Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009404.1 Hibiscus syriacus cultivar Beakdansim tig00113334_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: 40017
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:12611 original size:19 final size:19
Alignment explanation
Indices: 12587--12627 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12577 CTTAAATATA
* *
12587 GAGACATTTAGGAGTGGAT
1 GAGACATTGAGAAGTGGAT
12606 GAGACATTGAGAAGTGGAT
1 GAGACATTGAGAAGTGGAT
12625 GAG
1 GAG
12628 TTGCAAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.39, T:0.22
Consensus pattern (19 bp):
GAGACATTGAGAAGTGGAT
Found at i:12826 original size:38 final size:38
Alignment explanation
Indices: 12782--12861 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
12772 AGGCTTCAAG
*
12782 GCCACCAAGCAAGTTTATCTATCCCTAAGACTCAAGCA
1 GCCACCAAGCAAGTTTATCTACCCCTAAGACTCAAGCA
12820 GCCACCAAGCAAGTTTATCTACCCCTAAGACTCAAGCA
1 GCCACCAAGCAAGTTTATCTACCCCTAAGACTCAAGCA
12858 GCCA
1 GCCA
12862 GTGTAACATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.19
Consensus pattern (38 bp):
GCCACCAAGCAAGTTTATCTACCCCTAAGACTCAAGCA
Found at i:13813 original size:64 final size:65
Alignment explanation
Indices: 13659--13814 Score: 160
Period size: 64 Copynumber: 2.4 Consensus size: 65
13649 GAAGGTGTAT
* * * *
13659 CGATGCACAGGTAGTGCATCGATGCA--CTATTTTAATCTAAAAACATCGAATGCAATTGGTGCA
1 CGATGCACAGGTAGTGCATCGATGCATCCCA-TGTAATCAAAAAACATCGAATGCAATTGATGCA
*
13722 T
65 C
* * * * *
13723 CGATGCATAAGGCA-TGCATCGATGCATCCCA-GTAAT-AAACAAACATCGAATGTATTTTATGC
1 CGATGCA-CAGGTAGTGCATCGATGCATCCCATGTAATCAAA-AAACATCGAATGCAATTGATGC
13785 AC
64 AC
13787 CGATGCACAGGTAGTGCATCGATGCATC
1 CGATGCACAGGTAGTGCATCGATGCATC
13815 GATACACTGT
Statistics
Matches: 75, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
63 6 0.08
64 63 0.84
65 4 0.05
66 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (65 bp):
CGATGCACAGGTAGTGCATCGATGCATCCCATGTAATCAAAAAACATCGAATGCAATTGATGCAC
Found at i:14811 original size:105 final size:104
Alignment explanation
Indices: 14584--14803 Score: 370
Period size: 105 Copynumber: 2.1 Consensus size: 104
14574 GTCGAGGGTC
*
14584 TATGTGGTCCTTCGGA-ACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 TATGTGGTCCTTCGGACATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
* *
14648 CTTGATCCTTGGCATATGTATATAATTCTTAAGGAATGA
66 CTTGATCCCTAGCATATGTATATAATTCTTAAGGAATGA
*
14687 TATGTGGTCCTTCGAGACATATATATGTATTTTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TATGTGGTCCTTCG-GACATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
* *
14752 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
65 ACTTGATCCCTAGCATATGTATATAATTCTTAAGGAATGA
14792 TATGTGGTCCTT
1 TATGTGGTCCTT
14804 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 14 0.13
104 2 0.02
105 93 0.85
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (104 bp):
TATGTGGTCCTTCGGACATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
CTTGATCCCTAGCATATGTATATAATTCTTAAGGAATGA
Found at i:14886 original size:23 final size:23
Alignment explanation
Indices: 14810--14887 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
14800 CCTTATGGAC
*
14810 ATTATTATATGGCACTAT-GGTGCA
1 ATTA-TATGTGGCACT-TCGGTGCA
* * * *
14834 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
14857 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
14880 ATTATATG
1 ATTATATG
14888 AGCTGCGGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTTCGGTGCA
Found at i:15803 original size:181 final size:181
Alignment explanation
Indices: 15418--15802 Score: 630
Period size: 181 Copynumber: 2.1 Consensus size: 181
15408 ATTAAATTTT
* *
15418 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAATCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
15483 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTATATAAATTTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTATATAAAATTTTT
* *
15548 ATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTAATTAAA
131 ATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTAATTAAA
*
