Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006311.1 Hibiscus syriacus cultivar Beakdansim tig00015076_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: 54555
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1724 original size:16 final size:16
Alignment explanation
Indices: 1700--1747 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1690 GAAAAGAGAA
1700 AAAGATAAAAAAAATGG
1 AAAG-TAAAAAAAATGG
*
1717 AAAGTAAAAGAAATGG
1 AAAGTAAAAAAAATGG
*
1733 AATG-AAAAAGAAATG
1 AAAGTAAAAA-AAATG
1748 AAAAAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 19 0.70
17 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (16 bp):
AAAGTAAAAAAAATGG
Found at i:3217 original size:128 final size:127
Alignment explanation
Indices: 3009--3299 Score: 359
Period size: 128 Copynumber: 2.3 Consensus size: 127
2999 TTTAATTTTA
* * * * * * *
3009 AGATTTGATCTTCCTGAAGAACAGTGAAGCAAA-CCAACTTGATTCAACCTTCCTTGAAGAGTAG
1 AGATTTGATCTTCTTGAAGAGCAGTGAAGCAAATCAAACTCGATTCAACATTCCCTGAAGAGAAG
* * * * * * * *
3073 CGAAGTGAATCGAAGTTTCCAGATGTAACCTTCCTGAAAAGTAGTGAAGTAGGTCAAGTTCTT
66 CGAAGTGAATCAAAGTTTCCAGATCTAACATTCCTGAAAAGCAGTAAAATAGATCAAGTTC-C
* *
3136 AGATTTGATCTTTTTGAAGAGCAGTAAAGCAAATCAAACTCGATTCAACATTCCCTGAAGAGAAG
1 AGATTTGATCTTCTTGAAGAGCAGTGAAGCAAATCAAACTCGATTCAACATTCCCTGAAGAGAAG
* * ***
3201 CGAAGTGAATCAAAGTTTCCAGATCTATCATTCCTGAAGAGCAGTAAAATAGATCCTTTTCC
66 CGAAGTGAATCAAAGTTTCCAGATCTAACATTCCTGAAAAGCAGTAAAATAGATCAAGTTCC
*
3263 AGATTTGATCTTCTTGAAGAGCAGTGAAGCAAGTCAA
1 AGATTTGATCTTCTTGAAGAGCAGTGAAGCAAATCAA
3300 CCCTGATTTA
Statistics
Matches: 138, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
127 63 0.46
128 75 0.54
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (127 bp):
AGATTTGATCTTCTTGAAGAGCAGTGAAGCAAATCAAACTCGATTCAACATTCCCTGAAGAGAAG
CGAAGTGAATCAAAGTTTCCAGATCTAACATTCCTGAAAAGCAGTAAAATAGATCAAGTTCC
Found at i:3936 original size:23 final size:23
Alignment explanation
Indices: 3906--3959 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
3896 ATGCCGGTAA
3906 CACCAAA-TATGCCCACGCAGTAG
1 CACCAAATTA-GCCCACGCAGTAG
3929 CACCAAATTAGCCCACGCAGTAG
1 CACCAAATTAGCCCACGCAGTAG
3952 CACCAAAT
1 CACCAAAT
3960 CAGCACCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.37, C:0.35, G:0.15, T:0.13
Consensus pattern (23 bp):
CACCAAATTAGCCCACGCAGTAG
Found at i:5129 original size:2 final size:2
Alignment explanation
Indices: 5122--5156 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5112 TCTTTTATGG
*
5122 TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5157 GATGAATGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6404 original size:10 final size:10
Alignment explanation
Indices: 6390--6429 Score: 53
Period size: 10 Copynumber: 3.7 Consensus size: 10
6380 AAAACAGATC
6390 AAAAAGAAAA
1 AAAAAGAAAA
6400 CAAAATAGAGAAA
1 -AAAA-AGA-AAA
6413 AAAAAGAAAA
1 AAAAAGAAAA
6423 AAAAAGA
1 AAAAAGA
6430 CTTGAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.37
11 7 0.26
12 7 0.26
13 3 0.11
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:6404 original size:23 final size:22
Alignment explanation
Indices: 6374--6427 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
6364 TTTTCTTCAA
**
6374 AAAAAAAAAACAGATCAAAAAG
1 AAAAAAAAAACAGAAAAAAAAG
* *
6396 AAAACAAAATAGAGAAAAAAAAG
1 AAAA-AAAAAACAGAAAAAAAAG
