Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009495.1 Hibiscus syriacus cultivar Beakdansim tig00114702_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: 65459
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1262 original size:29 final size:29
Alignment explanation
Indices: 1152--1255 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
1142 TGACTGTGTA
**
1152 CTATTTTGGGAATTAATTCGAAATGGGTG
1 CTATTTTGGGAATTAATTCGAAAAAGGTG
*
1181 CTATTTTGGGAATTAATTC-AAAATA-GTT
1 CTATTTTGGGAATTAATTCGAAAA-AGGTG
* **
1209 CTTTTTTGTAAATTAATTCGAAAAAGGTG
1 CTATTTTGGGAATTAATTCGAAAAAGGTG
*
1238 CTATTTTGGTAATTAATT
1 CTATTTTGGGAATTAATT
1256 TTAAAAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 22 0.35
29 40 0.65
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (29 bp):
CTATTTTGGGAATTAATTCGAAAAAGGTG
Found at i:2248 original size:41 final size:41
Alignment explanation
Indices: 2197--2360 Score: 215
Period size: 42 Copynumber: 3.9 Consensus size: 41
2187 AAGTATTATT
2197 AGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTT-CC
1 AGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTACC
* *
2238 AGGTTCCTTTGCTATGTGCGAAGGTAAGCCTTACAGTTTACC
1 AGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTACC
* *
2280 AGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 AGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTACC
* *
2322 AGGTCCCTTTTGTTGTGTGCAAGGATAAACCTTAC-GTTT
1 AGGTCCC-TTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
2361 TCCTAGGCTC
Statistics
Matches: 112, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
41 39 0.35
42 50 0.45
43 23 0.21
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (41 bp):
AGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTACC
Found at i:2457 original size:19 final size:19
Alignment explanation
Indices: 2433--2470 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2423 GGTGAACCTA
2433 CACATTTTGGTGATTGGAT
1 CACATTTTGGTGATTGGAT
2452 CACATTTTGGTGATTGGAT
1 CACATTTTGGTGATTGGAT
2471 AAAAGTAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (19 bp):
CACATTTTGGTGATTGGAT
Found at i:7393 original size:28 final size:29
Alignment explanation
Indices: 7343--7397 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
7333 ATAACACCCT
*
7343 TTTCAAATTAATTCACAATATGTCACCAG
1 TTTCAAATTAATTCACAAAATGTCACCAG
7372 TTTCAAA-TAATT-ACTAAAATGTCACC
1 TTTCAAATTAATTCAC-AAAATGTCACC
7398 TGGTCAACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 2 0.08
28 15 0.62
29 7 0.29
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (29 bp):
TTTCAAATTAATTCACAAAATGTCACCAG
Found at i:7444 original size:17 final size:18
Alignment explanation
Indices: 7406--7446 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
7396 CCTGGTCAAC
*
7406 GGTCAACGGGTCGGGTCT
1 GGTCAACGGGTCGGGTCG
*
7424 GGTCAAC-GGTTGGGTCG
1 GGTCAACGGGTCGGGTCG
7441 GGTCAA
1 GGTCAA
7447 ACCGGTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.15, C:0.20, G:0.44, T:0.22
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:7455 original size:9 final size:9
Alignment explanation
Indices: 7441--7465 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
7431 GGTTGGGTCG
7441 GGTCAAACC
1 GGTCAAACC
7450 GGTCAAACC
1 GGTCAAACC
7459 GGTCAAA
1 GGTCAAA
7466 ATTGGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.28, G:0.24, T:0.12
Consensus pattern (9 bp):
GGTCAAACC
Found at i:40645 original size:10 final size:9
Alignment explanation
Indices: 40610--40708 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
40600 GCTGCTGGAA
*
40610 ACCGGTTTA
1 ACCGGTTTG
*
40619 ACCGGTTTTCA
1 ACCGG-TTT-G
40630 ACCGGTTCTG
1 ACCGGTT-TG
40640 ACCGGTTTG
1 ACCGGTTTG
*
40649 ACCGGTTTCA
1 ACCGGTTT-G
*
40659 ACCGGTTCG
1 ACCGGTTTG
40668 AACCGGTTTG
1 -ACCGGTTTG
*
40678 ACCGGTCTG
1 ACCGGTTTG
40687 ACTCGGTTTG
1 AC-CGGTTTG
*
40697 ACCGGTCTG
1 ACCGGTTTG
40706 ACC
1 ACC
40709 CGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:40654 original size:19 final size:19
Alignment explanation
Indices: 40611--40708 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
40601 CTGCTGGAAA
* * *
40611 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
40631 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
40650 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
40670 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
