Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007665.1 Hibiscus syriacus cultivar Beakdansim tig00026237_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: 50555
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.23
Found at i:3058 original size:11 final size:11
Alignment explanation
Indices: 3042--3074 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
3032 CGATAATGTC
3042 TCGCCGGAGCA
1 TCGCCGGAGCA
*
3053 TCGCCGGAGCG
1 TCGCCGGAGCA
3064 TCGCCGGAGCA
1 TCGCCGGAGCA
3075 CCACCGGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.36, G:0.39, T:0.09
Consensus pattern (11 bp):
TCGCCGGAGCA
Found at i:3480 original size:31 final size:32
Alignment explanation
Indices: 3445--3653 Score: 121
Period size: 32 Copynumber: 6.6 Consensus size: 32
3435 TTGCCCGGGG
** *
3445 TTGCCGATGGTGACCGAGACC-CCGTCTGGGT
1 TTGCCGATGGTGACCGAGACCACCCCCTGGGA
*
3476 TTGCCGATGGTGACCGAGGCCACCCCCTGGGA
1 TTGCCGATGGTGACCGAGACCACCCCCTGGGA
* * ** *
3508 CTGCCGATGGTGACCGAGGCTGCCGGGCCT-GG-
1 TTGCCGATGGTGACCGAGACCACC--CCCTGGGA
* * ** *
3540 -TGACCGA-GGCT-CCCG-CACCAATGGCCC-GGGG
1 TTG-CCGATGG-TGACCGAGACC-A-CCCCCTGGGA
* * *
3571 TTACCGATGGTGACCGAGA-CACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGACCACCC-CCTGGGA
*
3603 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGACCACCC-CCTGGGA
3636 TTGCCGATGGTGACCGAG
1 TTGCCGATGGTGACCGAG
3654 GCTCACGCAC
Statistics
Matches: 135, Mismatches: 27, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
30 6 0.04
31 34 0.25
32 60 0.44
33 32 0.24
34 3 0.02
ACGTcount: A:0.15, C:0.32, G:0.36, T:0.17
Consensus pattern (32 bp):
TTGCCGATGGTGACCGAGACCACCCCCTGGGA
Found at i:3610 original size:32 final size:32
Alignment explanation
Indices: 3574--3653 Score: 124
Period size: 33 Copynumber: 2.5 Consensus size: 32
3564 CCCGGGGTTA
* *
3574 CCGATGGTGACCGAGACACCCGTCTGGGTTTG
1 CCGATGGTGACCGAGACACCCGCCTGGGATTG
*
3606 CCGATGGTGACCGAGGCCACCCGCCTGGGATTG
1 CCGATGGTGACCGA-GACACCCGCCTGGGATTG
3639 CCGATGGTGACCGAG
1 CCGATGGTGACCGAG
3654 GCTCACGCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 15 0.34
33 29 0.66
ACGTcount: A:0.16, C:0.30, G:0.36, T:0.17
Consensus pattern (32 bp):
CCGATGGTGACCGAGACACCCGCCTGGGATTG
Found at i:3739 original size:167 final size:168
Alignment explanation
Indices: 3549--4120 Score: 948
Period size: 167 Copynumber: 3.4 Consensus size: 168
3539 GTGACCGAGG
*
3549 CTCCCGCACCAATGGCCCGGGGTTACCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* *
3614 GACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACGCACA-AGGGCCTGATGGT
66 GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGCCTGATGGT
3678 -ACCGAGACTCCCGCACCAACGCTCGGTTCTGTGCGGCA
131 GACCGAG-CTCCCGCACCAACGCTCGGTTCTGTGCGGCA
3716 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
3781 GACCGAGGCCACCCGCCTTGGATTGCCGATGGTG-CCGAGGCTCACGCACACGGGGCCTGATGGT
66 GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGCCTGATGGT
* *
3845 GACCGAGCTCCCCGCACCAAAGCTCGGTACTGT--GGCA
131 GACCGAGCT-CCCGCACCAACGCTCGGTTCTGTGCGGCA
3882 CTCCCGCACC-ATGG-CC-GGGTTGCCGATGGTGACCGAGACACCC-TCT-GGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* *
3942 GACCGAGGCCACCCGCCTTGGATTACCGATGGTGACCGAGGCGCACGCACACGGGGGCCTGATGG
66 GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACAC-GGGGCCTGATGG
4007 TGACCGAGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
130 TGACCGAGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
* **
4046 CTCCCCCCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGTTTTTGCCGATGG
1 CT-CCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGG
4111 TGACCGAGGC
65 TGACCGAGGC
4121 ACGCACACGT
Statistics
Matches: 380, Mismatches: 12, Indels: 23
0.92 0.03 0.06
Matches are distributed among these distances:
161 47 0.12
162 40 0.11
163 49 0.13
164 8 0.02
165 11 0.03
166 34 0.09
167 113 0.30
168 54 0.14
169 3 0.01
170 21 0.06
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.17
Consensus pattern (168 bp):
CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGCCTGATGGT
GACCGAGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
Found at i:3774 original size:32 final size:32
Alignment explanation
Indices: 3738--3819 Score: 112
Period size: 33 Copynumber: 2.6 Consensus size: 32
3728 TGGCCCGGGG
* *
3738 TTGCCGATGGTGACCGAGACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGACACCCGCCTGGGA
* *
3770 TTGCCGATGGTGACCGAGGCCACCCGCCTTGGA
1 TTGCCGATGGTGACCGA-GACACCCGCCTGGGA
3803 TTGCCGATGGTG-CCGAG
1 TTGCCGATGGTGACCGAG
3820 GCTCACGCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
31 1 0.02
32 21 0.47
33 23 0.51
ACGTcount: A:0.15, C:0.29, G:0.35, T:0.21
Consensus pattern (32 bp):
TTGCCGATGGTGACCGAGACACCCGCCTGGGA
Found at i:3807 original size:33 final size:33
Alignment explanation
Indices: 3738--3821 Score: 118
Period size: 32 Copynumber: 2.6 Consensus size: 33
3728 TGGCCCGGGG
* * *
3738 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
*
3770 TTGCCGATGGTGACCGAGGCCACCCGCCTTGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
3803 TTGCCGATGGTG-CCGAGGC
1 TTGCCGATGGTGACCGAGGC
3822 TCACGCACAC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
32 24 0.51
33 23 0.49
ACGTcount: A:0.14, C:0.30, G:0.36, T:0.20
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:3935 original size:30 final size:32
Alignment explanation
Indices: 3901--3981 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 32
3891 CATGGCCGGG
* *
3901 TTGCCGATGGTGACCGAGACACCC-TC-TGGT
1 TTGCCGATGGTGACCGAGACACCCGCCTTGGA
*
3931 TTGCCGATGGTGACCGAGGCCACCCGCCTTGGA
1 TTGCCGATGGTGACCGA-GACACCCGCCTTGGA
*
3964 TTACCGATGGTGACCGAG
1 TTGCCGATGGTGACCGAG
3982 GCGCACGCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 17 0.39
31 6 0.14
32 2 0.05
33 19 0.43
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.21
Consensus pattern (32 bp):
TTGCCGATGGTGACCGAGACACCCGCCTTGGA
Found at i:12021 original size:11 final size:11
Alignment explanation
Indices: 12005--12036 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
11995 CGATAATGTC
12005 TCGCCGGAGCG
1 TCGCCGGAGCG
12016 TCGCCGGAGCG
1 TCGCCGGAGCG
12027 TCGCCGGAGC
1 TCGCCGGAGC
12037 ACCACCGGGA
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:0.38, G:0.44, T:0.09
Consensus pattern (11 bp):
TCGCCGGAGCG
Found at i:12462 original size:32 final size:33
Alignment explanation
Indices: 12426--12489 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
12416 TGGCCCGGGG
*
12426 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGACACCCGCCTGGGT
*
12458 TTGCCGATGGTGACCGAGGCCACCCGCCTGGG
1 TTGCCGATGGTGACCGAGGACACCCGCCTGGG
12490 ACCGATGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.19
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGACACCCGCCTGGGT
Found at i:12497 original size:30 final size:30
Alignment explanation
Indices: 12429--12501 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 30
12419 CCCGGGGTTG
* *
12429 CCGATGGTGACCGAGACACCCGTCTGGGTTTG
1 CCGATGGTGACCGAGACACCCGCCTGGG--TA
*
12461 CCGATGGTGACCGAGGCCACCCGCCTGGG-A
1 CCGATGGTGACCGA-GACACCCGCCTGGGTA
12491 CCGATGGTGAC
1 CCGATGGTGAC
12502 TCACGCACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 11 0.30
32 14 0.38
33 12 0.32
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (30 bp):
CCGATGGTGACCGAGACACCCGCCTGGGTA
Found at i:12563 original size:128 final size:132
Alignment explanation
Indices: 12407--12681 Score: 459
Period size: 128 Copynumber: 2.1 Consensus size: 132
12397 TGCGGCACTA
12407 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
1 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
*
12472 CGAGGCCACCCGCCTGGGA-CCGATGGT-GA-CTCACGCACAAGGGGCCTGATGGTGACCGAGGC
66 CGAGGCCACCCGCCTGGGATCCGATGGTCGAGCTCACGCACAAGGGGCCTGATGGTGACCGAGAC
12534 TC
131 TC
12536 CCGCACCAATGGCCC-GGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
1 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
12600 CGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGATGGTGAC
66 CGAGGCCACCCGCCTGGGA-T-CCGATGGT---CGA-GCTCACGCACAAGGGGCCTGATGGTGAC
12665 CGAGACTC
125 CGAGACTC
12673 CCGCACCAA
1 CCGCACCAA
12682 CGCTCGGTTC
