Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 96 of 168
Found at i:28445498 original size:25 final size:25
Alignment explanation
Indices: 28445443--28445509 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
28445433 TTTTAAGTGT
*
28445443 TTTCAGTATAGT-CTATCTATAATAG
1 TTTCAGTATA-TACTATCTATAACAG
* *
28445468 TCTCAGTATATACTATCTATAGCAG
1 TTTCAGTATATACTATCTATAACAG
*
28445493 TTTCAGAATATACTATC
1 TTTCAGTATATACTATC
28445510 AAAGACAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.40
Consensus pattern (25 bp):
TTTCAGTATATACTATCTATAACAG
Found at i:28445518 original size:25 final size:25
Alignment explanation
Indices: 28445470--28445520 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
28445460 TATAATAGTC
* *
28445470 TCAGTATATACTATCTATAGCAGTT
1 TCAGAATATACTATCTAAAGCAGTT
28445495 TCAGAATATACTATC-AAAGACAGTT
1 TCAGAATATACTATCTAAAG-CAGTT
28445520 T
1 T
28445521 TAGTTTCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (25 bp):
TCAGAATATACTATCTAAAGCAGTT
Found at i:28445870 original size:18 final size:18
Alignment explanation
Indices: 28445839--28445886 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
28445829 TGTTGTTCGT
*
28445839 TTTCAAAACATTATTC-A
1 TTTCAAAACGTTATTCAA
*
28445856 TTTACAAATCGTTATTCAA
1 TTT-CAAAACGTTATTCAA
28445875 TTTCAAAACGTT
1 TTTCAAAACGTT
28445887 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (18 bp):
TTTCAAAACGTTATTCAA
Found at i:28458706 original size:22 final size:22
Alignment explanation
Indices: 28458673--28458719 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
28458663 ATTTGAATTT
* *
28458673 AAAATTTTTTAAA-TATATAAA
1 AAAATTTATTAAACTAAATAAA
28458694 AAAACTTTATTAAACTAAATAAA
1 AAAA-TTTATTAAACTAAATAAA
28458717 AAA
1 AAA
28458720 TTAATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATTTATTAAACTAAATAAA
Found at i:28459297 original size:25 final size:23
Alignment explanation
Indices: 28459269--28459319 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 23
28459259 GTTTAAAAGT
28459269 AATTCTAATATTATGATTA-TTTTAA
1 AATTCTAATA--AT-ATTATTTTTAA
*
28459294 AATTTTAATAATATTATTTTTAA
1 AATTCTAATAATATTATTTTTAA
28459317 AAT
1 AAT
28459320 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.17
23 11 0.46
25 9 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
AATTCTAATAATATTATTTTTAA
Found at i:28460895 original size:7 final size:7
Alignment explanation
Indices: 28460885--28460909 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28460875 ATTCGATTGA
28460885 TATTTAG
1 TATTTAG
28460892 TATTTAG
1 TATTTAG
28460899 TATTTAG
1 TATTTAG
28460906 TATT
1 TATT
28460910 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:28462054 original size:43 final size:45
Alignment explanation
Indices: 28462001--28462086 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
28461991 ATATTTTGAA
*
28462001 TATTTTGATATTATTTTATGTAA-AAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
*
28462044 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
28462087 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:28462121 original size:70 final size:69
Alignment explanation
Indices: 28462011--28462166 Score: 251
Period size: 70 Copynumber: 2.3 Consensus size: 69
28462001 TATTTTGATA
* * * *
28462011 TTATTTTATGTAA-AAAATAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
1 TTATTTGATGTAATAAAATAAAAAATTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAG
28462075 AAGT
66 AAGT
28462079 TTATTTGATGTAATAAAATAAAAAAATTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAAT-AAAAAATTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATA
28462144 GAAGT
65 GAAGT
*
28462149 TTATTTGATATAATAAAA
1 TTATTTGATGTAATAAAA
28462167 ACTCTAACCT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
68 12 0.15
69 5 0.06
70 64 0.79
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (69 bp):
TTATTTGATGTAATAAAATAAAAAATTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAG
AAGT
Found at i:28462156 original size:35 final size:35
Alignment explanation
Indices: 28462047--28462159 Score: 99
Period size: 35 Copynumber: 3.2 Consensus size: 35
28462037 TTTGAGTTAT
28462047 TTTGATATTATTTGATGTAATAAAATAGAAGTTTA
1 TTTGATATTATTTGATGTAATAAAATAGAAGTTTA
* * * ** * *
28462082 TTTGAT-GTA-ATAAAATAAAAAAATTTTCG-AG-TTA
1 TTTGATATTATTTGATGTAATAAAA---TAGAAGTTTA
28462116 TTTTGATATTATTTGATGTAATAAAATAGAAGTTTA
1 -TTTGATATTATTTGATGTAATAAAATAGAAGTTTA
28462152 TTTGATAT
1 TTTGATAT
28462160 AATAAAAACT
Statistics
Matches: 56, Mismatches: 14, Indels: 16
0.65 0.16 0.19
Matches are distributed among these distances:
33 9 0.16
34 7 0.12
35 24 0.43
36 7 0.12
37 9 0.16
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTGATATTATTTGATGTAATAAAATAGAAGTTTA
Found at i:28462230 original size:29 final size:29
Alignment explanation
Indices: 28462182--28462619 Score: 331
Period size: 29 Copynumber: 16.4 Consensus size: 29
28462172 AACCTAATTT
*
28462182 AACCCTAAACCCTAACCTAAATTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
**
28462212 AACCCTAACTTTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
28462241 AACCCTAACCCTAACCTAATTTAATGAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
28462270 AACCCTAACCCCTAACCTAAATTAATTACA
1 AACCCTAA-CCCTAACCTAATTTAATTAAA
28462300 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
28462329 AACCCT-A----AA-CT--CTTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
*
28462351 AACCCTAACCTTAACCTAATTTAATT-AA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
28462379 AA----AA-CCTAACTTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
28462403 AACCCTAAACCCTTAACTTAA---AATT-AA
1 AACCCT-AACCC-TAACCTAATTTAATTAAA
28462430 AACCCT-A-----ACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
28462453 AA-CC---C--TAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
28462476 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
28462505 AATCCTAAACCCT----T-A---ACTTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
*
28462527 AACCCTAAACCCTTAACTTAA---AATTAAA
1 AACCCT-AACCC-TAACCTAATTTAATTAAA
28462555 AA--CT----CTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
28462578 AACCCTAACCCTAACCTAATTTAATTTAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
28462607 AACCTTAAACCCT
1 AACCCT-AACCCT
28462620 TAACTTAAAA
Statistics
Matches: 337, Mismatches: 23, Indels: 96
0.74 0.05 0.21
Matches are distributed among these distances:
19 5 0.01
20 7 0.02
21 5 0.01
22 34 0.10
23 50 0.15
24 10 0.03
25 4 0.01
26 3 0.01
27 12 0.04
28 20 0.06
29 129 0.38
30 50 0.15
31 8 0.02
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.28
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:28462295 original size:59 final size:58
Alignment explanation
Indices: 28462182--28462619 Score: 304
Period size: 59 Copynumber: 8.2 Consensus size: 58
28462172 AACCTAATTT
* ** *
28462182 AACCCTAAACCCTAACCTAAATTAATTAAAAACCCTAACTTTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAA
* *
28462241 AACCCTAACCCTAACCTAATTTAATGAAAAACCCTAACCCCTAACCTAAATTAATTACA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCCTAACCTAAATTAATTAAA
*
28462300 AACCCTAACCCTAACCTAATTTAATTAAAAACCCT-A----AA-CT--CTTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAATTAA-TTAAA
* * *
28462351 AACCCTAACCTTAACCTAATTTAATT-AAAA----AA-CCTAACTTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAA
*
28462403 AACCCTAAACCCTTAACTTAA---AATT-AAAACCCTAA-CCTAA--T---TTAATT--A
1 AACCCT-AACCC-TAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAA
*
28462451 AA----AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAA
* * *
28462505 AATCCTAAACCCT----T-A---ACTTAAAAACCCTAAACCCTTAA-CTTAA--AATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAAAACCCT-AACCC-TAACCTAAATTAATTAAA
* *
28462555 AA--CT----CTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAA
*
28462607 AACCTTAAACCCT
1 AACCCT-AACCCT
28462620 TAACTTAAAA
Statistics
Matches: 304, Mismatches: 23, Indels: 104
0.71 0.05 0.24
Matches are distributed among these distances:
42 7 0.02
43 7 0.02
45 4 0.01
46 10 0.03
47 7 0.02
48 6 0.02
49 4 0.01
50 33 0.11
51 62 0.20
52 35 0.12
53 14 0.05
54 12 0.04
55 8 0.03
58 30 0.10
59 65 0.21
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.28
Consensus pattern (58 bp):
AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAA
Found at i:28462352 original size:22 final size:20
Alignment explanation
Indices: 28462320--28462365 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
28462310 CTAACCTAAT
28462320 TTAA-TTAAAAACCCTAAACTC
1 TTAACTTAAAAACCCT-AAC-C
28462341 TTAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACC
28462361 TTAAC
1 TTAAC
28462366 CTAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.25
21 7 0.29
22 11 0.46
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAACTTAAAAACCCTAACC
Found at i:28462366 original size:51 final size:51
Alignment explanation
Indices: 28462291--28462463 Score: 196
Period size: 51 Copynumber: 3.4 Consensus size: 51
28462281 CTAACCTAAA
* * *
28462291 TTAATTACAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACT-C
1 TTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACTAT
*
28462341 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAAACCT-AACTTAAT
1 TTAA-TTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAAC-T-AT
* *
28462394 TTAATTAAAAACCCTAAACCCTTAACTTAA---AATT-AAAACCCTAACCTAAT
1 TTAATTAAAAACCCT-AA-CCTTAACCTAATTTAATTAAAAACCCTAAACT-AT
28462444 TTAATTAAAAACCCTAACCT
1 TTAATTAAAAACCCTAACCT
28462464 AATTTAATTA
Statistics
Matches: 109, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
48 3 0.03
49 2 0.02
50 33 0.30
51 44 0.40
52 11 0.10
53 6 0.06
54 10 0.09
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (51 bp):
TTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACTAT
Found at i:28462400 original size:74 final size:74
Alignment explanation
Indices: 28462267--28462487 Score: 284
Period size: 73 Copynumber: 2.9 Consensus size: 74
28462257 TAATTTAATG
*
28462267 AAAAACCCTAACCCCTAACCTAAATTAATTACAAACCCTAACCCTAACCTAATTTAATTAAAAAC
1 AAAAACCCTAA-CCCTAACCTAATTTAATTA-AAA----AA-CCTAACCTAATTTAATTAAAAAC
*
28462332 CCTAAACTCTTAACTT
59 CCTAAACCCTTAACTT
* *
28462348 AAAAACCCTAACCTTAACCTAATTTAATTAAAAAACCTAACTTAATTTAATTAAAAACCCTAAAC
1 AAAAACCCTAACCCTAACCTAATTTAATTAAAAAACCTAACCTAATTTAATTAAAAACCCTAAAC
28462413 CCTTAACTT
66 CCTTAACTT
**** *
28462422 -AAAATTAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AAC
1 AAAAACCCTAACCCTAACCTAATTTAATTAAAAAACCTAACCTAATTTAATTAAAAACCCTAAAC
28462485 CCT
66 CCT
28462488 AACCTAATTT
Statistics
Matches: 129, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
72 6 0.05
73 53 0.41
74 37 0.29
75 2 0.02
79 3 0.02
80 17 0.13
81 11 0.09
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (74 bp):
