Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_40 ID=scaffold_40-JGI_221_v2.0
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: 26313
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 300 characters in sequence are not A, C, G, or T
Found at i:3531 original size:153 final size:150
Alignment explanation
Indices: 3326--3599 Score: 431
Period size: 152 Copynumber: 1.8 Consensus size: 150
3316 AATTTTTAAT
* * *
3326 TAATTAAATGTCATACTTTATTTTGTTGAGTAAATTTATATGTAGAATTTGTAAATCAAGTATTG
1 TAATTAAATGTAATACTTTATTTTGTTGAATAAATTTATATGTAGAATTTGTAAA-CAAGTATTA
*
3391 ATTTATCTGTCTATAAGAAAAATATTAATTTGACTTAAAGTTAAAGTCTTGCCTCTACCTCATCT
65 ATTTATCTATCTATAAGAAAAATATTAATTTGAC-TAAAGTTAAAGTCTTGCCTCTACCTCATCT
3456 TTTTTTTTTCCCCCTAGAGTGC
129 TTTTTTTTTCCCCCTAGAGTGC
*
3478 TAATTAAATGTAATGCTTTTATTTTGTTGAATAAATTTATATGTAGAATTTGTAAACAAGTATTA
1 TAATTAAATGTAATAC-TTTATTTTGTTGAATAAATTTATATGTAGAATTTGTAAACAAGTATTA
* * * * *
3543 ATTTTTCTATCTATAAGAAAAATGTTAATTTGACTGAATTTAATGTCTTGCCTCTAC
65 ATTTATCTATCTATAAGAAAAATATTAATTTGACTAAAGTTAAAGTCTTGCCTCTAC
3600 TTTCTCTCTT
Statistics
Matches: 111, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
151 20 0.18
152 53 0.48
153 38 0.34
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.45
Consensus pattern (150 bp):
TAATTAAATGTAATACTTTATTTTGTTGAATAAATTTATATGTAGAATTTGTAAACAAGTATTAA
TTTATCTATCTATAAGAAAAATATTAATTTGACTAAAGTTAAAGTCTTGCCTCTACCTCATCTTT
TTTTTTTCCCCCTAGAGTGC
Found at i:4647 original size:37 final size:37
Alignment explanation
Indices: 4597--4667 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
4587 CAAAATACGA
* * *
4597 ATTTTTTTTAAAAACACG-AAGATTTTTGAAACAATT
1 ATTTTTTTGAAAAACACGAAAAATTTTTAAAACAATT
4633 ATTTTCTTTGAAAAACACGAAAAATTTTTAAAACA
1 ATTTT-TTTGAAAAACACGAAAAATTTTTAAAACA
4668 CGAGAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 5 0.17
37 12 0.40
38 13 0.43
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (37 bp):
ATTTTTTTGAAAAACACGAAAAATTTTTAAAACAATT
Found at i:4667 original size:18 final size:18
Alignment explanation
Indices: 4644--4984 Score: 86
Period size: 18 Copynumber: 19.0 Consensus size: 18
4634 TTTTCTTTGA
4644 AAAACACGAAAAATTTTT
1 AAAACACGAAAAATTTTT
*
4662 AAAACACGAGAAA--TTT
1 AAAACACGAAAAATTTTT
* *
4678 AGAGACAC-AAAAATTCTTA
1 A-AAACACGAAAAATT-TTT
*
4697 AAAACATG-AAAATTTTT
1 AAAACACGAAAAATTTTT
* *
4714 GAAAACAC-AACAATTTTG
1 -AAAACACGAAAAATTTTT
* ***
4732 AAACACGCGAATTTTTTTTTT
1 AAA-ACACGAA--AAATTTTT
****
4753 GAAAAC-CAGATTTTTTTTT
1 -AAAACAC-GAAAAATTTTT
* * *
4772 GAAACGCG-AAAATTTGT
1 AAAACACGAAAAATTTTT
* * *
4789 GAAACACG-AGAATTATTG
1 AAAACACGAAAAATT-TTT
* *
4807 AAAACAC-ATAGATTTTT
1 AAAACACGAAAAATTTTT
4824 GAAAACACG-AAAATTTTT
1 -AAAACACGAAAAATTTTT
* *
4842 GAAACAC-AAAAGTTTTT
1 AAAACACGAAAAATTTTT
4859 AGAAAACACGAAAAATTTTT
1 --AAAACACGAAAAATTTTT
** * * *
4879 TGATCATTG--GAATTTTT
1 AAAACA-CGAAAAATTTTT
**
4896 GAAAACACG-AGGATTTTT
1 -AAAACACGAAAAATTTTT
* *
4914 GAAACACG-AAATTTTTT
1 AAAACACGAAAAATTTTT
4931 GAAAACACG--AAATTTTT
1 -AAAACACGAAAAATTTTT
* *
4948 GAAAGCACAAAAAATTTTT
1 -AAAACACGAAAAATTTTT
* *
4967 GAAACACGTAAAATTTTT
1 AAAACACGAAAAATTTTT
4985 GAAATACCGG
Statistics
Matches: 236, Mismatches: 59, Indels: 56
0.67 0.17 0.16
Matches are distributed among these distances:
16 8 0.03
17 77 0.33
18 101 0.43
19 29 0.12
20 10 0.04
21 8 0.03
22 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (18 bp):
AAAACACGAAAAATTTTT
Found at i:4831 original size:36 final size:34
Alignment explanation
Indices: 4767--4988 Score: 191
Period size: 35 Copynumber: 6.3 Consensus size: 34
4757 ACCAGATTTT
* * *
4767 TTTTTGAAACGCGAAAATTTGTG-AAACACGAGAA
1 TTTTTGAAACAC-AAAATTTTTGAAAACACGAAAA
