Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006695.1 Hibiscus syriacus cultivar Beakdansim tig00016655_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: 127750
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1557 original size:14 final size:14
Alignment explanation
Indices: 1538--1567 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1528 TCAATACCTT
1538 TTTGCATACATACA
1 TTTGCATACATACA
*
1552 TTTGCATACATTCA
1 TTTGCATACATACA
1566 TT
1 TT
1568 ATTCATTTCA
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:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTGCATACATACA
Found at i:8882 original size:1 final size:1
Alignment explanation
Indices: 8876--8933 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
8866 ATGCTTGAAG
* * * * * * *
8876 AAAAAAAAAAGAAAAAAAGAAAGAAACAAAAAAGAAAAAAAAGAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8934 GGGGGTCAAG
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.02, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:8892 original size:8 final size:8
Alignment explanation
Indices: 8879--8933 Score: 67
Period size: 8 Copynumber: 6.8 Consensus size: 8
8869 CTTGAAGAAA
8879 AAAAAAAG
1 AAAAAAAG
8887 AAAAAAAG
1 AAAAAAAG
*
8895 AAAGAAA-
1 AAAAAAAG
*
8902 CAAAAAAG
1 AAAAAAAG
8910 AAAAAAAAG
1 -AAAAAAAG
8919 AAAAAAAAG
1 -AAAAAAAG
8928 AAAAAA
1 AAAAAA
8934 GGGGGTCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 5 0.12
8 20 0.49
9 16 0.39
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:8892 original size:9 final size:9
Alignment explanation
Indices: 8878--8933 Score: 67
Period size: 9 Copynumber: 5.7 Consensus size: 9
8868 GCTTGAAGAA
8878 AAAAAAAAG
1 AAAAAAAAG
8887 AAAAAAAGAAAG
1 --AAAAA-AAAG
8899 AAACAAAAAAG
1 -AA-AAAAAAG
8910 AAAAAAAAG
1 AAAAAAAAG
8919 AAAAAAAAG
1 AAAAAAAAG
8928 AAAAAA
1 AAAAAA
8934 GGGGGTCAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
9 22 0.51
10 2 0.05
11 12 0.28
12 7 0.16
ACGTcount: A:0.88, C:0.02, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:8906 original size:23 final size:24
Alignment explanation
Indices: 8873--8934 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
8863 ATTATGCTTG
8873 AAGAAAAAAAAAAG-AAAAAAAGA
1 AAGAAAAAAAAAAGAAAAAAAAGA
*
8896 AAGAAACAAAAAAGAAAAAAAAGA
1 AAGAAAAAAAAAAGAAAAAAAAGA
*
8920 AAAAAAAGAAAAAAG
1 AAGAAAA-AAAAAAG
8935 GGGGTCAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 13 0.38
24 14 0.41
25 7 0.21
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (24 bp):
AAGAAAAAAAAAAGAAAAAAAAGA
Found at i:8908 original size:15 final size:14
Alignment explanation
Indices: 8876--8933 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
8866 ATGCTTGAAG
8876 AAAAAAA-AAAG--
1 AAAAAAAGAAAGAA
8887 AAAAAAAGAAAGAA
1 AAAAAAAGAAAGAA
8901 ACAAAAAAGAAA-AA
1 A-AAAAAAGAAAGAA
*
8915 AAAGAAAAAAAAGAA
1 AAA-AAAAGAAAGAA
8930 AAAA
1 AAAA
8934 GGGGGTCAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 7 0.17
12 4 0.10
13 2 0.05
14 12 0.30
15 15 0.38
ACGTcount: A:0.88, C:0.02, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAGAA
Found at i:8933 original size:11 final size:11
Alignment explanation
Indices: 8873--8926 Score: 76
Period size: 11 Copynumber: 5.0 Consensus size: 11
8863 ATTATGCTTG
8873 AAGAAAAAAAA
1 AAGAAAAAAAA
8884 AAGAAAAAAAGA
1 AAGAAAAAAA-A
*
8896 AAGAAACAAAA
1 AAGAAAAAAAA
8907 AAG--AAAAAA
1 AAGAAAAAAAA
8916 AAGAAAAAAAA
1 AAGAAAAAAAA
8927 GAAAAAAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 8 0.21
11 20 0.53
12 10 0.26
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:10415 original size:113 final size:114
Alignment explanation
Indices: 10210--10437 Score: 359
Period size: 113 Copynumber: 2.0 Consensus size: 114
10200 AGCAAGTACC
*
10210 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATATTATGGAAGTGTTCTTTGAGTTATCTG
* * * * * * *
10275 ATCTGGTTTGGTATGAACCCCAAAACCAATTATTGGATTTGAAAGATGA
66 ATCTGGTTCGGTAGGAACCACAAAACCAATCATTAGAATTAAAAGATGA
*
10324 ATGTGCTCATAGTAGAAAT-AGAAGACCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTG
1 ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATATTATGGAAGTGTTCTTTGAGTTATCTG
*
10388 ATCTGGTTCGGTAGGAACCACAGAACCAATCATTAGAATTAAAAGATGA
66 ATCTGGTTCGGTAGGAACCACAAAACCAATCATTAGAATTAAAAGATGA
10437 A
1 A
10438 CTGCATGATC
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
113 85 0.82
114 19 0.18
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (114 bp):
ATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATATTATGGAAGTGTTCTTTGAGTTATCTG
