Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006561.1 Hibiscus syriacus cultivar Beakdansim tig00016041_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 109290
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4364 original size:20 final size:21
Alignment explanation
Indices: 4335--4390 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
4325 TTTGTGCTTC
*
4335 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
4355 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
4377 ATGCATCGATGCAT
1 ATGCATCGATGCAT
4391 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:5963 original size:21 final size:21
Alignment explanation
Indices: 5921--5964 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5911 ACCCCGGGAG
*
5921 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
5942 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
5963 CT
1 CT
5965 CCTCCAGCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:6295 original size:18 final size:19
Alignment explanation
Indices: 6267--6303 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
6257 TGTTAAACTT
6267 TTTGATTTGGATGTTTATG
1 TTTGATTTGGATGTTTATG
6286 TTTG-TTTGGATGTTTATG
1 TTTGATTTGGATGTTTATG
6304 ATATTTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (19 bp):
TTTGATTTGGATGTTTATG
Found at i:6312 original size:17 final size:18
Alignment explanation
Indices: 6271--6314 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
6261 AAACTTTTTG
*
6271 ATTTGGATGTTTATGTTT
1 ATTTGGATGTTTATGTAT
*
6289 GTTTGGATGTTTATG-AT
1 ATTTGGATGTTTATGTAT
6306 ATTTGGATG
1 ATTTGGATG
6315 CTTGACTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (18 bp):
ATTTGGATGTTTATGTAT
Found at i:7127 original size:64 final size:65
Alignment explanation
Indices: 6982--7107 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 65
6972 GAATGCATTC
* ** *
6982 CATGCACCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAAG
1 CATGCACCGATGCA-TCAGGCTATTTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAAG
7046 A
65 A
*
7047 CATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTTCATGCATCGATGCACA
1 CATGCACCGATGCATCAGGCTATTTTTCAAAACATCGAATGCATTTCATGCATCGATGCACA
7108 CTTGGTGCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 37 0.67
65 18 0.33
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (65 bp):
CATGCACCGATGCATCAGGCTATTTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAAGA
Found at i:10962 original size:12 final size:11
Alignment explanation
Indices: 10942--10973 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
10932 ACAACAAACA
10942 GACAAAAAAAT
1 GACAAAAAAAT
*
10953 GATAAAAAAAT
1 GACAAAAAAAT
10964 GACAAAAAAA
1 GACAAAAAAA
10974 GTATTTATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.75, C:0.06, G:0.09, T:0.09
Consensus pattern (11 bp):
GACAAAAAAAT
Found at i:18136 original size:20 final size:20
Alignment explanation
Indices: 18111--18179 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
18101 ATTGCACATG
18111 AGCAAGA-TGCTGCTTGATTC
1 AGCAAGACT-CTGCTTGATTC
18131 AGCAAGACTCTGCTTGATTC
1 AGCAAGACTCTGCTTGATTC
18151 AGCAAGACTCTGCTTGATTC
1 AGCAAGACTCTGCTTGATTC
18171 AGCAAGACT
1 AGCAAGACT
18180 GTACATGAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 47 0.98
21 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (20 bp):
AGCAAGACTCTGCTTGATTC
Found at i:18200 original size:36 final size:37
Alignment explanation
Indices: 18106--18217 Score: 127
Period size: 36 Copynumber: 3.0 Consensus size: 37
18096 AAAGGATTGC
**
18106 ACATGAGCAAGATGCTGCTTGATTCAGCAAGACTCTGCT
1 ACATGAGCAAGACACTGCTTGATTCAGCAAGA--CTGCT
** * *
18145 TGATTCAGCAAGACTCTGCTTGATTCAGCAAGACTG-T
1 ACA-TGAGCAAGACACTGCTTGATTCAGCAAGACTGCT
*
18182 ACATGAGCAAGACACTGCTGGATTCAGCAAGACTGC
1 ACATGAGCAAGACACTGCTTGATTCAGCAAGACTGC
18218 CTCCTATCAA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
36 29 0.48
37 2 0.03
38 3 0.05
39 1 0.02
40 26 0.43
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (37 bp):
ACATGAGCAAGACACTGCTTGATTCAGCAAGACTGCT
Found at i:18212 original size:20 final size:20
Alignment explanation
Indices: 18120--18214 Score: 108
Period size: 20 Copynumber: 5.0 Consensus size: 20
18110 GAGCAAGATG
*
18120 CTGCTTGATTCAGCAAGACT
1 CTGCTTGATTCAGCAAGACA
*
18140 CTGCTTGATTCAGCAAGACT
1 CTGCTTGATTCAGCAAGACA
18160 CTGCTTGATTCAGCAAG--A
1 CTGCTTGATTCAGCAAGACA
** *
18178 CTG-TACA-TGAGCAAGACA
1 CTGCTTGATTCAGCAAGACA
*
18196 CTGCTGGATTCAGCAAGAC
1 CTGCTTGATTCAGCAAGAC
18215 TGCCTCCTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
16 7 0.11
17 2 0.03
18 7 0.11
19 2 0.03
20 46 0.72
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (20 bp):
CTGCTTGATTCAGCAAGACA
Found at i:21843 original size:41 final size:38
Alignment explanation
Indices: 21783--21859 Score: 91
Period size: 41 Copynumber: 1.9 Consensus size: 38
21773 ACATGACTTA
* *
21783 CACGTGGGTATAACGCGCCCATGTTCCGCGCTATACGC
1 CACGTGGGTATAACGCGCCCATGCTCAGCGCTATACGC
* *
21821 CACGTAGGGATATAGCGTCGCCCCTGCTCAGCGCTATAC
1 CACGT-GGG-TATAACG-CGCCCATGCTCAGCGCTATAC
21860 CTTGGTACGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 5 0.16
39 3 0.09
40 6 0.19
41 18 0.56
ACGTcount: A:0.19, C:0.34, G:0.26, T:0.21
Consensus pattern (38 bp):
CACGTGGGTATAACGCGCCCATGCTCAGCGCTATACGC
Found at i:22132 original size:15 final size:16
Alignment explanation
Indices: 22112--22159 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
22102 TCGTTATAAA
22112 TTTTATTATAATT-TT
1 TTTTATTATAATTATT
*
22127 TTTTATTATACTTATT
1 TTTTATTATAATTATT
* *
22143 GTTTATTATGATTATT
1 TTTTATTATAATTATT
22159 T
1 T
22160 AAAAAAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTTATTATAATTATT
Found at i:27197 original size:3 final size:3
Alignment explanation
Indices: 27191--27255 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
27181 ATTTTAAAAT
* *
27191 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA ATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
