Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 106 of 186
Found at i:34873908 original size:11 final size:11
Alignment explanation
Indices: 34873869--34873909 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
34873859 AAGTTTTATA
34873869 CAAAATAGTAG
1 CAAAATAGTAG
* *
34873880 CAACATAATAG
1 CAAAATAGTAG
*
34873891 TAAAATAGTAG
1 CAAAATAGTAG
34873902 CAAAATAG
1 CAAAATAG
34873910 GAAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:34876847 original size:43 final size:43
Alignment explanation
Indices: 34876785--34876943 Score: 223
Period size: 43 Copynumber: 3.7 Consensus size: 43
34876775 CAGATATAAG
*
34876785 TTCGGTTTAATGTAA-TGGCACTAAGTGTGCGATATAATTATAGC
1 TTCGG-TTAAT-TAATTGGCACTAAGTGTGCGATACAATTATAGC
* *
34876829 TTCGGCTAATTAATTGGCACTAAGTGTGCGATACGATTATAGC
1 TTCGGTTAATTAATTGGCACTAAGTGTGCGATACAATTATAGC
* *
34876872 TTCGGTTAATTAATTGGCACTAAGTGTGCGAAACCATTAT-GAC
1 TTCGGTTAATTAATTGGCACTAAGTGTGCGATACAATTATAG-C
*
34876915 TTCGGTTAATTAATTAGCACTAAGTGTGC
1 TTCGGTTAATTAATTGGCACTAAGTGTGC
34876944 AATTTTGTTG
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
42 4 0.04
43 97 0.92
44 5 0.05
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (43 bp):
TTCGGTTAATTAATTGGCACTAAGTGTGCGATACAATTATAGC
Found at i:34882548 original size:91 final size:91
Alignment explanation
Indices: 34882393--34882571 Score: 340
Period size: 91 Copynumber: 2.0 Consensus size: 91
34882383 AATTATAGAG
34882393 AATTGAATGACATGTATAAGTTAGATTTAATTCCTATTTTTAATAATAATATTGAAAAATGCAAT
1 AATTGAATGACATGTATAAGTTAGATTTAATTCCTATTTTTAATAATAATATTGAAAAATGCAAT
34882458 ACATGTATGTTGACTAAAATTACGAA
66 ACATGTATGTTGACTAAAATTACGAA
* *
34882484 AATTGAATGACATGTATAAGTTAGATTTAATTCTTGTTTTTAATAATAATATTGAAAAATGCAAT
1 AATTGAATGACATGTATAAGTTAGATTTAATTCCTATTTTTAATAATAATATTGAAAAATGCAAT
34882549 ACATGTATGTTGACTAAAATTAC
66 ACATGTATGTTGACTAAAATTAC
34882572 AAGAAACCCT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (91 bp):
AATTGAATGACATGTATAAGTTAGATTTAATTCCTATTTTTAATAATAATATTGAAAAATGCAAT
ACATGTATGTTGACTAAAATTACGAA
Found at i:34887946 original size:27 final size:27
Alignment explanation
Indices: 34887916--34888385 Score: 353
Period size: 27 Copynumber: 17.1 Consensus size: 27
34887906 GTTGTTAAGA
***
34887916 CCCTAGTTTGTAAAATTATTAAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
* *
34887943 CCCTAGTTTGTAAAATTATCGAAATTTC
1 CCCTAGTTTGTAAAATTACCGAAA-TAC
34887971 CCC-AGTTTGTAAAATTACCGAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
** **
34887997 CCCCGGTTTGTAAAATTATTGAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
*
34888024 CTCTAGTTTGTAAAATTACCGAAATA-
1 CCCTAGTTTGTAAAATTACCGAAATAC
* * *
34888050 CCTTCAGATTGTAAAATTATCGAAATAC
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * *
34888078 CTCTAGTTTTTAGAATTACCGAAATA-
1 CCCTAGTTTGTAAAATTACCGAAATAC
* * * *
34888104 CCATCGGATTGTAAAATTACCAAAATAC
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * *
34888132 CCTCGAATTGTCGATTTGTAAAATTACCAAAATAA
1 CC-C------TAG-TTTGTAAAATTACCGAAATAC
* *
34888167 CCCTAATTTTTAAAATTACCGAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
**
34888194 CCC-AAATTGTAAAATTACCGAAATA-
1 CCCTAGTTTGTAAAATTACCGAAATAC
* *
34888219 CCCTCAGATTGTAAAATTATCGAAATA-
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * * *
34888246 CCCTCGGATTGAAAAATTACCAAAATA-
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * *
34888273 CCCTCAGATTGTAAAATTATCAAAATAC
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * *
34888301 CCCTGGTTTGTGAAATTACTGAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
** * *
34888328 CTTTAGATTGTAAAATTACTGAAATA-
1 CCCTAGTTTGTAAAATTACCGAAATAC
*
34888354 CCCTCAGTTTGTAAAATTACTGAAATAC
1 CCCT-AGTTTGTAAAATTACCGAAATAC
34888382 CCCT
1 CCCT
34888386 GTAGGGTAAA
Statistics
Matches: 360, Mismatches: 64, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.01
26 31 0.09
27 284 0.79
28 18 0.05
34 2 0.01
35 22 0.06
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (27 bp):
CCCTAGTTTGTAAAATTACCGAAATAC
Found at i:34888006 original size:54 final size:53
Alignment explanation
Indices: 34887915--34888383 Score: 424
Period size: 54 Copynumber: 8.6 Consensus size: 53
34887905 GGTTGTTAAG
* *** *
34887915 ACCCTAGTTTGTAAAATTATTAAAATACCC-CTAGTTTGTAAAATTATCGAAATT
1 ACCCCAGTTTGTAAAATTACCGAAATACCCTC-AGATTGTAAAATTATCGAAA-T
* * * * *
34887969 TCCCCAGTTTGTAAAATTACCGAAATACCCCCGGTTTGTAAAATTATTGAAAT
1 ACCCCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* *
34888022 ACCTCTAGTTTGTAAAATTACCGAAATACCTTCAGATTGTAAAATTATCGAAAT
1 ACC-CCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* * * * * * *
34888076 ACCTCTAGTTTTTAGAATTACCGAAATACCATCGGATTGTAAAATTACCAAAAT
1 ACC-CCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* * *
34888130 ACCCTCGAATTGTCGATTTGTAAAATTACCAAAATAACCCT-A-ATTTTTAAAATTACCGAAAT
1 ACCC-C--A-----G-TTTGTAAAATTACCGAAAT-ACCCTCAGA-TTGTAAAATTATCGAAAT
**
34888192 ACCCCAAATTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
1 ACCCCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* * * * *
34888245 ACCCTCGGATTGAAAAATTACCAAAATACCCTCAGATTGTAAAATTATCAAAAT
1 ACCC-CAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* * * * *
34888299 ACCCCTGGTTTGTGAAATTACTGAAATACCTTTAGATTGTAAAATTA-CTGAAAT
1 ACCCC-AGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATC-GAAAT
*
34888353 ACCCTCAGTTTGTAAAATTACTGAAATACCC
1 ACCC-CAGTTTGTAAAATTACCGAAATACCC
34888384 CTGTAGGGTA
Statistics
Matches: 347, Mismatches: 49, Indels: 38
0.80 0.11 0.09
Matches are distributed among these distances:
52 5 0.01
53 44 0.13
54 251 0.72
55 2 0.01
56 1 0.00
59 1 0.00
61 3 0.01
62 36 0.10
63 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (53 bp):
ACCCCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
Found at i:34889947 original size:15 final size:15
Alignment explanation
Indices: 34889927--34889956 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34889917 TTTGGCCGAA
34889927 TAGGCACTCTTATTT
1 TAGGCACTCTTATTT
*
34889942 TAGGCATTCTTATTT
1 TAGGCACTCTTATTT
34889957 CTTTCTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (15 bp):
TAGGCACTCTTATTT
Found at i:34891897 original size:46 final size:47
Alignment explanation
Indices: 34891847--34891968 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 47
34891837 ACTGATACAT
* * *
34891847 GTCCCAGACATGTCTTACACTGGCT-TACGTTTCGAGGCCGATG-CAA
1 GTCCCAGACATGTCTTACACTGGCTCT-CGTCTCAAGACCGATGCCAA
* * * *
34891893 GTCCCAAACATGTCTTACACTAGCTCTCGTCTCAATACCGATGCCAT
1 GTCCCAGACATGTCTTACACTGGCTCTCGTCTCAAGACCGATGCCAA
34891940 GTCCCAGACATGGTCTTACACTGGCTCTC
1 GTCCCAGACAT-GTCTTACACTGGCTCTC
34891969 ATAATGTGGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 35 0.55
47 13 0.20
48 16 0.25
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (47 bp):
GTCCCAGACATGTCTTACACTGGCTCTCGTCTCAAGACCGATGCCAA
Found at i:34893393 original size:54 final size:53
Alignment explanation
Indices: 34893301--34893763 Score: 411
Period size: 54 Copynumber: 8.6 Consensus size: 53
34893291 GGTTGTTAAG
* * * *
34893301 ACCCTAGTTTGTAAAATTATTAAAATACCTCT-AGTTTGTAAAATTATCGAAAT
1 ACCCCAGTTTGTAAAATTACTGAAATACCCCTGA-TTTGTAAAATTATCGAAAT
* *
34893354 ACCACCAGTTTGTAAAATTACCGAAATACCCCTGATTTGTAAAATTACCGAAAT
1 ACC-CCAGTTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
* * * * ** * *
34893408 ACCCCCAATTTATGAAATTACCGAAATAGCTTCGGA-TTGTAAAATTATTGAAAT
1 A-CCCCAGTTTGTAAAATTACTGAAATA-CCCCTGATTTGTAAAATTATCGAAAT
* * * * *
34893462 ACCTCGGATTTGTAAAATTAGTGAAATACCCCCGATTTGTAAAATTAACGAAAT
1 ACCCCAG-TTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
* * * * * * *
34893516 ACCCTC-GAATTATAAAATTACTAAAATACCCTCAGA-TTGTAAAGTTACCAAAAT
1 ACCC-CAG-TTTGTAAAATTACTGAAATACCC-CTGATTTGTAAAATTATCGAAAT
* * * *
34893570 ACCCTCGGTTTGTAAAATTACCGAAATACCCTTGACTTGTAAAATTATCGAAAT
1 ACCC-CAGTTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
* * * *
34893624 ACCCCTGATTTATAAAATTACTGAAATACCCTTGAATTGTAAAATTATCGAAAT
1 ACCCCAG-TTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
*
34893678 ACCCCTAGTTTTTAAAATTA-TCGAAATACCCCTG-TTT-TAAAATTA-CTGAAAT
1 ACCCC-AGTTTGTAAAATTACT-GAAATACCCCTGATTTGTAAAATTATC-GAAAT
* *
34893730 ACCCCTAATTTGTAAAATTACTAAAATACCCCTG
1 ACCCC-AGTTTGTAAAATTACTGAAATACCCCTG
34893764 TAGGGTAAAA
Statistics
Matches: 340, Mismatches: 55, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
51 1 0.00
52 42 0.12
53 18 0.05
54 266 0.78
55 13 0.04
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (53 bp):
ACCCCAGTTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
Found at i:34893448 original size:81 final size:81
Alignment explanation
Indices: 34893308--34893760 Score: 427
Period size: 81 Copynumber: 5.6 Consensus size: 81
34893298 AAGACCCTAG
* * * * * * * *
34893308 TTTGTAAAATTATTAAAATACCTCTAGTTTGTAAAATTATCGAAATACCAC-CAGTTTGTAAAAT
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACC-CTCGGATTGTAAAAT
*
34893372 TACCGAAATACCCCTGA
65 TATCGAAATACCCCTGA
* * * * *
34893389 TTTGTAAAATTACCGAAATACCCCCAATTTATGAAATTACCGAAATAGCTTCGGATTGTAAAATT
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTCGGATTGTAAAATT
* * *
34893454 ATTGAAATACCTCGGA
66 ATCGAAATACCCCTGA
* * * * *
34893470 TTTGTAAAATTAGTGAAATACCCCCGATTTGTAAAATTAACGAAATACCCTCGAATTATAAAATT
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTCGGATTGTAAAATT
* *
34893535 A-CTAAAATACCCTCAGA
66 ATC-GAAATACCC-CTGA
* ** * ** *
34893552 -TTGTAAAGTTACCAAAATACCCTCGGTTTGTAAAATTACCGAAATACCCT-TGACTTGTAAAAT
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTCGGA-TTGTAAAAT
34893615 TATCGAAATACCCCTGA
65 TATCGAAATACCCCTGA
* ** * * * *
34893632 TTTATAAAATTACTGAAATACCCTTGAA-TTGTAAAATTATCGAAATACCC-CTAGTTTTTAAAA
1 TTTGTAAAATTACTGAAATACCC-CCAATTTGTAAAATTACCGAAATACCCTC-GGATTGTAAAA
34893695 TTATCGAAATACCCCTG-
64 TTATCGAAATACCCCTGA
* **
34893712 TTT-TAAAATTACTGAAATACCCCTAATTTGTAAAATTACTAAAATACCC
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCC
34893761 CTGTAGGGTA
Statistics
Matches: 303, Mismatches: 59, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
78 2 0.01
79 38 0.13
80 7 0.02
81 250 0.83
82 6 0.02
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (81 bp):
TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTCGGATTGTAAAATT
ATCGAAATACCCCTGA
Found at i:34893761 original size:27 final size:27
Alignment explanation
Indices: 34893302--34893762 Score: 329
Period size: 27 Copynumber: 17.1 Consensus size: 27
34893292 GTTGTTAAGA
* * *
34893302 CCCTAGTTTGTAAAATTATTAAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
* *
34893329 CTCTAGTTTGTAAAATTA-TCGAAATAC
1 CCCTAATTTGTAAAATTACT-GAAATAC
* *
34893356 CACC-AGTTTGTAAAATTACCGAAATAC
1 C-CCTAATTTGTAAAATTACTGAAATAC
* *
34893383 CCCTGATTTGTAAAATTACCGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
* * * *
34893410 CCCCAATTTATGAAATTACCGAAATAGC
1 CCCTAATTTGTAAAATTACTGAAATA-C
** ** *
34893438 TTCGGA-TTGTAAAATTATTGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
* ** *
