Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 18 of 206
Found at i:5526435 original size:21 final size:21
Alignment explanation
Indices: 5526409--5526449 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5526399 CTGTTTGGTT
5526409 GGTGAGAAAACTAAAGAAAAG
1 GGTGAGAAAACTAAAGAAAAG
*
5526430 GGTGAGAAAACTGAAGAAAA
1 GGTGAGAAAACTAAAGAAAA
5526450 TGGATTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.29, T:0.10
Consensus pattern (21 bp):
GGTGAGAAAACTAAAGAAAAG
Found at i:5527171 original size:16 final size:16
Alignment explanation
Indices: 5527134--5527175 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5527124 TTAATCATAT
*
5527134 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5527150 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5527165 TTAAAATATAT
1 TTAAAATATAT
5527176 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5527182 original size:14 final size:15
Alignment explanation
Indices: 5527143--5527184 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5527133 TTTAAACATA
*
5527143 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5527158 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5527172 A-TATAATTTAATA
1 ATTATAATTAAATA
5527185 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5529061 original size:11 final size:11
Alignment explanation
Indices: 5529047--5529073 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5529037 TTAGTACAAT
5529047 ACAAAAGTTTC
1 ACAAAAGTTTC
5529058 ACAAAAGTTTC
1 ACAAAAGTTTC
5529069 ACAAA
1 ACAAA
5529074 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:5536081 original size:24 final size:24
Alignment explanation
Indices: 5536054--5536102 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5536044 CATCTGTAGG
5536054 ATTATATGATATGACTATACAGAC
1 ATTATATGATATGACTATACAGAC
5536078 ATTATATGATATGACTATACAGAC
1 ATTATATGATATGACTATACAGAC
5536102 A
1 A
5536103 CACACACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATTATATGATATGACTATACAGAC
Found at i:5539716 original size:70 final size:71
Alignment explanation
Indices: 5539600--5539733 Score: 207
Period size: 70 Copynumber: 1.9 Consensus size: 71
5539590 AATTTCATTT
* * * *
5539600 ATGTTTATTAGATAATCAACTCTGTTACAAAACATATTTTGTTATAGGCAACCCTCAGATTTTTT
1 ATGTTTATTAGACAATAAACTCTG-TACAAAACATAATTTATTATAGGCAACCCTCAGATTTTTT
5539665 TTCCTCC
65 TTCCTCC
*
5539672 ATGTTTATTTGACAATAAACTCTG-ACAAAACATAATTTATTATAGGCAACCCTCAGATTTTT
1 ATGTTTATTAGACAATAAACTCTGTACAAAACATAATTTATTATAGGCAACCCTCAGATTTTT
5539734 CTTGTTTCAC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 36 0.63
72 21 0.37
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (71 bp):
ATGTTTATTAGACAATAAACTCTGTACAAAACATAATTTATTATAGGCAACCCTCAGATTTTTTT
TCCTCC
Found at i:5541530 original size:6 final size:6
Alignment explanation
Indices: 5541519--5541543 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5541509 AATTTATTTG
5541519 TTTGGC TTTGGC TTTGGC TTTGGC T
1 TTTGGC TTTGGC TTTGGC TTTGGC T
5541544 CTGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (6 bp):
TTTGGC
Found at i:5549842 original size:129 final size:129
Alignment explanation
Indices: 5549609--5549849 Score: 306
Period size: 129 Copynumber: 1.9 Consensus size: 129
5549599 CTTATTCCAC
* *
5549609 AAACGCCACTAAAGCTCATGTTATTTAGCGGCGCTTATCCCACAAACGCCACTAAAGGTCATGCT
1 AAACGCCACTAAAGCTCATGTTATTTAGCGGCGCTTATCCCACAAACGCCACTAAAGATCATACT
** * *
5549674 CTTTAGTGGCGCTTATTCCACAAACTTCGGTAAATGTCATGTTCTTTGGCAGCGCTTATCTCAA
66 CTTTAGTGGCGCTTATTCCACAAACGCCGCTAAAGGTCATGTTCTTTGGCAGCGCTTATCTCAA
* * * * * * * *
5549738 AAACGCCTCTAAAGGTCATGTTCTTTAGCGGTGCTTATCCCACAATCGCCGCTATAGATCTTAAC
1 AAACGCCACTAAAGCTCATGTTATTTAGCGGCGCTTATCCCACAAACGCCACTAAAGATCAT-AC
* *
5549803 T-TTTAGTGGCGCTT-TTCTCGCAAGCGCCGCTAAAGGTCATGTTCTTT
65 TCTTTAGTGGCGCTTATTC-CACAAACGCCGCTAAAGGTCATGTTCTTT
5549850 AGTGGCGCTT
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
128 3 0.03
129 89 0.95
130 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (129 bp):
AAACGCCACTAAAGCTCATGTTATTTAGCGGCGCTTATCCCACAAACGCCACTAAAGATCATACT
CTTTAGTGGCGCTTATTCCACAAACGCCGCTAAAGGTCATGTTCTTTGGCAGCGCTTATCTCAA
Found at i:5549858 original size:129 final size:129
Alignment explanation
Indices: 5549604--5549873 Score: 303
Period size: 129 Copynumber: 2.1 Consensus size: 129
5549594 TGTCGCTTAT
* *
5549604 TCCACAAACGCCACTAAAGCTCATGTTATTTAGCGGCGCTTATCCCACAAACGCCACTAAAGGTC
1 TCCAAAAACGCCACTAAAGCTCATGTTATTTAGCGGCGCTTATCCCACAAACGCCACTAAAGATC
* ** * * *
5549669 ATGCTCTTTAGTGGCGCTTATTCCACAAACTTCGGTAAATGTCATGTTCTTTGGCAGCGCTTATC
66 ATACTCTTTAGTGGCGCTTATTCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCAGCGCTT-TC
* * * * * * *
5549734 T-CAAAAACGCCTCTAAAGGTCATGTTCTTTAGCGGTGCTTATCCCACAATCGCCGCTATAGATC
1 TCCAAAAACGCCACTAAAGCTCATGTTATTTAGCGGCGCTTATCCCACAAACGCCACTAAAGATC
* * * **
5549798 TTAACT-TTTAGTGGCGCTT-TTCTCGCAAGCGCCGCTAAAGGTCATGTTCTTTAGTGGCGCTTT
66 AT-ACTCTTTAGTGGCGCTTATTC-CACAAACGCCGCTAAAGGTCATGTTCTTTAGCAGCGCTTT
*
5549861 T
129 C
5549862 TCCAAAAACGCC
1 TCCAAAAACGCC
5549874 GTAATAGATT
Statistics
Matches: 116, Mismatches: 21, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
128 5 0.04
129 108 0.93
130 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (129 bp):
TCCAAAAACGCCACTAAAGCTCATGTTATTTAGCGGCGCTTATCCCACAAACGCCACTAAAGATC
ATACTCTTTAGTGGCGCTTATTCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCAGCGCTTTC
Found at i:5549874 original size:43 final size:43
Alignment explanation
Indices: 5549597--5549874 Score: 249
Period size: 43 Copynumber: 6.5 Consensus size: 43
5549587 TTTACAATGT
* * *
5549597 CGCTTATTCCACAAACGCCACTAAAGCTCATGTTATTTAGCGG
1 CGCTTATTCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
* * * *
5549640 CGCTTATCCCACAAACGCCACTAAAGGTCATGCTCTTTAGTGG
1 CGCTTATTCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
** * * * *
5549683 CGCTTATTCCACAAACTTCGGTAAATGTCATGTTCTTTGGCAG
1 CGCTTATTCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
* *
5549726 CGCTTA-TCTCAAAAACGCCTCTAAAGGTCATGTTCTTTAGCGG
1 CGCTTATTC-CACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
* * * * * * *
5549769 TGCTTATCCCACAATCGCCGCTATAGATC-T-TAACTTTTAGTGG
1 CGCTTATTCCACAAACGCCGCTAAAGGTCATGT-TC-TTTAGCGG
* * *
5549812 CGCTT-TTCTCGCAAGCGCCGCTAAAGGTCATGTTCTTTAGTGG
1 CGCTTATTC-CACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
* *
5549855 CGCTTTTTCCAAAAACGCCG
1 CGCTTATTCCACAAACGCCG
5549875 TAATAGATTG
Statistics
Matches: 185, Mismatches: 42, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
41 1 0.01
42 6 0.03
43 171 0.92
44 6 0.03
45 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (43 bp):
CGCTTATTCCACAAACGCCGCTAAAGGTCATGTTCTTTAGCGG
Found at i:5551943 original size:25 final size:25
Alignment explanation
Indices: 5551909--5551990 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
5551899 TAATAAGACC
** * *
5551909 AAGTTATGTATTATGTATGTTATGT
1 AAGTTATGTAGAATGTAAGCTATGT
*
5551934 AAGTTGTGTAGAATGTAAGCTATGT
1 AAGTTATGTAGAATGTAAGCTATGT
*
5551959 AAGTTATGT-GAGT-TATA--TATGT
1 AAGTTATGTAGAATGTA-AGCTATGT
5551981 AAGTTATGTA
1 AAGTTATGTA
5551991 TAATATTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 14 0.29
23 2 0.04
24 4 0.08
25 28 0.58
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.44
Consensus pattern (25 bp):
AAGTTATGTAGAATGTAAGCTATGT
Found at i:5551972 original size:9 final size:9
Alignment explanation
Indices: 5551909--5552106 Score: 81
Period size: 9 Copynumber: 23.1 Consensus size: 9
5551899 TAATAAGACC
5551909 AAGTTATGT
1 AAGTTATGT
5551918 -A-TTATGT
1 AAGTTATGT
*
5551925 ATGTTATGT
1 AAGTTATGT
*
5551934 AAGTTGTGT
1 AAGTTATGT
*
5551943 -AG-AATGT
1 AAGTTATGT
*
5551950 AAGCTATGT
1 AAGTTATGT
5551959 AAGTTATGT
1 AAGTTATGT
*
5551968 GAGTTA--T
1 AAGTTATGT
5551975 -A--TATGT
1 AAGTTATGT
5551981 AAGTTATGT
1 AAGTTATGT
*
5551990 ATA-ATAT-T
1 A-AGTTATGT
*
5551998 AA-TTAATCGGCC
1 AAGTT-AT--G-T
*
5552010 AAGTTGTG-
1 AAGTTATGT
*
5552018 AA-TAATGT
1 AAGTTATGT
*
5552026 AAGTTATGA
1 AAGTTATGT
5552035 AAGTTATGT
1 AAGTTATGT
5552044 -A-TTATGT
1 AAGTTATGT
*
5552051 AAGTTATTT
1 AAGTTATGT
5552060 AAGTTATGTAAT
1 AAGTTATG---T
*
5552072 AAGTTGTGT
1 AAGTTATGT
5552081 -A-TTATGT
1 AAGTTATGT
*
5552088 AAGTTATTT
1 AAGTTATGT
5552097 AAGTTATGT
1 AAGTTATGT
5552106 A
1 A
5552107 TTACGAAATT
Statistics
Matches: 141, Mismatches: 23, Indels: 50
0.66 0.11 0.23
Matches are distributed among these distances:
4 2 0.01
6 2 0.01
7 27 0.19
8 17 0.12
9 78 0.55
10 2 0.01
12 11 0.08
13 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (9 bp):
AAGTTATGT
Found at i:5552038 original size:25 final size:25
Alignment explanation
Indices: 5552010--5552073 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
5552000 TTAATCGGCC
*
5552010 AAGTTGTGAATAATGTAAGTTATGA
1 AAGTTATGAATAATGTAAGTTATGA
* * **
5552035 AAGTTATGTATTATGTAAGTTATTT
1 AAGTTATGAATAATGTAAGTTATGA
5552060 AAGTTATGTAATAA
1 AAGTTATG-AATAA
5552074 GTTGTGTATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 28 0.90
26 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (25 bp):
AAGTTATGAATAATGTAAGTTATGA
Found at i:5552048 original size:16 final size:16
Alignment explanation
Indices: 5552029--5552094 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
5552019 ATAATGTAAG
5552029 TTATGAAAGTTATGTA
1 TTATGAAAGTTATGTA
* *
5552045 TTATGTAAGTTATTTAA
1 TTATGAAAGTTATGT-A
*
5552062 GTTATGTAATAAGTTGTGTA
1 -TTATG--A-AAGTTATGTA
*
5552082 TTATGTAAGTTAT
1 TTATGAAAGTTAT
5552095 TTAAGTTATG
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
16 19 0.50
17 1 0.03
18 5 0.13
19 5 0.13
20 1 0.03
21 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (16 bp):
TTATGAAAGTTATGTA
Found at i:5552082 original size:37 final size:37
Alignment explanation
Indices: 5552035--5552106 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
5552025 TAAGTTATGA
5552035 AAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAT
1 AAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAT
*
5552072 AAGTTGTGTATTATGTAAGTTATTTAAGTTATGTA
1 AAGTTATGTATTATGTAAGTTATTTAAGTTATGTA
5552107 TTACGAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (37 bp):
AAGTTATGTATTATGTAAGTTATTTAAGTTATGTAAT
Found at i:5552259 original size:30 final size:30
Alignment explanation
Indices: 5552179--5552364 Score: 162
Period size: 30 Copynumber: 6.1 Consensus size: 30
5552169 AAATTTTATC
* *
5552179 TTAATATTATATAAGTTATGCAATGAGAAA
1 TTAATATTATATAAGTTATGTAATTAGAAA
*
5552209 TTAATATTATATAAGTTATGTTATTAGAAA
1 TTAATATTATATAAGTTATGTAATTAGAAA
*
5552239 TTAATATTATATAAGTTATGTAATTCGAAA
1 TTAATATTATATAAGTTATGTAATTAGAAA
* * * * *
5552269 TTTTATCTTA-ATATTGTCTAAGTTATATA-AAA
1 -TTAATATTATATA-AGT-TATGTAAT-TAGAAA
