Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 204 of 226
Found at i:61062371 original size:14 final size:15
Alignment explanation
Indices: 61062342--61062375 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
61062332 AAATTTTAAA
61062342 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
61062357 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
61062371 TTTTA
1 TTTTA
61062376 GATAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:61064377 original size:28 final size:28
Alignment explanation
Indices: 61064339--61064955 Score: 748
Period size: 28 Copynumber: 23.2 Consensus size: 28
61064329 GAAGAACAAC
* *
61064339 CCTAACTTAACTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064367 CCTAATTTAACTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
61064395 CCTAATTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064423 -C----TTAACTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
61064446 CCTAATTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064474 CCTAATTTAATTTAACTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064502 -C----TTAACTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
61064525 CCTAATTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064553 CCTAATTTAATTTAATTAAAATCCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064581 CC-----TAATTTAATTAAAATCCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064604 CC-----TAATTTAGTTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
* * *
61064627 CCCTAACTTATTTTAATTAAAAACTCTAA
1 -CCTAATTTAATTTAATTAAAAACCCTAA
** *
61064656 CCCTAACCTAATTTAATTAAAAACACTAA
1 -CCTAATTTAATTTAATTAAAAACCCTAA
*
61064685 CCTAACTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
**
61064713 CCATAACCTAATTTAATTAAAAACCCTAA
1 CC-TAATTTAATTTAATTAAAAACCCTAA
*
61064742 CCTAACTTAATTTAATT-AAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
61064769 CCTAATTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064797 -C----TTAACTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
61064820 CCTAATTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064848 -C----TTAAATTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
61064871 CCTAATTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064899 CCTAAATTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
*
61064927 -C----TTAACTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA
61064950 CCTAAT
1 CCTAAT
61064956 CGAGCACATT
Statistics
Matches: 528, Mismatches: 28, Indels: 66
0.85 0.05 0.11
Matches are distributed among these distances:
23 146 0.28
24 7 0.01
27 31 0.06
28 273 0.52
29 71 0.13
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (28 bp):
CCTAATTTAATTTAATTAAAAACCCTAA
Found at i:61064422 original size:51 final size:51
Alignment explanation
Indices: 61064339--61064938 Score: 640
Period size: 51 Copynumber: 11.2 Consensus size: 51
61064329 GAAGAACAAC
* * *
61064339 CCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAACTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA-C----TTAATTTAATTAAAAACCCTAA
*
61064395 CCTAATTTAATTTAATTAAAAACCCTAACTTAACTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAACTTAATTTAATTAAAAACCCTAA
*
61064446 CCTAATTTAATTTAATTAAAAACCCTAACCTAATTTAATTTAACTAAA----AA
1 CCTAATTTAATTTAATTAAAAACCCTAACTTAATTTAA-TTAA--AAACCCTAA
* *
61064496 CCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAA
1 -CCTAATTTAATTTAATTAAAAACCCTAA-C----TTAATTTAATTAAAAACCCTAA
* * *
61064553 CCTAATTTAATTTAATTAAAATCCCTAACCTAATTTAATTAAAATCCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAACTTAATTTAATTAAAAACCCTAA
* * *
61064604 CCTAATTT-AGTTAA--AAACCCTAACCCTAACTTATTTTAATTAAAAACTCTAA
1 CCTAATTTAATTTAATTAAA----AACCCTAACTTAATTTAATTAAAAACCCTAA
**
61064656 CCCTAACCTAATTTAATTAAAAACACTAACCTAACTTAATTTAATTAAAAACCCTAA
1 -CCTAATTTAATTTAATT-AAAA-AC---CCTAACTTAATTTAATTAAAAACCCTAA
**
61064713 CCATAACCTAATTTAATTAAAAACCCTAACCTAACTTAATTTAATT-AAAACCCTAA
1 CC-TAATTTAATTTAATTAAAAA--C---CCTAACTTAATTTAATTAAAAACCCTAA
*
61064769 CCTAATTTAATTTAATTAAAAACCCTAACTTAACTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAACTTAATTTAATTAAAAACCCTAA
*
61064820 CCTAATTTAATTTAATTAAAAACCCTAACTTAAATTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAACTTAATTTAATTAAAAACCCTAA
61064871 CCTAATTTAATTTAATTAAAAACCCTAACCTAAATTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTTAATTAAAAACCCTAA-C----TTAATTTAATTAAAAACCCTAA
* *
61064927 CTTAACTTAATT
1 CCTAATTTAATT
61064939 AAAAACCCTA
Statistics
Matches: 479, Mismatches: 30, Indels: 70
0.83 0.05 0.12
Matches are distributed among these distances:
48 3 0.01
50 23 0.05
51 200 0.42
52 32 0.07
53 11 0.02
54 10 0.02
55 25 0.05
56 108 0.23
57 67 0.14
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.33
Consensus pattern (51 bp):
CCTAATTTAATTTAATTAAAAACCCTAACTTAATTTAATTAAAAACCCTAA
Found at i:61064467 original size:79 final size:79
Alignment explanation
Indices: 61064336--61064955 Score: 713
Period size: 79 Copynumber: 7.8 Consensus size: 79
61064326 GAGGAAGAAC
*
61064336 AACCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAACTTAATTAAAAACCCTAACCTAAT
1 AACCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAAT
61064401 TTAATTTAATTAAA
66 TTAATTTAATTAAA
61064415 AACCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAAT
1 AACCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAAT
*
61064480 TTAATTTAACTAAA
66 TTAATTTAATTAAA
61064494 AACCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAAT
1 AACCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAAT
61064559 TTAATTTAATTAAA
66 TTAATTTAATTAAA
* * * * *
61064573 ATCCCTAACCTAATTTAATTAAAATCCCTAACC-----TAATTTAGTTAAAAACCCTAACCCTAA
1 AACCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAA-CCTAA
* *
61064633 CTTATTTTAATTAAAAA
65 TTTAATTTAATT--AAA
* * * *
61064650 CTCTAACCCTAACCTAATTTAATTAAAAACACTAACCTAACTTAATTTAATTAAAAACCCTAACC
1 ----AACCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACC
**
61064715 ATAACCTAATTTAATTAAA
62 -TAATTTAATTTAATTAAA
*
61064734 AACCCTAACCTAACTTAATTTAATTAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAA-C
1 AACCCTAACTTAACTTAA-TT-A--AAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACC
*
61064798 ----TTAACTTAATTAAA
62 TAATTTAATTTAATTAAA
* *
61064812 AACCCTAACCTAATTTAATTTAATTAAAAACCCTAA-C----TTAAATTAATTAAAAACCCTAAC
1 AACCCTAA-C----TTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAAC
61064872 CTAATTTAATTTAATTAAA
61 CTAATTTAATTTAATTAAA
* *
61064891 AACCCTAACCTAAATTAATTTAATTAAAAACCCTAA-C----TTAACTTAATTAAAAACCCTAAC
1 AACCCTAA-C----TTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAAC
61064951 CTAAT
61 CTAAT
61064956 CGAGCACATT
Statistics
Matches: 487, Mismatches: 27, Indels: 54
0.86 0.05 0.10
Matches are distributed among these distances:
74 41 0.08
75 16 0.03
77 3 0.01
78 21 0.04
79 271 0.56
80 17 0.03
81 33 0.07
82 3 0.01
83 8 0.02
84 39 0.08
85 2 0.00
86 33 0.07
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (79 bp):
AACCCTAACTTAACTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAAT
TTAATTTAATTAAA
Found at i:61064609 original size:18 final size:19
Alignment explanation
Indices: 61064564--61064610 Score: 51
Period size: 23 Copynumber: 2.3 Consensus size: 19
61064554 CTAATTTAAT
61064564 TTAATTAAAATCCCTAACC
1 TTAATTAAAATCCCTAACC
61064583 TAATTTAATTAAAATCCCTAACC
1 ----TTAATTAAAATCCCTAACC
61064606 -TAATT
1 TTAATT
61064611 TAGTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
23 19 0.79
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAATTAAAATCCCTAACC
Found at i:61077887 original size:2 final size:2
Alignment explanation
Indices: 61077880--61077904 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61077870 ATACTCCCAA
61077880 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
61077905 CATGGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:61085633 original size:40 final size:40
Alignment explanation
Indices: 61085586--61085669 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
61085576 GGTCCAATTT
61085586 GTTTGTTCGATTCAATTGAAATAGTTTAATTTAATTTAGG
1 GTTTGTTCGATTCAATTGAAATAGTTTAATTTAATTTAGG
61085626 GTTTGTTCGATTCAATTGAAATAGTTTAATTTAATTTAGG
1 GTTTGTTCGATTCAATTGAAATAGTTTAATTTAATTTAGG
61085666 GTTT
1 GTTT
61085670 TTAGATATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.49
Consensus pattern (40 bp):
GTTTGTTCGATTCAATTGAAATAGTTTAATTTAATTTAGG
Found at i:61086851 original size:3 final size:3
Alignment explanation
Indices: 61086845--61086876 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
61086835 ATTATTAGTC
61086845 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
61086877 CCCTTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:61098332 original size:22 final size:22
Alignment explanation
Indices: 61098304--61098346 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
61098294 GATCCTTAAC
