Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004226.1 Hibiscus syriacus cultivar Beakdansim tig00009250_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: 68460
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:2140 original size:240 final size:240
Alignment explanation
Indices: 1717--2201 Score: 961
Period size: 240 Copynumber: 2.0 Consensus size: 240
1707 TTTAGTATGT
1717 CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
1 CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
1782 CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCATCTAGACACCATAACAAGAGGTTCT
66 CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCATCTAGACACCATAACAAGAGGTTCT
1847 CATAACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAA
131 CATAACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAA
1912 ACCTCCAAAGAAGAACTCAAAATAGAAAATATGATGAGGACTAAC
196 ACCTCCAAAGAAGAACTCAAAATAGAAAATATGATGAGGACTAAC
1957 CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
1 CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
*
2022 CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCATCTGGACACCATAACAAGAGGTTCT
66 CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCATCTAGACACCATAACAAGAGGTTCT
2087 CATAACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAA
131 CATAACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAA
2152 ACCTCCAAAGAAGAACTCAAAATAGAAAATATGATGAGGACTAAC
196 ACCTCCAAAGAAGAACTCAAAATAGAAAATATGATGAGGACTAAC
2197 CCTCT
1 CCTCT
2202 GAAAATGATA
Statistics
Matches: 244, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
240 244 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (240 bp):
CCTCTAAGTGTAATCAAGTATCAACATAAAACATAAATGTTTCAATCAACATGACATAACATACA
CATAATAGTCAAGTAAACTAATAAATCTAACTAATCATCATCTAGACACCATAACAAGAGGTTCT
CATAACCTTGTGTCTCCTTACAACCATACAAGATGAGGACGTTACTCTCCGAAGAGGAATCCTAA
ACCTCCAAAGAAGAACTCAAAATAGAAAATATGATGAGGACTAAC
Found at i:6303 original size:16 final size:16
Alignment explanation
Indices: 6282--6312 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6272 AATCATAATC
6282 AAACCTTAAATCATCA
1 AAACCTTAAATCATCA
6298 AAACCTTAAATCATC
1 AAACCTTAAATCATC
6313 TTCATCCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
AAACCTTAAATCATCA
Found at i:11199 original size:13 final size:13
Alignment explanation
Indices: 11181--11209 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11171 CTTAAGGAAC
11181 CGAAAGTCTAACT
1 CGAAAGTCTAACT
11194 CGAAAGTCTAACT
1 CGAAAGTCTAACT
11207 CGA
1 CGA
11210 TGAGTTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (13 bp):
CGAAAGTCTAACT
Found at i:23296 original size:31 final size:29
Alignment explanation
Indices: 23259--23330 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
23249 GGGACTAATT
* *
23259 TTTTTAAATTAATTCCAGAGACTAAATTGAA
1 TTTTT-AATTAATT-CAGAGACCAAAGTGAA
* *
23290 TTTTTAATTAAATTTAGGGACCAAAGTGAA
1 TTTTTAATT-AATTCAGAGACCAAAGTGAA
23320 TTTTTAATTAA
1 TTTTTAATTAA
23331 ATTTGAATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.06
30 25 0.69
31 9 0.25
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (29 bp):
TTTTTAATTAATTCAGAGACCAAAGTGAA
Found at i:24040 original size:18 final size:18
Alignment explanation
