Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 19 of 230
Found at i:5241897 original size:93 final size:93
Alignment explanation
Indices: 5241738--5241924 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
5241728 TTACACAGTT
5241738 TGGGAAGTATTACTCTTTTAAATGCCATACCCAAATTGCAATCAAGAATGAGATGAATATGGGTA
1 TGGGAAGTATTACTCTTTTAAATGCCATACCCAAATTGCAATCAAGAATGAGATGAATATGGGTA
5241803 AACCTAGTTCATCATGGATTGAGTTGGG
66 AACCTAGTTCATCATGGATTGAGTTGGG
5241831 TGGGAAGTATTACTCTTTTAAATGCCATACCCAAATTGCAATCAAGAATGAGATGAATATGGGTA
1 TGGGAAGTATTACTCTTTTAAATGCCATACCCAAATTGCAATCAAGAATGAGATGAATATGGGTA
5241896 AACCTAGTTCATCATGGATTGAGTTGGG
66 AACCTAGTTCATCATGGATTGAGTTGGG
5241924 T
1 T
5241925 ATGAAATTGC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (93 bp):
TGGGAAGTATTACTCTTTTAAATGCCATACCCAAATTGCAATCAAGAATGAGATGAATATGGGTA
AACCTAGTTCATCATGGATTGAGTTGGG
Found at i:5242681 original size:14 final size:15
Alignment explanation
Indices: 5242648--5242681 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
5242638 GACTATTAAG
5242648 TTTTTCTAATAATTC
1 TTTTTCTAATAATTC
5242663 TTTTTCTAATAATTC
1 TTTTTCTAATAATTC
5242678 TTTT
1 TTTT
5242682 ATTTGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTCTAATAATTC
Found at i:5248864 original size:6 final size:6
Alignment explanation
Indices: 5248855--5248921 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
5248845 AGAGAGGTAT
* * * *
5248855 GAAGTA GAAGGA GAAGGA GAAGGA GAGGGA GAATAAGA TGAAGGG GAAGGA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA G-A-AGGA -GAAGGA GAAGGA
* *
5248906 GAAGGG GAAGGG GAAG
1 GAAGGA GAAGGA GAAG
5248922 AAGAGGATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
6 43 0.86
7 3 0.06
8 3 0.06
9 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.51, T:0.04
Consensus pattern (6 bp):
GAAGGA
Found at i:5248936 original size:33 final size:33
Alignment explanation
Indices: 5248867--5248936 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
5248857 AGTAGAAGGA
* * *
5248867 GAAGGAGAAGGAGAGGGAGAATAAGATGAAGGG
1 GAAGGAGAAGGAGAGGGAGAAGAAGAGGAAGAG
* *
5248900 GAAGGAGAAGGGGAAGGG-GAAGAAGAGGATGAG
1 GAAGGAGAAGGAG-AGGGAGAAGAAGAGGAAGAG
5248933 GAAG
1 GAAG
5248937 AAGCACTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 27 0.87
34 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.51, T:0.04
Consensus pattern (33 bp):
GAAGGAGAAGGAGAGGGAGAAGAAGAGGAAGAG
Found at i:5261574 original size:34 final size:34
Alignment explanation
Indices: 5261534--5261602 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5261524 AGGATTTATG
5261534 TATGTTGATGGCATGAGTTAAAATATTATTATTT
1 TATGTTGATGGCATGAGTTAAAATATTATTATTT
5261568 TATGTTGATGGCATGAGTTAAAATATTATTATTT
1 TATGTTGATGGCATGAGTTAAAATATTATTATTT
5261602 T
1 T
5261603 TAATTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (34 bp):
TATGTTGATGGCATGAGTTAAAATATTATTATTT
Found at i:5262635 original size:16 final size:16
Alignment explanation
Indices: 5262616--5262653 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5262606 TTGGTATCTA
5262616 AATTTGACATTTTTTT
1 AATTTGACATTTTTTT
**
5262632 AATTTGATTTTTTTTT
1 AATTTGACATTTTTTT
5262648 AATTTG
1 AATTTG
5262654 GTACCTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.66
Consensus pattern (16 bp):
AATTTGACATTTTTTT
Found at i:5264843 original size:26 final size:26
Alignment explanation
Indices: 5264791--5264843 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
5264781 GTGTTGAAAT
**
5264791 GGAATAAAAAGATTTATAAAAAAAAA
1 GGAATAAAAAGATAAATAAAAAAAAA
*
5264817 GGAATAAAAAGA-AAATAATAAATAAA
1 GGAATAAAAAGATAAATAA-AAAAAAA
5264843 G
1 G
5264844 AGGGTTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (26 bp):
GGAATAAAAAGATAAATAAAAAAAAA
Found at i:5265394 original size:57 final size:57
Alignment explanation
Indices: 5265323--5265430 Score: 189
Period size: 57 Copynumber: 1.9 Consensus size: 57
5265313 TGGGTAGTTT
5265323 TATACGAGTATTTTGTCGATTGAGTGTTAGCTTGAATGATAATGATATTGTAGCTAG
1 TATACGAGTATTTTGTCGATTGAGTGTTAGCTTGAATGATAATGATATTGTAGCTAG
* * *
5265380 TATACGAGTGTTTTGTCGATTGAGTGTTGGCTTGATTGATAATGATATTGT
1 TATACGAGTATTTTGTCGATTGAGTGTTAGCTTGAATGATAATGATATTGT
5265431 TGTTAGTGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.25, C:0.06, G:0.26, T:0.43
Consensus pattern (57 bp):
TATACGAGTATTTTGTCGATTGAGTGTTAGCTTGAATGATAATGATATTGTAGCTAG
Found at i:5271418 original size:33 final size:33
Alignment explanation
Indices: 5271371--5271438 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
5271361 GGTGGTTGAC
* * *
5271371 GAGAGGGTCGAGAGTGTGTATTGTCGAGAGTGA
1 GAGAGGGTCAAGAGTGTGGATTGTCAAGAGTGA
5271404 GAGAGGGTCAAGAGTGTGGATTGTCAAGAGTGA
1 GAGAGGGTCAAGAGTGTGGATTGTCAAGAGTGA
5271437 GA
1 GA
5271439 TATGGTGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.06, G:0.44, T:0.22
Consensus pattern (33 bp):
GAGAGGGTCAAGAGTGTGGATTGTCAAGAGTGA
Found at i:5271431 original size:16 final size:16
Alignment explanation
Indices: 5271381--5271435 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
5271371 GAGAGGGTCG
* *
5271381 AGAGTGTGTATTGTCG
1 AGAGTGTGGATTGTCA
* **
5271397 AGAGTGAGAGAGGGTCA
1 AGAGTGTG-GATTGTCA
5271414 AGAGTGTGGATTGTCA
1 AGAGTGTGGATTGTCA
5271430 AGAGTG
1 AGAGTG
5271436 AGATATGGTG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 19 0.63
17 11 0.37
ACGTcount: A:0.27, C:0.05, G:0.42, T:0.25
Consensus pattern (16 bp):
AGAGTGTGGATTGTCA
Found at i:5277730 original size:29 final size:29
Alignment explanation
Indices: 5277693--5277756 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
5277683 AATGGGATAT
5277693 TACA-GATTGTATGGTGAACTCTTCAAAG
1 TACATGATTGTATGGTGAACTCTTCAAAG
*
5277721 TACATGATTGTATGGTGAACTCTTCATAG
1 TACATGATTGTATGGTGAACTCTTCAAAG
5277750 TACATGA
1 TACATGA
5277757 AACTATGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (29 bp):
TACATGATTGTATGGTGAACTCTTCAAAG
Found at i:5277763 original size:29 final size:29
Alignment explanation
Indices: 5277702--5277763 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
5277692 TTACAGATTG
***
5277702 TATGGTGAACTCTTCAAAGTACATGATTG
1 TATGGTGAACTCTTCAAAGTACATGAAAC
*
5277731 TATGGTGAACTCTTCATAGTACATGAAAC
1 TATGGTGAACTCTTCAAAGTACATGAAAC
5277760 TATG
1 TATG
5277764 CATGTATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (29 bp):
TATGGTGAACTCTTCAAAGTACATGAAAC
Found at i:5285959 original size:21 final size:21
Alignment explanation
Indices: 5285935--5286167 Score: 71
Period size: 21 Copynumber: 11.1 Consensus size: 21
5285925 TAGAAGGTTG
*
5285935 AACAGAAGCACATAAGTGCTA
1 AACAGAAGCACATAAGAGCTA
* * * *
5285956 AACAGAAACCCATAAGGGTTA
1 AACAGAAGCACATAAGAGCTA
* **
5285977 AACGGAAGCTTATAAGAGCTA
1 AACAGAAGCACATAAGAGCTA
* * * *
5285998 AAC-GAAAACCCAAAAG-GATTA
1 AACAG-AAGCACATAAGAG-CTA
* ** * *
5286019 AACAAAAGTTCAAAAGAGCTG
1 AACAGAAGCACATAAGAGCTA
* * * *
5286040 AAC-GAAAACCCATAAGGGTTA
1 AACAG-AAGCACATAAGAGCTA
* *
5286061 AACAGAAGCTCAAAAGAGCTA
1 AACAGAAGCACATAAGAGCTA
* * * *
5286082 AAC-GAAAACCCATAAGGGTTA
1 AACAG-AAGCACATAAGAGCTA
* *
5286103 AACAGAAGCTCA-AAAAGCTA
1 AACAGAAGCACATAAGAGCTA
* * * * *
5286123 AACGGAAACTCATATGAGTTA
1 AACAGAAGCACATAAGAGCTA
* *
5286144 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCACATAAGAGCTA
5286165 AAC
1 AAC
5286168 GAAAAGTAAA
Statistics
Matches: 149, Mismatches: 54, Indels: 18
0.67 0.24 0.08
Matches are distributed among these distances:
20 18 0.12
21 128 0.86
22 3 0.02
ACGTcount: A:0.49, C:0.18, G:0.19, T:0.14
Consensus pattern (21 bp):
AACAGAAGCACATAAGAGCTA
Found at i:5285998 original size:42 final size:42
Alignment explanation
Indices: 5285930--5286172 Score: 301
Period size: 42 Copynumber: 5.8 Consensus size: 42
5285920 AAAGCTAGAA
* * *
5285930 GGTTGAACAGAAGCACATAAGTGCTAAAC-AGAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACGA-AAACCCATAAG
* * *
5285972 GGTTAAACGGAAGCTTATAAGAGCTAAACGAAAACCCAAAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACGAAAACCCATAAG
* * * * *
5286014 GATTAAACAAAAGTTCAAAAGAGCTGAACGAAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACGAAAACCCATAAG
*
5286056 GGTTAAACAGAAGCTCAAAAGAGCTAAACGAAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACGAAAACCCATAAG
* * * *
5286098 GGTTAAACAGAAGCTCA-AAAAGCTAAACGGAAACTCATATG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACGAAAACCCATAAG
* *
5286139 AGTTAAACAGAAGCTCATGAGAGCTAAACGAAAA
1 GGTTAAACAGAAGCTCATAAGAGCTAAACGAAAA
5286173 GTAAACAAAA
Statistics
Matches: 173, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
41 36 0.21
42 136 0.79
43 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.14
Consensus pattern (42 bp):
GGTTAAACAGAAGCTCATAAGAGCTAAACGAAAACCCATAAG
Found at i:5295356 original size:37 final size:37
Alignment explanation
Indices: 5295315--5295523 Score: 177
Period size: 37 Copynumber: 5.6 Consensus size: 37
5295305 TTTTGGGACA
* *
5295315 TTAGCGCGTTTTGAAAAGCGCCACTAATGCTCAGAGT
1 TTAGCGCGTTTTAAAAAGCGCCGCTAATGCTCAGAGT
5295352 TTAGCAGCG-TTTAAAAAGCGCCGCTAATGCTCA-AGCT
1 TTAGC-GCGTTTTAAAAAGCGCCGCTAATGCTCAGAG-T
* ** * *
5295389 TTATTG-GCGTTTAAAAAAAATGTCGCTAATGC-CAGAGC
1 TTA--GCGCGTTT-TAAAAAGCGCCGCTAATGCTCAGAGT
*
5295427 TTAGCGCGATTTAAAAAAG-GCCGCTAATGC-CA-AGCT
1 TTAGCGCG-TTTTAAAAAGCGCCGCTAATGCTCAGAG-T
5295463 TTAGCGGCGTTTTTAAAAAGCG-CGCTAATGCTCAGAGT
1 TTAGC-GCG-TTTTAAAAAGCGCCGCTAATGCTCAGAGT
*
5295501 TTA-C-CATTTTTAAAAAGCGCCGC
1 TTAGCGC-GTTTTAAAAAGCGCCGC
5295524 AAAATATTAT
Statistics
Matches: 143, Mismatches: 13, Indels: 33
0.76 0.07 0.17
Matches are distributed among these distances:
35 15 0.10
36 23 0.16
37 65 0.45
38 20 0.14
39 20 0.14
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (37 bp):
TTAGCGCGTTTTAAAAAGCGCCGCTAATGCTCAGAGT
Found at i:5295481 original size:75 final size:76
Alignment explanation
Indices: 5295338--5295523 Score: 213
Period size: 74 Copynumber: 2.5 Consensus size: 76
5295328 AAAAGCGCCA
* **
5295338 CTAATGCTCAGAGTTTAGCAGCGTTTAAAAAGCGCCGCTAATGCTCAAGCTTTATTGGCGTTTAA
1 CTAATGCTCAGAGCTTAGCAGCGTTTAAAAAGCGCCGCTAATGCTCAAGCTTTAGCGGCGTTTAA
5295403 AAAAAATGTCG
66 AAAAAATGTCG
5295414 CTAATGC-CAGAGCTTAGC-GCGATTTAAAAAAG-GCCGCTAATGC-CAAGCTTTAGCGGCGTTT
1 CTAATGCTCAGAGCTTAGCAGCG-TTT-AAAAAGCGCCGCTAATGCTCAAGCTTTAGCGGCGTTT
** **
5295475 TTAAAAAGCG-CG
64 AAAAAAAATGTCG
* * **
5295487 CTAATGCTCAGAGTTTACCA-TTTTTAAAAAGCGCCGC
1 CTAATGCTCAGAGCTTAGCAGCGTTTAAAAAGCGCCGC
5295524 AAAATATTAT
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
72 6 0.06
73 17 0.18
74 34 0.36
75 24 0.26
76 13 0.14
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (76 bp):
CTAATGCTCAGAGCTTAGCAGCGTTTAAAAAGCGCCGCTAATGCTCAAGCTTTAGCGGCGTTTAA
AAAAAATGTCG
Found at i:5296116 original size:13 final size:13
Alignment explanation
Indices: 5296085--5296122 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5296075 GTTTAGGTTA
5296085 AGGGTTAGAGATTT
1 AGGGTTA-AGATTT
5296099 A-GGTTAAGATTT
1 AGGGTTAAGATTT
*
5296111 AGGGTTTAGATT
1 AGGGTTAAGATT
5296123 AATTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 14 0.64
14 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (13 bp):
AGGGTTAAGATTT
Found at i:5296126 original size:79 final size:81
Alignment explanation
Indices: 5296030--5296202 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 81
5296020 TCGGTGTGGC
* * **
5296030 TTAGGGTTTAAATTAATTAGTGTGTTTTAA-TCTATATTAAATAAGGTTTA-GGTTAAGGGTTAG
1 TTAGGGTTTAAATTAATTAAT-T-TTTTAATTATATATTAAATAAACTTTAGGGTTAAGGGTTAG
*
5296093 AGATTTAG-GTTA-AGAT
64 AGATTAAGAGTTAGAGAT
* *
5296109 TTAGGGTTTAGATTAATTAATTTTTTAATTATATATTAAATAAACTTTAGGGGTTAGGGGTTAGA
1 TTAGGGTTTAAATTAATTAATTTTTTAATTATATATTAAATAAACTTTA-GGGTTAAGGGTTAGA
* *
5296174 GGTTAAGAGTTAGTGAT
65 GATTAAGAGTTAGAGAT
5296191 TTAGGGTTTAAA
1 TTAGGGTTTAAA
5296203 GATTCGGAGT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
77 6 0.08
78 18 0.23
79 19 0.24
80 18 0.23
81 4 0.05
82 14 0.18
ACGTcount: A:0.33, C:0.01, G:0.23, T:0.43
Consensus pattern (81 bp):
TTAGGGTTTAAATTAATTAATTTTTTAATTATATATTAAATAAACTTTAGGGTTAAGGGTTAGAG
ATTAAGAGTTAGAGAT
Found at i:5310132 original size:33 final size:33
Alignment explanation
Indices: 5310085--5310152 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
5310075 GGTGGTTGAC
* * *
5310085 GAGAGGGTCGAGAGTGTGTATTGTCGAGAGTGA
1 GAGAGGGTCAAGAGTGTGGATTGTCAAGAGTGA
5310118 GAGAGGGTCAAGAGTGTGGATTGTCAAGAGTGA
1 GAGAGGGTCAAGAGTGTGGATTGTCAAGAGTGA
5310151 GA
1 GA
5310153 TATGGTGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.06, G:0.44, T:0.22
Consensus pattern (33 bp):
GAGAGGGTCAAGAGTGTGGATTGTCAAGAGTGA
Found at i:5310145 original size:16 final size:16
