Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009054.1 Hibiscus syriacus cultivar Beakdansim tig00112469_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: 53279
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1106 original size:20 final size:20
Alignment explanation
Indices: 1081--1118 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1071 TAGGTTTGAG
* *
1081 TATCGATATTTGATGAACAA
1 TATCGATACTAGATGAACAA
1101 TATCGATACTAGATGAAC
1 TATCGATACTAGATGAAC
1119 TAGGAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
TATCGATACTAGATGAACAA
Found at i:1942 original size:19 final size:18
Alignment explanation
Indices: 1902--1937 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1892 TAAAATTATC
*
1902 ACATGATATTTATATAAA
1 ACATGATATTAATATAAA
1920 ACAT-ATATTAATATAAA
1 ACATGATATTAATATAAA
1937 A
1 A
1938 TACATCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (18 bp):
ACATGATATTAATATAAA
Found at i:3727 original size:20 final size:20
Alignment explanation
Indices: 3702--3742 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3692 GGTCGTGCGT
3702 CGCCGCCTGAAAATGGTGGC
1 CGCCGCCTGAAAATGGTGGC
3722 CGCCGCCTGAAAATGGTGGC
1 CGCCGCCTGAAAATGGTGGC
3742 C
1 C
3743 ACCACCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.32, G:0.34, T:0.15
Consensus pattern (20 bp):
CGCCGCCTGAAAATGGTGGC
Found at i:5042 original size:106 final size:106
Alignment explanation
Indices: 4856--5608 Score: 1058
Period size: 106 Copynumber: 7.0 Consensus size: 106
4846 TGTACTGTTC
* * * *
4856 TGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTTTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
*
4921 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
4962 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATACTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
* *
5027 ACCAGCCGTCCCTTCGTTGTGAATTTTAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
5068 CGAGTCCAATATCATTCGCTGTGAAATTGAAATTGGCTTTGAAACTGGGAAATTGTTTGTTGAGA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
5133 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
5174 TGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
*
5239 ACCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * *
5280 TGAGTCCAATATCCTTTACTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGAC
* * * *
5345 GACCAGTCGTTCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
5387 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGAC
* * *
5452 GACCAGCCGTCCCTTCATTGTGAAGTTAAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * ** * *
5494 TAAGTCCAATATCCTTTGCTGTGAAGATGAAATTGGCTCTGAATGAAACT-TAAAAGTGGTTTAT
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAA-TTGTTTGT
* *
5558 TGACAACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
61 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
5604 CGAGT
1 TGAGT
5609 GGTGCGATAT
Statistics
Matches: 589, Mismatches: 52, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
106 346 0.59
107 184 0.31
110 52 0.09
111 7 0.01
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:5925 original size:14 final size:14
Alignment explanation
Indices: 5906--5932 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5896 CTAAAATCTT
5906 TCTGGAATCTTGAC
1 TCTGGAATCTTGAC
5920 TCTGGAATCTTGA
1 TCTGGAATCTTGA
5933 AGTTTCGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (14 bp):
TCTGGAATCTTGAC
Found at i:6613 original size:58 final size:58
Alignment explanation
Indices: 6550--6662 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
6540 CTTTTGTTCT
* * *
6550 TTTTTCTCTTTTTC-ATTTTTTCAATTTAGGGTGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTC-CTTTTTCTATTTTTTCAACTTAGGATGCCCTTTCAGGTTTTCACCCTAAACG
* * *
6608 TTTTTCCTTTTTCTTTTTTTTCGACTTAGGATGCCCTTTCAGGTTTTCATCCTAA
1 TTTTTCCTTTTTCTATTTTTTCAACTTAGGATGCCCTTTCAGGTTTTCACCCTAA
6663 GCGAAGTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 7 0.15
58 41 0.85
ACGTcount: A:0.13, C:0.22, G:0.12, T:0.52
Consensus pattern (58 bp):
TTTTTCCTTTTTCTATTTTTTCAACTTAGGATGCCCTTTCAGGTTTTCACCCTAAACG
Found at i:12825 original size:18 final size:18
Alignment explanation
Indices: 12790--12833 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
12780 AAGGTTAGTA
*
12790 AAATAAAAATAAATAAAT
1 AAATAAAAATAAAGAAAT
* *
12808 AAATAAAAATGACGAAAT
1 AAATAAAAATAAAGAAAT
12826 AAA-AAAAA
1 AAATAAAAA
12834 ACAAAAAGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (18 bp):
AAATAAAAATAAAGAAAT
Found at i:24031 original size:20 final size:21
Alignment explanation
Indices: 24006--24098 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
23996 TTTTCCCAAT
*
24006 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
24026 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
