Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 135 of 171
Found at i:41903542 original size:52 final size:53
Alignment explanation
Indices: 41903429--41903559 Score: 203
Period size: 52 Copynumber: 2.5 Consensus size: 53
41903419 GCACACAGAC
* * *
41903429 GTGTGTCAGGGTGTGTGTATATTGTTCTAAGGCACATGGGCTGACACATAGGA
1 GTGTGTCAGGGTGTGTGTATACTGTTCTAAGGCACATGGGCTAACACATAGCA
*
41903482 GTGTGTCAGGGTGTGTGTATACTGTTCTAAGG-ATATGGGCTAACACATGAGCA
1 GTGTGTCAGGGTGTGTGTATACTGTTCTAAGGCACATGGGCTAACACAT-AGCA
41903535 -TGTGTCAGGGTGTGTGTATACTGTT
1 GTGTGTCAGGGTGTGTGTATACTGTT
41903560 TTCAGACACA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
52 39 0.53
53 34 0.47
ACGTcount: A:0.21, C:0.12, G:0.34, T:0.33
Consensus pattern (53 bp):
GTGTGTCAGGGTGTGTGTATACTGTTCTAAGGCACATGGGCTAACACATAGCA
Found at i:41904141 original size:12 final size:12
Alignment explanation
Indices: 41904124--41904166 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
41904114 TCATGTTTGC
*
41904124 ATCTGTAACTAT
1 ATCTGTATCTAT
41904136 ATCTGTATC-AT
1 ATCTGTATCTAT
41904147 ATCTGTATCTAT
1 ATCTGTATCTAT
*
41904159 AACTGTAT
1 ATCTGTAT
41904167 TTGTGACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.44
Consensus pattern (12 bp):
ATCTGTATCTAT
Found at i:41904858 original size:33 final size:32
Alignment explanation
Indices: 41904812--41904877 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
41904802 AAGAAAGATA
* *
41904812 AATTCTATTAGGATTTGAAAAGGAGTAGTTTG
1 AATTCTATTAGGATTTAAAAAGGAGTACTTTG
*
41904844 AATTCTAGTTAGGATTTAAAAAGGATTACTTTG
1 AATTCTA-TTAGGATTTAAAAAGGAGTACTTTG
41904877 A
1 A
41904878 CTTTCAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (32 bp):
AATTCTATTAGGATTTAAAAAGGAGTACTTTG
Found at i:41906248 original size:18 final size:16
Alignment explanation
Indices: 41906225--41906266 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
41906215 TATTTTGAAA
41906225 AAAAATATAAAATTTTAT
1 AAAAATA-AAAA-TTTAT
*
41906243 AAAAATAGAAATTTAT
1 AAAAATAAAAATTTAT
41906259 AAAAATAA
1 AAAAATAA
41906267 TTAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 12 0.55
17 3 0.14
18 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AAAAATAAAAATTTAT
Found at i:41906323 original size:2 final size:2
Alignment explanation
Indices: 41906312--41906349 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
41906302 ATAAATGTAA
41906312 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41906350 ATCACTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41906900 original size:19 final size:19
Alignment explanation
Indices: 41906876--41906914 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41906866 ATTAATTATA
41906876 AATT-AATGAACTATATTTT
1 AATTAAATGAACT-TATTTT
*
41906895 AATTAAATTAACTTATTTT
1 AATTAAATGAACTTATTTT
41906914 A
1 A
41906915 TTTTTAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (19 bp):
AATTAAATGAACTTATTTT
Found at i:41927355 original size:18 final size:18
Alignment explanation
Indices: 41927340--41927374 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41927330 GAGAGCTCTA
41927340 CTAAACATGCGAGCTCAC
1 CTAAACATGCGAGCTCAC
*
41927358 CTAAACATGCAAGCTCA
1 CTAAACATGCGAGCTCA
41927375 ACCAAAGATA
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:0.37, C:0.31, G:0.14, T:0.17
Consensus pattern (18 bp):
CTAAACATGCGAGCTCAC
Found at i:41927390 original size:18 final size:17
Alignment explanation
Indices: 41927369--41927412 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
41927359 TAAACATGCA
41927369 AGCTCAACCAAAGA-TATG
1 AGCTC-ACC-AAGATTATG
41927387 AGCTCACCAAGATTATG
1 AGCTCACCAAGATTATG
*
41927404 AGCTTACCA
1 AGCTCACCA
41927413 TATCTGTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 15 0.62
18 5 0.21
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (17 bp):
AGCTCACCAAGATTATG
Found at i:41927516 original size:79 final size:79
Alignment explanation
Indices: 41927425--41927575 Score: 230
Period size: 79 Copynumber: 1.9 Consensus size: 79
41927415 TCTGTGAGCC
* * * * * *
41927425 TGCGAGCTCATTAAACTTTAGAAGTCACTATAGGTGCGAGCTTTATCAAGAGAACCCATACCTGC
1 TGCGAGCTCATTAAACCTGAGAAGTCACTAAAGGTGCAAGCTCTATCAAGAGAACCCATACATGC
41927490 AAGCTCACTAATAG
66 AAGCTCACTAATAG
* *
41927504 TGCGAGCTCATTAAACCTGAGAAGTCACTAAAGGTGCAAGCTCTATCAGGAGAATCCATACATGC
1 TGCGAGCTCATTAAACCTGAGAAGTCACTAAAGGTGCAAGCTCTATCAAGAGAACCCATACATGC
41927569 AAGCTCA
66 AAGCTCA
41927576 TTACTCTGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (79 bp):
TGCGAGCTCATTAAACCTGAGAAGTCACTAAAGGTGCAAGCTCTATCAAGAGAACCCATACATGC
AAGCTCACTAATAG
Found at i:41935703 original size:17 final size:17
Alignment explanation
Indices: 41935681--41935719 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
41935671 CTCCACCTTG
* *
41935681 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
41935698 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
41935715 ACAAG
1 ACAAG
41935720 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:41940512 original size:39 final size:39
Alignment explanation
Indices: 41940434--41940512 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 39
41940424 TATCATTCAA
* * *
41940434 AAATAATAATAATAATATTTTATTTAAATTTAATTATAT
1 AAATAATAATAATAAAATTTTATTTAAATTCAATAATAT
*
41940473 AAATATTAAT-ATAAAATTATTATTTTAAA-TCAATAATAT
1 AAATAATAATAATAAAATT-TTA-TTTAAATTCAATAATAT
41940512 A
1 A
41940513 TTTTTATTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
38 7 0.21
39 21 0.62
40 6 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (39 bp):
AAATAATAATAATAAAATTTTATTTAAATTCAATAATAT
Found at i:41952899 original size:33 final size:36
Alignment explanation
Indices: 41952857--41952923 Score: 104
Period size: 33 Copynumber: 1.9 Consensus size: 36
41952847 TGTTTATGTG
*
41952857 AAATTGAAGAGAAA-GAGAAGAG-AG-GCAAAGATC
1 AAATTGAAGAGAAAGGAAAAGAGAAGAGCAAAGATC
41952890 AAATTGAAGAGAAAGGAAAAGAGAAGAGCAAAGA
1 AAATTGAAGAGAAAGGAAAAGAGAAGAGCAAAGA
41952924 GTGAAAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 14 0.47
34 7 0.23
35 2 0.07
36 7 0.23
ACGTcount: A:0.58, C:0.04, G:0.30, T:0.07
Consensus pattern (36 bp):
AAATTGAAGAGAAAGGAAAAGAGAAGAGCAAAGATC
Found at i:41953825 original size:25 final size:24
Alignment explanation
Indices: 41953788--41953845 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
41953778 ACACTAGCGC
41953788 GCTCTCTG-TTTAGCAC-GTCTCGT
1 GCTCTCTGTTTTAGCACTGTCT-GT
* *
41953811 GCTCTCTGTTATTAGTACTGTGTGT
1 GCTCTCTGTT-TTAGCACTGTCTGT
41953836 GCTCTCTGTT
1 GCTCTCTGTT
41953846 GCCCAGCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 8 0.27
24 1 0.03
25 18 0.60
26 3 0.10
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (24 bp):
GCTCTCTGTTTTAGCACTGTCTGT
Found at i:41956304 original size:25 final size:25
Alignment explanation
Indices: 41956256--41956303 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
41956246 AAATTCAAAA
*
41956256 TATTTATAAAAAATTCTAAATTTTG
1 TATTTATAAAAAATTATAAATTTTG
*
41956281 TATTT-TAAAAAATTATAATTTTT
1 TATTTATAAAAAATTATAAATTTT
41956304 TTTAAATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTTATAAAAAATTATAAATTTTG
Found at i:41958400 original size:22 final size:21
Alignment explanation
Indices: 41958369--41958417 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
41958359 ACAAATTTTA
41958369 TTTTTCTCT-CGCTT-CTAGGAG
1 TTTTTCTCTCCG-TTGCT-GGAG
41958390 TTTTTCTTCTCCGTTGCTGGAG
1 TTTTTC-TCTCCGTTGCTGGAG
41958412 TTTTTC
1 TTTTTC
41958418 CATTGAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.24
22 15 0.60
23 4 0.16
ACGTcount: A:0.06, C:0.22, G:0.18, T:0.53
Consensus pattern (21 bp):
TTTTTCTCTCCGTTGCTGGAG
Found at i:41962532 original size:3 final size:3
Alignment explanation
Indices: 41962524--41962597 Score: 94
Period size: 3 Copynumber: 24.7 Consensus size: 3
41962514 AAACTTAATG
* * *
41962524 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTG TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
41962572 TTG TTG TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
41962598 TTCTATTTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41970247 original size:23 final size:25
Alignment explanation
Indices: 41970195--41970247 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
41970185 TGATTATCCA
** *
41970195 ATTTTAATTTTTTTTCAATTTAATC
1 ATTTTAATTTTTTTGAAATTAAATC
41970220 A-TTTAA-TTTTTTGAAATTAAAT-
1 ATTTTAATTTTTTTGAAATTAAATC
41970242 ATTTTA
1 ATTTTA
41970248 GTCTGCTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.04
23 17 0.71
24 5 0.21
25 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (25 bp):
ATTTTAATTTTTTTGAAATTAAATC
Found at i:41970500 original size:21 final size:21
Alignment explanation
Indices: 41970454--41970502 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
41970444 TAGAAATTAA
41970454 AAAAAAACATGTATTAAAGAT
1 AAAAAAACATGTATTAAAGAT
* *
41970475 TAAAAAATATGTATTAATA-AT
1 AAAAAAACATGTATTAA-AGAT
41970496 AAAAAAA
1 AAAAAAA
41970503 AAACCACACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (21 bp):
AAAAAAACATGTATTAAAGAT
Found at i:41971327 original size:20 final size:20
Alignment explanation
Indices: 41971304--41971368 Score: 98
Period size: 19 Copynumber: 3.4 Consensus size: 20
41971294 CTCTCTTAAC
*
41971304 AAAAATTTAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
41971324 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
*
41971344 -AAAATTCAAAATAA-TTAT
1 AAAAATTCAAAATAATTTTT
41971362 AAAAATT
1 AAAAATT
41971369 TTAAATTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
18 3 0.07
19 20 0.48
20 19 0.45
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:41971407 original size:19 final size:19
Alignment explanation
Indices: 41971351--41971412 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
41971341 TTTAAAATTC
*
41971351 AAAATAATTATAAAAATTTT
1 AAAA-AATTATAATAATTTT
*
41971371 ---AAATTATATATATTTTTT
1 AAAAAATTATA-ATA-ATTTT
41971389 AAAAAATTATAATAATTTT
1 AAAAAATTATAATAATTTT
41971408 AAAAA
1 AAAAA
41971413 TAATCTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
16 7 0.21
17 3 0.09
18 4 0.12
19 9 0.26
20 3 0.09
21 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAAATTATAATAATTTT
Found at i:41971413 original size:18 final size:18
Alignment explanation
Indices: 41971356--41971413 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
41971346 AATTCAAAAT
*
41971356 AATTATAAAAATTTT--A
1 AATTATAATAATTTTAAA
*
41971372 AATTATATATATTTTTTAAAA
1 AATTATA-ATA-ATTTT-AAA
41971393 AATTATAATAATTTTAAA
1 AATTATAATAATTTTAAA