34893464 CTCGGATTTGTAAAATTAGTGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
**
34893491 CCCCGATTTGTAAAATTAAC-GAAATAC
1 CCCTAATTTGTAAAATT-ACTGAAATAC
* * *
34893518 CCTCGAA-TTATAAAATTACTAAAATA-
1 CC-CTAATTTGTAAAATTACTGAAATAC
* **
34893544 CCCTCAGA-TTGTAAAGTTACCAAAATA-
1 CCCT-A-ATTTGTAAAATTACTGAAATAC
** *
34893571 CCCTCGGTTTGTAAAATTACCGAAATAC
1 CCCT-AATTTGTAAAATTACTGAAATAC
* * *
34893599 CCTTGACTTGTAAAATTA-TCGAAATAC
1 CCCTAATTTGTAAAATTACT-GAAATAC
* *
34893626 CCCTGATTTATAAAATTACTGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
*
34893653 CCTTGAA-TTGTAAAATTA-TCGAAATAC
1 CCCT-AATTTGTAAAATTACT-GAAATAC
* *
34893680 CCCTAGTTTTTAAAATTA-TCGAAATAC
1 CCCTAATTTGTAAAATTACT-GAAATAC
*
34893707 CCCT-GTTT-TAAAATTACTGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
*
34893732 CCCTAATTTGTAAAATTACTAAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
34893759 CCCT
1 CCCT
34893763 GTAGGGTAAA
Statistics
Matches: 363, Mismatches: 50, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
25 20 0.06
26 24 0.07
27 307 0.85
28 12 0.03
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (27 bp):
CCCTAATTTGTAAAATTACTGAAATAC
Found at i:34893771 original size:27 final size:27
Alignment explanation
Indices: 34893715--34893779 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
34893705 ACCCCTGTTT
* **
34893715 TAAAATTACTGAAATACCCCTAATTTG
1 TAAAATTACTAAAATACCCCTAATGGG
*
34893742 TAAAATTACTAAAATACCCCT-GTAGGG
1 TAAAATTACTAAAATACCCCTAAT-GGG
*
34893769 TAAAATGACTA
1 TAAAATTACTA
34893780 TTTTGCCCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (27 bp):
TAAAATTACTAAAATACCCCTAATGGG
Found at i:34904587 original size:127 final size:127
Alignment explanation
Indices: 34904359--34904612 Score: 463
Period size: 127 Copynumber: 2.0 Consensus size: 127
34904349 CTCCGAATCG
*
34904359 GATGATTTATTCATTTAACTTGTTCCGTAGAGATCCCTAAGTTATGTTATTATCCCTATTCAAGA
1 GATGATTTATTCATTTAACTTGTTCCGTAGAGATCCCTAAATTATGTTATTATCCCTATTCAAGA
34904424 CTAATAACGTCTAATCCCTAGATTGAATAACCGAGACTTTTCTCTAATTAACACTCTAGGGT
66 CTAATAACGTCTAATCCCTAGATTGAATAACCGAGACTTTTCTCTAATTAACACTCTAGGGT
*
34904486 GATGATTTATTCATTTAACTTGTTCCGTAGAGATCCCTAAATTATGTTATTATCCCTATTCAAGG
1 GATGATTTATTCATTTAACTTGTTCCGTAGAGATCCCTAAATTATGTTATTATCCCTATTCAAGA
* * *
34904551 CTAATAACGTCTAATCCCTATATTGAATAACTGAGACTTTTCTCTAATTAACACTTTAGGGT
66 CTAATAACGTCTAATCCCTAGATTGAATAACCGAGACTTTTCTCTAATTAACACTCTAGGGT
34904613 TGTATTAACT
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 122 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (127 bp):
GATGATTTATTCATTTAACTTGTTCCGTAGAGATCCCTAAATTATGTTATTATCCCTATTCAAGA
CTAATAACGTCTAATCCCTAGATTGAATAACCGAGACTTTTCTCTAATTAACACTCTAGGGT
Found at i:34910326 original size:71 final size:71
Alignment explanation
Indices: 34910111--34910328 Score: 188
Period size: 71 Copynumber: 3.1 Consensus size: 71
34910101 CCTTAAAAGG
34910111 CATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAATATGGTAAGTAATGA
1 CATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAATATGGTAAGTAATGA
34910176 TTAAAA
66 TTAAAA
* * ** * * * * *
34910182 CATTTGAA-T--A-GC-AAAATGTGTTTG-TACAAATG-GCA-ACAATGT--GATGAG-AATGGT
1 CATTTGAATTGAATGCTCAATTG-GCATGTTATAATTGAGTATA-AAGGTAATATG-GTAA--GT
* **
34910236 GATCCTTAAAA
61 AATGATTAAAA
34910247 GGCATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAATATGGTAAGTAAT
1 --CATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAATATGGTAAGTAAT
34910312 GATTAAAA
64 GATTAAAA
34910320 CATTTGAAT
1 CATTTGAAT
34910329 AGCAAAATGT
Statistics
Matches: 105, Mismatches: 24, Indels: 36
0.64 0.15 0.22
Matches are distributed among these distances:
63 5 0.05
64 2 0.02
65 16 0.15
66 10 0.10
67 13 0.12
68 2 0.02
70 2 0.02
71 22 0.21
72 10 0.10
73 16 0.15
74 2 0.02
75 5 0.05
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (71 bp):
CATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAATATGGTAAGTAATGA
TTAAAA
Found at i:34910345 original size:138 final size:138
Alignment explanation
Indices: 34910097--34910373 Score: 554
Period size: 138 Copynumber: 2.0 Consensus size: 138
34910087 AGGATGACTT
34910097 TGATCCTTAAAAGGCATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAAT
1 TGATCCTTAAAAGGCATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAAT
34910162 ATGGTAAGTAATGATTAAAACATTTGAATAGCAAAATGTGTTTGTACAAATGGCAACAATGTGAT
66 ATGGTAAGTAATGATTAAAACATTTGAATAGCAAAATGTGTTTGTACAAATGGCAACAATGTGAT
34910227 GAGAATGG
131 GAGAATGG
34910235 TGATCCTTAAAAGGCATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAAT
1 TGATCCTTAAAAGGCATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAAT
34910300 ATGGTAAGTAATGATTAAAACATTTGAATAGCAAAATGTGTTTGTACAAATGGCAACAATGTGAT
66 ATGGTAAGTAATGATTAAAACATTTGAATAGCAAAATGTGTTTGTACAAATGGCAACAATGTGAT
34910365 GAGAATGG
131 GAGAATGG
34910373 T
1 T
34910374 ACCTAATTGT
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (138 bp):
TGATCCTTAAAAGGCATTTGAATTGAATGCTCAATTGGCATGTTATAATTGAGTATAAAGGTAAT
ATGGTAAGTAATGATTAAAACATTTGAATAGCAAAATGTGTTTGTACAAATGGCAACAATGTGAT
GAGAATGG
Found at i:34917822 original size:9 final size:8
Alignment explanation
Indices: 34917797--34917832 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
34917787 TCAAAACTAC
34917797 AAAATTTA
1 AAAATTTA
34917805 AAAATTTA
1 AAAATTTA
34917813 AAAATATTA
1 AAAAT-TTA
34917822 ATAAATTTA
1 A-AAATTTA
34917831 AA
1 AA
34917833 TACGCTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 14 0.54
9 8 0.31
10 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATTTA
Found at i:34917829 original size:18 final size:16
Alignment explanation
Indices: 34917797--34917832 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
34917787 TCAAAACTAC
34917797 AAAATTTAAAAATTTA
1 AAAATTTAAAAATTTA
34917813 AAAATATTAATAAATTTA
1 AAAAT-TTAA-AAATTTA
34917831 AA
1 AA
34917833 TACGCTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 4 0.22
18 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTTAAAAATTTA
Found at i:34919898 original size:79 final size:82
Alignment explanation
Indices: 34919787--34919971 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
34919777 GCTACTCGTT
* * *
34919787 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
34919850 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
34919867 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
34919930 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
34919947 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
34919972 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:34919971 original size:40 final size:40
Alignment explanation
Indices: 34919768--34919971 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
34919758 CGGAATTTAA
** *
34919768 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
34919808 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
34919848 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
34919887 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
34919927 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
34919967 CCGGA
1 CCGGA
34919972 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:34931404 original size:34 final size:34
Alignment explanation
Indices: 34931365--34931435 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
34931355 AAATGCATTA
*
34931365 GTAATAGTATTACATAATCCCTCCAAATTAGTGT
1 GTAATAGTAGTACATAATCCCTCCAAATTAGTGT
34931399 GTAATAGTAGTACATAATCCCTCCAAATTAGTGT
1 GTAATAGTAGTACATAATCCCTCCAAATTAGTGT
34931433 GTA
1 GTA
34931436 CCATGACTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (34 bp):
GTAATAGTAGTACATAATCCCTCCAAATTAGTGT
Found at i:34937374 original size:46 final size:46
Alignment explanation
Indices: 34937324--34937685 Score: 379
Period size: 46 Copynumber: 7.8 Consensus size: 46
34937314 TGGTTGAGCA
34937324 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
34937370 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
34937415 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
34937463 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
34937508 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
34937556 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
34937601 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * **
34937649 CCCGAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
34937686 GCGGGTTACA
Statistics
Matches: 266, Mismatches: 23, Indels: 54
0.78 0.07 0.16
Matches are distributed among these distances:
42 6 0.02
43 15 0.06
45 9 0.03
46 120 0.45
47 87 0.33
48 9 0.03
50 14 0.05
51 6 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:34937480 original size:93 final size:93
Alignment explanation
Indices: 34937321--34937676 Score: 685
Period size: 93 Copynumber: 3.8 Consensus size: 93
34937311 GGATGGTTGA
34937321 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
34937386 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
34937414 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
34937479 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
34937507 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
34937572 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
34937600 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
34937665 TGAGTCCGAGTT
66 TGAGTCCGAGTT
34937677 TGCTTATGGG
Statistics
Matches: 260, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 260 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:34939221 original size:22 final size:22
Alignment explanation
Indices: 34939196--34939239 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34939186 ATAGGTTCTG
34939196 TACATACCTGTATCGCCTCGTA
1 TACATACCTGTATCGCCTCGTA
*
34939218 TACATACCTGTATTGCCTCGTA
1 TACATACCTGTATCGCCTCGTA
34939240 CTAACCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.34
Consensus pattern (22 bp):
TACATACCTGTATCGCCTCGTA
Found at i:34943066 original size:27 final size:26
Alignment explanation
Indices: 34943001--34943131 Score: 104
Period size: 27 Copynumber: 4.9 Consensus size: 26
34942991 AATACTTTAG
* *
34943001 TTTACTAAAATTACTGAAATACCC-CCA
1 TTTA-TAAAATTAC-CAAATACCCTCGA
* *
34943028 GTTGTAAAATTACCAAAGTACCCTCGA
1 TTTATAAAATTACCAAA-TACCCTCGA
**
34943055 TTTATAAAATTACCCAAATATTCTCGA
1 TTTATAAAATTA-CCAAATACCCTCGA
* *
34943082 TTTGTAAAATTACCGAAATACCGTCGA
1 TTTATAAAATTACC-AAATACCCTCGA
* *
34943109 TTGA-AAAATTACTAAAATACCCT
1 TTTATAAAATTAC-CAAATACCCT
34943132 TGTAAGGTAG
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
25 3 0.04
26 32 0.39
27 43 0.52
28 5 0.06
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (26 bp):
TTTATAAAATTACCAAATACCCTCGA
Found at i:34943155 original size:27 final size:27
Alignment explanation
Indices: 34943115--34943321 Score: 244
Period size: 27 Copynumber: 7.7 Consensus size: 27
34943105 TCGATTGAAA
* *
34943115 AATTACTA-AAATACCCTTGTAAGGTAG
1 AATTAC-AGAAATACCCCTGTAGGGTAG
*
34943142 AAATATC-GAAATACCCCTGTAGGGTAG
1 AATTA-CAGAAATACCCCTGTAGGGTAG
*
34943169 AATTACAGAAATACCCCTGTAGAGTAG
1 AATTACAGAAATACCCCTGTAGGGTAG
*
