Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001711.1 Hibiscus syriacus cultivar Beakdansim tig00003454_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: 4148933
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 13
Found at i:7082 original size:15 final size:16
Alignment explanation
Indices: 7053--7086 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
7043 TTTTTTTGGA
7053 TTTTTTTTGGCTTTTT
1 TTTTTTTTGGCTTTTT
*
7069 TTTTTTTTTG-TTTTT
1 TTTTTTTTGGCTTTTT
7084 TTT
1 TTT
7087 AAAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (16 bp):
TTTTTTTTGGCTTTTT
Found at i:7086 original size:11 final size:11
Alignment explanation
Indices: 7035--7072 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
7025 TTTTTTGAAA
7035 TTTTGGTTTTT
1 TTTTGGTTTTT
*
7046 TTTTGGATTTT
1 TTTTGGTTTTT
7057 TTTTGGCTTTTT
1 TTTTGG-TTTTT
7069 TTTT
1 TTTT
7073 TTTTTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.79
Consensus pattern (11 bp):
TTTTGGTTTTT
Found at i:11943 original size:26 final size:26
Alignment explanation
Indices: 11907--11958 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
11897 GTTACTAGTT
*
11907 ATGTAGCTAACATATAACTTAGCAAG
1 ATGTAGCTAACAGATAACTTAGCAAG
11933 ATGTAGCTAACAGATAACTTAGCAAG
1 ATGTAGCTAACAGATAACTTAGCAAG
11959 TACACATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (26 bp):
ATGTAGCTAACAGATAACTTAGCAAG
Found at i:23567 original size:19 final size:20
Alignment explanation
Indices: 23529--23571 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
23519 GAAACCCCTT
*
23529 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
23549 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
23568 TGAA
1 TGAA
23572 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:25830 original size:23 final size:24
Alignment explanation
Indices: 25802--25855 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
25792 AAAATCAGCA
25802 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
25825 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
25849 AAGAAAA
1 AAGAAAA
25856 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:25860 original size:24 final size:23
Alignment explanation
Indices: 25802--25861 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
25792 AAAATCAGCA
25802 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
25825 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
25849 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
25862 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:32450 original size:33 final size:33
Alignment explanation
Indices: 32371--32474 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
32361 ATACAATCTG
* *
32371 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
32407 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
32440 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
32473 TC
1 TC
32475 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:38125 original size:33 final size:33
Alignment explanation
Indices: 38046--38149 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
38036 ATACAATCTG
* *
38046 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
38082 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
38115 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
38148 TC
1 TC
38150 ATTCATAAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:43802 original size:33 final size:33
Alignment explanation
Indices: 43723--43826 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
43713 ATACAATCTG
* *
43723 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
43759 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
43792 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
43825 TC
1 TC
43827 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:45360 original size:24 final size:24
Alignment explanation
Indices: 45309--45360 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
45299 TCTCGGCACT
* * *
45309 TCAAATGACGTTTCTCTTGGAACT
1 TCAAATGACATTTCTCTTGAAACA
45333 TCAAATGACATTATCT-TTGAAACA
1 TCAAATGACATT-TCTCTTGAAACA
45357 TCAA
1 TCAA
45361 GAGATATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (24 bp):
TCAAATGACATTTCTCTTGAAACA
Found at i:48201 original size:12 final size:12
Alignment explanation
Indices: 48184--48216 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
48174 AATACAAAAG
48184 GAAGTGCAATGT
1 GAAGTGCAATGT
48196 GAAGTGCAATGT
1 GAAGTGCAATGT
48208 GAAGTGCAA
1 GAAGTGCAA
48217 AGTCAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.33, T:0.21
Consensus pattern (12 bp):
GAAGTGCAATGT
Found at i:51124 original size:24 final size:24
Alignment explanation
Indices: 51097--51143 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
51087 CCTCAATAAT
*
51097 CACAACTTGTGGCACTTCAAGTGA
1 CACAACTTGTGGAACTTCAAGTGA
* * *
51121 CACATCTTTTTGAACTTCAAGTG
1 CACAACTTGTGGAACTTCAAGTG
51144 GCATAACTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (24 bp):
CACAACTTGTGGAACTTCAAGTGA
Found at i:52591 original size:15 final size:15
Alignment explanation
Indices: 52558--52595 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
52548 CTCTTTTCAT
52558 TTTCTTTTGATTTTC
1 TTTCTTTTGATTTTC
**
52573 -TTCTTTTTCTTTTC
1 TTTCTTTTGATTTTC
52587 TTTCTTTTG
1 TTTCTTTTG
52596 TACTCCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTCTTTTGATTTTC
Found at i:52631 original size:6 final size:6
Alignment explanation
Indices: 52620--52661 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
52610 TGTAGGAGTC
*
52620 TTTTCT TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT CTTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT -TTTT
52662 GTTGTAGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 22 0.69
7 10 0.31
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:52640 original size:12 final size:12
Alignment explanation
Indices: 52620--52661 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
52610 TGTAGGAGTC
52620 TTTTCTTTTTCT
1 TTTTCTTTTTCT
*
52632 TTTTGTTTTTCT
1 TTTTCTTTTTCT
52644 TCTTTCTTTTTCT
1 T-TTTCTTTTTCT
52657 CTTTT
1 -TTTT
52662 GTTGTAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 12 0.46
13 13 0.50
14 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:53471 original size:19 final size:20
Alignment explanation
Indices: 53433--53475 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
53423 GAAACCCCTT
*
53433 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
53453 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
53472 TGAA
1 TGAA
53476 GCTAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:56118 original size:19 final size:21
Alignment explanation
Indices: 56094--56145 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
