Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003113.1 Hibiscus syriacus cultivar Beakdansim tig00006510_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: 51412
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Found at i:3971 original size:11 final size:12
Alignment explanation
Indices: 3940--3983 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
3930 TCAAAAATCA
3940 TAAAATAATTAT
1 TAAAATAATTAT
3952 T-AAAT--TTAT
1 TAAAATAATTAT
3961 TAAAAT-ATTA-
1 TAAAATAATTAT
3971 TAAAATAATTAT
1 TAAAATAATTAT
3983 T
1 T
3984 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:5371 original size:2 final size:2
Alignment explanation
Indices: 5366--5391 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5356 TCTCTCTCTC
5366 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5392 AGCTATAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6342 original size:27 final size:27
Alignment explanation
Indices: 6312--6368 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
6302 GACCTCTCAA
6312 TCCTAGTAACCGTCGTCCCCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
*
6339 TCCTAGTAACCGTCGTCCTCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
6366 TCC
1 TCC
6369 CCTCCTCCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.11, C:0.54, G:0.11, T:0.25
Consensus pattern (27 bp):
TCCTAGTAACCGTCGTCCCCCTCCCCC
Found at i:6566 original size:42 final size:42
Alignment explanation
Indices: 6520--6889 Score: 321
Period size: 42 Copynumber: 9.3 Consensus size: 42
6510 ACACCTCCTA
* *
6520 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTTCCCCCTC
* *
6562 CCCCTTCTCCTACTCCCCCTCCTCGTACACCTC-T-----TC
1 CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTTCCCCCTC
* * * *
6598 CACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCC-C
1 CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTTCCCCCTC
* * *
6639 CCCCTGCTCCTACTCCCCCTCCTCGTACA-C-C-T---CCTA
1 CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTTCCCCCTC
* * *
6675 TCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTT-CCCCCTC
* * *
6717 CTCCTGCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTTCCCCCTC
* * *
6759 CCCCTGCTCCTACTCCCCCTCCTCGTACA-C-C-T---CCTA
1 CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTTCCCCCTC
* * * *
6795 CCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTTCCCCCTC
* * * *
6837 CCCCTGCTCCTACTCCCCCTCCTCGTACACCTCCTACCCCTC
1 CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTTCCCCCTC
* *
6879 CACCTACTCCT
1 CCCCTCCTCCT
6890 CCCCCTCCCT
Statistics
Matches: 259, Mismatches: 48, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
35 2 0.01
36 79 0.31
37 3 0.01
38 3 0.01
39 3 0.01
40 2 0.01
41 26 0.10
42 139 0.54
43 2 0.01
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.25
Consensus pattern (42 bp):
CCCCTCCTCCTACTCCCCCTCCTCGCACACCTCTTCCCCCTC
Found at i:6578 original size:21 final size:21
Alignment explanation
Indices: 6490--6660 Score: 76
Period size: 21 Copynumber: 8.5 Consensus size: 21
6480 AACACGCCTC
* *
6490 CTCCCCCTCCCCCTCCTCGTA
1 CTCCCCCTCCCCCTCCACCTA
* * *
6511 CACCTCCTACCCCTCCACCTA
1 CTCCCCCTCCCCCTCCACCTA
* *
6532 CTCCCCCTCCTCGC-GCACCT-
1 CTCCCCCTCC-CCCTCCACCTA
* *
6552 CTTCCCCCTCCCCCTTCTCCTA
1 C-TCCCCCTCCCCCTCCACCTA
* * *
6574 CTCCCCCTCCTCGTACACCT-
1 CTCCCCCTCCCCCTCCACCTA
*
6594 CT-----TCCACCTCCACCTA
1 CTCCCCCTCCCCCTCCACCTA
**
6610 CTCCCCCTCCTAGCT-CACCT-
1 CTCCCCCTCC-CCCTCCACCTA
* *
6630 CTTCCCCC-CCCCCTGCTCCTA
1 C-TCCCCCTCCCCCTCCACCTA
6651 CTCCCCCTCC
1 CTCCCCCTCC
6661 TCGTACACCT
Statistics
Matches: 111, Mismatches: 24, Indels: 30
0.67 0.15 0.18
Matches are distributed among these distances:
15 10 0.09
16 2 0.02
19 2 0.02
20 18 0.16
21 73 0.66
22 6 0.05
ACGTcount: A:0.09, C:0.64, G:0.04, T:0.24
Consensus pattern (21 bp):
CTCCCCCTCCCCCTCCACCTA
Found at i:6589 original size:78 final size:78
Alignment explanation
Indices: 6496--6768 Score: 399
Period size: 78 Copynumber: 3.5 Consensus size: 78
6486 CCTCCTCCCC
6496 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
*
6561 CCCCCTTCTCCTA
66 CCCCCTGCTCCTA
* * *
6574 CTCCCCCTCCTCGTACACCT-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACC-CCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCC
6638 -CCCCCTGCTCCTA
65 TCCCCCTGCTCCTA
*
6651 CTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCC
*
6715 TCCTCCTGCTCCTA
65 TCCCCCTGCTCCTA
** * * * *
6729 CTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
6769 TACTCCCCCT
Statistics
Matches: 175, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
76 2 0.01
77 69 0.39
78 104 0.59
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (78 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
CCCCCTGCTCCTA
Found at i:6757 original size:21 final size:21
Alignment explanation
Indices: 6688--6759 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 21
6678 CTCCACCTAC
6688 TCCCCCTCCTCGCGCACCT-T
1 TCCCCCTCCTCGCGCACCTCT
*
6708 TCCCCCCTCCTC-CTGCTCCTAC-
1 T-CCCCCTCCTCGC-GCACCT-CT
6730 TCCCCCTCCTCGCGCACCTCT
1 TCCCCCTCCTCGCGCACCTCT
6751 TCCCCCTCC
1 TCCCCCTCC
6760 CCCTGCTCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
20 3 0.07
21 39 0.89
22 2 0.05
ACGTcount: A:0.04, C:0.64, G:0.07, T:0.25
Consensus pattern (21 bp):
TCCCCCTCCTCGCGCACCTCT
Found at i:6775 original size:21 final size:21
Alignment explanation
Indices: 6710--6780 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
6700 CGCACCTTTC
*
6710 CCCCCTCCTCCTGCTCCTACT
1 CCCCCTCCCCCTGCTCCTACT
* *
6731 CCCCCTCCTCGC-GCACCT-CTT
1 CCCCCTCC-CCCTGCTCCTAC-T
6752 CCCCCTCCCCCTGCTCCTACT
1 CCCCCTCCCCCTGCTCCTACT
6773 CCCCCTCC
1 CCCCCTCC
6781 TCGTACACCT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.07
21 36 0.88
22 2 0.05
ACGTcount: A:0.04, C:0.66, G:0.06, T:0.24
Consensus pattern (21 bp):
CCCCCTCCCCCTGCTCCTACT
Found at i:6791 original size:120 final size:120
Alignment explanation
Indices: 6606--6889 Score: 437
Period size: 120 Copynumber: 2.4 Consensus size: 120
6596 TCCACCTCCA
* *
6606 CCTACTCCCCCTCCTAGCTCACCTCTTCCCCC-CCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
* * *
6670 TCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTCCTGCT
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTT-CCCCCTCCCCCTGCT
*
6725 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
