Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005175.1 Hibiscus syriacus cultivar Beakdansim tig00011676_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: 44344
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:66 original size:22 final size:22
Alignment explanation
Indices: 37--89 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
27 CTATATCGGT
37 AATT-GAGTTGCAAAATTGGCG
1 AATTCGAGTTGCAAAATTGGCG
*
58 AATTCGAGTTGCGAAATTGGCG
1 AATTCGAGTTGCAAAATTGGCG
80 AATTCGAGTT
1 AATTCGAGTT
90 ACGGATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.30
Consensus pattern (22 bp):
AATTCGAGTTGCAAAATTGGCG
Found at i:1761 original size:33 final size:32
Alignment explanation
Indices: 1724--1951 Score: 131
Period size: 33 Copynumber: 6.9 Consensus size: 32
1714 GTAATTTAGT
* * *
1724 TTTTGGTAATTCGGGAGTTTTGGTTAACTCTGG
1 TTTTGGTAATTCAGGAATTTAGG-TAACTCTGG
* *
1757 TTTTGGT-ATCTCAGGAATTTAGGTAATTCTGA
1 TTTTGGTAAT-TCAGGAATTTAGGTAACTCTGG
* * ** *
1789 CTTAGGTAGCTCAGGAATTTTGGTAACTCTGG
1 TTTTGGTAATTCAGGAATTTAGGTAACTCTGG
* * *
1821 TTTCGGTAATTCATGAACTTTAGGTAATTCTGG
1 TTTTGGTAATTCAGGAA-TTTAGGTAACTCTGG
* * * *
1854 TTTTGGTAACTCGGGAACGTT-GGTAA-TTTAGGAG
1 TTTTGGTAATTCAGGAA-TTTAGGTAACTCT--G-G
* * * *
1888 CTTTGGTCGCATT-AGGAACTTTAGGCAATTCTGG
1 TTTTGGT--AATTCAGGAA-TTTAGGTAACTCTGG
*
1922 TTTCGGTAATTCAGGAACTTTAGGTAACTC
1 TTTTGGTAATTCAGGAA-TTTAGGTAACTC
1952 AGGAGCTTTG
Statistics
Matches: 147, Mismatches: 37, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
31 2 0.01
32 53 0.36
33 63 0.43
34 13 0.09
35 8 0.05
36 6 0.04
37 2 0.01
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (32 bp):
TTTTGGTAATTCAGGAATTTAGGTAACTCTGG
Found at i:1782 original size:65 final size:65
Alignment explanation
Indices: 1724--1879 Score: 181
Period size: 65 Copynumber: 2.4 Consensus size: 65
1714 GTAATTTAGT
* * *
1724 TTTTGGTAATTCGGGAGTTTTGGTTAACTCTGGTTTTGGT-ATCTCAGGAA-TTTAGGTAATTCT
1 TTTTGGTAACTCGGGAATTTTGG-TAACTCTGGTTTCGGTAAT-TCAGGAACTTTAGGTAATTCT
1787 GA
64 GA
* * * * * *
1789 CTTAGGTAGCTCAGGAATTTTGGTAACTCTGGTTTCGGTAATTCATGAACTTTAGGTAATTCTGG
1 TTTTGGTAACTCGGGAATTTTGGTAACTCTGGTTTCGGTAATTCAGGAACTTTAGGTAATTCTGA
**
1854 TTTTGGTAACTCGGGAACGTTGGTAA
1 TTTTGGTAACTCGGGAATTTTGGTAA
1880 TTTAGGAGCT
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
64 21 0.28
65 53 0.72
ACGTcount: A:0.22, C:0.12, G:0.26, T:0.40
Consensus pattern (65 bp):
TTTTGGTAACTCGGGAATTTTGGTAACTCTGGTTTCGGTAATTCAGGAACTTTAGGTAATTCTGA
Found at i:1807 original size:32 final size:32
Alignment explanation
Indices: 1761--1870 Score: 94
Period size: 32 Copynumber: 3.4 Consensus size: 32
1751 CTCTGGTTTT
*
1761 GGTATCTCAGGAATTTAGGTAATTCTGACTTA
1 GGTAACTCAGGAATTTAGGTAATTCTGACTTA
* * * ** *
1793 GGTAGCTCAGGAATTTTGGTAACTCTGGTTTC
1 GGTAACTCAGGAATTTAGGTAATTCTGACTTA
* * ** *
1825 GGTAATTCATGAACTTTAGGTAATTCTGGTTTT
1 GGTAACTCAGGAA-TTTAGGTAATTCTGACTTA
*
1858 GGTAACTCGGGAA
1 GGTAACTCAGGAA
1871 CGTTGGTAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
32 36 0.58
33 26 0.42
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (32 bp):
GGTAACTCAGGAATTTAGGTAATTCTGACTTA
Found at i:1919 original size:68 final size:69
Alignment explanation
Indices: 1835--1962 Score: 186