34943196 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACAGAAATACCCCTGTAGGGTAG
*
34943223 AATTATC-GAAATACCCTTGTAGGGTAG
1 AATTA-CAGAAATACCCCTGTAGGGTAG
* **
34943250 AAATACTA-AAATATTCCTGTAGGGTAG
1 AATTAC-AGAAATACCCCTGTAGGGTAG
34943277 AATTACTA-AAATACCCCTGTAGGGTAG
1 AATTAC-AGAAATACCCCTGTAGGGTAG
*
34943304 AATTACTGAAATACCCCT
1 AATTACAGAAATACCCCT
34943322 AGGGTGTTAA
Statistics
Matches: 157, Mismatches: 16, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.01
27 153 0.97
28 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (27 bp):
AATTACAGAAATACCCCTGTAGGGTAG
Found at i:34943222 original size:81 final size:81
Alignment explanation
Indices: 34943115--34943321 Score: 301
Period size: 81 Copynumber: 2.6 Consensus size: 81
34943105 TCGATTGAAA
* * * *
34943115 AATTACTAAAATACCCTTGTAAGGTAGAAATATCGAAATACCCCTGTAGGGTAGAATTAC-AGAA
1 AATTACTAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAGAAATACTA-AA
34943179 ATACCCCTGTAGAGTAG
65 ATACCCCTGTAGAGTAG
* *
34943196 AATTACTGAAATACCCCTGTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAGAAATACTAAAA
1 AATTACTAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAGAAATACTAAAA
** *
34943261 TATTCCTGTAGGGTAG
66 TACCCCTGTAGAGTAG
34943277 AATTACTAAAATACCCCTGTAGGGTAGAATTA-CTGAAATACCCCT
1 AATTACTAAAATACCCCTGTAGGGTAGAATTATC-GAAATACCCCT
34943322 AGGGTGTTAA
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.01
81 111 0.98
82 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (81 bp):
AATTACTAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAGAAATACTAAAA
TACCCCTGTAGAGTAG
Found at i:34943565 original size:27 final size:26
Alignment explanation
Indices: 34943535--34943616 Score: 101
Period size: 27 Copynumber: 3.1 Consensus size: 26
34943525 GGATGAAGCA
34943535 TTCTGGTGGCTATGCCACAAATATCTG
1 TTCTGGTGGCTATGCCAC-AATATCTG
*
34943562 TTCTGGTGGCTCTGCCACAATATCTG
1 TTCTGGTGGCTATGCCACAATATCTG
* * * *
34943588 TATTTGGTGACTTTGTCACAATATCTG
1 T-TCTGGTGGCTATGCCACAATATCTG
34943615 TT
1 TT
34943617 GACCGATCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 10 0.20
27 39 0.80
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (26 bp):
TTCTGGTGGCTATGCCACAATATCTG
Found at i:34943752 original size:22 final size:22
Alignment explanation
Indices: 34943724--34943782 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
34943714 CCCATTATCG
34943724 ATGGCTTTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
34943746 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
34943768 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
34943783 ACGTATTTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:34944022 original size:27 final size:26
Alignment explanation
Indices: 34943949--34944023 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
34943939 AGTGGATTTG
* * *
34943949 CCACATTATCTGTTTCTAGTGGCTATG
1 CCACAATATCTG-TTCTGGTGGCTATA
* * *
34943976 CCACAAATATCTATTTTGGTGGCTCTA
1 CCAC-AATATCTGTTCTGGTGGCTATA
34944003 CCACAATATCTGTATCTGGTG
1 CCACAATATCTGT-TCTGGTG
34944024 ACTTTGTCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 8 0.21
27 24 0.63
28 6 0.16
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (26 bp):
CCACAATATCTGTTCTGGTGGCTATA
Found at i:34948412 original size:25 final size:24
Alignment explanation
Indices: 34948384--34948430 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
34948374 AAGGGAATAG
34948384 GGGAAGGAA-ATGAGGAAAAATGAAA
1 GGGAAGGAAGA-GA-GAAAAATGAAA
*
34948409 GGGAATGAAGAGAGAAAAATGA
1 GGGAAGGAAGAGAGAAAAATGA
34948431 GAGAGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 10 0.50
26 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.36, T:0.09
Consensus pattern (24 bp):
GGGAAGGAAGAGAGAAAAATGAAA
Found at i:34948426 original size:24 final size:25
Alignment explanation
Indices: 34948398--34948446 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
34948388 AGGAAATGAG
*
34948398 GAAAAATGAAAG-GGAATGAAGAGA
1 GAAAAATGAAAGAGAAATGAAGAGA
*
34948422 GAAAAATGAGAGAGAAATGAAGAGA
1 GAAAAATGAAAGAGAAATGAAGAGA
34948447 TGACAAGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.08
Consensus pattern (25 bp):
GAAAAATGAAAGAGAAATGAAGAGA
Found at i:34954467 original size:44 final size:44
Alignment explanation
Indices: 34954412--34954499 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
34954402 CTCCTGCTAA
*
34954412 AGGGGCAGTGCCGACTAAAAATCAACATCCTACTGTTGGTCAAG
1 AGGGGCAGTGCCGACTAAAAATCAACATCCTACTGTTAGTCAAG
* * ** *
34954456 AGGGGCGGTGCCGACTGAAAATTGACCTCCTACTGTTAGTCAAG
1 AGGGGCAGTGCCGACTAAAAATCAACATCCTACTGTTAGTCAAG
34954500 GAGGAGGAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (44 bp):
AGGGGCAGTGCCGACTAAAAATCAACATCCTACTGTTAGTCAAG
Found at i:34966233 original size:46 final size:44
Alignment explanation
Indices: 34966129--34966236 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
34966119 TGTCTTTGAC
** * * *
34966129 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
34966173 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
34966219 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
34966237 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:34966805 original size:213 final size:213
Alignment explanation
Indices: 34966438--34966863 Score: 798
Period size: 213 Copynumber: 2.0 Consensus size: 213
34966428 ACCTCGATAC
34966438 AAAATGTGACTAAAGTTTACAATTTAGTCCTTTACTTTTTCTTTTCCCCGATCTAATCCCGAATT
1 AAAATGTGACTAAAGTTTACAATTTAGTCCTTTACTTTTTCTTTTCCCCGATCTAATCCCGAATT
34966503 TCGCTCTTCTTGATCTATAATAGCAAATTTAGCTTATTTAATATCAACATTTATCAAAACAACCC
66 TCGCTCTTCTTGATCTATAATAGCAAATTTAGCTTATTTAATATCAACATTTATCAAAACAACCC
* *
34966568 TTTACTCAAACTTTGGAAAAATCACATTTTTGCCCCTAAACTTTCACATATTTGCACTTTTGCCC
131 TTTACTCAAACTTTAGAAAAATCACATTTTTGCCCCTAAAATTTCACATATTTGCACTTTTGCCC
*
34966633 CAAGGCTCGTAAATTAAA
196 CAACGCTCGTAAATTAAA
* *
34966651 AAAATGTGACTAAAGTTTACAATTTAGTCCTTTCCTTTTTCTTTTCCCCGATCTACTCCCGAATT
1 AAAATGTGACTAAAGTTTACAATTTAGTCCTTTACTTTTTCTTTTCCCCGATCTAATCCCGAATT
*
34966716 TCGTTCTTCTTGATCTATAATAGCAAATTTAGCTTATTTAATATCAACATTTATCAAAACAACCC
66 TCGCTCTTCTTGATCTATAATAGCAAATTTAGCTTATTTAATATCAACATTTATCAAAACAACCC
34966781 TTTACTCAAACTTTAGAAAAATCACATTTTTGCCCCTAAAATTTCACATATTTGCACTTTTGCCC
131 TTTACTCAAACTTTAGAAAAATCACATTTTTGCCCCTAAAATTTCACATATTTGCACTTTTGCCC
34966846 CAACGCTCGTAAATTAAA
196 CAACGCTCGTAAATTAAA
34966864 CTTCATCCTA
Statistics
Matches: 207, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
213 207 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (213 bp):
AAAATGTGACTAAAGTTTACAATTTAGTCCTTTACTTTTTCTTTTCCCCGATCTAATCCCGAATT
TCGCTCTTCTTGATCTATAATAGCAAATTTAGCTTATTTAATATCAACATTTATCAAAACAACCC
TTTACTCAAACTTTAGAAAAATCACATTTTTGCCCCTAAAATTTCACATATTTGCACTTTTGCCC
CAACGCTCGTAAATTAAA
Found at i:34966996 original size:41 final size:42
Alignment explanation
Indices: 34966939--34967020 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 42
34966929 TTCACACACT
34966939 AACATGTACTTATGACTATTAGGTATTTTTA-CGATTAAGCC
1 AACATGTACTTATGACTATTAGGTATTTTTACCGATTAAGCC
34966980 AACATGTACTTATGACTATTAGGTATTTTTACCGATTAAGC
1 AACATGTACTTATGACTATTAGGTATTTTTACCGATTAAGC
34967021 GTTTTTACTC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 31 0.77
42 9 0.22
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (42 bp):
AACATGTACTTATGACTATTAGGTATTTTTACCGATTAAGCC
Found at i:34975344 original size:28 final size:28
Alignment explanation
Indices: 34975312--34975439 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 28
34975302 ATAGTAAGTC
*
34975312 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
34975340 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
34975369 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
34975397 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
34975426 CGCACACTTAGTGC
1 CGCACACTTAGTGC
34975440 CAATCTCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 44 0.49
29 45 0.51
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:34975402 original size:57 final size:57
Alignment explanation
Indices: 34975311--34975439 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
34975301 TATAGTAAGT
*
34975311 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
34975368 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
34975425 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
34975440 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:34980142 original size:14 final size:14
Alignment explanation
Indices: 34980123--34980216 Score: 61
Period size: 14 Copynumber: 6.4 Consensus size: 14
34980113 TGAATCCTCC
34980123 TATTTT-TTTATTCT
1 TATTTTATTTATT-T
34980137 TATTTTTACTTTATTT
1 TA-TTTTA-TTTATTT
34980153 TATTTTATTTATTT
1 TATTTTATTTATTT
* *
34980167 T-TCTT-TTTCTTT
1 TATTTTATTTATTT
34980179 TGATTTTTATTTTCATTT
1 T-A-TTTTA-TTT-ATTT
*
34980197 CAATTTTA-TTATTT
1 -TATTTTATTTATTT
34980211 TATTTT
1 TATTTT
34980217 GAAAAACATA
Statistics
Matches: 64, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
12 7 0.11
13 8 0.12
14 14 0.22
15 14 0.22
16 3 0.05
17 14 0.22
18 4 0.06
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (14 bp):
TATTTTATTTATTT
Found at i:34980186 original size:7 final size:6
Alignment explanation
Indices: 34980127--34980196 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
34980117 TCCTCCTATT
* * * * *
34980127 TTTTTA TTCTTA TTTTTA -CTTTA TTTTATT TTATTTA TTTTTC TTTTTC
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TT-TTTA TTTTTA TTTTTA
* *
34980176 TTTTGA TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTT
34980197 CAATTTTATT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 4 0.08
6 38 0.76
7 6 0.12
8 2 0.04
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:34980191 original size:17 final size:16
Alignment explanation
Indices: 34980129--34980206 Score: 61
Period size: 17 Copynumber: 4.8 Consensus size: 16
34980119 CTCCTATTTT
* *
34980129 TTTATTCTTATTTTTA
1 TTTATTTTTATTTTCA
34980145 CTTTA-TTTTATTTT-A
1 -TTTATTTTTATTTTCA
* *
34980160 TTTATTTTTCTTTTTCT
1 TTTATTTTT-ATTTTCA
34980177 TTTGATTTTTATTTTCA
1 TTT-ATTTTTATTTTCA
*
34980194 TTTCAATTTTATT
1 TTT-ATTTTTATT
34980207 ATTTTATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
14 4 0.08
15 5 0.10
16 12 0.24
17 23 0.46
18 6 0.12
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTATTTTTATTTTCA
Found at i:34983119 original size:13 final size:13
Alignment explanation
Indices: 34983103--34983135 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
34983093 TTTAATTAAA
*
34983103 TTAGTTAATTAGT
1 TTAGATAATTAGT
34983116 TTAGATAATTAGT
1 TTAGATAATTAGT
34983129 TTA-ATAA
1 TTAGATAA
34983136 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:34993683 original size:17 final size:18
Alignment explanation
Indices: 34993663--34993708 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
34993653 TTTTTATCAT
*
34993663 TTATCATTTTTCGGGCA-
1 TTATCATTTATCGGGCAC
* *
34993680 TTATAATTGATCGGGCAC
1 TTATCATTTATCGGGCAC
34993698 TT-TCATTTATC
1 TTATCATTTATC
