Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 211 of 228
Found at i:61698504 original size:3 final size:3
Alignment explanation
Indices: 61698496--61698531 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
61698486 CAACCGCTTG
* *
61698496 AGA AGA AGA AGC AGA AGA GGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
61698532 GAGTTGAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.03, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:61699809 original size:3 final size:3
Alignment explanation
Indices: 61699801--61699825 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
61699791 CTTTGTTTTC
61699801 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
61699826 TCTCCTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:61700668 original size:60 final size:60
Alignment explanation
Indices: 61700604--61700717 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
61700594 ATACCTATTT
* *
61700604 TTTTAAGGATT-TACAAATATTTCTAA-GTTGTTACCAAAAATTCTAAAAGTTTATTGAAAA
1 TTTTAAGG-TTATACAAAAATTTCTAATGAT-TTACCAAAAATTCTAAAAGTTTATTGAAAA
* *
61700664 TTTTAAGGTTATACAAAAATTTCTAATGATTTACCAATAATTCTAAGAGTTTAT
1 TTTTAAGGTTATACAAAAATTTCTAATGATTTACCAAAAATTCTAAAAGTTTAT
61700718 CAGTATTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 44 0.92
61 2 0.04
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (60 bp):
TTTTAAGGTTATACAAAAATTTCTAATGATTTACCAAAAATTCTAAAAGTTTATTGAAAA
Found at i:61700727 original size:20 final size:20
Alignment explanation
Indices: 61700682--61700735 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
61700672 TTATACAAAA
61700682 ATTTCTAATGATTTACCAAT
1 ATTTCTAATGATTTACCAAT
* * *
61700702 AATTCTAA-GAGTTTATCAGT
1 ATTTCTAATGA-TTTACCAAT
*
61700722 ATTTCTAAAGATTT
1 ATTTCTAATGATTT
61700736 CCTTAGTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (20 bp):
ATTTCTAATGATTTACCAAT
Found at i:61700819 original size:40 final size:41
Alignment explanation
Indices: 61700775--61700869 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
61700765 CATTTTGACA
** *
61700775 TACCAAAATTTCTAAAGGTTTCT-C-ACTATTTCTAA-GGATT
1 TACCAAAATTTCTAAAGGTTT-TACAAAAAATT-TAATGGATT
61700815 TACCAAAATTTCT-AAGGTTTTACAAAAAATTTAATGGATT
1 TACCAAAATTTCTAAAGGTTTTACAAAAAATTTAATGGATT
61700855 TACCAAAATTTCTAA
1 TACCAAAATTTCTAA
61700870 GGATAATTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
38 1 0.02
39 11 0.23
40 35 0.73
41 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (41 bp):
TACCAAAATTTCTAAAGGTTTTACAAAAAATTTAATGGATT
Found at i:61700845 original size:21 final size:20
Alignment explanation
Indices: 61700775--61700873 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
61700765 CATTTTGACA
61700775 TACCAAAATTTCTAAAGG-TT
1 TACCAAAATTTCT-AAGGATT
**
61700795 T-CTCACTATTTCTAAGGATT
1 TAC-CAAAATTTCTAAGGATT
*
61700815 TACCAAAATTTCTAAGGTTT
1 TACCAAAATTTCTAAGGATT
* *
61700835 TACAAAAAATT-TAATGGATT
1 TACCAAAATTTCTAA-GGATT
61700855 TACCAAAATTTCTAAGGAT
1 TACCAAAATTTCTAAGGAT
61700874 AATTTGGTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.12
20 52 0.81
21 4 0.06
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (20 bp):
TACCAAAATTTCTAAGGATT
Found at i:61700901 original size:20 final size:20
Alignment explanation
Indices: 61700876--61700922 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
61700866 CTAAGGATAA
* **
61700876 TTTGGTATAACCTTAGATGT
1 TTTGGTATAACCTAAGAAAT
61700896 TTTGGTATAACCTAAGAAAT
1 TTTGGTATAACCTAAGAAAT
61700916 TTTGGTA
1 TTTGGTA
61700923 GATCCTTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (20 bp):
TTTGGTATAACCTAAGAAAT
Found at i:61701027 original size:20 final size:20
Alignment explanation
Indices: 61700985--61701231 Score: 159
Period size: 20 Copynumber: 12.6 Consensus size: 20
61700975 GACACTAGGG
* *
61700985 AAATCTTTAGAAATATTT-TT
