Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004678.1 Hibiscus syriacus cultivar Beakdansim tig00010489_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: 94525
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4006 original size:21 final size:21
Alignment explanation
Indices: 3952--4000 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
3942 GGGAGCGTCA
3952 GTGCATCGATGCATACCCAAG
1 GTGCATCGATGCATACCCAAG
3973 GTGCATCGATGCATACCCAAG
1 GTGCATCGATGCATACCCAAG
3994 GTGCATC
1 GTGCATC
4001 AGTGCACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (21 bp):
GTGCATCGATGCATACCCAAG
Found at i:4169 original size:45 final size:45
Alignment explanation
Indices: 4064--4161 Score: 196
Period size: 45 Copynumber: 2.2 Consensus size: 45
4054 GGTGTACTAA
4064 GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCT
4109 GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCT
4154 GAGTGCAT
1 GAGTGCAT
4162 ATATGCATGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCT
Found at i:4244 original size:65 final size:65
Alignment explanation
Indices: 4102--4270 Score: 202
Period size: 65 Copynumber: 2.6 Consensus size: 65
4092 ATGTTTCAAA
*
4102 ATAGCCTGAGTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATATAT
1 ATAG-CTG-GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATAGAT
4166 GC
64 GC
* * *
4168 ATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGAT
1 ATAGCTGGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-CTGAGTGCATAGAT
4231 GC
64 GC
* * *
4233 ATAG-TATGTGCATCGATGCATGAAATGAATTCGATGTT
1 ATAGCT-GGTGCATCGATGCATAAAATGCATTCGATGTT
4271 CAATTTATTC
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
64 30 0.33
65 55 0.60
66 6 0.07
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (65 bp):
ATAGCTGGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATAGATGC
Found at i:4594 original size:2 final size:2
Alignment explanation
Indices: 4589--4722 Score: 261
Period size: 2 Copynumber: 67.5 Consensus size: 2
4579 ACACACACAC
4589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4715 AT AT -T AT A
1 AT AT AT AT A
4723 ATTGTTTCAA
Statistics
Matches: 131, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 130 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6315 original size:164 final size:164
Alignment explanation
Indices: 6044--6371 Score: 656
Period size: 164 Copynumber: 2.0 Consensus size: 164
6034 AGTAATCCAA
6044 CCTACCAATGTGATTCTAAGTTGCTCACGAGCTATCCTCTCACAGCATACTTAATAAAGTGATAT
1 CCTACCAATGTGATTCTAAGTTGCTCACGAGCTATCCTCTCACAGCATACTTAATAAAGTGATAT
6109 AATCTATGATACGTTAATTATACCCAATGTTAAATCTATAAAATTTACATGAACATTATTCATAG
66 AATCTATGATACGTTAATTATACCCAATGTTAAATCTATAAAATTTACATGAACATTATTCATAG
6174 TATTCAATTCATAATATGGTTAATTATGCATCAT
131 TATTCAATTCATAATATGGTTAATTATGCATCAT
6208 CCTACCAATGTGATTCTAAGTTGCTCACGAGCTATCCTCTCACAGCATACTTAATAAAGTGATAT
1 CCTACCAATGTGATTCTAAGTTGCTCACGAGCTATCCTCTCACAGCATACTTAATAAAGTGATAT
6273 AATCTATGATACGTTAATTATACCCAATGTTAAATCTATAAAATTTACATGAACATTATTCATAG
66 AATCTATGATACGTTAATTATACCCAATGTTAAATCTATAAAATTTACATGAACATTATTCATAG
6338 TATTCAATTCATAATATGGTTAATTATGCATCAT
131 TATTCAATTCATAATATGGTTAATTATGCATCAT
6372 TTATAAAACC
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (164 bp):
CCTACCAATGTGATTCTAAGTTGCTCACGAGCTATCCTCTCACAGCATACTTAATAAAGTGATAT
AATCTATGATACGTTAATTATACCCAATGTTAAATCTATAAAATTTACATGAACATTATTCATAG
TATTCAATTCATAATATGGTTAATTATGCATCAT
Found at i:7764 original size:30 final size:30
Alignment explanation
Indices: 7729--7797 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
7719 ACTAATTTTC
7729 AATTATCAAAATTATAATAAAATCAATCGT
1 AATTATCAAAATTATAATAAAATCAATCGT
*
7759 AATTATCAAAATTATAATAAAATCTATCGT
1 AATTATCAAAATTATAATAAAATCAATCGT
7789 AATTATCAA
1 AATTATCAA
7798 TTAAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (30 bp):
AATTATCAAAATTATAATAAAATCAATCGT
Found at i:13104 original size:33 final size:32
Alignment explanation
Indices: 13059--13181 Score: 119
Period size: 32 Copynumber: 3.9 Consensus size: 32
13049 AATGATCACT
*
13059 TTCATTTT-TATTTAATTAAGATTTGATAATA
1 TTCATTTTATATTTAATTAAGATTTGATAACA
*
13090 TTCATATTTATATTTCAA-TAAGATTTGATTACA
1 TTCAT-TTTATATTT-AATTAAGATTTGATAACA
* * *
13123 TTCATTTT-TAATTTAATTAAGATTTGGTCACT
1 TTCATTTTAT-ATTTAATTAAGATTTGATAACA
** *
13155 TTTGTTTT-TATTTAATTAAGATGTGAT