61098304 TTTGAAAGTAATTTAATGAAAA
1 TTTGAAAGTAATTTAATGAAAA
61098326 TTTGAAAGTAATTTAATGAAA
1 TTTGAAAGTAATTTAATGAAA
61098347 TTCAAGCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (22 bp):
TTTGAAAGTAATTTAATGAAAA
Found at i:61104970 original size:30 final size:30
Alignment explanation
Indices: 61104936--61104999 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
61104926 CACACGAGCG
*
61104936 TGTGTCACACACGGGCAACACACATGGGCA
1 TGTGTCACACACGGGCAACACACATAGGCA
*
61104966 TGTGTCACACACGGGCAACACACATAGGCG
1 TGTGTCACACACGGGCAACACACATAGGCA
61104996 TGTG
1 TGTG
61105000 ACCCAAGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (30 bp):
TGTGTCACACACGGGCAACACACATAGGCA
Found at i:61105533 original size:49 final size:49
Alignment explanation
Indices: 61105461--61105562 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
61105451 TCAAGAAGGG
* *
61105461 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACCAAGTTTAGCAATGT
* * *
61105510 ATAAATAGTGATAAGAGTTTAGACAGTGAAATACCAAGTTTAGCATTGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACCAAGTTTAGCAATGT
61105559 ATAA
1 ATAA
61105563 CATGAATCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAGTGAAAGACCAAGTTTAGCAATGT
Found at i:61107109 original size:44 final size:44
Alignment explanation
Indices: 61107056--61107214 Score: 193
Period size: 44 Copynumber: 3.6 Consensus size: 44
61107046 TGAGTAATCA
*
61107056 TGTAAGACCACGTCTGGGATGTTGGAATCGATTTGATATTTACG
1 TGTAAGACCACGTCTGGGATGTTGGCATCGATTTGATATTTACG
* *
61107100 TGTAAGACCACGTCTGAGACGTTGGCATCGATTTGATATTTACG
1 TGTAAGACCACGTCTGGGATGTTGGCATCGATTTGATATTTACG
* * *
61107144 TGTAAGACC-CTGTTTGGGACAG-TGGCATCGATGTT--TGA-TTACA
1 TGTAAGACCAC-GTCTGGGA-TGTTGGCATCGAT-TTGAT-ATTTACG
61107187 TGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCACGTCTGGGATGTTGGCAT
61107215 TGTACGAGCT
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
42 1 0.01
43 28 0.28
44 68 0.68
45 3 0.03
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGATGTTGGCATCGATTTGATATTTACG
Found at i:61114769 original size:18 final size:21
Alignment explanation
Indices: 61114727--61114771 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
61114717 AAAAAGTAGG
*
61114727 TTATATATTATTTTTCTAATA
1 TTATATATTATTTATCTAATA
61114748 TTATATATT-TTTAT-TAAT-
1 TTATATATTATTTATCTAATA
61114766 TTATAT
1 TTATAT
61114772 TTAAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 4 0.17
21 9 0.39
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATATATTATTTATCTAATA
Found at i:61114875 original size:58 final size:59
Alignment explanation
Indices: 61114747--61114866 Score: 158
Period size: 57 Copynumber: 2.1 Consensus size: 59
61114737 TTTTTCTAAT
* * * * *
61114747 ATTATATATT-TT-TATTAATTTATATTTAAATAATTATTATATTAAGAATGTTATTAA
1 ATTATATATTATTATTTTAAATTATATTTAAATAATAATTATATTAAGAATATGATTAA
*
61114804 ATTATATATTATTATTTTAAATTATATTT-AATAATAATTTTATTAA-AATATGATTAA
1 ATTATATATTATTATTTTAAATTATATTTAAATAATAATTATATTAAGAATATGATTAA
61114861 ATTATA
1 ATTATA
61114867 ATCCTATTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
57 25 0.45
58 17 0.31
59 13 0.24
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (59 bp):
ATTATATATTATTATTTTAAATTATATTTAAATAATAATTATATTAAGAATATGATTAA
Found at i:61115478 original size:29 final size:30
Alignment explanation
Indices: 61115434--61115495 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
61115424 ACTTATTTTA
61115434 TTGTTAAATTTGTTATTATTTTAAAGACAT
1 TTGTTAAATTTGTTATTATTTTAAAGACAT
* *
61115464 TTGTT-AATTTTTTATTATTTTAGAGACAT
1 TTGTTAAATTTGTTATTATTTTAAAGACAT
61115493 TTG
1 TTG
61115496 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.56
Consensus pattern (30 bp):
TTGTTAAATTTGTTATTATTTTAAAGACAT
Found at i:61116297 original size:13 final size:13
Alignment explanation
Indices: 61116275--61116310 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
61116265 GGTCTGCCCG
*
61116275 TATTAATTTTTTA
1 TATTATTTTTTTA
61116288 TATTATTTTTTTA
1 TATTATTTTTTTA
*
61116301 TATAATTTTT
1 TATTATTTTT
61116311 AAATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTATTTTTTTA
Found at i:61116477 original size:30 final size:30
Alignment explanation
Indices: 61116432--61116493 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
61116422 CTTAATAAGT
*
61116432 AAATACCTCTAAAATAATAACAGAATTAAC
1 AAATACCTCTAAAATAATAACAAAATTAAC
* *
61116462 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATACCTCTAAAATAATAACAAAATTAAC
61116492 AA
1 AA
61116494 TAAAGTAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (30 bp):
AAATACCTCTAAAATAATAACAAAATTAAC
Found at i:61118177 original size:25 final size:25
Alignment explanation
Indices: 61118149--61118200 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
61118139 AGTACGAAAA
* *
61118149 CAGACACAATACATAGAATCATAAT
1 CAGACAAAAAACATAGAATCATAAT
*
61118174 CAGATAAAAAACATAGAATCATAAT
1 CAGACAAAAAACATAGAATCATAAT
61118199 CA
1 CA
61118201 TAATCAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (25 bp):
CAGACAAAAAACATAGAATCATAAT
Found at i:61119041 original size:18 final size:16
Alignment explanation
Indices: 61119012--61119045 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
61119002 AAATCAAAGG
61119012 AAATTGAAAAAGAAGA
1 AAATTGAAAAAGAAGA
61119028 AAATGTGAAGAAAGAAGA
1 AAAT-TGAA-AAAGAAGA
61119046 GAAGAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (16 bp):
AAATTGAAAAAGAAGA
Found at i:61127086 original size:21 final size:22
Alignment explanation
Indices: 61127057--61127119 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 22
61127047 GGACTTTGTT
* *
61127057 CTGAGTATGATTCGTAAACAC-
1 CTGACTATGTTTCGTAAACACA
61127078 CTGACTATGTTTCGTAAAC-CA
1 CTGACTATGTTTCGTAAACACA
61127099 CTGACTATGTTTCGTAAACAC
1 CTGACTATGTTTCGTAAACAC
61127120 TTGGAGAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (22 bp):
CTGACTATGTTTCGTAAACACA
Found at i:61131678 original size:16 final size:16
Alignment explanation
Indices: 61131659--61131692 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
61131649 CAATAAATCG
61131659 AAAATAA-TCTAAATTT
1 AAAATAATTC-AAATTT
61131675 AAAATAATTCAAATTT
1 AAAATAATTCAAATTT
61131691 AA
1 AA
61131693 TTAAAAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAATTCAAATTT
Found at i:61132491 original size:21 final size:21
Alignment explanation
Indices: 61132445--61132495 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
61132435 AACACATAAC
*
61132445 CCCAAAACCTTAAACTTTAAA
1 CCCAAAACCTTAAACCTTAAA
* * *
61132466 TCCAAACCCTTAAACCTTGAA
1 CCCAAAACCTTAAACCTTAAA
61132487 CCCAAAACC
1 CCCAAAACC
61132496 CAAAACCCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.20
Consensus pattern (21 bp):
CCCAAAACCTTAAACCTTAAA
Found at i:61132501 original size:21 final size:21
Alignment explanation
Indices: 61132389--61132502 Score: 54
Period size: 21 Copynumber: 5.4 Consensus size: 21
61132379 AGCTCATAAC
* *
61132389 CCCAAACCCTTGAATCCAAAA
1 CCCAAAACCTTGAACCCAAAA
* **
61132410 CCC-AAACCGTGAACCCCGAA
1 CCCAAAACCTTGAACCCAAAA
* * *
61132430 CTCATAACACAT-AACCCCAAAA
1 CCCAAAAC-CTTGAA-CCCAAAA
** * * *
61132452 CCTTAAACTTTAAATCC-AAA
1 CCCAAAACCTTGAACCCAAAA
*
61132472 CCCTTAAACCTTGAACCCAAAA
1 CCC-AAAACCTTGAACCCAAAA
61132494 CCCAAAACC
1 CCCAAAACC
61132503 CAAACCCTAA
Statistics
Matches: 65, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
20 19 0.29
21 27 0.42
22 19 0.29
ACGTcount: A:0.43, C:0.38, G:0.04, T:0.15
Consensus pattern (21 bp):
CCCAAAACCTTGAACCCAAAA
Found at i:61133565 original size:7 final size:7
Alignment explanation
Indices: 61133555--61133580 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
61133545 ATTTTTTTAA
61133555 TTTAAAT
1 TTTAAAT
61133562 TTTAAAT
1 TTTAAAT
61133569 TTTAAAT
1 TTTAAAT
61133576 TTTAA
1 TTTAA
61133581 TTATTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAAAT
Found at i:61134047 original size:25 final size:25
Alignment explanation
Indices: 61134019--61134091 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
61134009 ATAGAACAGA
*
61134019 GCAGAACATATTAGAACAGGACAAG
1 GCAGAACATATCAGAACAGGACAAG
*
61134044 GCAGAACATATCAGAACAGGACAAA
1 GCAGAACATATCAGAACAGGACAAG
* * * *
61134069 CCAGAATATAACAGAATAGGACA
1 GCAGAACATATCAGAACAGGACA
61134092 GAGCTACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.11
Consensus pattern (25 bp):
GCAGAACATATCAGAACAGGACAAG
Found at i:61134798 original size:8 final size:8
Alignment explanation
Indices: 61134785--61134814 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
61134775 CAAGTTATTC
61134785 ATCATCAG
1 ATCATCAG
61134793 ATCATCAG
1 ATCATCAG
61134801 ATCATCAG
1 ATCATCAG
61134809 AT-ATCA
1 ATCATCA
61134815 AATTATATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.18
8 18 0.82
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (8 bp):
ATCATCAG
Found at i:61136973 original size:107 final size:107
Alignment explanation
Indices: 61136777--61136982 Score: 333