27240 TTA TTTA TTA ATA TTA
1 TTA -TTA TTA TTA TTA
27256 CAAAACCCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28595 original size:14 final size:15
Alignment explanation
Indices: 28578--28610 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28568 TATTATTAAG
28578 TTATATAA-ATATAT
1 TTATATAATATATAT
*
28592 TTATATAATATTTAT
1 TTATATAATATATAT
28607 TTAT
1 TTAT
28611 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:31091 original size:14 final size:14
Alignment explanation
Indices: 31053--31106 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
31043 ATTTTAAATA
*
31053 ATTTACATTTACAT
1 ATTTACATTTGCAT
* *
31067 TTTTATATTTGCAT
1 ATTTACATTTGCAT
31081 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
31096 CTTTGCATTTG
1 ATTTACATTTG
31107 TATTGCACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:34409 original size:16 final size:15
Alignment explanation
Indices: 34384--34414 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
34374 AAGAAAGAAG
34384 AAAAAAAAAGGAAAA
1 AAAAAAAAAGGAAAA
34399 AAAAGAAAAAGGAAAA
1 AAAA-AAAAAGGAAAA
34415 TTGAATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGGAAAA
Found at i:36822 original size:115 final size:115
Alignment explanation
Indices: 36659--37003 Score: 548
Period size: 115 Copynumber: 3.0 Consensus size: 115
36649 AGCAAGTGCC
* *
36659 ATGTGCTCGTAGTAGAAATAAGAATACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
36724 ATTTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGA
66 ATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGA
36774 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
*
36839 ATCTGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGA
66 ATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGA
* * * * *
36889 ATTTGCTCCTGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
* * * * * *
36954 ATCTGGTTCGGTAGGAACCAC-AGAACCAATCATTGGAATTAAAAGATGA
66 ATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGA
37003 A
1 A
37004 CTGCATGATC
Statistics
Matches: 214, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
114 25 0.12
115 189 0.88
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (115 bp):
ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
ATCTGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGA
Found at i:39216 original size:54 final size:54
Alignment explanation
Indices: 39127--39332 Score: 228
Period size: 54 Copynumber: 3.9 Consensus size: 54
39117 AGAAATCTTG
* * * *
39127 GCAGAAGCCAC-AGAAAAGGATGAATGTGTTGTCAAACGCTTTATGAACGTCTGA
1 GCAGAAACCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCTGA
* **
39181 GCAAAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
1 GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCTGA
* *
39235 GCAGAAGCCAC-AGAAAAGGATGAATGTGTTGTCAAGTG-TTT-T--ACATCTCGA
1 GCAGAAACCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCT-GA
* * *
39286 -CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTATGAAC
1 GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATGAAC
39333 CAGTGATTAT
Statistics
Matches: 128, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
50 36 0.28
51 6 0.05
52 1 0.01
53 5 0.04
54 78 0.61
55 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.24
Consensus pattern (54 bp):
GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCTGA
Found at i:39728 original size:22 final size:22
Alignment explanation
Indices: 39699--39753 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
39689 ATCTACACTC
*
39699 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
39721 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
39743 TTCAAAGATGA
1 TTCAAAGATGA
39754 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:40355 original size:24 final size:23
Alignment explanation
Indices: 40312--40356 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
40302 GTTCATAATG
*
40312 AGAAGAAATCATCTGAAGAAGGA
1 AGAAGAAATCATATGAAGAAGGA
40335 AGAAGAAATTCATAATG-AGAAG
1 AGAAGAAA-TCAT-ATGAAGAAG
40357 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 9 0.47
25 2 0.11
ACGTcount: A:0.53, C:0.07, G:0.24, T:0.16
Consensus pattern (23 bp):
AGAAGAAATCATATGAAGAAGGA
Found at i:40409 original size:113 final size:113
Alignment explanation
Indices: 40153--41850 Score: 2975
Period size: 113 Copynumber: 15.0 Consensus size: 113
40143 TAGCAAATGT
*
40153 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATTAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
40218 AGAA-G--GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
40263 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAAATCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
40328 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
40376 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
40441 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
40489 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
40554 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
40602 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
40667 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
40715 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
40780 AGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
40828 TCAAATCCATCATATGATTGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
40893 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
40941 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
41006 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
41054 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
41119 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
41167 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
41232 AGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
41280 TCAAATCCATCTTCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
