Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015090.1 Kokia drynarioides strain JFW-HI SEQ_130134, 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: 762378
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 242 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:777 original size:105 final size:104
Alignment explanation
Indices: 603--837 Score: 242
Period size: 105 Copynumber: 2.2 Consensus size: 104
593 AGCACAATAC
* * * * * **
603 TGAGCCTGATGTTGTCACTTATAATATATTGGTTGATGCGTATTGTAAGGCTGGGATCATTTCTA
1 TGAGCCTGATGTTGTCACGTATAGTATATTGGTTGATACGTATGGCAAGGAGGGGATCATTTCTA
* * * *
668 AAGCTGTAGACACTGTTGACGCAATGAGAAA-TCAAGATAT
66 AAGCTGTAAACACTATTGACACAATGAGAAACTC-AG-CAT
* *
708 TGAGCCTAATGTTGTCACGTATAGTATATTGGTTGATACTTATGGCAAGGAGGGGA-CGATTT-T
1 TGAGCCTGATGTTGTCACGTATAGTATATTGGTTGATACGTATGGCAAGGAGGGGATC-ATTTCT
* * *
771 CCAAGCTGTAAATACTATTGATACAATGAGAAAGCTCAGCAT
65 -AAAGCTGTAAACACTATTGACACAATGAGAAA-CTCAGCAT
* *
813 TGAACCTGATGTTGTTACGTATAGT
1 TGAGCCTGATGTTGTCACGTATAGT
838 GCATTAATAA
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
104 2 0.02
105 101 0.94
106 2 0.02
107 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33
Consensus pattern (104 bp):
TGAGCCTGATGTTGTCACGTATAGTATATTGGTTGATACGTATGGCAAGGAGGGGATCATTTCTA
AAGCTGTAAACACTATTGACACAATGAGAAACTCAGCAT
Found at i:4381 original size:24 final size:24
Alignment explanation
Indices: 4349--4397 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
4339 TAAGGTAAAA
4349 GTATCATGGCTTGTATTAGGAGTC
1 GTATCATGGCTTGTATTAGGAGTC
4373 GTATCATGGCTTGTATTAGGAGTC
1 GTATCATGGCTTGTATTAGGAGTC
4397 G
1 G
4398 GATTGCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.37
Consensus pattern (24 bp):
GTATCATGGCTTGTATTAGGAGTC
Found at i:7284 original size:3 final size:3
Alignment explanation
Indices: 7276--7314 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
7266 CAGATTTAAT
* * *
7276 TTC TTC TTC GTC TTC TTC TTC TGC TTC TTC TTC CTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
7315 AGATTCTCCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.36, G:0.05, T:0.59
Consensus pattern (3 bp):
TTC
Found at i:12856 original size:2 final size:2
Alignment explanation
Indices: 12844--12893 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
12834 TTAATGTTTG
* *
12844 AT AT AT A- AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12885 AT A- AT AT AT
1 AT AT AT AT AT
12894 TGGTGTAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:17490 original size:6 final size:6
Alignment explanation
Indices: 17479--17517 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
17469 CACCAATTTC
17479 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT
17518 CTCTGCTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:18455 original size:9 final size:9
Alignment explanation
Indices: 18443--18468 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
18433 GGCGGAGGTA
18443 TGGTGGTGC
1 TGGTGGTGC
18452 TGGTGGTGC
1 TGGTGGTGC
18461 TGGTGGTG
1 TGGTGGTG
18469 GCAGGCCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.58, T:0.35
Consensus pattern (9 bp):
TGGTGGTGC
Found at i:18590 original size:6 final size:6
Alignment explanation
Indices: 18581--18623 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
18571 AGTTGGCAAA
18581 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG G
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG G
18624 TTTATGGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (6 bp):
GGTTTG
Found at i:19401 original size:22 final size:20
Alignment explanation
Indices: 19384--19437 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
19374 GAAATTATTG
*
19384 TTTTAGATTTTTTTAATTTT
1 TTTTAGATATTTTTAATTTT
* *
19404 TTTTATATATTTTTAGA-TAT
1 TTTTAGATATTTTTA-ATTTT
*
19424 TTTTATATATTTTT
1 TTTTAGATATTTTT
19438 TAAATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (20 bp):
TTTTAGATATTTTTAATTTT
Found at i:19416 original size:10 final size:10
Alignment explanation
Indices: 19403--19437 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
19393 TTTTTAATTT
19403 TTTTTATATA
1 TTTTTATATA
*
19413 TTTTTAGATA
1 TTTTTATATA
19423 TTTTTATATA
1 TTTTTATATA
19433 TTTTT
1 TTTTT
19438 TAAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (10 bp):
TTTTTATATA
Found at i:30126 original size:59 final size:59
Alignment explanation
Indices: 30046--30178 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 59
30036 AAACAAAGTG
* * * * *
30046 AATAGTTGAGTGATCATTTTGTAACTTTTTATAGTTGTGTGACCAAAACAAAA-TTTACC
1 AATAGTTG-GTGACCAGTTTGTAACTTTTCATAGTTGAGTGACCAAAAAAAAAGTTTACC
** *
30105 AATAGTTGGTTGACCAGTTTGTAACTTTTCATAGTTGAGTGATGAAAAAAAAAGTTTACT
1 AATAGTTGG-TGACCAGTTTGTAACTTTTCATAGTTGAGTGACCAAAAAAAAAGTTTACC
30165 AATAGTTGGGTGAC
1 AATAGTT-GGTGAC
30179 TACTAGTGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
58 1 0.02
59 44 0.70
60 16 0.25
61 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (59 bp):
AATAGTTGGTGACCAGTTTGTAACTTTTCATAGTTGAGTGACCAAAAAAAAAGTTTACC
Found at i:32734 original size:14 final size:14
Alignment explanation
Indices: 32715--32743 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
32705 ATGTGGCGTG
32715 TCACGAATATCTCA
1 TCACGAATATCTCA
32729 TCACGAATATCTCA
1 TCACGAATATCTCA
32743 T
1 T
32744 TCTCGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (14 bp):
TCACGAATATCTCA
Found at i:35734 original size:10 final size:9
Alignment explanation
Indices: 35716--35749 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
35706 ATTTGAGTTT
35716 ATTCGAATA
1 ATTCGAATA
35725 ATTCGAAATA
1 ATTCG-AATA
*
35735 ATTAGAATA
1 ATTCGAATA
35744 ATTCGA
1 ATTCGA
35750 TTCGATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (9 bp):
ATTCGAATA
Found at i:61845 original size:17 final size:19
Alignment explanation
Indices: 61820--61858 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
61810 TAAACGTACA
61820 TTTTAAC-TT-TTTTTTTC
1 TTTTAACTTTATTTTTTTC
*
61837 TTTTTACTTTATTTTTTTC
1 TTTTAACTTTATTTTTTTC
61856 TTT
1 TTT
61859 CTTCTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTAACTTTATTTTTTTC
Found at i:72391 original size:23 final size:23
Alignment explanation
Indices: 72347--72392 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
72337 TGAAGTATTA
* *
72347 TTTAATAATAAAAATGTTTAAAT
1 TTTAATAATAAAAATATATAAAT
* *
72370 TTTAATTATAAAACTATATAAAT
1 TTTAATAATAAAAATATATAAAT
72393 ATCAACATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAATAATAAAAATATATAAAT
Found at i:74119 original size:15 final size:16
Alignment explanation
Indices: 74099--74147 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
74089 ATTAAATCAA
74099 TTTATTTCTTT-ATTT
1 TTTATTTCTTTCATTT
* *
74114 TTTATTTATTTCCTTT
1 TTTATTTCTTTCATTT
*
74130 TTTATCTTCTCTCATTT
1 TTTAT-TTCTTTCATTT
74147 T
1 T
74148 CCTCGTCTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 10 0.37
16 8 0.30
17 9 0.33
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTTCTTTCATTT
Found at i:85485 original size:12 final size:12
Alignment explanation
Indices: 85468--85500 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
85458 TCTTTACCTA
85468 TAGAACTTCAGT
1 TAGAACTTCAGT
85480 TAGAACTTCAGT
1 TAGAACTTCAGT
85492 TAGAACTTC
1 TAGAACTTC
85501 TACTAGGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (12 bp):
TAGAACTTCAGT
Found at i:87101 original size:204 final size:205
Alignment explanation
Indices: 86751--87213 Score: 811
Period size: 204 Copynumber: 2.3 Consensus size: 205
86741 CCATAAACAG
* *
86751 CGACGCGGTCATCTTCCTGATAAGATACCGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGA
1 CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGA
*
86816 GTAAATCTTCGAATCCTAACTTCCTGATGAGACACCGAGAAGCAGATCGAAGTAATAAACAGTTA
66 GTAAATCTTCGAATCCTAACTTCCTGATGAGACACCGAGAAGCAGATCGAAGAAATAAACAGTTA
86881 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC-GA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
86945 TTGAAACAAA
196 TTGAAACAAA
* * *
86955 CGACGCGGTCATCTTCCTGATGAGATACTGAGAATAAGACAAAATCAAACCCACGCTCGGTGTGA
1 CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGA
* * *
87020 GTAAATCTTCGAATCCTAGCTTCCTGATGAGACATCGAGAAGCAGATCGAAGAAATAAACGGTTA
66 GTAAATCTTCGAATCCTAACTTCCTGATGAGACACCGAGAAGCAGATCGAAGAAATAAACAGTTA
*
87085 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATTAGATACAGAGAAGCGGA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
87150 TTGAAACAAA
196 TTGAAACAAA
* *
87160 CGACGCAGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
1 CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
87214 TGTAAATCTT
Statistics
Matches: 244, Mismatches: 14, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
204 182 0.75
205 62 0.25
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (205 bp):
CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGA
GTAAATCTTCGAATCCTAACTTCCTGATGAGACACCGAGAAGCAGATCGAAGAAATAAACAGTTA
GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
TTGAAACAAA
Found at i:87562 original size:372 final size:372
Alignment explanation
Indices: 86877--87579 Score: 998
Period size: 372 Copynumber: 1.9 Consensus size: 372
86867 GTAATAAACA
* * *
86877 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
1 GTTAGCTCCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCGGATGAGATACAGACAAG
* * *
86942 CGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAATAAGACAAAATCAAACCC
66 CGATTGAAACAAAAGACGCGGTAATCTTCCTGATGAGATACTGAGAAGAAGACAAAATCAAACCC
* ** * *
87007 ACGCTCGGTGTGAGTAAATCTTCGAATCCTAGCTTCCTGATGAGACATCGAGAAGCAGATCGAAG
131 ACGCTCGGTATGAACAAATCTTCGAACCCCAGCTTCCTGATGAGACATCGAGAAGCAGATCGAAG
* * ** * * * * *
87072 AAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATTAGAT
196 AAATAAACGGTTAGCTTCCTGATGAAATACGGAGAAGTAAACCAAAATCATCTTCCTGATGAAAC
** * *
87137 ACAGAGAAGCGGATTGAAACAAACGACGCAGTCATCTTCTTGATGAGATACTGAGAAGAAGACCA
261 ACAGAGAAGCGGATCAAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
87202 AATCAAACCCACTGTAAATCTTTGAATCTCAGCTCCTGATGAGAATG
326 AATCAAACCCACTGTAAATCTTTGAATCTCAGCTCCTGATGAGAATG
*
87249 GTTAGCTCCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTTCGGATGAGATACAGACAAG
1 GTTAGCTCCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCGGATGAGATACAGACAAG
*
87314 CGAATTGAAACAAAAGACGCGGTAATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACC
66 CG-ATTGAAACAAAAGACGCGGTAATCTTCCTGATGAGATACTGAGAAGAAGACAAAATCAAACC
* * *
87379 CATGCTC-G-ATGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATA-CTGAGAAGCAGGTCGA
130 CACGCTCGGTATGAACAAATCTTCGAACCCCAGCTTCCTGATGAGACATC-GAGAAGCAGATCGA
* *
87441 AGTAATAAAACGGTTAGCTTCCTGATGAAATACGGGGAAGTAAACCAAAATCATCTTCCTGATGA
194 AGAAAT-AAACGGTTAGCTTCCTGATGAAATACGGAGAAGTAAACCAAAATCATCTTCCTGATGA
* ** * ** * *
87506 AACACAGAGAAGTGGATCAAAACAAGTGATATGGTCATCTTCCTGATGAGATACTGAGAATAAGG
258 AACACAGAGAAGCGGATCAAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGA
*
87571 CCAAGTCAA
323 CCAAATCAA
87580 TGAAACCAGA
Statistics