AAAAACCCTAACCCTAACCTAATTTAATTAAAAAACCTAACCTAATTTAATTAAAAACCCTAAAC
CCTTAACTT
Found at i:28462483 original size:18 final size:20
Alignment explanation
Indices: 28462364--28462479 Score: 61
Period size: 23 Copynumber: 5.0 Consensus size: 20
28462354 CCTAACCTTA
28462364 ACCTAATTTAATTAAAAAACC
1 ACCTAATTTAATT-AAAAACC
*
28462385 TAACTTAATTTAATTAAAAACCC
1 --ACCTAATTTAATTAAAAA-CC
* *
28462408 TAAACCCTTAACTTAAAATTAAAACCC
1 ---A-CC-TAA-TT-TAATTAAAAACC
28462435 TAACCTAATTTAATTAAAAACCC
1 --ACCTAATTTAATTAAAAA-CC
28462458 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
28462480 CTAACCCTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
22 15 0.19
23 38 0.49
24 5 0.06
25 3 0.04
26 5 0.06
27 4 0.05
28 8 0.10
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:28462502 original size:125 final size:124
Alignment explanation
Indices: 28462306--28462587 Score: 428
Period size: 125 Copynumber: 2.3 Consensus size: 124
28462296 TACAAACCCT
* *
28462306 AACCCTAACCTAATTTAATTAAAAACCCTAAACTCTTAACTTAAAAACCCTAACCTTAACCTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTCTTAACTTAAAAACCCTAACCCTAACCTAAT
*
28462371 TTAATTAAAAAACCT-AACTTAATTTAA-TTAAAAACCCTAAACCCTTAACTTAAAATT-AA
66 TTAATTAAAAAACCTAAAC---ACTTAACTTAAAAACCCTAAACCCTTAACTTAAAATTAAA
*
28462430 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAACCCTAACCTA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCT--CTTAACTTAAAAACCCTAACCCTAACCTA
* *
28462494 ATTTAATTAAAAATCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAATTAAA
64 ATTTAATTAAAAAACCTAAACACTTAACTTAAAAACCCTAAACCCTTAACTTAAAATTAAA
*
28462555 AACTCTAACCTAATTTAATTAAAAACCCTAACC
1 AACCCTAACCTAATTTAATTAAAAACCCTAACC
28462588 CTAACCTAAT
Statistics
Matches: 146, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
123 4 0.03
124 63 0.43
125 72 0.49
126 7 0.05
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (124 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCTCTTAACTTAAAAACCCTAACCCTAACCTAAT
TTAATTAAAAAACCTAAACACTTAACTTAAAAACCCTAAACCCTTAACTTAAAATTAAA
Found at i:28462526 original size:22 final size:22
Alignment explanation
Indices: 28462496--28462549 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
28462486 CTAACCTAAT
*
28462496 TTAA-TTAAAAATCCTAAACCC
1 TTAACTTAAAAACCCTAAACCC
28462517 TTAACTTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCTAAACCC
28462539 TTAACTTAAAA
1 TTAACTTAAAA
28462550 TTAAAAACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (22 bp):
TTAACTTAAAAACCCTAAACCC
Found at i:28462552 original size:102 final size:101
Alignment explanation
Indices: 28462320--28462629 Score: 372
Period size: 102 Copynumber: 3.1 Consensus size: 101
28462310 CTAACCTAAT
* ***** *
28462320 TTAA-TTAAAAACCCTAAACTCTTAACTTAAAAACCCTAACCTTAACCTAATTTAATT-AAAA--
1 TTAACTTAAAAACCCTAAACCCTTAACTTAAAATTAAAAACCCTAACCTAATTTAATTAAAAACC
*
28462381 --AA-CCTAACTTAATTTAATTAAAAACCCTAAACCC
66 CTAACCCTAACCTAATTTAATTAAAAA-CCTAAACCC
* *
28462415 TTAACTT-AAAA--TTAAAACCC-TAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAA
1 TTAACTTAAAAACCCT-AAACCCTTAACTTAA---AATTAAAAACCCTAACCTAATTTAATTAAA
28462476 AACCCTAACCCTAACCTAATTTAATTAAAAATCCTAAACCC
62 AACCCTAACCCTAACCTAATTTAATTAAAAA-CCTAAACCC
*
28462517 TTAACTTAAAAACCCTAAACCCTTAACTTAAAATTAAAAACTCTAACCTAATTTAATTAAAAACC
1 TTAACTTAAAAACCCTAAACCCTTAACTTAAAATTAAAAACCCTAACCTAATTTAATTAAAAACC
*
28462582 CTAACCCTAACCTAATTTAATTTAAAACCTTAAACCC
66 CTAACCCTAACCTAATTTAATTAAAAACC-TAAACCC
28462619 TTAACTTAAAA
1 TTAACTTAAAA
28462630 GCTCTAACCT
Statistics
Matches: 184, Mismatches: 15, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
93 8 0.04
94 5 0.03
95 8 0.04
96 23 0.12
97 4 0.02
101 4 0.02
102 114 0.62
103 4 0.02
104 6 0.03
105 8 0.04
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (101 bp):
TTAACTTAAAAACCCTAAACCCTTAACTTAAAATTAAAAACCCTAACCTAATTTAATTAAAAACC
CTAACCCTAACCTAATTTAATTAAAAACCTAAACCC
Found at i:28462610 original size:73 final size:74
Alignment explanation
Indices: 28462247--28462614 Score: 224
Period size: 73 Copynumber: 4.8 Consensus size: 74
28462237 TAAAAACCCT
* *
28462247 AACCCTAACCTAATTTAATGAAAAACCCTAACCCCTAACCTAAATTAA-TTACAAACCCTAACCC
1 AACCCTAACCTAATTTAATTAAAAACCCTAA-CCCTAACCTAATTTAATTTA-AAACCCT-----
28462311 TAACCTAATTTAATTAAA
59 TAACCTAA--TAATTAAA
* * * * * *
28462329 AACCCTAAACT--CTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAAACC-TAACTT
1 AACCCTAACCTAATTTAA-TTAAAAACCCTAACCCTAACCTAATTTAATTTAAAACCCTTAACCT
28462391 AATTTAATTAAA
65 AA--TAATTAAA
* **** *
28462403 AACCCTAAACC---CTTAACTT-AAAATTAAAACCCTAACCTAATTTAATTAAAAACCC-TAACC
1 AACCCT-AACCTAATTTAA-TTAAAAACCCTAACCCTAACCTAATTTAATTTAAAACCCTTAACC
28462463 TAATTTAATTAAAAA
64 TAA--TAATT--AAA
* * * **
28462478 CCCTAACCCTAACCTAATTTAATTAAAAATCCTAAACCCTTAACTTAA--AAACCCT-AAACCCT
1 ----AACCCTAACCTAATTTAATTAAAAACCCT-AACCC-TAACCTAATTTAA-TTTAAAACCCT
*
28462540 TAACTTAA-AATTAAA
59 TAACCTAATAATTAAA
*
28462555 AACTCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAAAA-CCTTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAAAACCCTTAA
28462615 ACCCTTAACT
Statistics
Matches: 234, Mismatches: 32, Indels: 50
0.74 0.10 0.16
Matches are distributed among these distances:
71 7 0.03
72 12 0.05
73 76 0.32
74 31 0.13
75 6 0.03
77 3 0.01
78 4 0.02
79 10 0.04
80 25 0.11
81 31 0.13
82 22 0.09
83 7 0.03
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (74 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAAAACCCTTAACCTA
ATAATTAAA
Found at i:28462639 original size:176 final size:172
Alignment explanation
Indices: 28462279--28462596 Score: 473
Period size: 176 Copynumber: 1.8 Consensus size: 172
28462269 AAACCCTAAC
* *
28462279 CCCTAACCTAAATTAATTACAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACTCTTA
1 CCCTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
*
28462344 ACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAAACCTAACTTAATTTAATTAAAAACCCT
66 ACTTAAAAACCCTAACCTTAACCTAA--TAATTAAAAAACCTAACCTAATTTAATTAAAAACCCT
* *
28462409 AAACCCTTAACTTAAAATTAAAACCCTAACCTAATTTAATTAAAAA
129 AAACCCTTAACCTAAAATTAAAACCCTAACC--ACTTAATTAAAAA
* *
28462455 CCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAATCCTAAACCCTTA
1 CCCTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
*
28462520 ACTTAAAAACCCTAAACCCTTAACTTAA-AATT-AAAAACTCTAACCTAATTTAATTAAAAACCC
66 ACTTAAAAACCCT-AA-CCTTAACCTAATAATTAAAAAAC-CTAACCTAATTTAATTAAAAACCC
28462583 T-AACCC-TAACCTAA
128 TAAACCCTTAACCTAA
28462597 TTTAATTTAA
Statistics
Matches: 132, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
173 7 0.05
174 11 0.08
175 28 0.21
176 74 0.56
177 2 0.02
178 10 0.08
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (172 bp):
CCCTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTA
ACTTAAAAACCCTAACCTTAACCTAATAATTAAAAAACCTAACCTAATTTAATTAAAAACCCTAA
ACCCTTAACCTAAAATTAAAACCCTAACCACTTAATTAAAAA
Found at i:28462779 original size:115 final size:116
Alignment explanation
Indices: 28462645--28462861 Score: 391
Period size: 116 Copynumber: 1.9 Consensus size: 116
28462635 AACCTTAACG
28462645 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAA-TTTACATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
*
28462709 CTTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
* * *
28462760 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAATAATTTTATATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
28462825 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
28462862 CAATTTATCA
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
115 46 0.47
116 51 0.53
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.43
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAAATATTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
Found at i:28462878 original size:17 final size:18
Alignment explanation
Indices: 28462837--28462878 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
28462827 TTTACTAACC
* *
28462837 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
28462855 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
28462872 ATTAATA
1 ATTAATA
28462879 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:28466110 original size:124 final size:125
Alignment explanation
Indices: 28465890--28466253 Score: 496
Period size: 124 Copynumber: 2.8 Consensus size: 125
28465880 CCCAAACATG
*
28465890 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
28465955 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAT-TTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATATTATTTCTTACATGAC
** **
28466014 CTACTGTAGCAAAAGCGCGTTGACGAGACCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
28466079 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAT-ATTATTTCTTACATGAC
*
28466140 CTACTGTAGCAAACTTGCGCGCAAAAGCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAA
1 CTACTGT-----A-------GCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAA
* **
28466205 ATAGCATCCTGCTAGAAGAGATTTTATACTATTTTATCAGAAACGTCAA
54 ATAGCATCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
28466254 CTCGAAATTA
Statistics
Matches: 210, Mismatches: 16, Indels: 14
0.88 0.07 0.06
Matches are distributed among these distances:
124 102 0.49
126 21 0.10
131 1 0.00
138 86 0.41
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATATTATTTCTTACATGAC
Found at i:28467854 original size:3 final size:3
Alignment explanation
Indices: 28467846--28467876 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28467836 GTCCCTTGCG
28467846 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28467877 AACACGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28472515 original size:90 final size:90
Alignment explanation
Indices: 28472318--28472593 Score: 331
Period size: 91 Copynumber: 3.0 Consensus size: 90
28472308 ATGGTTTTTG
* * *
28472318 CACGAAAGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTCTCCACTGATAACATGTCAGTTT
1 CACGCAAGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTCTCCAC-GATAACACGTCAATTT
* * *
28472383 GCTTATAAGAGCTCTCCAATCAATAA
65 GCTCATAAGAGCTTTCCAAACAATAA
* * * *
28472409 CACGCAAGATGCACATAATGCAAAGCCCGTATGATAAATATTCTCCTCGATAACACGTCAATTTG
1 CACGCAAGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTCTCCACGATAACACGTCAATTTG
* *
28472474 CTCATAAAAGTTTTCCAAACAATAA
66 CTCATAAGAGCTTTCCAAACAATAA
* ** * * * *
28472499 CATGTTAGATGCACATAGTGTACAA-CCCGTAGGCTAAATATTCTCCCCCAATAACGCGTCAATT
1 CACGCAAGATGCACATAGTGCA-AAGCCCGTAGGCTAAATATTCT-CCACGATAACACGTCAATT
28472563 TGCTCATAAGAGCTTT-CAAACTAATAA
64 TGCTCATAAGAGCTTTCCAAAC-AATAA
28472590 CACG
1 CACG
28472594 TCAAATCTTC
Statistics
Matches: 157, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
90 74 0.47
91 83 0.53
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (90 bp):
