Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 73
Found at i:2182821 original size:42 final size:41
Alignment explanation
Indices: 2182730--2182828 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
2182720 TTATTTTAGG
* * *
2182730 GGCATTTTTTATA-TAAATGTCGCTAAAGACTGTACTTTAGT
1 GGCA-TTTTTATACAAAATGCCGCTAAAGACTGTACTTTAAT
**
2182771 GGTGTTTTTATACAAAATGCCGCTATAA-ACTCGTACTTTAAT
1 GGCATTTTTATACAAAATGCCGCTA-AAGACT-GTACTTTAAT
2182813 GGCATTTTTATACAAA
1 GGCATTTTTATACAAA
2182829 CGCCGTAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 8 0.17
41 15 0.31
42 25 0.52
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (41 bp):
GGCATTTTTATACAAAATGCCGCTAAAGACTGTACTTTAAT
Found at i:2185936 original size:6 final size:7
Alignment explanation
Indices: 2185915--2185943 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2185905 TTCTCTCTTC
2185915 TTTATTT
1 TTTATTT
2185922 TTTATTT
1 TTTATTT
2185929 TTTA-TT
1 TTTATTT
2185935 TTTATTT
1 TTTATTT
2185942 TT
1 TT
2185944 GTGGTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:2185938 original size:13 final size:14
Alignment explanation
Indices: 2185915--2185943 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2185905 TTCTCTCTTC
2185915 TTTATTTTTTATTT
1 TTTATTTTTTATTT
2185929 TTTA-TTTTTATTT
1 TTTATTTTTTATTT
2185942 TT
1 TT
2185944 GTGGTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTATTTTTTATTT
Found at i:2186868 original size:128 final size:127
Alignment explanation
Indices: 2186700--2186964 Score: 311
Period size: 126 Copynumber: 2.1 Consensus size: 127
2186690 TGAAGAGTTT
* * * * *
2186700 TGGTTATC-AAAGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGACGACACAGCT
1 TGGTTATCTAAA-GTTGACACAGCTCCTACATGATGAGGAGATCAGATCAGGTGACGACACAGAT
* * * * *
2186764 CATACGTGATGAAGAGT-TCTGGCCATCTAAAGGTGATAACACGGTTCCACTTTGATGGGGACGG
65 CAT-C-TGATCAAGAGTAT-AGGCCATCTAAAGGTGATAACACGGTTCCACTCTAATGGGGACGA
2186828 C
127 C
* * * *
2186829 TGGTTATCTAAA-TTGACACAGCTCCTACATGATGAGGAGATCTGATCATGTGATGACACTGATC
1 TGGTTATCTAAAGTTGACACAGCTCCTACATGATGAGGAGATCAGATCAGGTGACGACACAGATC
* * * *
2186893 ATCTGTTCATGAGTATAGGCCATCTAAGGGTGATAACACGGTTCCACTCTAATGGGGATGAC
66 ATCTGATCAAGAGTATAGGCCATCTAAAGGTGATAACACGGTTCCACTCTAATGGGGACGAC
2186955 TGGTTATCTA
1 TGGTTATCTA
2186965 GGGGTGACAT
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
126 58 0.50
127 2 0.02
128 45 0.39
129 8 0.07
130 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (127 bp):
TGGTTATCTAAAGTTGACACAGCTCCTACATGATGAGGAGATCAGATCAGGTGACGACACAGATC
ATCTGATCAAGAGTATAGGCCATCTAAAGGTGATAACACGGTTCCACTCTAATGGGGACGAC
Found at i:2187412 original size:32 final size:33
Alignment explanation
Indices: 2187355--2187443 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 33
2187345 AAAATAAGAT
*
2187355 TTGTTTCAAGAGAAACGATCTCAAAGATGGTTG
1 TTGTTTCAAGAGAAACGATCTCAAAGATGATTG
* * * *
2187388 TTGTTTCTAGTGAAATGA-CTCAAAGATGATTT
1 TTGTTTCAAGAGAAACGATCTCAAAGATGATTG
* **
2187420 TTGTTTCAAAAGAAATTATCTCAA
1 TTGTTTCAAGAGAAACGATCTCAA
2187444 GAGACAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
32 26 0.57
33 20 0.43
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (33 bp):
TTGTTTCAAGAGAAACGATCTCAAAGATGATTG
Found at i:2187507 original size:129 final size:127
Alignment explanation
Indices: 2187356--2187604 Score: 285
Period size: 129 Copynumber: 1.9 Consensus size: 127
2187346 AAATAAGATT
* * *
2187356 TGTTTCAAGAGAAACGATCTCAAAGATGGT-TGTTGTTTCTAGTG-AA-ATGACTCAAAGATGAT
1 TGTTTCAAAAGAAACGATCTCAAAGATGATAT-TTGTTTCAAGTGAAACAT-ACTC-AA-AT-AT
*
2187418 TTTTGTTTCAAAAGAAATTATCTCAAGAGACAAAA-TTCGTTTCAAA-AGAAACGATTTTAAAGA
61 TTTT-TTTCAAAAGAAATTATCTCAAGAGACAAAACTTCGTTT-AAATAGAAACAATTTTAAAGA
2187481 TGGG
124 TGGG
*
2187485 TGTTTCAAAAGAAACTGA-CTCAAAGATTATAAAATTTGTTTCAAGTGAAACATACTCAAATATT
1 TGTTTCAAAAGAAAC-GATCTCAAAGATGAT---ATTTGTTTCAAGTGAAACATACTCAAATATT
** *
2187549 TTTTTTTTAAAGAAATTATCTCAAGAGACAAAACTTTGTTTAAATAGAAACAATTT
62 TTTTTTCAAAAGAAATTATCTCAAGAGACAAAACTTCGTTTAAATAGAAACAATTT
2187605 CAAATGTGAG
Statistics
Matches: 103, Mismatches: 8, Indels: 17
0.80 0.06 0.13
Matches are distributed among these distances:
129 55 0.53
130 24 0.23
131 2 0.02
132 13 0.13
133 7 0.07
134 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (127 bp):
TGTTTCAAAAGAAACGATCTCAAAGATGATATTTGTTTCAAGTGAAACATACTCAAATATTTTTT
TTCAAAAGAAATTATCTCAAGAGACAAAACTTCGTTTAAATAGAAACAATTTTAAAGATGGG
Found at i:2188191 original size:33 final size:32
Alignment explanation
Indices: 2188124--2188199 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
2188114 TTTGCATCAT
*
2188124 GATGTTGAATCCCCAAATATGCCCCAATAGTC
1 GATGTTGAATCCCCAAAGATGCCCCAATAGTC
* * *
2188156 GATGTTGATTGCCTCAAAGATGCTCCAAT-GTTC
1 GATGTTGAAT-CCCCAAAGATGCCCCAATAG-TC
*
2188189 GATTTTGAATC
1 GATGTTGAATC
2188200 TTTAAAGATG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
32 11 0.31
33 25 0.69
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGATGCCCCAATAGTC
Found at i:2189277 original size:13 final size:12
Alignment explanation
Indices: 2189244--2189368 Score: 62
Period size: 13 Copynumber: 9.8 Consensus size: 12
2189234 TCGCATATGC
2189244 TTTTTTCTTT-T
1 TTTTTTCTTTCT
2189255 TTTTTCTCTTTACT
1 TTTTT-TCTTT-CT
2189269 TTTTTTCTTTGCT
1 TTTTTTCTTT-CT
* *
2189282 TATTTTCTTTTT
1 TTTTTTCTTTCT
*
2189294 TCTTTTTCTTTGT
1 T-TTTTTCTTTCT
2189307 TCTTTATTGC--TCT
1 T-TTT-TT-CTTTCT
*
2189320 TTTTTTGCTTTAAT
1 TTTTTT-CTTT-CT
2189334 TTCTTTT-TTTCAT
1 TT-TTTTCTTTC-T
2189347 TTTTTT-TGTTCT
1 TTTTTTCT-TTCT
*
2189359 TTGTTTCTTT
1 TTTTTTCTTT
2189369 TTCCTTTGTT
Statistics
Matches: 92, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
11 9 0.10
12 23 0.25
13 44 0.48
14 11 0.12
15 5 0.05
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTTTCTTTCT
Found at i:2189290 original size:26 final size:25
Alignment explanation
Indices: 2189244--2189307 Score: 51
Period size: 25 Copynumber: 2.5 Consensus size: 25
2189234 TCGCATATGC
* * *
2189244 TTTTTTCTTTTTTTTTCTCT-TTACT
1 TTTTTTCTTTGTTATT-TCTCTTTCT
*
2189269 TTTTTTCTTTGCTTATTT-TCTTTTT
1 TTTTTTCTTTG-TTATTTCTCTTTCT
2189294 TCTTTTTCTTTGTT
1 T-TTTTTCTTTGTT
2189308 CTTTATTGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 1 0.03
25 17 0.53
26 14 0.44
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (25 bp):
TTTTTTCTTTGTTATTTCTCTTTCT
Found at i:2189355 original size:49 final size:45
Alignment explanation
Indices: 2189243--2189360 Score: 134
Period size: 49 Copynumber: 2.5 Consensus size: 45
2189233 TTCGCATATG
*
2189243 CTTTTTTCTTTTTTTT-TCTCTTTACTTTTTTTCTTTGCTTATTTT
1 CTTTTTTCTTTTTTTTGT-TCTTTACTTTTTTTCTTTGCTTAATTT
2189288 CTTTTTTCTTTTTCTTTGTTCTTTA-TTGCTCTTTT-TTTGCTTTAATTT
1 CTTTTTTCTTTTT-TTTGTTCTTTACTT--T-TTTTCTTTGC-TTAATTT
2189336 CTTTTTTTCATTTTTTTTGTTCTTT
1 C-TTTTTTC-TTTTTTTTGTTCTTT
2189361 GTTTCTTTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
45 15 0.23
46 9 0.14
47 7 0.11
48 11 0.17
49 17 0.27
50 5 0.08
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.76
Consensus pattern (45 bp):
CTTTTTTCTTTTTTTTGTTCTTTACTTTTTTTCTTTGCTTAATTT
Found at i:2192357 original size:21 final size:20
Alignment explanation
Indices: 2192333--2192372 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2192323 TAAAAATTAA
*
2192333 ATGCATATGCAAAATGCAAAG
1 ATGCAAATGC-AAATGCAAAG
*
2192354 ATGCAAATGCAGATGCAAA
1 ATGCAAATGCAAATGCAAA
2192373 AATATTGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.17
Consensus pattern (20 bp):
ATGCAAATGCAAATGCAAAG
Found at i:2195327 original size:13 final size:13
Alignment explanation
Indices: 2195309--2195348 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
2195299 TTGACCGGTT
2195309 TTGACCCGACCCG
1 TTGACCCGACCCG
2195322 TTGACCCGA-CC-
1 TTGACCCGACCCG
2195333 -TGACCCGACCCG
1 TTGACCCGACCCG
2195345 TTGA
1 TTGA
2195349 TCGTTGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 8 0.33
11 2 0.08
12 2 0.08
13 12 0.50
ACGTcount: A:0.17, C:0.42, G:0.23, T:0.17
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:2195534 original size:29 final size:29
Alignment explanation
Indices: 2195466--2195535 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
2195456 AAAAAATGTC
* *
2195466 ATTTTAGTAAATATTTTTAAAATGGTGCT
1 ATTTTAGTAATTAATTTTAAAATGGTGCT
*
2195495 ATTTTGGTAATTAATTTTAAAATGGTGCT
1 ATTTTAGTAATTAATTTTAAAATGGTGCT
*
2195524 ATTTTCGTAATT
1 ATTTTAGTAATT
2195536 TTTAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.50
Consensus pattern (29 bp):
ATTTTAGTAATTAATTTTAAAATGGTGCT
Found at i:2195555 original size:109 final size:109
Alignment explanation
Indices: 2195356--2195558 Score: 255
Period size: 109 Copynumber: 1.9 Consensus size: 109
2195346 TGATCGTTGA
* * *
2195356 CATTTTAGTAATTATTTTGAAACTGGTGACATATTGGGAATTAATTCGAAAAAGGTGATATTTTT
1 CATTTTAGTAAATATTTTGAAAATGGTGACATATTGGGAATTAATTCGAAAAAGGTGATATTTTC
* * *
2195421 ATAATTTTTTAAAAATGCTATTTTCGTAATTTTTGAAAAAATGT
66 ATAATTTTTAAAAAATACTAATTTCGTAATTTTTGAAAAAATGT
* * * ** * *
2195465 CATTTTAGTAAATATTTTTAAAATGGTG-CTATTTTGGTAATTAATTTTAAAATGGTGCTATTTT
1 CATTTTAGTAAATATTTTGAAAATGGTGAC-ATATTGGGAATTAATTCGAAAAAGGTGATATTTT
* *
2195529 CGTAATTTTTAAAAAATATTAATTTCGTAA
65 CATAATTTTTAAAAAATACTAATTTCGTAA
2195559 AATGGTTGAC
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
108 1 0.01
109 77 0.99
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.46
Consensus pattern (109 bp):
CATTTTAGTAAATATTTTGAAAATGGTGACATATTGGGAATTAATTCGAAAAAGGTGATATTTTC
ATAATTTTTAAAAAATACTAATTTCGTAATTTTTGAAAAAATGT
Found at i:2201899 original size:33 final size:33
Alignment explanation
Indices: 2201857--2201926 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
2201847 AGCATTAAAG
*
2201857 AAAATTTAGGGACAAGCCCTGAATTTACCCAAA
1 AAAATTTAGGGACAAACCCTGAATTTACCCAAA
*
2201890 AAAATTTAGGGACAAACCCTGAATTTACCCAAG
1 AAAATTTAGGGACAAACCCTGAATTTACCCAAA
2201923 AAAA
1 AAAA
2201927 GTTGGTGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (33 bp):
AAAATTTAGGGACAAACCCTGAATTTACCCAAA
Found at i:2202552 original size:21 final size:21
Alignment explanation
