Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005877.1 Hibiscus syriacus cultivar Beakdansim tig00013809_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: 114373
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5978 original size:17 final size:17
Alignment explanation
Indices: 5934--5968 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5924 TCGGGTATTA
5934 AATTATAATAAAAATAT
1 AATTATAATAAAAATAT
5951 AATTATAATAAAAATAT
1 AATTATAATAAAAATAT
5968 A
1 A
5969 TTTTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTATAATAAAAATAT
Found at i:6044 original size:24 final size:26
Alignment explanation
Indices: 6017--6070 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 26
6007 TGAATTTTAT
*
6017 TTATTTTTAAATA-ATTAA-AATAAA
1 TTATTTTTAAAAATATTAATAATAAA
*
6041 TTA-TTTTAAAAATATTAATATTAAA
1 TTATTTTTAAAAATATTAATAATAAA
6066 TTATT
1 TTATT
6071 AAAATAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 8 0.32
24 8 0.32
25 8 0.32
26 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTATTTTTAAAAATATTAATAATAAA
Found at i:6065 original size:25 final size:23
Alignment explanation
Indices: 6021--6070 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
6011 TTTTATTTAT
*
6021 TTTTAAATAATTAAAATAAATTA
1 TTTTAAAAAATTAAAATAAATTA
*
6044 TTTTAAAAATATTAATATTAAATTA
1 TTTTAAAAA-ATTAA-AATAAATTA
6069 TT
1 TT
6071 AAAATAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 5 0.22
25 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTTAAAAAATTAAAATAAATTA
Found at i:6855 original size:2 final size:2
Alignment explanation
Indices: 6848--6884 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6838 ATGTTTTTCA
6848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6885 ATTGAGTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7673 original size:21 final size:21
Alignment explanation
Indices: 7645--7758 Score: 94
Period size: 21 Copynumber: 5.4 Consensus size: 21
7635 ATTTTGAACT
7645 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
7666 ATCACAACGCGAACTTT-GACT--
1 ATCGCAA--CGAA-TTTGGAATAA
* *
7687 ATCACAACGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
7708 ATCGCAACGCAAACTTGGACT--
1 ATCGCAACG--AATTTGGAATAA
7729 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
7750 ATCGCAACG
1 ATCGCAACG
7759 CGAACTTCGA
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.03
19 15 0.20
21 39 0.52
23 16 0.21
24 3 0.04
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:7697 original size:42 final size:42
Alignment explanation
Indices: 7637--7777 Score: 219
Period size: 42 Copynumber: 3.3 Consensus size: 42
7627 TCGTTGCGAT
*
7637 TTTGAACTATCGCAACGAATTTGGAATAAATCACAACGCGAAC
1 TTTG-ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
7680 TTTGACTATCACAACGAACTTGGAATAAATCGCAACGCAAAC
1 TTTGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
7722 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTTGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
7764 TTCGACTATCGCAA
1 TTTGACTATCGCAA
7778 TGCGAACTTG
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 85 0.96
43 4 0.04
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (42 bp):
TTTGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:7774 original size:21 final size:21
Alignment explanation
Indices: 7670--7804 Score: 116
Period size: 21 Copynumber: 6.4 Consensus size: 21