Period size: 68 Copynumber: 1.9 Consensus size: 69
1825 GGTAATTCAT
* * * * *
1835 GAACTTTAGGTAATTCTGGTTTTGGTAACTCGGGAACGTT-GGTAATTTAGGAGCTTTGGTCGCA
1 GAACTTTAGGCAATTCTGGTTTCGGTAACTCAGGAACGTTAGGTAACTCAGGAGCTTTGGTCGCA
1899 TTAG
66 TTAG
* *
1903 GAACTTTAGGCAATTCTGGTTTCGGTAATTCAGGAACTTTAGGTAACTCAGGAGCTTTGG
1 GAACTTTAGGCAATTCTGGTTTCGGTAACTCAGGAACGTTAGGTAACTCAGGAGCTTTGG
1963 GTAATTCTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
68 35 0.67
69 17 0.33
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.35
Consensus pattern (69 bp):
GAACTTTAGGCAATTCTGGTTTCGGTAACTCAGGAACGTTAGGTAACTCAGGAGCTTTGGTCGCA
TTAG
Found at i:1953 original size:18 final size:18
Alignment explanation
Indices: 1926--1966 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1916 TTCTGGTTTC
*
1926 GGTAATTCAGGAACTTTA
1 GGTAACTCAGGAACTTTA
* *
1944 GGTAACTCAGGAGCTTTG
1 GGTAACTCAGGAACTTTA
1962 GGTAA
1 GGTAA
1967 TTCTGACTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (18 bp):
GGTAACTCAGGAACTTTA
Found at i:2138 original size:33 final size:32
Alignment explanation
Indices: 2068--2168 Score: 132
Period size: 33 Copynumber: 3.1 Consensus size: 32
2058 TTTGGCATTG
* *
2068 TTGGAAACTCGGGAACCTTAGGAACTTC-GGCT
1 TTGGCAACTCAGGAACCTTAGGAA-TTCAGGCT
*
2100 TTGGCAACTCAGGAATCTTAGGCAATTCAGGCT
1 TTGGCAACTCAGGAACCTTAGG-AATTCAGGCT
*
2133 TTGGCAACTCAGGAACCTTAGGTATTTCAGGCT
1 TTGGCAACTCAGGAACCTTAGG-AATTCAGGCT
2166 TTG
1 TTG
2169 AAATTTCCGA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
32 22 0.36
33 39 0.64
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.29
Consensus pattern (32 bp):
TTGGCAACTCAGGAACCTTAGGAATTCAGGCT
Found at i:2144 original size:15 final size:15
Alignment explanation
Indices: 2096--2145 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
2086 TAGGAACTTC
2096 GGCTTTGGCAACTCA
1 GGCTTTGGCAACTCA
* *
2111 GGAATCTTAGGCAATTCA
1 GG---CTTTGGCAACTCA
2129 GGCTTTGGCAACTCA
1 GGCTTTGGCAACTCA
2144 GG
1 GG
2146 AACCTTAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 15 0.54
18 13 0.46
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (15 bp):
GGCTTTGGCAACTCA
Found at i:6505 original size:18 final size:18
Alignment explanation
Indices: 6484--6518 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6474 CTTTTGATAA
* *
6484 CTCAGGAGCTTTGGGCAT
1 CTCAGGAACTTTAGGCAT
6502 CTCAGGAACTTTAGGCA
1 CTCAGGAACTTTAGGCA
6519 ATTCTGATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (18 bp):
CTCAGGAACTTTAGGCAT
Found at i:6534 original size:69 final size:68
Alignment explanation
Indices: 6365--6536 Score: 184
Period size: 69 Copynumber: 2.5 Consensus size: 68
6355 TTTTGAAAAT
* * * * * * * * *
6365 TCAGGAATTTTAGGAAATTATGATTTTGGCACCTCAGGAACATTTGGTAATTTAGGAGCTTTGGT
1 TCAGGAACTTTAGGCAATTCTGA-TTTGGTAACTCAGGAACATTTGATAACTCAGGAGCTTTGGG
6430 CACC
65 CACC
* * *
6434 T-AGAGAACTTTAGGCAATTCTAGCTTTGGTAATTCAGGAACTTTTGATAACTCAGGAGCTTTGG
1 TCAG-GAACTTTAGGCAATTCT-GATTTGGTAACTCAGGAACATTTGATAACTCAGGAGCTTTGG
*
6498 GCATC
64 GCACC
6503 TCAGGAACTTTAGGCAATTCTGATTTCGGTAACT
1 TCAGGAACTTTAGGCAATTCTGATTT-GGTAACT
6537 TTTGAACTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
68 6 0.07
69 75 0.89
70 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (68 bp):
