Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007672.1 Hibiscus syriacus cultivar Beakdansim tig00027365_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: 33251
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.22
Found at i:2849 original size:160 final size:164
Alignment explanation
Indices: 2493--3057 Score: 742
Period size: 160 Copynumber: 3.4 Consensus size: 164
2483 ACGTGTGCGT
* * **
2493 GCCTCAGTCACTATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
*
2558 GTGCGGGAGTACCGCACA-ACCGAGCGTTGGTGTGGGAGCCTCGTCACCATCAGGCCCCCGTGTG
65 GTGCGGGAGT---GCACAGACCGAGCGTTGGTGCGGGAGCCTCGTCACCATCAGGCCCCCGTGTG
* * * *
2622 CGTGCGCCTCGGTCACCATCAGTAATCCAAGGTGGGTG
127 CGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
* *
2660 GCCTCGGTCACCATCGGC-AACCTAGACGGGTGTCTCGATCACCATCGGCAACCCC-GCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
*
2723 TGC-GGA-TG-ACAGTACCGAGCTTTGGTGCGGGAGCCTCGTCACCATCAGGCCCCCGTGTGCGT
66 TGCGGGAGTGCACAG-ACCGAGCGTTGGTGCGGGAGCCTCGTCACCATCAGGCCCCCGTGTGCGT
* *
2785 GAGCCTCAGTCA-CATCGGCAATCTAAGGCGGGTG
130 GAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
* *
2819 GCGTCGATCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGAGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCG-GCCATTG
* * *
2884 GTACGGGAGTGCTGCACAGAACCGAGCGGTT-GTGCGGGAGTCTCGATCACCATCAGG-CCCCTT
65 GTGCGGGA--G-TGCACAG-ACCGAGC-GTTGGTGCGGGAGCCTCG-TCACCATCAGGCCCCCGT
*
2947 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
124 GTGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
2988 GCCTCGGTCACCATCGGCAAACCCAGAC----GTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
3049 GTGCGGGAG
65 GTGCGGGAG
3058 CCTCAGTCAC
Statistics
Matches: 354, Mismatches: 29, Indels: 34
0.85 0.07 0.08
Matches are distributed among these distances:
158 3 0.01
159 35 0.10
160 92 0.26
162 11 0.03
163 7 0.02
164 11 0.03
165 38 0.11
166 34 0.10
167 18 0.05
168 46 0.13
169 59 0.17
ACGTcount: A:0.19, C:0.33, G:0.31, T:0.18
Consensus pattern (164 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
TGCGGGAGTGCACAGACCGAGCGTTGGTGCGGGAGCCTCGTCACCATCAGGCCCCCGTGTGCGTG
AGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:2995 original size:33 final size:33
Alignment explanation
Indices: 2955--3141 Score: 120
Period size: 33 Copynumber: 5.6 Consensus size: 33
2945 TTGTGCGTGA
2955 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
* *
2988 GCCTCGGTCACCATCGGCAAACCCAGAC--GT-
1 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
* * *
3018 --CTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAATCCCAGG-C----G-G-GTG
* * ** * *
3056 AGCCTCAGTCACCATCATGC---CCCTTGTGCGTG
1 -GCCTCGGTCACCATC-GGCAATCCCAGGCGGGTG
*
3088 AGCCTCGGTCACCATCGGTAATCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
3122 GCCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
3142 ACCCGGGCCA
Statistics
Matches: 116, Mismatches: 21, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
28 22 0.19
29 1 0.01
31 3 0.03
32 17 0.15
33 45 0.39
34 9 0.08
37 1 0.01
39 4 0.03
41 12 0.10
42 2 0.02
ACGTcount: A:0.17, C:0.37, G:0.29, T:0.17
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
Found at i:11647 original size:169 final size:168
Alignment explanation
Indices: 11332--11908 Score: 917
Period size: 169 Copynumber: 3.4 Consensus size: 168
11322 ACGTGTGCGT
* **
11332 GCCTCGGTCACCATAGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
*
11397 TAC-GGAGTG-CGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGG-CCCCGTGT
* **