1 TTCATTTTATATTTAATTAAGATTTGAT
13182 TACTAAACAT
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
31 24 0.31
32 29 0.37
33 23 0.29
34 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.54
Consensus pattern (32 bp):
TTCATTTTATATTTAATTAAGATTTGATAACA
Found at i:13571 original size:41 final size:40
Alignment explanation
Indices: 13526--13635 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 40
13516 ATTCACGTTG
* *
13526 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTC
*
13567 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-GAAATCGCGTTGCGATTTTC
13608 CATTTCGCGTTGCGATAGTTGAAATCGC
1 CATTTCGCGTTGCGATAGTTGAAATCGC
13636 AACGCGATCT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 7 0.11
41 56 0.88
42 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
Found at i:13622 original size:20 final size:20
Alignment explanation
Indices: 13551--13623 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
13541 TAGTTGAAAA
*
13551 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
13571 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGAT-TTTCCATT
13592 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
13612 TCGCGTTGCGAT
1 TCGCGTTGCGAT
13624 AGTTGAAATC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:13635 original size:20 final size:21
Alignment explanation
Indices: 13530--13635 Score: 67
Period size: 20 Copynumber: 5.2 Consensus size: 21
13520 ACGTTGCATT
*
13530 TCGCATTGCGATAGTT-GAAAA
1 TCGCGTTGCGATAGTTCG-AAA
** * **
13551 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
* *
13571 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTCGAAA
* * **
13592 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
13612 TCGCGTTGCGATAGTT-GAAA
1 TCGCGTTGCGATAGTTCGAAA
13632 TCGC
1 TCGC
13636 AACGCGATCT
Statistics
Matches: 61, Mismatches: 21, Indels: 7
0.69 0.24 0.08
Matches are distributed among these distances:
20 34 0.56
21 27 0.44
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCGAAA
Found at i:13688 original size:21 final size:21
Alignment explanation
Indices: 13668--13809 Score: 139
Period size: 20 Copynumber: 6.9 Consensus size: 21
13658 ATTCGCGTTG
*
13668 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* ** *
13689 AAAATCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
*
13709 CATTTCGCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGT-TC
* *
13731 CA-GTCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
*
13750 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTC
* * *
13771 AAATTCGCGTTGCGAT-TTTC
1 CATTTCGCGTTGCGATAGTTC
13791 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
13810 CTACAGTTGT
Statistics
Matches: 93, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
19 3 0.03
20 44 0.47
21 43 0.46
22 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (21 bp):
CATTTCGCGTTGCGATAGTTC
Found at i:13746 original size:142 final size:142
Alignment explanation
Indices: 13497--13774 Score: 479
Period size: 142 Copynumber: 2.0 Consensus size: 142
13487 AATTCGCATT
*
13497 GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGT
1 GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGA
**
13562 TTTTCCATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
66 TTTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
13627 TGAAATCGCAAC
131 TGAAATCGCAAC
* *
13639 GCGATCTCCA-TCATCGCAAATTCGCGTTGCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG
1 GCGATCTCCACT-ATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCG
13703 ATTTTCCATTTCGCGTTGCGATAGTCTACAG-TCGCGTTGCGATTTTCCATTTCGCGTTGCGATA
65 ATTTTCCATTTCGCGTTGCGATAGT-TACAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATA
13767 GTTGAAAT
129 GTTGAAAT
13775 TCGCGTTGCG
Statistics
Matches: 129, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
141 1 0.01
142 125 0.97
143 3 0.02
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (142 bp):
GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGA
TTTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
TGAAATCGCAAC
Found at i:13766 original size:82 final size:83
Alignment explanation
Indices: 13668--13850 Score: 309
Period size: 82 Copynumber: 2.2 Consensus size: 83
13658 ATTCGCGTTG
13668 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
13733 GTCG-CGTTGCGATTTTC
66 GTCGTCGTTGCGATTTTC
*
