Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011605.1 Kokia drynarioides strain JFW-HI SEQ_126595, 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: 72316
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:3771 original size:12 final size:12
Alignment explanation
Indices: 3756--3964 Score: 98
Period size: 12 Copynumber: 18.2 Consensus size: 12
3746 AATAACAATC
*
3756 AAAACAGCAGCA
1 AAAACAGCAACA
* *
3768 AAAATAACAAC-
1 AAAACAGCAACA
3779 AAAAC---AACA
1 AAAACAGCAACA
* *
3788 AAAATAACAACA
1 AAAACAGCAACA
3800 AAAACAGCAACA
1 AAAACAGCAACA
* * *
3812 AAAATAACAGCA
1 AAAACAGCAACA
* *
3824 AAAATAGCAATA
1 AAAACAGCAACA
3836 AAAACAGCAACA
1 AAAACAGCAACA
* *
3848 AATAACAACATC-
1 AA-AACAGCAACA
*
3860 AAAACAGTAA-A
1 AAAACAGCAACA
* *
3871 AAAATAGC-ACC
1 AAAACAGCAACA
*
3882 AAAACAGCAACT
1 AAAACAGCAACA
*
3894 AAAACAG-TA-A
1 AAAACAGCAACA
* *
3904 AAAACAAC-ACC
1 AAAACAGCAACA
*
3915 AAAACAGTAA-A
1 AAAACAGCAACA
* *
3926 AAAATAGCAACC
1 AAAACAGCAACA
* *
3938 AAAACAGTAAAA
1 AAAACAGCAACA
* *
3950 AAAACCGCACCA
1 AAAACAGCAACA
3962 AAA
1 AAA
3965 CAACAATATA
Statistics
Matches: 142, Mismatches: 43, Indels: 24
0.68 0.21 0.11
Matches are distributed among these distances:
8 3 0.02
9 4 0.03
10 8 0.06
11 37 0.26
12 83 0.58
13 7 0.05
ACGTcount: A:0.66, C:0.21, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAACAGCAACA
Found at i:3772 original size:24 final size:22
Alignment explanation
Indices: 3744--3826 Score: 107
Period size: 24 Copynumber: 3.7 Consensus size: 22
3734 CCAAATAACC
3744 AAAATAACAATCAAAACAGCAGCA
1 AAAATAACAA-CAAAACAGCA-CA
3768 AAAATAACAACAAAACA--ACA
1 AAAATAACAACAAAACAGCACA
3788 AAAATAACAACAAAAACAGCAACA
1 AAAATAACAAC-AAAACAGC-ACA
*
3812 AAAATAACAGCAAAA
1 AAAATAACAACAAAA
3827 ATAGCAATAA
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
20 13 0.24
21 7 0.13
23 11 0.20
24 23 0.43
ACGTcount: A:0.70, C:0.19, G:0.05, T:0.06
Consensus pattern (22 bp):
AAAATAACAACAAAACAGCACA
Found at i:3774 original size:44 final size:44
Alignment explanation
Indices: 3723--3826 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 44
3713 AAAAACGCAT
* * * * *
3723 AAAAATAACATCCAAATAACCAAAATAACAATC-AAAACAGCAGC
1 AAAAATAACAACAAAACAACAAAAATAACAA-CAAAAACAGCAAC
3767 AAAAATAACAACAAAACAACAAAAATAACAACAAAAACAGCAAC
1 AAAAATAACAACAAAACAACAAAAATAACAACAAAAACAGCAAC
*
3811 AAAAATAACAGCAAAA
1 AAAAATAACAACAAAA
3827 ATAGCAATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 1 0.02
44 52 0.98
ACGTcount: A:0.68, C:0.20, G:0.04, T:0.08
Consensus pattern (44 bp):
AAAAATAACAACAAAACAACAAAAATAACAACAAAAACAGCAAC
Found at i:3791 original size:20 final size:20
Alignment explanation
Indices: 3723--3826 Score: 91
Period size: 24 Copynumber: 4.8 Consensus size: 20
3713 AAAAACGCAT
* * *
3723 AAAAATAACATCCAAATAAC
1 AAAAATAACAACAAAACAAC
*
3743 CAAAATAACAATCAAAACAGCAGC
1 AAAAATAACAA-CAAAACA--A-C
3767 AAAAATAACAACAAAACAAC
1 AAAAATAACAACAAAACAAC
3787 AAAAATAACAACAAAAACAGCAAC
1 AAAAATAACAAC--AAA-A-CAAC
*
3811 AAAAATAACAGCAAAA
1 AAAAATAACAACAAAA
3827 ATAGCAATAA
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
20 22 0.31
21 7 0.10
22 6 0.09
23 9 0.13
24 26 0.37
ACGTcount: A:0.68, C:0.20, G:0.04, T:0.08
Consensus pattern (20 bp):
AAAAATAACAACAAAACAAC
Found at i:3839 original size:36 final size:35
Alignment explanation
Indices: 3773--3863 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 35
3763 CAGCAAAAAT
*
3773 AACAACAAAACAACAAAAATAACAACAAAAACAGC
1 AACAAAAAAACAACAAAAATAACAACAAAAACAGC
* * *
3808 AACAAAAATAACAGCAAAAATAGCAATAAAAACAGC
1 AACAAAAA-AACAACAAAAATAACAACAAAAACAGC
*
3844 AACAAATAACAACATCAAAA
1 AACAAA-AA-AACAACAAAA
3864 CAGTAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
35 7 0.15
36 30 0.62
37 11 0.23
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (35 bp):
