Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003105.1 Hibiscus syriacus cultivar Beakdansim tig00006486_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: 73521
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6843 original size:19 final size:19
Alignment explanation
Indices: 6821--6891 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
6811 TACACTAGGG
6821 GAGTATCAATACCAGGGTT
1 GAGTATCAATACCAGGGTT
* **** *
6840 GAGTATCGATACTCCCCATAG
1 GAGTATCAATAC-CAGGGT-T
6861 GAGTATCAATACCAGGGTT
1 GAGTATCAATACCAGGGTT
*
6880 GAGTATCGATAC
1 GAGTATCAATAC
6892 TCCCCATAGG
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 22 0.59
20 4 0.11
21 11 0.30
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (19 bp):
GAGTATCAATACCAGGGTT
Found at i:6865 original size:40 final size:40
Alignment explanation
Indices: 6820--6912 Score: 177
Period size: 40 Copynumber: 2.3 Consensus size: 40
6810 GTACACTAGG
6820 GGAGTATCAATACCAGGGTTGAGTATCGATACTCCCCATA
1 GGAGTATCAATACCAGGGTTGAGTATCGATACTCCCCATA
6860 GGAGTATCAATACCAGGGTTGAGTATCGATACTCCCCATA
1 GGAGTATCAATACCAGGGTTGAGTATCGATACTCCCCATA
*
6900 GGAGTATCGATAC
1 GGAGTATCAATAC
6913 TTCTCCTTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (40 bp):
GGAGTATCAATACCAGGGTTGAGTATCGATACTCCCCATA
Found at i:6866 original size:21 final size:21
Alignment explanation
Indices: 6840--6913 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
6830 TACCAGGGTT
6840 GAGTATCGATACTCCCCATAG
1 GAGTATCGATACTCCCCATAG
* **** *
6861 GAGTATCAATAC-CAGGGT-T
1 GAGTATCGATACTCCCCATAG
6880 GAGTATCGATACTCCCCATAG
1 GAGTATCGATACTCCCCATAG
6901 GAGTATCGATACT
1 GAGTATCGATACT
6914 TCTCCTTTGT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 24 0.62
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (21 bp):
GAGTATCGATACTCCCCATAG
Found at i:12641 original size:21 final size:21
Alignment explanation
Indices: 12617--12680 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
12607 ATTATTATTC
12617 AATAAAAATAAATAAAAATAT
1 AATAAAAATAAATAAAAATAT
* *
12638 AATAAAAA-AGAATTATAAAT-G
1 AATAAAAATA-AA-TAAAAATAT
* *
12659 AATAAAATTCAATAAAAATAT
1 AATAAAAATAAATAAAAATAT
12680 A
1 A
12681 GTGTAAAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
20 7 0.21
21 20 0.61
22 6 0.18
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (21 bp):
AATAAAAATAAATAAAAATAT
Found at i:12645 original size:12 final size:10
Alignment explanation
Indices: 12617--12678 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
12607 ATTATTATTC
12617 AATAAAAATA
1 AATAAAAATA
12627 AATAAAAATA
1 AATAAAAATA
12637 TAATAAAAA-A
1 -AATAAAAATA
* *
12647 GAATTATAAATG
1 -AA-TAAAAATA
* *
12659 AATAAAATTC
1 AATAAAAATA
12669 AATAAAAATA
1 AATAAAAATA
12679 TAGTGTAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 26 0.63
11 15 0.37
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (10 bp):
AATAAAAATA
Found at i:12765 original size:18 final size:17
Alignment explanation
Indices: 12737--12775 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
12727 AATATTAATT
12737 TTAAAAAATATAAAATA
1 TTAAAAAATATAAAATA
* *
12754 TTAAATAAATATTAAATT
1 TTAAA-AAATATAAAATA
12772 TTAA
1 TTAA
12776 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAAATATAAAATA
Found at i:13544 original size:29 final size:31
Alignment explanation
Indices: 13478--13550 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 31
13468 TTATTATTCA
13478 TTAATTATTATTTTTAACAACAATTAATAATG
1 TTAA-TATTATTTTTAACAACAATTAATAATG
*
13510 TT--TATTCATTTTTAATAA-AATTAA-AAT-
1 TTAATATT-ATTTTTAACAACAATTAATAATG
13537 TTAATATTTATTTT
1 TTAATA-TTATTTT
13551 ATATTTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
27 2 0.06
28 3 0.08
29 17 0.47
30 12 0.33
32 2 0.06
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (31 bp):
TTAATATTATTTTTAACAACAATTAATAATG
Found at i:13635 original size:10 final size:10
Alignment explanation
Indices: 13620--13668 Score: 80
Period size: 10 Copynumber: 4.8 Consensus size: 10
13610 CTTTACATTA
13620 TATTTTTATT
1 TATTTTTATT
13630 TATTTTTATT
1 TATTTTTATT
13640 TATTTTTAATT
1 TATTTTT-ATT
*
13651 CATTTTTATT
1 TATTTTTATT
13661 TATTTTTA
1 TATTTTTA
13669 AAAAAATGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 27 0.75
11 9 0.25
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (10 bp):
