Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 17
Found at i:2899108 original size:24 final size:24
Alignment explanation
Indices: 2899076--2899122 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2899066 GAAATAATAT
*
2899076 ATATTTACATAAAGTATA-ATAGAG
1 ATATGTACATAAA-TATATATAGAG
2899100 ATATGTACATAAATATATATAGA
1 ATATGTACATAAATATATATAGA
2899123 TTAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (24 bp):
ATATGTACATAAATATATATAGAG
Found at i:2905006 original size:33 final size:33
Alignment explanation
Indices: 2904964--2905030 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2904954 CCTAGTACAG
2904964 ATGGTGGACACGACCTTATGTGTCATACGAATT
1 ATGGTGGACACGACCTTATGTGTCATACGAATT
*
2904997 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGAATT
2905030 A
1 A
2905031 GCACTACGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGAATT
Found at i:2912288 original size:33 final size:33
Alignment explanation
Indices: 2912246--2912312 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2912236 CCTAGTACAG
* *
2912246 ATGGTGGACATGACCTTATGTGTCATATGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
2912279 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
2912312 A
1 A
2912313 GCACTACGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:2912440 original size:44 final size:40
Alignment explanation
Indices: 2912391--2912486 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 40
2912381 TGGTATATGG
* *
2912391 TTATGGAATAATGGCAAGTGTATTGGTTAAATAAGCTTACAAGC
1 TTATGG-ATAATGACAAGTATATTGG-T-AA-AAGCTTACAAGC
* *
2912435 TTATGGATAAATGATAAGTATATTGGTAAAAGCTTACGAGC
1 TTATGGAT-AATGACAAGTATATTGGTAAAAGCTTACAAGC
2912476 TTATGGGATAA
1 TTAT-GGATAA
2912487 ATGGTAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
41 17 0.37
42 6 0.13
43 3 0.07
44 20 0.43
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (40 bp):
TTATGGATAATGACAAGTATATTGGTAAAAGCTTACAAGC
Found at i:2912663 original size:18 final size:18
Alignment explanation
Indices: 2912636--2912671 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2912626 AAGTTTATAC
*
2912636 TTAGCGTGTGATGATTTT
1 TTAGCCTGTGATGATTTT
2912654 TTAGCCTGTGATGATTTT
1 TTAGCCTGTGATGATTTT
2912672 CACGCGTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.25, T:0.50
Consensus pattern (18 bp):
TTAGCCTGTGATGATTTT
Found at i:2922714 original size:16 final size:16
Alignment explanation
Indices: 2922695--2922727 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2922685 CATTAATGCA
2922695 CCTCCCTCTTAATTGC
1 CCTCCCTCTTAATTGC
2922711 CCTCCCTCTTAATTGC
1 CCTCCCTCTTAATTGC
2922727 C
1 C
2922728 TTATCGGTTA
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:0.12, C:0.45, G:0.06, T:0.36
Consensus pattern (16 bp):
CCTCCCTCTTAATTGC
Found at i:2922848 original size:17 final size:18
Alignment explanation
Indices: 2922815--2922849 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2922805 CAGGCGCAGT
*
2922815 CTCACTTGTCTTTAATAC
1 CTCACTTGTCTTAAATAC
2922833 CTCACTT-TCTTAAATAC
1 CTCACTTGTCTTAAATAC
2922850 TACTATCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.43
Consensus pattern (18 bp):
CTCACTTGTCTTAAATAC
Found at i:2925565 original size:23 final size:23
Alignment explanation
Indices: 2925534--2925577 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2925524 TAAAAAAAAT
2925534 TATTATCTAATGACAAATATTTAA
1 TATTATCTAATGA-AAATATTTAA
*
2925558 TATT-TCTAATGATAATATTT
1 TATTATCTAATGAAAATATTT
2925578 GTAACTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (23 bp):
TATTATCTAATGAAAATATTTAA
Found at i:2925988 original size:7 final size:7
Alignment explanation
Indices: 2925828--2926065 Score: 83
Period size: 7 Copynumber: 33.7 Consensus size: 7
2925818 ATATGATAAG
*
2925828 GTTTAGG
1 GTTTAGA
2925835 GTTTAGA
1 GTTTAGA
2925842 GTTTAG-
1 GTTTAGA
2925848 GATTTAGA
1 G-TTTAGA
*
2925856 GTTTA-T
1 GTTTAGA
*
2925862 GTGATATGA
1 GT-TTA-GA
2925871 -TTTA-A
1 GTTTAGA
*
2925876 GGTTTAGG
1 -GTTTAGA
2925884 GTTTATG-
1 GTTTA-GA
2925891 GTTTAGA
1 GTTTAGA
2925898 GTTTAGA
1 GTTTAGA
*
2925905 GTTTA-T
1 GTTTAGA
*
2925911 GTAATAG-
1 GT-TTAGA
2925918 GATTTA-A
1 G-TTTAGA
2925925 GGTTTAGA
1 -GTTTAGA
*
2925933 GTTTAGT
1 GTTTAGA
2925940 GTTTA-A
1 GTTTAGA
2925946 GGTTTAGA
1 -GTTTAGA
2925954 GTTTAG-
1 GTTTAGA
2925960 GTGTTA-A
1 GT-TTAGA
2925967 GGTTTAG-
1 -GTTTAGA
2925974 GATTTAGA
1 G-TTTAGA
2925982 GTTTAGA
1 GTTTAGA
* *
2925989 ATTCAGA
1 GTTTAGA
2925996 GTTTTAGA
1 G-TTTAGA
*
2926004 GTTTA-T
1 GTTTAGA
*
2926010 GTGATATGA
1 GT-TTA-GA
2926019 -TTTA-A
1 GTTTAGA
*
2926024 GGTTTATA
1 -GTTTAGA
*
2926032 GTTTAGG
1 GTTTAGA
2926039 GTTTAGA
1 GTTTAGA
* *
2926046 GTTCAAA
1 GTTTAGA
2926053 GTTTTAGA
1 G-TTTAGA
2926061 GTTTA
1 GTTTA
2926066 TGTAATATGA
Statistics
Matches: 173, Mismatches: 26, Indels: 64
0.66 0.10 0.24
Matches are distributed among these distances:
5 2 0.01
6 11 0.06
7 137 0.79
8 23 0.13
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (7 bp):
GTTTAGA
Found at i:2926037 original size:57 final size:57
Alignment explanation
Indices: 2925963--2926101 Score: 208
Period size: 57 Copynumber: 2.4 Consensus size: 57
2925953 AGTTTAGGTG
* * * *
2925963 TTAAGGTTTA-GGATTTAGAGTTTAGAATTCAGAGTTTTAGAGTTTATGTGATATGAT
1 TTAAGGTTTATAG-TTTAGGGTTTAGAATTCAAAGTTTTAGAGTTTATGTAATATGAT
*
2926020 TTAAGGTTTATAGTTTAGGGTTTAGAGTTCAAAGTTTTAGAGTTTATGTAATATGAT
1 TTAAGGTTTATAGTTTAGGGTTTAGAATTCAAAGTTTTAGAGTTTATGTAATATGAT
2926077 TTAAGGTTTATATGTTTAGGGTTTA
1 TTAAGGTTTATA-GTTTAGGGTTTA
2926102 TATGTTAAGG
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
57 62 0.83
58 13 0.17
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (57 bp):
TTAAGGTTTATAGTTTAGGGTTTAGAATTCAAAGTTTTAGAGTTTATGTAATATGAT
Found at i:2926099 original size:15 final size:15
Alignment explanation
Indices: 2926070--2926114 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
2926060 AGTTTATGTA
*
2926070 ATATGATTTAAGGTTT
1 ATATG-TTTAGGGTTT
2926086 ATATGTTTAGGGTTT
1 ATATGTTTAGGGTTT
*
2926101 ATATGTTAAGGGTT
1 ATATGTTTAGGGTT
2926115 AGGGGTTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (15 bp):
ATATGTTTAGGGTTT
Found at i:2928040 original size:11 final size:10
Alignment explanation
Indices: 2928024--2928111 Score: 50
Period size: 11 Copynumber: 7.8 Consensus size: 10
2928014 TAACCCATCC
2928024 TCGAGCTTAA
1 TCGAGCTTAA
*
2928034 GTCGAGCTCACAA
1 -TCGAGCT--TAA
2928047 TCGAGCTTGAA
1 TCGAGCTT-AA
*
2928058 TCGAGCTCACAA
1 TCGAGCT--TAA
2928070 TCGAGCTTGAA
1 TCGAGCTT-AA
*
2928081 TCGAGCTCAAAA
1 TCGAGCT--TAA
2928093 TCGAGCTTCAA
1 TCGAGCTT-AA
*
2928104 TTGAGCTT
1 TCGAGCTT
2928112 GAGTCTTGAG
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
11 34 0.56
12 25 0.41
13 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (10 bp):
TCGAGCTTAA
Found at i:2928052 original size:12 final size:12
Alignment explanation
Indices: 2928035--2928099 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 12
2928025 CGAGCTTAAG
2928035 TCGAGCTCACAA
1 TCGAGCTCACAA
**
2928047 TCGAGCT-TGAA
1 TCGAGCTCACAA
2928058 TCGAGCTCACAA
1 TCGAGCTCACAA
**
2928070 TCGAGCT-TGAA
1 TCGAGCTCACAA
*
2928081 TCGAGCTCAAAA
1 TCGAGCTCACAA
2928093 TCGAGCT
1 TCGAGCT
2928100 TCAATTGAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 18 0.42
12 25 0.58
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (12 bp):
TCGAGCTCACAA
Found at i:2928054 original size:23 final size:23
Alignment explanation
Indices: 2928024--2928110 Score: 131
Period size: 23 Copynumber: 3.8 Consensus size: 23
2928014 TAACCCATCC
2928024 TCGAGCTT-AAGTCGAGCTCACAA
1 TCGAGCTTGAA-TCGAGCTCACAA
2928047 TCGAGCTTGAATCGAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
*
2928070 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCACAA
* *
2928093 TCGAGCTTCAATTGAGCT
1 TCGAGCTTGAATCGAGCT
2928111 TGAGTCTTGA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 58 0.97
24 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCACAA
Found at i:2932383 original size:17 final size:18
Alignment explanation
Indices: 2932350--2932384 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2932340 CAGGCGCAGT
*
2932350 CTCACTTGTCTTTAATAC
1 CTCACTTGTCTTAAATAC
2932368 CTCACTT-TCTTAAATAC
1 CTCACTTGTCTTAAATAC
2932385 TACTATCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.43
Consensus pattern (18 bp):
CTCACTTGTCTTAAATAC
Found at i:2941540 original size:131 final size:131
Alignment explanation
Indices: 2941306--2941557 Score: 459
Period size: 131 Copynumber: 1.9 Consensus size: 131
2941296 TCTATGATAT
2941306 TTTATTTTAATTTATGATTGTCAATAGTCTTTTAATAGTTTAGTTTCATGTTGTAGTCCGACTGT
1 TTTATTTTAATTTATGATTGTCAATAGTCTTTTAATAGTTTAGTTTCATGTTGTAGTCCGACTGT
*
2941371 CGATGCAGTTATATTTATTTGTATTTATATCAAATGATTAGTTTATTATATTTGTTGTTACATCG
66 CGATGCAATTATATTTATTTGTATTTATATCAAATGATTAGTTTATTATATTTGTTGTTACATCG
2941436 A
131 A
* **
2941437 TTTATTTTAATTTATGATTTTCAATAGTCTTTTAATAGTTTAGTTTCATGTTGTAGTCCGTTTGT
1 TTTATTTTAATTTATGATTGTCAATAGTCTTTTAATAGTTTAGTTTCATGTTGTAGTCCGACTGT
*
2941502 CGATGCAATTATATTTATTTGTATTTATGTCAAATGATTAGTTTATTATATTTGTT
66 CGATGCAATTATATTTATTTGTATTTATATCAAATGATTAGTTTATTATATTTGTT
2941558 ATATCGAAAT
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
131 116 1.00
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (131 bp):
TTTATTTTAATTTATGATTGTCAATAGTCTTTTAATAGTTTAGTTTCATGTTGTAGTCCGACTGT
CGATGCAATTATATTTATTTGTATTTATATCAAATGATTAGTTTATTATATTTGTTGTTACATCG
A
Found at i:2942316 original size:22 final size:23
Alignment explanation
Indices: 2942279--2942324 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2942269 TTAAATATTC
*
2942279 AAAAACAAAGCTAAAG-AGATGAA
1 AAAAAAAAAGCTAAAGCA-ATGAA
2942302 AAAAAAAAAGC-AAAGCAATGAA
1 AAAAAAAAAGCTAAAGCAATGAA
2942324 A
1 A
2942325 TCTTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.70, C:0.09, G:0.15, T:0.07
Consensus pattern (23 bp):
AAAAAAAAAGCTAAAGCAATGAA
Found at i:2946731 original size:32 final size:32
Alignment explanation
Indices: 2946677--2946737 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2946667 AATATACGGT
2946677 TAAAAAAAAGTAGTATTAATTTTATTATTGGC