Matches: 288, Mismatches: 40, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
370 1 0.00
371 50 0.17
372 173 0.60
373 64 0.22
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (372 bp):
GTTAGCTCCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCGGATGAGATACAGACAAG
CGATTGAAACAAAAGACGCGGTAATCTTCCTGATGAGATACTGAGAAGAAGACAAAATCAAACCC
ACGCTCGGTATGAACAAATCTTCGAACCCCAGCTTCCTGATGAGACATCGAGAAGCAGATCGAAG
AAATAAACGGTTAGCTTCCTGATGAAATACGGAGAAGTAAACCAAAATCATCTTCCTGATGAAAC
ACAGAGAAGCGGATCAAAACAAACGACACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
AATCAAACCCACTGTAAATCTTTGAATCTCAGCTCCTGATGAGAATG
Found at i:87957 original size:18 final size:18
Alignment explanation
Indices: 87934--88019 Score: 86
Period size: 18 Copynumber: 4.8 Consensus size: 18
87924 TTCATTTTGG
* *
87934 GTTTAAATTTAGTTTAAA
1 GTTTAAATTTAATTTTAA
**
87952 GTTTAAACTTTTCTTTTAA
1 GTTTAAA-TTTAATTTTAA
*
87971 GTTTAAATTTAA-ATTAA
1 GTTTAAATTTAATTTTAA
*
87988 GTTTAAAATTAATTTTAA
1 GTTTAAATTTAATTTTAA
88006 -TTTAAAATTTAATT
1 GTTT-AAATTTAATT
88020 AATTAAAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
17 18 0.32
18 23 0.41
19 15 0.27
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (18 bp):
GTTTAAATTTAATTTTAA
Found at i:87989 original size:17 final size:17
Alignment explanation
Indices: 87967--88021 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
87957 AACTTTTCTT
87967 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
* *
87984 TTAAGTTTAAAATTAATT
1 TTAAGTTTAAATTTAA-A
88002 TTAA-TTTAAAATTT-AA
1 TTAAGTTT-AAATTTAAA
88018 TTAA
1 TTAA
88022 TTAAAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 4 0.12
17 19 0.59
18 9 0.28
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:89719 original size:29 final size:29
Alignment explanation
Indices: 89681--90050 Score: 355
Period size: 29 Copynumber: 12.7 Consensus size: 29
89671 CCCTATAGGT
89681 CCCCAAAACTTCCAAAAATTCTATTTTTA
1 CCCCAAAACTTCCAAAAATTCTATTTTTA
** *
89710 CCCCCGAACTTTCAAAAA-TCTCATTTTTAA
1 CCCCAAAACTTCCAAAAATTCT-ATTTTT-A
* *
89740 CCCTAAAACTTCTAAAAATT-TCATTTTTA
1 CCCCAAAACTTCCAAAAATTCT-ATTTTTA
*
89769 CCCCTAAACTTCCAAAAATTCTATTTTTAA
1 CCCCAAAACTTCCAAAAATTCTATTTTT-A
*
89799 CCCCAAAACTTCCAAAAATTCCA-TTTTA
1 CCCCAAAACTTCCAAAAATTCTATTTTTA
*
89827 CCCTC-AAACTTTCAAAAA-TCTCATTTTTGA
1 CCC-CAAAACTTCCAAAAATTCT-ATTTTT-A
*
89857 CCCCAAAACTTCTAAAAATTCCT-TTTTTA
1 CCCCAAAACTTCCAAAAATT-CTATTTTTA
* * *
89886 TCCCTAAACTTCCAAAAA-TCCATTTTTAA
1 CCCCAAAACTTCCAAAAATTCTATTTTT-A
* * *
89915 CCTCGAAACTTCCAAAAATTCCATTTTTA
1 CCCCAAAACTTCCAAAAATTCTATTTTTA
** *
89944 CCCCTGAACTTCCAAAAA-TCCATTTTTGA
1 CCCCAAAACTTCCAAAAATTCTATTTTT-A
*
89973 CCCCAAAACTTCCAAAAATTCCA-TTTTA
1 CCCCAAAACTTCCAAAAATTCTATTTTTA
**
90001 CCCCTGAACTTCCAAAAATT-TCATTTTTAA
1 CCCCAAAACTTCCAAAAATTCT-ATTTTT-A
* *
90031 CCTCGAAACTTCCAAAAATT
1 CCCCAAAACTTCCAAAAATT
90051 ACAATTTTGC
Statistics
Matches: 286, Mismatches: 35, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
27 3 0.01
28 55 0.19
29 128 0.45
30 96 0.34
31 2 0.01
32 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
CCCCAAAACTTCCAAAAATTCTATTTTTA
Found at i:89854 original size:58 final size:59
Alignment explanation
Indices: 89681--90050 Score: 500
Period size: 58 Copynumber: 6.3 Consensus size: 59
89671 CCCTATAGGT
* ** *
89681 CCCCAAAACTTCCAAAAATTCTATTTTTACCCCCGAACTTTCAAAAATCTCATTTTTAA
1 CCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAA
* * *
89740 CCCTAAAACTTCTAAAAATTTCATTTTTACCCCTAAACTTCCAAAAAT-TCTATTTTTAA
1 CCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCTC-ATTTTTAA
* *
89799 CCCCAAAACTTCCAAAAATTCCA-TTTTA-CCCTCAAACTTTCAAAAATCTCATTTTTGA
1 CCCCAAAACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATCTCATTTTTAA
* * *
89857 CCCCAAAACTTCTAAAAATTCCTTTTTTATCCCTAAACTTCCAAAAATC-CATTTTTAA
1 CCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAA
* * * *
89915 CCTCGAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATC-CATTTTTGA
1 CCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAA
* *
89973 CCCCAAAACTTCCAAAAATTCCA-TTTTACCCCTGAACTTCCAAAAATTTCATTTTTAA
1 CCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAA
* *
90031 CCTCGAAACTTCCAAAAATT
1 CCCCAAAACTTCCAAAAATT
90051 ACAATTTTGC
Statistics
Matches: 276, Mismatches: 29, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
57 28 0.10
58 154 0.56
59 90 0.33
60 4 0.01
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (59 bp):
CCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAA
Found at i:90108 original size:116 final size:113
Alignment explanation
Indices: 89686--90091 Score: 490
Period size: 116 Copynumber: 3.5 Consensus size: 113
89676 TAGGTCCCCA
* * * * *
89686 AAACTTCCAAAAATTCTATTTTTACCCCCGAACTTTCAAAAATCTCATTTTTAACCCTAAAACTT
1 AAACTTCCAAAAATTC-AATTTTA-CCCTGAACTTCCAAAAATC-CATTTTTGACCCCAAAACTT
* * *
89751 CTAAAAATTTCATTTTTACCCCTAAACTTCCAAAAATTCTATTTTTAACCCCA
63 CTAAAAATTCCA-TTTTACCCCTAAACTTCCAAAAATTC-ATTTTTAACCTCG
* * *
89804 AAACTTCCAAAAATTCCATTTTACCCTCAAACTTTCAAAAATCTCATTTTTGACCCCAAAACTTC
1 AAACTTCCAAAAATTCAATTTTACCCT-GAACTTCCAAAAATC-CATTTTTGACCCCAAAACTTC
* * *
89869 TAAAAATTCCTTTTTTATCCCTAAACTTCCAAAAATCCATTTTTAACCTCG
64 TAAAAATTCC-ATTTTACCCCTAAACTTCCAAAAATTCATTTTTAACCTCG
*
89920 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCATTTTTGACCCCAAAACTTC
1 AAACTTCCAAAAATT-CAATTTTA-CCCTGAACTTCCAAAAATCCATTTTTGACCCCAAAACTTC
* *
89985 CAAAAATTCCATTTTACCCCTGAACTTCCAAAAATTTCATTTTTAACCTCG
64 TAAAAATTCCATTTTACCCCTAAACTTCCAAAAA-TTCATTTTTAACCTCG
* * *
90036 AAACTTCCAAAAATTACAATTTTGCTCCTGGA-TGTCCAAAAACTCCATTTTCGACC
1 AAACTTCCAAAAATT-CAATTTTAC-CCTGAACT-TCCAAAAA-TCCATTTTTGACC
90092 TTGAAACTCT
Statistics
Matches: 254, Mismatches: 26, Indels: 17
0.86 0.09 0.06
Matches are distributed among these distances:
115 23 0.09
116 108 0.43
117 103 0.41
118 20 0.08
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (113 bp):
AAACTTCCAAAAATTCAATTTTACCCTGAACTTCCAAAAATCCATTTTTGACCCCAAAACTTCTA
AAAATTCCATTTTACCCCTAAACTTCCAAAAATTCATTTTTAACCTCG
Found at i:93179 original size:29 final size:27
Alignment explanation
Indices: 93155--93215 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
93145 AGATTAATTC
* * *
93155 AAAAATTTGTTAATAGTAAATATTATT
1 AAAAATTTATTAATAATAAAAATTATT
93182 AAAATATTTTATTAATAATAAAAATTATT
1 AAAA-A-TTTATTAATAATAAAAATTATT
93211 AAAAA
1 AAAAA
93216 ATGTGAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 4 0.14
28 2 0.07
29 23 0.79
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
AAAAATTTATTAATAATAAAAATTATT
Found at i:93841 original size:18 final size:18
Alignment explanation
Indices: 93820--93865 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
93810 TTTTTTTATT
93820 TTTTAAATTTGTTATTAA
1 TTTTAAATTTGTTATTAA
** *
93838 TTTTGTATTTGTTATTAT
1 TTTTAAATTTGTTATTAA
*
93856 TTTTTAATTT
1 TTTTAAATTT
93866 TCTCTATTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTAAATTTGTTATTAA
Found at i:94455 original size:23 final size:22
Alignment explanation
Indices: 94413--94488 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 22
94403 TACTGAGTTA
*
94413 ATTTTTTTAAATAATTACTTTT
1 ATTTTTTTAAATAATGACTTTT
94435 ATTTTCTTTAAATTAA-GAC--TT
1 ATTTT-TTTAAA-TAATGACTTTT
* *
94456 A-TTTTTTAATTTAATGTATTATTT
1 ATTTTTTTAA-ATAATG-ACT-TTT
94480 ATTTTTTTA
1 ATTTTTTTA
94489 TTTTTCACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
19 8 0.19
20 4 0.10
21 4 0.10
22 5 0.12
23 8 0.19
24 6 0.14
25 7 0.17
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (22 bp):
ATTTTTTTAAATAATGACTTTT
Found at i:101871 original size:18 final size:18
Alignment explanation
Indices: 101840--101890 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
101830 TGGGATGGGG
101840 ATAAATTT--TTAATTAA
1 ATAAATTTAATTAATTAA
101856 ATAAATTTAATTAATTAA
1 ATAAATTTAATTAATTAA
*
101874 A-AATTTTAAATTAATTA
1 ATAAATTT-AATTAATTA
101891 CAATTAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 8 0.26
17 5 0.16
18 18 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAAATTTAATTAATTAA
Found at i:120937 original size:39 final size:39
Alignment explanation
Indices: 120894--121630 Score: 649
Period size: 39 Copynumber: 18.5 Consensus size: 39
120884 GGCAAATACA
* * * *
120894 CCATCTAATCTCTTACCCTGACCTTGGGACAGATTGAAC
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* ** * *
120933 CCATCCAATCTCTTACCCTGACAATAAGGCAGACTAAAG
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* * * *
120972 ATATCATCCAATCTCTTA-CCTCGACCATGAGGCACATTAAAG
1 ---CCATCCAATCTCTTACCCT-GACCATGGGGCAGATTGAAG
** * *
121014 CCATCTGATCTCTTACCCCGACCATGGGGCAGATTAAAG
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* * * *
121053 CCATCCAATCTCTTACTCTGACCATGGGACATATTAAAG
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* * * *
121092 CCGTCCAATCTCTTACCCCGACCATGGGGTAGAGTGAAG
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* * * *
121131 ACATCATCCAATCTTTTACCTTGACCATGGGGCAAACTGAAG
1 -C--CATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* * *
121173 TCATCCGATCTTTTA-CCTCGACCATGGGGCAGATTGAAG
1 CCATCCAATCTCTTACCCT-GACCATGGGGCAGATTGAAG
* * *
121212 CCATCTAATCTCTTACCCTGACAATGGGGTAGATTGAAG
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* *
121251 ACATCATCCAGTCTCTTA-CCTCGACCATGGGGCAGACTGAAG
1 -C--CATCCAATCTCTTACCCT-GACCATGGGGCAGATTGAAG
* * * *
121293 TCATCCGATCTTTTA-CCTCGACCATGGGGCAGATTAAAG
1 CCATCCAATCTCTTACCCT-GACCATGGGGCAGATTGAAG
* ** *
121332 CCATCTAATCTCTTACCCTGACCATAAGGTAGATTGAAG
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
*
121371 ACATCATCCAGTCTCTTA-CCTCGACCATGGGGCAGATTGAAG
1 -C--CATCCAATCTCTTACCCT-GACCATGGGGCAGATTGAAG
* *
121413 CCATCCAATCTCTTA-CCTCGACCAAGGGGGCAAATTGAAG
1 CCATCCAATCTCTTACCCT-GACC-ATGGGGCAGATTGAAG
* *
121453 CCATCCAATCTCTTACCCCGACCATGAGGCAGATTGAAG
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* * * ***
121492 TCATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAAG
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* * *
121531 ACATCATCCAATCTCTTACCCCGACCATGGAGTAGATTGAAG
1 -C--CATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* * * *
121573 CCATCCAATCTCTTACCATAACCATGAGGTAGATTGAAG
1 CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
* *
121612 CCATCCCATCTTTTACCCT
1 CCATCCAATCTCTTACCCT
121631 AACTAGAGGG
Statistics
Matches: 568, Mismatches: 106, Indels: 48
0.79 0.15 0.07
Matches are distributed among these distances:
38 2 0.00
39 360 0.63
40 44 0.08
41 13 0.02
42 149 0.26
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (39 bp):
CCATCCAATCTCTTACCCTGACCATGGGGCAGATTGAAG
Found at i:121045 original size:81 final size:78
Alignment explanation
Indices: 120895--121628 Score: 637
Period size: 81 Copynumber: 9.2 Consensus size: 78
120885 GCAAATACAC
* * * * * * *
120895 CATCTAATCTCTTACC-CTGACCTTGGGACAGATTGAACCCATCCAATCTCTTACCCTGACAATA
1 CATCCAATCTCTTACCTC-GACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATG
* * *
120959 AGGCAGACTAAAGATAT
65 GGGCAGATTGAAG---T
* * * **
