Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002072.1 Hibiscus syriacus cultivar Beakdansim tig00004229_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: 80012
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:4573 original size:112 final size:112
Alignment explanation
Indices: 4372--4600 Score: 370
Period size: 112 Copynumber: 2.0 Consensus size: 112
4362 CGAAATGCCA
* * **
4372 AAATGGTATTTCACCTCATTATGAATACCATGGGTGGCACATTTTATGTCGAAAATGCACTGTTA
1 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGAACATTTTATGTAAAAAATGCACTGTTA
*
4437 TGCATTAAGCAAAATTGATCGATAACTTTCATACACGAAGTATGTCG
66 TGCATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCG
*
4484 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGAACCTTTTATGTAAAAAATGCA-TCGTT
1 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGAACATTTTATGTAAAAAATGCACT-GTT
* *
4548 ATGCATTAAGCAAAATCGATTGATAACTTTCATACATGAAGTATGTCG
65 ATGCATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCG
4596 AAATG
1 AAATG
4601 CACCTATAAC
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
111 1 0.01
112 107 0.99
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (112 bp):
AAATGGTAATTCACCTCATTATGAATACCATGGGTGGAACATTTTATGTAAAAAATGCACTGTTA
TGCATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCG
Found at i:14228 original size:14 final size:16
Alignment explanation
Indices: 14209--14242 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
14199 CGAAATTGAA
14209 TAAAAAC-AA-AAAAT
1 TAAAAACGAATAAAAT
14223 TAAAAACGAATAAAAT
1 TAAAAACGAATAAAAT
14239 TAAA
1 TAAA
14243 TATAGATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 2 0.11
16 9 0.50
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (16 bp):
TAAAAACGAATAAAAT
Found at i:26981 original size:23 final size:23
Alignment explanation
Indices: 26951--27008 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
26941 ATACTGAAAA
26951 GAGTATCGATACACTTTACATAG
1 GAGTATCGATACACTTTACATAG
*
26974 GAGTATCGATACACTTTATATAG
1 GAGTATCGATACACTTTACATAG
*
26997 TAGTATCGATAC
1 GAGTATCGATAC
27009 CATGACCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (23 bp):
GAGTATCGATACACTTTACATAG
Found at i:31017 original size:17 final size:17
Alignment explanation
Indices: 30995--31039 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
30985 ATAAAGCAAT
*
30995 TAAATAAAGGTGATGAA
1 TAAATAAAGATGATGAA
31012 TAAATAAAGATGATGAA
1 TAAATAAAGATGATGAA
31029 TAAATAAAGAT
1 TAAATAAAGAT
31040 AAGAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (17 bp):
TAAATAAAGATGATGAA
Found at i:41771 original size:10 final size:10
Alignment explanation
Indices: 41726--41773 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
41716 AACGCTGGAA
41726 ACCGGTTTTG
1 ACCGGTTTTG
* *
41736 ACCAG-TTTA
1 ACCGGTTTTG
*
41745 ATCGGTTTTG
1 ACCGGTTTTG
41755 AACCGGTTTTG
1 -ACCGGTTTTG
41766 ACCGGTTT
1 ACCGGTTT
41774 GCCCTGTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
9 6 0.20
10 15 0.50
11 9 0.30
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:41806 original size:18 final size:18
Alignment explanation
Indices: 41783--41841 Score: 109
Period size: 18 Copynumber: 3.3 Consensus size: 18
41773 TGCCCTGTCA
*
41783 TGACCCGACCCAACCCGT
