Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402450.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5528.0, 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: 4078
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Found at i:390 original size:171 final size:170
Alignment explanation
Indices: 1--2735 Score: 2274
Period size: 171 Copynumber: 16.1 Consensus size: 170
* * * *
1 ACTTGAAGTCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGTCTTTTAAAGGCATAG
1 ACTTAAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG
* * * * * *
66 GTGACTATAAATAGACTTTTCTTTCCAATGAATAT-GTTTTCTTCATGTTT-TTCAAGTTAGACA
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTT-TAGGTAGACA
*
129 TTCAATTATAATCTGTTTTGA-TAAAAAATGT-AAAAAATTCA
129 TTCAATTATAATCTGTTTTTACT-AAAAATGTAAAAAAATTCA
* * * * * *
170 ACTTCAAA-TCAATTATGAGAGTATAAAACCATTTAAAGTGAGCAATAAGGCTTTGGAAGGCTTG
1 ACTT-AAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATA
** * * *
234 GGTGACTATAAATAGG-CTTTTCTTGCCAATGAATGGCTTTTTCGTT-AAGTTTATTTAGGCAAA
64 GGTGACTATAAAT-GGACTTTTCTTGCCAATGAATATCTTTTTC-TTCAAGTTTCTTTAGGTAGA
* ** * * *
297 CATTCAACTGCAATATGTTTTTACTAACAATGTAAAAAAATTTA
127 CATTCAATTATAATCTGTTTTTACTAAAAATGTAAAAAAATTCA
* * *
341 ACTTAAAGTTAATTATGAGATTATAAATTCATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAG
1 ACTTAAAGTCAATTATGAGATTATAAA-CCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG
* * * * **
406 GCGACTATAAATGGACATTTCTTGCTAATAAATATCTTTTAGTTC-AGATTT-TTTGAGGTAGAC
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAG-TTTCTTT-AGGTAGAC
* * *
469 ATTTAATTATAATCTGTTTTAACAAAAAATG-AAAAAACATTCA
128 ATTCAATTATAATCTGTTTTTACTAAAAATGTAAAAAA-ATTCA
* **
512 ACTTAAAGTCAATTACGAGATTATGAAACCATTTAAAATGAGTAATAAGG-TTTTGAAAGGCATA
1 ACTTAAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTG-AAGGCATA
* * * * *** *
576 GGTAACTATAAATAGACTTTTCTTACCAATGAGTATC-TTTTCTTCACA-TTTCCCAAGGTAAAC
64 GGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCA-AGTTTCTTTAGGTAGAC
* *
639 ATTCAATTATAATCTG-TTTTAATAAAAAATGTAAAAAAATTTA
128 ATTCAATTATAATCTGTTTTTACT-AAAAATGTAAAAAAATTCA
* ** * * * *
682 ACTTTAACACAATTATGAGATTATCAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGTATGG
1 ACTTAAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG
** * * ** *
747 GTGACTATAAATGGACTTTTCTTGTTAATGAATGGT-TTTTTCTTCACGTTTCTCAAGGTAGATA
65 GTGACTATAAATGGACTTTTCTTGCCAATGAAT-ATCTTTTTCTTCAAGTTTCTTTAGGTAGACA
* * *
811 TTTAATTATAATCTGTTTTAACAAAAAATG-AAAAAACATTCA
129 TTCAATTATAATCTGTTTTTACTAAAAATGTAAAAAA-ATTCA
* * * *
853 ACTTAAAGTCAATTATGAGATTATAAAACCATTTAATGCGAGTAATAAGCCATTGGAAGGCATAG
1 ACTTAAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG
* * * * *
918 GTGACTATAAATGGACTTTTCTTTCTAATGAATATCATTTTCTTCACATTTTC-TAAGGTAGACA
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCA-AGTTTCTTTAGGTAGACA
* * *
982 TCCAATT-TCAATATG-TTTTAATAAAAAATGTAAAAAAATTCA
129 TTCAATTAT-AATCTGTTTTTACT-AAAAATGTAAAAAAATTCA
* * * * ** *
1024 ATTTCAAA-TCAATTTTGAGATTATCAAATCATTTAAAGCAAGTAATAAGGCTTTTGAAGGTGTG
1 ACTT-AAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATA
* * * * * ** *
1088 GGTGATTATAAATGGACTTTTCTTGCCAACGAATAGCTTTTTCTTCATGCTTCTCAATGTAGACA