* *
4801 TTATTGAAAACACATAGATTTTTGAAAACACGAAAA
1 TTTTTG-AAACACA-AAATTTTTGAAAACACGAAAA
4837 TTTTTGAAACACAAAAGTTTTTAGAAAACACGAAAAA
1 TTTTTGAAACACAAAA-TTTTT-GAAAACACG-AAAA
* *** **
4874 TTTTTTG-ATCATTGGAATTTTTGAAAACACGAGGA
1 -TTTTTGAAACA-CAAAATTTTTGAAAACACGAAAA
*
4909 TTTTTGAAACACGAAATTTTTTGAAAACACG-AAA
1 TTTTTGAAACAC-AAAATTTTTGAAAACACGAAAA
4943 TTTTTGAAAGCACAAAAAATTTTTG-AAACACGTAAAA
1 TTTTTGAAA-CAC--AAAATTTTTGAAAACACG-AAAA
4980 TTTTTGAAA
1 TTTTTGAAA
4989 TACCGGAATT
Statistics
Matches: 152, Mismatches: 22, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
34 24 0.16
35 54 0.36
36 42 0.28
37 24 0.16
38 8 0.05
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (34 bp):
TTTTTGAAACACAAAATTTTTGAAAACACGAAAA
Found at i:4985 original size:18 final size:17
Alignment explanation
Indices: 4767--4988 Score: 175
Period size: 18 Copynumber: 12.5 Consensus size: 17
4757 ACCAGATTTT
*
4767 TTTTTGAAACGCGAAAA
1 TTTTTGAAACACGAAAA
* *
4784 TTTGTGAAACACGAGAA
1 TTTTTGAAACACGAAAA
* *
4801 TTATTGAAAACAC-ATAGA
1 TTTTTG-AAACACGA-AAA
4819 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
4837 TTTTTGAAACAC-AAAA
1 TTTTTGAAACACGAAAA
4853 GTTTTTAGAAAACACGAAAAA
1 -TTTTT-G-AAACACG-AAAA
* * *
4874 TTTTTTG-ATCATTG-GAA
1 -TTTTTGAAACA-CGAAAA
**
4891 TTTTTGAAAACACGAGGA
1 TTTTTG-AAACACGAAAA
*
4909 TTTTTGAAACACGAAAT
1 TTTTTGAAACACGAAAA
4926 TTTTTGAAAACACG-AAA
1 TTTTTG-AAACACGAAAA
*
4943 TTTTTGAAAGCACAAAAAA
1 TTTTTGAAA-CAC-GAAAA
4962 TTTTTGAAACACGTAAAA
1 TTTTTGAAACACG-AAAA
4980 TTTTTGAAA
1 TTTTTGAAA
4989 TACCGGAATT
Statistics
Matches: 166, Mismatches: 22, Indels: 33
0.75 0.10 0.15
Matches are distributed among these distances:
16 13 0.08
17 58 0.35
18 65 0.39
19 20 0.12
20 1 0.01
21 9 0.05
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:5002 original size:36 final size:35
Alignment explanation
Indices: 4600--5002 Score: 191
Period size: 36 Copynumber: 11.2 Consensus size: 35
4590 AATACGAATT
* * *** *
4600 TTTTTTAAAAACACGAAGATTTTTGAAACAATTAT
1 TTTTTTGAAAACACGAAAATTTTTGAAACACGAAA
*
4635 TTTCTTTGAAAAACACGAAAAATTTTTAAAACACGAGAA
1 TTT-TTTG-AAAACACG-AAAATTTTTGAAACACGA-AA
* * * * ** *
4674 -ATTTAG-AGACACAAAAATTCTTAAAAACATGAAA
1 TTTTTTGAAAACACGAAAATT-TTTGAAACACGAAA
* *
4708 ATTTTTGAAAACAC-AACAA-TTTTGAAACACGCGAATTTT
1 TTTTTTGAAAACACGAA-AATTTTTGAAACA--CGAA---A
*** *
4747 TTTTTTGAAAAC-CAGATTTTTTTTTGAAACGCGAAA
1 TTTTTTGAAAACAC-GA-AAATTTTTGAAACACGAAA
* * * *
4783 ATTTGTG-AAACACGAGAATTATTGAAAACAC-ATAGA
1 TTTTTTGAAAACACGAAAATTTTTG-AAACACGA-A-A
*
4819 -TTTTTGAAAACACGAAAATTTTTGAAACACAAAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACACGAAA
* * * *
4853 GTTTTTAGAAAACACGAAAAATTTTTTG-ATCATTGGAA
1 -TTTTTTGAAAACACG-AAAA-TTTTTGAAACA-CGAAA
**
4891 -TTTTTGAAAACACGAGGATTTTTGAAACACGAAA
1 TTTTTTGAAAACACGAAAATTTTTGAAACACGAAA
*
4925 TTTTTTGAAAACACG-AAATTTTTGAAAGCACAAAAA
1 TTTTTTGAAAACACGAAAATTTTTGAAA-CAC-GAAA
* * *
4961 ATTTTTG-AAACACGTAAAATTTTTGAAATACCGGAA
1 TTTTTTGAAAACACG-AAAATTTTTGAAACA-CGAAA
4997 TTTTTT
1 TTTTTT
5003 TTAACACAAA
Statistics
Matches: 278, Mismatches: 55, Indels: 69
0.69 0.14 0.17
Matches are distributed among these distances:
34 41 0.15
35 78 0.28
36 79 0.28
37 31 0.11
38 23 0.08
39 16 0.06
40 1 0.00
41 9 0.03
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (35 bp):
TTTTTTGAAAACACGAAAATTTTTGAAACACGAAA
Found at i:5170 original size:20 final size:19
Alignment explanation
Indices: 5126--5184 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
5116 CCTTATTATT
* *
5126 ATTTTTTTGGAAACGC-AA
1 ATTTTTTTTGAAACACGAA
*
5144 ATATTTTTTGAAACACGAGA
1 ATTTTTTTTGAAACACGA-A
5164 ATTTTTTTTGAAGACACGAA
1 ATTTTTTTTGAA-ACACGAA
5184 A
1 A