34993709 AAGCTTTAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (18 bp):
TTATCATTTATCGGGCAC
Found at i:35012470 original size:33 final size:33
Alignment explanation
Indices: 35012433--35012495 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
35012423 TGTATCTCTC
35012433 AATTACAAACAAGTAAACCCAAATCTAATTTGT
1 AATTACAAACAAGTAAACCCAAATCTAATTTGT
* *
35012466 AATTACAAACAATTAAACCTAAATCTAATT
1 AATTACAAACAAGTAAACCCAAATCTAATT
35012496 GTTAAGTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.29
Consensus pattern (33 bp):
AATTACAAACAAGTAAACCCAAATCTAATTTGT
Found at i:35012690 original size:28 final size:29
Alignment explanation
Indices: 35012631--35012695 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
35012621 TATTTGAAAG
* *
35012631 TTTTTATTTAATTCACTAAACTATTCAAAT
1 TTTTTTTTTAAATCACTAAACTATT-AAAT
**
35012661 TTTTTTTTTAAATCACTAGTCTATT-AAT
1 TTTTTTTTTAAATCACTAAACTATTAAAT
35012689 TTTTTTT
1 TTTTTTT
35012696 AAGTTTGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 10 0.32
30 21 0.68
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTTTTTTTAAATCACTAAACTATTAAAT
Found at i:35024070 original size:15 final size:16
Alignment explanation
Indices: 35024050--35024085 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
35024040 CTATGAGCGT
35024050 TTTTTATATTAT-TTA
1 TTTTTATATTATATTA
35024065 TTTTTATATTATATTA
1 TTTTTATATTATATTA
35024081 TTTTT
1 TTTTT
35024086 GTTTTAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTATATTATATTA
Found at i:35024527 original size:211 final size:209
Alignment explanation
Indices: 35024165--35024561 Score: 740
Period size: 211 Copynumber: 1.9 Consensus size: 209
35024155 TTTCTTCCCC
*
35024165 ATTGTTCGTTTTTTGTTCTTTCCAAAGTCCAATTTCATTTTTTTCTTATTTCTTTCATTTTATAT
1 ATTGTTCATTTTTTGTTCTTTCCAAAGTCCAATTTCATTTTTTTCTTATTTCTTTCATTTTATAT
* *
35024230 ACGTTACGTGTTGTCTGTCAAGATCAATCGTTCTTGTGTGTTTCGTTTTATCAGAGGTGAAGTGG
66 ACGTTACGTGTTGTCTGTCAAGACCAATCGTCCTTGTGTGTTTCGTTTTATCAGAGGTGAAGTGG
35024295 GTAAGTTTTGTTCATGAGAGTTTACGATAGAATTGCTTCTGCTTCTATTATTTGTTCATGAGAGT
131 GTAAGTTTTGTTCATGAGAGTTTACGATAGAATTGCTTCTGCTTCTATTATTTGTTCATGAGAGT
35024360 TTACGATAGCTTCT
196 TTACGATAGCTTCT
*
35024374 ATTGTTCATTTTTTGTTCTTTCCAAAGTCCAATTTCATTTTTTTTTCTTATTTCTTTCGTTTTAT
1 ATTGTTCATTTTTTGTTCTTTCCAAAGTCCAATTTCA--TTTTTTTCTTATTTCTTTCATTTTAT
35024439 ATACGTTACGTGTTGTCTGTCAAGACCAATCGTCCTTGTGTGTTTCGTTTTATCAGAGGTGAAGT
64 ATACGTTACGTGTTGTCTGTCAAGACCAATCGTCCTTGTGTGTTTCGTTTTATCAGAGGTGAAGT
35024504 GGGTAAGTTTTGTTCATGAGAGTTTACGATAGAATTGCTTCTGCTTCTATTATTTGTT
129 GGGTAAGTTTTGTTCATGAGAGTTTACGATAGAATTGCTTCTGCTTCTATTATTTGTT
35024562 AATTGCAGTT
Statistics
Matches: 182, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
209 36 0.20
211 146 0.80
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (209 bp):
ATTGTTCATTTTTTGTTCTTTCCAAAGTCCAATTTCATTTTTTTCTTATTTCTTTCATTTTATAT
ACGTTACGTGTTGTCTGTCAAGACCAATCGTCCTTGTGTGTTTCGTTTTATCAGAGGTGAAGTGG
GTAAGTTTTGTTCATGAGAGTTTACGATAGAATTGCTTCTGCTTCTATTATTTGTTCATGAGAGT
TTACGATAGCTTCT
Found at i:35028194 original size:17 final size:17
Alignment explanation
Indices: 35028172--35028207 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
35028162 GCATAATTCT
35028172 GGGTCACCAATGGTTAG
1 GGGTCACCAATGGTTAG
35028189 GGGTCACCAATGGTTAG
1 GGGTCACCAATGGTTAG
35028206 GG
1 GG
35028208 ATCATTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (17 bp):
GGGTCACCAATGGTTAG
Found at i:35028487 original size:21 final size:21
Alignment explanation
Indices: 35028461--35028510 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
35028451 ACAGTGAGTT
*
35028461 ACATGGGCATGTCTCCCCTTC
1 ACATGGGCATGTCTACCCTTC
* * *
35028482 ACATGGGCGTGTGTAGCCTTC
1 ACATGGGCATGTCTACCCTTC
35028503 ACATGGGC
1 ACATGGGC
35028511 TTATAGACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (21 bp):
ACATGGGCATGTCTACCCTTC
Found at i:35034781 original size:13 final size:13
Alignment explanation
Indices: 35034765--35034797 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
35034755 TTTAATTAAA
*
35034765 TTAGTTAATTAGT
1 TTAGATAATTAGT
35034778 TTAGATAATTAGT
1 TTAGATAATTAGT
35034791 TTA-ATAA
1 TTAGATAA
35034798 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:35045345 original size:17 final size:18
Alignment explanation
Indices: 35045325--35045370 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
35045315 TTTTTATCAT
*
35045325 TTATCATTTTTCGGGCA-
1 TTATCATTTATCGGGCAC
* *
35045342 TTATAATTGATCGGGCAC
1 TTATCATTTATCGGGCAC
35045360 TT-TCATTTATC
1 TTATCATTTATC
35045371 AAGCTTTAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (18 bp):
TTATCATTTATCGGGCAC
Found at i:35048611 original size:74 final size:74
Alignment explanation
Indices: 35048490--35048791 Score: 588
Period size: 74 Copynumber: 4.1 Consensus size: 74
35048480 TATTAAAAGC
35048490 TTATACGCCACATGACTTATACTTTATTTTATTATTTTATTAAATTTTTAATACAACAACCTAGT
1 TTATACGCCACATGACTTATACTTTATTTTATTATTTTATTAAATTTTTAATACAACAACCTAGT
35048555 TTTACAGAG
66 TTTACAGAG
35048564 TTATACGCCACATGACTTATACTTTATTTTATTATTTTATTAAATTTTTAATACAACAACCTAGT
1 TTATACGCCACATGACTTATACTTTATTTTATTATTTTATTAAATTTTTAATACAACAACCTAGT
35048629 TTTACAGAG
66 TTTACAGAG
35048638 TTATACGCCACATGACTTATACTTTATTTTATTATTTTATTAAATTTTTAATACAACAACCTAGT
1 TTATACGCCACATGACTTATACTTTATTTTATTATTTTATTAAATTTTTAATACAACAACCTAGT
35048703 TTTACAGAG
66 TTTACAGAG
*
35048712 TTATACGCCACATGACTTATACTTTATTTTATTATTTTATTAAATTTTTAATACAACACCCTAGT
1 TTATACGCCACATGACTTATACTTTATTTTATTATTTTATTAAATTTTTAATACAACAACCTAGT
35048777 TTTACAGAG
66 TTTACAGAG
35048786 -TATACG
1 TTATACG
35048792 TCAAAAATAG
Statistics
Matches: 227, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
73 6 0.03
74 221 0.97
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (74 bp):
TTATACGCCACATGACTTATACTTTATTTTATTATTTTATTAAATTTTTAATACAACAACCTAGT
TTTACAGAG
Found at i:35051697 original size:51 final size:50
Alignment explanation
Indices: 35051507--35051694 Score: 189
Period size: 51 Copynumber: 3.7 Consensus size: 50
35051497 AGTGAAAGTG
** * * *
35051507 ATGGTCATGTGTGTAGTACTATGTGCAGGCTATTACATGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATATGTACCGG-ATGGT
* * *
35051558 A-GGTCGCATGTGTAGTACTATGTGCAGGCTACTATACGTACCGGATTGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATATGTACCGGATGGT
* ** * * * *
35051607 TTCGAACACGTGTGGAGTACTATGTGCAGGCTACTATGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATATGTACCGGATGGT
**
35051658 AATGGTCACATGTGTAGTACTATGTTTAGGCTACTAT
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTAT
35051695 GTGAACCAAA
Statistics
Matches: 109, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 3 0.03
50 37 0.34
51 68 0.62
52 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATATGTACCGGATGGT
Found at i:35052892 original size:18 final size:19
Alignment explanation
Indices: 35052859--35052894 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35052849 ATAAATGTGG
*
35052859 TGCTTATCCATGCTTATAA
1 TGCTTATACATGCTTATAA
35052878 TGCTTATAC-TGCTTATA
1 TGCTTATACATGCTTATA
35052895 TTTATTTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (19 bp):
TGCTTATACATGCTTATAA
Found at i:35053078 original size:103 final size:103
Alignment explanation
Indices: 35052895--35053094 Score: 330
Period size: 103 Copynumber: 1.9 Consensus size: 103
35052885 ACTGCTTATA
* * * *
35052895 TTTATTTGGCTAGCATGTTTGGTGTGTATGCTTAGGCTTTGGACAAGTTGTGGCTGGGTTACGCC
1 TTTATTTGGCTAGCATATCTGGTGTGTATGCTTAGGCTTTGGACAAGTTGTGGCTGGATTACGCA
*
35052960 ACATTAAATTTATAAAATTATGCACTGAGATGTATATG
66 ACATTAAATTGATAAAATTATGCACTGAGATGTATATG
35052998 TTTATTTGGCTAGCATATCTGGTGTGTATGCTTAGGCTTT-GACCAAGTTGTGGCTGGATTACGC
1 TTTATTTGGCTAGCATATCTGGTGTGTATGCTTAGGCTTTGGA-CAAGTTGTGGCTGGATTACGC
*
35053062 AACATTAAATTGATAAAATTATGCATTGAGATG
65 AACATTAAATTGATAAAATTATGCACTGAGATG
35053095 GTAAATGCCT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 2 0.02
103 88 0.98
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
TTTATTTGGCTAGCATATCTGGTGTGTATGCTTAGGCTTTGGACAAGTTGTGGCTGGATTACGCA
ACATTAAATTGATAAAATTATGCACTGAGATGTATATG
Found at i:35055577 original size:35 final size:35
Alignment explanation
Indices: 35055536--35055604 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
35055526 GTAAATTGGA
35055536 AAATGGTAAAACTCGATATATTCGATATTGAAATT
1 AAATGGTAAAACTCGATATATTCGATATTGAAATT
35055571 AAATGGTAAAACTCGATATATTCGATATTGAAAT
1 AAATGGTAAAACTCGATATATTCGATATTGAAAT
35055605 GGAAAATGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.33
Consensus pattern (35 bp):
AAATGGTAAAACTCGATATATTCGATATTGAAATT
Found at i:35057711 original size:33 final size:33
Alignment explanation
Indices: 35057669--35057731 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
35057659 AGAACACTAG
*
35057669 TTGTCGCCATTTAGCCACCGTTGTTCAACCACA
1 TTGTCGCCATTTAGCCACCGTCGTTCAACCACA
35057702 TTGTCGCCATTTAGCCACCGTCGTTCAACC
1 TTGTCGCCATTTAGCCACCGTCGTTCAACC
35057732 GCTATCTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.19, C:0.35, G:0.16, T:0.30
Consensus pattern (33 bp):
TTGTCGCCATTTAGCCACCGTCGTTCAACCACA
Found at i:35068283 original size:9 final size:9
Alignment explanation
Indices: 35068255--35068284 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
35068245 AAATTACTTG
35068255 ATTAAATTA
1 ATTAAATTA
*
35068264 ACTAAATTA
1 ATTAAATTA
35068273 ATTAAATTA
1 ATTAAATTA
35068282 ATT
1 ATT
35068285 TCTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (9 bp):
ATTAAATTA
Found at i:35074352 original size:38 final size:40
Alignment explanation
Indices: 35074309--35074386 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
35074299 CTTTTTAAGC
35074309 TATTCAATTC-TTT-CTCATTTTAATAGAAACTATTCTCA
1 TATTCAATTCTTTTACTCATTTTAATAGAAACTATTCTCA
* *
35074347 TATTCAGTTCTTTTACTCATTTTAATAGTAACTATTCTCA
1 TATTCAATTCTTTTACTCATTTTAATAGAAACTATTCTCA
35074387 CTGTCATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 9 0.25
39 3 0.08
40 24 0.67
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (40 bp):
TATTCAATTCTTTTACTCATTTTAATAGAAACTATTCTCA
Found at i:35077984 original size:14 final size:14
Alignment explanation
Indices: 35077967--35077994 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35077957 TAAGATTTCC
35077967 GTTAAACAATTTTA
1 GTTAAACAATTTTA
35077981 GTTAAACAATTTTA
1 GTTAAACAATTTTA
35077995 ATAGAAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
GTTAAACAATTTTA
Found at i:35078232 original size:48 final size:48
Alignment explanation
Indices: 35078177--35078322 Score: 238
Period size: 48 Copynumber: 3.0 Consensus size: 48
35078167 CTTTGGGTTA
* * * *
35078177 AAATTGTGCCATTAAATGTTTATCATATCAGGGATTGAAGGAGTTGGT
1 AAATTGTGTCATTAGATATTTATCATATCAAGGATTGAAGGAGTTGGT
35078225 AAATTGTGTCATTAGATATTTATCATATCAAGGATTGAAGGAGTTGGT
1 AAATTGTGTCATTAGATATTTATCATATCAAGGATTGAAGGAGTTGGT
* *
35078273 AAATTGTGTCATTAGATATTTATCATATCAAGTATTGAAAGAGTTGGT
1 AAATTGTGTCATTAGATATTTATCATATCAAGGATTGAAGGAGTTGGT
35078321 AA
1 AA
35078323 TGGTGGTTCG
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 92 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (48 bp):