Period size: 107 Copynumber: 1.9 Consensus size: 107
61136767 TGGACTTAAA
* *
61136777 AAAATTTTGGTTGAATAAAATTCTATCACTAAACAAAATCTAACTCAAAACTTTTATAATTCTAA
1 AAAATTTTGATTGAATAAAATTCTATCACTAAACAAAATCTAACTCAAAACTTTTAAAATTCTAA
*
61136842 TTAACTTAGACCTATCAATTGAAAAAAAATTGAATGAAAATTT
66 TTAACTTAGACCTACCAATTG-AAAAAAATTGAATGAAAATTT
* * *
61136885 AAAA-TTTGATTGAATAAAATTCTTTGACTAAACAAAATCTGACTCAAAACTTTTAAAATTCTAA
1 AAAATTTTGATTGAATAAAATTCTATCACTAAACAAAATCTAACTCAAAACTTTTAAAATTCTAA
*
61136949 TTAACTTAGACCTGCCAATTGAAAAAAATTGAAT
66 TTAACTTAGACCTACCAATTGAAAAAAATTGAAT
61136983 TAAATTTTTG
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
106 13 0.14
107 74 0.81
108 4 0.04
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (107 bp):
AAAATTTTGATTGAATAAAATTCTATCACTAAACAAAATCTAACTCAAAACTTTTAAAATTCTAA
TTAACTTAGACCTACCAATTGAAAAAAATTGAATGAAAATTT
Found at i:61137179 original size:17 final size:17
Alignment explanation
Indices: 61137157--61137192 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
61137147 TTTCAGTATC
61137157 AACGATCAATATCAGTG
1 AACGATCAATATCAGTG
*
61137174 AACGATCACTATCAGTG
1 AACGATCAATATCAGTG
61137191 AA
1 AA
61137193 TAGAATGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (17 bp):
AACGATCAATATCAGTG
Found at i:61138805 original size:20 final size:21
Alignment explanation
Indices: 61138769--61138808 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
61138759 AAATGCCTAT
61138769 GAAAAGATGGCTTGGATTTAA
1 GAAAAGATGGCTTGGATTTAA
*
61138790 GAAAAGTTGG-TTGGATTTA
1 GAAAAGATGGCTTGGATTTA
61138809 TCAATGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.33
Consensus pattern (21 bp):
GAAAAGATGGCTTGGATTTAA
Found at i:61143216 original size:13 final size:13
Alignment explanation
Indices: 61143198--61143223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61143188 TGTATAAATT
61143198 GATTTTTAAATAA
1 GATTTTTAAATAA
61143211 GATTTTTAAATAA
1 GATTTTTAAATAA
61143224 CGATAAAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
GATTTTTAAATAA
Found at i:61143999 original size:5 final size:6
Alignment explanation
Indices: 61143971--61144011 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
61143961 AAAGGATCTC
*
61143971 AAAAAC AAACAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
61144012 CAAAACAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:61144579 original size:13 final size:14
Alignment explanation
Indices: 61144549--61144582 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
61144539 TATTTTGTAA
*
61144549 TTGGGCTCGGGTTG
1 TTGGGCTAGGGTTG
61144563 TTGGGCTAGGG-TG
1 TTGGGCTAGGGTTG
61144576 TTGGGCT
1 TTGGGCT
61144583 TATTTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.03, C:0.12, G:0.50, T:0.35
Consensus pattern (14 bp):
TTGGGCTAGGGTTG
Found at i:61144579 original size:44 final size:44
Alignment explanation
Indices: 61144516--61144607 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
61144506 TTGACTTGGT
61144516 TTGTTGGGCAAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
1 TTGTTGGGCAAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
*
61144560 TTGTTGGGCTAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
1 TTGTTGGGCAAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
61144604 TTGT
1 TTGT
61144608 AATGGGTAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.10, C:0.09, G:0.40, T:0.41
Consensus pattern (44 bp):
TTGTTGGGCAAGGGTGTTGGGCTTATTTTGTAATTGGGCTCGGG
Found at i:61145514 original size:132 final size:132
Alignment explanation
Indices: 61145288--61145816 Score: 792
Period size: 132 Copynumber: 4.0 Consensus size: 132
61145278 ATAAGACTAA
* * * *
61145288 TGGCTTCAATCTGCTTCCTTACTACTTTGGGAAGATAAGATTCACCGTCTAT-AATCTGCTCCAC
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT-TCGATCTGCTCCAC
* *
61145352 TACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCATTGCGGCTCAAGGAGATAGGAC
65 TACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGAC
61145417 TGG
130 TGG
* *
61145420 TGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATATGATTCACCGTCTTCGATCTGCTCCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
* * * * * * *
61145485 ACTACTCATGGAGACAAGATCTGCGATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGAAT
66 ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGACT
61145550 GG
131 GG
* * *
61145552 TGGCTTAAATTTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTTGATCTGCTTCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
*
61145617 ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACT
66 ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGACT
61145682 GG
131 GG
* * * * *
61145684 TGGCTTAAATCTACTTCCCTACTACATTGGGAAGATAAGATTCGCTGTCTTCGATCTGCGCCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
* *
61145749 ACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTC-AGAGAGATAGGAC
66 ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAG-GAGATAGGAC
61145813 TGG
130 TGG
61145816 T
1 T
61145817 CATGGTGTGA
Statistics
Matches: 358, Mismatches: 37, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
131 2 0.01
132 356 0.99
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (132 bp):
TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
ACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGACT
GG
Found at i:61145666 original size:44 final size:44
Alignment explanation
Indices: 61145613--61145798 Score: 119
Period size: 44 Copynumber: 4.2 Consensus size: 44
61145603 TGATCTGCTT
61145613 CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTC
1 CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTC
* * * * **** * *
61145657 CACTGCTGCTCAGGGAGATAGGA-CTGGTGGCTTAAATCTACTTC
1 CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTAC-TC
* * ** * * * *
61145701 C-CTACTACATT-GGGAAGATAAGAT-TCGCTGTCTTCGATCTGCGC
1 CACTACTGC-TTAGGG-AGACAAGATCT-GCAATCTTCAACCTACTC
* *
61145745 CACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTC
1 CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTC
*
61145789 CACTGCTGCT
1 CACTACTGCT
61145799 CAGAGAGATA
Statistics
Matches: 103, Mismatches: 31, Indels: 16
0.69 0.21 0.11
Matches are distributed among these distances:
43 20 0.19
44 62 0.60
45 21 0.20
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (44 bp):
CACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTC
Found at i:61153111 original size:63 final size:63
Alignment explanation
Indices: 61153038--61153164 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
61153028 CAAAACTTAC
61153038 AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
1 AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
61153101 AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
1 AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
61153164 A
1 A
61153165 GAGAAGATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.27
Consensus pattern (63 bp):
AATAATTCAAATTTAATAAAAATAAAACCCAAAATTAACTTTGTTGATACAGAAATACAACAA
Found at i:61154925 original size:20 final size:21
Alignment explanation
Indices: 61154888--61154931 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
61154878 TAAAAGAAAA
* *
61154888 AAAAATAGATTTATAAATTCT
1 AAAAATAGAATTAAAAATTCT
*
61154909 AAAAATA-AATTAAAAATTTT
1 AAAAATAGAATTAAAAATTCT
61154929 AAA
1 AAA
61154932 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAAATAGAATTAAAAATTCT
Found at i:61164883 original size:23 final size:23
Alignment explanation
Indices: 61164857--61164900 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
61164847 GAATAAATTG
61164857 ATGATTTAATTCATTAACAAAGC
1 ATGATTTAATTCATTAACAAAGC
61164880 ATGATTTAATTCATTAACAAA
1 ATGATTTAATTCATTAACAAA
61164901 ACATCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGATTTAATTCATTAACAAAGC
Found at i:61172649 original size:31 final size:32
Alignment explanation
Indices: 61172599--61172660 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
61172589 AATATATAAG
* *
61172599 TATGTATGTATATATATATAAATTAT-GAAAA
1 TATGTACGTATATAAATATAAATTATAGAAAA
* *
61172630 TATGTACGTGTATAAATATATATTATAGAAA
1 TATGTACGTATATAAATATAAATTATAGAAA
61172661 TGTATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (32 bp):
TATGTACGTATATAAATATAAATTATAGAAAA
Found at i:61172723 original size:3 final size:3
Alignment explanation
Indices: 61172715--61172755 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
61172705 AAAATGAGTA
61172715 AAT AAT AAT AAT AAT AAT AAT AAT CAAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
61172756 CAAGATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:61172820 original size:17 final size:17
Alignment explanation
Indices: 61172800--61172832 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
61172790 ATAAAATAGA
61172800 AATACAATAAC-AATAAT
1 AATACAA-AACTAATAAT
61172817 AATACAAAACTAATAA
1 AATACAAAACTAATAA
61172833 CAAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