1 TGACCCGACCCGACCCGT
41801 TGACCCGACCCGACCCGT
1 TGACCCGACCCGACCCGT
41819 TGACCCGACCCGACCCGT
1 TGACCCGACCCGACCCGT
41837 TGACC
1 TGACC
41842 GGTGCTATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.19, C:0.49, G:0.20, T:0.12
Consensus pattern (18 bp):
TGACCCGACCCGACCCGT
Found at i:41965 original size:29 final size:29
Alignment explanation
Indices: 41842--41978 Score: 102
Period size: 29 Copynumber: 4.8 Consensus size: 29
41832 CCCGTTGACC
****
41842 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCAAAATT
* *
41871 GGTGCTATTCTGGGAATTAATTC-GAACT
1 GGTGCTATTCTGGGAATTAATTCAAAATT
* * * *
41899 AGTGCTATTTTGGTAATT--TTCGGGAAAA-A
1 GGTGCTATTCTGGGAATTAATTC---AAAATT
* *
41928 AGTGATATTCTGGGAATTAATTCAAAATT
1 GGTGCTATTCTGGGAATTAATTCAAAATT
*
41957 GGTGCTATTTTGGGAATTAATT
1 GGTGCTATTCTGGGAATTAATT
41979 AGAAAAGGGT
Statistics
Matches: 86, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
26 3 0.03
28 21 0.24
29 57 0.66
30 2 0.02
31 3 0.03
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCAAAATT
Found at i:41989 original size:29 final size:28
Alignment explanation
Indices: 41933--42024 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 28
41923 AAAAAAGTGA
* **
41933 TATTCTGGGAATTAATTCAAAATTGGTGC
1 TATTTTGGGAATTAATT-AAAAAGGGTGC
41962 TATTTTGGGAATTAATTAGAAAAGGGTGC
1 TATTTTGGGAATTAATTA-AAAAGGGTGC
* * *
41991 AATTTTGGTAATTATTGTAAAAAGGGTGC
1 TATTTTGGGAATTAAT-TAAAAAGGGTGC
42020 TATTT
1 TATTT
42025 GTGTAAAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.02
29 51 0.94
30 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (28 bp):
TATTTTGGGAATTAATTAAAAAGGGTGC
Found at i:43127 original size:118 final size:118
Alignment explanation
Indices: 42798--43130 Score: 588
Period size: 112 Copynumber: 2.9 Consensus size: 118
42788 TTACTGTTAC
42798 TGGGTGATTGGTGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGT
1 TGGGTGATTGGTGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGT
42863 AAGTCCTTACTGGTGTGCAGGTGGGTGTACGGTTCTGGGGAACCTACACATTT
66 AAGTCCTTACTGGTGTGCAGGTGGGTGTACGGTTCTGGGGAACCTACACATTT
*
42916 T-GG-G--T-G-GTGATTGGATGGGAAAGTTATTACCGCATGCTCCTCAGCTTTGTGCTCAGGGT
1 TGGGTGATTGGTGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGT
42975 AAGTCCTTACTGGTGTGCAGGTGGGTGTACGGTTCTGGGGAACCTACACATTT
66 AAGTCCTTACTGGTGTGCAGGTGGGTGTACGGTTCTGGGGAACCTACACATTT
*
43028 TGGGTGATTGGTGTGATTGGATGGAAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGT
1 TGGGTGATTGGTGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGT
* *
43093 AAGTCCTTACTGGTGTGCAGGTAGGTGTATGGTTCTGG
66 AAGTCCTTACTGGTGTGCAGGTGGGTGTACGGTTCTGG
43131 AAAATATACA
Statistics
Matches: 204, Mismatches: 5, Indels: 12
0.92 0.02 0.05
Matches are distributed among these distances:
112 106 0.52
113 3 0.01
114 2 0.01
116 2 0.01
117 3 0.01
118 88 0.43
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.32
Consensus pattern (118 bp):
TGGGTGATTGGTGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGT
AAGTCCTTACTGGTGTGCAGGTGGGTGTACGGTTCTGGGGAACCTACACATTT
Found at i:44895 original size:18 final size:18
Alignment explanation
Indices: 44872--44943 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
44862 ACCGGTCACA
44872 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
