Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 15 of 210
Found at i:5129121 original size:24 final size:22
Alignment explanation
Indices: 5129071--5129121 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
5129061 ATATGCATGC
5129071 ATACA-TTTTTATAATATACGT
1 ATACATTTTTTATAATATACGT
* *
5129092 ACACATTTTTTATAATTTATATGT
1 ATACATTTTTTATAA--TATACGT
5129116 ATACAT
1 ATACAT
5129122 AGTTATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 9 0.38
24 11 0.46
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (22 bp):
ATACATTTTTTATAATATACGT
Found at i:5130185 original size:23 final size:25
Alignment explanation
Indices: 5130151--5130205 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
5130141 GATGTTTTTA
5130151 TATATATATTTTT-GGTGAAAATGTT
1 TATATAT-TTTTTAGGTGAAAATGTT
* * *
5130176 TATATCTTTTTTAGGTGAAATTTTT
1 TATATATTTTTTAGGTGAAAATGTT
5130201 TATAT
1 TATAT
5130206 GATGAACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (25 bp):
TATATATTTTTTAGGTGAAAATGTT
Found at i:5134282 original size:106 final size:106
Alignment explanation
Indices: 5134142--5134378 Score: 399
Period size: 106 Copynumber: 2.2 Consensus size: 106
5134132 GTTATTTTGT
5134142 ATTATTTTGATTTTTTTTTATAAAATTGAATGGAAATAAAATCCGACATCAAAGGTAATCGAACT
1 ATTATTTTGA--TTTTTTTATAAAATTGAATGGAAATAAAATCCGACATCAAAGGTAATCGAACT
*
5134207 AAATTTAAATGGTTTGAATTCAATTCATAGAT-TCTTAAAAAAA
64 AAATTTAAATGGTTTGAATTCAATTCACAGATAT-TTAAAAAAA
5134250 ATTATTTTGATTTTTTTATAAAATTGAATGGAAATAAAATCCGACATCAAAGGTAATCGAACTAA
1 ATTATTTTGATTTTTTTATAAAATTGAATGGAAATAAAATCCGACATCAAAGGTAATCGAACTAA
5134315 ATTTAAATGGTTTGAATTCAATTCACAGATATTTAAAAAAA
66 ATTTAAATGGTTTGAATTCAATTCACAGATATTTAAAAAAA
* *
5134356 ATTATTAT-ATTTTGTTA-AAAATT
1 ATTATTTTGATTTTTTTATAAAATT
5134379 ATTTTCACTA
Statistics
Matches: 125, Mismatches: 3, Indels: 6
0.93 0.02 0.04
Matches are distributed among these distances:
104 6 0.05
105 8 0.06
106 100 0.80
107 1 0.01
108 10 0.08
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.39
Consensus pattern (106 bp):
ATTATTTTGATTTTTTTATAAAATTGAATGGAAATAAAATCCGACATCAAAGGTAATCGAACTAA
ATTTAAATGGTTTGAATTCAATTCACAGATATTTAAAAAAA
Found at i:5137703 original size:18 final size:18
Alignment explanation
Indices: 5137681--5137814 Score: 114
Period size: 17 Copynumber: 7.7 Consensus size: 18
5137671 TGAAATTCGA
5137681 AAAATTTTTGAAAACACG
1 AAAATTTTTGAAAACACG
* * * *
5137699 GAAATCTTTG-CAATACG
1 AAAATTTTTGAAAACACG
* * *
5137716 AGAA-TTTTAAAAACATG
1 AAAATTTTTGAAAACACG
* *
5137733 AAAATTTCT-AAAACATG
1 AAAATTTTTGAAAACACG
5137750 AAAATTTTTGAAAACACG
1 AAAATTTTTGAAAACACG
* *
5137768 AGATTTTTTG-AAACACG
1 AAAATTTTTGAAAACACG
* * *
5137785 AAAATATTTGGAAATACG
1 AAAATTTTTGAAAACACG
5137803 AAAATTTTTGAA
1 AAAATTTTTGAA
5137815 GCACGAAGTT
Statistics
Matches: 89, Mismatches: 23, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
16 3 0.03
17 44 0.49
18 42 0.47
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.31
Consensus pattern (18 bp):
AAAATTTTTGAAAACACG
Found at i:5137782 original size:35 final size:35
Alignment explanation
Indices: 5137681--5137821 Score: 122
Period size: 35 Copynumber: 4.1 Consensus size: 35
5137671 TGAAATTCGA
* * * * *
5137681 AAAATTTTTGAAAACACGGAAATCTTTGCAATACG
1 AAAATATTTGAAAACACGAAAATTTTTGAAACACG
* * * * * *
5137716 AGAAT-TTTAAAAACATGAAAATTTCTAAAACATG
1 AAAATATTTGAAAACACGAAAATTTTTGAAACACG
* * *
5137750 AAAATTTTTGAAAACACGAGATTTTTTGAAACACG
1 AAAATATTTGAAAACACGAAAATTTTTGAAACACG
* * *
5137785 AAAATATTTGGAAATACGAAAATTTTTGAAGCACG
1 AAAATATTTGAAAACACGAAAATTTTTGAAACACG
5137820 AA
1 AA
5137822 GTTTTTTTTA
Statistics
Matches: 81, Mismatches: 24, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
34 24 0.30
35 57 0.70
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (35 bp):
AAAATATTTGAAAACACGAAAATTTTTGAAACACG
Found at i:5137892 original size:17 final size:17
Alignment explanation
Indices: 5137869--5137917 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
5137859 TTATTATTAT
5137869 TTTTTGAAACACGAGAAA
1 TTTTTGAAACACGA-AAA
*
5137887 -TTTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
*
5137904 TTTTTTAAACACGA
1 TTTTTGAAACACGA
5137918 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:5138412 original size:7 final size:7
Alignment explanation
Indices: 5138400--5138441 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
5138390 TTGGGCCCCC
5138400 CTTTTTT
1 CTTTTTT
5138407 CTTTTTT
1 CTTTTTT
5138414 CTTTTCTT
1 CTTTT-TT
*
5138422 CTCTTTT
1 CTTTTTT
5138429 C-TTTTT
1 CTTTTTT
5138435 CTTTTTT
1 CTTTTTT
5138442 TTCTACTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.16
7 20 0.65
8 6 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
CTTTTTT
Found at i:5138443 original size:15 final size:16
Alignment explanation
Indices: 5138401--5138445 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
5138391 TGGGCCCCCC
5138401 TTTT-TTCTTTTTTC-
1 TTTTCTTCTTTTTTCT
*
5138415 TTTTCTTCTCTTTTCT
1 TTTTCTTCTTTTTTCT
5138431 TTTTCTT-TTTTTTCT
1 TTTTCTTCTTTTTTCT
5138446 ACTGGGCTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 4 0.15
15 16 0.59
16 7 0.26
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTCTTTTTTCT
Found at i:5138692 original size:12 final size:11
Alignment explanation
Indices: 5138675--5138756 Score: 71
Period size: 12 Copynumber: 7.3 Consensus size: 11
5138665 TATTTTTTAT
5138675 TTTTTTTCTCTC
1 TTTTTTTCT-TC
*
5138687 TTTTTTTCGTTT
1 TTTTTTTC-TTC
5138699 TTCTTTTTCTTC
1 TT-TTTTTCTTC
5138711 TTCTTTTTCTT-
1 TT-TTTTTCTTC
*
5138722 TATTTTTC-T-
1 TTTTTTTCTTC
*
5138731 TTTTCTTCTTTC
1 TTTTTTTC-TTC
5138743 TTTTTTTCTTC
1 TTTTTTTCTTC
5138754 TTT
1 TTT
5138757 CTTCTTCCTC
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
9 7 0.12
10 6 0.10
11 8 0.14
12 31 0.53
13 7 0.12
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:5138699 original size:19 final size:17
Alignment explanation
Indices: 5138668--5138762 Score: 81
Period size: 18 Copynumber: 5.5 Consensus size: 17
5138658 CGTCTGTTAT
*
5138668 TTTTTATTTT-TTTTCTC
1 TTTTTCTTTTCTTTT-TC
*
5138685 TCTTT-TTTTCGTTTTTC
1 TTTTTCTTTTC-TTTTTC
5138702 TTTTTCTTCTTCTTTTTC
1 TTTTTCTT-TTCTTTTTC
*
5138720 TTTAT-TTTTCTTTTTC
1 TTTTTCTTTTCTTTTTC
5138736 TTCTTTCTTTT-TTTCTTC
1 TT-TTTCTTTTCTTT-TTC
5138754 TTTCTTCTT
1 TTT-TTCTT
5138763 CCTCCTTCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
16 15 0.23
17 18 0.27
18 30 0.45
19 3 0.05
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTTC
Found at i:5138703 original size:15 final size:14
Alignment explanation
Indices: 5138685--5138759 Score: 66
Period size: 15 Copynumber: 5.3 Consensus size: 14
5138675 TTTTTTTCTC
5138685 TCTTTTTTTCGTTTT
1 TCTTTTTTTC-TTTT
*
5138700 TCTTTTTCTTCTTCT
1 TCTTTTT-TTCTTTT
* *
5138715 T-TTTCTTTATTTT
1 TCTTTTTTTCTTTT
5138728 TC--TTTTTCTTCTT
1 TCTTTTTTTCTT-TT
5138741 TCTTTTTTTCTTCTT
1 TCTTTTTTTCTT-TT
5138756 TCTT
1 TCTT
5138760 CTTCCTCCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
12 6 0.12
13 10 0.20
14 4 0.08
15 26 0.53
16 3 0.06
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (14 bp):
TCTTTTTTTCTTTT
Found at i:5138705 original size:6 final size:6
Alignment explanation
Indices: 5138689--5138762 Score: 73
Period size: 6 Copynumber: 12.3 Consensus size: 6
5138679 TTTCTCTCTT
* *
5138689 TTTTTC GTTTTTC TTTTTC TTCTTC TTTTTC --TTTA TTTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
5138736 TTCTTTC TTTTT- TTCTTC TTTCTTC TT
1 TT-TTTC TTTTTC TTTTTC TTT-TTC TT
5138763 CCTCCTTCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
4 3 0.05
5 4 0.07
6 32 0.57
7 17 0.30
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:5138711 original size:28 final size:26
Alignment explanation
Indices: 5138668--5138759 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 26
5138658 CGTCTGTTAT
* *
5138668 TTTTTATTTTTTTTCTCTCTTTTTTTC
1 TTTTTCTTTTTCTTCT-TCTTTTTTTC
*
5138695 GTTTTTCTTTTTCTTCTTCTTTTTCTTTA
1 -TTTTTCTTTTTCTTCTTC-TTTT-TTTC
5138724 TTTTTCTTTTTCTTCTTTCTTTTTTTC
1 TTTTTCTTTTTCTTC-TTCTTTTTTTC
5138751 TTCTTTCTT
1 TT-TTTCTT
5138760 CTTCCTCCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.12
28 43 0.77
29 6 0.11
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.79
Consensus pattern (26 bp):
TTTTTCTTTTTCTTCTTCTTTTTTTC
Found at i:5138717 original size:25 final size:24
Alignment explanation
Indices: 5138677--5138763 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 24
5138667 TTTTTTATTT
5138677 TTTTTCTCTCTT-TTTTTCGTTTTTC
1 TTTTTCT-TCTTCTTTTTC-TTTTTC
5138702 TTTTTCTTCTTCTTTTTCTTTATT-
1 TTTTTCTTCTTCTTTTTCTTT-TTC
*
5138726 TTTCTTTTTCTTCTTTCTT-TTTTTC
1 TTT-TTCTTCTTCTTT-TTCTTTTTC
5138751 TTCTTTCTTCTTC
1 TT-TTTCTTCTTC
5138764 CTCCTTCTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
24 12 0.22
25 39 0.72
26 3 0.06
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTTTCTTCTTCTTTTTCTTTTTC
Found at i:5138731 original size:22 final size:21
Alignment explanation
Indices: 5138668--5138755 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 21
5138658 CGTCTGTTAT
*
5138668 TTTTTATTTTTTTTCTCTCTT-
1 TTTTTCTTTTTTTTCT-TCTTC
5138689 TTTTTCGTTTTTCTTTTTCTTCTTC
1 TTTTTC---TTT-TTTTTCTTCTTC
*
5138714 TTTTTCTTTATTTTTCTTTTTC
1 TTTTTCTTT-TTTTTCTTCTTC
5138736 TTCTTTC-TTTTTTTCTTCTT
1 TT-TTTCTTTTTTTTCTTCTT
5138756 TCTTCTTCCT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
21 15 0.26
22 18 0.32
23 4 0.07
24 7 0.12
25 13 0.23
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.80
Consensus pattern (21 bp):
TTTTTCTTTTTTTTCTTCTTC
Found at i:5139333 original size:30 final size:29
Alignment explanation
Indices: 5139296--5139416 Score: 93
Period size: 30 Copynumber: 4.1 Consensus size: 29
5139286 CAAGTGTAAT
* *
5139296 TTTGAGAAAATTTAGGGGTTAAAATATAA
1 TTTGAGAAAATTAAGGGGTCAAAATATAA
** * *
5139325 TTTCGAGAAGTTTATA--GGTTAAAATGTAA
1 TTT-GAGAAAATTA-AGGGGTCAAAATATAA
* * *
5139354 TTTTAGGAAAGTTAAGGGGTCAAAACATAA
1 TTTGA-GAAAATTAAGGGGTCAAAATATAA
* *
5139384 TTTTAAAAAAGTTAAGGGGTCAAAATATAA
1 TTTGAGAAAA-TTAAGGGGTCAAAATATAA
5139414 TTT
1 TTT
5139417 TTTATTTTTG
Statistics
Matches: 73, Mismatches: 13, Indels: 11
0.75 0.13 0.11
Matches are distributed among these distances:
28 2 0.03
29 27 0.37
30 43 0.59
31 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (29 bp):
TTTGAGAAAATTAAGGGGTCAAAATATAA
Found at i:5139417 original size:30 final size:30
Alignment explanation
Indices: 5139345--5139417 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
5139335 TTTATAGGTT
* **
5139345 AAAATGTAATTTTAGGAAAGTTAAGGGGTC
1 AAAATATAATTTTAAAAAAGTTAAGGGGTC
*
5139375 AAAACATAATTTTAAAAAAGTTAAGGGGTC
1 AAAATATAATTTTAAAAAAGTTAAGGGGTC
5139405 AAAATATAATTTT
1 AAAATATAATTTT
5139418 TTATTTTTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.32
Consensus pattern (30 bp):
AAAATATAATTTTAAAAAAGTTAAGGGGTC
Found at i:5139769 original size:78 final size:76
Alignment explanation
Indices: 5139682--5140567 Score: 1005
Period size: 78 Copynumber: 11.5 Consensus size: 76
5139672 CATGTGCCTA
* *
5139682 AGGCTCAACTCACC-CATCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAAATACCT
1 AGGCTCAACTCACCTC-TCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCT
5139746 CAGCGTGCGACCCG
65 CAGCGT--GACCCG
*
5139760 AGGCTCAACTCACCTCTCGCAATATGAGTTGAGTTTTTTGAAAAACAGAAATTGAAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTC
5139825 AGCGTGCGACCCG
66 AGCGT--GACCCG
*