13750 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
*
13815 GTTGTCGTTGCGATTTTC
66 GTCGTCGTTGCGATTTTC
*
13833 CAAATT--CGTTGCGATAGT
1 C-ATTTCGCGTTGCGATAGT
13851 CTACAGTTGT
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
82 79 0.82
83 14 0.15
84 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (83 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
GTCGTCGTTGCGATTTTC
Found at i:13826 original size:22 final size:22
Alignment explanation
Indices: 13798--13869 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
13788 TTCCATTTCG
13798 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
13820 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
13839 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
13861 CGTTGCGAT
1 CGTTGCGAT
13870 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:13843 original size:19 final size:19
Alignment explanation
Indices: 13819--13884 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
13809 TCTACAGTTG
13819 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
13838 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
13859 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
13879 TCGTTG
1 TCGTTG
13885 TGATAGTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:13890 original size:123 final size:121
Alignment explanation
Indices: 13668--13892 Score: 303
Period size: 123 Copynumber: 1.8 Consensus size: 121
13658 ATTCGCGTTG
*
13668 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACA
*
13733 GTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
65 GTCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
* * *
13791 CATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTA
* *
13854 CAGTTGTCGTTGCGATTTTCCAAATT-CGTTGTGATAGTT
63 CAGTCG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGTT
13893 TAAAAAAAAG
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
123 55 0.61
124 29 0.32
125 6 0.07
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.39
Consensus pattern (121 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAG
TCGCGTTGCGATTTTCCAATTCCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
Found at i:13891 original size:41 final size:40
Alignment explanation
Indices: 13668--13875 Score: 244
Period size: 41 Copynumber: 5.0 Consensus size: 40
13658 ATTCGCGTTG
* * *
13668 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTTGCGTTGCGATTTTC
*
13709 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTTGCGTTGCGATTTTC
*
13750 CATTTCGCGTTGCGATAGT-TGA-AATTCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTT-GCGTTGCGATTTTC
13791 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC
*
13833 CAAATT-CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 C-ATTTCCGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC
13874 CA
1 CA
13876 AATTCGTTGT
Statistics
Matches: 154, Mismatches: 6, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
40 4 0.03
41 128 0.83
42 19 0.12
43 3 0.02
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (40 bp):
CATTTCCGTTGCGATAGTCTACAGTTGCGTTGCGATTTTC
Found at i:13891 original size:82 final size:80
Alignment explanation
Indices: 13675--13875 Score: 273
Period size: 82 Copynumber: 2.5 Consensus size: 80
13665 TTGCATTTCG
*
13675 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGT
1 CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTC-CGTTGCGATAGTCTACAGTCGCGT
*
13740 TGCGATTTTCCATTTC
65 TGCGATTTTCCAATTC
*
13756 GCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTC
1 -CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTC-CGTTGCGATAGTCTACAGTCG-C
13821 GTTGCGATTTTCCAAATT-
63 GTTGCGATTTTCC-AATTC
*
13839 CGTTGCGATAGTCT-ACAGTT-GTCGTTGCGATTTTCCA
1 CGTTGCGATAGT-TGA-AATTCG-CGTTGCGATTTTCCA
13876 AATTCGTTGT
Statistics
Matches: 110, Mismatches: 4, Indels: 9
0.89 0.03 0.07
Matches are distributed among these distances:
82 74 0.67
83 33 0.30
84 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (80 bp):
CGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCCGTTGCGATAGTCTACAGTCGCGTT
GCGATTTTCCAATTC
Found at i:13979 original size:6 final size:6
Alignment explanation
Indices: 13968--14023 Score: 98
Period size: 6 Copynumber: 9.7 Consensus size: 6
13958 AGACACGTAT
13968 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
14015 GACC-C GACC
1 GACCAC GACC