44890 ACCCGACCCGACCTGTT-
1 ACCCGACCCGACCCGTTG
*
44907 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
44921 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
44939 ACCCG
1 ACCCG
44944 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 11 0.25
18 33 0.75
ACGTcount: A:0.17, C:0.49, G:0.19, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:44913 original size:31 final size:31
Alignment explanation
Indices: 44877--44943 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
44867 TCACAACCCG
*
44877 ACCCGACCCGTTGACCCGACCCGACCTGTTT
1 ACCCGACCCGTTGACCCGACCCGACCCGTTT
44908 ACCCGACCCGTTGACCCGACCCGACCCGTTT
1 ACCCGACCCGTTGACCCGACCCGACCCGTTT
44939 ACCCG
1 ACCCG
44944 TTGACCGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGACCCGTTT
Found at i:44942 original size:8 final size:8
Alignment explanation
Indices: 44930--44963 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
44920 GACCCGACCC
44930 GACCCGTT
1 GACCCGTT
*
44938 TACCCGTT
1 GACCCGTT
44946 GA-CCGTT
1 GACCCGTT
44953 GACCCGTT
1 GACCCGTT
44961 GAC
1 GAC
44964 TGGCGACCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:44943 original size:13 final size:13
Alignment explanation
Indices: 44894--44930 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
44884 CCGTTGACCC
*
44894 GACCCGACCTGTT
1 GACCCGACCCGTT
*
44907 TACCCGACCCGTT
1 GACCCGACCCGTT
44920 GACCCGACCCG
1 GACCCGACCCG
44931 ACCCGTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:44957 original size:15 final size:15
Alignment explanation
Indices: 44933--44963 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44923 CCGACCCGAC
*
44933 CCGTTTACCCGTTGA
1 CCGTTGACCCGTTGA
44948 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
44963 C
1 C
44964 TGGCGACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.35, G:0.23, T:0.29
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:46947 original size:24 final size:24
Alignment explanation
Indices: 46846--46954 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
46836 GATTATTTTA
* * *
46846 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTATGT
* * *
46870 TTTGACATCTGATCTGAAATATGT
1 TCTGATATCTGATCTGAATTATGT
* * *
46894 TCTGAT-TCCTAACCT-AGATTCTGT
1 TCTGATAT-CTGATCTGA-ATTATGT
46918 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
46942 TTTGATTTCTGAT
1 TCTGATATCTGAT
46955 ATCTCCGTTT
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
23 2 0.03
24 60 0.94
25 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:49831 original size:12 final size:12
Alignment explanation
Indices: 49806--49844 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
49796 TATAACCTAT
49806 ATGCAACT--AA
1 ATGCAACTAAAA
49816 ATGCAACTAAAA
1 ATGCAACTAAAA
49828 ATGCAACTAAAA
1 ATGCAACTAAAA
49840 ATGCA
1 ATGCA
49845 GTGCATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 8 0.30
12 19 0.70
ACGTcount: A:0.54, C:0.18, G:0.10, T:0.18
Consensus pattern (12 bp):
ATGCAACTAAAA
Found at i:50577 original size:20 final size:20
Alignment explanation
Indices: 50540--50578 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
50530 TTTCCACCAC
**
50540 ATGCAACTATATTCTCCTAA
1 ATGCAACTATATGATCCTAA
*
50560 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
