Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008172.1 Hibiscus syriacus cultivar Beakdansim tig00110763_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: 140334
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5420 original size:13 final size:13
Alignment explanation
Indices: 5394--5428 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
5384 CAATCCTGGC
5394 GACATACG-GGGT
1 GACATACGAGGGT
5406 GACATACGAGGGT
1 GACATACGAGGGT
5419 GACATACGAG
1 GACATACGAG
5429 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:5438 original size:11 final size:11
Alignment explanation
Indices: 5422--5448 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5412 CGAGGGTGAC
5422 ATACGAGCCAT
1 ATACGAGCCAT
5433 ATACGAGCCAT
1 ATACGAGCCAT
5444 ATACG
1 ATACG
5449 TCATACGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:5484 original size:22 final size:22
Alignment explanation
Indices: 5453--5532 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 22
5443 TATACGTCAT
*
5453 ACGAGCCAATGGGGAGGATGCA
1 ACGAGCCAATGGGGAGCATGCA
*
5475 ACGAGGCAATGGGGAGCATGCAGGAA
1 ACGAGCCAATGGGGAGCATGC----A
*
5501 TAGAGAGCCAATGGGGAGCATGCA
1 -A-CGAGCCAATGGGGAGCATGCA
5525 ACGAGCCA
1 ACGAGCCA
5533 TATACGAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 25 0.53
23 1 0.02
24 1 0.02
26 1 0.02
27 1 0.02
28 18 0.38
ACGTcount: A:0.34, C:0.19, G:0.39, T:0.09
Consensus pattern (22 bp):
ACGAGCCAATGGGGAGCATGCA
Found at i:5513 original size:28 final size:28
Alignment explanation
Indices: 5481--5646 Score: 188
Period size: 28 Copynumber: 5.6 Consensus size: 28
5471 TGCAACGAGG
5481 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
5509 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
* *
5542 CCACGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
5570 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
5603 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
5631 CAATGGGGAGCATGCA
1 CAATGGGGAGCATGCA
5647 ACGAGCCATA
Statistics
Matches: 116, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
28 52 0.45
29 10 0.09
30 4 0.03
31 4 0.03
32 10 0.09
33 36 0.31
ACGTcount: A:0.34, C:0.20, G:0.36, T:0.11
Consensus pattern (28 bp):
CAATGGGGAGCATGCAGGAATAGAGAGC
Found at i:5514 original size:50 final size:50
Alignment explanation
Indices: 5455--5651 Score: 178
Period size: 61 Copynumber: 3.5 Consensus size: 50
5445 TACGTCATAC
*
5455 GAGCCAATGGGGAGGATGCAACGAGGCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGGCAATGGGGAGCATGCAGGAATAGA
*
5505 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCCACGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGGCA-AT----------GGGGAGCATGCAGGAATAGA
5566 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAAC--G------A-G-G-CAATGGGGAGCATGCAGGAATAGA
5627 GAGCCAATGGGGAGCATGCAACGAG
1 GAGCCAATGGGGAGCATGCAACGAG
5652 CCATATACAA
Statistics
Matches: 122, Mismatches: 3, Indels: 42
0.73 0.02 0.25
Matches are distributed among these distances:
50 26 0.21
51 2 0.02
52 1 0.01
53 1 0.01
59 1 0.01
61 84 0.69
63 1 0.01
69 1 0.01
70 1 0.01
71 2 0.02
72 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.37, T:0.10
Consensus pattern (50 bp):
GAGCCAATGGGGAGCATGCAACGAGGCAATGGGGAGCATGCAGGAATAGA
Found at i:5570 original size:61 final size:61
Alignment explanation
Indices: 5475--5665 Score: 337
Period size: 61 Copynumber: 3.1 Consensus size: 61
5465 GGAGGATGCA
* *
5475 ACGAGGCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
5536 ACGAGCCCACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
5597 ACGAGCCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
5658 ACAAGCCA
1 ACGAGCCA
5666 TGCAGGAATA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 124 1.00
ACGTcount: A:0.35, C:0.21, G:0.34, T:0.10
Consensus pattern (61 bp):
ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
Found at i:5729 original size:29 final size:29
Alignment explanation
Indices: 5679--5787 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
5669 AGGAATAGAG
* *
5679 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
5708 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
5737 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
5766 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
5788 CCATTCCATC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:5904 original size:35 final size:37
Alignment explanation
Indices: 5837--5909 Score: 132
Period size: 35 Copynumber: 2.0 Consensus size: 37
5827 CATAGATTCC
5837 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
5874 TTCACGTGCT-CCCGCTGCA-TGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
5909 T
1 T
5910 GCATGCATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 17 0.47
36 9 0.25
37 10 0.28
ACGTcount: A:0.16, C:0.45, G:0.14, T:0.25
Consensus pattern (37 bp):
TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
Found at i:5937 original size:18 final size:18
Alignment explanation
Indices: 5914--5948 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5904 CCCAATGCAT
5914 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
5932 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
5949 TTATTGGTAC
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:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:6066 original size:23 final size:23
Alignment explanation
Indices: 6038--6083 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6028 AAAAGAAAGA
6038 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
6061 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
6084 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:6098 original size:25 final size:23
Alignment explanation
Indices: 6038--6098 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
6028 AAAAGAAAGA