AACAAAAAAACAACAAAAATAACAACAAAAACAGC
Found at i:3938 original size:23 final size:22
Alignment explanation
Indices: 3882--3966 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 22
3872 AAATAGCACC
* *
3882 AAAACAGCAACTAAAACAGTAA
1 AAAAAAGCAACCAAAACAGTAA
3904 AAAACAA-C-ACCAAAACAGTAA
1 AAAA-AAGCAACCAAAACAGTAA
3925 AAAAATAGCAACCAAAACAGTAA
1 AAAAA-AGCAACCAAAACAGTAA
3948 AAAAAACCGC-ACCAAAACA
1 AAAAAA--GCAACCAAAACA
3967 ACAATATAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.02
21 17 0.31
22 7 0.13
23 28 0.51
24 2 0.04
ACGTcount: A:0.65, C:0.22, G:0.07, T:0.06
Consensus pattern (22 bp):
AAAAAAGCAACCAAAACAGTAA
Found at i:6671 original size:72 final size:72
Alignment explanation
Indices: 6524--6671 Score: 197
Period size: 72 Copynumber: 2.1 Consensus size: 72
6514 GAGGAAAAGT
* * * * *
6524 ACCATTTAATTGATTTTCTGAAACATAAAAGAACTTCAAAGATGATAATTTCCCTGTAGACAATG
1 ACCATTTAATTGATTTCCTGAAACATAAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
**
6589 GAATTTG
66 GAATGGG
* * **
6596 ACCATTTAATTGATTTCCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATCGATGATG
1 ACCATTTAATTGATTTCCTGAAACATAAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
6661 GAATGGG
66 GAATGGG
6668 ACCA
1 ACCA
6672 GAAATTTTGT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (72 bp):
ACCATTTAATTGATTTCCTGAAACATAAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
GAATGGG
Found at i:7646 original size:21 final size:21
Alignment explanation
Indices: 7620--7662 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
7610 CAGCAGTGAA
7620 GGATTTATTTTGCCTCCTAGG
1 GGATTTATTTTGCCTCCTAGG
7641 GGATTTATTTTGCCTCCTAGG
1 GGATTTATTTTGCCTCCTAGG
7662 G
1 G
7663 CTGACTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (21 bp):
GGATTTATTTTGCCTCCTAGG
Found at i:10183 original size:29 final size:30
Alignment explanation
Indices: 10142--10216 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
10132 GATCAATTCA
* *
10142 AAATTTCACGTATAAAATTGCACA-AAATC
1 AAATTTCATGTATAAAATTGCACATAAACC
*
10171 AAATTTCATGTATATAATTGCACATTAAACC
1 AAATTTCATGTATAAAATTGCACA-TAAACC
10202 AAAGTTT-ATGTATAA
1 AAA-TTTCATGTATAA
10217 TTAAGATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 22 0.56
31 14 0.36
32 3 0.08
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.33
Consensus pattern (30 bp):
AAATTTCATGTATAAAATTGCACATAAACC
Found at i:15542 original size:29 final size:29
Alignment explanation
Indices: 15343--15691 Score: 436
Period size: 30 Copynumber: 11.9 Consensus size: 29
15333 ACTCGGGATG
* * * *
15343 AAAATGAAATTTTGGAAAAGCTCGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTG-GGGTT
*
15373 AAAATGTGATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
*
15403 AAAATGTAATTTTGGAAAAGCTTAGGGGTT
1 AAAATGTAATTTTGGAAAAG-TTTGGGGTT
*
15433 AAAATGTAATTTTGGAAAAGTTTTGGGGTC
1 AAAATGTAATTTTGGAAAAG-TTTGGGGTT
** *
15463 AAAACATAATTTTGGAAAAGTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
15492 CAAAATGTAATTTTGGAAAAGTTTGGGGTT
1 -AAAATGTAATTTTGGAAAAGTTTGGGGTT
*
15522 AAAATGTAATTTTGGAAAAGTTTGGTGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
* *
15551 AAAATGTAATTTT-G-AAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
*
15579 AAAATGTAATTTT-GAAAAGTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
**
15607 AAAACATAATTTTGGAAAAGTTTGGGG-T
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
* * *
15635 CAAATGTTATTTTGGAAAAGTTTGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTG-GGGTT
15665 AAAATGTAATTTTGGAAAAGTTTGGGG
1 AAAATGTAATTTTGGAAAAGTTTGGGG
15692 ACCTCTTGAG
Statistics
Matches: 279, Mismatches: 32, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
27 7 0.03
28 55 0.20
29 73 0.26
30 141 0.51
31 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTGGGGTT
Found at i:17657 original size:29 final size:29