1 AAATCCTTAGAAAT-TTTGGT
61701005 AAATCCTTAGAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* * *
61701025 AAAGCCTT-CAAATTCTGGT
1 AAATCCTTAGAAATTTTGGT
* *
61701044 AAATCTTTAGATATTTTGGT
1 AAATCCTTAGAAATTTTGGT
*
61701064 ATAA-CCTTAGGAATTTTGGT
1 A-AATCCTTAGAAATTTTGGT
* * *
61701084 AAATTCTTAGATATTTTGAT
1 AAATCCTTAGAAATTTTGGT
* * * *
61701104 ATAGCTTTAGAAATTTTGAT
1 AAATCCTTAGAAATTTTGGT
61701124 AAAAT-CTTAGAAA--TTGGT
1 -AAATCCTTAGAAATTTTGGT
* **
61701142 AAAACCTTAGAAATTTTAAT
1 AAATCCTTAGAAATTTTGGT
* * * *
61701162 GAAGCCTTAAAAACTTTGG-
1 AAATCCTTAGAAATTTTGGT
** * *
61701181 AAATATTTAGATATTTTGGC
1 AAATCCTTAGAAATTTTGGT
*
61701201 ATAA-CTTTAGAAATTTTGGT
1 A-AATCCTTAGAAATTTTGGT
61701221 AAATCCTTAGA
1 AAATCCTTAGA
61701232 TTTTTTTTGT
Statistics
Matches: 170, Mismatches: 46, Indels: 22
0.71 0.19 0.09
Matches are distributed among these distances:
17 3 0.02
18 12 0.07
19 34 0.20
20 115 0.68
21 6 0.04
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (20 bp):
AAATCCTTAGAAATTTTGGT
Found at i:61703203 original size:17 final size:17
Alignment explanation
Indices: 61703174--61703211 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
61703164 TTAATAAAAT
61703174 TTTTAAATATTTTATA-
1 TTTTAAATATTTTATAC
*
61703190 TTTTAATATTTTTTATAC
1 TTTTAA-ATATTTTATAC
61703208 TTTT
1 TTTT
61703212 GTAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAAATATTTTATAC
Found at i:61703235 original size:19 final size:19
Alignment explanation
Indices: 61703190--61703236 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
61703180 ATATTTTATA
* *
61703190 TTTTAATATTTTTTATACT
1 TTTTAATTTTTTTTATAAT
61703209 TTTGTAATTTTTTTCTA-AAT
1 TTT-TAATTTTTTT-TATAAT
61703229 TTTTAATT
1 TTTTAATT
61703237 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 14 0.58
21 2 0.08
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTAATTTTTTTTATAAT
Found at i:61703446 original size:20 final size:20
Alignment explanation
Indices: 61703423--61703489 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
61703413 ATTTTATGAT
61703423 TTTTATAAATTTTTTCTATA
1 TTTTATAAATTTTTTCTATA
* **
61703443 TTTTATAATAATTTTGATATA
1 TTTTATAA-ATTTTTTCTATA
** *
61703464 -TTTGCAATTTTTTTCTATA
1 TTTTATAAATTTTTTCTATA
61703483 TTTTATA
1 TTTTATA
61703490 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
19 8 0.24
20 17 0.50
21 9 0.26
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTATAAATTTTTTCTATA
Found at i:61703492 original size:19 final size:19
Alignment explanation
Indices: 61703432--61703494 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
61703422 TTTTTATAAA
61703432 TTTTTTCTATATTTTATAAT
1 TTTTTTCTATATTTTAT-AT
* ** *
61703452 AATTTTGATATATTTGCA-AT
1 -TTTTTTCTATATTT-TATAT
61703472 TTTTTTCTATATTTTATAT
1 TTTTTTCTATATTTTATAT
61703491 TTTT
1 TTTT
61703495 AATTTATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 2 0.06
21 11 0.34
22 1 0.03
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTTTCTATATTTTATAT
Found at i:61703498 original size:26 final size:27
Alignment explanation
Indices: 61703460--61703513 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
61703450 ATAATTTTGA
61703460 TATATTTGCAA-TT-TTTTTCTATATTT
1 TATATTTGCAATTTATTTTTCTA-ATTT
**
61703486 TATATTTTTAATTTATTTTTCTAATTT
1 TATATTTGCAATTTATTTTTCTAATTT
61703513 T
1 T
61703514 TAATAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 7 0.29
28 8 0.33
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (27 bp):
TATATTTGCAATTTATTTTTCTAATTT
Found at i:61708500 original size:38 final size:38
Alignment explanation
Indices: 61708449--61708524 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
61708439 TCTGAAGTAA
61708449 TCATGTATGACACCCAAATTCGAGAATTATATGGAAAC
1 TCATGTATGACACCCAAATTCGAGAATTATATGGAAAC
*
61708487 TCATGTATGACACCCAAATTTGAGAATTATATGGAAAC