1 TAAAAAAAAGTAGTATTAATTTTATTATTGGC
* *
2946709 TAAAAAAAGGTGGTACTT-ATTTTATTATT
1 TAAAAAAAAGTAGTA-TTAATTTTATTATT
2946738 ATTGTGCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (32 bp):
TAAAAAAAAGTAGTATTAATTTTATTATTGGC
Found at i:2947369 original size:20 final size:20
Alignment explanation
Indices: 2947311--2947370 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2947301 TAAATATAAT
* *
2947311 AAAATAATATTATTTATTAAC
1 AAAATAAT-TTATTTAATATC
2947332 AAAATAATTT-TTTAAATATC
1 AAAATAATTTATTT-AATATC
*
2947352 AGAATAATTTATTTAATAT
1 AAAATAATTTATTTAATAT
2947371 TATTTATGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.09
20 20 0.59
21 11 0.32
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATAATTTATTTAATATC
Found at i:2947416 original size:28 final size:28
Alignment explanation
Indices: 2947381--2947470 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
2947371 TATTTATGTC
2947381 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
2947409 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
* ** *
2947437 TATATT-TTATTAAAATAAAATTATTAT
1 AATATTATTATTAAAATATTATGATTAT
2947464 AA-ATTAT
1 AATATTAT
2947471 ATTTATTATT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 3 0.06
27 17 0.36
28 25 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:2947473 original size:31 final size:31
Alignment explanation
Indices: 2947410--2947478 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
2947400 TATATCTATA
*
2947410 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
2947440 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
2947471 A-TTTATTA
1 ATTTTATTA
2947479 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:2948124 original size:21 final size:20
Alignment explanation
Indices: 2948100--2948138 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2948090 CAAATACAAT
*
2948100 AAAATAATATTATTTATTAAA
1 AAAATAATAATA-TTATTAAA
2948121 AAAATAATAATATTATTA
1 AAAATAATAATATTATTA
2948139 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATAATAATATTATTAAA
Found at i:2948132 original size:27 final size:25
Alignment explanation
Indices: 2948097--2948165 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
2948087 CATCAAATAC
2948097 AATAAAATAATATTATTTATTAAAAA
1 AATAAAATAATATTATTT-TTAAAAA
* *
2948123 AATAATAATATTATTATTTTTAAAAT
1 AATAA-AATAATATTATTTTTAAAAA
* *
2948149 ATTAGAATAAT-TTATTT
1 AATAAAATAATATTATTT
2948166 AATATTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 6 0.16
25 5 0.14
26 14 0.38
27 12 0.32
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (25 bp):
AATAAAATAATATTATTTTTAAAAA
Found at i:2948147 original size:24 final size:25
Alignment explanation
Indices: 2948097--2948166 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 25
2948087 CATCAAATAC
2948097 AATAAAATAATATTATTTATTAAAAA
1 AATAAAATAATATTATTTATT-AAAA
*
2948123 AATAATAATATTATTATTT-TTAAAA
1 AATAA-AATAATATTATTTATTAAAA
* *
2948148 TATTAGAATAAT-TTATTTA
1 -AATAAAATAATATTATTTA
2948167 ATATTATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
24 6 0.16
25 9 0.24
26 10 0.27
27 12 0.32
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (25 bp):
AATAAAATAATATTATTTATTAAAA
Found at i:2948177 original size:14 final size:14
Alignment explanation
Indices: 2948158--2948225 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
2948148 TATTAGAATA
2948158 ATTTATTTAATATT
1 ATTTATTTAATATT
2948172 ATTTA--T-ATA--
1 ATTTATTTAATATT
2948181 ATTTATTTAATATT
1 ATTTATTTAATATT
*
2948195 ATTTATGTCAATATT
1 ATTTAT-TTAATATT
*
2948210 A-TTATTAAAATATT
1 ATTTATT-TAATATT
2948224 AT
1 AT
2948226 ATCTATAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
9 5 0.11
11 4 0.09
12 4 0.09
13 1 0.02
14 22 0.50
15 8 0.18
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:2948181 original size:23 final size:23
Alignment explanation
Indices: 2948155--2948200 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2948145 AAATATTAGA
2948155 ATAATTTATTTAATATTATTTAT
1 ATAATTTATTTAATATTATTTAT
2948178 ATAATTTATTTAATATTATTTAT
1 ATAATTTATTTAATATTATTTAT
2948201 GTCAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATAATTTATTTAATATTATTTAT
Found at i:2948239 original size:28 final size:28
Alignment explanation
Indices: 2948204--2948293 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
2948194 TATTTATGTC
2948204 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
2948232 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
* ** *
2948260 TATATT-TTATTAAAATAAAATTATTAT
1 AATATTATTATTAAAATATTATGATTAT
2948287 AA-ATTAT
1 AATATTAT
2948294 ATTTATTATT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 3 0.06
27 17 0.36
28 25 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:2948296 original size:31 final size:31
Alignment explanation
Indices: 2948233--2948301 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
2948223 TATATCTATA
*
2948233 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
2948263 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
2948294 A-TTTATTA
1 ATTTTATTA
2948302 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:2948300 original size:40 final size:42
Alignment explanation
Indices: 2948247--2948338 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 42
2948237 TATAAATAAA
*
2948247 AAATTATGA-TTATTATATT-TTATTAA-AATAA-AAT-TATTAT
1 AAATTAT-ATTTATTAT-TTATTA-TAATAATAATAATATATCAT
2948287 AAATTATATTTATTATTTATTATAATAATAATAATATATCAT
1 AAATTATATTTATTATTTATTATAATAATAATAATATATCAT
*
2948329 TAATTATATT
1 AAATTATATT
2948339 ATAATGAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
39 6 0.13
40 22 0.49
41 3 0.07
42 14 0.31
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (42 bp):
AAATTATATTTATTATTTATTATAATAATAATAATATATCAT
Found at i:2948672 original size:16 final size:16
Alignment explanation
Indices: 2948651--2948681 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2948641 TTGTTATGCC
2948651 TAACAATAACAAAACA
1 TAACAATAACAAAACA
2948667 TAACAATAACAAAAC
1 TAACAATAACAAAAC
2948682 CAGTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.19, G:0.00, T:0.13
Consensus pattern (16 bp):
TAACAATAACAAAACA
Found at i:2949104 original size:31 final size:31
Alignment explanation
Indices: 2949024--2949109 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
2949014 TATTTTTATT
*
2949024 AAAA-TATTATATCTATAATTTTA-T-AAATAA
1 AAAATTATAATAT-TAT-ATTTTATTAAAATAA
2949054 AAAATTATAATTATTATATTTTATTAAAATAA
1 AAAATTATAA-TATTATATTTTATTAAAATAA
*
2949086 AATTATTATAA-ATTATA-TTTATTA
1 AA-AATTATAATATTATATTTTATTA
2949110 TTTATTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
30 17 0.35
31 14 0.29
32 11 0.22
33 7 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (31 bp):
AAAATTATAATATTATATTTTATTAAAATAA
Found at i:2949111 original size:33 final size:32
Alignment explanation
Indices: 2949041--2949109 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
2949031 TATATCTATA
2949041 ATTTTA-T-AAATAAAAAATTATAATTATTAT
1 ATTTTATTAAAATAAAAAATTATAATTATTAT
*
2949071 ATTTTATTAAAATAAAATTATTATAA--ATTAT
1 ATTTTATTAAAATAAAA-AATTATAATTATTAT
2949102 A-TTTATTA
1 ATTTTATTA
2949110 TTTATTATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 13 0.37
31 7 0.20
32 8 0.23
33 7 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
ATTTTATTAAAATAAAAAATTATAATTATTAT
Found at i:2949137 original size:808 final size:792
Alignment explanation
Indices: 2946850--2949264 Score: 3340
Period size: 789 Copynumber: 3.0 Consensus size: 792
2946840 ATTGTTGTGC
* * * * * *
2946850 ATAACAAAACCGGTAAAAATTACCGAAAACATCATTATTTTAACAAAATCAGTAAAGTGCTA-CT
1 ATAACAAAACCGATAAAAATTACCAAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTATCG
* ** *
2946914 AGTTTTGTTATTTTTTACCCGTTTTGTTATTGTTGGATATTTTACCGGAAATGTTAAAAAACATT
66 A-TTTTGTTA-TTTTTACCGGTTTTGTTATTGTTGGGCATTTTACCAGAAATGTTAAAAAACATT
* * * *
2946979 GATGTTTTAGGTAGAAATAATAATGTTTTAGGTAATTTTTA-TCAGTTTTGTTAT--AC-TC-AT
129 GATGTTTTAGGTAGAAATAATAATATTTTAGGTAATTTTTACT-GGTTTTGTTATGCCCAACAAT
* ** **
2947039 --GAATAACAAAACTGGTAAAAATA-ACATTTTTAATGATAAAATTAGTAAACACGTATTATACA
193 AACAATAACAAAACCAGTAAAAATAGAC-TTTTTAATGATAAAATTAGTAAACACAAATTATACA
* ** **
2947101 AAATAATTTTAATTTTTTAGTTTGTAAGTTGCCACAATATAACTAATGAAAAAGGGACACGATAT
257 AATTAATTTTAATTTTTTAGTTTGTAAGTTGCCACAATATAACTAATGAAAAA-AAACAAAATAT
* *
2947166 TTCTATTTCGATATTAGCTTTATAATAATAAAATAAAAAAATAAAAAAAATTATATATAATTGCA
321 TTCTATTTCGATATTAGC--T-T--T-CT-AAATAAAAAAAT-AAAAAAATTATATATAATTACA
2947231 ATATAATTTTAAAAAATAATCATAATGAAGTGATGAAAAATAATCATAATTACAATATAACTATA
378 ATATAATTTTAAAAAATAATCATAATGAAGTGATGAAAAATAATCATAATTACAATATAACTATA
* * *
2947296 AACATTAAATATAATAAAATAATATTATTTATTAAC-----AA-AATA--ATTTT-TTAAATATC
443 AACATCAAATACAATAAAATAATATTATTTATTAACAAAATAATAATATTATTTTGTTAAATATT
*
2947352 AGAATAATTTATTTAATATTATTTATGTCAATATTATTATTAAAATATTATATCTATAATTTTAT
508 ATAATAATTTATTTAATATTATTTATGTCAATATTATTATTAAAATATTATATCTATAATTTTAT
2947417 AAATAAAAAATTATGATTATTATATTTTATTAAAATAAAATTATTATAAATTATATTTATTATTT
573 AAATAAAAAATTATGATTATTATATTTTATTAAAATAAAATTATTATAAATTATATTTATTATTT
*
2947482 ATTATAATAAGAATAATATATCATTAATTATATTATAATGAGAGAATAGTTAAACATATGCGTCG
638 ATTATAATAAGAATAATATATCATTAATTATATTATAATGAGAGAATAGTTAAACATATGTGTCG
* * *
2947547 ATACATTTTGCTAAAAGTATCGAAATATATGTTACATCGAAACCGATAATTATAATATAATAGGT
703 ATACATTTT-CTAAAAGTATCG--ACACATGTTACATCGAAACTGATAATTATAATATAATAGGT
2947612 AAATTTACAATGTAACTGGTATACAACA
765 AAATTTACAATGTAACTGGTATACAACA
* *
2947640 ATAATAAAACCGATAAAAATTACCGAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTATCG
1 ATAACAAAACCGATAAAAATTACCAAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTATCG
*
2947705 ATTTTGTTATTTTTACCGGTTTTGTTATTGTTTGGCATTTTACCAGAAATGTTAAAAAACATTGA
66 ATTTTGTTATTTTTACCGGTTTTGTTATTGTTGGGCATTTTACCAGAAATGTTAAAAAACATTGA
*
2947770 TGTTTTAGGTAGAAATAATAATGTTTTAGGTAATTTTTACTGGTTTTGTTATGCCCAACAATAAC
131 TGTTTTAGGTAGAAATAATAATATTTTAGGTAATTTTTACTGGTTTTGTTATGCCCAACAATAAC
*
2947835 AA-AAC----CGA-TAAAAATAGACTTTTTAATGATAAAATTAGTAAACACAAATTATACAAATT
196 AATAACAAAACCAGTAAAAATAGACTTTTTAATGATAAAATTAGTAAACACAAATTATACAAATT