41971411 AAT
1 AAT
41971414 AATCTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 7 0.21
17 2 0.06
18 10 0.29
19 4 0.12
20 3 0.09
21 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTATAATAATTTTAAA
Found at i:41971416 original size:12 final size:12
Alignment explanation
Indices: 41971408--41971435 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41971398 TAATAATTTT
41971408 AAAAATAATCTA
1 AAAAATAATCTA
41971420 AAAAATAATCTA
1 AAAAATAATCTA
41971432 AAAA
1 AAAA
41971436 GAGTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAATAATCTA
Found at i:41976930 original size:17 final size:17
Alignment explanation
Indices: 41976895--41976936 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
41976885 GGATAAAATA
*
41976895 GTTATAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
41976913 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
41976930 GTTAAAG
1 GTTAAAG
41976937 GCCAAGAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.24
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:41978644 original size:24 final size:24
Alignment explanation
Indices: 41978603--41978649 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41978593 AATTATACGA
*
41978603 ATAATAAATACAAAAAACAAATAT
1 ATAATAAATAAAAAAAACAAATAT
41978627 ATAA-AAATAAAAATAAACAAATA
1 ATAATAAATAAAAA-AAACAAATA
41978650 CGCAATGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (24 bp):
ATAATAAATAAAAAAAACAAATAT
Found at i:41978863 original size:30 final size:30
Alignment explanation
Indices: 41978789--41978987 Score: 215
Period size: 30 Copynumber: 6.7 Consensus size: 30
41978779 AAGGAAAAAT
* *
41978789 GGGGTCAAAATA-AAATTTTGGAAAGTTT-
1 GGGGTCAAAACATAATTTTTGGAAAGTTTA
* **
41978817 GGGG-CCAAATTTGAATTTTTGGAAAGTTTA
1 GGGGTCAAAACAT-AATTTTTGGAAAGTTTA
* * ** * * *
41978847 AGGGTTAAATTAGAATTTTTAGAAAGTTTG
1 GGGGTCAAAACATAATTTTTGGAAAGTTTA
*
41978877 GGGGTCAAAACATAATTTTTGGATAGTTTA
1 GGGGTCAAAACATAATTTTTGGAAAGTTTA
* *
41978907 AGGGTCAAAACATAATTTTTTTGAAAGTTTA
1 GGGGTCAAAACATAA-TTTTTGGAAAGTTTA
*
41978938 GGGGTCAAAACATAATTTTTTGAAAGTTTA
1 GGGGTCAAAACATAATTTTTGGAAAGTTTA
41978968 GGGGTCAAAACATAATTTTT
1 GGGGTCAAAACATAATTTTT
41978988 AAATAAAATT
Statistics
Matches: 143, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 5 0.03
28 4 0.03
29 15 0.10
30 89 0.62
31 30 0.21
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.37
Consensus pattern (30 bp):
GGGGTCAAAACATAATTTTTGGAAAGTTTA
Found at i:41978952 original size:61 final size:61
Alignment explanation
Indices: 41978830--41978987 Score: 228
Period size: 61 Copynumber: 2.6 Consensus size: 61
41978820 GCCAAATTTG
* ** * *
41978830 AATTTTTGGAAAGTTTAAGGGTTAAATTAGAA-TTTTTAGAAAGTTTGGGGGTCAAAACAT
1 AATTTTTGGAAAGTTTAAGGGTCAAAACATAATTTTTTAGAAAGTTTAGGGGTCAAAACAT
* *
41978890 AATTTTTGGATAGTTTAAGGGTCAAAACATAATTTTTTTGAAAGTTTAGGGGTCAAAACAT
1 AATTTTTGGAAAGTTTAAGGGTCAAAACATAATTTTTTAGAAAGTTTAGGGGTCAAAACAT
* *
41978951 AATTTTTTGAAAGTTTAGGGGTCAAAACATAATTTTT
1 AATTTTTGGAAAGTTTAAGGGTCAAAACATAATTTTT
41978988 AAATAAAATT
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
60 27 0.31
61 60 0.69
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (61 bp):
AATTTTTGGAAAGTTTAAGGGTCAAAACATAATTTTTTAGAAAGTTTAGGGGTCAAAACAT
Found at i:41979384 original size:20 final size:20
Alignment explanation
Indices: 41979351--41979390 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41979341 TTCTTTTAAA
*
41979351 AAAATGCTCCTTTCTCTCTC
1 AAAATCCTCCTTTCTCTCTC
*
41979371 AAAATCCTCTTTTCTCTCTC
1 AAAATCCTCCTTTCTCTCTC
41979391 CCTTTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.35, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATCCTCCTTTCTCTCTC
Found at i:41982601 original size:45 final size:45
Alignment explanation
Indices: 41982536--41982708 Score: 179
Period size: 45 Copynumber: 3.8 Consensus size: 45
41982526 AGGCTATACG
*
41982536 TAAAAGATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCAAGA
1 TAAAA-ATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCAAGA
* * *
41982582 TAAAAATGAGCAAGACCATAGTTGAAAGATGCTATGGCA-CAGGA
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCAAGA
* * * ** * *
41982626 CAGAAATGAGTAAGACCATGGCTGAAAGACCCTATGGCATCATGG
1 TAAAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCAAGA
* * * *
41982671 TAAACAA-GACTAAGTCCATAGCTGAAAGACGTTATGGC
1 TAAA-AATGAGTAAGACCATAGCTGAAAGATGCTATGGC
41982709 GACCTAGTAG
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
44 36 0.34
45 62 0.59
46 7 0.07
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (45 bp):
TAAAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCAAGA
Found at i:41982697 original size:89 final size:89
Alignment explanation
Indices: 41982542--41982708 Score: 212
Period size: 89 Copynumber: 1.9 Consensus size: 89
41982532 TACGTAAAAG
** *
41982542 ATGAGTAAGACCATAGCTAAAAGATGCTATGGCATCAAGATAAAAATGAGCAAGACCATAGTTGA
1 ATGAGTAAGACCATAGCTAAAAGACCCTATGGCATCAAGATAAAAATGAGCAAGACCATAGCTGA
*
41982607 AAGATGCTATGGCACAGGACAGAA
66 AAGACGCTATGGCACAGGACAGAA
* * * * *
41982631 ATGAGTAAGACCATGGCTGAAAGACCCTATGGCATCATGGTAAACAA-GA-CTAAGTCCATAGCT
1 ATGAGTAAGACCATAGCTAAAAGACCCTATGGCATCAAGATAAA-AATGAGC-AAGACCATAGCT
*
41982694 GAAAGACGTTATGGC
64 GAAAGACGCTATGGC
41982709 GACCTAGTAG
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
88 1 0.02
89 63 0.95
90 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (89 bp):
ATGAGTAAGACCATAGCTAAAAGACCCTATGGCATCAAGATAAAAATGAGCAAGACCATAGCTGA
AAGACGCTATGGCACAGGACAGAA
Found at i:41985998 original size:22 final size:19
Alignment explanation
Indices: 41985968--41986011 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
41985958 TCTTTCATGA
41985968 TTAACTTAATTAATCACTTAT
1 TTAACTTAATTAATC-C-TAT
41985989 TTAACCTTAATTAATCCTAT
1 TTAA-CTTAATTAATCCTAT
41986009 TTA
1 TTA
41986012 TAATCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 11 0.50
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAACTTAATTAATCCTAT
Found at i:41993159 original size:21 final size:21
Alignment explanation
Indices: 41993133--41993212 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
41993123 CCTAAAAAAA
41993133 GTCAACGGTCAACT-ATCAATT
1 GTCAACGGTCAA-TGATCAATT
* *
41993154 GTCAACGATCAATGATCAACT
1 GTCAACGGTCAATGATCAATT
* * *
41993175 GTTAACGGTCAATGGTCAATA
1 GTCAACGGTCAATGATCAATT
*
41993196 GTCAACGGTCAACGATC
1 GTCAACGGTCAATGATC
41993213 GGTCAACGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 1 0.02
21 47 0.98
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (21 bp):
GTCAACGGTCAATGATCAATT
Found at i:41993219 original size:18 final size:18
Alignment explanation
Indices: 41993195--41993243 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
41993185 AATGGTCAAT
41993195 AGTCAACGGTCAACGATC
1 AGTCAACGGTCAACGATC
* ** *
41993213 GGTCAACGAACAACGGTC
1 AGTCAACGGTCAACGATC
*
41993231 AGTCAACAGTCAA
1 AGTCAACGGTCAA
41993244 ACCTGAATTG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (18 bp):
AGTCAACGGTCAACGATC
Found at i:42000048 original size:23 final size:24
Alignment explanation
Indices: 42000021--42000074 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
42000011 AAATTTCACA
42000021 TTTTAATC-TTTAATGTTTA-TATT
1 TTTTAATCATTTAAT-TTTATTATT
*
42000044 TTTT-ATCAATTTGATTTTATTATT
1 TTTTAATC-ATTTAATTTTATTATT
42000068 TTTTAAT
1 TTTTAAT
42000075 TAAATTTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
23 8 0.31
24 13 0.50
25 2 0.08
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTAATCATTTAATTTTATTATT
Found at i:42000080 original size:26 final size:24
Alignment explanation
Indices: 42000036--42000089 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
42000026 ATCTTTAATG
*
42000036 TTTATATTTTTTATCAATTTGAT-
1 TTTATATTTTTTATAAATTTGATC
42000059 TTTATTATTTTTTAATTAAATTTGATC
1 TTTA-TATTTTTT-A-TAAATTTGATC
42000086 TTTA
1 TTTA
42000090 ACTTTTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.15
24 8 0.31
25 1 0.04
26 9 0.35
27 4 0.15
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTATATTTTTTATAAATTTGATC
Found at i:42001533 original size:23 final size:22
Alignment explanation
Indices: 42001499--42001542 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
42001489 TATTGTTATT
* *
42001499 ATATTACATAATATATTATATG
1 ATATAACATAATATATAATATG
42001521 ATATAACATTAATATATAATAT
1 ATATAACA-TAATATATAATAT
42001543 AATAGGAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATAACATAATATATAATATG
Found at i:42003366 original size:21 final size:21
Alignment explanation
Indices: 42003341--42003381 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42003331 TTAGAGTCAT
42003341 AAATAAT-TAATTAAAGTATTG
1 AAATAATATAA-TAAAGTATTG
*
42003362 AAATAATATAATCAAGTATT
1 AAATAATATAATAAAGTATT
42003382 ATTACATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (21 bp):
AAATAATATAATAAAGTATTG
Found at i:42003913 original size:7 final size:7
Alignment explanation
Indices: 42003901--42003931 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42003891 GTTTGAGTCA
42003901 CCCTTCT
1 CCCTTCT
42003908 CCCTTCT
1 CCCTTCT
42003915 CCCTTCT
1 CCCTTCT
42003922 CCCTTCT
1 CCCTTCT
42003929 CCC
1 CCC
42003932 ATTTCTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (7 bp):
CCCTTCT
Found at i:42011421 original size:18 final size:18
Alignment explanation
Indices: 42011390--42011424 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42011380 AAAAATCAAA
42011390 TAAAAGAAAAATTAAAAT
1 TAAAAGAAAAATTAAAAT
42011408 TAAAA-AAAATATTAAAA
1 TAAAAGAAAA-ATTAAAA
42011425 GAAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
TAAAAGAAAAATTAAAAT
Found at i:42023626 original size:2 final size:2
Alignment explanation
Indices: 42023619--42023662 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
42023609 TTAATATCTG
42023619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42023661 AT
1 AT
42023663 TTGATATGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42026702 original size:20 final size:19
Alignment explanation
Indices: 42026642--42026706 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 19
42026632 CAATAGAATG
42026642 AAAGAAAATAA-AAAATC-A
1 AAAGAAAA-AAGAAAATCGA
* * *
42026660 AAA-AGAAAAGAAAATGGG
1 AAAGAAAAAAGAAAATCGA
*
42026678 GAAGAAAAGAAGAAAATCGA
1 AAAGAAAA-AAGAAAATCGA
42026698 AAAGAAAAA
1 AAAGAAAAA
42026707 CACTACAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
16 2 0.06
17 8 0.23
18 5 0.14
19 4 0.11
20 16 0.46
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.06