AAATTGTGTCATTAGATATTTATCATATCAAGGATTGAAGGAGTTGGT
Found at i:35078376 original size:59 final size:60
Alignment explanation
Indices: 35078291--35078403 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 60
35078281 TCATTAGATA
* *
35078291 TTTATCATATCAAGTATTGAAAGAGTTGGTAATGGTGGTTCGAAGGTGGTGTGTTAAATG
1 TTTATCATATCAAGGATTGAAAGAGTTGGTAATGGTGATTCGAAGGTGGTGTGTTAAATG
* * *
35078351 TTTATCATATC-CGGATTGAAGGAGTTGGTAATGGTGATTCGGAGGTGGTGTGT
1 TTTATCATATCAAGGATTGAAAGAGTTGGTAATGGTGATTCGAAGGTGGTGTGT
35078404 GATAGGGTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 37 0.77
60 11 0.23
ACGTcount: A:0.25, C:0.06, G:0.33, T:0.36
Consensus pattern (60 bp):
TTTATCATATCAAGGATTGAAAGAGTTGGTAATGGTGATTCGAAGGTGGTGTGTTAAATG
Found at i:35084531 original size:8 final size:8
Alignment explanation
Indices: 35084518--35084547 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
35084508 TTCCCACAGG
35084518 TAATAAAA
1 TAATAAAA
35084526 TAATAAAA
1 TAATAAAA
35084534 TAATAAAA
1 TAATAAAA
35084542 TAATAA
1 TAATAA
35084548 TTTACTCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
TAATAAAA
Found at i:35090671 original size:194 final size:193
Alignment explanation
Indices: 35090312--35090703 Score: 493
Period size: 194 Copynumber: 2.0 Consensus size: 193
35090302 TCACACGACT
* * *
35090312 GTGTGCCTCACACAGATGAGACACACGCCCATGTTTCAGGCCATGTAACTTTTGAACTAGGGACA
1 GTGTGCCTCACACAGATGAGACACACGCCCATGTCTCAAGCCATGTAACTTTCGAACTAGGGACA
* *
35090377 CACGACCGTGTCCTAGCCTGTGTCCTCACCCGTGTAACTCGCTGAGTAGGGTCACATGGTCGTGT
66 CACGACCGTGTCCTAGCCTGTGTCCTCACCCGTGTAACTCACTGAGTAGGGTCACATGGTCATGT
* * * *
35090442 AACACACTTGTGTGCTAGGCTGTGTAACACTTTGAGTCGCCCCACATGCCCGTGTTGCCAGGCC
131 AACACACTCGTGTGCTAGGCCGTGTAACACTTTGAGTCACCCCACATGCACGTG-TGCCAGGCC
* * * *
35090506 GTGTGCCTCACACGGCTGAGACACACGCCTATGTCTCAAGCCGTGTAACTTTCGAACTAGGGACA
1 GTGTGCCTCACACAGATGAGACACACGCCCATGTCTCAAGCCATGTAACTTTCGAACTAGGGACA
** * *
35090571 CACGGTCGTGT-TTCAGCCTGTGTCCTCACCTGTGTAACTCACTGAGTA-GGTCCACATGGTCAT
66 CACGACCGTGTCCT-AGCCTGTGTCCTCACCCGTGTAACTCACTGAGTAGGGT-CACATGGTCAT
* ** * ** * *
35090634 GTCACATGCTCGTTTG-TCAGGCCGTGTAATGCTTTGAGTTACCCCACATGCATGTGTGCCAGGC
129 GTAACACACTCGTGTGCT-AGGCCGTGTAACACTTTGAGTCACCCCACATGCACGTGTGCCAGGC
35090698 C
193 C
*
35090699 ATGTG
1 GTGTG
35090704 TTCGGTCGTG
Statistics
Matches: 169, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
193 18 0.11
194 151 0.89
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (193 bp):
GTGTGCCTCACACAGATGAGACACACGCCCATGTCTCAAGCCATGTAACTTTCGAACTAGGGACA
CACGACCGTGTCCTAGCCTGTGTCCTCACCCGTGTAACTCACTGAGTAGGGTCACATGGTCATGT
AACACACTCGTGTGCTAGGCCGTGTAACACTTTGAGTCACCCCACATGCACGTGTGCCAGGCC
Found at i:35092712 original size:8 final size:8
Alignment explanation
Indices: 35092701--35092725 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35092691 ATTTCTATAG
35092701 ATAATAAA
1 ATAATAAA
35092709 ATAATAAA
1 ATAATAAA
35092717 ATAATAAA
1 ATAATAAA
35092725 A
1 A
35092726 ATTTACTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAATAAA
Found at i:35093893 original size:13 final size:14
Alignment explanation
Indices: 35093875--35093912 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
35093865 AATGAAAACA
35093875 ATTATATGAAA-AG
1 ATTATATGAAATAG
35093888 ATTATATGAGAATAG
1 ATTATATGA-AATAG
35093903 A-TATATGAAA
1 ATTATATGAAA
35093913 GGGACTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 9 0.39
15 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (14 bp):
ATTATATGAAATAG
Found at i:35094623 original size:10 final size:10
Alignment explanation
Indices: 35094608--35094641 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
35094598 TTGTATGTTA
35094608 TTTGGTGTGT
1 TTTGGTGTGT
*
35094618 TTTGGTATGT
1 TTTGGTGTGT
35094628 TTTGGTGTGT
1 TTTGGTGTGT
35094638 TTTG
1 TTTG
35094642 AATATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.35, T:0.62
Consensus pattern (10 bp):
TTTGGTGTGT
Found at i:35096792 original size:43 final size:42
Alignment explanation
Indices: 35096735--35097104 Score: 309
Period size: 43 Copynumber: 8.7 Consensus size: 42
35096725 TAAATTCAGT
*
35096735 GATACGGGGAATCAGCACATAGCAACCTCTTTCACAATCAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
* * * **
35096777 GATACGGTGGAATCAGCACTTAGCAACCACCTTT-ATATTCAGT
1 GATACGG-GGAATCAGCACATAGCAACC-CCTTTCACAATCAAA
* *
35096820 GATACGGGGAATCAACACATTGCAACCCCTTTCACAATCAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
* * * * * **
35096862 TATATGGTGGAATCAGCACTTAGCAACCACCTTT-ATATTCAGT
1 GATACGG-GGAATCAGCACATAGCAACC-CCTTTCACAATCAAA
* *
35096905 GATACGGGGAATCAACACATTGCAACCCCTTTCACAATCAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
* * * * * **
35096947 TATATGGTGGAATCAGCACTTAGCAACCACCTTT-ATATTCAGT
1 GATACGG-GGAATCAGCACATAGCAACC-CCTTTCACAATCAAA
* *
35096990 GATACGGGGAATCAACACATTGCAACCCCTTTCACAATCAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
* * * *
35097032 TATATGGTGGAATCAGCACTTAGCAACCACCTTT-AGAATCAATA
1 GATACGG-GGAATCAGCACATAGCAACC-CCTTTCACAATCAA-A
* * * * *
35097076 -ATTCGAGGATTCAGTACTTAGCAACCCCT
1 GATACGGGGAATCAGCACATAGCAACCCCT
35097105 CGGGGAATCT
Statistics
Matches: 256, Mismatches: 60, Indels: 25
0.75 0.18 0.07
Matches are distributed among these distances:
41 18 0.07
42 106 0.41
43 112 0.44
44 20 0.08
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (42 bp):
GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
Found at i:35097104 original size:85 final size:85
Alignment explanation
Indices: 35096699--35097066 Score: 648
Period size: 85 Copynumber: 4.3 Consensus size: 85
35096689 CCGTTACTCA
* * * * * * *
35096699 GTGGATTCAACACTTAGCAACCAGC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCT
1 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATTGCAACCC
* *
35096763 CTTTCACAATCAAAGATACG
66 CTTTCACAATCAAATATATG
35096783 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATTGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATTGCAACCC
35096848 CTTTCACAATCAAATATATG
66 CTTTCACAATCAAATATATG
35096868 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATTGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATTGCAACCC
35096933 CTTTCACAATCAAATATATG
66 CTTTCACAATCAAATATATG
35096953 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATTGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATTGCAACCC
35097018 CTTTCACAATCAAATATATG
66 CTTTCACAATCAAATATATG
35097038 GTGGAATCAGCACTTAGCAACCACCTTTA
1 GTGGAATCAGCACTTAGCAACCACCTTTA
35097067 GAATCAATAA
Statistics
Matches: 274, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
84 22 0.08
85 252 0.92
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (85 bp):
GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAACACATTGCAACCC
CTTTCACAATCAAATATATG
Found at i:35103040 original size:42 final size:42
Alignment explanation
Indices: 35102913--35103136 Score: 167
Period size: 42 Copynumber: 5.3 Consensus size: 42
35102903 CGGTGGATTA
* * *
35102913 AGCATTTAGCAACCACC-TTAAATTCAGTGATACG-GGAAATC
1 AGCACTTAGCAACCACCTTTAAATTCAATGATATGTGG-AATC
* * * *
35102954 AACACATAGCAACC-CCTTTCACAA-TCAAAGATACGGTGGAATC
1 AGCACTTAGCAACCACCTTT-A-AATTCAATGATA-TGTGGAATC
* * *
35102997 AGCACTTAGCAACCACCTTTATATTCAGTGATATGAGGAATC
1 AGCACTTAGCAACCACCTTTAAATTCAATGATATGTGGAATC
* *
35103039 AGCACATAGCAACC-CTTTTCACAA-TCAAAT-ATATTGTGGAATC
1 AGCACTTAGCAACCACCTTT-A-AATTC-AATGATA-TGTGGAATC
* * * *
35103082 AGTACTTAGCAACCACCTTTAGAATT-AATAATTTGGGGAATC
1 AGCACTTAGCAACCACCTTTA-AATTCAATGATATGTGGAATC
35103124 AGCACTTAGCAAC
1 AGCACTTAGCAAC
35103137 TCCTCGAGGA
Statistics
Matches: 144, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
40 2 0.01
41 17 0.12
42 58 0.40
43 55 0.38
44 12 0.08
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (42 bp):
AGCACTTAGCAACCACCTTTAAATTCAATGATATGTGGAATC
Found at i:35103045 original size:85 final size:85
Alignment explanation
Indices: 35102903--35103107 Score: 279
Period size: 85 Copynumber: 2.4 Consensus size: 85
35102893 ATCCTTTACT
* * *
35102903 CGGTGGATTAAGCATTTAGCAACCACC-TTAAATTCAGTGATACGGGAAATCAACACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGAAATCAACACATAGCAAC
35102967 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATCAAAGATA
* * *
35102987 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATATGAGG-AATCAGCACATAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACG-GGAAATCAACACATAGCAA
* *
35103051 CCCTTTTCACAATCAAATATA
65 CCCCTTTCACAATCAAAGATA
** *
35103072 TTGTGGAATCAGTACTTAGCAACCACCTTTAGAATT
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-AATT
35103108 AATAATTTGG
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
84 24 0.23
85 77 0.73
86 5 0.05
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.26
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGAAATCAACACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:35103122 original size:85 final size:85
Alignment explanation
Indices: 35102903--35103136 Score: 267
Period size: 85 Copynumber: 2.8 Consensus size: 85
35102893 ATCCTTTACT
* * * * * * *
35102903 CGGTGGATTAAGCATTTAGCAACCACC-TTAAATTCAGTGATACG-GGAAATCAACACATAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAATAATATGAGG-AATCAGCACATAGCAA
35102966 CCCCTTTCACAATCAAAGATA
65 CCCCTTTCACAATCAAAGATA
* * *
35102987 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATATGAGGAATCAGCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAATAATATGAGGAATCAGCACATAGCAAC
* *
35103052 CCTTTTCACAATCAAATATA
66 CCCTTTCACAATCAAAGATA
** * * * *
35103072 TTGTGGAATCAGTACTTAGCAACCACCTTTAGAATT-AATAATTTGGGGAATCAGCACTTAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-AATTCAATAATATGAGGAATCAGCACATAGCAA
35103136 C
65 C
35103137 TCCTCGAGGA
Statistics
Matches: 130, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
84 24 0.18
85 101 0.78
86 5 0.04
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAATAATATGAGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:35103970 original size:347 final size:348
Alignment explanation
Indices: 35103444--35104489 Score: 2031
Period size: 347 Copynumber: 3.0 Consensus size: 348
35103434 TTCTTTCTTG
*
35103444 AACTATAATAACACATTTAACTTATTTAACATGAAAATTCATCAACTTTGGCAAAATTATAATTT
1 AACTATAATAACACATTTAACTTATTTAACAGGAAAATTCATCAACTTTGGCAAAATTATAATTT
35103509 TGCCCCTAAACTTTTGCATATTTACACTTTTTCCCCAAAGCTCAGAAATTAAACTCCATCTCTTA
66 TGCCCCTAAACTTTTGCATATTTACACTTTTTCCCCAAAGCTCAGAAATTAAACTCCATCTCTTA
35103574 TTATTATGTTTTATGACATACTAAACATTTTTCTCTTCTATGGTAACATCAAATTCCCATTCTAA
131 TTATTATGTTTTATGACATACTAAACATTTTTCTCTTCTATGGTAACATCAAATTCCCATTCTAA
35103639 CACTTACTTATGAACATTAGGTATTTTTACCGATTATGTCGTTTTACTCGTTTTCACTTAAAATC
196 CACTTACTTATGAACATTAGGTATTTTTACCGATTATGTCGTTTTACTCGTTTTCACTTAAAATC
35103704 GCTTAGCAATAGTTGTTTAACATAATTTCAGCTATGGGTATTTTTCCAAATATAAACCCTAGGTT
261 GCTTAGCAATAGTTGTTTAACATAATTTCAGCTATGGGTATTTTTCCAAATATAAACCCTAGGTT
35103769 AAATTATTGCTAGAAATAGATAA
326 AAATTATTGCTAGAAATAGATAA
