Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009555.1 Hibiscus syriacus cultivar Beakdansim tig00116498_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: 23306
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.21
Found at i:4207 original size:31 final size:31
Alignment explanation
Indices: 4167--4252 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
4157 GCGTGAGCCC
*
4167 CGGTCACCATCGGCAATCCCAGGCGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGT-GCCT
* ** *
4199 C-GTCACCATCGGCAAAACCATACGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGTGCCT
*
4229 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
4253 CATTGGTGAG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
30 4 0.09
31 39 0.89
32 1 0.02
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (31 bp):
CGGTCACCATCGGCAAACCCAGGCGGTGCCT
Found at i:4394 original size:31 final size:32
Alignment explanation
Indices: 4297--4428 Score: 196
Period size: 32 Copynumber: 4.2 Consensus size: 32
4287 GTGCGTGAGG
* *
4297 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
4329 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
4361 CTCGGTCACCATCGGCAAACCCAGAC-GGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
4392 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
4424 CTCGG
1 CTCGG
4429 CAACCCCAGG
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
31 29 0.31
32 52 0.56
33 12 0.13
ACGTcount: A:0.18, C:0.37, G:0.30, T:0.14
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:4409 original size:63 final size:64
Alignment explanation
Indices: 4295--4428 Score: 200
Period size: 63 Copynumber: 2.1 Consensus size: 64
4285 TGGTGCGTGA
*
4295 GGCTCGGTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
* * * *
4359 GTCTCGGTCACCATCGGCAAACCCAGAC-GGT-GTCTCGGTCACCATCGGCAACCCCCGACGGGT
1 GGCTCGGTCACCATCGGC-AACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
4422 GGCTCGG
1 GGCTCGG
4429 CAACCCCAGG
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 35 0.56
64 20 0.32
65 8 0.13
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.14
Consensus pattern (64 bp):
GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:4581 original size:62 final size:63
Alignment explanation
Indices: 4478--4605 Score: 233
Period size: 62 Copynumber: 2.0 Consensus size: 63
4468 GAGAGTTGGT
4478 GGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC-GGTGC
1 GGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-GCAACCCCAGGCCACGGGTGC
4541 GGGGG-CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCACGGGTGC
1 GGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCACGGGTGC
4603 GGG
1 GGG
4606 AGTGCCGCAC
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
61 15 0.23
62 44 0.69
63 5 0.08
ACGTcount: A:0.14, C:0.41, G:0.35, T:0.10
Consensus pattern (63 bp):
GGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCACGGGTGC
Found at i:4754 original size:31 final size:32
Alignment explanation
Indices: 4640--4751 Score: 149
Period size: 31 Copynumber: 3.6 Consensus size: 32
4630 GTGCGTGAGG
* * *
4640 CTCGGTCACCATCGGCAATCCC-GGC-GGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
* *
4671 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
4703 CTCGGTCACCATC-GCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
4734 CTCGGTCACCATCGGCAA
1 CTCGGTCACCATCGGCAA
