Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007451.1 Hibiscus syriacus cultivar Beakdansim tig00020402_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: 42819
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Found at i:6973 original size:33 final size:32
Alignment explanation
Indices: 6936--7020 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
6926 GTGTGCGTGC
* * *
6936 GCCTCGGTCACCATCGGTAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGT
* *
6968 GGCCTCGGTCACCATCGACAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCAAGACGGGT
*
7001 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
7021 CCCCGGCCAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 18 0.40
33 27 0.60
ACGTcount: A:0.21, C:0.34, G:0.28, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGT
Found at i:7085 original size:169 final size:170
Alignment explanation
Indices: 6800--7378 Score: 988
Period size: 169 Copynumber: 3.4 Consensus size: 170
6790 ACGTGTGCGT
**
6800 GCCTCGGTCACCATCGGCAAAAACAGAC-GGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
6864 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
6929 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
6969 GCCTCGGTCACCATCGACAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
7033 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* **
7098 TGCGTGAGCCTCGGACACCATCGGCAATCCTGGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
7138 GCCTCGGTCACCATCGGTAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
7202 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCCCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
7266 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
7306 GCCTCGGTCACCATCGG-AAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
7370 GTGCGGGAG
66 GTGCGGGAG
7379 CCTCGGTCAC
Statistics
Matches: 388, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
167 38 0.10
168 77 0.20
169 246 0.63
170 27 0.07
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.17
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:7142 original size:33 final size:32
Alignment explanation
Indices: 7105--7189 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
7095 GTGTGCGTGA
* * ** *
7105 GCCTCGGACACCATCGGCAATCCTGGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
*
7137 GGCCTCGGTCACCATCGGTAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCCAGACGGGT
*
7170 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
7190 CCCCGGCCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 18 0.41
33 26 0.59
ACGTcount: A:0.19, C:0.34, G:0.31, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:7336 original size:32 final size:33
Alignment explanation
Indices: 7273--7492 Score: 161
Period size: 32 Copynumber: 6.6 Consensus size: 33
7263 TTGTGCGTGA
* *
7273 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
7306 GCCTCGGTCACCATCGG-AAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
* * * * *
7337 GTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCC-AG--A--CG-G-GTG
* * *
7377 AGCCTCGGTCACCATCAGGC---CCCTTG-TGCGTG
1 -GCCTCGGTCACCATC-GGCAAACCC-AGACGGGTG
**
7409 AGCCTCGGTCACCATCGGCAGTCCCAG--GGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
7441 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
7473 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
7493 CCCCGGGCCA
Statistics
Matches: 153, Mismatches: 18, Indels: 33
0.75 0.09 0.16
Matches are distributed among these distances:
31 43 0.28
32 58 0.38
33 23 0.15
34 4 0.03
35 1 0.01
37 1 0.01
38 1 0.01
39 5 0.03
41 14 0.09
42 3 0.02
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
Found at i:7395 original size:137 final size:136
Alignment explanation
Indices: 7230--7510 Score: 519
Period size: 137 Copynumber: 2.1 Consensus size: 136
7220 GAACCGAGCG
*
7230 TTGGTGCGGGAGTCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
7295 CCAGGCGGGTGGCCTCGGTCACCATCGG-AAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
66 CCA-G-GGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
7359 CCGGGCCA
129 CCGGGCCA
*
7367 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAGTC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
7432 CCAGGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC
66 CCAGGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC
7497 GGGCCA
131 GGGCCA
7503 TTGGTGCG
1 TTGGTGCG
7511 TAGTGCCGCA
Statistics
Matches: 141, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
135 22 0.16
136 53 0.38
137 66 0.47
ACGTcount: A:0.15, C:0.35, G:0.32, T:0.18
Consensus pattern (136 bp):
TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
CCAGGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC
GGGCCA
Found at i:7576 original size:136 final size:136
Alignment explanation
Indices: 7230--7582 Score: 459
Period size: 137 Copynumber: 2.6 Consensus size: 136
7220 GAACCGAGCG
* * *
7230 TTGGTGCGGGAGTCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
1 TTGGTGCGGGAG-CTCCGTCACCAACAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAACC
* *
7295 CCAGGCGGGTGGCCTCGGTCACCATCGGAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCC
65 CCCGACGGGTGGCCTCGGTCACCATCGGAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCC
7360 CGGGCCA
130 CGGGCCA
* * **
7367 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGC-AGT
1 TTGGTGCGGGAG-CTCCGTCACCAACAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAACC
*
7431 CCC-AGGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
65 CCCGACGGGTGGCCTCGGTCACCATCGG-AAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
7495 CCGGGCCA
129 CCGGGCCA
* * * * * *
7503 TTGGTGC-GTAG-TGCCG-CACAGAACCGG-GCGTTGGTGCGGGAGCCTCGGTCACCATCGGCAA
1 TTGGTGCGGGAGCT-CCGTCAC-CAACAGGCCCCTT-GTGCGTGAGCCTCGGTCACCATCGGCAA
7564 CCCCCGACGGGT-GCCTCGG
63 CCCCCGACGGGTGGCCTCGG
7583 CAACCCCAGG
Statistics
Matches: 193, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
133 7 0.04
134 31 0.16
135 36 0.19
136 59 0.31
137 60 0.31
ACGTcount: A:0.15, C:0.35, G:0.33, T:0.17
Consensus pattern (136 bp):
TTGGTGCGGGAGCTCCGTCACCAACAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAACCC
CCGACGGGTGGCCTCGGTCACCATCGGAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC
GGGCCA
Found at i:7894 original size:11 final size:11
Alignment explanation
Indices: 7878--7905 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
7868 TTCCCGTGGT
7878 GCTCCGGCGAC
1 GCTCCGGCGAC
7889 GCTCCGGCGAC
1 GCTCCGGCGAC
7900 GCTCCG
1 GCTCCG
7906 CGAGACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.46, G:0.36, T:0.11
Consensus pattern (11 bp):
GCTCCGGCGAC
Found at i:21513 original size:33 final size:32
Alignment explanation
Indices: 21476--21560 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
21466 GTGTGCGTGC
* * *
21476 GCCTCGGTCACCATCGGTAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGT
* *
21508 GGCCTCGGTCACCATCGACAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCAAGACGGGT
*
21541 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
21561 CCCCGGCCAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 18 0.40
33 27 0.60
ACGTcount: A:0.21, C:0.34, G:0.28, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGT
Found at i:21629 original size:169 final size:170
Alignment explanation
Indices: 21339--21920 Score: 997
Period size: 169 Copynumber: 3.4 Consensus size: 170
21329 ACGTGTGCGT
** *
21339 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCTATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
21404 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
21469 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
21509 GCCTCGGTCACCATCGACAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
21573 GTGCGGGAGTGCCGCACAGTACCGATCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* **
21638 TGCGTGAGCCTCGGACACCATCGGCAATCCTGGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
21678 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGAGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
21743 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCCCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
21807 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
21847 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
21912 GTGCGGGAG
66 GTGCGGGAG
21921 CCTCGGTCAC
Statistics
Matches: 387, Mismatches: 24, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
169 274 0.71
170 113 0.29
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.17
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:21721 original size:32 final size:33
Alignment explanation
Indices: 21645--21729 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
21635 GTGTGCGTGA
* * ** *
21645 GCCTCGGACACCATCGGCAATCCTGGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
21678 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
21710 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
21730 CCCCGAGCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 19 0.41
33 27 0.59
ACGTcount: A:0.19, C:0.35, G:0.31, T:0.15
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
Found at i:21856 original size:33 final size:33
Alignment explanation
Indices: 21814--22036 Score: 195
Period size: 32 Copynumber: 6.6 Consensus size: 33
21804 TTGTGCGTGA
*
21814 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
21847 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * *
21879 GTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
** * *
21919 AGCCTCGGTCACCATCAGGC---CCCTTGTGCGTG
1 -GCCTCGGTCACCATC-GGCAAACCCAGGCGGGTG
**
21951 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
21985 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
22017 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
22037 CCCCGGGCCA
Statistics
Matches: 156, Mismatches: 21, Indels: 27
0.76 0.10 0.13
Matches are distributed among these distances:
31 3 0.02
32 60 0.38
33 60 0.38
34 9 0.06
37 1 0.01
38 1 0.01
39 5 0.03
41 14 0.09
42 3 0.02
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
Found at i:21860 original size:65 final size:65
Alignment explanation
Indices: 21784--21999 Score: 231
Period size: 65 Copynumber: 3.2 Consensus size: 65
21774 GTGCGGGAGT
21784 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
* * * * * * *
21849 CTCGGTCACCATC-GGCAAACCC-AG-ACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATT
1 CTCGGTCACCATCAGGC---CCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGG-C---
*
21911 GGTGCGGGAGC
59 -G-G-GTG-GC
*
21922 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGC
1 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
21987 CTCGGTCACCATC
1 CTCGGTCACCATC
22000 GGCAAACCCA
Statistics
Matches: 120, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
64 3 0.03
65 55 0.46
66 4 0.03
67 4 0.03
68 1 0.01
70 1 0.01
71 4 0.03
72 4 0.03
73 41 0.34
74 3 0.03
ACGTcount: A:0.15, C:0.37, G:0.31, T:0.18
Consensus pattern (65 bp):
CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
Found at i:21935 original size:138 final size:138
Alignment explanation
Indices: 21771--22055 Score: 552
Period size: 138 Copynumber: 2.1 Consensus size: 138
21761 GAACCGAGCG
*
21771 TTGGTGCGGGAGTCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
21836 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
66 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
21901 CCGGGCCA
131 CCGGGCCA
*
21909 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAGTC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
21974 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
66 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
22039 CCGGGCCA
131 CCGGGCCA
22047 TTGGTGCGG
1 TTGGTGCGG
22056 TAGTGCCGCA
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 145 1.00
ACGTcount: A:0.15, C:0.35, G:0.32, T:0.18
Consensus pattern (138 bp):
TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
CCGGGCCA
Found at i:22025 original size:339 final size:339
Alignment explanation
Indices: 21339--22036 Score: 1018
Period size: 339 Copynumber: 2.1 Consensus size: 339
21329 ACGTGTGCGT
* *
21339 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCTATTG
1 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGAGCCATTG
*
21404 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
21469 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTGGCCTCGGTCACCATCGACAAACCCA
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTGGCCTCGGTCACCATCGACAAACCCA
*
21534 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGTGCGGGAGTGCCGCACAGTACCGAT
196 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGTGCGGGAGTGCCGCACAGTACCGAC
* * *
21599 CTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGTGCGTGAGCCTCGGACACCATCGGCA
261 CCTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCAGTGCGCGTGAGCCTCGGACACCATCGGCA
* ** *
21664 ATCCTGGGCGGGTG
326 AACCCAGACGGGTG
**
21678 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGAGCCATTG
1 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGAGCCATTG
* *
21743 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCCCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
21807 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTGGCCTCGGTCACCATCGACAAACCCA
*
21872 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGGAGCCT-CGGTCACCA-T-
196 GACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTGGTGCGGGAG--TGCCG-CA-CAGTA
* * * * *
21934 CAGGCCCCTT-GTGCGTGAGCCTCGGTCACCATC-GGCAGTCCCAG-GCGGGTG-GCCTCGGTCA
256 C-CGACCCTTGGTGCGGGAGCCTCGGTCACCATCAGGC---CCCAGTGCGCGTGAGCCTCGGACA
21995 CCATCGGCAAACCCAGACGGGT-
317 CCATCGGCAAACCCAGACGGGTG
*
22017 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
22037 CCCCGGGCCA
Statistics
Matches: 324, Mismatches: 26, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
338 98 0.30
339 155 0.48
340 52 0.16
341 13 0.04
342 6 0.02
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.17
Consensus pattern (339 bp):
GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGAGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTGGCCTCGGTCACCATCGACAAACCCA
GACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGTGCGGGAGTGCCGCACAGTACCGAC
CCTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCAGTGCGCGTGAGCCTCGGACACCATCGGCA
AACCCAGACGGGTG
Found at i:22440 original size:11 final size:11
Alignment explanation
Indices: 22426--22457 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
22416 TCCCGGTGGT
22426 GCTCCGGCGAC
1 GCTCCGGCGAC
22437 GCTCCGGCGAC
1 GCTCCGGCGAC
22448 GCTCCGGCGA
1 GCTCCGGCGA
22458 GACATTATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.44, G:0.38, T:0.09
Consensus pattern (11 bp):
GCTCCGGCGAC
Found at i:30627 original size:166 final size:164
Alignment explanation
Indices: 30345--30915 Score: 875
Period size: 166 Copynumber: 3.5 Consensus size: 164
30335 ACGTGTGCGT
**
30345 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCA-CATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
30409 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAG-ACCGAGC-TTGGTGCGGGAGCCTCGGTCACCATCAGG-CCCCGTG
* *
30474 TGCGTGGCGCCTCGGTCACCATCGGTAATCCAAGGCTG
128 TGCGT-GAGCCTCGGTCACCATCGGCAATCCAAGGCTG
*
30512 GCCTCGGTCACCATCGACAAA-CCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
30575 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
66 GTGCGGGAGTGCCGCACAG-ACCGAGC-TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
* **
30640 GCGTGAG-CTCGGACACCATCGGCAATCCTGGGCGGGTG
129 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGC---TG
30678 GCCTCGGTCACCATCGGCCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATT
1 GCCTCGGTCACCATCGG-CAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATT
* * *
30743 GGTGCGGGAGTGCCGCACAGAACGAGCGTGGTGCGGGAGTCTCGGTCACCATCAGGCCCC-TGTG
65 GGTGCGGGAGTGCCGCACAGACCGAGCTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGTG
* *
30807 CGTGAGCCTC-GTCACCATCGGCAATCCCAGGCGG
130 CGTGAGCCTCGGTCACCATCGGCAATCCAAGGCTG
30841 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGGGCCATT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAA-CCCCGGGCCATT
30906 GGTGCGGGAG
65 GGTGCGGGAG
30916 CCTCGGTCAC
Statistics
Matches: 377, Mismatches: 18, Indels: 22
0.90 0.04 0.05
Matches are distributed among these distances:
162 35 0.09
163 62 0.16
164 2 0.01
165 12 0.03
166 128 0.34
167 71 0.19
168 40 0.11
169 27 0.07
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.16
Consensus pattern (164 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGACCGAGCTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGTGC
GTGAGCCTCGGTCACCATCGGCAATCCAAGGCTG
Found at i:30690 original size:33 final size:32
Alignment explanation
Indices: 30647--30730 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 32
30637 TGTGCGTGAG
* * ** *
30647 CTCGGACACCATCGGCAATCCTGGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
*
30680 CTCGGTCACCATCGGCCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGG-CAAACCCAGACGGGTGC
30713 CTCGGTCACCATCGGCAA
1 CTCGGTCACCATCGGCAA
30731 CCCCGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.07
33 30 0.68
34 11 0.25
ACGTcount: A:0.19, C:0.36, G:0.30, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:30851 original size:30 final size:32
Alignment explanation
Indices: 30812--31028 Score: 135
Period size: 32 Copynumber: 6.6 Consensus size: 32
30802 CTGTGCGTGA
* *
30812 GCCTC-GTCACCATCGGCAATCCCAGGC-GG-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
30841 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
* * * *
30873 GTCTCGGTCACCATCGGCAACCCCCGGGCCATTGGTGCGGGA
1 GCCTCGGTCACCATCGGCAA---AC---CCA---G-ACGGGT
* * * *
30915 GCCTCGGTCACCA-CAGGC---CCCTTGTGCGTGA
1 GCCTCGGTCACCATC-GGCAAACCC-AG-ACGGGT
** *
30946 GCCTCGGTCACCATCGGCAGTCCCAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
30978 GCCTCGGTCACCATCGGCAAACCCAGAC-GGT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
*
31009 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
31029 CCCCGGGCCA
Statistics
Matches: 153, Mismatches: 16, Indels: 36
0.75 0.08 0.18
Matches are distributed among these distances:
29 5 0.03
30 20 0.13
31 47 0.31
32 49 0.32
33 3 0.02
34 3 0.02
35 1 0.01
36 1 0.01
38 3 0.02
41 2 0.01
42 19 0.12
ACGTcount: A:0.17, C:0.38, G:0.29, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:30884 original size:32 final size:30
Alignment explanation
Indices: 30812--30892 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
30802 CTGTGCGTGA
* *
30812 GCCTC-GTCACCATCGGCAATCCCAGGCGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGG
30841 GCCTCGGTCACCATCGGCAAACCCAGACGGG
1 GCCTCGGTCACCATCGGCAAACCCAGAC-GG
*
30872 TGTCTCGGTCACCATCGGCAA
1 -GCCTCGGTCACCATCGGCAA
30893 CCCCCGGGCC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.11
30 20 0.43
31 2 0.04
32 19 0.41