56084 CAACCAAGAG
*
56094 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
56113 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
56134 CATGTATTTTCA
1 CATGTATTTTCA
56146 AAGAAGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:56879 original size:21 final size:20
Alignment explanation
Indices: 56853--56904 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
56843 GGAGTGCAAA
56853 AAGAAAGAAAA-AAGACAAAAG
1 AAGAAAGAAAATAAG--AAAAG
*
56874 AAGAAA-AAAATCAGAAAAG
1 AAGAAAGAAAATAAGAAAAG
56893 AAGAAAAGAAAA
1 AAG-AAAGAAAA
56905 GAAAAACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 8 0.30
20 7 0.26
21 12 0.44
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (20 bp):
AAGAAAGAAAATAAGAAAAG
Found at i:56891 original size:26 final size:26
Alignment explanation
Indices: 56862--56915 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
56852 AAAGAAAGAA
56862 AAAAG-ACAAAAGAAGAA-AAAAATCAG
1 AAAAGAACAAAAGAA-AAGAAAAA-CAG
*
56888 AAAAGAAGAAAAGAAAAGAAAAACAG
1 AAAAGAACAAAAGAAAAGAAAAACAG
56914 AA
1 AA
56916 GTTCAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.02
Consensus pattern (26 bp):
AAAAGAACAAAAGAAAAGAAAAACAG
Found at i:56907 original size:18 final size:17
Alignment explanation
Indices: 56851--56909 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 17
56841 TTGGAGTGCA
* *
56851 AAAAGAAAGAAAAAAGAC
1 AAAAG-AAGAAAAAAAAG
56869 AAAAGAAGAAAAAAATCAG
1 AAAAGAAGAAAAAAA--AG
56888 AAAAGAAGAAAAGAAAAG
1 AAAAGAAGAAAA-AAAAG
56906 AAAA
1 AAAA
56910 ACAGAAGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 9 0.25
18 11 0.31
19 13 0.36
20 3 0.08
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAAAAAG
Found at i:60159 original size:19 final size:21
Alignment explanation
Indices: 60135--60186 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
60125 CGGCCAAGAG
*
60135 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
60154 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
60175 CATGTATTTTCA
1 CATGTATTTTCA
60187 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:62842 original size:11 final size:13
Alignment explanation
Indices: 62810--62839 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
62800 TGGCCAAATA
62810 TGAAAAGGTATGT
1 TGAAAAGGTATGT
62823 TGAAAAGGTATG-
1 TGAAAAGGTATGT
62835 TGAAA
1 TGAAA
62840 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:70464 original size:11 final size:13
Alignment explanation
Indices: 70432--70461 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
70422 TGGCCAAAGA
70432 TGAAAAGGTATGT
1 TGAAAAGGTATGT
70445 TGAAAAGGTATG-
1 TGAAAAGGTATGT
70457 TGAAA
1 TGAAA
70462 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:77431 original size:24 final size:24
Alignment explanation
Indices: 77404--77458 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
77394 CCAACTTTTC
77404 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
77427 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
*
77451 CTTCTTTT
1 TTTCTTTT
77459 CTGATTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 12 0.50
25 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:80832 original size:12 final size:12
Alignment explanation
Indices: 80815--80845 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
80805 TTTGCACTTC
80815 TCTTTTTGATTT
1 TCTTTTTGATTT
80827 TCTTTTTGATTT
1 TCTTTTTGATTT
80839 TCTTTTT
1 TCTTTTT
80846 TATTGAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.77
Consensus pattern (12 bp):
TCTTTTTGATTT
Found at i:83448 original size:24 final size:24
Alignment explanation
Indices: 83412--83479 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
83402 TTTTCTTTGC
*
83412 TTTTTC-TTCTTTTGAGTGTTGAA
1 TTTTTCTTTCTTTTGAGTGCTGAA
* *
83435 TTTTTCTTTATTTTGAGTGCTGGA
1 TTTTTCTTTCTTTTGAGTGCTGAA
83459 TTTTTCTTTCTTTTGAGTGCT
1 TTTTTCTTTCTTTTGAGTGCT
83480 TCACTTTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 6 0.15
24 34 0.85
ACGTcount: A:0.10, C:0.10, G:0.18, T:0.62
Consensus pattern (24 bp):
TTTTTCTTTCTTTTGAGTGCTGAA
Found at i:88511 original size:15 final size:15
Alignment explanation
Indices: 88493--88525 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
88483 TCTTCATTCC
88493 ATGGAACATCATCCT
1 ATGGAACATCATCCT
88508 ATGGAACATCATCCT
1 ATGGAACATCATCCT
88523 ATG
1 ATG
88526 TTTGCAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (15 bp):
ATGGAACATCATCCT
Found at i:91156 original size:19 final size:20
Alignment explanation
Indices: 91128--91167 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
91118 TAAAGTGAAT
91128 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
91148 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
91167 A
1 A
91168 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:91621 original size:19 final size:21
Alignment explanation
Indices: 91578--91629 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
91568 GAAACCCCTT
*
91578 TGAAAATATATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
91599 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
91618 TGAAGATACATG
1 TGAAAATACATG
91630 CTCTTGGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:92653 original size:20 final size:19
Alignment explanation
Indices: 92616--92654 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
92606 AAGTAAAGAT
**
92616 GTGAAAACATATGTTATGC
1 GTGAAAACATATAATATGC
92635 GTGAAAATCATATAATATGC
1 GTGAAAA-CATATAATATGC
92655 AAGTGAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
GTGAAAACATATAATATGC
Found at i:93639 original size:8 final size:8
Alignment explanation
Indices: 93626--93683 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
93616 TGAATTTCTT
93626 TTCTTTTC
1 TTCTTTTC
93634 TTCTTTTC
1 TTCTTTTC
93642 TTCTTTTC
1 TTCTTTTC
*
93650 TGATTTTTTC
1 T--TCTTTTC
93660 TTCTTTT-
1 TTCTTTTC
93667 TGTC-TTT-
1 T-TCTTTTC
93674 TTCTTTTC
1 TTCTTTTC
93682 TT
1 TT
93684 TTTGCACTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
6 2 0.05
7 8 0.19
8 26 0.60
10 7 0.16
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:93641 original size:18 final size:18
Alignment explanation
Indices: 93620--93685 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 18
93610 CTCTTTTGAA
93620 TTTCTTTTCTTTTCTTCT
1 TTTCTTTTCTTTTCTTCT
**
93638 TTTC--TTCTTTTCTGAT
1 TTTCTTTTCTTTTCTTCT
93654 TTT-TTCTTCTTTT-TGTCTT
1 TTTCTT-TTCTTTTCT-TC-T
93673 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
93686 TGCACTCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
16 13 0.34
17 1 0.03
18 11 0.29
19 11 0.29
20 2 0.05
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTCTTTTCTTTTCTTCT
Found at i:93649 original size:26 final size:27
