Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003462.1 Hibiscus syriacus cultivar Beakdansim tig00007317_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: 59209
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:56 original size:40 final size:40
Alignment explanation
Indices: 1--90 Score: 162
Period size: 40 Copynumber: 2.2 Consensus size: 40
1 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
*
41 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATTTGT
1 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
*
81 AAATCACAAC
1 AAATCGCAAC
91 ACTGAAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGT
Found at i:82 original size:20 final size:20
Alignment explanation
Indices: 1--90 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
*
1 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
21 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
41 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
**
61 AAATCGCAACGAGAATTTGT
1 AAATCGCAACGAGAATCCGT
*
81 AAATCACAAC
1 AAATCGCAAC
91 ACTGAAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:783 original size:24 final size:24
Alignment explanation
Indices: 744--790 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
734 AAATTTGGTC
744 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
768 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
791 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:980 original size:12 final size:12
Alignment explanation
Indices: 963--987 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
953 ATATAATCCT
963 GAAGAAGAAAAA
1 GAAGAAGAAAAA
975 GAAGAAGAAAAA
1 GAAGAAGAAAAA
987 G
1 G
988 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:3346 original size:72 final size:71
Alignment explanation
Indices: 3253--3485 Score: 270
Period size: 72 Copynumber: 3.3 Consensus size: 71
3243 GCAACGAGAG
*
3253 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAA-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
3318 AAATGAA
65 AAATGAA
3325 AATCGCAATGCGAAATGAAAATCGC-AATGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAAATGA-A-AATCGCAATGCGGAAATGAAAATCGCAATGC
3389 GAAATG-A
64 GAAATGAA
* * * * *
3396 AATCGCAACGAGAGAATCG-CAATGCGGAAATG-AAATCGTAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
3456 CG--A-GAG
63 CGAAATGAA
3462 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
3486 ACAATGCGAA
Statistics
Matches: 142, Mismatches: 10, Indels: 25
0.80 0.06 0.14
Matches are distributed among these distances:
65 3 0.02
66 16 0.11
67 2 0.01
68 2 0.01
70 20 0.14
71 24 0.17
72 68 0.48
73 3 0.02
74 4 0.03
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCGA
AATGAA
Found at i:3399 original size:52 final size:53
Alignment explanation
Indices: 3239--3507 Score: 376
Period size: 52 Copynumber: 5.1 Consensus size: 53
3229 CGGAAATTAC
*
3239 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
3286 AATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
3344 AATCGCAATGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATG-A
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
3396 AATCGCAACGAGAGAATCGCAATGCGGAAATG-AAATCGTAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
3448 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
3501 AATCGCA
1 AATCGCA
3508 TTGCGATTCT
Statistics
Matches: 200, Mismatches: 8, Indels: 22
0.87 0.03 0.10
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
51 17 0.09
52 79 0.40
53 79 0.40
55 2 0.01
58 13 0.06
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (53 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
Found at i:3513 original size:72 final size:69
Alignment explanation
Indices: 3220--3512 Score: 253
Period size: 72 Copynumber: 4.2 Consensus size: 69
3210 GCATTTGACT
** * * *
3220 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-C-AT
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATCGAT
3283 GAAA
66 GAAA
*
3287 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
3352 T-GA-GAGA
61 TCGATGAAA
* * * * *