CACGCAAGATGCACATAGTGCAAAGCCCGTAGGCTAAATATTCTCCACGATAACACGTCAATTTG
CTCATAAGAGCTTTCCAAACAATAA
Found at i:28478420 original size:26 final size:26
Alignment explanation
Indices: 28478382--28478451 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 26
28478372 AATAATGTGT
** *
28478382 AAAACAAGCTAAAATAAATAATC-TTC
1 AAAACAATTTAAAATAAATAA-CATAC
* *
28478408 AAAGCAATTTAAAAATAAATAACATAG
1 AAAACAATTT-AAAATAAATAACATAC
28478435 AAAACAATTTAAAATAA
1 AAAACAATTTAAAATAA
28478452 CATGTAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.63, C:0.10, G:0.04, T:0.23
Consensus pattern (26 bp):
AAAACAATTTAAAATAAATAACATAC
Found at i:28478705 original size:22 final size:21
Alignment explanation
Indices: 28478673--28478724 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
28478663 AACTTAAAAT
*
28478673 AAAT-AATAATAGAACGATTTA
1 AAATAAATAATAGAAAG-TTTA
*
28478694 AAATAAATAATATAAAGTTTA
1 AAATAAATAATAGAAAGTTTA
28478715 AAATAAATAA
1 AAATAAATAA
28478725 ATAAATACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATAAATAATAGAAAGTTTA
Found at i:28478722 original size:25 final size:24
Alignment explanation
Indices: 28478638--28478728 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 24
28478628 TGATTAACAT
*
28478638 AGTTTAAAATAAATAATATATTAAA
1 AGTTTAAAATAAATAA-ATAATAAA
**
28478663 AACTTAAAATAAAT-AATAATAGAA
1 AGTTTAAAATAAATAAATAATA-AA
*
28478687 CGATTTAAAATAAAT-AAT-AT-AA
1 AG-TTTAAAATAAATAAATAATAAA
28478709 AGTTTAAAATAAATAAATAA
1 AGTTTAAAATAAATAAATAA
28478729 ATACATTGCA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
21 12 0.22
22 6 0.11
23 6 0.11
24 5 0.09
25 26 0.47
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (24 bp):
AGTTTAAAATAAATAAATAATAAA
Found at i:28490251 original size:22 final size:22
Alignment explanation
Indices: 28490234--28490295 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
28490224 TAATAGTGAA
28490234 AAAACAACAAGAAAATAGCAAC
1 AAAACAACAAGAAAATAGCAAC
* * *
28490256 AAAATAACAAGAAAACAGCAAG
1 AAAACAACAAGAAAATAGCAAC
* *
28490278 AAAATAGCAAGAAAATAG
1 AAAACAACAAGAAAATAG
28490296 AAAAAGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.68, C:0.13, G:0.13, T:0.06
Consensus pattern (22 bp):
AAAACAACAAGAAAATAGCAAC
Found at i:28490259 original size:11 final size:11
Alignment explanation
Indices: 28490241--28490295 Score: 83
Period size: 11 Copynumber: 5.0 Consensus size: 11
28490231 GAAAAAACAA
28490241 CAAGAAAATAG
1 CAAGAAAATAG
* *
28490252 CAACAAAATAA
1 CAAGAAAATAG
*
28490263 CAAGAAAACAG
1 CAAGAAAATAG
28490274 CAAGAAAATAG
1 CAAGAAAATAG
28490285 CAAGAAAATAG
1 CAAGAAAATAG
28490296 AAAAAGAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.65, C:0.13, G:0.15, T:0.07
Consensus pattern (11 bp):
CAAGAAAATAG
Found at i:28490719 original size:22 final size:26
Alignment explanation
Indices: 28490693--28490750 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 26
28490683 TATATTTTAT
28490693 TTTAAAATATAAATA-T-AAAA-TAA
1 TTTAAAATATAAATATTAAAAATTAA
*
28490716 -TTAAAATAAAAATATTAAAAATTAA
1 TTTAAAATATAAATATTAAAAATTAA
28490741 TTTAAAATAT
1 TTTAAAATAT
28490751 CAAGAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 13 0.45
23 1 0.03
24 4 0.14
25 3 0.10
26 8 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TTTAAAATATAAATATTAAAAATTAA
Found at i:28490727 original size:15 final size:15
Alignment explanation
Indices: 28490695--28490735 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
28490685 TATTTTATTT
28490695 TAAAATA-T-AAATA
1 TAAAATATTAAAATA
28490708 TAAAATAATTAAAATA
1 TAAAAT-ATTAAAATA
28490724 -AAAATATTAAAA
1 TAAAATATTAAAA
28490736 ATTAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.24
14 8 0.32
15 6 0.24
16 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAATATTAAAATA
Found at i:28492565 original size:23 final size:23
Alignment explanation
Indices: 28492523--28492608 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
28492513 AATGTTTACA
*
28492523 AACATGTTCATTTAAC-TTAATTG
1 AACATGTTCA-TGAACATTAATTG
* * *
28492546 AATATGTTCATGAACATTAAATA
1 AACATGTTCATGAACATTAATTG
28492569 AACATGTTCATGAACATATAATTG
1 AACATGTTCATGAACAT-TAATTG
*
28492593 AACATATTCATGAACA
1 AACATGTTCATGAACA
28492609 ATGTTAATGA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 4 0.08
23 30 0.57
24 19 0.36
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (23 bp):
AACATGTTCATGAACATTAATTG
Found at i:28495644 original size:64 final size:64
Alignment explanation
Indices: 28495543--28495665 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
28495533 GGGACAAGGA
* * *
28495543 CACGGGCAAGTGTCCAGGCCATGTAACTCGCTGTTTACAAAATAATGATCACACGGGTGAACGG
1 CACGGGCAAGTGTCCAGGCCATGTAACTCACTGTTTACAAAATAAGGATCACACAGGTGAACGG
** * * *
28495607 CACGGGCGTGTGTCCAGGCCGTGTGACTCACTGTTTACAAAATAAGGATTACACAGGTG
1 CACGGGCAAGTGTCCAGGCCATGTAACTCACTGTTTACAAAATAAGGATCACACAGGTG
28495666 GAGGACACGA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (64 bp):
CACGGGCAAGTGTCCAGGCCATGTAACTCACTGTTTACAAAATAAGGATCACACAGGTGAACGG
Found at i:28495683 original size:64 final size:64
Alignment explanation
Indices: 28495552--28495695 Score: 166
Period size: 64 Copynumber: 2.3 Consensus size: 64
28495542 ACACGGGCAA
* * * * * ** *
28495552 GTGTCCAGGCCATGTAACTCGCTGTTTACAAAATAATGATCACACGGGTGAACGGCACGGGCGT
1 GTGTCCAGGCCGTGTGACTCACTGTTTACAAAATAAGGATCACACAGGTGAACGGCACGACCAT
* *
28495616 GTGTCCAGGCCGTGTGACTCACTGTTTACAAAATAAGGATTACACAGGTGGA-GGACACGACCAT
1 GTGTCCAGGCCGTGTGACTCACTGTTTACAAAATAAGGATCACACAGGTGAACGG-CACGACCAT
*
28495680 GTGT-TAGGCCGTGTGA
1 GTGTCCAGGCCGTGTGA
28495696 GACACACGGG
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
63 13 0.19
64 55 0.81
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (64 bp):
GTGTCCAGGCCGTGTGACTCACTGTTTACAAAATAAGGATCACACAGGTGAACGGCACGACCAT
Found at i:28495773 original size:54 final size:54
Alignment explanation
Indices: 28495667--28495773 Score: 178
Period size: 54 Copynumber: 2.0 Consensus size: 54
28495657 ACACAGGTGG
* *
28495667 AGGACACGACCATGTGTTAGGCCGTGTGAGACACACGGGCAAGCACATGGGCAA
1 AGGACACGACCATGTGTTAGGCCGTGTGAGACACACGGACAAGCACACGGGCAA
* *
28495721 AGGACACGACCATGTGTTAGGCCGTGTGAGACACACGGATAAGGACACGGGCA
1 AGGACACGACCATGTGTTAGGCCGTGTGAGACACACGGACAAGCACACGGGCA
28495774 TGTTCCAGGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.34, T:0.13
Consensus pattern (54 bp):
AGGACACGACCATGTGTTAGGCCGTGTGAGACACACGGACAAGCACACGGGCAA
Found at i:28496703 original size:14 final size:14
Alignment explanation
Indices: 28496684--28496712 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28496674 TATTGTCTAT
28496684 GCCGAATATAAGGG
1 GCCGAATATAAGGG
28496698 GCCGAATATAAGGG
1 GCCGAATATAAGGG
28496712 G
1 G
28496713 TTAGATCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.38, T:0.14
Consensus pattern (14 bp):
GCCGAATATAAGGG
Found at i:28497589 original size:18 final size:19
Alignment explanation
Indices: 28497559--28497595 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28497549 ATCAAAATTT
*
28497559 TATTTTAAATTTTTTTATA
1 TATTTTAAATTTTATTATA
28497578 TATTTT-AATTTTATTATA
1 TATTTTAAATTTTATTATA
28497596 CATACTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTAAATTTTATTATA
Found at i:28502647 original size:25 final size:24
Alignment explanation
Indices: 28502614--28502665 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
28502604 TGTGAAAGTA
* *
28502614 AAACACTAACTAATAAATAAAAA-T
1 AAACACTAA-AAAGAAATAAAAACT
28502638 AAACACCTAAAAAGAAATAAAAACT
1 AAACA-CTAAAAAGAAATAAAAACT
28502663 AAA
1 AAA
28502666 GAAAAGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.15
Consensus pattern (24 bp):
AAACACTAAAAAGAAATAAAAACT
Found at i:28504663 original size:21 final size:22
Alignment explanation
Indices: 28504634--28504674 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28504624 GATCCCCTTT
* *
28504634 ATTAGAATAAATAA-AAATAGC
1 ATTAAAATAAAAAATAAATAGC
28504655 ATTAAAATAAAAAATAAATA
1 ATTAAAATAAAAAATAAATA
28504675 TTAAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (22 bp):
ATTAAAATAAAAAATAAATAGC
Found at i:28504677 original size:19 final size:19
Alignment explanation
Indices: 28504655--28504691 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28504645 TAAAAATAGC
28504655 ATTAAAATAAAAAATAAAT
1 ATTAAAATAAAAAATAAAT
* *
28504674 ATTAAAATTAAAATTAAA
1 ATTAAAATAAAAAATAAA
28504692 GACAAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTAAAATAAAAAATAAAT
Found at i:28508863 original size:26 final size:26
Alignment explanation
Indices: 28508827--28508947 Score: 136
Period size: 26 Copynumber: 4.7 Consensus size: 26
28508817 AAAATTAATG
*
28508827 AAATACTCTCGATGGGTAAAATACCA
1 AAATACCCTCGATGGGTAAAATACCA
* **
28508853 AAATACCCTCGATGGGTAAATTATTA
1 AAATACCCTCGATGGGTAAAATACCA
28508879 AAATACCCTCGATGGG-AAAATTACCA
1 AAATACCCTCGATGGGTAAAA-TACCA
* * * * *
28508905 AAATAACCTCAATGGGTAAATTATCG
1 AAATACCCTCGATGGGTAAAATACCA
*
28508931 AAATACCCTCGAAGGGT
1 AAATACCCTCGATGGGT
28508948 CGAATGACCG
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
25 3 0.04
26 72 0.92
27 3 0.04
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (26 bp):
AAATACCCTCGATGGGTAAAATACCA
Found at i:28508890 original size:52 final size:53
Alignment explanation
Indices: 28508818--28508947 Score: 183
Period size: 52 Copynumber: 2.5 Consensus size: 53
28508808 TAATGGGAAA
* * * *
28508818 AAATTAATGAAATACTCTCGATGGGTAAAA-TACCAAAATACCCTCGATGGGT
1 AAATTATTGAAATACCCTCGATGGGTAAAATTACCAAAATAACCTCAATGGGT
*
28508870 AAATTATTAAAATACCCTCGATGGG-AAAATTACCAAAATAACCTCAATGGGT
1 AAATTATTGAAATACCCTCGATGGGTAAAATTACCAAAATAACCTCAATGGGT
* *
28508922 AAATTATCGAAATACCCTCGAAGGGT
1 AAATTATTGAAATACCCTCGATGGGT
28508948 CGAATGACCG
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 4 0.06
52 64 0.94
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (53 bp):
AAATTATTGAAATACCCTCGATGGGTAAAATTACCAAAATAACCTCAATGGGT
Found at i:28509228 original size:26 final size:26
Alignment explanation
Indices: 28509179--28509228 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
28509169 ACATATACTG
* **
28509179 TACTGGCAGCTCTGCTGCGTTATTAT
1 TACTGGCAGCTATGCTGCAATATTAT
28509205 TACTGGCAGCTATGCTGCAATATT
1 TACTGGCAGCTATGCTGCAATATT
28509229 GGTGTGTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTATGCTGCAATATTAT
Found at i:28511112 original size:29 final size:29
Alignment explanation
Indices: 28511080--28511137 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28511070 CTTGTAGAAA
28511080 AAGAAAAGATTGTAGAAGAAGTTAAGCAC
1 AAGAAAAGATTGTAGAAGAAGTTAAGCAC
28511109 AAGAAAAGATTGTAGAAGAAGTTAAGCAC
1 AAGAAAAGATTGTAGAAGAAGTTAAGCAC
28511138 TCGGAGCGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (29 bp):
AAGAAAAGATTGTAGAAGAAGTTAAGCAC
Found at i:28516034 original size:26 final size:26
Alignment explanation
Indices: 28516003--28516239 Score: 204