Alignment explanation
Indices: 93620--93685 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 27
93610 CTCTTTTGAA
93620 TTTCTTTTCTTTTCTTCTTTTCT-TC-T
1 TTTCTTTTCTTTTCTTCTTTT-TGTCTT
*
93646 TTTCTGATT-TTTTCTTCTTTTTGTCTT
1 TTTCT-TTTCTTTTCTTCTTTTTGTCTT
93673 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
93686 TGCACTCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.03
26 21 0.62
27 12 0.35
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (27 bp):
TTTCTTTTCTTTTCTTCTTTTTGTCTT
Found at i:93674 original size:17 final size:18
Alignment explanation
Indices: 93637--93678 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
93627 TCTTTTCTTC
93637 TTTTCTTCTTTTCTGATT
1 TTTTCTTCTTTTCTGATT
93655 TTTTCTTCTTTT-TG-TCT
1 TTTTCTTCTTTTCTGAT-T
93672 TTTTCTT
1 TTTTCTT
93679 TTCTTTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 10 0.43
18 12 0.52
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTCTTCTTTTCTGATT
Found at i:93972 original size:17 final size:19
Alignment explanation
Indices: 93940--93984 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
93930 AAGAATAAGT
93940 GAAAT-AATA-AAGAT-AA
1 GAAATGAATAGAAGATAAA
93956 GAAATGAATAGAA-ATAAA
1 GAAATGAATAGAAGATAAA
93974 GAAATG-ATAGA
1 GAAATGAATAGA
93985 GATGGCTGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 11 0.42
18 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (19 bp):
GAAATGAATAGAAGATAAA
Found at i:95268 original size:15 final size:16
Alignment explanation
Indices: 95248--95290 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
95238 AGTTATCATC
95248 ATAATAACTATAGAT-
1 ATAATAACTATAGATA
* *
95263 ATAATAAATATAGTTA
1 ATAATAACTATAGATA
*
95279 AAAATAACTATA
1 ATAATAACTATA
95291 TTAAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATA
Found at i:111857 original size:10 final size:10
Alignment explanation
Indices: 111842--111867 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
111832 CCCCAACTTC
111842 TTTCTTTTAT
1 TTTCTTTTAT
111852 TTTCTTTTAT
1 TTTCTTTTAT
111862 TTTCTT
1 TTTCTT
111868 CTTTTGAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTTAT
Found at i:112820 original size:36 final size:36
Alignment explanation
Indices: 112745--112846 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
112735 TTATAAGTTG
* *
112745 GTGATAATATAGGCGTGAT-ATGGTGATGGAATATG
1 GTGATGATATAGGCGTGATAATGGTGATGGAATATC
*
112780 GTGATGATATAGGCGTGATAATGGTGATGGACTATC
1 GTGATGATATAGGCGTGATAATGGTGATGGAATATC
*
112816 GTGATGATATAGGTGTGATAATGGTGATGGA
1 GTGATGATATAGGCGTGATAATGGTGATGGA
112847 TAGATTGTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 18 0.29
36 44 0.71
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.31
Consensus pattern (36 bp):
GTGATGATATAGGCGTGATAATGGTGATGGAATATC
Found at i:116174 original size:19 final size:20
Alignment explanation
Indices: 116136--116188 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
116126 GAAACCCCTT
*
116136 TGAAAATACATGATTTTTTTGA
1 TGAAAATACATGA--TTTTTAA
116158 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
116177 TGAAGATACATG
1 TGAAAATACATG
116189 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:117138 original size:30 final size:31
Alignment explanation
Indices: 117098--117157 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
117088 ACATGCTGTC
**
117098 ATGATATCTAAATGAAATGAAAACATAATAA
1 ATGATATCTAAAACAAATGAAAACATAATAA
* *
117129 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGAAAACATAATA
117158 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGAAAACATAATAA
Found at i:120432 original size:19 final size:20
Alignment explanation
Indices: 120394--120446 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
120384 GAAACCCCTT
*
120394 TGAAAATACATGATTTTTTTGA
1 TGAAAATACATGA--TTTTTAA
120416 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
120435 TGAAGATACATG
1 TGAAAATACATG
120447 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:121396 original size:30 final size:31
Alignment explanation
Indices: 121356--121415 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
121346 ACATGCTGTC
**
121356 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
121387 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
121416 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:122998 original size:17 final size:19
Alignment explanation
Indices: 122976--123019 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
122966 GTAGGAGTCT
122976 TTTTCTTTTCTCTT-TTG-
1 TTTTCTTTTCTCTTGTTGC
*
122993 TTTTCTTTTTTCTTGTTGC
1 TTTTCTTTTCTCTTGTTGC
123012 TTTT-TTTT
1 TTTTCTTTT
123020 TTGTTGTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 13 0.54
18 7 0.29
19 4 0.17
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTCTCTTGTTGC
Found at i:123020 original size:17 final size:18
Alignment explanation
Indices: 122974--123020 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
122964 ATGTAGGAGT
*
122974 CTTTTTCTTTTCTCTTTTG
1 CTTTTT-TTTTCTCTGTTG
*
122993 TTTTCTTTTTTCT-TGTTG
1 CTTT-TTTTTTCTCTGTTG
123011 CTTTTTTTTT
1 CTTTTTTTTT
123021 TGTTGTAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 6 0.25
18 7 0.29
19 9 0.38
20 2 0.08
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (18 bp):
CTTTTTTTTTCTCTGTTG
Found at i:123021 original size:18 final size:18
Alignment explanation
Indices: 122974--123026 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
122964 ATGTAGGAGT
122974 CTTTTTCTTTTCTCTT-TTG
1 CTTTTT-TTTT-TCTTGTTG
122993 -TTTTCTTTTTTCTTGTTG
1 CTTTT-TTTTTTCTTGTTG
*
123011 CTTTTTTTTTTGTTGT
1 CTTTTTTTTTTCTTGT
123027 AGCACTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.77
Consensus pattern (18 bp):
CTTTTTTTTTTCTTGTTG
Found at i:123384 original size:13 final size:13
Alignment explanation
Indices: 123366--123428 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
123356 TGAGGATGAA
123366 GGAATATGGTGAT
1 GGAATATGGTGAT
123379 GGAATATGGTGAT
1 GGAATATGGTGAT
*
123392 -G-ATATAGGCG-T
1 GGAATAT-GGTGAT
123403 -G-ATAATGGTGAT
1 GGAAT-ATGGTGAT
*
123415 GGACTATGGTGAT
1 GGAATATGGTGAT
123428 G
1 G
123429 ATATAGGCGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
11 11 0.26
12 7 0.17
13 23 0.55
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.38, T:0.30
Consensus pattern (13 bp):
GGAATATGGTGAT
Found at i:123454 original size:36 final size:36
Alignment explanation
Indices: 123371--123454 Score: 159
Period size: 36 Copynumber: 2.3 Consensus size: 36
123361 ATGAAGGAAT
*
123371 ATGGTGATGGAATATGGTGATGATATAGGCGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
123407 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
123443 ATGGTGATGGAC
1 ATGGTGATGGAC
123455 AAATTGTATC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
