Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001907.1 Hibiscus syriacus cultivar Beakdansim tig00003860_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: 72680
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:5438 original size:15 final size:16
Alignment explanation
Indices: 5420--5449 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5410 CAGCGGTTGG
5420 AAACCCTAG-GGTTTC
1 AAACCCTAGTGGTTTC
5435 AAACCCTAGTGGTTT
1 AAACCCTAGTGGTTT
5450 AGGTTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (16 bp):
AAACCCTAGTGGTTTC
Found at i:5547 original size:3 final size:3
Alignment explanation
Indices: 5539--5570 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
5529 ATATATATTA
5539 AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A
5571 TTAACGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:7615 original size:64 final size:63
Alignment explanation
Indices: 7532--7657 Score: 234
Period size: 64 Copynumber: 2.0 Consensus size: 63
7522 TGATGAAATT
*
7532 TATCTGGTGAAAAGTAGATTATTGGTAGGACACACTATCCGTCTCGTCTTCAACCATTTTATC
1 TATCTGGTGAAAAGTAGATTATTGGTAGGACACACTATCCGCCTCGTCTTCAACCATTTTATC
7595 TATCGTGGTGAAAAGTAGATTATTGGTAGGACACACTATCCGCCTCGTCTTCAACCATTTTAT
1 TATC-TGGTGAAAAGTAGATTATTGGTAGGACACACTATCCGCCTCGTCTTCAACCATTTTAT
7658 TCATTATGAC
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 4 0.07
64 57 0.93
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
TATCTGGTGAAAAGTAGATTATTGGTAGGACACACTATCCGCCTCGTCTTCAACCATTTTATC
Found at i:8843 original size:2 final size:2
Alignment explanation
Indices: 8836--8886 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
8826 TTAAAACAAC
8836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8878 TA TA TA TA T
1 TA TA TA TA T
8887 GCATATGATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9039 original size:12 final size:12
Alignment explanation
Indices: 9004--9040 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
8994 ATACGTGTGT
9004 GTATATATAT-A
1 GTATATATATAA
*
9015 -TATATATAAAA
1 GTATATATATAA
9026 GTATATATATAA
1 GTATATATATAA
9038 GTA
1 GTA
9041 ATTAAGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 8 0.36
11 1 0.05
12 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
GTATATATATAA
Found at i:9050 original size:16 final size:16
Alignment explanation
Indices: 9031--9065 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9021 TAAAAGTATA
9031 TATATAAGTAATTAAG
1 TATATAAGTAATTAAG
* *
9047 TATATATGTAATTATG
1 TATATAAGTAATTAAG
9063 TAT
1 TAT
9066 GATCAATGAT
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:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (16 bp):
TATATAAGTAATTAAG
Found at i:9110 original size:19 final size:19
Alignment explanation
Indices: 9071--9110 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9061 TGTATGATCA
*
9071 ATGATGTATGTACATATGT
1 ATGATGTATGTACATAAGT
*
9090 ATGATGTATGTAGATAAGT
1 ATGATGTATGTACATAAGT
9109 AT
1 AT
9111 ATATATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.40
Consensus pattern (19 bp):
ATGATGTATGTACATAAGT
Found at i:9291 original size:2 final size:2
Alignment explanation
Indices: 9263--9315 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
9253 ATGTATATGC
* * * *
9263 AT AT AT AC AT AT GT AT GT AT GT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9304 AT AT AT AT AT AT
1 AT AT AT AT AT AT
9316 CATAATTTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9687 original size:13 final size:13
Alignment explanation
Indices: 9664--9707 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
9654 TAAAATTAAT
*
9664 TTAATGATTATAA
1 TTAAGGATTATAA
**
9677 TTAAGTTTTATAA
1 TTAAGGATTATAA
9690 TATAAGGATTATAA
1 T-TAAGGATTATAA
9704 TTAA
1 TTAA
9708 TGTATAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (13 bp):
TTAAGGATTATAA
Found at i:12073 original size:32 final size:31
Alignment explanation
Indices: 12037--12113 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
12027 CGGGGCCGTG
*
12037 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
12069 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