14024 CGAGACGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.20
6 40 0.80
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:14538 original size:5 final size:5
Alignment explanation
Indices: 14528--14584 Score: 60
Period size: 6 Copynumber: 10.4 Consensus size: 5
14518 TCGTCTCGTC
*
14528 TCGGG TAGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG-GG
14577 TCGTGG TC
1 TCG-GG TC
14585 ATACGTGTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 21 0.43
6 28 0.57
ACGTcount: A:0.02, C:0.18, G:0.53, T:0.28
Consensus pattern (5 bp):
TCGGG
Found at i:14546 original size:15 final size:16
Alignment explanation
Indices: 14528--14579 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
14518 TCGTCTCGTC
14528 TCGGGTAGGGTCG-GG
1 TCGGGTAGGGTCGTGG
*
14543 TCGGGTCGGGTCGTGG
1 TCGGGTAGGGTCGTGG
*
14559 TCGTGGTCGTGGTCGTGG
1 TCG-GGTAG-GGTCGTGG
14577 TCG
1 TCG
14580 TGGTCATACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 12 0.36
16 5 0.15
17 5 0.15
18 11 0.33
ACGTcount: A:0.02, C:0.17, G:0.54, T:0.27
Consensus pattern (16 bp):
TCGGGTAGGGTCGTGG
Found at i:14562 original size:6 final size:6
Alignment explanation
Indices: 14536--14584 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
14526 TCTCGGGTAG
14536 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
14581 GGTC
1 GGTC
14585 ATACGTGTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.35
6 28 0.65
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:14692 original size:19 final size:19
Alignment explanation
Indices: 14668--14733 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
14658 TTAACTATCA
14668 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
14687 CAACGACAACTATAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
14709 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
14728 CAACGA
1 CAACGA
14734 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:14710 original size:22 final size:22
Alignment explanation
Indices: 14683--14754 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
14673 AATTTGGAAA
14683 ATCGCAACGACAACTATAGACT
1 ATCGCAACGACAACTATAGACT
* * **
14705 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTATAGACT
*
14724 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTATAGACT
14746 ATCGCAACG
1 ATCGCAACG
14755 CGAAATAGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTATAGACT
Found at i:14812 original size:61 final size:61
Alignment explanation
Indices: 14746--14914 Score: 180
Period size: 61 Copynumber: 2.8 Consensus size: 61
14736 ACTGTAGACT
* * *
14746 ATCGCAACGCGA-AATAGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGACAATAGAAAATCGCAACGCGAAATGCAA-AATCGCAACGCGAAATGGAAA
** ** *
14807 ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGACAATAGAAAATCGCAACGCGAAATGCAAAATCGCAACGCGAAATGGAAA
*** ** *
14868 ATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAATGGAAAATCGCA
1 ATCGCAACGCGACAAT-AGAAAATCGCAACGCGAAATGCAAAATCGCA
14915 GCGATTTTCA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
61 75 0.78
62 21 0.22
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (61 bp):
ATCGCAACGCGACAATAGAAAATCGCAACGCGAAATGCAAAATCGCAACGCGAAATGGAAA
Found at i:14858 original size:41 final size:41
Alignment explanation
Indices: 14677--14859 Score: 246
Period size: 41 Copynumber: 4.4 Consensus size: 41
14667 ACAACGAATT
* * *
14677 TGGAAAATCGCAACGACAACTATAGACTATCGCAA--CGAATT
1 TGGAAAATCGCAACG-CGACTGTAGACTATCGCAACGCGAA-A
*
14718 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGACTGTAGACTATCGCAACGCGAAA
* * *
14760 TAGAAAATCGCAACGCGAATTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAA
14801 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
14842 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
14860 AATGGAAAAT
Statistics
Matches: 129, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
40 1 0.01
41 109 0.84
42 15 0.12
43 4 0.03
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAA
Found at i:14858 original size:102 final size:100
Alignment explanation
Indices: 14746--14943 Score: 326
Period size: 102 Copynumber: 2.0 Consensus size: 100
14736 ACTGTAGACT
14746 ATCGCAACGCGAAATAGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGCGAAATAGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCG
14811 CAACGCGACTGT-AGACTATCGCAACGCGAAATGGAAA
