Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008394.1 Hibiscus syriacus cultivar Beakdansim tig00111160_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: 259054
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:788 original size:16 final size:19
Alignment explanation
Indices: 774--811 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
764 TGATTATTTG
774 ATTA-TTATTTTATTTAGGA
1 ATTAGTTATTTTATTTA-GA
793 ATTAGTTATTTTA-TTAGA
1 ATTAGTTATTTTATTTAGA
811 A
1 A
812 CTCTTTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 7 0.39
20 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (19 bp):
ATTAGTTATTTTATTTAGA
Found at i:2396 original size:10 final size:10
Alignment explanation
Indices: 2381--2405 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2371 GGAGTGATAA
2381 TAAATATTAT
1 TAAATATTAT
2391 TAAATATTAT
1 TAAATATTAT
2401 TAAAT
1 TAAAT
2406 CATTGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAAATATTAT
Found at i:3767 original size:35 final size:34
Alignment explanation
Indices: 3708--3819 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 34
3698 AAAACATTCC
* *
3708 TCAATTTCATTATAAATCCCAAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCAAATTTCAAAATAAT
*
3743 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTTCAAAATAAT
* *
3778 TCAATTACATTCTAAACCCCAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTTC-AAAATAAT
3813 TCAATTT
1 TCAATTT
3820 AAGGAGAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
34 5 0.07
35 59 0.88
36 3 0.04
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTTCAAAATAAT
Found at i:4880 original size:35 final size:34
Alignment explanation
Indices: 4824--4936 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
4814 AAAAAAGACA
* *
4824 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
* * *
4859 GTAATTTAATTATTTTGGAATTTAGAGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
4894 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
4929 GAAATTGA
1 GAAATTGA
4937 GAATTGTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 1 0.01
35 64 0.96
36 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:10219 original size:12 final size:12
Alignment explanation
Indices: 10204--10250 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
10194 CCGGTTTTTT
*
10204 AACCGGATAAAA
1 AACCGGTTAAAA
10216 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
10231 AACCGGTTAAAA
1 AACCGGTTAAAA
10243 AACCGGTT
1 AACCGGTT
10251 TTTATCCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:12536 original size:21 final size:21
Alignment explanation
Indices: 12512--12551 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12502 TTTATTTTAT
12512 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
12533 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
12552 AACTTGAAGT
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:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:12603 original size:33 final size:33
Alignment explanation
Indices: 12546--12643 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
12536 TTTGTTTCAA
12546 TTATCGAACTT-GAAG-TTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
12577 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
12610 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
12643 T
1 T
12644 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
31 11 0.18
32 4 0.06
33 47 0.76
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:12672 original size:13 final size:13
Alignment explanation
Indices: 12629--12683 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
12619 TTGGAAGTAT
12629 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
12642 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
12656 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
12669 TTAAGTATTTGAA
1 TTAAGTATTTCAA
12682 TT
1 TT
12684 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:13105 original size:15 final size:15
Alignment explanation
Indices: 13080--13135 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
13070 ATCTGGAATA
*
13080 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
13095 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
13110 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
13127 TTAAAACCG
1 TTAAAACCG
13136 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:13144 original size:21 final size:18
Alignment explanation
Indices: 13099--13132 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13089 GTTTTTTTAT
13099 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
13116 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
13133 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:13252 original size:15 final size:17
Alignment explanation
Indices: 13226--13257 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13216 TTCTATGGGA
13226 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
13242 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
13258 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:16792 original size:21 final size:20
Alignment explanation
Indices: 16762--16801 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16752 TAAATAATTT
* *
16762 TTTATTATTATACACATATG
1 TTTATTATTAAACAAATATG
16782 TTTATTTATTAAACAAATAT
1 TTTA-TTATTAAACAAATAT
16802 AAAAATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTATTATTAAACAAATATG
Found at i:25965 original size:12 final size:13
Alignment explanation
Indices: 25945--25980 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
25935 TAATTTAATA
25945 TAAATTTAAAATT
1 TAAATTTAAAATT
*
25958 T-TATTTAAAATT
1 TAAATTTAAAATT
25970 TAAATTTAAAA
1 TAAATTTAAAA
25981 GTATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:26795 original size:24 final size:23
Alignment explanation
Indices: 26744--26799 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
26734 TACTTTTTTC
*
26744 TATTAAAAAACACTTTTTTCACA
1 TATTAAAATACACTTTTTTCACA
*
26767 CATTAAAATACACATTTTTTCA-A
1 TATTAAAATACAC-TTTTTTCACA
26790 TTATTAAAAT
1 -TATTAAAAT
