Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 21 of 150
Found at i:5532414 original size:81 final size:82
Alignment explanation
Indices: 5532329--5532486 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 82
5532319 TTCAGTGTCA
* * *
5532329 GGTTAGGCTTTAGGGTTTAGATTAATCAGTGTGTTTTAA-TT-TATATTAAATAAGATTTAGGGG
1 GGTTAGGATTTAGGGTTTAGATTAATCAATAT-TTTTAATTTGTATATTAAATAAGATTTAGGGG
5532392 TTAG-AGGTTAGGGATTTG
65 TTAGTA-GTTAGGGATTTG
* * *
5532410 GGTTAGGATTTAGGGTTTTGATTAATTAATATTTTTAATTTGTATATTAAATAAGGTTTAGGGGT
1 GGTTAGGATTTAGGGTTTAGATTAATCAATATTTTTAATTTGTATATTAAATAAGATTTAGGGGT
5532475 TAGTAGTTAGGG
66 TAGTAGTTAGGG
5532487 TTAGGGGTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
80 6 0.09
81 29 0.43
82 32 0.47
83 1 0.01
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.44
Consensus pattern (82 bp):
GGTTAGGATTTAGGGTTTAGATTAATCAATATTTTTAATTTGTATATTAAATAAGATTTAGGGGT
TAGTAGTTAGGGATTTG
Found at i:5532644 original size:21 final size:21
Alignment explanation
Indices: 5532620--5532662 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5532610 AAAAGAGGGG
5532620 TTAGGGGTTAAAGGTTAAGGA
1 TTAGGGGTTAAAGGTTAAGGA
* *
5532641 TTAGGGGTTAAGGGTTATGGA
1 TTAGGGGTTAAAGGTTAAGGA
5532662 T
1 T
5532663 AGGTAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.40, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAAAGGTTAAGGA
Found at i:5537882 original size:42 final size:44
Alignment explanation
Indices: 5537821--5538080 Score: 184
Period size: 43 Copynumber: 6.1 Consensus size: 44
5537811 GATATGTTTT
* *
5537821 TAGCAGCGTTTGTGTG-AAAAGCGTCACTAAAGGT-TTGT-TCTA
1 TAGCAGCGTTTGTGGGAAAAAGCGCCACTAAAGGTCTT-TATCTA
*
5537863 TAGCAGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCTTTATCTA
1 TAGCAGCGTTTGTGGGAAAAAGCGCCACTAAAGGTCTTTATCTA
* * * * * *
5537907 TAGCAGCGTTTGT-GGAACAAGCACCGCTAAAAGTCCTGATCTA
1 TAGCAGCGTTTGTGGGAAAAAGCGCCACTAAAGGTCTTTATCTA
* * ** * * *
5537950 TAACGGCGTTTTGTGTGG---TTGCGCCGCTAAAGGTCCTAATCTA
1 TAGCAGCG-TTTGTG-GGAAAAAGCGCCACTAAAGGTCTTTATCTA
* * * *
5537993 TAGC-GACGTTTGT--GAAAAAGTGCCGCTAAAGGTCCTGATCTA
1 TAGCAG-CGTTTGTGGGAAAAAGCGCCACTAAAGGTCTTTATCTA
* * * *
5538035 TAGCGGCGTTTGTGGG-AAAA-CACCGCTAAAGGTCTTGATCTA
1 TAGCAGCGTTTGTGGGAAAAAGCGCCACTAAAGGTCTTTATCTA
5538077 TAGC
1 TAGC
5538081 GGCATTTATT
Statistics
Matches: 182, Mismatches: 23, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
39 1 0.01
42 76 0.42
43 78 0.43
44 25 0.14
46 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (44 bp):
TAGCAGCGTTTGTGGGAAAAAGCGCCACTAAAGGTCTTTATCTA
Found at i:5537974 original size:86 final size:84
Alignment explanation
Indices: 5537859--5538081 Score: 252
Period size: 85 Copynumber: 2.6 Consensus size: 84
5537849 AAAGGTTTGT
* * *
5537859 TCTATAGCAGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCTTTATCTATAGC-AGCGTTTGTGGA
1 TCTATAACGGCGTTTGTGGG--AAAGCGCCGCTAAAGGTCTTAATCTATAGCGA-CGTTTGT-GA
*
5537923 ACAAGCACCGCTAAAAGTCCTGA
62 AAAAGCACCGCTAAAAGTCCTGA
** *
5537946 TCTATAACGGCGTTTTGTGTGG-TTGCGCCGCTAAAGGTCCTAATCTATAGCGACGTTTGTGAAA
1 TCTATAACGGCG-TTTGTG-GGAAAGCGCCGCTAAAGGTCTTAATCTATAGCGACGTTTGTGAAA
** *
5538010 AAGTGCCGCTAAAGGTCCTGA
64 AAGCACCGCTAAAAGTCCTGA
* * * *
5538031 TCTATAGCGGCGTTTGTGGGAAAACACCGCTAAAGGTCTTGATCTATAGCG
1 TCTATAACGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTAATCTATAGCG
5538082 GCATTTATTT
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
83 2 0.02
84 30 0.26
85 32 0.28
86 32 0.28
87 11 0.10
88 6 0.05
89 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (84 bp):
TCTATAACGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTAATCTATAGCGACGTTTGTGAAAAA
GCACCGCTAAAAGTCCTGA
Found at i:5538081 original size:42 final size:43
Alignment explanation
Indices: 5537821--5538083 Score: 259
Period size: 42 Copynumber: 6.2 Consensus size: 43
5537811 GATATGTTTT
* * * * * *
5537821 TAGCAGCGTTTGTGTGAAAAGCGTCACTAAAGGT-TTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * *
5537863 TAGCAGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCTTTATCTA
1 TAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCCTGATCTA
* * *
5537907 TAGCAGCGTTTGT-GGAACAAGCACCGCTAAAAGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAA-AAGCGCCGCTAAAGGTCCTGATCTA
* ** *
5537950 TAACGGCGTTTTGTGTGG--TTGCGCCGCTAAAGGTCCTAATCTA
1 TAGCGGCG-TTTGTG-GGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * *
5537993 TAGCGACGTTTGT-GAAAAAGTGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* *
5538035 TAGCGGCGTTTGTGGGAAAA-CACCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
5538077 TAGCGGC
1 TAGCGGC
5538084 ATTTATTTCA
Statistics
Matches: 184, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
40 1 0.01
42 81 0.44
43 76 0.41
44 24 0.13
46 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:5540274 original size:19 final size:17
Alignment explanation
Indices: 5540248--5540287 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5540238 AAGAAAACAT
5540248 TTTGAAATTGAATAATGA
1 TTTGAAA-TGAATAATGA
*
5540266 TTTGTAAATGAATAATGT
1 TTTG-AAATGAATAATGA
5540284 TTTG
1 TTTG
5540288 GAAACGAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (17 bp):
TTTGAAATGAATAATGA
Found at i:5541333 original size:114 final size:113
Alignment explanation
Indices: 5541141--5541345 Score: 265
Period size: 114 Copynumber: 1.8 Consensus size: 113
5541131 TTTTTGAGCT
*
5541141 TTCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGTTCAGGCCTTTAGCGGCATTTTTG
1 TTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGTTCAGGCCTTTAGCGGCATTTTTG
*
5541206 AGAAAGTGCCGCAACAAAAACTAAGCCGAACTACACTGTTTTCTGACAA
66 AGAAAGCGCCGCAA-AAAAACTAAGCCGAACTACACTGTTTTCTGACAA
* * *
5541255 TTCGTGGGCTTTAGCGGCG-TTTTAAG-AATGCGCCGCTAATGCTT-AGGGCTTTAGCGGCGTTT
1 TTCG-GGGATTTAGCGGCGTTTTTAAGTAA-GCGCCGCTAATG-TTCAGGCCTTTAGCGGCATTT
* * *
5541317 TTGTTG-AAGCGTCGCAAAAAACCTAAGCC
63 TTG-AGAAAGCGCCGCAAAAAAACTAAGCC
5541346 CAACGGCGTC
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
113 13 0.16
114 51 0.65
115 15 0.19
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (113 bp):
TTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGTTCAGGCCTTTAGCGGCATTTTTG
AGAAAGCGCCGCAAAAAAACTAAGCCGAACTACACTGTTTTCTGACAA
Found at i:5542012 original size:14 final size:14
Alignment explanation
Indices: 5541967--5542006 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5541957 TATTAAATAA
*
5541967 GGTTTAGGGTTAGT
1 GGTTTGGGGTTAGT
* *
5541981 AGTTAGGGGTTAGT
1 GGTTTGGGGTTAGT
5541995 GGTTTGGGGTTA
1 GGTTTGGGGTTA
5542007 AGGGTTAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (14 bp):
GGTTTGGGGTTAGT
Found at i:5542376 original size:7 final size:7
Alignment explanation
Indices: 5542362--5542396 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
5542352 GGAATATTAC
5542362 GGTTTGG
1 GGTTTGG
*
5542369 GATTTGG
1 GGTTTGG
*
5542376 GGTTTAG
1 GGTTTGG
5542383 GGTTTGG
1 GGTTTGG
5542390 GGTTTGG
1 GGTTTGG
5542397 TTTTTGAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.06, C:0.00, G:0.51, T:0.43
Consensus pattern (7 bp):
GGTTTGG
Found at i:5543595 original size:147 final size:143
Alignment explanation
Indices: 5543318--5543787 Score: 372
Period size: 147 Copynumber: 3.2 Consensus size: 143
5543308 TACGTTGCTA
* *** * *
5543318 TTAGTGGCGCTTTACATC-AAACGCCGCAAAATTGTAATTTTGTTTA-ATGAAATGTTGTCGTTT
1 TTAGTGGCGCTTTAC-TCAAAACGCCGCAAAATTGTTATAACGTTTATA-GAAACG-TGCCGTTT
* * * * * * **
5543381 TGTCTATGGTATTAGTGGCGTTTTTATGAAAAGGCCACAAGCTTGAGTTAACTGTTGGGGAAACG
63 TG--TATGTTATTAGTGGCGTTTTT-CGAAAACGCCACAGGTTTGAGCTAACTGTTGATGAAACG
5543446 ACTTCG-TTTGAGCTTATAG
125 ACTTCGTTTTGA-CTTATAG
* *
5543465 TTAGTGGCGCTTTACTCAAAACACCGCAAAATTGTTCTAACGTTTATAGAAACGCTGCCGTTTTG
1 TTAGTGGCGCTTTACTCAAAACGCCGCAAAATTGTTATAACGTTTATAGAAACG-TGCCGTTTTG
* * * *
5543530 TAAATGTTATTAGTGGCGTTTTTGCGAAAACGCCACGGGTTTGAGGTAAGTGTTGATGAAGCGAC
65 T--ATGTTATTAGTGGCGTTTTT-CGAAAACGCCACAGGTTTGAGCTAACTGTTGATGAAACGAC
* *
5543595 TGCGTTTTGATTTATAG
127 TTCGTTTTGACTTATAG
* * *** * * * * * * *
5543612 TTTGTGGAGCTTCGGTTAAAACGCCGCAAAAATGTTTTAACATTTATTGATACGAGTCCGTTTTG
1 TTAGTGGCGCTTTACTCAAAACGCCGCAAAATTGTTATAACGTTTATAGAAACGTG-CCGTTTTG
* * * * * ** *
5543677 CTGTATTATTAGTGGCGTTTATTCAAAAACTCCACAGGTGTGAGCTATTTGTTGATGAAACGGCT
65 -TATGTTATTAGTGGCGTTT-TTCGAAAACGCCACAGGTTTGAGCTAACTGTTGATGAAACGACT
*
5543742 TCGTTTTGACTTTTAG
128 TCGTTTTGACTTATAG
* *
5543758 TTAGTGGCGC-TTATTTATAAACGCCGCAAA
1 TTAGTGGCGCTTTACTCA-AAACGCCGCAAA
5543788 TGGATAATTT
Statistics
Matches: 259, Mismatches: 55, Indels: 19
0.78 0.17 0.06
Matches are distributed among these distances:
145 5 0.02
146 85 0.33
147 162 0.63
148 7 0.03
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (143 bp):
TTAGTGGCGCTTTACTCAAAACGCCGCAAAATTGTTATAACGTTTATAGAAACGTGCCGTTTTGT
ATGTTATTAGTGGCGTTTTTCGAAAACGCCACAGGTTTGAGCTAACTGTTGATGAAACGACTTCG
TTTTGACTTATAG
Found at i:5545728 original size:13 final size:13
Alignment explanation
Indices: 5545712--5546061 Score: 233
Period size: 13 Copynumber: 26.5 Consensus size: 13
5545702 TTACTAAAAT
*
5545712 TTACTTTAATATA
1 TTACTTAAATATA
*
5545725 TTACTTGAATATA
1 TTACTTAAATATA
*
5545738 TTACTTAAATAAA
1 TTACTTAAATATA
*
5545751 TTACTTAAATACA
1 TTACTTAAATATA
*
5545764 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** * *
5545778 TTGGTTAAATTTC
1 TTACTTAAATATA
5545791 TTACTTAAATATA
1 TTACTTAAATATA
*
5545804 TTACTTGAATATA
1 TTACTTAAATATA
*
5545817 TTACTTAAATAAA
1 TTACTTAAATATA
*
5545830 TTACTTAAATACA
1 TTACTTAAATATA
*
5545843 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** * *
5545857 TTGGTTAAATTTC
1 TTACTTAAATATA
*
5545870 TTACTTAAATATG
1 TTACTTAAATATA
*
5545883 TTACTTAAATACA
1 TTACTTAAATATA
*