7660 GAATAAATCA
* *
7670 CAACGCGAACTTTGACTATCA
1 CAACGCGAACTTGGACTATCG
*
7691 CAA--CGAACTTGGAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
*
7712 CAACGCAAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
* *
7733 CAA--CGAATTTGGAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
*
7754 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTGGACTATCG
*
7775 CAATGCGAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
* *
7796 TAATGCGAA
1 CAACGCGAA
7805 TATGTAAATC
Statistics
Matches: 92, Mismatches: 14, Indels: 16
0.75 0.11 0.13
Matches are distributed among these distances:
19 19 0.21
21 54 0.59
23 19 0.21
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACGCGAACTTGGACTATCG
Found at i:10910 original size:6 final size:6
Alignment explanation
Indices: 10897--10948 Score: 68
Period size: 6 Copynumber: 8.5 Consensus size: 6
10887 TTTGGGCCGT
* * *
10897 CCACTC CTACTC CTACTC CCACTGG CCACTC CCACTC CCACTC CCACTC
1 CCACTC CCACTC CCACTC CCACT-C CCACTC CCACTC CCACTC CCACTC
10946 CCA
1 CCA
10949 TTTCCTCACC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 36 0.88
7 5 0.12
ACGTcount: A:0.17, C:0.60, G:0.04, T:0.19
Consensus pattern (6 bp):
CCACTC
Found at i:10933 original size:19 final size:18
Alignment explanation
Indices: 10897--10948 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
10887 TTTGGGCCGT
* *
10897 CCACTCCTACTCCTACTC
1 CCACTCCCACTCCCACTC
*
10915 CCACTGGCCACTCCCACTC
1 CCACT-CCCACTCCCACTC
10934 CCACTCCCACTCCCA
1 CCACTCCCACTCCCA
10949 TTTCCTCACC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.17, C:0.60, G:0.04, T:0.19
Consensus pattern (18 bp):
CCACTCCCACTCCCACTC
Found at i:10933 original size:25 final size:25
Alignment explanation
Indices: 10897--10944 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
10887 TTTGGGCCGT
* *
10897 CCACTCCTACTCCTACTCCCACTGG
1 CCACTCCCACTCCCACTCCCACTGG
10922 CCACTCCCACTCCCACTCCCACT
1 CCACTCCCACTCCCACTCCCACT
10945 CCCATTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.17, C:0.58, G:0.04, T:0.21
Consensus pattern (25 bp):
CCACTCCCACTCCCACTCCCACTGG
Found at i:11198 original size:13 final size:13
Alignment explanation
Indices: 11162--11201 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
11152 TCCGAAATAG
*
11162 TTAATTAAATTAT
1 TTAATTATATTAT
*
11175 TTACTTTATATTAT
1 TTA-ATTATATTAT
11189 TTAATTATATTAT
1 TTAATTATATTAT
11202 ATCTTATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:12964 original size:183 final size:183
Alignment explanation
Indices: 12656--13030 Score: 741
Period size: 183 Copynumber: 2.0 Consensus size: 183
12646 GTTGCTGGAC
12656 AGTTTCGGGGGTGAAGGCTTCGCGAGTTGTTTCGACAGGTTGTTGTTCAACTGATTCAAATAGGG
1 AGTTTCGGGGGTGAAGGCTTCGCGAGTTGTTTCGACAGGTTGTTGTTCAACTGATTCAAATAGGG
12721 GGTTAAAATTGGATTCAGATATGGATGGGCCATGTTTTTGCATGGGATTTGCATGGGTGTTATGT
66 GGTTAAAATTGGATTCAGATATGGATGGGCCATGTTTTTGCATGGGATTTGCATGGGTGTTATGT
12786 TGGGATCGTTTCTGCCTTCGGTCAACTAGCATCCACGGTCTGAACGACTCACT
131 TGGGATCGTTTCTGCCTTCGGTCAACTAGCATCCACGGTCTGAACGACTCACT
12839 AGTTTCGGGGGTGAAGGCTTCGCGAGTTGTTTCGACAGGTTGTTGTTCAACTGATTCAAATAGGG
1 AGTTTCGGGGGTGAAGGCTTCGCGAGTTGTTTCGACAGGTTGTTGTTCAACTGATTCAAATAGGG
12904 GGTTAAAATTGGATTCAGATATGGATGGGCCATGTTTTTGCATGGGATTTGCATGGGTGTTATGT
66 GGTTAAAATTGGATTCAGATATGGATGGGCCATGTTTTTGCATGGGATTTGCATGGGTGTTATGT
*
