Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008770.1 Hibiscus syriacus cultivar Beakdansim tig00111873_pilon, 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: 569103
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:465937 original size:34 final size:34
Alignment explanation
Indices: 465881--465964 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 34
465871 TTAACTTTTA
*
465881 AAAAAT-ATATTAAAATATTATATATATTTTAAAT
1 AAAAATAATATTAAAATAATATATAT-TTTTAAAT
* *
465915 AAAAATAAGATTAAAA-AATATATATTTTTATAT
1 AAAAATAATATTAAAATAATATATATTTTTAAAT
* *
465948 TAAATTAATATTAAAAT
1 AAAAATAATATTAAAAT
465965 GTTTAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
33 20 0.48
34 14 0.33
35 8 0.19
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (34 bp):
AAAAATAATATTAAAATAATATATATTTTTAAAT
Found at i:466053 original size:31 final size:31
Alignment explanation
Indices: 465995--466064 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
465985 AATATATTTA
**
465995 AAAATATATATTTTTAAGTGATGATAAAGAT-
1 AAAATATATATTTTTAAGTGAAAATAAA-ATC
*
466026 AAAATATATATTTTTATA-TTAAAATAAAATC
1 AAAATATATATTTTTA-AGTGAAAATAAAATC
466057 AAAATATA
1 AAAATATA
466065 CTTAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 2 0.06
31 31 0.91
32 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (31 bp):
AAAATATATATTTTTAAGTGAAAATAAAATC
Found at i:466104 original size:27 final size:29
Alignment explanation
Indices: 466051--466104 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
466041 ATATTAAAAT
466051 AAAATCAAAATATACTTAATAAATTAAGA
1 AAAATCAAAATATACTTAATAAATTAAGA
* *
466080 AAAAT-AAAA-ATATTTAATAAGTTAA
1 AAAATCAAAATATACTTAATAAATTAA
466105 AACAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
28 4 0.17
29 5 0.22
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAATCAAAATATACTTAATAAATTAAGA
Found at i:468048 original size:20 final size:22
Alignment explanation
Indices: 468023--468064 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
468013 ATCTCTGAAA
*
468023 ATTTT-AAT-TTTTTTTTATAT
1 ATTTTAAATATTTTCTTTATAT
468043 ATTTTAAATATTTTCTTTATAT
1 ATTTTAAATATTTTCTTTATAT
468065 TTTGTCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 3 0.16
22 11 0.58
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTTTAAATATTTTCTTTATAT
Found at i:469347 original size:44 final size:44
Alignment explanation
Indices: 469292--469597 Score: 136
Period size: 44 Copynumber: 7.1 Consensus size: 44
469282 TCAATAGATT
* * * ** * *
469292 AAAAGATTAGGGGCTTCAATTACAAATTTAGAAAGTGATATTGA
1 AAAAAATTAGGGACATCAATTACAAAGGTAAAAAATGATATTGA
*
469336 AAAAAATTAGGGACATCAATTATAAAGGTAAAAAATGATATTG-
1 AAAAAATTAGGGACATCAATTACAAAGGTAAAAAATGATATTGA
* * * * *
469379 AAAAAATTAAGTG-CCTCAAAGAATATAAATGTAAAAAA-G-T-TTGA
1 AAAAAATT-AGGGACATC--A-ATTACAAAGGTAAAAAATGATATTGA
* * * *
469423 TTAAAAAATTAGGGGGCTTCAATTATAAAGGTAAAAGATG--A--GA
1 --AAAAAATTA-GGGACATCAATTACAAAGGTAAAAAATGATATTGA
* * * * * *
469466 TAAAAACTAGGAGTC-TCAATTATAAAGGTAAAAAGTGAGATT--
1 AAAAAATTAGG-GACATCAATTACAAAGGTAAAAAATGATATTGA
* * * * **
469508 AAAAAATTACGGG-CTTCGATTATAAAGGTAGAAAGCGATATTGA
1 AAAAAATTA-GGGACATCAATTACAAAGGTAAAAAATGATATTGA
* * * *
469552 AAAAAA-TAGGGACCTCAATTATAAAGGTAAAAAGTGAGATTGA
1 AAAAAATTAGGGACATCAATTACAAAGGTAAAAAATGATATTGA
469595 AAA
1 AAA
469598 CATTAAGGAC
Statistics
Matches: 208, Mismatches: 33, Indels: 43
0.73 0.12 0.15
Matches are distributed among these distances:
40 22 0.11
41 10 0.05
42 35 0.17
43 49 0.24
44 59 0.28
45 5 0.02
46 25 0.12
47 3 0.01
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (44 bp):
AAAAAATTAGGGACATCAATTACAAAGGTAAAAAATGATATTGA
Found at i:469470 original size:42 final size:41
Alignment explanation
Indices: 469287--469685 Score: 268
Period size: 43 Copynumber: 9.3 Consensus size: 41
469277 GGGTCTCAAT
* * ** *
469287 AGATTAAAAGATTAGGGGCTTCAATTACAAATTTAGAAAGTG
1 AGATTAAAAAATTAGGGGCTTCAATTATAAAGGTA-AAAATG
* * *
469329 ATATTGAAAAAAATTAGGGACATCAATTATAAAGGTAAAAAATG
1 AGATT--AAAAAATTAGGGGCTTCAATTATAAAGGT-AAAAATG
* * * * * * *
469373 ATATTGAAAAAATTAAGTGCCTCAAAGAATATAAATGTAAAAAAGTT
1 AGATT-AAAAAATTAGGGGCTTC--A-ATTATAAAGGT-AAAAA-TG
*
469420 TGATTAAAAAATTAGGGGGCTTCAATTATAAAGGTAAAAGATG
1 AGATTAAAAAATTA-GGGGCTTCAATTATAAAGGTAAAA-ATG
* *
469463 AGA-T-AAAAACTAGGAG-TCTCAATTATAAAGGTAAAAAGTG
1 AGATTAAAAAATTAGGGGCT-TCAATTATAAAGGTAAAAA-TG
* * **
469503 AGATTAAAAAATTACGGGCTTCGATTATAAAGGTAGAAAGCG
1 AGATTAAAAAATTAGGGGCTTCAATTATAAAGGTA-AAAATG
* * * *
469545 ATATTGAAAAAAATAGGGACCTCAATTATAAAGGTAAAAAGTG
1 AGATT-AAAAAATTAGGGGCTTCAATTATAAAGGTAAAAA-TG
* ** *
469588 AGATTGAAAACATTAAGGACCTT-AATTATAAATGTAAAATATG
1 AGATT-AAAAAATT-AGGGGCTTCAATTATAAAGGTAAAA-ATG
* * * *
469631 GGGTT-AAAAATTAGGGGCTTCAATTATAAAGATAAAAAGG
1 AGATTAAAAAATTAGGGGCTTCAATTATAAAGGTAAAAATG
469671 AGATTACAAAAATTA
1 AGATTA-AAAAATTA
469686 AAGACCTTAA
Statistics
Matches: 277, Mismatches: 58, Indels: 44
0.73 0.15 0.12
Matches are distributed among these distances:
39 2 0.01
40 37 0.13
41 28 0.10
42 44 0.16
43 81 0.29
44 49 0.18
45 3 0.01
46 24 0.09
47 9 0.03
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (41 bp):
AGATTAAAAAATTAGGGGCTTCAATTATAAAGGTAAAAATG
Found at i:469640 original size:85 final size:84
Alignment explanation
Indices: 469336--469702 Score: 259
Period size: 83 Copynumber: 4.3 Consensus size: 84
469326 GTGATATTGA
* * * ** * *
469336 AAAAAATTAGGGACATCAATTATAAAGGTAAAAAATGATATTGAAAAAATTAAGTG-CCTCAAAG
1 AAAAAATTAAGGACCTTAATTATAAAGGTAAAAAGCGAGATTGAAAAAA-T-AGGGACCTC--A-
* * **
469400 AATATAAATGTAAAAAAGTTTGATT
61 ATTATAAAGGT-AAAAAGTGAGATT
* ** * * *
469425 AAAAAATTAGGGGGCTTCAATTATAAAGGT-AAAAGATGAGA-T-AAAAACTA-GGAGTCTCAAT
1 AAAAAATTAAGGACCTT-AATTATAAAGGTAAAAAG-CGAGATTGAAAAAATAGGGA-CCTCAAT
469486 TATAAAGGTAAAAAGTGAGATT
63 TATAAAGGTAAAAAGTGAGATT
* * * * *
469508 AAAAAATTACGG-GCTTCGATTATAAAGGTAGAAAGCGATATTGAAAAAAATAGGGACCTCAATT
1 AAAAAATTAAGGACCTT-AATTATAAAGGTAAAAAGCGAGATTG-AAAAAATAGGGACCTCAATT
469572 ATAAAGGTAAAAAGTGAGATT
64 ATAAAGGTAAAAAGTGAGATT
* * * * * *
469593 GAAAACATTAAGGACCTTAATTATAAATGTAAAATATG-G-GGTT-AAAAATTAGGGGCTTCAAT
1 -AAAAAATTAAGGACCTTAATTATAAAGGTAAAA-A-GCGAGATTGAAAAAATAGGGACCTCAAT