64 GGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAGGTAGACA
* * * *
1153 TTTAATTATAATATG-TTTTAATCAAAAATGAAAAAAAAACTT-A
129 TTCAATTATAATCTGTTTTTACT-AAAAATG-TAAAAAAA-TTCA
* * * * * *
1196 ACTTAAAGTGAATTATGATATTATCAAACCATTTAAAACGAGCAATAAGGCTTTTGATGGCATGG
1 ACTTAAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG
* * * * * *
1261 GTGACAATAAATGGACTTTTCTCGTCAATGAATATCATTTTCTTCATGTTT-TCTAGAGTAGACA
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAG-GTAGACA
* * *
1325 TTCAATTATAATATG-TTTTAATAAAAAATGTAAAAAGATTCA
129 TTCAATTATAATCTGTTTTTACT-AAAAATGTAAAAAAATTCA
* * * * *
1367 GCTTTAAA-TCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGGAAAGCTTA
1 AC-TTAAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATA
* ** * * * *
1431 GGTGACTATAAATAGG-CTTTTCTTACCAATGAATGGCTTTTTCTTCAAGCTTCCTTGGGCAGAC
64 GGTGACTATAAAT-GGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAGGTAGAC
* * * * *
1495 ATTTAA-CAGTAATCTGTTTTAACCAAAAATGTAAAAAAATTAA
128 ATTCAATTA-TAATCTGTTTTTACTAAAAATGTAAAAAAATTCA
* * * *
1538 ACTTAAAGTTAATTGTG-GCATTATAAAAGCATTTAAAGCGCA-TAATAAGGCTTCTGAAGGCAT
1 ACTTAAAGTCAATTATGAG-ATTAT-AAACCATTTAAAGCG-AGTAATAAGGCTTTTGAAGGCAT
* * * * *
1601 AGGTCACTATAAATGAACTTTTCTTGCCAATGAATATCTTTTTCTACATGTTTCTTGAGGTAGAC
63 AGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAGGTAGAC
* *
1666 ATTTAATTATAATCTG-TTTTAATAACAAATGTAAAAAAATTCA
128 ATTCAATTATAATCTGTTTTTACTAA-AAATGTAAAAAAATTCA
* * * * *
1709 ACTTCAAA-TCAATTATGAGATTATAAAACAATTTAAA-TGAGTAATAAGCCTTTTGAAGGCTTG
1 ACTT-AAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATA
* ** * ** * * *
1772 GGTGACTATAAATAGG--TTTTGCTTTCCAATGAATGGCTTTTTTTTCTGGTTTATTTAGGCAAA
64 GGTGACTATAAAT-GGACTTTT-CTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAGGTAGA
** * ** *
1835 CACCCAACTATAATCCATTTTAAC-AAATAATGTAAAAAAATTCA
127 CATTCAATTATAATCTGTTTTTACTAAA-AATGTAAAAAAATTCA
* * * *
1879 ACTTAAAGTCAATTATGAGATTCTAAATCCATTTAAAGGGAGTAATAAAGCTTTCGAAGGCATAG
1 ACTTAAAGTCAATTATGAGATTATAAA-CCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG
* * * * **
1944 GTGATTATAAATGGACTTTTCTTGCTAATGAATATCTTTTTCTACATGTTT-TCGAGGTAGACAT
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAGGTAGACAT
* * * *
2008 TTAATTATAATCTGTTTTAACAAAAAAT-AAAAAAACATTCA
130 TCAATTATAATCTGTTTTTACTAAAAATGTAAAAAA-ATTCA
* * * * *
2049 ACTTAAAATCAATTAT-AGAATTATGAAACAATTTAAAACGAGTAATAACGCTTTGGAAGGCATA
1 ACTTAAAGTCAATTATGAG-ATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATA
* ** *** * **
2113 GGTGACTATAAATGGACTTTTCCTGCCAATGAATA--------TTCACCTTTCCCGATGTAGTTA
64 GGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAGGTAGACA
* * * *
2170 TTTAATTATAAT-T-TATTTAAATAAAAAATAG-AAAAAAATTTA
129 TTCAATTATAATCTGT-TTTTACT-AAAAAT-GTAAAAAAATTCA
* * *
2212 ACTTAAAGTCAATTATGAGATTATAAATCCACTTGAAGCGAGTAAAAAGGC------A--CAT--
1 ACTTAAAGTCAATTATGAGATTATAAA-CCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG
* * *** * *
2267 GTGACTATAAATGGGCTTTTCTTGCCAATGAATATCCTTTTCTTCTTCTTTCCTGAGGTAGACAT
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAGGTAGACAT
* * * *
2332 TTAATTATAAT-TGATTTTAGCTAAAAATAG-AAAAACATTGA
