Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005559.1 Hibiscus syriacus cultivar Beakdansim tig00012893_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: 115158
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2871 original size:22 final size:22
Alignment explanation
Indices: 2843--2921 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
2833 GCACTTAACA
2843 ATGCATCGATGCATCCCTTGAT
1 ATGCATCGATGCATCCCTTGAT
*
2865 ATGCATCGATGCATCCGCATG--
1 ATGCATCGATGCATCC-CTTGAT
* *
2886 ATGCACCGATGCATGCCTTGAAT
1 ATGCATCGATGCATCCCTTG-AT
*
2909 GTGCATCGATGCA
1 ATGCATCGATGCA
2922 CAAGAATATG
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.06
21 14 0.30
22 16 0.34
23 14 0.30
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (22 bp):
ATGCATCGATGCATCCCTTGAT
Found at i:2933 original size:43 final size:43
Alignment explanation
Indices: 2843--2943 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 43
2833 GCACTTAACA
* *
2843 ATGCATCGATGCATCCCTTGATATGCATCGATGCATCCGCATG
1 ATGCATCGATGCATCCCTTGATATGCATCGATGCATCAGAATG
* * *
2886 ATGCACCGATGCATGCCTTGAATGTGCATCGATGCA-CAAGAAT-
1 ATGCATCGATGCATCCCTTG-ATATGCATCGATGCATC-AGAATG
2929 ATGCATCGATGCATC
1 ATGCATCGATGCATC
2944 GTCGGGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 32 0.65
44 17 0.35
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (43 bp):
ATGCATCGATGCATCCCTTGATATGCATCGATGCATCAGAATG
Found at i:5407 original size:21 final size:21
Alignment explanation
Indices: 5383--5422 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5373 TTTTCAAAGG
5383 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
5404 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
5423 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:5472 original size:19 final size:19
Alignment explanation
Indices: 5448--5486 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5438 TCGAATGCAT
5448 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
5467 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
5486 T
1 T
5487 GATTCAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:5511 original size:64 final size:65
Alignment explanation
Indices: 5383--5612 Score: 204
Period size: 64 Copynumber: 3.5 Consensus size: 65
5373 TTTTCAAAGG
*
5383 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGC
5446 ATTC
62 ATTC
* * *
5450 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTCAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
* * ** * ** * *
5514 GATGCATCGATGCACAATCCATGCATCGATGCAC-CA-GACTATTTTTCAAACATCGAATGTACT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATA-AATTAAAACATCGAATGCA-T
5577 T-
64 TC
* * *
5578 CATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACT
5613 AGGAGTCCAA
Statistics
Matches: 137, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
63 5 0.04
64 96 0.70
65 17 0.12
66 3 0.02
67 14 0.10
68 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
Found at i:6713 original size:15 final size:15
Alignment explanation
Indices: 6693--6723 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6683 CTTTATGTTG
6693 TCAGAATTACAAATT
1 TCAGAATTACAAATT
6708 TCAGAATTACAAATT
1 TCAGAATTACAAATT
6723 T
1 T
6724 TAGATTACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (15 bp):
TCAGAATTACAAATT
Found at i:16536 original size:18 final size:18
Alignment explanation
Indices: 16513--16566 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
16503 ATATAACAAC
16513 CTATTTTAATGTCGTTAA
1 CTATTTTAATGTCGTTAA
16531 CTA-TTTAA---C---AA
1 CTATTTTAATGTCGTTAA
16542 CCTATTTTAATGTCGTTAA
1 -CTATTTTAATGTCGTTAA
16561 CTATTT
1 CTATTT
16567 AACGGTTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
13 5 0.18
14 1 0.04
16 1 0.04
17 5 0.18
18 9 0.32
19 2 0.07
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (18 bp):
CTATTTTAATGTCGTTAA
Found at i:16541 original size:30 final size:30
Alignment explanation
Indices: 16501--16569 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
16491 TCGTTTGTAT
*
16501 CTATATAACAACCTATTTTAATGTCGTTAA
1 CTATTTAACAACCTATTTTAATGTCGTTAA
16531 CTATTTAACAACCTATTTTAATGTCGTTAA
1 CTATTTAACAACCTATTTTAATGTCGTTAA
16561 CTATTTAAC
1 CTATTTAAC
16570 GGTTGAGTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (30 bp):
CTATTTAACAACCTATTTTAATGTCGTTAA
Found at i:17075 original size:2 final size:2
Alignment explanation
Indices: 17068--17097 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17058 TAGCATGATA
17068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17098 TAATGGGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19855 original size:110 final size:110
Alignment explanation
Indices: 19662--19881 Score: 404
Period size: 110 Copynumber: 2.0 Consensus size: 110
19652 TAGGGATTAC
* *
19662 AACAATGTTCATTTATTAAGAAGATTAATGAAGTATTCTCCAAATTGTTTGAAGAGTGATTTTTA
1 AACAATGTTCATTTATTAAGAAGATTAATGAAGTATTCTCCAAATTGTTTGAAGAGTGACTGTTA
19727 ATTATTTTTAATAAAAGAACATCCTTTTTAAAATATAAGTGAATA
66 ATTATTTTTAATAAAAGAACATCCTTTTTAAAATATAAGTGAATA
*
