Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002768.1 Hibiscus syriacus cultivar Beakdansim tig00005706_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: 65622
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:13004 original size:65 final size:65
Alignment explanation
Indices: 12851--13007 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 65
12841 AATAGCAAGA
* * * *
12851 GTGCATCGATGCATGACTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTTG
1 GTGCATCGATGCATGATTGGTGCATCGATGCATCAAATACATTCGATGTTTTAATAACATCCATG
* * * * * *
12916 GTGTATCGGTGCATGGTAT-GTGCATCGATGCATGAAATACATTCGATG-TTTAATTTA-ATTCA
1 GTGCATCGATGCATGAT-TGGTGCATCGATGCATCAAATACATTCGATGTTTTAA-TAACATCCA
12978 TG
64 TG
12980 GTGCATCGATGCATGAATTGGTGCATCG
1 GTGCATCGATGCATG-ATTGGTGCATCG
13008 CTCTGAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
64 23 0.31
65 51 0.68
66 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGCATGATTGGTGCATCGATGCATCAAATACATTCGATGTTTTAATAACATCCATG
Found at i:16739 original size:20 final size:20
Alignment explanation
Indices: 16714--16755 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
16704 TAAAGATAAA
16714 GAAGACACAAAATTTACGTG
1 GAAGACACAAAATTTACGTG
16734 GAAGACACAAAATTTACGTG
1 GAAGACACAAAATTTACGTG
16754 GA
1 GA
16756 GAACCCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.19
Consensus pattern (20 bp):
GAAGACACAAAATTTACGTG
Found at i:18268 original size:76 final size:75
Alignment explanation
Indices: 18187--18334 Score: 226
Period size: 76 Copynumber: 2.0 Consensus size: 75
18177 TAAACTCAAA
18187 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
18251 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * * *
18263 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTATATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
18328 TTAATTA
66 TTAATTA
18335 GGATTTAGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 24 0.36
76 42 0.64
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:18360 original size:75 final size:76
Alignment explanation
Indices: 18214--18361 Score: 228
Period size: 75 Copynumber: 2.0 Consensus size: 76
18204 AACATTATAT
* * *
18214 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTA
18279 TATATTTTATC
66 TATATTTTATC
* *
18290 TTTATCTTTGTATTTTAGTTTATATAGG-TTTTAGTATTTTAATTAGGATTTAGAATATTATATT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTAT-TT
18354 AT-TATTTT
65 ATATATTTT
18362 TAGATATTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 36 0.55
76 30 0.45
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (76 bp):
TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTA
TATATTTTATC
Found at i:18363 original size:76 final size:76
Alignment explanation
Indices: 18214--18363 Score: 232
Period size: 76 Copynumber: 2.0 Consensus size: 76
18204 AACATTATAT
* *
18214 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTT
18279 TATATTTTATC
66 TATATTTTATC
* *
18290 TTTATCTTTGTATTTTAGTTTATATAGG-TTTTAGTATTTTAATTAGGATTTAGAATATTATATT
1 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTAT-TT
18354 ATTAT-TTTTA
65 -TTATATTTTA
18364 GATATTTTAG
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
75 30 0.44
76 34 0.50
77 4 0.06
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (76 bp):
TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTTT
TATATTTTATC
Found at i:19130 original size:18 final size:18
Alignment explanation
Indices: 19078--19121 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
19068 CCCCTTTTTA
*
19078 TATTTATTA-C-TATTAA
1 TATTTATTATCATATTAT
19094 TATTTATTATCATATTAT
1 TATTTATTATCATATTAT
