Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009194.1 Hibiscus syriacus cultivar Beakdansim tig00112776_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: 93063
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:960 original size:21 final size:20
Alignment explanation
Indices: 936--1054 Score: 105
Period size: 21 Copynumber: 5.8 Consensus size: 20
926 TCAGTTTTCC
936 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
957 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
978 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
997 ACAAATTCGCATTGCGATTTTCC
1 A-AAA-TCGCAACGCGATTTT-G
* * *
1020 AGAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
1040 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1055 ACACATAAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
19 1 0.01
20 18 0.22
21 59 0.73
22 2 0.02
23 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:982 original size:42 final size:41
Alignment explanation
Indices: 930--1054 Score: 119
Period size: 42 Copynumber: 3.0 Consensus size: 41
920 CGCAAATCAG
930 TTTTCCAAAATCGCAACGCGATTCTTGAAAATCGCAACGCGA
1 TTTTCCAAAATCGCAACGCGATT-TTGAAAATCGCAACGCGA
* * ** **
972 TTCTT-GAAAATCGCAATGCGATAGT-ACAAATTCGCATTGCGA
1 TT-TTCCAAAATCGCAACGCGATTTTGA-AAA-TCGCAACGCGA
* * *
1014 TTTTCCAGAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 TTTTCCAAAATCGCAACGCGATTTTGAAAATCGCAACGCGA
1055 ACACATAAAT
Statistics
Matches: 64, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
40 1 0.02
41 15 0.23
42 45 0.70
43 3 0.05
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (41 bp):
TTTTCCAAAATCGCAACGCGATTTTGAAAATCGCAACGCGA
Found at i:1047 original size:20 final size:20
Alignment explanation
Indices: 936--1073 Score: 75
Period size: 21 Copynumber: 6.7 Consensus size: 20
926 TCAGTTTTCC
* *
936 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
* *
957 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAAT-ATG
*
978 AAAATCGCAATGCG-ATA-G
1 AAAATCGCAACGCGAATATG
** * * *
996 TACAAATTCGCATTGCGATTTTCC
1 -A-AAA-TCGCAACGCGAATAT-G
*
1020 AGAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAATATG
* *
1040 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATG
1059 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
1074 TATCCGTAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 33 0.35
21 54 0.57
22 3 0.03
23 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:1083 original size:20 final size:20
Alignment explanation
Indices: 1022--1246 Score: 221
Period size: 20 Copynumber: 11.4 Consensus size: 20
1012 GATTTTCCAG
* ** *
1022 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1042 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1062 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1082 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1102 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1122 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1142 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1162 AATCGCAA-G-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1181 AATCGCAACGAGAATCTGT-
1 AATCGCAACGCGTATCCGTA
1200 AATCGCAA--CG-ATCCCGTA
1 AATCGCAACGCGTAT-CCGTA
* * *
1218 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1238 AATCACAAC
1 AATCGCAAC
1247 CTGAAATTTT
Statistics
Matches: 173, Mismatches: 22, Indels: 20
0.80 0.10 0.09
Matches are distributed among these distances:
16 2 0.01
17 4 0.02
18 9 0.05
19 25 0.14
20 129 0.75
21 4 0.02
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:4461 original size:33 final size:34
Alignment explanation
Indices: 4410--4607 Score: 174
Period size: 33 Copynumber: 5.7 Consensus size: 34
4400 CGGAAATTAC
* *
4410 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
4443 AATCCCAAC-ATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* * *
4476 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
4515 AAT-GCGGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
* *
4548 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
4581 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
4608 CGAGAGAATC
Statistics