66 C-A-GCGACTGTCA-ACTATCGCAACGCGAAATGGAAA
* *
14848 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGCGAAATAGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCG
* *
14913 CAGCGATTTTCAACTATCGCAACGCGAAATG
66 CAGCGACTGTCAACTATCGCAACGCGAAATG
14944 CAACGCGAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
100 25 0.27
101 2 0.02
102 64 0.70
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (100 bp):
ATCGCAACGCGAAATAGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGAAAATCG
CAGCGACTGTCAACTATCGCAACGCGAAATGGAAA
Found at i:14930 original size:39 final size:41
Alignment explanation
Indices: 14848--14943 Score: 178
Period size: 39 Copynumber: 2.4 Consensus size: 41
14838 GAAATGGAAA
14848 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
14889 ATCGCAACGCGAAATGGAAAATCGC-A-GCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
14928 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
14944 CAACGCGAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 29 0.53
40 1 0.02
41 25 0.45
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:16060 original size:14 final size:13
Alignment explanation
Indices: 16030--16068 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
16020 GTTTAATTTA
16030 TTTA-AATTTCAT
1 TTTATAATTTCAT
16042 TTTATAATTTCAT
1 TTTATAATTTCAT
16055 TTT-T-ATTT-AT
1 TTTATAATTTCAT
16065 TTTA
1 TTTA
16069 GTCCTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.20
11 4 0.16
12 5 0.20
13 11 0.44
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATAATTTCAT
Found at i:16646 original size:281 final size:280
Alignment explanation
Indices: 15961--16705 Score: 804
Period size: 281 Copynumber: 2.6 Consensus size: 280
15951 ATTTAGTTTA
* * ** **
15961 ATTTAATATTAATATCAGCTTCACATTTTACAATTATTTTGATTTGATCCCCGCATGTTGTTTAA
1 ATTTTATATTAATTTCAGCTTCACATTTTACAATTATTTCAATTTGATCCCTACATGTTGTTTAA
* *
16026 TTTATTTAAATTTCATTTTATAATTTCATTTTTATTTATTTTAGTCCTTAAAA-TATATTTTTTA
66 TTTATTTAAATTTCAGTTTATAATTTCATTTTTATTTAATTTAGTCCTTAAAATTATA-TTTTTA
* ** ** * * *
16090 TCTGAAATTGTGTCATGCTTATTAATATTTTTTTAATTTACTCCGAACCCTACTAATCACATCAT
130 TCCGAAATTG-CCCATAATTATTTATATTTTTGTAATTTACTCC-AA--ATAC-AATCACATCAT
* * * * *
16155 ATACTTTATTTTAAAACTTGTAAATTATAACATAATCTTCAAACTCAATATAATTTTGTTCATCA
190 AAACTTAATTTCAAAACCTGTAAATTATAACATAATCTTCAAACTCAATAAAATTTTGTTCATCA
* *
16220 ACTTTTTAAATGATGCAATCTAGTCT
255 ACTTTTTAAATGATACAATCTAGTCC
* * * *
16246 ATTTTTTATATTAATTT-AGCTTCATATTTTACATTTGTTTCAATTTGATCCCTACATGTTATTT
1 A--TTTTATATTAATTTCAGCTTCACATTTTACAATTATTTCAATTTGATCCCTACATGTTGTTT
* * * * * *
16310 AATTTATTTTAATTTTAGTTTATAATTTTATATTTATTTAATTCAGTCTTTAAAATTATATTTTT
64 AATTTATTTAAATTTCAGTTTATAATTTCATTTTTATTTAATTTAGTCCTTAAAATTATATTTTT
* *
16375 ATCCGAAATTAGCCCATAATTATTTCTATTTTTGTAATTTACTCTAAATA-AATCACATCATAAA
129 ATCCGAAATT-GCCCATAATTATTTATATTTTTGTAATTTACTCCAAATACAATCACATCATAAA
* ** *
16439 CTTAATTTCAAACCCTGTAAATTATATTATAATC-TCTAAA-TCCTATAAAATTATT-TTCA-CA
193 CTTAATTTCAAAACCTGTAAATTATAACATAATCTTC-AAACT-CAATAAAATT-TTGTTCATC-
*
16500 AACTTTTTAAATGGATACAATTTAGTCC
254 AACTTTTTAAAT-GATACAATCTAGTCC
* * ***
16528 ATTTTATATTAATTTCAACTTCACATTTTAGAATTATTTCAATTTGATCCCTTTGTGTTGTTTAA
1 ATTTTATATTAATTTCAGCTTCACATTTTACAATTATTTCAATTTGATCCCTACATGTTGTTTAA
* * * * * *
16593 TCTATTTGAATTTCAGTTTGTAATTTCATTTTTGTTCAATTTAGTCCTTAAAATTATATTTTCAT
66 TTTATTTAAATTTCAGTTTATAATTTCATTTTTATTTAATTTAGTCCTTAAAATTATATTTTTAT
* *
16658 -CAAAATTGGCCCGTAATTATTTATATATTTTTGTAATTTACTCCAAAT
131 CCGAAATT-GCCCATAATTA-TT-TATATTTTTGTAATTTACTCCAAAT
16706 CATATACAAT
Statistics
Matches: 383, Mismatches: 65, Indels: 27
0.81 0.14 0.06
Matches are distributed among these distances:
280 34 0.09
281 164 0.43
282 38 0.10
283 2 0.01
285 3 0.01
286 125 0.33
287 17 0.04
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (280 bp):
ATTTTATATTAATTTCAGCTTCACATTTTACAATTATTTCAATTTGATCCCTACATGTTGTTTAA
TTTATTTAAATTTCAGTTTATAATTTCATTTTTATTTAATTTAGTCCTTAAAATTATATTTTTAT
CCGAAATTGCCCATAATTATTTATATTTTTGTAATTTACTCCAAATACAATCACATCATAAACTT
AATTTCAAAACCTGTAAATTATAACATAATCTTCAAACTCAATAAAATTTTGTTCATCAACTTTT
TAAATGATACAATCTAGTCC
Found at i:18237 original size:37 final size:36
Alignment explanation
Indices: 18178--18297 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
18168 ATCACATTAT
* * *
18178 CATTTTTC-AACAAACATCTACCAAACATTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