5545896 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
5545910 TTGTTTAAATTTA
1 TTACTTAAATATA
* *
5545923 TTACCTAAATATG
1 TTACTTAAATATA
*
5545936 TTACTTAAATACA
1 TTACTTAAATATA
*
5545949 TTACTTACTAA-ATT
1 TTACTTA--AATATA
** *
5545963 TTGGTTAAATTTA
1 TTACTTAAATATA
*
5545976 TTACTTAAATATG
1 TTACTTAAATATA
*
5545989 TTACTTAAATACA
1 TTACTTAAATATA
*
5546002 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
5546016 TTGTTTAAATTTA
1 TTACTTAAATATA
*
5546029 TTACTTAAATATG
1 TTACTTAAATATA
*
5546042 TTACTTAAATACA
1 TTACTTAAATATA
5546055 TTACTTA
1 TTACTTA
5546062 CTAAAATTTA
Statistics
Matches: 254, Mismatches: 68, Indels: 30
0.72 0.19 0.09
Matches are distributed among these distances:
12 14 0.06
13 200 0.79
14 26 0.10
15 14 0.06
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:5545874 original size:53 final size:53
Alignment explanation
Indices: 5545815--5546070 Score: 449
Period size: 53 Copynumber: 4.8 Consensus size: 53
5545805 TACTTGAATA
**
5545815 TATTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
* *
5545868 TCTTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGTTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
* *
5545921 TATTACCTAAATATGTTACTTAAATACATTACTTACTAAATTTTGGTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
*
5545974 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGTTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
5546027 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
5546071 AAGTATATAT
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 192 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.46
Consensus pattern (53 bp):
TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
Found at i:5546374 original size:28 final size:28
Alignment explanation
Indices: 5546338--5546482 Score: 123
Period size: 28 Copynumber: 5.0 Consensus size: 28
5546328 AAAAATTTTT
*
5546338 ATATAAACTTACATAATACATTACTTAC
1 ATATAAACTTACATAATACATAACTTAC
* * **
5546366 ATATTAACTTACATAACTTA-TTAA-TATTT
1 ATATAAACTTACATAA--TACATAACT-TAC
*
5546395 ATATAAACTTACATAACTATCACATAAACTTAT
1 ATATAAACTTACAT-A--AT-ACAT-AACTTAC
*
5546428 ATGTAAACTTACATAATACATAACTTAC
1 ATATAAACTTACATAATACATAACTTAC
* *
5546456 ATGTTAACTTACATAATACATAACTTA
1 ATATAAACTTACATAATACATAACTTA
5546483 TAAAAAATTT
Statistics
Matches: 96, Mismatches: 11, Indels: 20
0.76 0.09 0.16
Matches are distributed among these distances:
28 48 0.50
29 20 0.21
30 6 0.06
31 1 0.01
32 3 0.03
33 17 0.18
34 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (28 bp):
ATATAAACTTACATAATACATAACTTAC
Found at i:5546379 original size:90 final size:89
Alignment explanation
Indices: 5546285--5546471 Score: 220
Period size: 90 Copynumber: 2.1 Consensus size: 89
5546275 ACTTACATAA
* *
5546285 TACATAACTTATATGTAA-ACTTACATATAA-TACATAACTTAT-A-AAAAATTTTTATATAAAC
1 TACATAAC-T-TAT-TAATACTTACATA-AACTACATAAC-TATCACAAAAACTTATATATAAAC
*
5546346 TTACATAATACATTACTTACATATTAACT
61 TTACATAATACATAACTTACATATTAACT
* * * *
5546375 TACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTAAACTTAC
1 TACATAACTTATTAATACTTACATAAAC-TACATAACTATCACAAAAACTTATATATAAACTTAC
*
5546440 ATAATACATAACTTACATGTTAACT
65 ATAATACATAACTTACATATTAACT
5546465 TACATAA
1 TACATAA
5546472 TACATAACTT
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
87 5 0.06
88 13 0.15
89 10 0.12
90 56 0.67
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (89 bp):
TACATAACTTATTAATACTTACATAAACTACATAACTATCACAAAAACTTATATATAAACTTACA
TAATACATAACTTACATATTAACT
Found at i:5546454 original size:16 final size:16
Alignment explanation
Indices: 5546433--5546482 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
5546423 CTTATATGTA
5546433 AACTTACATAATACAT
1 AACTTACATAATACAT
*
5546449 AACTTACAT-GT---T
1 AACTTACATAATACAT
5546461 AACTTACATAATACAT
1 AACTTACATAATACAT
5546477 AACTTA
1 AACTTA
5546483 TAAAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:5546530 original size:157 final size:158
Alignment explanation
Indices: 5546237--5546543 Score: 562
Period size: 157 Copynumber: 1.9 Consensus size: 158
5546227 ATATAAACTT
*
5546237 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTATATGTA
1 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTA
*
5546302 AACTTACATATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAATACATTACTTACA
66 AACTTACA-ATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACA
5546367 TATTAACTTACATAACTTATTAATATTTA
130 TATTAACTTACATAACTTATTAATATTTA
*
5546396 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTT
1 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTA
5546461 AACTTAC-ATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACAT
66 AACTTACAATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACAT
*
5546525 ATTAACTTACATAAGTTAT
131 ATTAACTTACATAACTTAT
5546544 CTACAAGCTT
Statistics
Matches: 144, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
157 74 0.51
159 70 0.49
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (158 bp):
TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTA
AACTTACAATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACAT
ATTAACTTACATAACTTATTAATATTTA
Found at i:5546556 original size:159 final size:160
Alignment explanation
Indices: 5546237--5546580 Score: 565
Period size: 159 Copynumber: 2.2 Consensus size: 160
5546227 ATATAAACTT
*
5546237 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTATATGTA
1 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTA
*
5546302 AACTTACATATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAATACATTACTTACA
66 AACTTACA-ATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACA
5546367 TATTAACTTACATAACTTATTAATA-TT-TA
130 TATTAACTTACATAACTTATTAATACTTATA
*
5546396 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTT
1 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTA
5546461 AACTTAC-ATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACAT
66 AACTTACAATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACAT
*
5546525 ATTAACTTACATAAGTTATCTACA-AGCTTATA
131 ATTAACTTACATAACTTAT-TA-ATA-CTTATA
*
5546557 TATAAACTTGCATAACT-T-ACATAA
1 TATAAACTTACATAACTATCACATAA
5546581 TAACATAACA
Statistics
Matches: 175, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
157 74 0.42
158 3 0.02
159 77 0.44
160 3 0.02
161 18 0.10
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (160 bp):
TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTA
AACTTACAATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACAT
ATTAACTTACATAACTTATTAATACTTATA
Found at i:5546579 original size:9 final size:9
Alignment explanation
Indices: 5546561--5546854 Score: 228
Period size: 9 Copynumber: 33.8 Consensus size: 9
5546551 CTTATATATA
*
5546561 AACTTGCAT
1 AACTTACAT
5546570 AACTTACAT
1 AACTTACAT
*
5546579 AA-TAACAT
1 AACTTACAT
5546587 AACAACTTACAT
1 ---AACTTACAT
5546599 AA--TACAT
1 AACTTACAT
* *
5546606 AGCATACAT
1 AACTTACAT
5546615 AACTTACAT
1 AACTTACAT
5546624 AACTTACAT
1 AACTTACAT
*
5546633 AA--TACAA
1 AACTTACAT
5546640 AACTTACAT
1 AACTTACAT
5546649 AACTTACAT
1 AACTTACAT
*
5546658 AA--TACAA
1 AACTTACAT
5546665 AACTTACAT
1 AACTTACAT
5546674 AACTTACAT
1 AACTTACAT
*
5546683 AACCTACAT
1 AACTTACAT
5546692 AA--TACATTT
1 AACTTACA--T
5546701 AACTTACAT
1 AACTTACAT
5546710 AACTTACAT
1 AACTTACAT
*
5546719 AATACATA-AT
1 -A-ACTTACAT
5546729 AACTTAC--
1 AACTTACAT
*
5546736 AACTTAAAT
1 AACTTACAT
*
5546745 AACATACAT
1 AACTTACAT
* **
5546754 TACTTTGAT
1 AACTTACAT
5546763 AACTTACAT
1 AACTTACAT
5546772 AACTTACAT
1 AACTTACAT
*
5546781 AA--TACAC
1 AACTTACAT
5546788 AACTTACAT
1 AACTTACAT
* *
5546797 AGCTTACTT
1 AACTTACAT
5546806 AA--TACAT
1 AACTTACAT
5546813 AACTTACAT
1 AACTTACAT
5546822 AACTT--AT
1 AACTTACAT
*
5546829 ACACGTACAT
1 A-ACTTACAT
5546839 AACTTACAT
1 AACTTACAT
*
5546848 AATTTAC
1 AACTTAC
5546855 TTAATACATA
Statistics
Matches: 227, Mismatches: 32, Indels: 52
0.73 0.10 0.17
Matches are distributed among these distances:
7 43 0.19
8 12 0.05
9 151 0.67
10 6 0.03
11 10 0.04
12 5 0.02
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:5546597 original size:157 final size:158
Alignment explanation
Indices: 5546237--5546606 Score: 529
Period size: 157 Copynumber: 2.3 Consensus size: 158
5546227 ATATAAACTT
* * * *
5546237 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTATATGTA
1 TATAAACTTACATAACTATCACATAAACTAACATGAAAACTTACATAATACATAACTTACATGTA
*
5546302 AACTTACATATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAATACATTACTTACA
66 AACTTACA-ATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACA
5546367 TATTAACTTACATAACTTATTAATATTTA
130 TATTAACTTACATAACTTATTAATATTTA
* * * *
5546396 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTT
1 TATAAACTTACATAACTATCACATAAACTAACATGAAAACTTACATAATACATAACTTACATGTA
5546461 AACTTAC-ATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACAT
66 AACTTACAATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACAT
*
5546525 ATTAACTTACATAAGTTATCTACA-AGCTTATA
131 ATTAACTTACATAACTTAT-TA-ATA--TT-TA
*
5546557 TATAAACTTGCATAACT-T-ACAT-AA-TAACAT-AACAACTTACATAATACATA
1 TATAAACTTACATAACTATCACATAAACTAACATGAA-AACTTACATAATACATA
5546607 GCATACATAA
Statistics
Matches: 197, Mismatches: 8, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
156 1 0.01
157 95 0.48
158 5 0.03
159 75 0.38
160 3 0.02
161 18 0.09
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.36
Consensus pattern (158 bp):
TATAAACTTACATAACTATCACATAAACTAACATGAAAACTTACATAATACATAACTTACATGTA
AACTTACAATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAACACATTACTTACAT
ATTAACTTACATAACTTATTAATATTTA
Found at i:5546621 original size:25 final size:25
Alignment explanation
