Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400659.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3846.0, 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: 4963
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.34
Warning! 280 characters in sequence are not A, C, G, or T
Found at i:68 original size:21 final size:21
Alignment explanation
Indices: 39--78 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29 GAATGGGTAA
39 TAATAAATGGAATTTTCTTGC
1 TAATAAATGGAATTTTCTTGC
* * *
60 TAATGAATGTATTTTTCTT
1 TAATAAATGGAATTTTCTT
79 CATGTTTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.50
Consensus pattern (21 bp):
TAATAAATGGAATTTTCTTGC
Found at i:482 original size:21 final size:21
Alignment explanation
Indices: 458--500 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
448 AAAGAATAGG
*
458 TGCCTATAAATGAACTTTTCT
1 TGCCCATAAATGAACTTTTCT
* * *
479 TGCCCATTAATGCATTTTTCT
1 TGCCCATAAATGAACTTTTCT
500 T
1 T
501 AACGTTTCTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (21 bp):
TGCCCATAAATGAACTTTTCT
Found at i:942 original size:171 final size:169
Alignment explanation
Indices: 367--1309 Score: 541
Period size: 171 Copynumber: 5.5 Consensus size: 169
357 ATAAAGTCTG
* * * * * * *
367 TTTTAA-CAAAAAATATACAAAAATTCAAC-TATAATTAATTATAAGATTA-CAAACCATTTCAA
1 TTTTAACCAAAAAGTA-AAAAAAATTTAACTTA-AATAAATTATGAGATTATAAAACCATTTAAA
* * * * * *
429 GCGTGTAATAAGGCTTTTGAAAGAATAGGTGCCTATAAAT-GAACTTTTCTTGCCCATTAATGCA
64 GCGAGTAATAAGGCTTTTGAAAGAATAGGTGAC-ATAAATAG-ACTTTTCTTGCCAATGAATACC
* * * * * *
493 TTTTTCTTAACGTTTCTCGTGGTGGACATTCAATTATAGTCTA
127 TTTTTCTTCACGTTTCTTGAGGTAGACATTCAATAATAATCTA
* * *** * * *
536 -TTTAATCAAAAATGT-AAAACAATTCGCCTTAAAATGAAGTATGAGATTATAAAACCATTTAGA
1 TTTTAACCAAAAA-GTAAAAAAAATTTAACTT-AAATAAATTATGAGATTATAAAACCATTTAAA
********** * * * * **
599 GCGAGTANNNNNNNNNNTGAAAGAATGGGTGACTATAAATGGACTTTTCTT-TCAATAAAT-GTT
64 GCGAGTAATAAGGCTTTTGAAAGAATAGGTGAC-ATAAATAGACTTTTCTTGCCAATGAATACCT
* * * * * * *
662 ATTTTGTACACATTTTTTGAGGTAGATATTCAATTAA-AGTCTG
128 -TTTTCTTCACGTTTCTTGAGGTAGACATTCAA-TAATAATCTA
** * * * **********
705 TTTTAAAGAAATATGT-AAAAAAATTCAACTTATAATCAATTATGAGATTANNNNNNNNNNTAAA
1 TTTTAACCAAA-AAGTAAAAAAAATTTAACTTA-AATAAATTATGAGATTATAAAACCATTTAAA
* *
769 GCGAGTAATAAGGCTTTTGAAGGAATAGGTGACAGTAAATAAACTTTTCTTGCCAATGAATACCT
64 GCGAGTAATAAGGCTTTTGAAAGAATAGGTGACA-TAAATAGACTTTTCTTGCCAATGAATACCT
** * * * *
834 TTTTCTTCACGTTTCTCAATGTAGACATTCAATGATAATATG
128 TTTTCTTCACGTTTCTTGAGGTAGACATTCAATAATAATCTA
*
876 TTTTAACCAAAACAGTAAAAATAATTTAACTTAAATAAATTATGAGATTATAAAACCATTTAAAG
1 TTTTAACCAAAA-AGTAAAAAAAATTTAACTTAAATAAATTATGAGATTATAAAACCATTTAAAG
* * * * * *
941 CGAGTAACAATGCTTTTGAAAGAAT-GGATGGCTATAAATGGACTTTTCTT-CTCAATAAATATC
65 CGAGTAATAAGGCTTTTGAAAGAATAGG-TGAC-ATAAATAGACTTTTCTTGC-CAATGAATACC
** * * * *
1004 AGTTTCTACATGTTTCTTGAGGCAG-CTATTCAATTAA-AGTCTA