130 TCAATTATAATCTGTTTTTA-CTAAAAAT-GTAAAAAAATTCA
* * ** * * *
2373 ACTTAAAGTTAATTATGAGATTAAAAAATTATTTAAAGCGAGTAATAAGGCTTTGGAATGCATAT
1 ACTTAAAGTCAATTATGAGATT-ATAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG
* * * *
2438 GAGACTATAAATGGACTTTTCTTGTCAATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACAT
65 GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAGGTAGACAT
* * *
2503 TCAATTATAATCTATTTTTA-AAAAAATATAAAAAAATTCA
130 TCAATTATAATCTGTTTTTACTAAAAATGTAAAAAAATTCA
* * * * * * *
2543 ACTTAAA-TCGATTATGAGATTATAAAACCATTTCAAGCAAGTAATAAGGGTTTTGAAGTCTTGG
1 ACTTAAAGTCAATTATGAGATTAT-AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAG
* ** * *
2607 GTGACTATAAATAGG-CTTTTCTTGCCATTGAATGGCTTTTTCTTC-AGATTTCCTTAGGCAGAC
65 GTGACTATAAAT-GGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAG-TTTCTTTAGGTAGAC
* ** * * *
2670 ATTCAACTGCATTCTG-TTTTAATAAAAAATATAAAAAAATTCA
128 ATTCAATTATAATCTGTTTTTACT-AAAAATGTAAAAAAATTCA
* *
2713 A-GTAACAATCAATTATGAGATTA
1 ACTTAA-AGTCAATTATGAGATTA
2736 GAAAATGAAC
Statistics
Matches: 2071, Mismatches: 391, Indels: 206
0.78 0.15 0.08
Matches are distributed among these distances:
153 32 0.02
155 3 0.00
157 1 0.00
161 90 0.04
162 20 0.01
163 67 0.03
164 8 0.00
167 1 0.00
168 7 0.00
169 214 0.10
170 498 0.24
171 941 0.45
172 187 0.09
173 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
ACTTAAAGTCAATTATGAGATTATAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCATAGG
TGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCAAGTTTCTTTAGGTAGACATT
CAATTATAATCTGTTTTTACTAAAAATGTAAAAAAATTCA
Found at i:684 original size:341 final size:338
Alignment explanation
Indices: 9--2735 Score: 2491
Period size: 341 Copynumber: 8.0 Consensus size: 338
1 ACTTGAAG
* * *
9 TCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGTCTTTT-AAAGGCATAGGTGACTA
1 TCAATTATGAGATTAT-AAATCATTTAAAGCGAGTAATAAGGCTTTTGAAA-GCATAGGTGACTA
* * * * * * * *
73 TAAATAGACTTTTCTTTCCAATGAATAT-GTTTTCTTCATGTTTTTCAAGTTAGACATTCAATTA
64 TAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGTAGACATTTAATTA
* * * *
137 TAATCTGTTTTGATAAAAAATGTAAAAAATTCAACTTCAAA-TCAATTATGAGAGTATAAAACCA
129 TAATCTGTTTTAACAAAAAATGAAAAAAATTCAACTT-AAAGTCAATTATGAGATTATAAAACCA
* * * * *
201 TTTAAAGTGAGCAATAAGGCTTTGGAAGGCTTGGGTGACTATAAATAGG-CTTTTCTTGCCAATG
193 TTTAAAGCGAGTAATAAGG-TTTTGAAGGCATAGGTGACTATAAAT-GGACTTTTCTTGCCAATG
** ** * * * * ** * * *
265 AATGGCTTTTTCGTT-A-AGTTTATTTAGGCAAACATTCAACTGCAATATGTTTTTACT-AACAA
256 AATATCTTTTTC-TTCACA-TTTCCTGAGGTAGACATTCAATTATAATCTG-TTTTAATAAAAAA
*
327 TGTAAAAAAATTTAACTTAAA
318 TGTAAAAAAATTCAACTTAAA
* *
348 GTTAATTATGAGATTATAAATTCATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGCGACTA
1 -TCAATTATGAGATTATAAA-TCATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGTGACTA
* * * ** * *
413 TAAATGGACATTTCTTGCTAATAAATATCTTTTAGTTCA-GATTTTTTGAGGTAGACATTTAATT
64 TAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACG-TTTCTCGAGGTAGACATTTAATT
* *
477 ATAATCTGTTTTAACAAAAAATGAAAAAACATTCAACTTAAAGTCAATTACGAGATTATGAAACC
128 ATAATCTGTTTTAACAAAAAATGAAAAAA-ATTCAACTTAAAGTCAATTATGAGATTATAAAACC
** * * *
542 ATTTAAAATGAGTAATAAGGTTTTGAAAGGCATAGGTAACTATAAATAGACTTTTCTTACCAATG
