Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398386.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1683.0, 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: 5059
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.28
Warning! 1016 characters in sequence are not A, C, G, or T
Found at i:545 original size:135 final size:135
Alignment explanation
Indices: 360--610 Score: 317
Period size: 135 Copynumber: 1.9 Consensus size: 135
350 GTATAGTCTA
* * *
360 TTTTGACCAAAAATATAAAAAATTTTAACTTAAAATAAAGTATAAGATTATAAAACCATTTAAAG
1 TTTTAACCAAAAATATAAAAAAATTCAACTTAAAATAAAGTATAAGATTATAAAACCATTTAAAG
* * * **
425 TGTGTAATAAGGCTTTCAAAGGACTGGGAGA-CATAAATGGACTTTTCTTGCTAAATAAGTGGCA
66 CGCGTAATAA-GCTTTCAAAGGAATGAAAGATCATAAATGGACTTTTCTTGCTAAATAAGTGGCA
489 AAACTG
130 AAACTG
* * * * *
495 TTTTAACCAAAACTGTAAAAAAATTCAACTTAAAAT-CAGTTATGATATTATAAAACCATTTAAA
1 TTTTAACCAAAAATATAAAAAAATTCAACTTAAAATAAAG-TATAAGATTATAAAACCATTTAAA
** * *
559 GCGCGTAATAAGCTTTTGAAGGAATGAAATATTATAAATGGACTTTTCTTGC
65 GCGCGTAATAAGCTTTCAAAGGAATGAAAGATCATAAATGGACTTTTCTTGC
611 CAATGAATGA
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
134 16 0.16
135 81 0.84
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (135 bp):
TTTTAACCAAAAATATAAAAAAATTCAACTTAAAATAAAGTATAAGATTATAAAACCATTTAAAG
CGCGTAATAAGCTTTCAAAGGAATGAAAGATCATAAATGGACTTTTCTTGCTAAATAAGTGGCAA
AACTG
Found at i:861 original size:171 final size:171
Alignment explanation
Indices: 492--2583 Score: 1697
Period size: 171 Copynumber: 12.2 Consensus size: 171
482 AGTGGCAAAA
** * * *
492 CTGTTTTAACCAAAACTGTAAAAAAATTCAACTTAAAATCAGTTATGATATTATAAAACCATTTA
1 CTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
** * * * *
557 AAGCGCGTAATAA-GCTTTTGAAGGAATGAAATATTATAAATGGACTTTTCTTGCCAATGAATGA
66 AAGCTAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGG
* * * **
621 CTTTTTCTACATGTTTCTCCAGACAATTATTCAATTATAGT
131 CTTTTTCTACACGTTTCTCGAGGCAAGCATTCAATTATAGT
* *
662 CTGTTTTAATGAAAAAGGTAAAAAAAATTCAACTT-AAATACAATTATGAGATTACAAAACCATT
1 CTGTTTTAATGAAAAATGT-AAAAAAATTCAACTTAAAAT-CAATTATGAGATTATAAAACCATT
* * * * * * * *
726 TAAGGCTAGTAATAAGGCTATTGAAAGTATGAGAGACTATAAATGGATTTTTCTTTCAAATAAAT
64 TAAAGCTAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAAT
* * *
791 GGCTTTCTCTACACGTTTCTTGAGGCAAGCATTTAATTATAGT
129 GGCTTTTTCTACACGTTTCTCGAGGCAAGCATTCAATTATAGT
****************************
834 CTGTTTTAATGAAAAATGTAAAAAAATTCAACTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTA
1 CTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * **
899 AAG-TGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTTCTTTACAATGAAT
66 AAGCT-AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGAC-TTTTCTTGCCAATGAAT
* * * *
963 -ACTTTTTTCTTCACATTTCTCGAGG-TAGACATTCAATTAT-GAT
129 GGC-TTTTTCTACACGTTTCTCGAGGCAAG-CATTCAATTATAG-T
* * * * * * *
