Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397651.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4247.0, 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: 2449
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.34
Warning! 109 characters in sequence are not A, C, G, or T
Found at i:550 original size:171 final size:170
Alignment explanation
Indices: 1--1496 Score: 670
Period size: 172 Copynumber: 8.7 Consensus size: 170
* * * * * *
1 AAATAGACTTTTCTTGCTAATGAATGCCTTTTTCTTCATGTTTCTCAAGGTAGAGAATCAATTAT
1 AAATAGACATTTCTTTCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGCTAGACATTCAATTAT
* ** * * *
66 AGTCTGTTTTAATAAAAAATCT-AAAAAAA-TCTTACTTAAAATCAATTATGAGATTATAAAACC
66 AATCTGTTTTAA-CCAAAATGTAAAAAAAATTC-AACTTAAAAT-AATTATAAGATTATAAAACC
* * * ** * *
129 ATTTAAAGTGAGTGATAAGGTTTTTGAAGAAATGGGTGGCTAT
128 ATTTAAAGAGAGTAATAAGGCTTTTGAAGAAATAAGAGACTAT
* * * * * * *
172 AAATAGACTTTTCTTACCAATGAATG-CTTATTT-ATCTATGTTTCTTGAGGCT-GATAATCAAT
1 AAATAGACATTTCTTTCCAATGAATGCCTT-TTTCTTC-ATGTTTC-TCAAGCTAGACATTCAAT
* * * * *
234 TATAGTCTGTTTTAACCAAAAATTTTAAAAAAATTCAGCTTAAAATCAATTATGAGATTATAAAA
63 TATAATCTGTTTTAACC-AAAATGTAAAAAAAATTCAACTTAAAAT-AATTATAAGATTATAAAA
* * ******************** ** * **
299 CTATTTAAAGCGNNNNNNNNNNNNNNNNNNNNAATGGGTGAAAAT
126 CCATTTAAAGAGAGTAATAAGGCTTTTGAAGAAATAAGAGACTAT
* ** * * **
344 AAATAGACTTTTCTGGCCAATGAATGCC-CTTTCTTCATGTTTCTCAAGCTGGATGTTCAATTAT
1 AAATAGACATTTCTTTCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGCTAGACATTCAATTAT
* * * * * * *
408 AATCTGTTTTAACCAATAATATAAAAAAAATTGAACCTAAAATCATTTTAAGACTGTAAAACCAT
66 AATCTGTTTTAACCAA-AATGTAAAAAAAATTCAACTTAAAATAATTATAAGATTATAAAACCAT
* *
473 TTAAAGCGAGTAATAGGGCTTTTGAAGAAATAAGAGACTAT
130 TTAAAGAGAGTAATAAGGCTTTTGAAGAAATAAGAGACTAT
* * * * *
514 AAATGGACATTTCTTTCCAATGAATGCTTTTTTCTTCATGTTTCTTGAGGCT-TACATTCAATTA
1 AAATAGACATTTCTTTCCAATGAATGCCTTTTTCTTCATGTTTC-TCAAGCTAGACATTCAATTA
** * * * * * * *
578 TTGTCTGTTTGAACTAAAAATGT-AAACAAATTCAACTTCAAATTGATTATGAGATTATAAAACT
65 TAATCTGTTTTAAC-CAAAATGTAAAAAAAATTCAACTT-AAAATAATTATAAGATTATAAAACC
* * * * *
642 ATTGAAAGTGAGCAATAATG-TGTTTGAAAAAATAAGAGACTAT
128 ATTTAAAGAGAGTAATAAGGCT-TTTGAAGAAATAAGAGACTAT
* * * * * *** * *
685 CAAT-G-GATTTTTTTGGCAATGAATGCCTTTTTCTTCATGTTTTTTGGGGC-AAACGTTCAATT
1 AAATAGACATTTCTTT-CCAATGAATGCCTTTTTCTTCATG-TTTCTCAAGCTAGACATTCAATT
* * * * *
747 CTAGTATGTTTTAATCGAAAATGTAAAAAAAATTCAACTTAAAATAAATTATCAGATTATAAAAC
64 ATAATCTGTTTTAA-CCAAAATGTAAAAAAAATTCAACTTAAAAT-AATTATAAGATTATAAAAC
* * * *
812 CATTTAAAAAGAGTAATATGGCTTTTGAAGGAAT-GGATGACTAT
127 CATTTAAAGAGAGTAATAAGGCTTTTGAAGAAATAAGA-GACTAT
* * * ** *
856 AAATAAACTTTTCTTACCAAT-ATATGCCTTTTTCTTCATGTTTCTCAATATAGACATTTAATTA
1 AAATAGACATTTCTTTCCAATGA-ATGCCTTTTTCTTCATGTTTCTCAAGCTAGACATTCAATTA
* ************************ * * *
920 TAATCTATTTTAACCAAAANNNNNNNNNNNNNNNNNNNNNNNNNCAATTTTGAGATTATAAAAGC
65 TAATCTGTTTTAACCAAAA--TGTAAAAAAAATTCAACTTAAAATAATTATAAGATTATAAAACC
