Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000295.1 Hibiscus syriacus cultivar Beakdansim tig00000541_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: 2017499
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 9 of 9
Found at i:1885797 original size:13 final size:13
Alignment explanation
Indices: 1885774--1885807 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1885764 AACGGGTCAA
1885774 CGGTT-AACGGGT
1 CGGTTCAACGGGT
1885786 CGGTTCAACGGGT
1 CGGTTCAACGGGT
*
1885799 CGGGTCAAC
1 CGGTTCAAC
1885808 ATGTCGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.18, C:0.24, G:0.38, T:0.21
Consensus pattern (13 bp):
CGGTTCAACGGGT
Found at i:1885815 original size:18 final size:18
Alignment explanation
Indices: 1885794--1885840 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1885784 GTCGGTTCAA
*
1885794 CGGGTCGGGTCAACATGT
1 CGGGTCGGGTCAACAGGT
* *
1885812 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACAGGT
1885830 CGGGTCGGGTC
1 CGGGTCGGGTC
1885841 TGGTTTTGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.21, G:0.47, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:1887915 original size:24 final size:24
Alignment explanation
Indices: 1887888--1887939 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1887878 AACGGATATA
*
1887888 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1887912 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1887936 TCAA
1 TCAA
1887940 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1888026 original size:24 final size:24
Alignment explanation
Indices: 1887911--1888026 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
1887901 CATAAATCAG
* *
1887911 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* *
1887935 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
1887959 GTCAAGTATCAGATCAAAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
1887983 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1888007 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1888027 TCAAATCAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 75 0.91
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1888035 original size:24 final size:24
Alignment explanation
Indices: 1887911--1888044 Score: 146
Period size: 24 Copynumber: 5.6 Consensus size: 24
1887901 CATAAATCAG
* *
1887911 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAA
*
1887935 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
1887959 GTCAAGTATCAGATCAAAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
1887983 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
*
1888007 GTCAAGTATCAGATCAGAATTCAA
1 GTCAAGTATCAGATCAGAATCCAA
* **
1888031 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
1888045 AAAATATTCA
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
23 5 0.05
24 88 0.93
25 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:1888042 original size:72 final size:71
Alignment explanation
Indices: 1887887--1888049 Score: 179
Period size: 72 Copynumber: 2.3 Consensus size: 71
1887877 AAACGGATAT
* * *
1887887 ATCAAAAATCAAAACATAAATCAGGTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAG
1 ATCAAAAATCAGATCA-AAATCAGGTCAAGTATCAGATCAGAAATCAGGTCAAGTAACAGATCAG
1887952 AATCCAA
65 AATCCAA
* ** * * *
1887959 GTCAAGTATCAGATCAAAATCCATGTC-AGATATCAGATCAG-AATCCATGTCAAGTATCAGATC
1 ATCAAAAATCAGATCAAAAT-CAGGTCAAG-TATCAGATCAGAAAT-CAGGTCAAGTAACAGATC
*
1888022 AGAATTCAA
63 AGAATCCAA
1888031 ATCAAAAATCAGAT-AAAAT
1 ATCAAAAATCAGATCAAAAT
1888050 ATTCATGTGA
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
71 14 0.19
72 61 0.81
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (71 bp):
ATCAAAAATCAGATCAAAATCAGGTCAAGTATCAGATCAGAAATCAGGTCAAGTAACAGATCAGA