18214 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
18250 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
18285 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
18298 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 35 0.46
36 13 0.17
37 28 0.37
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:18253 original size:21 final size:21
Alignment explanation
Indices: 18229--18289 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
18219 TTCAAAGAAA
18229 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
18250 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
18264 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
18285 CATTT
1 CATTT
18290 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:18306 original size:35 final size:36
Alignment explanation
Indices: 18180--18324 Score: 133
Period size: 35 Copynumber: 4.1 Consensus size: 36
18170 CACATTATCA
* *
18180 TTTTTCAACA-AACA-TCTACCAAACATTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
18215 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
18252 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
18288 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
18322 TTT
1 TTT
18325 AATAATTTCA
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 29 0.30
38 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:22853 original size:37 final size:35
Alignment explanation
Indices: 22794--22940 Score: 167
Period size: 35 Copynumber: 4.2 Consensus size: 35
22784 ATCCCATTAT
*
22794 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACAT-TACCAAACTTTG-AAAAC
*
22830 TATTTTTCAAAGAAACACTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACA-TTACCAAACTTTGAAAAC
22866 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACA-TTACCAAACTTTGAAAAC
****
22901 CATTTTTTCAAAG-TTGGTTACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAACATTACCAAACTTTGAAAAC
22935 CATTTT
1 CATTTT
22941 AATAATTTCA
Statistics
Matches: 99, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
33 4 0.04
34 10 0.10
35 43 0.43
36 13 0.13
37 28 0.28
38 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.32
Consensus pattern (35 bp):
CATTTTTCAAAGAAACATTACCAAACTTTGAAAAC
Found at i:29767 original size:16 final size:16
Alignment explanation
Indices: 29743--29776 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29733 TATCGCCGAT
*
29743 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
29759 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
29775 CG
1 CG
29777 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:30255 original size:36 final size:36
Alignment explanation
Indices: 30205--30276 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 36
30195 ACATCTATCA
*
30205 AAATTTTACCAAACTTTG-AAAAACATTTTTCAAAG
1 AAATTTTACCAAACTTTGAAAAAACATTTTCCAAAG
30240 AAATATTTACCAAACTTTGAAAAAACATTTTCCAAAG
1 AAAT-TTTACCAAACTTTGAAAAAACATTTTCCAAAG
30277 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 4 0.12
36 14 0.41
37 16 0.47
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (36 bp):
AAATTTTACCAAACTTTGAAAAAACATTTTCCAAAG
Found at i:30295 original size:35 final size:36
Alignment explanation
Indices: 30210--30296 Score: 106
Period size: 35 Copynumber: 2.4 Consensus size: 36
30200 TATCAAAATT
* *
30210 TTACCAAACTTTG-AAAAACATTTTTCAAAGAAATAT
1 TTACCAAACTTTGAAAAAACATTTTCCAAAG-AATAG
* *
30246 TTACCAAACTTTGAAAAAACATTTTCCAAAG-TTGG
1 TTACCAAACTTTGAAAAAACATTTTCCAAAGAATAG
*
30281 TTGCCAAACTTTGAAA
1 TTACCAAACTTTGAAA
30297 CTTTTAACAG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 16 0.36
36 13 0.29
37 16 0.36
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (36 bp):
TTACCAAACTTTGAAAAAACATTTTCCAAAGAATAG
Found at i:33759 original size:34 final size:34
Alignment explanation
Indices: 33712--33792 Score: 144
Period size: 34 Copynumber: 2.4 Consensus size: 34
33702 CGCTTCGAGA
33712 ATTCACTCCATCACTCCATCATTCGAGAGTGATG
1 ATTCACTCCATCACTCCATCATTCGAGAGTGATG
* *
33746 ATTCACTCTATCACTCCATCATTCGAGCGTGATG
1 ATTCACTCCATCACTCCATCATTCGAGAGTGATG
33780 ATTCACTCCATCA
1 ATTCACTCCATCA
33793 TGCGAGAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (34 bp):
ATTCACTCCATCACTCCATCATTCGAGAGTGATG
Found at i:35772 original size:27 final size:27
Alignment explanation