Indices: 23995--24046 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
23985 GAAATAGTCA
* *
23995 ACCATTTACCGTTGACCG
1 ACCATTGACTGTTGACCG
24013 ACCATTGACTGTTGACCG
1 ACCATTGACTGTTGACCG
* *
24031 ACCGTTGACTATTGAC
1 ACCATTGACTGTTGAC
24047 AACTGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (18 bp):
ACCATTGACTGTTGACCG
Found at i:26407 original size:152 final size:154
Alignment explanation
Indices: 26101--26411 Score: 590
Period size: 153 Copynumber: 2.0 Consensus size: 154
26091 GGAATCAGTT
26101 GACTTGGGATCTTTTTAAGGCACGATTTTGGATCCGCTACATCGAAGAGAGATACCTGCATGAGC
1 GACTTGGGATCTTTTTAAGGCACGATTTTGGATCCGCTACATCGAAGAGAGATACCTGCATGAGC
26166 GATGCCAAGAGTTTAAGAATTTGGAGTAGGGGATATGTTTGTTATGGATTATGAGATTGAGTTCA
66 GATGCCAAGAGTTTAAGAATTTGGAGTAGGGGATATGTTTGTTATGGATTATGAGATTGAGTTCA
*
26231 TCAGATTGACTCGGTATGTTATTG
131 TCAGATTGACTCGCTATGTTATTG
*
26255 GACTTGGGAT-TTTTTAAGGCACGTTTTTGGATCCGCTACATCGAAGAGAGATACCTGCATGAGC
1 GACTTGGGATCTTTTTAAGGCACGATTTTGGATCCGCTACATCGAAGAGAGATACCTGCATGAGC
26319 GATGCCAAGAGTTTAAGAATTTGGAGTA-GGGATATGTTTGTTATGGATTATGAGATTGAGTTCA
66 GATGCCAAGAGTTTAAGAATTTGGAGTAGGGGATATGTTTGTTATGGATTATGAGATTGAGTTCA
26383 TCAGATTGACTCGCTATGTTATTG
131 TCAGATTGACTCGCTATGTTATTG
26407 GACTT
1 GACTT
26412 ATTGGCACTG
Statistics
Matches: 155, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
152 64 0.41
153 81 0.52
154 10 0.06
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (154 bp):
GACTTGGGATCTTTTTAAGGCACGATTTTGGATCCGCTACATCGAAGAGAGATACCTGCATGAGC
GATGCCAAGAGTTTAAGAATTTGGAGTAGGGGATATGTTTGTTATGGATTATGAGATTGAGTTCA
TCAGATTGACTCGCTATGTTATTG
Found at i:28112 original size:2 final size:2
Alignment explanation
Indices: 28105--28142 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
28095 GAAAACATGA
*
28105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28143 CTAAATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28147 original size:8 final size:8
Alignment explanation
Indices: 28107--28149 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
28097 AAACATGAAT
*
28107 ATATATAT
1 ATATATAA
*
28115 ATATATAT
1 ATATATAA
*
28123 ATATATAT
1 ATATATAA
28131 ATATATAA
1 ATATATAA
*
28139 ATATCTAA
1 ATATATAA
28147 ATA
1 ATA
28150 GTTTCATTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (8 bp):
ATATATAA
Found at i:28256 original size:182 final size:182
Alignment explanation
Indices: 27944--28286 Score: 616
Period size: 182 Copynumber: 1.9 Consensus size: 182
27934 GGTTGACCAA
*
27944 ATATGATATATAAATTTCTAAATAGTTTCATTCCACATACAAGCATGGAAATGATTCTCCAATAT
1 ATATGATATATAAATATCTAAATAGTTTCATTCCACATACAAGCATGGAAATGATTCTCCAATAT
*
28009 CAACAACATCATAATAAAGCCTTAAATCATCAAAAACTAACATCCCCATCATCCATCCAATTCAA
66 CAACAACATCATAATAAAGCATTAAATCATCAAAAACTAACATCCCCATCATCCATCCAATTCAA
28074 GAAATTAATGTTTTAAGCATGGAAAACATGAATATATATATATATATATATAT
131 GAAATTAATGTTTTAAGCATGG-AAACATGAATATATATATATATATATATAT
* *
28127 ATAT-ATATATAAATATCTAAATAGTTTCATTCCTCATACAAGCATGGAAATGATTGTCCAATAT
1 ATATGATATATAAATATCTAAATAGTTTCATTCCACATACAAGCATGGAAATGATTCTCCAATAT
*
28191 CAACAACATCATAATAAAGCATTAAATCATCAAAAACTAACATCCCCTTCATCCATCCAATTCAA
66 CAACAACATCATAATAAAGCATTAAATCATCAAAAACTAACATCCCCATCATCCATCCAATTCAA
*
28256 GAACTTAATGTTTTAAGCATGGAAACATGAA
131 GAAATTAATGTTTTAAGCATGGAAACATGAA
28287 CTAATGGTAC