Statistics
Matches: 136, Mismatches: 1, Indels: 10
0.93 0.01 0.07
Matches are distributed among these distances:
128 68 0.50
129 15 0.11
131 8 0.06
135 2 0.01
137 43 0.32
ACGTcount: A:0.18, C:0.32, G:0.35, T:0.15
Consensus pattern (132 bp):
CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
CGAGGCCACCCGCCTGGGATCCGATGGTCGAGCTCACGCACAAGGGGCCTGATGGTGACCGAGAC
TC
Found at i:12617 original size:33 final size:33
Alignment explanation
Indices: 12554--12638 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
12544 ATGGCCCGGG
* * *
12554 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
12586 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
12619 TTGCCGATGGTGACCGAGGC
1 TTGCCGATGGTGACCGAGGC
12639 TCACGCACAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 17 0.35
33 32 0.65
ACGTcount: A:0.15, C:0.29, G:0.36, T:0.19
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:12740 original size:169 final size:170
Alignment explanation
Indices: 12533--13114 Score: 1008
Period size: 169 Copynumber: 3.4 Consensus size: 170
12523 GTGACCGAGG
12533 CTCCCGCACCAATGGCCC-GGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* *
12597 GACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACGCACA-AGGGGCCTGATGG
66 GACCGAGGCCACCCGCCTAGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
*
12661 TGACCGAGACTCCCGCACCAACGCTCGGTTCTGTGCGGCA
131 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
12701 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* *
12766 GACCGAGGCCACCCGCCCAGGATTGCCGATGGTGTCCGAGGCTCACGCACACGGGGGCCTGATGG
66 GACCGAGGCCACCCGCCTAGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
* *
12831 TGACCGAGGCTCCCGCACCAAAGCTCGGTACTGTGCGGCA
131 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
*
12871 CTCCCGCACCAATGG-CCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGTCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* * *
12935 GACCGAGGCCACCCGCCTTGGATTACCGATGGTGACCGAGGCGCACGCACACGGGGGCCTGATGG
66 GACCGAGGCCACCCGCCTAGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
*
13000 TGAACGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
131 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
**
13040 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGTTTTTTGCCGATGG
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTG-GGTTTGCCGATGG
13105 TGACCGAGGC
65 TGACCGAGGC
13115 ACGCACACGT
Statistics
Matches: 391, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
168 18 0.05
169 254 0.65
170 99 0.25
171 20 0.05
ACGTcount: A:0.16, C:0.33, G:0.34, T:0.17
Consensus pattern (170 bp):
CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
GACCGAGGCCACCCGCCTAGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
Found at i:12792 original size:33 final size:33
Alignment explanation
Indices: 12723--12807 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
12713 TGGCCCGGGG
* * ** *
12723 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCCAGGA
12755 TTGCCGATGGTGACCGAGGCCACCCGCCCAGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCCAGGA
*
12788 TTGCCGATGGTGTCCGAGGC
1 TTGCCGATGGTGACCGAGGC
12808 TCACGCACAC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 17 0.37
33 29 0.63
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.19
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCCAGGA
Found at i:12965 original size:33 final size:33
Alignment explanation
Indices: 12895--12976 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
12885 GCCGGGGTTG
* * * *
12895 CCGATGGTGACCGA-GACACCCGTCTGGGTTTG
1 CCGATGGTGACCGAGGCCACCCGCCTGGGATTA
* *
12927 TCGATGGTGACCGAGGCCACCCGCCTTGGATTA
1 CCGATGGTGACCGAGGCCACCCGCCTGGGATTA
12960 CCGATGGTGACCGAGGC
1 CCGATGGTGACCGAGGC
12977 GCACGCACAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 13 0.31
33 29 0.69
ACGTcount: A:0.17, C:0.29, G:0.34, T:0.20
Consensus pattern (33 bp):
CCGATGGTGACCGAGGCCACCCGCCTGGGATTA
Found at i:32050 original size:11 final size:11
Alignment explanation
Indices: 32034--32065 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
