Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 152 of 208
Found at i:46281245 original size:11 final size:11
Alignment explanation
Indices: 46281229--46281260 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
46281219 CTCTAATATT
46281229 CTCACAAATTC
1 CTCACAAATTC
46281240 CTCACAAATTC
1 CTCACAAATTC
*
46281251 CTCTCAAATT
1 CTCACAAATT
46281261 TCTATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (11 bp):
CTCACAAATTC
Found at i:46283114 original size:18 final size:18
Alignment explanation
Indices: 46283091--46283133 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
46283081 TGCTAGGTGC
* *
46283091 GTATCCTAGCCCTTCTAT
1 GTATCCTAACCCTTATAT
46283109 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
46283127 GTTTCCT
1 GTATCCT
46283134 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:46283379 original size:14 final size:14
Alignment explanation
Indices: 46283360--46283390 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
46283350 TATTTTGATA
46283360 TTATTTTGAATATT
1 TTATTTTGAATATT
46283374 TTATTTTGAATATT
1 TTATTTTGAATATT
46283388 TTA
1 TTA
46283391 ATATTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
TTATTTTGAATATT
Found at i:46283427 original size:49 final size:49
Alignment explanation
Indices: 46283368--46283568 Score: 330
Period size: 49 Copynumber: 4.1 Consensus size: 49
46283358 TATTATTTTG
* * *
46283368 AATATTTTATTTTGAATATTTTAATATTATTTGATGTAATAAAATACAA
1 AATAGTTTATTTTGAATATTTTGATATTATTTCATGTAATAAAATACAA
*
46283417 AATAGTTTATTTTGAATATTTTGATATTATTTGATGTAATAAAATACAA
1 AATAGTTTATTTTGAATATTTTGATATTATTTCATGTAATAAAATACAA
* *
46283466 AATAGTTTATTTTAAATATTTTGATATTATTTCATTTAATAAAATACAA
1 AATAGTTTATTTTGAATATTTTGATATTATTTCATGTAATAAAATACAA
* *
46283515 AATAGTTTATTTTGAATATTTTGATATTATTTCATTTAACAAAATACAA
1 AATAGTTTATTTTGAATATTTTGATATTATTTCATGTAATAAAATACAA
46283564 AATAG
1 AATAG
46283569 CTAATATTCT
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 145 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (49 bp):
AATAGTTTATTTTGAATATTTTGATATTATTTCATGTAATAAAATACAA
Found at i:46286999 original size:124 final size:124
Alignment explanation
Indices: 46286775--46287060 Score: 464
Period size: 124 Copynumber: 2.3 Consensus size: 124
46286765 CCCAAACATG
46286775 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * **
46286840 TTGAAGCGTTTTTATACAATTTTCTCAGAAACGTCAACTTGAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTATACAATTTGCTCACAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * *
46286899 CTATTGTAGCAAAAGTGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
46286964 TTGAAGCGTTTTTATACTATTTGCTCACAAACGTCAACTCAAAATTATTTTTTTAGGAC
66 TTGAAGCGTTTTTATACAATTTGCTCACAAACGTCAACTCAAAATTATTTTTTCAGGAC
* *
46287023 CTACTGTAGGAAAAGCACGTCCACGTGGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
46287061 CTTAATAAAT
Statistics
Matches: 147, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 147 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTTTATACAATTTGCTCACAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:46287415 original size:39 final size:40
Alignment explanation
Indices: 46287341--46287416 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
46287331 TACGTGGCAA
*
46287341 CAAAACGCGCCCTTGAGGGAGCGATTTTCGTCCACGTAAG
1 CAAAACGCGCCCTTCAGGGAGCGATTTTCGTCCACGTAAG
* *
46287381 CAAAGCGCGCCC-TCAGGGACGCGATTTTTG-CCACGT
1 CAAAACGCGCCCTTCAGGGA-GCGATTTTCGTCCACGT
46287417 CCCCTGACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 12 0.38
40 20 0.62
ACGTcount: A:0.22, C:0.30, G:0.28, T:0.20
Consensus pattern (40 bp):
CAAAACGCGCCCTTCAGGGAGCGATTTTCGTCCACGTAAG
Found at i:46288114 original size:19 final size:20
Alignment explanation
Indices: 46288073--46288123 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
46288063 CTGTTGGATG
46288073 AAAATTTTATATAATAAATTT
1 AAAATTTTATATAAT-AATTT
46288094 AAAATTTTA-AT-ATAATATT
1 AAAATTTTATATAATAAT-TT
*
46288113 AAAATATTATA
1 AAAATTTTATA
46288124 AATTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 12 0.44
20 3 0.11
21 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTTTATATAATAATTT
Found at i:46289618 original size:21 final size:19
Alignment explanation
Indices: 46289580--46289618 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
46289570 AATCTATATT
*
46289580 TCTCTTTATTTTATAATAA
1 TCTCTTTATTTAATAATAA
46289599 TCTCATTTATATTAATAATA
1 TCTC-TTTAT-TTAATAATA
46289619 TTGAATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TCTCTTTATTTAATAATAA
Found at i:46291003 original size:9 final size:8
Alignment explanation
Indices: 46290984--46291030 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 8
46290974 CCTGTTTAAC
46290984 TTTA-TTT
1 TTTATTTT
46290991 TTTATTATT
1 TTTATT-TT
46291000 TTTATTTT
1 TTTATTTT
46291008 TATTATTTCT
1 T-TTATTT-T
46291018 TTTATTTT
1 TTTATTTT
46291026 ATTTA
1 -TTTA
46291031 AAAAAAGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 4 0.11
8 5 0.14
9 24 0.69
10 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTATTTT
Found at i:46291009 original size:15 final size:16
Alignment explanation
Indices: 46290984--46291028 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
46290974 CCTGTTTAAC
46290984 TTTATTTTTTATTATT
1 TTTATTTTTTATTATT
46291000 TTTA-TTTTTATTATT
1 TTTATTTTTTATTATT
46291015 TCTT-TTATTTTATT
1 T-TTATT-TTTTATT
46291029 TAAAAAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 12 0.46
16 7 0.27
17 7 0.27
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTTTTATTATT
Found at i:46293718 original size:17 final size:17
Alignment explanation
Indices: 46293696--46293728 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46293686 GCATGCATAT
46293696 ATACATATAGATATAAC
1 ATACATATAGATATAAC
*
46293713 ATACATATATATATAA
1 ATACATATAGATATAA
46293729 ATAAGTTATA
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:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (17 bp):
ATACATATAGATATAAC
Found at i:46294101 original size:3 final size:3
Alignment explanation
Indices: 46294044--46294082 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
46294034 AACTAATACC
46294044 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46294083 CAAGATTAAT
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):
ATA
Found at i:46294763 original size:21 final size:20
Alignment explanation
Indices: 46294735--46294773 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
46294725 TGAGGAGAGC
*
46294735 CCAAATTTGGGTCAAAAATA
1 CCAAATTTGGGTAAAAAATA
*
46294755 CCAAGATTTTGGTAAAAAA
1 CCAA-ATTTGGGTAAAAAA
46294774 ACGGGCCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (20 bp):
CCAAATTTGGGTAAAAAATA
Found at i:46294771 original size:20 final size:20
Alignment explanation
Indices: 46294735--46294772 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46294725 TGAGGAGAGC
46294735 CCAAATTTGGGTCAAAAATA
1 CCAAATTTGGGTCAAAAATA
*
46294755 CCAAGATTTTGGT-AAAAA
1 CCAA-ATTTGGGTCAAAAA
46294773 AACGGGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
CCAAATTTGGGTCAAAAATA
Found at i:46295897 original size:37 final size:37
Alignment explanation
Indices: 46295836--46296018 Score: 316
Period size: 37 Copynumber: 5.0 Consensus size: 37
46295826 TACGTATGAT
* *
46295836 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
46295871 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
46295908 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
46295945 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
46295982 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
46296019 TAAAGCTATT
Statistics
Matches: 141, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
35 9 0.06
36 3 0.02
37 129 0.91
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:46296036 original size:46 final size:46
Alignment explanation
Indices: 46295982--46296355 Score: 295
Period size: 46 Copynumber: 7.6 Consensus size: 46
46295972 TAAGTGTAGC
* * **
46295982 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
46296028 TACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
46296074 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * * * *
46296126 CACTTATCACTTTCCACTTTCCACTTG-TCACTTGATCAG-ATAAG-TGTAGCTGAAG
1 CACTTATCAC-TT----TGT-CACTTGATCA---GATAAGTAT-AGCCGAAGCT--AT
**
46296181 CTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 C-A-CTT--ATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
46296231 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
46296277 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
46296329 CACTTATCACTTTTTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
46296356 AGTACTCAAA
Statistics
Matches: 269, Mismatches: 29, Indels: 60
0.75 0.08 0.17
Matches are distributed among these distances:
46 116 0.43
47 1 0.00
48 2 0.01
49 2 0.01
50 5 0.02
51 12 0.04
52 96 0.36
53 12 0.04
54 12 0.04
55 2 0.01
56 1 0.00
57 1 0.00
58 2 0.01
59 5 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:46296095 original size:52 final size:52
Alignment explanation
Indices: 46296029--46296349 Score: 378
Period size: 46 Copynumber: 6.2 Consensus size: 52
46296019 TAAAGCTATT
* *
46296029 ACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
1 ACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
*
46296082 ACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATC
1 ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
* *
46296134 ACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATC
1 AC--T----TTT-CACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
46296193 AC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
1 ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
*
46296239 AC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATC
1 ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
* * ** *
46296285 ACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATC
1 ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
46296337 ACTTTTTCACTTG
1 AC-TTTTCACTTG
46296350 ATCAGAAGTA
Statistics