Statistics
Matches: 154, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
181 9 0.06
182 141 0.92
183 4 0.03
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (182 bp):
ATATGATATATAAATATCTAAATAGTTTCATTCCACATACAAGCATGGAAATGATTCTCCAATAT
CAACAACATCATAATAAAGCATTAAATCATCAAAAACTAACATCCCCATCATCCATCCAATTCAA
GAAATTAATGTTTTAAGCATGGAAACATGAATATATATATATATATATATAT
Found at i:28959 original size:15 final size:15
Alignment explanation
Indices: 28935--28970 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
28925 GGATTATGTA
*
28935 ACTTTTTAAAATTAC
1 ACTTTATAAAATTAC
28950 ACTTTATAAAATTAC
1 ACTTTATAAAATTAC
28965 ACTTTA
1 ACTTTA
28971 GTCCTTGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (15 bp):
ACTTTATAAAATTAC
Found at i:29151 original size:19 final size:19
Alignment explanation
Indices: 29129--29171 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
29119 ATGGTATCAG
29129 TACTC-GGGATAGGTATCGA
1 TACTCAGGG-TAGGTATCGA
*
29148 TACTCAAGGGTTGGTATCGA
1 TACTC-AGGGTAGGTATCGA
29168 TACT
1 TACT
29172 ATAGGGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 13 0.62
21 3 0.14
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (19 bp):
TACTCAGGGTAGGTATCGA
Found at i:32595 original size:123 final size:123
Alignment explanation
Indices: 32357--32656 Score: 338
Period size: 123 Copynumber: 2.4 Consensus size: 123
32347 CTAAAGAATT
* * * * * *
32357 GTACTGTAGTAGT-TTTTTATACAAATGCCGCTATAAACT-AGTAATTTAGTGGCGTTTTTATAT
1 GTACTTTAGTGGTGTTTTTATACAAATGCCGCTATAGACTCA-TACTTTAGTGGCATTTTTATAC
* * ** *
32420 AAACACGTCTATATACTCATACTTTTGTGGCGGTTTTATACAAACGCTGCTATAAACTC
65 AAACACGTCTATAGACTCATACTTTAGTGGAAGTTTTATACAAACGCCGCTATAAACTC
*
32479 GTACTTTAGTGGTGTTTTTACACAAATGCCGCTATAGACTCATACTTTAGTGGCATTTTTATACA
1 GTACTTTAGTGGTGTTTTTATACAAATGCCGCTATAGACTCATACTTTAGTGGCATTTTTATACA
* * * * * *
32544 AACGCCG-CTATAGACTCGTACTTTAGTGGAATTTTTATACAAATGCCGCTATAGACTT
66 AAC-ACGTCTATAGACTCATACTTTAGTGGAAGTTTTATACAAACGCCGCTATAAACTC
* * * *
32602 GTACTTT-GTGGTGTTTGTGTTTAGAAACGCCGCTATAGACGCATACTTTAGTGGC
1 GTACTTTAGTGGTGTTT-T-TATACAAATGCCGCTATAGACTCATACTTTAGTGGC
32657 GTTTACATAA
Statistics
Matches: 150, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
122 20 0.13
123 96 0.64
124 34 0.23
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (123 bp):
GTACTTTAGTGGTGTTTTTATACAAATGCCGCTATAGACTCATACTTTAGTGGCATTTTTATACA
AACACGTCTATAGACTCATACTTTAGTGGAAGTTTTATACAAACGCCGCTATAAACTC
Found at i:32607 original size:82 final size:82
Alignment explanation
Indices: 32370--32660 Score: 318
Period size: 82 Copynumber: 3.5 Consensus size: 82
32360 CTGTAGTAGT
* * * * *
32370 TTTTTATACAAATGCCGCTATAAACTAGTAATTTAGTGGCGTTTTTATATAAA--CACGTCTATA
1 TTTTTATACAAACGCCGCTATAAACTCGTACTTTAGTGGAGTTTTTATACAAATGC-CG-CTATA
* *
32433 TACTCATACTTTTGTGGCG
64 GACTCATACTTTAGTGGCG
* * * *
32452 GTTTTATACAAACGCTGCTATAAACTCGTACTTTAGTGGTGTTTTTACACAAATGCCGCTATAGA
1 TTTTTATACAAACGCCGCTATAAACTCGTACTTTAGTGGAGTTTTTATACAAATGCCGCTATAGA
*
32517 CTCATACTTTAGTGGCA
66 CTCATACTTTAGTGGCG
* *
32534 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGAATTTTTATACAAATGCCGCTATAGA
1 TTTTTATACAAACGCCGCTATAAACTCGTACTTTAGTGGAGTTTTTATACAAATGCCGCTATAGA
** *
32599 CTTGTACTTT-GTGGTG
66 CTCATACTTTAGTGGCG
* * * * * *