Indices: 5546567--5546880 Score: 161
Period size: 25 Copynumber: 12.8 Consensus size: 25
5546557 TATAAACTTG
5546567 CATAACTTACATAA-T--A-ACATA
1 CATAACTTACATAACTACATACATA
*
5546588 -ACAACTTACATAA-TACATAGCATA
1 CATAACTTACATAACTACATA-CATA
5546612 CATAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
*
5546637 CAAAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
* *
5546662 CAAAACTTACATAACTTACATAACCTA
1 CATAACTTACATAAC-TACAT-ACATA
*
5546689 CATAA--TACATTTAACTTACATAACTTA
1 CATAACTTACA--TAAC-TACAT-ACATA
*
5546716 CATAA--TACATAA-T--A-ACTTA
1 CATAACTTACATAACTACATACATA
* * *
5546735 C--AACTTAAATAACATACATTACTTT
1 CATAACTTACATAAC-TACA-TACATA
*
5546760 GATAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
* * *
5546785 CACAACTTACATAGCTTACTTA-ATA
1 CATAACTTACATAAC-TACATACATA
*
5546810 CATAACTTACATAACT-TATACACGTA
1 CATAACTTACATAACTACATACA--TA
* *
5546836 CATAACTTACATAATTTACTTA-ATA
1 CATAACTTACATAA-CTACATACATA
* *
5546861 CATAAATTACTTAA-TACATA
1 CATAACTTACATAACTACATA
5546881 AATATATATC
Statistics
Matches: 240, Mismatches: 27, Indels: 50
0.76 0.09 0.16
Matches are distributed among these distances:
17 2 0.01
19 12 0.05
20 13 0.05
21 2 0.01
22 1 0.00
23 10 0.04
24 6 0.03
25 120 0.50
26 19 0.08
27 53 0.22
28 2 0.01
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (25 bp):
CATAACTTACATAACTACATACATA
Found at i:5546630 original size:34 final size:34
Alignment explanation
Indices: 5546567--5546870 Score: 186
Period size: 34 Copynumber: 9.3 Consensus size: 34
5546557 TATAAACTTG
*
5546567 CATAACTTACATAA-TAACATAACAACTTACATAATA
1 CATAACTTACATAACTTACAT---AACTTACATAATA
* *
5546603 CATAGCATACATAACTTACATAACTTAC---ATA
1 CATAACTTACATAACTTACATAACTTACATAATA
5546634 -AT-AC--A-A-AACTTACATAACTTACATAATA
1 CATAACTTACATAACTTACATAACTTACATAATA
* *
5546662 CAAAACTTACATAACTTACATAACCTACATAATA
1 CATAACTTACATAACTTACATAACTTACATAATA
5546696 CATTTAACTTACATAACTTACATAA--TAC---ATA
1 CA--TAACTTACATAACTTACATAACTTACATAATA
* * * *
5546727 -ATAACTTAC--AACTTAAATAACATACATTACTTT
1 CATAACTTACATAACTTACATAACTTACA-TA-ATA
* *
5546760 GATAACTTACATAACTTACATAA--TACACAACTTA
1 CATAACTTACATAACTTACATAACTTACATAA--TA
* *
5546794 CATAGCTTACTTAA--TACATAACTTACATAACT-
1 CATAACTTACATAACTTACATAACTTACATAA-TA
* * * *
5546826 TATACACGTACATAACTTACATAATTTACTTAATA
1 CATA-ACTTACATAACTTACATAACTTACATAATA
*
5546861 CATAAATTAC
1 CATAACTTAC
5546871 TTAATACATA
Statistics
Matches: 210, Mismatches: 28, Indels: 62
0.70 0.09 0.21
Matches are distributed among these distances:
25 16 0.08
26 11 0.05
27 1 0.00
28 14 0.07
29 2 0.01
30 5 0.02
31 6 0.03
32 11 0.05
33 11 0.05
34 69 0.33
35 17 0.08
36 42 0.20
37 5 0.02
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (34 bp):
CATAACTTACATAACTTACATAACTTACATAATA
Found at i:5546867 original size:123 final size:120
Alignment explanation
Indices: 5546640--5546867 Score: 284
Period size: 123 Copynumber: 1.9 Consensus size: 120
5546630 CATAATACAA
5546640 AACTTACATAACTTACATAATACAAAACTTACATAACTTACATAACCTACATAATACATTTAACT
1 AACTTACATAACTTACATAATACAAAACTTACATAACTTACATAA-CTACATAATACA-TTAACT
* *
5546705 TACATAACTTACATAATACATAATAACTTACAACTTAAATAACATACATTACTTTGAT
64 TA-ATAACGTACATAATACATAATAACTTACAACATAAATAACATACATTACTTTGAT
* * *
5546763 AACTTACATAACTTACATAATACACAACTTACATAGCTTACTTAA-TACATAACTTACA-TAACT
1 AACTTACATAACTTACATAATACAAAACTTACATAACTTACATAACTACATAA--TACATTAACT
*
5546826 T-ATACACGTACATAACTTACATAATTTACTTA-ATACATAAAT
64 TAATA-ACGTACATAA--TACATAA-TAACTTACA-ACATAAAT
5546868 TACTTAATAC
Statistics
Matches: 92, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
119 3 0.03
120 9 0.10
121 13 0.14
122 8 0.09
123 59 0.64
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (120 bp):
AACTTACATAACTTACATAATACAAAACTTACATAACTTACATAACTACATAATACATTAACTTA
ATAACGTACATAATACATAATAACTTACAACATAAATAACATACATTACTTTGAT
Found at i:5546882 original size:16 final size:16
Alignment explanation
Indices: 5546843--5546883 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
5546833 GTACATAACT
*
5546843 TACATAATTTACTTAA
1 TACATAAATTACTTAA
5546859 TACATAAATTACTTAA
1 TACATAAATTACTTAA
5546875 TACATAAAT
1 TACATAAAT
5546884 ATATATCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (16 bp):
TACATAAATTACTTAA
Found at i:5552401 original size:21 final size:21
Alignment explanation
Indices: 5552377--5552445 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
5552367 GTACAACTTA
*
5552377 AAGCAGAGGCGGCAACGAGGG
1 AAGCAGAGGCGGCAACGAGAG
* *
5552398 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAACGAGAG
* * *
5552419 AAGCAGAGGCTGCAGCGCGAG
1 AAGCAGAGGCGGCAACGAGAG
5552440 AAGCAG
1 AAGCAG
5552446 CAAGAGAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.43, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCGGCAACGAGAG
Found at i:5553028 original size:43 final size:42
Alignment explanation
Indices: 5552891--5553044 Score: 218
Period size: 42 Copynumber: 3.6 Consensus size: 42
5552881 TTCATGATGA
* * * *
5552891 AAGCGCCACTAAAGAACATTATCTTTAGCGGCATTTTTCTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTT
* * * *
5552933 AAGCGCCGCTAAATAACATTATCTTTAGCGGCGATTTTTTGT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTT
*
5552975 AACCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTTTT
5553018 AAGCGCCGCTAAAGAACATGATCTTTA
1 AAGCGCCGCTAAAGAACATGATCTTTA
5553045 ATAGCGTTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 66 0.67
43 33 0.33
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTT
Found at i:5553056 original size:85 final size:84
Alignment explanation
Indices: 5552894--5553057 Score: 229
Period size: 85 Copynumber: 1.9 Consensus size: 84
5552884 ATGATGAAAG
* * *
5552894 CGCCACTAAAGAACATTATCTTTAGCGGCATTTTTCTTTAAGCGCCGCTAAATAACATTATCTTT
1 CGCCACTAAAGAACATGATCTTTAGCGGCATTTTTCTTTAAGCGCCGCTAAAGAACATGATCTTT
* *
5552959 AGCGGCGATTTTTTGTAAC
66 AACAGCGATTTTTTGTAAC
* * *
5552978 CGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTTAAGCGCCGCTAAAGAACATGATCTT
1 CGCCACTAAAGAACATGATCTTTAGCGGCAT-TTTTCTTTAAGCGCCGCTAAAGAACATGATCTT
* *
5553043 TAATAGCGTTTTTTT
65 TAACAGCGATTTTTT
5553058 CTGTAAACGC
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
84 28 0.41
85 41 0.59
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (84 bp):
CGCCACTAAAGAACATGATCTTTAGCGGCATTTTTCTTTAAGCGCCGCTAAAGAACATGATCTTT
AACAGCGATTTTTTGTAAC
Found at i:5553144 original size:21 final size:21
Alignment explanation
Indices: 5553118--5553157 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5553108 GTTAGTGGCG
*
5553118 CTAAAAAGCGCCGCTAAAAGC
1 CTAAAAAACGCCGCTAAAAGC
5553139 CTAAAAAACGCCGCTAAAA
1 CTAAAAAACGCCGCTAAAA
5553158 ACCTGTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.28, G:0.15, T:0.10
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:5557984 original size:19 final size:18
Alignment explanation
Indices: 5557962--5558002 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
5557952 TTTAATTTCA
*
5557962 TTTTTTTGTTTTTTGTAAT
1 TTTTTTTATTTTTTG-AAT
5557981 TTTTTTTATTTTTTGAAT
1 TTTTTTTATTTTTTGAAT
5557999 TTTT
1 TTTT
5558003 AAAATTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTTTTATTTTTTGAAT
Found at i:5558344 original size:2 final size:2
Alignment explanation
Indices: 5558337--5558365 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5558327 ATGCATAATT
5558337 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 T
5558366 TTTTCCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5558777 original size:19 final size:20
Alignment explanation
Indices: 5558740--5558777 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5558730 ACCAAAATCA
* *
5558740 TTTTTTTCTTGATTTAAAGG
1 TTTTTTTCTTGAATAAAAGG
5558760 TTTTTTT-TTGAATAAAAG
1 TTTTTTTCTTGAATAAAAG
5558778 CATTATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTTTTTCTTGAATAAAAGG
Found at i:5579461 original size:96 final size:97
Alignment explanation
Indices: 5579349--5579523 Score: 237
Period size: 96 Copynumber: 1.8 Consensus size: 97
5579339 AAACACGAAG
* * * * *
5579349 AAGAAGAGCTTGAAAAGGT-GACAGAAAGCCATAAGCTTAAACGAAAGCCACCATCACCGTCATT
1 AAGAAGAGCTTGAAAAGGTAGAAAAAAAG-CATAAACTTAAACGAAAGCAACCATCACCGTCATC
*
5579413 GGAACGCGAA-AAGAAGATCGCTAAACCTGAAA
65 GGAACCCGAATAAGAAGATCGCTAAACCTGAAA
* * * *
5579445 AAGAAGAGCTTGAAAAGGTATAAAAAAAGTATAAACTTAAACGAAAGCAACCATCGCCTTCATCG
1 AAGAAGAGCTTGAAAAGGTAGAAAAAAAGCATAAACTTAAACGAAAGCAACCATCACCGTCATCG
5579510 GAACCCGAATAAGA
66 GAACCCGAATAAGA
5579524 GCTTGAAAGG
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
96 57 0.85
97 10 0.15
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (97 bp):
AAGAAGAGCTTGAAAAGGTAGAAAAAAAGCATAAACTTAAACGAAAGCAACCATCACCGTCATCG
GAACCCGAATAAGAAGATCGCTAAACCTGAAA
Found at i:5580576 original size:11 final size:11
Alignment explanation
Indices: 5580560--5580584 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5580550 GATTTGCTGA
5580560 TTTGAGTGATG
1 TTTGAGTGATG
5580571 TTTGAGTGATG
1 TTTGAGTGATG
5580582 TTT
1 TTT
5580585 TGGCTGATAA
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:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (11 bp):
TTTGAGTGATG
Found at i:5580672 original size:15 final size:15
Alignment explanation
Indices: 5580652--5580684 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5580642 AATTAGTGGA
5580652 GTAGTTATATATTAG
1 GTAGTTATATATTAG
5580667 GTAGTTATATATTAG
1 GTAGTTATATATTAG
5580682 GTA
1 GTA
5580685 ACTACTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
GTAGTTATATATTAG
Found at i:5597638 original size:28 final size:29
Alignment explanation
Indices: 5597607--5597667 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
5597597 TAAAAGACAA