192 ATTTAAAGCGAGTAATAAGGTTTTG-AAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATG
* ** *
607 AGTATC-TTTTCTTCACATTTCCCAAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATGT
256 AATATCTTTTTCTTCACATTTCCTGAGGTAGACATTCAATTATAATCTGTTTTAATAAAAAATGT
*
671 AAAAAAATTTAACTTTAACA
321 AAAAAAATTCAAC-TTAA-A
* * * *
691 -CAATTATGAGATTATCAAACCATTTAAAGTGAGTAATAAGGCTTTT-AAAGGTATGGGTGACTA
1 TCAATTATGAGATTAT-AAATCATTTAAAGCGAGTAATAAGGCTTTTGAAA-GCATAGGTGACTA
** * * *
754 TAAATGGACTTTTCTTGTTAATGAATGGT-TTTTTCTTCACGTTTCTCAAGGTAGATATTTAATT
64 TAAATGGACTTTTCTTGCCAATGAAT-ATCTTTTTCTTCACGTTTCTCGAGGTAGACATTTAATT
818 ATAATCTGTTTTAACAAAAAATGAAAAAACATTCAACTTAAAGTCAATTATGAGATTATAAAACC
128 ATAATCTGTTTTAACAAAAAATGAAAAAA-ATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* ** * * *
883 ATTTAATGCGAGTAATAAGCCATTGGAAGGCATAGGTGACTATAAATGGACTTTTCTTTCTAATG
192 ATTTAAAGCGAGTAATAAG-GTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATG
* * * * *
948 AATATCATTTTCTTCACATTTTCTAAGGTAGACATCCAATT-TCAATATGTTTTAATAAAAAATG
256 AATATCTTTTTCTTCACATTTCCTGAGGTAGACATTCAATTAT-AATCTGTTTTAATAAAAAATG
*
1012 TAAAAAAATTCAATTTCAAA
320 TAAAAAAATTCAACTT-AAA
* * * ** * *
1032 TCAATTTTGAGATTATCAAATCATTTAAAGCAAGTAATAAGGCTTTTGAAGGTGTGGGTGATTAT
1 TCAATTATGAGATTAT-AAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGTGACTAT
* * * * * *
1097 AAATGGACTTTTCTTGCCAACGAATAGCTTTTTCTTCATGCTTCTCAATGTAGACATTTAATTAT
65 AAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGTAGACATTTAATTAT
* * * *
1162 AATATGTTTTAATC-AAAAATGAAAAAAAAACTT-AACTTAAAGTGAATTATGATATTATCAAAC
130 AATCTGTTTTAA-CAAAAAATG--AAAAAAA-TTCAACTTAAAGTCAATTATGAGATTATAAAAC
* * * * * * *
1225 CATTTAAAACGAGCAATAAGGCTTTTGATGGCATGGGTGACAATAAATGGACTTTTCTCGTCAAT
191 CATTTAAAGCGAGTAATAAGG-TTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAAT
* ** * *
1290 GAATATCATTTTCTTCATGTTTTCT-AGAGTAGACATTCAATTATAATATGTTTTAATAAAAAAT
255 GAATATCTTTTTCTTCACATTTCCTGAG-GTAGACATTCAATTATAATCTGTTTTAATAAAAAAT
* *
1354 GTAAAAAGATTCAGCTTTAAA
319 GTAAAAAAATTCAAC-TTAAA
* * *
1375 TCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGGAAAGCTTAGGTGACTAT
1 TCAATTATGAGATTATAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGTGACTAT
* ** * * * * *
1440 AAATAGG-CTTTTCTTACCAATGAATGGCTTTTTCTTCAAGCTTCCTTG-GGCAGACATTTAA-C
65 AAAT-GGACTTTTCTTGCCAATGAATATCTTTTTCTTCACG-TTTCTCGAGGTAGACATTTAATT
* * * *
1502 AGTAATCTGTTTTAACCAAAAATGTAAAAAAATTAAACTTAAAGTTAATTGTG-GCATTATAAAA
128 A-TAATCTGTTTTAACAAAAAATG-AAAAAAATTCAACTTAAAGTCAATTATGAG-ATTATAAAA
* * * *
1566 GCATTTAAAGCGCA-TAATAAGGCTTCTGAAGGCATAGGTCACTATAAATGAACTTTTCTTGCCA
190 CCATTTAAAGCG-AGTAATAAGG-TTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCA
* ** * * *
1630 ATGAATATCTTTTTCTACATGTTTCTTGAGGTAGACATTTAATTATAATCTGTTTTAATAACAAA
253 ATGAATATCTTTTTCTTCACATTTCCTGAGGTAGACATTCAATTATAATCTGTTTTAATAAAAAA
1695 TGTAAAAAAATTCAACTTCAAA
318 TGTAAAAAAATTCAACTT-AAA
* * * * * *
1717 TCAATTATGAGATTATAAAACAATTTAAA-TGAGTAATAAGCCTTTTGAAGGCTTGGGTGACTAT
1 TCAATTATGAGATTATAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGTGACTAT
* ** * ** * ** * * *** *
1781 AAATAGG--TTTTGCTTTCCAATGAATGGCTTTTTTTTCTGGTTTATTTAGGCAAACACCCAACT