26800 GTTAAATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (23 bp):
TATTAAAATACACTTTTTTCACA
Found at i:36595 original size:42 final size:42
Alignment explanation
Indices: 36549--36628 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
36539 ATTTTTTATT
*
36549 TATATATTTTA-TAGTATTATTAGTT-TTTTATTTTATTTTACA
1 TATATATGTTATTAGTATT-TTAGTTATTTTA-TTTATTTTACA
* *
36591 TATATGTGTTATTAGTATTTTATTTATTTTATTTATTT
1 TATATATGTTATTAGTATTTTAGTTATTTTATTTATTT
36629 ATTATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
42 21 0.64
43 12 0.36
ACGTcount: A:0.26, C:0.01, G:0.06, T:0.66
Consensus pattern (42 bp):
TATATATGTTATTAGTATTTTAGTTATTTTATTTATTTTACA
Found at i:36636 original size:42 final size:39
Alignment explanation
Indices: 36539--36637 Score: 96
Period size: 42 Copynumber: 2.4 Consensus size: 39
36529 TTTAATTCTA
36539 ATTT-TTTATTTATATATTTTATAGTATTATTAGTTTTTT
1 ATTTATTTA-TTATATATTTTATAGTATTATTAGTTTTTT
* *
36578 ATTTTATTT-TACATATATGTGTTATTAGTATT-TTATTTATTTT
1 A-TTTATTTAT-TATATAT-T-TTA-TAGTATTATTAGTT-TTTT
36621 ATTTATTTATTATATAT
1 ATTTATTTATTATATAT
36638 ATCTATATGC
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
39 2 0.04
40 9 0.18
41 4 0.08
42 21 0.43
43 13 0.27
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (39 bp):
ATTTATTTATTATATATTTTATAGTATTATTAGTTTTTT
Found at i:48335 original size:105 final size:105
Alignment explanation
Indices: 48150--48907 Score: 1169
Period size: 105 Copynumber: 7.2 Consensus size: 105
48140 TTTTACCCAT
48150 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
48215 AAGGGACCGCTGGTTGTCAACAAACATTTCT-CAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAG
*
48255 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
48320 AAGGGACCGCTGGTTGTCAACAAACATTTCT-CAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAG
* *
48360 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
48425 AAGGGACCGCTGGTTGTCAACAAATATTTCT-CAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAG
* ** **
48465 AGTCAATTTCAACTTCACAGTGAAGGATATTGGACTTGAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
48530 AAGGGATCGCTGGTTGTCACCAAACATTTCTCCAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
* *
48570 AGCCAATTTC-A----A-AACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
48629 AAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
*
48669 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
48734 AAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
*
48774 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
48839 AAGGGACCGCTGGTTGTCAACAAA-ATTTC-CCAGTTTAAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATT-CAG
*
48879 ACAGCACAAGTTCAACTTCACAACGAAGG
1 --AGC-CAATTTCAACTTCACAACGAAGG
48908 GGCCGCTGGC
Statistics
Matches: 611, Mismatches: 30, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
99 88 0.14
100 2 0.00
103 3 0.00
104 9 0.01
105 482 0.79
106 2 0.00
107 3 0.00
108 22 0.04
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
Found at i:48992 original size:164 final size:166
Alignment explanation
Indices: 48715--49026 Score: 425
Period size: 164 Copynumber: 1.9 Consensus size: 166
48705 CCAGACAATG
* * *
48715 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAA
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCTCCAA-TT--A-CCAA
* **
48780 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGA
62 TTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGA
*
48845 CCGCTGGTTGTCAACAAAATTTCCCAGTTTAAAGACAGCA
127 CCGCTGGCTGTCAACAAAATTTCCCAGTTTAAAGACAGCA
*
48885 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTC-CCAA-T-CCAATTT
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAAC-ATTTCTCCAATTACCAATTT
* * * * *
48947 CAACTTCACAGA-AAATGATATTGGACTCGAGACAGCTCAAGTTCAACTTCACAACGAAGGGGCC
65 CAACTTCACA-ACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACC
49011 GCTGGCTGTCAACAAA
129 GCTGGCTGTCAACAAA
49027 CAACTTCCCA
Statistics
Matches: 127, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
164 76 0.60
165 1 0.01
168 1 0.01
170 44 0.35
171 5 0.04
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (166 bp):
CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCTCCAATTACCAATTTC
AACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGC
TGGCTGTCAACAAAATTTCCCAGTTTAAAGACAGCA
Found at i:49107 original size:106 final size:106
Alignment explanation
Indices: 48940--49188 Score: 401
Period size: 106 Copynumber: 2.3 Consensus size: 106
48930 ATTTCCCAAT
** * * *
48940 CCAATTTCAACTTCACAGAAAATGATATTGGACTCGAGACAGCTCAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAA
49005 GGGGCCGCTGGCTGTCAACAAACAACTTCCCAA-TTTCAGAG
66 GGGGCCGCTGGCTGTCAACAAAC-ACTTCCCAAGTTTCAGAG
49046 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAA
* *
49111 GGGGCCGCTGGTTGTCAACAAACACTTTCCAAGTTTCAGAG
66 GGGGCCGCTGGCTGTCAACAAACACTTCCCAAGTTTCAGAG
* *
49152 TCAATTTCAACTTCACAGCGAAGGATATTGGCCTCGA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
49189 AGCAACACAA
Statistics
Matches: 133, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
105 8 0.06
106 125 0.94
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAA
GGGGCCGCTGGCTGTCAACAAACACTTCCCAAGTTTCAGAG
Found at i:50874 original size:12 final size:13
Alignment explanation
Indices: 50857--50885 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
50847 GTGTTATTAG
50857 TATTTTA-TTATT
1 TATTTTATTTATT
50869 TATTTTATTTATT
1 TATTTTATTTATT
50882 TATT
1 TATT
50886 ATATATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:50943 original size:2 final size:2
Alignment explanation
Indices: 50933--50964 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
50923 TTACAAGTTA
*
50933 AT AT TT 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
50965 TTATCTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:52537 original size:2 final size:2
Alignment explanation
Indices: 52530--52563 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
52520 CTATTGGTAA
52530 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
52564 TGATAAATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54023 original size:17 final size:17