* * * * *
5552301 TTAGAAATTGATGTGTACTTA-GAAATTAGAAA
1 TTA-ATATT-ATAT-AAGTTATGTAATTAGAAA
5552333 TTAATATTATATAAGTTATGTAATTAGAAA
1 TTAATATTATATAAGTTATGTAATTAGAAA
5552363 TT
1 TT
5552365 TTATCTTAAT
Statistics
Matches: 121, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
29 4 0.03
30 73 0.60
31 17 0.14
32 21 0.17
33 4 0.03
34 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (30 bp):
TTAATATTATATAAGTTATGTAATTAGAAA
Found at i:5552388 original size:20 final size:20
Alignment explanation
Indices: 5552365--5552476 Score: 142
Period size: 20 Copynumber: 5.8 Consensus size: 20
5552355 ATTAGAAATT
5552365 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
5552385 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
* * *
5552405 TTAT-GT-A-ATTAGA-AATT
1 TTATCTTAATATTATATAA-G
5552422 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
*
5552442 TAATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
*
5552462 TTATCTTAATTTTAT
1 TTATCTTAATATTAT
5552477 GTAATTAGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
16 2 0.03
17 9 0.12
18 2 0.03
19 2 0.03
20 61 0.78
21 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.51
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:5552394 original size:57 final size:57
Alignment explanation
Indices: 5552333--5552465 Score: 257
Period size: 57 Copynumber: 2.3 Consensus size: 57
5552323 AAATTAGAAA
*
5552333 TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
1 TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATC
5552390 TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATC
1 TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATC
5552447 TTAATATTATATAAGTTAT
1 TTAATATTATATAAGTTAT
5552466 CTTAATTTTA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 75 1.00
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (57 bp):
TTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATC
Found at i:5552417 original size:94 final size:92
Alignment explanation
Indices: 5552160--5552442 Score: 311
Period size: 94 Copynumber: 3.0 Consensus size: 92
5552150 GAAATTGATG
* *
5552160 TGTAATTAGAAATTTTATCTTAATATTATATAAGTTATGCAATGAGAAATTAAT-ATTATATAAG
1 TGTAATTAGAAATTTTATCTTAATATTATATAAGTTAT-C--TTA-AAATTAATAATTATGTAA-
**
5552224 TTATGTTATTAGAAATTAATATTATATAAGTTA
61 TTA-GAAATTAGAAATTAATATTATATAAGTTA
* * * * *
5552257 TGTAATTCGAAATTTTATCTTAATATTGTCTAAGTTAT-ATAAAATTAGA-AATTGATGTGTACT
1 TGTAATTAGAAATTTTATCTTAATATTATATAAGTTATCTTAAAATTA-ATAATT-A--TGTAAT
5552320 TAGAAATTAGAAATTAATATTATATAAGTTA
62 TAGAAATTAGAAATTAATATTATATAAGTTA
*
5552351 TGTAATTAGAAATTTTATCTTAATATTATATAAGTTATCTTAATATTATATAAGTTATGTAATTA
1 TGTAATTAGAAATTTTATCTTAATATTATATAAGTTATCTTAAAATTA-ATAA-TTATGTAATTA
** **
5552416 GAAATTTTATCTTAATATTATATAAGT
64 GAAATTAGAAATTAATATTATATAAGT
5552443 AATCTTAATA
Statistics
Matches: 158, Mismatches: 20, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
92 6 0.04
93 5 0.03
94 93 0.59
95 11 0.07
96 6 0.04
97 37 0.23
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (92 bp):
TGTAATTAGAAATTTTATCTTAATATTATATAAGTTATCTTAAAATTAATAATTATGTAATTAGA
AATTAGAAATTAATATTATATAAGTTA
Found at i:5552851 original size:15 final size:15
Alignment explanation
Indices: 5552831--5552864 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
5552821 TAATTACGTA
5552831 AATTAAATAACTTTG
1 AATTAAATAACTTTG
5552846 AATTAAATAACTTTG
1 AATTAAATAACTTTG
5552861 AATT
1 AATT
5552865 CCGTCATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (15 bp):
AATTAAATAACTTTG
Found at i:5555007 original size:19 final size:19
Alignment explanation
Indices: 5554983--5555024 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5554973 CGTCGGGTTG
*
5554983 GGGGAACTGTTAGGGATTA
1 GGGGAAATGTTAGGGATTA
* *
5555002 GGGGAAATTTTAGGGATTT
1 GGGGAAATGTTAGGGATTA
5555021 GGGG
1 GGGG
5555025 GAGATGACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.45, T:0.29
Consensus pattern (19 bp):
GGGGAAATGTTAGGGATTA
Found at i:5555978 original size:21 final size:22
Alignment explanation
Indices: 5555954--5556009 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
5555944 CCGTAAATCT
5555954 TAAACCCTAAACT-ATAAACCC
1 TAAACCCTAAACTCATAAACCC
* * *
5555975 TAAACCCCAAA-TCGTAAACCT
1 TAAACCCTAAACTCATAAACCC
*
5555996 TAAACCTTAAACTC
1 TAAACCCTAAACTC
5556010 GTCAATTAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.45, C:0.32, G:0.02, T:0.21
Consensus pattern (22 bp):
TAAACCCTAAACTCATAAACCC
Found at i:5556006 original size:14 final size:14
Alignment explanation
Indices: 5555938--5556007 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
5555928 ATACTGTAAG
*
5555938 CCTT-AACCGTAAA
1 CCTTAAACCCTAAA
*
5555951 TCTTAAACCCTAAA
1 CCTTAAACCCTAAA
5555965 -CTATAAACCCTAAA
1 CCT-TAAACCCTAAA
** * *
5555979 CCCCAAATCGTAAA
1 CCTTAAACCCTAAA
*
5555993 CCTTAAACCTTAAA
1 CCTTAAACCCTAAA
5556007 C
1 C
5556008 TCGTCAATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 5 0.11
14 38 0.86
15 1 0.02
ACGTcount: A:0.43, C:0.31, G:0.03, T:0.23
Consensus pattern (14 bp):
CCTTAAACCCTAAA
Found at i:5556745 original size:114 final size:112
Alignment explanation
Indices: 5556536--5556980 Score: 390
Period size: 114 Copynumber: 3.9 Consensus size: 112
5556526 AAAACTGCGC
* ** * *
5556536 CGTTTTGGTTAACAA-TTTTGCGGCGCTTTCCCTAAAGCGCCACTAAAAGTTATTCTATAGCGGC
1 CGTTTTGGTCAA-AATTTTTGCGGCGC-TTCAGTAAAGCGCCACTAAAAGTGA-TATATAGCGGC
* * * *
5556600 GTTTTCAAATAAGCGCCGCTAATGCCTCTATAGGTCAAGCCGGAACGATG
63 GTTTTCAAGTAAGCGCCGCTAACGCCGCTATAGCTCAAGCCGGAACGATG
* * *
5556650 GGTTTTGGTCAAAATTTTTGCGGCGCTTCAGTAAAAGTGCCACTAAAAGCTGATATATAGCGGCT
1 CGTTTTGGTCAAAATTTTTGCGGCGCTTCAGT-AAAGCGCCACTAAAAG-TGATATATAGCGGCG
** * * * * *
5556715 TTTTCGGGTAAGCGCCGCTAACGGCGCTATAGCTCAAGACGAAACGTTT
64 TTTTCAAGTAAGCGCCGCTAACGCCGCTATAGCTCAAGCCGGAACGATG
* ** *** ** * * * ** * **
5556764 CGTTTCGGTTTAAATTTTTTTAGCATTTTTTAGTTAAGCGCCGCTAATTGAGGGATATAGCGGCG
1 CGTTTTGGTCAAAATTTTTGCGGC--GCTTCAGTAAAGCGCCACTAAAAGTGATATATAGCGGCG
* * ** *
5556829 TTTTCAGGTAAGCGCCGCTAATGCCTTTATAGGTCAAGCCGGAACGATG
64 TTTTCAAGTAAGCGCCGCTAACGCCGCTATAGCTCAAGCCGGAACGATG
*
5556878 CGTTTTGGTCAAAATTTTTGCGGCGCTTCAGTAGAAGCGCCACTACAAGCTGATATATAGCGGCG
1 CGTTTTGGTCAAAATTTTTGCGGCGCTTCAGTA-AAGCGCCACTAAAAG-TGATATATAGCGGCG
* * *
5556943 TTTTCGAGTAAGCGCCACTGACAG-CGCTATAGCTCAAG
64 TTTTCAAGTAAGCGCCGCTAAC-GCCGCTATAGCTCAAG
5556981 ATGAAACGTT
Statistics
Matches: 250, Mismatches: 73, Indels: 16
0.74 0.22 0.05
Matches are distributed among these distances:
112 5 0.02
113 17 0.07
114 209 0.84
115 14 0.06
116 5 0.02
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (112 bp):
CGTTTTGGTCAAAATTTTTGCGGCGCTTCAGTAAAGCGCCACTAAAAGTGATATATAGCGGCGTT
TTCAAGTAAGCGCCGCTAACGCCGCTATAGCTCAAGCCGGAACGATG
Found at i:5556989 original size:228 final size:228
Alignment explanation
Indices: 5556591--5557061 Score: 753
Period size: 228 Copynumber: 2.1 Consensus size: 228
5556581 AAAGTTATTC
*
5556591 TATAGCGGCGTTTTCAAATAAGCGCCGCTAATGCCTCTATAGGTCAAGCCGGAACGATGGGTTTT
1 TATAGCGGCGTTTTCAAATAAGCGCCGCTAATGCCTCTATAGGTCAAGCCGGAACGATGCGTTTT
* *
5556656 GGTCAAAATTTTTGCGGCGCTTCAGTAAAAGTGCCACTAAAAGCTGATATATAGCGGCTTTTTCG
66 GGTCAAAATTTTTGCGGCGCTTCAGTAAAAGCGCCACTAAAAGCTGATATATAGCGGCGTTTTCG
* * * * * ** *
5556721 GGTAAGCGCCGCTAACGGCGCTATAGCTCAAGACGAAACGTTTCGTTTCGGTTTAAATTTTTTTA
131 AGTAAGCGCCACTAACAGCGCTATAGCTCAAGACGAAACGTTGCATTTCGGTTTAAAAGTTTCTA
5556786 GCATTTTTTAGTTAAGCGCCGCTAATTGAGGGA
196 GCATTTTTTAGTTAAGCGCCGCTAATTGAGGGA
** *
5556819 TATAGCGGCGTTTTCAGGTAAGCGCCGCTAATGCCTTTATAGGTCAAGCCGGAACGATGCGTTTT
1 TATAGCGGCGTTTTCAAATAAGCGCCGCTAATGCCTCTATAGGTCAAGCCGGAACGATGCGTTTT
* *
5556884 GGTCAAAATTTTTGCGGCGCTTCAGTAGAAGCGCCACTACAAGCTGATATATAGCGGCGTTTTCG
66 GGTCAAAATTTTTGCGGCGCTTCAGTAAAAGCGCCACTAAAAGCTGATATATAGCGGCGTTTTCG
* * *
5556949 AGTAAGCGCCACTGACAGCGCTATAGCTCAAGATGAAACGTTGCATTTCGGTTTAAAAGTTTCTG
131 AGTAAGCGCCACTAACAGCGCTATAGCTCAAGACGAAACGTTGCATTTCGGTTTAAAAGTTTCTA
*
5557014 GCATTTTTTAGTTAAGCGCCGCTAATTGCGGGA
196 GCATTTTTTAGTTAAGCGCCGCTAATTGAGGGA
*
5557047 TATAACGGCGTTTTC
1 TATAGCGGCGTTTTC
5557062 TACAACCGCC
Statistics
Matches: 222, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
228 222 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (228 bp):
TATAGCGGCGTTTTCAAATAAGCGCCGCTAATGCCTCTATAGGTCAAGCCGGAACGATGCGTTTT
GGTCAAAATTTTTGCGGCGCTTCAGTAAAAGCGCCACTAAAAGCTGATATATAGCGGCGTTTTCG
AGTAAGCGCCACTAACAGCGCTATAGCTCAAGACGAAACGTTGCATTTCGGTTTAAAAGTTTCTA
GCATTTTTTAGTTAAGCGCCGCTAATTGAGGGA
Found at i:5557050 original size:114 final size:112
Alignment explanation
Indices: 5556704--5557061 Score: 316
Period size: 114 Copynumber: 3.1 Consensus size: 112
5556694 AAAAGCTGAT
* * * *
5556704 ATATAGCGGCTTTTTCGGGTAAGCGCCGCTAACGGCGCTATAGCTCAAGACGAAACGTTTCGTTT
1 ATATAGCGGCGTTTTCGAGTAAGCGCCGCT-ACAGCGCTATAGCTCAAGACGAAACGTTGCGTTT
* * *
5556769 CGGTTTAAATTTTTTTAGCATTTTTTAGTTAAGCGCCGCTAATTGAGGG
65 CGGTTTAAA-ATTTTTGGCATTTTTTAGTTAAGCGCCGCTAATTGCGGG
* * * *
5556818 ATATAGCGGCGTTTTC-AGGTAAGCGCCGCTA-ATGC-CTTTATAGGTCAAGCCGGAACGATGCG
1 ATATAGCGGCGTTTTCGA-GTAAGCGCCGCTACA-GCGC--TATAGCTCAAGACGAAACGTTGCG
* * ** * * * * **
5556880 TTTTGG-TCAAAATTTTTGCGGC--GCTTCAGTAGAAGCGCCACTACA-AGCTGAT
62 TTTCGGTTTAAAATTTTT--GGCATTTTTTAGT-TAAGCGCCGCTA-ATTGC-GGG
* * *
5556932 ATATAGCGGCGTTTTCGAGTAAGCGCCACTGACAGCGCTATAGCTCAAGATGAAACGTTGCATTT
1 ATATAGCGGCGTTTTCGAGTAAGCGCCGCT-ACAGCGCTATAGCTCAAGACGAAACGTTGCGTTT
*
5556997 CGGTTTAAAAGTTTCTGGCATTTTTTAGTTAAGCGCCGCTAATTGCGGG
65 CGGTTTAAAA-TTTTTGGCATTTTTTAGTTAAGCGCCGCTAATTGCGGG
*
5557046 ATATAACGGCGTTTTC
1 ATATAGCGGCGTTTTC
5557062 TACAACCGCC
Statistics
Matches: 186, Mismatches: 40, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
112 11 0.06
113 18 0.10
114 125 0.67
115 21 0.11
116 11 0.06
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (112 bp):
ATATAGCGGCGTTTTCGAGTAAGCGCCGCTACAGCGCTATAGCTCAAGACGAAACGTTGCGTTTC
GGTTTAAAATTTTTGGCATTTTTTAGTTAAGCGCCGCTAATTGCGGG
Found at i:5558752 original size:1 final size:1
Alignment explanation
Indices: 5558746--5558770 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5558736 CCACGAAACC
5558746 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
5558771 TGGAAACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5559112 original size:13 final size:13
Alignment explanation
Indices: 5559094--5559170 Score: 68
Period size: 13 Copynumber: 5.9 Consensus size: 13
5559084 AGTTCTTCAT
5559094 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
5559107 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
5559120 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
* * *
5559133 TACTTCTGAGAAG
1 TGCTTTTGAAAAG
5559146 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