ATCTGGTTCGGTAGGAACCACAAAACCAATCATTAGAATTAAAAGATGA
Found at i:11512 original size:113 final size:114
Alignment explanation
Indices: 11122--11744 Score: 1123
Period size: 113 Copynumber: 5.5 Consensus size: 114
11112 TAGCAAAGAT
* *
11122 TCAAATCCATCATTTGATGGATCAACTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAAGTTCATAATGAGAAGAACTCATCTG
11187 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
11236 TC-AATCCATCATTTGATGGATCAGTTTTTCCAGAG-AAAGTTCATAATGAGAATAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAAGTTCATAATGAGAAGAACTCATCTG
*
11299 AAGAA-GAAGAAGAAATTCATAATGAGAAGAAGTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
11347 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAAGTTCATAATGAGAAGAACTCATCTG
*
11412 AAGAAGGAAAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
11461 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAA-TTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAAGTTCATAATGAGAAGAACTCATCTG
11525 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
11574 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAAGTTCATAATGAGAAGAACTCATCTG
11638 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
11687 TCAAATCCATCATTTGATGGATCAACCTTTCCAGA-AAAAGTTCATAATGAGAAGAACT
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAAGTTCATAATGAGAAGAACT
11745 TGTTCAACTT
Statistics
Matches: 490, Mismatches: 14, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
111 44 0.09
112 66 0.13
113 298 0.61
114 82 0.17
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (114 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:11773 original size:73 final size:73
Alignment explanation
Indices: 11646--11783 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 73
11636 TGAAGAAGGA
* **
11646 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
1 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
11711 ACCTTTCC
66 ACCTTTCC
* ** *
11719 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATC
1 AGAAGAAA-TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
11783 A
65 A
11784 GCATTACCAG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 3 0.05
73 54 0.95
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (73 bp):
AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
ACCTTTCC
Found at i:11773 original size:186 final size:186
Alignment explanation
Indices: 11533--11930 Score: 573
Period size: 186 Copynumber: 2.1 Consensus size: 186
11523 TGAAGAAGGA
* **
11533 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
* * *
11597 AGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
65 AGCATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
*
11662 GAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACCTTTCC
130 GAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCC
* ** *
11719 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
**** *
11784 GCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 GCATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * *
11849 AGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTTCC
131 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCC
** *
11905 AGGTAGAGTTCATAATGAGAAGAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
11931 CGTCATCTGA
Statistics
Matches: 188, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
185 3 0.02
186 185 0.98
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (186 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
GCATTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCC
Found at i:11802 original size:73 final size:73
Alignment explanation
Indices: 11646--11817 Score: 193
Period size: 73 Copynumber: 2.4 Consensus size: 73
11636 TGAAGAAGGA
* **
11646 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATC
* *
11710 AACCTTTCC
65 AACATTACC
* ** *
11719 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
*
11784 GCATTACC
66 ACATTACC
**** *
11792 AGTTCGAGTTCATAATAAGAAGAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
11818 CATCTGAAGA
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 3 0.04
73 80 0.96
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (73 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCA
ACATTACC
Found at i:11806 original size:299 final size:298
Alignment explanation
Indices: 11428--12042 Score: 910
Period size: 299 Copynumber: 2.1 Consensus size: 298
11418 GAAAAAGAAA
* ** * *