4752 CCCCCGACTG
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
31 49 0.69
32 19 0.27
33 3 0.04
ACGTcount: A:0.20, C:0.35, G:0.29, T:0.17
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:4769 original size:31 final size:32
Alignment explanation
Indices: 4640--4769 Score: 142
Period size: 31 Copynumber: 4.2 Consensus size: 32
4630 GTGCGTGAGG
* *
4640 CTCGGTCACCATCGGCAATCCC-GGC-GGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
4671 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
4703 CTCGGTCACCATC-GCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* * *
4734 CTCGGTCACCATCGGCAACCCCCGAC-TGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
4765 CTCGG
1 CTCGG
4770 CAACCCCAGG
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
31 57 0.67
32 25 0.29
33 3 0.04
ACGTcount: A:0.18, C:0.37, G:0.28, T:0.17
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:4832 original size:94 final size:94
Alignment explanation
Indices: 4536--4905 Score: 304
Period size: 94 Copynumber: 3.9 Consensus size: 94
4526 CCCAGGCCAC
* *
4536 GGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-GCAACCCCAGGCCACGGG
1 GGTGCGGGGCCCTCGGTCACCATCGGCAACACCCGAC-GGTGCCTCGGCAACCCCAGGCCACGGG
*
4600 TGCGGGAGTGCCGCACAGAACCGAGCGTT-
65 TGCGGGAGTGCCGCACAGAACCGAGAGTTG
* * * *
4629 GGTGCGTGAGG--CTCGGTCACCATCGGCAA-TCCCGGCGGTGGCCTCGGTC-ACCATTGGCAAA
1 GGTGCG-G-GGCCCTCGGTCACCATCGGCAACACCCGACGGT-GCCTCGG-CAACC-----CCAG
** * * * * *
4690 GCCAGACGGGTGTCTCG-GTCACCATCGCA-AACCCAGA--CG
57 GCC--ACGGGTG-CGGGAGT-GCC-GCACAGAACCGAGAGTTG
* * *
4729 GGT-----G-TCTCGGTCACCATCGGCAACCCCCGACTGTGCCTCGGCAACCCCAGGCCACGGGT
1 GGTGCGGGGCCCTCGGTCACCATCGGCAACACCCGACGGTGCCTCGGCAACCCCAGGCCACGGGT
*
4788 GCGGGAGTGCCGCACAGAGCCGAGAGTTG
66 GCGGGAGTGCCGCACAGAACCGAGAGTTG
* **
4817 GGTGCGGGGCCCTCGGTCACCATCGGCAACACCCGACGGTGCCTCGGCAACCCCAGTCCATTGGT
1 GGTGCGGGGCCCTCGGTCACCATCGGCAACACCCGACGGTGCCTCGGCAACCCCAGGCCACGGGT
4882 GCGGGAGTGCCGCACAGAACCGAG
66 GCGGGAGTGCCGCACAGAACCGAG
4906 CGCTGGTGCG
Statistics
Matches: 216, Mismatches: 32, Indels: 57
0.71 0.10 0.19
Matches are distributed among these distances:
85 3 0.01
86 10 0.05
87 9 0.04
88 4 0.02
89 5 0.02
91 3 0.01
92 10 0.05
93 31 0.14
94 102 0.47
95 9 0.04
98 5 0.02
100 12 0.06
101 10 0.05
102 3 0.01
ACGTcount: A:0.18, C:0.35, G:0.34, T:0.13
Consensus pattern (94 bp):
GGTGCGGGGCCCTCGGTCACCATCGGCAACACCCGACGGTGCCTCGGCAACCCCAGGCCACGGGT
GCGGGAGTGCCGCACAGAACCGAGAGTTG
Found at i:4860 original size:342 final size:342
Alignment explanation
Indices: 4241--4886 Score: 1079
Period size: 342 Copynumber: 1.9 Consensus size: 342
4231 GTCACCATCG
**
4241 GCAACCCCAGGCCATTGGTGAGGGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCAC
1 GCAACCCCAGGCCACGGGTGAGGGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCAC
4306 CATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACC
66 CATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACC
*
4371 ATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAACCCC
131 ATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCC
* * *
4436 AGGCCACGGGTGCGGGAGTTCCGGACAGAGCCGAGAGTTGGTGGGGGTCCTCGGTCACCATCGGC
196 AGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGTGGGGGCCCTCGGTCACCATCGGC
*
4501 AACCCCCGACGGGTGCCTCGGCAACCCCAGGCCA-CGGTGCGGGGGCCTCGGTCACCATCGGCAA
261 AACACCCGACGGGTGCCTCGGCAACCCCAGGCCATCGGTGCGGGGGCCTCGGTCACCATCGGCAA