*
469655 TATAAAGATAAAAAG-GAGATT
63 TATAAAGGTAAAAAGTGAGATT
*
469676 ACAAAAATTAAAGACCTTAATTATAAA
1 A-AAAAATTAAGGACCTTAATTATAAA
469703 AAAATAAAAC
Statistics
Matches: 230, Mismatches: 34, Indels: 34
0.77 0.11 0.11
Matches are distributed among these distances:
82 20 0.09
83 56 0.24
84 39 0.17
85 37 0.16
86 29 0.13
87 9 0.04
88 6 0.03
89 18 0.08
90 16 0.07
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.26
Consensus pattern (84 bp):
AAAAAATTAAGGACCTTAATTATAAAGGTAAAAAGCGAGATTGAAAAAATAGGGACCTCAATTAT
AAAGGTAAAAAGTGAGATT
Found at i:473676 original size:24 final size:25
Alignment explanation
Indices: 473623--473684 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
473613 TGTCAAGGAA
* *
473623 TATATTCTTTTTTTATTTTATTTCT
1 TATATTATTTATTTATTTTATTTCT
*
473648 AATATTATTTATTTA-TTTA-TTCTT
1 TATATTATTTATTTATTTTATTTC-T
*
473672 TATATTATATATT
1 TATATTATTTATT
473685 AGATAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 3 0.10
24 16 0.52
25 12 0.39
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (25 bp):
TATATTATTTATTTATTTTATTTCT
Found at i:474779 original size:29 final size:32
Alignment explanation
Indices: 474727--474793 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 32
474717 CGTAGAGTGA
* *
474727 CTAAAGTAGAAATAATTCAAAAGTTTAATAAG
1 CTAAATTAGAAATAATTCAAAAGTATAATAAG
*
474759 -TAAATTAGAAA-AATT-AAAAGTATAGTAAG
1 CTAAATTAGAAATAATTCAAAAGTATAATAAG
474788 CTAAAT
1 CTAAAT
474794 AGGAGAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 12 0.39
30 9 0.29
31 10 0.32
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.28
Consensus pattern (32 bp):
CTAAATTAGAAATAATTCAAAAGTATAATAAG
Found at i:475415 original size:20 final size:19
Alignment explanation
Indices: 475390--475439 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 19
475380 AAATGAAATG
*
475390 AAGAAAGTATTAAATTTTAA
1 AAGAAAGTATTAAA-TATAA
475410 AAGAAA-TA--AAATATAA
1 AAGAAAGTATTAAATATAA
*
475426 AAAAAAGTATTAAA
1 AAGAAAGTATTAAA
475440 GGGAGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
16 9 0.36
17 5 0.20
19 5 0.20
20 6 0.24
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (19 bp):
AAGAAAGTATTAAATATAA
Found at i:476552 original size:19 final size:20
Alignment explanation
Indices: 476530--476569 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
476520 AGAAGAATGA
476530 AAGGG-AAAATGGTCATTGG
1 AAGGGAAAAATGGTCATTGG
476549 AAGGGAAAAATGGTCATTGG
1 AAGGGAAAAATGGTCATTGG
476569 A
1 A
476570 TAGCAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.40, C:0.05, G:0.35, T:0.20
Consensus pattern (20 bp):
AAGGGAAAAATGGTCATTGG
Found at i:478855 original size:18 final size:18
Alignment explanation
Indices: 478832--478869 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
478822 CGAGGGTTAT
*
478832 AAGTGGTCATTTGGGACA
1 AAGTGGTCATTCGGGACA
478850 AAGTGGTCATTCGGGACA
1 AAGTGGTCATTCGGGACA
478868 AA
1 AA
478870 TTTTAAGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.24
Consensus pattern (18 bp):
AAGTGGTCATTCGGGACA
Found at i:500375 original size:24 final size:24
Alignment explanation
Indices: 500330--500375 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
500320 CATGAACATG
**
500330 CTCGTTTGAAAGCTCATTTATTGA
1 CTCGTTTGAAAGCTCAAGTATTGA
500354 CTCGTTT-ATAAGCTCAAGTATT
1 CTCGTTTGA-AAGCTCAAGTATT
500376 TGATTCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (24 bp):
CTCGTTTGAAAGCTCAAGTATTGA
Found at i:500591 original size:23 final size:23
Alignment explanation
Indices: 500564--500620 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
500554 ATTCACGAAA
* *
500564 ATTAAATGAATATGTTCTCAAAC
1 ATTAAATGAACATGTTCGCAAAC
* * *
500587 TTTAAACGAACATGTTCGCGAAC
1 ATTAAATGAACATGTTCGCAAAC
500610 ATTAAATGAAC
1 ATTAAATGAAC
500621 TTAACACAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (23 bp):
ATTAAATGAACATGTTCGCAAAC
Found at i:501553 original size:65 final size:65
Alignment explanation
Indices: 501479--501611 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 65
501469 TTGATCCCTA
501479 TGTATTATTTGATAACTAATAAATTTAATAGTGCTTGACATCTAATGGTTCAATAAATTGAATCC
1 TGTATTATTTGATAACTAATAAATTTAATAGTGCTTGACATCTAATGGTTCAATAAATTGAATCC
*
501544 TGTATTATTTGATAACTAATAAATTTAATAGTGCTTGACATCTAATGGTTCACTAAATTGAATCC
1 TGTATTATTTGATAACTAATAAATTTAATAGTGCTTGACATCTAATGGTTCAATAAATTGAATCC
501609 TGT
1 TGT
501612 GATCTTTTCT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (65 bp):
TGTATTATTTGATAACTAATAAATTTAATAGTGCTTGACATCTAATGGTTCAATAAATTGAATCC
Found at i:503889 original size:16 final size:17
Alignment explanation
Indices: 503868--503901 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
503858 TTTTTTTATT
*
503868 ATTTAATATAAA-AATA
1 ATTTAAAATAAATAATA
503884 ATTTAAAATAAATAATA
1 ATTTAAAATAAATAATA
503901 A
1 A
503902 AATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATAAATAATA
Found at i:507510 original size:138 final size:141
Alignment explanation
Indices: 507252--507531 Score: 494
Period size: 138 Copynumber: 2.0 Consensus size: 141
507242 TTTCCTCCTT
*
507252 ACAACTGGATTTTCTCAGAAGTTCAAATTGCATGCTATCAGAAGAAAATGCATACCATCTTGAGT
1 ACAACTGGATTTTCTCAGAAGTTCAAATT--ATGCTATCAGAAGAAAATGCATACCATCTTGAGC
*
507317 ATTTGTTCACTAGTATAAGCCTCAGCAGATACACTGATTAAATCTTTCACTTGTAAAGAACTACA
64 ATTTGTTCACTAGTATAAGCCTCAGCAGATACACTGATTAAATCTTTCACCTGTAAAGAACTACA
507382 GTTAAAATGAGAG
129 GTTAAAATGAGAG
*
507395 ACAACTGGATTTTCTCAGAATTTCAAA-T-TGC-ATCAGAAGAAAATGCATACCATCTTGAGCAT
1 ACAACTGGATTTTCTCAGAAGTTCAAATTATGCTATCAGAAGAAAATGCATACCATCTTGAGCAT
507457 TTGTTCACTAGTATAAGCCTCAGCAGATACACTGATTAAATCTTTCACCTGTAAAGAACTACAGT
66 TTGTTCACTAGTATAAGCCTCAGCAGATACACTGATTAAATCTTTCACCTGTAAAGAACTACAGT
507522 TAAAATGAGA
131 TAAAATGAGA
507532 AAATGCATAC
Statistics
Matches: 134, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
138 104 0.78
139 3 0.02
142 1 0.01
143 26 0.19
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (141 bp):
ACAACTGGATTTTCTCAGAAGTTCAAATTATGCTATCAGAAGAAAATGCATACCATCTTGAGCAT
TTGTTCACTAGTATAAGCCTCAGCAGATACACTGATTAAATCTTTCACCTGTAAAGAACTACAGT
TAAAATGAGAG
Found at i:512567 original size:23 final size:23
Alignment explanation