**
6038 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
6061 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
6084 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
6099 AGAAAGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:6122 original size:21 final size:21
Alignment explanation
Indices: 6086--6159 Score: 96
Period size: 21 Copynumber: 3.4 Consensus size: 21
6076 GATTGCAGCC
*
6086 GAGAAA-GAAAGAAAGAAAGG
1 GAGAAAGGAAAGGAAGAAAGG
6106 GAGAAAGGAAAGGAAGAAAGG
1 GAGAAAGGAAAGGAAGAAAGG
6127 GAGAAAGGAAAGTAAGAAGAAAGG
1 GAGAAAGGAAAG---GAAGAAAGG
6151 GAGATAAGG
1 GAGA-AAGG
6160 TAAATTTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
20 6 0.12
21 25 0.52
24 13 0.27
25 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (21 bp):
GAGAAAGGAAAGGAAGAAAGG
Found at i:6138 original size:13 final size:13
Alignment explanation
Indices: 6088--6126 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
6078 TTGCAGCCGA
*
6088 GAAAGAAAGAAA-
1 GAAAGGAAGAAAG
*
6100 GAAAGGGAGAAAG
1 GAAAGGAAGAAAG
6113 GAAAGGAAGAAAG
1 GAAAGGAAGAAAG
6126 G
1 G
6127 GAGAAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (13 bp):
GAAAGGAAGAAAG
Found at i:6319 original size:41 final size:41
Alignment explanation
Indices: 6274--6362 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
6264 TATATGATTG
* *
6274 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
6315 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
6356 TTAGTTT
1 TTAGTTT
6363 GTATTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:6406 original size:46 final size:48
Alignment explanation
Indices: 6343--6434 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
6333 TTATATAGTT
6343 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* *
6388 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
6435 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 17 0.41
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:8748 original size:26 final size:24
Alignment explanation
Indices: 8690--8748 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
8680 CTAATAAACC
*
8690 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
8714 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
8742 TAATAAT
1 TAATAAT
8749 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:9584 original size:28 final size:30
Alignment explanation
Indices: 9544--9606 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
9534 ATTTTTTATA
*
9544 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
9574 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
9602 TAATA
1 TAATA
9607 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:9613 original size:28 final size:28
Alignment explanation
Indices: 9548--9613 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
9538 TTTATATAAT
*
9548 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
9576 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
9604 ATAATTTATA
1 ATAATATATA
9614 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:9616 original size:21 final size:21
Alignment explanation
Indices: 9583--9631 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
9573 CTAATATAAT
9583 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
9604 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
9625 ATTAACT
1 A-TAACT
9632 ATTTAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:10260 original size:28 final size:29
Alignment explanation
Indices: 10228--10306 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
10218 TATACCTTGG
*
10228 AGGTCGCCCGGATTGCATGGCGA-CTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
10256 AGGTCGCCTGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
10285 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
10307 TCCTATGGCG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 22 0.45
29 27 0.55
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.20
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:22167 original size:35 final size:35
Alignment explanation
Indices: 22109--22208 Score: 182
Period size: 35 Copynumber: 2.8 Consensus size: 35
22099 CGCGTTGATA
22109 ACTTTTATCAAGGTGTTTTAGTTTAGAGACAAGAAG
1 ACTTTTATCAA-GTGTTTTAGTTTAGAGACAAGAAG
22145 ACTTTTATCAAGTGTTTTAGTTTAGAGACAAGAAG
1 ACTTTTATCAAGTGTTTTAGTTTAGAGACAAGAAG
22180 ACTTTTATCAAGTGGTTTTAGTTTAGAGA
1 ACTTTTATCAAGT-GTTTTAGTTTAGAGA
22209 GGAGAAGAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
35 37 0.59
36 26 0.41
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (35 bp):
ACTTTTATCAAGTGTTTTAGTTTAGAGACAAGAAG
Found at i:24557 original size:2 final size:2
Alignment explanation
Indices: 24550--24578 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24540 TTTTTAAAAC
24550 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 A
24579 CCCCTATCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24818 original size:24 final size:24
Alignment explanation
Indices: 24791--24924 Score: 162
Period size: 24 Copynumber: 5.6 Consensus size: 24
24781 CATAATTCAT
* *
24791 GTCAAATATCATATCAAAATCCAG
1 GTCAAATATCATATCAGAATCCAA
* *
24815 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAATATCATATCAGAATCCAA
* *
24839 GTCAAGTATCATATCAGAATCCAT
1 GTCAAATATCATATCAGAATCCAA
* *
24863 GTCATATATCATATCAGAATCCAT
1 GTCAAATATCATATCAGAATCCAA
* *
24887 GTCAAGTATCATATCAGAATTCAA
1 GTCAAATATCATATCAGAATCCAA
24911 GTCGAAA-ATCATAT
1 GTC-AAATATCATAT
24925 AAAATATTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
24 94 0.98
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (24 bp):
GTCAAATATCATATCAGAATCCAA
Found at i:24922 original size:72 final size:72
Alignment explanation
Indices: 24788--24924 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
24778 AAGCATAATT
*
24788 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCATAT
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATCATAT
24853 CAGAATC
66 CAGAATC
* * * * *
24860 CATGTCATATATCATATCAGAATCCATGTCAAGTATCATATCAGAATTCAAGTCGAA-AATCATA
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTC-AAGAATCATA
24924 T
65 T
24925 AAAATATTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 56 0.97
73 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (72 bp):
CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATCATAT
CAGAATC
Found at i:32843 original size:24 final size:24
Alignment explanation
Indices: 32816--32863 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
32806 GCTTTACGTT
32816 GATTATTAATTCAATTACCACGGC
1 GATTATTAATTCAATTACCACGGC
*
32840 GATTATTAATTCAATTACCTCGGC
1 GATTATTAATTCAATTACCACGGC
32864 AATGATGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (24 bp):
GATTATTAATTCAATTACCACGGC
Found at i:47548 original size:14 final size:15
Alignment explanation
Indices: 47529--47561 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
47519 ACGTTTGTGA
*
47529 AAAAAG-AAGAAAAG
1 AAAAAGAAAAAAAAG
47543 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
47558 AAAA
1 AAAA
47562 TGTTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:50076 original size:18 final size:18
Alignment explanation
Indices: 50050--50103 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
50040 TTGTCACCAT
* *
50050 TGTCGTCATTGCCGCCAC
1 TGTCATCATCGCCGCCAC
*
50068 TGTCATCATCGTCGCCAC
1 TGTCATCATCGCCGCCAC
*
50086 TGTCATCATCGTCGCCAC
1 TGTCATCATCGCCGCCAC
50104 CGATATCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.15, C:0.39, G:0.19, T:0.28
Consensus pattern (18 bp):
TGTCATCATCGCCGCCAC
Found at i:50371 original size:22 final size:22
Alignment explanation
Indices: 50346--50387 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
50336 AATTTTTAAC
50346 TAATTTATAA-TTACATGTTTAG
1 TAATTTATAATTTA-ATGTTTAG
*
50368 TAATTTTTAATTTAATGTTT
1 TAATTTATAATTTAATGTTT
50388 TATAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (22 bp):
TAATTTATAATTTAATGTTTAG
Found at i:51343 original size:13 final size:14
Alignment explanation
Indices: 51321--51352 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
51311 GGTATTTGAG
51321 AAAATAAAATATTA
1 AAAATAAAATATTA
51335 AAAAT-AAATATTA
1 AAAATAAAATATTA
51348 AAAAT
1 AAAAT
51353 TAATTAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATAAAATATTA
Found at i:63166 original size:23 final size:23
Alignment explanation
Indices: 63137--63181 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
63127 ATGTATTTAT
*
63137 TAATAATTCTAATTTTCTAAGTC
1 TAATAATTCTAACTTTCTAAGTC
*
63160 TAATAATTTTAACTTTCTAAGT
1 TAATAATTCTAACTTTCTAAGT
63182 ATATTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (23 bp):
TAATAATTCTAACTTTCTAAGTC
Found at i:71562 original size:20 final size:22
Alignment explanation
Indices: 71532--71585 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
71522 TATAAATATA
71532 AAAATAATATTTAT-TAAT-TTT
1 AAAA-AATATTTATATAATATTT
71553 AAAAAATA-TTATATAATATTT
1 AAAAAATATTTATATAATATTT
*
71574 AAAATATATTTA
1 AAAAAATATTTA
71586 CAAATTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.14
20 8 0.28
21 14 0.48
22 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAAAATATTTATATAATATTT
Found at i:71592 original size:19 final size:21
Alignment explanation
Indices: 71550--71592 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
71540 ATTTATTAAT
*
71550 TTTAAAAAATATTATATAATA
1 TTTAAAAAATATTATACAATA
*
71571 TTTAAAATATATT-TACAA-A
1 TTTAAAAAATATTATACAATA
71590 TTT
1 TTT
71593 TCTTATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAAAAATATTATACAATA
Found at i:82196 original size:20 final size:20
Alignment explanation
Indices: 82151--82196 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
82141 GACCAACAAA
*
82151 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
82171 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
82190 ATCGCAA
1 ATCGCAA
82197 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:82287 original size:20 final size:21
Alignment explanation
Indices: 82262--82313 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
82252 TTTTCCCAAT
82262 TCGCAATGCGAATA-AGT-AAA
1 TCGCAATGCGAATAGA-TAAAA
* *
82282 TCGCAACGCGAATTGATAAAA
1 TCGCAATGCGAATAGATAAAA
82303 TCGCAATGCGA
1 TCGCAATGCGA
82314 TACTGACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATAGATAAAA
Found at i:82327 original size:20 final size:20
Alignment explanation
Indices: 82302--82415 Score: 165
Period size: 20 Copynumber: 5.7 Consensus size: 20
82292 AATTGATAAA
*
82302 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
82322 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
82342 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* **
82362 TTTACAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
82382 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
82402 TTCGCAACGAGATA
1 ATCGCAACGCGATA
82416 ATACAGAATC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:82588 original size:12 final size:12
Alignment explanation
Indices: 82569--82598 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
82559 CTCTCTGGCG
82569 ACATCCGTTCCT
1 ACATCCGTTCCT
*
82581 ATATCCGTTCCT
1 ACATCCGTTCCT
82593 ACATCC
1 ACATCC
82599 TTCTCCATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.20, C:0.40, G:0.07, T:0.33
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:82777 original size:20 final size:21
Alignment explanation
Indices: 82747--82788 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
82737 AGACATTCAT
*
82747 TTGACTATCGCAACGCGAAAA
1 TTGACTATCGCAACGAGAAAA
82768 TTGA-TATCGCAACGAGAAAA
1 TTGACTATCGCAACGAGAAAA
82788 T
1 T
82789 CGCAATGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (21 bp):