35103792 AACTATAATAACACATTTAACTTATTTAACAGGAAAATTCATCAACTTTGGCAAAATTATAATTT
1 AACTATAATAACACATTTAACTTATTTAACAGGAAAATTCATCAACTTTGGCAAAATTATAATTT
*
35103857 TGCCCCTAAACTTTTGCATATTTACAC-TTTTCCCCAAAGCTCAGAAATTAAACTTCATCTCTTA
66 TGCCCCTAAACTTTTGCATATTTACACTTTTTCCCCAAAGCTCAGAAATTAAACTCCATCTCTTA
35103921 TTATTATGTTTTATGACATACTAAACATTTTTCTCTTCTATGGTAACATCAAATTCCCATTCTAA
131 TTATTATGTTTTATGACATACTAAACATTTTTCTCTTCTATGGTAACATCAAATTCCCATTCTAA
35103986 CACTTACTTATGAACATTAGGTATTTTTACCGATTATGTCGTTTTACTCGTTTTCACTTAAAATC
196 CACTTACTTATGAACATTAGGTATTTTTACCGATTATGTCGTTTTACTCGTTTTCACTTAAAATC
35104051 GCTTAGCAATAGTTGTTTAACATAATTTCAGCTATGGGTATTTTTCCAAATATAAACCCTAGGTT
261 GCTTAGCAATAGTTGTTTAACATAATTTCAGCTATGGGTATTTTTCCAAATATAAACCCTAGGTT
35104116 AAATTATTGCTAGAAATAGATAA
326 AAATTATTGCTAGAAATAGATAA
35104139 AACTATAATAACACATTTAACTTATTTAACAGGAAAATTCATCAACTTTGGCAAAATTATAATTT
1 AACTATAATAACACATTTAACTTATTTAACAGGAAAATTCATCAACTTTGGCAAAATTATAATTT
35104204 TGCCCCTAAACTTTTGCATATTTACACTTTTTCCCCAAAGCTCAGAAATTAAACTCCATCTCTTA
66 TGCCCCTAAACTTTTGCATATTTACACTTTTTCCCCAAAGCTCAGAAATTAAACTCCATCTCTTA
35104269 TTATTATGTTTTATGACATACTAAACATTTTTCTCTTCTATGGTAACATCAAATTCCCATTCTAA
131 TTATTATGTTTTATGACATACTAAACATTTTTCTCTTCTATGGTAACATCAAATTCCCATTCTAA
*
35104334 CACTTACTTATGAACATTAGGTATTTTTACCGATTATGTCGTTTTACTCATTTTCACTTAAAATC
196 CACTTACTTATGAACATTAGGTATTTTTACCGATTATGTCGTTTTACTCGTTTTCACTTAAAATC
* *
35104399 GCTTAGCAAAAGTTGTTTAACATAATTTCAGCTATGGGTATTTTTCAAAATATAAACCCTAGGTT
261 GCTTAGCAATAGTTGTTTAACATAATTTCAGCTATGGGTATTTTTCCAAATATAAACCCTAGGTT
*
35104464 AAATTATTTCTAGAAATAGATAA
326 AAATTATTGCTAGAAATAGATAA
35104487 AAC
1 AAC
35104490 AAGTTACCGA
Statistics
Matches: 690, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
347 346 0.50
348 344 0.50
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (348 bp):
AACTATAATAACACATTTAACTTATTTAACAGGAAAATTCATCAACTTTGGCAAAATTATAATTT
TGCCCCTAAACTTTTGCATATTTACACTTTTTCCCCAAAGCTCAGAAATTAAACTCCATCTCTTA
TTATTATGTTTTATGACATACTAAACATTTTTCTCTTCTATGGTAACATCAAATTCCCATTCTAA
CACTTACTTATGAACATTAGGTATTTTTACCGATTATGTCGTTTTACTCGTTTTCACTTAAAATC
GCTTAGCAATAGTTGTTTAACATAATTTCAGCTATGGGTATTTTTCCAAATATAAACCCTAGGTT
AAATTATTGCTAGAAATAGATAA
Found at i:35106349 original size:26 final size:26
Alignment explanation
Indices: 35106318--35106382 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
35106308 ATTTCAACCT
35106318 ACAACTCGTGTGAGTAGGCCCATTTC
1 ACAACTCGTGTGAGTAGGCCCATTTC
35106344 ACAACTCGTGTGAGTAGGCCCATTTC
1 ACAACTCGTGTGAGTAGGCCCATTTC
* *
35106370 ATAGCTCGTGTGA
1 ACAACTCGTGTGA
35106383 TCAATGATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (26 bp):
ACAACTCGTGTGAGTAGGCCCATTTC
Found at i:35107928 original size:39 final size:40
Alignment explanation
Indices: 35107777--35107946 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
35107767 AGACTAAGAT
* * *
35107777 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
35107817 CCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* ** *
35107857 CCGAAGGCATTCGTCCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * * *
35107897 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
35107936 CCGAAGGCATT
1 CCGAAGGCATT
35107947 TGAACGAGGA
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
39 31 0.28
40 79 0.72
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:35107946 original size:79 final size:80
Alignment explanation
Indices: 35107800--35107946 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 80
35107790 TGCGAGATAC
* * * *
35107800 TAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
35107865 ATTCGTCCGAGTTGT
66 ATTCGTCCGAGTTGT
* * * *
35107880 TAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
35107944 ATT
66 ATT
35107947 TGAACGAGGA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 35 0.59
80 24 0.41
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGTCCGAGTTGT
Found at i:35107966 original size:79 final size:80
Alignment explanation
Indices: 35107799--35107981 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
35107789 GTGCGAGATA
* * * *
35107799 CTAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
35107864 CATTCGTCCGAGTTG
66 CATTCGAACGAGGAG
* * * * *
35107879 TTAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
35107943 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
35107958 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
35107982 TACGTGAATT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.16
79 47 0.55
80 24 0.28
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:35115842 original size:39 final size:40
Alignment explanation
Indices: 35115691--35115860 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
35115681 AGACTAAGAT
* * *
35115691 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
35115731 CCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* ** *
35115771 CCGAAGGCATTCGTCCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * * *
35115811 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
35115850 CCGAAGGCATT
1 CCGAAGGCATT
35115861 TGAACGAGGA
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
39 31 0.28
40 79 0.72
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:35115860 original size:79 final size:80
Alignment explanation
Indices: 35115714--35115860 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 80
35115704 TGCGAGATAC
* * * *
35115714 TAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
35115779 ATTCGTCCGAGTTGT
66 ATTCGTCCGAGTTGT
* * * *
35115794 TAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
35115858 ATT
66 ATT
35115861 TGAACGAGGA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 35 0.59
80 24 0.41
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGTCCGAGTTGT
Found at i:35115880 original size:79 final size:80
Alignment explanation
Indices: 35115713--35115895 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
35115703 GTGCGAGATA
* * * *
35115713 CTAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
35115778 CATTCGTCCGAGTTG
66 CATTCGAACGAGGAG
* * * * *
35115793 TTAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
35115857 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
35115872 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
35115896 TACGTGAATT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.16
79 47 0.55
80 24 0.28
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:35117680 original size:30 final size:30
Alignment explanation
Indices: 35117644--35117700 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
35117634 TATGTTGTCA
35117644 AATGCTTATTAACCAAAGTCGTTTTGGTCG
1 AATGCTTATTAACCAAAGTCGTTTTGGTCG
* *
35117674 AATGCTTGTTTACCAAAGTCGTTTTGG
1 AATGCTTATTAACCAAAGTCGTTTTGG
35117701 GATGAAGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (30 bp):
AATGCTTATTAACCAAAGTCGTTTTGGTCG
Found at i:35128525 original size:15 final size:15
Alignment explanation
Indices: 35128505--35128533 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35128495 ATGCGTCGCA
35128505 CACCATGTTATCAAT
1 CACCATGTTATCAAT
35128520 CACCATGTTATCAA
1 CACCATGTTATCAA
35128534 GCAACAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (15 bp):
CACCATGTTATCAAT
Found at i:35140600 original size:16 final size:16
Alignment explanation
Indices: 35140579--35140609 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35140569 TTCAGGAGTT
*
35140579 TTTTGTTTTCTTTATG
1 TTTTGTATTCTTTATG
35140595 TTTTGTATTCTTTAT
1 TTTTGTATTCTTTAT
35140610 TCTTCTGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TTTTGTATTCTTTATG
Found at i:35143959 original size:47 final size:46
Alignment explanation
Indices: 35143890--35144062 Score: 147
Period size: 47 Copynumber: 3.7 Consensus size: 46
35143880 TTACTTGTGT
* * * *
35143890 GCCAGTGTAA-AACATGTTTGGGACATGCACCAACCACAATATGATA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATC-ACCACAAAATGATA
** *
35143936 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGAATGAGT-
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCACCACA-A-AATGA-TA
* **
35143985 GCCAGTGTAAGA-CATGTCTGGGACATGCATCGACCTCGACGATGATA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATC-ACCAC-AAAATGATA
* *
35144032 GCCAGTGTAAGACC-TGTCTAGGACACGCATC
1 GCCAGTGTAAGACCATGTCTGGGACATGCATC
35144063 GGCTAAGAGT
Statistics
Matches: 103, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
46 11 0.11
47 53 0.51
48 21 0.20
49 17 0.17
50 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.21
Consensus pattern (46 bp):
GCCAGTGTAAGACCATGTCTGGGACATGCATCACCACAAAATGATA
Found at i:35144056 original size:95 final size:91
Alignment explanation
Indices: 35143888--35144107 Score: 271
Period size: 95 Copynumber: 2.4 Consensus size: 91
35143878 GATTACTTGT
* * * *
35143888 GTGCCAGTGTAAAACATGTTTGGGACATGCACCAACCACAATATGATAGCCAGTGTAAGACCATG
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCAACCACAAGATGATAGCCAGTGTAAGACCATG
* *
35143953 TCTGGGACATGGCATCGGCATAGAGAATGA
66 TCTAGGACA-CGCATCGGC-TA-AGAAT-A
* * *
35143983 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGACGATGATAGCCAGTGTAAGACC-T
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCAACCAC-AAGATGATAGCCAGTGTAAGACCAT
* *
35144047 GTCTAGGACACGCATCGGCTAAGAGTT
65 GTCTAGGACACGCATCGGCTAAGAATA
* *
35144074 GTGCTAGTGTAAGACATATCTGGGACATGCATCA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCA
35144108 GCGTGTATAG
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
91 31 0.28
92 4 0.04
93 2 0.02
94 8 0.07
95 44 0.40
96 21 0.19
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (91 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCAACCACAAGATGATAGCCAGTGTAAGACCATG
TCTAGGACACGCATCGGCTAAGAATA
Found at i:35144100 original size:44 final size:44
Alignment explanation
Indices: 35143936--35144106 Score: 164
Period size: 47 Copynumber: 3.7 Consensus size: 44
35143926 CAATATGATA
* *
35143936 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGAATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TA-AGAGT-TGT
* * *
35143985 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCT-CGACGATGAT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCG-GCTAAGA-GTTG-T
* * *
35144031 AGCCAGTGTAAGACCTGTCTAGGACACGCATCGGCTAAGAGTTGT
1 -GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGTTGT
* *
35144076 GCTAGTGTAAGACATATCTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
35144107 AGCGTGTATA
Statistics
Matches: 101, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
44 26 0.26
45 4 0.04
46 6 0.06
47 38 0.38
48 15 0.15
49 12 0.12
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (44 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGTTGT
Found at i:35144180 original size:49 final size:47
Alignment explanation
Indices: 35143890--35144206 Score: 208
Period size: 49 Copynumber: 6.7 Consensus size: 47
35143880 TTACTTGTGT
* * * * *
35143890 GCCAGTGTAA-AACATGTTTGGGACATGCACCAACCACAAT-ATGATA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATC-GCCTCAATGATGATA
