Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2841
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: 84759
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:12913 original size:41 final size:40
Alignment explanation
Indices: 12811--12968 Score: 190
Period size: 40 Copynumber: 3.9 Consensus size: 40
12801 CGTTTGTGGA
* * *
12811 AAAAAACGCTGCTATTGCTTTACCTTTAACGGCGTTTATG
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* *
12851 AAAAAATGCCGCTGTTGCTTTACCTTTTGCGGCGTTTATG
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* * * *
12891 AGAAAAATGCCACTATTACTTTACTTTTTACGGCGTTTACG
1 A-AAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* * * *
12932 CAAAAACGCTGCTAATGCTTTACCTTTTACGGCGTTT
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTT
12969 TCTATCCAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 66 0.67
41 33 0.33
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (40 bp):
AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
Found at i:12937 original size:81 final size:82
Alignment explanation
Indices: 12794--12968 Score: 208
Period size: 81 Copynumber: 2.1 Consensus size: 82
12784 TAAAAAAATA
* ** * * *
12794 TTTGCGGCGTTTGTGGAAAAAAACGCTGCTATTGCTTTACCTTTAACGGCGTTTATGAAAAAATG
1 TTTGCGGCGTTTATGGAAAAAAACGCCACTATTACTTTACCTTTAACGGCGTTTACGAAAAAACG
**
12859 CCGCTGTTGCTTTACCT
66 CCGCTAATGCTTTACCT
* * * * *
12876 TTTGCGGCGTTTAT-GAGAAAAATGCCACTATTACTTTACTTTTTACGGCGTTTACGCAAAAACG
1 TTTGCGGCGTTTATGGAAAAAAACGCCACTATTACTTTACCTTTAACGGCGTTTACGAAAAAACG
*
12940 CTGCTAATGCTTTACCT
66 CCGCTAATGCTTTACCT
*
12957 TTTACGGCGTTT
1 TTTGCGGCGTTT
12969 TCTATCCAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
81 65 0.83
82 13 0.17
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (82 bp):
TTTGCGGCGTTTATGGAAAAAAACGCCACTATTACTTTACCTTTAACGGCGTTTACGAAAAAACG
CCGCTAATGCTTTACCT
Found at i:16988 original size:15 final size:13
Alignment explanation
Indices: 16977--17009 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16967 GTGTGTGATG
16977 TGAATATATGTGT
1 TGAATATATGTGT
*
16990 TGAATATATG-AT
1 TGAATATATGTGT
17002 TGAATATA
1 TGAATATA
17010 CCTTGTGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
TGAATATATGTGT
Found at i:17898 original size:13 final size:13
Alignment explanation
Indices: 17875--17927 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
17865 AATTAAGGCA
*
17875 GTTCACGATAGGG
1 GTTCACCATAGGG
*
17888 GTTCGCCATAGGTG
1 GTTCACCATAGG-G
*
17902 AGTTCACGATAGGG
1 -GTTCACCATAGGG
17916 GTTCACCATAGG
1 GTTCACCATAGG
17928 TGAGTTTGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 21 0.64
14 2 0.06
15 10 0.30
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (13 bp):
GTTCACCATAGGG
Found at i:17914 original size:28 final size:28
Alignment explanation
Indices: 17874--17933 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
17864 GAATTAAGGC
*
17874 AGTTCACGATAGGGGTTCGCCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
17902 AGTTCACGATAGGGGTTCACCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
17930 AGTT
1 AGTT
17934 TGCCATAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (28 bp):
AGTTCACGATAGGGGTTCACCATAGGTG
Found at i:17945 original size:28 final size:28
Alignment explanation
Indices: 17886--17964 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
17876 TTCACGATAG
* * * *
17886 GGGTTCGCCATAGGTGAGTTCACGATAG
1 GGGTTCACCATAGGTGAGTTTACCATAA
*
17914 GGGTTCACCATAGGTGAGTTTGCCATAA
1 GGGTTCACCATAGGTGAGTTTACCATAA
*
17942 GGGTT-ACTCATATGTGAGTTTAC
1 GGGTTCAC-CATAGGTGAGTTTAC
17965 TAGACATAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.05
28 41 0.95
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
GGGTTCACCATAGGTGAGTTTACCATAA
Found at i:27904 original size:18 final size:19
Alignment explanation
Indices: 27867--27903 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
27857 TTTAAAAAAA
27867 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
27885 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
27904 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:27909 original size:18 final size:21
Alignment explanation
Indices: 27872--27914 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 21
27862 AAAAATATAA
*
27872 ATTTTAGAATTTTTATAAA-T
1 ATTTTAGAATTTTTAAAAATT
27892 ATTTT-GAA-TTTTAAAAATT
1 ATTTTAGAATTTTTAAAAATT
27911 ATTT
1 ATTT
27915 AAAATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTTTAGAATTTTTAAAAATT
Found at i:33122 original size:21 final size:21
Alignment explanation
Indices: 33093--33133 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33083 GATACTTGGT