TCAGGAACTTTAGGCAATTCTGATTTGGTAACTCAGGAACATTTGATAACTCAGGAGCTTTGGGC
ACC
Found at i:6994 original size:43 final size:44
Alignment explanation
Indices: 6947--7356 Score: 234
Period size: 43 Copynumber: 9.3 Consensus size: 44
6937 TATTCTTTTT
* * * *
6947 TTTTTTCAATCTCACTTTTTATCTTTATAATTGAAGTCTC-TAA
1 TTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGGCCCTTAA
* *
6990 -TTTTTCAATC-C-C--CTT---TTT-TAATTGA-GGCCCCTAA
1 TTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGGCCCTTAA
*
7024 TTTTTT-AATCTCATTTTTTTTTAACTTTATAATTGA-GGCCCTTAA
1 TTTTTTCAATCTCA---CTTTTTAACTTTATAATTGAGGGCCCTTAA
*
7069 GTTTTTTCAATCTCACTTTCTACCTTTTCTAACTTTATAATTGAGGG-CCATAA
1 -TTTTTTCAA--T--C--TC-A-CTTTT-TAACTTTATAATTGAGGGCCCTTAA
* * * *
7122 TTTTTT-AATCCCGCTTTTTTAACTTTACAATTGAGGG-CCATAA
1 TTTTTTCAATCTCAC-TTTTTAACTTTATAATTGAGGGCCCTTAA
* * *
7165 TTTTTT-AATCCCGCTTTTTTAACTTTACAATTGA-GGCCCTTAA
1 TTTTTTCAATCTCAC-TTTTTAACTTTATAATTGAGGGCCCTTAA
* * * *
7208 GTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGGACCC-TAA
1 -TTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGGCCCTTAA
* * * *
7252 TTTTTT-AATCTCACTTTTTTTAAAATTTTATAATTTA-AGCTCTTAA
1 TTTTTTCAATCTCAC--TTTTT--AACTTTATAATTGAGGGCCCTTAA
* * *
7298 TTTTTTTCAATCTCACTTTCTACCTTTATAATTGA-GGCCCCTAA
1 -TTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGGCCCTTAA
7342 GTTTTTTCAATCTCA
1 -TTTTTTCAATCTCA
7357 ATTATACATT
Statistics
Matches: 295, Mismatches: 36, Indels: 71
0.73 0.09 0.18
Matches are distributed among these distances:
33 3 0.01
34 14 0.05
35 9 0.03
38 2 0.01
40 1 0.00
41 3 0.01
42 19 0.06
43 69 0.23
44 67 0.23
45 27 0.09
46 24 0.08
47 9 0.03
48 8 0.03
49 2 0.01
51 3 0.01
52 10 0.03
53 22 0.07
54 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.49
Consensus pattern (44 bp):
TTTTTTCAATCTCACTTTTTAACTTTATAATTGAGGGCCCTTAA
Found at i:7322 original size:90 final size:87
Alignment explanation
Indices: 7144--7356 Score: 264
Period size: 90 Copynumber: 2.4 Consensus size: 87
7134 GCTTTTTTAA
* * * * * *
7144 CTTTACAATTGAGGGCCATAATTTTTTAATCCCGCTTTTTTAACTTTACAATTGAGGCCCTTAAG
1 CTTTATAATTGAGGACCCTAATTTTTTAATCTCACTTTTTTAACTTTACAATTGAAGCCCTTAAG
7209 TTTTTTCAATCTCAATTTCTAC
66 TTTTTTCAATCTCAATTTCTAC
* * * *
7231 CTTTATAATTGAGGACCCTAATTTTTTAATCTCACTTTTTTTAAAATTTTATAATTTAAGCTCTT
1 CTTTATAATTGAGGACCCTAATTTTTTAATCTCAC-TTTTTT--AACTTTACAATTGAAGCCCTT
* *
7296 AATTTTTTTCAATCTCACTTTCTAC
63 AAGTTTTTTCAATCTCAATTTCTAC
*
7321 CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCA
1 CTTTATAATTGAGGACCCTAA-TTTTTT-AATCTCA
7357 ATTATACATT
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
87 30 0.28
88 6 0.06
90 59 0.55
91 6 0.06
92 7 0.06
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.46
Consensus pattern (87 bp):
CTTTATAATTGAGGACCCTAATTTTTTAATCTCACTTTTTTAACTTTACAATTGAAGCCCTTAAG
TTTTTTCAATCTCAATTTCTAC
Found at i:7347 original size:44 final size:43
Alignment explanation
Indices: 7092--7390 Score: 230
Period size: 43 Copynumber: 6.8 Consensus size: 43
7082 CACTTTCTAC
* * * *
7092 CTTTTCTAACTTTATAATTGAGGGCCATAATTTTTTAATCCCG
1 CTTTTCTAACTTTATAATTGAGGCCCCTAATTTTTTAATCTCA
* * * * * *
7135 CTTTTTTAACTTTACAATTGAGGGCCATAATTTTTTAATCCCG