6419 AAAAAAAAA
1 AAAAAAAAA
6428 GACTTGAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.81, C:0.06, G:0.09, T:0.04
Consensus pattern (22 bp):
AAAAAAAAAACAGAAAAAAAAG
Found at i:7416 original size:14 final size:13
Alignment explanation
Indices: 7397--7439 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
7387 TTGTCCATAT
*
7397 TTTAGGATTTATAG
1 TTTAGGATTTAT-C
*
7411 TTTAGGAATTATC
1 TTTAGGATTTATC
*
7424 TTTAGGATATATC
1 TTTAGGATTTATC
7437 TTT
1 TTT
7440 TATTTTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.51
Consensus pattern (13 bp):
TTTAGGATTTATC
Found at i:18953 original size:2 final size:2
Alignment explanation
Indices: 18936--18974 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
18926 TATACATGTT
*
18936 TA TA T- TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18975 GTTATACCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21022 original size:21 final size:21
Alignment explanation
Indices: 20993--21039 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
20983 ATTCTGACTA
20993 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
21014 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
21035 TCGCA
1 TCGCA
21040 ACGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:21060 original size:20 final size:20
Alignment explanation
Indices: 21035--21228 Score: 158
Period size: 20 Copynumber: 9.3 Consensus size: 20
21025 TTTTCCTAAT
*
21035 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
21055 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
21076 TCGCAATGCGAGTACATAAA
1 TCGCAATGCGAATACGTAAA
* *
21096 TCGCATTGCGATTACGTAAATCTAAA
1 TCGCAATGCGAATACG------TAAA
* *
21122 TCGCATTGCGATTTACGT-AA
1 TCGCAATGCGA-ATACGTAAA
*
21142 TCGCAATGCGATTTACGTAAA
1 TCGCAATGCGA-ATACGTAAA
21163 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
21183 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
21203 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
*
21223 TTGCAA
1 TCGCAA
21229 CAAGATTCTG
Statistics
Matches: 147, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.01
20 97 0.66
21 29 0.20
26 15 0.10
27 5 0.03
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:21185 original size:41 final size:41
Alignment explanation
Indices: 21020--21228 Score: 185
Period size: 41 Copynumber: 5.0 Consensus size: 41
21010 AAATTCGCGT
* * * *
21020 TGCGATTTTCCTAATTCGCAACGCGAATACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAA
* * * * * *
21061 CGCGAATTT-GGAAAATCGCAATGCGAGTACATAAATCGCAT
1 TGCG-ATTTACGTAAATCGCAATGCGAATACGTAAATCGCAA
* *
21102 TGCGA-TTACGTAAATCTAAATCGCATTGCGATTTACGT-AATCGCAA
1 TGCGATTTACG------TAAATCGCAATGCGA-ATACGTAAATCGCAA
21148 TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAA
*
21189 TGCGA-TTACGTAAATCGCAATGCGAAT-CTGTAAATTGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATAC-GTAAATCGCAA
21229 CAAGATTCTG
Statistics
Matches: 137, Mismatches: 19, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
39 3 0.02
40 39 0.28
41 57 0.42
42 4 0.03
46 25 0.18
47 9 0.07
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (41 bp):
TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:22140 original size:24 final size:24
Alignment explanation
Indices: 22089--22142 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