12100 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
12114 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:12096 original size:63 final size:63
Alignment explanation
Indices: 11990--12113 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
11980 ACCTAAGGGA
* * ** *
11990 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
12053 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
12114 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:17052 original size:32 final size:31
Alignment explanation
Indices: 16966--17090 Score: 83
Period size: 31 Copynumber: 4.0 Consensus size: 31
16956 TACATAAGGG
* *
16966 AACATCTTAGGGCCTG-AGAGCCTACCCAAGA
1 AACATCTTAGGGCC-GCAGGGCCTACCTAAGA
* * * **
16997 TAGAT-TTCAGGGTCGTGGGGCCTACCTAAGA
1 AACATCTT-AGGGCCGCAGGGCCTACCTAAGA
* **
17028 ACACATCTTAGGGCTGCAGGGCCTACCCGAGA
1 A-ACATCTTAGGGCCGCAGGGCCTACCTAAGA
** * *
17060 ATGATCTTAGGGCCGTAGAGCCTACCTAAGA
1 AACATCTTAGGGCCGCAGGGCCTACCTAAGA
17091 GTCACATTAG
Statistics
Matches: 69, Mismatches: 21, Indels: 8
0.70 0.21 0.08
Matches are distributed among these distances:
30 3 0.04
31 43 0.62
32 21 0.30
33 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (31 bp):
AACATCTTAGGGCCGCAGGGCCTACCTAAGA
Found at i:17083 original size:63 final size:63
Alignment explanation
Indices: 16967--17090 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
16957 ACATAAGGGA
* * *
16967 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGTCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGCCGTAGAGCCTACCTAAGAAC
* *
17030 ACATCTTAGGG-CTGCAGGGCCTACCCGAGA-ATGATCTT-AGGGCCGTAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GAT-TTCAGGGCCGTAGAGCCTACCTAAGA
17091 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 4 0.08
63 47 0.89
64 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGCCGTAGAGCCTACCTAAGAAC
Found at i:22041 original size:32 final size:31
Alignment explanation
Indices: 22003--22079 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
21993 CGGGGCTGTG
*
22003 GGGCCTACCTAAGAACACATCTTAGGGCCGTA
1 GGGCCTACCTAAGAA-ACATCTTAGGGCCGCA
** **
22035 GGGCCTACCCGAGAATGATCTTAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTTAGGGCCGCA
*
22066 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
22080 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTTAGGGCCGCA
Found at i:29823 original size:32 final size:31
Alignment explanation
Indices: 29787--29862 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
29777 CGGGGCCGTG
*
29787 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** ** *
29819 GGGCCTACCCGAGAATGATCTCAGGGCCGTA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
29850 GAGCCTACCTAAG
1 GGGCCTACCTAAG
29863 TGTCACAATA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:29846 original size:63 final size:63
Alignment explanation
Indices: 29740--29862 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
29730 ACCTAAGGGA
* * * * *
29740 ACATCTTAGGGCATGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCACGAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAAC
* *
29803 ACATCTTAGGGC-CGCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGTAGAGCCTACCTAAG
1 ACATCTTAGGGCACG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGTAGAGCCTACCTAAG
29863 TGTCACAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCACGAGAGCCTACCCAAGATAGATCTCAGGGCCGTAGAGCCTACCTAAGAAC
Found at i:32746 original size:13 final size:13
Alignment explanation
Indices: 32728--32758 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
32718 AACGATCAAC
32728 GGTCAACGGGTCG
1 GGTCAACGGGTCG
32741 GGTCAACGGGTCG
1 GGTCAACGGGTCG
32754 GGTCA
1 GGTCA
32759 GGTTGTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.23, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:37731 original size:13 final size:13
Alignment explanation
Indices: 37713--37741 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
37703 ACCGGTCAAC
37713 GGTCAACGGGTCG
1 GGTCAACGGGTCG
37726 GGTCAACGGGTCG
1 GGTCAACGGGTCG
37739 GGT
1 GGT
37742 TGGGTCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:38887 original size:32 final size:31
Alignment explanation
