Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 23
Found at i:3958720 original size:19 final size:17
Alignment explanation
Indices: 3958627--3958748 Score: 71
Period size: 19 Copynumber: 7.1 Consensus size: 17
3958617 CCTCCTTTTA
3958627 TTTCTCTTTTTT-TCATT
1 TTTCT-TTTTTTCTCATT
*
3958644 TTTC-ATTTTT-TCATT
1 TTTCTTTTTTTCTCATT
*
3958659 TTTCATTTTTTAT-TCCCTT
1 TTTC-TTTTTT-TCT-CATT
*
3958678 TTCCATTTTTTT-TC--T
1 TTTC-TTTTTTTCTCATT
*
3958693 TTTCGTTTTTTCCATCATT
1 TTTC-TTTTTTTC-TCATT
3958712 TTTCTTTTTTTCTCATT
1 TTTCTTTTTTTCTCATT
3958729 TTTCTCATTTTTTCTC-TT
1 TTTCT--TTTTTTCTCATT
3958747 TT
1 TT
3958749 ATTTCTTCTT
Statistics
Matches: 87, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
15 24 0.28
17 21 0.24
18 15 0.17
19 27 0.31
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.72
Consensus pattern (17 bp):
TTTCTTTTTTTCTCATT
Found at i:3958730 original size:10 final size:10
Alignment explanation
Indices: 3958717--3958754 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
3958707 TCATTTTTCT
3958717 TTTTTTCTCA
1 TTTTTTCTCA
3958727 -TTTTTCTCA
1 TTTTTTCTCA
*
3958736 TTTTTTCTCT
1 TTTTTTCTCA
3958746 TTTATTTCT
1 TTT-TTTCT
3958755 TCTTCAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 9 0.36
10 11 0.44
11 5 0.20
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTCTCA
Found at i:3958748 original size:9 final size:9
Alignment explanation
Indices: 3958710--3958748 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
3958700 TTTTCCATCA
3958710 TTTTTCT-T
1 TTTTTCTCT
*
3958718 TTTTTCTCA
1 TTTTTCTCT
3958727 TTTTTCTCAT
1 TTTTTCTC-T
3958737 TTTTTCTCT
1 TTTTTCTCT
3958746 TTT
1 TTT
3958749 ATTTCTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 7 0.26
9 12 0.44
10 8 0.30
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:3971828 original size:36 final size:36
Alignment explanation
Indices: 3971781--3971952 Score: 162
Period size: 35 Copynumber: 4.8 Consensus size: 36
3971771 GAGCGTCTAC
* **
3971781 AATATAAGTTTTCAAAAACATTTTTTTTAAACTATAT-
1 AATAT-AGTTTTCAAAAA-ATGTTTTCAAAACTATATA
3971818 AATATAGTTTTC-AAAAATGTTTTCAAAACTATATA
1 AATATAGTTTTCAAAAAATGTTTTCAAAACTATATA
*
3971853 ATATATAGGTTTTC-AAAAATGCTTTCAAAAACTATATA
1 A-ATATA-GTTTTCAAAAAATGTTTTC-AAAACTATATA
* *
3971891 TTATATA-TTTT--AAAAATATTTTCAAAACTATAT-
1 -AATATAGTTTTCAAAAAATGTTTTCAAAACTATATA
*
3971924 AGTATATGTTTTC-AAAAATGTTTTCAAAA
1 AATATA-GTTTTCAAAAAATGTTTTCAAAA
3971953 AAACTATATA
Statistics
Matches: 117, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
32 4 0.03
34 29 0.25
35 30 0.26
36 16 0.14
37 22 0.19
38 16 0.14
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (36 bp):
AATATAGTTTTCAAAAAATGTTTTCAAAACTATATA
Found at i:3971852 original size:34 final size:34
Alignment explanation
Indices: 3971781--3971952 Score: 186
Period size: 34 Copynumber: 4.8 Consensus size: 34
3971771 GAGCGTCTAC
* **
3971781 AATATAAGTTTTCAAAAACATTTTTTTTAAACTATAT
1 AATAT-AGTTTTC-AAAA-ATGTTTTCAAAACTATAT
3971818 AATATAGTTTTCAAAAATGTTTTCAAAACTATAT
1 AATATAGTTTTCAAAAATGTTTTCAAAACTATAT
*
3971852 AATATATAGGTTTTCAAAAATGCTTTCAAAAACTATAT
1 -A-ATATA-GTTTTCAAAAATGTTTTC-AAAACTATAT
*
3971890 ATTATATA-TTTT-AAAAATATTTTCAAAACTATAT
1 A--ATATAGTTTTCAAAAATGTTTTCAAAACTATAT
*
3971924 AGTATATGTTTTCAAAAATGTTTTCAAAA
1 AATATA-GTTTTCAAAAATGTTTTCAAAA
3971953 AAACTATATA
Statistics
Matches: 119, Mismatches: 8, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
32 4 0.03
34 30 0.25
35 30 0.25
36 16 0.13
37 23 0.19
38 16 0.13
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (34 bp):
AATATAGTTTTCAAAAATGTTTTCAAAACTATAT
Found at i:3971907 original size:72 final size:72
Alignment explanation
Indices: 3971809--3971996 Score: 244
Period size: 72 Copynumber: 2.6 Consensus size: 72
3971799 CATTTTTTTT
* *
3971809 AAACTATATA--ATATAGTTTTCAAAAATGTTTTCAAAACTATATAATATATAGGTTTTCAAAAA
1 AAACTATATATTATATACTTTT-AAAAATATTTTCAAAACTATATAATATAT--GTTTTCAAAAA
3971872 TGCTTTC-AA
63 TGCTTTCAAA
* *
3971881 AAACTATATATTATATA-TTTTAAAAATATTTTCAAAACTATATAGTATATGTTTTCAAAAATGT
1 AAACTATATATTATATACTTTTAAAAATATTTTCAAAACTATATAATATATGTTTTCAAAAATGC
3971945 TTTCAAAA
66 TTTC-AAA
*
3971953 AAACTATATATTATATACTTTT-AAAACATTTT-AATAACTATATA
1 AAACTATATATTATATACTTTTAAAAATATTTTCAA-AACTATATA
3971997 TATTATATAT
Statistics
Matches: 106, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
70 17 0.16
71 2 0.02
72 74 0.70
73 8 0.08
74 5 0.05
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (72 bp):
AAACTATATATTATATACTTTTAAAAATATTTTCAAAACTATATAATATATGTTTTCAAAAATGC
TTTCAAA
Found at i:3971946 original size:12 final size:12
Alignment explanation
Indices: 3971929--3971953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3971919 TATATAGTAT
3971929 ATGTTTTCAAAA
1 ATGTTTTCAAAA
3971941 ATGTTTTCAAAA
1 ATGTTTTCAAAA
3971953 A
1 A
3971954 AACTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:3971997 original size:34 final size:33
Alignment explanation
Indices: 3971809--3972040 Score: 155
Period size: 34 Copynumber: 6.5 Consensus size: 33
3971799 CATTTTTTTT
* *
3971809 AAACTATATA--ATATAGTTTTCAAAAATGTTTTCA
1 AAACTATATATTATATA-TTTT-AAAAA-ATTTTAA
* *
3971843 AAACTATATAATATATAGGTTTTCAAAAATGCTTTCAA
1 AAACTATATATTATATA--TTTTAAAAAAT--TTT-AA
*
3971881 AAACTATATATTATATATTTTAAAAATATTTTCA
1 AAACTATATATTATATATTTTAAAAA-ATTTTAA
* * *
3971915 AAACTATATAGTATATGTTTTCAAAAATGTTTTCAAAA
1 AAACTATATATTATATATTTT-AAAAA-ATTTT---AA
*
3971953 AAACTATATATTATATACTTTTAAAACATTTTAA
1 AAACTATATATTATATA-TTTTAAAAAATTTTAA
* * *
3971987 TAACTATATA-TATTATATATATAAAAAATTATAAAA
1 AAACTATATATTA-TATAT-TTTAAAAAATT-T-TAA
*
3972023 AAATTATATATTATATAT
1 AAACTATATATTATATAT
3972041 GTATTTTTCA
Statistics
Matches: 161, Mismatches: 20, Indels: 32
0.76 0.09 0.15
Matches are distributed among these distances:
33 3 0.02
34 54 0.34
35 15 0.09
36 32 0.20
37 16 0.10
38 37 0.23
39 4 0.02
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (33 bp):
AAACTATATATTATATATTTTAAAAAATTTTAA
Found at i:3972013 original size:72 final size:72
Alignment explanation
Indices: 3971809--3972040 Score: 223
Period size: 72 Copynumber: 3.2 Consensus size: 72
3971799 CATTTTTTTT
** * *
3971809 AAACTATATA--ATATAGTTTTCAAAAATGTTTTCAAAACTATATAATATATAGGTTTTCAAAAA
1 AAACTATATATTATATA-TTTT-AAAAACATTTTCAAAACTATATAGTATATA--TTATCAAAAA
*
3971872 TGCTTTC--AA
62 TGTTTTCAAAA
* * *
3971881 AAACTATATATTATATATTTTAAAAATATTTTCAAAACTATATAGTATATGTTTTCAAAAATGTT
1 AAACTATATATTATATATTTTAAAAACATTTTCAAAACTATATAGTATATATTATCAAAAATGTT
3971946 TTCAAAA
66 TTCAAAA
3971953 AAACTATATATTATATACTTTT-AAAACATTTT-AATAACTATATA-TATTATATATAT-AAAAA
1 AAACTATATATTATATA-TTTTAAAAACATTTTCAA-AACTATATAGTA-TATAT-TATCAAAAA
* *
3972014 -ATTAT-AAAA
62 TGTTTTCAAAA
*
3972023 AAATTATATATTATATAT
1 AAACTATATATTATATAT
3972041 GTATTTTTCA
Statistics
Matches: 142, Mismatches: 10, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
69 1 0.01
70 36 0.25
71 7 0.05
72 83 0.58
73 10 0.07
74 5 0.04
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (72 bp):
AAACTATATATTATATATTTTAAAAACATTTTCAAAACTATATAGTATATATTATCAAAAATGTT
TTCAAAA
Found at i:3972023 original size:11 final size:12
Alignment explanation
Indices: 3972004--3972032 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3971994 ATATATTATA
3972004 TATATAAAAAAT
1 TATATAAAAAAT
3972016 TATA-AAAAAAT
1 TATATAAAAAAT
3972027 TATATA
1 TATATA
3972033 TTATATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TATATAAAAAAT
Found at i:3975878 original size:18 final size:20
Alignment explanation
Indices: 3975855--3975898 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3975845 ATCTTCTTAA
*
3975855 ATTTTAAAA-TTAT-TTTAT
1 ATTTTAAAATTTATATATAT
3975873 ATTTTAAAATTTATATATAT
1 ATTTTAAAATTTATATATAT
3975893 ATTTTA
1 ATTTTA
3975899 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 4 0.17
20 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTAAAATTTATATATAT
Found at i:3976369 original size:50 final size:50
Alignment explanation
Indices: 3976247--3976371 Score: 162
Period size: 50 Copynumber: 2.5 Consensus size: 50
3976237 TTAGCAGTAA
**
3976247 AGCGCACCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGC-CCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
* *
3976298 AGCGCCCCCCTGAACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTAT
1 AGCGCCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
* * *
3976347 AGCGCGGCCCCTGCAGCACGCTATA
1 AGCGC-CCCCCTGCACCGCGCTATA
3976372 TCTGTGTATC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
49 11 0.17
50 49 0.75
51 5 0.08
ACGTcount: A:0.18, C:0.35, G:0.30, T:0.17
Consensus pattern (50 bp):
AGCGCCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
Found at i:3976524 original size:12 final size:10
Alignment explanation
Indices: 3976483--3976523 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
3976473 TTTATCACAC
3976483 CAAATTCTCT
1 CAAATTCTCT
3976493 CAAATTCTCT
1 CAAATTCTCT
3976503 -AAATTTCTCT
1 CAAA-TTCTCT
*
3976513 CAAATACTCT
1 CAAATTCTCT
3976523 C
1 C
3976524 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:3978724 original size:3 final size:3
Alignment explanation
Indices: 3978708--3978769 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
3978698 ACCTGCGCAA
* * *
3978708 GAC GAC GAT AAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAT GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
3978756 GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GA
3978770 TGATGATGGT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (3 bp):
GAC
Found at i:3982626 original size:49 final size:51
Alignment explanation
Indices: 3982519--3982641 Score: 180
Period size: 49 Copynumber: 2.5 Consensus size: 51
3982509 TTATACAAAA
* *
3982519 CGCGGTATCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAAGTATGT
3982570 CGCGGTACCTGCCCCGCGCTATATAAAATTAT-T-AGGAGTAAAAGTATAG-
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAAGTAT-GT
**
3982619 CGCGGTACCTGATCCGCGCTATA
1 CGCGGTACCTGCCCCGCGCTATA
3982642 CCCCTACGTG
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
49 34 0.51
50 2 0.03
51 31 0.46
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (51 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAAGTATGT
Found at i:3982762 original size:51 final size:50
Alignment explanation
