Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 18
Found at i:2471737 original size:2 final size:2
Alignment explanation
Indices: 2471730--2471808 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
2471720 TTGTCCTTAT
2471730 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2471772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2471809 TAACAAGTTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2476698 original size:32 final size:32
Alignment explanation
Indices: 2476662--2476741 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
2476652 TGATTATCGA
* *
2476662 ATCAATTAATTTTCAGGTCG-GATTAATATTAT
1 ATCAATTAATTTTCAGGTCGAG-TCAATATCAT
*
2476694 ATCAATTAGA-TTTCGGGTCGAGTCAATATCAT
1 ATCAATTA-ATTTTCAGGTCGAGTCAATATCAT
* *
2476726 ACCAATTGATTTTCAG
1 ATCAATTAATTTTCAG
2476742 ACCAAATCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
31 1 0.03
32 36 0.92
33 2 0.05
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.39
Consensus pattern (32 bp):
ATCAATTAATTTTCAGGTCGAGTCAATATCAT
Found at i:2486154 original size:42 final size:42
Alignment explanation
Indices: 2485998--2486347 Score: 343
Period size: 43 Copynumber: 8.2 Consensus size: 42
2485988 TGAGAATAAA
* * * *
2485998 AAACGCCGCAATAGGTCAATATCTATTA-CGGCGTTTTTTGAAC
1 AAACGCCGCAAAAGGTC-AGACCTA-TAGCGGCGTTTTTGGAAC
* * *
2486041 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGAAC
* * ** * * *
2486084 AAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTGTAGAAA
1 AAACGCCGCAAAAGGTCA-GACCTATAGCGGCGTTTTTGGAAC
*
2486127 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGA-AC
* * *
2486170 GAACGCCGCAAAAGAG-AAGACCTATA-CTGGCGTTTTTAGAAC
1 AAACGCCGCAAAAG-GTCAGACCTATAGC-GGCGTTTTTGGAAC
* **
2486212 AAACGTCGCAAAAGGTCAGACCTATAGCAACGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGA-AC
*
2486255 AAACGCCGC--AAGGTCAGACCTATAACGGCGTTTTT-GAACTC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGAA--C
* *
2486296 AAACGCCGCAAAAAGTCAGACCTATAACGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGA-AC
2486339 AAACGCCGC
1 AAACGCCGC
2486348 TAATTACCTT
Statistics
Matches: 261, Mismatches: 32, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 34 0.13
42 55 0.21
43 165 0.63
44 3 0.01
45 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGAAC
Found at i:2486204 original size:85 final size:85
Alignment explanation
Indices: 2485998--2486347 Score: 374
Period size: 85 Copynumber: 4.1 Consensus size: 85
2485988 TGAGAATAAA
* * * * *
2485998 AAACGCCGCAATAG-GTCAATATCTATTACGGCGTTTTTTGAACAAACGCCGCAAAAGGTCGATA
1 AAACGCCGCAAAAGAGT-AAGACCTA-TACGGCGTTTTTAGAACAAACGCCGCAAAAGGTC-AGA
* *
2486062 TCTATAGCGGCGTTTTTGGA-AT
63 CCTATAGCGGCGTTTTTGGATAC
* ** * * *
2486084 AAACGCCGCAAAA-AGTTATGATATATAGCGGCGTTTGTAGAAAAAACGCCGCAAAAGGTCAGAT
1 AAACGCCGCAAAAGAG-TAAGACCTATA-CGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGAC
2486148 CTATAGCGGCGTTTTTGGATAC
64 CTATAGCGGCGTTTTTGGATAC
* *
2486170 GAACGCCGCAAAAGAG-AAGACCTATACTGGCGTTTTTAGAACAAACGTCGCAAAAGGTCAGACC
1 AAACGCCGCAAAAGAGTAAGACCTATAC-GGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACC
** *
2486234 TATAGCAACGTTTTTGGACAC
65 TATAGCGGCGTTTTTGGATAC
* *
2486255 AAACGCCGC--AAG-GTCAGACCTATAACGGCGTTTTT-GAACTCAAACGCCGCAAAAAGTCAGA
1 AAACGCCGCAAAAGAGTAAGACCTAT-ACGGCGTTTTTAGAA--CAAACGCCGCAAAAGGTCAGA
*
2486316 CCTATAACGGCGTTTTTGGATAC
63 CCTATAGCGGCGTTTTTGGATAC
2486339 AAACGCCGC
1 AAACGCCGC
2486348 TAATTACCTT
Statistics
Matches: 226, Mismatches: 28, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
82 4 0.02
83 20 0.09
84 50 0.22
85 89 0.39
86 60 0.27
87 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (85 bp):
AAACGCCGCAAAAGAGTAAGACCTATACGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCT
ATAGCGGCGTTTTTGGATAC
Found at i:2488920 original size:41 final size:41
Alignment explanation
Indices: 2488855--2489210 Score: 363
Period size: 41 Copynumber: 8.6 Consensus size: 41
2488845 TAAACTTGCA
* * * * *
2488855 GCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACG
1 GCGTTTGTATA-A-AAACGCCACTAAAGTACAAGTCTTTAGCG
* * **
2488898 GCGTTTGAATAAAAATGCCACTAAAGTACGCGTCTTTAGCG
1 GCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
* * *
2488939 GAGTTTGCATAAAAACGCCACTAAAGTATAAGTCTTTAGCG
1 GCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
* **
2488980 GCGTTTGTATAAAAACGCCACTAAATTATGAGTCTTTAGCG
1 GCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
* * * * * * * *
2489021 ACGTTTGTAAACACAAATGCCACTATAGTACATGTGTATAACG
1 GCGTTTGTATA-A-AAACGCCACTAAAGTACAAGTCTTTAGCG
* *
2489064 GCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCG
1 GCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
* * * *
2489105 GCGTTTGTATAAAAATGGCACTAAATTACGAGTCTTTAGCG
1 GCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
* * *
2489146 GCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCG
1 GCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
2489187 GCGTTTGT-TGAAAAAACGCCACTA
1 GCGTTTGTAT--AAAAACGCCACTA
2489211 TCGATGAACC
Statistics
Matches: 259, Mismatches: 50, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
40 1 0.00
41 204 0.79
42 16 0.06
43 38 0.15
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
GCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
Found at i:2489194 original size:166 final size:166
Alignment explanation
Indices: 2488850--2489211 Score: 496
Period size: 166 Copynumber: 2.2 Consensus size: 166
2488840 ATTTGTAAAC
* *
2488850 TTGCAGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATG
1 TTGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACG
** * *
2488915 CCACTAAAGTACGCGTCTTTAGCGGAGTTTGCATAAAAACGCCACTAAAGTATAAGTCTTTAGCG
66 CCACTAAAGTACAAGTCTATAGCGGAGTTTGCATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
* *
2488980 GCGTTTGTATAAAAACGCCACTAAATTATGAGTCTT
131 GCGTTTGTATAAAAACGCCACTAAAGTATGACTCTT
* * * * *
2489016 TAGCGACGTTTGTAAACACAAATGCCACTATAGTACATGTGTATAACGGCGTTTGTATAAAAACG
1 TTGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACG
* * * * * * *
2489081 CCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGGCACTAAATTACGAGTCTTTAGCG
66 CCACTAAAGTACAAGTCTATAGCGGAGTTTGCATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
2489146 GCGTTTGTATAAAAACGCCACTAAAGTACT-ACTCTT
131 GCGTTTGTATAAAAACGCCACTAAAGTA-TGACTCTT
*
2489182 TTGCGGCGTTTGTTGAA-A-AAACGCCACTAT
1 TTGCGGCGTTTG-TAAACACAAACGCCACTAT
2489212 CGATGAACCT
Statistics
Matches: 170, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
165 11 0.06
166 155 0.91
167 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (166 bp):
TTGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACG
CCACTAAAGTACAAGTCTATAGCGGAGTTTGCATAAAAACGCCACTAAAGTACAAGTCTTTAGCG
GCGTTTGTATAAAAACGCCACTAAAGTATGACTCTT
Found at i:2489229 original size:82 final size:81
Alignment explanation
Indices: 2488896--2489254 Score: 248
Period size: 82 Copynumber: 4.4 Consensus size: 81
2488886 AAGTGTATAA
* * * * * *
2488896 CGGCGTTTGAATAAAAATGCCACTAAAGTAC-GCGTCTTTAGCGGAGTTTGCATAAAAACGCCAC
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACAAC-TCTATAGCGGCGTTTGTATAAAAACGCCAC
* * *
2488960 TAAAGTA-TAAGTCTTTAG
65 TAATG-ACGAA-CCTTTAG
* ** * * * * *
2488978 CGGCGTTTGTATAAAAACGCCACTAAATTATGAGTCTTTAGCGACGTTTGTAAACACAAATGCCA
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATA-A-AAACGCCA
** *
2489043 CT-AT-A-GTACATGTGTATAA
64 CTAATGACG-A-ACCT-T-TAG
* * *
2489062 CGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGGCACT
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCACT
* **
2489127 AAATTACGAGTCTTTAG
66 -AATGACGAACCTTTAG
* * *
2489144 CGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAACGCCA
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTAT--AAAAACGCCA
*
2489208 CT-ATCGATGAACCTATT-G
64 CTAAT-GACGAACCT-TTAG
* *
2489226 CGGCGTTTTTATAAAAACGCTACTAAAGT
1 CGGCGTTTGTATAAAAACGCCACTAAAGT
2489255 TACCATTTGT
Statistics
Matches: 224, Mismatches: 38, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
81 4 0.02
82 137 0.61
83 18 0.08
84 62 0.28
85 2 0.01
86 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (81 bp):
CGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCCACT
AATGACGAACCTTTAG
Found at i:2489609 original size:31 final size:31
Alignment explanation
Indices: 2489574--2489650 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
2489564 TGCAAGTTTT
2489574 AAGTTTAGTGACCATAATGCATATTCCCTAG
1 AAGTTTAGTGACCATAATGCATATTCCCTAG
2489605 AAGTTTAGTGACCATAATGCATATTCCCTAG
1 AAGTTTAGTGACCATAATGCATATTCCCTAG
2489636 AAGTTTAGTGACCAT
1 AAGTTTAGTGACCAT
2489651 TCATGTAGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (31 bp):
AAGTTTAGTGACCATAATGCATATTCCCTAG
Found at i:2494909 original size:29 final size:29
Alignment explanation
Indices: 2494844--2494909 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
2494834 TTCTTTTGAT
2494844 TATTAAATTTTCAAAAGTTATAAAATTAA
1 TATTAAATTTTCAAAAGTTATAAAATTAA
*
2494873 TATCAAATTTT-ATTAAA-TTATAAAA-TAA
1 TATTAAATTTTCA--AAAGTTATAAAATTAA
2494901 TCATTAAAT
1 T-ATTAAAT
2494910 GTATTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 5 0.16
29 24 0.75
30 3 0.09
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (29 bp):
TATTAAATTTTCAAAAGTTATAAAATTAA
Found at i:2494915 original size:28 final size:29
Alignment explanation
Indices: 2494861--2494916 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2494851 TTTTCAAAAG
*
2494861 TTATAAAATTAATATCAAATTTTATTAAA
1 TTATAAAATTAATATCAAATTGTATTAAA
*
2494890 TTATAAAA-TAATCATTAAA-TGTATTAA
1 TTATAAAATTAAT-ATCAAATTGTATTAA
2494917 TTTTTACACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (29 bp):
TTATAAAATTAATATCAAATTGTATTAAA
Found at i:2496410 original size:49 final size:50
Alignment explanation
Indices: 2496333--2496431 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 50
2496323 GCAGGTACTG
* * *
2496333 GTTTGCAAAGCTTGAATATGTTCTTATTTCATCTTGTGGTAATTG-TTTT
1 GTTTACAAAGCTAGAAGATGTTCTTATTTCATCTTGTGGTAATTGCTTTT
2496382 GTTTACAAAGCTAGAAGATGTTCTTATTTCATCTTGTGGTAATTGCTTTT
1 GTTTACAAAGCTAGAAGATGTTCTTATTTCATCTTGTGGTAATTGCTTTT
2496432 TTTTGGTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 42 0.91
50 4 0.09
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.48
Consensus pattern (50 bp):
GTTTACAAAGCTAGAAGATGTTCTTATTTCATCTTGTGGTAATTGCTTTT
Found at i:2497372 original size:14 final size:14
Alignment explanation