Consensus pattern (19 bp):
AAAGAAAAAAGAAAATCGA
Found at i:42035085 original size:162 final size:162
Alignment explanation
Indices: 42034609--42035996 Score: 2311
Period size: 162 Copynumber: 8.6 Consensus size: 162
42034599 GCGTCCAATT
* * *
42034609 TGCAAACTCTGGAGATATCGGACTGCTCCCAATTGGAAGAAATAATCCAAGGTTCAGAAGTGTCA
1 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* ** * *
42034674 AACATAAGCCTCCACTGTTTAACGGAAGTAGTAGTTCAAAAATGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
*
42034739 CCCAATGTCTGTTGCTAAAAGCCTTGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* *
42034771 TGCAAACTCTGAAGATATTGGGCTGATCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGT--
1 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* *
42034834 -ACATAAGCCTCCAAAGTTTAAGGGGAA-TACTAGTTGAAAACTGCAATAATTTGAGGTATCTCT
66 GACATAAGCCTCCAAAGTTTAA-GGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
*
42034897 TCCTAATGTCTATTGCTAAAAGCCTTGGGAGAC
130 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
*
42034930 TGCAAACTCTGAAGATATTGGGCTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* * *
42034995 GACATAAGCCTCCAAAGTTTAACGGAAGTACTAGTTGAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
*
42035060 CCCAATGTCTATTGCTAAAAGCCTTGGGAAAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
42035092 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
*
42035157 GACATAAGCTTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
* *
42035222 CCCAGTGGCTATTGCTAAAAGCCTTGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* *
42035254 TGCAAACTCTGACGATATTGGACTGCCCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
*
42035319 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTACAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
*
42035384 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAT
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
*
42035416 TGCAAACTCTGAATATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
*
42035481 GACATAAGCTTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
* *
42035546 CCCAGTGTCTATTGCTAAAAGCCTTAGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* * * *
42035578 TGCAAACTCTGACGATATTTGACTGCTCCCAATTGGAAGAAATAATCCAAGGTTCAGAAGTATCA
1 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* *
42035643 GACATAAGCATCCAAAGTTTAAGGGAAGTAGCAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
* *
42035708 CCCAATGCCTATTGCTAAAAGCCTTGGG-GTAT
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAG-AC
* *
42035740 TGCAAGCTCTGAGGATA-TGGAACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTC
1 TGCAAACTCTGAAGATATTGG-ACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTC
42035804 AGACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
65 AGACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
*
42035869 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAT
130 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
*
42035902 TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* *
42035967 AACATATGCCTCCAAAGTTTAAGGGAAGTA
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTA
42035997 TGTGTTAAAC
Statistics
Matches: 1154, Mismatches: 63, Indels: 18
0.93 0.05 0.01
Matches are distributed among these distances:
159 145 0.13
160 4 0.00
161 7 0.01
162 994 0.86
163 4 0.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (162 bp):
TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
Found at i:42038984 original size:36 final size:36
Alignment explanation
Indices: 42038945--42039100 Score: 104
Period size: 36 Copynumber: 4.4 Consensus size: 36
42038935 CAGTAAAATC
* *
42038945 GACAAATGAGTGTGCCCAGCACT-GATCGATATAACC
1 GACAAATGAGTGTGCCCAGCACTAG-TCGATAAAACT
* * * * *
42038981 GACAAATAAATGTG-ACATGCACTAGTCGGTAAAATT
1 GACAAATGAGTGTGCCCA-GCACTAGTCGATAAAACT
** *
42039017 GACAAATGAGTGTGCCCAATA-TAGTCGATATAACT
1 GACAAATGAGTGTGCCCAGCACTAGTCGATAAAACT
* * * * * * *
42039052 GACAAATAAATGCGCCCTGCGCT-GATCGGTAAAATT
1 GACAAATGAGTGTGCCCAGCACTAG-TCGATAAAACT
42039088 GACAAATGAGTGT
1 GACAAATGAGTGT
42039101 TGATTCAATT
Statistics
Matches: 87, Mismatches: 28, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
35 28 0.32
36 56 0.64
37 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (36 bp):
GACAAATGAGTGTGCCCAGCACTAGTCGATAAAACT
Found at i:42039081 original size:71 final size:72
Alignment explanation
Indices: 42038919--42039100 Score: 217
Period size: 71 Copynumber: 2.5 Consensus size: 72
42038909 AACAATGAAT
* ** * * *
42038919 TGCGCCCTGCGTTGGCCAGTAAAATCGACAAATGAGTGTGCCCAGCACTGATCGATATAACCGAC
1 TGCGCCCTGCGCTGATCGGTAAAATTGACAAATGAGTGTGCCCAACACTGATCGATATAACCGAC
42038984 AAATAAA
66 AAATAAA
* * * * * *
42038991 TGTGACATGCACT-AGTCGGTAAAATTGACAAATGAGTGTGCCCAATA-T-AGTCGATATAACTG
1 TGCGCCCTGCGCTGA-TCGGTAAAATTGACAAATGAGTGTGCCCAACACTGA-TCGATATAACCG
42039053 ACAAATAAA
64 ACAAATAAA
42039062 TGCGCCCTGCGCTGATCGGTAAAATTGACAAATGAGTGT
1 TGCGCCCTGCGCTGATCGGTAAAATTGACAAATGAGTGT
42039101 TGATTCAATT
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
70 1 0.01
71 54 0.59
72 36 0.40
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (72 bp):
TGCGCCCTGCGCTGATCGGTAAAATTGACAAATGAGTGTGCCCAACACTGATCGATATAACCGAC
AAATAAA
Found at i:42039603 original size:105 final size:103
Alignment explanation
Indices: 42039471--42039760 Score: 373
Period size: 97 Copynumber: 2.9 Consensus size: 103
42039461 TAAATTGGCA
*
42039471 CCTATAATAT-AGTATT-AAATTCGACATAAACACTTATTTAATCCTAACATTTAATTTAACATA
1 CCTATAATATCAGCATTAAAATT-GACATAAACACTTATTTAATCCTAACATTTAATTTAACATA
*
42039534 AACATAATAGAAATGTCCAACTTTGAAAAAACACTTATTTG
65 AACATAATAGAAATGT-C-ACTTTGAAAAAACACTTATTCG
* *
42039575 CCTATAATATCAGCATTAAAATTGACATAAACACTCATTTAATCCTAACATTTTATTTAACATAA
1 CCTATAATATCAGCATTAAAATTGACATAAACACTTATTTAATCCTAACATTTAATTTAACATAA
* *
42039640 ACATAATAG-AATGT--C---GGAAAAACATTTATTCG
66 ACATAATAGAAATGTCACTTTGAAAAAACACTTATTCG
* ** *
42039672 CCTATAATATCAACATTAAAATCAACATAAACACTTATTTAATCCTAACATTTAA-TTAACAAAA
1 CCTATAATATCAGCATTAAAATTGACATAAACACTTATTTAATCCTAACATTTAATTTAACATAA
*
42039736 ACATAATAAAAATGTCTAGCTTTGA
66 ACATAATAGAAATGTC-A-CTTTGA
42039761 CAACACTTAA
Statistics
Matches: 162, Mismatches: 14, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
96 16 0.10
97 69 0.43
100 1 0.01
101 1 0.01
104 16 0.10
105 54 0.33
106 5 0.03
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (103 bp):
CCTATAATATCAGCATTAAAATTGACATAAACACTTATTTAATCCTAACATTTAATTTAACATAA
ACATAATAGAAATGTCACTTTGAAAAAACACTTATTCG
Found at i:42039797 original size:23 final size:23
Alignment explanation
Indices: 42039762--42039844 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
42039752 TAGCTTTGAC
* *
42039762 AACACTTAAAACATGCTTTGGAT
1 AACATTTAAAACATACTTTGGAT
* * *
42039785 GACATTTAAAACATATTTTGGGT
1 AACATTTAAAACATACTTTGGAT
* *
42039808 AACATTTAAAACTTACTTT-GAC
1 AACATTTAAAACATACTTTGGAT
*
42039830 AACATTTGAAACATA
1 AACATTTAAAACATA
42039845 TTTTTGCCGG
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
22 14 0.29
23 34 0.71
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (23 bp):
AACATTTAAAACATACTTTGGAT
Found at i:42042474 original size:192 final size:196
Alignment explanation
Indices: 42042147--42042535 Score: 651
Period size: 192 Copynumber: 2.0 Consensus size: 196
42042137 GCTTCGTCGA
*
42042147 CAACAATAGATAGTGGCACCTATTTTCATAAATAATTAAATTGAAAATTGAAAATTAAAACCCTA
1 CAACAATAGATAGTGGCACCTATTTTCATAAATAATCAAATTGAAAATTGAAAATTAAAACCCTA
* * *
42042212 ATCAACATAAATCAAAAAGATTTGGCATGTATGATAAAAAATACTGAATTCAAATATCAAATTCA
66 ATCAACATAAATCAAAAAGATTTGGCATGTATGATAAAAAATACCGAATCCAAATATCAAATCCA
*
42042277 TAAAATTTTGAAAACGAATCAACCCAAAAATAAT-GAAT-AA-T-GTTCTCAATTATTCAACATG
131 TAAAATTTTAAAAACGAATCAACCCAAAAATAATAGAATCAATTCGTTCTCAATTATTCAACATG
42042338 G
196 G
*
42042339 CAACAATAGATAGTGGCACCTATTTTCATAAATAATCAAATTGAAAATTGAAAATTAAAGCCCTA
1 CAACAATAGATAGTGGCACCTATTTTCATAAATAATCAAATTGAAAATTGAAAATTAAAACCCTA
*
42042404 ATCAACATAAATCCAAAAGATTTGGCATGTATGATAAAAAATACCGAATCCAAATATCAAATCCA
66 ATCAACATAAATCAAAAAGATTTGGCATGTATGATAAAAAATACCGAATCCAAATATCAAATCCA
* *
42042469 TAAAATTTTAAAAACGAATCAACCTAAAAATAATAAAGAATCAATTCGTTCTCAATTATTTAACA
131 TAAAATTTTAAAAACGAATCAACCCAAAAATAAT--AGAATCAATTCGTTCTCAATTATTCAACA
42042534 TG
194 TG
42042536 ACAAAACTCG
Statistics
Matches: 182, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
192 156 0.86
195 4 0.02
196 2 0.01
197 1 0.01
198 19 0.10
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (196 bp):
CAACAATAGATAGTGGCACCTATTTTCATAAATAATCAAATTGAAAATTGAAAATTAAAACCCTA
ATCAACATAAATCAAAAAGATTTGGCATGTATGATAAAAAATACCGAATCCAAATATCAAATCCA
TAAAATTTTAAAAACGAATCAACCCAAAAATAATAGAATCAATTCGTTCTCAATTATTCAACATG
G
Found at i:42042629 original size:31 final size:31
Alignment explanation
Indices: 42042570--42042638 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
42042560 AAATAATAGC
* * * *
42042570 AATTCAACTCTTTTTAAATGATTGATGATCA
1 AATTTAACTCTTTTTAAATAATTAATGATAA
*
42042601 AGTTTAACTCTTTTTATAA-AATTAATGATAA
1 AATTTAACTCTTTTTA-AATAATTAATGATAA
42042632 AATTTAA
1 AATTTAA
42042639 AAAAAATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (31 bp):
AATTTAACTCTTTTTAAATAATTAATGATAA
Found at i:42042891 original size:33 final size:33
Alignment explanation
Indices: 42042853--42042915 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
42042843 TCCCAATTAC
42042853 TGAAATTCCAAGGAAAGTGAGAGCAAAAGATAT
1 TGAAATTCCAAGGAAAGTGAGAGCAAAAGATAT
42042886 TGAAATTCCAAGGAAAGTGAGAGCAAAAGA
1 TGAAATTCCAAGGAAAGTGAGAGCAAAAGA
42042916 CTTGTCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.25, T:0.16
Consensus pattern (33 bp):
TGAAATTCCAAGGAAAGTGAGAGCAAAAGATAT
Found at i:42046316 original size:11 final size:12
Alignment explanation
Indices: 42046286--42046327 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
42046276 TTTTTATAAA
*
42046286 TTTTTCTTTTAACA
1 TTTTTCTTTT--CT
42046300 TTTTTCTTTT-T
1 TTTTTCTTTTCT
42046311 TTTTTCTTTTCT
1 TTTTTCTTTTCT
42046323 TTTTT
1 TTTTT
42046328 AAACACTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 10 0.38
12 6 0.23
14 10 0.38
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:42059493 original size:162 final size:162
Alignment explanation
Indices: 42059219--42059576 Score: 576
Period size: 162 Copynumber: 2.2 Consensus size: 162
42059209 GCGTCCAATT
* * ** *
42059219 TGCAAACTCTGGA-GATATCGGACTGCTCCCAATTGGAAGAAATAATCCAAGGTTCAGAAGTGTC
1 TGCAAACTCT-GACGATATTGGGCTGCTCCCAATTGGAAGAAATAATCCAAGACTCAGAAGTATC