** **
2947894 AATTTTAATTTTTTAGTTTGTAAGTTATCACAATATAACTAATGAAAAAAAGGAC-ACGTATTTC
261 AATTTTAATTTTTTAGTTTGTAAGTTGCCACAATATAACTAATGAAAAAAA--ACAAAATATTTC
*
2947958 AATTTCGATATTAGCTTTCTATTAATAAAATAAAAAAAATAAAAAAATTTATATATAATTACAAT
324 TATTTCGATATTAGCTTTC------T-AAAT-AAAAAAATAAAAAAA-TTATATATAATTACAAT
* * *
2948023 ATAA-TTTAAAAAAAAATCATAATGAAGTGATGAAAAATAATAATAATTAGAATATAACTATAAA
380 ATAATTTTAAAAAATAATCATAATGAAGTGATGAAAAATAATCATAATTACAATATAACTATAAA
*
2948087 CATCAAATACAATAAAATAATATTATTTATTAAAAAAATAATAATATTATTATTTTTAAAATATT
445 CATCAAATACAATAAAATAATATTATTTATTAACAAAATAAT-A-A-TATTA----T----T-TT
2948152 AGAATAATTTATTTAATATTATTTATATAATTTATTTAATATTATTTATGTCAATATTATTATTA
498 -G------TTA---AATATTA--TA-ATAATTTATTTAATATTATTTATGTCAATATTATTATTA
2948217 AAATATTATATCTATAATTTTATAAATAAAAAATTATGATTATTATATTTTATTAAAATAAAATT
550 AAATATTATATCTATAATTTTATAAATAAAAAATTATGATTATTATATTTTATTAAAATAAAATT
*
2948282 ATTATAAATTATATTTATTATTTATTATAATAATAATAATATATCATTAATTATATTATAATGAG
615 ATTATAAATTATATTTATTATTTATTATAATAAGAATAATATATCATTAATTATATTATAATGAG
*
2948347 AGAATAGTTAAACATATGTGTAGATACATTTTCTAAAAGTATCGACACATGTTACATCGAAACTG
680 AGAATAGTTAAACATATGTGTCGATACATTTTCTAAAAGTATCGACACATGTTACATCGAAACTG
*
2948412 ATAATTATAATATAATAGGTAAATTTACAATGT-ACCGGTATACAACA
745 ATAATTATAATATAATAGGTAAATTTACAATGTAACTGGTATACAACA
*
2948459 ATAACAAAACCGGTAAAAATTACCAAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTA-CA
1 ATAACAAAACCGATAAAAATTACCAAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTATC-
* * *
2948523 GGTTTTGTTATTTTTTTACCGGTTTTGTTATTGTTGGGCATTTTACCGGAAATGTTAAAAAATAT
65 GATTTTGTTA--TTTTTACCGGTTTTGTTATTGTTGGGCATTTTACCAGAAATGTTAAAAAACAT
*
2948588 TGATGTTTTAGGTAGAAATAATAATATTTTAGGTAATTTTTACCGGTTTTGTTTTGTTATGCCTA
128 TGATGTTTTAGGTAGAAATAATAATATTTTAGGTAATTTTTA-C----TGGTTTTGTTATGCC--
*
2948653 ACAATAACAAAACATAACAATAACAAAACCAGTAAAAATAGACTTTTTAATAATAAAATTAGTAA
186 -C---AAC---A-ATAACAATAACAAAACCAGTAAAAATAGACTTTTTAATGATAAAATTAGTAA
* *
2948718 ACACAAACTATACAAATTAATTTTAATTTTTTAGTTTGTAAGTTGCCACAATCTAACTAATGAAA
243 ACACAAATTATACAAATTAATTTTAATTTTTTAGTTTGTAAGTTGCCACAATATAACTAATGAAA
2948783 AAATAACAAAATATTTCTATTTCGATATTAGCTTTCT-AATAAAAAAATAAAAAAATTATATATA
308 AAA-AACAAAATATTTCTATTTCGATATTAGCTTTCTAAATAAAAAAATAAAAAAATTATATATA
* * *
2948847 ATTACAATATAATTTTAAAAAATAATCATAATAAAGCGATGAAAAAAAATCATAATTACAATATA
372 ATTACAATATAATTTTAAAAAATAATCATAATGAAGTGATGAAAAATAATCATAATTACAATATA
* *
2948912 ATTACAAACATCAAATACAATAAAATAATATTATTTATTAACAAAATAATAATATTATTTTGTTA
437 ACTATAAACATCAAATACAATAAAATAATATTATTTATTAACAAAATAATAATATTATTTTGTTA
* *
2948977 AATATTATAATAATTTTTTTAATATTATTTATGTCAATATTTTTATTAAAATATTATATCTATAA
502 AATATTATAATAATTTATTTAATATTATTTATGTCAATATTATTATTAAAATATTATATCTATAA
*
2949042 TTTTATAAATAAAAAATTATAATTATTATATTTTATTAAAATAAAATTATTATAAATTATATTTA
567 TTTTATAAATAAAAAATTATGATTATTATATTTTATTAAAATAAAATTATTATAAATTATATTTA
* *
2949107 TTATTTATTATAATAAGAATAATATATCATTAATTATATTATAATAAGAGAATAATTAAACATAT
632 TTATTTATTATAATAAGAATAATATATCATTAATTATATTATAATGAGAGAATAGTTAAACATAT
*
2949172 GTGTCGATACATTTTCTAAAAGTATCGACACATATGTTACATCGAAACTGATAATTATAATGTAA
697 GTGTCGATACATTTTCTAAAAGTATCGACAC--ATGTTACATCGAAACTGATAATTATAATATAA
2949237 TAGGTAAATTTACAATGTAACTGGTATA
760 TAGGTAAATTTACAATGTAACTGGTATA
2949265 AATATACCGG
Statistics
Matches: 1461, Mismatches: 81, Indels: 145
0.87 0.05 0.09
Matches are distributed among these distances:
784 1 0.00
786 1 0.00
787 1 0.00
789 313 0.21
790 99 0.07
791 3 0.00
792 1 0.00
793 2 0.00
794 5 0.00
795 2 0.00
796 1 0.00
797 1 0.00
798 2 0.00
800 1 0.00
804 1 0.00
808 211 0.14
809 4 0.00
810 49 0.03
811 15 0.01
814 3 0.00
817 3 0.00
818 1 0.00
819 81 0.06
820 58 0.04
821 93 0.06
822 15 0.01
823 198 0.14
826 15 0.01
829 1 0.00
830 5 0.00
831 1 0.00
832 25 0.02
833 108 0.07
834 3 0.00
835 1 0.00
836 8 0.01
837 3 0.00
841 4 0.00
842 121 0.08
843 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (792 bp):
ATAACAAAACCGATAAAAATTACCAAAAACATCATTATTTTAACAAAACCGGTAAAGCGCTATCG
ATTTTGTTATTTTTACCGGTTTTGTTATTGTTGGGCATTTTACCAGAAATGTTAAAAAACATTGA
TGTTTTAGGTAGAAATAATAATATTTTAGGTAATTTTTACTGGTTTTGTTATGCCCAACAATAAC
AATAACAAAACCAGTAAAAATAGACTTTTTAATGATAAAATTAGTAAACACAAATTATACAAATT
AATTTTAATTTTTTAGTTTGTAAGTTGCCACAATATAACTAATGAAAAAAAACAAAATATTTCTA
TTTCGATATTAGCTTTCTAAATAAAAAAATAAAAAAATTATATATAATTACAATATAATTTTAAA
AAATAATCATAATGAAGTGATGAAAAATAATCATAATTACAATATAACTATAAACATCAAATACA
ATAAAATAATATTATTTATTAACAAAATAATAATATTATTTTGTTAAATATTATAATAATTTATT
TAATATTATTTATGTCAATATTATTATTAAAATATTATATCTATAATTTTATAAATAAAAAATTA
TGATTATTATATTTTATTAAAATAAAATTATTATAAATTATATTTATTATTTATTATAATAAGAA
TAATATATCATTAATTATATTATAATGAGAGAATAGTTAAACATATGTGTCGATACATTTTCTAA
AAGTATCGACACATGTTACATCGAAACTGATAATTATAATATAATAGGTAAATTTACAATGTAAC
TGGTATACAACA
Found at i:2949645 original size:197 final size:196
Alignment explanation
Indices: 2949210--2949697 Score: 599
Period size: 197 Copynumber: 2.5 Consensus size: 196
2949200 CACATATGTT
* * *
2949210 ACATCGAAACTGATAATTATAATGTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGT-ACCGGTATAAATATA-CAG
* * * *
2949275 TTTTATAAGATAATATGT-TAACATAATGTATCGAAACAAATTTAAAAAGTGTCGATACATTTTG
64 TTTTATAAGAAAATAGGTCT-ATATAATATATCG-AACAAATTTAAAAAGTGTCGATACATTTTG
*
2949339 TCCATAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCAATC
127 TCCATAATGAATGCCAAACAAGGTGCACGCATAAAGTGTCGATACATTTA-TAAAAGTATCAATC
2949404 CCAAAA
191 CCAAAA
* *
2949410 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCCGGTAGAAATATATCAG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTA-CCGGTATAAATATA-CAG
* * **** *
2949475 TTTTATGAGAAAATAGGTCTATATAATATATCG-ACACATTTATGTTTGTGTCGATAC-TTTTTT
64 TTTTATAAGAAAATAGGTCTATATAATATATCGAACAAATTTA-AAAAGTGTCGATACATTTTGT
* * *
2949538 CCATAATGAATGGCC-AACAAGGTGCACGCCTAAAGTGTCGATACATTTA-AAATTGTATCGATC
128 CCATAATGAAT-GCCAAACAAGGTGCACGCATAAAGTGTCGATACATTTATAAA-AGTATCAATC
2949601 CCAAAA
191 CCAAAA
* * * *
2949607 ACATCGAAACCGATGATTATAATGTAATAGGTAAATTTACAATATTACCGGTATAAATATACCGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAAT-GTACCGGTATAAATATACAGT
* *
2949672 TTTAGTTAGAAAATAGGTCAATATAA
65 TTTA-TAAGAAAATAGGTCTATATAA
2949698 GTGCTACCTA
Statistics
Matches: 252, Mismatches: 29, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
196 9 0.04
197 87 0.35
198 58 0.23
199 14 0.06
200 83 0.33
201 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (196 bp):
ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACCGGTATAAATATACAGTT
TTATAAGAAAATAGGTCTATATAATATATCGAACAAATTTAAAAAGTGTCGATACATTTTGTCCA
TAATGAATGCCAAACAAGGTGCACGCATAAAGTGTCGATACATTTATAAAAGTATCAATCCCAAA
A
Found at i:2949780 original size:64 final size:64
Alignment explanation
Indices: 2949702--2949922 Score: 379
Period size: 64 Copynumber: 3.5 Consensus size: 64
2949692 ATATAAGTGC
** * * *
2949702 TACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTTATAATATTTTCGGTTAAA
1 TACCTATTTTATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
2949766 TACCTATTTTATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
1 TACCTATTTTATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
*
2949830 TACCTATTTTATTATATAAGTGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
1 TACCTATTTTATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
*
2949894 TACCTATTTTATTATATAAGCGATACCTA
1 TACCTATTTTATTATATAAGCGCTACCTA
2949923 TTACATTATA
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 149 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.44
Consensus pattern (64 bp):
TACCTATTTTATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
Found at i:2949919 original size:23 final size:23
Alignment explanation
Indices: 2949893--2949954 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
2949883 TTCCGGTTAA
*
2949893 ATACCTATTTTATTATATAAGCG
1 ATACCTATTATATTATATAAGCG
*
2949916 ATACCTATTACATTATATAAGCG
1 ATACCTATTATATTATATAAGCG
* *
2949939 TTACCTAATATATTAT
1 ATACCTATTATATTAT
2949955 TGTACTTGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (23 bp):
ATACCTATTATATTATATAAGCG
Found at i:2949931 original size:87 final size:86
Alignment explanation
Indices: 2949829--2950067 Score: 334
Period size: 87 Copynumber: 2.8 Consensus size: 86
2949819 TTCCGGTTAA
* *
2949829 ATACCTATTTTATTATATAAGTGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
1 ATACCTA-TTAATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
*
2949894 TACCTATTTTATTATATAAGCG
65 TACATATTTTATTATATAAGCG
* * *
2949916 ATACCTATTACATTATATAAGCGTTACCTAATATATTATTGTACTTGATAATATTTCAGGTTAAA
1 ATACCTATTA-ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
2949981 TACATATTTTATTATATAAGCG
65 TACATATTTTATTATATAAGCG
* * * * * * * *
2950003 TTACCTATTAATTATATAAACGCTACTTAATATGATATTATACTTAAAAATATTTTCGGTTAAAT
1 ATACCTATTAATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAAT
2950068 GAATAACCAA
Statistics
Matches: 134, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
86 47 0.35
87 87 0.65
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (86 bp):
ATACCTATTAATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAAT
ACATATTTTATTATATAAGCG
Found at i:2953630 original size:19 final size:19
Alignment explanation
Indices: 2953608--2953647 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2953598 TAATTGTAAT
2953608 TAACCCTTTTCACCATTGG
1 TAACCCTTTTCACCATTGG
*
2953627 TAACTCTTTTCACCATTGG
1 TAACCCTTTTCACCATTGG
2953646 TA
1 TA
2953648 CTTCTAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.40
Consensus pattern (19 bp):
TAACCCTTTTCACCATTGG
Found at i:2955996 original size:36 final size:34
Alignment explanation
Indices: 2955954--2956022 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2955944 ATAATACCCC
2955954 TCTATATATAATTTTTTTCAATTAAGTCACTGTT
1 TCTATATATAATTTTTTTCAATTAAGTCACTGTT
2955988 TCTATATATAATTTTTTTCAATTAAGTCACTGTT
1 TCTATATATAATTTTTTTCAATTAAGTCACTGTT
2956022 T
1 T
2956023 TTATTGAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.54
Consensus pattern (34 bp):
TCTATATATAATTTTTTTCAATTAAGTCACTGTT
Found at i:2966154 original size:4 final size:4
Alignment explanation