Indices: 2202503--2202555 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2202493 AAATGATCGG
* *
2202503 TTTGACCAGTTATTTTCAATG
1 TTTGACCGGTTATTTTCAATA
2202524 TTTGACCGGTTATTTTCAATA
1 TTTGACCGGTTATTTTCAATA
*
2202545 TTTTACCGGTT
1 TTTGACCGGTT
2202556 TGACCAGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (21 bp):
TTTGACCGGTTATTTTCAATA
Found at i:2202672 original size:29 final size:28
Alignment explanation
Indices: 2202640--2202775 Score: 86
Period size: 29 Copynumber: 4.9 Consensus size: 28
2202630 AATTTATTCA
*
2202640 AAAAGGGTGCTATTTTTGTAATTTTTTTT
1 AAAA-GGTGCTATTTTTGTAATTTTTTTG
2202669 AAAA--TGCTATTTTTCGTAA--TTTTTG
1 AAAAGGTGCTATTTTT-GTAATTTTTTTG
** * * *
2202694 AAAAAATGAC-ATTTTAGTAAATATTTTG
1 AAAAGGTG-CTATTTTTGTAATTTTTTTG
* * *
2202722 AAAATGGTGCTATATTGGTAATTAATTTT-
1 AAAA-GGTGCTATTTTTGTAATT-TTTTTG
*
2202751 AAAATGGTGCTATTTTCGTAATTTT
1 AAAA-GGTGCTATTTTTGTAATTTT
2202776 GAAAAAATAT
Statistics
Matches: 87, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
25 9 0.10
26 14 0.16
27 11 0.13
28 12 0.14
29 36 0.41
30 5 0.06
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.48
Consensus pattern (28 bp):
AAAAGGTGCTATTTTTGTAATTTTTTTG
Found at i:2202698 original size:26 final size:26
Alignment explanation
Indices: 2202647--2202725 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
2202637 TCAAAAAGGG
**
2202647 TGCTATTTTTGTAATTTTTTTTAAAA
1 TGCTATTTTTGTAATTTTTTGAAAAA
2202673 TGCTATTTTTCGTAA-TTTTTGAAAAAA
1 TGCTATTTTT-GTAATTTTTTG-AAAAA
* *
2202700 TGAC-ATTTTAGTAAATATTTTGAAAA
1 TG-CTATTTTTGT-AATTTTTTGAAAA
2202726 TGGTGCTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
26 17 0.39
27 21 0.48
28 6 0.14
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (26 bp):
TGCTATTTTTGTAATTTTTTGAAAAA
Found at i:2202704 original size:82 final size:81
Alignment explanation
Indices: 2202618--2202783 Score: 176
Period size: 82 Copynumber: 2.0 Consensus size: 81
2202608 TTAAAATTAG
* * * **
2202618 TGACATATT-GGGAAT-TTATTCAAAAAGGGTGCTATTTTTGTAATTTTTTTTAAAA-TGCTATT
1 TGACATATTAGGAAATATT-TT-AAAAAGGGTGCTATATTGGTAATTAATTTTAAAAGTGCTA-T
2202680 TTTCGTAATTTTTGAAAAAA
63 TTTCGTAA-TTTTGAAAAAA
* * * *
2202700 TGACATTTTAGTAAATATTTTGAAAATGGTGCTATATTGGTAATTAATTTTAAAATGGTGCTATT
1 TGACATATTAGGAAATATTTTAAAAAGGGTGCTATATTGGTAATTAATTTTAAAA--GTGCTATT
2202765 TTCGTAATTTTGAAAAAA
64 TTCGTAATTTTGAAAAAA
2202783 T
1 T
2202784 ATTAATTTCG
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
82 36 0.51
83 18 0.26
84 11 0.16
85 5 0.07
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (81 bp):
TGACATATTAGGAAATATTTTAAAAAGGGTGCTATATTGGTAATTAATTTTAAAAGTGCTATTTT
CGTAATTTTGAAAAAA
Found at i:2203574 original size:15 final size:16
Alignment explanation
Indices: 2203541--2203573 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2203531 TGATACTTGA
2203541 TTCCTGAATATTGATT
1 TTCCTGAATATTGATT
2203557 TTCCT-AATATCTGATT
1 TTCCTGAATAT-TGATT
2203573 T
1 T
2203574 CTGTATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (16 bp):
TTCCTGAATATTGATT
Found at i:2205923 original size:22 final size:22
Alignment explanation
Indices: 2205898--2205939 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2205888 TATGATGTAA
*
2205898 AATAAAAATATTTACAACATAT
1 AATAAAAACATTTACAACATAT
*
2205920 AATAATAACATTTACAACAT
1 AATAAAAACATTTACAACAT
2205940 GTACATACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAAAAACATTTACAACATAT
Found at i:2207294 original size:29 final size:30
Alignment explanation
Indices: 2207256--2207315 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
2207246 CTTCCTTGCT
2207256 TTATGTTTTTTTTTGCTGAATAATGAAATC
1 TTATGTTTTTTTTTGCTGAATAATGAAATC
2207286 TTATG-TTTTTTTTGCTGAATAATGAAATC
1 TTATGTTTTTTTTTGCTGAATAATGAAATC
2207315 T
1 T
2207316 GGTGTGTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (30 bp):
TTATGTTTTTTTTTGCTGAATAATGAAATC
Found at i:2207466 original size:3 final size:3
Alignment explanation
Indices: 2207458--2207515 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
2207448 AAATAGTAAT
2207458 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2207505 TAA TAA TAA TA
1 TAA TAA TAA TA
2207516 TACTATATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2209703 original size:21 final size:21
Alignment explanation
Indices: 2209679--2209724 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2209669 TGTAAACTTT
2209679 GTTTATTATTATGGAATTCAA
1 GTTTATTATTATGGAATTCAA
* * *
2209700 GTTTCTTGTTATGGATTTCAA
1 GTTTATTATTATGGAATTCAA
2209721 GTTT
1 GTTT
2209725 GTTTTCTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (21 bp):
GTTTATTATTATGGAATTCAA
Found at i:2210008 original size:44 final size:43
Alignment explanation
Indices: 2209960--2210060 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 43
2209950 TTTTACGTTC
*
2209960 ACAAATGCCACAATATGACATAAAATTAAGCGGCATTATTGGG
1 ACAAATGCCACAATATGACAGAAAATTAAGCGGCATTATTGGG
** ** * * *
2210003 AACAAATGCCATTATATGTTAGAAAATTTAGCGGCGTTTTTGGG
1 -ACAAATGCCACAATATGACAGAAAATTAAGCGGCATTATTGGG
2210047 ACAAAATGCCACAA
1 AC-AAATGCCACAA
2210061 AAGAAAAGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
43 2 0.04
44 44 0.96
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (43 bp):
ACAAATGCCACAATATGACAGAAAATTAAGCGGCATTATTGGG
Found at i:2212292 original size:15 final size:15
Alignment explanation
Indices: 2212272--2212305 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2212262 TTAGTCGGGA
* *
2212272 GGCAGATGTGGGGCG
1 GGCAGATGTAGAGCG
2212287 GGCAGATGTAGAGCG
1 GGCAGATGTAGAGCG
2212302 GGCA
1 GGCA
2212306 AGGTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.53, T:0.12
Consensus pattern (15 bp):
GGCAGATGTAGAGCG
Found at i:2214693 original size:23 final size:23
Alignment explanation
Indices: 2214667--2214735 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
2214657 CACCACAGCT
*
2214667 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
2214690 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
2214713 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
2214736 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2219531 original size:20 final size:20
Alignment explanation
Indices: 2219506--2219547 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2219496 ACTATATACA
2219506 CATCATCATATCAAATATAT
1 CATCATCATATCAAATATAT
2219526 CATCATCATATCAAATATAT
1 CATCATCATATCAAATATAT
2219546 CA
1 CA
2219548 CTTCACACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
CATCATCATATCAAATATAT
Found at i:2219719 original size:23 final size:23
Alignment explanation
Indices: 2219693--2219761 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
2219683 CACCACAGCT
*
2219693 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
2219716 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
2219739 CGTAGAATTGCACCGTAA-TGCCA
1 CGTAGAATTGCACCG-AAGTGCCA
2219762 TATAATAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2220040 original size:7 final size:7
Alignment explanation
Indices: 2220028--2220056 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2220018 TGTCATATAA
2220028 ATCACAT
1 ATCACAT
2220035 ATCACAT
1 ATCACAT
2220042 ATCACAT
1 ATCACAT
2220049 AT-ACAT
1 ATCACAT
2220055 AT
1 AT
2220057 AGACACATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCACAT
Found at i:2220728 original size:2 final size:2
Alignment explanation
Indices: 2220716--2220753 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2220706 GTGGTTATCT
2220716 TA TA T- 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
2220754 CAATAATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2220924 original size:18 final size:19
Alignment explanation
Indices: 2220901--2220943 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2220891 TTAGTCATGT
2220901 ATACATACAATC-AATATA
1 ATACATACAATCGAATATA
* *
2220919 ATACATATAATCGCATATA
1 ATACATACAATCGAATATA
2220938 AT-CATA
1 ATACATA
2220944 ACAAACACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACATACAATCGAATATA
Found at i:2221336 original size:21 final size:21
Alignment explanation
Indices: 2221312--2221354 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2221302 TCTGGTTTGT
* * *
2221312 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2221333 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2221354 T
1 T
2221355 AGCCAAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2223154 original size:3 final size:3
Alignment explanation
Indices: 2223148--2223173 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2223138 AATAATAATA
2223148 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2223174 AAAGATCCCT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2228949 original size:20 final size:20
Alignment explanation
Indices: 2228900--2228952 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
2228890 TACCGGAAGG
*
2228900 GGGTATCGATACCATAGTAG
1 GGGTATCGATACCATAGTAA
2228920 GGTAGTATCGATACCAT-GTTAA
1 GG--GTATCGATACCATAG-TAA
2228942 GGGTATCGATA
1 GGGTATCGATA
2228953 TTGAAGGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 11 0.38
21 1 0.03
22 17 0.59
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:2228949 original size:95 final size:93
Alignment explanation
Indices: 2228732--2228953 Score: 275
Period size: 93 Copynumber: 2.4 Consensus size: 93
2228722 GTACTGATGA
* * *
2228732 GGTATTATAGATACCATGGTAAGGGAATCGATATCAAGTAACATCGAACCTAATTTTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATATCAAGTAACATCGAACCTAATTTTGGTATCGA
* * *
2228797 TACTGGAGGGGTATCGGTACCATAGTAT
66 TACCGGAGGGGTATCGATACCATAGTAG
* * * * * ** *
2228825 AGTAGTATCGATACAATGGTGACGATATCGATATCAAG-ACACATCGAAGTTAATTTTGGTATGG
1 GGTAGTATCGATACCATGGTAAGGGTATCGATATCAAGTA-ACATCGAACCTAATTTTGGTATCG
2228889 ATACCGGAAGGGGGTATCGATACCATAGTAG
65 ATACCGG-A-GGGGTATCGATACCATAGTAG
*
2228920 GGTAGTATCGATACCATGTTAAGGGTATCGATAT
1 GGTAGTATCGATACCATGGTAAGGGTATCGATAT
2228954 TGAAGGGCCA
Statistics
Matches: 106, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
92 1 0.01
93 57 0.54
94 1 0.01
95 47 0.44