Alignment explanation
Indices: 53996--54064 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 17
53986 AAAATAGCAT
*
53996 AAATATAAATT-TTAAA
1 AAATATTAATTATTAAA
*
54012 AGAATATTAATTATTATA
1 A-AATATTAATTATTAAA
54030 AAATATTAATGATATTATTAA
1 AAATATTAAT--TATTA--AA
*
54051 AAATATCAATTATT
1 AAATATTAATTATT
54065 GATCTATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 1 0.02
17 18 0.42
18 5 0.12
19 9 0.21
21 10 0.23
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (17 bp):
AAATATTAATTATTAAA
Found at i:54047 original size:19 final size:18
Alignment explanation
Indices: 54014--54064 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
54004 ATTTTAAAAG
54014 AATATTAATTATTA-TAA
1 AATATTAATTATTATTAA
54031 AATATTAATGATATTATTAAA
1 AATATTAAT--TATTATT-AA
*
54052 AATATCAATTATT
1 AATATTAATTATT
54065 GATCTATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 9 0.31
19 9 0.31
20 1 0.03
21 10 0.34
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
AATATTAATTATTATTAA
Found at i:54274 original size:13 final size:13
Alignment explanation
Indices: 54258--54291 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
54248 TTGAGAAGGA
54258 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
*
54271 AAAAGAAAAAAAG
1 AAAAGAGAAAAAG
54284 AAAA-AGAA
1 AAAAGAGAA
54292 GATTAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:71463 original size:3 final size:3
Alignment explanation
Indices: 71455--71487 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
71445 TTGGCGTTTA
71455 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
71488 TTAATTCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:73518 original size:17 final size:17
Alignment explanation
Indices: 73485--73537 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
73475 ATGTTATGTC
*
73485 AAAAATAATTTAAAATT-
1 AAAAAT-ATTAAAAATTG
73502 ATAAAATATTAAAAATTG
1 A-AAAATATTAAAAATTG
73520 AAAAGATATATAAAAATT
1 AAAA-ATAT-TAAAAATT
73538 CAATACTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 13 0.42
18 10 0.32
19 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (17 bp):
AAAAATATTAAAAATTG
Found at i:79650 original size:25 final size:25
Alignment explanation
Indices: 79622--79670 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
79612 AAAATAATAT
79622 TTATTTAAAATTTACGAATTAATTA
1 TTATTTAAAATTTACGAATTAATTA
79647 TTATTTAAAATTTACGAATTAATT
1 TTATTTAAAATTTACGAATTAATT
79671 GACAATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (25 bp):
TTATTTAAAATTTACGAATTAATTA
Found at i:82969 original size:59 final size:60
Alignment explanation
Indices: 82854--82969 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
82844 TGGTCTCCCG
* * * * * *
82854 ACTAAAGGACGTTTCTTTGTTGAGTCTCTTGATTATTAAAAGTTATAAAATGATCCTCCA
1 ACTAAAGGACATTACTTTGTTGAATCTCTCGACTATTAAAAGTTACAAAATGATCCTCCA
* *
82914 ACTATAGGACATTACTTTGTTGAATC-CTCGACTATT-AAAGTTTACAAAATTATCCT
1 ACTAAAGGACATTACTTTGTTGAATCTCTCGACTATTAAAAG-TTACAAAATGATCCT
82970 GCTAGTCATA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
58 4 0.09
59 21 0.45
60 22 0.47
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (60 bp):
ACTAAAGGACATTACTTTGTTGAATCTCTCGACTATTAAAAGTTACAAAATGATCCTCCA
Found at i:90156 original size:60 final size:60
Alignment explanation
Indices: 90060--90224 Score: 163
Period size: 60 Copynumber: 2.8 Consensus size: 60
90050 ATTGAAATAT
** * *** * *
90060 TCAAAAGTTTGGGGACTAATTTAGAATGATGGTCATAGTTTGGGGATGAAACTAGAATGA-
1 TCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAGGGATAAAACTAGAA-GAC
* * ** * *
90120 TCAAAAGTTTAAGGACTAGTTTAAAATGAAATTCATAAATTAAGGATAAAATTAGAAGAC
1 TCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAGGGATAAAACTAGAAGAC
* *
90180 TCAAAAG-TTAAGGACCAATTTAAAATAAAAATCATAGTTTAGGGA
1 TCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAGGGA
90225 CATATGATTC
Statistics
Matches: 84, Mismatches: 20, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
59 33 0.39
60 51 0.61
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.28
Consensus pattern (60 bp):
TCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAGGGATAAAACTAGAAGAC
Found at i:90215 original size:59 final size:60
Alignment explanation
Indices: 90103--90215 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 60
90093 CATAGTTTGG
* * * * *
90103 GGATGAAACTAGAATGATCAAAAGTTTAAGGACTAGTTTAAAATGAAATTCATAAATTAA
1 GGATAAAACTAGAATGATCAAAAGTTTAAGGACCAATTTAAAATAAAAATCATAAATTAA
*
90163 GGATAAAATTAGAA-GACTCAAAAG-TTAAGGACCAATTTAAAATAAAAATCATA
1 GGATAAAACTAGAATGA-TCAAAAGTTTAAGGACCAATTTAAAATAAAAATCATA
90216 GTTTAGGGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 27 0.59
60 19 0.41
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (60 bp):
GGATAAAACTAGAATGATCAAAAGTTTAAGGACCAATTTAAAATAAAAATCATAAATTAA
Found at i:99471 original size:24 final size:24
Alignment explanation
Indices: 99444--99506 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
99434 GAGTAGAGGG
*
99444 TCTACGCGGTCCTTCAAGATAAAT
1 TCTACGTGGTCCTTCAAGATAAAT
99468 TCTACGTGGTCCTTCAAGATAAAT
1 TCTACGTGGTCCTTCAAGATAAAT
99492 TCTACGTGGTCCTTC
1 TCTACGTGGTCCTTC
99507 GGGACGTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (24 bp):
TCTACGTGGTCCTTCAAGATAAAT
Found at i:99658 original size:23 final size:23
Alignment explanation
Indices: 99624--99709 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
99614 ACATATTATA
99624 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
99647 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * * *
99670 CAGTC-CTTCGG-GACAAATTCTATG
1 -TGGCACTACGGTG-C-AATTCTACG
99694 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
99710 ATTTATACGA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
22 1 0.02
23 32 0.65
24 15 0.31
25 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:108749 original size:33 final size:33
Alignment explanation
Indices: 108712--108774 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
108702 TGTTTAAAGT
* *
108712 TTGGCTACCAATCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