41345 AGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
41393 TCAAATCCATCTTCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
41458 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
41506 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
41571 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
41619 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** * *
41684 AGGA-GAAGAA-AAAGTTCACAATGAGAAGAGCTTATTCAACCTTTCGC
66 AGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* ** * *
41731 AT-AATTCTATCACAGAAGCAGATAGATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
1 -TCAA----ATC-C---ATCATCT-GA-T-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA
* **
41795 GAACTCATCTGAAGAA-GAAGAAG---TTCACAATGAGAAGAGCTTGTTCAACCTTTTGC
54 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
41851 ATAATTCTAT
Statistics
Matches: 1538, Mismatches: 33, Indels: 24
0.96 0.02 0.02
Matches are distributed among these distances:
110 67 0.04
111 4 0.00
112 36 0.02
113 1335 0.87
116 3 0.00
117 1 0.00
120 35 0.02
121 2 0.00
122 1 0.00
123 54 0.04
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:41866 original size:120 final size:119
Alignment explanation
Indices: 41639--41992 Score: 501
Period size: 120 Copynumber: 2.9 Consensus size: 119
41629 CATCTGATGG
*
41639 ATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAGAAAAAGTTCACA
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-A--AGAAGAAAAAGTTCACA
*
41704 ATGAGAAGAGCTTATTCAACCTTTCGCATAATTCTATCACAGAAGCAGATAGATTAGC
63 ATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAG-AGATAGATTAGC
*
41762 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATG
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATG
* *
41827 AGAAGAGCTTGTTCAACCTTTTGCATAATTCTATTACAGAAAGAGATAGATTAGC
66 AGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAG-AAGAGATAGATTAGC
* * * *
41882 ATCAACCTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAGGGGAAAGAAAAAGTTCAT
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA---G-AAGAAAAAGTTCAC
* * * * *
41947 AATGAAAAGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAG
62 AATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAG
41993 GAAATAGGTC
Statistics
Matches: 209, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
120 110 0.53
121 3 0.01
122 1 0.00
123 47 0.22
124 48 0.23
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (119 bp):
ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATG
AGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGAGATAGATTAGC
Found at i:42209 original size:3 final size:3
Alignment explanation
Indices: 42201--42257 Score: 78
Period size: 3 Copynumber: 18.3 Consensus size: 3
42191 ATTTTAAAAT
*
42201 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TATA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA
*
42248 TTA ATA TTA T
1 TTA TTA TTA T
42258 AAAACCCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:43479 original size:15 final size:14
Alignment explanation
Indices: 43459--43518 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
43449 ATCCATTAGT
43459 TTTTAATATTATTA
1 TTTTAATATTATTA
* *
43473 CTTTTAATTTTTTTAA
1 -TTTTAATATTATT-A
*
43489 TTTTAATTATTGTTA
1 TTTTAA-TATTATTA
*
43504 TTTT-ATTTTATTA
1 TTTTAATATTATTA
43517 TT
1 TT
43519 ACGTTTGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
15 22 0.59
16 6 0.16
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTAATATTATTA
Found at i:43593 original size:14 final size:15
Alignment explanation
Indices: 43576--43608 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
43566 TATTATTAAG
43576 TTATATAA-ATATAT
1 TTATATAATATATAT
*
43590 TTATATAATATTTAT
1 TTATATAATATATAT
43605 TTAT
1 TTAT
43609 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:43966 original size:137 final size:135
Alignment explanation
Indices: 43686--43938 Score: 305
Period size: 137 Copynumber: 1.9 Consensus size: 135
43676 AAATAAACAT
* * * *
43686 ATTTTGATATGTATTTATTATTTAATATCTAAGAAAAGAGCTGTCTTAAAATACCTAGAAGTCCT
1 ATTTTAATATGTATTTATTATTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTCCT
* * * * *
43751 TTTCTGATATTCTTAAATAAATAAATGTCCTACTTTTATAAATTGTATATATTAATCTATTTTTA
66 TTTCTGATATTCTTAAATAAATAAATATCCTACTTTTATAAATTATAAATATTAATCTAATTATA
43816 GATAA
131 GATAA
* * * *
43821 ATGTTTTAATATTTATTTATTTTTTAATATCAAAGGAAGGAACTGTCTTAAAACACCTAGAAG-C
1 A--TTTTAATATGTATTTATTATTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTC
*
43885 TCTTTTCTGATATT-TCTAAATAAATAAATATCTTA-TTTATATAAATTAATAAAT
64 -CTTTTCTGATATTCT-TAAATAAATAAATATCCTACTTT-TATAAATT-ATAAAT
43939 TTACTTAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
135 1 0.01
136 5 0.05
137 90 0.90
138 4 0.04
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.44
Consensus pattern (135 bp):
ATTTTAATATGTATTTATTATTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTCCT
TTTCTGATATTCTTAAATAAATAAATATCCTACTTTTATAAATTATAAATATTAATCTAATTATA
GATAA
Found at i:49712 original size:16 final size:16
Alignment explanation
Indices: 49693--49731 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
49683 AAGCAGCCCA
49693 AACCGAAGTCAACCCG
1 AACCGAAGTCAACCCG
*
49709 AACCTAAGTCAACCCG
1 AACCGAAGTCAACCCG
*
49725 AATCGAA
1 AACCGAA
49732 AGCAATCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.33, G:0.15, T:0.10
Consensus pattern (16 bp):
AACCGAAGTCAACCCG
Found at i:50484 original size:2 final size:2
Alignment explanation
Indices: 50479--50504 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50469 AATTAAATTA
50479 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
50505 TATGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53270 original size:2 final size:2
Alignment explanation
Indices: 53265--53294 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53255 AAAAAGGAAA
53265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53295 CAAGTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53734 original size:2 final size:2