11428 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACC
*
11493 AGAGAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
66 AGAGAAAATTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
* *
11558 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAAT
131 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCCAG-GTAAAGTTCATAAT
11622 GAGAAGAACTCATC-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
195 GAGAAGAACTCATCAT-AAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
11686 CTCAAATCCATCATTTGATGGATCAACCTTTCCAGAAAAAG
258 CTCAAATCCATCACTTGATGGATCAACCTTTCCAGAAAAAG
* ** *
11727 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTACC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACC
**** * *
11792 AGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
66 AGAGAAAATTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
* * * * *
11857 TTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTTCCAGGTAGAGTTCATAATG
131 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCCAGGTAAAGTTCATAATG
* ** *
11922 AGAAGAACTCGTCATCTGAAGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
196 AGAAGAACTCATCATAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
11987 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAG
261 AAATCCATCACTTGATGGATCAACCTTTCCAGAAAAAG
12025 TTCATAATGAGAAGAACT
1 TTCATAATGAGAAGAACT
12043 CATCTGAAGA
Statistics
Matches: 283, Mismatches: 31, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
298 97 0.34
299 185 0.65
300 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (298 bp):
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACC
AGAGAAAATTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACATTTCCAGGTAAAGTTCATAATG
AGAAGAACTCATCATAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
AAATCCATCACTTGATGGATCAACCTTTCCAGAAAAAG
Found at i:11847 original size:113 final size:111
Alignment explanation
Indices: 11719--12213 Score: 455
Period size: 113 Copynumber: 4.4 Consensus size: 111
11709 CAACCTTTCC
* * * *
11719 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATT-GATGGATCA
* * * *
11784 GCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
65 GCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
* * *
11832 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCA
* *
11897 ACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGA
65 GCATTTCCAGATAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGA
* * * *
11947 A-TA-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCA
* * *
12009 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAGA
65 GCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
* * * * * *
12053 AGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTACATAATTTTATCACAGAAGATAT-A
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCAT--C-----AT-TGA
* * * * * *
12117 TTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAA
58 -T-GGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG-A
* * * *
12174 AGAAAAAGTTCATAATGAGAGGAGCTTATTCAACCTTTTG
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
12214 AATGACTCTA
Statistics
Matches: 319, Mismatches: 42, Indels: 34
0.81 0.11 0.09
Matches are distributed among these distances:
106 6 0.02
107 1 0.00
108 2 0.01
109 40 0.13
110 1 0.00
111 1 0.00
112 79 0.25
113 84 0.26
114 3 0.01
115 6 0.02
116 15 0.05
117 42 0.13
120 3 0.01
121 36 0.11
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (111 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTGATGGATCAG
CATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
Found at i:11975 original size:20 final size:20
Alignment explanation
Indices: 11911--11975 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
11901 TTCCAGGTAG
*
11911 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAATT
* * *
11931 CG-TCAT-CTGAAGAAGAATA
1 AGTTCATAATG-AGAAGAATT
*
11950 AATTCATAATGAGAAGAATT
1 AGTTCATAATGAGAAGAATT
*
11970 TGTTCA
1 AGTTCA
11976 ACCTTTTGCT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 17 0.53
21 2 0.06
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAATT
Found at i:11996 original size:112 final size:109
Alignment explanation
Indices: 11719--12091 Score: 462
Period size: 113 Copynumber: 3.4 Consensus size: 109
11709 CAACCTTTCC
* * **
11719 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA
* * * *
11784 GCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGA
66 GCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