Matches: 240, Mismatches: 14, Indels: 28
0.85 0.05 0.10
Matches are distributed among these distances:
46 88 0.37
50 1 0.00
52 83 0.35
53 17 0.07
54 1 0.00
58 3 0.01
59 47 0.20
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
ACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATC
Found at i:46296144 original size:59 final size:58
Alignment explanation
Indices: 46296071--46296197 Score: 218
Period size: 59 Copynumber: 2.2 Consensus size: 58
46296061 TAGCCGAAGC
*
46296071 TATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTT-TCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
46296130 TATCACTTTCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTT-CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
46296189 TATCACTTT
1 TATCACTTT
46296198 GTCACTTGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
58 1 0.02
59 64 0.98
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (58 bp):
TATCACTTTCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:46298504 original size:16 final size:16
Alignment explanation
Indices: 46298485--46298516 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
46298475 TTTGGGTTGT
*
46298485 TTTTTTTTTTTGTTTG
1 TTTTTTATTTTGTTTG
46298501 TTTTTTATTTTGTTTG
1 TTTTTTATTTTGTTTG
46298517 GGTTCATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.84
Consensus pattern (16 bp):
TTTTTTATTTTGTTTG
Found at i:46298861 original size:36 final size:37
Alignment explanation
Indices: 46298804--46298879 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
46298794 CACAATGGAG
46298804 AAAAAATATTTTTTTAATAGGTGGTC-GATGTGTCAAGT
1 AAAAAATA-TTTTTTAATAGGTGGTCAG-TGTGTCAAGT
46298842 AAAAAATA-TTTTTAATAGGTGGTCAGTGTGTCAAGT
1 AAAAAATATTTTTTAATAGGTGGTCAGTGTGTCAAGT
46298878 AA
1 AA
46298880 CATTGGTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 28 0.76
37 1 0.03
38 8 0.22
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (37 bp):
AAAAAATATTTTTTAATAGGTGGTCAGTGTGTCAAGT
Found at i:46300637 original size:20 final size:20
Alignment explanation
Indices: 46300588--46300628 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
46300578 TCTAGCCTAA
*
46300588 ACATCAACCAAACCACTCCC
1 ACATCAAACAAACCACTCCC
46300608 ACATCAAACAAACCACTCCC
1 ACATCAAACAAACCACTCCC
46300628 A
1 A
46300629 TATTAAACAT
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:0.44, C:0.46, G:0.00, T:0.10
Consensus pattern (20 bp):
ACATCAAACAAACCACTCCC
Found at i:46303489 original size:28 final size:28
Alignment explanation
Indices: 46303438--46303501 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
46303428 ATTTATATAC
46303438 TTTT-AAAATAATTTTAATGAA-TTTTAA
1 TTTTAAAAATAATTTTAAT-AATTTTTAA
*
46303465 TTTTAAAAATAAATTTTATATATTTTTTAA
1 TTTTAAAAAT-AATTTTA-ATAATTTTTAA
46303495 TTTTAAA
1 TTTTAAA
46303502 TAAATGCTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.12
28 5 0.16
29 8 0.25
30 15 0.47
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTTAAAAATAATTTTAATAATTTTTAA
Found at i:46320360 original size:24 final size:22
Alignment explanation
Indices: 46320319--46320383 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 22
46320309 ATTCTTCAAG
46320319 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
46320338 GATATGCAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
46320360 -ATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
46320381 GAT
1 GAT
46320384 TTTGTAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 13 0.33
21 19 0.49
22 7 0.18
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:46320365 original size:21 final size:19
Alignment explanation
Indices: 46320319--46320374 Score: 94
Period size: 19 Copynumber: 2.8 Consensus size: 19
46320309 ATTCTTCAAG
46320319 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46320338 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46320357 GATATATGCAATCTTAGA
1 G--ATATGCAATCTTAGA
46320375 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 20 0.57
21 15 0.43
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:46320439 original size:16 final size:16
Alignment explanation
Indices: 46320418--46320482 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
46320408 TTCGCTGTAT
46320418 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
46320434 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
46320450 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
46320466 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
46320482 T
1 T
46320483 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.38, C:0.06, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:46324209 original size:23 final size:22
Alignment explanation
Indices: 46324180--46324222 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
46324170 TACTTCACAC
*
46324180 ACATATATATTTTTCTTATATGT
1 ACATATATATGTTT-TTATATGT
46324203 ACATATATATGTTTTTATAT
1 ACATATATATGTTTTTATAT
46324223 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (22 bp):
ACATATATATGTTTTTATATGT
Found at i:46329145 original size:12 final size:12
Alignment explanation
Indices: 46329111--46329139 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
46329101 TTGGGCCTCG
46329111 AGGGATCATATA
1 AGGGATCATATA
46329123 AGGGATCATATA
1 AGGGATCATATA
46329135 AGGGA
1 AGGGA
46329140 CAATATGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.31, T:0.21
Consensus pattern (12 bp):
AGGGATCATATA
Found at i:46331858 original size:42 final size:42
Alignment explanation
Indices: 46331820--46331900 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
46331810 GAGTTTCCGT
46331820 TCAACTCTATCGAGCTTTTGTTTAACCCTTATGGGTTTCCAC
1 TCAACTCTATCGAGCTTTTGTTTAACCCTTATGGGTTTCCAC
* * * ** * *
46331862 TCAGCTTTTTCGAGCTTCCGTTCAACCCTTATGGTTTTC
1 TCAACTCTATCGAGCTTTTGTTTAACCCTTATGGGTTTC
46331901 TATTTAGCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.16, C:0.27, G:0.15, T:0.42
Consensus pattern (42 bp):
TCAACTCTATCGAGCTTTTGTTTAACCCTTATGGGTTTCCAC
Found at i:46340665 original size:30 final size:30
Alignment explanation
Indices: 46340643--46340744 Score: 138
Period size: 29 Copynumber: 3.5 Consensus size: 30
46340633 AGAGACTGCA
* *
46340643 ACAATGGCTTCCTTTTTAATAGAGATCGCC
1 ACAAAGGCTTCCTTTTTAATAGAGATAGCC
*
46340673 ATAAAGGCTTCC-TTTTAATAGAGATAGCC
1 ACAAAGGCTTCCTTTTTAATAGAGATAGCC
* *
46340702 ACAAAGGCTTCC--TTTAACAGAGATAGGC
1 ACAAAGGCTTCCTTTTTAATAGAGATAGCC
46340730 ACAAAGGCTTCCTTT
1 ACAAAGGCTTCCTTT
46340745 AAAAGAGATC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
28 26 0.41
29 27 0.42
30 11 0.17
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (30 bp):
ACAAAGGCTTCCTTTTTAATAGAGATAGCC
Found at i:46340726 original size:28 final size:28
Alignment explanation
Indices: 46340643--46340791 Score: 154
Period size: 28 Copynumber: 5.2 Consensus size: 28
46340633 AGAGACTGCA
* *
46340643 ACAATGGCTTCCTTTTTAATAGAGATCGCC
1 ACAAAGGCTTCC--TTTAATAGAGATAGCC
*
46340673 ATAAAGGCTTCCTTTTAATAGAGATAGCC
1 ACAAAGGCTTCC-TTTAATAGAGATAGCC
* *
46340702 ACAAAGGCTTCCTTTAACAGAGATAGGC
1 ACAAAGGCTTCCTTTAATAGAGATAGCC
* ***
46340730 ACAAAGGCTTCCTTTAAAAGAGATCTTC
1 ACAAAGGCTTCCTTTAATAGAGATAGCC
* * * *
46340758 ATAAAGACTTCCTTTAATAAATATAGCC
1 ACAAAGGCTTCCTTTAATAGAGATAGCC
46340786 ACAAAG
1 ACAAAG
46340792 ACTTACCTAT
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
28 63 0.63
29 27 0.27
30 10 0.10
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (28 bp):
ACAAAGGCTTCCTTTAATAGAGATAGCC
Found at i:46340739 original size:57 final size:57
Alignment explanation
Indices: 46340643--46340753 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 57
46340633 AGAGACTGCA
* * * * *
46340643 ACAATGGCTTCCTTTTTAATAGAGATCGCCATAAAGGCTTCCTTTTAATAGAGATAGCC
1 ACAAAGGCTTCC-TTTTAACAGAGATAGCCACAAAGGCTTCC-TTTAAAAGAGATAGCC
*
46340702 ACAAAGGCTTCC-TTTAACAGAGATAGGCACAAAGGCTTCCTTTAAAAGAGAT
1 ACAAAGGCTTCCTTTTAACAGAGATAGCCACAAAGGCTTCCTTTAAAAGAGAT
46340754 CTTCATAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 11 0.24
57 24 0.52
59 11 0.24
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (57 bp):
ACAAAGGCTTCCTTTTAACAGAGATAGCCACAAAGGCTTCCTTTAAAAGAGATAGCC
Found at i:46343302 original size:22 final size:22
Alignment explanation
Indices: 46343238--46343302 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
46343228 TACACACTGC
*
46343238 GTTGCGGATGAACCACCAGTAA
1 GTTGTGGATGAACCACCAGTAA
* * * ** *
46343260 TTTGTAGATAAACTGCTAGTAA
1 GTTGTGGATGAACCACCAGTAA
46343282 GTTGTGGATGAACCACCAGTA
1 GTTGTGGATGAACCACCAGTA
46343303 TTTGTATATT
Statistics
Matches: 30, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (22 bp):
GTTGTGGATGAACCACCAGTAA
Found at i:46349200 original size:41 final size:41
Alignment explanation
Indices: 46349097--46349289 Score: 183
Period size: 41 Copynumber: 4.6 Consensus size: 41
46349087 GTTACACGGT
* ** *
46349097 GGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCTG
1 GGAATCAGCACTTAGCAACCACCTTATAATC-AAGGATACTG
* *
46349139 GTGAAATCAGCACTTAGCAACCACCTTATAATCAATGATAATG
1 G-G-AATCAGCACTTAGCAACCACCTTATAATCAAGGATACTG
* * *
46349182 GGAATCAGCACATAGCAACC-CCTTTCACAATCAAGGATACGG
1 GGAATCAGCACTTAGCAACCACC-TT-ATAATCAAGGATACTG
* * *
46349224 TGGAATCGGCACTTAGCAACCACCTTATAATGAATGATACTG
1 -GGAATCAGCACTTAGCAACCACCTTATAATCAAGGATACTG
* * *
46349266 AGAATCAACACATAGCAACC-CCTT
1 GGAATCAGCACTTAGCAACCACCTT
46349290 TTTGATCAAT
Statistics
Matches: 124, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
40 6 0.05
41 35 0.28
42 26 0.21
43 29 0.23
44 28 0.23
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.22
Consensus pattern (41 bp):
GGAATCAGCACTTAGCAACCACCTTATAATCAAGGATACTG
Found at i:46349260 original size:84 final size:85
Alignment explanation
Indices: 46349129--46349290 Score: 254
Period size: 84 Copynumber: 1.9 Consensus size: 85
46349119 CTCATGTTCA
* * *
46349129 AAGGATCCTGGTGAAATCAGCACTTAGCAACCACCTTATAATCAATGATAATGGGAATCAGCACA
1 AAGGATACTGGTGAAATCAGCACTTAGCAACCACCTTATAATCAATGATAATGAGAATCAACACA
46349194 TAGCAACCCCTTTCACAATC
66 TAGCAACCCCTTTCACAATC
* * * *
