Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004775.1 Hibiscus syriacus cultivar Beakdansim tig00010770_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: 75573
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5055 original size:23 final size:23
Alignment explanation
Indices: 4984--5062 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
4974 ACACTTAACA
*
4984 GTGCATCGATGCATC-CCTTTGAAT
1 GTGCATCGATGTA-CACC-TTGAAT
* *
5008 GTGCATCGA--TACACCATGAAG
1 GTGCATCGATGTACACCTTGAAT
* *
5029 GTGCACCGATGTACTCCTTGAAT
1 GTGCATCGATGTACACCTTGAAT
5052 GTGCATCGATG
1 GTGCATCGATG
5063 CACAAGGACA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
21 13 0.30
22 3 0.07
23 19 0.43
24 9 0.20
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGTACACCTTGAAT
Found at i:7664 original size:20 final size:20
Alignment explanation
Indices: 7635--7672 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7625 TTTCAAAGGA
7635 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
* *
7655 ATGCATCGATGCATCAAT
1 ATGCACCGATGCACCAAT
7673 GAATAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:8811 original size:41 final size:41
Alignment explanation
Indices: 8751--8833 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
8741 CTAGTCGTTG
* * *
8751 CAGCCTTCGTGCATGGATGCACAGCAGGATGCATCAATGCA
1 CAGCCTTCGTGCATCGATGCACAGAAAGATGCATCAATGCA
* *
8792 CAGCCTT-GATGCATCGATGCACAGAAAGATGTATCGATGCA
1 CAGCCTTCG-TGCATCGATGCACAGAAAGATGCATCAATGCA
8833 C
1 C
8834 TAATTGAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.20
Consensus pattern (41 bp):
CAGCCTTCGTGCATCGATGCACAGAAAGATGCATCAATGCA
Found at i:8923 original size:21 final size:20
Alignment explanation
Indices: 8854--8995 Score: 142
Period size: 21 Copynumber: 6.8 Consensus size: 20
8844 CGGTGTTTGA
*
8854 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACAGG
*
8874 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCACTA---CAGG
*
8896 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTACAGG
8916 GATGCATGGATGCACTACAGG
1 G-TGCATGGATGCACTACAGG
* *
8937 GATGCATAGATGAAACTACAGGG
1 G-TGCATGGATG-CACTACA-GG
* *
8960 GTGCATAGATGAACTACAGGG
1 GTGCATGGATGCACTACA-GG
8981 GTGCATGGATGCACT
1 GTGCATGGATGCACT
8996 TTAACACACT
Statistics
Matches: 107, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.02
20 17 0.16
21 52 0.49
22 31 0.29
23 5 0.05
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.21
Consensus pattern (20 bp):
GTGCATGGATGCACTACAGG
Found at i:8980 original size:64 final size:63
Alignment explanation
Indices: 8855--8995 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 63
8845 GGTGTTTGAG
* * * ** * * *
8855 TGCATGGATGCACTACATGGTGCATCGATGCACTAGTGCAGGTGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTACAGGGTGCATAGATGAACTACAGCAGGTGCATAGATGAACTACAGGGA
* *
8918 TGCATGGATGCACTACAGGGATGCATAGATGAAACTACAG-GGGTGCATAGATGAACTACAGGGG
1 TGCATGGATGCACTACAGGG-TGCATAGATG-AACTACAGCAGGTGCATAGATGAACTACAGGGA
8982 TGCATGGATGCACT
1 TGCATGGATGCACT
8996 TTAACACACT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
63 19 0.29
64 42 0.64
65 5 0.08
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (63 bp):
TGCATGGATGCACTACAGGGTGCATAGATGAACTACAGCAGGTGCATAGATGAACTACAGGGA
Found at i:9135 original size:31 final size:31
Alignment explanation
Indices: 9075--9165 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
