Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397274.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_228.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2969030
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 66526 characters in sequence are not A, C, G, or T
File 1 of 8
Found at i:6088 original size:29 final size:30
Alignment explanation
Indices: 6056--6124 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
6046 TTGCATATGA
6056 CATGTAATAATAGTA-TTTTTTCAACATGG
1 CATGTAATAATAGTATTTTTTTCAACATGG
* *
6085 CATGTAATAGTGGTATTTTTTTTTTCAACATGG
1 CATGTAATAATAGTA---TTTTTTTCAACATGG
6118 CATGTAA
1 CATGTAA
6125 CAACATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.38
33 21 0.62
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.43
Consensus pattern (30 bp):
CATGTAATAATAGTATTTTTTTCAACATGG
Found at i:6340 original size:45 final size:45
Alignment explanation
Indices: 6259--6361 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
6249 ACAACTTAAC
* *** *
6259 CATGGCGT-TAACAATCTAACTATGGCGTGTTTCATGTTTTTGTA
1 CATGGTGTGTAACAATCTAACTATGGCGTGCAACATGTTTCTGTA
*
6303 TAT-GTCGTGTAACAATCTAA-TCATGGCGTGCAACATGTTTCTGTA
1 CATGGT-GTGTAACAATCTAACT-ATGGCGTGCAACATGTTTCTGTA
6348 CATGGTGTGTAACA
1 CATGGTGTGTAACA
6362 TAATGATGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
43 1 0.02
44 5 0.10
45 40 0.83
46 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (45 bp):
CATGGTGTGTAACAATCTAACTATGGCGTGCAACATGTTTCTGTA
Found at i:17864 original size:24 final size:25
Alignment explanation
Indices: 17811--17865 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
17801 TTGTAAATAG
*
17811 TAAAAATATAATTAGGAATAATTTT
1 TAAAAATATAATTAAGAATAATTTT
*
17836 T-AAAAT-TAATTAAGAGTAATTTT
1 TAAAAATATAATTAAGAATAATTTT
17859 TAAAAAT
1 TAAAAAT
17866 CATACATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 16 0.59
24 10 0.37
25 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (25 bp):
TAAAAATATAATTAAGAATAATTTT
Found at i:20677 original size:35 final size:35
Alignment explanation
Indices: 20616--20683 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
20606 TAGTTCTTCC
* *
20616 CTTATTCTAATTGTTTTGTATGAAGTATAATTTCA
1 CTTATTCTAATTGTTTTGTATAAAGTAAAATTTCA
20651 CTTATTCTAATTGTTTTGCT-TAAAGTAAAATTT
1 CTTATTCTAATTGTTTTG-TATAAAGTAAAATTT
20684 TATTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.51
Consensus pattern (35 bp):
CTTATTCTAATTGTTTTGTATAAAGTAAAATTTCA
Found at i:37854 original size:49 final size:49
Alignment explanation
Indices: 37794--38072 Score: 172
Period size: 50 Copynumber: 5.6 Consensus size: 49
37784 TGCTTTAAGG
* *
37794 GTCTTACAACTTGATTTTGAATGAACAATTTGGAGACTTCGTTTAAAGA
1 GTCTTACAACTTGATCTTGAATGAACAATTTAGAGACTTCGTTTAAAGA
* * * *
37843 GTCTTATAACTTAATCTTGAATGAACGATTTGGAGA-TT--TTACTAGAAGA
1 GTCTTACAACTTGATCTTGAATGAACAATTTAGAGACTTCGTT--TA-AAGA
** * * ** * * *
37892 GTCTTATGACTTGATATGGAATGAATGATTTAGAAACTTCG-CTATAAGG
1 GTCTTACAACTTGATCTTGAATGAACAATTTAGAGACTTCGTTTA-AAGA
* * * * * *
37941 GTTTTGACAACTTGATTTTGAATAAACAACTTAGAGACTTCGTTTCAAGG
1 GTCTT-ACAACTTGATCTTGAATGAACAATTTAGAGACTTCGTTTAAAGA
* * * ** *
37991 GTCTTGACGACTTAATCTTGAAAGAATGATTTAGAGACTTTGTTTCAAAG-
1 GTCTT-ACAACTTGATCTTGAATGAACAATTTAGAGACTTCGTTT-AAAGA
** **
38041 GTCTTTATGACTTGATCTTGAACAAACAATTT
1 GTC-TTACAACTTGATCTTGAATGAACAATTT
38073 GGATCACTTG
Statistics
Matches: 177, Mismatches: 43, Indels: 19
0.74 0.18 0.08
Matches are distributed among these distances:
46 2 0.01
48 4 0.02
49 74 0.42
50 91 0.51
51 6 0.03
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (49 bp):
GTCTTACAACTTGATCTTGAATGAACAATTTAGAGACTTCGTTTAAAGA
Found at i:38230 original size:49 final size:48
Alignment explanation
Indices: 38093--38325 Score: 206
Period size: 48 Copynumber: 4.8 Consensus size: 48
38083 GACCTAAGGT
* *
38093 TGGAACTTTAGAAAAGCTTTGATTCTTCAAATCTTT-TTCTTGGATTTG
1 TGGAACTTT-GAAAGGCTTTGGTTCTTCAAATCTTTCTTCTTGGATTTG
* * * * * *
38141 TGGAAATTTGGAAAGGCTTTAG-TCTTTAGATCTTCCTTCTTGGATTTA
1 TGGAACTTT-GAAAGGCTTTGGTTCTTCAAATCTTTCTTCTTGGATTTG
* * *
38189 TGGGACTCTTGAGAGACTTTGGTTCTTCAAATCTTTCTTCTT-GACTTTG
1 TGGAACT-TTGAAAGGCTTTGGTTCTTCAAATCTTTCTTCTTGGA-TTTG
* * * * * *
38238 TGGAACTTTGAAGAGGCTTTAGTTTTTCATA-CCTT-TTCTTAGATTTT
1 TGGAACTTTGAA-AGGCTTTGGTTCTTCAAATCTTTCTTCTTGGATTTG
* *
38285 TGGAACTCTAGAAAGGCTTTGGTTATTCAAATCTTTCTTCT
1 TGGAACT-TTGAAAGGCTTTGGTTCTTCAAATCTTTCTTCT
38326 AAAGGTTTGA
Statistics
Matches: 145, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
47 40 0.28
48 60 0.41
49 45 0.31
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (48 bp):
TGGAACTTTGAAAGGCTTTGGTTCTTCAAATCTTTCTTCTTGGATTTG
Found at i:38283 original size:96 final size:96
Alignment explanation
Indices: 38093--38325 Score: 269
Period size: 96 Copynumber: 2.4 Consensus size: 96
38083 GACCTAAGGT
* *
38093 TGGAACTTTAGAAA-AGCTTTGATTCTTCAAATCTTT-TTCTTGGATTTGTGGAAATTTGGAAAG
1 TGGAACTCTAGAAAGA-CTTTGGTTCTTCAAATCTTTCTTCTTGGATTTGTGGAAATTTGGAAAG
* *
38156 GCTTTAGTCTTTAGATCTTCCTTCTTGGATTTA
65 GCTTTAGTCTTTAGACCTT-CTTCTTAGATTTA
* * * *
38189 TGGGACTCTTGAGAGACTTTGGTTCTTCAAATCTTTCTTCTT-GACTTTGTGGAACTTT-GAAGA
1 TGGAACTCTAGAAAGACTTTGGTTCTTCAAATCTTTCTTCTTGGA-TTTGTGGAAATTTGGAA-A
* * *
38252 GGCTTTAGTTTTTCATACCTT-TTCTTAGATTTT
64 GGCTTTAGTCTTT-AGACCTTCTTCTTAGATTTA
* *
38285 TGGAACTCTAGAAAGGCTTTGGTTATTCAAATCTTTCTTCT
1 TGGAACTCTAGAAAGACTTTGGTTCTTCAAATCTTTCTTCT
38326 AAAGGTTTGA
Statistics
Matches: 116, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
96 80 0.69
97 31 0.27
98 5 0.04
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (96 bp):
TGGAACTCTAGAAAGACTTTGGTTCTTCAAATCTTTCTTCTTGGATTTGTGGAAATTTGGAAAGG
CTTTAGTCTTTAGACCTTCTTCTTAGATTTA
Found at i:40283 original size:58 final size:58
Alignment explanation
Indices: 40191--40328 Score: 152
Period size: 58 Copynumber: 2.4 Consensus size: 58
40181 TTGGATTGAG
* * * **
40191 AATTACATG-CTTAGCATATCGTGATACATACCTTAATATGTCTTGTCATACCAATGAA
1 AATTACATGCCTT-GCATGTCTTAATACATACCTTAATATGTCTCATCATACCAATGAA
* * * * **
40249 AATTACATGCCTTGCATGTCTTAATACATTCCTTAGTATGTCTCATTATACCATTGTG
1 AATTACATGCCTTGCATGTCTTAATACATACCTTAATATGTCTCATCATACCAATGAA
*
40307 AATTACATGCCATGCATGTCTT
1 AATTACATGCCTTGCATGTCTT
40329 GATATATATA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 64 0.96
59 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (58 bp):
AATTACATGCCTTGCATGTCTTAATACATACCTTAATATGTCTCATCATACCAATGAA
Found at i:40775 original size:29 final size:29
Alignment explanation
Indices: 40743--40798 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
40733 GTTTCTTTGA
* *
40743 TTCCATTCTTTTTAGTAGGGTTTTCCTGT
1 TTCCATTCTTTTGAATAGGGTTTTCCTGT
*
40772 TTCCATTCTTTTGAATAGGTTTTTCCT
1 TTCCATTCTTTTGAATAGGGTTTTCCT
40799 AATGCCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.12, C:0.18, G:0.14, T:0.55
Consensus pattern (29 bp):
TTCCATTCTTTTGAATAGGGTTTTCCTGT
Found at i:40806 original size:29 final size:29
Alignment explanation
Indices: 40745--40812 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
40735 TTCTTTGATT
* * ** *
40745 CCATTCTTTTTAGTAGGGTTTTCCTGTTT
1 CCATTCTTTTGAATAGGGTTTTCCTAATG
*
40774 CCATTCTTTTGAATAGGTTTTTCCTAATG
1 CCATTCTTTTGAATAGGGTTTTCCTAATG
*
40803 CCATTATTTT
1 CCATTCTTTT
40813 AAGACATTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (29 bp):
CCATTCTTTTGAATAGGGTTTTCCTAATG
Found at i:41127 original size:36 final size:36
Alignment explanation
Indices: 41059--41145 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
41049 GCTACTTCGA
* * * *
41059 CACCGTATGTAATTTATTCTCCATCGATTGCTTCAG
1 CACCATATGTGATTTATTCTCCATCCACTGCTTCAG
* **
41095 CACCATATGTGATTTGTTCTCCATCCACTGCTTTGG
1 CACCATATGTGATTTATTCTCCATCCACTGCTTCAG
* *
41131 AACCATACGTGATTT
1 CACCATATGTGATTT