46349214 AAGGATAC-GGTGGAATCGGCACTTAGCAACCACCTTATAATGAATGATACTGAGAATCAACACA
1 AAGGATACTGGTGAAATCAGCACTTAGCAACCACCTTATAATCAATGATAATGAGAATCAACACA
46349278 TAGCAACCCCTTT
66 TAGCAACCCCTTT
46349291 TTGATCAATG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 63 0.90
85 7 0.10
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (85 bp):
AAGGATACTGGTGAAATCAGCACTTAGCAACCACCTTATAATCAATGATAATGAGAATCAACACA
TAGCAACCCCTTTCACAATC
Found at i:46350190 original size:16 final size:17
Alignment explanation
Indices: 46350148--46350184 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
46350138 CCAAATTACC
46350148 AAAATA-CCC-AACTTA
1 AAAATACCCCTAACTTA
46350163 AAAATACCCCTAACTTA
1 AAAATACCCCTAACTTA
46350180 AAAAT
1 AAAAT
46350185 TTCCTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 3 0.15
17 11 0.55
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATACCCCTAACTTA
Found at i:46351266 original size:41 final size:40
Alignment explanation
Indices: 46351209--46351482 Score: 287
Period size: 41 Copynumber: 6.6 Consensus size: 40
46351199 GATCCCGGTC
46351209 GAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGG
1 GAATCAGCACTTAGCAACC-CCTTATAATCAATGATACGGG
* * * *
46351250 GAATCAACACATAGCAACCCCTTTCACAATCAAGGATACGGTG
1 GAATCAGCACTTAGCAACCCC-TT-ATAATCAATGATACGG-G
* * *
46351293 GAATCAGCACTTAGCAACCACCTTATAATCAATGATTCCGA
1 GAATCAGCACTTAGCAACC-CCTTATAATCAATGATACGGG
* * *
46351334 GAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGGTG
1 GAATCAGCACTTAGCAACCCC-TT-ATAATCAATGATACGG-G
* * *
46351377 GAATCGGCAGTTAGCAACCACCTTATAATCAATGATACGAG
1 GAATCAGCACTTAGCAACC-CCTTATAATCAATGATACGGG
* * * * *
46351418 GAATCAGCACATAGCAACCCCTTTTTGATCAATGATTCGAG
1 GAATCAGCACTTAGCAACCCC-TTATAATCAATGATACGGG
*
46351459 GAATCTGCACTTAGCAACCCCTTA
1 GAATCAGCACTTAGCAACCCCTTA
46351483 CATTCAAATA
Statistics
Matches: 192, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
40 8 0.04
41 91 0.47
42 51 0.27
43 38 0.20
44 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.22
Consensus pattern (40 bp):
GAATCAGCACTTAGCAACCCCTTATAATCAATGATACGGG
Found at i:46351317 original size:84 final size:84
Alignment explanation
Indices: 46351204--46351441 Score: 404
Period size: 84 Copynumber: 2.8 Consensus size: 84
46351194 CAAAGGATCC
* *
46351204 CGGTCGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
46351269 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* * *
46351288 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATTCCGAGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
46351353 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* * *
46351372 CGGTGGAATCGGCAGTTAGCAACCACCTTATAATCAATGATACGAGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
46351437 CCTTT
66 CCTTT
46351442 TTGATCAATG
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 143 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
CCTTTCACAATCAAGGATA
Found at i:46351423 original size:125 final size:125
Alignment explanation
Indices: 46351209--46351489 Score: 324
Period size: 125 Copynumber: 2.3 Consensus size: 125
46351199 GATCCCGGTC
* *
46351209 GAATCAGCACTTAGCAACCACC-TTATAATCAATGATACGGGGAATCAACACATAGCAACCCCTT
1 GAATCAGCACTTAGCAACC-CCTTTACAATCAAGGATACGGGGAATCAACACATAGCAACCCCTT
* *
46351273 TCACAATCAAGGATACGGTGGAATCAGCACTTAGCAACCACC-TTATAATCAATGATTCCGA-
65 TCACAATCAAGGATACGGAGGAATCAGCACATAGCAACC-CCTTTATAATCAATGATT-CGAG
* ** **
46351334 GAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGGTGGAATCGGCAGTTAGCAACCACC
1 GAATCAGCACTTAGCAACCCCTTT-ACAATCAAGGATACGG-GGAATCAACACATAGCAACC-CC
* * * *
46351399 -TT-ATAATCAATGATAC-GAGGAATCAGCACATAGCAACCCCTTTTTGATCAATGATTCGAG
63 TTTCACAATCAAGGATACGGAGGAATCAGCACATAGCAACCCCTTTATAATCAATGATTCGAG
* *
46351459 GAATCTGCACTTAGCAACCCC-TTACATTCAA
1 GAATCAGCACTTAGCAACCCCTTTACAATCAA
46351490 ATAATCTCGG
Statistics
Matches: 134, Mismatches: 16, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
123 7 0.05
124 9 0.07
125 72 0.54
126 26 0.19
127 18 0.13
128 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.22
Consensus pattern (125 bp):
GAATCAGCACTTAGCAACCCCTTTACAATCAAGGATACGGGGAATCAACACATAGCAACCCCTTT
CACAATCAAGGATACGGAGGAATCAGCACATAGCAACCCCTTTATAATCAATGATTCGAG
Found at i:46354485 original size:53 final size:53
Alignment explanation
Indices: 46354400--46354662 Score: 269
Period size: 53 Copynumber: 4.9 Consensus size: 53
46354390 AAAATTAAAT
* * *
46354400 TTCCTCATATGATTCCATAACCCACCAA-TTATGGTTTTACATGATATGGGCTTC
1 TTCC-CATATGATGCCATAACCCA-CAAGTTACGGTTTTACATGATATGGTCTTC
* *
46354454 TTCCCATATGATGCCATAACCCACAAGTTATGGTTTTACATGATATGGTTTTC
1 TTCCCATATGATGCCATAACCCACAAGTTACGGTTTTACATGATATGGTCTTC
* ** * * * * * *
46354507 TTCTCATATGATGTTATAACCCACCAGTTACGATCTTAAACGATATGGTATTC
1 TTCCCATATGATGCCATAACCCACAAGTTACGGTTTTACATGATATGGTCTTC
* * * *
46354560 TTTCCATATGATGCCATAACCCACTAGTTACGGTTTTACATGATATTGTC-CC
1 TTCCCATATGATGCCATAACCCACAAGTTACGGTTTTACATGATATGGTCTTC
* * * * * *
46354612 ATTCCCTTATGATGTCATAACTCACCAGTTACGATCTTACATGATATGGTC
1 -TTCCCATATGATGCCATAACCCACAAGTTACGGTTTTACATGATATGGTC
46354663 CTTAAATGTC
Statistics
Matches: 174, Mismatches: 33, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
52 4 0.02
53 166 0.95
54 4 0.02
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (53 bp):
TTCCCATATGATGCCATAACCCACAAGTTACGGTTTTACATGATATGGTCTTC
Found at i:46354589 original size:106 final size:106
Alignment explanation
Indices: 46354400--46354661 Score: 303
Period size: 106 Copynumber: 2.5 Consensus size: 106
46354390 AAAATTAAAT
* * * * * * **
46354400 TTCCTCATATGAT-TCCATAACCCACCAATTATGGTTTTACATGATATGGGCTTCTTCCCATATG
1 TTCC-CATATGATGT-CATAACCCACCAGTTACGATCTTAAACGATATGGTATTCTTCCCATATG
* **
46354464 ATGCCATAACCCACAAGTTATGGTTTTACATGATATGGTTTTC-
64 ATGCCATAACCCACAAGTTACGGTTTTACATGATATGG-TCCCA
* * *
46354507 TTCTCATATGATGTTATAACCCACCAGTTACGATCTTAAACGATATGGTATTCTTTCCATATGAT
1 TTCCCATATGATGTCATAACCCACCAGTTACGATCTTAAACGATATGGTATTCTTCCCATATGAT
* *
46354572 GCCATAACCCACTAGTTACGGTTTTACATGATATTGTCCCA
66 GCCATAACCCACAAGTTACGGTTTTACATGATATGGTCCCA
* * * *
46354613 TTCCCTTATGATGTCATAACTCACCAGTTACGATCTTACATGATATGGT
1 TTCCCATATGATGTCATAACCCACCAGTTACGATCTTAAACGATATGGT
46354662 CCTTAAATGT
Statistics
Matches: 131, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
105 2 0.02
106 125 0.95
107 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (106 bp):
TTCCCATATGATGTCATAACCCACCAGTTACGATCTTAAACGATATGGTATTCTTCCCATATGAT
GCCATAACCCACAAGTTACGGTTTTACATGATATGGTCCCA
Found at i:46357037 original size:29 final size:29
Alignment explanation
Indices: 46356995--46357052 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
46356985 CTTCTTCCGC
*
46356995 TTCCTCCATTCAATTGTTTATCATTCAGT
1 TTCCTCCATTCAATTATTTATCATTCAGT
46357024 TTCCTCCATTCAATTATTTATCATTCAGT
1 TTCCTCCATTCAATTATTTATCATTCAGT
46357053 ATTTATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.05, T:0.48
Consensus pattern (29 bp):
TTCCTCCATTCAATTATTTATCATTCAGT
Found at i:46362809 original size:30 final size:30
Alignment explanation
Indices: 46362775--46362835 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
46362765 TCTCAACACA
46362775 TTATATCATTCAGTCAAACATTCTCATATC
1 TTATATCATTCAGTCAAACATTCTCATATC
46362805 TTATATCATTCAGTCAAACATTCTCATATC
1 TTATATCATTCAGTCAAACATTCTCATATC
46362835 T
1 T
46362836 CATAACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (30 bp):
TTATATCATTCAGTCAAACATTCTCATATC
Found at i:46364615 original size:33 final size:33
Alignment explanation
Indices: 46364560--46364634 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 33
46364550 TGGCCCTGTC
** * * *
46364560 ATGGTCTTACGTTCATAGTGCCATA-ACCCAATT
1 ATGGTCTTACCATCAGAATGCCATAGA-CCAACT
*
46364593 ATGGTCTTACCATCAGAATGCCATAGACCAGCT
1 ATGGTCTTACCATCAGAATGCCATAGACCAACT
46364626 ATGGTCTTA
1 ATGGTCTTA
46364635 TATATATACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (33 bp):
ATGGTCTTACCATCAGAATGCCATAGACCAACT
Found at i:46372371 original size:24 final size:24
Alignment explanation
Indices: 46372344--46372389 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
46372334 AGAACAGTTC
*
46372344 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGGAAATGAAGGAGCAGCTT
* *
46372368 CAAAAGTAAATGAATGAGCAGC
1 CAAAAGGAAATGAAGGAGCAGC
46372390 AAAAAGTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.26, T:0.13
Consensus pattern (24 bp):
CAAAAGGAAATGAAGGAGCAGCTT
Found at i:46383427 original size:13 final size:13
Alignment explanation
Indices: 46383411--46383435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46383401 CCCTTTATGT
46383411 TTCTCCTTAAATG
1 TTCTCCTTAAATG
46383424 TTCTCCTTAAAT
1 TTCTCCTTAAAT
46383436 AACAAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.48
Consensus pattern (13 bp):
TTCTCCTTAAATG
Found at i:46384633 original size:13 final size:13
Alignment explanation
Indices: 46384601--46384625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46384591 ACATATCAAA
46384601 CTTACCATTCATT
1 CTTACCATTCATT
46384614 CTTACCATTCAT
1 CTTACCATTCAT
46384626 ATTTACCACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (13 bp):
CTTACCATTCATT
Found at i:46385181 original size:45 final size:44
Alignment explanation
Indices: 46385110--46385239 Score: 129
Period size: 45 Copynumber: 2.9 Consensus size: 44
46385100 TAATTCATCG
* * * * *
46385110 TTCCAAAG-AATGTCATGGCATTTTTCAACCATGGTCTTATGCAT
1 TTCCAAAGTAGTGTCATAGTATCTTTCAACTATGGTCTTAT-CAT
46385154 TTCCAAAGTAGTGTCATAGTATCTTTCAACTATGGTCTTGATCAT
1 TTCCAAAGTAGTGTCATAGTATCTTTCAACTATGGTCTT-ATCAT
* * * * *
46385199 TACCGATGT-GATGCCATAATATCTTTCAACTATGGTCTTAT
1 TTCCAAAGTAG-TGTCATAGTATCTTTCAACTATGGTCTTAT
46385240 TTGTATCAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 11 0.15
45 60 0.82
46 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (44 bp):
TTCCAAAGTAGTGTCATAGTATCTTTCAACTATGGTCTTATCAT
Found at i:46385262 original size:45 final size:44
Alignment explanation
Indices: 46385132--46385284 Score: 141
Period size: 45 Copynumber: 3.4 Consensus size: 44
46385122 TCATGGCATT
* * * * *