19772 AACAATGTTCATTTATTAAGAAGATTAATGAAGTATTCTCCAAATTGTTTGGAGAGTGACTGTTA
1 AACAATGTTCATTTATTAAGAAGATTAATGAAGTATTCTCCAAATTGTTTGAAGAGTGACTGTTA
*
19837 ATTATTTTTAATAAAAGAACATCCTTTTTGAAATATAAGTGAATA
66 ATTATTTTTAATAAAAGAACATCCTTTTTAAAATATAAGTGAATA
19882 GAAAATACAA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 106 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (110 bp):
AACAATGTTCATTTATTAAGAAGATTAATGAAGTATTCTCCAAATTGTTTGAAGAGTGACTGTTA
ATTATTTTTAATAAAAGAACATCCTTTTTAAAATATAAGTGAATA
Found at i:20151 original size:22 final size:22
Alignment explanation
Indices: 20123--20164 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20113 TATTTTTATT
20123 TGATAATAAATTTTTATTAAAA
1 TGATAATAAATTTTTATTAAAA
* *
20145 TGATAATATATTTTTGTTAA
1 TGATAATAAATTTTTATTAA
20165 TCGAATCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
TGATAATAAATTTTTATTAAAA
Found at i:21581 original size:19 final size:19
Alignment explanation
Indices: 21557--21603 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
21547 ACCAACTAAA
21557 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
21576 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
21595 TCGCAATGC
1 TCGCAATGC
21604 AATCTCCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (19 bp):
TCGCAATGCGATCGATAAT
Found at i:21687 original size:21 final size:21
Alignment explanation
Indices: 21661--21728 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
21651 ACTATCGTAT
* *
21661 TGCGATTTTCCAAATTCGCGA
1 TGCGATTTTCCGAATTCGCAA
21682 TGCGATTTTCCGAATTCGCAA
1 TGCGATTTTCCGAATTCGCAA
*
21703 TGCGATTTTCTGAATTCGCAA
1 TGCGATTTTCCGAATTCGCAA
21724 TGCGA
1 TGCGA
21729 ATATGTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (21 bp):
TGCGATTTTCCGAATTCGCAA
Found at i:21743 original size:20 final size:20
Alignment explanation
Indices: 21718--21780 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
21708 TTTTCTGAAT
21718 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
21738 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
21758 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
21778 TCG
1 TCG
21781 GAACGAGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:21801 original size:40 final size:39
Alignment explanation
Indices: 21710--21808 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 39
21700 CAATGCGATT
* *
21710 TTCTGA-ATTCGCAATGCGAATATGTAAATCGCAATGCGA
1 TTCTGATA-TCGCAATGCGAATATGTAAATCGCAACGAGA
* * * *
21749 ATATGTAAATCGCAATGCGAATATGTAAATCGGAACGAGA
1 TTCTG-ATATCGCAATGCGAATATGTAAATCGCAACGAGA
*
21789 TTCTGACTATCGCAACGCGA
1 TTCTGA-TATCGCAATGCGA
21809 TGCTGACTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
39 4 0.08
40 43 0.90
41 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (39 bp):
TTCTGATATCGCAATGCGAATATGTAAATCGCAACGAGA
Found at i:21828 original size:20 final size:20
Alignment explanation
Indices: 21777--21829 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
21767 GAATATGTAA
* * *
21777 ATCGGAACGAGATTCTGACT
1 ATCGCAACGCGATGCTGACT
21797 ATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATGCTGACT
*
21817 ATCGCAATGCGAT
1 ATCGCAACGCGAT
21830 TTTCAAAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATGCTGACT
Found at i:22030 original size:22 final size:22
Alignment explanation
Indices: 22005--22047 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
21995 GGCGACATTC
22005 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
22027 GTCCCCATCTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
22048 CGTCTATCTC
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:0.26, C:0.42, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:22470 original size:20 final size:20
Alignment explanation
Indices: 22445--22497 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
22435 CGATTTTAGT
22445 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
22465 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
22485 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
22498 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:24485 original size:20 final size:19
Alignment explanation
Indices: 24460--24526 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
24450 GCGATTCTCT
24460 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
*
24480 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-ATTCG
*
24500 CATTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
24518 TGTTGCGAT
1 CGTTGCGAT
24527 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.27
19 1 0.02
20 29 0.71
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:25107 original size:21 final size:21
Alignment explanation
Indices: 25017--25123 Score: 69
Period size: 21 Copynumber: 5.1 Consensus size: 21
25007 ACTCACCTGT
25017 CATCGTTCAAGAGG-CA-TCCC
1 CATCGTTCAAGAGGCCACT-CC
* **
25037 CTATCGTTCAAGAGGCCCCTAT
1 C-ATCGTTCAAGAGGCCACTCC
** *
25059 CATCCCTCAAGAGTCTC-CTCC
1 CATCGTTCAAGAGGC-CACTCC
* *
25080 CACCGTTCAAGAGGCCACTGC
1 CATCGTTCAAGAGGCCACTCC
*
25101 CATCGTTGAAGAGGTCC-CTCC
1 CATCGTTCAAGAGG-CCACTCC
25122 CA