41146 TTTATATCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (36 bp):
CACCATATGTGATTTATTCTCCATCCACTGCTTCAG
Found at i:43067 original size:38 final size:38
Alignment explanation
Indices: 43016--43094 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
43006 TTTTCATTCT
* *
43016 TTTGAATAGAA-TTTTCTTGATTCTGTTATTTTGAGACA
1 TTTGAATAAAATTTTTC-TGATTCTATTATTTTGAGACA
* * *
43054 TTTGAATAAAATTTTTCTGATTTTATTCTTTTGAGATA
1 TTTGAATAAAATTTTTCTGATTCTATTATTTTGAGACA
43092 TTT
1 TTT
43095 TATTTTTCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 30 0.86
39 5 0.14
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.54
Consensus pattern (38 bp):
TTTGAATAAAATTTTTCTGATTCTATTATTTTGAGACA
Found at i:43430 original size:6 final size:6
Alignment explanation
Indices: 43413--43446 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
43403 CGCAAGCATC
* *
43413 CATTGG CGTTGG CATTGG CATTGG CAGTGG CATT
1 CATTGG CATTGG CATTGG CATTGG CATTGG CATT
43447 TCACAAAGCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.15, C:0.18, G:0.35, T:0.32
Consensus pattern (6 bp):
CATTGG
Found at i:45795 original size:12 final size:12
Alignment explanation
Indices: 45778--45803 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
45768 ATAACTGAGC
45778 AAGTTCAAGTTG
1 AAGTTCAAGTTG
45790 AAGTTCAAGTTG
1 AAGTTCAAGTTG
45802 AA
1 AA
45804 TTGGTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (12 bp):
AAGTTCAAGTTG
Found at i:67308 original size:9 final size:10
Alignment explanation
Indices: 67274--67307 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
67264 CATTCAGATA
67274 TTATTTCTTT
1 TTATTTCTTT
67284 TT-TTTCTTT
1 TTATTTCTTT
67293 TTATTT-TTT
1 TTATTTCTTT
67302 TTATTT
1 TTATTT
67308 TATTTTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (10 bp):
TTATTTCTTT
Found at i:69339 original size:3 final size:3
Alignment explanation
Indices: 69331--69357 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
69321 ATTAGAAATT
69331 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
69358 CAAATAGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:77194 original size:4 final size:4
Alignment explanation
Indices: 77187--77229 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
77177 ATATATATAT
77187 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
77230 TAAGTGCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:83926 original size:91 final size:91
Alignment explanation
Indices: 83771--83949 Score: 322
Period size: 91 Copynumber: 2.0 Consensus size: 91
83761 TGATTTGAAT
83771 TAAAGTGTTAATAATATTTATTATTATATAAAAATAAAAAATTTAAAATTTTAATTGAAATAAAT
1 TAAAGTGTTAATAATATTTATTATTATATAAAAATAAAAAATTTAAAATTTTAATTGAAATAAAT
83836 AAAATTTAAATGTTATCTTATAAGCC
66 AAAATTTAAATGTTATCTTATAAGCC
* * * *
83862 TAAAGTGTTAATAATATTTATTGTTATATAAAACTAAAAAATTTAAAATTTTAGTTGAAGTAAAT
1 TAAAGTGTTAATAATATTTATTATTATATAAAAATAAAAAATTTAAAATTTTAATTGAAATAAAT
83927 AAAATTTAAATGTTATCTTATAA
66 AAAATTTAAATGTTATCTTATAA
83950 CCCCAAAATT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (91 bp):
TAAAGTGTTAATAATATTTATTATTATATAAAAATAAAAAATTTAAAATTTTAATTGAAATAAAT
AAAATTTAAATGTTATCTTATAAGCC
Found at i:90200 original size:19 final size:20
Alignment explanation
Indices: 90171--90213 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
90161 TTCATTACAA
* *
90171 AATATTTTTTAATTAATTTT
1 AATATTTTTTAAATAATTTG
90191 AATA-TTTTTAAATAATTTG
1 AATATTTTTTAAATAATTTG
90210 AATA
1 AATA
90214 CTAATATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AATATTTTTTAAATAATTTG
Found at i:96573 original size:19 final size:19
Alignment explanation
Indices: 96549--96591 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
96539 GGATTTGTTT
*
96549 GGAGTTCTA-AATTTAATTA
1 GGAGTTCTAGAA-GTAATTA
*
96568 GGAGTTGTAGAAGTAATTA
1 GGAGTTCTAGAAGTAATTA
96587 GGAGT
1 GGAGT
96592 AGTAGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (19 bp):
GGAGTTCTAGAAGTAATTA
Found at i:96596 original size:19 final size:19
Alignment explanation
Indices: 96562--96598 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
96552 GTTCTAAATT
*
96562 TAATTAGGAGTTGTAGAAG
1 TAATTAGGAGTAGTAGAAG
96581 TAATTAGGAGTAGTAGAA
1 TAATTAGGAGTAGTAGAA
96599 AATAGTGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (19 bp):
TAATTAGGAGTAGTAGAAG
Found at i:108654 original size:13 final size:13
Alignment explanation
Indices: 108633--108680 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
108623 GAGGGAATTG
*
108633 GAGAGGAGGAGGA
1 GAGAAGAGGAGGA
108646 GAGAAGAGGAGGA
1 GAGAAGAGGAGGA
*
108659 GAG-GGAGAGAGAGA
1 GAGAAGAG-GAG-GA
108673 GAGAAGAG
1 GAGAAGAG
108681 AGGGAGAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 3 0.10
13 18 0.62
14 5 0.17
15 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (13 bp):
GAGAAGAGGAGGA
Found at i:108656 original size:21 final size:24
Alignment explanation
Indices: 108632--108683 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
108622 GGAGGGAATT
108632 GGAGAGGA-GGAG-GAGAGA-AGA
1 GGAGAGGAGGGAGAGAGAGAGAGA
108653 GGAG-GAGAGGGAGAGAGAGAGAGA
1 GGAGAG-GAGGGAGAGAGAGAGAGA
*
108677 AGAGAGG
1 GGAGAGG
108684 GAGAGGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 4 0.16
23 6 0.24
24 7 0.28
25 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (24 bp):
GGAGAGGAGGGAGAGAGAGAGAGA
Found at i:108684 original size:21 final size:19
Alignment explanation
Indices: 108643--108688 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
108633 GAGAGGAGGA
*
108643 GGAGAGAAGAGGAGGAGAG
1 GGAGAGAAGAGGAAGAGAG
108662 GGAGAGAGAGAGAGAAGAGAG
1 GGAGAGA-AGAG-GAAGAGAG
108683 GGAGAG
1 GGAGAG
108689 GGAAAGGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 4 0.17
21 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (19 bp):
GGAGAGAAGAGGAAGAGAG
Found at i:114927 original size:44 final size:44
Alignment explanation
Indices: 114864--114953 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
114854 AAATCAGGAA
114864 CAAAAATTACAATATGTCGAAAAGTAAATCCTCTATTTGAAATC
1 CAAAAATTACAATATGTCGAAAAGTAAATCCTCTATTTGAAATC
114908 CAAAAATTACAATATGTCGAAAAGTAAATCCTCTATTTGAAATC
1 CAAAAATTACAATATGTCGAAAAGTAAATCCTCTATTTGAAATC
114952 CA
1 CA
114954 TACAAAGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (44 bp):
CAAAAATTACAATATGTCGAAAAGTAAATCCTCTATTTGAAATC
Found at i:115263 original size:13 final size:13
Alignment explanation
Indices: 115245--115270 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
115235 ATTTAACATG
115245 ACTGAAAAGGAGT
1 ACTGAAAAGGAGT
115258 ACTGAAAAGGAGT
1 ACTGAAAAGGAGT
115271 CTTCAGATAC
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:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (13 bp):
ACTGAAAAGGAGT
Found at i:121203 original size:5 final size:5
Alignment explanation
Indices: 121195--121228 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
121185 TTGTCTTGTA
121195 TCATC TCATC TCATC TCATC TCATC TCATC TCAT
1 TCATC TCATC TCATC TCATC TCATC TCATC TCAT
121229 GCTTAAACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (5 bp):
TCATC
Found at i:138394 original size:5 final size:5
Alignment explanation
Indices: 138384--138409 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
138374 GCACTGTATC
138384 GGCTT GGCTT GGCTT GGCTT GGCTT G
1 GGCTT GGCTT GGCTT GGCTT GGCTT G
138410 TTTACACCCC
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:0.00, C:0.19, G:0.42, T:0.38
Consensus pattern (5 bp):
GGCTT
Found at i:139306 original size:27 final size:26
Alignment explanation
Indices: 139265--139339 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
139255 CTTTGGTTGC
* *
139265 AAATAAAACTAATCAAGCCTAGACAGT
1 AAATAGAACTCATCAAGCCTAGA-AGT
* *
139292 AAATAGAACTCATCAGGCCTAGGATGT
1 AAATAGAACTCATCAAGCCTA-GAAGT
* *
139319 -AATTGAACTCATCATGCCTAG
1 AAATAGAACTCATCAAGCCTAG