19112 TATTTATTAT
1 TATTTATTAT
19122 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.36
17 1 0.04
18 15 0.60
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTATTATCATATTAT
Found at i:24587 original size:10 final size:10
Alignment explanation
Indices: 24569--24599 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
24559 ACCCATTTCG
24569 TTATATTTTTT
1 TTAT-TTTTTT
24580 TTATTTTTTT
1 TTATTTTTTT
24590 TTATTTTTTT
1 TTATTTTTTT
24600 AGCGAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:24782 original size:54 final size:52
Alignment explanation
Indices: 24685--24789 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 52
24675 GAATATTTAA
*
24685 CGAAAAAAACAGTGCAGAAAAACAGACTTGGTTCAAACTGTGCAGAAAAATT
1 CGAAAAAAACAGTGCAGAAAAACAGACTTGGTTCAAACAGTGCAGAAAAATT
* * **
24737 CGAACAAAACAGTGCAGAAAAAAACTA-ATTTGGTTTGAACAGTGCAGAAAAAT
1 CGAAAAAAACAGTGCAG--AAAAAC-AGACTTGGTTCAAACAGTGCAGAAAAAT
24790 ACACAGCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
52 16 0.36
54 28 0.62
55 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.18
Consensus pattern (52 bp):
CGAAAAAAACAGTGCAGAAAAACAGACTTGGTTCAAACAGTGCAGAAAAATT
Found at i:26535 original size:77 final size:75
Alignment explanation
Indices: 26443--26608 Score: 217
Period size: 75 Copynumber: 2.2 Consensus size: 75
26433 TTAAACTCAA
* * *
26443 ATTTAGGATAATATTTTAAAAATTATAT-TTTATCTTTGTATTTTTAGTTTAAATAGGTTTTTAG
1 ATTTAGGATATTATTTT-AAAATTATATCTTTATCTTTGTA-TTTTAGTTTAAA-AAGATTTTAG
26507 TATTTTAATTAAG
63 TATTTTAATTAAG
* * * *
26520 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAAAAGATTTTAGTAT
1 ATTTAGGATATTATTTTAAAATTATATCTTTATCTTTGTATTTTAGTTTAAAAAGATTTTAGTAT
*
26585 TTTAATTAGG
66 TTTAATTAAG
*
26595 ATTTAGAATATTAT
1 ATTTAGGATATTAT
26609 ATTATTATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
75 32 0.41
76 19 0.24
77 27 0.35
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAAAATTATATCTTTATCTTTGTATTTTAGTTTAAAAAGATTTTAGTAT
TTTAATTAAG
Found at i:26606 original size:75 final size:78
Alignment explanation
Indices: 26471--26621 Score: 220
Period size: 75 Copynumber: 2.0 Consensus size: 78
26461 AAAATTATAT
* * * *
26471 TTTATCTTTGTATTTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATTAT-T
1 TTTATCTTTGTATTTTTAGTTTAAATAAGATTTTAGTATTTTAATTAAGATTTAGAATATTATAT
26535 T-TTATATTTTATC
66 TATTAT-TTTTATC
*
26548 TTTATCTTTGTA-TTTTAGTTTAAA-AAGATTTTAGTATTTTAATTAGGATTTAGAATATTATAT
1 TTTATCTTTGTATTTTTAGTTTAAATAAGATTTTAGTATTTTAATTAAGATTTAGAATATTATAT
26611 TATTATTTTTA
66 TATTATTTTTA
26622 GATATTTTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
75 32 0.48
76 19 0.28
77 16 0.24
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (78 bp):
TTTATCTTTGTATTTTTAGTTTAAATAAGATTTTAGTATTTTAATTAAGATTTAGAATATTATAT
TATTATTTTTATC
Found at i:27303 original size:19 final size:18
Alignment explanation
Indices: 27252--27300 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
27242 AATCTCTTTA
*
27252 ATTTGTTTATTTAATTTTT
1 ATTT-TTTATTTAATTCTT
*
27271 TTCTTTTTATTTAATTCTT
1 AT-TTTTTATTTAATTCTT
27290 ATTTTTTATTT
1 ATTTTTTATTT
27301 TAACCACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 9 0.35
19 15 0.58
20 2 0.08
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTTTTATTTAATTCTT
Found at i:31527 original size:13 final size:13
Alignment explanation
Indices: 31505--31554 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
31495 TGATTCCAGT
*
31505 AACTGGTTTGACA
1 AACTGATTTGACA
**
31518 AACTGATTTGATT
1 AACTGATTTGACA
* *
31531 ATCTGATTTGAGA
1 AACTGATTTGACA
31544 AACTGATTTGA
1 AACTGATTTGA
31555 TTAATTCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (13 bp):