1 CA
25124 ACATTCTAGA
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
20 2 0.03
21 57 0.88
22 5 0.08
23 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCACTCC
Found at i:26562 original size:14 final size:14
Alignment explanation
Indices: 26525--26586 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
26515 TTGCTTGTTT
*
26525 AATTGATTTATAAA
1 AATTGATTTGTAAA
26539 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
26553 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
26568 TATTGATGTGTAAA
1 AATTGATTTGTAAA
26582 TAATT
1 -AATT
26587 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:26788 original size:20 final size:20
Alignment explanation
Indices: 26761--27045 Score: 315
Period size: 20 Copynumber: 14.8 Consensus size: 20
26751 GCGATTTTCT
* *
26761 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCA
* *
26781 CATTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
26801 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCA
*
26821 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
**
26841 CGTTGCGAT--T----TTTT
1 CGTTGCGATAGTCAAATTCA
*
26855 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
26875 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
* *
26895 CGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
26915 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
* *
26935 CGTTGCGAT--T---TTTGA
1 CGTTGCGATAGTCAAATTCA
* *
26950 -GTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCA
* *
26969 CGTTGCGATAGTCGAATACA
1 CGTTGCGATAGTCAAATTCA
*
26989 TGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
27009 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
27029 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
27046 GAATGTCTAA
Statistics
Matches: 222, Mismatches: 31, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
14 19 0.09
15 3 0.01
16 2 0.01
18 2 0.01
19 2 0.01
20 194 0.87
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:26861 original size:74 final size:74
Alignment explanation
Indices: 26783--26923 Score: 246
Period size: 74 Copynumber: 1.9 Consensus size: 74
26773 CAAATACCCA
* *
26783 TTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCTCGTTGCGATAGTCAAATTCGCGTTGCG
1 TTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCG
26848 ATTTTTTCG
66 ATTTTTTCG
* *
26857 TTGCGATAGTCAAATTCCCGTTGCGATAGTCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCG
1 TTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCG
26922 AT
66 AT
26924 AGTCAAATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (74 bp):
TTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCG
ATTTTTTCG
Found at i:26882 original size:94 final size:94
Alignment explanation
Indices: 26721--27037 Score: 463
Period size: 94 Copynumber: 3.4 Consensus size: 94
26711 CGCGAAAGTT
* * * * * * *
26721 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
1 AATTCGCGTTGCGATAGTCAAATTCACGTTGCGATTTTTTCGTTGCGATAGTCAAATTCCCGTTG
*
26786 CGATAATCAAATTCACGTTGCGATAGTCA
66 CGATAGTCAAATTCACGTTGCGATAGTCA
* *
26815 AATTCTCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTTCGTTGCGATAGTCAAATTCCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCACGTTGCGATTTTTTCGTTGCGATAGTCAAATTCCCGTTG
*
26880 CGATAGTCAAATTCACGTTGCAATAGTCA
66 CGATAGTCAAATTCACGTTGCGATAGTCA
** * *
26909 AATTCGCGTTGCGATAGTCAAATTCACGTTGCGATTTTTGAGTTGCGATAATCAAATTCGCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCACGTTGCGATTTTTTCGTTGCGATAGTCAAATTCCCGTTG
* * *
26974 CGATAGTCGAATACATGTTGCGATAGTCA
66 CGATAGTCAAATTCACGTTGCGATAGTCA
*
27003 AATTCACGTTGCGATAGTCAAATTCACGTTGCGAT
1 AATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT
27038 ATTCAAATGA
Statistics
Matches: 203, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 203 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (94 bp):
AATTCGCGTTGCGATAGTCAAATTCACGTTGCGATTTTTTCGTTGCGATAGTCAAATTCCCGTTG
CGATAGTCAAATTCACGTTGCGATAGTCA
Found at i:26954 original size:74 final size:74
Alignment explanation
Indices: 26876--27017 Score: 221
Period size: 74 Copynumber: 1.9 Consensus size: 74
26866 TCAAATTCCC
* * *
26876 GTTGCGATAGTCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCGATAGTCAAATTCACGTTGC
1 GTTGCGATAATCAAATTCACGTTGCAATAGTCAAATACACGTTGCGATAGTCAAATTCACGTTGC
26941 GATTTTTGA
66 GATTTTTGA
* * * *
26950 GTTGCGATAATCAAATTCGCGTTGCGATAGTCGAATACATGTTGCGATAGTCAAATTCACGTTGC
1 GTTGCGATAATCAAATTCACGTTGCAATAGTCAAATACACGTTGCGATAGTCAAATTCACGTTGC
27015 GAT
66 GAT
27018 AGTCAAATTC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (74 bp):
GTTGCGATAATCAAATTCACGTTGCAATAGTCAAATACACGTTGCGATAGTCAAATTCACGTTGC
GATTTTTGA
Found at i:26978 original size:54 final size:57
Alignment explanation
Indices: 26783--27045 Score: 211
Period size: 54 Copynumber: 4.6 Consensus size: 57
26773 CAAATACCCA
* * * *
26783 TTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCTCGTTGCGATAGTCAAATTCGCG
1 TTGCAATAATCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGATA-T--AATTCACG
* ** *
