Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001204.1 Hibiscus syriacus cultivar Beakdansim tig00002379_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: 80493
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1883 original size:31 final size:31
Alignment explanation
Indices: 1845--2000 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
1835 AGGGTCGAGG
1845 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1876 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1907 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1938 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1969 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2000 G
1 G
2001 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4003 original size:84 final size:81
Alignment explanation
Indices: 3754--4294 Score: 522
Period size: 84 Copynumber: 6.6 Consensus size: 81
3744 CCAACCAAAT
* * * * *
3754 ACCTTCGAGTTCGACCACGCTCAGTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCGAG-AG
* *
3819 GGCTATCTG-TAA-AAG
65 GGTTATCTGCCAACAAG
* * ** * * * * *
3834 ACCCTCGAGTTCGACTACGCTCAACTTTGAGGGCACATCATTTACAGTATAACTCAAGGCTATAA
1 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTCAAGGCGA-GA
* *
3899 GGGTTATCTGTCACCAAAG
64 GGGTTATCTGCCAAC-AAG
* * * **
3918 ACCTTCTAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAATCGATGAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCGA-GAG
3983 GGTTATCTGCCAACCCAAG
65 GGTTATCTGCCAA--CAAG
* * * * * *
4002 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGCAGTATGACTTAAGTCGATAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCGA-GAG
*
4067 GGCTATCTG-CAA-AAG
65 GGTTATCTGCCAACAAG
* * * * *
4082 ACCTTCGAGTTCGATTACACTCAGCTTCGAGTGCACATCATTTGCAGCATAACTCAAGGCTAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATTTGCAGCATAACTCAAGGCGAG-A
4147 GGGTTATCTGCCAACAAAG
64 GGGTTATCTGCCAAC-AAG
* * * * * *
4166 ACCTTTGAGTTCGATTACGCTCAGCT-CAACGGCACATCATTTGCGGTATAACTCAAGGCTAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTCAAGGCGAGAG
4230 GGTCTATCTGCC-A-AAG
65 GGT-TATCTGCCAACAAG
* *
4246 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACAT-ATTTACAGCATA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
4295 GCCCAATACC
Statistics
Matches: 381, Mismatches: 65, Indels: 31
0.80 0.14 0.06
Matches are distributed among these distances:
79 9 0.02
80 84 0.22
81 74 0.19
82 9 0.02
83 82 0.22
84 122 0.32
85 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (81 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCGAGAGG
GTTATCTGCCAACAAG
Found at i:4084 original size:164 final size:161
Alignment explanation
Indices: 3754--4294 Score: 640
Period size: 164 Copynumber: 3.3 Consensus size: 161
3744 CCAACCAAAT
* * *
3754 ACCTTCGAGTTCGACCACGCTCAGTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
* * * * * * *
3819 GGCTATCTG-TAA-AAGACCCTCGAGTTCGACTACGCTCAACTTTGAGGGCACATCATTTACAGT
66 GGTTATCTGCCAACAAGACCTTCGAGTTCGACTACGCTCAGC--TCAAGGCACATCATTTGCAGT
*
3882 ATAACTCAAGGCTATAAGGGTTATCTGTCACCAAAG
129 ATAACTCAAGGCTATAAGGGCTATCTG-CA--AAAG
* * *
3918 ACCTTCTAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAATCGATG-A
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA-GAA
*
3982 GGGTTATCTGCCAACCCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGCA
65 GGGTTATCTGCCAA--CAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTGCA
* * * *
4047 GTATGACTTAAGTCGATAAGGGCTATCTGCAAAAG
127 GTATAACTCAAGGCTATAAGGGCTATCTGCAAAAG
* * * * * * *
4082 ACCTTCGAGTTCGATTACACTCAGCTTCGAGTGCACATCATTTGCAGCATAACTCAAGGCTAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATTTGCAGCATAACTTAAGTCGAGAA
* * *
4147 GGGTTATCTGCCAACAAAGACCTTTGAGTTCGATTACGCTCAGCTCAACGGCACATCATTTGCGG
65 GGGTTATCTGCCAAC-AAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTGCAG
* * *
4212 TATAACTCAAGGCTAGAAGGTCTATCTGCCAAAG
128 TATAACTCAAGGCTATAAGGGCTATCTGCAAAAG
* *
4246 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACAT-ATTTACAGCATA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
4295 GCCCAATACC
Statistics
Matches: 321, Mismatches: 46, Indels: 22
0.83 0.12 0.06
Matches are distributed among these distances:
162 11 0.03
163 9 0.03
164 191 0.60
165 43 0.13
166 3 0.01
167 38 0.12
168 26 0.08
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (161 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
GGTTATCTGCCAACAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTGCAGTAT
AACTCAAGGCTATAAGGGCTATCTGCAAAAG
Found at i:4187 original size:248 final size:246
Alignment explanation
Indices: 3733--4296 Score: 730
Period size: 248 Copynumber: 2.3 Consensus size: 246
3723 CAAGAAAAGA
* * * * * *
3733 AGGGCTATTTGCCAACCAAATACCTTCGAGTTCGACCACGCTCAGTTCCAAGGCACATCATTTGC
1 AGGGTTATCTGCCAACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGC
* * *
3798 AGCATAGCTTAAGTCGAGAAGGGCTATCTGTAAAAGACCCTCGAGTTCGACTACGCTCAACTTTG
65 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCAAAAGACCCTCGAGTTCGACTACACTCAACTTCG
* * * *
3863 AGGGCACATCATTTACAGTATAACTCAAGGCTATAAGGGTTATCTGTCACCAAAGACCTTCTAGT
130 AGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCTAGT
* * *
3928 TCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAAATCGATG
195 TCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAACTCAAAGCGA-G
3981 AGGGTTATCTGCCAACCCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGC
1 AGGGTTATCTGCCAA-CCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGC
* * * * *
4046 AGTAT-GACTTAAGTCGATAAGGGCTATCTGCAAAAGACCTTCGAGTTCGATTACACTCAGCTTC
65 AGCATAG-CTTAAGTCGAGAAGGGCTATCTGCAAAAGACCCTCGAGTTCGACTACACTCAACTTC
* *
4110 GAGTGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTT-TGA
129 GAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCT-A
* * * * *
4174 GTTCGATTACGCTCAGCTCAACGGCACATCATTTGCGGTATAACTCAAGGCTAG
193 GTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAACTCAAAGCGAG
* *
4228 AAGGTCTATCTGCC-A--AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GACACAT-ATTTA
1 AGGGT-TATCTGCCAACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGA-ACATCATTTG
4288 CAGCATAGC
64 CAGCATAGC
4297 CCAATACCAG
Statistics
Matches: 278, Mismatches: 31, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
243 12 0.04
244 38 0.14
247 11 0.04
248 215 0.77
249 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (246 bp):
AGGGTTATCTGCCAACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAACATCATTTGCA
GCATAGCTTAAGTCGAGAAGGGCTATCTGCAAAAGACCCTCGAGTTCGACTACACTCAACTTCGA
GGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCTAGTT
CGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAACTCAAAGCGAG
Found at i:4776 original size:2 final size:2
Alignment explanation
Indices: 4763--4810 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
4753 TTTTGTTTGT
* *
4763 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4805 TA TA TA
1 TA TA TA
4811 GTAATATAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4907 original size:63 final size:62
Alignment explanation
Indices: 4840--4958 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 62
4830 TGTTTTTGAC
* * * *
4840 AAAATATAATATA-ATTTTTTCAGAAAATGATTTTCG-AAAATTTATATATTATATAGTATTTTT
1 AAAATATAATATATA-GTTTT-AAAAAAAGATTTTCGAAAAATTT-TATAATATATAGTATTTTT
*
4903 AAAATATAATATATAGTTTTAAAAAAAGATTTTTGAAAAATTTTATAATATATAGT
1 AAAATATAATATATAGTTTTAAAAAAAGATTTTCGAAAAATTTTATAATATATAGT
4959 TTAAAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
62 24 0.49
63 24 0.49
64 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (62 bp):
AAAATATAATATATAGTTTTAAAAAAAGATTTTCGAAAAATTTTATAATATATAGTATTTTT
Found at i:4909 original size:21 final size:20
Alignment explanation
Indices: 4885--4926 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4875 GAAAATTTAT
* *
4885 ATATTATATAGTATTTTTAAA
1 ATATAATATA-TAGTTTTAAA
4906 ATATAATATATAGTTTTAAA
1 ATATAATATATAGTTTTAAA
4926 A
1 A
4927 AAAGATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
ATATAATATATAGTTTTAAA
Found at i:4927 original size:21 final size:22
Alignment explanation
Indices: 4883--4927 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
4873 TCGAAAATTT
* *
4883 ATATATTATATAGTATTTTTAAA
1 ATATAATATATAG-ATTTTAAAA
4906 ATATAATATATAG-TTTTAAAA
1 ATATAATATATAGATTTTAAAA
4927 A
1 A
4928 AAGATTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