Indices: 512541--512590 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
512531 ATCAAGCACA
*
512541 ATAACATATTAGGTACCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
** *
512564 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
512587 ATAA
1 ATAA
512591 TTAAATAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTACCGCTTAT
Found at i:512654 original size:23 final size:23
Alignment explanation
Indices: 512628--512687 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
512618 ATCAAGAACA
*
512628 ATAATATATTAGGTACCGCTTAT
1 ATAATATAATAGGTACCGCTTAT
* *
512651 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTACCGCTTAT
*
512674 ATAATAAAATAGGT
1 ATAATATAATAGGT
512688 TAATTACTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAATATAATAGGTACCGCTTAT
Found at i:512669 original size:87 final size:87
Alignment explanation
Indices: 512523--512780 Score: 417
Period size: 87 Copynumber: 3.0 Consensus size: 87
512513 CATTTAACCG
*
512523 GAAACATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATA
1 GAAACATTATCAAGAACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATA
* *
512588 TAATTAAATAAGTTAATTACTT
66 TAATAAAATAAGTTAATTACTA
*
512610 GAAACATTATCAAGAACAATAATATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATA
1 GAAACATTATCAAGAACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATA
*
512675 TAATAAAATAGGTTAATTACTA
66 TAATAAAATAAGTTAATTACTA
* * * * *
512697 GAAACATTATCAAGTACAATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGTTTATA
1 GAAACATTATCAAGAACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATA
*
512762 TAATAAAATATGTTAATTA
66 TAATAAAATAAGTTAATTA
512781 TTTAATTTGT
Statistics
Matches: 159, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 159 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (87 bp):
GAAACATTATCAAGAACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATA
TAATAAAATAAGTTAATTACTA
Found at i:512741 original size:23 final size:23
Alignment explanation
Indices: 512715--512764 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
512705 ATCAAGTACA
*
512715 ATAACATATTAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
* * *
512738 ATAACGTAATAGGTAGCGTTTAT
1 ATAACATAATAGATAGCGCTTAT
512761 ATAA
1 ATAA
512765 TAAAATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:513575 original size:112 final size:112
Alignment explanation
Indices: 513241--513817 Score: 890
Period size: 112 Copynumber: 5.2 Consensus size: 112
513231 TGAAAGTATC
* *
513241 AAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAATTTCATTATAACAA
1 AAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAA
*
513306 AACCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTTAT
66 AACCGGTAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTTAT
* * * *
513353 AAAAATGTATTGATACGTTACAATATAACATGTAAAAATATGAC--AACCAGTTTCATTATGACA
1 AAAAA-GGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACA
*
513416 AAA-CGGTAAAATTTACCTGATATGTTGAATGTATCAATCCTTTTTAT
65 AAACCGGTAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTTAT
* *
513463 AAAAAGGATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAATTTCATTATGACAA
1 AAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAA
* *
513528 AACCGGTAAAATTTACCTGATATGTTGAAAGTATTAATCTTTTTTAT
66 AACCGGTAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTTAT
* *
513575 AAAAGGGATCGGTACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAA
1 AAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAA
* * *
513640 AACCGGTAAAATTTACCTGATATATTGAAAGTATCGATCTTTTTTAT
66 AACCGGTAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTTAT
* * *
513687 AAAAATGATCGATAATTTACAATATAACAGGTAAAAATATGACAAAATCAGTTTCATTATGACAA
1 AAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAA
* * * *
513752 AACCAGTAAAATTTACCTGATATATTGAAAGTATAAATACTTTTTAT
66 AACCGGTAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTTAT
*
513799 AAAAATGTATCGATACTTT
1 AAAAA-GGATCGATACTTT
513818 GTTGAAAATT
Statistics
Matches: 425, Mismatches: 35, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
109 35 0.08
110 47 0.11
111 41 0.10
112 258 0.61
113 44 0.10
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (112 bp):
AAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAA
AACCGGTAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTTAT
Found at i:514221 original size:87 final size:87
Alignment explanation
Indices: 514119--514327 Score: 328
Period size: 87 Copynumber: 2.4 Consensus size: 87
514109 TTTTCCACAG
* *
514119 AGGTAGCGCTTATATAATAAAATAGGTTAATTTTTGGAAACATTATCAAGCACAATAACATATTA
1 AGGTAGCGCTTATATAATAAAATAGGTTAATTATTGAAAACATTATCAAGCACAATAACATATTA
* * * *
514184 GGTACCGGTTATATAATGTAAT
66 AGTACCGCTTATAAAAAGTAAT
*
514206 AGGTAGTGCTTATATAATAAAATAGGTTAATTATTGAAAACATTATCAAGCACAATAACATATTA
1 AGGTAGCGCTTATATAATAAAATAGGTTAATTATTGAAAACATTATCAAGCACAATAACATATTA
*
514271 AGTAGCGCTTATAAAAAGTAAT
66 AGTACCGCTTATAAAAAGTAAT
* *
514293 AAGTAACGCTTATATAATAAAATAGGTTAATTATT
1 AGGTAGCGCTTATATAATAAAATAGGTTAATTATT
514328 TAATTTGTTA
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 111 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (87 bp):
AGGTAGCGCTTATATAATAAAATAGGTTAATTATTGAAAACATTATCAAGCACAATAACATATTA
AGTACCGCTTATAAAAAGTAAT
Found at i:514686 original size:36 final size:36
Alignment explanation
Indices: 514644--514716 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
514634 ACAAAACCGG
* *
514644 TAAAATTTACCTGATCTGTTGAAAGTATCGATCCTT
1 TAAAATTTACCTGATATGTTGAAAGTATCGAACCTT
514680 TAAAATTTACCTGATATGTTGAAAGTATCGAACCTT
1 TAAAATTTACCTGATATGTTGAAAGTATCGAACCTT
514716 T
1 T
514717 TTATAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (36 bp):
TAAAATTTACCTGATATGTTGAAAGTATCGAACCTT
Found at i:514837 original size:92 final size:92
Alignment explanation
Indices: 514680--514951 Score: 413
Period size: 92 Copynumber: 3.0 Consensus size: 92
514670 ATCGATCCTT
*
514680 TAAAATTTACCTGATATGTTGAAAGTATCGAA-CCTTTTTATAAAAATGATCGATACTTTACAAT
1 TAAAATTTACCTGATATGTTGAAAGTATC-AATCCTTTTTATAAAAAAGATCGATACTTTACAAT
*
514744 ATAAC-GAGTAAAAATATGACAAAACCGG
65 ATAACAG-GTAAAAATATGACAAAACCGA