3359 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAT-CGCAACGAGAGAATCGCAATGC
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA-A-AATCGCAAT-C
3421 GGAAATG-AA
63 -G--ATGAAA
* *
3430 ATCGTAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAAT-CG
3494 AAATGAAA
64 --ATGAAA
*
3502 ATCGCATTGCG
1 ATCGCAATGCG
3513 ATTCTCTCGT
Statistics
Matches: 183, Mismatches: 22, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
64 6 0.03
65 5 0.03
66 12 0.07
67 25 0.14
69 3 0.02
70 20 0.11
71 21 0.11
72 83 0.45
73 3 0.02
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (69 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATCGAT
GAAA
Found at i:3547 original size:20 final size:19
Alignment explanation
Indices: 3522--3619 Score: 127
Period size: 20 Copynumber: 5.4 Consensus size: 19
3512 GATTCTCTCG
3522 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3542 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3561 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3575 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3593 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3613 TTGCGAT
1 TTGCGAT
3620 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 8 0.11
17 3 0.04
18 6 0.09
19 18 0.26
20 26 0.37
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3547 original size:53 final size:51
Alignment explanation
Indices: 3490--3598 Score: 146
Period size: 53 Copynumber: 2.1 Consensus size: 51
3480 AAAATCACAA
3490 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGA-TTTCATTT-CGCAT
** ** **
3543 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCAT
3594 TGCGA
1 TGCGA
3599 TTTTCATTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 10 0.20
52 8 0.16
53 32 0.64
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.39
Consensus pattern (51 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCAT
Found at i:3627 original size:20 final size:18
Alignment explanation
Indices: 3503--3619 Score: 115
Period size: 20 Copynumber: 6.7 Consensus size: 18
3493 GAAATGAAAA
*
3503 TCGCATTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
3519 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
3536 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGA-TTTCATT
*
3556 TCGCATTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
3572 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
3588 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
3607 TCCGCATTGCGAT
1 T-CGCATTGCGAT
3620 AGTCATTTTT
Statistics
Matches: 86, Mismatches: 3, Indels: 21
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.14
15 3 0.03
16 14 0.16
17 5 0.06
18 8 0.09
19 19 0.22
20 25 0.29
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:3743 original size:14 final size:14
Alignment explanation
Indices: 3724--3760 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3714 CATCAATTAC
3724 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3738 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3752 ACAAATCAA
1 ACAAATCAA
3761 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:5162 original size:21 final size:21
Alignment explanation
Indices: 5132--5194 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
5122 GTGAATCGGG
5132 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * **
5153 CTCTTCAATGATGACAGTGG-C
1 CTCTTGAATGGTGGGAG-GGAC
*
5174 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
5195 TCTCGAGGAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:5663 original size:19 final size:19
Alignment explanation
Indices: 5639--5792 Score: 101
Period size: 19 Copynumber: 8.3 Consensus size: 19
5629 TAGTTTACTT
*
5639 TCGCAACACGAAACTTAAA
1 TCGCAACACGAAACTAAAA
* *
5658 TCGCAACGCGAAA-TGAGAA
1 TCGCAACACGAAACT-AAAA
*
5677 TCGCAACGA-GAAACCAAAA
1 TCGCAAC-ACGAAACTAAAA
* *
5696 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACTAAAA
*
5715 TCGCAACGCG-AACTGAAAA
1 TCGCAACACGAAACT-AAAA
*
5734 TCGCAA-ACG--AC-AGAA
1 TCGCAACACGAAACTAAAA
**
5749 TCGCAATGCGAAA-TGAAAA
1 TCGCAACACGAAACT-AAAA
*
5768 TCGCAACGCGAAA-TGAAAA
1 TCGCAACACGAAACT-AAAA