108745 TTGGCCACCAACCAAGATGAAATTTCCAAT
1 TTGGCCACCAACCAAGATGAAATTTCCAAT
108775 TTGCCAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (33 bp):
TTGGCCACCAACCAAGATGAAATTTCCAATAAG
Found at i:113491 original size:33 final size:33
Alignment explanation
Indices: 113445--113507 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
113435 TGTTCAAAGT
113445 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
* *
113478 TTGGTCACTAACCAAGATGAAATTTCCAAT
1 TTGGCCACCAACCAAGATGAAATTTCCAAT
113508 TTTCCAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (33 bp):
TTGGCCACCAACCAAGATGAAATTTCCAATAAG
Found at i:114585 original size:24 final size:24
Alignment explanation
Indices: 114541--114586 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
114531 AATTAATTAA
*
114541 TTTAAAAACAAAATAATTAAAAAT
1 TTTAAAAACAAAATAAATAAAAAT
*
114565 TTTAGAAA-AAAATAAAATAAAA
1 TTTAAAAACAAAAT-AAATAAAA
114587 TGTTAGCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (24 bp):
TTTAAAAACAAAATAAATAAAAAT
Found at i:125312 original size:23 final size:23
Alignment explanation
Indices: 125286--125331 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
125276 TCGGTACCCT
125286 CTTAGCCCCCTTAATTGACTTTC
1 CTTAGCCCCCTTAATTGACTTTC
125309 CTTAGCCCCCTTAATTGACTTTC
1 CTTAGCCCCCTTAATTGACTTTC
125332 AACAATCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.09, T:0.39
Consensus pattern (23 bp):
CTTAGCCCCCTTAATTGACTTTC
Found at i:135316 original size:24 final size:24
Alignment explanation
Indices: 135278--135347 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
135268 CAAAACAGAG
* *
135278 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
135302 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
135326 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
135348 CTATTTATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:136068 original size:29 final size:28
Alignment explanation
Indices: 136026--136099 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
136016 GTCAAACATT
*
136026 TTACACAAATAGCACCCTTTTTAAAATAA
1 TTAC-CAAATAGCACCCTTTTCAAAATAA
* *
136055 TTACCAATATAGCACCCTTTTCGAATTAA
1 TTACCAA-ATAGCACCCTTTTCAAAATAA
*
136084 TTCCCAAAATAGCACC
1 TTACC-AAATAGCACC
136100 AAAACCAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 34 0.87
30 2 0.05
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTCAAAATAA
Found at i:142310 original size:24 final size:24
Alignment explanation
Indices: 142278--142347 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
142268 CAAAACAGAG
* *
142278 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* *
142302 TCCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* *
142326 TCCAGGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
142348 CTATTTATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:143096 original size:29 final size:29
Alignment explanation
Indices: 143038--143111 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
143028 GTCAAACATT
* *
143038 TTACACAAATAGCACCTTTTTTAAAATAA
1 TTACACAAATAGCACCCTTTTCAAAATAA
* *
143067 TTAC-CAATATAGCACCCTTTTCGAATTAA
1 TTACACAA-ATAGCACCCTTTTCAAAATAA
*
143096 TT-CTCAAAATAGCACC
1 TTACAC-AAATAGCACC
143112 AAAACCAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 4 0.11
29 32 0.84
30 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.32
Consensus pattern (29 bp):
TTACACAAATAGCACCCTTTTCAAAATAA
Found at i:143164 original size:12 final size:13
Alignment explanation
Indices: 143141--143187 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 13
143131 GAATTGCATC
143141 GGTCAACGGGTCG
1 GGTCAACGGGTCG
143154 GGTCAACGGTCGGGTCG
1 GGTCAA----CGGGTCG
143171 GGTCAACGGGTCG
1 GGTCAACGGGTCG
143184 GGTC
1 GGTC
143188 GTGACCGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 17 0.57
17 13 0.43
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:143169 original size:17 final size:18
Alignment explanation
Indices: 143147--143188 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
143137 CATCGGTCAA
143147 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
143164 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
143182 CGGGTCG
1 CGGGTCG
143189 TGACCGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:144721 original size:54 final size:54
Alignment explanation
Indices: 144616--144730 Score: 121
Period size: 54 Copynumber: 2.1 Consensus size: 54
144606 ATATAAAATT
* *
144616 AATATTAAATTATTTTAAAATTTAAATTTATAATATTTATTTATCATATAA-TAA
1 AATATTAAATTATTTTAAAAATTAAA-TTATAAAATTTATTTATCATATAATTAA
*
144670 AATATTCAATTA-TTTAAAAATTAAA-TA-AAAATTATATTATATCATAAATAATTTAA
1 AATATTAAATTATTTTAAAAATTAAATTATAAAATT-TATT-TATCAT--ATAA-TTAA
144726 AATAT
1 AATAT
144731 ATTTATTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
50 5 0.10
51 6 0.12
52 6 0.12
53 12 0.23
54 15 0.29
56 8 0.15
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (54 bp):
AATATTAAATTATTTTAAAAATTAAATTATAAAATTTATTTATCATATAATTAA
Found at i:144727 original size:27 final size:26
Alignment explanation
Indices: 144697--144763 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 26
144687 AAATTAAATA
144697 AAAATTATATTATATCATAAATAATTT
1 AAAA-TATATTATATCATAAATAATTT
* * *
144724 AAAATATATT-TATTTATTAATTATTT
1 AAAATATATTATA-TCATAAATAATTT
144750 AAAA-ATAATTATAT
1 AAAATAT-ATTATAT
144764 ATGATAAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 4 0.12
26 24 0.71
27 6 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAATATATTATATCATAAATAATTT
Found at i:144796 original size:44 final size:43
Alignment explanation
Indices: 144729--144813 Score: 143
Period size: 44 Copynumber: 2.0 Consensus size: 43
144719 AATTTAAAAT
*
144729 ATATTTATTTATTAATTATTTAAAAATAATTATATATGATAAG
1 ATATATATTTATTAATTATTTAAAAATAATTATATATGATAAG
*
144772 ATATATATTTATTTAATTATTTAAAAATAATTATATGTGATA
1 ATATATATTTA-TTAATTATTTAAAAATAATTATATATGATA
144814 GAATCTACTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 10 0.26
44 29 0.74
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (43 bp):
ATATATATTTATTAATTATTTAAAAATAATTATATATGATAAG
Found at i:146336 original size:3 final size:3