*
5597607 AATCATTATA-TT-GTTTATGTAGTTAAAT
1 AATCATTATACTTCGTCTAT-TAGTTAAAT
*
5597635 AATC-TTGTACTTCGTCTATTAGTTAAAT
1 AATCATTATACTTCGTCTATTAGTTAAAT
5597663 AATCA
1 AATCA
5597668 GTCCATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
27 4 0.14
28 19 0.68
29 5 0.18
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (29 bp):
AATCATTATACTTCGTCTATTAGTTAAAT
Found at i:5602943 original size:52 final size:51
Alignment explanation
Indices: 5602835--5603007 Score: 185
Period size: 50 Copynumber: 3.4 Consensus size: 51
5602825 ATGATGCTTA
* * * *
5602835 AATGCATGATTTAA-TTAA-GATGCAAAC-TAAATGAACAAATGAG-TTTACTT
1 AATGCATGACTTAATTTAATGATGCAAACTTAACT-AAC--ATGAGAGTTACAT
* *
5602885 AATGCATGACTTAATTTAATGATGCAGACTTAAACTAACATGGGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTT-AACTAACATGAGAGTTACAT
* *
5602937 AATGCATGTCATAATTT-ATGATGCAAACTTAACTAACATGAGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAGAGTTACAT
* *
5602987 AATGCATGACTTTATTAAATG
1 AATGCATGACTTAATTTAATG
5603008 CAGAACACAT
Statistics
Matches: 103, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
50 45 0.44
51 23 0.22
52 28 0.27
53 4 0.04
54 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (51 bp):
AATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAGAGTTACAT
Found at i:5606912 original size:34 final size:34
Alignment explanation
Indices: 5606841--5606925 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
5606831 ATGACTCAAA
* *
5606841 AACAAGCTAATAAATTTAGCTTCTTACTCCCACT
1 AACAAGCTAACAAACTTAGCTTCTTACTCCCACT
** *
5606875 AACAAGCTAACAAACTTAGCTT-TCTACTTTCATT
1 AACAAGCTAACAAACTTAGCTTCT-TACTCCCACT
*
5606909 AACAAGTTAACAAACTT
1 AACAAGCTAACAAACTT
5606926 CCTAGAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
33 1 0.02
34 43 0.98
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (34 bp):
AACAAGCTAACAAACTTAGCTTCTTACTCCCACT
Found at i:5609197 original size:102 final size:102
Alignment explanation
Indices: 5609010--5609197 Score: 263
Period size: 102 Copynumber: 1.9 Consensus size: 102
5609000 AAAAAAGTAA
*
5609010 TTAAGCCCCTACTCTTTTTTTTTGCACTCAATTGGGTACTTGAATTTTCAAAATGCATCAAAAAG
1 TTAAGCCCCTACTCTTTTTTTTTGCACTCAATTGGGTACTTGAATTTTCAAAATGCATAAAAAAG
****
5609075 GCCCTCAAACTTTTTCAAAAAAAAAAAAGAGAAGCAT
66 GCCCTCAAACTTAAAAAAAAAAAAAAAAGAGAAGCAT
* * * *
5609112 TTAAGCCCTTGCTTTTTTTTTTTGGACTCAATTGGGTACTTGAATTTTCAAAATGCATAAAAAAA
1 TTAAGCCCCTACTCTTTTTTTTTGCACTCAATTGGGTACTTGAATTTTCAAAATGCAT-AAAAAA
*
5609177 TG-CCTCAAA-TTAAAAAAAAAA
65 GGCCCTCAAACTTAAAAAAAAAA
5609198 CAATTAAGTC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
101 8 0.11
102 61 0.81
103 6 0.08
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (102 bp):
TTAAGCCCCTACTCTTTTTTTTTGCACTCAATTGGGTACTTGAATTTTCAAAATGCATAAAAAAG
GCCCTCAAACTTAAAAAAAAAAAAAAAAGAGAAGCAT
Found at i:5609420 original size:9 final size:9
Alignment explanation
Indices: 5609345--5609550 Score: 84
Period size: 9 Copynumber: 22.0 Consensus size: 9
5609335 GACATATAGC
*
5609345 AAAAAATAT
1 AAAAATTAT
5609354 AAAAA-TAT
1 AAAAATTAT
5609362 -AAAA--AT
1 AAAAATTAT
5609368 AAAAATTAAT
1 AAAAATT-AT
*
5609378 AAAATTTAT
1 AAAAATTAT
*
5609387 AAGAATTAT
1 AAAAATTAT
**
5609396 CAAATTTTAGT
1 -AAAAATTA-T
5609407 AAAAATTAT
1 AAAAATTAT
*
5609416 AAAAATTGT
1 AAAAATTAT
5609425 AAAAAATTAT
1 -AAAAATTAT
*
5609435 AAAAAGTGTAAA
1 AAAAA-T-T-AT
5609447 AAAAATTAT
1 AAAAATTAT
5609456 -AAAATATAT
1 AAAAAT-TAT
*
5609465 AGAAA-TAT
1 AAAAATTAT
*
5609473 ATAAAATTTT
1 A-AAAATTAT
* **
5609483 ATAAAGTCGT
1 A-AAAATTAT
5609493 AAGAAGATTAT
1 AA-AA-ATTAT
*
5609504 AAAAAATAT
1 AAAAATTAT
*
5609513 AAAGAAATAT
1 AAA-AATTAT
*
5609523 -AAAATTCGT
1 AAAAATT-AT
5609532 AAAAAATTAT
1 -AAAAATTAT
*
5609542 AAAATTTAT
1 AAAAATTAT
5609551 CATACCAAAA
Statistics
Matches: 151, Mismatches: 26, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
6 2 0.01
7 8 0.05
8 15 0.10
9 54 0.36
10 53 0.35
11 13 0.09
12 6 0.04
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5609431 original size:19 final size:20
Alignment explanation
Indices: 5609407--5609459 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
5609397 AAATTTTAGT
*
5609407 AAAAATTATAAAAATTGT-A
1 AAAAATTATAAAAAGTGTAA
5609426 AAAAATTATAAAAAGTGTAAA
1 AAAAATTATAAAAAGTGT-AA
5609447 AAAAATTATAAAA
1 AAAAATTATAAAA
5609460 TATATAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (20 bp):
AAAAATTATAAAAAGTGTAA
Found at i:5609478 original size:29 final size:28
Alignment explanation
Indices: 5609409--5609546 Score: 77
Period size: 29 Copynumber: 4.8 Consensus size: 28
5609399 ATTTTAGTAA
* * *
5609409 AAATTAT-AAAAATTGTAAAAAATTATAA
1 AAATTATAAAAAATTATAAAATA-TATAG
* *
5609437 AAAGTGTAAAAAAAATTATAAAATATATAG
1 AAATTATAAAAA--ATTATAAAATATATAG
** * *
5609467 AAATATATAAAATTTTATAAAGTCGTA-AG
1 AAAT-TATAAAAAATTATAAAAT-ATATAG
*
5609496 AAGATTATAAAAAA-TATAAAGAAATATA-
1 AA-ATTATAAAAAATTATAAA-ATATATAG
*
5609524 AAATTCGTAAAAAATTATAAAAT
1 AAATT-ATAAAAAATTATAAAAT
5609547 TTATCATACC
Statistics
Matches: 82, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
27 3 0.04
28 23 0.28
29 30 0.37
30 11 0.13
31 15 0.18
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (28 bp):
AAATTATAAAAAATTATAAAATATATAG
Found at i:5609486 original size:50 final size:48
Alignment explanation
Indices: 5609427--5609528 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
5609417 AAAATTGTAA
* * * *
5609427 AAAATTATAAAAAGT-GTAAAAAAAATTATAAAATATATAGAA-ATATAT
1 AAAATTTTATAAAGTCGT-AAAAAAATTATAAAAAATATA-AAGAAATAT
* *
5609475 AAAATTTTATAAAGTCGTAAGAAGATTATAAAAAATATAAAGAAATAT
1 AAAATTTTATAAAGTCGTAAAAAAATTATAAAAAATATAAAGAAATAT
5609523 AAAATT
1 AAAATT
5609529 CGTAAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.04
48 42 0.91
49 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (48 bp):
AAAATTTTATAAAGTCGTAAAAAAATTATAAAAAATATAAAGAAATAT
Found at i:5609825 original size:28 final size:28
Alignment explanation
Indices: 5609774--5609843 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
5609764 TTAAATATTT
5609774 TTTTTATATTTTTATTAAAATTTAATGA
1 TTTTTATATTTTTATTAAAATTTAATGA
** *
5609802 TTTTTATAATTTTTA-TAACTTTTATTGA
1 TTTTTAT-ATTTTTATTAAAATTTAATGA
* *
5609830 TTTCTATTTTTTTA
1 TTTTTATATTTTTA
5609844 ATATTTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.17
28 23 0.64
29 7 0.19
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTTATATTTTTATTAAAATTTAATGA
Found at i:5610116 original size:89 final size:90
Alignment explanation
Indices: 5609957--5610183 Score: 303
Period size: 89 Copynumber: 2.5 Consensus size: 90
5609947 TCAAATGAGC
* * * * * * *
5609957 TTTTTGATTTATTTTGACAGTTCAAGTACCCAATTAAGTGTAAAATAAAAGCAGGGGCTTAATTG
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
*
5610022 CTTTTTT-GAAAAAGTTTGATGGCA
66 CTTTTTTCGAAAAAGTTTGAGGGCA
* * *
5610046 TTTTTGATGTATTTTAAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAAGTAGGGGCTTAACTA
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
* *
5610111 TTTTTTTCGAAAAAGTTTGAGGGCT
66 CTTTTTTCGAAAAAGTTTGAGGGCA
* * *
5610136 TTTTTGATGTATTTTGAAAGTTCAAATGCCTAATTGAGTGCAAAAAAA
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAA
5610184 GACTTAATTT
Statistics
Matches: 119, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 61 0.51
90 58 0.49
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (90 bp):
TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
CTTTTTTCGAAAAAGTTTGAGGGCA
Found at i:5618241 original size:31 final size:31
Alignment explanation
Indices: 5618205--5618265 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
5618195 CAAAAACACA
* *
5618205 AAAACAAAATCTGGGTCTTCGAGTTTAATTC
1 AAAACAAAAACTGGGTCTTCGAGTTAAATTC
* *
5618236 AAAACAAAAACTGGGTGTTTGAGTTAAATT
1 AAAACAAAAACTGGGTCTTCGAGTTAAATT
5618266 TTTTTTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (31 bp):
AAAACAAAAACTGGGTCTTCGAGTTAAATTC
Found at i:5620187 original size:22 final size:23
Alignment explanation
Indices: 5620140--5620187 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
5620130 ATGATTTGAC
* *
5620140 AAAGAACACAAATTTAAATATTA
1 AAAGAACACAAAATTAAATATAA
5620163 AAAGAGACA-AAAATTAAATA-AA
1 AAAGA-ACACAAAATTAAATATAA
5620185 AAA
1 AAA
5620188 CTAAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 15 0.68
24 3 0.14
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (23 bp):
AAAGAACACAAAATTAAATATAA
Found at i:5634581 original size:9 final size:10
Alignment explanation
Indices: 5634506--5634600 Score: 80
Period size: 9 Copynumber: 9.8 Consensus size: 10
5634496 TTGTTGCCGC
5634506 TATTATTATT
1 TATTATTATT
5634516 ATCATTATTATT
1 -T-ATTATTATT
5634528 TA-TATTTATAT
1 TATTA-TTAT-T
5634539 TATTATTA-T
1 TATTATTATT
5634548 TATTATTA-T
1 TATTATTATT
5634557 TATTATTA-T
1 TATTATTATT
*
5634566 CATTATTATT
1 TATTATTATT
5634576 TA-TATT-TCT
1 TATTATTAT-T
5634585 T-TTATTATT
1 TATTATTATT
5634594 TA-TATTA
1 TATTATTA
5634601 GTATTAGAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
8 1 0.01
9 45 0.62
10 8 0.11
11 8 0.11
12 11 0.15
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TATTATTATT
Found at i:5634593 original size:3 final size:3
Alignment explanation
Indices: 5634506--5634575 Score: 90
Period size: 3 Copynumber: 23.3 Consensus size: 3
5634496 TTGTTGCCGC
*
5634506 TAT TAT TAT TAT CAT TAT TAT T-T ATAT T-T ATAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT -TAT TAT TAT TAT TAT
*
5634551 TAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
5634576 TATATTTCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.03
3 55 0.93
4 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5638079 original size:19 final size:20
Alignment explanation