Matches: 133, Mismatches: 15, Indels: 29
0.75 0.08 0.16
Matches are distributed among these distances:
32 2 0.02
33 72 0.54
34 20 0.15
35 2 0.02
37 1 0.01
38 28 0.21
39 7 0.05
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:4483 original size:52 final size:52
Alignment explanation
Indices: 4424--4644 Score: 374
Period size: 52 Copynumber: 4.2 Consensus size: 52
4414 GCAACGAGAG
* *
4424 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGAAATGAA
4476 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
4529 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
4581 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT-TA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
4632 AATCGCATTGCGA
1 AATCGCAATGCGA
4645 TTCTCTCGTT
Statistics
Matches: 163, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
51 13 0.08
52 97 0.60
53 53 0.33
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:4573 original size:105 final size:103
Alignment explanation
Indices: 4424--4644 Score: 372
Period size: 105 Copynumber: 2.1 Consensus size: 103
4414 GCAACGAGAG
4424 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
4489 AATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AATGAAAATCGCAACGAGAGAATCGCAATGC-GAAAT-AA
* *
4529 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCG
*
4593 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTA
65 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAA
*
4632 AATCGCATTGCGA
1 AATCGCAATGCGA
4645 TTCTCTCGTT
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
103 13 0.12
104 5 0.05
105 92 0.83
106 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (103 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
AATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAA
Found at i:4618 original size:33 final size:33
Alignment explanation
Indices: 4476--4638 Score: 154
Period size: 33 Copynumber: 4.8 Consensus size: 33
4466 GCGAAATGAA
4476 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
4509 AATCGCAATGCGGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
4542 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
4581 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
4614 AATCGCAATGCGAAAT-TAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
4639 TTGCGATTCT
Statistics
Matches: 106, Mismatches: 12, Indels: 25
0.74 0.08 0.17
Matches are distributed among these distances:
31 5 0.05
32 11 0.10
33 43 0.41
34 20 0.19
35 1 0.01
36 2 0.02
38 10 0.09
39 7 0.07
40 7 0.07
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:4678 original size:52 final size:51
Alignment explanation
Indices: 4616--4729 Score: 174
Period size: 52 Copynumber: 2.2 Consensus size: 51
4606 AACGAGAGAA
*
4616 TCGCAATGCGAAATTAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATTAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** **
4667 TCCGCATTGCGATTTTATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATTAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
4719 TCGCATTGCGA
1 TCGCATTGCGA
4730 TTTTCATTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 11 0.19
52 46 0.81
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.40
Consensus pattern (51 bp):
TCGCATTGCGAAATTAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:4729 original size:19 final size:19
Alignment explanation
Indices: 4653--4749 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
4643 GATTCTCTCG
4653 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
4673 TTGCGATTTT-ATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4691 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4705 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4724 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4743 TTGCGAT
1 TTGCGAT
4750 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
14 6 0.09
16 9 0.13
17 4 0.06
18 10 0.14
19 30 0.43
20 10 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4739 original size:52 final size:52
Alignment explanation
Indices: 4634--4749 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
4624 CGAAATTAAA
4634 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTATT
4686 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTT-ATT
4738 TCGCATTGCGAT
1 TCGCATTGCGAT
4750 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 14 0.22
52 49 0.78
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTATT
Found at i:4757 original size:19 final size:18
Alignment explanation
Indices: 4634--4749 Score: 113
Period size: 19 Copynumber: 6.7 Consensus size: 18
4624 CGAAATTAAA
*
4634 TCGCATTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
4650 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
4667 TCCGCATTGCGATTTTATT
1 T-CGCATTGCGATTTCATT
*
4686 TCGCATTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
4702 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
4719 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
4738 TCGCATTGCGAT
1 TCGCATTGCGAT
4750 AGTCATTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
14 12 0.14
16 13 0.15
17 8 0.10
18 13 0.15
19 32 0.38
20 6 0.07
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:4757 original size:38 final size:37
Alignment explanation
Indices: 4634--4749 Score: 124
Period size: 33 Copynumber: 3.3 Consensus size: 37
4624 CGAAATTAAA
*
4634 TCGCATTGCGA-TTC-TCTCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTCATTTCGCATTGCGATTTTCATT
* *
4667 TCCGCATTGCGATTTTATTTCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTCATTTCGCATTGCGATTTTCATT
4702 TCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATTTCGCATTGCGATTTTCATT
4738 TCGCATTGCGAT
1 TCGCATTGCGAT
4750 AGTCATTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
32 6 0.09
33 18 0.27
34 12 0.18
35 7 0.10
36 11 0.16
37 1 0.01
38 12 0.18
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (37 bp):
TCGCATTGCGATTTCATTTCGCATTGCGATTTTCATT
Found at i:4874 original size:14 final size:14
Alignment explanation
Indices: 4855--4891 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4845 CATCAATTAC
4855 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4869 ACAAATCATCTTTT
1 ACAAATCAACTTTT
4883 ACAAATCAA
1 ACAAATCAA
4892 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:6844 original size:19 final size:19
Alignment explanation
Indices: 6804--6910 Score: 99
Period size: 19 Copynumber: 6.1 Consensus size: 19
6794 TAGTTTACTT
* *
6804 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
6824 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
6843 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
6857 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
6876 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
6890 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
6909 TC
1 TC
6911 TCAATGCGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 21
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.22
16 11 0.15
17 11 0.15
19 23 0.32
20 12 0.16
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:6860 original size:14 final size:14
Alignment explanation
Indices: 6841--6897 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6831 GCGAAATGAA
*
6841 AATCGCAACGACAG
1 AATCGCAACGAAAG
6855 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
6872 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
6888 AATCGCAACG
1 AATCGCAACG
6898 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:6868 original size:33 final size:33
Alignment explanation
Indices: 6822--6910 Score: 160
Period size: 33 Copynumber: 2.7 Consensus size: 33
6812 CGAAACTTAA
*
6822 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
6855 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
6888 AATCGCAACGCGAAATGAAAATC
1 AATCGCAACGCGAAATGAAAATC
6911 TCAATGCGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:6937 original size:19 final size:18
Alignment explanation
Indices: 6915--7057 Score: 103
Period size: 19 Copynumber: 8.3 Consensus size: 18
6905 AAAATCTCAA
6915 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
6934 TGCGAGTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
6948 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
6967 TGCGATTCT-TTT---GT
1 TGCGATTTTGTTTCGCGT
*
6981 TGCGATTCT-TTT---GT
1 TGCGATTTTGTTTCGCGT
*