TTGACTATCGCAACGAGAAAA
Found at i:82831 original size:14 final size:14
Alignment explanation
Indices: 82812--82865 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
82802 GAAAATCGCA
82812 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
82826 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
82843 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
82859 TTGCGAT
1 TTGCGAT
82866 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:82831 original size:33 final size:33
Alignment explanation
Indices: 82794--82864 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
82784 AAAATCGCAA
*
82794 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
82827 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
82860 TGCGA
1 TGCGA
82865 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:83011 original size:14 final size:14
Alignment explanation
Indices: 82992--83028 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
82982 CATCAATTAA
82992 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
83006 ACAAATCATCTTTT
1 ACAAATCAACATTT
83020 ACAAATCAA
1 ACAAATCAA
83029 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:84915 original size:20 final size:19
Alignment explanation
Indices: 84892--84959 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
84882 GAAACTTAAA
84892 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
84912 ATCGGAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
84932 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
84951 ATCGCAACG
1 ATCGCAACG
84960 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:84967 original size:14 final size:14
Alignment explanation
Indices: 84948--85038 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
84938 ATGCGAAATG
84948 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
84962 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
84981 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
84995 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
85011 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
85027 AAAATCTCAACG
1 AAAATCGCAACG
85039 CGAAACATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:85023 original size:32 final size:33
Alignment explanation
Indices: 84932--85043 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
84922 GGAAATGGCT
84932 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
84965 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
84998 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
85030 ATCTCAACGCGAAA
1 ATCGCAATGCGAAA
85044 CATAAATCGC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 28 0.36
33 49 0.64
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:85051 original size:65 final size:66
Alignment explanation
Indices: 84932--85054 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 66
84922 GGAAATGGCT
* *
84932 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
84997 A
66 A
*
84998 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCTCAACGCGAAA-CATAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
85055 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 1 0.02
65 36 0.68
66 16 0.30
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:85072 original size:19 final size:19
Alignment explanation
Indices: 85050--85165 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
85040 GAAACATAAA
85050 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
85069 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
85085 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
85101 TCGTATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
85117 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
***
85134 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCATT
85153 TCCGCATTGCGAT
1 T-CGCATTGCGAT
85166 AGTCATTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 19
0.75 0.08 0.18
Matches are distributed among these distances:
14 15 0.19
15 3 0.04
16 12 0.15
17 4 0.05
18 12 0.15
19 22 0.28
20 11 0.14
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:85091 original size:14 final size:14
Alignment explanation
Indices: 85072--85129 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
85062 TTTCATTTCG
85072 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
85086 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
85102 CGTATTGCGATTTTGT
1 CG--TTGCGATTTTGT
85118 CGTTGCGATTTT
1 CGTTGCGATTTT
85130 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:85136 original size:33 final size:33
Alignment explanation
Indices: 85055--85145 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
85045 ATAAATCGCA
*
85055 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
85088 TTGCGA-TTTCATTTCGTATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
85120 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
85146 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:85184 original size:20 final size:20
Alignment explanation
Indices: 85130--85173 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
85120 TTGCGATTTT
85130 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
85149 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
85169 CATTT
1 CATTT
85174 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:85686 original size:18 final size:18
Alignment explanation
Indices: 85660--85704 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
85650 GTCGATCAGA
* *
85660 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTAGGCGAGG
*
85678 TGATAGCTCTAGGCGAGG
1 TGATGGCTCTAGGCGAGG
85696 TGATGGCTC
1 TGATGGCTC
85705 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:87917 original size:18 final size:18
Alignment explanation
Indices: 87890--87935 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
