Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001672.1 Hibiscus syriacus cultivar Beakdansim tig00003345_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: 88724
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:337 original size:38 final size:37
Alignment explanation
Indices: 294--431 Score: 152
Period size: 38 Copynumber: 3.7 Consensus size: 37
284 GTGTATATAT
* *
294 ATAATCATCTACACAACAATCGGTTCATGTATACATGG
1 ATAATCATCTACACAACAATCTGTTCATG-ATATATGG
* * * * *
332 ATAATCATCTGCACAACAATATGTTCTTGACATATAG
1 ATAATCATCTACACAACAATCTGTTCATGATATATGG
* *
369 ATAATCATCTACACAACTATCTGTTCATGCATTTATGG
1 ATAATCATCTACACAACAATCTGTTCATG-ATATATGG
*
407 ATAACCATCT-CTACAACAATCTGTT
1 ATAATCATCTAC-ACAACAATCTGTT
432 AATCTGAAAT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
37 31 0.38
38 51 0.62
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (37 bp):
ATAATCATCTACACAACAATCTGTTCATGATATATGG
Found at i:374 original size:75 final size:75
Alignment explanation
Indices: 288--431 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 75
278 GTGTGTGTGT
* * *
288 ATATATATAATCATCTACACAACAATCGGTTCATGTATACATGGATAATCATCTGC-ACAACAAT
1 ATATAGATAATCATCTACACAACAATCGGTTCATGCATACATGGATAACCATCT-CTACAACAAT
352 ATGTTCTTGAC
65 ATGTTCTTGAC
* * ** *
363 ATATAGATAATCATCTACACAACTATCTGTTCATGCATTTATGGATAACCATCTCTACAACAATC
1 ATATAGATAATCATCTACACAACAATCGGTTCATGCATACATGGATAACCATCTCTACAACAATA
428 TGTT
66 TGTT
432 AATCTGAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 1 0.02
75 59 0.98
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (75 bp):
ATATAGATAATCATCTACACAACAATCGGTTCATGCATACATGGATAACCATCTCTACAACAATA
TGTTCTTGAC
Found at i:1511 original size:19 final size:19
Alignment explanation
Indices: 1487--1551 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1477 TTATGTAAGT
1487 TTTAAAAAACATTTTTGAC
1 TTTAAAAAACATTTTTGAC
** ** * *
1506 TTTAAAACTCAAATTTAAGT
1 TTTAAAAAACATTTTTGA-C
1526 TTTAAAAAACATTTTTGAC
1 TTTAAAAAACATTTTTGAC
1545 TTTAAAA
1 TTTAAAA
1552 CTCAAATTTC
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.42
Consensus pattern (19 bp):
TTTAAAAAACATTTTTGAC
Found at i:1525 original size:39 final size:39
Alignment explanation
Indices: 1482--1560 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1472 TTATTTTATG
1482 TAAGTTTTAAAAAACATTTTTGACTTTAAAACTCAAATT
1 TAAGTTTTAAAAAACATTTTTGACTTTAAAACTCAAATT
1521 TAAGTTTTAAAAAACATTTTTGACTTTAAAACTCAAATT
1 TAAGTTTTAAAAAACATTTTTGACTTTAAAACTCAAATT
1560 T
1 T
1561 CATCCATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (39 bp):
TAAGTTTTAAAAAACATTTTTGACTTTAAAACTCAAATT
Found at i:9733 original size:7 final size:7
Alignment explanation
Indices: 9715--9751 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
9705 TCCAAAGTTC
9715 TCTTCTCT
1 TCTTC-CT
9723 TCTTCCT
1 TCTTCCT
9730 TCTTCCT
1 TCTTCCT
9737 TCTTCCT
1 TCTTCCT
9744 TCTTCCT
1 TCTTCCT
9751 T
1 T
9752 TTTCATACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 24 0.83
8 5 0.17
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
TCTTCCT
Found at i:10961 original size:18 final size:18
Alignment explanation
Indices: 10938--11009 Score: 117
Period size: 18 Copynumber: 4.0 Consensus size: 18
10928 GAGGGATTAT
*
10938 TAGTGGTCCTTCTGGACA
1 TAGTGGTCCTTCAGGACA
*
10956 TAGTGGTCCTTCTGGACA
1 TAGTGGTCCTTCAGGACA
10974 TAGTGGTCCTTCAGGACA
1 TAGTGGTCCTTCAGGACA
*
10992 TAGTGGTCGTTCAGGACA
1 TAGTGGTCCTTCAGGACA
11010 AATATTCAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (18 bp):
TAGTGGTCCTTCAGGACA
Found at i:13848 original size:19 final size:18
Alignment explanation
Indices: 13823--13886 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 18
13813 TAATATATAT
13823 TTCTATAAAAATAAAATG
1 TTCTATAAAAATAAAATG
*
13841 TATCTATAAATTAATAAGAT-
1 T-TCTATAAA--AATAAAATG
*
13861 TTCTATAAATATAAATATG
1 TTCTATAAAAATAAA-ATG
13880 TTTCTAT
1 -TTCTAT
13887 CATGGTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 4 0.11
18 3 0.08
19 16 0.43
20 7 0.19
21 7 0.19
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (18 bp):
TTCTATAAAAATAAAATG
Found at i:17412 original size:42 final size:42
Alignment explanation
Indices: 17365--17496 Score: 125
Period size: 42 Copynumber: 3.1 Consensus size: 42
17355 TTCATACGTG
17365 TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATAT
1 TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATAT
* * *
17407 TCATA---T-CATT-AGT-ATACTTTATGCTATGC-ATCCCATTCATAT
1 TCATATTGTGCTTTGA-TCAT-C-TTAT--TTTGCAAT--CATGCATAT
17449 TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATAT
1 TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATAT
17491 TCATAT
1 TCATAT
17497 CATTAGTATA
Statistics
Matches: 70, Mismatches: 6, Indels: 28
0.67 0.06 0.27