*
6790 TCCTACCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
66 TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
* * * * *
6845 CCTACTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCT
1 CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCT
6890 CCCCCTCCCT
Statistics
Matches: 151, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
119 30 0.20
120 119 0.79
121 2 0.01
ACGTcount: A:0.09, C:0.61, G:0.05, T:0.25
Consensus pattern (120 bp):
CCTACTCCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
Found at i:6807 original size:78 final size:78
Alignment explanation
Indices: 6725--6896 Score: 310
Period size: 78 Copynumber: 2.2 Consensus size: 78
6715 TCCTCCTGCT
6725 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
6790 TCCTACCCCTCCA
66 TCCTACCCCTCCA
* *
6803 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
6868 TCCTACCCCTCCA
66 TCCTACCCCTCCA
6881 CCTACTCCTCCC-CCTC
1 CCTACTCC-CCCTCCTC
6897 CCTCTCCACC
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
78 87 0.98
79 2 0.02
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.24
Consensus pattern (78 bp):
CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCA
Found at i:6812 original size:21 final size:20
Alignment explanation
Indices: 6753--6943 Score: 69
Period size: 21 Copynumber: 9.6 Consensus size: 20
6743 GCACCTCTTC
* * *
6753 CCCCTCCCCCTGCTCCTACT
1 CCCCTCCACCTACTCCTCCT
* * *
6773 CCCCCTCCTCGTACACCTCCT
1 -CCCCTCCACCTACTCCTCCT
6794 ACCCCTCCACCTACTCCTCCT
1 -CCCCTCCACCTACTCCTCCT
***
6815 CCTAGCGCACCT-CT--T-C-
1 CCCCTC-CACCTACTCCTCCT
* * *
6831 CCCCTCCCCCTGCTCCTACT
1 CCCCTCCACCTACTCCTCCT
* * *
6851 CCCCCTCCTCGTACACCTCCT
1 -CCCCTCCACCTACTCCTCCT
6872 ACCCCTCCACCTACTCCT-C-
1 -CCCCTCCACCTACTCCTCCT
*
6891 CCCCT-C-CCT-CTCCACCT
1 CCCCTCCACCTACTCCTCCT
*
6908 CCCCCTCCACCTCCACCTCCACCT
1 -CCCCTCCACCT--A-CTCCTCCT
6932 CCACCTCCACCT
1 CC-CCTCCACCT
6944 CCACCTCCAC
Statistics
Matches: 127, Mismatches: 26, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.06
16 9 0.07
17 2 0.02
18 12 0.09
19 2 0.02
20 9 0.07
21 66 0.52
23 2 0.02
24 17 0.13
ACGTcount: A:0.10, C:0.64, G:0.03, T:0.23
Consensus pattern (20 bp):
CCCCTCCACCTACTCCTCCT
Found at i:6898 original size:6 final size:6
Alignment explanation
Indices: 6875--6954 Score: 108
Period size: 6 Copynumber: 13.3 Consensus size: 6
6865 ACCTCCTACC
* * * *
6875 CCTCCA CCTACT CCTCCC CCTCC- CTCTCCA CCTCCC CCTCCA CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
6923 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
6955 AGTTACCTGC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
5 1 0.02
6 64 0.97
7 1 0.02
ACGTcount: A:0.12, C:0.69, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTCCA
Found at i:10700 original size:20 final size:20
Alignment explanation
Indices: 10675--10749 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
10665 GATACTTTTT
10675 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
10695 AAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTC
10715 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
10735 AAGAGTTTTGAAACT
1 AAGAGTTTCGAAACT
10750 TTCCCTAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
AAGAGTTTCGAAACTATCTC
Found at i:15531 original size:11 final size:12
Alignment explanation
Indices: 15500--15543 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
15490 TCAAAAATCA
15500 TAAAATAATTAT
1 TAAAATAATTAT
15512 T-AAAT--TTAT
1 TAAAATAATTAT
15521 TAAAAT-ATTA-
1 TAAAATAATTAT
15531 TAAAATAATTAT
1 TAAAATAATTAT
15543 T
1 T
15544 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:16457 original size:2 final size:2
Alignment explanation
Indices: 16450--16474 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16440 CTATTAAAAT
16450 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16475 GGGAAGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16950 original size:2 final size:2
Alignment explanation
Indices: 16945--16972 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16935 TCTCTCTCTC
16945 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16973 GCTATAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17923 original size:27 final size:27
Alignment explanation
Indices: 17893--17947 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
17883 GACCTCTCAA
17893 TCCTAGTAACCGTCGTCCCCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
*
17920 TCCTAGTAACCGTCGTCCTCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
17947 T
1 T
17948 TCCCCTCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.11, C:0.53, G:0.11, T:0.25
Consensus pattern (27 bp):
TCCTAGTAACCGTCGTCCCCCTCCCCC
Found at i:18171 original size:78 final size:78
Alignment explanation
Indices: 18078--18351 Score: 399
Period size: 78 Copynumber: 3.5 Consensus size: 78
18068 CCTCCTCCCC
*
18078 CTCCCCCTCCTCGTACACCTCCTACCCCTCAACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
*
18143 CCCCCTTCTCCTA
66 CCCCCTGCTCCTA
* * *
18156 CTCCCCCTCCTCGTACACCT-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACC-CCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCC
18220 TCCCCCTGCTCCTA
65 TCCCCCTGCTCCTA
*
18234 CTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCC
*
18298 TCCTCCTGCTCCTA
65 TCCCCCTGCTCCTA
** * * * *
18312 CTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
18352 TACTCCCCCT
Statistics
Matches: 176, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
77 6 0.03
78 167 0.95
79 3 0.02
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.25
Consensus pattern (78 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
CCCCCTGCTCCTA
Found at i:18210 original size:21 final size:22
Alignment explanation
Indices: 18181--18364 Score: 73
Period size: 21 Copynumber: 9.0 Consensus size: 22
18171 CACCTCTTCC
*
18181 ACCTCCACCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
*
18203 AGCT-CACCT-CTTCCCCCTCC-
1 ACCTGCACCTAC-TCCCCCTCCT
* *
18223 CCCTGCTCCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
* * * **
18245 -CGTACACCTCCTATCCCTCC-
1 ACCTGCACCTACTCCCCCTCCT
18265 ACCT--A----CTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
*
18281 -CGC-GCACCTT-TCCCCCCTCCT
1 AC-CTGCACCTACT-CCCCCTCCT
*
18302 -CCTGCTCCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
18323 -CGC-GCACCT-CTTCCCCCTCC-