1 CTTTTCTAACTTTATAATTGAGGCCCCTAATTTTTTAATCTCA
* * *
7178 CTTTTTTAACTTTACAATTGAGGCCCTTAAGTTTTTTCAATCTCA
1 CTTTTCTAACTTTATAATTGAGGCCCCTAA-TTTTTT-AATCTCA
* * *
7223 -ATTTCTACCTTTATAATTGAGGACCCTAATTTTTTAATCTCA
1 CTTTTCTAACTTTATAATTGAGGCCCCTAATTTTTTAATCTCA
* * * * * *
7265 CTTTTTTTAAAATTTTATAATTTAAGCTCTTAATTTTTTTCAATCTCA
1 C-TTTTCT--AACTTTATAATTGAGGCCCCTAA-TTTTTT-AATCTCA
*
7313 C-TTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCA
1 CTTTTCTAACTTTATAATTGAGGCCCCTAA-TTTTTT-AATCTCA
* * * *
7357 --ATTAT-ACATTTATATTTGAGGCCCCTAGTTTTTT
1 CTTTTCTAAC-TTTATAATTGAGGCCCCTAATTTTTT
7391 TCGACCTCAA
Statistics
Matches: 213, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
42 14 0.07
43 96 0.45
44 64 0.30
45 5 0.02
46 20 0.09
47 6 0.03
48 8 0.04
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (43 bp):
CTTTTCTAACTTTATAATTGAGGCCCCTAATTTTTTAATCTCA
Found at i:7391 original size:43 final size:44
Alignment explanation
Indices: 7188--7416 Score: 157
Period size: 44 Copynumber: 5.2 Consensus size: 44
7178 CTTTTTTAAC
* * * *
7188 TTTACAATTGAGGCCCTTAAG-TTTTTTCAATCTCAATTTCTACC
1 TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCAA-TTATACA
* * * *
7232 TTTATAATTGAGGACCCTAA--TTTTTT-AATCTCACTTTTTTTAAAA
1 TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCA---ATTAT-ACA
* * * * * * *
7277 TTTTATAATTTAAGCTCTTAA-TTTTTTTCAATCTCACTTTCTACC
1 -TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCA-ATTATACA
7322 TTTATAATTGAGGCCCCTAAG-TTTTTTCAATCTCAATTATACA
1 TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCAATTATACA
* * * * *
7365 TTTATATTTGAGGCCCCT-AGTTTTTTTCGACCTCAATGTCTACT
1 TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCAAT-TATACA
7409 TTTATAAT
1 TTTATAAT
7417 CAATGTCTCT
Statistics
Matches: 146, Mismatches: 29, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
42 9 0.06
43 42 0.29
44 61 0.42
45 2 0.01
46 19 0.13
47 6 0.04
48 7 0.05
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (44 bp):
TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCAATTATACA
Found at i:7391 original size:44 final size:45
Alignment explanation
Indices: 7188--7392 Score: 158
Period size: 44 Copynumber: 4.6 Consensus size: 45
7178 CTTTTTTAAC
* * * *
7188 TTTACAATTGAGGCCCTTAAG-TTTTTTCAATCTCA-ATTTCTACC
1 TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCACA-TTATACA
* * * *
7232 TTTATAATTGAGGACCCTAA--TTTTTT-AATCTCACTTTTTTTAAAA
1 TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCAC--ATTAT-ACA
* * * * * * *
7277 TTTTATAATTTAAGCTCTTAA-TTTTTTTCAATCTCACTTTCTACC
1 -TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCACATTATACA
7322 TTTATAATTGAGGCCCCTAAG-TTTTTTCAATCTCA-ATTATACA
1 TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCACATTATACA
*
7365 TTTATATTTGAGGCCCCT-AGTTTTTTTC
1 TTTATAATTGAGGCCCCTAAGTTTTTTTC
7393 GACCTCAATG
Statistics
Matches: 129, Mismatches: 23, Indels: 19
0.75 0.13 0.11
Matches are distributed among these distances:
42 9 0.07
43 35 0.27
44 50 0.39
45 2 0.02
46 19 0.15
47 6 0.05
48 8 0.06
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.48
Consensus pattern (45 bp):
TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCACATTATACA
Found at i:7898 original size:17 final size:18
Alignment explanation
Indices: 7876--7913 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
7866 CTTGGGAAAA
*
7876 TTTGGT-AATTCAGGAAT
1 TTTGGTCAACTCAGGAAT
*
7893 TTTGGTCACCTCAGGAAT
1 TTTGGTCAACTCAGGAAT
7911 TTT
1 TTT
7914 AGGCAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (18 bp):
TTTGGTCAACTCAGGAAT
Found at i:9137 original size:21 final size:22
Alignment explanation
Indices: 9113--9162 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
9103 TACTTACGTT
9113 CTTAAAAAATATAATTT-ATTA
1 CTTAAAAAATATAATTTAATTA
* * *
9134 CTT-AATAATTTATTTTAATTA
1 CTTAAAAAATATAATTTAATTA
9155 CTTAAAAA
1 CTTAAAAA
9163 TAAATAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.43
21 10 0.43
22 3 0.13
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (22 bp):
CTTAAAAAATATAATTTAATTA
Found at i:9877 original size:23 final size:20
Alignment explanation
Indices: 9851--9903 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
9841 AAAATGTGCC
9851 ACAAAGACAGAGATAAACATGTA
1 ACAAAGACAGAG---AACATGTA
* *
9874 ACAAAGGCAGAGAACATGTC
1 ACAAAGACAGAGAACATGTA
9894 ACAAAGACAG
1 ACAAAGACAG
9904 TTATTGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.59
23 11 0.41
ACGTcount: A:0.53, C:0.17, G:0.21, T:0.09
Consensus pattern (20 bp):
ACAAAGACAGAGAACATGTA
Found at i:10584 original size:13 final size:13
Alignment explanation
Indices: 10566--10598 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
10556 AATAGTTAAA
*
10566 TTTTAAACAATAC
1 TTTTAAACAACAC
10579 TTTTAAACAACAC
1 TTTTAAACAACAC
10592 TTTTAAA
1 TTTTAAA
10599 AGTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTTAAACAACAC
Found at i:11528 original size:2 final size:2
Alignment explanation
Indices: 11521--11561 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11511 GAATAATACC
11521 TA 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 TA T
11562 TACATGAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11987 original size:15 final size:15
Alignment explanation
Indices: 11967--12025 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
11957 ACTCAGAAAT
11967 TTTTGGTAACTCTGG
1 TTTTGGTAACTCTGG
* *
11982 TTTTGGTAATTCAGG
1 TTTTGGTAACTCTGG
*
11997 AACTTTTGGTAATTCTGG
1 ---TTTTGGTAACTCTGG
*
12015 TTATGGTAACT
1 TTTTGGTAACT
12026 TGGGAACATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 22 0.61
18 14 0.39
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (15 bp):
TTTTGGTAACTCTGG
Found at i:12005 original size:18 final size:18
Alignment explanation
Indices: 11982--12053 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 18
11972 GTAACTCTGG
11982 TTTTGGTAATTCAGGAAC
1 TTTTGGTAATTCAGGAAC
*
12000 TTTTGGTAATTCTGG---
1 TTTTGGTAATTCAGGAAC
* *
12015 TTATGGTAACTT-GGGAAC
1 TTTTGGTAA-TTCAGGAAC
* *
12033 ATTTGGTAATTCAGGAGC
1 TTTTGGTAATTCAGGAAC
12051 TTT
1 TTT
12054 GGTCGCATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
15 10 0.24
16 2 0.05
17 2 0.05
18 27 0.66
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.42
Consensus pattern (18 bp):
TTTTGGTAATTCAGGAAC
Found at i:12032 original size:33 final size:33
Alignment explanation
Indices: 11882--12110 Score: 174
Period size: 33 Copynumber: 6.8 Consensus size: 33