Indices: 3982653--3982766 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 50
3982643 CCCTACGTGG
* * * * ** *
3982653 CGTATAGCGCGCTACAGGGGCCGCGCTATACCCACGTGGTGCCAGCTTAC
1 CGTATAGCGCGGTACAGGGGACGCGCTATACCAACGTGGCGCCAAATCAC
* * *
3982703 CGTATAGCGCGGTTCAGGGGACGCGCTATACCTAACGTGGCGCTAAATCAT
1 CGTATAGCGCGGTACAGGGGACGCGCTATACC-AACGTGGCGCCAAATCAC
3982754 CGTATAGCGCGGT
1 CGTATAGCGCGGT
3982767 GTAGGAGGCA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
50 29 0.55
51 24 0.45
ACGTcount: A:0.20, C:0.29, G:0.31, T:0.20
Consensus pattern (50 bp):
CGTATAGCGCGGTACAGGGGACGCGCTATACCAACGTGGCGCCAAATCAC
Found at i:3994192 original size:59 final size:59
Alignment explanation
Indices: 3994100--3994218 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 59
3994090 TAGAGATTCA
* * * *
3994100 CTATGATAATAACACTTCTAATCCACCTTGTTCCGTTCATAACGTTAATATTTGAATCT
1 CTATGAGAATAACACTTCTAATCCACCTTGTTCCATTCAAAACGTTAAGATTTGAATCT
*
3994159 CTATGAGAATAACACTTCTAATCCACCTTGTTCCATTCAAAACGTTAAGGTTTGAATCT
1 CTATGAGAATAACACTTCTAATCCACCTTGTTCCATTCAAAACGTTAAGATTTGAATCT
3994218 C
1 C
3994219 CGATCTTACT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (59 bp):
CTATGAGAATAACACTTCTAATCCACCTTGTTCCATTCAAAACGTTAAGATTTGAATCT
Found at i:3994860 original size:20 final size:20
Alignment explanation
Indices: 3994835--3994888 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3994825 GACCAACAAA
3994835 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
3994855 TTCGCAACTC-AGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
3994875 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
3994889 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:3994899 original size:20 final size:21
Alignment explanation
Indices: 3994876--3994923 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3994866 GTTTCCAATT
3994876 TCGCAACGCGAA-TATGTAAA
1 TCGCAACGCGAATTATGTAAA
** *
3994896 TCGCATTGCGAATTTTGTAAA
1 TCGCAACGCGAATTATGTAAA
3994917 TCGCAAC
1 TCGCAAC
3994924 ACAGAAGTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (21 bp):
TCGCAACGCGAATTATGTAAA
Found at i:3994942 original size:20 final size:20
Alignment explanation
Indices: 3994917--3994956 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3994907 ATTTTGTAAA
3994917 TCGCAACAC-AGAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
*
3994937 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
3994957 GTTTTTACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:3995129 original size:22 final size:22
Alignment explanation
Indices: 3995077--3995134 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
3995067 TCACTCTCTA
* *
3995077 CGACGACATCCGTCCCCATTTT
1 CGACGAAATCCGTCCCCATTTC
* * *
3995099 TGACAAAATTCGTCCCCATTTC
1 CGACGAAATCCGTCCCCATTTC
3995121 CGACGAAATCCGTC
1 CGACGAAATCCGTC
3995135 TATCTCCATC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.36, G:0.14, T:0.26
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATTTC
Found at i:3997686 original size:21 final size:21
Alignment explanation
Indices: 3997638--3997690 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
3997628 AGCCCTTCCC
*
3997638 GCCGTTCAAGAGGCCCCATCA
1 GCCGTTCAAGAGGCCCCACCA
* * *
3997659 -TCGTTCAAGAGGTCCCGCCA
1 GCCGTTCAAGAGGCCCCACCA
3997679 GCCGTTCAAGAG
1 GCCGTTCAAGAG
3997691 CCTGATTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.17
Consensus pattern (21 bp):
GCCGTTCAAGAGGCCCCACCA
Found at i:4006019 original size:22 final size:21
Alignment explanation
Indices: 4005977--4006016 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4005967 GAGCTTATTT
*
4005977 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
4005998 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4006017 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:4008726 original size:14 final size:14
Alignment explanation
Indices: 4008707--4008746 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4008697 TTTTGATTAA
4008707 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
4008721 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
4008735 TTGATTTGTAAA
1 TTGATTTGTAAA
4008747 TAAGAATTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:4008786 original size:66 final size:60
Alignment explanation
Indices: 4008657--4008796 Score: 181
Period size: 66 Copynumber: 2.2 Consensus size: 60
4008647 TTTTACATTG
4008657 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
** * * *
4008717 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTAATTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAG-ATT--TATTTT--TTGATTAATTGATTTGT
4008782 A
60 A
4008783 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
4008797 GTTTCTAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 17 0.25
61 13 0.19
62 3 0.04
64 5 0.07
66 31 0.45
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (60 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
Found at i:4008880 original size:20 final size:20
Alignment explanation
Indices: 4008855--4008944 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
4008845 GTTGAAGGTA
4008855 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
4008875 CAAATTCGCAACGCGAAA-T
1 CAAATTCGCAACGCGAAAGT
***
4008894 --AA---GCGTTGC-AATAGT
1 CAAATTCGCAACGCGAA-AGT
*
4008909 CAAATTCGAAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
4008929 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
4008945 TTTTCGGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.04
14 5 0.09
15 1 0.02
17 4 0.07
19 1 0.02
20 39 0.72
21 2 0.04
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:4009203 original size:39 final size:39
Alignment explanation
Indices: 4009149--4009235 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
4009139 TCAAGTTGTA
**
4009149 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTAACACCATATGAGATTTG
*
4009188 GATTTTGATTTCCTTTTGCTTAACACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTAACACCATATGAGATTTG
4009227 GATTTTGAT
1 GATTTTGAT
4009236 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTAACACCATATGAGATTTG
Found at i:4009497 original size:11 final size:11
Alignment explanation
Indices: 4009481--4009532 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
4009471 TTATACATAC
4009481 AATGTTCAAAT
1 AATGTTCAAAT
4009492 AATGTTCAAAT
1 AATGTTCAAAT
* *
4009503 AATGTACCCATAAC
1 AATGT--TCA-AAT
4009517 AATGTTCAAAT
1 AATGTTCAAAT
4009528 AATGT
1 AATGT
4009533 ACTCACAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 23 0.68
12 2 0.06
13 2 0.06
14 7 0.21
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:4009525 original size:25 final size:25
Alignment explanation
Indices: 4009492--4009547 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
4009482 ATGTTCAAAT
*
4009492 AATGTTCAAATAATGTACCCATAAC
1 AATGTTCAAATAATGTACCCACAAC
*
4009517 AATGTTCAAATAATGTACTCACAAC
1 AATGTTCAAATAATGTACCCACAAC
4009542 AATGTT
1 AATGTT
4009548 TAATTGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (25 bp):
AATGTTCAAATAATGTACCCACAAC
Found at i:4010020 original size:18 final size:18
Alignment explanation
Indices: 4009997--4010032 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4009987 AAGCCGGTTG
4009997 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
4010015 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
4010033 CCTTTTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:4010741 original size:12 final size:12
Alignment explanation
Indices: 4010724--4010749 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4010714 AGAGGCTCGA
4010724 AAAAACTCCATT
1 AAAAACTCCATT
4010736 AAAAACTCCATT
1 AAAAACTCCATT
4010748 AA
1 AA
4010750 CATAGTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAACTCCATT
Found at i:4012340 original size:24 final size:23
Alignment explanation
Indices: 4012309--4012360 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
4012299 TCACATCATC
4012309 AAAATCCGAGTATTGACCAAGAT
1 AAAATCCGAGTATTGACCAAGAT
*
4012332 AAAAGTCCGGGTATTGACCAAGAT
1 AAAA-TCCGAGTATTGACCAAGAT
*
4012356 CAAAT
1 AAAAT
4012361 TTCGAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (23 bp):
AAAATCCGAGTATTGACCAAGAT
Found at i:4012502 original size:12 final size:12
Alignment explanation
Indices: 4012485--4012518 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
4012475 GGTTGTGGGT
4012485 TTTGATATTGTG
1 TTTGATATTGTG
4012497 TTTGATATTGTG
1 TTTGATATTGTG
*
4012509 TTTGGTATTG
1 TTTGATATTG
4012519 GAAATGTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:4013152 original size:76 final size:77
Alignment explanation
Indices: 4013001--4013209 Score: 289
Period size: 76 Copynumber: 2.8 Consensus size: 77
4012991 CAAAGCCAAA
* * * * **
4013001 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACAGATT-CCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
4013065 TTTGGCCCCGAG
66 TTTGGCCCCGAG
*
4013077 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
4013142 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
4013153 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
4013210 TGTACAACGG
Statistics
Matches: 119, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
75 19 0.16
76 86 0.72
77 14 0.12
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:4018918 original size:21 final size:21
Alignment explanation
Indices: 4018881--4018966 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
4018871 TTTTGGTGCA
*
4018881 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
4018901 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
* *
4018922 GAAGGGGAACCAATTCCCCCCACA
1 G-A-GGGAACCGATTCCCCCC-CT
* *
4018946 G-GGGAATCGATACCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
4018966 G
1 G
4018967 GGGTTCTGTT
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
20 12 0.24
21 22 0.43
22 1 0.02
23 15 0.29
24 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.24, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:4020909 original size:17 final size:17
Alignment explanation
Indices: 4020887--4020934 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
4020877 TTTCAACATT
4020887 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
4020904 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
4020921 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