1 AC-CTGCACCTAC-TCCCCCTCCT
* *
18343 CCCTGCTCCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
18365 CGTACACCTC
Statistics
Matches: 123, Mismatches: 17, Indels: 44
0.67 0.09 0.24
Matches are distributed among these distances:
15 9 0.07
16 1 0.01
17 1 0.01
19 1 0.01
20 7 0.06
21 97 0.79
22 7 0.06
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (22 bp):
ACCTGCACCTACTCCCCCTCCT
Found at i:18253 original size:120 final size:118
Alignment explanation
Indices: 18110--18575 Score: 366
Period size: 120 Copynumber: 3.9 Consensus size: 118
18100 TACCCCTCAA
* * * * * *
18110 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCTCCTACTCC-CCCTCCTCGTACAC
1 CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACCTACTCCTACTCCTCCCACCTC-TAC-C
* *
18174 CTCTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCT
64 CTCCTCC-CCTCCACCTACTCCCCCTCCTCGCTCACCTCTTCCCCCTCCCCCTGCT
* * ** *
18230 CCTACTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCC
1 CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACCTACTCCTACTCCTC-C-CACCTCTACC
* * * *
18294 CCCCTCCTCCTGCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
64 CTCCTCC-CCTCCACCTACTCCCCCTCCTCGCTCACCTCTTCCCCCTCCCCCTGCT
* * * *
18350 CCTACTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCC
1 CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACCTACTCCTACTCCT--CCCACCTCTACC
* * * * *
18415 C-CCTCCCCCTGCTCCTACTCCCCCTCCTCG-T-ACAC-C-T---CCTACCCCTCCA
64 CTCCT-CCCCTCCACCTACTCCCCCTCCTCGCTCAC-CTCTTCCCCCTCCCCCTGCT
* * * * * * *
18464 CCTACT-CCCCTCCTAGCGCACCTCTTCCCCCTCC-CCTTGCTCCTACTCC-CCCTCCACGTACA
1 CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACC-TACTCCTACTCCTCCCACCTC-TAC-
* * * *
18526 CCTCCTACCCCTCCACCTACTCCTCCC-CCTCCCTCTCCACCTCCCCCTCC
63 CCTCCT-CCCCTCCACCTACTCC-CCCTCCTCGCTCACCTCTTCCCCCTCC
18576 ACCTCCACCT
Statistics
Matches: 284, Mismatches: 42, Indels: 41
0.77 0.11 0.11
Matches are distributed among these distances:
110 5 0.02
111 2 0.01
112 4 0.01
113 54 0.19
114 20 0.07
115 2 0.01
116 1 0.00
117 1 0.00
118 3 0.01
119 5 0.02
120 171 0.60
121 10 0.04
122 2 0.01
123 4 0.01
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.24
Consensus pattern (118 bp):
CCTACTCCCCCTCCTCGCACACCTCCTACCCCTCCACCTACTCCTACTCCTCCCACCTCTACCCT
CCTCCCCTCCACCTACTCCCCCTCCTCGCTCACCTCTTCCCCCTCCCCCTGCT
Found at i:18390 original size:78 final size:78
Alignment explanation
Indices: 18308--18548 Score: 439
Period size: 78 Copynumber: 3.1 Consensus size: 78
18298 TCCTCCTGCT
*
18308 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
18373 TCCTACCCCTCCA
66 TCCTACCCCTCCA
*
18386 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
18451 TCCTACCCCTCCA
66 TCCTACCCCTCCA
* *
18464 CCTACT-CCCCTCCTAGCGCACCTCTTCCCCCTCCCCTTGCTCCTACTCCCCCTCCACGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
18528 TCCTACCCCTCCA
66 TCCTACCCCTCCA
18541 CCTACTCC
1 CCTACTCC
18549 TCCCCCTCCC
Statistics
Matches: 157, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
77 74 0.47
78 83 0.53
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.24
Consensus pattern (78 bp):
CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCA
Found at i:18395 original size:21 final size:20
Alignment explanation
Indices: 18336--18602 Score: 73
Period size: 21 Copynumber: 13.5 Consensus size: 20
18326 GCACCTCTTC
* * *
18336 CCCCTCCCCCTGCTCCTACT
1 CCCCTCCACCTACTCCTCCT
* * *
18356 CCCCCTCCTCGTACACCTCCT
1 -CCCCTCCACCTACTCCTCCT
18377 ACCCCTCCACCTACTCCTCCT
1 -CCCCTCCACCTACTCCTCCT
***
18398 CCTAGCGCACCT-CT--T-C-
1 CCCCTC-CACCTACTCCTCCT
* * *
18414 CCCCTCCCCCTGCTCCTACT
1 CCCCTCCACCTACTCCTCCT
* * *
18434 CCCCCTCCTCGTACACCTCCT
1 -CCCCTCCACCTACTCCTCCT
18455 ACCCCTCCACCTACTCC-CCT
1 -CCCCTCCACCTACTCCTCCT
***
18475 CCTAGCGCACCT-CT--T-C-
1 CCCCTC-CACCTACTCCTCCT
* *
18491 CCCCTCC-CCTTGCTCCTACT
1 CCCCTCCACC-TACTCCTCCT
* *
18511 CCCCCTCCACGTACACCTCCT
1 -CCCCTCCACCTACTCCTCCT
18532 ACCCCTCCACCTACTCCT-C-
1 -CCCCTCCACCTACTCCTCCT
*
18551 CCCCT-C-CCT-CTCCACCT
1 CCCCTCCACCTACTCCTCCT
*
18568 CCCCCTCCACCTCCACCTCCACCT
1 -CCCCTCCACCT--A-CTCCTCCT
18592 CCACCTCCACC
1 CC-CCTCCACC
18603 AGTTACCTGC
Statistics
Matches: 180, Mismatches: 39, Indels: 51
0.67 0.14 0.19
Matches are distributed among these distances:
14 2 0.01
15 10 0.06
16 14 0.08
17 3 0.02
18 13 0.07
19 8 0.04
20 17 0.09
21 94 0.52
22 1 0.01
23 2 0.01
24 16 0.09
ACGTcount: A:0.11, C:0.63, G:0.04, T:0.22
Consensus pattern (20 bp):
CCCCTCCACCTACTCCTCCT
Found at i:18528 original size:42 final size:41
Alignment explanation
Indices: 18110--18549 Score: 359
Period size: 42 Copynumber: 11.1 Consensus size: 41
18100 TACCCCTCAA
** *
18110 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCT
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCT-CCCCTGCT
* *
18152 CCTACTCCCCCTCCTCGTACACCTCTTCCACCT---C--CA
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCTGCT
*
18188 CCTACTCCCCCTCCTAGCT-CACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCG-TACACCTCTTCCCCCT-CCCCTGCT
** * *
18230 CCTACTCCCCCTCCTCGTACA-C-C-T-CCTAT-CCCTCCA
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCTGCT
**
18266 CCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTCCTGCT
1 CCTACTCCCCCTCCTCGTACACCTCTT-CCCCCTCC-CCTGCT
**
18308 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCT-CCCCTGCT
* * *
18350 CCTACTCCCCCTCCTCGTACACCTCCTACCCCT---C--CA
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCTGCT
* * **
18386 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCT-CCCCTGCT
* * *
18428 CCTACTCCCCCTCCTCGTACACCTCCTACCCCT---C--CA
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCTGCT
* **
18464 CCTACT-CCCCTCCTAGCGCACCTCTTCCCCCTCCCCTTGCT
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCC-TGCT
* * * *
18505 CCTACTCCCCCTCCACGTACACCTCCTACCCCTCCACCTACT
1 CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCC-CCTGCT
18547 CCT
1 CCT
18550 CCCCCTCCCT
Statistics
Matches: 317, Mismatches: 50, Indels: 62
0.74 0.12 0.14
Matches are distributed among these distances:
35 21 0.07
36 89 0.28
37 2 0.01
38 8 0.03
39 1 0.00
40 6 0.02
41 10 0.03
42 174 0.55
43 6 0.02
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.25
Consensus pattern (41 bp):
CCTACTCCCCCTCCTCGTACACCTCTTCCCCCTCCCCTGCT
Found at i:18548 original size:18 final size:18