Indices: 2497350--2497406 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
2497340 GGTTCGTGAA
*
2497350 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
2497364 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
2497378 CG--T--TTATGTT
1 CGTTTGGTTATGTT
* *
2497388 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
2497402 CGTTT
1 CGTTT
2497407 ATGTTCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
12 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:2497378 original size:24 final size:24
Alignment explanation
Indices: 2497351--2497425 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
2497341 GTTCGTGAAC
* * *
2497351 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
2497375 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
2497399 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
2497423 GTT
1 GTT
2497426 TAACCCAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:2497996 original size:10 final size:10
Alignment explanation
Indices: 2497981--2498055 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
2497971 AGGTCTCCAA
2497981 CGTTTATGTT
1 CGTTTATGTT
2497991 CGTTTATGTT
1 CGTTTATGTT
2498001 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
2498012 ATGTTCGTGTT
1 -CGTTTATGTT
2498023 CGTTTATGTT
1 CGTTTATGTT
2498033 CG----TGTT
1 CGTTTATGTT
2498039 CGTTTATGTT
1 CGTTTATGTT
2498049 CGTTTAT
1 CGTTTAT
2498056 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:2498012 original size:16 final size:16
Alignment explanation
Indices: 2497987--2498051 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
2497977 CCAACGTTTA
2497987 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
2498003 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
2498019 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2498035 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2498051 T
1 T
2498052 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2498142 original size:16 final size:16
Alignment explanation
Indices: 2498121--2498153 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2498111 AAAAAAATTT
2498121 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2498137 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2498153 T
1 T
2498154 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2514408 original size:21 final size:21
Alignment explanation
Indices: 2514372--2514426 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
2514362 AATATACCAT
2514372 ATTAATATTAATAAATA-ATAAGA
1 ATTAAT-TT-ATAAATATATAA-A
*
2514395 ATTAATTTATAAATATTTAAA
1 ATTAATTTATAAATATATAAA
2514416 ATTAAATTTAT
1 ATT-AATTTAT
2514427 TATTATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.38
22 12 0.41
23 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTAATTTATAAATATATAAA
Found at i:2516267 original size:2 final size:2
Alignment explanation
Indices: 2516260--2516298 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2516250 TCCATTTACT
2516260 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2516299 CAGACCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2525877 original size:2 final size:2
Alignment explanation
Indices: 2525870--2525894 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2525860 ATTATATCGT
2525870 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2525895 TAATGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2530569 original size:24 final size:24
Alignment explanation
Indices: 2530542--2530589 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2530532 AATTAAACAC
2530542 TGATACAAGATTTTATATTATGGG
1 TGATACAAGATTTTATATTATGGG
*
2530566 TGATACAAGATTTTATATTTTGGG
1 TGATACAAGATTTTATATTATGGG
2530590 CGAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.44
Consensus pattern (24 bp):
TGATACAAGATTTTATATTATGGG
Found at i:2536508 original size:18 final size:18
Alignment explanation
Indices: 2536477--2536511 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2536467 ATTTTATTTA
2536477 ATTTTCTTAAAATGAAAC
1 ATTTTCTTAAAATGAAAC
* *
2536495 ATTTTTTTATAATGAAA
1 ATTTTCTTAAAATGAAA
2536512 GGAAAAATGC
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:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
ATTTTCTTAAAATGAAAC
Found at i:2537026 original size:17 final size:17
Alignment explanation
Indices: 2537006--2537040 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2536996 TCTCCCATAA
2537006 TTTTTAAAAATTCTAAT
1 TTTTTAAAAATTCTAAT
*
2537023 TTTTTAAAAATTTTAAT
1 TTTTTAAAAATTCTAAT
2537040 T
1 T
2537041 AGACCCCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTAAAAATTCTAAT
Found at i:2541074 original size:2 final size:2
Alignment explanation
Indices: 2541067--2541096 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2541057 AGCTCTCGTG
2541067 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2541097 GAAGTTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2542399 original size:22 final size:22
Alignment explanation
Indices: 2542364--2542408 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2542354 GTCAATATGT
* * * *
2542364 TCGTTTAGCGTTTATCAACATA
1 TCGTTTAACATTTACCAAAATA
2542386 TCGTTTAACATTTACCAAAATA
1 TCGTTTAACATTTACCAAAATA
2542408 T
1 T
2542409 TTATTTAGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (22 bp):
TCGTTTAACATTTACCAAAATA
Found at i:2551301 original size:12 final size:12
Alignment explanation
Indices: 2551284--2551325 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2551274 ATTTAATTAC
2551284 TAAATTTTATTT
1 TAAATTTTATTT
2551296 TAAATTTTATTT
1 TAAATTTTATTT
* *
2551308 GATATTTTATTT
1 TAAATTTTATTT
*
2551320 AAAATT
1 TAAATT
2551326 GATTTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
TAAATTTTATTT
Found at i:2551699 original size:29 final size:30
Alignment explanation
Indices: 2551667--2551737 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
2551657 CTAACATTTG
2551667 TTATTAAGGGCCTAA-TTTTTCAATACTTA
1 TTATTAAGGGCCTAATTTTTTCAATACTTA
* *
2551696 TTA-TAAGGGGGCTTAATTTTTTCAATATTTA
1 TTATTAA--GGGCCTAATTTTTTCAATACTTA
*
2551727 TTATTAGGGGC
1 TTATTAAGGGC
2551738 ATACTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 3 0.09
29 3 0.09
30 11 0.31
31 16 0.46
32 2 0.06
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (30 bp):
TTATTAAGGGCCTAATTTTTTCAATACTTA
Found at i:2551713 original size:30 final size:31
Alignment explanation
Indices: 2551674--2551736 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
2551664 TTGTTATTAA
2551674 GGGCCTAA-TTTTTCAATACTTATTATAAGG
1 GGGCCTAATTTTTTCAATACTTATTATAAGG
* * *
2551704 GGGCTTAATTTTTTCAATATTTATTATTAGG
1 GGGCCTAATTTTTTCAATACTTATTATAAGG
2551735 GG
1 GG
2551737 CATACTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (31 bp):
GGGCCTAATTTTTTCAATACTTATTATAAGG
Found at i:2551737 original size:30 final size:30
Alignment explanation
Indices: 2551651--2551737 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
2551641 TTGTCAATAT
* * *
2551651 TTTTTTCTAACATTTGTTATTAAGGGCCTAA
1 TTTTTTC-AATATTTATTATTAGGGGCCTAA
* * *
2551682 -TTTTTCAATACTTATTATAAGGGGGCTTAA
1 TTTTTTCAATATTTATTATTA-GGGGCCTAA
2551712 TTTTTTCAATATTTATTATTAGGGGC
1 TTTTTTCAATATTTATTATTAGGGGC
2551738 ATACTTTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 10 0.22
30 18 0.39
31 18 0.39
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.48
Consensus pattern (30 bp):
TTTTTTCAATATTTATTATTAGGGGCCTAA
Found at i:2552107 original size:17 final size:18
Alignment explanation
Indices: 2552081--2552118 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2552071 CATAGTGACG
*
2552081 ATACTAGCAGTGATTG-A
1 ATACTAGCAGTAATTGTA
*
2552098 ATACTTGCAGTAATTGTA
1 ATACTAGCAGTAATTGTA
2552116 ATA
1 ATA
2552119 TCATCAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (18 bp):
ATACTAGCAGTAATTGTA
Found at i:2554099 original size:16 final size:17
Alignment explanation
Indices: 2554071--2554102 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2554061 AAAATTATTT
2554071 TTTATTATTATTTTTAA
1 TTTATTATTATTTTTAA
2554088 TTTATT-TTATTTTTA
1 TTTATTATTATTTTTA
2554103 TAATTGAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTATTATTTTTAA
Found at i:2561696 original size:30 final size:30
Alignment explanation
Indices: 2561662--2561732 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
2561652 CGTGTATTCT
2561662 TGGAGACCTATGGAGGTTGTCGTATGCTCC
1 TGGAGACCTATGGAGGTTGTCGTATGCTCC
2561692 TGGAGACCTATGGAGGTTGTCGTATGCTCC
1 TGGAGACCTATGGAGGTTGTCGTATGCTCC
*
2561722 TGGAGAACTAT
1 TGGAGACCTAT
2561733 ATAGGTCACC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (30 bp):
TGGAGACCTATGGAGGTTGTCGTATGCTCC
Found at i:2568893 original size:23 final size:23
Alignment explanation
Indices: 2568867--2568914 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2568857 ATAAAGTACA
*
2568867 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2568890 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2568913 AT
1 AT
2568915 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2569664 original size:18 final size:18
Alignment explanation
Indices: 2569641--2569677 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2569631 CGAAATATAT
2569641 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2569659 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2569677 A
1 A
2569678 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2569907 original size:23 final size:23
Alignment explanation
Indices: 2569881--2569945 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
2569871 ATGCGAGATA
2569881 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
2569904 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
2569927 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
2569946 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:2570328 original size:21 final size:22
Alignment explanation
Indices: 2570303--2570354 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
2570293 ACACTTTACA
*
2570303 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
2570326 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
2570349 ATATAA
1 ATATAA
2570355 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:2570339 original size:23 final size:23
Alignment explanation
Indices: 2570313--2570375 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2570303 ATATAACCAC
2570313 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
2570336 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