4565 CCCCCGACGGGTGCCTC
326 CCCCCGACGGGTGCCTC
*
4582 GCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTC
1 GCAACCCCAGGCCACGGGTG-AGG-GTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTC
* *
4647 ACCATCGGCAATCCC-GGC-GGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCGGTC
64 ACCATCGGCAA-CCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTC
*
4710 ACCATC-GCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGAC-TGTGCCTCGGCAA
128 ACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAA
4773 CCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGCCCTCGGTCACC
192 CCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTT-GGTG-GGGGCCCTCGGTCACC
* *
4838 ATCGGCAACACCCGAC-GGTGCCTCGGCAACCCCAGTCCATTGGTGCGGG
255 ATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCATCGGTGCGGG
4887 AGTGCCGCAC
Statistics
Matches: 285, Mismatches: 13, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
341 82 0.29
342 108 0.38
343 92 0.32
344 3 0.01
ACGTcount: A:0.17, C:0.35, G:0.34, T:0.13
Consensus pattern (342 bp):
GCAACCCCAGGCCACGGGTGAGGGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCAC
CATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACC
ATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCC
AGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGTGGGGGCCCTCGGTCACCATCGGC
AACACCCGACGGGTGCCTCGGCAACCCCAGGCCATCGGTGCGGGGGCCTCGGTCACCATCGGCAA
CCCCCGACGGGTGCCTC
Found at i:13042 original size:33 final size:31
Alignment explanation
Indices: 13005--13092 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
12995 GCGTGAGCCC
*
13005 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGC-GGT-GCCT
* ** *
13038 CGGTCACCATCGGCAAAACCATACGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGTGCCT
*
13069 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
13093 CATTGGAGGG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
31 23 0.50
32 3 0.07
33 20 0.43
ACGTcount: A:0.20, C:0.38, G:0.27, T:0.15
Consensus pattern (31 bp):
CGGTCACCATCGGCAAACCCAGGCGGTGCCT
Found at i:13217 original size:32 final size:32
Alignment explanation
Indices: 13137--13267 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
13127 GTGCGTGAGG
* *
13137 CTCGGTCACCATCGGC-AACCC-GGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
13168 CTCGGTCACCATC-GCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
13199 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
13231 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
13263 CTCGG
1 CTCGG
13268 CAACCCCAGG
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
30 2 0.02
31 32 0.35
32 58 0.63
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:13413 original size:63 final size:62
Alignment explanation
Indices: 13314--13447 Score: 250
Period size: 63 Copynumber: 2.1 Consensus size: 62
13304 GCCGAGAGTT
*
13314 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-GCAACCCCAGGCCAC
13377 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCAC
13439 GGGTGCGGG
1 GGGTGCGGG
13448 AGTGCCGCAC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 24 0.34
63 46 0.66
ACGTcount: A:0.13, C:0.40, G:0.37, T:0.10
Consensus pattern (62 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCAC
Found at i:13424 original size:95 final size:94
Alignment explanation
Indices: 13199--13424 Score: 242