Alignment explanation
Indices: 18509--18602 Score: 100
Period size: 18 Copynumber: 5.1 Consensus size: 18
18499 CTTGCTCCTA
* *
18509 CTCCCCCTCCACGTACAC
1 CTCCCCCTCCACCTCCAC
* *
18527 CTCCTACCCCTCCACCTACTC
1 CT-C--CCCCTCCACCTCCAC
18548 CTCCCCCTCC-CTCTCCAC
1 CTCCCCCTCCAC-CTCCAC
18566 CTCCCCCTCCACCTCCAC
1 CTCCCCCTCCACCTCCAC
*
18584 CTCCACCTCCACCTCCAC
1 CTCCCCCTCCACCTCCAC
18602 C
1 C
18603 AGTTACCTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.02
18 47 0.71
19 2 0.03
20 1 0.02
21 15 0.23
ACGTcount: A:0.13, C:0.67, G:0.01, T:0.19
Consensus pattern (18 bp):
CTCCCCCTCCACCTCCAC
Found at i:18558 original size:6 final size:6
Alignment explanation
Indices: 18535--18602 Score: 84
Period size: 6 Copynumber: 11.3 Consensus size: 6
18525 ACCTCCTACC
* * * *
18535 CCTCCA CCTACT CCTCCC CCTCC- CTCTCCA CCTCCC CCTCCA CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
18583 CCTCCA CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CC
18603 AGTTACCTGC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
5 1 0.02
6 52 0.96
7 1 0.02
ACGTcount: A:0.12, C:0.69, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTCCA
Found at i:22278 original size:20 final size:20
Alignment explanation
Indices: 22253--22347 Score: 163
Period size: 20 Copynumber: 4.8 Consensus size: 20
22243 GATAATTTTT
*
22253 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTA
22273 AAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTA
22293 AAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTA
*
22313 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTA
*
22333 AAGAGTTTCCAAACT
1 AAGAGTTTCGAAACT
22348 TTCCCTAAAG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (20 bp):
AAGAGTTTCGAAACTATCTA
Found at i:22360 original size:40 final size:40
Alignment explanation
Indices: 22253--22363 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 40
22243 GATAATTTTT
22253 AAGAGTTTCGAAACTAT-CTCAAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCCT-AAGAGTTTCGAAACTATCTA
*
22293 AAGAGTTTCGAAACTAT-CTAAAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCCT-AAGAGTTTCGAAACTATCTA
* *
22333 AAGAGTTTCCAAACTTTCCCTAA-AGTTTCGA
1 AAGAGTTTCGAAACTAT-CCTAAGAGTTTCGA
22364 TACTTTGGCT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
40 61 0.94
41 2 0.03
42 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (40 bp):
AAGAGTTTCGAAACTATCCTAAGAGTTTCGAAACTATCTA
Found at i:24853 original size:2 final size:2
Alignment explanation
Indices: 24772--24834 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
24762 ATAATGTAAG
24772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24814 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
24835 CCACTTTAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26077 original size:108 final size:108
Alignment explanation
Indices: 25904--26104 Score: 384
Period size: 108 Copynumber: 1.9 Consensus size: 108
25894 AATACCAAAT
25904 AATCTGTGTCGAAGTAACACAAGCATCAATTTAGTAATGATTCATACATCAATAGTAAAATAAAA
1 AATCTGTGTCGAAGTAACACAAGCATCAATTTAGTAATGATTCATACATCAATAGTAAAATAAAA
*
25969 TACGTCATAAAATTAGTGTATCAAAATATACAAATGACATCAA
66 TACGTCATAAAATTAGTGTACCAAAATATACAAATGACATCAA
26012 AATCTGTGTCGAAGTAACACAAGCATCAATTTAGTAATGATTCATACATCAATAGTAAAATAAAA
1 AATCTGTGTCGAAGTAACACAAGCATCAATTTAGTAATGATTCATACATCAATAGTAAAATAAAA
*
26077 TATGTCATAAAATTAGTGTACCAAAATA
66 TACGTCATAAAATTAGTGTACCAAAATA
26105 AAGACAGATT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 91 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.28
Consensus pattern (108 bp):
AATCTGTGTCGAAGTAACACAAGCATCAATTTAGTAATGATTCATACATCAATAGTAAAATAAAA
TACGTCATAAAATTAGTGTACCAAAATATACAAATGACATCAA
Found at i:27208 original size:29 final size:29
Alignment explanation
Indices: 27170--27234 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
27160 GAAAATTTAG
27170 TATATTTTTAATAATATAAAAATATATTA
1 TATATTTTTAATAATATAAAAATATATTA
*
27199 TATATTTTTAATATTATAAAAATATATTA
1 TATATTTTTAATAATATAAAAATATATTA
27228 TATATTT
1 TATATTT
27235 ATATGATACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TATATTTTTAATAATATAAAAATATATTA
Found at i:27235 original size:27 final size:27
Alignment explanation
Indices: 27161--27235 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 27
27151 TCTTACTCAG
* * *
27161 AAAATTTAGTATATTTTTAATAATATA
1 AAAATATATTATATATTTAATAATATA
*
27188 AAAATATATTATATATTTTTAATATTATA
1 AAAATATATTATATA--TTTAATAATATA
27217 AAAATATATTATATATTTA
1 AAAATATATTATATATTTA
27236 TATGATACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 16 0.38
29 26 0.62
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
AAAATATATTATATATTTAATAATATA
Found at i:28681 original size:11 final size:12
Alignment explanation
Indices: 28650--28693 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
28640 TCAAAAATCA
28650 TAAAATAATTAT
1 TAAAATAATTAT
28662 T-AAAT--TTAT
1 TAAAATAATTAT
28671 TAAAAT-ATTA-
1 TAAAATAATTAT
28681 TAAAATAATTAT
1 TAAAATAATTAT
28693 T
1 T
28694 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:29281 original size:24 final size:23
Alignment explanation
Indices: 29251--29303 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
29241 TTACTTAGAG
29251 AAAAGGAGA-AAGAAAGACTCCTAA
1 AAAAGGA-ATAAGAAAG-CTCCTAA
**
29275 AAAAGGAATAAGACTGCTCCTAA
1 AAAAGGAATAAGAAAGCTCCTAA
29298 AAAAGG
1 AAAAGG
29304 CGTAAAACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.55, C:0.13, G:0.21, T:0.11
Consensus pattern (23 bp):
AAAAGGAATAAGAAAGCTCCTAA
Found at i:30054 original size:305 final size:301
Alignment explanation
Indices: 29503--30087 Score: 985
Period size: 305 Copynumber: 1.9 Consensus size: 301
29493 ATATATGCTA
* *
29503 TGATTCAATTACATAGTTTAAAACTTCTTAGTTTTACACTTTTTTAGGATCATTAGATGATAAGC
1 TGATTCAATTACATAGTTTAAAACTTATTAGTTTTACACTTTTTTAGGATCATTAGATGATAAGA
29568 AATCAAAGACTGAGATTAACATTAATAAATGAGAAGATATTCACTCAAAAAGAAAAACAAAAAGT
66 AATCAAAGACTGAGATTAACATTAATAAATGAGAAGATATTCACTCAAAAAGAAAAACAAAAAGT
*
29633 TAATCTTAGTCTTTGATTTCCCTCATTCAACTATTTTAAGGTGTAAAACTAAAACTTTTTTTATA
131 TAATCTTAGTCTTTGATTTCCCTCATCCAACTATTTTAAGGTGTAAAACTAAAACTTTTTTTATA
* *
29698 TAACCACTGGTATCTGATTTATTAATCGGCTAAAAAATTTTACATTATGTAATTGGATTCTCTCT
196 TAACCACTAGTATCTGATTTATTAATCGGCTAAAAAATTTTACACTATGTAATTGGATTCT-T-T
29763 CTCTCTATATATATATA-TATATATATGTATGTATGTATAGGCCG