AACTGATTTGACA
Found at i:35664 original size:89 final size:88
Alignment explanation
Indices: 35569--35741 Score: 258
Period size: 89 Copynumber: 2.0 Consensus size: 88
35559 GATAATTCCT
*
35569 AAAATAA-AGAAATAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAA
1 AAAATAATA-AAATAAATCCTAATTAAAACAATTAAAACTATTTAAACTAAAATACCTAAAACAA
*
35633 AGATAAGATAAAATATAATATAATA
65 AGATAAAATAAAA-ATAATATAATA
*** *
35658 AAAATAATATCCTAAATCCTAATTAAAATAATTAAAACTATTTAAACTAAAATACCTAAAACAAA
1 AAAATAATAAAATAAATCCTAATTAAAACAATTAAAACTATTTAAACTAAAATACCTAAAACAAA
*
35723 GATAAAATTAAAATAATAT
66 GATAAAATAAAAATAATAT
35742 CCTAAAACAT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
88 7 0.09
89 68 0.89
90 1 0.01
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (88 bp):
AAAATAATAAAATAAATCCTAATTAAAACAATTAAAACTATTTAAACTAAAATACCTAAAACAAA
GATAAAATAAAAATAATATAATA
Found at i:45106 original size:12 final size:12
Alignment explanation
Indices: 45089--45113 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45079 AAAGATAAAG
45089 ATTAAATAAATA
1 ATTAAATAAATA
45101 ATTAAATAAATA
1 ATTAAATAAATA
45113 A
1 A
45114 AATAGATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAATAAATA
Found at i:47716 original size:4 final size:4
Alignment explanation
Indices: 47707--47762 Score: 62
Period size: 4 Copynumber: 14.0 Consensus size: 4
47697 AGATAAATTA
* *
47707 AAAT AAAT AAAT AAAT AAAT AATTAT AAAA AAAT AAAA AAAT -AAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AA--AT AAAT AAAT AAAT AAAT AAAT AAAT
47756 -AAT AAAT
1 AAAT AAAT
47763 TTTAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 6 0.14
4 34 0.77
6 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:47734 original size:22 final size:22
Alignment explanation
Indices: 47709--47751 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
47699 ATAAATTAAA
* *
47709 ATAAATAAATAAATAAATAATT
1 ATAAAAAAATAAAAAAATAATT
47731 ATAAAAAAATAAAAAAATAAT
1 ATAAAAAAATAAAAAAATAAT
47752 AAATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAAAAAAATAAAAAAATAATT
Found at i:47760 original size:26 final size:27
Alignment explanation
Indices: 47705--47761 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
47695 AAAGATAAAT
* *
47705 TAAAATAAATAAATAAATAAATAATTA
1 TAAAATAAATAAAAAAATAAATAATAA
47732 TAAAA-AAATAAAAAAAT-AATAAATAA
1 TAAAATAAATAAAAAAATAAAT-AATAA
47758 TAAA
1 TAAA
47762 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 3 0.11
26 19 0.70
27 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (27 bp):
TAAAATAAATAAAAAAATAAATAATAA
Found at i:50450 original size:19 final size:19
Alignment explanation
Indices: 50426--50462 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50416 GTTATATTCG
50426 AACTTTTCTGCACAGTTCA
1 AACTTTTCTGCACAGTTCA
* *
50445 AACTTTTTTGCACTGTTC
1 AACTTTTCTGCACAGTTC
50463 GAACCAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (19 bp):
AACTTTTCTGCACAGTTCA
Found at i:50782 original size:19 final size:18
Alignment explanation
Indices: 50757--50810 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
50747 ATATCAAAGA
*
50757 AAAATAAAAACAAAAATG
1 AAAATAAAAATAAAAATG
* *
50775 AATCATAAAAATAAAATTG
1 AA-AATAAAAATAAAAATG
50794 AAAATAAAAATAAAAAT
1 AAAATAAAAATAAAAAT
50811 TGAACAAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (18 bp):
AAAATAAAAATAAAAATG
Found at i:50788 original size:6 final size:6
Alignment explanation
Indices: 50756--50810 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
50746 AATATCAAAG
* ** * *
50756 AAAAAT AAAAAC AAAAAT GAATCAT AAAAAT AAAATT GAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