Matches are distributed among these distances:
37 3 0.04
38 5 0.07
39 5 0.07
40 2 0.03
41 4 0.06
42 32 0.46
43 4 0.06
44 2 0.03
45 5 0.07
46 5 0.07
47 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (42 bp):
TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATAT
Found at i:17463 original size:84 final size:84
Alignment explanation
Indices: 17365--17536 Score: 335
Period size: 84 Copynumber: 2.0 Consensus size: 84
17355 TTCATACGTG
17365 TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATATTCATATCATTAGTATACTTTATG
1 TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATATTCATATCATTAGTATACTTTATG
17430 CTATGCATCCCATTCATAT
66 CTATGCATCCCATTCATAT
17449 TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATATTCATATCATTAGTATACTTTATG
1 TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATATTCATATCATTAGTATACTTTATG
*
17514 CTATGCATCCCATTCATGT
66 CTATGCATCCCATTCATAT
17533 TCAT
1 TCAT
17537 GACTTAAGTA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (84 bp):
TCATATTGTGCTTTGATCATCTTATTTTGCAATCATGCATATTCATATCATTAGTATACTTTATG
CTATGCATCCCATTCATAT
Found at i:17536 original size:42 final size:42
Alignment explanation
Indices: 17402--17536 Score: 122
Period size: 42 Copynumber: 3.2 Consensus size: 42
17392 TGCAATCATG
17402 CATATTCATATCATTAGTATACTTTATGCTATGCATCCCATT
1 CATATTCATATCATTAGTATACTTTATGCTATGCATCCCATT
* * *
17444 CATATTCATAT--TGT-GCTTTGATCATCTTAT--TTTGCAAT--CATG
1 CATATTCATATCAT-TAG-TAT-A-C-T-TTATGCTATGC-ATCCCATT
17486 CATATTCATATCATTAGTATACTTTATGCTATGCATCCCATT
1 CATATTCATATCATTAGTATACTTTATGCTATGCATCCCATT
*
17528 CATGTTCAT
1 CATATTCAT
17537 GACTTAAGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 28
0.67 0.07 0.26
Matches are distributed among these distances:
39 4 0.06
40 5 0.07
41 8 0.11
42 38 0.53
43 8 0.11
44 5 0.07
45 4 0.06
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (42 bp):
CATATTCATATCATTAGTATACTTTATGCTATGCATCCCATT
Found at i:18569 original size:30 final size:30
Alignment explanation
Indices: 18529--18585 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
18519 CTTAAAAGAG
* *
18529 TTTTGCAATACTGAGATTTAAATAATTTTA
1 TTTTACAATACTGAAATTTAAATAATTTTA
18559 TTTTACAATACTGAAATTTAAATAATT
1 TTTTACAATACTGAAATTTAAATAATT
18586 CATACAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTTACAATACTGAAATTTAAATAATTTTA
Found at i:18658 original size:54 final size:54
Alignment explanation
Indices: 18599--19428 Score: 442
Period size: 54 Copynumber: 15.4 Consensus size: 54
18589 ACAACTACAA
18599 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* * ** *
18653 TAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAA-TC-TA-TATTTTAA-AATAAATCAATCCATA--C
* * * * *
18713 TAAAATAAATCAATTCATACT-AAT-AA-AT-TA-TTTAAAATAAATCAATCCATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* * * *
18765 -AACTACA--A--T--AATAAATCAATCCATAATTTAAAAAAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
*
18813 AAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATC-A---AT-CT-AT--A-T-TTTAAAATAAATCAATCCATAC
** * * * *
18876 TTTTAAA--A--T-AAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATATTT
1 TAATAAATTATTTAAAATAAATCAAT-CT-AT--A-T-TTTAAAATAAATCAATCCATA--C
* * * * *
18933 TAAAATAAATCAATTCATACT-AAT-AA-AT-TA-TTTAAAATAAATCAATCCATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* *
18985 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* * ** *
19033 TAATAAATTATTTAAAATAAATCAATCAATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATC--TA-TATTTTAA-AATAAATCAATCCATA--C
* * ** * * *
19093 TAAAATAAATCAATCCATAGAAAT-AA-AT-TA-TTTAAAATAAATCAATCC--A-
1 T--AATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* * * *
19142 T-A-AAACTA--CAATAATAAATCAATCCATATTTTCAAATAAATCAATCCATAC
1 TAATAAATTATTTAA-AATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
*
19193 AAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* **
19247 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTGATAC
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
* * *
19301 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
*
19355 TAATAAATTATTTAAAAT--A--AA--T-TATTTTAAAATAAATCAATCCATATTTTA
1 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATA----C
19406 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTA-TTTAAAATAAAT
19429 TATTTTATAA
Statistics
Matches: 607, Mismatches: 85, Indels: 167
0.71 0.10 0.19
Matches are distributed among these distances:
43 6 0.01
44 11 0.02
45 10 0.02
46 1 0.00
47 30 0.05
48 66 0.11
49 9 0.01
50 11 0.02
51 10 0.02
52 13 0.02
53 5 0.01
54 285 0.47
55 11 0.02
56 5 0.01
57 10 0.02
58 44 0.07
59 7 0.01
60 4 0.01
61 6 0.01
62 27 0.04
63 11 0.02
64 23 0.04
65 2 0.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