4020935 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:4021689 original size:75 final size:76
Alignment explanation
Indices: 4021519--4021727 Score: 278
Period size: 75 Copynumber: 2.8 Consensus size: 76
4021509 CAAAGCCAAA
* * * * *
4021519 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCCATAGGAGGAACTGATTCCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCCATAGGAGGAACCGATTCCCCCTAAATAG
4021584 TTTTGGCCCCGAG
64 TTTTGGCCCCGAG
*
4021597 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAATAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAATAGTT
*
4021662 TT-GCTCCGAG
66 TTGGCCCCGAG
* * * * *
4021672 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCAATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCT
4021728 TGTACAACGG
Statistics
Matches: 118, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
74 17 0.14
75 40 0.34
76 36 0.31
78 25 0.21
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAATAGTT
TTGGCCCCGAG
Found at i:4022957 original size:20 final size:20
Alignment explanation
Indices: 4022932--4023091 Score: 69
Period size: 20 Copynumber: 8.0 Consensus size: 20
4022922 TTGCAAAATT
4022932 AAATTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
** *
4022952 AAATTC-AATTGTGAATTTG
1 AAATTCGCGTTGCGAATTTG
** *
4022971 ACTTTCGTGTTGCGAATTTAG
1 AAATTCGCGTTGCGAATTT-G
* *** *
4022992 AAAATCGCAACGCAAATTTGG
1 AAATTCGCGTTGCGAATTT-G
* **
4023013 AAAATCGCAATGCG-ATTT-
1 AAATTCGCGTTGCGAATTTG
*
4023031 ACATATTCGCGTTGCGAAATTG
1 A-A-ATTCGCGTTGCGAATTTG
* * *
4023053 AAA-ACTGGGTTGCGAAATT-
1 AAATTC-GCGTTGCGAATTTG
4023072 AGAATTCGCGTTGCGAATTT
1 A-AATTCGCGTTGCGAATTT
4023092 ATTGGTCATT
Statistics
Matches: 103, Mismatches: 28, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
18 1 0.01
19 17 0.17
20 54 0.52
21 30 0.29
22 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTTG
Found at i:4026308 original size:55 final size:55
Alignment explanation
Indices: 4026220--4026330 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
4026210 GATATCATTT
* *
4026220 ATAGGATTATATAAATCCTTTAATTTTTTTATCGATTTTGCCCTTAAACTTTAAA
1 ATAGGACTATATAAATCCTTTAATTTTTATATCGATTTTGCCCTTAAACTTTAAA
* *
4026275 ATAGGACTATATAAATCCTTTAATTTTTATATCGATTTTGCCGTTACACTTTAAA
1 ATAGGACTATATAAATCCTTTAATTTTTATATCGATTTTGCCCTTAAACTTTAAA
4026330 A
1 A
4026331 CGTTTTAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (55 bp):
ATAGGACTATATAAATCCTTTAATTTTTATATCGATTTTGCCCTTAAACTTTAAA
Found at i:4027634 original size:3 final size:3
Alignment explanation
Indices: 4027626--4027690 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
4027616 ATTTTTGTTT
** *
4027626 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
4027672 TTA -TA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
4027691 TACAAACAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:4027732 original size:26 final size:26
Alignment explanation
Indices: 4027696--4027747 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
4027686 TTATTTACAA
* *
4027696 ACAGTTACAAACAAAACTGGACCGGC
1 ACAGTTACAAACAAAACAGAACCGGC
4027722 ACAGTTACAAACAAAACAGAACCGGC
1 ACAGTTACAAACAAAACAGAACCGGC
4027748 CCAGACCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (26 bp):
ACAGTTACAAACAAAACAGAACCGGC
Found at i:4030023 original size:16 final size:16
Alignment explanation
Indices: 4030002--4030053 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
4029992 TCTTTCAAAT
4030002 TTTTTAT-TACTTATTA
1 TTTTTATATA-TTATTA
4030018 TTTTTATATATTATTA
1 TTTTTATATATTATTA
*
4030034 TTTTT-TATTTTATTTA
1 TTTTTATATATTA-TTA
4030050 TTTT
1 TTTT
4030054 ATTCAAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 6 0.18
16 25 0.76
17 2 0.06
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTATATATTATTA
Found at i:4032360 original size:7 final size:7
Alignment explanation
Indices: 4032325--4032365 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
4032315 TTTTCATATA
4032325 TGCATTT
1 TGCATTT
4032332 T-CATTT
1 TGCATTT
4032338 TGCATCTT
1 TGCAT-TT
4032346 TGCATTT
1 TGCATTT
*
4032353 TTCATTT
1 TGCATTT
4032360 TGCATT
1 TGCATT
4032366 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:4036530 original size:114 final size:114
Alignment explanation
Indices: 4036329--4036546 Score: 339
Period size: 114 Copynumber: 1.9 Consensus size: 114
4036319 GTGCCATGTT
* *
4036329 CTCGTAGTAGAAATAAGGAGCCCCAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
* * *
4036394 ATTTGGTATGAACCCTAAAACCAATCATTAGATTTGAAATATAAATTTG
66 ATTTGGTAGGAACCCCAAAACCAATCATTAGAATTGAAATATAAATTTG
* *
4036443 CTCGTAGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTGTCTGATTTG
1 CTCGTAGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
* *
4036508 -TTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAA
66 ATTT-GGTAGGAACCCCAAAACCAATCATTAGAATTGAAA
4036547 GATGAACTGC
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
113 3 0.03
114 91 0.97
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (114 bp):
CTCGTAGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
ATTTGGTAGGAACCCCAAAACCAATCATTAGAATTGAAATATAAATTTG
Found at i:4037801 original size:76 final size:76
Alignment explanation
Indices: 4037653--4037829 Score: 198
Period size: 76 Copynumber: 2.3 Consensus size: 76
4037643 TAACAAGAAA
* * * * *
4037653 CAAATGTTGGGGCATGCTGAAA-ACCCTTGTCAATCAGAATCAGGAATGTTGATGTATCCTAAAT
1 CAAATATTAGGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATGTTGATGTATCCTAAAC
* *
4037717 GTTTATATCAG
66 GCTCATATCAG
* ** *
4037728 CAAA-ATGCTAGGGCATGCTGAAAGCCCCTT-TCAATCAGAATGAAGAATGTTGATGTATTTTGA
1 CAAATAT--TAGGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATGTTGATGTATCCTAA
4037791 ACGCTCATATCAG
64 ACGCTCATATCAG
* *
4037804 CAAATATTGGGGCATGCTGAAGGCCC
1 CAAATATTAGGGCATGCTGAAAGCCC
4037830 ACAACATCCT
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
74 1 0.01
75 21 0.25
76 56 0.66
77 7 0.08
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (76 bp):
CAAATATTAGGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATGTTGATGTATCCTAAAC
GCTCATATCAG
Found at i:4039206 original size:22 final size:21
Alignment explanation
Indices: 4039163--4039216 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
4039153 ATTTACACTC
*
4039163 TTCAAAGATAATAGATCTCTT
1 TTCAAAGATGATAGATCTCTT
*
4039184 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGA-TCTCTT
4039206 TTCAAAGATGA
1 TTCAAAGATGA
4039217 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (21 bp):
TTCAAAGATGATAGATCTCTT
Found at i:4040016 original size:76 final size:76
Alignment explanation
Indices: 4039890--4040680 Score: 1438
Period size: 76 Copynumber: 10.4 Consensus size: 76
4039880 CTATTTCCCA
4039890 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4039955 AGCCTTAGGGT
66 AGCCTTAGGGT
4039966 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4040031 AGCCTTAGGGT
66 AGCCTTAGGGT
4040042 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4040107 AGCCTTAGGGT
66 AGCCTTAGGGT
4040118 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4040183 AGCCTTAGGGT
66 AGCCTTAGGGT
4040194 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4040259 AGCCTTAGGGT
66 AGCCTTAGGGT
*
4040270 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTAGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
4040335 AGCTTTAGGGT
66 AGCCTTAGGGT
4040346 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
4040411 ATCCTTAGGGT
66 AGCCTTAGGGT
* * *
4040422 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAGCCTTAGGGAGATTTTTGATGTTTTTA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
4040487 AAGCCTTAGGGT
65 AAGCCTTAGGGT
**
4040499 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
4040564 AACCTTAGGGT
66 AGCCTTAGGGT
* *
4040575 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTATTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
4040640 AACCTTAAGGC
66 AGCCTTAGGGT
*
4040651 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
4040681 TTAAGACCTC
Statistics
Matches: 695, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
76 625 0.90
77 70 0.10
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:4040846 original size:3 final size:3
Alignment explanation
Indices: 4040838--4040902 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
4040828 ATTTTTGTTT
** *
4040838 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
4040884 TTA -TA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
4040903 TACAAACAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:4040961 original size:26 final size:26
Alignment explanation
Indices: 4040909--4040963 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
4040899 TATTTACAAA
* *
4040909 CAGTTACAAACAAAACTGGACCAGCC
1 CAGTTACAAACAAAACAGAACCAGCC
*
4040935 CAGTTACAAACAAAACAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCAGCC
4040961 CAG
1 CAG
4040964 ACCAACCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.31, G:0.16, T:0.09
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCAGCC
Found at i:4043697 original size:1 final size:1
Alignment explanation
Indices: 4043691--4043722 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
4043681 CATTTTCGAT
4043691 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4043723 GCGAGTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4045316 original size:30 final size:31
Alignment explanation
Indices: 4045200--4045324 Score: 109
Period size: 30 Copynumber: 4.2 Consensus size: 31
4045190 TTTGTAATTA
* *
4045200 CTATTTTAGCCCTTTAAGTTTATAT-T-TTTG
1 CTATTTTAGTCCTTTAACTTT-TATGTATTTG
*
4045230 CTATTTTAGTCCTTTAACTTTCTAT-T-TTAG
1 CTATTTTAGTCCTTTAACTTT-TATGTATTTG
* * *
4045260 CTATTTCAGTCCCTTAAGTTTT-TGTATTTG
1 CTATTTTAGTCCTTTAACTTTTATGTATTTG
* * *
4045290 TTATTTTGGTCCTTTAA-TTTTATGTATTTA
1 CTATTTTAGTCCTTTAACTTTTATGTATTTG
4045320 CTATT
1 CTATT
4045325 CATCCCTTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
28 1 0.01
29 6 0.08
30 71 0.91
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.58
Consensus pattern (31 bp):
CTATTTTAGTCCTTTAACTTTTATGTATTTG
Found at i:4045324 original size:60 final size:60
Alignment explanation
Indices: 4045192--4045341 Score: 146
Period size: 60 Copynumber: 2.5 Consensus size: 60
4045182 CTGGTTTATT
* * * *
4045192 TGTAATTACTATTTTAG-CCCTTTAAGTTTATATTTTTGCTATTTTAGTCCTTTAACTTTC