Alignment explanation
Indices: 146328--146364 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
146318 TGACTATATA
146328 AAT AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
146365 GTAACAGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:151341 original size:2 final size:2
Alignment explanation
Indices: 151334--151387 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
151324 TTGTGTCATA
151334 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
151376 AT AT AT AT AT AT
1 AT AT AT AT AT AT
151388 CCATATACAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153348 original size:17 final size:17
Alignment explanation
Indices: 153308--153340 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
153298 TCTTTTAGAG
153308 AAAAAAATAATTTTTTT
1 AAAAAAATAATTTTTTT
153325 AAAAAAATAATTTTTT
1 AAAAAAATAATTTTTT
153341 AAAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAAAAATAATTTTTTT
Found at i:156538 original size:4 final size:4
Alignment explanation
Indices: 156529--156576 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
156519 TAGGGTGTAG
*
156529 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-A AT-A ATAA A-AA AGAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
156574 ATA
1 ATA
156577 TTCTTTTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
3 9 0.22
4 32 0.78
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:157521 original size:46 final size:46
Alignment explanation
Indices: 157468--157573 Score: 185
Period size: 46 Copynumber: 2.3 Consensus size: 46
157458 GCAAACCTAT
*
157468 TCTTATTATCATGAATGAAACAAACCGACTCTAAATTAAGCTATAA
1 TCTTATTATCATGAATGAAACAAACCGACCCTAAATTAAGCTATAA
* *
157514 TCTTATTATCATGAATGAAACAACCCGACCCTAAATTAAGCTATAT
1 TCTTATTATCATGAATGAAACAAACCGACCCTAAATTAAGCTATAA
157560 TCTTATTATCATGA
1 TCTTATTATCATGA
157574 CTTGTGGTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (46 bp):
TCTTATTATCATGAATGAAACAAACCGACCCTAAATTAAGCTATAA
Found at i:161042 original size:23 final size:23
Alignment explanation
Indices: 161007--161072 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
160997 CGTTGGTTGC
161007 TTTGATG-ACTGTACTGTAGCTAT
1 TTTGATGCA-TGTACTGTAGCTAT
*
161030 TTTGATGCATGTACTGTAGCTGT
1 TTTGATGCATGTACTGTAGCTAT
* *
161053 TTTGATACTTGTACTGTAGC
1 TTTGATGCATGTACTGTAGC
161073 AGTTTATTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.44
Consensus pattern (23 bp):
TTTGATGCATGTACTGTAGCTAT
Found at i:161156 original size:22 final size:22
Alignment explanation
Indices: 161117--161159 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
161107 TTATTTATCC
*
161117 ATAAAAATATTTGATTGAGTGA
1 ATAAAAATATATGATTGAGTGA
161139 ATAAAAATA-ATGACTTGAGTG
1 ATAAAAATATATGA-TTGAGTG
161160 GTTCTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (22 bp):
ATAAAAATATATGATTGAGTGA
Found at i:162208 original size:20 final size:21
Alignment explanation
Indices: 162183--162234 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
162173 TTTTCCCAAT
*
162183 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
162203 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
162224 TCGCAATGCGA
1 TCGCAATGCGA
162235 TAATACAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:162293 original size:20 final size:20
Alignment explanation
Indices: 162245--162296 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
162235 TAATACAAAA
* *
162245 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
162265 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
162285 TCGCAACGCGAT
1 TCGCAACGCGAT
162297 TTACATAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:162510 original size:22 final size:22
Alignment explanation
Indices: 162482--162525 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
162472 CACTCTCTCA
162482 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
162504 CCCATCTCTGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
162526 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:164077 original size:18 final size:18
Alignment explanation
Indices: 164056--164101 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
164046 CTCCACTTCG
* *
164056 AGAGCCATCACCTCGCCC
1 AGAGCCATCACCCCACCC
*
164074 AGAGCTATCACCCCACCC
1 AGAGCCATCACCCCACCC
164092 AGAGCCATCA
1 AGAGCCATCA
164102 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.46, G:0.15, T:0.11
Consensus pattern (18 bp):
AGAGCCATCACCCCACCC
Found at i:164866 original size:19 final size:19
Alignment explanation
Indices: 164844--164935 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
164834 GGAAATTACT
164844 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
164863 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
164877 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
164896 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
164910 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
164929 ATCGCAA
1 ATCGCAA
164936 CGAGGGAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 18 0.33
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 25 0.45
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:164886 original size:33 final size:33
Alignment explanation
Indices: 164844--164954 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
164834 GGAAATTACT
164844 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
164877 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
164909 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
164943 ATCGCAATGCGA
1 ATCGCAATGCGA
164955 TTTTCATTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 1 0.01
33 67 0.97
34 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:165101 original size:14 final size:14
Alignment explanation
Indices: 165082--165118 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
165072 CATCAATTAA
165082 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
165096 ACAAATCACCTTTT
1 ACAAATCAACTTTT
165110 ACAAATCAA
1 ACAAATCAA
165119 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:166541 original size:21 final size:21
Alignment explanation