120976 CATCCAATCTCTTACCTCGACCATGAGGCACATTAAAGCCATCTGATCTCTTACCCCGACCATGG
1 CATCCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGG
* *
121041 GGCAGATTAAAGC
66 GGCAGATTGAAGT
* * * *
121054 CATCCAATCTCTTA-CTCTGACCATGGGACATATTAAAGCCGTCCAATCTCTTACCCCGACCATG
1 CATCCAATCTCTTACCTC-GACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATG
* *
121118 GGGTAGAGTGAAGACAT
65 GGGCAGATTGAAG---T
* * * * * * * *
121135 CATCCAATCTTTTACCTTGACCATGGGGCAAACTGAAGTCATCCGATCTTTTACCTCGACCATGG
1 CATCCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGG
*
121200 GGCAGATTGAAGC
66 GGCAGATTGAAGT
* * * * *
121213 CATCTAATCTCTTACC-CTGACAATGGGGTAGATTGAAGACATCATCCAGTCTCTTACCTCGACC
1 CATCCAATCTCTTACCTC-GACCATGGGGCAGATTGAAG-C--CATCCAATCTCTTACCCCGACC
*
121277 ATGGGGCAGACTGAAGT
62 ATGGGGCAGATTGAAGT
* * * * * **
121294 CATCCGATCTTTTACCTCGACCATGGGGCAGATTAAAGCCATCTAATCTCTTACCCTGACCATAA
1 CATCCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGG
*
121359 GGTAGATTGAAGACAT
66 GGCAGATTGAAG---T
* * *
121375 CATCCAGTCTCTTACCTCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCTCGACCAAGG
1 CATCCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACC-ATG
* *
121440 GGGCAAATTGAAGC
65 GGGCAGATTGAAGT
* * * * ** ***
121454 CATCCAATCTCTTACCCCGACCATGAGGCAGATTGAAGTCATCCAATCTTTTACCCTAACCAAAA
1 CATCCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGG
121519 GGCAGATTGAAGACAT
66 GGCAGATTGAAG---T
* * * *** *
121535 CATCCAATCTCTTACCCCGACCATGGAGTAGATTGAAGCCATCCAATCTCTTACCATAACCATGA
1 CATCCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGG
* *
121600 GGTAGATTGAAGC
66 GGCAGATTGAAGT
* *
121613 CATCCCATCTTTTACC
1 CATCCAATCTCTTACC
121629 CTAACTAGAG
Statistics
Matches: 531, Mismatches: 104, Indels: 39
0.79 0.15 0.06
Matches are distributed among these distances:
77 3 0.01
78 150 0.28
79 53 0.10
80 1 0.00
81 309 0.58
82 15 0.03
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (78 bp):
CATCCAATCTCTTACCTCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCCCGACCATGG
GGCAGATTGAAGT
Found at i:121150 original size:120 final size:120
Alignment explanation
Indices: 120895--121616 Score: 733
Period size: 120 Copynumber: 6.0 Consensus size: 120
120885 GCAAATACAC
* * * * * * *
120895 CATCTAATCTCTTACCCTGACCTTGGGACAGATTGAACCCATCCAATCTCTTACC-CTGACAATA
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCTC-GACCATG
* * * * * * *
120959 AGGCAGACTAAAGATATCATCCAATCTCTTA-CCTCGACCATGAGGCACATTAAAG-C--
65 GGGCAGATTGAAG---CCATCCAATCTCTTACCCT-GACCATGAGGTAGATTGAAGACAT
** *
121015 CATCTGATCTCTTACCCCGACCATGGGGCAGATTAAAGCCATCCAATCTCTTA-CTCTGACCATG
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCTC-GACCATG
* * * * * * *
121079 GGACATATTAAAGCCGTCCAATCTCTTACCCCGACCATGGGGTAGAGTGAAGACAT
65 GGGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGAGGTAGATTGAAGACAT
* ** * * * * *
121135 CATCCAATCTTTTACCTTGACCATGGGGCAAACTGAAGTCATCCGATCTTTTACCTCGACCATGG
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCTCGACCATGG
* * *
121200 GGCAGATTGAAGCCATCTAATCTCTTACCCTGACAATGGGGTAGATTGAAGACAT
66 GGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGAGGTAGATTGAAGACAT
* * * * * *
121255 CATCCAGTCTCTTACCTCGACCATGGGGCAGACTGAAGTCATCCGATCTTTTACCTCGACCATGG
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCTCGACCATGG
* * *
121320 GGCAGATTAAAGCCATCTAATCTCTTACCCTGACCATAAGGTAGATTGAAGACAT
66 GGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGAGGTAGATTGAAGACAT
* * *
121375 CATCCAGTCTCTTACCTCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCTCGACCAAGG
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCTCGACC-ATG
* * *
121440 GGGCAAATTGAAGCCATCCAATCTCTTACCCCGACCATGAGGCAGATTGAAG---T
65 GGGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGAGGTAGATTGAAGACAT
* ** *** *
121493 CATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAAGACATCATCCAATCTCTTACCCCGACCA
1 CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAG-C--CATCCAATCTCTTACCTCGACCA
* * * * *
121558 TGGAGTAGATTGAAGCCATCCAATCTCTTACCATAACCATGAGGTAGATTGAAGCCAT
63 TGGGGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGAGGTAGATTGAAGACAT
121616 C
1 C
121617 CCATCTTTTA
Statistics
Matches: 514, Mismatches: 75, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
117 28 0.05
118 34 0.07
119 2 0.00
120 376 0.73
121 72 0.14
123 2 0.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (120 bp):
CATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTCTTACCTCGACCATGG
GGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGAGGTAGATTGAAGACAT
Found at i:123354 original size:3 final size:3
Alignment explanation
Indices: 123346--123389 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
123336 TTTGTTTTAT
123346 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
123390 TTGCGTTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:123601 original size:8 final size:8
Alignment explanation
Indices: 123588--123621 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
123578 AATCATAGTA
123588 TTATTATT
1 TTATTATT
123596 TTATTATT
1 TTATTATT
*
123604 TTATTGTT
1 TTATTATT
*
123612 GTATTATT
1 TTATTATT
123620 TT
1 TT
123622 CACCTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (8 bp):
TTATTATT
Found at i:130914 original size:22 final size:22
Alignment explanation
Indices: 130889--130948 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
130879 TATTTAACAA
*
130889 GTTTGTCCTCTCCGTTTAGGAC
1 GTTTGTCCTCTCCGTTTAGCAC
* *
130911 GTTTG-CGCTCTTCGTCTAGCAC
1 GTTTGTC-CTCTCCGTTTAGCAC
* *
130933 CTTTGTGCTCTCCGTT
1 GTTTGTCCTCTCCGTT
130949 CATTAGTGCA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.07, C:0.30, G:0.22, T:0.42
Consensus pattern (22 bp):
GTTTGTCCTCTCCGTTTAGCAC
Found at i:148503 original size:25 final size:25
Alignment explanation
Indices: 148437--148525 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 25
148427 ATTTAGTTTA
*
148437 TTTAAATTTAAATAAATT-AATAAAA
1 TTTAAATTTAAATAAATTAAAT-AAT
* **
148462 TTTACATAGAGAA-AAATTAAATAAT
1 TTTAAATTTA-AATAAATTAAATAAT
148487 TTTAAATTTAAATAAATTGATAATAAT
1 TTTAAATTTAAATAAATT-A-AATAAT
* *
148514 TATATATTTAAA
1 TTTAAATTTAAA
148526 ATTTATTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
24 2 0.04
25 26 0.52
26 6 0.12
27 16 0.32
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (25 bp):
TTTAAATTTAAATAAATTAAATAAT
Found at i:148885 original size:10 final size:11
Alignment explanation
Indices: 148863--148888 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
148853 ATGATGTCAT
148863 AATTTTAAAAA
1 AATTTTAAAAA
148874 AATTTTAAAAA
1 AATTTTAAAAA
148885 AATT
1 AATT
148889 CCTTCTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTTTAAAAA
Found at i:154997 original size:60 final size:59
Alignment explanation
Indices: 154925--155039 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 59
154915 AGTGATTATC
* * * * *
154925 TTAATATTAAATTTAATTTAATGTTTATCTTGTATAAACATTTTATTATTTTAATAAGAT
1 TTAATATAAAATTTAATCTAATATTTATCTTG-ATAAACATTATATTAATTTAATAAGAT
* *
154985 TTAATATAAAATTTAATCTAATATTTATCTTGATAAATATTATGTTAATTTAATA
1 TTAATATAAAATTTAATCTAATATTTATCTTGATAAACATTATATTAATTTAATA
155040 TTAAAGTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 19 0.40
60 29 0.60
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (59 bp):
TTAATATAAAATTTAATCTAATATTTATCTTGATAAACATTATATTAATTTAATAAGAT
Found at i:156323 original size:9 final size:9
Alignment explanation
Indices: 156309--156347 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
156299 TGAATTTTAC
156309 AATTCGAAT
1 AATTCGAAT
156318 AATTCGAAT
1 AATTCGAAT
*
156327 AATTCAAAT
1 AATTCGAAT
156336 AAATT-GAAT
1 -AATTCGAAT
156345 AAT
1 AAT
156348 AGATTGGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 3 0.11
9 20 0.74
10 4 0.15
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:156450 original size:18 final size:19
Alignment explanation
Indices: 156429--156469 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
156419 AATTACAAAA
*
156429 AAAATCAAAATAAT-TTTT
1 AAAATCAAAAAAATATTTT
*
156447 AAAATTAAAAAAATATTTT
1 AAAATCAAAAAAATATTTT
156466 AAAA
1 AAAA
156470 AAATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATCAAAAAAATATTTT
Found at i:156450 original size:21 final size:19
Alignment explanation
Indices: 156426--156482 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
156416 AAAAATTACA
156426 AAAAAAATCAAAATAATTTTT
1 AAAAAAATCAAAAT-A-TTTT
156447 AAAATTAAA--AAAATATTTT
1 AAAA--AAATCAAAATATTTT
156466 AAAAAAATCAAAA-ATTT
1 AAAAAAATCAAAATATTT
156483 ATATTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
17 3 0.09
18 4 0.12
19 12 0.38
20 1 0.03
21 9 0.28
23 3 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAAATCAAAATATTTT
Found at i:156478 original size:20 final size:22
Alignment explanation
Indices: 156426--156495 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
156416 AAAAATTACA
156426 AAAAAAATC-AAAATAATTTTT
1 AAAAAAATCAAAAATAATTTTT
*
156447 ---AAAATTAAAAA-AATATTTT
1 AAAAAAATCAAAAATAAT-TTTT
156466 AAAAAAATCAAAAATTTATATTTTT
1 AAAAAAATCAAAAA--TA-ATTTTT
156491 AAAAA
1 AAAAA
156496 TTATGATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
18 8 0.21
19 8 0.21
22 10 0.26
25 10 0.26
26 2 0.05
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAAAATCAAAAATAATTTTT
Found at i:156496 original size:16 final size:18
Alignment explanation
Indices: 156475--156508 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
156465 TAAAAAAATC
156475 AAAAATT-T-ATATTTTT
1 AAAAATTATGATATTTTT
156491 AAAAATTATGATATTTTT
1 AAAAATTATGATATTTTT
156509 TTAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AAAAATTATGATATTTTT
Found at i:160567 original size:22 final size:23
Alignment explanation
Indices: 160523--160567 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
160513 AAGTAATTAA
* *
160523 AAATAATTAATTAACATAATATT
1 AAATAATTAATAAAAATAATATT
*
160546 AAAT-ATTAATAAAAATATTATT
1 AAATAATTAATAAAAATAATATT
160568 GACAAATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATAATTAATAAAAATAATATT
Found at i:161873 original size:24 final size:24
Alignment explanation
Indices: 161846--161892 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
161836 AGTTTGACTG
161846 AAACAAATAAACAGAGTTTAATTT
1 AAACAAATAAACAGAGTTTAATTT
* *
161870 AAACTAATAAATAGAGTTTAATT
1 AAACAAATAAACAGAGTTTAATT
161893 AGAAGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTT
Found at i:163942 original size:6 final size:6
Alignment explanation
Indices: 163931--163975 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
163921 TGATCAAAAT
* * *
163931 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
163976 TATGAATTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:168479 original size:24 final size:25
Alignment explanation
Indices: 168447--168498 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
168437 AGTTTGACTG
* *
168447 AAACAAATAAATAAAATTTAATT-A
1 AAACAAATAAACAAAATGTAATTGA
*
168471 AAACTAATAAACAAAATGTAATTGA
1 AAACAAATAAACAAAATGTAATTGA