32615 TTTGTGTTTAGAAACGCCGCTATAGACGCATACTTTAGTGGCGTTT
1 TTT-T-TATACAAACGCCGCTATAAACTCGTACTTTAGTGGAGTTT
32661 ACATAAAAAA
Statistics
Matches: 178, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
81 7 0.04
82 134 0.75
83 36 0.20
84 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (82 bp):
TTTTTATACAAACGCCGCTATAAACTCGTACTTTAGTGGAGTTTTTATACAAATGCCGCTATAGA
CTCATACTTTAGTGGCG
Found at i:32641 original size:42 final size:41
Alignment explanation
Indices: 32343--32655 Score: 272
Period size: 41 Copynumber: 7.6 Consensus size: 41
32333 TCTTACTTTA
* * * * * *
32343 GCCGCTAAAGAATTGTACTGTAGTAGT-TTTTTATACAAAT
1 GCCGCTATAGACTCGTACTTTAGTGGTATTTTTATACAAAC
* * * ** *
32383 GCCGCTATAAACTAGTAATTTAGTGGCGTTTTTATATAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGTATTTTTATACAAAC
* * * * ***
32424 -ACGTCTATATACTCATACTTTTGTGGCGGTTTTATACAAAC
1 GCCG-CTATAGACTCGTACTTTAGTGGTATTTTTATACAAAC
* * * * *
32465 GCTGCTATAAACTCGTACTTTAGTGGTGTTTTTACACAAAT
1 GCCGCTATAGACTCGTACTTTAGTGGTATTTTTATACAAAC
* *
32506 GCCGCTATAGACTCATACTTTAGTGGCATTTTTATACAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGTATTTTTATACAAAC
* *
32547 GCCGCTATAGACTCGTACTTTAGTGGAATTTTTATACAAAT
1 GCCGCTATAGACTCGTACTTTAGTGGTATTTTTATACAAAC
* * * *
32588 GCCGCTATAGACTTGTACTTT-GTGGTGTTTGTGTTTAGAAAC
1 GCCGCTATAGACTCGTACTTTAGTGGTATTT-T-TATACAAAC
* *
32630 GCCGCTATAGACGCATACTTTAGTGG
1 GCCGCTATAGACTCGTACTTTAGTGG
32656 CGTTTACATA
Statistics
Matches: 221, Mismatches: 46, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
40 28 0.13
41 164 0.74
42 25 0.11
43 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (41 bp):
GCCGCTATAGACTCGTACTTTAGTGGTATTTTTATACAAAC
Found at i:37771 original size:22 final size:22
Alignment explanation
Indices: 37754--37807 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
37744 GTTGACCACT
37754 GTTGACCAGGACTTTGACCGGC
1 GTTGACCAGGACTTTGACCGGC
37776 GTTGACCAGGACTTTGACCGGC
1 GTTGACCAGGACTTTGACCGGC
37798 GTTGACCAGG
1 GTTGACCAGG
37808 CATTGAACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.22
Consensus pattern (22 bp):
GTTGACCAGGACTTTGACCGGC
Found at i:37772 original size:12 final size:11
Alignment explanation
Indices: 37735--37813 Score: 69
Period size: 10 Copynumber: 7.4 Consensus size: 11
37725 GCATTAACCA
37735 TTGA-CAGGCG
1 TTGACCAGGCG
37745 TTGACCA--CTG
1 TTGACCAGGC-G
*
37755 TTGACCAGGACT
1 TTGACCAGG-CG
37767 TTGACC-GGCG
1 TTGACCAGGCG
*
37777 TTGACCAGGACT
1 TTGACCAGG-CG
37789 TTGACC-GGCG
1 TTGACCAGGCG
*
37799 TTGACCAGGCA
1 TTGACCAGGCG
37810 TTGA
1 TTGA
37814 ACGACCTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
9 1 0.02
10 26 0.46
11 15 0.27
12 13 0.23
13 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.24
Consensus pattern (11 bp):
TTGACCAGGCG
Found at i:40093 original size:24 final size:24
Alignment explanation
Indices: 40066--40160 Score: 145
Period size: 24 Copynumber: 4.0 Consensus size: 24
40056 TTCTATTTGA
*
40066 ATTCTGATCTGATAATTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
40090 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
40114 ATTCTAATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
40138 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
