Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 53 of 210
Found at i:16189657 original size:57 final size:57
Alignment explanation
Indices: 16189553--16189816 Score: 433
Period size: 57 Copynumber: 4.6 Consensus size: 57
16189543 AAGCCAAAAA
*
16189553 AATTTAGGTTA-GTTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTA-GATTAGGGTTTTTAGTT
*
16189610 AATTTAGGTTAGCTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTT
* * *
16189667 AATTTATGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTAAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTT
*
16189724 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGATTAGATT-GGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTT
* *
16189780 AATTTAGGTTAGGTTTAGGGTTTTTAATCAAATTAGG
1 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGG
16189817 GTTTTTATTT
Statistics
Matches: 193, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
56 44 0.23
57 122 0.63
58 27 0.14
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (57 bp):
AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGATTAGGGTTTTTAGTT
Found at i:16189698 original size:86 final size:84
Alignment explanation
Indices: 16189553--16189816 Score: 379
Period size: 86 Copynumber: 3.1 Consensus size: 84
16189543 AAGCCAAAAA
*
16189553 AATTTAGGTTAGTTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAGG
1 AATTTAGGTTAGTTTAGGGTTTTTAATTAATTTA-GTTAGGATTAGGGTTTTTAGTTAATTTAGG
16189618 TTAGCTTTAGGGTTTTTAATT
65 TTAG-TTTAGGGTTTTTAATT
* * * *
16189639 AATTTAGGTTAGATTAGGGTTTTTAGTTAATTTATGTTAGGTTTAGGGTTTTTAATTAATTTAGG
1 AATTTAGGTTAGTTTAGGGTTTTTAATTAATTTA-GTTAGGATTAGGGTTTTTAGTTAATTTAGG
* *
16189704 TTAGATTAGGGTTTTAAATT
65 TTAGTTTAGGGTTTTTAATT
16189724 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGATTA-GATT-GGGTTTTTAGTTAATTTAG
1 AATTTAGGTTA-GTTTAGGGTTTTTAATTAATTTAG-TTAGGATTAGGGTTTTTAGTTAATTTAG
*
16189787 GTTAGGTTTAGGGTTTTTAATC
64 GTTA-GTTTAGGGTTTTTAATT
*
16189809 AAATTAGG
1 AATTTAGG
16189817 GTTTTTATTT
Statistics
Matches: 160, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
84 22 0.14
85 50 0.31
86 88 0.55
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (84 bp):
AATTTAGGTTAGTTTAGGGTTTTTAATTAATTTAGTTAGGATTAGGGTTTTTAGTTAATTTAGGT
TAGTTTAGGGTTTTTAATT
Found at i:16189895 original size:26 final size:25
Alignment explanation
Indices: 16189864--16189912 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
16189854 CTTAAAAAAT
16189864 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
**
16189890 TTCTATTTTATTACATCAAATAA
1 TTCTATCGTATTACATCAAATAA
16189913 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Found at i:16190054 original size:24 final size:24
Alignment explanation
Indices: 16190026--16190078 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
16190016 GGTGGTTGTT
*
16190026 CTTCCTCTGGTGCTGATTGTGGTC
1 CTTCCTCCGGTGCTGATTGTGGTC
* * *
16190050 CTTCCTCCGGTGGTGGTTGTGGTT
1 CTTCCTCCGGTGCTGATTGTGGTC
16190074 CTTCC
1 CTTCC
16190079 GGTTCGACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.02, C:0.26, G:0.30, T:0.42
Consensus pattern (24 bp):
CTTCCTCCGGTGCTGATTGTGGTC
Found at i:16190376 original size:18 final size:18
Alignment explanation
Indices: 16190332--16190377 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
16190322 TATTCGGAAA
* *
16190332 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
*
16190350 AGGGTACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
16190368 AGGAAACATA
1 AGGATACATA
16190378 CCTGACATCA
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:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:16191030 original size:7 final size:7
Alignment explanation
Indices: 16191020--16191044 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16191010 TTATATACAT
16191020 AATACTA
1 AATACTA
16191027 AATACTA
1 AATACTA
16191034 AATACTA
1 AATACTA
16191041 AATA
1 AATA
16191045 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:16192175 original size:30 final size:31
Alignment explanation
Indices: 16192122--16192185 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
16192112 GCCATTGATG
16192122 AAAATATAAAAAAAATTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
* *
16192153 AAAATAT-AAAAAAGTTATAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
16192183 AAA
1 AAA
16192186 TGGATTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (31 bp):
AAAATATAAAAAAAATTAAAATTATTTTAAA
Found at i:16192256 original size:22 final size:22
Alignment explanation
Indices: 16192231--16192281 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
16192221 AAATATGAGT
16192231 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
16192253 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
16192275 TTGAGAG
1 TTGAGAG
16192282 GATTAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:16209655 original size:15 final size:15
Alignment explanation
Indices: 16209635--16209663 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16209625 AAAAAAACAA
16209635 AAAAGGCATAATAAT
1 AAAAGGCATAATAAT
16209650 AAAAGGCATAATAA
1 AAAAGGCATAATAA
16209664 ATGGATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.17
Consensus pattern (15 bp):
AAAAGGCATAATAAT
Found at i:16214118 original size:28 final size:28
Alignment explanation
Indices: 16214064--16214128 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
16214054 GCACAGTGTG
* **
16214064 CCTGGAACTGAAACACTGGAATGTAGTA
1 CCTGGAACTGAAACACCGGAACATAGTA
* *
16214092 CCTGAAACTGAAACACCGGTACATAGTA
1 CCTGGAACTGAAACACCGGAACATAGTA
16214120 CCTGGAACT
1 CCTGGAACT
16214129 TTAATTACTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (28 bp):
CCTGGAACTGAAACACCGGAACATAGTA
Found at i:16228912 original size:4 final size:4
Alignment explanation
Indices: 16228899--16228929 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
16228889 TGGTTTTTCG
16228899 AATT -ATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT
16228930 GAAATTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
AATT
Found at i:16229085 original size:16 final size:18
Alignment explanation
Indices: 16229058--16229090 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16229048 TGGAATTGGG
16229058 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
16229075 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
16229091 TATAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:16232524 original size:21 final size:20
Alignment explanation
Indices: 16232491--16232529 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16232481 AATATACATC
16232491 TGTTTGTCAGAACATTTTGTT
1 TGTTTGTCAGAAC-TTTTGTT
**
16232512 TGTTTGTGTGAACTTTTG
1 TGTTTGTCAGAACTTTTG
16232530 GTTATTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (20 bp):
TGTTTGTCAGAACTTTTGTT
Found at i:16256654 original size:49 final size:49
Alignment explanation
Indices: 16256549--16256647 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
16256539 GCTACTTATA
* * *
16256549 ATGATTAAAATATTCGAATTTGAATATGCAGTTTTCACATCAAATCCCT
1 ATGATTAAAATATTCGAATTTGAATATGCAATATTCACACCAAATCCCT
16256598 ATGATTAAAATATTCGAATTTGAATATGCAATATTCACACCAAATCCCT
1 ATGATTAAAATATTCGAATTTGAATATGCAATATTCACACCAAATCCCT
16256647 A
1 A
16256648 GCATTAATGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (49 bp):
ATGATTAAAATATTCGAATTTGAATATGCAATATTCACACCAAATCCCT
Found at i:16260851 original size:18 final size:18
Alignment explanation
Indices: 16260816--16260851 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16260806 ACACCAATTT
*
16260816 ATTATTTGAGTTAATCGA
1 ATTATTTGAATTAATCGA
*
16260834 ATTATTTGAATTATTCGA
1 ATTATTTGAATTAATCGA
16260852 GTTGTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (18 bp):
ATTATTTGAATTAATCGA
Found at i:16262181 original size:29 final size:28
Alignment explanation
Indices: 16262139--16262194 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
16262129 CAATAATTTT
*
16262139 TATAATTTCTTTCT-ATTTTTATAATATG
1 TATAATTTCTTTCTGAATTTT-TAATATG
*
16262167 TATACATTTTTTTCTGAATTTTTAATAT
1 TATA-ATTTCTTTCTGAATTTTTAATAT
16262195 ATTTATTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 15 0.62
30 5 0.21
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.61
Consensus pattern (28 bp):
TATAATTTCTTTCTGAATTTTTAATATG
Found at i:16262686 original size:23 final size:23
Alignment explanation
Indices: 16262658--16262706 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16262648 TAAACTTTTT
* *
16262658 TATAAAATTCTAAAATATATAAA
1 TATAAAATTCTAAAAAATAAAAA
* *
16262681 TATAAATTTTTAAAAAATAAAAA
1 TATAAAATTCTAAAAAATAAAAA
16262704 TAT
1 TAT
16262707 TATATGAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TATAAAATTCTAAAAAATAAAAA
Found at i:16272655 original size:26 final size:26
Alignment explanation
Indices: 16272626--16272690 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
16272616 AGTTTAGCAA
16272626 TGCTTTTGAAAAGCGCTTTTATA-AAG
1 TGCTTTTGAAAAGCGCTTTTA-AGAAG
* *
16272652 TGC-TGTGCAAAAGTGCTTTTAAGAAG
1 TGCTTTTG-AAAAGCGCTTTTAAGAAG
* *
16272678 TACTTTTAAAAAG
1 TGCTTTTGAAAAG
16272691 TTTAGTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 4 0.13
26 25 0.81
27 2 0.06
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (26 bp):
TGCTTTTGAAAAGCGCTTTTAAGAAG
Found at i:16274958 original size:27 final size:27
Alignment explanation
Indices: 16274906--16274975 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
16274896 ACAAGAAACC
* * *
16274906 ATCAAAATTTTACAATTAAAATTTAAA
1 ATCAAAATTTTAAAACTAAAACTTAAA
16274933 ATCAAAATTTATAAAACT-AAACTTAAA
1 ATCAAAATTT-TAAAACTAAAACTTAAA
* * *
16274960 ACCAAATTTTTTAAAC
1 ATCAAAATTTTAAAAC
16274976 ATGTATCAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 5 0.14
27 26 0.72
28 5 0.14
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (27 bp):
ATCAAAATTTTAAAACTAAAACTTAAA
Found at i:16288611 original size:17 final size:17
Alignment explanation
Indices: 16288589--16288621 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