22079 GTATTCAAAA
*
22089 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
22113 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
22137 TTTGAT
1 TTTGAT
22143 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:24581 original size:20 final size:20
Alignment explanation
Indices: 24558--24632 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
24548 CAACGAGAAT
*
24558 ATGACTATCGCAACACGGAA
1 ATGACTATCGCAACGCGGAA
*
24578 ATGACTATCGCAATGCGGAA
1 ATGACTATCGCAACGCGGAA
* *
24598 TTGACTATCGCAACGTGGAA
1 ATGACTATCGCAACGCGGAA
24618 ATGACTATCGCAACG
1 ATGACTATCGCAACG
24633 AGAGAATCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (20 bp):
ATGACTATCGCAACGCGGAA
Found at i:24618 original size:40 final size:41
Alignment explanation
Indices: 24554--24630 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
24544 ATTGCAACGA
24554 GAATATGACTATCGCAACACGGAAATGACTATCGCAATGCG
1 GAATATGACTATCGCAACACGGAAATGACTATCGCAATGCG
**
24595 GAAT-TGACTATCGCAACGTGGAAATGACTATCGCAA
1 GAATATGACTATCGCAACACGGAAATGACTATCGCAA
24631 CGAGAGAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (41 bp):
GAATATGACTATCGCAACACGGAAATGACTATCGCAATGCG
Found at i:24658 original size:19 final size:19
Alignment explanation
Indices: 24634--24701 Score: 127
Period size: 19 Copynumber: 3.6 Consensus size: 19
24624 ATCGCAACGA
24634 GAGAATCGCAATGCGAAAT
1 GAGAATCGCAATGCGAAAT
24653 GAGAATCGCAATGCGAAAT
1 GAGAATCGCAATGCGAAAT
24672 GAGAATCGCAATGCGAAAT
1 GAGAATCGCAATGCGAAAT
*
24691 GAAAATCGCAA
1 GAGAATCGCAA
24702 CGAGTGAATC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.15
Consensus pattern (19 bp):
GAGAATCGCAATGCGAAAT
Found at i:24705 original size:71 final size:72
Alignment explanation
Indices: 24575--24736 Score: 193
Period size: 71 Copynumber: 2.2 Consensus size: 72
24565 TCGCAACACG
** * * **
24575 GAAATGACTATCGCAATGCGGAATTGACTATCGCAACGTGGAAATGACTATCGCAACGAGAGAAT
1 GAAATGAAAATCGCAATGCGGAAATGACAATCGCAAC-TGGAAATGAAAATCGCAACGAGAGAAT
24640 CGCAATGC
65 CGCAATGC
* * *
24648 GAAATGAGAATCGCAATGC-GAAATGAGAATCGCAA-TGCGAAATGAAAATCGCAACGAGTGAAT
1 GAAATGAAAATCGCAATGCGGAAATGACAATCGCAACTG-GAAATGAAAATCGCAACGAGAGAAT
24711 CGCAATGC
65 CGCAATGC
24719 GAAAATGGAAAATCGCAA
1 G-AAAT-GAAAATCGCAA
24737 CGCGTCACTC
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
70 2 0.03
71 31 0.40
72 17 0.22
73 27 0.35
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.17
Consensus pattern (72 bp):
GAAATGAAAATCGCAATGCGGAAATGACAATCGCAACTGGAAATGAAAATCGCAACGAGAGAATC
GCAATGC
Found at i:24781 original size:33 final size:34
Alignment explanation
Indices: 24744--24807 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
24734 CAACGCGTCA
**
24744 CTCGTTGCGATTTTCATTT-CGCATTGCGATTCT
1 CTCGTTGCGATAGTCATTTCCGCATTGCGATTCT
*
24777 CTCGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CTCGTTGCGATAGTCATTTCCGCATTGCGAT
24808 AGTCTGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 17 0.63
34 10 0.37
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (34 bp):
CTCGTTGCGATAGTCATTTCCGCATTGCGATTCT
Found at i:24928 original size:14 final size:14
Alignment explanation
Indices: 24909--24945 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
24899 CATCAATTAA
24909 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
24923 ACAAATCATCTTTT
1 ACAAATCAACATTT
