Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000509.1 Hibiscus syriacus cultivar Beakdansim tig00000968_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: 67844
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:8009 original size:21 final size:20
Alignment explanation
Indices: 7923--8080 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
7913 AAATGACCAA
**
7923 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
7942 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
7962 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
7982 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
8003 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
8024 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
8044 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
8065 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
8081 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:8073 original size:20 final size:20
Alignment explanation
Indices: 8048--8236 Score: 209
Period size: 20 Copynumber: 9.4 Consensus size: 20
8038 GATTTTCCAG
** *
8048 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
*
8068 AATCGCAACGCGAA-CACATA
1 AATCGCAACGCGAATC-CGTA
*
8088 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
8108 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
8128 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
**
8148 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
8168 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTA
**
8188 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
8208 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTA
*
8228 AATCACAAC
1 AATCGCAAC
8237 ACTGAAATTT
Statistics
Matches: 149, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:8968 original size:24 final size:24
Alignment explanation
Indices: 8929--8975 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
8919 AAATTTGGTC
8929 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
8953 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
8976 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:9166 original size:12 final size:12
Alignment explanation
Indices: 9149--9173 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9139 ATATAATCCT
9149 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9161 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9173 G
1 G
9174 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:11507 original size:33 final size:34
Alignment explanation
Indices: 11456--11660 Score: 152
Period size: 34 Copynumber: 5.8 Consensus size: 34
11446 CGGAAATTAC
* *
11456 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
11489 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* * *
11523 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
11562 AAT-GCGGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
* * *
11595 AATCGCAACGA-GAGAATCGCAATGCGGAAATAAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
*
11629 AATCGCAATGCGAAATGAAAATCGCATTGCGA
1 AATCGCAA--C--AATGAAAATCGCAATGCGA
11661 TTTTCATTTC
Statistics
Matches: 136, Mismatches: 17, Indels: 33
0.73 0.09 0.18
Matches are distributed among these distances:
32 2 0.01
33 41 0.30
34 50 0.37
36 2 0.01
38 7 0.05
39 33 0.24
40 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:11521 original size:20 final size:19
Alignment explanation
Indices: 11470--11660 Score: 205
Period size: 19 Copynumber: 10.7 Consensus size: 19
11460 GCAACGAGAG
11470 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
11489 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
11503 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
11523 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
11542 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
11556 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
11576 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
11595 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
11609 AATCGCAATGCGGAAATAAA
1 AATCGCAATGC-GAAATGAA
11629 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
11648 AATCGCATTGCGA
1 AATCGCAATGCGA
11661 TTTTCATTTC
Statistics
Matches: 145, Mismatches: 9, Indels: 36
0.76 0.05 0.19
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 3 0.02
17 7 0.05
19 60 0.41
20 41 0.28
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:11533 original size:53 final size:53
Alignment explanation
Indices: 11470--11654 Score: 327
Period size: 53 Copynumber: 3.5 Consensus size: 53
11460 GCAACGAGAG
* *
11470 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
11523 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
11576 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATAAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
11629 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
11655 TTGCGATTTT
Statistics
Matches: 128, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
53 127 0.99
54 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:11672 original size:19 final size:19