127 TTTTTCTTCACGTTTCTTGAGGTAGAC-ATTCAA-TAATAATCTA
** * *
1047 TTTTAAAGAAAAA-TATAAAAAAATTTAACTTATAA-ACAATTATGAGATTACAAAGCCATTTAA
1 TTTTAACCAAAAAGTA-AAAAAAATTTAACTTA-AATA-AATTATGAGATTATAAAACCATTTAA
* ********** *
1110 AGCGAGTAATAAAGCTTTTGAANNNNNNNNNNACAATAAATAGACTTTTCTTGCCAATGAATGCC
63 AGCGAGTAATAAGGCTTTTGAAAGAATAGGTGAC-ATAAATAGACTTTTCTTGCCAATGAATACC
* * *
1175 TTTTTCTTCGCATTTCTTGAGGTAGACATTCAATAATAGTCTA
127 TTTTTCTTCACGTTTCTTGAGGTAGACATTCAATAATAATCTA
* * * * ** *
1218 TTTTAACCAAATATGCAAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAATTATATAAA
1 TTTTAACCAAA-AAGTAAAAAAAATTTAACTT-AAATAAATTATGAGATTATAAAACCATTTAAA
*
1283 GTGAGTAATAAGGCTTTTGAAAGAATA
64 GCGAGTAATAAGGCTTTTGAAAGAATA
1310 AGAGACTATA
Statistics
Matches: 569, Mismatches: 172, Indels: 63
0.71 0.21 0.08
Matches are distributed among these distances:
168 15 0.03
169 59 0.10
170 152 0.27
171 263 0.46
172 78 0.14
173 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.34
Consensus pattern (169 bp):
TTTTAACCAAAAAGTAAAAAAAATTTAACTTAAATAAATTATGAGATTATAAAACCATTTAAAGC
GAGTAATAAGGCTTTTGAAAGAATAGGTGACATAAATAGACTTTTCTTGCCAATGAATACCTTTT
TCTTCACGTTTCTTGAGGTAGACATTCAATAATAATCTA
Found at i:1093 original size:342 final size:338
Alignment explanation
Indices: 358--1323 Score: 927
Period size: 342 Copynumber: 2.8 Consensus size: 338
348 AAGTGACAAA
* * ** *
358 TAAAGTCTGTTTTAACA-AAAAATATACAAAAATTCAAC-TATAATTAATTATAAGATTACAAA-
1 TAAAGTCTATTTTAA-AGAAAAATATAAAAAAATTCAACTTATAAACAATTATGAGATTACAAAG
* * * * *
420 CCATTTCAAGCGTGTAATAAGGCTTTTGAAAGAATAGGTGCCTATAAATGAACTTTTCTTGCCCA
65 CCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGTGAC-ATAAATAAACTTTTCTTGCCAA
* * * * * * * *
485 TTAATGCATTTTTCTTAACGTTTCTCGTGGTGGACATTCAATTATAGTCTATTTAATCAAAAATG
129 TGAATGCCTTTTTCTTCACGTTTCTCAT-GTAGACATTCAATAATAGTCTTTTTAACCAAAAA-G
* ** * * * ********
550 T-AAAACAATTCGCCTTAAAATGAAGTATGAGATTATAAAACCATTTAGAGCGAGTANNNNNNNN
192 TAAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAACAAGGCT
** * * * * * *
614 NNTGAAAGAATGGGTGACTATAAATGGACTTTTCTTTCAATAAATGTTATTTTGTACACATTTTT
257 TTTGAAAGAATGGATGACTATAAATGGACTTTTCTTTCAATAAATATCAGTTTCTACACATTTCT
*
679 TGAGGTAGATATTCAAT
322 TGAGGCAGATATTCAAT
* * * * ******
696 TAAAGTCTGTTTTAAAGAAATATGTAAAAAAATTCAACTTATAATCAATTATGAGATTANNNNNN
1 TAAAGTCTATTTTAAAGAAAAATATAAAAAAATTCAACTTATAAACAATTATGAGATTACAAAGC
**** *
761 NNNNTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACAGTAAATAAACTTTTCTTGCCAAT
66 CATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGTGACA-TAAATAAACTTTTCTTGCCAAT
* * * *
826 GAATACCTTTTTCTTCACGTTTCTCAATGTAGACATTCAATGATAATATGTTTTAACCAAAACAG
130 GAATGCCTTTTTCTTCACGTTTCTC-ATGTAGACATTCAATAATAGTCT-TTTTAACCAAAA-AG
* * *
891 TAAAAATAATTTAACTT-AAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAACAATGCT
192 TAAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAACAAGGCT
* **
955 TTTGAAAGAATGGATGGCTATAAATGGACTTTTCTTCTCAATAAATATCAGTTTCTACATGTTTC
257 TTTGAAAGAATGGATGACTATAAATGGACTTTTCTT-TCAATAAATATCAGTTTCTACACATTTC
*
1020 TTGAGGCAGCTATTCAAT
321 TTGAGGCAGATATTCAAT
*
1038 TAAAGTCTATTTTAAAGAAAAATATAAAAAAATTTAACTTATAAACAATTATGAGATTACAAAGC
1 TAAAGTCTATTTTAAAGAAAAATATAAAAAAATTCAACTTATAAACAATTATGAGATTACAAAGC
* ********** *
1103 CATTTAAAGCGAGTAATAAAGCTTTTGAANNNNNNNNNNACAATAAATAGACTTTTCTTGCCAAT
66 CATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGTGAC-ATAAATAAACTTTTCTTGCCAAT
* * * * *
1168 GAATGCCTTTTTCTTCGCATTTCTTGAGGTAGACATTCAATAATAGTCTATTTTAACCAAATATG
130 GAATGCCTTTTTCTTCACGTTTC-TCATGTAGACATTCAATAATAGTCT-TTTTAACCAAA-AAG
* * ** * * *
1233 CAAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAATTATATAAAGTGAGTAATAAGGCT
192 TAAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAACAAGGCT
*
1298 TTTGAAAGAATAAGA-GACTATAAATG
257 TTTGAAAGAAT-GGATGACTATAAATG
1324 TGCTCTTCTT
Statistics
Matches: 506, Mismatches: 108, Indels: 23
0.79 0.17 0.04
Matches are distributed among these distances:
337 1 0.00
338 33 0.07
339 19 0.04
340 91 0.18
341 81 0.16
342 215 0.42
343 64 0.13
344 2 0.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.33
Consensus pattern (338 bp):
TAAAGTCTATTTTAAAGAAAAATATAAAAAAATTCAACTTATAAACAATTATGAGATTACAAAGC
CATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATAGGTGACATAAATAAACTTTTCTTGCCAATG
AATGCCTTTTTCTTCACGTTTCTCATGTAGACATTCAATAATAGTCTTTTTAACCAAAAAGTAAA
AAAAATTCAACTTAAAATAAATTATGAGATTATAAAACCATTTAAAGCGAGTAACAAGGCTTTTG
AAAGAATGGATGACTATAAATGGACTTTTCTTTCAATAAATATCAGTTTCTACACATTTCTTGAG
GCAGATATTCAAT
Found at i:2678 original size:682 final size:666
Alignment explanation
Indices: 1918--3191 Score: 1345
Period size: 682 Copynumber: 1.9 Consensus size: 666
1908 TCGAGGTAAA
*
1918 CATTCAACAATAGTCTGTTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATNNNNN
1 CATTCAACAATAGTCAGTTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTAT-----
* * *
1983 NNNNNAACCATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGGGTGACTATAAA-CGAACTTTT
61 ----AAACCATTTAAAGCGAGTAATAAGACTTTCGAAAGAATGGGTGACTATAAATAGAA-TTTT
* * * * *****
2047 CTTGC-CAATGA-AT-TTATTTTTCTACAGGTTTTTCA-AGGTAGACATTCAATTATAGTNNNNN
121 CTT-CTCAAT-ACATGGTA-TTTTCTACAGGTTTCT-AGAGGCAGACATTCAATTAAAGTCTGTT
****** * * * *
2108 NNNNNTAAAAATATAAAAAAATATAACTTAAAATTAATTATGAGATTACAAAATCATTTACAGTG
182 TTAAAGAAAAATATAAAAAAATATAACTTAAAATCAATTATGAGATTACAAAACCATTTAAAGCG
* ** * *
2173 AGTAATAAGACCTTTT-AAAGAATAAGTGAGTATAAATGGACTTTTCTTGCCAATGAATGCCTTT
247 AATAATAAG-CCTTTTGAAAGAATAAGTGACAATAAATGGACTCTTCTTACCAATGAATGCCTTT
* * ** ** * * * * *
2237 TTCTTCATGTTTTTTGAGGCAGGCAT-TCAATTATAGTCTATTTTAATTAAAAGTGT-AA-ACAA
311 TTCTTCATATTTCTCAACACAGACATCT-AATTATAATCTATTTTAACTAAAAATGTAAATAAAA
* * *
2299 AT-TCAACATAAAATCAATTATGAGATTACAAAACTATTTAAAGCGAGTAATTAGGCTTTTGAAG