TATTTTTATT
Found at i:13646 original size:21 final size:21
Alignment explanation
Indices: 13620--13669 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
13610 CTTTACATTA
*
13620 TATTTTT-ATTTATTTTTATT
1 TATTTTTAATTCATTTTTATT
13640 TATTTTTAATTCATTTTTATT
1 TATTTTTAATTCATTTTTATT
13661 TATTTTTAA
1 TATTTTTAA
13670 AAAAATGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TATTTTTAATTCATTTTTATT
Found at i:15041 original size:22 final size:22
Alignment explanation
Indices: 15013--15063 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
15003 TCAACCGATC
*
15013 GAACCGGTCCGACCGGTCGGAA
1 GAACCGGTCCGACCGGTCGAAA
15035 GAACCGGTCCGACCGGTCGAAA
1 GAACCGGTCCGACCGGTCGAAA
15057 GAACCGG
1 GAACCGG
15064 ACGACGTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.31, G:0.35, T:0.08
Consensus pattern (22 bp):
GAACCGGTCCGACCGGTCGAAA
Found at i:18475 original size:2 final size:2
Alignment explanation
Indices: 18468--18499 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18458 AAATAACTAC
18468 AT 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 AT
18500 GTTCCTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18953 original size:30 final size:32
Alignment explanation
Indices: 18877--18974 Score: 164
Period size: 32 Copynumber: 3.1 Consensus size: 32
18867 ATCTTGGTAA
*
18877 AATGATTATGAGGTTAGAGACGATCTAGCATT
1 AATGGTTATGAGGTTAGAGACGATCTAGCATT
18909 AATGGTTATGAGGTTAGAGACGATCTAGCATT
1 AATGGTTATGAGGTTAGAGACGATCTAGCATT
*
18941 AATGG-T-TGAGGTTAGAGACGATCTAGCACT
1 AATGGTTATGAGGTTAGAGACGATCTAGCATT
18971 AATG
1 AATG
18975 ATAAAGGGCA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 27 0.42
31 1 0.02
32 36 0.56
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (32 bp):
AATGGTTATGAGGTTAGAGACGATCTAGCATT
Found at i:25410 original size:195 final size:196
Alignment explanation
Indices: 25025--25417 Score: 770
Period size: 195 Copynumber: 2.0 Consensus size: 196
25015 TCCCAAATCC
25025 TAGGTAAAATATTTTTGTAGCAAGATTAGCCAATAAAAGTTTATATAAACACCCCAAATCCAGAT
1 TAGGTAAAATATTTTTGTAGCAAGATTAGCCAATAAAAGTTTATATAAACACCCCAAATCCAGAT
*
25090 ACCGGCAAGCTCCAGGCAATCTGAACCACTTTTGTCTTGCTGATATTGGAGGATTTGGATATCAC
66 ACCAGCAAGCTCCAGGCAATCTGAACCACTTTTGTCTTGCTGATATTGGAGGATTTGGATATCAC
25155 AGACTTGTTTAATTGGTTTTTGTTCAGGACAATTACTCCTCCTTCGACAAAATAAAAAGAAATTG
131 AGACTTGTTTAATTGGTTTTTGTTCAGGACAATTACTCCTCCTTCGACAAAATAAAAAGAAATTG
25220 A
196 A
25221 TAGGTAAAATATTTTTGTAGCAAGATTAGCCAATAAAAGTTTATATAAACACCCCAAATCCAGAT
1 TAGGTAAAATATTTTTGTAGCAAGATTAGCCAATAAAAGTTTATATAAACACCCCAAATCCAGAT
25286 ACCAGCAAGCTCCAGGCAATCTGAACCAC-TTTGTCTTGCTGATATTGGAGGATTTGGATATCAC
66 ACCAGCAAGCTCCAGGCAATCTGAACCACTTTTGTCTTGCTGATATTGGAGGATTTGGATATCAC
25350 AGACTTGTTTAATTGGTTTTTGTTCAGGACAATTACTCCTCCTTCGACAAAATAAAAAGAAATTG
131 AGACTTGTTTAATTGGTTTTTGTTCAGGACAATTACTCCTCCTTCGACAAAATAAAAAGAAATTG
25415 A
196 A
25416 TA
1 TA
25418 ATGGTACCAA
Statistics
Matches: 196, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
195 103 0.53
196 93 0.47
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (196 bp):
TAGGTAAAATATTTTTGTAGCAAGATTAGCCAATAAAAGTTTATATAAACACCCCAAATCCAGAT
ACCAGCAAGCTCCAGGCAATCTGAACCACTTTTGTCTTGCTGATATTGGAGGATTTGGATATCAC
AGACTTGTTTAATTGGTTTTTGTTCAGGACAATTACTCCTCCTTCGACAAAATAAAAAGAAATTG
A
Found at i:28225 original size:16 final size:17
Alignment explanation
Indices: 28195--28227 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
28185 ACTCATAGGA
28195 CAATTCAGTGATGACAT
1 CAATTCAGTGATGACAT
28212 CAATTCAG-GATGACAT
1 CAATTCAGTGATGACAT
28228 AAGATGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (17 bp):
CAATTCAGTGATGACAT
Found at i:32841 original size:9 final size:9
Alignment explanation
Indices: 32827--32880 Score: 72
Period size: 9 Copynumber: 5.7 Consensus size: 9
32817 CTGCTGGAAA
32827 ACCGGTTTG
1 ACCGGTTTG
32836 ACCGGTTCTG
1 ACCGGTT-TG
32846 AACCGGTTTG
1 -ACCGGTTTG
*
32856 ACCGGTCTG
1 ACCGGTTTG
32865 AACCGGTTTG
1 -ACCGGTTTG
32875 ACCGGT
1 ACCGGT
32881 CTGAACTAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 21 0.52
10 12 0.30
11 7 0.17
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:32896 original size:19 final size:19
Alignment explanation
Indices: 32826--32886 Score: 113
Period size: 19 Copynumber: 3.2 Consensus size: 19