Found at i:134159 original size:13 final size:12
Alignment explanation
Indices: 134140--134225 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
134130 ATATAGGCGT
134140 GATATGGTGATG
1 GATATGGTGATG
134152 GAATATGGTGAT-
1 G-ATATGGTGATG
*
134164 GATATAGGCG-T-
1 GATAT-GGTGATG
134175 GATAATGGTGATG
1 GAT-ATGGTGATG
134188 GACTATGGTGAT-
1 GA-TATGGTGATG
*
134200 GATATAGGCG-T-
1 GATAT-GGTGATG
134211 GATAATGGTGATG
1 GAT-ATGGTGATG
134224 GA
1 GA
134226 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:134195 original size:36 final size:36
Alignment explanation
Indices: 134122--134226 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
134112 ATTTATAAGT
* *
134122 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
134157 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
134193 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
134227 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:137339 original size:13 final size:12
Alignment explanation
Indices: 137298--137347 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
137288 ACAATCTGTC
*
137298 CATCACCATTAT
1 CATCACCATAAT
137310 CA-CACC-TATAT
1 CATCACCATA-AT
137321 CATCACCATAAT
1 CATCACCATAAT
*
137333 CCATCACCATTAT
1 -CATCACCATAAT
137346 CA
1 CA
137348 CGCCTATATC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 1 0.03
11 8 0.25
12 10 0.31
13 13 0.41
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (12 bp):
CATCACCATAAT
Found at i:137412 original size:36 final size:36
Alignment explanation
Indices: 137295--137411 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 36
137285 GATACAATCT
*
137295 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * **
137331 ATCCATCACCATTATCACGCCTATATCATCACTACC
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
137367 TTCCATCACTATTTTCACGCCTATAACATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
137403 GTCCATCAC
1 GTCCATCAC
137412 TTTCACGCCA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:138935 original size:24 final size:25
Alignment explanation
Indices: 138882--138932 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
138872 AAAAATCAGA
*
138882 AAAG-AAATTGAAGCACTCCAAAAG
1 AAAGAAAATTGAAGCACTCAAAAAG
*
138906 AAAGAAAATTTAAGCACTCAAAAAG
1 AAAGAAAATTGAAGCACTCAAAAAG
138931 AA
1 AA
138933 GAAGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (25 bp):
AAAGAAAATTGAAGCACTCAAAAAG
Found at i:148706 original size:21 final size:19
Alignment explanation
Indices: 148673--148717 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
148663 TGTAGGAGTC
* *
148673 TTTTTCTTTTCTTTTTGTT
1 TTTTTCTTTTCTTGTTGCT
148692 TTTTTCTTCTTTCTTGTTGCT
1 TTTTTC-T-TTTCTTGTTGCT
148713 TTTTT
1 TTTTT
148718 GTTGTAGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 1 0.05
21 15 0.68
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTCTTGTTGCT
Found at i:149137 original size:35 final size:36
Alignment explanation
Indices: 149090--149157 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
149080 ATTTAGAAGT
*
149090 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCATGATAATGGTGATGGAATA
*
149125 TGGTGATGATATAGGCATGATAATGGTGATGGA
1 TGGTGATAATATAGGCATGATAATGGTGATGGA
149158 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCATGATAATGGTGATGGAATA
Found at i:161749 original size:30 final size:28
Alignment explanation
Indices: 161690--161749 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
161680 CTTTTTCTTC
* **
161690 TTTTGAGTGCTGGATTTTTTTCTTTTTT
1 TTTTGAGTGCTGCATTTTTTTCTGATTT
*
161718 TTTTGAGTGCTTCACTTTCTTTTCTGATTT
1 TTTTGAGTGCTGCA-TTT-TTTTCTGATTT
161748 TT
1 TT
161750 CTTTTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
29 3 0.12
30 11 0.42
ACGTcount: A:0.08, C:0.12, G:0.15, T:0.65
Consensus pattern (28 bp):
TTTTGAGTGCTGCATTTTTTTCTGATTT
Found at i:167024 original size:13 final size:13
Alignment explanation
Indices: 167006--167048 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
166996 GTCTCTAGCT
167006 AGCTCAAAAGTCC
1 AGCTCAAAAGTCC
*
167019 AGCTC--AAGT-T
1 AGCTCAAAAGTCC
167029 AGCTCAAAAGTCC
1 AGCTCAAAAGTCC
167042 AGCTCAA
1 AGCTCAA
167049 GTTAGCTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 5 0.20
11 4 0.16
12 4 0.16
13 12 0.48
ACGTcount: A:0.37, C:0.28, G:0.16, T:0.19
Consensus pattern (13 bp):
AGCTCAAAAGTCC
Found at i:167031 original size:23 final size:23
Alignment explanation
Indices: 167005--167055 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
166995 GGTCTCTAGC
167005 TAGCTCAAAAGTCCAGCTCAAGT
1 TAGCTCAAAAGTCCAGCTCAAGT
167028 TAGCTCAAAAGTCCAGCTCAAGT
1 TAGCTCAAAAGTCCAGCTCAAGT
167051 TAGCT
1 TAGCT
167056 ATGAGCTCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (23 bp):
TAGCTCAAAAGTCCAGCTCAAGT
Found at i:170385 original size:23 final size:24
Alignment explanation
Indices: 170354--170408 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
170344 GAAAAATCAG
*
170354 AAAAGAAATTGA-AGCACTCCAAA
1 AAAAGAAATTGACAGCACTCAAAA
* *
170377 AGAAGAAATTTACAGCACTCAAAA
1 AAAAGAAATTGACAGCACTCAAAA
170401 AAAAGAAA
1 AAAAGAAA
170409 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.60, C:0.15, G:0.13, T:0.13
Consensus pattern (24 bp):
AAAAGAAATTGACAGCACTCAAAA
Found at i:172171 original size:13 final size:12
Alignment explanation
Indices: 172152--172237 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
172142 ATATAGACAT
172152 GATATGGTGATG
1 GATATGGTGATG
172164 GAATATGGTGAT-
1 G-ATATGGTGATG
*
172176 GATATAGGCG-T-
1 GATAT-GGTGATG
172187 GATAATGGTGATG
1 GAT-ATGGTGATG
172200 GACTATGGTGAT-
1 GA-TATGGTGATG
*
172212 GATATAGGCG-T-
1 GATAT-GGTGATG
172223 GATAATGGTGATG
1 GAT-ATGGTGATG
172236 GA
1 GA
172238 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:172207 original size:36 final size:36
Alignment explanation
Indices: 172134--172238 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
172124 ATTTATAAGT
* * * *
172134 TGGTGATAATATAGACATGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
172169 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
172205 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
172239 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 18 0.28
36 47 0.72
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:177438 original size:11 final size:12
Alignment explanation
Indices: 177418--177447 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
177408 TTGGAGTCTT
177418 TTCTTTTTTTTA
1 TTCTTTTTTTTA
177430 TTCTTTTTTTTA
1 TTCTTTTTTTTA
177442 TTCTTT
1 TTCTTT
177448 CTCGTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (12 bp):
TTCTTTTTTTTA
Found at i:177870 original size:22 final size:23
Alignment explanation