*
5559159 TGTTTTTGAAAA
1 TGCTTTTGAAAA
5559171 ATTTGAGTGC
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
12 3 0.06
13 42 0.86
14 4 0.08
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:5564002 original size:36 final size:37
Alignment explanation
Indices: 5563921--5564004 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 37
5563911 TATTCTCTGT
* *
5563921 TTTGGTGTGTTCCAGTTGGACTAGCTATTTGGAGCCA
1 TTTGGTGTGTTTCAGATGGACTAGCTATTTGGAGCCA
* * *
5563958 -TTGCTGTGTTTCAGATGGATTAGCTCTTAT-GAG-CA
1 TTTGGTGTGTTTCAGATGGACTAGCTATT-TGGAGCCA
5563993 TTTGGTGTGTTT
1 TTTGGTGTGTTT
5564005 TGGTTGGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
35 2 0.05
36 36 0.92
37 1 0.03
ACGTcount: A:0.15, C:0.13, G:0.29, T:0.43
Consensus pattern (37 bp):
TTTGGTGTGTTTCAGATGGACTAGCTATTTGGAGCCA
Found at i:5566784 original size:20 final size:20
Alignment explanation
Indices: 5566757--5566813 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
5566747 ATAAATGGTG
5566757 AAAGGTATCGATACTTTCTT
1 AAAGGTATCGATACTTTCTT
5566777 CAAA-GTATC-ATTACTTTCTT
1 -AAAGGTATCGA-TACTTTCTT
*
5566797 AAAGGTATTGATACTTT
1 AAAGGTATCGATACTTT
5566814 TGACTTGGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.12
20 24 0.75
21 4 0.12
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (20 bp):
AAAGGTATCGATACTTTCTT
Found at i:5568767 original size:24 final size:24
Alignment explanation
Indices: 5568739--5568787 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5568729 GAATTTAGGA
*
5568739 TCCACTTGGACGTAAGTTTAGAGC
1 TCCACTTGGAAGTAAGTTTAGAGC
*
5568763 TCCACTTGGAATTAAGTTTAGAGC
1 TCCACTTGGAAGTAAGTTTAGAGC
5568787 T
1 T
5568788 TTCGCTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (24 bp):
TCCACTTGGAAGTAAGTTTAGAGC
Found at i:5570557 original size:11 final size:11
Alignment explanation
Indices: 5570541--5570566 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5570531 TACAAGAAAT
5570541 AAATTACTAAG
1 AAATTACTAAG
5570552 AAATTACTAAG
1 AAATTACTAAG
5570563 AAAT
1 AAAT
5570567 AATTCAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (11 bp):
AAATTACTAAG
Found at i:5584432 original size:40 final size:41
Alignment explanation
Indices: 5584318--5584432 Score: 110
Period size: 40 Copynumber: 2.8 Consensus size: 41
5584308 AAACACACTT
* * *
5584318 TTAGCGGCGTTTA-GAGAAAAACTGCCACAAAAGGTTACAAC
1 TTAGTGGCGTTTATGAGAAAAAC-GCCGCAAAAGCTTACAAC
* ** * *
5584359 TATAGTGGCGTTTGTGTCAAAAACGCTGGAAAAGCTTAGC-A-
1 T-TAGTGGCGTTTATGAGAAAAACGCCGCAAAAGCTTA-CAAC
5584400 TTAGTGGCGTTTATGAGAAAAACGCCGCAAAAG
1 TTAGTGGCGTTTATGAGAAAAACGCCGCAAAAG
5584433 TTCGAGTATT
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
40 27 0.47
41 2 0.03
42 21 0.36
43 8 0.14
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (41 bp):
TTAGTGGCGTTTATGAGAAAAACGCCGCAAAAGCTTACAAC
Found at i:5584629 original size:114 final size:114
Alignment explanation
Indices: 5584417--5584867 Score: 609
Period size: 114 Copynumber: 4.0 Consensus size: 114
5584407 CGTTTATGAG
* * * * * *
5584417 AAAAACGCCGCAAAAGTTCGAGTATTAGCGACGCTTTTCTAAAAATGCCGCAAAAATG-TAATCA
1 AAAAACGCCGCTATAGGTCGAGAATTAGCGACGCTTTTCTAAAAACGCCACAAAAATGTTAATCA
** * *
5584481 AAACACATCGTTCTATCTTGAGCTTTAGTGGCATTAGCGGCGCTTACAC
66 AAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAGCGACGCTTATAC
* *
5584530 AAAAACGCCGCTATAGGTCGAGAATTAGCGACGCTTTTTTAAAAACGCTACAAAAATGTTAATCA
1 AAAAACGCCGCTATAGGTCGAGAATTAGCGACGCTTTTCTAAAAACGCCACAAAAATGTTAATCA
*
5584595 AAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAGCGACGCTTATGC
66 AAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAGCGACGCTTATAC
* * * *
5584644 AAAAACGCCGCTAGAGGTCGAGAATTAGCGGCGCTCTTCTAAAAATGCCACAAAAATGTTAATCA
1 AAAAACGCCGCTATAGGTCGAGAATTAGCGACGCTTTTCTAAAAACGCCACAAAAATGTTAATCA
* *
5584709 AAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAACGACGCTTATTC
66 AAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAGCGACGCTTATAC
* * * * * ** *
5584758 AAAAATGCCACTATATGTCGAGAATTAGC-AGTGCTTTTCTAAAAACGTCGTAAACATGTTAATC
1 AAAAACGCCGCTATAGGTCGAGAATTAGCGA-CGCTTTTCTAAAAACGCCACAAAAATGTTAATC
* * *
5584822 AAAATGCATCGTTCTAGCTTAAGCTTTAGTGGCATTAGCGGCGCTT
65 AAAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAGCGACGCTT
5584868 TCCGGAAAAT
Statistics
Matches: 299, Mismatches: 37, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
113 50 0.17
114 249 0.83
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (114 bp):
AAAAACGCCGCTATAGGTCGAGAATTAGCGACGCTTTTCTAAAAACGCCACAAAAATGTTAATCA
AAATGCATCGTTCTATCTTGAGCTTTAGTGGCATTAGCGACGCTTATAC
Found at i:5585296 original size:14 final size:14
Alignment explanation
Indices: 5585261--5585451 Score: 81
Period size: 14 Copynumber: 13.4 Consensus size: 14
5585251 TTCCCAAAGA
*
5585261 TATGGTTTA-GGAT
1 TATGGTTTAGGGTT
5585274 TATGGTTTAGGGTT
1 TATGGTTTAGGGTT
* *
5585288 TACGGTTTAGAGTT
1 TATGGTTTAGGGTT
* *
5585302 TAAGGTTT-GTGTTT
1 TATGGTTTAG-GGTT
* *
5585316 TATGGTTTAAGATT
1 TATGGTTTAGGGTT
5585330 TATGGTTTAAGGGTT
1 TATGGTTT-AGGGTT
* **
5585345 T-TGGGTATATTGGGGA
1 TAT-GGT-T-TAGGGTT
*
5585361 T-TGGATTTTGGGTT
1 TATGG-TTTAGGGTT
*
5585375 T-TGGTGGTT-GGTTT
1 TATGGT--TTAGGGTT
* *
5585389 TGTGATTTACGGGTT
1 TATGGTTTA-GGGTT
*
5585404 TAAT-GTTTATGGTT
1 T-ATGGTTTAGGGTT
* *
5585418 TAGGGTTTAGGATT
1 TATGGTTTAGGGTT
*
5585432 TATGGTTTAAGGTT
1 TATGGTTTAGGGTT
5585446 TATGGT
1 TATGGT
5585452 ATATTGGGGA
Statistics
Matches: 135, Mismatches: 28, Indels: 29
0.70 0.15 0.15
Matches are distributed among these distances:
13 14 0.10
14 87 0.64
15 25 0.19
16 8 0.06
17 1 0.01
ACGTcount: A:0.17, C:0.01, G:0.32, T:0.49
Consensus pattern (14 bp):
TATGGTTTAGGGTT
Found at i:5585338 original size:21 final size:21
Alignment explanation
Indices: 5585264--5585338 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
5585254 CCAAAGATAT
* *
5585264 GGTTTA-GGATTATGGTTTAG
1 GGTTTATGGTTTATGGTTTAA
*
5585284 GGTTTACGGTTTA-GAGTTTAA
1 GGTTTATGGTTTATG-GTTTAA
* *
5585305 GGTTTGTGTTTTATGGTTTAA
1 GGTTTATGGTTTATGGTTTAA
*
5585326 GATTTATGGTTTA
1 GGTTTATGGTTTA
5585339 AGGGTTTTGG
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 7 0.16
21 36 0.82
22 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.49
Consensus pattern (21 bp):
GGTTTATGGTTTATGGTTTAA
Found at i:5585385 original size:21 final size:22
Alignment explanation
Indices: 5585341--5585390 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
5585331 ATGGTTTAAG
5585341 GGTTTTGGGTATATTGGGGATT
1 GGTTTTGGGTATATTGGGGATT
5585363 GGATTTTGGGT-T-TTGGTGG-TT
1 GG-TTTTGGGTATATTGG-GGATT
5585384 GGTTTTG
1 GGTTTTG
5585391 TGATTTACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.19
21 8 0.31
22 5 0.19
23 8 0.31
ACGTcount: A:0.08, C:0.00, G:0.42, T:0.50
Consensus pattern (22 bp):
GGTTTTGGGTATATTGGGGATT
Found at i:5585418 original size:7 final size:7
Alignment explanation
Indices: 5585408--5585451 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
5585398 CGGGTTTAAT
5585408 GTTTATG
1 GTTTATG
*
5585415 GTTTAGG
1 GTTTATG
5585422 GTTTA-G
1 GTTTATG
5585428 GATTTATG
1 G-TTTATG
*
5585436 GTTTAAG
1 GTTTATG
5585443 GTTTATG
1 GTTTATG
5585450 GT
1 GT
5585452 ATATTGGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 2 0.06
7 28 0.88
8 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (7 bp):
GTTTATG
Found at i:5585423 original size:21 final size:22
Alignment explanation
Indices: 5585394--5585447 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
5585384 GGTTTTGTGA
*
5585394 TTTACGGGTTTAATG-TTTATGG
1 TTTA-GGGTTTAAGGATTTATGG
5585416 TTTAGGGTTT-AGGATTTATGG
1 TTTAGGGTTTAAGGATTTATGG
*
5585437 TTTAAGGTTTA
1 TTTAGGGTTTA
5585448 TGGTATATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 22 0.79
22 4 0.14
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (22 bp):
TTTAGGGTTTAAGGATTTATGG
Found at i:5585476 original size:102 final size:101
Alignment explanation
Indices: 5585293--5585514 Score: 315
Period size: 102 Copynumber: 2.2 Consensus size: 101
5585283 GGGTTTACGG
* * * *
5585293 TTTAGAGTTTAAGGTTTGTGTTTTATGGTTTAAGATTTATGGTTTAAGGGTTTTGGGTATATTGG
1 TTTAGGGTTTAAGGTTTATGGTTTAGGGTTTAAGATTTATGGTTTAAGGGTTTTGGGTATATTGG
5585358 GGATTGGATTTTGGGTTTTGGTGGTTGG-TTTTGTGA
66 GGATTGGATTTTGGG-TTTGGTGGTTGGTTTTTGTGA
* *
5585394 TTTACGGGTTTAATGTTTATGGTTTAGGGTTTAGGATTTATGGTTTAA-GGTTTAT-GGTATATT
1 TTTA-GGGTTTAAGGTTTATGGTTTAGGGTTTAAGATTTATGGTTTAAGGGTTT-TGGGTATATT
*
5585457 GGGGATTGGATTTTAGGGTTTGGTGGTTGGTTTTTTGTGG
64 GGGGATTGGATTTT-GGGTTTGGTGGTTGG-TTTTTGTGA
5585497 TTTAGGGTTTAAGGTTTA
1 TTTAGGGTTTAAGGTTTA
5585515 GGATTTAATC
Statistics
Matches: 108, Mismatches: 8, Indels: 9
0.86 0.06 0.07
Matches are distributed among these distances:
101 43 0.40
102 54 0.50
103 11 0.10
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.50
Consensus pattern (101 bp):
TTTAGGGTTTAAGGTTTATGGTTTAGGGTTTAAGATTTATGGTTTAAGGGTTTTGGGTATATTGG
GGATTGGATTTTGGGTTTGGTGGTTGGTTTTTGTGA
Found at i:5586708 original size:27 final size:27
Alignment explanation
Indices: 5586678--5586747 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
5586668 TTTGGTACTG
5586678 GCATACTATTTTATGTATTTCCCATAT
1 GCATACTATTTTATGTATTTCCCATAT
5586705 GCATAC-AGTTTTAAT-TATTTCCCATAT
1 GCATACTA-TTTT-ATGTATTTCCCATAT
*
5586732 GCATACTGTTTTATGT
1 GCATACTATTTTATGT
5586748 TTAAATATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
26 3 0.08
27 33 0.87
28 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (27 bp):
GCATACTATTTTATGTATTTCCCATAT
Found at i:5590588 original size:13 final size:14
Alignment explanation
Indices: 5590572--5590600 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5590562 TTATAAATAT
5590572 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
5590585 TTATAATGGTTTAA
1 TTATAATGGTTTAA
5590599 TT
1 TT
5590601 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:5591371 original size:44 final size:43
Alignment explanation
Indices: 5591271--5591513 Score: 195
Period size: 43 Copynumber: 5.6 Consensus size: 43
5591261 CCAAATTAGC
* *
5591271 GGCGTTTGTA-AAAAAAGCACCGCTAAAGACCACGAATTATAGT
1 GGCGTTT-TATAAAAAAGCGCCGCTAAAGGCCACGAATTATAGT
* * *
5591314 GGCGTTTTATAAAAAAGTGCTGCTAAAGGCCACGAATTATAGC
1 GGCGTTTTATAAAAAAGCGCCGCTAAAGGCCACGAATTATAGT
* * * * *
5591357 AGCGTTTTTTTAAAAAAGCACCGCTAAAGGCCATGACTTATAGT
1 GGCG-TTTTATAAAAAAGCGCCGCTAAAGGCCACGAATTATAGT
* * * *
5591401 GGAGTTTTATAAAAAAGCGCCGTTAAAGGCCACGGCATT-TAGC
1 GGCGTTTTATAAAAAAGCGCCGCTAAAGGCCAC-GAATTATAGT
* * ** * * * * *
5591444 GGCATTTTCTATGATAGCACCGCTAAAGACCACGACCTT-TAGC
1 GGCGTTTTATAAAAAAGCGCCGCTAAAGGCCACGA-ATTATAGT
* * *
5591487 GGCATTTTCTATAAAAGCGCCGCTAAA
1 GGCGTTTTATAAAAAAGCGCCGCTAAA
5591514 AGTCAAGATC
Statistics