Found at i:18660 original size:22 final size:22
Alignment explanation
Indices: 18611--18659 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18601 ATAAATTATT
* **
18611 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
18633 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
18656 TAAA
1 TAAA
18660 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:18698 original size:26 final size:26
Alignment explanation
Indices: 18668--18814 Score: 96
Period size: 26 Copynumber: 5.7 Consensus size: 26
18658 AATTATTTAA
*
18668 AATAAATCAATTCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
* **
18694 AATAAATCAATCCAT---ATTTTAA-
1 AATAAATCAATCCATACAACTACAAT
* *
18716 AATAAATCAATTCATACTAA-TAAATTATTT
1 AATAAATCAATCCATAC-AACTACA--A--T
18746 AAAATAAATCAATCCATACAACTACAAT
1 --AATAAATCAATCCATACAACTACAAT
**
18774 AATAAATCAATCCATA-ATTTA-AA-
1 AATAAATCAATCCATACAACTACAAT
18797 AA-AAATCAATCCATACAA
1 AATAAATCAATCCATACAA
18815 ATAAATTATT
Statistics
Matches: 96, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
22 27 0.28
23 7 0.07
24 2 0.02
25 5 0.05
26 31 0.32
27 1 0.01
28 1 0.01
30 1 0.01
31 2 0.02
32 19 0.20
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.29
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:18701 original size:80 final size:80
Alignment explanation
Indices: 18614--18929 Score: 481
Period size: 80 Copynumber: 3.9 Consensus size: 80
18604 AATTATTTAA
*
18614 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
18679 TCATACAACTACAAT
66 CCATACAACTACAAT
*
18694 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
18759 CCATACAACTACAAT
66 CCATACAACTACAAT
* * *
18774 AATAAATCAATCCATAATTTAAAAAAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
18839 CCATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
*
18858 AAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
*
18923 ATTCATA
64 ATCCATA
18930 TTTTAAAATA
Statistics
Matches: 216, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
80 147 0.68
81 2 0.01
82 1 0.00
84 1 0.00
86 65 0.30
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:18740 original size:22 final size:23
Alignment explanation
Indices: 18665--18739 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
18655 ATAAATTATT
18665 TAAAATAAATCAATTCATAC-AA
1 TAAAATAAATCAATTCATACTAA
* **
18687 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATTCATACTAA
18713 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATACTAA
18736 TAAA
1 TAAA
18740 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAATAAATCAATTCATACTAA
Found at i:18802 original size:22 final size:23
Alignment explanation
Indices: 18742--18813 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 23
18732 CTAATAAATT
*
18742 ATTTAAAATAAATCAATCCATAC
1 ATTTAAAAAAAATCAATCCATAC
**
18765 AACTACAATAATAAATCAATCCATA-
1 ATTTA-AA-AA-AAATCAATCCATAC
18790 ATTTAAAAAAAATCAATCCATAC
1 ATTTAAAAAAAATCAATCCATAC
18813 A
1 A
18814 AATAAATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
22 13 0.32
23 6 0.15
24 4 0.10
25 4 0.10
26 13 0.32
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (23 bp):
ATTTAAAAAAAATCAATCCATAC
Found at i:18906 original size:22 final size:22
Alignment explanation
Indices: 18857--18905 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18847 ATAAATTATT
**
18857 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
18879 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
18902 TAAA
1 TAAA
18906 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:18935 original size:22 final size:22
Alignment explanation
Indices: 18909--18951 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
18899 TAATAAATTA
18909 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATTCATAT
18931 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATTCATA
18952 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAT
Found at i:18957 original size:18 final size:18
Alignment explanation
Indices: 18882--18960 Score: 51
Period size: 22 Copynumber: 4.4 Consensus size: 18
18872 CATATTTTAA
18882 AATAAATCAA-TCTATACT
1 AATAAATCAATTC-ATACT
* *
18900 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
*
18914 AATAAATCAATTCATATTTT
1 AATAAATCAATTCATA--CT
18934 AAAATAAATCAATTCATACT
1 --AATAAATCAATTCATACT
18954 AATAAAT
1 AATAAAT
18961 TATTTAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 18
0.67 0.07 0.26
Matches are distributed among these distances:
14 7 0.15
15 5 0.11
17 3 0.06
18 15 0.32
20 1 0.02
22 16 0.34
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:18960 original size:22 final size:22
Alignment explanation
Indices: 18911--18959 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
18901 ATAAATTATT
**
18911 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATTCATATAA
18933 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATA-TAA
18956 TAAA
1 TAAA
18960 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:19011 original size:80 final size:80
Alignment explanation
Indices: 18914--19219 Score: 540
Period size: 80 Copynumber: 3.8 Consensus size: 80
18904 AATTATTTAA
* * *
18914 AATAAATCAATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
18979 CCATACAACTACAAT
66 CCATACAACTACAAT
*
18994 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
*
19059 CAATACAACTACAAT
66 CCATACAACTACAAT
*
19074 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAGAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
*
19139 CCATAAAACTACAAT
66 CCATACAACTACAAT
*
19154 AATAAATCAATCCATATTTTCAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
19219 C
66 C
19220 TATATTTTAA
Statistics
Matches: 217, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 217 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:19040 original size:22 final size:23
Alignment explanation
Indices: 18965--19039 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
18955 ATAAATTATT
18965 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
18987 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
19013 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
19036 TAAA
1 TAAA
19040 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:19200 original size:22 final size:22
Alignment explanation
Indices: 19125--19199 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
19115 ATAAATTATT
19125 TAAAATAAATCAATCCATAAAA
1 TAAAATAAATCAATCCATAAAA
***
19147 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATAAAA
*
19173 TCAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
19196 TAAA
1 TAAA
19200 TTATTTAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
22 16 0.40
23 5 0.12
25 3 0.08
26 16 0.40
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Found at i:19254 original size:22 final size:22
Alignment explanation
Indices: 19205--19253 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
19195 ATAAATTATT
* **
19205 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
19227 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
19250 TAAA
1 TAAA
19254 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:19317 original size:380 final size:379
Alignment explanation
Indices: 18614--19331 Score: 1047
Period size: 380 Copynumber: 1.9 Consensus size: 379
18604 AATTATTTAA
*
18614 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
18679 TCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
66 TCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTAT
*
18744 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAATTTAAAAAAAATCAATCC
131 TTAAAATAAATCAATCCATAAAACTACAATAATAAATCAATCCATAATTTAAAAAAAATCAATCC
* ** **
18809 ATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
196 ATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAAATAAATAAAATAAATCAATAAA
* * *
18874 TATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAAT
261 TATTTTAAAATAAATCAATCTATACTAATAAATAATTGAAAATAAATCAAAT-ATATTTTAAAAT
*
18939 AAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
325 AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
18994 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA-
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
19058 TCAATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATAGAAATAAATTA
66 TC-ATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTA
* * *
19123 TTTAAAATAAATCAATCCATAAAACTACAATAATAAATCAATCCATATTTTCAAATAAATCAATC
130 TTTAAAATAAATCAATCCATAAAACTACAATAATAAATCAATCCATAATTTAAAAAAAATCAATC
* ** * **
19188 CATACAAATAAATTATTTAAAATAAATCAATCTATA-TTTTAAAATAAAT-CAATCCATACTAAT
195 CATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAAATAAATAAAATAAAT-C-AAT
** * *
19251 AAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTGATACT-AAT-AAAT-TA-
258 AAATAT-TTTAAAATAAATCAAT-C-TATACT--AATAAAT-AATTGAAAATAAATCAAATATAT
19311 TTTAAAATAAATCAATCCATA
317 TTTAAAATAAATCAATCCATA
19332 TTTTAAAATA
Statistics
Matches: 302, Mismatches: 27, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
378 5 0.02
379 12 0.04
380 259 0.86
381 3 0.01
382 4 0.01
383 3 0.01
384 10 0.03
385 6 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (379 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
TCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTAT
TTAAAATAAATCAATCCATAAAACTACAATAATAAATCAATCCATAATTTAAAAAAAATCAATCC
ATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAAATAAATAAAATAAATCAATAAA
TATTTTAAAATAAATCAATCTATACTAATAAATAATTGAAAATAAATCAAATATATTTTAAAATA
AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