* * * *
985 ATTTAAAGTGAGTAATAAGACTTTTGAAGGAAT-AGCTGACTAT
128 ATTTAAAGAGAGTAATAAGGCTTTTGAAGAAATAAG-AGACTAT
* * * * *
1028 AAATAGACTTTTCTTGCTAGTGAATG-CTTTTCTCTTCAAGTTTCT-AGATG-TAGACATTCAAT
1 AAATAGACATTTCTTTCCAATGAATGCCTTTT-TCTTCATGTTTCTCA-A-GCTAGACATTCAAT
* * * * * * * *
1090 CATAGTCTATTTTAACAAAAACTATAAAAAACATTTAACTTAAAATCAATTATGAGATTATAAAA
63 TATAATCTGTTTTAACCAAAA-TGTAAAAAAAATTCAACTTAAAAT-AATTATAAGATTATAAAA
* * * * ** *
1155 CAATTTAAAGTGAGTAATAAGGTTTTTGAAGGAATGGGTGACTAT
126 CCATTTAAAGAGAGTAATAAGGCTTTTGAAGAAATAAGAGACTAT
* * * * * *
1200 CAATGGACTTTTC-TTCTCAATGAATAG-CTTTTTCTACACT-TTTCTCAAGATAGGCATTCAAT
1 AAATAGACATTTCTTTC-CAATGAAT-GCCTTTTTCTTCA-TGTTTCTCAAGCTAGACATTCAAT
* * * *
1262 TATAGTCTGTTTTAACTAGATATG--AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
63 TATAATCTGTTTTAACCA-AAATGTAAAAAAAATTCAACTTAAAAT-AATTATAAGATTATAAAA
* * ** ** *
1325 CTATTTAGAGCTAGTAATAAGGCTTTTGAA-AGAATGGGTGACTAT
126 CCATTTAAAGAGAGTAATAAGGCTTTTGAAGA-AATAAGAGACTAT
* * * * * * * * *
1370 AAATAGACTTTTC-TTCTCAATAAATGGCTTTTTCTGCAAGTTTCCTGAGGC-AAACATTCAATG
1 AAATAGACATTTCTTTC-CAATGAATGCCTTTTTCTTCATGTTT-CTCAAGCTAGACATTCAATT
* * * *
1433 ATAGTCTGTTTTAATGCAAAATG-CAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
64 ATAATCTGTTTTAA-CCAAAATGTAAAAAAAATTCAACTTAAAAT-AATTATAAGATTATAAAAC
1497 TATTNNNNNN
Statistics
Matches: 1005, Mismatches: 272, Indels: 96
0.73 0.20 0.07
Matches are distributed among these distances:
169 8 0.01
170 277 0.28
171 344 0.34
172 357 0.36
173 19 0.02
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
AAATAGACATTTCTTTCCAATGAATGCCTTTTTCTTCATGTTTCTCAAGCTAGACATTCAATTAT
AATCTGTTTTAACCAAAATGTAAAAAAAATTCAACTTAAAATAATTATAAGATTATAAAACCATT
TAAAGAGAGTAATAAGGCTTTTGAAGAAATAAGAGACTAT
Found at i:1148 original size:172 final size:168
Alignment explanation
Indices: 1--2210 Score: 884
Period size: 171 Copynumber: 12.9 Consensus size: 168
* * * *
1 AAATAGACTTTTCTTGCT-AATGAAT-GCCTTTTTCTTCATGTTTCTCA-AGGTAGAGAATCAAT
1 AAATAGACTTTTCTT-CTCAATGAATAG-CTTTTTCTACAAGTTTCT-AGA-GTAGACATTCAAT
* * * *
63 TATAGTCTGTTTTAATAAAAAATCTAAAAAAA-TCTTACTTAAAATCAATTATGAGATTATAAAA
62 CATAGTCTGTTTT-A-ACAAAATATAAAAAAATTC-AACTTAAAATCAATTATGAGATTATAAAA
* * * * *
127 CCATTTAAAGTGAGTGATAAGGTTTTTGAAGAAATGGGTGGCTAT
124 CAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * *
172 AAATAGACTTTTCTTAC-CAATGAAT-GCTTATT-TATCTATGTTTCTTGAGGCT-GATAATCAA
1 AAATAGACTTTTCTT-CTCAATGAATAGCTTTTTCTA-C-AAGTTTCTAGA-G-TAGACATTCAA
* * *
233 TTATAGTCTGTTTTAACCAAAAATTTTAAAAAAATTCAGCTTAAAATCAATTATGAGATTATAAA
61 TCATAGTCTGTTTTAA-C-AAAA-TATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * ******************** **
298 ACTATTTAAAGCGNNNNNNNNNNNNNNNNNNNNAATGGGTGAAAAT
123 ACAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* ** * * * ** *
344 AAATAGACTTTTCTGGC-CAATGAAT-GCCCTTTCTTCATGTTTCTCA-AGCTGGATGTTCAATT
1 AAATAGACTTTTCT-TCTCAATGAATAGCTTTTTCTACAAGTTTCT-AGAG-TAGACATTCAATC