11460 GCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCAAGTG
130 GCGTGCGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
11499 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
* * * *
11564 TGCGGGAGTGCCGCACAGTACCGAGCTTTGGTACGGGAGCCTCGGTCACAATCAGGACCCCGTGT
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGG-CCCCGTGT
11629 GCGTGCGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
130 GCGTGCGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
* *
11668 GCCTCGGTCAGCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACACCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAAC-CCCGGCCATTG
* * * *
11733 GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGGCCCCTTCT
65 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
* *
11798 GCGTGAGCCTCGGTCACCATCGGCAA-CCCAGGCGGGTG
130 GCGTGCGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
* *
11836 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCGGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
11901 TGCGGGAG
66 TGCGGGAG
11909 CCTCGGTCAC
Statistics
Matches: 381, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
167 84 0.22
168 68 0.18
169 168 0.44
170 61 0.16
ACGTcount: A:0.19, C:0.33, G:0.32, T:0.16
Consensus pattern (168 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGTG
CGTGCGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:11715 original size:32 final size:33
Alignment explanation
Indices: 11635--11719 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
11625 GTGTGCGTGC
* *
11635 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
* *
11668 GCCTCGGTCAGCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
11700 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
11720 CACCGGGCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 18 0.39
33 28 0.61
ACGTcount: A:0.20, C:0.34, G:0.31, T:0.15
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
Found at i:11840 original size:32 final size:32
Alignment explanation
Indices: 11804--12022 Score: 159
Period size: 32 Copynumber: 6.7 Consensus size: 32
11794 TTCTGCGTGA
11804 GCCTCGGTCACCATCGGCAACCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAACCCAGGCGGGTG
*
11836 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGC-AACCCAGGCGGGTG
* * * *
11868 GTCTCGGTCACCATCGGTAACCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAACCCAGG-C----G-G-GTG
** * *
11907 AGCCTCGGTCACCATCAGGC--CCCTTGTGCGTG
1 -GCCTCGGTCACCATC-GGCAACCCAGGCGGGTG
11939 AGCCTC-GTCACCATCGGCAATCCCAGGC-GGTG
1 -GCCTCGGTCACCATCGGCAA-CCCAGGCGGGTG
*
11971 G-CTCGGTCACCATC-GCAAACCCAGAC-GGT-
1 GCCTCGGTCACCATCGGC-AACCCAGGCGGGTG
*
12000 GTCTCGGTCACCATCGGCAACCC
1 GCCTCGGTCACCATCGGCAACCC
12023 CGGGCCATTG
Statistics
Matches: 151, Mismatches: 18, Indels: 38
0.73 0.09 0.18
Matches are distributed among these distances:
29 1 0.01
30 35 0.23
31 29 0.19
32 46 0.30
33 16 0.11
34 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 4 0.03
40 14 0.09
41 2 0.01
ACGTcount: A:0.17, C:0.37, G:0.29, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAACCCAGGCGGGTG
Found at i:11842 original size:136 final size:135
Alignment explanation
Indices: 11668--12038 Score: 420
Period size: 136 Copynumber: 2.7 Consensus size: 135
11658 AAGGCGGGTG
* * * ** **
11668 GCCTCGGTCAGCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACACCGGGCCATTG
1 GCCTCGGTCACCATCGGC-AACCCAGGCGGGTGGCTCGGTCACCATCGGCAA-ACCCAG--ACGG
* * *
11733 GTG-CGGGAGT-ACCGCA-CAG-AA-CCGAG-CGTTGGTGCGGGAGTCTCGGTCACCATCAGGCC
62 GTGTCGCG-GTCA-C-CATCAGTAACCCGAGCCATTGGTGCGGGAGCCTCGGTCACCATCAGGCC