16288579 ATGGAATGTC
16288589 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
16288606 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
16288622 AAATCTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:16293197 original size:17 final size:17
Alignment explanation
Indices: 16293175--16293207 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
16293165 ATGGAATGTC
16293175 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
16293192 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
16293208 AAATCTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:16295932 original size:15 final size:15
Alignment explanation
Indices: 16295909--16295943 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
16295899 ATAATTATAA
16295909 TGAAAAGAATAAAAT
1 TGAAAAGAATAAAAT
*
16295924 TGAAGAGAATAAAAT
1 TGAAAAGAATAAAAT
16295939 T-AAAA
1 TGAAAA
16295944 AAAAGTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (15 bp):
TGAAAAGAATAAAAT
Found at i:16295999 original size:7 final size:7
Alignment explanation
Indices: 16295989--16296016 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
16295979 ATTCAAAATA
16295989 TAAATTT
1 TAAATTT
16295996 TAAATTT
1 TAAATTT
16296003 TAAATTT
1 TAAATTT
16296010 TAAATTT
1 TAAATTT
16296017 GAAGATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TAAATTT
Found at i:16296034 original size:21 final size:21
Alignment explanation
Indices: 16295983--16296044 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
16295973 TTCAAAATTC
* *
16295983 AAAATATAAATTTTAAATTTT
1 AAAATATAAATTTGAAATTTG
* *
16296004 AAATTTTAAATTTGAAGA-TTG
1 AAAATATAAATTTGAA-ATTTG
*
16296025 AAAATATAAAATTGGAAATT
1 AAAATAT-AAATTTGAAATT
16296045 GAGGATTGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (21 bp):
AAAATATAAATTTGAAATTTG
Found at i:16296052 original size:14 final size:15
Alignment explanation
Indices: 16296035--16296066 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16296025 AAAATATAAA
16296035 ATTGGAA-ATTGAGG
1 ATTGGAAGATTGAGG
16296049 ATT-GAAGATTGAGG
1 ATTGGAAGATTGAGG
16296063 ATTG
1 ATTG
16296067 AGAATTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.19
14 13 0.81
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (15 bp):
ATTGGAAGATTGAGG
Found at i:16296077 original size:14 final size:13
Alignment explanation
Indices: 16296039--16296077 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
16296029 TATAAAATTG
16296039 GAAATTGAGGATT
1 GAAATTGAGGATT
16296052 GAAGATTGAGGATT
1 GAA-ATTGAGGATT
*
16296066 GAGAATTTAGGA
1 GA-AATTGAGGA
16296078 AGGAAGAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 19 0.83
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.28
Consensus pattern (13 bp):
GAAATTGAGGATT
Found at i:16297204 original size:14 final size:14
Alignment explanation
Indices: 16297185--16297240 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
16297175 TTTGGGCCGG
16297185 TTGGGTTAGGGTAT
1 TTGGGTTAGGGTAT
16297199 TTGGGTT----TAAT
1 TTGGGTTAGGGT-AT
16297210 TTGGGTTAGGGTAT
1 TTGGGTTAGGGTAT
*
16297224 TTGGGTTAGGGTTT
1 TTGGGTTAGGGTAT
16297238 TTG
1 TTG
16297241 TAATGGACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 1 0.03
11 9 0.25
14 25 0.69
15 1 0.03
ACGTcount: A:0.12, C:0.00, G:0.39, T:0.48
Consensus pattern (14 bp):
TTGGGTTAGGGTAT
Found at i:16303691 original size:71 final size:71
Alignment explanation
Indices: 16303575--16303716 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
16303565 TTTAACTGTA
16303575 GGGGTGTGATAAATGCTTGTAATTCATGCATTTTAGGGTCTTATTGCTTTACTTTTTACCGATTT
1 GGGGTGTGATAAATGCTTGTAATTCATGCATTTTAGGGTCTTATTGCTTTACTTTTTACCGATTT
16303640 TTTAGC
66 TTTAGC
16303646 GGGGTGTGATAAATGCTTGTAATTCATGCATTTTAGGGTCTTATTGCTTTACTTTTTACCGATTT
1 GGGGTGTGATAAATGCTTGTAATTCATGCATTTTAGGGTCTTATTGCTTTACTTTTTACCGATTT
16303711 TTTAGC
66 TTTAGC
16303717 AAAATACCAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.20, C:0.13, G:0.21, T:0.46
Consensus pattern (71 bp):
GGGGTGTGATAAATGCTTGTAATTCATGCATTTTAGGGTCTTATTGCTTTACTTTTTACCGATTT
TTTAGC
Found at i:16307030 original size:25 final size:25
Alignment explanation
Indices: 16307002--16307054 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
16306992 ACTAATCGGT
* * *
16307002 GAGCACTGACGTGCTAATAATTAGA
1 GAGCACTAACGTGCTAAAAATGAGA
*
16307027 GAGCACTAATGTGCTAAAAATGAGA
1 GAGCACTAACGTGCTAAAAATGAGA
16307052 GAG
1 GAG
16307055 TGCGCTAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (25 bp):
GAGCACTAACGTGCTAAAAATGAGA
Found at i:16307425 original size:2 final size:2
Alignment explanation
Indices: 16307418--16307461 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
16307408 TCTTATTATC
16307418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16307460 AT
1 AT
16307462 TATTCTTAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16310713 original size:3 final size:3
Alignment explanation
Indices: 16310707--16310755 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
16310697 AATAAAAGAC
* * * *
16310707 TAA TAA TAA TAA TAA TAA TAA TAA TGAC CAA TAA AAA TAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
16310753 TAA
1 TAA
16310756 ATCAATTAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 36 0.97
4 1 0.03
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:16311854 original size:16 final size:16
Alignment explanation
Indices: 16311833--16311870 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
16311823 TGACTTGGGC
16311833 ATATTGGGTTTTCTGG
1 ATATTGGGTTTTCTGG
*
16311849 ATATTGGGTTTTGTGG
1 ATATTGGGTTTTCTGG
16311865 ATATTG
1 ATATTG
16311871 TAATTGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.03, G:0.32, T:0.50
Consensus pattern (16 bp):
ATATTGGGTTTTCTGG
Found at i:16312322 original size:51 final size:50
Alignment explanation
Indices: 16312267--16312362 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
16312257 AATCAGTTCC
* * *
16312267 ACTGCACCGCCTAGGAAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTA
1 ACTGCAACGCC-AGGAAAGTAAGATTCGCCATTGTAGCTTTAATCTTTTTA
* *
16312318 ACTGCAATGCCAGGGAAGTAAGATTCGCCATTGTAGCTTTAATCT
1 ACTGCAACGCCAGGAAAGTAAGATTCGCCATTGTAGCTTTAATCT
16312363 ATTCATTCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 31 0.77
51 9 0.22
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (50 bp):
ACTGCAACGCCAGGAAAGTAAGATTCGCCATTGTAGCTTTAATCTTTTTA
Found at i:16312343 original size:50 final size:51
Alignment explanation
Indices: 16312229--16312367 Score: 154
Period size: 51 Copynumber: 2.7 Consensus size: 51
16312219 TGTGATGTCG
* * * * * *
16312229 GGGAAGTAAGATTTGCTGTTGTAGCTTCAATCAGTTCCACTGCACCGCCTA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTGTTCAACTGCAACGCCTA
* * * * *
16312280 GGAAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCC-A
1 GGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTGTTCAACTGCAACGCCTA
* *
16312330 GGGAAGTAAGATTCGCCATTGTAGCTTTAATCTATTCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTGTTCA
16312368 TTCGCCATTG
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
50 34 0.47
51 38 0.53
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (51 bp):
GGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTGTTCAACTGCAACGCCTA
Found at i:16312745 original size:131 final size:131
Alignment explanation
Indices: 16312531--16312930 Score: 454
Period size: 131 Copynumber: 3.0 Consensus size: 131
16312521 CACTACTGCT
* *
16312531 CAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCATC
1 CAGGGAAATAAGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCATC
*
16312596 TTCGATCTGCTCCACTACTGCATAGGGAGATGAGATCTGTAATTT-TCAACCTATTCCACTGCCG
66 TTCGATCTGCTCCACTACTGCATAGGGAGATAAGATCTGTAATTTCT-AACCTATTCCACTGCCG
16312660 AC
130 AC
* * *
16312662 CAGGGAAATAAGACTTGTGGCTTAAATCTTCTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTC
1 CAGGGAAATAAGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCATC
* * * *
16312727 TTTGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAATTTCTAACCTATTCCACTGCTGA
66 TTCGATCTGCTCCACTACTGCATAGGGAGATAAGATCTGTAATTTCTAACCTATTCCACTGCCGA
16312792 C
131 C
* * * * * * * * *
16312793 CAGGGAGAT-AGAATTACTGGCTTCAATGTAC-TCCACTA-TAACCATAGGG-AGGTAA-AATCT
1 CAGGGAAATAAGACTT-GTGGCTTAAATCTGCTTCC-CTACT--CC-TGGGGAAGATAAGATTC-
* * * * *
16312853 GTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTATAATCTTC-AATCTATTCCA
60 GCCATCTTCGATCTGCTCCACTACTGCATAGGGAGATAAGATCTGTAAT-TTCTAACCTATTCCA
*
16312917 CTGCCAAC
124 CTGCCGAC
16312925 CAGGGA
1 CAGGGA
16312931 GATAGAATTA
Statistics
Matches: 232, Mismatches: 29, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
130 9 0.04
131 144 0.62
132 72 0.31
133 7 0.03
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (131 bp):
CAGGGAAATAAGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCATC
TTCGATCTGCTCCACTACTGCATAGGGAGATAAGATCTGTAATTTCTAACCTATTCCACTGCCGA
C
Found at i:16312913 original size:132 final size:132
Alignment explanation
Indices: 16312590--16313915 Score: 1618
Period size: 132 Copynumber: 10.0 Consensus size: 132
16312580 GATAAGATTC
* * * * *
16312590 GCCATCTTCGATCTGCTCCACTACTGCATAGGGAGATGAGATCTGTAATTTTCAACCTATTCCAC
1 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAC
* * * * * * ** *
16312655 TGCCGACCAGGGAAATAAGACTT-GTGGCTTAAATCTTCTTCC-C--T-ACTCTTGGGGAAGATA
66 TGCCGACCAGGGAGAT-AGAATTACTGGCTTCAATGTAC-TCCACTGTAAC-CTCAGGG-AGGTA
*
16312715 AGAT-T
127 AAATCT
* * * * *
16312720 CGCCGTCTTTGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAAT-TTCTAACCTATTCC
1 -GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTC-AATCTATTCC
* *
16312784 ACTGCTGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTATAACCAT-AGGGAGGTAA
64 ACTGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACC-TCAGGGAGGTAA
16312848 AATCT
128 AATCT
* * * *
16312853 GTCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCAC
1 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAC
* * *
16312918 TGCCAACCAGGGAGATAGAATTACTGGCTTCAATGTACTCTACTGTAACCTCAGGAAGGTAAAAT
66 TGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAA-
*
16312983 TTT
130 TCT
* * * * *
16312986 GTCATCTTCGATCTACTCCACTAGTGCTTAGGAAGACT-AGATTTGCT-ATCTTTAATCTATTCC
1 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGA-TAAGATCTG-TAATCTTCAATCTATTCC
* * *
16313049 ACTGCCAACCAGGAAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGCAGGTAAA
64 ACTGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAA
16313114 ATCT
129 ATCT
* * *
16313118 GCCATTTTCAATCTACTCCACTACTGCTTAGGGAGACT-AGATCTGCT-ATCTTTAATCTATTCC
1 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGA-TAAGATCTG-TAATCTTCAATCTATTCC
* * * * *
16313181 ACTGCCAACCAGGGAGATAGAGTTACTGACTTCAATGTACTCCATTGTACCCTCAGGGAGGTAAA
64 ACTGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAA
16313246 ATCT
129 ATCT
* * * *
16313250 ACCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAAATTTGTAATATTCAATCTATTCCAC
1 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAC
* * ** * * *
16313315 TGCTGCCCAAAGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATCACAGAGAGGTAAAAT
66 TGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAAT
16313380 CT
131 CT
*
16313382 GCCATTTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATAC-ATTCCA
1 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT-CTATTCCA
* * * * *
16313446 CTACTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAGCCTCAGGGAGGTAAAC
65 CTGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAA
*
16313511 TCC
130 TCT
* * * *
16313514 ACCATCTTCGATCTACTCCATTATTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCAC
1 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAC
* * * * * * *
16313579 TGCTGCCCAGGAAGATAGAATTACTAGCTTCAATGCACTCCACTGTAATCACAGGGAGGTAAAAT
66 TGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAAT
*
16313644 CC
131 CT
* * * * * *
16313646 GTCATCTTCGATCTACTCTACTACTACTTAGGGAGATAAAATCTGAAATCTTCAATCTATTCCAT
1 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAC
* * * *
16313711 TGCCGACCAGGGAGATAGAATTACTGGCTTCAATATATTCCATTGTAACCTCAAGGAGGTAAAAT
66 TGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAAT
16313776 CT
131 CT
16313778 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCCT-TAATCTTCAATCTATTCCA
1 GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGAT-CTGTAATCTTCAATCTATTCCA
* * *
16313842 CTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAA
65 CTGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAA
*
16313907 TCC
130 TCT
16313910 GCCATC
1 GCCATC
16313916 AACCTGCTCT
Statistics
Matches: 1044, Mismatches: 133, Indels: 35
0.86 0.11 0.03
Matches are distributed among these distances:
130 11 0.01
131 86 0.08
132 813 0.78
133 129 0.12
134 5 0.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (132 bp):
GCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAC
TGCCGACCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAAT
CT
Found at i:16312917 original size:44 final size:45
Alignment explanation
Indices: 16312813--16312918 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 45
16312803 GAATTACTGG
* * * * * *
16312813 CTTCAATGTACTCCACTA-TAACCATAGGGAGGTAAAATCTGTCAT
1 CTTCAATCTACTCCACTACTAA-CTTAGGGAGATAAGATCTATAAT
* *
16312858 CTTCGATCTGCTCCACTACT-ACTTAGGGAGATAAGATCTATAAT
1 CTTCAATCTACTCCACTACTAACTTAGGGAGATAAGATCTATAAT
*
16312902 CTTCAATCTATTCCACT
1 CTTCAATCTACTCCACT
16312919 GCCAACCAGG
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
44 32 0.65
45 16 0.33
46 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (45 bp):
CTTCAATCTACTCCACTACTAACTTAGGGAGATAAGATCTATAAT
Found at i:16313283 original size:44 final size:44
Alignment explanation
Indices: 16313100--16313887 Score: 259
Period size: 44 Copynumber: 17.9 Consensus size: 44
16313090 CCACTGTAAC
* * * *
16313100 CTCAGGCAGGTAAAATCTGCCATTTTCAATCTACTCCACTACTG
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTG
* * * * * * * **
16313144 CTTAGGGAGACT-AGATCTGCTATCTTTAATCTATTCCACTGCCAA
1 CTCAGGGAGA-TAAAATCTACCATCTTCAATCTACTCCACT-ACTG
* * * * * *
16313189 C-CAGGGAGATAGAGT-TACTGA-CTTCAATGTACTCCATTGTAC-C
1 CTCAGGGAGATAAAATCTAC-CATCTTCAATCTACTCCA--CTACTG
* *
16313232 CTCAGGGAGGTAAAATCTACCATCTTCGATCTACTCCACTACTG
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTG
* * *** * * *
16313276 CTTAGGGAGATAAAATTTGTAATATTCAATCTATTCCACTGCTG
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTG
* ** * *** * *
16313320 CCCAAAGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGTAAT-
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCAC--TACTG
* * * * * *
16313364 CACAGAGAGGTAAAATCTGCCATTTTCGATCTACTCCACTACTG
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTG
* * *** *
16313408 CTTAGGGAGATAAGATCTGTAATCTTCAATAC-ATTCCACTACTG
1 CTCAGGGAGATAAAATCTACCATCTTCAAT-CTACTCCACTACTG
* * *** * *
16313452 CCCAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACT-GTAG
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACT-G
* * * * * *
16313495 CCTCAGGGAGGTAAACTCCACCATCTTCGATCTACTCCATTATTG
1 -CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTG
* * ** * *
16313540 CTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCTG
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTG
* * * * * *
16313584 CCCAGGAAGATAGAAT-TACTAGCTTCAATGC-ACTCCACTGTAAT-
1 CTCAGGGAGATAAAATCTACCATCTTCAAT-CTACTCCAC--TACTG
* * *** * * *
16313628 CACAGGGAGGTAAAATCCGTCATCTTCGATCTACTCTACTACTA
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTG
* * * * * *
16313672 CTTAGGGAGATAAAATCTGA-AATCTTCAATCTATTCCATTGCCG
1 CTCAGGGAGATAAAATCT-ACCATCTTCAATCTACTCCACTACTG
* *** * * *
16313716 AC-CAGGGAGATAGAAT-TACTGGCTTCAATATATTCCATTGTAAC--
1 -CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCA--CT-ACTG
* * * *
16313760 CTCAAGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTG
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTG
* * * *
16313804 CTTAGGGAGATAAGATCCTTA--ATCTTCAATCTATTCCACTGCTG
1 CTCAGGGAGATAAAAT-C-TACCATCTTCAATCTACTCCACTACTG
* * *** *
16313848 CCCAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTA
1 CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTA
16313888 TAACCTCAGG
Statistics
Matches: 518, Mismatches: 186, Indels: 81
0.66 0.24 0.10
Matches are distributed among these distances:
41 2 0.00
42 4 0.01
43 103 0.20
44 319 0.62
45 87 0.17
46 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (44 bp):
CTCAGGGAGATAAAATCTACCATCTTCAATCTACTCCACTACTG
Found at i:16316174 original size:39 final size:38
Alignment explanation
Indices: 16316110--16316188 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
16316100 GACCTCTCCT
*
16316110 TTTTCTTTTCTTTTTTTTATTTTGATGTT-AATTATTA
1 TTTTCTCTTCTTTTTTTTATTTTGATGTTGAATTATTA
* * *
16316147 TTTTCTCTTCTTTTTTTGATTTTTTGATTTTGATTTATTA
1 TTTTCTCTTCTTTTTTT--TATTTTGATGTTGAATTATTA
16316187 TT
1 TT
16316189 ATTATTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 16 0.46
39 10 0.29
40 9 0.26
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.73
Consensus pattern (38 bp):
TTTTCTCTTCTTTTTTTTATTTTGATGTTGAATTATTA
Found at i:16316991 original size:25 final size:25
Alignment explanation
Indices: 16316963--16317028 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
16316953 AAGAAAGTCC
*
16316963 AAAAGAATGAAAGAATAATTA-TTCA
1 AAAAGAATGAAAGAA-AATTAGCTCA
*
16316988 AAAAGAATGAAAGAACATTAGCTCA
1 AAAAGAATGAAAGAAAATTAGCTCA
16317013 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
16317029 TGTATTTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 4 0.11
25 22 0.61
26 5 0.14
27 5 0.14
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (25 bp):
AAAAGAATGAAAGAAAATTAGCTCA
Found at i:16318177 original size:59 final size:59
Alignment explanation
Indices: 16318085--16318217 Score: 257
Period size: 59 Copynumber: 2.3 Consensus size: 59
16318075 CCAAAAATGA
*
16318085 AGAAAAAAAGAAAACCAAAATATGAACTTTGGAAAAGAAACTAACGTTTGAGTAAAAAG
1 AGAAATAAAGAAAACCAAAATATGAACTTTGGAAAAGAAACTAACGTTTGAGTAAAAAG
16318144 AGAAATAAAGAAAACCAAAATATGAACTTTGGAAAAGAAACTAACGTTTGAGTAAAAAG
1 AGAAATAAAGAAAACCAAAATATGAACTTTGGAAAAGAAACTAACGTTTGAGTAAAAAG
16318203 AGAAATAAAGAAAAC
1 AGAAATAAAGAAAAC
16318218 ATAAAAATAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 73 1.00
ACGTcount: A:0.59, C:0.08, G:0.17, T:0.17
Consensus pattern (59 bp):
AGAAATAAAGAAAACCAAAATATGAACTTTGGAAAAGAAACTAACGTTTGAGTAAAAAG
Found at i:16318307 original size:5 final size:5
Alignment explanation
Indices: 16318297--16318324 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16318287 ATTTTAAAAC
16318297 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
16318325 ATATTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:16320586 original size:13 final size:13
Alignment explanation
Indices: 16320527--16320588 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
16320517 TTTTTCTTGC
16320527 TAAGTTTTAAATT
1 TAAGTTTTAAATT
* *
16320540 T-AGTTCTGAATT
1 TAAGTTTTAAATT
16320552 TAAGTTTTCTATAATT
1 TAAG-TTT-TA-AATT
*
16320568 TTAGTTTTAAATT
1 TAAGTTTTAAATT
16320581 TAAGTTTT
1 TAAGTTTT
16320589 TTAAAAATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 10 0.26
13 14 0.36
14 4 0.10
15 4 0.10
16 7 0.18
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (13 bp):
TAAGTTTTAAATT
Found at i:16326891 original size:27 final size:25
Alignment explanation
Indices: 16326861--16326910 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
16326851 TTTAATGTAG
16326861 ATATTAATTAAATTTGGATTTCAAAGC
1 ATATTAA-TAAATTTGGA-TTCAAAGC
* *
16326888 ATATTTATGAATTTGGATTCAAA
1 ATATTAATAAATTTGGATTCAAA
16326911 ATTTGCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 9 0.43
27 6 0.29
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (25 bp):
ATATTAATAAATTTGGATTCAAAGC
Found at i:16331032 original size:29 final size:29
Alignment explanation