259 C-CTCTATATATATA-ACTATATATATGTATGTATGTATAGGCCG
* * *
29807 TGATTCAATTACATAGTTTAAAACTTATTAGTTTTACACTTTTTTAATGATCGTTGGATGATAAG
1 TGATTCAATTACATAGTTTAAAACTTATTAGTTTTACACTTTTTT-AGGATCATTAGATGATAAG
* * *
29872 AAATCAAAGGCTGAGATTAACATTAGTAAATGAGAAGATATTCACTGAAAAAGAAAAACAAAAAG
65 AAATCAAAGACTGAGATTAACATTAATAAATGAGAAGATATTCACTCAAAAAGAAAAACAAAAAG
*
29937 TTAATCTTAGTCTTTGATTTCCCTCATCCAACTATTTTAAGGTGTAAAACTAAAAGTTTTTTTTA
130 TTAATCTTAGTCTTTGATTTCCCTCATCCAACTATTTTAAGGTGTAAAACTAAAA-CTTTTTTTA
*
30002 TATAACCACTAGTATCTGATTTATTAATCTGCT-AAAAATTTTACACTATGTAATTGGATTCTTT
194 TATAACCACTAGTATCTGATTTATTAATCGGCTAAAAAATTTTACACTATGTAATTGGATTCTTT
30066 CCTCTATATATATAACTATATA
259 CCTCTATATATATAACTATATA
30088 CTAACTTAAT
Statistics
Matches: 265, Mismatches: 13, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
301 1 0.00
302 19 0.07
303 2 0.01
304 45 0.17
305 159 0.60
306 39 0.15
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (301 bp):
TGATTCAATTACATAGTTTAAAACTTATTAGTTTTACACTTTTTTAGGATCATTAGATGATAAGA
AATCAAAGACTGAGATTAACATTAATAAATGAGAAGATATTCACTCAAAAAGAAAAACAAAAAGT
TAATCTTAGTCTTTGATTTCCCTCATCCAACTATTTTAAGGTGTAAAACTAAAACTTTTTTTATA
TAACCACTAGTATCTGATTTATTAATCGGCTAAAAAATTTTACACTATGTAATTGGATTCTTTCC
TCTATATATATAACTATATATATGTATGTATGTATAGGCCG
Found at i:30321 original size:21 final size:20
Alignment explanation
Indices: 30235--30392 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
30225 AAATGACCAA
**
30235 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
30254 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
30274 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
30294 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
30315 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
30336 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
30356 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
30377 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
30393 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:30424 original size:20 final size:20
Alignment explanation
Indices: 30359--30568 Score: 201
Period size: 20 Copynumber: 10.5 Consensus size: 20
30349 CGATTTTCCA
* ** *
30359 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
30379 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
30399 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30419 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30439 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30459 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30479 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
30499 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
30519 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
30539 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
30559 AAATCACAAC
1 AAATCGCAAC
30569 ACTGAAATTT
Statistics
Matches: 158, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 154 0.97
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:31266 original size:24 final size:24
Alignment explanation
Indices: 31230--31284 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
31220 ATGAGTACTA
* * * *
31230 GTCAGTATTCGAAATTTGGTCTTG
1 GTCAATATCCGAAATTTGATATTG
*
31254 GTCAATATCCGAACTTTGATATTG
1 GTCAATATCCGAAATTTGATATTG
31278 GTCAATA
1 GTCAATA
31285 CACGGATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (24 bp):
GTCAATATCCGAAATTTGATATTG
Found at i:31489 original size:12 final size:12
Alignment explanation
Indices: 31472--31496 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31462 ATATAATCCT
31472 GAAGAAGAAAAA
1 GAAGAAGAAAAA
31484 GAAGAAGAAAAA
1 GAAGAAGAAAAA
31496 G
1 G
31497 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:33860 original size:19 final size:19
Alignment explanation
Indices: 33820--33917 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
33810 GATTCTCTCG
33820 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
33840 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
33859 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
33873 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
33892 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
33911 TTGCGAT
1 TTGCGAT
33918 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:33914 original size:52 final size:53
Alignment explanation
Indices: 33801--33917 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
33791 GAAATGAAAA
33801 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
33854 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
33906 TCGCATTGCGAT
1 TCGCATTGCGAT
33918 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:34043 original size:14 final size:14
Alignment explanation
Indices: 34024--34060 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
34014 CATCAATTAC
34024 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
34038 ACAAATCATCTTTT
1 ACAAATCAACTTTT
34052 ACAAATCAA
1 ACAAATCAA
34061 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:35184 original size:27 final size:27
Alignment explanation
Indices: 35154--35211 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
35144 GACCTCCCAA
35154 TCCTAGTAACCGTCGTCCCCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
*
35181 TCCTAGTAACCGTCGTCCTCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
35208 TCCT
1 TCCT
35212 CAACGGCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.10, C:0.53, G:0.10, T:0.26
Consensus pattern (27 bp):
TCCTAGTAACCGTCGTCCCCCTCCCCC
Found at i:35404 original size:21 final size:22
Alignment explanation
Indices: 35354--35412 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
35344 CCTACCCCTC
35354 CACCTAC-TCCCCCTCCTCGCG
1 CACCTACTTCCCCCTCCTCGCG
35375 CACCT-CTTCCCCCTCC-C-CTG
1 CACCTACTTCCCCCTCCTCGC-G
*
35395 CTCCTACTT-CCCCTCCTC
1 CACCTACTTCCCCCTCCTC
35413 ATACACCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.03
20 14 0.42
21 18 0.55
ACGTcount: A:0.07, C:0.63, G:0.05, T:0.25
Consensus pattern (22 bp):
CACCTACTTCCCCCTCCTCGCG
Found at i:35407 original size:77 final size:77
Alignment explanation
Indices: 35327--35760 Score: 411
Period size: 77 Copynumber: 5.6 Consensus size: 77
35317 CACGCCTCCT
35327 CCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCC
1 CCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCC
*
35392 CTGCTCCTACTT