ATATAATATATAGATTTTAAAA
Found at i:4954 original size:39 final size:39
Alignment explanation
Indices: 4906--5068 Score: 224
Period size: 38 Copynumber: 4.2 Consensus size: 39
4896 TATTTTTAAA
4906 ATATAATATATAGTTTTAAAAAAAGATTTTTGAAAAATT
1 ATATAATATATAGTTTTAAAAAAAGATTTTTGAAAAATT
* *
4945 TTATAATATATAG-TTTAAAAAAATATTTTTTGAAAAATT
1 ATATAATATATAGTTTTAAAAAAAGA-TTTTTGAAAAATT
* * *
4984 CTATAGTATATAGTTTT-AAAAAACATTTTTGAAAAATT
1 ATATAATATATAGTTTTAAAAAAAGATTTTTGAAAAATT
* *
5022 ATATAATATATAGTTTTAAAAATAG-TTTTTGAAAACTT
1 ATATAATATATAGTTTTAAAAAAAGATTTTTGAAAAATT
*
5060 AGATAATAT
1 ATATAATAT
5069 TTTTTAAAAC
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
38 59 0.54
39 48 0.44
40 3 0.03
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (39 bp):
ATATAATATATAGTTTTAAAAAAAGATTTTTGAAAAATT
Found at i:4973 original size:38 final size:39
Alignment explanation
Indices: 4906--5068 Score: 206
Period size: 39 Copynumber: 4.2 Consensus size: 39
4896 TATTTTTAAA
*
4906 ATATAATATATAGTTTTAAAAAA-AGATTTTTGAAAAATT
1 ATATAATATATAGTTTAAAAAAATAG-TTTTTGAAAAATT
* *
4945 TTATAATATATAGTTTAAAAAAATATTTTTTGAAAAATT
1 ATATAATATATAGTTTAAAAAAATAGTTTTTGAAAAATT
* * * *
4984 CTATAGTATATAGTTTTAAAAAACA-TTTTTGAAAAATT
1 ATATAATATATAGTTTAAAAAAATAGTTTTTGAAAAATT
* *
5022 ATATAATATATAGTTT-TAAAAATAGTTTTTGAAAACTT
1 ATATAATATATAGTTTAAAAAAATAGTTTTTGAAAAATT
*
5060 AGATAATAT
1 ATATAATAT
5069 TTTTTAAAAC
Statistics
Matches: 109, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
37 6 0.06
38 47 0.43
39 55 0.50
40 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (39 bp):
ATATAATATATAGTTTAAAAAAATAGTTTTTGAAAAATT
Found at i:5018 original size:77 final size:77
Alignment explanation
Indices: 4907--5056 Score: 239
Period size: 77 Copynumber: 1.9 Consensus size: 77
4897 ATTTTTAAAA
* * *
4907 TATAATATATAGTTTTAAAAAAAGATTTTTGAAAAATTTTATAATATATAGTTTAAAAAAATATT
1 TATAATATATAGTTTTAAAAAAACATTTTTGAAAAATTATATAATATATAGTTT-AAAAAATAGT
4972 TTTTGAAAAATTC
65 TTTTGAAAAATTC
* *
4985 TATAGTATATAGTTTT-AAAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAATAGTT
1 TATAATATATAGTTTTAAAAAAACATTTTTGAAAAATTATATAATATATAGTTTAAAAAATAGTT
5049 TTTGAAAA
66 TTTGAAAA
5057 CTTAGATAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
76 17 0.25
77 35 0.52
78 15 0.22
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.43
Consensus pattern (77 bp):
TATAATATATAGTTTTAAAAAAACATTTTTGAAAAATTATATAATATATAGTTTAAAAAATAGTT
TTTGAAAAATTC
Found at i:5125 original size:24 final size:24
Alignment explanation
Indices: 5080--5126 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5070 TTTTAAAACA
*
5080 TTTTGAAAACTATATAACATATAG
1 TTTTGAAAACTATATAAAATATAG
* *
5104 TTTTGAAAACTTTTTAAAATATA
1 TTTTGAAAACTATATAAAATATA
5127 ATATATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (24 bp):
TTTTGAAAACTATATAAAATATAG
Found at i:5176 original size:30 final size:31
Alignment explanation
Indices: 5115--5178 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
5105 TTTGAAAACT
*
5115 TTTTAAAATATAATATATAGTTTAAAAAATA
1 TTTTAAAATATAATATATAGTATAAAAAATA
* *
5146 TTTTGAAATAT-ATATATTA-TATAAATAATA
1 TTTTAAAATATAATATA-TAGTATAAAAAATA
5176 TTT
1 TTT
5179 AGTATATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTTAAAATATAATATATAGTATAAAAAATA
Found at i:5189 original size:3 final size:3
Alignment explanation
Indices: 5183--5212 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5173 ATATTTAGTA
5183 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5213 TTAATTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:6976 original size:2 final size:2
Alignment explanation
Indices: 6969--7058 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
6959 TCCGACAGTA
6969 AT AT AT AT AT 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 AT AT AT AT AT
7011 AT AT AT AT AT 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 AT AT AT AT AT
7053 AT AT AT
1 AT AT AT
7059 TTGATATCGT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9154 original size:13 final size:14
Alignment explanation
Indices: 9132--9168 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
9122 GTCAAAGAAA
9132 GTCAACGGTCAACG