33093 AAAAGGTATAGATACTTTTTG
1 AAAAGGTATAGATACTTTTTG
* *
33114 AAAATGTATTGATACTTTTT
1 AAAAGGTATAGATACTTTTT
33134 ATCATTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (21 bp):
AAAAGGTATAGATACTTTTTG
Found at i:38819 original size:11 final size:11
Alignment explanation
Indices: 38797--38854 Score: 80
Period size: 11 Copynumber: 5.2 Consensus size: 11
38787 AACTAATCCT
38797 CTCTCAAATTTC
1 CTCTC-AATTTC
38809 CTCTCAATTTC
1 CTCTCAATTTC
*
38820 CTCTAAATTTC
1 CTCTCAATTTC
*
38831 CTCTCAATTTG
1 CTCTCAATTTC
*
38842 CTCTCAAATTC
1 CTCTCAATTTC
38853 CT
1 CT
38855 TCCAAATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 36 0.88
12 5 0.12
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:38854 original size:22 final size:23
Alignment explanation
Indices: 38797--38851 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
38787 AACTAATCCT
38797 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
38820 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
38842 CTCTCAAATT
1 CTCTCAAATT
38852 CCTTCCAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.44
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:38862 original size:34 final size:34
Alignment explanation
Indices: 38797--38872 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
38787 AACTAATCCT
* *
38797 CTCTCAAATTTCCTCTCAATTTCCTCTAAATTTC
1 CTCTCAAATTTCCTCTCAAATTCCTCCAAATTTC
*
38831 CTCTC-AATTTGCTCTCAAATTCCTTCCAAATTT-
1 CTCTCAAATTTCCTCTCAAATTCC-TCCAAATTTC
*
38864 CTCTGAAAT
1 CTCTCAAAT
38873 CCATATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.25, C:0.30, G:0.03, T:0.42
Consensus pattern (34 bp):
CTCTCAAATTTCCTCTCAAATTCCTCCAAATTTC
Found at i:38867 original size:22 final size:22
Alignment explanation
Indices: 38796--38872 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
38786 AAACTAATCC
38796 TCTCTCAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
38818 TC-CTCTAAATTTCCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
38840 TGCTCTCAAA-TTCCT-TCCAAATT
1 T-CTCTCAAATTTCCTCT-C-AATT
*
38863 TCTCTGAAAT
1 TCTCTCAAAT
38873 CCATATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
21 4 0.08
22 32 0.67
23 9 0.19
24 3 0.06
ACGTcount: A:0.25, C:0.30, G:0.03, T:0.43
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:38890 original size:51 final size:51
Alignment explanation
Indices: 38832--38931 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
38822 CTAAATTTCC
38832 TCTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTGAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTCT-CAAATTTCTCTGAAATCCATATTTAA
* * * *
38883 TCTCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTGAAATCCATATTT
38932 TTAAATAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.44
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTGAAATCCATATTTAA
Found at i:40087 original size:7 final size:7
Alignment explanation
Indices: 40075--40100 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40065 TAGTCTATTG
40075 GTATTTA
1 GTATTTA
40082 GTATTTA
1 GTATTTA
40089 GTATTTA
1 GTATTTA
40096 GTATT
1 GTATT
40101 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:41535 original size:128 final size:129
Alignment explanation
Indices: 41303--41691 Score: 525
Period size: 128 Copynumber: 3.0 Consensus size: 129
41293 TTTAATTGAC
* * * *
41303 AAACCTTAAACCCTTAACCTAAAAACCCTAACCCTAAACCTTAAAACTCCTAACTCTTAAATTAA
1 AAACCTTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTTAAAAC-CCTAACCCTTAACTT-A
* * *
41368 AAACCCTAAACCCTTAACTTAAAAATCATAAA-CTCTTAACCTAAAAACCCTAACTCCTTAACTT
64 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCT-TTAACTTAAAAACCCTAACTCCTTAACTT
41432 AA
128 AA
* * *
41434 AAACCTTAAACCCTTAAATTAAAAACTCTAAACCCTTAA-CTTAAAACCCTACCCCTTAACTT-A
1 AAACCTTAAACCCTTAACTTAAAAACCCT-AACCCTTAACCTTAAAACCCTAACCCTTAACTTAA
* **
41497 AACCCTAAACCTTTAACTTAAAAACCCTAAACCTTTAACTTAAAAACTTTAA-TCCCTTAACTTA
65 AACCCTAAACCCTTAACTTAAAAACCCTAAACCTTTAACTTAAAAACCCTAACT-CCTTAACTTA
41561 A
129 A
* * *
41562 AAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAATCCTAACCCTTAACTTAAA
1 AAACCTTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTTAAAACCCTAACCCTTAACTTAAA
* * * *
41627 ACCCTAACCCCTTAACTTAAAAACCCTAACCCCTTAACTTAAAAACCCTAACCCCTTAACTTAA
66 ACCCTAAACCCTTAACTTAAAAACCCTAAACCTTTAACTTAAAAACCCTAACTCCTTAACTTAA
41691 A
1 A
41692 GACCCTAACC
Statistics
Matches: 226, Mismatches: 26, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
127 10 0.04
128 101 0.45
129 61 0.27
130 12 0.05
131 34 0.15
132 8 0.04
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (129 bp):
AAACCTTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTTAAAACCCTAACCCTTAACTTAAA
ACCCTAAACCCTTAACTTAAAAACCCTAAACCTTTAACTTAAAAACCCTAACTCCTTAACTTAA
Found at i:41701 original size:22 final size:22
Alignment explanation
Indices: 41303--41699 Score: 474
Period size: 22 Copynumber: 18.4 Consensus size: 22
41293 TTTAATTGAC
* *
41303 AAACCTTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
41325 AAACCCT-AACCCTAAACCTT-A
1 AAACCCTAAACCCTTAA-CTTAA
* *
41346 AAACTCCT-AACTCTTAAATTAA
1 AAAC-CCTAAACCCTTAACTTAA
41368 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* * * *
41390 AAATCATAAACTCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
41412 AAACCCT-AACTCCTTAACTTAA
1 AAACCCTAAAC-CCTTAACTTAA
* *
41434 AAACCTTAAACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
*
41456 AAACTCTAAACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAA
*
41477 AAACCCT-ACCCCTTAACTT--
1 AAACCCTAAACCCTTAACTTAA
*
41496 AAACCCTAAACCTTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
41518 AAACCCTAAACCTTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
** *
41540 AAACTTTAATCCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
41562 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
41584 AAACCCT-AACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
41605 AAATCCT-AACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAA
*
41625 AAACCCTAACCCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
41647 AAACCCTAACCCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
41669 AAACCCTAACCCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
41691 AGACCCTAA
1 AAACCCTAA
41700 CCTGTAACAC
Statistics
Matches: 326, Mismatches: 38, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
19 7 0.02
20 28 0.09
21 69 0.21
22 219 0.67
23 3 0.01
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.25
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:42121 original size:46 final size:46
Alignment explanation
Indices: 42054--42284 Score: 390
Period size: 46 Copynumber: 5.0 Consensus size: 46
42044 ACATTGCTAT
*
42054 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
42100 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
42146 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTAAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* *
42192 AACTCAGTATGGTTTTTTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* *
42238 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
42284 A
1 A
42285 CTTTGCCATA
Statistics
Matches: 173, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 173 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:44776 original size:21 final size:21
Alignment explanation
Indices: 44740--44900 Score: 180
Period size: 21 Copynumber: 7.6 Consensus size: 21
44730 ATTACATAAC
*
44740 CCCTTAACTT-AAAACCCTAG
1 CCCTTAACTTAAAAACCCTAA
44760 CCCTTAACTTAAAAACCCTAAA
1 CCCTTAACTTAAAAACCCT-AA
* * *
44782 CCCTTAATTTTAAAACCGTAA
1 CCCTTAACTTAAAAACCCTAA
* * *
44803 CCCTTAAATTAAGAACCATAAA
1 CCCTTAACTTAAAAACCCT-AA
* * *
44825 CCCTTAACTTTAAAATCGTAA
1 CCCTTAACTTAAAAACCCTAA
* *
44846 CCCTTAAATAAAAAACCCTAA
1 CCCTTAACTTAAAAACCCTAA
*
44867 CACTTAACTTAAAAACCCTAA
1 CCCTTAACTTAAAAACCCTAA
44888 CCCTTAACTTAAA
1 CCCTTAACTTAAA
44901 TATAATTTGA
Statistics
Matches: 116, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
20 10 0.09
21 73 0.63
22 33 0.28
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.26
Consensus pattern (21 bp):
CCCTTAACTTAAAAACCCTAA
Found at i:44798 original size:43 final size:43
Alignment explanation
Indices: 44740--44900 Score: 200
Period size: 43 Copynumber: 3.8 Consensus size: 43
44730 ATTACATAAC
* *
44740 CCCTTAAC-TTAAAACCCTAGCCCTTAACTTAAAAACCCTAAA
1 CCCTTAACTTTAAAACCCTAACCCTTAAATTAAAAACCCTAAA
* * * *
44782 CCCTTAATTTTAAAACCGTAACCCTTAAATTAAGAACCATAAA
1 CCCTTAACTTTAAAACCCTAACCCTTAAATTAAAAACCCTAAA
* * *
44825 CCCTTAACTTTAAAATCGTAACCCTTAAATAAAAAACCCT-AA
1 CCCTTAACTTTAAAACCCTAACCCTTAAATTAAAAACCCTAAA
* * *
44867 CACTTAACTTAAAAACCCTAACCCTTAACTTAAA
1 CCCTTAACTTTAAAACCCTAACCCTTAAATTAAA
44901 TATAATTTGA
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 37 0.37
43 64 0.63
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.26
Consensus pattern (43 bp):
CCCTTAACTTTAAAACCCTAACCCTTAAATTAAAAACCCTAAA
Found at i:44882 original size:85 final size:85
Alignment explanation
Indices: 44734--44899 Score: 217
Period size: 85 Copynumber: 2.0 Consensus size: 85
44724 CGGGCTATTA
* * * * * * *
44734 CATAACCCCTTAACTTAAAACCCTAGCCCTTAACTTAAAAACCCTAAACCCTTAATTTTAAAACC
1 CATAAACCCTTAACTTAAAACCCTAACCCTTAAATAAAAAACCCTAAACACTTAACTTAAAAACC