* * * * * * *
406 ATAATCTGTTTTAACCAATAATATAAAAAAAATTGAACCTAAAATC-ATTTTAAGACTGTAAAAC
63 ATAGTCTGTTTTAA-CAA-AATAT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * * * ** *
470 CATTTAAAGCGAGTAATAGGGCTTTTGAAGAAATAAGAGACTAT
125 AATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * * *
514 AAATGGACATTTCTT-TCCAATGAAT-GCTTTTTTCTTCATGTTTCTTGAGGCT-TACATTCAAT
1 AAATAGACTTTTCTTCT-CAATGAATAGC-TTTTTCTACAAGTTTCTAGA-G-TAGACATTCAAT
* * * * * * **
576 TATTGTCTGTTTGAACTAAAAATGTAAACAAATTCAACTTCAAATTGATTATGAGATTATAAAAC
62 CATAGTCTGTTTTAAC--AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * * * ** ** *
641 TATTGAAAGTGAGCAATAATG-TGTTTGAAAAAATAAGAGACTAT
125 AATTTAAAGTGAGTAATAAGGCT-TTTGAAGGAATGGGTGACTAT
* * * ** * * * * * * * *
685 CAATGGA-TTTTTTTGGCAATGAAT-GCCTTTTTCTTCATGTTTTTTGGGGCAAACGTTCAATTC
1 AAATAGACTTTTCTTCTCAATGAATAG-CTTTTTCTACAAG-TTTCTAGAGTAGACATTCAA-TC
* * * *
748 -TAGTATGTTTTAATCGAAAATGTAAAAAAAATTCAACTTAAAATAAATTATCAGATTATAAAAC
63 ATAGTCTGTTTTAA-C-AAAATAT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* ** * *
812 CATTTAAAAAGAGTAATATGGCTTTTGAAGGAATGGATGACTAT
125 AATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * *
856 AAATAAACTTTTCTTAC-CAAT--ATATGCCTTTTTCTTCATGTTTCTCA-ATATAGACATTTAA
1 AAATAGACTTTTCTT-CTCAATGAATA-G-CTTTTTCTACAAGTTTCT-AGA-GTAGACATTCAA
* * * *********************** *
917 TTATAATCTATTTTAACCAAAANNNNNNNNNNNNNNNNNNNNNNNNNCAATTTTGAGATTATAAA
61 TCATAGTCTGTTTTAA-CAAAA--TATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * *
982 AGC-ATTTAAAGTGAGTAATAAGACTTTTGAAGGAATAGCTGACTAT
123 A-CAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* *
1028 AAATAGACTTTTCTTGCT-AGTGAAT-GCTTTTCTCTTCAAGTTTCTAGATGTAGACATTCAATC
1 AAATAGACTTTTCTT-CTCAATGAATAGCTTTT-TCTACAAGTTTCTAGA-GTAGACATTCAATC
* *
1091 ATAGTCTATTTTAACAAAAACTATAAAAAACATTTAACTTAAAATCAATTATGAGATTATAAAAC
63 ATAGTCTGTTTTAAC-AAAA-TATAAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAAC
*
1156 AATTTAAAGTGAGTAATAAGGTTTTTGAAGGAATGGGTGACTAT
125 AATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * ** * *
1200 CAATGGACTTTTCTTCTCAATGAATAGCTTTTTCTACACTTTTCTCA-AGATAGGCATTCAATTA
1 AAATAGACTTTTCTTCTCAATGAATAGCTTTTTCTACAAGTTTCT-AGAG-TAGACATTCAATCA
* * *
1264 TAGTCTGTTTTAACTAGATATGAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTAT
64 TAGTCTGTTTTAACAAAATAT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAAT
* *
1329 TTAGAGCT-AGTAATAAGGCTTTTGAAAGAATGGGTGACTAT
128 TTAAAG-TGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * * *
1370 AAATAGACTTTTCTTCTCAATAAATGGCTTTTTCTGCAAGTTTCCT-GAGGCAAACATTCAATGA
1 AAATAGACTTTTCTTCTCAATGAATAGCTTTTTCTACAAGTTT-CTAGA-GTAGACATTCAATCA
** *
1434 TAGTCTGTTTTAATGCAAAATGCAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTA
64 TAGTCTGTTTTAA--CAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAA
********** * *
1499 TTNNNNNNNNNNAATAAGGCTTTTAAAGGAATGGGTAACTAT