ATCCAA
Found at i:1890177 original size:16 final size:17
Alignment explanation
Indices: 1890156--1890188 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1890146 CGAAAGCATA
*
1890156 AAATTT-GACTTTTCGG
1 AAATTTGGAATTTTCGG
1890172 AAATTTGGAATTTTCGG
1 AAATTTGGAATTTTCGG
1890189 TCAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (17 bp):
AAATTTGGAATTTTCGG
Found at i:1892483 original size:24 final size:24
Alignment explanation
Indices: 1892456--1892507 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1892446 AACGGATATA
*
1892456 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1892480 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1892504 TCAA
1 TCAA
1892508 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1892508 original size:24 final size:24
Alignment explanation
Indices: 1892476--1892594 Score: 143
Period size: 24 Copynumber: 5.0 Consensus size: 24
1892466 AAACATAAAT
*
1892476 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
* *
1892500 CAGGTCAAGTAACATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1892524 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1892548 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
* *
1892572 CATGTCAAGTATCAAATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
1892595 TCAAATCGAA
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:1892610 original size:48 final size:48
Alignment explanation
Indices: 1892515--1892612 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 48
1892505 CAAGTAACAT
* ** *
1892515 ATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATATCAG
1 ATCAGAATCCAAGTCAAGTATCAAATCAGAATCCAAATCAGAAATCAG
* *
1892563 ATCAGAATCCATGTCAAGTATCAAATCAGAATTCAAATC-GAAAATCAG
1 ATCAGAATCCAAGTCAAGTATCAAATCAGAATCCAAATCAG-AAATCAG
1892611 AT
1 AT
1892613 AAAATATTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 1 0.02
48 42 0.98
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAATCCAAGTCAAGTATCAAATCAGAATCCAAATCAGAAATCAG
Found at i:1895086 original size:15 final size:15
Alignment explanation
Indices: 1895066--1895099 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1895056 GGTCAACGTC
*
1895066 GGTCAACGATCAATG
1 GGTCAACGATCAACG
*
1895081 GGTCAACGGTCAACG
1 GGTCAACGATCAACG
1895096 GGTC
1 GGTC
1895100 GGGTCAACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (15 bp):
GGTCAACGATCAACG
Found at i:1895106 original size:13 final size:13
Alignment explanation
Indices: 1895088--1895117 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1895078 ATGGGTCAAC
*
1895088 GGTCAACGGGTCG
1 GGTCAACAGGTCG
1895101 GGTCAACAGGTCG
1 GGTCAACAGGTCG
1895114 GGTC
1 GGTC
1895118 GGGTAAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:1895117 original size:18 final size:18
Alignment explanation
Indices: 1895094--1895154 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
1895084 CAACGGTCAA
1895094 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
1895112 CGGGTCGGGT-AA-A---
1 CGGGTCGGGTCAACAGGT
* * *
1895125 CGGGTTGGGTAAACGGGT
1 CGGGTCGGGTCAACAGGT
1895143 CGGGTCGGGTCA
1 CGGGTCGGGTCA
1895155 GGTTATGACC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
13 9 0.26
14 2 0.06
16 1 0.03
17 2 0.06
18 20 0.59
ACGTcount: A:0.16, C:0.18, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:1895128 original size:13 final size:13
Alignment explanation
Indices: 1895112--1895147 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1895102 GTCAACAGGT
1895112 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
*
1895125 CGGGTTGGGTAAA
1 CGGGTCGGGTAAA
1895138 CGGGTCGGGT
1 CGGGTCGGGT
1895148 CGGGTCAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.14, G:0.50, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1895144 original size:31 final size:31