5139838 AGGCTCAACTCACCTCTCGCAATATGAGTTGAGTTTTTTGAAAAACAGAAATTG-AAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTC
* *
5139902 AGCGTAACCTG
66 AGCGTGACCCG
* *
5139913 AGGCTTAACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAAACAGAAATT-AAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAAACAGAAATTGAAAAATACCT
*
5139976 CAGCGTAAAACCCG
65 CAGCGT--GACCCG
* *
5139990 AGGCTCAACTCAGCTCTCGCATTATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTGAAAAATACCT
*
5140055 CTG-GATGACCCG
65 CAGCG-TGACCCG
* * * *
5140067 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAACAGAAACTG-AAATTACTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTGAAAAATACCT
5140131 CAG-GATGACCCG
65 CAGCG-TGACCCG
* * * *
5140143 AGGCTCAACTCAGCTCTCGCATTATGAGTTGATTCTTGATTTGATTTTTTTAAA-AGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TT--TTTGA------AAAACAGAAATTGAA
* *
5140207 AAATACCTCGGCTTGCAGCCCG
57 AAATACCTCAGCGTG-A-CCCG
*
5140229 AGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTG-AAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTC
5140291 AGCGTGACCCG
66 AGCGTGACCCG
* * * * *
5140302 AAGCTCAACTCACTTCTCGCATTATGAGTTGA--TTTTTGAAAAATAGGAATTG-AAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTC
*
5140364 AACGTGACCCG
66 AGCGTGACCCG
* * * *
5140375 AGGCTCAACTCACCTCTCACATTATGAGTTGA-TTTTTTGGAAAATAGAAATT-AAAATATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAA-ATACCT
*
5140438 CGGCGTGTGACCCG
65 CAGC--GTGACCCG
* * * *
5140452 AAGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTT-AAAAACAGAAATTTAAAAGAAATGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAA-TT-GAA-AAATAC
* *
5140516 CTCGGCATGTGACCTG
63 CTCAGC--GTGACCCG
*
5140532 AAGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
5140568 AAAAGACAAA
Statistics
Matches: 721, Mismatches: 54, Indels: 64
0.86 0.06 0.08
Matches are distributed among these distances:
73 101 0.14
74 28 0.04
75 89 0.12
76 58 0.08
77 153 0.21
78 154 0.21
79 21 0.03
80 54 0.07
81 7 0.01
83 8 0.01
84 14 0.02
85 1 0.00
86 33 0.05
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (76 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTC
AGCGTGACCCG
Found at i:5139991 original size:230 final size:228
Alignment explanation
Indices: 5139602--5140567 Score: 1087
Period size: 230 Copynumber: 4.2 Consensus size: 228
5139592 CCCGGCATGC
* * * * * *
5139602 GACCCGAAGCTCAACTCACCTCTTG-AATTATGTGTTGA-TCTTCGAAAAACAAAAATCGAAAAT
1 GACCCGAAGCTCAACTCACCTCTCGCAA-TATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAT
** ** * ** *
5139665 ACCTTGGCATGTG-CCTAAGGCTCAACTCACC-CATCGCAATATGAGTTGATTTTTTTTAACAAC
65 ACCTCAGC--GTGACCCGAGGCTCAACTCACCTC-TCGCATTATGAGTTGATTTTTTGAAAAAAC
* *
5139728 AGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAG
127 AGAAATTAAAAAATACCTCAGCGTGCAACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
5139793 TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTG
191 TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTG
*
5139831 CGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAGTTTTTTGAAAAACAGAAATTGAAAA
1 -GACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAA
* * *
5139896 TACCTCAGCGTAACCTGAGGCTTAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAG
64 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAG
** * *
5139961 AAATT-AAAAATACCTCAGCGTAAAACCCGAGGCTCAACTCAGCTCTCGCATTATGAGTTGATTT
129 AAATTAAAAAATACCTCAGCGTGCAACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--T
*
5140025 TTTTTGAAAAACAGAAATTGAAAAATACCTCTG-GAT-
192 TTTTTGAAAAACAGAAATTGAAAAATACCTCAGCG-TG
* * * *
5140061 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAACAGAAACTGAAAT
1 GACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAAACAGAAATTGAAAA
* *
5140126 TACTTCAG-GATGACCCGAGGCTCAACTCAGCTCTCGCATTATGAGTTGATTCTTGATTTGATTT
64 TACCTCAGCG-TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-T-TT--TTTGA---
** * * * *
5140190 TTTTAAA-AGAAATTAAAAAATACCTCGGCTTGCAGCCCGAGGCTCAACTCACTTCTCGCAATAT
121 --AAAAACAGAAATTAAAAAATACCTCAGCGTGCAACCCGAGGCTCAACTCACCTCTCGCAATAT
5140254 GAGTTGA-TTTTTGAAAAACAGAAATTG-AAAATACCTCAGCGT-
184 GAGTTGATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTG
* * * *
5140296 GACCCGAAGCTCAACTCACTTCTCGCATTATGAGTTGA-TTTTTGAAAAATAGGAATTGAAAATA
1 GACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATA
* * * *
5140360 CCTCAACGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTG-GAAAATAGAA
66 CCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAA
* * ** * *
5140424 ATTAAAATATACCTCGGCGTGTGACCCGAAGCTCAACTCACCTCTCGCAATATAAGTTGATTTTT
131 ATTAAAAAATACCTCAGCGTGCAACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * * * *
5140489 TTAAAAACAGAAATTTAAAAGAAATGCCTCGGCATG
196 TGAAAAACAGAAA-TT-GAA-AAATACCTCAGCGTG
*
5140525 TGACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 -GACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
5140568 AAAAGACAAA
Statistics
Matches: 635, Mismatches: 71, Indels: 59
0.83 0.09 0.08
Matches are distributed among these distances:
222 3 0.00
223 56 0.09
224 16 0.03
225 2 0.00
227 1 0.00
228 15 0.02
229 38 0.06
230 188 0.30
231 90 0.14
232 93 0.15
233 1 0.00
234 5 0.01
235 48 0.08
236 21 0.03
238 7 0.01
239 51 0.08
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (228 bp):
GACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATA
CCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAACAGAA
ATTAAAAAATACCTCAGCGTGCAACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
TGAAAAACAGAAATTGAAAAATACCTCAGCGTG
Found at i:5140025 original size:77 final size:76
Alignment explanation
Indices: 5139572--5140567 Score: 972
Period size: 77 Copynumber: 13.0 Consensus size: 76
5139562 ATTTTTTATT
* * * * * *
5139572 AAAAA-AGAAATCAAAAATAGCC-CGGCATGCGACCCGAAGCTCAACTCACCTCTTG-AATTATG
1 AAAAACAGAAATTAAAAATA-CCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAA-TATG
* * *
5139634 TGTTGA-TCTTCG
64 AGTTGATTTTTTG
* ** ** * **
5139646 AAAAACAAAAATCGAAAATACCTTGGCATGTG-CCTAAGGCTCAACTCACC-CATCGCAATATGA
1 AAAAACAGAAATTAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTC-TCGCAATATGA
*
5139709 GTTGATTTTTTTT
65 GTTGA-TTTTTTG
* *
5139722 AACAACAGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATT-AAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
5139787 GTTGAGTTTTTTG
65 GTTGA-TTTTTTG
*
5139800 AAAAACAGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATT-AAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
5139865 GTTGAGTTTTTTG
65 GTTGA-TTTTTTG
* * * * *
5139878 AAAAACAGAAATTGAAAATACCTCAGC--GTAACCTGAGGCTTAACTCACCTCTCGCATTATGAG
1 AAAAACAGAAATTAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
5139941 TTGATTTTTTG
66 TTGATTTTTTG
*** * *
5139952 AAAAAACAGAAATTAAAAATACCTCAGCGTAAAACCCGAGGCTCAACTCAGCTCTCGCATTATGA
1 -AAAAACAGAAATTAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
5140017 GTTGATTTTTTTTG
65 GTTGA--TTTTTTG
* * *
5140031 AAAAACAGAAATTGAAAAATACCTCTG-G-ATGACCCGAGGCTCAACTCACCTCTCGCATTATGA
1 AAAAACAGAAATT-AAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
5140094 GTTGATTTTTTTTG
65 GTTGA--TTTTTTG
* * * * * * *
5140108 AAAAACAGAAACTGAAATTACTTCAG-G-ATGACCCGAGGCTCAACTCAGCTCTCGCATTATGAG
1 AAAAACAGAAATTAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
5140171 TTGATTCTTGATTTG
66 TTGA-T-TT--TTTG
* * *
5140186 ATTTTTTTAAA-AGAAATTAAAAAATACCTCGGC-T-TGCAGCCCGAGGCTCAACTCACTTCTCG
1 A------AAAACAGAAATT-AAAAATACCTCAGCGTGTG-A-CCCGAGGCTCAACTCACCTCTCG
5140248 CAATATGAGTTGA-TTTTTG
57 CAATATGAGTTGATTTTTTG
* * * *
5140267 AAAAACAGAAATTGAAAATACCTCAGC--GTGACCCGAAGCTCAACTCACTTCTCGCATTATGAG
1 AAAAACAGAAATTAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
5140330 TTGA-TTTTTG
66 TTGATTTTTTG
* * * * * *
5140340 AAAAATAGGAATTGAAAATACCTCAAC--GTGACCCGAGGCTCAACTCACCTCTCACATTATGAG
1 AAAAACAGAAATTAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
5140403 TTGATTTTTTG
66 TTGATTTTTTG
* * * * *
5140414 GAAAATAGAAATTAAAATATACCTCGGCGTGTGACCCGAAGCTCAACTCACCTCTCGCAATATAA
1 AAAAACAGAAATTAAAA-ATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
*
5140479 GTTGATTTTTTT
65 GTTGATTTTTTG
* * * * *
5140491 AAAAACAGAAATTTAAAAGAAATGCCTCGGCATGTGACCTGAAGCTCAACTCACCTCTCGCAATA
1 AAAAACAGAAA-TT--AA-AAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATA
5140556 TGAGTTGATTTT
62 TGAGTTGATTTT
5140568 AAAAGACAAA
Statistics
Matches: 800, Mismatches: 83, Indels: 72
0.84 0.09 0.08
Matches are distributed among these distances:
73 102 0.13
74 61 0.08
75 109 0.14
76 71 0.09
77 171 0.21
78 149 0.19
79 20 0.03
80 54 0.07
81 7 0.01
83 8 0.01
84 14 0.02
85 1 0.00
86 33 0.04
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (76 bp):
AAAAACAGAAATTAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTG
Found at i:5140308 original size:73 final size:73
Alignment explanation
Indices: 5140197--5140589 Score: 430
Period size: 73 Copynumber: 5.2 Consensus size: 73
5140187 TTTTTTTAAA
* * *
5140197 AGAAATTAAAAAATACCTCGGCTTGCAGCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
1 AGAAATT-AAAAATACCTCGGCGTG-A-CCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGAT
5140262 TTTTGAAAAAC
63 TTTTGAAAAAC
* * * *
5140273 AGAAATTGAAAATACCTCAGCGTGACCCGAAGCTCAACTCACTTCTCGCATTATGAGTTGATTTT
1 AGAAATTAAAAATACCTCGGCGTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
5140338 TGAAAAAT
66 TGAAAAAC
* * ** * * *
5140346 AGGAATTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTT
1 AGAAATTAAAAATACCTCGGCGTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT
* *
5140411 TTGGAAAAT
65 TTGAAAAAC
*
5140420 AGAAATTAAAATATACCTCGGCGTGTGACCCGAAGCTCAACTCACCTCTCGCAATATAAGTTGAT
1 AGAAATTAAAA-ATACCTCGGC--GTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
5140485 TTTTTTAAAAAC
62 TTTTTGAAAAAC
* *
5140497 AGAAATTTAAAAGAAATGCCTCGGCATGTGACCTGAAGCTCAACTCACCTCTCGCAATATGAGTT
1 AGAAA-TT--AA-AAATACCTCGGC--GTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTT
5140562 GA-TTTT-AAAAGAC
60 GATTTTTGAAAA-AC
*
5140575 AAAAATTGAAAAATA
1 AGAAATT-AAAAATA
5140590 TAATTCTTGA
Statistics
Matches: 278, Mismatches: 30, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
73 101 0.36
74 21 0.08
75 26 0.09
76 9 0.03
77 57 0.21
78 12 0.04
80 50 0.18
81 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (73 bp):
AGAAATTAAAAATACCTCGGCGTGACCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TGAAAAAC
Found at i:5140313 original size:159 final size:148
Alignment explanation
Indices: 5139562--5140567 Score: 943
Period size: 152 Copynumber: 6.5 Consensus size: 148
5139552 TTTATTCTTT
* * *
5139562 ATTTTTTATTAAAAA-AGAAATCAAAAATAGCC-CGGCATGCGACCCGAAGCTCAACTCACCTCT
1 ATTTTTT-TGAAAAATAGAAATTAAAAATA-CCTCGGCAT--GACCCGAGGCTCAACTCACCTCT
* * * * * * * ** * ** *
5139625 TGAATTATGTGTTGA-TCTTCGAAAAACAAAAATCGAAAATACCTTGGCATGTGCCTAAGGCTCA
62 CGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAA-GCTCA
* *
5139689 ACTCACCCATCGCAATATGAGTTG
126 ACTCACTC-TCGCATTATGAGTTG
* * * * *
5139713 ATTTTTTTTAACAACAGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTC
1 ATTTTTTTGAAAAATAGAAATT-AAAAATACCTCGGCAT--GACCCGAGGCTCAACTCACCTCTC
* *
5139778 GCAATATGAGTTGAGTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGCGACCCGAGGCT
63 GCATTATGAGTTGA-TTTTTTGAAAAACAGAAATTG-AAAATACCTCAGCGT--GACCCGAAGCT
*
5139843 CAACTCACCTCTCGCAATATGAGTTG
124 CAACTCA-CTCTCGCATTATGAGTTG
* * * * * * * *
5139869 AGTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTAACCTGAGGCTTAACTCACCTCTCGCA