139340 GAGGTAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 1 0.02
26 18 0.44
27 20 0.49
28 2 0.05
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (26 bp):
AAATAGAACTCATCAAGCCTAGAAGT
Found at i:139337 original size:26 final size:26
Alignment explanation
Indices: 139297--139346 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
139287 ACAGTAAATA
*
139297 GAACTCATCAGGCCTAGGATGTAATT
1 GAACTCATCAGGCCTAGGAGGTAATT
*
139323 GAACTCATCATGCCTAGGAGGTAA
1 GAACTCATCAGGCCTAGGAGGTAA
139347 AATTACTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (26 bp):
GAACTCATCAGGCCTAGGAGGTAATT
Found at i:161021 original size:19 final size:18
Alignment explanation
Indices: 160988--161023 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
160978 GAATATAAAT
*
160988 TTAAATATTTATTTTTTA
1 TTAAAAATTTATTTTTTA
161006 TTAAAAATTATATTTTTT
1 TTAAAAATT-TATTTTTT
161024 TACTTAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAAAAATTTATTTTTTA
Found at i:161232 original size:24 final size:25
Alignment explanation
Indices: 161200--161249 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 25
161190 TCGATAATAT
161200 AAATATAAATATTTATTT-TTT-ATTA
1 AAATATAAAT-TTT-TTTATTTAATTA
161225 AAAT-TAAATTTTTTTATTTAATTA
1 AAATATAAATTTTTTTATTTAATTA
161249 A
1 A
161250 CTTATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.13
23 6 0.26
24 10 0.43
25 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AAATATAAATTTTTTTATTTAATTA
Found at i:162012 original size:480 final size:463
Alignment explanation
Indices: 161377--162275 Score: 1117
Period size: 480 Copynumber: 1.9 Consensus size: 463
161367 GTTATTATTA
* * *
161377 TTTATTTAAGAATTAAAATTTATATATCATTAAATACTTTTAGCTCAAGAACACAAATTTAAATA
1 TTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTTAGCTCAAAAACACAAATTTAAATA
* * *
161442 TTTATTTTCATTAAAATTAGATTATTTTTCTTAATTAATTTATTAAGTTAACTCTCACATATTTA
66 TTTATTTTCACTAAAATTAGATTATTTTTCTTAATTAACTTATTAAGTTAACTCTCACACATTTA
* * *
161507 CGTTAGGATTTAAAATTTAGTTA-TTTAATCTTTATAAATTTTTACGTCAATTGTTATAGTTTTA
131 CATTAAGATTTAAAATTTAGTTATTTTAA-ATTTATAAATTTTTACGTCAATTGTTATAGTTTTA
* *** *
161571 CGTCAAAACTTATCTATATCAATTTTAAACTATAAT-T-ATTTTTATCCTCATTATTCTTTATTT
195 CATCAAAACTTATCTATATCAATTTTAAACTATAATATAAAAATTATCATCATTATT-TTTATTT
* *
161634 AAAAATTAAAATTTATATACCATTAAATACTTTTAGTCCGAGAATATAAATTTAAATATTTTTTT
259 AAAAATTAAAATTTATATACCATTAAATAATTTTAGTACGAGAATATAAATTT-AA-ATTTTTTT
* * *
161699 CACTAAAATTAATTTTGTTTACTTAATTGACTTGTTACATTAACTTTTACACAT-TTACGTTAAG
322 -ACTAAAATTAAATTT-TTT-CTTAATTGACTTGTTAAATTAAC-TCT-CACATATTACGTTAAG
*
161763 ATTTAAAATTTAATTAT-TTTACTTTTATAAGTTTTTACGTCAAGTTTTTTTATGTTAATTTCAA
382 ATTTAAAATTTAATTATCTTGAC-TTTATAAGTTTTTACGTCAAGTTTTTTTATGTTAATTTCAA
161827 ACTATAATTATTTTTATC
446 ACTATAATTATTTTTATC
* ** * * *
161845 TTTATNNNNNNNNNNTTAAAAATTAAAATTTGTATATTGTTAAACACTTTTAGTTCAAAAATATA
1 TTTAT----------TTAAAAATTAAAATTTATATATCATTAAACACTTTTAGCTCAAAAACACA
* * * *
161910 AATTTAAATATTTATTTTTTTACTAAAATTAGATTATTTTAT-TTAATTGACTTGTTATGTTAAC
56 AATTTAAATATTTA--TTTTCACTAAAATTAGATTATTTT-TCTTAATTAACTTATTAAGTTAAC
* * ** *
161974 TCTCACACATTTACATTAAGATTTAAGATTTAGTTATTTTAAATTTATAAGTTTTTTTGTTAATT
118 TCTCACACATTTACATTAAGATTTAAAATTTAGTTATTTTAAATTTATAAATTTTTACGTCAATT
* ** * * * *
162039 GTTATAGTTTTATATCAAGGCTTATTTATGTCAATTTTAAACTATAATAATAAAAATTATTATTA
183 GTTATAGTTTTACATCAAAACTTATCTATATCAATTTTAAACTATAAT-ATAAAAATTATCATCA
* *
162104 TTATTTTTATTTAAAAATTAAAATTTATATATCATTAAATAATTTTAGTATGAGAATATAAATTT
247 TTATTTTTATTTAAAAATTAAAATTTATATACCATTAAATAATTTTAGTACGAGAATATAAATTT
*
162169 AAATTTTTTTATTAAAATTAAATTTTTTCTTAATTGACTTGTTAAATTAACTCTCACATATTACG
312 AAATTTTTTTACTAAAATTAAATTTTTTCTTAATTGACTTGTTAAATTAACTCTCACATATTACG
* *
162234 TTAAGATTTTAAATTTAATTATCTTGACTTTATGAGTTTTTA
377 TTAAGATTTAAAATTTAATTATCTTGACTTTATAAGTTTTTA
162276 TATTAATTTT
Statistics
Matches: 365, Mismatches: 47, Indels: 30
0.83 0.11 0.07
Matches are distributed among these distances:
468 5 0.01
475 5 0.01
476 41 0.11
477 26 0.07
478 58 0.16
479 13 0.04
480 140 0.38
481 8 0.02
482 57 0.16
483 12 0.03
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.49
Consensus pattern (463 bp):
TTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTTAGCTCAAAAACACAAATTTAAATA
TTTATTTTCACTAAAATTAGATTATTTTTCTTAATTAACTTATTAAGTTAACTCTCACACATTTA
CATTAAGATTTAAAATTTAGTTATTTTAAATTTATAAATTTTTACGTCAATTGTTATAGTTTTAC
ATCAAAACTTATCTATATCAATTTTAAACTATAATATAAAAATTATCATCATTATTTTTATTTAA
AAATTAAAATTTATATACCATTAAATAATTTTAGTACGAGAATATAAATTTAAATTTTTTTACTA
AAATTAAATTTTTTCTTAATTGACTTGTTAAATTAACTCTCACATATTACGTTAAGATTTAAAAT
TTAATTATCTTGACTTTATAAGTTTTTACGTCAAGTTTTTTTATGTTAATTTCAAACTATAATTA
TTTTTATC
Found at i:167897 original size:21 final size:21
Alignment explanation
Indices: 167873--167914 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
167863 GGTAACTAAA
*
167873 TTTTAAATTTCATTTAATTTT
1 TTTTAAATTTCATCTAATTTT
* *
167894 TTTTAATTTTTATCTAATTTT
1 TTTTAAATTTCATCTAATTTT
167915 ATTAATCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTAAATTTCATCTAATTTT
Found at i:174970 original size:2 final size:2
Alignment explanation
Indices: 174963--174989 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
174953 ATTCTCCCTT
174963 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 T
174990 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:179566 original size:2 final size:2
Alignment explanation
Indices: 179559--179602 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
179549 GGTCCTATGC
179559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
179601 AT
1 AT
179603 TTCTAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180844 original size:24 final size:24
Alignment explanation
Indices: 180816--180872 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
180806 CAACTTAACT
180816 ATGACATGTCAAATGTTTTTGTAG
1 ATGACATGTCAAATGTTTTTGTAG
*
180840 ATGACATGTCAAATGTTTTTGTAT
1 ATGACATGTCAAATGTTTTTGTAG
*
180864 ATGGCATGT
1 ATGACATGT
180873 AATAACCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (24 bp):
ATGACATGTCAAATGTTTTTGTAG
Found at i:180926 original size:39 final size:39
Alignment explanation
Indices: 180883--180960 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
180873 AATAACCAAT
* ** * *
180883 GTATAACAATCTAATTAGGATGTGTCACATGTTTTTGTA
1 GTATAACAACCTAACCAGGATATGTCACATATTTTTGTA
*
180922 GTATAACAACCTAACCATGATATGTCACATATTTTTGTA
1 GTATAACAACCTAACCAGGATATGTCACATATTTTTGTA
180961 CATGATGTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (39 bp):
GTATAACAACCTAACCAGGATATGTCACATATTTTTGTA
Found at i:186986 original size:22 final size:22
Alignment explanation
Indices: 186961--187030 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
186951 AATTAAAAAA
186961 AATTATTTATTTTTTAATTTTT
1 AATTATTTATTTTTTAATTTTT
* ** *
186983 AATTATATATTTAATAAATTTT
1 AATTATTTATTTTTTAATTTTT
*
187005 AATTTTTTATATTTTTATATTTTT
1 AATTATTTAT-TTTTTA-ATTTTT
187029 AA
1 AA
187031 AAAATTATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 26 0.70
23 4 0.11
24 7 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
AATTATTTATTTTTTAATTTTT
Found at i:187175 original size:26 final size:28
Alignment explanation
Indices: 187146--187197 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
187136 TTTTTAACAA
187146 TTATTT-TTTTTT-ATATATAAAATCAG
1 TTATTTCTTTTTTAATATATAAAATCAG
187172 TTATTTCTTTTTTAATATATAAAATC
1 TTATTTCTTTTTTAATATATAAAATC
187198 TATTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 6 0.25
27 6 0.25
28 12 0.50
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (28 bp):
TTATTTCTTTTTTAATATATAAAATCAG
Found at i:200196 original size:15 final size:17
Alignment explanation
Indices: 200165--200196 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
200155 TTTTTTAATT
200165 TTTTCATAAATTTAAAA