15599 AAATATTAAATATATTATATATAACATATGGG-TTAAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
*
15663 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATT-AAAAA-TTATATAAAATT
*
15728 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
128 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTT-AATTAAA
* *
15783 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
15803 AATTATAAAA
Statistics
Matches: 190, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
180 3 0.02
181 103 0.54
182 5 0.03
183 62 0.33
184 17 0.09
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (181 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTATATAAAATTTTT
ATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTAATTAAA
Found at i:19650 original size:7 final size:7
Alignment explanation
Indices: 19638--19668 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
19628 GTCAAAGAAA
19638 GTCAACG
1 GTCAACG
19645 GTCAACG
1 GTCAACG
19652 GTCAACG
1 GTCAACG
19659 GTCAACG
1 GTCAACG
19666 GTC
1 GTC
19669 GGGTCGGGTC
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:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:19675 original size:5 final size:5
Alignment explanation
Indices: 19665--19710 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
19655 AACGGTCAAC
*
19665 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTC
19711 AACGGTCAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 33 0.89
7 4 0.11
ACGTcount: A:0.04, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:19702 original size:27 final size:27
Alignment explanation
Indices: 19651--19723 Score: 119
Period size: 27 Copynumber: 2.6 Consensus size: 27
19641 AACGGTCAAC
19651 GGTCAACGGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTC-A-GGTCGGGTCGGGTCG
*
19680 GGTCAACGGTCGGGTCGGGTCGGGTCG
1 GGTCAACGGTCAGGTCGGGTCGGGTCG
19707 GGTCAACGGTCAGGTCG
1 GGTCAACGGTCAGGTCG
19724 AGTCAGACCG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 31 0.74
29 11 0.26
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.18
Consensus pattern (27 bp):
GGTCAACGGTCAGGTCGGGTCGGGTCG
Found at i:19723 original size:22 final size:22
Alignment explanation
Indices: 19658--19705 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
19648 AACGGTCAAC
19658 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
19680 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
19702 GGTC
1 GGTC
19706 GGGTCAACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:19742 original size:9 final size:9
Alignment explanation
Indices: 19725--19822 Score: 79
Period size: 9 Copynumber: 10.2 Consensus size: 9
19715 GTCAGGTCGA
*
19725 GTCAGACCG
1 GTCAAACCG
19734 GTCAAACCG
1 GTCAAACCG
*
19743 GTTCAGACCG
1 G-TCAAACCG
19753 GTCAAACCG
1 GTCAAACCG
*
19762 GTTCGAACCAG
1 G-TCAAACC-G
* *
19773 TTGAAACCG
1 GTCAAACCG
19782 GTCAAACCG
1 GTCAAACCG
19791 GTCAGAACCG
1 GTCA-AACCG
*
19801 GTTGAAAACCG
1 G-T-CAAACCG
*
19812 GTTAAACCG
1 GTCAAACCG
19821 GT
1 GT
19823 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
9 37 0.51
10 26 0.36
11 8 0.11
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
GTCAAACCG
Found at i:19748 original size:19 final size:19
Alignment explanation
Indices: 19726--19823 Score: 92
Period size: 19 Copynumber: 5.1 Consensus size: 19
19716 TCAGGTCGAG
19726 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
19745 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
19764 TC-GAACCAGTTGAAACCGG-
1 TCAG-ACC-GGTCAAACCGGT
*
19783 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
19803 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
19823 T
1 T
19824 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.06
19 35 0.53
20 18 0.27
21 9 0.14
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:19782 original size:29 final size:31
Alignment explanation
Indices: 19749--19823 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
19739 ACCGGTTCAG
19749 ACCGGTCAAACCGGTTC-GAACCAGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCAGTTGAAA
*
19778 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCAGTTGAAA
*
19808 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