Indices: 2966145--2966177 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
2966135 GTGTGGTTCA
*
2966145 AATT AATT AATT AATT AATT AATT AACT AATT A
1 AATT AATT AATT AATT AATT AATT AATT AATT A
2966178 TGCTTTTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (4 bp):
AATT
Found at i:2970943 original size:3 final size:3
Alignment explanation
Indices: 2970935--2970966 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2970925 AATCAAAGGT
2970935 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2970967 TATTGTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2973150 original size:11 final size:11
Alignment explanation
Indices: 2973131--2973160 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2973121 AAAATTCCCA
*
2973131 ATTGGATTCCT
1 ATTGCATTCCT
2973142 ATTGCATTCCT
1 ATTGCATTCCT
2973153 ATTGCATT
1 ATTGCATT
2973161 TGTGCTACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (11 bp):
ATTGCATTCCT
Found at i:2976320 original size:19 final size:19
Alignment explanation
Indices: 2976296--2976352 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
2976286 AATCAAGTCG
*
2976296 AGAACAAAAAAAAAAGAAA
1 AGAACAAAAGAAAAAGAAA
*
2976315 AGAACAAAGGAAAAAGAGAA
1 AGAACAAAAGAAAAAGA-AA
2976335 A-AA-AAAAGAAAAAGAAA
1 AGAACAAAAGAAAAAGAAA
2976352 A
1 A
2976353 ATGGGAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.09
18 11 0.32
19 17 0.50
20 3 0.09
ACGTcount: A:0.81, C:0.04, G:0.16, T:0.00
Consensus pattern (19 bp):
AGAACAAAAGAAAAAGAAA
Found at i:2976340 original size:12 final size:12
Alignment explanation
Indices: 2976301--2976353 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
2976291 AGTCGAGAAC
2976301 AAAAA-AAAAAG
1 AAAAAGAAAAAG
2976312 -AAAAGAACAAAGG
1 AAAAAGAA-AAA-G
2976325 AAAAAGAGAAAA-
1 AAAAAGA-AAAAG
2976337 AAAAAGAAAAAG
1 AAAAAGAAAAAG
2976349 AAAAA
1 AAAAA
2976354 TGGGAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
10 4 0.11
11 6 0.17
12 15 0.42
13 1 0.03
14 9 0.25
15 1 0.03
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:2976351 original size:24 final size:25
Alignment explanation
Indices: 2976306--2976370 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
2976296 AGAACAAAAA
2976306 AAAAAGAAAAGAACAAAGGAAAAA-GAG
1 AAAAA-AAAAGAA-AAAGGAAAAATG-G
2976333 AAAAAAAAAGAAAAA-GAAAAATGG
1 AAAAAAAAAGAAAAAGGAAAAATGG
* *
2976357 GAAAATAAAGAAAA
1 AAAAAAAAAGAAAA
2976371 CATATCAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 19 0.54
25 4 0.11
26 7 0.20
27 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAAAAAAAGAAAAAGGAAAAATGG
Found at i:2978870 original size:64 final size:66
Alignment explanation
Indices: 2978757--2978930 Score: 244
Period size: 64 Copynumber: 2.7 Consensus size: 66
2978747 TGAGATTATT
* *
2978757 TCTCAAAACAAAGTTTCGTCTCGTTTGAGACAATTTCCCTTGAACATAAACCTTTAAAATTGTTT
1 TCTCGAAACAAAGTTTCGTCTCGTTTGAGACAATTTCCCTTGAAAATAAACCTTTAAAATTGTTT
2978822 C
66 C
* * * * * *
2978823 TCTTGAAACAAAGTTTCGTCTTG-TTGGGACAATTTCTCTT-AAAATAAACCTTTGAGATTGTTT
1 TCTCGAAACAAAGTTTCGTCTCGTTTGAGACAATTTCCCTTGAAAATAAACCTTTAAAATTGTTT
2978886 C
66 C
* *
2978887 TCTCGAAACAAAGTTTCGTCTCGCTTGAGACAGTTTCCCTTGAA
1 TCTCGAAACAAAGTTTCGTCTCGTTTGAGACAATTTCCCTTGAA
2978931 GCCCATTTCG
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
64 42 0.45
65 29 0.31
66 22 0.24
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (66 bp):
TCTCGAAACAAAGTTTCGTCTCGTTTGAGACAATTTCCCTTGAAAATAAACCTTTAAAATTGTTT
C
Found at i:2979678 original size:135 final size:135
Alignment explanation
Indices: 2979467--2979721 Score: 336
Period size: 135 Copynumber: 1.9 Consensus size: 135
2979457 CCTCAATACA
* * * * * *
2979467 AAGGAACAATATCGTTCACCGATCATATCTCCTCAACGTAAAGGAGCATGTCATCCTCAGACAAT
1 AAGGAACAATATCGTCCACCGACCAGATCTCCTCAACATAAAGGAGCATGTCACCCTCAGACAAG
* * **
2979532 CATACTTCTCAATACGAAGAAACTGTGTTGTCT-TCAAATTATCCAAATACGTCTAGACTTCCTC
66 CAGACTTCTCAACACGAAGAAACCATGTTGTCTCT-AAATTATCCAAATACGTCTAGACTTCCTC
2979596 AACATG
130 AACATG
* * *
2979602 AAGGAACAATGTTGTCCACCGACCAGATCT-CTCAACAT-AAGGAGCAATGTTACCCTCAGACAA
1 AAGGAACAATATCGTCCACCGACCAGATCTCCTCAACATAAAGGAGC-ATGTCACCCTCAGACAA
*
2979665 GCAGACTTCCTCAACACGAAGGAACCATGTTGTCTCTAAATTATCCAAATACGTCTA
65 GCAGACTT-CTCAACACGAAGAAACCATGTTGTCTCTAAATTATCCAAATACGTCTA
2979722 AACGTTTCAT
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
133 7 0.07
134 28 0.27
135 67 0.65
136 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.25
Consensus pattern (135 bp):
AAGGAACAATATCGTCCACCGACCAGATCTCCTCAACATAAAGGAGCATGTCACCCTCAGACAAG
CAGACTTCTCAACACGAAGAAACCATGTTGTCTCTAAATTATCCAAATACGTCTAGACTTCCTCA
ACATG
Found at i:2979986 original size:102 final size:104
Alignment explanation
Indices: 2979762--2980000 Score: 293
Period size: 102 Copynumber: 2.3 Consensus size: 104
2979752 TCAGACGACC
* * * *
2979762 CGACTTCCTCAACAAGAAGGAACATCATCATATGAAAGCGACCAAAACTCTTCAACATGGATGAG
1 CGACTTCCTCAACAAGAAGGAACAACGTCATCTGAAAGCGACCAAAACTCTTCAACATGGATGAA
* * *
2979827 CAATGTCGTTTTCAACACCAGATTATCTCTAGATTGACT
66 CAATGACGTCTTCAACACCAAATTATCTCTAGATTGACT
* * * * *
2979866 CGAGTTCCTCAACAAGAA-GAACAACGTCATCTGAAAGTGGCCATAACT-TTCAACATTGATGAA
1 CGACTTCCTCAACAAGAAGGAACAACGTCATCTGAAAGCGACCAAAACTCTTCAACATGGATGAA
* *
2979929 CATTGACGTCTTCAACACCAAATTATCTCTATATTGACT
66 CAATGACGTCTTCAACACCAAATTATCTCTAGATTGACT
* ** * *
2979968 CGACTTCCTGAATGAGAAGGAATAATGTCATCT
1 CGACTTCCTCAACAAGAAGGAACAACGTCATCT
2980001 CAACAAAAAG
Statistics
Matches: 114, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
102 61 0.54
103 36 0.32
104 17 0.15
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.26
Consensus pattern (104 bp):
CGACTTCCTCAACAAGAAGGAACAACGTCATCTGAAAGCGACCAAAACTCTTCAACATGGATGAA
CAATGACGTCTTCAACACCAAATTATCTCTAGATTGACT
Found at i:2980108 original size:126 final size:126
Alignment explanation
Indices: 2979873--2980111 Score: 315
Period size: 126 Copynumber: 1.9 Consensus size: 126
2979863 ACTCGAGTTC
* * * *
2979873 CTCAACAAGAAGAACAACGTCATCTGAAAGTGGCCATAACTTTCAACATTGATGAACATTGACGT
1 CTCAACAAAAAGAACAACGTCATCTGAAAGCGGCCATAACTTTCAACATTGATGAACAATGACAT
* *
2979938 CTTCAACACCAAATTATCTCTATATTGACTCGACTTCCTGAATGAGAAGGAATAATGTCAT
66 CTTCAACACCAAATTATCTCCATATTGACCCGACTTCCTGAATGAGAAGGAATAATGTCAT
* * * *
2979999 CTCAACAAAAAGGAACAATGTCATCTGAAAGCGGCCATAACTCTTTAACA-TGAATGAGCAATGT
1 CTCAACAAAAA-GAACAACGTCATCTGAAAGCGGCCATAACT-TTCAACATTG-ATGAACAATGA
*
2980063 CATC-TCAACA-CAAATTATCTCCATATT-ACCCCGACTTCCTTAATGAGAA
63 CATCTTCAACACCAAATTATCTCCATATTGA-CCCGACTTCCTGAATGAGAA
2980112 TGAACAACTT
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
125 1 0.01
126 44 0.45
127 36 0.37
128 17 0.17
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (126 bp):
CTCAACAAAAAGAACAACGTCATCTGAAAGCGGCCATAACTTTCAACATTGATGAACAATGACAT
CTTCAACACCAAATTATCTCCATATTGACCCGACTTCCTGAATGAGAAGGAATAATGTCAT
Found at i:2981682 original size:51 final size:51
Alignment explanation
Indices: 2981554--2981683 Score: 181
Period size: 51 Copynumber: 2.5 Consensus size: 51
2981544 CTTGATGTGA
* *
2981554 TACTTTCAATTTATGCATTTTGGTCAATGTTTATTTATGATTAAGCTATTT
1 TACTTTCATTTTATGCATTTTGGTCACTGTTTATTTATGATTAAGCTATTT
* * * * *
2981605 TACTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTGATTTAGTTATTGT
1 TACTTTCATTTTATGCATTTTGGTCACTGTTTATTTATGATTAAGCTATT-T
2981657 T-CTTTCATTTTATGCATTTTGGTCACT
1 TACTTTCATTTTATGCATTTTGGTCACT
2981684 TGTTATGCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 67 0.97
52 2 0.03
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.56
Consensus pattern (51 bp):
TACTTTCATTTTATGCATTTTGGTCACTGTTTATTTATGATTAAGCTATTT
Found at i:2982857 original size:16 final size:16
Alignment explanation
Indices: 2982836--2982866 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2982826 ATAAATAAAC
*
2982836 GAACATAAATGAACAT
1 GAACATAAACGAACAT
2982852 GAACATAAACGAACA
1 GAACATAAACGAACA
2982867 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (16 bp):
GAACATAAACGAACAT
Found at i:2982962 original size:14 final size:14
Alignment explanation
Indices: 2982945--2982984 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2982935 AACAAACATA
*
2982945 AACGAACACGAACG
1 AACGAACACAAACG
*
2982959 AACGAACATAAACG
1 AACGAACACAAACG
2982973 AAC-AACACAAAC
1 AACGAACACAAAC
2982985 ACACAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.57, C:0.28, G:0.12, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:2983275 original size:12 final size:10
Alignment explanation
Indices: 2983248--2983291 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
2983238 AACATAAATG
2983248 AACGAACATA
1 AACGAACATA
2983258 AACGAACATA
1 AACGAACATA
*
2983268 TAATCGAACATT
1 -AA-CGAACATA
*
2983280 CACGAACATA
1 AACGAACATA
2983290 AA
1 AA
2983292 TGAATGAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 18 0.64
11 3 0.11
12 7 0.25
ACGTcount: A:0.55, C:0.20, G:0.09, T:0.16
Consensus pattern (10 bp):
AACGAACATA
Found at i:2986548 original size:18 final size:19
Alignment explanation
Indices: 2986503--2986541 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2986493 TATAAATCCA
2986503 TAATTTATTTTTAAAAATT
1 TAATTTATTTTTAAAAATT
*
2986522 TAATTTATTTTTAAATATT
1 TAATTTATTTTTAAAAATT
2986541 T
1 T
2986542 GATTATTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATTTATTTTTAAAAATT
Found at i:2986766 original size:5 final size:5
Alignment explanation
Indices: 2986756--2986806 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
2986746 ATCTATTGAT
2986756 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2986806 A
1 A
2986807 AAAGCCATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:2992149 original size:20 final size:20
Alignment explanation
Indices: 2992105--2992402 Score: 152
Period size: 20 Copynumber: 14.6 Consensus size: 20
2992095 AATGACCAAT
* *
2992105 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
2992124 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* ** ***
2992144 AAAATCACAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
2992164 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
2992184 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