Alignment explanation
Indices: 17570--17887 Score: 317
Period size: 30 Copynumber: 10.9 Consensus size: 29
17560 ACTCGAGATG
* * ** *
17570 AAAATGAAATTTTAGAAAAGCTCGGGGGTC
1 AAAATGTAATTTTGGAAAAG-TTTGGGGTT
* *
17600 AAAATGTGATTTTGGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
* *
17630 AAAATGTAATTTTGAAAAAGCTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
*
17659 AAACA--TAATTTTGGAAAAGTTTGGGGTC
1 AAA-ATGTAATTTTGGAAAAGTTTGGGGTT
**
17687 AAAACATAATTTTGGAAAAGTTT-GGGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
17715 CAAAATGTAATTTT-GAAAAGTTTAGGGGTCT
1 -AAAATGTAATTTTGGAAAAGTTT-GGGGT-T
* * *
17746 -AAATATATTTTTGGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTT-GGGGTT
*
17775 AAAATGTAATTTTGGAAAAGTTTGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
** *
17804 AAAACATAATTTTGGAAAAGTTTAGGG-T
1 AAAATGTAATTTTGGAAAAGTTTGGGGTT
*
17832 CAAATGTAATTTTGGAAAAGTTTGGCGGTT
1 AAAATGTAATTTTGGAAAAGTTTGG-GGTT
* *
17862 AAAATATAATTTT-GAAAAATTTGGGG
1 AAAATGTAATTTTGGAAAAGTTTGGGG
17888 ACCTCTTGAG
Statistics
Matches: 241, Mismatches: 35, Indels: 26
0.80 0.12 0.09
Matches are distributed among these distances:
27 1 0.00
28 60 0.25
29 87 0.36
30 92 0.38
31 1 0.00
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTGGGGTT
Found at i:17705 original size:58 final size:57
Alignment explanation
Indices: 17608--17880 Score: 320
Period size: 58 Copynumber: 4.7 Consensus size: 57
17598 TCAAAATGTG
* * * * *
17608 ATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGAAAAAGCTTGGGGTTAAACA-TA
1 ATTTTGGAAAAGTTT-GGGGTTAAAATATAATTTTGGAAAAGTTTAGGGTTAAA-AGTA
* *
17666 ATTTTGGAAAAGTTTGGGGTCAAAACATAATTTTGGAAAAGTTT-GGGTTCAAAATGTA
1 ATTTTGGAAAAGTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGGTT-AAAA-GTA
*
17724 ATTTT-GAAAAGTTTAGGGGTCT-AAATATATTTTTGGAAAAGTTTAAGGGTTAAAATGTA
1 ATTTTGGAAAAGTTT-GGGGT-TAAAATATAATTTTGGAAAAGTTT-AGGGTTAAAA-GTA
* * * *
17783 ATTTTGGAAAAGTTTGAGGTTAAAACATAATTTTGGAAAAGTTTAGGGTCAAATGTA
1 ATTTTGGAAAAGTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGGTTAAAAGTA
*
17840 ATTTTGGAAAAGTTTGGCGGTTAAAATATAATTTTGAAAAA
1 ATTTTGGAAAAGTTTGG-GGTTAAAATATAATTTTGGAAAA
17881 TTTGGGGACC
Statistics
Matches: 188, Mismatches: 17, Indels: 20
0.84 0.08 0.09
Matches are distributed among these distances:
56 6 0.03
57 54 0.29
58 77 0.41
59 37 0.20
60 14 0.07
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.36
Consensus pattern (57 bp):
ATTTTGGAAAAGTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGGGTTAAAAGTA
Found at i:17758 original size:87 final size:86
Alignment explanation
Indices: 17594--17886 Score: 353
Period size: 87 Copynumber: 3.4 Consensus size: 86
17584 GAAAAGCTCG
* * *
17594 GGGGTCAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGAAAAAGCTT-GGGGT
1 GGGGTCAAAATATAATTTTGGAAAAGTTT--GGGTTAAAATGTAATTTTG-AAAAGTTTAGGGGT
*
17658 -TAAACATAATTTTGGAAAAGTTT
63 CTAAATATAATTTTGGAAAAGTTT
*
17681 GGGGTCAAAACATAATTTTGGAAAAGTTTGGGTTCAAAATGTAATTTTGAAAAGTTTAGGGGTCT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTGGGTT-AAAATGTAATTTTGAAAAGTTTAGGGGTCT
*
17746 AAATATATTTTTGGAAAAGTTT
65 AAATATAATTTTGGAAAAGTTT
* * * **
17768 AAGGGTTAAAATGTAATTTTGGAAAAGTTTGAGGTTAAAACATAATTTTGGAAAAGTTTA-GGGT
1 -GGGGTCAAAATATAATTTTGGAAAAGTTTG-GGTTAAAATGTAATTTT-GAAAAGTTTAGGGGT
*
17832 C-AAATGTAATTTTGGAAAAGTTT
63 CTAAATATAATTTTGGAAAAGTTT
* *
17855 GGCGGTTAAAATATAATTTT-GAAAAATTTGGG
1 GG-GGTCAAAATATAATTTTGGAAAAGTTTGGG
17887 GACCTCTTGA
Statistics
Matches: 182, Mismatches: 17, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
85 14 0.08
86 29 0.16
87 83 0.46
88 42 0.23
89 14 0.08
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (86 bp):
GGGGTCAAAATATAATTTTGGAAAAGTTTGGGTTAAAATGTAATTTTGAAAAGTTTAGGGGTCTA
AATATAATTTTGGAAAAGTTT
Found at i:20025 original size:14 final size:14