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (93 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATATCAAGTAACATCGAACCTAATTTTGGTATCGA
TACCGGAGGGGTATCGATACCATAGTAG
Found at i:2229523 original size:59 final size:59
Alignment explanation
Indices: 2229277--2229744 Score: 636
Period size: 59 Copynumber: 7.9 Consensus size: 59
2229267 GATTACCAAA
* * ** *
2229277 AGGGCAATTCGTGTGCTAAAATGTCAAGAAATTCATACTAAGTTTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
* * * * *
2229336 AGGGCACTTTGTGTGATAA-TTGAGAAGGAATTCATAATAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
*
2229394 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATAATAATAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTC---ATACTAAGTGTATGAATTTCCATAT
* * *
2229456 AAGGCACTTCGTGTGCTAACATGAGAAGGAATTCATAATAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
* *
2229515 AAGGCACTTCGTGTGCTAACATGAGAAGAAATTTATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
*
2229574 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
* ***
2229633 AGGGCACTTCGTGTGCTAACATGAGAA-AGAATTCATACCAAGTGTATGAATTTGTGTAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGA-AATTCATACTAAGTGTATGAATTTCCATAT
* * * * *
2229692 AGGGCACTTCATGTGCTATA-ATGAGAATAAATTCATATTAAATATATGAATTT
1 AGGGCACTTCGTGTGCTA-ACATGAGAAGAAATTCATACTAAGTGTATGAATTT
2229745 TCGTATTAAA
Statistics
Matches: 371, Mismatches: 31, Indels: 14
0.89 0.07 0.03
Matches are distributed among these distances:
58 50 0.13
59 262 0.71
60 2 0.01
62 57 0.15
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTATGAATTTCCATAT
Found at i:2229782 original size:177 final size:177
Alignment explanation
Indices: 2229279--2229809 Score: 525
Period size: 177 Copynumber: 3.0 Consensus size: 177
2229269 TTACCAAAAG
* * ** * *
2229279 GGCAATTCGTGTGCTAAAATG-TCAAGAAATTCAT-ACTAAGTTTATGAATTTCCATATAGGGCA
1 GGCACTTCGTGTGCTAACATGAGAAAG-AATTCATAAC-AAGTGTATGAATTTCCATATAAGGCA
** * * * * * * **
2229342 CTTTGTGTGATAA-TTGAGAAGGAATTCATAATAAGTGTATGAATTTCCATATAGGGCACTTCGT
64 CTTCATGTGCTAACATGAGAAGAAATTCATACTAAATATATGAATTTCCATATAGAACACTTCGT
* * * * *
2229406 GTGCTAACATGAGAAGAAATTCATAATAATAAGTGTATGAATTTCCATATAA
129 GTGCCAAAATGAGAAGGAATTC---ACACTAAGTGTATGAATTTCCATATAA
* *
2229458 GGCACTTCGTGTGCTAACATGAGAAGGAATTCATAATAAGTGTATGAATTTCCATATAAGGCACT
1 GGCACTTCGTGTGCTAACATGAGAAAGAATTCATAACAAGTGTATGAATTTCCATATAAGGCACT
* * * * **
2229523 TCGTGTGCTAACATGAGAAGAAATTTATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGT
66 TCATGTGCTAACATGAGAAGAAATTCATACTAAATATATGAATTTCCATATAGAACACTTCGTGT
* * * *
2229588 GCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAG
131 GCCAAAATGAGAAGGAATTCACACTAAGTGTATGAATTTCCATATAA
* *** *
2229635 GGCACTTCGTGTGCTAACATGAGAAAGAATTCATACCAAGTGTATGAATTTGTGTATAGGGCACT
1 GGCACTTCGTGTGCTAACATGAGAAAGAATTCATAACAAGTGTATGAATTTCCATATAAGGCACT
* * * *
2229700 TCATGTGCTATA-ATGAGAATAAATTCATATTAAATATATGAATTTTCGTATTA-AACACCTT-G
66 TCATGTGCTA-ACATGAGAAGAAATTCATACTAAATATATGAATTTCCATA-TAGAACA-CTTCG
* * * * *
2229762 TGTGCCAAAATGATAAGGAATTCACATTACGTTTTTGAATTTCCATAT
128 TGTGCCAAAATGAGAAGGAATTCACACTAAGTGTATGAATTTCCATAT
2229810 GAGAAATAAA
Statistics
Matches: 304, Mismatches: 42, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
177 166 0.55
178 6 0.02
179 61 0.20
180 71 0.23
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (177 bp):
GGCACTTCGTGTGCTAACATGAGAAAGAATTCATAACAAGTGTATGAATTTCCATATAAGGCACT
TCATGTGCTAACATGAGAAGAAATTCATACTAAATATATGAATTTCCATATAGAACACTTCGTGT
GCCAAAATGAGAAGGAATTCACACTAAGTGTATGAATTTCCATATAA
Found at i:2235476 original size:55 final size:55
Alignment explanation
Indices: 2235379--2235505 Score: 168
Period size: 55 Copynumber: 2.3 Consensus size: 55
2235369 ATTACCAAAT
* * * *
2235379 GGCACTATGT-GTACAAAACTAAGAAATTGATAATTAGTTTATGAATTTCTGTAT-
1 GGCACT-TGTGGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
* *
2235433 GGACACTTTTTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
1 GG-CACTTGTGGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
2235489 GGCACTTGTGGTGCAAA
1 GGCACTTGTGGTGCAAA
2235506 CATGGTAAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
54 4 0.06
55 57 0.90
56 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (55 bp):
GGCACTTGTGGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
Found at i:2242122 original size:55 final size:55
Alignment explanation
Indices: 2241972--2242122 Score: 223
Period size: 55 Copynumber: 2.7 Consensus size: 55
2241962 ACTATATGTA
* * *
2241972 CAAAACTAAGAAATTGATAATAAGTTTATGAATTTCCGTATGGGAACTTTGTGTG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGAACTTTGTGCG
*
2242027 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGTACTTTGTGCG
1 CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGAACTTTGTGCG
** *
2242082 CAAAA-TCAAGAAATTCATGGTAAGTTTATGAATTTTTGTAT
1 CAAAACT-AAGAAATTCATAATAAGTTTATGAATTTCTGTAT
2242123 TAGTAGTGGG
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 1 0.01
55 87 0.99
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (55 bp):
CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGAACTTTGTGCG
Found at i:2244536 original size:35 final size:34
Alignment explanation
Indices: 2244497--2244605 Score: 102
Period size: 35 Copynumber: 3.3 Consensus size: 34
2244487 AGCACGACTG
*
2244497 GTAATTCCTATCTTTGGAAGATTCAGTCGATGCTA
1 GTAATTCCTATCTTTGG-AGGTTCAGTCGATGCTA
* * *
2244532 GTAATTCCT-TGTAT--AGGTTCAGGCCGA--CTA
1 GTAATTCCTATCTTTGGAGGTTCA-GTCGATGCTA
* *
2244562 GTAATTCCTATCTTTGGCAGGTTCAGTTGCTGCTA
1 GTAATTCCTATCTTTGG-AGGTTCAGTCGATGCTA
2244597 GTAATTCCT
1 GTAATTCCT
2244606 TGTATAGGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
30 12 0.21
31 9 0.16
32 4 0.07
33 2 0.03
34 10 0.17
35 21 0.36
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (34 bp):
GTAATTCCTATCTTTGGAGGTTCAGTCGATGCTA
Found at i:2244539 original size:65 final size:65
Alignment explanation
Indices: 2244444--2244621 Score: 277
Period size: 65 Copynumber: 2.7 Consensus size: 65
2244434 GTAAGAAGAG
* * *
2244444 TTTGGCAGGTTCAGTCGATGCTCGTGATTCCTTGTATAGGTTCAGCACGACTGGTAATTCCTATC
1 TTTGGCAGGTTCAGTCGATGCTAGTAATTCCTTGTATAGGTTCAGCACGACTAGTAATTCCTATC
* *
2244509 TTTGGAAGATTCAGTCGATGCTAGTAATTCCTTGTATAGGTTCAGGC-CGACTAGTAATTCCTAT
1 TTTGGCAGGTTCAGTCGATGCTAGTAATTCCTTGTATAGGTTCA-GCACGACTAGTAATTCCTAT
2244573 C
65 C
* *
2244574 TTTGGCAGGTTCAGTTGCTGCTAGTAATTCCTTGTATAGGTTCAGCAC
1 TTTGGCAGGTTCAGTCGATGCTAGTAATTCCTTGTATAGGTTCAGCAC
2244622 CAAATGATAA
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
64 2 0.02
65 98 0.96
66 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (65 bp):
TTTGGCAGGTTCAGTCGATGCTAGTAATTCCTTGTATAGGTTCAGCACGACTAGTAATTCCTATC
Found at i:2244563 original size:30 final size:30
Alignment explanation
Indices: 2244528--2244618 Score: 94
Period size: 30 Copynumber: 2.9 Consensus size: 30
2244518 TTCAGTCGAT
2244528 GCTAGTAATTCCTTGTATAGGTTCAG-GCC
1 GCTAGTAATTCCTTGTATAGGTTCAGTGCC
* * *
2244557 GACTAGTAATTCCTATCTTTGGCAGGTTCAGTTGCT
1 G-CTAGTAATTCCT-TGTAT---AGGTTCAG-TGCC
2244593 GCTAGTAATTCCTTGTATAGGTTCAG
1 GCTAGTAATTCCTTGTATAGGTTCAG
2244619 CACCAAATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
29 1 0.02
30 12 0.24
31 11 0.22
34 11 0.22
35 12 0.24
36 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (30 bp):
GCTAGTAATTCCTTGTATAGGTTCAGTGCC
Found at i:2244694 original size:31 final size:31
Alignment explanation
Indices: 2244659--2244741 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 31
2244649 GCGACCCTTA
* * **
2244659 GGTAGGTTATGTGGCCCCAAGATTTTTCTTG
1 GGTAGGCTCTGTGGCCCCAAGAACTTTCTTG
* * *
2244690 GGTAGGCCCCGTGGCCCCGAGAACTTTCTTG
1 GGTAGGCTCTGTGGCCCCAAGAACTTTCTTG
*
2244721 GGTAGGCTCTGAGGCCCCAAG
1 GGTAGGCTCTGTGGCCCCAAG
2244742 GTGCTCCCTT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.16, C:0.25, G:0.33, T:0.27
Consensus pattern (31 bp):
GGTAGGCTCTGTGGCCCCAAGAACTTTCTTG
Found at i:2250018 original size:18 final size:19
Alignment explanation
Indices: 2249995--2250075 Score: 89
Period size: 18 Copynumber: 4.3 Consensus size: 19
2249985 TTTACTTAAT
2249995 TTATTATTATTA-AAATTA
1 TTATTATTATTATAAATTA
2250013 TTATTATTATTATAAA-TA
1 TTATTATTATTATAAATTA
*
2250031 TTATTATTA-TATTATATATA
1 TTATTATTATTA-TAAAT-TA
*
2250051 TTA-TATTATTATTAAATAA
1 TTATTATTATTA-TAAATTA
2250070 TTATTA
1 TTATTA
2250076 CAAGCCTAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.04
18 26 0.48
19 12 0.22
20 14 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTATTATTATAAATTA
Found at i:2250075 original size:3 final size:3
Alignment explanation
Indices: 2249995--2250064 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
2249985 TTTACTTAAT
** * *
2249995 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2250042 TTA -TA TATA TTA -TA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
2250065 AATAATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2251551 original size:3 final size:3
Alignment explanation
Indices: 2251536--2251613 Score: 147
Period size: 3 Copynumber: 26.0 Consensus size: 3
2251526 TTCAATATAT
*
2251536 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2251584 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2251614 CAAATATATA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2251671 original size:23 final size:23
Alignment explanation
Indices: 2251636--2251679 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2251626 TAATAAATAA
** *
2251636 TATTTATTTATTTATTTTTATCC
1 TATTTATAAATTTAATTTTATCC
2251659 TATTTATAAATTTAATTTTAT
1 TATTTATAAATTTAATTTTAT
2251680 AAATTAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTATAAATTTAATTTTATCC
Found at i:2251851 original size:128 final size:129
Alignment explanation
Indices: 2251711--2251942 Score: 328
Period size: 127 Copynumber: 1.8 Consensus size: 129
2251701 ATTATATTTA
* * *
2251711 AATATATATTTATTT-TTCAATATTAAGAAATG-GCAGTCTTAAAGCAACTGGATGTCCATTTTC
1 AATATATATTTATTTATT--ATATTAAGAAAGGAGCAGTCTTAAAGCAACTAGAAG-CCATTTTC
*
2251774 TGATATTTTTAAATAAATAAATATTTTATTT-TT-ATAGATTATATAAATTATTTTTAATGTTTT
