Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 16 of 208
Found at i:4860863 original size:17 final size:17
Alignment explanation
Indices: 4860843--4860879 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4860833 AAACAACAAC
4860843 CAGCAAAAAAAAAGCAG
1 CAGCAAAAAAAAAGCAG
* *
4860860 CAGCAGAAAAAAGGCAG
1 CAGCAAAAAAAAAGCAG
4860877 CAG
1 CAG
4860880 GCCTGTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.19, G:0.24, T:0.00
Consensus pattern (17 bp):
CAGCAAAAAAAAAGCAG
Found at i:4860902 original size:19 final size:19
Alignment explanation
Indices: 4860874--4860920 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4860864 AGAAAAAAGG
*
4860874 CAGCAGGCCTG-TCCAAGCC
1 CAGCAAGCCTGATCC-AGCC
*
4860893 CAGCAAGCCTGATCCAGTC
1 CAGCAAGCCTGATCCAGCC
4860912 CAGCAAGCC
1 CAGCAAGCC
4860921 CAGAATAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.26, C:0.40, G:0.23, T:0.11
Consensus pattern (19 bp):
CAGCAAGCCTGATCCAGCC
Found at i:4861522 original size:18 final size:18
Alignment explanation
Indices: 4861501--4861616 Score: 89
Period size: 17 Copynumber: 6.4 Consensus size: 18
4861491 ACGATATTTC
4861501 TTTTAAAAAAATTTCGTG
1 TTTTAAAAAAATTTCGTG
4861519 TTTTCAAAAAAATTCTCGTG
1 TTTT-AAAAAAATT-TCGTG
* * *
4861539 -TTT-CAAAATTTTCATG
1 TTTTAAAAAAATTTCGTG
**
4861555 -TTTCCAAAAATTTCCGTG
1 TTTTAAAAAAATTT-CGTG
*
4861573 -TTT-CAAAAATTTCGTG
1 TTTTAAAAAAATTTCGTG
4861589 TTTTCAAAAAAATTCTCGTG
1 TTTT-AAAAAAATT-TCGTG
*
4861609 TTTCAAAA
1 TTTTAAAA
4861617 TCTTCGTGCT
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
16 11 0.13
17 26 0.31
18 10 0.12
19 23 0.28
20 13 0.16
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAAATTTCGTG
Found at i:4861563 original size:36 final size:36
Alignment explanation
Indices: 4861507--4861629 Score: 171
Period size: 35 Copynumber: 3.5 Consensus size: 36
4861497 TTTCTTTTAA
4861507 AAAAATTTCGTGTTTTCAAAAAAATTCTCGTGTTTC
1 AAAAATTTCGTGTTTTCAAAAAAATTCTCGTGTTTC
* * * *
4861543 AAAATTTTCATG-TTTCCAAAAATTTC-CGTGTTTC
1 AAAAATTTCGTGTTTTCAAAAAAATTCTCGTGTTTC
4861577 AAAAATTTCGTGTTTTCAAAAAAATTCTCGTGTTTC
1 AAAAATTTCGTGTTTTCAAAAAAATTCTCGTGTTTC
*
4861613 -AAAATCTTCGTGCTTTC
1 AAAAAT-TTCGTGTTTTC
4861630 TTTCTTTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
34 18 0.24
35 29 0.39
36 28 0.37
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (36 bp):
AAAAATTTCGTGTTTTCAAAAAAATTCTCGTGTTTC
Found at i:4862076 original size:12 final size:12
Alignment explanation
Indices: 4862059--4862084 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4862049 TCCGCTGCAA
4862059 AATAAAGTAATC
1 AATAAAGTAATC
4862071 AATAAAGTAATC
1 AATAAAGTAATC
4862083 AA
1 AA
4862085 AATATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (12 bp):
AATAAAGTAATC
Found at i:4865585 original size:30 final size:26
Alignment explanation
Indices: 4865521--4865621 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 26
4865511 TGGTTTGGGC
*
4865521 TCATATATTGGTGGGTTGTTG-GGAGGT
1 TCATACATTGGT-GGTT-TTGTGGAGGT
*
4865548 TGATACATTGGTGGTTTTAGTGGCTTAGGT
1 TCATACATTGGTGGTTTT-GTGG---AGGT
* * *
4865578 TCGTACATTGGAGGCTTTTTTGGAGGT
1 TCATACATTGGTGG-TTTTGTGGAGGT
4865605 TCATACATTGGTGGTTT
1 TCATACATTGGTGGTTT
4865622 GGGTTCATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
25 2 0.03
26 8 0.13
27 28 0.47
30 18 0.30
31 4 0.07
ACGTcount: A:0.16, C:0.08, G:0.34, T:0.43
Consensus pattern (26 bp):
TCATACATTGGTGGTTTTGTGGAGGT
Found at i:4865605 original size:57 final size:57
Alignment explanation
Indices: 4865542--4865726 Score: 178
Period size: 57 Copynumber: 3.4 Consensus size: 57
4865532 TGGGTTGTTG
* *
4865542 GGAGGTTGATACATTGGTGGTTTTAGTGGCTTAGGTTCGTACATTGGAGGCTTTTTT
1 GGAGGTTCATACATTGGTGGTTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTTT
* * *
4865599 GGAGGTTCATACATTGGTGGTTTGGGT-TCATCAGGTT--T-C-TT------TTTCTTT
1 GGAGGTTCATACATTGGTGGTTTTGGTGGC-TTAGGTTCGTACATTGGAGGCTTT-TTT
* ** *
4865647 GGAGGTGT-ATAAACCGGTGGCTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTTT
1 GGAGGT-TCATACATTGGTGGTTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTTT
4865704 GGAGGTTCATACATTGGTGGTTT
1 GGAGGTTCATACATTGGTGGTTT
4865727 GGGTTCAGGT
Statistics
Matches: 97, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
47 3 0.03
48 29 0.30
49 2 0.02
50 1 0.01
51 1 0.01
52 2 0.02
53 2 0.02
54 1 0.01
55 1 0.01
56 2 0.02
57 50 0.52
58 3 0.03
ACGTcount: A:0.15, C:0.11, G:0.32, T:0.42
Consensus pattern (57 bp):
GGAGGTTCATACATTGGTGGTTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTTT
Found at i:4865623 original size:105 final size:105
Alignment explanation
Indices: 4865509--4865772 Score: 304
Period size: 105 Copynumber: 2.5 Consensus size: 105
4865499 TGGTGGCTTA
* * * * ** *
4865509 GGTGGTTTGGGCTCAT-ATATTGGTGGGTTGTTGGGAGGT-TGATACATTGGTGGTTTTAGTGGC
1 GGTGGTTTGGGCTCATCAGATTGCT-GGTTCTTGGGAGGTGT-ATAAACCGGTGGCTTTAGTGGC
4865572 TTAGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATT
64 TTAGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATT
* * * ** * *
4865614 GGTGGTTTGGGTTCATCAGGTTTCTTTTTCTTTGGAGGTGTATAAACCGGTGGCTTTGGTGGCTT
1 GGTGGTTTGGGCTCATCAGATTGCTGGTTCTTGGGAGGTGTATAAACCGGTGGCTTTAGTGGCTT
4865679 AGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATT
66 AGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATT
* * ** *
4865719 GGTGGTTTGGG-T--TCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTT
1 GGTGGTTTGGGCTCATCAGATTGCTGGTTCTTGGGAGGTGTATAAACCGGTGGCTTT
4865773 GGCTCGGGCT
Statistics
Matches: 142, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
102 41 0.29
104 1 0.01
105 95 0.67
106 5 0.04
ACGTcount: A:0.14, C:0.11, G:0.33, T:0.42
Consensus pattern (105 bp):
GGTGGTTTGGGCTCATCAGATTGCTGGTTCTTGGGAGGTGTATAAACCGGTGGCTTTAGTGGCTT
AGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATT
Found at i:4865768 original size:45 final size:45
Alignment explanation
Indices: 4865701--4866003 Score: 326
Period size: 45 Copynumber: 6.7 Consensus size: 45
4865691 TGGAGGCTTT
* ** * *
4865701 TTTGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTC
1 TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGGCTTCTCCTTC
* *
4865746 TTTGGAGGTGT-ATAAACCGGTGGCTTT-GGCTCGGGCTTCTCCTTC
1 TTTGGAGGT-TCATAAACCGGTGG-TTTGGGTTCAGGCTTCTCCTTC
* * * *
4865791 TTTGGAGGTTCATATACGGGTGGTTTGGGTTCAGGTTTCTCTTTC
1 TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGGCTTCTCCTTC
* * * *
4865836 TTTGGAGGTGT-ATAAACCGGTGATTTTGGCTCAGGTTTCTCCTTC
1 TTTGGAGGT-TCATAAACCGGTGGTTTGGGTTCAGGCTTCTCCTTC
* * *
4865881 TTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGCTTCTCCTTC
1 TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGGCTTCTCCTTC
* * * *
4865926 TTTGGAGGTTCATACACTGGTGGTTTGGGTTCAGGCTTCTCTTTT
1 TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGGCTTCTCCTTC
* *
4865971 TTTGGAGGTGT-ATAAACCGGTGGCTTAGGTTCA
1 TTTGGAGGT-TCATAAACCGGTGGTTTGGGTTCA
4866004 TATGGTGGTG
Statistics
Matches: 218, Mismatches: 33, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
44 5 0.02
45 207 0.95
46 6 0.03
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.41
Consensus pattern (45 bp):
TTTGGAGGTTCATAAACCGGTGGTTTGGGTTCAGGCTTCTCCTTC
Found at i:4865783 original size:105 final size:104
Alignment explanation
Indices: 4865557--4865774 Score: 386
Period size: 105 Copynumber: 2.1 Consensus size: 104
4865547 TTGATACATT
* *
4865557 GGTGGTTTTAGTGGCTTAGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATTGGTGGTTT
1 GGTGGCTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATTGGTGGTTT
*
4865622 GGGTTCATCAGGTTTCTTTTTCTTTGGAGGTGTATAAACC
66 GGGTT-ATCAGGTTTCTCTTTCTTTGGAGGTGTATAAACC
4865662 GGTGGCTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATTGGTGGTTT
1 GGTGGCTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATTGGTGGTTT
4865727 GGG-T-TCAGGTTTCTCTTTCTTTGGAGGTGTATAAACC
66 GGGTTATCAGGTTTCTCTTTCTTTGGAGGTGTATAAACC
4865764 GGTGGCTTTGG
1 GGTGGCTTTGG
4865775 CTCGGGCTTC
Statistics
Matches: 110, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
102 43 0.39
104 1 0.01
105 66 0.60
ACGTcount: A:0.14, C:0.12, G:0.33, T:0.42
Consensus pattern (104 bp):
GGTGGCTTTGGTGGCTTAGGTTCGTACATTGGAGGCTTTTTTGGAGGTTCATACATTGGTGGTTT
GGGTTATCAGGTTTCTCTTTCTTTGGAGGTGTATAAACC
Found at i:4865813 original size:90 final size:89
Alignment explanation
Indices: 4865701--4865979 Score: 389
Period size: 90 Copynumber: 3.1 Consensus size: 89
4865691 TGGAGGCTTT
* *
4865701 TTTGGAGGTTCATACATTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
1 TTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
*
4865766 TGGCTTTGGCTCGGGCTTCTCCTTC
66 TGG-TTTGGCTCAGGCTTCTCCTTC
*
4865791 TTTGGAGGTTCATATACGGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
1 TTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
* *
4865856 TGATTTTGGCTCAGGTTTCTCCTTC
66 TG-GTTTGGCTCAGGCTTCTCCTTC
* * * * *
4865881 TTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGCTTCTCCTTCTTTGGAGGT-TCATACACTG
1 TTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGT-ATAAACCG
* * *
4865945 GTGGTTTGGGTTCAGGCTTCTCTTTT
65 GTGGTTT-GGCTCAGGCTTCTCCTTC
4865971 TTTGGAGGT
1 TTTGGAGGT
4865980 GTATAAACCG
Statistics
Matches: 169, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
89 4 0.02
90 165 0.98
ACGTcount: A:0.12, C:0.16, G:0.29, T:0.42
Consensus pattern (89 bp):
TTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGG
TGGTTTGGCTCAGGCTTCTCCTTC
Found at i:4865948 original size:135 final size:135
Alignment explanation
Indices: 4865731--4865992 Score: 411
Period size: 135 Copynumber: 1.9 Consensus size: 135
4865721 TGGTTTGGGT
* *
4865731 TCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTGGCTTTGGCTCGGGCTTCTCCTTCTTTGG
1 TCAGGTTTCTCCTTCTTTGGAGGTGTATAAACCGGTGGCTTTGGCTCAGGCTTCTCCTTCTTTGG
* *
4865796 AGGTTCATATACGGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCGGTGATT
66 AGGTTCATACACGGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTGATT
4865861 TTGGC
131 TTGGC
* * *
4865866 TCAGGTTTCTCCTTCTTTGGAGGT-TCATATACTGGTGG-TTTAGGTTCAGGCTTCTCCTTCTTT
1 TCAGGTTTCTCCTTCTTTGGAGGTGT-ATAAACCGGTGGCTTT-GGCTCAGGCTTCTCCTTCTTT
* *
4865929 GGAGGTTCATACACTGGTGGTTTGGGTTCAGGCTTCTCTTTTTTTGGAGGTGTATAAACCGGTG
64 GGAGGTTCATACACGGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTG
4865993 GCTTAGGTTC
Statistics
Matches: 116, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
134 4 0.03
135 112 0.97
ACGTcount: A:0.13, C:0.17, G:0.29, T:0.41
Consensus pattern (135 bp):
TCAGGTTTCTCCTTCTTTGGAGGTGTATAAACCGGTGGCTTTGGCTCAGGCTTCTCCTTCTTTGG
AGGTTCATACACGGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACCGGTGATT
TTGGC
Found at i:4867243 original size:74 final size:74
Alignment explanation
Indices: 4867121--4867264 Score: 218
Period size: 74 Copynumber: 1.9 Consensus size: 74
4867111 TTCGGATTTT
* * * * *
4867121 AAAAAGGGATCATGCTCAGTAAGTTAGGACGCGATCTTTTCTTCATTCCTGAGATCGTTTAAAAC
1 AAAAAGGGATCATGCCCAATAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAAC
4867186 TTGAGAAAA
66 TTGAGAAAA
*
4867195 AAAAAGGGATCATGCCCAATAAGTTAGGACACGAT-TTCTTCTTAATTCCCGAGATCGTTTATAA
1 AAAAAGGGATCATGCCCAATAAGTTAGGACACGATCTT-TTCTTAATTCCCGAGATCGTTTAAAA
4867259 CTTGAG
65 CTTGAG
4867265 TTTGAAAAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 2 0.03
74 61 0.97
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (74 bp):
AAAAAGGGATCATGCCCAATAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAAC
TTGAGAAAA
Found at i:4867718 original size:51 final size:51
Alignment explanation
Indices: 4867612--4867708 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
4867602 GAAAATGAAT
*
4867612 AAAATTATAAAAATGTAAAAAGATATATATGTATGTATATATATGTATATA
1 AAAATTATAAAAATGTAAAAAGATATATATGTATGTATATATATATATATA
4867663 AAAATTAT-AAAATGTAAAAA-ATATATATAAGTATGTATATATATAT
1 AAAATTATAAAAATGTAAAAAGATATATAT--GTATGTATATATATAT
4867709 TCATGAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
49 8 0.19
50 12 0.28
51 23 0.53
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (51 bp):
AAAATTATAAAAATGTAAAAAGATATATATGTATGTATATATATATATATA
Found at i:4874617 original size:45 final size:45
Alignment explanation
Indices: 4874554--4875045 Score: 331
Period size: 45 Copynumber: 10.7 Consensus size: 45
4874544 CATACGGTGG
*
4874554 TTTCTTTGGAT-GTTCATAAACTGGTGGCTTGGGTCCTGGTTTCTC
1 TTTCTTTGG-TGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * * *
4874599 TTTCTTTGGTGGTACATAAACTGGTGGTTTTGGTGGTT-TAGGCTCATAAACTGG
1 TTTCTTTGGTGGTTCATAAACTGGTGG-CTT-G-GGTTCT-GG-T--T--TCT-C
* * * * *
4874653 TGGCTTCTTCGGAGGTTGATAAACTGGTGGTTTGGGTTCTGGTTTTTC
1 T---TTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * *
4874701 TTTCTTTGGTGGTGT-ATAAACCGGTGGCTTAGGCTT-AGGCTTT-TC
1 TTTCTTTGGTGGT-TCATAAACTGGTGGCTT-GGGTTCTGG-TTTCTC
* * * *
4874746 CTTCTTTGGTGGTTCATACACTGGTGGCTTGGGTTCAGGCTTCTC
1 TTTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * * *
4874791 TTTCTTTGGTGGGGT-ATAAACTGGTGGCTTAGGCTCAGGCTTT-TC
1 TTTCTTTGGT-GGTTCATAAACTGGTGGCTTGGGTTCTGG-TTTCTC
* * * * * *
4874836 CTTCTTTGGTGGTTCATATACTGGTGGTTTGTGTTCAGGCTTCTC
1 TTTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * *
4874881 TTTCTTTGGAGGTGT-ATAAACTGGTGGCTTTGGTTCGGGCTTT-TCC
1 TTTCTTTGGTGGT-TCATAAACTGGTGGCTTGGGTTCTGG-TTTCT-C
* * *
4874927 TTT-TTTGGTGATTCATATACTGGTGGCTTGGGTTCTGGCTTCTC
1 TTTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * * *
4874971 TTTCTTTGGTGGTGT-ATAAACTGGTGGTTTAGGTTCAGGTTTTTC
1 TTTCTTTGGTGGT-TCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
* * * *
4875016 CTTCTTTGGAGGTTCATAGACAGGTGGCTT
1 TTTCTTTGGTGGTTCATAAACTGGTGGCTT
4875046 ATGTTCATAA
Statistics
Matches: 351, Mismatches: 63, Indels: 66
0.73 0.13 0.14
Matches are distributed among these distances:
44 21 0.06
45 258 0.74
46 23 0.07
47 2 0.01
48 6 0.02
49 2 0.01
51 2 0.01
53 3 0.01
54 7 0.02
55 2 0.01
56 3 0.01
57 22 0.06
ACGTcount: A:0.12, C:0.15, G:0.29, T:0.43
Consensus pattern (45 bp):
TTTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCTGGTTTCTC
Found at i:4874750 original size:90 final size:90
Alignment explanation
Indices: 4874656--4875045 Score: 539
Period size: 90 Copynumber: 4.3 Consensus size: 90
4874646 AAACTGGTGG
* * * * * * * *
4874656 CTTCTTCGGAGGTTGATAAACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGTGGTGTATAAA
1 CTTCTTTGGTGGTTCATATACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
*
4874721 CCGGTGGCTTAGGCTT-AGGCTTTTC
66 CTGGTGGCTTAGG-TTCAGGCTTTTC
* *
4874746 CTTCTTTGGTGGTTCATACACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGGGTATAAA
1 CTTCTTTGGTGGTTCATATACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
*
4874811 CTGGTGGCTTAGGCTCAGGCTTTTC
66 CTGGTGGCTTAGGTTCAGGCTTTTC
* * *
4874836 CTTCTTTGGTGGTTCATATACTGGTGGTTTGTGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAA
1 CTTCTTTGGTGGTTCATATACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
* *
4874901 CTGGTGGCTTTGGTTCGGGCTTTTC
66 CTGGTGGCTTAGGTTCAGGCTTTTC
* * *
4874926 CTTTTTTGGTGATTCATATACTGGTGGCTTGGGTTCTGGCTTCTCTTTCTTTGGTGGTGTATAAA
1 CTTCTTTGGTGGTTCATATACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
* *
4874991 CTGGTGGTTTAGGTTCAGGTTTTTC
66 CTGGTGGCTTAGGTTCAGGCTTTTC
* * *
4875016 CTTCTTTGGAGGTTCATAGACAGGTGGCTT
1 CTTCTTTGGTGGTTCATATACTGGTGGCTT
4875046 ATGTTCATAA
Statistics
Matches: 265, Mismatches: 34, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
89 1 0.00
90 264 1.00
ACGTcount: A:0.12, C:0.16, G:0.29, T:0.44
Consensus pattern (90 bp):
CTTCTTTGGTGGTTCATATACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
CTGGTGGCTTAGGTTCAGGCTTTTC
Found at i:4875052 original size:45 final size:44
Alignment explanation
Indices: 4874656--4875052 Score: 375
Period size: 45 Copynumber: 8.8 Consensus size: 44
4874646 AAACTGGTGG
* * * * * *
4874656 CTTCTTCGGAGGTTGATAAACTGGTGGTTTGGGTTCTGGTTTTTC
1 CTTCTTTGGTGGTT-ATAAACTGGTGGCTTAGGTTCAGGCTTTTC
* *
4874701 TTTCTTTGGTGGTGTATAAACCGGTGGCTTAGGCTT-AGGCTTTTC
1 CTTCTTTGGTGGT-TATAAACTGGTGGCTTAGG-TTCAGGCTTTTC
* * *
4874746 CTTCTTTGGTGGTTCATACACTGGTGGCTTGGGTTCAGGCTTCTC
1 CTTCTTTGGTGGTT-ATAAACTGGTGGCTTAGGTTCAGGCTTTTC
* * *
4874791 TTTCTTTGGTGGGGTATAAACTGGTGGCTTAGGCTCAGGCTTTTC
1 CTTCTTTGGT-GGTTATAAACTGGTGGCTTAGGTTCAGGCTTTTC
* * *
4874836 CTTCTTTGGTGGTTCATATACTGGTGG-TTTGTGTTCAGGCTTCTC
1 CTTCTTTGGTGGTT-ATAAACTGGTGGCTTAG-GTTCAGGCTTTTC
* * * *
4874881 TTTCTTTGGAGGTGTATAAACTGGTGGCTTTGGTTCGGGCTTTTC
1 CTTCTTTGGTGGT-TATAAACTGGTGGCTTAGGTTCAGGCTTTTC
* * * * * *
4874926 CTTTTTTGGTGATTCATATACTGGTGGCTTGGGTTCTGGCTTCTC
1 CTTCTTTGGTGGTT-ATAAACTGGTGGCTTAGGTTCAGGCTTTTC
* * *
4874971 TTTCTTTGGTGGTGTATAAACTGGTGGTTTAGGTTCAGGTTTTTC
1 CTTCTTTGGTGGT-TATAAACTGGTGGCTTAGGTTCAGGCTTTTC
* * * *
4875016 CTTCTTTGGAGGTTCATAGACAGGTGGCTTATGTTCA
1 CTTCTTTGGTGGTT-ATAAACTGGTGGCTTAGGTTCA
4875053 TAAGGTGGGG
Statistics
Matches: 287, Mismatches: 53, Indels: 24
0.79 0.15 0.07
Matches are distributed among these distances:
44 11 0.04
45 264 0.92
46 12 0.04
ACGTcount: A:0.12, C:0.16, G:0.29, T:0.44
Consensus pattern (44 bp):
CTTCTTTGGTGGTTATAAACTGGTGGCTTAGGTTCAGGCTTTTC
Found at i:4875416 original size:20 final size:20
Alignment explanation
Indices: 4875391--4875431 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4875381 GAAATTTTGG
4875391 ACTACGGATACACAAGGCTT
1 ACTACGGATACACAAGGCTT
4875411 ACTACGGATACACAAGGCTT
1 ACTACGGATACACAAGGCTT
4875431 A
1 A
4875432 GTCATGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ACTACGGATACACAAGGCTT
Found at i:4876242 original size:64 final size:64
Alignment explanation
Indices: 4876141--4876268 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
4876131 AATGAAAGTG
4876141 ACTAAGAATTTTTTTTTAAAATTAGCTTAGGGTAATTGGCTAATTGATCCTTGTCCATTTTAGT
1 ACTAAGAATTTTTTTTTAAAATTAGCTTAGGGTAATTGGCTAATTGATCCTTGTCCATTTTAGT
* *
4876205 ACTAAGAATTTTTTTTTCAATTTAGCTTAGGGTAATTGGCTAATTGATCCTTGTCCATTTTAGT
1 ACTAAGAATTTTTTTTTAAAATTAGCTTAGGGTAATTGGCTAATTGATCCTTGTCCATTTTAGT
4876269 CTCTCAACCT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.46
Consensus pattern (64 bp):
ACTAAGAATTTTTTTTTAAAATTAGCTTAGGGTAATTGGCTAATTGATCCTTGTCCATTTTAGT
Found at i:4877593 original size:19 final size:18
Alignment explanation
Indices: 4877565--4877603 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
4877555 TTAGCAAGTC
*
4877565 TTGAAAACTTCTATATAT
1 TTGAAAACTTCTATAAAT
*
4877583 TTGAGAAACTTGTATAAAT
1 TTGA-AAACTTCTATAAAT
4877602 TT
1 TT
4877604 ATTTACTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (18 bp):
TTGAAAACTTCTATAAAT
Found at i:4884379 original size:21 final size:21
Alignment explanation
Indices: 4884353--4884403 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
4884343 ATTCATACGA
*
4884353 AAATTTTAAAATATA-TATTCT
1 AAATTTTAAAATATACTAAT-T
* *
4884374 AAATTTAAAAATTTACTAATT
1 AAATTTTAAAATATACTAATT
4884395 AAATTTTAA
1 AAATTTTAA
4884404 CTATAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTTTAAAATATACTAATT
Found at i:4885956 original size:20 final size:17
Alignment explanation
Indices: 4885922--4885955 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4885912 CATGAAGGGT
4885922 CGGAATAATTTTCATCA
1 CGGAATAATTTTCATCA
*
4885939 CGGAATAATATTCATCA
1 CGGAATAATTTTCATCA
4885956 TTGCCTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (17 bp):
CGGAATAATTTTCATCA
Found at i:4886604 original size:90 final size:90
Alignment explanation
Indices: 4886532--4886923 Score: 528
Period size: 90 Copynumber: 4.4 Consensus size: 90
4886522 TGGAGGCTTA
* * * * *
4886532 TAAGCCGGTGGCTTCTCCTTCTTTGGTGGTCCATACACTGGTGGTTTGGGCTCAGGCTGCTCTTT
1 TAAGCC-GTGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTT
4886597 CTTTGGTGGTGTATAAACTGGTGGCT
65 CTTTGGTGGTGTATAAACTGGTGGCT
* * *
4886623 TAGGCTC-AGGCTTTTCCTTCTTTGGGGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTT
1 TAAGC-CGTGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTT
4886687 CTTTGGTGGTGTATAAACTGGTGGCT
65 CTTTGGTGGTGTATAAACTGGTGGCT
* * *
4886713 TAGGTTC-AGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTT
1 TAAG-CCGTGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTT
4886777 CTTTGGTGGTGTATAAACTGGTGGCT
65 CTTTGGTGGTGTATAAACTGGTGGCT
* * *
4886803 TAGGTTC-AGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGG-TT-GG-TCAGGCTTCTCTTT
1 TAAG-CCGTGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTT
*
4886864 CTTTGGAGGTGTATAAACTGGTGGCT
65 CTTTGGTGGTGTATAAACTGGTGGCT
* * *
4886890 TAGGCTC-AGGCTTTTCCTTCTTTGGTGGTTCATA
1 TAAGC-CGTGGCTTTTCCTTCTTTGGAGGTTCATA
4886924 GACAGGGGGC
Statistics
Matches: 286, Mismatches: 12, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
87 70 0.24
88 2 0.01
89 2 0.01
90 207 0.72
91 4 0.01
92 1 0.00
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (90 bp):
TAAGCCGTGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTC
TTTGGTGGTGTATAAACTGGTGGCT
Found at i:4886763 original size:180 final size:177
Alignment explanation
Indices: 4886541--4886923 Score: 658
Period size: 180 Copynumber: 2.1 Consensus size: 177
4886531 ATAAGCCGGT
* *
4886541 GGCTTCTCCTTCTTTGGTGGTCCATACACTGGTGGTTTGGGCTCAGGCTGCTCTTTCTTTGGTGG
1 GGCTTTTCCTTCTTTGGTGGTTCATACACTGGTGGTTTGGGCTCAGGCTGCTCTTTCTTTGGTGG
*
4886606 TGTATAAACTGGTGGCTTAGGCTCAGGCTTTTCCTTCTTTGGGGGTTCATATACTGGTGGTTTGG
66 TGTATAAACTGGTGGCTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGG-TT-G
* *
4886671 GCTCAGGCTTCTCTTTCTTTGGTGGTGTATAAACTGGTGGCTTAGGTTCA
129 G-TCAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCA
* * *
4886721 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGG
1 GGCTTTTCCTTCTTTGGTGGTTCATACACTGGTGGTTTGGGCTCAGGCTGCTCTTTCTTTGGTGG
*
4886786 TGTATAAACTGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTGGT
66 TGTATAAACTGGTGGCTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTGGT
4886851 CAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCA
131 CAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCA
4886898 GGCTTTTCCTTCTTTGGTGGTTCATA
1 GGCTTTTCCTTCTTTGGTGGTTCATA
4886924 GACAGGGGGC
Statistics
Matches: 193, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
177 71 0.37
178 2 0.01
179 2 0.01
180 118 0.61
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (177 bp):
GGCTTTTCCTTCTTTGGTGGTTCATACACTGGTGGTTTGGGCTCAGGCTGCTCTTTCTTTGGTGG
TGTATAAACTGGTGGCTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTGGT
CAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTAGGCTCA
Found at i:4886936 original size:45 final size:45
Alignment explanation
Indices: 4886541--4886923 Score: 447
Period size: 45 Copynumber: 8.6 Consensus size: 45
4886531 ATAAGCCGGT
* * * *
4886541 GGCTTCTCCTTCTTTGGTGGTCCATACACTGGTGGTTTGGGCTCA
1 GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
* *
4886586 GGCTGCTCTTTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGCTCA
1 GGCTTCTCCTTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCA
* * * * *
4886631 GGCTTTTCCTTCTTTGGGGGTTCATATACTGGTGGTTTGGGCTCA
1 GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
* *
4886676 GGCTTCTCTTTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGTTCA
1 GGCTTCTCCTTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCA
* * * * *
4886721 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCA
1 GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
* *
4886766 GGCTTCTCTTTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGTTCA
1 GGCTTCTCCTTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCA
* * *
4886811 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGG-TT-GG-TCA
1 GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
* *
4886853 GGCTTCTCTTTCTTTGGAGGTGT-ATAAACTGGTGGCTTAGGCTCA
1 GGCTTCTCCTTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCA
*
4886898 GGCTTTTCCTTCTTTGGTGGTTCATA
1 GGCTTCTCCTTCTTTGGTGGTTCATA
4886924 GACAGGGGGC
Statistics
Matches: 283, Mismatches: 44, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
42 33 0.12
43 5 0.02
44 8 0.03
45 235 0.83
46 2 0.01
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (45 bp):
GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
Found at i:4888270 original size:16 final size:15
Alignment explanation
Indices: 4888249--4888279 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4888239 GGTGCTTTCC
4888249 TTTTCTTTTCTTTTTT
1 TTTTCTTTT-TTTTTT
4888265 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
4888280 GCATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:4888279 original size:11 final size:11
Alignment explanation
Indices: 4888244--4888279 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
4888234 ACCATGGTGC
* *
4888244 TTTCCTTTTCT
1 TTTCTTTTTTT
4888255 TTTCTTTTTTT
1 TTTCTTTTTTT
4888266 TTTCTTTTTTT
1 TTTCTTTTTTT
4888277 TTT
1 TTT
4888280 GCATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:4888512 original size:15 final size:14
Alignment explanation
Indices: 4888494--4888524 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4888484 GGTGCTTTCC
4888494 TTTTCTTTTCTTTTT
1 TTTTCTTTT-TTTTT
4888509 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
4888523 TT
1 TT
4888525 GCATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:4888521 original size:245 final size:245
Alignment explanation
Indices: 4888088--4889062 Score: 1809
Period size: 245 Copynumber: 4.0 Consensus size: 245
4888078 CATATTATCA
*
4888088 AGGATTTACATCAATTATATTATTTTCTTATTTCTTCATATCATTTCAATACGAATGAATTCACA
1 AGGATTTACATCAATTATATTATTTTCTTATTTCTTCTTATCATTTCAATACGAATGAATTCACA
*
4888153 CTCCATACTTAAATTCGGATTTAATTCTATTTAATCCATATAAGTCTATATAAAAGTAAATCCTT
66 CTCCATACTTAAATTCGGATTTAATTCTATTTAATCCATATAAGTCTATATAAAAGTAAGTCCTT
4888218 TGTTTACACATGCACCACCATGGTGCTTTCCTTTTCTTTTCTTTTTTTTT-TCTTTTTTTTTTGC
131 TGTTTACACATGCACCACCATGGTGCTTTCCTTTTCTTTTCTTTTTTTTTCT-TTTTTTTTTTGC
4888282 ATTTTAAAAAATGTTAAATTTTAATTTTGACCTCTCTATTATGTCTAAATT
195 ATTTTAAAAAATGTTAAATTTTAATTTTGACCTCTCTATTATGTCTAAATT
4888333 AGGATTTACATCAATTATATTATTTTCTTATTTCTTCTTATCATTTCAATACGAATGAATTCACA
1 AGGATTTACATCAATTATATTATTTTCTTATTTCTTCTTATCATTTCAATACGAATGAATTCACA
4888398 CTCCATACTTAAATTCGGATTTAATTCTATTTAATCCATATAAGTCTATATAAAAGTAAGTCCTT
66 CTCCATACTTAAATTCGGATTTAATTCTATTTAATCCATATAAGTCTATATAAAAGTAAGTCCTT
4888463 TGTTTACACATGCACCACCATGGTGCTTTCCTTTTCTTTTCTTTTTTTTTCTTTTTTTTTTTGCA
131 TGTTTACACATGCACCACCATGGTGCTTTCCTTTTCTTTTCTTTTTTTTTCTTTTTTTTTTTGCA
4888528 TTTTAAAAAATGTTAAATTTTAATTTTGACCTCTCTATTATGTCTAAATT
196 TTTTAAAAAATGTTAAATTTTAATTTTGACCTCTCTATTATGTCTAAATT
4888578 AGGATTTACATCAATTATATTATTTTCTTATTTCTTCTTATCATTTCAATACGAATGAATTCACA
1 AGGATTTACATCAATTATATTATTTTCTTATTTCTTCTTATCATTTCAATACGAATGAATTCACA
4888643 CTCCATACTTAAATTCGGATTTAATTCTATTTAATCCATATAAGTCTATATAAAAGTAAGTCCTT
66 CTCCATACTTAAATTCGGATTTAATTCTATTTAATCCATATAAGTCTATATAAAAGTAAGTCCTT
4888708 TGTTTACACATGCACCACCATGGTGCTTTCCTTTTCTTTTCTTTTTTTTTCTTTTTTTTTTTTGC
131 TGTTTACACATGCACCACCATGGTGCTTTCCTTTTCTTTTCTTTTTTTTTC-TTTTTTTTTTTGC
4888773 ATTTTAAAAAATGTTAAATTTTAATTTTGACCTCTCTATTATGTCTAAATT
195 ATTTTAAAAAATGTTAAATTTTAATTTTGACCTCTCTATTATGTCTAAATT
4888824 AGGATTTACATCAATTATATTATTTTCTTATTTCTTCTTATCA-TT---T-CGAATGAATTCACA
1 AGGATTTACATCAATTATATTATTTTCTTATTTCTTCTTATCATTTCAATACGAATGAATTCACA
4888884 CTCCATACTTAAATTCGGATTTAATTCTATTTAATCCATATAAGTCTATATAAAAGTAAGTCCTT
66 CTCCATACTTAAATTCGGATTTAATTCTATTTAATCCATATAAGTCTATATAAAAGTAAGTCCTT
4888949 TGTTTACACATGCACCACCATGGTGCTTT-C----CTTTTC--TTTTTTTC--TTTTTTTTTGCA
131 TGTTTACACATGCACCACCATGGTGCTTTCCTTTTCTTTTCTTTTTTTTTCTTTTTTTTTTTGCA
4889005 TTTTAAAAAATGTTAAATTTTAATTTTGACCTCTCTATTATGTCTAAATT
196 TTTTAAAAAATGTTAAATTTTAATTTTGACCTCTCTATTATGTCTAAATT
4889055 AGGATTTA
1 AGGATTTA
4889063 GCCTCTATAC
Statistics
Matches: 726, Mismatches: 2, Indels: 18
0.97 0.00 0.02
Matches are distributed among these distances:
231 70 0.10
234 8 0.01
236 6 0.01
240 1 0.00
241 108 0.15
242 1 0.00
245 424 0.58
246 108 0.15
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.48
Consensus pattern (245 bp):
AGGATTTACATCAATTATATTATTTTCTTATTTCTTCTTATCATTTCAATACGAATGAATTCACA
CTCCATACTTAAATTCGGATTTAATTCTATTTAATCCATATAAGTCTATATAAAAGTAAGTCCTT
TGTTTACACATGCACCACCATGGTGCTTTCCTTTTCTTTTCTTTTTTTTTCTTTTTTTTTTTGCA
TTTTAAAAAATGTTAAATTTTAATTTTGACCTCTCTATTATGTCTAAATT
Found at i:4888522 original size:10 final size:10
Alignment explanation
Indices: 4888493--4888522 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
4888483 TGGTGCTTTC
*
4888493 CTTTTCTTTT
1 CTTTTTTTTT
4888503 CTTTTTTTTT
1 CTTTTTTTTT
4888513 CTTTTTTTTT
1 CTTTTTTTTT
4888523 TTGCATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:4888757 original size:15 final size:14
Alignment explanation
Indices: 4888739--4888770 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
4888729 GGTGCTTTCC
4888739 TTTTCTTTTCTTTTT
1 TTTTCTTTT-TTTTT
4888754 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
4888768 TTT
1 TTT
4888771 GCATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:4889420 original size:17 final size:17
Alignment explanation
Indices: 4889398--4889434 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4889388 ATTGAAAACT
4889398 CTTCTTGAAATTTCAAA
1 CTTCTTGAAATTTCAAA
**
4889415 CTTCTTGCCATTTCAAA
1 CTTCTTGAAATTTCAAA
4889432 CTT
1 CTT
4889435 GTACAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.43
Consensus pattern (17 bp):
CTTCTTGAAATTTCAAA
Found at i:4889988 original size:9 final size:9
Alignment explanation
Indices: 4889974--4890016 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
4889964 GTTTTCGAAT
4889974 TCGAATAAC
1 TCGAATAAC
4889983 TCGAATAAC
1 TCGAATAAC
*
4889992 TCGAATAAT
1 TCGAATAAC
*
4890001 TCGAATAAT
1 TCGAATAAC
4890010 TCGAATA
1 TCGAATA
4890017 TCAAACTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (9 bp):