1 GTCAACGGTCAACG
9146 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
9159 GTCAACGGTC
1 GTCAACGGTC
9169 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:9180 original size:17 final size:17
Alignment explanation
Indices: 9158--9190 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9148 CACGGTCAAC
9158 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
9175 GGTCAACGGTCGGGTC
1 GGTCAACGGTCGGGTC
9191 AACAGTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:9185 original size:7 final size:7
Alignment explanation
Indices: 9132--9168 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
9122 GTCAAAGAAA
9132 GTCAACG
1 GTCAACG
9139 GTCAACG
1 GTCAACG
9146 GTC-ACG
1 GTCAACG
9152 GTCAACG
1 GTCAACG
9159 GTCAACG
1 GTCAACG
9166 GTC
1 GTC
9169 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:15750 original size:6 final size:7
Alignment explanation
Indices: 15728--15782 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
15718 GTCAAAGAAA
*
15728 GTCAATG
1 GTCAACG
15735 GTCAACG
1 GTCAACG
15742 GTC-ACG
1 GTCAACG
15748 GTCAACG
1 GTCAACG
15755 GTC-ACG
1 GTCAACG
15761 GTCAACG
1 GTCAACG
*
15768 GTC--GG
1 GTCAACG
15773 GTCAACG
1 GTCAACG
15780 GTC
1 GTC
15783 GGGTCGGGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 4 0.10
6 12 0.29
7 25 0.61
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:15757 original size:20 final size:21
Alignment explanation
Indices: 15728--15782 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
15718 GTCAAAGAAA
*
15728 GTCAATGGTCAACGGTC-ACG
1 GTCAACGGTCAACGGTCAACG
15748 GTCAACGGTC-ACGGTCAACG
1 GTCAACGGTCAACGGTCAACG
*
15768 GTC--GGGTCAACGGTC
1 GTCAACGGTCAACGGTC
15783 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 4 0.13
19 12 0.39
20 15 0.48
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (21 bp):
GTCAACGGTCAACGGTCAACG
Found at i:15787 original size:12 final size:13
Alignment explanation
Indices: 15734--15782 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
15724 GAAAGTCAAT
15734 GGTCAACGGTCAC
1 GGTCAACGGTCAC
15747 GGTCAACGGTCAC
1 GGTCAACGGTCAC
*
15760 GGTCAACGGTC-G
1 GGTCAACGGTCAC
15772 GGTCAACGGTC
1 GGTCAACGGTC
15783 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 11 0.31
13 24 0.69
ACGTcount: A:0.20, C:0.29, G:0.35, T:0.16
Consensus pattern (13 bp):
GGTCAACGGTCAC
Found at i:15811 original size:19 final size:19
Alignment explanation
Indices: 15789--15858 Score: 113
Period size: 19 Copynumber: 3.7 Consensus size: 19
15779 GGTCGGGTCG
*
15789 GGTCAACCCGGTTCAAACC
1 GGTCAAACCGGTTCAAACC
*
15808 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
15827 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCAAACC
15846 GGTCAAACCGGTT
1 GGTCAAACCGGTT
15859 TTCCAGCAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:15815 original size:9 final size:9
Alignment explanation
Indices: 15789--15857 Score: 84
Period size: 9 Copynumber: 7.3 Consensus size: 9
15779 GGTCGGGTCG
*
15789 GGTCAACCC
1 GGTCAAACC
15798 GGTTCAAACC
1 GG-TCAAACC
15808 GGTCAAACC
1 GGTCAAACC
*
15817 GGTTCAGACC
1 GG-TCAAACC
15827 GGTCAAACC
1 GGTCAAACC
*
15836 GGTTCGAACC
1 GG-TCAAACC
15846 GGTCAAACC
1 GGTCAAACC
15855 GGT
1 GGT
15858 TTTCCAGCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
9 28 0.54
10 24 0.46
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:20250 original size:6 final size:6
Alignment explanation
Indices: 20241--20271 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
20231 TTCCAAATTC
20241 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
20272 ATATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:23777 original size:23 final size:23
Alignment explanation
Indices: 23746--23829 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
23736 TTTGTGTTTA
23746 TTCATTTAATGTTCACGAATAT-
1 TTCATTTAATGTTCACGAATATG
* * *
23768 TATCATTTAATGTTTACAAATGTG
1 T-TCATTTAATGTTCACGAATATG
* **
23792 TTCATTTGATGTTCACGAACGTG
1 TTCATTTAATGTTCACGAATATG
* *
23815 TTCGTTTAATATTCA
1 TTCATTTAATGTTCA
23830 TTTAACGTTC
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 1 0.02
23 48 0.96
24 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (23 bp):