2992205 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * * *
2992228 AAAATTGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
2992248 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
2992268 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
2992288 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2992311 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
2992331 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
2992351 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
2992371 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
2992391 AAAATCGTAACG
1 AAAATCGCAACG
2992403 TTAAAAAGAA
Statistics
Matches: 217, Mismatches: 50, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
19 17 0.08
20 158 0.73
21 14 0.06
23 28 0.13
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2992296 original size:40 final size:40
Alignment explanation
Indices: 2992209--2992389 Score: 236
Period size: 40 Copynumber: 4.4 Consensus size: 40
2992199 GCTTCCAAGT
* * *
2992209 TCGCAACGCGATTTAGAAGAAAATTGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTA-TAG--AATCGCAATGCGATTGAGAGAA
* *
2992252 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTATAGAATCGCAATGCGATTGAGAGAA
* *
2992292 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTA-TAG--AATCGCAATGCGATTGAGAGAA
*
2992335 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTATAGAATCGCAATGCGATTGAGAGAA
2992375 TCGCAACGCGATTTA
1 TCGCAACGCGATTTA
2992390 GAAAATCGTA
Statistics
Matches: 122, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
40 68 0.56
41 2 0.02
42 4 0.03
43 48 0.39
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (40 bp):
TCGCAACGCGATTTATAGAATCGCAATGCGATTGAGAGAA
Found at i:2992314 original size:83 final size:83
Alignment explanation
Indices: 2992209--2992392 Score: 332
Period size: 83 Copynumber: 2.2 Consensus size: 83
2992199 GCTTCCAAGT
* * *
2992209 TCGCAACGCGATTTAGAAGAAAATTGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
*
2992274 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAA
2992292 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
2992357 GCAATGCGATTGAGAGAA
66 GCAATGCGATTGAGAGAA
2992375 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
2992393 AATCGTAACG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 97 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
GCAATGCGATTGAGAGAA
Found at i:2992429 original size:20 final size:20
Alignment explanation
Indices: 2992389--2992430 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2992379 AACGCGATTT
* *
2992389 AGAAAATCGTAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
2992409 AGAAAATCGCAACGGTCAAAA
1 AGAAAATCGCAACGGT-AAAA
2992430 A
1 A
2992431 AATAGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:2992521 original size:6 final size:6
Alignment explanation
Indices: 2992510--2992563 Score: 99
Period size: 6 Copynumber: 9.0 Consensus size: 6
2992500 GACACGTATT
*
2992510 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG CCCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2992558 ACCACG
1 ACCACG
2992564 CCCAGTCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2996065 original size:14 final size:14
Alignment explanation
Indices: 2996046--2996072 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2996036 TCAAAAAATA
2996046 TTAAATTAATATAT
1 TTAAATTAATATAT
2996060 TTAAATTAATATA
1 TTAAATTAATATA
2996073 AATATTAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAATTAATATAT
Found at i:2996091 original size:24 final size:24
Alignment explanation
Indices: 2996064--2996126 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
2996054 ATATATTTAA
2996064 ATTAATATAAATATTAAAGTATAC
1 ATTAATATAAATATTAAAGTATAC
* *
2996088 ATTAATATAAATATTAAATTATAT
1 ATTAATATAAATATTAAAGTATAC
*
2996112 ATTTAAAATAAATAT
1 A-TTAATATAAATAT
2996127 ATATTGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 23 0.66
25 12 0.34
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
ATTAATATAAATATTAAAGTATAC
Found at i:2997755 original size:56 final size:56
Alignment explanation
Indices: 2997669--2997779 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
2997659 GGACTTAAGC
*
2997669 TAAGAATCATTTATCTTGAAAGTTCATAAGCTCCTTTAGTCTTGTCTGAGATGTTG
1 TAAGAATCATTTATCCTGAAAGTTCATAAGCTCCTTTAGTCTTGTCTGAGATGTTG
2997725 TAAGAATCATTTATCCTGAAAGTTCATAAGCTCCTTTAGTCTTGTCTGAGATGTT
1 TAAGAATCATTTATCCTGAAAGTTCATAAGCTCCTTTAGTCTTGTCTGAGATGTT
2997780 TTCTCACACT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (56 bp):
TAAGAATCATTTATCCTGAAAGTTCATAAGCTCCTTTAGTCTTGTCTGAGATGTTG
Found at i:3005742 original size:50 final size:51
Alignment explanation
Indices: 3005667--3005766 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 51
3005657 ACATTTTTAC
3005667 ATACGTAAATGCCATGCATGTATATGTTAAGCTCTATGTTTGATT-TAGAG
1 ATACGTAAATGCCATGCATGTATATGTTAAGCTCTATGTTTGATTATAGAG
3005717 ATACGTAAATGCCATGCATGTATATGTTAAGCTCTATGTTTGATTATAGA
1 ATACGTAAATGCCATGCATGTATATGTTAAGCTCTATGTTTGATTATAGA
3005767 AACTCTGAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 45 0.92
51 4 0.08
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (51 bp):
ATACGTAAATGCCATGCATGTATATGTTAAGCTCTATGTTTGATTATAGAG
Found at i:3008360 original size:20 final size:21
Alignment explanation
Indices: 3008315--3008366 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
3008305 GTGTATTCTC
*
3008315 ATTTT-ATAATAATTTATTAA
1 ATTTTAATAATAATTTATAAA
*
3008335 A-TTTAATAATTATTT-TAAA
1 ATTTTAATAATAATTTATAAA
*
3008354 ATTTTAATGATAA
1 ATTTTAATAATAA
3008367 AAAATGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTAATAATAATTTATAAA
Found at i:3011643 original size:18 final size:18
Alignment explanation
Indices: 3011622--3011675 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
3011612 ACCATAATGG
*
3011622 TATTTAAATAATATTATT
1 TATTAAAATAATATTATT
3011640 TATTAAAATAATATTATT
1 TATTAAAATAATATTATT
3011658 TATTAAAATAATA-TATT
1 TATTAAAATAATATTATT
3011675 T
1 T
3011676 TTTATAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
17 5 0.14
18 30 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTAAAATAATATTATT
Found at i:3011657 original size:21 final size:20
Alignment explanation
Indices: 3011632--3011680 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
3011622 TATTTAAATA
3011632 ATATTATTTATTAAAAT-A-
1 ATATTATTTATTAAAATAAT
3011650 ATATTATTTATTAAAATAAT
1 ATATTATTTATTAAAATAAT
*
3011670 ATATTTTTTAT
1 ATATTATTTAT
3011681 AAACACGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 17 0.61
19 1 0.04
20 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTATTTATTAAAATAAT
Found at i:3016594 original size:23 final size:23
Alignment explanation
Indices: 3016568--3016618 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3016558 TACATTTTTA
3016568 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAATT
* **
3016591 ATATTATAATAATATAATTGATT
1 ATATTATAATAAAATAATCAATT
3016614 ATATT
1 ATATT
3016619 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAATT
Found at i:3017156 original size:14 final size:15
Alignment explanation
Indices: 3017120--3017163 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
3017110 TTTTAGAAAT
*
3017120 GTAATTCATTTTCCA
1 GTAATTCATTTTTCA
3017135 GTAATTCATTTTTCA
1 GTAATTCATTTTTCA
*
3017150 G-AATTCAATTTTCA
1 GTAATTCATTTTTCA
3017164 AAAAACCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.48
Consensus pattern (15 bp):
GTAATTCATTTTTCA
Found at i:3017473 original size:26 final size:26
Alignment explanation
Indices: 3017437--3017493 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
3017427 TGACAACTTG
3017437 CAAGATTGGTTAAATATTCTAATTAA
1 CAAGATTGGTTAAATATTCTAATTAA
3017463 CAAGATTGGTTAAATATTCTAATTAA
1 CAAGATTGGTTAAATATTCTAATTAA
3017489 CAAGA
1 CAAGA
3017494 AAAAGACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (26 bp):
CAAGATTGGTTAAATATTCTAATTAA
Found at i:3020148 original size:108 final size:108
Alignment explanation
Indices: 3019865--3020155 Score: 330
Period size: 108 Copynumber: 2.6 Consensus size: 108
3019855 TATTTTCCAG
* * ** ***
3019865 AACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGCGGT
1 AACCATACACCCACCAGCACACCAGTAAGGACTTACCCTAAGCACAAAGCAAAGGAGCCTGAAAT
* *
3019930 AATAACTTTCCCATCCAATCACTCCAATCACCAAAATGTGTAGGTTCCCCAT
66 AATAAC-TT----TCC---CA-TCCAATCACCAAAATGTATAGGTTCCCCAA
* * * * ** *
3019982 AACTATACACCCACCTGCACACCAGTAAGGACTTACTCTGAGCACAAAGCCGAGGAGCCTGCAAT
1 AACCATACACCCACCAGCACACCAGTAAGGACTTACCCTAAGCACAAAGCAAAGGAGCCTGAAAT
3020047 AATAACTTTCCCATCCAATCACCAAAATGTATAGGTTCCCCAA
66 AATAACTTTCCCATCCAATCACCAAAATGTATAGGTTCCCCAA
* * *
3020090 AACCATACACCCACCAGCACACCAGTAATGACTTACCCTAAGCACACAGCAAATGAGCCTGAAAT
1 AACCATACACCCACCAGCACACCAGTAAGGACTTACCCTAAGCACAAAGCAAAGGAGCCTGAAAT
3020155 A
66 A
3020156 CTTCCCTCAA
Statistics
Matches: 158, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
108 84 0.53
109 2 0.01
112 3 0.02
116 2 0.01
117 67 0.42
ACGTcount: A:0.35, C:0.33, G:0.14, T:0.18
Consensus pattern (108 bp):
AACCATACACCCACCAGCACACCAGTAAGGACTTACCCTAAGCACAAAGCAAAGGAGCCTGAAAT
AATAACTTTCCCATCCAATCACCAAAATGTATAGGTTCCCCAA
Found at i:3021062 original size:13 final size:13
Alignment explanation
Indices: 3021044--3021074 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3021034 TATGGTCAAC
*
3021044 GGTCAACGGGTCG
1 GGTCAACGGGTAG
3021057 GGTCAACGGGTAG
1 GGTCAACGGGTAG
3021070 GGTCA
1 GGTCA
3021075 GGTCGGACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTAG
Found at i:3027447 original size:117 final size:117
Alignment explanation
Indices: 3027149--3027432 Score: 444
Period size: 117 Copynumber: 2.4 Consensus size: 117
3027139 TATATATTTT
* * *
3027149 CCAGAACCATACACCCACCTGCACACCAGTAAGAACTTACCCTGAGCACAAAGCCGAGGAGCTTA
1 CCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
* * *
3027214 CGGTAATAATTTTCCCATCCAATCACTCCGATCACCAAAATGTGTAGGTTCC
66 CGGTAATAACTTTCCCATCCAATCACTCCAATCACCAAAATATGTAGGTTCC
* * * *
3027266 CCATAACCATACACTCACCTGCATACCAGTAAGGACTTGCCCTGAGCACAAAGCCGAGGAGCCTG
1 CCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