19824 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.56
30 15 0.37
31 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCAGTTGAAA
Found at i:19812 original size:30 final size:29
Alignment explanation
Indices: 19766--19822 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
19756 AAACCGGTTC
19766 GAACCAGTTGAAACCGGTCAAACCGGTCA
1 GAACCAGTTGAAACCGGTCAAACCGGTCA
* *
19795 GAACCGGTTGAAAACCGGTTAAACCGGT
1 GAACCAGTTG-AAACCGGTCAAACCGGT
19823 TTCCAGCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (29 bp):
GAACCAGTTGAAACCGGTCAAACCGGTCA
Found at i:26987 original size:7 final size:7
Alignment explanation
Indices: 26975--27005 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
26965 GTCAAAGAAA
26975 GTCAACG
1 GTCAACG
26982 GTCAACG
1 GTCAACG
26989 GTCAACG
1 GTCAACG
26996 GTCAACG
1 GTCAACG
27003 GTC
1 GTC
27006 GGGTCGGGTC
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:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:27039 original size:27 final size:27
Alignment explanation
Indices: 26988--27060 Score: 119
Period size: 27 Copynumber: 2.6 Consensus size: 27
26978 AACGGTCAAC
*
26988 GGTCAACGGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCGGGTCG
27017 GGTCAACGGTCGGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCGGGTCG
27044 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
27061 AGTCAGACCG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
27 32 0.74
29 11 0.26
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (27 bp):
GGTCAACGGTCGGGTCGGGTCGGGTCG
Found at i:27060 original size:5 final size:5
Alignment explanation
Indices: 27002--27047 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
26992 AACGGTCAAC
*
27002 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTC
27048 AACGGTCGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 33 0.89
7 4 0.11
ACGTcount: A:0.04, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:27060 original size:22 final size:22
Alignment explanation
Indices: 26995--27042 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
26985 AACGGTCAAC
26995 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
27017 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
27039 GGTC
1 GGTC
27043 GGGTCAACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:27085 original size:19 final size:19
Alignment explanation
Indices: 27063--27160 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
27053 TCGGGTCGAG
27063 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
27082 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
27101 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
27120 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
27140 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
27160 T
1 T
27161 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:27091 original size:10 final size:9
Alignment explanation
Indices: 27062--27159 Score: 88
Period size: 9 Copynumber: 10.2 Consensus size: 9
27052 GTCGGGTCGA
*
27062 GTCAGACCG
1 GTCAAACCG
27071 GTCAAACCG
1 GTCAAACCG
*
27080 GTTCAGACCG
1 G-TCAAACCG
27090 GTCAAACCG
1 GTCAAACCG
*
27099 GTTCGAACCG
1 G-TCAAACCG
*
27109 GTTGAAACCG
1 G-TCAAACCG
27119 GTCAAACCG
1 GTCAAACCG
27128 GTCAGAACCG
1 GTCA-AACCG
*
27138 GTTGAAAACCG
1 G-T-CAAACCG
*
27149 GTTAAACCG
1 GTCAAACCG
27158 GT
1 GT
27160 TTCCAGCAGC
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
9 36 0.48
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (9 bp):
GTCAAACCG
Found at i:27118 original size:29 final size:28
Alignment explanation
Indices: 27074--27160 Score: 61
Period size: 29 Copynumber: 3.0 Consensus size: 28
27064 CAGACCGGTC
*
27074 AAACCGGTTCAGACCGGTCAAACCGGTTCG
1 AAACCGG-TCAAACCGGTCAAACCGGTT-G
* *
27104 -AACCGGTTGAAACCGGTCAAACCGG-TC
1 AAACCGG-TCAAACCGGTCAAACCGGTTG
* *
27131 AGAACCGGTTGAAAACCGGTTAAACCGGTT
1 A-AACCGG-T-CAAACCGGTCAAACCGGTT
27161 TCCAGCAGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 31 0.65
30 15 0.31
31 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (28 bp):
AAACCGGTCAAACCGGTCAAACCGGTTG