168496 AAA
1 AAA
168499 ATTATTTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (25 bp):
AAACAAATAAACAAAATGTAATTGA
Found at i:171969 original size:6 final size:6
Alignment explanation
Indices: 171935--171996 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
171925 TAATAGGAAT
* * * *
171935 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*
171982 TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTT
171997 TGATCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 40 0.85
7 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:174535 original size:24 final size:24
Alignment explanation
Indices: 174496--174552 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
174486 TAAACTTATA
* *
174496 AGAGTTTGATTGAAAC-AAATAAAT
1 AGAGTTTAATTAAAACTAAA-AAAT
* *
174520 ATAGTTTAATTAAAACTAGAAAAT
1 AGAGTTTAATTAAAACTAAAAAAT
174544 AGAGTTTAA
1 AGAGTTTAA
174553 CTGAAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.32
Consensus pattern (24 bp):
AGAGTTTAATTAAAACTAAAAAAT
Found at i:174724 original size:27 final size:27
Alignment explanation
Indices: 174693--174747 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
174683 TATTTTCCGG
174693 ACTAAGATAAATGAAAACATAAAACGA
1 ACTAAGATAAATGAAAACATAAAACGA
174720 ACTAAGATAAATGAAAACATAAAACGA
1 ACTAAGATAAATGAAAACATAAAACGA
174747 A
1 A
174748 TCTTTTGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.15
Consensus pattern (27 bp):
ACTAAGATAAATGAAAACATAAAACGA
Found at i:175983 original size:20 final size:20
Alignment explanation
Indices: 175958--176026 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
175948 TTCAAGGTTT
175958 GGGTTCAAGCTTT-AGATTCA
1 GGGTTCAAG-TTTAAGATTCA
*
175978 GGGTTCATGGTTTCAAGATTCA
1 GGGTTCA-AGTTT-AAGATTCA
* *
176000 AGGTTCGAGTTTAAGATTCAA
1 GGGTTCAAGTTTAAGATTC-A
176021 GGGTTC
1 GGGTTC
176027 GAGGTTTAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
20 17 0.43
21 11 0.28
22 12 0.30
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.35
Consensus pattern (20 bp):
GGGTTCAAGTTTAAGATTCA
Found at i:175999 original size:22 final size:20
Alignment explanation
Indices: 175958--176034 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 20
175948 TTCAAGGTTT
*
175958 GGGTTCAAGCTTT-AGATTCA
1 GGGTTCGAG-TTTAAGATTCA
175978 GGGTTC-ATGGTTTCAAGATTCA
1 GGGTTCGA--GTTT-AAGATTCA
*
176000 AGGTTCGAGTTTAAGATTCAA
1 GGGTTCGAGTTTAAGATTC-A
176021 GGGTTCGAGGTTTA
1 GGGTTCGA-GTTTA
176035 GGGATTAAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.02
20 16 0.33
21 13 0.27
22 17 0.35
23 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.35
Consensus pattern (20 bp):
GGGTTCGAGTTTAAGATTCA
Found at i:176471 original size:23 final size:23
Alignment explanation
Indices: 176437--176481 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
176427 TAAGCGTACC
176437 TAGACATACTTAA-GGCTATGTTG
1 TAGACATACTTAATGGCT-TGTTG
176460 TAGA-ATACCTTAATGGCTTGTT
1 TAGACATA-CTTAATGGCTTGTT
176482 TGGAAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (23 bp):
TAGACATACTTAATGGCTTGTTG
Found at i:177765 original size:19 final size:20
Alignment explanation
Indices: 177741--177783 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
177731 TCATTTGTTT
177741 TTATT-AATTTACAATT-TAA
1 TTATTAAATTTA-AATTGTAA
177760 TTATTAAATTTAAATTGTAA
1 TTATTAAATTTAAATTGTAA
177780 TTAT
1 TTAT
177784 ATTTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TTATTAAATTTAAATTGTAA
Found at i:178019 original size:17 final size:17
Alignment explanation
Indices: 177997--178030 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
177987 TTTACTTGTC
177997 CTCAAGTAAACAAAAGT
1 CTCAAGTAAACAAAAGT
178014 CTCAAGTAAACAAAAGT
1 CTCAAGTAAACAAAAGT
178031 TAGCAAAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (17 bp):
CTCAAGTAAACAAAAGT
Found at i:178273 original size:13 final size:12
Alignment explanation
Indices: 178255--178287 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
178245 ATAAATATTT
178255 TTTTTCTTTTCTC
1 TTTTTCTTTT-TC
178268 TTTTTC-TTTTC
1 TTTTTCTTTTTC
178279 TTTTTCTTT
1 TTTTTCTTT
178288 CTTTTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 5 0.26
13 6 0.32
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:178275 original size:6 final size:6
Alignment explanation
Indices: 178255--178287 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
178245 ATAAATATTT
178255 TTTTTC TTTTCTC TTTTTC -TTTTC TTTTTC TTT
1 TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC TTT
178288 CTTTTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:178288 original size:10 final size:11
Alignment explanation
Indices: 178255--178293 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
178245 ATAAATATTT
178255 TTTTTCTTTTCTC
1 TTTTTC-TTT-TC
178268 TTTTTCTTTTC
1 TTTTTCTTTTC
178279 TTTTTC-TTTC
1 TTTTTCTTTTC
178289 TTTTT
1 TTTTT
178294 ATGTGATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.35
11 8 0.31
12 3 0.12
13 6 0.23
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:178884 original size:17 final size:17
Alignment explanation
Indices: 178864--178910 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
178854 GACAATGTAG
178864 ATGCAACGACAATAAAA
1 ATGCAACGACAATAAAA
* * *
178881 ATGCAATGACATTAATA
1 ATGCAACGACAATAAAA
*
178898 ATGCAAGGACAAT
1 ATGCAACGACAAT
178911 TATACTATAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (17 bp):
ATGCAACGACAATAAAA
Found at i:195620 original size:38 final size:38
Alignment explanation
Indices: 195548--195753 Score: 156
Period size: 38 Copynumber: 5.5 Consensus size: 38
195538 TCGGGCTATG
* * ** *
195548 TGCCTAGCAAG-CTTCGTGCTGGTGACATTGGGCTTTA
1 TGCCTAGCAGGCCTTCGTGCTAGTGTTATTAGGCTTTA
*
195585 TGCCTAGTAGGCCTTCGTGCTAGTGTTATTAGGCTTTA
1 TGCCTAGCAGGCCTTCGTGCTAGTGTTATTAGGCTTTA
* *
195623 TG-CTAGCAGGCCTTCGTG-TCAATGTTATCAGGCTTTA
1 TGCCTAGCAGGCCTTCGTGCT-AGTGTTATTAGGCTTTA
* * * * * *
195660 TGCCTAGCAGGCCTTTGTG-TCGGTGTTA-TCGAGATATG
1 TGCCTAGCAGGCCTTCGTGCT-AGTGTTATTAG-GCTTTA
* * ** *
195698 TGCCTAGCAGG-TTTCGTGC-AGGTGATATCGGGGTTTA
1 TGCCTAGCAGGCCTTCGTGCTA-GTGTTATTAGGCTTTA
195735 TGCCTAGCAGGCCTTCGTG
1 TGCCTAGCAGGCCTTCGTG
195754 TCGGTGTTAT
Statistics
Matches: 134, Mismatches: 27, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
36 1 0.01
37 66 0.49
38 67 0.50
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (38 bp):
TGCCTAGCAGGCCTTCGTGCTAGTGTTATTAGGCTTTA
Found at i:195686 original size:75 final size:76
Alignment explanation
Indices: 195513--195819 Score: 216
Period size: 75 Copynumber: 4.1 Consensus size: 76
195503 TAATATCAGG
* * * * * * * * * * * *
195513 CTAGCAAGCCTTAGTGCCGGTGTTA-TCGGGCTATGTGCCTAGCAAGCTTCGTGCTGGTGACATT
1 CTAGCAGGCCTTCGTGTCGGTGTTATTAGAGATATATGCCTAGCAGGCTTCGTGCAGATGATATC
*
195577 GGGCTTTATGC
66 AGGCTTTATGC
* * * * *
195588 CTAGTAGGCCTTCGTG-CTAGTGTTATTAG-GCTTTATG-CTAGCAGGCCTTCGTGTCA-ATGTT
1 CTAGCAGGCCTTCGTGTC-GGTGTTATTAGAGATATATGCCTAGCAGG-CTTCGTG-CAGATGAT
195649 ATCAGGCTTTATGC
63 ATCAGGCTTTATGC
* * * * *
195663 CTAGCAGGCCTTTGTGTCGGTGTTA-TCGAGATATGTGCCTAGCAGGTTTCGTGCAGGTGATATC
1 CTAGCAGGCCTTCGTGTCGGTGTTATTAGAGATATATGCCTAGCAGGCTTCGTGCAGATGATATC
* *
195727 GGGGTTTATGC
66 AGGCTTTATGC
* * * * * * *
195738 CTAGCAGGCCTTCGTGTCGGTGTTA-TCGAGTTATATGCCCAACAGACTTCATGTC-GGTGATAT
1 CTAGCAGGCCTTCGTGTCGGTGTTATTAGAGATATATGCCTAGCAGGCTTCGTG-CAGATGATAT
* *
195801 CAGGTTTTATAC
65 CAGGCTTTATGC
195813 CTAGCAG
1 CTAGCAG
195820 ACTTTGTGCC
Statistics
Matches: 186, Mismatches: 37, Indels: 18
0.77 0.15 0.07
Matches are distributed among these distances:
74 12 0.06
75 161 0.87
76 13 0.07
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (76 bp):
CTAGCAGGCCTTCGTGTCGGTGTTATTAGAGATATATGCCTAGCAGGCTTCGTGCAGATGATATC
AGGCTTTATGC
Found at i:195802 original size:150 final size:147
Alignment explanation
Indices: 195513--195902 Score: 387
Period size: 150 Copynumber: 2.6 Consensus size: 147
195503 TAATATCAGG
* * * * *
195513 CTAGCAAGCCTTAGTGCCGGTGTTATCGGGCTATGTGCCTAGCAAGCTTCGTGCTGGTGACATTG
1 CTAGC-AGCCTTTGTGCCGGTGTTATCGGGCTATGTGCCTAGCAGGTTTCGTGC-GGTGATATCG
* * * * * * * *
195578 GGCTTTATGCCTAGTAGGCCTTCGTGCTAGTGTTATTAGGCTTTATGCTAGCAGGCCTTCGTGTC
64 GGGTTTATGCCTAGCAGGCCTTCGTGC-GGTGTTATGAGGCTTTATGCCAACAGGACTTCATGTC
* *
195643 AATGTTATCAGGCTTTATGC
128 AATGATATCAGGCTTTATAC
* * *
195663 CTAGCAGGCCTTTGTGTCGGTGTTATCGAGATATGTGCCTAGCAGGTTTCGTGCAGGTGATATCG
1 CTAGCA-GCCTTTGTGCCGGTGTTATCGGGCTATGTGCCTAGCAGGTTTCGTGC-GGTGATATCG
195728 GGGTTTATGCCTAGCAGGCCTTCGTGTCGGTGTTATCGA-G-TTATATGCCCAACA-GACTTCAT
64 GGGTTTATGCCTAGCAGGCCTTCGTG-CGGTGTTAT-GAGGCTT-TATG-CCAACAGGACTTCAT
** *
195790 GTCGGTGATATCAGGTTTTATAC
125 GTCAATGATATCAGGCTTTATAC
* * * * *
195813 CTAGCAGACTTTGTGCCGGTATTGTCGGGCTATGTGCCTATCAGGCTTT-GTGGCGGTGTTATC-
1 CTAGCAGCCTTTGTGCCGGTGTTATCGGGCTATGTGCCTAGCAGG-TTTCGT-GCGGTGATATCG
*
195876 GGGTTATGTGCCTAGCAGG-CTTCGTGC
64 GGGTT-TATGCCTAGCAGGCCTTCGTGC
195903 CGATGTTAAT
Statistics
Matches: 201, Mismatches: 31, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
147 1 0.00
148 12 0.06
149 57 0.28
150 125 0.62
151 6 0.03
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (147 bp):
CTAGCAGCCTTTGTGCCGGTGTTATCGGGCTATGTGCCTAGCAGGTTTCGTGCGGTGATATCGGG
GTTTATGCCTAGCAGGCCTTCGTGCGGTGTTATGAGGCTTTATGCCAACAGGACTTCATGTCAAT
GATATCAGGCTTTATAC
Found at i:195910 original size:37 final size:37
Alignment explanation
Indices: 195526--195910 Score: 249
Period size: 37 Copynumber: 10.3 Consensus size: 37
195516 GCAAGCCTTA
* * *
195526 GTGCCGGTGTTATCGGGCTATGTGCCTAGCAAGCTTC
1 GTGCCGGTGTTATCGGGTTATATGCCTAGCAGGCTTC
* ** * *
195563 GTGCTGGTGACATTGGGCTT-TATGCCTAGTAGGCCTTC
1 GTGCCGGTGTTATCGGG-TTATATGCCTAGCAGG-CTTC
** * *
195601 GTGCTAGTGTTATTAGGCTT-TATG-CTAGCAGGCCTTC
1 GTGCCGGTGTTA-TCGGGTTATATGCCTAGCAGG-CTTC
* ** * *
195638 GTGTCAATGTTATCAGGCTT-TATGCCTAGCAGGCCTTT
1 GTGCCGGTGTTATC-GGGTTATATGCCTAGCAGG-CTTC
* * * * *
195676 GTGTCGGTGTTATCGAGATATGTGCCTAGCAGGTTTC
1 GTGCCGGTGTTATCGGGTTATATGCCTAGCAGGCTTC
* *
195713 GTGCAGGTGATATCGGGGTT-TATGCCTAGCAGGCCTTC
1 GTGCCGGTGTTATC-GGGTTATATGCCTAGCAGG-CTTC
* * * * *
195751 GTGTCGGTGTTATCGAGTTATATGCCCAACAGACTTC
1 GTGCCGGTGTTATCGGGTTATATGCCTAGCAGGCTTC
* * * * * * * *
195788 ATGTCGGTGATATCAGGTTTTATACCTAGCAGACTTT
1 GTGCCGGTGTTATCGGGTTATATGCCTAGCAGGCTTC
* * * * * *
195825 GTGCCGGTATTGTCGGGCTATGTGCCTATCAGGCTTT
1 GTGCCGGTGTTATCGGGTTATATGCCTAGCAGGCTTC
* *
195862 GTGGCGGTGTTATCGGGTTATGTGCCTAGCAGGCTTC
1 GTGCCGGTGTTATCGGGTTATATGCCTAGCAGGCTTC
*
195899 GTGCCGATGTTA
1 GTGCCGGTGTTA
195911 ATTGAGATAT
Statistics
Matches: 269, Mismatches: 70, Indels: 18
0.75 0.20 0.05
Matches are distributed among these distances:
36 1 0.00
37 182 0.68
38 83 0.31
39 3 0.01
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (37 bp):
GTGCCGGTGTTATCGGGTTATATGCCTAGCAGGCTTC
Found at i:202921 original size:383 final size:383
Alignment explanation
Indices: 202210--202975 Score: 1309
Period size: 383 Copynumber: 2.0 Consensus size: 383
202200 ACCTAATCTA
*
202210 GAGTTAGTGGTATTTATAACACTAAGTGTGAGCTTAAAAGCCTCACAACTGTCCCAAAACTTAGG