63 TGATATTTCTAAATAAATAAATATTTTATTTATTAATAGATTATATAAATTATTTTTAATGTTTT
2251837 TT
128 TT
* * * * *
2251839 AATATTTATTTATTTATTGTATTAAGAAAGGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGA
1 AATATATATTTATTTATTATATTAAGAAAGGAGCAGTCTTAAAGCAACTAGAAGCCATTTTCTGA
2251904 TATTTCTAAATAAATAAATATTTTATTTATTAATAGATT
66 TATTTCTAAATAAATAAATATTTTATTTATTAATAGATT
2251943 TTTTTATATA
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
127 48 0.53
128 34 0.37
129 9 0.10
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (129 bp):
AATATATATTTATTTATTATATTAAGAAAGGAGCAGTCTTAAAGCAACTAGAAGCCATTTTCTGA
TATTTCTAAATAAATAAATATTTTATTTATTAATAGATTATATAAATTATTTTTAATGTTTTTT
Found at i:2254857 original size:21 final size:22
Alignment explanation
Indices: 2254812--2254884 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
2254802 CATACATGCA
*
2254812 TTTACATTTTGTATCTGTGCAT
1 TTTACATTTTGTATCTGTACAT
*
2254834 TTT-CATTTTGTATTCT-TACTT
1 TTTACATTTTGTA-TCTGTACAT
* *
2254855 TTTACATCTTTGAAT-TGCACAT
1 TTTACAT-TTTGTATCTGTACAT
*
2254877 TTTGCATT
1 TTTACATT
2254885 CTTATTTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 17 0.41
22 19 0.46
23 5 0.12
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTACATTTTGTATCTGTACAT
Found at i:2257470 original size:15 final size:15
Alignment explanation
Indices: 2257452--2257495 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 15
2257442 AGAAGAAGCA
2257452 AAAAAGGAAAAAAAC
1 AAAAAGGAAAAAAAC
2257467 AAAAAGGAAAAAAAAC
1 AAAAAGG-AAAAAAAC
2257483 AAAAA-GAAAAAAA
1 AAAAAGGAAAAAAA
2257496 AGGAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.25
15 8 0.29
16 13 0.46
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAGGAAAAAAAC
Found at i:2257480 original size:10 final size:10
Alignment explanation
Indices: 2257478--2257512 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2257468 AAAAGGAAAA
*
2257478 AAAACAAAAAG
1 AAAA-AAAAGG
2257489 AAAAAAAAGG
1 AAAAAAAAGG
2257499 AAAAAAAAGG
1 AAAAAAAAGG
2257509 AAAA
1 AAAA
2257513 TTTAATCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:2257502 original size:15 final size:15
Alignment explanation
Indices: 2257452--2257496 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
2257442 AGAAGAAGCA
*
2257452 AAAAAGGAAAAAAAC
1 AAAAAGAAAAAAAAC
2257467 AAAAAGGAAAAAAAAC
1 AAAAA-GAAAAAAAAC
2257483 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
2257497 GGAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAC
Found at i:2262254 original size:22 final size:22
Alignment explanation
Indices: 2262225--2262279 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2262215 ATCTACACTC
2262225 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
2262247 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2262269 TTCAAAGATGA
1 TTCAAAGATGA
2262280 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2263068 original size:166 final size:166
Alignment explanation
Indices: 2262793--2263117 Score: 555
Period size: 166 Copynumber: 2.0 Consensus size: 166
2262783 AAAATGAGCA
2262793 TTATCTTGAGATTGGGACATGTTACCCAATCAACATGTTATTTCAAAAGAATAATGAGAAAACGA
1 TTATCTTGAGATTGGGACATGTTACCCAATCAACATGTTATTTCAAAAGAATAATGAGAAAACGA
* *
2262858 TTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTATGAAAACGATTTCC
66 TTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTCC
*
2262923 TTAGTTTTTTTTACTTAGTAAACTATTTCCTACAGCC
131 TTAG-TTTTTTTACTTAGCAAACTATTTCCTACAGCC
* ** *
2262960 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTGAAA-AATAATGGGAAAACGA
1 TTATCTTGAGATTGGGACATGTTACCCAATCAACATGTTATTTCAAAAGAATAATGAGAAAACGA
2263024 -TTCTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTC
66 TTTC-CATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTC
2263088 CTTAGTTTTTTTACTTAGCAAACTATTTCC
130 CTTAGTTTTTTTACTTAGCAAACTATTTCC
2263118 AACATCTGTA
Statistics
Matches: 150, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
165 27 0.18
166 78 0.52
167 45 0.30
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (166 bp):
TTATCTTGAGATTGGGACATGTTACCCAATCAACATGTTATTTCAAAAGAATAATGAGAAAACGA
TTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATTTCC
TTAGTTTTTTTACTTAGCAAACTATTTCCTACAGCC
Found at i:2263667 original size:303 final size:304
Alignment explanation
Indices: 2263120--2264206 Score: 1972
Period size: 303 Copynumber: 3.6 Consensus size: 304
2263110 CTATTTCCAA
*
2263120 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2263185 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * * *
2263250 GAAGTTTTCAAAGCCTTAGGGTCATTTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
2263315 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTAC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
*
2263380 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTA-GGT
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
2263423 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263488 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
2263553 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
2263618 AGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
*
2263683 AAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
2263727 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263791 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
2263856 GATGTTTTCAAAACCTTAGGATCA-CTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTC
131 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
2263919 GGGAGC-TTTTGATGTTTTCAAAGCCTTAGGGTCATTTGTAAGTCCTACAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
2263983 AAAAAG-CTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
2264026 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2264090 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * *
2264155 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTT
131 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
2264207 TTAAGACCTC
Statistics
Matches: 762, Mismatches: 19, Indels: 9
0.96 0.02 0.01
Matches are distributed among these distances:
298 16 0.02
299 170 0.22
300 87 0.11
301 15 0.02
302 29 0.04
303 393 0.52
304 52 0.07
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (304 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC
AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
Found at i:2264207 original size:76 final size:76
Alignment explanation
Indices: 2263120--2264206 Score: 1972
Period size: 76 Copynumber: 14.4 Consensus size: 76
2263110 CTATTTCCAA
*
2263120 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263185 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2263196 CATCTGTAAGTCCTACAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGAAGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263261 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2263272 CATTTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263337 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2263348 CATCTGTAAGTCCTACAGTGCATGATGTTTACAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263413 AGCCTTA-GGT
66 AGCCTTAGGGT
2263423 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263488 AGCCTTAGGGT
66 AGCCTTAGGGT
2263499 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263564 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2263575 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263640 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2263651 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263716 AGCCTTAGGGT
66 AGCCTTAGGGT
2263727 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263791 AGCCTTAGGGT
66 AGCCTTAGGGT
2263802 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
2263867 AACCTTAGGAT
66 AGCCTTAGGGT
2263878 CA-CTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2263940 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2263951 CATTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAG-CTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2264015 AGCCTTAGGGT
66 AGCCTTAGGGT
2264026 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2264090 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2264101 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
2264166 AACCTTCGGGT
66 AGCCTTAGGGT
* *
2264177 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
2264207 TTAAGACCTC
Statistics
Matches: 976, Mismatches: 28, Indels: 14
0.96 0.03 0.01
Matches are distributed among these distances:
73 26 0.03
74 59 0.06
75 307 0.31
76 584 0.60
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:2264448 original size:3 final size:3
Alignment explanation
Indices: 2264374--2264437 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
2264364 TTATTAAAAT
* *
2264374 TTA TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2264420 TATA TTA -TA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA
2264438 AATAATTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 6 0.11
3 44 0.83
4 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2265389 original size:16 final size:16
Alignment explanation
Indices: 2265368--2265402 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2265358 TTTCATAAGG
2265368 GGTAAACCCCTTCCGC
1 GGTAAACCCCTTCCGC
*
2265384 GGTAAACCCCTTCTGC
1 GGTAAACCCCTTCCGC
2265400 GGT
1 GGT
2265403 GTTCCATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.37, G:0.23, T:0.23
Consensus pattern (16 bp):
GGTAAACCCCTTCCGC
Found at i:2265935 original size:3 final size:3
Alignment explanation
Indices: 2265927--2265961 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2265917 ATATATTTAT
2265927 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2265962 CAAATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2266014 original size:22 final size:22
Alignment explanation
Indices: 2265986--2266027 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2265976 AAATAATATT
* *
2265986 TATTTATTATTTATTTTTATCC
1 TATTTATAATTTAATTTTATCC
2266008 TATTTATAATTTAATTTTAT
1 TATTTATAATTTAATTTTAT