1 TGTATTTACTATTTCAGTCCC-TTAAGTTTATATATTTGCTATTTTAGTCCTTTAACTTTA
* * * * * *
4045252 TAT-TTTAGCTATTTCAGTCCCTTAAGTTTTTGTATTTGTTATTTTGGTCCTTTAATTTTA
1 TGTATTTA-CTATTTCAGTCCCTTAAGTTTATATATTTGCTATTTTAGTCCTTTAACTTTA
*
4045312 TGTATTTACTA-TTCA-TCCCTTTAAATTTAT
1 TGTATTTACTATTTCAGTCCC-TTAAGTTTAT
4045342 GTTAATTTTA
Statistics
Matches: 73, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
58 4 0.05
59 15 0.21
60 47 0.64
61 7 0.10
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (60 bp):
TGTATTTACTATTTCAGTCCCTTAAGTTTATATATTTGCTATTTTAGTCCTTTAACTTTA
Found at i:4046316 original size:6 final size:6
Alignment explanation
Indices: 4046302--4046401 Score: 51
Period size: 6 Copynumber: 16.7 Consensus size: 6
4046292 TCCATAATTT
* * * * * *
4046302 CATATA CATACA CATACA TATACG CATACG CATACA CATACG CATACG
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
** * * * * *
4046350 CATATG CATACG CATACG CATATC- CATATC- CATATA CATATA CATATA
1 CATACA CATACA CATACA CATA-CA CATA-CA CATACA CATACA CATACA
4046398 CATA
1 CATA
4046402 TGCATATGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
6 82 0.99
7 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (6 bp):
CATACA
Found at i:4046335 original size:18 final size:18
Alignment explanation
Indices: 4046308--4046371 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
4046298 ATTTCATATA
* *
4046308 CATACACATACATATACG
1 CATACGCATACACATACG
4046326 CATACGCATACACATACG
1 CATACGCATACACATACG
**
4046344 CATACGCATATGCATACG
1 CATACGCATACACATACG
4046362 CATACGCATA
1 CATACGCATA
4046372 TCCATATCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (18 bp):
CATACGCATACACATACG
Found at i:4046372 original size:18 final size:18
Alignment explanation
Indices: 4046321--4046395 Score: 89
Period size: 18 Copynumber: 4.2 Consensus size: 18
4046311 ACACATACAT
*
4046321 ATACGCATACGCATACAC
1 ATACGCATACGCATATAC
*
4046339 ATACGCATACGCATATGC
1 ATACGCATACGCATATAC
*
4046357 ATACGCATACGCATATCC
1 ATACGCATACGCATATAC
**
4046375 ATATC-CATATACATATAC
1 ATA-CGCATACGCATATAC
4046393 ATA
1 ATA
4046396 TACATATGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
18 49 0.98
19 1 0.02
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.24
Consensus pattern (18 bp):
ATACGCATACGCATATAC
Found at i:4046402 original size:6 final size:6
Alignment explanation
Indices: 4046368--4046469 Score: 73
Period size: 6 Copynumber: 17.3 Consensus size: 6
4046358 TACGCATACG
* * * * *
4046368 CATATC CATATC CATATA CATATA CATATA CATATG CATATG CAGATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
* * * * * * * *
4046416 C--ATG CAGATA TAGATA CATATA CAGATA TATATA CAGATA CAGATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
4046462 CATATA CA
1 CATATA CA
4046470 GATGCAGATG
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
4 3 0.04
6 76 0.96
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (6 bp):
CATATA
Found at i:4046470 original size:18 final size:18
Alignment explanation
Indices: 4046380--4046489 Score: 80
Period size: 18 Copynumber: 6.2 Consensus size: 18
4046370 TATCCATATC
* *
4046380 CATATACATATACATATA
1 CATATACAGATACAGATA
* * *
4046398 CATATGCATATGCAGATA
1 CATATACAGATACAGATA
* *
4046416 C--ATGCAGATATAGATA
1 CATATACAGATACAGATA
* *
4046432 CATATACAGATATATATA
1 CATATACAGATACAGATA
* *
4046450 CAGATACAGATACATATA
1 CATATACAGATACAGATA
* * *
4046468 CAGATGCAGATGCAGATA
1 CATATACAGATACAGATA
4046486 CATA
1 CATA
4046490 GGTGTATGCG
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.17
18 63 0.83
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (18 bp):
CATATACAGATACAGATA
Found at i:4046785 original size:6 final size:6
Alignment explanation
Indices: 4046678--4046882 Score: 122
Period size: 6 Copynumber: 34.2 Consensus size: 6
4046668 TATCCATATG
* * * * * * * *
4046678 CGTATG CGTATA CATATG CGTATG CGTATA CATATG CATATG CGTATA
1 CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA
* * * * * * * * *
4046726 CATATG CGTATG CGTATA CGTATA CATATG CGTATG CATATA CATATG
1 CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA
* * * * * * *
4046774 CGTATA CGTATA CATATG CATATA TGTATA CATATG CGTATA TGTATA
1 CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA
* * * * * * * *
4046822 CATATG TGTATA TGTATA CGTATA TGTATA TGTATA CGTATG CATATA
1 CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA CGTATA
4046870 CGTATA CGTATA C
1 CGTATA CGTATA C
4046883 AGATACAGAT
Statistics
Matches: 154, Mismatches: 45, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 154 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (6 bp):
CGTATA
Found at i:4046815 original size:18 final size:18
Alignment explanation
Indices: 4046494--4047096 Score: 431
Period size: 18 Copynumber: 33.2 Consensus size: 18
4046484 TACATAGGTG
* * *
4046494 TATGCGTATCCATATGCA
1 TATGCGTATGCGTATACA
*
4046512 TATGCGTATGCGTATCCA
1 TATGCGTATGCGTATACA
* * *
4046530 TTTGCGTATGTGTATCCA
1 TATGCGTATGCGTATACA
*
4046548 TATGCGTATGCGTATCCA
1 TATGCGTATGCGTATACA
*
4046566 TATGCGTATGCGTATCCA
1 TATGCGTATGCGTATACA
*
4046584 TATGCGTATGCGTATCCA
1 TATGCGTATGCGTATACA
*
4046602 TATGCGTATGCGTATTCA
1 TATGCGTATGCGTATACA
* *
4046620 TATACGTATGCGTATCCA
1 TATGCGTATGCGTATACA
* *
4046638 TATGCATATGCGTATCCA
1 TATGCGTATGCGTATACA
*
4046656 TATGCGTATGCGTATCCA
1 TATGCGTATGCGTATACA
4046674 TATGCGTATGCGTATACA
1 TATGCGTATGCGTATACA
4046692 TATGCGTATGCGTATACA
1 TATGCGTATGCGTATACA
*
4046710 TATGCATATGCGTATACA
1 TATGCGTATGCGTATACA
4046728 TATGCGTATGCGTATACGTATACA
1 TATGCGTAT--G----CGTATACA
*
4046752 TATGCGTATGCATATACA
1 TATGCGTATGCGTATACA
*
4046770 TATGCGTATACGTATACA
1 TATGCGTATGCGTATACA
* **
4046788 TATGCATATATGTATACA
1 TATGCGTATGCGTATACA
**
4046806 TATGCGTATATGTATACA
1 TATGCGTATGCGTATACA
* ** *
4046824 TATGTGTATATGTATACG
1 TATGCGTATGCGTATACA
** ** *
4046842 TATATGTATATGTATACG
1 TATGCGTATGCGTATACA
* * *
4046860 TATGCATATACGTATACG
1 TATGCGTATGCGTATACA
* * *
4046878 TATACAG-ATACAG-ATATA
1 TATGC-GTATGC-GTATACA
* *
4046896 GATGCAG-ATGCAG-ATGCA
1 TATGC-GTATGC-GTATACA
* * * * *
4046914 GATACATATACATATACA
1 TATGCGTATGCGTATACA
* * * *
4046932 TATACATATGCATATGCA
1 TATGCGTATGCGTATACA
* * *
4046950 TATGCATATGCATATGCA
1 TATGCGTATGCGTATACA
* * *
4046968 TATGCATATGCATATGCA
1 TATGCGTATGCGTATACA
* *
4046986 TATGCATATGCATATACA
1 TATGCGTATGCGTATACA
* * * *
4047004 TATACATATACATATACA
1 TATGCGTATGCGTATACA
* * *
4047022 TATGCATATGCATATGCA
1 TATGCGTATGCGTATACA
* *
4047040 TATGCATATGCATATACA
1 TATGCGTATGCGTATACA
* * * *
4047058 TATGCATATACATATGCA
1 TATGCGTATGCGTATACA
* *
4047076 TATGCATATGCATATACA
1 TATGCGTATGCGTATACA
4047094 TAT
1 TAT
4047097 ACATATACAT
Statistics
Matches: 517, Mismatches: 58, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
18 497 0.96
19 1 0.00
20 1 0.00
22 1 0.00
24 17 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (18 bp):
TATGCGTATGCGTATACA
Found at i:4046834 original size:36 final size:36
Alignment explanation
Indices: 4046494--4047186 Score: 431
Period size: 36 Copynumber: 19.1 Consensus size: 36
4046484 TACATAGGTG
* * * *
4046494 TATGCGTATCCATATGCATATGCGTATGCGTATCCA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * * *
4046530 TTTGCGTATGTGTATCCATATGCGTATGCGTATCCA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* *
4046566 TATGCGTATGCGTATCCATATGCGTATGCGTATCCA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * *
4046602 TATGCGTATGCGTATTCATATACGTATGCGTATCCA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * *
4046638 TATGCATATGCGTATCCATATGCGTATGCGTATCCA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
4046674 TATGCGTATGCGTATACATATGCGTATGCGTATACA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
*
4046710 TATGCATATGCGTATACATATGCGTATGCGTATACGTATACA
1 TATGCGTATGCGTATACATATGCGTAT--G----CGTATACA
* *
4046752 TATGCGTATGCATATACATATGCGTATACGTATACA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* ** **
4046788 TATGCATATATGTATACATATGCGTATATGTATACA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* ** * ** ** *
4046824 TATGTGTATATGTATACGTATATGTATATGTATACG
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * * * * *
4046860 TATGCATATACGTATACGTATACAG-ATACAG-ATATA
1 TATGCGTATGCGTATACATATGC-GTATGC-GTATACA
* * * * * * *
4046896 GATGCAG-ATGCAG-ATGCAGATACATATACATATACA
1 TATGC-GTATGC-GTATACATATGCGTATGCGTATACA
* * * * * * *
4046932 TATACATATGCATATGCATATGCATATGCATATGCA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * * * *
4046968 TATGCATATGCATATGCATATGCATATGCATATACA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * * * * * *
4047004 TATACATATACATATACATATGCATATGCATATGCA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * * * * *
4047040 TATGCATATGCATATACATATGCATATACATATGCA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * * * * *
4047076 TATGCATATGCATATACATATACATATACATATACA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * * * * * * *
4047112 TATACATATACATATACATATACATATACATATACA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
* * * * * * * *
4047148 TATACATATACATATACATATACATATACATATACA
1 TATGCGTATGCGTATACATATGCGTATGCGTATACA
4047184 TAT
1 TAT
4047187 ATACATATAC
Statistics
Matches: 576, Mismatches: 67, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
36 539 0.94
37 3 0.01
38 1 0.00
42 33 0.06
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (36 bp):
TATGCGTATGCGTATACATATGCGTATGCGTATACA
Found at i:4047953 original size:6 final size:6
Alignment explanation
Indices: 4046704--4047952 Score: 1599
Period size: 6 Copynumber: 210.3 Consensus size: 6
4046694 TGCGTATGCG
* * * * * * * *
4046704 TATACA TATGCA TATGCG TATACA TATGCG TATGCG TATACG TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * * * * * * **
4046752 TATGCG TATGCA TATACA TATGCG TATACG TATACA TATGCA TATATG
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * ** *** ** * **
4046800 TATACA TATGCG TATATG TATACA TATGTG TATATG TATACG TATATG
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
** * * * * * * *
4046848 TATATG TATACG TATGCA TATACG TATACG TATACA GATACA GATATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * * * * * * *
4046896 GATGCA GATGCA GATGCA GATACA TATACA TATACA TATACA TATGCA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * * * * * * *
4046944 TATGCA TATGCA TATGCA TATGCA TATGCA TATGCA TATGCA TATGCA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * * *
4046992 TATGCA TATACA TATACA TATACA TATACA TATGCA TATGCA TATGCA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * * * * *
4047040 TATGCA TATGCA TATACA TATGCA TATACA TATGCA TATGCA TATGCA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047088 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047136 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATAC--A
4047186 TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047232 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047280 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047328 TATACA TATACA TATACA TATACA TACATACA TATAC- -ATACA TATACA
1 TATACA TATACA TATACA TATACA T--ATACA TATACA TATACA TATACA
* *
4047376 TATACA TATAC- -ATACA TATAC- -ATACA TATGCA CATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* *
4047420 TACATACA TATAC- -ATACA TATACA TATACA TATACA TACATA TGCATACA
1 T--ATACA TATACA TATACA TATACA TATACA TATACA TATACA T--ATACA
*
4047470 TATAC- -ATACA TATACA TATACA TATACA TATGCA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
4047516 TATACA TATAC- -ATACA TATGCA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047562 TATACA TATACA TAT-CA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047609 TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047655 TATACA TATACA TATAC- -ATACA TATACA TATACACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TAT--ACA TATACA TATACA
4047703 TATACA TATACA TATACA TATAC- -ATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047749 TATACA TATACA TATACA TATACA TATACA TATAC- -ATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047795 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047843 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
4047891 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* *
4047939 TACACA TACACA TA
1 TATACA TATACA TA
4047953 CCATGTATCC
Statistics
Matches: 1143, Mismatches: 67, Indels: 66
0.90 0.05 0.05
Matches are distributed among these distances:
4 44 0.04
5 5 0.00
6 1066 0.93
8 28 0.02
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:4049736 original size:4 final size:4
Alignment explanation
Indices: 4049712--4049811 Score: 71
Period size: 4 Copynumber: 23.2 Consensus size: 4
4049702 CATGTTAGAT
*
4049712 ATAA AAAA ATAAA ATTAA ATAA ATAAA ATAA ATAA ATAA ATTCAA CCA-AA
1 ATAA ATAA AT-AA A-TAA ATAA AT-AA ATAA ATAA ATAA A-T-AA --ATAA
*
4049762 ATAA A-AA AGAA ATAAA ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA AT-AA AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA
4049811 A
1 A
4049812 GCATAGAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 24
0.75 0.03 0.22
Matches are distributed among these distances:
3 5 0.06
4 49 0.60
5 23 0.28
6 3 0.04
8 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:4049774 original size:26 final size:26
Alignment explanation
Indices: 4049745--4049804 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
4049735 TAAAATAAAT
* *
4049745 AAATAAATTCAACCAAAATAAAAAAG
1 AAATAAATTAAAACAAAATAAAAAAG
* * * *
4049771 AAATAAAATAAAATAAAATAATAAAT
1 AAATAAATTAAAACAAAATAAAAAAG
4049797 AAATAAAT
1 AAATAAAT
4049805 AAATAAAGCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (26 bp):
AAATAAATTAAAACAAAATAAAAAAG
Found at i:4049779 original size:5 final size:5
Alignment explanation
Indices: 4049717--4049811 Score: 67
Period size: 5 Copynumber: 19.6 Consensus size: 5
4049707 TAGATATAAA
* * * **
4049717 AAAAT AAAAT TAAAT -AAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
4049764 AAAAA AGAAAT AAAAT AAAAT AAAAT AATAA- ATAAAT -AAAT -AAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AA-AAT A-AAAT AAAAT AAAAT
4049809 AAA
1 AAA
4049812 GCATAGAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
4 20 0.27
5 46 0.63
6 7 0.10
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:4051458 original size:105 final size:106
Alignment explanation
Indices: 4051150--4051571 Score: 581
Period size: 105 Copynumber: 4.0 Consensus size: 106
4051140 AGCATTGTTC
* * **
4051150 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
4051215 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* * *
4051256 CGAGTCCAATAACCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** ** *
4051315 AGAAGTGGTCCCTTCGTCGTGGAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* *
4051356 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
4051420 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* * *
4051461 -GAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGTAGTTGTTTGTTGAC
1 CG-AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
*
4051525 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
4051567 CGAGT
1 CGAGT
4051572 GTCACGATAT
Statistics
Matches: 280, Mismatches: 27, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
100 82 0.29
101 3 0.01
102 5 0.02
104 4 0.01
105 100 0.36
106 85 0.30
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
Found at i:4052337 original size:67 final size:65
Alignment explanation
Indices: 4052206--4052656 Score: 275
Period size: 65 Copynumber: 6.7 Consensus size: 65
4052196 AATATATCTG
* * * * **
4052206 TTGTTTCATGAGAAACGGTCTCAAGGGAAATAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
4052271 TT
64 TT
* *
4052273 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
4052338 T
65 T
* ** * * * *
4052339 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
* *
4052404 ACAAA-ACT
57 TCAAAGATT
* * * * * * * * * *
4052412 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * *
4052477 TTGTTTCAAGGGAAACTGTCTCAA--GAGGCAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
*
4052540 ACAAA-ATT
57 TCAAAGATT
* * * * * * *** *
4052548 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
4052612 TATGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTGTTTTAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
4052657 AAAAGCAATC
Statistics
Matches: 300, Mismatches: 60, Indels: 51
0.73 0.15 0.12
Matches are distributed among these distances:
63 20 0.07
64 22 0.07
65 91 0.30
66 4 0.01
67 24 0.08
68 32 0.11
70 2 0.01
71 26 0.09
72 6 0.02
73 68 0.23
74 5 0.02
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:4052390 original size:36 final size:36
Alignment explanation
Indices: 4052338--4052598 Score: 263
Period size: 36 Copynumber: 7.4 Consensus size: 36
4052328 ATTCAAAGAT
* *
4052338 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
4052374 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * *
4052410 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
4052447 TTTGTTTCAAAGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
4052476 TTTGTTTCAAGGGAAACTGTCTCAAGAG-G-CAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
4052510 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
4052546 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
4052583 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
4052599 TGTTTTCAAT
Statistics
Matches: 186, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.01
29 18 0.10
30 1 0.01
31 1 0.01
34 29 0.16
35 1 0.01
36 68 0.37
37 66 0.35
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:4052435 original size:37 final size:36
Alignment explanation
Indices: 4052350--4052461 Score: 127
Period size: 37 Copynumber: 3.1 Consensus size: 36
4052340 TGTTTCAAGG
* * * * *
4052350 GAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
4052386 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
* * * *
4052423 GAAACTGTCTCAAGGGAGACGAAATTTGTTTC-AAA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
4052458 GAAA
1 GAAA
4052462 ACATATTCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
35 7 0.11
36 28 0.42
37 31 0.47
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:4052564 original size:37 final size:36
Alignment explanation
Indices: 4052480--4052598 Score: 188
Period size: 37 Copynumber: 3.3 Consensus size: 36
4052470 AAATATTTTG
4052480 TTTCAAGGGAAACTGTCTCAAGAG-G-CAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
*
4052514 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTA
* *
4052551 TTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
4052587 TTTCAAGGGAAA
1 TTTCAAGGGAAA
4052599 TGTTTTCAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
34 24 0.31
35 1 0.01
36 20 0.26
37 33 0.42
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:4052580 original size:136 final size:137
Alignment explanation
Indices: 4052275--4052646 Score: 469
Period size: 136 Copynumber: 2.7 Consensus size: 137
4052265 GAAGATTTTG
* * * * * *
4052275 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTT
* *
4052340 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
66 TGTTTCAAGGGAAACTGTCTCAAGA-AGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGA
4052405 CAAAACTT
130 CAAAACTT
* * * * * *
4052413 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTT
* *
4052478 TGTTTCAAGGGAAACTGTCTCAAG-AGGCAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGAC
66 TGTTTCAAGGGAAACTGTCTCAAGAAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGAC
*
4052542 AAAATTT
131 AAAACTT
* * * * * * *
4052549 TGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTC-AATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTT
* *
4052613 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA
66 -TGTTTCAAGGGAAACTGTCTCAA-GAAGACAAA
4052647 TTTGTTTTAA
Statistics
Matches: 199, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
135 6 0.03
136 109 0.55
137 1 0.01
138 83 0.42
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (137 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAATATTT
TGTTTCAAGGGAAACTGTCTCAAGAAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGAC
AAAACTT
Found at i:4053046 original size:18 final size:18
Alignment explanation
Indices: 4053019--4053054 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4053009 TGTTGAATCC
* *
4053019 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
4053037 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
4053055 TTGATGTTGA
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:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:4053484 original size:22 final size:22
Alignment explanation