1 ATTTTTTTGAAAAATAGAAATTAAAAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCA
* * *
5139934 TTATGAGTTGATTTTTTGAAAAAACAGAAATTAAAAATACCTCAGCGTAAAACCCGAGGCTCAAC
66 TTATGAGTTGATTTTTTG-AAAAACAGAAATTGAAAATACCTCAGCGT--GACCCGAAGCTCAAC
5139999 TCAGCTCTCGCATTATGAGTTG
128 TCA-CTCTCGCATTATGAGTTG
*
5140021 ATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCTGG-ATGACCCGAGGCTCAACTCACCTCTC
1 A-TTTTTTTGAAAAATAGAAATT-AAAAATACCTC-GGCATGACCCGAGGCTCAACTCACCTCTC
* * * *
5140085 GCATTATGAGTTGATTTTTTTTGAAAAACAGAAACTGAAATTACTTCAG-GATGACCCGAGGCTC
63 GCATTATGAGTTGA--TTTTTTGAAAAACAGAAATTGAAAATACCTCAGCG-TGACCCGAAGCTC
5140149 AACTCAGCTCTCGCATTATGAGTTG
125 AACTCA-CTCTCGCATTATGAGTTG
* *
5140174 ATTCTTGATTTGATTTTTTTAAA-AGAAATTAAAAAATACCTCGGCTTGCAGCCCGAGGCTCAAC
1 ATT-TT--TTTGA------AAAATAGAAATT-AAAAATACCTCGGCATG-A-CCCGAGGCTCAAC
* *
5140238 TCACTTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCG
54 TCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCG
5140302 AAGCTCAACTCACTTCTCGCATTATGAGTTG
119 AAGCTCAACTCAC-TCTCGCATTATGAGTTG
* * ** * *
5140333 A--TTTTTGAAAAATAGGAATTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTCACA
1 ATTTTTTTGAAAAATAGAAATTAAAAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCA
* * * *
5140396 TTATGAGTTGATTTTTTGGAAAATAGAAATTAAAATATACCTCGGCGTGTGACCCGAAGCTCAAC
66 TTATGAGTTGATTTTTTGAAAAACAGAAATTGAAA-ATACCTCAGC--GTGACCCGAAGCTCAAC
* *
5140461 TCACCTCTCGCAATATAAGTTG
128 TCA-CTCTCGCATTATGAGTTG
* * * *
5140483 ATTTTTTT-AAAAACAGAAATTTAAAAGAAATGCCTCGGCATGTGACCTGAAGCTCAACTCACCT
1 ATTTTTTTGAAAAATAGAAA-TT--AA-AAATACCTCGGCA--TGACCCGAGGCTCAACTCACCT
*
5140547 CTCGCAATATGAGTTGATTTT
60 CTCGCATTATGAGTTGATTTT
5140568 AAAAGACAAA
Statistics
Matches: 729, Mismatches: 82, Indels: 82
0.82 0.09 0.09
Matches are distributed among these distances:
146 33 0.05
147 21 0.03
148 25 0.03
149 6 0.01
150 42 0.06
151 25 0.03
152 112 0.15
153 106 0.15
154 69 0.09
155 65 0.09
156 53 0.07
157 45 0.06
158 1 0.00
159 67 0.09
160 21 0.03
161 4 0.01
162 34 0.05
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (148 bp):
ATTTTTTTGAAAAATAGAAATTAAAAATACCTCGGCATGACCCGAGGCTCAACTCACCTCTCGCA
TTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAAGCTCAACTCA
CTCTCGCATTATGAGTTG
Found at i:5141474 original size:28 final size:27
Alignment explanation
Indices: 5141443--5141509 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
5141433 TCATCTTGAT
*
5141443 TTTTATTTTTCT-TTTCTTTCCTTTTTTG
1 TTTTATTTTT-TGTTTCTCT-CTTTTTTG
* *
5141471 TTTTCTTTTTTGTTTCTCTGTTTTTTG
1 TTTTATTTTTTGTTTCTCTCTTTTTTG
*
5141498 TTTTTTTTTTTG
1 TTTTATTTTTTG
5141510 GTTTTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.56
28 15 0.44
ACGTcount: A:0.01, C:0.10, G:0.07, T:0.81
Consensus pattern (27 bp):
TTTTATTTTTTGTTTCTCTCTTTTTTG
Found at i:5141508 original size:12 final size:12
Alignment explanation
Indices: 5141464--5141518 Score: 65
Period size: 12 Copynumber: 4.2 Consensus size: 12
5141454 TTTTCTTTCC
*
5141464 TTTTTTGTTTTC
1 TTTTTTGTTTTT
5141476 TTTTTTGTTTCTCT
1 TTTTTTGTTT-T-T
5141490 GTTTTTTGTTTTT
1 -TTTTTTGTTTTT
5141503 TTTTTTGGTTTTT
1 TTTTTT-GTTTTT
5141516 TTT
1 TTT
5141519 AGGCATAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
12 16 0.42
13 11 0.29
14 1 0.03
15 10 0.26
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:5142370 original size:439 final size:438
Alignment explanation
Indices: 5141553--5142431 Score: 1589
Period size: 439 Copynumber: 2.0 Consensus size: 438
5141543 CTGAGTTCAC
5141553 TGGATTAGGTAATTCTTTCCCATCCATCTCAGTGAGAATCAAAGCCCCTCCCGAGAATGCCTTTT
1 TGGATTAGGTAATTCTTTCCCATCCATCTCAGTGAGAATCAAAGCCCCTCCCGAGAATGCCTTTT
* *
5141618 TTACAACGTATGGCCTTTCCCAATTTGGTGACCATTTTCCTTGAAAGTCTTTTTGTATCGGGAGG
66 TTACAACGTATGGCCCTTCCCAATTTGGTGACCATTTTCCTCGAAAGTCTTTTTGTATCGGGAGG
*
5141683 ATTTTTCTTAACACAAGTTCCCCTTCGCGGAATTCTCTTGGTCGCACCTTCTTATTATGGGCCGT
131 ATTTTTCTTAACACAAGTTCCCCTTCGCAGAATTCTCTTGGTCGCACCTTCTTATTATGGGCCGT
5141748 GATCATTCTTTTCTGATACATCTGTCCATGACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGGT
196 GATCATTCTTTTCTGATACATCTGTCCATGACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGGT
*
5141813 TTAGTTGATCATATCGAGCTTGAACCCATTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCGC
261 TTAGTTGATCATATCGAGCTTGAACCCACTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCGC
* *
5141878 ATGGATAGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAAGGGA-G
326 AGGGATAGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAA-AGATG
* *
5141942 TTGCCCCCGTAGACGTCTGTACAGAGGTGCGATATGCGTACAAAGTGAA
390 TTGCCCCCGTAGACGTCCGTACAGAGGTGCGATATGCGTACAAAGCGAA
* * *
5141991 TGGATTAGGTAATTCTTTCTCATCCATCTCGGTGAGAATCAGAGCCCCTCCCGAGAATGCCTTTT
1 TGGATTAGGTAATTCTTTCCCATCCATCTCAGTGAGAATCAAAGCCCCTCCCGAGAATGCC-TTT
5142056 TTTACAACGTATGGCCCTTCCCAATTTGGTGACCATTTTCCTCGAAAGTCTTTTTGTATCGGGAG
65 TTTACAACGTATGGCCCTTCCCAATTTGGTGACCATTTTCCTCGAAAGTCTTTTTGTATCGGGAG
* *
5142121 GATTTTTCTTAGCACAAGTTCCCCTTCGCAGAATTCTCTTGGTCGCACCTTTTTATTATGGGCCG
130 GATTTTTCTTAACACAAGTTCCCCTTCGCAGAATTCTCTTGGTCGCACCTTCTTATTATGGGCCG
*
5142186 TGATCATTCTTTTCTGATACATCTGTCTATGACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGG
195 TGATCATTCTTTTCTGATACATCTGTCCATGACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGG
*
5142251 TTTAGTTGATCATATCGAGCTTGAATCCACTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCG
260 TTTAGTTGATCATATCGAGCTTGAACCCACTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCG
*
5142316 CAGGGATGGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAAAGATG
325 CAGGGATAGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAAAGATG
5142381 TTGCCCCCGTAGACGTCCGTACAGAGGTGCGATATGCGTACAAAGCGAA
390 TTGCCCCCGTAGACGTCCGTACAGAGGTGCGATATGCGTACAAAGCGAA
5142430 TG
1 TG
5142432 ATAGCTTCTC
Statistics
Matches: 423, Mismatches: 16, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
438 60 0.14
439 363 0.86
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (438 bp):
TGGATTAGGTAATTCTTTCCCATCCATCTCAGTGAGAATCAAAGCCCCTCCCGAGAATGCCTTTT
TTACAACGTATGGCCCTTCCCAATTTGGTGACCATTTTCCTCGAAAGTCTTTTTGTATCGGGAGG
ATTTTTCTTAACACAAGTTCCCCTTCGCAGAATTCTCTTGGTCGCACCTTCTTATTATGGGCCGT
GATCATTCTTTTCTGATACATCTGTCCATGACAAATTGCCTTCAAGCGCTTCCCTTCAATAAGGT
TTAGTTGATCATATCGAGCTTGAACCCACTCTGATTCTTCTAACTTTGTCTCCATTAAGACGCGC
AGGGATAGGATCTCTACTTTGATAGGCAGAACGACTTCCATCCCGTAGACCAGAGAAAAAGATGT
TGCCCCCGTAGACGTCCGTACAGAGGTGCGATATGCGTACAAAGCGAA
Found at i:5149267 original size:35 final size:34
Alignment explanation
Indices: 5149228--5149437 Score: 165
Period size: 35 Copynumber: 6.0 Consensus size: 34
5149218 AAAAAATGAG
**
5149228 AATTTTGAAATTCGAAAAATTTTTGAAAACACGAA
1 AATTTTGAAACACG-AAAATTTTTGAAAACACGAA
* * * *
5149263 AATTTTTGCAATACGAGAA-TTTTAAAAACACGAA
1 AA-TTTTGAAACACGAAAATTTTTGAAAACACGAA
*
5149297 AATTTCTAAAACACGAAAATTTTTGAAAACACGAGA
1 AATTT-TGAAACACGAAAATTTTTGAAAACACGA-A
** * *
5149333 TTTTTTGAAACACGAAAATTTTTGGAAATACGAA
1 AATTTTGAAACACGAAAATTTTTGAAAACACGAA
* * **
5149367 AATTTTTGAAGCATGAAGTTTTTTTTTG-AAACACGAGA
1 AA-TTTTGAAACACGAA---AATTTTTGAAAACACGA-A
*
5149405 AATTTTGAAAACATGAAAATTTTTG-AAACACGA
1 AATTTTG-AAACACGAAAATTTTTGAAAACACGA
5149438 TTATTTTTTT
Statistics
Matches: 141, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
33 3 0.02
34 26 0.18
35 69 0.49
36 14 0.10
37 12 0.09
38 17 0.12
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (34 bp):
AATTTTGAAACACGAAAATTTTTGAAAACACGAA
Found at i:5149445 original size:17 final size:17
Alignment explanation
Indices: 5149243--5149437 Score: 176
Period size: 17 Copynumber: 11.1 Consensus size: 17
5149233 TGAAATTCGA
5149243 AAAATTTTTGAAAACACG
1 AAAATTTTTG-AAACACG
* *
5149261 AAAATTTTTGCAATACG
1 AAAATTTTTGAAACACG
* **
5149278 AGAATTTTAAAAACACG
1 AAAATTTTTGAAACACG
* *
5149295 AAAATTTCTAAAACACG
1 AAAATTTTTGAAACACG
5149312 AAAATTTTTGAAAACACG
1 AAAATTTTTG-AAACACG
* *
5149330 AGATTTTTTGAAACACG
1 AAAATTTTTGAAACACG
*
5149347 AAAATTTTTGGAAATACG
1 AAAATTTTT-GAAACACG
* *
5149365 AAAATTTTTGAAGCATG
1 AAAATTTTTGAAACACG
**
5149382 AAGTTTTTTTTTGAAACACG
1 AA---AATTTTTGAAACACG
*
5149402 AGAAA-TTTTGAAAACATG
1 A-AAATTTTTG-AAACACG
5149420 AAAATTTTTGAAACACG
1 AAAATTTTTGAAACACG
5149437 A
1 A
5149438 TTATTTTTTT
Statistics
Matches: 141, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
17 75 0.53
18 53 0.38
20 12 0.09
21 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31
Consensus pattern (17 bp):
AAAATTTTTGAAACACG
Found at i:5149944 original size:13 final size:13
Alignment explanation
Indices: 5149921--5149966 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 13
5149911 TGGGCCCCCC
5149921 TTTTTTC-TTTCT
1 TTTTTTCTTTTCT
5149933 TTTTTTCTTTTCT
1 TTTTTTCTTTTCT
5149946 TCTCTTTTCTTTTTCT
1 T-T-TTTTC-TTTTCT
5149962 TTTTT
1 TTTTT
5149967 CTGCTGGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.23
13 6 0.20
14 4 0.13
15 6 0.20
16 7 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:5149951 original size:10 final size:9
Alignment explanation
Indices: 5149923--5149957 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 9
5149913 GGCCCCCCTT
5149923 TTTTCTTTC
1 TTTTCTTTC
5149932 TTTT-TTTC
1 TTTTCTTTC
5149940 TTTTCTTCTC
1 TTTTCTT-TC
5149950 TTTTCTTT
1 TTTTCTTT
5149958 TTCTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:5149967 original size:13 final size:13
Alignment explanation
Indices: 5149920--5149968 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
5149910 TTGGGCCCCC
*
5149920 CTTTTTTCTTTCT
1 CTTTTTTCTTTTT
5149933 -TTTTTTCTTTTCTT
1 CTTTTTTC-TTT-TT
*
5149947 CTCTTTTCTTTTT
1 CTTTTTTCTTTTT
5149960 CTTTTTTCT
1 CTTTTTTCT
5149969 GCTGGGCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 7 0.23
13 13 0.43
14 4 0.13
15 6 0.20
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
CTTTTTTCTTTTT
Found at i:5150054 original size:16 final size:16
Alignment explanation
Indices: 5150035--5150066 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5150025 GGTACCAGCT
5150035 GCTGGACTGGGCCTGC
1 GCTGGACTGGGCCTGC
*
5150051 GCTGGATTGGGCCTGC
1 GCTGGACTGGGCCTGC
5150067 TGTGGCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.28, G:0.44, T:0.22
Consensus pattern (16 bp):
GCTGGACTGGGCCTGC
Found at i:5150220 original size:6 final size:6
Alignment explanation
Indices: 5150211--5150290 Score: 67
Period size: 6 Copynumber: 13.5 Consensus size: 6
5150201 TTTCTCTCTT
* * * * *
5150211 TTTTTC TTTTTTC TATTTC TATTTC TATTTC TATTTC TATTTC --TTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
5150258 TTTTTC TTTTTC TTCTTTC TTTTT- TTCTTC TTT
1 TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TTT
5150291 CTTCCTCCTC
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
4 4 0.06
5 4 0.06
6 46 0.70
7 12 0.18
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:5150264 original size:28 final size:27
Alignment explanation
Indices: 5150226--5150292 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
5150216 CTTTTTTCTA
*
5150226 TTTCTATTTCTATTTC-TATTTCTATTT
1 TTTCTTTTTCTATTTCTTATTTCT-TTT
* *
5150253 CTTTCTTTTTCTTTTTCTTCTTTCTTTT
1 -TTTCTTTTTCTATTTCTTATTTCTTTT
5150281 TTTCTTCTTTCT
1 TTTCTT-TTTCT
5150293 TCCTCCTCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.18
28 22 0.65
29 6 0.18
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTCTTTTTCTATTTCTTATTTCTTTT
Found at i:5150291 original size:15 final size:16
Alignment explanation
Indices: 5150245--5150294 Score: 68