11872 GGTATTTCAT
* * *
11882 GTTTTGGTAATTCAGG-AGTTTTGGGTAATTCTA
1 GTTTTGGTAACTCAGGAACTTTT-GGTAATTCTG
* *
11915 GTTTTGGTATCTCAGGAA-TTTTAGGTAATTTTG
1 GTTTTGGTAACTCAGGAACTTTT-GGTAATTCTG
* * * *
11948 GCTTTGGTAACTCAGAAATTTTTGGTAACTCTG
1 GTTTTGGTAACTCAGGAACTTTTGGTAATTCTG
*
11981 GTTTTGGTAATTCAGGAACTTTTGGTAATTCTG
1 GTTTTGGTAACTCAGGAACTTTTGGTAATTCTG
* ** * *
12014 GTTATGGTAACTTGGGAACATTTGGTAATTCAGG
1 GTTTTGGTAACTCAGGAACTTTTGGTAATTC-TG
* ** * * * *
12048 AGCTTTGGTCGCATCAGAAACTTTAGGGAATTTTG
1 -GTTTTGGTAAC-TCAGGAACTTTTGGTAATTCTG
* * *
12083 ATTTTGGTAATTCAAGAACTTTTGGTAA
1 GTTTTGGTAACTCAGGAACTTTTGGTAA
12111 CACATGAGCT
Statistics
Matches: 149, Mismatches: 42, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
33 116 0.78
34 12 0.08
35 8 0.05
36 13 0.09
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (33 bp):
GTTTTGGTAACTCAGGAACTTTTGGTAATTCTG
Found at i:13302 original size:18 final size:18
Alignment explanation
Indices: 13279--13321 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
13269 ATTTAATTTG
*
13279 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
13297 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
13315 TTTATTT
1 TTTATTT
13322 TAAAAACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:15401 original size:30 final size:29
Alignment explanation
Indices: 15361--15525 Score: 172
Period size: 29 Copynumber: 5.6 Consensus size: 29
15351 CACATTCGAA
* *
15361 AATTTCCAAAATGTCAACTTTTTTCAAAAT
1 AATTCCCAGAATGTC-ACTTTTTTCAAAAT
* *
15391 AATTCTCAAAATGTCACCTTTTTTCAAAAT
1 AATTCCCAGAATGTCA-CTTTTTTCAAAAT
* * *
15421 ATTTCCTAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACTTTTTTCAAAAT
* * *
15450 ATTTTCTAGAATGTCACATTTTTT-AAAAT
1 AATTCCCAGAATGTCAC-TTTTTTCAAAAT
* *
15479 ATTTCCCAGAATGTCACATTTTTCACAAA-
1 AATTCCCAGAATGTCACTTTTTTCA-AAAT
15508 AATTCCCAGAATGTCACT
1 AATTCCCAGAATGTCACT
15526 GGGTCGGGTC
Statistics
Matches: 117, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.04
29 66 0.56
30 46 0.39
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (29 bp):
AATTCCCAGAATGTCACTTTTTTCAAAAT
Found at i:15495 original size:58 final size:59
Alignment explanation
Indices: 15362--15524 Score: 190
Period size: 58 Copynumber: 2.8 Consensus size: 59
15352 ACATTCGAAA
* * *
15362 ATTT-CCAAAATGTCAACTTTTTTCAAAATAATTCTCAAAATGTCACCTTTTTTCAAAAT
1 ATTTCCCAGAATGTC-ACATTTTTCAAAATAATTCTCAAAATGTCACATTTTTTCAAAAT
* * * *
15421 ATTTCCTAGAATGTCACCTTTTTCAAAAT-ATTTTCTAGAATGTCACATTTTTT-AAAAT
1 ATTTCCCAGAATGTCACATTTTTCAAAATAATTCTC-AAAATGTCACATTTTTTCAAAAT
* *
15479 ATTTCCCAGAATGTCACATTTTTCACAAA-AATTCCCAGAATGTCAC
1 ATTTCCCAGAATGTCACATTTTTCA-AAATAATTCTCAAAATGTCAC
15525 TGGGTCGGGT
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
58 43 0.48
59 39 0.43
60 8 0.09
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (59 bp):
ATTTCCCAGAATGTCACATTTTTCAAAATAATTCTCAAAATGTCACATTTTTTCAAAAT
Found at i:22861 original size:29 final size:29
Alignment explanation
Indices: 22821--23007 Score: 215
Period size: 29 Copynumber: 6.6 Consensus size: 29
22811 ACATTCGAAA
*
22821 ATTT-CCAAAATGTCACCTTTTTCAAAAT
1 ATTTCCCAGAATGTCACCTTTTTCAAAAT
* * * *
22849 AATTCTCAGAATGTCACATTTTTTAAAAT
1 ATTTCCCAGAATGTCACCTTTTTCAAAAT