1 TCATGTATGACACCCAAATTCGAGAATTATATGGAAAC
61708525 GAGCATAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (38 bp):
TCATGTATGACACCCAAATTCGAGAATTATATGGAAAC
Found at i:61709050 original size:17 final size:17
Alignment explanation
Indices: 61709028--61709080 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
61709018 AAAGAATTGA
61709028 ACATATCCATGTAGGAC
1 ACATATCCATGTAGGAC
* *
61709045 ACATAT--A-GAATTGA-
1 ACATATCCATGTA-GGAC
61709059 ACATATCCATGTAGGAC
1 ACATATCCATGTAGGAC
61709076 ACATA
1 ACATA
61709081 CATGTATCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
14 8 0.30
15 3 0.11
16 3 0.11
17 13 0.48
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.25
Consensus pattern (17 bp):
ACATATCCATGTAGGAC
Found at i:61709058 original size:31 final size:31
Alignment explanation
Indices: 61709020--61709080 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
61709010 AAAACTTTAA
61709020 AGAATTGAACATATCCATGTAGGACACATAT
1 AGAATTGAACATATCCATGTAGGACACATAT
61709051 AGAATTGAACATATCCATGTAGGACACATA
1 AGAATTGAACATATCCATGTAGGACACATA
61709081 CATGTATCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (31 bp):
AGAATTGAACATATCCATGTAGGACACATAT
Found at i:61713059 original size:24 final size:24
Alignment explanation
Indices: 61713008--61713059 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
61712998 ATATCGGTTT
* *
61713008 TTTTTTACTTTGATATTTAAATAT
1 TTTTTTACTTTGATACTTAAATAA
*
61713032 TTTTTTA-TTGTGATACTTATATAA
1 TTTTTTACTT-TGATACTTAAATAA
61713056 TTTT
1 TTTT
61713060 ATCAGTGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (24 bp):
TTTTTTACTTTGATACTTAAATAA
Found at i:61713154 original size:11 final size:11
Alignment explanation
Indices: 61713140--61713165 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61713130 AAAAAAATAT
61713140 AATTAATTTAA
1 AATTAATTTAA
61713151 AATTAATTTAA
1 AATTAATTTAA
61713162 AATT
1 AATT
61713166 TTCTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTAATTTAA
Found at i:61716314 original size:24 final size:24
Alignment explanation
Indices: 61716283--61716329 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
61716273 ATTTTAATTA
61716283 ATATAATATACATAAAT-CATACTT
1 ATATAATATACAT-AATCCATACTT
61716307 ATATAATATACATAATCCATACT
1 ATATAATATACATAATCCATACT
61716330 AACAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAATATACATAATCCATACTT
Found at i:61717637 original size:22 final size:21
Alignment explanation
Indices: 61717612--61717655 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
61717602 AAGCATATGA
* *
61717612 AAATGATTTGGTTATATTCAAT
1 AAATAATTTGGTTA-ATACAAT
61717634 AAATAATTTGGTTAATACAAT
1 AAATAATTTGGTTAATACAAT
61717655 A
1 A
61717656 CTTATATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (21 bp):
AAATAATTTGGTTAATACAAT
Found at i:61717664 original size:22 final size:22
Alignment explanation
Indices: 61717617--61717709 Score: 59
Period size: 22 Copynumber: 4.2 Consensus size: 22
61717607 TATGAAAATG
* *
61717617 ATTTGGTTATATTCAATAAATA-
1 ATTTGGTTA-ATACAATACATAT
*
61717639 ATTTGGTTAATACAATACTTAT
1 ATTTGGTTAATACAATACATAT
* * *
61717661 ATTT-GATAA-GCATATGA-AAAT
1 ATTTGGTTAATACA-AT-ACATAT
*
61717682 GATTTGGTTAATACAATACTTAT
1 -ATTTGGTTAATACAATACATAT
61717705 ATTTG
1 ATTTG
61717710 ATAAGCATAT
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
20 2 0.04
21 17 0.32
22 24 0.45
23 8 0.15
24 2 0.04
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (22 bp):
ATTTGGTTAATACAATACATAT
Found at i:61717689 original size:44 final size:44
Alignment explanation
Indices: 61717634--61717727 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
61717624 TATATTCAAT
*
61717634 AAATAATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
61717678 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
61717722 AAATGA