Alignment explanation
Indices: 5310095--5310149 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
5310085 GAGAGGGTCG
* *
5310095 AGAGTGTGTATTGTCG
1 AGAGTGTGGATTGTCA
* **
5310111 AGAGTGAGAGAGGGTCA
1 AGAGTGTG-GATTGTCA
5310128 AGAGTGTGGATTGTCA
1 AGAGTGTGGATTGTCA
5310144 AGAGTG
1 AGAGTG
5310150 AGATATGGTG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 19 0.63
17 11 0.37
ACGTcount: A:0.27, C:0.05, G:0.42, T:0.25
Consensus pattern (16 bp):
AGAGTGTGGATTGTCA
Found at i:5316439 original size:29 final size:29
Alignment explanation
Indices: 5316402--5316465 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
5316392 AATGGGATAT
5316402 TACA-GATTGTATGGTGAACTCTTCAAAG
1 TACATGATTGTATGGTGAACTCTTCAAAG
*
5316430 TACATGATTGTATGGTGAACTCTTCATAG
1 TACATGATTGTATGGTGAACTCTTCAAAG
5316459 TACATGA
1 TACATGA
5316466 AACTATGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (29 bp):
TACATGATTGTATGGTGAACTCTTCAAAG
Found at i:5316472 original size:29 final size:29
Alignment explanation
Indices: 5316411--5316472 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
5316401 TTACAGATTG
***
5316411 TATGGTGAACTCTTCAAAGTACATGATTG
1 TATGGTGAACTCTTCAAAGTACATGAAAC
*
5316440 TATGGTGAACTCTTCATAGTACATGAAAC
1 TATGGTGAACTCTTCAAAGTACATGAAAC
5316469 TATG
1 TATG
5316473 CATGTATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (29 bp):
TATGGTGAACTCTTCAAAGTACATGAAAC
Found at i:5324671 original size:41 final size:41
Alignment explanation
Indices: 5324604--5324831 Score: 223
Period size: 41 Copynumber: 5.6 Consensus size: 41
5324594 GAAGGTTGCA
* *
5324604 GAAGCACATAAGTGCTAAAC-AGAAACCCATAAGGGTTAAAC
1 GAAGCTCATAAGAGCTAAACGA-AAACCCATAAGGGTTAAAC
* * * * *
5324645 GGAGCTTATAAGAGCTAAACGAAAACCCAAAAGGATTAAAA
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAAC
* * *
5324686 AAAGTTCA-AA-AGCTGAACGAAAACCCATAAGGGTTAAAC
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAAC
*
5324725 AGAAGCTCAAAAGAGCTAAACGAAAA-CCATAAGGGTTAAAC
1 -GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAAC
* * * * * * *
5324766 AAAGCTCAAAAAAGCTAAACGGAAACTCAT-ATGATTAAAC
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAAC
*
5324806 AGAAGCTCATGAGAGCTAAACGAAAA
1 -GAAGCTCATAAGAGCTAAACGAAAA
5324832 GTAAACAAAA
Statistics
Matches: 152, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
39 25 0.16
40 38 0.25
41 76 0.50
42 13 0.09
ACGTcount: A:0.50, C:0.17, G:0.18, T:0.14
Consensus pattern (41 bp):
GAAGCTCATAAGAGCTAAACGAAAACCCATAAGGGTTAAAC
Found at i:5324784 original size:20 final size:20
Alignment explanation
Indices: 5324720--5324785 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
5324710 CCATAAGGGT
5324720 TAAACAGAAGCTCAAAAGAGC
1 TAAACA-AAGCTCAAAAGAGC
* * * *
5324741 TAAACGAAAAC-CATAAGGGT
1 TAAAC-AAAGCTCAAAAGAGC
*
5324761 TAAACAAAGCTCAAAAAAGC
1 TAAACAAAGCTCAAAAGAGC
5324781 TAAAC
1 TAAAC
5324786 GGAAACTCAT
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
19 4 0.12
20 21 0.62
21 8 0.24
22 1 0.03
ACGTcount: A:0.55, C:0.18, G:0.15, T:0.12
Consensus pattern (20 bp):
TAAACAAAGCTCAAAAGAGC
Found at i:5324804 original size:81 final size:81
Alignment explanation
Indices: 5324617--5324831 Score: 240
Period size: 81 Copynumber: 2.7 Consensus size: 81
5324607 GCACATAAGT
* * * *
5324617 GCTAAAC-AGAAACCCATAAGGGTTAAAC-GGAGCTTATAAGAGCTAAACGAAAACCCAAAAGGA
1 GCTAAACGA-AAACCCATAAGGATTAAACAGAAGCTCAAAAGAGCTAAACGAAAACCCAAAAGGA
*
5324680 TTAAAAAAAGTTCAAAA
65 TTAAAAAAAGCTCAAAA
* * * *
5324697 GCTGAACGAAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACGAAAA-CCATAAGGGT
1 GCTAAACGAAAACCCATAAGGATTAAACAGAAGCTCAAAAGAGCTAAACGAAAACCCAAAAGGAT
*
5324761 TAAACAAAGCTCAAAAAA
66 TAAAAAAAGCTC--AAAA
* * * **
5324779 GCTAAACGGAAACTCAT-ATGATTAAACAGAAGCTCATGAGAGCTAAACGAAAA
1 GCTAAACGAAAACCCATAAGGATTAAACAGAAGCTCAAAAGAGCTAAACGAAAA
5324832 GTAAACAAAA
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
80 43 0.37
81 55 0.47
82 18 0.16
ACGTcount: A:0.50, C:0.17, G:0.18, T:0.14
Consensus pattern (81 bp):
GCTAAACGAAAACCCATAAGGATTAAACAGAAGCTCAAAAGAGCTAAACGAAAACCCAAAAGGAT
TAAAAAAAGCTCAAAA
Found at i:5334083 original size:41 final size:41
Alignment explanation
Indices: 5334038--5334269 Score: 297
Period size: 41 Copynumber: 5.7 Consensus size: 41
5334028 TTTTGGGACA
* *
5334038 TTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCAGAGCT
1 TTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGAGCT
*
5334079 TTAGCAGCGTTTTTAAAAAAGCGCCGCTAATGCTCA-AGCTT
1 TTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGAGC-T
** * ** *
5334120 TTATTGGCGTTTTAAAAAAAATGTCGCTAATGCTCAGAGCT
1 TTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGAGCT
* *
5334161 TTAGCGGCGATTTTAAAAAAGAGCCGCTAATGCTCA-AGCTT
1 TTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGAGC-T
* * *
5334202 TTAGCGGCGTTTTTAGAAAAGCGCTGCTAATGCTCAGAGAT
1 TTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGAGCT
*
5334243 TTAGCGGCATTTTTAAAAAAGCGCCGC
1 TTAGCGGCGTTTTTAAAAAAGCGCCGC
5334270 AAAAATATTT
Statistics
Matches: 162, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
40 6 0.04
41 151 0.93
42 5 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (41 bp):
TTAGCGGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGAGCT
Found at i:5334608 original size:14 final size:15
Alignment explanation
Indices: 5334589--5334622 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
5334579 TATAGTTTAG
5334589 GGTTTAATA-TATAT
1 GGTTTAATAGTATAT
5334603 GGTTT-ATAGTATAT
1 GGTTTAATAGTATAT
5334617 GGTTTA
1 GGTTTA
5334623 GGGTATATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (15 bp):
GGTTTAATAGTATAT
Found at i:5334628 original size:14 final size:14
Alignment explanation
Indices: 5334598--5334634 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5334588 GGGTTTAATA
*
5334598 TATATGGTTTATAG
1 TATATGGTTTAGAG
*
5334612 TATATGGTTTAGGG
1 TATATGGTTTAGAG
5334626 TATATGGTT
1 TATATGGTT
5334635 AATTTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (14 bp):
TATATGGTTTAGAG
Found at i:5334888 original size:13 final size:13
Alignment explanation
Indices: 5334857--5334894 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5334847 TTAGGGGTTA
5334857 AGGGTTAGAGATTT
1 AGGGTTA-AGATTT
5334871 A-GGTTAAGATTT
1 AGGGTTAAGATTT
*
5334883 AGGGTTTAGATT
1 AGGGTTAAGATT
5334895 AATTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 14 0.64
14 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (13 bp):
AGGGTTAAGATTT
Found at i:5334899 original size:81 final size:83
Alignment explanation
Indices: 5334800--5334975 Score: 232
Period size: 81 Copynumber: 2.1 Consensus size: 83
5334790 TCGGTGTGGC
* * **
5334800 TTAGGGTTTAAATTAATTAGTGTGTTTTAA-TCTATATTAAATAAGGTTTAGGGGTTAAGGGTTA
1 TTAGGGTTTAAATTAATTAAT-TGTTTTAATTATATATTAAATAAACTTTAGGGGTTAAGGGTTA
*
5334864 GAGATTTAG-GTTA-AGAT
65 GAGATTAAGAGTTAGAGAT
* * *
5334881 TTAGGGTTTAGATTAATTAATTTTTTTAATTATATATTAAATAAACTTTAGGGGTTAGGGGTTAG
1 TTAGGGTTTAAATTAATTAATTGTTTTAATTATATATTAAATAAACTTTAGGGGTTAAGGGTTAG
* *
5334946 AGGTTAAGAGTTAGTGAT
66 AGATTAAGAGTTAGAGAT
5334964 TTAGGGTTTAAA
1 TTAGGGTTTAAA
5334976 GATTCGGAGT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
80 7 0.09
81 56 0.69
82 4 0.05
83 14 0.17
ACGTcount: A:0.32, C:0.01, G:0.24, T:0.43
Consensus pattern (83 bp):
TTAGGGTTTAAATTAATTAATTGTTTTAATTATATATTAAATAAACTTTAGGGGTTAAGGGTTAG
AGATTAAGAGTTAGAGAT
Found at i:5336921 original size:13 final size:13
Alignment explanation
Indices: 5336903--5336928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5336893 TTATAAAATT
5336903 TTTACATTTTACA
1 TTTACATTTTACA
5336916 TTTACATTTTACA
1 TTTACATTTTACA
5336929 AAGCTCTAGC
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:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTACATTTTACA
Found at i:5338000 original size:41 final size:41
Alignment explanation
Indices: 5337955--5338045 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
5337945 ACCGGCACTT
*
5337955 AGCCTGCTAGACATATAGTCTGAAATATTTCACCAGCATTA
1 AGCCTGCTAGACATATAGTCTGAAATATTTCACCAGCAATA
* * * *
5337996 AGCCTGCTAGACATTTAGTCTGAAGTGTTTCACCGGCAATA
1 AGCCTGCTAGACATATAGTCTGAAATATTTCACCAGCAATA
5338037 AGCCTGCTA
1 AGCCTGCTA
5338046 AGCGCTAAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACATATAGTCTGAAATATTTCACCAGCAATA
Found at i:5345520 original size:41 final size:40
Alignment explanation
Indices: 5345475--5345576 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 40
5345465 TGATTCAGTA
5345475 CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCA-TTAGCCTGCTAGACATATAGTCTGAAATATTT
* * *
5345516 CACCGGCATTAAGCCTGCTAGACATTTAGTCTGAAGTGTTT
1 CACCGGCATT-AGCCTGCTAGACATATAGTCTGAAATATTT
*
5345557 CACCGGCAATAAGCCTGCTA
1 CACCGGC-ATTAGCCTGCTA
5345577 AGCGCTAAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
40 2 0.04
41 51 0.93
42 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
CACCGGCATTAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:5345591 original size:41 final size:41
Alignment explanation
Indices: 5345475--5345591 Score: 112
Period size: 41 Copynumber: 2.9 Consensus size: 41
5345465 TGATTCAGTA
* * * * *
5345475 CACCGGCACTTAGCCTGCTAGACA-TATAGTCTGAAATATTT
1 CACCGGCAATAAGCCTGCTAGACACTA-AGCCTGAAGTGTTT
* * * *
5345516 CACCGGCATTAAGCCTGCTAGACATTTAGTCTGAAGTGTTT
1 CACCGGCAATAAGCCTGCTAGACACTAAGCCTGAAGTGTTT
*
5345557 CACCGGCAATAAGCCTGCTA-AGCGCTAAGCCTGAA
1 CACCGGCAATAAGCCTGCTAGA-CACTAAGCCTGAA
5345592 AATCTCAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 1 0.02
41 62 0.97
42 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (41 bp):
CACCGGCAATAAGCCTGCTAGACACTAAGCCTGAAGTGTTT
Found at i:5347172 original size:13 final size:13
Alignment explanation
Indices: 5347154--5347178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5347144 CAATCAAATG
5347154 CACACAAAATAAA
1 CACACAAAATAAA
5347167 CACACAAAATAA
1 CACACAAAATAA
5347179 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:5347730 original size:36 final size:36
Alignment explanation
Indices: 5347673--5347742 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
5347663 GAGATTAGTC
* *
5347673 GATTTCTTGTGAGAAGATAGGAGATTGAGTTTGGCA
1 GATTACTTGTGAGAAGATAGGAGATTAAGTTTGGCA
* *
5347709 GATTACTTGTTAGAAGTTAGGAGATTAAGTTTGG
1 GATTACTTGTGAGAAGATAGGAGATTAAGTTTGG
5347743 ATAAAATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (36 bp):
GATTACTTGTGAGAAGATAGGAGATTAAGTTTGGCA
Found at i:5349394 original size:47 final size:47
Alignment explanation
Indices: 5349310--5349399 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 47
5349300 ATAATTTTTT
* * *
5349310 TAAAGGTTATGTTTTTAGCGGTGTTTTTGTGAGAAGCGTCGCTAAGC
1 TAAAGGTTATGTTTTTAGCGGCGTTTGTGTGAAAAGCGTCGCTAAGC
5349357 TAAAGGTT-TGTTCTTTAGCGGCGTTTGTGAT-AAAAGCGTCGCT
1 TAAAGGTTATGTT-TTTAGCGGCGTTTGTG-TGAAAAGCGTCGCT
5349400 GAAGGTCATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
46 4 0.11
47 33 0.87
48 1 0.03
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (47 bp):
TAAAGGTTATGTTTTTAGCGGCGTTTGTGTGAAAAGCGTCGCTAAGC
Found at i:5349469 original size:43 final size:41
Alignment explanation
Indices: 5349422--5349653 Score: 181
Period size: 43 Copynumber: 5.6 Consensus size: 41
5349412 TTTTCACGGT
* *
5349422 GTTTGTGGGAAAAGCGTCACTAAAGGTCGTAGTCTATAGCTAC
1 GTTTGTGGGAAAAGCGCCGCTAAAGGTCGT-GTCTATAGC-AC
* * * *
5349465 GTTTGTGGTAAAAGTGCCGCTAAAGGTCGTGTTTTAGAGCAGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGGTCGTG-TCTATAGCA-C
* *
5349508 GTTTGTGGGAAAAGCGCCGCTAAAGGTTGTGGTCTATAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGGTCGT-GTCTATAGC-AC
* *
5349551 GTTTGT-GG---A---CCGCTAAAGGTCGTGGTCCATAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGGTCGT-GTCTATAGC-AC
* * * *
5349587 GTTTGTGGGAAAAGTGCTGCTAAAGGTCATGGTCTATAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGGTCGT-GTCTATAGC-AC
* *
5349630 GTTTTTGAGAAAAGCGCCGCTAAA
1 GTTTGTGGGAAAAGCGCCGCTAAA
5349654 CGCTAAAGAT
Statistics
Matches: 157, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
36 31 0.20
37 2 0.01
39 1 0.01
40 1 0.01
42 4 0.03
43 117 0.75
44 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (41 bp):
GTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGTCTATAGCAC
Found at i:5349492 original size:86 final size:86
Alignment explanation
Indices: 5349372--5349653 Score: 222
Period size: 86 Copynumber: 3.4 Consensus size: 86
5349362 GTTTGTTCTT
* * * * * * *
5349372 TAGCGGCGTTTGTGATAAAAGCGTCGCTGAAGGTCATGATTTTTCA-CGGTGTTTGTGGGAAAAG
1 TAGCGACGTTTGTGGTAAAAGCGCCGCTAAAGGTCATG-TTTTACAGCAGCGTTTGTGGGAAAAG
*