26843 TTGCGAT--T----TTTTCGTTGCGATAGTCAAATTCCCGTTGCGATAGTCAAATTCACG
1 TTGCAATAATCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGATA-T--AATTCACG
* * *
26897 TTGCAATAGTCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT-T-TTTGA-G
1 TTGCAATAATCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGATATAATTCACG
* * * *
26951 TTGCGATAATCAAATTCGCGTTGCGATAGTCGAATACATGTTGCGATAGTCAAATTCACG
1 TTGCAATAATCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGATA-T--AATTCACG
* * * *
27011 TTGCGATAGTCAAATTCACGTTGCGATATTCAAAT
1 TTGCAATAATCAAATTCGCGTTGCGATAGTCAAAT
27046 GAATGTCTAA
Statistics
Matches: 170, Mismatches: 21, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
54 91 0.54
55 3 0.02
56 2 0.01
58 2 0.01
59 3 0.02
60 69 0.41
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (57 bp):
TTGCAATAATCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGATATAATTCACG
Found at i:29299 original size:14 final size:14
Alignment explanation
Indices: 29280--29316 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29270 TCCCGTGGCA
29280 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAT
*
29294 TTTTCTTTGGGGAT
1 TTTTCTTCGGGGAT
29308 TTCTTCTTC
1 TT-TTCTTC
29317 TTCTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.05, C:0.16, G:0.22, T:0.57
Consensus pattern (14 bp):
TTTTCTTCGGGGAT
Found at i:29540 original size:24 final size:24
Alignment explanation
Indices: 29506--29559 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
29496 CTAAAACATC
29506 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
29530 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
29554 ATCAAA
1 ATCAAA
29560 TTTCGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:30405 original size:20 final size:20
Alignment explanation
Indices: 30380--30484 Score: 138
Period size: 20 Copynumber: 5.2 Consensus size: 20
30370 GAAATTCAGT
*
30380 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
30400 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
* *
30420 GTTGCGATAATCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
*
30440 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
30460 ATTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
30480 ATTGC
1 GTTGC
30485 AATTTACATA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:30494 original size:20 final size:21
Alignment explanation
Indices: 30454--30509 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
30444 CGACAGTCAG
*
30454 AATCGCATTGCG-ATAGT-CAT
1 AATCGCATTGCGAAT-TTACAT
30474 AATCGCATTGC-AATTTACAT
1 AATCGCATTGCGAATTTACAT
*
30494 ATTCGCATTGCGAATT
1 AATCGCATTGCGAATT
30510 CGGAAAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 26 0.84
21 4 0.13
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (21 bp):
AATCGCATTGCGAATTTACAT
Found at i:30527 original size:21 final size:21
Alignment explanation
Indices: 30503--30548 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
30493 TATTCGCATT
30503 GCGAATTCGGAAAATCACAAC
1 GCGAATTCGGAAAATCACAAC
* * *
30524 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCACAAC
30545 GCGA
1 GCGA
30549 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCACAAC
Found at i:33990 original size:2 final size:2
Alignment explanation
Indices: 33983--34018 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33973 CCTTAGATTA
33983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34019 TAGGTCAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38663 original size:23 final size:23
Alignment explanation
Indices: 38636--38682 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
38626 ATCATTCGCC
* *
38636 AAAATTAACCTAAAACATATAAA
1 AAAATTAACCTAAAAAACATAAA
* *
38659 AAAATTCAGCTAAAAAACATAAA
1 AAAATTAACCTAAAAAACATAAA
38682 A
1 A
38683 TGATCAGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.66, C:0.13, G:0.02, T:0.19
Consensus pattern (23 bp):
AAAATTAACCTAAAAAACATAAA
Found at i:40272 original size:2 final size:2
Alignment explanation
Indices: 40260--40299 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
40250 ACGAGGGAAG
40260 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40300 GCTTGTAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40414 original size:2 final size:2
Alignment explanation
Indices: 40402--40454 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
40392 ATAAAGTAAA
*
40402 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40442 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
40455 AGTAAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42304 original size:107 final size:106
Alignment explanation
Indices: 41985--42646 Score: 1041
Period size: 107 Copynumber: 6.4 Consensus size: 106
41975 GTATTGTTCC
* * * * * * *
41985 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
42050 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
42091 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
42156 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
