Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007825.1 Hibiscus syriacus cultivar Beakdansim tig00110163_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: 2082551
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:1938314 original size:2 final size:2
Alignment explanation
Indices: 1938307--1938341 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1938297 TTCTTGATAT
1938307 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1938342 TTGGTGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1940492 original size:2 final size:2
Alignment explanation
Indices: 1940485--1940519 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1940475 AAATAGCAGT
1940485 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 T
1940520 CCATCGTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1953206 original size:2 final size:2
Alignment explanation
Indices: 1953199--1953248 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1953189 TGATTCAATC
1953199 AT AT AT 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 AT AT AT
1953241 AT AT AT AT
1 AT AT AT AT
1953249 CATTTCCAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1955345 original size:24 final size:24
Alignment explanation
Indices: 1955308--1955368 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
1955298 ATAGTGTAAT
1955308 AATCAAAATATTTTTATAAATTTTC
1 AATC-AAATATTTTTATAAATTTTC
*
1955333 ATTCAAATATTTTTATAAATTTTC
1 AATCAAATATTTTTATAAATTTTC
1955357 AATCAAATATTT
1 AATCAAATATTT
1955369 ATAATTCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 31 0.91
25 3 0.09
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (24 bp):
AATCAAATATTTTTATAAATTTTC
Found at i:1956690 original size:8 final size:8
Alignment explanation
Indices: 1956677--1956703 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1956667 AAATATATAG
1956677 AAAAATTT
1 AAAAATTT
1956685 AAAAATTT
1 AAAAATTT
1956693 AAAAATTT
1 AAAAATTT
1956701 AAA
1 AAA
1956704 GGTCTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAAATTT
Found at i:1956786 original size:19 final size:19
Alignment explanation
Indices: 1956734--1956786 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1956724 CAAAAAAAGT
*
1956734 TTAAAAAATAAATTACATAA
1 TTAAAAAA-AAATTACAAAA
**
1956754 TTAAAAAATTATTA-AAAA
1 TTAAAAAAAAATTACAAAA
1956772 TTAAAACAAAAATTA
1 TTAAAA-AAAAATTA
1956787 TAATTAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 9 0.33
19 10 0.37
20 8 0.30
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAAAAAAATTACAAAA
Found at i:1964015 original size:23 final size:23
Alignment explanation
Indices: 1963989--1964034 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1963979 AGTCAATCTC
1963989 GCATTCACTCGTGTATGTCATAA
1 GCATTCACTCGTGTATGTCATAA
1964012 GCATTCACTCGTGTATGTCATAA
1 GCATTCACTCGTGTATGTCATAA
1964035 TGACCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (23 bp):
GCATTCACTCGTGTATGTCATAA
Found at i:1976277 original size:23 final size:23
Alignment explanation
Indices: 1976251--1976295 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1976241 CACCACAGCT
*
1976251 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1976274 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1976296 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1976462 original size:150 final size:149
Alignment explanation
Indices: 1976263--1976578 Score: 571
Period size: 150 Copynumber: 2.1 Consensus size: 149
1976253 TATAAATGCA
1976263 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
1976327 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTTTCC-AGACTTCACACATGT
* *
1976392 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
1976413 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1976478 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTTTCCAGACTTCACACATGTTC
*
1976543 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
1976562 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1976579 CCCTCTACAC
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
149 51 0.32
150 110 0.68
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:1981824 original size:2 final size:2
Alignment explanation