Indices: 35742--35799 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 27
35732 AAATGATTGT
35742 AATA-CACTGGATATATGAAATGACCAA-
1 AATACCACTGGA-ATA-GAAATGACCAAG
*
35769 AATACCCCTGGAATAGAAATGACCAAG
1 AATACCACTGGAATAGAAATGACCAAG
35796 AATA
1 AATA
35800 TCACCAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.39
27 11 0.39
28 6 0.21
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (27 bp):
AATACCACTGGAATAGAAATGACCAAG
Found at i:36941 original size:24 final size:24
Alignment explanation
Indices: 36842--36943 Score: 132
Period size: 24 Copynumber: 4.2 Consensus size: 24
36832 ATTTCCGATT
* *
36842 TGAATTCTGTTATGATACCTGACA
1 TGAATTCTGATATGATACTTGACA
* *
36866 TGGATTCTGATATGATACTTGACC
1 TGAATTCTGATATGATACTTGACA
* *
36890 TGGATTCTGATCTGATACTTGACA
1 TGAATTCTGATATGATACTTGACA
* *
36914 TGAATTCTGATCTGATACTTGACT
1 TGAATTCTGATATGATACTTGACA
36938 TGAATT
1 TGAATT
36944 ATGTTTCGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACA
Found at i:38225 original size:19 final size:19
Alignment explanation
Indices: 38201--38245 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
38191 GCTTCATTTC
* * *
38201 TGAATTTTTGTGATTTGAG
1 TGAATTTCTCTGACTTGAG
38220 TGAATTTCTCTGACTTGAG
1 TGAATTTCTCTGACTTGAG
38239 TGAATTT
1 TGAATTT
38246 ATTGGATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.49
Consensus pattern (19 bp):
TGAATTTCTCTGACTTGAG
Found at i:40979 original size:20 final size:20
Alignment explanation
Indices: 40956--41021 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
40946 TATGCACCGC
40956 TGCACTCATTAATGCATCGA
1 TGCACTCATTAATGCATCGA
*
40976 TGCACTCATTGATGCATCGA
1 TGCACTCATTAATGCATCGA
*
40996 TGCA--C-TTACATGAATCGA
1 TGCACTCATTA-ATGCATCGA
41014 TGCACTCA
1 TGCACTCA
41022 GGATTTTATG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 2 0.05
18 13 0.33
20 24 0.62
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (20 bp):
TGCACTCATTAATGCATCGA
Found at i:46765 original size:21 final size:21
Alignment explanation
Indices: 46739--46860 Score: 86
Period size: 21 Copynumber: 5.6 Consensus size: 21
46729 TTGTGCATAA
46739 TGCATCGATACACTATGAAGG
1 TGCATCGATACACTATGAAGG
* * *
46760 TGCATCAATGCATCCCTATGAATG
1 TGCATCGAT--A-CACTATGAAGG
*
46784 TGCATCGATACACCATGAAGG
1 TGCATCGATACACTATGAAGG
* * * *
46805 TGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACT--ATGAAGG
* *
46828 TGCATCGATGCACTCA-GCA-G
1 TGCATCGATACACT-ATGAAGG
46848 TGCATCGATACAC
1 TGCATCGATACAC
46861 CAGTCGGGAT
Statistics
Matches: 80, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
20 13 0.16
21 29 0.36
22 2 0.03
23 19 0.24
24 17 0.21
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACTATGAAGG
Found at i:46803 original size:45 final size:44
Alignment explanation
Indices: 46739--46836 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 44
46729 TTGTGCATAA
* *
46739 TGCATCGATACACTATGAAGGTGCATCAATGCA-TCCCTATGAATG
1 TGCATCGATACACCATGAAGGTGCACCAATGCACT-CCT-TGAATG
*
46784 TGCATCGATACACCATGAAGGTGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACCATGAAGGTGCACCAATGCACTCCTTGAATG
46828 TGCATCGAT
1 TGCATCGAT
46837 GCACTCAGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
44 15 0.31
45 33 0.67
46 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (44 bp):
TGCATCGATACACCATGAAGGTGCACCAATGCACTCCTTGAATG
Found at i:46830 original size:23 final size:23
Alignment explanation
Indices: 46739--46842 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 23
46729 TTGTGCATAA
* *
46739 TGCATCGATACACT--ATGAAGG
1 TGCATCGATGCACTCCATGAATG
*
46760 TGCATCAATGCA-TCCCTATGAATG
1 TGCATCGATGCACT-CC-ATGAATG
* *
46784 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACTCCATGAATG
* *
46805 TGCACCGATGCACTCCTTGAATG
1 TGCATCGATGCACTCCATGAATG
46828 TGCATCGATGCACTC
1 TGCATCGATGCACTC
46843 AGCAGTGCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 24 0.37
22 3 0.05
23 23 0.35
24 14 0.22
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACTCCATGAATG
Found at i:51318 original size:24 final size:24
Alignment explanation
Indices: 51207--51308 Score: 123
Period size: 24 Copynumber: 4.2 Consensus size: 24
51197 ATTTCTGATT
* *
51207 TGAATTCTGTTATGATACCTGACA
1 TGAATTCTGATATGATACTTGACA
* * *
51231 TGGATTATGATATGATACTTGACG
1 TGAATTCTGATATGATACTTGACA
* **
51255 TGGATTCTGATCCGATACTTGACA
1 TGAATTCTGATATGATACTTGACA
*
51279 TGAATTCTGATATGATACTTGACT
