Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1759
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: 21110
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:2110 original size:19 final size:20
Alignment explanation
Indices: 2072--2111 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2062 ATTGAGATGT
2072 AATTAAATAATAAAAAATAA
1 AATTAAATAATAAAAAATAA
* *
2092 AATTAAA-ATTAAGAAATAA
1 AATTAAATAATAAAAAATAA
2111 A
1 A
2112 GTAACAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (20 bp):
AATTAAATAATAAAAAATAA
Found at i:6104 original size:20 final size:20
Alignment explanation
Indices: 6067--6105 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6057 GCCACTCATT
* * *
6067 TTTCTTTTTTTTCGTTTTTG
1 TTTCCTTTTTTACATTTTTG
6087 TTTCCTTTTTTACATTTTT
1 TTTCCTTTTTTACATTTTT
6106 TTGTTAAGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTCCTTTTTTACATTTTTG
Found at i:7303 original size:32 final size:29
Alignment explanation
Indices: 7266--7788 Score: 312
Period size: 32 Copynumber: 17.3 Consensus size: 29
7256 TTTGAAAAAA
7266 GTTGCCACTGACTTACGTGGGCTTTAAAAAGG
1 GTTGCCACTGACTT--GTGGGCTTT-AAAAGG
** ** * **
7298 GTTGCCACCAAAAGTGTGGACTTTTGAAAAAC
1 GTTGCCA-CTGACTTGTGGGC-TTT-AAAAGG
* **
7330 GATGCCACCAACTTGTGCGGGCTTTAAAAGG
1 GTTGCCACTGACTTGT--GGGCTTTAAAAGG
* * * *
7361 GTTCCCACTGACTTGTGCGGGTTTTGAGAGAG
1 GTTGCCACTGACTTGT--GGGCTTTAAAAG-G
* *
7393 GTTCCCACCGACTTGTGTGGGCTTTGAAAAGG
1 GTTGCCACTGAC-T-TGTGGGCTTT-AAAAGG
** *
7425 GTTGCCACCAACTTGTGGGCTTTCAAATGG
1 GTTGCCACTGACTTGTGGGCTTT-AAAAGG
*
7455 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGG
1 GTTGCCACTGAC-T-TGTGGGCTTT-AAAAGG
** *
7487 GTTGCCACCAACTTGTGGGCTTTCAAATGG
1 GTTGCCACTGACTTGTGGGCTTT-AAAAGG
* *
7517 GTTGCCACCGACTTATGTGGGCTTTCAAATGG
1 GTTGCCACTGAC-T-TGTGGGCTTT-AAAAGG
** *
7549 GTTGCCACCAACTTGTGTAGGCTTTGAAATA-A
1 GTTGCCACTGACTTGTG--GGCTTT-AAA-AGG
* * *
7581 GTTGCCACCGACTTGTGTCGGCTTTGAAATGA
1 GTTGCCACTGACTTGTG--GGCTTT-AAAAGG
* * *
7613 GTTACCACTAACTTGTGGGCTTTGAAA-G
1 GTTGCCACTGACTTGTGGGCTTTAAAAGG
*
7641 G-TGCCACTGACTTGTGGGCTTTGAAA-G
1 GTTGCCACTGACTTGTGGGCTTTAAAAGG
*
7668 G-TGCCACTGACTTGTGGGCTTTGAAAGG
1 GTTGCCACTGACTTGTGGGCTTTAAAAGG
* *
7696 G-TGCCACTGACTTATGGGCTTTGAAA-G
1 GTTGCCACTGACTTGTGGGCTTTAAAAGG
* * *
7723 G-TGCCACTAATTTGTGGGCTTTGAAAA-A
1 GTTGCCACTGACTTGTGGGCTTT-AAAAGG
*
7751 G-TGCCACTGACTTGTGGGCTTTCAAAAAG
1 GTTGCCACTGACTTGTGGGCTTT-AAAAGG
7780 G-TGCCACTG
1 GTTGCCACTG
7789 GTTTTGTAGA
Statistics
Matches: 410, Mismatches: 62, Indels: 41
0.80 0.12 0.08
Matches are distributed among these distances:
27 70 0.17
28 54 0.13
29 11 0.03
30 62 0.15
31 43 0.10
32 157 0.38
33 10 0.02
34 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (29 bp):
GTTGCCACTGACTTGTGGGCTTTAAAAGG
Found at i:7474 original size:62 final size:61
Alignment explanation
Indices: 7266--8171 Score: 463
Period size: 57 Copynumber: 15.3 Consensus size: 61
7256 TTTGAAAAAA
* ** * ** * **
7266 GTTGCCACTGACTTACGTGGGCTTTAAAAAGGGTTGCCACCAAAAGTGTGGACTTTTGAAAAAC
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACC-AACTTGTGGGC-TTTG-AAAGG
* * * * ** * *
7330 GATGCCACCAACTTGTGCGGGCTTT-AAAAGGGTTCCCACTGACTTGTGCGGGTTTTGAGAGAG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGT--GGGCTTTGAAAG-G
* *