* * * *
514772 TAAAATTTACATGATATGTTGAAAGTATTAATCCTTTTTATAAAAAGGATCGGTACTTTACAATA
1 TAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTTATAAAAAAGATCGATACTTTACAATA
*
514837 TAACAGGTAAAAAAATGACAAAACCGA
66 TAACAGGTAAAAATATGACAAAACCGA
* * *
514864 TAAAATTTACCTGATATGTTGAAAGTATCGATCTTTTTTATAAAAAAGATCGATAGTTTACAATA
1 TAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTTATAAAAAAGATCGATACTTTACAATA
*
514929 TAACATGTAAAAATATGACAAAA
66 TAACAGGTAAAAATATGACAAAA
514952 TCAGTTTCAT
Statistics
Matches: 163, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
91 2 0.01
92 160 0.98
93 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (92 bp):
TAAAATTTACCTGATATGTTGAAAGTATCAATCCTTTTTATAAAAAAGATCGATACTTTACAATA
TAACAGGTAAAAATATGACAAAACCGA
Found at i:515514 original size:87 final size:87
Alignment explanation
Indices: 515352--515556 Score: 295
Period size: 87 Copynumber: 2.4 Consensus size: 87
515342 TTCCACAAAA
* * * **
515352 GTAGCGCTTATATAATAAAATAGATTAATTATTGGAAACATTATCAAGCACAATAACATATTAGG
1 GTAGCACTTATATAATAAAATAGATTAATTACTGGAAACATTATCAAACACAATAACATATTAAA
*
515417 TACCAGTTATATAATGTAATAG
66 TACCAGTTATATAAAGTAATAG
* * *
515439 GTAGTACTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACAGAATAACATATTAAA
1 GTAGCACTTATATAATAAAATAGATTAATTACTGGAAACATTATCAAACACAATAACATATTAAA
* *
515504 TAGC-GCTTATATAAAGTAATAT
66 TACCAG-TTATATAAAGTAATAG
515526 GTAGCACTTATATAATAAAATAGATTAATTA
1 GTAGCACTTATATAATAAAATAGATTAATTA
515557 TTTAATTTGT
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 1 0.01
87 103 0.99
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (87 bp):
GTAGCACTTATATAATAAAATAGATTAATTACTGGAAACATTATCAAACACAATAACATATTAAA
TACCAGTTATATAAAGTAATAG
Found at i:515981 original size:111 final size:113
Alignment explanation
Indices: 515797--516032 Score: 352
Period size: 111 Copynumber: 2.1 Consensus size: 113
515787 GTATTAATAC
* * *
515797 TTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAATTATGACAAAACCAGTTTCATTA
1 TTTATAAAAATGGATCGATACTTTACAATATAACATGTAAAAATATGAAAAAACCAGTTTCATTA
* * * * *
515862 TGAGAAAACCGCTAAAATTTATCTGATATGTTGAAAGTATCGATTCTT
66 TGACAAAACCGATAAAATTTACCTGATATGTTGAAAGTATAGATACTT
*
515910 TTTATAAAAA-GGATCGATACTTTACAATATAACA-GATAAAAATAT-AAAAAACTAGTTTCATT
1 TTTATAAAAATGGATCGATACTTTACAATATAACATG-TAAAAATATGAAAAAACCAGTTTCATT
*
515972 ATGACAAAACCGATAAAATTTACCTGATATTTTGAAAGTATAGATACTT
65 ATGACAAAACCGATAAAATTTACCTGATATGTTGAAAGTATAGATACTT
516021 TTTATAAAAATG
1 TTTATAAAAATG
516033 TATCAATAGT
Statistics
Matches: 111, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
111 69 0.62
112 32 0.29
113 10 0.09
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (113 bp):
TTTATAAAAATGGATCGATACTTTACAATATAACATGTAAAAATATGAAAAAACCAGTTTCATTA
TGACAAAACCGATAAAATTTACCTGATATGTTGAAAGTATAGATACTT
Found at i:516399 original size:20 final size:20
Alignment explanation
Indices: 516374--516416 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
516364 AAGTATGGAC
516374 ACTTATATATATTTATCGAT
1 ACTTATATATATTTATCGAT
516394 ACTTATATATATTTATCGAT
1 ACTTATATATATTTATCGAT
516414 ACT
1 ACT
516417 ACCGATAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (20 bp):
ACTTATATATATTTATCGAT
Found at i:518034 original size:35 final size:35
Alignment explanation
Indices: 517983--518052 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
517973 ACAATGCAGA
*
517983 CATCGGAGTGTAGAGAAGGGGATGCAAATGTATGT
1 CATCAGAGTGTAGAGAAGGGGATGCAAATGTATGT
*
518018 CATCAGAGTGTAGAGAAGTGGATGCAAATGTATGT
1 CATCAGAGTGTAGAGAAGGGGATGCAAATGTATGT
518053 GTAACTACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.34, T:0.24
Consensus pattern (35 bp):
CATCAGAGTGTAGAGAAGGGGATGCAAATGTATGT
Found at i:520268 original size:29 final size:28
Alignment explanation
Indices: 520220--520282 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 28
520210 GTTAATGGTA
*
520220 AAATTGAATAGAAGTTAGAGGAAATACT
1 AAATTTAATAGAAGTTAGAGGAAATACT
520248 AACATTTAATAGAAGTTAGAGGAAATACT
1 AA-ATTTAATAGAAGTTAGAGGAAATACT
520277 AAATTT
1 AAATTT
520283 TTCAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (28 bp):
AAATTTAATAGAAGTTAGAGGAAATACT
Found at i:521879 original size:16 final size:17
Alignment explanation
Indices: 521846--521879 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
521836 CCATTTTGTT
*
521846 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
521863 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
521879 T
1 T
521880 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:524112 original size:15 final size:13
Alignment explanation
Indices: 524081--524105 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
524071 GGGGCTTGAG
524081 AGAGAAAAATAAA
1 AGAGAAAAATAAA
524094 AGAGAAAAATAA
1 AGAGAAAAATAA
524106 CAAAGAGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (13 bp):
AGAGAAAAATAAA
Found at i:526930 original size:34 final size:34
Alignment explanation
Indices: 526857--526930 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
526847 TACATCAATG
526857 CAAATATACATCAACACATACATACATGATACAT
1 CAAATATACATCAACACATACATACATGATACAT
* * * *
526891 GAAATATGCATCAA-ACATTCATCATCATG-TGCAT
1 CAAATATACATCAACACATACAT-A-CATGATACAT
526925 CAAATA
1 CAAATA
526931 CATTTTTCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
33 7 0.21
34 22 0.67
35 4 0.12
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.26
Consensus pattern (34 bp):
CAAATATACATCAACACATACATACATGATACAT
Found at i:527331 original size:36 final size:35
Alignment explanation
Indices: 527240--527332 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 35
527230 ATACAAAGTG
*
527240 TTGTCTCGCTTGAGACAATTTTCTAAAAACAAATT
1 TTGTCTCGCTTGAGACATTTTTCTAAAAACAAATT
* * * *
527275 TTGTCTCACTTGAAATATTTTCTCTCAAAACAAATT
1 TTGTCTCGCTTGAGACATTTT-TCTAAAAACAAATT
*
527311 TTGTCTTGCTTGAGACATTTTT
1 TTGTCTCGCTTGAGACATTTTT
527333 TCTTTAAACA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
35 18 0.38
36 30 0.62
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (35 bp):
TTGTCTCGCTTGAGACATTTTTCTAAAAACAAATT
Found at i:527541 original size:132 final size:130
Alignment explanation