Indices: 1981817--1981865 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1981807 ATTATATCAT
1981817 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
1981859 TA TA TA T
1 TA TA TA T
1981866 GATTAAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1987797 original size:40 final size:40
Alignment explanation
Indices: 1987753--1987856 Score: 154
Period size: 40 Copynumber: 2.6 Consensus size: 40
1987743 TAAAAGCAAC
* *
1987753 ACAAACCAGATTCATACTAGCCCTAACAGTTGGACGATTG
1 ACAAACCAGATTCATACTAGCCCAAACAGTTGGACGATGG
** *
1987793 ACAAACCAGATTCATACCCGCTCAAACAGTTGGACGATGG
1 ACAAACCAGATTCATACTAGCCCAAACAGTTGGACGATGG
*
1987833 ACAAACCAGATTCATACTAACCCA
1 ACAAACCAGATTCATACTAGCCCA
1987857 GATCCATTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.19
Consensus pattern (40 bp):
ACAAACCAGATTCATACTAGCCCAAACAGTTGGACGATGG
Found at i:1989745 original size:85 final size:84
Alignment explanation
Indices: 1989600--1989786 Score: 320
Period size: 85 Copynumber: 2.2 Consensus size: 84
1989590 TTATTTAATA
* *
1989600 AATAAATGAAAACGAACATAAACGAATAATTTTTTTTGTTTATGTTCGTTTATTAAGGAATATAA
1 AATAAAT--AAACGAACATAAACGAATAATTTTTTTTGTTCATGCTCGTTTATTAAGGAATATAA
1989665 CTTGTTCATGTTCGTTCATTT
64 CTTGTTCATGTTCGTTCATTT
*
1989686 AATAAATAAACGAATATAAACGAATAATTTTTTTTTGTTCATGCTCGTTTATTAAGGAATATAAC
1 AATAAATAAACGAACATAAACGAATAA-TTTTTTTTGTTCATGCTCGTTTATTAAGGAATATAAC
1989751 TTGTTCATGTTCGTTCATTT
65 TTGTTCATGTTCGTTCATTT
1989771 AATAAATAAACGAACA
1 AATAAATAAACGAACA
1989787 CGAACATAAA
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
84 19 0.20
85 70 0.73
86 7 0.07
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (84 bp):
AATAAATAAACGAACATAAACGAATAATTTTTTTTGTTCATGCTCGTTTATTAAGGAATATAACT
TGTTCATGTTCGTTCATTT
Found at i:1990677 original size:24 final size:24
Alignment explanation
Indices: 1990624--1990669 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1990614 AGATTGGATT
*
1990624 AAACATAAATAAATGAACATAAAC
1 AAACATAAATAAACGAACATAAAC
*
1990648 AAACATAACTAAACGAACATAA
1 AAACATAAATAAACGAACATAA
1990670 CCGAACATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.15
Consensus pattern (24 bp):
AAACATAAATAAACGAACATAAAC
Found at i:1996758 original size:21 final size:21
Alignment explanation
Indices: 1996734--1996787 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1996724 TGTCTTTGCA
1996734 ATAAACCTTAAACTATAAACC
1 ATAAACCTTAAACTATAAACC
* * *
1996755 ATAAATCATAAACTATATACC
1 ATAAACCTTAAACTATAAACC
*
1996776 TTAAACCTTAAA
1 ATAAACCTTAAA
1996788 TCTAAATCTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAAACCTTAAACTATAAACC
Found at i:2008006 original size:45 final size:46
Alignment explanation
Indices: 2007920--2008025 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 46
2007910 GATGCACTGG
** *
2007920 TAGTGCATCGATGCACTCTTTTAAAATAAAAAGATCAAATGCA-AT
1 TAGTGCATCGATGCACTCCATTAAAATAAAAACATCAAATGCATAT
* *
2007965 TAGTGCATCGATGCA-TCCCATTAATAAT-AAAACATCGAATGCATTT
1 TAGTGCATCGATGCACT-CCATTAA-AATAAAAACATCAAATGCATAT
*
2008011 TA-TGCACCGATGCAC
1 TAGTGCATCGATGCAC
2008026 AAGTAGTGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 1 0.02
45 44 0.86
46 6 0.12
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (46 bp):
TAGTGCATCGATGCACTCCATTAAAATAAAAACATCAAATGCATAT
Found at i:2008470 original size:39 final size:39
Alignment explanation
Indices: 2008427--2008513 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
2008417 ATATGAGAAC
*
2008427 ATGACATGAGCTACATGATCACAAGAGAAATGACATGAA
1 ATGACATGAACTACATGATCACAAGAGAAATGACATGAA
2008466 ATGACATGAACTACATGATCACAAGAGAAATGACAT-AA
1 ATGACATGAACTACATGATCACAAGAGAAATGACATGAA
*
2008504 GT-ACATGAAC
1 ATGACATGAAC
2008514 ATATGAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 8 0.17
38 3 0.07
39 35 0.76
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.18
Consensus pattern (39 bp):
ATGACATGAACTACATGATCACAAGAGAAATGACATGAA
Found at i:2013427 original size:29 final size:29
Alignment explanation
Indices: 2013382--2013462 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2013372 TTTTATATGT
*
2013382 TCATGTA-CTAATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
2013410 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
2013439 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
