Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 79 of 204
Found at i:24528676 original size:22 final size:22
Alignment explanation
Indices: 24528643--24528684 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
24528633 AAAATGTTCT
24528643 AAAAATTCT-AAAATAAAAATG
1 AAAAATTCTAAAAATAAAAATG
*
24528664 AAAAACTTTTAAAAATAAAAA
1 AAAAA-TTCTAAAAATAAAAA
24528685 AAAAACCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAATTCTAAAAATAAAAATG
Found at i:24532934 original size:28 final size:27
Alignment explanation
Indices: 24532868--24532934 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
24532858 TGATGAATTA
**
24532868 TTTTTTATATAATATATTTTTAATAAC
1 TTTTTTATATAATATACGTTTAATAAC
*
24532895 TTTTATTTTATAATATACGTTTAA-AAGC
1 TTTT-TTATATAATATACGTTTAATAA-C
24532923 TATTTTTATATA
1 T-TTTTTATATA
24532935 TTTCATCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 6 0.18
28 24 0.73
29 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTTTTATATAATATACGTTTAATAAC
Found at i:24536610 original size:23 final size:23
Alignment explanation
Indices: 24536584--24536629 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
24536574 TATAAGAAAA
24536584 CTCTACTTTAACATCATTTTCAT
1 CTCTACTTTAACATCATTTTCAT
24536607 CTCTACTTTAACATCATTTTCAT
1 CTCTACTTTAACATCATTTTCAT
24536630 GTTTTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (23 bp):
CTCTACTTTAACATCATTTTCAT
Found at i:24539050 original size:13 final size:13
Alignment explanation
Indices: 24539032--24539065 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
24539022 ATTCATTTAG
24539032 CATTTCACATTTT
1 CATTTCACATTTT
*
24539045 CATTTCAAGATTTT
1 CATTTC-ACATTTT
24539059 CATTTCA
1 CATTTCA
24539066 AATGTCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (13 bp):
CATTTCACATTTT
Found at i:24539057 original size:14 final size:14
Alignment explanation
Indices: 24539040--24539066 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24539030 AGCATTTCAC
24539040 ATTTTCATTTCAAG
1 ATTTTCATTTCAAG
24539054 ATTTTCATTTCAA
1 ATTTTCATTTCAA
24539067 ATGTCCCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.52
Consensus pattern (14 bp):
ATTTTCATTTCAAG
Found at i:24539409 original size:43 final size:43
Alignment explanation
Indices: 24539348--24539432 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
24539338 TGCTCACATG
*
24539348 AGCTGTGGGTCGGGATGTTAGGCTACACGATGCTGTTTACACA
1 AGCTGTGGGTCAGGATGTTAGGCTACACGATGCTGTTTACACA
24539391 AGCTGTGGGTCAGGATGTTAGGCTACACGATGCTGTTTACAC
1 AGCTGTGGGTCAGGATGTTAGGCTACACGATGCTGTTTACAC
24539433 TAATAGCGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (43 bp):
AGCTGTGGGTCAGGATGTTAGGCTACACGATGCTGTTTACACA
Found at i:24558816 original size:26 final size:25
Alignment explanation
Indices: 24558761--24558817 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
24558751 TTACAAACCC
* *
24558761 ACAAAATATGACAAATAATCATATT
1 ACAAAATATAACAAATAATAATATT
24558786 ACAAAATA-AACAAATAAATAATAATT
1 ACAAAATATAACAAAT-AATAAT-ATT
24558812 ACAAAA
1 ACAAAA
24558818 AAATGTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 13 0.46
26 9 0.32
ACGTcount: A:0.65, C:0.11, G:0.02, T:0.23
Consensus pattern (25 bp):
ACAAAATATAACAAATAATAATATT
Found at i:24560029 original size:4 final size:4
Alignment explanation
Indices: 24560020--24560054 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
24560010 ATCATCACAA
24560020 CCAC CCAC CCAC CCAC CCAC CCAC CCAAC CCAC CC
1 CCAC CCAC CCAC CCAC CCAC CCAC CC-AC CCAC CC
24560055 CATTCTCTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.26, C:0.74, G:0.00, T:0.00
Consensus pattern (4 bp):
CCAC
Found at i:24574486 original size:38 final size:41
Alignment explanation
Indices: 24574424--24574504 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 41
24574414 TAAAAAGCAT
* * *
24574424 TTATATTAAAAAGCACTACCATAAATATAATGAGTATTTTA
1 TTATATTAAAAAGCACTACAATAAATATAATAAATATTTTA
24574465 TTATATTAAAAA-CAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAGCACTACAATAAATATAATAAATATTTTA
24574503 TT
1 TT
24574505 GTGTTAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 21 0.57
39 1 0.03
40 3 0.08
41 12 0.32
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (41 bp):
TTATATTAAAAAGCACTACAATAAATATAATAAATATTTTA
Found at i:24575872 original size:43 final size:43
Alignment explanation
Indices: 24575819--24576129 Score: 347
Period size: 43 Copynumber: 7.3 Consensus size: 43
24575809 TTTTAGAAAT
* * * *
24575819 AAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTAACAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCACAC
* * *
24575862 AAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCACAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCACAC
* * *
24575905 AAACGCCGCTAAAGATCATGACTTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCACAC
* * * * * *
24575948 AACCGTCACTAAAGATCATGACTTTTAGCAGCACTTTTC-CTAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCAC-AC
* * *
24575991 AAAAGCCGCTATAGGTCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCACAC
* * * * *
24576034 AAACGCCGCTATAGATCATCACTTTTAACGACACTTTTCTCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCACAC
* * * *
24576077 AAACGCTGCTATAAAACAT-ACCTTTAGCGGCGCTTTTCACAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCACAC
24576119 AAACGCCGCTA
1 AAACGCCGCTA
24576130 AAAACATATC
Statistics
Matches: 229, Mismatches: 37, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
42 29 0.13
43 199 0.87
44 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCACAC
Found at i:24576462 original size:43 final size:43
Alignment explanation
Indices: 24576396--24576482 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
24576386 ACATATGCAA
* * *
24576396 GGTAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
* *
24576439 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
24576482 G
1 G
24576483 TACATCATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:24579816 original size:15 final size:15
Alignment explanation
Indices: 24579795--24579826 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
24579785 ATAAATGAAA
24579795 AATATATA-T-AATT
1 AATATATATTAAATT
24579808 AATATATATTAAATT
1 AATATATATTAAATT
24579823 AATA
1 AATA
24579827 ATAATACGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATATATTAAATT
Found at i:24580540 original size:15 final size:13
Alignment explanation
Indices: 24580501--24580572 Score: 56
Period size: 15 Copynumber: 5.1 Consensus size: 13
24580491 ACTAGTTTAT
24580501 CTAAACACTAAACC
1 CTAAAC-CTAAACC
*
24580515 ATAAACCTAAACC
1 CTAAACCTAAACC
24580528 CTAAAATCCTAAACC
1 CT-AAA-CCTAAACC
*
24580543 CTTAACAC-ATAACC
1 CTAAAC-CTA-AACC
24580557 TCTAAACCTTAAACC
1 -CTAAACC-TAAACC
24580572 C
1 C
24580573 CAGCCTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
13 10 0.21
14 17 0.36
15 19 0.40
16 1 0.02
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (13 bp):
CTAAACCTAAACC
Found at i:24580590 original size:7 final size:7
Alignment explanation
Indices: 24580580--24580691 Score: 59
Period size: 7 Copynumber: 15.7 Consensus size: 7
24580570 CCCCAGCCTT
24580580 TAAACCA
1 TAAACCA
24580587 TAAACCA
1 TAAACCA
*
24580594 TAAATCA
1 TAAACCA
* *
24580601 TAACCCC
1 TAAACCA
24580608 TAAACTCA
1 TAAAC-CA
*
24580616 TAATCCA
1 TAAACCA
*
24580623 TAAACCT
1 TAAACCA
24580630 TAAA--A
1 TAAACCA
*
24580635 TAGTAACTCC
1 TA--AAC-CA
*
24580645 TAAACCT
1 TAAACCA
24580652 TAAACTC-
1 TAAAC-CA
24580659 TAAACCA
1 TAAACCA
* *
24580666 TATACCC
1 TAAACCA
24580673 TAAACCA
1 TAAACCA
* *
24580680 AAAACCT
1 TAAACCA
24580687 TAAAC
1 TAAAC
24580692 TATAGTGATA
Statistics
Matches: 78, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
5 2 0.03
6 1 0.01
7 64 0.82
8 9 0.12
10 2 0.03
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:24580633 original size:22 final size:22
Alignment explanation
Indices: 24580608--24580677 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
24580598 TCATAACCCC
24580608 TAAACTCATAATCCATAAACCT
1 TAAACTCATAATCCATAAACCT
*
24580630 TAAAAT-AGTAACTCC-TAAACCT
1 TAAACTCA-TAA-TCCATAAACCT
* * *
24580652 TAAACTC-TAAACCATATACCC
1 TAAACTCATAATCCATAAACCT
24580673 TAAAC
1 TAAAC
24580678 CAAAAACCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.05
21 14 0.36
22 20 0.51
23 3 0.08
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (22 bp):
TAAACTCATAATCCATAAACCT
Found at i:24581087 original size:41 final size:40
Alignment explanation
Indices: 24581000--24581233 Score: 247
Period size: 41 Copynumber: 5.8 Consensus size: 40
24580990 AAAAAAATTT
* * *** *
24581000 GCGGCGCTTTTTCAAAAACGCC-ATAAA-ATAGAGGATTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCGAGCATTA
* *
24581038 GCGGCGCTTTTTTAAAAACGCTGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGCCC-GAGCATTA
** * *
24581079 GCGGCGCTTTTCCAAAAACGCCGCTAAAAACACGAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCT-AAAGCCCGAGCATTA
* *
24581120 GCGGCGCTTTTTAAAAAATGCCGCTAAAACCCTGAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGCCC-GAGCATTA
* *
24581161 GCGGCGCTTTTTCAAAAGCGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAG-CCCGAGCATTA
* * *
24581202 GCGGCACTTTTTAAAAAATGCCACTAAAGCCC
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGCCC
24581234 CGAAAACTCA
Statistics
Matches: 165, Mismatches: 25, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
38 20 0.12
39 4 0.02
40 9 0.05
41 124 0.75
42 8 0.05
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (40 bp):
GCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCGAGCATTA
Found at i:24581131 original size:82 final size:82
Alignment explanation
Indices: 24581000--24581233 Score: 330
Period size: 82 Copynumber: 2.9 Consensus size: 82
24580990 AAAAAAATTT
* * * * * *
24581000 GCGGCGCTTTTTCAAAAACGCC-AT-AAAATA-GAGGATTAGCGGCGCTTTTTTAAAAACGCTGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
24581062 TAAAGCCCTGAGCATTA
66 TAAAGCCCTGAGCATTA
*
24581079 GCGGCGCTTTTCCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
*
24581144 TAAAACCCTGAGCATTA
66 TAAAGCCCTGAGCATTA
* * * * *
24581161 GCGGCGCTTTTTCAAAAGCGCCGCTAAAGACCCGAGCATTAGCGGCACTTTTTAAAAAATGCCAC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
24581226 TAAAGCCC
66 TAAAGCCC
24581234 CGAAAACTCA
Statistics
Matches: 137, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 21 0.15
80 1 0.01
81 5 0.04
82 110 0.80
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (82 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
TAAAGCCCTGAGCATTA
Found at i:24581236 original size:41 final size:41
Alignment explanation
Indices: 24581034--24581236 Score: 253
Period size: 41 Copynumber: 5.0 Consensus size: 41
24581024 AAAATAGAGG
* * *
24581034 ATTAGCGGCGCTTTTTTAAAAACGCTGCTAAAGCCCTGAGC
1 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCCGAGC
** ** *
24581075 ATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAAACACGAGC
1 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCCGAGC
* * *
24581116 ATTAGCGGCGCTTTTTAAAAAATGCCGCTAAAACCCTGAGC
1 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCCGAGC
* * *
24581157 ATTAGCGGCGCTTTTTCAAAAGCGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCCGAGC
* * *
24581198 ATTAGCGGCACTTTTTAAAAAATGCCACTAAAGCCCCGA
1 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCCGA
24581237 AAACTCAGAA
Statistics
Matches: 137, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 137 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCCGAGC
Found at i:24581359 original size:40 final size:39
Alignment explanation
Indices: 24581284--24581402 Score: 125
Period size: 39 Copynumber: 3.1 Consensus size: 39
24581274 GCGGTGCTTA
* * *
24581284 TTGGAAAACGCCTCTAATGCTC-ATTTTTAGTGGCGTTT
1 TTGGAAAACGCCGCTAATACTCGATTTTTAGCGGCGTTT
* *
24581322 TTCGGAAAGCGCCGCTAATACTCGATCTTTAGCGGCGTTT
1 TT-GGAAAACGCCGCTAATACTCGATTTTTAGCGGCGTTT
** * *
24581362 TTTTAAAACGCCGCTAATGA-TTGATTTTTAGCGGAGTTT
1 TTGGAAAACGCCGCTAAT-ACTCGATTTTTAGCGGCGTTT
24581401 TT
1 TT
24581403 TTATCCAAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.03
39 48 0.72
40 17 0.25
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (39 bp):
TTGGAAAACGCCGCTAATACTCGATTTTTAGCGGCGTTT
Found at i:24585425 original size:18 final size:18
Alignment explanation
Indices: 24585402--24585456 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
24585392 TATCTTTGGG
24585402 TCTTTACTTTCTTTTTAT
1 TCTTTACTTTCTTTTTAT
* * *
24585420 TCTTTATTTTATTCTTAT
1 TCTTTACTTTCTTTTTAT
*
24585438 T-TTTAC--TCTTTCTAT
1 TCTTTACTTTCTTTTTAT
24585453 TCTT
1 TCTT
24585457 ATATTTCATA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 7 0.24
16 2 0.07
17 4 0.14
18 16 0.55
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTTACTTTCTTTTTAT
Found at i:24590061 original size:18 final size:19
Alignment explanation
Indices: 24590024--24590060 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
24590014 TTTTAAAAAA
*
24590024 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
24590042 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
24590061 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:24590066 original size:18 final size:21
Alignment explanation
Indices: 24590029--24590072 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
24590019 AAAAATATAA
*
24590029 ATTTTAGAATTTTTATAAA-T
1 ATTTTAGAATTTTTAAAAATT
24590049 ATTTT-GAA-TTTTAAAAATT
1 ATTTTAGAATTTTTAAAAATT
24590068 ATTTT
1 ATTTT
24590073 TATTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTTTAGAATTTTTAAAAATT
Found at i:24590079 original size:19 final size:18
Alignment explanation
Indices: 24590037--24590079 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
24590027 AAATTTTAGA
*
24590037 ATTTTTATAAATATTTTG
1 ATTTTTAAAAATATTTTG
* *
24590055 AATTTTAAAAATTATTTTT
1 ATTTTTAAAAA-TATTTTG
24590074 ATTTTT
1 ATTTTT
24590080 TTGTAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTTAAAAATATTTTG
Found at i:24590532 original size:51 final size:52
Alignment explanation
Indices: 24590472--24590572 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 52
24590462 TTCATTTTCA
24590472 TTTTAGAGAAAACCAAAATCATTTCCAAATGATT-CCATTTCTCCATTTTTG
1 TTTTAGAGAAAACCAAAATCATTTCCAAATGATTCCCATTTCTCCATTTTTG
* * * *
24590523 TTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCCGTTTCTCCATTTT
1 TTTTAGAGAAAACCAAAATCATTTCCAAATGATTCCCATTTCTCCATTTT
24590573 CACCATTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 31 0.69
52 14 0.31
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (52 bp):
TTTTAGAGAAAACCAAAATCATTTCCAAATGATTCCCATTTCTCCATTTTTG
Found at i:24597782 original size:50 final size:50
Alignment explanation
Indices: 24597706--24597806 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
24597696 ACCTTATTGT
* **
24597706 AATCAATGTCAAATAGAAGAAAAGTAGTTCTCTATTGATTCTACTTGTGC
1 AATCAATGTCAAATAGAAGAAAAGTAGTTCTATAAGGATTCTACTTGTGC
* *
24597756 AATCAATGTCAAATAGAAGAATAGTAGTTCTATAAGGATTTTACTTGTGC
1 AATCAATGTCAAATAGAAGAAAAGTAGTTCTATAAGGATTCTACTTGTGC
24597806 A
1 A
24597807 GCCTGGTCCG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (50 bp):
AATCAATGTCAAATAGAAGAAAAGTAGTTCTATAAGGATTCTACTTGTGC
Found at i:24606391 original size:40 final size:40
Alignment explanation
Indices: 24606336--24606471 Score: 195
Period size: 40 Copynumber: 3.4 Consensus size: 40
24606326 GCTTGTATAG
*
24606336 GTTTGCACTTTGGTGCTTCAGATTGCACAATTGTGCCTTT
1 GTTTGCACTTTGGTGCTTCTGATTGCACAATTGTGCCTTT
* *
24606376 GTTTGCACTTTGGTGCCTCTGATTGCACAATCGTG-CTTCT
1 GTTTGCACTTTGGTGCTTCTGATTGCACAATTGTGCCTT-T
* *
24606416 GTTTGCACTTCGGTG-TCTCTGGTTGCACAATTGTGCCTTT
1 GTTTGCACTTTGGTGCT-TCTGATTGCACAATTGTGCCTTT
24606456 GTTTGCACTTTGGTGC
1 GTTTGCACTTTGGTGC
24606472 CCCTATCAGC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
39 3 0.04
40 78 0.93
41 3 0.04
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.42
Consensus pattern (40 bp):
GTTTGCACTTTGGTGCTTCTGATTGCACAATTGTGCCTTT
Found at i:24606472 original size:20 final size:20
Alignment explanation
Indices: 24606336--24606472 Score: 93
Period size: 20 Copynumber: 6.8 Consensus size: 20
24606326 GCTTGTATAG
*
24606336 GTTTGCACTTTGGTG-CTTCA
1 GTTTGCACTTTGGTGCCTT-T
* *
24606356 GATTGCACAATT-GTGCCTTT
1 GTTTGCAC-TTTGGTGCCTTT
*
24606376 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTTTGGTGCCTTT
* ** *
24606396 GATTGCACAATCGTG-CTTCT
1 GTTTGCACTTTGGTGCCTT-T
* * *
24606416 GTTTGCACTTCGGTGTCTCT
1 GTTTGCACTTTGGTGCCTTT
* *
24606436 GGTTGCACAATT-GTGCCTTT
1 GTTTGCAC-TTTGGTGCCTTT
24606456 GTTTGCACTTTGGTGCC
1 GTTTGCACTTTGGTGCC
24606473 CCTATCAGCA
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
19 6 0.07
20 72 0.84
21 8 0.09
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.42
Consensus pattern (20 bp):
GTTTGCACTTTGGTGCCTTT
Found at i:24609728 original size:28 final size:28
Alignment explanation
Indices: 24609664--24609736 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
24609654 ATGACTTTAC
24609664 CATATATGTGGAAGTCCACAAGGACAAT
1 CATATATGTGGAAGTCCACAAGGACAAT
* *
24609692 CTTACATGTGGAAGTCCACAAGGA-AATT
1 CATATATGTGGAAGTCCACAAGGACAA-T
* *
24609720 CATGTATGTGAAAGTCC
1 CATATATGTGGAAGTCC
24609737 GCAGGACTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.05
28 36 0.95
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (28 bp):
CATATATGTGGAAGTCCACAAGGACAAT
Found at i:24621003 original size:35 final size:34
Alignment explanation
Indices: 24620880--24621063 Score: 98
Period size: 33 Copynumber: 5.5 Consensus size: 34
24620870 ATGTTTATAT
* * * * *
24620880 GTAAGACCATAGTTGGGCTATGACATTTTAATGAA
1 GTAAGACCATAGCTGGGATATGGCATATTGAT-AA
* * * *
24620915 --AAGACCATAACTGGGTTATGACACT-TTGA-AC
1 GTAAGACCATAGCTGGGATATGGCA-TATTGATAA
* * *
24620946 GTAAGACCAT-GGTTGGACTATGGCAGTATTTATAA
1 GTAAGACCATAGCTGGGA-TATGGCA-TATTGATAA
*
24620981 GTAAGACCATAGCTGGGATATGGCAT-TCTGATGA
1 GTAAGACCATAGCTGGGATATGGCATAT-TGATAA
* * *
24621015 -TAAGACCATAACTGGGTTATGGCACTA-CGA-AA
1 GTAAGACCATAGCTGGGATATGGCA-TATTGATAA
*
24621047 GTAAGACCATGGCTGGG
1 GTAAGACCATAGCTGGG
24621064 CCATGGAAAT
Statistics
Matches: 115, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
31 1 0.01
32 4 0.03
33 77 0.67
34 10 0.09
35 18 0.16
36 5 0.04
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (34 bp):
GTAAGACCATAGCTGGGATATGGCATATTGATAA
Found at i:24621025 original size:101 final size:101
Alignment explanation
Indices: 24620845--24621069 Score: 297
Period size: 101 Copynumber: 2.2 Consensus size: 101
24620835 GAGTTGACAG
* * * * * *
24620845 GTAATACCATGGTTGGACCATGGCAATGTTTATATGTAAGACCATAGTTGGGCTATGACATTTTA
1 GTAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTGGGATATGACATTCTA
** *
24620910 ATGAAAAGACCATAACTGGGTTATGACACTTTGAAC
66 ATGAAAAGACCATAACTGGGTTATGACACTACGAAA
* * * *
24620946 GTAAGACCATGGTTGGACTATGGCAGTATTTATAAGTAAGACCATAGCTGGGATATGGCATTCTG
1 GTAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTGGGATATGACATTCTA
* *
24621011 ATGATAAGACCATAACTGGGTTATGGCACTACGAAA
66 ATGAAAAGACCATAACTGGGTTATGACACTACGAAA
* *
24621047 GTAAGACCATGGCTGGGCCATGG