46385132 TTTCAACCATGGTCTTATGCATTTCCA-AAGTAGTGTCATAGTATC
1 TTTCAACTATGGTCTTAT-CA-TTACAGATGTAATGTCATAATATC
* * *
46385177 TTTCAACTATGGTCTTGATCATTACCGATGTGATGCCATAATATC
1 TTTCAACTATGGTCTT-ATCATTACAGATGTAATGTCATAATATC
*
46385222 TTTCAACTATGGTCTTAT-TTGTATCAGAT-TCAATGTCATAATATC
1 TTTCAACTATGGTCTTATCAT-TA-CAGATGT-AATGTCATAATATC
*
46385267 TTTCAACTATAGTCTTAT
1 TTTCAACTATGGTCTTAT
46385285 ATAGTTTTTA
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
43 1 0.01
44 8 0.09
45 79 0.88
46 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (44 bp):
TTTCAACTATGGTCTTATCATTACAGATGTAATGTCATAATATC
Found at i:46392539 original size:22 final size:22
Alignment explanation
Indices: 46392512--46392553 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
46392502 TTCTTTCTCC
46392512 TTCCTTCATTATTCTTTTTGTT
1 TTCCTTCATTATTCTTTTTGTT
** *
46392534 TTCCTTTGTTTTTCTTTTTG
1 TTCCTTCATTATTCTTTTTG
46392554 GTTGGAGTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (22 bp):
TTCCTTCATTATTCTTTTTGTT
Found at i:46393204 original size:22 final size:23
Alignment explanation
Indices: 46393176--46393233 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
46393166 TGTAACTCAC
46393176 TCACACGGGCA-TGTGCATCTTAT
1 TCACACGGGCAGTGTGCATCTT-T
*
46393199 T-ACACGGG-AGTGTGCCTCTTT
1 TCACACGGGCAGTGTGCATCTTT
46393220 TCACACGGGC-GTGT
1 TCACACGGGCAGTGT
46393234 AGACCTCCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.10
22 27 0.87
23 1 0.03
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (23 bp):
TCACACGGGCAGTGTGCATCTTT
Found at i:46396952 original size:6 final size:6
Alignment explanation
Indices: 46396943--46396971 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
46396933 GTCTAAGAAA
46396943 ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
46396972 ATGAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:46397196 original size:5 final size:5
Alignment explanation
Indices: 46397109--46397186 Score: 52
Period size: 5 Copynumber: 14.6 Consensus size: 5
46397099 ATAAGAATAA
* * *
46397109 AAAAT AAAAT AAAAT AGATTAGT AAAAT AAAAAT ATATAAT ATAA- CAAAT
1 AAAAT AAAAT AAAAT A-A--AAT AAAAT -AAAAT A-A-AAT AAAAT AAAAT
46397159 AATAA- AAAAT AAAAT AAAAT AAAAT AAA
1 AA-AAT AAAAT AAAAT AAAAT AAAAT AAA
46397187 GGAAATGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
4 4 0.07
5 37 0.64
6 9 0.16
7 5 0.09
8 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:46409022 original size:12 final size:12
Alignment explanation
Indices: 46409005--46409034 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
46408995 CCTCACGCGC
46409005 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
46409017 CCGTGTGTTAGG
1 CCGTGTGCTAGG
46409029 CCGTGT
1 CCGTGT
46409035 AACAACCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.23, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:46410077 original size:30 final size:30
Alignment explanation
Indices: 46410037--46410178 Score: 124
Period size: 30 Copynumber: 4.7 Consensus size: 30
46410027 GATGGTTAAT
* * *
46410037 CTATCTCTTTTCGTAATTTGATAATTGAAG
1 CTATCCCTTTTCATAATTTGATAGTTGAAG
* * * * **
46410067 TTATCCCTTTTCATAGTTCGACAGTCAAAG
1 CTATCCCTTTTCATAATTTGATAGTTGAAG
*
46410097 CTATCCCTTTTCATAATTTGATAGCTGAAG
1 CTATCCCTTTTCATAATTTGATAGTTGAAG
* * **
46410127 CTATCCCTTTTCATAAATCGATAGCCGAAG
1 CTATCCCTTTTCATAATTTGATAGTTGAAG
* *
46410157 CCATCCCTCTTCA-AAGTTTGAT
1 CTATCCCTTTTCATAA-TTTGAT
46410179 GGTCGTCACA
Statistics
Matches: 88, Mismatches: 23, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
29 2 0.02
30 86 0.98
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.38
Consensus pattern (30 bp):
CTATCCCTTTTCATAATTTGATAGTTGAAG
Found at i:46410163 original size:60 final size:60
Alignment explanation
Indices: 46410043--46410178 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 60
46410033 TAATCTATCT
* * * ** * *
46410043 CTTTTCGTAATTTGATAATTGAAGTTATCCCTTTTCATAGTTCGACAGTCAAAGCTATCC
1 CTTTTCATAATTTGATAACTGAAGCTATCCCTTTTCATAAATCGACAGCCAAAGCCATCC
* * *
46410103 CTTTTCATAATTTGATAGCTGAAGCTATCCCTTTTCATAAATCGATAGCCGAAGCCATCC
1 CTTTTCATAATTTGATAACTGAAGCTATCCCTTTTCATAAATCGACAGCCAAAGCCATCC
*
46410163 CTCTTCA-AAGTTTGAT
1 CTTTTCATAA-TTTGAT
46410179 GGTCGTCACA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.03
60 62 0.97
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (60 bp):
CTTTTCATAATTTGATAACTGAAGCTATCCCTTTTCATAAATCGACAGCCAAAGCCATCC
Found at i:46410460 original size:16 final size:15
Alignment explanation
Indices: 46410441--46410483 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
46410431 GAATCATTCT
46410441 ATTCAATTTAACTAAA
1 ATTCAATTTAA-TAAA
46410457 ATTCACATTTTAATAAA
1 ATTCA-A-TTTAATAAA
46410474 ATTACAATTT
1 ATT-CAATTT
46410484 TGCCCCTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 8 0.33
17 9 0.38
18 7 0.29
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTCAATTTAATAAA
Found at i:46414932 original size:16 final size:16
Alignment explanation
Indices: 46414911--46414942 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46414901 ACTCATTTTA
46414911 GAGAAATTGTAGTTGT
1 GAGAAATTGTAGTTGT
46414927 GAGAAATTGTAGTTGT
1 GAGAAATTGTAGTTGT
46414943 ACTTTGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (16 bp):
GAGAAATTGTAGTTGT
Found at i:46418241 original size:15 final size:15
Alignment explanation
Indices: 46418221--46418297 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
46418211 TTATGGAAAG
*
46418221 TCAAATATATGGTTA
1 TCAAATATATGGATA
*
46418236 TCAAATA-ATGGAAA
1 TCAAATATATGGATA
* *
46418250 GTCAAAGATATGGGTA
1 -TCAAATATATGGATA
*
46418266 TCAAATAT-TGGAAAA
1 TCAAATATATGG-ATA
* *
46418281 TCAAAGATATGGGTA
1 TCAAATATATGGATA
46418296 TC
1 TC
46418298 GAGATATTGG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
14 8 0.17
15 31 0.66
16 8 0.17
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (15 bp):
TCAAATATATGGATA
Found at i:46418249 original size:30 final size:30
Alignment explanation
Indices: 46418213--46418297 Score: 134
Period size: 30 Copynumber: 2.8 Consensus size: 30
46418203 ATCTGTATTT
* *
46418213 ATGGAAAGTCAAATATATGGTTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
46418243 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
46418273 TTGGAAAATCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
46418298 GAGATATTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.27
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:46422881 original size:15 final size:15
Alignment explanation
Indices: 46422861--46422932 Score: 58
Period size: 15 Copynumber: 4.8 Consensus size: 15
46422851 TTATGGAAAG
*
46422861 TCAAATATATGGTTA
1 TCAAATATATGGATA
*
46422876 TCAAATA-ATGGAAA
1 TCAAATATATGGATA
* *
46422890 GTCAAAGATATGGGTA
1 -TCAAATATATGGATA
*
46422906 TCAAATAT-TGGAAAA
1 TCAAATATATGG-ATA
*
46422921 TCAAAGATATGG
1 TCAAATATATGG
46422933 GTATTGAGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
14 8 0.18
15 28 0.64
16 8 0.18
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (15 bp):
TCAAATATATGGATA
Found at i:46422889 original size:30 final size:30
Alignment explanation
Indices: 46422853--46422936 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
46422843 ATCTGTATTT
* *
46422853 ATGGAAAGTCAAATATATGGTTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
46422883 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
46422913 TTGGAAAATCAAAGATATGGGTAT
1 ATGGAAAGTCAAAGATATGGGTAT
46422937 TGAGATATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:46429164 original size:35 final size:35
Alignment explanation
Indices: 46429120--46429202 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 35
46429110 GCGCTGGCCG
* *
46429120 GTAATATCGACAATAAATATGTCTAGCACTAGTCA
1 GTAAAATCGACAATAAATATGTCCAGCACTAGTCA
*
46429155 GTAAAATCGACAATAAATGTGTCCAGCACTAGTCA
1 GTAAAATCGACAATAAATATGTCCAGCACTAGTCA
* *
46429190 GTATAACCGACAA
1 GTAAAATCGACAA
46429203 ATCGAGTGCC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (35 bp):
GTAAAATCGACAATAAATATGTCCAGCACTAGTCA
Found at i:46438411 original size:49 final size:50
Alignment explanation
Indices: 46438326--46438433 Score: 114
Period size: 49 Copynumber: 2.2 Consensus size: 50
46438316 TTTCCTATGC
* * * ** *
46438326 GCTAGTGATAGTGGCACTCTGATGCAATTTAGTAA-TTTCGCACTTTGGT
1 GCTAATGATAGTGGCACTCCGATACAATCCAGTAATTTTCACACTTTGGT
* * *
46438375 GCTAATGATAGTGGCACTCCGATACAGTCCATTAATTTTTACACTTTGGT
1 GCTAATGATAGTGGCACTCCGATACAATCCAGTAATTTTCACACTTTGGT
46438425 G-TAA-GATAG
1 GCTAATGATAG
46438434 CGTATGCACG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
48 5 0.10
49 31 0.63
50 13 0.27
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (50 bp):
GCTAATGATAGTGGCACTCCGATACAATCCAGTAATTTTCACACTTTGGT
Found at i:46447423 original size:21 final size:23
Alignment explanation
Indices: 46447399--46447442 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
46447389 GAAATAAAAC
*
46447399 TCAAAAAAAGTT-TAAAT-TATT
1 TCAAAAAAAATTATAAATATATT
46447420 TCAAAAAAAATTATAAATATATT
1 TCAAAAAAAATTATAAATATATT
46447443 CAACTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 5 0.25
23 4 0.20
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (23 bp):
TCAAAAAAAATTATAAATATATT
Found at i:46452796 original size:18 final size:18
Alignment explanation
Indices: 46452764--46452798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46452754 TTGTTTATCG
**
46452764 CTCCAAAAGTGCTTTTGC
1 CTCCAAAAGAACTTTTGC
46452782 CTCCAAAAGAACTTTTG
1 CTCCAAAAGAACTTTTG
46452799 AAACGCAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (18 bp):
CTCCAAAAGAACTTTTGC
Found at i:46458630 original size:88 final size:88
Alignment explanation
Indices: 46458481--46458658 Score: 266
Period size: 88 Copynumber: 2.0 Consensus size: 88
46458471 CCACGAGGTG
* * * *
46458481 TGGCATGGTGGTTATTCCCCTTGTGCCTCAACCATGTAGTTGAAAGTTCAACCTTGTTCATGGGA
1 TGGCATGGTGGCTATTCCCCTTATGCCTCAACCATGTAGTTGAAAGTTCAACCTCGCTCATGGGA
* * *
46458546 ATGTAACACATTTTGTGGCTGGT
66 ATGGAACACATTTTGCGGCTAGT
* *
46458569 TGGCATGGTGGCTATTCTCCTTATGCCTCAACCATGTAGTTGAGAGTTCAACCTCGCTCATGGGA