2570359 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2570376 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2570757 original size:21 final size:22
Alignment explanation
Indices: 2570732--2570783 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
2570722 ACACTTTACA
*
2570732 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
2570755 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
2570778 ATATAA
1 ATATAA
2570784 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:2570768 original size:23 final size:23
Alignment explanation
Indices: 2570742--2570804 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2570732 ATATAACCAC
2570742 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
2570765 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
2570788 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2570805 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2570886 original size:430 final size:431
Alignment explanation
Indices: 2569883--2571333 Score: 2865
Period size: 430 Copynumber: 3.4 Consensus size: 431
2569873 GCGAGATAGA
2569883 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
2569948 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
2570012 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
2570077 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
2570142 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
2570207 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
2570272 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
2570313 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
2570378 TTACCTATTTTATTGAAAGTGTCCATAC-TTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
2570442 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
2570507 ATTTCATTTGCAC-AAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
2570571 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
2570636 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
2570701 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
2570742 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
2570807 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
2570872 TGTAATTTATGTTTCAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
2570936 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
196 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
2571001 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
261 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
2571066 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
326 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
2571131 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
391 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
2571172 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
2571237 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
2571302 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
2571334 ACTGCGAATT
Statistics
Matches: 1016, Mismatches: 1, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
429 396 0.39
430 606 0.60
431 14 0.01
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (431 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
Found at i:2571187 original size:21 final size:22
Alignment explanation
Indices: 2571162--2571213 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
2571152 ACACTTTACA
*
2571162 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
2571185 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
2571208 ATATAA
1 ATATAA
2571214 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:2571198 original size:23 final size:23
Alignment explanation
Indices: 2571172--2571234 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2571162 ATATAACCAC
2571172 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
2571195 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
2571218 TACCTATTACATCATAT
1 TACCTATTACATTATAT
2571235 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:2573770 original size:184 final size:184
Alignment explanation
Indices: 2573461--2574132 Score: 1236
Period size: 184 Copynumber: 3.7 Consensus size: 184
2573451 TTTTAAATGG
* *
2573461 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2573526 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTTTTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
2573591 GATGTATAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2573645 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2573710 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
2573775 AATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
* *
2573829 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
2573894 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
2573959 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2574013 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
* **
2574078 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
2574133 ATGTTGAAAG
Statistics
Matches: 471, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 471 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:2575610 original size:3 final size:3
Alignment explanation
Indices: 2575602--2575688 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
2575592 ACTTGTTTGG
* * * **
2575602 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
2575650 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2575689 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:2575625 original size:18 final size:18
Alignment explanation
Indices: 2575602--2575703 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
2575592 ACTTGTTTGG
2575602 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
2575620 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
2575638 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
2575656 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
2575674 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
2575692 AGCTTCATCTTC
1 ATCATCATCTTC
2575704 TGCGACCGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:2575669 original size:42 final size:42
Alignment explanation
Indices: 2575610--2575700 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
2575600 GGATCATCAT
*
2575610 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
2575652 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
2575694 CTTCATC
1 CTTCATC
2575701 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:2577638 original size:200 final size:200
Alignment explanation
Indices: 2577161--2578783 Score: 3042
Period size: 200 Copynumber: 8.1 Consensus size: 200
2577151 TTTAAATTTG
* *
2577161 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
2577226 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
2577291 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTATGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2577355 AAAAA
196 AAAAA
*
2577360 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
2577425 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2577490 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2577555 AAAAA
196 AAAAA
2577560 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
2577625 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2577690 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2577755 AAAAA
196 AAAAA
2577760 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
2577825 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
2577890 CGACAC--TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2577952 AAAAA
196 AAAAA
2577957 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
2578022 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2578087 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2578151 AAAAA
196 AAAAA
2578156 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
2578221 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2578286 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2578351 AAAAA
196 AAAAA
2578356 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
2578421 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
2578486 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2578550 AAAAA
196 AAAAA
*
2578555 TATCGACACACACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
2578620 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2578685 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2578750 AAAAA
196 AAAAA
*
2578755 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
2578784 TGACCCTTAA
Statistics
Matches: 1394, Mismatches: 24, Indels: 11
0.98 0.02 0.01
Matches are distributed among these distances:
197 189 0.14
198 4 0.00
199 529 0.38
200 672 0.48
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
AAAAA
Found at i:2577902 original size:399 final size:399
Alignment explanation
Indices: 2577161--2578783 Score: 3038
Period size: 399 Copynumber: 4.1 Consensus size: 399
2577151 TTTAAATTTG
* *
2577161 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
2577226 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
2577291 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTATGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
*
2577356 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
*
2577421 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTG
2577486 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
2577551 GAAAAAAAA
391 GAAAAAAAA
2577560 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
2577625 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2577690 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2577755 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
*
2577820 GTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTAAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTT
* *
2577885 GGGATCGACAC--TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT
325 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
2577947 GGAAAAAAAA
390 GGAAAAAAAA
2577957 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
2578022 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2578087 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
2578151 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
*
2578216 GTATAATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTAAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTT
2578281 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
325 GGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
2578346 GGAAAAAAAA
390 GGAAAAAAAA
2578356 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
2578421 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
2578486 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
*
2578551 AAAATATCGACACACACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
*
2578616 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTG
2578681 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
2578746 GAAAAAAAA
391 GAAAAAAAA
*
2578755 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
2578784 TGACCCTTAA
Statistics
Matches: 1197, Mismatches: 22, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
396 143 0.12
397 245 0.20
398 61 0.05
399 554 0.46
400 194 0.16
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (399 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTAAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
GAAAAAAAA
Found at i:2578892 original size:19 final size:19
Alignment explanation
Indices: 2578865--2578909 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2578855 ATTCACATAA
*
2578865 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
2578884 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
2578903 AAAATTA
1 AAAATTA
2578910 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:2580736 original size:33 final size:33
Alignment explanation
Indices: 2580699--2580764 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2580689 CATCTTAATA
*
2580699 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
2580732 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
2580765 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:2582902 original size:24 final size:24
Alignment explanation
Indices: 2582865--2582917 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2582855 CCGTTCTATC
2582865 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
2582889 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
2582913 TATTT
1 TATTT
2582918 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:2583256 original size:20 final size:20
Alignment explanation
Indices: 2583230--2583275 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
2583220 CACTTTTAAA
2583230 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
2583249 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
2583270 TTTACC
1 TTTACC
2583276 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:2589529 original size:23 final size:23
Alignment explanation
Indices: 2589499--2589562 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
2589489 GACCCAAAAT
2589499 AATAAAAAATATTATTTTTATGC
1 AATAAAAAATATTATTTTTATGC
* *
2589522 AATAAAAACTATTATTTTTATTC
1 AATAAAAAATATTATTTTTATGC
*
2589545 AATAAAAAACATTGATTT
1 AATAAAAAATATT-ATTT
2589563 AATCAAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 32 0.89
24 4 0.11
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (23 bp):
AATAAAAAATATTATTTTTATGC
Found at i:2590539 original size:23 final size:21
Alignment explanation
Indices: 2590512--2590554 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2590502 ATATAAAAAA
2590512 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
2590533 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
2590554 T
1 T
2590555 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:2593015 original size:22 final size:21
Alignment explanation
Indices: 2592990--2593037 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
2592980 AACGTGCCAA
2592990 AAAGTAAAAGAAAACTTGTCAT
1 AAAGTAAAA-AAAACTTGTCAT
** *
2593012 AAAGGTAGTAAAAACTTGTTAT
1 AAA-GTAAAAAAAACTTGTCAT
2593034 AAAG
1 AAAG
2593038 ACAAACTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 17 0.77
23 4 0.18
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (21 bp):
AAAGTAAAAAAAACTTGTCAT
Found at i:2593091 original size:18 final size:17
Alignment explanation
Indices: 2593048--2593091 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2593038 ACAAACTTAT
2593048 TAAAAATAAAAAAACAA
1 TAAAAATAAAAAAACAA
*
2593065 TAGAAAATAAAAGAACAA
1 TA-AAAATAAAAAAACAA
2593083 TAAAGAATA
1 TAAA-AATA
2593092 TCAGTCAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.14
Consensus pattern (17 bp):
TAAAAATAAAAAAACAA
Found at i:2606044 original size:63 final size:64
Alignment explanation
Indices: 2605972--2606092 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 64
2605962 GCATCTACTG
** * *
2605972 TTTACCAAAATGGTCATTTTGGCCTTTAAAT-TTTT-TTCTCGAGCATTTTGGCCCCCCCAAACA
1 TTTACCAAAATAATCACTTTGACCTTT-AATCTTTTATTCTCGAGCATTTTGGCCCCCCCAAACA
* * * *
2606035 TTTATCAAAATAATCACTTTGACCTTTATTCTTTTATTCTGGAGCATTTTGGTCCCCC
1 TTTACCAAAATAATCACTTTGACCTTTAATCTTTTATTCTCGAGCATTTTGGCCCCCC
2606093 AACGTGTCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
62 2 0.04
63 26 0.54
64 20 0.42
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (64 bp):
TTTACCAAAATAATCACTTTGACCTTTAATCTTTTATTCTCGAGCATTTTGGCCCCCCCAAACA
Found at i:2606730 original size:2 final size:2
Alignment explanation
Indices: 2606721--2606795 Score: 81
Period size: 2 Copynumber: 40.5 Consensus size: 2
2606711 AAAATATAAA
* *
2606721 AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2606758 AT A- AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2606796 ATTGGGGCGG
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
1 6 0.10
2 57 0.90
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2606754 original size:26 final size:26
Alignment explanation
Indices: 2606713--2606787 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
2606703 TAATATAAAA
2606713 AATAT-AAAATATTATATATATAATT
1 AATATAAAAATATTATATATATAATT
2606738 AATATAAAAATATTATATATATAATT
1 AATATAAAAATATTATATATATAATT
* * *
2606764 TATATATATATATATATATATATA
1 AATATAAAAATAT-TATATATATA
2606788 TATATATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 5 0.11
26 30 0.67
27 10 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATATAAAAATATTATATATATAATT
Found at i:2611370 original size:11 final size:11
Alignment explanation
Indices: 2611318--2611371 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
2611308 TTTCCATTAC
2611318 AATTAT-TTTT
1 AATTATATTTT
*
2611328 AATTATTTTTT
1 AATTATATTTT
*
2611339 ATTTTATATTAATT
1 A-ATTATATT--TT
2611353 AATTATATTTT
1 AATTATATTTT
2611364 AATTATAT
1 AATTATAT
2611372 ACTAAGACGC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 6 0.16
11 15 0.41
12 6 0.16
13 7 0.19
14 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
AATTATATTTT
Found at i:2627981 original size:41 final size:41
Alignment explanation
Indices: 2627935--2628017 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
2627925 ATGAACCATG
2627935 AAGTAAAAGTAACAAGACACATGAAGTTCACGTTTGTCTAA
1 AAGTAAAAGTAACAAGACACATGAAGTTCACGTTTGTCTAA
2627976 AAGTAAAAGTAACAAGACACATGAAGTTCACGTTTGTCTAA
1 AAGTAAAAGTAACAAGACACATGAAGTTCACGTTTGTCTAA
2628017 A
1 A
2628018 CATTCGATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (41 bp):
AAGTAAAAGTAACAAGACACATGAAGTTCACGTTTGTCTAA
Found at i:2628236 original size:19 final size:19
Alignment explanation
Indices: 2628212--2628278 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 19
2628202 TATATAGTAT
2628212 AATTATAAGAATAATATTA
1 AATTATAAGAATAATATTA
*
2628231 AATTATTCAAATGTTATAAGTA-T-
1 AATTA-T--AA-G-AATAA-TATTA
2628254 AATTATAAGAATAATATTA
1 AATTATAAGAATAATATTA
2628273 AATTAT
1 AATTAT
2628279 TCAAATGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
17 2 0.05
18 5 0.13
19 12 0.32
20 3 0.08
22 3 0.08
23 6 0.16
24 5 0.13
25 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (19 bp):
AATTATAAGAATAATATTA
Found at i:2628255 original size:42 final size:42
Alignment explanation
Indices: 2628201--2628291 Score: 173
Period size: 42 Copynumber: 2.1 Consensus size: 42
2628191 ATTTTATATA
2628201 TTATATAGTATAATTATAAGAATAATATTAAATTATTCAAATG
1 TTATA-AGTATAATTATAAGAATAATATTAAATTATTCAAATG
2628244 TTATAAGTATAATTATAAGAATAATATTAAATTATTCAAATG
1 TTATAAGTATAATTATAAGAATAATATTAAATTATTCAAATG
2628286 TTATAA
1 TTATAA
2628292 CAAATACAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 43 0.90
43 5 0.10
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (42 bp):
TTATAAGTATAATTATAAGAATAATATTAAATTATTCAAATG
Found at i:2628757 original size:60 final size:60
Alignment explanation
Indices: 2628622--2628779 Score: 151
Period size: 60 Copynumber: 2.6 Consensus size: 60
2628612 TATAATTTGG
* * * * * * * *
2628622 GATGAAATTGTAATGTTAAAAAATTTGAGGGCCAATTTATAATGAAGATCACAGTTTGGG
1 GATGAAATTGAAATATTAAAAAGTTTGAGGACTAATTTAAAATGAAGATCACAGTTTAGA
* * *
2628682 GATGAAACTGAAATATTCAAAAGTTTGAGGACTAATTTAAAATGATAG-TCATAGTTTAGA
1 GATGAAATTGAAATATTAAAAAGTTTGAGGACTAATTTAAAATGA-AGATCACAGTTTAGA
** *
2628742 GATGAAATTTG-AATATTTGAAAGTTTAAGGA-TAATTTA
1 GATGAAA-TTGAAATATTAAAAAGTTTGAGGACTAATTTA
2628780 GAATTAAGGT
Statistics
Matches: 81, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 7 0.09
60 70 0.86
61 4 0.05
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (60 bp):
GATGAAATTGAAATATTAAAAAGTTTGAGGACTAATTTAAAATGAAGATCACAGTTTAGA
Found at i:2628864 original size:29 final size:31
Alignment explanation
Indices: 2628830--2628899 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
2628820 TCTATTTTAA
2628830 ATTAATCTTTAAACT-TTAAAAT-ATTCTAT
1 ATTAATCTTTAAACTATTAAAATCATTCTAT
* * *
2628859 ATTAATCTTCACACTATTAATATCATTCTAT
1 ATTAATCTTTAAACTATTAAAATCATTCTAT
* *
2628890 TTTGATCTTT
1 ATTAATCTTT
2628900 CCATTAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 13 0.39
30 6 0.18
31 14 0.42
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.50
Consensus pattern (31 bp):
ATTAATCTTTAAACTATTAAAATCATTCTAT
Found at i:2636835 original size:2 final size:2
Alignment explanation
Indices: 2636828--2636864 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2636818 GATCCTAACC
2636828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2636865 ACTTATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2637124 original size:4 final size:4
Alignment explanation
Indices: 2637115--2637141 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2637105 AAAACAGTTA
2637115 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
2637142 TATGCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2637149 original size:8 final size:8
Alignment explanation
Indices: 2637119--2637168 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