7393 GTTCCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTCAAATGG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTGAAA-GG
*
7455 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTCAAATGG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTGAAA-GG
* * * **
7517 GTTGCCACCGACTTATGTGGGCTTTCAAATGGGTTGCCACCAACTTGTGTAGGCTTTGAAATAA
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTG--GGCTTTGAAA-GG
* * * * *
7581 GTTGCCACCGACTTGTGTCGGCTTTGAAATGAGTTACCACTAACTTGTGGGCTTTGAAA-G
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTGAAAGG
* **
7641 G-TGCCACTGAC-T-TGTGGGCTTTG-AAA-GG-TGCCACTGACTTGTGGGCTTTGAAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTGAAAGG
* * * * **
7696 G-TGCCACTGAC-T-TATGGGCTTTG-AAA-GG-TGCCACTAATTTGTGGGCTTTGAAAAA
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTGAAAGG
* * * **** * *
7751 G-TGCCACTGAC-T-TGTGGGCTTTCAAAAAGG-TGCCACTGGTTTTGTAGACTTTG--A--
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCAC-CAACTTGTGGGCTTTGAAAGG
** * **
7805 --TGCCACTAAC-T-TGTAGGCTTTG-AAAGTGG-TGCCACTGACTTGTGGGCTTTGAAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAG-GGTTGCCACCAACTTGTGGGCTTTGAAAGG
* * * * *
7861 TGCCACTAACTTGCCACCGACTTGTGTCGGCTTTGAAATGAGTTACCACTAACTTGTGGGCTTTG
1 -G--------TTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTG
7926 AAA-G
57 AAAGG
* * *** *
7930 G-TGCTACTGAC-T-TGTGGGCTTTG-AAA-GG-TGCCATTGACTTGCGGGCTTTGAAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTGAAAGG
* **** *
7985 G-TGCCACTGAC-T-TGTGGGCTTTCGAAAA-GG-TGCCACTGGTTTGTGGACTTTGAAA-G
1 GTTGCCACCGACTTGTGTGGGCTTT-GAAAAGGGTTGCCACCAACTTGTGGGCTTTGAAAGG
* * * * ** * *
8041 GATGCCACTGAC-T-TGTAGGCTTTG-AAAGGGGTGCCACTGATTTATGGGCTTT-AGAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTGA-AAGG
** * * *** *
8099 G-TGCCACTAAC-T-TGTGGGC-TTAAAAAGGGGTGCCAATGACTTGTGGGCTTTGGAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTGAAAGG
*
8156 G-TGCCACTGACTTGTG
1 GTTGCCACCGACTTGTG
8172 GACTTAAAAG
Statistics
Matches: 698, Mismatches: 101, Indels: 91
0.78 0.11 0.10
Matches are distributed among these distances:
52 14 0.02
53 27 0.04
54 45 0.06
55 99 0.14
56 17 0.02
57 148 0.21
58 16 0.02
59 19 0.03
60 1 0.00
62 132 0.19
63 39 0.06
64 93 0.13
67 8 0.01
68 2 0.00
69 12 0.02
70 26 0.04
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (61 bp):
GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGGGCTTTGAAAGG
Found at i:7501 original size:94 final size:92
Alignment explanation
Indices: 7266--7786 Score: 409
Period size: 94 Copynumber: 5.8 Consensus size: 92
7256 TTTGAAAAAA
* ** * * ** * **
7266 GTTGCCACTGACTTACGTGGGCTTTAAAAAGGGTTGCCACCAAAAGTGTGGACTTTTGAAAAACG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTGTGTGGGC-TTTGAAAAGGG
* *
7331 ATGCCACCAACTTGTGCGGGCTTTAAAAGG
65 TTGCCACCAACTTGT--GGGCTTTCAAAGG
* * * * * *
7361 GTTCCCACTGACTTGTGCGGGTTTTG-AGAGAGGTTCCCACCGACTTGTGTGGGCTTTGAAAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAG-GGTTGCCACCGAC-TGTGTGGGCTTTGAAAAGG
7425 GTTGCCACCAACTTGTGGGCTTTCAAATGG
64 GTTGCCACCAACTTGTGGGCTTTCAAA-GG
* * *
7455 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCAACT-TGTGGGCTTTCAAATGGGT
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAAGGGT
*
7519 TGCCACCGACTTATGTGGGCTTTCAAATGG
66 TGCCACCAAC-T-TGTGGGCTTTCAAA-GG
* * * * * *
7549 GTTGCCACCAACTTGTGTAGGCTTTGAAATA-AGTTGCCACCGACTTGTGTCGGCTTTGAAATGA