Alignment explanation
Indices: 53727--53765 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
53717 TATTAAAGAA
53727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53766 ATAATAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53846 original size:18 final size:17
Alignment explanation
Indices: 53823--53865 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
53813 ATATATACAT
53823 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
53841 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
53858 ATAA-AATA
1 ATAATAATA
53866 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:53866 original size:58 final size:57
Alignment explanation
Indices: 53745--53866 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 57
53735 ATATATATAT
* * *
53745 ATATATATATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTA
1 ATATATATATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATAA--TA
53805 ATATATATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-A
1 ATATATATATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAATA
53863 ATAT
1 ATAT
53867 CCATATAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
58 5 0.09
60 27 0.48
61 9 0.16
62 4 0.07
63 11 0.20
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (57 bp):
ATATATATATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATAATA
Found at i:54292 original size:37 final size:36
Alignment explanation
Indices: 54244--54345 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
54234 ATAGTAGAAC
*
54244 TCTATCATATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
54281 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
54315 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
54346 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 33 0.55
37 27 0.45
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:55183 original size:105 final size:105
Alignment explanation
Indices: 54876--55602 Score: 1122
Period size: 105 Copynumber: 7.0 Consensus size: 105
54866 CATTGTTCCA
* * * ** * * *
54876 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * * *
54941 CAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
54982 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
55042 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
55082 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
55147 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
55187 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
55252 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
55292 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
55357 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
55397 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
55462 ATCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
55502 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
55567 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
55603 CCTCGAGTGC
Statistics
Matches: 577, Mismatches: 38, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
100 83 0.14
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.01
105 407 0.71
106 75 0.13
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:56335 original size:68 final size:65
Alignment explanation
Indices: 56245--56402 Score: 217
Period size: 68 Copynumber: 2.4 Consensus size: 65
56235 AAGATATCTG
* * **
56245 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
56310 TT
64 TT
* * *
56312 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
56377 T
65 T
*
56378 TTGTTTCAAGAGAAACTATCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
56403 ATAGACGAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 22 0.27
66 3 0.04
67 24 0.30
68 32 0.40
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:56378 original size:67 final size:67
Alignment explanation
Indices: 56232--56428 Score: 220
Period size: 65 Copynumber: 2.9 Consensus size: 67
56222 GGAAACGATC
* * * *
56232 TCAAAGATATCTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAA
56297 TAAAT
63 TAAAT
** * *
56302 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAA
56367 AT
66 AT
* ** * *
56369 TCAAAGA-TTT-TGTTTCAAGAGAAACTATCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTGTTTTAAGGGAAA
56429 CTGTCTCAAG
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
65 38 0.35
66 7 0.06
67 23 0.21
68 32 0.29
69 3 0.03
70 6 0.06
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:56425 original size:36 final size:35
Alignment explanation
Indices: 56378--56658 Score: 281
Period size: 36 Copynumber: 8.0 Consensus size: 35
56368 TTCAAAGATT
* *
56378 TTGTTTCAAGAGAAACTATCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
56414 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
56449 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGATAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
56487 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
56516 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
56551 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
56588 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
56623 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
56659 CTCTTCTAGT
Statistics
Matches: 204, Mismatches: 25, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 135 0.66
37 33 0.16
38 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:56489 original size:138 final size:137
Alignment explanation
Indices: 56326--56638 Score: 412
Period size: 138 Copynumber: 2.3 Consensus size: 137
56316 TTTCAAGAGT
* ** * *
56326 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGAGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGAGA
* *
56391 AACTATCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTATCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
56455 TCCAAAAGA
129 TCCAAAAGA