6995 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
7014 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
7033 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
7053 TGCGA
1 TGCGA
7058 AAGTAAACTA
Statistics
Matches: 105, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
14 35 0.33
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 47 0.45
20 13 0.12
ACGTcount: A:0.08, C:0.15, G:0.28, T:0.48
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:6957 original size:33 final size:32
Alignment explanation
Indices: 6915--7040 Score: 130
Period size: 33 Copynumber: 3.8 Consensus size: 32
6905 AAAATCTCAA
6915 TGCGATTTTGGTTTCGCGTTGCGAGTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGA-TTTGTCGT
* *
6948 TGCGATTTTGGTTTCGCGTTGCGATTCTTTTGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TGTCGT
* * ** *
6981 TGCGATTCTTTTGTTGCGATTTTC-ATTTCG-CGT
1 TGCGA-T-TTTGGTTTCGCGTTGCGATTT-GTCGT
7014 TGCGATTTTGGTTTCGCGTTGCGATTT
1 TGCGATTTTGGTTTCGCGTTGCGATTT
7041 TAAGTTTCGT
Statistics
Matches: 74, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
31 11 0.15
32 7 0.09
33 41 0.55
34 4 0.05
35 11 0.15
ACGTcount: A:0.07, C:0.16, G:0.28, T:0.49
Consensus pattern (32 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTGTCGT
Found at i:6984 original size:14 final size:14
Alignment explanation
Indices: 6965--7001 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
6955 TTGGTTTCGC
6965 GTTGCGATTCTTTT
1 GTTGCGATTCTTTT
6979 GTTGCGATTCTTTT
1 GTTGCGATTCTTTT
6993 GTTGCGATT
1 GTTGCGATT
7002 TTCATTTCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.54
Consensus pattern (14 bp):
GTTGCGATTCTTTT
Found at i:7238 original size:93 final size:93
Alignment explanation
Indices: 7102--7384 Score: 532
Period size: 93 Copynumber: 3.1 Consensus size: 93
7092 ATGGATTGCA
7102 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
7166 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
7194 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
7259 TAGCAGAATTGGTAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
7287 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
7352 TAGTAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
7380 TTACT
1 TTACT
7385 AAGCAATCTA
Statistics
Matches: 186, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 4 0.02
93 182 0.98
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:9104 original size:20 final size:20
Alignment explanation
Indices: 9073--9169 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
9063 TTTTGGTTGA
9073 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*** *
9093 AATGACTGTCGCAACGAGATA
1 AATGAAAATCGCAACGAGA-G
9114 AATGAAAATCGCAAC--GAG
1 AATGAAAATCGCAACGAGAG
*
9132 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
9147 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
9167 AAT
1 AAT
9170 CGCAACGCGA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.07
17 2 0.03
19 14 0.23
20 19 0.32
21 12 0.20
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:9139 original size:14 final size:14
Alignment explanation
Indices: 9120--9176 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
9110 GATAAATGAA
9120 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
9134 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
9153 AATCGCAACGAGAG
1 AATCGCAACGAGAG
9167 AATCGCAACG
1 AATCGCAACG
9177 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:9153 original size:33 final size:33
Alignment explanation
Indices: 9071--9193 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
9061 TCTTTTGGTT
*
9071 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAACGC
9110 GATAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 G--AAATGAAAATCGCAACGAGAGAATCGCAACGC
9145 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
9178 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
9194 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 9 0.11
38 1 0.01
39 1 0.01
40 1 0.01
41 21 0.26
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:9229 original size:14 final size:14
Alignment explanation
