Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006787.1 Hibiscus syriacus cultivar Beakdansim tig00017203_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: 72159
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6992 original size:20 final size:21
Alignment explanation
Indices: 6934--6992 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
6924 CAGAACCTGT
*
6934 GGGGGTATCGATTCCC-TCAA
1 GGGGGTATCAATTCCCTTCAA
* *
6954 GGAGGGAATCAGTTCCCCTTCAA
1 GG-GGGTATCAATT-CCCTTCAA
6977 -GGGGTATCAATTCCCT
1 GGGGGTATCAATTCCCT
6993 CTGCCCTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 6 0.19
21 17 0.55
22 4 0.13
23 4 0.13
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (21 bp):
GGGGGTATCAATTCCCTTCAA
Found at i:7539 original size:5 final size:5
Alignment explanation
Indices: 7529--7554 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
7519 TTAAGGTTTC
7529 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
7555 ATATATGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:12923 original size:20 final size:21
Alignment explanation
Indices: 12876--12929 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
12866 AAACCATTCA
* *
12876 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACACCATT-G
12898 GGGGGAATCGGTACACCATT-
1 GGGGGAATCGGTACACCATTG
12918 GGGGGAATCGGT
1 GGGGGAATCGGT
12930 TCCCTCTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.19, C:0.20, G:0.43, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACACCATTG
Found at i:13544 original size:21 final size:21
Alignment explanation
Indices: 13510--13563 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
13500 CACAACAGCT
* * *
13510 GATTCTGATTCCATATCCGCC
1 GATTCAGATGCCATACCCGCC
13531 GATTCAGATGCCATACCCGCC
1 GATTCAGATGCCATACCCGCC
*
13552 TATTCAGATGCC
1 GATTCAGATGCC
13564 TCCACTGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (21 bp):
GATTCAGATGCCATACCCGCC
Found at i:17092 original size:16 final size:16
Alignment explanation
Indices: 17071--17105 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17061 TAAAAGCCAT
17071 TTTGAGAATTTGAAAG
1 TTTGAGAATTTGAAAG
* *
17087 TTTGAGAGTTTGATAG
1 TTTGAGAATTTGAAAG
17103 TTT
1 TTT
17106 CAGAGTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (16 bp):
TTTGAGAATTTGAAAG
Found at i:17110 original size:16 final size:16
Alignment explanation
Indices: 17079--17112 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17069 ATTTTGAGAA
*
17079 TTTGAAAGTTTGAGAG
1 TTTGAAAGTTTCAGAG
*
17095 TTTGATAGTTTCAGAG
1 TTTGAAAGTTTCAGAG
17111 TT
1 TT
17113 ATGGAGTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.44
Consensus pattern (16 bp):
TTTGAAAGTTTCAGAG
Found at i:26537 original size:65 final size:65
Alignment explanation
Indices: 26433--26576 Score: 200
Period size: 65 Copynumber: 2.2 Consensus size: 65
26423 TTCAAAAATT
*
26433 CTTTGAATTATGGGCAATTTCATCCCTACTTTTAGCAAAGACCTTGGTACCACCTT-GACGCTTA
1 CTTTGAATTATGGGCAACTTCATCCCTACTTTTAGCAAAGACCTTGGTACCA-CTTCGACGCTTA
26497 C
65 C
* ** * *
26498 CTTTGAATTGTGGGCAACTTCATCTTTGCTTTTAGCAAAGACCTTGGTACCACTTCGACGCTTAT
1 CTTTGAATTATGGGCAACTTCATCCCTACTTTTAGCAAAGACCTTGGTACCACTTCGACGCTTAC
**
26563 CGCTGAATTATGGG
1 CTTTGAATTATGGG
26577 ATATTAGCGA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 3 0.04
65 66 0.96
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (65 bp):
CTTTGAATTATGGGCAACTTCATCCCTACTTTTAGCAAAGACCTTGGTACCACTTCGACGCTTAC
Found at i:28467 original size:14 final size:14
Alignment explanation
Indices: 28448--28477 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28438 TTAAATGATA
28448 AACGAACACAAATG
1 AACGAACACAAATG