40688 CTCGGTTTGACCGG-TCTGA
1 C-CGGTTTGACCGGTTCTGA
40707 CC
1 CC
40709 CGACCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.09
19 39 0.57
20 15 0.22
21 8 0.12
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:40672 original size:29 final size:30
Alignment explanation
Indices: 40609--40683 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
40599 GGCTGCTGGA
*
40609 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
40640 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
40668 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
40684 CTGACTCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:40693 original size:29 final size:28
Alignment explanation
Indices: 40610--40708 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 28
40600 GCTGCTGGAA
* *
40610 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAACCGGTTC-G
*
40640 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTCTCAACCGGTTCG
* *
40668 AACCGGTTTGACCGGTCT-GACTCGGTTTG
1 -ACCGGTTTGACCGGTCTCAAC-CGGTTCG
*
40697 ACCGGTCTGACC
1 ACCGGTTTGACC
40709 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 14 0.23
29 35 0.56
30 13 0.21
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:40707 original size:9 final size:9
Alignment explanation
Indices: 40630--40734 Score: 63
Period size: 9 Copynumber: 11.3 Consensus size: 9
40620 CCGGTTTTCA
40630 ACCGGTTCTG
1 ACCGG-TCTG
*
40640 ACCGGTTTG
1 ACCGGTCTG
* *
40649 ACCGGTTTCA
1 ACCGGTCT-G
40659 ACCGGT-TCG
1 ACCGGTCT-G
*
40668 AACCGGTTTG
1 -ACCGGTCTG
40678 ACCGGTCTG
1 ACCGGTCTG
*
40687 ACTCGGTTTG
1 AC-CGGTCTG
40697 ACCGGTCTG
1 ACCGGTCTG
** *
40706 ACCCGACCCG
1 A-CCGGTCTG
40716 ACC-GT-TG
1 ACCGGTCTG
40723 ACCGGTCTG
1 ACCGGTCTG
40732 ACC
1 ACC
40735 CGACCCGACC
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
7 4 0.05
8 2 0.03
9 37 0.49
10 32 0.42
11 1 0.01
ACGTcount: A:0.14, C:0.32, G:0.29, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:40741 original size:5 final size:5
Alignment explanation
Indices: 40731--40788 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
40721 TGACCGGTCT
* *
40731 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
40780 GACCC GACC
1 GACCC GACC
40789 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:40759 original size:22 final size:22
Alignment explanation
Indices: 40705--40795 Score: 146
Period size: 22 Copynumber: 4.0 Consensus size: 22
40695 TGACCGGTCT
40705 GACCCGACCCGACCGTTGACCGGTC
1 GACCCGACCCGACCGTTGACC---C
40730 TGACCCGACCCGACCGTTGACCC
1 -GACCCGACCCGACCGTTGACCC
40753 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
40775 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
40796 GTTGACCGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
22 43 0.66
23 1 0.02
26 21 0.32
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:40797 original size:7 final size:7
Alignment explanation
Indices: 40785--40815 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
40775 GACCCGACCC
40785 GACCGTT
1 GACCGTT
40792 GACCGTT
1 GACCGTT
40799 GACCGTT
1 GACCGTT
40806 GACCGTT
1 GACCGTT
40813 GAC
1 GAC
40816 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:48009 original size:10 final size:9
Alignment explanation
Indices: 47974--48072 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
47964 GCTGCTGGAA
*
47974 ACCGGTTTA
1 ACCGGTTTG
*
47983 ACCGGTTTTCA
1 ACCGG-TTT-G
47994 ACCGGTTCTG
1 ACCGGTT-TG
48004 ACCGGTTTG
1 ACCGGTTTG
*
48013 ACCGGTTTCA
1 ACCGGTTT-G
*
48023 ACCGGTTCG
1 ACCGGTTTG
48032 AACCGGTTTG
1 -ACCGGTTTG
*
48042 ACCGGTCTG
1 ACCGGTTTG
48051 ACTCGGTTTG
1 AC-CGGTTTG
*
48061 ACCGGTCTG
1 ACCGGTTTG
48070 ACC
1 ACC
48073 CGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:48018 original size:19 final size:19
Alignment explanation
Indices: 47975--48072 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
47965 CTGCTGGAAA
* * *
47975 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
47995 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
48014 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
48034 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
48052 CTCGGTTTGACCGG-TCTGA
1 C-CGGTTTGACCGGTTCTGA
48071 CC
1 CC
48073 CGACCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.09
19 39 0.57
20 15 0.22
21 8 0.12
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:48036 original size:29 final size:30