Indices: 16330992--16331068 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
16330982 TTTTTCTCGG
* * *
16330992 GTTACATTTTAGACACTTATGTTTGAAAT
1 GTTACGTTTTAGTCACTTATATTTGAAAT
*
16331021 GTTATGTTTTAGTCACTTATATTTGAAAT
1 GTTACGTTTTAGTCACTTATATTTGAAAT
16331050 GTTACGTTTTAGTCACTTA
1 GTTACGTTTTAGTCACTTA
16331069 CGTTATCGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.48
Consensus pattern (29 bp):
GTTACGTTTTAGTCACTTATATTTGAAAT
Found at i:16332020 original size:22 final size:23
Alignment explanation
Indices: 16331995--16332037 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
16331985 TTAAATTTGG
*
16331995 AAATT-TGGAAAATAAAAATATT
1 AAATTCTGAAAAATAAAAATATT
*
16332017 AAATTCTTAAAAATAAAAATA
1 AAATTCTGAAAAATAAAAATA
16332038 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATTCTGAAAAATAAAAATATT
Found at i:16332338 original size:18 final size:18
Alignment explanation
Indices: 16332293--16332327 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16332283 GGCCCAACTC
*
16332293 ATATTAAATATATATTTA
1 ATATAAAATATATATTTA
*
16332311 ATATATAATATATATTT
1 ATATAAAATATATATTT
16332328 GATTAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAAAATATATATTTA
Found at i:16334029 original size:18 final size:18
Alignment explanation
Indices: 16334006--16334043 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16333996 GTTTCTGTCC
16334006 TTATA-TTACATTTAAATT
1 TTATATTTA-ATTTAAATT
*
16334024 TTATATTTAATTTATATT
1 TTATATTTAATTTAAATT
16334042 TT
1 TT
16334044 TAAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATTTAATTTAAATT
Found at i:16334428 original size:10 final size:10
Alignment explanation
Indices: 16334407--16334454 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
16334397 TTCTTTCAAC
16334407 TCTCTC-AAT
1 TCTCTCAAAT
*
16334416 TCTTTCAAAT
1 TCTCTCAAAT
16334426 TCTCTCAAAT
1 TCTCTCAAAT
* *
16334436 CCTCTC-AAG
1 TCTCTCAAAT
16334445 TCTCTCAAAT
1 TCTCTCAAAT
16334455 ATCTAGTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 12 0.39
10 19 0.61
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.40
Consensus pattern (10 bp):
TCTCTCAAAT
Found at i:16334431 original size:19 final size:18
Alignment explanation
Indices: 16334397--16334452 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
16334387 ATTTACATTC
16334397 TTCTTTCAACTCTCTCAA
1 TTCTTTCAACTCTCTCAA
*
16334415 TTCTTTCAAATTCTCTCAAA
1 TTCTTTC-AACTCTCTC-AA
* * *
16334435 TCCTCTCAAGTCTCTCAA
1 TTCTTTCAACTCTCTCAA
16334453 ATATCTAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.28
19 16 0.50
20 7 0.22
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (18 bp):
TTCTTTCAACTCTCTCAA
Found at i:16334634 original size:15 final size:15
Alignment explanation
Indices: 16334614--16334665 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
16334604 GGTAAGACCG
16334614 TAATTTAATTTTTTT
1 TAATTTAATTTTTTT
** *
16334629 TAATTTCAATAATGTT
1 TAATTT-AATTTTTTT
*
16334645 AAATTTAATTTTTTT
1 TAATTTAATTTTTTT
16334660 ATAATT
1 -TAATT
16334666 ATGTTTTTGT
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
TAATTTAATTTTTTT
Found at i:16337623 original size:3 final size:3
Alignment explanation
Indices: 16337615--16337653 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
16337605 AACCTCTACG
*
16337615 AGA AGA AGA AGA AGA AGA AGA ATA AGA AGA AGAA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AG
16337654 GAAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:16338328 original size:25 final size:28
Alignment explanation
Indices: 16338296--16338362 Score: 90
Period size: 25 Copynumber: 2.6 Consensus size: 28
16338286 AGATTCTTTG
16338296 AAGCTAGTGTTAGCAGAAT-C-GAACCA
1 AAGCTAGTGTTAGCAGAATCCTGAACCA
*
16338322 AA-CTAGTGTTAGC--AATCCTGATCCA
1 AAGCTAGTGTTAGCAGAATCCTGAACCA
16338347 AAGCTAGTGTTAGCAG
1 AAGCTAGTGTTAGCAG
16338363 CCCGATAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 3 0.09
24 1 0.03
25 18 0.51
26 13 0.37
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (28 bp):
AAGCTAGTGTTAGCAGAATCCTGAACCA
Found at i:16341211 original size:32 final size:32
Alignment explanation
Indices: 16341166--16341231 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
16341156 CTTATATTAT
* *
16341166 TTTTTAATTTTTAA-AATATATATTTATTTTTA
1 TTTTTAATATTTAATAA-ATATATATATTTTTA
* *
16341198 TTTTTAGTATTTAATAAATTTATATATTTTTA
1 TTTTTAATATTTAATAAATATATATATTTTTA
16341230 TT
1 TT
16341232 GATTATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (32 bp):
TTTTTAATATTTAATAAATATATATATTTTTA
Found at i:16344666 original size:20 final size:20
Alignment explanation
Indices: 16344641--16344678 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16344631 TACATATTTG
*
16344641 CATATATAATACATAATATA
1 CATATATAATAAATAATATA
16344661 CATATATAATAAATAATA
1 CATATATAATAAATAATA
16344679 AATAATATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
CATATATAATAAATAATATA
Found at i:16344684 original size:27 final size:28
Alignment explanation
Indices: 16344626--16344686 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
16344616 TGTCATAATC
* * * *
16344626 TAATATACATATTTGCATATATAATACA
1 TAATATACATATATGAATAAATAATAAA
16344654 TAATATACATATAT-AATAAATAATAAA
1 TAATATACATATATGAATAAATAATAAA
16344681 TAATAT
1 TAATAT
16344687 CGAATCTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (28 bp):
TAATATACATATATGAATAAATAATAAA
Found at i:16345176 original size:21 final size:20
Alignment explanation
Indices: 16345143--16345186 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
16345133 TTATTTATAA
*
16345143 TAATTATAATTAATTAATATT
1 TAATTATAATTAAATAAT-TT
**
16345164 TAATTATGTTTAAATAATTT
1 TAATTATAATTAAATAATTT
16345184 TAA
1 TAA
16345187 AAAAATATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTATAATTAAATAATTT
Found at i:16345536 original size:6 final size:6
Alignment explanation
Indices: 16345525--16345549 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16345515 ATAATATATG
16345525 TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA T
16345550 CCATATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:16347011 original size:153 final size:149
Alignment explanation
Indices: 16346826--16347296 Score: 644
Period size: 152 Copynumber: 3.1 Consensus size: 149
16346816 AAAACCCCTT
* *
16346826 AAAAATACGAACAAAGGCCGAAATGAGGGTTTTTTTTAAATTTATTTAAAAAACACATTAAATTA
1 AAAAATACGAACAAAGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAATTA
16346891 ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTT
66 ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA-TA-AAAATAGTATATTTTT
*
16346956 TTAAAGTAATAAACTCTGGGGA
129 TTAAAGTAATAAAATCT-GGGA
* * *
16346978 AAAAATACGAACAAATGGCCGAAATAAGGG-TTTTTTTAAATTTATTTAAAAAATACAGTAAACT
1 AAAAATACGAACAAA-GGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAATT
* * * * * *
16347042 AATACATTTCTAACATGATGTACTAAAATAATTTAAAATAATTAAATACAAAAATAATATTTTTT
65 AATACATTTCAAACATAATGTACTAAAATAATGTAAAATAA-TAAA-ATAAAAATAGTATATTTT
*
16347107 TATTGAAAGTAATAAAATCTGAGA
128 T-TT-AAAGTAATAAAATCTGGGA
* *
16347131 AAAAATACAAACAAAGGGCCGAAATAA-GGTTTTTTTTAATTTTATTTAAAAAACACACTAAATT
1 AAAAATACGAACAAA-GGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAATT
*
16347195 AATACATTTCAAATC-TAATGTACTAAAATAATGTAAAATAAAAAAATAAAGAATAGTATATTTT
65 AATACATTTCAAA-CATAATGTACTAAAATAATGTAAAATAATAAAATAAA-AATAGTATATTTT
* *
16347259 TTAAAAGTAATAAAAT-TCGGAA
128 TTTAAAGTAATAAAATCT-GGGA
16347281 AAAAATACGAACAAAG
1 AAAAATACGAACAAAG
16347297 AGCCAAAACA
Statistics
Matches: 281, Mismatches: 29, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
149 2 0.01
150 29 0.10
151 5 0.02
152 115 0.41
153 114 0.41
154 16 0.06
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (149 bp):
AAAAATACGAACAAAGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAATTA
ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAAAAATAGTATATTTTTTT
AAAGTAATAAAATCTGGGA
Found at i:16347015 original size:152 final size:148
Alignment explanation
Indices: 16346826--16347296 Score: 640
Period size: 153 Copynumber: 3.1 Consensus size: 148
16346816 AAAACCCCTT
* *
16346826 AAAAATACGAACAAAGGCCGAAATGAGGGTTTTTTTTAAATTTATTTAAAAAACACATTAAATTA
1 AAAAATACGAACAAAGGCCGAAATAAGGG-TTTTTTTAAATTTATTTAAAAAACACACTAAATTA
16346891 ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTT
65 ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA-TA-AAAATAGTATATTTTT
*
16346956 TTAAAGTAATAAACTCTGGGGA
128 TTAAAGTAATAAAATCT-GGGA
* * *
16346978 AAAAATACGAACAAATGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAATACAGTAAACTA
1 AAAAATACGAACAAA-GGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACACACTAAATTA
* * * * * *
16347043 ATACATTTCTAACATGATGTACTAAAATAATTTAAAATAATTAAATACAAAAATAATATTTTTTT
65 ATACATTTCAAACATAATGTACTAAAATAATGTAAAATAA-TAAA-ATAAAAATAGTATATTTTT
*
16347108 ATTGAAAGTAATAAAATCTGAGA
128 -TT-AAAGTAATAAAATCTGGGA
* * *
16347131 AAAAATACAAACAAAGGGCCGAAATAAGGTTTTTTTTAATTTTATTTAAAAAACACACTAAATTA
1 AAAAATACGAACAAA-GGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACACACTAAATTA
*
16347196 ATACATTTCAAATC-TAATGTACTAAAATAATGTAAAATAAAAAAATAAAGAATAGTATATTTTT
65 ATACATTTCAAA-CATAATGTACTAAAATAATGTAAAATAATAAAATAAA-AATAGTATATTTTT
* *
16347260 TAAAAGTAATAAAAT-TCGGAA
128 TTAAAGTAATAAAATCT-GGGA
16347281 AAAAATACGAACAAAG
1 AAAAATACGAACAAAG
16347297 AGCCAAAACA
Statistics
Matches: 281, Mismatches: 30, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
149 2 0.01
150 29 0.10
151 5 0.02
152 113 0.40
153 116 0.41
154 16 0.06
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (148 bp):
AAAAATACGAACAAAGGCCGAAATAAGGGTTTTTTTAAATTTATTTAAAAAACACACTAAATTAA
TACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATAAAAATAGTATATTTTTTTA
AAGTAATAAAATCTGGGA
Found at i:16348545 original size:19 final size:19
Alignment explanation
Indices: 16348521--16348557 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16348511 ATCATATGTT
*
16348521 TGTTATGTGTTAAAATATG
1 TGTTATATGTTAAAATATG
*