11792 CCTTCTGCGTGA
124 CCTTCTGCGTGA
11804 GCCTCGGTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTG
1 GCCTCGGTCACCATCGGCAACCCAGGCGGGTGG-CTCGGTCACCATCGGCAAACCCAGACGGGTG
* * * *
11869 TCTCGGTCACCATCGGTAACCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGT
65 TCGCGGTCACCATCAGTAACCCGAGCCATTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTCT
11934 GCGTGA
130 GCGTGA
11940 GCCTC-GTCACCATCGGCAATCCCAGGC-GGTGGCTCGGTCACCATC-GCAAACCCAGAC-GGTG
1 GCCTCGGTCACCATCGGCAA-CCCAGGCGGGTGGCTCGGTCACCATCGGCAAACCCAGACGGGTG
* * * *
12001 TCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGG
65 TCGCGGTCACCATCAGTAA-CCCGAGCCATTGGTGCGG
12039 AGTGCCGCAC
Statistics
Matches: 211, Mismatches: 15, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
132 24 0.11
133 40 0.19
134 18 0.09
135 40 0.19
136 89 0.42
ACGTcount: A:0.17, C:0.35, G:0.31, T:0.17
Consensus pattern (135 bp):
GCCTCGGTCACCATCGGCAACCCAGGCGGGTGGCTCGGTCACCATCGGCAAACCCAGACGGGTGT
CGCGGTCACCATCAGTAACCCGAGCCATTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTCTG
CGTGA
Found at i:11922 original size:104 final size:102
Alignment explanation
Indices: 11797--11985 Score: 256
Period size: 103 Copynumber: 1.8 Consensus size: 102
11787 AGGCCCCTTC
* *
11797 TGCGTGAGCCTCGGTCACCATC-GGCAACCCAGGCGGGTG-GCCTCGGTCACCATCGGCAAACCC
1 TGCGGGAGCCTCGGTCACCATCAGGC--CCCAGGCGCGTGAGCCTC-GTCACCATCGGCAAACCC
*
11860 AGACGGGTGTCTCGGTCACCATCGGTAACCCGGGCCATTGG
63 AGAC-GGTGGCTCGGTCACCATCGGTAACCCGGGCCATTGG
** * * *
11901 TGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGTCACCATCGGCAATCCCAGG
1 TGCGGGAGCCTCGGTCACCATCAGGCCCCAGGCGCGTGAGCCTCGTCACCATCGGCAAACCCAGA
11966 CGGTGGCTCGGTCACCATCG
66 CGGTGGCTCGGTCACCATCG
11986 CAAACCCAGA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
102 18 0.24
103 28 0.37
104 26 0.35
105 3 0.04
ACGTcount: A:0.16, C:0.35, G:0.31, T:0.17
Consensus pattern (102 bp):
TGCGGGAGCCTCGGTCACCATCAGGCCCCAGGCGCGTGAGCCTCGTCACCATCGGCAAACCCAGA
CGGTGGCTCGGTCACCATCGGTAACCCGGGCCATTGG
Found at i:11980 original size:31 final size:31
Alignment explanation
Indices: 11945--12019 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 31
11935 CGTGAGCCTC
* *
11945 GTCACCATCGGCAATCCCAGGCGGTGGCTCG
1 GTCACCATCGGCAAACCCAGACGGTGGCTCG
*
11976 GTCACCATC-GCAAACCCAGACGGTGTCTCG
1 GTCACCATCGGCAAACCCAGACGGTGGCTCG
12006 GTCACCATCGGCAA
1 GTCACCATCGGCAA
12020 CCCCGGGCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 27 0.68
31 13 0.32
ACGTcount: A:0.21, C:0.36, G:0.27, T:0.16
Consensus pattern (31 bp):
GTCACCATCGGCAAACCCAGACGGTGGCTCG
Found at i:12087 original size:132 final size:134
Alignment explanation
Indices: 11761--12038 Score: 429
Period size: 136 Copynumber: 2.1 Consensus size: 134
11751 GAACCGAGCG
* * *
11761 TTGGTGCGGGAGTCTCGGTCACCATCAGGCCCCTTCTGCGTGAGCCTCGGTCACCATCGGCAACC
1 TTGGTGCGGGAG-CTCCGTCACCAACAGGCCCCTTGTGCGTGAGCCTC-GTCACCATCGGCAACC
*
11826 CAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCC
64 CAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCC
11891 GGGCCA
129 GGGCCA
* *
11897 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGTCACCATCGGCAATCC
1 TTGGTGCGGGAG-CTCCGTCACCAACAGGCCCCTTGTGCGTGAGCCTCGTCACCATCGGCAA-CC
11962 CAGGC-GGTGG-CTCGGTCACCATC-GCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCC
64 CAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAA-CC
12023 CGGGCCA
128 CGGGCCA
12030 TTGGTGCGG
1 TTGGTGCGG
12039 AGTGCCGCAC
Statistics
Matches: 137, Mismatches: 3, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
132 22 0.16
133 30 0.22