1 TGGCATGGTGGCTATTCCCCTTATGCCTCAACCATGTAGTTGAAAGTTCAACCTCGCTCATGGGA
*
46458634 ATGGAATACATTTTGCGGCTAGT
66 ATGGAACACATTTTGCGGCTAGT
46458657 TG
1 TG
46458659 TTTTATCTCT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (88 bp):
TGGCATGGTGGCTATTCCCCTTATGCCTCAACCATGTAGTTGAAAGTTCAACCTCGCTCATGGGA
ATGGAACACATTTTGCGGCTAGT
Found at i:46462955 original size:33 final size:34
Alignment explanation
Indices: 46462918--46463003 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 34
46462908 CTATGTTTGC
* *
46462918 TGTGTTGGTTGGATT-AGCTCTTATGAGTAT-TGG
1 TGTGTTGGTTGGATTGA-CTCGTATGAGCATCTGG
** *
46462951 TGTGTTGGAGGGATTGACTCGTGTGAGCATCTGG
1 TGTGTTGGTTGGATTGACTCGTATGAGCATCTGG
*
46462985 TGTGTTTGGTTGGAATGAC
1 TGTG-TTGGTTGGATTGAC
46463004 GATGTAATCT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
33 23 0.55
34 8 0.19
35 11 0.26
ACGTcount: A:0.15, C:0.08, G:0.37, T:0.40
Consensus pattern (34 bp):
TGTGTTGGTTGGATTGACTCGTATGAGCATCTGG
Found at i:46467941 original size:16 final size:15
Alignment explanation
Indices: 46467919--46467961 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
46467909 CATGGTTCTA
46467919 TATTTTTTTAATTTT
1 TATTTTTTTAATTTT
*
46467934 TAATTTTTTTTACTTTT
1 T-A-TTTTTTTAATTTT
*
46467951 TATTATTTTAA
1 TATTTTTTTAA
46467962 AAGCATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 13 0.57
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTTTTAATTTT
Found at i:46474096 original size:21 final size:21
Alignment explanation
Indices: 46474050--46474096 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
46474040 AATTCATAAT
46474050 TTAT-TTTTAAAAAATATGAA
1 TTATATTTTAAAAAATATGAA
** * *
46474070 AAATATTTTCAAAAATATTAA
1 TTATATTTTAAAAAATATGAA
46474091 TTATAT
1 TTATAT
46474097 AAAACTTCAT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TTATATTTTAAAAAATATGAA
Found at i:46477642 original size:41 final size:41
Alignment explanation
Indices: 46477493--46477642 Score: 194
Period size: 41 Copynumber: 3.6 Consensus size: 41
46477483 CATTGAATGT
* ** * *
46477493 AAGGGGTTGCTAAGTGCAGATTACCTGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATCAAA
* *
46477534 AAGGGGTTGTTAAGTGCAGATTCCCCTTAAAAAT-TGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCC--AAAACTCTGATCAAA
*
46477576 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATAAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATCAAA
*
46477617 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCAGATTCCCC
46477643 GAATTATTAA
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
40 5 0.05
41 55 0.58
42 33 0.35
43 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATCAAA
Found at i:46477682 original size:83 final size:83
Alignment explanation
Indices: 46477493--46477674 Score: 215
Period size: 83 Copynumber: 2.2 Consensus size: 83
46477483 CATTGAATGT
* ** * * * *
46477493 AAGGGGTTGCTAAGTGCAGATTACCTGAATCACTGATCAAAAAGGGGTTGTTAAGTGCAGATTCC
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATAAAAAAGGGGTTGCTAAGTGCAGATTCC
* *
46477558 CCTTAAAAATTGATCAAA
66 CCTGAAAAATTAATCAAA
*
46477576 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATAAAAAAGGGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATAAAAAAGGGGTTGCTAAGTGCAGATTCC
** *
46477641 CC-GAATTATTAATTC-TA
66 CCTGAAAAATTAA-TCAAA
46477658 AAGGTGGTTGCTAAGTG
1 AAGG-GGTTGCTAAGTG
46477675 TTGATTCCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
82 11 0.13
83 73 0.87
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (83 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTGATAAAAAAGGGGTTGCTAAGTGCAGATTCC
CCTGAAAAATTAATCAAA
Found at i:46477760 original size:41 final size:41
Alignment explanation
Indices: 46477493--46477765 Score: 153
Period size: 41 Copynumber: 6.6 Consensus size: 41
46477483 CATTGAATGT
* * * *
46477493 AAGGGGTTGCTAAGTGCAGATTACCTGAATCACTG-ATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGAAT-ATA
* * * ** * *
46477534 AAGGGGTTGTTAAGTGCAGATTCCCCTTAAAAATTG-ATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCC-GAATCACTGAAT-ATA
* * * * *
46477576 AAGGGGTTGCTAAGTGCAGATTCCCCAAAACTCTG-ATAAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGAAT-ATA
* * *
46477617 AAGGGGTTGCTAAGTGCTGATTCCCCGAATTA-TTAATTCTA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGAA-TATA
* ** * * *
46477658 AAGGTGGTTGCTAAGTGTTGATTCCATTGTATC-CTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGAATCAC-TGAATAT-A
* * * *
46477702 AAAGGGTTGTTATGTGCTGATTCCCCGTATCACTGAATAT-
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGAATATA
46477742 AAGGTGGTTGCTAAGTGCTGATTC
1 AAGG-GGTTGCTAAGTGCTGATTC
46477766 TACCGAGTAA
Statistics
Matches: 182, Mismatches: 40, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
40 4 0.02
41 83 0.46
42 66 0.36
43 23 0.13
44 6 0.03
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGAATATA
Found at i:46481215 original size:18 final size:17
Alignment explanation
Indices: 46481194--46481241 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
46481184 AAAATAAAAA
46481194 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAA-TGAAT
*
46481212 AACGATTTGTAAATGAAT
1 AACGTTTTG-AAATGAAT
**
46481230 AATATTTTGAAA
1 AACGTTTTGAAA
46481242 ACAAGCGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (17 bp):
AACGTTTTGAAATGAAT
Found at i:46481490 original size:22 final size:22
Alignment explanation
Indices: 46481465--46481511 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
46481455 AGAATTTCTT
* *
46481465 CATTCTACTCTCTATGTTGCGA
1 CATTCAACCCTCTATGTTGCGA
* *
46481487 CATTGAACCCTCTGTGTTGCGA
1 CATTCAACCCTCTATGTTGCGA
46481509 CAT
1 CAT
46481512 AGTGACCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (22 bp):
CATTCAACCCTCTATGTTGCGA
Found at i:46489413 original size:489 final size:489
Alignment explanation
Indices: 46488495--46489471 Score: 1765
Period size: 489 Copynumber: 2.0 Consensus size: 489
46488485 GTTTGGGGTA
* *
46488495 TTGACTTTCTTGGTCCTTTCCCTCCGTTTTTTGGTCATAAGTACATATTAGTAGCAGTAGACTAT
1 TTGACTTTCTCGGTCCTTTCCCTCCGTCTTTTGGTCATAAGTACATATTAGTAGCAGTAGACTAT
46488560 ATGTCTAAATGGGCTGAGGCAGAGGCATATCCGACAAACGATGCTAAGGTTGTAATGAAGTTTTT
66 ATGTCTAAATGGGCTGAGGCAGAGGCATATCCGACAAACGATGCTAAGGTTGTAATGAAGTTTTT
*
46488625 GCAGAAACATGTGTTCATAAGGTTTGGAACCCCAAGAGCCATCATCAGTGATGAAGGATCCCACT
131 GCAGAAACATATGTTCATAAGGTTTGGAACCCCAAGAGCCATCATCAGTGATGAAGGATCCCACT
46488690 TTGTGAACAAGTGATTGAAATGGTTATTAGATAAACATGAAGTGAAACACAAGGTCACTACAGCT
196 TTGTGAACAAGTGATTGAAATGGTTATTAGATAAACATGAAGTGAAACACAAGGTCACTACAGCT
* * *
46488755 TATCATCTGTAGACGAATGGGCAAGCTGAACTGGCAAACAAGGAGATCAAAGGCATACTTGAGAA
261 TACCATCTGTAGACGAATGGACAAGCTGAACTGGCAAACAAAGAGATCAAAGGCATACTTGAGAA
*
46488820 GGTAGTTTGCCCGAACAGACGAGATTGGTCCAAAAGACTGGATGATGCTTTATGGGCTTACAAGA
326 GGTAGTTTGCCCGAACAGACGAGATTGGTCCAAAAGACTGAATGATGCTTTATGGGCTTACAAGA
* *
46488885 CAGCATACAAGACACCTTTAGGGACGTCACCTTATAGGTTAGTCTTTGGGAAAGCCTGCCATCTA
391 CAGCATACAAGACACCTTTAGGGACGTCACCCTATAGGTTAGTCCTTGGGAAAGCCTGCCATCTA
46488950 CCCTTGGAGTTAGAACACAAAGCTTATTGGGCTG
456 CCCTTGGAGTTAGAACACAAAGCTTATTGGGCTG
*
46488984 TTGACTTTCTCGGTCCTTTCCCTCCGTCTTTTGGTCATAAGTACATATTATTAGCAGTAGACTAT
1 TTGACTTTCTCGGTCCTTTCCCTCCGTCTTTTGGTCATAAGTACATATTAGTAGCAGTAGACTAT
* *
46489049 ATGTCTAAGTGGGCTGAGGCAGAGGCATATCCGACAAATGATGCTAAGGTTGTAATGAAGTTTTT
66 ATGTCTAAATGGGCTGAGGCAGAGGCATATCCGACAAACGATGCTAAGGTTGTAATGAAGTTTTT
* *
46489114 GCAGAAACATATGTTTATAGGGTTTGGAACCCCAAGAGCCATCATCAGTGATGAAGGATCCCACT
131 GCAGAAACATATGTTCATAAGGTTTGGAACCCCAAGAGCCATCATCAGTGATGAAGGATCCCACT
*
46489179 TTGTGAACAAGTGATTGAAATGGTTATTAGATAAACATGAAGTGAAACACAAGGTCGCTACAGCT
196 TTGTGAACAAGTGATTGAAATGGTTATTAGATAAACATGAAGTGAAACACAAGGTCACTACAGCT
*
46489244 TACCATCTGTAGACGAATGGACAAGTTGAACTGGCAAACAAAGAGATCAAAGGCATACTTGAGAA
261 TACCATCTGTAGACGAATGGACAAGCTGAACTGGCAAACAAAGAGATCAAAGGCATACTTGAGAA
* * * *
46489309 GGTAGTTTGCCCGAACTGACGAGATTGGTCCAAAAGACTGAATGATTCTTTGTGGGCTTATAAGA
326 GGTAGTTTGCCCGAACAGACGAGATTGGTCCAAAAGACTGAATGATGCTTTATGGGCTTACAAGA
*
46489374 CAGCATACAAGACACCTTTAGGGATGTCACCCTATAGGTTAGTCCTTGGGAAAGCCTGCCATCTA
391 CAGCATACAAGACACCTTTAGGGACGTCACCCTATAGGTTAGTCCTTGGGAAAGCCTGCCATCTA
46489439 CCCTTGGAGTTAGAACACAAAGCTTATTGGGCT
456 CCCTTGGAGTTAGAACACAAAGCTTATTGGGCT
46489472 CTCCAACGAC
Statistics
Matches: 467, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
489 467 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (489 bp):
TTGACTTTCTCGGTCCTTTCCCTCCGTCTTTTGGTCATAAGTACATATTAGTAGCAGTAGACTAT
ATGTCTAAATGGGCTGAGGCAGAGGCATATCCGACAAACGATGCTAAGGTTGTAATGAAGTTTTT
GCAGAAACATATGTTCATAAGGTTTGGAACCCCAAGAGCCATCATCAGTGATGAAGGATCCCACT
TTGTGAACAAGTGATTGAAATGGTTATTAGATAAACATGAAGTGAAACACAAGGTCACTACAGCT
TACCATCTGTAGACGAATGGACAAGCTGAACTGGCAAACAAAGAGATCAAAGGCATACTTGAGAA
GGTAGTTTGCCCGAACAGACGAGATTGGTCCAAAAGACTGAATGATGCTTTATGGGCTTACAAGA
CAGCATACAAGACACCTTTAGGGACGTCACCCTATAGGTTAGTCCTTGGGAAAGCCTGCCATCTA
CCCTTGGAGTTAGAACACAAAGCTTATTGGGCTG
Found at i:46490284 original size:16 final size:15
Alignment explanation
Indices: 46490251--46490292 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
46490241 AAATGATAAT
46490251 TATTAATATATAATTA
1 TATTAAT-TATAATTA
*
46490267 TATTCATTATAATATA
1 TATTAATTATAAT-TA
46490283 TATTAATTAT
1 TATTAATTAT
46490293 TATCAGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:46506110 original size:31 final size:31
Alignment explanation
Indices: 46506072--46506134 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
46506062 AGTTGGTAAG
46506072 TTAATTTACTTATCACATACAAGGCTAGACA
1 TTAATTTACTTATCACATACAAGGCTAGACA
46506103 TTAATTTACTTATCACATACAAGGCTAGACA
1 TTAATTTACTTATCACATACAAGGCTAGACA
46506134 T
1 T
46506135 GGCTTTTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (31 bp):
TTAATTTACTTATCACATACAAGGCTAGACA
Found at i:46517380 original size:15 final size:15
Alignment explanation
Indices: 46517347--46517379 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
46517337 CATCCATTAA
46517347 TTTTCCTTTCTTTTT
1 TTTTCCTTTCTTTTT
46517362 TTTTCCTTT-TTTTT
1 TTTTCCTTTCTTTTT
46517376 TTTT