1006 TTATTTTAACT-TAAAGTGTAAAAAAAATCAACTTAAAATCAATTATGAGATTAAAAAACTATTT
1 CTGTTTTAA-TGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * **
1070 AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTTTTCTTATCAATGAATG
65 AAAGCTAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * * *
1135 GCTTTTTCTACATGTTTCTCGAGGCAGGCACTCAGTTATTGT
130 GCTTTTTCTACACGTTTCTCGAGGCAAGCATTCAATTATAGT
*
1177 CTGTTTTAATGAAAAATGTAAAAACAA-TCAACTTAAAATCAATTATGAGATTATAAAATCATTT
1 CTGTTTTAATGAAAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * ** * *
1241 AAAGCTAGTAATAAGG-TTTTGAAAGAATGGGTTACTATAAATGGAATTTTCTTGCTAATGAATG
65 AAAGCTAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * * * * *
1305 TCTTTTCCTTCACTTTTCTTGAGGTAA-CATTCAATTATAAT
130 GCTTTTTCTACACGTTTCTCGAGGCAAGCATTCAATTATAGT
* ** * * * *
1346 CTATTTTAACAAAAAATGTAAAAAAAAAATTGAACCTAAAATCGATTTTGAGATTATAAAACCAT
1 CTGTTTTAATGAAAAATGT---AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
** * * * * *
1411 TTAAAG-TGAGTAATACTGCTTTTAAAAGAATGGGTGACTATAAATGGACTTTGCTTGCCAATGA
63 TTAAAGCT-AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGA
* * *
1475 AT-G-TGTTTTCTTA-ACATTTCTTGAGG-TAGACATTCAATTATTA-T
127 ATGGCT-TTTTC-TACACGTTTCTCGAGGCAAG-CATTCAATTA-TAGT
** * **
1519 CTGTTTTAACCAAAAATGAAAAAAAAATAAAACTTAAAATCAATTATGAGATTATAAAACCATTT
1 CTGTTTTAATGAAAAATG-TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * * * * *
1584 GAAGCGAGTAATATGGCTTTTGAAGGAATAAGAGACTATAAATTGACTTTTCTT-CTGAATAAAA
65 AAAGCTAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGC-CAATGAAT
** * * *
1648 GTATTTTTCTACATGTTTTTCAAGGC-AGACAATT-AATTATAGT
129 GGCTTTTTCTACACGTTTCTCGAGGCAAG-C-ATTCAATTATAGT
* ** * * * * * *
1691 CCGTTTTAACAAAAAATGT-AAAACATTGAACCTCAAATGAATTATGAGATTATGAAACCATTTA
1 CTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * * * * * *
1755 AAGCGAGTAATAAGGGTCTCGAAGGAATGAGAGACAATAAATGTACTTTTATTACCAATGAATGT
66 AAGCTAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGG
** * * *
1820 CTTTTTCCT-CATATTTCTCGA--TATAGACATTTAATTATAAT
131 CTTTTT-CTACACGTTTCTCGAGGCA-AG-CATTCAATTATAGT
* ** * * * * *
1861 TTGTTTTAACCAAAAAAGTAAAAAAAAATTGAACTTAAAATTAATTTTGAGACTATAAAACCATT
1 CTGTTTTAATGAAAAATGT--AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * * *
1926 TAAAGCGAGTAATAAGGCTTTTGAAGGAACGA-TGACTATAAATAGACTTTTCTTGCCAATAAAT
64 TAAAGCTAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAAT
* *
1990 -GCTTTTTCTTCACGTTTCTTGA-G-ATAGACATTCAATTATAGT
129 GGCTTTTTCTACACGTTTCTCGAGGCA-AG-CATTCAATTATAGT
* * * * *
2032 CTGTTTTAAT-AAAAATATTAATAAAAATTGAACATAAAATCAATTTTGAGATTATAAAACTATT
1 CTGTTTTAATGAAAAAT-GTAA-AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * *
2096 TAAAG-TGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT-ACAATTGA
64 TAAAGCT-AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAA-TGA