40161 AATAATGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:46764 original size:24 final size:24
Alignment explanation
Indices: 46737--46855 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
46727 TTCGATTTGA
46737 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
46761 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
46785 ATTATGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
46809 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
46833 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
46856 AATTATGTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 85 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:46773 original size:48 final size:48
Alignment explanation
Indices: 46719--46855 Score: 152
Period size: 48 Copynumber: 2.9 Consensus size: 48
46709 TGAATATTTT
* * *
46719 ATCTGATTTTCGATTTGAATTCTGATCTGATACTTGACATGGATTCTG
1 ATCTGATTTTCGACTTGGATTATGATCTGATACTTGACATGGATTCTG
* * *
46767 ATCTGA-TATCTGACATGGATTATGATCTGATACTTGACTTGGATTCTG
1 ATCTGATTTTC-GACTTGGATTATGATCTGATACTTGACATGGATTCTG
* * * *
46815 ATATGATACTT-GACTTGGATTTTGATATGATACTTGACATG
1 ATCTGAT-TTTCGACTTGGATTATGATCTGATACTTGACATG
46856 AATTATGTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
47 3 0.04
48 69 0.95
50 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.42
Consensus pattern (48 bp):
ATCTGATTTTCGACTTGGATTATGATCTGATACTTGACATGGATTCTG
Found at i:55704 original size:18 final size:18
Alignment explanation
Indices: 55681--55716 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55671 TTATTTGTAC
55681 TTAACATTAGTATTATTA
1 TTAACATTAGTATTATTA
*
55699 TTAACATTATTATTATTA
1 TTAACATTAGTATTATTA
55717 AGTCCAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (18 bp):
TTAACATTAGTATTATTA
Found at i:57125 original size:40 final size:40
Alignment explanation
Indices: 57081--57183 Score: 179
Period size: 40 Copynumber: 2.6 Consensus size: 40
57071 TCAGCTGTTA
57081 TTTTACTCCTATTTTGATCACTCTACAATGACATGGATTG
1 TTTTACTCCTATTTTGATCACTCTACAATGACATGGATTG
* *
57121 TTTTACTCATATTTTGATCCCTCTACAATGACATGGATTG
1 TTTTACTCCTATTTTGATCACTCTACAATGACATGGATTG
*
57161 TTTTACTCCTATTTTGATAACTC
1 TTTTACTCCTATTTTGATCACTC
57184 AATTGAGAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (40 bp):
TTTTACTCCTATTTTGATCACTCTACAATGACATGGATTG
Found at i:60984 original size:68 final size:68
Alignment explanation
Indices: 60875--61230 Score: 588
Period size: 68 Copynumber: 5.2 Consensus size: 68
60865 TAAAGGATTG
*
60875 TGAGGCCTAACTGTGCTTATGACA-AGAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTA
1 TGAGGCCTAACTGTGCTTATGACAGA-AAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTG
60939 CCTT
65 CCTT
* *
60943 TGAGGCCTAACTGTACTTATGGCAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
1 TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
61008 CTT
66 CTT
* * *
61011 TGAGGCCTAACTGTGCTTATGACAGAAAGATGTCATATATGCCAGTTAGATGAAAGGCAAAGTGC
1 TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
*
61076 TTT
66 CTT
* *
61079 TGAGGCCTAACTGTGCTTATGACAGAAATGTATCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
1 TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
61144 CTT
66 CTT
* * *
61147 TAAGGCCTAACTGTGCTTATAAGAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