16348540 TGTTATATGTTAATATAT
1 TGTTATATGTTAAAATAT
16348558 CATATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (19 bp):
TGTTATATGTTAAAATATG
Found at i:16348809 original size:14 final size:15
Alignment explanation
Indices: 16348792--16348832 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
16348782 AGAACATGCG
16348792 GTCTTAGG-TTTAAA
1 GTCTTAGGATTTAAA
16348806 GTC-TAGGATTTAAA
1 GTCTTAGGATTTAAA
* *
16348820 GTTTTAGCATTTA
1 GTCTTAGGATTTA
16348833 TTTATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 4 0.17
14 11 0.48
15 8 0.35
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (15 bp):
GTCTTAGGATTTAAA
Found at i:16349989 original size:21 final size:21
Alignment explanation
Indices: 16349909--16349981 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
16349899 CAAAACAACA
*
16349909 GTTTCTCCCCTCGTTCTTGTTG
1 GTTTCT-CCCTCGTTCTTGCTG
*
16349931 GTTTCTCCCTTGTTCTTGCTG
1 GTTTCTCCCTCGTTCTTGCTG
* * *
16349952 GTTTGTCTCTCGTTTTTGCTG
1 GTTTCTCCCTCGTTCTTGCTG
16349973 GTTTCTCCC
1 GTTTCTCCC
16349982 CTCATTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 37 0.86
22 6 0.14
ACGTcount: A:0.00, C:0.29, G:0.19, T:0.52
Consensus pattern (21 bp):
GTTTCTCCCTCGTTCTTGCTG
Found at i:16350843 original size:2 final size:2
Alignment explanation
Indices: 16350803--16350828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16350793 TCCGCATTCA
16350803 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16350829 CCCTGACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16352236 original size:40 final size:39
Alignment explanation
Indices: 16352170--16352305 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 39
16352160 GCGTTTGGAC
* *
16352170 AAAAAGCGCCACTAAAAATTGAGCATTAGCGGCGCTTTTAT
1 AAAAA-CGCCGCTAAAAATAGAGCATTAGCGGCGCTTTT-T
** *
16352211 AAAAACGCCGCTAAAGGTAGAGCATTAGCGGTGCTTTTT
1 AAAAACGCCGCTAAAAATAGAGCATTAGCGGCGCTTTTT
*
16352250 AGAAAACGCCGCTAAAAATA-AGCATTAGCGGCGTTTTTT
1 A-AAAACGCCGCTAAAAATAGAGCATTAGCGGCGCTTTTT
*
16352289 GAAAAGCGCCGC-AAAAA
1 -AAAAACGCCGCTAAAAA
16352306 GCCTAAGCCC
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
38 5 0.06
39 28 0.34
40 45 0.54
41 5 0.06
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATAGAGCATTAGCGGCGCTTTTT
Found at i:16352398 original size:41 final size:41
Alignment explanation
Indices: 16352341--16352541 Score: 285
Period size: 41 Copynumber: 4.9 Consensus size: 41
16352331 TGAGTTTTTG
*
16352341 GGGCCTTTAGAGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
16352382 GGGCCTTTAGCGGCGTTTTTGGAGAAGTGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
16352423 GGGCCTTTAGCGGCGTTTTCGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* * * * *
16352464 GGGCCTTTAGCGGCATTTTTTAAGAAGTGCCGCTGATGCTT
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
** *
16352505 GGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
16352542 AATAAAATCT
Statistics
Matches: 139, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 139 1.00
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
Found at i:16353232 original size:7 final size:7
Alignment explanation
Indices: 16353222--16353252 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
16353212 AGATTATGAA
16353222 ATTAGGG
1 ATTAGGG
*
16353229 ATTATGG
1 ATTAGGG
16353236 ATTAGGG
1 ATTAGGG
16353243 ATTAGGG
1 ATTAGGG
16353250 ATT
1 ATT
16353253 CTAATTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (7 bp):
ATTAGGG
Found at i:16353233 original size:15 final size:14
Alignment explanation
Indices: 16353213--16353246 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16353203 AAGGTTTATA
16353213 GATTATGAAATTAGG
1 GATTATG-AATTAGG
*
16353228 GATTATGGATTAGG
1 GATTATGAATTAGG
16353242 GATTA
1 GATTA
16353247 GGGATTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (14 bp):
GATTATGAATTAGG
Found at i:16353351 original size:15 final size:16
Alignment explanation
Indices: 16353331--16353362 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
16353321 TTAAGATCAG
16353331 TTATGGATTT-AGGGT
1 TTATGGATTTAAGGGT
16353346 TTATGGATTTAAGGGT
1 TTATGGATTTAAGGGT
16353362 T
1 T
16353363 AGGTTTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (16 bp):
TTATGGATTTAAGGGT
Found at i:16353437 original size:19 final size:18
Alignment explanation
Indices: 16353413--16353473 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
16353403 TAATGTTTAG
16353413 GGGTTAGGGATTCTGGGT
1 GGGTTAGGGATTCTGGGT
*
16353431 CGGGTTAGGG-TT-T-AG-
1 -GGGTTAGGGATTCTGGGT
*
16353446 GGATTAGGGATTCTGGGTT
1 GGGTTAGGGATTCTGGG-T
16353465 GGGTTAGGG
1 GGGTTAGGG
16353474 TTTAGAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 17 0.52
ACGTcount: A:0.13, C:0.05, G:0.49, T:0.33
Consensus pattern (18 bp):
GGGTTAGGGATTCTGGGT
Found at i:16353444 original size:33 final size:33
Alignment explanation
Indices: 16353407--16353478 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
16353397 ATTAAATAAT
*
16353407 GTTTAGGGGTTAGGGATTCTGGGTCGGGTTAGG
1 GTTTAGGGATTAGGGATTCTGGGTCGGGTTAGG
*
16353440 GTTTAGGGATTAGGGATTCTGGGTTGGGTTAGG
1 GTTTAGGGATTAGGGATTCTGGGTCGGGTTAGG
16353473 GTTTAG
1 GTTTAG
16353479 AATTTAGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.14, C:0.04, G:0.46, T:0.36
Consensus pattern (33 bp):
GTTTAGGGATTAGGGATTCTGGGTCGGGTTAGG
Found at i:16353630 original size:119 final size:114
Alignment explanation
Indices: 16353354--16353639 Score: 324
Period size: 115 Copynumber: 2.5 Consensus size: 114
16353344 GTTTATGGAT
* ** *
16353354 TTAAGGGTTAGGTTTAGATTAATTAGTGGGTTTTAATTTATATATTAAATAATGTTTAGGGGTTA
1 TTAAGGTTTAGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTA
* ** * * * * *
16353419 GGGATTCTGGGTCGGGTTAGGGTTTAGGGATTAGGGATTCTGGGTTGGG
66 GGGATTCTGGGTAGAATTAGGATTCAGGGATTAGAGATTCGGGGTAGGG
* *
16353468 TTAGGGTTTAGAATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTTAGGGGTT
1 TTAAGGTTTAG-GTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTTAGGGGTT
*
16353533 A-GGAGTT-TGGGGTTAAGAATTAGTGATTCAGGGTTTAGAGATTCGGGGTCAGGG
65 AGGGA-TTCT-GGG-T-AGAATTAG-GATTCAGGGATTAGAGATTCGGGGT-AGGG
* * *
16353587 TTAAGGTTTAAGGTTTAGATTAATTAGTATTTTTTTATTTATATACTAAATAA
1 TTAAGGTTT-AGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAA
16353640 GTTCTTATAT
Statistics
Matches: 144, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
114 13 0.09
115 55 0.38
116 1 0.01
117 5 0.03
118 20 0.14
119 48 0.33
120 2 0.01
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.42
Consensus pattern (114 bp):
TTAAGGTTTAGGTTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTA
GGGATTCTGGGTAGAATTAGGATTCAGGGATTAGAGATTCGGGGTAGGG
Found at i:16354559 original size:146 final size:145
Alignment explanation
Indices: 16354394--16354673 Score: 400
Period size: 145 Copynumber: 1.9 Consensus size: 145
16354384 AAGATTTTTA
*
16354394 GCAAAAGATAAGCAATAGCGGC-ATTTTTATAAAAAACGCCACAAAAAATAATTTTACTTAAAAA
1 GCAAAAGATAAGCAATAGCGACGATTTTTATAAAAAACGCCACAAAAAATAATTTTA-TTAAAAA
* * * * *
16354458 AAATAGCGCCCTCTTAGCATAGCAAAATAGTGTCGCTTTATTCTAAATAAAATAATTTTTTGCGG
65 AAATAGCGCCATCTTA-CATAGCAAAACAGCGTCGCTTTATTCCAAATAAAATAATTTTTTACGG
16354523 CGTTTTTCATAAACGCC
129 CGTTTTTCATAAACGCC
* * * * **
16354540 GCAAAAGTTAATCAATAGCGACGTTTTTTTTAAAAAACGCCACAAAAAATAATTTTATTTTAAAA
1 GCAAAAGATAAGCAATAGCGACGATTTTTATAAAAAACGCCACAAAAAATAATTTTATTAAAAAA
* * *
16354605 AATAGCGCCATTTTATATAGCAAAACAGCGTCGTTTTATTCCAAATAAAATAATTTTTTACGGCG
66 AATAGCGCCATCTTACATAGCAAAACAGCGTCGCTTTATTCCAAATAAAATAATTTTTTACGGCG
16354670 TTTT
131 TTTT
16354674 GATAAAAACG
Statistics
Matches: 118, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
145 48 0.41
146 38 0.32
147 32 0.27
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (145 bp):
GCAAAAGATAAGCAATAGCGACGATTTTTATAAAAAACGCCACAAAAAATAATTTTATTAAAAAA
AATAGCGCCATCTTACATAGCAAAACAGCGTCGCTTTATTCCAAATAAAATAATTTTTTACGGCG
TTTTTCATAAACGCC
Found at i:16354683 original size:146 final size:146
Alignment explanation
Indices: 16354394--16354688 Score: 398
Period size: 146 Copynumber: 2.0 Consensus size: 146
16354384 AAGATTTTTA
*
16354394 GCAAAAGATAAGCAATAGCGGCATTTTTATAAAAAACGCCACAAAAAATAATTTTACTTAAAAAA
1 GCAAAAGATAAGCAATAGCGACATTTTTATAAAAAACGCCACAAAAAATAATTTTACTTAAAAAA
* * * * *
16354459 AATAGCGCCCTCTTAGCATAGCAAAATAGTGTCGCTTTATTCTAAATAAAATAATTTTTTGCGGC
66 AATAGCGCCATCTTAGCATAGCAAAACAGCGTCGCTTTATTCCAAATAAAATAATTTTTTACGGC
*
16354524 GTTTTTCATAAACGCC
131 GTTTTTCAAAAACGCC
* * * * **
16354540 GCAAAAGTTAATCAATAGCGACGTTTTTTTTAAAAAACGCCACAAAAAATAATTTTA-TTTTAAA
1 GCAAAAGATAAGCAATAGCGAC-ATTTTTATAAAAAACGCCACAAAAAATAATTTTACTTAAAAA
* * *
16354604 AAATAGCGCCATTTTA-TATAGCAAAACAGCGTCGTTTTATTCCAAATAAAATAATTTTTTACGG
65 AAATAGCGCCATCTTAGCATAGCAAAACAGCGTCGCTTTATTCCAAATAAAATAATTTTTTACGG
16354668 CGTTTTGAT-AAAAACGCC
130 CGTTTT--TCAAAAACGCC
16354686 GCA
1 GCA
16354689 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 16, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
145 48 0.37
146 49 0.38
147 33 0.25
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (146 bp):
GCAAAAGATAAGCAATAGCGACATTTTTATAAAAAACGCCACAAAAAATAATTTTACTTAAAAAA
AATAGCGCCATCTTAGCATAGCAAAACAGCGTCGCTTTATTCCAAATAAAATAATTTTTTACGGC
GTTTTTCAAAAACGCC
Found at i:16357352 original size:25 final size:25
Alignment explanation
Indices: 16357298--16357349 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
16357288 TTTATATTGA
16357298 TTTATAATTTGATCATATGTATGGG
1 TTTATAATTTGATCATATGTATGGG
* *
16357323 GTTATAATTTGATCATAT-TATTGG
1 TTTATAATTTGATCATATGTATGGG
16357347 TTT
1 TTT
16357350 TATCAACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.27, C:0.04, G:0.17, T:0.52
Consensus pattern (25 bp):
TTTATAATTTGATCATATGTATGGG
Found at i:16358430 original size:43 final size:43
Alignment explanation
Indices: 16358370--16358460 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
16358360 CTTTGAGTTC
* *
16358370 ATTA-CAAGATTTCCTTGATTAA-ATAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGA-AAATGCATTATATCTTTT