1 TGAATTCTGATATGATACTTGACA
51303 TGAATT
1 TGAATT
51309 ATGTTTTGAT
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACA
Found at i:52004 original size:23 final size:23
Alignment explanation
Indices: 51974--52017 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
51964 ACATGTTTTA
51974 ATAAAAGTTTTAAATCTTCCGCT
1 ATAAAAGTTTTAAATCTTCCGCT
*
51997 ATAAAAGTTTTAAATTTTCCG
1 ATAAAAGTTTTAAATCTTCCG
52018 TCCTCGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (23 bp):
ATAAAAGTTTTAAATCTTCCGCT
Found at i:57078 original size:32 final size:32
Alignment explanation
Indices: 57013--57115 Score: 120
Period size: 32 Copynumber: 3.2 Consensus size: 32
57003 CAGTGCTCGA
*
57013 CTCGTTAA-AAAATTTTGTTGCTCAAGTCG-TG
1 CTCGTTAAGAAAA-TTTGTTGCTCAACTCGTTG
* *
57044 CTCGTTAAGAAAATTTGTTGCTCGATTCGTTG
1 CTCGTTAAGAAAATTTGTTGCTCAACTCGTTG
* * **
57076 CTCATTAAGAAAATTTGTTGTTCCCCTCGTTG
1 CTCGTTAAGAAAATTTGTTGCTCAACTCGTTG
57108 CTCGTTAA
1 CTCGTTAA
57116 TCTTACTGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
31 22 0.35
32 40 0.65
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (32 bp):
CTCGTTAAGAAAATTTGTTGCTCAACTCGTTG
Found at i:62161 original size:41 final size:41
Alignment explanation
Indices: 62093--62172 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
62083 CCAACGGTGT
* *
62093 TGAACATTGATACATGAATATATCAAAGCTGAACTGATAAC
1 TGAACATTGATACACGAATATACCAAAGCTGAACTGATAAC
*
62134 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATA
1 TGAACATTGATACACGAATATACCAAAGCTGAACTGATA
62173 TGTACTCACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (41 bp):
TGAACATTGATACACGAATATACCAAAGCTGAACTGATAAC
Found at i:62438 original size:20 final size:20
Alignment explanation
Indices: 62413--62465 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
62403 TAGAAATACT
62413 CCATACTGAAAATTTATAAA
1 CCATACTGAAAATTTATAAA
62433 CCATACTGAAAATTTATAAA
1 CCATACTGAAAATTTATAAA
*
62453 TCATACTGAAAAT
1 CCATACTGAAAAT
62466 AAAATGAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (20 bp):
CCATACTGAAAATTTATAAA
Found at i:67703 original size:22 final size:22
Alignment explanation
Indices: 67678--67725 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
67668 ATTTTGTCGT
*
67678 AAAAACTCAACCATCAAAAAAC
1 AAAAAATCAACCATCAAAAAAC
* * *
67700 AAAAAATTAACCATTAAATAAC
1 AAAAAATCAACCATCAAAAAAC
67722 AAAA
1 AAAA
67726 TATGAAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAAAATCAACCATCAAAAAAC
Found at i:69122 original size:32 final size:32
Alignment explanation
Indices: 69086--69163 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
69076 TCGGGGCCAT
*
69086 AGGGCCTACCTAAGAACAT-ATCTTAGGGCCGC
1 AGGGCCTACCTAAGAA-ATGATCTCAGGGCCGC
**
69118 AGGGCCTACCCGAG-AATGATCTCAGGGCCGC
1 AGGGCCTACCTAAGAAATGATCTCAGGGCCGC
*
69149 AGAGCCTACCTAAGA
1 AGGGCCTACCTAAGA
69164 GTCACATTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
30 2 0.05
31 24 0.63
32 12 0.32
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.15
Consensus pattern (32 bp):
AGGGCCTACCTAAGAAATGATCTCAGGGCCGC
Found at i:80934 original size:22 final size:20
Alignment explanation
Indices: 80891--80928 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
80881 TTCAGACTGA
*
80891 ATAGTATCGGTACCTCTCCT
1 ATAGTATCGATACCTCTCCT
*
80911 ATAGTATCGATACTTCTC
1 ATAGTATCGATACCTCTC
80929 TTCTATGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (20 bp):
ATAGTATCGATACCTCTCCT
Found at i:80943 original size:22 final size:22
Alignment explanation
Indices: 80904--80945 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
80894 GTATCGGTAC
*
80904 CTCTCCTATAGTATCGATACTT
1 CTCTCCTATAGTACCGATACTT
* *
80926 CTCTTCTATGGTACCGATAC
1 CTCTCCTATAGTACCGATAC
80946 CCACTTCGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (22 bp):
CTCTCCTATAGTACCGATACTT
Found at i:88095 original size:31 final size:29
Alignment explanation
Indices: 88038--88105 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 29
88028 AAGCCTTAGA
* *
88038 AAAATTTGGGGACCATTCAATAATTTTTG
1 AAAAGTTGGGGACCATTCAATAATTTTGG
*
88067 AAAAGTTGGGGAACCAATTCGATAATTTTGG
1 AAAAGTTGGGG-ACC-ATTCAATAATTTTGG
88098 AAAAGTTG
1 AAAAGTTG
88106 TGAATGGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 10 0.29
30 3 0.09
31 21 0.62
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (29 bp):
AAAAGTTGGGGACCATTCAATAATTTTGG
Done.