1 GTTGCCACCGACTTGTGTGGGCTTTGAAA-AGGGTTGCCACCGAC-TGTGTGGGCTTTGAAAAGG
* * *
7613 GTTACCACTAACTTGTGGGCTTTGAAA-G
64 GTTGCCACCAACTTGTGGGCTTTCAAAGG
* *
7641 G-TGCCACTGAC-T-TGTGGGCTTTG-AAA-GG-TGCCACTGACT-TGTGGGCTTTG-AAAGGG-
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAAGGGT
** * *
7697 TGCCACTGACTTATGGGCTTTGAAA-G
66 TGCCACCAACTTGTGGGCTTTCAAAGG
* * * * * *
7723 G-TGCCA-CTAATT-TGTGGGCTTTGAAAA-AG-TGCCACTGACT-TGTGGGCTTTCAAAAAGG-
1 GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAAGGGT
7781 TGCCAC
66 TGCCAC
7787 TGGTTTTGTA
Statistics
Matches: 360, Mismatches: 54, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
81 1 0.00
82 41 0.11
83 29 0.08
84 21 0.06
85 1 0.00
86 9 0.03
87 2 0.01
88 2 0.01
89 10 0.03
90 1 0.00
91 8 0.02
92 28 0.08
93 12 0.03
94 106 0.29
95 59 0.16
96 30 0.08
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (92 bp):
GTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAAGGGT
TGCCACCAACTTGTGGGCTTTCAAAGG
Found at i:7654 original size:27 final size:28
Alignment explanation
Indices: 7348--7873 Score: 368
Period size: 32 Copynumber: 18.0 Consensus size: 28
7338 CAACTTGTGC
* *
7348 GGGCTTTAAAAGGGTTCCCACTGACTTGT
1 GGGCTTTGAAAGGG-TGCCACTGACTTGT
* * * *
7377 GCGGGTTTTGAGAGAGGTTCCCACCGACTTGTGT
1 --GGGCTTTGA-A-AGGGTGCCACTGAC-T-TGT
**
7411 GGGCTTTGAAAAGGGTTGCCACCAACTTGT
1 GGGCTTTG-AAAGGG-TGCCACTGACTTGT
* *
7441 GGGCTTTCAAATGGGTTGCCACCGACTTGTGT
1 GGGCTTTGAAA-GGG-TGCCACTGAC-T-TGT
**
7473 GGGCTTTGAAAAGGGTTGCCACCAACTTGT
1 GGGCTTTG-AAAGGG-TGCCACTGACTTGT
* *
7503 GGGCTTTCAAATGGGTTGCCACCGACTTATGT
1 GGGCTTTGAAA-GGG-TGCCACTGAC-T-TGT
* **
7535 GGGCTTTCAAATGGGTTGCCACCAACTTGT
1 GGGCTTTGAAA-GGG-TGCCACTGACTTGT
* * *
7565 GTAGGCTTTGAAATAAGTTGCCACCGACTTGT
1 G--GGCTTTG-AA-AGGGTGCCACTGACTTGT
* * *
7597 GTCGGCTTTGAAATGAGTTACCACTAACTTGT
1 G--GGCTTTGAAA-G-GGTGCCACTGACTTGT
7629 GGGCTTTGAAA-GGTGCCACTGACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
7656 GGGCTTTGAAA-GGTGCCACTGACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
*
7683 GGGCTTTGAAAGGGTGCCACTGACTTAT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
* *
7711 GGGCTTTGAAA-GGTGCCACTAATTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
**
7738 GGGCTTTGAAAAAGTGCCACTGACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
* * **
7766 GGGCTTTCAAAAAGGTGCCACTGGTTTTGT
1 GGGCTTT-GAAAGGGTGCCACT-GACTTGT
* * *
7796 AGACTTTG--A---TGCCACTAACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
*
7819 AGGCTTTGAAAGTGGTGCCACTGACTTGT
1 GGGCTTTGAAAG-GGTGCCACTGACTTGT
*
7848 GGGCTTTGAAA-GGTGCCACTAACTTG
1 GGGCTTTGAAAGGGTGCCACTGACTTG
7874 CCACCGACTT
Statistics
Matches: 418, Mismatches: 48, Indels: 62
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.03
24 7 0.02
25 1 0.00
27 90 0.22
28 46 0.11
29 41 0.10
30 71 0.17
31 17 0.04
32 119 0.28
33 11 0.03
34 4 0.01
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (28 bp):
GGGCTTTGAAAGGGTGCCACTGACTTGT
Found at i:7707 original size:28 final size:28
Alignment explanation
Indices: 7348--8172 Score: 377
Period size: 28 Copynumber: 28.1 Consensus size: 28
7338 CAACTTGTGC
* *
7348 GGGCTTTAAAAGGGTTCCCACTGACTTGT
1 GGGCTTTGAAAGGG-TGCCACTGACTTGT
* * * *
7377 GCGGGTTTTGAGAGAGGTTCCCACCGACTTGTGT
1 --GGGCTTTGA-A-AGGGTGCCACTGAC-T-TGT