Found at i:19337 original size:22 final size:22
Alignment explanation
Indices: 19311--19413 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
19301 TAATAAATTA
*
19311 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
*
19333 TTTAAAATAAATAAATCTATACT
1 TTTAAAATAAATAAATCCATA-T
** * ** **
19356 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-AAATCCA-TAT
*
19380 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
*
19402 TTTATAATAAAT
1 TTTAAAATAAAT
19414 TATTTTAAAA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
22 33 0.55
23 12 0.20
24 13 0.22
25 2 0.03
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:19385 original size:15 final size:15
Alignment explanation
Indices: 19356--19473 Score: 148
Period size: 15 Copynumber: 7.5 Consensus size: 15
19346 AATCTATACT
19356 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
19370 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
19385 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
19407 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
19422 AATAAATTATTTTAT
1 AATAAATTATTTTAA
19437 AATAAATTATTTTAA
1 AATAAATTATTTTAA
19452 AATAAATTATTTTAA
1 AATAAATTATTTTAA
19467 AATAAAT
1 AATAAAT
19474 AACCTTATTA
Statistics
Matches: 92, Mismatches: 4, Indels: 15
0.83 0.04 0.14
Matches are distributed among these distances:
14 9 0.10
15 65 0.71
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:19391 original size:69 final size:67
Alignment explanation
Indices: 19302--19458 Score: 228
Period size: 69 Copynumber: 2.3 Consensus size: 67
19292 AATTGATACT
*
19302 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATAAATCTATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAAT-AAT-TATA-AAATAAATTAT
19365 TTTAA
63 TTTAA
* * *
19370 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATTATAAAATAAATTATTTT
*
19435 AT
66 AA
19437 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
19459 TATTTTAAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
66 9 0.11
67 29 0.35
68 11 0.13
69 33 0.40
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATTATAAAATAAATTATTTT
AA
Found at i:22137 original size:19 final size:20
Alignment explanation
Indices: 22113--22158 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
22103 CAAAATGACC
*
22113 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
22132 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
22152 CAATTTC
1 CAATTTC
22159 CAGCATAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:23334 original size:31 final size:31
Alignment explanation
Indices: 23299--23359 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
23289 ATAACTTTTT
*
23299 AAAATCACACTTTTGGTCTCTAAAATTTTAG
1 AAAATCACACTTTTGGTCCCTAAAATTTTAG
* ** *
23330 AAAATTACTTTTTTGGTCCCTAAACTTTTA
1 AAAATCACACTTTTGGTCCCTAAAATTTTA
23360 AATCTTTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (31 bp):
AAAATCACACTTTTGGTCCCTAAAATTTTAG
Found at i:25589 original size:16 final size:16
Alignment explanation
Indices: 25558--25602 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
25548 ATTTGGTATT
*
25558 TTTATACATTTTATTTA
1 TTTATA-ATTTAATTTA
25575 TTTATAATTTAATTTA
1 TTTATAATTTAATTTA
*
25591 TTGAATAATTTA
1 TT-TATAATTTA
25603 TTTTTGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTATAATTTAATTTA
Found at i:25605 original size:16 final size:16
Alignment explanation
Indices: 25567--25610 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
25557 TTTTATACAT
*
25567 TTTATTTATT-TATAA
1 TTTATTTATTGAATAA
25582 TTTAATTTATTGAATAA
1 TTT-ATTTATTGAATAA
25599 TTTATTT-TTGAA
1 TTTATTTATTGAA
25611 CATTGTGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 8 0.31
16 11 0.42
17 7 0.27
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTATTTATTGAATAA
Found at i:31838 original size:21 final size:21
Alignment explanation
Indices: 31814--31853 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31804 TTCCTACACA
31814 ACTTATCTAATAT-CCTTTTAT
1 ACTTAT-TAATATACCTTTTAT
*
31835 ACTTATTTATATACCTTTT
1 ACTTATTAATATACCTTTT
31854 TTCTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTTATTAATATACCTTTTAT
Found at i:32288 original size:21 final size:18
Alignment explanation
Indices: 32244--32317 Score: 121
Period size: 18 Copynumber: 3.9 Consensus size: 18
32234 ACTGTATATT
32244 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
32262 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
32281 TTTGTCCCGAAGGACCACTA
1 --TGTCCCGAAGGACCACTA
32301 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
32318 CCTTAAGAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
18 34 0.64
19 1 0.02
20 1 0.02
21 17 0.32
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:32290 original size:39 final size:39