5185 ATTTCGAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 13 0.38
19 1 0.03
20 14 0.41
21 6 0.18
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
ATTTTTTTTGAAACACGAA
Found at i:5171 original size:21 final size:21
Alignment explanation
Indices: 5142--5188 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
5132 TTGGAAACGC
*
5142 AAATATTTTTTGAA-ACACGA
1 AAATTTTTTTTGAAGACACGA
*
5162 GAATTTTTTTTGAAGACACGA
1 AAATTTTTTTTGAAGACACGA
5183 AAATTT
1 AAATTT
5189 CGAAGCACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (21 bp):
AAATTTTTTTTGAAGACACGA
Found at i:5400 original size:23 final size:23
Alignment explanation
Indices: 5344--5413 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
5334 CTCATTTATT
5344 AAAAATATTAAAAAT-TAAATTAA
1 AAAAATA-TAAAAATATAAATTAA
*
5367 ATTAAAT-TAAAAATATAAA-TACA
1 A-AAAATATAAAAATATAAATTA-A
5390 AAAAATATAAAAATACATAAATTA
1 AAAAATATAAAAAT--ATAAATTA
5414 CTAATAACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
22 13 0.34
23 14 0.37
24 4 0.11
25 5 0.13
26 2 0.05
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAATATAAAAATATAAATTAA
Found at i:5547 original size:6 final size:6
Alignment explanation
Indices: 5536--5600 Score: 57
Period size: 6 Copynumber: 11.2 Consensus size: 6
5526 ATTGAACCTT
** *
5536 TTTTTC TTTTTC -TTCCC TTTTTTC TTTTT- TTTTCC TTTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC
5584 --TTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC T
5601 GCTGAGCTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
4 4 0.09
5 7 0.15
6 28 0.60
7 8 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:5556 original size:19 final size:18
Alignment explanation
Indices: 5535--5600 Score: 91
Period size: 18 Copynumber: 3.8 Consensus size: 18
5525 AATTGAACCT
5535 TTTTTTCTTTTTCTTCCC
1 TTTTTTCTTTTTCTTCCC
* *
5553 TTTTTTCTTTTTTTTTCC
1 TTTTTTCTTTTTCTTCCC
*
5571 TTTTTTCTTTTTCTT-TC
1 TTTTTTCTTTTTCTTCCC
5588 -TTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
5601 GCTGAGCTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.30
17 1 0.02
18 30 0.68
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTCTTTTTCTTCCC
Found at i:5591 original size:24 final size:23
Alignment explanation
Indices: 5554--5598 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
5544 TTTCTTCCCT
*
5554 TTTTTCTTTTTTTTTCCTTTTTTC
1 TTTTTCTTTCTTTTT-CTTTTTTC
5578 TTTTTCTTTCTTTTTCTTTTT
1 TTTTTCTTTCTTTTTCTTTTT
5599 CTGCTGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTCTTTTTCTTTTTTC
Found at i:5755 original size:17 final size:17
Alignment explanation
Indices: 5735--5768 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5725 AAATGGCCTG
5735 CTGCTTT-TTTTCTTTTT
1 CTGCTTTGTTTT-TTTTT
5752 CTGCTTTGTTTTTTTTT
1 CTGCTTTGTTTTTTTTT
5769 GGGCCGGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (17 bp):
CTGCTTTGTTTTTTTTT
Found at i:5895 original size:12 final size:12
Alignment explanation
Indices: 5880--5934 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
5870 TTATTTTCTT
5880 TTTTCTTTTTTC
1 TTTTCTTTTTTC
5892 TTTT-TTTCTTTC
1 TTTTCTTT-TTTC
*
5904 TTTTCTTCTTTC
1 TTTTCTTTTTTC
5916 -TTTCTTTTCTTC
1 TTTTCTTTT-TTC
5928 -TTTCTTT
1 TTTTCTTT
5935 CTTTTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
11 10 0.26
12 26 0.68
13 2 0.05
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:5896 original size:8 final size:8
Alignment explanation
Indices: 5873--5939 Score: 66
Period size: 8 Copynumber: 8.1 Consensus size: 8
5863 AAAAAAATTA
5873 TTTTC-TT
1 TTTTCTTT
5880 TTTTC-TT
1 TTTTCTTT
5887 TTTTCTTT
1 TTTTCTTT
5895 TTTTCTTT
1 TTTTCTTT
5903 CTTTTCTTCTT
1 -TTTTC-T-TT
5914 TCTTTCTTT
1 T-TTTCTTT
*
5923 TCTTCTTT
1 TTTTCTTT
*