127 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * *
1541 AAATGGACTTTTCTTCTCAATCAAT-GGTTTTTCTACAAGTTTTCCA-AGGCA-AGCATTCAAGT
1 AAATAGACTTTTCTTCTCAATGAATAGCTTTTTCTACAAG-TTTCTAGA-GTAGA-CATTCAA-T
* * * * * * *
1603 -GTAGTCTGTTTTAATGAAAAATTTAAACAAATTCAGCTTAAAATCAATTATGGGATTATAAAAN
62 CATAGTCTGTTTTAA--CAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
***********************
1667 NNNNNNNNNNNNNNNNNNNNNNNTTTGAAGGAATGGGTGACTAT
125 AATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * * * * *
1711 AAATGGACTTTTCTTGTCAATGAAT-GCCTTTTCTTTCATGTTTCTCGAGGTAGACATTCAGTTA
1 AAATAGACTTTTCTTCTCAATGAATAGCTTTTTC-TACAAGTTTCTAGA-GTAGACATTCAATCA
* * ** * *
1775 TAATCTGTTTTAACCAATAATGTAAAAAAA-TGGACTTAAAATCAATTATTAGATTATAAAAGAA
64 TAGTCTGTTTTAA-CAA-AATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAA
* * * *
1839 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATAACAAT
127 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * * ** * **
1881 AAATGGACTTTTCTTCTCAATGAAT-GGTTTTTCTACACATTTTCAAG-GTATATGTTTAATTTT
1 AAATAGACTTTTCTTCTCAATGAATAGCTTTTTCTACA-AGTTTCTAGAGTAGACATTCAATCAT
* * * ***********
1944 AGTCTGTTTTCACCAAAATGTTAAAAAATTTCAACTTAAAATCAATTATGAGNNNNNNNNNNTAT
65 AGTCTGTTTT-AACAAAAT-ATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAAT
* *
2009 TTAAAGTGAATAATAAAGCTTTTGAAGGAATAGGG-GACTAT
128 TTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGGTGACTAT
* * *
2050 AAATGGACTTTTCTT-TCCAATGAAT-GCTTGTTTCTTCACA-TTTCTAGAGGTAGACATTAAAT
1 AAATAGACTTTTCTTCT-CAATGAATAGCTT-TTTCTACA-AGTTTCTAGA-GTAGACATTCAAT
* * ******** * *
2112 TATAGTTTGTTNNNNNNNNNNATATAAAAAAATTCAACTTAAAATCAATTATGAGTTTACAAAAC
62 CATAGTCTGTT--TTAACAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * * * *
2177 AATTTAAAGCGAGTAGTAAAGTTTTTGAACGAAT
125 AATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT
2211 AGAAAAGCAA
Statistics
Matches: 1539, Mismatches: 418, Indels: 164
0.73 0.20 0.08
Matches are distributed among these distances:
167 3 0.00
168 30 0.02
169 92 0.06
170 509 0.33
171 526 0.34
172 366 0.24
173 11 0.01
174 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Consensus pattern (168 bp):
AAATAGACTTTTCTTCTCAATGAATAGCTTTTTCTACAAGTTTCTAGAGTAGACATTCAATCATA
GTCTGTTTTAACAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTA
AAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
Found at i:1292 original size:514 final size:488
Alignment explanation
Indices: 464--1413 Score: 919
Period size: 514 Copynumber: 1.9 Consensus size: 488
454 TTTAAGACTG
* * *
464 TAAAACCATTTAAAGCGAGTAATAGGGCTTTTGAAGAAATAAGAGACTATAAATGGACATTTCTT
1 TAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGAAATAAGAGACTATAAATAGACATTTCTT
* * * * * * * *
529 TCCAATGAATGCTTTTTTCTTCATGTTTCTTGAGGCTTACATTCAATTATTGTCTGTTTGAACTA
66 GCCAATGAATGCTTTTCTCTTCAAGTTTCTAGAGGCTGACATTCAATCATAGTCTATTTGAACTA
* * * ** *
594 AAAATGTAAACAAATTCAACTTCAAATTGATTATGAGATTATAAAACTATTGAAAGTGAGCAATA