Alignment explanation
Indices: 20006--20041 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
19996 GAAAAGTAAT
20006 TCATTTTCCAAAAA
1 TCATTTTCCAAAAA
*
20020 TCATTTTCCGAAAA
1 TCATTTTCCAAAAA
*
20034 CCATTTTC
1 TCATTTTC
20042 AATTAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (14 bp):
TCATTTTCCAAAAA
Found at i:37073 original size:30 final size:31
Alignment explanation
Indices: 37033--37104 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
37023 GTTACATTTA
* *
37033 ACAAAGCAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTAAACTTATCGAAAA-GTG
*
37063 ACAAAACAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
37094 ACAAAACAGTC
1 ACAAAACAGTC
37105 CTATTGGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 17 0.46
31 15 0.41
32 5 0.14
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.19
Consensus pattern (31 bp):
ACAAAACAGTCACTAAACTTATCGAAAAGTG
Found at i:37962 original size:30 final size:31
Alignment explanation
Indices: 37892--37963 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
37882 GTAAGTAGAG
*
37892 GACTGTTTTGTCACTTTTCGATAACTTTAAT
1 GACTGTTTTGTCACTTTTCGATAACTTGAAT
* *
37923 GACTGTTTTGTCACATTTTC-A-AAGTTGAGT
1 GACTGTTTTGTCAC-TTTTCGATAACTTGAAT
*
37953 GATTGTTTTGT
1 GACTGTTTTGT
37964 TAAATGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 16 0.44
31 15 0.42
32 5 0.14
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCGATAACTTGAAT
Found at i:40523 original size:69 final size:69
Alignment explanation
Indices: 40287--40594 Score: 277
Period size: 69 Copynumber: 4.5 Consensus size: 69
40277 TCGTTTTCTT
* * * * *
40287 CAAGAAAAAGAGC-CACCTGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGAGAAACGACCTC
1 CAAGAAAATGAGCTC-CATGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACAACGTC
**
40351 CCCTC
65 AACTC
* * * ** *
40356 CAAGGAGAA-GAGC-CACATGTTCCTGGACATGAAGAACCGTTGGAAATGTTAGATAAACAACGT
1 CAA-GAAAATGAGCTC-CATGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACAACGT
40419 CGAA-TC
64 C-AACTC
* * ** ** * * *
40425 CAAGAAAATG-GACACCATATAACCCGACATGAAGAGCCATCGGAAATGCTAGATAAACGACGTC
1 CAAGAAAATGAG-CTCCATGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACAACGTC
*
40489 TACTC
65 AACTC
* * *
40494 CAAGTAAATGAGCTCCATGTTGATGGACATGAAGAGCTC-TCAGAAATGCTAGATACACAACGTC
1 CAAGAAAATGAGCTCCATGTTGCTGGACATGAAGAGC-CGTCAGAAATGCTAGATAAACAACGTC
40558 AACTC
65 AACTC
*
40563 CAAGAAAATGAGCTCCCTGTTGCTGGACATGA
1 CAAGAAAATGAGCTCCATGTTGCTGGACATGA
40595 GCTAGATAAA
Statistics
Matches: 192, Mismatches: 39, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
68 6 0.03
69 179 0.93
70 7 0.04
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (69 bp):
CAAGAAAATGAGCTCCATGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACAACGTCA
ACTC
Found at i:40540 original size:138 final size:138
Alignment explanation
Indices: 40312--40572 Score: 332
Period size: 138 Copynumber: 1.9 Consensus size: 138
40302 CCTGTTGCTG
* *
40312 GACATGAAGAGCCGTCAGAAATGCTAGAGAAACGACCTCCCCTCCAAGGAGAAGAGCCACATGTT
1 GACATGAAGAGCCATCAGAAATGCTAGAGAAACGACCTCCACTCCAAGGAGAAGAGCCACATGTT
* ** *
40377 CCTGGACATGAAGAACCGTTGGAAATGTTAGATAAACAACGTCGAA-TCCAAGAAAATGGACACC
66 CATGGACATGAAGAACCGTCAGAAATGCTAGATAAACAACGTC-AACTCCAAGAAAATGGACACC
40441 ATATAACCC
130 ATATAACCC
* * * * *
40450 GACATGAAGAGCCATCGGAAATGCTAGATAAACGACGTCTACTCCAAGTA-AATGAGCTC-CATG
1 GACATGAAGAGCCATCAGAAATGCTAGAGAAACGACCTCCACTCCAAGGAGAA-GAGC-CACATG
* * *
40513 TTGATGGACATGAAGAGCTC-TCAGAAATGCTAGATACACAACGTCAACTCCAAGAAAATG
64 TTCATGGACATGAAGAAC-CGTCAGAAATGCTAGATAAACAACGTCAACTCCAAGAAAATG
40573 AGCTCCCTGT
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
137 4 0.04
138 99 0.94
139 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (138 bp):
GACATGAAGAGCCATCAGAAATGCTAGAGAAACGACCTCCACTCCAAGGAGAAGAGCCACATGTT