Indices: 527376--527670 Score: 346
Period size: 132 Copynumber: 2.2 Consensus size: 130
527366 GAAACAAAAA
* * * *
527376 AAAATCATCTTTGAGTTTGTTTCTATTGGAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 AAAATAATCTTTGAG-TTGTTTCTCTTGAAACAAATTTTGTCTCCATTGAGACAGTTTCTCTTGA
527441 AACAC-AAAACTTTGAGTATGTTTCACTTAAAAC-AAGTTTTGTCTCTC-TTGAGACAGTTTCTT
65 AACACTAAAA-TTTGA-TATGTTTCACTTAAAACAAAGTTTTGTCTC-CATTGAGACAGTTTCTT
*
527503 TTGG
127 TGGG
* * *
527507 AACACA-AATCTTTGAGTCTGTTTCTCGTGAAACAAGTTTTGTCTCTATTGAGACAGTTTCTCTT
1 AA-A-ATAATCTTTGAGT-TGTTTCTCTTGAAACAAATTTTGTCTCCATTGAGACAGTTTCTCTT
* * * * * * *
527571 GAAACTCTTATATTTGATTTGTTTCCCTTGAAACAAAGTTTTTTCTCCATTGAGACAGTTTCTTT
63 GAAACACTAAAATTTGATATGTTTCACTTAAAACAAAGTTTTGTCTCCATTGAGACAGTTTCTTT
527636 GGG
128 GGG
*
527639 AAAATCATCTTTGAGTTGGTTTCTCTTGAAAC
1 AAAATAATCTTTGAGTT-GTTTCTCTTGAAAC
527671 CAAAATCCCT
Statistics
Matches: 139, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
130 2 0.01
131 42 0.30
132 92 0.66
133 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.42
Consensus pattern (130 bp):
AAAATAATCTTTGAGTTGTTTCTCTTGAAACAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAA
ACACTAAAATTTGATATGTTTCACTTAAAACAAAGTTTTGTCTCCATTGAGACAGTTTCTTTGGG
Found at i:527661 original size:66 final size:63
Alignment explanation
Indices: 527376--527670 Score: 274
Period size: 66 Copynumber: 4.5 Consensus size: 63
527366 GAAACAAAAA
* * * *
527376 AAAATCATCTTTGAGTTTGTTTCTATTGGAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAATCATCTTTGAG-TTGTTTCTCTTGAAACAAGTTTTGTCTCCATTGAGACAGTTTCTCTTG
* * * *
527440 AAACA-CAAAACTTTGAGTATGTTTCACTTAAAACAAGTTTTGTCTCTC-TTGAGACAGTTTCTT
1 AAA-ATC--ATCTTTGAGT-TGTTTCTCTTGAAACAAGTTTTGTCTC-CATTGAGACAGTTTCTC
527503 TTGG
61 TT-G
* * *
527507 AACACA-AATCTTTGAGTCTGTTTCTCGTGAAACAAGTTTTGTCTCTATTGAGACAGTTTCTCTT
1 AA-A-ATCATCTTTGAGT-TGTTTCTCTTGAAACAAGTTTTGTCTCCATTGAGACAGTTTCTCTT
527571 G
63 G
* * * * *
527572 AAACTCTTATATTTGATTTGTTTCCCTTGAAACAAAGTTTTTTCTCCATTGAGACAGTTTCT-TT
1 AAAATC--ATCTTTGAGTTGTTTCTCTTGAAAC-AAGTTTTGTCTCCATTGAGACAGTTTCTCTT
527636 GGG
63 --G
527639 AAAATCATCTTTGAGTTGGTTTCTCTTGAAAC
1 AAAATCATCTTTGAGTT-GTTTCTCTTGAAAC
527671 CAAAATCCCT
Statistics
Matches: 189, Mismatches: 27, Indels: 28
0.77 0.11 0.11
Matches are distributed among these distances:
64 5 0.03
65 29 0.15
66 142 0.75
67 10 0.05
68 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.42
Consensus pattern (63 bp):
AAAATCATCTTTGAGTTGTTTCTCTTGAAACAAGTTTTGTCTCCATTGAGACAGTTTCTCTTG
Found at i:527842 original size:83 final size:83
Alignment explanation
Indices: 527705--527915 Score: 217
Period size: 83 Copynumber: 2.5 Consensus size: 83
527695 TCCTCATCGT
** * * * ** * * * *
527705 GTAGGAACTGTGTTATCCCCTGACCAGATCTCCTCATTACATAAGAGCCGTGTCACCCCTAGATA
1 GTAGGAACCATGTCATCCACTGACCAGACCTCCTCAACACGTAGGGGCCCTGTCACCCCTAGATA
527770 ACCAGCCGTACTCATCAC
66 ACCAGCCGTACTCATCAC
**
527788 GTAGGAACCATGTCATCCA-TCGACCAGACCTCCTCAACACGTAGGGGCCCTGTCACCTGTAGAT
1 GTAGGAACCATGTCATCCACT-GACCAGACCTCCTCAACACGTAGGGGCCCTGTCACCCCTAGAT
* * * *
527852 AACTAGTCTTCCTCATCAC
65 AACCAGCCGTACTCATCAC
** * *
527871 GTAGGAACTGTGTCATCCACTGACCAGATCTCCTCATCACGTAGG
1 GTAGGAACCATGTCATCCACTGACCAGACCTCCTCAACACGTAGG
527916 AGCCATGTTA
Statistics
Matches: 105, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
82 1 0.01
83 103 0.98
84 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (83 bp):
GTAGGAACCATGTCATCCACTGACCAGACCTCCTCAACACGTAGGGGCCCTGTCACCCCTAGATA
ACCAGCCGTACTCATCAC
Found at i:528139 original size:14 final size:14
Alignment explanation
Indices: 528120--528171 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
528110 CAAAAAATAT
528120 TTATTAATTTATTA
1 TTATTAATTTATTA
*
528134 TTATTATTTTATT-
1 TTATTAATTTATTA
528147 TATATT-A-TTATTA
1 T-TATTAATTTATTA
528160 TTTATTAATTTA
1 -TTATTAATTTA
528172 CATTTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 5 0.16
13 5 0.16
14 18 0.58
15 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTAATTTATTA
Found at i:528158 original size:23 final size:22
Alignment explanation
Indices: 528119--528171 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
528109 ACAAAAAATA
528119 TTTATTAATTTATTATTATTAT
1 TTTATTAATTTATTATTATTAT
*
528141 TTTATT--TATATTATTATTA-
1 TTTATTAATTTATTATTATTAT
528160 TTTATTAATTTA
1 TTTATTAATTTA
528172 CATTTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.22
20 12 0.44
21 3 0.11
22 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATTAATTTATTATTATTAT
Found at i:529828 original size:30 final size:30
Alignment explanation
Indices: 529751--529834 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
529741 TAAGTTCCTA
** *
529751 TTTTGTTGTTTTAACCCTTTAAGTTTCTAT
1 TTTTGTTGTTTTAGTCCTTTAAATTTCTAT
****
529781 TTTTAACATTTTAGTCCTTTAAATTTCTAT
1 TTTTGTTGTTTTAGTCCTTTAAATTTCTAT
*
529811 TTTTGTTGTTTTGGTCCTTTAAAT
1 TTTTGTTGTTTTAGTCCTTTAAAT
529835 CGAATATGAT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTTGTTGTTTTAGTCCTTTAAATTTCTAT
Found at i:532062 original size:108 final size:106
Alignment explanation
Indices: 531892--532516 Score: 333
Period size: 108 Copynumber: 5.6 Consensus size: 106
531882 GGGTTATGGA
* * ** * * * *
531892 AATCCGACGATAACA-AAATAGGTTAATTACTTAATTTGTTATTAGTATTATGAACATATTAGGT
1 AATCCGACGATAACATAACT-GGTTAATTACTGAAAATATTATAAGCATAAT-AACATATTAGGT
* *
531956 AACGCCTAAAATGTTACCAAAATTTAAGCTGATGCAACCTTAGG
64 AACGCCTAAAATGTTACCAAAGTTTAAGCTGATG-AGCCTTAGG
* *
532000 AATCTGACGATAACATAACTGGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTA
1 AATCCGACGATAACATAACTGGTTAATTACTGAAAATATTAT-AAGCATAATAACATATTAGGTA
* * * * *** * * * *
532065 GCGCTTATGTAACGTAATAGGTAGCACCTTTTTAAAGTTGATGGGGCTTTGG
65 ACGC----CTAA---AAT-GTTACCA-AAGTTT-AAGCTGATGAGCCTTAGG
* * * ** * * * *
532117 AAATCCGACGATAA-AAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGG
1 -AATCCGACGATAACATAACT-GGTTAATTACTGAAAATATTATAAGCATAAT-AACATATTAGG
* *
532181 TAACTCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGA
63 TAACGCCTAAAATGTTACCAAAGTTTAAGCTGAT-GAGCCTTAGG
* * * *
532226 AATCCAACGATAACATAACCGGTTAATTACTTG-AAATATTATCAAACATAACAACATATTAGGT