131 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTGAAAGTGAGCAATA
* * * * *
659 ATGTGTTTGAAAAAATAAGAGACTATCAATGGATTTTTTTGGCAATGAATGCCTTTTTCTTCATG
196 AGGTGTTTGAAAAAATAAGAGACTATCAATGGATTTTCTTCGCAATGAATGCCTTTTTCTACATC
* *** * * *
724 TTTTTTGGGGCAAACGTTCAATTCTAGTATGTTTTAATCGAAAATGTAAAAAAAATTCAACTTAA
261 TTTTCTCAAGCAAACATTCAATTATAGTATGTTTTAATAGAAAATG-AAAAAAAATTCAACTTAA
* *
789 AATAAATTATCAGATTATAAAACCATTTAAAAAGAGTAATATGGCTTTTGAAGGAATGGATGACT
325 AATAAATTATCAGATTATAAAACCATTTAAAAAGAGTAATAAGGCTTTTGAAAGAATGGATGACT
* * *
854 ATAAATAAACTTTTCTTAC-CAATATATGCCTTTTTCTTCATGTTTCTCAATATAGACATTTAAT
390 ATAAATAAACTTTTCTT-CTCAATAAATGCCTTTTTCTGCAAGTTTCTCAATATAGACATTTAAT
918 TATAATCTATTTTAACCAAAANNNNNNNNNNNNNNNNNNNNNNNNNCAATTTTGAGATTA
454 TATAATCTATTTTAACCAAAA-------------------------CAATTTTGAGATTA
* * * * *
978 TAAAAGCATTTAAAGTGAGTAATAAGACTTTTGAAGGAAT-AGCTGACTATAAATAGACTTTTCT
1 TAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGAAATAAG-AGACTATAAATAGACATTTCT
* * * *
1042 TGCTAGTGAATGCTTTTCTCTTCAAGTTTCTAGATG-TAGACATTCAATCATAGTCTATTTTAAC
65 TGCCAATGAATGCTTTTCTCTTCAAGTTTCTAGAGGCT-GACATTCAATCATAGTCTATTTGAAC
* * *
1106 -AAAAACTATAAAAAACATTTAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGTGAGT
129 TAAAAA-TATAAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAACAATTGAAAGTGAGC
* ** ** * *
1170 AATAAGGTTTTTGAAGGAATGGGTGACTATCAATGGACTTTTCTTCTCAATGAATAG-CTTTTTC
192 AATAAGGTGTTTGAAAAAATAAGAGACTATCAATGGA-TTTTCTTCGCAATGAAT-GCCTTTTTC
* * *
1234 TACA-CTTTTCTCAAG-ATAGGCATTCAATTATAGTCTGTTTTAACTAG-ATATG-AAAAAAATT
255 TACATCTTTTCTCAAGCA-A-ACATTCAATTATAGTATGTTTTAA-TAGAAAATGAAAAAAAATT
* * * * ***
1295 CAACTTAAAATCAATTATGAGATTATAAAACTATTTAGAGCTAGTAATAAGGCTTTTGAAAGAAT
317 CAACTTAAAATAAATTATCAGATTATAAAACCATTTAAAAAGAGTAATAAGGCTTTTGAAAGAAT
* * *
1360 GGGTGACTATAAATAGACTTTTCTTCTCAATAAATGGCTTTTTCTGCAAGTTTC
382 GGATGACTATAAATAAACTTTTCTTCTCAATAAATGCCTTTTTCTGCAAGTTTC
1414 CTGAGGCAAA
Statistics
Matches: 360, Mismatches: 66, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
513 9 0.03
514 222 0.62
515 78 0.22
516 48 0.13
517 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.36
Consensus pattern (488 bp):
TAAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGAAATAAGAGACTATAAATAGACATTTCTT
GCCAATGAATGCTTTTCTCTTCAAGTTTCTAGAGGCTGACATTCAATCATAGTCTATTTGAACTA
AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTGAAAGTGAGCAATA
AGGTGTTTGAAAAAATAAGAGACTATCAATGGATTTTCTTCGCAATGAATGCCTTTTTCTACATC
TTTTCTCAAGCAAACATTCAATTATAGTATGTTTTAATAGAAAATGAAAAAAAATTCAACTTAAA
ATAAATTATCAGATTATAAAACCATTTAAAAAGAGTAATAAGGCTTTTGAAAGAATGGATGACTA
TAAATAAACTTTTCTTCTCAATAAATGCCTTTTTCTGCAAGTTTCTCAATATAGACATTTAATTA
TAATCTATTTTAACCAAAACAATTTTGAGATTA
Found at i:1362 original size:170 final size:168
Alignment explanation
Indices: 1--2185 Score: 960
Period size: 170 Copynumber: 12.8 Consensus size: 168
* * * * *
1 AAATAGACTTTTCTTGCT-AATGAATGCCTTTTTCTTCA-TGTTTCTCAAGGTAGAGAATCAATT