42059283 AAACATAAGCCTCCAAAGTTTAACGAAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
65 AAACATAAGCCTCCAAAGTTTAACGAAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
42059348 TCCCAATGTCTATTGCTAAAAGCCTT-GAGAGAC
130 TCCCAATGTCTATTGCTAAAAGCCTTAG-GAGAC
*
42059381 TGCAAACTCTGACAATATTGGGCTGCTCCCAATTGGAAGAAATAATCCAAGACTCAGAAGTATCA
1 TGCAAACTCTGACGATATTGGGCTGCTCCCAATTGGAAGAAATAATCCAAGACTCAGAAGTATCA
* * * *
42059446 AATATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAGCTGCAATAATTTGAGGTATCTCTT
66 AACATAAGCCTCCAAAGTTTAACGAAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
42059511 CCCAATGTCTATTGCTAAAAGCCTTAGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTAGGAGAC
* *
42059543 TGCAAACTCTGACGATATTGAGCTGCTTCCAATT
1 TGCAAACTCTGACGATATTGGGCTGCTCCCAATT
42059577 ATTTTTTATG
Statistics
Matches: 181, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
161 2 0.01
162 178 0.98
163 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (162 bp):
TGCAAACTCTGACGATATTGGGCTGCTCCCAATTGGAAGAAATAATCCAAGACTCAGAAGTATCA
AACATAAGCCTCCAAAGTTTAACGAAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
CCCAATGTCTATTGCTAAAAGCCTTAGGAGAC
Found at i:42062699 original size:30 final size:32
Alignment explanation
Indices: 42062612--42062700 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 32
42062602 TATTTAAAAT
* *
42062612 ATAATTAATATATTC-TA-ATTAAATTTTATAA
1 ATAATTAATAT-TTCATATATTAAAATATATAA
*
42062643 ATAATTAATA-TTAAT-TACTTAGAAATATAT-A
1 ATAATTAATATTTCATATA-TTA-AAATATATAA
42062674 A-AATTAATATTTCATATATTAAAATAT
1 ATAATTAATATTTCATATATTAAAATAT
42062701 TAACAATAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
29 2 0.04
30 16 0.33
31 22 0.46
32 8 0.17
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (32 bp):
ATAATTAATATTTCATATATTAAAATATATAA
Found at i:42071729 original size:6 final size:6
Alignment explanation
Indices: 42071709--42071779 Score: 60
Period size: 6 Copynumber: 12.3 Consensus size: 6
42071699 AAATCCACTT
* * **
42071709 TTTAAA TTT-AT TTTAAA TTT-AA TTTAAG TTTAAA TTTATT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
42071755 TTTAAA ATT--A TTCTAAA TTTAAA TT
1 TTTAAA TTTAAA TT-TAAA TTTAAA TT
42071780 ATTAAAAAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 35 0.70
7 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:42071740 original size:17 final size:17
Alignment explanation
Indices: 42071720--42071779 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
42071710 TTAAATTTAT
*
42071720 TTTAAATTTAATTTAAG
1 TTTAAATTTAATTTAAA
*
42071737 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-ATTTAAA
*
42071755 TTTAAAATT-ATTCTAAA
1 TTTAAATTTAATT-TAAA
42071772 TTTAAATT
1 TTTAAATT
42071780 ATTAAAAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 2 0.06
17 21 0.58
18 13 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:42071741 original size:11 final size:11
Alignment explanation
Indices: 42071709--42071776 Score: 57
Period size: 11 Copynumber: 6.0 Consensus size: 11
42071699 AAATCCACTT
*
42071709 TTTAAATTTAT
1 TTTAAATTTAA
42071720 TTTAAATTTAA
1 TTTAAATTTAA
*
42071731 TTTAAGTTTAAA
1 TTTAAATTT-AA
**
42071743 TTTATTTTTAAA
1 TTTAAATTT-AA
*
42071755 TTTAAAATT-A
1 TTTAAATTTAA
42071765 TTCTAAATTTAA
1 TT-TAAATTTAA
42071777 ATTATTAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
10 3 0.07
11 24 0.52
12 19 0.41
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:42072464 original size:3 final size:3
Alignment explanation
Indices: 42072456--42072502 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
42072446 TCACTGTCAT
42072456 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42072503 TTAAAACGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42073548 original size:24 final size:22
Alignment explanation
Indices: 42073520--42073577 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
42073510 ATTAATTTTG
42073520 TATTTATCATTTATTTTGATTCA
1 TATTTATCATTTATTTT-ATTCA
* *
42073543 TAATTTGT-ATTTTATTTTTTTCA
1 T-ATTTATCA-TTTATTTTATTCA
42073566 TATTTATTCATT
1 TATTTA-TCATT
42073578 CTTTATGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
22 4 0.14
23 10 0.36
24 14 0.50
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (22 bp):
TATTTATCATTTATTTTATTCA
Found at i:42081354 original size:208 final size:208
Alignment explanation
Indices: 42080713--42081483 Score: 1063
Period size: 209 Copynumber: 3.7 Consensus size: 208
42080703 AATGAGATGT
* *
42080713 TCATCTTCCTGATGAAATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAAA
* * * *
42080778 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAAT-AA-AGCT--CTTT
66 CCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGAGTTACCTTT
* ** * *
42080839 CTGATGGGATACAGAGAAGTGAACCAGATTTGTCTTCTTGATGAGACACAGAGAAATGGATCAAA
131 CTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCAAA
*
42080904 ACAAGTGATGCGA
196 ACAAGTGATGCGG
* *
42080917 TCATCTTCCTGATGAGATATTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGC-AA
* * * *
42080982 A-CTTCGAACCTCAGCTTCCTAATGAGATACTGAGAAGCTGGTCGAAGCAATAAAGAGATTAACT
65 ACCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGAG-TTACCT
* * * * *
42081046 TTCTAATAAGATATAGAGAAGTAAACCAGATCCATCTTCCTGATGAGACACAGAGAAGTGGATCA
129 TTCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
*
42081111 AAACAAGTGATGCAG
194 AAACAAGTGATGCGG
* *
42081126 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGTGAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAG-CAA
* * * *
42081191 A-CTTCAAACCCCAGCTTCTTGATGAGATATTGAGAAGCAGGTCGAAGTAAT-AAGCAGTTACCT
65 ACCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAG-AGTTACCT
* * * *
42081254 TTCTGATGAGATATAGAGAAGTGAACCAGATCCGTCTTCCTGATAAGACACAAAGAAGTGAATCA
129 TTCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCA
*
42081319 AAACAACTGATGCGG
194 AAACAAGTGATGCGG
* * *
42081334 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATAAAACCTAGCTCAAAGCGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAAA
* * *
42081399 CCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAGTAAAGCGGTTACC-T
66 CCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAG-AGTTACCTT
42081463 TCTTGATGAGATACAGAGAAG
130 TC-TGATGAGATACAGAGAAG
42081484 AGGATTAAAA
Statistics
Matches: 502, Mismatches: 54, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
204 103 0.21
205 5 0.01
206 2 0.00
207 4 0.01
208 183 0.36
209 205 0.41
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (208 bp):
TCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAAA
CCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGAGTTACCTTT
CTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGATCAAA
ACAAGTGATGCGG
Found at i:42081922 original size:18 final size:17
Alignment explanation
Indices: 42081901--42081943 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
42081891 AAACCCACTT
**
42081901 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTCGAAA
*
42081919 TTTAAAATTATTCGAAA
1 TTTAAATTTATTCGAAA
42081936 TTTAAATT
1 TTTAAATT
42081944 ATTAAAAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTCGAAA
Found at i:42082674 original size:3 final size:3
Alignment explanation
Indices: 42082666--42082749 Score: 107
Period size: 3 Copynumber: 28.0 Consensus size: 3
42082656 AAAAGAGCAT
** * *
42082666 TAA TAA TAA TGG TAA TAA TAA -ATA TAC TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
*
42082711 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42082750 GTTTAAAGGA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.01
3 68 0.97
4 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42083819 original size:30 final size:30
Alignment explanation
Indices: 42083785--42083893 Score: 125
Period size: 29 Copynumber: 3.7 Consensus size: 30
42083775 TTGAACTATC
42083785 CAAAAATCATATTTTAACCCCCGAACTTTT
1 CAAAAATCATATTTTAACCCCCGAACTTTT
* * * *
42083815 CAAAAAT-A-ATATTGACCCTCAAACTTTT
1 CAAAAATCATATTTTAACCCCCGAACTTTT
* * * *
42083843 TAAAAATTACATTTTAACCCTCGAAC-TTT
1 CAAAAATCATATTTTAACCCCCGAACTTTT
42083872 CAAAAATCATATTTTAACCCCC
1 CAAAAATCATATTTTAACCCCC
42083894 TAAAACTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
28 22 0.34
29 23 0.35
30 20 0.31
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (30 bp):
CAAAAATCATATTTTAACCCCCGAACTTTT
Found at i:42083841 original size:28 final size:28
Alignment explanation
Indices: 42083798--42083928 Score: 86
Period size: 28 Copynumber: 4.5 Consensus size: 28
42083788 AAATCATATT
* *
42083798 TTAACCCCCGAACTTTTCAAAAATAATA
1 TTAACCCTCAAACTTTTCAAAAATAATA
* * *
42083826 TTGACCCTCAAACTTTTTAAAAATTACATT
1 TTAACCCTCAAACTTTTCAAAAA-TA-ATA
* *
42083856 TTAACCCTCGAAC-TTTCAAAAATCATATT
1 TTAACCCTCAAACTTTTCAAAAAT-A-ATA
* * * *
42083885 TTAACCCCCTAAAACTTTTTAAAATTACATT
1 TTAA--CCCTCAAACTTTTCAAAAATA-ATA
42083916 TTAACCC-CAAACT
1 TTAACCCTCAAACT
42083929 CTCCAAAACT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
28 25 0.30
29 21 0.26
30 13 0.16
31 15 0.18
32 8 0.10
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.34
Consensus pattern (28 bp):
TTAACCCTCAAACTTTTCAAAAATAATA
Found at i:42083886 original size:29 final size:30
Alignment explanation
Indices: 42083785--42083891 Score: 130
Period size: 28 Copynumber: 3.7 Consensus size: 30
42083775 TTGAACTATC
*
42083785 CAAAAATCATATTTTAACCCCCGAACTTTT
1 CAAAAATCATATTTTAACCCTCGAACTTTT
* * *
42083815 CAAAAAT-A-ATATTGACCCTCAAACTTTT
1 CAAAAATCATATTTTAACCCTCGAACTTTT
* * *
42083843 TAAAAATTACATTTTAACCCTCGAAC-TTT
1 CAAAAATCATATTTTAACCCTCGAACTTTT
42083872 CAAAAATCATATTTTAACCC
1 CAAAAATCATATTTTAACCC
42083892 CCTAAAACTT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
28 22 0.34
29 22 0.34
30 20 0.31
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34
Consensus pattern (30 bp):
CAAAAATCATATTTTAACCCTCGAACTTTT
Found at i:42083909 original size:31 final size:31
Alignment explanation
Indices: 42083830--42083923 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
42083820 ATAATATTGA
42083830 CCCTCAAACTTTTTAAAAATTACATTTTAA--
1 CCCTCAAACTTTTT-AAAATTACATTTTAACC
* ** * *
42083860 CCCTCGAACTTTCAAAAATCATATTTTAACC
1 CCCTCAAACTTTTTAAAATTACATTTTAACC
*
42083891 CCCTAAAACTTTTTAAAATTACATTTTAACC
1 CCCTCAAACTTTTTAAAATTACATTTTAACC
42083922 CC
1 CC
42083924 AAACTCTCCA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 13 0.25
30 11 0.22
31 27 0.53
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (31 bp):
CCCTCAAACTTTTTAAAATTACATTTTAACC
Found at i:42084355 original size:97 final size:98