5349436 CGTCACTAAAGGTCGTAGTCTA
65 CGCCACTAAAGGTCGTAGTCTA
* * * *
5349458 TAGCTACGTTTGTGGTAAAAGTGCCGCTAAAGGTCGTGTTTTAGAGCAGCGTTTGTGGGAAAAGC
1 TAGCGACGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGTTTTACAGCAGCGTTTGTGGGAAAAGC
* * *
5349523 GCCGCTAAAGGTTGTGGTCTA
66 GCCACTAAAGGTCGTAGTCTA
* * * ** * * *
5349544 TAGCGGCGTTTGTGG----A---CCGCTAAAGGTCGTGGTCCATAGCGGCGTTTGTGGGAAAAGT
1 TAGCGACGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGTTTTACAGCAGCGTTTGTGGGAAAAGC
** * *
5349602 GCTGCTAAAGGTCATGGTCTA
66 GCCACTAAAGGTCGTAGTCTA
* *
5349623 TAGCGGCGTTTTTGAG-AAAAGCGCCGCTAAA
1 TAGCGACGTTTGTG-GTAAAAGCGCCGCTAAA
5349654 CGCTAAAGAT
Statistics
Matches: 161, Mismatches: 27, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
79 67 0.42
80 1 0.01
82 1 0.01
83 1 0.01
85 5 0.03
86 86 0.53
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.28
Consensus pattern (86 bp):
TAGCGACGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGTTTTACAGCAGCGTTTGTGGGAAAAGC
GCCACTAAAGGTCGTAGTCTA
Found at i:5349576 original size:36 final size:36
Alignment explanation
Indices: 5349524--5349594 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
5349514 GGGAAAAGCG
* *
5349524 CCGCTAAAGGTTGTGGTCTATAGCGGCGTTTGTGGA
1 CCGCTAAAGGTCGTGGTCCATAGCGGCGTTTGTGGA
5349560 CCGCTAAAGGTCGTGGTCCATAGCGGCGTTTGTGG
1 CCGCTAAAGGTCGTGGTCCATAGCGGCGTTTGTGG
5349595 GAAAAGTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.15, C:0.20, G:0.37, T:0.28
Consensus pattern (36 bp):
CCGCTAAAGGTCGTGGTCCATAGCGGCGTTTGTGGA
Found at i:5349612 original size:79 final size:79
Alignment explanation
Indices: 5349481--5349633 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 79
5349471 GGTAAAAGTG
* ** **
5349481 CCGCTAAAGGTCGTGTTTTAGAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTGTGGTCTATA
1 CCGCTAAAGGTCGTGGTCCAGAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTATA
5349546 GCGGCGTTTGTGGA
66 GCGGCGTTTGTGGA
* * * *
5349560 CCGCTAAAGGTCGTGGTCCATAGCGGCGTTTGTGGGAAAAGTGCTGCTAAAGGTCATGGTCTATA
1 CCGCTAAAGGTCGTGGTCCAGAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTATA
5349625 GCGGCGTTT
66 GCGGCGTTT
5349634 TTGAGAAAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (79 bp):
CCGCTAAAGGTCGTGGTCCAGAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTATA
GCGGCGTTTGTGGA
Found at i:5354684 original size:19 final size:19
Alignment explanation
Indices: 5354660--5354705 Score: 71
Period size: 16 Copynumber: 2.6 Consensus size: 19
5354650 GTTCCAAGTC
5354660 AGAGATTTTGCAGATCTGA
1 AGAGATTTTGCAGATCTGA
5354679 AGAGA--TT-CAGATCTGA
1 AGAGATTTTGCAGATCTGA
5354695 AGAGATTTTGC
1 AGAGATTTTGC
5354706 TTCGGTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 14 0.58
17 2 0.08
18 2 0.08
19 6 0.25
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (19 bp):
AGAGATTTTGCAGATCTGA
Found at i:5362601 original size:6 final size:6
Alignment explanation
Indices: 5362590--5362620 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5362580 GCCCTTGTGC
5362590 ATACTG ATACTG ATACTG ATACTG ATACTG A
1 ATACTG ATACTG ATACTG ATACTG ATACTG A
5362621 ATTGGGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
ATACTG
Found at i:5363412 original size:37 final size:37
Alignment explanation
Indices: 5363371--5363447 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
5363361 CGGTTTGTAT
* *
5363371 AGACACGTTGTCTGCGTCTTGATAGTATTGTAAGAGG
1 AGACACATTGTCTGCGTCTTGATAGCATTGTAAGAGG
*
5363408 AGACACATTGTCTGCGTCTTGATAGCATTGTTAGAGG
1 AGACACATTGTCTGCGTCTTGATAGCATTGTAAGAGG
5363445 AGA
1 AGA
5363448 TGCATTATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (37 bp):
AGACACATTGTCTGCGTCTTGATAGCATTGTAAGAGG
Found at i:5364945 original size:71 final size:70
Alignment explanation
Indices: 5364796--5364930 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 70
5364786 GAATTATGGG
* * **
5364796 ACCACACGCCCGTGTGGCCCACACACTCAGATTGGCCTTGCCCGTGTGGATCACACGGCCTGGCC
1 ACCACACGCCCGTGTGGCCCACACACTCAGATTGGCCTAGCCCGTATGGATCACACGGCCACGCC
5364861 CAAAA
66 CAAAA
* * *
5364866 ACTCACACGCCCGTGTGGCCCACACGC-CTGACTTGGCCTAGCCCGTATGGCTCACACGGCCACG
1 AC-CACACGCCCGTGTGGCCCACACACTCAGA-TTGGCCTAGCCCGTATGGATCACACGGCCACG
5364930 C
64 C
5364931 TTCGGCCACC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
70 5 0.09
71 51 0.91
ACGTcount: A:0.19, C:0.41, G:0.24, T:0.16
Consensus pattern (70 bp):
ACCACACGCCCGTGTGGCCCACACACTCAGATTGGCCTAGCCCGTATGGATCACACGGCCACGCC
CAAAA
Found at i:5370273 original size:11 final size:11
Alignment explanation
Indices: 5370257--5370318 Score: 74
Period size: 11 Copynumber: 5.7 Consensus size: 11
5370247 TTTAATCACT
5370257 TTAATATTAAA
1 TTAATATTAAA
5370268 TTAATA-TAATA
1 TTAATATTAA-A
* *
5370279 TAAATATTAAG
1 TTAATATTAAA
*
5370290 TTACTATTAAA
1 TTAATATTAAA
5370301 TTAA-ATTAAA
1 TTAATATTAAA
5370311 TTAATATT
1 TTAATATT
5370319 TACAAGATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
10 13 0.31
11 26 0.62
12 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:5371641 original size:6 final size:6
Alignment explanation
Indices: 5371602--5371640 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5371592 TTAACCAATG
** *
5371602 AAAATA AAGGTA AAAATA AAAATA AAAATA AAATTA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
5371641 TCAATGATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:5377212 original size:19 final size:19
Alignment explanation
Indices: 5377166--5377226 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
5377156 ATAAAATTAC
*
5377166 TCAAAATAAAATTAATATTAA
1 TCAACATAAAATTAA-A-TAA
* *
5377187 TAAAACA-AATAATTAAGTAA
1 T-CAACATAA-AATTAAATAA
5377207 TCAACATAAAATTAAATAA
1 TCAACATAAAATTAAATAA
5377226 T
1 T
5377227 TATTTAACTC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
19 14 0.44
20 6 0.19
21 3 0.09
22 9 0.28
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
TCAACATAAAATTAAATAA
Found at i:5380277 original size:20 final size:20
Alignment explanation
Indices: 5380242--5380290 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5380232 ATCATGGTCT
*
5380242 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
5380261 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
5380281 TTGCTTACTT
1 TTGCTTACTT
5380291 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:5380680 original size:50 final size:50
Alignment explanation
Indices: 5380582--5380688 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
5380572 ACAGGAGATT
* * * * *
5380582 TCTCATATTGGTGCCCATGCCATGTCCCAGACAAGGTATTACGGGGGACC
1 TCTCATATCGGTGCCAACGCCATGTCCCAGACAAGGTAGTACAGGGGACC
* * * *
5380632 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCGTACATGGGACC
1 TCTCATATCGGTGCCAACGCCATGTCCCAGACAAGGTAGTACAGGGGACC
*
5380682 TTTCATA
1 TCTCATA
5380689 ATCTCAATAA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.25
Consensus pattern (50 bp):
TCTCATATCGGTGCCAACGCCATGTCCCAGACAAGGTAGTACAGGGGACC
Found at i:5380763 original size:36 final size:36
Alignment explanation
Indices: 5380723--5380794 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
5380713 CCCAGACATG
*
5380723 GTCTTATATGGGATCTCATTCCCTTAATGTCATGAC
1 GTCTTACATGGGATCTCATTCCCTTAATGTCATGAC
*
5380759 GTCTTACATGGGATCTCATTCCCTTAATGTCGTGAC
1 GTCTTACATGGGATCTCATTCCCTTAATGTCATGAC
5380795 ACTTGTATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (36 bp):
GTCTTACATGGGATCTCATTCCCTTAATGTCATGAC
Found at i:5384958 original size:18 final size:17
Alignment explanation
Indices: 5384930--5384970 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
5384920 TCTGGGCGTA
*
5384930 TGGGCCACACGTGCACG
1 TGGGCCACACGGGCACG
*
5384947 TGGGCTCACACGGGCATG
1 TGGGC-CACACGGGCACG
5384965 TGGGCC
1 TGGGCC
5384971 CATATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.15, C:0.32, G:0.39, T:0.15
Consensus pattern (17 bp):
TGGGCCACACGGGCACG
Found at i:5399653 original size:40 final size:40
Alignment explanation
Indices: 5399554--5399660 Score: 99
Period size: 40 Copynumber: 2.6 Consensus size: 40
5399544 TTATACAGGA
* * * * **
5399554 TTTGTACTTTAGTGCCTCCATTTGCACTTTGATGCCTCTG
1 TTTGCACTTCAGTGCCTCTATTCGCACTACGATGCCTCTG
* * * *
5399594 TATGCAGTTC-GCTGTCTCTATTCGCACTACGGTGCCTCTG
1 TTTGCACTTCAG-TGCCTCTATTCGCACTACGATGCCTCTG
5399634 TTTGCACTTCAGTGCCTCTATTACGCA
1 TTTGCACTTCAGTGCCTCTATT-CGCA
5399661 TTTCCAATGC
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
39 1 0.02
40 45 0.88
41 5 0.10
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (40 bp):
TTTGCACTTCAGTGCCTCTATTCGCACTACGATGCCTCTG
Found at i:5407710 original size:18 final size:18
Alignment explanation
Indices: 5407687--5407746 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
5407677 ATTTAAAAAA
*
5407687 TTAATTGTCTTAAGTAAT
1 TTAATTGTATTAAGTAAT
** * *
5407705 TTAATTAAAATTAA-AAAA
1 TTAATT-GTATTAAGTAAT
*
5407723 TTAATTGTTTTAAGTAAT
1 TTAATTGTATTAAGTAAT
5407741 TTAATT
1 TTAATT
5407747 AAAGTTAAAT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
17 4 0.13
18 22 0.73
19 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (18 bp):
TTAATTGTATTAAGTAAT
Found at i:5407723 original size:36 final size:36
Alignment explanation
Indices: 5407679--5407755 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
5407669 TGTTTATAAT
5407679 TTAAAAAATTAATTGTCTTAAGTAATTTAATTAAAA
1 TTAAAAAATTAATTGTCTTAAGTAATTTAATTAAAA
* *
5407715 TTAAAAAATTAATTGTTTTAAGTAATTTAATTAAAG
1 TTAAAAAATTAATTGTCTTAAGTAATTTAATTAAAA
5407751 TTAAA
1 TTAAA
5407756 TTAAGAAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.43
Consensus pattern (36 bp):
TTAAAAAATTAATTGTCTTAAGTAATTTAATTAAAA
Found at i:5408141 original size:28 final size:28
Alignment explanation
Indices: 5408109--5408174 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
5408099 TACACTAATA
*
5408109 GTCACCTAACTATTAG-TAAATTTATTTT
1 GTCACCCAACTATTAGTTAAATTT-TTTT
5408137 GTCACCCAACTATTAGTTAAATTTTTTT
1 GTCACCCAACTATTAGTTAAATTTTTTT
5408165 GTCACCCAAC
1 GTCACCCAAC
5408175 AATGAACAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 29 0.81
29 7 0.19
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (28 bp):
GTCACCCAACTATTAGTTAAATTTTTTT
Found at i:5408901 original size:13 final size:15
Alignment explanation
Indices: 5408869--5408905 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
5408859 GTAAACAAAA
5408869 TTTTTAGTACTTAAAT
1 TTTTTAGTACTT-AAT
5408885 TTTTTA-TACTT-AT
1 TTTTTAGTACTTAAT
5408898 TTTTTAGT
1 TTTTTAGT
5408906 TAATCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.40
14 1 0.05
15 5 0.25
16 6 0.30
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTAGTACTTAAT
Found at i:5410691 original size:18 final size:18
Alignment explanation
Indices: 5410653--5410687 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5410643 GTATGGTTCA
5410653 CTCGTGTAGGCCCACACG
1 CTCGTGTAGGCCCACACG
5410671 CTCGTGT-GGCCCACACG
1 CTCGTGTAGGCCCACACG
5410688 GCTCAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.14, C:0.40, G:0.29, T:0.17
Consensus pattern (18 bp):
CTCGTGTAGGCCCACACG
Found at i:5418254 original size:18 final size:18
Alignment explanation
Indices: 5418231--5418265 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5418221 GACCAATAAT
*
5418231 CCCACATGCCCGTGTGGG
1 CCCACACGCCCGTGTGGG
*
5418249 CCCACACGCTCGTGTGG
1 CCCACACGCCCGTGTGG
5418266 CTTACACAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.40, G:0.31, T:0.17
Consensus pattern (18 bp):
CCCACACGCCCGTGTGGG
Found at i:5420061 original size:20 final size:21
Alignment explanation
Indices: 5420036--5420078 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
5420026 TTTATTTTCC
*
5420036 TATTAAAATTTTATTAT-TTT
1 TATTAAAATATTATTATCTTT
5420056 TATTAAAATATTATTATCTTT
1 TATTAAAATATTATTATCTTT
5420077 TA
1 TA
5420079 CAAGAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTAAAATATTATTATCTTT
Found at i:5420184 original size:29 final size:29
Alignment explanation
Indices: 5420098--5420186 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
5420088 CATGATAATA
* * *
5420098 ATAACTATTTTAAAACTTAAGAGACG-ATA
1 ATAATTATTTTAAAATTTAAGAGA-GAATT
* * * *
5420127 ATAATTATTTTAAACTTTAGGAAATAATT
1 ATAATTATTTTAAAATTTAAGAGAGAATT
* *
5420156 ATTATTATTTTAAATTTTAAGAGAGAATT
1 ATAATTATTTTAAAATTTAAGAGAGAATT
5420185 AT
1 AT
5420187 GATAATCATA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (29 bp):
ATAATTATTTTAAAATTTAAGAGAGAATT
Found at i:5441719 original size:88 final size:87
Alignment explanation
Indices: 5441560--5442518 Score: 310
Period size: 88 Copynumber: 10.9 Consensus size: 87
5441550 GATTGTAGAT
* * ** *