24047 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
24067 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
24088 TCGCAATGCGA
1 TCGCAATGCGA
24099 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:24051 original size:41 final size:41
Alignment explanation
Indices: 24006--24098 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
23996 TTTTCCCAAT
24006 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
24047 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
24088 TCGCAATGCGA
1 TCGCAATGCGA
24099 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:24111 original size:41 final size:41
Alignment explanation
Indices: 24025--24159 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
24015 GAATAAGTAA
* *
24025 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
24066 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
24107 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
24148 TTCGCAACGCGA
1 ATCGCAACGCGA
24160 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:24112 original size:20 final size:20
Alignment explanation
Indices: 24087--24181 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
24077 AATTGGGAAA
*
24087 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
24107 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
24128 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
24148 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
24168 TTCGCAACGAGATA
1 ATCGCAACGCGATA
24182 ATGCATAATC
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:24397 original size:22 final size:22
Alignment explanation
Indices: 24369--24411 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
24359 CACTCTCTCA
24369 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
24391 CCCATCTCCGGCGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
24412 ATATCTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.44, G:0.16, T:0.19
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:24701 original size:20 final size:20
Alignment explanation
Indices: 24676--24713 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24666 CGATTCTCTC
24676 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
24696 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
24714 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:26059 original size:18 final size:18
Alignment explanation
Indices: 26033--26077 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
26023 TCCACTTCGG
*
26033 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
26051 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
26069 GAGCCATCA
1 GAGCCATCA
26078 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:26613 original size:19 final size:20
Alignment explanation
Indices: 26559--26625 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
26549 TAGTTTACTT
* *
26559 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
26579 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
26599 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
26618 TCGCAACG
1 TCGCAACG
26626 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:26633 original size:14 final size:14
Alignment explanation
Indices: 26614--26671 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
26604 ATGCGAAATG
*
26614 AAAATCGCAACGAC
1 AAAATCGCAACGAA
26628 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
26644 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
26660 AAAATCGCAACG
1 AAAATCGCAACG
26672 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:26656 original size:32 final size:33
Alignment explanation
Indices: 26598--26688 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
26588 GGAAATGGCT
*
26598 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
26631 ATCGCAATGCGAAATG-AAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
26663 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
26689 TGCGATTTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:26724 original size:14 final size:14
Alignment explanation
Indices: 26705--26762 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
26695 TTCTGTTTCG
26705 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
26719 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
26735 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
26751 CGTTGCGATTTT
1 CGTTGCGATTTT
26763 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:26769 original size:33 final size:32
Alignment explanation
Indices: 26689--26778 Score: 144
Period size: 33 Copynumber: 2.8 Consensus size: 32
26679 AAAATCGCAA
* *
26689 TGCGATTTCTGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTC-ATTTCGCATTGCGATTTTGTCGT
26722 TGCGATTTCATTTCGCATTGCGATTTTGTCGT
1 TGCGATTTCATTTCGCATTGCGATTTTGTCGT