Indices: 9210--9266 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
9200 TTTGGTTTCG
9210 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
9224 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
9243 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
9257 CGTTGCGATT
1 CGTTGCGATT
9267 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:9242 original size:33 final size:33
Alignment explanation
Indices: 9194--9274 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
9184 AAAATCGCAA
**
9194 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
9227 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
9260 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
9275 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:9277 original size:21 final size:21
Alignment explanation
Indices: 9251--9326 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
9241 CGCGTTGCGA
9251 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
9272 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
9292 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
9313 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
9327 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:9307 original size:41 final size:41
Alignment explanation
Indices: 9250--9327 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
9240 TCGCGTTGCG
*
9250 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
9291 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
9328 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:9448 original size:33 final size:33
Alignment explanation
Indices: 9406--9476 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
9396 AATACTAACT
9406 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
9439 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
9472 TGAAA
1 TGAAA
9477 TCTAAGTGAA
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:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:9876 original size:20 final size:20
Alignment explanation
Indices: 9851--10043 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
9841 CTTTAAATAT
9851 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9871 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
9893 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9912 CGCGTTGTGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
9932 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
9952 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
9972 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9992 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
10012 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
10032 CGCGTTGCGATT
1 CGCGTTGCGATT
10044 CTGGAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 129 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:11106 original size:21 final size:21
Alignment explanation
Indices: 11065--11104 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
11055 GTTTAAATAA
*
11065 ATATTATAAAAATCTCTAAAT
1 ATATTATAAAAATCCCTAAAT
11086 ATATT-TAAAAATCCCTAAA
1 ATATTATAAAAATCCCTAAA
11105 ATTCCTCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATTATAAAAATCCCTAAAT
Found at i:16323 original size:58 final size:58
Alignment explanation
Indices: 16252--16417 Score: 148
Period size: 57 Copynumber: 2.9 Consensus size: 58
16242 GTATGTATAA
* *
16252 TTTGGGG-TGAAATTGGAATGTTTAAAAAGTTTAGAGATCAATTTAGAATGA-A-AATTG
1 TTTGGGGATGAAATTGAAAT-TTT-AAAAGTTTAGAGATCAATTTAGAATGATAGAATAG
* * * *
16309 TTTGGGGATGAAATTAAAATTTTCAAAAGGTT-GAGGATTAATTTA-ATATGATAGTCATAG
1 TTTGGGGATGAAATTGAAATTTT-AAAAGTTTAGA-GATCAATTTAGA-ATGATAG-AATAG
* *
16369 TTT-AGGATGAAATTGAAACATTTAAAAGTTTAGAGATCAA-TTAGAATGA
1 TTTGGGGATGAAATTGAAA-TTTTAAAAGTTTAGAGATCAATTTAGAATGA
16418 GAATCATATT
Statistics
Matches: 88, Mismatches: 12, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
56 3 0.03
57 30 0.34
58 18 0.20
59 26 0.30
60 11 0.12
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (58 bp):
TTTGGGGATGAAATTGAAATTTTAAAAGTTTAGAGATCAATTTAGAATGATAGAATAG
Found at i:22220 original size:24 final size:24
Alignment explanation
Indices: 22184--22261 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 24