5441560 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCC-AAG-A-TAG
1 CTTATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGACGAAG-ATCTTATC-TCCCTAAGCAGTAG
*
5441622 TGGGAAGCAGATTTAAGCCACCAAGC
64 T-GG-AGCAGATTGAAGCCACCAAGC
* * * *
5441648 CTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGA-CGAAGATCTTATCTCCCTAAGCAGTAGT
* ** * *
5441713 GGAGCAGATCGAAGACGGCGAA-T
65 GGAGCAGATTGAAG-CCACCAAGC
* * * * * * *
5441736 CTTATCTTTCC-AAG-A-TAGTGGAAAGCAGATTTAAGCCACCAAG-CCTTGTCTCCCTGAGCAG
1 CTTATC-TCCCTAAGCAGTAGTGG--AGAAGATTGAAG--ACGAAGATCTTATCTCCCTAAGCAG
* * * ** *
5441797 CAGTGGAGAAGGTTGAAG--ATTGAAGAT
61 TAGTGGAGCAGATTGAAGCCA-CCAAG-C
* * ** *
5441824 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCC-AAG-A-TAG
1 CTTATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGACGAAG-ATCTTATC-TCCCTAAGCAGTAG
* *
5441886 TGGGAAGCAGCTTTAAGCCACCAAGC
64 T-GG-AGCAGATTGAAGCCACCAAGC
* * * * *
5441912 CTTGTCTCCCTGAGCAGCAGTGGAGAAGATTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGA-CGAAGATCTTATCTCCCTAAGCAGTAGT
* **** *
5441977 GGAGCAGATCGAAGACGGTGAA-T
65 GGAGCAGATTGAAG-CCACCAAGC
* * * * * * **
5442000 CTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAG-CCTTGTCTCCCGGAGCAG
1 CTTATC-TCCCTAAGCAGTAGT-GG-AGAAGATTGAAG--ACGAAGATCTTATCTCCCTAAGCAG
* * * ** *
5442061 CAGTGGAGAAGGTTGAAG--ATTGAAGAT
61 TAGTGGAGCAGATTGAAGCCA-CCAAG-C
* * ** *
5442088 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCC-AAG-A-TAG
1 CTTATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGACGAAG-ATCTTATC-TCCCTAAGCAGTAG
*
5442150 TGGGAAGCAGATTTAAGCCACCAAGC
64 T-GG-AGCAGATTGAAGCCACCAAGC
* * * * * * * *
5442176 CTTGTCTCCCTGAGCAGCAGTTGAGAAGGTTGAAGATTGTAGATCTTATCTTCCTAAGCAGTAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGA-CGAAGATCTTATCTCCCTAAGCAGTAGT
* ** * *
5442241 GGAGCAGATCGAAGACGGCGAA-T
65 GGAGCAGATTGAAG-CCACCAAGC
* * * * * * *
5442264 CTTATCTTTCC-AAG-A-TAGTGAGAAGCAGATTTAAGCCACCAAG-CCTTGTCTCCCTGAGCAG
1 CTTATC-TCCCTAAGCAGTAGTG-G-AGAAGATTGAAG--ACGAAGATCTTATCTCCCTAAGCAG
* * * *** *
5442325 CAGTGGAGAAGGTTGAAG--ATTGTAGAT
61 TAGTGGAGCAGATTGAAGCCA-CCAAG-C
* * * ** *
5442352 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCGAATCTTATCTTTCC-AAG-A-TAG
1 CTTATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGACGAAG-ATCTTATC-TCCCTAAGCAGTAG
*
5442414 TGGGAAGCAGATTTAAGCCACCAAGC
64 T-GG-AGCAGATTGAAGCCACCAAGC
* * * * * * * *
5442440 CTTGTCTCCCTGAGTAGCAGCGGAGAAAATTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGA-CGAAGATCTTATCTCCCTAAGCAGTAGT
*
5442505 GGAGCAGATCGAAG
65 GGAGCAGATTGAAG
5442519 ATGGTGAATC
Statistics
Matches: 626, Mismatches: 172, Indels: 146
0.66 0.18 0.15
Matches are distributed among these distances:
86 38 0.06
87 37 0.06
88 443 0.71
89 71 0.11
90 37 0.06
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (87 bp):
CTTATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGACGAAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATTGAAGCCACCAAGC
Found at i:5441745 original size:132 final size:132
Alignment explanation
Indices: 5441508--5442645 Score: 1981
Period size: 132 Copynumber: 8.6 Consensus size: 132
5441498 ATTGGTGAAA
* * *
5441508 CACCAAGCCTTGTCTCCCTAAGTAGTAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
5441573 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5441638 GC
131 GC
* *
5441640 CACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
5441705 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5441770 GC
131 GC
*
5441772 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
5441837 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGCTTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5441902 GC
131 GC
*
5441904 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGATTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
5441969 GCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5442034 GC
131 GC
* *
5442036 CACCAAGCCTTGTCTCCCGGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
5442101 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5442166 GC
131 GC
* *
5442168 CACCAAGCCTTGTCTCCCTGAGCAGCAGTTGAGAAGGTTGAAGATTGTAGATCTTATCTTCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
5442233 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGAGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5442298 GC
131 GC
5442300 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* *
5442365 GCAGTAGTGGAGTAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
5442430 GC
131 GC
* * **
5442432 CACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAAATTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * * *
5442497 GCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTACCTTTCCAAGATAGTGGG-AGACAGATTTG
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAG-CAGATTTA
5442561 AGC
130 AGC
* * * * **
5442564 CACCAAGCTTTGTCTCCCTGAGAAACAGCGGAGAAAATTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
5442629 GCAGTAGTGGAGCAGAT
66 GCAGTAGTGGAGCAGAT
5442646 TAAAGCCGAC
Statistics
Matches: 969, Mismatches: 36, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
131 2 0.00
132 967 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:5445260 original size:41 final size:41
Alignment explanation
Indices: 5445231--5445400 Score: 313
Period size: 41 Copynumber: 4.1 Consensus size: 41
5445221 TTAAAGTCTA
*
5445231 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
5445272 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
5445313 ATTCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
5445354 ATTCAATTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
5445395 ATTCAA
1 ATTCAA
5445401 GAATAATTTC
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 127 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (41 bp):
ATTCAATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:5447565 original size:98 final size:98
Alignment explanation
Indices: 5447451--5447642 Score: 330
Period size: 98 Copynumber: 2.0 Consensus size: 98
5447441 AAAAATCATG
* *
5447451 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTCGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
5447516 AAATCTTGGATAAGTGGATGTTCTTTTAAATTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAATTA
* *
5447549 AAGGAAATATTCCGAGTTCGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGGTTTCTT
1 AAGGAAATATTCCGAGTTCGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
* *
5447614 AAATTTTGGATGAGTGGATGTTCTTTTAA
66 AAATCTTGGATAAGTGGATGTTCTTTTAA
5447643 TATTTTTATT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTCGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAATTA
Found at i:5451194 original size:40 final size:39
Alignment explanation
Indices: 5451096--5451318 Score: 198
Period size: 40 Copynumber: 5.6 Consensus size: 39
5451086 TCCTCGTTCA
* * * * *
5451096 AATGCCTTCGAGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
5451135 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
5451174 GAATGCCTTCGGGACTTAACCCCGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
5451214 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
5451254 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
5451295 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
5451319 CAGCATTCAA
Statistics
Matches: 154, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
39 39 0.25
40 103 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:5451327 original size:41 final size:41
Alignment explanation
Indices: 5451250--5451327 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
5451240 TTTGTATCTC
* * *
5451250 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
5451291 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
5451328 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:5453678 original size:27 final size:27
Alignment explanation
Indices: 5453647--5453751 Score: 140
Period size: 27 Copynumber: 3.9 Consensus size: 27
5453637 ATCTGACCGA
*
5453647 AATACCCCCATAAGGTAAAATGACCAG
1 AATACCCCCATAGGGTAAAATGACCAG
* *
5453674 AATACCCTCATAGGGTAAAATGACCAA
1 AATACCCCCATAGGGTAAAATGACCAG
*
5453701 AATAACCCCATAGGGTAAAATGACC-G
1 AATACCCCCATAGGGTAAAATGACCAG
* *
5453727 AAATACTCTCATAGGGTAAAATGAC
1 -AATACCCCCATAGGGTAAAATGAC
5453752 TGTTATACCC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (27 bp):
AATACCCCCATAGGGTAAAATGACCAG
Found at i:5453722 original size:54 final size:54
Alignment explanation
Indices: 5453640--5453751 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
5453630 GGTCGATATC
* *
5453640 TGACCGAAATACCCCCATAAGGTAAAATGACC-AGAATACCCTCATAGGGTAAAA
1 TGACCAAAATAACCCCATAAGGTAAAATGACCGA-AATACCCTCATAGGGTAAAA
* *
5453694 TGACCAAAATAACCCCATAGGGTAAAATGACCGAAATACTCTCATAGGGTAAAA
1 TGACCAAAATAACCCCATAAGGTAAAATGACCGAAATACCCTCATAGGGTAAAA
5453748 TGAC
1 TGAC
5453752 TGTTATACCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 52 0.98
55 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.18
Consensus pattern (54 bp):
TGACCAAAATAACCCCATAAGGTAAAATGACCGAAATACCCTCATAGGGTAAAA
Found at i:5454875 original size:19 final size:19
Alignment explanation
Indices: 5454853--5454895 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
5454843 CCAAAATACC
5454853 GATCCTCCTCCAGTCCACA
1 GATCCTCCTCCAGTCCACA
*
5454872 GATCCTCCTCCAGTCCACC
1 GATCCTCCTCCAGTCCACA
5454891 GATCC
1 GATCC
5454896 ACCTTCGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.49, G:0.12, T:0.21
Consensus pattern (19 bp):
GATCCTCCTCCAGTCCACA
Found at i:5468417 original size:201 final size:190
Alignment explanation
Indices: 5468042--5468424 Score: 457
Period size: 201 Copynumber: 2.0 Consensus size: 190
5468032 ACAAGTGCCT
*
5468042 CCTATCCACTACCCTCCAGCCTTAAAAAATTATTTTTTTCTTTTGCATAACAGACTAATGATTGG
1 CCTATCCACTACCCTCCACCCTTAAAAAATTATTTTTTTCTTTTGCATAACAGACTAATGATTGG
* ** * * **
5468107 GGTAAAAAAAAAGGGTCGTGTCACCTTTCCACCACCGACACCATAGCATTTTTGTAAATAATGGG
66 GGTAAAAAAAAAGGGTCGTGCCACCGCTCCACCACCCAAACCATAGCATTTTCATAAATAATGGG
* * * *
5468172 AGTGGGATACTATTTTGGTAAATTTTTATTGTTTTTATATTATACAGGTAAAAAAAACCA
131 AGTGAGATACTATTTTGATAAATTTTTATTATTTTTATATTATACAAGTAAAAAAAACCA
* *
5468232 CCTATCCACTACCCTTCACCCTTAAAAAACTT-TTTTTGTTGTTTTGCATAACAGACTAATGATT
1 CCTATCCACTACCCTCCACCCTTAAAAAA-TTATTTTT-TTCTTTTGCATAACAGACTAATGATT
* * *
5468296 AAGGTCAAAGGTCAAAAAAAATAAGGGTGGTGCCACCGCTCTACCACCCAAACTATA-CGATTTT
64 --GG-----GGT--AAAAAAA-AAGGGTCGTGCCACCGCTCCACCACCCAAACCATAGC-ATTTT
*
5468360 CATAAATAATGGGAGTGAGATA-TCATTTTGATAATTTTTTATTATTTTTATATTATACAAGTAA
118 CATAAATAATGGGAGTGAGATACT-ATTTTGATAAATTTTTATTATTTTTATATTATACAAGTAA
5468424 A
182 A
5468425 GCAGCCCATT
Statistics
Matches: 161, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
190 32 0.20
191 27 0.17
193 2 0.01
198 3 0.02
200 9 0.06
201 88 0.55
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (190 bp):
CCTATCCACTACCCTCCACCCTTAAAAAATTATTTTTTTCTTTTGCATAACAGACTAATGATTGG
GGTAAAAAAAAAGGGTCGTGCCACCGCTCCACCACCCAAACCATAGCATTTTCATAAATAATGGG
AGTGAGATACTATTTTGATAAATTTTTATTATTTTTATATTATACAAGTAAAAAAAACCA
Found at i:5470959 original size:24 final size:24
Alignment explanation
Indices: 5470914--5470972 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
5470904 ATTTTATATT
* *
5470914 AAATATATATTTTTATTTTTAATC
1 AAATATATATTTATATTATTAATC
5470938 AAATATATA-TTATATATATTAA--
1 AAATATATATTTATAT-TATTAATC
*
5470960 ATATATATATTTA
1 AAATATATATTTA
5470973 ATATGGGTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 8 0.27
23 8 0.27
24 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
AAATATATATTTATATTATTAATC
Found at i:5470976 original size:24 final size:23
Alignment explanation
Indices: 5470908--5470976 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 23
5470898 GCCCAAATTT
* *
5470908 TATATTAAATATATATTTTTATT
1 TATATTAAATATATATATTTATA
* * *
5470931 TTTAATCAA-ATATATA-TTATA
1 TATATTAAATATATATATTTATA
5470952 TATATTAAATATATATATTTA-A
1 TATATTAAATATATATATTTATA
5470974 TAT
1 TAT
5470977 GGGTCGGGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
21 10 0.28
22 17 0.47
23 9 0.25
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATTAAATATATATATTTATA
Found at i:5473066 original size:26 final size:26
Alignment explanation
Indices: 5473009--5473066 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
5472999 CTTCAGCCTT
*
5473009 TTTTTTTTTGGTATATTTTGGTAAATA
1 TTTTTTTTGGGTATATTTTGGT-AATA
*
5473036 ATTTTTTTGGGATATATTTTGGT-ATA
1 TTTTTTTTGGG-TATATTTTGGTAATA
5473062 TTTTT
1 TTTTT
5473067 ATTTCTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.26
27 9 0.33