42197 GATTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGAGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAGTTGTTTATTGACA
42262 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
42304 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG-TTGTTTATTGACA
*
42369 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
42411 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC------TG-GAA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * *
42468 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
42509 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT---A---A-AA-TTGTTTATCGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
42566 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
42607 GAGTCCAGTATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
42647 GGTAAAACCT
Statistics
Matches: 530, Mismatches: 20, Indels: 19
0.93 0.04 0.03
Matches are distributed among these distances:
98 179 0.34
100 3 0.01
101 2 0.00
106 149 0.28
107 197 0.37
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:42525 original size:98 final size:98
Alignment explanation
Indices: 42356--42647 Score: 494
Period size: 98 Copynumber: 3.0 Consensus size: 98
42346 ATTGAGAAGT
* *
42356 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
42421 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAA
* *
42454 TTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
**
42519 TCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAA
* * * *
42552 TTGTTTATCGAAAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAGTA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
42617 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGG
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGG
42648 GTAAAACCTG
Statistics
Matches: 180, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 180 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (98 bp):
TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAA
Found at i:42538 original size:43 final size:43
Alignment explanation
Indices: 42477--42636 Score: 131
Period size: 43 Copynumber: 3.4 Consensus size: 43
42467 ACCAACGGTC
*
42477 CCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGTCCAGTAT
* * * ** *
42520 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGTTTATCGAAAACCAGTGGT
1 CCTTCGTCGTGAAGTTGAACTT-G--C----ATTGTCTA--G-AGTCCAGT-AT
*
42574 CCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAGTAT
1 -CCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGTCCAGTAT
*
42618 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
42637 ATTGGCTCTG
Statistics
Matches: 90, Mismatches: 15, Indels: 24
0.70 0.12 0.19
Matches are distributed among these distances:
43 38 0.42
44 2 0.02
45 6 0.07
46 2 0.02
48 6 0.07
50 7 0.08
52 2 0.02
53 5 0.06
54 2 0.02
55 20 0.22
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGTCCAGTAT
Found at i:43428 original size:9 final size:9
Alignment explanation
Indices: 43405--43451 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
43395 CACCTTATTT
43405 TCTTTTCT-
1 TCTTTTCTC
43413 T-TTTTCTC
1 TCTTTTCTC
43421 TCTTTTCTC
1 TCTTTTCTC
43430 -CTTTT-TC
1 TCTTTTCTC
*
43437 TCTTTTTTC
1 TCTTTTCTC
43446 TCTTTT
1 TCTTTT
43452 TTCCAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 8 0.23
8 12 0.34
9 15 0.43
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
TCTTTTCTC
Found at i:43436 original size:18 final size:17
Alignment explanation
Indices: 43405--43452 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
43395 CACCTTATTT
43405 TCTTTTCT-TTTTTCTC
1 TCTTTTCTCTTTTTCTC
43421 TCTTTTCTCCTTTTTCTC
1 TCTTTTCT-CTTTTTCTC
*
43439 TTTTTTCTCTTTTT
1 TCTTTTCTCTTTTT
43453 TCCAATTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 15 0.52
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TCTTTTCTCTTTTTCTC
Found at i:43452 original size:9 final size:9
Alignment explanation
Indices: 43410--43454 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
43400 TATTTTCTTT
43410 TCTTTTTTC
1 TCTTTTTTC
*
43419 TCTCTTTTC
1 TCTTTTTTC
*
43428 TCCTTTTTC
1 TCTTTTTTC
43437 TCTTTTTTC
1 TCTTTTTTC
43446 TCTTTTTTC
1 TCTTTTTTC
43455 CAATTTAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (9 bp):
TCTTTTTTC
Found at i:50983 original size:18 final size:17
Alignment explanation
Indices: 50944--50986 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
50934 ATTATATGGA
50944 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
50960 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
50978 TATTATTAT
1 TATTATTAT
50987 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:56908 original size:2 final size:2
Alignment explanation
Indices: 56901--56979 Score: 88
Period size: 2 Copynumber: 39.5 Consensus size: 2
56891 GAAAATAATT
* * ** *
56901 TA TA TA TA TA TA TG TA -A TA TA TA TG TGA CG TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
*
56943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56980 GTTTATAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:59765 original size:17 final size:17
Alignment explanation