87880 CTCCACTTCG
* *
87890 AGAGTCATCACCTCGCCC
1 AGAGCCATCACCTCACCC
*
87908 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
87926 AGAGCCATCA
1 AGAGCCATCA
87936 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.41, G:0.15, T:0.15
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:88416 original size:20 final size:20
Alignment explanation
Indices: 88391--88436 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
88381 TAGTTTACTT
88391 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* *
88411 TCGCAACGCGAAAATGGCTA
1 TCGCAACACGAAAATGACTA
88431 TCGCAA
1 TCGCAA
88437 AGCGAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:88441 original size:20 final size:20
Alignment explanation
Indices: 88399--88443 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
88389 TTTCGCAACA
*
88399 CGAAAATGACTATCGCAACG
1 CGAAAATGACTATCGCAAAG
*
88419 CGAAAATGGCTATCGCAAAG
1 CGAAAATGACTATCGCAAAG
88439 CGAAA
1 CGAAA
88444 TAAAAATCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.13
Consensus pattern (20 bp):
CGAAAATGACTATCGCAAAG
Found at i:88525 original size:14 final size:14
Alignment explanation
Indices: 88506--88557 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
88496 TCATTTCTCA
88506 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
88520 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
88537 CTTTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
88553 TTGCG
1 TTGCG
88558 TGTTGCGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 11 0.35
15 3 0.10
16 4 0.13
17 4 0.13
18 3 0.10
19 6 0.19
ACGTcount: A:0.08, C:0.17, G:0.25, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:88527 original size:32 final size:33
Alignment explanation
Indices: 88486--88557 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
88476 TTGTGTTTCG
*
88486 CGTTGCGA-TTTCATTTCTCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
*
88518 CGTTGCGATTTTCATTTCGCTTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
88551 CGTTGCG
1 CGTTGCG
88558 TGTTGCGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
32 8 0.22
33 29 0.78
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.49
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:90394 original size:20 final size:20
Alignment explanation
Indices: 90366--90414 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
90356 GTTGAAGGCA
*
90366 AAACAGACTGTCGCAACACG
1 AAACTGACTGTCGCAACACG
90386 AAACTGACTGTCGCAACACG
1 AAACTGACTGTCGCAACACG
90406 AAACTGACT
1 AAACTGACT
90415 ATTGCAACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (20 bp):
AAACTGACTGTCGCAACACG
Found at i:90421 original size:20 final size:20
Alignment explanation
Indices: 90366--90422 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
90356 GTTGAAGGCA
* *
90366 AAACAGACTGTCGCAACACG
1 AAACTGACTATCGCAACACG
*
90386 AAACTGACTGTCGCAACACG
1 AAACTGACTATCGCAACACG
*
90406 AAACTGACTATTGCAAC
1 AAACTGACTATCGCAAC
90423 GAGAGAATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.28, G:0.18, T:0.16
Consensus pattern (20 bp):
AAACTGACTATCGCAACACG
Found at i:90463 original size:33 final size:33
Alignment explanation
Indices: 90418--90551 Score: 157
Period size: 33 Copynumber: 4.1 Consensus size: 33
90408 ACTGACTATT
*
90418 GCAACGAGAGAATCGCAATGCGAAATGAAAATC
1 GCAACGAAAGAATCGCAATGCGAAATGAAAATC
* * *
90451 ACAACGAAAGAATCGTAATTCGAAATGAAAATC
1 GCAACGAAAGAATCGCAATGCGAAATGAAAATC
*
90484 GCAACGAGAGAATCGC-ATCGCGAAATGAAAATC
1 GCAACGAAAGAATCGCAAT-GCGAAATGAAAATC
* *
90517 GCAAAGACAA-AATCGCAACGCGAAACT-AAAATC
1 GCAACGA-AAGAATCGCAATGCGAAA-TGAAAATC
90550 GC
1 GC
90552 GTTGCGATTT
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
32 2 0.02
33 81 0.94
34 3 0.03
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (33 bp):
GCAACGAAAGAATCGCAATGCGAAATGAAAATC
Found at i:90541 original size:66 final size:66
Alignment explanation
Indices: 90418--90551 Score: 175
Period size: 66 Copynumber: 2.0 Consensus size: 66
90408 ACTGACTATT
* * **
90418 GCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGAAAGAATCGTAATTCGAAA-TGAAAA
1 GCAACGAGAGAATCGCAATGCGAAATGAAAATCACAAAGAAAGAATCGCAACGCGAAACT-AAAA
90482 TC
65 TC
*
90484 GCAACGAGAGAATCGC-ATCGCGAAATGAAAATCGCAAAGACAA-AATCGCAACGCGAAACTAAA
1 GCAACGAGAGAATCGCAAT-GCGAAATGAAAATCACAAAGA-AAGAATCGCAACGCGAAACTAAA
90547 ATC
64 ATC
90550 GC
1 GC
90552 GTTGCGATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
65 2 0.03
66 55 0.92
67 3 0.05
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (66 bp):
GCAACGAGAGAATCGCAATGCGAAATGAAAATCACAAAGAAAGAATCGCAACGCGAAACTAAAAT
C
Found at i:90595 original size:33 final size:33
Alignment explanation
Indices: 90551--90628 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
90541 ACTAAAATCG
*
90551 CGTTGCGATTTTAATTTAGCTTTGCGATT-TACT
1 CGTTGCGATTTTAATTTAGCATTGCGATTCTA-T
* * *
90584 CTTTGCGATTTTCATTTCGCATTGCGATTCTAT
1 CGTTGCGATTTTAATTTAGCATTGCGATTCTAT
90617 CGTTGCGATTTT
1 CGTTGCGATTTT
90629 TGAGACCTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 37 0.95
34 2 0.05
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.49
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTAGCATTGCGATTCTAT
Found at i:91064 original size:94 final size:94
Alignment explanation
Indices: 90952--91140 Score: 315
Period size: 94 Copynumber: 2.0 Consensus size: 94
90942 TTTATTTCAA
* * *
90952 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTTATAGTGTTAAAGAATACACAGTTT
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGATAAAGAATACACAGTTT
*
91017 AGCAGAATTGGCAGCAACCGAACAAATTT
66 AGCAGAATTGACAGCAACCGAACAAATTT
*
91046 ACTTTCAACCAAAAGACAAATCAAAGACAAATACTAACTTCACAGTGATAAAGAATACACAGTTT
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGATAAAGAATACACAGTTT
* *