* *
16358412 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATGTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
16358455 ATTACC
1 ATTACC
16358461 TTGCATATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 4 0.09
43 38 0.88
44 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:16358896 original size:43 final size:43
Alignment explanation
Indices: 16358835--16359038 Score: 313
Period size: 43 Copynumber: 4.7 Consensus size: 43
16358825 CAAAAAACGT
*
16358835 CGCTAAAGGT-TATGGTCTTTAGCGGCGTTTGTGGGGAAAGCGC
1 CGCTAAAGGTCT-TGGTCTTTAGCGGCGTTTGTGGGAAAAGCGC
* *
16358878 CGCTAAAGGTCTTTGTCTTTAGCGGCGTTTGTGAGAAAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGC
* * *
16358921 CGCTAATGCTCTTGGTCTTTAGCGGCGTTTGTTGGAAAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGC
16358964 CGCTAAAGGT-TATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGC
1 CGCTAAAGGTCT-TGGTCTTTAGCGGCGTTTGTGGGAAAAGCGC
*
16359007 CGCTAAAGGTCTTGTTCTTTAGCGGCGTTTGT
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT
16359039 TTCTAAAAAC
Statistics
Matches: 146, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.01
43 143 0.98
44 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.31
Consensus pattern (43 bp):
CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGC
Found at i:16359946 original size:23 final size:23
Alignment explanation
Indices: 16359920--16359965 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
16359910 CTAATAATAG
*
16359920 ATACCCAAATGATGAAACGAAAA
1 ATACCCAAATGATCAAACGAAAA
16359943 ATACCCAAATGATCAAACGAAAA
1 ATACCCAAATGATCAAACGAAAA
16359966 TGGGAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.13
Consensus pattern (23 bp):
ATACCCAAATGATCAAACGAAAA
Found at i:16360307 original size:47 final size:48
Alignment explanation
Indices: 16360219--16360316 Score: 171
Period size: 47 Copynumber: 2.0 Consensus size: 48
16360209 ACTTTGATCA
16360219 GAGGAGGGCACGGGGTTTGGGACTTTGATCGGTGGAAGAGGGGAAATGG
1 GAGGAGGGCACGGGGTTT-GGACTTTGATCGGTGGAAGAGGGGAAATGG
*
16360268 GAGGAGGGCACGGGGTTT-GAGTTTGATCGGTGGAAGAGGGGAAATGG
1 GAGGAGGGCACGGGGTTTGGACTTTGATCGGTGGAAGAGGGGAAATGG
16360315 GA
1 GA
16360317 ATGGGGAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 30 0.62
49 18 0.38
ACGTcount: A:0.23, C:0.07, G:0.51, T:0.18
Consensus pattern (48 bp):
GAGGAGGGCACGGGGTTTGGACTTTGATCGGTGGAAGAGGGGAAATGG
Found at i:16360376 original size:30 final size:30
Alignment explanation
Indices: 16360337--16360510 Score: 275
Period size: 30 Copynumber: 5.9 Consensus size: 30
16360327 TGCACTGTAT
*
16360337 TAGTATATTTTAAAAATAAAAAAATATATG
1 TAGTGTATTTTAAAAATAAAAAAATATATG
* *
16360367 TAGTGTATTTTAAAAAT--AAATATATATA
1 TAGTGTATTTTAAAAATAAAAAAATATATG
*
16360395 TAGTGTACTTTAAAAATAAAAAAATATATG
1 TAGTGTATTTTAAAAATAAAAAAATATATG
16360425 TAGTGTATTTTAAAAATAAAAAAATATATG
1 TAGTGTATTTTAAAAATAAAAAAATATATG
16360455 TAGTGTATTTTAAAAAT-AAAAAATATATG
1 TAGTGTATTTTAAAAATAAAAAAATATATG
*
16360484 TAGTCTATTTT-AAAATAAAAAAATATA
1 TAGTGTATTTTAAAAATAAAAAAATATA
16360511 GTTTATATTT
Statistics
Matches: 133, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
28 30 0.23
29 32 0.24
30 71 0.53
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.37
Consensus pattern (30 bp):
TAGTGTATTTTAAAAATAAAAAAATATATG
Found at i:16360435 original size:58 final size:58
Alignment explanation
Indices: 16360345--16360510 Score: 255
Period size: 58 Copynumber: 2.9 Consensus size: 58
16360335 ATTAGTATAT
*
16360345 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAATATATATATAGTGTAC
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAATATATATAGTGTAC
* *
16360403 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATATATGTAGTGTAT
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAAT--AAAAATATATATAGTGTAC
* *
16360463 TTTAAAAAT-AAAAAATATATGTAGTCTATTTT-AAAATAAAAAAATATA
1 TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAATATATA
16360511 GTTTATATTT
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
56 9 0.09
58 44 0.44
59 22 0.22
60 25 0.25
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (58 bp):
TTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAATATATATAGTGTAC
Found at i:16360499 original size:88 final size:88
Alignment explanation
Indices: 16360337--16360510 Score: 287
Period size: 88 Copynumber: 2.0 Consensus size: 88
16360327 TGCACTGTAT
* *
16360337 TAGTATATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAATATATATATAGTGTA
1 TAGTATATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAATATATATAGTCTA
16360402 CTTTAAAAATAAAAAAATATATG
66 CTTTAAAAATAAAAAAATATATG
* *
16360425 TAGTGTATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTCT
1 TAGTATATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAAT-AAAAATATATATAGTCT
*
16360490 A-TTTTAAAATAAAAAAATATA
65 ACTTTAAAAATAAAAAAATATA
16360511 GTTTATATTT
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 65 0.81
89 15 0.19
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.37
Consensus pattern (88 bp):
TAGTATATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAATATATATAGTCTA
CTTTAAAAATAAAAAAATATATG
Found at i:16364077 original size:21 final size:21
Alignment explanation
Indices: 16364052--16364104 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
16364042 CATTGTTTCC
* *
16364052 AATCTCACCGCTATAGTATCCT
1 AATCTCACCGCTACAGTA-ACT
16364074 -ATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACT
16364094 AATCTCACCGC
1 AATCTCACCGC
16364105 CACCTCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.28, C:0.36, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACT
Found at i:16377696 original size:41 final size:41
Alignment explanation
Indices: 16377651--16377741 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
16377641 ACTGGCACTT
*
16377651 AGCCTGCTAGACATATAGTCTGAAA-TATTTCACCGGCATTA
1 AGCCTGCTAGACATATAGTCT-AAAGTATTTCACCGGCAATA
* *
16377692 AGCCTGCTAGACATTTAGTCTAAAGTGTTTCACCGGCAATA
1 AGCCTGCTAGACATATAGTCTAAAGTATTTCACCGGCAATA
16377733 AGCCTGCTA
1 AGCCTGCTA
16377742 AGCGCTAAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 3 0.07
41 43 0.93
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACATATAGTCTAAAGTATTTCACCGGCAATA
Found at i:16378147 original size:2 final size:2
Alignment explanation
Indices: 16378140--16378203 Score: 62
Period size: 2 Copynumber: 33.0 Consensus size: 2
16378130 CAAATTCAAG
* * * *
16378140 TA TA TA TA TA CA TA TA GA TA CA TA TA TA -A T- TA TT TGA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
16378180 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
16378204 CCTTTATACC
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:16379367 original size:13 final size:13
Alignment explanation
Indices: 16379349--16379373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16379339 CAATCAAATG
16379349 CACACAAAATAAA
1 CACACAAAATAAA
16379362 CACACAAAATAA
1 CACACAAAATAA
16379374 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:16386886 original size:13 final size:13
Alignment explanation
Indices: 16386868--16386892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16386858 CAATCAAATG
16386868 CACACAAAATAAA
1 CACACAAAATAAA
16386881 CACACAAAATAA
1 CACACAAAATAA
16386893 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:16389038 original size:16 final size:17
Alignment explanation
Indices: 16389013--16389045 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16389003 CTTTCCCCCT
*
16389013 ACTTTCTCACTT-TATC
1 ACTTTATCACTTATATC
16389029 ACTTTATCACTTATATC
1 ACTTTATCACTTATATC
16389046 TGAAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (17 bp):
ACTTTATCACTTATATC
Found at i:16391065 original size:25 final size:26
Alignment explanation
Indices: 16391033--16391087 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
16391023 TTATTAAATT
*
16391033 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
16391058 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
16391083 A-ATAT
1 ATATAT
16391088 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:16391254 original size:39 final size:40
Alignment explanation
Indices: 16391211--16391315 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
16391201 TTCCATTATG
16391211 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
16391250 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
16391295 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
16391316 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:16391309 original size:45 final size:44
Alignment explanation
Indices: 16391209--16391318 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
16391199 TTTTCCATTA
16391209 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
16391248 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
16391293 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
16391319 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:16391348 original size:16 final size:16
Alignment explanation
Indices: 16391299--16391350 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
16391289 GATTTGCTAT
* *
16391299 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
16391315 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
16391331 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
16391347 TACA
1 TACA
16391351 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:16398200 original size:15 final size:15
Alignment explanation
Indices: 16398180--16398235 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
16398170 AAACAATAAC
16398180 AATAATAATAACATT
1 AATAATAATAACATT
* *
16398195 AATAATAATAGCAAT
1 AATAATAATAACATT
* * *
16398210 AAAAACAATGA-ATT
1 AATAATAATAACATT
16398224 AAATAATAATAA
1 -AATAATAATAA
16398236 TAAAAAGGGA
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
14 2 0.07
15 28 0.93
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (15 bp):
AATAATAATAACATT