50579 TATGAGATCT
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:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:55602 original size:11 final size:11
Alignment explanation
Indices: 55586--55634 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
55576 TTTTTTTATT
55586 GAATTGATATG
1 GAATTGATATG
55597 GAATTGATATG
1 GAATTGATATG
55608 GAATTGAT-TG
1 GAATTGATATG
**
55618 GAA-TGGCATG
1 GAATTGATATG
55628 GAATTGA
1 GAATTGA
55635 AGCTGAGAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 2 0.06
10 10 0.30
11 21 0.64
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.33
Consensus pattern (11 bp):
GAATTGATATG
Found at i:59696 original size:31 final size:31
Alignment explanation
Indices: 59661--59738 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
59651 GACCATTATG
59661 TAATTTTTGAAAAGTTAAGGGACCAAATTGA
1 TAATTTTTGAAAAGTTAAGGGACCAAATTGA
* *
59692 TAATTTTTGAAAAGTTAGGGGGCCAAATTGA
1 TAATTTTTGAAAAGTTAAGGGACCAAATTGA
* *
59723 TACTTTTGGAAAAGTT
1 TAATTTTTGAAAAGTT
59739 GTAGATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (31 bp):
TAATTTTTGAAAAGTTAAGGGACCAAATTGA
Found at i:61349 original size:59 final size:59
Alignment explanation
Indices: 61217--61395 Score: 236
Period size: 59 Copynumber: 3.1 Consensus size: 59
61207 AACAAGCTGA
* * **
61217 ATATTCAGGATTGCGCTAAAGTATAACTAGTGTATATGGT-GGCACGACCTTATGTGTC
1 ATATTCGGGATTGCACTAAAGTATAACTAGTGCGTATGGTGGGCACGACCTTATGTGTC
* * *
61275 ACATTCGGGATTGCACTAAAGTATAACTAGTGCGTATGGTGGGAACGACCATATGTGTC
1 ATATTCGGGATTGCACTAAAGTATAACTAGTGCGTATGGTGGGCACGACCTTATGTGTC
* * * *
61334 ATATTCGGGACTGCACTAATGCATAACTAGTGCAG-ATGGTGGGCATGACCTTATGTGTC
1 ATATTCGGGATTGCACTAAAGTATAACTAGTGC-GTATGGTGGGCACGACCTTATGTGTC
61393 ATA
1 ATA
61396 CTAGGGTTAG
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
58 35 0.33
59 69 0.66
60 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (59 bp):
ATATTCGGGATTGCACTAAAGTATAACTAGTGCGTATGGTGGGCACGACCTTATGTGTC
Found at i:61886 original size:16 final size:15
Alignment explanation
Indices: 61861--61894 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
61851 CTGCAATTTC
*
61861 TTAATATAATTAGTA
1 TTAATATAATTAATA
61876 TTAATTATAATTAATA
1 TTAA-TATAATTAATA
61892 TTA
1 TTA
61895 TGATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:67945 original size:59 final size:57
Alignment explanation
Indices: 67872--68057 Score: 185
Period size: 59 Copynumber: 3.2 Consensus size: 57
67862 CAGCAGGCTG
* * * *
67872 CATATTCGTGATTGCGCTGAAGTATAACTAATGTATATGGTGGGTACAACCTTATGTGT
1 CATATTCGGGATTGCACT-AAGTATAACTAGTG-ATATGGTGGGCACAACCTTATGTGT
* * *
67931 CATATTCGGGATTGCAATAATTATAACTAGTGAGTATAGTGGGCACAA-CTGTATGTGT
1 CATATTCGGGATTGCACTAAGTATAACTAGTGA-TATGGTGGGCACAACCT-TATGTGT
* * * * * *
67989 CATATTCGTGATTGTACTAATGTATAACTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGATTGCACTAA-GTATAACTAGT-GATATGGTGGGCACAACCTTATGTGT
*
68048 CATACTCGGG
1 CATATTCGGG
68058 TTAGAAGTAT
Statistics
Matches: 104, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
57 3 0.03
58 48 0.46
59 50 0.48
60 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (57 bp):
CATATTCGGGATTGCACTAAGTATAACTAGTGATATGGTGGGCACAACCTTATGTGT
Found at i:67979 original size:58 final size:59
