Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008411.1 Hibiscus syriacus cultivar Beakdansim tig00111186_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: 84986
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:2690 original size:18 final size:19
Alignment explanation
Indices: 2659--2705 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
2649 CGGCCAAGAG
*
2659 CATGTATCTTCATT-TAAAT
1 CATGTAT-TTCATTAAAAAT
2678 CATGTATTTCATTAAAAAT
1 CATGTATTTCATTAAAAAT
2697 CATGTATTT
1 CATGTATTT
2706 TCAAAGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (19 bp):
CATGTATTTCATTAAAAAT
Found at i:3093 original size:13 final size:11
Alignment explanation
Indices: 3052--3136 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 11
3042 ACAATCTGTC
3052 CATCACCATTAT
1 CATCACCA-TAT
3064 CA-CACCTATAT
1 CATCACC-ATAT
3075 CATCACCATAGT
1 CATCACCATA-T
3087 CCATCACCATTAT
1 -CATCACCA-TAT
*
3100 CA-CGCCTATAT
1 CATCACC-ATAT
3111 CATCACCATATT
1 CATCACCATA-T
3123 CCATCACCATAT
1 -CATCACCATAT
3135 CA
1 CA
3137 CGCCTATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 25 0.40
12 16 0.26
13 19 0.31
14 2 0.03
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:3096 original size:36 final size:36
Alignment explanation
Indices: 3049--3153 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
3039 GATACAATCT
*
3049 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
3085 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
3121 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
3154 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:3564 original size:18 final size:22
Alignment explanation
Indices: 3524--3568 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 22
3514 GTGCTACAAC
3524 AAAAAAAGCAACAAGAAAGAAG
1 AAAAAAAGCAACAAGAAAGAAG
3546 AAAAAAA-CAA-AAG-AA-AAG
1 AAAAAAAGCAACAAGAAAGAAG
3564 AAAAA
1 AAAAA
3569 GACTCCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 3 0.13
21 3 0.13
22 7 0.30
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (22 bp):
AAAAAAAGCAACAAGAAAGAAG
Found at i:3798 original size:16 final size:16
Alignment explanation
Indices: 3779--3812 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3769 TTTCTTACTA
3779 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
3795 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
3811 TT
1 TT
3813 GTTTCATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCATTTCTTTATTC
Found at i:6668 original size:19 final size:20
Alignment explanation
Indices: 6644--6694 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
6634 CGGCCAAGAG
* *
6644 CATGTATCTTCATT-TAAAT
1 CATGTATTTTCATTAAAAAT
6663 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
6683 CATGTATTTTCA
1 CATGTATTTTCA
6695 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:7079 original size:13 final size:11
Alignment explanation
Indices: 7038--7139 Score: 84
Period size: 11 Copynumber: 8.7 Consensus size: 11
7028 ACAATCTGTC
7038 CATCACCATTAT
1 CATCACCA-TAT
7050 CA-CACCTATAT
1 CATCACC-ATAT
7061 CATCACCATAGT
1 CATCACCATA-T
7073 CCATCACCATTAT
1 -CATCACCA-TAT
*
7086 CA-CGCCTATAT
1 CATCACC-ATAT
7097 CATCACCATATT
1 CATCACCATA-T
7109 CCATCACCATAT
1 -CATCACCATAT
7121 CA-CACCTATAT
1 CATCACC-ATAT
*
7132 TATCACCA
1 CATCACCA
7140 ACTTATAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 23
0.75 0.03 0.23
Matches are distributed among these distances:
10 4 0.05
11 31 0.41
12 20 0.26
13 19 0.25
14 2 0.03
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:7082 original size:36 final size:36
Alignment explanation
Indices: 7035--7139 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
7025 GATACAATCT
7035 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
*
7071 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
* *
7107 TTCCATCACCA-TATCACACCTATATTATCACCA
1 GTCCATCACCATTATCACACCTATATCATCACCA
7140 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACACCTATATCATCACCATA
Found at i:9613 original size:10 final size:9
Alignment explanation
Indices: 9578--9676 Score: 81
Period size: 10 Copynumber: 10.3 Consensus size: 9
9568 GCTGCTGGAA
*
9578 ACCGGTTTA
1 ACCGGTTTG
*
9587 ACCGGTTTTCA
1 ACCGG-TTT-G
9598 ACCGGTTCTG
1 ACCGGTT-TG
9608 ACCGGTTTG
1 ACCGGTTTG
*
9617 ACCGGTTTCA
1 ACCGGTTT-G
*
9627 ACCGGTTCG
1 ACCGGTTTG
9636 AACCGGTTTG
1 -ACCGGTTTG
*
9646 ACCGGTCTG
1 ACCGGTTTG
*
9655 AATCGGTTTG
1 -ACCGGTTTG
*
9665 ACCGGTCTG
1 ACCGGTTTG
9674 ACC
1 ACC
9677 CGACCGACCG
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.46
11 7 0.09
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:9622 original size:19 final size:19
Alignment explanation
Indices: 9579--9676 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 19
9569 CTGCTGGAAA
* * *
9579 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