1 TTTTCATAAATTTAAAA
200182 TTTTCA-AAA-TTAAAA
1 TTTTCATAAATTTAAAA
200197 GTGTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTCATAAATTTAAAA
Found at i:204701 original size:97 final size:97
Alignment explanation
Indices: 204535--204731 Score: 313
Period size: 97 Copynumber: 2.0 Consensus size: 97
204525 TCACCTTCTT
* * * *
204535 TGCATGTTGTATGTGTAAGCTCATAAGATCTCATGTAAACAACAAAACCACAATGAAGCACTGCT
1 TGCATGTTGTACGTGCAAGCTAATAAGATCTCATATAAACAACAAAACCACAATGAAGCACTGCT
* *
204600 GGAGTTCCAATTTTAGTTATCTTATGAATTTG
66 GGAGTTCAAATTTTAGTTATCTTATGAATCTG
* *
204632 TGCATGTTGTACGTGCAAGCTAATAAGGTCTCATATAAACAACAAGACCACAATGAAGCACTGCT
1 TGCATGTTGTACGTGCAAGCTAATAAGATCTCATATAAACAACAAAACCACAATGAAGCACTGCT
*
204697 GGAGTTCAAATTTTAGTTATCTTTTGAATCTG
66 GGAGTTCAAATTTTAGTTATCTTATGAATCTG
204729 TGC
1 TGC
204732 CTTTTGATAG
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (97 bp):
TGCATGTTGTACGTGCAAGCTAATAAGATCTCATATAAACAACAAAACCACAATGAAGCACTGCT
GGAGTTCAAATTTTAGTTATCTTATGAATCTG
Found at i:215653 original size:6 final size:6
Alignment explanation
Indices: 215634--215667 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
215624 GGGAAGGAGA
* *
215634 GGAAAG GGAGGG GGAAGG GGAAGG GGAAGG GGAA
1 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGAA
215668 AACACGGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GGAAGG
Found at i:226874 original size:139 final size:139
Alignment explanation
Indices: 226714--227117 Score: 452
Period size: 139 Copynumber: 3.0 Consensus size: 139
226704 GGGACTCAGG
226714 GTAAGCAGGGTGGCCGACGGCAACGAGGACGTTGCAGGAATCGGGTGAGAGAGAGTTTGCCGGAA
1 GTAAGCAGGGTGGCCGACGGCAACGAGGACGTTGCAGGAATCGGGTGAGAGAGAGTTTGCCGGAA
226779 TCGAATGGGAGAGAGTGTCACGAGGAAAGTGCCTCTATCTCACATCGGACAAGAACGAGAGGTCT
66 TCGAATGGGAGAGAGTGTCACGAGGAAAGTGCCTCTATCTCACATCGGACAAGAACGAGAGGTCT
226844 TGAGCTCCC
131 TGAGCTCCC
226853 GTAAGCAGGGTGGCCGACGGCAACGAGGACGTTGCAGGAATCGGGTGAGAGAGAGTTTGCCGGAA
1 GTAAGCAGGGTGGCCGACGGCAACGAGGACGTTGCAGGAATCGGGTGAGAGAGAGTTTGCCGGAA
* * * * * * * * ** ** * *
226918 TC-CACGAGGACGTTGCAG-G-AATCGGGTGAAGAGAG-GTTTGCCGGA-ATC-GA-ATG--GGA
66 TCGAATG-GGA-G-AG-AGTGTCA-CGAG-GAA-AGTGCCTCTATCTCACATCGGACAAGAACGA
*
226974 GAGAG---T--G-TCAC
124 GAG-GTCTTGAGCTCCC
*
226985 G--AG-AGGGTGGCCG--GGCAACGAAGACGTTGCAGGAATCGGGTGAGAGAGAGTTTGCCGGAA
1 GTAAGCAGGGTGGCCGACGGCAACGAGGACGTTGCAGGAATCGGGTGAGAGAGAGTTTGCCGGAA
227045 TCGAATGGGAGAGAGTGTCACGAGGAAAGTGCCTCTATCTCACATCGGACAAGAACGAGAGGTCT
66 TCGAATGGGAGAGAGTGTCACGAGGAAAGTGCCTCTATCTCACATCGGACAAGAACGAGAGGTCT
227110 TGAGCTCC
131 TGAGCTCC
227118 TTATAAGCGG
Statistics
Matches: 211, Mismatches: 31, Indels: 51
0.72 0.11 0.17
Matches are distributed among these distances:
123 3 0.01
124 9 0.04
125 8 0.04
126 4 0.02
127 53 0.25
128 3 0.01
129 15 0.07
130 2 0.01
131 1 0.00
132 4 0.02
133 2 0.01
134 2 0.01
135 1 0.00
137 5 0.02
138 3 0.01
139 72 0.34
140 4 0.02
141 8 0.04
142 9 0.04
143 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.38, T:0.16
Consensus pattern (139 bp):
GTAAGCAGGGTGGCCGACGGCAACGAGGACGTTGCAGGAATCGGGTGAGAGAGAGTTTGCCGGAA
TCGAATGGGAGAGAGTGTCACGAGGAAAGTGCCTCTATCTCACATCGGACAAGAACGAGAGGTCT
TGAGCTCCC
Found at i:226918 original size:25 final size:25
Alignment explanation
Indices: 226884--226966 Score: 68
Period size: 25 Copynumber: 3.5 Consensus size: 25
226874 AACGAGGACG
226884 TTGCAGGAATCGGGTGAGAGAGAGT
1 TTGCAGGAATCGGGTGAGAGAGAGT
* *** *
226909 TTGCCGGAATC-CACGAG-GA-CG-
1 TTGCAGGAATCGGGTGAGAGAGAGT
226930 TTGCAGGAATCGGGTGA-AGAGAGGT
1 TTGCAGGAATCGGGTGAGAGAGA-GT
*
226955 TTGCCGGAATCG
1 TTGCAGGAATCG
226967 AATGGGAGAG
Statistics
Matches: 42, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
21 10 0.24
22 5 0.12
23 2 0.05
24 4 0.10
25 21 0.50
ACGTcount: A:0.25, C:0.16, G:0.40, T:0.19
Consensus pattern (25 bp):
TTGCAGGAATCGGGTGAGAGAGAGT
Found at i:226942 original size:46 final size:46
Alignment explanation
Indices: 226875--226965 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
226865 GCCGACGGCA
226875 ACGAGGACGTTGCAGGAATCGGGTG-AGAGAGAGTTTGCCGGAATCC
1 ACGAGGACGTTGCAGGAATCGGGTGAAGAGAG-GTTTGCCGGAATCC
226921 ACGAGGACGTTGCAGGAATCGGGTGAAGAGAGGTTTGCCGGAATC
1 ACGAGGACGTTGCAGGAATCGGGTGAAGAGAGGTTTGCCGGAATC
226966 GAATGGGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 38 0.86
47 6 0.14
ACGTcount: A:0.26, C:0.16, G:0.40, T:0.18
Consensus pattern (46 bp):
ACGAGGACGTTGCAGGAATCGGGTGAAGAGAGGTTTGCCGGAATCC
Found at i:231133 original size:5 final size:5
Alignment explanation
Indices: 231123--231148 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
231113 AATCATATAC
231123 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
231149 AGATGGGGCA
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):
ATAAA
Found at i:235544 original size:31 final size:28
Alignment explanation
Indices: 235509--235584 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 28
235499 AATTATTACT
*
235509 TATAAAAACTTATTTAACTTAAA-AATAAAA
1 TATAAAAA-TTATTTAA-TGAAATAAT-AAA
235539 GTATAAATAATTGATTTAATGAAATAATAAA
1 -TATAAA-AATT-ATTTAATGAAATAATAAA
235570 -ATAAAAATTATTTAA
1 TATAAAAATTATTTAA
235585 AAATTTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
27 6 0.15
28 4 0.10
29 5 0.12
31 15 0.37
32 11 0.27
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (28 bp):
TATAAAAATTATTTAATGAAATAATAAA
Found at i:235588 original size:25 final size:27
Alignment explanation
Indices: 235527--235598 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 27
235517 CTTATTTAAC
*
235527 TTAAAAATAA-AAGTATAAATAATTGAT
1 TTAAAAATAATAA-AATAAATAATTGAT
235554 TTAATGAAATAATAAAATAAA-AATT-AT
1 TTAA--AAATAATAAAATAAATAATTGAT
**
235581 TTAAAAATTTTAAAATAA
1 TTAAAAATAATAAAATAA
235599 TTTAAGGGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 12 0.31
27 10 0.26
28 4 0.10
29 11 0.28
30 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
TTAAAAATAATAAAATAAATAATTGAT
Found at i:238993 original size:2 final size:2
Alignment explanation
Indices: 238986--239012 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
238976 TCATAGGAGA
238986 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
239013 CACATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:240959 original size:2 final size:2
Alignment explanation
Indices: 240952--240982 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
240942 ATACTTATTA
240952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
240983 AAGATTAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:281716 original size:17 final size:17
Alignment explanation
Indices: 281694--281731 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
281684 ATTATCTTTT
281694 AATTAATATT-TTAAAAA
1 AATTAA-ATTATTAAAAA
*
281711 AATTAAATTATTTAAAA
1 AATTAAATTATTAAAAA
281728 AATT
1 AATT
281732 TTAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTAAATTATTAAAAA
Found at i:300518 original size:139 final size:138
Alignment explanation
Indices: 300106--300611 Score: 480
Period size: 139 Copynumber: 3.6 Consensus size: 138
300096 GGGGAAAACT
* * * * **
300106 TTCACAAATTGGATTAAAATTCGATTTTTAGAGTTCGATGTATAAAATAATAATTTATTTATAAT
1 TTCAAAAATTGAATTAAAGTTCGATTTTT-GAATTCGATGTATAAAATAATAATCCATTTATAAT
** * * * * * *
300171 TACCATCCGTAAAATTTCAAGTCATAATTTTTATTTAATTATTTGAAATCAAATCATTTCAAATC
65 TAATATTCGTAAAATTTCAAGTCATAATTTTTATTTAATCACTTGAAATCGAATCATTTCAAGTT
300236 AAAAAAAAA
130 AAAAAAAAA
* * * *** *
300245 -TCAAAAATTGAATTAAAGTTTGATTTTTAAAATTTGATGTATAAAATAATAATCCACCAATAGT
1 TTCAAAAATTGAATTAAAGTTCGATTTTT-GAATTCGATGTATAAAATAATAATCCATTTATAAT
* * * * * *
300309 TAGTATTCGTAAAATTTCAAGTTATGATTTTTATTTAATCACTTGGAATCGGATCATTTCAAGTC
65 TAATATTCGTAAAATTTCAAGTCATAATTTTTATTTAATCACTTGAAATCGAATCATTTCAAGTT
300374 AAAAAAAAA
130 AAAAAAAAA
* * * * *