32816 GCTGCTGGAA
32826 AACCGGTTTGACCGGTTCTG
1 AACCGGTTTGACCGG-TCTG
32846 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
32865 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
32884 AAC
1 AAC
32887 TAGGTTGACC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 26 0.63
20 15 0.37
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:32912 original size:17 final size:17
Alignment explanation
Indices: 32890--32947 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
32880 TCTGAACTAG
32890 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
32907 GTTGACCCGACCCGAAT
1 GTTGACCCGACCCGACT
32924 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
32941 GTTGACC
1 GTTGACC
32948 GTTGACCGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.19, C:0.38, G:0.24, T:0.19
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:32953 original size:7 final size:7
Alignment explanation
Indices: 32941--32973 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
32931 CGACCCGACT
32941 GTTGACC
1 GTTGACC
32948 GTTGACC
1 GTTGACC
32955 G-TGACC
1 GTTGACC
32961 GTTGACC
1 GTTGACC
32968 GTTGAC
1 GTTGAC
32974 TTTCTTTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GTTGACC
Found at i:32961 original size:13 final size:13
Alignment explanation
Indices: 32943--32969 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32933 ACCCGACTGT
32943 TGACCGTTGACCG
1 TGACCGTTGACCG
32956 TGACCGTTGACCG
1 TGACCGTTGACCG
32969 T
1 T
32970 TGACTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.26
Consensus pattern (13 bp):
TGACCGTTGACCG
Found at i:33916 original size:32 final size:31
Alignment explanation
Indices: 33843--33919 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
33833 TTAATGTGAC
* *
33843 TCTTAGGTAGGCTCTGCGACCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
** * **
33874 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGACCCTAAGAT-CAT
33906 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
33920 CATGGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
Found at i:36775 original size:15 final size:15
Alignment explanation
Indices: 36752--36829 Score: 138
Period size: 15 Copynumber: 5.2 Consensus size: 15
36742 CGTAGGACTC
36752 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
36767 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
36782 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
36797 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
36812 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
36827 CTA
1 CTA
36830 TTATACCCTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:36788 original size:30 final size:30
Alignment explanation
Indices: 36752--36829 Score: 156
Period size: 30 Copynumber: 2.6 Consensus size: 30
36742 CGTAGGACTC
36752 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
36782 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
36812 CTACATCCCGAAGGACTA
1 CTACATCCCGAAGGACTA
36830 TTATACCCTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGGA
Found at i:36956 original size:29 final size:29
Alignment explanation
Indices: 36914--36987 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
36904 TTTCATATGT
36914 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
36942 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
36971 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
36988 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:37020 original size:12 final size:12
Alignment explanation
Indices: 37003--37048 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
36993 TATCATGTTC
*
37003 TCATATCACAGG
1 TCATATCACAGA
*
37015 TCATATCACATA
1 TCATATCACAGA
*
37027 TCATATCACATA
1 TCATATCACAGA
*
37039 GCATATCACA
1 TCATATCACA
37049 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:37034 original size:24 final size:24
Alignment explanation
Indices: 37003--37049 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
36993 TATCATGTTC
*
37003 TCATATCACA-GGTCATATCACATA
1 TCATATCACATAG-CATATCACATA
37027 TCATATCACATAGCATATCACAT
1 TCATATCACATAGCATATCACAT
37050 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (24 bp):
TCATATCACATAGCATATCACATA
Found at i:37049 original size:12 final size:12
Alignment explanation