Period size: 95 Copynumber: 2.4 Consensus size: 94
13189 AGACGGGTGT
* *
13199 CTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCC
13264 TCGGCAACCCCAGGCCACGGGTGCGGGAG
66 TCGGCAACCCCAGGCCACGGGTGCGGGAG
* * * * * ***** *
13293 TTCCGGACA-GAGCCG-AGAGTTGGGTGCGGG-GTCCTCGGTCACCATCGGCAACCCCCGACGGG
1 CT-CGGTCACCATCGGCA-AACCCAG-ACGGGTG-CCTCGGTCACCATCGGCAACCCCCGACGGG
*
13355 TGCCTCGGCAACCCCAGGCCACGGGTGCGGGGG
62 TGCCTCGGCAACCCCAGGCCACGGGTGCGGGAG
* *
13388 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCG
1 -CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCG
13425 CAACCCCAGG
Statistics
Matches: 99, Mismatches: 25, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
93 1 0.01
94 7 0.07
95 83 0.84
96 7 0.07
97 1 0.01
ACGTcount: A:0.16, C:0.37, G:0.35, T:0.12
Consensus pattern (94 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCC
TCGGCAACCCCAGGCCACGGGTGCGGGAG
Found at i:13511 original size:93 final size:93
Alignment explanation
Indices: 13378--13759 Score: 294
Period size: 93 Copynumber: 4.1 Consensus size: 93
13368 CCAGGCCACG
* *
13378 GGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-GCAACCCCAGGCCACGGG
1 GGTGCGTGGG-CTCGGTCACCATCGGCAACCCCAGACGGGTGCCTCGGCAACCCCAGGCCACGGG
13442 TGCGGGAGTGCCGCACAGAACCGAGCGTT
65 TGCGGGAGTGCCGCACAGAACCGAGCGTT
* * * *
13471 GGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTC-ACCATTGGCAAAG
1 GGTGCGTG-GGCTCGGTCACCATCGGCAACCCCAGACGGGT-GCCTCGG-CAACC-----CCAGG
** * *
13535 CCAGACGGGTGTCTCG-GT-CAC-CATCGGCAAACCCAGACG--
58 CC--ACGGGTG-CGGGAGTGC-CGCA-CAG--AACCGAG-CGTT
*
13574 GGT--GT---CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAA-CCCAGGCCACGGGT
1 GGTGCGTGGGCTCGGTCACCATCGGCAACCCCAGACGGGTGCCTCGGCAACCCCAGGCCACGGGT
* *
13633 GCGGGAGTGCCGCACAGAGCCGAGAGTT
66 GCGGGAGTGCCGCACAGAACCGAGCGTT
* * **
13661 GGGTGCGGGGGCCTC-GTCACCATCGGCAACACCC--ACGGGTGCCTCGGCAACCCCAGTCCATT
1 -GGTGCGTGGG-CTCGGTCACCATCGGCAAC-CCCAGACGGGTGCCTCGGCAACCCCAGGCCACG
*
13723 GGTGC-GGAGTGCCGCACAGAACCGAGCGCTG
63 GGTGCGGGAGTGCCGCACAGAACCGAGCG-TT
13754 GGTGCG
1 GGTGCG
13760 GCAGCCTCGC
Statistics
Matches: 228, Mismatches: 28, Indels: 67
0.71 0.09 0.21
Matches are distributed among these distances:
85 1 0.00
86 5 0.02
87 2 0.01
88 15 0.07
89 3 0.01
90 6 0.03
92 43 0.19
93 63 0.28
94 13 0.06
95 6 0.03
96 9 0.04
97 27 0.12
100 5 0.02
101 5 0.02
102 12 0.05
103 5 0.02
104 6 0.03
105 2 0.01
ACGTcount: A:0.17, C:0.34, G:0.35, T:0.13
Consensus pattern (93 bp):
GGTGCGTGGGCTCGGTCACCATCGGCAACCCCAGACGGGTGCCTCGGCAACCCCAGGCCACGGGT
GCGGGAGTGCCGCACAGAACCGAGCGTT
Found at i:13518 original size:157 final size:157
Alignment explanation
Indices: 13231--13519 Score: 449
Period size: 157 Copynumber: 1.8 Consensus size: 157
13221 AGACGGGTGT
* *
13231 CTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTTC
1 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
13296 CGGACAGAGCCGAGAGTTGGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC
66 CGCACAGAACCGAGAGTTGGGTGCGGGG-CCTCGGTCACCATCGGCAACCCCAGACGGGTGCCTC
13361 GGCAACCCCAGGCCACGGGTGCGGGGGC
130 GGCAACCCCAGGCCACGGGTGCGGGGGC
13389 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-GCAACCCCAGGCCACGGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
13453 CGCACAGAACCGAGCGTT-GGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCC
66 CGCACAGAACCGAGAGTTGGGTGCG-G-GGCCTCGGTCACCATCGGCAACCCCAGACGGGT-GCC