28 11 0.41
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.64
Consensus pattern (26 bp):
TTTTTTTTGGGTATATTTTGGTAATA
Found at i:5479135 original size:74 final size:74
Alignment explanation
Indices: 5479032--5479171 Score: 221
Period size: 74 Copynumber: 1.9 Consensus size: 74
5479022 CATTAAAACT
5479032 AGTAATAATTGCTCTCTTATATTACTTTGTGACATTTTACATCACTCACCATAACATACAACTTA
1 AGTAATAATTGCTCTCTTATATTACTTTGTGACATTTTACATCACTCACCATAACATACAACTTA
5479097 ACTAAAATC
66 ACTAAAATC
* * *
5479106 AGTAATAATTGCAT-TTTTATA-TACTTTTGTGACATTTTACATCACTGACCATAACATCCAACT
1 AGTAATAATTGC-TCTCTTATATTAC-TTTGTGACATTTTACATCACTCACCATAACATACAACT
5479169 TAA
64 TAA
5479172 TTATTATTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
73 3 0.05
74 57 0.93
75 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (74 bp):
AGTAATAATTGCTCTCTTATATTACTTTGTGACATTTTACATCACTCACCATAACATACAACTTA
ACTAAAATC
Found at i:5481294 original size:3 final size:3
Alignment explanation
Indices: 5481286--5481314 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5481276 GATTTAGTCC
5481286 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5481315 CCTATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5487706 original size:43 final size:43
Alignment explanation
Indices: 5487659--5487795 Score: 111
Period size: 44 Copynumber: 3.2 Consensus size: 43
5487649 AAAACAAAGC
5487659 CTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGAAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGAAGCAGAT
* * * * * * * *
5487702 CTTGCCTTCC-T-GCATTAACAGCGAAGCAGATTGAA-AA-CAAAGC
1 CTTGCC-TCCATCG-GTT-GCAGTGAAGCTGGTTAAAGAAGCAGA-T
*
5487745 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGA-AGCAGAT
*
5487789 ATTGCCT
1 CTTGCCT
5487796 TCCTAAGTAC
Statistics
Matches: 67, Mismatches: 18, Indels: 17
0.66 0.18 0.17
Matches are distributed among these distances:
42 19 0.28
43 21 0.31
44 24 0.36
45 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.26
Consensus pattern (43 bp):
CTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGAAGCAGAT
Found at i:5487757 original size:86 final size:87
Alignment explanation
Indices: 5487612--5488321 Score: 989
Period size: 86 Copynumber: 8.2 Consensus size: 87
5487602 AAAAAAAAGT
* * *
5487612 AGATCTTGCCTTCCT-ACATTAACAACGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTG
1 AGATCTTGCCTTCCTGA-AGTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
*
5487676 CAGTGAAGCTGGTTAAAGA-AGC
65 CAGTGGAGCTGGTTAAAGATAGC
* * *
5487698 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATTGAAAACAAAGCCTTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGAAGTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGC
5487763 AGTGGAGCTGGTTAAAGATAGC
66 AGTGGAGCTGGTTAAAGATAGC
* * ** * * *
5487785 AGATATTGCCTTCCT-AAGT-ACTAGCGGAGCAGATAAAAAACAAAGCCCTACCTCCATCTGTTG
1 AGATCTTGCCTTCCTGAAGTAAC-AGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
5487848 CAGTGGAGCTGGTTAAAGATAGC
65 CAGTGGAGCTGGTTAAAGATAGC
* *
5487871 AGATCTTGCCTTCCT-AAGT-ACTAGCGGAGTAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
1 AGATCTTGCCTTCCTGAAGTAAC-AGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
*
5487934 CAGTGGAGCTGGTTAAAGATAAC
65 CAGTGGAGCTGGTTAAAGATAGC
** * * *
5487957 AGATCTTGCCTTCCT-AAGT-ACTAATGGAGCAGATCAAAAACAAAGCCTTGCCTCCATCTGTTG
1 AGATCTTGCCTTCCTGAAGTAAC-AGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
5488020 CAGTGGAGCTGGTTAAAGATAGC
65 CAGTGGAGCTGGTTAAAGATAGC
* *
5488043 AGATCTTGCCTTCCT-AAGT-ACTAGCGGAGCAGATCGAAAACAAAGCCTTGCCTCCATCTGTTG
1 AGATCTTGCCTTCCTGAAGTAAC-AGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
5488106 CAGTGGAGCTGGTTAAAGATAGC
65 CAGTGGAGCTGGTTAAAGATAGC
* * *
5488129 AGATCTTGCCTTCCT-AAGT-ACTAACGGAGCAGATCGAAAACAAAGCCTTACCTCCATCGGTTG
1 AGATCTTGCCTTCCTGAAGTAAC-AGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
*
5488192 TAGTGGAGCTGGTTAAAGATAGC
65 CAGTGGAGCTGGTTAAAGATAGC
* *
5488215 AGATCTTGCCTTCCTG-CGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTACCTCCATCGGTTG
1 AGATCTTGCCTTCCTGAAG-TAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
5488279 CAGTGGAGCTGGTTAAAGATAGC
65 CAGTGGAGCTGGTTAAAGATAGC
5488302 AGATCTTGCCTTCCT-AAGTA
1 AGATCTTGCCTTCCTGAAGTA
5488322 CTAGTGGAGC
Statistics
Matches: 577, Mismatches: 40, Indels: 14
0.91 0.06 0.02
Matches are distributed among these distances:
85 2 0.00
86 478 0.83
87 95 0.16
88 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (87 bp):
AGATCTTGCCTTCCTGAAGTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGC
AGTGGAGCTGGTTAAAGATAGC
Found at i:5487912 original size:172 final size:172
Alignment explanation
Indices: 5487612--5488335 Score: 1123
Period size: 172 Copynumber: 4.2 Consensus size: 172
5487602 AAAAAAAAGT
* * *
5487612 AGATCTTGCCTTCCTACATTAAC-AACGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTG
1 AGATCTTGCCTTCCTA-AGT-ACTAACGGAGCAGATCAAAAACAAAGCCTTACCTCCATCGGTTG
* * * *
5487676 CAGTGAAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATTGAAAAC
64 CAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT-AAGTAACAGCGAAGCAGATCGAAAAC
5487740 AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGC
128 AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGC
* * * * *
5487785 AGATATTGCCTTCCTAAGTACTAGCGGAGCAGATAAAAAACAAAGCCCTACCTCCATCTGTTGCA
1 AGATCTTGCCTTCCTAAGTACTAACGGAGCAGATCAAAAACAAAGCCTTACCTCCATCGGTTGCA
* *
5487850 GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGT-ACTAGCGGAGTAGATCGAAAACAA
66 GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTAAC-AGCGAAGCAGATCGAAAACAA
*
5487914 AGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAAC
130 AGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGC
* * *
5487957 AGATCTTGCCTTCCTAAGTACTAATGGAGCAGATCAAAAACAAAGCCTTGCCTCCATCTGTTGCA
1 AGATCTTGCCTTCCTAAGTACTAACGGAGCAGATCAAAAACAAAGCCTTACCTCCATCGGTTGCA
*
5488022 GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGT-ACTAGCGGAGCAGATCGAAAACAA
66 GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTAAC-AGCGAAGCAGATCGAAAACAA
*
5488086 AGCCTTGCCTCCATCTGTTGCAGTGGAGCTGGTTAAAGATAGC
130 AGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGC
* *
5488129 AGATCTTGCCTTCCTAAGTACTAACGGAGCAGATCGAAAACAAAGCCTTACCTCCATCGGTTGTA
1 AGATCTTGCCTTCCTAAGTACTAACGGAGCAGATCAAAAACAAAGCCTTACCTCCATCGGTTGCA
**
5488194 GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAA
66 GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAG-TAACAGCGAAGCAGATCGAAAACAA
*
5488259 AGCCTTACCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGC
130 AGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGC
**
5488302 AGATCTTGCCTTCCTAAGTACTAGTGGAGCAGAT
1 AGATCTTGCCTTCCTAAGTACTAACGGAGCAGAT
5488336 TGAAGAGGGC
Statistics
Matches: 510, Mismatches: 36, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
171 4 0.01
172 377 0.74
173 127 0.25
174 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (172 bp):
AGATCTTGCCTTCCTAAGTACTAACGGAGCAGATCAAAAACAAAGCCTTACCTCCATCGGTTGCA
GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTAACAGCGAAGCAGATCGAAAACAAA
GCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGC
Found at i:5487985 original size:44 final size:44
Alignment explanation
Indices: 5487763--5488151 Score: 152
Period size: 44 Copynumber: 9.0 Consensus size: 44
5487753 CATCGGTTGC
* *
5487763 AGTGGAGCTGGTTAAAGATAGCAGATATTGCCTTCCTAAGTACT
1 AGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTAAGTACT
* * * * * * * ** *
5487807 AGCGGAGC-AGATAAA-A-AACAAAGCCCTACC-TCCATCTGTTGC-
1 AGTGGAGCTGGTTAAAGATAACAGA-TCTTGCCTTCC-TAAG-TACT
*
5487849 AGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTACT
1 AGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTAAGTACT
* * * * * ** *
5487893 AGCGGAG-TAGATCGAAA-ACAA-AG-CCTTGCC-TCCATCGGTTGC-
1 AGTGGAGCT-GGT-TAAAGATAACAGATCTTGCCTTCC-TAAG-TACT
5487935 AGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTAAGTACT
1 AGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTAAGTACT
* * * * * * * ** *
5487979 AATGGAGCAGATCAAAAACAA-AG-CCTTGCC-TCCATCTGTTGC-
1 AGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCC-TAAG-TACT
*
5488021 AGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTACT
1 AGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTAAGTACT
* * * * * * ** *
5488065 AGCGGAGCAGATCGAAA-ACAA-AG-CCTTGCC-TCCATCTGTTGC-
1 AGTGGAGCTGGT-TAAAGATAACAGATCTTGCCTTCC-TAAG-TACT
*
5488107 AGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTACT
1 AGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTAAGTACT
5488151 A
1 A
5488152 ACGGAGCAGA
Statistics
Matches: 232, Mismatches: 81, Indels: 64
0.62 0.21 0.17
Matches are distributed among these distances:
41 22 0.09
42 73 0.31
43 40 0.17
44 75 0.32
45 22 0.09
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (44 bp):
AGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTAAGTACT
Found at i:5488027 original size:42 final size:42
Alignment explanation
Indices: 5487640--5488114 Score: 123
Period size: 42 Copynumber: 11.1 Consensus size: 42
5487630 TTAACAACGA
* *
5487640 AGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGA
1 AGCAGATCAAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGG
* * * * * * * *
5487682 AGCTGGTTAAAGAAGCAGA-TCTTGCCTTCC-TGCA-TTAACAGCGA
1 AGCAGATCAAA-AA-CAAAGCCTTGCC-TCCAT-CAGTT-GCAGTGG
** *
5487726 AGCAGATTGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGG
1 AGCAGATCAAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGG
* * * * ** * * *
5487768 AGCTGGTTAAAGATAGCAGA-TATTGCCTTCC-TAAG-TACTAGCGG
1 AGCAGATCAAA-A-A-CAAAGCCTTGCC-TCCATCAGTTGC-AGTGG
* * * *
5487812 AGCAGATAAAAAACAAAGCCCTACCTCCATCTGTTGCAGTGG
1 AGCAGATCAAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGG
* * * * * * * *
5487854 AGCTGGTTAAAGATAGCAGA-TCTTGCCTTCC-TAAG-TACTAGCGG
1 AGCAGATCAAA-A-A-CAAAGCCTTGCC-TCCATCAGTTGC-AGTGG
* * *
5487898 AGTAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGG
1 AGCAGATCAAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGG
* * * * * * * * *
5487940 AGCTGGTTAAAGATAACAGATCTTGCCTTCC-TAAG-TACTAATGG
1 AGCAGATCAAAAACAA-AG-CCTTGCC-TCCATCAGTTGC-AGTGG
*
5487984 AGCAGATCAAAAACAAAGCCTTGCCTCCATCTGTTGCAGTGG
1 AGCAGATCAAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGG
* * * * * * * *
5488026 AGCTGGTTAAAGATAGCAGA-TCTTGCCTTCC-TAAG-TACTAGCGG
1 AGCAGATCAAA-A-A-CAAAGCCTTGCC-TCCATCAGTTGC-AGTGG
* *
5488070 AGCAGATCGAAAACAAAGCCTTGCCTCCATCTGTTGCAGTGG
1 AGCAGATCAAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGG
5488112 AGC
1 AGC
5488115 TGGTTAAAGA
Statistics
Matches: 293, Mismatches: 102, Indels: 76
0.62 0.22 0.16
Matches are distributed among these distances:
41 21 0.07
42 103 0.35
43 48 0.16
44 100 0.34
45 21 0.07
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (42 bp):
AGCAGATCAAAAACAAAGCCTTGCCTCCATCAGTTGCAGTGG
Found at i:5488070 original size:258 final size:258
Alignment explanation
Indices: 5487612--5488335 Score: 1145
Period size: 258 Copynumber: 2.8 Consensus size: 258
5487602 AAAAAAAAGT
* * *
5487612 AGATCTTGCCTTCCTACATTAAC-AACGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTG
1 AGATCTTGCCTTCCTA-AGT-ACTAACGGAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
* * *
5487676 CAGTGAAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATTGAAAAC
64 CAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGTA-TAACAGCGAAGCAGATCGAAAAC
*
5487740 AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATATTGCCTTCCTAAGTA
128 AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTA
5487805 CTAGCGGAGCAGATAAAAAACAAAGCCCTACCTCCATCTGTTGCAGTGGAGCTGGTTAAAGATAG
193 CTAGCGGAGCAGATAAAAAACAAAGCCCTACCTCCATCTGTTGCAGTGGAGCTGGTTAAAGATAG
5487870 C
258 C
* *
5487871 AGATCTTGCCTTCCTAAGTACTAGCGGAGTAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCA
1 AGATCTTGCCTTCCTAAGTACTAACGGAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCA
* * *
5487936 GTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTAAGTACTAA-TG-G-AGCAGATCAAAAAC
66 GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT--GTA-TAACAGCGAAGCAGATCGAAAAC
*
5487998 AAAGCCTTGCCTCCATCTGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTA
128 AAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTA
** * *
5488063 CTAGCGGAGCAGATCGAAAACAAAGCCTTGCCTCCATCTGTTGCAGTGGAGCTGGTTAAAGATAG
193 CTAGCGGAGCAGATAAAAAACAAAGCCCTACCTCCATCTGTTGCAGTGGAGCTGGTTAAAGATAG
5488128 C
258 C
* *
5488129 AGATCTTGCCTTCCTAAGTACTAACGGAGCAGATCGAAAACAAAGCCTTACCTCCATCGGTTGTA