Period size: 26 Copynumber: 9.0 Consensus size: 26
28515993 TAATGGGCTA
*
28516003 AAATTACCAAAATACCCTTGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
*
28516029 CAATTACCAAAATACCCTCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
*** * *
28516055 AAATTAATGAAACACCTTCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
* * * *
28516081 AAATTATCGAAATTCCATCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
* * ** * *
28516107 AAGTTATCAAAATACCCTTAATAGAT
1 AAATTACCAAAATACCCTCGATGGGT
*
28516133 AAATTACTAAAATACCCTCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
* *
28516159 AAATTACTAAAATACGCTCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
* * * * *
28516185 AAATTATCGAAATACCCTCAAAGGTT
1 AAATTACCAAAATACCCTCGATGGGT
* * *
28516211 AAAAATTATCGAAATACCCTCGAAGGGT
1 --AAATTACCAAAATACCCTCGATGGGT
28516239 A
1 A
28516240 GAATGACTAT
Statistics
Matches: 171, Mismatches: 38, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
26 147 0.86
28 24 0.14
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (26 bp):
AAATTACCAAAATACCCTCGATGGGT
Found at i:28516398 original size:26 final size:26
Alignment explanation
Indices: 28516350--28516399 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
28516340 AGATATACTG
* * *
28516350 TACTGGCAGCTCTATTGCGATATTAT
1 TACTGGCAGCTATACTGCAATATTAT
28516376 TACTGGCAGCTATACTGCAATATT
1 TACTGGCAGCTATACTGCAATATT
28516400 GGTGTGTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (26 bp):
TACTGGCAGCTATACTGCAATATTAT
Found at i:28526302 original size:2 final size:2
Alignment explanation
Indices: 28526295--28526321 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28526285 CATAATCACC
28526295 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28526322 GAATTAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28526513 original size:19 final size:21
Alignment explanation
Indices: 28526491--28526538 Score: 73
Period size: 19 Copynumber: 2.3 Consensus size: 21
28526481 TTTAAAAATA
28526491 TTTTAAAATA-TTTTTTT-AT
1 TTTTAAAATACTTTTTTTAAT
28526510 TTTTAAAATACTTTTTTTAAT
1 TTTTAAAATACTTTTTTTAAT
28526531 TTTCTAAA
1 TTT-TAAA
28526539 TTTTTTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.38
20 7 0.27
21 5 0.19
22 4 0.15
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAAAATACTTTTTTTAAT
Found at i:28526518 original size:29 final size:33
Alignment explanation
Indices: 28526462--28526524 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 33
28526452 CCGAATATAA
28526462 TAAATATATATTTTTTATTTTTAAAAATA-TTT
1 TAAATATATATTTTTTATTTTTAAAAATACTTT
28526494 TAAA-ATAT-TTTTTTATTTTT-AAAATACTTT
1 TAAATATATATTTTTTATTTTTAAAAATACTTT
28526524 T
1 T
28526525 TTTAATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 6 0.20
30 16 0.53
31 4 0.13
32 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (33 bp):
TAAATATATATTTTTTATTTTTAAAAATACTTT
Found at i:28529790 original size:25 final size:25
Alignment explanation
Indices: 28529737--28529800 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
28529727 GTAACCAAGC
* *
28529737 TTTAACTGGGAAAAAGATAGCAGAG
1 TTTAACTGGGAAAAAGATAGCAAAA
*
28529762 TTTAATTGGGAAAAAGATAGCAAAA
1 TTTAACTGGGAAAAAGATAGCAAAA
*
28529787 TTTAACTAGGAAAA
1 TTTAACTGGGAAAA
28529801 GAGACTCGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.23
Consensus pattern (25 bp):
TTTAACTGGGAAAAAGATAGCAAAA
Found at i:28539598 original size:30 final size:30
Alignment explanation
Indices: 28539562--28539665 Score: 190
Period size: 30 Copynumber: 3.5 Consensus size: 30
28539552 TGGCTTACAC
28539562 GCCCGTGTGGCCCATACGACCTACTTGGCA
1 GCCCGTGTGGCCCATACGACCTACTTGGCA
28539592 GCCCGTGTGGCCCATACGACCTACTTGGCA
1 GCCCGTGTGGCCCATACGACCTACTTGGCA
28539622 GCCCGTGTGGCCCATACGACCTACTTGGCA
1 GCCCGTGTGGCCCATACGACCTACTTGGCA
* *
28539652 GCCCATGTTGCCCA
1 GCCCGTGTGGCCCA
28539666 CATGGCCTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.16, C:0.38, G:0.26, T:0.20
Consensus pattern (30 bp):
GCCCGTGTGGCCCATACGACCTACTTGGCA
Found at i:28540297 original size:18 final size:18
Alignment explanation
Indices: 28540274--28540322 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
28540264 AAGCAGATTG
* *
28540274 AAAATAGAGAAGGAAAAC
1 AAAATAGAAAAAGAAAAC
28540292 AAAATAGAAAAAGAAAAC
1 AAAATAGAAAAAGAAAAC
* *
28540310 -CAAGAGAAAAAGA
1 AAAATAGAAAAAGA
28540323 GAAAGAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.04
Consensus pattern (18 bp):
AAAATAGAAAAAGAAAAC
Found at i:28541923 original size:3 final size:3
Alignment explanation
Indices: 28541915--28541975 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
28541905 TCTAAGCTAG
28541915 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28541963 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
28541976 AAATTTTATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28543955 original size:19 final size:17
Alignment explanation
Indices: 28543908--28543948 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
28543898 ATTAGGCCGT
28543908 GTGGGCCACACGGGCTC
1 GTGGGCCACACGGGCTC
28543925 GTGGGCCACACGGGCTC
1 GTGGGCCACACGGGCTC
28543942 GTGGGCC
1 GTGGGCC
28543949 CCACACGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.10, C:0.34, G:0.44, T:0.12
Consensus pattern (17 bp):
GTGGGCCACACGGGCTC
Found at i:28544179 original size:17 final size:17
Alignment explanation
Indices: 28544157--28544189 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28544147 GACCCCTAAT
28544157 TGACTGAAATGATTATA
1 TGACTGAAATGATTATA
*
28544174 TGACTGATATGATTAT
1 TGACTGAAATGATTAT
28544190 GCATGTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (17 bp):
TGACTGAAATGATTATA
Found at i:28547538 original size:28 final size:28
Alignment explanation
Indices: 28547501--28547615 Score: 81
Period size: 28 Copynumber: 3.9 Consensus size: 28
28547491 ATAACTGCAT
28547501 ATATATATTATATATAATAAACCCACAC
1 ATATATATTATATATAATAAACCCACAC
* ** *
28547529 ATATATATTATGTATAGCAGAA-CTACAC
1 ATATATATTATATATAATA-AACCCACAC
**
28547557 ATATATATGTACTAAGTATATAGTTGACCCACAC
1 ATATATAT-TA-T-A-TATA-A-TAAACCCACAC
*
28547591 AAATATATTATATAT-ATAACACCCA
1 ATATATATTATATATAATAA-ACCCA
28547616 TGCACGTAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 18
0.68 0.14 0.19
Matches are distributed among these distances:
27 1 0.02
28 35 0.54
29 4 0.06
30 4 0.06
31 1 0.02
32 5 0.08
33 3 0.05
34 12 0.18
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (28 bp):
ATATATATTATATATAATAAACCCACAC
Found at i:28553094 original size:20 final size:20
Alignment explanation
Indices: 28553069--28553109 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28553059 AGTTCGGCCA
*
28553069 ACAAACCACCATCATTGGTT
1 ACAAACCACCATCACTGGTT
28553089 ACAAACCACCATCACTGGTT
1 ACAAACCACCATCACTGGTT
28553109 A
1 A
28553110 GACTCAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (20 bp):
ACAAACCACCATCACTGGTT
Found at i:28556697 original size:29 final size:28
Alignment explanation
Indices: 28556665--28556730 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
28556655 CCTATAACTG
*
28556665 CATATATATTATATATAATAGAACCCACA
1 CATATATATTATATATAACAGAA-CCACA
**
28556694 CATAT-TCATTATATATGGCAGAACCACA
1 CATATAT-ATTATATATAACAGAACCACA
28556722 CATATATAT
1 CATATATAT
28556731 GTACTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (28 bp):
CATATATATTATATATAACAGAACCACA
Found at i:28556797 original size:34 final size:34
Alignment explanation
Indices: 28556759--28556864 Score: 133
Period size: 34 Copynumber: 3.1 Consensus size: 34
28556749 ACTCATACAA
28556759 ATATATTATACATATAACACCCATGCACTTAAAT
1 ATATATTATACATATAACACCCATGCACTTAAAT
* * ** *
28556793 ATATATTATATATATACCACCCATGCACGCATAT
1 ATATATTATACATATAACACCCATGCACTTAAAT
* *
28556827 ATATATTATTCATATAACACCCATGTA-TGTAAAT
1 ATATATTATACATATAACACCCATGCACT-TAAAT
28556861 ATAT
1 ATAT
28556865 TATAGAGAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.35
Consensus pattern (34 bp):
ATATATTATACATATAACACCCATGCACTTAAAT
Found at i:28558307 original size:40 final size:39
Alignment explanation
Indices: 28558263--28558373 Score: 107
Period size: 40 Copynumber: 2.8 Consensus size: 39
28558253 TGTTTGGACA
* * *
28558263 AAAAACGCTGCTAAAAAGCGAGCATTAGCTGCGCATTTAG
1 AAAAACGCAGCTAAAAAG-GAGCATTAGCGGCACATTTAG
* * * * *
28558303 AAAAACACAGCTAAAATGAAGCATTAGCGGCACTTTTTG
1 AAAAACGCAGCTAAAAAGGAGCATTAGCGGCACATTTAG
*
28558342 AAAAACGCCA-CTAAAAATAGAGCATTAGCGGC
1 AAAAACG-CAGCTAAAAA-GGAGCATTAGCGGC
28558374 GTTTATAATG
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
39 28 0.49
40 29 0.51
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (39 bp):
AAAAACGCAGCTAAAAAGGAGCATTAGCGGCACATTTAG
Found at i:28558345 original size:39 final size:40
Alignment explanation
Indices: 28558273--28558373 Score: 100
Period size: 39 Copynumber: 2.5 Consensus size: 40
28558263 AAAAACGCTG
** * *
28558273 CTAAAAAGCGAGCATTAGCTGCGCATTTAGAAAAAC-ACA
1 CTAAAAATAGAGCATTAGCGGCACATTTAGAAAAACGACA
* * *
28558312 GCT-AAAAT-GAAGCATTAGCGGCACTTTTTGAAAAACGCCA
1 -CTAAAAATAG-AGCATTAGCGGCACATTTAGAAAAACGACA
28558352 CTAAAAATAGAGCATTAGCGGC
1 CTAAAAATAGAGCATTAGCGGC
28558374 GTTTATAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
38 1 0.02
39 28 0.55
40 21 0.41
41 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (40 bp):
CTAAAAATAGAGCATTAGCGGCACATTTAGAAAAACGACA
Found at i:28558533 original size:41 final size:41
Alignment explanation
Indices: 28558433--28558717 Score: 270
Period size: 41 Copynumber: 7.0 Consensus size: 41
28558423 TGAGGCTTTG
* * * * * *
28558433 GGGACTTTAGCGGCGTTTTTTAAAAAGTGCCACTAATGAT-G
1 GGGA-TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
* * *
28558474 GGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTGT
1 GGGATTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
* * * **
28558515 GGGATTTAGCGGCTTTTTTTAAGAAGCGCCGCTAATGTTGG
1 GGGATTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
*
28558556 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
1 GGGATTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
* ** **
28558597 GGGTTTTAGCGATGTTTTTGAAGAAGCATCGCTAATGCTCT
1 GGGATTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
* * * * * *
28558638 TGGATTTAACGGCGTTTTAG-GGAAAGTGCCGCTATTGCTCT
1 GGGATTTAGCGGCGTTTTTGAAG-AAGCGCCGCTAATGCTCT
* * *
28558679 AGGCTTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGCTC
1 GGGATTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
28558718 GAGGGTTTTT
Statistics
Matches: 197, Mismatches: 44, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
40 45 0.23
41 152 0.77
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (41 bp):
GGGATTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
Found at i:28558669 original size:123 final size:121
Alignment explanation
Indices: 28558430--28558726 Score: 312
