Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000319.1 Hibiscus syriacus cultivar Beakdansim tig00000601_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: 80175
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1735 original size:17 final size:17
Alignment explanation
Indices: 1713--1746 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1703 TATTGGCCGT
1713 AGGTCGCCATGCACTCC
1 AGGTCGCCATGCACTCC
1730 AGGTCGCCATGCACTCC
1 AGGTCGCCATGCACTCC
1747 GGGCGACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.24, T:0.18
Consensus pattern (17 bp):
AGGTCGCCATGCACTCC
Found at i:1790 original size:12 final size:12
Alignment explanation
Indices: 1773--1797 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1763 CTCAAACAGA
1773 GAGAATGAACGT
1 GAGAATGAACGT
1785 GAGAATGAACGT
1 GAGAATGAACGT
1797 G
1 G
1798 TTGCATAGCA
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:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:1859 original size:29 final size:28
Alignment explanation
Indices: 1826--1910 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 28
1816 TCCCAACACA
1826 TAGGTCGCCATGTCCTCCGGGCGACCTTG
1 TAGGTCGCCATG-CCTCCGGGCGACCTTG
*
1855 TAGGTCGCCATGCCCTCCGGGCGACATTG
1 TAGGTCGCCATG-CCTCCGGGCGACCTTG
*
1884 TAGGTCGCCATGCACTCCGGGTGACCT
1 TAGGTCGCCATGC-CTCCGGGCGACCT
1911 ACCCTCGCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 1 0.02
29 50 0.98
ACGTcount: A:0.13, C:0.34, G:0.31, T:0.22
Consensus pattern (28 bp):
TAGGTCGCCATGCCTCCGGGCGACCTTG
Found at i:1962 original size:23 final size:23
Alignment explanation
Indices: 1929--1987 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1919 TCGGCTTCCT
*
1929 TCGGATTCCCTCGCATAGCTCGC
1 TCGGATGCCCTCGCATAGCTCGC
* *
1952 TCGGATGCCCTCGCATAGTTCGT
1 TCGGATGCCCTCGCATAGCTCGC
*
1975 TCGGATGGCCTCG
1 TCGGATGCCCTCG
1988 GTCGGATGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.12, C:0.34, G:0.27, T:0.27
Consensus pattern (23 bp):
TCGGATGCCCTCGCATAGCTCGC
Found at i:2020 original size:34 final size:34
Alignment explanation
Indices: 1975--2040 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1965 CATAGTTCGT
*
1975 TCGGATGGCCTCGGTCGGATGACCTCGGATGCTC
1 TCGGATAGCCTCGGTCGGATGACCTCGGATGCTC
2009 TCGGATAGCCTCGGTCGGATGACCTCGGATGC
1 TCGGATAGCCTCGGTCGGATGACCTCGGATGC
2041 CCAGCGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.14, C:0.29, G:0.35, T:0.23
Consensus pattern (34 bp):
TCGGATAGCCTCGGTCGGATGACCTCGGATGCTC
Found at i:2954 original size:5 final size:5
Alignment explanation
Indices: 2941--2977 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
2931 CAATGAGTTG
* *
2941 AAATA AAATG AAATA AAATG AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
2978 CCCTCAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:2954 original size:10 final size:10
Alignment explanation
Indices: 2939--2977 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
2929 TCCAATGAGT
2939 TGAAATAAAA
1 TGAAATAAAA
2949 TGAAATAAAA
1 TGAAATAAAA
2959 TGAAATAAAA
1 TGAAATAAAA
*
2969 TAAAATAAA
1 TGAAATAAA
2978 CCCTCAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (10 bp):
TGAAATAAAA
Found at i:11730 original size:25 final size:25
Alignment explanation
Indices: 11702--11749 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
11692 ATAACTCTTT
11702 TATA-AAAATATATTTATAAAAATTG
1 TATATAAAATATA-TTATAAAAATTG
* *
11727 TATATAAAATCTATTGTAAAAAT
1 TATATAAAATATATTATAAAAAT
11750 AATTAGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
TATATAAAATATATTATAAAAATTG
Found at i:14804 original size:25 final size:25
Alignment explanation
Indices: 14776--14823 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
14766 AAAAAATATT
*
14776 TTAACTATCTATTTTAATAAAAAAA
1 TTAAATATCTATTTTAATAAAAAAA
* *
14801 TTAAATGTTTATTTTAATAAAAA
1 TTAAATATCTATTTTAATAAAAA
14824 TACTTTAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
TTAAATATCTATTTTAATAAAAAAA
Found at i:22232 original size:2 final size:2
Alignment explanation
Indices: 22225--22266 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
22215 ACCGCGAATG
22225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22266 T
1 T
22267 TTTTGTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29007 original size:17 final size:18
Alignment explanation
Indices: 28970--29014 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28960 TGAAGTAGAT
*
28970 AATATTTAAAAAAAATAA
1 AATAATTAAAAAAAATAA
*
28988 AATAATTAAAAATAAT-A
1 AATAATTAAAAAAAATAA
29005 AATAA-TAAAA
1 AATAATTAAAA
29015 TATTTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 5 0.20
17 6 0.24
18 14 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAATTAAAAAAAATAA
Found at i:37706 original size:21 final size:21
Alignment explanation
Indices: 37682--37731 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
37672 ACCGAAAACA
*
37682 TTATTATTTCTACCGGTTTTG
1 TTATTATTTCTACCAGTTTTG
* *
37703 TTATTTTTTCTACCAGTTTTT
1 TTATTATTTCTACCAGTTTTG
37724 TTATTATT
1 TTATTATT
37732 GACATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (21 bp):
TTATTATTTCTACCAGTTTTG
Found at i:40441 original size:3 final size:3
Alignment explanation
Indices: 40433--40464 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40423 TTTTACGTTA
40433 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40465 ATGTAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41020 original size:21 final size:21
Alignment explanation
Indices: 40994--41091 Score: 87
Period size: 21 Copynumber: 4.7 Consensus size: 21
40984 ATCAGTTTCC
40994 AAAATCGCAACGCGATTATTG
1 AAAATCGCAACGCGATTATTG
* *
41015 AAAATCGCAATGCGA-TAGT-
1 AAAATCGCAACGCGATTATTG
** *
41034 ACAAATTCGCATTGCGATT-TTCC
1 A-AAA-TCGCAACGCGATTATT-G
*
41057 AAAATCGCAACGCGAATA-TG
1 AAAATCGCAACGCGATTATTG