1 AAATGA
61717728 AAGTCGAGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (44 bp):
AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
Found at i:61731901 original size:68 final size:68
Alignment explanation
Indices: 61731729--61731901 Score: 204
Period size: 69 Copynumber: 2.5 Consensus size: 68
61731719 CTTTCCAAGG
* *** *
61731729 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTAATTTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACCCCGAGGTATTTTAATTTTGT
61731794 TTT
66 TTT
* ** * *
61731797 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACCCCGAGGTATTTTAGTTTAT
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACCCCGAGGTATTTTAATTT-T
61731862 GTTTT
64 GTTTT
** *
61731867 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
61731902 TTTAATTTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
68 31 0.35
69 53 0.60
70 5 0.06
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (68 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACCCCGAGGTATTTTAATTTTGT
TTT
Found at i:61732231 original size:79 final size:76
Alignment explanation
Indices: 61731919--61732256 Score: 425
Period size: 72 Copynumber: 4.4 Consensus size: 76
61731909 TTTGTTTTTC
* * *
61731919 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
*
61731984 GTTGTTAAAAA
66 GTTTTTAAAAA
**
61731995 AAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
*
61732060 G-TTTT---CA
66 GTTTTTAAAAA
* ** * * *
61732067 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTAAATTTCT
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
*
61732132 GTTTTCAAAAAA
66 GTTTT-TAAAAA
* * * *
61732144 AAAATCAACTTATATTGCGAGAGGTGAGTTAAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAG---ACACGCTGAGGTAATTTCAATT
61732208 TCTGTTTTTTAAAAA
63 TCTG-TTTTTAAAAA
*
61732223 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGC
61732257 TTCAGATTAC
Statistics
Matches: 229, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
72 63 0.28
73 3 0.01
75 3 0.01
76 62 0.27
77 34 0.15
79 60 0.26
80 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (76 bp):
AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
GTTTTTAAAAA
Found at i:61732278 original size:79 final size:77
Alignment explanation
Indices: 61731919--61732281 Score: 425
Period size: 79 Copynumber: 4.8 Consensus size: 77
61731909 TTTGTTTTTC
* * *
61731919 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAG-GACACGCTGAGGTAATTTCAATTTC
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGAGACACGCTGAGGTATTTTCAATTTC
*
61731983 TGTTGTTAAAAA
66 TGTTTTTAAAAA
** *
61731995 AAAATCAACTTATATTGCGAGAAATGAGTTGAGCCTCA-AGACACGCTGAGGTAATTTCAATTTC
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGAGACACGCTGAGGTATTTTCAATTTC
*
61732059 TG-TTTT---CA
66 TGTTTTTAAAAA
* ** * *
61732067 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCA-AGACACGTTGAGGTATTTTAAATTTC
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGAGACACGCTGAGGTATTTTCAATTTC
*
61732131 TGTTTTCAAAAAA
66 TGTTTT-TAAAAA
* * ** *
61732144 AAAATCAACTTATATTGCGAGAGGTGAGTTAAGCCTCGGTTCACATGCTGAGGTATTTTCAATTT
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAG-AGACACGCTGAGGTATTTTCAATTT
61732209 CTGTTTTTTAAAAA
65 CTG-TTTTTAAAAA
* * * * *
61732223 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATTACACACTGTGGTATTTT
1 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGA-GACACGCTGAGGTATTTT
61732282 TTCAATTCAT
Statistics
Matches: 245, Mismatches: 32, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
72 63 0.26
73 3 0.01
75 3 0.01
76 61 0.25
77 34 0.14
79 77 0.31
80 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (77 bp):
AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGAGACACGCTGAGGTATTTTCAATTTC
TGTTTTTAAAAA
Found at i:61732495 original size:72 final size:72