**
7411 GGGCTTTGAAAAGGGTTGCCACCAACTTGT
1 GGGCTTTG-AAAGGG-TGCCACTGACTTGT
* *
7441 GGGCTTTCAAATGGGTTGCCACCGACTTGTGT
1 GGGCTTTGAAA-GGG-TGCCACTGAC-T-TGT
**
7473 GGGCTTTGAAAAGGGTTGCCACCAACTTGT
1 GGGCTTTG-AAAGGG-TGCCACTGACTTGT
* *
7503 GGGCTTTCAAATGGGTTGCCACCGACTTATGT
1 GGGCTTTGAAA-GGG-TGCCACTGAC-T-TGT
* **
7535 GGGCTTTCAAATGGGTTGCCACCAACTTGT
1 GGGCTTTGAAA-GGG-TGCCACTGACTTGT
* * *
7565 GTAGGCTTTGAAATAAGTTGCCACCGACTTGT
1 G--GGCTTTG-AA-AGGGTGCCACTGACTTGT
* * *
7597 GTCGGCTTTGAAATGAGTTACCACTAACTTGT
1 G--GGCTTTGAAA-G-GGTGCCACTGACTTGT
7629 GGGCTTTGAAA-GGTGCCACTGACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
7656 GGGCTTTGAAA-GGTGCCACTGACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
*
7683 GGGCTTTGAAAGGGTGCCACTGACTTAT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
* *
7711 GGGCTTTGAAA-GGTGCCACTAATTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
**
7738 GGGCTTTGAAAAAGTGCCACTGACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
* * **
7766 GGGCTTTCAAAAAGGTGCCACTGGTTTTGT
1 GGGCTTT-GAAAGGGTGCCACT-GACTTGT
* * *
7796 AGACTTTG--A---TGCCACTAACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
*
7819 AGGCTTTGAAAGTGGTGCCACTGACTTGT
1 GGGCTTTGAAAG-GGTGCCACTGACTTGT
* *
7848 GGGCTTTGAAA-GGTGCCACTAACTTGCCAC
1 GGGCTTTGAAAGGGTGCCACTGACTTG---T
* * ** * * * * *
7878 CGACTTGTG-TCGGCTTTG-AAATGAGTT-A
1 GGGCTT-TGAAAGG--GTGCCACTGACTTGT
*** * ** *
7906 CCACTAACTTG--TGGGCTTTGAAAGGTG-CTACTGACTT
1 GGGCT---TTGAAAGGG---TGCCA-CTGACT--TG---T
** ** * * *
7943 GTGGGCTTTGAAAGGTGCCATTGACTTGC
1 G-GGCTTTGAAAGGGTGCCACTGACTTGT
7972 GGGCTTTGAAAGGGTGCCACTGACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
* **
8000 GGGCTTTCGAAAAGGTGCCACTGGTTTGT
1 GGGCTTT-GAAAGGGTGCCACTGACTTGT
* *
8029 GGACTTTGAAAGGATGCCACTGACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
* * *
8057 AGGCTTTGAAAGGGGTGCCACTGATTTAT
1 GGGCTTTGAAA-GGGTGCCACTGACTTGT
*
8086 GGGCTTT-AGAAGGGTGCCACTAACTTGT
1 GGGCTTTGA-AAGGGTGCCACTGACTTGT
** *
8114 GGGCTTAAAAAGGGGTGCCAATGACTTGT
1 GGGCTTTGAAA-GGGTGCCACTGACTTGT
*
8143 GGGCTTTGGAAGGGTGCCACTGACTTGT
1 GGGCTTTGAAAGGGTGCCACTGACTTGT
8171 GG
1 GG
8173 ACTTAAAAGA
Statistics
Matches: 627, Mismatches: 108, Indels: 121
0.73 0.13 0.14
Matches are distributed among these distances:
23 11 0.02
24 7 0.01
25 1 0.00
27 90 0.14
28 144 0.23
29 114 0.18
30 79 0.13
31 24 0.04
32 128 0.20
33 16 0.03
34 9 0.01
35 2 0.00
37 2 0.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (28 bp):
GGGCTTTGAAAGGGTGCCACTGACTTGT
Found at i:7885 original size:38 final size:42
Alignment explanation
Indices: 7834--7916 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 42
7824 TTGAAAGTGG
* *
7834 TGCCACTGACTTGTG-GGCTTTGAAA-G-G-TGCCACTAACT
1 TGCCACCGACTTGTGCGGCTTTGAAATGAGTTACCACTAACT
7872 TGCCACCGACTTGTGTCGGCTTTGAAATGAGTTACCACTAACT
1 TGCCACCGACTTGTG-CGGCTTTGAAATGAGTTACCACTAACT
7915 TG
1 TG
7917 TGGGCTTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
38 14 0.37
40 10 0.26
41 1 0.03
42 1 0.03
43 12 0.32
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (42 bp):
TGCCACCGACTTGTGCGGCTTTGAAATGAGTTACCACTAACT
Found at i:8212 original size:37 final size:38
Alignment explanation
Indices: 8171--8248 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 38
8161 ACTGACTTGT
*
8171 GGACTTAAAAGAATGCCATGGAGTTGTGGAC-TTAAAA