1 GTAAGACCATGGTTGGACCATGG
24621070 AAATGCATGT
Statistics
Matches: 106, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 106 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (101 bp):
GTAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTGGGATATGACATTCTA
ATGAAAAGACCATAACTGGGTTATGACACTACGAAA
Found at i:24623363 original size:9 final size:10
Alignment explanation
Indices: 24623348--24623393 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
24623338 GGAAGAGAGA
24623348 AAGAAAGGAG
1 AAGAAAGGAG
24623358 -AGAAAGGAG
1 AAGAAAGGAG
*
24623367 AAGAAAAGAAG
1 AAG-AAAGGAG
*
24623378 AAG-AAGAAG
1 AAGAAAGGAG
24623387 AAGAAAG
1 AAGAAAG
24623394 AAAGAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 18 0.56
10 5 0.16
11 9 0.28
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (10 bp):
AAGAAAGGAG
Found at i:24623398 original size:20 final size:21
Alignment explanation
Indices: 24623339--24623404 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 21
24623329 GCACCCACCG
24623339 GAAGAGAGAAAGAAAGGAGAGAAA
1 GAAGA-AGAAAGAAA-GA-AGAAA
*
24623363 GGAGAAGAAA-AGAAGAAG-AA
1 GAAGAAGAAAGA-AAGAAGAAA
*
24623383 GAAGAAGAAAGAAAGAAAAAA
1 GAAGAAGAAAGAAAGAAGAAA
24623404 G
1 G
24623405 GTAATGTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 16 0.44
21 6 0.17
22 3 0.08
23 7 0.19
24 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
GAAGAAGAAAGAAAGAAGAAA
Found at i:24623398 original size:23 final size:21
Alignment explanation
Indices: 24623339--24623399 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
24623329 GCACCCACCG
*
24623339 GAAGAGAGAAAGAAAGGAGAGA
1 GAAGA-AGAAAGAAAGAAGAGA
*
24623361 -AAGGAG-AAGAAAAGAAGAAGAA
1 GAAGAAGAAAG-AAAGAAG-AG-A
24623383 GAAGAAGAAAGAAAGAA
1 GAAGAAGAAAGAAAGAA
24623400 AAAAGGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
19 3 0.10
20 8 0.26
21 5 0.16
22 1 0.03
23 11 0.35
24 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
GAAGAAGAAAGAAAGAAGAGA
Found at i:24623445 original size:47 final size:47
Alignment explanation
Indices: 24623394--24623487 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
24623384 AAGAAGAAAG
24623394 AAAGAAAAAAGGTAATGTATAATTTTAGTAAATAATTTTGTTTATAA
1 AAAGAAAAAAGGTAATGTATAATTTTAGTAAATAATTTTGTTTATAA
*
24623441 AAAGAAAAAAGGTAATGTATTATTTTAGTAAATAATTTTGTTTATAA
1 AAAGAAAAAAGGTAATGTATAATTTTAGTAAATAATTTTGTTTATAA
24623488 TTTAAAGAGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (47 bp):
AAAGAAAAAAGGTAATGTATAATTTTAGTAAATAATTTTGTTTATAA
Found at i:24624045 original size:102 final size:100
Alignment explanation
Indices: 24623927--24624211 Score: 407
Period size: 101 Copynumber: 2.8 Consensus size: 100
24623917 TTATAGTTAT
* * *
24623927 TTATTTTGTTAATAATTTATGGGATTAGG-T-TACAAATTGTTAGTGTTTAGTATTGAGTTTTGT
1 TTATTTTGTTAGTAATTTAT--GATTAGGTTATATAAATTGTTAGTGTTTAGT-TTGTGTTTTGT
*
24623990 GATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTTAG
63 GATTTTTTAGTAATGTAATTTAAAAAAAA-AATTTATAG
24624029 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTATGTGTTTTGTGA
1 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTT-TGTGTTTTGTGA
* * *
24624094 TTTTTTAGTAATTTATTTTAAAAAATAAATTTATAG
65 TTTTTTAGTAATGTAATTTAAAAAAAAAATTTATAG
* *
24624130 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTCAGTGTTTAGTTTAGTGTTTTGTAA
1 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTT-GTGTTTTGTGA
24624195 TTTTTT--TAATGTAATTT
65 TTTTTTAGTAATGTAATTT
24624212 TTATATAATT
Statistics
Matches: 168, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
99 9 0.05
100 8 0.05
101 77 0.46
102 74 0.44
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.54
Consensus pattern (100 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTGTGTTTTGTGAT
TTTTTAGTAATGTAATTTAAAAAAAAAATTTATAG
Found at i:24624079 original size:50 final size:50
Alignment explanation
Indices: 24624024--24624181 Score: 142
Period size: 50 Copynumber: 3.1 Consensus size: 50
24624014 AAAAATAATT
*
24624024 TTTAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTG
1 TTTAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTAAGTG
* * * * ** * *** *
24624074 TTTAGTTATGTGTT-TT-GTGATTTTTTAGTAATTTATTTTAAAAAATAAAT-
1 TTTAGTTAT-T-TTGTTAGTAATTTATGATTAGGTTA-TATAAATTGTAAGTG
*
24624124 TTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTCAGTG
1 TT-TAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTAAGTG
24624175 TTTAGTT
1 TTTAGTT
24624182 TAGTGTTTTG
Statistics
Matches: 77, Mismatches: 24, Indels: 14
0.67 0.21 0.12
Matches are distributed among these distances:
49 2 0.03
50 40 0.52
51 33 0.43
52 2 0.03
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (50 bp):
TTTAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTAAGTG
Found at i:24624209 original size:14 final size:16
Alignment explanation
Indices: 24624190--24624228 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
24624180 TTTAGTGTTT
24624190 TGTAATTTTT-T-TAA
1 TGTAATTTTTATATAA
24624204 TGTAATTTTTATATAA
1 TGTAATTTTTATATAA
*
24624220 TTTAATTTT
1 TGTAATTTT
24624229 ATTTGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
TGTAATTTTTATATAA
Found at i:24624564 original size:3 final size:3
Alignment explanation
Indices: 24624556--24624627 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
24624546 ATTTGCAACA
24624556 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24624604 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
24624628 CGCATATCAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:24626732 original size:76 final size:75
Alignment explanation
Indices: 24626575--24626875 Score: 442
Period size: 75 Copynumber: 4.0 Consensus size: 75
24626565 AATAACTTCA
* * * *
24626575 TATTTATGTAATGAATTTTT-TCCATTTTATTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
1 TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
*
24626639 GTTAACTTTG
66 GTAAACTTTG
* * *
24626649 TATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTTATGGTTTTTTTTGCAATTTAAAT
1 TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATGG-TTTTTTTGCAATTTAAAT
24626714 AGTAAACTTTG
65 AGTAAACTTTG
*
24626725 TATTTATGTAATGACTTTTTCGCTATTTCAGTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
1 TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
24626790 GTAAACTTTG
66 GTAAACTTTG
* * * *
24626800 TATTTATGTAATGACTTTTTCACTATTTCAGTTATCAATTTTATGTTTTTTTTTGTAATTTAAAT
1 TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATG-GTTTTTTTGCAATTTAAAT
*
24626865 AAATAAACTTT
65 -AGTAAACTTT
24626876 AGACTAACTT
Statistics
Matches: 212, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
74 19 0.09
75 97 0.46
76 87 0.41
77 9 0.04
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.55
Consensus pattern (75 bp):
TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
GTAAACTTTG
Found at i:24626841 original size:151 final size:151
Alignment explanation
Indices: 24626562--24626875 Score: 463
Period size: 151 Copynumber: 2.1 Consensus size: 151
24626552 GTTTTGTAAT
** * * *
24626562 ATAAAT-AACTTCATATTTATGTAATGAATTTTTTCCATTTTATTTATCAATTTTATGGTTTTTT
1 ATAAATAAACTTTGTATTTATGTAATGAACTTTTTCCATTTCAGTTATCAATTTTATGGTTTTTT
* ** * *
24626626 TGCAATTTAAATAGTTAACTTTGTATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTT
66 TGCAATTTAAATAGTAAACTTTGTATTTATGTAATGACTTTTTCACCATTTCAGTTATCAATTTT
24626691 ATGGTTTTTTTTGCAATTTAA
131 ATGGTTTTTTTTGCAATTTAA
*
24626712 AT-AGTAAACTTTGTATTTATGTAATG-ACTTTTTCGCTATTTCAGTTATCAATTTTATGGTTTT
1 ATAAATAAACTTTGTATTTATGTAATGAACTTTTTC-C-ATTTCAGTTATCAATTTTATGGTTTT
*
24626775 TTTGCAATTTAAATAGTAAACTTTGTATTTATGTAATGACTTTTTCACTATTTCAGTTATCAATT
64 TTTGCAATTTAAATAGTAAACTTTGTATTTATGTAATGACTTTTTCACCATTTCAGTTATCAATT
* *
24626840 TTATGTTTTTTTTTGTAATTTAA
129 TTATGGTTTTTTTTGCAATTTAA
24626863 ATAAATAAACTTT
1 ATAAATAAACTTT
24626876 AGACTAACTT
Statistics
Matches: 145, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
149 9 0.06
150 21 0.14
151 106 0.73
152 9 0.06
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (151 bp):
ATAAATAAACTTTGTATTTATGTAATGAACTTTTTCCATTTCAGTTATCAATTTTATGGTTTTTT
TGCAATTTAAATAGTAAACTTTGTATTTATGTAATGACTTTTTCACCATTTCAGTTATCAATTTT
ATGGTTTTTTTTGCAATTTAA
Found at i:24629779 original size:21 final size:20
Alignment explanation
Indices: 24629750--24629795 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
24629740 CGAAATGCAA
24629750 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
24629771 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
24629791 T-AACC
1 TCAACC
24629796 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:24631980 original size:19 final size:20
Alignment explanation
Indices: 24631951--24631988 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
24631941 TGCCACCCAT
*
24631951 AAAATAATAATTTAAAAAAC
1 AAAATAATAATATAAAAAAC
24631971 AAAA-AATAATATAAAAAA
1 AAAATAATAATATAAAAAA
24631989 GTAGTTGCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAATAATATAAAAAAC
Found at i:24634414 original size:43 final size:44
Alignment explanation
Indices: 24634346--24634435 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 44
24634336 TGTTGTGGCT
* * * * *
24634346 TTTGTAGCTAGAATCGCCTCAAAAGATCATGTTCTTTAGCGGCG
1 TTTGTAGCTAAAAGCGCCTCAAAAGATCATATTCTATAGCGCCG
*
24634390 TTTGTAG-TAAAAGCGCCTCTAAAGATCATATTCTATAGCGCCG
1 TTTGTAGCTAAAAGCGCCTCAAAAGATCATATTCTATAGCGCCG
24634433 TTT
1 TTT
24634436 TCTCACATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 33 0.82
44 7 0.17
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (44 bp):