41077 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
41092 ACACATAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 21 0.33
21 36 0.57
22 4 0.06
23 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTATTG
Found at i:41082 original size:20 final size:20
Alignment explanation
Indices: 41058--41251 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
41048 CGATTTTCCA
** *
41058 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
41078 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
41098 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
41118 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
41138 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
41158 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
41178 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
41198 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
41218 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
41238 AAATCGCAACGCGA
1 AAATCGCAACGCGA
41252 TATTTAAAGC
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:41671 original size:33 final size:33
Alignment explanation
Indices: 41632--41702 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
41622 TTCACTTAGA
* *
41632 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
41665 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
41698 TTTCA
1 TTTCA
41703 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:41839 original size:41 final size:38
Alignment explanation
Indices: 41775--41891 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
41765 TTCAATTTGC
* *
41775 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
41813 AGAATGACTGTCGCAACGAGAGAAATGACAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
41854 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
41887 AGAAT
1 AGAAT
41892 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:41855 original size:21 final size:21
Alignment explanation
Indices: 41782--41857 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
41772 TGCAGAAGAG
* *
41782 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
41803 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
41823 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
41844 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
41858 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:41861 original size:14 final size:14
Alignment explanation
Indices: 41842--41898 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
41832 GAGAAATGAC
41842 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
41856 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
41875 AATCGCAACGAGAG
1 AATCGCAACGAGAG
41889 AATCGCAACG
1 AATCGCAACG
41899 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:41879 original size:33 final size:33
Alignment explanation
Indices: 41834--41914 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
41824 CGCAACGAGA
*
41834 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
41867 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
41900 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
41915 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:41932 original size:19 final size:19
Alignment explanation
Indices: 41910--42007 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
41900 GAAACCAAAA
*
41910 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
41929 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
41943 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
41962 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
41976 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
41995 TCGCGTTGCGATT
1 TCGCGTTGCGATT
42008 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
16 4 0.07
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:41951 original size:14 final size:14
Alignment explanation
Indices: 41932--42021 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
41922 TTTCATTTCG
41932 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
41946 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
41965 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
41979 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
41996 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
42012 CGTTGCGATT
1 CGTTGCGATT
42022 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 2 0.03
16 7 0.11
17 7 0.11
18 2 0.03
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:41961 original size:33 final size:33
Alignment explanation
Indices: 41915--42029 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
41905 CAAAATCGCA
*
41915 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
41948 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
41981 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
42014 TTGCGATTTTCATTTC
1 TTGCGATTGTCATTTC
42030 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:42838 original size:19 final size:19
Alignment explanation
Indices: 42814--42913 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
42804 AAAATTGACT
42814 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
42833 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
42852 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
42866 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
42885 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
42905 ATCACAATG
1 ATCGCAATG
42914 GGAGAATCGC
Statistics
Matches: 72, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.54
20 17 0.24
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:42943 original size:53 final size:53
Alignment explanation
Indices: 42814--42930 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
42804 AAAATTGACT
*
42814 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCACAACGAGAGA
* *