1 GGACTTAAAAGAATACCATGGAGTTGTGGACTTTAAAA
* *
8208 GGACTTTAAAGGATACCATGGAGTTGTGGACTTTAAAA
1 GGACTTAAAAGAATACCATGGAGTTGTGGACTTTAAAA
8246 GGA
1 GGA
8249 TGCCACGGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 28 0.76
38 9 0.24
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.26
Consensus pattern (38 bp):
GGACTTAAAAGAATACCATGGAGTTGTGGACTTTAAAA
Found at i:8238 original size:27 final size:27
Alignment explanation
Indices: 8208--9473 Score: 1293
Period size: 27 Copynumber: 46.4 Consensus size: 27
8198 GGACTTAAAA
* *
8208 GGACTTTAAAGGATACCATGGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
8235 GGACTTTAAAAGGATGCCACGGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
* *
8263 GGACTTAAAAGGATGCCACAGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* * *
8290 GGACTTAAAAGGATACCACAGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* * *
8317 GGACTTTAAAAGGATGCAATGGAGTTAT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
* * *
8345 AGATTTTAAACGAGTGCCACGGAGTTGT
1 GGACTTTAAAGGA-TGCCACGGAGTTGT
* *
8373 GGACTTAAAAGGATGCCACGAAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
*
8400 GGACTTTAAAAGGACGCCACGGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
*
8428 GGACTTTAAAAGGATGCCACAGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
*
8456 GGACTTTAAAAGGATGCCACAGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
*
8484 GGAC-TTAAAGGGATGCCACGGAGTTAT
1 GGACTTTAAA-GGATGCCACGGAGTTGT
* *
8511 GGACTTAAAAGGATGCCATGGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
*
8538 AGACTTTAAAAGGATGCCACGGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
8566 GGACTTTAAAAAGG-TGCCACGGAGTTGT
1 GGACTTT--AAAGGATGCCACGGAGTTGT
*
8594 GGACTTAAAAGGATGCCACGGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* *
8621 GGACTTAAAAGGATGCCACGGAGTTAT
1 GGACTTTAAAGGATGCCACGGAGTTGT
8648 GGACTTTAAAAGGATGCCACGGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
* *
8676 GGAC-----A--ATGCCACGAAGTTAT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* *
8696 GGACTTAAAAGGATGCCACGGAGTTAT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* * * * *
8723 GGACTTAAAAAGATGCCACAGAATTAT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* * *
8750 GGGCTTTAAAAGGGTGCCACAGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
** * * * *
8778 TAACTTAAAAGGGGTGCCACGAAGTTAT
1 GGACTTTAAA-GGATGCCACGGAGTTGT
*
8806 GGACTTAAAAGGATGCCACGGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* *
8833 GGACTTTAAAAGGGTGCCACAGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
* *
8861 GAACTTAAAATGG-TGCCACGGAGTTGT
1 GGACTTTAAA-GGATGCCACGGAGTTGT
* *
8888 GGACTTAAAAGGATGCTACGGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* *
8915 GGACTTTAAAAGGGTGCCACAGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
* *
8943 GGACTTTATAGGGTGCCACGGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* ** * *
8970 GGACTTAAAAAGGATGCCACAAAATTAT
1 GGACTT-TAAAGGATGCCACGGAGTTGT
8998 GGACTTTAAAGGGATGCCACGGAGTTGT
1 GGACTTTAAA-GGATGCCACGGAGTTGT
* *
9026 GGACTTAAAAGGATGCCACGAAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* *
9053 AGG-CTTTAAAAGAGTGCCATGGAGTTGT
1 -GGACTTTAAAGGA-TGCCACGGAGTTGT
* *
9081 GGACTTAAAAAGGGTGCCACGGAGTTGT
1 GGACTT-TAAAGGATGCCACGGAGTTGT