375 ATGT-AACATAAAATCAATTATGAGATTACAAAACTATTTAAAGAGAATAATAAGGCTTTTGAAG
* *
2363 GAATATG-CGACT-ATAAATGGACTTTTCTT-GTCAATGAATAC-CTTTTCTTCACGTTTCTCAA
439 GAAT-TGACGA-TAATAAATAGACTTTTCTTACT-AATGAATACACTTTTCTTCACGTTTCTCAA
*
2424 GGTAGGCATTCAACAATAATCTGTTTGAACCAAAAATGTAAAAAAAATT-AACTTAAAATCAATT
501 GGTAGGCATTCAACAATAATATGTTTGAACCAAAAA-GTAAAAAAAATTAAACTTAAAATCAATT
2488 ATGAGATTATAAAACCANNNNNNNNNNGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
565 ATGAGATTATAAAACCA----------GTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGG
2553 ACTTTTTTTATCAATTAATGCCTTTTCTTCATATTTCTTAAAGTAGG
620 ACTTTTTTTATCAATTAATGCCTTTTCTTCATATTTCTTAAAGTAGG
* *
2600 CATTCAACAATAGTCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATGAATTANNNNNN
1 CATTCAACAATAGTCAGTTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTA------
* * *
2665 NNNNAAACCATTTAAAGCGAGTAATAATACTTTTGAAAGAATGGGTGACTATAAATAGAATTTTC
60 ---TAAACCATTTAAAGCGAGTAATAAGACTTTCGAAAGAATGGGTGACTATAAATAGAATTTTC
* *
2730 TTCTCAATACATGGTATTTTCTACATGTTTCTAGAGGCAGATATTCAATTAAAGTCTGTTTTAAA
122 TTCTCAATACATGGTATTTTCTACAGGTTTCTAGAGGCAGACATTCAATTAAAGTCTGTTTTAAA
* * * *
2795 GAAAAATGTAAAAAAATTTAACTTATAATCAATTATGAGGTTACAAAACCATTTAAAGCGAATAA
187 GAAAAATATAAAAAAATATAACTTAAAATCAATTATGAGATTACAAAACCATTTAAAGCGAATAA
* * * *
2860 TAAGGCTTTTGAAGGAATACGTGACAATAAATGGACTCTTCTTACCAATGAATGCCTTTTTCTTT
252 TAAGCCTTTTGAAAGAATAAGTGACAATAAATGGACTCTTCTTACCAATGAATGCCTTTTTCTTC
* *
2925 ATATTTCTCAACATAGACATCTAATTATAATCTATTTTTACTAAAAATGTAAAAATAAAAATGTA
317 ATATTTCTCAACACAGACATCTAATTATAATCTATTTTAACTAAAAATGT--AAATAAAAATGTA
* * * * *
2990 ACTTAAAATCAATTTTGGGATTATAAAACTATTTAAAGATAATAATAAGGCTTTTGAAGGAATTG
380 ACATAAAATCAATTATGAGATTACAAAACTATTTAAAGAGAATAATAAGGCTTTTGAAGGAATTG
* * * * * *
3055 ATGATAATAAATAGACTTTTCTTACTAATGAATGCATTTTTCTTCATGTTTCTCAATGTAGGTAT
445 ACGATAATAAATAGACTTTTCTTACTAATGAATACACTTTTCTTCACGTTTCTCAAGGTAGGCAT
*** * * * *
3120 TCAGTTATAATATGTTTTAACCAAAAAGTAAAAAAACTTAAACTTAAAATTAATTTTGAGATTAT
510 TCAACAATAATATGTTTGAACCAAAAAGTAAAAAAAATTAAACTTAAAATCAATTATGAGATTAT
3185 AAAACCA
575 AAAACCA
3192 TTTAATTCGA
Statistics
Matches: 486, Mismatches: 80, Indels: 47
0.79 0.13 0.08
Matches are distributed among these distances:
681 8 0.02
682 290 0.60
683 6 0.01
685 5 0.01
686 98 0.20
687 79 0.16
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.34
Consensus pattern (666 bp):
CATTCAACAATAGTCAGTTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAACC
ATTTAAAGCGAGTAATAAGACTTTCGAAAGAATGGGTGACTATAAATAGAATTTTCTTCTCAATA
CATGGTATTTTCTACAGGTTTCTAGAGGCAGACATTCAATTAAAGTCTGTTTTAAAGAAAAATAT
AAAAAAATATAACTTAAAATCAATTATGAGATTACAAAACCATTTAAAGCGAATAATAAGCCTTT
TGAAAGAATAAGTGACAATAAATGGACTCTTCTTACCAATGAATGCCTTTTTCTTCATATTTCTC
AACACAGACATCTAATTATAATCTATTTTAACTAAAAATGTAAATAAAAATGTAACATAAAATCA
ATTATGAGATTACAAAACTATTTAAAGAGAATAATAAGGCTTTTGAAGGAATTGACGATAATAAA