42866 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCACAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCACAACGAGAGA
42919 ATCGCAATGCGA
1 ATCGCAATGCGA
42931 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 29 0.48
53 32 0.52
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCACAACGAGAGA
Found at i:42948 original size:19 final size:19
Alignment explanation
Indices: 42920--43068 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
42910 AATGGGAGAA
* *
42920 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
42939 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
42955 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
42972 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
42991 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
43007 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
43024 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
43040 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
43057 TCCGCATTGCGA
1 T-CGCATTGCGA
43069 AATGTAATGG
Statistics
Matches: 107, Mismatches: 7, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
14 18 0.17
16 21 0.20
17 19 0.18
18 2 0.02
19 41 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:42983 original size:52 final size:52
Alignment explanation
Indices: 42920--43036 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
42910 AATGGGAGAA
*
42920 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
42972 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
43024 TCGCATTGCGATT
1 TCGCATTGCGATT
43037 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:43014 original size:33 final size:33
Alignment explanation
Indices: 42977--43068 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
42967 TCATTTCGCA
42977 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
43010 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
43043 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
43069 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:43015 original size:14 final size:14
Alignment explanation
Indices: 42996--43050 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
42986 TCATTTCGCA
42996 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
43010 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
43027 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
43043 TTGCGATT
1 TTGCGATT
43051 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:43151 original size:19 final size:19
Alignment explanation
Indices: 43127--43224 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
43117 AAAATTGACT
43127 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
43146 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
43165 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
43179 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
43198 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
43218 ATCGCAA
1 ATCGCAA
43225 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:43256 original size:53 final size:53
Alignment explanation
Indices: 43127--43243 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
43117 AAAATTGACT
43127 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
43179 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
43232 ATCGCAATGCGA
1 ATCGCAATGCGA
43244 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:45570 original size:12 final size:12
Alignment explanation
Indices: 45553--45577 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45543 TCTTCGGGGA
45553 CTTTTTCTTCTT
1 CTTTTTCTTCTT
45565 CTTTTTCTTCTT
1 CTTTTTCTTCTT
45577 C
1 C
45578 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:45785 original size:24 final size:24
Alignment explanation
Indices: 45751--45797 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
45741 CTGAAACATC
45751 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
45775 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
45798 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:46727 original size:20 final size:20
Alignment explanation
Indices: 46477--46726 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
46467 AAATTTCAGT
* * *
46477 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
46497 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
46517 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
46537 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
46557 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
46577 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
46597 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
46617 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
46637 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
46657 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
46677 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
46697 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
46717 GTTGCGATTT
1 GTTGCGATTT
46727 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:46743 original size:21 final size:21
Alignment explanation
Indices: 46713--46795 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
46703 ATTTTCATAT
*
46713 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
46734 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
46755 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
46776 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
46796 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:46786 original size:42 final size:43
Alignment explanation
Indices: 46693--46791 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
46683 ATTTATGTGT
* *
46693 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
46734 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
46776 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