Indices: 166475--166541 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
166465 GTGAATCGGG
*
166475 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
166495 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
166517 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
166538 CTCT
1 CTCT
166542 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:166580 original size:41 final size:41
Alignment explanation
Indices: 166514--166596 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
166504 CGATGACAGT
* * *
166514 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAG
* * *
166555 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAG
166596 G
1 G
166597 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.22
Consensus pattern (41 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAG
Found at i:168638 original size:39 final size:37
Alignment explanation
Indices: 168595--168723 Score: 131
Period size: 39 Copynumber: 3.5 Consensus size: 37
168585 TCTTTTGGTT
*
168595 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACG-GA-AATGAAAATCGCAACGC
** * * *
168634 GAAATGACTATCGCGAC---CA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGGAAATGAAAATCGCAACGC
*
168667 GAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CG-GAAATGAAAATCGCAACGC
168706 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
168724 CGTTGCGATT
Statistics
Matches: 73, Mismatches: 11, Indels: 13
0.75 0.11 0.13
Matches are distributed among these distances:
33 26 0.36
34 2 0.03
38 3 0.04
39 42 0.58
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGGAAATGAAAATCGCAACGC
Found at i:168646 original size:19 final size:19
Alignment explanation
Indices: 168595--168725 Score: 146
Period size: 19 Copynumber: 7.1 Consensus size: 19
168585 TCTTTTGGTT
*
168595 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
168614 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
168634 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
168652 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
168667 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
168687 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
168706 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
168725 G
1 G
168726 TTGCGATTAT
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.11
15 2 0.02
18 2 0.02
19 46 0.48
20 35 0.37
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:169354 original size:21 final size:22
Alignment explanation
Indices: 169330--169421 Score: 65
Period size: 20 Copynumber: 4.5 Consensus size: 22
169320 AAGTATCTTG
169330 TTGCGATTTTGT-ATTATCGCA
1 TTGCGATTTTGTAATTATCGCA
* *
169351 TTGCGA--TAGTAAGTATCGCA
1 TTGCGATTTTGTAATTATCGCA
* *
169371 TTGCGATTTTCTCAA-T-TCGCG
1 TTGCGATTTTGT-AATTATCGCA
*
169392 TTGCGA--TT-TACTTATTCGCA
1 TTGCGATTTTGTAATTA-TCGCA
169412 TTGCGATTTT
1 TTGCGATTTT
169422 CCCAATTCGC
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
17 1 0.02
18 2 0.04
19 5 0.09
20 24 0.44
21 16 0.29
22 5 0.09
23 2 0.04
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (22 bp):
TTGCGATTTTGTAATTATCGCA
Found at i:169377 original size:20 final size:20
Alignment explanation
Indices: 169284--169377 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
169274 CGCTATGTAA
* *
169284 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
169304 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
** * *
169324 ATCTTGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
169345 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
169365 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
169378 TTTCTCAATT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.73
21 11 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:169396 original size:41 final size:41
Alignment explanation
Indices: 169305--169439 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
169295 AAAGTCAGTA
* *** * *
169305 TCGCGTTGCGAAAGTAAGTATCTTGTTGCGATTTTGT-ATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
*
169345 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* ** *
169387 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCTCAAT
169428 TCGCGTTGCGAT
1 TCGCGTTGCGAT
169440 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:169410 original size:20 final size:20
Alignment explanation
Indices: 169366--169458 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
169356 ATAGTAAGTA
*
169366 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
169387 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
169407 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTAAT
* *
169428 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
169448 TCGCATTGCGA
1 TCGCATTGCGA
169459 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:169440 original size:41 final size:41
Alignment explanation
Indices: 169366--169458 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
169356 ATAGTAAGTA
*
169366 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
169407 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
169448 TCGCATTGCGA
1 TCGCATTGCGA
169459 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:170696 original size:17 final size:17
Alignment explanation
Indices: 170674--170707 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
170664 TTGTTAATAT
170674 ATAAATTGT-TTTATTTA
1 ATAAATT-TATTTATTTA
170691 ATAAATTTATTTATTTA
1 ATAAATTTATTTATTTA
170708 TAGTTTCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATAAATTTATTTATTTA
Found at i:172472 original size:5 final size:5
Alignment explanation
Indices: 172462--172527 Score: 132
Period size: 5 Copynumber: 13.2 Consensus size: 5
172452 GTATTTTCTC
172462 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
172512 ATTAT ATTAT ATTAT A
1 ATTAT ATTAT ATTAT A
172528 GGGCAAACTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 61 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:189884 original size:28 final size:28
Alignment explanation
Indices: 189829--189884 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
