATTCAATTCTAATCTATTTTAACTAAAAATGTAAAAAGATTTCAAATTTAAATC
AATTTTGAGATTATAAAACCATTAAAAGTGAGTAATAAGGCTTTTAAAGGAATCGGTGACTATAA
ATGGACTTTGCTTTCCAATAAATGCTTACTTCTTCATGTTTCTCAAGCTAAACA
Found at i:5480 original size:343 final size:344
Alignment explanation
Indices: 4028--5483 Score: 1590
Period size: 343 Copynumber: 4.2 Consensus size: 344
4018 NNNNNNNNNA
* * * *
4028 TAGACGTTCAATTATAATATGTTTTAACTAGAAAAGCAAAAAAAGTTTGAGCTTAAAATCAATTT
1 TAGACATTCAATTATAATATGTTTTAAATAGAAAAGTAAAAAAA-TTTGAACTTAAAATCAATTT
* * * * * *
4093 TGAGATTATAAAATCATTTAAAGTGACTGATAAGGCTTTTCAAGCAATGGGTGACTACAAATAGA
65 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGA
** * ** * * * * * *
4158 CTTTTCTTATCAATGAATGCCTTTTAATTTACGTTTATCGAGGTAGACATTCAATTATAGTCTGT
130 CTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTAT
* * * * * * *
4223 TTTAACCAAAAGTATA-AAAAAATTCAACTTTAGATCAATTATGACATTAAAAAACCATTTAAAG
195 TTTAACCAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAG
* * * * * * * *
4287 CGAGTAATACGACTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTT-
260 TGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTCTCTTACCAATGAATTCTTA
* * * *
4351 TTGTCCTCATGTTTCTAAAAG-
325 CT-TCTTTATGTTTCT-TAAGC
* * ** * * * * * * * *
4372 TAGGCAATCAATCCTACTCTGTTTTAACTA-AAAATTTATAAAGAA-TTCAGA-TTTAAATCGAT
1 TAGACATTCAATTATAATATGTTTTAAATAGAAAA-GTA-AAAAAATTTGA-ACTTAAAATCAAT
* ** * * * *
4434 TTTGAGATTAAAAAATTATTAAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATTATAAATG
63 TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATA
* * * * * * *
4499 GACTTTGCTTTCCAATAAATGCTTTTTTCTTCATGTTTCTCAAGGTGGACCTTAAATTGTAGTCT
128 GACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCT
* * *
4564 ATTTTAACCAAAAATGTACAAAAAATTCAAGTTTGAATCAATTTTGAGATTATAAAACAATTTAA
193 ATTTTAACCAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAA
* * * * * * * *
4629 ACTGAGTGATAAGGCTCTTGAAGGAATGGGTGTCTATAAATGGACTTTTCTTGCCAATGATTTCT
258 AGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTCTCTTACCAATGAATTCT
** * *
4694 TTTTTCTTTACGTTTCTTAAGG
323 TACTTCTTTATGTTTCTTAAGC
* * * * * *
4716 TAGACATTCAATTATAGTCCAT-TTTGACAGA-AAAAGTAAAAAAA-TTCAACTTAAAATTAATT
1 TAGACATTCAATTATAAT--ATGTTTTAAATAGAAAAGTAAAAAAATTTGAACTTAAAATCAATT
* * * * * *
4778 ATG-GCATTACAAAACTATTTACAA-CGAGTAATAAGGCTTTCGAAGGT-ATGGGTGGCTATAAA
64 TTGAG-ATTATAAAACCATTTA-AAGTGAGTAATAAGGCTTTTGAA-GTAATGGGTGACTATAAA
* * * * *
4840 TAGAATTTTCTTGCTAATGAATGCTTTTCTCTTCGTGTTTCTCAAAGTAGACATTCAATTCTAGT
126 TAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGT
* *
4905 CTATTTTAACCAAAAATGTACAAAGATTTCAAATTTAAATCAATTTTGAGATTATAAAACCATTT
191 CTATTTTAACCAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTT
* * * *
4970 AAAGTGAGTAATAAGGTTTTTAAAGGAATCGGTGACTATAAATGGATTTCTCTTACCTATGAATT
256 AAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTCTCTTACCAATGAATT
5035 CTTACTTCTTTATGTTTCTTAAGC
321 CTTACTTCTTTATGTTTCTTAAGC
* * *
5059 TAAACATTCAATTATAATATGTTTTGACA-AGAAAAGTAAAAGAATTTGAACTTAAAATCAATTT
1 TAGACATTCAATTATAATATGTTTT-AAATAGAAAAGTAAAAAAATTTGAACTTAAAATCAATTT
* * ** * **
5123 TGAGAATATAAAACCATTTAAAGTGATTAATTTGGCGTTTGAAGTAATAAGTGACTATAAATAGA
65 TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGA
* *
5188 CTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCATGGTAGACATTCAATTCTAGTCTAT
130 CTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTAT
*
5253 TTTAA-CAAAAATGTACAAAACATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAG
195 TTTAACCAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAG
* * * *
5317 TGAGTAATAAGGCTTTTAAAGGAATAGCTGACTATAAATGGACTTCTCTTACCCATGAATGCTTA
260 TGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTCTCTTACCAATGAATTCTTA
*
5382 CTTCTTTATGTTTCTTGAGC
325 CTTCTTTATGTTTCTTAAGC
*
5402 TAGACATTCAATTATAATATATTTTAAATAGAAAAGTAAAAAAATTTGAACTTAAAATCAATTTT
1 TAGACATTCAATTATAATATGTTTTAAATAGAAAAGTAAAAAAATTTGAACTTAAAATCAATTTT
*
5467 GAGAATATAAAACCATT
66 GAGATTATAAAACCATT
5484 NNNNNNNNNN
Statistics
Matches: 931, Mismatches: 161, Indels: 41
0.82 0.14 0.04
Matches are distributed among these distances:
341 2 0.00
342 8 0.01
343 632 0.68
344 271 0.29
345 17 0.02
346 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (344 bp):
TAGACATTCAATTATAATATGTTTTAAATAGAAAAGTAAAAAAATTTGAACTTAAAATCAATTTT
GAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGTAATGGGTGACTATAAATAGAC
TTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTATT
TTAACCAAAAATGTACAAAAAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGT
GAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTCTCTTACCAATGAATTCTTAC
TTCTTTATGTTTCTTAAGC
Done.