12969 TGGGATCGTTTCTGCCTTCGGTCAACTAGCATCCACGGTCTGACCGACTCACT
131 TGGGATCGTTTCTGCCTTCGGTCAACTAGCATCCACGGTCTGAACGACTCACT
13022 AGTTTCGGG
1 AGTTTCGGG
13031 CTTGGTTTGT
Statistics
Matches: 191, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 191 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (183 bp):
AGTTTCGGGGGTGAAGGCTTCGCGAGTTGTTTCGACAGGTTGTTGTTCAACTGATTCAAATAGGG
GGTTAAAATTGGATTCAGATATGGATGGGCCATGTTTTTGCATGGGATTTGCATGGGTGTTATGT
TGGGATCGTTTCTGCCTTCGGTCAACTAGCATCCACGGTCTGAACGACTCACT
Found at i:19210 original size:12 final size:12
Alignment explanation
Indices: 19171--19229 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
19161 AAAAAATAAA
19171 TAATAAAATATT
1 TAATAAAATATT
19183 T--T-AAATATT
1 TAATAAAATATT
** *
19192 TTTTAAAATGTT
1 TAATAAAATATT
19204 TAAT-AAATATT
1 TAATAAAATATT
*
19215 TAGTAAAATATT
1 TAATAAAATATT
19227 TAA
1 TAA
19230 AATATTCCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
11 10 0.27
12 18 0.49
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
TAATAAAATATT
Found at i:19212 original size:23 final size:23
Alignment explanation
Indices: 19174--19229 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
19164 AAATAAATAA
**
19174 TAAAATATTT--TAAATATTTTT
1 TAAAATATTTAATAAATATTTAG
*
19195 TAAAATGTTTAATAAATATTTAG
1 TAAAATATTTAATAAATATTTAG
19218 TAAAATATTTAA
1 TAAAATATTTAA
19230 AATATTCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 9 0.31
23 20 0.69
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TAAAATATTTAATAAATATTTAG
Found at i:20878 original size:29 final size:29
Alignment explanation
Indices: 20843--20924 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
20833 AAACTAAATT
*
20843 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
20872 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
20901 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
20925 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:25647 original size:29 final size:29
Alignment explanation
Indices: 25612--25693 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
25602 AAACTAAATT
*
25612 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
25641 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
25670 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
25694 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:46466 original size:44 final size:44
Alignment explanation
Indices: 46416--46548 Score: 248
Period size: 44 Copynumber: 3.0 Consensus size: 44
46406 ATGGGGTGAG
*
46416 TGGTCAACGGGTCAGGTATGCAGCCAATGGTCCAAGTAAGCATT
1 TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
46460 TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
1 TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
*
46504 TGGTCAACGGGTCAGGTATGCAGCCAACGGTTCAAGTAAGCATT
1 TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
46548 T
1 T
46549 AACTGTCCAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 87 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (44 bp):
TGGTCAACGGGTCAGGTATGCAGCCAACGGTCCAAGTAAGCATT
Found at i:46489 original size:20 final size:20
Alignment explanation
Indices: 46464--46533 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
46454 AGCATTTGGT
46464 CAACGGGTCAGGTATGCAGC
1 CAACGGGTCAGGTATGCAGC
* * *
46484 CAAC-GGTCCAAGTAAGCATTTGGT
1 CAACGGGT-CAGGTATGCA----GC
46508 CAACGGGTCAGGTATGCAGC