3027331 CGGTAATAACTTTCCCATCCAATCACTCCAATCACCAAAATATGTATGG-TCC
66 CGGTAATAACTTTCCCATCCAATCACTCCAATCACCAAAATATGTA-GGTTCC
* *
3027383 CCAGAACCATACACCCACCAGCACACCAGTAAGGACTTACCCTAAGCACA
1 CCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACA
3027433 CAACAAATGA
Statistics
Matches: 150, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
117 148 0.99
118 2 0.01
ACGTcount: A:0.33, C:0.34, G:0.15, T:0.18
Consensus pattern (117 bp):
CCAGAACCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
CGGTAATAACTTTCCCATCCAATCACTCCAATCACCAAAATATGTAGGTTCC
Found at i:3034589 original size:54 final size:54
Alignment explanation
Indices: 3034453--3034590 Score: 188
Period size: 54 Copynumber: 2.6 Consensus size: 54
3034443 GATAGATGGT
* * * * *
3034453 GTGCCCACGCCTTAACTGAAGGCTTCTTATGCGGTAGTTCTGGATGAATAAGCC
1 GTGCCCACGCCTTAACTGAAGACTTCTTCTACGGTAGCTCTGGATAAATAAGCC
* * *
3034507 GTGCTCACGCCTTAACTGGAGACTTCTTCTACGGTAGCTCAT-GATAAATAAGTC
1 GTGCCCACGCCTTAACTGAAGACTTCTTCTACGGTAGCTC-TGGATAAATAAGCC
3034561 GTGCCCACGCCTTAACTGAAGACTTCTTCT
1 GTGCCCACGCCTTAACTGAAGACTTCTTCT
3034591 GTGTTAGGTC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 72 0.99
55 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (54 bp):
GTGCCCACGCCTTAACTGAAGACTTCTTCTACGGTAGCTCTGGATAAATAAGCC
Found at i:3036199 original size:29 final size:28
Alignment explanation
Indices: 3036152--3036260 Score: 89
Period size: 29 Copynumber: 3.7 Consensus size: 28
3036142 TGACTCGTGT
* *
3036152 TTTAAATTGATCCCTAAACTTTTAAATA
1 TTTAAATTCATCCCCAAACTTTTAAATA
*
3036180 TTTAAATTTCATCCCCAAAC-TATAACTATCA
1 TTTAAA-TTCATCCCCAAACTTTTAA--AT-A
3036211 TTCTAAATT-AGTCCCCAAACTTTTGAACAT-
1 TT-TAAATTCA-TCCCCAAACTTTT-AA-ATA
*
3036241 TTTAATTTCATCCCCAAACT
1 TTTAAATTCATCCCCAAACT
3036261 ATGGCTTTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
28 10 0.15
29 26 0.39
30 6 0.09
31 14 0.21
32 8 0.12
33 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39
Consensus pattern (28 bp):
TTTAAATTCATCCCCAAACTTTTAAATA
Found at i:3036234 original size:60 final size:59
Alignment explanation
Indices: 3036154--3036324 Score: 191
Period size: 60 Copynumber: 2.8 Consensus size: 59
3036144 ACTCGTGTTT
* *
3036154 TAAATTGATCCCTAAACTTTTAAATATTTAAATTTCATCCCCAAACTATAACTATCATTC
1 TAAATTG-TCCCCAAACTTTTAAACATTTAAATTTCATCCCCAAACTATAACTATCATTC
* * ** *
3036214 TAAATTAGTCCCCAAACTTTTGAACATTTTAATTTCATCCCCAAACTATGGCTTTCATTC
1 TAAATT-GTCCCCAAACTTTTAAACATTTAAATTTCATCCCCAAACTATAACTATCATTC
* ** *
3036274 TAAATTGGTCCCCCAAACTTTTTGAACATTCCAATTTGA-CCCCAAACTATA
1 TAAATT-GT-CCCCAAAC-TTTTAAACATTTAAATTTCATCCCCAAACTATA
3036325 CACGTATATT
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
60 59 0.61
61 20 0.21
62 17 0.18
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (59 bp):
TAAATTGTCCCCAAACTTTTAAACATTTAAATTTCATCCCCAAACTATAACTATCATTC
Found at i:3036320 original size:61 final size:60
Alignment explanation
Indices: 3036184--3036324 Score: 194
Period size: 60 Copynumber: 2.3 Consensus size: 60
3036174 TAAATATTTA
**
3036184 AATTTCATCCCCAAACTATAACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTTT
1 AATTTCATCCCCAAACTATAACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTCC
** * *
3036244 AATTTCATCCCCAAACTATGGCTTTCATTCTAAATTGGTCCCCCAAACTTTTTGAACATTCC
1 AATTTCATCCCCAAACTATAACTATCATTCTAAATTAGT-CCCCAAAC-TTTTGAACATTCC
*
3036306 AATTTGA-CCCCAAACTATA
1 AATTTCATCCCCAAACTATA
3036325 CACGTATATT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
60 35 0.49
61 19 0.27
62 17 0.24
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.35
Consensus pattern (60 bp):
AATTTCATCCCCAAACTATAACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTCC
Found at i:3036573 original size:60 final size:60
Alignment explanation
Indices: 3036472--3036623 Score: 148
Period size: 60 Copynumber: 2.5 Consensus size: 60
3036462 ATAAAATTAG
* ** ** * *
3036472 AATATTCAAAAGTTTGGGGACTAATTTAGAAAGAGGGTCATAGTCTAG-GGATGAACTCAG
1 AATACTCAAAAGTTTAAGGACTAATTTAGAAAGAGAATCATAGT-TAGAGGATGAAATCAA
* * *
3036532 AATGCTCAAAAGTTTAAGGACTAATTTAGAATA-AGAATCATAGTTTGAGGATGAAATTAA
1 AATACTCAAAAGTTTAAGGACTAATTTAGAA-AGAGAATCATAGTTAGAGGATGAAATCAA
* * *
3036592 AATATTCAAAAATTTAAGGATTAATTTA-AAAG
1 AATACTCAAAAGTTTAAGGACTAATTTAGAAAG
3036624 GAAGTTTATA
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
58 1 0.01
59 4 0.05
60 69 0.92
61 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (60 bp):
AATACTCAAAAGTTTAAGGACTAATTTAGAAAGAGAATCATAGTTAGAGGATGAAATCAA
Found at i:3038803 original size:20 final size:21
Alignment explanation
Indices: 3038763--3038809 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
3038753 TATATTTATA
3038763 TAAAAAAGTATAATAAGATAC
1 TAAAAAAGTATAATAAGATAC
3038784 TAAAAAAGTATAATAA-ATAC
1 TAAAAAAGTATAATAAGATAC
3038804 -AAAAAA
1 TAAAAAA
3038810 CGGAAAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 16 0.62
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.21
Consensus pattern (21 bp):
TAAAAAAGTATAATAAGATAC
Found at i:3040778 original size:105 final size:105
Alignment explanation
Indices: 3040607--3041208 Score: 1033
Period size: 105 Copynumber: 5.7 Consensus size: 105
3040597 TGACAGTCAA
*** *
3040607 CGGTCCCTTCGTCGTGAAGTTGAACTTATACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
*
3040672 AAATTGGCTCTGAAATTGAGAAATGTTGGTTGACAACCAG
66 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAG
3040712 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
* ** *
3040777 AAATTGACTCTGGGATTGAGAAATGGTTGTTGACAACCAG
66 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAG
*
3040817 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGGGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
3040882 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAG
66 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAG
*
3040922 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
*
3040987 AAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAACCAG
66 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAG
* *
3041027 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
* *
3041092 AAATTGGCTCTGAAATTAAGAAATGTTTATTGACAACCAG
66 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAG
* * *
3041132 TGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
1 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
3041197 AAATTGGCTCTG
66 AAATTGGCTCTG
3041209 GGTAAAACCT
Statistics
Matches: 473, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 473 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAG
Found at i:3042043 original size:47 final size:49
Alignment explanation
Indices: 3041968--3042062 Score: 131
Period size: 47 Copynumber: 2.0 Consensus size: 49
3041958 ATTTTCCCTT
* * *
3041968 CTTTTTTCTTTTCTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAA
1 CTTTTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAA
* *
3042017 CTTTTTT-TTTTC-CGACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 CTTTTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
3042063 GCGAAGTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 29 0.71
48 5 0.12
49 7 0.17
ACGTcount: A:0.14, C:0.27, G:0.15, T:0.44
Consensus pattern (49 bp):
CTTTTTTCTTTTCTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAA
Found at i:3053246 original size:20 final size:21
Alignment explanation
Indices: 3053206--3053252 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
3053196 TATATTTATA
3053206 TAAAAAAGTATAATAAGATAC
1 TAAAAAAGTATAATAAGATAC
3053227 TAAAAAAGTATAATAA-ATAC
1 TAAAAAAGTATAATAAGATAC
3053247 -AAAAAA
1 TAAAAAA
3053253 CGGAAAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 16 0.62
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.21
Consensus pattern (21 bp):
TAAAAAAGTATAATAAGATAC
Found at i:3055897 original size:2 final size:2
Alignment explanation
Indices: 3055890--3055937 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
3055880 GGACCCAATT
* * * *
3055890 TC TC TC TC TC TC TC TC TC CC TC TC CC TC TC CC TC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3055932 TC TC TC
1 TC TC TC
3055938 AATATAGGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (2 bp):
TC
Found at i:3062490 original size:31 final size:31
Alignment explanation
Indices: 3062452--3062513 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3062442 ATACATTTTG
3062452 GTACTTAAACTCGGTTT-AACGGTGTAATTTA
1 GTACTTAAACTCGGTTTGAA-GGTGTAATTTA
* *
3062483 GTACTTAAATTTGGTTTGAAGGTGTAATTTA
1 GTACTTAAACTCGGTTTGAAGGTGTAATTTA
3062514 ACATGGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (31 bp):
GTACTTAAACTCGGTTTGAAGGTGTAATTTA
Found at i:3069040 original size:61 final size:60
Alignment explanation
Indices: 3068948--3069066 Score: 159
Period size: 61 Copynumber: 2.0 Consensus size: 60
3068938 TACGTTTAAG
* * *
3068948 GATATACATATATTAGGACAAAGCAGCAATTTAGTTTTATAAATAGC-TTATAAATAAAAA
1 GATACACATATATTAGGACAAAACAGCAATTTAATTTTATAAATA-CTTTATAAATAAAAA
* * *
3069008 GATACACATATATTTAGGATAAAACAGTAATTTAATTTTATAAATACTTTATGAATAAA
1 GATACACATATA-TTAGGACAAAACAGCAATTTAATTTTATAAATACTTTATAAATAAA
3069067 TAAAAAATGG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
60 12 0.24
61 39 0.76
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (60 bp):
GATACACATATATTAGGACAAAACAGCAATTTAATTTTATAAATACTTTATAAATAAAAA
Found at i:3069390 original size:2 final size:2
Alignment explanation
Indices: 3069383--3069412 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3069373 TTTCTAATTA
3069383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3069413 GTATTTGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3077248 original size:60 final size:59
Alignment explanation
Indices: 3077139--3077252 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 59
3077129 ACTATGGCTA
* *
3077139 TCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATGTCATCCCCAAACTATGATCT
1 TCATTCTAAATTAGTCCCCAAACTTTTGAACATTCCAATGTCATCCCC-AACTATGATCT
* *
3077199 TCATTCTAAATT-GATCCCCAAACTTTTTGAACATTCCAATTTTAT-CCCAACTAT
1 TCATTCTAAATTAG-TCCCCAAAC-TTTTGAACATTCCAATGTCATCCCCAACTAT