Matches: 160, Mismatches: 36, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
42 3 0.02
43 120 0.75
44 37 0.23
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (43 bp):
GGCGTTTTATAAAAAAGCGCCGCTAAAGGCCACGAATTATAGT
Found at i:5591383 original size:87 final size:86
Alignment explanation
Indices: 5591281--5591513 Score: 247
Period size: 87 Copynumber: 2.7 Consensus size: 86
5591271 GGCGTTTGTA
* * *
5591281 AAAAAAGCACCGCTAAAGACCACGAATTATAGTGGCGTTTTATAAAAAAGTGCTGCTAAAGGCCA
1 AAAAAAGCACCGCTAAAGACCACGAATTATAGTGGAGTTTTATAAAAAAGCGCCGCTAAAGGCCA
* *
5591346 C-GAATTATAGCAGCGTTTTTTT
66 CGGAATT-TAGCAGC-ATTTTCT
* * * *
5591368 AAAAAAGCACCGCTAAAGGCCATGACTTATAGTGGAGTTTTATAAAAAAGCGCCGTTAAAGGCCA
1 AAAAAAGCACCGCTAAAGACCACGAATTATAGTGGAGTTTTATAAAAAAGCGCCGCTAAAGGCCA
* *
5591433 CGGCATTTAGCGGCATTTTCT
66 CGGAATTTAGCAGCATTTTCT
** * * * * *
5591454 ATGATAGCACCGCTAAAGACCACGACCTT-TAGCGGCA-TTTTCTATAAAAGCGCCGCTAAA
1 AAAAAAGCACCGCTAAAGACCACGA-ATTATAGTGG-AGTTTTATAAAAAAGCGCCGCTAAA
5591514 AGTCAAGATC
Statistics
Matches: 123, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
86 50 0.41
87 69 0.56
88 4 0.03
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (86 bp):
AAAAAAGCACCGCTAAAGACCACGAATTATAGTGGAGTTTTATAAAAAAGCGCCGCTAAAGGCCA
CGGAATTTAGCAGCATTTTCT
Found at i:5591527 original size:43 final size:43
Alignment explanation
Indices: 5591370--5591537 Score: 135
Period size: 43 Copynumber: 3.9 Consensus size: 43
5591360 GTTTTTTTAA
* * * * *
5591370 AAAAGCACCGCTAAAGGCCATGA-CTTATAGTGG-AGTTTTATAA
1 AAAAGCACCGCTAAAGACCAAGACCTT-TAGCGGCA-TTTTCTAT
* * * * * *
5591413 AAAAGCGCCGTTAAAGGCCACGGCATTTAGCGGCATTTTCTAT
1 AAAAGCACCGCTAAAGACCAAGACCTTTAGCGGCATTTTCTAT
* * *
5591456 GATAGCACCGCTAAAGACCACGACCTTTAGCGGCATTTTCTAT
1 AAAAGCACCGCTAAAGACCAAGACCTTTAGCGGCATTTTCTAT
* * *
5591499 AAAAGCGCCGCTAAA-AGTCAAGATCTTTAGCGGCATTTT
1 AAAAGCACCGCTAAAGA-CCAAGACCTTTAGCGGCATTTT
5591538 TTTCAAAGAA
Statistics
Matches: 101, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.01
43 97 0.96
44 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (43 bp):
AAAAGCACCGCTAAAGACCAAGACCTTTAGCGGCATTTTCTAT
Found at i:5591573 original size:35 final size:35
Alignment explanation
Indices: 5591524--5591602 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
5591514 AGTCAAGATC
*
5591524 TTTAGCGGCATTTTTTTCAAAGAAACGCCGCAAGT
1 TTTAGCGGCATTTTTTTCAAAGAAACACCGCAAGT
** *
5591559 TTTAGCGGTGTTTTTTTCAAATAAACACCGCAAGT
1 TTTAGCGGCATTTTTTTCAAAGAAACACCGCAAGT
5591594 TTTAGCGGC
1 TTTAGCGGC
5591603 CTTGTCTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (35 bp):
TTTAGCGGCATTTTTTTCAAAGAAACACCGCAAGT
Found at i:5603810 original size:22 final size:22
Alignment explanation
Indices: 5603782--5603847 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
5603772 TTTATTGTTC
5603782 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
5603804 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
5603826 AGCCATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
5603848 TGCCCATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:5619858 original size:27 final size:27
Alignment explanation
Indices: 5619824--5619889 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
5619814 TACAACATAT
5619824 AGTCATTTTATAACATAGGGGCATAAC
1 AGTCATTTTATAACATAGGGGCATAAC
** * *
5619851 AGTCATTTTACCACGTGGGGGCATAAC
1 AGTCATTTTATAACATAGGGGCATAAC
*
5619878 AATCATTTTATA
1 AGTCATTTTATA
5619890 TCTACTTGGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (27 bp):
AGTCATTTTATAACATAGGGGCATAAC
Found at i:5624175 original size:22 final size:22
Alignment explanation
Indices: 5624149--5624190 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5624139 TTTGAATAAT
*
5624149 TAAATAAATTGAAT-AATAAACC
1 TAAAT-AATTCAATAAATAAACC
5624171 TAAATAATTCAATAAATAAA
1 TAAATAATTCAATAAATAAA
5624191 AACTGAGCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAATAATTCAATAAATAAACC
Found at i:5628830 original size:14 final size:13
Alignment explanation
Indices: 5628807--5628848 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5628797 TAATCTTTGA
5628807 TTTATTATTTTAT
1 TTTATTATTTTAT
5628820 TTTAGTTA-TTTAT
1 TTTA-TTATTTTAT
*
5628833 TTTAATTGTTTTAT
1 TTT-ATTATTTTAT
5628847 TT
1 TT
5628849 GACTTGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:5629221 original size:17 final size:17
Alignment explanation
Indices: 5629201--5629239 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5629191 AAAAACGTAC
*
5629201 AAAAAATAAAATACAAA
1 AAAAAATAAAAAACAAA
* *
5629218 AAAAACTAAAAAATAAA
1 AAAAAATAAAAAACAAA
5629235 AAAAA
1 AAAAA
5629240 TTTGGGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (17 bp):
AAAAAATAAAAAACAAA
Found at i:5631870 original size:72 final size:72
Alignment explanation
Indices: 5631780--5631924 Score: 227
Period size: 72 Copynumber: 2.0 Consensus size: 72
5631770 TCAAGGAGAG
* *
5631780 ATACTTGGTCCATACTGATTTGGGATATCAAAATAATATATTTGATCCTGGAGATACTTTTGGCG
1 ATACTTGATCCATACTGATTTGGGATATCAAAATAATATATTTGATCCTAGAGATACTTTTGGCG
*
5631845 CAGAAGA
66 CACAAGA
* * * *
5631852 ATACTTGATCCATACTGATTTGGGATATCAAAATCATATCTTTGATCCTAGAGATAGTTTTGGTG
1 ATACTTGATCCATACTGATTTGGGATATCAAAATAATATATTTGATCCTAGAGATACTTTTGGCG
5631917 CACAAGA
66 CACAAGA
5631924 A
1 A
5631925 AGAATAGGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (72 bp):
ATACTTGATCCATACTGATTTGGGATATCAAAATAATATATTTGATCCTAGAGATACTTTTGGCG
CACAAGA
Found at i:5633810 original size:32 final size:32
Alignment explanation
Indices: 5633769--5633832 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
5633759 AGAAACTAGA
5633769 ATTAATAAGCTTTAATTCAATTGCTTTTTCAT
1 ATTAATAAGCTTTAATTCAATTGCTTTTTCAT
5633801 ATTAATAAGCTTTAATTCAATTGCTTTTTCAT
1 ATTAATAAGCTTTAATTCAATTGCTTTTTCAT
5633833 TCTCTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (32 bp):
ATTAATAAGCTTTAATTCAATTGCTTTTTCAT
Found at i:5639998 original size:51 final size:48
Alignment explanation
Indices: 5639940--5640126 Score: 212
Period size: 51 Copynumber: 3.7 Consensus size: 48
5639930 CCAATTCACA
*
5639940 TAGTAGCCTGCACATAGTACTACACATGTGACCTTTCTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC--TCT-ATCCGGTACACG
* ** * * *
5639991 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-C--CTCTATCCGGTACACG
* *
5640042 TAGTAGCCTGCACATAGTACTACACATGCGACCTATGATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCTCT-A-TCCGGTACACG
*
5640092 TAGTAGCCTGCACATAGTACTACACATGTGGCCTC
1 TAGTAGCCTGCACATAGTACTACACATGTGACCTC
5640127 GCAACTTCAC
Statistics
Matches: 113, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 41 0.36
51 67 0.59
52 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (48 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCTCTATCCGGTACACG
Found at i:5641188 original size:27 final size:27
Alignment explanation
Indices: 5641158--5641467 Score: 324
Period size: 27 Copynumber: 11.5 Consensus size: 27
5641148 CTAAAATCGG
*
5641158 GATGGGTAAAATTACTGAAATACACTC
1 GATGGGTAAAATTACTGAAATACCCTC
5641185 GATGGGTAAAATTACTGAAATACCCTC
1 GATGGGTAAAATTACTGAAATACCCTC
* *
5641212 AATGGGTAAAATTAAC-GAAATAACCTC
1 GATGGGTAAAATT-ACTGAAATACCCTC
* * *
5641239 GATGGGTAAAATTACCGGAATACCCGC
1 GATGGGTAAAATTACTGAAATACCCTC
* * *
5641266 AATAGGTAAAATTACTAAAATACCCTC
1 GATGGGTAAAATTACTGAAATACCCTC
* *
5641293 GAAT-GGTAAAATTTCTAAAATACCCTC
1 G-ATGGGTAAAATTACTGAAATACCCTC
* * *
5641320 AATGGTTAAAATTA-TCGTAATACCC-C
1 GATGGGTAAAATTACT-GAAATACCCTC
*
5641346 TGATGGGTAAAATTA-TCGAAATACCCTT
1 -GATGGGTAAAATTACT-GAAATACCCTC
** *
5641374 GATGGGTAAAATTACCAAAATACCCTT
1 GATGGGTAAAATTACTGAAATACCCTC
* * *
5641401 GAAGGGTAAAATTACTGAAATACGCTT
1 GATGGGTAAAATTACTGAAATACCCTC
* *
5641428 GATGGGTAAAATTATTGAAATACCCTT
1 GATGGGTAAAATTACTGAAATACCCTC
*
5641455 GATGGGTTAAATT
1 GATGGGTAAAATT
5641468 GAGTGCTAGG
Statistics
Matches: 241, Mismatches: 34, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
26 6 0.02
27 231 0.96
28 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (27 bp):
GATGGGTAAAATTACTGAAATACCCTC
Found at i:5641633 original size:29 final size:27
Alignment explanation
Indices: 5641591--5641676 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
5641581 AGTATTGTTT
*
5641591 CTGGTGGCTCTGCCACACACATACTGATA
1 CTGGTGGCTATGCCACA-A-ATACTGATA
* *
5641620 CTGGTGGCTATGCCACAATTACTGTTA
1 CTGGTGGCTATGCCACAAATACTGATA
* *
5641647 CTGGTGGCTTTGCCACATATACT-ATA
1 CTGGTGGCTATGCCACAAATACTGATA
5641673 CTGG
1 CTGG
5641677 CAGCTCTGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 6 0.12
27 27 0.54
28 1 0.02
29 16 0.32
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAAATACTGATA
Found at i:5641720 original size:26 final size:26
Alignment explanation
Indices: 5641671--5641720 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5641661 ACATATACTA
* **
5641671 TACTGGCAGCTCTGCTGCGTTATTAT
1 TACTGGCAGCTATGCTGCAATATTAT
5641697 TACTGGCAGCTATGCTGCAATATT
1 TACTGGCAGCTATGCTGCAATATT
5641721 TGTGTGTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTATGCTGCAATATTAT
Found at i:5641869 original size:28 final size:28
Alignment explanation
Indices: 5641820--5641876 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
5641810 CATACTTGGA
* *
5641820 CCATACTGATACTGTATCGGGCTTAGGC
1 CCATACTGATACTATATCGGGCTAAGGC
* *
5641848 CCATACTGATTCTATATTGGGCTAAGGC
1 CCATACTGATACTATATCGGGCTAAGGC
5641876 C
1 C
5641877 ACACTGCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (28 bp):
CCATACTGATACTATATCGGGCTAAGGC
Found at i:5642705 original size:11 final size:11
Alignment explanation
Indices: 5642679--5642711 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5642669 AATATTGTAT
*
5642679 TTATTATCTT-
1 TTATTATTTTA
5642689 TTATTATTTTA
1 TTATTATTTTA
5642700 TTATTATTTTA
1 TTATTATTTTA
5642711 T
1 T
5642712 ATCAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:5645770 original size:22 final size:22
Alignment explanation
Indices: 5645745--5645826 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
5645735 ATCTTAGTAA
5645745 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
5645767 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
5645789 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
5645811 CATGAGAGCTTAGTAC
1 CATGAGAGCTTAGTAC
5645827 CTTATCATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:5649667 original size:27 final size:27
Alignment explanation
Indices: 5648624--5649655 Score: 1187
Period size: 27 Copynumber: 38.4 Consensus size: 27
5648614 CTCCAAAATA
* *
5648624 GGTAAAATGACCAAAATACCCCAATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * * *
5648651 GGTAAAATGACCAAAATATCCCTATAA
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5648678 GATAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