1 CAACGGGTCAGGTATGCAGC
46528 CAACGG
1 CAACGG
46534 TTCAAGTAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 3 0.08
20 19 0.50
24 13 0.34
25 3 0.08
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.17
Consensus pattern (20 bp):
CAACGGGTCAGGTATGCAGC
Found at i:46511 original size:24 final size:24
Alignment explanation
Indices: 46444--46513 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
46434 TGCAGCCAAT
46444 GGTCCAAGTAAGCATTTGGTCAAC
1 GGTCCAAGTAAGCATTTGGTCAAC
* * *
46468 GGGT-CAGGTATGCA----GCCAAC
1 -GGTCCAAGTAAGCATTTGGTCAAC
46488 GGTCCAAGTAAGCATTTGGTCAAC
1 GGTCCAAGTAAGCATTTGGTCAAC
46512 GG
1 GG
46514 GTCAGGTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 11
0.67 0.12 0.22
Matches are distributed among these distances:
19 3 0.09
20 13 0.38
24 15 0.44
25 3 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (24 bp):
GGTCCAAGTAAGCATTTGGTCAAC
Found at i:46566 original size:32 final size:32
Alignment explanation
Indices: 46527--46596 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
46517 AGGTATGCAG
*
46527 CCAACGGTTCAAGTAAGCATTTAACTGTCCAA
1 CCAACGGTCCAAGTAAGCATTTAACTGTCCAA
46559 CCAACGGTCCAAGTAAGCATTTAACTGTCCAA
1 CCAACGGTCCAAGTAAGCATTTAACTGTCCAA
46591 CTCAAC
1 C-CAAC
46597 TTTCCATCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (32 bp):
CCAACGGTCCAAGTAAGCATTTAACTGTCCAA
Found at i:49500 original size:15 final size:15
Alignment explanation
Indices: 49480--49511 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49470 TTCATATGTT
49480 ATATTAATTAAAATA
1 ATATTAATTAAAATA
*
49495 ATATTAATTAAATTA
1 ATATTAATTAAAATA
49510 AT
1 AT
49512 TTTTTAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATTAATTAAAATA
Found at i:50832 original size:3 final size:3
Alignment explanation
Indices: 50824--50876 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
50814 TTTTCCCACC
*
50824 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
50872 ATT AT
1 ATT AT
50877 AAGATGAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:52014 original size:90 final size:90
Alignment explanation
Indices: 51913--52092 Score: 324
Period size: 90 Copynumber: 2.0 Consensus size: 90
51903 TAAACCAAAA
51913 AAATTATAAACAGATACTATAAGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTTT
1 AAATTATAAACAGATACTATAAGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTTT
*
51978 TTGTCATTTAAACACACAAAAATGT
66 TGGTCATTTAAACACACAAAAATGT
* *
52003 AAATTATAAACAGTTACTATAGGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTTT
1 AAATTATAAACAGATACTATAAGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTTT
*
52068 TGGTCATTTAAGCACACAAAAATGT
66 TGGTCATTTAAACACACAAAAATGT
52093 GGTGAACGGT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (90 bp):
AAATTATAAACAGATACTATAAGGTAATTTTGTGTGTGTGAATTATCATTGAATCCGGTTGTTTT
TGGTCATTTAAACACACAAAAATGT
Found at i:61684 original size:12 final size:12
Alignment explanation
Indices: 61669--61694 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61659 TATCGTAACG
61669 GGAAATTCGAGA
1 GGAAATTCGAGA
61681 GGAAATTCGAGA
1 GGAAATTCGAGA
61693 GG
1 GG
61695 TATATAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.38, T:0.15
Consensus pattern (12 bp):
GGAAATTCGAGA
Found at i:64852 original size:245 final size:245
Alignment explanation
Indices: 64140--64874 Score: 1447
Period size: 244 Copynumber: 3.0 Consensus size: 245