**
9109 GGACTCAAAAGGATGCCACGGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
** * *
9136 GGACTTTAAAAAAGTGCCACAGAGTCGT
1 GGACTTTAAAGGA-TGCCACGGAGTTGT
* * *
9164 AGACTTTAAAGGGTGCCACAGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* * *
9191 GGACTTAAAAGGGTACCAC-GAGATTGT
1 GGACTTTAAAGGATGCCACGGAG-TTGT
* *
9218 GAACTTTAAAAAGATGCCACGGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
* * * *
9246 GGACTTAAAAGGGTGCCACAGAGTTAT
1 GGACTTTAAAGGATGCCACGGAGTTGT
9273 GGAC-TTAAAGGGATGCCACGGAGTTGT
1 GGACTTTAAA-GGATGCCACGGAGTTGT
* *
9300 GGACTTTAAAAGGGTACCACGGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
* *
9328 GGACTTTAAAGGGTGCCACAGAG-TGTT
1 GGACTTTAAAGGATGCCACGGAGTTG-T
* * * *
9355 GGACTTAAAAGGGTGCTATGGAG-TGTT
1 GGACTTTAAAGGATGCCACGGAGTTG-T
* *
9382 GGACTTAAAAGGGTGCCACGGAGTTGT
1 GGACTTTAAAGGATGCCACGGAGTTGT
* * *
9409 GGACTTAAAAGGATGCCATGGAGTTAT
1 GGACTTTAAAGGATGCCACGGAGTTGT
*
9436 GGACTTTAAAAGGGTGCCACGGAGTTGT
1 GGACTTT-AAAGGATGCCACGGAGTTGT
9464 GGACTTTAAA
1 GGACTTTAAA
9474 AGAAAAGGTT
Statistics
Matches: 1052, Mismatches: 148, Indels: 78
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.02
22 1 0.00
25 1 0.00
26 19 0.02
27 530 0.50
28 468 0.44
29 16 0.02
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (27 bp):
GGACTTTAAAGGATGCCACGGAGTTGT
Found at i:8292 original size:55 final size:55
Alignment explanation
Indices: 8208--9475 Score: 1442
Period size: 55 Copynumber: 23.2 Consensus size: 55
8198 GGACTTAAAA
* * *
8208 GGACTTTAAAGGATACCATGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
1 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * *
8263 GGACTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGATACCACAGAGTTGT
1 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * * * * *
8317 GGACTTTAAAAGGATGCAATGGAGTTATAGA-TTTTAAACGAGTGCCACGGAGTTGT
1 GGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGA-TGCCACGGAGTTGT
* *
8373 GGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGACGCCACGGAGTTGT
1 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* *
8428 GGACTTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGT
1 GGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * *
8484 GGACTTAAAGGGATGCCACGGAGTTATGGAC-TTAAAAGGATGCCATGGAGTTGT
1 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
*
8538 AGACTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAAGG-TGCCACGGAGTTGT
1 GGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTT-AAAAGGATGCCACGGAGTTGT
*
8594 GGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTAT
1 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* *
8648 GGACTTTAAAAGGATGCCACGGAGTTGTGGAC------A--ATGCCACGAAGTTAT
1 GGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * * * *
8696 GGACTTAAAAGGATGCCACGGAGTTATGGAC-TTAAAAAGATGCCACAGAATTAT
1 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * * ** * * *
8750 GGGCTTTAAAAGGGTGCCACAGAGTTGTTAAC-TTAAAAGGGGTGCCACGAAGTTAT
1 GGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAA-GGATGCCACGGAGTTGT
* *
8806 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGT
1 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* *
8861 GAACTTAAAATGG-TGCCACGGAGTTGTGGAC-TTAAAAGGATGCTACGGAGTTGT
1 GGACTTAAAA-GGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * * *
8915 GGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTT-ATAGGGTGCCACGGAGTTGT