AATACAAAACTAATAAT
Found at i:61174089 original size:17 final size:17
Alignment explanation
Indices: 61174036--61174090 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
61174026 TCATGGGTTG
* *
61174036 TTTGGGTTT-AATTTGT
1 TTTGGGTTTGTATTAGT
*
61174052 TTTGGGTTTGTTAATAG-
1 TTTGGGTTTG-TATTAGT
*
61174069 TTTGGGTTTGTATTGGT
1 TTTGGGTTTGTATTAGT
61174086 TTTGG
1 TTTGG
61174091 CCCCGGGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 13 0.42
17 15 0.48
18 3 0.10
ACGTcount: A:0.11, C:0.00, G:0.31, T:0.58
Consensus pattern (17 bp):
TTTGGGTTTGTATTAGT
Found at i:61176141 original size:31 final size:31
Alignment explanation
Indices: 61176049--61176143 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
61176039 GGCAAATTAC
*
61176049 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
61176080 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
61176111 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
61176142 AA
1 AA
61176144 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:61181027 original size:15 final size:15
Alignment explanation
Indices: 61181009--61181038 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61180999 TTTTTTTTGC
61181009 GCTTTTTTGCTTTTT
1 GCTTTTTTGCTTTTT
*
61181024 GCTTTTTTTCTTTTT
1 GCTTTTTTGCTTTTT
61181039 TTTACGCTTT
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:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (15 bp):
GCTTTTTTGCTTTTT
Found at i:61181673 original size:31 final size:32
Alignment explanation
Indices: 61181635--61181697 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
61181625 AGGCAAATTA
61181635 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
61181666 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
61181698 GTTGACACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:61183145 original size:31 final size:29
Alignment explanation
Indices: 61183110--61183181 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 29
61183100 ACATATACCT
61183110 ATATACATATATAAGCA-ATTATATAATAATA
1 ATATACATATATAAGCATA-TATAT-ATAA-A
*
61183141 ATATA-ATAT-GAAGCATATATATATAAA
1 ATATACATATATAAGCATATATATATAAA
*
61183168 ATTTACATA-ATAAG
1 ATATACATATATAAG
61183182 TATAAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 5 0.14
28 10 0.29
29 10 0.29
30 5 0.14
31 5 0.14
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (29 bp):
ATATACATATATAAGCATATATATATAAA
Found at i:61186573 original size:20 final size:20
Alignment explanation
Indices: 61186548--61186587 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
61186538 AAATTAAGCC
*
61186548 TAAAAA-ATTATATTTATTTT
1 TAAAAATATT-TATTAATTTT
61186568 TAAAAATATTTATTAATTTT
1 TAAAAATATTTATTAATTTT
61186588 AATATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAAATATTTATTAATTTT
Found at i:61186849 original size:23 final size:25
Alignment explanation
Indices: 61186823--61186873 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
61186813 TGTTTTTTAT
61186823 TTTAAAAAATAATG-AG-T-AATATA
1 TTTAAAAAAT-ATGTAGTTCAATATA
*
61186846 TTTATAAAATATGTAGTTCAATATA
1 TTTAAAAAATATGTAGTTCAATATA
61186871 TTT
1 TTT
61186874 TAAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.12
23 11 0.46
24 1 0.04
25 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (25 bp):
TTTAAAAAATATGTAGTTCAATATA
Found at i:61193012 original size:21 final size:22
Alignment explanation
Indices: 61192988--61193035 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
61192978 CCATTGCTTG
*
61192988 TGGCTATACAA-TTGTTTGCAA
1 TGGCTATACAATTTATTTGCAA
* *
61193009 TGGCTATATAATTTATTTGCAG
1 TGGCTATACAATTTATTTGCAA
61193031 TGGCT
1 TGGCT
61193036 CCATCTGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (22 bp):
TGGCTATACAATTTATTTGCAA
Found at i:61193866 original size:23 final size:23
Alignment explanation
Indices: 61193797--61193869 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
61193787 GTATATTAAA
61193797 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
*** * * *
61193820 ATATAA-TATTTTTA-ATTGA-A
1 ATATAATTAAAATCATTTTGATT
61193840 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
61193863 ATATAAT
1 ATATAAT
61193870 ATTAATATAA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 6 0.17
21 8 0.23
22 8 0.23
23 13 0.37
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATAATTAAAATCATTTTGATT
Found at i:61194423 original size:67 final size:69
Alignment explanation
Indices: 61194310--61194440 Score: 194
Period size: 67 Copynumber: 1.9 Consensus size: 69
61194300 TTTGTCTCTC
* * *
61194310 AATTATTTTTATAAAATTTAATTTGCATCTTCAATTCTTTGATAGTGTGTTCTAA-ATTAATATT
1 AATTATTTTTATAAAATGTAATTTGCAACTTCAACTCTTTGATAGTGTGTTCTAATATTAATATT
61194374 GTTT
66 GTTT
* * *
61194378 AATTTTTTTTATAAAGTGTAA-TTGCAACTTCAACTCTTTGATAGTGTGTTCTAATTTTAATAT
1 AATTATTTTTATAAAATGTAATTTGCAACTTCAACTCTTTGATAGTGTGTTCTAATATTAATAT
61194441 GTTGCAGTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 31 0.55
68 25 0.45
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (69 bp):
AATTATTTTTATAAAATGTAATTTGCAACTTCAACTCTTTGATAGTGTGTTCTAATATTAATATT
GTTT
Found at i:61197360 original size:26 final size:27
Alignment explanation
Indices: 61197320--61197401 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 27
61197310 TAAGAACATT
*
61197320 TTATGAAATTATATTTAATAATAATTA
1 TTATTAAATTATATTTAATAATAATTA
* *
61197347 TT-TTAAATTGTATTTAATCATATATT-
1 TTATTAAATTATATTTAATAATA-ATTA
* *
61197373 TTAATTAAAATATATTTAATATTAATTA
1 TT-ATTAAATTATATTTAATAATAATTA
61197401 T
1 T
61197402 AGTATCATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 19 0.43
27 8 0.18
28 17 0.39
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (27 bp):
TTATTAAATTATATTTAATAATAATTA
Found at i:61197466 original size:37 final size:37
Alignment explanation
Indices: 61197408--61197591 Score: 99
Period size: 37 Copynumber: 4.8 Consensus size: 37
61197398 TTATAGTATC
* * *
61197408 ATATATTATG-ATTTGAATAAATTATATAAGAATATGA
1 ATATATTAAGAATTTTATTAAATTATATAAGAATAT-A
**
61197445 AT-TATTAAGAATTTTATTAAATTATATATTTTAAT-TAA
1 ATATATTAAGAATTTTATTAAATTATATA--AGAATAT-A
* * * * * *
61197483 ATATATTTAATAATATTTATGTTAATTTATATTTTACAGTATC
1 ATATA-TTAAGAAT-TTTA--TTAAATTATA--TAAGAATATA
* * *
61197526 ATATATTATG-ATTTGAGTAAATTAATATAAGAATATTA
1 ATATATTAAGAATTTTATTAAATT-ATATAAGAATA-TA
61197564 AT-TATTAAGAATTTTATTAAATTATATA
1 ATATATTAAGAATTTTATTAAATTATATA
61197592 TTTTAATTAA
Statistics
Matches: 108, Mismatches: 25, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
36 6 0.06
37 34 0.31
38 23 0.21
39 8 0.07
40 10 0.09
41 6 0.06
42 3 0.03
43 16 0.15
44 1 0.01
45 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.48
Consensus pattern (37 bp):
ATATATTAAGAATTTTATTAAATTATATAAGAATATA
Found at i:61197475 original size:17 final size:17
Alignment explanation
Indices: 61197455--61197488 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
61197445 ATTATTAAGA
61197455 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
61197472 ATTTTAATTAAATATAT
1 ATTTTAATTAAATATAT
61197489 TTAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:61197525 original size:118 final size:119
Alignment explanation
Indices: 61197402--61197624 Score: 396
Period size: 119 Copynumber: 1.9 Consensus size: 119
61197392 TATTAATTAT
61197402 AGTATCATATATTATGATTTGAATAAATT-ATATAAGAATATGAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAATAAATTAATATAAGAATATGAATTATTAAGAATTTTATTAAA
*
61197466 TTATATATTTTAATT-AAATATATTTAATAATATTTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTAAAATATATTTAATAA-AATTATGTTAATTTATATTTTAC
* *
61197520 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAATAAATTAATATAAGAATATGAATTATTAAGAATTTTATTAAA
61197585 TTATATATTTTAATTAAAATATATTTAATAAAATTATGTT
66 TTATATATTTTAATTAAAATATATTTAATAAAATTATGTT
61197625 TAAATATGAT
Statistics
Matches: 100, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
118 28 0.28
119 57 0.57
120 15 0.15
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (119 bp):
AGTATCATATATTATGATTTGAATAAATTAATATAAGAATATGAATTATTAAGAATTTTATTAAA
TTATATATTTTAATTAAAATATATTTAATAAAATTATGTTAATTTATATTTTAC
Found at i:61197602 original size:18 final size:18
Alignment explanation
Indices: 61197574--61197621 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 18
61197564 ATTATTAAGA
61197574 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
61197591 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
*
61197607 A-TTTAATAAAATTAT
1 ATTTTAATTAAATTAT
61197622 GTTTAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.33
16 5 0.19
17 7 0.26
18 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:61197613 original size:15 final size:15
Alignment explanation
Indices: 61197587--61197627 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
61197577 TTATTAAATT
61197587 ATATATTTTAATTAAA
1 ATATATTTTAA-TAAA
61197603 ATATA-TTTAATAAA
1 ATATATTTTAATAAA
61197617 AT-TATGTTTAA