5931 CTTTCTTT
1 TTTTCTTT
5939 T
1 T
5940 CCAATCAGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
7 12 0.24
8 22 0.43
9 8 0.16
10 3 0.06
11 6 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCTTT
Found at i:5915 original size:16 final size:16
Alignment explanation
Indices: 5873--5940 Score: 95
Period size: 16 Copynumber: 4.3 Consensus size: 16
5863 AAAAAAATTA
*
5873 TTTTCTTTTTTC-TT-
1 TTTTCTTCTTTCTTTC
*
5887 TTTTCTTTTTTTCTTTC
1 TTTTC-TTCTTTCTTTC
5904 TTTTCTTCTTTCTTTC
1 TTTTCTTCTTTCTTTC
5920 TTTTCTTCTTTCTTTC
1 TTTTCTTCTTTCTTTC
5936 TTTTC
1 TTTTC
5941 CAATCAGCCC
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
14 5 0.10
15 7 0.14
16 33 0.66
17 5 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTCTTCTTTCTTTC
Found at i:6050 original size:9 final size:10
Alignment explanation
Indices: 6036--6089 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
6026 CCTTTCCCCC
6036 TTTTTC-TCT
1 TTTTTCTTCT
6045 TTTTTCTTCT
1 TTTTTCTTCT
*
6055 TTTTTTTTCT
1 TTTTTCTTCT
*
6065 TTTTGCTTGCT
1 TTTTTCTT-CT
6076 TGTTTT-TT-T
1 T-TTTTCTTCT
6085 TTTTT
1 TTTTT
6090 TATTTCTTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 4 0.11
9 8 0.21
10 18 0.47
11 5 0.13
12 3 0.08
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:6065 original size:20 final size:22
Alignment explanation
Indices: 6036--6090 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
6026 CCTTTCCCCC
*
6036 TTTTTCTCTTTTTTCTT-CTT-
1 TTTTTTTCTTTTTTCTTGCTTG
*
6056 TTTTTTTCTTTTTGCTTGCTTG
1 TTTTTTTCTTTTTTCTTGCTTG
6078 TTTTTTT-TTTTTT
1 TTTTTTTCTTTTTT
6091 ATTTCTTGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.50
21 8 0.27
22 7 0.23
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (22 bp):
TTTTTTTCTTTTTTCTTGCTTG
Found at i:6098 original size:21 final size:22
Alignment explanation
Indices: 6051--6098 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
6041 CTCTTTTTTC
*
6051 TTCTT-TTTTTTTCTTTTTGCT
1 TTCTTGTTTTTTTCTTTTTGAT
* *
6072 TGCTTGTTTTTTT-TTTTTTAT
1 TTCTTGTTTTTTTCTTTTTGAT
6093 TTCTTG
1 TTCTTG
6099 CCTCTTGGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.79
Consensus pattern (22 bp):
TTCTTGTTTTTTTCTTTTTGAT
Found at i:6468 original size:29 final size:30
Alignment explanation
Indices: 6416--6522 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 30
6406 AAATGCAGTA
* * ** *
6416 AAAGTTTTGGGGCCAAAACATAATTTTGAG
1 AAAGTTTAGGGGTCAAAATGTAATTTCGAG
* *
6446 AAAG-TTATGGGTCAAAATGTAATTTCGAT
1 AAAGTTTAGGGGTCAAAATGTAATTTCGAG
** *
6475 AAAGTTTAGGGGTTGAAATGTAATTTC-AA
1 AAAGTTTAGGGGTCAAAATGTAATTTCGAG
*
6504 AAAATTTAGGGGTCAAAAT
1 AAAGTTTAGGGGTCAAAAT
6523 ACATTTTTTT
Statistics
Matches: 62, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 39 0.63
30 23 0.37
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (30 bp):
AAAGTTTAGGGGTCAAAATGTAATTTCGAG
Found at i:13756 original size:23 final size:20
Alignment explanation
Indices: 13714--13757 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 20
13704 AAATTGACTA
13714 TTTTTTATATTTTTTAATTT
1 TTTTTTATATTTTTTAATTT
13734 TTTTGTTATATATTTTTAGATTT
1 TTTT-TTATAT-TTTTTA-ATTT
13757 T
1 T
13758 AAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 6 0.29
23 5 0.24
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTTATATTTTTTAATTT
Found at i:15934 original size:18 final size:18
Alignment explanation
Indices: 15894--15960 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
15884 TTTTTTTAAT
*
15894 TTTTATAAATATACAT-A
1 TTTTATATATATACATGA
* *
15911 -TATATATATATACATGT
1 TTTTATATATATACATGA
*
15928 TTTTATATAT-TTCTATGA
1 TTTTATATATATAC-ATGA
*
15946 TTTTATGTATATACA
1 TTTTATATATATACA
15961 CACATATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