1 AAATGGACTTTTCTT-CTCAATGAATG-CTTTTTCTACACT-TTTCTCAAGATAGACATTCAATT
* *
64 ATAGTCTGTTTTAA-TAAAAAATCTAAAAAAA-TCTTACTTAAAATCAATTATGAGATTATAAAA
63 ATAGTCTGTTTTAACT--AAAATGTAAAAAAATTC-AACTTAAAATCAATTATGAGATTATAAAA
* * * * *
127 CCATTTAAAGTGAGTGATAAGGTTTTTGAAGAAATGGGTGGCTAT
125 CAATTTAAAGT-AGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * * * *
172 AAATAGACTTTTCTTAC-CAATGAATGCTTATT-TATCTA-TGTTTCTTGAGGCT-GATAATCAA
1 AAATGGACTTTTCTT-CTCAATGAATGCTTTTTCTA-C-ACT-TTTC-TCAAGATAGACATTCAA
* * *
233 TTATAGTCTGTTTTAACCAAAAATTTTAAAAAAATTCAGCTTAAAATCAATTATGAGATTATAAA
61 TTATAGTCTGTTTTAA-CTAAAA-TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * ****************** **
298 ACTATTTAAAG-CGNNNNNNNNNNNNNNNNNNNNAATGGGTGAAAAT
124 ACAATTTAAAGTAG--TAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * ** * * * **
344 AAATAGACTTTTCTGGC-CAATGAATGCCCTTTCTTCA-TGTTTCTCAAGCTGGATGTTCAATTA
1 AAATGGACTTTTCT-TCTCAATGAATGCTTTTTCTACACT-TTTCTCAAGATAGACATTCAATTA
* * * * * * * * * *
407 TAATCTGTTTTAACCAATAATATAAAAAAAATTGAACCTAAAATC-ATTTTAAGACTGTAAAACC
64 TAGTCTGTTTTAACTAA-AATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACA
* * * ** *
471 ATTTAAAGCGAGTAATAGGGCTTTTGAAGAAATAAGAGACTAT
127 ATTTAAAG-TAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * * *
514 AAATGGACATTTCTT-TCCAATGAATGCTTTTTTCTTCA-TGTTTCTTGAGGCT-TACATTCAAT
1 AAATGGACTTTTCTTCT-CAATGAATGC-TTTTTCTACACT-TTTC-TCAAGATAGACATTCAAT
* * * * **
576 TATTGTCTGTTTGAACTAAAAATGTAAACAAATTCAACTTCAAATTGATTATGAGATTATAAAAC
62 TATAGTCTGTTTTAACT-AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * * * ** ** *
641 TATTGAAAGTGAGCAATAATG-TGTTTGAAAAAATAAGAGACTAT
126 AATTTAAAGT-AGTAATAAGGCT-TTTGAAGGAATGGGTGACTAT
* * ** * * * *** *
685 CAATGGA-TTTTTTTGGCAATGAATGCCTTTTTCTTCATGTTTTTTGGGGCA-A-ACGTTCAATT
1 AAATGGACTTTTCTTCTCAATGAATG-CTTTTTCTACA-CTTTTCTCAAG-ATAGACATTCAATT
* * * * *
747 CTAGTATGTTTTAATCGAAAATGTAAAAAAAATTCAACTTAAAATAAATTATCAGATTATAAAAC
63 ATAGTCTGTTTTAA-CTAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * *
812 CATTTAAAAAG-AGTAATATGGCTTTTGAAGGAATGGATGACTAT
126 AATTT--AAAGTAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
** * * *
856 AAATAAACTTTTCTTAC-CAAT-ATATGCCTTTTTCTTCA-TGTTTCTCAATATAGACATTTAAT
1 AAATGGACTTTTCTT-CTCAATGA-ATG-CTTTTTCTACACT-TTTCTCAAGATAGACATTCAAT
* * * *********************** *
918 TATAATCTATTTTAACCAAAANNNNNNNNNNNNNNNNNNNNNNNNNCAATTTTGAGATTATAAAA
62 TATAGTCTGTTTTAACTAAAA--TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* * *
983 GC-ATTTAAAGTGAGTAATAAGACTTTTGAAGGAATAGCTGACTAT
125 -CAATTTAAAGT-AGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * **
1028 AAATAGACTTTTCTTGCT-AGTGAATGCTTTTCTCTTCAAGTTTCT--AGATGTAGACATTCAAT
1 AAATGGACTTTTCTT-CTCAATGAATGCTTTT-TCTACACTTTTCTCAAGA--TAGACATTCAAT
* * * * *
1090 CATAGTCTATTTTAACAAAAACTATAAAAAACATTTAACTTAAAATCAATTATGAGATTATAAAA
62 TATAGTCTGTTTTAACTAAAA-TGTAAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAAAA
*
1155 CAATTTAAAGTGAGTAATAAGGTTTTTGAAGGAATGGGTGACTAT
125 CAATTTAAAGT-AGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* *
1200 CAATGGACTTTTCTTCTCAATGAATAGCTTTTTCTACACTTTTCTCAAGATAGGCATTCAATTAT
1 AAATGGACTTTTCTTCTCAATGAAT-GCTTTTTCTACACTTTTCTCAAGATAGACATTCAATTAT
* *
1265 AGTCTGTTTTAACTAGATATG-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTAT
65 AGTCTGTTTTAACTA-AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAAT
* *
1329 TTAGAGCTAGTAATAAGGCTTTTGAAAGAATGGGTGACTAT
129 TTAAAG-TAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * * * * *
1370 AAATAGACTTTTCTTCTCAATAAATGGCTTTTTCTGCAAGTTTCCTGAGGCA-A-ACATTCAATG
1 AAATGGACTTTTCTTCTCAATGAAT-GCTTTTTCTAC-ACTTTTCTCAAG-ATAGACATTCAATT
*
1433 ATAGTCTGTTTTAA-TGCAAAATGCAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
63 ATAGTCTGTTTTAACT--AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* ********* * *
1497 TATTNNNNNNNNNNAATAAGGCTTTTAAAGGAATGGGTAACTAT
126 AATT-TAAAGTAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * *
1541 AAATGGACTTTTCTTCTCAATCAATGGTTTTTCTACAAGTTTTC-CAAGGCA-AG-CATTCAAGT
1 AAATGGACTTTTCTTCTCAATGAATGCTTTTTCTAC-ACTTTTCTCAA-G-ATAGACATTCAATT
* * * * *
1603 GTAGTCTGTTTTAA-TGAAAAATTTAAACAAATTCAGCTTAAAATCAATTATGGGATTATAAAAN
63 ATAGTCTGTTTTAACT--AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-
***********************
1667 NNNNNNNNNNNNNNNNNNNNNNNTTTGAAGGAATGGGTGACTAT
125 CAATTTAAAGTAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * * *
1711 AAATGGACTTTTCTTGTCAATGAATGCCTTTTCTTTCA-TGTTTCTCGAGGTAGACATTCAGTTA
1 AAATGGACTTTTCTTCTCAATGAATGCTTTTTC-TACACT-TTTCTCAAGATAGACATTCAATTA
* * ** * *
1775 TAATCTGTTTTAACCAATAATGTAAAAAAA-TGGACTTAAAATCAATTATTAGATTATAAAAGAA
64 TAGTCTGTTTTAACTAA-AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAA
* * * *
1839 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGATAACAAT
128 TTTAAAG-TAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
* * * * ** * *
1881 AAATGGACTTTTCTTCTCAATGAATGGTTTTTCTACACATTT-TCAAGGTATATGTTTAATTTTA
1 AAATGGACTTTTCTTCTCAATGAATGCTTTTTCTACACTTTTCTCAAGATAGACATTCAATTATA
* * * ***********
1945 GTCTGTTTTCACCAAAATGTTAAAAAATTTCAACTTAAAATCAATTATGAGNNNNNNNNNNTATT
66 GTCTGTTTTAACTAAAATG-TAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATT
* *
2010 TAAAGTGAATAATAAAGCTTTTGAAGGAATAGGG-GACTAT
130 TAAAGT-AGTAATAAGGCTTTTGAAGGAAT-GGGTGACTAT
* * * *
2050 AAATGGACTTTTCTT-TCCAATGAATGCTTGTTTCTTCACATTTCT-AGAGGTAGACATTAAATT
1 AAATGGACTTTTCTTCT-CAATGAATGCTT-TTTCTACACTTTTCTCA-AGATAGACATTCAATT
* ********* * * *
2113 ATAGTTTGTTNNNNNNNNNNATATAAAAAAATTCAACTTAAAATCAATTATGAGTTTACAAAACA
63 ATAGTCTGTT-TTAACTAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACA
2178 ATTTAAAG
127 ATTTAAAG
2186 CGAGTAGTAA
Statistics
Matches: 1520, Mismatches: 406, Indels: 176
0.72 0.19 0.08
Matches are distributed among these distances:
167 4 0.00
168 36 0.02