Alignment explanation
Indices: 1895092--1895152 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1895082 GTCAACGGTC
*
1895092 AACGGGTCGGGTCAACAGGTCGGGTCGGGTA
1 AACGGGTCGGGTAAACAGGTCGGGTCGGGTA
* *
1895123 AACGGGTTGGGTAAACGGGTCGGGTCGGGT
1 AACGGGTCGGGTAAACAGGTCGGGTCGGGT
1895153 CAGGTTATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.48, T:0.18
Consensus pattern (31 bp):
AACGGGTCGGGTAAACAGGTCGGGTCGGGTA
Found at i:1896561 original size:65 final size:63
Alignment explanation
Indices: 1896446--1896651 Score: 202
Period size: 65 Copynumber: 3.2 Consensus size: 63
1896436 ATTTGAGGTG
* * * * *
1896446 ATGCACCGATGCATCACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATTGAATGCATTCC
1 ATGCACCGATGCATCACCATGCATCGATGCACT-CTGAATAT-TTTAAAACATTGAATGCATTTC
* * *
1896510 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTT-AAAACATTGAATGCATTTC
* * * **
1896575 ATGCATCGATGCA-CAAGCCATGCATCGATGCACGCAGGCTATTTTAAAAC-TTCGAATGCATTT
1 ATGCACCGATGCATC-A-CCATGCATCGATGCACTCTGAATATTTTAAAACATT-GAATGCATTT
1896638 C
63 C
*
1896639 ATGCATCGATGCA
1 ATGCACCGATGCA
1896652 CACTTGGTGC
Statistics
Matches: 120, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
63 2 0.02
64 48 0.40
65 70 0.58
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTAAAACATTGAATGCATTTC
Found at i:1905210 original size:64 final size:65
Alignment explanation
Indices: 1905057--1905218 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
1905047 GAATTAATTG
* * **** * *
1905057 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGAATCGATACACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGAATCGATACACGCAGAATATTTTCA
* * * ** *
1905122 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACGCAGGCTATTTT-T
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGAATCGATACACGCAGAATATTTTCA
1905186 AAACATCGAATGCATTTCATGCATCGATGCACA
1 AAACATCGAATGCATTTCATGCATCGATGCACA
1905219 CTTGGTGCAC
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 32 0.39
65 50 0.61
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGAATCGATACACGCAGAATATTTTCA
Found at i:1913576 original size:15 final size:15
Alignment explanation
Indices: 1913556--1913585 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1913546 CAAAAATCTT
1913556 TTAAAATAATAAACA
1 TTAAAATAATAAACA
1913571 TTAAAATAATAAACA
1 TTAAAATAATAAACA
1913586 CCAACTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
TTAAAATAATAAACA
Found at i:1914379 original size:55 final size:55
Alignment explanation
Indices: 1914314--1914428 Score: 203
Period size: 55 Copynumber: 2.1 Consensus size: 55
1914304 ATTTTACTAT
* *
1914314 TGGAAATATGCTCCAAGTTGGCATGAATTAAATTAAACTTTACTTTGTAAGTTCA
1 TGGAAATATGCTCCAACTTGGCATGAATTAAATTAAACCTTACTTTGTAAGTTCA
*
1914369 TGGAAATATGCTCCAACTTGGCATGAATTAAATTAAACCTTACTTTGTATGTTCA
1 TGGAAATATGCTCCAACTTGGCATGAATTAAATTAAACCTTACTTTGTAAGTTCA
1914424 TGGAA
1 TGGAA
1914429 CAATATCGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (55 bp):
TGGAAATATGCTCCAACTTGGCATGAATTAAATTAAACCTTACTTTGTAAGTTCA
Found at i:1921055 original size:24 final size:22
Alignment explanation
Indices: 1921028--1921102 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 22
1921018 TATATCAAAA
1921028 ATCATAAAATAATCCAGGTCAAGT
1 ATCA-AAAA-AATCCAGGTCAAGT
*
1921052 ATCAGATCAAAATCCAGGTCAAGT
1 ATCA-A-AAAAATCCAGGTCAAGT
* *
1921076 ATTCAATCAGAATCCAGGTCAAGT
1 A-TCAA-AAAAATCCAGGTCAAGT
1921100 ATC
1 ATC
1921103 CGATCAGAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.04
24 39 0.85
25 5 0.11
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (22 bp):
ATCAAAAAAATCCAGGTCAAGT
Found at i:1921073 original size:12 final size:13
Alignment explanation
Indices: 1921038--1921120 Score: 61