TTCATTTAATGTTCACGAATATG
Found at i:24396 original size:23 final size:23
Alignment explanation
Indices: 24364--24497 Score: 178
Period size: 23 Copynumber: 5.8 Consensus size: 23
24354 AAACTTAAGC
* * *
24364 CGATTAAAGCTCGATTTAGAACT
1 CGATTCAAGCTCGATTTGGAGCT
*
24387 CAATTCAAGCTCGATTTGGAGCT
1 CGATTCAAGCTCGATTTGGAGCT
* *
24410 CGATTCAAGCTCAATTTGGAGTT
1 CGATTCAAGCTCGATTTGGAGCT
* *
24433 CAATTCAAGCTCAATTTGGAGCT
1 CGATTCAAGCTCGATTTGGAGCT
*
24456 TGATTCAAGCTCGATTTGGAGCT
1 CGATTCAAGCTCGATTTGGAGCT
*
24479 TGATTCAAGCTCGATTTGG
1 CGATTCAAGCTCGATTTGG
24498 TTAATGTTGA
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 99 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (23 bp):
CGATTCAAGCTCGATTTGGAGCT
Found at i:25883 original size:21 final size:20
Alignment explanation
Indices: 25851--25901 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
25841 AAACCATTTA
* *
25851 ATTATATATTTTGACACTATT
1 ATTAT-TATTTTTACAATATT
*
25872 ATTATTATTTTTATAATATT
1 ATTATTATTTTTACAATATT
25892 ATGTATTATT
1 AT-TATTATT
25902 GTTGTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTATTATTTTTACAATATT
Found at i:26342 original size:21 final size:21
Alignment explanation
Indices: 26277--26346 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
26267 AGGGTTTAGG
* *
26277 GTTTAGTAATTAGGAATTAAG
1 GTTTAGGAATTAGGAATTAAT
* ** * * *
26298 GATTAGGCTTTATGATTTAGT
1 GTTTAGGAATTAGGAATTAAT
*
26319 GTTTAGGAGTTAGGAATTAAT
1 GTTTAGGAATTAGGAATTAAT
26340 GTTTAGG
1 GTTTAGG
26347 GTTGAGGGAT
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.01, G:0.27, T:0.41
Consensus pattern (21 bp):
GTTTAGGAATTAGGAATTAAT
Found at i:28241 original size:149 final size:149
Alignment explanation
Indices: 28042--28342 Score: 566
Period size: 149 Copynumber: 2.0 Consensus size: 149
28032 AGAGCTCGTG
*
28042 TCCTATTTTGAAGATTGGGGCTTGATTTGTATATGATTGGGAATCTGTGTAATTGTTATTGTCTG
1 TCCTATTTTGAAGATTAGGGCTTGATTTGTATATGATTGGGAATCTGTGTAATTGTTATTGTCTG
28107 ATTTATCATTGATAAAGTCCTATCACAATACGAAATTAGACCCTACACTTCAGTTTTATGATAAG
66 ATTTATCATTGATAAAGTCCTATCACAATACGAAATTAGACCCTACACTTCAGTTTTATGATAAG
28172 AACTGTTGTTATTTGGTCC
131 AACTGTTGTTATTTGGTCC
* * *
28191 TCCTATTTTGAAGATTAGGGCTTGTTTTGTATATGATTTGGAATCTGTGTAATTGTTTTTGTCTG
1 TCCTATTTTGAAGATTAGGGCTTGATTTGTATATGATTGGGAATCTGTGTAATTGTTATTGTCTG
28256 ATTTATCATTGATAAAGTCCTATCACAATACGAAATTAGACCCTACACTTCAGTTTTATGATAAG
66 ATTTATCATTGATAAAGTCCTATCACAATACGAAATTAGACCCTACACTTCAGTTTTATGATAAG
28321 AACTGTTGTTATTTGGTCC
131 AACTGTTGTTATTTGGTCC
28340 TCC
1 TCC
28343 ATTGTGTGCC
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (149 bp):
TCCTATTTTGAAGATTAGGGCTTGATTTGTATATGATTGGGAATCTGTGTAATTGTTATTGTCTG
ATTTATCATTGATAAAGTCCTATCACAATACGAAATTAGACCCTACACTTCAGTTTTATGATAAG
AACTGTTGTTATTTGGTCC
Found at i:30803 original size:19 final size:20
Alignment explanation
Indices: 30767--30804 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30757 GTTTGTTGTT
*
30767 TTTTTTTTCTTTTCTCTGTA
1 TTTTTTTTCTGTTCTCTGTA
30787 TTTTTTTTCTGTT-TCTGT
1 TTTTTTTTCTGTTCTCTGT
30805 CTCTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.76
Consensus pattern (20 bp):
TTTTTTTTCTGTTCTCTGTA
Found at i:31319 original size:3 final size:3
Alignment explanation
Indices: 31311--31377 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
31301 TAATATAAAT
31311 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31359 TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
31378 TGGATAAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:31717 original size:116 final size:115
Alignment explanation
Indices: 31513--32487 Score: 1261
Period size: 116 Copynumber: 8.6 Consensus size: 115
31503 ATTGAATAAA
* * ** *
31513 TTCTTC-TCTTTCTTCAGAT--GAGTTCTTCTCATTATGAACTTTCT-GCTGGGGATGATGATCC
1 TTCTTCTTCCTTCTTCAGATACGAGTTCTTCTCATTATGAAC--TCTACCTGGCAAAGATGATCC
*
31574 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 ATCAAGTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
31626 TTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCA
1 TTCTTCTTCCTTCTTCAGAT-ACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATGATCCA
* * *
31691 TCAAATGATGAATTCAAGCAAAAGATTGAGCAAGTTCTTCTTATTATGAAC