Indices: 177842--177893 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
177832 ATTTATAAGT
177842 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
177864 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
177887 TGGTGAT
1 TGGTGAT
177894 GGACTATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:177885 original size:36 final size:38
Alignment explanation
Indices: 177844--177923 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 38
177834 TTATAAGTTG
177844 GTGATAATATAGGCG-T-GA-TATGGTGATGATATAGGC
1 GTGATAATAT-GGCGATGGACTATGGTGATGATATAGGC
*
177880 GTGAT-A-ATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATGGCGATGGACTATGGTGATGATATAGGC
*
177916 ATGATAAT
1 GTGATAAT
177924 GGTGATGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
33 3 0.08
34 3 0.08
35 3 0.08
36 27 0.73
37 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (38 bp):
GTGATAATATGGCGATGGACTATGGTGATGATATAGGC
Found at i:177924 original size:36 final size:36
Alignment explanation
Indices: 177862--177933 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
177852 ATAGGCGTGA
*
177862 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
177898 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCATGATAATGGTGATGGAC
177934 AGATTGTATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCATGATAATGGTGATGGAC
Found at i:179818 original size:19 final size:20
Alignment explanation
Indices: 179794--179844 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
179784 CGGCCAAGAG
* *
179794 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
179813 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
179833 CATGTATTTTCA
1 CATGTATTTTCA
179845 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:186575 original size:19 final size:20
Alignment explanation
Indices: 186534--186584 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
186524 GAAACCCCTT
*
186534 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
186554 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
186573 TGAAGATACATG
1 TGAAAATACATG
186585 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:204571 original size:33 final size:33
Alignment explanation
Indices: 204529--204597 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
204519 GTTGATGAAT
*
204529 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
204562 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
204595 GAA
1 GAA
204598 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:207006 original size:30 final size:31
Alignment explanation
Indices: 206954--207013 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
206944 CTTAGCTTTA
**
206954 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
**
206984 TATTATGTTTGTATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
207014 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:207711 original size:19 final size:20
Alignment explanation
Indices: 207663--207713 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
207653 CTTAATAAAG
207663 GAAATAATAAT-ATAAGTAAT
1 GAAATAA-AATAATAAGTAAT
207683 GAAA-ATAAATAATAAG-AAT
1 GAAATA-AAATAATAAGTAAT
207702 GAAATAAAATAA
1 GAAATAAAATAA
207714 AGAAAGGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (20 bp):
GAAATAAAATAATAAGTAAT
Found at i:208164 original size:19 final size:20
Alignment explanation
Indices: 208126--208168 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
208116 GAAACCCCTT
*
208126 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
208146 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
208165 TGAA
1 TGAA
208169 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:209495 original size:17 final size:17
Alignment explanation
Indices: 209454--209498 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
209444 AAAGTGCTAC
*
209454 AAAAAAAAAACAACAAG
1 AAAAAGAAAACAACAAG
209471 AAAGAAGAAAACAA-AAG
1 AAA-AAGAAAACAACAAG
209488 AGAAAAGAAAA
1 A-AAAAGAAAA
209499 AGACTCCTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAACAACAAG
Found at i:214711 original size:36 final size:36
Alignment explanation
Indices: 214664--214779 Score: 169
Period size: 36 Copynumber: 3.2 Consensus size: 36
214654 ATACAATCTG
*
214664 TCCATCACCATTATCATGCCTATATCATCACCATAA
1 TCCATCACCATTATCACGCCTATATCATCACCATAA
***
214700 TCCATCACCATTATCACGCCTATATCATCACCACCT
1 TCCATCACCATTATCACGCCTATATCATCACCATAA
* * *
214736 TCCATCACCATTTTCACGCCTATAACATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAA
214772 TCCATCAC
1 TCCATCAC
214780 TTTCACGCCA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.30, C:0.38, G:0.03, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAA
Found at i:217737 original size:13 final size:13
Alignment explanation
Indices: 217721--217772 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
217711 CATTCTCTTT
217721 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
217734 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
*
217747 TTCTTTTATCTTTTT
1 TTC-TTT-TCTTTTC
217762 TTC-TTTCTTTT
1 TTCTTTTCTTTT
217773 TGCACTCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
12 6 0.17
13 18 0.50
14 3 0.08
15 9 0.25
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:218075 original size:19 final size:20
Alignment explanation
Indices: 218027--218077 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
218017 CTTAATAAAG
218027 GAAATAATAAT-ATAAGTAAT
1 GAAATAA-AATAATAAGTAAT
218047 GAAA-ATAAATAATAAG-AAT
1 GAAATA-AAATAATAAGTAAT
218066 GAAATAAAATAA
1 GAAATAAAATAA
218078 AGAAATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (20 bp):
GAAATAAAATAATAAGTAAT
Found at i:218084 original size:18 final size:18
Alignment explanation
Indices: 218027--218085 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 18
218017 CTTAATAAAG
*
218027 GAAATAATAATATAAGTAAT
1 GAAATAA-AATA-AAGAAAT
218047 GAAA-ATAAATAATA-AGAAT
1 GAAATA-AAATAA-AGA-AAT
218066 GAAATAAAATAAAGAAAT
1 GAAATAAAATAAAGAAAT
218084 GA
1 GA
218086 TAGAGATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 7 0.21
19 20 0.61
20 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (18 bp):
GAAATAAAATAAAGAAAT
Found at i:218528 original size:19 final size:20
Alignment explanation
Indices: 218490--218532 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
218480 GAAACCCCTT
*
218490 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
218510 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
218529 TGAA
1 TGAA
218533 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:219468 original size:30 final size:31
Alignment explanation
Indices: 219429--219488 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
219419 ACATGCTGCC
**
219429 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