* * * * *
56464 AACTGTCTCAAGGGAGACGATATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGAGA
* * * * * *
56529 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTATCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
56594 CAAGAGA
131 CAAAAGA
*
56601 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAA-AGAAA
56639 CTGTCTCAAG
Statistics
Matches: 151, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
137 44 0.29
138 107 0.71
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGAGA
AACTATCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:56537 original size:102 final size:102
Alignment explanation
Indices: 56414--56660 Score: 293
Period size: 101 Copynumber: 2.4 Consensus size: 102
56404 TAGACGAAAA
*
56414 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGA
*
56479 GACGATATTTGTTTCAA-AGAAAACATATTCAAATATT
65 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * ** *
56516 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
* * *
56581 ACGAAATTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAAT
66 ACGAAATTTGTTTCAAGAGAAAACATAT-TC-----A-A-ATATT
56624 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
56661 CTTCTAGTGA
Statistics
Matches: 123, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
100 2 0.02
101 42 0.34
102 39 0.32
106 1 0.01
107 1 0.01
108 38 0.31
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:56680 original size:35 final size:36
Alignment explanation
Indices: 56520--56692 Score: 188
Period size: 36 Copynumber: 4.8 Consensus size: 36
56510 AATATTTTGT
* * **
56520 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
56556 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATCTGC
* *
56592 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATCTGC
56628 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATCTGC
* * * *
56662 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAA
56693 TCTTGTTTTA
Statistics
Matches: 124, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
34 6 0.05
35 21 0.17
36 97 0.78
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.23
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:56700 original size:71 final size:72
Alignment explanation
Indices: 56520--56710 Score: 226
Period size: 72 Copynumber: 2.7 Consensus size: 72
56510 AATATTTTGT
* * * *
56520 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGA
** *
56585 AATTTGT
66 AAACTGC
56592 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGA
56656 AAACT-C
66 AAACTGC
* * * * * *
56662 TTCTAGTGAAAACGGTCTCAAGCGAGAC-AAATCTTGTTTTAAGAAAAAC
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAAT-TTGTTTCAAGAGAAAC
56711 AATCATGAGT
Statistics
Matches: 104, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
70 10 0.10
71 35 0.34
72 59 0.57
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (72 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGA
AAACTGC
Found at i:57163 original size:18 final size:18
Alignment explanation
Indices: 57136--57171 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57126 TGTTGAATCC
* *
57136 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
57154 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
57172 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:57611 original size:22 final size:22
Alignment explanation
Indices: 57585--57639 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
57575 TTGTGTTTGG
*
57585 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
57607 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
57629 TCAAAGGTTTG
1 TCAAAGGTTTG
57640 ATGGGACAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:58333 original size:23 final size:22
Alignment explanation
Indices: 58262--58361 Score: 73
Period size: 23 Copynumber: 4.4 Consensus size: 22
58252 GCATGTGCTT
* *
58262 TTTGTTCCTCTTTCTTTTTTATTC
1 TTTGTT-CTTTTTCTCTTTT-TTC
58286 -TTGTT-TTTTTC-CTTTTTTCC
1 TTTGTTCTTTTTCTCTTTTTT-C
58306 TTTTGTTCTTGTTTCTCTTTTTTC
1 -TTTGTTCTT-TTTCTCTTTTTTC
*
58330 TTTGTT-TTTTTTTGCTTCTTTTC
1 TTTGTTCTTTTTCT-CTT-TTTTC
*
58353 TTTTTTCTT
1 TTTGTTCTT
58362 CTTGATTGGA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
19 2 0.03
20 5 0.08
21 9 0.14
22 10 0.16
23 23 0.37
24 7 0.11
25 7 0.11
ACGTcount: A:0.01, C:0.17, G:0.06, T:0.76
Consensus pattern (22 bp):
TTTGTTCTTTTTCTCTTTTTTC
Found at i:58360 original size:7 final size:7
Alignment explanation
Indices: 58272--58361 Score: 67
Period size: 7 Copynumber: 11.9 Consensus size: 7
58262 TTTGTTCCTC
58272 TTTCTTT
1 TTTCTTT
*
58279 TTTATTCT
1 TTTCTT-T
58287 TGTT-TTT
1 T-TTCTTT
*
58294 TTCCTTT
1 TTTCTTT
58301 TTTCCTTT
1 TTT-CTTT
58309 TGTTCTTGT
1 T-TTCTT-T
58318 TTCTCTTT
1 TT-TCTTT
58326 TTTCTTT
1 TTTCTTT
58333 GTTT-TTT
1 -TTTCTTT
58340 TTTGCTTCT
1 TTT-CTT-T
58349 TTTCTTT
1 TTTCTTT
58356 TTTCTT
1 TTTCTT
58362 CTTGATTGGA
Statistics
Matches: 69, Mismatches: 3, Indels: 22
0.73 0.03 0.23
Matches are distributed among these distances:
6 4 0.06
7 27 0.39
8 24 0.35
9 14 0.20
ACGTcount: A:0.01, C:0.16, G:0.06, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:59486 original size:8 final size:8
Alignment explanation
Indices: 59470--59508 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
59460 AATGTAGATG
59470 AAAATGCA
1 AAAATGCA
*
59478 AAAAGGCA
1 AAAATGCA
59486 AAAATGC-
1 AAAATGCA
59493 AAAATGCA
1 AAAATGCA
*
59501 AGAATGCA
1 AAAATGCA
59509 TGAAATATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:59496 original size:15 final size:15
Alignment explanation
Indices: 59470--59508 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
59460 AATGTAGATG
59470 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
59486 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
59501 AGAATGCA
1 AAAATGCA
59509 TGAAATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:62426 original size:14 final size:14
Alignment explanation