1 GGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
** * * *
8970 GGACTTAAAAAGGATGCCACAAAATTATGGACTTTAAAGGGATGCCACGGAGTTGT
1 GGACTT-AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* *
9026 GGACTTAAAAGGATGCCACGAAGTTGTAGG-CTTTAAAA-GAGTGCCATGGAGTTGT
1 GGACTTAAAAGGATGCCACGGAGTTGT-GGACTTTAAAAGGA-TGCCACGGAGTTGT
* *
9081 GGACTTAAAAAGGGTGCCACGGAGTTGTGGAC-TCAAAAGGATGCCACGGAGTTGT
1 GGACTT-AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * * * * *
9136 GGACTTTAAAA-AAGTGCCACAGAGTCGTAGACTTT-AAAGGGTGCCACAGAGTTGT
1 GGAC-TTAAAAGGA-TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * * *
9191 GGACTTAAAAGGGTACCAC-GAGATTGTGAACTTTAAAAAGATGCCACGGAGTTGT
1 GGACTTAAAAGGATGCCACGGAG-TTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * * *
9246 GGACTTAAAAGGGTGCCACAGAGTTATGGAC-TTAAAGGGATGCCACGGAGTTGT
1 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
* * * *
9300 GGACTTTAAAAGGGTACCACGGAGTTGTGGACTTT-AAAGGGTGCCACAGAG-TGTT
1 GGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTG-T
* * * *
9355 GGACTTAAAAGGGTGCTATGGAG-TGTTGGAC-TTAAAAGGGTGCCACGGAGTTGT
1 GGACTTAAAAGGATGCCACGGAGTTG-TGGACTTTAAAAGGATGCCACGGAGTTGT
* * *
9409 GGACTTAAAAGGATGCCATGGAGTTATGGACTTTAAAAGGGTGCCACGGAGTTGT
1 GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
9464 GGACTTTAAAAG
1 GGAC-TTAAAAG
9476 AAAAGGTTGC
Statistics
Matches: 1044, Mismatches: 122, Indels: 93
0.83 0.10 0.07
Matches are distributed among these distances:
47 26 0.02
48 18 0.02
50 1 0.00
52 1 0.00
53 13 0.01
54 221 0.21
55 578 0.55
56 180 0.17
57 6 0.01
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (55 bp):
GGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGT
Found at i:8686 original size:20 final size:20
Alignment explanation
Indices: 8661--8699 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8651 CTTTAAAAGG
* *
8661 ATGCCACGGAGTTGTGGACA
1 ATGCCACGAAGTTATGGACA
8681 ATGCCACGAAGTTATGGAC
1 ATGCCACGAAGTTATGGAC
8700 TTAAAAGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (20 bp):
ATGCCACGAAGTTATGGACA
Found at i:9487 original size:33 final size:33
Alignment explanation
Indices: 9388--9546 Score: 151
Period size: 34 Copynumber: 5.1 Consensus size: 33
9378 TGTTGGACTT
*
9388 AAAAGGGTGCCACGGAGTTGTGGAC-TT-----
1 AAAAGGTTGCCACGGAGTTGTGGACTTTAAAAG
* * *
9415 AAAAGGATGCCATGGAGTTATGGACTTTAAAAG
1 AAAAGGTTGCCACGGAGTTGTGGACTTTAAAAG
9448 ----GG-TGCCACGGAGTTGTGGACTTTAAAAG
1 AAAAGGTTGCCACGGAGTTGTGGACTTTAAAAG
* *
9476 AAAAGGTTGCCACAGAGTTATGGACTTTAAAAG
1 AAAAGGTTGCCACGGAGTTGTGGACTTTAAAAG
* *
9509 AAAAAGGTTGCCATGGAGTTGTGGATTTTGAAAAG
1 -AAAAGGTTGCCACGGAGTTGTGGACTTT-AAAAG
9544 AAA
1 AAA
9547 TGCCACTAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
27 22 0.20
28 26 0.24
29 2 0.02
32 2 0.02
33 24 0.22
34 27 0.25
35 5 0.05
ACGTcount: A:0.35, C:0.11, G:0.30, T:0.25
Consensus pattern (33 bp):
AAAAGGTTGCCACGGAGTTGTGGACTTTAAAAG
Found at i:9519 original size:34 final size:34
Alignment explanation
Indices: 9443--9546 Score: 147
Period size: 33 Copynumber: 3.1 Consensus size: 34
9433 TATGGACTTT
*
9443 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAAG-
1 AAAAGGTTGCCACGGAGTTGTGGACTTTAAAAGA
* *
9476 AAAAGGTTGCCACAGAGTTATGGACTTTAAAAGA
1 AAAAGGTTGCCACGGAGTTGTGGACTTTAAAAGA
* *
9510 AAAAGGTTGCCATGGAGTTGTGGATTTTGAAAAGA