32024 CGATAATGTC
32034 TCGCCGGAGCG
1 TCGCCGGAGCG
32045 TCGCCGGAGCG
1 TCGCCGGAGCG
32056 TCGCCGGAGC
1 TCGCCGGAGC
32066 ACCACCGGGA
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:0.38, G:0.44, T:0.09
Consensus pattern (11 bp):
TCGCCGGAGCG
Found at i:32518 original size:33 final size:33
Alignment explanation
Indices: 32455--32670 Score: 183
Period size: 33 Copynumber: 6.6 Consensus size: 33
32445 TGGCCCGGGG
* * *
32455 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
32487 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
* * * ** *
32520 CTGCCGATGGTGACCGAGGCTCACGCACAAGGGC
1 TTGCCGATGGTGACCGAGGC-CACCCGCCTGGGA
* * *** * *
32554 CTGACCGA-GGCT-CCCGCA--CCAATGGCCCGGGG
1 TTG-CCGATGG-TGACCG-AGGCCACCCGCCTGGGA
* * *
32586 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
32618 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
32651 TTGCCGATGGTGACCGAGGC
1 TTGCCGATGGTGACCGAGGC
32671 TCACGCACAA
Statistics
Matches: 146, Mismatches: 29, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
31 6 0.04
32 54 0.37
33 64 0.44
34 16 0.11
35 6 0.04
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:32603 original size:131 final size:132
Alignment explanation
Indices: 32436--32689 Score: 492
Period size: 131 Copynumber: 1.9 Consensus size: 132
32426 GTGCGGCACT
32436 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
1 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
32501 CGAGGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACGCACAA-GGGCCTGACCGAGGC
66 CGAGGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGACCGAGGC
32565 TC
131 TC
32567 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
1 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
*
32632 CGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGA
66 CGAGGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGA
32690 TGGTGACCGA
Statistics
Matches: 121, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
131 113 0.93
132 8 0.07
ACGTcount: A:0.17, C:0.33, G:0.35, T:0.15
Consensus pattern (132 bp):
CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
CGAGGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGACCGAGGC
TC
Found at i:32824 original size:33 final size:33
Alignment explanation
Indices: 32755--32839 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
32745 TGGCCCGGGG
* * ** *
32755 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCCAGGA
32787 TTGCCGATGGTGACCGAGGCCACCCGCCCAGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCCAGGA
32820 TTGCCGATGGTGACCGAGGC
1 TTGCCGATGGTGACCGAGGC
32840 TCACGCACAC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 17 0.36
33 30 0.64
ACGTcount: A:0.16, C:0.31, G:0.35, T:0.18
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCCAGGA
Found at i:33001 original size:33 final size:32
Alignment explanation
Indices: 32927--33007 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 32
32917 GCCGGGGTTG
* * * *
32927 CCGATGGTGACCGA-GACACCCGTCTGGGTTT
1 CCGATGGTGACCGAGGCCACCCGCCTGGATTA
*
32958 GCGATGGTGACCGAGGCCACCCGCCTTGGATTA
1 CCGATGGTGACCGAGGCCACCCGCC-TGGATTA
32991 CCGATGGTGACCGAGGC
1 CCGATGGTGACCGAGGC
33008 GCACGCACAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 13 0.31
32 8 0.19
33 21 0.50
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.19
Consensus pattern (32 bp):
CCGATGGTGACCGAGGCCACCCGCCTGGATTA
Found at i:33033 original size:168 final size:170
Alignment explanation
Indices: 32564--33143 Score: 1033
Period size: 169 Copynumber: 3.4 Consensus size: 170
32554 CTGACCGAGG
32564 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* *
32629 GACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACGCACA-AGGGGCCTGATGG
66 GACCGAGGCCACCCGCCTAGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
*
32693 TGACCGAGACTCCCGCACCAACGCTCGGTTCTGTGCGGCA
131 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
32733 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
*
32798 GACCGAGGCCACCCGCCCAGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
66 GACCGAGGCCACCCGCCTAGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
* *
32863 TGACCGAGGCTCCCGCACCAAAGCTCGGTACTGTGCGGCA
131 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
32903 CTCCCGCACCAATGG-CCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTG-CGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* * *
32966 GACCGAGGCCACCCGCCTTGGATTACCGATGGTGACCGAGGCGCACGCACACGGGGGCCTGATGG
66 GACCGAGGCCACCCGCCTAGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
33031 TGA-CGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
131 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
**
33070 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGTTTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
33135 GACCGAGGC
66 GACCGAGGC
33144 ACGCACACGT
Statistics
Matches: 394, Mismatches: 14, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
167 49 0.12
168 110 0.28
169 171 0.43
170 64 0.16
ACGTcount: A:0.16, C:0.33, G:0.34, T:0.17
Consensus pattern (170 bp):
CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
GACCGAGGCCACCCGCCTAGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
Found at i:41077 original size:11 final size:11
Alignment explanation
Indices: 41061--41093 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
41051 CGATAATGTC
41061 TCGCCGGAGCA
1 TCGCCGGAGCA
*
41072 TCGCCGGAGCG
1 TCGCCGGAGCA
41083 TCGCCGGAGCA
1 TCGCCGGAGCA
41094 CCACCGGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.36, G:0.39, T:0.09
Consensus pattern (11 bp):
TCGCCGGAGCA
Found at i:41545 original size:33 final size:33
Alignment explanation
Indices: 41482--41568 Score: 131
Period size: 33 Copynumber: 2.7 Consensus size: 33
41472 TGGCCCGGGG
* * *
41482 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
41514 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
*
41547 CTGCCGATGGTGACCGAGGCCA
1 TTGCCGATGGTGACCGAGGCCA
41569 TGGTGACCGA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 17 0.34
33 33 0.66
ACGTcount: A:0.16, C:0.31, G:0.36, T:0.17
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:41573 original size:15 final size:15
Alignment explanation
Indices: 41553--41581 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41543 GGGACTGCCG
41553 ATGGTGACCGAGGCC
1 ATGGTGACCGAGGCC
41568 ATGGTGACCGAGGC
1 ATGGTGACCGAGGC
41582 TCCCGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.24, G:0.41, T:0.14
Consensus pattern (15 bp):
ATGGTGACCGAGGCC
Found at i:41615 original size:121 final size:121
Alignment explanation
Indices: 41463--41687 Score: 441
Period size: 121 Copynumber: 1.9 Consensus size: 121
41453 GTGCGGCACT
41463 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
1 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
41528 CGAGGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCCATGGTGACCGAGGCTC
66 CGAGGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCCATGGTGACCGAGGCTC
41584 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
1 CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
*
41649 CGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGC
66 CGAGGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGC
41688 TCACGCACAA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 103 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (121 bp):
CCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
CGAGGCCACCCGCCTGGGACTGCCGATGGTGACCGAGGCCATGGTGACCGAGGCTC
Found at i:41666 original size:33 final size:33
Alignment explanation
Indices: 41603--41687 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
41593 TGGCCCGGGG
* * *
41603 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
41635 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
41668 TTGCCGATGGTGACCGAGGC
1 TTGCCGATGGTGACCGAGGC
41688 TCACGCACAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 17 0.35
33 32 0.65
ACGTcount: A:0.15, C:0.29, G:0.36, T:0.19
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:41840 original size:33 final size:33