2266028 AATTAGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTATAATTTAATTTTATCC
Found at i:2268230 original size:14 final size:14
Alignment explanation
Indices: 2268213--2268243 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2268203 ACCTTGAAAT
2268213 AATCAAATTGATTG
1 AATCAAATTGATTG
2268227 AATCAAATTGATTG
1 AATCAAATTGATTG
2268241 AAT
1 AAT
2268244 TTGAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (14 bp):
AATCAAATTGATTG
Found at i:2268366 original size:19 final size:18
Alignment explanation
Indices: 2268317--2268371 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
2268307 GTGAGGAAAA
2268317 TTTTAA-AAA-AATATATT
1 TTTTAATAAATAA-ATATT
* *
2268334 TTTTATTAACTAAATATT
1 TTTTAATAAATAAATATT
2268352 GTTTTAATAAATAAATATT
1 -TTTTAATAAATAAATATT
2268371 T
1 T
2268372 CAAAAATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 5 0.16
18 8 0.26
19 18 0.58
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTTAATAAATAAATATT
Found at i:2275510 original size:40 final size:40
Alignment explanation
Indices: 2275458--2275923 Score: 376
Period size: 40 Copynumber: 11.6 Consensus size: 40
2275448 ATTCTTATGA
* * * *
2275458 TTGAGTGTGTATCACATTCAATATATAAGCATTATTATAG
1 TTGAGTGTGTATCTCATTCAATACATCACCATTATTATAG
* * * *
2275498 TTGGGTTTGTATC-C-TGTATAATACATCACCATTTATTGTAG
1 TTGAGTGTGTATCTCAT-T-CAATACATCACCA-TTATTATAG
* * *
2275539 TTGAGTGTGCATC-C-TGTGTAATACATCATCATTATTATAG
1 TTGAGTGTGTATCTCAT-T-CAATACATCACCATTATTATAG
* * **
2275579 TTGAGTGTGTGTCTCATGCAATACATCACCATTATTGCAG
1 TTGAGTGTGTATCTCATTCAATACATCACCATTATTATAG
* * * *
2275619 TTGGGTGTATATC-CTATACAATACATCACTATTATTATAG
1 TTGAGTGTGTATCTC-ATTCAATACATCACCATTATTATAG
* * * * *
2275659 TTGGGTGTGTATCTCATGCCATATATCACCATTATTATGG
1 TTGAGTGTGTATCTCATTCAATACATCACCATTATTATAG
* *
2275699 TT-ATGTGTGTATCTCATGCAATACAACACCATTATTATAG
1 TTGA-GTGTGTATCTCATTCAATACATCACCATTATTATAG
* *
2275739 TTCAGTGTGTATCAT-ATTCAATAAATCACCATTATTATAG
1 TTGAGTGTGTATC-TCATTCAATACATCACCATTATTATAG
* * *
2275779 TTGGGGTGTGTATCTCGTAT-AATATATCACCATTATTATAG
1 TT-GAGTGTGTATCTCAT-TCAATACATCACCATTATTATAG
* *
2275820 TTGAGTGTGTATCTCGTAT-AATATATCACCATTATTATAG
1 TTGAGTGTGTATCTCAT-TCAATACATCACCATTATTATAG
* * * * * * * *
2275860 CTGAGTGCGTATCACATTCAATATATTACAATTCTTGTAG
1 TTGAGTGTGTATCTCATTCAATACATCACCATTATTATAG
*
2275900 TT-AGGTGTGTATCTCATACAATAC
1 TTGA-GTGTGTATCTCATTCAATAC
2275924 GACACCACTC
Statistics
Matches: 352, Mismatches: 59, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
38 1 0.00
39 5 0.01
40 274 0.78
41 70 0.20
42 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (40 bp):
TTGAGTGTGTATCTCATTCAATACATCACCATTATTATAG
Found at i:2275912 original size:161 final size:159
Alignment explanation
Indices: 2275569--2275882 Score: 373
Period size: 161 Copynumber: 2.0 Consensus size: 159
2275559 ATACATCATC
* * * * *
2275569 ATTATTATAGTTGAGTGTGTGTC-TCATGCAATACATCACCATTATTGCAGTTGGGTGTATATCC
1 ATTATTATAGTTCAGTGTGTATCAT-ATTCAATAAATCACCATTATTACAGTTGGGTGTATATCC
* * * *
2275633 TATACAATACATCACTATTATTATAGTTGGGTGTGTATCTCATGCCATATATCACCATTATTATG
65 TATA-AATACATCACCATTATTATAGTTGAGTGTGTATCTCATACAATATATCACCATTATTATG
* * * * *
2275698 GTTATGTGTGTATCTCATGCAATACAACACC
129 CTGATGTGCGTATCACATGCAATACAACACA
* *
2275729 ATTATTATAGTTCAGTGTGTATCATATTCAATAAATCACCATTATTATAGTTGGGGTGTGTATCT
1 ATTATTATAGTTCAGTGTGTATCATATTCAATAAATCACCATTATTACAGTT-GGGTGTATATC-
* * *
2275794 CGTAT-AATATATCACCATTATTATAGTTGAGTGTGTATCTCGTATAATATATCACCATTATTAT
64 C-TATAAATACATCACCATTATTATAGTTGAGTGTGTATCTCATACAATATATCACCATTATTAT
*
2275858 AGCTGA-GTGCGTATCACATTCAATA
128 -GCTGATGTGCGTATCACATGCAATA
2275883 TATTACAATT
Statistics
Matches: 130, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
160 44 0.34
161 79 0.61
162 4 0.03
163 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (159 bp):
ATTATTATAGTTCAGTGTGTATCATATTCAATAAATCACCATTATTACAGTTGGGTGTATATCCT
ATAAATACATCACCATTATTATAGTTGAGTGTGTATCTCATACAATATATCACCATTATTATGCT
GATGTGCGTATCACATGCAATACAACACA
Found at i:2276027 original size:70 final size:70
Alignment explanation
Indices: 2275944--2276084 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
2275934 TTGTATTTAG
2275944 GCGTGTATCCCATATAATAGATCACTTCAATTATCAGTGTCAATACCAATATCCTAGTACTTATA
1 GCGTGTATCCCATATAATAGATCACTTCAATTATCAGTGTCAATACCAATATCCTAGTACTTATA
2276009 CTATA
66 CTATA
2276014 GCGTGTATCCCATATAATAGATCACTTCAATTATCAGTGTCAATACCAATATCCTAGTACTTATA
1 GCGTGTATCCCATATAATAGATCACTTCAATTATCAGTGTCAATACCAATATCCTAGTACTTATA
2276079 CTATA
66 CTATA
2276084 G
1 G
2276085 AATAGTTTTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (70 bp):
GCGTGTATCCCATATAATAGATCACTTCAATTATCAGTGTCAATACCAATATCCTAGTACTTATA
CTATA
Found at i:2276205 original size:39 final size:38
Alignment explanation
Indices: 2276055--2276205 Score: 140
Period size: 39 Copynumber: 3.9 Consensus size: 38
2276045 TATCAGTGTC
* * *
2276055 AATACCAATATCCTAGTACTTATACTATAGAATAGTTTT
1 AATACCAATATCCTGGTACCTATA-TTTAGAATAGTTTT
* * * * *
2276094 AATACCACTATCCTCGTAACTATAGTTTGGAATAGTTTC
1 AATACCAATATCCTGGTACCTATA-TTTAGAATAGTTTT
* * * *
2276133 AATACCAATATCCTGATATCTATAATCTCGAATAGTTTT
1 AATACCAATATCCTGGTACCTAT-ATTTAGAATAGTTTT
* *
2276172 AATGCCAATATACTGGTACCTATATTGTAGAATA
1 AATACCAATATCCTGGTACCTATATT-TAGAATA
2276206 CTTGTATTGT
Statistics
Matches: 89, Mismatches: 21, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
38 2 0.02
39 86 0.97
40 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (38 bp):
AATACCAATATCCTGGTACCTATATTTAGAATAGTTTT
Found at i:2276205 original size:78 final size:78
Alignment explanation
Indices: 2276053--2276205 Score: 177
Period size: 78 Copynumber: 2.0 Consensus size: 78
2276043 ATTATCAGTG
* * *
2276053 TCAATACCAATATCCTAGTACTTATACTATAGAATAGTTTTAATACCACTATCCTCGTAACTATA
1 TCAATACCAATATCCTAGTACTTATAATATAGAATAGTTTTAATACCAATATACTCGTAACTATA
*
2276118 GTTTGGAATAGTT
66 GTTTAGAATAGTT
* * * * *
2276131 TCAATACCAATATCCT-GATA-TCTATAATCTCGAATAGTTTTAATGCCAATATACTGGTACCTA
1 TCAATACCAATATCCTAG-TACT-TATAATATAGAATAGTTTTAATACCAATATACTCGTAACTA
2276194 TA-TTGTAGAATA
64 TAGTT-TAGAATA
2276206 CTTGTATTGT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
77 4 0.06
78 59 0.94
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (78 bp):
TCAATACCAATATCCTAGTACTTATAATATAGAATAGTTTTAATACCAATATACTCGTAACTATA
GTTTAGAATAGTT
Found at i:2286873 original size:19 final size:19
Alignment explanation
Indices: 2286845--2286914 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
2286835 ATGTGTTGGA
* * *
2286845 GAAACCAGATTTTAGGCTG
1 GAAACTAGATTTTAAGTTG
*
2286864 GAAACTAGATTTTAAGTTA
1 GAAACTAGATTTTAAGTTG
* *
2286883 GAATCCT-GATTTTATGTTG
1 GAA-ACTAGATTTTAAGTTG
2286902 GAAACTAGATTTT
1 GAAACTAGATTTT
2286915 TGGGTTTAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.05
19 37 0.90
20 2 0.05
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (19 bp):
GAAACTAGATTTTAAGTTG
Found at i:2292574 original size:26 final size:25
Alignment explanation
Indices: 2292538--2292593 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 25
2292528 ATCGAAGTGC
2292538 TACACATAAGGTCGTGCCCACCATAA
1 TACACATAAGGTCGTGCCCACCAT-A
*
2292564 TACACATAAGGTTGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATA
2292589 TACAC
1 TACAC
2292594 TTAGTGTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.21
Consensus pattern (25 bp):
TACACATAAGGTCGTGCCCACCATA
Found at i:2297279 original size:24 final size:23
Alignment explanation
Indices: 2297234--2297280 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2297224 ATTTGGCTCA
*
2297234 TGATCTTCCAGTCATCTTGGATG
1 TGATCTTCCAGTCATCTAGGATG
2297257 TGATCTTGCCAG-CATCTAAGGATG
1 TGATCTT-CCAGTCATCT-AGGATG
2297281 CTACAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (23 bp):
TGATCTTCCAGTCATCTAGGATG
Found at i:2300838 original size:241 final size:241
Alignment explanation
Indices: 2300414--2300872 Score: 805
Period size: 241 Copynumber: 1.9 Consensus size: 241
2300404 AGAGAATTAG
2300414 AGGATCAATCTTGTGGTTTACCCTTTTCTTTTAAAACATAATTCCCTCCCCCGTTTTTTATATCT
1 AGGATCAATCTTGTGGTTTACCCTTTTCTTTTAAAACATAATTCCCTCCCCCGTTTTTTATATCT
* *
2300479 GTGCGGTGCCTCCACTGGTTTTTCCCCCCTTTTCTTTGTTTCTTCCTCATCTCCGTTTGTCGATT
66 GTGCGGTGCCTCCACTGGTTTTT-CCCCCTTTTCTTTGTTTCTTCCTCATCGCCGTTTGTCAATT
2300544 CAATATCATCAGATAGTCAAGGTAAGTCACCAGTCATCATCTCAACAATACTCTATCTTAACCTT
130 CAATATCATCAGATAGTCAAGGTAAGTCACCAGTCATCATCTCAACAATACTCTATCTTAACCTT
2300609 GGCACTTGCCATCGATGTTGGGAAGAAACCGTGAGCATTGGCTCTTA
195 GGCACTTGCCATCGATGTTGGGAAGAAACCGTGAGCATTGGCTCTTA
2300656 AGGATCAATCTTGTGGTTTACCCTTTTTCTTTTAAAACATAATTCCCTCCCCCGTTTTTTATATC
1 AGGATCAATCTTGTGGTTTACCC-TTTTCTTTTAAAACATAATTCCCTCCCCCGTTTTTTATATC
*
2300721 TGTGCGGTGCCTCCACTGGTTTTT-CTCCTTTTCTTTGTTTCTTCCTCATCGCCGTTTGT-AACT
65 TGTGCGGTGCCTCCACTGGTTTTTCCCCCTTTTCTTTGTTTCTTCCTCATCGCCGTTTGTCAA-T
* * * * *
2300784 TCAATGTCATCTGATAGTCAAGGTAAGTCACCAGTCATCTTCTCGACAATACTCTTTCTTAACCT
129 TCAATATCATCAGATAGTCAAGGTAAGTCACCAGTCATCATCTCAACAATACTCTATCTTAACCT
2300849 TGGCACTTGCCATCGATGTTGGGA
194 TGGCACTTGCCATCGATGTTGGGA
2300873 GATGTTGGGA
Statistics
Matches: 207, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
240 1 0.00
241 118 0.57
242 23 0.11
243 65 0.31
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (241 bp):
AGGATCAATCTTGTGGTTTACCCTTTTCTTTTAAAACATAATTCCCTCCCCCGTTTTTTATATCT
GTGCGGTGCCTCCACTGGTTTTTCCCCCTTTTCTTTGTTTCTTCCTCATCGCCGTTTGTCAATTC
AATATCATCAGATAGTCAAGGTAAGTCACCAGTCATCATCTCAACAATACTCTATCTTAACCTTG
GCACTTGCCATCGATGTTGGGAAGAAACCGTGAGCATTGGCTCTTA
Found at i:2303939 original size:18 final size:18
Alignment explanation
Indices: 2303916--2303953 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2303906 AGGGCTAGAC
2303916 CAACTTAGAGTAAAGGTT
1 CAACTTAGAGTAAAGGTT
2303934 CAACTTAGAGTAAAGGTT
1 CAACTTAGAGTAAAGGTT
2303952 CA
1 CA
2303954 GATAGATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (18 bp):
CAACTTAGAGTAAAGGTT
Found at i:2309821 original size:30 final size:30
Alignment explanation
Indices: 2309787--2309869 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 30
2309777 GATATAAAAT