5787 TCGCAA
1 TCGCAA
5793 TGCGATTTTG
Statistics
Matches: 112, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.08
16 2 0.02
17 2 0.02
18 7 0.06
19 92 0.82
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACACGAAACTAAAA
Found at i:5681 original size:38 final size:39
Alignment explanation
Indices: 5639--5792 Score: 137
Period size: 38 Copynumber: 4.2 Consensus size: 39
5629 TAGTTTACTT
* * *
5639 TCGCAACACGAAACT-TAAATCGCAACGCGAAATGAGAA
1 TCGCAACACGAAACTGAAAATCGCAACGCGAAATCAAAA
* *
5677 TCGCAACGA-GAAAC-CAAAATCGCAACGCGAAACCAAAA
1 TCGCAAC-ACGAAACTGAAAATCGCAACGCGAAATCAAAA
* * *
5715 TCGCAACGCG-AACTGAAAATCGCAA-ACG--A-CAGAA
1 TCGCAACACGAAACTGAAAATCGCAACGCGAAATCAAAA
** *
5749 TCGCAATGCGAAA-TGAAAATCGCAACGCGAAATGAAAA
1 TCGCAACACGAAACTGAAAATCGCAACGCGAAATCAAAA
5787 TCGCAA
1 TCGCAA
5793 TGCGATTTTG
Statistics
Matches: 95, Mismatches: 12, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
34 25 0.26
35 5 0.05
37 6 0.06
38 58 0.61
39 1 0.01
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (39 bp):
TCGCAACACGAAACTGAAAATCGCAACGCGAAATCAAAA
Found at i:5797 original size:19 final size:19
Alignment explanation
Indices: 5655--5797 Score: 159
Period size: 19 Copynumber: 7.7 Consensus size: 19
5645 CACGAAACTT
5655 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
* * **
5674 GAATCGCAACGAGAAACCA
1 AAATCGCAACGCGAAATGA
**
5693 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAATGA
*
5712 AAATCGCAACGCGAACTGA
1 AAATCGCAACGCGAAATGA
* *
5731 AAATCGCAA-ACGACA-G-
1 AAATCGCAACGCGAAATGA
*
5747 -AATCGCAATGCGAAATGA
1 AAATCGCAACGCGAAATGA
5765 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
*
5784 AAATCGCAATGCGA
1 AAATCGCAACGCGA
5798 TTTTGGTTTC
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
15 8 0.08
16 4 0.04
17 2 0.02
18 3 0.03
19 87 0.84
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
AAATCGCAACGCGAAATGA
Found at i:5828 original size:14 final size:14
Alignment explanation
Indices: 5809--5899 Score: 56
Period size: 14 Copynumber: 5.9 Consensus size: 14
5799 TTTGGTTTCG
5809 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
5823 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
* *
5840 CGCGTTGCAATTCTGT
1 --CGTTGCGATTTTGT
*
5856 CGTTGCGATTTTCATT
1 CGTTGCGATTTT--GT
* *
5872 CGCGTTGCGATTCTCT
1 --CGTTGCGATTTTGT
5888 CGTTGCGATTTT
1 CGTTGCGATTTT
5900 AAGTTTCGTG
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 33 0.55
15 1 0.02
16 3 0.05
17 1 0.02
18 12 0.20
19 10 0.17
ACGTcount: A:0.09, C:0.20, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5835 original size:33 final size:33
Alignment explanation
Indices: 5793--5915 Score: 167
Period size: 33 Copynumber: 3.7 Consensus size: 33
5783 AAAATCGCAA
*
5793 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
*
5826 TGCGATTTTGGTTTCGCGTTGCAATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
5859 TGCGATTTT-CATTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
5891 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
5916 AAGTAAACTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
32 28 0.35
33 40 0.51
34 11 0.14
ACGTcount: A:0.10, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:5847 original size:19 final size:19
Alignment explanation
Indices: 5793--5847 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
5783 AAAATCGCAA
5793 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5812 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5826 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5845 TGC
1 TGC
5848 AATTCTGTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 12 0.39
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 15 0.48
ACGTcount: A:0.05, C:0.16, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:8117 original size:21 final size:21
Alignment explanation
Indices: 8075--8117 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
8065 TTTCTGGGTT
* * *
8075 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
8096 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
8117 A
1 A