** * * * *
2159 ATACCTTTTTCTTCACGTTTGTCGAGGTACA-CATTCAATTATAAT
127 ATGGCTTTTTCTACACGTTTCTCGAGGCA-AGCATTCAATTATAGT
* * * *
2204 ATGTTTTAAAT-AAAATTATAAAAAAATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTT
1 CTGTTTT-AATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * *
2268 AAAG-TGAGTAATAAGGCTTTCGAAGGAATGAGAGAATATAAATGGACTTTTTTTGCCAATGAAT
65 AAAGCT-AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAAT
* * *
2332 AGCTTTTTCTACATGTTTCTCGAGGTAAGCATTCAATTATAGT
129 GGCTTTTTCTACACGTTTCTCGAGGCAAGCATTCAATTATAGT
*
2375 CTGTTTTAATGAAAAATGTAAAACAAATTCAACTT-AAATACAATTATGAGAGTCA-AAAACCAT
1 CTGTTTTAATGAAAAATGTAAAA-AAATTCAACTTAAAAT-CAATTATGAGA-TTATAAAACCAT
* * * *
2438 TTAAGGGTAGTAATAAGGCTTTTGAAGGCACA-G-GAGACTGTAAATGGACATTTCTT-CCAAGT
63 TTAAAGCTAGTAATAAGGCTTTTGAAGG-A-ATGAGAGACTATAAATGGACTTTTCTTGCCAA-T
* * * *
2500 AAATGGCTTTCTCTACACGTTTC-CTTAGGCAGGCATTCAATTATAGT
125 GAATGGCTTTTTCTACACGTTTCTC-GAGGCAAGCATTCAATTATAGT
*
2547 CTGTTTTAATGAAAAATGTAAAAATATTCAACTTAAA
1 CTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAA
2584 NNNNNNNNNN
Statistics
Matches: 1543, Mismatches: 312, Indels: 132
0.78 0.16 0.07
Matches are distributed among these distances:
169 31 0.02
170 290 0.19
171 546 0.35
172 518 0.34
173 153 0.10
174 5 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (171 bp):
CTGTTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
AAGCTAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGG
CTTTTTCTACACGTTTCTCGAGGCAAGCATTCAATTATAGT
Found at i:1244 original size:343 final size:342
Alignment explanation
Indices: 492--2583 Score: 1688
Period size: 343 Copynumber: 6.1 Consensus size: 342
482 AGTGGCAAAA
* * * * *
492 CTGTTTTAACCAAAACTGTAAAAAAATTCAACTTAAAATCAGTTATGATATTATAAAACCATTTA
1 CTGTTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * * *
557 AAGCGCGTAATAA-GCTTTTGAAGGAATGAA-ATATTATAAATGGACTTTTCTTGCCAATGAATG
66 AAGTGAGTAATAAGGCTTTTGAAGGAAT-AAGAGACTATAAATAGACTTTTCTTTCCAATGAAT-
* * * ** * *
620 AC-TTTTTCTACATGTTTCTCCAGACA-ATTATTCAATTATAGTCTGTTTTAA-TGAAAAAGGTA
129 ACTTTTTTCTTCACGTTTCTCGAGGTAGA-CATTCAATTATAGTCTGTTTTAACT-AAAAATGT-
* * * * * *
682 AAAAAAATTCAA-CTTAAATACAATTATGAGATTACAAAACCATTTAAGGCTAGTAATAAGGCTA
191 AAAAAAATTGAACCTAAAAT-CAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTT
* * * * * * *
746 TTGAA-AGTATGAGAGACTATAAATGGATTTTTCTTTCAAATAAATGGCTTTCTCTACACGTTTC
255 TTGAAGA-AATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGGCTTTTTCTACACGTTTC
* * * *
810 TTGAGGCA-AGCATTTAATTATAGT
319 TCGAGGTAGA-CATTCAATTATAAT
* * ****************************
834 CTGTTTTAATGAAAAATGTAAAAAAATTCAACTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTA
1 CTGTTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
*
899 AAGTGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTTCTTTACAATGAATA
66 AAGTGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATAGAC-TTTTCTTTCCAATGAATA
* * * * *
964 CTTTTTTCTTCACATTTCTCGAGGTAGACATTCAATTAT-GATTTATTTTAACTTAAAGTGTAAA
130 CTTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAG-TCTGTTTTAACTAAAAATGTAAA
* * * * *
1028 AAAAATCAACTTAAAATCAATTATGAGATTAAAAAACTATTTAAAGCGAGTAATAAGGCTTTTGA
194 AAAATTGAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA
* *
1093 AGAAATGAGTGACTATAAATGGACTTTTCTTATCAATGAATGGCTTTTTCTACATGTTTCTCGAG
259 AGAAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGGCTTTTTCTACACGTTTCTCGAG
* * * * **
1158 GCAGGCACTCAGTTATTGT
324 GTAGACATTCAATTATAAT
* * *
1177 CTGTTTTAATGAAAAATGTAAAAACAATCAACTTAAAATCAATTATGAGATTATAAAATCATTTA
1 CTGTTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* ** ** * * * *
1242 AAGCT-AGTAATAAGG-TTTTGAAAGAATGGGTTACTATAAATGGAATTTTCTTGCTAATGAAT-
66 AAG-TGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTCTTTCCAATGAATA
* * * * * * *
1304 GTCTTTTCCTTCACTTTTCTTGAGGTA-ACATTCAATTATAATCTATTTTAACAAAAAATGTAAA
130 CT-TTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGT---
* * * **
1368 AAAAAAATTGAACCTAAAATCGATTTTGAGATTATAAAACCATTTAAAGTGAGTAATACTGCTTT
191 AAAAAAATTGAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * * *
1433 T-AAAAGAATGGGTGACTATAAATGGACTTTGCTTGCCAATGAAT-G-TGTTTTCTTA-ACATTT
256 TGAAGA-AATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGGCT-TTTTC-TACACGTTT
* *
1494 CTTGAGGTAGACATTCAATTATTAT
318 CTCGAGGTAGACATTCAATTATAAT
* * *
1519 CTGTTTTAACCAAAAATGAAAAAAAAATAAAACTTAAAATCAATTATGAGATTATAAAACCATTT
1 CTGTTTTAATCAAAAATGTAAAAAAAAT-CAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * * *
1584 GAAGCGAGTAATATGGCTTTTGAAGGAATAAGAGACTATAAATTGACTTTTC-TTCTGAAT-AAA
65 AAAGTGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTCTTTC-CAATGAAT
* * * * * * * *
1647 AGTATTTTTCTACATGTTTTTCAAGGCAGACAATT-AATTATAGTCCGTTTTAACAAAAAATGT-
129 ACT-TTTTTCTTCACGTTTCTCGAGGTAGAC-ATTCAATTATAGTCTGTTTTAACTAAAAATGTA
* * * * * * *
1710 AAAACATTGAACCTCAAATGAATTATGAGATTATGAAACCATTTAAAGCGAGTAATAAGGGTCTC
192 AAAAAATTGAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
* * * * * * **
1775 GAAGGAATGAGAGACAATAAATGTACTTTTATTACCAATGAATGTCTTTTTCCT-CATATTTCTC
257 GAAGAAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGGCTTTTT-CTACACGTTTCTC
** *
1839 GATATAGACATTTAATTATAAT
321 GAGGTAGACATTCAATTATAAT
* * * * * * *
1861 TTGTTTTAACCAAAAAAGTAAAAAAAAATTGAACTTAAAATTAATTTTGAGACTATAAAACCATT
1 CTGTTTTAATCAAAAATGT-AAAAAAAA-TCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * *
1926 TAAAGCGAGTAATAAGGCTTTTGAAGG-A-ACGATGACTATAAATAGACTTTTCTTGCCAATAAA
64 TAAAGTGAGTAATAAGGCTTTTGAAGGAATAAGA-GACTATAAATAGACTTTTCTTTCCAATGAA
* * * *
1989 TGC-TTTTTCTTCACGTTTCTTGAGATAGACATTCAATTATAGTCTGTTTTAA-TAAAAATATTA
128 TACTTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAAT-GTA
* * * *
2052 ATAAAAATTGAACATAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTT
192 A-AAAAATTGAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTT
* * * ** * *
2117 TGAAGGAATGGGTGACTATAAATAGACTTTTCTTA-CAATTGAATACCTTTTTCTTCACGTTTGT
256 TGAAGAAATGAGTGACTATAAATGGACTTTTCTTACCAA-TGAATGGCTTTTTCTACACGTTTCT
*
2181 CGAGGTACACATTCAATTATAAT
320 CGAGGTAGACATTCAATTATAAT
* * * * *
2204 ATGTTTTAAAT-AAAATTATAAAAAAATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTT
1 CTGTTTT-AATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * *
2268 AAAGTGAGTAATAAGGCTTTCGAAGGAATGAGAGAATATAAATGGACTTTT-TTTGCCAATGAAT
65 AAAGTGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTCTTT-CCAATGAAT
* *
2332 AGC-TTTTTCTACATGTTTCTCGAGGTA-AGCATTCAATTATAGTCTGTTTTAA-TGAAAAATGT
129 A-CTTTTTTCTTCACGTTTCTCGAGGTAGA-CATTCAATTATAGTCTGTTTTAACT-AAAAATGT
* * * *
2394 AAAACAAATTCAA-CTTAAATACAATTATGAGAGTCA-AAAACCATTT-AAGGGTAGTAATAAGG
191 AAAA-AAATTGAACCTAAAAT-CAATTATGAGA-TTATAAAACCATTTAAAGCG-AGTAATAAGG
* * * * * *
2456 CTTTTGAAGGCACA-G-GAGACTGTAAATGGACATTTCTT-CCAAGTAAATGGCTTTCTCTACAC
252 CTTTTGAA-G-AAATGAGTGACTATAAATGGACTTTTCTTACCAA-TGAATGGCTTTTTCTACAC
* * * *
2518 GTTTC-CTTAGGCAGGCATTCAATTATAGT
314 GTTTCTC-GAGGTAGACATTCAATTATAAT
* * *
2547 CTGTTTTAATGAAAAATGTAAAAATATTCAACTTAAA
1 CTGTTTTAATCAAAAATGTAAAAAAAATCAACTTAAA
2584 NNNNNNNNNN
Statistics
Matches: 1382, Mismatches: 310, Indels: 115
0.76 0.17 0.06
Matches are distributed among these distances:
340 38 0.03
341 219 0.16
342 250 0.18
343 717 0.52
344 125 0.09
345 30 0.02
346 3 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (342 bp):
CTGTTTTAATCAAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
AAGTGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATAGACTTTTCTTTCCAATGAATAC
TTTTTTCTTCACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAA
AATTGAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
AAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATGGCTTTTTCTACACGTTTCTCGAGGT
AGACATTCAATTATAAT
Found at i:1623 original size:514 final size:515
Alignment explanation
Indices: 492--2583 Score: 1881
Period size: 514 Copynumber: 4.1 Consensus size: 515
482 AGTGGCAAAA
* * * *
492 CTGTTTTAACCAAAACTG-TAAAAAAATTCAACTTAAAATCAGTTATGATATTATAAAACCATTT
1 CTGTTTTAACCAAAAATGAAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * **
556 AAAGCGCGTAATAA-GCTTTTGAAGGAATGAA-ATATTATAAATGGACTTTTCTTGCCAATGAAT
66 AAAGCGAGTAATAAGGCTTTTGAAGGAAT-AAGAGACTATAAATGGACTTTTCTTATCAATGAAT
* * * *
619 GACTTTTTCTACATGTTTCTCCAGACA-ATTATTCAATTATAGTCTGTTTTAATGAAAAAGGTAA
130 GACTTTTTCTACATGTTTCTCGAGGCAGA-CATTCAATTATAGTCTGTTTTAATGAAAAATGTAA
* * *
683 AAAAAATTCAACTT-AAATACAATTATGAGATTACAAAACCATTTAAGGCTAGTAATAAGGCTAT
194 AAACAATTCAACTTAAAAT-CAATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCT-T
* * * * * * **
747 T-GAAAGTATGAGAGACTATAAATGGATTTTTCTTTCAAATAAATGGC-TTTCTCTACACGTTTC