24937 ACAAATCAA
1 ACAAATCAA
24946 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:26383 original size:21 final size:20
Alignment explanation
Indices: 26365--26403 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
26355 GAGGGATAAT
26365 AGGGGCCTCTTGAATGATAG
1 AGGGGCCTCTTGAATGATAG
*
26385 GGGAGGCCTCTTGAATGAT
1 AGG-GGCCTCTTGAATGAT
26404 GACAGGTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (20 bp):
AGGGGCCTCTTGAATGATAG
Found at i:26915 original size:20 final size:20
Alignment explanation
Indices: 26890--26957 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
26880 AAACTTAAAT
*
26890 TCGCAACGCGAAAATGATTA
1 TCGCAACGCGAAAATGACTA
* *
26910 TCGCAATGCAAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
26930 TCGCAATGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
26950 TCGCAACG
1 TCGCAACG
26958 AGAGAATCGC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:27024 original size:20 final size:20
Alignment explanation
Indices: 26996--27042 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
26986 CAACAACAAA
*
26996 ATTGTAATGCGAAAATGACT
1 ATTGCAATGCGAAAATGACT
**
27016 ATTGCAATGCGAATTTGACT
1 ATTGCAATGCGAAAATGACT
*
27036 ATAGCAA
1 ATTGCAA
27043 CGAGAGAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (20 bp):
ATTGCAATGCGAAAATGACT
Found at i:27108 original size:20 final size:20
Alignment explanation
Indices: 27083--27206 Score: 161
Period size: 20 Copynumber: 6.5 Consensus size: 20
27073 ATTGCGATTC
**
27083 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
27103 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
27123 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
27143 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
27157 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
27177 TTGCAATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
27197 TTGCGATAGT
1 TTGCGATAGT
27207 AAACTATTCT
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
18 6 0.07
20 72 0.79
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:29042 original size:20 final size:20
Alignment explanation
Indices: 28997--29036 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28987 CTGAAACTTT
28997 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
29017 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
29037 CTATCGTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:29156 original size:20 final size:20
Alignment explanation
Indices: 29110--29158 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
29100 GCGATTCTCT
29110 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** **
29130 CACTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
29150 CGTTGCGAT
1 CGTTGCGAT
29159 TCACTCATTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:29743 original size:20 final size:20
Alignment explanation
Indices: 29716--29790 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
29706 GCTATGTAAA
29716 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
29736 TTGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
*
29756 TCGCATTGCGATTGACGTAT
1 TCGCATTGCGATTTACGTAT
29776 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
29791 GGAAAATCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:29774 original size:40 final size:40
Alignment explanation