8118 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:8177 original size:66 final size:68
Alignment explanation
Indices: 8097--8247 Score: 225
Period size: 67 Copynumber: 2.2 Consensus size: 68
8087 ACCCATTCAA
*
8097 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
8161 -GG
66 GGG
* * * **
8163 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
8228 GGG
66 GGG
*
8231 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
8248 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 22 0.29
67 36 0.47
68 18 0.24
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
GGG
Found at i:8604 original size:29 final size:28
Alignment explanation
Indices: 8547--8617 Score: 106
Period size: 29 Copynumber: 2.5 Consensus size: 28
8537 CATATTATGA
*
8547 TACATGACATGAATTATATTAAATGTAT
1 TACATGACATGAATTATATGAAATGTAT
*
8575 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATT-ATATGAAATGTAT
*
8604 TGCATGACATGAAT
1 TACATGACATGAAT
8618 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 15 0.38
29 24 0.62
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (28 bp):
TACATGACATGAATTATATGAAATGTAT
Found at i:8674 original size:30 final size:30
Alignment explanation
Indices: 8632--8708 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
8622 AGAAAAAGTT
* *
8632 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
8663 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
8693 ATATGACTACGTGATA
1 ATATGACTATGTGATA
8709 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:10144 original size:21 final size:21
Alignment explanation
Indices: 10118--10194 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
10108 CGCGTTGCGA
*
10118 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
10139 TTCTCTCGTTGCAGATAGTCAT
1 TTCTCTCGTTGC-GATTTTCAT
*
10161 TT-TCACGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
10181 TTCTCTCGTTGCGA
1 TTCTCTCGTTGCGA
10195 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:10316 original size:33 final size:33
Alignment explanation
Indices: 10274--10344 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
10264 AATACTAACT
10274 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
10307 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
10340 TGAAA
1 TGAAA
10345 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:10729 original size:20 final size:20
Alignment explanation
Indices: 10702--10956 Score: 291
Period size: 20 Copynumber: 12.7 Consensus size: 20
10692 CTTTAAAAAT
*
10702 CGCGTTGCGATTTACGGATT
1 CGCGTTGCGATTTACGGATA
* *
10722 CTCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
10742 TGTCGTTGTGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
10763 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
10783 CACATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
10803 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
10823 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
10844 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
10864 CACATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
10884 CGCGTTGCGATTTACGAATA
1 CGCGTTGCGATTTACGGATA
*
10904 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
10924 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
10944 CGCGTTGCGATTT
1 CGCGTTGCGATTT
10957 TCATATTCGC
Statistics
Matches: 198, Mismatches: 30, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
20 164 0.83
21 34 0.17
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:10841 original size:81 final size:81
Alignment explanation
Indices: 10706--10934 Score: 388
Period size: 81 Copynumber: 2.8 Consensus size: 81
10696 AAAAATCGCG
* * *
10706 TTGCGATTTACGGATTCTCGTTGCGATTTTACGTATTGTCGTTGTGATTTACGGATACGCGTTGC
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGC
10771 GATATACGGATACACA
66 GATATACGGATACACA
10787 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGC
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGC
10852 GATATACGGATACACA
66 GATATACGGATACACA
* ***
10868 TTGCGATTTACGGATACGCGTTGCGA-TTTACGAATACACGTTGCGATTTACGGATACGCGTTGC