1 TTTT
46517380 TTTGCTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTCCTTTCTTTTT
Found at i:46517761 original size:15 final size:14
Alignment explanation
Indices: 46517720--46517769 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
46517710 ATTTTTAGAA
*
46517720 AAAAAATTT-AATT
1 AAAATATTTAAATT
*
46517733 AAAAT-GTTAAATT
1 AAAATATTTAAATT
46517746 AAAATATTTAAAATT
1 AAAATATTT-AAATT
*
46517761 ATAATATTT
1 AAAATATTT
46517770 TGGTTTCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 13 0.43
14 2 0.07
15 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
AAAATATTTAAATT
Found at i:46527195 original size:27 final size:27
Alignment explanation
Indices: 46527165--46527221 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
46527155 GAGGAACAGG
* **
46527165 TATAAAAATTTAATTTTGTGGTGAAGT
1 TATAAAAACTTAATTTTGTGAAGAAGT
*
46527192 TATAAAAACTTGATTTTGTGAAGAAGT
1 TATAAAAACTTAATTTTGTGAAGAAGT
46527219 TAT
1 TAT
46527222 CTGCAGGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.42
Consensus pattern (27 bp):
TATAAAAACTTAATTTTGTGAAGAAGT
Found at i:46527344 original size:184 final size:184
Alignment explanation
Indices: 46527035--46527401 Score: 716
Period size: 184 Copynumber: 2.0 Consensus size: 184
46527025 ACTACATGAA
46527035 TATCTGCAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAACAATACCT
1 TATCTGCAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAACAATACCT
*
46527100 ACCTTGCCACATGTGACCATAGGGTGTGTATTAGTTGGTATAGAAATTGGACTTTGAGGAACAGG
66 ACCTTGCCACATGTGACCATAGGGTGTGTATTAATTGGTATAGAAATTGGACTTTGAGGAACAGG
46527165 TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAGT
131 TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAGT
46527219 TATCTGCAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAACAATACCT
1 TATCTGCAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAACAATACCT
*
46527284 GCCTTGCCACATGTGACCATAGGGTGTGTATTAATTGGTATAGAAATTGGACTTTGAGGAACAGG
66 ACCTTGCCACATGTGACCATAGGGTGTGTATTAATTGGTATAGAAATTGGACTTTGAGGAACAGG
46527349 TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAG
131 TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAG
46527402 GTATAGAATA
Statistics
Matches: 181, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 181 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (184 bp):
TATCTGCAGGATTAGAAGGTATATTGGTTGCTATATATGCATTCAATTAAGGTTTAACAATACCT
ACCTTGCCACATGTGACCATAGGGTGTGTATTAATTGGTATAGAAATTGGACTTTGAGGAACAGG
TATAAAAATTTAATTTTGTGGTGAAGTTATAAAAACTTGATTTTGTGAAGAAGT
Found at i:46527482 original size:27 final size:27
Alignment explanation
Indices: 46527346--46527495 Score: 178
Period size: 27 Copynumber: 5.6 Consensus size: 27
46527336 TTTGAGGAAC
* * * *
46527346 AGGTATAAAAATTTAATTTTGTGGTGA
1 AGGTATAGAAACTTGATTTTGTGATGA
* * *
46527373 AGTTATAAAAACTTGATTTTGTGAAGA
1 AGGTATAGAAACTTGATTTTGTGATGA
46527400 AGGTATAGAATA-TTGATTTTGTGATGA
1 AGGTATAGAA-ACTTGATTTTGTGATGA
* * *
46527427 AGGTATGGAAAATTGATTTTGTGAAGA
1 AGGTATAGAAACTTGATTTTGTGATGA
46527454 AGGTATAGAAACTTGATTTTGT-AGTGA
1 AGGTATAGAAACTTGATTTTGTGA-TGA
46527481 AGGTATAGAAACTTG
1 AGGTATAGAAACTTG
46527496 TGAAGGCAAC
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.02
27 104 0.97
28 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (27 bp):
AGGTATAGAAACTTGATTTTGTGATGA
Found at i:46531607 original size:45 final size:45
Alignment explanation
Indices: 46531523--46531674 Score: 173
Period size: 45 Copynumber: 3.4 Consensus size: 45
46531513 TATGGTATTA
* ** *
46531523 AGCTATGGTCTTACTCAT-TTCTATCAG-GATGGCAGAGCATCTTTC
1 AGCTATGGTCTTACTCATCTT-TAT-GGTGATACCATAGCATCTTTC
* * * *
46531568 AACTATGGTTTTACTCATCTTTATGGTGATGCCATAGCATCTTTT
1 AGCTATGGTCTTACTCATCTTTATGGTGATACCATAGCATCTTTC
* *
46531613 AGCTATGGTCTTACACATCTTTATGGTGATACCATAGCATTTTTC
1 AGCTATGGTCTTACTCATCTTTATGGTGATACCATAGCATCTTTC
*
46531658 AGCTAAGGTCTTACTCA
1 AGCTATGGTCTTACTCA
46531675 ATTTAAACGT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.01
45 88 0.97
46 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (45 bp):
AGCTATGGTCTTACTCATCTTTATGGTGATACCATAGCATCTTTC
Found at i:46533365 original size:43 final size:42
Alignment explanation
Indices: 46533258--46533375 Score: 109
Period size: 43 Copynumber: 2.8 Consensus size: 42
46533248 GATTTGAGAT
* *
46533258 TTACATGTAAGACCATGTCTGGGACA-TCGACATCGTATACGA
1 TTACATGTAAGACCACGTCTGGGACAGT-GGCATCGTATACGA
* * * *
46533300 TTTCGTGTAAGACC-CTGCCTGGGACAGTGGCATCG-ATAGTTGA
1 TTACATGTAAGACCAC-GTCTGGGACAGTGGCATCGTATA--CGA
46533343 TTACATGTAAGACCACGTCTGGGAC-GTTGGCAT
1 TTACATGTAAGACCACGTCTGGGACAG-TGGCAT
46533376 TGTAAGAGCT
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
41 3 0.05
42 28 0.46
43 29 0.48
44 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (42 bp):
TTACATGTAAGACCACGTCTGGGACAGTGGCATCGTATACGA
Found at i:46534843 original size:2 final size:2
Alignment explanation
Indices: 46534836--46534876 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
46534826 GTTAATGTCG
46534836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46534877 TAATGTTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46535996 original size:26 final size:26
Alignment explanation
Indices: 46535960--46536017 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
46535950 GATAAAGGTG
*
46535960 AACTGAATAAGGACTATATCGAAATC
1 AACTAAATAAGGACTATATCGAAATC
46535986 AACTAAATAAGGACTATATCGAAATC
1 AACTAAATAAGGACTATATCGAAATC
46536012 AACTAA
1 AACTAA
46536018 CTTGTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (26 bp):
AACTAAATAAGGACTATATCGAAATC
Found at i:46541546 original size:3 final size:3
Alignment explanation
Indices: 46541538--46541622 Score: 116
Period size: 3 Copynumber: 28.3 Consensus size: 3
46541528 TTTCTATCAT
* * * * * *
46541538 TTC TTC TTC TTC TAC TAC TTC TAC TTC TAC TTC GTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
46541586 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
46541623 CAAAGAGCAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.05, C:0.32, G:0.01, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:46550519 original size:55 final size:55
Alignment explanation
Indices: 46550454--46550679 Score: 254
Period size: 55 Copynumber: 3.9 Consensus size: 55
46550444 ACGTGCTACG
* *
46550454 TAACAATCGATTTAAACATATAAAAAATCGATTCAAAATAAGTAGTATTCTAACA
1 TAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGTAGTATTCCAACA
* ** * *
46550509 TAATAATCGATTTAAATGTATAAACAATCGATTCAAAAGCAGTAGTATTCCAACA
1 TAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGTAGTATTCCAACA
* * * *
46550564 TAACAATCAATTTAAACATATAAAAAATTGATTCAAAAGAAGAAGAAGAAGAAGTATTCCACCA
1 TAACAATCGATTTAAACATATAAAAAATCGATTC--------AA-AAGAAGTAGTATTCCAACA
* *
46550628 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGTAATATTCCA
1 TAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGTAGTATTCCA
46550680 CAAATTAAGA
Statistics
Matches: 141, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
55 90 0.64
56 2 0.01
63 2 0.01
64 47 0.33
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (55 bp):
TAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGTAGTATTCCAACA
Found at i:46559034 original size:7 final size:7
Alignment explanation
Indices: 46559022--46559048 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
46559012 GTTATTTTTT
46559022 AAAATTA
1 AAAATTA
46559029 AAAATTA
1 AAAATTA
46559036 AAAATTA
1 AAAATTA
46559043 AAAATT
1 AAAATT
46559049 TTGGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATTA
Found at i:46568717 original size:20 final size:20
Alignment explanation
Indices: 46568692--46568732 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
46568682 ATCCTTCAAC
* *
46568692 TTAATCTTATTCAGCTTTGT
1 TTAATCTCATTCAACTTTGT
46568712 TTAATCTCATTCAACTTTGT
1 TTAATCTCATTCAACTTTGT
46568732 T
1 T
46568733 CTATTTTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (20 bp):
TTAATCTCATTCAACTTTGT
Found at i:46571663 original size:9 final size:9
Alignment explanation
Indices: 46571651--46571687 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
46571641 ATAATATCAA
46571651 AAATTAAAT
1 AAATTAAAT
46571660 AAATTAAAT
1 AAATTAAAT
46571669 AAA-TAAAT
1 AAATTAAAT
*
46571677 -AATAAAAT
1 AAATTAAAT
46571685 AAA
1 AAA
46571688 CAAACAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
7 2 0.08
8 9 0.36
9 14 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAATTAAAT
Found at i:46573525 original size:17 final size:17
Alignment explanation
Indices: 46573498--46573530 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
46573488 TCACTATATT
46573498 TTTATTTCACATATTCAC
1 TTTATTTCACA-ATTCAC
46573516 TTTA-TTCACAATTCA
1 TTTATTTCACAATTCA
46573531 TAAAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTCACAATTCAC
Found at i:46573777 original size:51 final size:51
Alignment explanation
Indices: 46573720--46573820 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
46573710 TTACTTTTCT
46573720 AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATTC
1 AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATTC
46573771 AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATT
1 AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATT
46573821 TTGTAACACC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.42
Consensus pattern (51 bp):
AACACTTTTATATCACTATTCACTTCATTTAAACCTTTAATCACAATATTC
Found at i:46574916 original size:39 final size:39
Alignment explanation
Indices: 46574873--46574971 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
46574863 CACATTCAGT
** *
46574873 TTTAAGCATATATCACGTTACACATGTAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
46574912 TTTAAGCATATATCACAATACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
46574951 TTCAAGCATATATCATAATAC
1 TTTAAGCATATATCACAATAC
46574972 TCAAAAACAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACATAACA
Found at i:46575235 original size:14 final size:14
Alignment explanation
Indices: 46575216--46575247 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
46575206 CAAAATCATT