1 AGATCTTGCCTTCCTAAGTACTAACGGAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCA
5488194 GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGT-TAACAGCGAAGCAGATCGAAAACA
66 GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT--GTATAACAGCGAAGCAGATCGAAAACA
*
5488258 AAGCCTTACCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTAC
129 AAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTAC
*
5488323 TAGTGGAGCAGAT
194 TAGCGGAGCAGAT
5488336 TGAAGAGGGC
Statistics
Matches: 428, Mismatches: 30, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
256 3 0.01
257 3 0.01
258 293 0.68
259 123 0.29
260 1 0.00
261 5 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (258 bp):
AGATCTTGCCTTCCTAAGTACTAACGGAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCA
GTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGTATAACAGCGAAGCAGATCGAAAACAAA
GCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTAAGTACTA
GCGGAGCAGATAAAAAACAAAGCCCTACCTCCATCTGTTGCAGTGGAGCTGGTTAAAGATAGC
Found at i:5488464 original size:87 final size:87
Alignment explanation
Indices: 5488352--5488595 Score: 274
Period size: 87 Copynumber: 2.8 Consensus size: 87
5488342 GGGCAAATAT
* * * * *
5488352 TATCTTCCTAAGCAATAGTGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTAAGCAGTAGTGGA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGCCGCTAGTCCTATCTCCCTAAGCAGTAGTGGA
*
5488417 GCAGGTCGAAGATGGTAGATCC
66 GCAGGTCAAAGATGGTAGATCC
* * * ** *
5488439 TATCTCCCTAAGTAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGT-GTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGCCGCTAG-TCCTATCTCCCTAAGCAGTAGTGG
*
5488503 AGCAGGTCAAAGATGGTAGATCT
65 AGCAGGTCAAAGATGGTAGATCC
* * * * * * * *
5488526 TATCTCCCTAAGCAGTAGTGGAGAAGATTGAAGACGGCGAATCTTATCTTCCTAAGCAGTAGTGA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAG-CCGCTAGTCCTATCTCCCTAAGCAGTAGTGG
5488591 AGCAG
65 AGCAG
5488596 ATTTAGGCCA
Statistics
Matches: 128, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
87 99 0.77
88 29 0.23
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (87 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGCCGCTAGTCCTATCTCCCTAAGCAGTAGTGGA
GCAGGTCAAAGATGGTAGATCC
Found at i:5488517 original size:43 final size:44
Alignment explanation
Indices: 5488392--5488548 Score: 280
Period size: 44 Copynumber: 3.6 Consensus size: 44
5488382 AAGCCACTAG
*
5488392 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
*
5488436 TCCTATCTCCCTAAGTAGTAGTGGAGCAGGTCAAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
5488480 TCCTATCTCCCTAAGCAGT-GTGGAGCAGGTCAAAGATGGTAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
*
5488523 TCTTATCTCCCTAAGCAGTAGTGGAG
1 TCCTATCTCCCTAAGCAGTAGTGGAG
5488549 AAGATTGAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
43 42 0.39
44 66 0.61
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (44 bp):
TCCTATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGGTAGA
Found at i:5488571 original size:44 final size:44
Alignment explanation
Indices: 5488314--5488598 Score: 261
Period size: 44 Copynumber: 6.5 Consensus size: 44
5488304 ATCTTGCCTT
* * * * * ** *
5488314 CCTAAGTACTAGTGGAGCAGATTGAAGAGGGCAAATATTATCTT
1 CCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCCTATCTC
* * * ****
5488358 CCTAAGCAATAGTGAAGCAGATTTAAGCCACTAG-TCCTATCTC
1 CCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCCTATCTC
* *
5488401 CCTAAGCAGTAGTGGAGCAGGTCGAAGATGGTAGATCCTATCTC
1 CCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCCTATCTC
* * **
5488445 CCTAAGTAGTAGTGGAGCAGGTCAAAGATGGTAGATCCTATCTC
1 CCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCCTATCTC
* ** *
5488489 CCTAAGCAGT-GTGGAGCAGGTCAAAGATGGTAGATCTTATCTC
1 CCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCCTATCTC
* * * * *
5488532 CCTAAGCAGTAGTGGAGAAGATTGAAGACGG-CGAATCTTATCTT
1 CCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAG-ATCCTATCTC
*
5488576 CCTAAGCAGTAGTGAAGCAGATT
1 CCTAAGCAGTAGTGGAGCAGATT
5488599 TAGGCCACCA
Statistics
Matches: 203, Mismatches: 35, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
43 74 0.36
44 129 0.64
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (44 bp):
CCTAAGCAGTAGTGGAGCAGATTGAAGATGGTAGATCCTATCTC
Found at i:5488639 original size:44 final size:44
Alignment explanation
Indices: 5488586--5488685 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 44
5488576 CCTAAGCAGT
* * * * *
5488586 AGTGAAGCAGATTTAGGCCACCAG-TCTTATCTTTCTGAGGTTAC
1 AGTGGAGCAGATTGAAGCCA-CAGATCTTATCTCTCTGAGATTAC
*
5488630 AGTGGAGCAGATTGAAGCCAGAGATCTTATCTCTCTGAGATTAC
1 AGTGGAGCAGATTGAAGCCACAGATCTTATCTCTCTGAGATTAC
5488674 AGTGGAGCAGAT
1 AGTGGAGCAGAT
5488686 CACATCTAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 2 0.04
44 47 0.96
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (44 bp):
AGTGGAGCAGATTGAAGCCACAGATCTTATCTCTCTGAGATTAC
Found at i:5490149 original size:3 final size:3
Alignment explanation
Indices: 5490141--5490166 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5490131 GATTTAGTCC
5490141 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
5490167 CCTATTTGTT
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):
TAT
Found at i:5493054 original size:18 final size:18
Alignment explanation
Indices: 5493031--5493065 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5493021 GAAGACAGAG
*
5493031 GGCAAAAACAGTGGAAAT
1 GGCAAAAACAGTAGAAAT
5493049 GGCAAAAACAGTAGAAA
1 GGCAAAAACAGTAGAAA
5493066 CAACAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.11, G:0.26, T:0.09
Consensus pattern (18 bp):
GGCAAAAACAGTAGAAAT
Found at i:5511488 original size:29 final size:31
Alignment explanation
Indices: 5511456--5511528 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
5511446 ACGTTTCTGC
**
5511456 TTTAGTCACTCATA-TTT-AAAATTTTTTAT
1 TTTAGTCACTCATATTTTCAAAATTTAATAT
* * *
5511485 TTTAGTCAATAATATTTTCGAAATTTAATAT
1 TTTAGTCACTCATATTTTCAAAATTTAATAT
5511516 TTTAGTCACTCAT
1 TTTAGTCACTCAT
5511529 CTGTTAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 12 0.34
30 3 0.09
31 20 0.57
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTAGTCACTCATATTTTCAAAATTTAATAT
Found at i:5511786 original size:11 final size:11
Alignment explanation
Indices: 5511772--5511797 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5511762 AATACATACA
5511772 AAATTATAAAT
1 AAATTATAAAT
5511783 AAATTATAAAT
1 AAATTATAAAT
5511794 AAAT
1 AAAT
5511798 GAATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATTATAAAT
Found at i:5514929 original size:20 final size:20
Alignment explanation
Indices: 5514906--5514971 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
5514896 TAATAGAAAG
5514906 AAATCAAAGGATTGAGAATC
1 AAATCAAAGGATTGAGAATC
* * * **
5514926 AAATCAATGTAATG-GAAAG
1 AAATCAAAGGATTGAGAATC
*
5514945 AAATCAAAAGATTGAGAATC
1 AAATCAAAGGATTGAGAATC
5514965 AAATCAA
1 AAATCAA
5514972 TGTAAACAAG
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCAAAGGATTGAGAATC
Found at i:5514949 original size:39 final size:39
Alignment explanation
Indices: 5514895--5514976 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
5514885 AAGCAAAACA
*
5514895 GTAATAGAAAGAAATCAAAGGATTGAGAATCAAATCAAT
1 GTAATAGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
*
5514934 GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
1 GTAATAGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
5514973 GTAA
1 GTAA
5514977 ACAAGATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (39 bp):
GTAATAGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
Found at i:5516038 original size:332 final size:335
Alignment explanation
Indices: 5515426--5516099 Score: 1228
Period size: 332 Copynumber: 2.0 Consensus size: 335
5515416 AAACGCGCCG
5515426 TATCACTCCATGACCTGCGCGTGTGACCCGACCCAGGGAGGATCCGCGTGCTTTTAAGCGGAGGG
1 TATCACTCCATGACCTGCGCGTGTGACCCGACCCAGGGAGGATCCGCGTGCTTTTAAGCGGAGGG
*
5515491 GTAAATTACGCTTTTAGCCCCTCTGCCTTTTAACATTTTTCCAATTGAGTTTTTTTTTTATTTTT
66 GTAAATTACGCTTTTAGCCCCTCTGCCTTTTAACATTTTTACAATTGAG----TTTTTTATTTTT
5515556 AAATTTGCCCTCTAATTTATTTACAATTTCAATTCAGTCCTAATGTGAACGACGTCGTTTAGAGG
127 AAATTTGCCCTCTAATTTATTTACAATTTCAATTCAGTCCTAATGTGAACGACGTCGTTTAGAGG
*
5515621 AGAAGGGCCAATTTCCTTTCCAGCCCCTCTGCATTCTTTACGCGTTCAATATGGTCCTTGAGACT
192 AGAAGGGCCAATTTCCTTTCCAGCCCCTCTGCATTCTTTACGCGTTCAATATGGTCCCTGAGACT
*
5515686 TCAATTATTTGCGAATTTGCCTTAG-TTTTTTATTATAATTTAAAATTAGTCCTTTTTTAGGATT
257 TCAATTATTTGCGAATTTGCCTTAGTTTTTTTATTACAATTTAAAATTAGTCCTTTTTTAGGATT
5515750 AATTAATTTCAAAA
322 AATTAATTTCAAAA
*
5515764 TATCACTCCATGACCTGCGCGTGTGACCCGACCCAGGGAGGATCCGCGTGTTTTTAAGCGGAGGG
1 TATCACTCCATGACCTGCGCGTGTGACCCGACCCAGGGAGGATCCGCGTGCTTTTAAGCGGAGGG
*
5515829 GTAAATTATGCTTTTAGCCCCTCTGCCTTTTAACATTTTTACAATTGAG-TTTTT-TTTTTAAAT
66 GTAAATTACGCTTTTAGCCCCTCTGCCTTTTAACATTTTTACAATTGAGTTTTTTATTTTTAAAT
*
5515892 TTTCCCTCTAATTTATTTACAATTTCAATTCAGTCCTAATGTGAACGACGTCGTTTAGAGGAGAA
131 TTGCCCTCTAATTTATTTACAATTTCAATTCAGTCCTAATGTGAACGACGTCGTTTAGAGGAGAA
*
5515957 GGGCCAATTTCCTTTCTAGCCCCTCTGCATTCTTTACGCGTTCAATATGGTCCCTGAGACTTCAA
196 GGGCCAATTTCCTTTCCAGCCCCTCTGCATTCTTTACGCGTTCAATATGGTCCCTGAGACTTCAA
5516022 TTATTTGCGAATTTGCCTTAGTTTTTTTATTACAATTTAAAATTAGTCCTTTTTTAGGATTAATT
261 TTATTTGCGAATTTGCCTTAGTTTTTTTATTACAATTTAAAATTAGTCCTTTTTTAGGATTAATT
5516087 AATTTCAAAA
326 AATTTCAAAA
5516097 TAT
1 TAT
5516100 TTTCTTTTTC
Statistics
Matches: 328, Mismatches: 7, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
332 157 0.48
333 60 0.18
338 111 0.34
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (335 bp):
TATCACTCCATGACCTGCGCGTGTGACCCGACCCAGGGAGGATCCGCGTGCTTTTAAGCGGAGGG
GTAAATTACGCTTTTAGCCCCTCTGCCTTTTAACATTTTTACAATTGAGTTTTTTATTTTTAAAT
TTGCCCTCTAATTTATTTACAATTTCAATTCAGTCCTAATGTGAACGACGTCGTTTAGAGGAGAA
GGGCCAATTTCCTTTCCAGCCCCTCTGCATTCTTTACGCGTTCAATATGGTCCCTGAGACTTCAA
TTATTTGCGAATTTGCCTTAGTTTTTTTATTACAATTTAAAATTAGTCCTTTTTTAGGATTAATT
AATTTCAAAA
Found at i:5516205 original size:20 final size:20
Alignment explanation
Indices: 5516182--5516235 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
5516172 TATGTACGTA
*
5516182 TATATATATATAATACTTTC
1 TATATATATATAATAATTTC
* * *
5516202 TATACATATTTTATAATTTC
1 TATATATATATAATAATTTC
5516222 TATATATATATAAT
1 TATATATATATAAT
5516236 CATTATCTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (20 bp):
TATATATATATAATAATTTC
Found at i:5516314 original size:100 final size:102
Alignment explanation
Indices: 5516122--5516332 Score: 309
Period size: 102 Copynumber: 2.1 Consensus size: 102
5516112 TTTTTAAGTT
* * * * *
5516122 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATGTACGTATATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATGTACGTATATAT
*
5516187 ATATATAATACTTTCTATACATATTTTATAATTTCTA
66 ATATATAATACTTTCTATACACATTTTATAATTTCTA
*
5516224 TATATATATAATCATTATCTTTATGATCTATATGTTTATTAACTTATATATATGTACGTATATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATGTACGTATATAT
* * *
5516289 GTAT-T-ATATTTTCTATCCACATTTTATAATTTCTA
66 ATATATAATACTTTCTATACACATTTTATAATTTCTA
*
5516324 TATGTATAT
1 TATATATAT
5516333 TTTCTTTATT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 35 0.36
101 1 0.01
102 62 0.63
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (102 bp):
TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATGTACGTATATAT
ATATATAATACTTTCTATACACATTTTATAATTTCTA
Found at i:5521269 original size:14 final size:15
Alignment explanation
Indices: 5521250--5521278 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5521240 AAAATAATAG
5521250 CAAAGAAAAA-AAAA
1 CAAAGAAAAAGAAAA
5521264 CAAAGAAAAAGAAAA
1 CAAAGAAAAAGAAAA
5521279 AGGAGAGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (15 bp):
CAAAGAAAAAGAAAA
Found at i:5522856 original size:132 final size:132
Alignment explanation
Indices: 5522627--5523302 Score: 1005
Period size: 132 Copynumber: 5.1 Consensus size: 132
5522617 TCGAAGACTC
** * *
5522627 CAGATCTTATCTCCCTAATTAGTAGCGAAGCAGATCGAAGGTGGCGGATTTTACCTCTCTGTGGT
1 CAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTGTGGT
* * * *
5522692 TACAATGGAGTACATTGAAGCCAGTAATTCTACTTTCTTGGACAACAGTGGAATATATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGAT
5522757 TT
131 TT
* * *
5522759 CAGATTTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTGTGGT
1 CAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTGTGGT
* * ** *
5522824 TATAGTGGAGTACATTGAAGCCAGTAGTTCTACTTCCCTGGGTAACAGTAGAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGAT
5522889 TT
131 TT
* * *
5522891 CAGATCTTATCTCCTTAAGCAG-ATGTGGAGCAGATCGAAGATGGTGGATTTTACCTCTCTGTGG