65 TCAAGTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * * *
31742 TTCTTCTTCCTTCTTCA-A-ATGAGTTCTTCTCATTATGAAC-CTTCTCTGGCAAAAATAATCCA
1 TTCTTCTTCCTTCTTCAGATACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATGATCCA
*
31804 TCAAGTGATGAATTCAA-AAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 TCAAGTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * *
31854 TTCTTCTTCCTTCTTCAGAT--GAGTTCTTCTCATTATGAAC-CTTCTCTGGCAAAAATAATCCA
1 TTCTTCTTCCTTCTTCAGATACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATGATCCA
* * *
31916 TCAAATGATGAATTCAAGCAAAAGATTGAGCAAGTTCTTCTTATTATGAAC
65 TCAAGTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * * *
31967 TTCTTCTTCCTTCTTCA-A-ATGAGTTCTTCTCATTATGAAC-CTTCTCTGGCAAAAATAATCCA
1 TTCTTCTTCCTTCTTCAGATACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATGATCCA
32029 TCAAGTGATGAATTCAA--AAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 TCAAGTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * *
32078 TTCTTCTTCCTTCTTCAGAT--GAGTTCTTCTCATTATGAAC-CTTCTCTGGCAAAAATAATCCA
1 TTCTTCTTCCTTCTTCAGATACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATGATCCA
* * *
32140 TCAAGTGATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 TCAAGTGATGAATTCAAG-CAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * *
32191 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCA
1 TTCTTCTTCCTTCTTCAGAT-ACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATGATCCA
* ** *
32256 TCAAGTGATGGATTTGAGCTAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 TCAAGTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * * *
32307 TTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCA
1 TTCTTCTTCCTTCTTCAGAT-ACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATGATCCA
* ** *
32372 TCAAGTGATGGATTTGAGCTAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 TCAAGTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * *
32423 TTCTTCTTCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGATGATCCA
1 TTCTTCTTCCTTCTTCAGAT-ACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATGATCCA
32488 CCAGATGATG
Statistics
Matches: 801, Mismatches: 40, Indels: 39
0.91 0.05 0.04
Matches are distributed among these distances:
110 1 0.00
111 104 0.13
112 110 0.14
113 213 0.27
114 13 0.02
115 4 0.00
116 332 0.41
117 24 0.03
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (115 bp):
TTCTTCTTCCTTCTTCAGATACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATGATCCAT
CAAGTGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
Found at i:33191 original size:47 final size:50
Alignment explanation
Indices: 33121--33226 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 50
33111 TCTAAATTCA
*
33121 ATGCT-TGATTCTGTCCAA--TCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGATTCTGTCCAACCACAGATAACTCAAAGAACACTTCCAGAAG
33168 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGATTCTGTCCAACC--A-CAGATAACTCAAAGAACACTTCCAGAAG
33220 ATGCTAT
1 ATGCTAT
33227 TGGCAAATTC
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
47 15 0.29
48 2 0.04
52 35 0.67
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (50 bp):
ATGCTATGATTCTGTCCAACCACAGATAACTCAAAGAACACTTCCAGAAG
Found at i:33219 original size:130 final size:130
Alignment explanation
Indices: 33059--33356 Score: 587
Period size: 130 Copynumber: 2.3 Consensus size: 130
33049 CACTTCTTCG
33059 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATG
1 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATG
33124 CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
66 CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
33189 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATG
1 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATG
33254 CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
66 CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
33319 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTAT
33357 GTTCTGTCCA
Statistics
Matches: 166, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 166 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (130 bp):
GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATG
CTTGATTCTGTCCAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:33344 original size:52 final size:52
Alignment explanation
Indices: 33268--33668 Score: 757
Period size: 52 Copynumber: 7.7 Consensus size: 52
33258 ATTCTGTCCA
33268 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
*
33320 ATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
*
33372 ATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
33424 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
* *
33476 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTTCTATCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
33528 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
*
33580 ATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
33632 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
33669 TGGCATATTC
Statistics
Matches: 339, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 339 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (52 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
Found at i:47131 original size:25 final size:24
Alignment explanation
Indices: 47087--47145 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
47077 TAGTTTGTTG
*
47087 TTTTTTTCTTTTCTTTTCTCTGTAT
1 TTTTTTTCTTTTCTTATCTCT-TAT
*
47112 TTTTTTTCTGTTTC-TATCTCTTCT
1 TTTTTTTCT-TTTCTTATCTCTTAT
47136 TTTTGTTTCT
1 TTTT-TTTCT
47146 CTCTGTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.20
25 20 0.67
26 4 0.13
ACGTcount: A:0.03, C:0.17, G:0.05, T:0.75
Consensus pattern (24 bp):
TTTTTTTCTTTTCTTATCTCTTAT
Found at i:47644 original size:3 final size:3
Alignment explanation
Indices: 47636--47693 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
47626 TAATATAAAT
47636 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47684 TAA TAA TAA T
1 TAA TAA TAA T
47694 GGATAAAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52395 original size:27 final size:26
Alignment explanation
Indices: 52357--52423 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
52347 TATATGTATA
52357 AATAATTATATTTATTGATATAAAAAT
1 AATAATTATATTTATT-ATATAAAAAT
* * *
52384 AATAATTTTATTTATTTTCTAAAAAT
1 AATAATTATATTTATTATATAAAAAT
*
52410 ATATAATTAAATTT
1 A-ATAATTATATTT
52424 TAATATACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
AATAATTATATTTATTATATAAAAAT
Found at i:60152 original size:58 final size:58
Alignment explanation
Indices: 60082--60197 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
60072 AGACGGCATA
60082 AAGGATGGGGATAGGTGTGACCTCAAAGCTCATTCTCTTTGATACTTCCCTTTTTCGT
1 AAGGATGGGGATAGGTGTGACCTCAAAGCTCATTCTCTTTGATACTTCCCTTTTTCGT
60140 AAGGATGGGGATAGGTGTGACCTCAAAGCTCATTCTCTTTGATACTTCCCTTTTTCGT
1 AAGGATGGGGATAGGTGTGACCTCAAAGCTCATTCTCTTTGATACTTCCCTTTTTCGT
60198 TGTTATCTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (58 bp):
AAGGATGGGGATAGGTGTGACCTCAAAGCTCATTCTCTTTGATACTTCCCTTTTTCGT
Found at i:61703 original size:20 final size:20
Alignment explanation
Indices: 61680--61784 Score: 165
Period size: 20 Copynumber: 5.2 Consensus size: 20
61670 TGCGATTTTC
61680 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
61700 CAAATTCGCTACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
61720 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
*
61740 TAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
61760 TAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
61780 CAAAT
1 CAAAT
61785 ATTTTTACGC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:63953 original size:21 final size:21
Alignment explanation
Indices: 63929--63978 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
63919 GTTAGGGGAA
* * *
63929 TTACGTGATGAGGTTGTTGCT
1 TTACGTGATGAGGTCGGTACT
*
63950 TTACGTCATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
63971 TTACGTGA
1 TTACGTGA
63979 AGATAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.14, G:0.30, T:0.38
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:64416 original size:21 final size:22
Alignment explanation
Indices: 64385--64482 Score: 91
Period size: 21 Copynumber: 4.7 Consensus size: 22
64375 CGATGCACCT
* *
64385 ATCATCATTCAAGAGGCGCCTC
1 ATCATCGTTCAAGAGGCCCCTC