2637109 CAGTTAATAC
*
2637119 ATACATAC
1 ATACATAT
*
2637127 ATACATAC
1 ATACATAT
2637135 ATACATAT
1 ATACATAT
*
2637143 ATGCATAT
1 ATACATAT
*
2637151 ATATATAT
1 ATACATAT
*
2637159 ATATATAT
1 ATACATAT
2637167 AT
1 AT
2637169 GCATGTGTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (8 bp):
ATACATAT
Found at i:2637149 original size:12 final size:12
Alignment explanation
Indices: 2637119--2637168 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
2637109 CAGTTAATAC
*
2637119 ATACATACATAC
1 ATACATACATAT
2637131 ATACATACATAT
1 ATACATACATAT
* *
2637143 ATGCATATATAT
1 ATACATACATAT
* *
2637155 ATATATATATAT
1 ATACATACATAT
2637167 AT
1 AT
2637169 GCATGTGTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (12 bp):
ATACATACATAT
Found at i:2637919 original size:41 final size:41
Alignment explanation
Indices: 2637816--2637939 Score: 232
Period size: 41 Copynumber: 3.0 Consensus size: 41
2637806 CCTACTACCT
*
2637816 TACCTCCCCCTCCCCCTATTACATATGGGAATAGGGTCAGC
1 TACCTCCCCCTCACCCTATTACATATGGGAATAGGGTCAGC
2637857 TACCT-CCCCTCACCCTATTACATATGGGAATAGGGTCAGC
1 TACCTCCCCCTCACCCTATTACATATGGGAATAGGGTCAGC
2637897 TACCTCCCCCTCACCCTATTACATATGGGAATAGGGTCAGC
1 TACCTCCCCCTCACCCTATTACATATGGGAATAGGGTCAGC
2637938 TA
1 TA
2637940 ATTTTATTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
40 39 0.48
41 42 0.52
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.25
Consensus pattern (41 bp):
TACCTCCCCCTCACCCTATTACATATGGGAATAGGGTCAGC
Found at i:2638753 original size:20 final size:20
Alignment explanation
Indices: 2638728--2638779 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2638718 ATAATAGAAA
2638728 GAATCGATGCTTAGCCGAAG
1 GAATCGATGCTTAGCCGAAG
2638748 GAATCGATGCTTAGCCGAAG
1 GAATCGATGCTTAGCCGAAG
2638768 GAATCGATGCTT
1 GAATCGATGCTT
2638780 TGTCTTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (20 bp):
GAATCGATGCTTAGCCGAAG
Found at i:2643488 original size:27 final size:28
Alignment explanation
Indices: 2643458--2643510 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
2643448 TAAGTATAAG
2643458 TTCATCTCATA-AATAATTAA-AATATCA
1 TTCAT-TCATATAATAATTAATAATATCA
*
2643485 TTCATTTATATAATAATTAATAATAT
1 TTCATTCATATAATAATTAATAATAT
2643511 TATAAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 14 0.61
28 5 0.22
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (28 bp):
TTCATTCATATAATAATTAATAATATCA
Found at i:2644465 original size:14 final size:14
Alignment explanation
Indices: 2644431--2644468 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2644421 ATATTTTAAA
*
2644431 ATATTTA-AATAAT
1 ATATTTATAAAAAT
2644444 ATATTTTATAAAAAT
1 ATA-TTTATAAAAAT
2644459 ATATTTATAA
1 ATATTTATAA
2644469 TTATTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 11 0.50
15 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATTTATAAAAAT
Found at i:2651951 original size:40 final size:40
Alignment explanation
Indices: 2651896--2652007 Score: 215
Period size: 40 Copynumber: 2.8 Consensus size: 40
2651886 TGTTTCATGC
*
2651896 TTATATTTGATATATAGTTAGGTTTGTCTCTAGCTTATGT
1 TTATATTTGATATATAGCTAGGTTTGTCTCTAGCTTATGT
2651936 TTATATTTGATATATAGCTAGGTTTGTCTCTAGCTTATGT
1 TTATATTTGATATATAGCTAGGTTTGTCTCTAGCTTATGT
2651976 TTATATTTGATATATAGCTAGGTTTGTCTCTA
1 TTATATTTGATATATAGCTAGGTTTGTCTCTA
2652008 ACTTGTTTGG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (40 bp):
TTATATTTGATATATAGCTAGGTTTGTCTCTAGCTTATGT
Found at i:2654817 original size:228 final size:228
Alignment explanation
Indices: 2654418--2655751 Score: 1217
Period size: 228 Copynumber: 5.9 Consensus size: 228
2654408 GACATAACAG
* * * *
2654418 ATGCAGATCTTTGTGAAAACTCTTACCGGTAAGACCATCACCCTGGAGGTGGAAAGCTCAGACAC
1 ATGCAGATCTTTGTGAAAACCCTTACCGGAAAGACCATCACTCTGGAGGTGGAGAGCTCAGACAC
* * * *
2654483 AATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAAGGGATCCCTCCCGACCAACAGAGGCTT-
66 AATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAACAGAGG-TTG
* * ** * * *
2654547 ATCTTTGCTGGAAAACAGCTTGAGGATGGCCGTACACTTGCTGATTACAACATCCAAAAGGAGTC
130 ATCTTTGCTGGGAAACAGCTGGAGGATGGTAGGACACTTGCTGACTATAACATCCAAAAGGAGTC
* * *
2654612 TACCCTTCACCTT-GTCCTTCGGCTCAGGGGTGGT
195 TACCCTCCA-CTTGGTCCTTCGTCTCAGGGGTGGC
* * * * * *
2654646 ATGCAGATCTTTGTAAAAACCCTTACTGGAAAGACAATTACTCTGGAGGTGGAAAGCTCCGACAC
1 ATGCAGATCTTTGTGAAAACCCTTACCGGAAAGACCATCACTCTGGAGGTGGAGAGCTCAGACAC
* * * * *
2654711 AATCGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATTCCTCCAGACCAACAGAGGCTT-
66 AATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAACAGAGG-TTG
* * * ** * * *
2654775 ATATTTGCTGGTAAACAACTGGAGGATGGCCGCACCCTTGCTGACTACAACATCCAGAAA-GAGT
130 ATCTTTGCTGGGAAACAGCTGGAGGATGGTAGGACACTTGCTGACTATAACATCCA-AAAGGAGT
*
2654839 CTACCCTGCACCTT-GTCCTTCGTCTCAGGGGTGGC
194 CTACCCTCCA-CTTGGTCCTTCGTCTCAGGGGTGGC
* * * *
2654874 ATGCAGATCTTTGTGAAAACCCTTACCGGCAAGACAATCACTCTTGAGGTGGAGAGCTCCGACAC
1 ATGCAGATCTTTGTGAAAACCCTTACCGGAAAGACCATCACTCTGGAGGTGGAGAGCTCAGACAC
* * * * *
2654939 AATTGATAATGTGAAGGCTAAGATTCAGGACAAGG-AGGGCATCCCACCGGACCAGCAGAGGTTA
66 AATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAAGGG-ATCCCACCAGACCAACAGAGGTTG
* * * * * * *
2655003 ATTTTTGCTGGGAAACAGCTTGAAGATGGTAGGACCCTAGCAGACTATAACATTCAAAAGGAGTC
130 ATCTTTGCTGGGAAACAGCTGGAGGATGGTAGGACACTTGCTGACTATAACATCCAAAAGGAGTC
* * * *
2655068 TACCCTCCACTTGGT-GTTGCGTCTCCGAGGCGGC
195 TACCCTCCACTTGGTCCTT-CGTCTCAGGGGTGGC
* * * * * * * * * * *
2655102 ATGCAAATTTTTGTGAAGACTCTTACAGGAAAGACTATTAC-CTTGGAAGTTGAGAGTTCAGATA
1 ATGCAGATCTTTGTGAAAACCCTTACCGGAAAGACCATCACTC-TGGAGGTGGAGAGCTCAGACA
* * * * * * *
2655166 CAATTGACAATGTGAAAGCTAAGATCCAGGACAAGGAGGGGATTCCACCAGATCAACAGAGGCTG
65 CAATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAACAGAGGTTG
* * * * * *
2655231 ATCTTCGCTGGCAAGCAGCTGGAGGATGGTAGGACACTTGCTGATTATAATATTCAGAAA-GAGT
130 ATCTTTGCTGGGAAACAGCTGGAGGATGGTAGGACACTTGCTGACTATAACATCCA-AAAGGAGT
* * *
2655295 CAACCCTCCACTTGGTCCTCCGTCTGC-GGGGTGGG
194 CTACCCTCCACTTGGTCCTTCGTCT-CAGGGGTGGC
* * * *
2655330 ATGCAGATTTTTGTGAAAA-CCTTGACCGGTAAGACCATTACAT-TGGAGGTGGAGAGCTCTGAC
1 ATGCAGATCTTTGTGAAAACCCTT-ACCGGAAAGACCATCAC-TCTGGAGGTGGAGAGCTCAGAC
* * * * * *
2655393 ACAATTGATAACGTTAAGGCCAAAATCCAGGATAAGG-AGGGAATCCCACCTGACCAGCAGAGGT
64 ACAATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAAGGG-ATCCCACCAGACCAACAGAGGT
* * * * * * *
2655457 TGATCTTTGC-CGGAAAGCAGCTTGAGGACGGGAGGACTCTTGCTGACTATAACATTCAGAAGGA
128 TGATCTTTGCTGGGAAA-CAGCTGGAGGATGGTAGGACACTTGCTGACTATAACATCCAAAAGGA
* * * * * * * *
2655521 GTCAACCCTACATTTGGT-CTTGCGCCTTAGAGGAGGG
192 GTCTACCCTCCACTTGGTCCTT-CGTCTCAGGGGTGGC
* * * * * * * *
2655558 ATGCAGATATTTGTCAAGA-CCTTGACTGGAAAAACCATCACCCTGGAGGTTGAGAGCTCGGACA
1 ATGCAGATCTTTGTGAAAACCCTT-ACCGGAAAGACCATCACTCTGGAGGTGGAGAGCTCAGACA
* * * * * *
2655622 CAATTGACAATGTGAAAGCAAAGATCCAGGACAAGGAGGGGATTCCC-CCAGATCAGCAGAGGTT
65 CAATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAAGGGA-TCCCACCAGACCAACAGAGGTT
* * * * * * *
2655686 GATCTTTGCTGGGAAGCAGTTGGAGGATGGTCGAACTCTTGCTGATTATAACATCCAGAAGGAGT
129 GATCTTTGCTGGGAAACAGCTGGAGGATGGTAGGACACTTGCTGACTATAACATCCAAAAGGAGT
2655751 C
194 C
2655752 CACTCTGCAC
Statistics
Matches: 915, Mismatches: 168, Indels: 46
0.81 0.15 0.04
Matches are distributed among these distances:
227 28 0.03
228 865 0.95
229 22 0.02
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (228 bp):
ATGCAGATCTTTGTGAAAACCCTTACCGGAAAGACCATCACTCTGGAGGTGGAGAGCTCAGACAC
AATTGATAATGTGAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAACAGAGGTTGA
TCTTTGCTGGGAAACAGCTGGAGGATGGTAGGACACTTGCTGACTATAACATCCAAAAGGAGTCT
ACCCTCCACTTGGTCCTTCGTCTCAGGGGTGGC
Found at i:2655292 original size:456 final size:453
Alignment explanation
Indices: 2654418--2655772 Score: 1520
Period size: 456 Copynumber: 3.0 Consensus size: 453
2654408 GACATAACAG
* * *
2654418 ATGCAGATCTTTGTGAAAACTCTTACCGGTAAGACCATCACCCTGGAGGTGGAAAGCTCAGACAC
1 ATGCAGATCTTTGTGAAAACCCTTACCGGTAAGACCATCACTCTGGAGGTGGAGAGCTCAGACAC
* *
2654483 AATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAAGGGATCCCTCCCGACCAACAGAGGCTTA
66 AATTGATAATGTCAAGGCCAAGATCCAGGATAAGG-AGGGATCCCACCCGACCAGCAGAGG-TTA
* * * * * *
2654548 TCTTTGCTGGAAAACAGCTTGAGGATGGCCGTACACTTGCTGATTACAACATCCAAAAGGAGTCT
129 TCTTTGCTGGGAAACAGCTTGAGGATGGCAGGACACTTGCTGACTATAACATTCAAAAGGAGTCT
* * * * * * *
2654613 ACCCTTCACCTT-GTCCTT-CGGCTCAGGGGTGGTATGCAGATCTTTGTAAAAACCCTTACTGGA
194 ACCCTACA-CTTGGT-CTTGCGCCTCAGAGGAGGCATGCAGATATTTGTAAAGA-CCTTACTGGA
* * * * * * * * *
2654676 AAGACAATTA-CTCTGGAGGTGGAAAGCTCCGACACAATCGATAATGTCAAGGCCAAGATCCAAG
256 AAGACAATTACCT-TGGAGGTTGAGAGCTCAGACACAATTGACAATGTGAAAGCAAAGATCCAGG
* * * * * * * * *
2654740 ACAAGGAAGGGATTCCTCCAGACCAACAGAGGCTTATATTTGCTGGTAAACAACTGGAGGATGGC
320 ACAAGGAGGGGATTCCACCAGATCAACAGAGGCTGATCTTTGCTGGCAAGCAGCTGGAGGATGGT
* * * * *
2654805 CGCACCCTTGCTGACTACAACATCCAGAAAGAGTCTACCCTGCACCTTGTCCTTCGTCT-CAGGG
385 CGAACACTTGCTGATTATAACATCCAGAAAGAGTCAACCCTGCACCTTGTCCTTCGTCTGC-GGG
2654869 GTGGC
449 GTGGC
* * * *
2654874 ATGCAGATCTTTGTGAAAACCCTTACCGGCAAGACAATCACTCTTGAGGTGGAGAGCTCCGACAC
1 ATGCAGATCTTTGTGAAAACCCTTACCGGTAAGACCATCACTCTGGAGGTGGAGAGCTCAGACAC
* * * * *
2654939 AATTGATAATGTGAAGGCTAAGATTCAGGACAAGGAGGGCATCCCACCGGACCAGCAGAGGTTAA
66 AATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAGGG-ATCCCACCCGACCAGCAGAGGTT-A
* * * * * *
2655004 TTTTTGCTGGGAAACAGCTTGAAGATGGTAGGACCCTAGCAGACTATAACATTCAAAAGGAGTCT
129 TCTTTGCTGGGAAACAGCTTGAGGATGGCAGGACACTTGCTGACTATAACATTCAAAAGGAGTCT
* * * * * * * * *
2655069 ACCCTCCACTTGGTGTTGCGTCTCCGAGGCGGCATGCAAATTTTTGTGAAGACTCTTACAGGAAA
194 ACCCTACACTTGGTCTTGCGCCTCAGAGGAGGCATGCAGATATTTGTAAAGAC-CTTACTGGAAA
* * * * *
2655134 GACTATTACCTTGGAAGTTGAGAGTTCAGATACAATTGACAATGTGAAAGCTAAGATCCAGGACA
258 GACAATTACCTTGGAGGTTGAGAGCTCAGACACAATTGACAATGTGAAAGCAAAGATCCAGGACA
* * *
2655199 AGGAGGGGATTCCACCAGATCAACAGAGGCTGATCTTCGCTGGCAAGCAGCTGGAGGATGGTAGG
323 AGGAGGGGATTCCACCAGATCAACAGAGGCTGATCTTTGCTGGCAAGCAGCTGGAGGATGGTCGA
* * * *
2655264 ACACTTGCTGATTATAATATTCAGAAAGAGTCAACCCTCCA-CTTGGTCCTCCGTCTGCGGGGTG
388 ACACTTGCTGATTATAACATCCAGAAAGAGTCAACCCTGCACCTT-GTCCTTCGTCTGCGGGGTG
*
2655328 GG
452 GC
* * *
2655330 ATGCAGATTTTTGTGAAAA-CCTTGACCGGTAAGACCATTACAT-TGGAGGTGGAGAGCTCTGAC
1 ATGCAGATCTTTGTGAAAACCCTT-ACCGGTAAGACCATCAC-TCTGGAGGTGGAGAGCTCAGAC
* * * *
2655393 ACAATTGATAACGTTAAGGCCAAAATCCAGGATAAGGAGGGAATCCCACCTGACCAGCAGAGGTT
64 ACAATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAGGG-ATCCCACCCGACCAGCAGAGGTT