CATGGACATGAAGAACCGTCAGAAATGCTAGATAAACAACGTCAACTCCAAGAAAATGGACACCA
TATAACCC
Found at i:40592 original size:138 final size:137
Alignment explanation
Indices: 40287--40594 Score: 320
Period size: 138 Copynumber: 2.2 Consensus size: 137
40277 TCGTTTTCTT
* *
40287 CAAGAAAAAGAGCCACCTGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGAGAAACGACCTCC
1 CAAGAAAATGAGCC-CCTGTTGCTGGACATGAAGAGCCATCAGAAATGCTAGAGAAACGACCTCC
* * ** *
40352 CCTCCAAGGAGAAGAGCCACATGTTCCTGGACATGAAGAACCGTTGGAAATGTTAGATAAACAAC
65 ACTCCAAGGAGAAGAGCCACATGTTCATGGACATGAAGAACCGTCAGAAATGCTAGATAAACAAC
40417 GTCGAATC
130 GTCGAATC
* * ** ** * * *
40425 CAAGAAAATG-GACACCATATAACCCGACATGAAGAGCCATCGGAAATGCTAGATAAACGACGTC
1 CAAGAAAATGAG-C-CCCTGTTGCTGGACATGAAGAGCCATCAGAAATGCTAGAGAAACGACCTC
* * * * *
40489 TACTCCAAGTA-AATGAGCTC-CATGTTGATGGACATGAAGAGCTC-TCAGAAATGCTAGATACA
64 CACTCCAAGGAGAA-GAGC-CACATGTTCATGGACATGAAGAAC-CGTCAGAAATGCTAGATAAA
40551 CAACGTC-AACTC
126 CAACGTCGAA-TC
40563 CAAGAAAATGAGCTCCCTGTTGCTGGACATGA
1 CAAGAAAATGAGC-CCCTGTTGCTGGACATGA
40595 GCTAGATAAA
Statistics
Matches: 135, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
137 5 0.04
138 126 0.93
139 4 0.03
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (137 bp):
CAAGAAAATGAGCCCCTGTTGCTGGACATGAAGAGCCATCAGAAATGCTAGAGAAACGACCTCCA
CTCCAAGGAGAAGAGCCACATGTTCATGGACATGAAGAACCGTCAGAAATGCTAGATAAACAACG
TCGAATC
Found at i:40638 original size:54 final size:54
Alignment explanation
Indices: 40541--40645 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
40531 TCTCAGAAAT
* ** * *
40541 GCTAGATACACAACGTCAACTCCAAGAAAATGAGCTCCCTGTTGCTGGACATGA
1 GCTAGATAAACAACGTCAACTCCAAGAAAACAAGCTCCATGTTGCCGGACATGA
* * *
40595 GCTAGATAAACAACGTCGACTCCAAGAAAACAAGTTTCATGTTGCCGGACA
1 GCTAGATAAACAACGTCAACTCCAAGAAAACAAGCTCCATGTTGCCGGACA
40646 CGAAGAGACC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (54 bp):
GCTAGATAAACAACGTCAACTCCAAGAAAACAAGCTCCATGTTGCCGGACATGA
Found at i:42366 original size:120 final size:120
Alignment explanation
Indices: 40644--42350 Score: 2605
Period size: 120 Copynumber: 14.2 Consensus size: 120
40634 TGTTGCCGGA
* * * * * * * * *
40644 CACGAAGAGACCTTGAAAAGGCCACATAAAAGA-AGTCGACTCCAAGAAGATGTTGATGGGCACG
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACA-TCGACTCCGAGAACATGTTGATGGCCACG
* * * * * *
40708 AAGAGCCTTC-GAAAATTCTAGATAAAAGACGTCAACTCCAAGAAGATGTTGATGGG
65 AAGTGCCCTCAG-AAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* *
40764 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCAACTCCGAGAACATGTTGATGGCCATGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
* **
40829 AGTGCCCTC-GAAAATGCTAGATAAAAGACGTCGACTTCGAGAAGATGTTGATAAC
66 AGTGCCCTCAG-AAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
** *
40884 CACGAAGAGCCCTTAAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGTCACGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
* *
40949 AGTGCCCTC-GAAAATGCTAGATAAAAGACGTCGACTCCAAGAAAATGTTGATGGC
66 AGTGCCCTCAG-AAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* *
41004 CACGAAGAGCCCACGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCATGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
* *
41069 AGTGCCCTCGGAAATGCTAGATAAAAGACGTCGACTTCGAGAAGATGTTGATGGC
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* * * * *
41124 CACGAAGAGCCCTGGGAAATGCTAGGTGAAAGACATCAACTCCGTGAACATGTTGATGGCCACGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
* * *
41189 AGTGCCCTTAGAAATGCTAGATAAAAGACGTCGACTTCGAGAAGATGTTGATGGG
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
*
41244 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGTGAACATGTTGATGGCCACGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
* * *
41309 AGTGCCCTTAGAAATGCTAGATAAAAGACGTCGACTTCGAGAAGATGTTGATGGG
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