Alignment explanation
Indices: 61732414--61732554 Score: 246
Period size: 72 Copynumber: 2.0 Consensus size: 72
61732404 TCAAAATTAG
* *
61732414 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTA
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGTGTTTTA
61732479 ATTTCAA
66 ATTTCAA
* *
61732486 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGTTTTTTA
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGTGTTTTA
61732551 ATTT
66 ATTT
61732555 ATGTTTCAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (72 bp):
CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGTGTTTTA
ATTTCAA
Found at i:61732707 original size:159 final size:160
Alignment explanation
Indices: 61732414--61732707 Score: 416
Period size: 159 Copynumber: 1.8 Consensus size: 160
61732404 TCAAAATTAG
* * ** *
61732414 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTA
1 CTCATATTACAAGAAGTGAGTTGAGCCTCGAAGCACGCTGAGGTATTTTCAATTTTTGTGTTTAA
** * * * * *
61732479 ATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTG
66 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGATATTTTCAAATTCTA
61732544 TTTTTTAATTTATGTTTCAAAAAAAATCAA
131 TTTTTTAATTTATGTTTCAAAAAAAATCAA
*
61732574 CTCATATTACGAGAAGTGAGTTGAGCCTC-AAG-ACGCTGAGGTAATTTT-AATTTTTGT-TTGT
1 CTCATATTACAAGAAGTGAGTTGAGCCTCGAAGCACGCTGAGGT-ATTTTCAATTTTTGTGTT-T
61732635 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGATATTTTCAAATT
64 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGATATTTTCAAATT
61732700 CTATTTTT
128 CTATTTTT
61732708 ATCAAAAAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
157 2 0.02
158 20 0.17
159 70 0.59
160 26 0.22
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (160 bp):
CTCATATTACAAGAAGTGAGTTGAGCCTCGAAGCACGCTGAGGTATTTTCAATTTTTGTGTTTAA
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGATATTTTCAAATTCTA
TTTTTTAATTTATGTTTCAAAAAAAATCAA
Found at i:61732736 original size:77 final size:73
Alignment explanation
Indices: 61732546--61732749 Score: 240
Period size: 71 Copynumber: 2.8 Consensus size: 73
61732536 AATTTTTGTT
* * *
61732546 TTTTAATTTATG-TT-TCAAAAAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCAAGACG
1 TTTTAATTTTTGTTTATC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACG
*
61732609 CTGAGGTAA
65 CTGAGATAA
*
61732618 TTTTAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
1 TTTTAATTTTTGTTTATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG--AC
61732681 GCTGAGAT-A
64 GCTGAGATAA
* *
61732690 TTTTCAAATTCTATT-TTTATCAAAAAAATCAACTTATATTGTGAGAGGTGAGTTGAGCCT
1 TTTT--AATT-T-TTGTTTATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
61732750 TAAATATTAA
Statistics
Matches: 115, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
71 39 0.34
72 16 0.14
73 11 0.10
74 6 0.05
75 6 0.05
76 2 0.02
77 35 0.30
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (73 bp):
TTTTAATTTTTGTTTATCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACGC
TGAGATAA
Found at i:61743578 original size:13 final size:11
Alignment explanation
Indices: 61743569--61743611 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
61743559 ACCAAAAATT
61743569 TATTTTAAAAA
1 TATTTTAAAAA
*
61743580 T-TTTAAAAAA
1 TATTTTAAAAA
61743590 TTATTTTAAAAA
1 -TATTTTAAAAA
61743602 TATTTTAAAA
1 TATTTTAAAA
61743612 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 8 0.29
11 12 0.43
12 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:61743587 original size:22 final size:23
Alignment explanation
Indices: 61743562--61743613 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
61743552 AATAAATACC
61743562 AAAAATTTATTTTAAAAAT-TTT
1 AAAAATTTATTTTAAAAATATTT
*
61743584 AAAAAATTATTTTAAAAATATTT
1 AAAAATTTATTTTAAAAATATTT
*
61743607 TAAAATT
1 AAAAATT
61743614 AAAAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAAATTTATTTTAAAAATATTT
Found at i:61743600 original size:11 final size:11
Alignment explanation
Indices: 61743563--61743614 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
61743553 ATAAATACCA
61743563 AAAATTTATTTT
1 AAAA-TTATTTT
61743575 AAAA--ATTTT
1 AAAATTATTTT
61743584 AAAAAATTATTTT
1 --AAAATTATTTT
*
61743597 AAAAATATTTT
1 AAAATTATTTT
61743608 AAAATTA
1 AAAATTA
61743615 AAAAAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 5 0.15
11 20 0.59
12 4 0.12
13 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:61743641 original size:18 final size:17
Alignment explanation
Indices: 61743617--61743715 Score: 107
Period size: 17 Copynumber: 5.9 Consensus size: 17
61743607 TAAAATTAAA
61743617 AAAATTAAAAATGTATTTT
1 AAAATTAAAAA--TATTTT
61743636 -AAATTAAAAATATTTT
1 AAAATTAAAAATATTTT
*
61743652 AAAATTAAAAAAATTTT
1 AAAATTAAAAATATTTT
*
61743669 -AAA--AAAAGTATTTT
1 AAAATTAAAAATATTTT
* **
61743683 AAAATTAAAAAAATTAA
1 AAAATTAAAAATATTTT
61743700 AAAATTAAAAATATTT
1 AAAATTAAAAATATTT
61743716 ATTATATTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
14 9 0.13
15 3 0.04
16 9 0.13
17 36 0.54
18 10 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AAAATTAAAAATATTTT
Found at i:61743655 original size:28 final size:29
Alignment explanation
Indices: 61743585--61743656 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 29
61743575 AAAAATTTTA
61743585 AAAAATTATTTTAAAA-ATATTTTAAAATT
1 AAAAA-TATTTTAAAATATATTTTAAAATT
* * *
61743614 AAAAA-AATTAAAAATGTATTTT-AAATT
1 AAAAATATTTTAAAATATATTTTAAAATT
61743641 AAAAATATTTTAAAAT
1 AAAAATATTTTAAAAT
61743657 TAAAAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 17 0.47
28 14 0.39
29 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (29 bp):
AAAAATATTTTAAAATATATTTTAAAATT
Found at i:61743684 original size:31 final size:32
Alignment explanation
Indices: 61743617--61743715 Score: 110
Period size: 31 Copynumber: 3.0 Consensus size: 32
61743607 TAAAATTAAA
*
61743617 AAAATTAAAAATGTATTTTAAATTAAAAATATTTT
1 AAAATTAAAAA--AATTTTAAA-TAAAAATATTTT
*
61743652 AAAATTAAAAAAATTTTAAA-AAAAGTATTTT
1 AAAATTAAAAAAATTTTAAATAAAAATATTTT
**
61743683 AAAATTAAAAAAATTAAAAAATTAAAAATATTT
1 AAAATTAAAAAAATT-TTAAA-TAAAAATATTT
61743716 ATTATATTCA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
31 25 0.45
32 3 0.05
33 8 0.14
34 9 0.16
35 11 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (32 bp):
AAAATTAAAAAAATTTTAAATAAAAATATTTT
Found at i:61743704 original size:48 final size:46
Alignment explanation
Indices: 61743608--61743715 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 46
61743598 AAAATATTTT
* * **
61743608 AAAATTAAAAAAA--TTAAAAATGTATTTTAAATTAAAAATATTTT
1 AAAATTAAAAAAATTTTAAAAAAGTATTTTAAATTAAAAAAATTAA
61743652 AAAATTAAAAAAATTTTAAAAAAAGTATTTTAAAATTAAAAAAATTAA
1 AAAATTAAAAAAATTTT-AAAAAAGTATTTT-AAATTAAAAAAATTAA
*
61743700 AAAATTAAAAATATTT
1 AAAATTAAAAAAATTT
61743716 ATTATATTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 13 0.24
46 2 0.04
47 12 0.22
48 28 0.51
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (46 bp):
AAAATTAAAAAAATTTTAAAAAAGTATTTTAAATTAAAAAAATTAA
Found at i:61753654 original size:78 final size:78
Alignment explanation
Indices: 61753554--61753715 Score: 324
Period size: 78 Copynumber: 2.1 Consensus size: 78
61753544 ATGACCAATC
61753554 AACCACCAGTCCAATTTGAAAAAACATTGAAAATCACATGGAGTTGTAGCATTGACTACAATCTA
1 AACCACCAGTCCAATTTGAAAAAACATTGAAAATCACATGGAGTTGTAGCATTGACTACAATCTA
61753619 CACAGGAAAGAAA
66 CACAGGAAAGAAA
61753632 AACCACCAGTCCAATTTGAAAAAACATTGAAAATCACATGGAGTTGTAGCATTGACTACAATCTA
1 AACCACCAGTCCAATTTGAAAAAACATTGAAAATCACATGGAGTTGTAGCATTGACTACAATCTA
61753697 CACAGGAAAGAAA
66 CACAGGAAAGAAA
61753710 AACCAC
1 AACCAC
61753716 TTACATGATT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 84 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (78 bp):