* * * * *
2655458 GATCTTTGC-CGGAAAGCAGCTTGAGGACGGGAGGACTCTTGCTGACTATAACATTCAGAAGGAG
128 -ATCTTTGCTGGGAAA-CAGCTTGAGGATGGCAGGACACTTGCTGACTATAACATTCAAAAGGAG
* * * * *
2655522 TCAACCCTACATTTGGTCTTGCGCCTTAGAGGAGGGATGCAGATATTTGTCAAGACCTTGACTGG
191 TCTACCCTACACTTGGTCTTGCGCCTCAGAGGAGGCATGCAGATATTTGTAAAGACCTT-ACTGG
* * * * *
2655587 AAAAACCATCACCCTGGAGGTTGAGAGCTCGGACACAATTGACAATGTGAAAGCAAAGATCCAGG
255 AAAGACAATTACCTTGGAGGTTGAGAGCTCAGACACAATTGACAATGTGAAAGCAAAGATCCAGG
* * * * *
2655652 ACAAGGAGGGGATTCCCCCAGATCAGCAGAGGTTGATCTTTGCTGGGAAGCAGTTGGAGGATGGT
320 ACAAGGAGGGGATTCCACCAGATCAACAGAGGCTGATCTTTGCTGGCAAGCAGCTGGAGGATGGT
* * * *
2655717 CGAACTCTTGCTGATTATAACATCCAGAAGGAGTCCACTCTGCACCTTGTCCTTCG
385 CGAACACTTGCTGATTATAACATCCAGAAAGAGTCAACCCTGCACCTTGTCCTTCG
2655773 CCTCCGTGGT
Statistics
Matches: 752, Mismatches: 134, Indels: 26
0.82 0.15 0.03
Matches are distributed among these distances:
455 27 0.04
456 718 0.95
457 7 0.01
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (453 bp):
ATGCAGATCTTTGTGAAAACCCTTACCGGTAAGACCATCACTCTGGAGGTGGAGAGCTCAGACAC
AATTGATAATGTCAAGGCCAAGATCCAGGATAAGGAGGGATCCCACCCGACCAGCAGAGGTTATC
TTTGCTGGGAAACAGCTTGAGGATGGCAGGACACTTGCTGACTATAACATTCAAAAGGAGTCTAC
CCTACACTTGGTCTTGCGCCTCAGAGGAGGCATGCAGATATTTGTAAAGACCTTACTGGAAAGAC
AATTACCTTGGAGGTTGAGAGCTCAGACACAATTGACAATGTGAAAGCAAAGATCCAGGACAAGG
AGGGGATTCCACCAGATCAACAGAGGCTGATCTTTGCTGGCAAGCAGCTGGAGGATGGTCGAACA
CTTGCTGATTATAACATCCAGAAAGAGTCAACCCTGCACCTTGTCCTTCGTCTGCGGGGTGGC
Found at i:2660209 original size:13 final size:13
Alignment explanation
Indices: 2660191--2660217 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2660181 CCTTCTACCC
2660191 ACGTCGCCTTTGT
1 ACGTCGCCTTTGT
2660204 ACGTCGCCTTTGT
1 ACGTCGCCTTTGT
2660217 A
1 A
2660218 TCTTCCTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.11, C:0.30, G:0.22, T:0.37
Consensus pattern (13 bp):
ACGTCGCCTTTGT
Found at i:2661583 original size:25 final size:21
Alignment explanation
Indices: 2661556--2661598 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2661546 CAAACTCCAT
*
2661556 ATTCTA-TTTGCCCAACTAAC
1 ATTCTATTTTTCCCAACTAAC
2661576 ATTCTATTTTTCCCAACTAAC
1 ATTCTATTTTTCCCAACTAAC
2661597 AT
1 AT
2661599 ATAGGAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTCTATTTTTCCCAACTAAC
Found at i:2665357 original size:23 final size:26
Alignment explanation
Indices: 2665309--2665363 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
2665299 ATGAGAAAAA
2665309 AGAAA-AAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTT
*
2665334 ATAAATAAAAT-ATTTAT-T-TATTT
1 AGAAATAAAATAATTTATATATATTT
2665357 AGAAATA
1 AGAAATA
2665364 TCAGAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 10 0.37
26 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTT
Found at i:2665437 original size:23 final size:22
Alignment explanation
Indices: 2665413--2665457 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2665403 CTTCAATATT
*
2665413 AATAAATATTAATTTAATAATTTA
1 AATAAA-ATTAAATT-ATAATTTA
2665437 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATTATAATTT
2665458 TTTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 7 0.35
24 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATAAAATTAAATTATAATTTA
Found at i:2667030 original size:3 final size:3
Alignment explanation
Indices: 2667024--2667092 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
2667014 TATTATTTTT
* *
2667024 TAA TAA TAA TAA TAA T-A TATA TTA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
2667069 TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
2667093 ATAAAAAAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.93
4 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2667089 original size:18 final size:18
Alignment explanation
Indices: 2667024--2667092 Score: 113
Period size: 18 Copynumber: 3.8 Consensus size: 18
2667014 TATTATTTTT
2667024 TAATAATAATAATAA-TA
1 TAATAATAATAATAATTA
*
2667041 TATATTATAATAATAATTA
1 TA-ATAATAATAATAATTA
2667060 TAATAATAATAATAATTA
1 TAATAATAATAATAATTA
2667078 TAATAATAATAATAA
1 TAATAATAATAATAA
2667093 ATAAAAAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
17 2 0.04
18 42 0.88
19 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATAATAATAATAATTA
Found at i:2667456 original size:124 final size:121
Alignment explanation
Indices: 2667236--2667528 Score: 346
Period size: 124 Copynumber: 2.4 Consensus size: 121
2667226 GTTGAATAAA
* * *
2667236 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCGCTGG---GGATGATGTTGAC
1 TTCTT-TCTTT-TTCAGATGAGTTCTTCTCATTATGAAC-TTTCTCTGGAAAGGATGATGCTAAC
* * * * *
2667298 CTATTTCCTTATGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAATTTT
63 ATATTTCCTTATGTGATAAAATCATTCAAAAGGTTGAACAAGCTCTTCTCATTATGAA---C
* *
2667360 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATATA
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACATA
* * *
2667425 TCTT-CTTCTGTGATAAAATTATGT-AAAAGGTTGAACAAGCTCTTCTCATTGTGAAC
66 T-TTCCTTATGTGATAAAATCAT-TCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
*
2667481 TTC-TTCTTTTTCAGATGAGTTTTTCTCATTATGAACTTTCTCTGGAAA
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
2667529 AGCTGATCCA
Statistics
Matches: 150, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
120 44 0.29
121 11 0.07
122 27 0.18
123 5 0.03
124 60 0.40
125 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (121 bp):
TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACATA
TTTCCTTATGTGATAAAATCATTCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
Found at i:2667826 original size:113 final size:113
Alignment explanation
Indices: 2667449--2668232 Score: 913
Period size: 113 Copynumber: 7.0 Consensus size: 113
2667439 AAAATTATGT
* * * * *
2667449 AAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC-T--TT-TTCAGATGAGTTTTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
**** * * * *
2667510 TATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGGATTTGAGC
66 TATGAACTCGAACTGGAAATGTTGATCCATCGAA-TGATGAATTTAAGC
* * *
2667558 AAAAGGTTGAACAAATTCTTCCCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTCT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* ** * * * * *
2667619 CATTATGAACTATACCTGGCAATGTTAATCCATCAAATTGATGAATTTTAAAC
63 TATTATGAACTCGAACTGGAAATGTTGATCCATCGAA-TGATGAA-TTTAAGC
* * * *
2667672 AAAAGGTTGCACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTTAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
* * *
2667737 TATGAACTCGAACTGGTAATGTTGATCCATTGAATGATGAATTCAAGC
66 TATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAGC
* * *
2667785 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGATTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
* * * * *
2667850 TATGAACTCTAACTGGTAATGTTGATCCATTGAATCATGAATTCAAGC
66 TATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAGC
**
2667898 AAAAAGTTGAGTAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
*
2667963 TATGAACTCGAACTGGAAATGTTGATCCACCGAATGATGAATTTAAGC
66 TATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAGC
*
2668011 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTT-TTCA
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT-A
* * *
2668075 TTTTGAACTCGAACTGGAAATGTTGATCCACCGAATGATGGATTTAAGC
65 TTATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAGC
* * * *
2668124 AAAAAGTTGAACAAGTTTTTCTCATTATGAACTTTTTCTGCCTTCTTCAGATGAATTCTTCTTAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
**** * * * *
2668189 TATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTT
66 TATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTT
2668233 GAATCTTTGC
Statistics
Matches: 595, Mismatches: 66, Indels: 24
0.87 0.10 0.04
Matches are distributed among these distances:
106 3 0.01
107 2 0.00
108 2 0.00
109 34 0.06
112 38 0.06
113 418 0.70
114 43 0.07
115 39 0.07
116 1 0.00
117 5 0.01
118 10 0.02
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
TATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAGC
Found at i:2669098 original size:115 final size:114
Alignment explanation
Indices: 2668937--2669166 Score: 363
Period size: 115 Copynumber: 2.0 Consensus size: 114
2668927 GATCATGCAG
* * * *
2668937 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCTTACCGAACCAGATCAGACAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGACAACTCAAAGA
2669002 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCACA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCACA
* * *
2669051 TTCATCTTTCAAATCCAATGATTAGTT-TTTAGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGT--GGTTCATACCAAACCAGATCAGACAACTCAAA
*
2669115 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
64 GAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCACA
2669166 T
1 T
2669167 GGCACTTGCT
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
113 2 0.02
114 24 0.23
115 80 0.75
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGACAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCACA
Found at i:2669205 original size:115 final size:113
Alignment explanation
Indices: 2668974--2669192 Score: 300
Period size: 115 Copynumber: 1.9 Consensus size: 113
2668964 CTGTGGTTCT
*
2668974 TACCGAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCT
1 TACCAAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCT
* * * ** *
2669039 ACTATGAGCACATTCATCTTTCAAATCCAATGATTAGTTTTTAGGGTTCA
66 ACTATGAGCACATGCATCTTGC--ATCCAATGAATAGTTTGGAGGATTCA
* *
2669089 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCT
1 TACCAAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCT
*
2669154 ACTATGAGCACATGGCA-CTTGC-TCCAATTAAT-GTTTGGA
66 ACTATGAGCACAT-GCATCTTGCATCCAATGAATAGTTTGGA
2669193 CTGGAATATC
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
111 5 0.05
112 8 0.09
115 79 0.84
116 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (113 bp):
TACCAAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCT
ACTATGAGCACATGCATCTTGCATCCAATGAATAGTTTGGAGGATTCA
Found at i:2677824 original size:15 final size:15
Alignment explanation
Indices: 2677801--2677832 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2677791 TGAAATGAAT
2677801 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2677816 AATGTATGTATGCAA
1 AATGAATGTATGCAA
2677831 AA
1 AA
2677833 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2681696 original size:23 final size:26
Alignment explanation