300383 TTCAAAAATTGAATTAAAGTTCGATTTTTGCAACTCAATGCATAAAAAAATAATCCATTTATACT
1 TTCAAAAATTGAATTAAAGTTCGATTTTTG-AATTCGATGTATAAAATAATAATCCATTTATAAT
* * * * *
300448 TAATATTCGTAAAATTTTAAATCATAAGTGTCATTTAATCACTTGAAATCGAATCATTTCAAGTT
65 TAATATTCGTAAAATTTCAAGTCATAATTTTTATTTAATCACTTGAAATCGAATCATTTCAAGTT
* ***
300513 GAAAAATTT
130 AAAAAAAAA
* ** * * *
300522 TTCAAAAATT-AGATTAGAGTTC-ATTTAACGAAGTTCGATGTATAGAATAATAGTTCATTTATA
1 TTCAAAAATTGA-ATTAAAGTTCGATTT-TTGAA-TTCGATGTATAAAATAATAATCCATTTATA
*
300585 ATTAATACTT-GCAAAATTTCAAAGTCA
63 ATTAATA-TTCGTAAAATTTC-AAGTCA
300612 CATATTTCCT
Statistics
Matches: 296, Mismatches: 64, Indels: 13
0.79 0.17 0.03
Matches are distributed among these distances:
138 121 0.41
139 168 0.57
140 7 0.02
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.38
Consensus pattern (138 bp):
TTCAAAAATTGAATTAAAGTTCGATTTTTGAATTCGATGTATAAAATAATAATCCATTTATAATT
AATATTCGTAAAATTTCAAGTCATAATTTTTATTTAATCACTTGAAATCGAATCATTTCAAGTTA
AAAAAAAA
Found at i:304655 original size:28 final size:29
Alignment explanation
Indices: 304591--304660 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
304581 TAAAAAAATA
*
304591 AAATAAA-TTTTTATTTATCTTTTACATG
1 AAATAAATTTTTTATTTATCTTTTACATC
*
304619 AAATTAAATTTTTTATTT-T-TATTTAGATC
1 AAA-TAAATTTTTTATTTATCT-TTTACATC
304648 AAATAAATTTTTT
1 AAATAAATTTTTT
304661 TATTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 14 0.38
29 14 0.38
30 9 0.24
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (29 bp):
AAATAAATTTTTTATTTATCTTTTACATC
Found at i:329346 original size:17 final size:16
Alignment explanation
Indices: 329324--329364 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
329314 AACTAGTTAT
* *
329324 ATATATATAATTTTTAA
1 ATATATATAATATAT-A
329341 ATATATATAATATATA
1 ATATATATAATATATA
329357 ATATATAT
1 ATATATAT
329365 TTAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATATAATATATA
Found at i:331631 original size:20 final size:19
Alignment explanation
Indices: 331604--331657 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
331594 AAATTATATT
331604 TTTTTATTATATTTTAAAA
1 TTTTTATTATATTTTAAAA
*
331623 TTTTATATT-TATTTTTAAA
1 TTTT-TATTATATTTTAAAA
331642 TTTTT-TTATAATTTTA
1 TTTTTATTAT-ATTTTA
331658 TCTCTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 22 0.73
20 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTATTATATTTTAAAA
Found at i:331697 original size:30 final size:32
Alignment explanation
Indices: 331637--331697 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 32
331627 ATATTTATTT
*
331637 TTAAATTTTTTTATAATTTTATCTCTTCAAATA
1 TTAAATTTTTTTAT-ATTTTATCACTTCAAATA
*
331670 TTAAA-TTTTTTAT-TTTTGTCACTTCAAA
1 TTAAATTTTTTTATATTTTATCACTTCAAA
331698 CTTAAAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 13 0.50
32 8 0.31
33 5 0.19
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (32 bp):
TTAAATTTTTTTATATTTTATCACTTCAAATA
Found at i:340092 original size:14 final size:14
Alignment explanation
Indices: 340069--340101 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
340059 GACAAAAGCC
*
340069 AAAAAGAAGAAGAA
1 AAAAACAAGAAGAA
340083 AAAAACAAGAAGAA
1 AAAAACAAGAAGAA
340097 AAAAA
1 AAAAA
340102 ACAAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAACAAGAAGAA
Found at i:356262 original size:14 final size:14
Alignment explanation
Indices: 356243--356269 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
356233 AATTTCGGAA
356243 TATGATACCATATG
1 TATGATACCATATG
356257 TATGATACCATAT
1 TATGATACCATAT
356270 CATCTCTAAA
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:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (14 bp):
TATGATACCATATG
Found at i:356368 original size:6 final size:6
Alignment explanation
Indices: 356357--356381 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
356347 ATTATGAGTG
356357 AATTTT AATTTT AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT A
356382 TAATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:369224 original size:26 final size:31
Alignment explanation
Indices: 369151--369245 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 31
369141 AATATATTTT
* *
369151 TAATGTTATACATTTTATTTTTATTTTTATTA
1 TAATATTATATATTTTATTTTTA-TTTTATTA
*
369183 TAATATTATATATTTTATTTTTATTTCTTTAATA
1 TAATATTATATATTTTATTTTTA--T-TTTATTA
* * *
369217 TAATTTTTTATATTGTATATTTTATTTTA
1 TAATATTATATATTTTAT-TTTTATTTTA
369246 ATTTCTTCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
32 25 0.46
33 3 0.06
34 21 0.39
35 5 0.09
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (31 bp):
TAATATTATATATTTTATTTTTATTTTATTA
Found at i:369229 original size:34 final size:33
Alignment explanation
Indices: 369151--369244 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 33
369141 AATATATTTT
* * *
369151 TAATGTTATACATTTTATTTTTA-TTTTTATTA
1 TAATATTATATATTTTATTTTTATTTTTTAATA
369183 TAATATTATATATTTTATTTTTATTTCTTTAATA
1 TAATATTATATATTTTATTTTTATTT-TTTAATA
* * *
369217 TAATTTTTTATATTGTATATTTTATTTT
1 TAATATTATATATTTTAT-TTTTATTTT
369245 AATTTCTTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 21 0.40
33 2 0.04
34 22 0.42
35 8 0.15
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (33 bp):
TAATATTATATATTTTATTTTTATTTTTTAATA
Found at i:369341 original size:14 final size:14
Alignment explanation
Indices: 369324--369350 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
369314 ATATTATATA
369324 TTTTATTTTAATTT
1 TTTTATTTTAATTT
369338 TTTTATTTTAATT
1 TTTTATTTTAATT
369351 ATAACATTAC
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTTAATTT
Found at i:371078 original size:33 final size:33
Alignment explanation
Indices: 371036--371109 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
371026 TAACCAGCTC
* *
371036 CCTCCATTCCCATTTCCACCTCCCTTTGGTGTT
1 CCTCCATTCCCATTTCCACCTCCCTTTGGTCTA
371069 CCTCCATTCCCATTTCCACCTCCCTTTGGTCTA
1 CCTCCATTCCCATTTCCACCTCCCTTTGGTCTA
371102 CCTCCATT
1 CCTCCATT
371110 TGGTCTACCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.11, C:0.45, G:0.07, T:0.38
Consensus pattern (33 bp):
CCTCCATTCCCATTTCCACCTCCCTTTGGTCTA
Found at i:371104 original size:15 final size:15
Alignment explanation
Indices: 371086--371124 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
371076 TCCCATTTCC
*
371086 ACCTCCCTTTGGTCT
1 ACCTCCATTTGGTCT
371101 ACCTCCATTTGGTCT
1 ACCTCCATTTGGTCT
371116 ACCTCCATT
1 ACCTCCATT
371125 CCCTGGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.38, G:0.10, T:0.38
Consensus pattern (15 bp):
ACCTCCATTTGGTCT
Found at i:372794 original size:18 final size:18
Alignment explanation
Indices: 372766--372820 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
372756 ACTTAATTAG
372766 TATTAATTAAAATATTATT
1 TATTAA-TAAAATATTATT
* *
372785 TATTAATAAATTAATATT
1 TATTAATAAAATATTATT
* *
372803 TTTTAAT-ATATATTATT
1 TATTAATAAAATATTATT
372820 T
1 T
372821 TTTACTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 8 0.27
18 16 0.53
19 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTAATAAAATATTATT
Found at i:372877 original size:15 final size:15
Alignment explanation
Indices: 372859--372957 Score: 53
Period size: 15 Copynumber: 6.5 Consensus size: 15
372849 CGTAATAAAA
*
372859 TAATAAATAATATTT
1 TAATAAATAATAATT
*
372874 TAATTAATAATAATT
1 TAATAAATAATAATT
* *
372889 TATTTAATTTAA-AATT
1 TA-ATAA-ATAATAATT
* **
372905 AAATTTTATAA-AATT
1 TAA-TAAATAATAATT
372920 TAATTAAAT-ATAATT
1 TAA-TAAATAATAATT
372935 TAATTAAAT-ATAATT
1 TAA-TAAATAATAATT
*
372950 TAAAAAAT
1 TAATAAAT
372958 TCTATTTAGT
Statistics
Matches: 66, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
14 5 0.08
15 50 0.76
16 8 0.12
17 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATAAATAATAATT
Found at i:372883 original size:19 final size:19
Alignment explanation