65 AAAT-GGACTTTT-CTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGTAGACATTTAATT
** * * *
1844 ATAATCCATTTTAACAAATAATGTAAAAAAATTCAACTTAAAGTCAATTATGAGATTCTAAATCC
128 ATAATCTGTTTTAACAAAAAATG-AAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * *
1909 ATTTAAAGGGAGTAATAAAGCTTTCGAAGGCATAGGTGATTATAAATGGACTTTTCTTGCTAATG
192 ATTTAAAGCGAGTAAT-AAGGTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATG
* ** * * * *
1974 AATATCTTTTTCTACATGTTTTC-GAGGTAGACATTTAATTATAATCTGTTTTAACAAAAAAT-A
256 AATATCTTTTTCTTCACATTTCCTGAGGTAGACATTCAATTATAATCTGTTTTAATAAAAAATGT
2037 AAAAAACATTCAACTTAAAA
321 AAAAAA-ATTCAACTT-AAA
* * * *
2057 TCAATTAT-AGAATTATGAAA-CAATTTAAAACGAGTAATAACGCTTTGGAAGGCATAGGTGACT
1 TCAATTATGAG-ATTAT-AAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGTGACT
* * * * **
2120 ATAAATGGACTTTTCCTGCCAATGAATA--------TTCACCTTTCCCGATGTAGTTATTTAATT
63 ATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGTAGACATTTAATT
* * * * * *
2177 ATAATTTATTTAAATAAAAAATAGAAAAAAATTTAACTTAAAGTCAATTATGAGATTATAAATCC
128 ATAATCTGTTTTAACAAAAAAT-GAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * *
2242 ACTTGAAGCGAGT-A-AA-------AAGGCACATGTGACTATAAATGGGCTTTTCTTGCCAATGA
192 ATTTAAAGCGAGTAATAAGGTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGA
* * * *
2298 ATATCCTTTTCTTCTTC-TTTCCTGAGGTAGACATTTAATTATAAT-TGATTTTAGCT-AAAAAT
257 ATATCTTTTTCTTC-ACATTTCCTGAGGTAGACATTCAATTATAATCTG-TTTTA-ATAAAAAAT
* *
2360 AG-AAAAACATTGAACTTAAA
319 -GTAAAAAAATTCAACTTAAA
* * * * * * *
2380 GTTAATTATGAGATTAAAAAATTATTTAAAGCGAGTAATAAGGCTTTGGAATGCATATGAGACTA
1 -TCAATTATGAGATT-ATAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGTGACTA
* * *
2445 TAAATGGACTTTTCTTGTCAATGAATATCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTA
64 TAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGTAGACATTTAATTA
* *
2510 TAATCTATTTTTAA-AAAAATAT-AAAAAAATTCAACTTAAA-TCGATTATGAGATTATAAAACC
129 TAATCT-GTTTTAACAAAAA-ATGAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACC
* * * * * *
2572 ATTTCAAGCAAGTAATAAGGGTTTTGAAGTCTTGGGTGACTATAAATAGG-CTTTTCTTGCCATT
192 ATTTAAAGCGAGTAATAA-GGTTTTGAAGGCATAGGTGACTATAAAT-GGACTTTTCTTGCCAAT
** * * * * ** * *
2636 GAATGGCTTTTTCTTCAGATTTCCTTAGGCAGACATTCAACTGCATTCTGTTTTAATAAAAAATA
255 GAATATCTTTTTCTTCACATTTCCTGAGGTAGACATTCAATTATAATCTGTTTTAATAAAAAATG
* *
2701 TAAAAAAATTCAAGTAACAA
320 TAAAAAAATTCAACTTA-AA
2721 TCAATTATGAGATTA
1 TCAATTATGAGATTA
2736 GAAAATGAAC
Statistics
Matches: 1988, Mismatches: 308, Indels: 183
0.80 0.12 0.07
Matches are distributed among these distances:
323 56 0.03
324 116 0.06
325 8 0.00
330 32 0.02
331 18 0.01
332 36 0.02
333 86 0.04
334 1 0.00
339 13 0.01
340 267 0.13
341 584 0.29
342 484 0.24
343 271 0.14
344 16 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (338 bp):
TCAATTATGAGATTATAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGTGACTATA
AATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCTCGAGGTAGACATTTAATTATA
ATCTGTTTTAACAAAAAATGAAAAAAATTCAACTTAAAGTCAATTATGAGATTATAAAACCATTT
AAAGCGAGTAATAAGGTTTTGAAGGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATAT
CTTTTTCTTCACATTTCCTGAGGTAGACATTCAATTATAATCTGTTTTAATAAAAAATGTAAAAA
AATTCAACTTAAA
Found at i:2277 original size:153 final size:156
Alignment explanation
Indices: 2105--2591 Score: 369
Period size: 161 Copynumber: 3.0 Consensus size: 156
2095 AACGCTTTGG
* *
2105 AAGGCATAGGTGACTATAAATGGACTTTTCCTGCCAATGAATA-TTC-AC-CTTTCCCGATGTAG
1 AAGGCACAGGTGACTATAAATGGACTTTTCCTGCCAATGAATATTTCTACTCTTTCCCGAGGTAG
** * *
2167 TTATTTAATTATAATTTA-TTTAAATAAAAAATAGAAAAAAATTTAACTTAAAGTCAATTATGAG
66 ACATTTAATTATAATTGATTTTAAAT-AAAAATAGAAAAAAATTGAACTTAAAGTCAATTATGAG
2231 ATTATAAATCCACTTGAAGCGAGTAAA
130 ATTATAAATCCACTTGAAGCGAGTAAA
* * * * *
2258 AAGGCACATGTGACTATAAATGGGCTTTTCTTGCCAATGAATATCCTTTTCTTCTTCTTTCCTGA
1 AAGGCACAGGTGACTATAAATGGACTTTTCCTGCCAATGAATA----TTTCTAC-TCTTTCCCGA
** * *
2323 GGTAGACATTTAATTATAATTGATTTTAGCTAAAAATAGAAAAACATTGAACTTAAAGTTAATTA
61 GGTAGACATTTAATTATAATTGATTTTAAATAAAAATAGAAAAAAATTGAACTTAAAGTCAATTA
* * * * *
2388 TGAGATTAAAAAAT-TATTTAAAGCGAGTAAT
126 TGAGATT-ATAAATCCACTTGAAGCGAGTAAA
* * * * * *
2419 AAGGCTTTGGAATGCATATGAGACTATAAATGGACTTTTCTTGTCAATGAATATCTTTTTCTTCA
1 AAGGC------A--C--AGGTGACTATAAATGGACTTTTCCTGCCAATGAATA----TTTCTACT
** * * * *
2484 CGTTTCTTGAGGTAGACATTCAATTATAATCT-ATTTTTAA-AAAAATATAAAAAAATTCAACTT
52 C-TTTCCCGAGGTAGACATTTAATTATAAT-TGATTTTAAATAAAAATAGAAAAAAATTGAACTT
* * * * * *
2547 AAA-TCGATTATGAGATTATAAAACCATTTCAAGCAAGTAAT
115 AAAGTCAATTATGAGATTATAAATCCACTTGAAGCGAGTAAA
2588 AAGG
1 AAGG
2592 GTTTTGAAGT
Statistics
Matches: 271, Mismatches: 40, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
153 39 0.14
158 3 0.01
159 1 0.00
161 83 0.31
162 10 0.04
167 1 0.00
168 4 0.01
169 31 0.11
170 24 0.09
171 74 0.27
172 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (156 bp):
AAGGCACAGGTGACTATAAATGGACTTTTCCTGCCAATGAATATTTCTACTCTTTCCCGAGGTAG
ACATTTAATTATAATTGATTTTAAATAAAAATAGAAAAAAATTGAACTTAAAGTCAATTATGAGA
TTATAAATCCACTTGAAGCGAGTAAA
Found at i:2963 original size:291 final size:290
Alignment explanation
Indices: 2475--3030 Score: 694
Period size: 292 Copynumber: 1.9 Consensus size: 290
2465 ATGAATATCT
* *
2475 TTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAATCTATTTTTAAAAAAATATAAAAAAAT
1 TTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTTAAAAAAATATAAAAAAAT
* * * * * * * *
2540 TCAACTTAAATCGATTATGAGATTATAAAACCATTTCAAGCAAGTAATAAGGGTTTTGAAGTCTT
66 GCAACTTAAATCAATTATGAGATTATAAAACCATTTAAAACAAGTAATAAAGCTTTCGAAGTCAT
* * * * *
2605 GGGTGACTATAAATAGGCTTTTCTTGCCATTGAATGGCTTTTTCTTCAGATTTCCTTAGGCAGAC
131 AGGTGACTATAAATAGGCTTTTCTTGCCAATAAATAGCTTTTTCTTCAGATTTCCTGAGGCAGAC
* *
2670 ATTCAACTGCATTCTGTTTTAATAAAAAATATAAAAAAATTCAA-GTAACAATCAATTATGAGAT
196 ATTCAACTACAATCTGTTTTAAT-AAAAATATAAAAAAATTCAACGTAA-AATCAATTATGAGAT
2734 TAGAAAATGAACTTTTTTACCAATGAATGGTA
259 TAGAAAATGAACTTTTTTACCAATGAATGGTA
* *
2766 TTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATTATTTA-TTTTAATGAAAAATAT-AAAAA
1 TTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTTAA--AAAAATATAAAAAA
* * * *
2829 ATGCAACTTAAAATCAATTATGAGATTGTAAAACCGTTTAAAACTAGTAATAAAGCTTTCGACGT
64 ATGCAACTT-AAATCAATTATGAGATTATAAAACCATTTAAAACAAGTAATAAAGCTTTCGAAGT
* * * *