9599 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
9618 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
9638 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
9657 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
9675 CC
1 CC
9677 CGACCGACCG
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.07
19 39 0.58
20 15 0.22
21 8 0.12
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:9640 original size:29 final size:30
Alignment explanation
Indices: 9577--9676 Score: 118
Period size: 29 Copynumber: 3.4 Consensus size: 30
9567 GGCTGCTGGA
*
9577 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
9608 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
9636 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
9665 -ACCGGTCTGACC
1 AACCGGTTTGACC
9677 CGACCGACCG
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.19
29 37 0.60
30 13 0.21
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:9697 original size:5 final size:5
Alignment explanation
Indices: 9689--9750 Score: 63
Period size: 5 Copynumber: 11.8 Consensus size: 5
9679 ACCGACCGTT
* *
9689 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GA-CC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC
9737 GACCC GACCC GACC
1 GACCC GACCC GACC
9751 GTTGATCGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
4 2 0.04
5 39 0.81
6 1 0.02
7 6 0.12
ACGTcount: A:0.19, C:0.52, G:0.23, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:9708 original size:22 final size:22
Alignment explanation
Indices: 9673--9755 Score: 152
Period size: 22 Copynumber: 3.9 Consensus size: 22
9663 TGACCGGTCT
9673 GACCCGA-CCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
9694 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
9716 GACCCGACCCGACCGTTGA-CC
1 GACCCGACCCGACCGTTGACCC
9737 GACCCGACCCGACCGTTGA
1 GACCCGACCCGACCGTTGA
9756 TCGTTGACCG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
21 28 0.46
22 33 0.54
ACGTcount: A:0.19, C:0.47, G:0.24, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:9721 original size:43 final size:43
Alignment explanation
Indices: 9673--9755 Score: 150
Period size: 43 Copynumber: 1.9 Consensus size: 43
9663 TGACCGGTCT
9673 GACCCGA-CCGACCGTTGACCCGACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGA-CCGACCCGACCCGACCGTTGACCC
9716 GACCCGACCCGACCGTTGACCGACCCGACCCGACCGTTGA
1 GACCCGACCCGACCGTTGACCGACCCGACCCGACCGTTGA
9756 TCGTTGACCG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.19, C:0.47, G:0.24, T:0.10
Consensus pattern (43 bp):
GACCCGACCCGACCGTTGACCGACCCGACCCGACCGTTGACCC
Found at i:16961 original size:10 final size:9
Alignment explanation
Indices: 16926--17024 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
16916 GCTGCTGGAA
*
16926 ACCGGTTTA
1 ACCGGTTTG
*
16935 ACCGGTTTTCA
1 ACCGG-TTT-G
16946 ACCGGTTCTG
1 ACCGGTT-TG
16956 ACCGGTTTG
1 ACCGGTTTG
*
16965 ACCGGTTTCA
1 ACCGGTTT-G
*
16975 ACCGGTTCG
1 ACCGGTTTG
*
16984 AACTGGTTTG
1 -ACCGGTTTG
*
16994 ACCGGTCTG
1 ACCGGTTTG
*
17003 AATCGGTTTG
1 -ACCGGTTTG
*
17013 ACCGGTCTG
1 ACCGGTTTG
17022 ACC
1 ACC
17025 CGACCCGACC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
9 32 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:16970 original size:19 final size:19
Alignment explanation
Indices: 16927--17024 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
16917 CTGCTGGAAA
* * *
16927 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
16947 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
16966 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
*
16986 CTGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
17005 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
17023 CC
1 CC
17025 CGACCCGACC
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
18 5 0.08
19 38 0.58
20 14 0.22
21 8 0.12
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.31
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:16991 original size:29 final size:29
Alignment explanation
Indices: 16926--17024 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
16916 GCTGCTGGAA
*
16926 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
16956 ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* * * *
16984 AACTGGTTTGACCGGTCTGAATCGGTT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
*
17013 ACCGGTCTGACC
1 ACCGGTTTGACC
17025 CGACCCGACC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 11 0.18
29 36 0.60
30 13 0.22
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:17031 original size:5 final size:5
Alignment explanation
Indices: 17021--17100 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
17011 TGACCGGTCT
* *
17021 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
* *