Indices: 372859--372897 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
372849 CGTAATAAAA
372859 TAATAAATAATAT-TTTAAT
1 TAAT-AATAATATATTTAAT
*
372878 TAATAATAATTTATTTAAT
1 TAATAATAATATATTTAAT
372897 T
1 T
372898 TAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAATAATATATTTAAT
Found at i:383439 original size:32 final size:32
Alignment explanation
Indices: 383392--383452 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
383382 AAATTGATTA
* *
383392 AAACTAATACGCTTTTAATATTATTATCAACT
1 AAACCAATACACTTTTAATATTATTATCAACT
383424 AAACCAATACACTTTTAATATTATTATCA
1 AAACCAATACACTTTTAATATTATTATCA
383453 TAGTTAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (32 bp):
AAACCAATACACTTTTAATATTATTATCAACT
Found at i:383642 original size:23 final size:21
Alignment explanation
Indices: 383602--383643 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
383592 TAATTATTAT
*
383602 AATTTTTTTTTTACAAATTTA
1 AATTTTTTTTTTAAAAATTTA
383623 AATTATTTTTTTATAAAAATT
1 AATT-TTTTTTT-TAAAAATT
383644 AGTTTCGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTTTTTTTTAAAAATTTA
Found at i:390394 original size:21 final size:20
Alignment explanation
Indices: 390364--390404 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
390354 TTTACATAAT
390364 TATTAATATTGTACGATACG
1 TATTAATATTGTACGATACG
* *
390384 TATTACATATTTTATGATACG
1 TATTA-ATATTGTACGATACG
390405 GTATGATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (20 bp):
TATTAATATTGTACGATACG
Found at i:394659 original size:3 final size:3
Alignment explanation
Indices: 394651--394675 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
394641 TACTCCCCTG
394651 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
394676 GTATCAGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:397390 original size:2 final size:2
Alignment explanation
Indices: 397385--397417 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
397375 TGTCATGAGA
397385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
397418 AAGAGGAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:397592 original size:22 final size:22
Alignment explanation
Indices: 397548--397594 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
397538 CATCAGAACT
*
397548 AACCAAAAAAATAATTTAGTTG
1 AACCAAAAAAATAATTAAGTTG
*
397570 AACC-AAAAAATAATTGAATTTG
1 AACCAAAAAAATAATT-AAGTTG
397592 AAC
1 AAC
397595 AAGTCATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.26
Consensus pattern (22 bp):
AACCAAAAAAATAATTAAGTTG
Found at i:410620 original size:26 final size:26
Alignment explanation
Indices: 410591--410646 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
410581 CTTAAAATTT
* *
410591 AACAGATTAAAACCCAAGATAGTAGG
1 AACAGATTAAAACACAAGACAGTAGG
410617 AACAGATTAAAACACAAGACAGTAGG
1 AACAGATTAAAACACAAGACAGTAGG
410643 AACA
1 AACA
410647 CTAGAAGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (26 bp):
AACAGATTAAAACACAAGACAGTAGG
Found at i:411307 original size:2 final size:2
Alignment explanation
Indices: 411294--411326 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
411284 TCACAGTAAC
*
411294 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
411327 GGCTTATGGC
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:424384 original size:2 final size:2
Alignment explanation
Indices: 424375--424406 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
424365 TTTTTTCAAT
424375 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
424407 TATCGATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:424975 original size:33 final size:32
Alignment explanation
Indices: 424938--425136 Score: 104
Period size: 33 Copynumber: 5.9 Consensus size: 32
424928 TTTGAATGTC
424938 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTATTATAAT-TT
* *
424971 ATATATTTTATTTTTATTTCTTTAATATAATTT
1 ATATATTTTATTTTTATTT-ATTATTATAATTT
*
425004 TTATATTATATATATTTTAATTTATT-TTACTTATATTAT
1 ATATATT-T-TAT-TTTT-ATTTATTATTA--TA-ATT-T
* *
425043 ATAAATTTTAATTTTT-TTTA-TATT-TTATTT
1 ATATATTTT-ATTTTTATTTATTATTATAATTT
* * * * *
425073 -TATTTTTTGATTCTTACATTATATATTTTATTTT
1 ATATATTTT-ATTTTTA-TTTAT-TATTATAATTT
* *
425107 A-ATATTTTTATTTTAATTATAATATTATAA
1 ATATA-TTTTATTTTTATT-TATTATTATAA
425137 AATATTTTTA
Statistics
Matches: 125, Mismatches: 22, Indels: 38
0.68 0.12 0.21
Matches are distributed among these distances:
29 11 0.09
30 1 0.01
31 6 0.05
32 1 0.01
33 38 0.30
34 24 0.19
35 15 0.12
36 6 0.05
37 11 0.09
38 6 0.05
39 6 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (32 bp):
ATATATTTTATTTTTATTTATTATTATAATTT
Found at i:425031 original size:26 final size:27
Alignment explanation
Indices: 424991--425066 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 27
424981 TTTTTATTTC
* *
424991 TTTAATATAATTTTTATATTATATATAT
1 TTTAAT-TTATTTTTATATTATATAAAT
425019 TTTAATTTATTTTACTTATATTATATAAAT
1 TTTAATTTA-TTT--TTATATTATATAAAT
425049 TTTAATTT-TTTTTATATT
1 TTTAATTTATTTTTATATT
425067 TTATTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 7 0.16
27 2 0.05
28 12 0.28
30 22 0.51
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTAATTTATTTTTATATTATATAAAT
Found at i:425039 original size:30 final size:30
Alignment explanation
Indices: 425004--425062 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
424994 AATATAATTT
*
425004 TTATATTATATATATTTTAATTTATTTTAC
1 TTATATTATATAAATTTTAATTTATTTTAC
*
425034 TTATATTATATAAATTTTAATTTTTTTTA
1 TTATATTATATAAATTTTAATTTATTTTA
425063 TATTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
TTATATTATATAAATTTTAATTTATTTTAC
Found at i:425117 original size:14 final size:15
Alignment explanation
Indices: 425093--425123 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
425083 TTCTTACATT
425093 ATATATTTTATTTTA
1 ATATATTTTATTTTA
425108 ATAT-TTTTATTTTA
1 ATATATTTTATTTTA
425122 AT
1 AT
425124 TATAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:425887 original size:18 final size:18
Alignment explanation
Indices: 425853--425890 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
425843 GTTTTTAAAT
*
425853 ATTTTATACATTTTTATA
1 ATTTTATACATTATTATA
425871 ATTTT-TACATTAATTATA
1 ATTTTATACATT-ATTATA
425889 AT
1 AT
425891 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTATACATTATTATA
Found at i:432690 original size:3 final size:3
Alignment explanation
Indices: 432682--432707 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
432672 TTATACACTA
432682 GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GC
432708 CGCCACAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.35, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:434187 original size:46 final size:46
Alignment explanation
Indices: 434102--434239 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 46
434092 CAAAAGTCTC
* *
434102 TAGGCTTTGTAAAAAG-GAA-ACTATAAATTTCGCGGACTTTCTAAT
1 TAGGCATTGTAAAAAGAGAACA-TATAAATTTCGTGGACTTTCTAAT
* * *
434147 TAGGCGTTGTAAAAAGAGAACATATAAATTTCGTGAACTTTCTTAT
1 TAGGCATTGTAAAAAGAGAACATATAAATTTCGTGGACTTTCTAAT
434193 TAGGCATTGTAAAAAGAGAACATATAAATTTCGTGGACTTTCTAAT
1 TAGGCATTGTAAAAAGAGAACATATAAATTTCGTGGACTTTCTAAT
434239 T
1 T
434240 TGCCTTGTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
45 15 0.18
46 68 0.81
47 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (46 bp):
TAGGCATTGTAAAAAGAGAACATATAAATTTCGTGGACTTTCTAAT
Found at i:437068 original size:30 final size:30
Alignment explanation
Indices: 437034--437092 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
437024 CAGGAGGCGG
*
437034 GGCATTCCAGGCCGTGGTGGAGGTGGAGCA
1 GGCATTCCAGGCCGTGGAGGAGGTGGAGCA
* *
437064 GGCATTCCAGGTCGTGGAGGCGGTGGAGC
1 GGCATTCCAGGCCGTGGAGGAGGTGGAGC
437093 TGGAGGTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.47, T:0.17
Consensus pattern (30 bp):
GGCATTCCAGGCCGTGGAGGAGGTGGAGCA