TTTGTAGCTAAAAGCGCCTCAAAAGATCATATTCTATAGCGCCG
Found at i:24635057 original size:23 final size:23
Alignment explanation
Indices: 24635022--24635072 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
24635012 GGGAAATAAA
* *
24635022 AAAAATAAGTTAGGGAATTGGGG
1 AAAATTAAATTAGGGAATTGGGG
*
24635045 AAAATTAAATTAGGGATTTGGGG
1 AAAATTAAATTAGGGAATTGGGG
24635068 AAAAT
1 AAAAT
24635073 GATTTGGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.25
Consensus pattern (23 bp):
AAAATTAAATTAGGGAATTGGGG
Found at i:24635206 original size:41 final size:40
Alignment explanation
Indices: 24635150--24635285 Score: 139
Period size: 40 Copynumber: 3.3 Consensus size: 40
24635140 ATTCGCGGTG
* * * *
24635150 TTTATGGGCAAAATGCCGTTATTGCTTTACCTTTAGCGGCG
1 TTTATGAG-AAAATGCCGCTATTGCTTTACCTTTTGCGGCA
*
24635191 TTTATGAGAAGAATGCCGCTATTGTTTTTAACCTTTTGCGGCA
1 TTTATGAGAA-AATGCCGCTATTG-CTTT-ACCTTTTGCGGCA
* * *
24635234 TTTATGCA-AAAACGCCACTATTGCTTTACCTTTTGCTGCA
1 TTTATG-AGAAAATGCCGCTATTGCTTTACCTTTTGCGGCA
*
24635274 TTTATGGGAAAA
1 TTTATGAGAAAA
24635286 ATGACGTTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
40 24 0.30
41 22 0.28
42 14 0.17
43 19 0.24
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (40 bp):
TTTATGAGAAAATGCCGCTATTGCTTTACCTTTTGCGGCA
Found at i:24635275 original size:40 final size:41
Alignment explanation
Indices: 24635169--24635279 Score: 127
Period size: 43 Copynumber: 2.7 Consensus size: 41
24635159 AAAATGCCGT
* * * *
24635169 TATTGCTTTACCTTTAGCGGCGTTTATGAGAAGAATGCCGC
1 TATTGCTTTACCTTTTGCGGCATTTATGAGAAGAACGCCAC
*
24635210 TATTGTTTTTAACCTTTTGCGGCATTTATGCA-AA-AACGCCAC
1 TATTG-CTTT-ACCTTTTGCGGCATTTATG-AGAAGAACGCCAC
*
24635252 TATTGCTTTACCTTTTGCTGCATTTATG
1 TATTGCTTTACCTTTTGCGGCATTTATG
24635280 GGAAAAATGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
40 18 0.30
41 8 0.13
42 14 0.23
43 19 0.32
44 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (41 bp):
TATTGCTTTACCTTTTGCGGCATTTATGAGAAGAACGCCAC
Found at i:24635724 original size:16 final size:17
Alignment explanation
Indices: 24635686--24635728 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
24635676 CTCAAGTGCA
*
24635686 TTTTCTTTTGAGTGTTT
1 TTTTCTTTTGAGTCTTT
* *
24635703 TGTTCTTTTG-TTCTTT
1 TTTTCTTTTGAGTCTTT
24635719 TTTTCTTTTG
1 TTTTCTTTTG
24635729 CATTTTTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.02, C:0.09, G:0.14, T:0.74
Consensus pattern (17 bp):
TTTTCTTTTGAGTCTTT
Found at i:24640687 original size:20 final size:20
Alignment explanation
Indices: 24640648--24640689 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
24640638 ATCTCAAATC
**
24640648 TTTTATTAGTTTGATTTTTT
1 TTTTATTAGTTTGAAATTTT
*
24640668 TTTTCTTAGTTTGAAATTTT
1 TTTTATTAGTTTGAAATTTT
24640688 TT
1 TT
24640690 AAGCCCTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (20 bp):
TTTTATTAGTTTGAAATTTT
Found at i:24660274 original size:36 final size:36
Alignment explanation
Indices: 24660227--24660298 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
24660217 CATACACATA
24660227 GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
1 GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
24660263 GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
1 GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
24660299 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (36 bp):
GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
Found at i:24667003 original size:27 final size:27
Alignment explanation
Indices: 24666957--24667049 Score: 127
Period size: 27 Copynumber: 3.4 Consensus size: 27
24666947 TCCAAAATAC
24666957 GCCACAAAGGC-AGTTCATACAGAGTAT
1 GCCACAAAGGCTA-TTCATACAGAGTAT
*
24666984 GCTACAAAGGCTATAT-ATACAGAGTAT
1 GCCACAAAGGCTAT-TCATACAGAGTAT
* *
24667011 GCCACAAGGGCTATTCATTCAGAGTAT
1 GCCACAAAGGCTATTCATACAGAGTAT
24667038 GCCACAAAGGCT
1 GCCACAAAGGCT
24667050 GATAGGATGC
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 55 0.95
28 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (27 bp):
GCCACAAAGGCTATTCATACAGAGTAT
Found at i:24671617 original size:30 final size:30
Alignment explanation
Indices: 24671581--24671639 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
24671571 TACGAGCTTT
24671581 GGGGAAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGAAAAAGTGTAAATATGCAAAAGTTTA
* * * *
24671611 GGGGAAAAATTGTAATTTTGCCAAAGTTT
1 GGGGAAAAAGTGTAAATATGCAAAAGTTT
24671640 GAGTCAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.29
Consensus pattern (30 bp):
GGGGAAAAAGTGTAAATATGCAAAAGTTTA
Found at i:24672220 original size:51 final size:50
Alignment explanation
Indices: 24672165--24672302 Score: 204
Period size: 50 Copynumber: 2.7 Consensus size: 50
24672155 AATGGCCACA
* * *
24672165 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGCCTTGGTCACG
1 TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGAAAG-CTTGATCACG
* *
24672216 TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAGCTTGATCACG
1 TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGAAAGCTTGATCACG
* *
24672266 TGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGA
1 TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGA
24672303 TGACAATGGT
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 42 0.54
51 36 0.46
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGAAAGCTTGATCACG
Found at i:24672282 original size:50 final size:51
Alignment explanation
Indices: 24672165--24672291 Score: 202
Period size: 51 Copynumber: 2.5 Consensus size: 51
24672155 AATGGCCACA
* * * * *
24672165 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGCCTTGGTCACG
1 TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAGCCTTGATCACG
24672216 TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAG-CTTGATCACG
1 TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAGCCTTGATCACG
24672266 TGTGTAGTACTATGTGTAGGCTACTA
1 TGTGTAGTACTATGTGTAGGCTACTA
24672292 CGTGTATCGG
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
50 35 0.49
51 36 0.51
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAGCCTTGATCACG
Found at i:24675015 original size:9 final size:9
Alignment explanation
Indices: 24675001--24675040 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
24674991 GTAGTGATTC
24675001 AATTCGGTT
1 AATTCGGTT
*
24675010 AATTCGGGT
1 AATTCGGTT
*
24675019 AATTCGTTT
1 AATTCGGTT
24675028 AATTCGGTT
1 AATTCGGTT
24675037 AATT
1 AATT
24675041 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:24682936 original size:21 final size:21
Alignment explanation
Indices: 24682899--24682967 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
24682889 CGCCCAAGTC
*
24682899 GTGTGGCTT-CACACATGGCT
1 GTGTGGCTTCCTCACATGGCT
* *
24682919 GTGTGGCTTCCTCACATGCCC
1 GTGTGGCTTCCTCACATGGCT
*
24682940 GTGAGGCTTCCTCACAT-GCTT
1 GTGTGGCTTCCTCACATGGC-T
24682961 GTGTGGC
1 GTGTGGC
24682968 CAGACCGTGC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 10 0.25
21 30 0.75
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.30
Consensus pattern (21 bp):
GTGTGGCTTCCTCACATGGCT
Found at i:24688025 original size:10 final size:10
Alignment explanation
Indices: 24688010--24688034 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
24688000 GCCTAAGATG
24688010 TGAATTGCAT
1 TGAATTGCAT
24688020 TGAATTGCAT
1 TGAATTGCAT
24688030 TGAAT
1 TGAAT
24688035 ATGAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (10 bp):
TGAATTGCAT
Found at i:24688697 original size:24 final size:24
Alignment explanation
Indices: 24688623--24688703 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
24688613 TGGCTATCCG
24688623 GAGCTTCCCGATTAATTGCTCTTCA-
1 GAGCTTCCCGATT-ATTGCTCTT-AT
* **
24688648 GAGCTACCCG-TTATTGGCTCGCAT
1 GAGCTTCCCGATTATT-GCTCTTAT
24688672 GAGCTTCCCGATTA-TGACTCTTAT
1 GAGCTTCCCGATTATTG-CTCTTAT
24688696 GAGCTTCC
1 GAGCTTCC
24688704 TATTATACAG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 5 0.11
24 29 0.63
25 12 0.26
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (24 bp):
GAGCTTCCCGATTATTGCTCTTAT
Found at i:24688741 original size:25 final size:25
Alignment explanation
Indices: 24688713--24688766 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
24688703 CTATTATACA
* *
24688713 GCTCAGATAAGCTTCCCGTTACATG
1 GCTCACATAAGCTTCCCATTACATG
* *
24688738 GCTCACATGAGCTTCCCATTATATG
1 GCTCACATAAGCTTCCCATTACATG
24688763 GCTC
1 GCTC
24688767 GAGAGAGAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (25 bp):
GCTCACATAAGCTTCCCATTACATG
Found at i:24693329 original size:6 final size:6
Alignment explanation
Indices: 24693315--24693362 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
24693305 TTATTATTCG
* * *
24693315 TCTCTC TCTCAC TCTCAC TCT--C TCACTC TCTCAC TCTCAC TCTCAC
1 TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC
24693361 TC
1 TC
24693363 ACTCACACGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 3 0.08
6 33 0.92
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (6 bp):
TCTCAC
Found at i:24693337 original size:14 final size:14
Alignment explanation
Indices: 24693318--24693368 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
24693308 TTATTCGTCT
24693318 CTCTCTCACTCTCA
1 CTCTCTCACTCTCA
*
24693332 CTCTCTCACTCTCT
1 CTCTCTCACTCTCA
*
24693346 CACTCTCACTCTCA
1 CTCTCTCACTCTCA
*
24693360 CTCACTCAC
1 CTCTCTCAC
24693369 ACGCACATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.16, C:0.51, G:0.00, T:0.33
Consensus pattern (14 bp):
CTCTCTCACTCTCA
Found at i:24693368 original size:8 final size:8