169 88 0.06
170 516 0.34
171 491 0.32
172 365 0.24
173 17 0.01
174 3 0.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35
Consensus pattern (168 bp):
AAATGGACTTTTCTTCTCAATGAATGCTTTTTCTACACTTTTCTCAAGATAGACATTCAATTATA
GTCTGTTTTAACTAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTT
AAAGTAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
Found at i:1645 original size:341 final size:342
Alignment explanation
Indices: 964--1665 Score: 823
Period size: 341 Copynumber: 2.1 Consensus size: 342
954 NNNNNNNNNN
* *
964 CAATTTTGAGATTATAAAAGCATTTAAAGTGAGTAATAAGACTTTTGAAGGAATAGCTGACTATA
1 CAATTATGAGATTATAAAAGCATTTAAAGTGAGTAATAAGACTTTTGAAAGAATAGCTGACTATA
* * * * * *
1029 AATAGACTTTTCTTGCTAGTGAATGCTTTTCTCTTCAAGTTTCTAGATGTAGACATTCAATCATA
66 AATAGACTTTTCTTGCTAATAAATGCTTTTCTCTGCAAGTTTCTAGAGGCAAACATTCAATCATA
* *
1094 GTCTATTTTAACAAAAACTATAAAAAACATTTAACTTAAAATCAATTATGAGATTATAAAACAAT
131 GTCTATTTTAACAAAAACTACAAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACAAT
* * * * *
1159 TTAAAGTGAGTAATAAGGTTTTTGAAGGAATGGGTGACTATCAATGGACTTTTCTTCTCAATGAA
196 TTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTAACTATAAATGGACTTTTCTTCTCAATCAA
* * * * *
1224 TAGCTTTTTCTACACTTTTCTCAAGATAGGCATTCAATTATAGTCTGTTTTAACTAGATATGAAA
261 TAGCTTTTTCTACACTTTTCTCAAGACAAGCATTCAAGTATAGTCTGTTTTAACTAAAAATGAAA
1289 AAAATTCAACTTAAAAT
326 AAAATTCAACTTAAAAT
* * * *
1306 CAATTATGAGATTATAAAA-CTATTTAGAGCT-AGTAATAAGGCTTTTGAAAGAATGGGTGACTA
1 CAATTATGAGATTATAAAAGC-ATTTAAAG-TGAGTAATAAGACTTTTGAAAGAATAGCTGACTA
1369 TAAATAGACTTTTCTT-CTCAATAAATGGCTTTT-TCTGCAAGTTTCCT-GAGGCAAACATTCAA
64 TAAATAGACTTTTCTTGCT-AATAAAT-GCTTTTCTCTGCAAGTTT-CTAGAGGCAAACATTCAA
* * *
1431 TGATAGTCTGTTTTAATGC-AAAA-TGCAAAAAA-ATTCAACTTAAAATCAATTATGAGATTATA
126 TCATAGTCTATTTTAA--CAAAAACTACAAAAAACATTCAACTTAAAATCAATTATGAGATTATA
* **********
1493 AAACTATTNNNNNNNNNNAATAAGGCTTTTAAAGGAATGGGTAACTATAAATGGACTTTTCTTCT
189 AAACAATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTAACTATAAATGGACTTTTCTTCT
* * * *
1558 CAATCAAT-GGTTTTTCTACAAGTTTTC-CAAGGCAAGCATTCAAGTGTAGTCTGTTTTAA-TGA
254 CAATCAATAGCTTTTTCTAC-ACTTTTCTCAAGACAAGCATTCAAGTATAGTCTGTTTTAACT-A
* * *
1620 AAAATTTAAACAAATTCAGCTTAAAAT
317 AAAA-TGAAAAAAATTCAACTTAAAAT
*
1647 CAATTATGGGATTATAAAA
1 CAATTATGAGATTATAAAA
1666 NNNNNNNNNN
Statistics
Matches: 304, Mismatches: 46, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
339 1 0.00
340 40 0.13
341 132 0.43
342 117 0.38
343 13 0.04
344 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (342 bp):
CAATTATGAGATTATAAAAGCATTTAAAGTGAGTAATAAGACTTTTGAAAGAATAGCTGACTATA
AATAGACTTTTCTTGCTAATAAATGCTTTTCTCTGCAAGTTTCTAGAGGCAAACATTCAATCATA
GTCTATTTTAACAAAAACTACAAAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACAAT
TTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTAACTATAAATGGACTTTTCTTCTCAATCAA
TAGCTTTTTCTACACTTTTCTCAAGACAAGCATTCAAGTATAGTCTGTTTTAACTAAAAATGAAA
AAAATTCAACTTAAAAT
Done.