3077253 ATGTATATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 7 0.15
60 23 0.48
61 18 0.38
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (59 bp):
TCATTCTAAATTAGTCCCCAAACTTTTGAACATTCCAATGTCATCCCCAACTATGATCT
Found at i:3077473 original size:60 final size:60
Alignment explanation
Indices: 3077370--3077530 Score: 207
Period size: 60 Copynumber: 2.7 Consensus size: 60
3077360 TTTGGATGAA
* * * **
3077370 TTTGGGAATAAAATTGGAA-GATTCAAAAGTTTAGGGACCAATTTAGAAAGAGGTTCATAG
1 TTTGGGGATGAAATTGGAATG-TTCAAAAGTTTAAGGACCAATTTAGAAAGAGAATCATAG
* * *
3077430 TTTGGGGGTGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAATCATAG
1 TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAAAGAGAATCATAG
* * *
3077490 TTTGGGGATGAAATTAGAATATTCAAACGTTTAAGGACCAA
1 TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACCAA
3077531 ACGAAAATTA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 86 0.99
61 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (60 bp):
TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAAAGAGAATCATAG
Found at i:3079550 original size:22 final size:22
Alignment explanation
Indices: 3079525--3079569 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3079515 AGAATTAATC
*
3079525 AAAGGCCTTGGTAGATAAGATA
1 AAAGGCCTTGGAAGATAAGATA
* *
3079547 AAAGGCTTTTGAAGATAAGATA
1 AAAGGCCTTGGAAGATAAGATA
3079569 A
1 A
3079570 TATAGGACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.24
Consensus pattern (22 bp):
AAAGGCCTTGGAAGATAAGATA
Found at i:3082533 original size:19 final size:18
Alignment explanation
Indices: 3082486--3082532 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3082476 CGATTAAGTA
3082486 AAATATATATAATATTTC
1 AAATATATATAATATTTC
*
3082504 AAGATAAATATCAATA-TTC
1 AA-ATATATAT-AATATTTC
3082523 AAATAT-TATA
1 AAATATATATA
3082533 TTTTATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 5 0.20
19 12 0.48
20 4 0.16
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATATATATAATATTTC
Found at i:3083290 original size:42 final size:42
Alignment explanation
Indices: 3083243--3083325 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
3083233 GAAGTGCCAA
* * * *
3083243 GTTTGTATACGATTGTCCTTGATCATATGTGTGAACAAGTTC
1 GTTTGTAAACGAGTGTCCTTCATCATATATGTGAACAAGTTC
* *
3083285 GTTTGTAAACGAGTGTGCTTCATCTTATATGTGAACAAGTT
1 GTTTGTAAACGAGTGTCCTTCATCATATATGTGAACAAGTT
3083326 GTCTTCAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (42 bp):
GTTTGTAAACGAGTGTCCTTCATCATATATGTGAACAAGTTC
Found at i:3085143 original size:3 final size:3
Alignment explanation
Indices: 3085135--3085186 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
3085125 CTTGTTTGTA
**
3085135 TAT TAT TAT CGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3085183 TAT T
1 TAT T
3085187 TACATTTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3088824 original size:31 final size:32
Alignment explanation
Indices: 3088788--3088849 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3088778 ATTTTACATG
3088788 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
3088819 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
3088850 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:3091779 original size:18 final size:17
Alignment explanation
Indices: 3091735--3091781 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
3091725 GAGTGCAAAG
*
3091735 ATCAAACCAAAGAAAAA
1 ATCAAAGCAAAGAAAAA
3091752 A-CAAAGAGCAAAGAGAAAA
1 ATC-AA-AGCAAAGA-AAAA
3091771 ATCAAAGCAAA
1 ATCAAAGCAAA
3091782 AATCAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 13 0.52
19 7 0.28
20 1 0.04
ACGTcount: A:0.68, C:0.15, G:0.13, T:0.04
Consensus pattern (17 bp):
ATCAAAGCAAAGAAAAA
Found at i:3091784 original size:12 final size:11
Alignment explanation
Indices: 3091765--3091802 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
3091755 AAGAGCAAAG
3091765 AGAAAAATCAA
1 AGAAAAATCAA
3091776 AGCAAAAATCAA
1 AG-AAAAATCAA
*
3091788 AGAAAAAGCAA
1 AGAAAAATCAA
3091799 AGAA
1 AGAA
3091803 CAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:3092994 original size:4 final size:4
Alignment explanation
Indices: 3092985--3093022 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
3092975 AAAAGTATAC
*
3092985 ACAT ACAT ACAT ACAT ACAT AC-- ACAC ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3093023 GATACATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.06
4 29 0.94
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (4 bp):
ACAT
Found at i:3093009 original size:22 final size:22
Alignment explanation
Indices: 3092981--3093022 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3092971 CGAGAAAAGT
*
3092981 ATACACATACATACATACATAC
1 ATACACACACATACATACATAC
3093003 ATACACACACATACATACAT
1 ATACACACACATACATACAT
3093023 GATACATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (22 bp):
ATACACACACATACATACATAC
Found at i:3093668 original size:105 final size:102
Alignment explanation
Indices: 3093481--3093719 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 102
3093471 TGAGAATATT
** *
3093481 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTGTGAATTTGATTCACT
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTGTGAATTTGATTCACT
*
3093546 TAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TAAAACAAAATTAATCTCA-CTTGAGATCG-TG-TTC--TCA
* * *
3093586 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATT-TCGAATTTGTTTCAC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTGT-GAATTTGATTCAC
* *
3093650 ATT-AAACAAAGTTGATCTCACTTGAGATCGTGTTCTCA
65 -TTAAAACAAAATTAATCTCACTTGAGATCGTGTTCTCA
* *
3093688 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
3093720 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 29 0.25
103 3 0.03
104 6 0.05
105 76 0.64
106 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTGTGAATTTGATTCACT
TAAAACAAAATTAATCTCACTTGAGATCGTGTTCTCA
Found at i:3093710 original size:36 final size:33
Alignment explanation
Indices: 3093665--3093783 Score: 105
Period size: 36 Copynumber: 3.4 Consensus size: 33
3093655 ACAAAGTTGA
*
3093665 TCTCACTTGAGATCGTGTTCTCAAAAACAAACTTTG
1 TCTCACTTGAGA-C-T-TTCTCAAAAACAAATTTTG
*
3093701 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGAC--TTTCTC-AAAAACAAATTTTG
* * *
3093737 TCTCATTTGAGACTATATCT-TAAAGCAAATTTTG
1 TCTCACTTGAGACT-T-TCTCAAAAACAAATTTTG
*
3093771 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
3093784 ATCGTTTTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
34 24 0.34
35 7 0.10
36 39 0.56
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (33 bp):
TCTCACTTGAGACTTTCTCAAAAACAAATTTTG
Found at i:3093771 original size:34 final size:36
Alignment explanation
Indices: 3093683--3093784 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
3093673 GAGATCGTGT
* *
3093683 TCTC-AAAAACAAACTTTGTCTCGCTTGAGACAATT
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
** *
3093718 TCTCTAAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
*
3093754 TCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
3093785 TCGTTTTCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 23 0.40
35 5 0.09
36 29 0.51
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
Found at i:3094058 original size:29 final size:28
Alignment explanation
Indices: 3094026--3094162 Score: 131
Period size: 29 Copynumber: 4.9 Consensus size: 28
3094016 TCTTGAGACA
3094026 GTTTCTCTTGGAAAAAAATCTTTGAGTTT
1 GTTTCT-TTGGAAAAAAATCTTTGAGTTT
***
3094055 GTTTCTTTGGAAAAAAAATCTTTGAGACA
1 GTTTCTTTGG-AAAAAAATCTTTGAGTTT
3094084 GTTTCTCTT--AAAAAAATCTTTGAGTTT
1 GTTTCT-TTGGAAAAAAATCTTTGAGTTT
* * * *
3094111 GTTCCTTTTGAATAAATATTTTTGAG-TT
1 GTTTCTTTGGAA-AAAAATCTTTGAGTTT
*
3094139 GTTTCTTTTG--AAAAATCTTTGAGT
1 GTTTCTTTGGAAAAAAATCTTTGAGT
3094163 CTATTTATTT
Statistics
Matches: 90, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
25 11 0.12
26 2 0.02
27 20 0.22
28 17 0.19
29 38 0.42
30 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.46
Consensus pattern (28 bp):
GTTTCTTTGGAAAAAAATCTTTGAGTTT
Found at i:3094135 original size:56 final size:56
Alignment explanation
Indices: 3094018--3094162 Score: 177
Period size: 56 Copynumber: 2.6 Consensus size: 56
3094008 TTTGTCTCTC
*
3094018 TTGAGACAGTTTCTCTTGGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAAAAAAATCT
1 TTGAGACAGTTTCTCTT--AAAAAAATCTTTGAGTTTGTTCCTTTGGAAAAAAAATCT
* * * *
3094076 TTGAGACAGTTTCTCTTAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAATATTT
1 TTGAGACAGTTTCTCTTAAAAAAATCTTTGAGTTTGTTCCTTTGGAAAAAAAATCT
** **
3094132 TTGAG-TTGTTTCT-TTTGAAAAATCTTTGAGT
1 TTGAGACAGTTTCTCTTAAAAAAATCTTTGAGT
3094163 CTATTTATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
54 16 0.21
55 6 0.08
56 39 0.50
58 17 0.22
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.45
Consensus pattern (56 bp):
TTGAGACAGTTTCTCTTAAAAAAATCTTTGAGTTTGTTCCTTTGGAAAAAAAATCT
Found at i:3094236 original size:52 final size:53
Alignment explanation
Indices: 3094173--3094276 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 53
3094163 CTATTTATTT
3094173 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
* * *
3094225 TGAAACGAAGTTTTGTCTCTCTTGATACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
3094277 ATAGTTTCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 34 0.72
54 13 0.28
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:3094318 original size:29 final size:31
Alignment explanation
Indices: 3094264--3094327 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
3094254 ATTTTGTGAA
3094264 AAAAATCTTTGAGATAGTTTCCTTT-GAAAC
1 AAAAATCTTTGAGATAGTTTCCTTTGGAAAC
* *
3094294 AAAAATCTTTGAGTTTGTTT-CTTTGGAAAC
1 AAAAATCTTTGAGATAGTTTCCTTTGGAAAC
3094324 AAAA
1 AAAA
3094328 TTTTGTCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (31 bp):
AAAAATCTTTGAGATAGTTTCCTTTGGAAAC
Found at i:3094328 original size:29 final size:30
Alignment explanation
Indices: 3094256--3094332 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
3094246 TTGATACAAT
3094256 TTTGTGAAA-AAAATCTTTGAGATAGTTTCC
1 TTTG-GAAACAAAATCTTTGAGATAGTTTCC