189819 TCAACATATA
* *
189829 TTTTAATATTTTAATAATTGATTTTAAT
1 TTTTAATATTTTAATAATTGAATATAAT
*
189857 TTTTTATATTTTAATTAATT-AATATAAT
1 TTTTAATATTTTAA-TAATTGAATATAAT
189885 ATGCGTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTAATATTTTAATAATTGAATATAAT
Found at i:192943 original size:23 final size:23
Alignment explanation
Indices: 192900--192975 Score: 145
Period size: 23 Copynumber: 3.3 Consensus size: 23
192890 TTAAATTCAT
192900 AAAATTTATATAA-TTTTTTTAC
1 AAAATTTATATAATTTTTTTTAC
192922 AAAATTTATATAATTTTTTTTAC
1 AAAATTTATATAATTTTTTTTAC
192945 AAAATTTATATAATTTTTTTTAC
1 AAAATTTATATAATTTTTTTTAC
192968 AAAATTTA
1 AAAATTTA
192976 AAAGATAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 13 0.25
23 40 0.75
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
AAAATTTATATAATTTTTTTTAC
Found at i:203418 original size:11 final size:11
Alignment explanation
Indices: 203395--203426 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
203385 TGTAATTAAT
203395 TATTTATATATA
1 TATTTA-ATATA
203407 TATTTAATATA
1 TATTTAATATA
203418 TATTTAATA
1 TATTTAATA
203427 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:203430 original size:3 final size:3
Alignment explanation
Indices: 203422--203486 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
203412 AATATATATT
*
203422 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
203470 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
203487 TGGATAAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:204492 original size:113 final size:113
Alignment explanation
Indices: 203623--204489 Score: 1202
Period size: 113 Copynumber: 7.6 Consensus size: 113
203613 ATTGAATAAA
* * * * * * *
203623 TTCTTCTCTCTCTCCAGATGAGTTCTTCTTATTATGAACTTTTTGCTGTG-GATGATGATCCATC
1 TTCTTC-CT-TCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTG-GAAAAGATAATCCATC
* * *
203687 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTC
62 AAATGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * * * *
203739 TTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATC
1 TTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCCATC
* * *
203803 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTC
62 AAATGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
*
203855 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAATT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAA-A
**
203920 TGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
65 TGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
*
203969 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAATT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAA-A
**
204034 TGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
65 TGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * *
204083 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAAT
* *
204148 GATAGAATT-AGGCAGAAGGTTGAACAAATTCTTCTCATTATGAATTTC
66 GAT-GAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * *
204196 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATAATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAAT
* * *
204261 GATGAATTCAGGTAACAGGTTGAACAAATTCTTCTCATTATGAATTTC
66 GATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * * *
204309 TTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAAT
* *
204374 GATAGAATT-AGGCAGAAGGTTGAACAAATTCTTCTCATTATGAATTTC
66 GAT-GAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * *
204422 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTAATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAAT
204487 GAT
66 GAT
204490 AGATTTGAAT
Statistics
Matches: 695, Mismatches: 46, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
112 8 0.01
113 337 0.48
114 237 0.34
115 3 0.00
116 90 0.13
117 19 0.03
118 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAAAT
GATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
Found at i:205277 original size:83 final size:83
Alignment explanation
Indices: 205138--205450 Score: 529
Period size: 83 Copynumber: 3.8 Consensus size: 83
205128 GTAGTTCTTA
* *
205138 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTTCAA
205203 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
205221 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTTCAA
205286 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * * *
205304 CTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAAAAATTCATC-TTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTTC-A
205368 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
*
205387 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTTCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTTCA
205451 GTTAATGTTT
Statistics
Matches: 215, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
82 2 0.01
83 210 0.98
84 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTTCAA
ATTCAATGATTGGTTCTG
Found at i:206553 original size:9 final size:9
Alignment explanation
Indices: 206539--206590 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
206529 ACCTTGACCC
206539 CTCTTTTTT
1 CTCTTTTTT
206548 CTCTTTTTTT
1 CTC-TTTTTT
*
206558 CTTTTTTTT
1 CTCTTTTTT
*
206567 TTCTTTTTTT
1 CTC-TTTTTT
*
206577 TTCTTTTTT
1 CTCTTTTTT
*
206586 TTCTT
1 CTCTT
206591 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 21 0.55
10 17 0.45
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
CTCTTTTTT
Found at i:206565 original size:11 final size:10
Alignment explanation
Indices: 206542--206587 Score: 74
Period size: 10 Copynumber: 4.5 Consensus size: 10
206532 TTGACCCCTC
*
206542 TTTTTTCTCT
1 TTTTTTCTTT
206552 TTTTTTCTTTT
1 TTTTTTC-TTT
206563 TTTTTTCTTT
1 TTTTTTCTTT
206573 TTTTTTCTTT
1 TTTTTTCTTT
206583 TTTTT
1 TTTTT
206588 CTTCAAGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:206568 original size:21 final size:21
Alignment explanation
Indices: 206542--206587 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
206532 TTGACCCCTC
206542 TTTTTTCTCTTTTTTTCTTTT
1 TTTTTTCTCTTTTTTTCTTTT
*
206563 TTTTTTCTTTTTTTTTCTTTT
1 TTTTTTCTCTTTTTTTCTTTT
206584 TTTT
1 TTTT