1 ATATAT-TTTAA
61197628 ATATGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.09
14 6 0.26
15 10 0.43
16 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATATATTTTAATAAA
Found at i:61197757 original size:18 final size:17
Alignment explanation
Indices: 61197729--61197763 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61197719 AATTATAAGA
*
61197729 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
61197746 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
61197764 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:61197846 original size:156 final size:156
Alignment explanation
Indices: 61197562--61197876 Score: 596
Period size: 156 Copynumber: 2.0 Consensus size: 156
61197552 ATAAGAATAT
61197562 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAATTATGTTTA
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAATTATGTTTA
*
61197627 AATATGATTAAATTATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
61197692 AATCATTTACCAAAACAAATTTATGC
131 AATCATTTACCAAAACAAATTTATGC
61197718 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAA-AATTATGTTT
61197782 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
65 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
61197847 TAATCATTTACCAAAACAATTTTATGC
130 TAATCATTTACCAAAACAAATTTATGC
61197874 TAA
1 TAA
61197877 GGGTATTCTA
Statistics
Matches: 156, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
155 47 0.30
156 109 0.70
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAATTATGTTTA
AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAT
AATCATTTACCAAAACAAATTTATGC
Found at i:61197993 original size:44 final size:45
Alignment explanation
Indices: 61197928--61198018 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
61197918 ACCTCTATTC
* * *
61197928 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
61197972 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
61198017 CA
1 CA
61198019 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:61198020 original size:16 final size:16
Alignment explanation
Indices: 61197999--61198034 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
61197989 GATTAGCTAT
61197999 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
61198015 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
61198031 TACA
1 TACA
61198035 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:61198819 original size:16 final size:16
Alignment explanation
Indices: 61198791--61198838 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
61198781 AATCAAAAAC
61198791 AATCAAAACTTAAAATA
1 AATCAAAA-TTAAAATA
* *
61198808 ATTCAAATTTAATAA-A
1 AATCAAAATTAA-AATA
61198824 AATCAAAATTAAAAT
1 AATCAAAATTAAAAT
61198839 TAACTTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 2 0.08
16 15 0.60
17 8 0.32
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (16 bp):
AATCAAAATTAAAATA
Found at i:61202177 original size:9 final size:9
Alignment explanation
Indices: 61202163--61202199 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
61202153 TATAGTTTGA
61202163 TATTCGAAT
1 TATTCGAAT
61202172 TATTCGAAT
1 TATTCGAAT
*
61202181 TATTCGAGT
1 TATTCGAAT
61202190 TATTCGAAT
1 TATTCGAAT
61202199 T
1 T
61202200 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:61221358 original size:15 final size:15
Alignment explanation
Indices: 61221326--61221370 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
61221316 TAATTCTTTG
*
61221326 ATTTATATTCATATAT
1 ATTTATA-TCATACAT
*
61221342 ATTTATATCATCCAT
1 ATTTATATCATACAT
61221357 ATTTAT-TCATACAT
1 ATTTATATCATACAT
61221371 TCAAAGTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 7 0.27
15 12 0.46
16 7 0.27
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTATATCATACAT
Found at i:61221864 original size:16 final size:16
Alignment explanation
Indices: 61221836--61221883 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
61221826 AATCAAAAAC
61221836 AATCAAAACTTAAAATA
1 AATCAAAA-TTAAAATA
* *
61221853 ATTCAAATTTAATAA-A
1 AATCAAAATTAA-AATA
61221869 AATCAAAATTAAAAT
1 AATCAAAATTAAAAT
61221884 TAACTTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 2 0.08
16 15 0.60
17 8 0.32
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (16 bp):
AATCAAAATTAAAATA
Found at i:61225481 original size:21 final size:20
Alignment explanation
Indices: 61225423--61225486 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
61225413 CCTGATCAGT
61225423 ATACGACACATAAGTGCCTG
1 ATACGACACATAAGTGCCTG
* * *
61225443 AAACGACACACGAGGTGCCTG
1 ATACGACACA-TAAGTGCCTG
61225464 ATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTG
61225485 AT
1 AT
61225487 CGGCAAAGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.25
21 27 0.75
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
ATACGACACATAAGTGCCTG
Found at i:61225764 original size:14 final size:12
Alignment explanation
Indices: 61225745--61225788 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
61225735 TATTCATAAA
61225745 TTAATTCACTTTAT
1 TTAATTCA-TTT-T
61225759 TTAATTCATTTT
1 TTAATTCATTTT
*
61225771 TTAAATCCATTTT
1 TT-AATTCATTTT
61225784 TTAAT
1 TTAAT
61225789 CAAATTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 6 0.21
13 14 0.50
14 8 0.29
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAATTCATTTT
Found at i:61226603 original size:30 final size:28
Alignment explanation
Indices: 61226560--61226617 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
61226550 TTTTCTTCCC
61226560 CTGTTTTCGTCTCTTTCTCTGTTTCTTTT
1 CTGTTTTCGTCTCTTTCTCTG-TTCTTTT
* *
61226589 CTGTTCTTCTTCTCTTTTTCTGTTCTTTT
1 CTGTT-TTCGTCTCTTTCTCTGTTCTTTT
61226618 ATTTCATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.00, C:0.24, G:0.09, T:0.67
Consensus pattern (28 bp):
CTGTTTTCGTCTCTTTCTCTGTTCTTTT
Found at i:61227523 original size:20 final size:20
Alignment explanation
Indices: 61227498--61227537 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
61227488 AAATTAAGCC
*
61227498 TAAAAAAATATATTTATTTT
1 TAAAAAAATATATTAATTTT
* *
61227518 TAAAAATATTTATTAATTTT
1 TAAAAAAATATATTAATTTT
61227538 AATACTGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAAAAATATATTAATTTT
Found at i:61227538 original size:19 final size:18
Alignment explanation
Indices: 61227501--61227539 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
61227491 TTAAGCCTAA
*
61227501 AAAAATATATTTATTTTT
1 AAAAATATATTTAATTTT
*
61227519 AAAAATATTTATTAATTTT
1 AAAAATATAT-TTAATTTT
61227538 AA
1 AA
61227540 TACTGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAAATATATTTAATTTT
Found at i:61227795 original size:23 final size:26
Alignment explanation
Indices: 61227764--61227823 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 26
61227754 TATTTTTTAT
*
61227764 TTTAAAAAATAATG-AG-T-AATATA
1 TTTATAAAATAATGTAGTTCAATATA
61227787 TTTATAAAAT-ATGTAGTTCAATATA
1 TTTATAAAATAATGTAGTTCAATATA
*
61227812 TTT-TAAATTAAT
1 TTTATAAAATAAT
61227824 TTTTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 3 0.10
23 11 0.35
24 6 0.19
25 11 0.35
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (26 bp):
TTTATAAAATAATGTAGTTCAATATA
Found at i:61234039 original size:21 final size:21
Alignment explanation
Indices: 61234013--61234053 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61234003 AGACGAGCAA
* *
61234013 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
61234034 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
61234054 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:61239391 original size:16 final size:16
Alignment explanation
Indices: 61239367--61239401 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
61239357 AAATTTGACG
* *
61239367 AAAATATTAATAATAT
1 AAAAAATTAAAAATAT
61239383 AAAAAATTAAAAATAT
1 AAAAAATTAAAAATAT
61239399 AAA
1 AAA
61239402 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATTAAAAATAT
Found at i:61239661 original size:23 final size:24
Alignment explanation
Indices: 61239630--61239687 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
61239620 TTAAATTCGT
61239630 ATTTGTATTATTTATAAATTT-AGA
1 ATTT-TATTATTTATAAATTTAAGA
**
61239654 ATTTTATT-TTTATATTTTTAAGA
1 ATTTTATTATTTATAAATTTAAGA
*
61239677 ATTTAATTATT
1 ATTTTATTATT
61239688 CATTTATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.31
23 14 0.48
24 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (24 bp):
ATTTTATTATTTATAAATTTAAGA
Found at i:61244205 original size:20 final size:20
Alignment explanation
Indices: 61244131--61244206 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
61244121 GACTGTATAG
*
61244131 AATTTTATAATTTTTTTCTTC
1 AATTTTATAATTTTTTT-TAC
** * *
61244152 --TTTTACGA-TTTTTATAA
1 AATTTTATAATTTTTTTTAC
61244169 AATTTTATAATTTTTTTTAC
1 AATTTTATAATTTTTTTTAC
61244189 AATTCTTAT-ATTTTTTTT
1 AATT-TTATAATTTTTTTT
61244207 CTAGTTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.02
18 5 0.12