*
35143936 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-AGA-GAATGAGT-
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATC-GCCTCA-ATG-ATGA-TA
* *
35143985 GCCAGTGTAAGA-CATGTCTGGGACATGCATCGACCTCGACGATGATA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCG-CCTCAATGATGATA
* * *
35144032 GCCAGTGTAAGACC-TGTCTAGGACACGCATCGGCT-AA-GAGTTG-T-
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCGCCTCAATGA--TGATA
* * * ** ** *
35144076 GCTAGTGTAAGA-CATATCTGGGACATGCATCAGCGTGTATAGACAAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATC-GCCTCAAT-GATGATA
* * *
35144124 GCTAGTATAAGACCATGTCTGGGACATGTTATCAGCCTCAATGATGATA
1 GCCAGTGTAAGACCATGTCTGGGACATG-CATC-GCCTCAATGATGATA
* *
35144173 GCCAGTATAAGACCATGTCCGGGACATGACATCG
1 GCCAGTGTAAGACCATGTCTGGGACATG-CATCG
35144207 GCAACATATC
Statistics
Matches: 213, Mismatches: 36, Indels: 42
0.73 0.12 0.14
Matches are distributed among these distances:
43 1 0.00
44 27 0.13
45 4 0.02
46 17 0.08
47 55 0.26
48 36 0.17
49 63 0.30
50 10 0.05
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.22
Consensus pattern (47 bp):
GCCAGTGTAAGACCATGTCTGGGACATGCATCGCCTCAATGATGATA
Found at i:35147648 original size:16 final size:18
Alignment explanation
Indices: 35147610--35147650 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
35147600 ATAGAAGAAC
35147610 AGAAGAAGAAACAATAAAA
1 AGAA-AAGAAACAATAAAA
*
35147629 AGAAAAGAAA-AA-AAAT
1 AGAAAAGAAACAATAAAA
35147645 AGAAAA
1 AGAAAA
35147651 AGGTGACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
18 6 0.29
19 4 0.19
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (18 bp):
AGAAAAGAAACAATAAAA
Found at i:35152809 original size:22 final size:22
Alignment explanation
Indices: 35152784--35152828 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
35152774 AAATTAGTTT
*
35152784 TGACTAAA-GTATAACATTCATA
1 TGACTAAATGAATAAC-TTCATA
35152806 TGACTAAATGAATAACTTCATA
1 TGACTAAATGAATAACTTCATA
35152828 T
1 T
35152829 ATGCACATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (22 bp):
TGACTAAATGAATAACTTCATA
Found at i:35153125 original size:40 final size:40
Alignment explanation
Indices: 35153067--35153234 Score: 239
Period size: 40 Copynumber: 4.2 Consensus size: 40
35153057 TCTTCAGGAT
35153067 TTAG-CCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
*
35153106 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * * *
35153146 TTAGCCCGGATATAACCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * * *
35153186 ATAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
*
35153226 TTAGTCCGG
1 TTAGCCCGG
35153235 TTATCATCCG
Statistics
Matches: 112, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Found at i:35155358 original size:19 final size:18
Alignment explanation
Indices: 35155307--35155360 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
35155297 TATTTTAGCC
*
35155307 ATTTTTATTTTATTTTAT
1 ATTTTTATTTTAATTTAT
*
35155325 ATTTTTGTTTTTAATTTA-
1 ATTTTT-ATTTTAATTTAT
35155343 ATTTTTACTTTCTAATTT
1 ATTTTTA-TTT-TAATTT
35155361 TTCTTTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTATTTTAATTTAT
Found at i:35156180 original size:31 final size:31
Alignment explanation
Indices: 35156116--35156190 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
35156106 CGTGTGGGCT
* * ** *
35156116 ACACGGGCATGTGGGCCCACATGGGTAGTCC
1 ACACGGGCGTGTGGGCCCAAATGGACAGGCC
*
35156147 ACACGGGCGTGTGGGCCTAAATGGACAGGCC
1 ACACGGGCGTGTGGGCCCAAATGGACAGGCC
* *
35156178 ACATGGGTGTGTG
1 ACACGGGCGTGTG
35156191 AGCCGATTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.20, C:0.24, G:0.39, T:0.17
Consensus pattern (31 bp):
ACACGGGCGTGTGGGCCCAAATGGACAGGCC
Found at i:35160271 original size:17 final size:17
Alignment explanation
Indices: 35160244--35160288 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
35160234 GTCTTCCTCG
35160244 ATTTCTTTATTCTTTATT
1 ATTT-TTTATTCTTTATT
*
35160262 -TTATTTTATTTTTTATT
1 ATT-TTTTATTCTTTATT
35160279 ATTTTTTATT
1 ATTTTTTATT
35160289 ATTATTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTTTTATTCTTTATT
Found at i:35160296 original size:27 final size:26
Alignment explanation
Indices: 35160250--35160374 Score: 75
Period size: 27 Copynumber: 4.8 Consensus size: 26
35160240 CTCGATTTCT
* *
35160250 TTATTCTTTATTTTATTTTATTTTTTA
1 TTATTTTTTATTTTATTTTA-GTTTTA
35160277 TTATTTTTTATTATTA-TTTAGTTTTA
1 TTATTTTTTATT-TTATTTTAGTTTTA
** *
35160303 TT-TTTTTTCCTTT-TTTT-GTGTTA
1 TTATTTTTTATTTTATTTTAGTTTTA
* *
35160326 TTATTATGTTTA-TTAATTTTTA-TACTTA
1 TTATT-T-TTTATTTTA-TTTTAGT-TTTA
35160354 TT-TTTTTTATTCTTATTTTAG
1 TTATTTTTTATT-TTATTTTAG
35160375 CTATCGTATG
Statistics
Matches: 77, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
23 7 0.09
24 7 0.09
25 14 0.18
26 17 0.22
27 24 0.31
28 8 0.10
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (26 bp):
TTATTTTTTATTTTATTTTAGTTTTA
Found at i:35160302 original size:6 final size:5
Alignment explanation
Indices: 35160256--35160373 Score: 50
Period size: 5 Copynumber: 22.8 Consensus size: 5
35160246 TTCTTTATTC
35160256 TTTAT TTTAT TTTAT TTT-T TATTAT TTT-T TATTATT ATTTAGT TTTAT
1 TTTAT TTTAT TTTAT TTTAT T-TTAT TTTAT T-TTA-T -TTTA-T TTTAT
** * * *
35160304 TTT-T TTTCC TTT-T TTTGT GTTAT TATTAT GTTTA- TTAATT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT -TTTAT TTTA-T TTTAT
*
35160349 ACTTAT TTT-T TTTAT TCTTAT TTTA
1 -TTTAT TTTAT TTTAT T-TTAT TTTA
35160374 GCTATCGTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
4 18 0.20
5 38 0.43
6 25 0.28
7 6 0.07
8 1 0.01
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:35161341 original size:12 final size:11
Alignment explanation
Indices: 35161306--35161383 Score: 52
Period size: 11 Copynumber: 7.0 Consensus size: 11
35161296 GTAGATTTTA
35161306 TTTGTTTTCTT
1 TTTGTTTTCTT
*
35161317 TTTAGCTTTCTT
1 TTT-GTTTTCTT
35161329 TTTGTTTTCCTT
1 TTTGTTTT-CTT
*
35161341 TTATG-TTTATT
1 TT-TGTTTTCTT
* *
35161352 TTTATTTT-TA
1 TTTGTTTTCTT
* *
35161362 GTTGTTTTATT
1 TTTGTTTTCTT
*
35161373 TTTATTTTCTT
1 TTTGTTTTCTT
35161384 AGACTTATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
10 8 0.16
11 23 0.45
12 18 0.35
13 2 0.04
ACGTcount: A:0.09, C:0.08, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTGTTTTCTT
Found at i:35161353 original size:23 final size:23
Alignment explanation
Indices: 35161306--35161359 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
35161296 GTAGATTTTA
* *
35161306 TTTGTTTTCTTTTTAGCTTTCTT
1 TTTGTTTTCCTTTTAGCTTTATT
35161329 TTTGTTTTCCTTTTATG-TTTATT
1 TTTGTTTTCCTTTTA-GCTTTATT
*
35161352 TTTATTTT
1 TTTGTTTT
35161360 TAGTTGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.76
Consensus pattern (23 bp):
TTTGTTTTCCTTTTAGCTTTATT
Found at i:35163229 original size:30 final size:30
Alignment explanation
Indices: 35163193--35163251 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
35163183 GGAGCCACAC
* *
35163193 GGGCTAGGCACATGCCTATGTGACCCAAAT
1 GGGCTAGACACATGCCCATGTGACCCAAAT
35163223 GGGCTAGACACATGCCCATGTGACCCAAA
1 GGGCTAGACACATGCCCATGTGACCCAAA
35163252 CGAGATAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (30 bp):
GGGCTAGACACATGCCCATGTGACCCAAAT
Found at i:35163261 original size:30 final size:30
Alignment explanation
Indices: 35163201--35163264 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
35163191 ACGGGCTAGG
* * * *
35163201 CACATGCCTATGTGACCCAAATGGGCTAGA
1 CACATGCCCATGTGACCCAAACGAGATAGA
35163231 CACATGCCCATGTGACCCAAACGAGATAGA
1 CACATGCCCATGTGACCCAAACGAGATAGA
35163261 CACA
1 CACA
35163265 CTGCTTCCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.30, G:0.20, T:0.16
Consensus pattern (30 bp):
CACATGCCCATGTGACCCAAACGAGATAGA
Found at i:35167962 original size:29 final size:30
Alignment explanation
Indices: 35167898--35167959 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
35167888 GGGTTGGGTC
35167898 AAATTTTTATAAAATGCTCAAATGAAAGTT
1 AAATTTTTATAAAATGCTCAAATGAAAGTT
* *
35167928 AAATTTTTTTAAAATGTTCAAAT-AAGAGTT
1 AAATTTTTATAAAATGCTCAAATGAA-AGTT
35167958 AA
1 AA
35167960 TTTAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.39
Consensus pattern (30 bp):
AAATTTTTATAAAATGCTCAAATGAAAGTT
Found at i:35168611 original size:6 final size:6
Alignment explanation
Indices: 35168591--35168633 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
35168581 TTTACGTCAA
*
35168591 AATTTT AATTAAT AATTAT AATTAT AATTAT AATTAT AATTAT
1 AATTAT AATT-AT AATTAT AATTAT AATTAT AATTAT AATTAT
35168634 TACGATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 30 0.86
7 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTAT
Found at i:35175353 original size:49 final size:48
Alignment explanation
Indices: 35175292--35175422 Score: 167
Period size: 49 Copynumber: 2.7 Consensus size: 48
35175282 ACATCAAAGT
35175292 CGATGTCATGTCCCAGACAGGTCTTACACT-GACTT-TCATATATCAAGGA
1 CGATG-CATGTCCCAGACAGGTCTTACACTAG-CTTGT-ATATATCAAGGA
* * * *
35175341 CGATGCTGTGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCGAGGT
1 CGATGC-ATGTCCCAGACAGGTCTTACACTAGCTTGTATATATCAAGGA
*
35175390 CGATGCATGTCCCAGACATGTCTTACACTAGCT
1 CGATGCATGTCCCAGACAGGTCTTACACTAGCT
35175423 CTCGTCTCAA
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
48 26 0.36
49 45 0.62
50 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (48 bp):
CGATGCATGTCCCAGACAGGTCTTACACTAGCTTGTATATATCAAGGA
Found at i:35175455 original size:46 final size:45
Alignment explanation
Indices: 35175392--35175513 Score: 151
Period size: 46 Copynumber: 2.7 Consensus size: 45
35175382 CTCGAGGTCG
*
35175392 ATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAAT-T-CCA
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCTC--AT-AATGTGCCA
*
35175438 ATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTGGCCA
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAATGT-GCCA
*
35175484 ATGCATGTCCCA-AGCATGCCTTACACTAGC
1 ATGCATGTCCCAGA-CATGTCTTACACTAGC
35175514 ACACATATCA
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
43 3 0.04
44 2 0.03
45 1 0.01
46 62 0.91
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAATGTGCCA
Found at i:35182715 original size:47 final size:44
Alignment explanation
Indices: 35182611--35182731 Score: 154
Period size: 44 Copynumber: 2.7 Consensus size: 44
35182601 TATACGTGCT
* *
35182611 GATGCATGTCCTAGACATGTCTTACACTAGCACAAAACTTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACAAAACTTAGCC
* * *
35182655 GATGAATGTCCCAGACATGTCTTACACTGGCTA-ACATCTTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-ACAAAACTT--A-GCC
35182702 GATGCATGTCCCAGACATGTCTTACACTGG
1 GATGCATGTCCCAGACATGTCTTACACTGG
35182732 AAGTCGTCTC
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 33 0.49
45 1 0.01
46 1 0.01
47 32 0.48
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACAAAACTTAGCC
Found at i:35182757 original size:47 final size:46
Alignment explanation
Indices: 35182612--35182780 Score: 150
Period size: 47 Copynumber: 3.7 Consensus size: 46
35182602 ATACGTGCTG
* * * * *