Alignment explanation
Indices: 32241--32317 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
32231 GGCACTGTAT
32241 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
1 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
32280 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACT
1 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACT
32318 CCTTAAGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.21
Consensus pattern (39 bp):
ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
Found at i:37532 original size:21 final size:18
Alignment explanation
Indices: 37488--37561 Score: 121
Period size: 18 Copynumber: 3.9 Consensus size: 18
37478 ATTTTATATT
37488 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
37506 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
37525 TTTGTCCCGAAGGACCACTA
1 --TGTCCCGAAGGACCACTA
37545 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
37562 CCGCAAGAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
18 34 0.64
19 1 0.02
20 1 0.02
21 17 0.32
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:37539 original size:39 final size:39
Alignment explanation
Indices: 37485--37561 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
37475 GGCATTTTAT
37485 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
1 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
37524 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACT
1 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACT
37562 CCGCAAGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.21
Consensus pattern (39 bp):
ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
Found at i:38379 original size:64 final size:65
Alignment explanation
Indices: 38270--38394 Score: 166
Period size: 64 Copynumber: 1.9 Consensus size: 65
38260 TTCCCTTGAC
38270 GGGTGCATCGATGCACTATCTATGCATCGATACATAAATCCCATTCGATGTT-TTTATTTTAAGG
1 GGGTGCATCGATGCACTATCTATGCATCGATACATAAATCCCATTCGATGTTATTTATTTTAAGG
* * **
38334 GGGTGCATCGATGCACT-CCTTATGCATCGATGCACT-AATTGCATTCGATGTTCATTTATTT
1 GGGTGCATCGATGCACTATC-TATGCATCGATACA-TAAATCCCATTCGATGTT-ATTTATTT
38395 GAGAGTACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
63 1 0.02
64 44 0.83
65 1 0.02
66 7 0.13
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (65 bp):
GGGTGCATCGATGCACTATCTATGCATCGATACATAAATCCCATTCGATGTTATTTATTTTAAGG
Found at i:40634 original size:25 final size:26
Alignment explanation
Indices: 40601--40649 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
40591 TATATTATGT
* *
40601 TTATAGTTAGATATGATATGCATACA
1 TTATAGTTACATATCATATGCATACA
*
40627 TTAT-GTTACATATCATGTGCATA
1 TTATAGTTACATATCATATGCATA
40650 TGTTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (26 bp):
TTATAGTTACATATCATATGCATACA
Found at i:63679 original size:21 final size:23
Alignment explanation
Indices: 63655--63751 Score: 66
Period size: 21 Copynumber: 4.6 Consensus size: 23
63645 TGGTGCATGG
63655 CGTGATGAGGTA-TGGT-CTTTA
1 CGTGATGAGGTAGTGGTACTTTA
* *
63676 CGTGGTGAGGTAGAGGT--TTTA
1 CGTGATGAGGTAGTGGTACTTTA
* * *
63697 CGCGATGA--CAGTGGTGCTTTA
1 CGTGATGAGGTAGTGGTACTTTA
* *
63718 CGTGGTGAGGTA-T-CTACTTTA
1 CGTGATGAGGTAGTGGTACTTTA
*
63739 CGTGTTGAGGTAG
1 CGTGATGAGGTAG
63752 CCGCTCTACG
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
19 5 0.09
21 48 0.83
22 4 0.07
23 1 0.02
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.34
Consensus pattern (23 bp):
CGTGATGAGGTAGTGGTACTTTA
Found at i:64117 original size:42 final size:42
Alignment explanation
Indices: 64071--64158 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
64061 ACTCTCCTAT
*
64071 CGTTCAAGAAG-TCTCTATCATCCTTCAAGAGGCCCCTCTCAC
1 CGTTCAAGAAGCCCT-TATCATCCTTCAAGAGGCCCCTCTCAC
* * * * *
64113 CGTTCAAGATGCCCTTGTTATCGTTCAAGAGGTCCCTCTCAC
1 CGTTCAAGAAGCCCTTATCATCCTTCAAGAGGCCCCTCTCAC
64155 CGTT
1 CGTT
64159 AGAGAATCTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 37 0.95
43 2 0.05
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (42 bp):
CGTTCAAGAAGCCCTTATCATCCTTCAAGAGGCCCCTCTCAC
Found at i:64118 original size:21 final size:21
Alignment explanation
Indices: 64094--64158 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
64084 TCTATCATCC
64094 TTCAAGAGGCCCCTCTCACCG
1 TTCAAGAGGCCCCTCTCACCG
* * * * *
64115 TTCAAGATGCCCTTGTTATCG
1 TTCAAGAGGCCCCTCTCACCG
*
64136 TTCAAGAGGTCCCTCTCACCG
1 TTCAAGAGGCCCCTCTCACCG
64157 TT
1 TT
64159 AGAGAATCTG
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.34, G:0.18, T:0.29
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTCACCG
Found at i:65497 original size:13 final size:14
Alignment explanation
Indices: 65472--65504 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
65462 AAATTGATGT