26754 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGA-TTTCATTTCGCATTGCGAT
26779 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 26 0.48
33 28 0.52
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (32 bp):
TGCGATTTCATTTCGCATTGCGATTTTGTCGT
Found at i:28827 original size:14 final size:14
Alignment explanation
Indices: 28808--28863 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
28798 CGAAATGGCT
28808 ATCGCAATGAGAAA
1 ATCGCAATGAGAAA
28822 ATCGCAATGCGAAATGAAA
1 ATCGCAAT--G--A-GAAA
*
28841 ATCGCAACGAGAAA
1 ATCGCAATGAGAAA
28855 ATCGCAATG
1 ATCGCAATG
28864 CGATTTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (14 bp):
ATCGCAATGAGAAA
Found at i:28840 original size:19 final size:17
Alignment explanation
Indices: 28817--28866 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
28807 TATCGCAATG
28817 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
28835 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
28850 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
28867 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:28879 original size:33 final size:33
Alignment explanation
Indices: 28789--28866 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
28779 AAAACAGACT
* *** *
28789 ATCGCAACGCGAAATGGCTATCGCAATGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
28822 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
28855 ATCGCAATGCGA
1 ATCGCAATGCGA
28867 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:28910 original size:20 final size:20
Alignment explanation
Indices: 28885--28922 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28875 TCGCATTGCG
*
28885 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
28905 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
28923 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:29989 original size:24 final size:24
Alignment explanation
Indices: 29962--30015 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
29952 GTATTCGAAA
*
29962 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
29986 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
30010 TTTGAT
1 TTTGAT
30016 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:30207 original size:12 final size:12
Alignment explanation
Indices: 30190--30214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30180 ATATAATCCT
30190 GAAGAAGAAAAA
1 GAAGAAGAAAAA
30202 GAAGAAGAAAAA
1 GAAGAAGAAAAA
30214 G
1 G
30215 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:32556 original size:19 final size:19
Alignment explanation
Indices: 32501--32630 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
32491 GGAAATTACT
32501 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
32519 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
32533 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
32552 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
32566 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
32585 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
32599 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
32618 ATCGCAACGCGAA
1 ATCGCAATGCGAA
32631 TTTAATTTCG
Statistics
Matches: 83, Mismatches: 13, Indels: 31
0.65 0.10 0.24
Matches are distributed among these distances:
13 1 0.01
14 26 0.31
15 2 0.02
16 8 0.10
17 4 0.05
18 10 0.12
19 32 0.39
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:32559 original size:33 final size:33
Alignment explanation
Indices: 32501--32626 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
32491 GGAAATTACT
32501 ATCGCAATGCGAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
32533 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
32565 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
32599 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
32627 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
32 17 0.20
33 66 0.79
34 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:32601 original size:66 final size:65
Alignment explanation
Indices: 32502--32633 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 65
32492 GAAATTACTA
*
32502 TCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
32567 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
32632 T
65 T
32633 T
1 T
32634 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 15 0.23
66 49 0.77
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (65 bp):
TCGCAATGCGAAATGAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:32668 original size:19 final size:19
Alignment explanation
Indices: 32626--32669 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
32616 AAATCGCAAC
*
32626 GCGAATTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
*
32645 GCGATTTTATTTTCGCGTT
1 GCGATTTTAATTTCGCGTT
32664 GCGATT
1 GCGATT