*
28462 AACGAACATAAATG
1 AACGAACACAAATG
28476 AA
1 AA
28478 TGGGTCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:38896 original size:24 final size:24
Alignment explanation
Indices: 38864--38951 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
38854 GATATCAGAA
*
38864 ATCAAAACAGAATTCAGATAAGAT
1 ATCAGAACAGAATTCAGATAAGAT
* * * *
38888 ATCAGAACATAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATAAGAT
*
38912 ATCAGAACAGAATTCAGGTAATG-T
1 ATCAGAACAGAATTCAGATAA-GAT
*
38936 ATCATAACAGAATTCA
1 ATCAGAACAGAATTCA
38952 AGTCGAAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 51 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATAAGAT
Found at i:38917 original size:12 final size:12
Alignment explanation
Indices: 38859--38928 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
38849 ACGGAGATAT
*
38859 CAGAAATCAAAA
1 CAGAAATCAGAA
*
38871 CAGAATTCAGATA
1 CAGAAATCAGA-A
*
38884 -AGATATCAGAA
1 CAGAAATCAGAA
* *
38895 CA-TAATCCAGAT
1 CAGAAAT-CAGAA
38907 CAGAAATCAGAA
1 CAGAAATCAGAA
*
38919 CAGAATTCAG
1 CAGAAATCAG
38929 GTAATGTATC
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
11 3 0.07
12 37 0.84
13 4 0.09
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:38962 original size:48 final size:48
Alignment explanation
Indices: 38857--38965 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
38847 AAACGGAGAT
* * *
38857 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACATAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
* *
38905 ATCAGAAATCAGAACAGAATTCAGGTAATG-TATCATAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAA-TCAAG
38954 -TC-GAAAATCAGA
1 ATCAG-AAATCAGA
38966 TAAAATATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
47 1 0.02
48 47 0.89
49 5 0.09
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
Found at i:41604 original size:16 final size:17
Alignment explanation
Indices: 41574--41606 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41564 AAACCGATCC
41574 AAAAAACCGATAACCGA
1 AAAAAACCGATAACCGA
*
41591 AAAAAATCGA-AACCGA
1 AAAAAACCGATAACCGA
41607 TTTAGTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.21, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAACCGATAACCGA
Found at i:42838 original size:23 final size:23
Alignment explanation
Indices: 42806--42851 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42796 TTGGTTCGTC
*
42806 GATCGAAGGTCGGACGACGAGTA
1 GATCGAAGGTCAGACGACGAGTA
* *
42829 GATCGGAGGTCAGACGGCGAGTA
1 GATCGAAGGTCAGACGACGAGTA
42852 TATCATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.41, T:0.13
Consensus pattern (23 bp):
GATCGAAGGTCAGACGACGAGTA
Found at i:44346 original size:22 final size:22
Alignment explanation
Indices: 44320--44365 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
44310 TATACTAGAT
*
44320 AATCTATTATATATTCCTGTAA
1 AATCTAGTATATATTCCTGTAA
44342 AATCTAGTATATATTCCTGTAA
1 AATCTAGTATATATTCCTGTAA
44364 AA
1 AA
44366 CCAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (22 bp):
AATCTAGTATATATTCCTGTAA
Found at i:49158 original size:14 final size:13
Alignment explanation
Indices: 49128--49178 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
49118 TAAAACATAT
*
49128 TAAATATTAAATAA
1 TAAATA-TAATTAA
49142 TAAATATAATTATA
1 TAAATATAATTA-A
*
49156 TAATTATAATTAA
1 TAAATATAATTAA
*
49169 AAAATA-AATT
1 TAAATATAATT
49179 TGGGGTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 10 0.31
14 18 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAATATAATTAA
Found at i:61646 original size:16 final size:16
Alignment explanation
Indices: 61625--61661 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