134 13 0.09
135 19 0.14
136 53 0.39
ACGTcount: A:0.16, C:0.35, G:0.31, T:0.18
Consensus pattern (134 bp):
TTGGTGCGGGAGCTCCGTCACCAACAGGCCCCTTGTGCGTGAGCCTCGTCACCATCGGCAACCCA
GGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGG
GCCA
Found at i:12420 original size:11 final size:11
Alignment explanation
Indices: 12406--12437 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
12396 TCCCGGTGGT
12406 GCTCCGGCGAC
1 GCTCCGGCGAC
*
12417 GCTCCGGCGAT
1 GCTCCGGCGAC
12428 GCTCCGGCGA
1 GCTCCGGCGA
12438 GACATTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.38, T:0.12
Consensus pattern (11 bp):
GCTCCGGCGAC
Found at i:20250 original size:32 final size:33
Alignment explanation
Indices: 20174--20258 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
20164 GTGTGCGTGC
* * *
20174 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTA
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTA
*
20207 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTA
*
20239 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
20259 CCCCGACCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 19 0.40
33 28 0.60
ACGTcount: A:0.21, C:0.34, G:0.28, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGTA
Found at i:20318 original size:169 final size:170
Alignment explanation
Indices: 20037--20610 Score: 874
Period size: 169 Copynumber: 3.4 Consensus size: 170
20027 ACGTGTGCGT
** * *
20037 GCCTCGGTCACCATCGGCAAAAACAGACAGGTGTCTCGGTCACCATCGGCAACCCCGGGTCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
20102 GTGGGGGAGTGTCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCATG
* * *
20167 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTA
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
20207 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GACCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
20271 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACAATCAGGCCCCCATG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCATG
* *
20336 TGCGTGAGCCTCAGTCACCATCGGCAATCCAAGACGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
* *
20376 GCCTCGGTCACCATGGGCAAACCTAGACGGGTGTC-CTGGTCACCATCGGCAACCCCGGG-CATT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTC-GGTCACCATCGGCAACCCCGGGCCATT
* *
20439 GGT-CGGGAGTGCCGCACAGAACCGAGCGTTGGTGC-GGAGTCTCGGTCACCATCAGG-CCCCTT
65 GGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCAT
*
20501 GTGCGT-AGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
130 GTGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
* * *
20541 GCCTTGGTCACCATCGGCAAACTCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
20606 GTGCG
66 GTGCG
20611 AGAGCCTCGG
Statistics
Matches: 367, Mismatches: 32, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
165 83 0.23
166 19 0.05
167 21 0.06
168 31 0.08
169 159 0.43
170 54 0.15
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCATG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:20427 original size:32 final size:33
Alignment explanation
Indices: 20343--20427 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
20333 ATGTGCGTGA
* *
20343 GCCTCAGTCACCATCGGCAATCCAAGACGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
* *
20376 GCCTCGGTCACCATGGGCAAACCTAGACGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
20409 TCCT-GGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
20428 CCCCGGGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 14 0.30
33 32 0.70
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
Found at i:20587 original size:32 final size:33