1 TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
61212 CTT
66 CTT
61215 TGAGGCCTAACTGTGC
1 TGAGGCCTAACTGTGC
61231 AATTGGTAGA
Statistics
Matches: 266, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
68 265 1.00
69 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (68 bp):
TGAGGCCTAACTGTGCTTATGACAGAAAGGTGTCATATAAGCCAGTTAGATGAAAGGCTAAGTGC
CTT
Found at i:61365 original size:81 final size:81
Alignment explanation
Indices: 61219--61858 Score: 877
Period size: 81 Copynumber: 7.9 Consensus size: 81
61209 TGCCTTTGAG
* * *
61219 GCCTAACTGTGCAATTGGTAGAAAGGTACTAATTATTCCAGTTAGATGAACAGTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
61284 GAGTAAAAGAATAATG
66 GAGTAAAAGAATAATA
* * * * * *
61300 GACTTACTGTGCAATTGGTAGAAAGATACCAATTATGCCTA-TTAGATGAATGGTTTAGTATCGT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCC-AGTTAGATGAACGGTTTAATACCGT
61364 TGAGTAAAAGAATAATA
65 TGAGTAAAAGAATAATA
* * * * *
61381 GTCTAATTGTGCAACTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAATGTTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
61446 GAGTAAATGAATAATA
66 GAGTAAAAGAATAATA
* ** ** *
61462 GACTAACTGTGCAATTGGTAGAAAGGTGTCAATTATGTTAGTTAGATGAACGGTTTAATATCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
61527 GAGTAAAAGAATAATG
66 GAGTAAAAGAATAATA
*
61543 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATACCAGTTAGATGAACGGTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
61608 GAGTAAAAGAATCATA
66 GAGTAAAAGAATAATA
* *
61624 GCCTAACTGTGCAATGGGTAGAAATGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
61689 GAGTAAAATAATAATA
66 GAGTAAAAGAATAATA
* * * * *
61705 GCCTAAATGTGCAATTGGTATAAAGGTACCAATTATGCCAATTAGATTAACAGTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
* *
61770 GAGTAAAGGAATAATG
66 GAGTAAAAGAATAATA
* * * * * * *
61786 GCCTAACTATGCAATTGGTAGAAGGGTGCCAATTATGTCAGTTAGATGAACGGTTAAACACGGTT
1 GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
*
61851 GAGCAAAA
66 GAGTAAAA
61859 ACGAAAGGTT
Statistics
Matches: 488, Mismatches: 69, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
80 1 0.00
81 486 1.00
82 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (81 bp):
GCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
GAGTAAAAGAATAATA
Found at i:62034 original size:2 final size:2
Alignment explanation
Indices: 62029--62077 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
62019 ATGATATATA
*
62029 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
62071 TG TG TG T
1 TG TG TG T
62078 ATATATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:63396 original size:97 final size:97
Alignment explanation
Indices: 63193--63472 Score: 294
Period size: 97 Copynumber: 3.0 Consensus size: 97
63183 AAAAAGTTTG
* * *
63193 ATAATTACAATAATTATCTT-TCTTTT-AA-ATATAAAATCTATCTCAACTC--ATATTAGGTTC
1 ATAATTACAATAATTAT-TTCTCTTTTAAATATATAAAATATATTTCAACTCAGATATTA--TTT
* * * * * *
63253 TATCA-AATAAATATTTATATTTTAGTAAAGTTTG
63 TATCATAATATATATATATATATTAATAAAGATTA
*
63287 ATAATTTCAATAATTATTTCTCTTTTAAATATATAAAAT-TATTTCAACTCAGATATTATTTTAT
1 ATAATTACAATAATTATTTCTCTTTTAAATATATAAAATATATTTCAACTCAGATATTATTTTAT
**
63351 CATATATATATATATATATATTAATTGAGATTA
66 CATA-ATATATATATATATATTAATAAAGATTA
* * **