Indices: 29714--29790 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
29704 GCGCTATGTA
* *
29714 AATCGCATTGCGATTTACGTATTTGCATTGCGATTTACGT
1 AATCGCATTGCGATTGACGTATTCGCATTGCGATTTACGT
29754 AATCGCATTGCGATTGACGTATTCGCATTGCGATTTA
1 AATCGCATTGCGATTGACGTATTCGCATTGCGATTTA
29791 GGAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (40 bp):
AATCGCATTGCGATTGACGTATTCGCATTGCGATTTACGT
Found at i:30826 original size:90 final size:88
Alignment explanation
Indices: 30675--30850 Score: 298
Period size: 90 Copynumber: 2.0 Consensus size: 88
30665 CCTAACACAC
30675 CCTTTTATAGCCAAGTTACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
1 CCTTTTATAGCCAAGTTACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
* *
30740 TTAATTAATTGGAATTTAATAAT
66 TTAATTAATTGAAATTAAATAAT
* *
30763 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTA-CCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
30828 ATTTAATTAATTGAAATTAAATA
64 ATTTAATTAATTGAAATTAAATA
30851 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 17 0.21
89 16 0.20
90 49 0.60
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (88 bp):
CCTTTTATAGCCAAGTTACCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAAATAAT
Found at i:35401 original size:12 final size:12
Alignment explanation
Indices: 35380--35413 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35370 TAATTAAAAC
*
35380 AAAAACATAATA
1 AAAAAAATAATA
*
35392 AAAAGAATAATA
1 AAAAAAATAATA
35404 AAAAAAATAA
1 AAAAAAATAA
35414 AATAAACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAAAAATAATA
Found at i:37782 original size:41 final size:40
Alignment explanation
Indices: 37737--37834 Score: 92
Period size: 42 Copynumber: 2.4 Consensus size: 40
37727 GGATTGCCCA
* *
37737 AAGGACTTATCATCTTGCTC-AAATGACTTA-TAGATGACATG
1 AAGGACTTATCATCATGCTCGAAA-GACTTACT-GATGAC-CG
* * *
37778 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCG
1 AAGGACTT-ATCATCATGCTCGAAAGACTTACTGATGACCG
37819 AAGGACTTACTCATCA
1 AAGGACTTA-TCATCA
37835 AGAAACCCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
40 1 0.02
41 20 0.43
42 21 0.46
43 4 0.09
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (40 bp):
AAGGACTTATCATCATGCTCGAAAGACTTACTGATGACCG
Found at i:38107 original size:42 final size:41
Alignment explanation
Indices: 38000--38107 Score: 99
Period size: 42 Copynumber: 2.6 Consensus size: 41
37990 AGGTCTTATG
* *
38000 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAAACTAATA
1 GATGACCCGAAGGACTTATCATCATGCTCGAAAAACTAATA
* * * * * * *
38041 GATGAACCGAAGGATTTAAGCATCATGCTCGAAATATTTATT
1 GATGACCCGAAGGACTT-ATCATCATGCTCGAAAAACTAATA
**
38083 GATTTCCCGAAGGACTTACTCATCA
1 GATGACCCGAAGGACTTA-TCATCA
38108 AGAAACCCTT
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
41 15 0.29
42 36 0.71
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCGAAAAACTAATA
Found at i:38129 original size:273 final size:274
Alignment explanation
Indices: 37318--38165 Score: 1178
Period size: 273 Copynumber: 3.1 Consensus size: 274
37308 TTTCGGTTTC
* *
37318 AGTTGTCATCAAGGAACCCTTAAAAAATAGGCTTAGCTTCCTTTAAAAATTCTTTGGAGATAACC
1 AGTTGTCATCAAGGAACCC-T-AAAAATAGGCTTAGCTTCCTTTAAAAATTATTTGGAGATAATC
** * * * *
37383 ATC-A-AAACCCCTGAAAATCAGACTTAATTTCTAAAAACTCATTTGAAAACATCCTGCCCAAAG