64130 ATGGGTTTAA
64140 AATAATAACAGAAGAATAGTTTAGGTACCCGATTTGAT-AAAAAAACAGTTTAGGTACTTAAAAC
1 AATAATAACAGAAGAATAGTTTAGGTACCCGATTTGATAAAAAAAACAGTTTAGGTACTTAAAAC
64204 AAAAAAAACAGCATAGTTTGAGGGCTGATTTTTCATTTAAGCCTAATTTTAATTGTAAAGTAGTC
66 AAAAAAAACAGCATAGTTTGAGGGCTGATTTTTCATTTAAGCCTAATTTTAATTGTAAAGTAGTC
64269 GGGGTCGGGTAGGGTTTTAAACCCTAGACTCGACTCTAACCCCGACCGACCTTTTATATATAAAA
131 GGGGTCGGGTAGGGTTTTAAACCCTAGACTCGACTCTAACCCCGACCGACCTTTTATATATAAAA
64334 CACGACCTGTCCTAATTTGACCCTACCCAAATCCGATTTTTTGTTAAAAG
196 CACGACCTGTCCTAATTTGACCCTACCCAAATCCGATTTTTTGTTAAAAG
64384 AATAATAACAGAAGAATAGTTTAGGTACCCGATTTGATAAAAAAAACAGTTTAGGTACTTAAAAC
1 AATAATAACAGAAGAATAGTTTAGGTACCCGATTTGATAAAAAAAACAGTTTAGGTACTTAAAAC
64449 -AAAAAAACAGCATAGTTTGAGGGCTGATTTTTCATTTAAGCCTAATTTTAATTGTAAAGTAGTC
66 AAAAAAAACAGCATAGTTTGAGGGCTGATTTTTCATTTAAGCCTAATTTTAATTGTAAAGTAGTC
64513 GGGGTCGGGTAGGGTTTTAAACCCTAGACTCGACTCTAACCCCGACCGACCTTTTATATATAAAA
131 GGGGTCGGGTAGGGTTTTAAACCCTAGACTCGACTCTAACCCCGACCGACCTTTTATATATAAAA
64578 CACGACCTGTCCTAATTTGACCCTACCCAAATCCGATTTTTTGTTAAAAG
196 CACGACCTGTCCTAATTTGACCCTACCCAAATCCGATTTTTTGTTAAAAG
64628 AATAATAACAGAAGAATAGTTTAGGTACCCGATTTGATAAAAAAAACAGTTTAGGTACTTAAAAC
1 AATAATAACAGAAGAATAGTTTAGGTACCCGATTTGATAAAAAAAACAGTTTAGGTACTTAAAAC
64693 AAAAAAAACAGCATAGTTTGAGGGCTGATTTTTCATTTAAGCCTAATTTTAATTGTAAAGTAGTC
66 AAAAAAAACAGCATAGTTTGAGGGCTGATTTTTCATTTAAGCCTAATTTTAATTGTAAAGTAGTC
64758 GGGGTCGGGTAGGGTTTTAAACCCTAGACTCGACTCTAACCCCGACCGACCTTTTATATATAAAA
131 GGGGTCGGGTAGGGTTTTAAACCCTAGACTCGACTCTAACCCCGACCGACCTTTTATATATAAAA
*
64823 CACGACCTGTCCTCATTTGACCCTACCCAAATCCGATTTTTTGTTAAAAG
196 CACGACCTGTCCTAATTTGACCCTACCCAAATCCGATTTTTTGTTAAAAG
64873 AA
1 AA
64875 AACCTAACTC
Statistics
Matches: 488, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
244 282 0.58
245 206 0.42
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (245 bp):
AATAATAACAGAAGAATAGTTTAGGTACCCGATTTGATAAAAAAAACAGTTTAGGTACTTAAAAC
AAAAAAAACAGCATAGTTTGAGGGCTGATTTTTCATTTAAGCCTAATTTTAATTGTAAAGTAGTC
GGGGTCGGGTAGGGTTTTAAACCCTAGACTCGACTCTAACCCCGACCGACCTTTTATATATAAAA
CACGACCTGTCCTAATTTGACCCTACCCAAATCCGATTTTTTGTTAAAAG
Found at i:65167 original size:60 final size:59
Alignment explanation
Indices: 65098--65214 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 59
65088 GTACACATGG
* * * *
65098 TCTCTGACTATATAG-TGTTATTTTTTTGAGTT-TTCCGACTATTAAAAGTTATAAAATGA
1 TCTCTGACTATA-AGATGTTACTTTGTTAAGTTACT-CGACTATTAAAAGTTATAAAATGA
*
65157 TCTCTCGACTATAGGATGTTACTTTGTTAAGTTACTCGACTATTAAAAGTTATAAAAT
1 TCTCT-GACTATAAGATGTTACTTTGTTAAGTTACTCGACTATTAAAAGTTATAAAAT
65215 AGTTATTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 6 0.12
60 43 0.86
61 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.43
Consensus pattern (59 bp):
TCTCTGACTATAAGATGTTACTTTGTTAAGTTACTCGACTATTAAAAGTTATAAAATGA
Found at i:71632 original size:45 final size:45
Alignment explanation
Indices: 71567--71653 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
71557 AATTAATTAC
71567 TATTGATGTGGCTGCCTGTTATCAATACATCATCAAAACGACGAT
1 TATTGATGTGGCTGCCTGTTATCAATACATCATCAAAACGACGAT
*
71612 TATTGATGTGGCTGCTTGTTATCAATACATCATCAAAACGAC
1 TATTGATGTGGCTGCCTGTTATCAATACATCATCAAAACGAC
71654 ACCGTTTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (45 bp):
TATTGATGTGGCTGCCTGTTATCAATACATCATCAAAACGACGAT