61615 TCGAAGTTTC
61625 TTTTCCTTTTGATTTA
1 TTTTCCTTTTGATTTA
*
61641 TTTTCCTTTTGATTTC
1 TTTTCCTTTTGATTTA
61657 TTTTC
1 TTTTC
61662 AAGTTCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTTCCTTTTGATTTA
Found at i:65844 original size:20 final size:20
Alignment explanation
Indices: 65808--65845 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
65798 ATCTTATTCC
*
65808 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTTCATTCCCA
65828 CTGATAAT-TTTACATTCC
1 CTGATAATCTTT-CATTCC
65846 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (20 bp):
CTGATAATCTTTCATTCCCA
Found at i:67637 original size:20 final size:20
Alignment explanation
Indices: 67614--67663 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
67604 GCAAATTTGG
* *
67614 AATTCGCAAGACAGAAGTCA
1 AATTCGCAACACAAAAGTCA
67634 AATTCGCAACACAAAAGTCA
1 AATTCGCAACACAAAAGTCA
67654 AATTCGCAAC
1 AATTCGCAAC
67664 TCGATTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (20 bp):
AATTCGCAACACAAAAGTCA
Found at i:67761 original size:20 final size:19
Alignment explanation
Indices: 67677--67789 Score: 93
Period size: 20 Copynumber: 5.7 Consensus size: 19
67667 ATTTTGACAA
*
67677 TTTCGTAACAC-ATATTTCTT
1 TTTCGCAACACGAT-TTT-TT
* *
67697 TTTCACAACACGATTTTTAA
1 TTTCGCAACACGATTTTT-T
* *
67717 TTTCGCAACTCGATTTTTGA
1 TTTCGCAACACGATTTTT-T
*
67737 ATTCGCAACACGAATTTTTT
1 TTTCGCAACACG-ATTTTTT
* *
67757 TTTCGCAACTCGATATTCTT
1 TTTCGCAACACGAT-TTTTT
67777 TTTCGCAACACGA
1 TTTCGCAACACGA
67790 ATTGTTTGGG
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
19 3 0.04
20 65 0.86
21 8 0.11
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.42
Consensus pattern (19 bp):
TTTCGCAACACGATTTTTT
Found at i:67781 original size:60 final size:60
Alignment explanation
Indices: 67656--67785 Score: 142
Period size: 60 Copynumber: 2.1 Consensus size: 60
67646 AAAAGTCAAA
*
67656 TTCGCAACTCGATTTTGACAATTTCGTAACACATATTTCTTTTTCACAACACGATTTTTAAT
1 TTCGCAACTCGATTTTGA-AATTTCGCAACACATATTTCTTTTTCACAACACGATTTTT-AT
* * *
67718 TTCGCAACTCGATTTTTG-AA-TTCGCAACACGA-ATTTTTTTTTCGCAACTCGATATTCTT-T
1 TTCGCAACTCGA-TTTTGAAATTTCGCAACAC-ATATTTCTTTTTCACAACACGAT-TT-TTAT
67778 TTCGCAAC
1 TTCGCAAC
67786 ACGAATTGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
60 36 0.60
61 5 0.08
62 14 0.23
63 5 0.08
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (60 bp):
TTCGCAACTCGATTTTGAAATTTCGCAACACATATTTCTTTTTCACAACACGATTTTTAT
Found at i:67782 original size:40 final size:40
Alignment explanation
Indices: 67690--67792 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
67680 CGTAACACAT
*
67690 ATTTCTTTTTCACAACACG-ATTTTTAATTTCGCAACTCG
1 ATTTCTTTTTCGCAACACGAATTTTTAATTTCGCAACTCG
* *
67729 ATTT-TTGAATTCGCAACACGAATTTTT-TTTTCGCAACTCG
1 ATTTCTT--TTTCGCAACACGAATTTTTAATTTCGCAACTCG
67769 ATATTCTTTTTCGCAACACGAATT
1 AT-TTCTTTTTCGCAACACGAATT
67793 GTTTGGGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
38 2 0.04
39 4 0.07
40 39 0.71
41 8 0.15
42 2 0.04
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (40 bp):
ATTTCTTTTTCGCAACACGAATTTTTAATTTCGCAACTCG
Found at i:68728 original size:24 final size:24
Alignment explanation
Indices: 68701--68747 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
68691 AGTCAGTATT
68701 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
*
68725 CGAACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
68748 TCAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:68759 original size:24 final size:24
Alignment explanation
Indices: 68706--68752 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
68696 GTATTCGAAA
*