Alignment explanation
Indices: 42084182--42084378 Score: 279
Period size: 97 Copynumber: 2.0 Consensus size: 98
42084172 TCCAAAATAT
* * *
42084182 TTAAAATCGAGGCAATATTCCTTTATGTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCAC
1 TTAAAATCGAGGCAATATTCCTTTATCTAGGGTTTTGAAAATTTGTCCCTTAACTTACTAGGCAC
* *
42084247 GATTTTTCTTCAAACCAGGATAATCGAATACCC
66 GACTTTTCTTCAAACCAGGATAATCAAATACCC
* * * * *
42084280 TTAAAA-CGAGGCAATGTTTCTTTATCTATGGTTTTGAAAATTTGTCCCTTAACTTACTATGCGC
1 TTAAAATCGAGGCAATATTCCTTTATCTAGGGTTTTGAAAATTTGTCCCTTAACTTACTAGGCAC
* *
42084344 GACTTTTCTTCAAATCGGGATAATCAAATACCC
66 GACTTTTCTTCAAACCAGGATAATCAAATACCC
42084377 TT
1 TT
42084379 TTCCAGGGTT
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
97 81 0.93
98 6 0.07
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (98 bp):
TTAAAATCGAGGCAATATTCCTTTATCTAGGGTTTTGAAAATTTGTCCCTTAACTTACTAGGCAC
GACTTTTCTTCAAACCAGGATAATCAAATACCC
Found at i:42085496 original size:24 final size:24
Alignment explanation
Indices: 42085452--42085505 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
42085442 ATTTATGAAA
42085452 TAATTT-TTTAGTTAAAATCT-AT
1 TAATTTATTTAGTTAAAATCTAAT
* *
42085474 TTATTTATTTCAGTTAAATTCTAAT
1 TAATTTATTT-AGTTAAAATCTAAT
42085499 TAATTTA
1 TAATTTA
42085506 AATTATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 3 0.12
24 10 0.38
25 8 0.31
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TAATTTATTTAGTTAAAATCTAAT
Found at i:42086068 original size:28 final size:27
Alignment explanation
Indices: 42086037--42086112 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 27
42086027 CCACTTATAA
* *
42086037 GATAGTCCTAATGAACTTTCACATGTAC
1 GATAGTCCTAATGGACTTTCACATAT-C
*
42086065 GATAGTCCTAATGGGC-TTCACATATC
1 GATAGTCCTAATGGACTTTCACATATC
* *
42086091 GATAGTTCTAACGGACTTTCAC
1 GATAGTCCTAATGGACTTTCAC
42086113 TGGATTATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.34
27 13 0.32
28 14 0.34
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (27 bp):
GATAGTCCTAATGGACTTTCACATATC
Found at i:42086360 original size:53 final size:53
Alignment explanation
Indices: 42086272--42086395 Score: 146
Period size: 53 Copynumber: 2.4 Consensus size: 53
42086262 TAGTCCAACA
* * * *
42086272 GAACCTTCACAAAGCC-GAATACCATTAATATCATTCT-TTGTACAATTC-GCCC
1 GAACCTCCGCAAAGCCACAATACCATTAATATCATTCTCCT-TAC-ATTCTGCCC
*
42086324 GATCCTCCGCAAAGCCACAATACCATTAATATCATTCTCCTTACATTCTGCCC
1 GAACCTCCGCAAAGCCACAATACCATTAATATCATTCTCCTTACATTCTGCCC
* *
42086377 TAACCTCCGCGAAGCCACA
1 GAACCTCCGCAAAGCCACA
42086396 TATATAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
52 17 0.28
53 43 0.70
54 1 0.02
ACGTcount: A:0.31, C:0.34, G:0.10, T:0.26
Consensus pattern (53 bp):
GAACCTCCGCAAAGCCACAATACCATTAATATCATTCTCCTTACATTCTGCCC
Found at i:42087033 original size:31 final size:29
Alignment explanation
Indices: 42086979--42087042 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
42086969 AAAAATTAAC
*
42086979 AATTCAACTCTTTCTGAAATTGATGGTCA
1 AATTCAACTCTTTCTGAAATTGATGGCCA
* *
42087008 AATTTAACTCTTTTTGTAAAATTGATGGCCA
1 AATTCAACTCTTTCTG--AAATTGATGGCCA
42087039 AATT
1 AATT
42087043 GACAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 14 0.47
31 16 0.53
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (29 bp):
AATTCAACTCTTTCTGAAATTGATGGCCA
Found at i:42087667 original size:27 final size:28
Alignment explanation
Indices: 42087616--42087674 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
42087606 GAGAAATCTA
**
42087616 AAAAGTAAAAAACTAAATCGTTAAAAAC
1 AAAAGTAAAAAACTAAATCCCTAAAAAC
* *
42087644 AAAAGTAAAATACT-AATCCCTAAAAAT
1 AAAAGTAAAAAACTAAATCCCTAAAAAC
42087671 AAAA
1 AAAA
42087675 ATTGTGCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.64, C:0.12, G:0.05, T:0.19
Consensus pattern (28 bp):
AAAAGTAAAAAACTAAATCCCTAAAAAC
Found at i:42087675 original size:28 final size:29
Alignment explanation
Indices: 42087614--42087675 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
42087604 TTGAGAAATC
**
42087614 TAAAAAGTAAAAAACTAAATCGTTAAAAA
1 TAAAAAGTAAAAAACTAAATCCCTAAAAA
* *
42087643 -CAAAAGTAAAATACT-AATCCCTAAAAA
1 TAAAAAGTAAAAAACTAAATCCCTAAAAA
42087670 TAAAAA
1 TAAAAA
42087676 TTGTGCAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (29 bp):
TAAAAAGTAAAAAACTAAATCCCTAAAAA
Found at i:42094032 original size:162 final size:162
Alignment explanation
Indices: 42093838--42095066 Score: 2111
Period size: 162 Copynumber: 7.6 Consensus size: 162
42093828 GCGTCCAATT
* * *
42093838 TGCAAACTCTGAAGATATCGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAAAAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
*
42093903 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTGTCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
42093968 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* *
42094000 TGCAAACTCTGAAGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTTA
1 TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* *
42094065 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCTAAACTGCAACAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
*
42094130 CCCAATGTCTATTGCTAAAAGCCATGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* * *
42094162 TGCAAACTTTGACGGTATTGGGCTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
*
42094227 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTATTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
42094292 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* * *
42094324 TGCAAACTTTGAAGATATTGGATTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
42094389 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
* *
42094454 CCCAATGTCTATTGCTAAAAGCTTTGGGAGAT
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
*
42094486 TGCAAACTCTGACGATCTTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* *
42094551 GACATAAGCCTCCAAAGTTTAAGGGAAATAGTATTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
* *
42094616 CCCAGTGTCTATTGCTAAAAGCCTTAGGAGAC
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
* * *
42094648 TGCAAACTCTGACGATATTTGACTGCTCCCAATTGGAAGAAATAATCCAAGGTTCAGAAGTATCA
1 TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* *
42094713 GACATAAGCATCCAAAGTTTAAGGGAAGTAGCAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
* *
42094778 CCCAATGCCTATTGCTAAAAGCCTTGGG-GTAT
131 CCCAATGTCTATTGCTAAAAGCCTTGGGAG-AC
* *
42094810 TGCAAGCTCTGAGGATA-TGGAACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTC
1 TGCAAACTCTGACGATATTGG-ACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTC
42094874 AGACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
65 AGACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCT
*
42094939 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAT
130 TCCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
42094972 TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
1 TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
* *
42095037 AACATATGCCTCCAAAGTTTAAGGGAAGTA
66 GACATAAGCCTCCAAAGTTTAAGGGAAGTA
42095067 TGTGTTAAAC
Statistics
Matches: 1006, Mismatches: 57, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
161 3 0.00
162 999 0.99
163 4 0.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (162 bp):
TGCAAACTCTGACGATATTGGACTGCTCCCAATTGGAAGAAATAATCCAAGGCTCAGAAGTGTCA
GACATAAGCCTCCAAAGTTTAAGGGAAGTAGTAGTTCAAAACTGCAATAATTTGAGGTATCTCTT
CCCAATGTCTATTGCTAAAAGCCTTGGGAGAC
Found at i:42096375 original size:23 final size:22
Alignment explanation
Indices: 42096349--42096397 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
42096339 TTTTGAGAAG
42096349 TTAAAATATAATTTAATCATTT
1 TTAAAATATAATTTAATCATTT
** *
42096371 ATTAATTTATAATTTCATCATTT
1 -TTAAAATATAATTTAATCATTT
42096394 TTAA
1 TTAA
42096398 GGAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAATATAATTTAATCATTT
Found at i:42097561 original size:20 final size:20
Alignment explanation
Indices: 42097536--42097577 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
42097526 TTGAAGCTTC
42097536 TTGGCGTTGACTGGTTATGA
1 TTGGCGTTGACTGGTTATGA
42097556 TTGGCGTTGACTGGTTATGA
1 TTGGCGTTGACTGGTTATGA
42097576 TT
1 TT
42097578 TGCTTACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.43
Consensus pattern (20 bp):
TTGGCGTTGACTGGTTATGA
Found at i:42098742 original size:24 final size:23
Alignment explanation
Indices: 42098707--42098764 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
42098697 AATATAATCT
*
42098707 AATTAA-ATTTTATAAATAATTAA
1 AATTAATA-TTTAGAAATAATTAA
* *
42098730 TATTAATTATTTAGAAATATTTAA
1 AATTAA-TATTTAGAAATAATTAA
42098754 AATTAATATTT
1 AATTAATATTT
42098765 CATATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 10 0.34
24 18 0.62
25 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATATTTAGAAATAATTAA
Found at i:42098976 original size:13 final size:13
Alignment explanation
Indices: 42098958--42098982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42098948 TTTAAATCAA
42098958 ACTTCTCAAAAGT
1 ACTTCTCAAAAGT
42098971 ACTTCTCAAAAG
1 ACTTCTCAAAAG
42098983 CAATGCTAAA
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:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTCTCAAAAGT
Found at i:42102499 original size:80 final size:79
Alignment explanation
Indices: 42102355--42102514 Score: 232
Period size: 80 Copynumber: 2.0 Consensus size: 79
42102345 TACTTTAAAC
* ** * * * *
42102355 CAAATCCGTCAATTCATGGCACCTGGTGCCTAGCGGATATACCGCGATAATTGAGCCCAGCTCTA
1 CAAAACCGTCAATTCATGGCACCCAGTGCCTAGCAGATATACCGCAATAAATGAGCCCAACTCTA
42102420 GTTGGATTAACCAA
66 GTTGGATTAACCAA
42102434 CAAAACCGATCAATTCATGGCACCCAGTGCCTAGCAGATGA-ACCGCAATAAATGAGCCCAACTC
1 CAAAACCG-TCAATTCATGGCACCCAGTGCCTAGCAGAT-ATACCGCAATAAATGAGCCCAACTC
42102498 TAGTTGGATTAACCAA
64 TAGTTGGATTAACCAA
42102514 C
1 C
42102515 GGGTTTGCAC
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
79 7 0.10
80 64 0.89
81 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (79 bp):
CAAAACCGTCAATTCATGGCACCCAGTGCCTAGCAGATATACCGCAATAAATGAGCCCAACTCTA
GTTGGATTAACCAA
Found at i:42102936 original size:17 final size:17
Alignment explanation
Indices: 42102916--42102967 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
42102906 TTTAATTTTT
*
42102916 TTTTAAGATTAAATTTG
1 TTTTAAGATTAAATTTA
42102933 TTTTAA-ATTTAAATTTA
1 TTTTAAGA-TTAAATTTA
*
42102950 TTTTAAGTTTAAATTTA
1 TTTTAAGATTAAATTTA
42102967 T
1 T
42102968 CTTTGAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 1 0.03
17 30 0.97
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTTAAGATTAAATTTA
Found at i:42102977 original size:35 final size:34
Alignment explanation
Indices: 42102906--42102999 Score: 100
Period size: 34 Copynumber: 2.7 Consensus size: 34
42102896 CTGAACCCTT
* * * *
42102906 TTTAATTTTTTTTTAAGATTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAGTTTAAATTTATTTTAAA
*
42102940 TTTAAATTTATTTTAAGTTTAAATTTATCTTTGAA
1 TTTAAATTTATTTTAAGTTTAAATTTAT-TTTAAA
* *
42102975 TTTCAAA-TTATTATAAATTTAAATT
1 TTT-AAATTTATTTTAAGTTTAAATT
42103000 GAAAGTCCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
34 24 0.47
35 24 0.47
36 3 0.06
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGTTTAAATTTATTTTAAA
Found at i:42103659 original size:3 final size:3
Alignment explanation
Indices: 42103646--42103688 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
42103636 ATAAATATGG
* *
42103646 TAA TAAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAT TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42103689 ATAACATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42104793 original size:29 final size:29
Alignment explanation
Indices: 42104761--42105043 Score: 118
Period size: 29 Copynumber: 9.6 Consensus size: 29
42104751 ACCTTCGAAC
* *
42104761 TTTCTAAAATTCCATTTTGACCCTAATTT
1 TTTCAAAAATTCCATTTTTACCCTAATTT
* * **
42104790 TTTCCAAAAAATACATTTTTACCCCTAA-AC
1 TTT-CAAAAATTCCATTTTTA-CCCTAATTT
*
42104820 TTTCCAAAATTCCATTTTTACCCTAATTT
1 TTTCAAAAATTCCATTTTTACCCTAATTT
* * **
42104849 CTCCAAAAATTACCA-TTTTACCCCTAA-AC
1 TTTCAAAAATT-CCATTTTTA-CCCTAATTT
* * *
42104878 TTCCAAAAATTCCATTTTTAACCTCGATTT
1 TTTCAAAAATTCCATTTTTACCCT-AATTT
* * * * *
42104908 CTCCACAAATTACCA-TTTCACCTCTAA--A
1 TTTCAAAAATT-CCATTTTTACC-CTAATTT
* *
42104936 CTTCAAAATTTTCCATTTTTGA-CCTCAATTT
1 TTTCAAAA-ATTCCATTTTT-ACCCT-AATTT
* * *
42104967 TTCCAAAAATACCA-TTTTACCCTCGAA--C
1 TTTCAAAAATTCCATTTTTACCCT--AATTT
* * *
42104995 TTTCAAAAATTTCATTTTTAACCTCGATTT
1 TTTCAAAAATTCCATTTTTACCCT-AATTT
*
42105025 TTCCAAAAATTACCATTTT
1 TTTCAAAAATT-CCATTTT
42105044 ACACCCAAAT
Statistics
Matches: 185, Mismatches: 47, Indels: 42
0.68 0.17 0.15
Matches are distributed among these distances:
28 36 0.19
29 69 0.37
30 57 0.31
31 23 0.12
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.40
Consensus pattern (29 bp):
TTTCAAAAATTCCATTTTTACCCTAATTT
Found at i:42104821 original size:59 final size:59
Alignment explanation
Indices: 42104758--42105045 Score: 336
Period size: 59 Copynumber: 4.9 Consensus size: 59
42104748 TTGACCTTCG
* * * *
42104758 AACTTTCTAAAATTCCATTTTGACCCT-AATTTTTTCCAAAAAATA-CATTTTTACCCCTA
1 AACTTTCAAAAATTCCATTTTTAACCTCAA-TTTTTCCAAAAATTACCA-TTTTACCCCTA
* * *
42104817 AACTTTCCAAAATTCCATTTTTACCCT-AATTTCTCCAAAAATTACCATTTTACCCCTA
1 AACTTTCAAAAATTCCATTTTTAACCTCAATTTTTCCAAAAATTACCATTTTACCCCTA
* * * * * *
42104875 AACTTCCAAAAATTCCATTTTTAACCTCGATTTCTCCACAAATTACCATTTCACCTCTA
1 AACTTTCAAAAATTCCATTTTTAACCTCAATTTTTCCAAAAATTACCATTTTACCCCTA
* * *
42104934 AAC-TTCAAAATTTTCCATTTTTGACCTCAATTTTTCCAAAAA-TACCATTTTA-CCCTCG
1 AACTTTCAAAA-ATTCCATTTTTAACCTCAATTTTTCCAAAAATTACCATTTTACCCCT-A
* *
42104992 AACTTTCAAAAATTTCATTTTTAACCTCGATTTTTCCAAAAATTACCATTTTAC
1 AACTTTCAAAAATTCCATTTTTAACCTCAATTTTTCCAAAAATTACCATTTTAC
42105046 ACCCAAATGT
Statistics
Matches: 198, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
57 3 0.02
58 93 0.47
59 102 0.52
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (59 bp):
AACTTTCAAAAATTCCATTTTTAACCTCAATTTTTCCAAAAATTACCATTTTACCCCTA
Found at i:42104824 original size:30 final size:30
Alignment explanation
Indices: 42104790--42104897 Score: 127
Period size: 29 Copynumber: 3.7 Consensus size: 30
42104780 ACCCTAATTT
*
42104790 TTTCCAAAAAATACATTTTTACCCCTAAAC
1 TTTCCAAAAATTACATTTTTACCCCTAAAC
* *
42104820 TTTCC-AAAATTCCATTTTTA-CCCT-AAT
1 TTTCCAAAAATTACATTTTTACCCCTAAAC
42104847 TTCTCCAAAAATTACCA-TTTTACCCCTAAAC
1 TT-TCCAAAAATTA-CATTTTTACCCCTAAAC
*
42104878 -TTCCAAAAATTCCATTTTTA
1 TTTCCAAAAATTACATTTTTA
42104898 ACCTCGATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
27 4 0.06
28 9 0.14
29 39 0.59
30 12 0.18
31 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (30 bp):
TTTCCAAAAATTACATTTTTACCCCTAAAC
Found at i:42104935 original size:117 final size:116
Alignment explanation
Indices: 42104766--42105042 Score: 323
Period size: 117 Copynumber: 2.4 Consensus size: 116
42104756 CGAACTTTCT
* * * * * * *
42104766 AAAATTCCATTTTGACCCT-AATTTTTTCCAAAAAATA-CATTTTTACCCCTAAACTTTCCAAAA
1 AAAATTCCATTTTTAACCTCGA-TTTCTCCAAAAATTACCA-TTTCACCTCTAAAC-TT-CAAAA
42104829 -TTCCATTTTT-ACC-CTAATTTCTCCAAAAATTACCATTTTACCC-CTAAACTTCCA
62 TTTCCATTTTTGACCTC-AATTTCTCCAAAAA-TACCATTTTACCCTC-AAACTTCCA
*
42104883 AAAATTCCATTTTTAACCTCGATTTCTCCACAAATTACCATTTCACCTCTAAACTTCAAAATTTT
1 AAAATTCCATTTTTAACCTCGATTTCTCCAAAAATTACCATTTCACCTCTAAACTTCAAAA-TTT
* * *
42104948 CCATTTTTGACCTCAATTTTTCCAAAAATACCATTTTACCCTCGAACTTTCA
65 CCATTTTTGACCTCAATTTCTCCAAAAATACCATTTTACCCTCAAACTTCCA
* *
42105000 AAAATTTCATTTTTAACCTCGATTTTTCCAAAAATTACCATTT
1 AAAATTCCATTTTTAACCTCGATTTCTCCAAAAATTACCATTT
42105043 TACACCCAAA
Statistics
Matches: 139, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
115 5 0.04
116 2 0.01
117 111 0.80
118 20 0.14
119 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (116 bp):
AAAATTCCATTTTTAACCTCGATTTCTCCAAAAATTACCATTTCACCTCTAAACTTCAAAATTTC
CATTTTTGACCTCAATTTCTCCAAAAATACCATTTTACCCTCAAACTTCCA
Found at i:42105072 original size:59 final size:59
Alignment explanation
Indices: 42104788--42105045 Score: 296
Period size: 58 Copynumber: 4.4 Consensus size: 59
42104778 TGACCCTAAT
* * * * *
42104788 TTTTTCCAAAAAATA-CATTTTTACCC-CTAAACTTTCCAAAATTCCATTTTTACCCT-AA
1 TTTTTCCAAAAATTACCA-TTTTACCCTCTAAAC-TTCAAAAATTTCATTTTTAACCTCGA
* *
42104846 TTTCTCCAAAAATTACCATTTTACCC-CTAAACTTCCAAAAATTCCATTTTTAACCTCGA
1 TTTTTCCAAAAATTACCATTTTACCCTCTAAACTT-CAAAAATTTCATTTTTAACCTCGA
* * * * * *
42104905 TTTCTCCACAAATTACCATTTCA-CCTCTAAACTTCAAAATTTTCCATTTTTGACCTCAA
1 TTTTTCCAAAAATTACCATTTTACCCTCTAAACTTCAAAAATTT-CATTTTTAACCTCGA
*
42104964 TTTTTCCAAAAA-TACCATTTTACCCTC-GAACTTTCAAAAATTTCATTTTTAACCTCGA
1 TTTTTCCAAAAATTACCATTTTACCCTCTAAAC-TTCAAAAATTTCATTTTTAACCTCGA
42105022 TTTTTCCAAAAATTACCATTTTAC
1 TTTTTCCAAAAATTACCATTTTAC
42105046 ACCCAAATGT
Statistics
Matches: 174, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
57 2 0.01
58 92 0.53
59 80 0.46
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (59 bp):
TTTTTCCAAAAATTACCATTTTACCCTCTAAACTTCAAAAATTTCATTTTTAACCTCGA
Found at i:42105072 original size:117 final size:117
Alignment explanation
Indices: 42104766--42105106 Score: 310
Period size: 117 Copynumber: 2.9 Consensus size: 117
42104756 CGAACTTTCT
* * * * * * *
42104766 AAAATTCCATTTTGACCCT-AATTTTTTCCAAAAAATA-CATTTTTACCCCTAAACTTTCCAAAA
1 AAAATTCCATTTTTAACCTCGA-TTTCTCCAAAAATTACCA-TTTCACCTCTAAAC-TT-CAAAA
* * *
42104829 -TTCCATTTTT-A-CCCTAATTTCTCCAAAAATTACCATTTTACCCCTAAACTTCCA
62 TTTTCATTTTTGACCCCGAATTTTTCCAAAAA-TACCATTTTACCCCTAAACTTCCA
*
42104883 AAAATTCCATTTTTAACCTCGATTTCTCCACAAATTACCATTTCACCTCTAAACTTCAAAATTTT
1 AAAATTCCATTTTTAACCTCGATTTCTCCAAAAATTACCATTTCACCTCTAAACTTCAAAATTTT
* * *
42104948 CCATTTTTGACCTC-AATTTTTCCAAAAATACCATTTTA-CCCTCGAACTTTCA
66 -CATTTTTGACCCCGAATTTTTCCAAAAATACCATTTTACCCCT-AAACTTCCA
* *
42105000 AAAATTTCATTTTTAACCTCGATTTTTCCAAAAATTACCATTTTACACC-C-AAA-TGTCTAAAA
1 AAAATTCCATTTTTAACCTCGATTTCTCCAAAAATTACCA-TTT-CACCTCTAAACT-TC--AAA
* * * *
42105062 ATTTT-GTTTTTGACCCCGAACTTTTCC-AAATTACCATTTTGCCCC
61 ATTTTCATTTTTGACCCCGAATTTTTCCAAAAATACCATTTTACCCC
42105107 CCGAGTGACC
Statistics
Matches: 189, Mismatches: 21, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
115 5 0.03
116 9 0.05
117 129 0.68
118 32 0.17
119 14 0.07
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.38
Consensus pattern (117 bp):
AAAATTCCATTTTTAACCTCGATTTCTCCAAAAATTACCATTTCACCTCTAAACTTCAAAATTTT
CATTTTTGACCCCGAATTTTTCCAAAAATACCATTTTACCCCTAAACTTCCA
Found at i:42112111 original size:25 final size:24
Alignment explanation
Indices: 42111987--42112137 Score: 145
Period size: 23 Copynumber: 6.4 Consensus size: 24
42111977 ACACTAGCGC
*
42111987 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTGT-GT
*
42112010 GCTCTCTG-ATTAGCACTATGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
*
42112033 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
* *
42112056 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
*
42112079 ACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTGTGT
*
42112104 GCTCTCTGT-TGCCTAGCACT-TATGT
1 GCTCTCTGTAT---TAGCACTGTGTGT
42112129 GCTCTCTGT
1 GCTCTCTGT
42112138 TAGTACTTTG
Statistics
Matches: 112, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
23 69 0.62
24 3 0.03
25 33 0.29
26 7 0.06
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTGTGT
Found at i:42114466 original size:18 final size:18
Alignment explanation
Indices: 42114439--42114482 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
42114429 CATATGTGAA
42114439 GGAAAAGAAGAAAGAGAT
1 GGAAAAGAAGAAAGAGAT
* **
42114457 GGAAAGGAAGCGAGAGAT
1 GGAAAAGAAGAAAGAGAT
42114475 GAGAAAAG
1 G-GAAAAG
42114483 CACGACTGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.39, T:0.05
Consensus pattern (18 bp):
GGAAAAGAAGAAAGAGAT
Found at i:42118744 original size:18 final size:18
Alignment explanation
Indices: 42118721--42118756 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42118711 CATCTAATAC
* *
42118721 TGTTCCTTGTAATTATTT
1 TGTTCCTTATAAATATTT
42118739 TGTTCCTTATAAATATTT
1 TGTTCCTTATAAATATTT
42118757 GGCATTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.58
Consensus pattern (18 bp):
TGTTCCTTATAAATATTT
Found at i:42119321 original size:49 final size:49
Alignment explanation
Indices: 42119179--42119623 Score: 289
Period size: 49 Copynumber: 9.1 Consensus size: 49
42119169 TACAGGTCTC
* * * *
42119179 AGTACCAC-GAAACATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCC
1 AGTACCACAGAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
* * * * ** *
42119227 AGTACCAC-GAAGACACAAGGGGAAAGGTTTAAGTCGCAGTGGCGAACTTT
1 AGTACCACAGAAG-CATAAAGGGAAAGATTTAAGCCGCAACGGCGAA-TCT
* *
42119277 A-TACCTCAGAAGCATAAAGGGAAAGATTTAAGCCGCAACAGCGAATCT
1 AGTACCACAGAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
* * * * * *
42119325 AGTAACACA-AAG-ATATGGAGGGAAAGGTTTAAGTCGCAACGGAGAACCT
1 AGTACCACAGAAGCATA--AAGGGAAAGATTTAAGCCGCAACGGCGAATCT
* * * * * ** *
42119374 TGTACCTCAAAATCATGAATAGAAAGATTTAAGCCGCAACGGCGAATCC