11828 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGG
1 A-G-A-AA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGG
* *
11893 ATTAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
62 ATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* * * *
11944 AGAATAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
1 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATC
* *
12008 AGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGA
65 AGCATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
12053 AGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTT
1 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
12092 ACATAATTTT
Statistics
Matches: 230, Mismatches: 24, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
108 2 0.01
109 44 0.19
110 2 0.01
111 1 0.00
112 81 0.35
113 84 0.37
114 2 0.01
115 2 0.01
116 12 0.05
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (109 bp):
AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGGATCA
GCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
Found at i:12229 original size:121 final size:123
Alignment explanation
Indices: 12012--12301 Score: 357
Period size: 121 Copynumber: 2.4 Consensus size: 123
12002 TGGATCAGCT
*
12012 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG---AAG-AAGAAGAAGTTCACAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCACAATGAGA
* * * * * *
12073 AGAGCTTGTTCAACCTTTTACATAATTTTATCACAGAA-GATATA-TTAGCATCAACC
66 AGAGCTTATTCAACCTTTTACATAACTCTATCACAGAAGGAAATAGTCAACATCAACC
*
12129 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCACAATGAGA
* * *
12194 GGAGCTTATTCAACCTTTTGA-ATGACTCTATCACAGAAGGAAATAGGTCAACATCATCC
66 AGAGCTTATTCAACCTTTT-ACATAACTCTATCACAGAAGGAAATA-GTCAACATCAACC
*
12253 ---CCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAA-AAAGA-AAGAA
12302 TTTATTCAAC
Statistics
Matches: 150, Mismatches: 12, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
117 37 0.25
120 3 0.02
121 54 0.36
122 37 0.25
123 5 0.03
124 14 0.09
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (123 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAAAAGTTCACAATGAGA
AGAGCTTATTCAACCTTTTACATAACTCTATCACAGAAGGAAATAGTCAACATCAACC
Found at i:12453 original size:3 final size:3
Alignment explanation
Indices: 12445--12497 Score: 61
Period size: 3 Copynumber: 16.3 Consensus size: 3
12435 TTTTTATTTA
*
12445 ATT ATT ATT ATT AATA ATT ATT ATT ATAT ATAT ATTT ATT ATT ATT ATT
1 ATT ATT ATT ATT -ATT ATT ATT ATT AT-T AT-T A-TT ATT ATT ATT ATT
12494 ATT A
1 ATT A
12498 AAAAAATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 34 0.76
4 10 0.22
5 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:12480 original size:24 final size:22
Alignment explanation
Indices: 12445--12498 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 22
12435 TTTTTATTTA
12445 ATTATTATTATTAATAATTATT
1 ATTATTATTATTAATAATTATT
*
12467 ATTA-TA-TA-T-ATATTTATT
1 ATTATTATTATTAATAATTATT
12485 ATTATTATTATTAA
1 ATTATTATTATTAA
12499 AAAAATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 12 0.44
19 3 0.11
20 4 0.15
21 3 0.11
22 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTATTATTATTAATAATTATT
Found at i:16933 original size:30 final size:31
Alignment explanation
Indices: 16891--16975 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
16881 AAATTATATA
*
16891 TTTAATATCTAAATTATTAATTTTGATC-AGT
1 TTTAATACCTAAATTATTAATTTTGATCTA-T
* *
16922 TTTAATA-CTAAACTATTAATTATGATCTAT
1 TTTAATACCTAAATTATTAATTTTGATCTAT
*
16952 TTTAGTACCTAAACTT-TTAATTTT
1 TTTAATACCTAAA-TTATTAATTTT
16976 TTAAAAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 25 0.54
31 20 0.43
32 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTAATACCTAAATTATTAATTTTGATCTAT
Found at i:27418 original size:14 final size:14
Alignment explanation
Indices: 27399--27428 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
27389 TTAGGTGTTT
27399 TGATTTAAGTCTTA
1 TGATTTAAGTCTTA
27413 TGATTTAAGTCTTA
1 TGATTTAAGTCTTA
27427 TG
1 TG
27429 TTCTTCAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (14 bp):
TGATTTAAGTCTTA
Found at i:45908 original size:93 final size:93
Alignment explanation
Indices: 45749--45932 Score: 359
Period size: 93 Copynumber: 2.0 Consensus size: 93
45739 TAGGGTTTAA
*
45749 AATTTTTTCATTATCGATTTCGTTGAAAGTTAGAGGAGATCATCGCCGTTAATGAAAGAATCATG
1 AATTTTTTCATTATCGATTTCGTTGAAAATTAGAGGAGATCATCGCCGTTAATGAAAGAATCATG
45814 TGTTTTTGAATAAATAAATAAATAAAAT
66 TGTTTTTGAATAAATAAATAAATAAAAT