* *
2309787 ATTTTTTATTATACAATAAGTGTGTGTGTA
1 ATTTTTTATTATGCAGTAAGTGTGTGTGTA
2309817 ATTTTTTATTATGCAGTAAG-GTGTGTGTA
1 ATTTTTTATTATGCAGTAAGTGTGTGTGTA
* *
2309846 TTTTTTTATAATGCAGTAAGTGTG
1 ATTTTTTATTATGCAGTAAGTGTG
2309870 AGTAAATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 27 0.56
30 21 0.44
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (30 bp):
ATTTTTTATTATGCAGTAAGTGTGTGTGTA
Found at i:2309919 original size:56 final size:54
Alignment explanation
Indices: 2309846--2309977 Score: 169
Period size: 54 Copynumber: 2.4 Consensus size: 54
2309836 GGTGTGTGTA
* * *
2309846 TTTTTTTATAATGCAGTAAGTGTGAGTAAATTTAATATATATTTATGTGTGTATGC
1 TTTTTTTATTATGCAGTACGTGTGAGT--ATTTAATATATATGTATGTGTGTATGC
* * *
2309902 TTTTTTTATTATGCAGTACGTGTGTGTGTTTAATATATATGTATGTGTGTGTGC
1 TTTTTTTATTATGCAGTACGTGTGAGTATTTAATATATATGTATGTGTGTATGC
*
2309956 --TTTTTATTATGCAATACGTGTG
1 TTTTTTTATTATGCAGTACGTGTG
2309978 TATGTTTAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
52 21 0.30
54 24 0.35
56 24 0.35
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.50
Consensus pattern (54 bp):
TTTTTTTATTATGCAGTACGTGTGAGTATTTAATATATATGTATGTGTGTATGC
Found at i:2309940 original size:54 final size:54
Alignment explanation
Indices: 2309846--2309993 Score: 183
Period size: 52 Copynumber: 2.7 Consensus size: 54
2309836 GGTGTGTGTA
* * * * *
2309846 TTTTTTTATAATGCAGTAAGTGTGAGTAAATTTAATATATATTTATGTGTGTATGC
1 TTTTTTTATTATGCAGTACGTGTGTGT--GTTTAATATATATGTATGTGTGTATGC
*
2309902 TTTTTTTATTATGCAGTACGTGTGTGTGTTTAATATATATGTATGTGTGTGTGC
1 TTTTTTTATTATGCAGTACGTGTGTGTGTTTAATATATATGTATGTGTGTATGC
* * *
2309956 --TTTTTATTATGCAATACGTGTGTATGTTTAATGTATAT
1 TTTTTTTATTATGCAGTACGTGTGTGTGTTTAATATATAT
2309994 ATGAAATGTC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
52 35 0.42
54 24 0.29
56 24 0.29
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.51
Consensus pattern (54 bp):
TTTTTTTATTATGCAGTACGTGTGTGTGTTTAATATATATGTATGTGTGTATGC
Found at i:2309976 original size:25 final size:24
Alignment explanation
Indices: 2309904--2309978 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
2309894 GTGTATGCTT
*
2309904 TTTTTATTATGCAGTACGTGTGTG
1 TTTTTATTATGCAATACGTGTGTG
* **
2309928 TGTTTAATATATATG-TATGTGTGTGTG
1 T-TTT--TAT-TATGCAATACGTGTGTG
2309955 CTTTTTATTATGCAATACGTGTGT
1 -TTTTTATTATGCAATACGTGTGT
2309979 ATGTTTAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 11
0.68 0.12 0.20
Matches are distributed among these distances:
24 5 0.13
25 14 0.37
27 14 0.37
28 5 0.13
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.51
Consensus pattern (24 bp):
TTTTTATTATGCAATACGTGTGTG
Found at i:2310079 original size:54 final size:52
Alignment explanation
Indices: 2309992--2310111 Score: 161
Period size: 54 Copynumber: 2.3 Consensus size: 52
2309982 TTTAATGTAT
*
2309992 ATATGAAATGTCTGTGTGACTTATTATAATATAAAGGGTGTGTGATCTT-TTA
1 ATATGAAATGTGTGTGTGACTTATTATAATATAAAGGGTGTGTG-TCTTGTTA
* * *
2310044 ATATGAAATGTGTGTGAGTGAGTTTTTATAATATAAAGGGTGTGTGTGTTGTTA
1 ATATGAAATGTGTGT--GTGACTTATTATAATATAAAGGGTGTGTGTCTTGTTA
*
2310098 ATACGAAATGTGTG
1 ATATGAAATGTGTG
2310112 AGTTTTTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
52 14 0.23
53 3 0.05
54 43 0.72
ACGTcount: A:0.30, C:0.03, G:0.26, T:0.41
Consensus pattern (52 bp):
ATATGAAATGTGTGTGTGACTTATTATAATATAAAGGGTGTGTGTCTTGTTA
Found at i:2310133 original size:24 final size:24
Alignment explanation
Indices: 2310061--2310135 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
2310051 ATGTGTGTGA
*
2310061 GTGAGTTTTTATAATATAAAGG-GT
1 GTGAGTTTTTATAATAT-GAGGTGT
* * * **
2310085 GTGTGTGTTGT-TAATACGAAATGT
1 GTGAGT-TTTTATAATATGAGGTGT
2310109 GTGAGTTTTTATAATATGAGGTGT
1 GTGAGTTTTTATAATATGAGGTGT
2310133 GTG
1 GTG
2310136 TTTTCGAAAG
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
23 4 0.11
24 30 0.81
25 3 0.08
ACGTcount: A:0.27, C:0.01, G:0.29, T:0.43
Consensus pattern (24 bp):
GTGAGTTTTTATAATATGAGGTGT
Found at i:2310209 original size:24 final size:20
Alignment explanation
Indices: 2310149--2310208 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
2310139 TCGAAAGGTA
2310149 AACCACCGGAAGTAACTAAC
1 AACCACCGGAAGTAACTAAC
2310169 AACCACCGGAAGTAACTAAC
1 AACCACCGGAAGTAACTAAC
*
2310189 AACCACCGGAAGTAATTAAC
1 AACCACCGGAAGTAACTAAC
2310209 TGATTTCAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.12
Consensus pattern (20 bp):
AACCACCGGAAGTAACTAAC
Found at i:2312196 original size:15 final size:15
Alignment explanation
Indices: 2312178--2312218 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2312168 TTCATGGGGT
*
2312178 AAGAAGACAACGTCA
1 AAGAAGAAAACGTCA
*
2312193 AAGAAGAAAATGTCA
1 AAGAAGAAAACGTCA
2312208 AAGAAGGAAAA
1 AAGAA-GAAAA
2312219 AGAAAACATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.61, C:0.10, G:0.22, T:0.07
Consensus pattern (15 bp):
AAGAAGAAAACGTCA
Found at i:2315640 original size:13 final size:12
Alignment explanation
Indices: 2315619--2315660 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
2315609 AATGACGTGC
2315619 AATGCGCGTCATA
1 AATG-GCGTCATA
2315632 AATGAGCGTCATA
1 AATG-GCGTCATA
2315645 AAT-GCGTTCATA
1 AATGGCG-TCATA
2315657 AATG
1 AATG
2315661 CATGTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 3 0.12
12 8 0.31
13 15 0.58
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (12 bp):
AATGGCGTCATA
Found at i:2315657 original size:12 final size:13
Alignment explanation
Indices: 2315640--2315682 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
2315630 TAAATGAGCG
2315640 TCATAAATGCGT-
1 TCATAAATGCGTA
* *
2315652 TCATAAATGCATG
1 TCATAAATGCGTA
*
2315665 TCAAAAATGCGTA
1 TCATAAATGCGTA
2315678 TCATA
1 TCATA
2315683 GATTTATGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (13 bp):
TCATAAATGCGTA
Found at i:2315657 original size:25 final size:26
Alignment explanation
Indices: 2315627--2315682 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
2315617 GCAATGCGCG
*
2315627 TCATAAATG-AGCGTCATAAATGCGT-
1 TCATAAATGCA-CGTCAAAAATGCGTA
*
2315652 TCATAAATGCATGTCAAAAATGCGTA
1 TCATAAATGCACGTCAAAAATGCGTA
2315678 TCATA
1 TCATA
2315683 GATTTATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (26 bp):
TCATAAATGCACGTCAAAAATGCGTA
Found at i:2334317 original size:19 final size:18
Alignment explanation
Indices: 2334293--2334328 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2334283 TAATTGGTGA
*
2334293 GATTTAATTTGTATTTTTG
1 GATTTAAATTG-ATTTTTG
2334312 GATTTAAATTGATTTTT
1 GATTTAAATTGATTTTT
2334329 CATGTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (18 bp):
GATTTAAATTGATTTTTG
Found at i:2337424 original size:2 final size:2
Alignment explanation
Indices: 2337417--2337446 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2337407 TACATACATG
2337417 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
2337447 CACACACAGT
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):
TA
Found at i:2337638 original size:33 final size:34
Alignment explanation
Indices: 2337583--2337666 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
2337573 CGTGTACATT
* * *
2337583 TGATGATTGCACCTGGAGTGCAT-TTTTTGTATC
1 TGATGATTGCACCTAGACTGCATATTTATGTATC
* * *
2337616 TGATTATTGCACCTATACTGCATATTTATGTTTC
1 TGATGATTGCACCTAGACTGCATATTTATGTATC
**
2337650 TGATGATAACACCTAGA
1 TGATGATTGCACCTAGA
2337667 GTACTTATTA
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
33 19 0.47
34 21 0.52
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (34 bp):
TGATGATTGCACCTAGACTGCATATTTATGTATC
Found at i:2342513 original size:30 final size:31
Alignment explanation
Indices: 2342456--2342517 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
2342446 CGCGATCGAG
*
2342456 GTGCGATTGAGAGAACTTTTGGATTGAAATC
1 GTGCGATTGAGAGAACTTTTAGATTGAAATC
**
2342487 GTGCGATTGAGAG-TTTTTTAGATTGAAATC
1 GTGCGATTGAGAGAACTTTTAGATTGAAATC
2342517 G
1 G
2342518 CGCGCTCGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.35
Consensus pattern (31 bp):
GTGCGATTGAGAGAACTTTTAGATTGAAATC
Found at i:2343288 original size:15 final size:15
Alignment explanation
Indices: 2343246--2343288 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2343236 TTTTAAATAT
*
2343246 ATAAATATACAAAAC
1 ATAAATATAAAAAAC
* *
2343261 ATAAACATAAAAAAT
1 ATAAATATAAAAAAC
2343276 ACTAAATATAAAA
1 A-TAAATATAAAA
2343289 GTTAAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAATATAAAAAAC
Found at i:2343714 original size:15 final size:16
Alignment explanation
Indices: 2343694--2343723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2343684 TTTATAAATA
2343694 AATTTT-AATTTTATG
1 AATTTTAAATTTTATG
2343709 AATTTTAAATTTTAT
1 AATTTTAAATTTTAT
2343724 TTTTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
AATTTTAAATTTTATG
Found at i:2345673 original size:19 final size:19
Alignment explanation
Indices: 2345649--2345688 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2345639 TTTAGTATAA
*
2345649 ATACTTAGGAGGATTATCG
1 ATACTTAGGAGGATTACCG
2345668 ATACTTAGGAGGATTACCG
1 ATACTTAGGAGGATTACCG
2345687 AT
1 AT
2345689 GGTATTACCA
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:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (19 bp):
ATACTTAGGAGGATTACCG
Found at i:2348079 original size:31 final size:31
Alignment explanation
Indices: 2348039--2348099 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2348029 TTGAATGTTC
*
2348039 AAAATAAAAATAC-AAAATTATACGAATGACT
1 AAAACAAAAATACGAAAA-TATACGAATGACT
* *
2348070 AAAACAAAAATACGAGAATATATGAATGAC
1 AAAACAAAAATACGAAAATATACGAATGAC
2348100 CATATAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.20
Consensus pattern (31 bp):
AAAACAAAAATACGAAAATATACGAATGACT
Found at i:2349041 original size:22 final size:21
Alignment explanation
Indices: 2349016--2349057 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2349006 TGAGTTCACT
2349016 ATGGATGCTTAAGTTTTCTTTA
1 ATGGATGCTT-AGTTTTCTTTA
* *
2349038 ATGGATGGTTTGTTTTCTTT
1 ATGGATGCTTAGTTTTCTTT
2349058 TTATGCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55