219460 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
219489 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:219979 original size:33 final size:33
Alignment explanation
Indices: 219937--220005 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
219927 GTTGATGAAT
*
219937 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
219970 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
220003 GAA
1 GAA
220006 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:225186 original size:33 final size:33
Alignment explanation
Indices: 225144--225212 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
225134 GTTGATGAAT
*
225144 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
225177 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
225210 GAA
1 GAA
225213 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:235306 original size:26 final size:26
Alignment explanation
Indices: 235271--235335 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
235261 TGGTTAGGGT
235271 ATAGAAATGGTTATGGTAAAGGTAGG
1 ATAGAAATGGTTATGGTAAAGGTAGG
235297 ATAGAAATGGTTATGGTAAAGGTAGG
1 ATAGAAATGGTTATGGTAAAGGTAGG
*
235323 ATAGAAAAGGTTA
1 ATAGAAATGGTTA
235336 AGAAAAGGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (26 bp):
ATAGAAATGGTTATGGTAAAGGTAGG
Found at i:235613 original size:6 final size:6
Alignment explanation
Indices: 235602--235645 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
235592 GATGTAGGAG
*
235602 TCTTTT TC-TTT TCTTTT TATTTT TCTTATT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
235646 TTTGTTGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:236044 original size:35 final size:37
Alignment explanation
Indices: 235998--236068 Score: 119
Period size: 35 Copynumber: 2.0 Consensus size: 37
235988 TTAGAAGTTG
235998 GTGATAATATAGGCGTGAT-ATGGTGATGGA-ATATA
1 GTGATAATATAGGCGTGATAATGGTGATGGACATATA
*
236033 GTGATGATATAGGCGTGATAATGGTGATGGACATAT
1 GTGATAATATAGGCGTGATAATGGTGATGGACATAT
236069 TGTATCTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 18 0.55
36 11 0.33
37 4 0.12
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.31
Consensus pattern (37 bp):
GTGATAATATAGGCGTGATAATGGTGATGGACATATA
Found at i:236761 original size:18 final size:20
Alignment explanation
Indices: 236738--236775 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
236728 TGGAAGGCAA
236738 ACTT-CCAT-CATTTGAGCT
1 ACTTCCCATGCATTTGAGCT
*
236756 ACTTCCCATGTATTTGAGCT
1 ACTTCCCATGCATTTGAGCT
236776 GAAGATGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.39
Consensus pattern (20 bp):
ACTTCCCATGCATTTGAGCT
Found at i:237400 original size:12 final size:13
Alignment explanation
Indices: 237375--237403 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
237365 CATCACTATC
237375 TTTCTTTCTTTCA
1 TTTCTTTCTTTCA
237388 TTTCTTT-TTTCA
1 TTTCTTTCTTTCA
237400 TTTC
1 TTTC
237404 CATTACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTCTTTCA
Found at i:244348 original size:2 final size:2
Alignment explanation
Indices: 244341--244417 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
244331 TGGTAGCAGA
244341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244383 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 A
244418 AGTTGGTGAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:247597 original size:35 final size:37
Alignment explanation
Indices: 247551--247630 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
247541 TTTGAGAATT
*
247551 TGGTGATGATATAGGCATGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
* *
247586 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
*
247623 TGGGGATG
1 TGGTGATG
247631 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
Found at i:251206 original size:6 final size:6
Alignment explanation
Indices: 251195--251236 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
251185 GATGTAGGAG
*
251195 TCTTTT TC-TTT TCTTTT TATTTT TCTTTT T-TTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCT-TTT T
251237 TGTTGCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 10 0.32
6 17 0.55
7 4 0.13
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (6 bp):
TCTTTT
Found at i:251218 original size:12 final size:11
Alignment explanation
Indices: 251195--251237 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
251185 GATGTAGGAG
*
251195 TCTTTTTCTTT
1 TCTTTTTTTTT
251206 TCTTTTTATTTT
1 TCTTTTT-TTTT
251218 TCTTTTTTTTT
1 TCTTTTTTTTT
251229 TCTCTTTTT
1 TCT-TTTTT
251238 GTTGCTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 14 0.48
12 15 0.52
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:251229 original size:17 final size:17
Alignment explanation
Indices: 251197--251228 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
251187 TGTAGGAGTC
251197 TTTTTCTTTTCTTTTTA
1 TTTTTCTTTTCTTTTTA
251214 TTTTTCTTTT-TTTTT
1 TTTTTCTTTTCTTTTT
251229 TCTCTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTTA
Found at i:251245 original size:23 final size:23
Alignment explanation
Indices: 251196--251246 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
251186 ATGTAGGAGT
* *
251196 CTTTTTCTTTTCTTTTTATTTTT
1 CTTTTTCTTTTCTTTTTATGTTG
*
251219 CTTTTTTTTTTCTCTTTT-TGTTG
1 CTTTTTCTTTTCT-TTTTATGTTG
251242 CTTTT
1 CTTTT
251247 GTTGCAGCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (23 bp):
CTTTTTCTTTTCTTTTTATGTTG
Found at i:251662 original size:35 final size:37
Alignment explanation
Indices: 251623--251702 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
251613 TTTGAGAATT
* *
251623 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGAGTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGAGTA
*
251658 TGGTGATGATATAGGCATGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGAGTA
*
251695 TGGGGATG
1 TGGTGATG
251703 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.29, C:0.03, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCATGATAATGGAAGATGGAGTA
Found at i:253345 original size:21 final size:23
Alignment explanation
Indices: 253295--253349 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
253285 CAAAGAAATC
*
253295 AAAGCACTCATAAGAAGAAATTG
1 AAAGCACTCATAAGAAAAAATTG
253318 AAAGCACTCA-AA-AAAAAAGTTG
1 AAAGCACTCATAAGAAAAAA-TTG
253340 -AAGCACTCAT
1 AAAGCACTCAT
253350 CAACAATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 14 0.48
22 5 0.17
23 10 0.34
ACGTcount: A:0.53, C:0.16, G:0.15, T:0.16
Consensus pattern (23 bp):
AAAGCACTCATAAGAAAAAATTG
Found at i:254570 original size:12 final size:11
Alignment explanation
Indices: 254549--254591 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
254539 TGCTGGAAAC
254549 AAGATAAAAAA
1 AAGATAAAAAA
*