66 CTGCTCCTACTC
* * * *
35404 CCCCTCCTCATACACCT-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCA-CTCTTCCCCCTCC
1 CCCCTCCTCGTACACCTCCTACC-CCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT-C
35467 CCCTGCTCCTACTC
64 CCCTGCTCCTACTC
*
35481 CCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCC-CCT
1 CCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCC-
*
35544 CCTCCTCCTACTC
65 CCTGCTCCTACTC
* ** * * * * * *
35557 CCCCCCCTCGCGCACCTCTTCCCCCTCC-CCTCCTCGTACACCTCCTACCCTTCCACCTAC-TCC
1 CCCCTCCTCGTACACCTCCTACCCCTCCACCTACTC---CCCCTCCT-CGC--GCACCT-CTTCC
* * *
35620 TCCTCCTAGC-GCACCT-CTTC
59 CCCTCC--CCTGCTCCTAC-TC
* * * * * * * *
35640 CCCCTCCCCCTGCTCCTACTCCCCCTCCACCTACTCCCCCTCCTAGCACACCTCTTCCCCCTCCC
1 CCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCC
35705 CTGCTCCTACT-
66 CTGCTCCTACTC
* *
35716 CCCCTCCACGTACACCTCCTACTCCTCCACCTACTCCTCCC-CCTC
1 CCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC-CCCTCCTC
35761 CCTCTCCCCT
Statistics
Matches: 287, Mismatches: 49, Indels: 43
0.76 0.13 0.11
Matches are distributed among these distances:
75 8 0.03
76 83 0.29
77 113 0.39
78 26 0.09
79 2 0.01
80 1 0.00
81 12 0.04
82 6 0.02
83 29 0.10
84 7 0.02
ACGTcount: A:0.10, C:0.61, G:0.04, T:0.24
Consensus pattern (77 bp):
CCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCC
CTGCTCCTACTC
Found at i:35431 original size:21 final size:19
Alignment explanation
Indices: 35375--35431 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
35365 CCTCCTCGCG
* *
35375 CACCTCTTCCCCCTCCCCTG
1 CACCTCTT-CCCCTCCCATA
*
35395 CTCCTACTTCCCCTCCTCATA
1 CACCT-CTTCCCCTCC-CATA
35416 CACCTCTTCCACCTCC
1 CACCTCTTCC-CCTCC
35432 ACCTACTCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.11, C:0.60, G:0.02, T:0.28
Consensus pattern (19 bp):
CACCTCTTCCCCTCCCATA
Found at i:35540 original size:21 final size:22
Alignment explanation
Indices: 35508--35581 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 22
35498 CCTATCCCTC
*
35508 CACCTACT-CCCCCTCCTCGCG
1 CACCTATTCCCCCCTCCTCGCG
35529 CACCT-TTCCCCCCCTCCT--C-
1 CACCTATT-CCCCCCTCCTCGCG
* *
35548 CTCCTACTCCCCCC-CCTCGCG
1 CACCTATTCCCCCCTCCTCGCG
*
35569 CACCTCTTCCCCC
1 CACCTATTCCCCC
35582 TCCCCTCCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 3 0.07
19 10 0.24
20 4 0.10
21 15 0.37
22 9 0.22
ACGTcount: A:0.07, C:0.66, G:0.05, T:0.22
Consensus pattern (22 bp):
CACCTATTCCCCCCTCCTCGCG
Found at i:35581 original size:22 final size:22
Alignment explanation
Indices: 35516--35588 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 22
35506 TCCACCTACT
*
35516 CCCCCTCCTCGCGCACCT-TTC
1 CCCCCCCCTCGCGCACCTCTTC
*
35537 CCCCCCTCCT--C-CTCCTAC-T-
1 CCCCCC-CCTCGCGCACCT-CTTC
35556 CCCCCCCCTCGCGCACCTCTTC
1 CCCCCCCCTCGCGCACCTCTTC
35578 CCCCTCCCCTC
1 CCCC-CCCCTC
35589 CTCGTACACC
Statistics
Matches: 40, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
18 3 0.08
19 10 0.25
20 4 0.10
21 10 0.25
22 7 0.17
23 6 0.15
ACGTcount: A:0.04, C:0.68, G:0.05, T:0.22
Consensus pattern (22 bp):
CCCCCCCCTCGCGCACCTCTTC
Found at i:35663 original size:15 final size:15
Alignment explanation
Indices: 35643--35682 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
35633 CCTCTTCCCC
* *
35643 CTCCCCCTGCTCCTA
1 CTCCCCCTCCACCTA
35658 CTCCCCCTCCACCTA
1 CTCCCCCTCCACCTA
35673 CTCCCCCTCC
1 CTCCCCCTCC
35683 TAGCACACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.07, C:0.68, G:0.03, T:0.23
Consensus pattern (15 bp):
CTCCCCCTCCACCTA
Found at i:35682 original size:21 final size:21
Alignment explanation
Indices: 35638--35682 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35628 GCGCACCTCT
* * *
35638 TCCCCCTCCCCCTGCTCCTAC
1 TCCCCCTCCACCTACTCCCAC
*
35659 TCCCCCTCCACCTACTCCCCC
1 TCCCCCTCCACCTACTCCCAC
35680 TCC
1 TCC
35683 TAGCACACCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.69, G:0.02, T:0.22
Consensus pattern (21 bp):
TCCCCCTCCACCTACTCCCAC
Found at i:35703 original size:102 final size:99
Alignment explanation
Indices: 35481--35664 Score: 253
Period size: 102 Copynumber: 1.8 Consensus size: 99
35471 GCTCCTACTC
* * *
35481 CCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTCGCGCACCTTTCCCCCCCTCC
1 CCCCACCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTAGCGCACCTTTCCCCCCCCCC
35546 TCCTCCTACTCCCCCCCCTCGCGCACCTCTTCCCCCT
66 TCCTCCTACT--CCCCCCTC-CGCACCTCTTCCCCCT
* *
35583 CCCCTCCTCGTACACCTCCTA-CCCTTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCC
1 CCCCACCTCGTACACCTCCTATCCC-TCCACCTACTCCCCCTCCTAGCGCACCT-TTCCCCC-CC
*
35647 CCCTGCTCCTACTCCCCC
63 CCCTCCTCCTACTCCCCC
35665 TCCACCTACT
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
101 3 0.04
102 52 0.69
103 7 0.09
104 13 0.17
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.24
Consensus pattern (99 bp):
CCCCACCTCGTACACCTCCTATCCCTCCACCTACTCCCCCTCCTAGCGCACCTTTCCCCCCCCCC
TCCTCCTACTCCCCCCTCCGCACCTCTTCCCCCT
Found at i:35744 original size:21 final size:22
Alignment explanation
Indices: 35708--35778 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 22
35698 CCCTCCCCTG
*
35708 CTCCTACTCCCCTCCACGTACAC
1 CTCCTACT-CCCTCCACCTACAC
*
35731 CTCCTACT-CCTCCACCTACTC
1 CTCCTACTCCCTCCACCTACAC
** * *
35752 CTCCCCCTCCCTCTCCCCTCCAC
1 CTCCTACTCCCTC-CACCTACAC
35775 CTCC
1 CTCC
35779 CCCTCCACCT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 17 0.44
22 4 0.10
23 18 0.46
ACGTcount: A:0.11, C:0.63, G:0.01, T:0.24
Consensus pattern (22 bp):
CTCCTACTCCCTCCACCTACAC
Found at i:35760 original size:6 final size:6
Alignment explanation
Indices: 35739--35817 Score: 83
Period size: 6 Copynumber: 13.3 Consensus size: 6
35729 ACCTCCTACT
* * * *
35739 CCTCCA CCTACT CCTCCC CCTCC- CTCTCC- CCTCCA CCTCCC CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
35786 CCTCCA CCTTCC- CCTCCA CCTCCA CCTCCA CC
1 CCTCCA CC-TCCA CCTCCA CCTCCA CCTCCA CC
35818 AGCTACCTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
5 8 0.13
6 52 0.83
7 3 0.05
ACGTcount: A:0.10, C:0.70, G:0.00, T:0.20
Consensus pattern (6 bp):
CCTCCA
Found at i:35791 original size:18 final size:18
Alignment explanation
Indices: 35751--35814 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
35741 TCCACCTACT
* *
35751 CCTCCCCCTCCCTCTCC-
1 CCTCCACCTCCCCCTCCA
35768 CCTCCACCTCCCCCTCCA
1 CCTCCACCTCCCCCTCCA
*
35786 CCTCCACCTTCCCCTCCA