Indices: 59743--59778 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
59733 TCAAAGAAGA
59743 AAAAGTTCAGAATAAAT
1 AAAAGTTCAGAATAAAT
59760 AAAAGTTCAGAATAAAT
1 AAAAGTTCAGAATAAAT
59777 AA
1 AA
59779 GGAAGAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.22
Consensus pattern (17 bp):
AAAAGTTCAGAATAAAT
Found at i:66741 original size:13 final size:13
Alignment explanation
Indices: 66725--66765 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
66715 AATTTCGTTT
66725 TTTATCTTTATAA
1 TTTATCTTTATAA
66738 TTTAGATC-TT-TAA
1 TTT--ATCTTTATAA
66751 TTTATCTTTATAA
1 TTTATCTTTATAA
66764 TT
1 TT
66766 GGATCTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 3 0.12
12 2 0.08
13 14 0.58
14 2 0.08
15 3 0.12
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTATCTTTATAA
Found at i:66834 original size:43 final size:43
Alignment explanation
Indices: 66773--67018 Score: 160
Period size: 43 Copynumber: 5.7 Consensus size: 43
66763 ATTGGATCTT
* *
66773 ATTTTTTTAATCTTACTTTTTACCTTTATAATTAAGGCTTATG
1 ATTTTTTCAATCTCACTTTTTACCTTTATAATTAAGGCTTATG
* * * * *
66816 ATTTTTTCAATCACACTTTATACTTTTATAATTGA-GCTCCATG
1 ATTTTTTCAATCTCACTTTTTACCTTTATAATTAAGGCT-TATG
* * * * * *
66859 ATTTTTTTAGTTTCACTTTATACCTTTATAAATTGAGG-TCATAG
1 ATTTTTTCAATCTCACTTTTTACCTTTAT-AATTAAGGCTTAT-G
* * * * * * *
66903 TTTTTTTTAATCTCACTTTTTATCTTTATAGCTTATGCCCCTA--
1 ATTTTTTCAATCTCACTTTTTACCTTTATA-ATTAAG-GCTTATG
* * * *
66946 ATTTTTTCAATCACACTTTTTACTTTTATAATTAAGAC-TATTA
1 ATTTTTTCAATCTCACTTTTTACCTTTATAATTAAGGCTTA-TG
* * *
66989 ATTTTTTCAATTTTACATTTTACCTTTATA
1 ATTTTTTCAATCTCACTTTTTACCTTTATA
67019 TAATTGAGAC
Statistics
Matches: 157, Mismatches: 36, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
40 2 0.01
41 1 0.01
42 7 0.04
43 110 0.70
44 35 0.22
45 1 0.01
46 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (43 bp):
ATTTTTTCAATCTCACTTTTTACCTTTATAATTAAGGCTTATG
Found at i:66894 original size:44 final size:42
Alignment explanation
Indices: 66756--66932 Score: 169
Period size: 43 Copynumber: 4.2 Consensus size: 42
66746 TTTAATTTAT
* * * *
66756 CTTTATAATTG-GATC-TTATTTTTTTAATCTTACTTTTTAC
1 CTTTATAATTGAGCTCATGATTTTTTTAATCTCACTTTATAC
* * * *
66796 CTTTATAATTAAGGCTTATGATTTTTTCAATCACACTTTATAC
1 CTTTATAATTGA-GCTCATGATTTTTTTAATCTCACTTTATAC
* * *
66839 TTTTATAATTGAGCTCCATGATTTTTTTAGTTTCACTTTATAC
1 CTTTATAATTGAGCT-CATGATTTTTTTAATCTCACTTTATAC
* * * *
66882 CTTTATAAATTGAGGTCATAGTTTTTTTTAATCTCACTTTTTAT
1 CTTTAT-AATTGAGCTCAT-GATTTTTTTAATCTCACTTTATAC
66926 CTTTATA
1 CTTTATA
66933 GCTTATGCCC
Statistics
Matches: 109, Mismatches: 22, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
40 10 0.09
42 5 0.05
43 61 0.56
44 33 0.30
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (42 bp):
CTTTATAATTGAGCTCATGATTTTTTTAATCTCACTTTATAC
Found at i:67036 original size:45 final size:43
Alignment explanation
Indices: 66944--67047 Score: 118
Period size: 43 Copynumber: 2.3 Consensus size: 43
66934 CTTATGCCCC
* * *
66944 TAATTTTTTCAATCACACTTTTTACTTTTATAATTAAGACTAT
1 TAATTTTTTCAATTACACATTTTACTTTTATAATTAAGACCAT
** * *
66987 TAATTTTTTCAATTTTACATTTTACCTTTATATAATTGAGACCCT
1 TAATTTTTTCAATTACACATTTTA-CTTT-TATAATTAAGACCAT
67032 TAATTTTTTTCAATTA
1 TAA-TTTTTTCAATTA
67048 ATGCATCTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 20 0.40
44 4 0.08
45 15 0.30
46 11 0.22
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.53
Consensus pattern (43 bp):
TAATTTTTTCAATTACACATTTTACTTTTATAATTAAGACCAT
Found at i:67675 original size:21 final size:21
Alignment explanation
Indices: 67651--67715 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
67641 AACAATTCTC
* *
67651 TTCATGAAACGATTAAGTCCT
1 TTCATAAAAAGATTAAGTCCT
* *
67672 TTCATAAAAAGGTTAAGCCCT
1 TTCATAAAAAGATTAAGTCCT
* *
67693 TTCATCAAAAGAATAAGTCCT
1 TTCATAAAAAGATTAAGTCCT
67714 TT
1 TT
67716 AATCGAAAGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.32
Consensus pattern (21 bp):
TTCATAAAAAGATTAAGTCCT
Found at i:67724 original size:21 final size:21
Alignment explanation
Indices: 67685--67724 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
67675 ATAAAAAGGT
*
67685 TAAGCCCTTTCATCAAAAGAA
1 TAAGCCCTTTAATCAAAAGAA
* *
67706 TAAGTCCTTTAATCGAAAG
1 TAAGCCCTTTAATCAAAAG
67725 GGTACGTTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (21 bp):
TAAGCCCTTTAATCAAAAGAA
Found at i:69064 original size:24 final size:24
Alignment explanation
Indices: 69037--69082 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
69027 ATAAGTCTAG
*
69037 ATTTAATACTT-TGATACATGATTC
1 ATTTAATA-TTATGAAACATGATTC
*
69061 ATTTCATATTATGAAACATGAT
1 ATTTAATATTATGAAACATGAT
69083 ATGAGTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (24 bp):
ATTTAATATTATGAAACATGATTC
Found at i:69996 original size:20 final size:20
Alignment explanation
Indices: 69971--70024 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
69961 GTTTGTGAGC
*
69971 ATTGGTACTGTTCACATAGT
1 ATTGGTACTATTCACATAGT
*
69991 ATTGGTACTATTCACGTAGT
1 ATTGGTACTATTCACATAGT
* *
70011 ATAGGTATTATTCA