Indices: 38851--38927 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
38841 TGGGGCCGTG
*
38851 GGGCCTACCTAAGAACACATCTTAGGGCCACA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
** ** *
38883 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
38914 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
38928 GTAACTTTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:41802 original size:18 final size:18
Alignment explanation
Indices: 41781--41826 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
41771 CACCGGTCAA
*
41781 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAACGGGT
*
41799 CGGGTTGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
41817 CGGGTCGGGT
1 CGGGTCGGGT
41827 TGTGACCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.09, C:0.17, G:0.52, T:0.22
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:43908 original size:32 final size:32
Alignment explanation
Indices: 43832--43925 Score: 86
Period size: 32 Copynumber: 3.0 Consensus size: 32
43822 ACCTAAGGGA
* * *
43832 ACATCTTAGGGCC-TGAGAGCCTACCCAAG-AT
1 ACATCTTAGGGCCGTG-GGGCCTACCTAAGAAC
*
43863 AGAT-TTCAGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTT-AGGGCCGTGGGGCCTACCTAAGAAC
** *
43895 ACATCTTAGGGCCGCAGGGCCTACCTGAGAA
1 ACATCTTAGGGCCGTGGGGCCTACCTAAGAA
43926 TGATCTCAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
30 2 0.04
31 20 0.39
32 27 0.53
33 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.18
Consensus pattern (32 bp):
ACATCTTAGGGCCGTGGGGCCTACCTAAGAAC
Found at i:43935 original size:63 final size:63
Alignment explanation
Indices: 43832--43955 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
43822 ACCTAAGGGA
* ** *
43832 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* **
43895 ACATCTTAGGGCC-GCAGGGCCTACCTGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
43956 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:43940 original size:31 final size:32
Alignment explanation
Indices: 43868--43955 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 32
43858 AAGATAGATT
**
43868 TCAGGGCCGTGGGGCCTACCTAAGAACACATC
1 TCAGGGCCGCAGGGCCTACCTAAGAACACATC
* * **
43900 TTAGGGCCGCAGGGCCTACCTGAGAA-TGATC
1 TCAGGGCCGCAGGGCCTACCTAAGAACACATC
*
43931 TCAGGGCCGCAGAGCCTACCTAAGA
1 TCAGGGCCGCAGGGCCTACCTAAGA
43956 GTCACATTAG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 25 0.53
32 22 0.47
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (32 bp):
TCAGGGCCGCAGGGCCTACCTAAGAACACATC
Found at i:49270 original size:13 final size:13
Alignment explanation
Indices: 49252--49294 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
49242 ACCGGTCAAC
49252 GGTCAACGGGTCG
1 GGTCAACGGGTCG
49265 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
49278 GGCCAACGGGTCG
1 GGTCAACGGGTCG
49291 GGTC
1 GGTC
49295 GGGTTGTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.14, C:0.26, G:0.47, T:0.14
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:50270 original size:13 final size:13
Alignment explanation
Indices: 50252--50300 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 13
50242 ACCGGTCAAC
50252 GGTCAACGGGTCG
1 GGTCAACGGGTCG
50265 GGTCAACGGGTCAGGTTG
1 GGTCAACGGGTC-----G
50283 GGTCAACGGGTCG
1 GGTCAACGGGTCG
50296 GGTCA
1 GGTCA
50301 GGTTGTGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 18 0.58
18 13 0.42
ACGTcount: A:0.16, C:0.20, G:0.45, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:54309 original size:13 final size:13
Alignment explanation
Indices: 54291--54333 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
54281 ACCGGTCAAC
54291 GGTCAACGGGTCG
1 GGTCAACGGGTCG
54304 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
54317 GGTCAACGGGTCA
1 GGTCAACGGGTCG
54330 GGTC
1 GGTC
54334 GGGTTGTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:59275 original size:13 final size:13
Alignment explanation
Indices: 59257--59286 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
59247 GGTCAATAGT
59257 GGTCAACGGGTCG
1 GGTCAACGGGTCG
59270 GGTCAACGGGTCG
1 GGTCAACGGGTCG
59283 GGTC
1 GGTC