1 GAGTTAGTGGTATTTACAACACTAAGTGTGAGCTTAAAAGCCTCACAACTGTCCCAAAACTTAGG
202275 TAATATCACTCAAATCTCTAGTACATTAGCAACCACAAATATATATGCTCTTCCACCTGAAACTT
66 TAATATCACTCAAATCTCTAGTACATTAGCAACCACAAATATATATGCTCTTCCACCTGAAACTT
* *
202340 CCTCACCTTCTAGATCCTCTAGCATGTCAATACCTGATCATTTTACAACTACACATCAAGACTCA
131 CATCACCTTCTAGATCCTCTAGCATGTCAATACCTGATCATGTTACAACTACACATCAAGACTCA
* * *
202405 ACATCTAGTCAAAACCAAAACCAAACACTTCTAGCTACCAACTATCATCCTATGGTTATAAGAAG
196 ACATCTAGTCAAAACCAAAACCAAACACTTCTAACTACAAACTATCATCCTATGGTTACAAGAAG
202470 TAAACTAGGAATTTTCAAACCTAAGGCATATGTCACCAAGGTAACAAGTTCATCAGATGTTGCTA
261 TAAACTAGGAATTTTCAAACCTAAGGCATATGTCACCAAGGTAACAAGTTCATCAGATGTTGCTA
* *
202535 TTACTACTAATTCATCCTCTAATGTTCCAAGTAACTTTCATGAAGCAATGGTCTCACC
326 TTACTACTAATTCATCCTCTAATGTTCCAAGTAACATTCATGAAGAAATGGTCTCACC
* * * * *
202593 GAGTTAGTGGTATTTCCAACACTAAGTGTGAGCTTAGAAGCCTCACAGCTTTTCCAAAACTTAGG
1 GAGTTAGTGGTATTTACAACACTAAGTGTGAGCTTAAAAGCCTCACAACTGTCCCAAAACTTAGG
* * * *
202658 TAATATCAGTCCAATCTCTAGTACATTAGCAACCATAAATATATTTGCTCTTCCACCTGAAACTT
66 TAATATCACTCAAATCTCTAGTACATTAGCAACCACAAATATATATGCTCTTCCACCTGAAACTT
*
202723 CATCACCTTCTAGATCCTCTAGCATGTCAATACCTGATCATGTTACAACTACACATCAGGACTCA
131 CATCACCTTCTAGATCCTCTAGCATGTCAATACCTGATCATGTTACAACTACACATCAAGACTCA
* *
202788 ACATCTAGTTAAAACCAAAACCAAACACTT-TCAACTACAAACTGTCATCCTATGGTTACAAGAA
196 ACATCTAGTCAAAACCAAAACCAAACACTTCT-AACTACAAACTATCATCCTATGGTTACAAGAA
*
202852 GTAAACTAGGAATTTTCAAACCTAAGGCATATGTCACCAAGGTAACAAGTTCATCAGATGTTTCT
260 GTAAACTAGGAATTTTCAAACCTAAGGCATATGTCACCAAGGTAACAAGTTCATCAGATGTTGCT
* *
202917 ATTACTACTAATTTATCCTCTGATGTTCCAAGTAACATTCATGAAGAAATGGTCTCACC
325 ATTACTACTAATTCATCCTCTAATGTTCCAAGTAACATTCATGAAGAAATGGTCTCACC
202976 ACAGTGGCAA
Statistics
Matches: 359, Mismatches: 23, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
382 1 0.00
383 358 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (383 bp):
GAGTTAGTGGTATTTACAACACTAAGTGTGAGCTTAAAAGCCTCACAACTGTCCCAAAACTTAGG
TAATATCACTCAAATCTCTAGTACATTAGCAACCACAAATATATATGCTCTTCCACCTGAAACTT
CATCACCTTCTAGATCCTCTAGCATGTCAATACCTGATCATGTTACAACTACACATCAAGACTCA
ACATCTAGTCAAAACCAAAACCAAACACTTCTAACTACAAACTATCATCCTATGGTTACAAGAAG
TAAACTAGGAATTTTCAAACCTAAGGCATATGTCACCAAGGTAACAAGTTCATCAGATGTTGCTA
TTACTACTAATTCATCCTCTAATGTTCCAAGTAACATTCATGAAGAAATGGTCTCACC
Found at i:205429 original size:26 final size:26
Alignment explanation
Indices: 205397--205451 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
205387 CAACCAGGAA
205397 TGTCGCTGCATGAACATGT-ATAGAAT
1 TGTCGCTGCATGAACATGTCA-AGAAT
205423 TGTCGCTGCATGAACATGTCAAGAAT
1 TGTCGCTGCATGAACATGTCAAGAAT
205449 TGT
1 TGT
205452 GCCCTGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 27 0.96
27 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCAAGAAT
Found at i:208617 original size:14 final size:14
Alignment explanation
Indices: 208598--208628 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
208588 TTAGTACTAT
*
208598 TATTTAAGATTTAA
1 TATTTAAGAATTAA
208612 TATTTAAGAATTAA
1 TATTTAAGAATTAA
208626 TAT
1 TAT
208629 CAATATTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TATTTAAGAATTAA
Found at i:208717 original size:14 final size:15
Alignment explanation
Indices: 208676--208729 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
208666 TGTTTAAGAA
*
208676 TTAAAGATTTAGGGT
1 TTAAAGATTTAGAGT
*
208691 TTAAAGTTTTAGAGT
1 TTAAAGATTTAGAGT
208706 TTAAA-ATTTAGAGT
1 TTAAAGATTTAGAGT
208720 CTTAAA-ATTT
1 -TTAAAGATTT
208730 TATTTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
14 8 0.23
15 27 0.77
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (15 bp):
TTAAAGATTTAGAGT
Found at i:211880 original size:39 final size:39
Alignment explanation
Indices: 211713--212094 Score: 281
Period size: 39 Copynumber: 9.7 Consensus size: 39
211703 ATGGTAGCTT
* *
211713 TAATCTGCCCCATGATCGGGGTAAGAGATTGGTATGTCT-
1 TAATCTGCCCCATGATCGGGGTAAGAGATCGG-ATGGCTG
* ** *
211752 TCAATTTGCCCTC-TGATTAGGGTAA-AGATTGGAT-GCT-
1 T-AATCTGCCC-CATGATCGGGGTAAGAGATCGGATGGCTG
* * * **
211789 TCGATCTGCCCTATGGTCATGGTAAGAGATC-GATGGCTG
1 T-AATCTGCCCCATGATCGGGGTAAGAGATCGGATGGCTG
* ** *
211828 TGATCTGCCCCATGATCGGGGTAAGAGATCGGATTACTA
1 TAATCTGCCCCATGATCGGGGTAAGAGATCGGATGGCTG
* * ** *
211867 CAATCTGCCCCATGATCGAGGTAAGAGATTAGATGACTG
1 TAATCTGCCCCATGATCGGGGTAAGAGATCGGATGGCTG
* * * *
211906 TGATCTGCCCCATGATCGAGGTAAGAGATGGGATGGTTG
1 TAATCTGCCCCATGATCGGGGTAAGAGATCGGATGGCTG
* ** *
211945 TAATCTGACCCATGATCAAGGTAAGAGATTCGGATGGTTG
1 TAATCTGCCCCATGATCGGGGTAAGAGA-TCGGATGGCTG
* * * * * *
211985 TGATCTGCCCCATGATCGGAGTAAGAGATCGGGTAGTTA
1 TAATCTGCCCCATGATCGGGGTAAGAGATCGGATGGCTG
* * * ** *
212024 TGATCTACCTCATGATCAAGGTAAGAGATCAGATGATGGTTG
1 TAATCTGCCCCATGATCGGGGTAAGAGATC-G--GATGGCTG
*
212066 CAATCTGCCCCATGATCGGGGTAAGAGAT
1 TAATCTGCCCCATGATCGGGGTAAGAGAT
212095 TGGCGATAGT
Statistics
Matches: 275, Mismatches: 57, Indels: 19
0.78 0.16 0.05
Matches are distributed among these distances:
37 23 0.08
38 34 0.12
39 137 0.50
40 52 0.19
41 1 0.00
42 28 0.10
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (39 bp):
TAATCTGCCCCATGATCGGGGTAAGAGATCGGATGGCTG
Found at i:212011 original size:157 final size:157
Alignment explanation
Indices: 211792--212094 Score: 400
Period size: 157 Copynumber: 1.9 Consensus size: 157
211782 GGATGCTTCG
* * *
211792 ATCTGCCCTATGGTCATGGTAAGAGATCGATGGCTGTGATCTGCCCCATGATCGGGGTAAGAGAT
1 ATCTGCCCTATGATCAAGGTAAGAGATCGATGGCTGTGATCTGCCCCATGATCGGAGTAAGAGAT
* * * *
211857 CGGATTA-CTACAATCTGCCCCATGATCGAGGTAAGAGATTAGATGACT-G-TG-ATCTGCCCCA
66 CGG-GTAGCTACAATCTACCCCATGATCAAGGTAAGAGATCAGATGA-TGGTTGAATCTGCCCCA
211918 TGATCGAGGTAAGAGATGGGATGGTTGTA
129 TGATCGAGGTAAGAGATGGGATGGTTGTA
*
211947 ATCTGACCC-ATGATCAAGGTAAGAGATTCGGATGGTTGTGATCTGCCCCATGATCGGAGTAAGA
1 ATCTG-CCCTATGATCAAGGTAAGAGA-TC-GATGGCTGTGATCTGCCCCATGATCGGAGTAAGA
* ** *
212011 GATCGGGTAGTTATGATCTACCTCATGATCAAGGTAAGAGATCAGATGATGGTTGCAATCTGCCC
63 GATCGGGTAGCTACAATCTACCCCATGATCAAGGTAAGAGATCAGATGATGGTTG-AATCTGCCC
*
212076 CATGATCGGGGTAAGAGAT
127 CATGATCGAGGTAAGAGAT
212095 TGGCGATAGT
Statistics
Matches: 127, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
155 20 0.16
156 8 0.06
157 71 0.56
158 2 0.02
160 26 0.20
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (157 bp):
ATCTGCCCTATGATCAAGGTAAGAGATCGATGGCTGTGATCTGCCCCATGATCGGAGTAAGAGAT
CGGGTAGCTACAATCTACCCCATGATCAAGGTAAGAGATCAGATGATGGTTGAATCTGCCCCATG
ATCGAGGTAAGAGATGGGATGGTTGTA
Found at i:212474 original size:49 final size:49
Alignment explanation
Indices: 212414--213055 Score: 295
Period size: 49 Copynumber: 13.3 Consensus size: 49
212404 GCTGTTGTGA
* *
212414 CTTAAACCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCAG
1 CTTAAATCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGG
* * * * * * * ** *
212463 CTTCAATCTTTCTCAT-CATGT-TTC-TGAGGTACAAGGTTCGCCATTATGA
1 CTTAAATCTTTC-CCTCCATATCTTCAT--GGTACCAGATTCGTCGTTGCGG
* *
212512 CTTAAA-CATTTCCCTCCATATCTTCGTGGTACCAGATTCGCCGTTGCGG
1 CTTAAATC-TTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGG
* * * *
212561 CTTCAATCTTT-CCTAGCATGT-TTC-TGAGGTA-CA-A----T-GTTGCGA
1 CTTAAATCTTTCCCT-CCATATCTTCAT--GGTACCAGATTCGTCGTTGCGG
* * * * *
212603 CTTAAACCTTTCCCTCCATATCTTCGTTGTACCAAATTCGTCATTGCGG
1 CTTAAATCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGG
* * ** * * * * **
212652 CTTTAATATTTCCCAGCATGT-TTCTAAGGTACAAGGTTCGTCGTTGCAA
1 CTTAAATCTTTCCCTCCATATCTTC-ATGGTACCAGATTCGTCGTTGCGG
* *
212701 CTTAAACCTTTCCCTCCATATCTTCGTGGTACCAGATTCGTCGTTGCGG
1 CTTAAATCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGG
* * * * * * * * *
212750 CTTTAATCTTTCCCTTCATGT-TTCTAAGGTACAAGGTTC-ACTGTTGTGA
1 CTTAAATCTTTCCCTCCATATCTTC-ATGGTACCAGATTCGTC-GTTGCGG
* * * * *
212799 CTTAAACCTTTCCCTTCATATCTTCATGGTACTAGATTCGTCATTGTGG
1 CTTAAATCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGG
* * * * * *
212848 CTTAAATCTTTCCCTTCATGT-TTC-TGAGGTACAAGGTTCGCCGTTGCGA
1 CTTAAATCTTTCCCTCCATATCTTCAT--GGTACCAGATTCGTCGTTGCGG
* ** * * * *
212897 CTTAAACCTTTCCCTCCATATCTTTGTGGTACTAGATTCGCCATTGTGG
1 CTTAAATCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGG
* * * * * *** * *
212946 CTT--ATTTTTCCCTTCATGT-TTC-TGAGGTACAAGGTTTACCGTTGTGA
1 CTTAAATCTTTCCCTCCATATCTTCAT--GGTACCAGATTCGTCGTTGCGG
* * * * **
212993 CTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCATCGTTATGG
1 CTTAAATCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGG
213042 CTTAAATCTTTCCC
1 CTTAAATCTTTCCC
213056 ATCTCATCTC
Statistics
Matches: 437, Mismatches: 119, Indels: 74
0.69 0.19 0.12
Matches are distributed among these distances:
42 22 0.05
43 8 0.02
44 2 0.00
45 1 0.00
46 2 0.00
47 35 0.08
48 25 0.06
49 321 0.73
50 18 0.04
51 3 0.01
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (49 bp):
CTTAAATCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGG
Found at i:212518 original size:98 final size:98
Alignment explanation
Indices: 212348--213058 Score: 855
Period size: 98 Copynumber: 7.3 Consensus size: 98
212338 TTAGGGTATA
* * * ** * * *
212348 AGATTCATCGTTACGGCTTCAATATTTCCCTATCAAATTTTTGAGGTACAAGGTTAGCTGTTGTG
1 AGATTCGTCGTTGCGGCTTCAATCTTTCCC-ATCATGTTTCTGAGGTACAAGGTTCGCCGTTGTG
*
212413 ACTTAAACCTTTCCCTCCATATCTTCATGGTACC
65 ACTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * *
212447 AGATTCGTCGTTGCAGCTTCAATCTTTCTCATCATGTTTCTGAGGTACAAGGTTCGCCATTATGA
1 AGATTCGTCGTTGCGGCTTCAATCTTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGTGA
*
212512 CTTAAACATTTCCCTCCATATCTTCGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * *
212545 AGATTCGCCGTTGCGGCTTCAATCTTTCCTAGCATGTTTCTGAGGTACAA---T----GTTGCGA
1 AGATTCGTCGTTGCGGCTTCAATCTTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGTGA
*
212603 CTTAAACCTTTCCCTCCATATCTTCGTTGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * * * * **
212636 AAATTCGTCATTGCGGCTTTAATATTTCCCAGCATGTTTCTAAGGTACAAGGTTCGTCGTTGCAA
1 AGATTCGTCGTTGCGGCTTCAATCTTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGTGA
212701 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * *
212734 AGATTCGTCGTTGCGGCTTTAATCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACTGTTGTGA
1 AGATTCGTCGTTGCGGCTTCAATCTTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGTGA
* * *
212799 CTTAAACCTTTCCCTTCATATCTTCATGGTACT
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * *
212832 AGATTCGTCATTGTGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGA
1 AGATTCGTCGTTGCGGCTTCAATCTTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGTGA
* *
212897 CTTAAACCTTTCCCTCCATATCTTTGTGGTACT
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* * * * * **
212930 AGATTCGCCATTGTGGCTT--ATTTTTCCCTTCATGTTTCTGAGGTACAAGGTTTACCGTTGTGA
1 AGATTCGTCGTTGCGGCTTCAATCTTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGTGA
*
212993 CTTAAACCTTTCCCTCCATATCTTCGTGGTACT
66 CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
* ** *
213026 AGATTCATCGTTATGGCTTAAATCTTTCCCATC
1 AGATTCGTCGTTGCGGCTTCAATCTTTCCCATC