91111 AGTAGAATTGACAGCAACCGAATAAATTT
66 AGCAGAATTGACAGCAACCGAACAAATTT
91140 A
1 A
91141 TTAAGCAATC
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 88 1.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGATAAAGAATACACAGTTT
AGCAGAATTGACAGCAACCGAACAAATTT
Found at i:92678 original size:20 final size:19
Alignment explanation
Indices: 92647--92735 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 19
92637 TCTTTTGGTT
92647 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
92666 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
92687 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
92706 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
92720 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
92736 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 2 0.04
19 11 0.20
20 29 0.52
21 2 0.04
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:92733 original size:33 final size:34
Alignment explanation
Indices: 92672--92735 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
92662 ACGAGATAAT
**
92672 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGGAAATGAAAATCGCAACGA
92706 GAGAATCGCAACGC-GAAATGAAAATCGCAA
1 GAGAATCGCAACGCGGAAATGAAAATCGCAA
92736 TGCGATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGAAAATCGCAACGA
Found at i:92758 original size:19 final size:19
Alignment explanation
Indices: 92736--92802 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
92726 AAAATCGCAA
* *
92736 TGCGATTTTGGTTTTGCGT
1 TGCGATTTTGATTTCGCGT
*
92755 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
92774 TGCGATAATT-ATTTCCGCGT
1 TGCGAT-TTTGATTT-CGCGT
92794 TGCGATTTT
1 TGCGATTTT
92803 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:93353 original size:20 final size:20
Alignment explanation
Indices: 93328--93541 Score: 182
Period size: 20 Copynumber: 10.6 Consensus size: 20
93318 GCTATGTAAA
93328 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
93348 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
93368 TCGCATTGCGATTTCCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
93389 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
93409 TCGCATTACGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * * *
93429 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACG-TAT
** * *
93450 TCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGT-AT
*
93470 TCGCATTGCGATAGT-CAGTA-
1 TCGCATTGCGAT-TTAC-GTAT
* **
93490 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACGTAT
* *
93511 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACGTAT
93531 TCGCATTGCGA
1 TCGCATTGCGA
93542 ATTGAGAAAA
Statistics
Matches: 156, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
20 111 0.71
21 42 0.27
22 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:93400 original size:41 final size:41
Alignment explanation
Indices: 93326--93541 Score: 199
Period size: 41 Copynumber: 5.3 Consensus size: 41
93316 GCGCTATGTA
93326 AATCGCATTGCGATTTACGT-ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGTAATTCGCATTGCGATTTACGT
* * * *
93366 ATTCGCATTGCGATTTCCCTAATTCGCATTGCGATTTACTT
1 AATCGCATTGCGATTTACGTAATTCGCATTGCGATTTACGT
* * * *
93407 AATCGCATTACGATTTACGT-ATTCGCATTGCGAATTATGAA
1 AATCGCATTGCGATTTACGTAATTCGCATTGCGATTTACG-T
** * * *
93448 AATCGCAACGCGA-ATACGTAAATCGCATTGCGATAGT-CAGT
1 AATCGCATTGCGATTTACGTAATTCGCATTGCGAT-TTAC-GT
* ** * *
93489 -ATCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
1 AATCGCATTGCGATTTACGTAATTCGCATTGCGATTTACGT
*
93529 ATTCGCATTGCGA
1 AATCGCATTGCGA
93542 ATTGAGAAAA
Statistics
Matches: 136, Mismatches: 32, Indels: 15
0.74 0.17 0.08
Matches are distributed among these distances:
40 50 0.37
41 84 0.62
42 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (41 bp):
AATCGCATTGCGATTTACGTAATTCGCATTGCGATTTACGT
Found at i:93423 original size:61 final size:60
Alignment explanation
Indices: 93328--93541 Score: 220
Period size: 61 Copynumber: 3.5 Consensus size: 60
93318 GCTATGTAAA
* *
93328 TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTCCCTAAT
1 TCGCATTGCGATTTACTTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTCCC-AAT
* ** *
93389 TCGCATTGCGATTTACTTAATCGCATTACGATTTACGTATTCGCATTGCGAATTAT-GAAAA
1 TCGCATTGCGATTTACTTAATCGCATTGCGATTTACGTATTCGCATTGCG-ATT-TCCCAAT
** * * *
93450 TCGCAACGCGA-ATACGTAAATCGCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTAC-TTAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGA-TTTCCCAAT
* *
93511 TCGCGTTGCGATTTACTTATTCGCATTGCGA
1 TCGCATTGCGATTTACTTAATCGCATTGCGA
93542 ATTGAGAAAA
Statistics
Matches: 124, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
60 5 0.04
61 108 0.87
62 10 0.08
63 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (60 bp):
TCGCATTGCGATTTACTTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTCCCAAT
Found at i:94102 original size:44 final size:44
Alignment explanation
Indices: 94039--94127 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
94029 TTGGTTACTG
94039 ATCCTAGGGAGCTTGAGAAAATTCGTCAAAGGTGACAAGTCATA
1 ATCCTAGGGAGCTTGAGAAAATTCGTCAAAGGTGACAAGTCATA
94083 ATCCTAGGGAGCTTGAGAAAATTCGTCAAAGGTGACAAGTCATA
1 ATCCTAGGGAGCTTGAGAAAATTCGTCAAAGGTGACAAGTCATA
94127 A
1 A
94128 GCTGTTGTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (44 bp):
ATCCTAGGGAGCTTGAGAAAATTCGTCAAAGGTGACAAGTCATA
Found at i:97070 original size:20 final size:20
Alignment explanation
Indices: 97045--97116 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
97035 AGTTTCCAAT
97045 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* * *
97065 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* *
97085 TTTGCAATGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
97105 TTCGCAACGCGA
1 TTCGCAACGCGA
97117 ACTCTAATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:97128 original size:20 final size:20