Alignment explanation
Indices: 11650--11733 Score: 115
Period size: 19 Copynumber: 4.6 Consensus size: 19
11640 GAAATGAAAA
11650 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
11669 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
11685 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
11702 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
11721 TCCGCATTGCGAT
1 T-CGCATTGCGAT
11734 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 26 0.46
20 11 0.19
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:11859 original size:14 final size:14
Alignment explanation
Indices: 11840--11876 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
11830 CATCAATTAA
11840 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
11854 ACAAATCATCTTTT
1 ACAAATCAACTTTT
11868 ACAAATCAA
1 ACAAATCAA
11877 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:13841 original size:19 final size:19
Alignment explanation
Indices: 13799--13938 Score: 146
Period size: 19 Copynumber: 7.6 Consensus size: 19
13789 TAGTTTACTT
* *
13799 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
13819 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
13838 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
13857 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
13876 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
13890 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
13909 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
13928 TCGCAATGCGA
1 TCGCAACGCGA
13939 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 5 0.05
19 69 0.70
20 12 0.12
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:13901 original size:33 final size:34
Alignment explanation
Indices: 13815--13917 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 34
13805 CACGAAACTT
*
13815 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAAC--G--ACC
13853 AAAATCGCAACGCGAAATGAAAATCGCAACGA-C
1 AAAATCGCAACGCGAAATGAAAATCGCAACGACC
* *
13886 AGAATCGCAATGCGAAATGAAAATCGCAACGA
1 AAAATCGCAACGCGAAATGAAAATCGCAACGA
13918 GAAATGAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
33 31 0.50
34 1 0.02
36 1 0.02
38 29 0.47
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (34 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGACC
Found at i:13909 original size:52 final size:52
Alignment explanation
Indices: 13834--13933 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
13824 ACGCGAAATG
*
13834 AGAATCGCAACGAGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AGAATCGCAACGAGAAACCAAAATCGCAACGAGAAATGAAAATCGCAACGAC
* * **
13886 AGAATCGCAATGCGAAATGAAAATCGCAACGAGAAATGAAAATCGCAA
1 AGAATCGCAACGAGAAACCAAAATCGCAACGAGAAATGAAAATCGCAA
13934 TGCGATTTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.49, C:0.21, G:0.20, T:0.10
Consensus pattern (52 bp):
AGAATCGCAACGAGAAACCAAAATCGCAACGAGAAATGAAAATCGCAACGAC
Found at i:15950 original size:20 final size:20
Alignment explanation
Indices: 15920--16016 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
15910 TTTTGGTTGA
15920 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
** *
15940 AATGACTATCGCAACGAGATA
1 AATGAAAATCGCAACGAGA-G
15961 AATGAAAATCGCAAC--GAG
1 AATGAAAATCGCAACGAGAG
*
15979 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
15994 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
16014 AAT
1 AAT
16017 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 14 0.23
20 20 0.32
21 13 0.21
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:15986 original size:14 final size:14
Alignment explanation
Indices: 15967--16023 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
15957 GATAAATGAA
15967 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
15981 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
16000 AATCGCAACGAGAG
1 AATCGCAACGAGAG
16014 AATCGCAACG
1 AATCGCAACG
16024 CGAAATGAAA
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:16001 original size:33 final size:33
Alignment explanation
Indices: 15918--16040 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
15908 TCTTTTGGTT
*
15918 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGA
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAACGC
15957 GATAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 G--AAATGAAAATCGCAACGAGAGAATCGCAACGC
15992 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
16025 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
16041 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 48 0.59
35 10 0.12
37 2 0.02
38 1 0.01
39 4 0.05
41 16 0.20
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:16083 original size:21 final size:21
Alignment explanation
Indices: 16057--16127 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
16047 TTTGGTTTCG
16057 CGTTGCGATTTTCATTTCTCT
1 CGTTGCGATTTTCATTTCTCT
** *
16078 CGTTGCAGATAGTCATTT-TCG
1 CGTTGC-GATTTTCATTTCTCT
16099 CGTTGCGATTTTCATTTCTCT
1 CGTTGCGATTTTCATTTCTCT
16120 CGTTGCGA