1 CAGATCTTATCTCCCTAAGCAGTA-GCGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTGTGG
* *
5522955 TTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGACAATAGTGGAATAGATTGAAGA
65 TTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGA
5523020 TTT
130 TTT
* * * * *
5523023 CAGATCTTATCTCCCTAAGCAGTAGCGAAGCAGATCGAAGATGACAGATTTTACCTTTTTGTGGT
1 CAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTGTGGT
*
5523088 TATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGAT
5523153 TT
131 TT
* *
5523155 CAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAATATAGCGGATTTTACCTCTCTGTGGT
1 CAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTGTGGT
* * **
5523220 TACAGCGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGGAGTGGAATAGATTGAAGAT
66 TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGAT
5523285 TGT
131 T-T
* *
5523288 GA-ATCCTATCTCCCT
1 CAGATCTTATCTCCCT
5523303 TGTCAGCAGT
Statistics
Matches: 489, Mismatches: 52, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
131 1 0.00
132 485 0.99
133 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (132 bp):
CAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTGTGGT
TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGAT
TT
Found at i:5523314 original size:44 final size:44
Alignment explanation
Indices: 5523266--5523410 Score: 229
Period size: 44 Copynumber: 3.3 Consensus size: 44
5523256 CCTGGGCAGG
*
5523266 AGTGGAATAGATTGAAGATTGTGAATCCTATCTCCCTTGTCAGC
1 AGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTTGTCAGC
5523310 AGTGGAATAGGTTGAAGATTGTGAATCCTATCT-CCTTGGTCAGC
1 AGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTT-GTCAGC
* * * *
5523354 GGTGGAATAGGTTGAAGATTGAGAATCCTATCTCCCTGGTTAGC
1 AGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTTGTCAGC
5523398 AGTGGAATAGGTT
1 AGTGGAATAGGTT
5523411 TAAAGTAAAC
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
43 4 0.04
44 86 0.92
45 3 0.03
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (44 bp):
AGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTTGTCAGC
Found at i:5524030 original size:20 final size:20
Alignment explanation
Indices: 5524005--5524070 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
5523995 TAATGGAAAG
5524005 AAATCAAAGGATTGAGAATC
1 AAATCAAAGGATTGAGAATC
* * * **
5524025 AAATCAATGTAATG-GAAAG
1 AAATCAAAGGATTGAGAATC
*
5524044 AAATCAAAAGATTGAGAATC
1 AAATCAAAGGATTGAGAATC
5524064 AAATCAA
1 AAATCAA
5524071 TGTAAACAAG
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCAAAGGATTGAGAATC
Found at i:5524048 original size:39 final size:39
Alignment explanation
Indices: 5523994--5524075 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
5523984 AAGCAAAACA
*
5523994 GTAATGGAAAGAAATCAAAGGATTGAGAATCAAATCAAT
1 GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
5524033 GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
1 GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
5524072 GTAA
1 GTAA
5524076 ACAAGATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (39 bp):
GTAATGGAAAGAAATCAAAAGATTGAGAATCAAATCAAT
Found at i:5524049 original size:19 final size:19
Alignment explanation
Indices: 5523993--5524051 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
5523983 GAAGCAAAAC
5523993 AGTAATGGAAAGAAATCAA
1 AGTAATGGAAAGAAATCAA
* * **
5524012 AGGATTGAGAATCAAATCAA
1 AGTAATG-GAAAGAAATCAA
*
5524032 TGTAATGGAAAGAAATCAA
1 AGTAATGGAAAGAAATCAA
5524051 A
1 A
5524052 AGATTGAGAA
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (19 bp):
AGTAATGGAAAGAAATCAA
Found at i:5524266 original size:14 final size:14
Alignment explanation
Indices: 5524247--5524276 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5524237 TACTGTGTTC
*
5524247 TTTTATTATTTTTA
1 TTTTATTATTATTA
5524261 TTTTATTATTATTA
1 TTTTATTATTATTA
5524275 TT
1 TT
5524277 ATTTTCTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:5524271 original size:17 final size:17
Alignment explanation
Indices: 5524249--5524281 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5524239 CTGTGTTCTT
*
5524249 TTATTATTTTTATTTTA
1 TTATTATTATTATTTTA
5524266 TTATTATTATTATTTT
1 TTATTATTATTATTTT
5524282 CTCCTTGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTATTATTATTTTA
Found at i:5524987 original size:20 final size:20
Alignment explanation
Indices: 5524964--5525012 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5524954 ATGTACGTAT
*
5524964 ATATATAATACTTTCTATAC
1 ATATATAATAATTTCTATAC
* * *
5524984 ATATTTTATAATTTCTATAT
1 ATATATAATAATTTCTATAC
5525004 ATATATAAT
1 ATATATAAT
5525013 CATTATCTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATAATAATTTCTATAC
Found at i:5525018 original size:100 final size:99
Alignment explanation
Indices: 5524901--5525109 Score: 294
Period size: 100 Copynumber: 2.1 Consensus size: 99
5524891 TTTTTAAGTT
* * * * *
5524901 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAAC-T-TATATATATGTACGTATAT
*
5524966 A-TATAATACTTTCTATACATATTTTATAATTTCTA
64 AGTATAATACTTTCTATACACATTTTATAATTTCTA
*
5525001 TATATATATAATCATTATCTTTATGATCTATATGTTTATTAACTTATATATATGTACGTATATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATGTACGTATATA-
* *
5525066 GTATTATACTTTCTATCCACATTTTATAATTTCTA
65 GTATAATACTTTCTATACACATTTTATAATTTCTA
*
5525101 TATGTATAT
1 TATATATAT
5525110 TTTCTTTATT
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
98 20 0.21
99 1 0.01
100 76 0.78
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.53
Consensus pattern (99 bp):
TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATGTACGTATATAG
TATAATACTTTCTATACACATTTTATAATTTCTA
Found at i:5528798 original size:989 final size:989
Alignment explanation
Indices: 5526882--5528858 Score: 3936
Period size: 989 Copynumber: 2.0 Consensus size: 989
5526872 CCGAGACTTT
*
5526882 ATGATACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACC
1 ATGATACGGGGTTGCACGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACC
5526947 CTAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTG
66 CTAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTG
5527012 AAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAA
131 AAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAA
5527077 ACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAA
196 ACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAA
5527142 TCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTT
261 TCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTT
5527207 AAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAG
326 AAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAG
5527272 TAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTC
391 TAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTC
5527337 GAAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAA
456 GAAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAA
5527402 GAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAG
521 GAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAG
5527467 AAAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATG
586 AAAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATG
5527532 ATAAGTGTTTAACAAGGTGGACAGTCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAAT
651 ATAAGTGTTTAACAAGGTGGACAGTCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAAT
5527597 TAGAAAACTAAAATAAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTT
716 TAGAAAACTAAAATAAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTT
5527662 ATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAAAAT
781 ATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAAAAT
5527727 AAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGAT
846 AAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGAT
5527792 GGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTG
911 GGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTG
5527857 ACTCGTATCATTCA
976 ACTCGTATCATTCA
5527871 ATGATACGGGGTTGCACGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACC
1 ATGATACGGGGTTGCACGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACC
5527936 CTAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTG
66 CTAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTG
5528001 AAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAA
131 AAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAA
5528066 ACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAA
196 ACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAA
5528131 TCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTT
261 TCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTT
5528196 AAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAG
326 AAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAG
5528261 TAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTC
391 TAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTC
5528326 GAAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAA
456 GAAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAA
5528391 GAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAG
521 GAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAG
5528456 AAAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATG
586 AAAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATG
5528521 ATAAGTGTTTAACAAGGTGGACAGTCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAAT
651 ATAAGTGTTTAACAAGGTGGACAGTCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAAT
5528586 TAGAAAACTAAAATAAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTT
716 TAGAAAACTAAAATAAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTT
5528651 ATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAAAAT
781 ATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAAAAT
5528716 AAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGAT
846 AAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGAT
*
5528781 GGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCTCCTTCAAGAATTTGGGCTTTTGTG
911 GGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTG
5528846 ACTCGTATCATTC
976 ACTCGTATCATTC
5528859 CTCCCTTCCT
Statistics
Matches: 986, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
989 986 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (989 bp):
ATGATACGGGGTTGCACGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAACC
CTAAACAATTAGATCTGAAACGAAACAGAAAATTAAAAGATTAGATTTTTGAATTTTCAGATCTG
AAATAAAATCCCCAAATCAGCAAAGAATCAAATTGAGAATAGAAATAAGTGTTAGGGTTCTTGAA
ACCCTCAAGGAGATTGTGATTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAA
TCTAATTTCACCCAAAAAGAGTATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTT
AAGATAGAAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAG
TAGAAATAAAGAAAGAATTGACAGTAAGAAATTAAAAGATAAGTCCTAAGAAGCCTTGAAATCTC
GAAAGATCTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAAAGAATATCAATGGCAAGAA
GAAGGTTGAAGATGGCTCCCACAATCACAAGATTGTTAAAACAACTTCTAAAGAAAACTCAAGAG
AAAAATCTTGGAGAAAACTCAAAGAAAATTCTGCTCTCAACAAATCTGAAATTTTAATAATAATG
ATAAGTGTTTAACAAGGTGGACAGTCATGCCTTTAAATAGGCCTTATAACTAGTCCTAATCTAAT
TAGAAAACTAAAATAAAAAAAACTCCTAATTATTTTAATATGGAAATTCGGTCAAAGGTCATTTT
ATCTGGGACTCTTGGACTGAATATTGACATAAAAATTTAAACTAAGTAAATAAATAAATAAAAAT
AAAAATAAAACTTTACAACTTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGTATGGAT
GGATTTCTTGATTGGGCTGGGAATTTGCTTATTGGGCCTCGCCTTCAAGAATTTGGGCTTTTGTG
ACTCGTATCATTCA
Found at i:5530123 original size:23 final size:22
Alignment explanation
Indices: 5530071--5530123 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
5530061 TTCCACGTCT
*
5530071 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
5530093 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
5530116 TTTCTTTT
1 TTTCTTTT
5530124 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:5547422 original size:1 final size:1
Alignment explanation
Indices: 5547411--5547454 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
5547401 CTTCACTTGG
* * * *
5547411 AAAAAAGAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5547455 GGAGAGGCCA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:5547432 original size:11 final size:11
Alignment explanation
Indices: 5547411--5547454 Score: 81
Period size: 11 Copynumber: 4.1 Consensus size: 11
5547401 CTTCACTTGG
5547411 AAAAAAG-AAA
1 AAAAAAGAAAA
5547421 AAAAAAGAAAA
1 AAAAAAGAAAA
5547432 AAAAAAGAAAA
1 AAAAAAGAAAA
5547443 AAAAAAGAAAA
1 AAAAAAGAAAA
5547454 A
1 A
5547455 GGAGAGGCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 7 0.21
11 26 0.79