22174 CAAAGTCTAA
*
22184 ACACCAAAGTAACAATCCACAAAC
1 ACACCAAACTAACAATCCACAAAC
*
22208 ACACCAAACTAAC-AT--AC-TAC
1 ACACCAAACTAACAATCCACAAAC
* * *
22228 A-ACCAAAGTAACAAACCACAAAT
1 ACACCAAACTAACAATCCACAAAC
*
22251 ACAACAAACTA
1 ACACCAAACTA
22262 TCATATTACA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 10 0.24
20 4 0.10
21 2 0.05
22 2 0.05
23 4 0.10
24 19 0.46
ACGTcount: A:0.56, C:0.31, G:0.03, T:0.10
Consensus pattern (24 bp):
ACACCAAACTAACAATCCACAAAC
Found at i:22247 original size:43 final size:43
Alignment explanation
Indices: 22186--22273 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
22176 AAGTCTAAAC
* *
22186 ACCAAAGTAACAATCCACAAACACACCAAACTAACATACTACA
1 ACCAAAGTAACAAACCACAAACACAACAAACTAACATACTACA
* * *
22229 ACCAAAGTAACAAACCACAAATACAACAAACTATCATATTACA
1 ACCAAAGTAACAAACCACAAACACAACAAACTAACATACTACA
22272 AC
1 AC
22274 AATTCTTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.55, C:0.30, G:0.02, T:0.14
Consensus pattern (43 bp):
ACCAAAGTAACAAACCACAAACACAACAAACTAACATACTACA
Found at i:22248 original size:19 final size:19
Alignment explanation
Indices: 22202--22248 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
22192 GTAACAATCC
22202 ACAAA-CAC-ACCAAACTA
1 ACAAACCACAACCAAACTA
* * *
22219 ACATACTACAACCAAAGTA
1 ACAAACCACAACCAAACTA
22238 ACAAACCACAA
1 ACAAACCACAA
22249 ATACAACAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 4 0.17
18 2 0.09
19 17 0.74
ACGTcount: A:0.57, C:0.32, G:0.02, T:0.09
Consensus pattern (19 bp):
ACAAACCACAACCAAACTA
Found at i:24885 original size:21 final size:21
Alignment explanation
Indices: 24861--24921 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
24851 AACTTTGAAA
24861 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
24882 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
24896 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
24917 AAATG
1 AAATG
24922 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:24899 original size:35 final size:36
Alignment explanation
Indices: 24826--24972 Score: 187
Period size: 35 Copynumber: 4.2 Consensus size: 36
24816 TGAAAGTATT
***
24826 AAAATGGTTTTC-AAGTTTGGT-AAT-CAACTTTGAA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-A
24860 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
24895 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
* * *
24931 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
24967 AAAATG
1 AAAATG
24973 ATAATGGGAT
Statistics
Matches: 102, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
34 12 0.12
35 45 0.44
36 17 0.17
37 28 0.27
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
Found at i:24972 original size:72 final size:69
Alignment explanation
Indices: 24826--24969 Score: 184
Period size: 72 Copynumber: 2.1 Consensus size: 69
24816 TGAAAGTATT
24826 AAAATGGTTTTCAAGTTTGGTAATCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 AAAATGGTTTTCAAGTTTGGTAATCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
*
24891 TTTG
66 GTTG
*** * *
24895 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-AAAAATAGTTTTTCAAAGTTTGGTAGATG
1 AAAATGGTTTTC-AAGTTTGGT-AAT-CAACTTTGAAAAAAT-GGTTTTCAAAGTTTGGTAAATG
24959 TTT-GTTG
62 TTTCGTTG
24966 AAAA
1 AAAA
24970 ATGATAATGG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
69 12 0.18
70 9 0.14
71 16 0.25
72 28 0.43
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (69 bp):
AAAATGGTTTTCAAGTTTGGTAATCAACTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
GTTG
Found at i:27064 original size:19 final size:20
Alignment explanation
Indices: 27013--27073 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
27003 CCGTTTTGAT
*
27013 CGGTTTCGATCGGT-TCGAAC
1 CGGTTTCGACCGGTCT-GAAC
27033 CGGTTTCGACCGGTCTGAAC
1 CGGTTTCGACCGGTCTGAAC
27053 CGGTTT-GACCGGTCTG-AC
1 CGGTTTCGACCGGTCTGAAC
27071 CGG
1 CGG
27074 ACCCGACTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 5 0.13
19 10 0.26
20 23 0.59
21 1 0.03
ACGTcount: A:0.13, C:0.28, G:0.33, T:0.26
Consensus pattern (20 bp):
CGGTTTCGACCGGTCTGAAC
Found at i:27065 original size:9 final size:9
Alignment explanation