Found at i:16400034 original size:50 final size:49
Alignment explanation
Indices: 16399971--16400430 Score: 217
Period size: 50 Copynumber: 9.2 Consensus size: 49
16399961 TGCAATTTCA
* *
16399971 GGAAGTAAGATTCACCGTCGTGGCTTCAATCTATTTACTTGCAATGTCGG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCT-TTTACTTGCAATGTCGG
* * * * * * * *
16400021 GGAAATGAGATTCACTGTCGTAGCTTCAATCTGTTCCGCTGCATTGCCTG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTAC-TTGCAATGTCGG
* * * * * * *
16400071 GGAAGTAAGTTTCACCATTGTGGCTTCAATCTTTTGAGTTGCGATGTCGG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTT-ACTTGCAATGTCGG
* * * * * *
16400121 GGAAGTGAGATTCACCGTCATAGCTTCAATCTGTTCCGCTGC-ATCGCCTG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTAC-TTGCAAT-GTCGG
* * * * * * **
16400171 GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTTAG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATC-TTTTACTTGCAATGTCGG
* * * * * * * *
16400221 GGAAGTAAGATCCACTGTTGTAGCTTCAATCTGTTCCATTGCAACG-CTAG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTAC-TTGCAATGTC-GG
* * * * * * * *
16400271 GAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATC-TTTTACTTGCAATGTCGG
* * * * * * *
16400321 GGAAGTGAGATCCGCTGTTGTAGCTTCAATCTGTTCCAC-TGCAACG-CTAG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCT-TT-TACTTGCAATGTC-GG
* * * * * * * *
16400371 GAAAGTAAGATCCACTGTTGTAGCTTCAATCTTTTAATTGCAATGCCAG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTACTTGCAATGTCGG
*
16400420 GGAAGTAAGAT
1 GGAAGTGAGAT
16400431 CCGCTATTGT
Statistics
Matches: 321, Mismatches: 74, Indels: 31
0.75 0.17 0.07
Matches are distributed among these distances:
48 1 0.00
49 30 0.09
50 280 0.87
51 10 0.03
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (49 bp):
GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTACTTGCAATGTCGG
Found at i:16400145 original size:100 final size:100
Alignment explanation
Indices: 16399971--16400513 Score: 601
Period size: 100 Copynumber: 5.4 Consensus size: 100
16399961 TGCAATTTCA
* * * * * * * *
16399971 GGAAGTAAGATTCACCGTCGTGGCTTCAATCTATTTACTTGCAATGTCGGGGAAATGAGATTCAC
1 GGAAGTAAGATCCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGAGATCCAC
* *
16400036 TGTCGTAGCTTCAATCTGTTCCGCTGCATTGCCTG
66 TGTCGTAGCTTCAATCTGTTCCACTGCATCGCCTG
* * * * * * * * *
16400071 GGAAGTAAGTTTCACCATTGTGGCTTCAATCTTTTGAGTTGCGATGTCGGGGAAGTGAGATTCAC
1 GGAAGTAAGATCCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGAGATCCAC
* * *
16400136 CGTCATAGCTTCAATCTGTTCCGCTGCATCGCCTG
66 TGTCGTAGCTTCAATCTGTTCCACTGCATCGCCTG
* * * *
16400171 GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTTAGGGAAGTAAGATCCAC
1 GGAAGTAAGATCCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGAGATCCAC
* * *
16400236 TGTTGTAGCTTCAATCTGTTCCATTGCAACG-CTAG
66 TGTCGTAGCTTCAATCTGTTCCACTGCATCGCCT-G
* * * *
16400271 GAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGAGATCCGC
1 GGAAGTAAGATCCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGAGATCCAC
* *
16400336 TGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAG
66 TGTCGTAGCTTCAATCTGTTCCACTGCATCGCCT-G
* * * * *
16400371 GAAAGTAAGATCCACTGTTGTAGCTTCAATC-TTTTAATTGCAATGCCAGGGAAGTAAGATCCGC
1 GGAAGTAAGATCCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGAGATCCAC
* *
16400435 TATTGTAGCTTCAATCTGTTCCACTGCAAT-G-CTAG
66 TGTCGTAGCTTCAATCTGTTCCACTGC-ATCGCCT-G
* * * *
16400470 GAAAGTAAGATCCGCTGTTGTAGCTTCAATCATTTTAATTGCAA
1 GGAAGTAAGATCCACCGTTGTAGCTTCAATCTTTTTAATTGCAA
16400514 ACTATGGTTT
Statistics
Matches: 399, Mismatches: 41, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
99 94 0.24
100 305 0.76
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (100 bp):
GGAAGTAAGATCCACCGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGAGATCCAC
TGTCGTAGCTTCAATCTGTTCCACTGCATCGCCTG
Found at i:16400481 original size:50 final size:50
Alignment explanation
Indices: 16400141--16400500 Score: 458
Period size: 50 Copynumber: 7.2 Consensus size: 50
16400131 TTCACCGTCA
**
16400141 TAGCTTCAATCTGTTCCGCTGC-ATCGCCT-GGGAAGTAAGATCCGCTGTTG
1 TAGCTTCAATCTGTTCCATTGCAAT-G-CTAGGGAAGTAAGATCCGCTGTTG
* ** * *
16400191 TAGCTTCAATCTTTTTAATTGCAATGTTAGGGAAGTAAGATCCACTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
* *
16400241 TAGCTTCAATCTGTTCCATTGCAACGCTAGGAAAGTAAGATCCGCTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
* ** *
16400291 TAGCTTCAATCTTTTTAATTGCAATG-TCAGGGAAGTGAGATCCGCTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCT-AGGGAAGTAAGATCCGCTGTTG
* * * *
16400341 TAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCACTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
** * *
16400391 TAGCTTCAATCT-TTTAATTGCAATGCCAGGGAAGTAAGATCCGCTATTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
* *
16400440 TAGCTTCAATCTGTTCCACTGCAATGCTAGGAAAGTAAGATCCGCTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
16400490 TAGCTTCAATC
1 TAGCTTCAATC
16400501 ATTTTAATTG
Statistics
Matches: 263, Mismatches: 42, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
49 43 0.16
50 217 0.83
51 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (50 bp):
TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
Found at i:16400632 original size:44 final size:45
Alignment explanation
Indices: 16400518--16400737 Score: 157
Period size: 45 Copynumber: 5.0 Consensus size: 45
16400508 TTGCAAACTA
* * * * *
16400518 TGGTTTCTTCGATTTGCTTCGCTGTTAGTACAAGAAGGCAAGATC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGC
* * *
16400563 TGCTATCTTC-ATTCTGCTCCGCTGTCAGTACAGGAAGGCAAG-GC
1 TGGTGTCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGC
* * *
16400607 TGGTGTCTTCGATCTGCTTCACTGTCAAG-GCAGGAAGGCAAGATC
1 TGGTGTCTTCGATCTGCTTCGCTGTC-AGTACAGGAAGGCAAGAGC
* * * * * * * * *
16400652 TGTTGTCTTCAACCAGCTCCACT-ACA--ACCGAGAGAGGCAAG-GT
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAG-GA-AGGCAAGAGC
* *
16400695 TTGTGTCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGA
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
16400738 TCTTTTGTCT
Statistics
Matches: 133, Mismatches: 32, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
42 2 0.02
43 19 0.14
44 51 0.38
45 58 0.44
46 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.28
Consensus pattern (45 bp):
TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGC
Found at i:16401094 original size:88 final size:88
Alignment explanation
Indices: 16400598--16401092 Score: 785
Period size: 88 Copynumber: 5.6 Consensus size: 88
16400588 CAGTACAGGA
* * * * *
16400598 AGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCAAGGCAGGAAGGCAAGATCTGTTGTCTTCA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
16400663 ACCAGCTCCA-CTACAACCGAGAG
66 ACCAGCTCCATC-ACAACCGAGAG
* * *
16400686 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTTTTGTCTTCA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
*
16400751 ACTAGCTCCATCACAACCGAGAG
66 ACCAGCTCCATCACAACCGAGAG
*
16400774 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTGTCTTCA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
16400839 ACCAGCTCCATCACAACCGAGAG
66 ACCAGCTCCATCACAACCGAGAG
16400862 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
*
16400927 ACCAACTCCATCACAACCGAGAG
66 ACCAGCTCCATCACAACCGAGAG
* * * *
16400950 AGGCAAGGTTTCTGTCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTTTTGTCTTCA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
* *
16401015 ATCAGCTCCATCACAACTGAGAG
66 ACCAGCTCCATCACAACCGAGAG
* * * *
16401038 AGGCAAGGTTTGTTTCTTCGACCTACTTCACTGTTAATGCAGGAAGGCAAGATCT
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
16401093 TTAACTTCGT
Statistics
Matches: 378, Mismatches: 28, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
88 377 1.00
89 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (88 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
ACCAGCTCCATCACAACCGAGAG
Found at i:16402328 original size:15 final size:15
Alignment explanation
Indices: 16402301--16402374 Score: 66
Period size: 15 Copynumber: 5.0 Consensus size: 15
16402291 TTAGCCTCTC
*
16402301 CATTTTT-ACTTTTT
1 CATTTTTCATTTTTT
*
16402315 CATTTTTTCATTTTCT
1 CA-TTTTTCATTTTTT
16402331 CATTTTTCATTTTTT
1 CATTTTTCATTTTTT
*
16402346 CA-TCTT--TTTTTT
1 CATTTTTCATTTTTT
16402358 CATTTTCATCATTTTTT
1 CATTTT--TCATTTTTT
16402375 TTGACTCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
12 8 0.17
13 2 0.04
14 5 0.10
15 20 0.42
16 7 0.15
17 6 0.12
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (15 bp):
CATTTTTCATTTTTT
Found at i:16402363 original size:8 final size:8
Alignment explanation
Indices: 16402310--16402354 Score: 65
Period size: 8 Copynumber: 5.6 Consensus size: 8
16402300 CCATTTTTAC
16402310 TTTTTCAT
1 TTTTTCAT
16402318 TTTTTCAT
1 TTTTTCAT
*
16402326 TTTCTCA-
1 TTTTTCAT
16402333 TTTTTCAT
1 TTTTTCAT
16402341 TTTTTCAT
1 TTTTTCAT
16402349 CTTTTT
1 -TTTTT
16402355 TTTCATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 6 0.18
8 22 0.67
9 5 0.15
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCAT
Found at i:16402363 original size:9 final size:9
Alignment explanation
Indices: 16402310--16402375 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
16402300 CCATTTTTAC
16402310 TTTTTCA-T
1 TTTTTCATT
16402318 TTTTTCA-T
1 TTTTTCATT
*
16402326 TTTCTCA--
1 TTTTTCATT
16402333 TTTTTCATT
1 TTTTTCATT
*
16402342 TTTTCATCTTT
1 TTTT--TCATT
16402353 TTTTTCATT
1 TTTTTCATT
**
16402362 TTCATCATT
1 TTTTTCATT
16402371 TTTTT
1 TTTTT
16402376 TGACTCAAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
7 6 0.13
8 14 0.30
9 18 0.39
11 8 0.17
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCATT
Found at i:16402363 original size:18 final size:18
Alignment explanation
Indices: 16402317--16402376 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
16402307 TACTTTTTCA
16402317 TTTTTTCATTTTC-TC--
1 TTTTTTCATTTTCATCTT
*
16402332 ATTTTTCATTTTTTCATCTT