9065 AAACTTTGAA
9075 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
9104 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
9135 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
9166 CCTTAAATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:10445 original size:19 final size:19
Alignment explanation
Indices: 10402--10449 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
10392 TCTAAATCCT
* *
10402 TTTTCAAAATTTCTTTTTG
1 TTTTCAAAATCTATTTTTG
10421 TCTTTCAAAATCTATTTTTG
1 T-TTTCAAAATCTATTTTTG
10441 TTTTCAAAA
1 TTTTCAAAA
10450 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.27, C:0.12, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTCAAAATCTATTTTTG
Found at i:11372 original size:34 final size:32
Alignment explanation
Indices: 11310--11379 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
11300 ACCTTACAAC
* *
11310 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
11342 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
11376 TCCC
1 TCCC
11380 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:11772 original size:20 final size:21
Alignment explanation
Indices: 11743--11837 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
11733 GCAGCCTTCG
*
11743 TGCATGGATGCACA-ACAGGA
1 TGCATCGATGCACAGACAGGA
* **
11763 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAGACAGGA
* * **
11784 TGTATCGATGCACAGCCTTGA
1 TGCATCGATGCACAGACAGGA
11805 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACAGACAGGA
11825 TGCATCGATGCAC
1 TGCATCGATGCAC
11838 TAATTGCATT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
20 28 0.43
21 37 0.57
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.21
Consensus pattern (21 bp):
TGCATCGATGCACAGACAGGA
Found at i:11790 original size:21 final size:21
Alignment explanation
Indices: 11761--11837 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
11751 TGCACAACAG
11761 GATGCATCGATGCACAGCCTT
1 GATGCATCGATGCACAGCCTT
*
11782 GATGTATCGATGCACAGCCTT
1 GATGCATCGATGCACAGCCTT
***
11803 GATGCATCGATGCACAG-AAG
1 GATGCATCGATGCACAGCCTT
11823 GATGCATCGATGCAC
1 GATGCATCGATGCAC
11838 TAATTGCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 15 0.29
21 36 0.71
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (21 bp):
GATGCATCGATGCACAGCCTT
Found at i:11905 original size:22 final size:23
Alignment explanation
Indices: 11858--11935 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 23
11848 CGGTGTTTGA
11858 GTGCATGGATGCAC---TGCATG
1 GTGCATGGATGCACTAGTGCATG
*
11878 GTGCATTGATGCACTAGTGCA-G
1 GTGCATGGATGCACTAGTGCATG
*
11900 GTGCATGGATGCAC---TGCAGGG
1 GTGCATGGATGCACTAGTGCA-TG
11921 GTGCATGGATGCACT
1 GTGCATGGATGCACT
11936 TTGACACCCT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.08
20 13 0.26
21 15 0.30
22 14 0.28
23 4 0.08
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (23 bp):
GTGCATGGATGCACTAGTGCATG
Found at i:12036 original size:29 final size:29
Alignment explanation
Indices: 12015--12072 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
12005 AAACTTTGAA
12015 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
12044 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
12073 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:12062 original size:30 final size:30
Alignment explanation
Indices: 12015--12074 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