Indices: 27002--27073 Score: 54
Period size: 10 Copynumber: 7.6 Consensus size: 9
26992 AGGGCTGAAA
*
27002 ACCGTTTTG
1 ACCGGTTTG
*
27011 ATCGGTTTCG
1 ACCGGTTT-G
* *
27021 ATCGGTTCG
1 ACCGGTTTG
27030 AACCGGTTTCG
1 -ACCGGTTT-G
*
27041 ACCGGTCTG
1 ACCGGTTTG
27050 AACCGGTTTG
1 -ACCGGTTTG
*
27060 ACCGGTCTG
1 ACCGGTTTG
27069 ACCGG
1 ACCGG
27074 ACCCGACTGA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
9 21 0.41
10 29 0.57
11 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:34417 original size:15 final size:14
Alignment explanation
Indices: 34399--34437 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
34389 TTTTTAAATA
34399 AAAATTTTAATTTTT
1 AAAATTTTAA-TTTT
*
34414 AAAATGATTAATTTT
1 AAAAT-TTTAATTTT
34429 AAAATTTTA
1 AAAATTTTA
34438 GCATTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 14 0.67
16 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
AAAATTTTAATTTT
Found at i:41422 original size:21 final size:21
Alignment explanation
Indices: 41396--41435 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41386 CAGAACCCCA
*
41396 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
41417 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
41436 TCAAAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:41470 original size:21 final size:21
Alignment explanation
Indices: 41417--41479 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
41407 ATTCCCCTGT
41417 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* * *
41440 AGGAGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
*
41461 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
41480 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 19 0.56
22 3 0.09
23 12 0.35
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:50826 original size:15 final size:15
Alignment explanation
Indices: 50803--50866 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 15
50793 TATCCGATTC
*
50803 GAATTAAATAAATTT
1 GAATAAAATAAATTT
*
50818 GAATAAAAT-TA-TT
1 GAATAAAATAAATTT
*
50831 --A-AAAATAAATAT
1 GAATAAAATAAATTT
*
50843 GAATTAAATAAATTT
1 GAATAAAATAAATTT
50858 GAATAAAAT
1 GAATAAAAT
50867 TATTAAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
10 5 0.14
11 2 0.05
12 1 0.03
13 2 0.05
14 2 0.05
15 25 0.68
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (15 bp):
GAATAAAATAAATTT
Found at i:50848 original size:40 final size:40
Alignment explanation
Indices: 50803--50882 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
50793 TATCCGATTC
50803 GAATTAAATAAATTTGAATAAAATTATTAAAAATAAATAT
1 GAATTAAATAAATTTGAATAAAATTATTAAAAATAAATAT
50843 GAATTAAATAAATTTGAATAAAATTATTAAAAATAAATAT
1 GAATTAAATAAATTTGAATAAAATTATTAAAAATAAATAT
50883 TTAAATATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (40 bp):
GAATTAAATAAATTTGAATAAAATTATTAAAAATAAATAT
Found at i:53049 original size:15 final size:15
Alignment explanation
Indices: 53026--53110 Score: 59
Period size: 15 Copynumber: 5.7 Consensus size: 15
53016 AAAGGCAATG
* *
53026 AAGATAAATAAACTA
1 AAGAAAAATAAAATA
53041 AAGAAAAATAAAATA
1 AAGAAAAATAAAATA
*
53056 AAG-GAAATAAAAATA
1 AAGAAAAAT-AAAATA
*
53071 AATG-AAAATAAGGA-A
1 AA-GAAAAATAA-AATA
* *
53086 AATAAGAATAAAATA
1 AAGAAAAATAAAATA
*
53101 AAGGAAAATA
1 AAGAAAAATA
53111 CTAATAATTG
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
14 5 0.09
15 43 0.80
16 6 0.11
ACGTcount: A:0.72, C:0.01, G:0.12, T:0.15
Consensus pattern (15 bp):
AAGAAAAATAAAATA
Found at i:53056 original size:20 final size:20
Alignment explanation
Indices: 53031--53110 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
53021 CAATGAAGAT
*
53031 AAATAAACTAAAGAAAAATA
1 AAATAAAATAAAGAAAAATA
** *
53051 AAATAAAGGAAATAAAAAT-
1 AAATAAAATAAAGAAAAATA
*
53070 AAATGAAAAT-AAGGAAAATA
1 AAAT-AAAATAAAGAAAAATA
*
53090 AGAATAAAATAAAGGAAAATA
1 A-AATAAAATAAAGAAAAATA
53111 CTAATAATTG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
19 11 0.22
20 25 0.51
21 13 0.27
ACGTcount: A:0.72, C:0.01, G:0.11, T:0.15
Consensus pattern (20 bp):
AAATAAAATAAAGAAAAATA
Found at i:53088 original size:25 final size:24
Alignment explanation