TAGACTTTTCTTACTAATGAATACACTTTTCTTCACGTTTCTCAAGGTAGGCATTCAACAATAAT
ATGTTTGAACCAAAAAGTAAAAAAAATTAAACTTAAAATCAATTATGAGATTATAAAACCAGTAA
TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTATCAATTAATGCCTTTTCTTCA
TATTTCTTAAAGTAGG
Found at i:2691 original size:170 final size:169
Alignment explanation
Indices: 1348--3286 Score: 960
Period size: 171 Copynumber: 11.3 Consensus size: 169
1338 ACAAATGAAA
* * * * * * * **
1348 GACTATAAAAGAACTTTTCTTACCAATGAATGTCTTTTTCTTTATGTTTCTCAAGGTAAACACTT
1 GACTATAAATGGACTTTTCTTATCAATGAATG-CCTTTTCTTCATATTTCTTAAGGTAGGCA-TT
** * * * ** *
1413 -AATTATTGTCTGTTTTGACCAGAAATGTAAAAAAATTCAACTTAAAATTTATTATGAGATTATA
64 CAACAATAGTCTGTTTTAACCAAAAATGTAAAAAAATT-AACTTAAAATCAATTATGAGATTACA
* * ******
1477 AAACCGTTTAAAGCGAGTAATAAGGCTTTTGAAAGANNNNNN
128 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
***** * ** * * * * * *
1519 NNNNGTAAATAGACTTTTCTTGCCCATTAATGCTTTTTTCTTCA-AGTTTCATGAGGTAGACATT
1 GACTATAAATGGACTTTTCTTATCAATGAATGC-CTTTTCTTCATA-TTTCTTAAGGTAGGCATT
* ** * * * * * * * *
1583 GAATTATTGTCTGTTTTAACTAAAAATGT-ACAAAATTCCATTTAAAATTAGTTATGAGATTA-T
64 CAACAATAGTCTGTTTTAACCAAAAATGTAAAAAAATT-AACTTAAAATCAATTATGAGATTACA
* ** * *
1646 AAACCATTTAAAGTGAGTAATAACTCTTTTGAAAGAATGGGT
128 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
** * * ** * * * *
1688 GACTATAAATGGACTTTTCTTGGCAATGAATATCTTTTTCTTCACGTTTTTTGAGGCAGACATTC
1 GACTATAAATGGACTTTTCTTATCAATGAAT-GCCTTTTCTTCATATTTCTTAAGGTAGGCATTC
** * * * ********** *
1753 AATTATAGCCTGTTTTAGCCAAAAATGTAAAAAAATCANNNNNNNNNNAATTATGAGATTATAAA
65 AACAATAGTCTGTTTTAACCAAAAATGTAAAAAAATTAACTTAAAATCAATTATGAGATTACAAA
*
1818 ACCATTTAAAG-GAAGTAATAAGGATTTTGAAGGAAT-GAGT
130 ACCATTTAAAGCG-AGTAATAAGGCTTTTGAAGGAATAG-GT
*********** * * * * **
1858 GACTATAAATGGNNNNNNNNNNCCAATAAATGTCTTTTTCTTCATGTTT-TTCGAGGTAAACATT
1 GACTATAAATGGACTTTTCTTATCAATGAATG-CCTTTTCTTCATATTTCTT-AAGGTAGGCATT
* * *********
1922 CAACAATAGTCTGTTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATNNNNNNNNN
64 CAACAATAGTCTGTTTTAACCAAAAATGTAAAAAAATT-AACTTAAAATCAATTATGAGATTACA
* * * *
1987 NAACCATTTAAAGCGAGTAATAAGGCTTTCGAAAGAATGGGT
128 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
* * ** *** * ** *
2029 GACTATAAACGAACTTTTCTTGCCAATGAATTTATTTTTCTACAGGTTT-TTCAAGGTAGACATT
1 GACTATAAATGGACTTTTCTTATCAATGAA-TGCCTTTTCTTCATATTTCTT-AAGGTAGGCATT
** *********** * *
2093 CAATTATAGTNNNNNNNNNNTAAAAATATAAAAAAATATAACTTAAAATTAATTATGAGATTACA
64 CAACAATAGTCTGTTTTAACCAAAAATGTAAAAAAAT-TAACTTAAAATCAATTATGAGATTACA
* * * * * *
2158 AAATCATTTACAGTGAGTAATAAGACCTTTT-AAAGAATAAGT
128 AAACCATTTAAAGCGAGTAATAAG-GCTTTTGAAGGAATAGGT
* ** * * * *
2200 GAGTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTTTTGAGGCAGGCATTC
1 GACTATAAATGGACTTTTCTTATCAATGAATGCC-TTTTCTTCATATTTCTTAAGGTAGGCATTC
** * ** * * *
2265 AATTATAGTCTATTTTAATTAAAAGTGTAAACAAATTCAACATAAAATCAATTATGAGATTACAA