13516 TCGG
128 TCGG
13520 TCACCATTGG
Statistics
Matches: 120, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
156 33 0.28
157 51 0.43
158 36 0.30
ACGTcount: A:0.16, C:0.36, G:0.36, T:0.12
Consensus pattern (157 bp):
CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
CGCACAGAACCGAGAGTTGGGTGCGGGGCCTCGGTCACCATCGGCAACCCCAGACGGGTGCCTCG
GCAACCCCAGGCCACGGGTGCGGGGGC
Found at i:13556 original size:32 final size:32
Alignment explanation
Indices: 13482--13615 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
13472 GTGCGTGAGG
* *
13482 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
13515 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
13547 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
13579 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
13611 CTCGG
1 CTCGG
13616 CAACCCAGGC
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 65 0.71
33 26 0.29
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:13564 original size:158 final size:157
Alignment explanation
Indices: 13165--13582 Score: 522
Period size: 158 Copynumber: 2.7 Consensus size: 157
13155 CCCGGCGGGT
* * *
13165 GGCCTCGGTCACCATC-GCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATAGGCAAAGCCAGACGGGT
*
13229 GTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGT
66 GTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-GCAACCCCAGGCCACGGGTGCGGGAGT
* * *
13294 TCCGGACAGAGCCGAGAGTTGGGTGCGG
130 GCCGCACAGAACCGAGAGTTGGGTGCGG
* * ** * * ***
13322 GGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG-CAACCCCAGGCCACGGGTG-CGG
1 GG-CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTC-ACCATAGGCAAAGCCAGACGG
* *
13385 GGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCACGGGTGCGGGAG
64 GTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCACGGGTGCGGGAG
*
13450 TGCCGCACAGAACCGAGCGTT-GGTGCGTG
129 TGCCGCACAGAACCGAGAGTTGGGTGCG-G
* * *
13479 AGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGG
1 -GGCCTCGGTCACCATCGGCAAACCCAGACGGGT-GCCTCGGTCACCATAGGCAAAGCCAGACGG
* * *
13543 GTGTCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCG
64 GTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCG
13583 GTCACCATCG
Statistics
Matches: 218, Mismatches: 35, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
156 33 0.15
157 62 0.28
158 95 0.44
159 28 0.13
ACGTcount: A:0.17, C:0.35, G:0.34, T:0.13
Consensus pattern (157 bp):
GGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATAGGCAAAGCCAGACGGGT
GTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCACGGGTGCGGGAGTG
CCGCACAGAACCGAGAGTTGGGTGCGG
Found at i:13767 original size:92 final size:93
Alignment explanation
Indices: 13583--13768 Score: 268
Period size: 92 Copynumber: 2.0 Consensus size: 93
13573 GGGTGTCTCG
*
13583 GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCAGGCCACGGGTGCGGGAGTGCCGCAC
1 GTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCAGGCCACGGGTGCGGGAGTGCCGCAC
* * **
13648 AGAGCCGAGAGTTGGGTGCGGGGGCCTC
66 AGAACCGAGAGCTGGGTGCGGCAGCCTC
* **
13676 GTCACCATCGGCAACACCC-ACGGGTGCCTCGGCAACCCCAGTCCATTGGTGC-GGAGTGCCGCA
1 GTCACCATCGGCAACACCCGACGGGTGCCTCGGCAA-CCCAGGCCACGGGTGCGGGAGTGCCGCA
*
13739 CAGAACCGAGCGCTGGGTGCGGCAGCCTC
65 CAGAACCGAGAGCTGGGTGCGGCAGCCTC
13768 G
1 G
13769 CACAGCGTCG
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
92 52 0.63