32670 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:32700 original size:19 final size:19
Alignment explanation
Indices: 32635--32701 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
32625 CGCGAATTTA
32635 ATTTCGCGTTGCGATTTT-
1 ATTTCGCGTTGCGATTTTC
32653 ATTTTCGCGTTGCGA--TTC
1 A-TTTCGCGTTGCGATTTTC
*
32671 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
32687 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
32702 AGTACTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:32827 original size:14 final size:14
Alignment explanation
Indices: 32808--32844 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
32798 CATCAATTAA
32808 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
32822 ACAAATCACCTTTT
1 ACAAATCAACTTTT
32836 ACAAATCAA
1 ACAAATCAA
32845 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:34262 original size:21 final size:21
Alignment explanation
Indices: 34196--34262 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
34186 GTGAATCGGG
*
34196 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
34216 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
34238 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
34259 CTCT
1 CTCT
34263 CGAGGAATAA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:34281 original size:42 final size:42
Alignment explanation
Indices: 34235--34318 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
34225 CGATGACAGT
* * *
34235 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATAATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATAATAGG
* * * *
34277 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATAATAGG
34319 CGAGTCGGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATAATAGG
Found at i:36391 original size:33 final size:33
Alignment explanation
Indices: 36334--36432 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
36324 ACGAGATAAT
*
36334 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
36368 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
36401 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
36433 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:36426 original size:19 final size:19
Alignment explanation
Indices: 36309--36474 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
36299 TCTTTTGGTT
*
36309 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
36328 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
36348 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
36366 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
36382 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
36400 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
36415 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
36435 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
36454 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
36473 GA
1 GA
36475 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.36
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:36492 original size:19 final size:19
Alignment explanation
Indices: 36470--36536 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
36460 AAAATCGCAA
*
36470 TGCGATTTTGGTTTCGAGT
1 TGCGATTTTGATTTCGAGT
* *
36489 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGAGT
* *
36508 TGCGATAGTT-ATTTCCGCGT
1 TGCGAT-TTTGATTT-CGAGT
36528 TGCGATTTT
1 TGCGATTTT
36537 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGATTTCGAGT
Found at i:36528 original size:20 final size:19
Alignment explanation
Indices: 36481--36533 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
36471 GCGATTTTGG
* **
36481 TTTCGAGTTGCGATTTTTA
1 TTTCGCGTTGCGATAGTTA
36500 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
36519 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
36534 TTTCATTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:37120 original size:21 final size:19
Alignment explanation
Indices: 37096--37224 Score: 80
Period size: 20 Copynumber: 6.3 Consensus size: 19
37086 AAGTATCTCG
37096 TTGCGATTTTTTATTATCGCA
1 TTGCGATTTTTTA-T-TCGCA
** *
37117 TTGCGA-TAGTAAGTATCGCA
1 TTGCGATTTTTTA-T-TCGCA
** *
37137 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTT--TTATTCGCA
37158 TTGCGATTTATTTATTCGCA
1 TTGCGATTT-TTTATTCGCA
* *
37178 TTGCGATTTTTCCAATTCGCG
1 TTGCGATTTTT--TATTCGCA
*
37199 TTGCGATTTACTTATTCGCA
1 TTGCGATTT-TTTATTCGCA
37219 TTGCGA
1 TTGCGA
37225 ATTGGGAAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
19 2 0.02
20 43 0.51
21 35 0.41
22 3 0.04
23 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTTTATTCGCA
Found at i:37143 original size:20 final size:20
Alignment explanation
Indices: 37050--37143 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
37040 CGCTATGTAA
* *
37050 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