213059 TCATCTCCAT
Statistics
Matches: 535, Mismatches: 68, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
91 78 0.15
94 1 0.00
95 1 0.00
96 87 0.16
98 343 0.64
99 25 0.05
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (98 bp):
AGATTCGTCGTTGCGGCTTCAATCTTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGTGA
CTTAAACCTTTCCCTCCATATCTTCGTGGTACC
Found at i:212732 original size:189 final size:189
Alignment explanation
Indices: 212406--213058 Score: 826
Period size: 189 Copynumber: 3.4 Consensus size: 189
212396 CAAGGTTAGC
* * *
212406 TGTTGTGACTTAAACCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCAGCTTCAATC
1 TGTTGTGACTTAAACCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCATTGCGGCTTAAATC
* * ** *
212471 TTTCTCATCATGTTTCTGAGGTACAAGGTTCGCCATTATGACTTAAACATTTCCCTCCATATCTT
66 TTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTT
*
212536 CGTGGTACCAGATTCGCCGTTGCGGCTTCAATCTTT-CCTAGCATGTTTCTGAGGTACAA-
131 CGTGGTACCAGATTCGCCGTTGCGGCTT-AATCTTTCCCT-TCATGTTTCTGAGGTACAAG
* * * * * *
212595 TGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTTGTACCAAATTCGTCATTGCGGCTTTAATA
1 TGTTGTGACTTAAACCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCATTGCGGCTTAAATC
* * * *
212660 TTTCCCAGCATGTTTCTAAGGTACAAGGTTCGTCGTTGCAACTTAAACCTTTCCCTCCATATCTT
66 TTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTT
* *
212725 CGTGGTACCAGATTCGTCGTTGCGGCTTTAATCTTTCCCTTCATGTTTCTAAGGTACAAGG
131 CGTGGTACCAGATTCGCCGTTGCGGC-TTAATCTTTCCCTTCATGTTTCTGAGGTACAA-G
* * *
212786 TTCACTGTTGTGACTTAAACCTTTCCCTTCATATCTTCATGGTACTAGATTCGTCATTGTGGCTT
1 -----TGTTGTGACTTAAACCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCATTGCGGCTT
*
212851 AAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
61 AAATCTTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCAT
* * * * *
212916 ATCTTTGTGGTACTAGATTCGCCATTGTGGCTT-ATTTTTCCCTTCATGTTTCTGAGGTACAAGG
126 ATCTTCGTGGTACCAGATTCGCCGTTGCGGCTTAATCTTTCCCTTCATGTTTCTGAGGTACAA-G
* * * * **
212980 TTTACCGTTGTGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCATCGTTATGGCTT
1 --T---GTTGTGACTTAAACCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCATTGCGGCTT
213045 AAATCTTTCCCATC
61 AAATCTTTCCCATC
213059 TCATCTCCAT
Statistics
Matches: 403, Mismatches: 49, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
189 162 0.40
190 5 0.01
191 1 0.00
194 96 0.24
195 2 0.00
196 137 0.34
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (189 bp):
TGTTGTGACTTAAACCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCATTGCGGCTTAAATC
TTTCCCATCATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTT
CGTGGTACCAGATTCGCCGTTGCGGCTTAATCTTTCCCTTCATGTTTCTGAGGTACAAG
Found at i:215066 original size:6 final size:6
Alignment explanation
Indices: 215055--215112 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
215045 TCATCTTGAC
*
215055 TTTCTT TTTC-- TTCCTT TTTCTTT TCTTCTTT TTTCTT TTTCTTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTC-TT T-TTC-TT TTTCTT TTTC-TT TTTCTT
215105 TTT-TT TTT
1 TTTCTT TTT
215113 TAAAAGATGC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
4 3 0.07
5 5 0.11
6 18 0.40
7 12 0.27
8 7 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:215108 original size:15 final size:15
Alignment explanation
Indices: 215055--215113 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
215045 TCATCTTGAC
*
215055 TTTCTTTTTCTTCCTT
1 TTTCTTTTT-TTCTTT
*
215071 TTTCTTTTCTTCTTT
1 TTTCTTTTTTTCTTT
215086 TTTC--TTTTTCTTT
1 TTTCTTTTTTTCTTT
215099 TTTCTTTTTTT-TTT
1 TTTCTTTTTTTCTTT
215113 T
1 T
215114 AAAAGATGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.32
14 4 0.11
15 14 0.37
16 8 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTTTTTCTTT
Found at i:215108 original size:21 final size:21
Alignment explanation
Indices: 215055--215113 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
215045 TCATCTTGAC
215055 TTTCTTTTTCTTCCTTTTTCTTT
1 TTTCTTTTT-TT-CTTTTTCTTT
215078 TCTTC-TTTTTTCTTTTTCTTT
1 T-TTCTTTTTTTCTTTTTCTTT
215099 TTTCTTTTTTT-TTTT
1 TTTCTTTTTTTCTTTT
215114 AAAAGATGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.21
21 17 0.50
22 2 0.06
23 5 0.15
24 3 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTCTTTTTTTCTTTTTCTTT
Found at i:215110 original size:16 final size:15
Alignment explanation
Indices: 215055--215106 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
215045 TCATCTTGAC
*
215055 TTTCTTTTTCTTCCTT
1 TTTC-TTTTCTTCTTT
215071 TTTCTTTTCTTCTTT
1 TTTCTTTTCTTCTTT
215086 TTTC-TTT-TTCTTT
1 TTTCTTTTCTTCTTT
215099 TTTCTTTT
1 TTTCTTTT
215107 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.29
14 6 0.18
15 14 0.41
16 4 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTCTTCTTT
Found at i:215190 original size:18 final size:18
Alignment explanation
Indices: 215149--215181 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
215139 TCTTGACCTT
215149 TTCTT-TCTTTTCTTTTC
1 TTCTTCTCTTTTCTTTTC
215166 TTCTTCTCTTTT-TTTT
1 TTCTTCTCTTTTCTTTT
215182 ATCTCTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTCTTCTCTTTTCTTTTC
Found at i:222679 original size:17 final size:17
Alignment explanation
Indices: 222657--222691 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
222647 GAATAAGAAC
222657 TTATCTAATGAGATATT
1 TTATCTAATGAGATATT
* *
222674 TTATCTATTTAGATATT
1 TTATCTAATGAGATATT
222691 T
1 T
222692 ATATTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (17 bp):
TTATCTAATGAGATATT
Found at i:224097 original size:27 final size:28
Alignment explanation
Indices: 224067--224119 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
224057 TATATTATAT
* *
224067 TATTTTA-ATATTTAATAATTTTATACA
1 TATTTTATATATTAAAAAATTTTATACA
*
224094 TATTTTATTTATTAAAAAATTTTATA
1 TATTTTATATATTAAAAAATTTTATA
224120 TAGTCATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TATTTTATATATTAAAAAATTTTATACA
Found at i:231837 original size:21 final size:21
Alignment explanation
Indices: 231804--231877 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
231794 GAGTTTTTAA
*
231804 TATCGGTAAAAGTAAAACTTG
1 TATCGGTAGAAGTAAAACTTG
*
231825 TATCAGTAGAAGTAAAACTTG
1 TATCGGTAGAAGTAAAACTTG
**
231846 TATCGGTAGAAG-AGTCACTTG
1 TATCGGTAGAAGTA-AAACTTG
231867 TATCGGTAGAA
1 TATCGGTAGAA
231878 CTGTCGCATG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 1 0.02
21 46 0.98
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (21 bp):
TATCGGTAGAAGTAAAACTTG
Found at i:231889 original size:21 final size:21
Alignment explanation
Indices: 231844--231898 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
231834 AAGTAAAACT
* *
231844 TGTATCGGTAGAAGAGTCACT
1 TGTATCGGTAGAACAGTCACA
* *
231865 TGTATCGGTAGAACTGTCGCA
1 TGTATCGGTAGAACAGTCACA
*
231886 TGTATTGGTAGAA
1 TGTATCGGTAGAA
231899 GTCTACACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (21 bp):
TGTATCGGTAGAACAGTCACA
Found at i:238576 original size:21 final size:21
Alignment explanation
Indices: 238552--238609 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
238542 TAGAAGTAAA
238552 ACTTGTATAGGTAGAACAGTC
1 ACTTGTATAGGTAGAACAGTC
* * *
238573 ACTTGTATCGATAGAACTGTC
1 ACTTGTATAGGTAGAACAGTC
* *
238594 GCTTGTATTGGTAGAA
1 ACTTGTATAGGTAGAA
238610 GTCTACACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (21 bp):
ACTTGTATAGGTAGAACAGTC
Found at i:244078 original size:23 final size:23
Alignment explanation
Indices: 244051--244135 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
244041 GGTGTTACAA
* ** *
244051 AAATCATATTAATGTTTAATCAC
1 AAATCACATTAACATTTAAGCAC
244074 AAATCACATTAACATTTAAGCAC
1 AAATCACATTAACATTTAAGCAC
*
244097 AAATCACATTAGCATTTAAGCAC
1 AAATCACATTAACATTTAAGCAC
*
244120 AAATCATATTAACATT
1 AAATCACATTAACATT
244136 GTAACACCCA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.32
Consensus pattern (23 bp):
AAATCACATTAACATTTAAGCAC
Found at i:246513 original size:20 final size:20
Alignment explanation
Indices: 246486--246536 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
246476 GTTAGTAAAA
246486 AAAGTCAACGGTCAA-AGTT
1 AAAGTCAACGGTCAACAGTT
*
246505 AACAGTCAACGGTCAACGGTT
1 AA-AGTCAACGGTCAACAGTT
246526 AAAGTCAACGG
1 AAAGTCAACGG
246537 GTCAGTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 22 0.76
21 5 0.17
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAAGTCAACGGTCAACAGTT
Found at i:246535 original size:13 final size:13
Alignment explanation
Indices: 246486--246536 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
246476 GTTAGTAAAA
246486 AAAGTCAACGGTC
1 AAAGTCAACGGTC
* *
246499 AAAGTTAACAGTC
1 AAAGTCAACGGTC
* *
246512 AACGGTCAACGGTT
1 AA-AGTCAACGGTC
246526 AAAGTCAACGG
1 AAAGTCAACGG
246537 GTCAGTCAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
13 21 0.70
14 9 0.30
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.18
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:248626 original size:20 final size:20
Alignment explanation
Indices: 248601--248652 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
248591 TCATTAAGCT
* **
248601 TTAATTAACCCTTTTTATTC
1 TTAATTAACCCTATTTATAA
*
248621 TTAATTAAACCTATTTATAA
1 TTAATTAACCCTATTTATAA
248641 TTAATATAACCC
1 TTAAT-TAACCC
248653 ATGATAACCC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATTAACCCTATTTATAA
Found at i:248923 original size:23 final size:22
Alignment explanation
Indices: 248900--249090 Score: 193
Period size: 23 Copynumber: 8.3 Consensus size: 22
248890 TGTTAAAAAC
* *
248900 ATTTAAGCCTAAATCATATTAAC
1 ATTTAAGCC-AAATCACATTAAT
* * *
248923 ATTTAAGCATAAATCATATTAAC
1 ATTTAAGC-CAAATCACATTAAT
*
248946 ATTTAAGCATAAATCACATTAAT
1 ATTTAAGC-CAAATCACATTAAT
*
248969 ATTTAAGCACAAAATCGCATTAAT
1 ATTTAAGC-C-AAATCACATTAAT
* *
248993 ATTTAAGTACAAATCATATTAAT
1 ATTTAAG-CCAAATCACATTAAT
249016 ATTTAAGCACAAATCACATTAAT
1 ATTTAAGC-CAAATCACATTAAT
*
249039 ATTTAAGCACAAATCACAATAAT
1 ATTTAAGC-CAAATCACATTAAT
* *
249062 AATAAAGCACAAATCACATTAAT
1 ATTTAAGC-CAAATCACATTAAT
249085 ATTTAA
1 ATTTAA
249091 CACATTTAAT
Statistics
Matches: 148, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
23 128 0.86
24 20 0.14
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.32
Consensus pattern (22 bp):
ATTTAAGCCAAATCACATTAAT
Found at i:248967 original size:46 final size:46
Alignment explanation
Indices: 248900--249094 Score: 250
Period size: 46 Copynumber: 4.2 Consensus size: 46
248890 TGTTAAAAAC
* * * * *
248900 ATTTAAGC-CTAAATCATATTAACATTTAAGCATAAATCATATTAAC
1 ATTTAAGCAC-AAATCACATTAATATTTAAGCACAAATCACATTAAT
* *
248946 ATTTAAGCATAAATCACATTAATATTTAAGCACAAAATCGCATTAAT
1 ATTTAAGCACAAATCACATTAATATTTAAGCAC-AAATCACATTAAT
* *
248993 ATTTAAGTACAAATCATATTAATATTTAAGCACAAATCACATTAAT
1 ATTTAAGCACAAATCACATTAATATTTAAGCACAAATCACATTAAT
* * *
249039 ATTTAAGCACAAATCACAATAATAATAAAGCACAAATCACATTAAT
1 ATTTAAGCACAAATCACATTAATATTTAAGCACAAATCACATTAAT
249085 ATTTAA-CACA
1 ATTTAAGCACA
249095 TTTAATCACA
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
45 4 0.03