Indices: 5638038--5638081 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5638028 TCTTTTTGCA
**
5638038 TTCATCCATAAGCATTACCT
1 TTCATCCATAAGCATTAAAT
*
5638058 TTCAT-CATATGCATTAAAT
1 TTCATCCATAAGCATTAAAT
5638077 TTCAT
1 TTCAT
5638082 AAAATGTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (20 bp):
TTCATCCATAAGCATTAAAT
Found at i:5638222 original size:20 final size:21
Alignment explanation
Indices: 5638182--5638222 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5638172 ACAAAAGCCA
* *
5638182 TAGATCAAATGTTAGAGAGAT
1 TAGAACAAATGTTAGAAAGAT
5638203 TAGAACAAAT-TTAGAAAGAT
1 TAGAACAAATGTTAGAAAGAT
5638223 ATGTAAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.27
Consensus pattern (21 bp):
TAGAACAAATGTTAGAAAGAT
Found at i:5644511 original size:37 final size:37
Alignment explanation
Indices: 5644470--5644568 Score: 144
Period size: 37 Copynumber: 2.7 Consensus size: 37
5644460 CATATATCGG
* *
5644470 TATGGAATACCAGAAAGGATTATATATCATATGTCAA
1 TATGGAATGCCAGAAAGGATCATATATCATATGTCAA
* **
5644507 TATGGAATGCCAAAAAGGATCATATATCATATGTCGG
1 TATGGAATGCCAGAAAGGATCATATATCATATGTCAA
*
5644544 TATAGAATGCCAGAAAGGATCATAT
1 TATGGAATGCCAGAAAGGATCATAT
5644569 CTAACAATGC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.27
Consensus pattern (37 bp):
TATGGAATGCCAGAAAGGATCATATATCATATGTCAA
Found at i:5646243 original size:44 final size:44
Alignment explanation
Indices: 5646175--5646458 Score: 248
Period size: 44 Copynumber: 6.3 Consensus size: 44
5646165 CTACCATAGT
* * * * *
5646175 AAATATTATATCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTAA
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
* * * * *
5646219 AAATCCTATAC-CTCTGAAGTTGCAGTGG-GTCAGATTGAATATACCATAG
1 AAATCTTAT-CTCCCTGAAGTTGCAATGGAG-CAGATT--A-A-AGC-TAC
* * * * *
5646268 GAATCTTATCTTCATAAAGTTGCAATGGAGCAGATGAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
* * * *
5646312 CAATCTTATCTCCCTGAAGTTGTATTGGAGCAAATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
* * *
5646356 TAATCTTATCTCCCTGAAGTTGCAATAGAGCATATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
* * * *
5646400 AAGTCGTATCTCCCTGAAGTTGTAATGGAGCAAATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
*
5646444 CAATCTTATCTCCCT
1 AAATCTTATCTCCCT
5646459 TAAAGCTCCA
Statistics
Matches: 192, Mismatches: 39, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
43 1 0.01
44 155 0.81
45 2 0.01
46 2 0.01
47 2 0.01
48 3 0.02
49 26 0.14
50 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
Found at i:5646396 original size:88 final size:88
Alignment explanation
Indices: 5646269--5646463 Score: 284
Period size: 88 Copynumber: 2.2 Consensus size: 88
5646259 ATACCATAGG
* * * *
5646269 AATCTTATCTTCATAAAGTTGCAATGGAGCAGATGAAAGCTACCAA-TCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAATAGAGCAGATGAAAGCTA-CAAGTCGTATCTCCCTGAAGTT
* *
5646333 GTATTGGAGCAAATTAAAGCTACT
65 GTAATGGAGCAAATTAAAGCTACC
* * *
5646357 AATCTTATCTCCCTGAAGTTGCAATAGAGCATATTAAAGCTACAAGTCGTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAATAGAGCAGATGAAAGCTACAAGTCGTATCTCCCTGAAGTTG
5646422 TAATGGAGCAAATTAAAGCTACC
66 TAATGGAGCAAATTAAAGCTACC
5646445 AATCTTATCTCCCTTAAAG
1 AATCTTATCTCCC-TAAAG
5646464 CTCCAAGGAC
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
87 3 0.03
88 88 0.93
89 4 0.04
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (88 bp):
AATCTTATCTCCCTAAAGTTGCAATAGAGCAGATGAAAGCTACAAGTCGTATCTCCCTGAAGTTG
TAATGGAGCAAATTAAAGCTACC
Found at i:5648047 original size:6 final size:6
Alignment explanation
Indices: 5648036--5648120 Score: 107
Period size: 6 Copynumber: 14.2 Consensus size: 6
5648026 TTGTTGCCCC
* * * * *
5648036 TATTAT TATTAT TATTGT TATTGT TATTGT TATTGT TATTGT TATTAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
* *
5648084 TATTAT TATTAT TATTAT TATTAT TCTCAT TATTAT T
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT T
5648121 TATCTTTCTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (6 bp):
TATTAT
Found at i:5652330 original size:20 final size:20
Alignment explanation
Indices: 5652278--5652330 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
5652268 ATTTTGATGT
*
5652278 GTTAAAATGATTTAAACTTG
1 GTTAAAATCATTTAAACTTG
** * **
5652298 GTTGGAATTATTTGGACTTG
1 GTTAAAATCATTTAAACTTG
5652318 GTTAAAATCATTT
1 GTTAAAATCATTT
5652331 TCACTTTATT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (20 bp):
GTTAAAATCATTTAAACTTG
Found at i:5664629 original size:152 final size:153
Alignment explanation
Indices: 5664425--5664773 Score: 413
Period size: 152 Copynumber: 2.3 Consensus size: 153
5664415 TATAGATTTG
* * * *
5664425 ATTTTAGTCAACAATGTTAAATGGAACAGTTATGAGAATTTAAGAGTTTGGTTGAAAACCTTTAA
1 ATTTTAATCAACAATGTTAAATGGAGCACTT-TGAGAATTTAAGAGTTTGGTTGAAAACCTTCAA
** * *
5664490 GAA-TTGATTGAGAATCTTAATCAATGATGTTAAATGGATCATTTTTAAGAATTTAGGG-CTT-G
65 -AATTTGATTGAGAATCTTAATCAACAATGTTAAATGGAGCACTTTTAAGAATTTAGGGACTTGG
* *
5664552 -AAAATCTTTTAAGATTTGATTGCAA
129 CAAAATC-TTTAAGATTTAATTGAAA
* * **
5664577 ATTTTAATCAACAATGTTAAATGGAGCACTTTGGAGAATTT-GGGGATTTGGTTGAAAGTCTTCA
1 ATTTTAATCAACAATGTTAAATGGAGCACTTT-GAGAATTTAAGAG-TTTGGTTGAAAACCTTCA
* *
5664641 AAATTTGATTGAGAATCTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGG
64 AAATTTGATTGAGAATCTTAATCAACAATGTTAAATGGAGCACTTTTAAGAATTTAGGGACTTGG
*
5664706 TCAAAATCTTTCAGATTTAATTGAAA
129 -CAAAATCTTTAAGATTTAATTGAAA
* * *
5664732 ATTTTTATGAACAATGTT-AATGGAGCACTTTTTAGAATTTAA
1 ATTTTAATCAACAATGTTAAATGGAGCAC-TTTGAGAATTTAA
5664774 AATCTTTAAA
Statistics
Matches: 167, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
151 5 0.03
152 102 0.61
153 2 0.01
154 18 0.11
155 34 0.20
156 6 0.04
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (153 bp):
ATTTTAATCAACAATGTTAAATGGAGCACTTTGAGAATTTAAGAGTTTGGTTGAAAACCTTCAAA
ATTTGATTGAGAATCTTAATCAACAATGTTAAATGGAGCACTTTTAAGAATTTAGGGACTTGGCA
AAATCTTTAAGATTTAATTGAAA
Found at i:5664667 original size:78 final size:76
Alignment explanation
Indices: 5664425--5664772 Score: 316
Period size: 78 Copynumber: 4.6 Consensus size: 76
5664415 TATAGATTTG
* * * * * * *
5664425 ATTTTAGTCAACAATGTTAAATGGAACAGTTATGAGAATTTA-AGAGTTTGGTTGAAAACCTTT-
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGA-TTTGG-TCAAAATCTTTC
*
5664488 AAGAATTGATTGAGA
64 AA-ATTTGATTGA-A
* ** * * * * *
5664503 ATCTTAATCAATGATGTTAAATGGATCATTTTTAAGAATTTAGGG-CTT-G--AAAATCTTTTAA
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGGTCAAAATCTTTCAA
5664564 GATTTGATTGCAA
66 -ATTTGATTG-AA
* * * *
5664577 ATTTTAATCAACAATGTTAAATGGAGCACTTTGGAGAATTTGGGGATTTGGTTGAAAGTC-TTCA
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGG-TCAAAATCTTTC-
5664641 AAATTTGATTGAGA
64 AAATTTGATTGA-A
* *
5664655 ATCTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGGTCAAAATCTTTCAG
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGGTCAAAATCTTTCAA
*
5664720 ATTTAATTGAAA
66 ATTTGATTG-AA
* * *
5664732 ATTTTTATGAACAATGTT-AATGGAGCACTTTTTAGAATTTA
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTA
5664773 AAATCTTTAA
Statistics
Matches: 224, Mismatches: 34, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
73 8 0.04
74 49 0.22
75 3 0.01
76 24 0.11
77 34 0.15
78 98 0.44
79 8 0.04
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (76 bp):
ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGGTCAAAATCTTTCAA
ATTTGATTGAA
Found at i:5669252 original size:240 final size:240
Alignment explanation
Indices: 5668829--5669307 Score: 931
Period size: 240 Copynumber: 2.0 Consensus size: 240
5668819 ATACACTTAA
5668829 CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
1 CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
*
5668894 ACTGGATAGTTTGAAGGGATCTCCGATGATTTCCAACCCGAGCGAGCCTTCGGAACACCATAAAC
66 ACTGGATAGTTTGAAGGGATCTCCGACGATTTCCAACCCGAGCGAGCCTTCGGAACACCATAAAC
5668959 ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
131 ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
5669024 GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAAC
196 GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAAC
5669069 CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
1 CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
* *
5669134 ACTGGATAGTTTGATGGGATCTCCGACGATTTCCAACCCGAGCGAGCCTTCGGAACACTATAAAC
66 ACTGGATAGTTTGAAGGGATCTCCGACGATTTCCAACCCGAGCGAGCCTTCGGAACACCATAAAC
5669199 ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
131 ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
5669264 GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAA
196 GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAA
5669308 TACAATAAAA
Statistics
Matches: 236, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
240 236 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (240 bp):
CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
ACTGGATAGTTTGAAGGGATCTCCGACGATTTCCAACCCGAGCGAGCCTTCGGAACACCATAAAC
ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAAC
Found at i:5670473 original size:43 final size:43
Alignment explanation
Indices: 5670410--5670571 Score: 132
Period size: 43 Copynumber: 3.8 Consensus size: 43
5670400 TACCGTAACA
* * *** * *
5670410 ATGCC-ATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCACATATCG
*
5670452 ATGCCAATAG-CCCAGCCATGGTCTTACACAAAATCACATATCG
1 ATGCCAAT-GTCCCAGACATGGTCTTACACAAAATCACATATCG
* * * * *
5670495 ATGCCAATGTCCTAGACATGGTCTTACACGAAGTCTCATATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCACATATCG
* * * * *
5670538 ATTCC-ATATCCCATATATGGTCTTACACATAATC
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATC
5670572 TCGGTAACCC
Statistics
Matches: 95, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
42 28 0.29