Alignment explanation
Indices: 20508--20729 Score: 143
Period size: 32 Copynumber: 6.6 Consensus size: 33
20498 CTTGTGCGTA
* *
20508 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
* *
20541 GCCTTGGTCACCATCGGCAAACTCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
* * * * * *
20573 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGAG
1 GCCTCGGTCACCATCGGCAAACCC-AG--A--CG-G-GTG
* * *
20613 AGCCTCGGTCACCATCAGGC---CCCTTG-TGCGTG
1 -GCCTCGGTCACCATC-GGCAAACCC-AGACGGGTG
* *
20645 AGCCTCGGTCACCATCGGC-ATCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
20678 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
* *
20710 GTCTCGGTCACTATCGGCAA
1 GCCTCGGTCACCATCGGCAA
20730 CCCCGGGCCA
Statistics
Matches: 149, Mismatches: 26, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
31 3 0.02
32 74 0.50
33 47 0.32
34 1 0.01
35 1 0.01
37 1 0.01
38 1 0.01
39 5 0.03
41 14 0.09
42 2 0.01
ACGTcount: A:0.17, C:0.35, G:0.30, T:0.18
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
Found at i:20640 original size:137 final size:136
Alignment explanation
Indices: 20467--20748 Score: 494
Period size: 137 Copynumber: 2.1 Consensus size: 136
20457 GAACCGAGCG
*
20467 TTGGTGCGGAGTCTCGGTCACCATCAGGCCCCTTGTGCGT-AGCCTCGGTCACCATCGGCAATCC
1 TTGGTGCGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGC-ATCC
* * *
20531 CAGGCGGGTGGCCTTGGTCACCATCGGCAAACTCAGACGGGTGTCTCGGTCACCATCGGTAACCC
65 CAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCC
20596 CGGGCCA
130 CGGGCCA
20603 TTGGTGCGAGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCATCC
1 TTGGTGCG-GAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCATCC
*
20668 CAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACTATCGGCAACCC
65 CAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCC
20733 CGGGCCA
130 CGGGCCA
20740 TTGGTGCGG
1 TTGGTGCGG
20749 GAGTGCCGCA
Statistics
Matches: 139, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
136 9 0.06
137 111 0.80
138 19 0.14
ACGTcount: A:0.16, C:0.34, G:0.31, T:0.19
Consensus pattern (136 bp):
TTGGTGCGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCATCCC
AGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC
GGGCCA
Found at i:20813 original size:137 final size:137
Alignment explanation
Indices: 20467--20820 Score: 452
Period size: 137 Copynumber: 2.6 Consensus size: 137
20457 GAACCGAGCG
* * *
20467 TTGGTGCG-GAGTCTCGGTCACCATCAGGCCCCTTGTGC-GTAGCCTCGGTCACCATCGGCAATC
1 TTGGTGCGAGAG-CTCCGTCACCAACAGGCCCCTTGTGCGGGAGCCTCGGTCACCATCGGCAATC
* * *
20530 CCAGGCGGGTGGCCTTGGTCACCATCGGCAAACTCAGACGGGTGTCTCGGTCACCATCGGTAACC
65 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
20595 CCGGGCCA
130 CCGGGCCA
* * *
20603 TTGGTGCGAGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGC-ATC
1 TTGGTGCGAGAG-CTCCGTCACCAACAGGCCCCTTGTGCGGGAGCCTCGGTCACCATCGGCAATC
*
20667 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACTATCGGCAACC
65 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
20732 CCGGGCCA
130 CCGGGCCA
* * * * *
20740 TTGGTGCGGGAG-TGCCG-CACAGAACCGG-GCGTTGGTGCGGGAGCCTCGGTCACCATCGGCAA
1 TTGGTGCGAGAGCT-CCGTCAC-CAACAGGCCCCTT-GTGCGGGAGCCTCGGTCACCATCGGCAA
* * *
20802 CCCCCGACGGGT-GCCTCGG
63 TCCCAGGCGGGTGGCCTCGG
20821 CAACCCCAGG
Statistics
Matches: 194, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
135 7 0.04
136 46 0.24
137 122 0.63
138 19 0.10
ACGTcount: A:0.16, C:0.34, G:0.32, T:0.18
Consensus pattern (137 bp):
TTGGTGCGAGAGCTCCGTCACCAACAGGCCCCTTGTGCGGGAGCCTCGGTCACCATCGGCAATCC
CAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCC
CGGGCCA
Found at i:29041 original size:31 final size:32
Alignment explanation
Indices: 28969--29051 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
28959 CTGTGCGTGC
* * *
28969 GCCTCGGTCACCATCGGTAATCCAAGGCGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGTG
*
29001 GCCTCGGTCACCATCGGCAAACCCAGACGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGTG
*
29032 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
29052 CCCGGCCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 19 0.41
32 27 0.59
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGTG
Found at i:29131 original size:165 final size:166
Alignment explanation
Indices: 28836--29398 Score: 932
Period size: 165 Copynumber: 3.4 Consensus size: 166
28826 ACGTGTGCGT
**
28836 GCCTCGGTCACCATCGGCAAAAACAGACGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGT
28901 GCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCA-GCCCCCTGTGC
66 GCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCTGTGC
* *
28965 GTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGTG
131 GTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGTG
29001 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAA-CCCGGCCATT-GT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGT
* *
29064 GCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGTG
66 GCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCC-TGTG
29129 CGTGAGCCTCGGTC-CCATCGGCAATCCAAGGCGGGTG
130 CGTGAGCCTCGGTCACCATCGGCAATCCAAGGC-GGTG
29166 GCCTCGGTCACCATCGGCAAA-CCAGACGG-GTCTCGGTCACCATCGGCAACCCCGGCCATTGGT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGT
*
29229 GCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG--CCCTGTGC
66 GCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCTGTGC
*
29292 GTGAGCCTCGGTCACCATCGGCAATCCCAGGCGG-G
131 GTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGTG
*
29327 GCCTCGGTCACCATC-GCAAACCCAGACGGGTGTCTC-GTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
29390 GTGCGGGAG
64 GTGCGGGAG
29399 CCTCGTCACC
Statistics
Matches: 377, Mismatches: 11, Indels: 22
0.92 0.03 0.05
Matches are distributed among these distances:
160 5 0.01
161 22 0.06
162 39 0.10
163 115 0.31
164 51 0.14
165 145 0.38
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.16
Consensus pattern (166 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGT
GCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCTGTGC
GTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGTG
Found at i:29184 original size:33 final size:31
Alignment explanation
Indices: 29134--29214 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 31
29124 GTGTGCGTGA
* *
29134 GCCTCGGTC-CCATCGGCAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACC-AGACGGGT
29165 GGCCTCGGTCACCATCGGCAAACCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCAGACGGGT
29197 --CTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
29215 CCCCGGCCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 18 0.39
32 16 0.35
33 12 0.26
ACGTcount: A:0.20, C:0.36, G:0.30, T:0.15
Consensus pattern (31 bp):
GCCTCGGTCACCATCGGCAAACCAGACGGGT
Found at i:29334 original size:31 final size:31
Alignment explanation
Indices: 29296--29509 Score: 133
Period size: 30 Copynumber: 6.7 Consensus size: 31
29286 CTGTGCGTGA
29296 GCCTCGGTCACCATCGGCAATCCCAGGCGGG-
1 GCCTCGGTCACCATCGGCAA-CCCAGGCGGGT
*
29327 GCCTCGGTCACCATC-GCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGC-AACCCAGGCGGGT
* * *