Alignment explanation
Indices: 24693316--24693366 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
24693306 TATTATTCGT
*
24693316 CTCTCTCT
1 CTCTCTCA
*
24693324 CACTCTCA
1 CTCTCTCA
24693332 CTCTCTCA
1 CTCTCTCA
24693340 CTCTCTCA
1 CTCTCTCA
* *
24693348 CTCTCACT
1 CTCTCTCA
*
24693356 CTCACTCA
1 CTCTCTCA
24693364 CTC
1 CTC
24693367 ACACGCACAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.14, C:0.51, G:0.00, T:0.35
Consensus pattern (8 bp):
CTCTCTCA
Found at i:24695085 original size:19 final size:19
Alignment explanation
Indices: 24695063--24695106 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
24695053 GTCTGGTATA
*
24695063 GATACTGTTTTAGTATATC
1 GATACTGTTTTAGGATATC
*
24695082 GATACCTTTTTTAGGATATC
1 GATA-CTGTTTTAGGATATC
24695102 GATAC
1 GATAC
24695107 CTTAGTGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (19 bp):
GATACTGTTTTAGGATATC
Found at i:24695095 original size:20 final size:20
Alignment explanation
Indices: 24695070--24695109 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
24695060 ATAGATACTG
*
24695070 TTTTAGTATATCGATACCTT
1 TTTTAGGATATCGATACCTT
24695090 TTTTAGGATATCGATACCTT
1 TTTTAGGATATCGATACCTT
24695110 AGTGCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTTAGGATATCGATACCTT
Found at i:24698292 original size:27 final size:27
Alignment explanation
Indices: 24698254--24698317 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
24698244 TAACTAACTG
*
24698254 TAATACCCCTATAGGGTAAAATGACCA
1 TAATGCCCCTATAGGGTAAAATGACCA
* *
24698281 TAATGCCCCTATAGGGTAAACTGACCG
1 TAATGCCCCTATAGGGTAAAATGACCA
*
24698308 TAAAGCCCCT
1 TAATGCCCCT
24698318 GAAAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (27 bp):
TAATGCCCCTATAGGGTAAAATGACCA
Found at i:24698427 original size:27 final size:27
Alignment explanation
Indices: 24698387--24698615 Score: 282
Period size: 27 Copynumber: 8.5 Consensus size: 27
24698377 GATTGATTTT
* * *
24698387 TAGGGTAAAATGACCATAATGCCCCTT
1 TAGGGTAAACTGACCGTAATGCCCCTG
* * *
24698414 TAAGGTAAACTGACTGTAATACCCCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
* * *
24698441 TAGGGTAAAATGACTGTAATACCCCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
*
24698468 TAGGGTAAACTGACCGTAATGCCTCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
* *
24698495 TAGGGTAAACTGACCATAATGCCCCCG
1 TAGGGTAAACTGACCGTAATGCCCCTG
24698522 TAGGGTAAACTGACCGTAATGCCCCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
*
24698549 T-GAGGTAAACTGACCGTAATCCCCCTG
1 TAG-GGTAAACTGACCGTAATGCCCCTG
* * *
24698576 TAGGGTAAAATGACTGTAATACCCCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
*
24698603 GAGGGTAAA-TGAC
1 TAGGGTAAACTGAC
24698616 TATTTTGCAC
Statistics
Matches: 178, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
26 5 0.03
27 172 0.97
28 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (27 bp):
TAGGGTAAACTGACCGTAATGCCCCTG
Found at i:24698675 original size:23 final size:24
Alignment explanation
Indices: 24698649--24698701 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
24698639 GATTGAATTA
24698649 TCTGTGGTT-AAATGACTAATTTG
1 TCTGTGGTTGAAATGACTAATTTG
* ** *
24698672 TCTGTGTTTGGTATGACTGATTTG
1 TCTGTGGTTGAAATGACTAATTTG
24698696 TCTGTG
1 TCTGTG
24698702 ATTTGAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.47
Consensus pattern (24 bp):
TCTGTGGTTGAAATGACTAATTTG
Found at i:24698711 original size:24 final size:24
Alignment explanation
Indices: 24698659--24698717 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
24698649 TCTGTGGTTA
*
24698659 AATGACTAATTTGTCTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTTGG
*
24698683 TATGACTGATTTGTCTGTGATTT-G
1 AATGACTGATTTGTCTGTG-TTTGG
24698707 AATGACTGATT
1 AATGACTGATT
24698718 CTGAGCATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGTTTGG
Found at i:24698823 original size:27 final size:27
Alignment explanation
Indices: 24698781--24698845 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
24698771 ATGGAGGAAG
*
24698781 TACTGTT-CTAGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
24698806 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
*
24698834 TACTATTACTGG
1 TACTGTTACTGG
24698846 CAGCTTTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 7 0.21
27 24 0.71
28 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:24698851 original size:27 final size:27
Alignment explanation
Indices: 24698799--24698851 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
24698789 TAGTGGCTCT
* **
24698799 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTATTACTGGCAGCTTG
24698826 GCCACATAT-ACTATTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
24698852 TGCTGCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTG
Found at i:24698898 original size:26 final size:26
Alignment explanation
Indices: 24698843--24698898 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
24698833 ATACTATTAC
* *
24698843 TGGCAGCTTTGCTGCGATACTGCTGC
1 TGGCAGCTTTGCTGCGATACTACTGA
* *
24698869 TGGCAGCTTTGCTGTGATGCTACTGA
1 TGGCAGCTTTGCTGCGATACTACTGA
24698895 TGGC
1 TGGC
24698899 TTTGTGCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.12, C:0.23, G:0.32, T:0.32
Consensus pattern (26 bp):
TGGCAGCTTTGCTGCGATACTACTGA
Found at i:24699009 original size:32 final size:32
Alignment explanation
Indices: 24698889--24699010 Score: 156
Period size: 32 Copynumber: 3.8 Consensus size: 32
24698879 GCTGTGATGC
*
24698889 TACTGATGGCTTTGTGCCAATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
24698921 TACTAATAGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
**
24698953 TACTGATGAATTTGTG-CGAATCATATTACCGT
1 TACTGATGGCTTTGTGCCG-ATCATATTACCGT
* * *
24698985 TACTGATGGCTGTGTACCGGTCATAT
1 TACTGATGGCTTTGTGCCGATCATAT
24699011 CACTACTACT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
31 2 0.03
32 72 0.95
33 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:24699009 original size:64 final size:64
Alignment explanation
Indices: 24698889--24699010 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
24698879 GCTGTGATGC
** * *
24698889 TACTGATGGCTTTGTGCCAATCATATTACCGTTACTAATAGCTTTGTGCCGATCATATTACCGT
1 TACTGATGAATTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATTACCGT
* * * *
24698953 TACTGATGAATTTGTGCGAATCATATTACCGTTACTGATGGCTGTGTACCGGTCATAT
1 TACTGATGAATTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATAT
24699011 CACTACTACT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (64 bp):
TACTGATGAATTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATTACCGT
Found at i:24699031 original size:64 final size:64
Alignment explanation
Indices: 24698896--24699044 Score: 163
Period size: 64 Copynumber: 2.3 Consensus size: 64
24698886 TGCTACTGAT
* * * ** * *
24698896 GGCTTTGTGCCAATCATATTACCGTTACTAATAGCTTTGTGCCGATCATATTACCGTTACTGAT
1 GGCTTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATCACCACTACTAAA
** * * * * *
24698960 GAATTTGTGCGAATCATATTACCGTTACTGATGGCTGTGTACCGGTCATATCACTACTACTAAA
1 GGCTTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATCACCACTACTAAA
*
24699024 GGCTTTGTGCCAATGATATTA
1 GGCTTTGTGCCAATCATATTA
24699045 TTGTACTTAT
Statistics
Matches: 67, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (64 bp):
GGCTTTGTGCCAATCATATTACCGTTACTAATAGCTGTGTACCGATCATATCACCACTACTAAA
Found at i:24713421 original size:2 final size:2
Alignment explanation
Indices: 24713414--24713438 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24713404 TGAGAACATT
24713414 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 T
24713439 CTCAAATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24716927 original size:17 final size:17
Alignment explanation
Indices: 24716905--24716939 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24716895 TATACATTTC
*
24716905 TGTTTCGTTTCTTCTTT
1 TGTTTCGTTTATTCTTT
*
24716922 TGTTTCTTTTATTCTTT
1 TGTTTCGTTTATTCTTT
24716939 T
1 T
24716940 ATTTTATTTC
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:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (17 bp):
TGTTTCGTTTATTCTTT
Found at i:24717181 original size:16 final size:17
Alignment explanation
Indices: 24717145--24717181 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
24717135 TAATATAATT
24717145 TATAATATTTTAATTAA
1 TATAATATTTTAATTAA
*
24717162 -ATAATATTTTTA-TAA
1 TATAATATTTTAATTAA
24717177 TATAA
1 TATAA
24717182 ATCAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATATTTTAATTAA
Found at i:24724165 original size:21 final size:23
Alignment explanation
Indices: 24724140--24724214 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
24724130 GACATACGAG
*
24724140 GTGTCT-A-ATAATACACATAAA
1 GTGTCTGAGATAAGACACATAAA
*
24724161 GTGTCTGAGATACGACACATAAA
1 GTGTCTGAGATAAGACACATAAA
*
24724184 GTGTCTGATG-TACGACACATAAA
1 GTGTCTGA-GATAAGACACATAAA
*
24724207 GTGCCTGA
1 GTGTCTGA
24724215 TCGGCAAACC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
21 6 0.12
22 1 0.02
23 40 0.83
24 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (23 bp):
GTGTCTGAGATAAGACACATAAA
Found at i:24724178 original size:23 final size:23
Alignment explanation
Indices: 24724152--24724215 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
24724142 GTCTAATAAT
24724152 ACACATAAAGTGTCTGA-GATACG
1 ACACATAAAGTGTCTGATG-TACG
24724175 ACACATAAAGTGTCTGATGTACG
1 ACACATAAAGTGTCTGATGTACG
*
24724198 ACACATAAAGTGCCTGAT
1 ACACATAAAGTGTCTGAT
24724216 CGGCAAACCG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (23 bp):
ACACATAAAGTGTCTGATGTACG