2894 CATAGGTGAGTATAAAT-GGACTTTTCTTGTCAATAAATATCTTTTTCTTCCTG-TTT-CTCGA-
128 CATAGGTGACTATAAATAGG-CTTTTCTTGCCAATAAATAGCTTTTTCTT-CAGATTTCCT-GAG
* * * * *
2955 GTAGACATTCAATTATAATCTGTTTTAATAAAAATGTAAAAAAATTCAACTTAAAATCAATTATG
190 GCAGACATTCAACTACAATCTGTTTTAATAAAAATATAAAAAAATTCAACGTAAAATCAATTATG
*
3020 AGATTATAAAA
255 AGATTAGAAAA
3031 ACAAATAAAG
Statistics
Matches: 225, Mismatches: 33, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
290 46 0.20
291 82 0.36
292 95 0.42
293 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (290 bp):
TTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTTAAAAAAATATAAAAAAAT
GCAACTTAAATCAATTATGAGATTATAAAACCATTTAAAACAAGTAATAAAGCTTTCGAAGTCAT
AGGTGACTATAAATAGGCTTTTCTTGCCAATAAATAGCTTTTTCTTCAGATTTCCTGAGGCAGAC
ATTCAACTACAATCTGTTTTAATAAAAATATAAAAAAATTCAACGTAAAATCAATTATGAGATTA
GAAAATGAACTTTTTTACCAATGAATGGTA
Found at i:3389 original size:171 final size:169
Alignment explanation
Indices: 2766--3825 Score: 887
Period size: 171 Copynumber: 6.3 Consensus size: 169
2756 ATGAATGGTA
* * * * * * *
2766 TTTTCTTCACGTTTCTTGAGGCAAACATTCAATTATTATTTATTTTAATGAAAAA-TATAAAAAA
1 TTTTCTTCACGTTTC-TCAAGTAGACATTCAATTATAATCTATTTTAATAAAAAATTA-AAAAAA
* * * * * * *
2830 TGCAACTTAAAATCAATTATGAGATTGTAAAACCGTTTAAAACT-AGTAATAAAGCTTTCGACGT
64 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTT-AAAGTGAGTAATAAGGCTTTCGAAGG
* *
2894 CATAGGTGAGTATAAATGGACTTTTCTTGT-CAATAAATATCT
128 CATAGGTGACTATAAATGGACTTTTCTT-TCCAATGAATATCT
* *
2936 TTTTCTTC-CTGTTTCTCGAGTAGACATTCAATTATAATCTGTTTTAAT-AAAAATGTAAAAAAA
1 TTTTCTTCAC-GTTTCTCAAGTAGACATTCAATTATAATCTATTTTAATAAAAAAT-TAAAAAAA
* ** ** * *
2999 TTCAACTTAAAATCAATTATGAGATTATAAAAACAAATAAAGCAAGTAATAGGGCTTTCAAAGGC
64 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGC
* ** * * *
3064 ATGGGTGAGGATAAAATGGACTTTTCTCAT-CAGTGAA-AGGC-
129 ATAGGTGACTAT-AAATGGACTTTTCT-TTCCAATGAATA-TCT
** * * * * *
3105 TTTTCTTCATATTTCTTGAGGTAGACATTCAATTATAATCTATTGTAA-ACAGAAATGAAAAAAA
1 TTTTCTTCACGTTTC-TCAAGTAGACATTCAATTATAATCTATTTTAATA-AAAAATTAAAAAAA
* * * ** * *
3169 TTGAACTCAAAGTCAATTATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGT
64 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGC
*
3234 ATAGGTGACTATAAATGAACTTTTCTTTCCAATGAATATCT
129 ATAGGTGACTATAAATGGACTTTTCTTTCCAATGAATATCT
* * *
3275 TTTTCTTCACGTTTCCCAAGTAAGACTTTCAATTATAATTTATTTTAATAAAAAATATAAAAAAA
1 TTTTCTTCACGTTTCTCAAGT-AGACATTCAATTATAATCTATTTTAATAAAAAAT-TAAAAAAA
* * * * **
3340 TTTAACTTCAAATCAATTCTGAGAGTATAAAACCATTTAAAGTGAGTAATAAGGCTTGGGAAGGC
64 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGC
* * * * **
3405 CTGGGTGACTATCAATAGG-CTTTTCTTGCCAATGAATGGCT
129 ATAGGTGACTATAAAT-GGACTTTTCTTTCCAATGAATATCT
* * * * * * * * *
3446 TTTTCTTCAAGTTTTATTAGGCAGACATTCAACTGTAATCTGTTTTAACT-AAAAATGTTAAAAA
1 TTTTCTTCACG-TTTCTCAAGTAGACATTCAATTATAATCTATTTTAA-TAAAAAAT-TAAAAAA
* * * * * *
3510 ATTCAACTTAAAGTCAATTATAATATTATAAATCCATTTAAAGTGAGTAATAAGGCTTTCAAAAG
63 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGG
* *
3575 CATAGGTGACTATAAATGGACTTTTCTTGCTAATGAATATCT
128 CATAGGTGACTATAAATGGACTTTTCTTTCCAATGAATATCT
* *
3617 TTTTCTTCA-GATTTCTTGAGGTAG--A--C-ATT-T-A---A--TT-ATAAAAAATTAAAAAAC