50805 AAAAAT
1 AAAAAT
50811 TGAACAAACG
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 34 0.89
7 4 0.11
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:50811 original size:19 final size:19
Alignment explanation
Indices: 50757--50814 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
50747 ATATCAAAGA
*
50757 AAAATAAAAACAAAAA-TG
1 AAAATAAAAATAAAAATTG
*
50775 AATCATAAAAAT-AAAATTG
1 AA-AATAAAAATAAAAATTG
50794 AAAATAAAAATAAAAATTG
1 AAAATAAAAATAAAAATTG
50813 AA
1 AA
50815 CAAACGGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 14 0.41
19 20 0.59
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAATAAAAATAAAAATTG
Found at i:54773 original size:21 final size:21
Alignment explanation
Indices: 54749--54796 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
54739 ATGCAATTAG
*
54749 CTTTTCCTGGGACGTAACCAA
1 CTTTTCCTAGGACGTAACCAA
* *
54770 CTTTTCCTAGGACGTGACCAT
1 CTTTTCCTAGGACGTAACCAA
54791 CTTTTC
1 CTTTTC
54797 TTGTAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (21 bp):
CTTTTCCTAGGACGTAACCAA
Found at i:57777 original size:20 final size:20
Alignment explanation
Indices: 57747--57791 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
57737 GTTTGTGGTC
*
57747 GTTTCTAGCCG-TTGGGGAT
1 GTTTTTAGCCGTTTGGGGAT
57766 GATTTTTAGCCGTTTGGGGAT
1 G-TTTTTAGCCGTTTGGGGAT
57787 GTTTT
1 GTTTT
57792 CTCTACAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 13 0.57
21 9 0.39
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (20 bp):
GTTTTTAGCCGTTTGGGGAT
Found at i:58076 original size:20 final size:20
Alignment explanation
Indices: 58048--58158 Score: 150
Period size: 20 Copynumber: 5.5 Consensus size: 20
58038 TCCTAATTCA
58048 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* ** *
58068 CAATACGAATTTGGAAAATCG
1 CAATGCGAA-TACGTAAATCG
58089 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
58109 CAATGCGAATATGTAAATCG
1 CAATGCGAATACGTAAATCG
*
58129 CAATGTGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
58149 CAATGTGAAT
1 CAATGCGAAT
58159 CTAACTATCG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 63 0.80
21 16 0.20
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:58139 original size:40 final size:41
Alignment explanation
Indices: 58048--58158 Score: 170
Period size: 40 Copynumber: 2.7 Consensus size: 41
58038 TCCTAATTCA
* *
58048 CAATGCGAATACGTAAATCGCAATACGAATTTGGAAAATCG
1 CAATGCGAATACGTAAATCGCAATGCGAATATGGAAAATCG
*
58089 CAATGCGAATACGTAAATCGCAATGCGAATAT-GTAAATCG
1 CAATGCGAATACGTAAATCGCAATGCGAATATGGAAAATCG
* *
58129 CAATGTGAATACGTAAATCGCAATGTGAAT
1 CAATGCGAATACGTAAATCGCAATGCGAAT
58159 CTAACTATCG
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 35 0.54
41 30 0.46
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (41 bp):
CAATGCGAATACGTAAATCGCAATGCGAATATGGAAAATCG
Found at i:58168 original size:20 final size:20
Alignment explanation
Indices: 58145--58232 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
58135 GAATACGTAA
* *
58145 ATCGCAATGTGAATCTAACT
1 ATCGCAATGAGAATCTGACT
58165 ATCGCAATGCA-AATCTGACT
1 ATCGCAATG-AGAATCTGACT
* *
58185 ATCACAATGAGATTCTGACT
1 ATCGCAATGAGAATCTGACT
* * *
58205 ATTGCAACGAGATTCTGACT
1 ATCGCAATGAGAATCTGACT
58225 ATCGCAAT
1 ATCGCAAT
58233 ACTGAATTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.02
20 56 0.98
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (20 bp):
ATCGCAATGAGAATCTGACT
Found at i:58169 original size:40 final size:38
Alignment explanation
Indices: 58048--58174 Score: 146
Period size: 40 Copynumber: 3.2 Consensus size: 38
58038 TCCTAATTCA
* *
58048 CAATGCGAATACGTAAATCGCAATACGAATTTGGAAAATCG