65472 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
65486 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
*
65499 TTTTGT
1 ATTTGT
65505 TTAATTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:65584 original size:62 final size:63
Alignment explanation
Indices: 65483--65616 Score: 173
Period size: 62 Copynumber: 2.1 Consensus size: 63
65473 TTTGTAAAAG
* *
65483 TTGATTTGTAAAGTTGTTTTGTTTAATTGATGAGGAAATAA-GAAT-TTTTTTGCTTGTTTAA
1 TTGATTTGTAAAGTTGATTTATTTAATTGATGAGGAAATAATGAATATTTTTTGCTTGTTTAA
* * *** *
65544 TTGATTTGTAAAAGTTGATTTATTTAATTGATGTGTAAATAATTTTTATTTTTTGCTTGTTTAG
1 TTGATTTGT-AAAGTTGATTTATTTAATTGATGAGGAAATAATGAATATTTTTTGCTTGTTTAA
65608 TTGATTTGT
1 TTGATTTGT
65617 TGTTTTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
61 9 0.15
62 28 0.45
63 1 0.02
64 24 0.39
ACGTcount: A:0.26, C:0.01, G:0.18, T:0.54
Consensus pattern (63 bp):
TTGATTTGTAAAGTTGATTTATTTAATTGATGAGGAAATAATGAATATTTTTTGCTTGTTTAA
Found at i:68051 original size:24 final size:24
Alignment explanation
Indices: 68017--68070 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
68007 CTGAAACATC
*
68017 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAA
* *
68041 ATCAAAGTCCGGGTATTGACCAAA
1 ATCAAAATCCGAGTATTGACCAAA
68065 ATCAAA
1 ATCAAA
68071 TTTCAAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAA
Found at i:69048 original size:20 final size:20
Alignment explanation
Indices: 69025--69094 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
69015 TAAAATTCTT
69025 GTTGCGAATTCAAAAATCGA
1 GTTGCGAATTCAAAAATCGA
* * *
69045 GTTGCTACA-ACAAAATTCGCA
1 GTTGCGA-ATTCAAAAATCG-A
* *
69066 -TTGTGAATTCAGAAATCGA
1 GTTGCGAATTCAAAAATCGA
69085 GTTGCGAATT
1 GTTGCGAATT
69095 TGAAATTCAG
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
19 2 0.05
20 33 0.89
21 2 0.05
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (20 bp):
GTTGCGAATTCAAAAATCGA
Found at i:69133 original size:20 final size:20
Alignment explanation
Indices: 69110--69152 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
69100 TTCAGTGTTT
69110 CGATTTACAAATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
*
69130 CGATTTACATATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
69150 CGA
1 CGA
69153 ATTTGGAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTG
Found at i:77782 original size:36 final size:37
Alignment explanation
Indices: 77742--77817 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 37
77732 TTTTTATATT
77742 TTTAATTTTGTAAA-AAAATTATATAAATATTATA-AA
1 TTTAATTTTGTAAAGAAAA-TATATAAATATTATACAA
* *
77778 TTTAATTTTTTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAAGAAAATATATAAATATTATACAA
77815 TTT
1 TTT
77818 GTAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 27 0.75
37 9 0.25
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAGAAAATATATAAATATTATACAA
Found at i:79265 original size:14 final size:14
Alignment explanation
Indices: 79243--79317 Score: 96
Period size: 14 Copynumber: 5.3 Consensus size: 14
79233 TCAGTAATAT
*
79243 GTTCGTTTATGTTC
1 GTTCGTTTATATTC
*
79257 GTTCATTTATATTC
1 GTTCGTTTATATTC
79271 GTTCGTTTTATATTC
1 GTTCG-TTTATATTC
*
79286 GTTCGTTTATGTTC
1 GTTCGTTTATATTC
* *
79300 GTTTGTTTATATTT
1 GTTCGTTTATATTC
79314 GTTC
1 GTTC
79318 ATTTGTGTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
14 38 0.73
15 14 0.27
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.60
Consensus pattern (14 bp):
GTTCGTTTATATTC
Found at i:79522 original size:10 final size:10
Alignment explanation
Indices: 79507--79552 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
79497 AAAGAAAAAA
*
79507 ATTTATTTTC
1 ATTTATGTTC
79517 ATTTATGTTC
1 ATTTATGTTC
*
79527 GTTTATGTTC
1 ATTTATGTTC
79537 ATTTATGTTC
1 ATTTATGTTC
79547 ATTTAT
1 ATTTAT
79553 TGTGTTCGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (10 bp):
ATTTATGTTC
Found at i:79564 original size:13 final size:13
Alignment explanation
Indices: 79542--79601 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
79532 TGTTCATTTA
*
79542 TGTTCATTTATTG
1 TGTTCGTTTATTG
79555 TGTTCGTTTA---
1 TGTTCGTTTATTG
* * *
79565 CGTTCGTTCATTTT
1 TGTTCGTTTA-TTG
79579 TGTTCGTTTATTG
1 TGTTCGTTTATTG
79592 TGTTCGTTTA
1 TGTTCGTTTA
79602 CATTAGTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
10 8 0.22
13 21 0.57
14 8 0.22
ACGTcount: A:0.10, C:0.12, G:0.18, T:0.60
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:79583 original size:37 final size:37
Alignment explanation
Indices: 79533--79644 Score: 143
Period size: 37 Copynumber: 3.0 Consensus size: 37
79523 GTTCGTTTAT
* * *
79533 GTTCATTTATGTTCATTTATTGTGTTCGTTTACGTTC
1 GTTCATTTATGTTCGTTTATTGTGTTCGTTTACATTA
*
79570 GTTCATTTTTGTTCGTTTATTGTGTTCGTTTACATTA
1 GTTCATTTATGTTCGTTTATTGTGTTCGTTTACATTA