Alignment explanation
Indices: 97041--97133 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
97031 ACCCAGTTTC
97041 CAATTTCGCAACGCGATAGT
1 CAATTTCGCAACGCGATAGT
* * * *
97061 CAAATTCGCAACACAAAAGT
1 CAATTTCGCAACGCGATAGT
*
97081 CAAATTT-GCAATGCGATAGT
1 C-AATTTCGCAACGCGATAGT
* *
97101 CAAATTCGCAACGCGA-ACT
1 CAATTTCGCAACGCGATAGT
97120 CTAATTTCGCAACG
1 C-AATTTCGCAACG
97134 TGAATAGTAA
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 7 0.12
20 46 0.81
21 4 0.07
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.23
Consensus pattern (20 bp):
CAATTTCGCAACGCGATAGT
Found at i:97539 original size:20 final size:20
Alignment explanation
Indices: 97500--97619 Score: 118
Period size: 20 Copynumber: 5.8 Consensus size: 20
97490 CAACGCGATT
*
97500 TTGTGATTTT-CTAAATTCGCG
1 TTGTGATTTTACT--ATTCACG
*
97521 TTGTGATTTTACTATTCGCG
1 TTGTGATTTTACTATTCACG
* *
97541 TTATGATTTTACCATTCACG
1 TTGTGATTTTACTATTCACG
97561 TTGCT-ATTTTACTATTCACG
1 TTG-TGATTTTACTATTCACG
*
97581 TTGCGATATTTACTATTCACG
1 TTGTGAT-TTTACTATTCACG
**
97602 TTCCGATTTTTACTATTC
1 TTGTGA-TTTTACTATTC
97620 CCGCTGCGAT
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
20 45 0.52
21 39 0.45
22 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.48
Consensus pattern (20 bp):
TTGTGATTTTACTATTCACG
Found at i:97629 original size:21 final size:21
Alignment explanation
Indices: 97514--97632 Score: 118
Period size: 20 Copynumber: 5.8 Consensus size: 21
97504 GATTTTCTAA
* *
97514 ATTCGCGTTGTGA-TTTTACT
1 ATTCACGTTGCGATTTTTACT
* ** *
97534 ATTCGCGTTATGA-TTTTACC
1 ATTCACGTTGCGATTTTTACT
*
97554 ATTCACGTTGCTA-TTTTACT
1 ATTCACGTTGCGATTTTTACT
*
97574 ATTCACGTTGCGATATTTACT
1 ATTCACGTTGCGATTTTTACT
*
97595 ATTCACGTTCCGATTTTTACT
1 ATTCACGTTGCGATTTTTACT
* *
97616 ATTCCCGCTGCGATTTT
1 ATTCACGTTGCGATTTT
97633 GGAAACTGAG
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
20 45 0.54
21 39 0.46
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.46
Consensus pattern (21 bp):
ATTCACGTTGCGATTTTTACT
Found at i:101923 original size:224 final size:226
Alignment explanation
Indices: 101525--101967 Score: 734
Period size: 224 Copynumber: 2.0 Consensus size: 226
101515 CTATCCTTTT
* *
101525 TATCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTT
1 TATCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTT
**
101590 AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTT
66 AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTT
101655 GTGTAAATGAAATTATTAAATTAATATTGTAGATGGAAAACATGAAACACTATTAAAAAAATTGA
131 GTGTAAATGAAATTATTAAATTAATATTGTAGATGGAAAACATGAAACACTATTAAAAAAATTGA
101720 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTT-AAAAAAGTATA
*
101752 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATC-TTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
101817 TTAATATTGTTAAATTT-AAAT-T-CA-AA-ATTTTATAAAATATCAAAACAATCAAATAAAATT
64 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* * * *
101877 TTGTGTAAATTAAATTATTAAATTAATATTGTTGGTGGAAAACATGAAACACTATTAAATAAATT
129 TTGTGTAAATGAAATTATTAAATTAATATTGTAGATGGAAAACATGAAACACTATTAAAAAAATT
101942 GAAACATAAATTACATAACTTTAAAA
194 GAAACATAAATTACATAACTTTAAAA
101968 GCAGTTTTAA
Statistics
Matches: 204, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
223 4 0.02
224 115 0.56
225 2 0.01
226 1 0.00
227 5 0.02
228 36 0.18
229 41 0.20
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TATCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGATGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:102076 original size:20 final size:19
Alignment explanation
Indices: 102033--102077 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
102023 CGATATACCA
*
102033 GGTAAAAATATGATAAATC
1 GGTAAAAATATGATAAACC
102052 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGAT-AAACC
102072 GGTAAA
1 GGTAAA
102078 TTTAAAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.53, C:0.09, G:0.18, T:0.20
Consensus pattern (19 bp):
GGTAAAAATATGATAAACC
Found at i:104597 original size:33 final size:33
Alignment explanation
Indices: 104555--104620 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
104545 AAATAGATGG
*
104555 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
104588 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
104621 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:105865 original size:23 final size:23
Alignment explanation
Indices: 105839--105902 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
105829 AAAGGTAAAC
*
105839 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
105862 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
105885 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
105903 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:105909 original size:23 final size:23
Alignment explanation
Indices: 105839--105911 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
105829 AAAGGTAAAC
* **
105839 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
105862 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
105885 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
105908 ATAT
1 ATAT
105912 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:112087 original size:35 final size:35
Alignment explanation
Indices: 112016--112087 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
112006 GGATCGTAAC
* *
112016 ACTGACCTTTTAAATACCTTAAGAATGATTGATAT
1 ACTGACCTTTTAAATACCCTAAGAATGATTCATAT
*
112051 ACTGACCTTTTAAATACCCTAAGAATGATTCTTAT
1 ACTGACCTTTTAAATACCCTAAGAATGATTCATAT
112086 AC
1 AC
112088 ATTACTGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (35 bp):
ACTGACCTTTTAAATACCCTAAGAATGATTCATAT
Found at i:112437 original size:28 final size:26
Alignment explanation