254560 TAAGATTAAAAA
1 -AAGATAAAAAA
*
254572 AAGATAAATAA
1 AAGATAAAAAA
254583 AAGATAAAA
1 AAGATAAAA
254592 GAATTGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.16
Consensus pattern (11 bp):
AAGATAAAAAA
Found at i:258420 original size:19 final size:20
Alignment explanation
Indices: 258373--258423 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
258363 GAAACCCCTT
*
258373 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
258393 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
* *
258412 TTAAGATACATG
1 TGAAAATACATG
258424 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:259536 original size:127 final size:127
Alignment explanation
Indices: 259386--259645 Score: 520
Period size: 127 Copynumber: 2.0 Consensus size: 127
259376 TATAAAGCTA
259386 AGTAAAGATGTGAAAACATATGTTATGCATGAAAATCATATAGTTGCAAGTGAATGATAACATAT
1 AGTAAAGATGTGAAAACATATGTTATGCATGAAAATCATATAGTTGCAAGTGAATGATAACATAT
259451 GATTATTCAAGCATAGTTTAAGATGCAAAAGTATGCTCATAATAATATATAGTGCATAAATG
66 GATTATTCAAGCATAGTTTAAGATGCAAAAGTATGCTCATAATAATATATAGTGCATAAATG
259513 AGTAAAGATGTGAAAACATATGTTATGCATGAAAATCATATAGTTGCAAGTGAATGATAACATAT
1 AGTAAAGATGTGAAAACATATGTTATGCATGAAAATCATATAGTTGCAAGTGAATGATAACATAT
259578 GATTATTCAAGCATAGTTTAAGATGCAAAAGTATGCTCATAATAATATATAGTGCATAAATG
66 GATTATTCAAGCATAGTTTAAGATGCAAAAGTATGCTCATAATAATATATAGTGCATAAATG
259640 AGTAAA
1 AGTAAA
259646 TATAATATAA
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 133 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.30
Consensus pattern (127 bp):
AGTAAAGATGTGAAAACATATGTTATGCATGAAAATCATATAGTTGCAAGTGAATGATAACATAT
GATTATTCAAGCATAGTTTAAGATGCAAAAGTATGCTCATAATAATATATAGTGCATAAATG
Found at i:260102 original size:36 final size:35
Alignment explanation
Indices: 260009--260119 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
259999 TTGGTGGTTA
* * * *
260009 TATAGGCATGAAATGGTGATAGAAGATGGTAATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
260044 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
260079 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
260115 T-TAGG
1 TATAGG
260120 TAGTATCTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 43 0.64
36 24 0.36
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:260749 original size:19 final size:19
Alignment explanation
Indices: 260702--260742 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
260692 AGCAACTAGG
260702 TGTGACTTGGCTTCCATCT
1 TGTGACTTGGCTTCCATCT
260721 TGTGACTTGGCTTCCATCT
1 TGTGACTTGGCTTCCATCT
260740 TGT
1 TGT
260743 ATCTTGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (19 bp):
TGTGACTTGGCTTCCATCT
Found at i:262152 original size:9 final size:9
Alignment explanation
Indices: 262138--262169 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
262128 ATGGGAGTGC
262138 AAAAGAAAG
1 AAAAGAAAG
262147 AAAAGAAAG
1 AAAAGAAAG
262156 AAAAGAAA-
1 AAAAGAAAG
262164 AAAAGA
1 AAAAGA
262170 TGAAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:264269 original size:13 final size:12
Alignment explanation
Indices: 264250--264335 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
264240 AAATAGGCGT
264250 GATATGGTGATG
1 GATATGGTGATG
264262 GAATATGGTGAT-
1 G-ATATGGTGATG
*
264274 GATATAGGCG-T-
1 GATAT-GGTGATG
264285 GATAATGGTGATG
1 GAT-ATGGTGATG
264298 GACTATGGTGAT-
1 GA-TATGGTGATG
*
264310 GATATAGGCG-T-
1 GATAT-GGTGATG
264321 GATAATGGTGATG
1 GAT-ATGGTGATG
264334 GA
1 GA
264336 CATATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:264305 original size:36 final size:36
Alignment explanation
Indices: 264232--264336 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
264222 ATTTATAAGT
* * *
264232 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
264267 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
264303 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
264337 ATATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:271334 original size:19 final size:20
Alignment explanation
Indices: 271310--271360 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
271300 CGGCCAAGAG
*
271310 CATGTATCTTCATTAAAA-T
1 CATGTATTTTCATTAAAATT
271329 CATGTATTTTCATTAAAATT
1 CATGTATTTTCATTAAAATT
271349 CATGTATTTTCA
1 CATGTATTTTCA
271361 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAATT
Found at i:271857 original size:36 final size:35
Alignment explanation
Indices: 271764--271874 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
271754 TTGGTGGTTA
* * * *
271764 TATAGGTGTAAAATGGTGATAGAAGATGGTAATGA
1 TATAGGCGTAAAATGGTGATGGAAGATGGTGATGT
* ** *
271799 TATAGGCATTCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTAAAATGGTGATGGAAGATGGTGATGT
271834 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGT-AAAATGGTGATGGAAGATGGTGATGT
271870 T-TAGG
1 TATAGG
271875 TAGTATCTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
35 39 0.62
36 24 0.38
ACGTcount: A:0.33, C:0.03, G:0.34, T:0.30
Consensus pattern (35 bp):
TATAGGCGTAAAATGGTGATGGAAGATGGTGATGT
Found at i:276156 original size:36 final size:35
Alignment explanation
Indices: 276063--276173 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
276053 TTGGTGGTTA
* * *
276063 TATAGGCGTGAAATGGTGATAGAAGATGGTAATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
276098 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
276133 TATAGGCATGAAAATGGTGATGGAAGAAGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
276169 T-TAGG
1 TATAGG
276174 TAGTATCTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 43 0.65
36 23 0.35
ACGTcount: A:0.33, C:0.04, G:0.36, T:0.27
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:278126 original size:6 final size:6
Alignment explanation
Indices: 278115--278155 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
278105 GTACTGCAAC
278115 AAAAAG AAAAAG AAAACA- AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAA
278156 AATACTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 1 0.03
6 31 0.94
7 1 0.03
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:279550 original size:22 final size:20
Alignment explanation
Indices: 279525--279564 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
279515 ATGTTTGTTT
279525 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
279547 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
279565 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:283786 original size:22 final size:20
Alignment explanation
Indices: 283761--283800 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
283751 ATGTTTGTTT
283761 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
283783 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
283801 CATCATCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:296948 original size:19 final size:20