1 AATCCGACGATAACATAACTGGTTAATTAC-TGAAAATATTAT-AAGCATAATAACATATTAGGT
* * * *** * *
532290 AGCGCTTATGTAACGTAATAGGTAGCGC-CTTTTTAAAGCTGATGAGGCTTTGG
64 AACGC----CTAA---AAT-GTTA-C-CAAAGTTT-AAGCTGATGAGCCTTAGG
* * * * ** * * * *
532343 AAATCCGATGGTAACA-AAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGG
1 -AATCCGACGATAACATAACT-GGTTAATTACTGAAAATATTATAAGCATAAT-AACATATTAGG
*
532407 TAACGCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGA
63 TAACGCCTAAAATGTTACCAAAGTTTAAGCTGAT-GAGCCTTAGG
* * * * *
532452 AATCTGACGATAACATAACCGGTTAATTACTGTAAACATTATTAAGAATAATAACATATTAGGTA
1 AATCCGACGATAACATAACTGGTTAATTACTGAAAATATTA-TAAGCATAATAACATATTAGGTA
532517 GCACTTATGT
Statistics
Matches: 373, Mismatches: 106, Indels: 76
0.67 0.19 0.14
Matches are distributed among these distances:
108 146 0.39
109 46 0.12
110 8 0.02
111 6 0.02
112 6 0.02
114 6 0.02
115 6 0.02
116 8 0.02
117 36 0.10
118 105 0.28
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (106 bp):
AATCCGACGATAACATAACTGGTTAATTACTGAAAATATTATAAGCATAATAACATATTAGGTAA
CGCCTAAAATGTTACCAAAGTTTAAGCTGATGAGCCTTAGG
Found at i:532176 original size:118 final size:117
Alignment explanation
Indices: 532052--532634 Score: 436
Period size: 118 Copynumber: 5.1 Consensus size: 117
532042 CAAGCATAAT
* * * *
532052 AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCACCTTTTTAAAGTTGATGGGGCTTTGG
1 AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCACATTTTT-AAGCTGATGGGGCCTTAG
*
532117 AAATCCGACGATAAAAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATC
65 AAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATC
* ** * * ** *
532170 AACATATTAGGTA--AC-T-CCTAA---AAT-GTTACCA-AAGTTTAAGCTGATGGAGCCTTAGA
1 AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCACATTTTTAAGCTGATGGGGCCTTAGA
* * ** * * * * * *
532226 AATCCAACGATAACATAACCGGTTAATTACTTGAA-ATATTATCA-AACATAAC
66 AATCCGACGATAACAAAATAGGTTAATTACTT-AATTTGTTATTAGTA-TTATC
* * * * *
532278 AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGAGGCTTTGG
1 AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCACATTTTT-AAGCTGATGGGGCCTTAG
* *
532343 AAATCCGATGGTAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATC
65 AAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATC
* * * * ** *
532396 AACATATTAGGTAACGC----CTAA---AAT-GTTACCA-AAGTTTAAGCTGATGGAGCCTTAGA
1 AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCACATTTTTAAGCTGATGGGGCCTTAGA
* * ** *** * *
532452 AATCTGACGATAACATAACCGGTTAATTACTGTAA-ACATTATTAAGAATAAT-
66 AATCCGACGATAACAAAATAGGTTAATTACT-TAATTTGTTATT-AGTATTATC
* * * * * *
532504 AACATATTAGGTAGCACTTATGTAACGTAATAGGTAGCGCATTATTGAAGTTGATAGGACCTTAG
1 AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCACATT-TTTAAGCTGATGGGGCCTTAG
* * * * *
532569 AAATCCAACGATAACAAAATATGTTAATTATTTAATTTGTTATCAATATTATC
65 AAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATC
532622 AACATATTAGGTA
1 AACATATTAGGTA
532635 ATGCCTAAAA
Statistics
Matches: 339, Mismatches: 98, Indels: 56
0.69 0.20 0.11
Matches are distributed among these distances:
107 1 0.00
108 124 0.37
109 17 0.05
110 10 0.03
111 7 0.02
112 6 0.02
114 6 0.02
115 7 0.02
116 9 0.03
117 14 0.04
118 137 0.40
119 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (117 bp):
AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCACATTTTTAAGCTGATGGGGCCTTAGA
AATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATC
Found at i:532176 original size:226 final size:226
Alignment explanation
Indices: 531779--532675 Score: 1332
Period size: 226 Copynumber: 4.0 Consensus size: 226
531769 AAAAAATATA
* * *
531779 GACGATAACATAACCAGTTAATTA-TTAGAAACATTATCAAGCATAATAACATATTCGGTAGCGC
1 GACGATAACATAACCGGTTAATTACTGA-AAACATTATCAAGCATAATAACATATTAGGTAGCGC
* * *
531843 TTATATAATGTAATAGGTAACGCATTTTTAAAGCTGATGGGG-TTATGGAAATCCGACGATAACA
65 TTATGTAACGTAATAGGTAGCGCATTTTTAAAGCTGATGGGGCTT-TGGAAATCCGACGATAACA
*
531907 AAATAGGTTAATTACTTAATTTGTTATTAGTATTATGAACATATTAGGTAACGCCTAAAATGTTA
129 AAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTA
* * *
531972 CCAAAATTTAAGCTGATGCAACCTTAGGAATCT
194 CCAAAATTTAAGCTGATGGAGCCTTAGAAATCT
*
532005 GACGATAACATAACTGGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
1 GACGATAACATAACCGGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* * * *
532070 TATGTAACGTAATAGGTAGCACCTTTTTAAAGTTGATGGGGCTTTGGAAATCCGACGATAAAAAA
66 TATGTAACGTAATAGGTAGCGCATTTTTAAAGCTGATGGGGCTTTGGAAATCCGACGATAACAAA
*
532135 ATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACTCCTAAAATGTTACC
131 ATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACC
* *
532200 AAAGTTTAAGCTGATGGAGCCTTAGAAATCC
196 AAAATTTAAGCTGATGGAGCCTTAGAAATCT
* * * *
532231 AACGATAACATAACCGGTTAATTACTTG-AAATATTATCAAACATAACAACATATTAGGTAGCGC
1 GACGATAACATAACCGGTTAATTAC-TGAAAACATTATCAAGCATAATAACATATTAGGTAGCGC
* * * *
532295 TTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGAGGCTTTGGAAATCCGATGGTAACAA
65 TTATGTAACGTAATAGGTAGCGCATTTTTAAAGCTGATGGGGCTTTGGAAATCCGACGATAACAA
532360 AATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAC
130 AATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAC
*
532425 CAAAGTTTAAGCTGATGGAGCCTTAGAAATCT
195 CAAAATTTAAGCTGATGGAGCCTTAGAAATCT
* * * *
532457 GACGATAACATAACCGGTTAATTACTGTAAACATTATTAAGAATAATAACATATTAGGTAGCACT
1 GACGATAACATAACCGGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* * * * * * * *
532522 TATGTAACGTAATAGGTAGCGCATTATTGAAGTTGATAGGACCTTAGAAATCCAACGATAACAAA
66 TATGTAACGTAATAGGTAGCGCATTTTTAAAGCTGATGGGGCTTTGGAAATCCGACGATAACAAA
* * * * * *
532587 ATATGTTAATTATTTAATTTGTTATCAATATTATCAACATATTAGGTAATGCCTAAAATGTTAAC
131 ATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACC
*
532652 AAAATTTAAGCTAATGGAGCCTTA
196 AAAATTTAAGCTGATGGAGCCTTA
532676 AGAATACAAC
Statistics
Matches: 609, Mismatches: 58, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
225 2 0.00
226 601 0.99
227 6 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (226 bp):
GACGATAACATAACCGGTTAATTACTGAAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
TATGTAACGTAATAGGTAGCGCATTTTTAAAGCTGATGGGGCTTTGGAAATCCGACGATAACAAA
ATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACC
AAAATTTAAGCTGATGGAGCCTTAGAAATCT
Found at i:536715 original size:19 final size:19
Alignment explanation
Indices: 536691--536741 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
536681 GAAAAAATTT
536691 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
536710 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
536729 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
536742 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:536783 original size:65 final size:63
Alignment explanation
Indices: 536585--536792 Score: 201
Period size: 65 Copynumber: 3.2 Consensus size: 63
536575 GCACCAAGTG
* **
536585 TGCATCGATGCATGAAATGCATTCGATGTTTAAGAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTCAA-AAA-ATTCTGATGCATCGATGCATGGAC-TG
536649 -
63 A
* *
536649 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAATT-TAGAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG--TTCAAAAAATTCT-GA-TGCATCGATGCATGGACT
536711 GA
62 GA
* * **
536713 GTGCATCGGTGCATGGAATGCATTCGATGTTCAATTAATTCATCGATGCATCGATGCATGGACTG
1 -TGCATCGATGCATGAAATGCATTCGATGTTCAAAAAATTC-T-GATGCATCGATGCATGGACTG
536778 A
63 A
*
536779 TGCATCGGTGCATG
1 TGCATCGATGCATG
536793 CCTTTGAATA
Statistics
Matches: 122, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
63 10 0.08
64 46 0.38
65 60 0.49
66 6 0.05
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTCAAAAAATTCTGATGCATCGATGCATGGACTGA
Found at i:537413 original size:8 final size:8
Alignment explanation
Indices: 537390--537427 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
537380 AAATTAAGTT
*
537390 CAAACATT
1 CAAACATC
*
537398 CAAGCATC
1 CAAACATC
537406 CAAACATC
1 CAAACATC
537414 CAAACATC
1 CAAACATC
537422 CAAACA
1 CAAACA
537428 AACATAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.50, C:0.34, G:0.03, T:0.13
Consensus pattern (8 bp):
CAAACATC
Found at i:543213 original size:22 final size:21
Alignment explanation
Indices: 543171--543210 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
543161 GAGTTTGTTT
*
543171 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
543192 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
543211 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:545285 original size:19 final size:19
Alignment explanation
Indices: 545261--545311 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
545251 GAAAAAATTC
545261 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
545280 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
545299 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
545312 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:545296 original size:65 final size:65
Alignment explanation
Indices: 545154--545313 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
545144 TGCACCAAGT
* ***
545154 GTGCATCGATGCATGAAATGCATTCGATG-TTTAAGAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTAAGAAATAGCCAGATGCATCGATGCATGGAGA
* **
545218 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAA-AAA-ATTCAGAGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTT-AAGAAATAGCCAGA-TGCATCGATGCATGGA
545281 GA
64 GA
* *
545283 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
545314 CAATTAATTC
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 32 0.39
65 49 0.59
66 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTAAGAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:545888 original size:19 final size:20
Alignment explanation
Indices: 545866--545907 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
545856 ATTTAATCAA
*
545866 TTTTGTCACATTTTAACC-G
1 TTTTGTCAAATTTTAACCTG
545885 TTTTGTCAAATTTTAACCTG
1 TTTTGTCAAATTTTAACCTG
545905 TTT
1 TTT
545908 AGAAATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (20 bp):
TTTTGTCAAATTTTAACCTG
Found at i:550391 original size:230 final size:230
Alignment explanation
Indices: 549980--550396 Score: 633
Period size: 230 Copynumber: 1.8 Consensus size: 230
549970 ATAGTAAAAT
* * *
549980 GGTTTCCTTCAATGGAATCGGAATACTCTCTACTACAAGTATCGGTACATTTATACAACCTATAA
1 GGTTTCCGTCAATGGAATCGGAATACTCTCTACTACAAGTATCAGTACATTTATACAACCTACAA
* *
550045 TATCATTTTCTACCTATAATATTATATACAAGTATCGATATTTATTTTCTACCCATAATATCACT
66 TATCATTTTCTACCTATAATATTATATAAAAGTATCGATATTTATTTTCTACCCAGAATATCACT
* * *
550110 TTCTAACTCTAATCGGTCCCAAATCCTTCTTTGTTTTAAAATCCTCAAACCCATAAACCCTAATC
131 TTCTAACTCTAATCGGTCCCAAATCCTTCTTTCTTTGAAAATCCCCAAACCCATAAACCCTAATC
550175 CCTATTTCTAAATACTATAATACTAAAAAAACTAG
196 CCTATTTCTAAATACTATAATACTAAAAAAACTAG
* **
550210 GGTTTCCGTCAAAT-GAATGGGAATACTCTCTACTACAAGTATCAGTACATTTATACAATGTACA
1 GGTTTCCGTC-AATGGAATCGGAATACTCTCTACTACAAGTATCAGTACATTTATACAACCTACA
*
550274 ATATCATTTTCTACCTATAATATTATATAAAAGTATCGATATTTATTTTCTACCCAGAATATTAC
65 ATATCATTTTCTACCTATAATATTATATAAAAGTATCGATATTTATTTTCTACCCAGAATATCAC
* * * * *
550339 TTTCT-ACATGTCATCGGTCTCAAATGCTTTTTTACTTTGAAAA-CCCCAAACCCATAAA
130 TTTCTAAC-TCTAATCGGTCCCAAATCCTTCTTT-CTTTGAAAATCCCCAAACCCATAAA
550397 ACCTCTATTT
Statistics
Matches: 167, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
229 2 0.01
230 155 0.93
231 10 0.06
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (230 bp):
GGTTTCCGTCAATGGAATCGGAATACTCTCTACTACAAGTATCAGTACATTTATACAACCTACAA
TATCATTTTCTACCTATAATATTATATAAAAGTATCGATATTTATTTTCTACCCAGAATATCACT
TTCTAACTCTAATCGGTCCCAAATCCTTCTTTCTTTGAAAATCCCCAAACCCATAAACCCTAATC
CCTATTTCTAAATACTATAATACTAAAAAAACTAG
Found at i:562902 original size:50 final size:52
Alignment explanation
Indices: 562823--562921 Score: 139
Period size: 50 Copynumber: 1.9 Consensus size: 52
562813 AATACTTCGC
* * * *
562823 TTAGGATGAAAACCGGAGAGGGCGTCCTAAGTTGA-AAAA-AAAAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAAAACGT
*
562873 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAAAA
562922 GAGGAAAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 30 0.71
51 4 0.10
52 8 0.19
ACGTcount: A:0.47, C:0.13, G:0.25, T:0.14
Consensus pattern (52 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAAAACGT
Found at i:562930 original size:17 final size:18
Alignment explanation
Indices: 562908--562941 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