1 CCTCCACCTCCCCCTCCA
35804 CCTCCACCTCC
1 CCTCCACCTCC
35815 ACCAGCTACC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 15 0.36
18 27 0.64
ACGTcount: A:0.08, C:0.72, G:0.00, T:0.20
Consensus pattern (18 bp):
CCTCCACCTCCCCCTCCA
Found at i:39563 original size:20 final size:20
Alignment explanation
Indices: 39538--39612 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
39528 GATACTTTTT
39538 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
* *
39558 AAGAGTTTTGAAACTATCTA
1 AAGAGTTTCGAAACTATCTC
39578 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
39598 AAGAGTTTTGAAACT
1 AAGAGTTTCGAAACT
39613 TTCCCTAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (20 bp):
AAGAGTTTCGAAACTATCTC
Found at i:44351 original size:11 final size:12
Alignment explanation
Indices: 44320--44363 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
44310 TCAAAAATCA
44320 TAAAATAATTAT
1 TAAAATAATTAT
44332 T-AAAT--TTAT
1 TAAAATAATTAT
44341 TAAAAT-ATTA-
1 TAAAATAATTAT
44351 TAAAATAATTAT
1 TAAAATAATTAT
44363 T
1 T
44364 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:45738 original size:2 final size:2
Alignment explanation
Indices: 45733--45758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45723 TCTCTCTCTC
45733 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
45759 AGCTATAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46700 original size:27 final size:27
Alignment explanation
Indices: 46670--46724 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
46660 GACCTCTCAA
46670 TCCTAGTAACCGTCGTCCCCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
*
46697 TCCTAGTAACCGTCGTCCTCCTCCCCC
1 TCCTAGTAACCGTCGTCCCCCTCCCCC
46724 T
1 T
46725 TCCCCTCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.11, C:0.53, G:0.11, T:0.25
Consensus pattern (27 bp):
TCCTAGTAACCGTCGTCCCCCTCCCCC
Found at i:46880 original size:25 final size:26
Alignment explanation
Indices: 46827--46883 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
46817 TCCGAATAAA
* *
46827 CCTCCCTCTCCGAACACGCCTCCTCCC
1 CCTCCCCCTCCGAACAC-CCTCCTACC
*
46854 CCTCCCCCTCCGTACA-CCTCCTACC
1 CCTCCCCCTCCGAACACCCTCCTACC
46879 CCTCC
1 CCTCC
46884 ACCTACTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 13 0.48
27 14 0.52
ACGTcount: A:0.11, C:0.65, G:0.05, T:0.19
Consensus pattern (26 bp):
CCTCCCCCTCCGAACACCCTCCTACC
Found at i:46930 original size:41 final size:42
Alignment explanation
Indices: 46885--47240 Score: 296
Period size: 41 Copynumber: 9.0 Consensus size: 42
46875 TACCCCTCCA
*
46885 CCTACTCCCCCTCCTCGCGCA-CTCTTCCCCCTCCCCCTTCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
** * *
46926 CCTACTCCCCCTCCTCGTACACCTCTTCCACCT----C--CA
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
* *
46962 CCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
** ** *
47004 CCTACTCCCCCTCCTCGTACA-C-C-T---CCTATCCCT-CC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
*
47039 CCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTT-CCCCCTCCCCCTGCT
47081 CCTACT-CCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
** * * *
47122 CCTACTCCCCCTCCTCGTACA-C-C-T---CCT-ACCCTCCA
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
* *
47157 CCTACTCCTCCTCCTAGCGCACCTCTT-CCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
** * *
47198 CCTACT-CCCCTCCTCGTACACCTC-TACCCCTCCACCCTACT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCC-CCCTGCT
47239 CC
1 CC
47241 CCCTCCCTCT
Statistics
Matches: 251, Mismatches: 39, Indels: 50
0.74 0.11 0.15
Matches are distributed among these distances:
35 42 0.17
36 42 0.17
37 2 0.01
38 2 0.01
39 3 0.01
40 27 0.11
41 83 0.33
42 50 0.20
ACGTcount: A:0.09, C:0.61, G:0.05, T:0.25
Consensus pattern (42 bp):
CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCT
Found at i:46950 original size:77 final size:77
Alignment explanation
Indices: 46855--47123 Score: 352
Period size: 77 Copynumber: 3.5 Consensus size: 77
46845 CCTCCTCCCC
46855 CTCCCCCT-C-CGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACTCTTCCCCCTC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACTCTTCCCCCTC
*
46918 CCCCTTCTCCTA
66 CCCCTGCTCCTA
* * *
46930 CTCCCCCTCCTCGTACACCT-CTTCCACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACC-CCTCCACCTACTCCCCCTCCTCGCGCA-CTCTTCCCCC
46994 TCCCCCTGCTCCTA
64 TCCCCCTGCTCCTA
*
47008 CTCCCCCTCCTCGTACACCTCCTATCCCTCC-CCTACTCCCCCTCCTCGCGCAC-CTTTCCCCCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACTC-TT-CCCCC
*
47071 TCCTCCTGCTCCTA
64 TCCCCCTGCTCCTA
** * * * *
47085 CT-CCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCC
1 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCC
47124 TACTCCCCCT
Statistics
Matches: 171, Mismatches: 15, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
75 9 0.05
76 31 0.18
77 80 0.47
78 48 0.28
79 3 0.02
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (77 bp):
CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACTCTTCCCCCTC
CCCCTGCTCCTA
Found at i:46984 original size:21 final size:22
Alignment explanation
Indices: 46955--47018 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
46945 CACCTCTTCC
*
46955 ACCTCCACCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
*
46977 AGCT-CACCT-CTTCCCCCTCC-
1 ACCTGCACCTAC-TCCCCCTCCT
* *
46997 CCCTGCTCCTACTCCCCCTCCT
1 ACCTGCACCTACTCCCCCTCCT
47019 CGTACACCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.09
21 27 0.79
22 4 0.12
ACGTcount: A:0.09, C:0.62, G:0.03, T:0.25
Consensus pattern (22 bp):
ACCTGCACCTACTCCCCCTCCT
Found at i:47071 original size:21 final size:21
Alignment explanation
Indices: 47045--47111 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 21
47035 CTCCCCTACT
47045 CCCCCTCCTCGCGCACCTTTC
1 CCCCCTCCTCGCGCACCTTTC
* *
47066 CCCCCTCCTC-CTGCTCC-TAC
1 CCCCCTCCTCGC-GCACCTTTC
*
47086 TCCCCTCCTCGCGCACCTCTTC
1 CCCCCTCCTCGCGCACCT-TTC
47108 CCCC
1 CCCC
47112 TCCCCCTGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
20 16 0.44
21 15 0.42
22 5 0.14
ACGTcount: A:0.04, C:0.64, G:0.07, T:0.24
Consensus pattern (21 bp):
CCCCCTCCTCGCGCACCTTTC
Found at i:47113 original size:21 final size:21
Alignment explanation
Indices: 47044--47114 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
47034 CCTCCCCTAC
47044 TCCCCCTCCTCGCGCACCT-T