2013463 ATATCACATA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 7 0.15
29 36 0.75
30 5 0.10
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:2014110 original size:64 final size:64
Alignment explanation
Indices: 2013914--2014136 Score: 204
Period size: 64 Copynumber: 3.5 Consensus size: 64
2013904 TGAAGGTATA
* ** ** * ** *
2013914 CATCGATGCACTA-TTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTACTGGGAT
1 CATCGATGCACTACTT-ATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAGAT
2013977 G
64 G
* * *
2013978 CATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAACGGGATG
1 CATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATG
** *
2014042 CATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGCTTTTATT-TTAAA-AGAGT
1 CATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAGA-T
*
2014105 T
64 G
* *
2014106 CATCGATGCACTA-TCAATGCATCGATACACC
1 CATCGATGCACTACT-TATGCATCGATGCACC
2014137 TTCAAACAAT
Statistics
Matches: 134, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
63 5 0.04
64 121 0.90
65 8 0.06
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (64 bp):
CATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATG
Found at i:2017678 original size:12 final size:12
Alignment explanation
Indices: 2017661--2017685 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2017651 ATTCAAATAC
2017661 ATATGTGATATG
1 ATATGTGATATG
2017673 ATATGTGATATG
1 ATATGTGATATG
2017685 A
1 A
2017686 GAACATGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
ATATGTGATATG
Found at i:2017723 original size:29 final size:29
Alignment explanation
Indices: 2017684--2017764 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
2017674 TATGTGATAT
2017684 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
2017714 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
2017743 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
2017765 ACATATGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 37 0.76
30 5 0.10
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:2017867 original size:15 final size:15
Alignment explanation
Indices: 2017849--2017882 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2017839 GAGGGTATAA
2017849 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
2017864 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
2017879 TAGT
1 TAGT
2017883 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:2020003 original size:9 final size:9
Alignment explanation
Indices: 2019989--2020047 Score: 64
Period size: 9 Copynumber: 6.2 Consensus size: 9
2019979 CTTGCTGTCA
2019989 TCATCGTCG
1 TCATCGTCG
2019998 TCATCGTCATCG
1 TCATCG---TCG
* *
2020010 TCACCATCG
1 TCATCGTCG
2020019 TCATCGTCG
1 TCATCGTCG
2020028 TCATCGTCG
1 TCATCGTCG
*
2020037 TCGTCGTCG
1 TCATCGTCG
2020046 TC
1 TC
2020048 CTGAGCAGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
9 35 0.83
12 7 0.17
ACGTcount: A:0.12, C:0.36, G:0.20, T:0.32
Consensus pattern (9 bp):
TCATCGTCG
Found at i:2020009 original size:15 final size:15
Alignment explanation
Indices: 2019989--2020044 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
2019979 CTTGCTGTCA
2019989 TCATCGTCGTCATCG
1 TCATCGTCGTCATCG
**
2020004 TCATCGTCACCATCG
1 TCATCGTCGTCATCG
2020019 TCATCGTCGTCATCG
1 TCATCGTCGTCATCG
*
2020034 TCGTCGTCGTC
1 TCATCGTCGTC
2020045 GTCCTGAGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.12, C:0.36, G:0.20, T:0.32
Consensus pattern (15 bp):
TCATCGTCGTCATCG
Found at i:2033262 original size:81 final size:80
Alignment explanation
Indices: 2033095--2033404 Score: 439
Period size: 79 Copynumber: 3.9 Consensus size: 80
2033085 TGTAAGTCAT
2033095 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATA-CCTTAGGTTGGTTCCTTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCTTTTGCTGTG
2033159 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
* *
2033174 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGCATATCTTTAGGTTGGTTCCCTTTTGCTGT
1 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTT-CCTTTTGCTGT
2033239 GTGCATAAGGTAACCC
65 GTGCATAAGGTAACCC
* * *
2033255 TACGGACCTAAGGATATATTGGGTAGGCCCTAAGGTATATCCTTAGGTTGGTTCCTTAAT--TGT
1 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCTT-TTGCTGT
*