19 12 0.29
20 20 0.48
21 4 0.10
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (20 bp):
AATTTTATAATTTTTTTTAC
Found at i:61244262 original size:27 final size:28
Alignment explanation
Indices: 61244212--61244273 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
61244202 TTTTTCTAGT
* *
61244212 TTTTTAATAAAATTTAAATATTTTTATA
1 TTTTTATTAAAATTTAAATATTTTAATA
61244240 TTTTTATTAAAATTTAAAT-TTTTAATA
1 TTTTTATTAAAATTTAAATATTTTAATA
61244267 TTTTTAT
1 TTTTTAT
61244274 CACATGTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 14 0.44
28 18 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTATTAAAATTTAAATATTTTAATA
Found at i:61247554 original size:16 final size:16
Alignment explanation
Indices: 61247533--61247578 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
61247523 AAAAACTTGA
*
61247533 ATTAGAGGTGTATTGG
1 ATTAGAGGTGTAATGG
61247549 ATTAGAGGTGTAATGG
1 ATTAGAGGTGTAATGG
*
61247565 AATAGAGGTGTAAT
1 ATTAGAGGTGTAAT
61247579 AGCAAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (16 bp):
ATTAGAGGTGTAATGG
Found at i:61247623 original size:45 final size:44
Alignment explanation
Indices: 61247557--61247651 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
61247547 GGATTAGAGG
* *
61247557 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
61247602 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
61247646 TGTAAT
1 TGTAAT
61247652 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:61247821 original size:25 final size:25
Alignment explanation
Indices: 61247789--61247843 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
61247779 TAATTTAATC
*
61247789 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
61247813 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
61247838 ATATAT
1 ATATAT
61247844 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:61248025 original size:47 final size:46
Alignment explanation
Indices: 61247974--61248134 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
61247964 GATTTAATAA
61247974 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
61248021 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
61248062 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
61248109 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
61248135 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:61253023 original size:124 final size:124
Alignment explanation
Indices: 61252855--61253145 Score: 512
Period size: 124 Copynumber: 2.3 Consensus size: 124
61252845 TTATTTCGAG
* *
61252855 TTGACGTTTCTG-GACAAATAGTATAAAATCGCGCCCTCGAGGATGCTAATTGGGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGT
*
61252919 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTTT
61252979 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
* *
61253044 AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAATAAATATTTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTTT
*
61253103 TTGACGTTTCTGAACAAATAGTATAAAATCGCGCCCTCGTGGA
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGA
61253146 CGCGATTTTG
Statistics
Matches: 160, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
124 159 0.99
125 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCGCCCTCGTGGATGCTAATTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTTT
Found at i:61256376 original size:56 final size:56
Alignment explanation
Indices: 61256287--61256411 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
61256277 TATGTAAAAC
* **
61256287 TATGTAAAATTATTAAGCCCAATAACTTCTGTTAATGGTTAGTAA-ATTTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGA-TTATCAAAT
*
61256343 TATGTAAAATTATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGATTATCAAAT
*
61256399 TAGGTAAAATTAT
1 TATGTAAAATTAT
61256412 GTTATGGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 62 0.98
57 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCAAAAAAGTCTGTTAATGGTTAGTAAGATTATCAAAT
Found at i:61256431 original size:23 final size:23
Alignment explanation
Indices: 61256405--61256466 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
61256395 AAATTAGGTA
* *
61256405 AAATTATGTTATGGTTTTTAAAT
1 AAATTAGGTTAAGGTTTTTAAAT
* *
61256428 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAAGGTTTTTAAAT
61256451 AAATTAGGTTAAGGTT
1 AAATTAGGTTAAGGTT
61256467 AGGGGTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (23 bp):
AAATTAGGTTAAGGTTTTTAAAT
Found at i:61256467 original size:29 final size:29
Alignment explanation
Indices: 61256433--61256675 Score: 396
Period size: 29 Copynumber: 8.4 Consensus size: 29
61256423 TAAATAAATT
61256433 AGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
61256462 AGGTTAGGGGTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
61256491 AGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
61256520 AGGTTAGGGGTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
61256549 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
* * *
61256578 AAGTTAGGGGTTTTAATCAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
61256607 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
* *
61256636 GGGTTAAGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
61256665 GGGTTAGGGTT
1 AGGTTAGGGTT
61256676 AGGGTATGAA
Statistics
Matches: 199, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 199 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (29 bp):
AGGTTAGGGTTTTTAATTAAATTAGGTTA
Found at i:61257912 original size:7 final size:7
Alignment explanation
Indices: 61257902--61257934 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
61257892 TTATATACAT
61257902 AATACTA
1 AATACTA
61257909 AATACTA
1 AATACTA
61257916 AATACTA
1 AATACTA
61257923 AATACTA
1 AATACTA
*
61257930 TATAC
1 AATAC
61257935 CGGTCCCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACTA
Found at i:61259175 original size:38 final size:37
Alignment explanation
Indices: 61259086--61259158 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
61259076 GTCTCCAAAT
* *
61259086 TCACATTTCAATTC-AATTTCACTTTTTCACTTTCAA
1 TCACAATTCAATTCAAAATTCACTTTTTCACTTTCAA
*
61259122 TCACAATTCAATTCAAAATTCACTTTTTCATTTTCAA
1 TCACAATTCAATTCAAAATTCACTTTTTCACTTTCAA
61259159 ATCAATATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 13 0.39
37 20 0.61
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (37 bp):
TCACAATTCAATTCAAAATTCACTTTTTCACTTTCAA
Found at i:61259386 original size:3 final size:3
Alignment explanation
Indices: 61259378--61259407 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
61259368 AATCTCACTC
61259378 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
61259408 CTTATACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:61261340 original size:11 final size:11
Alignment explanation
Indices: 61261324--61261403 Score: 85
Period size: 11 Copynumber: 7.3 Consensus size: 11
61261314 TTTAAATAGG
61261324 AATTTGAGAGA
1 AATTTGAGAGA
61261335 AATTTGAGAGGA
1 AATTTGAGA-GA
61261347 AA-TTGAGAGCA
1 AATTTGAGAG-A
*
61261358 AA-TTCAGAGA
1 AATTTGAGAGA
61261368 AATTTGAGAGA
1 AATTTGAGAGA
**
61261379 ATATTAAAGAGA
1 A-ATTTGAGAGA
61261391 AA-TTGAGAGA
1 AATTTGAGAGA
61261401 AAT
1 AAT
61261404 GATTTAGTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
10 12 0.21
11 33 0.57
12 13 0.22
ACGTcount: A:0.49, C:0.03, G:0.25, T:0.24
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:61261367 original size:33 final size:33
Alignment explanation
Indices: 61261330--61261403 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
61261320 TAGGAATTTG
*
61261330 AGAGAAATTTGAGAGGAA-ATT-GAGAGCAAATTC
1 AGAGAAATTTGAGA-GAATATTAAAGAG-AAATTC
*
61261363 AGAGAAATTTGAGAGAATATTAAAGAGAAATTG
1 AGAGAAATTTGAGAGAATATTAAAGAGAAATTC
61261396 AGAGAAAT
1 AGAGAAAT
61261404 GATTTAGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 3 0.08
33 30 0.81
34 4 0.11
ACGTcount: A:0.50, C:0.03, G:0.26, T:0.22
Consensus pattern (33 bp):
AGAGAAATTTGAGAGAATATTAAAGAGAAATTC
Found at i:61266447 original size:33 final size:33
Alignment explanation
Indices: 61266392--61266471 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
61266382 GTATATTGAT
*
61266392 GATGCAGCCGTGTACAGCAATGCCGCGTGTATC
1 GATGGAGCCGTGTACAGCAATGCCGCGTGTATC
* *
61266425 GATGGAGCCGTGTGCAGGAATGCCGCGTGTATC
1 GATGGAGCCGTGTACAGCAATGCCGCGTGTATC
61266458 GATGGAGCCGTGTA
1 GATGGAGCCGTGTA
61266472 TATCAGAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.21
Consensus pattern (33 bp):
GATGGAGCCGTGTACAGCAATGCCGCGTGTATC
Found at i:61267067 original size:27 final size:28
Alignment explanation
Indices: 61267010--61267067 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
61267000 CAGCCCAGCC
** * *
61267010 TAATTTATTATTTAATAATTAAAATTTA
1 TAATTTATTATTTAATAAAAAAAACTAA
*
61267038 TAATTTTTTA-TTAATAAAAAAAACTAA
1 TAATTTATTATTTAATAAAAAAAACTAA
61267065 TAA
1 TAA
61267068 GCGAAGGACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATTTATTATTTAATAAAAAAAACTAA