Indices: 37016--37049 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
37006 TATCACAGGT
*
37016 CATATCACATAT
1 CATATCACATAG
37028 CATATCACATAG
1 CATATCACATAG
37040 CATATCACAT
1 CATATCACAT
37050 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (12 bp):
CATATCACATAG
Found at i:37466 original size:64 final size:62
Alignment explanation
Indices: 37358--37582 Score: 229
Period size: 64 Copynumber: 3.5 Consensus size: 62
37348 TAATGAAGGT
* * * ***
37358 ATGCATCGATGCACTACTGATGCATCGGTGCATCCAAGGT--ATTCGATGTAGTATTATTGTTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CCAA-TTACATTCGATGT--TATTATTAACGG
37421 G
62 G
* *
37422 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTACATTCGATGTTTCATTAATAACGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATG-TT-ATTATTAACGGG
* ****
37486 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTTATTATTTAAAAAT
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTATTA-TTAACGGG
**
37549 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
37583 ATTCATATAA
Statistics
Matches: 138, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
62 5 0.04
63 11 0.08
64 121 0.88
65 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTATTATTAACGGG
Found at i:43180 original size:15 final size:15
Alignment explanation
Indices: 43157--43204 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
43147 CGTAGGACTC
43157 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
43172 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
43187 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
43202 CTA
1 CTA
43205 TTATACCCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:43331 original size:29 final size:29
Alignment explanation
Indices: 43289--43362 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
43279 TTTCATATGT
43289 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
43317 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
43346 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
43363 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:43395 original size:12 final size:12
Alignment explanation
Indices: 43378--43423 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
43368 TATCATGTTC
*
43378 TCATATCACAGG
1 TCATATCACAGA
*
43390 TCATATCACATA
1 TCATATCACAGA
*
43402 TCATATCACATA
1 TCATATCACAGA
*
43414 GCATATCACA
1 TCATATCACA
43424 TGAACATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (12 bp):
TCATATCACAGA
Found at i:43409 original size:24 final size:24
Alignment explanation
Indices: 43378--43424 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43368 TATCATGTTC
*
43378 TCATATCACA-GGTCATATCACATA
1 TCATATCACATAG-CATATCACATA
43402 TCATATCACATAGCATATCACAT
1 TCATATCACATAGCATATCACAT
43425 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (24 bp):
TCATATCACATAGCATATCACATA
Found at i:43424 original size:12 final size:12
Alignment explanation
Indices: 43391--43424 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
43381 TATCACAGGT
*
43391 CATATCACATAT
1 CATATCACATAG
43403 CATATCACATAG
1 CATATCACATAG
43415 CATATCACAT
1 CATATCACAT
43425 GAACATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (12 bp):
CATATCACATAG
Found at i:43841 original size:64 final size:64
Alignment explanation
Indices: 43733--43893 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
43723 TAATGAAGGT
* * * * ***
43733 ATGCATCGATGCACTACTGATGCATCGGTGCATCCAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCCAAGGCATTCGATGT-GTCATTAATAACGGG
* * *
43797 ATGCATCGATGCACTCCTTATGCATCGATGCA-CCAATTGCATTCGATGTTTCATTAATAACGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCCAA-GGCATTCGATGTGTCATTAATAACGGG
43861 ATGCATCGATGCACTACTTATGCATCGATGCAT
1 ATGCATCGATGCACTACTTATGCATCGATGCAT
43894 TTATTACATT
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 5 0.06
64 78 0.94
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATCCAAGGCATTCGATGTGTCATTAATAACGGG
Found at i:43904 original size:64 final size:65
Alignment explanation
Indices: 43794--43957 Score: 199
Period size: 64 Copynumber: 2.6 Consensus size: 65
43784 TATTATTGTT
* *
43794 GGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTT-TCA-TTAATAA
1 GGGATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTATCATTTAA-AA
*
43857 C
65 A