*
44799 GTAACCCTTAAATTAAGAAC
66 CTAACCCTTAAATTAAGAAC
* *
44819 CATAAACCCTTAACTTTAAAATCGTAACCCTTAAATAAAAAACCCT-AACACTTAACTTAAAAAC
1 CATAAACCCTTAAC-TTAAAACCCTAACCCTTAAATAAAAAACCCTAAACACTTAACTTAAAAAC
*
44883 CCTAACCCTTAACTTAA
65 CCTAACCCTTAAATTAA
44900 ATATAATTTG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
85 43 0.62
86 26 0.38
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.26
Consensus pattern (85 bp):
CATAAACCCTTAACTTAAAACCCTAACCCTTAAATAAAAAACCCTAAACACTTAACTTAAAAACC
CTAACCCTTAAATTAAGAAC
Found at i:48083 original size:27 final size:27
Alignment explanation
Indices: 48052--48229 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
48042 TAAATTGTAC
48052 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
48079 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
48105 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
48133 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
48161 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
48188 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
48215 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
48230 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:48166 original size:82 final size:81
Alignment explanation
Indices: 48053--48208 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
48043 AAATTGTACA
* *
48053 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
48117 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
48134 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
48199 TGCGAGTTGA
65 TGCGAATTGA
48209 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:48220 original size:82 final size:81
Alignment explanation
Indices: 48049--48229 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
48039 GATTAAATTG
* *
48049 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
48114 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
48130 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
48194 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
48212 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
48230 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:56249 original size:27 final size:27
Alignment explanation
Indices: 56218--56395 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
56208 TAAATTGTAC
56218 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
56245 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
56271 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
56299 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
56327 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
56354 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
56381 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
56396 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:56332 original size:82 final size:81
Alignment explanation
Indices: 56219--56374 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
56209 AAATTGTACA
* *
56219 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
56283 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
56300 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
56365 TGCGAGTTGA
65 TGCGAATTGA
56375 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:56386 original size:82 final size:81
Alignment explanation
Indices: 56215--56395 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
56205 GATTAAATTG
* *
56215 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
56280 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
56296 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
56360 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
56378 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
56396 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:60877 original size:27 final size:27
Alignment explanation
Indices: 60846--61023 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
60836 TAAATTGTAC
60846 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
60873 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
60899 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
60927 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
60955 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
60982 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
61009 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
61024 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:60960 original size:82 final size:81
Alignment explanation
Indices: 60847--61002 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
60837 AAATTGTACA