37070 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
37090 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
37111 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
37131 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
37144 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:37162 original size:41 final size:40
Alignment explanation
Indices: 37071--37205 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 40
37061 AAAGTCAGTA
* * * ** *
37071 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
37111 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
* **
37153 TCGCGTTGCGAT-TTATTTATTCGCATTGCGATTTTTCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGA-TTTTCCAAT
37194 TCGCGTTGCGAT
1 TCGCGTTGCGAT
37206 TTACTTATTC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 70 0.88
42 6 0.08
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (40 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:37176 original size:20 final size:20
Alignment explanation
Indices: 37151--37224 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
37141 GATTTTCCCA
*
37151 ATTCGCGTTGCGATTTATTT
1 ATTCGCATTGCGATTTATTT
*
37171 ATTCGCATTGCGATTT-TTCCA
1 ATTCGCATTGCGATTTATT--T
* *
37192 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTATTT
37212 ATTCGCATTGCGA
1 ATTCGCATTGCGA
37225 ATTGGGAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.04
20 27 0.60
21 15 0.33
22 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (20 bp):
ATTCGCATTGCGATTTATTT
Found at i:37206 original size:41 final size:41
Alignment explanation
Indices: 37132--37224 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
37122 ATAGTAAGTA
*
37132 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTATTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
37173 TCGCATTGCGATTTTTCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
37214 TCGCATTGCGA
1 TCGCATTGCGA
37225 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:38437 original size:2 final size:2
Alignment explanation
Indices: 38432--38481 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
38422 CATATATTTT
* * *
38432 TA TA TA TA CA TA TA TA TT TA TA TA TA TA TA TA TA TC TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38473 TA T- TA TA TA
1 TA TA TA TA TA
38482 GTCTACAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38438 original size:10 final size:10
Alignment explanation
Indices: 38423--38481 Score: 54
Period size: 10 Copynumber: 6.3 Consensus size: 10
38413 AATTTCGTCC
*
38423 ATATATTTTT
1 ATATATTTAT
**
38433 ATATATACAT
1 ATATATTTAT
38443 ATATATTTAT
1 ATATATTTAT
38453 ATATA--TAT
1 ATATATTTAT
*
38461 ATATATCTAT
1 ATATATTTAT
38471 -TATA-TTAT
1 ATATATTTAT
38479 ATA
1 ATA
38482 GTCTACAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
8 11 0.28
9 6 0.15
10 23 0.57
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (10 bp):
ATATATTTAT
Found at i:38445 original size:18 final size:18
Alignment explanation
Indices: 38422--38466 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
38412 TAATTTCGTC
*
38422 CATATATTTTTATATATA
1 CATATATATTTATATATA
38440 CATATATATTTATATATA
1 CATATATATTTATATATA
*
38458 TATATATAT
1 CATATATAT
38467 CTATTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
CATATATATTTATATATA
Found at i:38592 original size:64 final size:63
Alignment explanation
Indices: 38512--38639 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 63
38502 ATACGTATAT
38512 AATATATGATTTTTAAAAT-ACCTTTGAAAACTATATAATATATAG-TTTTTAAAACATTTTTAG
1 AATATATGATTTTTAAAATCA-CTTTG-AAACT-TAT-ATATATAGTTTTTTAAAACATTTTT-G
38575 AAA
61 AAA
* **
38578 AATATAT-A-TTTTAAAATCATTTTGAAACTTATATATATAGTTTTTTTTAACATTTTTGAAA
1 AATATATGATTTTTAAAATCACTTTGAAACTTATATATATAGTTTTTTAAAACATTTTTGAAA
38639 A
1 A
38640 CTTATATGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
61 13 0.23
62 17 0.30
63 5 0.09
64 13 0.23
65 2 0.04
66 7 0.12
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (63 bp):
AATATATGATTTTTAAAATCACTTTGAAACTTATATATATAGTTTTTTAAAACATTTTTGAAA
Found at i:38678 original size:14 final size:15
Alignment explanation
Indices: 38657--38696 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
38647 GTAATATATA
38657 AATTTTTAAAA-AAT
1 AATTTTTAAAATAAT
* *
38671 ATTTTTTAAAATTAT
1 AATTTTTAAAATAAT
38686 AATTTTTAAAA
1 AATTTTTAAAA
38697 CATTTTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTTTAAAATAAT
Found at i:38722 original size:26 final size:27
Alignment explanation
Indices: 38661--38722 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
38651 TATATAAATT
* *
38661 TTTAAAAAATATTTTTTAAAATTATAA
1 TTTAAAAAACATTTTTGAAAATTATAA
** *
38688 TTTTTAAAACATTTTTGAAAA-TATAG
1 TTTAAAAAACATTTTTGAAAATTATAA
38714 TTTAAAAAA
1 TTTAAAAAA