64 ATCAAGAAATACCTGAAAATCAGACTTAGTTTCTAAAAACTCATTTGAGAACATCCTGTCTAAAG
* * * *
37446 GTCTTATGGATGGCTCGAA-AACTTATCATCTTGCTCGAAAGGCTTATAGATGACCGAAGAATTT
129 GTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCGAAGGATTT
* * *
37510 AAGCATCATTCTCAAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAA
194 AAGCATCATGCTCGAAAGACTTACTGATTGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAA
*
37575 TTAAGCTTAGTTTCTT
259 TCAAGCTTAGTTTCTT
* *
37591 AGTTGTCATCAAGGAACACCTAAAAATTAGGC-TAGCTTCATATAAAAATTATTTGGAGATAATC
1 AGTTGTCATCAAGGAAC-CCTAAAAA-TAGGCTTAGCTTCCTTTAAAAATTATTTGGAGATAATC
* * **
37655 ATCAAG-AATCTCCTGAAAATCTGACTTAGTTTCTAAAAACTCATTTGAGAACATGTTGT-TCAA
64 ATCAAGAAAT-ACCTGAAAATCAGACTTAGTTTCTAAAAACTCATTTGAGAACATCCTGTCT-AA
* * *
37718 AGGTCTTATGGATTGCCCAAAGGACTTATCATCTTGCTC-AAATGACTTATAGATGACATGAAGG
127 AGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAA-GACTTATAGATGAC-CGAAGG
*
37782 ATTTAAGCATCATGCTCGAAAGACTTACTGA-TGGCCGAAGGACTTACTCATCAAGAAACCCTTG
190 ATTTAAGCATCATGCTCGAAAGACTTACTGATTGCCCGAAGGACTTACTCATCAAGAAACCCTTG
* *
37846 AAAATCAAGCTTTGTTTTTT
255 AAAATCAAGCTTAGTTTCTT
37866 AGTTGTCATCAAGGAATCCCT-AAAATAGGCTTAGCTTCCTTTAAAAA-TATTTGGAGATAATCA
1 AGTTGTCATCAAGGAA-CCCTAAAAATAGGCTTAGCTTCCTTTAAAAATTATTTGGAGATAATCA
* * *
37929 TCAAGAAATACCTGAAAACCAGGCTTAGTTTCT-AAAACTCATTTGAGAACATCCTGTCTGAAGG
65 TCAAGAAATACCTGAAAATCAGACTTAGTTTCTAAAAACTCATTTGAGAACATCCTGTCTAAAGG
* *
37993 TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAAACTAATAGATGAACCGAAGGATTT
130 TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATG-ACCGAAGGATTT
* * * *
38058 AAGCATCATGCTCGAAATATTTATTGATTTCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAA
194 AAGCATCATGCTCGAAAGACTTACTGATTGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAA
38123 TCAAGCTTAGTTTCTT
259 TCAAGCTTAGTTTCTT
*
38139 AGTTATCATCAAGGAACCCCTAAAAAT
1 AGTTGTCATCAAGGAA-CCCTAAAAAT
38166 CTTCCTTTTA
Statistics
Matches: 508, Mismatches: 50, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
272 139 0.27
273 146 0.29
274 93 0.18
275 96 0.19
276 34 0.07
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (274 bp):
AGTTGTCATCAAGGAACCCTAAAAATAGGCTTAGCTTCCTTTAAAAATTATTTGGAGATAATCAT
CAAGAAATACCTGAAAATCAGACTTAGTTTCTAAAAACTCATTTGAGAACATCCTGTCTAAAGGT
CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCGAAGGATTTAA
GCATCATGCTCGAAAGACTTACTGATTGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAATC
AAGCTTAGTTTCTT
Found at i:40197 original size:13 final size:13
Alignment explanation
Indices: 40163--40272 Score: 81
Period size: 13 Copynumber: 8.8 Consensus size: 13
40153 ATTTGATCAT
*
40163 TTTTCTTTCTTTC
1 TTTTCTTTTTTTC
40176 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
*
40189 TTTTC-TTTTTCC
1 TTTTCTTTTTTTC
40201 TTTT-TTCTTTTT-
1 TTTTCTT-TTTTTC
40213 TTTTCTATTTTTTC
1 TTTTCT-TTTTTTC
* *
40227 -CTTC-CTTTTTC
1 TTTTCTTTTTTTC
*
40238 TTTAT-TTTGTTTC
1 TTT-TCTTTTTTTC
* *
40251 TTTT-TCTTTTTG
1 TTTTCTTTTTTTC
40263 TTTTCTTTTT
1 TTTTCTTTTT
40273 GTGTGTGTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
11 6 0.08
12 26 0.34
13 43 0.57
14 1 0.01
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:40198 original size:19 final size:19
Alignment explanation
Indices: 40163--40261 Score: 107
Period size: 19 Copynumber: 5.3 Consensus size: 19
40153 ATTTGATCAT