93 31 0.37
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.12
Consensus pattern (93 bp):
GTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCAGGCCACGGGTGCGGGAGTGCCGCAC
AGAACCGAGAGCTGGGTGCGGCAGCCTC
Found at i:21936 original size:32 final size:29
Alignment explanation
Indices: 21897--21980 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 29
21887 GCGTGAGCCC
*
21897 CGGTCACCATCGGCAATCCCAGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGCGGGT---CT
* *
21929 CGGTCACCATCGGCAAAACCATACGGGTCT
1 CGGTCACCATCGGCAAACCCA-GCGGGTCT
*
21959 CGGTCACCATCGGCAACCCCAG
1 CGGTCACCATCGGCAAACCCAG
21981 GCCAGTTGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 21 0.47
32 19 0.42
33 5 0.11
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.14
Consensus pattern (29 bp):
CGGTCACCATCGGCAAACCCAGCGGGTCT
Found at i:22071 original size:32 final size:32
Alignment explanation
Indices: 22030--22158 Score: 169
Period size: 31 Copynumber: 4.2 Consensus size: 32
22020 GTGCGTGAGG
* *
22030 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
22062 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
22094 CTCGGTCA-CATCGGCAAACCCA-AC-GGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
22123 CTCGGTCACCATCGGCAACCCCCGAC-GGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
22154 CTCGG
1 CTCGG
22159 CAACCCCAGG
Statistics
Matches: 89, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
29 13 0.15
30 14 0.16
31 25 0.28
32 25 0.28
33 12 0.13
ACGTcount: A:0.19, C:0.37, G:0.29, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:22137 original size:61 final size:63
Alignment explanation
Indices: 22028--22158 Score: 171
Period size: 61 Copynumber: 2.1 Consensus size: 63
22018 TGGTGCGTGA
*
22028 GGCTCGGTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGAC-GGT
* * * *
22092 GTCTCGGTCA-CATCGGCAAACCCA-AC-GGT-GTCTCGGTCACCATCGGCAACCCCCGACGGT
1 GGCTCGGTCACCATCGGC-AACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGT
22152 GGCTCGG
1 GGCTCGG
22159 CAACCCCAGG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
60 9 0.15
61 25 0.42
62 3 0.05
63 8 0.13
64 15 0.25
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.15
Consensus pattern (63 bp):
GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGT
Found at i:22307 original size:59 final size:60
Alignment explanation
Indices: 22203--22329 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 60
22193 GCCGAGAGTT
*
22203 GGTGC-GGGTCCTCGTCACCATCGGCAACCCCCGACGGTGCCTCGGCAACCCCAGGCC-CG
1 GGTGCGGGGGCCTCGTCACCATCGGCAACCCCCGA-GGTGCCTCGGCAACCCCAGGCCACG
22262 GGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCG-GGTGCCTCGGCAACCCCAGGCCACG
1 GGTGCGGGGGCCTC-GTCACCATCGGCAACCCCCGAGGTGCCTCGGCAACCCCAGGCCACG
22322 GGTGCGGG
1 GGTGCGGG
22330 AGTGCCGCAC
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
59 27 0.42
60 17 0.27
61 20 0.31
ACGTcount: A:0.13, C:0.41, G:0.35, T:0.11
Consensus pattern (60 bp):
GGTGCGGGGGCCTCGTCACCATCGGCAACCCCCGAGGTGCCTCGGCAACCCCAGGCCACG
Found at i:22342 original size:150 final size:152
Alignment explanation
Indices: 22123--22400 Score: 413
Period size: 150 Copynumber: 1.8 Consensus size: 152
22113 CCAACGGTGT
* *
22123 CTCGGTCACCATCGGCAACCCCCGACGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGAGTTCCG
1 CTCGGTCACCATCGGCAACCCCCGA-GGTGCCTCGGCAACCCCAGGCCACGGGTGCGGAGTGCCG