Period size: 12 Copynumber: 6.8 Consensus size: 13
1921028 ATCATAAAAT
1921038 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
1921051 TAT-CAGATCAA-
1 AATCCAGGTCAAG
1921062 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
1921075 TATTCA-ATC-AG
1 AATCCAGGTCAAG
1921086 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
1921099 TATCC-GATC-AG
1 AATCCAGGTCAAG
1921110 AATCCAGGTCA
1 AATCCAGGTCA
1921121 GGTATTATAA
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
11 14 0.28
12 24 0.48
13 12 0.24
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:1921108 original size:24 final size:24
Alignment explanation
Indices: 1921038--1921125 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
1921028 ATCATAAAAT
* *
1921038 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCCGATCAG
* *
1921062 AATCCAGGTCAAGTATTCAATCAG
1 AATCCAGGTCAAGTATCCGATCAG
1921086 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
1921110 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
1921126 TATAATAGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:1948551 original size:24 final size:22
Alignment explanation
Indices: 1948524--1948598 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 22
1948514 TATATCAAAA
1948524 ATCATAAAATAATCCAGGTCAAGT
1 ATCA-AAAA-AATCCAGGTCAAGT
*
1948548 ATCAGATCAAAATCCAGGTCAAGT
1 ATCA-A-AAAAATCCAGGTCAAGT
* *
1948572 ATTCAATCAGAATCCAGGTCAAGT
1 A-TCAA-AAAAATCCAGGTCAAGT
1948596 ATC
1 ATC
1948599 CGATCAGAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.04
24 39 0.85
25 5 0.11
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (22 bp):
ATCAAAAAAATCCAGGTCAAGT
Found at i:1948569 original size:12 final size:13
Alignment explanation
Indices: 1948534--1948599 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 13
1948524 ATCATAAAAT
1948534 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
1948547 TAT-CAGATCAA-
1 AATCCAGGTCAAG
1948558 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
1948571 TATTCA-ATC-AG
1 AATCCAGGTCAAG
1948582 AATCCAGGTCAAG
1 AATCCAGGTCAAG
*
1948595 TATCC
1 AATCC
1948600 GATCAGAATC
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
11 8 0.21
12 18 0.47
13 12 0.32
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:1948604 original size:24 final size:24
Alignment explanation
Indices: 1948534--1948614 Score: 117
Period size: 24 Copynumber: 3.4 Consensus size: 24
1948524 ATCATAAAAT
* *
1948534 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCCGATCAG
* *
1948558 AATCCAGGTCAAGTATTCAATCAG
1 AATCCAGGTCAAGTATCCGATCAG
1948582 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
1948606 AATCTAGGT
1 AATCCAGGT
1948615 TAGGTATTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:1949598 original size:18 final size:18
Alignment explanation
Indices: 1949575--1949609 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1949565 TGCCATCTGG
*
1949575 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1949593 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1949610 GTCATTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1950864 original size:18 final size:18
Alignment explanation
Indices: 1950841--1950875 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1950831 GTTAACGCCG
1950841 GTCAACGGGTCGGGTCGA
1 GTCAACGGGTCGGGTCGA
1950859 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
1950876 GGTTGTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGA
Found at i:1956225 original size:18 final size:19
Alignment explanation
Indices: 1956202--1956240 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1956192 TTTAAGTAGT
*
1956202 AATAAAAACGATT-AAGTA
1 AATAAAAACAATTAAAGTA
*
1956220 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