* *
60847 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
60911 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
60928 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
60993 TGCGAGTTGA
65 TGCGAATTGA
61003 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:61014 original size:82 final size:81
Alignment explanation
Indices: 60843--61023 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
60833 GATTAAATTG
* *
60843 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
60908 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
60924 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
60988 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
61006 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
61024 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:63317 original size:40 final size:40
Alignment explanation
Indices: 62981--63308 Score: 566
Period size: 40 Copynumber: 8.2 Consensus size: 40
62971 GTTATATAGT
62981 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
63021 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
* *
63061 CGGGCTAAGTTCCGAAGAGCATTTGTGCTAGTGATGTATT
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
* *
63101 CGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATGTGTC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
*
63141 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
*
63181 CGGGCTAAGTTCCGAAGAGCATTCGGGCTAGTGATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
* *
63221 CGGGCTAAGTTCCGAAGAGCATTCGCGCTAGTAATGTATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
*
63261 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATC
1 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
*
63301 CAGGCTAA
1 CGGGCTAA
63309 ACCTCGAAGG
Statistics
Matches: 271, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 271 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
Found at i:63421 original size:29 final size:28
Alignment explanation
Indices: 63340--63435 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 28
63330 GAGTTATGAG
* * * *
63340 GCACTGTGTGTGCAAGTTCTTCAACTGA
1 GCACTATGTGTGCGAGTTCTTTAATTGA
**
63368 GCACTATGTGTGCGAGATT-GGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTTAATTGA
*
63396 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTCTTTAATTGA
*
63425 GCGCTATGTGT
1 GCACTATGTGT
63436 ACGAAATCAG
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
28 31 0.56
29 24 0.44
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTATGTGTGCGAGTTCTTTAATTGA
Found at i:66907 original size:48 final size:48
Alignment explanation
Indices: 66692--66904 Score: 363
Period size: 48 Copynumber: 4.4 Consensus size: 48
66682 TATATATGTG
66692 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
66740 TGTGGTAAAGCCGAATGGTTAATGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
** *
66788 TGCAGTAAAGCCGAATGGCTAATATGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
* *
66836 TGTGGTAAAGCCGAATGGCTAGTGTGAACTATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
*
66884 TGTGGTAAAGCCAAATGGCTA
1 TGTGGTAAAGCCGAATGGCTA
66905 GTGATTCGGC
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 154 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATA
Found at i:69800 original size:56 final size:54
Alignment explanation
Indices: 69740--69891 Score: 225
Period size: 56 Copynumber: 2.8 Consensus size: 54
69730 TCCCAGACAG
*
69740 GGTCTTACTCGCACACATATATCGAAGTCACATATCAATGCCAACATATAAAACGT
1 GGTCTTACTCGCACACATATATCGAAGTCACATATCGATGCCAACATAT-AAA-GT
* *
69796 GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATAAAGT
1 GGTCTTACTCGCACACATATATCGAAGTCACATATCGATGCCAACATATAAAGT
* *
69850 GGTCTTACTCGCATACATATATTAGAA-TCACATATCGATGCC
1 GGTCTTACTCGCACACATATA-TCGAAGTCACATATCGATGCC
69892 TCATATACAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
54 37 0.42
55 6 0.07
56 46 0.52
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (54 bp):
GGTCTTACTCGCACACATATATCGAAGTCACATATCGATGCCAACATATAAAGT
Found at i:78091 original size:40 final size:40
Alignment explanation
Indices: 78046--78189 Score: 216
Period size: 40 Copynumber: 3.6 Consensus size: 40
78036 CTTGCGCAAG
* * * * *
78046 GCCTTCGAGTCTTAGCCCGGATGTGGTCTCTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
*
78086 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
* *
78126 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
78166 GCCTTCGGGTCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
78190 CATTCGAATA
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCGCTAGCACAAAT
Done.