17070 GACCT GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
17101 GTTGATCGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 50 0.79
7 13 0.21
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:17047 original size:22 final size:22
Alignment explanation
Indices: 17021--17105 Score: 161
Period size: 22 Copynumber: 3.9 Consensus size: 22
17011 TGACCGGTCT
17021 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
17043 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
17065 GACCCGACCTGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
17087 GACCCGACCCGACCGTTGA
1 GACCCGACCCGACCGTTGA
17106 TCGTTGACCG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.19, C:0.47, G:0.24, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:32949 original size:25 final size:20
Alignment explanation
Indices: 32893--32932 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
32883 AATGAAAATG
32893 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
32913 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
32933 TGAAATGGAT
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:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (20 bp):
AAATGGAAAAAGGAAAGAAT
Found at i:33164 original size:36 final size:36
Alignment explanation
Indices: 33090--33191 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
33080 AAATGGAATT
**
33090 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
33125 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
33161 TGGTGATGATATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
33192 AACAGATTGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.33
36 43 0.67
ACGTcount: A:0.27, C:0.04, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
Found at i:33374 original size:19 final size:20
Alignment explanation
Indices: 33350--33400 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
33340 ACGCCAAGAG
* *
33350 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
33369 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
33389 CATGTATTTTCA
1 CATGTATTTTCA
33401 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:37424 original size:19 final size:20
Alignment explanation
Indices: 37400--37450 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
37390 CGGCCAAGAG
* *
37400 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
37419 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
37439 CATGTATTTTCA
1 CATGTATTTTCA
37451 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:40558 original size:90 final size:91
Alignment explanation
Indices: 40405--40586 Score: 285
Period size: 90 Copynumber: 2.0 Consensus size: 91
40395 GGGAAATGAT
* *
40405 GCTTGGCCGAATAGGGAGATAGCTCTTCATCTTGGCGCCTAAATAAACCTCATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCTCATGCAAGGCACATG
*
40469 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* *
40495 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCTCATGCAAGGCACATG
* **
40560 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
40586 G
1 G
40587 GTGTTCTAGG
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 60 0.72
91 23 0.28
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCTCATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:43464 original size:36 final size:36
Alignment explanation
Indices: 43423--43571 Score: 199
Period size: 36 Copynumber: 4.1 Consensus size: 36
43413 ATTTATAAGT
* * * * *
43423 TGGTGATAATATGGGTGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *
43459 TGGTGACGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
43495 TGGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
43531 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
43567 TGGTG
1 TGGTG
43572 TTGGACATAT
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 99 1.00
ACGTcount: A:0.30, C:0.04, G:0.38, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:43561 original size:23 final size:23
Alignment explanation
Indices: 43466--43561 Score: 56
Period size: 25 Copynumber: 4.0 Consensus size: 23
43456 ATATGGTGAC
43466 GATATAGGCGTGATAATGGAGAT
1 GATATAGGCGTGATAATGGAGAT
* * *
43489 GGACTAT-GGTGATGATAAAGGCG-T
1 -GA-TATAGGCG-TGATAATGGAGAT
* *
43513 GATA-ATG-GTGATGGACTATGGTGAT
1 GATATAGGCGTGAT--A--ATGGAGAT
43538 GATATAGGCGTGATAATGGAGAT
1 GATATAGGCGTGATAATGGAGAT
43561 G
1 G
43562 GAAGATGGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 21
0.65 0.10 0.25
Matches are distributed among these distances:
20 4 0.07
21 1 0.02
22 4 0.07
23 10 0.19
24 10 0.19
25 18 0.33
26 2 0.04
27 5 0.09
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.27
Consensus pattern (23 bp):
GATATAGGCGTGATAATGGAGAT
Found at i:43963 original size:19 final size:20
Alignment explanation
Indices: 43916--43966 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
43906 GAAATCCCTT