AACCACCAGTCCAATTTGAAAAAACATTGAAAATCACATGGAGTTGTAGCATTGACTACAATCTA
CACAGGAAAGAAA
Found at i:61759966 original size:60 final size:58
Alignment explanation
Indices: 61759845--61759971 Score: 141
Period size: 58 Copynumber: 2.2 Consensus size: 58
61759835 TGAATTTAGT
* * ** **
61759845 TTCAATTTTCAATTTGGTACTTGAGTTATTTTATTTCAATTTGGTACTTAAGTTTGGC
1 TTCAATGTTCAATTTGATACTTGAGTTATTTTATTTCAATTAAGTACTTAAGTTTAAC
*
61759903 TTCAATGTTCAATTTGATACTTGAGTTCTTTT-TTATCCCAATTAAGTATCTT-AGTTTAAC
1 TTCAATGTTCAATTTGATACTTGAGTTATTTTATT-T--CAATTAAGTA-CTTAAGTTTAAC
61759963 TTCAATGTT
1 TTCAATGTT
61759972 TGGTACCTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 2 0.03
58 30 0.52
60 23 0.40
61 3 0.05
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (58 bp):
TTCAATGTTCAATTTGATACTTGAGTTATTTTATTTCAATTAAGTACTTAAGTTTAAC
Found at i:61766282 original size:21 final size:21
Alignment explanation
Indices: 61766249--61766304 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
61766239 CACGGTCTAC
*
61766249 CCACACGGCCGTGT-CCTTCAG
1 CCACACGGTCGTGTCCCTT-AG
*
61766270 CCACATGGTCGTGTCCCTTAG
1 CCACACGGTCGTGTCCCTTAG
*
61766291 CCACACGGTTGTGT
1 CCACACGGTCGTGT
61766305 ATTCCTGCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.14, C:0.36, G:0.25, T:0.25
Consensus pattern (21 bp):
CCACACGGTCGTGTCCCTTAG
Found at i:61766339 original size:23 final size:21
Alignment explanation
Indices: 61766290--61766341 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
61766280 GTGTCCCTTA
*
61766290 GCCACACGGTTGTGTATTCCT
1 GCCACACAGTTGTGTATTCCT
*
61766311 GCCACACAGTTGTGTATTCTT
1 GCCACACAGTTGTGTATTCCT
*
61766332 GTCACACAGT
1 GCCACACAGT
61766342 CTAAATCCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (21 bp):
GCCACACAGTTGTGTATTCCT
Found at i:61766401 original size:21 final size:21
Alignment explanation
Indices: 61766365--61766420 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
61766355 CACGATCTGC
* *
61766365 CCACACGGTCGTGTCCCTCAG
1 CCACATGGTTGTGTCCCTCAG
* *
61766386 CTACATGGTTGTGTCCCTTAG
1 CCACATGGTTGTGTCCCTCAG
61766407 CCACATGGTTGTGT
1 CCACATGGTTGTGT
61766421 ATTCCTGTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.30, G:0.25, T:0.30
Consensus pattern (21 bp):
CCACATGGTTGTGTCCCTCAG
Found at i:61766447 original size:95 final size:95
Alignment explanation
Indices: 61766270--61766548 Score: 283
Period size: 95 Copynumber: 2.9 Consensus size: 95
61766260 TGTCCTTCAG
* * * * * ** *
61766270 CCACATGGTCGTGTCCCTTAGCCACACGGTTGTGTATTCC-T-GCCACACAGTTGTGTATTCTTG
1 CCACACGGTCGTGTCCCTCAGCTACATGGTTGTG--TCCCTTAGCCACATGGTTGTGTATTCCTG
* *
61766333 TCACACAGTCTAAATCCTCCCACACGATCTGC
64 TCACACAGTCTGAACCCTCCCACACGATCTGC
61766365 CCACACGGTCGTGTCCCTCAGCTACATGGTTGTGTCCCTTAGCCACATGGTTGTGTATTCCTGTC
1 CCACACGGTCGTGTCCCTCAGCTACATGGTTGTGTCCCTTAGCCACATGGTTGTGTATTCCTGTC
* * * * *
61766430 ATACGGTCTGAACCCTCCTATACGGTCTGC
66 ACACAGTCTGAACCCTCCCACACGATCTGC
* ** * * * * * * *
61766460 TCACACGACCATATCCCTCAGCTACATAGTCGTGTCTCTCAGCCACATGGTTGTGTATTCCTATC
1 CCACACGGTCGTGTCCCTCAGCTACATGGTTGTGTCCCTTAGCCACATGGTTGTGTATTCCTGTC
* *
61766525 ACACAGTTTGAACCCTCTCACACG
66 ACACAGTCTGAACCCTCCCACACG
61766549 GCCGTGTGGT
Statistics
Matches: 151, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
93 3 0.02
94 1 0.01
95 147 0.97
ACGTcount: A:0.20, C:0.33, G:0.18, T:0.29
Consensus pattern (95 bp):
CCACACGGTCGTGTCCCTCAGCTACATGGTTGTGTCCCTTAGCCACATGGTTGTGTATTCCTGTC
ACACAGTCTGAACCCTCCCACACGATCTGC
Found at i:61769360 original size:30 final size:30
Alignment explanation
Indices: 61769326--61769395 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
61769316 CGGCACATGA
* *
61769326 CCATGTGAACCGCCCGTATGCAGCACACGG
1 CCATGTCAACCGCACGTATGCAGCACACGG
* * **
61769356 CCATGTCAACCGCATGTGTGTGGCACACGG