Period size: 15 Copynumber: 3.2 Consensus size: 16
5150235 CTATTTCTAT
*
5150245 TTCTATTTCTTTCTTT-
1 TTCTTTTTC-TTCTTTC
5150261 TTCTTTTTCTTCTTTC
1 TTCTTTTTCTTCTTTC
5150277 TT-TTTTTCTTCTTTC
1 TTCTTTTTCTTCTTTC
5150292 TTC
1 TTC
5150295 CTCCTCCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 21 0.68
16 10 0.32
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTTCTTCTTTC
Found at i:5150292 original size:19 final size:20
Alignment explanation
Indices: 5150250--5150293 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
5150240 TCTATTTCTA
*
5150250 TTTCTTTCTTTTTCTTTTTC
1 TTTCTTTCTTTTTCTTCTTC
5150270 -TTCTTTCTTTTT-TTCTTC
1 TTTCTTTCTTTTTCTTCTTC
5150288 TTTCTT
1 TTTCTT
5150294 CCTCCTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTTTCTTTTTCTTCTTC
Found at i:5150294 original size:7 final size:7
Alignment explanation
Indices: 5150251--5150294 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
5150241 CTATTTCTAT
5150251 TTCTTTC
1 TTCTTTC
5150258 TT-TTTC
1 TTCTTTC
5150264 TT-TTTC
1 TTCTTTC
5150270 TTCTTTC
1 TTCTTTC
*
5150277 TTTTTTTC
1 -TTCTTTC
5150285 TTCTTTC
1 TTCTTTC
5150292 TTC
1 TTC
5150295 CTCCTCCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 12 0.36
7 15 0.45
8 6 0.18
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTCTTTC
Found at i:5150913 original size:30 final size:29
Alignment explanation
Indices: 5150887--5150964 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
5150877 AGAAGTTCAT
*
5150887 AGGTTAAAATGTAATTTTAGAAAAGTTAA
1 AGGTTAAAATGTAATTTTAAAAAAGTTAA
* ***
5150916 AGGGTCAAAACACAATTTTAAAAAAGTTAA
1 A-GGTTAAAATGTAATTTTAAAAAAGTTAA
*
5150946 GGGGTTAAAATGTAATTTT
1 -AGGTTAAAATGTAATTTT
5150965 TTTATTTTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
29 1 0.03
30 36 0.97
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (29 bp):
AGGTTAAAATGTAATTTTAAAAAAGTTAA
Found at i:5150981 original size:17 final size:17
Alignment explanation
Indices: 5150956--5150990 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5150946 GGGGTTAAAA
*
5150956 TGTAATTTTTTTATTTT
1 TGTAATTTTTGTATTTT
*
5150973 TGTATTTTTTGTATTTT
1 TGTAATTTTTGTATTTT
5150990 T
1 T
5150991 TTTGAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (17 bp):
TGTAATTTTTGTATTTT
Found at i:5150992 original size:10 final size:9
Alignment explanation
Indices: 5150960--5150991 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5150950 TTAAAATGTA
5150960 ATTTTTT-T
1 ATTTTTTGT
5150968 A-TTTTTGT
1 ATTTTTTGT
5150976 ATTTTTTGT
1 ATTTTTTGT
5150985 ATTTTTT
1 ATTTTTT
5150992 TTGAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 5 0.23
8 3 0.14
9 14 0.64
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (9 bp):
ATTTTTTGT
Found at i:5151925 original size:20 final size:20
Alignment explanation
Indices: 5151888--5151925 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5151878 TATGTTTTGT
*
5151888 TATATTAATCTACTTTTTTA
1 TATATTAATCTACATTTTTA
5151908 TATATGTAATCT-CATTTT
1 TATAT-TAATCTACATTTT
5151926 ACGATAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (20 bp):
TATATTAATCTACATTTTTA
Found at i:5156777 original size:17 final size:18
Alignment explanation
Indices: 5156755--5156794 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
5156745 ACCCAAACCG
*
5156755 ATAAAACCCA-ACATAAA
1 ATAAAACCCAGAAATAAA
5156772 ATAAAACCCAGAAATAAA
1 ATAAAACCCAGAAATAAA
5156790 A-AAAA
1 ATAAAA
5156795 ATGGACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.70, C:0.17, G:0.03, T:0.10
Consensus pattern (18 bp):
ATAAAACCCAGAAATAAA
Found at i:5156795 original size:18 final size:17
Alignment explanation
Indices: 5156757--5156795 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5156747 CCAAACCGAT
* *
5156757 AAAACCCAACATAAAAT
1 AAAACCCAAAATAAAAA
5156774 AAAACCCAGAAATAAAAA
1 AAAACCCA-AAATAAAAA
5156792 AAAA
1 AAAA
5156796 TGGACCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.08
Consensus pattern (17 bp):
AAAACCCAAAATAAAAA
Found at i:5158769 original size:5 final size:5
Alignment explanation
Indices: 5158761--5158793 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
5158751 TTTATTGCAA
5158761 AAAAG AAAAG AAAAG AAAAG AAAAG AAATAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AA
5158794 GGACATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:5179266 original size:22 final size:21
Alignment explanation
Indices: 5179220--5179266 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
5179210 TATTAAACTA
5179220 ATTAGTTTTTTTTATTATTACT
1 ATTAGTTTTTTTTATTATTA-T
*
5179242 ATTATTTTTCTTTTATTTATT-T
1 ATTAGTTTT-TTTTA-TTATTAT
5179264 ATT
1 ATT
5179267 TATTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 12 0.55
23 5 0.23
24 5 0.23
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (21 bp):
ATTAGTTTTTTTTATTATTAT
Found at i:5180675 original size:22 final size:23
Alignment explanation
Indices: 5180643--5180685 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
5180633 TATTTTTCAA
5180643 TTTCTTGTTTTACCTT-TTTCCTT
1 TTTCTTGTTTTA-CTTATTTCCTT
5180666 TTTCTT-TTTTACTTATTTCC
1 TTTCTTGTTTTACTTATTTCC
5180686 CCTCTCTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 10 0.53
23 6 0.32
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTCTTGTTTTACTTATTTCCTT
Found at i:5183555 original size:15 final size:16
Alignment explanation
Indices: 5183525--5183558 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5183515 TTTTTTAGAA
5183525 AAAACATTAACAAAAC
1 AAAACATTAACAAAAC
*
5183541 AAAACA-TAACTAAAC
1 AAAACATTAACAAAAC
5183556 AAA
1 AAA
5183559 GAAGACGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.71, C:0.18, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAACATTAACAAAAC
Found at i:5183683 original size:12 final size:12
Alignment explanation
Indices: 5183668--5183710 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5183658 CCTGCTCCTG
5183668 CTCCACCTCCAA
1 CTCCACCTCCAA
*
5183680 CTCCACCGCCAA
1 CTCCACCTCCAA
** *
5183692 CAGCACCTCCTA
1 CTCCACCTCCAA
5183704 CTCCACC
1 CTCCACC
5183711 ACCTACACCA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.23, C:0.58, G:0.05, T:0.14
Consensus pattern (12 bp):
CTCCACCTCCAA
Found at i:5183722 original size:24 final size:24
Alignment explanation
Indices: 5183670--5183722 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5183660 TGCTCCTGCT
*
5183670 CCACCTCCAACTCCACCGCCAACA
1 CCACCTCCAACTCCACCACCAACA
* * *
5183694 GCACCTCCTACTCCACCACCTACA
1 CCACCTCCAACTCCACCACCAACA
5183718 CCACC
1 CCACC
5183723 ACCAGCACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.58, G:0.04, T:0.11
Consensus pattern (24 bp):
CCACCTCCAACTCCACCACCAACA
Found at i:5183750 original size:9 final size:9
Alignment explanation
Indices: 5183738--5183853 Score: 51
Period size: 9 Copynumber: 12.9 Consensus size: 9
5183728 CACCACCAAA
*
5183738 TCCACCGAC
1 TCCACCGAG
5183747 TCCACCG-G
1 TCCACCGAG
* *
5183755 TTCCTCCAAG
1 -TCCACCGAG
* *
5183765 TCCATCGAC
1 TCCACCGAG
5183774 TCCACCG-G
1 TCCACCGAG
* *
5183782 TACCTCCAAG
1 T-CCACCGAG
*
5183792 TCCACCGAC
1 TCCACCGAG
5183801 TCCACCG-G
1 TCCACCGAG
* *
5183809 TACCTCCAAG
1 T-CCACCGAG
*
5183819 TCCACCGAC
1 TCCACCGAG
5183828 TCCACCG-G
1 TCCACCGAG
* *
5183836 TTCCTCCAAG
1 -TCCACCGAG
5183846 TCCACCGA
1 TCCACCGA
5183854 ATCCTCCGGT
Statistics
Matches: 74, Mismatches: 25, Indels: 16
0.64 0.22 0.14
Matches are distributed among these distances:
8 2 0.03
9 66 0.89
10 6 0.08
ACGTcount: A:0.21, C:0.47, G:0.15, T:0.17
Consensus pattern (9 bp):
TCCACCGAG
Found at i:5183751 original size:27 final size:27
Alignment explanation
Indices: 5183733--5183878 Score: 229
Period size: 27 Copynumber: 5.4 Consensus size: 27
5183723 ACCAGCACCA
* *
5183733 CCAAATCCACCGACTCCACCGGTTCCT
1 CCAAGTCCACCGACTCCACCGGTACCT
*
5183760 CCAAGTCCATCGACTCCACCGGTACCT
1 CCAAGTCCACCGACTCCACCGGTACCT
5183787 CCAAGTCCACCGACTCCACCGGTACCT
1 CCAAGTCCACCGACTCCACCGGTACCT
*
5183814 CCAAGTCCACCGACTCCACCGGTTCCT
1 CCAAGTCCACCGACTCCACCGGTACCT
* * *
5183841 CCAAGTCCACCGAATCCTCCGGTTCCT
1 CCAAGTCCACCGACTCCACCGGTACCT
5183868 CCAAGTCCACC
1 CCAAGTCCACC
5183879 CAAACCACCA
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 112 1.00
ACGTcount: A:0.21, C:0.47, G:0.14, T:0.18
Consensus pattern (27 bp):
CCAAGTCCACCGACTCCACCGGTACCT
Found at i:5183887 original size:81 final size:78
Alignment explanation
Indices: 5183723--5183911 Score: 243
Period size: 81 Copynumber: 2.4 Consensus size: 78
5183713 CTACACCACC
* * * *
5183723 ACCAGCACCACCAAATCCACCGACTCCACCGGTTCCTCCAAGTCCATCGACTCCACCGGTACCTC
1 ACCACCACCACCAAGTCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCACCGGTACCTC
* *
5183788 CAAGTCCACCGAC
66 CAAGTCCACCCAA
* * * *
5183801 TCCACCGGTACCTCCAAGTCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCTCCGGTTC
1 ACCACC---ACCACCAAGTCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCACCGGTAC
5183866 CTCCAAGTCCACCCAA
63 CTCCAAGTCCACCCAA
* *
5183882 ACCACCACCACCAAGTCCACCTACACCACC
1 ACCACCACCACCAAGTCCACCGACTCCACC
5183912 AAAGGGAGTA
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
78 25 0.27
81 69 0.73
ACGTcount: A:0.25, C:0.49, G:0.12, T:0.15
Consensus pattern (78 bp):
ACCACCACCACCAAGTCCACCGACTCCACCGGTTCCTCCAAGTCCACCGAATCCACCGGTACCTC
CAAGTCCACCCAA
Found at i:5191932 original size:18 final size:18
Alignment explanation
Indices: 5191909--5191974 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
5191899 TCTAAAATTT
5191909 ACATTTAAAAAAATATAA
1 ACATTTAAAAAAATATAA
5191927 ACATTTTAAAAAAATA-AA
1 ACA-TTTAAAAAAATATAA
*
5191945 A-ATTCTAAATAATATATAA
1 ACATT-TAAA-AAAATATAA
* *
5191964 AAAATTAAAAA
1 ACATTTAAAAA
5191975 TTTTCTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 2 0.05
17 5 0.12
18 13 0.32
19 19 0.46
20 2 0.05
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
ACATTTAAAAAAATATAA
Found at i:5191936 original size:19 final size:18
Alignment explanation
Indices: 5191912--5191965 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
5191902 AAAATTTACA
5191912 TTTAAAAAAATATAAACAT
1 TTTAAAAAAATATAAA-AT
5191931 TTTAAAAAAATA-AAAAT
1 TTTAAAAAAATATAAAAT
* *
5191948 TCTAAATAATATATAAAA
1 TTTAAA-AAAATATAAAA
5191966 AATTAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 7 0.23
18 8 0.26
19 16 0.52
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
TTTAAAAAAATATAAAAT
Found at i:5191953 original size:17 final size:19
Alignment explanation
Indices: 5191909--5191964 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
5191899 TCTAAAATTT
5191909 ACATT-TAAAAAAATATAA
1 ACATTCTAAAAAAATATAA
*
5191927 ACATTTTAAAAAAATA-AA
1 ACATTCTAAAAAAATATAA
*
5191945 A-ATTCTAAATAATATATAA
1 ACATTCTAAA-AAAATATAA
5191964 A
1 A
5191965 AAATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 7 0.21
18 13 0.39
19 13 0.39
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
ACATTCTAAAAAAATATAA
Found at i:5198299 original size:49 final size:49
Alignment explanation
Indices: 5198242--5198335 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 49
5198232 TGTCTAGAAC
* * *
5198242 TACCCATAACTCTTCATCAACCCATAAATAAGAGGATAATATGCTTCAG
1 TACCCATAACTCCTCACCAACCCATAAATAAGAAGATAATATGCTTCAG
* * *
5198291 TACCCATAATTCCTCCCCAACCCATAAATAAGAATATAATATGCT
1 TACCCATAACTCCTCACCAACCCATAAATAAGAAGATAATATGCT
5198336 CCAAAAGGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (49 bp):
TACCCATAACTCCTCACCAACCCATAAATAAGAAGATAATATGCTTCAG
Found at i:5205167 original size:88 final size:88
Alignment explanation
Indices: 5205018--5205194 Score: 275