Indices: 62409--62435 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62399 TATATTACAT
62409 AAATAAAAATAATC
1 AAATAAAAATAATC
62423 AAATAAAAATAAT
1 AAATAAAAATAAT
62436 TAAGAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAAAATAATC
Found at i:62616 original size:49 final size:50
Alignment explanation
Indices: 62503--62630 Score: 111
Period size: 49 Copynumber: 2.5 Consensus size: 50
62493 ATATATGACT
* * **
62503 AAATAAAGATAATTACA-ATATATATATAGTAATATTAGACTTATAAGTAAAA
1 AAATAAAGA-AA-TA-ATATATATATATAATAATAATAGAAATATAAGTAAAA
* *
62555 TATTAAAGAAAT-ATATATATATATAATAATAATA-AAATAT-AGTAAAA
1 AAATAAAGAAATAATATATATATATAATAATAATAGAAATATAAGTAAAA
*
62602 AAATAAATGAAAATAATTTAATATATATA
1 AAATAAA-G-AAATAATAT-ATATATATA
62631 TATATACATA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
47 12 0.19
48 6 0.10
49 22 0.35
50 4 0.06
51 11 0.18
52 7 0.11
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (50 bp):
AAATAAAGAAATAATATATATATATAATAATAATAGAAATATAAGTAAAA
Found at i:62663 original size:18 final size:17
Alignment explanation
Indices: 62640--62682 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
62630 ATATATACAT
*
62640 ATAATAATAATACCATGA
1 ATAATAATAATA-AATGA
*
62658 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
62675 ATAA-AATA
1 ATAATAATA
62683 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:63122 original size:37 final size:36
Alignment explanation
Indices: 63074--63175 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
63064 ATAGTAGAAC
*
63074 TCTATCATATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
63111 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
63145 TCTATCCTATTTTTAAGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
63176 TAGGACACAC
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 32 0.54
37 27 0.46
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:68506 original size:21 final size:21
Alignment explanation
Indices: 68482--68548 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
68472 TCATCGCCAC
68482 CTCCACCACCACAAAATTCCT
1 CTCCACCACCACAAAATTCCT
* **
68503 CTCCACC-TC-C-ATTTTCAC-
1 CTCCACCACCACAAAATTC-CT
68521 CTCCACCACCACAAAATTCCT
1 CTCCACCACCACAAAATTCCT
*
68542 CGCCACC
1 CTCCACC
68549 TCCATCTTCG
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
18 11 0.32
19 3 0.09
20 3 0.09
21 17 0.50
ACGTcount: A:0.27, C:0.51, G:0.01, T:0.21
Consensus pattern (21 bp):
CTCCACCACCACAAAATTCCT
Found at i:68510 original size:27 final size:27
Alignment explanation
Indices: 68452--68513 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
68442 CCCAGGCCAT
* *
68452 CACCACCACCACCACGAAATTCATCGC
1 CACCTCCACCACCACAAAATTCATCGC
* *
68479 CACCTCCACCACCACAAAATTCCTCTC
1 CACCTCCACCACCACAAAATTCATCGC
68506 CACCTCCA
1 CACCTCCA
68514 TTTTCACCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.52, G:0.03, T:0.15
Consensus pattern (27 bp):
CACCTCCACCACCACAAAATTCATCGC
Found at i:68523 original size:39 final size:39
Alignment explanation
Indices: 68479--68567 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
68469 AATTCATCGC
* *
68479 CACCTCCACCACCACAAAATTCCTCTCCACCTCCATTTT
1 CACCTCCACCACCACAAAATTCCTCGCCACCTCCATCTT
68518 CACCTCCACCACCACAAAATTCCTCGCCACCTCCATCTT
1 CACCTCCACCACCACAAAATTCCTCGCCACCTCCATCTT
*
68557 CGCCTCCACCA
1 CACCTCCACCA
68568 GCACCAACTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.25, C:0.52, G:0.02, T:0.21
Consensus pattern (39 bp):
CACCTCCACCACCACAAAATTCCTCGCCACCTCCATCTT
Found at i:68719 original size:36 final size:36
Alignment explanation
Indices: 68679--68789 Score: 213
Period size: 36 Copynumber: 3.1 Consensus size: 36
68669 TTCAACTCCG
*
68679 CCATCACCACCAGCAGTACCACCAAATTCGCCACCA
1 CCATCTCCACCAGCAGTACCACCAAATTCGCCACCA
68715 CCATCTCCACCAGCAGTACCACCAAATTCGCCACCA
1 CCATCTCCACCAGCAGTACCACCAAATTCGCCACCA
68751 CCATCTCCACCAGCAGTACCACCAAATTCGCCACCA
1 CCATCTCCACCAGCAGTACCACCAAATTCGCCACCA
68787 CCA
1 CCA
68790 CCACGAACTC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.32, C:0.48, G:0.08, T:0.13
Consensus pattern (36 bp):
CCATCTCCACCAGCAGTACCACCAAATTCGCCACCA
Found at i:72646 original size:46 final size:46
Alignment explanation
Indices: 72561--72687 Score: 190
Period size: 46 Copynumber: 2.8 Consensus size: 46
72551 TTATAATTTA
*
72561 TTTTTTT-TAATATTTG-TA-T-AAGTGTTTAACTTTTTGCCAATAT
1 TTTTTTTCTAATATTTGTTATTAAAG-GTTTAATTTTTTGCCAATAT
72604 TTTTTTTCTAATATTTGTTATTAAAGGTTTAATTTTTTGCCAATAT
1 TTTTTTTCTAATATTTGTTATTAAAGGTTTAATTTTTTGCCAATAT
* *
72650 TTTTTTTCTAATATTTGTTATTAAAAGTTCAATTTTTT
1 TTTTTTTCTAATATTTGTTATTAAAGGTTTAATTTTTT
72688 CAATACTTAA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
43 7 0.09
44 9 0.12
45 2 0.03
46 56 0.73
47 3 0.04
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (46 bp):
TTTTTTTCTAATATTTGTTATTAAAGGTTTAATTTTTTGCCAATAT
Found at i:76723 original size:28 final size:29
Alignment explanation
Indices: 76682--76790 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
76672 CTAGTGGAAA
76682 TACCTAATTTTCCAATATTCAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
76711 TACCT-ATTTTCCAATATTCAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
76739 TACCTAATTTTCCAATATTCAATGAGCATT
1 TACCTAATTTTCCAATATTCAATGAGCA-T
76769 TACCTAATTTTCCAATA-TCAAT
1 TACCTAATTTTCCAATATTCAAT
76791 ATTCAATGAG
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
28 28 0.36
29 32 0.41
30 18 0.23
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (29 bp):
TACCTAATTTTCCAATATTCAATGAGCAT
Found at i:76749 original size:57 final size:58
Alignment explanation
Indices: 76682--76790 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 58
76672 CTAGTGGAAA
76682 TACCTAATTTTCCAATATTCAATGAGCA-TTACCT-ATTTTCCAATATTCAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCATTTACCTAATTTTCCAATA-TCAATGAGCAT
76739 TACCTAATTTTCCAATATTCAATGAGCATTTACCTAATTTTCCAATATCAAT
1 TACCTAATTTTCCAATATTCAATGAGCATTTACCTAATTTTCCAATATCAAT