1956239 AA
1 AA
1956241 AAATAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:1983781 original size:18 final size:18
Alignment explanation
Indices: 1983754--1983800 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1983744 ACCGGTCAAC
1983754 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
1983772 GGTTAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1983790 GGTCAACGGGT
1 GGTCAACGGGT
1983801 AGGTAAACGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1983855 original size:11 final size:10
Alignment explanation
Indices: 1983825--1983874 Score: 59
Period size: 9 Copynumber: 5.1 Consensus size: 10
1983815 ACGGGTCGTG
1983825 ACCGGTC-AA
1 ACCGGTCAAA
1983834 ACCGGTCAAA
1 ACCGGTCAAA
1983844 ACCGGTTCAAA
1 ACCGG-TCAAA
* *
1983855 ATCGGT-TAA
1 ACCGGTCAAA
1983864 ACCGGTCAAA
1 ACCGGTCAAA
1983874 A
1 A
1983875 TCGATTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 14 0.41
10 11 0.32
11 9 0.26
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1990123 original size:11 final size:11
Alignment explanation
Indices: 1990107--1990133 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1990097 CAGAAATACG
1990107 GAAATCGGTAT
1 GAAATCGGTAT
1990118 GAAATCGGTAT
1 GAAATCGGTAT
1990129 GAAAT
1 GAAAT
1990134 ACCTTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.26
Consensus pattern (11 bp):
GAAATCGGTAT
Found at i:1990983 original size:21 final size:21
Alignment explanation
Indices: 1990957--1991005 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1990947 GTCAACGGGT
* **
1990957 CGGGTCGGGTTAACGGGTCGA
1 CGGGTCGGGTAAACGGGTAAA
*
1990978 CGGGTCAGGTAAACGGGTAAA
1 CGGGTCGGGTAAACGGGTAAA
1990999 CGGGTCG
1 CGGGTCG
1991006 TGACCGGTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.45, T:0.16
Consensus pattern (21 bp):
CGGGTCGGGTAAACGGGTAAA
Found at i:1991028 original size:10 final size:10
Alignment explanation
Indices: 1991008--1991051 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
1990998 ACGGGTCGTG
1991008 ACCGGTC-AA
1 ACCGGTCAAA
1991017 ACCGGTCAAA
1 ACCGGTCAAA
*
1991027 ACCGGT-TAA
1 ACCGGTCAAA
*
1991036 ACCGATCAAA
1 ACCGGTCAAA
1991046 ACCGGT
1 ACCGGT
1991052 TTTCAGCGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.36, C:0.30, G:0.20, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1991052 original size:19 final size:19
Alignment explanation
Indices: 1991008--1991052 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1990998 ACGGGTCGTG
* *
1991008 ACCGGTCAAACCGGTCAAA
1 ACCGGTTAAACCGATCAAA
1991027 ACCGGTTAAACCGATCAAA
1 ACCGGTTAAACCGATCAAA
1991046 ACCGGTT
1 ACCGGTT
1991053 TTCAGCGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.16
Consensus pattern (19 bp):
ACCGGTTAAACCGATCAAA
Found at i:1999804 original size:24 final size:24
Alignment explanation
Indices: 1999777--1999827 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1999767 TATATCAAAA
* *
1999777 ATCAAAACATAATTTAGGTCAAGT
1 ATCAAAACAGAATCTAGGTCAAGT
* * *
1999801 ATCAGATCAGAATCTAGGTCATGT
1 ATCAAAACAGAATCTAGGTCAAGT
1999825 ATC
1 ATC
1999828 CTATCAGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
ATCAAAACAGAATCTAGGTCAAGT
Found at i:1999833 original size:24 final size:24
Alignment explanation
Indices: 1999791--1999837 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1999781 AAACATAATT
1999791 TAGGTCAAGTATCAGATCAGAATC
1 TAGGTCAAGTATCAGATCAGAATC
* **
1999815 TAGGTCATGTATCCTATCAGAAT
1 TAGGTCAAGTATCAGATCAGAAT
1999838 TCGGGTCAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
TAGGTCAAGTATCAGATCAGAATC
Found at i:1999844 original size:24 final size:24
Alignment explanation
Indices: 1999817--1999864 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1999807 TCAGAATCTA
* * *
1999817 GGTCATGTATCCTATCAGAATTCG