Alignment explanation
Indices: 296924--296964 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
296914 GTCCAAGAGT
296924 ATGTATCTTCATT-AAAATC
1 ATGTATCTTCATTAAAAATC
*
296943 ATGTATTTTCATTAAAAATC
1 ATGTATCTTCATTAAAAATC
296963 AT
1 AT
296965 ATATTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (20 bp):
ATGTATCTTCATTAAAAATC
Found at i:296962 original size:20 final size:19
Alignment explanation
Indices: 296924--296973 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
296914 GTCCAAGAGT
*
296924 ATGTATCTTCATTAAAATC
1 ATGTATTTTCATTAAAATC
296943 ATGTATTTTCATTAAAAATC
1 ATGTATTTTCATT-AAAATC
*
296963 ATATATTTTCA
1 ATGTATTTTCA
296974 AATGGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (19 bp):
ATGTATTTTCATTAAAATC
Found at i:301315 original size:36 final size:36
Alignment explanation
Indices: 301268--301372 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
301258 GATACAATCT
301268 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
301304 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
301340 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
301373 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:301330 original size:11 final size:11
Alignment explanation
Indices: 301271--301355 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 11
301261 ACAATCTGTC
301271 CATCACCATTAT
1 CATCACCA-TAT
*
301283 CA-CGCCTATAT
1 CATCACC-ATAT
301294 CATCACCATAGT
1 CATCACCATA-T
301306 CCATCACCATTAT
1 -CATCACCA-TAT
301319 CA-CACCTATAT
1 CATCACC-ATAT
301330 CATCACCATATT
1 CATCACCATA-T
301342 CCATCACCATAT
1 -CATCACCATAT
301354 CA
1 CA
301356 CGCCTATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 25 0.40
12 16 0.26
13 19 0.31
14 2 0.03
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:305018 original size:36 final size:36
Alignment explanation
Indices: 304971--305075 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
304961 GATACAATCT
304971 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
305007 GTCCATCACCATTATCACGCCTATATCATTACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
305043 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
305076 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:311686 original size:13 final size:11
Alignment explanation
Indices: 311645--311729 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
311635 ACAATCTGTC
311645 CATCACCATTAT
1 CATCACCA-TAT
*
311657 CA-CGCCTATAT
1 CATCACC-ATAT
311668 CATCACCATAGT
1 CATCACCATA-T
311680 CCATCACCATTAT
1 -CATCACCA-TAT
*
311693 CA-CGCCTATAT
1 CATCACC-ATAT
311704 CATCACCATATT
1 CATCACCATA-T
311716 CCATCACCATAT
1 -CATCACCATAT
311728 CA
1 CA
311730 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:311689 original size:36 final size:36
Alignment explanation
Indices: 311642--311746 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
311632 GATACAATCT
311642 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
311678 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
311714 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
311747 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:315748 original size:36 final size:36
Alignment explanation
Indices: 315701--315771 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
315691 ATACAATCTT
*
315701 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATACCATCACCATAG
315737 TCCATCACCATTATCACGCCTATACCATCACCATA
1 TCCATCACCATTATCACGCCTATACCATCACCATA
315772 TAACGCCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.27
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATACCATCACCATAG
Found at i:315780 original size:22 final size:23
Alignment explanation
Indices: 315738--315791 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
315728 TCACCATAGT
*
315738 CCATCACCATTATCACGCCTATA
1 CCATCACCATTATAACGCCTATA
315761 CCATCACCA-TATAACGCCTATA
1 CCATCACCATTATAACGCCTATA
**
315783 TTATCACCA
1 CCATCACCA
315792 ACTTATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.33, C:0.37, G:0.04, T:0.26
Consensus pattern (23 bp):
CCATCACCATTATAACGCCTATA
Found at i:317845 original size:33 final size:33
Alignment explanation
Indices: 317803--317871 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
317793 GTTGATGAAT
*
317803 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
317836 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
317869 GAA
1 GAA
317872 TATGATGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:326042 original size:33 final size:34
Alignment explanation
Indices: 326000--326091 Score: 136
Period size: 33 Copynumber: 2.7 Consensus size: 34
325990 AGATACAATC
326000 GTCCATCACCATTATCACGCCTAT-ATCACCATA
1 GTCCATCACCATTATCACGCCTATCATCACCATA
326033 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCC--TATCATCACCATA
326069 -TACCATCACCA-TATCACGCCTAT
1 GT-CCATCACCATTATCACGCCTAT
326092 TTTATCACCA
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
33 24 0.44
35 13 0.24
36 18 0.33
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.27
Consensus pattern (34 bp):
GTCCATCACCATTATCACGCCTATCATCACCATA
Found at i:326075 original size:13 final size:13
Alignment explanation
Indices: 326024--326082 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
326014 TCACGCCTAT
326024 ATCACCATAGT-CC
1 ATCACCATA-TACC
*
326037 ATCACCAT-TATC
1 ATCACCATATACC
* *
326049 A-CGCC-TATATC
1 ATCACCATATACC
326060 ATCACCATATACC
1 ATCACCATATACC
326073 ATCACCATAT
1 ATCACCATAT
326083 CACGCCTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 1 0.03
11 9 0.24
12 5 0.13
13 23 0.61
ACGTcount: A:0.34, C:0.36, G:0.03, T:0.27
Consensus pattern (13 bp):
ATCACCATATACC
Found at i:326091 original size:35 final size:35
Alignment explanation
Indices: 326000--326101 Score: 140
Period size: 35 Copynumber: 2.9 Consensus size: 35
325990 AGATACAATC
326000 GTCCATCACCATTATCACGCC--TATATCACCATA
1 GTCCATCACCATTATCACGCCTATATATCACCATA
326033 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATAT-ATCACCATA
*
326069 -TACCATCACCA-TATCACGCCTATTTTATCACCA
1 GT-CCATCACCATTATCACGCCTA-TATATCACCA
326102 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
33 21 0.33
35 22 0.35
36 20 0.32
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.28
Consensus pattern (35 bp):
GTCCATCACCATTATCACGCCTATATATCACCATA
Found at i:329974 original size:24 final size:21
Alignment explanation
Indices: 329940--329982 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
329930 TCCATAAAAC
*
329940 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
329962 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
329983 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Done.