76791 ATTCAATGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
57 28 0.56
58 11 0.22
59 11 0.22
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (58 bp):
TACCTAATTTTCCAATATTCAATGAGCATTTACCTAATTTTCCAATATCAATGAGCAT
Found at i:77415 original size:28 final size:29
Alignment explanation
Indices: 77360--77419 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 29
77350 AATTCGGTGA
77360 ATTCAATATGTCATTCTCACCAGGAACTCCC
1 ATTCAATATGTC--TCTCACCAGGAACTCCC
*
77391 ATTCAATATGTC-CTCACTAGGAACTCCC
1 ATTCAATATGTCTCTCACCAGGAACTCCC
77419 A
1 A
77420 AACTCTTGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 16 0.57
31 12 0.43
ACGTcount: A:0.30, C:0.32, G:0.10, T:0.28
Consensus pattern (29 bp):
ATTCAATATGTCTCTCACCAGGAACTCCC
Found at i:82164 original size:57 final size:58
Alignment explanation
Indices: 82097--82205 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 58
82087 CTAATGGAAA
*
82097 TACCTAATTTTCCAATATTCAAAGAGGA-TTACCT-ATTTTCCAATATTCAATGACCAT
1 TACCTAATTTTCCAATATTCAAAGAGCATTTACCTAATTTTCCAATA-TCAATGACCAT
*
82154 TACCTAATTTTCCAATATTCAATGAGCATTTACCTAATTTTCCAATATCAAT
1 TACCTAATTTTCCAATATTCAAAGAGCATTTACCTAATTTTCCAATATCAAT
82206 ATTCAATGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
57 26 0.54
58 11 0.23
59 11 0.23
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.39
Consensus pattern (58 bp):
TACCTAATTTTCCAATATTCAAAGAGCATTTACCTAATTTTCCAATATCAATGACCAT
Found at i:82173 original size:29 final size:29
Alignment explanation
Indices: 82097--82205 Score: 168
Period size: 29 Copynumber: 3.8 Consensus size: 29
82087 CTAATGGAAA
* *
82097 TACCTAATTTTCCAATATTCAAAGAGGAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
*
82126 TACCT-ATTTTCCAATATTCAATGACCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
82154 TACCTAATTTTCCAATATTCAATGAGCATT
1 TACCTAATTTTCCAATATTCAATGAGCA-T
82184 TACCTAATTTTCCAATA-TCAAT
1 TACCTAATTTTCCAATATTCAAT
82206 ATTCAATGAG
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
28 25 0.34
29 31 0.42
30 18 0.24
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.39
Consensus pattern (29 bp):
TACCTAATTTTCCAATATTCAATGAGCAT
Found at i:82853 original size:6 final size:6
Alignment explanation
Indices: 82844--82868 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
82834 TACTAATGCA
82844 TATAAT TATAAT TATAAT TATAAT T
1 TATAAT TATAAT TATAAT TATAAT T
82869 TTTATTTGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATAAT
Found at i:82899 original size:19 final size:18
Alignment explanation
Indices: 82844--82905 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
82834 TACTAATGCA
* * *
82844 TATAATTATAATTATAAT
1 TATAATTTTTATTATATT
*
82862 TATAATTTTTATTTGTATT
1 TATAATTTTTA-TTATATT
82881 TATATATTTTTATTATATT
1 TATA-ATTTTTATTATATT
82900 TA-AATT
1 TATAATT
82906 GATAAAATCC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.08
18 10 0.27
19 17 0.46
20 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TATAATTTTTATTATATT
Found at i:83911 original size:16 final size:16
Alignment explanation
Indices: 83890--83923 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
83880 TTACTATTCA
*
83890 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
83906 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
83922 CG
1 CG
83924 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:85746 original size:16 final size:13
Alignment explanation
Indices: 85713--85747 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
85703 CCCATAACAC
85713 CGCAGCAGAATGG
1 CGCAGCAGAATGG
85726 CGCAGCAGAATGG
1 CGCAGCAGAATGG
*
85739 CGTAGCAGA
1 CGCAGCAGA
85748 GTGCATGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.37, T:0.09
Consensus pattern (13 bp):
CGCAGCAGAATGG
Found at i:88003 original size:35 final size:36
Alignment explanation
Indices: 87957--88044 Score: 108
Period size: 36 Copynumber: 2.5 Consensus size: 36
87947 TTGTTAAAAG
*
87957 TTTCAAAGTTTGG-CAA-CCAACTTTGAAAAATGTTT
1 TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATG-TT
****
87992 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGTT
1 TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATGTT
88028 TTTCAAAGTTTGGTAAA
1 TTTCAAAGTTTGGTAAA
88045 ATTTTGGTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 13 0.28
36 21 0.46
37 12 0.26
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATGTT
Found at i:89208 original size:7 final size:7
Alignment explanation
Indices: 89196--89229 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
89186 TTCTTGGCAA
89196 GAAGAAG
1 GAAGAAG
89203 GAAGAAG
1 GAAGAAG
89210 GAAGAAG
1 GAAGAAG
*
89217 GAATAA-
1 GAAGAAG
89223 GAAGAAG
1 GAAGAAG
89230 AAAAAGCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (7 bp):
GAAGAAG
Found at i:90420 original size:10 final size:10
Alignment explanation
Indices: 90405--90436 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
90395 ACAAGTAGAA
90405 AAGCCCAAGC
1 AAGCCCAAGC
90415 AAGCCCAAGC
1 AAGCCCAAGC
90425 AAGCCCAAGC
1 AAGCCCAAGC
90435 AA
1 AA
90437 TGTTGACAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.44, C:0.38, G:0.19, T:0.00
Consensus pattern (10 bp):
AAGCCCAAGC
Found at i:90786 original size:18 final size:18
Alignment explanation
Indices: 90765--90799 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
90755 ATTAATAATT
90765 ATAAAATTAAAAATATTA
1 ATAAAATTAAAAATATTA
90783 ATAAAATTAAAAATATT
1 ATAAAATTAAAAATATT
90800 TAGTTCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAATTAAAAATATTA
Found at i:91048 original size:2 final size:2
Alignment explanation
Indices: 91041--91068 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
91031 TGTTTGTATG
91041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91069 ATTGTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:94170 original size:20 final size:20
Alignment explanation
Indices: 94145--94219 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