1 CGTTGCGA
16128 CTCTTCTGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 9 0.21
21 24 0.57
22 9 0.21
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (21 bp):
CGTTGCGATTTTCATTTCTCT
Found at i:16253 original size:19 final size:19
Alignment explanation
Indices: 16229--16277 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 19
16219 CGAGAGAATA
16229 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
16248 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
16262 GCAACGCGAAATGAAA
1 GCAACGCGAAATGAAA
16278 TCTACGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 10
0.66 0.06 0.29
Matches are distributed among these distances:
14 10 0.43
15 1 0.04
16 2 0.09
17 2 0.09
18 1 0.04
19 7 0.30
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.08
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:16253 original size:33 final size:33
Alignment explanation
Indices: 16207--16277 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
16197 AATACTAACT
*
16207 TGAAAATCTCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
*
16240 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
16273 TGAAA
1 TGAAA
16278 TCTACGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:16671 original size:20 final size:20
Alignment explanation
Indices: 16646--16918 Score: 388
Period size: 20 Copynumber: 13.6 Consensus size: 20
16636 CTTTAAAAAT
16646 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
16666 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
16686 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
16707 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
16727 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
16747 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
16767 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
16787 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
16807 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
16827 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
16847 CACGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
16867 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
16887 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
16907 CGCGTTGCGATT
1 CGCGTTGCGATT
16919 CTGGAAAATC
Statistics
Matches: 228, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
20 210 0.92
21 18 0.08
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:22078 original size:25 final size:25
Alignment explanation
Indices: 22018--22078 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
22008 TCTACAAAAA
22018 TATTTTATTA-TATTATATATTTAT
1 TATTTTATTATTATTATATATTTAT
22042 T-TATTTATTATTATTAATATATTT-T
1 TAT-TTTATTATTATT-ATATATTTAT
22067 TATTTTATTATT
1 TATTTTATTATT
22079 TTTGCAGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
23 1 0.03
24 8 0.24
25 15 0.45
26 9 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TATTTTATTATTATTATATATTTAT
Found at i:22080 original size:8 final size:8
Alignment explanation
Indices: 22018--22080 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
22008 TCTACAAAAA
22018 TATTTTAT
1 TATTTTAT
*
22026 TATATTA-
1 TATTTTAT
22033 TATATTTAT
1 TAT-TTTAT
22042 T-TATTTAT
1 TAT-TTTAT
*
22050 TATTATTAA
1 TATT-TTAT
22059 TATATTT-T
1 TAT-TTTAT
22067 TATTTTAT
1 TATTTTAT
22075 TATTTT
1 TATTTT
22081 TGCAGGCCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
7 6 0.13
8 28 0.62
9 10 0.22
10 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TATTTTAT
Found at i:26650 original size:3 final size:3
Alignment explanation
Indices: 26642--26670 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
26632 TAATATAAAT
26642 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
26671 TGGATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27162 original size:113 final size:113
Alignment explanation
Indices: 26807--27680 Score: 1154
Period size: 113 Copynumber: 7.7 Consensus size: 113
26797 TTTGAATAAA
* * ** *
26807 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGATGATCCATC
* * * * *
26871 AGATGAT-GAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AAATGATGGATTTC-AGCTAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
26920 TTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAA-ATAATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACCTTCTCTGG-AAAAGATGATCC
* * ** * *
26984 ATCAAGTGAT-GAATTCAGAAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAATGATGGATTTCAGCTAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
27035 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
* * * *
27100 AGTGATGGATTTGAGCTAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 AATGATGGATTTCAGCTAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * * *
27148 TTCTTCTTCTTTCTTCAGATAACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATGATCC
* * *
27212 ATCAAATGATGAATTTAAGCAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
62 ATCAAATGATGGATTTCAGC-TAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
27265 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