12005 AAACTTTGAA
12015 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
12044 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
12075 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:12415 original size:89 final size:89
Alignment explanation
Indices: 12309--12557 Score: 331
Period size: 89 Copynumber: 2.8 Consensus size: 89
12299 AAGAGTACAA
* * *
12309 ATTCTTCTTATTTCAGATTTGGTCTTCCTAAAGAAGCAGTGAAGCAAATCAATATTGAGTCTGAT
1 ATTCTTCTTATTTCAGATTTGGTCTTCCTAAAGAAACAGCGAAGCAAATCAATCTTGAGTCTGAT
* *
12374 CTCCCCGGAAAAGTAGTATAGCAT
66 CTCCCCGGAAAAGTAGTAGAACAT
* * * *
12398 ATTCTTTTTATTTCAGATTTAGTCTTCCTAAAGAATA-AGCGAAGAAAATCAATCTTGAATCTGA
1 ATTCTTCTTATTTCAGATTTGGTCTTCCTAAAGAA-ACAGCGAAGCAAATCAATCTTGAGTCTGA
* * *
12462 TCTCCCCGGAAGAGTAGTGGAATAT
65 TCTCCCCGGAAAAGTAGTAGAACAT
* **
12487 GTTCTTCTTATTTCAGATTTGGTCTTCCTAAAGAAACAGCGAAGCAAAT-AATCCTCAAGTCTGA
1 ATTCTTCTTATTTCAGATTTGGTCTTCCTAAAGAAACAGCGAAGCAAATCAAT-CTTGAGTCTGA
12551 TCTCCCC
65 TCTCCCC
12558 TAAAATAAGA
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
88 4 0.03
89 134 0.97
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (89 bp):
ATTCTTCTTATTTCAGATTTGGTCTTCCTAAAGAAACAGCGAAGCAAATCAATCTTGAGTCTGAT
CTCCCCGGAAAAGTAGTAGAACAT
Found at i:12698 original size:55 final size:55
Alignment explanation
Indices: 12544--12700 Score: 172
Period size: 55 Copynumber: 2.8 Consensus size: 55
12534 ATAATCCTCA
* * * * *
12544 AGTCTGATCTCCCCTAAAATAAGAGTGGAACAGACTCATTTTCCAAAGATTTTTCG
1 AGTCTTATCT-CCCTAAAAGAAGAGTGGAGCAGACTCGTTTTCCAAAGATTTCTCG
* * * * *
12600 AGTCTTCTCTCCTTGAAAGAAGTGTGGAGCAGGAC-CGTCTTCCAAAGATTTCTCG
1 AGTCTTATCTCCCTAAAAGAAGAGTGGAGCA-GACTCGTTTTCCAAAGATTTCTCG
* * *
12655 AGTCTTATCTCCCTAAAAGAAAAGTGTAGCAAACTCGTTTTCCAAA
1 AGTCTTATCTCCCTAAAAGAAGAGTGGAGCAGACTCGTTTTCCAAA
12701 ATTGATCTGA
Statistics
Matches: 81, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
54 2 0.02
55 68 0.84
56 11 0.14
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (55 bp):
AGTCTTATCTCCCTAAAAGAAGAGTGGAGCAGACTCGTTTTCCAAAGATTTCTCG
Found at i:12861 original size:82 final size:81
Alignment explanation
Indices: 12694--12863 Score: 182
Period size: 82 Copynumber: 2.1 Consensus size: 81
12684 CAAACTCGTT
* * * * *
12694 TTCCAAAATTGATCTGACTACCCGAAAAGAGGAATAAATCATGTCTAATATCCCCTGAAAGAAGA
1 TTCCAAAATTGATCTAACTACCCGAAAAGAGGAACAAATCAAGTATAATATCCCCTAAAAGAAGA
* * * *
12759 GTAGAGTAGACTCGTT
66 GTAGAGCAGACCCATG
* *
12775 TTCCAAAATT-ATTCTAACTACCCGAAAA-AGTTGAACAAATCAAGTATGATATCCCTTAAAAGA
1 TTCCAAAATTGA-TCTAACTACCCGAAAAGAG--GAACAAATCAAGTATAATATCCCCTAAAAGA
* *
12838 AGAGTGGAGCATACCCATG
63 AGAGTAGAGCAGACCCATG
12857 TTCCAAA
1 TTCCAAA
12864 GAATTTTCGA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
80 3 0.04
81 25 0.34
82 45 0.62
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (81 bp):
TTCCAAAATTGATCTAACTACCCGAAAAGAGGAACAAATCAAGTATAATATCCCCTAAAAGAAGA
GTAGAGCAGACCCATG
Found at i:12897 original size:55 final size:55
Alignment explanation
Indices: 12826--12973 Score: 190
Period size: 55 Copynumber: 2.7 Consensus size: 55
12816 AAGTATGATA
* *
12826 TCCCTTAAAAGAAGAGTGGAGCATACCCATGTTCCAAAGAATTT-TCGAGTCTTATC
1 TCCC-TAAAAGAAGAGTGGAGCAGACCCATCTTCCAAAG-ATTTATCGAGTCTTATC
* * *
12882 TCGCTAAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTATCGAGTTTTATC
1 TCCCTAAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTATCGAGTCTTATC
* * * *
12937 TCCCAAAAAGAAAAGTGGAGCAGTCTCATCTTCCAAA
1 TCCCTAAAAGAAGAGTGGAGCAGACCCATCTTCCAAA
12974 ATTGATCTGA
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
54 4 0.05
55 73 0.91
56 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (55 bp):
TCCCTAAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTATCGAGTCTTATC
Found at i:13029 original size:81 final size:82
Alignment explanation
Indices: 12943--13119 Score: 259
Period size: 81 Copynumber: 2.2 Consensus size: 82
12933 TATCTCCCAA
* *
12943 AAAGAAAAGTGGAGCAGTCTCATCTTCCAAAATTGATCTGACTACCCGAAAAAG-GGAACATATC
1 AAAGAAAAGTGGAGCAGACCCATCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAACATATC
13007 AAGT-CTGATCTCCCCTG
66 AAGTCCT-ATCTCCCCTG
* * * * *
13024 AAAGAATAGTTGAGCAGACCCGTCTTCCAAAATTGATCTTACTACCTGAAAAAGAGGAACATATC
1 AAAGAAAAGTGGAGCAGACCCATCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAACATATC
13089 AAGTCCTATCTCCCCTG
66 AAGTCCTATCTCCCCTG
*
13106 AAAGAAGAGTGGAG
1 AAAGAAAAGTGGAG
13120 TGGATTTCCC
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
81 47 0.55
82 36 0.42
83 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (82 bp):
AAAGAAAAGTGGAGCAGACCCATCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAACATATC
AAGTCCTATCTCCCCTG
Found at i:13054 original size:273 final size:273
Alignment explanation
Indices: 12541--13119 Score: 754
Period size: 273 Copynumber: 2.1 Consensus size: 273
12531 CAAATAATCC
* * * * *
12541 TCAAGTCTGATCTCCCCTAAAATAAGAGTGGAACAGACTCATTTTCCAAAGATTTTTCGAGTCTT
1 TCAAGTCTGATCTCCCCTAAAAGAAGAGTGGAGCAGACCCATGTTCCAAAGAATTTTCGAGTCTT
* * * * *
12606 CTCTCCTTGAAAGAAGTGTGGAGCAGGACCGTCTTCCAAAGATTTCTCGAGTCTTATCTCCCTAA
66 ATCTCCTTAAAAGAAGAGTGGAGCAGGACCGTCTTCCAAAGATTTATCGAGTCTTATCTCCCAAA
* * * * *
12671 AAGAAAAGTGTAGCAAACTCGTTTTCCAAAATTGATCTGACTACCCGAAAAGAGGAATAAATCAT
131 AAGAAAAGTGGAGCAAACTCATCTTCCAAAATTGATCTGACTACCCGAAAAGAGGAACAAATCAA
* * *
12736 GTCTAATATCCCCTGAAAGAAGAGTAGAGTAGACTCGTTTTCCAAAATT-ATTCTAACTACCCGA
196 GTCTAATATCCCCTGAAAGAAGAGTAGAGCAGACCCGTCTTCCAAAATTGA-TCTAACTACCCGA
**
12800 AAAAGTTGAACAAA
260 AAAAGAGGAACAAA
* * * *
12814 TCAAGTATGATATCCCTTAAAAGAAGAGTGGAGCATACCCATGTTCCAAAGAATTTTCGAGTCTT
1 TCAAGTCTGATCTCCCCTAAAAGAAGAGTGGAGCAGACCCATGTTCCAAAGAATTTTCGAGTCTT
*
12879 ATCTCGC-TAAAAGAAGAGTGGAGCA-GACCCGTCTTCCAAAGATTTATCGAGTTTTATCTCCCA
66 ATCTC-CTTAAAAGAAGAGTGGAGCAGGA-CCGTCTTCCAAAGATTTATCGAGTCTTATCTCCCA
** *
12942 AAAAGAAAAGTGGAGCAGTCTCATCTTCCAAAATTGATCTGACTACCCGAAAA-AGGGAACATAT
129 AAAAGAAAAGTGGAGCAAACTCATCTTCCAAAATTGATCTGACTACCCGAAAAGA-GGAACAAAT
* * * * * *
13006 CAAGTCTGATCTCCCCTGAAAGAATAGTTGAGCAGACCCGTCTTCCAAAATTGATCTTACTACCT
193 CAAGTCTAATATCCCCTGAAAGAAGAGTAGAGCAGACCCGTCTTCCAAAATTGATCTAACTACCC
*
13071 GAAAAAGAGGAACATA
258 GAAAAAGAGGAACAAA
*
13087 TCAAGTCCT-ATCTCCCCTGAAAGAAGAGTGGAG
1 TCAAGT-CTGATCTCCCCTAAAAGAAGAGTGGAG
13120 TGGATTTCCC
Statistics
Matches: 262, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
272 3 0.01
273 256 0.98
274 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (273 bp):
TCAAGTCTGATCTCCCCTAAAAGAAGAGTGGAGCAGACCCATGTTCCAAAGAATTTTCGAGTCTT
ATCTCCTTAAAAGAAGAGTGGAGCAGGACCGTCTTCCAAAGATTTATCGAGTCTTATCTCCCAAA
AAGAAAAGTGGAGCAAACTCATCTTCCAAAATTGATCTGACTACCCGAAAAGAGGAACAAATCAA
GTCTAATATCCCCTGAAAGAAGAGTAGAGCAGACCCGTCTTCCAAAATTGATCTAACTACCCGAA