68706 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCAGAAC
68730 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTGGTCAATAC-CAGA
68753 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGAAC
Found at i:68977 original size:3 final size:3
Alignment explanation
Indices: 68934--68962 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
68924 ATATAACCCT
68934 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
68963 GTCCCAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:71016 original size:21 final size:20
Alignment explanation
Indices: 70992--71062 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 20
70982 ATGTGGATCC
70992 TGAACGATGGGAGGGGATTCT
1 TGAACGATGGGAGGGG-TTCT
*
71013 TGAACGATGGGAGGAGGCTCT
1 TGAACGATGGGAGG-GGTTCT
*
71034 TGAACGATGGGATGGGTCTCT
1 TGAACGATGGGAGGGGT-TCT
71055 TGAACGAT
1 TGAACGAT
71063 AAGAGCTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 2 0.04
21 41 0.91
22 2 0.04
ACGTcount: A:0.24, C:0.13, G:0.39, T:0.24
Consensus pattern (20 bp):
TGAACGATGGGAGGGGTTCT
Found at i:71079 original size:21 final size:21
Alignment explanation
Indices: 71055--71104 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
71045 ATGGGTCTCT
*
71055 TGAACGATAAGAGCTGAATCC
1 TGAACAATAAGAGCTGAATCC
** *
71076 TGAACAATGGGAGGTGAATCC
1 TGAACAATAAGAGCTGAATCC
71097 TGAACAAT
1 TGAACAAT
71105 GGTAGGTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (21 bp):
TGAACAATAAGAGCTGAATCC
Found at i:71080 original size:42 final size:42
Alignment explanation
Indices: 70988--71089 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
70978 TTGAATGTGG
** * *
70988 ATCCTGAACGATGGGAGGGGATTCTTGAACGATGGGAGGAGG
1 ATCCTGAACGATGGGAGGGGATTCTTGAACGATAAGAGCAGA
* * * *
71030 CTCTTGAACGATGGGATGGG-TCTCTTGAACGATAAGAGCTGA
1 ATCCTGAACGATGGGAGGGGAT-TCTTGAACGATAAGAGCAGA
*
71072 ATCCTGAACAATGGGAGG
1 ATCCTGAACGATGGGAGG
71090 TGAATCCTGA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (42 bp):
ATCCTGAACGATGGGAGGGGATTCTTGAACGATAAGAGCAGA
Found at i:71105 original size:21 final size:21
Alignment explanation
Indices: 71069--71112 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
71059 CGATAAGAGC
71069 TGAATCCTGAACAATGGGAGG
1 TGAATCCTGAACAATGGGAGG
*
71090 TGAATCCTGAACAATGGTAGG
1 TGAATCCTGAACAATGGGAGG
71111 TG
1 TG
71113 GATCAGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.23
Consensus pattern (21 bp):
TGAATCCTGAACAATGGGAGG
Found at i:71446 original size:21 final size:20
Alignment explanation
Indices: 71422--71505 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 20
71412 CCTCGTCACA
71422 TAAAACAACTACCTCACCACG
1 TAAAAC-ACTACCTCACCACG
* ** *
71443 TAAAACACCATTGTCATCACG
1 TAAAACACTA-CCTCACCACG
71464 TAAAACAACTACCTCACCACG
1 TAAAAC-ACTACCTCACCACG
* *
71485 TAAAGACCCTACCTCATCACG
1 TAAA-ACACTACCTCACCACG
71506 CCATGCATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
20 3 0.06
21 42 0.84
22 5 0.10
ACGTcount: A:0.39, C:0.36, G:0.07, T:0.18
Consensus pattern (20 bp):
TAAAACACTACCTCACCACG
Found at i:71505 original size:42 final size:41
Alignment explanation
Indices: 71397--71505 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 41
71387 GAAATAATCT
* * * *
71397 CACGTAGAGCACCGACCTCGTCACATAAAACAACTACCTCAC
1 CACGTAAAACACC-ACCTCATCACGTAAAACAACTACCTCAC
**
71439 CACGTAAAACACCATTGTCATCACGTAAAACAACTACCTCAC
1 CACGTAAAACACCA-CCTCATCACGTAAAACAACTACCTCAC
71481 CACGTAAAGAC-CCTACCTCATCACG
1 CACGTAAA-ACACC-ACCTCATCACG
71506 CCATGCATCA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 52 0.93
43 3 0.05
ACGTcount: A:0.37, C:0.37, G:0.10, T:0.17
Consensus pattern (41 bp):
CACGTAAAACACCACCTCATCACGTAAAACAACTACCTCAC
Done.