Found at i:30228 original size:21 final size:21
Alignment explanation
Indices: 30202--30243 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
30192 ACGAATTCAA
30202 TGTAGCAGTGCATCGATGCAC
1 TGTAGCAGTGCATCGATGCAC
*
30223 TGTAGCAGTGTATCGATGCAC
1 TGTAGCAGTGCATCGATGCAC
30244 AATATTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TGTAGCAGTGCATCGATGCAC
Found at i:30288 original size:21 final size:21
Alignment explanation
Indices: 30264--30304 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30254 CGAAATTTAG
* *
30264 TGCATTGGTGCACTGTAGCAA
1 TGCATCGGTGCACTATAGCAA
*
30285 TGCATCGTTGCACTATAGCA
1 TGCATCGGTGCACTATAGCA
30305 CTATTTATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCATCGGTGCACTATAGCAA
Found at i:32293 original size:19 final size:19
Alignment explanation
Indices: 32240--32332 Score: 62
Period size: 19 Copynumber: 4.9 Consensus size: 19
32230 ATTACAAATT
* *
32240 TTATTTTCTGAATCAGAAC
1 TTATTTTCAGAATCATAAC
* * *
32259 TTATTTCCATATTCATAAC
1 TTATTTTCAGAATCATAAC
* *
32278 TTATTTTCAGACTCATAGC
1 TTATTTTCAGAATCATAAC
** *
32297 TTATTGGCA-AATTCATAGC
1 TTATTTTCAGAA-TCATAAC
* *
32316 TAATTTTCAGATTCATA
1 TTATTTTCAGAATCATA
32333 GTTCACTTTT
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
18 1 0.02
19 54 0.96
20 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (19 bp):
TTATTTTCAGAATCATAAC
Found at i:32300 original size:38 final size:38
Alignment explanation
Indices: 32240--32333 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 38
32230 ATTACAAATT
* * * * *
32240 TTATTTTCTGAATCAGAACTTATTTCCATATTCATAAC
1 TTATTTTCAGAATCATAGCTTATTGCCAAATTCATAAC
* * *
32278 TTATTTTCAGACTCATAGCTTATTGGCAAATTCATAGC
1 TTATTTTCAGAATCATAGCTTATTGCCAAATTCATAAC
* *
32316 TAATTTTCAGATTCATAG
1 TTATTTTCAGAATCATAG
32334 TTCACTTTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.43
Consensus pattern (38 bp):
TTATTTTCAGAATCATAGCTTATTGCCAAATTCATAAC
Found at i:32333 original size:19 final size:19
Alignment explanation
Indices: 32258--32333 Score: 80
Period size: 19 Copynumber: 4.0 Consensus size: 19
32248 TGAATCAGAA
* * *
32258 CTTATTTCCATATTCATAA
1 CTTATTTTCAGATTCATAG
*
32277 CTTATTTTCAGACTCATAG
1 CTTATTTTCAGATTCATAG
** *
32296 CTTATTGGCAAATTCATAG
1 CTTATTTTCAGATTCATAG
*
32315 CTAATTTTCAGATTCATAG
1 CTTATTTTCAGATTCATAG
32334 TTCACTTTTA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (19 bp):
CTTATTTTCAGATTCATAG
Found at i:35872 original size:60 final size:60
Alignment explanation
Indices: 35749--35864 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
35739 TTCTCCTGAT
* * * * *
35749 TATAGGATATTGCTTTGTTGAGTCTCTTGACTATTAAAAGTTATAAAATTCTCTCTCAAC
1 TATAGGATATTGCTTTGTTGAGTCTCCTGACTATTAAAACTTACAAAATACTCACTCAAC
* *
35809 TATAGGA-AGTTGCTTTGTTGAGT-TCACTGACTATTAAAACTTGCAAAATAGTCACT
1 TATAGGATA-TTGCTTTGTTGAGTCTC-CTGACTATTAAAACTTACAAAATACTCACT
35865 TGACTATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (60 bp):
TATAGGATATTGCTTTGTTGAGTCTCCTGACTATTAAAACTTACAAAATACTCACTCAAC
Found at i:37673 original size:23 final size:23
Alignment explanation
Indices: 37642--37710 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
37632 CACCACAACT
* *
37642 CGTATAATTACACTGAAGTGCCA
1 CGTAGAATTGCACTGAAGTGCCA
* *
37665 CGTAGAATTGCACTGGAGTGCCG
1 CGTAGAATTGCACTGAAGTGCCA
* *
37688 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACTGAAGTGCCA
37711 TATAATAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACTGAAGTGCCA
Found at i:37917 original size:103 final size:103
Alignment explanation
Indices: 37733--37931 Score: 362
Period size: 103 Copynumber: 1.9 Consensus size: 103
37723 ATCCATAAGA
* *
37733 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
37798 TCACACATGTTCCAAAGAATACATATATGTCTCGAAAG
66 TCACACATGTTCCAAAGAATACATATATGTCTCGAAAG
* *
37836 ACCATATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACTAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
37901 TCACACATGTTCCAAAGAATACATATATGTC
66 TCACACATGTTCCAAAGAATACATATATGTC
37932 CCGATGGACC
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 92 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCTCGAAAG
Done.