206588 CTTCAAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (21 bp):
TTTTTTCTCTTTTTTTCTTTT
Found at i:217272 original size:18 final size:17
Alignment explanation
Indices: 217226--217275 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
217216 AAATACTTGC
*
217226 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
217244 AAATATTATAAAAAATAAT
1 AAATA-AATAAAAAAT-AT
217263 AAATAAATAAAAA
1 AAATAAATAAAAA
217276 TTTTGAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 19 0.70
19 7 0.26
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:219354 original size:11 final size:11
Alignment explanation
Indices: 219331--219362 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
219321 TGTAATTAAT
219331 TATTTATATATA
1 TATTTA-ATATA
219343 TATTTAATATA
1 TATTTAATATA
219354 TATTTAATA
1 TATTTAATA
219363 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:219366 original size:3 final size:3
Alignment explanation
Indices: 219358--219434 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
219348 AATATATATT
*
219358 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
219406 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
219435 TGGATAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:229221 original size:13 final size:14
Alignment explanation
Indices: 229182--229238 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 14
229172 ATATTTGTAT
229182 TTAGTACTTTTTTA
1 TTAGTACTTTTTTA
* *
229196 TT-GTAGTTGTTTA
1 TTAGTACTTTTTTA
229209 TTAG-ACTTTTTTA
1 TTAGTACTTTTTTA
*
229222 TT-GTAATTTTTTTA
1 TTAGT-ACTTTTTTA
229236 TTA
1 TTA
229239 TTTATTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 1 0.03
13 20 0.59
14 13 0.38
ACGTcount: A:0.21, C:0.04, G:0.11, T:0.65
Consensus pattern (14 bp):
TTAGTACTTTTTTA
Found at i:229238 original size:27 final size:27
Alignment explanation
Indices: 229163--229226 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
229153 AGATTTTATT
* * *
229163 TTTTTTATTATATTTGTAT-TTAGTAC
1 TTTTTTATTGTAGTTGTTTATTAGTAC
229189 TTTTTTATTGTAGTTGTTTATTAG-AC
1 TTTTTTATTGTAGTTGTTTATTAGTAC
229215 TTTTTTATTGTA
1 TTTTTTATTGTA
229227 ATTTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 30 0.88
27 4 0.12
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (27 bp):
TTTTTTATTGTAGTTGTTTATTAGTAC
Found at i:230283 original size:14 final size:15
Alignment explanation
Indices: 230249--230287 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
230239 TCATATAATC
230249 ATAATAAACAATAAGT
1 ATAATAAA-AATAAGT
*
230265 ATAATAAAAA-AATT
1 ATAATAAAAATAAGT
230279 ATAATAAAA
1 ATAATAAAA
230288 TTACCTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 2 0.09
16 8 0.36
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAATAAAAATAAGT
Found at i:233498 original size:21 final size:21
Alignment explanation
Indices: 233472--233524 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
233462 AACCGTTAGA
* **
233472 TGTTGACGTGATATTTTACGG
1 TGTTGACATGATAGCTTACGG
*
233493 TGTTGATATGATAGCTTACGG
1 TGTTGACATGATAGCTTACGG
*
233514 TGTTAACATGA
1 TGTTGACATGA
233525 CGATCCGCGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (21 bp):
TGTTGACATGATAGCTTACGG
Found at i:236692 original size:31 final size:31
Alignment explanation
Indices: 236622--236692 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
236612 ATTATTTTTT
* *
236622 AATTT-ACCTCTAAATTCTAGATAAAATATT
1 AATTTAACCCCTAAATTCTAGATAAAATATC
* *
236652 AACTAAACCCCTAAACTT-TAGATAAAATATC
1 AATTTAACCCCTAAA-TTCTAGATAAAATATC
236683 AATTTAACCC
1 AATTTAACCC
236693 TTTAACTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 3 0.09
31 28 0.85
32 2 0.06
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (31 bp):
AATTTAACCCCTAAATTCTAGATAAAATATC
Found at i:243965 original size:14 final size:14
Alignment explanation
Indices: 243936--243981 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
243926 TTTTAAAATT
243936 TTTATTTAA-A-AA
1 TTTATTTAATATAA
243948 -TTATTTAATGAT-A
1 TTTATTTAAT-ATAA
243961 TTTATTTAATATAA
1 TTTATTTAATATAA
243975 TTTATTT
1 TTTATTT
243982 TTATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 8 0.28
13 4 0.14
14 17 0.59
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TTTATTTAATATAA
Found at i:245218 original size:21 final size:22
Alignment explanation
Indices: 245189--245236 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
245179 AGAATTATTA
* *
245189 TAATATTTTAAAATTAAT-AAT
1 TAATTTTTTAAAATAAATAAAT
*
245210 TAATTTTTTATAATAAATAAAT
1 TAATTTTTTAAAATAAATAAAT
245232 TAATT
1 TAATT
245237 ATTATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTTTTTAAAATAAATAAAT
Found at i:245241 original size:21 final size:22
Alignment explanation
Indices: 245207--245252 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
245197 TAAAATTAAT
*
245207 AATTAATTTTTTATAATAAATA
1 AATTAATTTATTATAATAAATA
*
245229 AATTAA-TTATTATATTAAATA
1 AATTAATTTATTATAATAAATA
245250 AAT
1 AAT
245253 ATCATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTAATTTATTATAATAAATA
Found at i:251091 original size:16 final size:16
Alignment explanation
Indices: 251070--251103 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
251060 TTACTATTCA
*
251070 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
251086 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
251102 CG
1 CG
251104 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:251874 original size:15 final size:16
Alignment explanation
Indices: 251854--251885 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
251844 TGGCAGATCC
251854 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
251869 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
251885 A
1 A
251886 GAAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:258109 original size:12 final size:12
Alignment explanation
Indices: 258092--258116 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
258082 CAAATTAAAG
258092 ATATATATACAT
1 ATATATATACAT
258104 ATATATATACAT
1 ATATATATACAT
258116 A
1 A
258117 CAGTTGGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATACAT
Done.