16 13 0.34
17 2 0.05
18 21 0.55
19 2 0.05
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.52
Consensus pattern (18 bp):
TTTTATATATATACATGA
Found at i:19450 original size:7 final size:8
Alignment explanation
Indices: 19400--19507 Score: 56
Period size: 8 Copynumber: 12.5 Consensus size: 8
19390 GATTCCATAA
19400 AAAAAAAG
1 AAAAAAAG
19408 AAAAAAGAGGG
1 AAAAAA-A--G
19419 AAAAAAAG
1 AAAAAAAG
19427 AAAAATCAA-
1 AAAAA--AAG
**
19436 AGTCAAAAG
1 A-AAAAAAG
19445 AAAAAAAG
1 AAAAAAAG
**
19453 AAAAAATC
1 AAAAAAAG
**
19461 AATCAAAG
1 AAAAAAAG
19469 TCAAAAATAAG
1 --AAAAA-AAG
*
19480 AGAAAAAG
1 AAAAAAAG
19488 AAAAAAAG
1 AAAAAAAG
*
19496 AGAAAAAG
1 AAAAAAAG
19504 AAAA
1 AAAA
19508 GAAAAATGAG
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
8 49 0.66
9 7 0.09
10 8 0.11
11 10 0.14
ACGTcount: A:0.75, C:0.05, G:0.15, T:0.06
Consensus pattern (8 bp):
AAAAAAAG
Found at i:19491 original size:16 final size:16
Alignment explanation
Indices: 19471--19507 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 16
19461 AATCAAAGTC
19471 AAAAATAAGAGAAAAAG
1 AAAAA-AAGAGAAAAAG
19488 AAAAAAAGAGAAAAAG
1 AAAAAAAGAGAAAAAG
19504 AAAA
1 AAAA
19508 GAAAAATGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAG
Found at i:20901 original size:48 final size:50
Alignment explanation
Indices: 20846--21871 Score: 419
Period size: 50 Copynumber: 20.6 Consensus size: 50
20836 AGTGGAACAG
* *
20846 ATTGAAGCTACAATGGTGAATCTCACTTCCCCG-CGTTACAATT-AAAAA
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* * * *
20894 ATTGAAGCTACAACGGCGAATCTTC-TTTCCCCGACATTGCAATTCAAAAG
1 ATTGAAGCTACAACGGTGAATC-TCACTTCCCCGACATTACAATTCAAAAA
* * * * * * **** * *
20944 ATTGAAGCCACAACGGTGAATCTTACTTCTCAGGCGA-TGCAGCGGAACAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC-ATTACAATTCAAAAA
* * * * *
20994 ATTGAAGCTACGACGGCGAATCTTACTTCCCTGACATTACAATTCAAAAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* * * * ** *
21044 ATTGAAGCTACAACGATGAATCTTACTTCCCAGGCGATGTAGC---GGAAAAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC-AT-TA-CAATTCAAAAA
* * * * * *
21094 ATTGAAGCTACGACAGTGAATCTCACCTCCCCAACATTGCAATTCAAAAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* * * ** * ** * **** *
21144 ATTGAAGCTACAACGGCGAATCTTACTTTCTAGGCGGTGCAGCGGAATAA
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
** * *
21194 ATTGAAGCTACAACGACGAATCTCACTTCCCCGACATTGCAATTCAAAAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* * * * ** * **** * *
21244 ATTGAAGCTACAACGGTGAATCTTACTTTCCAGGCGGTGCAGCGGAATAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* * * *
21294 ATTGAAGCTACAACGGTGAATCTTC-TTTCCCCGACATTGCAATTTAAAAG
1 ATTGAAGCTACAACGGTGAATC-TCACTTCCCCGACATTACAATTCAAAAA
* * *** * * **** * *
21344 ATTGAAGCCACAACGGTGAATCTTACTTCTTAGGCGA-TGCAGCGGAACAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC-ATTACAATTCAAAAA
* * ** *
21394 ATTGAAGCTACGACGGCGAATCTTGCTTCCCCGACATTACAATTCAAAAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* * * * * **** *
21444 ATTGAAGCTACAACGGTGAATCTTACTTTCCAGGCGA-TGCAGCGGAAAAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC-ATTACAATTCAAAAA
* * * * *
21494 ATTGAAGCTACGACAGTGAATCTCACCTCCCCGACATTGCAATTCAAAAT
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* * * * * * **** * *
21544 ATTGAAGCTACAACGGTGAATCTTACTTTCCAGGCAGTGCAGCGGAATAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* * * * *
21594 ATTGAAGCTACAACGGCGAATCTTC-TTTCCCTGACATTGCAATTCAAAAG
1 ATTGAAGCTACAACGGTGAATC-TCACTTCCCCGACATTACAATTCAAAAA
* * * *** * * * * *
21644 ATTGAAGCCACAACGGCGAATCTTACTTCTTAGGCAATGC-A-GCAGAACAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCA-AA-AA