1 CAATGCGAATACGTAAATCGCAATGCGAATCT---AAATCG
*
58089 CAATGCGAATACGTAAATCGCAATGCGAATATGTAAATCG
1 CAATGCGAATACGTAAATCGCAATGCG-A-ATCTAAATCG
* *
58129 CAATGTGAATACGTAAATCGCAATGTGAATCTAACTATCG
1 CAATGCGAATACGTAAATCGCAATGCGAATCTAA--ATCG
58169 CAATGC
1 CAATGC
58175 AAATCTGACT
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
38 5 0.07
39 1 0.01
40 40 0.53
41 26 0.34
42 1 0.01
43 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (38 bp):
CAATGCGAATACGTAAATCGCAATGCGAATCTAAATCG
Found at i:61553 original size:34 final size:33
Alignment explanation
Indices: 61465--61560 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
61455 TCATTTGACT
* **
61465 ATCGCAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
61499 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
61532 ATCGCAATGCGAAAATGAAAATCACAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
61561 CAAATTTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:61616 original size:14 final size:14
Alignment explanation
Indices: 61597--61650 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
61587 CATTTTCGCA
61597 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
61611 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
61628 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
61644 TTGCGAT
1 TTGCGAT
61651 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:61618 original size:34 final size:34
Alignment explanation
Indices: 61575--61670 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
61565 TTTAGTTTCG
61575 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
61609 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
61642 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
61671 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:63797 original size:20 final size:20
Alignment explanation
Indices: 63774--63902 Score: 150
Period size: 20 Copynumber: 6.5 Consensus size: 20
63764 GAAACTTAAA
63774 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
63794 ATCGCAAAGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
63814 ATCGCAAAGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
63834 ATCACAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * **
63854 ATCGCAATGTGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* **
63874 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
63894 ATCGCAACG
1 ATCGCAACG
63903 AGAGAATCGC
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 95 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:63990 original size:20 final size:20
Alignment explanation
Indices: 63967--64033 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
63957 CAAATTCACT
63967 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
63987 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
64007 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
64027 TTGCGAT
1 TTGCGAT
64034 TTTGTTGTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:64054 original size:34 final size:34
Alignment explanation
Indices: 64007--64100 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 34
63997 CATTTTCGCA
* * * * * *
64007 TTGCGATAGTCATTTTTGCGTTGCGATTTTGTTG
1 TTGCAATAGTCATTTTCGCATTGCGATTCTCTCG
**
64041 TTGCAATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCAATAGTCATTTTCGCATTGCGATTCTCTCG
64074 TTGCAATAGTCATTTTCGCATTGCGAT
1 TTGCAATAGTCATTTTCGCATTGCGAT
64101 AATAAACTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
33 26 0.53
34 23 0.47
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.46
Consensus pattern (34 bp):
TTGCAATAGTCATTTTCGCATTGCGATTCTCTCG
Done.