38723 AGGCATTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (27 bp):
TTTAAAAAACATTTTTGAAAATTATAA
Found at i:39723 original size:30 final size:30
Alignment explanation
Indices: 39689--39761 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
39679 CCCGAAGGAC
*
39689 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAA
39719 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAA
* *
39749 CTGTCCATAGGTC
1 CTATCCAGAGGTC
39762 CCGAATAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGATAA
Found at i:39863 original size:63 final size:62
Alignment explanation
Indices: 39748--39871 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
39738 ATCCTCGATA
* * *
39748 ACTGTCCATAGGTCCCGAATAACCTAGGTAAATTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAATAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
39810 ACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAATA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
39872 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 24 0.44
63 30 0.55
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAATAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:39867 original size:32 final size:31
Alignment explanation
Indices: 39747--39874 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
39737 GATCCTCGAT
* * * * *
39747 AACTGTCCATAGGTCCCGAATAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
39778 AATTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
39809 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
39841 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
39872 AAC
1 AAC
39875 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
30 4 0.05
31 48 0.61
32 23 0.29
33 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:41255 original size:21 final size:21
Alignment explanation
Indices: 41225--41269 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
41215 ATTCTGTCGT
* *
41225 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
41246 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
41267 TTG
1 TTG
41270 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:46922 original size:15 final size:15
Alignment explanation
Indices: 46902--46946 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
46892 CTGAGAATAC
*
46902 AAAATAAAAGCGGAA
1 AAAATAATAGCGGAA
* *
46917 AAAATAATACCCGAA
1 AAAATAATAGCGGAA
*
46932 AAATTAATAGCGGAA
1 AAAATAATAGCGGAA
46947 TTCAGCCAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.13
Consensus pattern (15 bp):
AAAATAATAGCGGAA
Found at i:47241 original size:20 final size:21
Alignment explanation
Indices: 47216--47256 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
47206 AGCTAAACTT
47216 GACAA-TTGTGTTGAAATCCC
1 GACAATTTGTGTTGAAATCCC
47236 GACAATTTGTGTTGAAATCCC
1 GACAATTTGTGTTGAAATCCC
47257 ACCGAAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (21 bp):
GACAATTTGTGTTGAAATCCC
Found at i:49572 original size:24 final size:25
Alignment explanation
Indices: 49522--49575 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
49512 TTTTATATTG
49522 AAAATTTTAAGAGATATAAAATTAT
1 AAAATTTTAAGAGATATAAAATTAT
*
49547 AAAATTTTGAGAGA-A-ACAAATTAT
1 AAAATTTTAAGAGATATA-AAATTAT
49571 AAAAT
1 AAAAT
49576 AAAAAAATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 1 0.04
24 13 0.48
25 13 0.48
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.31
Consensus pattern (25 bp):
AAAATTTTAAGAGATATAAAATTAT
Found at i:49591 original size:14 final size:14
Alignment explanation
Indices: 49571--49616 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
49561 AACAAATTAT
49571 AAAATAAAAAAATA
1 AAAATAAAAAAATA
*
49585 CAAAT-AAAAAATAA
1 AAAATAAAAAAAT-A
49599 AAAATAAAAAAATA
1 AAAATAAAAAAATA
49613 AAAA
1 AAAA
49617 AATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.25
14 14 0.50
15 7 0.25
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:49619 original size:8 final size:7
Alignment explanation
Indices: 49571--49617 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
49561 AACAAATTAT
49571 AAAATAA
1 AAAATAA
49578 AAAA-ATA
1 AAAATA-A
*
49585 CAAATAA
1 AAAATAA
49592 AAAATAA
1 AAAATAA
49599 AAAATAAA
1 AAAAT-AA
49607 AAAATAA
1 AAAATAA
49614 AAAA
1 AAAA
49618 ATTTCAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 1 0.03
7 26 0.74
8 8 0.23
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:50973 original size:31 final size:30
Alignment explanation
Indices: 50938--50995 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
50928 ACTTAATAAA
* *
50938 TTTAATGATGATTTTATAACTTTTTAAACAT
1 TTTAATAATAATTTTATAA-TTTTTAAACAT
50969 TTTAATAATAATTTTATAATTTTTAAA
1 TTTAATAATAATTTTATAATTTTTAAA
50996 AGTTCAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTAATAATAATTTTATAATTTTTAAACAT
Done.