46 87 0.66
47 40 0.31
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (46 bp):
ATTTAAGCACAAATCACATTAATATTTAAGCACAAATCACATTAAT
Found at i:249106 original size:10 final size:10
Alignment explanation
Indices: 249085--249157 Score: 85
Period size: 10 Copynumber: 7.4 Consensus size: 10
249075 TCACATTAAT
249085 ATTTAA-CAC
1 ATTTAATCAC
249094 ATTTAATCAC
1 ATTTAATCAC
249104 ATTTAATCAC
1 ATTTAATCAC
* *
249114 ATATAACCAC
1 ATTTAATCAC
* *
249124 ATATAGTCAC
1 ATTTAATCAC
*
249134 ATATAATCAC
1 ATTTAATCAC
*
249144 ATTTAATCAT
1 ATTTAATCAC
249154 ATTT
1 ATTT
249158 TATGATAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
9 6 0.11
10 50 0.89
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.37
Consensus pattern (10 bp):
ATTTAATCAC
Found at i:249320 original size:66 final size:66
Alignment explanation
Indices: 249227--249363 Score: 195
Period size: 66 Copynumber: 2.1 Consensus size: 66
249217 TATACACGAA
* * * *
249227 TCTCCAAACACACCAAATGACTCATAGAGT-AGAACATATCCCACAAGTGAAGCATATAGCTAAC
1 TCTCCAAACACAACAAAAGACTCATAGAGTCA-AACATATCCCAAAAGTGAAGCATAAAGCTAAC
249291 AC
65 AC
* **
249293 TCTCCAAACACAACAAAAGACTTATAGAGTCAAACATATCCCAAAAGTGAAGTGTAAAGCTAACA
1 TCTCCAAACACAACAAAAGACTCATAGAGTCAAACATATCCCAAAAGTGAAGCATAAAGCTAACA
249358 C
66 C
249359 TCTCC
1 TCTCC
249364 TTATTTCCCC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
66 62 0.98
67 1 0.02
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19
Consensus pattern (66 bp):
TCTCCAAACACAACAAAAGACTCATAGAGTCAAACATATCCCAAAAGTGAAGCATAAAGCTAACA
C
Found at i:249753 original size:107 final size:107
Alignment explanation
Indices: 249627--249822 Score: 286
Period size: 107 Copynumber: 1.8 Consensus size: 107
249617 CACTGTCAGG
* * * *
249627 TGACATGAATAACATACCAATATATTTTCTATCTCATGGCACAAAAAACATACTCACATATTTA-
1 TGACATGAATAACATACCAACATATTTACTATCACATGGCACAAAAAACATACCCACATATTTAT
249691 CTGTCACATGGCATGAATAACATACTCACATATTACTATCACA
66 C-GTCACATGGCATGAATAACATACTCACATATTACTATCACA
* * * * *
249734 TGACATGAATAACATACCAACATATTTACTGTCACATGGCCCGAATAACATACCCTCATATTTAT
1 TGACATGAATAACATACCAACATATTTACTATCACATGGCACAAAAAACATACCCACATATTTAT
*
249799 CGTCTCATGGCATGAATAACATAC
66 CGTCACATGGCATGAATAACATAC
249823 CAACAAATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 77 0.99
108 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.29
Consensus pattern (107 bp):
TGACATGAATAACATACCAACATATTTACTATCACATGGCACAAAAAACATACCCACATATTTAT
CGTCACATGGCATGAATAACATACTCACATATTACTATCACA
Found at i:249766 original size:71 final size:72
Alignment explanation
Indices: 249633--249835 Score: 216
Period size: 71 Copynumber: 2.8 Consensus size: 72
249623 CAGGTGACAT
* * * * ** *
249633 GAATAACATACCAATATATTT-TCTATCTCATGGCACAAAAAACATACTC-ACATATTTACTGTC
1 GAATAACATACCCACATATTTATC-ATCACATGACATGAATAACATAC-CAACATATTTACTGTC
*
249696 ACATGGCAT
64 ACATGGCAC
*
249705 GAATAACATACTCACATA-TTA-CTATCACATGACATGAATAACATACCAACATATTTACTGTCA
1 GAATAACATACCCACATATTTATC-ATCACATGACATGAATAACATACCAACATATTTACTGTCA
*
249768 CATGGCCC
65 CATGGCAC
* * * * *
249776 GAATAACATACCCTCATATTTATCGTCTCATGGCATGAATAACATACCAACAAATTTACT
1 GAATAACATACCCACATATTTATCATCACATGACATGAATAACATACCAACATATTTACT
249836 TTCATAACAA
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
70 1 0.01
71 59 0.53
72 50 0.45
73 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (72 bp):
GAATAACATACCCACATATTTATCATCACATGACATGAATAACATACCAACATATTTACTGTCAC
ATGGCAC
Found at i:249823 original size:36 final size:36
Alignment explanation
Indices: 249612--249835 Score: 218
Period size: 36 Copynumber: 6.2 Consensus size: 36
249602 TCAACAAAAT
* ** * * *
249612 ATATTCACTGTCAGGTGACATGAATAACATACCAAT
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * * ** * *
249648 ATATTTTCTATCTCATGGCACAAAAAACATACTCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
*
249684 ATATTTACTGTCACATGGCATGAATAACATACTCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * *
249720 ATA-TTACTATCACATGACATGAATAACATACCAAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
** *
249755 ATATTTACTGTCACATGGCCCGAATAACATACCCTC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
249791 ATATTTA-TCGTCTCATGGCATGAATAACATACCAAC
1 ATATTTACT-GTCACATGGCATGAATAACATACCCAC
*
249827 AAATTTACT
1 ATATTTACT
249836 TTCATAACAA
Statistics
Matches: 150, Mismatches: 35, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
35 32 0.21
36 117 0.78
37 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.29
Consensus pattern (36 bp):
ATATTTACTGTCACATGGCATGAATAACATACCCAC
Found at i:251720 original size:18 final size:18
Alignment explanation
Indices: 251699--251746 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
251689 TTATCGATTC
*
251699 GGTTCAGTCAACGGGTCA
1 GGTTCAGTCAACGGGACA
* *
251717 GGTTCGGTCAGCGGGACA
1 GGTTCAGTCAACGGGACA
251735 GGTTCGAGTCAA
1 GGTTC-AGTCAA
251747 TCTAAATTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (18 bp):
GGTTCAGTCAACGGGACA
Found at i:253858 original size:61 final size:61
Alignment explanation
Indices: 253746--253860 Score: 140
Period size: 61 Copynumber: 1.9 Consensus size: 61
253736 TTAATTTTAT
* * * * * **
253746 TTATAATTTTTTATATTATTAAATATAAATAATTAAATATATATTTTAATAATATTGGATA
1 TTATAATATTTTATATTAATAAATATAAAAAATTAAAAATATAATAAAATAATATTGGATA
** *
253807 TTATAATATTTTATATTAATACTTTTAAAAAATTAAAAATATAATAAAATAATA
1 TTATAATATTTTATATTAATAAATATAAAAAATTAAAAATATAATAAAATAATA
253861 ATATTATGCT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
61 44 1.00
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (61 bp):
TTATAATATTTTATATTAATAAATATAAAAAATTAAAAATATAATAAAATAATATTGGATA
Found at i:257698 original size:12 final size:12
Alignment explanation
Indices: 257672--257806 Score: 113
Period size: 12 Copynumber: 11.8 Consensus size: 12
257662 ACAATAAATA
* *
257672 AACAACCAAAGC
1 AACAACAAAAAC
*
257684 AACAGCAAAAAC
1 AACAACAAAAAC
257696 AACAAC-AAAAC
1 AACAACAAAAAC
257707 AACAAC-AAAA-
1 AACAACAAAAAC
*
257717 AA-AACAAAAAT
1 AACAACAAAAAC
* *
257728 AACTACAAAAAT
1 AACAACAAAAAC
257740 AACAAC-AAAAC
1 AACAACAAAAAC
*
257751 AACAATAAAAA-
1 AACAACAAAAAC
*
257762 AA-AACAAAAAT
1 AACAACAAAAAC
* * *
257773 AGCAACAAAGAT
1 AACAACAAAAAC
257785 AACAACAAAAAC
1 AACAACAAAAAC
*
257797 AACACCAAAA
1 AACAACAAAA
257807 CAGTAAAAAA
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
9 3 0.03
10 13 0.13
11 29 0.28
12 57 0.56
ACGTcount: A:0.72, C:0.21, G:0.03, T:0.04
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:257701 original size:3 final size:3
Alignment explanation
Indices: 257683--257755 Score: 51
Period size: 3 Copynumber: 25.0 Consensus size: 3
257673 ACAACCAAAG
* * * * * *
257683 CAA CAG CAA AAA CAA CAA CAA -AA CAA CAA CAA AAA AAA CAA AAA TAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* * *
257730 CTA CAA AAA TAA CAA CAA -AA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
257756 TAAAAAAAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.73, C:0.22, G:0.01, T:0.04
Consensus pattern (3 bp):
CAA
Found at i:257717 original size:24 final size:23
Alignment explanation
Indices: 257690--257881 Score: 103
Period size: 23 Copynumber: 8.3 Consensus size: 23
257680 AAGCAACAGC
257690 AAAAACAACAACAAAACAACAACA
1 AAAAACAACAA-AAAACAACAACA
* *
257714 AAAAA-AAC-AAAAATAACTAC-
1 AAAAACAACAAAAAACAACAACA
* *
257734 AAAAATAACAACAAAACAACAATA
1 AAAAACAACAA-AAAACAACAACA
*
257758 AAAAAAAACAAAAATAGCAACAA-A
1 AAAAACAACAAAAA-A-CAACAACA
* * *
257782 GATAACAAC-AAAAACAACACCA
1 AAAAACAACAAAAAACAACAACA
** *
257804 AAACAGTAAAAAAAAACAAC-ACA
1 AAA-AACAACAAAAAACAACAACA
* *
257827 AAAAA-AACTAAANAAAAAAAAAC-
1 AAAAACAAC-AAA-AAACAACAACA
* * * *
257850 CAAAATAATAAAAAACAACACCA
1 AAAAACAACAAAAAACAACAACA
257873 AAACAACAA
1 AAA-AACAA
257882 TATAATTTTT
Statistics
Matches: 126, Mismatches: 27, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
20 5 0.04
21 19 0.15
22 16 0.13
23 40 0.32
24 40 0.32
25 6 0.05
ACGTcount: A:0.74, C:0.18, G:0.02, T:0.05
Consensus pattern (23 bp):
AAAAACAACAAAAAACAACAACA
Found at i:257816 original size:45 final size:44
Alignment explanation
Indices: 257684--257806 Score: 165
Period size: 45 Copynumber: 2.8 Consensus size: 44
257674 CAACCAAAGC
* *
257684 AACAGCAAAAACAACAACAAAACAACAACAAAAAAAACAAAAAT
1 AACAACAAAAATAACAACAAAACAACAACAAAAAAAACAAAAAT
* *
257728 AACTACAAAAATAACAACAAAACAACAATAAAAAAAAACAAAAAT
1 AACAACAAAAATAACAACAAAACAACAA-CAAAAAAAACAAAAAT
* * *
257773 AGCAACAAAGATAACAACAAAAACAACACCAAAA
1 AACAACAAAAATAACAAC-AAAACAACAACAAAA
257807 CAGTAAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 25 0.37
45 34 0.50
46 9 0.13
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.05
Consensus pattern (44 bp):
AACAACAAAAATAACAACAAAACAACAACAAAAAAAACAAAAAT
Found at i:257829 original size:12 final size:11
Alignment explanation
Indices: 257660--257831 Score: 109
Period size: 12 Copynumber: 15.3 Consensus size: 11
257650 AATAACATCT
* *
257660 AAACAATAAAT
1 AAACAACAAAA
*
257671 AAACAACCAAAG
1 AAACAA-CAAAA
* *
257683 CAACAGCAAAA
1 AAACAACAAAA
257694 ACAACAACAAAA
1 A-AACAACAAAA
*
257706 CAACAAC-AAA
1 AAACAACAAAA
257716 AAA-AACAAAA
1 AAACAACAAAA
*
257726 ATAACTACAAAA
1 A-AACAACAAAA
257738 ATAACAACAAAA
1 A-AACAACAAAA
* *
257750 CAACAATAAAA
1 AAACAACAAAA
257761 AAA-AACAAAA
1 AAACAACAAAA
*
257771 ATAGCAACAAAGA
1 A-AACAACAAA-A
*
257784 TAACAACAAAA
1 AAACAACAAAA
*
257795 ACAACACCAAAA
1 A-AACAACAAAA
* **
257807 CAGTAA-AAAA
1 AAACAACAAAA
257817 AAACAACACAAA
1 AAACAACA-AAA
257829 AAA
1 AAA
257832 AACTAAANAA
Statistics
Matches: 123, Mismatches: 27, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
9 3 0.02
10 23 0.19
11 34 0.28
12 62 0.50
13 1 0.01
ACGTcount: A:0.73, C:0.19, G:0.03, T:0.05
Consensus pattern (11 bp):
AAACAACAAAA
Found at i:257831 original size:14 final size:14
Alignment explanation
Indices: 257812--257881 Score: 52
Period size: 15 Copynumber: 4.8 Consensus size: 14
257802 CAAAACAGTA
257812 AAAAAAAACAACAC
1 AAAAAAAACAACAC
*
257826 AAAAAAAACTAA-ANA
1 AAAAAAAAC-AACA-C
* *
257841 AAAAAAAACCAAAAT
1 AAAAAAAA-CAACAC
257856 AATAAAAAACAACAC
1 AA-AAAAAACAACAC
* *
257871 CAAAACAACAA
1 AAAAAAAACAA
257882 TATAATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 18 0.40
15 19 0.42
16 8 0.18
ACGTcount: A:0.77, C:0.17, G:0.00, T:0.04
Consensus pattern (14 bp):
AAAAAAAACAACAC
Found at i:259219 original size:25 final size:26
Alignment explanation
Indices: 259174--259222 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
259164 TATCTTCCAT
259174 AATATTTATGTAATTAATATATTTAA
1 AATATTTATGTAATTAATATATTTAA
*
259200 AATA-TTATG-AATATATTATATTT
1 AATATTTATGTAAT-TAATATATTT
259223 TGTTACAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
AATATTTATGTAATTAATATATTTAA
Found at i:262874 original size:21 final size:21
Alignment explanation
Indices: 262848--262891 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
262838 TATTTTTTTT
* *
262848 ATTTTTTTATAATTTTAATTA
1 ATTTTTTCAAAATTTTAATTA
*
262869 ATTTTTTCAAAATTTTCATTA