35182612 ATGCATGTCCTAGACATGTCTTACACTAGCACAAAACTT---AGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCA-ACATCTTCGAAGCCA
* * *
35182656 ATGAATGTCCCAGACATGTCTTACACTGGCTAACATCTTCGAGGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGC-AACATCTTCGAAGCCA
* *
35182703 ATGCATGTCCCAGACATGTCTTACACTGG-AA-GTCGTCTCTAAGCCA
1 ATGCATGTCCCAGACATGTCTTACACTGGCAACATC-T-TCGAAGCCA
*
35182749 ATGCCATGTCCCAGACATGGTCTTATACTGGC
1 ATG-CATGTCCCAGACAT-GTCTTACACTGGC
35182781 TCTTACATAA
Statistics
Matches: 104, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
44 34 0.33
45 4 0.04
46 9 0.09
47 46 0.44
48 11 0.11
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCAACATCTTCGAAGCCA
Found at i:35189127 original size:55 final size:55
Alignment explanation
Indices: 35189055--35189173 Score: 143
Period size: 55 Copynumber: 2.2 Consensus size: 55
35189045 AGTATGAGAC
* * * * *
35189055 ACTGACTTTAGGGCACGGCCATGACACATGCCCGTGTGGCCTACCCGTGGGCAAT
1 ACTGACTTTAGGACACGGCCATGACACACGCCCGTGTGCCCTAACCGTGGACAAT
* *
35189110 ACTGACTTATA-GACACGGCGATGACACACGTCCGTGTGCCCTAACCGTGGACAAT
1 ACTGACTT-TAGGACACGGCCATGACACACGCCCGTGTGCCCTAACCGTGGACAAT
*
35189165 ATTGA-TTTA
1 ACTGACTTTA
35189174 AAAGTTTAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.04
54 2 0.04
55 49 0.89
56 2 0.04
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (55 bp):
ACTGACTTTAGGACACGGCCATGACACACGCCCGTGTGCCCTAACCGTGGACAAT
Found at i:35193322 original size:40 final size:40
Alignment explanation
Indices: 35193267--35193484 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
35193257 CGGATGATAA
* * * *
35193267 CCGGGCTAAGCCCCGACGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
35193307 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
35193347 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35193387 CCGAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35193427 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
35193467 CC-GGATAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
35193485 TACTTAGTTG
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 16 0.10
40 145 0.90
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:35201702 original size:5 final size:6
Alignment explanation
Indices: 35201692--35201761 Score: 53
Period size: 5 Copynumber: 12.0 Consensus size: 6
35201682 GATAGTATTT
*
35201692 TATTAA T-TTAA TATTAAAA TGATT-A TCTTAA TATTAA -ATTAA T-TTAA
1 TATTAA TATTAA TATT--AA T-ATTAA TATTAA TATTAA TATTAA TATTAA
35201739 TATTAA -ATTAA -ATTTAA TATTAA
1 TATTAA TATTAA TA-TTAA TATTAA
35201762 AGTAATTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
5 23 0.43
6 23 0.43
7 1 0.02
8 3 0.06
9 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (6 bp):
TATTAA
Found at i:35201708 original size:11 final size:11
Alignment explanation
Indices: 35201692--35201761 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
35201682 GATAGTATTT
35201692 TATTAATTTAA
1 TATTAATTTAA
35201703 TATTAA---AA
1 TATTAATTTAA
35201711 TGATT-ATCTTAA
1 T-ATTAAT-TTAA
*
35201723 TATTAAATTAA
1 TATTAATTTAA
35201734 T-TTAATATTAA
1 TATTAAT-TTAA
35201745 -ATTAAATTTAA
1 TATT-AATTTAA
35201756 TATTAA
1 TATTAA
35201762 AGTAATTATG
Statistics
Matches: 47, Mismatches: 2, Indels: 20
0.68 0.03 0.29
Matches are distributed among these distances:
8 4 0.09
9 3 0.06
10 4 0.09
11 26 0.55
12 10 0.21
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (11 bp):
TATTAATTTAA
Found at i:35201738 original size:16 final size:16
Alignment explanation
Indices: 35201693--35201768 Score: 89
Period size: 17 Copynumber: 4.4 Consensus size: 16
35201683 ATAGTATTTT
35201693 ATTAATTTAATATTAAA
1 ATTAATTTAATATT-AA
*
35201710 ATGATTATCTTAATATTAA
1 AT--TAAT-TTAATATTAA
35201729 ATTAATTTAATATTAA
1 ATTAATTTAATATTAA
35201745 ATTAAATTTAATATTAA
1 ATT-AATTTAATATTAA
*
35201762 AGTAATT
1 ATTAATT
35201769 ATGTTTAATC
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
16 17 0.33
17 20 0.38
19 7 0.13
20 8 0.15
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTAATTTAATATTAA
Found at i:35206278 original size:3 final size:3
Alignment explanation
Indices: 35206270--35206304 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
35206260 GCATTACTCT
35206270 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35206305 TAAAGCTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:35211876 original size:18 final size:18
Alignment explanation
Indices: 35211833--35211867 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35211823 AAATATAATT
*
35211833 ATTAGTTTTATTATTATG
1 ATTATTTTTATTATTATG
*
35211851 ATTATTTTTATTTTTAT
1 ATTATTTTTATTATTAT
35211868 TTTTATTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
ATTATTTTTATTATTATG
Found at i:35211888 original size:6 final size:6
Alignment explanation
Indices: 35211838--35211876 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
35211828 TAATTATTAG
* **
35211838 TTTTAT TATTAT GATTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
35211877 CGTTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:35216925 original size:20 final size:20
Alignment explanation
Indices: 35216900--35216940 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35216890 TTATACAAAA
35216900 TATCTTACGGACACCGTCAT
1 TATCTTACGGACACCGTCAT
35216920 TATCTTACGGACACCGTCAT
1 TATCTTACGGACACCGTCAT
35216940 T
1 T
35216941 CTTAATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (20 bp):
TATCTTACGGACACCGTCAT
Found at i:35219910 original size:25 final size:25
Alignment explanation
Indices: 35219863--35219911 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
35219853 GGACAGTGAG
*
35219863 TTAGAGACTCAAATAGACCAGGAAA
1 TTAGAGACTCAAATAGAACAGGAAA
*
35219888 TTAGAGACTCAAATAGAATAGGAA
1 TTAGAGACTCAAATAGAACAGGAA
35219912 CTCTATCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18
Consensus pattern (25 bp):
TTAGAGACTCAAATAGAACAGGAAA
Found at i:35234995 original size:46 final size:46
Alignment explanation
Indices: 35234942--35235115 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
35234932 TGGTTGAGCA
35234942 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATG
* * * *
35234988 TCCGAACTCTTTGAGTTGAGTCCGAGTT--C-GAGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAA-T--G
** * *
35235033 CATCCGGGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATG
*
35235081 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTAT
35235116 GGGCGGGTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 7 0.07
44 1 0.01
45 3 0.03
46 58 0.55
47 25 0.24
48 1 0.01
49 1 0.01
50 5 0.05
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATG
Found at i:35235098 original size:93 final size:93
Alignment explanation
Indices: 35234939--35235109 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
35234929 GGATGGTTGA
* *
35234939 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATGTCCGAACTCTTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGTCCGAACTCGTTGAGT
35235004 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
** * *
35235032 GCATCCGGGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGTCC-GAACTCGTTGAG
35235096 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
35235110 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:35238151 original size:46 final size:48
Alignment explanation
Indices: 35238079--35238181 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 48
35238069 GACAGGACAG
* * * *
35238079 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
*
35238125 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
35238173 GACAGGAAT
1 GACAGGAAT
35238182 AATTTATGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 27 0.54
47 1 0.02
48 22 0.44
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
Found at i:35241476 original size:13 final size:13
Alignment explanation
Indices: 35241451--35241491 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
35241441 GCTCGCCAGG
*
35241451 GACACGCCCGTGT
1 GACATGCCCGTGT
*
35241464 GACATGCCTGTGT
1 GACATGCCCGTGT
*
35241477 TACATGCCCGTGT
1 GACATGCCCGTGT
35241490 GA
1 GA
35241492 ATCGTACTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.24
Consensus pattern (13 bp):
GACATGCCCGTGT
Found at i:35265064 original size:92 final size:93
Alignment explanation
Indices: 35264898--35265069 Score: 233
Period size: 92 Copynumber: 1.9 Consensus size: 93
35264888 GGGTATAATA
* *
35264898 CCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCACACTAAGTCGACGCCATGTCCCAGA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACACTAAGTCGACGCCATGTCCCAGA
35264963 CATGATCTTACACTGACACATCATGTAG
66 CATGATCTTACACTGACACATCATGTAG
** * * *
35264991 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTC-GTCTCAATGTTGATGCCATGTCCCG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACACT-AA-GTCGACGCCATGTCCCA
*
35265053 GACATGGTCTTACACTG
64 GACATGATCTTACACTG
35265070 GCTCTCGTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
90 2 0.03
91 17 0.25
92 44 0.64
93 6 0.09
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (93 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACACTAAGTCGACGCCATGTCCCAGA
CATGATCTTACACTGACACATCATGTAG
Found at i:35266230 original size:40 final size:38
Alignment explanation
Indices: 35266175--35266298 Score: 167
Period size: 40 Copynumber: 3.1 Consensus size: 38
35266165 GCCTAACCTA
35266175 GAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCGAG-TACTATATCC-GGCTAAGTCCC
35266215 GAAGGCATTTGTGCGAAGTACTATATCCAGGCTAAGTCCC
1 GAAGGCATTTGTGCG-AGTACTATATCC-GGCTAAGTCCC
* * * *
35266255 GAAGGCATTCGAGCGAGTAGCTATATCCGGTTAAATCCC
1 GAAGGCATTTGTGCGAGTA-CTATATCCGGCTAAGTCCC
35266294 GAAGG
1 GAAGG
35266299 TAATTGGCTT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
39 18 0.23
40 57 0.74
41 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (38 bp):
GAAGGCATTTGTGCGAGTACTATATCCGGCTAAGTCCC
Found at i:35271647 original size:46 final size:45
Alignment explanation
Indices: 35271513--35271763 Score: 186
Period size: 46 Copynumber: 5.4 Consensus size: 45
35271503 GCCATGTCTG
* * * *
35271513 AGACATGGTCTTACACTAGCTCTCACACT-AGGTCGATGTAATGTCCC
1 AGACAT-GTCTTACACTAGCTCTCA-TCTGAGGCCAATG-CATGTCCC
* * * *
35271560 AAACATGGTCTTACACTGGCACATCATGT-A-GCCAATGCATGTCCC
1 AGACAT-GTCTTACACTAGCTC-TCATCTGAGGCCAATGCATGTCCC
* * *
35271605 AGACATGTTTTACACTGGCT-TACATCTCGAGGCCGATGCATGTCCC
1 AGACATGTCTTACACTAGCTCT-CATCT-GAGGCCAATGCATGTCCC
* ** * * * *
35271651 AAACATGTCTTACACTAGCTCTGGTCTCAATGCCGATGTCATGTTCC
1 AGACATGTCTTACACTAGCTCTCATCT-GAGGCCAATG-CATGTCCC
* * *
35271698 AGACATGGTCTTACATTAGCTCTCATAATGTGGCCAATGCATGTCCC
1 AGACAT-GTCTTACACTAGCTCTCAT-CTGAGGCCAATGCATGTCCC
35271745 AGACATGTCTTACACTAGC
1 AGACATGTCTTACACTAGC
35271764 ACACAAATGA
Statistics
Matches: 163, Mismatches: 32, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 4 0.02
44 12 0.07
45 13 0.08
46 60 0.37
47 47 0.29
48 25 0.15
49 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (45 bp):
AGACATGTCTTACACTAGCTCTCATCTGAGGCCAATGCATGTCCC
Done.