Period size: 123 Copynumber: 2.4 Consensus size: 121
28558420 TACTGAGGCT
* * * * * *
28558430 TTGGGGACTTTAGCGGCGTTTTTTAAAAAGTGCCACTAATGAT-GGGGCTTTAGCAGCGTTTTTG
1 TTGGGGGCTTTAGCGGCG-TTTTTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCAGCGTTTTTG
* * * *
28558494 AAGAAGCGCCGCTAATGCTGTGGGATTTAGCGGCTTTTTTTAAGAAGCGCCGCTAATG
65 AAGAAGCACCGCTAATGCTCTGGGATTTAACGGC-TGTTTTAAGAAGCGCCGCTAATG
* * *
28558552 TTGGGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGGTTTTAGC-GATGTTTTT
1 TTGGGGGCTTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGCTCAGGGTTTTAGCAG-CGTTTTT
* * * * *
28558616 GAAGAAGCATCGCTAATGCTCTTGGATTTAACGGC-GTTTTAGGGAAAGTGCCGCTATTG
64 GAAGAAGCACCGCTAATGCTCTGGGATTTAACGGCTGTTTTA-AG-AAGCGCCGCTAATG
* ***
28558675 CTCTAGGCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCGAGGGTTTT
1 TTGGGGGCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTC-AGGGTTTT
28558727 TAGGGTTAAC
Statistics
Matches: 146, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
121 10 0.07
122 53 0.36
123 83 0.57
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.33
Consensus pattern (121 bp):
TTGGGGGCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCAGGGTTTTAGCAGCGTTTTTGA
AGAAGCACCGCTAATGCTCTGGGATTTAACGGCTGTTTTAAGAAGCGCCGCTAATG
Found at i:28558837 original size:7 final size:7
Alignment explanation
Indices: 28558827--28558886 Score: 59
Period size: 7 Copynumber: 8.7 Consensus size: 7
28558817 AGAGTTTTGA
28558827 GTTTAGG
1 GTTTAGG
*
28558834 GTTTATG
1 GTTTAGG
*
28558841 GTGTA-G
1 GTTTAGG
28558847 GTTTAGG
1 GTTTAGG
* *
28558854 GCTTGGG
1 GTTTAGG
*
28558861 GTTTGGG
1 GTTTAGG
*
28558868 GTTTAAG
1 GTTTAGG
28558875 GTTTAGG
1 GTTTAGG
28558882 GTTTA
1 GTTTA
28558887 CGTTTTAATG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
6 5 0.12
7 38 0.88
ACGTcount: A:0.13, C:0.02, G:0.42, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:28558982 original size:21 final size:21
Alignment explanation
Indices: 28558958--28558998 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28558948 TAGGGGTTGA
* *
28558958 TGTTTATGGTTTACGGTTTAG
1 TGTTAATGATTTACGGTTTAG
*
28558979 TGTTAATGATTTAGGGTTTA
1 TGTTAATGATTTACGGTTTA
28558999 CAATGCATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.51
Consensus pattern (21 bp):
TGTTAATGATTTACGGTTTAG
Found at i:28560568 original size:31 final size:31
Alignment explanation
Indices: 28560530--28560609 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
28560520 TTGGATTTTA
28560530 ATTGGTTTTTGCAGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCAGCTAAGATGGTACCTTCT
28560561 ATTGGTTTTTGCTA-CTAAGATGGTACCTTCT
1 ATTGGTTTTTGC-AGCTAAGATGGTACCTTCT
* * *
28560592 AGTGATTTTTGCTGCTAA
1 ATTGGTTTTTGCAGCTAA
28560610 ATCAACCATG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.44
Consensus pattern (31 bp):
ATTGGTTTTTGCAGCTAAGATGGTACCTTCT
Found at i:28562329 original size:5 final size:5
Alignment explanation
Indices: 28562319--28562345 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28562309 GATTCTTGTT
28562319 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
28562346 GGCAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:28563667 original size:43 final size:43
Alignment explanation
Indices: 28563569--28563804 Score: 246
Period size: 43 Copynumber: 5.5 Consensus size: 43
28563559 ATGTTTTTGT
* * * * * *
28563569 GGCGTTTTTGCGAGAAGCGTCGCTAAAGGT-TTG-TACTATAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGAT-CTATAGC
* * **
28563611 AGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGATATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
* * *
28563654 GGCGCTTT-TGGGAAAAGCACCGCTAAATGTCTTGATCTATAGC
1 GGCG-TTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
** * *
28563697 GGCGTTTGT-ATAGAAGCGCCGCTAAAGGTCCCGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
** *
28563739 GGCGTTTGTGAAAAAAGCACCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
28563782 GGCGTTTGTGGGAAAAGCGCCGC
1 GGCGTTTGTGGGAAAAGCGCCGC
28563805 AAACGTTTGT
Statistics
Matches: 162, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
42 63 0.39
43 96 0.59
44 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
Found at i:28563717 original size:85 final size:85
Alignment explanation
Indices: 28563625--28563790 Score: 244
Period size: 85 Copynumber: 2.0 Consensus size: 85
28563615 TTTGTGGGAA
** ** * *
28563625 AAGCGCCGCTAAAGGTCTTGAGATATAGCGGCGCTTT-TGGGAAAAGCACCGCTAAATGTCTTGA
1 AAGCGCCGCTAAAGGTCCCGAGATATAGCGGCG-TTTGTGAAAAAAGCACCGCTAAAGGTCCTGA
28563689 TCTATAGCGGCGTTTGTATAG
65 TCTATAGCGGCGTTTGTATAG
**
28563710 AAGCGCCGCTAAAGGTCCCGATCTATAGCGGCGTTTGTGAAAAAAGCACCGCTAAAGGTCCTGAT
1 AAGCGCCGCTAAAGGTCCCGAGATATAGCGGCGTTTGTGAAAAAAGCACCGCTAAAGGTCCTGAT
28563775 CTATAGCGGCGTTTGT
66 CTATAGCGGCGTTTGT
28563791 GGGAAAAGCG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 3 0.04
85 69 0.96
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (85 bp):
AAGCGCCGCTAAAGGTCCCGAGATATAGCGGCGTTTGTGAAAAAAGCACCGCTAAAGGTCCTGAT
CTATAGCGGCGTTTGTATAG
Found at i:28567804 original size:31 final size:31
Alignment explanation
Indices: 28567737--28567802 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
28567727 TTAATAAAGT
* * *
28567737 TAAAATTGTACTTTAATTTTCTTATAAATAA
1 TAAAATTGTAATTTAATCTTCTTAAAAATAA
* *
28567768 TAAAATTTTAATTTAATCTT-TTAAAAATTA
1 TAAAATTGTAATTTAATCTTCTTAAAAATAA
28567798 TAAAA
1 TAAAA
28567803 ATATAAACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (31 bp):
TAAAATTGTAATTTAATCTTCTTAAAAATAA
Found at i:28569183 original size:20 final size:19
Alignment explanation
Indices: 28569147--28569189 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
28569137 AAAACTTAAG
*
28569147 TATAT-TTTTTAATTTGTT
1 TATATCTTTTAAATTTGTT
28569165 TATATCTTTTAAATATTGTT
1 TATATCTTTTAAAT-TTGTT
28569185 T-TATC
1 TATATC
28569190 AATAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
TATATCTTTTAAATTTGTT
Found at i:28569350 original size:154 final size:154
Alignment explanation
Indices: 28568970--28569442 Score: 609
Period size: 154 Copynumber: 3.1 Consensus size: 154
28568960 ACATTACAAA
* * *
28568970 TATATTATATTTTAAAAACTTAAGTATAATTTTTAATTTGGTTATATGTTTTAAATATTATTTTA
1 TATATTATATTTCAAAAACTTAAGTAT-ATTTTTAATTTGATTATATCTTTTAAATATTATTTTA
* * * * * *
28569035 TTAATAATTTTATTTAATATATCGTTA-TTAAATAACAATTTTATAAAACATACGAGCAATCCGT
65 TCAATAATTTTATTTAATATATCATTATTTAAATAATAATTTTATAAAACACACAAGCAACCCGT
* * *
28569099 ACATCACATGGGAT-AAAAAACTAG
130 GCATCACACGAGATAAAAAAACTAG
* * * *
28569123 TATATTATATCTCGAAAACTTAAGTATATTTTTTAATTTGTTTATATCTTTTAAATATTGTTTTA
1 TATATTATATTTCAAAAACTTAAGTATA-TTTTTAATTTGATTATATCTTTTAAATATTATTTTA
* *
28569188 TCAATAATTTTATTTAATATATCTTTATTTAAATAATGATTTTATAAAACACACAAGCAACCCGT
65 TCAATAATTTTATTTAATATATCATTATTTAAATAATAATTTTATAAAACACACAAGCAACCCGT
*
28569253 GCATCACGCGAGATAAAAAAACTAG
130 GCATCACACGAGATAAAAAAACTAG
* *
28569278 TATATTATATTTCAAAAACTTAAGTATATTTTAAATTTTGATTATATCTTTTAAATATT-TTTAA
1 TATATTATATTTCAAAAACTTAAGTATATTTTTAA-TTTGATTATATCTTTTAAATATTATTTTA
* * * *
28569342 TCAATAATTTTATTTAACATATCATTATTTAAATAATAATTTTATAAAGCACACTTA-CAACCCA
65 TCAATAATTTTATTTAATATATCATTATTTAAATAATAATTTTATAAAACACAC-AAGCAACCCG
*
28569406 TGCATCACAC-AGGA-AAAAAAATTAG
129 TGCATCACACGA-GATAAAAAAACTAG
28569431 T-TATTTATATTT
1 TATA-TTATATTT
28569443 AAAGCTTTGA
Statistics
Matches: 283, Mismatches: 30, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
152 3 0.01
153 102 0.36
154 119 0.42
155 59 0.21
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (154 bp):
TATATTATATTTCAAAAACTTAAGTATATTTTTAATTTGATTATATCTTTTAAATATTATTTTAT
CAATAATTTTATTTAATATATCATTATTTAAATAATAATTTTATAAAACACACAAGCAACCCGTG
CATCACACGAGATAAAAAAACTAG
Found at i:28570691 original size:134 final size:134
Alignment explanation
Indices: 28570383--28571186 Score: 1321
Period size: 134 Copynumber: 6.0 Consensus size: 134
28570373 AACTTAGTCA
*
28570383 AACTACTTTCAAGTTTATTTCCATCTTTT-AAGTGCCAAATCATTTTGGAACTATTTGAG-TCAA
1 AACTAC-TT-AAGTTTATTTCCAT-TTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTC-A
* * *
28570446 AGACTTTACTTCAATAAGGCAGTGAAATAAATTATGTATTTG---ACTATTGTGTTGCTTGTAAA
62 AGACTTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAA
28570508 CTTAATTG
127 CTTAATTG
*
28570516 AACTACTTAAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTGAAGAC
1 AACTACTTAAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTCAAGAC
28570581 TTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACTTA
66 TTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACTTA
28570646 ATTG
131 ATTG
*
28570650 AACTACTTAAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTGAAGAC
1 AACTACTTAAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTCAAGAC
28570715 TTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACTTA
66 TTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACTTA
28570780 ATTG
131 ATTG
28570784 AACTACTTAAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTCAAGAC
1 AACTACTTAAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTCAAGAC
28570849 TTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACTTA
66 TTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACTTA
28570914 ATTG
131 ATTG
28570918 AACTACTTAAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTCAAGAC
1 AACTACTTAAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTCAAGAC
28570983 TTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACTTA
66 TTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACTTA
*
28571048 ATCG
131 ATTG
* * * * * * *
28571052 AATTGCTTTCAAGTTTATTTCCGTCTTTCAAGTGCCAAATCATTTTGGAACTATTTGAGTCCAAA
1 AACTAC-TT-AAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTCAAG
* * * * * * * *
28571117 ACTTTACTTCAATAAGGCAGTGAAATGAATTATGTATTTGTAAACTACTGTGTTGGTTGTGAACT
64 ACTTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACT
28571182 TAATT
129 TAATT
28571187 ATATTTTTAG
Statistics
Matches: 641, Mismatches: 23, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
130 4 0.01
131 83 0.13
132 3 0.00
133 6 0.01
134 432 0.67
135 2 0.00
136 111 0.17
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (134 bp):
AACTACTTAAGTTTATTTCCATTTTTCAAGTGCCAAATCATTTTGAAACTATTTGAGTTCAAGAC
TTTATTTCAATAAGACAGTGAAATAAATCATGTATTTGCAAACTATTGTGTTGCTTGTAAACTTA
ATTG
Found at i:28572693 original size:13 final size:13
Alignment explanation
Indices: 28572667--28572721 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
28572657 GAATAACATA
28572667 TAAATATCAATAAT
1 TAAATAT-AATAAT
28572681 TAAATATAATAAT
1 TAAATATAATAAT
28572694 T--A-ATAATACATT
1 TAAATATAATA-A-T
*
28572706 TAAATAGAATAAT
1 TAAATATAATAAT
28572719 TAA
1 TAA
28572722 TAATAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 2 0.06
13 11 0.31
14 9 0.26
15 5 0.14