Found at i:80728 original size:20 final size:20
Alignment explanation
Indices: 80705--80775 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
80695 CACAGAATGT
80705 AAGATTACCAGTTGGAATAA
1 AAGATTACCAGTTGGAATAA
*
80725 AAGATTATCAGTTGGAATAA
1 AAGATTACCAGTTGGAATAA
* *
80745 AAGATTATCAGTGGGAATAA
1 AAGATTACCAGTTGGAATAA
*
80765 AATATTACCAG
1 AAGATTACCAG
80776 GGAATATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (20 bp):
AAGATTACCAGTTGGAATAA
Found at i:85602 original size:16 final size:18
Alignment explanation
Indices: 85581--85624 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
85571 TTTAAAATAA
*
85581 AAATATTTAAAGTTA-T-
1 AAATATTTAAAATTATTC
85597 AAATA--TAAAATTATTC
1 AAATATTTAAAATTATTC
85613 AAATATTTAAAA
1 AAATATTTAAAA
85625 AATTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 7 0.30
15 1 0.04
16 10 0.43
18 5 0.22
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATATTTAAAATTATTC
Found at i:85623 original size:24 final size:23
Alignment explanation
Indices: 85570--85624 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
85560 TTATTTAATT
*
85570 TTTTAAAATAAAAATATTTAAAG
1 TTTTAAAATAAAAATATTCAAAG
* *
85593 TTATAAATATAAAATTATTCAAA-
1 TTTTAAA-ATAAAAATATTCAAAG
85616 TATTTAAAA
1 T-TTTAAAA
85625 AATTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TTTTAAAATAAAAATATTCAAAG
Found at i:85898 original size:25 final size:25
Alignment explanation
Indices: 85870--85918 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
85860 CTGGATTAAT
*
85870 CGAGATTTACAAAATTTAAATTAGC
1 CGAGACTTACAAAATTTAAATTAGC
* *
85895 CGAGACTTACAAATTTTAGATTAG
1 CGAGACTTACAAAATTTAAATTAG
85919 TTGAAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (25 bp):
CGAGACTTACAAAATTTAAATTAGC
Found at i:85929 original size:25 final size:25
Alignment explanation
Indices: 85874--85929 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
85864 ATTAATCGAG
*
85874 ATTTACAAAATTTAAATTAGCCGAG
1 ATTTACAAAATTTAAATTAGCCGAA
* * * **
85899 ACTTACAAATTTTAGATTAGTTGAA
1 ATTTACAAAATTTAAATTAGCCGAA
85924 ATTTAC
1 ATTTAC
85930 TATGTATTCT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (25 bp):
ATTTACAAAATTTAAATTAGCCGAA
Found at i:106617 original size:36 final size:35
Alignment explanation
Indices: 106533--106620 Score: 108
Period size: 36 Copynumber: 2.5 Consensus size: 35
106523 AGTCATATAT
* *
106533 TCGGGTCGGGTCCGGTCGGGTGAAACCTTAATTTCG
1 TCGGGTCGGGTCGGGTCCGGTGAAACCTT-ATTTCG
106569 TCGGGTCGGGTCGGGTCACGGTGAAACCCTT-TCTTC-
1 TCGGGTCGGGTCGGGTC-CGGTGAAA-CCTTAT-TTCG
106605 TCGGGTCGGGTCGGGT
1 TCGGGTCGGGTCGGGT
106621 GGCCCAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
36 33 0.70
37 10 0.21
38 4 0.09
ACGTcount: A:0.10, C:0.24, G:0.39, T:0.27
Consensus pattern (35 bp):
TCGGGTCGGGTCGGGTCCGGTGAAACCTTATTTCG
Found at i:108117 original size:2 final size:2
Alignment explanation
Indices: 108110--108134 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
108100 ATGGAGATGT
108110 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
108135 GAGTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:108357 original size:2 final size:2
Alignment explanation
Indices: 108350--108382 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
108340 TGATCTTACC
108350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
108383 TATGTTGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.