562898 CCTAAATTGA
562908 GAAAAGA-AAAAAAAGAG
1 GAAAAGAGAAAAAAAGAG
*
562925 GAAAAGAGAATAAAAGA
1 GAAAAGAGAAAAAAAGA
562942 AGAGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (18 bp):
GAAAAGAGAAAAAAAGAG
Found at i:563869 original size:105 final size:105
Alignment explanation
Indices: 563687--564330 Score: 933
Period size: 105 Copynumber: 6.2 Consensus size: 105
563677 AGGTTTTACC
* *
563687 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
563752 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
563792 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
563857 ACGAAGGGACCGCTGGTTGTCACCAAACA-TT-TCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
563895 CAGAGCCAATTTCAACTTCA-AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
563959 ACGAAGGGACCGCTGGTTGTCAACAAACA--TCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
*
563997 CAGAGCCAATTTCAACTTCACAAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCAC-AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
564062 GACGAAGGGACCGCTGGTTGTCAATAAACATTTC-CCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAA-TT
*
564103 CAGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
564168 ACGAAGGGA------GTTGTCAACAAACATCTCT-CAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAAT-T
* * * * * * *
564202 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCGACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
564267 ACGAAGGGA-CGACTGACTGTCAACGAATA-ATTTCT-CAATT
66 ACGAAGGGACCG-CTGGTTGTCAAC-AA-ACATTTCTCCAATT
* *
564307 CCATAGCCAATTCCAACTTCACAA
1 -CAGAGCCAATTTCAACTTCACAA
564331 ACAGATTGAC
Statistics
Matches: 497, Mismatches: 25, Indels: 33
0.90 0.05 0.06
Matches are distributed among these distances:
98 1 0.00
99 86 0.17
101 1 0.00
102 98 0.20
103 27 0.05
104 73 0.15
105 155 0.31
106 55 0.11
107 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
Found at i:564317 original size:311 final size:306
Alignment explanation
Indices: 563687--564332 Score: 944
Period size: 311 Copynumber: 2.1 Consensus size: 306
563677 AGGTTTTACC
* *
563687 CAGAGCCAATTTCAACTTCAC-AGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCACAAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
563751 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCACAAC
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCACAAC
*
563816 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACC
131 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA---C--GTTGTCAAC
* * *
563881 AAACATTTCCAATTCAGAGCCAATTTCAACTTCAAACGAAGGATATTGGACTCCAGACAACGCAA
191 AAACATCTCCAATTCAGAGCCAATTTCAACTTCAAACGAAGGATATTGGACTCAAGACAACACAA
* * **
563946 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCAAATT
256 GCTCAACTTCACAACGAAGGGACCGCTGACTGTCAACAAACATCTCAAATT
*
563997 CAGAGCCAATTTCAACTTCACAAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCAC
1 CAGAGCCAATTTCAACTTCACAAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
564062 GACGAAGGGACCGCTGGTTGTCAATAAACATTTC-CCAATTTCAGAGCCAATTTCAACTTCGCAA
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAA-TTCAGAGCCAATTTCAACTTCACAA
564126 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA-GTTGTCAACAAAC
130 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACGTTGTCAACAAAC
* *
564190 ATCTCTCAATGTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAG
195 ATCTC-CAAT-TCAGAGCCAATTTCAACTTCA-AACGAAGGATATTGGACTCAAGACAACACAAG
*
564255 CTCGACTTCACAACGAAGGGA-CGACTGACTGTCAACGAATA-ATTTCTC-AATT
257 CTCAACTTCACAACGAAGGGACCG-CTGACTGTCAAC-AA-ACA--TCTCAAATT
* *
564307 CCATAGCCAATTCCAACTTCACAAAC
1 -CAGAGCCAATTTCAACTTCACAAAC
564333 AGATTGACTC
Statistics
Matches: 306, Mismatches: 19, Indels: 21
0.88 0.05 0.06
Matches are distributed among these distances:
305 16 0.05
306 4 0.01
307 23 0.08
308 56 0.18
309 3 0.01
310 30 0.10
311 174 0.57
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (306 bp):
CAGAGCCAATTTCAACTTCACAAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCACAAC
GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACGTTGTCAACAAACA
TCTCCAATTCAGAGCCAATTTCAACTTCAAACGAAGGATATTGGACTCAAGACAACACAAGCTCA
ACTTCACAACGAAGGGACCGCTGACTGTCAACAAACATCTCAAATT
Found at i:566936 original size:190 final size:192
Alignment explanation
Indices: 566594--566970 Score: 526
Period size: 190 Copynumber: 2.0 Consensus size: 192
566584 TTACGACACC
* * * *
566594 TTCAACATATCCGGTAGCTCTTTACTAGATTTGTCATATTGAAACCTATTTTGTCATATTTTAAC
1 TTCAACATATCCGATAGCTCTTTACTAGATTTGTCATATGGAAACCGATTTTCTCATATTTTAAC
* * *
566659 CTGTTATGTTGTTATGTACGATACATGTTTATAAAATATCGATACTTTATAAGCGCTATTATTGC
66 ATGTTATGTTGTTATGTACAATACATGTTTATAAAATATCGATACTTTATAAGAGCTATTATTGC
* *
566724 AATTCTTTTAAATTCTTAAAGTATCGATAATATGATACATATACTTATAAAAGTATCAATAT
131 AATTCTTTTAAATTCATAAAGTATCGATAATATGATACATATACTTAGAAAAGTATCAATAT
* * *
566786 TTCAACA-ATCCGATAGTTCTTTACTGGTTTTGTCATATGGAAACCGATTTTCT-ATATTTTAAC
1 TTCAACATATCCGATAGCTCTTTACTAGATTTGTCATATGGAAACCGATTTTCTCATATTTTAAC
* * ** * * * *
566849 AT-TTATGTTGTTATGTATTAATACATGTTTCTAATGTCTCTATACTTTATAGGAGTTATTATTG
66 ATGTTATGTTGTTATGTA-CAATACATGTTTATAAAATATCGATACTTTATAAGAGCTATTATTG
* *
566913 CAATTCTTTTAAATTCATAAAGTATCGATAATTTGATGCATATACTTAGAAAAGTATC
130 CAATTCTTTTAAATTCATAAAGTATCGATAATATGATACATATACTTAGAAAAGTATC
566971 GATACAAATT
Statistics
Matches: 162, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
189 15 0.09
190 101 0.62
191 39 0.24
192 7 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (192 bp):
TTCAACATATCCGATAGCTCTTTACTAGATTTGTCATATGGAAACCGATTTTCTCATATTTTAAC
ATGTTATGTTGTTATGTACAATACATGTTTATAAAATATCGATACTTTATAAGAGCTATTATTGC
AATTCTTTTAAATTCATAAAGTATCGATAATATGATACATATACTTAGAAAAGTATCAATAT
Found at i:567700 original size:20 final size:21
Alignment explanation
Indices: 567651--567701 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
567641 ATTGGTATAA
*
567651 TTACACATTTTATCCTCAATAT
1 TTACACATTTTATCCTC-AGAT
567673 TTACACATTTTATCCTC-GAT
1 TTACACATTTTATCCTCAGAT
*
567693 TTATACATT
1 TTACACATT
567702 CTTTTTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.47
Consensus pattern (21 bp):
TTACACATTTTATCCTCAGAT
Done.