63384 ATAATTACAATAAATATTTCTCTTTTAAATATAT-AAATATATTTCAACTCAGAAAAGATTTTAT
1 ATAATTACAATAATTATTTCTCTTTTAAATATATAAAATATATTTCAACTCAGATATTATTTTAT
*
63448 CATAA-A-A-ATATATATTTTAATAAAG
66 CATAATATATATATATATATTAATAAAG
63473 TTTGATATTT
Statistics
Matches: 159, Mismatches: 19, Indels: 17
0.82 0.10 0.09
Matches are distributed among these distances:
93 17 0.11
94 23 0.14
95 20 0.13
96 15 0.09
97 84 0.53
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (97 bp):
ATAATTACAATAATTATTTCTCTTTTAAATATATAAAATATATTTCAACTCAGATATTATTTTAT
CATAATATATATATATATATTAATAAAGATTA
Found at i:63539 original size:82 final size:81
Alignment explanation
Indices: 63412--63574 Score: 209
Period size: 82 Copynumber: 2.0 Consensus size: 81
63402 TCTCTTTTAA
*
63412 ATATATAAATATATTTCAACTCAGAAAAGATTTTATCATAAAAATATATATTTTAATAAAGTTTG
1 ATATATAAATATATTTCAACTCAGAAAAGATTCTATCATAAAAATATATA-TTTAATAAAGTTTG
* * *
63477 ATATTTATAATATATAT
65 ATAATTAGAATAAATAT
* * ** * ** *
63494 ATATATATATATATTTCAACTGAGATTATATTCTATTTTATAAATATATATTTAATAAAGTTTGA
1 ATATATAAATATATTTCAACTCAGAAAAGATTCTATCATAAAAATATATATTTAATAAAGTTTGA
63559 TAATTAGAATAAATAT
66 TAATTAGAATAAATAT
63575 CTCCTTTTTA
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
81 28 0.41
82 41 0.59
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (81 bp):
ATATATAAATATATTTCAACTCAGAAAAGATTCTATCATAAAAATATATATTTAATAAAGTTTGA
TAATTAGAATAAATAT
Found at i:63620 original size:9 final size:9
Alignment explanation
Indices: 63606--63665 Score: 79
Period size: 9 Copynumber: 6.8 Consensus size: 9
63596 TTATATTTAC
63606 AATAATTAT
1 AATAATTAT
63615 AATAATTATT
1 AATAATTA-T
* *
63625 TATAGTTAT
1 AATAATTAT
63634 AATAATTAT
1 AATAATTAT
63643 AAT-ATTA-
1 AATAATTAT
63650 AATAATTAT
1 AATAATTAT
63659 AATAATT
1 AATAATT
63666 TGTTTTAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
7 3 0.07
8 8 0.18
9 26 0.59
10 7 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (9 bp):
AATAATTAT
Found at i:63625 original size:28 final size:28
Alignment explanation
Indices: 63593--63646 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
63583 TAAATATTTA
*
63593 TATTTATATTTACAATAATTATAATAAT
1 TATTTATAGTTACAATAATTATAATAAT
*
63621 TATTTATAGTTATAATAATTATAATA
1 TATTTATAGTTACAATAATTATAATA
63647 TTAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
TATTTATAGTTACAATAATTATAATAAT
Found at i:63653 original size:16 final size:17
Alignment explanation
Indices: 63610--63662 Score: 72
Period size: 16 Copynumber: 3.1 Consensus size: 17
63600 ATTTACAATA
*
63610 ATTATAATAATTATTTAT
1 ATTATAATAATTA-TAAT
63628 AGTTATAATAATTATAAT
1 A-TTATAATAATTATAAT
63646 ATTA-AATAATTATAAT
1 ATTATAATAATTATAAT
63662 A
1 A
63663 ATTTGTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 13 0.39
17 3 0.09
18 5 0.15
19 12 0.36
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTATAATAATTATAAT
Found at i:65439 original size:10 final size:10
Alignment explanation
Indices: 65424--65454 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
65414 GGGATGGACA
*
65424 TGGGTCAGGT
1 TGGGTCGGGT
65434 TGGGTCGGGT
1 TGGGTCGGGT
65444 TGGGTCGGGT
1 TGGGTCGGGT
65454 T
1 T
65455 TTTGGTCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.03, C:0.10, G:0.55, T:0.32
Consensus pattern (10 bp):
TGGGTCGGGT
Done.