Alignment explanation
Indices: 47973--48047 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
47963 GGCTGCTGGA
*
47973 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
48004 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
48032 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
48048 CTGACTCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:48057 original size:29 final size:28
Alignment explanation
Indices: 47974--48072 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 28
47964 GCTGCTGGAA
* *
47974 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAACCGGTTC-G
*
48004 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTCTCAACCGGTTCG
* *
48032 AACCGGTTTGACCGGTCT-GACTCGGTTTG
1 -ACCGGTTTGACCGGTCTCAAC-CGGTTCG
*
48061 ACCGGTCTGACC
1 ACCGGTTTGACC
48073 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 14 0.23
29 35 0.56
30 13 0.21
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:48071 original size:9 final size:9
Alignment explanation
Indices: 47994--48098 Score: 63
Period size: 9 Copynumber: 11.3 Consensus size: 9
47984 CCGGTTTTCA
47994 ACCGGTTCTG
1 ACCGG-TCTG
*
48004 ACCGGTTTG
1 ACCGGTCTG
* *
48013 ACCGGTTTCA
1 ACCGGTCT-G
48023 ACCGGT-TCG
1 ACCGGTCT-G
*
48032 AACCGGTTTG
1 -ACCGGTCTG
48042 ACCGGTCTG
1 ACCGGTCTG
*
48051 ACTCGGTTTG
1 AC-CGGTCTG
48061 ACCGGTCTG
1 ACCGGTCTG
** *
48070 ACCCGACCCG
1 A-CCGGTCTG
48080 ACC-GT-TG
1 ACCGGTCTG
48087 ACCGGTCTG
1 ACCGGTCTG
48096 ACC
1 ACC
48099 CGACCCGACC
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
7 4 0.05
8 2 0.03
9 37 0.49
10 32 0.42
11 1 0.01
ACGTcount: A:0.14, C:0.32, G:0.29, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:48105 original size:5 final size:5
Alignment explanation
Indices: 48095--48152 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
48085 TGACCGGTCT
* *
48095 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
48144 GACCC GACC
1 GACCC GACC
48153 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:48123 original size:22 final size:22
Alignment explanation
Indices: 48069--48159 Score: 146
Period size: 22 Copynumber: 4.0 Consensus size: 22
48059 TGACCGGTCT
48069 GACCCGACCCGACCGTTGACCGGTC
1 GACCCGACCCGACCGTTGACC---C
48094 TGACCCGACCCGACCGTTGACCC
1 -GACCCGACCCGACCGTTGACCC
48117 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
48139 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
48160 GTTGACCGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
22 43 0.66
23 1 0.02
26 21 0.32
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:48161 original size:7 final size:7
Alignment explanation
Indices: 48149--48179 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
48139 GACCCGACCC
48149 GACCGTT
1 GACCGTT
48156 GACCGTT
1 GACCGTT
48163 GACCGTT
1 GACCGTT
48170 GACCGTT
1 GACCGTT
48177 GAC
1 GAC
48180 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:54693 original size:34 final size:35
Alignment explanation
Indices: 54637--54707 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 35
54627 CGTCACTAAC
*
54637 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
54672 AGTAAGGCCCTG-GCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
54706 AG
1 AG
54708 AAATCTTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 23 0.66
35 12 0.34
ACGTcount: A:0.31, C:0.30, G:0.31, T:0.08
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
Found at i:54818 original size:24 final size:23
Alignment explanation
Indices: 54790--54876 Score: 93
Period size: 24 Copynumber: 3.7 Consensus size: 23
54780 ATTCAAGTCA
* *
54790 AGTATCATATCAGAATCCATATC
1 AGTATCAGATCAGAATCCATGTC
*
54813 ATGTATCAGATTAGAATCCATGTC
1 A-GTATCAGATCAGAATCCATGTC
* *
54837 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCATGTC
* *
54860 AGGTATCATAACAGAAT
1 A-GTATCAGATCAGAAT
54877 TCAAATTTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
23 21 0.40
24 32 0.60
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCATGTC
Found at i:54876 original size:47 final size:48
Alignment explanation
Indices: 54786--54876 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 48
54776 CATAATTCAA
* * * **
54786 GTCAAGTATCATATCAGAATCCATATCATGTATCAGATTAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAATCCAT
* *
54834 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAAT
54877 TCAAATTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 31 0.86