* *
3094286 TTT-GAAACAAAAATCTTTGAGTTTGTTT-C
1 TTTGGAAAC-AAAATCTTTGAGATAGTTTCC
3094315 TTTGGAAACAAAAT-TTTG
1 TTTGGAAACAAAATCTTTG
3094333 TCTCTCTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 8 0.19
29 9 0.21
30 25 0.60
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (30 bp):
TTTGGAAACAAAATCTTTGAGATAGTTTCC
Found at i:3094761 original size:66 final size:66
Alignment explanation
Indices: 3094685--3094835 Score: 241
Period size: 66 Copynumber: 2.3 Consensus size: 66
3094675 TTTGTTTCCT
* *
3094685 TTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAGATACCCACATTTGATATCGTTTCT
1 TTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTTCT
3094750 A
66 A
* * *
3094751 TTGAAACAAAATTTTGTCTCTCGAGACAACTTTTTTTGAAAATGCCCACCTTTGAGATCGTTTCT
1 TTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTTCT
3094816 A
66 A
*
3094817 TTAAAAC-AAATTTTGTCTC
1 TTGAAACAAAATTTTGTCTC
3094836 GCATGAGACA
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 12 0.15
66 67 0.85
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (66 bp):
TTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTTCT
A
Found at i:3095633 original size:46 final size:44
Alignment explanation
Indices: 3095580--3095813 Score: 157
Period size: 46 Copynumber: 5.4 Consensus size: 44
3095570 TAACCAGCCG
3095580 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC
1 TCCTCATCACGTAGGAACCGTGTTATCACC--TAGATGGCCAGATC
* * * * * *
3095626 TCTTCATCACGTATGAGCCGTGTCAT-TCCTCGA---CCAGATC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTAGATGGCCAGATC
* * ** *
3095666 TCCTCATCACGTAGGAGCCGTGTCAATCA--TAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGT-TATCACCTAGATGGCCAGATC
*
3095708 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTTATCACC--TAGATGGCCAGATC
* * * * * * * *
3095755 TCTTCATCACGTATGAGCAGTGTCATC-CCTCGA---CTAGATT
1 TCCTCATCACGTAGGAACCGTGTTATCACCTAGATGGCCAGATC
3095795 TCCTCATCACGTAGGAACC
1 TCCTCATCACGTAGGAACC
3095814 ATGTCACCCT
Statistics
Matches: 147, Mismatches: 30, Indels: 28
0.72 0.15 0.14
Matches are distributed among these distances:
40 50 0.34
41 2 0.01
42 5 0.03
43 32 0.22
45 4 0.03
46 53 0.36
47 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (44 bp):
TCCTCATCACGTAGGAACCGTGTTATCACCTAGATGGCCAGATC
Found at i:3095674 original size:40 final size:40
Alignment explanation
Indices: 3095619--3095819 Score: 134
Period size: 40 Copynumber: 4.8 Consensus size: 40
3095609 CTTTAGATGG
* * *
3095619 CCAGATCTCTTCATCACGTATGAGCCGTGTCATTCCTCGA
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCATTCCTAGA
* *
3095659 CCAGATCTCCTCATCACGTAGGAGCCGTGTCAATCATAGATAA
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCATTCCTAG---A
* * * *
3095702 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGATC-TCCTCATCACGTAGGAGCCGTGTCAT-TCC--TAGA
* * * * * *
3095745 TGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGA
1 ---CCAGATCTCCTCATCACGTAGGAGCCGTGTCATTCCTAGA
* * * *
3095788 CTAGATTTCCTCATCACGTAGGAACCATGTCA
1 CCAGATCTCCTCATCACGTAGGAGCCGTGTCA
3095820 CCCTTAGATG
Statistics
Matches: 123, Mismatches: 27, Indels: 22
0.72 0.16 0.13
Matches are distributed among these distances:
40 58 0.47
42 1 0.01
43 32 0.26
44 1 0.01
45 2 0.02
46 28 0.23
47 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTAGGAGCCGTGTCATTCCTAGA
Found at i:3095718 original size:43 final size:43
Alignment explanation
Indices: 3095564--3095731 Score: 132
Period size: 40 Copynumber: 3.9 Consensus size: 43
3095554 AGTTTGTCAC
*
3095564 CATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGT-TAT
1 CATAGATAACCAGACC-TCCTCATCACGTAGGAACCGTGTCAAT
** * * * * *
3095606 CACCTTTAGATGGCCAGATCTCTTCATCACGTATGAGCCGTGTCATT
1 CA----TAGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAAT
* * * *
3095653 CCTCG---ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAAT
1 CATAGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAAT
3095693 CATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 CATAGATAACCAGACC-TCCTCATCACGTAGGAACCGTGT
3095732 TATCACCTTT
Statistics
Matches: 98, Mismatches: 18, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
40 34 0.35
42 3 0.03
43 29 0.30
46 29 0.30
47 3 0.03
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (43 bp):
CATAGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAAT
Found at i:3095799 original size:129 final size:129
Alignment explanation
Indices: 3095564--3095819 Score: 449
Period size: 129 Copynumber: 2.0 Consensus size: 129
3095554 AGTTTGTCAC
*
3095564 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATCTCT
1 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
* * * *
3095629 TCATCACGTATGAGCCGTGTCATTCCTCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAAT
66 TCATCACGTATGAGCAGTGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAACCATGTCAAT
3095693 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
* *
3095758 TCATCACGTATGAGCAGTGTCATCCCTCGACTAGATTTCCTCATCACGTAGGAACCATGTCA
66 TCATCACGTATGAGCAGTGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAACCATGTCA
3095820 CCCTTAGATG
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 120 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (129 bp):
CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
TCATCACGTATGAGCAGTGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAACCATGTCAAT
Found at i:3096025 original size:3 final size:3
Alignment explanation
Indices: 3096017--3096071 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
3096007 CTTGTTTGTA
**
3096017 TAT TAT TAT CGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3096065 TAT TAT T
1 TAT TAT T
3096072 TAATTTACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3100221 original size:8 final size:8
Alignment explanation
Indices: 3100210--3100239 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3100200 ATAATTTATT
3100210 AATAAAAA
1 AATAAAAA
3100218 AATAAAAAA
1 AAT-AAAAA
3100227 AATAAAAA
1 AATAAAAA
3100235 AATAA
1 AATAA
3100240 TAATAAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AATAAAAA
Found at i:3100762 original size:20 final size:20
Alignment explanation
Indices: 3100727--3100764 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3100717 TCACACCAAA
* *
3100727 TTCTCTCAATTTCTCTTAAC
1 TTCTCTCAAATACTCTTAAC
3100747 TTCTCTCAAATACTCTTA
1 TTCTCTCAAATACTCTTA
3100765 TAATCTCTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (20 bp):
TTCTCTCAAATACTCTTAAC
Found at i:3100820 original size:25 final size:26
Alignment explanation
Indices: 3100782--3100846 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
3100772 TTCTAAGGTA
*
3100782 TATTTTATTATATTTTTAATATTTT-G
1 TATTTAATT-TATTTTTAATATTTTAG
*
3100808 TATTTAATTTA--TTTAATATTTTACT
1 TATTTAATTTATTTTTAATATTTTA-G
3100833 TATTTAATTT-TTTT
1 TATTTAATTTATTTT
3100847 ACAGATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
23 11 0.33
25 12 0.36
26 10 0.30
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (26 bp):
TATTTAATTTATTTTTAATATTTTAG
Found at i:3100847 original size:25 final size:23
Alignment explanation
Indices: 3100794--3100847 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 23
3100784 TTTTATTATA
3100794 TTTTTAATATTTTGTATTTAATT
1 TTTTTAATATTTTGTATTTAATT
* *
3100817 TATTTAATATTTTACTTATTTAATT
1 TTTTTAATATTTT--GTATTTAATT
3100842 TTTTTA
1 TTTTTA
3100848 CAGATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 12 0.46
25 14 0.54
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTAATATTTTGTATTTAATT
Found at i:3102438 original size:12 final size:12
Alignment explanation
Indices: 3102421--3102451 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3102411 TTTTTCTTTA
3102421 TAATATATGAAT
1 TAATATATGAAT
3102433 TAATATATGAAT
1 TAATATATGAAT
3102445 TAATATA
1 TAATATA
3102452 AAATAATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
TAATATATGAAT
Found at i:3103531 original size:15 final size:15
Alignment explanation
Indices: 3103508--3103552 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
3103498 CGTAGGACTC
3103508 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
* *
3103523 CTACGTCCCGAAGAA
1 CTACATCCCGAAGGA
3103538 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
3103553 ATATTATACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.33, C:0.33, G:0.20, T:0.13
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:3103681 original size:29 final size:29
Alignment explanation
Indices: 3103641--3103717 Score: 147
Period size: 29 Copynumber: 2.7 Consensus size: 29
3103631 TTCATATGTC
3103641 CATGTA-CTCATGTCATTTCTCTTGTGAT
1 CATGTAGCTCATGTCATTTCTCTTGTGAT
3103669 CATGTAGCTCATGTCATTTCTCTTGTGAT
1 CATGTAGCTCATGTCATTTCTCTTGTGAT
3103698 CATGTAGCTCATGTCATTTC
1 CATGTAGCTCATGTCATTTC
3103718 ATATCATGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 6 0.12
29 42 0.88
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
CATGTAGCTCATGTCATTTCTCTTGTGAT
Found at i:3103746 original size:12 final size:12
Alignment explanation
Indices: 3103729--3103776 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
3103719 TATCATGTTC
3103729 TCATATCACATG
1 TCATATCACATG
*
3103741 TCATATCACATA
1 TCATATCACATG
3103753 TCATATCACATAG
1 TCATATCACAT-G
3103766 -CATATCACATG
1 TCATATCACATG
3103777 AACATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 1 0.03
12 32 0.97
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATG
Found at i:3104192 original size:64 final size:64
Alignment explanation
Indices: 3104124--3104244 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 64
3104114 CATAAAAGGT
* ** * *
3104124 ATTCGATGTAGTATTATTGCTGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGC
1 ATTCGATGTAGTACTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
**
3104188 ATTCGATGTTTTACTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCAC
1 ATTCGATGTAGTACTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCAC
3104245 ATTCATACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (64 bp):
ATTCGATGTAGTACTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
Done.