43 67 0.71
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACAAAATCACATATCG
Found at i:5681827 original size:30 final size:30
Alignment explanation
Indices: 5681791--5681856 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
5681781 ATGTTAGCGG
* *
5681791 GTGACTGTTTTGTTATTTTCTTAAAGTTTA
1 GTGACTGTTTTGTTATTTTCTCAAAGTTGA
5681821 GTGACTGTTTTGTTATTTTCTCAAAGTTGA
1 GTGACTGTTTTGTTATTTTCTCAAAGTTGA
5681851 GTGACT
1 GTGACT
5681857 CTTGGTGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.52
Consensus pattern (30 bp):
GTGACTGTTTTGTTATTTTCTCAAAGTTGA
Found at i:5685983 original size:29 final size:29
Alignment explanation
Indices: 5685941--5686027 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
5685931 CTCAGAGCCC
5685941 CCCATGTGCAATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
**
5685970 CCCATGTGTGATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
*
5685999 CTCATGTGCAATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
5686028 AAGTGCTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (29 bp):
CCCATGTGCAATGCTATAAGTTATTTAGA
Found at i:5688989 original size:15 final size:15
Alignment explanation
Indices: 5688943--5688991 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5688933 AAGGCTATTT
* *
5688943 TTGATAAATTAAATA
1 TTGAAAAATTAAATG
*
5688958 TT-AAAAATGTAAGTG
1 TTGAAAAAT-TAAATG
5688973 TTGAAAAATTAAATG
1 TTGAAAAATTAAATG
5688988 TTGA
1 TTGA
5688992 TTTTAAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.18
15 17 0.61
16 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (15 bp):
TTGAAAAATTAAATG
Found at i:5689101 original size:5 final size:5
Alignment explanation
Indices: 5689091--5689115 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5689081 AATGAATTAG
5689091 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
5689116 CTGAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:5690533 original size:21 final size:21
Alignment explanation
Indices: 5690520--5690569 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
5690510 GTGTCCCCTC
5690520 CACATGGGCATGTGTGTCCTT
1 CACATGGGCATGTGTGTCCTT
5690541 CACATGGGCATGTGTGTCCTT
1 CACATGGGCATGTGTGTCCTT
5690562 CACATGGG
1 CACATGGG
5690570 TGTGTTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.30
Consensus pattern (21 bp):
CACATGGGCATGTGTGTCCTT
Found at i:5690538 original size:23 final size:23
Alignment explanation
Indices: 5690508--5690559 Score: 81
Period size: 21 Copynumber: 2.3 Consensus size: 23
5690498 TCACACGAGC
5690508 GTGTGTCCCCTCCACATGGGCAT
1 GTGTGTCCCCTCCACATGGGCAT
*
5690531 GTGTGT--CCTTCACATGGGCAT
1 GTGTGTCCCCTCCACATGGGCAT
5690552 GTGTGTCC
1 GTGTGTCC
5690560 TTCACATGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 20 0.77
23 6 0.23
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.31
Consensus pattern (23 bp):
GTGTGTCCCCTCCACATGGGCAT
Found at i:5692051 original size:17 final size:17
Alignment explanation
Indices: 5692031--5692090 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
5692021 ATTAATTAAT
5692031 TTTAAAAATT-TAAAAAA
1 TTTAAAAATTAT-AAAAA
*
5692048 TTTAAAAACTATAAAAA
1 TTTAAAAATTATAAAAA
5692065 TTT-AAAATTATAAAAA
1 TTTAAAAATTATAAAAA
5692081 TTATAAAAAT
1 TT-TAAAAAT
5692091 ATTTTCTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
16 14 0.37
17 18 0.47
18 6 0.16
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTAAAAATTATAAAAA
Found at i:5692063 original size:16 final size:17
Alignment explanation
Indices: 5692043--5692089 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
5692033 TAAAAATTTA
5692043 AAAAATTTAAAAACTAT
1 AAAAATTTAAAAACTAT
*
5692060 AAAAATTT-AAAATTAT
1 AAAAATTTAAAAACTAT
5692076 AAAAATTATAAAAA
1 AAAAATT-TAAAAA
5692090 TATTTTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 14 0.52
17 9 0.33
18 4 0.15
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATTTAAAAACTAT
Found at i:5692071 original size:25 final size:26
Alignment explanation
Indices: 5692033--5692090 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
5692023 TAATTAATTT
5692033 TAAAAATTTAAAAAATT-TAAAAACTA
1 TAAAAATTT-AAAAATTATAAAAACTA
*
5692059 TAAAAATTT-AAAATTATAAAAATTA
1 TAAAAATTTAAAAATTATAAAAACTA
5692084 TAAAAAT
1 TAAAAAT
5692091 ATTTTCTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 6 0.20
25 15 0.50
26 9 0.30
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAAAATTTAAAAATTATAAAAACTA
Found at i:5692080 original size:9 final size:8
Alignment explanation
Indices: 5692031--5692090 Score: 68
Period size: 9 Copynumber: 7.1 Consensus size: 8
5692021 ATTAATTAAT
5692031 TTTAAAAA
1 TTTAAAAA
5692039 TTTAAAAAA
1 TTT-AAAAA
5692048 TTTAAAAA
1 TTTAAAAA
*
5692056 CTATAAAAA
1 -TTTAAAAA
5692065 TTT-AAAA
1 TTTAAAAA
5692072 TTATAAAAA
1 TT-TAAAAA
5692081 TTATAAAAA
1 TT-TAAAAA
5692090 T
1 T
5692091 ATTTTCTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
7 6 0.13
8 11 0.24
9 29 0.63
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (8 bp):
TTTAAAAA
Found at i:5694163 original size:2 final size:2
Alignment explanation
Indices: 5694158--5694185 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5694148 CTCTTTTTCT
5694158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5694186 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5697307 original size:3 final size:3
Alignment explanation
Indices: 5697299--5697337 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5697289 TCTAGAGCAG
5697299 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
5697338 CATTTTTGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5699128 original size:2 final size:2
Alignment explanation
Indices: 5699121--5699149 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5699111 GGCTTAGAAT
5699121 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 T
5699150 TTTTTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5699248 original size:7 final size:8
Alignment explanation
Indices: 5699232--5699256 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5699222 GTCTCTTTTC
5699232 TTTTATTT
1 TTTTATTT
5699240 TTTTATTT
1 TTTTATTT
5699248 TTTTATTT
1 TTTTATTT
5699256 T
1 T
5699257 ATAACACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:5701481 original size:29 final size:29
Alignment explanation
Indices: 5701443--5701506 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
5701433 TGTGTGTCGC
* * *
5701443 CACACAGTCGTGTGGTAGGCCGTGTATGG
1 CACACGGTCGTGTAGTAGGCCGTGTAAGG
*
5701472 CACACGGTCGTGTAGTAGGTCGTGTAAGG
1 CACACGGTCGTGTAGTAGGCCGTGTAAGG
5701501 CACACG
1 CACACG
5701507 ACAGTGTGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (29 bp):
CACACGGTCGTGTAGTAGGCCGTGTAAGG
Found at i:5702018 original size:18 final size:19
Alignment explanation
Indices: 5701995--5702043 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
5701985 GTTGTAAAGT
*
5701995 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
5702013 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
5702032 TTTAATTTTTAT
1 TTT-ATTTTTAT
5702044 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:5702023 original size:22 final size:22
Alignment explanation
Indices: 5701994--5702043 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5701984 AGTTGTAAAG
* *
5701994 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
5702015 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
5702038 TTTTAT
1 TTTTAT
5702044 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:5703201 original size:5 final size:5
Alignment explanation
Indices: 5703187--5703289 Score: 91
Period size: 5 Copynumber: 20.4 Consensus size: 5
5703177 ATGGGGGTAG
* * * * * *
5703187 GATAT GATTT GATTT GATAT GATAT GATAA GCTAT GATTT GATTT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
* * * *
5703237 GATAT GATAT GATAG GATAG GATAG GATCT G-TAT GAAATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT G--ATAT GATAT GATAT
5703288 GA
1 GA
5703290 AATATTAAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
4 3 0.04
5 76 0.92
7 4 0.05
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (5 bp):
GATAT
Found at i:5703225 original size:30 final size:30
Alignment explanation
Indices: 5703189--5703245 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
5703179 GGGGGTAGGA
5703189 TATGATTTGATTTGATATGATATGATAAGC
1 TATGATTTGATTTGATATGATATGATAAGC
5703219 TATGATTTGATTTGATATGATATGATA
1 TATGATTTGATTTGATATGATATGATA
5703246 TGATAGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (30 bp):
TATGATTTGATTTGATATGATATGATAAGC
Found at i:5705527 original size:25 final size:25
Alignment explanation
Indices: 5705499--5705549 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5705489 AAATGTCAAG
*
5705499 TTTAG-TACCAAATTAAACCAAAAAA
1 TTTAGATACCAAATTAAA-AAAAAAA
*
5705524 TTTAGATACTAAATTAAAAAAAAAA
1 TTTAGATACCAAATTAAAAAAAAAA
5705549 T
1 T
5705550 CAAATTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27
Consensus pattern (25 bp):
TTTAGATACCAAATTAAAAAAAAAA
Found at i:5709473 original size:21 final size:21
Alignment explanation
Indices: 5709431--5709473 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5709421 TTTGATTGAC
* * *
5709431 AAAATATAATATTATTTTAAA
1 AAAATATAATATCACTTAAAA
*
5709452 AAAATATCATATCACTTAAAA
1 AAAATATAATATCACTTAAAA
5709473 A
1 A
5709474 CATATTTTTA
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:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATATAATATCACTTAAAA
Found at i:5720068 original size:94 final size:94
Alignment explanation
Indices: 5719907--5720094 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
5719897 CGGCTAAATC
5719907 TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