Found at i:438075 original size:15 final size:15
Alignment explanation
Indices: 438055--438094 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
438045 TTTATTTTAT
438055 AAAAAATAAAAATAA
1 AAAAAATAAAAATAA
438070 AAAAAA-ACAAAATAA
1 AAAAAATA-AAAATAA
438085 AGAAAAATAA
1 A-AAAAATAA
438095 CAAGCCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 14 0.64
16 6 0.27
17 1 0.05
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.10
Consensus pattern (15 bp):
AAAAAATAAAAATAA
Found at i:450141 original size:2 final size:2
Alignment explanation
Indices: 450134--450164 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
450124 TAAGAAACGT
450134 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
450165 GAAACGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:450338 original size:3 final size:3
Alignment explanation
Indices: 450330--450355 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
450320 AAACTACAAA
450330 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
450356 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:451359 original size:13 final size:13
Alignment explanation
Indices: 451341--451370 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
451331 AATCTATCAC
*
451341 TTTTCTTTCTTTT
1 TTTTCTTCCTTTT
451354 TTTTCTTCCTTTT
1 TTTTCTTCCTTTT
451367 TTTT
1 TTTT
451371 GTTTTTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTCCTTTT
Found at i:470130 original size:32 final size:32
Alignment explanation
Indices: 470094--470158 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
470084 AAATCTTAAA
470094 AGGAATAAGAGTAACTAACAAATAACTTCTAC
1 AGGAATAAGAGTAACTAACAAATAACTTCTAC
*
470126 AGGAATATGAGTAACTAACAAATAACTTCTAC
1 AGGAATAAGAGTAACTAACAAATAACTTCTAC
470158 A
1 A
470159 ATATCATGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.23
Consensus pattern (32 bp):
AGGAATAAGAGTAACTAACAAATAACTTCTAC
Found at i:492089 original size:11 final size:10
Alignment explanation
Indices: 492071--492117 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
492061 ATATACAATC
492071 AATATTATAT
1 AATATTATAT
492081 AATATTTATAT
1 AATA-TTATAT
*
492092 AATGTTAT-T
1 AATATTATAT
*
492101 AA-ATTATAA
1 AATATTATAT
492110 AATATTAT
1 AATATTAT
492118 TTCAAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
8 4 0.13
9 5 0.16
10 13 0.42
11 9 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (10 bp):
AATATTATAT
Found at i:492117 original size:18 final size:20
Alignment explanation
Indices: 492071--492118 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
492061 ATATACAATC
*
492071 AATATTATATAATATTTATAT
1 AATATTAT-TAATATTTATAA
*
492092 AATGTTATTAA-A-TTATAA
1 AATATTATTAATATTTATAA
492110 AATATTATT
1 AATATTATT
492119 TCAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 13 0.54
19 1 0.04
20 3 0.12
21 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AATATTATTAATATTTATAA
Found at i:510803 original size:33 final size:33
Alignment explanation
Indices: 510766--510831 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
510756 AGCATGTCAT
510766 GCGTTACAGGTGTTGCT-TTGATTTAGAATGCCA
1 GCGTTACAGGTGTTGCTCTT-ATTTAGAATGCCA
* *
510799 GCGTTATAGGTGTTGCTCTTATTTGGAATGCCA
1 GCGTTACAGGTGTTGCTCTTATTTAGAATGCCA
510832 TAATGCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (33 bp):
GCGTTACAGGTGTTGCTCTTATTTAGAATGCCA
Found at i:516330 original size:25 final size:25
Alignment explanation
Indices: 516274--516334 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
516264 TTACTAAATT
* *
516274 AATAAAATAATAAAAATGAATATAA
1 AATAAAATAATAAAAAAGAACATAA
*
516299 AATAAAATAATAATAAAAGCACATAA
1 AATAAAATAATAA-AAAAGAACATAA
516325 AA-AAAA-AATA
1 AATAAAATAATA
516335 GTATCTACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.12
25 17 0.53
26 11 0.34
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (25 bp):
AATAAAATAATAAAAAAGAACATAA
Found at i:529914 original size:2 final size:2
Alignment explanation
Indices: 529907--529945 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
529897 TGCTGAGTTG
529907 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
529946 TGGTTAGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:532997 original size:9 final size:10
Alignment explanation
Indices: 532978--533002 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
532968 TTGATTTATG
532978 TTTTTGTTTT
1 TTTTTGTTTT
532988 TTTTTGTTTT
1 TTTTTGTTTT
532998 TTTTT
1 TTTTT
533003 ACACTAGAAT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:542273 original size:69 final size:69
Alignment explanation
Indices: 542199--542331 Score: 212
Period size: 69 Copynumber: 1.9 Consensus size: 69
542189 TGGATTCTAG
* * * *
542199 AATTTCTAGCTACAATTAGGGTTTTTTTTCTTGTTAATGGTGTTCCTGTTAACCCATTTTGGATT
1 AATTTCTAGCTACAATTAGGGTTTTTTTCCTTGTTAATGGTGCTCCCGTTAACCCATTTCGGATT
542264 TTGA
66 TTGA
* *
542268 AATTTCTAGCTACAGTTAGGGTTTTTTTCCTTGTTAATGGTGCTCCCGTTAACCTATTTCGGAT
1 AATTTCTAGCTACAATTAGGGTTTTTTTCCTTGTTAATGGTGCTCCCGTTAACCCATTTCGGAT
542332 GGAGTGTGGG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.47
Consensus pattern (69 bp):
AATTTCTAGCTACAATTAGGGTTTTTTTCCTTGTTAATGGTGCTCCCGTTAACCCATTTCGGATT
TTGA
Found at i:546706 original size:13 final size:13
Alignment explanation
Indices: 546685--546717 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
546675 AAATTATTTG
546685 ATAAATTTTTTTT
1 ATAAATTTTTTTT
*
546698 ATAAGTTTTTTTT
1 ATAAATTTTTTTT
546711 ATAAATT
1 ATAAATT
546718 ATAACTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
ATAAATTTTTTTT
Found at i:551604 original size:55 final size:56
Alignment explanation
Indices: 551531--551641 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
551521 TCAACAATAT
* *
551531 TCCTAACTAATTTA-TTTTTTTAGGCTAGGCTATGGGATTGTGGGCAATATGCTGG
1 TCCTAACTAATTTATTTTTTTTAGGCTAGGCTATGGGATTATGGGCAACATGCTGG
*
551586 TCCTAACTAATTTATTTTTTTTAGGCTAGGCTATGGGATTATGGGCACCATGCTGG
1 TCCTAACTAATTTATTTTTTTTAGGCTAGGCTATGGGATTATGGGCAACATGCTGG
551642 CTGGGCTATG
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 14 0.27
56 38 0.73
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (56 bp):
TCCTAACTAATTTATTTTTTTTAGGCTAGGCTATGGGATTATGGGCAACATGCTGG
Found at i:561971 original size:2 final size:2
Alignment explanation
Indices: 561964--561988 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
561954 CATTATGCCC
561964 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
561989 CAAATTTACA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:568981 original size:28 final size:28
Alignment explanation
Indices: 568931--568988 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
568921 CTTATGGCTG
* * * *
568931 CCCTTGACAAAGATTTGTTTTGTAAGAC
1 CCCTTGACAAAAATATCTCTTGTAAGAC
568959 CCCTTGACAAAAATATCTCTTGTAAGAC
1 CCCTTGACAAAAATATCTCTTGTAAGAC
568987 CC
1 CC
568989 TTTTAAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (28 bp):
CCCTTGACAAAAATATCTCTTGTAAGAC
Found at i:577863 original size:23 final size:21
Alignment explanation
Indices: 577820--577863 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
577810 ATAAAAATAA
*
577820 AATAGAATAATAATAGGATTT
1 AATAGAATAATAATAGAATTT
577841 AATAGCAATAGATAATAGAATTT
1 AATAG-AATA-ATAATAGAATTT
577864 TCTAATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (21 bp):
AATAGAATAATAATAGAATTT
Found at i:588842 original size:61 final size:60
Alignment explanation
Indices: 588763--588906 Score: 154
Period size: 56 Copynumber: 2.5 Consensus size: 60
588753 ACGTAAATCA
* * * *
588763 TAAAAACATCAAATCACAAGAAATGTATGTAAAAGGAAACTTAATT-ATAAAGTATTAATGG
1 TAAAAATATCAAATCACAAGAAATGTATG--AAAGCAAACCTAATTCACAAAGTATTAATGG
* * *
588824 TAAAAATATCAAATCACAA-TAA---ATGAAAGCATACCTAATTCACAAGGTATTAATGG
1 TAAAAATATCAAATCACAAGAAATGTATGAAAGCAAACCTAATTCACAAAGTATTAATGG
* *
588880 TAAAAATGTCAAATCACAAGAAGTGTA