2033318 GTGCTTAAGGTAACCC
65 GTGCATAAGGTAACCC
* * ** *
2033334 TACGGATCTAAGGATGTCCTTGGGTA-GATCCAAGGTATATCCTTAGGTTGGCTCCCCTTTTTGC
1 TACGGACCTAAGGATAT-CTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGG-T-TCC-TTTTGC
2033398 TGTGTGC
62 TGTGTGC
2033405 TGAGGGCAAG
Statistics
Matches: 206, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
79 93 0.45
80 24 0.12
81 80 0.39
82 2 0.01
83 7 0.03
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (80 bp):
TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCTTTTGCTGTG
TGCATAAGGTAACCC
Found at i:2033382 original size:160 final size:161
Alignment explanation
Indices: 2033095--2033404 Score: 457
Period size: 160 Copynumber: 1.9 Consensus size: 161
2033085 TGTAAGTCAT
* *
2033095 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATACCTTAGGTTGGTTCCTTTTGCTGTGT
1 TACGGACCTAAGGATATATTGGGTAGGCCCCAAGGTATACCTTAGGTTGGTTCCTTAT-CTGTGT
* *
2033160 GCATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGCATATCTTTAGGTTGG
65 GCATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGACCCAAGGCATATCCTTAGGTTGG
*
2033225 -TTCCC-TTTTGCTGTGTGCATAAGGTAACCC
130 CTCCCCTTTTTGCTGTGTGCATAAGGTAACCC
*
2033255 TACGGACCTAAGGATATATTGGGTAGGCCCTAAGGTATATCCTTAGGTTGGTTCCTTAAT-TGTG
1 TACGGACCTAAGGATATATTGGGTAGGCCCCAAGGTATA-CCTTAGGTTGGTTCCTT-ATCTGTG
* * * * *
2033319 TGCTTAAGGTAACCCTACGGATCTAAGGATGTCCTTGGGTA-GATCCAAGGTATATCCTTAGGTT
64 TGCATAAGGTAACCCTACGGACCTAAGGATAT-CTTGGGTAGGACCCAAGGCATATCCTTAGGTT
2033383 GGCTCCCCTTTTTGCTGTGTGC
128 GGCTCCCCTTTTTGCTGTGTGC
2033405 TGAGGGCAAG
Statistics
Matches: 134, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
160 91 0.68
161 29 0.22
162 14 0.10
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (161 bp):
TACGGACCTAAGGATATATTGGGTAGGCCCCAAGGTATACCTTAGGTTGGTTCCTTATCTGTGTG
CATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGACCCAAGGCATATCCTTAGGTTGGC
TCCCCTTTTTGCTGTGTGCATAAGGTAACCC
Found at i:2048576 original size:10 final size:10
Alignment explanation
Indices: 2048561--2048589 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2048551 TAATTATTTT
2048561 AAAAAAATTA
1 AAAAAAATTA
2048571 AAAAAAATTA
1 AAAAAAATTA
2048581 AAAAAAATT
1 AAAAAAATT
2048590 TGAGGGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:2049665 original size:2 final size:2
Alignment explanation
Indices: 2049660--2049694 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2049650 AGTGTGTGTG
* *
2049660 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2049695 GTGTAGGTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2058418 original size:37 final size:37
Alignment explanation
Indices: 2058345--2058419 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
2058335 GTTGGAAAAT
* *
2058345 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
2058382 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
2058419 A
1 A
2058420 ATATTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:2062882 original size:30 final size:29
Alignment explanation
Indices: 2062833--2062912 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 29
2062823 TCATTTTTTT
* *
2062833 TAATATTTTCATTATTTTTTAGCGTATAA
1 TAATATTTTCATCATTTTTTAGCATATAA
* *
2062862 TAATATTTTTAGTCATTTTTTAGCATCTAA
1 TAATATTTTCA-TCATTTTTTAGCATATAA
2062892 TAATATTTTCGATCATTTTTT
1 TAATATTTTC-ATCATTTTTT
2062913 TTGAAAATCC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 10 0.23
30 33 0.75
31 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (29 bp):
TAATATTTTCATCATTTTTTAGCATATAA
Found at i:2066408 original size:25 final size:25
Alignment explanation
Indices: 2066380--2066428 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2066370 TGTATTGCTT
*
2066380 CAATGTAT-ATAATCAATTATTATAA
1 CAAT-TATCATAATCAATTACTATAA
*
2066405 CAATTATCATAATCAGTTACTATA
1 CAATTATCATAATCAATTACTATA
2066429 TTGGATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (25 bp):
CAATTATCATAATCAATTACTATAA
Found at i:2066410 original size:12 final size:13
Alignment explanation
Indices: 2066387--2066419 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2066377 CTTCAATGTA
2066387 TATAATCAATTAT
1 TATAATCAATTAT
2066400 TATAA-CAATTAT
1 TATAATCAATTAT
*
2066412 CATAATCA
1 TATAATCA