1 AAAAGGTTGCCACGGAGTTGTGGACTTT-AAAAGA
9545 AA
1 AA
9547 TGCCACTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.48
34 24 0.39
35 8 0.13
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.24
Consensus pattern (34 bp):
AAAAGGTTGCCACGGAGTTGTGGACTTTAAAAGA
Found at i:10920 original size:21 final size:21
Alignment explanation
Indices: 10887--10926 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
10877 GCTTTTGTAC
* * *
10887 TTTTTTTGTTTTTTTTTTCAA
1 TTTTTGTGCTTTTTCTTTCAA
10908 TTTTTGTGCTTTTTCTTTC
1 TTTTTGTGCTTTTTCTTTC
10927 GACTTTTTCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.10, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTGTGCTTTTTCTTTCAA
Found at i:19757 original size:15 final size:15
Alignment explanation
Indices: 19737--19784 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
19727 TATCCTAAAT
19737 CCAAAATAATTCAAA
1 CCAAAATAATTCAAA
19752 CCAAAATAACTT-AAA
1 CCAAAATAA-TTCAAA
* *
19767 CCTAAAATGATGCAAA
1 CC-AAAATAATTCAAA
19783 CC
1 CC
19785 CATAATCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.54, C:0.23, G:0.04, T:0.19
Consensus pattern (15 bp):
CCAAAATAATTCAAA
Found at i:20179 original size:16 final size:16
Alignment explanation
Indices: 20147--20191 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
20137 ATTATTTCAA
20147 GTTCGAG-CTTATTTGG
1 GTTCGAGCCTT-TTTGG
* *
20163 GTTTGGGCCTTTTTGG
1 GTTCGAGCCTTTTTGG
20179 GTTCGAGCCTTTT
1 GTTCGAGCCTTTT
20192 CGAGTTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.07, C:0.16, G:0.31, T:0.47
Consensus pattern (16 bp):
GTTCGAGCCTTTTTGG
Found at i:20441 original size:15 final size:17
Alignment explanation
Indices: 20392--20441 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
20382 TAAAACCTAT
20392 ATTTATAATAAA-AATTA
1 ATTTAT-ATAAATAATTA
20409 ATTTATATATAATAAATTA
1 ATTTATATA-AAT-AATTA
20428 ATTT-T-TAAATAATT
1 ATTTATATAAATAATT
20442 TATTATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.13
16 6 0.20
17 10 0.33
18 1 0.03
19 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTATATAAATAATTA
Found at i:20446 original size:19 final size:19
Alignment explanation
Indices: 20392--20440 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
20382 TAAAACCTAT
20392 ATTTAT-AATAA-AAATTA
1 ATTTATAAATAATAAATTA
*
20409 ATTTATATATAATAAATTA
1 ATTTATAAATAATAAATTA
*
20428 ATTTTTAAATAAT
1 ATTTATAAATAAT
20441 TTATTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 6 0.22
18 4 0.15
19 17 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTATAAATAATAAATTA
Found at i:20821 original size:63 final size:60
Alignment explanation
Indices: 20722--20850 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 60
20712 ATACTCACCT
* *
20722 AAAACCAAAACCTAAGTTTTTCCCTTTTTTAGTCGCAACTATTATTTT-CTTTAGCATTAGTA
1 AAAACCAAAACCTAAGTTTTTCCCTTTTGTAATCGCAACTATTATTTTAC--T-GCATTAGTA
* * *
20784 AAAACCTAAAGCCTAATTTTTTTCCC-TTTGTAATCGCAACTCTTATTTTACTGCATTAGTA
1 AAAACC-AAAACCTAA-GTTTTTCCCTTTTGTAATCGCAACTATTATTTTACTGCATTAGTA
20845 AAAACC
1 AAAACC
20851 CAAATTTGCT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
61 15 0.25
62 7 0.12
63 28 0.47
64 9 0.15
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.40
Consensus pattern (60 bp):
AAAACCAAAACCTAAGTTTTTCCCTTTTGTAATCGCAACTATTATTTTACTGCATTAGTA
Done.