Indices: 112379--112437 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
112369 GATTGGGTCA
* * *
112379 TTTTTTAAGTTTGATATTCTAGTTGG
1 TTTTTTAAGTATGATATTCGAGTCGG
*
112405 TTTTTTAAGTATGATATTCGGGTCGAG
1 TTTTTTAAGTATGATATTCGAGTCG-G
112432 TTTTTT
1 TTTTTT
112438 TAAAAATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (26 bp):
TTTTTTAAGTATGATATTCGAGTCGG
Found at i:112454 original size:29 final size:31
Alignment explanation
Indices: 112422--112491 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
112412 AGTATGATAT
*
112422 TCGGGTC-GAGTTTTTTT-AAAAATTTCGAA
1 TCGGGTCGGAGTTTTTTTAAAAAAATTCGAA
*
112451 TCGGGTCGGATTTTTTTTAAAAAAATTCGAA
1 TCGGGTCGGAGTTTTTTTAAAAAAATTCGAA
*
112482 TTCGAGTCGG
1 -TCGGGTCGG
112492 GTCGGGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 7 0.20
30 9 0.26
31 11 0.31
32 8 0.23
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (31 bp):
TCGGGTCGGAGTTTTTTTAAAAAAATTCGAA
Found at i:112475 original size:32 final size:30
Alignment explanation
Indices: 112420--112491 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 30
112410 TAAGTATGAT
112420 ATTCGGGTC-GAGTTTTTTTAAAAATTTCGA
1 ATTCGGGTCGGAGTTTTTTTAAAAA-TTCGA
*
112450 A-TCGGGTCGGATTTTTTTTAAAAAAATTCGA
1 ATTCGGGTCGGAGTTTTTTT--AAAAATTCGA
*
112481 ATTCGAGTCGG
1 ATTCGGGTCGG
112492 GTCGGGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 7 0.19
30 10 0.28
31 6 0.17
32 13 0.36
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (30 bp):
ATTCGGGTCGGAGTTTTTTTAAAAATTCGA
Found at i:112524 original size:33 final size:33
Alignment explanation
Indices: 112481--112566 Score: 111
Period size: 32 Copynumber: 2.6 Consensus size: 33
112471 AAAAATTCGA
* *
112481 ATTCGAGTCGGGTCGGGTTTTTTTAAGTTTGAT
1 ATTCGGGTCGGGTCGGGTTTTTTTAAGTGTGAT
**
112514 ATTCGGGTCGGGTC-GAATTTTTTAAGTGTGAT
1 ATTCGGGTCGGGTCGGGTTTTTTTAAGTGTGAT
*
112546 ATTCGGGTCGGATTCGGGTTT
1 ATTCGGGTCGG-GTCGGGTTT
112567 AGGATGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 26 0.59
33 15 0.34
34 3 0.07
ACGTcount: A:0.15, C:0.10, G:0.33, T:0.42
Consensus pattern (33 bp):
ATTCGGGTCGGGTCGGGTTTTTTTAAGTGTGAT
Found at i:125249 original size:41 final size:42
Alignment explanation
Indices: 125162--125251 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
125152 TTTTCCGTTC
* * *
125162 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCC
1 GTGTTTGTTTCACGTAATTCATTTTCCGGAAAATATTTTCCA
125204 GTGTTTGTTTCACGTAATTCATTTTCC-GAAAATATTTTCCA
1 GTGTTTGTTTCACGTAATTCATTTTCCGGAAAATATTTTCCA
125245 GTGTTTG
1 GTGTTTG
125252 GTTGGAGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 19 0.42
42 26 0.58
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.47
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCATTTTCCGGAAAATATTTTCCA
Found at i:125497 original size:21 final size:21
Alignment explanation
Indices: 125455--125509 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
125445 TCAAATATTA
*
125455 ATTATTAAAATATTTAAAATAT
1 ATTATTAATAT-TTTAAAATAT
*
125477 -TTATTAATATTTCTAATATAT
1 ATTATTAATATTT-TAAAATAT
*
125498 ATTTTTAATATT
1 ATTATTAATATT
125510 ATAATAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTAATATTTTAAAATAT
Found at i:125514 original size:21 final size:23
Alignment explanation
Indices: 125473--125515 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
125463 AATATTTAAA
*
125473 ATATTTATTAATATTTCTAATAT
1 ATATTTATTAATATTTATAATAT
125496 ATATTT-TTAATA-TTATAATA
1 ATATTTATTAATATTTATAATA
125516 AATTAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTTATTAATATTTATAATAT
Found at i:125607 original size:50 final size:48
Alignment explanation
Indices: 125506--125608 Score: 111
Period size: 50 Copynumber: 2.1 Consensus size: 48
125496 ATATTTTTAA
* * *
125506 TATTATAATAAATTAATCAATTATATATAATAATATAAGATATAATTT
1 TATTTTAATAAATTAATAAATTATATATAATAATATAAGATATAATAT
* *
125554 TATTTTAATAATATATAATAAATTATTATATATTTAATA-ATGA-ATAATAT
1 TATTTTAATAA-AT-TAATAAATTA-TATATA-ATAATATAAGATATAATAT
125604 TATTT
1 TATTT
125609 ATATATTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
48 10 0.22
49 2 0.04
50 20 0.43
51 9 0.20
52 5 0.11
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (48 bp):
TATTTTAATAAATTAATAAATTATATATAATAATATAAGATATAATAT
Found at i:125619 original size:28 final size:28
Alignment explanation
Indices: 125527--125620 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 28
125517 ATTAATCAAT
* *
125527 TATATATAATAATATA-AGATATAATTT-
1 TATATTTAATAATATATA-ATATTATTTA
125554 TAT-TTTAATAATATATAATAAATTA-TTA
1 TATATTTAATAATATATAAT--ATTATTTA
125582 TATATTTAATAATGA-ATAATATTATTTA
1 TATATTTAATAAT-ATATAATATTATTTA
125610 TATATTTAATA
1 TATATTTAATA
125621 TTAATCTATA
Statistics
Matches: 58, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
26 13 0.22
27 10 0.17
28 20 0.34
29 14 0.24
30 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TATATTTAATAATATATAATATTATTTA
Found at i:126039 original size:34 final size:34
Alignment explanation
Indices: 125971--126039 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
125961 ATGTTTTCAG
* **
125971 AAAAATGTAATTCATTTTTCGGAAAACATTTTCC
1 AAAAATGTAATTCATTTTTCAGAAAACAAATTCC
**
126005 AAAAATGTAATTCATTTTTCAGAATTCAAATTCC
1 AAAAATGTAATTCATTTTTCAGAAAACAAATTCC
126039 A
1 A
126040 GTAATTCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (34 bp):
AAAAATGTAATTCATTTTTCAGAAAACAAATTCC
Found at i:126044 original size:29 final size:29
Alignment explanation
Indices: 126011--126069 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
126001 TTCCAAAAAT
126011 GTAATTCATTTTTCAGAATTCAAATTCCA
1 GTAATTCATTTTTCAGAATTCAAATTCCA
* * *
126040 GTAATTCATTTTTCATAATTTAATTTCCA
1 GTAATTCATTTTTCAGAATTCAAATTCCA
126069 G
1 G
126070 AAAACCAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (29 bp):
GTAATTCATTTTTCAGAATTCAAATTCCA
Done.