40163 TTTTCTTTC-TTTC-TTTTC
1 TTTT-TTTCTTTTCTTTTTC
40181 TTTTTTTCTTTTCTTTTTC
1 TTTTTTTCTTTTCTTTTTC
*
40200 CTTTTTTCTTTT-TTTTTC
1 TTTTTTTCTTTTCTTTTTC
* *
40218 TATTTTTTCCTTCCTTTTTC
1 T-TTTTTTCTTTTCTTTTTC
*
40238 TTTATTTT-GTTTCTTTTTC
1 TTT-TTTTCTTTTCTTTTTC
40257 TTTTT
1 TTTTT
40262 GTTTTCTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
17 4 0.06
18 16 0.23
19 39 0.56
20 11 0.16
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.80
Consensus pattern (19 bp):
TTTTTTTCTTTTCTTTTTC
Found at i:43483 original size:13 final size:13
Alignment explanation
Indices: 43465--43489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43455 TGATCAAAAC
43465 AATTAATATAATT
1 AATTAATATAATT
43478 AATTAATATAAT
1 AATTAATATAAT
43490 AAAAACAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTAATATAATT
Found at i:43500 original size:1 final size:1
Alignment explanation
Indices: 43490--43528 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
43480 TTAATATAAT
* * *
43490 AAAAACAAAAAAATAAAAAAATAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43529 CATAAATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.03, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:43501 original size:8 final size:8
Alignment explanation
Indices: 43485--43525 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
43475 ATTAATTAAT
43485 ATAATAAAA
1 ATAA-AAAA
*
43494 ACAAAAAA
1 ATAAAAAA
43502 ATAAAAAA
1 ATAAAAAA
43510 ATAAAAAA
1 ATAAAAAA
43518 A-AAAAAA
1 ATAAAAAA
43525 A
1 A
43526 AAACATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 7 0.23
8 20 0.67
9 3 0.10
ACGTcount: A:0.88, C:0.02, G:0.00, T:0.10
Consensus pattern (8 bp):
ATAAAAAA
Found at i:45518 original size:14 final size:15
Alignment explanation
Indices: 45489--45521 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
45479 AAATAACTTC
*
45489 TCAAATTATTTATCA
1 TCAAATTATGTATCA
45504 TCAAATTA-GTATCA
1 TCAAATTATGTATCA
45518 TCAA
1 TCAA
45522 TGTACATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (15 bp):
TCAAATTATGTATCA
Found at i:47530 original size:29 final size:29
Alignment explanation
Indices: 47494--47556 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
47484 GAGATGCCGG
*
47494 AGCTCTCCTCAATAACCATAAATTGCCTT
1 AGCTCTCCTCAACAACCATAAATTGCCTT
*
47523 AGCTCTCCTCAACAACCATAAATTTCCTT
1 AGCTCTCCTCAACAACCATAAATTGCCTT
47552 AGCTC
1 AGCTC
47557 GCTAGCTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.30
Consensus pattern (29 bp):
AGCTCTCCTCAACAACCATAAATTGCCTT
Found at i:50755 original size:12 final size:13
Alignment explanation
Indices: 50738--50774 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
50728 GAGAGAGAGA
50738 AAATAAAT-AAGG
1 AAATAAATAAAGG
50750 AAATAAATAAAGG
1 AAATAAATAAAGG
50763 -AATAAATTAAAG
1 AAATAAA-TAAAG
50775 CATAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (13 bp):
AAATAAATAAAGG
Found at i:52376 original size:23 final size:23
Alignment explanation
Indices: 52342--52404 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
52332 ATTGCATATT
*
52342 CATGTTATTAATTCATGGCATTG
1 CATGTTACTAATTCATGGCATTG
52365 CATGTTACTAATTCATGGCATTG
1 CATGTTACTAATTCATGGCATTG
* *
52388 CATGGTACTACTTCATG
1 CATGTTACTAATTCATG
52405 TAGCAATGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (23 bp):
CATGTTACTAATTCATGGCATTG
Done.