45842 AATTTTTTCATTATCGATTTCGTTGAAAATTAGAGGAGATCATCGCCGTTAATGAAAGAATCATG
1 AATTTTTTCATTATCGATTTCGTTGAAAATTAGAGGAGATCATCGCCGTTAATGAAAGAATCATG
45907 TGTTTTTGAATAAATAAATAAATAAA
66 TGTTTTTGAATAAATAAATAAATAAA
45933 TAAAAGATAC
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (93 bp):
AATTTTTTCATTATCGATTTCGTTGAAAATTAGAGGAGATCATCGCCGTTAATGAAAGAATCATG
TGTTTTTGAATAAATAAATAAATAAAAT
Found at i:46171 original size:2 final size:2
Alignment explanation
Indices: 46166--46199 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46156 ATGAAAATTA
46166 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
46200 GAAATAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62678 original size:2 final size:2
Alignment explanation
Indices: 62673--62742 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
62663 ATATATGAAA
62673 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
62715 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
62743 GAAATAATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90669 original size:258 final size:262
Alignment explanation
Indices: 90318--90838 Score: 1005
Period size: 258 Copynumber: 2.0 Consensus size: 262
90308 TTTCAAAAAC
90318 CCCAACTGCCTCAGCAACTTCAAAAAAACAACCTCTAGAAATTAAGGCCCTGCCCAACTCATCAT
1 CCCAACTGCCTCAGCAACTTCAAAAAAACAACCTCTAGAAATTAAGGCCCTGCCCAACTCATCAT
90383 TGGACACCCCTCTGGATACCTCCTTCTCGTCCCTCTCGTT-TTCCAATCCTGTACATTATGATTC
66 TGGACACCCCTCTGGATACCTCCTTCTCGTCCCTCTCGTTCTTCCAATCCTGTACATTATGATTC
90447 CAAATC-TTCTGCATTTCGACCTAC-TAAAATATCTTATGACTTCTGATTAGTTTCCTAGCAA-C
131 CAAATCTTTCTGCATTTCGACCTACATAAAATATCTTATGACTTCTGATTAGTTTCCTAGCAACC
90509 GGAGCAGTCTTCATGGATAACGAACTTGCAGAACCTTCTTGTGAACCAGCTCTTGAATTTAACAA
196 GGAGCAGTCTTCATGGATAACGAACTTGCAGAACCTTCTTGTGAACCAGCTCTTGAATTTAACAA
90574 CT
261 CT
90576 CCCAACTGCCTCAGCAACTTCAAAAAAACAACCTCTAGAAATTAAGGCCCTGCCCAACTCATCAT
1 CCCAACTGCCTCAGCAACTTCAAAAAAACAACCTCTAGAAATTAAGGCCCTGCCCAACTCATCAT
90641 TGGACACCCCTCTGGATACCTCCTTCTCGTCCCTCTCGTTCTTCCAATCCTGTACATTATGATTC
66 TGGACACCCCTCTGGATACCTCCTTCTCGTCCCTCTCGTTCTTCCAATCCTGTACATTATGATTC
90706 CAAATCTTTCTGCATTTCGACCTACTATAAAATATCTTATGACTTCTGATTAGTTTCCTAGCAAC
131 CAAATCTTTCTGCATTTCGACCTAC-ATAAAATATCTTATGACTTCTGATTAGTTTCCTAGCAAC
90771 CGGAGCAGTCTTCATGGATAACGAACTTGCAGAACCTTCTTGTGAACCAGCTCTTGAATTTAACA
195 CGGAGCAGTCTTCATGGATAACGAACTTGCAGAACCTTCTTGTGAACCAGCTCTTGAATTTAACA
90836 ACT
260 ACT
90839 TTAAACCACC
Statistics
Matches: 258, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
258 105 0.41
259 30 0.12
260 18 0.07
262 37 0.14
263 68 0.26
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.30
Consensus pattern (262 bp):
CCCAACTGCCTCAGCAACTTCAAAAAAACAACCTCTAGAAATTAAGGCCCTGCCCAACTCATCAT
TGGACACCCCTCTGGATACCTCCTTCTCGTCCCTCTCGTTCTTCCAATCCTGTACATTATGATTC
CAAATCTTTCTGCATTTCGACCTACATAAAATATCTTATGACTTCTGATTAGTTTCCTAGCAACC
GGAGCAGTCTTCATGGATAACGAACTTGCAGAACCTTCTTGTGAACCAGCTCTTGAATTTAACAA
CT
Found at i:94287 original size:25 final size:25
Alignment explanation
Indices: 94259--94308 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
94249 GACATTAATC
94259 ATGTTTATAGTTCAATCTATTAAAA
1 ATGTTTATAGTTCAATCTATTAAAA
*
94284 ATGTTTGTAGTTCAATCTATTAAAA
1 ATGTTTATAGTTCAATCTATTAAAA
94309 TGTAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (25 bp):
ATGTTTATAGTTCAATCTATTAAAA
Found at i:112355 original size:11 final size:11
Alignment explanation
Indices: 112339--112364 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
112329 TATTTCTATC
112339 TCCATCTTCTA
1 TCCATCTTCTA
112350 TCCATCTTCTA
1 TCCATCTTCTA
112361 TCCA
1 TCCA
112365 GAATACACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.42
Consensus pattern (11 bp):
TCCATCTTCTA
Found at i:123241 original size:4 final size:4
Alignment explanation
Indices: 123232--123257 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
123222 TGTGTTTTTG
123232 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
123258 AGATACAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:124327 original size:31 final size:31
Alignment explanation
Indices: 124261--124320 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
124251 TTGGATTTGA
* *
124261 TATTATCTTTACATTTGATTAAATTTGTGTC
1 TATTATCTTTACATTCGATTAAATTTATGTC
* *
124292 TATTATCTTTCCGATTCGTTTAAATTTAT
1 TATTATCTTTAC-ATTCGATTAAATTTAT
124321 TTTATTAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.46
32 13 0.54
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (31 bp):
TATTATCTTTACATTCGATTAAATTTATGTC
Done.