AAAGAGGAACAAA
Found at i:14417 original size:19 final size:17
Alignment explanation
Indices: 14392--14435 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
14382 TTGATTTCCA
14392 TATATTTTAATTTGGATT
1 TATATTTTAATTTGG-TT
*
14410 TCATATTTT-ATTTTGTT
1 T-ATATTTTAATTTGGTT
14427 TATATTTTA
1 TATATTTTA
14436 GTCACTAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 7 0.30
17 3 0.13
18 6 0.26
19 7 0.30
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (17 bp):
TATATTTTAATTTGGTT
Found at i:21992 original size:15 final size:16
Alignment explanation
Indices: 21965--22004 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
21955 CTTTATTATC
21965 TTATTTCATCTTTCAT
1 TTATTTCATCTTTCAT
*
21981 TTATTT-ATCTTTTAT
1 TTATTTCATCTTTCAT
21996 TTATTTCAT
1 TTATTTCAT
22005 TCTAATCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTCATCTTTCAT
Found at i:27843 original size:13 final size:13
Alignment explanation
Indices: 27825--27850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27815 CGAGAGAAAA
27825 TATTAAAATAAAT
1 TATTAAAATAAAT
27838 TATTAAAATAAAT
1 TATTAAAATAAAT
27851 CACATCACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAAAATAAAT
Found at i:34679 original size:63 final size:63
Alignment explanation
Indices: 34607--34731 Score: 250
Period size: 63 Copynumber: 2.0 Consensus size: 63
34597 ATTTTAAAAA
34607 CTATAAATACAACATAAAAAATCATATATATAAACTAAAAAGTACATTGCAATTTACAAGTAT
1 CTATAAATACAACATAAAAAATCATATATATAAACTAAAAAGTACATTGCAATTTACAAGTAT
34670 CTATAAATACAACATAAAAAATCATATATATAAACTAAAAAGTACATTGCAATTTACAAGTA
1 CTATAAATACAACATAAAAAATCATATATATAAACTAAAAAGTACATTGCAATTTACAAGTA
34732 GAGGAGCACA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (63 bp):
CTATAAATACAACATAAAAAATCATATATATAAACTAAAAAGTACATTGCAATTTACAAGTAT
Found at i:43077 original size:21 final size:21
Alignment explanation
Indices: 43051--43102 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
43041 GGGAGCATGT
43051 GTGCATCGATGCATAGTCAAG
1 GTGCATCGATGCATAGTCAAG
43072 GTGCATCGATGCATAGTCAAG
1 GTGCATCGATGCATAGTCAAG
43093 GTGCATCGAT
1 GTGCATCGAT
43103 CCATCAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATAGTCAAG
Found at i:45570 original size:22 final size:22
Alignment explanation
Indices: 45552--45593 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45542 AAAAAAATTT
*
45552 ATTTCAAAAATTTTCAAAAAAA
1 ATTTCAAAAATTTTCAAAATAA
*
45574 ATTTCAAAAATTTTGAAAAT
1 ATTTCAAAAATTTTCAAAAT
45594 GACGAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
ATTTCAAAAATTTTCAAAATAA
Found at i:45995 original size:23 final size:22
Alignment explanation
Indices: 45969--46048 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
45959 TACTGCTGAG
45969 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
* * *
45991 GTGCATCGGTGCACCTTC-ATGA
1 -TGCATCGATGCACATTCAAGGA
* *
46013 TGTATCGATGCACATTTATAGGA
1 TGCATCGATGCACATTCA-AGGA
46036 TGCATCGATGCAC
1 TGCATCGATGCAC
46049 TGGATAGTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 13 0.28
22 3 0.07
23 30 0.65
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:55437 original size:110 final size:110
Alignment explanation
Indices: 55235--55441 Score: 299
Period size: 110 Copynumber: 1.9 Consensus size: 110
55225 GCTTCCCAGT
* * *
55235 TTTAGAGCCAATTTTAACTTCAAAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTTAGAGCCAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