1 TAAAAATATCAAATCACAAGAAATGTA
588907 CGGAAAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
55 12 0.18
56 31 0.46
57 4 0.06
60 3 0.04
61 18 0.26
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.25
Consensus pattern (60 bp):
TAAAAATATCAAATCACAAGAAATGTATGAAAGCAAACCTAATTCACAAAGTATTAATGG
Found at i:590810 original size:25 final size:23
Alignment explanation
Indices: 590751--590803 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
590741 TCTATATTTA
*
590751 TTTATATTAAAAAAATTTACAATT
1 TTTATATTAAAAAAATTTA-TATT
*
590775 ATTTATTATTAAAAATATTTATATT
1 -TTTA-TATTAAAAAAATTTATATT
590800 TTTA
1 TTTA
590804 ATAATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 7 0.28
26 14 0.56
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTATATTAAAAAAATTTATATT
Found at i:597759 original size:12 final size:12
Alignment explanation
Indices: 597742--597766 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
597732 TTTAATTTTA
597742 TGAATATAAATT
1 TGAATATAAATT
597754 TGAATATAAATT
1 TGAATATAAATT
597766 T
1 T
597767 ATGTGATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TGAATATAAATT
Found at i:606964 original size:29 final size:29
Alignment explanation
Indices: 606909--606964 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
606899 GAATCATACT
****
606909 TTAACTTTAGTCAATGGTTTTTGCTCAGC
1 TTAACTTTAGTCAATGGTTGCCACTCAGC
*
606938 TTAACTTTAGTCAATTGTTGCCACTCA
1 TTAACTTTAGTCAATGGTTGCCACTCA
606965 ATCAATGGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (29 bp):
TTAACTTTAGTCAATGGTTGCCACTCAGC
Found at i:612391 original size:23 final size:23
Alignment explanation
Indices: 612365--612410 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
612355 AATTTTACGA
* *
612365 ATTAAATTGATTTGATAATTAAT
1 ATTAAATTGATTTAATAACTAAT
* *
612388 ATTATATTTATTTAATAACTAAT
1 ATTAAATTGATTTAATAACTAAT
612411 TAAATATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
ATTAAATTGATTTAATAACTAAT
Found at i:614977 original size:38 final size:39
Alignment explanation
Indices: 614902--614985 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 39
614892 ATAGTTATTT
***
614902 CCTTTCATAATATAACTATTTTGTAGTTATATCTAATAA
1 CCTTTCATAATATAACTATTTAAAAGTTATATCTAATAA
*
614941 TCTTTCATAATATAACTA-TTAAAAGTTATATCTAATAA
1 CCTTTCATAATATAACTATTTAAAAGTTATATCTAATAA
614979 CCTTTCA
1 CCTTTCA
614986 ATTAAAAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 23 0.57
39 17 0.43
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (39 bp):
CCTTTCATAATATAACTATTTAAAAGTTATATCTAATAA
Found at i:618699 original size:21 final size:21
Alignment explanation
Indices: 618661--618700 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
618651 GATTTAGTTG
* *
618661 AATTAAAGTTCCATATTAATC
1 AATTAAAGTTCAAAATTAATC
*
618682 AATTAAAGTTGAAAATTAA
1 AATTAAAGTTCAAAATTAA
618701 ATTTGAATTT
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:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (21 bp):
AATTAAAGTTCAAAATTAATC
Found at i:626815 original size:2 final size:2
Alignment explanation
Indices: 626808--626834 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
626798 ACACCACATT
626808 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 T
626835 TTATGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:632425 original size:15 final size:15
Alignment explanation
Indices: 632405--632451 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
632395 AAGGGGGCAT
632405 GAGATCAGAGTAGGG
1 GAGATCAGAGTAGGG
632420 GAGATCAGAGTAGGG
1 GAGATCAGAGTAGGG
632435 GAGATCAGAGTAGGG
1 GAGATCAGAGTAGGG
632450 GA
1 GA
632452 TCTGCATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.47, T:0.13
Consensus pattern (15 bp):
GAGATCAGAGTAGGG
Found at i:633507 original size:20 final size:19
Alignment explanation
Indices: 633482--633524 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
633472 CACCCCATTA
* *
633482 ATTTTTTATTTATTTTTTAT
1 ATTTTTTATTT-TGTTTAAT
633502 A-TTTTTATTTTGTTTAAT
1 ATTTTTTATTTTGTTTAAT
633520 ATTTT
1 ATTTT
633525 AGGTTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 7 0.35
19 12 0.60
20 1 0.05
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
ATTTTTTATTTTGTTTAAT
Found at i:633521 original size:18 final size:19
Alignment explanation
Indices: 633479--633524 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
633469 CTCCACCCCA
*
633479 TTAAT-TTTTTATTTATTT
1 TTAATATTTTTATTTATGT
*
633497 TTTATATTTTTATTT-TGT
1 TTAATATTTTTATTTATGT
633515 TTAATATTTT
1 TTAATATTTT
633525 AGGTTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTAATATTTTTATTTATGT
Found at i:634732 original size:27 final size:26
Alignment explanation
Indices: 634671--634731 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
634661 TAAGTCAAAT
*
634671 AAAAAAACTAAAGAATTTACAAAGTC
1 AAAAAAATTAAAGAATTTACAAAGTC
634697 AAAAGAAATTAAAGAATTTACGAAAAGTC
1 AAAA-AAATTAAAGAATTTAC--AAAGTC
*
634726 TAAAAA
1 AAAAAA
634732 TGATATATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.13
27 15 0.50
28 2 0.07
29 9 0.30
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.20
Consensus pattern (26 bp):
AAAAAAATTAAAGAATTTACAAAGTC
Found at i:640059 original size:2 final size:2
Alignment explanation
Indices: 640052--640077 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
640042 TTTATAGTCA
640052 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
640078 TTGAATGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:642397 original size:25 final size:25
Alignment explanation
Indices: 642368--642417 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
642358 TTGAAGTTGT
642368 TTTACTAGAAAATTCAGAGTTAGGC
1 TTTACTAGAAAATTCAGAGTTAGGC
*
642393 TTTACTAGATAATTCAGAGTTAGGC
1 TTTACTAGAAAATTCAGAGTTAGGC
642418 CATTCAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (25 bp):
TTTACTAGAAAATTCAGAGTTAGGC
Found at i:661856 original size:27 final size:27
Alignment explanation
Indices: 661826--661879 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
661816 TTTGTTACAC
661826 GTGTAATATCACGGGCTTGCCCTTTTT
1 GTGTAATATCACGGGCTTGCCCTTTTT
*
661853 GTGTAATATCACGGGCTTTCCCTTTTT
1 GTGTAATATCACGGGCTTGCCCTTTTT
661880 TAAAAACTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (27 bp):
GTGTAATATCACGGGCTTGCCCTTTTT
Found at i:665285 original size:28 final size:26
Alignment explanation
Indices: 665233--665292 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
665223 TATTAATGAA
* *
665233 TAATATATTTTTATATATTTTAGTAGTT
1 TAATATATTTTAACATATTTTAGTA--T
665261 TAATATATTTTAACAT-TTTTAAGTAT
1 TAATATATTTTAACATATTTT-AGTAT
665287 TAATAT
1 TAATAT
665293 TAAATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.24
27 4 0.14
28 18 0.62
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (26 bp):
TAATATATTTTAACATATTTTAGTAT
Found at i:666168 original size:11 final size:11
Alignment explanation
Indices: 666154--666182 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
666144 TAATAAAAAC
666154 TTAAAGGTTAA
1 TTAAAGGTTAA
666165 TTAAA-GTTAA
1 TTAAAGGTTAA
666175 TTAAAGGT
1 TTAAAGGT
666183 ATCATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (11 bp):
TTAAAGGTTAA
Found at i:668193 original size:54 final size:54
Alignment explanation
Indices: 668091--668193 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
668081 CAAGAGGTTG
* * *
668091 AGATTAAGTCGTCAAGACATTTGAAGTGAAGATATTAGGCTTACTTCATAATTA
1 AGATTAAGCCGTCAAGACATTTGAAGTGAAGATATCAAGCTTACTTCATAATTA
* * * *
668145 AGATTAAGCCGTCAAGCCCTTT-AACGTGAAGATATCAAGTTTAGTTCAT
1 AGATTAAGCCGTCAAGACATTTGAA-GTGAAGATATCAAGCTTACTTCAT
668194 GATTTTTGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 2 0.05
54 39 0.95
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (54 bp):
AGATTAAGCCGTCAAGACATTTGAAGTGAAGATATCAAGCTTACTTCATAATTA
Done.