Indices: 2681653--2681702 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
2681643 GAAAAAAGAA
*
2681653 AAAATAATTTATATATATTTATAAAT
1 AAAATAATTTATATATATTTAGAAAT
2681679 AAAAT-ATTTAT-T-TATTTAGAAAT
1 AAAATAATTTATATATATTTAGAAAT
2681702 A
1 A
2681703 TCAGAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
AAAATAATTTATATATATTTAGAAAT
Found at i:2683358 original size:3 final size:3
Alignment explanation
Indices: 2683352--2683417 Score: 105
Period size: 3 Copynumber: 22.0 Consensus size: 3
2683342 TATTATTTTT
* *
2683352 TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2683400 TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
2683418 ATAAAAAAGG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2688240 original size:16 final size:16
Alignment explanation
Indices: 2688216--2688249 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2688206 TTAAGATTAA
*
2688216 AATTATTTTTTATTTT
1 AATTATTTTTAATTTT
*
2688232 AATTGTTTTTAATTTT
1 AATTATTTTTAATTTT
2688248 AA
1 AA
2688250 CACTAAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
AATTATTTTTAATTTT
Found at i:2708988 original size:144 final size:143
Alignment explanation
Indices: 2708728--2709057 Score: 617
Period size: 144 Copynumber: 2.3 Consensus size: 143
2708718 GACAATAACA
2708728 GCTTCCATCACCATATCCCTTGTTAGTAACTTCATAAGCTTTGTCACCACCATTCTCATCACCAC
1 GCTTCCATCACCATAT-CCTTGTTAGTAACTTCATAAGCTTTGTCACCACCATTCTCATCACCAC
2708793 CACCACTTCCAGCAGCCGATTTGTTTCGATTTGCAACAAAGAAACCCAAAACAAGGGCTGAAAGG
65 CACCACTTCCAGCAGCCGATTTGTTTCGATTTGCAACAAAGAAACCCAAAACAAGGGCTGAAAGG
2708858 TGTTGAATTTCGTT
130 TGTTGAATTTCGTT
2708872 GCTTCCATCACCATATCCGTTGTTAGTAACTTCATAAGCTTTGTCACCACCATTCTCATCACCAC
1 GCTTCCATCACCATATCC-TTGTTAGTAACTTCATAAGCTTTGTCACCACCATTCTCATCACCAC
2708937 CACCACTTCCAGCAGCCGATTTGTTTCGATTTGCAACAAAGAAACCCAAAACAAGGGCTGAAAGG
65 CACCACTTCCAGCAGCCGATTTGTTTCGATTTGCAACAAAGAAACCCAAAACAAGGGCTGAAAGG
2709002 TGTTGAATTTCGTT
130 TGTTGAATTTCGTT
2709016 GCTTCCATCACCATAT-CTCTGATTAGTAACTTCATAAGCTTT
1 GCTTCCATCACCATATCCT-TG-TTAGTAACTTCATAAGCTTT
2709058 TCCACATATT
Statistics
Matches: 183, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
142 1 0.01
143 5 0.03
144 177 0.97
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (143 bp):
GCTTCCATCACCATATCCTTGTTAGTAACTTCATAAGCTTTGTCACCACCATTCTCATCACCACC
ACCACTTCCAGCAGCCGATTTGTTTCGATTTGCAACAAAGAAACCCAAAACAAGGGCTGAAAGGT
GTTGAATTTCGTT
Found at i:2710932 original size:24 final size:24
Alignment explanation
Indices: 2710905--2710956 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2710895 TAACTCAAAA
2710905 TTAACAAATAA-ATATTTAAATATT
1 TTAACAAATAATATATTTAAA-ATT
* * *
2710929 TTAACATATAATTTTTTTAAAATT
1 TTAACAAATAATATATTTAAAATT
2710953 TTAA
1 TTAA
2710957 ATATAAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAACAAATAATATATTTAAAATT
Found at i:2711000 original size:34 final size:33
Alignment explanation
Indices: 2710961--2711025 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
2710951 TTTTAAATAT
* *
2710961 AAACTCTAATTTATATTTAAATAATAAAAATAAA
1 AAACTCTAACTTA-ATATAAATAATAAAAATAAA
* *
2710995 AAACTCTAACTTAATATAATTAGTAAAAATA
1 AAACTCTAACTTAATATAAATAATAAAAATA
2711026 TTAAAGACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (33 bp):
AAACTCTAACTTAATATAAATAATAAAAATAAA
Found at i:2712607 original size:29 final size:28
Alignment explanation
Indices: 2712561--2712758 Score: 242
Period size: 29 Copynumber: 7.0 Consensus size: 28
2712551 GACCCGACTC
*
2712561 GGTGATATTTTG-GAAATTATTTCGAAGAC
1 GGTGATATTTTGAG-AATTATTTCGAA-AA
2712590 GGTGATATTTTGAGAATTATTTCGAAAAA
1 GGTGATATTTTGAGAATTATTTCG-AAAA
*
2712619 GGTGATATTTTGGGAATTATTTCGAAAA
1 GGTGATATTTTGAGAATTATTTCGAAAA
* *
2712647 -GTGATATTTTGGGAATTATTACGAACAA
1 GGTGATATTTTGAGAATTATTTCGAA-AA
* *
2712675 TGTGATATTTT-AGGAATTATTTCAAAAAA
1 GGTGATATTTTGA-GAATTATTTC-GAAAA
* *
2712704 TGTGATATTTTGGGAATTATTTCGAAAA
1 GGTGATATTTTGAGAATTATTTCGAAAA
2712732 -GTGATATTTTGAGAATTATTTCGAAAA
1 GGTGATATTTTGAGAATTATTTCGAAAA
2712759 AATATTATTT
Statistics
Matches: 153, Mismatches: 9, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
27 50 0.33
28 10 0.07
29 88 0.58
30 5 0.03
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (28 bp):
GGTGATATTTTGAGAATTATTTCGAAAA
Found at i:2712680 original size:56 final size:54
Alignment explanation
Indices: 2712562--2712758 Score: 259
Period size: 56 Copynumber: 3.5 Consensus size: 54
2712552 ACCCGACTCG
* * *
2712562 GTGATATTTTGGAAATTATTTCGAAGACGGTGATATTTTGAGAATTATTTCGAAAAA
1 GTGATATTTTGGGAATTATTTCGAA-A-AGTGATATTTTGGGAATTATTTCG-AAAA
*
2712619 GGTGATATTTTGGGAATTATTTCGAAAAGTGATATTTTGGGAATTATTACGAACAA
1 -GTGATATTTTGGGAATTATTTCGAAAAGTGATATTTTGGGAATTATTTCGAA-AA
* *
2712675 TGTGATATTTTAGGAATTATTTCAAAAAATGTGATATTTTGGGAATTATTTCGAAAA
1 -GTGATATTTTGGGAATTATTTC-GAAAA-GTGATATTTTGGGAATTATTTCGAAAA
*
2712732 GTGATATTTTGAGAATTATTTCGAAAA
1 GTGATATTTTGGGAATTATTTCGAAAA
2712759 AATATTATTT
Statistics
Matches: 125, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
55 6 0.05
56 64 0.51
57 7 0.06
58 48 0.38
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.40
Consensus pattern (54 bp):
GTGATATTTTGGGAATTATTTCGAAAAGTGATATTTTGGGAATTATTTCGAAAA
Found at i:2712709 original size:85 final size:84
Alignment explanation
Indices: 2712562--2712798 Score: 316
Period size: 85 Copynumber: 2.8 Consensus size: 84
2712552 ACCCGACTCG
* ** * *
2712562 GTGATATTTTGGAAATTATTTCGAAGACGGTGATATTTT-GAGAATTATTTCGAAAAAGGTGATA
1 GTGATATTTTGGGAATTATTTCGAA-AAAGTGATATTTTAG-GAATTATTTCAAAAAATGTGATA
2712626 TTTTGGGAATTATTTCGAAAA
64 TTTTGGGAATTATTTCGAAAA
* *
2712647 GTGATATTTTGGGAATTATTACGAACAATGTGATATTTTAGGAATTATTTCAAAAAATGTGATAT
1 GTGATATTTTGGGAATTATTTCGAA-AAAGTGATATTTTAGGAATTATTTCAAAAAATGTGATAT
2712712 TTTGGGAATTATTTCGAAAA
65 TTTGGGAATTATTTCGAAAA
* * * * *
2712732 GTGATATTTTGAGAATTATTTCGAAAAAAT-ATTATTTTAGAAATTATTTTAAAAAATGTGTTAT
1 GTGATATTTTGGGAATTATTTCGAAAAAGTGA-TATTTTAGGAATTATTTCAAAAAATGTGATAT
2712796 TTT
65 TTT
2712799 CGTAATAATT
Statistics
Matches: 136, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
83 1 0.01
84 35 0.26
85 99 0.73
86 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (84 bp):
GTGATATTTTGGGAATTATTTCGAAAAAGTGATATTTTAGGAATTATTTCAAAAAATGTGATATT
TTGGGAATTATTTCGAAAA
Found at i:2712797 original size:29 final size:29
Alignment explanation
Indices: 2712562--2712798 Score: 139
Period size: 29 Copynumber: 8.3 Consensus size: 29
2712552 ACCCGACTCG
* ** * **
2712562 GTGATATTTTGGAAATTATTTCGAAGACG
1 GTGATATTTTAGAAATTATTTTAAAAAAT
** *
2712591 GTGATATTTT-GAGAATTATTTCGAAAAAG
1 GTGATATTTTAGA-AATTATTTTAAAAAAT
* * **
2712620 GTGATATTTTGGGAATTA-TTTCGAAAA-
1 GTGATATTTTAGAAATTATTTTAAAAAAT
* * *** *
2712647 GTGATATTTTGGGAATTATTACGAACAAT
1 GTGATATTTTAGAAATTATTTTAAAAAAT
* *
2712676 GTGATATTTTAGGAATTATTTCAAAAAAT
1 GTGATATTTTAGAAATTATTTTAAAAAAT
* * **
2712705 GTGATATTTTGGGAATTA-TTTCGAAAA-
1 GTGATATTTTAGAAATTATTTTAAAAAAT
*
2712732 GTGATATTTT-GAGAATTATTTCGAAAAAAT
1 GTGATATTTTAGA-AATTATTT-TAAAAAAT
*
2712762 AT--TATTTTAGAAATTATTTTAAAAAAT
1 GTGATATTTTAGAAATTATTTTAAAAAAT
*
2712789 GTGTTATTTT
1 GTGATATTTT
2712799 CGTAATAATT
Statistics
Matches: 171, Mismatches: 26, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
26 1 0.01
27 41 0.24
28 34 0.20
29 93 0.54
30 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (29 bp):
GTGATATTTTAGAAATTATTTTAAAAAAT
Found at i:2724266 original size:3 final size:3
Alignment explanation
Indices: 2724258--2724283 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2724248 TTTTTTCTTC
2724258 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2724284 ATACTGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2724668 original size:13 final size:13
Alignment explanation
Indices: 2724639--2724737 Score: 52
Period size: 13 Copynumber: 8.0 Consensus size: 13
2724629 AAATTATCAA
2724639 AATAAAATA-AAT
1 AATAAAATATAAT
*
2724651 -TTAAAATATAAT
1 AATAAAATATAAT
*
2724663 AATAAAA-A-AAG
1 AATAAAATATAAT
*
2724674 AATACAAAT-GAAT
1 AATA-AAATATAAT
* *
2724687 GACTAAATTATCAA-
1 -AATAAAATAT-AAT
2724701 AATAAAATA-AAT
1 AATAAAATATAAT
*
2724713 -TTAAAATATAAT
1 AATAAAATATAAT
*
2724725 AATAAAAAATAAT
1 AATAAAATATAAT
2724738 TTTTTAAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 21
0.66 0.12 0.22
Matches are distributed among these distances:
11 22 0.34
12 10 0.16
13 27 0.42
14 3 0.05
15 2 0.03
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (13 bp):
AATAAAATATAAT
Found at i:2724682 original size:62 final size:62
Alignment explanation
Indices: 2724607--2724733 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
2724597 TGATGCCAAT
2724607 AAAAGAATACAAATGAATGACTAAATTATCAAAATAAAATAAATTTAAAATATAATAATAAA
1 AAAAGAATACAAATGAATGACTAAATTATCAAAATAAAATAAATTTAAAATATAATAATAAA
2724669 AAAAGAATACAAATGAATGACTAAATTATCAAAATAAAATAAATTTAAAATATAATAATAAA
1 AAAAGAATACAAATGAATGACTAAATTATCAAAATAAAATAAATTTAAAATATAATAATAAA
2724731 AAA
1 AAA
2724734 TAATTTTTTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (62 bp):
AAAAGAATACAAATGAATGACTAAATTATCAAAATAAAATAAATTTAAAATATAATAATAAA
Found at i:2727497 original size:20 final size:20
Alignment explanation
Indices: 2727469--2727508 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2727459 TCCTAATTCA
*
2727469 CAATGCGAATACGTAAATCG
1 CAATACGAATACGTAAATCG
2727489 CAATACGAATACGTAAATCG
1 CAATACGAATACGTAAATCG
2727509 TAACGCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (20 bp):
CAATACGAATACGTAAATCG
Found at i:2727517 original size:20 final size:20
Alignment explanation
Indices: 2727473--2727518 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2727463 AATTCACAAT
*
2727473 GCGAATACGTAAATCGCAAT
1 GCGAATACGTAAATCGCAAC
* *
2727493 ACGAATACGTAAATCGTAAC
1 GCGAATACGTAAATCGCAAC
2727513 GCGAAT
1 GCGAAT
2727519 CTGACTATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
GCGAATACGTAAATCGCAAC
Found at i:2727528 original size:20 final size:20
Alignment explanation
Indices: 2727505--2727571 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
2727495 GAATACGTAA
* *
2727505 ATCGTAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
2727525 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2727545 ATCACAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2727565 ATCGCAA
1 ATCGCAA
2727572 TACTGAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2727882 original size:74 final size:74
Alignment explanation