TCGAATAAC
Found at i:4891939 original size:25 final size:26
Alignment explanation
Indices: 4891886--4891948 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
4891876 ATTTGTACAT
4891886 ATTATAAAAAATGTATAAACATATGA
1 ATTATAAAAAATGTATAAACATATGA
*
4891912 ATTATAAAACATG-A-AAACATAAAT-A
1 ATTATAAAAAATGTATAAACAT--ATGA
4891937 ATTATAAAAAAT
1 ATTATAAAAAAT
4891949 ATGAATGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 6 0.18
25 13 0.39
26 14 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (26 bp):
ATTATAAAAAATGTATAAACATATGA
Found at i:4892118 original size:12 final size:12
Alignment explanation
Indices: 4892101--4892143 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
4892091 ATATGTAAGT
4892101 ATAATAAATATA
1 ATAATAAATATA
*
4892113 AAAAT-AATAGTA
1 ATAATAAATA-TA
*
4892125 ATAATAAAAATA
1 ATAATAAATATA
4892137 ATAATAA
1 ATAATAA
4892144 CTATTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 4 0.15
12 19 0.73
13 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (12 bp):
ATAATAAATATA
Found at i:4893769 original size:22 final size:22
Alignment explanation
Indices: 4893744--4893790 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4893734 CTAAGAGAAG
* * *
4893744 TAAACAGGATAGCTATAAGCTA
1 TAAACAGAATAGCTACAAGCCA
*
4893766 TAAACAGAATGGCTACAAGCCA
1 TAAACAGAATAGCTACAAGCCA
4893788 TAA
1 TAA
4893791 GTACATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (22 bp):
TAAACAGAATAGCTACAAGCCA
Found at i:4893836 original size:32 final size:32
Alignment explanation
Indices: 4893782--4893916 Score: 132
Period size: 32 Copynumber: 4.3 Consensus size: 32
4893772 GAATGGCTAC
* * *
4893782 AAGCCATAAGT-ACA-TAATATGATTGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
4893812 AAGCCATCAGTAGCAGTGATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
4893844 CATCTATCAGTAAC-GATAATATCATCGGCACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
* *
4893876 AAGCCATCAGTAACAGTCATATAATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
4893908 AAGCCATCA
1 AAGCCATCA
4893917 ATAGCATTGC
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
30 10 0.12
31 3 0.04
32 71 0.84
33 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:4893994 original size:27 final size:27
Alignment explanation
Indices: 4893963--4894026 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
4893953 AGCAAAAATG
* *
4893963 CCAGTAATAGT-ATATGTGGCCA-AGCTA
1 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
4893990 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
4894017 CCAGT-ACAGT
1 CCAGTAACAGT
4894027 ACTTCTTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 7 0.21
27 24 0.73
28 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:4894118 original size:24 final size:24
Alignment explanation
Indices: 4894091--4894196 Score: 104
Period size: 24 Copynumber: 4.4 Consensus size: 24
4894081 CCATACTCAG
4894091 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
* *
4894115 AATCAGTCATACCATTCACAGACA
1 AATCAGTCATACAAATCACAGACA
* ** *
4894139 AATCAATCATTTAAATCACAGGCA
1 AATCAGTCATACAAATCACAGACA
* ** * *
4894163 CATCAGTCATTTACATCACATACA
1 AATCAGTCATACAAATCACAGACA
*
4894187 AATCAATCAT
1 AATCAGTCAT
4894197 TTACACTCGA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.24
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:4894168 original size:48 final size:47
Alignment explanation
Indices: 4894103--4894199 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 47
4894093 TCAGTCATAC
4894103 AAATCACAGACAAATCAGTCA-TACCATTCACAGACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTA-CA-TCACAGACAAATCAATCATTT
* * *
4894151 AAATCACAGGCACATCAGTCATTTACATCACATACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCA-TTACATCACAGACAAATCAATCATTT
4894199 A
1 A
4894200 CACTCGAGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 40 0.91
49 2 0.05
50 2 0.05
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (47 bp):
AAATCACAGACAAATCAGTCATTACATCACAGACAAATCAATCATTT
Found at i:4894197 original size:24 final size:24
Alignment explanation
Indices: 4894105--4894201 Score: 108
Period size: 24 Copynumber: 4.0 Consensus size: 24
4894095 AGTCATACAA
*
4894105 ATCACAGACAAATCAGTCA--TACC
1 ATCACAGACAAATCAATCATTTA-C
*
4894128 ATTCACAGACAAATCAATCATTTAA
1 A-TCACAGACAAATCAATCATTTAC
* * *
4894153 ATCACAGGCACATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
*
4894177 ATCACATACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
4894201 A
1 A
4894202 CTCGAGGGGC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
23 1 0.02
24 57 0.93
25 1 0.02
26 2 0.03
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.25
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:4894250 original size:26 final size:26
Alignment explanation
Indices: 4894193--4894278 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
4894183 TACAAATCAA
* * ** *
4894193 TCATTTACACTCGAGGGGCAAAATAG
1 TCATTTACCCTCCAGGGGCATTATGG
*
4894219 TAATTTACCCTCCAGGGGCATTATGG
1 TCATTTACCCTCCAGGGGCATTATGG
* * * *
4894245 TCATTTTACCTTACAGGGGTATTTTGG
1 TCA-TTTACCCTCCAGGGGCATTATGG
4894272 TCATTTA
1 TCATTTA
4894279 AACCTATGGG
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
26 26 0.54
27 22 0.46
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (26 bp):
TCATTTACCCTCCAGGGGCATTATGG
Found at i:4894261 original size:27 final size:27
Alignment explanation
Indices: 4894222--4894401 Score: 118
Period size: 27 Copynumber: 6.7 Consensus size: 27
4894212 AAAATAGTAA
* * *
4894222 TTTACCCTCCAGGGGCATTATGGTCAT
1 TTTACCTTACAGGGGTATTATGGTCAT
*
4894249 TTTACCTTACAGGGGTATTTTGGTCAT
1 TTTACCTTACAGGGGTATTATGGTCAT
* ** *
4894276 TTAAACC-TATGGGGGTATTACGGTCAT
1 TT-TACCTTACAGGGGTATTATGGTCAT
** *
4894303 TTTACCTTATGGGGGTATTTTGGTCAT
1 TTTACCTTACAGGGGTATTATGGTCAT
**
4894330 TTTATCC-TATGGGGGTATT-TCGGTCAT
1 TTTA-CCTTACAGGGGTATTAT-GGTCAT
* * *
4894357 TTTACCCTATA-GGGTATT-TCCGTCAT
1 TTTACCTTACAGGGGTATTAT-GGTCAT
* **
4894383 TCTACCTTATGGGGGTATT
1 TTTACCTTACAGGGGTATT
4894402 TCAGTCATTT
Statistics
Matches: 130, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
26 28 0.22
27 97 0.75
28 5 0.04
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.41
Consensus pattern (27 bp):
TTTACCTTACAGGGGTATTATGGTCAT
Found at i:4894408 original size:27 final size:27
Alignment explanation
Indices: 4894243--4894411 Score: 200
Period size: 27 Copynumber: 6.3 Consensus size: 27
4894233 GGGGCATTAT
** *
4894243 GGTCATTTTACCTTACAGGGGTATTTT
1 GGTCATTTTACCTTATGGGGGTATTTC
* *
4894270 GGTCATTTAAACC-TATGGGGGTATTAC
1 GGTCATTT-TACCTTATGGGGGTATTTC
*
4894297 GGTCATTTTACCTTATGGGGGTATTTT
1 GGTCATTTTACCTTATGGGGGTATTTC
4894324 GGTCATTTTATCC-TATGGGGGTATTTC
1 GGTCATTTTA-CCTTATGGGGGTATTTC
* *
4894351 GGTCATTTTACCCTAT-AGGGTATTTC
1 GGTCATTTTACCTTATGGGGGTATTTC
* *
4894377 CGTCATTCTACCTTATGGGGGTATTTC
1 GGTCATTTTACCTTATGGGGGTATTTC
*
4894404 AGTCATTT
1 GGTCATTT
4894412 AACAACCTTT
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
26 27 0.22
27 89 0.74
28 5 0.04
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (27 bp):
GGTCATTTTACCTTATGGGGGTATTTC
Found at i:4894409 original size:80 final size:81
Alignment explanation
Indices: 4894260--4894411 Score: 216
Period size: 80 Copynumber: 1.9 Consensus size: 81
4894250 TTACCTTACA
* * * * **
4894260 GGGGTATTTTGGTCATTTAAACCTATGGGGGTATTACGGTCATTTTACCTTATGGGGGTATTTTG
1 GGGGTATTTCGGTCATTTAAACCTATGAGGGTATTACCGTCATTCTACCTTATGGGGGTATTTCA
4894325 GTCATTTTATCCTATG
66 GTCATTTTATCCTATG
* * *
4894341 GGGGTATTTCGGTCATTTTACCCTAT-AGGGTATTTCCGTCATTCTACCTTATGGGGGTATTTCA
1 GGGGTATTTCGGTCATTTAAACCTATGAGGGTATTACCGTCATTCTACCTTATGGGGGTATTTCA
4894405 GTCATTT
66 GTCATTT
4894412 AACAACCTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
80 39 0.63
81 23 0.37
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.43
Consensus pattern (81 bp):
GGGGTATTTCGGTCATTTAAACCTATGAGGGTATTACCGTCATTCTACCTTATGGGGGTATTTCA
GTCATTTTATCCTATG
Found at i:4895362 original size:13 final size:13
Alignment explanation
Indices: 4895344--4895400 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
4895334 TTATCCAACT
4895344 CAACCCAATTACC
1 CAACCCAATTACC
4895357 CAACCCAATTA-C
1 CAACCCAATTACC
4895369 CAACCC-A--ACC
1 CAACCCAATTACC
*
4895379 CAACCTAATTACC
1 CAACCCAATTACC
4895392 CAACCCAAT
1 CAACCCAAT
4895401 AAAACTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 1 0.03
10 6 0.16
11 2 0.05
12 7 0.18
13 22 0.58
ACGTcount: A:0.40, C:0.46, G:0.00, T:0.14
Consensus pattern (13 bp):
CAACCCAATTACC
Found at i:4895382 original size:22 final size:23
Alignment explanation
Indices: 4895354--4895399 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
4895344 CAACCCAATT
4895354 ACCCAACCCAATTA-CCAACCCA
1 ACCCAACCCAATTACCCAACCCA
*
4895376 ACCCAACCTAATTACCCAACCCA
1 ACCCAACCCAATTACCCAACCCA
4895399 A
1 A
4895400 TAAAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.41, C:0.48, G:0.00, T:0.11
Consensus pattern (23 bp):
ACCCAACCCAATTACCCAACCCA
Found at i:4895394 original size:18 final size:18
Alignment explanation
Indices: 4895332--4895399 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
4895322 TAATAAATAA
* * *
4895332 AATTATCCAACTCAACCC
1 AATTACCCAACCCAACCT
*
4895350 AATTACCCAACCCAA-TT
1 AATTACCCAACCCAACCT
***
4895367 ACCAACCCAACCCAACCT
1 AATTACCCAACCCAACCT
4895385 AATTACCCAACCCAA
1 AATTACCCAACCCAA
4895400 TAAAACTAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
17 12 0.32
18 26 0.68
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (18 bp):
AATTACCCAACCCAACCT
Found at i:4895435 original size:39 final size:39
Alignment explanation
Indices: 4895385--4895497 Score: 183
Period size: 39 Copynumber: 2.9 Consensus size: 39
4895375 AACCCAACCT
*
4895385 AATTACCCAACCCAATAAAACTAAAACTAAAGTTTACCC
1 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
4895424 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