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (13 bp):
TAAATATAATAAT
Found at i:28572708 original size:25 final size:25
Alignment explanation
Indices: 28572680--28572737 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
28572670 ATATCAATAA
*
28572680 TTAAATATAATAATTAATAATACAT
1 TTAAATATAATAATTAATAATAAAT
*
28572705 TTAAATAGAATAATTAATAATAAAT
1 TTAAATATAATAATTAATAATAAAT
28572730 TTAAATAT
1 TTAAATAT
28572738 GTCTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
TTAAATATAATAATTAATAATAAAT
Found at i:28580294 original size:20 final size:20
Alignment explanation
Indices: 28580269--28580312 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28580259 TATTTGGTCC
*
28580269 TGTTCTATTTTGATTTGGTT
1 TGTTCTACTTTGATTTGGTT
* *
28580289 TGTTCTACTTTGTTTTGTTT
1 TGTTCTACTTTGATTTGGTT
28580309 TGTT
1 TGTT
28580313 TTGTTATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (20 bp):
TGTTCTACTTTGATTTGGTT
Found at i:28582638 original size:22 final size:22
Alignment explanation
Indices: 28582610--28582654 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28582600 GAGTGTTAGC
28582610 TAAAAGCTTCACTTATGGGATA
1 TAAAAGCTTCACTTATGGGATA
*
28582632 TAAAAGCTTTACTTATGGGATA
1 TAAAAGCTTCACTTATGGGATA
28582654 T
1 T
28582655 GTTCGATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (22 bp):
TAAAAGCTTCACTTATGGGATA
Found at i:28586792 original size:15 final size:14
Alignment explanation
Indices: 28586753--28586809 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
28586743 AAAGAGAAAT
*
28586753 TAAAATAAAATTAA
1 TAAAATAAAATAAA
28586767 TAATCAA-AAAATGAAA
1 TAA--AATAAAAT-AAA
*
28586783 TAAAATAAAATAAC
1 TAAAATAAAATAAA
28586797 TGAAAATAAAATA
1 T-AAAATAAAATA
28586810 TGTATCTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 8 0.22
15 21 0.58
16 7 0.19
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (14 bp):
TAAAATAAAATAAA
Found at i:28588184 original size:15 final size:15
Alignment explanation
Indices: 28588161--28588190 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28588151 TCGTAAACTT
*
28588161 GAGTGAAAAGATAAA
1 GAGTAAAAAGATAAA
28588176 GAGTAAAAAGATAAA
1 GAGTAAAAAGATAAA
28588191 CATTAGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.13
Consensus pattern (15 bp):
GAGTAAAAAGATAAA
Found at i:28595796 original size:599 final size:602
Alignment explanation
Indices: 28594642--28595852 Score: 1910
Period size: 599 Copynumber: 2.0 Consensus size: 602
28594632 ATCACTATCA
28594642 AGAGTGGTAAACAAACTTGGGAGCCGACTACAGACTCTACTATAGCACCTCAAGATACTAGTAAA
1 AGAGTGGTAAACAAACTTGGGAGCCGACTACAGACTCTACTATAGCACCTCAAGATACTAGTAAA
*
28594707 GTAATCCCTGGTGAGAAGGTTGAATCTTAAGAGCTTGTCGATGTACCAGAAAAATAAGTTCCACA
66 GTAATCCCTGGTGAGAAGGTTGAATCTTAAGAGCTTGTCGATGTACCAAAAAAATAAGTTCCACA
* *
28594772 AATTGTCTCTCAGATGCCTAATGTCTGACCCTCAAAACTGTCGACGCAATCAAAGGTGTCGACGC
131 AATTGTCACTCAGATGCCTAATGTCAGACCCTCAAAACTGTCGACGCAATCAAA---GT---CG-
* *
28594837 AATCAGAAGTATCTCTACCTTTACCTTTTCCATAAAGATTTAGGAAAAAGGAGCAAGATAAGTAG
189 -AT----A-TATCTCTACCTTTACCTTTTCCACAAAGATTCAGGAAAAAGGAGCAAGATAAGTAG
* * *
28594902 TACCAACATTTATCGAACACACTGAAGCAACTTCAGGTCAATATTCCTTTAGTAGACACTCTTAT
248 TACCAACAGTTATCGAACACACTGAAGCAACTTCAGGCCAATATTCCTTCAGTAGACACTCTTAT
* *
28594967 GTAAATTCTGAATTATGGGAAGTTTATGAAGGAGCTCTTGTCCAAGAAGAAGAAGCTCATTGATA
313 GGAAATTCTGAATTATGGGAAGTTTATGAAGGAGCTCTTCTCCAAGAAGAAGAAGCTCATTGATA
* * *
28595032 TGGAAACTATTGCACTCATAGAAGGCTGTAGTACTATTTTTACAAATATGTTACCACCCAAAATG
378 TGGAAACTATTGCACTCACAGAAGGCTGTAGTACTATTTTGACAAATAAGTTACCACCCAAAATG
* * *
28595097 AAAGATCCTGGGAGCTTTACTATCCCATGTTCAATTGGCAACCATTATTTTGGTAAAACTTTATG
443 AAAGATCCTGGGAGCTTTACTATCCCATATTCAATTGACAACCATTATTTGGGTAAAACTTTATG
*
28595162 CGACTTGGGAGCTAGCATCAACCTAATGCCACTATCTACTTTCAGAAATTTGGGAATTAGTCACA
508 CGACTTGGAAGCTAGCATCAACCTAATGCCACTATCTACTTTCAGAAATTTGGGAATTAGTCACA
28595227 TGAAACCTACTGCAGTGACATTACAACTTAC
573 T-AAACCTACTGCAGTGACATTACAACTTAC
* * *
28595258 AGAGTGGTAAACAAA-TTGGGGAGCCGACTATAGACTCTACTATAGCACCTCATGATACTAGTGA
1 AGAGTGGTAAACAAACTT-GGGAGCCGACTACAGACTCTACTATAGCACCTCAAGATACTAGTAA
* *
28595322 AGTGATCCTTGGTGAGAAGGTTGAATCTTAAGAGCTTGTCGATGTACCAAAAAAATAAGTTCCAC
65 AGTAATCCCTGGTGAGAAGGTTGAATCTTAAGAGCTTGTCGATGTACCAAAAAAATAAGTTCCAC
28595387 AAATTGTCACTCAGATGCCTAATGTCAGACCCTCAAAACTGTCGACGCAATCAAA-T-G-T-TAT
130 AAATTGTCACTCAGATGCCTAATGTCAGACCCTCAAAACTGTCGACGCAATCAAAGTCGATATAT
* * * * *
28595448 CTTTACTTTTACCTTTTCCACAAAGATTCAGGGAAAAGGAGCAAGATAAGTAGTATCAACAGTTC
195 CTCTACCTTTACCTTTTCCACAAAGATTCAGGAAAAAGGAGCAAGATAAGTAGTACCAACAGTTA
* *
28595513 TCGAACACACTGAAGCAACTTTAGGCCAATATTCCTTCAGTAGACACTCTTATGGAAATTCTTAA
260 TCGAACACACTGAAGCAACTTCAGGCCAATATTCCTTCAGTAGACACTCTTATGGAAATTCTGAA
*
28595578 TTATGGGAAGTTTATGAAGGAGCTCTTCTCTAAGAAGAAGAAGCTCATTGATATGGAAACTATTG
325 TTATGGGAAGTTTATGAAGGAGCTCTTCTCCAAGAAGAAGAAGCTCATTGATATGGAAACTATTG
* *
28595643 CACTCACAGAAGGCTGTAGTACTATTTTGATAAATAAGTTACCACCCAAAATGAAAGATCTTGGG
390 CACTCACAGAAGGCTGTAGTACTATTTTGACAAATAAGTTACCACCCAAAATGAAAGATCCTGGG
**
28595708 AGCTTTACTATCCCATATTCAATTGACAACCATTATTTGGGTAAGGCTTTATGCGACTTGGAAGC
455 AGCTTTACTATCCCATATTCAATTGACAACCATTATTTGGGTAAAACTTTATGCGACTTGGAAGC
* * *
28595773 TATCATCAACCTAATGCCACTATCTACTTTCAGAAATTTGGGAATTAGTCACATTAACCTACTGT
520 TAGCATCAACCTAATGCCACTATCTACTTTCAGAAATTTGGGAATTAGTCACATAAACCTACTGC
*
28595838 AGTGACATTGCAACT
585 AGTGACATTACAACT
28595853 AGCTGATCGA
Statistics
Matches: 556, Mismatches: 38, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
598 23 0.04
599 355 0.64
605 1 0.00
608 1 0.00
612 1 0.00
615 2 0.00
616 173 0.31
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (602 bp):
AGAGTGGTAAACAAACTTGGGAGCCGACTACAGACTCTACTATAGCACCTCAAGATACTAGTAAA
GTAATCCCTGGTGAGAAGGTTGAATCTTAAGAGCTTGTCGATGTACCAAAAAAATAAGTTCCACA
AATTGTCACTCAGATGCCTAATGTCAGACCCTCAAAACTGTCGACGCAATCAAAGTCGATATATC
TCTACCTTTACCTTTTCCACAAAGATTCAGGAAAAAGGAGCAAGATAAGTAGTACCAACAGTTAT
CGAACACACTGAAGCAACTTCAGGCCAATATTCCTTCAGTAGACACTCTTATGGAAATTCTGAAT
TATGGGAAGTTTATGAAGGAGCTCTTCTCCAAGAAGAAGAAGCTCATTGATATGGAAACTATTGC
ACTCACAGAAGGCTGTAGTACTATTTTGACAAATAAGTTACCACCCAAAATGAAAGATCCTGGGA
GCTTTACTATCCCATATTCAATTGACAACCATTATTTGGGTAAAACTTTATGCGACTTGGAAGCT
AGCATCAACCTAATGCCACTATCTACTTTCAGAAATTTGGGAATTAGTCACATAAACCTACTGCA
GTGACATTACAACTTAC
Found at i:28601565 original size:17 final size:17
Alignment explanation
Indices: 28601543--28601575 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28601533 GTTCGTGTAC
*
28601543 ATTGTCGTTGCATTTTT
1 ATTGTCATTGCATTTTT
28601560 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
28601576 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:28608412 original size:7 final size:7
Alignment explanation
Indices: 28608400--28608431 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
28608390 TTATCTGATC
28608400 AGTGACA
1 AGTGACA
28608407 AGTGACA
1 AGTGACA
28608414 AGTGACA
1 AGTGACA
*
28608421 AGTGATA
1 AGTGACA
28608428 AGTG
1 AGTG
28608432 GTAGCTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (7 bp):
AGTGACA
Found at i:28608460 original size:58 final size:57
Alignment explanation
Indices: 28608359--28608469 Score: 213
Period size: 58 Copynumber: 1.9 Consensus size: 57
28608349 TTCTGATCAA
28608359 TGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGACAAG
1 TGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGACAAG
28608416 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGA
1 TGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACAAGTGA
28608470 TAAATGTGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 21 0.40
58 32 0.60
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (57 bp):
TGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGACAAG
Found at i:28613220 original size:36 final size:37
Alignment explanation
Indices: 28613157--28613240 Score: 143
Period size: 36 Copynumber: 2.3 Consensus size: 37
28613147 ATCAGTGACA
28613157 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* *
28613194 AGTGATAAGTGGTAG-TTTAGCTACACTTATTTGATT
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
28613230 AGTGATAAGTG
1 AGTGATAAGTG
28613241 ACAAGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 30 0.67
37 15 0.33
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:28613260 original size:87 final size:88
Alignment explanation
Indices: 28613145--28613379 Score: 306
Period size: 87 Copynumber: 2.7 Consensus size: 88
28613135 TGAGTACTTC
*
28613145 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGGTAG-
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGGTAGC
* *
28613209 TTTAGCTACACTTATTTGATTAG
66 TTTAGCTACACTTATCTGATCAG
28613232 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGATAAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC-------AGTGATAAG
*
28613297 TGGTAGCTTTAGCTGCACTTATCTGATCAG
59 TGGTAGCTTTAGCTACACTTATCTGATCAG
*
28613327 TGATAAGTGACAAGTG---A----TAGCTTTAGCTGCACTTATCTGATCAGTGATAAGTG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTG
28613380 ACAAGTGATA
Statistics
Matches: 135, Mismatches: 5, Indels: 22
0.83 0.03 0.14
Matches are distributed among these distances:
81 11 0.08
87 48 0.36
88 24 0.18
92 1 0.01
94 15 0.11
95 36 0.27
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (88 bp):
TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGGTAGC
TTTAGCTACACTTATCTGATCAG
Found at i:28613274 original size:51 final size:51
Alignment explanation
Indices: 28613194--28613481 Score: 401
Period size: 44 Copynumber: 6.0 Consensus size: 51
28613184 TTATCTGATC
* *
28613194 AGTGATAAGTGGTAG-TTTAGCTACACTTATTTGATTAGTGATAAGTGACA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACA
28613244 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTG---A-T---A
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACA
*
28613288 AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGATAAGTGACA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACA
*
28613339 AGTG---A----TAGCTTTAGCTGCACTTATCTGATCAGTGATAAGTGACA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACA
* *
28613383 AGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCGGTGACAAGTGACA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACA
*
28613433 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGA
28613482 TAAATGTGAT
Statistics
Matches: 215, Mismatches: 7, Indels: 31
0.85 0.03 0.12
Matches are distributed among these distances:
44 84 0.39
47 3 0.01
48 3 0.01
50 62 0.29
51 63 0.29
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (51 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGACA
Found at i:28616319 original size:22 final size:22
Alignment explanation
Indices: 28616289--28616344 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
28616279 TAGGTACCAT
*
28616289 TGTCGACGCATTGAAATCTTAC
1 TGTCAACGCATTGAAATCTTAC
28616311 TGTCAACGCATTGAAATCTTAC