1 TTTTCTTCACG-TTTC-TCAAGTAGACATTCAATTATAATCTATTTTAATAAAAAATTAAAAAA-
* * *
3668 ATTCAACTTAAAATCAATTATGAGATTATGAAACCATTTAAAAG-GAGTAATAAAG-TTTTGAAA
63 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT-AAAGTGAGTAATAAGGCTTTCG-AA
* *
3731 GGCATAGGTGACTATAAATGGACTTTTCTTTCCAATTAGTATCT
126 GGCATAGGTGACTATAAATGGACTTTTCTTTCCAATGAATATCT
* * * * * * * *
3775 TTTTCTTCACATTTCCTGAGGTAAATATTAAATTTTAATCTGTTTTAATAA
1 TTTTCTTCACGTTT-CTCAAGTAGACATTCAATTATAATCTATTTTAATAA
3826 GGCATGGGTG
Statistics
Matches: 711, Mismatches: 138, Indels: 81
0.76 0.15 0.09
Matches are distributed among these distances:
157 10 0.01
158 111 0.16
159 7 0.01
160 1 0.00
163 3 0.00
164 2 0.00
165 2 0.00
166 2 0.00
167 1 0.00
168 9 0.01
169 127 0.18
170 182 0.26
171 247 0.35
172 7 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (169 bp):
TTTTCTTCACGTTTCTCAAGTAGACATTCAATTATAATCTATTTTAATAAAAAATTAAAAAAATT
CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGCAT
AGGTGACTATAAATGGACTTTTCTTTCCAATGAATATCT
Found at i:3706 original size:158 final size:158
Alignment explanation
Indices: 3496--3797 Score: 430
Period size: 158 Copynumber: 1.9 Consensus size: 158
3486 TGTTTTAACT
* * *
3496 AAAAATGTTAAAAAATTCAACTTAAAGTCAATTATAATATTATAAATCCATTT-AAAGTGAGTAA
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAATCCATTTAAAAG-GAGTAA
* *
3560 TAAGGCTTTCAAAAGCATAGGTGACTATAAATGGACTTTTCTTGCTAATGAATATCTTTTTCTTC
65 TAAAGCTTTCAAAAGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTC
* *
3625 AGATTTCTTGAGGTAGACATTTAATTATA
130 ACATTTCCTGAGGTAGACATTTAATTATA
*
3654 AAAAAT-TAAAAAACATTCAACTTAAAATCAATTATGAGATTATGAAA-CCATTTAAAAGGAGTA
1 AAAAATGTAAAAAA-ATTCAACTTAAAATCAATTATAAGATTAT-AAATCCATTTAAAAGGAGTA
* * * * * *
3717 ATAAAGTTTTGAAAGGCATAGGTGACTATAAATGGACTTTTCTTTCCAATTAGTATCTTTTTCTT
64 ATAAAGCTTTCAAAAGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTT
3782 CACATTTCCTGAGGTA
129 CACATTTCCTGAGGTA
3798 AATATTAAAT
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
157 6 0.05
158 114 0.90
159 7 0.06
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (158 bp):
AAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTATAAATCCATTTAAAAGGAGTAAT
AAAGCTTTCAAAAGCATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCA
CATTTCCTGAGGTAGACATTTAATTATA
Found at i:3914 original size:95 final size:95
Alignment explanation
Indices: 3729--3917 Score: 213
Period size: 95 Copynumber: 2.0 Consensus size: 95
3719 AAAGTTTTGA
* ** * * *
3729 AAGGCATAGGTGACTATAAATGGACTTTTCTTTCCAATTAGTATCTTTTTCTTCACATTTCCTGA
1 AAGGCATAGGTGACTATAAATAGACTTTTCTTTCCAACGAATAGCTTTTTCTTCACATTTCCTAA
* * * *
3794 GGTAAATATTAAATTTTAATCTGTTTTAAT
66 CGTAAACATTAAATTATAATATGTTTTAAT
* *
3824 AAGGCATGGGTGACTATAAATAGACTTTT-TTTACCAACGAATGGCTTTTTCTTCACATTT-CTC
1 AAGGCATAGGTGACTATAAATAGACTTTTCTTT-CCAACGAATAGCTTTTTCTTCACATTTCCT-
*
3887 AACGTAGACATGT-AATTATAATATGTTTTAA
64 AACGTAAACAT-TAAATTATAATATGTTTTAA
3918 CCAAAAATAA
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
94 5 0.06
95 72 0.92
96 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (95 bp):
AAGGCATAGGTGACTATAAATAGACTTTTCTTTCCAACGAATAGCTTTTTCTTCACATTTCCTAA
CGTAAACATTAAATTATAATATGTTTTAAT
Done.