46792 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:51552 original size:22 final size:23
Alignment explanation
Indices: 51522--51570 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
51512 TTTATTCGTA
* * *
51522 TATGTATTTTATTATTTT-TTTT
1 TATGAATTTTAATATTTTCTTTG
51544 TATGAATTTTAATATTTTCTTTG
1 TATGAATTTTAATATTTTCTTTG
51567 TATG
1 TATG
51571 GTCTTGTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.67
Consensus pattern (23 bp):
TATGAATTTTAATATTTTCTTTG
Found at i:57586 original size:60 final size:60
Alignment explanation
Indices: 57414--57595 Score: 199
Period size: 60 Copynumber: 3.0 Consensus size: 60
57404 TGTATTTAGG
* * ** * * *
57414 GATGAAGTTGGAATATTCAAAAGTTTGGGGACCAATTTAGAAAGAAG-GTCATAGTTTAGG-
1 GATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTA-AAATAAGAGTTATAGTTT-GGA
* * * *
57474 GATGAAATT-AGAATGTTCAAAAGTTTAAGGACTAATTTATAATGAGAATTATAGTTTGGA
1 GATGAAATTGA-AATATTCAAAAGTTTAAGGACTAATTTAAAATAAGAGTTATAGTTTGGA
* *
57534 GATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAAAATTAGAGTTATAATTTGGA
1 GATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAAAATAAGAGTTATAGTTTGGA
57594 GA
1 GA
57596 CATGTGATGT
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
59 6 0.06
60 95 0.93
61 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.32
Consensus pattern (60 bp):
GATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAAAATAAGAGTTATAGTTTGGA
Found at i:60422 original size:4 final size:4
Alignment explanation
Indices: 60413--60466 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
60403 TAAGAATTTG
60413 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
60461 ATCT AT
1 ATCT AT
60467 ATGTTTATCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:64530 original size:54 final size:54
Alignment explanation
Indices: 64465--64606 Score: 230
Period size: 54 Copynumber: 2.6 Consensus size: 54
64455 TCTTTTACAG
* * * *
64465 TAGCTCGGGATGGATAAACCGTGCCCACGCCTTAACTGAAGACTTCTTTTGCGT
1 TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTAACTGAAGACTTCTTGTGCGT
* *
64519 TAGTTCTGGATGAATAAGCCGTGCCCAAGCCTTAACTGAAGACTTCTTGTGCGT
1 TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTAACTGAAGACTTCTTGTGCGT
64573 TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTA
1 TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTA
64607 TGCGAACGCC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 80 1.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.27
Consensus pattern (54 bp):
TAGCTCTGGATGAATAAGCCGTGCCCACGCCTTAACTGAAGACTTCTTGTGCGT
Found at i:65825 original size:45 final size:45
Alignment explanation
Indices: 65755--65841 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
65745 TTACACGACA
* *
65755 ATAGTATAGACAAATTTTGAGACTAATA-CAGCAAACATTATTTTC
1 ATAGTATAGACAAATTCTGAAACTAATACCA-CAAACATTATTTTC
* *
65800 ATAGTCTAGATAAATTCTGAAACTAATACCACAAACATTATT
1 ATAGTATAGACAAATTCTGAAACTAATACCACAAACATTATT
65842 GTCGTTACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 35 0.95
46 2 0.05
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (45 bp):
ATAGTATAGACAAATTCTGAAACTAATACCACAAACATTATTTTC
Found at i:73181 original size:2 final size:2
Alignment explanation
Indices: 73174--73202 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
73164 TCGATCTACA
73174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73203 ATTTCTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73473 original size:84 final size:85
Alignment explanation
Indices: 73259--73555 Score: 465
Period size: 85 Copynumber: 3.5 Consensus size: 85
73249 AATGATGTGT
* * * *
73259 GCTTCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
*
73324 CAAGC--AGATTTATGACGGGG
66 C-ATCTTA-ATTTATGACGGGG
* *
73344 GCTTCAATGACGCGCAATGTAAGTTATACATACGTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
*
73409 CATCTTAATTTATGAC-GGT
66 CATCTTAATTTATGACGGGG
73428 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
73493 CATCTTAATTTATGACGGGG
66 CATCTTAATTTATGACGGGG
* *
73513 GCTTCAATGACGCGCAATGTATGTCATACATGCGCGTCATAAA
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAA
73556 AAATTCATGT
Statistics
Matches: 196, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
84 83 0.42
85 112 0.57
86 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (85 bp):
GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
CATCTTAATTTATGACGGGG
Found at i:75105 original size:7 final size:7
Alignment explanation
Indices: 75093--75122 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
75083 ACCAAAACTG
75093 AACTGAT
1 AACTGAT
75100 AACTGAT
1 AACTGAT
75107 AACTGAT
1 AACTGAT
*
75114 AACTAAT
1 AACTGAT
75121 AA
1 AA
75123 GCACTCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (7 bp):
AACTGAT
Found at i:75242 original size:18 final size:18
Alignment explanation
Indices: 75219--75266 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
75209 AATCTATGCA
75219 TGATAACTGTAAAAAATC
1 TGATAACTGTAAAAAATC
*
75237 TGATAACTGT-AAACATC
1 TGATAACTGTAAAAAATC
75254 TGATAACTG-AAAA
1 TGATAACTGTAAAA
75267 TCATTTGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (18 bp):
TGATAACTGTAAAAAATC
Found at i:75277 original size:18 final size:17
Alignment explanation
Indices: 75219--75310 Score: 85
Period size: 18 Copynumber: 5.2 Consensus size: 17
75209 AATCTATGCA
*
75219 TGATAACTGTAAAAAATC
1 TGATAACTG-AAAACATC
*
75237 TGATAACTGTAAACATC
1 TGATAACTGAAAACATC
*
75254 TGATAACTGAAAATCATT
1 TGATAACTGAAAA-CATC
* *
75272 TGATAACTAAAAATCATA
1 TGATAACTGAAAA-CATC
* * *
75290 TGATAATTGTAAATATC
1 TGATAACTGAAAACATC
75307 TGAT
1 TGAT
75311 GTCCACTTGT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
17 24 0.39
18 38 0.61
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
TGATAACTGAAAACATC
Done.