5648705 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * **
5648732 GATAAAATGACTGAAATACCCTTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
5648759 GGTAAACTAACCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
5648786 GGTAAAATAACTGAAATAGCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* ** *
5648813 GGTAGAATGGTCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5648840 TGT--AATGACCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
5648865 GGTAAAATCACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5648892 GGTAGAATGACCGAAATAACCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
5648919 GGTAGAATGATCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
5648946 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
5648973 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5649000 GGTAGAATGACCGAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
5649027 GATAAAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
5649054 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* **
5649081 GGTAAAATGACTGAAATACCCTTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * * *
5649108 GATAAAATGGCTGAAATACCCCCATAA
1 GGTAAAATGACCGAAATACCCCCATAG
*
5649135 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
5649162 GGTAGAACGACTGAAATA-CCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5649188 GGTAAAATGATCGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
5649215 GGTAGAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
** *
5649242 GGTAAAATGACCGAAATACCCTTATAA
1 GGTAAAATGACCGAAATACCCCCATAG
* * **
5649269 GGTAAAATGACTGAAATACACTTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5649296 GATAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5649323 GGTAAAATAACTGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * * *
5649350 GGTAGAACGACTGAAATA-CCCCATTG
1 GGTAAAATGACCGAAATACCCCCATAG
*
5649376 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
5649403 GGTAAAATGACCGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
** *
5649430 GGTAAAATGATTGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
5649457 GATAAAATGACC-AAATTACCCCCATAG
1 GGTAAAATGACCGAAA-TACCCCCATAG
* * * *
5649484 GGTAGAATGATCGAAGTACCCTCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5649511 GGTGAAATGACC-AAGATGCCCCCATAG
1 GGTAAAATGACCGAA-ATACCCCCATAG
* * *
5649538 GGAAAAATGATCGAATTACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5649565 GGTAAAATGACCAAAATGCCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
5649592 GGTAAAATGACCAAAATGCCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
5649619 GGTAAAATGACC-AAGATGCCCCCATAG
1 GGTAAAATGACCGAA-ATACCCCCATAG
5649646 GGTAAAATGA
1 GGTAAAATGA
5649656 TTGTTATACC
Statistics
Matches: 854, Mismatches: 142, Indels: 18
0.84 0.14 0.02
Matches are distributed among these distances:
25 20 0.02
26 50 0.06
27 780 0.91
28 4 0.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAG
Found at i:5655320 original size:12 final size:12
Alignment explanation
Indices: 5655286--5655320 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5655276 AGACACAACC
* *
5655286 GTGTGGAAGGCT
1 GTGTGAAAGGTT
5655298 GTGTGAAAGGTT
1 GTGTGAAAGGTT
5655310 GTGTGAAAGGT
1 GTGTGAAAGGT
5655321 CCTAGGCCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.03, G:0.46, T:0.29
Consensus pattern (12 bp):
GTGTGAAAGGTT
Found at i:5661897 original size:27 final size:27
Alignment explanation
Indices: 5661788--5661906 Score: 150
Period size: 27 Copynumber: 4.4 Consensus size: 27
5661778 ATTTGTTCCT
*
5661788 TGTAGGGTAAAATGACCGTAATGCCCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
* *
5661815 TATAGGGTAAAATGATCCTAATGCCCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
* * ** *
5661842 TATAGGGTAAAATGATCGGAACACTCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
5661869 TGTAGGGTAAAATGATCGTAATGCCCC
1 TGTAGGGTAAAATGATCGTAATGCCCC
5661896 TGGT-GGGTAAA
1 T-GTAGGGTAAA
5661907 TGACTATTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
27 76 0.97
28 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (27 bp):
TGTAGGGTAAAATGATCGTAATGCCCC
Found at i:5661954 original size:23 final size:23
Alignment explanation
Indices: 5661927--5661997 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
5661917 TGCCCCTCGA
* *
5661927 GGTTAAATGATTGTTTTGTCTGT
1 GGTTAAATGACTGATTTGTCTGT
5661950 GGTTAAATGACTGATTTGTCTGT
1 GGTTAAATGACTGATTTGTCTGT
* **
5661973 GTTTGGTATGACTGATTTGTCTGT
1 GGTT-AAATGACTGATTTGTCTGT
5661997 G
1 G
5661998 ATTTGAATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 24 0.57
24 18 0.43
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (23 bp):
GGTTAAATGACTGATTTGTCTGT
Found at i:5662007 original size:24 final size:23
Alignment explanation
Indices: 5661932--5662009 Score: 93
Period size: 24 Copynumber: 3.3 Consensus size: 23
5661922 CTCGAGGTTA
* * * *
5661932 AATGATTGTTTTGTCTGTGGTTA
1 AATGACTGATTTGTCTGTGTTTG
5661955 AATGACTGATTTGTCTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTT-G
*
5661979 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTG-TTTG
5662003 AATGACT
1 AATGACT
5662010 AATTCTGAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 19 0.40
24 25 0.53
25 3 0.06
ACGTcount: A:0.19, C:0.08, G:0.26, T:0.47
Consensus pattern (23 bp):
AATGACTGATTTGTCTGTGTTTG
Found at i:5662225 original size:32 final size:32
Alignment explanation
Indices: 5662173--5662290 Score: 112
Period size: 32 Copynumber: 3.7 Consensus size: 32
5662163 GCGATGCTAC
**
5662173 TGATGGCTTTGTGCTAATCATAGTACCATTAT
1 TGATGGCTTTGTGCCGATCATAGTACCATTAT
* * * * *
5662205 TGATGGATTTGTCCCGATCATATTACCACTAC
1 TGATGGCTTTGTGCCGATCATAGTACCATTAT
* * * * *
5662237 CGATGGCTGTGTGCCGGTAAT-GTTACCGTTAT
1 TGATGGCTTTGTGCCGATCATAG-TACCATTAT
5662269 TGATGGCTTTGTGCCGATCATA
1 TGATGGCTTTGTGCCGATCATA
5662291 TCACTGCTAC
Statistics
Matches: 63, Mismatches: 21, Indels: 3
0.72 0.24 0.03
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATAGTACCATTAT
Found at i:5662314 original size:64 final size:64
Alignment explanation
Indices: 5662196--5662315 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 64
5662186 CTAATCATAG
* *
5662196 TACCATTATTGATGGATTTGTCCCGATCATATTACCACTACCGATGGCTGTGTGCCGGTAATGT
1 TACCATTATTGATGGATTTGTCCCGATCATATCACCACTACCGATAGCTGTGTGCCGGTAATGT
* * * ** * *
5662260 TACCGTTATTGATGGCTTTGTGCCGATCATATCACTGCTACTGATAGCTTTGTGCC
1 TACCATTATTGATGGATTTGTCCCGATCATATCACCACTACCGATAGCTGTGTGCC
5662316 AATGACATTA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 47 1.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (64 bp):
TACCATTATTGATGGATTTGTCCCGATCATATCACCACTACCGATAGCTGTGTGCCGGTAATGT
Found at i:5662357 original size:22 final size:21
Alignment explanation
Indices: 5662332--5662395 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
5662322 ATTACTGTAC
5662332 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* * * *
5662354 TTATAGCTTATAACTATCCTGT
1 TTATGGCTT-TAGCCATTCTGT
5662376 TTATGGCTCTTAGCCATTCT
1 TTATGGCT-TTAGCCATTCT
5662396 AATTACTGGC
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:5662419 original size:26 final size:26
Alignment explanation
Indices: 5662390--5662442 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
5662380 GGCTCTTAGC
* * *
5662390 CATTCTAATTACTGGCAGCTCTGCTG
1 CATTATAACTACTGGCAGCTATGCTG
* *
5662416 CATTATTACTACTGGTAGCTATGCTG
1 CATTATAACTACTGGCAGCTATGCTG
5662442 C
1 C
5662443 GATATTGGTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (26 bp):
CATTATAACTACTGGCAGCTATGCTG
Found at i:5668277 original size:26 final size:26
Alignment explanation
Indices: 5668241--5668295 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
5668231 CAGCACCGAC
5668241 CCGCTTACAACTGGAGATTACCTGTA
1 CCGCTTACAACTGGAGATTACCTGTA
5668267 CCGCTTACAACTGGAGATTACCTGTA
1 CCGCTTACAACTGGAGATTACCTGTA
5668293 CCG
1 CCG
5668296 TTAAATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (26 bp):
CCGCTTACAACTGGAGATTACCTGTA
Found at i:5668543 original size:27 final size:26
Alignment explanation
Indices: 5668491--5668569 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
5668481 ACATAAGGCC
*
5668491 ATAACAGTCATTTCATCTCCTA-GGGGT
1 ATAACAGTCATTTTA-C-CCTATGGGGT
5668518 ATAACAGTCATTTTACCCTATTGGGGT
1 ATAACAGTCATTTTACCCTA-TGGGGT
* * *
5668545 A-ATTCGGTCATTTTACCCTGTGGGG
1 ATA-ACAGTCATTTTACCCTATGGGG
5668570 GTAATTCGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
25 4 0.09
26 7 0.16
27 34 0.76
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (26 bp):
ATAACAGTCATTTTACCCTATGGGGT
Found at i:5668570 original size:27 final size:27
Alignment explanation
Indices: 5668525--5668775 Score: 364
Period size: 27 Copynumber: 9.2 Consensus size: 27
5668515 GGTATAACAG
* * *
5668525 TCATTTTACCCTATTGGGGTAATTCGG
1 TCATTTTACCCTGTGGGGGTAATTCGA
5668552 TCATTTTACCCTGTGGGGGTAATTCGA
1 TCATTTTACCCTGTGGGGGTAATTCGA
*
5668579 TTATTTTACCCTGTGGGGGTAATTCGA
1 TCATTTTACCCTGTGGGGGTAATTCGA
*
5668606 TCATTTTACCCTGTGGTGGTAATTCGA
1 TCATTTTACCCTGTGGGGGTAATTCGA
5668633 TCATTTTACCCTGTGGGGGTAATTTC-A
1 TCATTTTACCCTGTGGGGGTAA-TTCGA
5668660 TCATTTTACCCTGTGGGGGGTTAATTC-A
1 TCATTTTACCCTGT-GGGGG-TAATTCGA
5668688 GTCATTTTACCCTGTGGGGGTAATTCGA
1 -TCATTTTACCCTGTGGGGGTAATTCGA
* *
5668716 TCATTTTACCCTATGGGGGTAATT-TA
1 TCATTTTACCCTGTGGGGGTAATTCGA
*
5668742 GTCATTTTACCCTGTGGGGCTAATTCGA
1 -TCATTTTACCCTGTGGGGGTAATTCGA
5668770 TCATTT
1 TCATTT
5668776 ATTAACCTCT
Statistics
Matches: 205, Mismatches: 12, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
26 1 0.00
27 168 0.82
28 19 0.09
29 17 0.08
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (27 bp):
TCATTTTACCCTGTGGGGGTAATTCGA
Found at i:5668724 original size:83 final size:82
Alignment explanation
Indices: 5668522--5668760 Score: 360
Period size: 83 Copynumber: 2.9 Consensus size: 82
5668512 AGGGGTATAA
* * * *
5668522 CAGTCATTTTACCCTATTGGGGTAATTCGGTCATTTTACCCTGTGGGGGTAA-TTCGATTATTTT
1 CAGTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTGTGGGGGTAATTTC-ATCATTTT
5668586 ACCCTGT-GGGGGTAATT
65 ACCCTGTGGGGGGTAATT
*
5668603 C-GATCATTTTACCCTGTGGTGGTAATTCGATCATTTTACCCTGTGGGGGTAATTTCATCATTTT
1 CAG-TCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTGTGGGGGTAATTTCATCATTTT
5668667 ACCCTGTGGGGGGTTAATT
65 ACCCTGTGGGGGG-TAATT
*
5668686 CAGTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTATGGGGGTAATTT-AGTCATTTT
1 CAGTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTGTGGGGGTAATTTCA-TCATTTT
5668750 ACCCTGTGGGG
65 ACCCTGTGGGG
5668761 CTAATTCGAT
Statistics
Matches: 145, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
80 1 0.01
81 60 0.41
82 9 0.06
83 74 0.51