48 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAATCCAT
Found at i:56010 original size:18 final size:18
Alignment explanation
Indices: 55989--56024 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55979 CTTCCATCCG
*
55989 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
56007 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
56025 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:57223 original size:7 final size:7
Alignment explanation
Indices: 57207--57256 Score: 61
Period size: 7 Copynumber: 7.3 Consensus size: 7
57197 GGTCAACGTG
57207 GGTC-AC
1 GGTCAAC
57213 GGTCAAC
1 GGTCAAC
57220 GGTCAAC
1 GGTCAAC
57227 GGTCAAC
1 GGTCAAC
57234 GGGTCAAC
1 -GGTCAAC
57242 GGGTC-A-
1 -GGTCAAC
57248 GGTCAAC
1 GGTCAAC
57255 GG
1 GG
57257 GTCGGGTCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 4 0.10
6 5 0.12
7 19 0.47
8 12 0.30
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (7 bp):
GGTCAAC
Found at i:57264 original size:18 final size:18
Alignment explanation
Indices: 57227--57281 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
57217 AACGGTCAAC
57227 GGTCAACGGGTCAACGGGTCA
1 GGTCAACGGGT---CGGGTCA
57248 GGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
*
57266 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
57282 AAACGGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCA
Found at i:57277 original size:13 final size:13
Alignment explanation
Indices: 57235--57265 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
57225 ACGGTCAACG
57235 GGTCAACGGGTCA
1 GGTCAACGGGTCA
*
57248 GGTCAACGGGTCG
1 GGTCAACGGGTCA
57261 GGTCA
1 GGTCA
57266 GGTCAACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:59436 original size:22 final size:23
Alignment explanation
Indices: 59379--59458 Score: 99
Period size: 24 Copynumber: 3.4 Consensus size: 23
59369 CATAATTCAA
*
59379 GTCAGTATCATATCAGAATCCAT
1 GTCAGTATCAGATCAGAATCCAT
* *
59402 ATCATGTATCAGATTAGAATCCAT
1 GTCA-GTATCAGATCAGAATCCAT
*
59426 GTCA-TATCAGATCAGAATCCAG
1 GTCAGTATCAGATCAGAATCCAT
59448 GTCAGGTATCA
1 GTCA-GTATCA
59459 TAACGAATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
22 20 0.42
23 3 0.06
24 25 0.52
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (23 bp):
GTCAGTATCAGATCAGAATCCAT
Found at i:60608 original size:18 final size:18
Alignment explanation
Indices: 60587--60622 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
60577 CTTCCATCCG
*
60587 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
60605 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
60623 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:61816 original size:15 final size:15
Alignment explanation
Indices: 61796--61835 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
61786 TGGTCAACGT
61796 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
61811 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
61826 GGGTCAACGG
1 GGGTCAACGG
61836 GTCAGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:61817 original size:8 final size:8
Alignment explanation
Indices: 61796--61851 Score: 77
Period size: 8 Copynumber: 7.6 Consensus size: 8
61786 TGGTCAACGT
61796 GGGTCAAC
1 GGGTCAAC
61804 -GGTCAAC
1 GGGTCAAC
61811 GGGTCAAC
1 GGGTCAAC
61819 -GGTCAAC
1 GGGTCAAC
61826 GGGTCAAC
1 GGGTCAAC
61834 GGGTC-A-
1 GGGTCAAC
61840 -GGTCAAC
1 GGGTCAAC
61847 GGGTC
1 GGGTC
61852 GGGTCAGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
5 4 0.09
6 1 0.02
7 15 0.35
8 23 0.53
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.14
Consensus pattern (8 bp):
GGGTCAAC
Found at i:61856 original size:18 final size:18
Alignment explanation
Indices: 61819--61873 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
61809 ACGGGTCAAC
61819 GGTCAACGGGTCAACGGGTCA
1 GGTCAACGGGT---CGGGTCA
61840 GGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
*
61858 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
61874 AAACGGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCA
Found at i:61869 original size:13 final size:13
Alignment explanation
Indices: 61827--61857 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
61817 ACGGTCAACG
61827 GGTCAACGGGTCA
1 GGTCAACGGGTCA
*
61840 GGTCAACGGGTCG
1 GGTCAACGGGTCA
61853 GGTCA
1 GGTCA
61858 GGTCAACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCA
Done.