46575216 GTACATATAGGTAA
1 GTACATATAGGTAA
46575230 GTACATATAGGTAA
1 GTACATATAGGTAA
46575244 GTAC
1 GTAC
46575248 TTACAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (14 bp):
GTACATATAGGTAA
Found at i:46577227 original size:16 final size:15
Alignment explanation
Indices: 46577202--46577245 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
46577192 GGGAGATTTC
46577202 TTTTCTTTTTTCCATAT
1 TTTTC-TTTTTCC-TAT
*
46577219 TTTTCTTTTTCCTTT
1 TTTTCTTTTTCCTAT
46577234 TCTTTCTTTTTC
1 T-TTTCTTTTTC
46577246 TCCCTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 17 0.68
17 5 0.20
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTTTTTCCTAT
Found at i:46582778 original size:22 final size:22
Alignment explanation
Indices: 46582747--46582800 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
46582737 ATACATATAT
46582747 TATATTATATG-AGTGGGTCTTAC
1 TATA-TATATGCA-TGGGTCTTAC
*
46582770 TATATATATGCATGGGTCTTAT
1 TATATATATGCATGGGTCTTAC
46582792 TATATATAT
1 TATATATAT
46582801 TATAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (22 bp):
TATATATATGCATGGGTCTTAC
Found at i:46583194 original size:18 final size:18
Alignment explanation
Indices: 46583158--46583226 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
46583148 GTGTAATATT
* * *
46583158 GTGAACCATGTTAACTTG
1 GTGAACTATATTAATTTG
* *
46583176 GTGAATTATATTATTTTG
1 GTGAACTATATTAATTTG
* *
46583194 GCGAACTATGTTAATTTG
1 GTGAACTATATTAATTTG
* *
46583212 GTGATCTGTATTAAT
1 GTGAACTATATTAAT
46583227 ATGACGAAAT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (18 bp):
GTGAACTATATTAATTTG
Found at i:46583951 original size:17 final size:16
Alignment explanation
Indices: 46583931--46584005 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 16
46583921 TATTATTCGG
46583931 TATGAACTGATATTTCA
1 TATGAACT-ATATTTCA
**
46583948 TATGAACTATTATTTTG
1 TATGAACTA-TATTTCA
* * **
46583965 CATGAGCTATCATTTGG
1 TATGAACTAT-ATTTCA
*
46583982 TATGAACTGTTATTTCA
1 TATGAACT-ATATTTCA
46583999 TATGAAC
1 TATGAAC
46584006 AAATTTTTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
16 2 0.04
17 42 0.93
18 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (16 bp):
TATGAACTATATTTCA
Found at i:46583961 original size:51 final size:51
Alignment explanation
Indices: 46583897--46584005 Score: 157
Period size: 51 Copynumber: 2.1 Consensus size: 51
46583887 TATGATGGAG
* * *
46583897 TATGAATTGTTATTTTGCAT-AGACTATTATTCGGTATGAACTGATATTTCA
1 TATGAACTATTATTTTGCATGAG-CTATCATTCGGTATGAACTGATATTTCA
* *
46583948 TATGAACTATTATTTTGCATGAGCTATCATTTGGTATGAACTGTTATTTCA
1 TATGAACTATTATTTTGCATGAGCTATCATTCGGTATGAACTGATATTTCA
46583999 TATGAAC
1 TATGAAC
46584006 AAATTTTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
51 50 0.96
52 2 0.04
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (51 bp):
TATGAACTATTATTTTGCATGAGCTATCATTCGGTATGAACTGATATTTCA
Found at i:46585695 original size:101 final size:101
Alignment explanation
Indices: 46585473--46585676 Score: 338
Period size: 101 Copynumber: 2.0 Consensus size: 101
46585463 ATGCATTTGT
46585473 ATCATTCAAGAGCATATGCATGTAGTTATTTTAGTCACAAAACTATAATCATATTTTATTGATAT
1 ATCATTCAAGAGCATATGCATGTAGTTATTTTAGTCACAAAACTATAATCATATTTTATTGATAT
*
46585538 CATAATAACATTTGCAGTTGTTTATGAAGCATTCGC
66 CATAATAACATTTGCAGCTGTTTATGAAGCATTCGC
* ** *
46585574 ATCATTCAAGAGCATATGCATGTGGTTATTTTAGTCATGAAACTATAATCATATTTTATTGTTAT
1 ATCATTCAAGAGCATATGCATGTAGTTATTTTAGTCACAAAACTATAATCATATTTTATTGATAT
*
46585639 CATAATAACATTTGCA-CTGCTTTATGAAGCATTTGC
66 CATAATAACATTTGCAGCTG-TTTATGAAGCATTCGC
46585675 AT
1 AT
46585677 TATCTTGGAT
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 2 0.02
101 94 0.98
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (101 bp):
ATCATTCAAGAGCATATGCATGTAGTTATTTTAGTCACAAAACTATAATCATATTTTATTGATAT
CATAATAACATTTGCAGCTGTTTATGAAGCATTCGC
Found at i:46586155 original size:30 final size:27
Alignment explanation
Indices: 46586121--46586200 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 27
46586111 ATTGTCGAAG
46586121 TTCTGGTTTTGCCTAGTAAGTCCTTTCAAA
1 TTCTGGTTTTGCCTAG---GTCCTTTCAAA
*
46586151 TTCTGGTTTCT-CCTAGGTTCTTTCCAATA
1 TTCTGGTTT-TGCCTAGGTCCTTT-CAA-A
*
46586180 TTTCTGGTTCTGCCTAGGTCC
1 -TTCTGGTTTTGCCTAGGTCC
46586201 GTTGTTGAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
27 6 0.14
28 3 0.07
29 2 0.05
30 30 0.71
31 1 0.02
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (27 bp):
TTCTGGTTTTGCCTAGGTCCTTTCAAA
Found at i:46586169 original size:90 final size:89
Alignment explanation
Indices: 46585943--46586242 Score: 302
Period size: 90 Copynumber: 3.3 Consensus size: 89
46585933 TTCTGAAATC
* * * *
46585943 CTGGTTTCGCCTAGTAAGTCCTTTCAAATTCTGGTTCCACCCAAGTTCATTTCGAGATTTATAGT
1 CTGGTTTTGCCTAGTAAGTCCTTTCAAATTCTGGTTTCACCCAGGTTC-TTTCGAAATTTATAGT
* * *
46586008 TTCGCCCAAGTCCATTATCAAAGTT
65 TTTGCCCAAGTCCATTGTCGAAGTT
* * * *
46586033 ATGGTTTCAT-CC-AGTAAGTCCTTTCAAATTCTTG-TTCGGCCCAGGTT-TGTTCTGAAAGTTA
1 CTGGTTT--TGCCTAGTAAGTCCTTTCAAATTCTGGTTTC-ACCCAGGTTCT-TTC-GAAATTTA
46586094 TAGTTTTGCCCAAGTCCATTGTCGAAGTT
61 TAGTTTTGCCCAAGTCCATTGTCGAAGTT
* * * * *
46586123 CTGGTTTTGCCTAGTAAGTCCTTTCAAATTCTGGTTTCTCCTAGGTTCTTTCCAATATTTCTGGT
1 CTGGTTTTGCCTAGTAAGTCCTTTCAAATTCTGGTTTCACCCAGGTTCTTTCGAA-ATTTATAGT
* * * * *
46586188 TCTGCCTAGGTCCGTTGTTGAAGTT
65 TTTGCCCAAGTCCATTGTCGAAGTT
* *
46586213 TTGGTTTTGCCTAGTAAGTCCTTTGAAATT
1 CTGGTTTTGCCTAGTAAGTCCTTTCAAATT
46586243 TTGATTTCGC
Statistics
Matches: 174, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
88 2 0.01
89 9 0.05
90 157 0.90
91 6 0.03
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (89 bp):
CTGGTTTTGCCTAGTAAGTCCTTTCAAATTCTGGTTTCACCCAGGTTCTTTCGAAATTTATAGTT
TTGCCCAAGTCCATTGTCGAAGTT
Found at i:46586275 original size:90 final size:90
Alignment explanation
Indices: 46586102--46586311 Score: 221
Period size: 90 Copynumber: 2.3 Consensus size: 90
46586092 TATAGTTTTG
* * * *
46586102 CCCAAGTCCATTGTCGAAGTTCTGGTTTTGCCTAGTAAGTCCTTTCAAATTCTGGTTTCTCCTAG
1 CCCAGGTCCATTGTCGAAGTTTTGGTTTTGCCTAGTAAGTCCTTTCAAATTCTGATTTCGCCTAG
* * *
46586167 GTTCTTTCCAATATTTCTGG-TTCTG
66 CTTCTTTCCAATAGTTCTGGTTTC-A
* * * * *
46586192 CCTAGGTCCGTTGTTGAAGTTTTGGTTTTGCCTAGTAAGTCCTTTGAAATTTTGATTTCG-CTCA
1 CCCAGGTCCATTGTCGAAGTTTTGGTTTTGCCTAGTAAGTCCTTTCAAATTCTGATTTCGCCT-A
* *
46586256 -CTTCTATTGTCGA-AGTTCTGGTTTCA
65 GCTTCT-TT-CCAATAGTTCTGGTTTCA
*
46586282 CCCAGGTCTATTGTCGAAGTTTTGGTTTTG
1 CCCAGGTCCATTGTCGAAGTTTTGGTTTTG
46586312 TCCAGGTCCA
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
89 6 0.06
90 87 0.89
91 5 0.05
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.43
Consensus pattern (90 bp):
CCCAGGTCCATTGTCGAAGTTTTGGTTTTGCCTAGTAAGTCCTTTCAAATTCTGATTTCGCCTAG
CTTCTTTCCAATAGTTCTGGTTTCA
Found at i:46586333 original size:30 final size:29
Alignment explanation
Indices: 46586261--46586345 Score: 98
Period size: 30 Copynumber: 2.9 Consensus size: 29
46586251 GCTCACTTCT
* ** *
46586261 ATTGTCGAAGTTCTGGTTTCACCCAGGTCT
1 ATTGTCGAAGTT-TTGTTTTGCCCAGGTCC
*
46586291 ATTGTCGAAGTTTTGGTTTTGTCCAGGTCC
1 ATTGTCGAAGTTTT-GTTTTGCCCAGGTCC
*
46586321 ATTGTTGAAGTTTTGTTTTGCCCAG
1 ATTGTCGAAGTTTTGTTTTGCCCAG
46586346 TAACTTCTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 11 0.23
30 36 0.77
ACGTcount: A:0.15, C:0.18, G:0.25, T:0.42
Consensus pattern (29 bp):
ATTGTCGAAGTTTTGTTTTGCCCAGGTCC
Found at i:46586482 original size:29 final size:30
Alignment explanation
Indices: 46586425--46586488 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
46586415 AGAATTTCTA
46586425 GTTTCACCCAGGTCCATTGTTAAAGTTTTG
1 GTTTCACCCAGGTCCATTGTTAAAGTTTTG
* *
46586455 GTTTCA-CCAGGTCTATTTTTCAAA-TTTTG
1 GTTTCACCCAGGTCCATTGTT-AAAGTTTTG
46586484 GTTTC
1 GTTTC
46586489 GTCCAGTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (30 bp):
GTTTCACCCAGGTCCATTGTTAAAGTTTTG
Found at i:46586841 original size:78 final size:78
Alignment explanation
Indices: 46586753--46586896 Score: 182
Period size: 78 Copynumber: 1.8 Consensus size: 78
46586743 GTCAAACTTG
* * * * **
46586753 TTTTCAAAAATAGGTTGAGCCTGGGGATTGTTATTGAGGTCCTTTTAGTGTTTTTTCA-TTTTAT
1 TTTTCAAAAATAGGTTGAACCTCGAGATTGTCATCAAGGTCCTTTTAGT-TTTTTTCATTTTTAT
46586817 TAGGGTTGAATTCA
65 TAGGGTTGAATTCA
* * * *
46586831 TTTTCGAAAATGGGTTGAACCTCGAGATTGTCGTCAAGGTCGTTTTAGTTTTTTTCATTTTTATT
1 TTTTCAAAAATAGGTTGAACCTCGAGATTGTCATCAAGGTCCTTTTAGTTTTTTTCATTTTTATT
46586896 A
66 A
46586897 AAAGTTAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 8 0.15
78 47 0.85
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.47
Consensus pattern (78 bp):
TTTTCAAAAATAGGTTGAACCTCGAGATTGTCATCAAGGTCCTTTTAGTTTTTTTCATTTTTATT
AGGGTTGAATTCA
Found at i:46586956 original size:79 final size:77
Alignment explanation
Indices: 46586786--46586960 Score: 197
Period size: 79 Copynumber: 2.2 Consensus size: 77
46586776 GGGATTGTTA
** * * * *
46586786 TTGAGGTCCTTTTAGTGTTTTTTCATTTTATTAGGGTTGAATTCATTTTCGAAAATGGGTTGAAC
1 TTGAGGTCCTTTTAGT-TTTTTTCATTTTATTAAAGTTAAATCCATTTCCAAAAATGGGTTGAAC
* *
46586851 CTCGAGATTGTCG
65 CACGAGATTGCCG
** * * *
46586864 TCAAGGTCGTTTTAGTTTTTTTCATTTTTATTAAAAGTTAAATCCATTTCCAAAAATGGTTTGAG
1 TTGAGGTCCTTTTAGTTTTTTTCA-TTTTATT-AAAGTTAAATCCATTTCCAAAAATGGGTTGAA
46586929 CCACGAGATTGCCG
64 CCACGAGATTGCCG
*
46586943 TTGAGTTCCTTTTAGTTT
1 TTGAGGTCCTTTTAGTTT
46586961 AATTTTGTCA
Statistics
Matches: 78, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
77 8 0.10
78 20 0.26
79 50 0.64
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (77 bp):
TTGAGGTCCTTTTAGTTTTTTTCATTTTATTAAAGTTAAATCCATTTCCAAAAATGGGTTGAACC
ACGAGATTGCCG
Found at i:46588722 original size:24 final size:24
Alignment explanation
Indices: 46588689--46588740 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
46588679 TTCGTAAGTC
** *
46588689 AAATAAATTATGTTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
46588713 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
46588737 AAAT
1 AAAT
46588741 TTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:46589105 original size:16 final size:15
Alignment explanation