65 AACAATAGTCTGTTTTAACCAAAAATGTAAAAAAATT-AACTTAAAATCAATTATGAGATTACAA
* * * *
2330 AACTATTTAAAGCGAGTAATTAGGCTTTTGAAGGAATATGC
129 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
* * ** *
2371 GACTATAAATGGACTTTTCTTGTCAATGAATACCTTTTCTTCACGTTTCTCAAGGTAGGCATTCA
1 GACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTCTTCATATTTCTTAAGGTAGGCATTCA
* * *
2436 ACAATAATCTGTTTGAACCAAAAATGTAAAAAAAATTAACTTAAAATCAATTATGAGATTATAAA
66 ACAATAGTCTGTTTTAACCAAAAATGT-AAAAAAATTAACTTAAAATCAATTATGAGATTACAAA
********** *
2501 ACCANNNNNNNNNNGTAATAAGGCTTTTGAAGGAATGGGT
130 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
* * *
2541 GACTATAAATGGACTTTTTTTATCAATTAATGCCTTTTCTTCATATTTCTTAAAGTAGGCATTCA
1 GACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTCTTCATATTTCTTAAGGTAGGCATTCA
* * * **********
2606 ACAATAGTCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATGAATTANNNNNNNNNNAA
66 ACAATAGTCTGTTTTAACCAAAAATGTAAAAAAATT-AACTTAAAATCAATTATGAGATTACAAA
** * *
2671 ACCATTTAAAGCGAGTAATAATACTTTTGAAAGAATGGGT
130 ACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
* * * ** * * * **
2711 GACTATAAATAGAATTTTCTTCTCAAT-ACATGGTATTTTCTACATGTTTC-TAGAGGCAGATAT
1 GACTATAAATGGACTTTTCTTATCAATGA-AT-GCCTTTTCTTCATATTTCTTA-AGGTAGGCAT
* ** * *
2774 TCAATTAA-AGTCTGTTTTAAAGAAAAATGTAAAAAAATTTAACTTATAATCAATTATGAGGTTA
63 TCAA-CAATAGTCTGTTTTAACCAAAAATGTAAAAAAA-TTAACTTAAAATCAATTATGAGATTA
* *
2838 CAAAACCATTTAAAGCGAATAATAAGGCTTTTGAAGGAATACGT
126 CAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
* * * * * ** *
2882 GACAATAAATGGACTCTTCTTACCAATGAATGCCTTTTTCTTTATATTTCTCAACATAGACA-TC
1 GACTATAAATGGACTTTTCTTATCAATGAATGCC-TTTTCTTCATATTTCTTAAGGTAGGCATTC
** * * * * * *
2946 TAATTATAATCTATTTTTACTAAAAATGTAAAAATAAAAATGTAACTTAAAATCAATTTTGGGAT
65 -AACAATAGTCTGTTTTAACCAAAAATGT---AA-AAAAAT-TAACTTAAAATCAATTATGAGAT
* * ** * * *
3011 TATAAAACTATTTAAAGATAATAATAAGGCTTTTGAAGGAATTGAT
124 TACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
* * * * * *
3057 GA-TAATAAATAGACTTTTCTTA-CTAATGAATGCATTTTTCTTCATGTTTCTCAATGTAGGTAT
1 GACT-ATAAATGGACTTTTCTTATC-AATGAATGC-CTTTTCTTCATATTTCTTAAGGTAGGCAT
*** * * * *
3120 TCAGTTATAATATGTTTTAACCAAAAA-GTAAAAAAACTTAAACTTAAAATTAATTTTGAGATTA
63 TCAACAATAGTCTGTTTTAACCAAAAATGTAAAAAAA-TT-AACTTAAAATCAATTATGAGATTA
* ** * * **
3184 TAAAACCATTTAATTCGAGTAATAAGACTTTTAAAGGAATTA-AA
126 CAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA-TAGGT
* ** * * * * *
3228 GACTATAAATAGACTTTTCTTGCCAATAAATACTTTTTTCTTCACATTTCTCAAGGTAG
1 GACTATAAATGGACTTTTCTTATCAATGAATGC-CTTTTCTTCATATTTCTTAAGGTAG
3287 NNNNNNNNNN
Statistics
Matches: 1346, Mismatches: 375, Indels: 94
0.74 0.21 0.05
Matches are distributed among these distances:
169 129 0.10
170 412 0.31
171 647 0.48
172 19 0.01
174 6 0.00
175 131 0.10
176 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
GACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTCTTCATATTTCTTAAGGTAGGCATTCA
ACAATAGTCTGTTTTAACCAAAAATGTAAAAAAATTAACTTAAAATCAATTATGAGATTACAAAA
CCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGT
Found at i:3160 original size:511 final size:498
Alignment explanation
Indices: 2157--3268 Score: 1013
Period size: 511 Copynumber: 2.2 Consensus size: 498
2147 ATGAGATTAC
* * * * * *
2157 AAAATCATTTACAGTGAGTAATAAGACCTTTTAAAGAATAAGTGAGTATAAATGGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAGACCTTTTAAAGAATAAGTGACTATAAATAGAATTTTCTTG
* * * * * **
2222 CCAATGAATGCCTTTTTCTTCATGTTTTTTGAGGCAGGCATTCAATTATAGTCTATTTTAATTAA
66 CCAATGAATGCCTTTTTCTACATGTTTCTAGAGGCAGACATTCAATTAAAGTCTATTTTAAAGAA
* * * * *
2287 AAGTGTAAACAAATTCAACATAAAATCAATTATGAGATTACAAAACTATTTAAAGCGAGTAATTA
131 AAATGTAAAAAAATTCAACATAAAATCAATTATGAGATTACAAAACCATTTAAAGCGAATAATAA
* * * ** *
2352 GGCTTTTGAAGGAATATGCGACTATAAATGGACTTTTCTTGTCAATGAATACCTTTTCTTCACGT
196 GGCTTTTGAAGGAATACGCGACAATAAATGGACTCTTCTTACCAATGAATACCTTTTCTTCACAT
** * *
2417 TTCTCAAGGTAGGCATTCAACAATAATCTGTTTGAACCAAAAATGTAAAAAAAATTAACTTAAAA
261 TTCTCAACATAGACATTCAACAATAATCTATTTGAACCAAAAATGTAAAAAAAATTAACTTAAAA
*********** *
2482 TCAATTATGAGATTATAAAACCANNNNNNNNNNGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
326 TCAATTATGAGATTATAAAACCATTTAAAGATAATAATAAGGCTTTTGAAGGAATGGATGACTAT
* * * *
2547 AAATGGACTTTTTTTATCAATTAATGCCTTTTCTTCATATTTCTTAAAGTAGGCATTCAACAATA
391 AAATAGACTTTTCTTATCAATGAATGCCTTTTCTTCATATTTCTCAAAGTAGGCATTCAACAATA
* *
2612 GTCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATGAATT
456 ATCAGTTTTAACCAAAAATGT-AAAAAA-T-AACTTAAAATGAATT
* **
2658 ANNNNNNNNNNAAACCATTTAAAGCGAGTAATAATA-CTTTTGAAAGAATGGGTGACTATAAATA
1 A----------AAACCATTTAAAGCGAGTAATAAGACCTTTT-AAAGAATAAGTGACTATAAATA
* *
2722 GAATTTTCTT-CTCAAT-ACATG-GTATTTTCTACATGTTTCTAGAGGCAGATATTCAATTAAAG
55 GAATTTTCTTGC-CAATGA-ATGCCT-TTTTCTACATGTTTCTAGAGGCAGACATTCAATTAAAG
* * * * *
2784 TCTGTTTTAAAGAAAAATGTAAAAAAATTTAACTTATAATCAATTATGAGGTTACAAAACCATTT
117 TCTATTTTAAAGAAAAATGTAAAAAAATTCAACATAAAATCAATTATGAGATTACAAAACCATTT
* *
2849 AAAGCGAATAATAAGGCTTTTGAAGGAATACGTGACAATAAATGGACTCTTCTTACCAATGAATG
182 AAAGCGAATAATAAGGCTTTTGAAGGAATACGCGACAATAAATGGACTCTTCTTACCAATGAATA
* * ** ** *
2914 CCTTTTTCTTTATATTTCTCAACATAGACA-TCTAATTATAATCTATTTTTACTAAAAATGTAAA
247 CC-TTTTCTTCACATTTCTCAACATAGACATTC-AACAATAATCTATTTGAACCAAAAATGT--A
* * *
2978 AATAAAAATGTAACTTAAAATCAATTTTGGGATTATAAAACTATTTAAAGATAATAATAAGGCTT
308 AA-AAAAAT-TAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGATAATAATAAGGCTT
* * *
3043 TTGAAGGAATTGATGA-TAATAAATAGACTTTTCTTA-CTAATGAATGCATTTTTCTTCATGTTT
371 TTGAAGGAATGGATGACT-ATAAATAGACTTTTCTTATC-AATGAATGC-CTTTTCTTCATATTT
* * ***
3106 CTCAATGTAGGTATTCAGTTATAAT-ATGTTTTAACCAAAAA-GTAAAAAAACTTAAACTTAAAA
433 CTCAAAGTAGGCATTCAACAATAATCA-GTTTTAACCAAAAATGT-AAAAAA--T-AACTT--AA
3169 TTAATTTTGAGATTAT