*
55300 CAACGAAGGGACGACTGATTGTCAACAAACAAATTTTTAGTTTCA
66 CAACGAAGGGACGACTGACTGTCAACAAACAAATTTTTAGTTTCA
* * *
55345 TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTTAGAGCCAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
** * *
55410 CAGTGAAAGGG-CGGCTGACTGTTAACAAACAA
66 CAACG-AAGGGACGACTGACTGTCAACAAACAA
55442 TTTCCAGAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
110 80 0.94
111 5 0.06
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (110 bp):
TTTAGAGCCAATTTCAACTTCAAAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGACGACTGACTGTCAACAAACAAATTTTTAGTTTCA
Found at i:56950 original size:16 final size:15
Alignment explanation
Indices: 56913--56986 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 15
56903 ATTCTTTTTC
*
56913 ATATATCATTATTATTT
1 ATATAT-ATTTTTA-TT
56930 ATATATATTTTTATT
1 ATATATATTTTTATT
* *
56945 ACTATA-ATTATATGTT
1 A-TATATATT-TTTATT
56961 ATATATATTTATTATT
1 ATATATATTT-TTATT
*
56977 TTATATATTT
1 ATATATATTT
56987 CATTTTATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
15 11 0.23
16 30 0.64
17 6 0.13
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (15 bp):
ATATATATTTTTATT
Found at i:57006 original size:14 final size:14
Alignment explanation
Indices: 56989--57041 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
56979 ATATATTTCA
56989 TTTTATCTTTTATT
1 TTTTATCTTTTATT
*
57003 TTTTATCTTCTA-T
1 TTTTATCTTTTATT
*
57016 TTTTATTTTTGTATT
1 TTTTATCTTT-TATT
57031 GTTATTATCTT
1 -TT-TTATCTT
57042 CTTTATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 9 0.29
14 13 0.42
15 1 0.03
16 2 0.06
17 6 0.19
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTATCTTTTATT
Found at i:57017 original size:26 final size:27
Alignment explanation
Indices: 56972--57052 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 27
56962 TATATATTTA
56972 TTATTTTATATAT-TTC-ATTTTATCTT
1 TTATTTTAT-TATCTTCTATTTTATCTT
*
56998 TTATTTT-TTATCTTCTATTTTTATTTT
1 TTATTTTATTATCTTCTA-TTTTATCTT
57025 TGTATTGTTATTATCTTCTTTATTTTAT
1 T-TATT-TTATTATCTTC--TATTTTAT
57053 GTATTTTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
24 3 0.07
25 4 0.09
26 8 0.17
27 9 0.20
28 4 0.09
29 2 0.04
30 8 0.17
31 6 0.13
32 2 0.04
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (27 bp):
TTATTTTATTATCTTCTATTTTATCTT
Found at i:57019 original size:27 final size:31
Alignment explanation
Indices: 56988--57052 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
56978 TATATATTTC
56988 ATTTTATCTTT-TATT-TT-TTATCTTCTAT
1 ATTTTATCTTTGTATTGTTATTATCTTCTAT
* *
57016 -TTTTATTTTTGTATTGTTATTATCTTCTTT
1 ATTTTATCTTTGTATTGTTATTATCTTCTAT
57046 ATTTTAT
1 ATTTTAT
57053 GTATTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 9 0.29
28 4 0.13
29 2 0.06
30 10 0.32
31 6 0.19
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (31 bp):
ATTTTATCTTTGTATTGTTATTATCTTCTAT
Found at i:60244 original size:93 final size:95
Alignment explanation
Indices: 60097--60283 Score: 283
Period size: 93 Copynumber: 2.0 Consensus size: 95
60087 TACCATTGAG
** * * *
60097 GTAGTATTGATACCATGGTAAGGGTATCGATACCAAACAACATCGAATCTAAATTTGGTATCGAT
1 GTAGTATCAATACCATGGTAAGGGCATCGATACCAAACAACATCAAACCTAAATTTGGTATCGAT
60162 ACCGGAA-GGGGTATCGGTACCATAGTATT
66 ACCGGAAGGGGGTATCGGTACCATAGTATT
60191 GTAGTATCAATACCATGGTAA-GGCATCGATA-CAAGGA-AACATCAAACCTAAATTTGGTATCG