Indices: 46589080--46589110 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
46589070 CCCATATTAG
46589080 TTTTTTTTATAAAAT
1 TTTTTTTTATAAAAT
46589095 TTTTATTTTATAAAAT
1 TTTT-TTTTATAAAAT
46589111 AAATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTTTTATAAAAT
Found at i:46590014 original size:32 final size:32
Alignment explanation
Indices: 46589973--46590037 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
46589963 AAACTTCATA
46589973 ATCTGCAAGGGAGAGGGAAAGAGAGATTTCTT
1 ATCTGCAAGGGAGAGGGAAAGAGAGATTTCTT
46590005 ATCTGCAAGGGAGAGGGAAAGAGAGATTTCTT
1 ATCTGCAAGGGAGAGGGAAAGAGAGATTTCTT
46590037 A
1 A
46590038 CCTGAGTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.09, G:0.34, T:0.22
Consensus pattern (32 bp):
ATCTGCAAGGGAGAGGGAAAGAGAGATTTCTT
Found at i:46590820 original size:16 final size:15
Alignment explanation
Indices: 46590795--46590829 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
46590785 TCTGATGTGA
46590795 GAAAAGTACAGTGTT
1 GAAAAGTACAGTGTT
46590810 GAAATAGTACAGTGTT
1 GAAA-AGTACAGTGTT
46590826 GAAA
1 GAAA
46590830 CAAGCACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.26
Consensus pattern (15 bp):
GAAAAGTACAGTGTT
Found at i:46598532 original size:14 final size:15
Alignment explanation
Indices: 46598513--46598564 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
46598503 GTTAGCGAAC
46598513 AAAATAAATAAATA-
1 AAAATAAATAAATAT
* *
46598527 AAAATAAACATATAT
1 AAAATAAATAAATAT
*
46598542 AAAATAAAATAAAAAT
1 AAAAT-AAATAAATAT
*
46598558 AGAATAA
1 AAAATAA
46598565 TTTATATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 12 0.40
15 7 0.23
16 11 0.37
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAAATAAATAT
Found at i:46599278 original size:10 final size:10
Alignment explanation
Indices: 46599236--46599286 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
46599226 ATTAGCGAAC
46599236 AAAATAAATA
1 AAAATAAATA
*
46599246 AATATAAATA
1 AAAATAAATA
* *
46599256 AACATATAT-
1 AAAATAAATA
46599265 AAAATAAATA
1 AAAATAAATA
46599275 AAAATAGAATA
1 AAAATA-AATA
46599286 A
1 A
46599287 TTTATATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 7 0.21
10 22 0.65
11 5 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (10 bp):
AAAATAAATA
Found at i:46599801 original size:724 final size:726
Alignment explanation
Indices: 46598372--46599827 Score: 2546
Period size: 724 Copynumber: 2.0 Consensus size: 726
46598362 AAGTGTATCT
46598372 AGGGTTGAGTGGTCACCAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
1 AGGGTTGAGTGGTCACCAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
* *
46598437 TGCAGACTTAGAGACATAATTTTTCCTATTCAATTTTTTTTGTGTTTTCTTTGTTGGACAAAACA
66 TACAGACTTAGAGACATAATTTTTCCTATTCAA---TTTTTGTGTTTTCTTTGTTGGAAAAAACA
*
46598502 CGTTAGCGAACAAAATAAATAAATAAAAATAAACATATATAAAATAAAATAAAAATAGAATAATT
128 CATTAGCGAACAAAATAAATAAATAAAAATAAACATATATAAAATAAAATAAAAATAGAATAATT
* *
46598567 TATATTTAATTTTTCAAATACGAAAAATAATCAAAACCGTAACAAAAGTTGAAATCAAAAGGGAG
193 TATATTTAATTTTTCAAATACGAAAAACAATCAAAACCATAACAAAAGTTGAAATCAAAAGGGAG
46598632 AATAGAGATTTTACTAAATGTTTAGGCCTATTAAAAAAATTTCCTTAAGACATATTCATTCACTC
258 AATAGAGATTTTACTAAATGTTTAGGCCTATTAAAAAAATTTCCTTAAGACATATTCATTCACTC
*
46598697 CTATGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAGGATACAACAAGAACAATGACCAAAGT
323 CTATGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAGGATACAACAAGAACAATGACCAAAGC
* * * *
46598762 AGTAGCACCTCTGCAGCGATCTACGAACAAACGATGTCTTTTTCTATCATCGGAACATTTGAAAA
388 AGTAGCACATCTACAGCGATCAACGAACAAACGACGTCTTTTTCTATCATCGGAACATTTGAAAA
*
46598827 ATATAGAGAGGAAAAGAAAAGTTTTGAGAGAAAAAAAATTTCGGTGTGAAATAATATTAGAGTGT
453 ATATAGAGAGGAAAAGAAAAGTTTTGAGAGAAAAAAAATTTCGGTGTGAAAGAATATTAGAGTGT
*
46598892 CTAATACTACAGAATTTGTAGCCTTTTATAGGCATTGGGAATGTTGAAATTTTGGAAATTTTCCA
518 CTAATACTACAGAATTTGTAGCCTTTTATAGGCATTGAGAATGTTGAAATTTTGGAAATTTTCCA
46598957 CAAAATCTGCCATTAATGAACAAATAAATCAAATTTGATTTAAAGATTAAATCAAATTGATTGGA
583 CAAAATCTGCCATTAATGAACAAATAAATCAAATTTGATTTAAAGATTAAATCAAATTGATTGGA
* *
46599022 ATCAAATAAATAATATAAATGTCCTTATATAAACAGATAATGTAGGAAAAATAATTTTGTGTTGA
648 ATCAAATAAATAAGATAAATGTCATTATATAAACAGATAATGTAGGAAAAATAATTTTGTGTTGA
46599087 GCTAAAATATCCGC
713 GCTAAAATATCCGC
46599101 AGGGTTGAGTGGTCACCAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
1 AGGGTTGAGTGGTCACCAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
*
46599166 TACAGACTTAGAGACATAATTTTTCCTATTCAA-TTTT-T-TTTTCTTTGTTGGAAAAAATACAT
66 TACAGACTTAGAGACATAATTTTTCCTATTCAATTTTTGTGTTTTCTTTGTTGGAAAAAACACAT
*
46599228 TAGCGAACAAAATAAATAAATATAAATAAACATATATAAAAT-AAATAAAAATAGAATAATTTAT
131 TAGCGAACAAAATAAATAAATAAAAATAAACATATATAAAATAAAATAAAAATAGAATAATTTAT
46599292 ATTTAATTTTTCAAATACGAAAAACAATCAAAACCATAACAAAAGTTGAAATCAAAAGGGAGAAT
196 ATTTAATTTTTCAAATACGAAAAACAATCAAAACCATAACAAAAGTTGAAATCAAAAGGGAGAAT
*
46599357 AGAGATTTTACTAAATGTTTAGGCCTCTTAAAAACAATTTCCTTAAGACATATTCATTCACTCCT
261 AGAGATTTTACTAAATGTTTAGGCCTATTAAAAA-AATTTCCTTAAGACATATTCATTCACTCCT
46599422 ATGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAGGATACAACAAGAACAATGACCAAAGCAG
325 ATGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAGGATACAACAAGAACAATGACCAAAGCAG
*
46599487 TAGCACATCTATAGCGATCAACGAACAAACGACGTCTTTTTCTATCA-CTGGAACATTT-AACAA
390 TAGCACATCTACAGCGATCAACGAACAAACGACGTCTTTTTCTATCATC-GGAACATTTGAA-AA
* * *
46599550 ATATAGAGAGGAAAAAGAAAAGTTTTGAGAGAAACAGAATTTTGGTGTGAAAGAATATTAGAGTG
453 ATATAGAGAGG-AAAAGAAAAGTTTTGAGAGAAAAAAAATTTCGGTGTGAAAGAATATTAGAGTG
* *
46599615 TCTAATACTGCAGAATTTGTAGTCTTTTATAGGCATTGAGAATGTTGAAATTTTGGAAATTTTCC
517 TCTAATACTACAGAATTTGTAGCCTTTTATAGGCATTGAGAATGTTGAAATTTTGGAAATTTTCC
* * * *
46599680 ACAAAATCTGTCATTAATGAGCAAATAAATCAAATTTGATTTAAAGATTAAATCAATTTTATTGG
582 ACAAAATCTGCCATTAATGAACAAATAAATCAAATTTGATTTAAAGATTAAATCAAATTGATTGG
*
46599745 AATCAAATAAATAAGATAAATGTCATTATATAAACAGATTATGTAGGAAAAATAATTTTGTGTTG
647 AATCAAATAAATAAGATAAATGTCATTATATAAACAGATAATGTAGGAAAAATAATTTTGTGTTG
*
46599810 AGCTAAAATATCTGC
712 AGCTAAAATATCCGC
46599825 AGG
1 AGG
46599828 TCCACTCTAG
Statistics
Matches: 694, Mismatches: 29, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
722 121 0.17
723 220 0.32
724 252 0.36
725 4 0.01
729 97 0.14
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (726 bp):
AGGGTTGAGTGGTCACCAAGTAGCTCATTGTCTATATAAGCAACCTTAGGGTCACCGGGATTCTA
TACAGACTTAGAGACATAATTTTTCCTATTCAATTTTTGTGTTTTCTTTGTTGGAAAAAACACAT
TAGCGAACAAAATAAATAAATAAAAATAAACATATATAAAATAAAATAAAAATAGAATAATTTAT
ATTTAATTTTTCAAATACGAAAAACAATCAAAACCATAACAAAAGTTGAAATCAAAAGGGAGAAT
AGAGATTTTACTAAATGTTTAGGCCTATTAAAAAAATTTCCTTAAGACATATTCATTCACTCCTA
TGGTACTTGGAGAAACGTTGGTCGAATGTCTCCCAGGATACAACAAGAACAATGACCAAAGCAGT
AGCACATCTACAGCGATCAACGAACAAACGACGTCTTTTTCTATCATCGGAACATTTGAAAAATA
TAGAGAGGAAAAGAAAAGTTTTGAGAGAAAAAAAATTTCGGTGTGAAAGAATATTAGAGTGTCTA
ATACTACAGAATTTGTAGCCTTTTATAGGCATTGAGAATGTTGAAATTTTGGAAATTTTCCACAA
AATCTGCCATTAATGAACAAATAAATCAAATTTGATTTAAAGATTAAATCAAATTGATTGGAATC
AAATAAATAAGATAAATGTCATTATATAAACAGATAATGTAGGAAAAATAATTTTGTGTTGAGCT
AAAATATCCGC
Found at i:46599924 original size:16 final size:14
Alignment explanation
Indices: 46599887--46599923 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
46599877 CAGGTGTGCC
46599887 ATATATATACACAT
1 ATATATATACACAT
46599901 ATATATATACACAT
1 ATATATATACACAT
*
46599915 CTATATATA
1 ATATATATA
46599924 TGTGGGATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATATATACACAT
Found at i:46607763 original size:2 final size:2
Alignment explanation
Indices: 46607756--46607795 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
46607746 AAATCCCATC
46607756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46607796 TTATTGGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46608668 original size:28 final size:29
Alignment explanation
Indices: 46608588--46608670 Score: 105
Period size: 30 Copynumber: 2.9 Consensus size: 29
46608578 TAGTAGTAGT
*
46608588 GTGTGGGCCATAGCCCAATACAGTAACAGA
1 GTGTGGGCCTTAGCCCAATACAGTAACA-A
*
46608618 GTGTGGGCCTTATCCCAATACAGTAAC-A
1 GTGTGGGCCTTAGCCCAATACAGTAACAA
* * *
46608646 GTGTGGGTCTTAGCCTAAAACAGTA
1 GTGTGGGCCTTAGCCCAATACAGTA
46608671 TTCAGTACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 22 0.47
30 25 0.53
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (29 bp):
GTGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:46608806 original size:26 final size:26
Alignment explanation
Indices: 46608777--46608874 Score: 108
Period size: 26 Copynumber: 3.8 Consensus size: 26
46608767 GCCAACACAT
46608777 CGTAGCAAAGCTGCCAGTAATAATAA
1 CGTAGCAAAGCTGCCAGTAATAATAA
* * *
46608803 CGTAGCAAAGTTGCCAGTAACAGTAA
1 CGTAGCAAAGCTGCCAGTAATAATAA
* * *
46608829 CGTAGTAGAGCTACCAGT-ATCAATAA
1 CGTAGCAAAGCTGCCAGTAAT-AATAA
* *
46608855 CGCAGCAAAGCTGCTAGTAA
1 CGTAGCAAAGCTGCCAGTAA
46608875 CAGTATTTGT
Statistics
Matches: 56, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
25 1 0.02
26 54 0.96
27 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (26 bp):
CGTAGCAAAGCTGCCAGTAATAATAA
Found at i:46609073 original size:27 final size:27
Alignment explanation
Indices: 46609054--46609272 Score: 257
Period size: 27 Copynumber: 8.2 Consensus size: 27
46609044 GGGTATAACA
*
46609054 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
**
46609081 GTCATTTTACCCT-TCAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
46609107 ATCATTTTAACCT-TCGAGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* ** *
46609134 ATCATTTTACCCT-TCAAGGGTATTTCT
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* *
46609161 GTCATTTTACCCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
46609188 GTTATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
46609215 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
46609242 GTCA-TTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
46609268 GTCAT
1 GTCAT
46609273 ATATCGACTT
Statistics
Matches: 169, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
26 47 0.28
27 121 0.72
28 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Done.