1 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
** *
4895463 AATTA-CCAACATAATAAAAATAAAACTAAAGTCTA
1 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTA
4895498 ACTCTTAAGT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
38 27 0.39
39 43 0.61
ACGTcount: A:0.52, C:0.25, G:0.03, T:0.20
Consensus pattern (39 bp):
AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
Found at i:4895652 original size:17 final size:17
Alignment explanation
Indices: 4895632--4895694 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
4895622 TAATTTCAAG
4895632 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
4895649 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
4895667 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
4895686 AATTATGTA
1 AATTATGTA
4895695 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:4895656 original size:37 final size:37
Alignment explanation
Indices: 4895629--4895703 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
4895619 TGTTAATTTC
* *
4895629 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
* *
4895666 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
4895703 A
1 A
4895704 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
Found at i:4895716 original size:9 final size:9
Alignment explanation
Indices: 4895702--4895732 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4895692 GTAGTGATTC
*
4895702 AATTCGGGT
1 AATTCGGTT
4895711 AATTCGGTT
1 AATTCGGTT
4895720 AATTCGGTT
1 AATTCGGTT
4895729 AATT
1 AATT
4895733 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4898595 original size:15 final size:15
Alignment explanation
Indices: 4898577--4898608 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4898567 CATTTTACTA
*
4898577 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
4898592 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
4898607 TT
1 TT
4898609 TGTACGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:4899486 original size:25 final size:25
Alignment explanation
Indices: 4899447--4899494 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
4899437 TTGTAGAGAG
*
4899447 AAAATTCTCTGAAGAGATTATTTCAA
1 AAAATTCTCTAAAGAGATT-TTTCAA
*
4899473 AAAATT-TCTAAAGATATTTTTC
1 AAAATTCTCTAAAGAGATTTTTC
4899495 TGATTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 10 0.50
26 6 0.30
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (25 bp):
AAAATTCTCTAAAGAGATTTTTCAA
Found at i:4903054 original size:30 final size:29
Alignment explanation
Indices: 4902991--4903056 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
4902981 TTAAAAATTA
*
4902991 AAAAAATTAATTTTTTATATATTATTTTC
1 AAAAATTTAATTTTTTATATATTATTTTC
* *
4903020 AAAAATTTTATTTTTTATATTTTTAATTTT-
1 AAAAATTTAATTTTTTATA-TATT-ATTTTC
4903050 AAAAATT
1 AAAAATT
4903057 CAAATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 17 0.53
30 10 0.31
31 5 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
AAAAATTTAATTTTTTATATATTATTTTC
Found at i:4904797 original size:45 final size:46
Alignment explanation
Indices: 4904733--4904821 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 46
4904723 TTAAGTCCTT
* *
4904733 TTTTATTTTAATTCTTTTATTCA-TTGATTTACTTATTTATTATTTC
1 TTTTATTTTAATTCATTTATTCACTT-ATTTACTTATATATTATTTC
* *
4904779 TTTTATTTT-ATTCATTTATTTACTTATTTATTTATATATTATT
1 TTTTATTTTAATTCATTTATTCACTTATTTACTTATATATTATT
4904822 CATCTATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 27 0.71
46 11 0.29
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.69
Consensus pattern (46 bp):
TTTTATTTTAATTCATTTATTCACTTATTTACTTATATATTATTTC
Found at i:4904809 original size:4 final size:4
Alignment explanation
Indices: 4904748--4904866 Score: 66
Period size: 4 Copynumber: 29.5 Consensus size: 4
4904738 TTTTAATTCT
* * * * *
4904748 TTTA TTCA TTGA TTTA CTTA TTTA -TTA TTTCT TTTA TTTTA TTCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA -TTTA TTTA TTTA
* * * * *
4904797 TTTA CTTA TTTA TTTA TATA -TTA TTCA TCTA TTTA CTT- TTTA TTTTAA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTT-A
*
4904845 TTCT- TTTA TTCA TTTA TTTA TT
1 TT-TA TTTA TTTA TTTA TTTA TT
4904867 ATTCCTTCAC
Statistics
Matches: 85, Mismatches: 21, Indels: 18
0.69 0.17 0.15
Matches are distributed among these distances:
3 8 0.09
4 63 0.74
5 12 0.14
6 2 0.02
ACGTcount: A:0.24, C:0.08, G:0.01, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:4904980 original size:14 final size:15
Alignment explanation
Indices: 4904961--4904990 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4904951 GCCTTTACTA
4904961 TTATTATTA-CTATT
1 TTATTATTATCTATT
4904975 TTATTATTATCTATT
1 TTATTATTATCTATT
4904990 T
1 T
4904991 ATCTACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTATTATCTATT
Found at i:4905284 original size:26 final size:25
Alignment explanation
Indices: 4905224--4905292 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
4905214 TTAAATTACT
*
4905224 TTATTTATTAATACTA-TAATATGA
1 TTATTTATTAATACTATTAATATAA
* *
4905248 TTATAAATATTAATACTATTATTATAA
1 TTAT--TTATTAATACTATTAATATAA
*
4905275 TTATGTTATTATTACTAT
1 TTAT-TTATTAATACTAT
4905293 AGGATTCCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 4 0.11
26 22 0.61
27 10 0.28
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (25 bp):
TTATTTATTAATACTATTAATATAA
Found at i:4916778 original size:44 final size:44
Alignment explanation
Indices: 4916655--4916820 Score: 174
Period size: 44 Copynumber: 3.6 Consensus size: 44
4916645 TCACCATAGT
* *
4916655 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-CTTACC
1 AAATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGC-TA-C
* * * * *
4916700 ATGGCGAATCTTATCTCTCTGAAGTTGTAATGGAGCAAATTAAAGCTAC
1 A-----AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTAC
*
4916749 AAATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTAT
1 AAATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTAC
4916793 AAATCTTATCTCCCTGAAGA-TGCAGTGG
1 AAATCTTATCTCCCTGAA-ATTGCAGTGG
4916821 GTTAGGATGA
Statistics
Matches: 103, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
44 63 0.61
45 2 0.02
49 2 0.02
50 35 0.34
51 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTAC
Found at i:4917985 original size:22 final size:22
Alignment explanation
Indices: 4917957--4918016 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
4917947 CGAGACCCGA
4917957 CCCGTGTGGCTCAAATTACATG
1 CCCGTGTGGCTCAAATTACATG
* *
4917979 CCCGTGTGGC-CTAGA-CACATG
1 CCCGTGTGGCTC-AAATTACATG
4918000 CCCGTGTGGCTCAAATT
1 CCCGTGTGGCTCAAATT
4918017 TGATGAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (22 bp):
CCCGTGTGGCTCAAATTACATG
Found at i:4918628 original size:10 final size:10
Alignment explanation
Indices: 4918578--4918630 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
4918568 AAGGACAAGG
4918578 AAGAAGAACCGA
1 AAGAAGAA--GA
4918590 AAGAAGAAG-
1 AAGAAGAAGA
*
4918599 AAGAAGGAGA
1 AAGAAGAAGA
4918609 AAG-AGAAAGA
1 AAGAAG-AAGA
4918619 AAGAAGAAGA
1 AAGAAGAAGA
4918629 AA
1 AA
4918631 AAACATAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 10 0.28
10 16 0.44
11 2 0.06
12 8 0.22
ACGTcount: A:0.66, C:0.04, G:0.30, T:0.00
Consensus pattern (10 bp):
AAGAAGAAGA
Found at i:4922293 original size:102 final size:101
Alignment explanation
Indices: 4922084--4922275 Score: 255
Period size: 102 Copynumber: 1.9 Consensus size: 101
4922074 AGTGACCATA
* *
4922084 TGGTGGCTTCTTGGGAGACTCATATACTGGTGGTTTAGGTTCTGGCTTCTCTTTCTTTGGTGGTG
1 TGGTGGCTTCTTGGGAGACTCATAAACTGGTGGTTTAGGTTCTGGCTTCTCTTTCTTTGGAGGTG
* *
4922149 CATAAACCGGTGGCTTTGGTGGCTTAGGCTCATACAC
66 CATAAACCGGTGGCTTT-GAGGCTCAGGCTCATACAC
* * * * *
4922186 TGGTGGCTTCTTTGGAGGCTTATAAACTGGTGGTTT-GAGTTCTGGTTTTTCTTTCTTTGGAGGT
1 TGGTGGCTTCTTGGGAGACTCATAAACTGGTGGTTTAG-GTTCTGGCTTCTCTTTCTTTGGAGGT
*
4922250 GCATAAACTGGTGG-TTT-AGGCTCAGG
65 GCATAAACCGGTGGCTTTGAGGCTCAGG
4922276 TTTTTCCTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
99 7 0.09
101 4 0.05
102 68 0.86
ACGTcount: A:0.14, C:0.16, G:0.31, T:0.39
Consensus pattern (101 bp):
TGGTGGCTTCTTGGGAGACTCATAAACTGGTGGTTTAGGTTCTGGCTTCTCTTTCTTTGGAGGTG
CATAAACCGGTGGCTTTGAGGCTCAGGCTCATACAC
Found at i:4922326 original size:90 final size:90
Alignment explanation
Indices: 4922192--4922499 Score: 388
Period size: 90 Copynumber: 3.4 Consensus size: 90
4922182 ACACTGGTGG
* * * * *
4922192 CTTCTTTGGAGGCTT-ATAAACTGGTGGTTTGAGTTC-TGGTTTTTCTTTCTTTGGAGGTGCATA
1 CTTCTTTGGTGG-TTCATAAACCGGTGGTTTGTGTTCAT-GCTTTTCTTTCTTTGGAGGTGTATA
*
4922255 AACTGGTGGTTTAGGCTCAGGTTTTTC
64 AACTGGTGGTTTAGGCTCAGGCTTTTC
* * *
4922282 CTTCTTTGGTGGTTCATACACCGGTGGCTTGTGTTCATGCTTTTCTTTCTTTGGTGGTGTATAAA
1 CTTCTTTGGTGGTTCATAAACCGGTGGTTTGTGTTCATGCTTTTCTTTCTTTGGAGGTGTATAAA
*
4922347 CCGGTGGTTTAGGCTCAGGCTTTTC
66 CTGGTGGTTTAGGCTCAGGCTTTTC
* * * * *
4922372 CTTCTTTGGAGGTTCATATACTGGTGGTTTCG-GTTCAGGCTTCTCTTTCTTTGGAGGTGTATAA
1 CTTCTTTGGTGGTTCATAAACCGGTGGTTT-GTGTTCATGCTTTTCTTTCTTTGGAGGTGTATAA
* * *
4922436 ACTGGTGGCTTAGGTTCAGGCTTCTC
65 ACTGGTGGTTTAGGCTCAGGCTTTTC
* *
4922462 CTTCTTTGGTGGTTCATAAACCGGAGGTTTATGTTCAT
1 CTTCTTTGGTGGTTCATAAACCGGTGGTTTGTGTTCAT
4922500 ATGGTGGCGG
Statistics
Matches: 187, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
89 2 0.01
90 183 0.98
91 2 0.01
ACGTcount: A:0.14, C:0.17, G:0.27, T:0.43
Consensus pattern (90 bp):
CTTCTTTGGTGGTTCATAAACCGGTGGTTTGTGTTCATGCTTTTCTTTCTTTGGAGGTGTATAAA
CTGGTGGTTTAGGCTCAGGCTTTTC
Found at i:4922443 original size:135 final size:135
Alignment explanation
Indices: 4922192--4922492 Score: 349
Period size: 135 Copynumber: 2.2 Consensus size: 135
4922182 ACACTGGTGG
* * * * * *
4922192 CTTCTTTGGAGGCTTATAAACTGGTGGTTT-GAGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAA
1 CTTCTTTGGTGG-TTATAAACCGGTGGTTTAGAGCTCAGGCTTTTCCTTCTTTGGAGGTGCATAA
* * * * *
4922256 ACTGGTGGTTTAGGCTCAGGTTTTTCCTTCTTTGGTGGTTCATACACCGGTGGCTT-GTGTTCAT