Indices: 4053458--4053512 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4053448 TTGTGTTTGG
4053458 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATAC
* *
4053480 TCAAAGGCTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATAC
4053502 TCAAAGGTTTG
1 TCAAAGGTTTG
4053513 ATGGGATAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATAC
Found at i:4054172 original size:28 final size:26
Alignment explanation
Indices: 4054136--4054235 Score: 105
Period size: 25 Copynumber: 3.7 Consensus size: 26
4054126 GCATGTGCTT
4054136 TTTTGTCCTTTTTTCTTTTTGATTTTTG
1 TTTT-TCCTTTTTTCTTTTTG-TTTTTG
*
4054164 TTCTTTCCTTTTTTCCTTTTGTTTTTG
1 TT-TTTCCTTTTTTCTTTTTGTTTTTG
* *
4054191 TTTCT-CTTTTTTCTTTGTT-TTTTTT
1 TTTTTCCTTTTTTCTTT-TTGTTTTTG
*
4054216 TTTTTGCTTCTTTTCTTTTT
1 TTTTTCCTT-TTTTCTTTTT
4054236 TTCTTCTTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
25 19 0.30
26 9 0.14
27 16 0.25
28 17 0.27
29 2 0.03
ACGTcount: A:0.01, C:0.14, G:0.07, T:0.78
Consensus pattern (26 bp):
TTTTTCCTTTTTTCTTTTTGTTTTTG
Found at i:4054207 original size:23 final size:26
Alignment explanation
Indices: 4054141--4054212 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 26
4054131 TGCTTTTTTG
*
4054141 TCCTTTTTTCTTTTTGATTTTTGTTCTT
1 TCCTTTTTTC-TTTTG-TTTTTGTTCTC
4054169 TCCTTTTTTCCTTTTGTTTTTGTT-TC
1 TCCTTTTTT-CTTTTGTTTTTGTTCTC
4054195 T-CTTTTTTC-TTTGTTTTT
1 TCCTTTTTTCTTTTGTTTTT
4054213 TTTTTTTTGC
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
23 9 0.21
24 1 0.02
25 7 0.17
26 2 0.05
27 8 0.19
28 14 0.33
29 1 0.02
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.76
Consensus pattern (26 bp):
TCCTTTTTTCTTTTGTTTTTGTTCTC
Found at i:4054215 original size:27 final size:25
Alignment explanation
Indices: 4054134--4054237 Score: 88
Period size: 26 Copynumber: 4.0 Consensus size: 25
4054124 TTGCATGTGC
*
4054134 TTTTTTGTC-CTTTTTTCTTTTTGATT
1 TTTTTTTTCTCTTTTTTCTTTTT--TT
* *
4054160 TTTGTTCTTTC-CTTTTTTCCTTTTGT
1 TTT-TT-TTTCTCTTTTTTCTTTTTTT
*
4054186 TTTTGTTTCTCTTTTTTCTTTGTTTT
1 TTTTTTTTCTCTTTTTTCTTT-TTTT
4054212 TTTTTTTT-TGCTTCTTTTCTTTTTTT
1 TTTTTTTTCT-CTT-TTTTCTTTTTTT
4054238 CTTCTTGATT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
24 4 0.06
25 12 0.18
26 24 0.37
27 10 0.15
28 15 0.23
ACGTcount: A:0.01, C:0.13, G:0.07, T:0.79
Consensus pattern (25 bp):
TTTTTTTTCTCTTTTTTCTTTTTTT
Found at i:4054219 original size:19 final size:19
Alignment explanation
Indices: 4054197--4054243 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
4054187 TTTGTTTCTC
4054197 TTTTTTCTT-TGTTT-TTTT
1 TTTTTTCTTCT-TTTCTTTT
4054215 TTTTTTGCTTCTTTTCTTTT
1 TTTTTT-CTTCTTTTCTTTT
*
4054235 TTTCTTCTT
1 TTTTTTCTT
4054244 GATTGGATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.24
19 9 0.36
20 10 0.40
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (19 bp):
TTTTTTCTTCTTTTCTTTT
Found at i:4057266 original size:4 final size:4
Alignment explanation
Indices: 4057242--4057336 Score: 54
Period size: 4 Copynumber: 22.2 Consensus size: 4
4057232 CATGTTAGAT
*
4057242 ATAA AAAA ATAAA ATTAA ATAA ATAAA ATAA ATAA ATAA ATTCAA CCA-AA
1 ATAA ATAA AT-AA A-TAA ATAA AT-AA ATAA ATAA ATAA A-T-AA --ATAA
*
4057292 AT-A A-AA AGAA ATAAA ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA AT-AA AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA A
4057337 GCATATAAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
3 6 0.08
4 42 0.56
5 23 0.31
6 3 0.04
8 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:4057308 original size:5 final size:5
Alignment explanation
Indices: 4057247--4057320 Score: 66
Period size: 5 Copynumber: 15.4 Consensus size: 5
4057237 TAGATATAAA
* * * **
4057247 AAAAT AAAAT TAAAT -AAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
4057294 AAAA- AGAAAT AAAAT AAAAT AAAAT AA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AA
4057321 TAAATAAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
4 13 0.23
5 43 0.75
6 1 0.02
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:4059453 original size:497 final size:496
Alignment explanation
Indices: 4058795--4059788 Score: 1915
Period size: 492 Copynumber: 2.0 Consensus size: 496
4058785 ATACAATGAG
4058795 ATTATTTTTATGTTTTTTGTTTTTATATATTTCTATCAGTTTGAATTAAGTTGAACTTAGAACCA
1 ATTATTTTTATGTTTTTTGTTTTTATATATTTCTATCAGTTTGAATTAAGTTGAACTTAGAACCA
4058860 TTTAGAATCTATGTAAATATAATTAAATAAATTCAGATTTTAAAATAAATTTATTTTAAGTTTTA
66 TTTAGAATCTATGTAAATATAATTAAATAAATTCAGATTTTAAAATAAATTTATTTTAAGTTTTA
4058925 ATTTAAAAATAATTAAATTTTTAATTTTAAAAAGAGGGATGAACTATCTAAGGGTAAACTATATA
131 ATTTAAAAATAATTAAATTTTTAATTTTAAAAAGAGGGATGAACTATCTAAGGGTAAAC---ATA
4058990 TTTAGTGCCTAAACTATTACTTTTTTATGTTTTGGTACCTAAATCTTATTTTGTTACAAAACATA
193 -TTAGTGCCTAAACTATTAC-TTTTTATGTTTTGGTACCTAAATCTTATTTTGTTACAAAACATA
4059055 CCTAACGTTTAATTTAAGTTTCATTTTGGTACATCGCCTTTAAAAACTTAACGGTGATATTGATG
256 CCTAACGTTTAATTTAAGTTTCATTTTGGTACATCGCCTTTAAAAACTTAACGGTGATATTGATG
4059120 TGTCACCCACCATAAGGTAATGAGACAACACCATTGGAAAAAAATAGAAAAATTTCATATCAACA
321 TGTCACCCACCATAAGGTAATGAGACAACACCATTGGAAAAAAATAGAAAAATTTCATATCAACA
4059185 ATCTGTTAATTTTTTAACGACATGTACCAAATTAAAACTTAAACT-AATATTAGGTATGGTTTTG
386 ATCTGTTAATTTTTTAACGACATGTACCAAATTAAAACTTAAACTAAATATTAGGTATGGTTTTG
4059249 -AAAAATAT-AAATTTAGGTAAAAAACAAAAC-AAAGTAATAGTTT
451 AAAAAATATAAAATTTAGGTAAAAAACAAAACAAAAGTAATAGTTT
4059292 ATTATTTTTATGTTTTTTGTTTTTATATATTTCTATCAGTTTGAATTAAGTTGAACTTAGAACCA
1 ATTATTTTTATGTTTTTTGTTTTTATATATTTCTATCAGTTTGAATTAAGTTGAACTTAGAACCA
4059357 TTTAGAATCTATGTAAATATAATTAAATAAATTCAGATTTTAAAATAAATTTATTTTAAGTTTTA
66 TTTAGAATCTATGTAAATATAATTAAATAAATTCAGATTTTAAAATAAATTTATTTTAAGTTTTA
4059422 ATTTAAAAATAATTAAATTTTTAATTTTAAAAAGAGGGATGAACTATCTAAGGGTAAACATATTA
131 ATTTAAAAATAATTAAATTTTTAATTTTAAAAAGAGGGATGAACTATCTAAGGGTAAACATATTA
4059487 GTGCCTAAACTATTACTTTTTATGTTTTGGTACCTAAATCTTATTTTGTTACAAAACATACCTAA
196 GTGCCTAAACTATTACTTTTTATGTTTTGGTACCTAAATCTTATTTTGTTACAAAACATACCTAA
4059552 CGTTTAATTTAAGTTTCATTTTGGTACATCGCCTTTAAAAACTTAACGGTGATATTGATGTGTCA
261 CGTTTAATTTAAGTTTCATTTTGGTACATCGCCTTTAAAAACTTAACGGTGATATTGATGTGTCA
4059617 CCCACCATAAGGTAATGAGACAACACCATTGGAAAAAAATAGAAAAATTTCATATCAACAATCTG
326 CCCACCATAAGGTAATGAGACAACACCATTGGAAAAAAATAGAAAAATTTCATATCAACAATCTG
4059682 TTAATTTTTTAACGACATGTACCAAATTAAAACTTAAACTAAATATTAGGTATGGTTTTGAAAAA
391 TTAATTTTTTAACGACATGTACCAAATTAAAACTTAAACTAAATATTAGGTATGGTTTTGAAAAA
4059747 ATATAAAATTTAGGTAAAAAACAAAACAAAAGTAATAGTTT
456 ATATAAAATTTAGGTAAAAAACAAAACAAAAGTAATAGTTT
4059788 A
1 A
4059789 AGTACTAAAT
Statistics
Matches: 493, Mismatches: 0, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
492 219 0.44
493 38 0.08
494 11 0.02
495 22 0.04
496 14 0.03
497 189 0.38
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (496 bp):
ATTATTTTTATGTTTTTTGTTTTTATATATTTCTATCAGTTTGAATTAAGTTGAACTTAGAACCA
TTTAGAATCTATGTAAATATAATTAAATAAATTCAGATTTTAAAATAAATTTATTTTAAGTTTTA
ATTTAAAAATAATTAAATTTTTAATTTTAAAAAGAGGGATGAACTATCTAAGGGTAAACATATTA
GTGCCTAAACTATTACTTTTTATGTTTTGGTACCTAAATCTTATTTTGTTACAAAACATACCTAA
CGTTTAATTTAAGTTTCATTTTGGTACATCGCCTTTAAAAACTTAACGGTGATATTGATGTGTCA
CCCACCATAAGGTAATGAGACAACACCATTGGAAAAAAATAGAAAAATTTCATATCAACAATCTG
TTAATTTTTTAACGACATGTACCAAATTAAAACTTAAACTAAATATTAGGTATGGTTTTGAAAAA
ATATAAAATTTAGGTAAAAAACAAAACAAAAGTAATAGTTT
Found at i:4061643 original size:105 final size:105
Alignment explanation
Indices: 4061387--4061634 Score: 381
Period size: 105 Copynumber: 2.4 Consensus size: 105
4061377 AGATACCATT
* * * *
4061387 GACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCGCATATAATACATTGGTTGATGCTTA
1 GACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCACATATAGTACATTGGTTGATACCTA
4061452 TTGCAAGGAGGGAATGGTTTCTAAAGCTGAAGATATTGTC
66 TTGCAAGGAGGGAATGGTTTCTAAAGCTGAAGATATTGTC
* * * *
4061492 GACTCCATGAGAAAGCAAGGCATTGAACCTAATGTTGTCACATATAGTATATTGGTTGATACCTA
1 GACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCACATATAGTACATTGGTTGATACCTA
*
4061557 TTGCAAGGAGGGAATGGTTTGC-AAAGCTGAAGGTATTGTC
66 TTGCAAGGAGGGAATGGTTT-CTAAAGCTGAAGATATTGTC
* *
4061597 GACACAATGAGAAAGCAAGGCATTGAGCTTGATGTTGT
1 GACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGT
4061635 TTCCTATAGC
Statistics
Matches: 128, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
105 127 0.99
106 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (105 bp):
GACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCACATATAGTACATTGGTTGATACCTA
TTGCAAGGAGGGAATGGTTTCTAAAGCTGAAGATATTGTC
Found at i:4063382 original size:24 final size:24
Alignment explanation
Indices: 4063355--4063402 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4063345 AAACGTAGAT
*
4063355 ATCAGAAATCAAAACTGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
4063379 ATCAGATATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
4063403 GTAATGTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:4065512 original size:43 final size:43
Alignment explanation
Indices: 4065451--4065536 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
4065441 AAGCATAAAG
4065451 AGGTAGTAAAGTATTACTTCGATTTCCGTGCAATACTGATCAA
1 AGGTAGTAAAGTATTACTTCGATTTCCGTGCAATACTGATCAA
4065494 AGGTAGTAAAGTATTACTTCGATTTCCGTGCAATACTGATCAA
1 AGGTAGTAAAGTATTACTTCGATTTCCGTGCAATACTGATCAA
4065537 CCATTAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (43 bp):
AGGTAGTAAAGTATTACTTCGATTTCCGTGCAATACTGATCAA
Found at i:4067141 original size:26 final size:26
Alignment explanation
Indices: 4067112--4067162 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
4067102 ACCGGTCATA
4067112 ACCCGACCCGTTGA-TCCGACCTGTTT
1 ACCCGACCCGTTGACT-CGACCTGTTT
4067138 ACCCGACCCGTTGACTCGACCTGTT
1 ACCCGACCCGTTGACTCGACCTGTT
4067163 GACTCGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.16, C:0.39, G:0.20, T:0.25
Consensus pattern (26 bp):
ACCCGACCCGTTGACTCGACCTGTTT
Found at i:4067166 original size:13 final size:13
Alignment explanation
Indices: 4067115--4067168 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
4067105 GGTCATAACC
4067115 CGACCCGTTGA-T
1 CGACCCGTTGACT
* * *
4067127 CCGACCTGTTTACC
1 -CGACCCGTTGACT
4067141 CGACCCGTTGACT
1 CGACCCGTTGACT
*
4067154 CGACCTGTTGACT
1 CGACCCGTTGACT
4067167 CG
1 CG
4067169 TTGACTGTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.15, C:0.37, G:0.22, T:0.26
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:4068490 original size:18 final size:18