Alignment explanation
Indices: 41771--41855 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
41761 TGGCCCGGGG
* * *
41771 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
*
41803 TTGCCGATGGTGACCGAGGCCACCCGCCTTGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
41836 TTGCCGATGGTGACCGAGGC
1 TTGCCGATGGTGACCGAGGC
41856 TCACGCACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
32 17 0.35
33 31 0.65
ACGTcount: A:0.15, C:0.29, G:0.35, T:0.20
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:41999 original size:169 final size:170
Alignment explanation
Indices: 41581--42160 Score: 1051
Period size: 169 Copynumber: 3.4 Consensus size: 170
41571 GTGACCGAGG
41581 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* *
41646 GACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACGCACA--AGGGCCTGATGG
66 GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
*
41709 TGACCGAGACTCCCGCACCAACGCTCGGTTCTGTGCGGCA
131 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
41749 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
41814 GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
66 GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
* *
41879 TGACCGAGGCTCCCGCACCAAAGCTCGGTACTGTGCGGCA
131 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
41919 CTCCCGCACCAATGG-CCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* *
41983 GACCGAGGCCACCCGCCTTGGATTACCGATGGTGACCGAGGCGCACGCACACGGGGGCCTGATGG
66 GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
42048 TGA-CGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
131 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
**
42087 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGTTTTTGCCGATGGT
1 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
42152 GACCGAGGC
66 GACCGAGGC
42161 ACGCACACGT
Statistics
Matches: 398, Mismatches: 11, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
168 164 0.41
169 171 0.43
170 63 0.16
ACGTcount: A:0.16, C:0.33, G:0.34, T:0.17
Consensus pattern (170 bp):
CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
GACCGAGGCCACCCGCCTTGGATTGCCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
Found at i:42012 original size:33 final size:33
Alignment explanation
Indices: 41943--42024 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
41933 GCCGGGGTTG
* * * *
41943 CCGATGGTGACCGA-GACACCCGTCTGGGTTTG
1 CCGATGGTGACCGAGGCCACCCGCCTGGGATTA
*
41975 CCGATGGTGACCGAGGCCACCCGCCTTGGATTA
1 CCGATGGTGACCGAGGCCACCCGCCTGGGATTA
42008 CCGATGGTGACCGAGGC
1 CCGATGGTGACCGAGGC
42025 GCACGCACAC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 14 0.32
33 30 0.68
ACGTcount: A:0.17, C:0.30, G:0.34, T:0.18
Consensus pattern (33 bp):
CCGATGGTGACCGAGGCCACCCGCCTGGGATTA
Found at i:50469 original size:91 final size:93
Alignment explanation
Indices: 50314--50495 Score: 278
Period size: 91 Copynumber: 2.0 Consensus size: 93
50304 TGCGAGGCTG
* *
50314 CCGCACCCAGCGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCA-CC
1 CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
*
50378 -CGGGTGTTGCCGATGGTGACCGAGGCC
66 GCGGGGGTTGCCGATGGTGACCGAGGCC
* ** *
50405 CCGCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
50470 GTCGGGGGTTGCCGATGGTGACCGAG
66 G-CGGGGGTTGCCGATGGTGACCGAG
50496 ACACCCGTCT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
91 56 0.69
92 2 0.02
94 23 0.28
ACGTcount: A:0.12, C:0.36, G:0.35, T:0.16
Consensus pattern (93 bp):
CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
GCGGGGGTTGCCGATGGTGACCGAGGCC
Found at i:50495 original size:32 final size:32
Alignment explanation
Indices: 50459--50555 Score: 149
Period size: 32 Copynumber: 3.0 Consensus size: 32
50449 CCTGGGGTTG
* * *
50459 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
50491 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
50523 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
50555 C
1 C
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.20
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Done.