* * ** ** * * *
21694 ATTTAAGCTACGACGGCAAATCTTGCTTCCCCAACATTGCAATTCAAAAT
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* * * * ** *
21744 ATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGATGTAGC---GGAAAAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGAC-AT-TA-CAATTCAAAAA
* * ** *
21794 ATTGAAGCTACGACAGTGAATCTCACTTCCCCGACATTGTAATTCAAAAG
1 ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
* *
21844 ATTGAAGCTACAACGGCGAATCTTACTT
1 ATTGAAGCTACAACGGTGAATCTCACTT
21872 TCCAGGAAGT
Statistics
Matches: 721, Mismatches: 227, Indels: 58
0.72 0.23 0.06
Matches are distributed among these distances:
47 1 0.00
48 31 0.04
49 23 0.03
50 647 0.90
51 12 0.02
52 5 0.01
53 2 0.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (50 bp):
ATTGAAGCTACAACGGTGAATCTCACTTCCCCGACATTACAATTCAAAAA
Found at i:21024 original size:100 final size:100
Alignment explanation
Indices: 20894--21917 Score: 1348
Period size: 100 Copynumber: 10.2 Consensus size: 100
20884 CAATTAAAAA
* *
20894 ATTGAAGCTACAACGGCGAATCTT-CTTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAAC
1 ATTGAAGCTACGACGGCGAATCTTAC-TTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAAC
20958 GGTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
65 GGTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
* *
20994 ATTGAAGCTACGACGGCGAATCTTACTTCCCTGACATTACAATTCAAAAGATTGAAGCTACAACG
1 ATTGAAGCTACGACGGCGAATCTTACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAACG
* * * *
21059 ATGAATCTTACTTCCCAGGCGATGTAGCGGAAAAG
66 GTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
* * * * *
21094 ATTGAAGCTACGACAGTGAATCTCACCTCCCCAACATTGCAATTCAAAAGATTGAAGCTACAACG
1 ATTGAAGCTACGACGGCGAATCTTACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAACG
* * * *
21159 GCGAATCTTACTT-TCTAGGCGGTGCAGCGGAATAA
66 GTGAATCTTACTTCTC-AGGCGATGCAGCGGAACAG
* * *
21194 ATTGAAGCTACAACGACGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAACG
1 ATTGAAGCTACGACGGCGAATCTTACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAACG
* *
21259 GTGAATCTTACTT-TCCAGGCGGTGCAGCGGAATAG
66 GTGAATCTTACTTCT-CAGGCGATGCAGCGGAACAG
* * * *
21294 ATTGAAGCTACAACGGTGAATCTT-CTTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAAC
1 ATTGAAGCTACGACGGCGAATCTTAC-TTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAAC
*
21358 GGTGAATCTTACTTCTTAGGCGATGCAGCGGAACAG
65 GGTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
* *
21394 ATTGAAGCTACGACGGCGAATCTTGCTTCCCCGACATTACAATTCAAAAGATTGAAGCTACAACG
1 ATTGAAGCTACGACGGCGAATCTTACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAACG
*
21459 GTGAATCTTACTT-TCCAGGCGATGCAGCGGAAAAG
66 GTGAATCTTACTTCT-CAGGCGATGCAGCGGAACAG
* * * * *
21494 ATTGAAGCTACGACAGTGAATCTCACCTCCCCGACATTGCAATTCAAAATATTGAAGCTACAACG
1 ATTGAAGCTACGACGGCGAATCTTACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAACG
*
21559 GTGAATCTTACTT-TCCAGGC-AGTGCAGCGGAATAG
66 GTGAATCTTACTTCT-CAGGCGA-TGCAGCGGAACAG
* * *
21594 ATTGAAGCTACAACGGCGAATCTT-CTTTCCCTGACATTGCAATTCAAAAGATTGAAGCCACAAC
1 ATTGAAGCTACGACGGCGAATCTTAC-TTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAAC
* * * *
21658 GGCGAATCTTACTTCTTAGGCAATGCAGCAGAACAG
65 GGTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
* * * * *
21694 ATTTAAGCTACGACGGCAAATCTTGCTTCCCCAACATTGCAATTCAAAATATTGAAGCTACAACG
1 ATTGAAGCTACGACGGCGAATCTTACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAACG
* * * *
21759 GCGAATCTTACTTCCCAGGCGATGTAGCGGAAAAG
66 GTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
* * * *
21794 ATTGAAGCTACGACAGTGAATCTCACTTCCCCGACATTGTAATTCAAAAGATTGAAGCTACAACG
1 ATTGAAGCTACGACGGCGAATCTTACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAACG
* *
21859 GCGAATCTTACTT-TCCAGG-AAGTGCAGCGGAACAG
66 GTGAATCTTACTTCT-CAGGCGA-TGCAGCGGAACAG
* *
21894 ATTGAAGCCACAACGGCGAATCTT
1 ATTGAAGCTACGACGGCGAATCTT
21918 GATTTTTCTA
Statistics
Matches: 814, Mismatches: 96, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
99 6 0.01
100 801 0.98
101 7 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (100 bp):
ATTGAAGCTACGACGGCGAATCTTACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTACAACG
GTGAATCTTACTTCTCAGGCGATGCAGCGGAACAG
Found at i:21439 original size:300 final size:301
Alignment explanation
Indices: 20889--21971 Score: 1542
Period size: 300 Copynumber: 3.6 Consensus size: 301
20879 CGTTACAATT
* * * *
20889 AAAAAATTGAAGCTACAACGGCGAATCTTC-TTTCCCCGACATTGCAATTCAAAAGATTGAAGCC
1 AAAAGATTGAAGCTACAACAGCGAATC-TCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCT
*
20953 ACAACGGTGAATCTTAC-TTCTCAGGC-GATGCAGCGGAACAGATTGAAGCTACGACGGCGAATC
65 ACAACGGTGAATCTTACTTTC-CAGGCAG-TGCAGCGGAACAGATTGAAGCTACAACGGCGAATC
* * * ** **
21016 TTAC-TTCCCTGACATTACAATTCAAAAGATTGAAGCTACAACGATGAATCTTACTTCCCAGGCG
128 TTACTTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTTAGGCG
* * * * ** *
21080 ATGTAGCGGAAAAGATTGAAGCTACGACAGTGAATCTCACCTCCCCAACATTGCAATTCAAAAGA
193 ATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTGCTTCCCCAACATTGCAATTCAAAAGA
* *
21145 TTGAAGCTACAACGGCGAATCTTACTTTCTAGGCGGTGCAGCGG
258 TTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGG
21189 AATAA-ATTGAAGCTACAAC-GACGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGC
1 AA-AAGATTGAAGCTACAACAG-CGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGC
* * *
21252 TACAACGGTGAATCTTACTTTCCAGGCGGTGCAGCGGAATAGATTGAAGCTACAACGGTGAATCT
64 TACAACGGTGAATCTTACTTTCCAGGCAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCT
* *
21317 T-CTTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCTTAGGCGA
129 TACTTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTTAGGCGA
* *
21381 TGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTGCTTCCCCGACATTACAATTCAAAAGAT
194 TGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTTGCTTCCCCAACATTGCAATTCAAAAGAT
*
21446 TGAAGCTACAACGGTGAATCTTACTTTCCAGGCGATGCAGCGG
259 TGAAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGG
* * * *
21489 AAAAGATTGAAGCTACGACAGTGAATCTCACCTCCCCGACATTGCAATTCAAAATATTGAAGCTA
1 AAAAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTA
*
21554 CAACGGTGAATCTTACTTTCCAGGCAGTGCAGCGGAATAGATTGAAGCTACAACGGCGAATCTT-
66 CAACGGTGAATCTTACTTTCCAGGCAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTA
* *
21618 CTTTCCCTGACATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTTAGGCAATG
131 CTTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTTAGGCGATG
* * * *
21683 CAGCAGAACAGATTTAAGCTACGACGGCAAATCTTGCTTCCCCAACATTGCAATTCAAAATATTG
196 CAGCGGAACAGATTGAAGCTACGACGGCGAATCTTGCTTCCCCAACATTGCAATTCAAAAGATTG
* *
21748 AAGCTACAACGGCGAATCTTACTTCCCAGGCGATGTAGCGG
261 AAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGG
* * *
21789 AAAAGATTGAAGCTACGACAGTGAATCTCACTTCCCCGACATTGTAATTCAAAAGATTGAAGCTA
1 AAAAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTA
* * *
21854 CAACGGCGAATCTTACTTTCCAGGAAGTGCAGCGGAACAGATTGAAGCCACAACGGCGAATCTTG
66 CAACGGTGAATCTTACTTTCCAGGCAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTT-
** * * *
21919 A-TTT-TTCTACATTGTAATT-AAAAGATTG-AGCCCGCAACGGCGAATCTTACTTC
130 ACTTTCCCCGACATTGCAATTCAAAAGATTGAAG-CCACAACGGCGAATCTTACTTC
21972 CTCGATGAAC
Statistics
Matches: 716, Mismatches: 56, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
298 2 0.00
299 36 0.05
300 668 0.93
301 10 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (301 bp):
AAAAGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCTA
CAACGGTGAATCTTACTTTCCAGGCAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTA
CTTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTCTTAGGCGATG
CAGCGGAACAGATTGAAGCTACGACGGCGAATCTTGCTTCCCCAACATTGCAATTCAAAAGATTG
AAGCTACAACGGCGAATCTTACTTTCCAGGCGATGCAGCGG
Found at i:22460 original size:132 final size:132
Alignment explanation
Indices: 22074--22479 Score: 614
Period size: 132 Copynumber: 3.1 Consensus size: 132
22064 AGTTGCAGTA
* * * * *
22074 GAGCTGATCGAAGATGGTGAATCTTATCTTTCCAAGATAGTGGAGAAGTAGATTTAAACCATTAG
1 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAG
* * *
22139 TCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTCCAAGATTCTATCACCCTAAGCAGTA
66 TCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAA-ATTCTGTCACCCTAAGCAGTA
22204 GTG
130 GTG
*
22207 GAGTAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAG
1 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAG
* * * *
22272 TCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCCGTCACCCTAAACAGTAA
66 TCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAATTCTGTCACCCTAAGCAGTAG
22337 TG
131 TG
* *
22339 GAGCAGATTGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAG
1 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAG
** * * * *
22404 TCCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGACTGTAAACTCTGTCCCCCTAAGCAGTAG
66 TCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAATTCTGTCACCCTAAGCAGTAG
22469 TG
131 TG
22471 GAGCAGATC
1 GAGCAGATC
22480 AACAATAACG
Statistics
Matches: 246, Mismatches: 27, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
132 147 0.60
133 99 0.40
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (132 bp):
GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAG
TCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAATTCTGTCACCCTAAGCAGTAG
TG
Found at i:22965 original size:23 final size:23
Alignment explanation
Indices: 22922--22966 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
22912 GCCACCAACC
*
22922 CTCTGCCACCGACGCCACTGACT
1 CTCTGCCACCAACGCCACTGACT
* *
22945 CTCTGCCACCAACTCCTCTGAC
1 CTCTGCCACCAACGCCACTGAC
22967 ACCTGCAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.49, G:0.13, T:0.20
Consensus pattern (23 bp):
CTCTGCCACCAACGCCACTGACT
Found at i:24613 original size:14 final size:16
Alignment explanation
Indices: 24579--24616 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
24569 TAAAATATAC
24579 ATATATACATACTTTT
1 ATATATACATACTTTT
**
24595 ATATATACATGTTTTT
1 ATATATACATACTTTT
24611 ATATAT
1 ATATAT
24617 TTCTATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATATACATACTTTT
Found at i:24615 original size:18 final size:18
Alignment explanation
Indices: 24579--24639 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
24569 TAAAATATAC
*
24579 ATATATACAT-ACTTT-T
1 ATATATACATGATTTTAT
*
24595 ATATATACATGTTTTTAT
1 ATATATACATGATTTTAT
*
24613 ATAT-TTCTATGATTTTAT
1 ATATATAC-ATGATTTTAT
*
24631 GTATATACA
1 ATATATACA
24640 CACATATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 10 0.29
17 5 0.14
18 18 0.51
19 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (18 bp):
ATATATACATGATTTTAT
Found at i:26240 original size:26 final size:26
Alignment explanation
Indices: 26201--26257 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
26191 ATGACAACAT
* *
26201 CTTTGATTTGTTTGAGCTCTAGAAAA
1 CTTTGATTTATTTGAGCTCAAGAAAA
26227 CTTTGATTTATTTGAGCTCAAGAAAA
1 CTTTGATTTATTTGAGCTCAAGAAAA
26253 CTTTG
1 CTTTG
26258 GAGCTAAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (26 bp):
CTTTGATTTATTTGAGCTCAAGAAAA
Done.