65 ACTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGAGGTTCATAAACCGGTGGCTTAG-GTTCAG
*
4922320 GCTTTTC
129 GCTTCTC
* * *
4922327 TTTCTTTGGTGGTGTATAAACCGGTGGTTTAG-GCTCAGGCTTTTCCTTCTTTGGAGGTTCATAT
1 CTTCTTTGGTGGT-TATAAACCGGTGGTTTAGAGCTCAGGCTTTTCCTTCTTTGGAGGTGCATAA
* * * *
4922391 ACTGGTGGTTTCGGTTCAGGCTTCTCTTTCTTTGGAGGTGT-ATAAACTGGTGGCTTAGGTTCAG
65 ACTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGAGGT-TCATAAACCGGTGGCTTAGGTTCAG
4922455 GCTTCTC
129 GCTTCTC
*
4922462 CTTCTTTGGTGGTTCATAAACCGGAGGTTTA
1 CTTCTTTGGTGGTT-ATAAACCGGTGGTTTA
4922493 TGTTCATATG
Statistics
Matches: 140, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
134 2 0.01
135 135 0.96
136 3 0.02
ACGTcount: A:0.14, C:0.17, G:0.27, T:0.43
Consensus pattern (135 bp):
CTTCTTTGGTGGTTATAAACCGGTGGTTTAGAGCTCAGGCTTTTCCTTCTTTGGAGGTGCATAAA
CTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGAGGTTCATAAACCGGTGGCTTAGGTTCAGGC
TTCTC
Found at i:4922481 original size:45 final size:45
Alignment explanation
Indices: 4922192--4922498 Score: 309
Period size: 45 Copynumber: 6.8 Consensus size: 45
4922182 ACACTGGTGG
* *
4922192 CTTCTTTGGAGGCTT-ATAAACTGGTGGTTT-GAGTTCTGGTTTTTC
1 CTTCTTTGGAGG-TTCATAAACTGGTGGTTTAG-GTTCAGGCTTTTC
* * * *
4922237 TTTCTTTGGAGGTGCATAAACTGGTGGTTTAGGCTCAGGTTTTTC
1 CTTCTTTGGAGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
* * * * *
4922282 CTTCTTTGGTGGTTCATACACCGGTGGCTT-GTGTTCATGCTTTTC
1 CTTCTTTGGAGGTTCATAAACTGGTGGTTTAG-GTTCAGGCTTTTC
* * * *
4922327 TTTCTTTGGTGGTGT-ATAAACCGGTGGTTTAGGCTCAGGCTTTTC
1 CTTCTTTGGAGGT-TCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
* * *
4922372 CTTCTTTGGAGGTTCATATACTGGTGGTTTCGGTTCAGGCTTCTC
1 CTTCTTTGGAGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
* * *
4922417 TTTCTTTGGAGGTGT-ATAAACTGGTGGCTTAGGTTCAGGCTTCTC
1 CTTCTTTGGAGGT-TCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
* * * *
4922462 CTTCTTTGGTGGTTCATAAACCGGAGGTTTATGTTCA
1 CTTCTTTGGAGGTTCATAAACTGGTGGTTTAGGTTCA
4922499 TATGGTGGCG
Statistics
Matches: 219, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
44 4 0.02
45 211 0.96
46 4 0.02
ACGTcount: A:0.14, C:0.17, G:0.27, T:0.43
Consensus pattern (45 bp):
CTTCTTTGGAGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
Found at i:4925133 original size:19 final size:19
Alignment explanation
Indices: 4925109--4925146 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
4925099 AATTGTTTAA
4925109 TATAAAAATT-TAAAGAAAT
1 TATAAAAATTATAAA-AAAT
4925128 TATAAAAATTATAAAAAAT
1 TATAAAAATTATAAAAAAT
4925147 CATTTCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TATAAAAATTATAAAAAAT
Found at i:4926508 original size:27 final size:29
Alignment explanation
Indices: 4926450--4926508 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 29
4926440 TACTTAAAAG
*
4926450 AAAACATATTAGACAAAATAAAAACCACA
1 AAAAAATATTAGACAAAATAAAAACCACA
*
4926479 AAAAAATATT-GACAAAAT-AAAATCACA
1 AAAAAATATTAGACAAAATAAAAACCACA
4926506 AAA
1 AAA
4926509 CTATGAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 11 0.39
28 8 0.29
29 9 0.32
ACGTcount: A:0.68, C:0.14, G:0.03, T:0.15
Consensus pattern (29 bp):
AAAAAATATTAGACAAAATAAAAACCACA
Found at i:4932250 original size:19 final size:18
Alignment explanation
Indices: 4932215--4932250 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4932205 AACTTTTTTA
*
4932215 TCAAATTAACCCTAAAAC
1 TCAAATTAACACTAAAAC
4932233 TCAAATTAAACACTAAAA
1 TCAAATT-AACACTAAAA
4932251 AGTTAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (18 bp):
TCAAATTAACACTAAAAC
Found at i:4955578 original size:30 final size:30
Alignment explanation
Indices: 4955542--4955601 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
4955532 ATTTAACAAG
4955542 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
4955572 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
4955602 TAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:4955653 original size:14 final size:14
Alignment explanation
Indices: 4955636--4955665 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4955626 TTTAAATAAA
4955636 AACAACAAAATAGT
1 AACAACAAAATAGT
*
4955650 AACAACATAATAGT
1 AACAACAAAATAGT
4955664 AA
1 AA
4955666 AATGGTAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (14 bp):
AACAACAAAATAGT
Found at i:4962531 original size:2 final size:2
Alignment explanation
Indices: 4962524--4962554 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4962514 CAGTAAGAAC
4962524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4962555 AATGGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4962982 original size:2 final size:2
Alignment explanation
Indices: 4962970--4963006 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
4962960 TTTCAATTGT
* *
4962970 TA TA TA AA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4963007 GAATATGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4963007 original size:10 final size:10
Alignment explanation
Indices: 4962978--4963012 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
4962968 GTTATATAAA
*
4962978 TATATATATA
1 TATATATATG
4962988 TATATATATG
1 TATATATATG
4962998 TATATATATG
1 TATATATATG
*
4963008 AATAT
1 TATAT
4963013 GAAGTAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (10 bp):
TATATATATG
Found at i:4963872 original size:70 final size:70
Alignment explanation
Indices: 4963791--4963925 Score: 270
Period size: 70 Copynumber: 1.9 Consensus size: 70
4963781 AATCCACATC
4963791 AATTTATAATATTAAAATTCAACAAATATTAGAAAGACTATTATTTTACCAGACCTTGGTCATCA
1 AATTTATAATATTAAAATTCAACAAATATTAGAAAGACTATTATTTTACCAGACCTTGGTCATCA
4963856 ATAAT
66 ATAAT
4963861 AATTTATAATATTAAAATTCAACAAATATTAGAAAGACTATTATTTTACCAGACCTTGGTCATCA
1 AATTTATAATATTAAAATTCAACAAATATTAGAAAGACTATTATTTTACCAGACCTTGGTCATCA
4963926 TATTCAATGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (70 bp):
AATTTATAATATTAAAATTCAACAAATATTAGAAAGACTATTATTTTACCAGACCTTGGTCATCA
ATAAT
Found at i:4967167 original size:22 final size:22
Alignment explanation
Indices: 4967134--4967187 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
4967124 TAATTAAATC
4967134 ATTTCTCT-AATTTCCTCTC-A
1 ATTTCTCTCAATTTCCTCTCAA
4967154 ATTTGCTCTCAATTTCCTCTCAA
1 ATTT-CTCTCAATTTCCTCTCAA
4967177 ATTTCTCTCAA
1 ATTTCTCTCAA
4967188 ATCCCTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 4 0.13
21 4 0.13
22 18 0.58
23 5 0.16
ACGTcount: A:0.22, C:0.30, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTCTCTCAATTTCCTCTCAA
Found at i:4967189 original size:11 final size:11
Alignment explanation
Indices: 4967134--4967187 Score: 69
Period size: 11 Copynumber: 5.1 Consensus size: 11
4967124 TAATTAAATC
4967134 ATTT-CTCT-A
1 ATTTCCTCTCA
4967143 ATTTCCTCTCA
1 ATTTCCTCTCA
*
4967154 ATTTGCTCTCA
1 ATTTCCTCTCA
4967165 ATTTCCTCTCAA
1 ATTTCCTCTC-A
4967177 ATTT-CTCTCA
1 ATTTCCTCTCA
4967187 A
1 A
4967188 ATCCCTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
9 4 0.10
10 6 0.15
11 25 0.62
12 5 0.12
ACGTcount: A:0.22, C:0.30, G:0.02, T:0.46
Consensus pattern (11 bp):
ATTTCCTCTCA
Found at i:4969055 original size:18 final size:18
Alignment explanation
Indices: 4969032--4969074 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4969022 TGCCAGGTGC
* *
4969032 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
4969050 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
4969068 GTTTCCT
1 GTATCCT
4969075 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:4969342 original size:21 final size:21
Alignment explanation
Indices: 4969315--4969362 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4969305 CCAACATCGA
*
4969315 CAACCAG-ATACCCTACCGGAG
1 CAACCAGAAT-CCCCACCGGAG
*
4969336 GAACCAGAATCCCCACCGGAG
1 CAACCAGAATCCCCACCGGAG
4969357 CAACCA
1 CAACCA
4969363 TAACCCCCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.35, C:0.40, G:0.19, T:0.06
Consensus pattern (21 bp):
CAACCAGAATCCCCACCGGAG
Found at i:4969370 original size:21 final size:21
Alignment explanation
Indices: 4969315--4969370 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
4969305 CCAACATCGA
*
4969315 CAACCAGATA-CCCTACCGGAG
1 CAACCAGA-ACCCCCACCGGAG
* *
4969336 GAACCAGAATCCCCACCGGAG
1 CAACCAGAACCCCCACCGGAG
*
4969357 CAACCATAACCCCC
1 CAACCAGAACCCCC
4969371 GCCGAAAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.34, C:0.43, G:0.16, T:0.07
Consensus pattern (21 bp):
CAACCAGAACCCCCACCGGAG
Found at i:4981531 original size:18 final size:17
Alignment explanation
Indices: 4981503--4981537 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4981493 ATATTTCACA
4981503 TCTTTTTTTTTTACTTC
1 TCTTTTTTTTTTACTTC
*
4981520 TCTTTGTTTTTTTTCTTC
1 TCTTT-TTTTTTTACTTC
4981538 AAACTGGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (17 bp):
TCTTTTTTTTTTACTTC
Found at i:4984287 original size:15 final size:15
Alignment explanation
Indices: 4984267--4984296 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4984257 TTAATAAAAA
*
4984267 TAAAAATATTATATT
1 TAAAAATATAATATT
4984282 TAAAAATATAATATT
1 TAAAAATATAATATT
4984297 CACAAACCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAAATATAATATT
Found at i:4995375 original size:2 final size:2
Alignment explanation
Indices: 4995368--4995406 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4995358 ATCTCAATTT
4995368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4995407 CATAACCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5000181 original size:55 final size:55
Alignment explanation
Indices: 5000097--5000205 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
5000087 ATCTAAAGCA
*
5000097 CCAAGCAAAGGCTTAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
1 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
*
5000152 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAATGAAACACAAAGAAAT
1 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAAT
5000206 ATATCACAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.17
Consensus pattern (55 bp):
CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
Found at i:5019558 original size:23 final size:23
Alignment explanation
Indices: 5019532--5019599 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
5019522 ATTATAATTA
5019532 TAAATTGATTTACATTTATTAGT
1 TAAATTGATTTACATTTATTAGT
*
5019555 TAAA---A-ATA-A-TTA-TAGTT
1 TAAATTGATTTACATTTATTAG-T
5019572 ATAAATTGATTTACATTTATTAGT
1 -TAAATTGATTTACATTTATTAGT
5019596 TAAA
1 TAAA
5019600 AATATGTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 18
0.63 0.04 0.33
Matches are distributed among these distances:
16 3 0.09
17 4 0.12
18 5 0.15
19 2 0.06
20 1 0.03
21 1 0.03
22 2 0.06
23 9 0.26
24 4 0.12
25 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (23 bp):
TAAATTGATTTACATTTATTAGT
Found at i:5019564 original size:41 final size:41
Alignment explanation
Indices: 5019519--5019603 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
5019509 AAAAGTTGTG
5019519 ATAATTATAATTATAAATTGATTTACATTTATTAGTTAAAA
1 ATAATTATAATTATAAATTGATTTACATTTATTAGTTAAAA
*
5019560 ATAATTATAGTTATAAATTGATTTACATTTATTAGTTAAAA
1 ATAATTATAATTATAAATTGATTTACATTTATTAGTTAAAA
5019601 ATA
1 ATA
5019604 TGTGTATTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (41 bp):
ATAATTATAATTATAAATTGATTTACATTTATTAGTTAAAA
Found at i:5023244 original size:16 final size:14
Alignment explanation
Indices: 5023225--5023267 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
5023215 TTTTAATTTT
5023225 TTAAAATATTAAATTA
1 TTAAAATATTAAA--A
*
5023241 TTAAATTATTAAAA
1 TTAAAATATTAAAA
5023255 TT-AAATATTAAAA
1 TTAAAATATTAAAA
5023268 CATTCAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 3 0.12
16 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAATATTAAAA
Found at i:5023263 original size:13 final size:13
Alignment explanation
Indices: 5023228--5023267 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 13
5023218 TAATTTTTTA
5023228 AAATATTAAATTATT
1 AAATATTAAA--ATT
5023243 AAATTATTAAAATT
1 AAA-TATTAAAATT
5023257 AAATATTAAAA
1 AAATATTAAAA
5023268 CATTCAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.33
14 6 0.25
15 3 0.12
16 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATATTAAAATT
Found at i:5027990 original size:21 final size:20
Alignment explanation
Indices: 5027957--5027995 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5027947 GATATACGTT
5027957 TGTTTGTCAGAACATTTTGTC
1 TGTTTGTCAGAAC-TTTTGTC
**
5027978 TGTTTGTGTGAACTTTTG
1 TGTTTGTCAGAACTTTTG
5027996 GTTATTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.51
Consensus pattern (20 bp):
TGTTTGTCAGAACTTTTGTC
Found at i:5029318 original size:10 final size:10
Alignment explanation
Indices: 5029302--5029332 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5029292 AATAGTTATT
5029302 AAAAATTAAA
1 AAAAATTAAA
*
5029312 GAAAATTAAA
1 AAAAATTAAA
5029322 AAAAATTAAA
1 AAAAATTAAA
5029332 A
1 A
5029333 GAGGTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:5039583 original size:13 final size:15
Alignment explanation
Indices: 5039565--5039596 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5039555 CACCAAATTT
5039565 AAACCC-AAT-TAAA
1 AAACCCTAATATAAA
5039578 AAACCCTAATATAAA
1 AAACCCTAATATAAA
5039593 AAAC
1 AAAC
5039597 TTCAAAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 3 0.18
15 8 0.47
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (15 bp):
AAACCCTAATATAAA
Found at i:5044755 original size:15 final size:15
Alignment explanation
Indices: 5044735--5044772 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5044725 GTTTTCCAGA
5044735 GGAGTCAATGGTAGT
1 GGAGTCAATGGTAGT
*
5044750 GGAGTCAATTGTAGT
1 GGAGTCAATGGTAGT
*
5044765 GGACTCAA
1 GGAGTCAA
5044773 GGGGAGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (15 bp):
GGAGTCAATGGTAGT
Found at i:5049377 original size:40 final size:39
Alignment explanation
Indices: 5049323--5049456 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 39
5049313 ACCAGTTTGG
5049323 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATAATTCGAAGT-ATAAATTGA
* * * * *
5049363 CACCTAGTGTCTCATCGGCTAA-ACTGAAG--TAAATTGG
1 CACCCAGTGCCTCATCGGATAATTC-GAAGTATAAATTGA
*
5049400 CACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATTCGAAGTA-TAAATTGA
*
5049441 CACCCAGTGTCTCATC
1 CACCCAGTGCCTCATC
5049457 AACTCGAAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
37 22 0.29
38 7 0.09
39 2 0.03
40 23 0.30
41 22 0.29
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATTCGAAGTATAAATTGA
Found at i:5049437 original size:41 final size:41
Alignment explanation
Indices: 5049323--5049456 Score: 152
Period size: 37 Copynumber: 3.4 Consensus size: 41
5049313 ACCAGTTTGG
*
5049323 CACCCAGTGCCTCATCGGA-TAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATTAATTCGAAGTAGTAAATTGA
* * * * * *
5049363 CACCTAGTGTCTCATCGGCTAAACT-G-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGGATTAATTCGAAGTAGTAAATTGA
*
5049400 CACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGATTAATTCGAAGTAGTAAATTGA
*
5049441 CACCCAGTGTCTCATC
1 CACCCAGTGCCTCATC
5049457 AACTCGAAGT
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 27 0.36
38 1 0.01
39 2 0.03
40 17 0.23
41 27 0.36
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGGATTAATTCGAAGTAGTAAATTGA
Found at i:5050349 original size:5 final size:5
Alignment explanation
Indices: 5050339--5050401 Score: 53
Period size: 5 Copynumber: 12.8 Consensus size: 5
5050329 CCCTTTCCCT
* *
5050339 TTTTC TTTTC -TTTC TTTTC CTTTC TGTTTC GTTTTGC TTGTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC -TTTT-C TTTTC TTTTC
5050385 -TTT- TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTT
5050402 ATTTATTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 13 0.27
5 23 0.48
6 10 0.21
7 2 0.04
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:5051098 original size:29 final size:30
Alignment explanation
Indices: 5051029--5051090 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
5051019 AATCCAACTT
5051029 ATAAAATTAATAAAAATTCACTATATGTGC
1 ATAAAATTAATAAAAATTCACTATATGTGC
*
5051059 ATAAAATTAATAAAATTTCACTATATGTGC
1 ATAAAATTAATAAAAATTCACTATATGTGC
5051089 AT
1 AT
5051091 CTATTAATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (30 bp):
ATAAAATTAATAAAAATTCACTATATGTGC
Found at i:5052423 original size:25 final size:25
Alignment explanation
Indices: 5052392--5052451 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
5052382 ATTATTATGG
*
5052392 TTTTGTCTACAGTTTCGTGATTTTA
1 TTTTGTCCACAGTTTCGTGATTTTA
* *
5052417 TTTTGTCCATAGTTTTGTGATTTTA
1 TTTTGTCCACAGTTTCGTGATTTTA
*
5052442 TTTTGACCAC
1 TTTTGTCCAC
5052452 TCTTATATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.55
Consensus pattern (25 bp):
TTTTGTCCACAGTTTCGTGATTTTA
Found at i:5057477 original size:25 final size:24
Alignment explanation
Indices: 5057416--5057477 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
5057406 AAGCGGTAAG
**
5057416 AAACTTGAGCTTGAGCTCAACTCA
1 AAACTTGAGCTTGAGCTCAAAGCA
* *
5057440 AAATTTGAGGCTTGAGACTCAAAGCT
1 AAACTTGA-GCTTGAG-CTCAAAGCA
*
5057466 AGACTTGAGCTT
1 AAACTTGAGCTT
5057478 AACGGAGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 7 0.23
25 11 0.37
26 12 0.40
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (24 bp):
AAACTTGAGCTTGAGCTCAAAGCA
Found at i:5067056 original size:27 final size:26
Alignment explanation
Indices: 5067000--5067072 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 26
5066990 ATTATTAATC
*
5067000 TTTTTATAATTAATTATTAAATTATTA
1 TTTTTAT-ATTAATTATTAAATTATCA
*
5067027 TTTTTATATTAA-TATGTTAATATATCA
1 TTTTTATATTAATTAT-TAAAT-TATCA
* *
5067054 TTTATA-ATTAAAT-TTAAAT
1 TTTTTATATTAATTATTAAAT
5067073 AAAAATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 7 0.18
26 15 0.38
27 17 0.44
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
TTTTTATATTAATTATTAAATTATCA
Found at i:5067063 original size:26 final size:25
Alignment explanation
Indices: 5067002--5067072 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
5066992 TATTAATCTT
*
5067002 TTTATAATTAATTATTAAATTATTA
1 TTTATAATTAATTATTAAATTATCA
* *
5067027 TTTTTATATTAA-TATGTTAATATATCA
1 TTTATA-ATTAATTAT-TAAAT-TATCA
*
5067054 TTTATAATTAAAT-TTAAAT
1 TTTATAATTAATTATTAAAT
5067073 AAAAATATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
25 12 0.32
26 15 0.41
27 10 0.27
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (25 bp):
TTTATAATTAATTATTAAATTATCA
Found at i:5067286 original size:16 final size:15
Alignment explanation
Indices: 5067237--5067287 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
5067227 CCAATATAAG
5067237 TATATAATAT-AATA
1 TATATAATATAAATA
*
5067251 TACATAGATATAAA-A
1 TATATA-ATATAAATA
5067266 TTATATAATTATAAATA
1 -TATATAA-TATAAATA
5067283 TATAT
1 TATAT
5067288 TCAAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 18 0.60
17 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
TATATAATATAAATA
Found at i:5075506 original size:34 final size:34
Alignment explanation
Indices: 5075468--5075666 Score: 209
Period size: 34 Copynumber: 5.8 Consensus size: 34
5075458 AAATGACGAA
* * *
5075468 TGAACATGAGAGATTCCCTACAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGCG
* * *
5075502 TGAACATGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-GAAATGATGCG
* *
5075537 TGAACAGGAAATATTCCCTGCAAGAAATGATGCG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGCG
* * *
5075571 TGAATAGGAAAGATTCCCTGCAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGCG
* * **
5075605 TGAACAAGAGAGATTCCCTGCAACAAAAAAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-GAAATGATGCG
* * * *
5075640 TGAATAGGAAATATTCCCTCCAAGAAA
1 TGAACAGGAGAGATTCCCTGCAAGAAA
5075667 AGACAAGTGA
Statistics
Matches: 138, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