1 TGTCAACGCATTGAAATCTTAC
28616333 TGTCAACGCATT
1 TGTCAACGCATT
28616345 CCATAAGTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (22 bp):
TGTCAACGCATTGAAATCTTAC
Found at i:28624038 original size:27 final size:27
Alignment explanation
Indices: 28623999--28624254 Score: 314
Period size: 27 Copynumber: 9.5 Consensus size: 27
28623989 CTTATCAGTA
28623999 CGGTCATTTTACCCTATGGGGGTATTT
1 CGGTCATTTTACCCTATGGGGGTATTT
* * *
28624026 TGGTCATTTTACCCTACGAGGGTATTT
1 CGGTCATTTTACCCTATGGGGGTATTT
28624053 CGGTCATTTTACCCTATGGGGGTATTT
1 CGGTCATTTTACCCTATGGGGGTATTT
*** * * *
28624080 TAATCAGTTTACACTATAGGGGTATTT
1 CGGTCATTTTACCCTATGGGGGTATTT
* *
28624107 CAGTTATTTTACCCTATGGGGGTATTT
1 CGGTCATTTTACCCTATGGGGGTATTT
*
28624134 CGGTCATTTTACCCTATGGAGGTATTT
1 CGGTCATTTTACCCTATGGGGGTATTT
* * *
28624161 TGGTAATTTTACCCTATTGGGGTATTT
1 CGGTCATTTTACCCTATGGGGGTATTT
** *
28624188 CAATCATTTTACCCTATGGAGGTATTT
1 CGGTCATTTTACCCTATGGGGGTATTT
* **
28624215 CGGTCATTCTACCCTATAAGGGTATTT
1 CGGTCATTTTACCCTATGGGGGTATTT
*
28624242 TGGTCATTTTACC
1 CGGTCATTTTACC
28624255 TATTTTGGGG
Statistics
Matches: 190, Mismatches: 39, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 190 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (27 bp):
CGGTCATTTTACCCTATGGGGGTATTT
Found at i:28624970 original size:30 final size:30
Alignment explanation
Indices: 28624934--28624995 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
28624924 AACAACAACC
28624934 TCCTCAAATCCCAATATCCCTCCTCAATTA
1 TCCTCAAATCCCAATATCCCTCCTCAATTA
*
28624964 TCCTCAAATCCCAATATCCCTCCTTAATTA
1 TCCTCAAATCCCAATATCCCTCCTCAATTA
28624994 TC
1 TC
28624996 TCTATAACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (30 bp):
TCCTCAAATCCCAATATCCCTCCTCAATTA
Found at i:28627788 original size:36 final size:35
Alignment explanation
Indices: 28627748--28627819 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 35
28627738 CATCTCCGGA
28627748 GCTTGGCAAATAAGGAAAGTGATCTTTTGAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTG-AGATAT
* *
28627784 GCTTGGCAAATATGGAAGGTGATCTTTTGAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
28627819 G
1 G
28627820 TGATCCTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 7 0.21
36 27 0.79
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
Found at i:28632942 original size:36 final size:35
Alignment explanation
Indices: 28632895--28632966 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 35
28632885 CATCTCCGGA
28632895 GCTTGGCAAATAAAGAAAGTGATCTTTTGAAGATAT
1 GCTTGGCAAATAAAGAAAGTGATCTTTTG-AGATAT
**
28632931 GCTTGGCAAATATGGAAAGTGATCTTTTGAGATAT
1 GCTTGGCAAATAAAGAAAGTGATCTTTTGAGATAT
28632966 G
1 G
28632967 TGATCCTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 7 0.21
36 27 0.79
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.32
Consensus pattern (35 bp):
GCTTGGCAAATAAAGAAAGTGATCTTTTGAGATAT
Found at i:28643996 original size:19 final size:19
Alignment explanation
Indices: 28643956--28644000 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28643946 GTCCAAAACA
*
28643956 AAAATAGTCCCAAGAGTCC
1 AAAATAGTCCCAACAGTCC
*
28643975 AAAATAGT-CCAACAGTATC
1 AAAATAGTCCCAACAGT-CC
28643994 AAAATAG
1 AAAATAG
28644001 AGTAAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.18
Consensus pattern (19 bp):
AAAATAGTCCCAACAGTCC
Found at i:28659364 original size:15 final size:15
Alignment explanation
Indices: 28659344--28659374 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28659334 CCAACCTTCA
28659344 AATTTTACCTCAATT
1 AATTTTACCTCAATT
28659359 AATTTTACCTCAATT
1 AATTTTACCTCAATT
28659374 A
1 A
28659375 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:28663176 original size:93 final size:92
Alignment explanation
Indices: 28663044--28663238 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
28663034 TTGATTTTAG
* *
28663044 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
28663108 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
28663136 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
28663201 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
28663229 CAAATTCATA
1 TAAATTCATA
28663239 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:28663296 original size:17 final size:17
Alignment explanation
Indices: 28663271--28663304 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28663261 ATAATTTTAA
*
28663271 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
28663288 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
28663305 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:28663306 original size:15 final size:16
Alignment explanation
Indices: 28663271--28663309 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
28663261 ATAATTTTAA
*
28663271 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
28663288 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
28663303 ATTTAAT
1 ATTTAAT
28663310 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:28663313 original size:17 final size:18
Alignment explanation
Indices: 28663275--28663314 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
28663265 TTTTAAATTT
*
28663275 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
28663293 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
28663309 TATTAA
1 TATTAA
28663315 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:28663429 original size:15 final size:15
Alignment explanation
Indices: 28663394--28663445 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28663384 TTAAGAATTT
*
28663394 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28663408 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28663422 TATTTAATAATAAT-
1 TATTTAATTATAATA
28663436 TATGTTAATT
1 TAT-TTAATT
28663446 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28663436 original size:120 final size:120
Alignment explanation
Indices: 28663270--28663561 Score: 459
Period size: 120 Copynumber: 2.4 Consensus size: 120
28663260 AATAATTTTA
* * *
28663270 AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAATATTAATTAT-TTGAAATTT-TCT
1 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATAATTATGTT--AATTTATAT
* *
28663331 TTTATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAAT-TTTATTTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTT-TTAAG
28663389 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
28663454 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTTTTAAG
28663509 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
28663562 TAAATATGAT
Statistics
Matches: 162, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
119 23 0.14
120 128 0.79
121 11 0.07
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTTTTAAG
Found at i:28663526 original size:59 final size:59
Alignment explanation
Indices: 28663343--28663526 Score: 148
Period size: 59 Copynumber: 3.1 Consensus size: 59
28663333 TATAGTATCA
* *
28663343 TATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAGAATTTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATTAAAT
* * * * * * * *
28663402 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-CAGTAT
1 TATATTATGATTTGAGTA-AAT-TCATATAAGAAT-ATTAT-TT-ATTAAGAATTTTATTA-AAT
28663461 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTT-TTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAGAATATT-ATTTATTAAGAATTTTATTAAAT
28663522 TATAT
1 TATAT
28663527 ATTTTAATTA
Statistics
Matches: 92, Mismatches: 18, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
56 6 0.07
57 10 0.11
58 9 0.10
59 19 0.21
60 7 0.08
61 12 0.13
62 10 0.11
63 13 0.14
64 6 0.07
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (59 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATTAAAT
Found at i:28663544 original size:16 final size:16
Alignment explanation
Indices: 28663523--28663564 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28663513 TTATTAAATT
*
28663523 ATATATTTTAATTATA
1 ATATATTTTAATAATA
28663539 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
28663554 AT-TATGTTTAA
1 ATATAT-TTTAA
28663565 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:28663549 original size:15 final size:15
Alignment explanation
Indices: 28663514--28663555 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28663504 TTAAGAATTT
*
28663514 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28663528 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28663542 TATTTAATAATAAT
1 TATTTAATTATAAT
28663556 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28663711 original size:123 final size:126
Alignment explanation
Indices: 28663518--28663772 Score: 462
Period size: 123 Copynumber: 2.0 Consensus size: 126
28663508 GAATTTTATT
*
28663518 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTATTTA
1 AAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTATTTA
28663583 TTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
66 TTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
28663642 AAATTATAT-TTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTATTTA
1 AAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTATTTA
*
28663706 TTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAAC
66 TTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
28663768 AAATT
1 AAATT
28663773 TCTGCTAAGG
Statistics
Matches: 126, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
123 62 0.49
124 11 0.09
126 53 0.42
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (126 bp):
AAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTATTTA
TTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
Found at i:28663921 original size:16 final size:16
Alignment explanation
Indices: 28663900--28663938 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28663890 TTGATTTGCT
*
28663900 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
28663916 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
28663932 ATTACAC
1 ATTACAC
28663939 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:28663939 original size:16 final size:16
Alignment explanation
Indices: 28663913--28663969 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
28663903 ACACAGCTTT
* *
28663913 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
28663929 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
28663945 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
28663961 TCCAATACA
1 TCCAATACA
28663970 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:28667957 original size:24 final size:24
Alignment explanation
Indices: 28667925--28667970 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
28667915 TGGTAGAGGT
*
28667925 GACACGTGTGTTGCAACCGAATCA
1 GACACGTGTGGTGCAACCGAATCA
28667949 GACACGTGTGGTGCAACCGAAT
1 GACACGTGTGGTGCAACCGAAT