84 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (82 bp):
CAGTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCCTGTGGGGGTAATTTCATCATTTTA
CCCTGTGGGGGGTAATT
Found at i:5668747 original size:137 final size:135
Alignment explanation
Indices: 5668525--5668775 Score: 398
Period size: 137 Copynumber: 1.8 Consensus size: 135
5668515 GGTATAACAG
* * *
5668525 TCATTTTACCCTATTGGGGTAATTCGGTCATTTTACCCTGTGGGGGTAATTCGATTATTTTACCC
1 TCATTTTACCCTATGGGGGTAATTCAGTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCC
* *
5668590 TGTGGGGGTAATTCGATCATTTTACCCTGTGGTGG-TAATTCGATCATTTTACCCTGTGGGGGTA
66 TATGGGGGTAATTAGATCATTTTACCCTGTGG-GGCTAATTCGATCATTTTACCCTGTGGGGGTA
5668654 ATTTCA
130 ATTTCA
*
5668660 TCATTTTACCCTGTGGGGGGTTAATTCAGTCATTTTACCCTGTGGGGGTAATTCGATCATTTTAC
1 TCATTTTACCCTAT-GGGGG-TAATTCAGTCATTTTACCCTGTGGGGGTAATTCGATCATTTTAC
5668725 CCTATGGGGGTAATTTAG-TCATTTTACCCTGTGGGGCTAATTCGATCATTT
64 CCTATGGGGGTAA-TTAGATCATTTTACCCTGTGGGGCTAATTCGATCATTT
5668776 ATTAACCTCT
Statistics
Matches: 106, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
135 13 0.12
136 6 0.06
137 84 0.79
138 3 0.03
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (135 bp):
TCATTTTACCCTATGGGGGTAATTCAGTCATTTTACCCTGTGGGGGTAATTCGATCATTTTACCC
TATGGGGGTAATTAGATCATTTTACCCTGTGGGGCTAATTCGATCATTTTACCCTGTGGGGGTAA
TTTCA
Found at i:5669381 original size:24 final size:24
Alignment explanation
Indices: 5669356--5669402 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5669346 CCCAAATCCC
*
5669356 AATATTCTCTCCTCAAATCTCTCCA
1 AATATCCT-TCCTCAAATCTCTCCA
*
5669381 AATATCCTTCCTCAATTCTCTC
1 AATATCCTTCCTCAAATCTCTC
5669403 TATGATCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATCCTTCCTCAAATCTCTCCA
Found at i:5671484 original size:28 final size:29
Alignment explanation
Indices: 5671431--5671490 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
5671421 GTATCAGTAT
* *
5671431 AGTGTGGTCCATAGCCCAATACAGTAA-C
1 AGTGTGGGCCATAGCCCAAAACAGTAATC
* *
5671459 AGTGTGGGCCTTAGCCCAAAATAGTAATC
1 AGTGTGGGCCATAGCCCAAAACAGTAATC
5671488 AGT
1 AGT
5671491 ACAAATCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (29 bp):
AGTGTGGGCCATAGCCCAAAACAGTAATC
Found at i:5672090 original size:27 final size:27
Alignment explanation
Indices: 5671877--5672110 Score: 260
Period size: 27 Copynumber: 8.7 Consensus size: 27
5671867 TATGCTATAG
*
5671877 GGGTATTTCGATCATTTTACCCTTTCG-
1 GGGTATTTCGATAATTTTACCC-TTCGA
* * * *
5671904 GAGTATTTCAATAATTTTATCCTTCTA
1 GGGTATTTCGATAATTTTACCCTTCGA
*
5671931 GGGTATTTCGATAATTTTACCTTTC-A
1 GGGTATTTCGATAATTTTACCCTTCGA
* **
5671957 GGGGTATTTTGATAATTTTACCCTTTAA
1 -GGGTATTTCGATAATTTTACCCTTCGA
*
5671985 GGTTATTTC-ATTAATTTTACCCTTCGA
1 GGGTATTTCGA-TAATTTTACCCTTCGA
*
5672012 GGGTATTT-AAGTAATTTTACCCTTCGA
1 GGGTATTTCGA-TAATTTTACCCTTCGA
5672039 GGGTATTTCGATAATTTTACCCTTCGA
1 GGGTATTTCGATAATTTTACCCTTCGA
* *
5672066 GGGTAATTCGGTAATTTTACCCTTCGA
1 GGGTATTTCGATAATTTTACCCTTCGA
* * *
5672093 CGTTATTTCGATTATTTT
1 GGGTATTTCGATAATTTT
5672111 TTGGCCCAAG
Statistics
Matches: 175, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.03
27 168 0.96
28 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACCCTTCGA
Found at i:5683574 original size:27 final size:27
Alignment explanation
Indices: 5683544--5683723 Score: 247
Period size: 27 Copynumber: 6.7 Consensus size: 27
5683534 CAACCCATAG
* * * *
5683544 GGGTATTTCGGTCATTTTACCTTTCAA
1 GGGTATTTCAGTAATTTTACCCTTCGA
** * *
5683571 GGGTATTTTGGTAATTTTATCCTTTGA
1 GGGTATTTCAGTAATTTTACCCTTCGA
5683598 GGGTATTTC-GATAATTTTACCCTTC-A
1 GGGTATTTCAG-TAATTTTACCCTTCGA
5683624 GGGGTATTTCAGTAATTTTACCCTTCGA
1 -GGGTATTTCAGTAATTTTACCCTTCGA
5683652 GGGTATTTCAGTAATTTTACCCTTCGA
1 GGGTATTTCAGTAATTTTACCCTTCGA
5683679 GGGTATTTCAGTAATTTTACCCTTCGA
1 GGGTATTTCAGTAATTTTACCCTTCGA
*
5683706 GGGTATTTTAGTAATTTT
1 GGGTATTTCAGTAATTTT
5683724 TCACCCCAAG
Statistics
Matches: 139, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
26 2 0.01
27 135 0.97
28 2 0.01
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.44
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTACCCTTCGA
Found at i:5689373 original size:28 final size:28
Alignment explanation
Indices: 5689331--5689429 Score: 162
Period size: 28 Copynumber: 3.5 Consensus size: 28
5689321 GCAGTAACAG
*
5689331 TAGCCCAATACAGTAATAATGTGGGCCT
1 TAGCCCAATACAGTAACAATGTGGGCCT
*
5689359 TTGCCCAATACAGTAACAATGTGGGCCT
1 TAGCCCAATACAGTAACAATGTGGGCCT
5689387 TAGCCCAATACAGTAACAATGTGGGCCT
1 TAGCCCAATACAGTAACAATGTGGGCCT
* *
5689415 AAGCCCAATATAGTA
1 TAGCCCAATACAGTA
5689430 TCAGTACAGT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (28 bp):
TAGCCCAATACAGTAACAATGTGGGCCT
Found at i:5689811 original size:27 final size:27
Alignment explanation
Indices: 5689781--5689869 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
5689771 TTTCATCTGC
5689781 TAGGGGTATAAGAGTCATTTTACCCTA
1 TAGGGGTATAAGAGTCATTTTACCCTA
**
5689808 TAGGGGTA-ATTCAGTCATTTTACCCTA
1 TAGGGGTATA-AGAGTCATTTTACCCTA
* ** *
5689835 TAAGGGTAATTCG-GTCATTTTACCCTG
1 TAGGGGT-ATAAGAGTCATTTTACCCTA
*
5689862 TGGGGGTA
1 TAGGGGTA
5689870 ATTCGGTTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
26 2 0.04
27 47 0.94
28 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (27 bp):
TAGGGGTATAAGAGTCATTTTACCCTA
Found at i:5689870 original size:27 final size:27
Alignment explanation
Indices: 5689793--5689908 Score: 160
Period size: 27 Copynumber: 4.3 Consensus size: 27
5689783 GGGGTATAAG
5689793 AGTCATTTTACCCTATAGGGGTAATTC
1 AGTCATTTTACCCTATAGGGGTAATTC
*
5689820 AGTCATTTTACCCTATAAGGGTAATTC
1 AGTCATTTTACCCTATAGGGGTAATTC
* * *
5689847 GGTCATTTTACCCTGTGGGGGTAATTC
1 AGTCATTTTACCCTATAGGGGTAATTC
* * * *
5689874 GGTTATTATACCCTATGGGGGTAATTC
1 AGTCATTTTACCCTATAGGGGTAATTC
5689901 AGTCATTT
1 AGTCATTT
5689909 ATTAACCTCT
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (27 bp):
AGTCATTTTACCCTATAGGGGTAATTC
Found at i:5699023 original size:69 final size:69
Alignment explanation
Indices: 5698908--5699043 Score: 245
Period size: 69 Copynumber: 2.0 Consensus size: 69
5698898 GTTCTGTACC
*
5698908 TAGTTGGGCTTTGACCTTTCTTATCTCTCATTTATCTGTCGCTGCTATCAACATGTCATCAACAT
1 TAGTTGGGCTTTGACCTTTCTTATCTCTCATTTATCTGTCACTGCTATCAACATGTCATCAACAT
5698973 AACT
66 AACT
* *
5698977 TAGTTGGGCTTTGACCTTTCTTATCTCTCATTTATCTTTCATTGCTATCAACATGTCATCAACAT
1 TAGTTGGGCTTTGACCTTTCTTATCTCTCATTTATCTGTCACTGCTATCAACATGTCATCAACAT
5699042 AA
66 AA
5699044 AGGAGTAGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.42
Consensus pattern (69 bp):
TAGTTGGGCTTTGACCTTTCTTATCTCTCATTTATCTGTCACTGCTATCAACATGTCATCAACAT
AACT
Found at i:5701075 original size:27 final size:27
Alignment explanation
Indices: 5701055--5701127 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
5701045 TTACCCTATT
*
5701055 GGGCTATTTCAGTTATTTTACCCTTCA
1 GGGCTATTTCAGTAATTTTACCCTTCA
* * *
5701082 GGGGTATTTCGGTAATTTTACCCTTTAA
1 GGGCTATTTCAGTAATTTTACCC-TTCA
5701110 GGG-TATTTC-GATAATTTT
1 GGGCTATTTCAG-TAATTTT
5701128 CCAGCCCATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 33 0.82
28 6 0.15
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (27 bp):
GGGCTATTTCAGTAATTTTACCCTTCA
Found at i:5705377 original size:27 final size:27
Alignment explanation
Indices: 5705356--5705554 Score: 231
Period size: 27 Copynumber: 7.3 Consensus size: 27
5705346 AGGGGTATAA
* * *
5705356 CAGTTATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTGTGGGGGTAATT
* *
5705383 C-GATCATTTTACCCTATAAGGGGTAATT
1 CAG-TCATTTTACCCTGT-GGGGGTAATT
** *
5705411 C-GATCATTTTACCCAATGGGGTTAATT
1 CAG-TCATTTTACCCTGTGGGGGTAATT
* *
5705438 CAGTTATTTTACCTTGTGGGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
* *
5705465 CGGTTATTTTACCCTGTGGGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
5705492 CAGTCATTTTACCCTGTGGGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
*
5705519 CAGTCATTTTACCCTGTGGGGTTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
*
5705546 CGGTCATTT
1 CAGTCATTT
5705555 ATTGACCTCT
Statistics
Matches: 152, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
26 1 0.01
27 126 0.83
28 25 0.16
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (27 bp):
CAGTCATTTTACCCTGTGGGGGTAATT
Found at i:5705512 original size:81 final size:82
Alignment explanation
Indices: 5705356--5705554 Score: 267
Period size: 81 Copynumber: 2.4 Consensus size: 82
5705346 AGGGGTATAA
* * *
5705356 CAGTTATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAAGGGGTAATTCGATCATTTT
1 CAGTTATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATAAGGGGTAATTCGATCATTTT
*
5705421 ACCCAATGGGGTTAATT
66 ACCCAATGGGGGTAATT
* * * *
5705438 CAGTTATTTTACCTTGTGGGGGTAATTCGGTTATTTTACCCTGT-GGGGGTAATTC-AGTCATTT
1 CAGTTATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATAAGGGGTAATTCGA-TCATTT
**
5705501 TACCCTGTGGGGGTAATT
65 TACCCAATGGGGGTAATT
* *
5705519 CAGTCATTTTACCCTGTGGGGTTAATTCGGTCATTT
1 CAGTTATTTTACCCTGTGGGGGTAATTCGGTCATTT
5705555 ATTGACCTCT
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
80 1 0.01
81 63 0.62
82 38 0.37
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (82 bp):
CAGTTATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATAAGGGGTAATTCGATCATTTT
ACCCAATGGGGGTAATT
Found at i:5708827 original size:27 final size:27
Alignment explanation
Indices: 5708795--5708973 Score: 202
Period size: 27 Copynumber: 6.7 Consensus size: 27
5708785 TATGTTATAG
*
5708795 GGGTATTTCAGG-CATTTTACCCTTCGA
1 GGGTATTTC-GGTAATTTTACCCTTCGA
*
5708822 GAGTATTTCGGTAATTTT-CTCCTTCGA
1 GGGTATTTCGGTAATTTTAC-CCTTCGA
* * * *
5708849 GGGTATTTTGATAATTTTACCTTTCGG
1 GGGTATTTCGGTAATTTTACCCTTCGA
* * **
5708876 GGGTATTTCAGTAATTTTTCCCTTTAA
1 GGGTATTTCGGTAATTTTACCCTTCGA
5708903 GGGTATTTCGGTAATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
* *
5708930 GGGTATTTTGGTAATTTTACCCTTCAA
1 GGGTATTTCGGTAATTTTACCCTTCGA
*
5708957 GGGAATTT-GGTAATTTT
1 GGGTATTTCGGTAATTTT
5708974 CTGGCCTAAG
Statistics
Matches: 127, Mismatches: 22, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
26 12 0.09
27 114 0.90
28 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.44
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCTTCGA
Found at i:5708909 original size:81 final size:81
Alignment explanation
Indices: 5708794--5708950 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 81
5708784 TTATGTTATA
* *
5708794 GGGGTATTTCAGGCATTTTACCCTTCGAGAGTATTTCGGTAATTTT-CTCCTTCGAGGGTATTTT
1 GGGGTATTTCAGGAATTTTACCCTTCAAGAGTATTTCGGTAATTTTAC-CCTTCGAGGGTATTTT
5708858 GATAATTTTACCTTTCG
65 GATAATTTTACCTTTCG
* * * *
5708875 GGGGTATTTCAGTAATTTTTCCCTTTAAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTG
1 GGGGTATTTCAGGAATTTTACCCTTCAAGAGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTG
*
5708940 GTAATTTTACC
66 ATAATTTTACC
5708951 CTTCAAGGGA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
81 67 0.99
82 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (81 bp):
GGGGTATTTCAGGAATTTTACCCTTCAAGAGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTG
ATAATTTTACCTTTCG
Found at i:5709980 original size:26 final size:24
Alignment explanation
Indices: 5709927--5709985 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
5709917 ATTATTATAT
* *
5709927 TATTAAT-AAATTTTTATTTTTAA
1 TATTAATAAAATTTTAATTTTCAA
*
5709950 AATTAATAAAATATTATAATTTTCAA
1 TATTAATAAAAT-TT-TAATTTTCAA
*
5709976 TATTATTAAA
1 TATTAATAAA
5709986 CATACAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 6 0.21
24 4 0.14
25 2 0.07
26 16 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTAATAAAATTTTAATTTTCAA
Found at i:5712504 original size:43 final size:43
Alignment explanation
Indices: 5712436--5712704 Score: 245
Period size: 43 Copynumber: 6.3 Consensus size: 43
5712426 CGCTATTGAC
** * *
5712436 AACGCCGCTAAAGATCATGGTCTTTAGCGGCACTTTTGCCACA
1 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACA
* * * * * *
5712479 AACGTCGCTAGATATCATGACCTTTAGCAGCGCTTCTACTACA
1 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACA
* ** * * * *
5712522 AACGCCGCTAAAGATGATGGTCTTTAGTGACGCTTTTAACGCA
1 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACA
* * * *
5712565 AACGCCGCTAAAGATCATGGCCTTTAGCGGCGCTTATACTAGA
1 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACA
* **
5712608 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTATTACA
1 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACA
* ** * * *
5712651 AACGTCGCTATAA-AAAATGACTTTTAGCGACGCTTTT-TCACA
1 AACGCCGCTA-AAGATCATGACCTTTAGCGGCGCTTTTACCACA
5712693 AACGCCGCTAAA
1 AACGCCGCTAAA
5712705 AACATGCTTT
Statistics
Matches: 181, Mismatches: 44, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
41 2 0.01
42 13 0.07
43 164 0.91
44 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (43 bp):
AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTACCACA
Found at i:5712642 original size:86 final size:86
Alignment explanation
Indices: 5712436--5712704 Score: 274
Period size: 86 Copynumber: 3.1 Consensus size: 86
5712426 CGCTATTGAC
* ** * * *
5712436 AACGCCGCTAAAGATCATGGTCTTTAGCGGCACTTTTGCCACAAACGTCGCTAGATATCATGACC
1 AACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTAACACAAACGCCGCTAAAGATCATGACC
*
5712501 TTTAGCAGCGCTTCTACTACA
66 TTTAGCAGCGCTTATACTACA
* * * * *
5712522 AACGCCGCTAAAGATGATGGTCTTTAGTGACGCTTTTAACGCAAACGCCGCTAAAGATCATGGCC
1 AACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTAACACAAACGCCGCTAAAGATCATGACC
* *
5712587 TTTAGCGGCGCTTATACTAGA
66 TTTAGCAGCGCTTATACTACA
** * ** * **
5712608 AACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTATTACAAACGTCGCTATAA-AAAATGAC
1 AACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTAACACAAACGCCGCTA-AAGATCATGAC
* * *
5712672 TTTTAGC-GACGCTTTTTC-ACA
65 CTTTAGCAG-CGCTTATACTACA
5712693 AACGCCGCTAAA
1 AACGCCGCTAAA
5712705 AACATGCTTT
Statistics
Matches: 150, Mismatches: 31, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
85 15 0.10
86 133 0.89
87 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (86 bp):
AACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTAACACAAACGCCGCTAAAGATCATGACC
TTTAGCAGCGCTTATACTACA
Found at i:5712677 original size:129 final size:128
Alignment explanation
Indices: 5712436--5712704 Score: 335
Period size: 129 Copynumber: 2.1 Consensus size: 128
5712426 CGCTATTGAC
* * * * * *
5712436 AACGCCGCTAAAGATCATGGTCTTTAGCGGCACTTTTGCCACAAACGTCGCTAGATATCATGACC
1 AACGCCGCTAAAGATCATGGCCTTTAGCGGCACTTATACCACAAACGCCGCTAAAGATCATGACC
** * * *
5712501 TTTAGCAGCGCTTCTACTACAAACGCCGCTAAAGATGATGGTCTTTAGTGACGCTTTTAACGCA
66 TTTAGCAGCGCTTCTACTACAAACGCCGCTAAAGAAAATGCTCTTTAGCGACGCTTTT-ACACA
* * *
5712565 AACGCCGCTAAAGATCATGGCCTTTAGCGGCGCTTATACTAGAAACGCCGCTAAAGATCATGACC
1 AACGCCGCTAAAGATCATGGCCTTTAGCGGCACTTATACCACAAACGCCGCTAAAGATCATGACC
* * * *
5712630 TTTAGCGGCGCTTCTATTACAAACGTCGCTATAA-AAAATGACT-TTTAGCGACGCTTTTTCACA
66 TTTAGCAGCGCTTCTACTACAAACGCCGCTA-AAGAAAATG-CTCTTTAGCGACGCTTTTACACA
5712693 AACGCCGCTAAA
1 AACGCCGCTAAA
5712705 AACATGCTTT
Statistics
Matches: 120, Mismatches: 18, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
128 15 0.12
129 102 0.85
130 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (128 bp):
AACGCCGCTAAAGATCATGGCCTTTAGCGGCACTTATACCACAAACGCCGCTAAAGATCATGACC
TTTAGCAGCGCTTCTACTACAAACGCCGCTAAAGAAAATGCTCTTTAGCGACGCTTTTACACA
Found at i:5712754 original size:22 final size:24
Alignment explanation
Indices: 5712729--5712772 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
5712719 AAAAATTAAT
5712729 TAAATAATAT-TTAT-TTTTATAA
1 TAAATAATATATTATGTTTTATAA
*
5712751 TAAATACTATATTATGTTTTAT
1 TAAATAATATATTATGTTTTAT
5712773 TTTTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TAAATAATATATTATGTTTTATAA
Found at i:5714913 original size:39 final size:40
Alignment explanation
Indices: 5714844--5714950 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
5714834 TATTTTTTGC
* *
5714844 GGTGTTTTTAAAGTAGCGCCGCTAAAGCTCAATCTATAG-G
1 GGTGTTTTT-AAGAAGCGCCGCTAATGCTCAATCTATAGTG
*
5714884 GGTGTTTTTAAGAAGCGCCACTAATGCTCAATCTATAGTG
1 GGTGTTTTTAAGAAGCGCCGCTAATGCTCAATCTATAGTG
*
5714924 GAGT-TTTTTAAAAAGCGCCGCTAATGC
1 G-GTGTTTTTAAGAAGCGCCGCTAATGC
5714951 CTCTTATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 26 0.43
40 32 0.53
41 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (40 bp):
GGTGTTTTTAAGAAGCGCCGCTAATGCTCAATCTATAGTG
Found at i:5714932 original size:40 final size:38
Alignment explanation
Indices: 5714847--5714950 Score: 136
Period size: 39 Copynumber: 2.7 Consensus size: 38
5714837 TTTTTGCGGT
* * *
5714847 GTTTTTAAAGTAGCGCCGCTAAAGCTCAATCTATAGGG
1 GTTTTTTAAGAAGCGCCGCTAATGCTCAATCTATAGGG
*
5714885 GTGTTTTTAAGAAGCGCCACTAATGCTCAATCTATAGTGG
1 GT-TTTTTAAGAAGCGCCGCTAATGCTCAATCTATAG-GG
*
5714925 AGTTTTTTAAAAAGCGCCGCTAATGC
1 -GTTTTTTAAGAAGCGCCGCTAATGC
5714951 CTCTTATTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.04
39 30 0.53
40 23 0.40
41 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (38 bp):
GTTTTTTAAGAAGCGCCGCTAATGCTCAATCTATAGGG
Found at i:5715683 original size:14 final size:14
Alignment explanation
Indices: 5715664--5715714 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
5715654 CTAAACCCTA
5715664 AACCCCTAACTCTT
1 AACCCCTAACTCTT
5715678 AACCCCTAACGTC-T
1 AACCCCTAAC-TCTT
*
5715692 AACCCCTTAACCCTT
1 AACCCC-TAACTCTT
5715707 -ACCCCTAA
1 AACCCCTAA
5715715 ACCTTAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 3 0.09
14 23 0.70
15 7 0.21
ACGTcount: A:0.29, C:0.45, G:0.02, T:0.24
Consensus pattern (14 bp):
AACCCCTAACTCTT
Found at i:5715717 original size:14 final size:13
Alignment explanation
Indices: 5715630--5715714 Score: 57
Period size: 14 Copynumber: 6.2 Consensus size: 13
5715620 CTAAACCCAA
5715630 AACCCTAA-CCC-
1 AACCCTAACCCCT
*
5715641 AACCCTTGAATCCCT
1 AACCC-T-AACCCCT
5715656 AAACCCTAAACCCCT
1 -AACCCT-AACCCCT
*
5715671 AACTCTTAACCCCT
1 AAC-CCTAACCCCT
*
5715685 AACGTCTAACCCCTT
1 AAC-CCTAACCCC-T
*
5715700 AACCCTTACCCCT
1 AACCCTAACCCCT
5715713 AA
1 AA
5715715 ACCTTAAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
11 5 0.08
12 1 0.02
13 5 0.08
14 30 0.51
15 13 0.22
16 5 0.08
ACGTcount: A:0.32, C:0.45, G:0.02, T:0.21
Consensus pattern (13 bp):
AACCCTAACCCCT
Found at i:5715731 original size:21 final size:21
Alignment explanation
Indices: 5715707--5715786 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 21
5715697 CTTAACCCTT
*
5715707 ACCCCTAAACCTTAAATCCCA
1 ACCCATAAACCTTAAATCCCA
*
5715728 ACCCATAAACCAT-AATCCCTA
1 ACCCATAAACCTTAAATCCC-A
* * * *
5715749 ATCCGTAATCCCTAAA-CCCA
1 ACCCATAAACCTTAAATCCCA
*
5715769 TACTCCTTAAACCTTAAA
1 -AC-CCATAAACCTTAAA
5715787 ATAGTACCCC
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 7 0.16
21 25 0.56
22 13 0.29
ACGTcount: A:0.39, C:0.38, G:0.01, T:0.23
Consensus pattern (21 bp):
ACCCATAAACCTTAAATCCCA
Found at i:5716223 original size:41 final size:41
Alignment explanation
Indices: 5716127--5716366 Score: 270
Period size: 41 Copynumber: 5.9 Consensus size: 41
5716117 TAAAATGTTT
* *
5716127 TTAGCGGCGCTTTTTC-AAAACTGCAGCTAAAGCCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAAC-GCCGCTAAAACCCCGAGCA
* * *
5716168 TTAGTGGCGC-TTTTCAAAAACGCCGCTAAAATCTCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* *
5716208 TTAGCGACGCTTTTTCAAAAACGCCG-TAAAAACCCCAAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCT-AAAACCCCGAGCA
* *
5716249 TTAGCGGCGCTTTTTCAAAAATGCAGCTAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * * * **
5716290 TTAGCAGCACTTTTTAAAAAACGCCGCTAAAACACAAAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* ** *
5716331 TTAGCGGCACTTTTTTGAAAACGCCGCTAAAGCCCC
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCC
5716367 CGAAAGGTAA
Statistics
Matches: 167, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
40 29 0.17
41 137 0.82
42 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
Found at i:5723710 original size:26 final size:24
Alignment explanation
Indices: 5723657--5723715 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
5723647 ATTATTATAT
* *
5723657 TATTAAT-AAATTTTTATTTTTAA
1 TATTAATAAAATTTTAATTTTCAA
*
5723680 AATTAATAAAATATTATAATTTTCAA
1 TATTAATAAAAT-TT-TAATTTTCAA
*
5723706 TATTATTAAA
1 TATTAATAAA
5723716 CATACATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 6 0.21
24 4 0.14
25 2 0.07
26 16 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTAATAAAATTTTAATTTTCAA
Found at i:5731375 original size:26 final size:24
Alignment explanation
Indices: 5731322--5731380 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
5731312 ATTATTATAT
* *
5731322 TATTAAT-AAATTTTTATTTTTAA
1 TATTAATAAAATTTTAATTTTCAA
*
5731345 AATTAATAAAATATTATAATTTTCAA
1 TATTAATAAAAT-TT-TAATTTTCAA
*
5731371 TATTATTAAA
1 TATTAATAAA
5731381 CATACATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 6 0.21
24 4 0.14
25 2 0.07
26 16 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTAATAAAATTTTAATTTTCAA
Found at i:5737449 original size:17 final size:18
Alignment explanation
Indices: 5737412--5737450 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5737402 AAATCTATAG
*
5737412 TTCTGTTGTAAACAGGAA
1 TTCTGTTATAAACAGGAA
*
5737430 TTCTGTTATGAACA-GAA
1 TTCTGTTATAAACAGGAA
5737447 TTCT
1 TTCT
5737451 TATCTCAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (18 bp):
TTCTGTTATAAACAGGAA
Found at i:5742263 original size:17 final size:18
Alignment explanation