* *
22878 ATTTCCTAGAATATCACC-TTTTCAAAAAT
1 ATTTCCCAGAATGTCACCTTTTTC-AAAAT
22907 ATTTCCCAGAATGTCACCTTTTT-AAAAT
1 ATTTCCCAGAATGTCACCTTTTTCAAAAT
*
22935 ATTTCCCAGAATGTCACATTTTTTCAAAAT
1 ATTTCCCAGAATGTCAC-CTTTTTCAAAAT
*
22965 ATTTCCCAGAATGTCA-CATTTTCAAAA-
1 ATTTCCCAGAATGTCACCTTTTTCAAAAT
* *
22992 A-ATCTCAGAATGTCAC
1 ATTTCCCAGAATGTCAC
23008 TGGGTCGGGT
Statistics
Matches: 135, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
26 12 0.09
27 1 0.01
28 38 0.28
29 59 0.44
30 25 0.19
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.37
Consensus pattern (29 bp):
ATTTCCCAGAATGTCACCTTTTTCAAAAT
Found at i:23037 original size:17 final size:18
Alignment explanation
Indices: 23009--23048 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
22999 GAATGTCACT
23009 GGGTCGGGTCAACGGGAA
1 GGGTCGGGTCAACGGGAA
*
23027 GGGTC-GGTCAACGGGTA
1 GGGTCGGGTCAACGGGAA
23044 GGGTC
1 GGGTC
23049 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.15
Consensus pattern (18 bp):
GGGTCGGGTCAACGGGAA
Found at i:24062 original size:12 final size:12
Alignment explanation
Indices: 24045--24070 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24035 CTAAGTGTTT
24045 GGTGAGAAAATC
1 GGTGAGAAAATC
24057 GGTGAGAAAATC
1 GGTGAGAAAATC
24069 GG
1 GG
24071 CATTTTGTTA
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):
GGTGAGAAAATC
Found at i:27563 original size:2 final size:2
Alignment explanation
Indices: 27556--27591 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27546 TTACATATTA
27556 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
27592 GTTGGGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28957 original size:15 final size:15
Alignment explanation
Indices: 28937--28989 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
28927 ATGAATTTTA
28937 GGTAATTCTGACTTT
1 GGTAATTCTGACTTT
28952 GGTAATT-TAGGAACTTTT
1 GGTAATTCT--G-AC-TTT
*
28970 GGTAATTCTGATTTT
1 GGTAATTCTGACTTT
28985 GGTAA
1 GGTAA
28990 CTCGAGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 1 0.03
15 15 0.47
16 2 0.06
17 3 0.09
18 10 0.31
19 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.45
Consensus pattern (15 bp):
GGTAATTCTGACTTT
Found at i:28974 original size:33 final size:32
Alignment explanation
Indices: 28932--29076 Score: 105
Period size: 33 Copynumber: 4.3 Consensus size: 32
28922 ATCTCATGAA
28932 TTTTAGGTAATTCTGACTTTGGTAATTTAGGAAC
1 TTTT-GGTAATTCTGACTTTGGTAA-TTAGGAAC
* * *
28966 TTTTGGTAATTCTGATTTTGGTAACTCGAGAA-
1 TTTTGGTAATTCTGACTTTGGTAATTAG-GAAC
* *
28998 TGTTTGGTAATTCAGGAGCTTTGGTCGCATTAGGAAC
1 T-TTTGGTAATTC-TGA-CTTTGGT--AATTAGGAAC
* * * *
29035 TTTAGGCAATTCTG-GTTTCGGTAATTCAGGAAA
1 TTTTGGTAATTCTGACTTT-GGTAATT-AGGAAC
29068 TTTTGGTAA
1 TTTTGGTAA
29077 CTCAAGAGCT
Statistics
Matches: 86, Mismatches: 16, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
32 6 0.07
33 48 0.56
34 9 0.10
35 7 0.08
36 12 0.14
37 4 0.05
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (32 bp):
TTTTGGTAATTCTGACTTTGGTAATTAGGAAC
Found at i:29046 original size:69 final size:69
Alignment explanation
Indices: 28958--29090 Score: 171
Period size: 69 Copynumber: 1.9 Consensus size: 69
28948 CTTTGGTAAT
* * * * *