* *
22188 ACAGAGCCGAGAGTTGGTGCG-G-GTCCTC-GTCACCATCGGCAACCCCCGACGGT-GCCTCGGC
65 ACAGAACCGAGAGTTGGTGCGTGAG-CCTCGGTCACCATCGGCAACCCCAGACGGTGGCCTCGGC
22249 AACCCCAGGCCCGGGTGCGGGGGC
129 AACCCCAGGCCCGGGTGCGGGGGC
22273 CTCGGTCACCATCGGCAACCCCCG-GGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCG
1 CTCGGTCACCATCGGCAACCCCCGAGGTGCCTCGGCAACCCCAGGCCACGGGTGC-GGAGTGCCG
* * * *
22337 CACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGTGGCCTCGG
65 -ACAGAACCGAGAGTTGGTGCGTGAGCCTCGGTCACCATCGGCAACCCCAGACGGTGGCCTCGG
22401 TCACCATTGG
Statistics
Matches: 114, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
148 29 0.25
149 8 0.07
150 43 0.38
151 4 0.04
152 23 0.20
153 7 0.06
ACGTcount: A:0.15, C:0.37, G:0.35, T:0.13
Consensus pattern (152 bp):
CTCGGTCACCATCGGCAACCCCCGAGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGAGTGCCGA
CAGAACCGAGAGTTGGTGCGTGAGCCTCGGTCACCATCGGCAACCCCAGACGGTGGCCTCGGCAA
CCCCAGGCCCGGGTGCGGGGGC
Found at i:22434 original size:31 final size:31
Alignment explanation
Indices: 22364--22494 Score: 172
Period size: 32 Copynumber: 4.2 Consensus size: 31
22354 GTGCGTGAGG
* *
22364 CTCGGTCACCATCGGCAATCCCAGGCGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGT-GC
* * *
22396 CTCGGTCACCATTGGCAAAGCCAGACGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGTGC
*
22427 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGAC-GGTGC
* *
22459 CTCGGTCACCATCGGCAACCCCCGACGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGTGC
22490 CTCGG
1 CTCGG
22495 CAACCCCAGG
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
31 34 0.39
32 54 0.61
ACGTcount: A:0.18, C:0.37, G:0.29, T:0.16
Consensus pattern (31 bp):
CTCGGTCACCATCGGCAAACCCAGACGGTGC
Found at i:22463 original size:63 final size:63
Alignment explanation
Indices: 22364--22494 Score: 174
Period size: 63 Copynumber: 2.1 Consensus size: 63
22354 GTGCGTGAGG
* * * * *
22364 CTCGGTCACCATCGGCAATCCCAGGCGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGTGC
* * *
22427 CTCGGTCACCATCGGCAAACCCAGACGG-GTGTCTCGGTCACCATCGGCAACCCCCGACGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGTG-GCCTCGGTCACCATCGGCAAACCCAGACGGTGC
22490 CTCGG
1 CTCGG
22495 CAACCCCAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
62 1 0.02
63 58 0.98
ACGTcount: A:0.18, C:0.37, G:0.29, T:0.16
Consensus pattern (63 bp):
CTCGGTCACCATCGGCAAACCCAGACGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGTGC
Found at i:22637 original size:94 final size:94
Alignment explanation
Indices: 22459--22642 Score: 273
Period size: 94 Copynumber: 2.0 Consensus size: 94
22449 AGACGGGTGT
*
22459 CTCGGTCACCATCGGCAACCCCCGACGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGAGTGCCG
1 CTCGGTCACCATCGGCAACACCCGACGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGAGTGCCG
* *
22524 CACAGAGCCGAGAGTTGGG-TGCGGGGGC
66 CACAGAGACGAGAGCTGGGTTGCGGGGGC
* **
22552 CTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACACCCGAC-GGTGCCTCGGCAACCCCAGGCCACGGGTGC-GGAGTGC
*
22617 CGCACAGA-ACGAGCGCTGGGTTGCGG
64 CGCACAGAGACGAGAGCTGGGTTGCGG
22643 CAGCCTCGCA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
93 25 0.31
94 36 0.44
95 20 0.25
ACGTcount: A:0.17, C:0.35, G:0.36, T:0.12
Consensus pattern (94 bp):
CTCGGTCACCATCGGCAACACCCGACGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGAGTGCCG
CACAGAGACGAGAGCTGGGTTGCGGGGGC
Done.