34 85 0.62
35 53 0.38
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.21
Consensus pattern (34 bp):
TGAACAGGAGAGATTCCCTGCAAGAAATGATGCG
Found at i:5075585 original size:69 final size:68
Alignment explanation
Indices: 5075468--5075667 Score: 211
Period size: 69 Copynumber: 2.9 Consensus size: 68
5075458 AAATGACGAA
* * * * * * *
5075468 TGAACATGAGAGATTCCCTACAAGAAATGATGTGTGAACATGAGAGATTCCCTGCAACAAAATAA
1 TGAACAAGAAAGATTCCCTGCAAGAAATGATGCGTGAATAGGAAAGATTCCCTGCAA-AAAATAA
5075533 TGCG
65 TGCG
* * * *
5075537 TGAACAGGAAATATTCCCTGCAAGAAATGATGCGTGAATAGGAAAGATTCCCTGCAAGAAATGAT
1 TGAACAAGAAAGATTCCCTGCAAGAAATGATGCGTGAATAGGAAAGATTCCCTGCAAAAAATAAT
*
5075602 GTG
66 GCG
* * ** * *
5075605 TGAACAAGAGAGATTCCCTGCAACAAAAAAATGCGTGAATAGGAAATATTCCCTCCAAGAAAA
1 TGAACAAGAAAGATTCCCTGCAA-GAAATGATGCGTGAATAGGAAAGATTCCCTGCAA-AAAA
5075668 GACAAGTGAA
Statistics
Matches: 109, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
68 28 0.26
69 78 0.72
70 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.20
Consensus pattern (68 bp):
TGAACAAGAAAGATTCCCTGCAAGAAATGATGCGTGAATAGGAAAGATTCCCTGCAAAAAATAAT
GCG
Found at i:5075638 original size:103 final size:103
Alignment explanation
Indices: 5075478--5075666 Score: 333
Period size: 103 Copynumber: 1.8 Consensus size: 103
5075468 TGAACATGAG
* *
5075478 AGATTCCCTACAAGAAATGATGTGTGAACATGAGAGATTCCCTGCAACAAAATAATGCGTGAACA
1 AGATTCCCTACAAGAAATGATGTGTGAACAAGAGAGATTCCCTGCAACAAAAAAATGCGTGAACA
*
5075543 GGAAATATTCCCTGCAAGAAATGATGCGTGAATAGGAA
66 GGAAATATTCCCTCCAAGAAATGATGCGTGAATAGGAA
* *
5075581 AGATTCCCTGCAAGAAATGATGTGTGAACAAGAGAGATTCCCTGCAACAAAAAAATGCGTGAATA
1 AGATTCCCTACAAGAAATGATGTGTGAACAAGAGAGATTCCCTGCAACAAAAAAATGCGTGAACA
5075646 GGAAATATTCCCTCCAAGAAA
66 GGAAATATTCCCTCCAAGAAA
5075667 AGACAAGTGA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 81 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (103 bp):
AGATTCCCTACAAGAAATGATGTGTGAACAAGAGAGATTCCCTGCAACAAAAAAATGCGTGAACA
GGAAATATTCCCTCCAAGAAATGATGCGTGAATAGGAA
Found at i:5075934 original size:14 final size:13
Alignment explanation
Indices: 5075904--5075941 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
5075894 AGTTTCCAAA
*
5075904 TTTTCAAATTGAG
1 TTTTCAAATTAAG
5075917 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
5075931 TTTTCAAATTA
1 TTTTCAAATTA
5075942 CAAATATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:5081677 original size:22 final size:22
Alignment explanation
Indices: 5081630--5081671 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5081620 TATATATTTA
*
5081630 AAAAAATTATTAAAAATTCACC
1 AAAAAATCATTAAAAATTCACC
5081652 AAAAAATCATTAAAAATTCA
1 AAAAAATCATTAAAAATTCA
5081672 TTAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAAATCATTAAAAATTCACC
Found at i:5081678 original size:10 final size:11
Alignment explanation
Indices: 5081631--5081677 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
5081621 ATATATTTAA
5081631 AAAAATT-ATT
1 AAAAATTCATT
**
5081641 AAAAATTCACC
1 AAAAATTCATT
*
5081652 AAAAAATCATT
1 AAAAATTCATT
5081663 AAAAATTCATT
1 AAAAATTCATT
5081674 AAAA
1 AAAA
5081678 TAAAAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 7 0.23
11 23 0.77
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAAATTCATT
Found at i:5083399 original size:24 final size:23
Alignment explanation
Indices: 5083367--5083421 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
5083357 ATTAACCATG
5083367 TTTAAATTAAATTGTT-TATGATTT
1 TTTAAATTAAATT-TTATAT-ATTT
5083391 TTTAAATTAAATTTTACTATATTT
1 TTTAAATTAAATTTTA-TATATTT
5083415 TTTAAAT
1 TTTAAAT
5083422 ATTAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 2 0.07
24 24 0.83
25 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTAAATTAAATTTTATATATTT
Found at i:5083436 original size:25 final size:24
Alignment explanation
Indices: 5083367--5083436 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
5083357 ATTAACCATG
* *
5083367 TTTAAAT-TAAATTGTTTATGATTT
1 TTTAAATATTAATTTTTTAT-ATTT
* *
5083391 TTTAAAT-TAAATTTTACTATATTT
1 TTTAAATATTAATTTT-TTATATTT
5083415 TTTAAATATTAATTTATTTATA
1 TTTAAATATTAATTT-TTTATA
5083437 ATTGAATAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 25 0.64
25 13 0.33
26 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (24 bp):
TTTAAATATTAATTTTTTATATTT
Found at i:5088913 original size:14 final size:14
Alignment explanation
Indices: 5088871--5088926 Score: 76
Period size: 14 Copynumber: 3.8 Consensus size: 14
5088861 CAAGCTAATA
5088871 ACTAACTGTTAACT
1 ACTAACTGTTAACT
*
5088885 AACTACAACTATTAACT
1 -ACT--AACTGTTAACT
5088902 ACTAACTGTTAACT
1 ACTAACTGTTAACT
5088916 ACTAACTGTTA
1 ACTAACTGTTA
5088927 CAACCTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
14 21 0.57
15 3 0.08
16 3 0.08
17 10 0.27
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (14 bp):
ACTAACTGTTAACT
Found at i:5088919 original size:17 final size:17
Alignment explanation
Indices: 5088871--5088919 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5088861 CAAGCTAATA
5088871 ACTAACTGTTAACTAACT
1 ACTAACTGTTAACT-ACT
*
5088889 AC-AACTATT-A--ACT
1 ACTAACTGTTAACTACT
5088902 ACTAACTGTTAACTACT
1 ACTAACTGTTAACTACT
5088919 A
1 A
5088920 ACTGTTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 9
0.69 0.06 0.25
Matches are distributed among these distances:
13 5 0.20
14 6 0.24
15 1 0.04
16 1 0.04
17 10 0.40
18 2 0.08
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (17 bp):
ACTAACTGTTAACTACT
Found at i:5093323 original size:56 final size:58
Alignment explanation
Indices: 5093201--5093370 Score: 186
Period size: 58 Copynumber: 3.0 Consensus size: 58
5093191 TATTTTGGAT
** *
5093201 CTGAACTTGGTAATTGTTCCTATATTGGGGTTTAAAATTTTTTTGTCCAAGTTAGTTC
1 CTGAACTTGACAATTGTTCCTATATTGGGGCTTAAAATTTTTTTGTCCAAGTTAGTTC
*
5093259 CTGAACTTGACAATTGTTCCTTTATT-GGGCTT-AAATTTTTTTGTCCAAGTTAG-TC
1 CTGAACTTGACAATTGTTCCTATATTGGGGCTTAAAATTTTTTTGTCCAAGTTAGTTC
* * * ** * * *
5093314 ATTGGACTTGACAATTGTT-CTCATGTTGAAGCTTGAACTTTTTTTATCCAAGTTAGT
1 -CTGAACTTGACAATTGTTCCT-ATATTGGGGCTTAAAATTTTTTTGTCCAAGTTAGT
5093371 CCATGATATT
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
55 4 0.04
56 40 0.42
57 9 0.09
58 42 0.44
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (58 bp):
CTGAACTTGACAATTGTTCCTATATTGGGGCTTAAAATTTTTTTGTCCAAGTTAGTTC
Found at i:5097454 original size:51 final size:51
Alignment explanation
Indices: 5097378--5097494 Score: 200
Period size: 51 Copynumber: 2.3 Consensus size: 51
5097368 ACTTCTGATC
5097378 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATC-AGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAG-GACA
* *
5097429 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGGACA
5097480 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
5097495 ATGTGATCCG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 61 0.97
52 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGGACA
Found at i:5100924 original size:21 final size:21
Alignment explanation
Indices: 5100881--5100924 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5100871 TCTCAACTTA
**
5100881 TATTTTCAATAATTTAATCTT
1 TATTTTCAATAATTTAAAATT
* *
5100902 TATTTTTAATATTTTAAAATT
1 TATTTTCAATAATTTAAAATT
5100923 TA
1 TA
5100925 AGTCTAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTCAATAATTTAAAATT
Found at i:5100934 original size:28 final size:28
Alignment explanation
Indices: 5100880--5100948 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
5100870 CTCTCAACTT
*
5100880 ATATTTTCAATAATTTAATCTTTATTTTTA
1 ATATTTT-AA-AATTTAATCTTAATTTTTA
5100910 ATATTTTAAAATTTAAGTC-TAATTTTTA
1 ATATTTTAAAATTTAA-TCTTAATTTTTA
*
5100938 ATATTATAAAA
1 ATATTTTAAAA
5100949 AATATTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 25 0.69
29 4 0.11
30 7 0.19
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (28 bp):
ATATTTTAAAATTTAATCTTAATTTTTA
Found at i:5101075 original size:20 final size:20
Alignment explanation
Indices: 5101050--5101091 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5101040 AATAATTATG
5101050 TTGGAATGAGATTTACAATT
1 TTGGAATGAGATTTACAATT
5101070 TTGGAATGAGATTTACAATT
1 TTGGAATGAGATTTACAATT
5101090 TT
1 TT
5101092 AAATATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (20 bp):
TTGGAATGAGATTTACAATT
Found at i:5103332 original size:16 final size:17
Alignment explanation
Indices: 5103299--5103334 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5103289 CAAACCCAAT
*
5103299 AAACTAAACCTAAGCCC
1 AAACCAAACCTAAGCCC
5103316 AAACCAAACCT-AGCCC
1 AAACCAAACCTAAGCCC
5103332 AAA
1 AAA
5103335 AAAAAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.50, C:0.36, G:0.06, T:0.08
Consensus pattern (17 bp):
AAACCAAACCTAAGCCC
Found at i:5104280 original size:3 final size:3
Alignment explanation
Indices: 5104272--5104330 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
5104262 ACTATTTAAT
5104272 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5104320 TTA TTA TTA TT
1 TTA TTA TTA TT
5104331 GTCTATTTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5106865 original size:19 final size:18
Alignment explanation
Indices: 5106828--5106870 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5106818 ATACAAATAA
* *
5106828 TTTTAAACATTTTTTAAT
1 TTTTAAAAATTTATTAAT
5106846 TTTTAAAAATTTAATTAAT
1 TTTTAAAAATTT-ATTAAT
*
5106865 TGTTAA
1 TTTTAA
5106871 TGTGACGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTAAAAATTTATTAAT
Found at i:5108290 original size:28 final size:28
Alignment explanation
Indices: 5108259--5108312 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5108249 ACCTAAATAA
*
5108259 TATAAAAAATA-ATTAATTACTAAAAAGG
1 TATAAAAAATAGAATAATTAC-AAAAAGG
*
5108287 TATAGAAAATAGAATAATTACAAAAA
1 TATAAAAAATAGAATAATTACAAAAA
5108313 TAGGCATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (28 bp):
TATAAAAAATAGAATAATTACAAAAAGG
Done.