** *
79607 GTTTGTTTATGTTCGTTCATTTGTGTTCGTTTATCATT
1 GTTCATTTATGTTCGTTTA-TTGTGTTCGTTTA-CATT
79645 TAAATGAACG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
37 48 0.74
38 13 0.20
39 4 0.06
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (37 bp):
GTTCATTTATGTTCGTTTATTGTGTTCGTTTACATTA
Found at i:79729 original size:16 final size:16
Alignment explanation
Indices: 79710--79744 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
79700 CAAACAAGAA
*
79710 TATGTTCGTGTTTGTT
1 TATGTTCGTGTTCGTT
79726 TATGTTCGTGTTCGTT
1 TATGTTCGTGTTCGTT
79742 TAT
1 TAT
79745 TTGTTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.09, G:0.23, T:0.60
Consensus pattern (16 bp):
TATGTTCGTGTTCGTT
Found at i:82185 original size:12 final size:12
Alignment explanation
Indices: 82160--82217 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
82150 ACGAAGATAT
* *
82160 CAGAAATCAAAA
1 CAGAATTCAGAA
*
82172 CAGAATTCATAA
1 CAGAATTCAGAA
*
82184 CAGAATCCAGAA
1 CAGAATTCAGAA
*
82196 CAGAAATCAGAA
1 CAGAATTCAGAA
82208 CAGAATTCAG
1 CAGAATTCAG
82218 GTCATTTATC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:82252 original size:24 final size:24
Alignment explanation
Indices: 82196--82254 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
82186 GAATCCAGAA
*
82196 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAAGT
***
82220 CATTTATCAGAACAGAATTCAAGT
1 CAGAAATCAGAACAGAATTCAAGT
*
82244 CGGAAATCAGA
1 CAGAAATCAGA
82255 TAAAATATTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAAGT
Found at i:84747 original size:14 final size:15
Alignment explanation
Indices: 84728--84759 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
84718 TGGTCAACTC
84728 CGGTCAAC-GGTCAA
1 CGGTCAACGGGTCAA
84742 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
84757 CGG
1 CGG
84760 GTCGGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:84772 original size:18 final size:18
Alignment explanation
Indices: 84749--84817 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
84739 CAACGGTCAA
84749 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
84767 CGGGTCAA-----CGGGT
1 CGGGTCAACGGGTCGGGT
*
84780 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
84798 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
84816 CG
1 CG
84818 TGTTGTGACC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 12 0.27
18 32 0.73
ACGTcount: A:0.13, C:0.22, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:84780 original size:8 final size:7
Alignment explanation
Indices: 84728--84759 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
84718 TGGTCAACTC
84728 CGGTCAA
1 CGGTCAA
84735 CGGTCAA
1 CGGTCAA
84742 CGGTCAA
1 CGGTCAA
84749 CGGGTCAA
1 C-GGTCAA
84757 CGG
1 CGG
84760 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:84790 original size:31 final size:31
Alignment explanation
Indices: 84749--84815 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
84739 CAACGGTCAA
*
84749 CGGGTCAACGGGTCGGGTCGGGTCAACGGGT
1 CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
84780 CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
1 CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
84811 CGGGT
1 CGGGT
84816 CGTGTTGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.16
Consensus pattern (31 bp):
CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
Found at i:84816 original size:13 final size:13
Alignment explanation
Indices: 84762--84798 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
84752 GTCAACGGGT
84762 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
84775 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
84788 CGGGTCGGGTC
1 CGGGTCGGGTC
84799 GGGTCAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:86978 original size:12 final size:12
Alignment explanation
Indices: 86953--87010 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
86943 ACGAAGATAT
* *
86953 CAGAAATCAAAA
1 CAGAATTCAGAA
*
86965 CAGAATTCATAA
1 CAGAATTCAGAA
* *
86977 CAGAATCCAGAT
1 CAGAATTCAGAA
*
86989 CAGAAATCAGAA
1 CAGAATTCAGAA
87001 CAGAATTCAG
1 CAGAATTCAG
87011 GTCATTTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.52, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:87045 original size:24 final size:24
Alignment explanation
Indices: 86965--87047 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
86955 GAAATCAAAA
* * *
86965 CAGAATTCATAACAGAA-TCCAGAT
1 CAGAAATCAGAACAGAATTCAAG-T
*
86989 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAAGT
***
87013 CATTTATCAGAACAGAATTCAAGT
1 CAGAAATCAGAACAGAATTCAAGT
*
87037 CGGAAATCAGA
1 CAGAAATCAGA
87048 TAAAATATTT
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
24 43 0.93
25 3 0.07
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAAGT
Done.