* *
27330 AATGATGGA-TTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAT
66 AATGATGGATTTCAGCT-AAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
27378 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
* *
27443 AATGATGGA-TTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAT
66 AATGATGGATTTCAGCT-AAAGGTTGAACAAATTCTTCTCATTATGAAC
*
27491 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAA-ATAATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG-AAAAGATGATCCATC
* * *
27555 AAGTGAT-GAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 AAATGATGGATTTCAGCT-AAAGGTTGAACAAATTCTTCTCATTATGAAC
*
27604 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
*
27669 AATGATAGATTT
66 AATGATGGATTT
27681 GAATCTTTGC
Statistics
Matches: 698, Mismatches: 45, Indels: 35
0.90 0.06 0.04
Matches are distributed among these distances:
111 4 0.01
112 50 0.07
113 374 0.54
114 66 0.09
115 53 0.08
116 75 0.11
117 76 0.11
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCA
AATGATGGATTTCAGCTAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:28379 original size:83 final size:83
Alignment explanation
Indices: 28233--28557 Score: 517
Period size: 83 Copynumber: 3.9 Consensus size: 83
28223 GCACTTCTTT
* *
28233 AGATCAAATAACTCAAAGAACATTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
* ** *
28298 GCTTGGTTCTGTTAAACC
66 GCTTGATTCTGTCCAATC
* *
28316 ATG-TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCAA
1 A-GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAA
*
28380 TGATTGATTCTGTCCAATC
65 TGCTTGATTCTGTCCAATC
28399 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
*
28464 GCTTGATTTTGTCCAATC
66 GCTTGATTCTGTCCAATC
* *
28482 AGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCATATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
*
28547 GCTTGGTTCTG
66 GCTTGATTCTG
28558 GGATATCACA
Statistics
Matches: 223, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
82 1 0.00
83 221 0.99
84 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (83 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
GCTTGATTCTGTCCAATC
Found at i:40286 original size:13 final size:15
Alignment explanation
Indices: 40264--40300 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
40254 TTTGACATAA
40264 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
40276 AAATAAAATACTTGC
1 AAATAAAATACTTGC
40291 AAATAAAATA
1 AAATAAAATA
40301 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:40339 original size:18 final size:17
Alignment explanation
Indices: 40291--40341 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
40281 AAATACTTGC
*
40291 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
40309 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
40327 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
40342 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:42515 original size:3 final size:3
Alignment explanation
Indices: 42507--42571 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
42497 TAATATAAAT
42507 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42555 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
42572 TGGATAAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52847 original size:18 final size:19
Alignment explanation
Indices: 52824--52869 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
52814 GTAATAAAAT
*
52824 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
*
52842 ATT-AAATAAGTAGAAGCA
1 ATTAAAATAAGTAAAAGCA
52860 ATTAAAATAA
1 ATTAAAATAA
52870 AAATAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 12 0.50
19 6 0.25
ACGTcount: A:0.61, C:0.04, G:0.11, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:61826 original size:28 final size:29
Alignment explanation
Indices: 61795--61850 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
61785 ATATGATTTG
61795 AAAAAAAATAAGA-TTTAGATACCAAAAT
1 AAAAAAAATAAGAGTTTAGATACCAAAAT
* *
61823 AAAAAAAATAATAGTTTAGATACTAAAA
1 AAAAAAAATAAGAGTTTAGATACCAAAA
61851 ATGTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.23
Consensus pattern (29 bp):
AAAAAAAATAAGAGTTTAGATACCAAAAT
Found at i:62786 original size:22 final size:22
Alignment explanation
Indices: 62760--62807 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
62750 CCAAACGACT
62760 AAAACATATCA-AAAGACATAAG
1 AAAACATATCATAAAGACAT-AG
* *
62782 AAAACGTATTATAAAGACATAG
1 AAAACATATCATAAAGACATAG
62804 AAAA
1 AAAA
62808 TCGTGTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAACATATCATAAAGACATAG
Found at i:62818 original size:23 final size:23
Alignment explanation
Indices: 62760--62819 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
62750 CCAAACGACT
*
62760 AAAACATATCA-AAAGACATAAG
1 AAAACGTATCATAAAGACATAAG
*
62782 AAAACGTATTATAAAGACAT-AG
1 AAAACGTATCATAAAGACATAAG
*
62804 AAAATCGTGTCATAAA
1 AAAA-CGTATCATAAA
62820 AGTAGAGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.20
Consensus pattern (23 bp):
AAAACGTATCATAAAGACATAAG
Done.