Alignment explanation
Indices: 4068464--4068499 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4068454 TCGAAAGGAC
*
4068464 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
4068482 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
4068500 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:4069113 original size:18 final size:18
Alignment explanation
Indices: 4069087--4069122 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4069077 TCGAAAGGAC
*
4069087 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
4069105 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
4069123 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:4070200 original size:24 final size:23
Alignment explanation
Indices: 4070173--4070228 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
4070163 AATTATTTTA
* *
4070173 TCTGATTTTCGACTTGAATTCTGT
1 TCTGATTTT-GACCTGAATTATGT
**
4070197 TCTGATACATGACCTGAATTATGT
1 TCTGAT-TTTGACCTGAATTATGT
4070221 TCTGATTT
1 TCTGATTT
4070229 CTTATATGGA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (23 bp):
TCTGATTTTGACCTGAATTATGT
Found at i:4070242 original size:48 final size:48
Alignment explanation
Indices: 4070190--4070283 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
4070180 TTCGACTTGA
* *
4070190 ATTCTGTTCTGATA-CATGACCTGAATTATGTTCTGATTTCTTATATGG
1 ATTCTGTTCTAATATC-TGACCTGAATTATGTTCTGATTTCTGATATGG
** * *
4070238 ATTCTGTTCTAATATCTGTTCTGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTAATATCTGACCTGAATTATGTTCTGATTTCTGATAT
4070284 CTCCGTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (48 bp):
ATTCTGTTCTAATATCTGACCTGAATTATGTTCTGATTTCTGATATGG
Found at i:4070245 original size:24 final size:24
Alignment explanation
Indices: 4070211--4070283 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
4070201 ATACATGACC
*
4070211 TGAATTATGTTCTGATTTCTTATA
1 TGAATTCTGTTCTGATTTCTTATA
* * * *
4070235 TGGATTCTGTTCTAATATCTGT-TC
1 TGAATTCTGTTCTGATTTCT-TATA
* *
4070259 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTTATA
4070283 T
1 T
4070284 CTCCGTTTAA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTTATA
Found at i:4070255 original size:12 final size:12
Alignment explanation
Indices: 4070238--4070279 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
4070228 TCTTATATGG
4070238 ATTCTGTTCT-A
1 ATTCTGTTCTGA
4070249 ATATCTGTTCTGA
1 AT-TCTGTTCTGA
*
4070262 ATTCTGTTTTGA
1 ATTCTGTTCTGA
*
4070274 TTTCTG
1 ATTCTG
4070280 ATATCTCCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 2 0.07
12 22 0.81
13 3 0.11
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (12 bp):
ATTCTGTTCTGA
Found at i:4072980 original size:10 final size:10
Alignment explanation
Indices: 4072965--4073028 Score: 74
Period size: 10 Copynumber: 6.1 Consensus size: 10
4072955 CATTTAAATG
4072965 ATAAACGAAC
1 ATAAACGAAC
4072975 ATAAACGAAC
1 ATAAACGAAC
*
4072985 GTAAACGAAC
1 ATAAACGAAC
*
4072995 ATAAACAAACAC
1 ATAAAC-GA-AC
4073007 AATAAACGAAC
1 -ATAAACGAAC
*
4073018 ATAAATGAAC
1 ATAAACGAAC
4073028 A
1 A
4073029 ACACAAACAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
10 34 0.74
11 3 0.07
12 3 0.07
13 6 0.13
ACGTcount: A:0.61, C:0.19, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:4073013 original size:33 final size:32
Alignment explanation
Indices: 4072975--4073039 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
4072965 ATAAACGAAC
*
4072975 ATAAACGAACGTAAACGAACATAAACAAACACA
1 ATAAACGAACATAAACGAACA-AAACAAACACA
* *
4073008 ATAAACGAACATAAATGAACAACACAAACACA
1 ATAAACGAACATAAACGAACAAAACAAACACA
4073040 CACAAAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 10 0.34
33 19 0.66
ACGTcount: A:0.62, C:0.22, G:0.08, T:0.09
Consensus pattern (32 bp):
ATAAACGAACATAAACGAACAAAACAAACACA
Found at i:4073298 original size:14 final size:14
Alignment explanation
Indices: 4073276--4073335 Score: 84
Period size: 14 Copynumber: 4.1 Consensus size: 14
4073266 GCCCTCTGTT
*
4073276 CGAATATAAATGAA
1 CGAACATAAATGAA
*
4073290 CGAACATAAATAAA
1 CGAACATAAATGAA
4073304 CGAACATAAATGAA
1 CGAACATAAATGAA
4073318 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
4073334 CG
1 CG
4073336 TTCATGAACG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
14 33 0.80
15 3 0.07
16 5 0.12
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.17
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:4086571 original size:33 final size:33
Alignment explanation
Indices: 4086528--4086590 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
4086518 AGAACAAATT
* *
4086528 ATGATTGCATAAACATAACCAAATATTATAGCA
1 ATGATGGCATAAACACAACCAAATATTATAGCA
*
4086561 ATGATGGCATAAACACAACCAATTATTATA
1 ATGATGGCATAAACACAACCAAATATTATA
4086591 CCAAATTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.27
Consensus pattern (33 bp):
ATGATGGCATAAACACAACCAAATATTATAGCA
Found at i:4087554 original size:14 final size:14
Alignment explanation
Indices: 4087532--4087566 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
4087522 TTAAGTGACA
4087532 AGAATGCTGATTGC
1 AGAATGCTGATTGC
*
4087546 AGCATGCTGATTGC
1 AGAATGCTGATTGC
4087560 AGAATGC
1 AGAATGC
4087567 AATTTGTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (14 bp):
AGAATGCTGATTGC
Found at i:4090473 original size:18 final size:17
Alignment explanation
Indices: 4090434--4090468 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4090424 CCCTTTAAAA
4090434 ATTTTAAATTTTCTTAT
1 ATTTTAAATTTTCTTAT
4090451 ATTTTAAATTTT-TTAT
1 ATTTTAAATTTTCTTAT
4090467 AT
1 AT
4090469 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTAAATTTTCTTAT
Found at i:4090530 original size:24 final size:24
Alignment explanation
Indices: 4090487--4090538 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4090477 ATTAATTATC
*
4090487 TAATTTTACACCCCTAAAAT-TTT
1 TAATTTCACACCCCTAAAATCTTT
4090510 ATAATTTCACACCCTCT-AAATCTTT
1 -TAATTTCACACCC-CTAAAATCTTT
4090535 TAAT
1 TAAT
4090539 ATAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATTTCACACCCCTAAAATCTTT
Found at i:4090765 original size:28 final size:28
Alignment explanation
Indices: 4090734--4090830 Score: 113
Period size: 31 Copynumber: 3.3 Consensus size: 28
4090724 TATTTTATTC
*
4090734 AATATAAACATCACATTTAATATTTTAA
1 AATATAAATATCACATTTAATATTTTAA
* *
4090762 AATAGAAATATCACATTAAATATCTTAATAA
1 AATATAAATATCACATTTAATAT-TT--TAA
* *
4090793 AATATAAATATCATATTTAACATTTTAAA
1 AATATAAATATCACATTTAATATTTT-AA
4090822 AATATAAAT
1 AATATAAAT
4090831 TTCTTATTGG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
28 21 0.36
29 13 0.22
30 2 0.03
31 22 0.38
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37
Consensus pattern (28 bp):
AATATAAATATCACATTTAATATTTTAA
Found at i:4093919 original size:14 final size:14
Alignment explanation
Indices: 4093900--4093933 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
4093890 CCAAACACAT
4093900 GCCCAA-CAGAACCG
1 GCCCAATCAG-ACCG
4093914 GCCCAATCAGACCG
1 GCCCAATCAGACCG
4093928 GCCCAA
1 GCCCAA
4093934 ACCCAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.32, C:0.44, G:0.21, T:0.03
Consensus pattern (14 bp):
GCCCAATCAGACCG
Found at i:4095219 original size:2 final size:2
Alignment explanation
Indices: 4095212--4095259 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
4095202 TTTAATTTAG
* *
4095212 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA GT- TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
4095253 TA TA TA T
1 TA TA TA T
4095260 TTTAGGATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.93
3 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (2 bp):
TA
Found at i:4101253 original size:8 final size:8
Alignment explanation
Indices: 4101234--4101262 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4101224 CTCATTTATA
4101234 AAAAAAGG
1 AAAAAAGG
4101242 -AAAAAGG
1 AAAAAAGG
4101249 AAAAAAGG
1 AAAAAAGG
4101257 AAAAAA
1 AAAAAA
4101263 AATTGAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:4106560 original size:45 final size:45
Alignment explanation
Indices: 4106506--4106619 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 45
4106496 GGGAGTTTTT
* * * ** * * *
4106506 TGATATTTTCAAAACCTTTGTGTCATCTGTAAGCCCTTCAGTTCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
4106551 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
*
4106596 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
4106620 AGCTTTTTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 46 0.79
46 4 0.07
47 8 0.14
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
Found at i:4106637 original size:76 final size:76
Alignment explanation
Indices: 4106557--4106769 Score: 331
Period size: 76 Copynumber: 2.8 Consensus size: 76
4106547 TTCATGATGT
4106557 TTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAG
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAG
4106622 CTTTTTGATAC
66 CTTTTTGATAC
* * *
4106633 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAGGATATTTTCAAAAAGCCTTCGGGAG
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAG
*
4106698 CTTTTTGATAT
66 CTTTTTGATAC
** * * *
4106709 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
4106770 TCATCTATAA
Statistics
Matches: 126, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
74 8 0.06
75 4 0.03
76 114 0.90
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (76 bp):
TTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAG
CTTTTTGATAC
Found at i:4106681 original size:121 final size:123
Alignment explanation
Indices: 4106453--4106695 Score: 346
Period size: 121 Copynumber: 2.0 Consensus size: 123
4106443 CTATTTCCAA
* * *
4106453 CATCCATAAGACCTGCAGTGCAGAATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATATTTTCAA
1 CATCCATAAGACCTACAGTGCAGAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTCAA
* * ** * * * * * *
4106518 AACCTTTGTGTCATCTGTAAGCCCTTCAGTTCATGATGTTTTC-AAAA-CCTTCGGGT
66 AACCTTCGGGTCATCCATAAGACCTGCAATGCAGGATATTTTCAAAAAGCCTTCGGGT
*
4106574 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTCAA
1 CATCCATAAGACCTACAGTGCAGAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTCAA
4106639 AACCTTCGGGTCATCCATAAGACCTGCAATGCAGGATATTTTCAAAAAGCCTTCGGG
66 AACCTTCGGGTCATCCATAAGACCTGCAATGCAGGATATTTTCAAAAAGCCTTCGGG
4106696 AGCTTTTTGA
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