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGC
10932 GAT
66 GAT
10935 TTATGTGTTC
Statistics
Matches: 141, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
80 37 0.26
81 104 0.74
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (81 bp):
TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGC
GATATACGGATACACA
Found at i:15962 original size:2 final size:2
Alignment explanation
Indices: 15955--15984 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15945 TGAGTTCACA
15955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15985 GCTATTGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25742 original size:20 final size:20
Alignment explanation
Indices: 25717--25775 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
25707 TCGTAACACG
*
25717 AAAGTCGAATTCGCAACGCC
1 AAAGTCAAATTCGCAACGCC
25737 AAAGTCAAATTCGCAACGCC
1 AAAGTCAAATTCGCAACGCC
25757 AAAGTCAAATTCGCAACGC
1 AAAGTCAAATTCGCAACGC
25776 AAATAGTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAGTCAAATTCGCAACGCC
Found at i:25794 original size:40 final size:40
Alignment explanation
Indices: 25717--25794 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
25707 TCGTAACACG
* * *
25717 AAAGTCGAATTCGCAACGCCAAAGTCAAATTCGCAACGCC
1 AAAGTCAAATTCGCAACGCAAAAGTCAAATTCACAACGCC
*
25757 AAAGTCAAATTCGCAACGCAAATAGTTAAATT-ACAACG
1 AAAGTCAAATTCGCAACGCAAA-AGTCAAATTCACAACG
25795 ATAATATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 25 0.76
41 8 0.24
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.18
Consensus pattern (40 bp):
AAAGTCAAATTCGCAACGCAAAAGTCAAATTCACAACGCC
Found at i:25808 original size:40 final size:40
Alignment explanation
Indices: 25764--25859 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
25754 GCCAAAGTCA
* *
25764 AATTCGCAACGCAAATAGTTAAATTACAACGATAATATGT
1 AATTCGCAACGCAAATAGGTAAATCACAACGATAATATGT
** *
25804 AATTCGCAACGCGCATAGGTAAATCGCAACGATAATATGT
1 AATTCGCAACGCAAATAGGTAAATCACAACGATAATATGT
* *
25844 AAATCACAACGCAAAT
1 AATTCGCAACGCAAAT
25860 TCTCCAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (40 bp):
AATTCGCAACGCAAATAGGTAAATCACAACGATAATATGT
Found at i:25813 original size:20 final size:20
Alignment explanation
Indices: 25790--25854 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
25780 AGTTAAATTA
*
25790 CAACGATAATATGTAATTCG
1 CAACGATAATATGTAAATCG
*** *
25810 CAACGCGCATAGGTAAATCG
1 CAACGATAATATGTAAATCG
*
25830 CAACGATAATATGTAAATCA
1 CAACGATAATATGTAAATCG
25850 CAACG
1 CAACG
25855 CAAATTCTCC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.22
Consensus pattern (20 bp):
CAACGATAATATGTAAATCG
Found at i:25973 original size:126 final size:126
Alignment explanation
Indices: 25827--26072 Score: 375
Period size: 126 Copynumber: 2.0 Consensus size: 126
25817 CATAGGTAAA
* * * *
25827 TCGCAACGATAATATGTAAATCACAACGCAAATTCTCCAAATTCGCAACTCGAATTTCGCAATGC
1 TCGCAACGAGAATAGGTAAATCACAACACAAATTCTCCAAATTCGCAACTCGAATTTCGCAACGC
*
25892 TAATTACCGATATAGGCAATTAGCGTTGCGAAAACGAAATTCACGTTGCGATTTTCCAAAT
66 TAATGACCGATATAGGCAATTAGCGTTGCGAAAACGAAATTCACGTTGCGATTTTCCAAAT
* * * *
25953 TCGCAACGCGAATAGGTAAATCGCAACACGAATTCTCCAAATTCGCAACTTGAATTTCGCAACGC
1 TCGCAACGAGAATAGGTAAATCACAACACAAATTCTCCAAATTCGCAACTCGAATTTCGCAACGC
* * * *
26018 TAATGACTGATATAGGTAATTAGCGTTGCGAAAATGAAATTCACGTTGTGATTTT
66 TAATGACCGATATAGGCAATTAGCGTTGCGAAAACGAAATTCACGTTGCGATTTT
26073 GGAGAATAGC
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
126 107 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (126 bp):
TCGCAACGAGAATAGGTAAATCACAACACAAATTCTCCAAATTCGCAACTCGAATTTCGCAACGC
TAATGACCGATATAGGCAATTAGCGTTGCGAAAACGAAATTCACGTTGCGATTTTCCAAAT
Found at i:26108 original size:147 final size:152
Alignment explanation
Indices: 25935--26247 Score: 413
Period size: 158 Copynumber: 2.1 Consensus size: 152
25925 ACGAAATTCA
* *
25935 CGTTGCGATTTTCCAAATTCGCAACGCGAATAGGTAAATCGC-AACACG-AAT-TC-TC-CAAAT
1 CGTTGCGATTTTCCAAATTCGCAACGCGAATAGGTAAATCGCAAACACGAAATCGCAACGCAAAT
* * *
25995 TCGCAACTTGAATTTCGCAACGCTAATGACTGA-TATAGGTAATTAGCGTTGCGAAAATGAAATT
66 TCACAACTCGAATTTCGCAACGCTAATGAC-CACTATAGGTAATTAGCGTTGCGAAAATGAAATT