28667971 TAGATCGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (24 bp):
GACACGTGTGGTGCAACCGAATCA
Found at i:28672571 original size:23 final size:23
Alignment explanation
Indices: 28672541--28672588 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28672531 TTAAAACATA
* *
28672541 TAAATATTTCATAT-ATTAATAT
1 TAAATATTTAATATAATTAAGAT
28672563 TAAAGTATTTAATATAATTAAGAT
1 TAAA-TATTTAATATAATTAAGAT
28672587 TA
1 TA
28672589 TATAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
24 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TAAATATTTAATATAATTAAGAT
Found at i:28681079 original size:44 final size:44
Alignment explanation
Indices: 28680566--28681050 Score: 693
Period size: 44 Copynumber: 11.0 Consensus size: 44
28680556 TTGGTGAAAC
*
28680566 TGCAAATCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
* *
28680610 TGCAAGTTCTATCTCCCTGAACAGTAGTGGAATAGGTTGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
* * *
28680654 TGCAAGTCTTATCTCCCTGAACCGCAGTGGAATAGGTTAAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
* * *
28680698 TGCAAGTCCTATCTCCCTGAACAGTAGTAGAATATGTTGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
* * *
28680742 TACAAGTCCTATCTCCCTGAACAGTAGTTGAATAGGTTGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
* * * * **
28680786 TGTAAGTCCCACCTCCCTAAACAGCAGTGTTATAGGTTGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
* * *
28680830 TGCAAGTCCTATCTCCCTGAGCAGCAATGGAATAGGCTGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
*
28680874 TGCAAGTCCTATCTCCCTGAACAGC-GTGGAATACGTTGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
* * *
28680917 TGTAAGTCCTATCTCCCTGGACAGCAATGGAATAGGTTGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
* * *
28680961 TGTAAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTCGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
* *
28681005 TGTAAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGAT
1 TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
28681049 TG
1 TG
28681051 TAGATCCTGT
Statistics
Matches: 394, Mismatches: 46, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
43 38 0.10
44 356 0.90
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
TGCAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGAT
Found at i:28681672 original size:7 final size:7
Alignment explanation
Indices: 28681660--28681690 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28681650 AATTACAATT
28681660 ACCTAAA
1 ACCTAAA
28681667 ACCTAAA
1 ACCTAAA
*
28681674 ACCCAAA
1 ACCTAAA
28681681 ACCTAAA
1 ACCTAAA
28681688 ACC
1 ACC
28681691 CATACCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.35, G:0.00, T:0.10
Consensus pattern (7 bp):
ACCTAAA
Found at i:28682703 original size:3 final size:3
Alignment explanation
Indices: 28682697--28682737 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
28682687 TTTTGTACTG
*
28682697 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28682738 TCTTCTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28682957 original size:22 final size:21
Alignment explanation
Indices: 28682901--28682957 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
28682891 AAGATGTAGT
28682901 ATGCTATTATTTTTAAATTATC
1 ATGC-ATTATTTTTAAATTATC
* **
28682923 AT-TAACATGTTTTAAATTTATC
1 ATGCATTAT-TTTTAAA-TTATC
28682945 ATGCATTATTTTT
1 ATGCATTATTTTT
28682958 TAGTCTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 13 0.50
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (21 bp):
ATGCATTATTTTTAAATTATC
Found at i:28685096 original size:52 final size:52
Alignment explanation
Indices: 28685039--28685151 Score: 174
Period size: 53 Copynumber: 2.2 Consensus size: 52
28685029 CCTTTATGTA
28685039 AAAAAAATTACATTTTGGGCTGTCATTGGCTG-CACCAGTATACGAAAAAATT
1 AAAAAAATTACATTTT-GGCTGTCATTGGCTGACACCAGTATACGAAAAAATT
** *
28685091 CAAAAATCTTATATTTTGGCTGTCATTGGCTGACACCAGTATACGAAAAAATT
1 -AAAAAAATTACATTTTGGCTGTCATTGGCTGACACCAGTATACGAAAAAATT
28685144 AAAAAAAT
1 AAAAAAAT
28685152 AAATTTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
52 21 0.39
53 33 0.61
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (52 bp):
AAAAAAATTACATTTTGGCTGTCATTGGCTGACACCAGTATACGAAAAAATT
Found at i:28685156 original size:158 final size:160
Alignment explanation
Indices: 28684944--28685251 Score: 462
Period size: 161 Copynumber: 1.9 Consensus size: 160
28684934 TTTTTTTTAC
** *
28684944 ATTTTGGACTGTCATTGGCCGACACCAGTATACGAAAAAATTTTTAAAAAAAA-TTTTGCTGGTT
1 ATTTTGGACTGTCATTGGCCGACACCAGTATACGAAAAAATTTAAAAAAAAAATTTTTGCTGGTA
* *
28685008 GCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAATTACATTTTGGGCTGTCATTGG-CTGC
66 GCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAAATACATTTT-GGCTGTCATTGGTCGGC
28685072 ACCAGTATACGAAAAAATTCAAAAATCTTAT
130 ACCAGTATACGAAAAAATTCAAAAATCTTAT
* *
28685103 ATTTTGG-CTGTCATTGGCTGACACCAGTATACGAAAAAA-TTAAAAAAATAAATTTTTTTGGTG
1 ATTTTGGACTGTCATTGGCCGACACCAGTATACGAAAAAATTTAAAAAAA-AAA--TTTTTGCTG
* * *
28685166 GTAGTCTGGCAATTGCCGGCACCACCTTTATGTAAAAAAAAATACATTTTGGCTGTTATTGGTCG
63 GTAGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAAATACATTTTGGCTGTCATTGGTCG
28685231 GCACCAGTATACGAAAAAATT
128 GCACCAGTATACGAAAAAATT
28685252 GAATTTTTTT
Statistics
Matches: 134, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
157 7 0.05
158 34 0.25
159 7 0.05
160 11 0.08
161 75 0.56
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (160 bp):
ATTTTGGACTGTCATTGGCCGACACCAGTATACGAAAAAATTTAAAAAAAAAATTTTTGCTGGTA
GCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAAATACATTTTGGCTGTCATTGGTCGGCA
CCAGTATACGAAAAAATTCAAAAATCTTAT
Found at i:28685227 original size:108 final size:108
Alignment explanation
Indices: 28685103--28685512 Score: 488
Period size: 108 Copynumber: 3.9 Consensus size: 108
28685093 AAAATCTTAT
* *
28685103 ATTTTGGCTGTCATTGGCTGACACCAGTATACGAAAAAA-TTAAAAAAATAAATTTTTTTGGTGG
1 ATTTGGGCTGTCATTGGCTGGCACCAGTATACGAAAAAATTTAAAAAAA-AAATTTTTTTGGTGG
* * *
28685167 TAGTCTGGCAATTGCCGGCACCACCTTTATGTAAAAAAAAATAC
65 TGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAAATAC
* * * * *
28685211 ATTTTGGCTGTTATTGG-TCGGCACCAGTATACGAAAAAA-TT------GAATTTTTTTTTGTGG
1 ATTTGGGCTGTCATTGGCT-GGCACCAGTATACGAAAAAATTTAAAAAAAAAATTTTTTTGGTGG
28685268 TGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAAATTTAC
65 TGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAAA--TAC
* * *
28685314 ATTATGGGCTATCATTAGCCGGCACCAGTATAC-AAAAAATTTTAAAAAAAAAATTTTTTTGGTG
1 ATT-TGGGCTGTCATTGGCTGGCACCAGTATACGAAAAAA-TTTAAAAAAAAAATTTTTTTGGTG
* *
28685378 GTGGCCTGGCAATGGCCGGCACCACCTATATGT-AAAAAAATTAC
64 GTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAAATAC
* *
28685422 ATTTCGGGCTGTCATTGGCAGGCACCAGTATACGAAAAAATTTGAAAAAAAAA---TTTTGGTGG
1 ATTT-GGGCTGTCATTGGCTGGCACCAGTATACGAAAAAATTTAAAAAAAAAATTTTTTTGGTGG
**
28685484 TGGCCTACCAATGGCCGGCACCACCTTTA
65 TGGCCTGGCAATGGCCGGCACCACCTTTA
28685513 CGGGAAAAAA
Statistics
Matches: 262, Mismatches: 25, Indels: 33
0.82 0.08 0.10
Matches are distributed among these distances:
101 51 0.19
103 12 0.05
104 23 0.09
105 37 0.14
107 2 0.01
108 80 0.31
109 6 0.02
110 7 0.03
111 44 0.17
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (108 bp):
ATTTGGGCTGTCATTGGCTGGCACCAGTATACGAAAAAATTTAAAAAAAAAATTTTTTTGGTGGT
GGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAAAATAC
Found at i:28686637 original size:55 final size:54
Alignment explanation
Indices: 28686570--28686691 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 54
28686560 CATCTTTTTT
* *
28686570 TCATTCATTTCAAAAAAAAATTTCTACATCTAACACCCCTTTTTTTCATTCAATC
1 TCATTTATTTCAAAAAAAAATTTCTACATCTAACA-CCCTTTTCTTCATTCAATC
**** ** * *
28686625 TCATTTATTTCAATTTTATTTTTCTATATCTAACACCCTTTTCTTCATTCAGTC
1 TCATTTATTTCAAAAAAAAATTTCTACATCTAACACCCTTTTCTTCATTCAATC
28686679 TCATTTATTTCAA
1 TCATTTATTTCAA
28686692 TTTTATTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
54 30 0.53
55 27 0.47
ACGTcount: A:0.29, C:0.23, G:0.01, T:0.48
Consensus pattern (54 bp):
TCATTTATTTCAAAAAAAAATTTCTACATCTAACACCCTTTTCTTCATTCAATC
Found at i:28686685 original size:54 final size:55
Alignment explanation
Indices: 28686590--28686710 Score: 208
Period size: 54 Copynumber: 2.2 Consensus size: 55
28686580 CAAAAAAAAA
*
28686590 TTTCTACATCTAACACCCCTTTTTTTCATTCAATCTCATTTATTTCAATTTTATT
1 TTTCTACATCTAACACCCCTTTTCTTCATTCAATCTCATTTATTTCAATTTTATT
* *
28686645 TTTCTATATCTAACA-CCCTTTTCTTCATTCAGTCTCATTTATTTCAATTTTATT
1 TTTCTACATCTAACACCCCTTTTCTTCATTCAATCTCATTTATTTCAATTTTATT
28686699 TTTCTACATCTA
1 TTTCTACATCTA
28686711 CACTACACCA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
54 48 0.77
55 14 0.23
ACGTcount: A:0.23, C:0.23, G:0.01, T:0.53
Consensus pattern (55 bp):
TTTCTACATCTAACACCCCTTTTCTTCATTCAATCTCATTTATTTCAATTTTATT
Found at i:28686755 original size:22 final size:22
Alignment explanation
Indices: 28686725--28686767 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28686715 ACACCAAAAC
* *
28686725 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGACGCTTTTTT
28686747 AGGCCTTTAGCGACGCTTTTT
1 AGGCCTTTAGCGACGCTTTTT
28686768 AGCACCGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGACGCTTTTTT
Found at i:28686897 original size:43 final size:43
Alignment explanation
Indices: 28686849--28687202 Score: 453
Period size: 43 Copynumber: 8.3 Consensus size: 43
28686839 TTTTAGAAAT
*
28686849 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCTCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
28686892 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCAG
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
28686935 AAA---CGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
28686975 AAACGCCGCTAATGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * **
28687018 AAGCGCCGCTAAAGACCATGACTTTTAGCGGCGGTTTTAGCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
28687061 AAACGCCGCTAAAGACAAAGACCTTTAGCGGCGTTTTTCCTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * **
28687104 AAACACCGCTAAAGACCATGACCTTTAGCGACGATTTTCCCGT
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * **
28687147 AAACGCCGCTAAAGACCATGACTTTTAGCGACGCTTTTGACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
28687190 AAATGCCGCTAAA
1 AAACGCCGCTAAA
28687203 AATATATCTT
Statistics
Matches: 271, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
40 39 0.14
43 232 0.86
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:28687222 original size:17 final size:17
Alignment explanation
Indices: 28687200--28687241 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
28687190 AAATGCCGCT
28687200 AAAAATATATCTTTTAA
1 AAAAATATATCTTTTAA
* *
28687217 AAAAATATATTTTTTCA
1 AAAAATATATCTTTTAA
*
28687234 AATAATAT
1 AAAAATAT
28687242 TTATTTCTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAATATATCTTTTAA
Done.