121 94 0.89
122 4 0.04
123 8 0.08
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (123 bp):
CATCCATAAGACCTACAGTGCAGAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATACTTTCAA
AACCTTCGGGTCATCCATAAGACCTGCAATGCAGGATATTTTCAAAAAGCCTTCGGGT
Found at i:4106757 original size:45 final size:45
Alignment explanation
Indices: 4106703--4106797 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
4106693 GGGAGCTTTT
* * * *
4106703 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
4106748 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
*
4106793 AGATG
1 TGATG
4106798 ATAGGACCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
Found at i:4107005 original size:37 final size:38
Alignment explanation
Indices: 4106957--4107028 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 38
4106947 TTTCGTTTTT
* *
4106957 TTATTATTATTAAATTAAT-AATAATAATAATAATATA
1 TTATTATTATTAAATAAATAAATAATAACAATAATATA
*
4106994 TTATTATTATTAAATAAATAAATAATTACAATAAT
1 TTATTATTATTAAATAAATAAATAATAACAATAAT
4107029 CTCAGAACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 18 0.58
38 13 0.42
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (38 bp):
TTATTATTATTAAATAAATAAATAATAACAATAATATA
Found at i:4107077 original size:14 final size:15
Alignment explanation
Indices: 4107058--4107091 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
4107048 CCAAACATAA
4107058 GCCCAA-CAGAACCG
1 GCCCAATCAGAACCG
4107072 GCCCAATCAGAACCG
1 GCCCAATCAGAACCG
4107087 GCCCA
1 GCCCA
4107092 GACCTAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.32, C:0.44, G:0.21, T:0.03
Consensus pattern (15 bp):
GCCCAATCAGAACCG
Found at i:4108760 original size:65 final size:63
Alignment explanation
Indices: 4108689--4108848 Score: 223
Period size: 65 Copynumber: 2.5 Consensus size: 63
4108679 AATTAAATTG
* *
4108689 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
4108753 A
63 A
* * *
4108754 AACATCGAATGCATTTGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
*
4108818 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
4108849 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
63 1 0.01
64 30 0.34
65 51 0.59
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:4108848 original size:17 final size:19
Alignment explanation
Indices: 4108820--4108868 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4108810 TATTTTGAAA
4108820 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
4108838 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
4108857 CACCGATGCACT
1 CATCGATGCACT
4108869 AAAGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:4115097 original size:19 final size:20
Alignment explanation
Indices: 4115073--4115110 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
4115063 TAAATTAAAT
4115073 ATTAGATAG-ATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
4115092 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
4115111 TTATTCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:4115121 original size:26 final size:26
Alignment explanation
Indices: 4115092--4115179 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 26
4115082 ATCAGTTTTA
4115092 ATTAGATAGAATCAGTTTTTTATTCT
1 ATTAGATAGAATCAGTTTTTTATTCT
* * ** *
4115118 ATTAGTTATTAAT-AGGATCATTT-TT-A
1 ATTAGATA-GAATCA-G-TTTTTTATTCT
4115144 ATTAGATAGAATCAGTTTTTTATTCT
1 ATTAGATAGAATCAGTTTTTTATTCT
*
4115170 ATTAGTTAGA
1 ATTAGATAGA
4115180 TAGGATCATT
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
24 4 0.09
25 6 0.13
26 25 0.56
27 6 0.13
28 4 0.09
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (26 bp):
ATTAGATAGAATCAGTTTTTTATTCT
Found at i:4115150 original size:52 final size:52
Alignment explanation
Indices: 4115072--4115199 Score: 208
Period size: 52 Copynumber: 2.5 Consensus size: 52
4115062 CTAAATTAAA
*
4115072 TATTAGATA-GATCAGTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTA-ATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
4115124 TATTAATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
*
4115176 TA--GATAGGATCATTTTTAATTAGA
1 TATTAATAGGATCATTTTTAATTAGA
4115200 ATCATTTTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
50 21 0.29
51 3 0.04
52 49 0.67
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
Found at i:4115157 original size:20 final size:20
Alignment explanation
Indices: 4115125--4115163 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4115115 TCTATTAGTT
*
4115125 ATTAATAGGATCA-TTTTTA
1 ATTAATAGAATCAGTTTTTA
4115144 ATTAGATAGAATCAGTTTTT
1 ATTA-ATAGAATCAGTTTTT
4115164 TATTCTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTAATAGAATCAGTTTTTA
Found at i:4117880 original size:98 final size:96
Alignment explanation
Indices: 4117705--4117900 Score: 365
Period size: 98 Copynumber: 2.0 Consensus size: 96
4117695 CCGGGGGAGA
4117705 ATGACTCGAAATGAGTTTTTGGGAACAAACTCCTTGCCAAAATCGGTTGTAAATAGCTCAGTGGA
1 ATGACTCGAAATGAGTTTTTGGGAACAAACTCCTTGCCAAAATCGGTTGTAAATAGCTCAGTGGA
4117770 ACCAATTCATATTTCCGTAACTAATCCTAGG
66 ACCAATTCATATTTCCGTAACTAATCCTAGG
*
4117801 ATGACTCTGAAATGATTTTTTGGGAACAAACATCCTTGCCAAAATCGGTTGTAAATAGCTCAGTG
1 ATGACTC-GAAATGAGTTTTTGGGAACAAAC-TCCTTGCCAAAATCGGTTGTAAATAGCTCAGTG
4117866 GAACCAATTCATATTTCCGTAACTAATCCTAGG
64 GAACCAATTCATATTTCCGTAACTAATCCTAGG
4117899 AT
1 AT
4117901 TTCACAACCT
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
96 7 0.07
97 22 0.23
98 68 0.70
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (96 bp):
ATGACTCGAAATGAGTTTTTGGGAACAAACTCCTTGCCAAAATCGGTTGTAAATAGCTCAGTGGA
ACCAATTCATATTTCCGTAACTAATCCTAGG
Found at i:4132488 original size:19 final size:18
Alignment explanation
Indices: 4132464--4132583 Score: 80
Period size: 17 Copynumber: 7.1 Consensus size: 18
4132454 ATTTTGCTTG
4132464 AAGAAGAAATAAAAGAGAA
1 AAGAAGAAA-AAAAGAGAA
*
4132483 AAGAAGAAAAAATGAGAA
1 AAGAAGAAAAAAAGAGAA
*
4132501 AA-AAGAAAAAATGATGAA
1 AAGAAGAAAAAAAGA-GAA
**
4132519 AA-AA-AAACGAA-A-AA
1 AAGAAGAAAAAAAGAGAA
*
4132533 AAG-AGAAAAAATG-GAA
1 AAGAAGAAAAAAAGAGAA
*
4132549 AA-AGGAAGAAAAAGAGAA
1 AAGAAGAA-AAAAAGAGAA
*
4132567 AA-ATGAAAAAAA-AGAA
1 AAGAAGAAAAAAAGAGAA
4132583 A
1 A
4132584 TAAAAGGAGG
Statistics
Matches: 83, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
14 5 0.06
15 4 0.05
16 13 0.16
17 26 0.31
18 26 0.31
19 9 0.11
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.05
Consensus pattern (18 bp):
AAGAAGAAAAAAAGAGAA
Found at i:4132521 original size:18 final size:17
Alignment explanation
Indices: 4132467--4132583 Score: 92
Period size: 18 Copynumber: 6.4 Consensus size: 17
4132457 TTGCTTGAAG
*
4132467 AAGAAATAAAAGAGAAAA
1 AAGAAA-AAATGAGAAAA
4132485 GAAGAAAAAATGAGAAAA
1 -AAGAAAAAATGAGAAAA
4132503 AAGAAAAAATGATGAAAAAAA
1 AAGAAAAAATGA-G---AAAA
*
4132524 AACGAAAAAAAGAGAAAA
1 AA-GAAAAAATGAGAAAA
* *
4132542 AATGGAAAAAGGA-AGAAA
1 AA-GAAAAAATGAGA-AAA
*
4132560 AAGAGAAAAATGAAAAAA
1 AAGA-AAAAATGAGAAAA
4132578 AAGAAA
1 AAGAAA
4132584 TAAAAGGAGG
Statistics
Matches: 83, Mismatches: 7, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
17 16 0.19
18 44 0.53
19 7 0.08
21 7 0.08
22 9 0.11
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.05
Consensus pattern (17 bp):
AAGAAAAAATGAGAAAA
Found at i:4132525 original size:21 final size:21
Alignment explanation
Indices: 4132499--4132543 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
4132489 AAAAAATGAG
*
4132499 AAAAAA-GAAAAAATGATGAAA
1 AAAAAACGAAAAAAAGA-GAAA
4132520 AAAAAACGAAAAAAAGAGAAA
1 AAAAAACGAAAAAAAGAGAAA
4132541 AAA
1 AAA
4132544 TGGAAAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAAACGAAAAAAAGAGAAA
Found at i:4132579 original size:58 final size:58
Alignment explanation
Indices: 4132469--4132579 Score: 138
Period size: 57 Copynumber: 1.9 Consensus size: 58
4132459 GCTTGAAGAA
* **
4132469 GAAATAAAAGAGAAAAGAAGAAAAAATGAGAAAAAAGAAAAAATGATGAAAAAAAAAC
1 GAAATAAAAGAGAAAAGAAGAAAAAAGGAGAAAAAAGAAAAAATGAAAAAAAAAAAAC
*
4132527 GAAA-AAAAGAGAAAA-AATGGAAAAAGGA-AGAAAAAGAGAAAAATGAAAAAAAA
1 GAAATAAAAGAGAAAAGAA-GAAAAAAGGAGA-AAAAAGA-AAAAATGAAAAAAAA
4132580 GAAATAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
56 3 0.07
57 26 0.57
58 17 0.37
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.05
Consensus pattern (58 bp):
GAAATAAAAGAGAAAAGAAGAAAAAAGGAGAAAAAAGAAAAAATGAAAAAAAAAAAAC
Found at i:4132583 original size:9 final size:9
Alignment explanation
Indices: 4132467--4132589 Score: 63
Period size: 9 Copynumber: 13.3 Consensus size: 9
4132457 TTGCTTGAAG
*
4132467 AAGAAATAA
1 AAGAAAAAA
*
4132476 AAGAGAAAAG
1 AAGA-AAAAA
4132486 AAG-AAAAA
1 AAGAAAAAA
* *
4132494 ATGAGAAAA
1 AAGAAAAAA
4132503 AAGAAAAAA
1 AAGAAAAAA
*
4132512 TGATGAAAAAA
1 --AAGAAAAAA
4132523 AA-ACGAAAAA
1 AAGA--AAAAA
4132533 AAGAGAAAAA
1 AAGA-AAAAA
* *
4132543 ATG-GAAAA
1 AAGAAAAAA
* *
4132551 AGGAAGAAA
1 AAGAAAAAA
*
4132560 AAGAGAAAA
1 AAGAAAAAA
*
4132569 ATGAAAAAA
1 AAGAAAAAA
*
4132578 AAGAAATAA
1 AAGAAAAAA
4132587 AAG
1 AAG
4132590 GAGGGTTCAA
Statistics
Matches: 85, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
8 13 0.15
9 42 0.49
10 21 0.25
11 9 0.11
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.06
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:4133967 original size:51 final size:51
Alignment explanation
Indices: 4133902--4134317 Score: 537
Period size: 51 Copynumber: 8.0 Consensus size: 51
4133892 GAAGCAAATT
* *
4133902 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
4133953 AGTTCGTTAAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
4134004 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
*
4134055 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
4134106 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * *
4134157 CGTTTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACA
1 AG-TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACA
* * * * *
4134213 CGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* ** * *
4134264 TGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
4134318 CCGTTTTATT
Statistics
Matches: 327, Mismatches: 27, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
50 1 0.00
51 236 0.72
52 12 0.04
54 2 0.01
55 44 0.13
56 30 0.09
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (51 bp):
AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Done.