Indices: 5742224--5742264 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5742214 CTAAATCTAC
*
5742224 AATTCTGTTGTAAACAGG
1 AATTCTGTTATAAACAGG
*
5742242 AATTCTGTTATGAACA-G
1 AATTCTGTTATAAACAGG
5742259 AATTCT
1 AATTCT
5742265 TATCTCAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
AATTCTGTTATAAACAGG
Found at i:5744123 original size:26 final size:24
Alignment explanation
Indices: 5744070--5744128 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
5744060 ATTATTATAT
* *
5744070 TATTAAT-AAATTTTTATTTTTAA
1 TATTAATAAAATTTTAATTTTCAA
*
5744093 AATTAATAAAATATTATAATTTTCAA
1 TATTAATAAAAT-TT-TAATTTTCAA
*
5744119 TATTATTAAA
1 TATTAATAAA
5744129 CATACATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 6 0.21
24 4 0.14
25 2 0.07
26 16 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTAATAAAATTTTAATTTTCAA
Found at i:5751845 original size:26 final size:26
Alignment explanation
Indices: 5751816--5751876 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
5751806 ATATTATTAT
* *
5751816 ATTATTAATAA-ATTTTTATTTTTAAA
1 ATTATTAA-AATATTATAATTTTTAAA
* *
5751842 ATTAATAAAATATTATAATTTTTAAT
1 ATTATTAAAATATTATAATTTTTAAA
5751868 ATTATTAAA
1 ATTATTAAA
5751877 CATACATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTATTAAAATATTATAATTTTTAAA
Found at i:5751887 original size:25 final size:25
Alignment explanation
Indices: 5751832--5751887 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
5751822 AATAAATTTT
*
5751832 TATTTTTAAAATTAATAAAATATTA
1 TATTTTTAAAATTAATAAAATATCA
* *
5751857 TAATTTTTAATATTATTAAACATA-CA
1 T-ATTTTTAAAATTAATAAA-ATATCA
5751883 TATTT
1 TATTT
5751888 AATTATCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
26 18 0.69
27 3 0.12
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTTTTAAAATTAATAAAATATCA
Found at i:5758523 original size:27 final size:27
Alignment explanation
Indices: 5758493--5758546 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5758483 ATATACGTAC
5758493 ATATA-AAATAAATAAATAAATAAATAT
1 ATATATAAATAAA-AAATAAATAAATAT
* * *
5758520 ATATATAGATTAAAAATAATTAAATAT
1 ATATATAAATAAAAAATAAATAAATAT
5758547 TCAATACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
ATATATAAATAAAAAATAAATAAATAT
Found at i:5758661 original size:20 final size:21
Alignment explanation
Indices: 5758622--5758663 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5758612 AATATTCGTT
*
5758622 AAAAAGAATAAATATGTACATA
1 AAAAACAATAAATA-GTACATA
5758644 AAAAACAATAAATA-TACATA
1 AAAAACAATAAATAGTACATA
5758664 TATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAAACAATAAATAGTACATA
Found at i:5758687 original size:20 final size:20
Alignment explanation
Indices: 5758664--5758702 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5758654 AATATACATA
*
5758664 TATATATAAAAATAATTACG
1 TATATAAAAAAATAATTACG
5758684 TATATAAAAAAATAATTAC
1 TATATAAAAAAATAATTAC
5758703 ATTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
TATATAAAAAAATAATTACG
Found at i:5760472 original size:45 final size:45
Alignment explanation
Indices: 5760399--5760521 Score: 167
Period size: 45 Copynumber: 2.7 Consensus size: 45
5760389 GTTTATTTAT
* * *
5760399 TCTGCCCCACTGCAATTTCAAGGG-GATAAGACTTGCTTTCTTAAG
1 TCTGCTCCACTGCAACTTC-AGGGAGATAAGACTCGCTTTCTTAAG
* **
5760444 TCTGCTCCATTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTAAG
*
5760489 TATGCTCCACTGCAACTTCAGGGAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT
5760522 AGATGCGATC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 4 0.06
45 65 0.94
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTAAG
Found at i:5760841 original size:99 final size:99
Alignment explanation
Indices: 5760662--5760842 Score: 274
Period size: 99 Copynumber: 1.8 Consensus size: 99
5760652 CCATCTTCAG
* *
5760662 TCTTTTAAATTGCAATGTAGGGAAACAGGATTCGCCGTCGTAGCTTCATTCCGTTCCACTACACC
1 TCTTTTAAATTGCAATGTAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCCGTTCCACTACACC
**
5760727 GCCAGGGAAGTAAGATTCGCTGTTGCGACTTTAA
66 GCCAGGGAAACAAGATTCGCTGTTGCGACTTTAA
* * * *
5760761 TCTTTTTAATTG-AATGTTGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTGTTCCACTACAC
1 TCTTTTAAATTGCAATG-TAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCCGTTCCACTACAC
5760825 CGCCAGGGAAACAAGATT
65 CGCCAGGGAAACAAGATT
5760843 TGTCATTGTG
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 4 0.05
99 69 0.95
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (99 bp):
TCTTTTAAATTGCAATGTAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCCGTTCCACTACACC
GCCAGGGAAACAAGATTCGCTGTTGCGACTTTAA
Found at i:5761160 original size:88 final size:88
Alignment explanation
Indices: 5761063--5761235 Score: 240
Period size: 88 Copynumber: 2.0 Consensus size: 88
5761053 AAGACTAATG
* * * * *
5761063 TCTTCGATCTGCTTCACTGCCAGCACAGGAAGGCGAGATCTTCT-ATCTTCAACCTACTCCACTG
1 TCTTCGATCTACTTCACTGCCAACACAGGAAGACAAGATCTGCTAAT-TTCAACCTACTCCACTG
*
5761127 CTGCTCAAGGAGACAAGGCTGGTA
65 CTACTCAAGGAGACAAGGCTGGTA
* *
5761151 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAATATCTGCTAATTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAACACAGGAAGACAAGATCTGCTAATTTCAACCTACTCCACTGC
* *
5761216 TACTCAGGGAGATAAGGCTG
66 TACTCAAGGAGACAAGGCTG
5761236 AAGTTTCACC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 72 0.97
89 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (88 bp):
TCTTCGATCTACTTCACTGCCAACACAGGAAGACAAGATCTGCTAATTTCAACCTACTCCACTGC
TACTCAAGGAGACAAGGCTGGTA
Found at i:5773821 original size:21 final size:22
Alignment explanation
Indices: 5773781--5773822 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5773771 AATATTCGTT
*
5773781 AAAAAGAATAAATATGTACATGA
1 AAAAACAATAAATA-GTACATGA
5773804 AAAAACAATAAATA-TACAT
1 AAAAACAATAAATAGTACAT
5773823 ATATATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAAACAATAAATAGTACATGA
Found at i:5774449 original size:140 final size:141
Alignment explanation
Indices: 5774284--5774547 Score: 444
Period size: 140 Copynumber: 1.9 Consensus size: 141
5774274 GCCAAGAACT
5774284 TTTAAAAAAAATTCATTTTCTCATTGTTTTTAAAAAAAAACAGAAATCCTTTTAAAAAAGGCTCT
1 TTTAAAAAAAATTCATTTTCTCATTGTTTTT-AAAAAAAACAGAAATCCTTTTAAAAAAGGCTCT
* *
5774349 CCCCT-CCCAGTTC-TCTGGCCAAGGTAAGGGAATCAGCCAGTCGTCAGCCACCGCGCCGGCTTT
65 CCCCTCCCCAGTTCTTC-GGCCAAGGTAAGGGAATCAGCCAATCGTCAGCCACAGCGCCGGCTTT
5774412 AAGCAAAAAAAAA
129 AAGCAAAAAAAAA
*
5774425 TTTAAAAAAAA-TCATTTTCTCATTGTTTTTAAAAAAAACAGAAATCCTTTTGAAAAAGGCTCTC
1 TTTAAAAAAAATTCATTTTCTCATTGTTTTTAAAAAAAACAGAAATCCTTTTAAAAAAGGCTCTC
* *
5774489 CCCTCCCCAGTTCTTCGGCCAAGGTTAGGGCATCAGCCAATCGTCAGCCACAGCGCCGG
66 CCCTCCCCAGTTCTTCGGCCAAGGTAAGGGAATCAGCCAATCGTCAGCCACAGCGCCGG
5774548 TCGTCGGTCT
Statistics
Matches: 116, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
139 37 0.32
140 66 0.57
141 13 0.11
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (141 bp):
TTTAAAAAAAATTCATTTTCTCATTGTTTTTAAAAAAAACAGAAATCCTTTTAAAAAAGGCTCTC
CCCTCCCCAGTTCTTCGGCCAAGGTAAGGGAATCAGCCAATCGTCAGCCACAGCGCCGGCTTTAA
GCAAAAAAAAA
Found at i:5782734 original size:7 final size:7
Alignment explanation
Indices: 5782724--5782775 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
5782714 TGAGAGCTAA
*
5782724 GAGAGTT
1 GAGAGAT
5782731 GAGAGA-
1 GAGAGAT
5782737 GAG-GAT
1 GAGAGAT
5782743 GAGAGAT
1 GAGAGAT
5782750 GAGAGAT
1 GAGAGAT
5782757 GAGAGGGAT
1 GAGA--GAT
*
5782766 CAGAGAT
1 GAGAGAT
5782773 GAG
1 GAG
5782776 GGTTGAGGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 2 0.05
6 6 0.16
7 24 0.63
9 6 0.16
ACGTcount: A:0.38, C:0.02, G:0.46, T:0.13
Consensus pattern (7 bp):
GAGAGAT
Found at i:5782757 original size:14 final size:14
Alignment explanation
Indices: 5782724--5782775 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 14
5782714 TGAGAGCTAA
*
5782724 GAGAGTTGAGAGA-
1 GAGAGATGAGAGAT
5782737 GAG-GATGAGAGAT
1 GAGAGATGAGAGAT
5782750 GAGAGATGAGAGGGAT
1 GAGAGATGAGA--GAT
*
5782766 CAGAGATGAG
1 GAGAGATGAG
5782776 GGTTGAGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 8 0.24
13 6 0.18
14 7 0.21
16 12 0.36
ACGTcount: A:0.38, C:0.02, G:0.46, T:0.13
Consensus pattern (14 bp):
GAGAGATGAGAGAT
Found at i:5793515 original size:16 final size:17
Alignment explanation
Indices: 5793488--5793522 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5793478 AGAGAGTTGA
5793488 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
5793505 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
5793521 GA
1 GA
5793523 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:5796182 original size:17 final size:18
Alignment explanation
Indices: 5796160--5796194 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5796150 CAATTTGGGT
5796160 CATGTGGGCC-ACACGGG
1 CATGTGGGCCTACACGGG
5796177 CATGTGGGCCTACACGGG
1 CATGTGGGCCTACACGGG
5796195 TGAACATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.17, C:0.29, G:0.40, T:0.14
Consensus pattern (18 bp):
CATGTGGGCCTACACGGG
Found at i:5802319 original size:17 final size:16
Alignment explanation
Indices: 5802299--5802350 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
5802289 TTCAAAATAA
5802299 TTTATTTATTTATTTAT
1 TTTATTTATTTA-TTAT
*
5802316 TTTATTTAAATTATTAT
1 TTTATTT-ATTTATTAT
* *
5802333 TTTTTTTA-TAATTAT
1 TTTATTTATTTATTAT
5802348 TTT
1 TTT
5802351 TGTATTAGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 9 0.29
16 1 0.03
17 17 0.55
18 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTTATTTATTAT
Found at i:5803412 original size:26 final size:23
Alignment explanation
Indices: 5803359--5803417 Score: 55
Period size: 26 Copynumber: 2.4 Consensus size: 23
5803349 ATTATTATTT
* *
5803359 TATTAATAAATTTTTATTTTTAA
1 TATTAATAAATTTTAATTTTCAA
*
5803382 AATTAATACAATATTATAATTTTCAA
1 TATTAATA-AAT-TT-TAATTTTCAA
*
5803408 TATTATTAAA
1 TATTAATAAA
5803418 CATACATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 7 0.25
24 3 0.11
25 4 0.14
26 14 0.50
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTAATAAATTTTAATTTTCAA
Found at i:5806698 original size:50 final size:51
Alignment explanation
Indices: 5806577--5806712 Score: 166
Period size: 50 Copynumber: 2.7 Consensus size: 51
5806567 TAGATAATCG
* * * * * ** * *
5806577 TCACATGTGTAGTACTATGTACAGGCTACTATGTGTACTGGTAGGCTTTGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAAGCTTTGA
5806628 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAAG-TTTGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAAGCTTTGA
* *
5806678 TCACGTGTGTAGTACTATGTGAAGGCAACTACGTG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTG
5806713 TATCGAATGA
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 37 0.50
51 37 0.50
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAAGCTTTGA
Done.