Found at i:24724541 original size:16 final size:17
Alignment explanation
Indices: 24724520--24724551 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
24724510 TAATAATAAT
24724520 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
24724536 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
24724552 GCTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:24725241 original size:17 final size:17
Alignment explanation
Indices: 24725216--24725251 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
24725206 TTCAAATGGT
*
24725216 TTCTGTTTCTTTTCTTC
1 TTCTGTTTCTTTTATTC
*
24725233 TTCTTTTTCTTTTATTC
1 TTCTGTTTCTTTTATTC
24725250 TT
1 TT
24725252 TTATTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (17 bp):
TTCTGTTTCTTTTATTC
Found at i:24725468 original size:30 final size:27
Alignment explanation
Indices: 24725432--24725496 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
24725422 TTTCCTATAA
*
24725432 TATAATATCTTAACTTTAATTAATATAATT
1 TATAATATCTTAA--TTAAATAATAT-ATT
* *
24725462 TATAATATTTTAATTAAATAATATTTT
1 TATAATATCTTAATTAAATAATATATT
24725489 TATAATAT
1 TATAATAT
24725497 AAATCAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 10 0.31
30 12 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TATAATATCTTAATTAAATAATATATT
Found at i:24725498 original size:16 final size:17
Alignment explanation
Indices: 24725462--24725498 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
24725452 TAATATAATT
24725462 TATAATATTTTAATTAA
1 TATAATATTTTAATTAA
*
24725479 -ATAATATTTTTA-TAA
1 TATAATATTTTAATTAA
24725494 TATAA
1 TATAA
24725499 ATCAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATAATATTTTAATTAA
Found at i:24728812 original size:36 final size:37
Alignment explanation
Indices: 24728765--24728855 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
24728755 GTCTCCAAAT
* *
24728765 TCACATTTCAATTCAATTTCACTTTTTCACTTTCAA-
1 TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
* *
24728801 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAAG
1 TCACAATTCAATTC-AATTTCACTTTTCCACTTTCAAG
*
24728839 TCA-ATATTCATTTCAAT
1 TCACA-ATTCAATTCAAT
24728856 CCCACACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
36 13 0.28
37 22 0.48
38 11 0.24
ACGTcount: A:0.32, C:0.23, G:0.01, T:0.44
Consensus pattern (37 bp):
TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
Found at i:24729563 original size:9 final size:9
Alignment explanation
Indices: 24729551--24729582 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
24729541 TTTTCCATTC
24729551 TTTCTTTCT
1 TTTCTTTCT
24729560 TTTCTTTCT
1 TTTCTTTCT
*
24729569 TTCCTTTCT
1 TTTCTTTCT
24729578 TTTCT
1 TTTCT
24729583 CCATGTGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:24729564 original size:13 final size:13
Alignment explanation
Indices: 24729542--24729579 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
24729532 AACTCTAGTT
*
24729542 TTTCCATTCTTTC
1 TTTCCTTTCTTTC
*
24729555 TTTCTTTTCTTTC
1 TTTCCTTTCTTTC
24729568 TTTCCTTTCTTT
1 TTTCCTTTCTTT
24729580 TCTCCATGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCCTTTCTTTC
Found at i:24729790 original size:24 final size:24
Alignment explanation
Indices: 24729745--24729790 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
24729735 TACACATTTA
* * *
24729745 ATTATTATTACCATACACTTGTCT
1 ATTATCATCACCATACAATTGTCT
*
24729769 ATTATCATCACCATCCAATTGT
1 ATTATCATCACCATACAATTGT
24729791 TCTTAGTTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.41
Consensus pattern (24 bp):
ATTATCATCACCATACAATTGTCT
Found at i:24729969 original size:31 final size:30
Alignment explanation
Indices: 24729933--24730007 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 30
24729923 TACATTTGCC
*
24729933 ATAATTCAATTTATCTCTTAAT-ATAATA-TTT
1 ATAATT-AATTTATAT-TTAATAAT-ATACTTT
24729964 ATAATTTAA-TTA-ATTTAATAATATACTTT
1 ATAA-TTAATTTATATTTAATAATATACTTT
24729993 ATAATTAATTTATAT
1 ATAATTAATTTATAT
24730008 ATTTATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
28 12 0.32
29 13 0.34
30 5 0.13
31 6 0.16
32 2 0.05
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (30 bp):
ATAATTAATTTATATTTAATAATATACTTT
Found at i:24740796 original size:11 final size:11
Alignment explanation
Indices: 24740780--24740804 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24740770 GAACAGTGCT
24740780 GACGTGGCCGC
1 GACGTGGCCGC
24740791 GACGTGGCCGC
1 GACGTGGCCGC
24740802 GAC
1 GAC
24740805 TTGCCCCGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.36, G:0.44, T:0.08
Consensus pattern (11 bp):
GACGTGGCCGC
Found at i:24740940 original size:11 final size:11
Alignment explanation
Indices: 24740918--24740990 Score: 112
Period size: 11 Copynumber: 6.6 Consensus size: 11
24740908 AACTAATCCT
24740918 CTCTCAAATTTC
1 CTCTC-AATTTC
24740930 CTCTCAATTTC
1 CTCTCAATTTC
*
24740941 CTCTCAACTTC
1 CTCTCAATTTC
24740952 CTCTCAATTTC
1 CTCTCAATTTC
*
24740963 CTTTCAATTTC
1 CTCTCAATTTC
24740974 CTCTCAATTTC
1 CTCTCAATTTC
24740985 CT-TCAA
1 CTCTCAA
24740991 AAATTCTCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
10 4 0.07
11 48 0.84
12 5 0.09
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:24741087 original size:12 final size:12
Alignment explanation
Indices: 24741072--24741102 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
24741062 TTTTAAATAA
24741072 TTTTAAAATTTT
1 TTTTAAAATTTT
*
24741084 TTTTTAAATTTT
1 TTTTAAAATTTT
24741096 TTTTAAA
1 TTTTAAA
24741103 CCGTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:24741099 original size:11 final size:11
Alignment explanation
Indices: 24741059--24741102 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
24741049 CTTAACTCCC
24741059 TTTTTTTAAAT
1 TTTTTTTAAAT
** *
24741070 AATTTTAAAATT
1 TTTTTTTAAA-T
24741082 TTTTTTTAAAT
1 TTTTTTTAAAT
24741093 TTTTTTTAAA
1 TTTTTTTAAA
24741103 CCGTAAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:24742216 original size:7 final size:7
Alignment explanation
Indices: 24742204--24742228 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
24742194 AGTCGATTGA
24742204 TATTTAG
1 TATTTAG
24742211 TATTTAG
1 TATTTAG
24742218 TATTTAG
1 TATTTAG
24742225 TATT
1 TATT
24742229 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:24742897 original size:18 final size:18
Alignment explanation
Indices: 24742870--24742909 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
24742860 CAGGTGCGTT
* *
24742870 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATATA
24742888 TCCTAACCCTTATATATA
1 TCCTAACCCTTATATATA
24742906 TCCT
1 TCCT
24742910 TTTCCGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATATA
Found at i:24743366 original size:25 final size:25
Alignment explanation
Indices: 24743338--24743455 Score: 131
Period size: 25 Copynumber: 4.9 Consensus size: 25
24743328 TATTTTAATA
24743338 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
24743363 TTATTTGATGTAATAAAATAGAACT
1 TTATTTGATGTAATAAAATAGAAGT
* * ** *
24743388 TT-TTT--T-TAGTTATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
24743407 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
24743433 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
24743456 ATTTTTGAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 9 0.12
22 1 0.01
23 1 0.01
24 9 0.12
25 50 0.67
26 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:24743441 original size:70 final size:70
Alignment explanation
Indices: 24743328--24743461 Score: 250
Period size: 70 Copynumber: 1.9 Consensus size: 70
24743318 ATATTTTGAA
*
24743328 TATTTTAATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAACTTTTTT
1 TATTTTAATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTT
24743393 TTAGT
66 TTAGT
*
24743398 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTT
1 TATTTTAATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTT
24743462 GAATATTTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.48
Consensus pattern (70 bp):
TATTTTAATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTT
TTAGT
Found at i:24743509 original size:10 final size:9
Alignment explanation
Indices: 24743459--24743509 Score: 75
Period size: 9 Copynumber: 5.6 Consensus size: 9
24743449 AATAGAAATT
*
24743459 TTTGAATAT
1 TTTGAATAA
24743468 TTTGAATAA
1 TTTGAATAA
24743477 TTTGAATAA
1 TTTGAATAA
24743486 TTTGAATAA
1 TTTGAATAA
*
24743495 TTTGATATTA
1 TTTGA-ATAA
24743505 TTTGA
1 TTTGA
24743510 GAATTCTACT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
9 31 0.79
10 8 0.21
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (9 bp):
TTTGAATAA
Found at i:24743678 original size:44 final size:45
Alignment explanation
Indices: 24743531--24744241 Score: 633
Period size: 44 Copynumber: 16.0 Consensus size: 45
24743521 ACCATTAATA
* *
24743531 CCCTTAACTTAAAAACACTAACCTAATTTAATTAAAAACCCTAAC
1 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
** * * *
24743576 CTAATTTAA-TTAAAAACCTTAAACC--CTTAACTTAAAAACCCTAAC
1 C--CCTTAACTTAAAAACCCT-AACCTAATTAAATTAAAAACCCTAAC
** * * * *
24743621 CTAATTAAATTAAAAACTCAAACCTAATTAAATTAAAAATCCT-AC
1 C-CCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
24743666 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA-
1 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
24743710 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA-
1 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
24743754 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA-
1 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
* *