Consensus pattern (21 bp):
ATGGATGCTTAGTTTTCTTTA
Found at i:2350941 original size:22 final size:21
Alignment explanation
Indices: 2350916--2350957 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2350906 TGAGTTAACT
2350916 ATGGATGCTTAAGTTTTCTTTA
1 ATGGATGCTTAA-TTTTCTTTA
* *
2350938 ATGGATGGTTTATTTTCTTT
1 ATGGATGCTTAATTTTCTTT
2350958 TTATGCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.55
Consensus pattern (21 bp):
ATGGATGCTTAATTTTCTTTA
Found at i:2358014 original size:171 final size:171
Alignment explanation
Indices: 2357729--2358059 Score: 646
Period size: 171 Copynumber: 1.9 Consensus size: 171
2357719 TAAAAATCTC
2357729 ATCCAACACTCTAGAACTAAGCATATTGAAATTAGACATCACTTCATTAGAGACCATGTCACTAA
1 ATCCAACACTCTAGAACTAAGCATATTGAAATTAGACATCACTTCATTAGAGACCATGTCACTAA
2357794 GGAATATGTAGTTCTAGAATTTGTTGATACTTTGCATCAATTAGCGGATATTTTTTACAAAACCT
66 GGAATATGTAGTTCTAGAATTTGTTGATACTTTGCATCAATTAGCGGATA-TTTTTACAAAACCT
2357859 TTATACAAAGAAAGA-TTTGGAAACTTAGGAATTTAACTAAA
130 TTATACAAAGAAAGATTTTGGAAACTTAGGAATTTAACTAAA
2357900 ATCCAACACTCTAGAACTAAGCATATTGAAATTAGACATCACTTCATTAGAGACCATGTCACTAA
1 ATCCAACACTCTAGAACTAAGCATATTGAAATTAGACATCACTTCATTAGAGACCATGTCACTAA
2357965 GGAATATGTAGTTCTAGAATTTGTTGATACTTTGCATCAATTAGCGGATATTTTTACAAAACCTT
66 GGAATATGTAGTTCTAGAATTTGTTGATACTTTGCATCAATTAGCGGATATTTTTACAAAACCTT
2358030 TATACAAAGAAAGATTTTGGAAACTTAGGA
131 TATACAAAGAAAGATTTTGGAAACTTAGGA
2358060 GAGAATTAAG
Statistics
Matches: 159, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
170 29 0.18
171 130 0.82
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (171 bp):
ATCCAACACTCTAGAACTAAGCATATTGAAATTAGACATCACTTCATTAGAGACCATGTCACTAA
GGAATATGTAGTTCTAGAATTTGTTGATACTTTGCATCAATTAGCGGATATTTTTACAAAACCTT
TATACAAAGAAAGATTTTGGAAACTTAGGAATTTAACTAAA
Found at i:2359570 original size:15 final size:15
Alignment explanation
Indices: 2359550--2359579 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2359540 CTTTTCATTT
2359550 TGGGTTAAATAATGA
1 TGGGTTAAATAATGA
*
2359565 TGGGTTATATAATGA
1 TGGGTTAAATAATGA
2359580 GAATGAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (15 bp):
TGGGTTAAATAATGA
Found at i:2361238 original size:65 final size:63
Alignment explanation
Indices: 2361169--2361328 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 63
2361159 AAATAAATTG
* * *
2361169 AACATCGAATGCATTTCATGCATCGATGCACATACCATGAATCGATGCACTGAGGAT-TTTATGA
1 AACATCAAATGCATTTGATGCATCGATGCACA-ACCATGAATCGATGCACTCAGGATATTT-TG-
2361233 A
63 A
* * * *
2361234 AACATCAAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCAAATGCATTTGATGCATCGATGCA-CAACCATGAATCGATGCACTCAGGATATTTTGA
*
2361298 AACATCAAATGCACTTGATGCATCGATGCAC
1 AACATCAAATGCATTTGATGCATCGATGCAC
2361329 TGTTAGTGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 49 0.58
66 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCAAATGCATTTGATGCATCGATGCACAACCATGAATCGATGCACTCAGGATATTTTGA
Found at i:2365216 original size:23 final size:23
Alignment explanation
Indices: 2365182--2365255 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
2365172 GGAATCGATA
*
2365182 CCCCCTTT-AAGGGCAACCAATT
1 CCCCCTTTGAAGGGGAACCAATT
*
2365204 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCTTTGAAGGGGAACCAATT
* *
2365227 CCCCCTTTGAAGGGGAATCTATT
1 CCCCCTTTGAAGGGGAACCAATT
2365250 CCCCCT
1 CCCCCT
2365256 GTAGGGTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 8 0.17
23 39 0.83
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACCAATT
Found at i:2370395 original size:22 final size:22
Alignment explanation
Indices: 2370364--2370407 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2370354 ATTCACGAAC
*
2370364 ATATTCGTTTATCGTTTGTTTA
1 ATATTCGTTTATCGTTCGTTTA
* *
2370386 ATATTGGTTTATTGTTCGTTTA
1 ATATTCGTTTATCGTTCGTTTA
2370408 TATGTTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.07, G:0.16, T:0.59
Consensus pattern (22 bp):
ATATTCGTTTATCGTTCGTTTA
Found at i:2373251 original size:18 final size:18
Alignment explanation
Indices: 2373224--2373266 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2373214 GACCGGTCAT
**
2373224 GACCCGACCCGTTGACCC
1 GACCCGACCCGACGACCC
*
2373242 GACCCTACCCGACGACCC
1 GACCCGACCCGACGACCC
2373260 GACCCGA
1 GACCCGA
2373267 TCTGACCGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.51, G:0.21, T:0.07
Consensus pattern (18 bp):
GACCCGACCCGACGACCC
Found at i:2373322 original size:29 final size:29
Alignment explanation
Indices: 2373289--2373392 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 29
2373279 CAGTTGACTA
2373289 GTGCTATTCTGGGAATTAATTCGGTTTTG
1 GTGCTATTCTGGGAATTAATTCGGTTTTG
* * *
2373318 GTGCTATTCTAGAAATTAATTTGGTTTTG
1 GTGCTATTCTGGGAATTAATTCGGTTTTG
* *** *
2373347 GTGCTATTTTGGGAATTAATTCGAAATGG
1 GTGCTATTCTGGGAATTAATTCGGTTTTG
*
2373376 GTGCTATTCTGGTAATT
1 GTGCTATTCTGGGAATT
2373393 TTTTTAAAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (29 bp):
GTGCTATTCTGGGAATTAATTCGGTTTTG
Found at i:2373435 original size:86 final size:86
Alignment explanation
Indices: 2373317--2373490 Score: 267
Period size: 86 Copynumber: 2.0 Consensus size: 86
2373307 ATTCGGTTTT
* * * *** *
2373317 GGTGCTATTCTAGAAATTAATTTGGTTTTGGTGCTATTTTGGGAATTAATTCGAAATGGGTGCTA
1 GGTGATATTCTAGAAAATAATTAGAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTA
*
2373382 TTCTGGTAATTTTTTTAAAAA
66 TTCTGGTAATTATTTTAAAAA
2373403 GGTGATATTCTAGAAAATAATTAGAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTA
1 GGTGATATTCTAGAAAATAATTAGAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTA
*
2373468 TTTTGGTAATTATTTTAAAAA
66 TTCTGGTAATTATTTTAAAAA
2373489 GG
1 GG
2373491 GTGCTATTTG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (86 bp):
GGTGATATTCTAGAAAATAATTAGAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTA
TTCTGGTAATTATTTTAAAAA
Found at i:2373440 original size:29 final size:29
Alignment explanation
Indices: 2373315--2373469 Score: 89
Period size: 29 Copynumber: 5.4 Consensus size: 29
2373305 TAATTCGGTT
* ***
2373315 TTGGTGCTATTCTAGAAATTAATTTGGTT
1 TTGGTGCTATTCTAGAAATTAATTAGAAA
* * * *
2373344 TTGGTGCTATTTTGGGAATTAATTCGAAA
1 TTGGTGCTATTCTAGAAATTAATTAGAAA
* * * **
2373373 TGGGTGCTATTCTGGTAATTTTTTTA-AAA
1 TTGGTGCTATTCTAG-AAATTAATTAGAAA
* * *
2373402 -AGGTGATATTCTAGAAAATAATTAGAAA
1 TTGGTGCTATTCTAGAAATTAATTAGAAA
* * * *
2373430 TTGGTGCTATTTTGGGAATTAATTCGAAA
1 TTGGTGCTATTCTAGAAATTAATTAGAAA
**
2373459 AGGGTGCTATT
1 TTGGTGCTATT
2373470 TTGGTAATTA
Statistics
Matches: 93, Mismatches: 30, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
27 6 0.06
28 14 0.15
29 68 0.73
30 5 0.05
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.41
Consensus pattern (29 bp):
TTGGTGCTATTCTAGAAATTAATTAGAAA
Found at i:2373470 original size:29 final size:29
Alignment explanation
Indices: 2373346--2373499 Score: 130
Period size: 29 Copynumber: 5.3 Consensus size: 29
2373336 ATTTGGTTTT
*
2373346 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAAAG
* * * ** *
2373375 GGTGCTATTCTGGTAATT-TTTTTAAAAA
1 GGTGCTATTTTGGGAATTAATTCGAAAAG
* * * * * * **
2373403 GGTGATATTCTAGAAAATAATTAGAAATT
1 GGTGCTATTTTGGGAATTAATTCGAAAAG
2373432 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTCGAAAAG
* * **
2373461 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCGAAAAG
2373490 GGTGCTATTT
1 GGTGCTATTT
2373500 GTGTAAAATG
Statistics
Matches: 96, Mismatches: 28, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
28 19 0.20
29 77 0.80
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAAAG
Found at i:2374545 original size:42 final size:41
Alignment explanation
Indices: 2374433--2374683 Score: 376
Period size: 42 Copynumber: 6.0 Consensus size: 41
2374423 GAAGTATTAT
* *
2374433 CAGGTCCCTTTGATGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
2374475 CAGGTCCCTTTTGCTGTGTGCAAGGGTAAACCTTACAGTTTCC
1 CAGGTCCC-TTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
*
2374518 CAGGTCCCTTTGCTGTGTGCTAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
2374560 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
* *
2374602 CAGGTCCCTTTACTGTCTGCGAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
2374644 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTT
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
2374684 TCCTAGGCTC
Statistics
Matches: 192, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
41 6 0.03
42 146 0.76
43 40 0.21
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCC
Found at i:2374627 original size:84 final size:84
Alignment explanation
Indices: 2374433--2374683 Score: 423
Period size: 84 Copynumber: 3.0 Consensus size: 84
2374423 GAAGTATTAT
2374433 CAGGTCCCTTTGA-TGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCA
1 CAGGTCCCTTT-ACTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCC-TTTGCTGTGTGCA
2374497 AGGGTAAACCTTACAGTTTCC
64 AGGGTAAACCTTACAGTTTCC
* *
2374518 CAGGTCCCTTTGCTGTGTGCTAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTACTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
*
2374583 GGTAAGCCTTACAGTTTCC
66 GGTAAACCTTACAGTTTCC
* *
2374602 CAGGTCCCTTTACTGTCTGCGAAGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTACTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
*
2374667 GATAAACCTTACAGTTT
66 GGTAAACCTTACAGTTT
2374684 TCCTAGGCTC
Statistics
Matches: 156, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
84 109 0.70
85 47 0.30
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.32
Consensus pattern (84 bp):
CAGGTCCCTTTACTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
GGTAAACCTTACAGTTTCC
Found at i:2374648 original size:21 final size:21
Alignment explanation
Indices: 2374583--2374648 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
2374573 TGTGTGCAAG
2374583 GGTAAGCCTTACAGTTTCCCA
1 GGTAAGCCTTACAGTTTCCCA
* * * **
2374604 GGT--CCCTTTACTGTCTGCGAA
1 GGTAAGCC-TTACAGT-TTCCCA
2374625 GGTAAGCCTTACAGTTTCCCA
1 GGTAAGCCTTACAGTTTCCCA
2374646 GGT
1 GGT
2374649 CCCTTTGCTG
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 15 0.48
22 6 0.19
23 2 0.06