1 GGTCAGGTATCATAACAGAATTCG
1999841 GGTCAGGTATCATAACAGAATTCG
1 GGTCAGGTATCATAACAGAATTCG
1999865 AATCAGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (24 bp):
GGTCAGGTATCATAACAGAATTCG
Found at i:1999870 original size:24 final size:24
Alignment explanation
Indices: 1999823--1999870 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1999813 TCTAGGTCAT
* * **
1999823 GTATCCTATCAGAATTCGGGTCAG
1 GTATCATAACAGAATTCGAATCAG
1999847 GTATCATAACAGAATTCGAATCAG
1 GTATCATAACAGAATTCGAATCAG
1999871 AAATCAGGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (24 bp):
GTATCATAACAGAATTCGAATCAG
Found at i:2001649 original size:7 final size:7
Alignment explanation
Indices: 2001637--2001666 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2001627 TTTATCCATG
2001637 CATTTAT
1 CATTTAT
2001644 CATTTAT
1 CATTTAT
2001651 CATTTAT
1 CATTTAT
*
2001658 AATTTAT
1 CATTTAT
2001665 CA
1 CA
2001667 ACATGTTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (7 bp):
CATTTAT
Found at i:2003411 original size:16 final size:18
Alignment explanation
Indices: 2003390--2003422 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2003380 AAGCAAACTT
2003390 TGTTTA-TAAAA-AAATG
1 TGTTTATTAAAACAAATG
2003406 TGTTTATTAAAACAAAT
1 TGTTTATTAAAACAAAT
2003423 AAGAGATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (18 bp):
TGTTTATTAAAACAAATG
Found at i:2012289 original size:80 final size:80
Alignment explanation
Indices: 2012037--2012309 Score: 368
Period size: 81 Copynumber: 3.4 Consensus size: 80
2012027 TTGGGTCCTA
* * * * *
2012037 TGGGCCTACCCAAGGATATCCTTAGATCTGAAGGGTTACCTTAAGGACACAAAAAAAGGGAACCA
1 TGGGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACAC-AACAAAGGGAACCA
2012102 ACCTAAGGATATACCT
65 ACCTAAGGATATACCT
* * * *
2012118 TGGGTCTACCCAAGGACATCCTTAGATCCATAGGGTTACCTTAAGCACATAGCAAAAGGGAACCA
1 TGGGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAAC-AAAGGGAACCA
2012183 ACCTAAGGATATACCT
65 ACCTAAGGATATACCT
* * * * *
2012199 TGGGCCTACCCAAGGGCATCCTTAGAACCGTTGGGTTACCTTATGCACACAACAAAGGGAACAAA
1 TGGGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAGGGAACCAA
*
2012264 CCTAAGGATATGCCT
66 CCTAAGGATATACCT
* *
2012279 TGGGCCTACCCAA-GATATCCTTAGGTCCGTA
1 TGGGCCTACCCAAGGACATCCTTAGATCCGTA
2012310 AGGACTTGTA
Statistics
Matches: 167, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
79 13 0.08
80 39 0.23
81 115 0.69
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (80 bp):
TGGGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAGGGAACCAA
CCTAAGGATATACCT
Found at i:2017465 original size:78 final size:79
Alignment explanation
Indices: 2017212--2017474 Score: 279
Period size: 78 Copynumber: 3.4 Consensus size: 79
2017202 GGGCCTATGT
* * * *
2017212 GCCTACCCAAGGATATCCTTAGATCCGTATGGTTACCTTAAG-CACAATACAAAAGAGAACCAAC
1 GCCTACCCAA-GATATCCTTAGATCCGTAGGGTTACCTCAAGCCAC-ACACAAAAGGGAACCAAC
* * *
2017276 CTATGTATATACCTTG
64 CTAAGGATATGCCTTG
* * *
2017292 G-TTA-CC-A-ACATCCTTTGATCCGTAGGGTTACCTCAAGCACACACACAAAAGGGAACCAACC
1 GCCTACCCAAGATATCCTTAGATCCGTAGGGTTACCTCAAGC-CACACACAAAAGGGAACCAACC
*
2017353 TTAGGATATGCCTTG
65 TAAGGATATGCCTTG
*** * *
2017368 AGCCTACCCAAGGGCTCCTTAGATCCGTAGGGTTACCTCATGCCACA-GC-AAAGGGAACCAACC
1 -GCCTACCCAAGATATCCTTAGATCCGTAGGGTTACCTCAAGCCACACACAAAAGGGAACCAACC
2017431 TAAGGATATGCCTTAG
65 TAAGGATATGCCTT-G
*
2017447 GCCTACCCAAGATATCCTTAGGTCCGTA
1 GCCTACCCAAGATATCCTTAGATCCGTA
2017475 AGGACTTACA
Statistics
Matches: 152, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
75 26 0.17
76 28 0.18
77 5 0.03
78 55 0.36
79 6 0.04
80 6 0.04
81 26 0.17
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (79 bp):
GCCTACCCAAGATATCCTTAGATCCGTAGGGTTACCTCAAGCCACACACAAAAGGGAACCAACCT
AAGGATATGCCTTG
Done.