29358 GTCTC-GTCACCATCGGTAACCCCGGGCCATTGGTGCGGGA
1 GCCTCGGTCACCATCGGCAA---C---CCA---G-GCGGGT
* * *
29398 GCCTC-GTCACCATCGGC--CCCTTGTGCGTGA
1 GCCTCGGTCACCATCGGCAACCC-AG-GCGGGT
*
29428 GCCTCGGTCACCATC-GCAATCCCAGG-GTG-
1 GCCTCGGTCACCATCGGCAA-CCCAGGCGGGT
*
29457 GCCTCGGTCACCATCGGCAA-CCAGACGGGT
1 GCCTCGGTCACCATCGGCAACCCAGGCGGGT
*
29487 GTCTCGGTCACCATCGGCAACCC
1 GCCTCGGTCACCATCGGCAACCC
29510 CGGCCATTGG
Statistics
Matches: 148, Mismatches: 13, Indels: 44
0.72 0.06 0.21
Matches are distributed among these distances:
28 4 0.03
29 17 0.11
30 62 0.42
31 34 0.23
32 3 0.02
33 4 0.03
35 1 0.01
36 3 0.02
39 1 0.01
40 19 0.13
ACGTcount: A:0.17, C:0.38, G:0.29, T:0.17
Consensus pattern (31 bp):
GCCTCGGTCACCATCGGCAACCCAGGCGGGT
Found at i:29336 original size:132 final size:132
Alignment explanation
Indices: 29166--29527 Score: 353
Period size: 130 Copynumber: 2.8 Consensus size: 132
29156 AAGGCGGGTG
* * * * **
29166 GCCTCGGTCACCATCGGCAA-ACCAGAC-GGGTCTCGGTCACCATCGGCAACCCCGGCCATTGGT
1 GCCTCGGTCACCATCGGCAATCCCAGGCGGGGCCTCGGTCACCATCGGCAACCCCAG--ACGGGT
* *
29229 G-CGGGAGTGC-CGCA-CAG-AA-CCGAG-CGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCC
64 GTC--GAGT-CAC-CATCAGTAACCCGAGCCATTGGTGCGGGAGCCTC-GTCACCATC-GGCCCC
29287 -TGTGCGTGA
123 TTGTGCGTGA
*
29296 GCCTCGGTCACCATCGGCAATCCCAGGCGGGGCCTCGGTCACCATC-GCAAACCCAGACGGGTGT
1 GCCTCGGTCACCATCGGCAATCCCAGGCGGGGCCTCGGTCACCATCGGCAACCCCAGACGGGTGT
** * *
29360 CTCGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGTCACCATCGGCCCCTTGTGCG
66 CGAGTCACCATCAGTAA-CCCGAGCCATTGGTGCGGGAGCCTCGTCACCATCGGCCCCTTGTGCG
29425 TGA
130 TGA
*
29428 GCCTCGGTCACCATC-GCAATCCCAGG-GTGGCCTCGGTCACCATCGGCAA--CCAGACGGGTGT
1 GCCTCGGTCACCATCGGCAATCCCAGGCGGGGCCTCGGTCACCATCGGCAACCCCAGACGGGTG-
* *
29489 CTCG-GTCACCATCGGCAACCCCG-GCCATTGGTGCGGGAG
65 -TCGAGTCACCATCAGTAA-CCCGAGCCATTGGTGCGGGAG
29528 TGCCGCACAG
Statistics
Matches: 202, Mismatches: 16, Indels: 29
0.82 0.06 0.12
Matches are distributed among these distances:
127 3 0.01
128 5 0.02
129 34 0.17
130 58 0.29
131 46 0.23
132 56 0.28
ACGTcount: A:0.17, C:0.35, G:0.31, T:0.17
Consensus pattern (132 bp):
GCCTCGGTCACCATCGGCAATCCCAGGCGGGGCCTCGGTCACCATCGGCAACCCCAGACGGGTGT
CGAGTCACCATCAGTAACCCGAGCCATTGGTGCGGGAGCCTCGTCACCATCGGCCCCTTGTGCGT
GA
Found at i:29563 original size:130 final size:131
Alignment explanation
Indices: 29255--29527 Score: 396
Period size: 130 Copynumber: 2.1 Consensus size: 131
29245 GAACCGAGCG
* * *
29255 TTGGTGCGGGAGTCTCGGTCACCATCAGG-CCC-TGTGCGTGAGCCTCGGTCACCATCGGCAATC
1 TTGGTGCGGGAGCCTC-GTCA-CAACCGGCCCCTTGTGCGTGAGCCTCGGTCACCATC-GCAATC
*
29318 CCAGGCGGGGCCTCGGTCACCATCGCAAACCCAGACGGGTGTCTCGTCACCATCGGTAACCCCGG
63 CCAGGCGGGGCCTCGGTCACCATCGCAAACCCAGACGGGTGTCTCGTCACCATCGGCAACCCCGG
29383 GCCA
128 GCCA
* *
29387 TTGGTGCGGGAGCCTCGTCACCATCGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGCAATCCCA
1 TTGGTGCGGGAGCCTCGTCACAACCGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGCAATCCCA
*
29452 GG-GTGGCCTCGGTCACCATCGGC-AA-CCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GG
66 GGCGGGGCCTCGGTCACCATC-GCAAACCCAGACGGGTGTCTC-GTCACCATCGGCAACCCCGGG
29513 CCA
129 CCA
29516 TTGGTGCGGGAG
1 TTGGTGCGGGAG
29528 TGCCGCACAG
Statistics
Matches: 130, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
129 32 0.25
130 39 0.30
131 20 0.15
132 39 0.30
ACGTcount: A:0.16, C:0.35, G:0.31, T:0.18
Consensus pattern (131 bp):
TTGGTGCGGGAGCCTCGTCACAACCGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGCAATCCCA
GGCGGGGCCTCGGTCACCATCGCAAACCCAGACGGGTGTCTCGTCACCATCGGCAACCCCGGGCC
A
Done.