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:5548513 original size:50 final size:50
Alignment explanation
Indices: 5548457--5548617 Score: 130
Period size: 50 Copynumber: 3.2 Consensus size: 50
5548447 TTGAAGCCGT
*
5548457 AACGGTGAATCTTACTCCCCTGGCAGTGCAGTGGAACAGATTGAAGCTAC
1 AACGGTGAATCTTACTCCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTAC
* * * ** * * * *
5548507 AGCGGTGAATCCTGT-TTCCTC-GATATTGCAAT-TAAAAGATTGAAGCTGC
1 AACGGTGAAT-CT-TACTCCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTAC
* * * **
5548556 AACGGCGAATCTTACTCCCTTGGCGGTGCAGTGGAATGGATTGAAGCTAC
1 AACGGTGAATCTTACTCCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTAC
* *
5548606 GACGGAGAATCT
1 AACGGTGAATCT
5548618 CGTTTCCCTG
Statistics
Matches: 80, Mismatches: 26, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
47 1 0.01
48 5 0.06
49 28 0.35
50 39 0.49
51 6 0.08
52 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (50 bp):
AACGGTGAATCTTACTCCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTAC
Found at i:5548829 original size:100 final size:98
Alignment explanation
Indices: 5548425--5548876 Score: 496
Period size: 99 Copynumber: 4.5 Consensus size: 98
5548415 TTACTCGTAC
* * * * * *
5548425 CCCTGAGATTGCATTTAAAAGTTTGAAGCCGTAACGGTGAATCTTACTCCCCTGGCAGTGCAGTG
1 CCCTGACATTGCAATTAAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCAGTGCAGTG
* * *
5548490 GAACAGATTGAAGCTAC-AGCGGTGAATCCTGTTT
66 GAACAGATTAAAGCTACGA-CGG-AAATCTTGTTT
* * *
5548524 -CCTCGATATTGCAATTAAAAGATTGAAGCTGCAACGGCGAATCTTAC-TCCCTTGGCGGTGCAG
1 CCCT-GACATTGCAATTAAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCC-TGGCAGTGCAG
** * *
5548587 TGGAATGGATTGAAGCTACGACGGAGAATCTCGTTT
64 TGGAACAGATTAAAGCTACGACGGA-AATCTTGTTT
** * * * **
5548623 CCCTGACATTATAATTAAAAGATTGAAGCCGTAACGGCGAATCTTACTCCCCTAGTGGTGCAGTG
1 CCCTGACATTGCAATTAAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCAGTGCAGTG
* * **
5548688 GAACAAATTAAAGCTACAAACAAAAAATCTTGTTT
66 GAACAGATTAAAGCTAC-GAC-GGAAATCTTGTTT
* * *
5548723 CCCTGACATTGCAATTAAAAAGATTGAGGCCGCAACAGCAAATCTTACTTCCCTGGCAGTGCAGT
1 CCCTGACATTGCAATT-AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCAGTGCAGT
* * *
5548788 GGAACATATTAAAGCTACGATGGCAAATCTTGCTT
65 GGAACAGATTAAAGCTACGACGG-AAATCTTGTTT
5548823 CCCTGACATTGCAATTAAAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCCT
1 CCCTGACATTGCAATT-AAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCCT
5548877 AGCATAGACA
Statistics
Matches: 295, Mismatches: 48, Indels: 19
0.81 0.13 0.05
Matches are distributed among these distances:
98 6 0.02
99 137 0.46
100 94 0.32
101 58 0.20
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (98 bp):
CCCTGACATTGCAATTAAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCAGTGCAGTG
GAACAGATTAAAGCTACGACGGAAATCTTGTTT
Found at i:5548867 original size:50 final size:50
Alignment explanation
Indices: 5548712--5548876 Score: 168
Period size: 50 Copynumber: 3.3 Consensus size: 50
5548702 TACAAACAAA
** * *
5548712 AAATCTTGTTTCCCTGACATTGCAATTAAAAAGATTGAGGCCGCAACAGC
1 AAATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCCGCAACGGC
* * * ** * * * ** * *
5548762 AAATCTTACTTCCCTGGCAGTGCAGTGGAACATATTAAAGCTACGATGGC
1 AAATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCCGCAACGGC
*
5548812 AAATCTTGCTTCCCTGACATTGCAATTAAAAAGATTGAAGCCGCAACGGC
1 AAATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCCGCAACGGC
*
5548862 GAATCTTACTTCCCT
1 AAATCTTACTTCCCT
5548877 AGCATAGACA
Statistics
Matches: 84, Mismatches: 31, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (50 bp):
AAATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCCGCAACGGC
Found at i:5549103 original size:87 final size:83
Alignment explanation
Indices: 5548957--5549655 Score: 274
Period size: 87 Copynumber: 8.3 Consensus size: 83
5548947 CCACAGATCT
* * ** * * *
5548957 TATCTCCTTAAGCAGTAGTGGAGCAGATT-GCATCAAGTCTTATCTCCTTAAGCAGTAGTGGAGC
1 TATCTCCCTAAGCAGTAGTGGAGCTGATTAAAAACAAATCTTATCTCC-TAAGTAGTAGTGGAGC
5549021 AGACGGAAGAAACCAATCC
65 AGACGGAAGAAACCAATCC
**
5549040 TATCTCCCTAAAGTTGTAGTGGAGCTGATTAAAACCACAAATCTTATCTCTCTAAGTAGTAGTGG
1 TATCTCCCT-AAGCAGTAGTGGAGCTGATTAAAA--ACAAATCTTATCTC-CTAAGTAGTAGTGG
* * *
5549105 AGCAGATC----G-CATCAAGTCT
62 AGCAGA-CGGAAGAAACCAA-TCC
* * * * * *
5549124 TATCTCCCTAAGCAGTAGTAGAG-TAGATGGAAGAAACCAATCCTATCTCCTTGAAGTTGCAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCT-GAT-TAA-AAACAAATCTTATCTCC-T-AAGTAGTAGTG
** ** * *
5549188 GAGTGGA-TTAA-AACCACAGATCT
61 GAGCAGACGGAAGAAAC-CA-ATCC
* *** * * *
5549211 TATCTCCCTAAGCAGTAGTGGAGCAGA-TCGTATCAAGTCTTATCTCCCTAAGTAGTAGTGAAGC
1 TATCTCCCTAAGCAGTAGTGGAGCTGATTAAAAACAAATCTTATCT-CCTAAGTAGTAGTGGAGC
5549275 AGACGGAAGAAACCAATCC
65 AGACGGAAGAAACCAATCC
** * * *
5549294 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAACCATAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCT-AAGCAGTAGTGGAGCTGATTAAAAACA-A-ATCTTATCT-CCTAAGTAGTAGTGG
* * ** * *
5549359 AGTAGATC-GCA-TTA--AGTCT
62 AGCAGA-CGGAAGAAACCAATCC
* * * * *** *
5549378 TATCTCCCTAAGCAGTAGTGGAGCAGATGGAAGAAACCAATCCTATCTCCTTGAAGTTCCAGTGA
1 TATCTCCCTAAGCAGTAGTGGAGCTGAT-TAA-AAACAAATCTTATCTCC-T-AAGTAGTAGTGG
* *** *
5549443 AG-TGA-ATTA-AAACCATAGATCT
62 AGCAGACGGAAGAAACC--A-ATCC
* * *** * * **
5549465 TATCTCCCTAAGCAGTAGTGCAGCAGA-TCGCATCAAGTCTTATCTCCTTAACCAGTAGTGGAGC
1 TATCTCCCTAAGCAGTAGTGGAGCTGATTAAAAACAAATCTTATCTCC-TAAGTAGTAGTGGAGC
*
5549529 AGACAGAAGAAACCAATCC
65 AGACGGAAGAAACCAATCC
** * * * *
5549548 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCT-AAGCAGTAGTGGAGCTGATTAAAA--ACAAATCTTATCT-CCTAAGTAGTAGTGG
* *
5549613 AGCAGATC----G-AATCAAGTCT
62 AGCAGA-CGGAAGAAACCAA-TCC
5549632 TATCTCCCTAAGCAGTAGTGGAGC
1 TATCTCCCTAAGCAGTAGTGGAGC
5549656 AGATCGCATC
Statistics
Matches: 454, Mismatches: 114, Indels: 96
0.68 0.17 0.14
Matches are distributed among these distances:
82 6 0.01
83 128 0.28
84 141 0.31
85 19 0.04
86 8 0.02
87 145 0.32
88 7 0.02
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (83 bp):
TATCTCCCTAAGCAGTAGTGGAGCTGATTAAAAACAAATCTTATCTCCTAAGTAGTAGTGGAGCA
GACGGAAGAAACCAATCC
Found at i:5549129 original size:127 final size:127
Alignment explanation
Indices: 5548903--5549658 Score: 1188
Period size: 127 Copynumber: 6.0 Consensus size: 127
5548893 AAAAAGAAAA
* * *
5548903 AAACCAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCTTAA
1 AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAA
* *
5548968 GCAGTAGTGGAGCAGATTGCATCAAGTCTTATCTCCTTAAGCAGTAGTGGAGCAGACGGAAG
66 GCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGGAAG
* * * *
5549030 AAACCAATCCTATCTCCCTAAAGTTGTAGTGGAGCTGATTAAAACCACAAATCTTATCTCTCTAA
1 AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAA
* * * *
5549095 GTAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGAGTAGATGGAAG
66 GCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGGAAG
* * *
5549157 AAACCAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCCCTAA
1 AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAA
* * *
5549222 GCAGTAGTGGAGCAGATCGTATCAAGTCTTATCTCCCTAAGTAGTAGTGAAGCAGACGGAAG
66 GCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGGAAG
* *
5549284 AAACCAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAACCATAGATCTTATCTCCCTAA
1 AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAA
* * *
5549349 GCAGTAGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATGGAAG
66 GCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGGAAG
* * * * * * *
5549411 AAACCAATCCTATCTCCTTGAAGTTCCAGTGAAGTGAATTAAAACCATAGATCTTATCTCCCTAA
1 AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAA
* * * *
5549476 GCAGTAGTGCAGCAGATCGCATCAAGTCTTATCTCCTTAACCAGTAGTGGAGCAGACAGAAG
66 GCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGGAAG
5549538 AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAA
1 AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAA
*
5549603 GCAGTAGTGGAGCAGATCGAATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
66 GCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
5549659 TCGCATCAAG
Statistics
Matches: 566, Mismatches: 63, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
127 566 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (127 bp):
AAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGGAAG
Found at i:5550039 original size:19 final size:19
Alignment explanation
Indices: 5550015--5550055 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
5550005 AAAGCCCAGG
5550015 CAAAACCCAATACCCAAA-A
1 CAAAACCCAA-ACCCAAATA
5550034 CAAAACCCAAACCCAAATA
1 CAAAACCCAAACCCAAATA
5550053 CAA
1 CAA
5550056 CTAAACCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.59, C:0.37, G:0.00, T:0.05
Consensus pattern (19 bp):
CAAAACCCAAACCCAAATA
Found at i:5551322 original size:18 final size:21
Alignment explanation
Indices: 5551299--5551342 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5551289 CATATACATG
5551299 CATACA-TTTT-A-TAATACA
1 CATACATTTTTAATTAATACA
5551317 CATACATTTTTAATTAATACA
1 CATACATTTTTAATTAATACA
5551338 CATAC
1 CATAC
5551343 TTATACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 1 0.04
21 12 0.52
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (21 bp):
CATACATTTTTAATTAATACA
Found at i:5552063 original size:108 final size:106
Alignment explanation
Indices: 5551867--5552195 Score: 360
Period size: 106 Copynumber: 3.1 Consensus size: 106
5551857 ATAAAAAAGA
* *
5551867 AAAATTTCT-AAATAAGGCAATATTTTGCGTTTGAAAAATT-GAGAAAACATGCCCTAACGTGCT
1 AAAATTT-TAAAATAAGGCAATATTTTGCGTTTG-GAAATTCGAGAAAACATGCCCTAATGTGCT
* *
5551930 GGGTTTTGATTTCTCGTTCGACCAAAATAGCCAAATACCCTTTTT
64 GGGTTTCGATTTCTCGTTCGACC-AAATAGCCAAATACCC-TTTC
* * * * * *
5551975 AAAATTTTAAAATAAGACCATATTTCGCGTTTGGAAATTCGAGAAAACGTGCCCTAATATGTTGG
1 AAAATTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGG
* * * * * *
5552040 GTTTCGATTACTCGTTTGGCCAAATAGTCGAATATCCTTTC
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATACCCTTTC
* * ** * *
5552081 GAAATTCTAAAACGAGGCAATGTTTTGCGTTTGGAAATTCGAGAGAACATGCCCTAATGTGCTGG
1 AAAATTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGG
* * *
5552146 GTTTCGATTTCTCGTTCGACTAAATAGCCCAATATCCTCTT-
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATACCCT-TTC
5552187 -AAATTTTAA
1 AAAATTTTAA
5552196 TCCATGTCGT
Statistics
Matches: 183, Mismatches: 35, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
105 8 0.04
106 88 0.48
107 21 0.11
108 66 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (106 bp):
AAAATTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGG
GTTTCGATTTCTCGTTCGACCAAATAGCCAAATACCCTTTC
Found at i:5555405 original size:27 final size:28
Alignment explanation
Indices: 5555360--5555413 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
5555350 ATGCTGTCTT
5555360 GAAACCTAAGAAACGAGAAAACAACAAA
1 GAAACCTAAGAAACGAGAAAACAACAAA
*
5555388 GAAA-CTAAGTAAAC-AGAAAATAACAA
1 GAAACCTAAG-AAACGAGAAAACAACAA
5555414 CAATGACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.65, C:0.15, G:0.13, T:0.07
Consensus pattern (28 bp):
GAAACCTAAGAAACGAGAAAACAACAAA
Found at i:5561683 original size:56 final size:56
Alignment explanation
Indices: 5561621--5561735 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
5561611 GAAGCCAAAT
*
5561621 TAAGTGACCATATCATATGTATCATATATATATACTAGTGTATCATGTAATTAAGG
1 TAAGTGACCATATCATATGTATCATATATATACACTAGTGTATCATGTAATTAAGG
5561677 TAAGTGACCATATCATATGTATCATATATATACACTAGTGTATCATGTAATTAAGG
1 TAAGTGACCATATCATATGTATCATATATATACACTAGTGTATCATGTAATTAAGG
5561733 TAA
1 TAA
5561736 TTGTTTAGGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (56 bp):
TAAGTGACCATATCATATGTATCATATATATACACTAGTGTATCATGTAATTAAGG
Found at i:5562277 original size:49 final size:49
Alignment explanation
Indices: 5562222--5562372 Score: 177
Period size: 49 Copynumber: 3.2 Consensus size: 49
5562212 TGACATCCCG
*
5562222 GATTGCCCGACAACAATGATTTTCTCAGTTTGAACAATCTGTCACCCTA
1 GATTGCCCGACAACGATGATTTTCTCAGTTTGAACAATCTGTCACCCTA
* * * * ** *
5562271 GATTGCCC-AGCAACGGTGA--ATCT-A-TGTGAACAATTTACCACCTTA
1 GATTGCCCGA-CAACGATGATTTTCTCAGTTTGAACAATCTGTCACCCTA
*
5562316 GGTTGCCCGACAACGATGATTTTCTCAGTTTGAACAATCTGTCACCCTA
1 GATTGCCCGACAACGATGATTTTCTCAGTTTGAACAATCTGTCACCCTA
5562365 GATTGCCC
1 GATTGCCC
5562373 AGCAAGGGTG
Statistics
Matches: 79, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
45 31 0.39
46 2 0.03
47 6 0.08
48 2 0.03
49 38 0.48
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (49 bp):
GATTGCCCGACAACGATGATTTTCTCAGTTTGAACAATCTGTCACCCTA
Done.