*** *
43858 GGGATGCATCGATGCACTACTTATGCATCGATGCATTTATTACATTCGATGTTATTATTTAAAAA
1 GGGATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTATCATTTAAAAA
** **
43923 TAG-TGCATCGATGCACTACCAATGCATCGATGCAC
1 GGGATGCATCGATGCACTACTTATGCATCGATGCAC
43958 ATTCATATAA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 77 0.90
65 5 0.06
66 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (65 bp):
GGGATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTATCATTTAAAAA
Found at i:48854 original size:7 final size:7
Alignment explanation
Indices: 48842--48882 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
48832 CCGACCCAAT
48842 CGTTGAC
1 CGTTGAC
48849 CGTTGAC
1 CGTTGAC
48856 CGTTGAC
1 CGTTGAC
*
48863 TG-TGAC
1 CGTTGAC
48869 CGTTGAC
1 CGTTGAC
48876 CGTTGAC
1 CGTTGAC
48883 TTTATTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (7 bp):
CGTTGAC
Found at i:48870 original size:13 final size:14
Alignment explanation
Indices: 48842--48882 Score: 66
Period size: 13 Copynumber: 3.0 Consensus size: 14
48832 CCGACCCAAT
48842 CGTTGACCGTTGAC
1 CGTTGACCGTTGAC
*
48856 CGTTGACTG-TGAC
1 CGTTGACCGTTGAC
48869 CGTTGACCGTTGAC
1 CGTTGACCGTTGAC
48883 TTTATTTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (14 bp):
CGTTGACCGTTGAC
Found at i:48870 original size:20 final size:20
Alignment explanation
Indices: 48845--48883 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
48835 ACCCAATCGT
48845 TGACCGTTGACCGTTGACTG
1 TGACCGTTGACCGTTGACTG
48865 TGACCGTTGACCGTTGACT
1 TGACCGTTGACCGTTGACT
48884 TTATTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (20 bp):
TGACCGTTGACCGTTGACTG
Found at i:49820 original size:63 final size:63
Alignment explanation
Indices: 49752--49875 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
49742 CTAATGTGAC
* * * * *
49752 TCTTAGGTAGGCTCTACGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGACCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
49815 TCTTAGGTAGGCCCCACGACCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGACCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
49876 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGACCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:49826 original size:32 final size:31
Alignment explanation
Indices: 49752--49828 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
49742 CTAATGTGAC
* *
49752 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * **
49783 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
49815 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
49829 CACGACCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:51619 original size:17 final size:17
Alignment explanation
Indices: 51597--51648 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
51587 AATTTATTAC
51597 AAATAATTTAAATAAAA
1 AAATAATTTAAATAAAA
* *
51614 AAATAAATAAAATAAAA
1 AAATAATTTAAATAAAA
*
51631 AATATAATGTAAATAAAA
1 AA-ATAATTTAAATAAAA
51649 CGTATATCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (17 bp):
AAATAATTTAAATAAAA
Found at i:67264 original size:17 final size:15
Alignment explanation
Indices: 67242--67281 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
67232 AAATTAGGTT
67242 TTTAAAAAATAATAATA
1 TTTAAAAAA-AATAA-A
67259 TTTAAAAAAAATAAA
1 TTTAAAAAAAATAAA
67274 TTTCAAAA
1 TTT-AAAA
67282 TAAACAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 9 0.41
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TTTAAAAAAAATAAA
Found at i:67265 original size:16 final size:15
Alignment explanation
Indices: 67246--67284 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
67236 TAGGTTTTTA
67246 AAAAATAATAATATTT
1 AAAAATAATAA-ATTT
*
67262 AAAAAAAATAAATTT
1 AAAAATAATAAATTT
*
67277 CAAAATAA
1 AAAAATAA
67285 ACAGATTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAATAATAAATTT
Found at i:67565 original size:22 final size:21
Alignment explanation
Indices: 67516--67565 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
67506 TAATTTAAAA
67516 TAATTTAATAAATTTAATTTT
1 TAATTTAATAAATTTAATTTT
*
67537 TATATTTAA-AAACTTTATTATTT
1 TA-ATTTAATAAA-TTTAAT-TTT
67560 TAATTT
1 TAATTT
67566 TTTTCCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.20
22 15 0.60
23 5 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATTTAATAAATTTAATTTT
Done.