2066420 GTTACTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TATAATCAATTAT
Found at i:2068749 original size:9 final size:9
Alignment explanation
Indices: 2068735--2068823 Score: 67
Period size: 9 Copynumber: 11.0 Consensus size: 9
2068725 TTAATAACAG
2068735 ATAAATATA
1 ATAAATATA
2068744 ATAAATATA
1 ATAAATATA
2068753 AT-AATAATA
1 ATAAAT-ATA
2068762 AT-AATAT-
1 ATAAATATA
2068769 -TAAATAT-
1 ATAAATATA
2068776 -TAAATAT-
1 ATAAATATA
2068783 -TAAATATA
1 ATAAATATA
2068791 AT-AATA-A
1 ATAAATATA
*
2068798 TTAAAATATA
1 AT-AAATATA
2068808 AT-AATA-A
1 ATAAATATA
2068815 ATAAATATA
1 ATAAATATA
2068824 GTAATTAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
6 1 0.01
7 24 0.35
8 17 0.25
9 25 0.36
10 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATAAATATA
Found at i:2068758 original size:12 final size:12
Alignment explanation
Indices: 2068741--2068828 Score: 69
Period size: 12 Copynumber: 7.4 Consensus size: 12
2068731 ACAGATAAAT
2068741 ATAATAAATATA
1 ATAATAAATATA
2068753 ATAAT-AATAATA
1 ATAATAAAT-ATA
*
2068765 ATATTAAATATTAA
1 ATAATAAATA-T-A
*
2068779 ATATTAAATATA
1 ATAATAAATATA
2068791 ATAAT-AAT-TA
1 ATAATAAATATA
*
2068801 A-AATATA-ATA
1 ATAATAAATATA
2068811 ATAAATAAATATA
1 AT-AATAAATATA
*
2068824 GTAAT
1 ATAAT
2068829 TAAAATAGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
9 3 0.05
10 7 0.11
11 6 0.10
12 26 0.42
13 9 0.15
14 11 0.18
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (12 bp):
ATAATAAATATA
Found at i:2068776 original size:7 final size:7
Alignment explanation
Indices: 2068764--2068789 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2068754 TAATAATAAT
2068764 AATATTA
1 AATATTA
2068771 AATATTA
1 AATATTA
2068778 AATATTA
1 AATATTA
2068785 AATAT
1 AATAT
2068790 AATAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTA
Found at i:2068810 original size:29 final size:28
Alignment explanation
Indices: 2068717--2068864 Score: 116
Period size: 29 Copynumber: 5.4 Consensus size: 28
2068707 GGATCTTTCA
* *
2068717 AATTAAAAT-TAATAACAGATAAAT-AT
1 AATTAAAATATAATAATAAATAAATAAT
2068743 AA-T-AAATATAATAAT-AAT-AATAAT
1 AATTAAAATATAATAATAAATAAATAAT
*
2068767 -ATT-AAATATTAAATATTAAATATAATAAT
1 AATTAAAATA-T-AATAATAAATA-AATAAT
2068796 AATTAAAATATAATAATAAATAAATATAGT
1 AATTAAAATATAATAATAAATAAATA-A-T
* * **
2068826 AATTAAAATA-GATATTTTATAAATAAT
1 AATTAAAATATAATAATAAATAAATAAT
*
2068853 AATTATAATATA
1 AATTAAAATATA
2068865 TTTTGTAAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
23 4 0.04
24 14 0.14
25 8 0.08
26 7 0.07
27 13 0.13
28 5 0.05
29 28 0.28
30 15 0.15
31 5 0.05
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (28 bp):
AATTAAAATATAATAATAAATAAATAAT
Found at i:2068832 original size:17 final size:16
Alignment explanation
Indices: 2068741--2068828 Score: 81
Period size: 17 Copynumber: 5.3 Consensus size: 16
2068731 ACAGATAAAT
2068741 ATAATAAATATAATAATA
1 ATAATAAATA-AAT-ATA
*
2068759 ATAATAATATTAAATATT
1 ATAATAA-A-TAAATATA
*
2068777 A-AAT-ATTAAATATA
1 ATAATAAATAAATATA
*
2068791 ATAATAATTAAAATATA
1 ATAATAAAT-AAATATA
2068808 ATAATAAATAAATATA
1 ATAATAAATAAATATA
*
2068824 GTAAT
1 ATAAT
2068829 TAAAATAGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
14 8 0.13
15 3 0.05
16 15 0.25
17 18 0.30
18 10 0.17
19 4 0.07
20 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (16 bp):
ATAATAAATAAATATA
Found at i:2068931 original size:14 final size:14
Alignment explanation
Indices: 2068899--2068949 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2068889 AAATTATATG
* * *
2068899 TATAATACATTAAA
1 TATAATATAATAAT
2068913 TATAATA-AATAAT
1 TATAATATAATAAT
*
2068926 TAATAATATTATAAT
1 T-ATAATATAATAAT
2068941 TATAATATA
1 TATAATATA
2068950 TTTTGAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 5 0.16
14 20 0.65
15 6 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TATAATATAATAAT
Found at i:2068948 original size:33 final size:32
Alignment explanation
Indices: 2068738--2068949 Score: 92
Period size: 33 Copynumber: 6.6 Consensus size: 32
2068728 ATAACAGATA
* *
2068738 AATATAATAAATATAATAATAATAATAA-TATT
1 AATATAATAATTATAAT-ATAATAATAATTAAT
2068770 AAATATTAA-ATATTA-AATATAATAATAATTAA-
1 -AATA-TAATA-ATTATAATATAATAATAATTAAT
2068802 AATATAATAA-TA-AATA-AATATAGTAATTAA-