26059 CACGTTGTGATTTTGGAGAATAG
130 CACGTTGTGATTTTGGAGAATAG
* * * *
26082 CGTTGTGATTTTCCAAATTCGCAACGCTAATAGGTAAATCGCAATGATAATATGTAAATCGCAAC
1 CGTTGCGATTTTCCAAATTCGCAACGCGAATAGGTAAATCGC----A-AACACG-AAATCGCAAC
*
26147 GCAAATTCACAACTCGAATTTCGCAACGCTAATTACCACTATAGGTAATTAGCGTTGCGAAAATG
60 GCAAATTCACAACTCGAATTTCGCAACGCTAATGACCACTATAGGTAATTAGCGTTGCGAAAATG
* *
26212 AAATTCGCGTTGTGATTTTGGAGAATCG
125 AAATTCACGTTGTGATTTTGGAGAATAG
26240 CGTTGCGA
1 CGTTGCGA
26248 AAACGAAAAT
Statistics
Matches: 141, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
147 40 0.28
153 4 0.03
155 3 0.02
156 1 0.01
157 2 0.01
158 91 0.65
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (152 bp):
CGTTGCGATTTTCCAAATTCGCAACGCGAATAGGTAAATCGCAAACACGAAATCGCAACGCAAAT
TCACAACTCGAATTTCGCAACGCTAATGACCACTATAGGTAATTAGCGTTGCGAAAATGAAATTC
ACGTTGTGATTTTGGAGAATAG
Found at i:26125 original size:20 final size:20
Alignment explanation
Indices: 26100--26148 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
26090 TTTTCCAAAT
26100 TCGCAACGCTAATAGGTAAA
1 TCGCAACGCTAATAGGTAAA
* * *
26120 TCGCAATGATAATATGTAAA
1 TCGCAACGCTAATAGGTAAA
26140 TCGCAACGC
1 TCGCAACGC
26149 AAATTCACAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (20 bp):
TCGCAACGCTAATAGGTAAA
Found at i:26341 original size:20 final size:20
Alignment explanation
Indices: 26318--26382 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
26308 TGACTTTTGT
*
26318 GTTGCGATTTATATATTCGC
1 GTTGCGATTTACATATTCGC
*
26338 GTTGCGATTTACATATTCGA
1 GTTGCGATTTACATATTCGC
26358 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
26378 GTTGC
1 GTTGC
26383 AAATTTGGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:26431 original size:20 final size:20
Alignment explanation
Indices: 26408--26446 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
26398 CGTTGCCCTT
*
26408 TTGGAACTTGTGTTGCGAAA
1 TTGGAACTTGCGTTGCGAAA
**
26428 TTGGAGTTTGCGTTGCGAA
1 TTGGAACTTGCGTTGCGAA
26447 TTTGTTAGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.36
Consensus pattern (20 bp):
TTGGAACTTGCGTTGCGAAA
Found at i:38128 original size:15 final size:15
Alignment explanation
Indices: 38106--38138 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
38096 ACTATTAATT
38106 AATAAAAAATAATTTA
1 AATAAAAAAT-ATTTA
38122 AATAAAAAATATTTA
1 AATAAAAAATATTTA
38137 AA
1 AA
38139 AATAGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAAAAATATTTA
Found at i:51397 original size:29 final size:29
Alignment explanation
Indices: 51371--51465 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
51361 GTTTTCCAGC
51371 TTAGTCCCTGAACTTTATCTTGGTCCACA
1 TTAGTCCCTGAACTTTATCTTGGTCCACA
** * ** *
51400 TTAGTCTTTGAACTTGA-CAATTTTTCCAAA
1 TTAGTCCCTGAACTTTATC--TTGGTCCACA
*
51430 CTTAGTCCCTGAACTTTATTTTGGTCCACA
1 -TTAGTCCCTGAACTTTATCTTGGTCCACA
51460 TTAGTC
1 TTAGTC
51466 TGTGGACTTG
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
28 1 0.02
29 20 0.41
30 14 0.29
31 14 0.29
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (29 bp):
TTAGTCCCTGAACTTTATCTTGGTCCACA
Found at i:51442 original size:60 final size:59
Alignment explanation
Indices: 51362--51475 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 59
51352 AACTTGGCAG
* *
51362 TTTTCCAGCTTAGTCCCTGAACTTTATCTTGGTCCACATTAGTCTTTGAACTTGACAAT
1 TTTTCCAACTTAGTCCCTGAACTTTATCTTGGTCCACATTAGTCTGTGAACTTGACAAT
* *
51421 TTTTCCAAACTTAGTCCCTGAACTTTATTTTGGTCCACATTAGTCTGTGGACTTG
1 TTTTCC-AACTTAGTCCCTGAACTTTATCTTGGTCCACATTAGTCTGTGAACTTG
51476 GCACTTTATC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 6 0.12
60 44 0.88
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (59 bp):
TTTTCCAACTTAGTCCCTGAACTTTATCTTGGTCCACATTAGTCTGTGAACTTGACAAT
Found at i:58794 original size:18 final size:19
Alignment explanation
Indices: 58758--58794 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
58748 CACGGAATGT
58758 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
58778 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
58795 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Done.