41364 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
*
41429 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCAAGAAGATGTTGATGGC
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
**
41484 CACGAAGAGCCCTTAAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
*
41549 AGTGCCCTC-GAAAATGCTAGATAAAAGACGTCGACTCCAAGAAGATGTTGATGGC
66 AGTGCCCTCAG-AAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* * *
41604 CACGAAGAGCCCACGGAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCATGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
* *
41669 AGTGCCCTCGGAAATGCTAGATAAAAGACGTCGACTTCGAGAAGATGTTGATGGC
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* * * * * *
41724 CACGAAGAGCCCTGGGAAATGCTAGGTGAAAGACATCAACTCCGTGAACATGTTGATGGCCATGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
* *
41789 AGTGCCCTTAGAAATGCTAGATAAAAGACGTCGACTTCGAGAAGATGTTGATGGC
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* * * *
41844 CACGAAGAGCCCTCGAAAATGCTTGGTGAAAGACATCAACTCCGAGAACATGTCGATGGCCACGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
*
41909 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGG
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* *
41964 CACGAAGAGCCCTCGGAAATGCTAGATGAAAGACATCAACTCCGAGAACATGTTGATGGCCACGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
*
42029 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGG
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* *
42084 CACAAAGAGCCCTCGAAAATGCTAGGTGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
* *
42149 AGTGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAAGATGTTGATGGC
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* * *
42204 CACGAAGAGCCCTTGGAAATGCTAGATGAAAGATATCGACTCCGAGAACATGTTGATGGCCACGA
1 CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
* * * * *
42269 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCAAGAAAATATTTATGGA
66 AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
* * *
42324 CATGAAGAGCCCTGGGAAATGCTAGAT
1 CACGAAGAGCCCTCGAAAATGCTAGAT
42351 AAACGACGTG
Statistics
Matches: 1478, Mismatches: 105, Indels: 8
0.93 0.07 0.01
Matches are distributed among these distances:
119 1 0.00
120 1474 1.00
121 3 0.00
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.19
Consensus pattern (120 bp):
CACGAAGAGCCCTCGAAAATGCTAGATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGA
AGTGCCCTCAGAAATGCTAGATAAAAGACGTCGACTCCGAGAAGATGTTGATGGC
Found at i:42374 original size:60 final size:60
Alignment explanation
Indices: 40669--42366 Score: 2154
Period size: 60 Copynumber: 28.3 Consensus size: 60
40659 AAAAGGCCAC
* * * * * * *
40669 ATAAAAGAAGTCGACTCCAAGAAGATGTTGATGGGCACGAAGAGCCTTCGAAAATTCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * * *
40729 ATAAAAGACGTCAACTCCAAGAAGATGTTGATGGGCACGAAGAGCCCTCGAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * * * *
40789 ATGAAAGACATCAACTCCGAGAACATGTTGATGGCCATGAAGTGCCCTCGAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * ** ***
40849 ATAAAAGACGTCGACTTCGAGAAGATGTTGATAACCACGAAGAGCCCTTAAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * * *
40909 ATGAAAGACATCGACTCCGAGAACATGTTGATGGTCACGAAGTGCCCTCGAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
40969 ATAAAAGACGTCGACTCCAAGAAAATGTTGATGGCCACGAAGAGCCCACGAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
41029 ATGAAAGACATCGACTCCGAGAACATGTTGATGGCCATGAAGTGCCCTCGGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * *
41089 ATAAAAGACGTCGACTTCGAGAAGATGTTGATGGCCACGAAGAGCCCTGGGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * * * * **
41149 GTGAAAGACATCAACTCCGTGAACATGTTGATGGCCACGAAGTGCCCTTAGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
41209 ATAAAAGACGTCGACTTCGAGAAGATGTTGATGGGCACGAAGAGCCCTCGAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * * **
41269 ATGAAAGACATCGACTCCGTGAACATGTTGATGGCCACGAAGTGCCCTTAGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
41329 ATAAAAGACGTCGACTTCGAGAAGATGTTGATGGGCACGAAGAGCCCTCGAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
41389 ATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGAAGTGCCCTCAGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * ***
41449 ATAAAAGACGTCGACTCCAAGAAGATGTTGATGGCCACGAAGAGCCCTTAAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
41509 ATGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGAAGTGCCCTCGAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * *
41569 ATAAAAGACGTCGACTCCAAGAAGATGTTGATGGCCACGAAGAGCCCACGGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
41629 ATGAAAGACATCGACTCCGAGAACATGTTGATGGCCATGAAGTGCCCTCGGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * *
41689 ATAAAAGACGTCGACTTCGAGAAGATGTTGATGGCCACGAAGAGCCCTGGGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * * * * * **
41749 GTGAAAGACATCAACTCCGTGAACATGTTGATGGCCATGAAGTGCCCTTAGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
41809 ATAAAAGACGTCGACTTCGAGAAGATGTTGATGGCCACGAAGAGCCCTCGAAAATGCTTG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * * * * *
41869 GTGAAAGACATCAACTCCGAGAACATGTCGATGGCCACGAAGTGCCCTCAGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* *
41929 ATAAAAGACGTCGACTCCGAGAAGATGTTGATGGGCACGAAGAGCCCTCGGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * * *
41989 ATGAAAGACATCAACTCCGAGAACATGTTGATGGCCACGAAGTGCCCTCAGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
42049 ATAAAAGACGTCGACTCCGAGAAGATGTTGATGGGCACAAAGAGCCCTCGAAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * *
42109 GTGAAAGACATCGACTCCGAGAACATGTTGATGGCCACGAAGTGCCCTCGGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * *
42169 ATAAAAGACGTCGACTCCAAGAAGATGTTGATGGCCACGAAGAGCCCTTGGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* ** * *
42229 ATGAAAGATATCGACTCCGAGAACATGTTGATGGCCACGAAGTGCCCTCAGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* * * * * * *
42289 ATAAAAGACGTCGACTCCAAGAAAATATTTATGGACATGAAGAGCCCTGGGAAATGCTAG
1 ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
* *
42349 ATAAACGACGTGGACTCC
1 ATAAAAGACGTCGACTCC
42367 AAAAAAATGA
Statistics
Matches: 1402, Mismatches: 236, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 1402 1.00
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.19
Consensus pattern (60 bp):
ATAAAAGACGTCGACTCCGAGAACATGTTGATGGCCACGAAGAGCCCTCGGAAATGCTAG
Found at i:48799 original size:20 final size:21
Alignment explanation
Indices: 48774--48813 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
48764 AACAGATATT
48774 ATATTTTTATTCAAA-ATTTA
1 ATATTTTTATTCAAACATTTA
48794 ATATTTTTATTCAAACATTT
1 ATATTTTTATTCAAACATTT
48814 TCCATCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTTTTATTCAAACATTTA
Found at i:58727 original size:33 final size:32
Alignment explanation
Indices: 58686--58748 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 32
58676 TTATTAAGAT
58686 TATTTAAAAATTTTGTAAAAA-T-AAAAAATAAA
1 TATTT-AAAATTTT-TAAAAATTCAAAAAATAAA
58718 TATTATAAAATTTTTAAAAATTCAAAAAATA
1 TATT-TAAAATTTTTAAAAATTCAAAAAATA
58749 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 6 0.21
32 13 0.46
33 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (32 bp):
TATTTAAAATTTTTAAAAATTCAAAAAATAAA
Found at i:60398 original size:12 final size:13
Alignment explanation
Indices: 60373--60403 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
60363 TGCAAATGTA
60373 TCATTTCTCATTT
1 TCATTTCTCATTT
60386 TCATTTC-CATTT
1 TCATTTCTCATTT
60398 TCATTT
1 TCATTT
60404 TGAGAAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:61195 original size:17 final size:17
Alignment explanation