1 GTAGTATCAATACCATGGTAAGGGCATCGATACCAA--ACAACATCAAACCTAAATTTGGTATCG
60253 ATACCGGAAGGGGGTATCGGTACCATAGTAT
64 ATACCGGAAGGGGGTATCGGTACCATAGTAT
60284 AGAAGTATTG
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
92 3 0.04
93 41 0.48
94 41 0.48
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (95 bp):
GTAGTATCAATACCATGGTAAGGGCATCGATACCAAACAACATCAAACCTAAATTTGGTATCGAT
ACCGGAAGGGGGTATCGGTACCATAGTATT
Found at i:60298 original size:94 final size:94
Alignment explanation
Indices: 60099--60304 Score: 292
Period size: 94 Copynumber: 2.2 Consensus size: 94
60089 CCATTGAGGT
* * *
60099 AGTATTGATACCATGGTAAGGGTATCGATACCAAACAACATCGAATCTAAATTTGGTATCGATAC
1 AGTATTGATACCATGGTAAGGGCATCGATACCAAACAACATCAAACCTAAATTTGGTATCGATAC
* *
60164 CGGAAGGGGTATCGGTACCATAGTATTGT
66 CGGAAGGGGTATCGGTACCATAGTATAGA
**
60193 AGTATCAATACCATGGTAA-GGCATCGATA-CAAGGA-AACATCAAACCTAAATTTGGTATCGAT
1 AGTATTGATACCATGGTAAGGGCATCGATACCAA--ACAACATCAAACCTAAATTTGGTATCGAT
60255 ACCGGAAGGGGGTATCGGTACCATAGTATAGA
64 ACCGGAA-GGGGTATCGGTACCATAGTATAGA
*
60287 AGTATTGATACCAGGGTA
1 AGTATTGATACCATGGTA
60305 GCAATATCGA
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
92 3 0.03
93 41 0.41
94 55 0.56
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (94 bp):
AGTATTGATACCATGGTAAGGGCATCGATACCAAACAACATCAAACCTAAATTTGGTATCGATAC
CGGAAGGGGTATCGGTACCATAGTATAGA
Found at i:60776 original size:54 final size:54
Alignment explanation
Indices: 60633--60769 Score: 177
Period size: 53 Copynumber: 2.6 Consensus size: 54
60623 TTACCAAATA
* * *
60633 GGCACTAAGTGTGCATTCCATGGAATTCATCCTATATGGATTAATAACCGTTTC
1 GGCACTAAGTGTGCATTCCATGGAATTCATCCTATGTGGATGAATAAACGTTTC
* * * *
60687 GGCACTCAG-GTGCATTCCACGGAATTCATCCTATGTGGATGAATAAATGTTTT
1 GGCACTAAGTGTGCATTCCATGGAATTCATCCTATGTGGATGAATAAACGTTTC
* * *
60740 GGCAATAAGTGTGCATTTCATGGGATTCAT
1 GGCACTAAGTGTGCATTCCATGGAATTCAT
60770 AATATGTTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
53 45 0.64
54 25 0.36
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTCCATGGAATTCATCCTATGTGGATGAATAAACGTTTC
Found at i:64188 original size:21 final size:21
Alignment explanation
Indices: 64162--64242 Score: 144
Period size: 21 Copynumber: 3.9 Consensus size: 21
64152 CAATTAAAAA
* *
64162 TCAAGGAGCTTTACTTCATAG
1 TCAAGGCGCCTTACTTCATAG
64183 TCAAGGCGCCTTACTTCATAG
1 TCAAGGCGCCTTACTTCATAG
64204 TCAAGGCGCCTTACTTCATAG
1 TCAAGGCGCCTTACTTCATAG
64225 TCAAGGCGCCTTACTTCA
1 TCAAGGCGCCTTACTTCA
64243 AAGCCATAGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (21 bp):
TCAAGGCGCCTTACTTCATAG
Found at i:68766 original size:20 final size:20
Alignment explanation
Indices: 68741--68784 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
68731 TTAACTTTTT
* *
68741 TTTTCTCTTTCTTCCTTAAC
1 TTTTCTATTTCATCCTTAAC
*
68761 TTTTCTATTTCATCTTTAAC
1 TTTTCTATTTCATCCTTAAC
68781 TTTT
1 TTTT
68785 ACTTTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTCTATTTCATCCTTAAC
Found at i:72079 original size:23 final size:23
Alignment explanation
Indices: 72052--72100 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
72042 TGGTAGTTGG
72052 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGAATATTTA-ACTTTAT
*
72075 TTTAATGGAATATTTAAGTTTAT
1 TTTAATGGAATATTTAACTTTAT
72098 TTT
1 TTT
72101 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (23 bp):
TTTAATGGAATATTTAACTTTAT
Done.