Alignment explanation
Indices: 67893--68057 Score: 185
Period size: 58 Copynumber: 2.8 Consensus size: 59
67883 TTGCGCTGAA
* *
67893 GTATAACTAATGTA-TATGGTGGGTACAACCTTATGTGTCATATTCGGGATTGCAATAAT
1 GTATAACTAGTG-AGTATGGTGGGCACAACCTTATGTGTCATATTCGGGATTGCAATAAT
* * * *
67952 -TATAACTAGTGAGTATAGTGGGCACAA-CTGTATGTGTCATATTCGTGATTGTACTAAT
1 GTATAACTAGTGAGTATGGTGGGCACAACCT-TATGTGTCATATTCGGGATTGCAATAAT
* * * *
68010 GTATAACTAGTACAG-ATGGTGGACACGACCTTATGTGTCATACTCGGG
1 GTATAACTAGT-GAGTATGGTGGGCACAACCTTATGTGTCATATTCGGG
68058 TTAGAAGTAT
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
57 3 0.03
58 47 0.53
59 35 0.39
60 4 0.04
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (59 bp):
GTATAACTAGTGAGTATGGTGGGCACAACCTTATGTGTCATATTCGGGATTGCAATAAT
Found at i:73597 original size:11 final size:11
Alignment explanation
Indices: 73583--73607 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
73573 TAAAAATAAA
73583 AAAGAAAAGAG
1 AAAGAAAAGAG
73594 AAAGAAAAGAG
1 AAAGAAAAGAG
73605 AAA
1 AAA
73608 AGTTCCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAG
Found at i:75875 original size:134 final size:132
Alignment explanation
Indices: 75586--75861 Score: 319
Period size: 134 Copynumber: 2.1 Consensus size: 132
75576 GTCATAGGTG
** **
75586 CATTTCGACATA-AATTGTGTATAATGGTTATCGATCGATTTTGTGTAATGCATAATGGTGCATT
1 CATTTCGACATACAATCATGTATAAAAGTTATCGATCGATTTTGTGTAATGCATAATGGTGCATT
* *
75650 TTCGTATCACTAAGTCTACTTTCAACACTAGATATGCAATCATGGTATTCATAATGAGTTTATGA
66 TTCGTATCACTAAGTATACTTT--ACACTA-ATATGCAATCATGGAATTCATAATGAGTTTATGA
75715 ATTAC
128 ATTAC
* * * *
75720 CATTTTGATATACAATTATGTATAAAAGTTATCGATCGATTTTGT-TTATGCATAATGGTGCATT
1 CATTTCGACATACAATCATGTATAAAAGTTATCGATCGATTTTGTGTAATGCATAATGGTGCATT
* * * *
75784 TTCGTATCAGTACTAGATATACTTT-CACT-ATGTG-TATCCATGGAATTCATAATGAGTTTGTG
66 TTCGTATCACTA--AG-TATACTTTACACTAATATGCAAT-CATGGAATTCATAATGAGTTTATG
*
75846 AATTTC
127 AATTAC
75852 CATTTCGACA
1 CATTTCGACA
75862 CTTCGGTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
131 2 0.02
132 39 0.32
134 43 0.35
135 29 0.24
136 2 0.02
137 7 0.06
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (132 bp):
CATTTCGACATACAATCATGTATAAAAGTTATCGATCGATTTTGTGTAATGCATAATGGTGCATT
TTCGTATCACTAAGTATACTTTACACTAATATGCAATCATGGAATTCATAATGAGTTTATGAATT
AC
Found at i:79447 original size:112 final size:112
Alignment explanation
Indices: 79249--79466 Score: 382
Period size: 112 Copynumber: 1.9 Consensus size: 112
79239 CGAAGTGCCT
*
79249 AAATGGTGATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGCACCGTTA
1 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGCACCGTTA
*
79314 TGCATTAAGCAAAATAAATCGATAACTTTCATACACGAAGTCTGTCA
66 TGCATTAAACAAAATAAATCGATAACTTTCATACACGAAGTCTGTCA
* *
79361 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGTATCGTTA
1 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGCACCGTTA
**
79426 TGCATTAAACAAAATCGATCGATAACTTTCATACACGAAGT
66 TGCATTAAACAAAATAAATCGATAACTTTCATACACGAAGT
79467 ATGTTGAAAT
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 100 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (112 bp):
AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGCACCGTTA
TGCATTAAACAAAATAAATCGATAACTTTCATACACGAAGTCTGTCA
Done.