1 ATTGGTACTATTCA
70025 TACAGTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTGGTACTATTCACATAGT
Found at i:71619 original size:37 final size:38
Alignment explanation
Indices: 71569--71648 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 38
71559 TGTTCGGGTT
71569 GGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGAGTC
1 GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTC
*
71606 GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTC
1 GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTC
71644 GGGTC
1 GGGTC
71649 AGTGTCGGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 8 0.20
38 33 0.80
ACGTcount: A:0.11, C:0.11, G:0.40, T:0.38
Consensus pattern (38 bp):
GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAGTC
Found at i:71892 original size:38 final size:37
Alignment explanation
Indices: 71831--71919 Score: 124
Period size: 38 Copynumber: 2.4 Consensus size: 37
71821 TTTATTTTGT
*
71831 TCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGAG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAG
* *
71868 TCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTC-GGGTTTTTTAAGTGTGATATTCGGGTCGAG
*
71906 TTGGGTTCGGGTTT
1 TCGGG-TCGGGTTT
71920 AGGGTGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 7 0.16
38 36 0.80
39 2 0.04
ACGTcount: A:0.11, C:0.09, G:0.38, T:0.42
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAG
Found at i:71901 original size:264 final size:266
Alignment explanation
Indices: 71385--71911 Score: 839
Period size: 269 Copynumber: 2.0 Consensus size: 266
71375 TATTCGGGTT
* *
71385 GGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCG
1 GGGTTCGGGTTTAGGGTGAAAAAAACCAGACCGACCCAAAAATATATATAATTCAGGTCGGGTCG
* * *
71450 GATTAAGTCATTGTTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTGAA
66 GATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGAGTCGAGTTGAA
* * *
71515 TTTCTAATTCATATATTGGGGTCGGGTTGGGTGAAACTTTATTTTGTTCGGGTTGGGTCGGGTTT
131 TTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTC--G--GGGTCGGGTTT
*
71580 TTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCG
192 TTTAAGTGTGATATTCGGGTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCG
71645 GGTCAGTGTC
257 GGTCAGTGTC
71655 GGGTTCGGGTTTAGGGT-AAAAAAACCAGACCGACCCAAAAATATATATAATTC-GGCTCGGGTC
1 GGGTTCGGGTTTAGGGTGAAAAAAACCAGACCGACCCAAAAATATATATAATTCAGG-TCGGGTC
*
71718 GGATTAAGTCACTGTTTTTATTAAAT-AAACT-TTTATTATTATTATTTCGGGTCGAGTCGAGTT
65 GGATTAAGTCACTGTTTTTATTAAATAAAAATATTT-TT-TTATTATTTCGGGTCGAGTCGAGTT
*
71781 GGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTC-GGGTCGGGTTTT
128 GAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGGTCGGGTTTT
* *
71845 TTAAGTGTGATATTTGGGTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTGG
193 TTAAGTGTGATATTCGGGTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGG
71910 GT
258 GT
71912 TCGGGTTTAG
Statistics
Matches: 241, Mismatches: 13, Indels: 12
0.91 0.05 0.05
Matches are distributed among these distances:
264 76 0.32
267 3 0.01
268 8 0.03
269 137 0.57
270 17 0.07
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.38
Consensus pattern (266 bp):
GGGTTCGGGTTTAGGGTGAAAAAAACCAGACCGACCCAAAAATATATATAATTCAGGTCGGGTCG
GATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGAGTCGAGTTGAA
TTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGGTCGGGTTTTTTA
AGTGTGATATTCGGGTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTC
AGTGTC
Found at i:72491 original size:44 final size:44
Alignment explanation
Indices: 72442--72553 Score: 215
Period size: 44 Copynumber: 2.5 Consensus size: 44
72432 TGAACAAAAC
72442 ATAATATGAAATTGGATTCCAATTTCATTTCCTGCCAACCAAAT
1 ATAATATGAAATTGGATTCCAATTTCATTTCCTGCCAACCAAAT
72486 ATAATATGAAATTGGATTCCAATTTCATTTCCTGCCAACCAAAT
1 ATAATATGAAATTGGATTCCAATTTCATTTCCTGCCAACCAAAT
*
72530 AGAATATGAAATTGGATTCCAATT
1 ATAATATGAAATTGGATTCCAATT
72554 CTTACAGATT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (44 bp):
ATAATATGAAATTGGATTCCAATTTCATTTCCTGCCAACCAAAT
Found at i:77683 original size:64 final size:63
Alignment explanation
Indices: 77598--77758 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
77588 TTGTTTAAGG
* * * *
77598 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * *
77662 TGCATCGATGCATAAGGAGTGCATCGATACATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
77726 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
77759 ACCTTCATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 20 0.24
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:77927 original size:22 final size:22
Alignment explanation
Indices: 77899--77950 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
77889 TTATCAAGTA
77899 AGATCGATCAAGGAAAGATAAC
1 AGATCGATCAAGGAAAGATAAC
77921 AGATCGATCAAGGAAAGATAAC
1 AGATCGATCAAGGAAAGATAAC
77943 AGATCGAT
1 AGATCGAT
77951 ATTGACTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.15
Consensus pattern (22 bp):
AGATCGATCAAGGAAAGATAAC
Found at i:78258 original size:2 final size:2
Alignment explanation