Period size: 88 Copynumber: 2.0 Consensus size: 88
5205008 TAGGTTCAAT
* *
5205018 CTCCCAATTTTATAGTCCTTCATTCATTGATAATACACTTACTGTTTTTCTTTTTTTTGGAATCC
1 CTCCCAATTCTATAGTCCTTCATTCATTAATAATACACTTACTGTTTTTCTTTTTTTTGGAATCC
5205083 TTATGCAGATCACTTGATCTTCA
66 TTATGCAGATCACTTGATCTTCA
* ** * *
5205106 CTCCCAATTCTATAGTCCTTCACTT-GTTAATAATGTACTTACTGTTTTTTTTTTTTTTGGAATT
1 CTCCCAATTCTATAGTCCTTCA-TTCATTAATAATACACTTACTGTTTTTCTTTTTTTTGGAATC
5205170 CTTATGCAGATCACTTGATCTTCA
65 CTTATGCAGATCACTTGATCTTCA
5205194 C
1 C
5205195 AAAAGGCTCA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 79 0.98
89 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (88 bp):
CTCCCAATTCTATAGTCCTTCATTCATTAATAATACACTTACTGTTTTTCTTTTTTTTGGAATCC
TTATGCAGATCACTTGATCTTCA
Found at i:5222034 original size:27 final size:28
Alignment explanation
Indices: 5221981--5222036 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
5221971 TATGTTCCCC
*
5221981 AATTTTTTTTTAATTTTATCTCAACTTCT
1 AATTTTTTTTT-ATTTTAACTCAACTTCT
5222010 AATTTTTTTTT-TTTTAACTTC-ACTTCT
1 AATTTTTTTTTATTTTAAC-TCAACTTCT
5222037 GATACAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 12 0.48
28 2 0.08
29 11 0.44
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (28 bp):
AATTTTTTTTTATTTTAACTCAACTTCT
Found at i:5226403 original size:15 final size:15
Alignment explanation
Indices: 5226385--5226451 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
5226375 TTATAATTAA
5226385 ATAAATTTTAATATT
1 ATAAATTTTAATATT
*
5226400 AT-AATAATTAATATTAT
1 ATAAAT-TTTAATA-T-T
*
5226417 ATAAACTTTTAA-ATA
1 ATAAA-TTTTAATATT
5226432 ATAAATTTT-ATATT
1 ATAAATTTTAATATT
5226446 -TAAATT
1 ATAAATT
5226452 GGGAACCCAC
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
13 7 0.17
14 9 0.21
15 13 0.31
16 2 0.05
17 4 0.10
18 6 0.14
19 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
ATAAATTTTAATATT
Found at i:5226778 original size:14 final size:14
Alignment explanation
Indices: 5226759--5226789 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5226749 CAAATTTTAA
5226759 AAAATATAAAAATT
1 AAAATATAAAAATT
*
5226773 AAAATATAAAGATT
1 AAAATATAAAAATT
5226787 AAA
1 AAA
5226790 TCCGTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:5232071 original size:2 final size:2
Alignment explanation
Indices: 5232064--5232098 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5232054 GCTACTCTAT
* *
5232064 TA TA TA TA TA AA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5232099 TTCTACATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5235985 original size:20 final size:20
Alignment explanation
Indices: 5235960--5235997 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5235950 GTGTTTATCT
5235960 TAAATTAAAATAACTAGAGA
1 TAAATTAAAATAACTAGAGA
5235980 TAAATTAAAATAACTAGA
1 TAAATTAAAATAACTAGA
5235998 TTTCAGCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (20 bp):
TAAATTAAAATAACTAGAGA
Found at i:5238209 original size:221 final size:223
Alignment explanation
Indices: 5237814--5238258 Score: 876
Period size: 221 Copynumber: 2.0 Consensus size: 223
5237804 ATAATTTTAT
5237814 TTGAATTAATTATAAAATAATTTATAAATATTGATATGAAATTATATATTTTATTATCTTTCAAG
1 TTGAATTAATTATAAAATAATTTATAAATATTGATATGAAATTATATATTTTATTATCTTTCAAG
5237879 CAGAAATATGAGCTTTTGAATAGATGGAGCTGGATTCAGGTCCGGTCTTAATTTTTTTTTTTAAT
66 CAGAAATATGAGCTTTTGAATAGATGGAGCTGGATTCAGGTCCGGTCTTAATTTTTTTTTTTAAT
5237944 CGGATCTTGACAGGTGAACTTTTATTTAGGTTTTGGGCTTGGGCTTCCGATTATTTCCGAGAATT
131 CGGATCTTGACAGGTGAACTTTTATTTAGGTTTTGGGCTTGGGCTTCCGATTATTTCCGAGAATT
5238009 CTTAATGTACTTACTTTCTCACGCGCCC
196 CTTAATGTACTTACTTTCTCACGCGCCC
5238037 TTGAATTAA-T-TAAAATAATTTATAAATATTGATATGAAATTATATATTTTATTATCTTTCAAG
1 TTGAATTAATTATAAAATAATTTATAAATATTGATATGAAATTATATATTTTATTATCTTTCAAG
5238100 CAGAAATATGAGCTTTTGAATAGATGGAGCTGGATTCAGGTCCGGTCTTAATTTTTTTTTTTAAT
66 CAGAAATATGAGCTTTTGAATAGATGGAGCTGGATTCAGGTCCGGTCTTAATTTTTTTTTTTAAT
5238165 CGGATCTTGACAGGTGAACTTTTATTTAGGTTTTGGGCTTGGGCTTCCGATTATTTCCGAGAATT
131 CGGATCTTGACAGGTGAACTTTTATTTAGGTTTTGGGCTTGGGCTTCCGATTATTTCCGAGAATT
5238230 CTTAATGTACTTACTTTCTCACGCGCCC
196 CTTAATGTACTTACTTTCTCACGCGCCC
5238258 T
1 T
5238259 CTGATTGGTT
Statistics
Matches: 222, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
221 212 0.95
222 1 0.00
223 9 0.04
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (223 bp):
TTGAATTAATTATAAAATAATTTATAAATATTGATATGAAATTATATATTTTATTATCTTTCAAG
CAGAAATATGAGCTTTTGAATAGATGGAGCTGGATTCAGGTCCGGTCTTAATTTTTTTTTTTAAT
CGGATCTTGACAGGTGAACTTTTATTTAGGTTTTGGGCTTGGGCTTCCGATTATTTCCGAGAATT
CTTAATGTACTTACTTTCTCACGCGCCC
Found at i:5241898 original size:20 final size:20
Alignment explanation
Indices: 5241848--5241898 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5241838 TTGTTCAAAA
* *
5241848 ATAATAATAATAATTTAATT
1 ATAAAAATATTAATTTAATT
5241868 ATAAAAATATTAATATTAA-T
1 ATAAAAATATTAAT-TTAATT
*
5241888 ATAAAATTATT
1 ATAAAAATATT
5241899 TTATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAAAAATATTAATTTAATT
Found at i:5243747 original size:30 final size:30
Alignment explanation
Indices: 5243711--5243780 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
5243701 ATAATCTAAT
* *
5243711 AATATTATAAAATGAAGGAAGGAAAGAAAG
1 AATATTAGAAAATGAAGAAAGGAAAGAAAG
*
5243741 AATATTAGAAAATGAAGAAATGAAAGAAAG
1 AATATTAGAAAATGAAGAAAGGAAAGAAAG
5243771 AATATTAGAA
1 AATATTAGAA
5243781 TTTGTTGGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.19
Consensus pattern (30 bp):
AATATTAGAAAATGAAGAAAGGAAAGAAAG
Found at i:5245406 original size:49 final size:46
Alignment explanation
Indices: 5245281--5245406 Score: 132
Period size: 45 Copynumber: 2.7 Consensus size: 46
5245271 AATATAGATG
* * * *
5245281 AAAATATATTGATATTTG-TATGAACTATTTGAAATTTTTTACATATT
1 AAAATATA-TGATATTTGAAAT-AATTATTTGAAATATTTTACATATA
*
5245328 AAAGTA-ATGATATTTGAAATAAGTT-TTTGAAATATTTTACATATAA
1 AAAATATATGATATTTGAAATAA-TTATTTGAAATATTTTACATAT-A
5245374 AAAATAATAGTGATATTTGAAATAATTATTTGA
1 AAAAT-ATA-TGATATTTGAAATAATTATTTGA
5245407 TTTTATTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
45 29 0.44
46 8 0.12
47 6 0.09
48 3 0.05
49 20 0.30
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (46 bp):
AAAATATATGATATTTGAAATAATTATTTGAAATATTTTACATATA
Found at i:5245859 original size:2 final size:2
Alignment explanation
Indices: 5245852--5245887 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5245842 TGAGAATGGA
5245852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5245888 TTAAAAGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5253074 original size:24 final size:24
Alignment explanation
Indices: 5253025--5253075 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5253015 AATGGCCTAC
* ** *
5253025 ATACATATACATATACGTATGTAT
1 ATACATAAACATATACACATGCAT
5253049 ATACATAAACATATACACATGCAT
1 ATACATAAACATATACACATGCAT
5253073 ATA
1 ATA
5253076 AAACAGGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (24 bp):
ATACATAAACATATACACATGCAT
Found at i:5259035 original size:4 final size:4
Alignment explanation
Indices: 5259026--5259066 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
5259016 AGATGGTTAA
* * *
5259026 TATG TATG TATG TATG AATG AATG TATG TATG TATG CATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
5259067 GTAGTTTCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (4 bp):
TATG
Found at i:5274918 original size:2 final size:2
Alignment explanation
Indices: 5274911--5274973 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
5274901 ATGGGAAAAT
*
5274911 GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5274953 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
5274974 GATTATTATC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5287277 original size:9 final size:9
Alignment explanation
Indices: 5287268--5287336 Score: 102
Period size: 9 Copynumber: 7.7 Consensus size: 9
5287258 TCAATTCGGG
*
5287268 TAATTTGGG
1 TAATTTGGT
5287277 TAATTTGGT
1 TAATTTGGT
*
5287286 TAATTCGGT
1 TAATTTGGT
* *
5287295 TAATTCGGG
1 TAATTTGGT
5287304 TAATTTGGT
1 TAATTTGGT
5287313 TAATTTGGT
1 TAATTTGGT
5287322 TAATTTGGT
1 TAATTTGGT
5287331 TAATTT
1 TAATTT
5287337 TTAACCAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (9 bp):
TAATTTGGT
Found at i:5287289 original size:18 final size:18
Alignment explanation
Indices: 5287260--5287336 Score: 100
Period size: 18 Copynumber: 4.3 Consensus size: 18
5287250 GTAGTGATTC
* *
5287260 AATTCGGGTAATTTGGGT
1 AATTTGGGTAATTTGGTT
* *
5287278 AATTTGGTTAATTCGGTT
1 AATTTGGGTAATTTGGTT
*
5287296 AATTCGGGTAATTTGGTT
1 AATTTGGGTAATTTGGTT
*
5287314 AATTTGGTTAATTTGGTT
1 AATTTGGGTAATTTGGTT
5287332 AATTT
1 AATTT
5287337 TTAACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (18 bp):
AATTTGGGTAATTTGGTT
Found at i:5287291 original size:27 final size:27
Alignment explanation
Indices: 5287260--5287336 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
5287250 GTAGTGATTC
*
5287260 AATTCGGGTAATTTGGGTAATTTGGTT
1 AATTCGGTTAATTTGGGTAATTTGGTT
*
5287287 AATTCGGTTAATTCGGGTAATTTGGTT
1 AATTCGGTTAATTTGGGTAATTTGGTT
* *
5287314 AATTTGGTTAATTTGGTTAATTT
1 AATTCGGTTAATTTGGGTAATTT
5287337 TTAACCAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (27 bp):
AATTCGGTTAATTTGGGTAATTTGGTT
Found at i:5287556 original size:9 final size:9
Alignment explanation
Indices: 5287547--5287615 Score: 102
Period size: 9 Copynumber: 7.7 Consensus size: 9
5287537 TCAATTCGGG
*
5287547 TAATTTGGG
1 TAATTTGGT
5287556 TAATTTGGT
1 TAATTTGGT
*
5287565 TAATTCGGT
1 TAATTTGGT
* *
5287574 TAATTCGGG
1 TAATTTGGT
5287583 TAATTTGGT
1 TAATTTGGT
5287592 TAATTTGGT
1 TAATTTGGT
5287601 TAATTTGGT
1 TAATTTGGT
5287610 TAATTT
1 TAATTT
5287616 TTAACCAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (9 bp):
TAATTTGGT
Found at i:5287568 original size:18 final size:18
Alignment explanation
Indices: 5287539--5287615 Score: 100
Period size: 18 Copynumber: 4.3 Consensus size: 18
5287529 GTAGTGATTC
* *
5287539 AATTCGGGTAATTTGGGT
1 AATTTGGGTAATTTGGTT
* *
5287557 AATTTGGTTAATTCGGTT
1 AATTTGGGTAATTTGGTT
*
5287575 AATTCGGGTAATTTGGTT
1 AATTTGGGTAATTTGGTT
*
5287593 AATTTGGTTAATTTGGTT
1 AATTTGGGTAATTTGGTT
5287611 AATTT
1 AATTT
5287616 TTAACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (18 bp):
AATTTGGGTAATTTGGTT
Found at i:5287570 original size:27 final size:27
Alignment explanation
Indices: 5287539--5287615 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
5287529 GTAGTGATTC
*
5287539 AATTCGGGTAATTTGGGTAATTTGGTT
1 AATTCGGTTAATTTGGGTAATTTGGTT
*
5287566 AATTCGGTTAATTCGGGTAATTTGGTT
1 AATTCGGTTAATTTGGGTAATTTGGTT
* *
5287593 AATTTGGTTAATTTGGTTAATTT
1 AATTCGGTTAATTTGGGTAATTT
5287616 TTAACCAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (27 bp):
AATTCGGTTAATTTGGGTAATTTGGTT
Found at i:5287594 original size:279 final size:279
Alignment explanation
Indices: 5287094--5287652 Score: 1109
Period size: 279 Copynumber: 2.0 Consensus size: 279
5287084 AATCCAAACT
5287094 TAAGTATCCAACCCAACCCAACCCAATTACATAACTCAACTCAATCATAAAAATTACAAATAATT
1 TAAGTATCCAACCCAACCCAACCCAATTACATAACTCAACTCAATCATAAAAATTACAAATAATT
5287159 TAATAAATAAAAATAAATTTTCAATTATGTGTTAATTTCAAGACTTATGTAATATTAGTGATTCA
66 TAATAAATAAAAATAAATTTTCAATTATGTGTTAATTTCAAGACTTATGTAATATTAGTGATTCA
5287224 AACACTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTTGGGTAATTTGGTTAA
131 AACACTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTTGGGTAATTTGGTTAA
5287289 TTCGGTTAATTCGGGTAATTTGGTTAATTTGGTTAATTTGGTTAATTTTTAACCAAAAATAAAGA
196 TTCGGTTAATTCGGGTAATTTGGTTAATTTGGTTAATTTGGTTAATTTTTAACCAAAAATAAAGA
5287354 ACAAATAATTTTCGGTTAA
261 ACAAATAATTTTCGGTTAA
5287373 TAAGTATCCAACCCAACCCAACCCAATTACATAACTCAACTCAATCATAAAAATTACAAATAATT
1 TAAGTATCCAACCCAACCCAACCCAATTACATAACTCAACTCAATCATAAAAATTACAAATAATT
5287438 TAATAAATAAAAATAAATTTTCAATTATGTGTTAATTTCAAGACTTATGTAATATTAGTGATTCA
66 TAATAAATAAAAATAAATTTTCAATTATGTGTTAATTTCAAGACTTATGTAATATTAGTGATTCA
5287503 AACACTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTTGGGTAATTTGGTTAA
131 AACACTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTTGGGTAATTTGGTTAA
5287568 TTCGGTTAATTCGGGTAATTTGGTTAATTTGGTTAATTTGGTTAATTTTTAACCAAAAATAAAGA
196 TTCGGTTAATTCGGGTAATTTGGTTAATTTGGTTAATTTGGTTAATTTTTAACCAAAAATAAAGA
*
5287633 ACATATAATTTTCGGTTAA
261 ACAAATAATTTTCGGTTAA
5287652 T
1 T
5287653 TCGGTTAACC
Statistics
Matches: 279, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
279 279 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (279 bp):
TAAGTATCCAACCCAACCCAACCCAATTACATAACTCAACTCAATCATAAAAATTACAAATAATT
TAATAAATAAAAATAAATTTTCAATTATGTGTTAATTTCAAGACTTATGTAATATTAGTGATTCA
AACACTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTTGGGTAATTTGGTTAA
TTCGGTTAATTCGGGTAATTTGGTTAATTTGGTTAATTTGGTTAATTTTTAACCAAAAATAAAGA
ACAAATAATTTTCGGTTAA
Found at i:5287882 original size:50 final size:53
Alignment explanation
Indices: 5287789--5287909 Score: 185
Period size: 50 Copynumber: 2.3 Consensus size: 53
5287779 ACACCCCTAT
*
5287789 TGTCAATGGTCGGCACCACCAATACAAAAAAAAAGAAATTTTGGGTGCTGGCC
1 TGTCAATGGCCGGCACCACCAATACAAAAAAAAAGAAATTTTGGGTGCTGGCC
* *
5287842 TGTCAATGACCGGCACCACCAATAC-GAAAAAAA-AAA-TTTGGGTGCTGGCC
1 TGTCAATGGCCGGCACCACCAATACAAAAAAAAAGAAATTTTGGGTGCTGGCC
*
5287892 TGTCAATGGCAGGCACCA
1 TGTCAATGGCCGGCACCA
5287910 GTAGTTCCCA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
50 30 0.48
51 3 0.05
52 7 0.11
53 23 0.37
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (53 bp):
TGTCAATGGCCGGCACCACCAATACAAAAAAAAAGAAATTTTGGGTGCTGGCC
Found at i:5287950 original size:13 final size:13
Alignment explanation
Indices: 5287932--5287956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5287922 AAAAATTGGC
5287932 TTTATTTAAATTA
1 TTTATTTAAATTA
5287945 TTTATTTAAATT
1 TTTATTTAAATT
5287957 TCACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATTTAAATTA
Found at i:5296951 original size:51 final size:50
Alignment explanation
Indices: 5296871--5297652 Score: 759
Period size: 51 Copynumber: 15.8 Consensus size: 50
5296861 AGTCATTATG
* * * * *
5296871 GCGAATCTTTTTTCCCGGGCGTTGTAGTGGAACAGATTAAAGCTGGAGACA
1 GCGAATCTTATTT-CCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * * *
5296922 ACGAATTTTATTTTCCTAGCGTTGCAGTGGAACATATTAAAGCTGAAGGCA
1 GCGAATCTTA-TTTCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * * * * * * *
5296973 GTGAATCTTATTTCTTTAGCGTTGTAGTGGGATAGATTAAAGTTGAAGGCG
1 GCGAATCTTATTTC-CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* *
5297024 GTGAATCTTATTTCCATGGCGTTGCAGT-----AGATTAAAGTTGAAGGCA
1 GCGAATCTTATTTCC-TGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * *
5297070 GCGAATCTTTTTTCTTTAGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
1 GCGAATCTTATTTC-CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * * * *
5297121 ACGAATCTTATTTCTCTGGCATTGTAGT-----AGATTAAATCTGAAGGTA
1 GCGAATCTTATTTC-CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * *
5297167 GCGAATCTTATTTCCTTGGTGTTACAGTGGAACATATTAAAGCTGAAGGCA
1 GCGAATCTTATTTCC-TGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * * *
5297218 GTGAATCTTATTTCCTTGCGTTGCAGT-----AGATTAAAGCTGAAAGTA
1 GCGAATCTTATTTCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* *
5297263 GCGAATCTTTTTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAAGCA
1 GCGAATCTTATTTCC-TGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
*
5297314 GCGAATCTTATTTCTCTGGCGTTGCAAT---A-A-ATTAAAGCTGAAGGCA
1 GCGAATCTTATTTC-CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
*
5297360 GCGAATCTTATTTCCTTGGCGTTACAGTGGAACAGATTAAAGCTGAAGGCA
1 GCGAATCTTATTTCC-TGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * * *
5297411 TCGGATCTTTTTTCCTTGGCGTTGCAGTGGAACAAATTAAAGCTGAAGGCA
1 GCGAATCTTATTTCC-TGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* *
5297462 GCGAATCTTATTTCCCTGGCGTTGCAGT-----AGATTAAAACTGAAGGTA
1 GCGAATCTTATTT-CCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * * *
5297508 GCAAATCTTATTTCTTTGGCGTTACAGTGGAACAGATTAAAGCTGAAGACA
1 GCGAATCTTATTTC-CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * * *
5297559 GCAAATCTTATTTCTCTGACGTTGCAGTGGAATAGATTAAAGCTAAAGGCA
1 GCGAATCTTATTTC-CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
* * *
5297610 ACGAATCTTTTTTCTCAGGCGTTGCAGTGGAACAGATTAAAGC
1 GCGAATCTTATTTC-CTGGCGTTGCAGTGGAACAGATTAAAGC
5297653 CACAAATTAT
Statistics
Matches: 607, Mismatches: 89, Indels: 70
0.79 0.12 0.09
Matches are distributed among these distances:
45 31 0.05
46 165 0.27
47 1 0.00
48 1 0.00
49 1 0.00
50 14 0.02
51 388 0.64
52 6 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (50 bp):
GCGAATCTTATTTCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCA
Found at i:5297093 original size:97 final size:96
Alignment explanation
Indices: 5296871--5297637 Score: 729
Period size: 97 Copynumber: 7.8 Consensus size: 96
5296861 AGTCATTATG
* ** * * * ** *
5296871 GCGAATCTTTTTTCCCGGGCGTTGTAGTGGAACAGATTAAAGCTGGAGACAACGAATTTTATTTT
1 GCGAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTA-TTT
* *
5296936 CCTAGCGTTGCAGTGGAACATATTAAAGCTGAAGGCA
65 CCTGGCGTTGCAGT-----AGATTAAAGCTGAAGGCA
* * * * * * * *
5296973 GTGAATCTTATTTCTTTAGCGTTGTAGTGGGATAGATTAAAGTTGAAGGCGGTGAATCTTATTTC
1 GCGAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATTTC
*
5297038 CATGGCGTTGCAGTAGATTAAAGTTGAAGGCA
66 C-TGGCGTTGCAGTAGATTAAAGCTGAAGGCA
* * * **
5297070 GCGAATCTTTTTTCTTTAGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAACGAATCTTATTTC
1 GCGAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATTTC
* * * *
5297135 TCTGGCATTGTAGTAGATTAAATCTGAAGGTA
66 -CTGGCGTTGCAGTAGATTAAAGCTGAAGGCA
* * *
5297167 GCGAATCTTATTTCCTTGGTGTTACAGTGGAACATATTAAAGCTGAAGGCAGTGAATCTTATTTC
1 GCGAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATTTC
* * *
5297232 CTTGCGTTGCAGTAGATTAAAGCTGAAAGTA
66 CTGGCGTTGCAGTAGATTAAAGCTGAAGGCA
* * *
5297263 GCGAATCTTTTTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAAGCAGCGAATCTTATTTC
1 GCGAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATTTC
* *
5297328 TCTGGCGTTGCAATAAATTAAAGCTGAAGGCA
66 -CTGGCGTTGCAGTAGATTAAAGCTGAAGGCA
* * *
5297360 GCGAATCTTATTTCCTTGGCGTTACAGTGGAACAGATTAAAGCTGAAGGCA-TCGGATCTTTTTT
1 GCGAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGT-GAATCTTATTT
*
5297424 CCTTGGCGTTGCAGTGGAACAAATTAAAGCTGAAGGCA
65 CC-TGGCGTTGCAGT-----AGATTAAAGCTGAAGGCA
* * * **
5297462 GCGAATCTTATTTCCCTGGCGTTGCAGT-----AGATTAAAACTGAAGGTAGCAAATCTTATTTC
1 GCGAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATTTC
* * *
5297522 TTTGGCGTTACAGTGGAACAGATTAAAGCTGAAGACA
66 -CTGGCGTTGCAGT-----AGATTAAAGCTGAAGGCA
* * * * ** *
5297559 GCAAATCTTATTT-CTCTGACGTTGCAGTGGAATAGATTAAAGCTAAAGGCAACGAATCTTTTTT
1 GCGAATCTTATTTCCT-TGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATTT
*
5297623 CTCAGGCGTTGCAGT
65 C-CTGGCGTTGCAGT
5297638 GGAACAGATT
Statistics
Matches: 560, Mismatches: 87, Indels: 36
0.82 0.13 0.05
Matches are distributed among these distances:
96 87 0.16
97 329 0.59
98 1 0.00
101 5 0.01
102 138 0.25
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (96 bp):
GCGAATCTTATTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATTTC
CTGGCGTTGCAGTAGATTAAAGCTGAAGGCA
Found at i:5297100 original size:148 final size:148
Alignment explanation
Indices: 5296904--5297637 Score: 794
Period size: 148 Copynumber: 5.0 Consensus size: 148
5296894 GTAGTGGAAC
* * * * *
5296904 AGATTAAAGCTGGAGACAACGAATTTTATTTTCC-TAGCGTTGCAGTGGAACATATTAAAGCTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTA-TTTCCTTAGCGTTGCAGTGGAACAGATTAAAGCTGA
* * * * * * *
5296968 AGGCAGTGAATCTTATTTCTTTAGCGTTGTAGTGGGATAGATTAAAGTTGAAGGCGGTGAATCTT
65 AGGCAGCGAATCTTATTTCTTTGGCGTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTT
5297033 ATTTCCATGGCGTTGCAGT
130 ATTTCCATGGCGTTGCAGT
* * *
5297052 AGATTAAAGTTGAAGGCAGCGAATCTTTTTTCTTTAGCGTTGCAGTGGAACAGATTAAAGCTGAA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTAGCGTTGCAGTGGAACAGATTAAAGCTGAA
* * * * * *
5297117 GGCAACGAATCTTATTTCTCTGGCATT---GT--AGTAGATTAAATCTGAAGGTAGCGAATCTTA
66 GGCAGCGAATCTTATTTCTTTGGCGTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTA
* * *
5297177 TTTCCTTGGTGTTACAGT
131 TTTCCATGGCGTTGCAGT
* *
5297195 GGAACATATTAAAGCTGAAGGCAGTGAATCTTATTTCCTT-GCGTTGCAGT-----AGATTAAAG
1 -----AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTAGCGTTGCAGTGGAACAGATTAAAG
* * * * * *
5297254 CTGAAAGTAGCGAATCTTTTTTCCTTGGCGTTGCAGTGGAACAGATTAAAGCTGAAAGCAGCGAA
61 CTGAAGGCAGCGAATCTTATTTCTTTGGCGTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAA
*
5297319 TCTTATTTCTC-TGGCGTTGCAAT
126 TCTTATTTC-CATGGCGTTGCAGT
* * *
5297342 AAATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTACAGTGGAACAGATTAAAGCTGAA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTAGCGTTGCAGTGGAACAGATTAAAGCTGAA
* * * * * *
5297407 GGCATCGGATCTTTTTTCCTTGGCGTTGCAGTGGAACAAATTAAAGCTGAAGGCAGCGAATCTTA
66 GGCAGCGAATCTTATTTCTTTGGCGTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTA
*
5297472 TTTCCCTGGCGTTGCAGT
131 TTTCCATGGCGTTGCAGT
* * * * * *
5297490 AGATTAAAACTGAAGGTAGCAAATCTTATTTCTTTGGCGTTACAGTGGAACAGATTAAAGCTGAA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTAGCGTTGCAGTGGAACAGATTAAAGCTGAA
* * * * * * *
5297555 GACAGCAAATCTTATTTCTCTGACGTTGCAGTGGAATAGATTAAAGCTAAAGGCAACGAATCTTT
66 GGCAGCGAATCTTATTTCTTTGGCGTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTA
5297620 TTTCTCA-GGCGTTGCAGT
131 TTTC-CATGGCGTTGCAGT
5297638 GGAACAGATT
Statistics
Matches: 494, Mismatches: 72, Indels: 40
0.82 0.12 0.07
Matches are distributed among these distances:
142 67 0.14
143 48 0.10
145 4 0.01
147 54 0.11
148 320 0.65
149 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (148 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTAGCGTTGCAGTGGAACAGATTAAAGCTGAA
GGCAGCGAATCTTATTTCTTTGGCGTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTA
TTTCCATGGCGTTGCAGT
Found at i:5297867 original size:143 final size:143
Alignment explanation
Indices: 5297608--5298093 Score: 677
Period size: 143 Copynumber: 3.4 Consensus size: 143
5297598 AAGCTAAAGG
* * * *
5297608 CAACGAATCTTTTTTCTCAGGCGTTGCAGTGGAACAGATTAAAGCCACAAATTATGATGGATCTT
1 CAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCCACAAATTATGGTGGATCTT
* * * *
5297673 ATCTTTTTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTACAGTGG
66 ATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGG
*
5297738 AGTAGACTGAAGA
131 AGCAGACTGAAGA
* * ** * *
5297751 AAACGAATCTTATTTCCTTGGCGTTGCAGTGTTACAGATTAAAGCTACAAATTATGGTGGATCCT
1 CAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCCACAAATTATGGTGGATCTT
* * * * * *
5297816 ATCTTCTTGAAGTTGTAGTGAAACAGATTGAAGCCACTACCCTTATCTCCCTGAAGTTGCAGCGA
66 ATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGG
5297881 AGCAGACTGAAGA
131 AGCAGACTGAAGA
* * * **
5297894 CAGC-AGATCCTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCAGATCT
1 CAACGA-ATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCCACAAATTATGGTGGATCT
* *
5297958 TATCTTCTTGAAGTTGCAGTGGAGTAGATTGATGCCACCAGCCTTATCTCCCTGAAGTTGCAGCG
65 TATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCG
5298023 GAGCAGACTGAAGA
130 GAGCAGACTGAAGA
* * *
5298037 CAGCGAATCTTATTTCCCTGGTGTTGCAGTGGAACAGATTAAAGCCACAAGTTATGG
1 CAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCCACAAATTATGG
5298094 GAAGTTGCAG
Statistics
Matches: 299, Mismatches: 42, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
142 1 0.00
143 297 0.99
144 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (143 bp):
CAACGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCCACAAATTATGGTGGATCTT
ATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGG
AGCAGACTGAAGA
Found at i:5298019 original size:44 final size:44
Alignment explanation
Indices: 5297956--5298161 Score: 181
Period size: 44 Copynumber: 4.8 Consensus size: 44
5297946 TATGGCAGAT
* * * * *
5297956 CTTATCTTCTTGAAGTTGCAGTGGAGTAGATTGATGCCACCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAAC
* * * * *
5298000 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CCAAC
* ** * *
5298045 CTTATTTCCCTGGTGTTGCAGTGGAACAGATTAAAGCCA-CAA-
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAAC
* ** **
5298087 GTTA--T--GGGAAGTTGCAGTGGAGCAGATCAAAGCCACCAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAAC
5298127 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
5298162 AGTAGTAAAT
Statistics
Matches: 124, Mismatches: 31, Indels: 14
0.73 0.18 0.08
Matches are distributed among these distances:
38 24 0.19
39 3 0.02
40 4 0.03
42 4 0.03
43 2 0.02
44 54 0.44
45 33 0.27
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAAC
Found at i:5299618 original size:23 final size:23
Alignment explanation
Indices: 5299592--5299636 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5299582 TTTAGCCTCT
5299592 TTTTGTTTCTGTCTTG-GTTTTAA
1 TTTTGTTT-TGTCTTGTGTTTTAA
*
5299615 TTTTGTTTTGTGTTGTGTTTTA
1 TTTTGTTTTGTCTTGTGTTTTA
5299637 CTTATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.69
Consensus pattern (23 bp):
TTTTGTTTTGTCTTGTGTTTTAA
Found at i:5299753 original size:3 final size:3
Alignment explanation
Indices: 5299739--5299785 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
5299729 CGTGAACTTC
* *
5299739 ATT ATT AGT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5299786 GTTTTCATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5299790 original size:8 final size:8
Alignment explanation
Indices: 5299747--5299798 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 8
5299737 TCATTATTAG
5299747 TATTATTAT
1 TATTATT-T
*
5299756 TACTATTAT
1 TATTATT-T
5299765 TATTATTAT
1 TATTATT-T
5299774 TATTATTT
1 TATTATTT
*
5299782 TATTGTTT
1 TATTATTT
5299790 TCATTATTT
1 T-ATTATTT
5299799 CACTTATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
8 9 0.24
9 29 0.76
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (8 bp):
TATTATTT
Found at i:5303482 original size:20 final size:22
Alignment explanation
Indices: 5303446--5303487 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5303436 AATGCTTCTC
*
5303446 AAAAATACTTTTAGGGA-AAAA
1 AAAAACACTTTTAGGGACAAAA
5303467 AAAAACACTTTT-GGGACAAAA
1 AAAAACACTTTTAGGGACAAAA
5303488 GCATTCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.21
Consensus pattern (22 bp):
AAAAACACTTTTAGGGACAAAA
Found at i:5308971 original size:12 final size:12
Alignment explanation
Indices: 5308954--5308979 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5308944 TAATCCTCTC
5308954 AATTTCCTTCCA
1 AATTTCCTTCCA
5308966 AATTTCCTTCCA
1 AATTTCCTTCCA
5308978 AA
1 AA
5308980 ATTCTCTCAA
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:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTCCTTCCA
Found at i:5309031 original size:51 final size:51
Alignment explanation
Indices: 5308952--5309073 Score: 183
Period size: 51 Copynumber: 2.4 Consensus size: 51
5308942 TCTAATCCTC
* *
5308952 TCAATTTCCTTCCAAATTTCCTTCCAAAATTCTCTCAAACCCATCTTTAATT
1 TCAATTTCC-TCCCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
* *
5309004 TCAATTTCCTCCCAATTTCCTTTCAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCCCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
5309055 TCAATTTCC-CCTCAATTTC
1 TCAATTTCCTCC-CAATTTC
5309074 ATTTTTTAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
50 2 0.03
51 54 0.83
52 9 0.14
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (51 bp):
TCAATTTCCTCCCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
Found at i:5309109 original size:30 final size:31
Alignment explanation
Indices: 5309074--5309138 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
5309064 CCTCAATTTC
5309074 ATTTTTT-AAAATAATTTTAAA-TTTTTTAT
1 ATTTTTTAAAAATAATTTTAAATTTTTTTAT
5309103 ATTTTTTAAAAATAATTTTAAATTTTTTTAT
1 ATTTTTTAAAAATAATTTTAAATTTTTTTAT
5309134 ATTTT
1 ATTTT
5309139 CATCAATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 7 0.21
30 14 0.41
31 13 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
ATTTTTTAAAAATAATTTTAAATTTTTTTAT
Found at i:5310044 original size:7 final size:7
Alignment explanation
Indices: 5310032--5310056 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5310022 AGTCGATTGA
5310032 TATTTAG
1 TATTTAG
5310039 TATTTAG
1 TATTTAG
5310046 TATTTAG
1 TATTTAG
5310053 TATT
1 TATT
5310057 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:5310734 original size:18 final size:18
Alignment explanation
Indices: 5310708--5310742 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5310698 AGGTGTGTTT
* *
5310708 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
5310726 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
5310743 TCCTTTTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:5326365 original size:124 final size:124
Alignment explanation
Indices: 5326145--5326988 Score: 1652
Period size: 124 Copynumber: 6.8 Consensus size: 124
5326135 CAAACTTGCT
5326145 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
5326210 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
66 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
5326269 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
5326334 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
66 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
5326393 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
5326458 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
66 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
5326517 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
5326582 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
66 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
5326641 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
5326706 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
66 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
5326765 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
5326830 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
66 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
* *
5326889 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTCCCCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
* *
5326954 GAAGCGATTTTATACTATTTGCTCAAAAACGTCAA
66 TAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
5326989 CTCGAAATAA
Statistics
Matches: 716, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 716 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (124 bp):
ACTGTAGCAAAATCGCGTCCACGAGGGTCCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
TAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
Found at i:5327194 original size:29 final size:28
Alignment explanation
Indices: 5327136--5327196 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
5327126 GATTTCCCGG
*
5327136 AAAATGGACCATTCCGGTAAATAATCAA
1 AAAATGGACCATTCCGGTAAATAATAAA
* * **
5327164 AAAATCGGCCCATTTCGGTAAATTTTAAA
1 AAAAT-GGACCATTCCGGTAAATAATAAA
5327193 AAAA
1 AAAA
5327197 AAACGACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (28 bp):
AAAATGGACCATTCCGGTAAATAATAAA
Found at i:5330259 original size:4 final size:4
Alignment explanation
Indices: 5330250--5330274 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5330240 AAACATAAAT
5330250 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
5330275 CCCACACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:5332186 original size:14 final size:14
Alignment explanation
Indices: 5332164--5332206 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5332154 CTCATAATGT
5332164 TTATATTTATTATA
1 TTATATTTATTATA
* *
5332178 TTATTTTTATTATT
1 TTATATTTATTATA
5332192 TTATATCTT-TTATA
1 TTATAT-TTATTATA
5332206 T
1 T
5332207 AAATACATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATATTTATTATA
Found at i:5332512 original size:20 final size:20
Alignment explanation
Indices: 5332484--5332523 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5332474 CTCACCAACC
* *
5332484 AATTTATTTTTTACTAATTA
1 AATTGATTTTGTACTAATTA
*
5332504 AATTGATTTTGTATTAATTA
1 AATTGATTTTGTACTAATTA
5332524 TTTGAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
AATTGATTTTGTACTAATTA
Found at i:5334389 original size:60 final size:60
Alignment explanation
Indices: 5334318--5334438 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
5334308 TAGAAATATT
5334318 ATTATTTTTAATTAAGTCGAACTCAATTTTACTTTTCTTTTTTAAGAATAAAGGCAGACA
1 ATTATTTTTAATTAAGTCGAACTCAATTTTACTTTTCTTTTTTAAGAATAAAGGCAGACA
*
5334378 ATTATTTTTAATTAAGTCGAACTCAATTTTACTTTTCTTTTTTAAGAATAAAGGCATACA
1 ATTATTTTTAATTAAGTCGAACTCAATTTTACTTTTCTTTTTTAAGAATAAAGGCAGACA
5334438 A
1 A
5334439 ATAAATAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (60 bp):
ATTATTTTTAATTAAGTCGAACTCAATTTTACTTTTCTTTTTTAAGAATAAAGGCAGACA
Found at i:5337942 original size:17 final size:16
Alignment explanation
Indices: 5337920--5337969 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
5337910 AACTTATATT
5337920 AAATATATATAAATAAA
1 AAATATATA-AAATAAA
**
5337937 AAATATATAAAAATATT
1 AAATATAT-AAAATAAA
5337954 AAATAT-TAAAATAAA
1 AAATATATAAAATAAA
5337969 A
1 A
5337970 TAAAATATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.25
16 1 0.04
17 19 0.68
18 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATATATAAAATAAA
Found at i:5337973 original size:17 final size:18
Alignment explanation
Indices: 5337919--5337977 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 18
5337909 AAACTTATAT
5337919 TAAATATATATAAAT-AAA
1 TAAATATATA-AAATAAAA
* *
5337937 -AAATATATAAAA-ATAT
1 TAAATATATAAAATAAAA
5337953 TAAATAT-TAAAATAAAA
1 TAAATATATAAAATAAAA
5337970 TAAA-ATAT
1 TAAATATAT
5337978 GTTAATCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
16 11 0.33
17 22 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAATATATAAAATAAAA
Found at i:5351121 original size:17 final size:18
Alignment explanation
Indices: 5351096--5351136 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
5351086 CATGAATATT
*
5351096 ATATATATT-ATATTAAA
1 ATATCTATTAATATTAAA
5351113 ATATCTATTAATATTAAA
1 ATATCTATTAATATTAAA
5351131 A-ATCTA
1 ATATCTA
5351137 CACGCTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATCTATTAATATTAAA
Found at i:5352355 original size:28 final size:29
Alignment explanation
Indices: 5352316--5352376 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
5352306 AACAAACTTA
5352316 AAACTTTTAAAATCAATAATATTAAAATT