Indices: 61173--61207 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61163 ACTCAAGTAT
* *
61173 TCTACTCGTGAGGCCTA
1 TCTACTCATAAGGCCTA
61190 TCTACTCATAAGGCCTA
1 TCTACTCATAAGGCCTA
61207 T
1 T
61208 GAGACAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (17 bp):
TCTACTCATAAGGCCTA
Found at i:62830 original size:18 final size:17
Alignment explanation
Indices: 62777--62848 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
62767 TTAAAATTAT
*
62777 TTAAAAAATTTATAAAAAA
1 TTAAAAAA--TATTAAAAA
*
62796 TT--AAAATA-TATAAA
1 TTAAAAAATATTAAAAA
* *
62810 TTATAAAATTTTTAAAAA
1 TTA-AAAAATATTAAAAA
62828 TTAAAAAATATTAAAAA
1 TTAAAAAATATTAAAAA
62845 TTAA
1 TTAA
62849 TTAATTGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 6 0.14
15 2 0.05
17 24 0.57
18 8 0.19
19 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAAATATTAAAAA
Found at i:63606 original size:12 final size:12
Alignment explanation
Indices: 63589--63702 Score: 95
Period size: 12 Copynumber: 9.6 Consensus size: 12
63579 ATAACATCCA
*
63589 AACAACCAAAAT
1 AACAACAAAAAT
* *
63601 AACAACCAAAAC
1 AACAACAAAAAT
* *
63613 AGCAGCAAAAAT
1 AACAACAAAAAT
* * *
63625 AATAGC-AAAAC
1 AACAACAAAAAT
63636 AACAACAAAAAT
1 AACAACAAAAAT
* *
63648 AGCACCAAAAAT
1 AACAACAAAAAT
* *
63660 AATAGCAAAAAT
1 AACAACAAAAAT
* *
63672 AGCAACAAAAAC
1 AACAACAAAAAT
63684 AACAACAAAAAT
1 AACAACAAAAAT
63696 AACAACA
1 AACAACA
63703 TCAAAACAGT
Statistics
Matches: 79, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
11 8 0.10
12 71 0.90
ACGTcount: A:0.67, C:0.21, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:63641 original size:35 final size:34
Alignment explanation
Indices: 63595--63697 Score: 125
Period size: 35 Copynumber: 2.9 Consensus size: 34
63585 TCCAAACAAC
* *
63595 CAAAATAACAACCAAAACAGCAGCAAAAATAATAG
1 CAAAA-AACAACAAAAACAGCAACAAAAATAATAG
* *
63630 CAAAACAACAACAAAAATAGCACCAAAAATAATAG
1 CAAAA-AACAACAAAAACAGCAACAAAAATAATAG
*
63665 CAAAAATAGCAACAAAAACAACAACAAAAATAA
1 CAAAAA-A-CAACAAAAACAGCAACAAAAATAA
63698 CAACATCAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
34 1 0.02
35 37 0.63
36 21 0.36
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.08
Consensus pattern (34 bp):
CAAAAAACAACAAAAACAGCAACAAAAATAATAG
Found at i:63727 original size:20 final size:20
Alignment explanation
Indices: 63704--63781 Score: 95
Period size: 20 Copynumber: 3.8 Consensus size: 20
63694 ATAACAACAT
63704 CAAAACAGTAAAAAAAGCAC
1 CAAAACAGTAAAAAAAGCAC
* *
63724 CAAAACAGTAAAAAAATAACGC
1 CAAAACAGT-AAAAAA-AGCAC
*
63746 CAAAACAG-CAAAAAAGCAAC
1 CAAAACAGTAAAAAAAGC-AC
63766 CAAAACAGTAAAAAAA
1 CAAAACAGTAAAAAAA
63782 AAATAGCATC
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 2 0.04
20 23 0.48
21 12 0.25
22 11 0.23
ACGTcount: A:0.67, C:0.19, G:0.09, T:0.05
Consensus pattern (20 bp):
CAAAACAGTAAAAAAAGCAC
Found at i:68054 original size:24 final size:24
Alignment explanation
Indices: 68025--68088 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
68015 AGAAATAATC
*
68025 TTTCAATTAAATTCTTTTTATTTG
1 TTTCAATTAAACTCTTTTTATTTG
*
68049 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTTTTTATTTG
68073 TTTCAATTAAACTCTT
1 TTTCAATTAAACTCTT
68089 ATCAGTTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTTTTTATTTG
Found at i:68096 original size:21 final size:22
Alignment explanation
Indices: 68025--68096 Score: 56
Period size: 24 Copynumber: 3.1 Consensus size: 22
68015 AGAAATAATC
* **
68025 TTTCAATTAAATTCTTTTTATTTG
1 TTTCAATTAAA--CTCTTTATCAG
**
68049 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTC--TTTATCAG
68073 TTTCAATTAAACTC-TTATCAG
1 TTTCAATTAAACTCTTTATCAG
68094 TTT
1 TTT
68097 AGATTATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
21 8 0.19
22 2 0.05
24 33 0.77
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTCAATTAAACTCTTTATCAG
Done.