257 TCGAAAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTC-CTACATATTTC
* * * * ** * ****
810 TTGAGGCAAGCATTTAATTATAGTCTGTTTTAATGAAAAATGT--AAAAAAATTCAA-CTNNNNN
321 TCGAGGTAAGCATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAAAATTGAACCT-AAAA
*********************** * *
872 NNNNNNNNNNNNNNNNNNNNNNNTTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAAGAGACTAT
385 TCAATTTTGAGACTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTAT
** * *
937 AAATAGACTTTTTCTTTACAATGAATACTTTTTTCTTCACATTTCTCGAGGTAGACATTCAATTA
450 AAATAGAC-TTTTCTTGCCAATGAAT--GTTTTTCTTCACATTTCTTGAGGTAGACATTCAATTA
*
1002 TGAT
512 TTAT
* * ** * * * *
1006 TTATTTTAACTTAAAGTGTAAAAAAAA-TCAACTTAAAATCAATTATGAGATTAAAAAACTATTT
1 CTGTTTTAACCAAAAATGAAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * *
1070 AAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTGACTATAAATGGACTTTTCTTATCAATGAATG
66 AAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTATCAATGAATG
* * * * *
1135 GCTTTTTCTACATGTTTCTCGAGGCAGGCACTCAGTTATTGTCTGTTTTAATGAAAAATGTAAAA
131 ACTTTTTCTACATGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAA
* *
1200 ACAA-TCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCTAGTAATAAGG-TTTTGA
196 ACAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTCGA
* ** * * * *
1263 AAGAATGGGTTACTATAAATGGAATTTTCTTGCTAATGAATGTCTTTTCCTTCACT-TTTCTTGA
261 AAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTCCTACA-TATTTCTCGA
* *
1327 GGTAA-CATTCAATTATAATCTATTTTAACAAAAAATGTAAAAAAAAAATTGAACCTAAAATCGA
325 GGTAAGCATTCAATTATAATCTGTTTTAACAAAAAATGT-AAAAAAAAATTGAACCTAAAATCAA
* ** * * *
1391 TTTTGAGATTATAAAACCATTTAAAGTGAGTAATACTGCTTTTAAAAGAATGGGTGACTATAAAT
389 TTTTGAGACTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAAT
* * *
1456 GGACTTTGCTTGCCAATGAATGTGTTTTCTTAACATTTCTTGAGGTAGACATTCAATTATTAT
454 AGACTTTTCTTGCCAATGAATGT-TTTTCTTCACATTTCTTGAGGTAGACATTCAATTATTAT
**
1519 CTGTTTTAACCAAAAATGAAAAAAAAATAAAACTTAAAATCAATTATGAGATTATAAAACCATTT
1 CTGTTTTAACCAAAAATGAAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
* * * * * * *
1584 GAAGCGAGTAATATGGCTTTTGAAGGAATAAGAGACTATAAATTGACTTTTCTTCTGAATAAAAG
66 AAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTATCAATGAATG
* * * **
1649 TA-TTTTTCTACATGTTTTTCAAGGCAGACAATT-AATTATAGTCCGTTTTAACAAAAAATGT-A
131 -ACTTTTTCTACATGTTTCTCGAGGCAGAC-ATTCAATTATAGTCTGTTTTAATGAAAAATGTAA
* * * * * * * *
1711 AAAC-ATTGAACCTCAAATGAATTATGAGATTATGAAACCATTTAAAGCGAGTAATAAGGGTCTC
194 AAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTC
* * * * *
1775 GAAGGAATGAGAGACAATAAATGTACTTTTATTACCAATGAATGTCTTTTTCCT-CATATTTCTC
259 GAAAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGTC-TTTTCCTACATATTTCTC
* * *
1839 GA--TATAGACATTTAATTATAATTTGTTTTAACCAAAAAA-GTAAAAAAAAATTGAACTTAAAA