Indices: 53046--53102 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
53036 AACTAAAGAA
53046 AAATAAAATAAAGGAAATAAAAAT
1 AAATAAAATAAAGGAAATAAAAAT
*
53070 AAATGAAAAT-AAGGAAAATAAGAAT
1 AAAT-AAAATAAAGG-AAATAAAAAT
53095 AAAATAAA
1 -AAATAAA
53103 GGAAAATACT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 8 0.28
25 17 0.59
26 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (24 bp):
AAATAAAATAAAGGAAATAAAAAT
Found at i:53198 original size:22 final size:21
Alignment explanation
Indices: 53162--53212 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
53152 AAATACAAAT
* *
53162 GAAAATAAATATAAAAATAAAA
1 GAAAA-AAGTATAAAAAGAAAA
53184 GAATAAAAGTATAAAAAGAAAA
1 GAA-AAAAGTATAAAAAGAAAA
53206 GAAAAAA
1 GAAAAAA
53213 CAAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 20 0.77
23 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (21 bp):
GAAAAAAGTATAAAAAGAAAA
Found at i:53219 original size:22 final size:22
Alignment explanation
Indices: 53172--53242 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
53162 GAAAATAAAT
* **
53172 ATAAAAATAAAAGAATAAAAGT
1 ATAAAAAGAAAAGAATAAAAAA
53194 ATAAAAAGAAAAGAA-AAAACAA
1 ATAAAAAGAAAAGAATAAAA-AA
53216 ATAAAATA-AGAAA-AATAAAAAA
1 ATAAAA-AGA-AAAGAATAAAAAA
*
53238 GTAAA
1 ATAAA
53243 TATATGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 4 0.10
22 29 0.71
23 8 0.20
ACGTcount: A:0.77, C:0.01, G:0.08, T:0.13
Consensus pattern (22 bp):
ATAAAAAGAAAAGAATAAAAAA
Found at i:53237 original size:8 final size:8
Alignment explanation
Indices: 53158--53242 Score: 53
Period size: 8 Copynumber: 9.9 Consensus size: 8
53148 AGGAAAATAC
53158 AAATGAAAA
1 AAAT-AAAA
*
53167 TAAATATAA
1 -AAATAAAA
53176 AAATAAAA
1 AAATAAAA
*
53184 GAATAAAA
1 AAATAAAA
**
53192 GTATAAAA
1 AAATAAAA
*
53200 AGAAAAGAAA
1 A-AATA-AAA
*
53210 AAACAAATA
1 AAATAAA-A
53219 AAATAAGAA
1 AAATAA-AA
53228 AAATAAAA
1 AAATAAAA
*
53236 AAGTAAA
1 AAATAAA
53243 TATATGAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
8 31 0.51
9 21 0.34
10 9 0.15
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.14
Consensus pattern (8 bp):
AAATAAAA
Found at i:54295 original size:89 final size:89
Alignment explanation
Indices: 54144--54322 Score: 349
Period size: 89 Copynumber: 2.0 Consensus size: 89
54134 TATTACTACC
*
54144 CATCAGACTGGAGGGTAAGTTGTTGCACTGCAACGTGATGTTAGTTTACTTATAAAATTTTAGAG
1 CATCAGACTGGAGGGTAAGTTGTTGCACTGCAACGTGATGTTAATTTACTTATAAAATTTTAGAG
54209 TATAAATTTATAAAACTTTAAGAG
66 TATAAATTTATAAAACTTTAAGAG
54233 CATCAGACTGGAGGGTAAGTTGTTGCACTGCAACGTGATGTTAATTTACTTATAAAATTTTAGAG
1 CATCAGACTGGAGGGTAAGTTGTTGCACTGCAACGTGATGTTAATTTACTTATAAAATTTTAGAG
54298 TATAAATTTATAAAACTTTAAGAG
66 TATAAATTTATAAAACTTTAAGAG
54322 C
1 C
54323 GAAAACAAAG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (89 bp):
CATCAGACTGGAGGGTAAGTTGTTGCACTGCAACGTGATGTTAATTTACTTATAAAATTTTAGAG
TATAAATTTATAAAACTTTAAGAG
Found at i:61624 original size:22 final size:22
Alignment explanation
Indices: 61593--61635 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
61583 CTTATTTATT
61593 TATATATTAAATATCTTTTTTA
1 TATATATTAAATATCTTTTTTA
* * *
61615 TATATCTTAATTATGTTTTTT
1 TATATATTAAATATCTTTTTT
61636 CTACTCTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (22 bp):
TATATATTAAATATCTTTTTTA
Found at i:81810 original size:20 final size:21
Alignment explanation
Indices: 81776--81816 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
81766 TGCAGAGTTT
81776 TCATCCCCAAACGGCTAGAAA
1 TCATCCCCAAACGGCTAGAAA
81797 TCATCCCC-AACGGCTAGAAA
1 TCATCCCCAAACGGCTAGAAA
81817 CGACCACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.37, C:0.34, G:0.15, T:0.15
Consensus pattern (21 bp):
TCATCCCCAAACGGCTAGAAA
Found at i:89069 original size:38 final size:38
Alignment explanation
Indices: 89015--89088 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
89005 TGGAATGGAC
* *
89015 GACATGTTCTCTTTTGCGGTATGTAAATTTATATGCTT
1 GACATGTTCTCCTTTGCAGTATGTAAATTTATATGCTT
89053 GACATGTTCTCCTTTGCAGTATGTAAATTTATATGC
1 GACATGTTCTCCTTTGCAGTATGTAAATTTATATGC
89089 ATGGTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.45
Consensus pattern (38 bp):
GACATGTTCTCCTTTGCAGTATGTAAATTTATATGCTT
Done.