1 TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
5719972 CTTATGTGATGAAAGCTAAGAGGGATGTT
66 CTTATGTGATGAAAGCTAAGAGGGATGTT
*
5720001 TGGTTTGGTACTGGGAGGACAGATGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
1 TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
*
5720066 CTTATGTGGTGAAAGCTAAGAGGGATGTT
66 CTTATGTGATGAAAGCTAAGAGGGATGTT
5720095 GATCTACCTG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.30, C:0.10, G:0.33, T:0.27
Consensus pattern (94 bp):
TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
CTTATGTGATGAAAGCTAAGAGGGATGTT
Found at i:5722126 original size:72 final size:72
Alignment explanation
Indices: 5722009--5722153 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
5721999 CTTCTTTTAG
*
5722009 GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGTTGTATCGTGCGAA
1 GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGCTGTATCGTGCGAA
5722074 GGTATGT
66 GGTATGT
5722081 GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGCTGTATCGTGCGAA
1 GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGCTGTATCGTGCGAA
5722146 GGTATGT
66 GGTATGT
5722153 G
1 G
5722154 TTGATTTTTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (72 bp):
GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGCTGTATCGTGCGAA
GGTATGT
Found at i:5722567 original size:54 final size:54
Alignment explanation
Indices: 5722478--5722585 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
5722468 AGAGACTTTC
* *
5722478 ATTTTGGGTCACACGGGCGTGTGCTTTAACGTGTGCTAGACCGTGTAACTCTCT
1 ATTTTGGGTCACACGGGCGTGTGCTTCAACGTGTGCTAAACCGTGTAACTCTCT
* * * *
5722532 ATTTTGGGTCACACGGGGGTGTGC-TCAGCCTTGTGCTAAACCGTGTAATTCTCT
1 ATTTTGGGTCACACGGGCGTGTGCTTCA-ACGTGTGCTAAACCGTGTAACTCTCT
5722586 GAGTTGCCCC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 2 0.04
54 45 0.96
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (54 bp):
ATTTTGGGTCACACGGGCGTGTGCTTCAACGTGTGCTAAACCGTGTAACTCTCT
Found at i:5734667 original size:9 final size:9
Alignment explanation
Indices: 5734653--5734685 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
5734643 CGCATAGCCT
5734653 ATACATGCC
1 ATACATGCC
5734662 ATACATGCC
1 ATACATGCC
5734671 ATACATGCC
1 ATACATGCC
5734680 ATACAT
1 ATACAT
5734686 TCAAACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.24
Consensus pattern (9 bp):
ATACATGCC
Found at i:5739841 original size:2 final size:2
Alignment explanation
Indices: 5739834--5739866 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5739824 AATGTACATG
*
5739834 TA TA TA TA TA CA 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 T
5739867 GAAAGTATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5739875 original size:14 final size:13
Alignment explanation
Indices: 5739833--5739884 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
5739823 TAATGTACAT
*
5739833 GTATATATATACA
1 GTATATATATAAA
*
5739846 -TATATATATATA
1 GTATATATATAAA
5739858 -TATATATATGAAA
1 GTATATATAT-AAA
*
5739871 GTATACATATAAA
1 GTATATATATAAA
5739884 G
1 G
5739885 AAAAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 20 0.59
13 6 0.18
14 8 0.24
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (13 bp):
GTATATATATAAA
Found at i:5740381 original size:15 final size:14
Alignment explanation
Indices: 5740361--5740411 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
5740351 TAAACTAGTG
*
5740361 TAATAACAATATCAA
1 TAATAACATTAT-AA
*
5740376 TAATAATATTAGTAA
1 TAATAACATTA-TAA
5740391 TAATAACATTGATAA
1 TAATAACATT-ATAA
5740406 TAATAA
1 TAATAA
5740412 TAAATTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (14 bp):
TAATAACATTATAA
Found at i:5740409 original size:18 final size:18
Alignment explanation
Indices: 5740383--5740427 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5740373 CAATAATAAT
* *
5740383 ATTAGTAATAATAACATTG
1 ATTAATAATAATAA-ATTA
5740402 A-TAATAATAATAAATTA
1 ATTAATAATAATAAATTA
5740419 ATTAATAAT
1 ATTAATAAT
5740428 CTAATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.78
19 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (18 bp):
ATTAATAATAATAAATTA
Found at i:5741672 original size:17 final size:17
Alignment explanation
Indices: 5741652--5741693 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5741642 TGGACTGTTA
* *
5741652 TTTTATTTGGTTTTTAT
1 TTTTATTTGGATTTGAT
*
5741669 TTTTATTTTGATTTGAT
1 TTTTATTTGGATTTGAT
5741686 TTTTATTT
1 TTTTATTT
5741694 ATTATGGGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (17 bp):
TTTTATTTGGATTTGAT
Found at i:5748081 original size:14 final size:16
Alignment explanation
Indices: 5748047--5748083 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5748037 TTTATAATAT
*
5748047 AAATTCAATGATTATA
1 AAATTTAATGATTATA
5748063 AAATTTAAT-ATTA-A
1 AAATTTAATGATTATA
5748077 AAATTTA
1 AAATTTA
5748084 GTACTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 8 0.40
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (16 bp):
AAATTTAATGATTATA
Found at i:5758430 original size:32 final size:33
Alignment explanation
Indices: 5758394--5758462 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
5758384 TTTTCATATG
* ** * *
5758394 TTTTTACGTTTTTGTTTTCTTTTTCTT-TTTTC
1 TTTTTACCTTTTTCCTTTCTTCTTATTGTTTTC
*
5758426 TTTTTCCCTTTTTCCTTTCTTCTTATTGTTTTC
1 TTTTTACCTTTTTCCTTTCTTCTTATTGTTTTC
5758459 TTTT
1 TTTT
5758463 CTCCTTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.03, C:0.17, G:0.04, T:0.75
Consensus pattern (33 bp):
TTTTTACCTTTTTCCTTTCTTCTTATTGTTTTC
Found at i:5759096 original size:63 final size:63
Alignment explanation
Indices: 5758995--5759154 Score: 187
Period size: 63 Copynumber: 2.5 Consensus size: 63
5758985 ACGACCGTAT
* * * * *
5758995 GCCATGTAACTCACTGTTTAGAATTTATAGTCACACGGGCTAAAGACACGGACATGTGTCCAG
1 GCCATGTAACTCACTGTTTTGAATTTAGAGTCAAACGGGCCAAAGACACGGACATGTGTCCAA
* * * * * *
5759058 GCCATGTAATTCATTGTTTTGAATTTAGGGTCAAACGGGCCAGAGACACGGGCTTGTGTCCAA
1 GCCATGTAACTCACTGTTTTGAATTTAGAGTCAAACGGGCCAAAGACACGGACATGTGTCCAA
*
5759121 GCCGTGTAACTCACTGTTTTGGGAATTT-GAGTCA
1 GCCATGTAACTCACTGTTTT--GAATTTAGAGTCA
5759155 TACTGCCGTG
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
63 69 0.86
64 5 0.06
65 6 0.08
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (63 bp):
GCCATGTAACTCACTGTTTTGAATTTAGAGTCAAACGGGCCAAAGACACGGACATGTGTCCAA
Found at i:5759796 original size:18 final size:18
Alignment explanation
Indices: 5759773--5759833 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
5759763 GACTCTACAT
*
5759773 TTGTATCTGAATTTGTAA
1 TTGTATCTGAATATGTAA
*
5759791 TTGTATCTG-ATATGT-T
1 TTGTATCTGAATATGTAA
* *
5759807 TTGTATCTAAATCTGTAA
1 TTGTATCTGAATATGTAA
*
5759825 GTGTATCTG
1 TTGTATCTG
5759834 GTATGTTCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
16 8 0.24
17 10 0.29
18 16 0.47
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (18 bp):
TTGTATCTGAATATGTAA
Found at i:5759824 original size:34 final size:34
Alignment explanation
Indices: 5759772--5759847 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
5759762 GGACTCTACA
* * *
5759772 TTTGTATCTGAATTTGTAATTGTATCTGATATGT
1 TTTGTATCTAAATCTGTAAGTGTATCTGATATGT
*
5759806 TTTGTATCTAAATCTGTAAGTGTATCTGGTATGT
1 TTTGTATCTAAATCTGTAAGTGTATCTGATATGT
*
5759840 TCTGTATC
1 TTTGTATC
5759848 CATTTCTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.50
Consensus pattern (34 bp):
TTTGTATCTAAATCTGTAAGTGTATCTGATATGT
Found at i:5770134 original size:4 final size:4
Alignment explanation
Indices: 5770125--5770218 Score: 188
Period size: 4 Copynumber: 23.5 Consensus size: 4
5770115 TATCTAAACA
5770125 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5770173 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
5770219 TTGTTTGTTT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 90 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:5770293 original size:23 final size:23
Alignment explanation
Indices: 5770248--5770310 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
5770238 TTATTAACAT
***
5770248 TGTTCGTGAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
5770271 TGTTCGTGAACATGTTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
**
5770294 -GTTAAATGAACATGTTC
1 TGTT-CGTGAACATGTTC
5770311 GTAAACATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:5770340 original size:14 final size:14
Alignment explanation
Indices: 5770321--5770352 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
5770311 GTAAACATTA
5770321 AACAAATGAACATG
1 AACAAATGAACATG
5770335 AACAAATGAACATG
1 AACAAATGAACATG
5770349 AACA
1 AACA
5770353 CACATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12
Consensus pattern (14 bp):
AACAAATGAACATG
Found at i:5772194 original size:125 final size:125
Alignment explanation
Indices: 5771972--5772224 Score: 461
Period size: 125 Copynumber: 2.0 Consensus size: 125
5771962 CATAAAGTGA
* *
5771972 ATTTGCGATTCCTTGTTTCCCACTTAAACTATAAACAGTTGAGTTACCATTTAATTCAAGACAAT
1 ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
5772037 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCCACCCCCATTTTATTATTAATT
66 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCCACCCCCATTTTATTATTAATT
5772097 ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
1 ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
* **
5772162 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTTCCCACCCCTGTTTTATTATTAATT
66 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCCACCCCCATTTTATTATTAATT
5772222 ATT
1 ATT
5772225 ATTATATTTT
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 123 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (125 bp):
ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCCACCCCCATTTTATTATTAATT
Found at i:5774144 original size:16 final size:17
Alignment explanation
Indices: 5774123--5774155 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5774113 AAAATCAACC
5774123 AAAAAAGAAAA-GAAAA
1 AAAAAAGAAAAGGAAAA
5774139 AAAAAAGAAAAGGAAAA
1 AAAAAAGAAAAGGAAAA
5774156 CAAATCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGGAAAA
Found at i:5777334 original size:8 final size:7
Alignment explanation
Indices: 5777306--5777333 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5777296 TTGTAAATTA
5777306 AATTTTT
1 AATTTTT
5777313 AATTTTT
1 AATTTTT
5777320 AATTTTT
1 AATTTTT
5777327 AATTTTT
1 AATTTTT
5777334 TTCTTAGCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
AATTTTT
Found at i:5777435 original size:14 final size:14
Alignment explanation
Indices: 5777411--5777444 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5777401 TTAAAAAATG
*
5777411 TATTATTTATAAAA
1 TATTATATATAAAA
*
5777425 TTTTATATATAAAA
1 TATTATATATAAAA
5777439 TATTAT
1 TATTAT
5777445 TGTATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATATATAAAA
Found at i:5777543 original size:14 final size:14
Alignment explanation
Indices: 5777524--5777551 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5777514 GAAGCAAAAT
5777524 AAATTCAATATAAA
1 AAATTCAATATAAA
5777538 AAATTCAATATAAA
1 AAATTCAATATAAA
5777552 TTTGAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATTCAATATAAA
Found at i:5789647 original size:9 final size:9
Alignment explanation
Indices: 5789630--5789675 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
5789620 TAAGTTTTCG
5789630 AATTCGAAT
1 AATTCGAAT
*
5789639 AACTCGAAT
1 AATTCGAAT
5789648 AATTCGAAT
1 AATTCGAAT
*
5789657 AATTCAAAT
1 AATTCGAAT
5789666 AATTCGAAT
1 AATTCGAAT
5789675 A
1 A
5789676 TCAAACTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5789785 original size:5 final size:5
Alignment explanation
Indices: 5789775--5789799 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5789765 AGAACTTTTA
5789775 CTCCC CTCCC CTCCC CTCCC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC
5789800 AACCCCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:5790675 original size:5 final size:5
Alignment explanation
Indices: 5790665--5790690 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5790655 CTCGAAAATT
5790665 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
5790691 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:5790807 original size:2 final size:2
Alignment explanation
Indices: 5790795--5790845 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
5790785 TTCTCCCCCA
*
5790795 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5790835 -T AT GT AT AT AT
1 AT AT AT AT AT AT
5790846 TTTTTTAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5791679 original size:5 final size:5
Alignment explanation
Indices: 5791669--5791694 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5791659 AAAATCACTT
5791669 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
5791695 CTTTTTCGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:5792003 original size:9 final size:9
Alignment explanation
Indices: 5791989--5792019 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5791979 GTTAAACGAA
5791989 TCGAGTTAT
1 TCGAGTTAT
*
5791998 TCGAGTTAA
1 TCGAGTTAT
5792007 TCGAGTTAT
1 TCGAGTTAT
5792016 TCGA
1 TCGA
5792020 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5797118 original size:18 final size:18
Alignment explanation
Indices: 5797069--5797118 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
5797059 TAAGAAAACA
*
5797069 TTTTGAAATTGAATAATG
1 TTTTGAAAATGAATAATG
* *
5797087 ATTTGTAAATGAATAATG
1 TTTTGAAAATGAATAATG
*
5797105 TTTTGAAAACGAAT
1 TTTTGAAAATGAAT
5797119 GATGCGATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (18 bp):
TTTTGAAAATGAATAATG
Found at i:5797491 original size:25 final size:25
Alignment explanation
Indices: 5797445--5797493 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5797435 CTGTCTTTGA
** *
5797445 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATAATGAAACTACTATAGG
*
5797470 TAGTATATAATGAGACTACTATAG
1 TAGTATATAATGAAACTACTATAG
5797494 ATAGACAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (25 bp):
TAGTATATAATGAAACTACTATAGG
Found at i:5803643 original size:22 final size:22
Alignment explanation
Indices: 5803612--5803655 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5803602 TTTGAAATAA
5803612 GTTAGATTCATAGTGAGCCAAC
1 GTTAGATTCATAGTGAGCCAAC
*
5803634 GTTAGTTTCATAGTGAGCCAAC
1 GTTAGATTCATAGTGAGCCAAC
5803656 ACATAATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (22 bp):
GTTAGATTCATAGTGAGCCAAC
Found at i:5809154 original size:21 final size:21
Alignment explanation
Indices: 5809115--5809154 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5809105 GGCCATGTAG
*
5809115 AAAACATAAATTTAAAAATGA
1 AAAACATAAATATAAAAATGA
* *
5809136 AAAATATAAATATATAAAT
1 AAAACATAAATATAAAAAT
5809155 TGTTTGTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAACATAAATATAAAAATGA
Found at i:5814931 original size:49 final size:49
Alignment explanation
Indices: 5814859--5814956 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
5814849 CTCCCAGAAG
5814859 ATAAAGACATAAATGTGACTGACTGGA-TCGACAATACATCAGATTGGAC
1 ATAAAGACATAAATGTGACTGACTGGACT-GACAATACATCAGATTGGAC
**
5814908 ATAAAGACATAAATGTGACTGACTGGACTGACAATACATTGGATTGGAC
1 ATAAAGACATAAATGTGACTGACTGGACTGACAATACATCAGATTGGAC
5814957 TCATGTAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 45 0.98
50 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.23
Consensus pattern (49 bp):
ATAAAGACATAAATGTGACTGACTGGACTGACAATACATCAGATTGGAC
Found at i:5816097 original size:13 final size:13
Alignment explanation
Indices: 5816079--5816104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5816069 TTGAATTATC
5816079 ATCATAATACATA
1 ATCATAATACATA
5816092 ATCATAATACATA
1 ATCATAATACATA
5816105 TGAGAGGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
ATCATAATACATA
Found at i:5817362 original size:17 final size:17
Alignment explanation
Indices: 5817340--5817378 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5817330 ATCATTTGGA
5817340 CCACACAGGCATGTGGG
1 CCACACAGGCATGTGGG
* *
5817357 CCACACGGGCGTGTGGG
1 CCACACAGGCATGTGGG
*
5817374 TCACA
1 CCACA
5817379 TTGGCTGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.36, T:0.13
Consensus pattern (17 bp):
CCACACAGGCATGTGGG
Found at i:5823668 original size:31 final size:31
Alignment explanation
Indices: 5823593--5823660 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
5823583 TTACAAAATG
* **
5823593 GTCATTGAACTATTTGAAAGTTTTCATTGAA
1 GTCACTGAACTATTCAAAAGTTTTCATTGAA
* *
5823624 GTCACTGAACTATTCAAAAGTTTTTATTTAA
1 GTCACTGAACTATTCAAAAGTTTTCATTGAA
5823655 GTCACT
1 GTCACT
5823661 AGGCTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAGTTTTCATTGAA
Found at i:5839675 original size:30 final size:29
Alignment explanation
Indices: 5839639--5839707 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
5839629 TGATTGACCC
* *
5839639 ATCCCTTTTCGTAATTCGATAACCGAAGTT
1 ATCCCTTTTCGTAATTCGACAACC-AAATT
* * *
5839669 ATCCCTTTTTGTAGTTCGACAGCCAAATT
1 ATCCCTTTTCGTAATTCGACAACCAAATT
5839698 ATCCCTTTTC
1 ATCCCTTTTC
5839708 ATTGTTTGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCGTAATTCGACAACCAAATT
Found at i:5839821 original size:30 final size:30
Alignment explanation
Indices: 5839725--5839807 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
5839715 GACGGTCATC
* *
5839725 ACCATCCCTTTTCATAATTTGATAGCCAAA
1 ACCATCCCTTTTCATAGTTCGATAGCCAAA
* *
5839755 GCTATCCCTTTTCATAGTTCGATAGCCAAA
1 ACCATCCCTTTTCATAGTTCGATAGCCAAA
5839785 ACCATCCCTTTTCATAGTTCGAT
1 ACCATCCCTTTTCATAGTTCGAT
5839808 GATCGTCACC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (30 bp):
ACCATCCCTTTTCATAGTTCGATAGCCAAA
Found at i:5839824 original size:89 final size:89
Alignment explanation
Indices: 5839637--5839856 Score: 271
Period size: 89 Copynumber: 2.5 Consensus size: 89
5839627 GATGATTGAC
* * * ** **
5839637 CCATCCCTTTTCGTAATTCGATAACCGAAGTTATCCCTTTTTGTAGTTCGACAGCCAAATTATCC
1 CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGACAGCCAAACCATCC
* * *
5839702 CTTTTCATTGTTTGACGGTCATCA
66 CTTTTCATAGTTCGACGATCATCA
* * *
5839726 CCATCCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTCATAGTTCGATAGCCAAAACCATC
1 CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGACAGCC-AAACCATC
* *
5839791 CCTTTTCATAGTTCGATGATCGTCA
65 CCTTTTCATAGTTCGACGATCATCA
* *
5839816 CCATCCTTTTTCATAA-TCGATAGTCGAAGCTATCCCTTTTC
1 CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTC
5839857 GATTTGTCAA
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 70 0.63
90 41 0.37
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (89 bp):
CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGACAGCCAAACCATCC
CTTTTCATAGTTCGACGATCATCA
Found at i:5840676 original size:16 final size:15
Alignment explanation
Indices: 5840650--5840679 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5840640 TATCTTATTT
5840650 TAATTACTTAATTAC
1 TAATTACTTAATTAC
5840665 TAATTCACTTAATTA
1 TAATT-ACTTAATTA
5840680 ACCTTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTACTTAATTAC
Found at i:5843423 original size:25 final size:24
Alignment explanation
Indices: 5843389--5843443 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
5843379 GAGCTATAAA
* *
5843389 CGGTAAGCTCATACGAGCTGAGTAT
1 CGGTAAGCTCATAAGAGCTG-GAAT
*
5843414 CGGTAAGCTCATAAGAGTTGGAAT
1 CGGTAAGCTCATAAGAGCTGGAAT
5843438 CGGTAA
1 CGGTAA
5843444 CCCTAATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (24 bp):
CGGTAAGCTCATAAGAGCTGGAAT
Done.