Indices: 2727761--2727908 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
2727751 CGACATCCTT
*
2727761 CCCCATCCGGCAACAGGTTTTAGTTTCGCAGCTCGTTTGTTTAGTAAATTAATTTACAATAATGA
1 CCCCATCCAGCAACAGGTTTTAGTTTCGCAGCTCGTTTGTTTAGTAAATTAATTTACAATAATGA
2727826 AATCATCTA
66 AATCATCTA
*
2727835 CCCCATCCAGCAACATGTTTTAGTTTCGCAGCTCGTTTGTTTAGTAAATTAATTTACAATAATGA
1 CCCCATCCAGCAACAGGTTTTAGTTTCGCAGCTCGTTTGTTTAGTAAATTAATTTACAATAATGA
2727900 AATCATCTA
66 AATCATCTA
2727909 ATGTTGATCA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (74 bp):
CCCCATCCAGCAACAGGTTTTAGTTTCGCAGCTCGTTTGTTTAGTAAATTAATTTACAATAATGA
AATCATCTA
Found at i:2728519 original size:24 final size:24
Alignment explanation
Indices: 2728487--2728540 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2728477 GTATTCGAAA
2728487 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
2728511 TTTGATCTTGGTTAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2728535 TTTGAT
1 TTTGAT
2728541 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2730934 original size:20 final size:20
Alignment explanation
Indices: 2730909--2731017 Score: 166
Period size: 20 Copynumber: 5.5 Consensus size: 20
2730899 CAACGCGGAA
2730909 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
2730929 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
2730949 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
* *
2730969 ATCGTAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
2730989 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
2731009 ATCGCAACG
1 ATCGCAACG
2731018 AGAGAATCGC
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 77 0.96
21 3 0.04
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:2731129 original size:33 final size:33
Alignment explanation
Indices: 2731067--2731162 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
2731057 CTTAGTTTCG
* *
2731067 CGTTGAGATTTTCATTTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
2731101 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
2731134 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
2731163 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 33 0.59
34 23 0.41
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2731287 original size:14 final size:14
Alignment explanation
Indices: 2731268--2731304 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2731258 CATCAATTAA
2731268 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2731282 ACAAATCATCTTTT
1 ACAAATCAACATTT
2731296 ACAAATCAA
1 ACAAATCAA
2731305 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2733301 original size:20 final size:20
Alignment explanation
Indices: 2733278--2733343 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
2733268 ACTTAAAATT
2733278 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
2733298 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
* **
2733318 GCAATGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
2733338 GCAACG
1 GCAACG
2733344 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:2733407 original size:34 final size:34
Alignment explanation
Indices: 2733366--2733521 Score: 118
Period size: 34 Copynumber: 4.4 Consensus size: 34
2733356 TGCGATTTTC
2733366 ATTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
* *
2733400 AATTCGCATTGCGATAATCATTTTCGCATTGCGATAGTCA
1 ATTTCGCATTGCGAT--TC--TCTCG--TTGCGATAGTCA
* * * * * * * **
2733440 TTTTCGCGTTGTGATTTTGTTGTTGCGAT-TTTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
2733473 ATTTCGCATTGCGATTCTCTCGTTAG-GATAGTCA
1 ATTTCGCATTGCGATTCTCTCGTT-GCGATAGTCA
* *
2733507 TTTTCGCGTTGCGAT
1 ATTTCGCATTGCGAT
2733522 AGTCATTTTC
Statistics
Matches: 91, Mismatches: 23, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
33 22 0.24
34 36 0.40
36 5 0.05
38 5 0.05
40 23 0.25
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
Found at i:2733440 original size:20 final size:20
Alignment explanation
Indices: 2733388--2733544 Score: 101
Period size: 20 Copynumber: 8.5 Consensus size: 20
2733378 GATTCTCTCG
**
2733388 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2733408 TTGCGATAATCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2733428 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
2733448 TTGTGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
** *
2733462 TTGCGATTTTTA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2733481 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
2733495 TTAG-GATAGTCATTTTCGCG
1 TT-GCGATAGTCATTTTCGCA
2733515 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2733535 TTGCGATAGT
1 TTGCGATAGT
2733545 AAACTATTCT
Statistics
Matches: 110, Mismatches: 11, Indels: 32
0.72 0.07 0.21
Matches are distributed among these distances:
14 11 0.10
15 1 0.01
16 12 0.11
17 5 0.05
18 5 0.05
19 8 0.07
20 68 0.62
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2735469 original size:20 final size:20
Alignment explanation
Indices: 2735419--2735508 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
2735409 TCTGAAACTT
*
2735419 AAAATCACAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
2735439 AAAATCACAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
2735459 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
2735479 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
2735498 AAAATCGCAAC
1 AAAATCGCAAC
2735509 GACAGAATCG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 48 0.80
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:2735862 original size:22 final size:22
Alignment explanation
Indices: 2735837--2735898 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
2735827 ATTTCGCCGT
*
2735837 AGATGGAGATTGATATCGTC-A
1 AGATGGAGACTGATATCGTCGA
* *
2735858 GAGATGGGGACTGATTTCGTCGA
1 -AGATGGAGACTGATATCGTCGA
* *
2735881 AGATGGGGACGGATATCG
1 AGATGGAGACTGATATCG
2735899 CCTTAGAGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.37, T:0.24
Consensus pattern (22 bp):
AGATGGAGACTGATATCGTCGA
Found at i:2736139 original size:21 final size:21
Alignment explanation
Indices: 2736115--2736160 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2736105 TATTCGCATT
2736115 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
2736136 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2736157 GCGA
1 GCGA
2736161 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2749396 original size:12 final size:15
Alignment explanation
Indices: 2749352--2749393 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
2749342 TCTCATGAAA
*
2749352 GGAGAATAAGAGAGG
1 GGAGAAGAAGAGAGG
2749367 GGAGAAGAAGAGAGG
1 GGAGAAGAAGAGAGG
2749382 GGAGAAGAAGAG
1 GGAGAAGAAGAG
2749394 GGAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (15 bp):
GGAGAAGAAGAGAGG
Found at i:2749998 original size:9 final size:9
Alignment explanation
Indices: 2749969--2749998 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2749959 ATGATTTTGT
2749969 ATTTTTATA
1 ATTTTTATA
*
2749978 ATCTTTATA
1 ATTTTTATA
2749987 ATTTTTATA
1 ATTTTTATA
2749996 ATT
1 ATT
2749999 GAAATCTTAT
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:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:2755144 original size:30 final size:30
Alignment explanation
Indices: 2755082--2755299 Score: 171
Period size: 30 Copynumber: 7.3 Consensus size: 30
2755072 TTATTGAATT
**
2755082 TATTTTATTCTTTTCTTAAC-TA-AAATATA
1 TATTTTATTCTTACCTTAACTTATAAA-ATA
* *
2755111 TATTTTAATATTACCTTAACTTATAAAATA
1 TATTTTATTCTTACCTTAACTTATAAAATA
* *
2755141 TATTTTATTCCTACCTTAACTTA-ATAATA
1 TATTTTATTCTTACCTTAACTTATAAAATA
* *
2755170 TATTTTAATT-TTATCTTAACTTGAT-ACATA
1 TATTTT-ATTCTTACCTTAACTT-ATAAAATA
* * *
2755200 TATTATATTCTTAACTTATA-TTATTAAATA
1 TATTTTATTCTTACCTTA-ACTTATAAAATA
* * * *
2755230 TATTATATTTTTACCTTAAATTATTAAATA
1 TATTTTATTCTTACCTTAACTTATAAAATA
** *
2755260 T-TATTTATTCTTATATTAACTTAAAAATATA
1 TAT-TTTATTCTTACCTTAACTTATAAA-ATA
2755291 TATTTTATT
1 TATTTTATT
2755300 TTAATTTTAG
Statistics
Matches: 153, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
29 44 0.29
30 94 0.61
31 14 0.09
32 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (30 bp):
TATTTTATTCTTACCTTAACTTATAAAATA
Found at i:2755171 original size:59 final size:58
Alignment explanation
Indices: 2755082--2755302 Score: 214
Period size: 59 Copynumber: 3.7 Consensus size: 58
2755072 TTATTGAATT
* *
2755082 TATTTTATTCTTTTCTTAAC-TAAAATATATATTTTAATATTACCTTAACTTATAAAATA
1 TATTTTATTCTTATCTTAACTTAAAA-ATATATTTTAATTTTACCTTAACTTAT-AAATA
* * * * *
2755141 TATTTTATTCCTACCTTAACTTAATAATATATTTTAATTTTATCTTAACTTGATACATA
1 TATTTTATTCTTATCTTAACTTAAAAATATATTTTAATTTTACCTTAACTT-ATAAATA
* * * * * *
2755200 TATTATATTCTTAACTTATA-TTATTAAATATATTATATTTTTACCTTAAATTATTAAATA
1 TATTTTATTCTTATCTTA-ACTTA-AAAATATATTTTAATTTTACCTTAACTTA-TAAATA
* *
2755260 T-TATTTATTCTTATATTAACTTAAAAATATATATTTTATTTTA
1 TAT-TTTATTCTTATCTTAACTTAAAAATATAT-TTTAATTTTA
2755303 ATTTTAGAAA
Statistics
Matches: 130, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
59 73 0.56
60 57 0.44
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (58 bp):
TATTTTATTCTTATCTTAACTTAAAAATATATTTTAATTTTACCTTAACTTATAAATA
Found at i:2762500 original size:23 final size:23
Alignment explanation
Indices: 2762462--2762506 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2762452 GTACCATGTC
*
2762462 ATGTCAGCTACAATATCATCACT
1 ATGTCAGCTACAATATAATCACT
2762485 ATGTCAGCTATC-ATATAATCAC
1 ATGTCAGCTA-CAATATAATCAC
2762507 CTCATCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (23 bp):
ATGTCAGCTACAATATAATCACT
Found at i:2764259 original size:36 final size:36
Alignment explanation
Indices: 2764189--2764259 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 36
2764179 TATATTTTTT
*
2764189 ATTTTGTAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTGTAAAAAAATTATATAAATATTATCAATTTA
* *
2764225 ATTTT-TAAAGAAAA-TATATAATTATTTTACAATTT
1 ATTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
2764260 GTAATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (36 bp):
ATTTTGTAAAAAAATTATATAAATATTATCAATTTA
Found at i:2764282 original size:18 final size:18
Alignment explanation
Indices: 2764236--2764283 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2764226 TTTTTAAAGA
*
2764236 AAATATATAATTATTTTAC
1 AAATATATAA-TATTATAC
* *
2764255 -AATTTGTAATATTATAC
1 AAATATATAATATTATAC
2764272 AAATATATAATA
1 AAATATATAATA
2764284 AGAACAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
AAATATATAATATTATAC
Done.