28958 TTAGGAACTTTTGGTAATTCTGATTTTGGTAACTC--GAGAATGTTTGGTAATTCAGGAGCTTTG
1 TTAGGAACTTTAGGCAATTCTGATTTCGGTAACTCAGGA-AAT-TTTGGTAACTCAAGAGCTTTG
29021 GTCGCA
64 GTCGCA
* *
29027 TTAGGAACTTTAGGCAATTCTGGTTTCGGTAATTCAGGAAATTTTGGTAACTCAAGAGCTTTGG
1 TTAGGAACTTTAGGCAATTCTGATTTCGGTAACTCAGGAAATTTTGGTAACTCAAGAGCTTTGG
29091 AAATTCTGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 50 0.91
70 3 0.05
71 2 0.04
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.38
Consensus pattern (69 bp):
TTAGGAACTTTAGGCAATTCTGATTTCGGTAACTCAGGAAATTTTGGTAACTCAAGAGCTTTGGT
CGCA
Found at i:29231 original size:33 final size:33
Alignment explanation
Indices: 29189--29330 Score: 148
Period size: 33 Copynumber: 4.3 Consensus size: 33
29179 TTTGGCACTG
*
29189 TTGGAAACTCAAGAACCTTAGGAACTTC-GGACT
1 TTGGCAACTCAAGAACCTTAGGAACTTCAGG-CT
* * *
29222 TTGGTAACTCAGGAACTTTAGGAACTTCAGGCT
1 TTGGCAACTCAAGAACCTTAGGAACTTCAGGCT
* *
29255 TTGGCAACTCAAGAACCGTGGGCAA-TTCAGGCT
1 TTGGCAACTCAAGAACCTTAGG-AACTTCAGGCT
*
29288 TTGGCAACTCAAGAACC-TA-GACAATTCAGGCT
1 TTGGCAACTCAAGAACCTTAGGA-ACTTCAGGCT
* *
29320 TAGGTAACTCA
1 TTGGCAACTCA
29331 GGTATTTTAG
Statistics
Matches: 94, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.01
31 2 0.02
32 18 0.19
33 69 0.73
34 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (33 bp):
TTGGCAACTCAAGAACCTTAGGAACTTCAGGCT
Found at i:36600 original size:21 final size:22
Alignment explanation
Indices: 36553--36633 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 22
36543 ACACTAGTTA
36553 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCA-CCCTTGAAT
* * *
36576 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
36597 GTGCATCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
36620 GTGCATCGATGCAC
1 GTGCATCGATGCAC
36634 TCTGCTATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.36
23 32 0.64
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:39420 original size:65 final size:64
Alignment explanation
Indices: 39300--39448 Score: 183
Period size: 65 Copynumber: 2.3 Consensus size: 64
39290 TTTTGAATGC
* * ***
39300 ATTTTATGCACCGATGCACAACCATGCATCGATGCACTCAGGATTTTATTGAAACATCGAATTG
1 ATTTTGTGCACCGATGCACAACCATGCATCGATGCACCCAGGATTTTATTGAAACATCGAAGCA
* * * *
39364 ATTTTGTGCACCGATGCACAAGTCATGCATCGATGTACCCCGGCTATTT-TTGAAACATCGAAGC
1 ATTTTGTGCACCGATGCACAA-CCATGCATCGATGCACCCAGGAT-TTTATTGAAACATCGAAGC
39428 A
64 A
*
39429 AATTTGTGCACCGATGCACA
1 ATTTTGTGCACCGATGCACA
39449 CCCTAGTGTA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 20 0.27
65 50 0.68
66 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
ATTTTGTGCACCGATGCACAACCATGCATCGATGCACCCAGGATTTTATTGAAACATCGAAGCA
Found at i:41162 original size:36 final size:36
Alignment explanation
Indices: 41122--41253 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 36
41112 ACGTTTCTGG
41122 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* * *
41158 ACATTGATACACGAATGCATCAAAGCTTATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* * * *
41194 ACATTGATATATGAATGTGCCAAAGATGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
41230 ACATTGATACACGAATGTATCAAA
1 ACATTGATACACGAATGTACCAAA
41254 TCTATTAATG
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Done.