1 AAACTTTTAAAATCAATAATATTAAAATT
** *
5352345 AAAC-TTTAAAATCAATGTTATTAAGATT
1 AAACTTTTAAAATCAATAATATTAAAATT
5352373 AAAC
1 AAAC
5352377 CAATTGGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.36
Consensus pattern (29 bp):
AAACTTTTAAAATCAATAATATTAAAATT
Found at i:5352536 original size:20 final size:19
Alignment explanation
Indices: 5352494--5352533 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5352484 AGCTGGTTTC
5352494 TAATTTTTAAATAATTTAT
1 TAATTTTTAAATAATTTAT
5352513 TAATTTTT--ATAATTT-T
1 TAATTTTTAAATAATTTAT
5352529 TAATT
1 TAATT
5352534 AATCAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 7 0.33
19 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATTTTTAAATAATTTAT
Found at i:5356487 original size:29 final size:28
Alignment explanation
Indices: 5356437--5356491 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
5356427 TCTTCACAAA
*
5356437 TTCAGAATTTAGTCCTTATACTTTTATT
1 TTCAGAATTTAGCCCTTATACTTTTATT
5356465 TTCATGAATTTAGACCCTT-TACTTTTA
1 TTCA-GAATTTAG-CCCTTATACTTTTA
5356492 AGATTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 16 0.67
30 4 0.17
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.51
Consensus pattern (28 bp):
TTCAGAATTTAGCCCTTATACTTTTATT
Found at i:5358587 original size:12 final size:12
Alignment explanation
Indices: 5358572--5358596 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5358562 TCCATTTTAA
5358572 TATATTAAATAT
1 TATATTAAATAT
5358584 TATATTAAATAT
1 TATATTAAATAT
5358596 T
1 T
5358597 GTTAGTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATTAAATAT
Found at i:5359991 original size:24 final size:24
Alignment explanation
Indices: 5359963--5360009 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5359953 TATATATACC
5359963 AATTCAATCA-ATA-TAAATTCAATA
1 AATTC-ATCACATACTAAA-TCAATA
5359987 AATTCATCACATACTAAATCAAT
1 AATTCATCACATACTAAATCAAT
5360010 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCATCACATACTAAATCAATA
Found at i:5360843 original size:333 final size:336
Alignment explanation
Indices: 5360359--5361023 Score: 1000
Period size: 333 Copynumber: 2.0 Consensus size: 336
5360349 CTTAGACTAG
*
5360359 ATTTAACTCCCTAATTTCACTTAAATCCCTAAATTTTAATTTTTCACAATTTAATCCCTAATACT
1 ATTTAACTCCCTAATTTCACTTAAATCCCTAAATTTCAATTTTTCACAATTTAATCCCTAATACT
*
5360424 CAAAATTTACAATTTATTCTACAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATCAATTT
66 CAAAATTTAAAATTTATTCTACAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATCAATTT
* *
5360489 AATCCCTAATACTAAAATTATTCAACATAAACATCA-CTTAAAAACTTAATAATTTCTAAAATTT
131 AATCCCTAATACTAAAATTATTCAACATAAACAACATC-TAAAAACTCAATAATTTCTAAAATTT
* * *
5360553 TGACATGGGTC-GGATAGTATTTAATATCAGGATTCCAAAAATATAAAAATTACAA-AAAA-AAC
195 TGACATGGATCTGG-TAGTATTTAATACCAGGATTCCAAAAACATAAAAATTACAAGAAAAGAAC
* * * * * *
5360615 TAAA-T-TAACTAATTAAATTTTAAACCCTTGAAATCCTAACTTTTGTCCTTTTTTCTTTCTTTT
259 TAAATTATAACCAATTAAACTTTAAACCCTTAAAACCCTAACTTTTCTCCTTCTTTCTTTCTTTT
5360678 TTTTCTAAACAAA
324 TTTTCTAAACAAA
** * *
5360691 ATTTAACTTTCTAATTTCACTTAAATCCCTAAATTTCAATATTTTCACAATTTAGTCCCTATTAC
1 ATTTAACTCCCTAATTTCACTTAAATCCCTAAATTTCAAT-TTTTCACAATTTAATCCCTAATAC
*
5360756 TCAAAATTTAAAATTTATTCTATAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATCAATT
65 TCAAAATTTAAAATTTATTCTACAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATCAATT
* *
5360821 TAATCTCTAATACTAAAATTATTCAACATTAACAACATCTAAAAACTCAATAATTTCTAAAATTT
130 TAATCCCTAATACTAAAATTATTCAACATAAACAACATCTAAAAACTCAATAATTTCTAAAATTT
* * *
5360886 TGACATGGATCTGGTAGTATTTAATACCGGGATTCTAAAAACATAAAAATTACAAGAAAATGGAC
195 TGACATGGATCTGGTAGTATTTAATACCAGGATTCCAAAAACATAAAAATTACAAGAAAA-GAAC
* * *
5360951 TAAATTGACTAACCAATTGAGCTTTGAACCCTTAAAACCCTAACTTTTCTCCTTCTTTCTTTCTT
259 TAAATT-A-TAACCAATTAAACTTTAAACCCTTAAAACCCTAACTTTTCTCCTTCTTTCTTTCTT
5361016 TTTTTTCT
322 TTTTTTCT
5361024 TCCCTTTCTT
Statistics
Matches: 297, Mismatches: 26, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
332 37 0.12
333 191 0.64
334 7 0.02
336 6 0.02
337 1 0.00
340 55 0.19
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (336 bp):
ATTTAACTCCCTAATTTCACTTAAATCCCTAAATTTCAATTTTTCACAATTTAATCCCTAATACT
CAAAATTTAAAATTTATTCTACAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATCAATTT
AATCCCTAATACTAAAATTATTCAACATAAACAACATCTAAAAACTCAATAATTTCTAAAATTTT
GACATGGATCTGGTAGTATTTAATACCAGGATTCCAAAAACATAAAAATTACAAGAAAAGAACTA
AATTATAACCAATTAAACTTTAAACCCTTAAAACCCTAACTTTTCTCCTTCTTTCTTTCTTTTTT
TTCTAAACAAA
Found at i:5361070 original size:5 final size:5
Alignment explanation
Indices: 5361006--5361096 Score: 53
Period size: 5 Copynumber: 17.4 Consensus size: 5
5360996 TTTCTCCTTC
* * * *
5361006 TTTC- TTTCT TTT-T TTTC- TTCCC TTTCT TTCCT TTTCT GTTTCG TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT -TTTCT TTTCT
*
5361054 TTCTCT CCTTCT TTTCT ATTTCTT TTTCT TTTACT TTATCT TT
1 TT-TCT -TTTCT TTTCT -TTTC-T TTTCT TTT-CT TT-TCT TT
5361097 ATAATATAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
4 11 0.16
5 28 0.41
6 26 0.38
7 3 0.04
ACGTcount: A:0.03, C:0.24, G:0.02, T:0.70
Consensus pattern (5 bp):
TTTCT
Found at i:5361642 original size:18 final size:19
Alignment explanation
Indices: 5361606--5361642 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5361596 AAAAATATAA
*
5361606 ATTTTAAATTTTTATAAAT
1 ATTTTAAATTTTTAAAAAT
5361625 ATTTTAAA-TTTTAAAAAT
1 ATTTTAAATTTTTAAAAAT
5361643 TAATTTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTAAATTTTTAAAAAT
Found at i:5361649 original size:19 final size:19
Alignment explanation
Indices: 5361608--5361650 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5361598 AAATATAAAT
* *
5361608 TTTAAATTTTTATAAATAT
1 TTTAAATTTTTAAAAATAA
5361627 TTTAAA-TTTTAAAAATTAA
1 TTTAAATTTTTAAAAA-TAA
5361646 TTTAA
1 TTTAA
5361651 CCTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAAATTTTTAAAAATAA
Found at i:5365952 original size:14 final size:14
Alignment explanation
Indices: 5365929--5365968 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
5365919 AATATTTTAA
5365929 AAATTATAAAAAAT
1 AAATTATAAAAAAT
* *
5365943 TAATTTTAAAAAAT
1 AAATTATAAAAAAT
5365957 AAATTCATAAAA
1 AAATT-ATAAAA
5365969 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTATAAAAAAT
Found at i:5367058 original size:29 final size:30
Alignment explanation
Indices: 5367011--5367072 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
5367001 TGTTTGATTT
5367011 TTTAATAATATAATGACTAAATTAAT-CCA
1 TTTAATAATATAATGACTAAATTAATCCCA
* *
5367040 TTTAATAATA-GATGAACTAATTTAATCCCA
1 TTTAATAATATAATG-ACTAAATTAATCCCA
5367070 TTT
1 TTT
5367073 TTGTAATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 3 0.10
29 20 0.69
30 6 0.21
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (30 bp):
TTTAATAATATAATGACTAAATTAATCCCA
Found at i:5368638 original size:24 final size:24
Alignment explanation
Indices: 5368602--5368667 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
5368592 GAAGCTCATC
*
5368602 CGAGCC-ATAATCGGGAAGTTCAAG
1 CGAGCCAAT-ATCGGGAAATTCAAG
* * *
5368626 GGAGCCAATATCGAGAAATTCGAG
1 CGAGCCAATATCGGGAAATTCAAG
*
5368650 CGAGTCAATATCGGGAAA
1 CGAGCCAATATCGGGAAA
5368668 CTCATAAAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 32 0.94
25 2 0.06
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (24 bp):
CGAGCCAATATCGGGAAATTCAAG
Found at i:5368699 original size:28 final size:28
Alignment explanation
Indices: 5368659--5368726 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
5368649 GCGAGTCAAT
* *
5368659 ATCGGGAAACTCATAAAAGAACCTTTAA
1 ATCGGGAAGCTCATAAAAAAACCTTTAA
*
5368687 ATCGGGAAGCTCATAAAAAAACTTTTAA
1 ATCGGGAAGCTCATAAAAAAACCTTTAA
* *
5368715 ATCAGAAAGCTC
1 ATCGGGAAGCTC
5368727 CGAAGAGCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.22
Consensus pattern (28 bp):
ATCGGGAAGCTCATAAAAAAACCTTTAA
Found at i:5371027 original size:2 final size:2
Alignment explanation
Indices: 5371020--5371052 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5371010 AAATGATAAA
*
5371020 AC AC AC AC AC AC AC AC AC AC AC AA AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5371053 TATAATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5376020 original size:31 final size:31
Alignment explanation
Indices: 5375985--5376067 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 31
5375975 AATATACCTA
5375985 TAGTCTCTTTACTTTTTAAATTTTAGGAATT
1 TAGTCTCTTTACTTTTTAAATTTTAGGAATT
* * *
5376016 TAGTCT-TTGTA-TTTGT-AGTTTTAGGCATT
1 TAGTCTCTT-TACTTTTTAAATTTTAGGAATT
* * *
5376045 TAATGTCTTTACTTTTTAGATTT
1 TAGTCTCTTTACTTTTTAAATTT
5376068 CAAAATTCAG
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
29 17 0.43
30 12 0.30
31 11 0.28
ACGTcount: A:0.22, C:0.08, G:0.13, T:0.57
Consensus pattern (31 bp):
TAGTCTCTTTACTTTTTAAATTTTAGGAATT
Found at i:5377044 original size:22 final size:23
Alignment explanation
Indices: 5377018--5377064 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
5377008 AGTTAGACTT
*
5377018 AAATTTTAATTT-AAAAAATAAA
1 AAATTTAAATTTCAAAAAATAAA
*
5377040 AAATTTAAATTTCACAAAATAAA
1 AAATTTAAATTTCAAAAAATAAA
5377063 AA
1 AA
5377065 TATAGGGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATTTAAATTTCAAAAAATAAA
Found at i:5379802 original size:84 final size:84
Alignment explanation
Indices: 5379563--5379815 Score: 335
Period size: 84 Copynumber: 3.0 Consensus size: 84
5379553 GCAACTTAAT
* * * * * *
5379563 TATCACTAGCTTTGACGAAACCATCACTAATGAAAGTAGCAATCAACATAATATAGTTGTTGCGG
1 TATCATTAGCTATGATGAAACCGTCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGTGG
* *
5379628 AAAAGGGCATCGAAACGCC
66 AAGAGGGCATCGAAATGCC
* * *
5379647 TATCATTAGCTATGATGAAACCGTTACTAATGAAAGAAGCAATCAACATAATATAGTTGTTATAG
1 TATCATTAGCTATGATGAAACCGTCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGTGG
* *
5379712 AAGAGGGCACCGAAATGTC
66 AAGAGGGCATCGAAATGCC
* * * *
5379731 TGTCATTAGCTATGATGAAACTGTCGCTAATGAAAGAAGCAATCAACATAATATAGTTGATGTGG
1 TATCATTAGCTATGATGAAACCGTCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGTGG
* *
5379796 ATGAGGGCTTCGAAATGCC
66 AAGAGGGCATCGAAATGCC
5379815 T
1 T
5379816 TCTAACCTAA
Statistics
Matches: 145, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 145 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (84 bp):
TATCATTAGCTATGATGAAACCGTCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGTGG
AAGAGGGCATCGAAATGCC
Found at i:5385839 original size:39 final size:39
Alignment explanation
Indices: 5385796--5385873 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
5385786 TGTCGTTAAT
5385796 TATGTTTTGTTTTAATTCTGTTCTTTAAGTGCAATTAGC
1 TATGTTTTGTTTTAATTCTGTTCTTTAAGTGCAATTAGC
5385835 TATGTTTTGTTTTAATTCTGTTCTTTAAGTGCAATTAGC
1 TATGTTTTGTTTTAATTCTGTTCTTTAAGTGCAATTAGC
5385874 CAAAACGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (39 bp):
TATGTTTTGTTTTAATTCTGTTCTTTAAGTGCAATTAGC
Found at i:5388095 original size:32 final size:32
Alignment explanation
Indices: 5388059--5388141 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 32
5388049 TCTATTTACA
5388059 AGGGATTCCAACAGATTTCTATCATTAATTAT
1 AGGGATTCCAACAGATTTCTATCATTAATTAT
5388091 AGGGATTCCAATACCATCAGATTTCTATCATTAATTAT
1 AGGGATTCC---A--A-CAGATTTCTATCATTAATTAT
5388129 AGGGATTCCAACA
1 AGGGATTCCAACA
5388142 CTCCCCATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
32 11 0.24
33 1 0.02
35 2 0.04
37 1 0.02
38 30 0.67
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
AGGGATTCCAACAGATTTCTATCATTAATTAT
Done.