1 AATATAATAATTATAATATAATA-A-TAATTAAT
* * *
2068832 AATA-GATATTTTATAA-ATAATAATTA-TAAT
1 AATATAATA-ATTATAATATAATAATAATTAAT
* ** * *
2068862 ATATTTTGTAAATTTTGAA-ATAATGAAAAATT-AT
1 A-ATATAAT-AATTAT-AATATAAT-AATAATTAAT
*
2068896 ATGTATAATACATTA-AATATAATAAATAATTAAT
1 A-ATATAATA-ATTATAATATAAT-AATAATTAAT
*
2068930 AATATTATAATTATAATATA
1 AATATAATAATTATAATATA
2068950 TTTTGAAATT
Statistics
Matches: 137, Mismatches: 21, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
28 4 0.03
29 13 0.09
30 18 0.13
31 11 0.08
32 26 0.19
33 42 0.31
34 22 0.16
35 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (32 bp):
AATATAATAATTATAATATAATAATAATTAAT
Found at i:2070821 original size:21 final size:21
Alignment explanation
Indices: 2070795--2070839 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2070785 GATTTCTGGG
* *
2070795 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2070816 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2070837 CAA
1 CAA
2070840 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2071689 original size:31 final size:31
Alignment explanation
Indices: 2071651--2071837 Score: 331
Period size: 31 Copynumber: 6.0 Consensus size: 31
2071641 AGGGTCGAGG
2071651 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2071682 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2071713 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2071744 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2071775 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
2071806 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2071837 G
1 G
2071838 GTCCTTCGGG
Statistics
Matches: 152, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 151 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2074808 original size:21 final size:21
Alignment explanation
Indices: 2074782--2074826 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2074772 GATTTCTGGG
* *
2074782 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2074803 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2074824 CAA
1 CAA
2074827 CGACAGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2075667 original size:31 final size:31
Alignment explanation
Indices: 2075620--2075791 Score: 303
Period size: 31 Copynumber: 5.6 Consensus size: 31
2075610 AGGGTCGAGG
2075620 GTTTACCTA-GTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2075650 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2075681 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2075712 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2075743 GTTTACCTATGTTCTTCGGGACAT-TGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2075773 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
2075792 AATCTATGTA
Statistics
Matches: 137, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
30 32 0.23
31 105 0.77
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2077009 original size:36 final size:36
Alignment explanation
Indices: 2076934--2077036 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
2076924 ATTTATAAGT
* *
2076934 TGGTGATAATATAGGC-TGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2076968 T-GTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2077003 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
2077037 ATATTGTATC
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
33 13 0.20
34 5 0.08
35 14 0.22
36 32 0.50
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:2079544 original size:13 final size:13
Alignment explanation
Indices: 2079526--2079550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2079516 GGTCAAAGGA
2079526 GGTCAACGGTCAC
1 GGTCAACGGTCAC
2079539 GGTCAACGGTCA
1 GGTCAACGGTCA
2079551 ACGATTGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTCAACGGTCAC
Found at i:2079594 original size:19 final size:19
Alignment explanation
Indices: 2079555--2079594 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2079545 CGGTCAACGA
* * *
2079555 TTGGGTCGGGTCGGTCGGG
1 TTGGGTCGGGTCAGACCGG
2079574 TTGGGTCGGGTCAGACCGG
1 TTGGGTCGGGTCAGACCGG
2079593 TT
1 TT
2079595 CATACCGGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.17, G:0.50, T:0.28
Consensus pattern (19 bp):
TTGGGTCGGGTCAGACCGG
Done.