ACGTcount: A:0.20, C:0.38, G:0.27, T:0.15
Consensus pattern (30 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGG
Found at i:39400 original size:32 final size:32
Alignment explanation
Indices: 39361--39440 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
39351 GTGTGCGTGC
* * *
39361 GCCTCGGTCACCATCG-TAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGACAAACCAAGACGGGT
*
39392 GGCCTCGGTCACCATCGACAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGACAAACCAAGACGGGT
*
39425 GTCTCGGTCACCATCG
1 GCCTCGGTCACCATCG
39441 GCAACCCCGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 31 0.74
33 11 0.26
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (32 bp):
GCCTCGGTCACCATCGACAAACCAAGACGGGT
Found at i:39648 original size:166 final size:166
Alignment explanation
Indices: 39225--39796 Score: 904
Period size: 166 Copynumber: 3.4 Consensus size: 166
39215 ACGTGTGCGT
**
39225 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
*
39290 TGCGGGAGTGTCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACCATCAGGCCCCCGTGT
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCG-TCACCATCAGG-CCCCGTGT
* *
39355 GCGTGCGCCTCGGTCACCATCGTAATCCAAGGCGGGTG
129 GCGTGAGCCTCGGTCACCATCGCAATCCAAGGCGGGTG
*
39393 GCCTCGGTCACCATCGACAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
* *
39458 TGC-GGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGTG
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTC-GTCACCATCAGGCCCCGTGTG
* **
39522 CGTGAGCCTCGGACACCATCGCAATCCTGGGC-GGTG
130 CGTGAGCCTCGGTCACCATCGCAATCCAAGGCGGGTG
39558 GCCTCGGTCACCATC-GCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
* * *
39622 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGC-GTAGTCTC-TCACCATCAGGCCCCTTGTG
65 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTCACCATCAGGCCCCGTGTG
*
39685 CGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
130 CGTGAGCCTCGGTCACCATC-GCAATCCAAGGCGGGTG
39723 GCCTCGGTC-CACATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATT
1 GCCTCGGTCAC-CATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATT
39787 GGTGCGGGAG
64 GGTGCGGGAG
39797 CCTCGGTCAC
Statistics
Matches: 377, Mismatches: 20, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
163 38 0.10
164 50 0.13
165 54 0.14
166 122 0.32
167 47 0.12
168 66 0.18
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.17
Consensus pattern (166 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTCACCATCAGGCCCCGTGTGC
GTGAGCCTCGGTCACCATCGCAATCCAAGGCGGGTG
Found at i:39730 original size:33 final size:33
Alignment explanation
Indices: 39690--39908 Score: 134
Period size: 32 Copynumber: 6.6 Consensus size: 33
39680 TTGTGCGTGA
*
39690 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
39723 GCCTCGGTC-CACATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCAC-CATCGGCAAACCCAGGCGGGTG
* * * *
39755 GTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
** * *
39795 AGCCTCGGTCACCATCAGGC---CCCTTGTGCGTG
1 -GCCTCGGTCACCATC-GGCAAACCCAGGCGGGTG
* **
39827 ATCCTC-GTCACCATC-GCAGTCCCA-G-GGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
39857 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
39889 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
39909 CCCCGGGCCA
Statistics
Matches: 146, Mismatches: 21, Indels: 39
0.71 0.10 0.19
Matches are distributed among these distances:
29 6 0.04
30 13 0.09
31 17 0.12
32 51 0.35
33 34 0.23
34 1 0.01
37 1 0.01
38 1 0.01
39 5 0.03
41 14 0.10
42 3 0.02
ACGTcount: A:0.17, C:0.37, G:0.30, T:0.17
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
Found at i:39874 original size:134 final size:138
Alignment explanation
Indices: 39665--39927 Score: 464
Period size: 134 Copynumber: 1.9 Consensus size: 138
39655 GCGTAGTCTC
39665 TCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGG
1 TCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGG
39730 TCCACATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
66 TCCACATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
39795 AGCCTCGG
131 AGCCTCGG
* *
39803 TCACCATCAGGCCCCTTGTGCGTGATCCTC-GTCACCATC-GCAGTCCCA-G-GGGTGGCCTCGG
1 TCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGG
39864 T-CACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGG
66 TCCA-CATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGG
39928 TAGTGCCGCA
Statistics
Matches: 122, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
133 2 0.02
134 73 0.60
135 1 0.01
136 8 0.07
137 9 0.07
138 29 0.24
ACGTcount: A:0.16, C:0.37, G:0.30, T:0.17
Consensus pattern (138 bp):
TCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGG
TCCACATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
AGCCTCGG
Done.