323 GAGGTA-AG-CATTCAATTATAATCTGTTTTAA-CAAAAAATGTAAAAAAAAATTGAACCTAAAA
* * * *
1901 TTAATTTTGAGACTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-CGATGACTAT
385 TCAATTTTGAGACTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTAT
* * *
1965 AAATAGACTTTTCTTGCCAATAAATGCTTTTTCTTCACGTTTCTTGAGATAGACATTCAATTA-T
450 AAATAGACTTTTCTTGCCAATGAATG-TTTTTCTTCACATTTCTTGAGGTAGACATTCAATTATT
2029 AGT
514 A-T
* * * * * *
2032 CTGTTTTAA-TAAAAAT-ATTAATAAAAATTGAACATAAAATCAATTTTGAGATTATAAAACTAT
1 CTGTTTTAACCAAAAATGA--AAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* ** * *
2095 TTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTA-CAATTGA
64 TTAAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTATCAA-TGA
* * * * * * * * *
2159 AT-ACCTTTTTCTTCACGTTTGTCGAGGTACACATTCAATTATAATATGTTTTAAAT-AAAATTA
128 ATGA-CTTTTTCTACATGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTT-AATGAAAAATG
*
2222 TAAAAA-AATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTTAAAG-TGAGTAATAAGGC
191 TAAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCT-AGTAATAAGGC
* * * * *
2285 TTTCGAAGGAATGAGAGAATATAAATGGACTTTTTTTGCCAATGAATAG-CTTTTTCTACATGTT
255 TTTCGAAAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAAT-GTCTTTTCCTACATATT
* ** * * *
2349 TCTCGAGGTAAGCATTCAATTATAGTCTGTTTTAATGAAAAATGT-AAAACAAATTCAA-CTTAA
319 TCTCGAGGTAAGCATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAAAATTGAACCTAAA
* * * * * *
2412 ATACAATTATGAGAGTCA-AAAACCATTT-AAGGGTAGTAATAAGGCTTTTGAAGGCACAGGAGA
384 AT-CAATTTTGAGACT-ATAAAACCATTTAAAGTG-AGTAATAAGGCTTTTGAAGGAATAGGTGA
* * * * * * * * *
2475 CTGTAAATGGACATTTCTT-CCAAGTAAATGGCTTTCTCTACACGTTTCCTT-AGGCAGGCATTC
446 CTATAAATAGACTTTTCTTGCCAA-TGAAT-G-TTTTTCTTCACATTT-CTTGAGGTAGACATTC
2538 AATTA-TAGT
507 AATTATTA-T
** * *
2547 CTGTTTTAATGAAAAATG-TAAAAATATTCAACTTAAA
1 CTGTTTTAACCAAAAATGAAAAAAAAATTCAACTTAAA
2584 NNNNNNNNNN
Statistics
Matches: 1290, Mismatches: 238, Indels: 100
0.79 0.15 0.06
Matches are distributed among these distances:
511 2 0.00
512 56 0.04
513 434 0.34
514 539 0.42
515 239 0.19
516 20 0.02
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (515 bp):
CTGTTTTAACCAAAAATGAAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
AAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTTTCTTATCAATGAATG
ACTTTTTCTACATGTTTCTCGAGGCAGACATTCAATTATAGTCTGTTTTAATGAAAAATGTAAAA
ACAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCTTTCGA
AAGAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTCCTACATATTTCTCGAG
GTAAGCATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAAAATTGAACCTAAAATCAATT
TTGAGACTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAG
ACTTTTCTTGCCAATGAATGTTTTTCTTCACATTTCTTGAGGTAGACATTCAATTATTAT
Found at i:3277 original size:170 final size:172
Alignment explanation
Indices: 2860--3279 Score: 435
Period size: 172 Copynumber: 2.5 Consensus size: 172