94135 TGCAGCCTTC
*
94145 ATGCATGGATGCACAGCAGG
1 ATGCATCGATGCACAGCAGG
* **
94165 ATGCATCAATGCACAGCCTTG
1 ATGCATCGATGCACAG-CAGG
*
94186 ATGCATCGATGCACAGAAGG
1 ATGCATCGATGCACAGCAGG
94206 ATGCATCGATGCAC
1 ATGCATCGATGCAC
94220 TAATTGCATT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (20 bp):
ATGCATCGATGCACAGCAGG
Found at i:94197 original size:41 final size:41
Alignment explanation
Indices: 94137--94219 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
94127 CTAGCCGTTG
* *
94137 CAGCCTTCATGCATGGATGCACAGCAGGATGCATCAATGCA
1 CAGCCTTCATGCATCGATGCACAGAAGGATGCATCAATGCA
* *
94178 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1 CAGCCTTCATGCATCGATGCACAGAAGGATGCATCAATGCA
94219 C
1 C
94220 TAATTGCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (41 bp):
CAGCCTTCATGCATCGATGCACAGAAGGATGCATCAATGCA
Found at i:94309 original size:21 final size:20
Alignment explanation
Indices: 94240--94338 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 20
94230 CGGTGTTTGA
* *
94240 GTGCATGGATGCACTGTATG
1 GTGCATGGATGCACTGCAGG
*
94260 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
94282 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
94302 GATGCATGAATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
94324 GTGCATGGATGCACT
1 GTGCATGGATGCACT
94339 TTGACACCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.22
21 29 0.43
22 17 0.25
23 3 0.04
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:94439 original size:29 final size:29
Alignment explanation
Indices: 94418--94475 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
94408 AAACTTTGAA
94418 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
94447 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
94476 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:94465 original size:30 final size:30
Alignment explanation
Indices: 94418--94477 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
94408 AAACTTTGAA
94418 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
94447 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
94478 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:97049 original size:33 final size:33
Alignment explanation
Indices: 97002--97088 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
96992 ACAAAGTTTA
*
97002 CGAT-AATTGAAATACTT-AAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAT-CTTCCAAGTT
*
97034 TGATAAATTCAAATACTTAAAATCTTCCAAGTT
1 CGATAAATTCAAATACTTAAAATCTTCCAAGTT
97067 CGATAAATTCAAATACTTAAAA
1 CGATAAATTCAAATACTTAAAA
97089 ACGATCACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
32 3 0.06
33 43 0.86
34 4 0.08
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAATCTTCCAAGTT
Found at i:98330 original size:21 final size:21
Alignment explanation
Indices: 98278--98340 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
98268 CTAGCCATTG
*
98278 CAGCCTTCG-TGCATGGATGCA
1 CAGCCTT-GATGCATCGATGCA
* *
98299 CA-ACATGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
98319 CAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
98340 C
1 C
98341 TAATTGCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.43
21 19 0.54
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (21 bp):
CAGCCTTGATGCATCGATGCA
Found at i:98410 original size:21 final size:20
Alignment explanation
Indices: 98361--98439 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 20
98351 CGGTGTTTGA
98361 GTGCATGGATGCACT-AGTGCAG
1 GTGCATGGATGCACTGA-TG--G
98383 GTGCATGGATGCACTGATGG
1 GTGCATGGATGCACTGATGG
*
98403 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTG-ATGG
98425 GTGCATGGATGCACT
1 GTGCATGGATGCACT
98440 TTGACACCCT
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
20 2 0.04
21 29 0.55
22 21 0.40
23 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGATGG
Found at i:98540 original size:29 final size:29
Alignment explanation
Indices: 98519--98576 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
98509 AAACTTTGAA
98519 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
98548 TAAATTCAATTCAAGTCCAAAAATCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
98577 TGCCTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:98566 original size:30 final size:30
Alignment explanation
Indices: 98519--98578 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
98509 AAACTTTGAA
98519 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
98548 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATT-AAGTCCAAAAATCATTTTG
98579 CCTTAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:100217 original size:17 final size:18
Alignment explanation
Indices: 100191--100242 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 18
100181 AAATCATTTA
100191 AATTAGAATTAAATAATAT
1 AATTA-AATTAAATAATAT
*
100210 AA-TAAATTAAATATTAT
1 AATTAAATTAAATAATAT
100227 AATTAAATTCAAATAA
1 AATTAAATT-AAATAA
100243 CAATTCGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 14 0.48
18 8 0.28
19 7 0.24
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AATTAAATTAAATAATAT
Found at i:101021 original size:16 final size:16
Alignment explanation
Indices: 101000--101032 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
100990 TAATAAATAA
101000 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
101016 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
101032 A
1 A
101033 AATTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:103116 original size:16 final size:18
Alignment explanation
Indices: 103095--103139 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
103085 AATATTGCCA
103095 GTAATCTTATT-CCA-TG
1 GTAATCTTATTCCCACTG
103111 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
103131 GTAATCTTA
1 GTAATCTTA
103140 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 3 0.12
20 10 0.40
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Done.