1 TTTTTTCA--TTTTCATCTT
16402352 TTTTTTCATTTTCATCATT
1 TTTTTTCATTTTCATC-TT
16402371 TTTTTT
1 TTTTTT
16402377 GACTCAAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 7 0.19
17 5 0.14
18 10 0.27
19 8 0.22
20 7 0.19
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTCATTTTCATCTT
Found at i:16403224 original size:7 final size:7
Alignment explanation
Indices: 16403178--16403216 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
16403168 CTCCTTTTTC
16403178 TTTT-TT
1 TTTTCTT
16403184 TTTTCTT
1 TTTTCTT
16403191 TTTTCTT
1 TTTTCTT
16403198 TTTTCTT
1 TTTTCTT
16403205 TTTTCTCT
1 TTTTCT-T
16403213 TTTT
1 TTTT
16403217 TTATTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 4 0.13
7 22 0.71
8 5 0.16
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:16406628 original size:2 final size:2
Alignment explanation
Indices: 16406623--16406647 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16406613 AAATATATAA
16406623 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
16406648 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16407017 original size:3 final size:3
Alignment explanation
Indices: 16407009--16407073 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
16406999 ATGTAGAAAC
* * ** * *
16407009 AAT AAT AAT AAT AAT AAC ATT AAT AAT AAT AGC AAT AAA AAC AAT GAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
16407058 TA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
16407074 AAAGGGACTA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
2 1 0.02
3 43 0.91
4 3 0.06
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:16408556 original size:25 final size:27
Alignment explanation
Indices: 16408501--16408559 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
16408491 GTTTTAAAAT
* *
16408501 TTATTTTTATACAATAATAATAGTATT
1 TTATTTTTATAAAATAATAATAGTATG
16408528 TTATTTTT-TAAAAT-ATAATTA-TATG
1 TTATTTTTATAAAATAATAA-TAGTATG
16408553 TTATTTT
1 TTATTTT
16408560 ACTACTCCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.48
26 7 0.24
27 8 0.28
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (27 bp):
TTATTTTTATAAAATAATAATAGTATG
Found at i:16408691 original size:45 final size:47
Alignment explanation
Indices: 16408625--16408715 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 47
16408615 CATTTTAACC
*
16408625 TACTAAATAATTAACTAAATTACATAGTATTTATTATAAATTATTTA
1 TACTAAATAATTAACTAAATTACATAGTACTTATTATAAATTATTTA
*
16408672 TACTAAAT-A-TAACTAAATTACATAGTACTTATTATTAATTATTT
1 TACTAAATAATTAACTAAATTACATAGTACTTATTATAAATTATTT
16408716 GTATTTGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 33 0.79
46 1 0.02
47 8 0.19
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (47 bp):
TACTAAATAATTAACTAAATTACATAGTACTTATTATAAATTATTTA
Found at i:16418110 original size:18 final size:19
Alignment explanation
Indices: 16418072--16418112 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
16418062 CCGGAAAATG
16418072 AATAATTATGTTTATTAAA
1 AATAATTATGTTTATTAAA
*
16418091 AATAATTTAT-TTTATAAAA
1 AATAA-TTATGTTTATTAAA
16418110 AAT
1 AAT
16418113 GCAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AATAATTATGTTTATTAAA
Found at i:16426982 original size:5 final size:5
Alignment explanation
Indices: 16426962--16427016 Score: 94
Period size: 5 Copynumber: 11.0 Consensus size: 5
16426952 CTTTCTTTCA
16426962 CCTT- CCTTC CCTTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC
1 CCTTC CCTTC CC-TTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC
16427012 CCTTC
1 CCTTC
16427017 TTTTTCTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.08
5 40 0.82
6 5 0.10
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (5 bp):
CCTTC
Found at i:16427941 original size:157 final size:157
Alignment explanation
Indices: 16427655--16427970 Score: 587
Period size: 157 Copynumber: 2.0 Consensus size: 157
16427645 CAGTTGAGTA
16427655 ATCTAAAGAGAACATCTAACCAAACTAAATGATGCAGAGAATGATACAACAATTACCACATAATT
1 ATCTAAAGAGAACATCTAACCAAACTAAATGATGCAGAGAATGATACAACAATTACCACATAATT
16427720 TGCTTCATTCACAAATATTTCCTCAAAGAACATACTTGCATCTCAATTCAATGCTTTTGAAGGCA
66 TGCTTCATTCACAAATATTTCCTCAAAGAACATACTTGCATCTCAATTCAATGCTTTTGAAGGCA
16427785 AACAAAAGTCCAGAACATTACAATGTC
131 AACAAAAGTCCAGAACATTACAATGTC
* *
16427812 ATCTAAAGAGCACATCTAACCAAACTAAATGATGCAGAGAATGATACGACAATTACCACATAATT
1 ATCTAAAGAGAACATCTAACCAAACTAAATGATGCAGAGAATGATACAACAATTACCACATAATT
*
16427877 TGCTTCATTCACAAATATTTCCTCAAAGAACATGCTTGCATCTCAATTCAATGCTTTTGAAGGCA
66 TGCTTCATTCACAAATATTTCCTCAAAGAACATACTTGCATCTCAATTCAATGCTTTTGAAGGCA
* *
16427942 AACAAAAGTCCAGATCATTGCAATGTC
131 AACAAAAGTCCAGAACATTACAATGTC
16427969 AT
1 AT
16427971 TTCCAAAAAT
Statistics
Matches: 154, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.27
Consensus pattern (157 bp):
ATCTAAAGAGAACATCTAACCAAACTAAATGATGCAGAGAATGATACAACAATTACCACATAATT
TGCTTCATTCACAAATATTTCCTCAAAGAACATACTTGCATCTCAATTCAATGCTTTTGAAGGCA
AACAAAAGTCCAGAACATTACAATGTC
Found at i:16432383 original size:20 final size:20
Alignment explanation
Indices: 16432358--16432397 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16432348 CGTAAAATAA
*
16432358 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
16432378 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
16432398 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:16432387 original size:34 final size:35
Alignment explanation
Indices: 16432343--16432409 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16432333 TAGTAAAATG
*
16432343 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* *
16432377 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
16432410 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:16434773 original size:28 final size:27
Alignment explanation
Indices: 16434726--16434779 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
16434716 TTCTTAGTAA
* *
16434726 TGAAGAAGCTGAAGATGAGAACGGAGT
1 TGAAGAAGCTGAAGAAGAGAAAGGAGT
*
16434753 TGAAGAAGGTTGAAGAAGAGAAAGGAG
1 TGAAGAA-GCTGAAGAAGAGAAAGGAG
16434780 AAAGGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.44, C:0.04, G:0.39, T:0.13
Consensus pattern (27 bp):
TGAAGAAGCTGAAGAAGAGAAAGGAGT
Found at i:16446461 original size:22 final size:22
Alignment explanation
Indices: 16446366--16446463 Score: 124
Period size: 22 Copynumber: 4.5 Consensus size: 22
16446356 TTTTCACTGG
* *
16446366 TCTCATGTTTAACGAACTAAAC
1 TCTCATGTTTAACGTACTAAGC
* **
16446388 CCTCATGGCTAACGTACTAAGC
1 TCTCATGTTTAACGTACTAAGC
**
16446410 TCTCATGGCTAACGTACTAAGC
1 TCTCATGTTTAACGTACTAAGC
*
16446432 TCTCATGTTTCACGTACTAAGC
1 TCTCATGTTTAACGTACTAAGC
16446454 TCTCATGTTT
1 TCTCATGTTT
16446464 GAACAATAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.33
Consensus pattern (22 bp):
TCTCATGTTTAACGTACTAAGC
Found at i:16453611 original size:22 final size:22
Alignment explanation
Indices: 16453549--16453634 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
16453539 ATTGTTCAAA
* **
16453549 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
16453571 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
16453593 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
16453615 CATGAGGGTTTAGTTCGTTA
1 CATGAGAGCTTAGTACGTTA
16453635 AACACAAACA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:16473616 original size:47 final size:47
Alignment explanation
Indices: 16473565--16473673 Score: 173
Period size: 47 Copynumber: 2.3 Consensus size: 47
16473555 AGTAATGCAA
*
16473565 ATAAACTGCCAATAATCAAAATTGTGGACAAGCCACCAAAATCGCAG
1 ATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCGCAG
* *
16473612 ATAAACTGCCAATAATCAAAATCGTGGAGAAGCCACCAAAATCGTAG
1 ATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCGCAG
* *
16473659 AAAAAATGCCAATAA
1 ATAAACTGCCAATAA
16473674 CGTCCACCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.17
Consensus pattern (47 bp):
ATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCGCAG
Found at i:16477080 original size:25 final size:27
Alignment explanation
Indices: 16477052--16477119 Score: 88
Period size: 25 Copynumber: 2.6 Consensus size: 27
16477042 AAAATTGGTA
*
16477052 AGACATTTTCCATTCT-TCTCT-A-AGT
1 AGACATTTTCCATTCTCT-TCTAACAGC
16477077 AGACATTTTCCATTCTCTTCTAAGCAGC
1 AGACATTTTCCATTCTCTTCTAA-CAGC
16477105 AGACATTTTCCATTC
1 AGACATTTTCCATTC
16477120 CTCAAAGCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 19 0.50
26 2 0.05
28 17 0.45
ACGTcount: A:0.25, C:0.26, G:0.09, T:0.40
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAACAGC
Found at i:16479432 original size:15 final size:15
Alignment explanation
Indices: 16479407--16479454 Score: 87
Period size: 15 Copynumber: 3.1 Consensus size: 15
16479397 TAAGTGGTAC
16479407 TTTCAATGCTTTCATT
1 TTTC-ATGCTTTCATT
16479423 TTTCATGCTTTCATT
1 TTTCATGCTTTCATT
16479438 TTTCATGCTTTCATT
1 TTTCATGCTTTCATT
16479453 TT
1 TT
16479455 AAGTGGTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 28 0.88
16 4 0.12
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (15 bp):
TTTCATGCTTTCATT
Found at i:16479436 original size:8 final size:8
Alignment explanation
Indices: 16479406--16479451 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
16479396 ATAAGTGGTA
16479406 CTTTCAATG
1 CTTTC-ATG
16479415 CTTTCAT-
1 CTTTCATG
*
16479422 TTTTCATG
1 CTTTCATG
16479430 CTTTCAT-
1 CTTTCATG
*
16479437 TTTTCATG
1 CTTTCATG
16479445 CTTTCAT
1 CTTTCAT
16479452 TTTAAGTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
7 12 0.39
8 14 0.45
9 5 0.16
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (8 bp):
CTTTCATG
Found at i:16481033 original size:35 final size:36
Alignment explanation
Indices: 16480985--16481053 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
16480975 ATTTGTTAGA
16480985 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
16481021 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
16481054 ATGGTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Done.