Found at i:61267605 original size:19 final size:20
Alignment explanation
Indices: 61267573--61267641 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
61267563 CATGTGGCAA
61267573 AAAAATTATAAAAAATTATT
1 AAAAATTATAAAAAATTATT
* *
61267593 AAAAGTTAT-AAAAGTTATT
1 AAAAATTATAAAAAATTATT
**
61267612 AAATTTTAATAAAAAA-TA--
1 AAAAATT-ATAAAAAATTATT
61267630 AAAAATTATAAA
1 AAAAATTATAAA
61267642 TGTATCAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 5 0.12
18 5 0.12
19 14 0.35
20 12 0.30
21 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAATTATAAAAAATTATT
Found at i:61267614 original size:10 final size:10
Alignment explanation
Indices: 61267573--61267614 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
61267563 CATGTGGCAA
*
61267573 AAAAATTATA
1 AAAAATTATT
61267583 AAAAATTATT
1 AAAAATTATT
*
61267593 AAAAGTTA-T
1 AAAAATTATT
*
61267602 AAAAGTTATT
1 AAAAATTATT
61267612 AAA
1 AAA
61267615 TTTTAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (10 bp):
AAAAATTATT
Found at i:61267783 original size:21 final size:20
Alignment explanation
Indices: 61267757--61267802 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
61267747 TGTTGTGACA
61267757 AAAATTGATAAAAAAATTAAT
1 AAAATTGAT-AAAAAATTAAT
* * *
61267778 AAAATTTATAGAAAATTTAT
1 AAAATTGATAAAAAATTAAT
61267798 AAAAT
1 AAAAT
61267803 GCTTCTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATTGATAAAAAATTAAT
Found at i:61267864 original size:21 final size:21
Alignment explanation
Indices: 61267821--61267864 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
61267811 TAGTATGGTA
* *
61267821 TTTTTATATATTTCTTTATAC
1 TTTTTATATATTTCTTAAAAC
61267842 TTTTTATA-ATTTTCTTAAAAC
1 TTTTTATATA-TTTCTTAAAAC
61267863 TT
1 TT
61267865 AATAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTATATATTTCTTAAAAC
Found at i:61268277 original size:7 final size:7
Alignment explanation
Indices: 61268261--61268305 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
61268251 CCTTAAGCCT
*
61268261 AAAAATA
1 AAAAAGA
61268268 AAAAAGA
1 AAAAAGA
61268275 AAAAAGAA
1 AAAAAG-A
61268283 AAAAAGA
1 AAAAAGA
*
61268290 AATAAGA
1 AAAAAGA
*
61268297 AATAAGA
1 AAAAAGA
61268304 AA
1 AA
61268306 TAAAAATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 28 0.80
8 7 0.20
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (7 bp):
AAAAAGA
Found at i:61268285 original size:15 final size:15
Alignment explanation
Indices: 61268267--61268298 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
61268257 GCCTAAAAAT
61268267 AAAAAAGAAAAAAGA
1 AAAAAAGAAAAAAGA
*
61268282 AAAAAAGAAATAAGA
1 AAAAAAGAAAAAAGA
61268297 AA
1 AA
61268299 TAAGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAAAGA
Found at i:61268287 original size:22 final size:22
Alignment explanation
Indices: 61268261--61268310 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
61268251 CCTTAAGCCT
*
61268261 AAAAATAAAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAAAAAAGAA
* *
61268283 AAAAAGAAATAAGAAATAAGAA
1 AAAAAGAAAAAAGAAAAAAGAA
61268305 ATAAAA
1 A-AAAA
61268311 ATTATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (22 bp):
AAAAAGAAAAAAGAAAAAAGAA
Found at i:61268306 original size:7 final size:7
Alignment explanation
Indices: 61268271--61268312 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
61268261 AAAAATAAAA
*
61268271 AAGAAAA
1 AAGAAAT
*
61268278 AAGAAAAA
1 AAG-AAAT
61268286 AAGAAAT
1 AAGAAAT
61268293 AAGAAAT
1 AAGAAAT
61268300 AAGAAAT
1 AAGAAAT
61268307 AA-AAAT
1 AAGAAAT
61268313 TATAAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 4 0.12
7 22 0.67
8 7 0.21
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (7 bp):
AAGAAAT
Found at i:61274260 original size:7 final size:7
Alignment explanation
Indices: 61274233--61274267 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
61274223 TAATGTTGTT
61274233 TTTATTA
1 TTTATTA
*
61274240 TTTCTTA
1 TTTATTA
*
61274247 GTTATTA
1 TTTATTA
61274254 TTTATTA
1 TTTATTA
61274261 TTTATTA
1 TTTATTA
61274268 ATAAAAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:61274961 original size:3 final size:3
Alignment explanation
Indices: 61274953--61274991 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
61274943 AAGTGAAAAT
61274953 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61274992 CCTCCCTTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:61275205 original size:26 final size:26
Alignment explanation
Indices: 61275131--61275205 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 26
61275121 TATTTATTTT
* * *
61275131 TAAAAAACTAAAAAGTTCAAAACATA
1 TAAAAATCTAAAAAATTCAAAATATA
* **
61275157 T-ATAAT-TTTAAAATTCACGAAATATA
1 TAAAAATCTAAAAAATTCA--AAATATA
61275183 TAAAAATCTAAAAAATTCAAAAT
1 TAAAAATCTAAAAAATTCAAAAT
61275206 TAAAGAATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
24 8 0.22
25 3 0.08
26 12 0.33
27 4 0.11
28 9 0.25
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.28
Consensus pattern (26 bp):
TAAAAATCTAAAAAATTCAAAATATA
Found at i:61278393 original size:23 final size:23
Alignment explanation
Indices: 61278348--61278393 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
61278338 AATTGGCCGG
* *
61278348 AATTAAATTATTTTATTTAAAAA
1 AATTAAATTATTTAATATAAAAA
* *
61278371 AATTAATTTATTTAATATCAAAA
1 AATTAAATTATTTAATATAAAAA
61278394 TCGAGAGGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTAAATTATTTAATATAAAAA
Found at i:61279942 original size:30 final size:30
Alignment explanation
Indices: 61279906--61279965 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
61279896 TGTGGCAATC
*
61279906 CACATACTTTTATAAAAATTCAAACGAATT
1 CACATACTTTTATAAAAATTCAAAAGAATT
*
61279936 CACATACTTTTATAAAAATTGAAAAGAATT
1 CACATACTTTTATAAAAATTCAAAAGAATT
61279966 AATAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.33
Consensus pattern (30 bp):
CACATACTTTTATAAAAATTCAAAAGAATT
Found at i:61295043 original size:16 final size:15
Alignment explanation
Indices: 61295022--61295085 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 15
61295012 TTGAAATTAA
61295022 ATTATATATATTTATT
1 ATTATATAT-TTTATT
*
61295038 ATTATA-ATTTTATA
1 ATTATATATTTTATT
* *
61295052 ATTTTATAATTTTAAT
1 ATTATAT-ATTTTATT
* *
61295068 AGTGTATATTTTATT
1 ATTATATATTTTATT
61295083 ATT
1 ATT
61295086 TAAAAAAGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 10 0.26
15 11 0.29
16 17 0.45
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTATATATTTTATT
Found at i:61295052 original size:8 final size:8
Alignment explanation
Indices: 61295039--61295065 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
61295029 ATATTTATTA
61295039 TTATAATT
1 TTATAATT
61295047 TTATAATT
1 TTATAATT
61295055 TTATAATT
1 TTATAATT
61295063 TTA
1 TTA
61295066 ATAGTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTATAATT
Found at i:61295057 original size:22 final size:23
Alignment explanation
Indices: 61295023--61295085 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
61295013 TGAAATTAAA
61295023 TTATATATATTTATTATTATAAT-T
1 TTATA-AT-TTTATTATTATAATAT
* *
61295047 TTATAATTTTATAATTTTAATAGT
1 TTATAATTTTATTATTATAATA-T
*
61295071 GTAT-ATTTTATTATT
1 TTATAATTTTATTATT
61295086 TAAAAAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 12 0.36
23 12 0.36
24 9 0.27
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (23 bp):
TTATAATTTTATTATTATAATAT
Found at i:61296711 original size:25 final size:27
Alignment explanation
Indices: 61296681--61296744 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
61296671 TTTTTAATCA
61296681 ATATATCTACATA-CT-TATATTTTTT
1 ATATATCTACATATCTATATATTTTTT
*
61296706 ATATATGCTACA-ATCTATATGTTTTTT
1 ATATAT-CTACATATCTATATATTTTTT
* *
61296733 TTATATATACAT
1 ATATATCTACAT
61296745 GTATATACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 7 0.22
26 11 0.34
27 14 0.44
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.53
Consensus pattern (27 bp):
ATATATCTACATATCTATATATTTTTT
Found at i:61296946 original size:23 final size:24
Alignment explanation
Indices: 61296920--61296966 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
61296910 ACATATGCAC
61296920 ATACTTACA-TTTTATTT-TATATA
1 ATACTTACAGTTTT-TTTCTATATA
61296943 ATACTTACAGTTTTTTTCTATATA
1 ATACTTACAGTTTTTTTCTATATA
61296967 TGTATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (24 bp):
ATACTTACAGTTTTTTTCTATATA
Found at i:61308816 original size:44 final size:44
Alignment explanation
Indices: 61308746--61309513 Score: 560
Period size: 44 Copynumber: 17.4 Consensus size: 44
61308736 GGATGGATTG
* * * * *
61308746 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTAGCGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGT
* * * **
61308790 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTAGTAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATT-GGCGTGAAGT
* * * * * *
61308834 GGATCGAAGA-CGCAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGT
* * * * *
61308878 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGT
* * *
61308922 AGATCGAAGATAGCAGGTCCTATCTTCCTATATT-G-GTAGAAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCGT-G-AAGT
* * * *
61308966 GGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGT
* * *
61309010 AGATCGAAGA-AGGCAAATCTTGTCTTCATGTATTGGCGTGAAGT
1 AGATCGAAGATA-GCAGATCTTGTCTTCCTATATTGGCGTGAAGT
* * * *
61309054 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGT
* * * *
61309098 GGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGT
* * * *
61309142 AGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGT
* * * *
61309186 AGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGT
* * * *
61309230 GGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGT
* * * * *
61309274 AGATC-ACAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAATT
1 AGATCGA-AGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGT
* * * **
61309318 AGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG-GAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTG-GCGTGAAGT
* * * * *
61309362 GGATCCAAGATA-CAGATCTTGTCTTCCCATACTGGTGGTGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGT
* * *
61309406 AGATCGAAGAAAGCAGATCTTGTC--CCTGTATTTGACAGTGGAA-T
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATA-TTGGC-GT-GAAGT
* * * * * * *
61309450 AGATTGAGGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGC
1 AGATCGAAGATAGCAGATCTTGTCTTCCTATA-TTGGC-GTGAAGT
* *
61309496 AGATCGATGATGGCAGAT
1 AGATCGAAGATAGCAGAT
61309514 TTTACCTCCC
Statistics
Matches: 564, Mismatches: 130, Indels: 58
0.75 0.17 0.08
Matches are distributed among these distances:
42 3 0.01
43 106 0.19
44 323 0.57
45 103 0.18
46 29 0.05
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGT
Found at i:61308983 original size:132 final size:132
Alignment explanation
Indices: 61308746--61309429 Score: 1172
Period size: 132 Copynumber: 5.2 Consensus size: 132
61308736 GGATGGATTG
* *
61308746 AGATCGCAGAAAGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
* * *
61308811 ATCTTCCTATATTAGTAGGAAGTGGATCGAAGACGCAGATCTTGTCTTCCCATACTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
61308876 GT
131 GT
* *
61308878 AGATCGCAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
*
61308943 ATCTTCCTATATTGGTAGAAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
61309008 GT
131 GT
* *
61309010 AGATCGAAGAAGGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
1 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
61309075 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
61309140 GT
131 GT
* * *
61309142 AGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCT
1 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
61309207 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
66 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
61309272 GT
131 GT
* *
61309274 AGATC-ACAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAATTAGATCGAAGATAGCAGGTCC
1 AGATCGA-AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCC
* * * * *
61309338 TATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATACTGGTGGTGA
65 TATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGA
61309403 AGT
130 AGT
61309406 AGATCGAAGAAAGCAGATCTTGTC
1 AGATCGAAGAAAGCAGATCTTGTC
61309430 CCTGTATTTG
Statistics
Matches: 525, Mismatches: 25, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
131 1 0.00
132 523 1.00
133 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (132 bp):
AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCT
ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
GT
Found at i:61310506 original size:30 final size:31
Alignment explanation
Indices: 61310441--61310508 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
61310431 AAATCTATTC
*
61310441 TTTTTC-TTTTTCTTTTTTTCTCTGTTTGCA
1 TTTTTCTTTTTTCTTTTTTTCTCTATTTGCA
* * * *
61310471 GTTTTCTTTTTTCTTTTTTTTTTTATTT-TA
1 TTTTTCTTTTTTCTTTTTTTCTCTATTTGCA
61310501 TTTTTCTT
1 TTTTTCTT
61310509 CTCTTTCGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.79
Consensus pattern (31 bp):
TTTTTCTTTTTTCTTTTTTTCTCTATTTGCA
Found at i:61311333 original size:2 final size:2
Alignment explanation
Indices: 61311326--61311354 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61311316 AATGTTAAAC
61311326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61311355 AAATTCAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61311446 original size:24 final size:26
Alignment explanation
Indices: 61311419--61311480 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
61311409 TTTTTAATCA
61311419 ATATATCTACATA-CT-TATATTTTT
1 ATATATCTACATATCTATATATTTTT
*
61311443 ATATATGCTACA-ATCTATATGTTTTT
1 ATATAT-CTACATATCTATATATTTTT
* *
61311469 TTATATATACAT
1 ATATATCTACAT
61311481 GTATATACAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 7 0.23
25 11 0.35
26 13 0.42
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.52
Consensus pattern (26 bp):
ATATATCTACATATCTATATATTTTT
Found at i:61311704 original size:26 final size:24
Alignment explanation
Indices: 61311656--61311703 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
61311646 ACATATGCAC
61311656 ATACTTACATTTTTATTTTATATA
1 ATACTTACATTTTTATTTTATATA
*
61311680 ATACTTACAGTTTTT-TTCTATATA
1 ATACTTACA-TTTTTATTTTATATA
61311704 TGTATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.56
Consensus pattern (24 bp):
ATACTTACATTTTTATTTTATATA
Found at i:61322586 original size:25 final size:26
Alignment explanation
Indices: 61322556--61322618 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
61322546 TTTTTAATCA
61322556 ATATATCTACATA-CTTATAT-TTTTT
1 ATATATCTACATATC-TATATGTTTTT
61322581 ATATATGCTACA-ATCTATATGTTTTT
1 ATATAT-CTACATATCTATATGTTTTT
* *
61322607 TTATATATACAT
1 ATATATCTACAT
61322619 GTATATACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.52
Consensus pattern (26 bp):
ATATATCTACATATCTATATGTTTTT
Found at i:61322842 original size:26 final size:24
Alignment explanation
Indices: 61322794--61322841 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
61322784 ACATATGCAC
61322794 ATACTTACATTTTTATTTTATATA
1 ATACTTACATTTTTATTTTATATA
*
61322818 ATACTTACAGTTTTT-TTCTATATA
1 ATACTTACA-TTTTTATTTTATATA
61322842 TGTATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.56
Consensus pattern (24 bp):
ATACTTACATTTTTATTTTATATA
Found at i:61328110 original size:26 final size:25
Alignment explanation
Indices: 61328058--61328119 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
61328048 TCTAAAATCA
*
61328058 TAACAAAATTAACAATAAAACAATAG
1 TAACAAAA-TAACAACAAAACAATAG
* * *
61328084 TTATAAAATAACAACAAAATAAGTAG
1 TAACAAAATAACAACAAAACAA-TAG
61328110 TAACAAAATA
1 TAACAAAATA
61328120 GTGAAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.21
Consensus pattern (25 bp):
TAACAAAATAACAACAAAACAATAG
Found at i:61336522 original size:129 final size:129
Alignment explanation
Indices: 61336287--61336530 Score: 328
Period size: 129 Copynumber: 1.9 Consensus size: 129
61336277 TCAACAAAGA
* *
61336287 TGAGTCTCATTGATCCTAGCTTCAAAGTTTGCATCGCTACTTCTTCCTTTAAGTCCGATACACAA
1 TGAGCCTCATTGATCCTAGCTTCAAAGTTTGCATCGCTACTTCTTCCTCTAAGTCCGATACACAA
* * **
61336352 TTCACCTTTTCCTTAGATGGAAGCTTCGTCAACGACTCAACAAGCTCCGTAGCTTTCCTAGAAT
66 CTCACCTCTTCCTTAGATGGAAGCCCCGTCAACGACTCAACAAGCTCCGTAGCTTTCCTAGAAT
* * * * * *
61336416 TGAGCCTCATTGGTCTTAGCTTCAATGTTTGCATTGCTACTTCTTCCTCTAAGTTCGATGCACAA
1 TGAGCCTCATTGATCCTAGCTTCAAAGTTTGCATCGCTACTTCTTCCTCTAAGTCCGATACACAA
* ** *
61336481 CTCACCTCTTCCTTA-AGTGGAAGCCCCTTTGATGACTCAACAAGCTCCGT
66 CTCACCTCTTCCTTAGA-TGGAAGCCCCGTCAACGACTCAACAAGCTCCGT
61336531 CGTTGCCTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
128 1 0.01
129 97 0.99
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.34
Consensus pattern (129 bp):
TGAGCCTCATTGATCCTAGCTTCAAAGTTTGCATCGCTACTTCTTCCTCTAAGTCCGATACACAA
CTCACCTCTTCCTTAGATGGAAGCCCCGTCAACGACTCAACAAGCTCCGTAGCTTTCCTAGAAT
Found at i:61339455 original size:84 final size:84
Alignment explanation
Indices: 61339307--61339466 Score: 295
Period size: 84 Copynumber: 1.9 Consensus size: 84
61339297 TTTGATGCTC
61339307 GCTTTTCTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATTCAAAAGTGCTT
1 GCTTTTCTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATTCAAAAGTGCTT
61339372 TGAAGGTGACCTAATTCCT
66 TGAAGGTGACCTAATTCCT
*
61339391 GCTTTTGTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATTCCAAAA-TGCT
1 GCTTTTCTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATT-CAAAAGTGCT
61339455 TTGAAGGTGACC
65 TTGAAGGTGACC
61339467 CAAATATTCC
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
84 69 0.93
85 5 0.07
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (84 bp):
GCTTTTCTCAATCTCAATGGAGTTTTGTTTAAGGATCAAATTTGTTGCTTGATTCAAAAGTGCTT
TGAAGGTGACCTAATTCCT
Done.