24743798 CCCTTAACTTAAAAACACTAACCTAATTAAATTAAAAAACCTAAC
1 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
** * * *
24743843 CTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAAC
1 C-CCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
** * * *
24743887 CTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAAC
1 C-CCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
** * * *
24743931 CTAATTTAA-TTAAAAACCCTAACCCAATTAAATTAAAAACCTTAAA
1 C--CCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
24743977 CCCTTAACTTAAAAACCCTAACCTAATTAAAATT-AAAACCCTAAC
1 CCCTTAACTTAAAAACCCTAACCTAATT-AAATTAAAAACCCTAAC
** * * *
24744022 CTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAA-
1 C-CCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
* * * *
24744065 CCTTAATAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAAC
1 CCCT--TAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
** * * *
24744110 CTAATTTAA-TTAAAACCCCTAAACCCT-A--AACTTCAAAACCCTAAC
1 C--CCTTAACTTAAAAACCCT-AA-CCTAATTAAATTAAAAACCCTAAC
** *** *
24744155 CTATT-ACTTAAAAACCCTAACCCCCTTAACTTAAAAACCCTAA-
1 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
* * *
24744198 CCCTTAACTTTAAAACCCTAAACTAATTTAATTAAAAACCCTAA
1 CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA
24744242 ACTAAATTAA
Statistics
Matches: 570, Mismatches: 67, Indels: 59
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.00
42 4 0.01
43 20 0.04
44 361 0.63
45 89 0.16
46 84 0.15
47 10 0.02
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (45 bp):
CCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
Found at i:24743789 original size:111 final size:111
Alignment explanation
Indices: 24743530--24744251 Score: 894
Period size: 111 Copynumber: 6.5 Consensus size: 111
24743520 AACCATTAAT
* * * *
24743530 ACCCTTAACTTAAAAACACTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCT
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
* *
24743595 TAAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACTCAA
66 T-AACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* * * ** *
24743642 ACCTAATTAAATTAAAAATCCT-ACC-CCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAAC
1 ACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAAC
24743705 CCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
64 CCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* * *
24743753 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACAC
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
* * *
24743816 TAACCTAATTAAATTAAAAAACCTAACCTAATTAAATTAAAAACCCTA
66 TAACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* *
24743864 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCC
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
* * *
24743927 TAACCTAATTTAA-TTAAAAACCCTAACCCAATTAAATTAAAAACCTTAA
66 TAACC---CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT-A
24743976 ACCCTTAACTTAAAAACCCTAACCTAATTAAAATT-AAAACCCTAACCTAATTAAATTAAAAACC
1 ACCCTTAACTTAAAAACCCTAACCTAATT-AAATTAAAAACCCTAACCTAATTAAATTAAAAACC
24744040 CTAACCCTTAACTTAAAAACCCTAACCTTAA-TAAATTAAAAACCCTA
65 CTAACCCTTAACTTAAAAACCCTAACC-TAATTAAATTAAAAACCCTA
* * * *
24744087 ACCCTTAACTTAAAAACCCTAACCTAATTTAATTAAAACCCCTAAACCCT-A--AACTTCAAAAC
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT-AA-CCTAATTAAATTAAAAAC
* *** *
24744149 CCTAA-CCTATTACTTAAAAACCCTAACCCCCTTAACTTAAAAACCCTA
64 CCTAACCCT-TAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* * * *
24744197 ACCCTTAACTTTAAAACCCTAAACTAATTTAATTAAAAACCCTAAACTAAATTAA
1 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCT-AATTAA
24744252 TAATTTTACA
Statistics
Matches: 540, Mismatches: 48, Indels: 44
0.85 0.08 0.07
Matches are distributed among these distances:
108 2 0.00
109 37 0.07
110 95 0.18
111 242 0.45
112 119 0.22
113 13 0.02
114 32 0.06
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (111 bp):
ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
TAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
Found at i:24744129 original size:23 final size:23
Alignment explanation
Indices: 24743534--24744252 Score: 584
Period size: 23 Copynumber: 32.2 Consensus size: 23
24743524 ATTAATACCC
*
24743534 TTAACTTAAAAACACTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
24743558 TTAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
* *
24743581 TTAATTAAAAACCTTAAACC---C
1 TTAATTAAAAACCCT-AACCTAAT
24743602 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
* * *
24743626 TAAATTAAAAACTCAAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
* * **
24743649 TAAATTAAAAATCCT-ACC--CC
1 TTAATTAAAAACCCTAACCTAAT
24743669 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
* *
24743693 TAAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
24743713 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
* *
24743737 TAAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
24743757 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
* *
24743781 TAAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
*
24743801 TTAACTTAAAAACACTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
* *
24743825 TAAATTAAAAAACCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
* *
24743848 TAAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
24743868 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
* *
24743892 TAAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
24743912 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
*
24743936 TTAATTAAAAACCCTAACCCAAT
1 TTAATTAAAAACCCTAACCTAAT
* * *
24743959 TAAATTAAAAACCTTAAACC---C
1 TTAATTAAAAACCCT-AACCTAAT
24743980 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
*
24744004 TAAAATT-AAAACCCTAACCTAAT
1 T-TAATTAAAAACCCTAACCTAAT
* *
24744027 TAAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
24744047 TTAACTTAAAAACCCTAACCTTAA-
1 TTAA-TTAAAAACCCTAACC-TAAT
* *
24744071 TAAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
24744091 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
*
24744115 TTAATTAAAACCCCTAAACCCTAA-
1 TTAATTAAAAACCCT-AA-CCTAAT
* *
24744139 --ACTTCAAAACCCTAACCT-A-
1 TTAATTAAAAACCCTAACCTAAT
* ***
24744158 TTACTTAAAAACCCTAACC-CCC
1 TTAATTAAAAACCCTAACCTAAT
*
24744180 TTAACTTAAAAACCCTAACC---C
1 TTAA-TTAAAAACCCTAACCTAAT
* *
24744201 TTAACTTTAAAACCCTAAACTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
* *
24744225 TTAATTAAAAACCCTAAACTAAA
1 TTAATTAAAAACCCTAACCTAAT
24744248 TTAAT
1 TTAAT
24744253 AATTTTACAT
Statistics
Matches: 573, Mismatches: 66, Indels: 113
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.00
20 27 0.05
21 166 0.29
22 44 0.08
23 278 0.49
24 50 0.09
25 7 0.01
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (23 bp):
TTAATTAAAAACCCTAACCTAAT
Found at i:24744440 original size:111 final size:111
Alignment explanation
Indices: 24744246--24744466 Score: 415
Period size: 111 Copynumber: 2.0 Consensus size: 111
24744236 CCCTAAACTA
*
24744246 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACCGGTACTAACAATT
* *
24744311 AATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAATC
66 AATAATTTTATATAATTTGAAAATTTTACTAACCATTAATACAATC
24744357 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACCGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACCGGTACTAACAATT
24744422 AATAATTTTATATAATTTGAAAATTTTACTAACCATTAATACAAT
66 AATAATTTTATATAATTTGAAAATTTTACTAACCATTAATACAAT
24744467 TTATCAATTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (111 bp):
AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACCGGTACTAACAATT
AATAATTTTATATAATTTGAAAATTTTACTAACCATTAATACAATC
Found at i:24750701 original size:18 final size:18
Alignment explanation
Indices: 24750678--24750729 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
24750668 AAAATTAAAA
***
24750678 TTAAAAAATAAAAACTCT
1 TTAAAAAATAAAAAAGAT
*
24750696 TTAAAATATAAAAAAGAT
1 TTAAAAAATAAAAAAGAT
24750714 TTAAAAATATAAAAAA
1 TTAAAAA-ATAAAAAA
24750730 ATTCAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (18 bp):
TTAAAAAATAAAAAAGAT
Found at i:24754276 original size:21 final size:21
Alignment explanation
Indices: 24754252--24754293 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
24754242 AACACAATAG
24754252 ATAAAGATAGAAACATAAACA
1 ATAAAGATAGAAACATAAACA
24754273 ATAAAGATAGAAACATAAACA
1 ATAAAGATAGAAACATAAACA
24754294 TTCATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (21 bp):
ATAAAGATAGAAACATAAACA
Found at i:24755946 original size:15 final size:15
Alignment explanation
Indices: 24755926--24755956 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
24755916 TTCAGCAGAT
24755926 AATTTGCATAGCATC
1 AATTTGCATAGCATC
24755941 AATTTGCATAGCATC
1 AATTTGCATAGCATC
24755956 A
1 A
24755957 TTCATGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (15 bp):
AATTTGCATAGCATC
Found at i:24759225 original size:21 final size:22
Alignment explanation
Indices: 24759200--24759244 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
24759190 TTTGGGTCGT
*
24759200 TTTAGATTGTATTAGTG-TTGG
1 TTTAGATTGTATTAGGGTTTGG
* *
24759221 TTTAGGTTGTTTTAGGGTTTGG
1 TTTAGATTGTATTAGGGTTTGG
24759243 TT
1 TT
24759245 CATGGTGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.13, C:0.00, G:0.31, T:0.56
Consensus pattern (22 bp):
TTTAGATTGTATTAGGGTTTGG
Found at i:24759471 original size:21 final size:20
Alignment explanation
Indices: 24759447--24759488 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
24759437 TTATGGGTTC
24759447 GGTTTGGGATTATAGTGTTTA