1 ATTTTTTCAAAATTTTAATTA
262890 AT
1 AT
262892 CTCACAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTTCAAAATTTTAATTA
Found at i:279913 original size:41 final size:43
Alignment explanation
Indices: 279834--279920 Score: 142
Period size: 41 Copynumber: 2.1 Consensus size: 43
279824 AAACTGCCTC
*
279834 GATTTGAGACTACAGATGATTAAAAAAAAAAACTAACCTACGA
1 GATTTGAGACTACAGATGATTAAAAAAAAAAACCAACCTACGA
*
279877 GATTTGAGACTACAGATGA-T-AAAAAAAAAACCAACCTGCGA
1 GATTTGAGACTACAGATGATTAAAAAAAAAAACCAACCTACGA
279918 GAT
1 GAT
279921 GGCAGACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 22 0.52
42 1 0.02
43 19 0.45
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (43 bp):
GATTTGAGACTACAGATGATTAAAAAAAAAAACCAACCTACGA
Found at i:280115 original size:16 final size:18
Alignment explanation
Indices: 280094--280128 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
280084 CTTTTTCCTA
280094 AAACTT-CAACAC-AAAC
1 AAACTTCCAACACTAAAC
280110 AAACTTCCAACACTAAAC
1 AAACTTCCAACACTAAAC
280128 A
1 A
280129 CACACACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 6 0.35
18 5 0.29
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.14
Consensus pattern (18 bp):
AAACTTCCAACACTAAAC
Found at i:280425 original size:19 final size:20
Alignment explanation
Indices: 280401--280451 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
280391 GTGAATACCC
280401 ATTAAAATATTTTT-CACCT
1 ATTAAAATATTTTTCCACCT
*
280420 ATTAAATTATTTTTCCACCT
1 ATTAAAATATTTTTCCACCT
280440 ATTAAAA-ATTTT
1 ATTAAAATATTTT
280452 AACTTGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAAAATATTTTTCCACCT
Found at i:298368 original size:36 final size:36
Alignment explanation
Indices: 298328--298404 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
298318 TGATGATTGT
** * *
298328 TGTGAAAGTGAATATGTGGGTATGTTCTTCATGCCA
1 TGTGAAAGAAAATATATGGGTATGTTCTTCATGCAA
**
298364 TGTGACTGAAAATATATGGGTATGTTCTTCATGCAA
1 TGTGAAAGAAAATATATGGGTATGTTCTTCATGCAA
298400 TGTGA
1 TGTGA
298405 TTGATTATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.36
Consensus pattern (36 bp):
TGTGAAAGAAAATATATGGGTATGTTCTTCATGCAA
Found at i:300416 original size:65 final size:65
Alignment explanation
Indices: 300341--300465 Score: 157
Period size: 65 Copynumber: 1.9 Consensus size: 65
300331 AATATTATTA
** * *
300341 TTTTATAAAATTTATAAAATTTTA-ACTTTTTTATATATATTTT-AGATTTTTTAAAAATTATAA
1 TTTTATAAAATACA-AAAATTTTAGAATTTTTTATAAATATTTTCA-A-TTTTTAAAAATTATAA
300404 TGT
63 TGT
*
300407 TTTTA-AAAATACAAAAATTTTAGAATTTTTTATAAATATTTTCAATTTTTGAAAATTAT
1 TTTTATAAAATACAAAAATTTTAGAATTTTTTATAAATATTTTCAATTTTTAAAAATTAT
300466 TTTGATTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
64 22 0.42
65 24 0.46
66 6 0.12
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (65 bp):
TTTTATAAAATACAAAAATTTTAGAATTTTTTATAAATATTTTCAATTTTTAAAAATTATAATGT
Found at i:300462 original size:19 final size:21
Alignment explanation
Indices: 300430--300468 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
300420 AAAATTTTAG
*
300430 AATTTTTTATAAA-TATTTTC
1 AATTTTTGATAAATTATTTTC
300450 AATTTTTGA-AAATTATTTT
1 AATTTTTGATAAATTATTTT
300469 GATTATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (21 bp):
AATTTTTGATAAATTATTTTC
Found at i:302857 original size:30 final size:30
Alignment explanation
Indices: 302821--302935 Score: 95
Period size: 30 Copynumber: 3.6 Consensus size: 30
302811 AGTTTAGGAA
302821 CTTGAGAAGACTCGATATCTCATTCAAGAG
1 CTTGAGAAGACTCGATATCTCATTCAAGAG
* * * *
302851 CTTGAGAATATTCGATATCTCTTTCAAGAT
1 CTTGAGAAGACTCGATATCTCATTCAAGAG
* * *
302881 CTTGGGATTAAGAAGACTTGATATCTCGTTCGAGAG
1 CTT--G----AGAAGACTCGATATCTCATTCAAGAG
* *
302917 CTTGGGAAGACTCAATATC
1 CTTGAGAAGACTCGATATC
302936 GTGTTTAGGA
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
30 41 0.62
32 1 0.02
34 1 0.02
36 23 0.35
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (30 bp):
CTTGAGAAGACTCGATATCTCATTCAAGAG
Found at i:303000 original size:66 final size:66
Alignment explanation
Indices: 302808--303000 Score: 201
Period size: 66 Copynumber: 2.9 Consensus size: 66
302798 ACACCTTACG
* * * * * *
302808 AGGAGTTTAGGAACTTGAGAAGACTCGATATCTCATTCAAGAGCTTGAGAATATTCGATATCTCT
1 AGGAGCTTAGG-A-TTGAGAAGACTTGATATCTCATTCAGGAGCTTGGGAAGATTCAATATCTCT
302873 TTC
64 TTC
* * * * * * *
302876 AAGATCTTGGGATTAAGAAGACTTGATATCTCGTTC-GAGAGCTTGGGAAGACTCAATATCGTGT
1 AGGAGCTTAGGATTGAGAAGACTTGATATCTCATTCAG-GAGCTTGGGAAGATTCAATATC-TCT
302940 TT-
64 TTC
* *
302942 AGGAGCTTAGGATTGAGAATACTTGATATCTCATTCAGGAGCTTGGGAAGATTTAATAT
1 AGGAGCTTAGGATTGAGAAGACTTGATATCTCATTCAGGAGCTTGGGAAGATTCAATAT
303001 TTGATTTTTT
Statistics
Matches: 101, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
66 88 0.87
67 6 0.06
68 7 0.07
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (66 bp):
AGGAGCTTAGGATTGAGAAGACTTGATATCTCATTCAGGAGCTTGGGAAGATTCAATATCTCTTT
C
Found at i:305090 original size:24 final size:24
Alignment explanation
Indices: 305062--305132 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
305052 AGAAATAATC
* *
305062 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTAGTTG
*
305086 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAGTTAAACTCTATTTAGTTG
* *
305110 TTTGAGTCAAACTCT-TATTAGTT
1 TTTCAGTTAAACTCTAT-TTAGTT
305133 TAGATTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAGTTG
Found at i:308605 original size:6 final size:6
Alignment explanation
Indices: 308596--308624 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
308586 TAGTTATAGT
308596 AGCAGG AGCAGG AGCAGG AGCAGG AGCAG
1 AGCAGG AGCAGG AGCAGG AGCAGG AGCAG
308625 AAGGTGAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.48, T:0.00
Consensus pattern (6 bp):
AGCAGG
Found at i:314776 original size:12 final size:12
Alignment explanation
Indices: 314761--314788 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
314751 CAGCCCTCTT
314761 CCTCCTCCTCCA
1 CCTCCTCCTCCA
314773 CCTCCTCCTCCA
1 CCTCCTCCTCCA
314785 CCTC
1 CCTC
314789 TAACACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.68, G:0.00, T:0.25
Consensus pattern (12 bp):
CCTCCTCCTCCA
Found at i:317080 original size:69 final size:69
Alignment explanation
Indices: 316969--317104 Score: 202
Period size: 69 Copynumber: 2.0 Consensus size: 69
316959 CATAGTGTGT
* *
316969 CATACCTTAACCTTGACTGGATGATGGACTCTGTATATGTGACTCGTATACTTTGATGTAAATAA
1 CATACCTTAACCTTGACTGGATGATGAACTATGTATATGTGACTCGTATACTTTGATGTAAATAA
317034 AAAC
66 AAAC
* * * *
317038 CATACCTTAATCC-TGAGTGGATGATGAATTATGTATGTGTGACTCGTATACTTTGATGTAAGTA
1 CATACCTTAA-CCTTGACTGGATGATGAACTATGTATATGTGACTCGTATACTTTGATGTAAATA
317102 AAA
65 AAA
317105 GCCTGAGTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 58 0.97
70 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (69 bp):
CATACCTTAACCTTGACTGGATGATGAACTATGTATATGTGACTCGTATACTTTGATGTAAATAA
AAAC
Found at i:320758 original size:21 final size:21
Alignment explanation
Indices: 320734--320783 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
320724 GAAGTTCTAC
*
320734 CGATACAAGTTTGGGTACTAA
1 CGATACAAGTATGGGTACTAA
* *
320755 CGATACAAGTATGGGTATTAC
1 CGATACAAGTATGGGTACTAA
320776 CGATACAA
1 CGATACAA
320784 CCCATCCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (21 bp):
CGATACAAGTATGGGTACTAA
Found at i:321826 original size:158 final size:158
Alignment explanation
Indices: 321551--321858 Score: 402
Period size: 158 Copynumber: 1.9 Consensus size: 158
321541 ACATGTAGTG
*
321551 CTCACACGAGCTGTGAAATGGGCTTGCTCACACGAGCTATGGGTCGAGATGTTAGGATACATGAT
1 CTCACACGAGCTGTGAAATGGGCTTGCTCACACGAGCTATGGGTCGAGATGTTAGGATACACGAT
** * * * * * **
321616 GCTGTTCACATGAGCTGTAGATAATCCGTAATAAATGTTAGATCTCAACCATCGGTAGGACATCT
66 GCTACTCACACGAGCTATAGAGAACCCGCAATAAATGCCAGATCTCAACCATCGGTAGGACATCT
* *
321681 AAGACCAGCACTTATATAACTTGTAATA
131 AAGAACAGCACTCATATAACTTGTAATA
* * * *
321709 CTCACACGAGCTGTGAAGTGGG-TCTGCTCGCACGAGCTGTGGGTCGAGATGTTAGGCTACACGA
1 CTCACACGAGCTGTGAAATGGGCT-TGCTCACACGAGCTATGGGTCGAGATGTTAGGATACACGA
* * * * *
321773 TGCTACTCAGACGAGCTATGGAGAACCCGCAATAAATGCCGGATCTTAGCCATCGGTAGGACATC
65 TGCTACTCACACGAGCTATAGAGAACCCGCAATAAATGCCAGATCTCAACCATCGGTAGGACATC
*
321838 TAAGAACAGTACTCATATAAC
130 TAAGAACAGCACTCATATAAC
321859 CTATAATCCT
Statistics
Matches: 127, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
157 1 0.01
158 126 0.99
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (158 bp):
CTCACACGAGCTGTGAAATGGGCTTGCTCACACGAGCTATGGGTCGAGATGTTAGGATACACGAT
GCTACTCACACGAGCTATAGAGAACCCGCAATAAATGCCAGATCTCAACCATCGGTAGGACATCT
AAGAACAGCACTCATATAACTTGTAATA
Found at i:325069 original size:13 final size:13
Alignment explanation
Indices: 325051--325075 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
325041 TCACTGCATT
325051 TAATTTTAAATTG
1 TAATTTTAAATTG
325064 TAATTTTAAATT
1 TAATTTTAAATT
325076 TCAAATCTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TAATTTTAAATTG
Found at i:333168 original size:16 final size:16
Alignment explanation
Indices: 333149--333187 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
333139 TTATTGATAT
333149 TTTTATTTATTT-GAAA
1 TTTTATTT-TTTAGAAA
333165 TTTTATTTTTTAGAAA
1 TTTTATTTTTTAGAAA
333181 TATTTAT
1 T-TTTAT
333188 GAAAAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 13 0.62
17 5 0.24
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTATTTTTTAGAAA
Found at i:335364 original size:36 final size:36
Alignment explanation
Indices: 335273--335352 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
335263 TAGTAATAGG
335273 CATGACCTTCGGGTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTTCGGGTCAATAGGGAGTAAAATGAGCAT
*
335309 CATGACCTTCGGGTCAATAGGGAGTAAAATTAGCAT
1 CATGACCTTCGGGTCAATAGGGAGTAAAATGAGCAT
335345 CATGACCT
1 CATGACCT
335353 CAGGGTTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (36 bp):
CATGACCTTCGGGTCAATAGGGAGTAAAATGAGCAT
Found at i:340771 original size:36 final size:36
Alignment explanation
Indices: 340724--340803 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
340714 TGGTAACAGG
340724 CATGACCTTCGGGTCAACAGAGAGTAAAATGAGCAT
1 CATGACCTTCGGGTCAACAGAGAGTAAAATGAGCAT
* *
340760 CATGACCTTCGGTTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTCGGGTCAACAGAGAGTAAAATGAGCAT
340796 CATGACCT
1 CATGACCT
340804 AAAGGTCAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (36 bp):
CATGACCTTCGGGTCAACAGAGAGTAAAATGAGCAT
Found at i:340813 original size:36 final size:35
Alignment explanation
Indices: 340735--340824 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 35
340725 ATGACCTTCG
* **
340735 GGTCAACAGAGAGTAAAATGAGCATCATGACCTTC
1 GGTCAACAGGGAGTAAAATGAGCATCATGACCTAA
340770 GGTTCAACAGGGAGTAAAATGAGCATCATGACCTAAA
1 GG-TCAACAGGGAGTAAAATGAGCATCATGACCT-AA
340807 GGTCAACAAGGGA-TAAAA
1 GGTCAAC-AGGGAGTAAAA
340825 CGAATAACGA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
35 2 0.04
36 40 0.82
37 7 0.14
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (35 bp):
GGTCAACAGGGAGTAAAATGAGCATCATGACCTAA
Done.