1 AGTACCACAGAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
* * * * * * *
42119423 AGTACAAC-GAAG-ATATGGAGGGAAAGGTTTAAGTCTCAACGGTGAACCT
1 AGTACCACAGAAGCATA--AAGGGAAAGATTTAAGCCGCAACGGCGAATCT
* ** * * *
42119472 TGTACCTTAGAAGCATGAAGGGAAAGATTTAAGCTGCAATGGCGAATCT
1 AGTACCACAGAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
* * * * *
42119521 AGTACCAC-GAAGACACAAAGGGAAAGATTTAAGTCGCAATGACGAACCT
1 AGTACCACAGAAG-CATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
* * ** * * *
42119570 AGTACCCCAGAAGCATGAA-GGAAA-ATTTAAATCGTAACGACGAATTT
1 AGTACCACAGAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
42119617 AGTACCA
1 AGTACCA
42119624 TGCAGATTAA
Statistics
Matches: 296, Mismatches: 87, Indels: 29
0.72 0.21 0.07
Matches are distributed among these distances:
47 29 0.10
48 28 0.09
49 219 0.74
50 16 0.05
51 4 0.01
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (49 bp):
AGTACCACAGAAGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCT
Found at i:42119380 original size:98 final size:98
Alignment explanation
Indices: 42119191--42119599 Score: 459
Period size: 98 Copynumber: 4.2 Consensus size: 98
42119181 TACCACGAAA
* * *
42119191 CATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACGAAGACA-CAAGGGGAAAGGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTAACACGAAGACATGAA-GGGAAAGGT
** * * *
42119255 TTAAGTCGCAGTGGCGAACTTTATACCTCAGAAG
65 TTAAGTCGCAACGGAGAACCTTGTACCTCAGAAG
* * * * * *
42119289 CATAAAGGGAAAGATTTAAGCCGCAACAGCGAATCTAGTAACACAAAGATATGGAGGGAAAGGTT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTAACACGAAGACATGAAGGGAAAGGTT
* *
42119354 TAAGTCGCAACGGAGAACCTTGTACCTCAAAAT
66 TAAGTCGCAACGGAGAACCTTGTACCTCAGAAG
** * *
42119387 CATGAATAGAAAGATTTAAGCCGCAACGGCGAATCCAGT-ACAACGAAGATATGGAGGGAAAGGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTAAC-ACGAAGACATGAAGGGAAAGGT
* * *
42119451 TTAAGTCTCAACGGTGAACCTTGTACCTTAGAAG
65 TTAAGTCGCAACGGAGAACCTTGTACCTCAGAAG
* * * * ** *
42119485 CATGAAGGGAAAGATTTAAGCTGCAATGGCGAATCTAGTACCACGAAGACACAAAGGGAAAGATT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTAACACGAAGACATGAAGGGAAAGGTT
* * *
42119550 TAAGTCGCAA-TGACGAACCTAGTACCCCAGAAG
66 TAAGTCGCAACGGA-GAACCTTGTACCTCAGAAG
42119583 CATGAA-GGAAA-ATTTAA
1 CATGAAGGGAAAGATTTAA
42119600 ATCGTAACGA
Statistics
Matches: 263, Mismatches: 44, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
96 6 0.02
97 8 0.03
98 247 0.94
99 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (98 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTAACACGAAGACATGAAGGGAAAGGTT
TAAGTCGCAACGGAGAACCTTGTACCTCAGAAG
Found at i:42120048 original size:17 final size:17
Alignment explanation
Indices: 42120025--42120135 Score: 143
Period size: 17 Copynumber: 6.5 Consensus size: 17
42120015 CTAAACCCTT
42120025 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
42120042 ATTAAATTTGTTTTTAA
1 TTTAAATTTATTTTAAA
*
42120059 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
42120076 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
42120093 TTTAAATTTATCTTTGAA
1 TTTAAATTTAT-TTTAAA
*
42120111 TTTGAAA-TTATTATAAA
1 TTT-AAATTTATTTTAAA
42120128 TTTAAATT
1 TTTAAATT
42120136 GAAAGTCCAA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
16 3 0.04
17 62 0.77
18 12 0.15
19 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:42120066 original size:6 final size:6
Alignment explanation
Indices: 42120025--42120102 Score: 56
Period size: 6 Copynumber: 13.7 Consensus size: 6
42120015 CTAAACCCTT
* * ** * *
42120025 TTTAAA TTT-AT TTTAAA ATTAAA TTT-GT TTTTAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
42120070 TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
42120103 TCTTTGAATT
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
5 15 0.28
6 39 0.72
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:42120797 original size:3 final size:3
Alignment explanation
Indices: 42120789--42120822 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42120779 AAATATATGT
42120789 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
42120823 GATGATGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42122078 original size:58 final size:58
Alignment explanation
Indices: 42121957--42122120 Score: 174
Period size: 58 Copynumber: 2.8 Consensus size: 58
42121947 TGAACTTTCC
* ** *
42121957 AAAATTCCATTTTTAACT-CGATTTCGCCAAAAATTACCATTTTACCCCCAAACTTCTA
1 AAAATTCCATTTTTGACTCCGATTTTTCC-AAAATTACCATTTTACCCCCAAACTACTA
*
42122015 GAAATTCCATTTTTGACTCCGATTTTTCCAAAATTACCATTTTACCCCCAAA-TAACTA
1 AAAATTCCATTTTTGACTCCGATTTTTCCAAAATTACCATTTTACCCCCAAACT-ACTA
** ** * *
42122073 AAAATTTTATTTTTGAC-CCTGA-ACTTCCCAAATTACCATTTTGCCCCC
1 AAAATTCCATTTTTGACTCC-GATTTTTCCAAAATTACCATTTTACCCCC
42122121 CAAGTGACCA
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
57 25 0.27
58 58 0.64
59 8 0.09
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (58 bp):
AAAATTCCATTTTTGACTCCGATTTTTCCAAAATTACCATTTTACCCCCAAACTACTA
Found at i:42123318 original size:61 final size:60
Alignment explanation
Indices: 42123205--42123320 Score: 196
Period size: 61 Copynumber: 1.9 Consensus size: 60
42123195 CTCTCCCATC
*
42123205 ACCAATATTCATGACTATACACATATAATATATACAATTTTCCACCCAATCATTTCAATT
1 ACCAATATTCATGAATATACACATATAATATATACAATTTTCCACCCAATCATTTCAATT
* *
42123265 ACCAATATTCATGAATATACATATATAAATATATGCAATTTTCCACCCAATCATTT
1 ACCAATATTCATGAATATACACATAT-AATATATACAATTTTCCACCCAATCATTT
42123321 ATACTAAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 24 0.46
61 28 0.54
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.35
Consensus pattern (60 bp):
ACCAATATTCATGAATATACACATATAATATATACAATTTTCCACCCAATCATTTCAATT
Found at i:42127637 original size:2 final size:2
Alignment explanation
Indices: 42127630--42127664 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
42127620 TTCCATGAGA
*
42127630 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
42127665 TTACATTTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:42127685 original size:10 final size:10
Alignment explanation
Indices: 42127670--42127708 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
42127660 GATATTTACA
42127670 TTTCGATTAT
1 TTTCGATTAT
42127680 TTTCGA-TA-
1 TTTCGATTAT
42127688 TTTCGATTAT
1 TTTCGATTAT
42127698 TTTCGATTAT
1 TTTCGATTAT
42127708 T
1 T
42127709 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 6 0.22
9 4 0.15
10 17 0.63
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (10 bp):
TTTCGATTAT
Found at i:42127692 original size:18 final size:18
Alignment explanation
Indices: 42127669--42127704 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42127659 TGATATTTAC
42127669 ATTTCGATTATTTTCGAT
1 ATTTCGATTATTTTCGAT
42127687 ATTTCGATTATTTTCGAT
1 ATTTCGATTATTTTCGAT
42127705 TATTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (18 bp):
ATTTCGATTATTTTCGAT
Found at i:42131949 original size:19 final size:19
Alignment explanation
Indices: 42131921--42131962 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
42131911 ACAAAAAATT
*
42131921 CTTCCAATGTATCGGTCTC
1 CTTCCAATGTATCGGTCTA
*
42131940 CTTCCCATGTATCGGTCTA
1 CTTCCAATGTATCGGTCTA
42131959 CTTC
1 CTTC
42131963 ATATTCCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.33, G:0.14, T:0.38
Consensus pattern (19 bp):
CTTCCAATGTATCGGTCTA
Found at i:42132766 original size:24 final size:25
Alignment explanation
Indices: 42132738--42132797 Score: 90
Period size: 24 Copynumber: 2.5 Consensus size: 25
42132728 ACTAATAAGG
*
42132738 GTTTAACTT-AAACAAATAAACAGA
1 GTTTAACTTGAAACAAATAAACAAA
42132762 GTTTAA-TTGAAACAAATAAACAAA
1 GTTTAACTTGAAACAAATAAACAAA
42132786 GTTTAAC-TGAAA
1 GTTTAACTTGAAA
42132798 GATTATTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
23 2 0.06
24 31 0.94
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (25 bp):
GTTTAACTTGAAACAAATAAACAAA
Found at i:42138957 original size:11 final size:13
Alignment explanation
Indices: 42138930--42138967 Score: 62
Period size: 12 Copynumber: 3.1 Consensus size: 13
42138920 AACCACTAAA
42138930 TTTACTTAAATAT
1 TTTACTTAAATAT
42138943 TTTA-TTAAA-AT
1 TTTACTTAAATAT
42138954 TTTACTTAAATAT
1 TTTACTTAAATAT
42138967 T
1 T
42138968 CACAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.26
12 10 0.43
13 7 0.30
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTACTTAAATAT
Found at i:42140831 original size:42 final size:42
Alignment explanation
Indices: 42140772--42140891 Score: 204
Period size: 42 Copynumber: 2.8 Consensus size: 42
42140762 TGTTCGCAGG
*
42140772 CACACGGGGGTGTGTCCAGGGTGTGTGTGGCACATAGGCTAC
1 CACACGGGGGTGTGTCCAGGGTGTGTGTGGCACACAGGCTAC
*
42140814 CACACGGGGGTGTGTCCAGGGTGTGTGTGGCACACAGGCTAG
1 CACACGGGGGTGTGTCCAGGGTGTGTGTGGCACACAGGCTAC
*
42140856 CACACGGAGGTGTGTCCAGGTGTGTGTGTGGCACAC
1 CACACGGGGGTGTGTCCAGG-GTGTGTGTGGCACAC
42140892 GAGTTGGCAC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 59 0.80
43 15 0.20
ACGTcount: A:0.17, C:0.22, G:0.41, T:0.21
Consensus pattern (42 bp):
CACACGGGGGTGTGTCCAGGGTGTGTGTGGCACACAGGCTAC
Found at i:42141557 original size:29 final size:29
Alignment explanation
Indices: 42141524--42141610 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
42141514 ATGGATAAGG
42141524 GTATCATGTCTGCATCTGTAACTGTATCT
1 GTATCATGTCTGCATCTGTAACTGTATCT
** *
42141553 GTATCATGTCTGCATCCCTAACTATAAT-T
1 GTATCATGTCTGCATCTGTAACTGT-ATCT
* *
42141582 GTGA-CATGACTGCATCTGTAATTGTATCT
1 GT-ATCATGTCTGCATCTGTAACTGTATCT
42141611 CTAATTCGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 2 0.04
29 42 0.89
30 3 0.06
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (29 bp):
GTATCATGTCTGCATCTGTAACTGTATCT
Found at i:42141653 original size:29 final size:29
Alignment explanation
Indices: 42141583--42141668 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
42141573 ACTATAATTG
*
42141583 TGACATGACTGCATCTGTAATTGTATCTC
1 TGACATGACTGTATCTGTAATTGTATCTC
* *
42141612 T-A-ATTCGAATGTATTTGTAATTGTATCTC
1 TGACA-T-GACTGTATCTGTAATTGTATCTC
*
42141641 TGACATGACTGTATCTGTAACTGTATCT
1 TGACATGACTGTATCTGTAATTGTATCT
42141669 ATATTTTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
27 1 0.02
28 2 0.04
29 41 0.87
30 2 0.04
31 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (29 bp):
TGACATGACTGTATCTGTAATTGTATCTC
Found at i:42147900 original size:99 final size:99
Alignment explanation
Indices: 42147783--42147975 Score: 282
Period size: 99 Copynumber: 1.9 Consensus size: 99
42147773 AACACATAAG
* * * *
42147783 AAAATAAATCTCTACTAAATATGTAATACTACAT-TAATGTAAAAATTAAAATACTGTTAAGATG