2850 NNNNNNNNNN
*
2860 AGTAATAAGGCTTTTGAAAGAATGAGAGACTATAAATGGACTTTTTTTGCCAATGAATAGC-TTT
1 AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTTTTG-CAATGAATAGCTTTT
* *
2924 TTC-TACATGTTTCTTGAGGTAAGCATTCAATTATAGTCTGTTGTAATAAAAAATGTAAAATAAA
65 TTCAT-CACGTTTCTTGAGGCAAGCATTCAATTATAGTCTGTTGTAATAAAAAATGTAAAATAAA
2988 TTCAACTTAAATATAATTATGAGACTCAAAAACCATTTAAGGGT
129 TTCAACTTAAATATAATTATGAGACTCAAAAACCATTTAAGGGT
* * * * * * *
3032 AGTAATAAGGCTTTTGAAGGCACGGGAGACTGTAAATGGA-TATTTTTTCCAAGTAAATGGCTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACT-TTTTTTGCAA-TGAATAGCTTT
* * * *
3096 CTCCA-CACGTTTCTTGAGGCAGGCATTCAATTATAGTCTGTT-TATTAAAAAATGTAAAA-AAA
64 TTTCATCACGTTTCTTGAGGCAAGCATTCAATTATAGTCTGTTGTAATAAAAAATGTAAAATAAA
********** * *
3158 TTCAACTTAAA-ATCAATTNNNNNNNNNNAAAACTATTTAA-AGT
129 TTCAACTTAAATAT-AATTATGAGACTCAAAAACCATTTAAGGGT
* * * * *
3201 GAGTAATAAGGCTTTTGGAGGAATAAAAGACTATAAATCGACTTTTCTTAGCAATGAAT-GCTTT
1 -AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTT-TTTGCAATGAATAGCTTT
3265 TTTCATCACGTTTCT
64 TTTCATCACGTTTCT
3280 CTGGGTAAAC
Statistics
Matches: 200, Mismatches: 39, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
169 12 0.06
170 77 0.38
171 26 0.13
172 81 0.41
173 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.34
Consensus pattern (172 bp):
AGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTTTTGCAATGAATAGCTTTTT
TCATCACGTTTCTTGAGGCAAGCATTCAATTATAGTCTGTTGTAATAAAAAATGTAAAATAAATT
CAACTTAAATATAATTATGAGACTCAAAAACCATTTAAGGGT
Found at i:3666 original size:169 final size:160
Alignment explanation
Indices: 3361--3667 Score: 312
Period size: 169 Copynumber: 1.9 Consensus size: 160
3351 NNNNNNNNNN
* * *
3361 TATTTAAAGCGAGTAATAAGGCTCTTGAAAGAATGGGAGACAATAAATGGACTTATCTTATTAAT
1 TATTTAAAACGAGTAATAAGGCTCTTGAAAGAATGGGAGACAATAAATGGAATTATCTTATCAAT
* *** * *
3426 GAATGGCTTTTTCTACATGTTTCTCGAGGTAGGTACTCAATTATAGTCTGTTTTAAGAAAAAATA
66 GAATGGCTTTTTCTACATGTTTCTCAAGGTAAACACTCAATTATAATCTGTTTTAACAAAAAATA
3491 TAAAAAAATAAACTTNNNNNNNNNNATGAGATTATAAAAC
131 TAAAAAAATAAACTT----------ATGAGATTATAAAAC
* * ** * * *
3531 TATTTAAAACGAGTAATAATG-TTTTGAAAGAATGGGTTACTATAAATGGAATTTTCTTGTCAAT
1 TATTTAAAACGAGTAATAAGGCTCTTGAAAGAATGGGAGACAATAAATGGAATTATCTTATCAAT
* * * *
3595 GAATGGCTTTTTCTTCACT-TTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAGT
66 GAATGGCTTTTTCTACA-TGTTTCTCAAGGTAAACACTCAATTATAATCTGTTTTAACAAAAAAT
*
3659 GTAAAAAAA
130 ATAAAAAAA
3668 AATTAAACTT
Statistics
Matches: 115, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
169 95 0.83
170 20 0.17
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.35
Consensus pattern (160 bp):
TATTTAAAACGAGTAATAAGGCTCTTGAAAGAATGGGAGACAATAAATGGAATTATCTTATCAAT
GAATGGCTTTTTCTACATGTTTCTCAAGGTAAACACTCAATTATAATCTGTTTTAACAAAAAATA
TAAAAAAATAAACTTATGAGATTATAAAAC
Done.