**
43916 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
43936 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
43955 TGAAGATACATG
1 TGAAAATACATG
43967 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:50219 original size:19 final size:20
Alignment explanation
Indices: 50195--50245 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
50185 CAGCCAAGAG
* *
50195 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
50214 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
50234 CATGTATTTTCA
1 CATGTATTTTCA
50246 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:56336 original size:24 final size:24
Alignment explanation
Indices: 56301--56379 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
56291 ACTTGGAGCC
*
56301 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGA-CACAACTTGTGGAACT
* * *
56325 TCAAGTGACACATCTTTTTGAACT
1 TCAAGTGACACAACTTGTGGAACT
* *
56349 TCAAGTGGCATAA-TTGTTGGAACT
1 TCAAGTGACACAACTTG-TGGAACT
56373 TCAAGTG
1 TCAAGTG
56380 GCATAATTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.05
24 39 0.89
25 3 0.07
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (24 bp):
TCAAGTGACACAACTTGTGGAACT
Found at i:56400 original size:24 final size:24
Alignment explanation
Indices: 56344--56394 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
56334 ACATCTTTTT
56344 GAACTTCAAGTGGCATAATTGTTG
1 GAACTTCAAGTGGCATAATTGTTG
56368 GAACTTCAAGTGGCATAATTGTTG
1 GAACTTCAAGTGGCATAATTGTTG
56392 GAA
1 GAA
56395 TGTCAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (24 bp):
GAACTTCAAGTGGCATAATTGTTG
Found at i:62157 original size:19 final size:21
Alignment explanation
Indices: 62114--62165 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
62104 GAAACCCCTT
62114 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
62135 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
62154 TGAAGATACATG
1 TGAAAATACATG
62166 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:65517 original size:8 final size:8
Alignment explanation
Indices: 65506--65530 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
65496 TCTTTTTCTT
65506 TTCTTTTC
1 TTCTTTTC
65514 TTCTTTTC
1 TTCTTTTC
65522 TTCTTTTC
1 TTCTTTTC
65530 T
1 T
65531 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:66243 original size:19 final size:20
Alignment explanation
Indices: 66201--66251 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
66191 GAAACCCCTT
66201 TGAAAATACATGATTTTAAA
1 TGAAAATACATGATTTTAAA
66221 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
66240 TGAAGATACATG
1 TGAAAATACATG
66252 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:69603 original size:8 final size:8
Alignment explanation
Indices: 69592--69616 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
69582 TCTTTTTCTT
69592 TTCTTTTC
1 TTCTTTTC
69600 TTCTTTTC
1 TTCTTTTC
69608 TTCTTTTC
1 TTCTTTTC
69616 T
1 T
69617 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:70330 original size:19 final size:21
Alignment explanation
Indices: 70287--70338 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
70277 GAAACCCCTT
70287 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
70308 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
70327 TGAAGATACATG
1 TGAAAATACATG
70339 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:75280 original size:90 final size:91
Alignment explanation
Indices: 75127--75308 Score: 249
Period size: 90 Copynumber: 2.0 Consensus size: 91
75117 TGAAAATAAT
* * * **
75127 GCTTGGCCGAATAGGGAGATAGCTCTTCATCTTGGCGTCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCCCCTAAATAAACCACATGCAAGGCACATG
*
75191 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * *
75217 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCCCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCCCCTAAATAAACCACATGCAAGGCACATG
* **
75282 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
75308 G
1 G
75309 GTGTTCTAGG
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
90 56 0.71
91 23 0.29
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (91 bp):
GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCCCCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:83488 original size:90 final size:91
Alignment explanation
Indices: 83307--83480 Score: 260
Period size: 90 Copynumber: 1.9 Consensus size: 91
83297 CCTAGAACAC
*
83307 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
83372 AAGAGTTCTCTCCCTATTCAACCAAG
66 AAGAGCTCTCTCCCTATTCAACCAAG
** * * * * *
83398 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
83462 AAGAGCTCTCTCCCTATTC
66 AAGAGCTCTCTCCCTATTC
83481 GGCCAAGCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 55 0.74
91 19 0.26
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCAACCAAG
Done.