1 AAAATAAATATCTACTAAATATATAATACTA-ATCTAATGTAAAAATTAAAATAATGCTAAGATG
* *
42147847 ACTATA-TAAAAATTTTCAATAAATAAAAATGTAAA
65 AATATATTAAAAA-TGTCAATAAATAAAAATGTAAA
* *
42147882 AAAATAAATATGTACTAAATATATAATACTAATCTAATGTAAACATTAAAATAATGCTAAGATGA
1 AAAATAAATATCTACTAAATATATAATACTAATCTAATGTAAAAATTAAAATAATGCTAAGATGA
42147947 ATATATTAAAAATGTCAATAAATAAAAAT
66 ATATATTAAAAATGTCAATAAATAAAAAT
42147976 ATATAAAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
98 2 0.02
99 76 0.90
100 6 0.07
ACGTcount: A:0.55, C:0.07, G:0.06, T:0.32
Consensus pattern (99 bp):
AAAATAAATATCTACTAAATATATAATACTAATCTAATGTAAAAATTAAAATAATGCTAAGATGA
ATATATTAAAAATGTCAATAAATAAAAATGTAAA
Found at i:42148001 original size:99 final size:98
Alignment explanation
Indices: 42147778--42148009 Score: 265
Period size: 99 Copynumber: 2.3 Consensus size: 98
42147768 TTTAAAACAC
* * * * * *
42147778 ATAAGAAAATAAATCTCTACTAAATATGTAATACTACATTAATGTAAAAATTAAAATACTGTTAA
1 ATAAAAAAATAAATATGTAC-AAATATATAATACTACATTAATGTAAAAATTAAAATAATGCTAA
* *
42147843 GATGACTATATAAAAATTTTCAATAAATAAAAAT
65 GATGAATATATAAAAATTGTCAATAAATAAAAAT
* *
42147877 GTAAAAAAATAAATATGTACTAAATATATAATACTA-ATCTAATGTAAACATTAAAATAATGCTA
1 ATAAAAAAATAAATATGTAC-AAATATATAATACTACAT-TAATGTAAAAATTAAAATAATGCTA
42147941 AGATGAATATATTAAAAA-TGTCAATAAATAAAAAT
64 AGATGAATATA-TAAAAATTGTCAATAAATAAAAAT
*
42147976 ATATAAAATTATTAAATAT-TA-AAATAATATAATA
1 ATA-AAAA--AATAAATATGTACAAAT-ATATAATA
42148010 TAAATATTTT
Statistics
Matches: 115, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
98 2 0.02
99 85 0.74
100 18 0.16
101 2 0.02
102 8 0.07
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (98 bp):
ATAAAAAAATAAATATGTACAAATATATAATACTACATTAATGTAAAAATTAAAATAATGCTAAG
ATGAATATATAAAAATTGTCAATAAATAAAAAT
Found at i:42153607 original size:11 final size:12
Alignment explanation
Indices: 42153574--42153632 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
42153564 ATATTAGTTA
42153574 ATAATAATAA-T
1 ATAATAATAATT
*
42153585 ATAATACTAATT
1 ATAATAATAATT
42153597 A-AATAATAATTT
1 ATAATAATAA-TT
* *
42153609 ATATTATTATATT
1 ATAATAATA-ATT
*
42153622 ATAATATTAAT
1 ATAATAATAAT
42153633 AAATTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 16 0.41
12 7 0.18
13 15 0.38
14 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:42159718 original size:11 final size:12
Alignment explanation
Indices: 42159680--42159743 Score: 51
Period size: 11 Copynumber: 5.3 Consensus size: 12
42159670 ATATATTAGT
*
42159680 TAATAATAATAA
1 TAATTATAATAA
*
42159692 TAA-TATAATAC
1 TAATTATAATAA
42159703 TAATTA-AATAA
1 TAATTATAATAA
* *
42159714 TAATTTATATTAT
1 TAA-TTATAATAA
*
42159727 TATATTATAATAT
1 TA-ATTATAATAA
42159740 TAAT
1 TAAT
42159744 AAATTAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 16 0.38
12 10 0.24
13 15 0.36
14 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATTATAATAA
Found at i:42162582 original size:16 final size:18
Alignment explanation
Indices: 42162550--42162583 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42162540 TGAGTATTTC
42162550 GAATATAAAGACTAAAAT
1 GAATATAAAGACTAAAAT
42162568 GAATA-AAAGAC-AAAAT
1 GAATATAAAGACTAAAAT
42162584 ATGTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (18 bp):
GAATATAAAGACTAAAAT
Found at i:42168746 original size:11 final size:11
Alignment explanation
Indices: 42168730--42168805 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
42168720 AAAGCTCACT
42168730 TTAATATTAAA
1 TTAATATTAAA
42168741 TTAATA--AAA
1 TTAATATTAAA
*
42168750 -TATTATTAAA
1 TTAATATTAAA
*
42168760 ATAAGTATTAAA
1 TTAA-TATTAAA
42168772 TTTAAT-TTAATA
1 -TTAATATTAA-A
42168784 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
42168797 ATAATATTA
1 TTAATATTA
42168806 TTTTTGGGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 19 0.37
12 13 0.25
13 6 0.12
14 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:42172764 original size:18 final size:18
Alignment explanation
Indices: 42172724--42172765 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
42172714 TTATAGAAAA
42172724 CATTTT-TTTCTTCTTTT
1 CATTTTCTTTCTTCTTTT
*
42172741 CTTTTTCTTTCTT-TTTCT
1 CATTTTCTTTCTTCTTT-T
42172759 CATTTTC
1 CATTTTC
42172766 ATTTTTCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (18 bp):
CATTTTCTTTCTTCTTTT
Found at i:42173373 original size:17 final size:18
Alignment explanation
Indices: 42173336--42173375 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
42173326 AACAAAAAGG
*
42173336 ATGCAATGACAAAATAAA
1 ATGCAAGGACAAAATAAA
*
42173354 ATGCAAGGACAATA-AAA
1 ATGCAAGGACAAAATAAA
42173371 ATGCA
1 ATGCA
42173376 TGAAAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.57, C:0.12, G:0.15, T:0.15
Consensus pattern (18 bp):
ATGCAAGGACAAAATAAA
Found at i:42184399 original size:20 final size:20
Alignment explanation
Indices: 42184374--42184450 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
42184364 AAATCAAGTT
42184374 AAAATGATTTTAAACAAATC
1 AAAATGATTTTAAACAAATC
* * *
42184394 AAAATGATTTCAATCAAGTC
1 AAAATGATTTTAAACAAATC
* **
42184414 AAAATCATTTT-AACATTTC
1 AAAATGATTTTAAACAAATC
*
42184433 AAAATGTTTTTCAAACAA
1 AAAATGATTTT-AAACAA
42184451 GTCATAATAG
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
19 14 0.32
20 26 0.59
21 4 0.09
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATGATTTTAAACAAATC
Found at i:42184424 original size:40 final size:40
Alignment explanation
Indices: 42184365--42184454 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
42184355 ACAATTTTAA
* *
42184365 AATCAAGTTAAAATGATTTTAAACAAATCAAAATG-ATTTC
1 AATCAAGTCAAAATCATTTT-AACAAATCAAAATGTATTTC
** *
42184405 AATCAAGTCAAAATCATTTTAACATTTCAAAATGTTTTTC
1 AATCAAGTCAAAATCATTTTAACAAATCAAAATGTATTTC
*
42184445 AAACAAGTCA
1 AATCAAGTCA
42184455 TAATAGCTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 12 0.28
40 31 0.72
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (40 bp):
AATCAAGTCAAAATCATTTTAACAAATCAAAATGTATTTC
Found at i:42186664 original size:26 final size:26
Alignment explanation
Indices: 42186629--42186693 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
42186619 CCCTGGGCCT
42186629 TAAACCTTAAACCCTAACCCAAAACC
1 TAAACCTTAAACCCTAACCCAAAACC
* ** *
42186655 TAAACCTTAAACTCTAACCCTGAATC
1 TAAACCTTAAACCCTAACCCAAAACC
42186681 TCAAACCTTAAAC
1 T-AAACCTTAAAC
42186694 ATCAAAGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 23 0.68
27 11 0.32
ACGTcount: A:0.43, C:0.34, G:0.02, T:0.22
Consensus pattern (26 bp):
TAAACCTTAAACCCTAACCCAAAACC
Found at i:42189140 original size:7 final size:7
Alignment explanation
Indices: 42189128--42189202 Score: 66
Period size: 7 Copynumber: 11.0 Consensus size: 7
42189118 AACCATGAAT
42189128 CTTAAAC
1 CTTAAAC
42189135 CTTAAAC
1 CTTAAAC
*
42189142 CCTAAA-
1 CTTAAAC
*
42189148 CATAAAC
1 CTTAAAC
42189155 CTTAAA-
1 CTTAAAC
42189161 CTTAAAAC
1 CTT-AAAC
42189169 C-TAAAC
1 CTTAAAC
*
42189175 TTTAAAC
1 CTTAAAC
**
42189182 CCCAAAC
1 CTTAAAC
42189189 CTTAAAC
1 CTTAAAC
*
42189196 CATAAAC
1 CTTAAAC
42189203 TCTAAACTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
6 12 0.22
7 41 0.76
8 1 0.02
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (7 bp):
CTTAAAC
Found at i:42189155 original size:13 final size:13
Alignment explanation
Indices: 42189130--42189209 Score: 79
Period size: 14 Copynumber: 5.8 Consensus size: 13
42189120 CCATGAATCT
42189130 TAAACCTTAAACCC
1 TAAA-CTTAAACCC
* *
42189144 TAAACATAAACCT
1 TAAACTTAAACCC
*
42189157 TAAACTTAAAACC
1 TAAACTTAAACCC
42189170 TAAACTTTAAACCC
1 TAAAC-TTAAACCC
* *
42189184 CAAACCTTAAACCA
1 TAAA-CTTAAACCC
42189198 TAAACTCTAAAC
1 TAAACT-TAAAC
42189210 TCAAACCATG
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
13 24 0.44
14 29 0.54
15 1 0.02
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAACTTAAACCC
Found at i:42189155 original size:20 final size:20
Alignment explanation
Indices: 42189130--42189209 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
42189120 CCATGAATCT
42189130 TAAACCTTAAACCCTAAACA
1 TAAACCTTAAACCCTAAACA
* *
42189150 TAAACCTTAAA-CTTAAAACC
1 TAAACCTTAAACCCT-AAACA
* * *
42189170 TAAACTTTAAACCCCAAACCT
1 TAAACCTTAAACCCTAAA-CA
* *
42189191 TAAACCATAAACTCTAAAC
1 TAAACCTTAAACCCTAAAC
42189210 TCAAACCATG
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
19 2 0.04
20 29 0.62
21 16 0.34
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAACCTTAAACCCTAAACA
Found at i:42189217 original size:20 final size:20
Alignment explanation
Indices: 42189177--42189236 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
42189167 ACCTAAACTT
* *
42189177 TAAACCCCAAACCTTAAACCA
1 TAAACCTCAAA-CTCAAACCA
42189198 TAAA-CTCTAAACTCAAACCA
1 TAAACCTC-AAACTCAAACCA
* *
42189218 TGAACCTCAAACTCGAACC
1 TAAACCTCAAACTCAAACC
42189237 TCAAGTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 23 0.70
21 10 0.30
ACGTcount: A:0.45, C:0.35, G:0.03, T:0.17
Consensus pattern (20 bp):
TAAACCTCAAACTCAAACCA
Found at i:42189258 original size:7 final size:7
Alignment explanation
Indices: 42189248--42189490 Score: 60
Period size: 7 Copynumber: 35.9 Consensus size: 7
42189238 CAAGTTTAAA
42189248 GTTTAGG
1 GTTTAGG
42189255 GTTTA-G
1 GTTTAGG
*
42189261 GTTTAAG
1 GTTTAGG
*
42189268 ATTTAGG
1 GTTTAGG
* *
42189275 GTTCAAG
1 GTTTAGG
*
42189282 GTTTA-A
1 GTTTAGG
42189288 GTTTA-G
1 GTTTAGG
*
42189294 GTTTAAG
1 GTTTAGG
*
42189301 GTTTAATG
1 GTTT-AGG
* *
42189309 TTTTA-T
1 GTTTAGG
*
42189315 GTTTGGG
1 GTTTAGG
42189322 GTTTAGG
1 GTTTAGG
42189329 GTTTAGG
1 GTTTAGG
**
42189336 GTTTAAT
1 GTTTAGG
* *
42189343 ATTTAGC
1 GTTTAGG
* **
42189350 ATTTAAA
1 GTTTAGG
42189357 GTTTAGG
1 GTTTAGG
* *
42189364 GTTCAAG
1 GTTTAGG
42189371 GTTTA-G
1 GTTTAGG
42189377 GTTT-GAG
1 GTTTAG-G
*
42189384 GTTTAAAG
1 GTTT-AGG
42189392 GTTATA--
1 GTT-TAGG
42189398 GTTTAGG
1 GTTTAGG
* *
42189405 GTTCAAG
1 GTTTAGG
* *
42189412 GTCTAAG
1 GTTTAGG
* * *
42189419 GCTCAAG
1 GTTTAGG
42189426 GTTT-GG
1 GTTTAGG
*
42189432 GTTCA-G
1 GTTTAGG
42189438 GTTTA-G
1 GTTTAGG
42189444 GTTT-GG
1 GTTTAGG
42189450 GTTTAGG
1 GTTTAGG
*
42189457 GTTTGGG
1 GTTTAGG
* *
42189464 GTTCAAG
1 GTTTAGG
*
42189471 GTTTAAG
1 GTTTAGG
* *
42189478 ATTCAGG
1 GTTTAGG
42189485 GTTTAG
1 GTTTAG
42189491 TGTACCAAAA
Statistics
Matches: 171, Mismatches: 51, Indels: 28
0.68 0.20 0.11
Matches are distributed among these distances:
5 2 0.01
6 46 0.27
7 112 0.65
8 10 0.06
9 1 0.01
ACGTcount: A:0.22, C:0.04, G:0.32, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Done.