59287 GGGTTGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:64295 original size:23 final size:23
Alignment explanation
Indices: 64266--64316 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
64256 CAACGGTCAA
64266 CGGGTCGAGTCAACGGGTCGGGT
1 CGGGTCGAGTCAACGGGTCGGGT
* *
64289 CGGGTCGGGTCAACTGGTCGGGT
1 CGGGTCGAGTCAACGGGTCGGGT
64312 CGGGT
1 CGGGT
64317 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.20
Consensus pattern (23 bp):
CGGGTCGAGTCAACGGGTCGGGT
Found at i:64309 original size:13 final size:13
Alignment explanation
Indices: 64260--64312 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
64250 ACCGATCAAC
64260 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
64273 AGTCAACGGGTCG
1 GGTCAACGGGTCG
64286 GGT---CGGGTCG
1 GGTCAACGGGTCG
*
64296 GGTCAACTGGTCG
1 GGTCAACGGGTCG
64309 GGTC
1 GGTC
64313 GGGTTGTGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 10 0.29
13 24 0.71
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:65286 original size:2 final size:2
Alignment explanation
Indices: 65274--65354 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
65264 CGACCGATAG
*
65274 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65316 TA TA TA 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 TA TA TA T
65355 TAATTTTAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:66937 original size:30 final size:30
Alignment explanation
Indices: 66894--66953 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
66884 AAAAATTCAA
* *
66894 GGACTAAATTGAAATTTTAATTAAATTTAG
1 GGACCAAAGTGAAATTTTAATTAAATTTAG
66924 GGACCAAAGTGAAATTTTAATTAAATTTAG
1 GGACCAAAGTGAAATTTTAATTAAATTTAG
66954 ATCTAAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (30 bp):
GGACCAAAGTGAAATTTTAATTAAATTTAG
Found at i:67443 original size:32 final size:33
Alignment explanation
Indices: 67396--67459 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
67386 ATGCAAAAAG
*
67396 GGTACCAATACCCCCCAGGGGTATGCATACCCA
1 GGTACCAATACCCCCCAGGGGTATCCATACCCA
*
67429 GGTACCGATA-CCCCCAGGGGTATCCATACCC
1 GGTACCAATACCCCCCAGGGGTATCCATACCC
67460 CCTGGTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.25, C:0.38, G:0.22, T:0.16
Consensus pattern (33 bp):
GGTACCAATACCCCCCAGGGGTATCCATACCCA
Found at i:67457 original size:18 final size:18
Alignment explanation
Indices: 67407--67461 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
67397 GTACCAATAC
*
67407 CCCCCAGGGGTATGCATA
1 CCCCCAGGGGTATCCATA
67425 --CCCA--GGTA-CCGATA
1 CCCCCAGGGGTATCC-ATA
67439 CCCCCAGGGGTATCCATA
1 CCCCCAGGGGTATCCATA
67457 CCCCC
1 CCCCC
67462 TGGTTGCAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
13 1 0.03
14 7 0.23
16 8 0.27
18 12 0.40
19 2 0.07
ACGTcount: A:0.22, C:0.42, G:0.22, T:0.15
Consensus pattern (18 bp):
CCCCCAGGGGTATCCATA
Found at i:70094 original size:87 final size:85
Alignment explanation
Indices: 69940--70109 Score: 259
Period size: 87 Copynumber: 2.0 Consensus size: 85
69930 ACCAAACACA
* *
69940 CCTTTTTAGCCAGTTATCCTAATCATATTAGACTTTTATTTTCAAATTAATTAAATCTATATTTA
1 CCTTTTTAGCCAGTTACCCTAATCATATTAGACATTTATTTTCAAATTAATTAAATCTATATTTA
* *
70005 ATTAATTAGAATTTAATAAT
66 ATTAATTAAAATTAAATAAT
* **
70025 CCTTTTATATCCAGTTACCCTAATCATATTAGGGATTTATTATTCAAATTAATTAAATCTATATT
1 CCTTTT-TAGCCAGTTACCCTAATCATATTAGACATTTATT-TTCAAATTAATTAAATCTATATT
70090 TAATTAATTAAAATTAAATA
64 TAATTAATTAAAATTAAATA
70110 TTAGAGATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
85 6 0.08
86 29 0.38
87 41 0.54
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (85 bp):
CCTTTTTAGCCAGTTACCCTAATCATATTAGACATTTATTTTCAAATTAATTAAATCTATATTTA
ATTAATTAAAATTAAATAAT
Found at i:70139 original size:20 final size:21
Alignment explanation
Indices: 70071--70140 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
70061 TTATTATTCA
*
70071 AATTAATTAAATC-TATATTT
1 AATTAATTAAAACATATATTT
* * *
70091 AATTAATTAAAATTAAATATTAG
1 AATTAATTAAAA-CATATATT-T
70114 AGATT-ATTAAAACATATATTT
1 A-ATTAATTAAAACATATATTT
70135 AATTAA
1 AATTAA
70141 CTCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 14 0.37
21 2 0.05
22 11 0.29
23 8 0.21
24 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAACATATATTT
Done.