1 GGTTTGGGATTAT-GTGTTTA
* *
24759468 GGTTTGGGGTTATGTTTTTA
1 GGTTTGGGATTATGTGTTTA
24759488 G
1 G
24759489 TGTGGTGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (20 bp):
GGTTTGGGATTATGTGTTTA
Found at i:24759735 original size:32 final size:32
Alignment explanation
Indices: 24759689--24759797 Score: 148
Period size: 32 Copynumber: 3.4 Consensus size: 32
24759679 GTTAGTTCGG
* * *
24759689 GTTTAGTACAGTTTGGGTGTAGGTCTGTTTGA
1 GTTTAGTACGGTTTGTGTGTAAGTCTGTTTGA
*
24759721 GTTTAATACGGTTTGTGTGTAAGTCTGTTTGA
1 GTTTAGTACGGTTTGTGTGTAAGTCTGTTTGA
*
24759753 GTTTAGTACGATTTGTGTGTAAGT-TAGTTTGA
1 GTTTAGTACGGTTTGTGTGTAAGTCT-GTTTGA
*
24759785 GTTTAGTATGGTT
1 GTTTAGTACGGTT
24759798 CAAGTTTTAG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 1 0.01
32 67 0.99
ACGTcount: A:0.18, C:0.05, G:0.30, T:0.47
Consensus pattern (32 bp):
GTTTAGTACGGTTTGTGTGTAAGTCTGTTTGA
Found at i:24762118 original size:23 final size:23
Alignment explanation
Indices: 24762053--24762151 Score: 85
Period size: 23 Copynumber: 4.3 Consensus size: 23
24762043 CATATTGTAG
** *
24762053 GTTGTTTCACTGTTGTTTTTAGT
1 GTTGTTTCACTACTGTTTTTAAT
* * *
24762076 ATTGTTTCACTGCCGTTTTTAAT
1 GTTGTTTCACTACTGTTTTTAAT
* *
24762099 GTTGTTTCACTACTGCTTTTAAA
1 GTTGTTTCACTACTGTTTTTAAT
24762122 GTT-TTTC-CGTTACTGTTTTTAAT
1 GTTGTTTCAC--TACTGTTTTTAAT
*
24762145 ATTGTTT
1 GTTGTTT
24762152 GGATATTGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
21 1 0.02
22 4 0.07
23 53 0.87
24 3 0.05
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (23 bp):
GTTGTTTCACTACTGTTTTTAAT
Found at i:24762370 original size:14 final size:14
Alignment explanation
Indices: 24762351--24762385 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
24762341 AAGTATAAAT
24762351 TACCTTAAAATGAC
1 TACCTTAAAATGAC
*
24762365 TACCTTAAAATGAT
1 TACCTTAAAATGAC
24762379 TACCTTA
1 TACCTTA
24762386 TCATGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (14 bp):
TACCTTAAAATGAC
Found at i:24763331 original size:187 final size:187
Alignment explanation
Indices: 24762995--24763365 Score: 432
Period size: 187 Copynumber: 2.0 Consensus size: 187
24762985 AAAAACCGAG
* * * * * * *
24762995 CAACAAAATTTATTCACACATGCAGAGGTAGCAAGTGTACACCCCAACCTATTGCATGCTCGTAC
1 CAACAAAACTCATTCACACATGCAGAAGTAACAAATGTACACCACAACCTATTGCATGCTCATAC
* * * **
24763060 AAAAATAAACTCAAAAATATATAGGAAGGAATTTGCTGCAGTAGTGTGGGATAACTCTGGTCAAG
66 AAAAATAAACTCAAAAATATATA-GAAGAAATTTGCTGCAATAGTGTGAGATAACAATGGTCAAG
* *
24763125 ACTCATTTAAAACTCATAGAAAGCTTGATAAATAAGAA-CTATTAGGAAAACAACCATAGAGC
130 ACTCATTTAAAAATCATAGAAAACTT-A-AAA-AAGAATC-ATT-GGAAAACAACCATAGAGC
* * *
24763187 CAACAAAACTCATTCACACATGTAGAAGTAACAAATGTACA-TACAA-CTATATGCCTGCTCATA
1 CAACAAAACTCATTCACACATGCAGAAGTAACAAATGTACACCACAACCTAT-TGCATGCTCATA
* * *
24763250 CAAAAATAAAC-CCAAAA-ATAT-GAAGAAATTTGTTGCAATAGTGTGAGATAACAATGGTTAA-
65 CAAAAATAAACTCAAAAATATATAGAAGAAATTTGCTGCAATAGTGTGAGATAACAATGGTCAAG
*
24763311 ATCTCATTTAAAAATCATAGAAAACTTAATAAAGAATCATTGGAAAACAACCATA
130 A-CTCATTTAAAAATCATAGAAAACTTAAAAAAGAATCATTGGAAAACAACCATA
24763366 AAGCTTCAGA
Statistics
Matches: 155, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
183 14 0.09
184 8 0.05
185 3 0.02
186 2 0.01
187 56 0.36
189 4 0.03
190 9 0.06
191 24 0.15
192 35 0.23
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.24
Consensus pattern (187 bp):
CAACAAAACTCATTCACACATGCAGAAGTAACAAATGTACACCACAACCTATTGCATGCTCATAC
AAAAATAAACTCAAAAATATATAGAAGAAATTTGCTGCAATAGTGTGAGATAACAATGGTCAAGA
CTCATTTAAAAATCATAGAAAACTTAAAAAAGAATCATTGGAAAACAACCATAGAGC
Found at i:24768778 original size:13 final size:13
Alignment explanation
Indices: 24768760--24768820 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
24768750 AGTTTTTCAT
24768760 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
24768773 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
*
24768786 TGTTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
24768799 TGCTTTTCAAAAG
1 TGCTTTTGAGAAG
24768812 TGCTTTTGA
1 TGCTTTTGA
24768821 AACATTTGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.43
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:24768794 original size:26 final size:26
Alignment explanation
Indices: 24768760--24768820 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
24768750 AGTTTTTCAT
*
24768760 TGCTTTTGAGAAGTGCTTTTCAGAAG
1 TGCTTTTGAGAAGTGCTTTTCAAAAG
*
24768786 TGTTTTTGAGAAGTGCTTTTCAAAAG
1 TGCTTTTGAGAAGTGCTTTTCAAAAG
24768812 TGCTTTTGA
1 TGCTTTTGA
24768821 AACATTTGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.43
Consensus pattern (26 bp):
TGCTTTTGAGAAGTGCTTTTCAAAAG
Found at i:24770002 original size:21 final size:21
Alignment explanation
Indices: 24769978--24770022 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
24769968 TAAGCTGACA
24769978 ACAAATTGAACAGCATTGCCT
1 ACAAATTGAACAGCATTGCCT
*
24769999 ACAAATTGAATAGCATTGCCT
1 ACAAATTGAACAGCATTGCCT
24770020 ACA
1 ACA
24770023 TACCAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (21 bp):
ACAAATTGAACAGCATTGCCT
Found at i:24770031 original size:21 final size:21
Alignment explanation
Indices: 24769989--24770031 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
24769979 CAAATTGAAC
***
24769989 AGCATTGCCTACAAATTGAAT
1 AGCATTGCCTACAAACCAAAT
*
24770010 AGCATTGCCTACATACCAAAT
1 AGCATTGCCTACAAACCAAAT
24770031 A
1 A
24770032 TTTTTAATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (21 bp):
AGCATTGCCTACAAACCAAAT
Found at i:24781329 original size:30 final size:30
Alignment explanation
Indices: 24781288--24781345 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
24781278 GGTGGAATGA
* *
24781288 GAGGGAAGTAAAAGTTTTAGGGGGAAAGTGG
1 GAGGGAAGTAAAAATTTT-GGGAGAAAGTGG
24781319 GAGGG-AGTAAAAATTTTGGGAGAAAGT
1 GAGGGAAGTAAAAATTTTGGGAGAAAGT
24781346 AAAGAGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
30 11 0.44
31 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (30 bp):
GAGGGAAGTAAAAATTTTGGGAGAAAGTGG
Found at i:24782455 original size:25 final size:25
Alignment explanation
Indices: 24782384--24782481 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 25
24782374 AGATACACCA
24782384 CAGCTCTCACGAGCTTCCC-ATTATT
1 CAGCTCTCACGAGCTTCCCGA-TATT
* * ** *
24782409 TAGCTCTTATAAGCATCCCGATATT
1 CAGCTCTCACGAGCTTCCCGATATT
*
24782434 CAGCTCTCACGAGCTTCTCGATATT
1 CAGCTCTCACGAGCTTCCCGATATT
** **
24782459 TGGCTCTCTTGAGCTTCCCGATA
1 CAGCTCTCACGAGCTTCCCGATA
24782482 AATGGCTCGC
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
25 55 0.98
26 1 0.02
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.34
Consensus pattern (25 bp):
CAGCTCTCACGAGCTTCCCGATATT
Found at i:24782565 original size:50 final size:50
Alignment explanation
Indices: 24782469--24782565 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 50
24782459 TGGCTCTCTT
* *
24782469 GAGCTTCCCGATAAATGGCTCGCAAGAGCTTCCCGTTATATAGCTCGGAA
1 GAGCTTCCCGATAAATAGCTCGCAAGAGCTTCCCGTTACATAGCTCGGAA
* *
24782519 GAGCTTCCC-ATTATATAGCTCGGAAGAGCTTCCCGTTTACAT-GCTCG
1 GAGCTTCCCGA-TAAATAGCTCGCAAGAGCTTCCCG-TTACATAGCTCG
24782566 TATGAGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 1 0.02
50 35 0.85
51 5 0.12
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (50 bp):
GAGCTTCCCGATAAATAGCTCGCAAGAGCTTCCCGTTACATAGCTCGGAA
Found at i:24782572 original size:25 final size:25
Alignment explanation
Indices: 24782469--24782555 Score: 129
Period size: 25 Copynumber: 3.5 Consensus size: 25
24782459 TGGCTCTCTT
* * * *
24782469 GAGCTTCCCGATAAATGGCTCGCAA
1 GAGCTTCCCGTTATATAGCTCGGAA
24782494 GAGCTTCCCGTTATATAGCTCGGAA
1 GAGCTTCCCGTTATATAGCTCGGAA
*
24782519 GAGCTTCCCATTATATAGCTCGGAA
1 GAGCTTCCCGTTATATAGCTCGGAA
24782544 GAGCTTCCCGTT
1 GAGCTTCCCGTT
24782556 TACATGCTCG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCGGAA
Found at i:24788335 original size:16 final size:16
Alignment explanation
Indices: 24788314--24788345 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24788304 AATTATCTTC
*
24788314 ATGCATATCCACAAGT
1 ATGCATAACCACAAGT
24788330 ATGCATAACCACAAGT
1 ATGCATAACCACAAGT
24788346 TAGATGAGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (16 bp):
ATGCATAACCACAAGT
Found at i:24788769 original size:21 final size:22
Alignment explanation
Indices: 24788728--24788770 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24788718 TAATACTCCC
24788728 AAAGAATAATTAGACATAAAAT
1 AAAGAATAATTAGACATAAAAT
* *
24788750 AAAGAATAGTTAG-TATAAAAT
1 AAAGAATAATTAGACATAAAAT
24788771 TAGAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (22 bp):
AAAGAATAATTAGACATAAAAT
Found at i:24792757 original size:25 final size:25
Alignment explanation
Indices: 24792679--24792846 Score: 107
Period size: 25 Copynumber: 6.8 Consensus size: 25
24792669 TAAGCTCATA
*
24792679 AGAGCC-TTAATCAGGAAGCT-CATG
1 AGAGCCATTAATCGGGAAGCTCCA-G
* * * *
24792703 TGAGCCAATAA-CGGGTAA-CTCTAA
1 AGAGCCATTAATCGGG-AAGCTCCAG
*
24792727 AGAGCCATTAATCGGGAAGCTCCGG
1 AGAGCCATTAATCGGGAAGCTCCAG
* * * *
24792752 ATAGCCA-TATATTGGAAAGCTCAAG
1 AGAGCCATTA-ATCGGGAAGCTCCAG
* **
24792777 TGAGCCA-T-ATCGGGAAGCTTTAG
1 AGAGCCATTAATCGGGAAGCTCCAG
* *
24792800 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCGGGAAGCTC-CAG
*
24792826 AGAGCCTTTAATCGGGAAGCT
1 AGAGCCATTAATCGGGAAGCT
24792847 TACGAAGAGC
Statistics
Matches: 107, Mismatches: 28, Indels: 16
0.71 0.19 0.11
Matches are distributed among these distances:
23 17 0.16
24 24 0.22
25 46 0.43
26 20 0.19
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (25 bp):
AGAGCCATTAATCGGGAAGCTCCAG
Done.