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (21 bp):
GGTAAGCCTTACAGTTTCCCA
Found at i:2380912 original size:29 final size:29
Alignment explanation
Indices: 2380852--2381016 Score: 109
Period size: 29 Copynumber: 5.7 Consensus size: 29
2380842 ACCGTTAACT
* *** *
2380852 GGTGCTATTCT-AGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
2380880 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* ** * **
2380909 GGTGCTAATT-TGGTAATTTTTTTGAAAAAAA
1 GGTGCT-ATTCTGGGAATTAATTCG--AAATG
* * * *
2380940 GTTGATATTCTAGGAATTAATTCGAAATT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
2380969 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* * *
2380998 GGTTCTATTTTGGTAATTA
1 GGTGCTATTCTGGGAATTA
2381017 TTTTAAAAGG
Statistics
Matches: 104, Mismatches: 28, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
28 11 0.11
29 71 0.68
30 6 0.06
31 16 0.15
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:2381015 original size:89 final size:87
Alignment explanation
Indices: 2380857--2381024 Score: 246
Period size: 89 Copynumber: 1.9 Consensus size: 87
2380847 TAACTGGTGC
*** *
2380857 TATTCTAGAATTAATTCGGTTTTGGTGCTATTCTGGGAATTAATTCGAAATGGGTGCTAATTTGG
1 TATTCTAGAATTAATTCGAAATTGGTGCTATTCTGGGAATTAATTCGAAAAGGGTGCTAATTTGG
*
2380922 TAATTTTTTTGAAAAAAAGTTGA
66 TAATTATTTT-AAAAAAAGTTGA
* * *
2380945 TATTCTAGGAATTAATTCGAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTTCTATTTTG
1 TATTCTA-GAATTAATTCGAAATTGGTGCTATTCTGGGAATTAATTCGAAAAGGGTGCTAATTTG
2381010 GTAATTATTTTAAAA
65 GTAATTATTTTAAAA
2381025 GGGTACTATT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 11 0.15
89 60 0.85
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (87 bp):
TATTCTAGAATTAATTCGAAATTGGTGCTATTCTGGGAATTAATTCGAAAAGGGTGCTAATTTGG
TAATTATTTTAAAAAAAGTTGA
Found at i:2381033 original size:28 final size:29
Alignment explanation
Indices: 2380952--2381035 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
2380942 TGATATTCTA
** *
2380952 GGAATTAATTCGAAATTGGTGCTATTTTG
1 GGAATTAATTCGAAAAGGGTACTATTTTG
*
2380981 GGAATTAATTCGAAAAGGGTTCTATTTTG
1 GGAATTAATTCGAAAAGGGTACTATTTTG
* **
2381010 GTAATT-ATTTTAAAAGGGTACTATTT
1 GGAATTAATTCGAAAAGGGTACTATTT
2381036 GTGTAAAATG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 17 0.35
29 31 0.65
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (29 bp):
GGAATTAATTCGAAAAGGGTACTATTTTG
Found at i:2382078 original size:42 final size:41
Alignment explanation
Indices: 2381966--2382257 Score: 388
Period size: 42 Copynumber: 6.8 Consensus size: 41
2381956 GAAGTATTAT
*
2381966 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
2382008 CAGGTCCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCC-TTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
*
2382051 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
2382093 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAATTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
*
2382135 CAGGTCCTTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
2382177 CAGGTCCCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTTTCC
1 CAGGT--CCCTTTGCTGTGTGCAAGG-TAAGCCTTACAG-TTTCC
* * *
2382222 TAGG-CTCCTCTGCTTTGTGCACAGGTTAAGCCTTAC
1 CAGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
2382258 TGGTGTATAG
Statistics
Matches: 226, Mismatches: 13, Indels: 20
0.87 0.05 0.08
Matches are distributed among these distances:
41 2 0.01
42 120 0.53
43 59 0.26
44 37 0.16
45 8 0.04
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCC
Found at i:2384067 original size:44 final size:44
Alignment explanation
Indices: 2384004--2384091 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
2383994 CTAAGATATT
2384004 ATCAAACATAGTCCCAGACTTCACCTGACAAAAACAAACAAACA
1 ATCAAACATAGTCCCAGACTTCACCTGACAAAAACAAACAAACA
2384048 ATCAAACATAGTCCCAGACTTCACCTGACAAAAACAAACAAACA
1 ATCAAACATAGTCCCAGACTTCACCTGACAAAAACAAACAAACA
2384092 TTTTTCTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.50, C:0.30, G:0.07, T:0.14
Consensus pattern (44 bp):
ATCAAACATAGTCCCAGACTTCACCTGACAAAAACAAACAAACA
Found at i:2392604 original size:43 final size:43
Alignment explanation
Indices: 2392556--2392672 Score: 155
Period size: 47 Copynumber: 2.6 Consensus size: 43
2392546 GTAAGTATGC
2392556 AAATAAGCTTACGAGCTTATGAATAATGGCAAGTA-TATTGATA
1 AAATAAGCTTACGAGCTTATGAATAATGGCAAGTAGT-TTGATA
* *
2392599 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAGTTTGGTA
1 AAATAAGCTTACGAGCTTAT-GAA--T-AATGGCAAGTAGTTTGATA
2392646 AAATAAGCTTACGAGCTTATGAGATAA
1 AAATAAGCTTACGAGCTTATGA-ATAA
2392673 ATGGTAAGAG
Statistics
Matches: 66, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
43 20 0.30
44 5 0.08
45 1 0.02
46 3 0.05
47 36 0.55
48 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.31
Consensus pattern (43 bp):
AAATAAGCTTACGAGCTTATGAATAATGGCAAGTAGTTTGATA
Found at i:2393606 original size:145 final size:145
Alignment explanation
Indices: 2393343--2393633 Score: 582
Period size: 145 Copynumber: 2.0 Consensus size: 145
2393333 CTATAATCTG
2393343 TATAGGTATAATTATACGGGTTATGAGTGTTACAGTTTAAATGCTCGAAAACACCCCACACGAGT
1 TATAGGTATAATTATACGGGTTATGAGTGTTACAGTTTAAATGCTCGAAAACACCCCACACGAGT
2393408 CCTAGTAAACTTAGGACCTTTAAAACCAAGGTTTTAAACAGGGTATCAAATAGAGTTCGTGGTCA
66 CCTAGTAAACTTAGGACCTTTAAAACCAAGGTTTTAAACAGGGTATCAAATAGAGTTCGTGGTCA
2393473 CGTTTTCAGTCGCAT
131 CGTTTTCAGTCGCAT
2393488 TATAGGTATAATTATACGGGTTATGAGTGTTACAGTTTAAATGCTCGAAAACACCCCACACGAGT
1 TATAGGTATAATTATACGGGTTATGAGTGTTACAGTTTAAATGCTCGAAAACACCCCACACGAGT
2393553 CCTAGTAAACTTAGGACCTTTAAAACCAAGGTTTTAAACAGGGTATCAAATAGAGTTCGTGGTCA
66 CCTAGTAAACTTAGGACCTTTAAAACCAAGGTTTTAAACAGGGTATCAAATAGAGTTCGTGGTCA
2393618 CGTTTTCAGTCGCAT
131 CGTTTTCAGTCGCAT
2393633 T
1 T
2393634 GTGTTTATCG
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 146 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (145 bp):
TATAGGTATAATTATACGGGTTATGAGTGTTACAGTTTAAATGCTCGAAAACACCCCACACGAGT
CCTAGTAAACTTAGGACCTTTAAAACCAAGGTTTTAAACAGGGTATCAAATAGAGTTCGTGGTCA
CGTTTTCAGTCGCAT
Found at i:2397952 original size:18 final size:18
Alignment explanation
Indices: 2397904--2397960 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 18
2397894 CATATGAATT
2397904 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
2397922 TGAAATATCCCGAAGGACCACTA
1 TG-----TCCCGAAGGACCACTA
2397945 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
2397961 GTAGAACCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
18 16 0.47
23 18 0.53
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2405952 original size:18 final size:18
Alignment explanation
Indices: 2405929--2405992 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
2405919 TTCATTGAAA
2405929 AACCGAAAAACCGAACCG
1 AACCGAAAAACCGAACCG
2405947 AACCGAAAAACCCGAACCG
1 AACCGAAAAA-CCGAACCG
*
2405966 TTAA---AAAACCCGAACCG
1 --AACCGAAAAACCGAACCG
2405983 AACCGAAAAA
1 AACCGAAAAA
2405993 ACCGGTTTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 8 0.21
18 18 0.47
19 8 0.21
21 2 0.05
ACGTcount: A:0.52, C:0.31, G:0.14, T:0.03
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:2405963 original size:14 final size:14
Alignment explanation
Indices: 2405944--2405984 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
2405934 AAAAACCGAA
2405944 CCGAACCGAAAAAC
1 CCGAACCGAAAAAC
2405958 CCGAACCGTTAAAAAAC
1 CCGAACCG---AAAAAC
2405975 CCGAACCGAA
1 CCGAACCGAA
2405985 CCGAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.42
17 14 0.58
ACGTcount: A:0.46, C:0.34, G:0.15, T:0.05
Consensus pattern (14 bp):
CCGAACCGAAAAAC
Found at i:2409686 original size:53 final size:53
Alignment explanation
Indices: 2409602--2409782 Score: 197
Period size: 53 Copynumber: 3.5 Consensus size: 53
2409592 AAGATGTTTC
* * * * **
2409602 AAAAGGAGAGTCTTTAATTTATGGATAATGATGTATGCAAACAAGAAATTAGG
1 AAAAGGTGAGTCTTTCATTTATAGACAATGATGTATGCAGGCAAGAAATTAGG
* * *
2409655 AAAAGGTGAATCTTTCATTTATAGACGATGATGTATGCAGGCAATAAATTAGG
1 AAAAGGTGAGTCTTTCATTTATAGACAATGATGTATGCAGGCAAGAAATTAGG
* * * * *
2409708 AAAA-ATGAGT-TTT-ATTTATGGACAATGTTGTATGCGGGTAAGAAATTAGG
1 AAAAGGTGAGTCTTTCATTTATAGACAATGATGTATGCAGGCAAGAAATTAGG
* *
2409758 AAAAAGTGAGTTTTTCATTTATAGA
1 AAAAGGTGAGTCTTTCATTTATAGA
2409783 TGATGATATA
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
50 35 0.33
51 8 0.08
52 7 0.07
53 56 0.53
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (53 bp):
AAAAGGTGAGTCTTTCATTTATAGACAATGATGTATGCAGGCAAGAAATTAGG
Found at i:2409809 original size:53 final size:53
Alignment explanation
Indices: 2409629--2409814 Score: 184
Period size: 53 Copynumber: 3.6 Consensus size: 53
2409619 TTTATGGATA
* * * * * *
2409629 ATGATGTATGCAAACAAGAAATTAGGAAAAGGTGAATCTTTCATTTATAGACG
1 ATGATGTATGCGAGCAACAAATTAGGAAAAAGTGAGTTTTTCATTTATAGACG
* * *
2409682 ATGATGTATGC-AGGCAATAAATTAGGAAAAA-TGAG-TTTT-ATTTATGGACA
1 ATGATGTATGCGA-GCAACAAATTAGGAAAAAGTGAGTTTTTCATTTATAGACG
* * * * *
2409732 ATGTTGTATGCGGGTAAGAAATTAGGAAAAAGTGAGTTTTTCATTTATAGATG
1 ATGATGTATGCGAGCAACAAATTAGGAAAAAGTGAGTTTTTCATTTATAGACG
* *
2409785 ATGATATATACGAGCAACAAATTA-GAAAAA
1 ATGATGTATGCGAGCAACAAATTAGGAAAAA
2409815 TATGAGTCTC
Statistics
Matches: 108, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
50 35 0.32
51 7 0.06
52 14 0.13
53 52 0.48
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (53 bp):
ATGATGTATGCGAGCAACAAATTAGGAAAAAGTGAGTTTTTCATTTATAGACG
Found at i:2413659 original size:38 final size:39
Alignment explanation
Indices: 2413588--2413679 Score: 123
Period size: 38 Copynumber: 2.4 Consensus size: 39
2413578 TTCAATGATT
*
2413588 TATTTTCTTTTACAAACGAGGAAAATAAATCCAACAACA
1 TATTTTCTTTTACAAAAGAGGAAAATAAATCCAACAACA
* * **
2413627 TATTTTCTTTTACAAAATA-GAAAATAAATCCAATAATT
1 TATTTTCTTTTACAAAAGAGGAAAATAAATCCAACAACA
*
2413665 TACTTTCTTTTACAA
1 TATTTTCTTTTACAA
2413680 CTCAGAATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 30 0.64
39 17 0.36
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.37
Consensus pattern (39 bp):
TATTTTCTTTTACAAAAGAGGAAAATAAATCCAACAACA
Done.