Indices: 78251--78283 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
78241 CATGAGTTAG
*
78251 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78284 GGAATTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:81612 original size:64 final size:64
Alignment explanation
Indices: 81537--81679 Score: 184
Period size: 64 Copynumber: 2.2 Consensus size: 64
81527 ATTGTTTAAG
*
81537 GTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G
1 GTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTATGCATCGATGCAT-AGTG
81600 -A
63 TA
* * * *
81601 GTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGTA
1 GTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTA
81666 GTGCATCGATGCAT
1 GTGCATCGATGCAT
81680 ACCTTCATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 47 0.67
65 21 0.30
66 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTA
Found at i:83165 original size:26 final size:26
Alignment explanation
Indices: 83106--83166 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
83096 TTATTCAAAT
*
83106 TAAATTT-TATCTTATAATATAAAAA
1 TAAATTTATATCTCATAATATAAAAA
*
83131 TAAGTATTTATATCTCA-AATACTGAAAA
1 TAA--ATTTATATCTCATAATA-TAAAAA
83159 TAAATTTA
1 TAAATTTA
83167 AAATTTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 3 0.10
26 5 0.17
27 8 0.27
28 14 0.47
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (26 bp):
TAAATTTATATCTCATAATATAAAAA
Found at i:84502 original size:2 final size:2
Alignment explanation
Indices: 84497--84538 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
84487 AAAATTTTTA
84497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84539 CATTTGTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86254 original size:20 final size:20
Alignment explanation
Indices: 86229--86269 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
86219 ATCCTTAGTA
*
86229 GCTGACATGTTTTTTTCATG
1 GCTGACATGTTCTTTTCATG
86249 GCTGACATGTTCTTTTCATG
1 GCTGACATGTTCTTTTCATG
86269 G
1 G
86270 ATTCTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
GCTGACATGTTCTTTTCATG
Found at i:109513 original size:22 final size:22
Alignment explanation
Indices: 109469--109513 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
109459 GATCTATTAT
* * *
109469 TTTATTTAAATTTAATTACAAA
1 TTTATGTAAATTTAATAAAAAA
109491 TTTATGTAAATTTAATAAAAAA
1 TTTATGTAAATTTAATAAAAAA
109513 T
1 T
109514 CAACATTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTATGTAAATTTAATAAAAAA
Found at i:111450 original size:36 final size:36
Alignment explanation
Indices: 111410--111524 Score: 112
Period size: 36 Copynumber: 3.2 Consensus size: 36
111400 TGATCGGTGA
111410 TGAACCTATATAAGGAATTACCAGCTTGATCAGAAT
1 TGAACCTATATAAGGAATTACCAGCTTGATCAGAAT
* * *
111446 TGAACCTGCA-AAAAAGAATTACCAGC-CGATC-G-AT
1 TGAACCT--ATATAAGGAATTACCAGCTTGATCAGAAT
* **
111480 GCTGAACCTATATGAGGAATTACCAATTTGATCAGAAT
1 --TGAACCTATATAAGGAATTACCAGCTTGATCAGAAT
111518 TGAACCT
1 TGAACCT
111525 GCAGAGACTT
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
34 3 0.05
35 12 0.19
36 29 0.47
37 15 0.24
38 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (36 bp):
TGAACCTATATAAGGAATTACCAGCTTGATCAGAAT
Found at i:111542 original size:72 final size:72
Alignment explanation
Indices: 111386--111527 Score: 212
Period size: 72 Copynumber: 2.0 Consensus size: 72
111376 TTAGGTCTAT
* ** * *
111386 AAAGAATTATCAGATGATCGGTGATGAACCTATATAAGGAATTACCAGCTTGATCAGAATTGAAC
1 AAAGAATTACCAGCCGATCGATGATGAACCTATATAAGGAATTACCAACTTGATCAGAATTGAAC
111451 CTGCAAA
66 CTGCAAA
* * *
111458 AAAGAATTACCAGCCGATCGATGCTGAACCTATATGAGGAATTACCAATTTGATCAGAATTGAAC
1 AAAGAATTACCAGCCGATCGATGATGAACCTATATAAGGAATTACCAACTTGATCAGAATTGAAC
111523 CTGCA
66 CTGCA
111528 GAGACTTCAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (72 bp):
AAAGAATTACCAGCCGATCGATGATGAACCTATATAAGGAATTACCAACTTGATCAGAATTGAAC
CTGCAAA
Found at i:112996 original size:24 final size:24
Alignment explanation
Indices: 112971--113077 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
112961 AAACGGAGAT
* *
112971 ATCAGAAATCAAAACATAATTCAT
1 ATCAGAAATCAAAACAGAATTCAG
* * *
112995 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
113019 GTTAGGAATCAAAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
113043 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
*
113067 ACCAGAAATCA
1 ATCAGAAATCA
113078 GATAAAATAT
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:113077 original size:48 final size:48
Alignment explanation
Indices: 112973--113077 Score: 111
Period size: 48 Copynumber: 2.2 Consensus size: 48
112963 ACGGAGATAT
* * * ***
112973 CAGAAATCAAAACATAATTCATATCAGATATCAGAACAGAATCCAGGT
1 CAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCAAAC
* * * * *
113021 TAGGAATCAAAACAGATTTCAGATCAGATGTCAAAACAGAATTCAAAC
1 CAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCAAAC
113069 CAGAAATCA
1 CAGAAATCA
113078 GATAAAATAT
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (48 bp):
CAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCAAAC
Done.