491 --AA---TGA-A-T-T
** * *
3185 AAAACCATTTAATTCGAGTAATAAGA-CTTTTAAAGGAATTAA-AGACTATAAATAGACTTTTCT
1 AAAACCATTTAAAGCGAGTAATAAGACCTTTTAAA-GAA-TAAGTGACTATAAATAGAATTTTCT
* * *
3248 TGCCAATAAATACTTTTTTCT
64 TGCCAATGAATGCCTTTTTCT
3269 TCACATTTCT
Statistics
Matches: 485, Mismatches: 86, Indels: 64
0.76 0.14 0.10
Matches are distributed among these distances:
501 1 0.00
510 8 0.02
511 202 0.42
512 43 0.09
514 3 0.01
515 8 0.02
516 92 0.19
517 113 0.23
518 4 0.01
519 2 0.00
521 2 0.00
524 3 0.01
525 1 0.00
526 1 0.00
527 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.35
Consensus pattern (498 bp):
AAAACCATTTAAAGCGAGTAATAAGACCTTTTAAAGAATAAGTGACTATAAATAGAATTTTCTTG
CCAATGAATGCCTTTTTCTACATGTTTCTAGAGGCAGACATTCAATTAAAGTCTATTTTAAAGAA
AAATGTAAAAAAATTCAACATAAAATCAATTATGAGATTACAAAACCATTTAAAGCGAATAATAA
GGCTTTTGAAGGAATACGCGACAATAAATGGACTCTTCTTACCAATGAATACCTTTTCTTCACAT
TTCTCAACATAGACATTCAACAATAATCTATTTGAACCAAAAATGTAAAAAAAATTAACTTAAAA
TCAATTATGAGATTATAAAACCATTTAAAGATAATAATAAGGCTTTTGAAGGAATGGATGACTAT
AAATAGACTTTTCTTATCAATGAATGCCTTTTCTTCATATTTCTCAAAGTAGGCATTCAACAATA
ATCAGTTTTAACCAAAAATGTAAAAAATAACTTAAAATGAATT
Found at i:4265 original size:169 final size:169
Alignment explanation
Indices: 3945--4373 Score: 388
Period size: 169 Copynumber: 2.5 Consensus size: 169
3935 NNNNNNNNNN
* * * *
3945 ATGAGATTATAAAATCATTTAAAGCGCGTAATAAGGCTTTTGAAAGAATGAGTAGCTATAAATAG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTCAAAGAATGAGTAGCTATAAATAA
* * * * * * * *
4010 ACTTTTCTTGCCCATGAATGCTTTTTTTTTCACGTTTCTTGAGGTGAACATTCAATTATAGTCAA
66 ACTTTTCTTGCCAATAAATGCTATTTTCTACACATTTCTTGAGGAGAACATTCAATTAAAGTCAA
* *
4075 TTTAACTAAATTATAAAAAAATTTGGCTCAAAATGAATT
131 TTTAACAAAAATATAAAAAAATTTGGCTCAAAATGAATT
* * *
4114 ATGAGATTATAAAACCATTTAAAGTGAGTAATAATGCTTTTCAATGAATG-G-ATGACTATAAAT
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTCAAAGAATGAGTA-G-CTATAAAT
** * *
4177 AAACTTTT-TTTTCAATAAATGGTATTTTCTACACATTTCTTGAGGCAG-ATATTCAATTAAAGT
64 AAACTTTTCTTGCCAATAAATGCTATTTTCTACACATTTCTTGAGG-AGAACATTCAATTAAAGT
* * *** * * *
4240 CTATTTTAAAGAAAAATAT-AAAAAATTCAACTTATAATCAATT
128 C-AATTT-AACAAAAATATAAAAAAATTTGGCTCAAAATGAATT
** * * * * * *
4283 ATGAGAACACAAAACCATATAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGT-GATAATAAATG
1 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTCAAAGAATGAGTAGCT-ATAAAT-
* *
4347 AAA-TTTTCTTGCTAATGAATGC-ATTTT
64 AAACTTTTCTTGCCAATAAATGCTATTTT
4374 TCATCATATT
Statistics
Matches: 206, Mismatches: 44, Indels: 20
0.76 0.16 0.07
Matches are distributed among these distances:
167 1 0.00
168 45 0.22
169 139 0.67
170 21 0.10
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (169 bp):
ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTCAAAGAATGAGTAGCTATAAATAA
ACTTTTCTTGCCAATAAATGCTATTTTCTACACATTTCTTGAGGAGAACATTCAATTAAAGTCAA
TTTAACAAAAATATAAAAAAATTTGGCTCAAAATGAATT
Done.