64407 AT-ATCGTTCAAGAGGCCCCTC
1 ATCATCGTTCAAGAGGCCCCTC
*
64428 ATCATCG---AAGAAGCCCCTC
1 ATCATCGTTCAAGAGGCCCCTC
* * *
64447 -CCACCGTTCAAGAGGCCCAT-
1 ATCATCGTTCAAGAGGCCCCTC
*
64467 GTCATCGTTCAAGAGG
1 ATCATCGTTCAAGAGG
64483 TCCCACCCGT
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.06
19 11 0.18
21 41 0.66
22 6 0.10
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (22 bp):
ATCATCGTTCAAGAGGCCCCTC
Found at i:64430 original size:40 final size:41
Alignment explanation
Indices: 64386--64482 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 41
64376 GATGCACCTA
* * *
64386 TCATCATTCAAGAGGCGCCTCATATCGTTCAAGAGGCCC-C
1 TCATCATTCAAGAGGCCCCTCACACCGTTCAAGAGGCCCAC
* * *
64426 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCATG
1 TCATCATTC-AAGAGGCCCCTCACACCGTTCAAGAGGCCCA-C
*
64468 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
64483 TCCCACCCGT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
39 2 0.04
40 31 0.69
42 10 0.22
43 2 0.04
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (41 bp):
TCATCATTCAAGAGGCCCCTCACACCGTTCAAGAGGCCCAC
Found at i:65687 original size:15 final size:16
Alignment explanation
Indices: 65653--65688 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
65643 ACTCTTTAAA
65653 TGGTTTGAAAATATTT
1 TGGTTTGAAAATATTT
65669 TGGTTTGAAAATA-TT
1 TGGTTTGAAAATATTT
65684 TGGTT
1 TGGTT
65689 AAGTACCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (16 bp):
TGGTTTGAAAATATTT
Found at i:65936 original size:14 final size:14
Alignment explanation
Indices: 65917--65956 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
65907 TTTTGATTAA
65917 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
65931 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
65945 TTGATTTGTAAA
1 TTGATTTGTAAA
65957 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:65968 original size:62 final size:63
Alignment explanation
Indices: 65866--66006 Score: 196
Period size: 66 Copynumber: 2.2 Consensus size: 63
65856 TTTTACATTG
*
65866 AAAGTTGATTTGTTTAATTGATGAGAAAATAAGATTTA-TTTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGAAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTA
** * *
65927 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGAAAATAAGAATTA-TTTTTT-CTTGATTAATTGATTTGT
65992 A
63 A
65993 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
66007 GTTTCTAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
61 17 0.24
62 17 0.24
64 5 0.07
66 31 0.44
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.52
Consensus pattern (63 bp):
AAAGTTGATTTGTTTAATTGATGAGAAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTA
Found at i:66494 original size:18 final size:18
Alignment explanation
Indices: 66471--66506 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
66461 AAGCCGGTTG
*
66471 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
66489 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
66507 CCTTTTGCTT
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:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:67485 original size:24 final size:24
Alignment explanation
Indices: 67458--67507 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
67448 ATAAATAACC
67458 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
67482 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
67506 AA
1 AA
67508 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:73088 original size:24 final size:24
Alignment explanation
Indices: 73061--73110 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
73051 ATAAAGAACC
73061 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAATCTTAAACAT-CCATTA
*
73085 AAAATAAATTTTAAACATCCATTA
1 AAAATAAATCTTAAACATCCATTA
73109 AA
1 AA
73111 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATAAATCTTAAACATCCATTA
Found at i:76164 original size:12 final size:12
Alignment explanation
Indices: 76143--76176 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
76133 GGTTGTGGGT
*
76143 TTTGAGATTGTG
1 TTTGATATTGTG
76155 TTTGATATTGTG
1 TTTGATATTGTG
*
76167 TTTGGTATTG
1 TTTGATATTG
76177 GAAATGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Done.