1 TCCCCCTCCTCGCGCACCTCT
*
47064 TCCCCCCTCCTC-CTGCTCCTAC-
1 T-CCCCCTCCTCGC-GCACCT-CT
47086 T-CCCCTCCTCGCGCACCTCT
1 TCCCCCTCCTCGCGCACCTCT
47106 TCCCCCTCC
1 TCCCCCTCC
47115 CCCTGCTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
19 1 0.02
20 17 0.40
21 23 0.55
22 1 0.02
ACGTcount: A:0.04, C:0.63, G:0.07, T:0.25
Consensus pattern (21 bp):
TCCCCCTCCTCGCGCACCTCT
Found at i:47122 original size:118 final size:117
Alignment explanation
Indices: 46962--47240 Score: 411
Period size: 118 Copynumber: 2.4 Consensus size: 117
46952 TCCACCTCCA
* *
46962 CCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACT-CCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
* *
47027 TCCTATCCCTCC-CCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTCCTGCT
65 TCCTA-CCCTCCACCTACTCCCCCTCCTAGCGCACCTCTT--CCCCTCCCCCTGCT
*
47081 CCTACTCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCT
1 CCTACTCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCT
*
47146 CCTACCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCTCCCCCTGCT
66 CCTACCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCTCCCCCTGCT
* * *
47198 CCTACTCCCCTCCTCGTACACCTC-TACCCCTCCACCCTACTCC
1 CCTACTCCCCTCCTCGCACACCTCTTCCCCCTCC-CCCTGCTCC
47241 CCCTCCCTCT
Statistics
Matches: 148, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
116 8 0.05
117 49 0.33
118 83 0.56
119 8 0.05
ACGTcount: A:0.09, C:0.61, G:0.05, T:0.25
Consensus pattern (117 bp):
CCTACTCCCCTCCTCGCACACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCT
CCTACCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCTCCCCCTGCT
Found at i:47130 original size:21 final size:21
Alignment explanation
Indices: 47066--47135 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
47056 CGCACCTTTC
*
47066 CCCCCTCCTCCTGCTCCTACT
1 CCCCCTCCCCCTGCTCCTACT
* *
47087 -CCCCTCCTCGC-GCACCT-CTT
1 CCCCCTCC-CCCTGCTCCTAC-T
47107 CCCCCTCCCCCTGCTCCTACT
1 CCCCCTCCCCCTGCTCCTACT
47128 CCCCCTCC
1 CCCCCTCC
47136 TCGTACACCT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 1 0.03
20 15 0.38
21 22 0.56
22 1 0.03
ACGTcount: A:0.04, C:0.66, G:0.06, T:0.24
Consensus pattern (21 bp):
CCCCCTCCCCCTGCTCCTACT
Found at i:47246 original size:76 final size:77
Alignment explanation
Indices: 47081--47246 Score: 268
Period size: 76 Copynumber: 2.2 Consensus size: 77
47071 TCCTCCTGCT
*
47081 CCTACT-CCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
47145 TCCTACCCTCCA
66 TCCTACCCTCCA
*
47157 CCTACTCCTCCTCCTAGCGCACCTCTT-CCCCTCCCCCTGCTCCTACT-CCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
47220 T-CTACCCCTCCA
66 TCCTA-CCCTCCA
47232 CCCTACTCCCCCTCC
1 -CCTACTCCCCCTCC
47247 CTCTCACCTC
Statistics
Matches: 84, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
74 3 0.04
75 24 0.29
76 39 0.46
77 18 0.21
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.24
Consensus pattern (77 bp):
CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCTCCA
Found at i:47256 original size:35 final size:36
Alignment explanation
Indices: 47122--47246 Score: 128
Period size: 35 Copynumber: 3.4 Consensus size: 36
47112 TCCCCCTGCT
47122 CCTACTCCCCCTCCTCGTACACCTCCTA-CCCTCCA-
1 CCTACTCCCCCTCCTCGTACACCT-CTACCCCTCCAC
* * ** * *
47157 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCTCCCC
1 CCTACTCCCCCTCCTCGTACACCTCTACCCCTCCAC
*
47193 CTGCTCCTACTCCCCTCCTCGTACACCTCTACCCCTCCAC
1 C--CTACT-C-CCCCTCCTCGTACACCTCTACCCCTCCAC
47233 CCTACTCCCCCTCC
1 CCTACTCCCCCTCC
47247 CTCTCACCTC
Statistics
Matches: 70, Mismatches: 14, Indels: 11
0.74 0.15 0.12
Matches are distributed among these distances:
34 2 0.03
35 26 0.37
36 8 0.11
37 1 0.01
38 8 0.11
39 1 0.01
40 24 0.34
ACGTcount: A:0.11, C:0.61, G:0.04, T:0.24
Consensus pattern (36 bp):
CCTACTCCCCCTCCTCGTACACCTCTACCCCTCCAC
Found at i:47262 original size:6 final size:6
Alignment explanation
Indices: 47246--47300 Score: 78
Period size: 6 Copynumber: 9.3 Consensus size: 6
47236 ACTCCCCCTC
*
47246 CCTCTCA CCTCCC CCT-C- CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA
1 CCTC-CA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA
47293 CCTCCA CC
1 CCTCCA CC
47301 AGTTACCTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
4 3 0.07
5 2 0.04
6 36 0.80
7 4 0.09
ACGTcount: A:0.13, C:0.69, G:0.00, T:0.18
Consensus pattern (6 bp):
CCTCCA
Found at i:47285 original size:75 final size:73
Alignment explanation
Indices: 47081--47273 Score: 205
Period size: 76 Copynumber: 2.6 Consensus size: 73
47071 TCCTCCTGCT
* **
47081 CCTACT-CCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCT-ACGCACCTC-T-CCCCTCCCCCACCTCCTACT-CCCCTCCTCGTACACC
47145 TCCTACCCTCCA
62 TCCTACCCTCCA
* **
47157 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCTCCCCCTGCTCCTACTCCCCTCCTCGTACACCT-
1 CCTACTCCCCCTCCTA-CGCACCTC-TCCCCTCCCCCACCTCCTACTCCCCTCCTCGTACACCTC
47221 CTACCCCTCCA
64 CTA-CCCTCCA
*
47232 CCCTACTCCCCCTCCCT-CTCACCTC-CCCCTCCCTCCACCTCC
1 -CCTACTCCCCCT-CCTACGCACCTCTCCCCTCCC-CCACCTCC
47274 ACCTCCACCT
Statistics
Matches: 105, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
73 8 0.08
74 9 0.09
75 31 0.30
76 37 0.35
77 20 0.19
ACGTcount: A:0.09, C:0.63, G:0.04, T:0.24
Consensus pattern (73 bp):
CCTACTCCCCCTCCTACGCACCTCTCCCCTCCCCCACCTCCTACTCCCCTCCTCGTACACCTCCT
ACCCTCCA
Found at i:48931 original size:38 final size:33
Alignment explanation
Indices: 48866--48936 Score: 79
Period size: 34 Copynumber: 2.0 Consensus size: 33
48856 TCTTTTGAGA
48866 TTATTTATTAAATTATAGATATCATTAAATATTT
1 TTATTTATTAAATTATAGATATCATTAAA-ATTT
* *
48900 TTATTTATTTATTTATAGGATGATCCGATTAAAATTT
1 TTATTTATTAAATTATA-GAT-AT-C-ATTAAAATTT
48937 AAAAATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 15 0.48
35 3 0.10
36 2 0.06
37 5 0.16
38 6 0.19
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (33 bp):
TTATTTATTAAATTATAGATATCATTAAAATTT
Found at i:50968 original size:20 final size:20
Alignment explanation
Indices: 50943--51017 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
50933 GATACTTTTT
50943 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
50963 AAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTC
50983 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
51003 AAGAGTTTTGAAACT
1 AAGAGTTTCGAAACT
51018 TTCCCTAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
AAGAGTTTCGAAACTATCTC
Done.