1 CCATGTCAACCGCACGTATGCAGCACACGG
61769386 CCATGTCAAC
1 CCATGTCAAC
61769396 AGTTCGTGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.17
Consensus pattern (30 bp):
CCATGTCAACCGCACGTATGCAGCACACGG
Found at i:61778470 original size:20 final size:20
Alignment explanation
Indices: 61778445--61778489 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
61778435 GATATTCTTA
*
61778445 TCTCTTTGGGATAAATTTGC
1 TCTCTTTGGGATAAATCTGC
61778465 TCTCTTTGGGATAAATCTGC
1 TCTCTTTGGGATAAATCTGC
61778485 TCTCT
1 TCTCT
61778490 CAATATGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (20 bp):
TCTCTTTGGGATAAATCTGC
Found at i:61790121 original size:7 final size:7
Alignment explanation
Indices: 61790111--61790171 Score: 68
Period size: 7 Copynumber: 8.7 Consensus size: 7
61790101 TTAGGGTCAT
61790111 AGGTCTA
1 AGGTCTA
61790118 AGGTCTA
1 AGGTCTA
*
61790125 AGGGCTA
1 AGGTCTA
*
61790132 AGGTTTA
1 AGGTCTA
*
61790139 GGGTCTA
1 AGGTCTA
*
61790146 AGGTTTA
1 AGGTCTA
*
61790153 AGGTTTA
1 AGGTCTA
61790160 AGGTCTA
1 AGGTCTA
*
61790167 GGGTC
1 AGGTC
61790172 CAGGTTCAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.25, C:0.10, G:0.34, T:0.31
Consensus pattern (7 bp):
AGGTCTA
Found at i:61790135 original size:21 final size:21
Alignment explanation
Indices: 61790111--61790166 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
61790101 TTAGGGTCAT
*
61790111 AGGTCTAAGGTCTAAGGGCTA
1 AGGTTTAAGGTCTAAGGGCTA
* **
61790132 AGGTTTAGGGTCTAAGGTTTA
1 AGGTTTAAGGTCTAAGGGCTA
61790153 AGGTTTAAGGTCTA
1 AGGTTTAAGGTCTA
61790167 GGGTCCAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.32, T:0.32
Consensus pattern (21 bp):
AGGTTTAAGGTCTAAGGGCTA
Found at i:61791728 original size:2 final size:2
Alignment explanation
Indices: 61791721--61791746 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61791711 TAAACAAGTC
61791721 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
61791747 TAATGTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61793977 original size:3 final size:3
Alignment explanation
Indices: 61793969--61793996 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
61793959 TAAATAAAAT
61793969 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
61793997 GCAAGGCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:61794491 original size:2 final size:2
Alignment explanation
Indices: 61794484--61794508 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61794474 CTTGGACCTC
61794484 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 T
61794509 TTTAAACATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61794990 original size:14 final size:14
Alignment explanation
Indices: 61794967--61794996 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61794957 GCCGAAAGGT
61794967 AAATAAGGAGAACC
1 AAATAAGGAGAACC
*
61794981 AAATATGGAGAACC
1 AAATAAGGAGAACC
61794995 AA
1 AA
61794997 GTTCCTAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.13, G:0.20, T:0.10
Consensus pattern (14 bp):
AAATAAGGAGAACC
Found at i:61795634 original size:38 final size:40
Alignment explanation
Indices: 61795577--61795652 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
61795567 TTTAATCCTC
*
61795577 TAAAATAAATAAAAAAATA-TTTAATCTCTTCAAAATTGA
1 TAAAATAAATAAAAAAATATTTTAATCTCTTAAAAATTGA
*
61795616 TAAAAT-AATAAAATAATATTTTAATCTCTTAAAAATT
1 TAAAATAAATAAAAAAATATTTTAATCTCTTAAAAATT
61795653 TATTCTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 11 0.32
39 23 0.68
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (40 bp):
TAAAATAAATAAAAAAATATTTTAATCTCTTAAAAATTGA
Found at i:61796242 original size:15 final size:15
Alignment explanation
Indices: 61796222--61796255 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
61796212 TTTTATTTTT
61796222 ATTATATATTTTGAA
1 ATTATATATTTTGAA
*
61796237 ATTATATATTTTGTA
1 ATTATATATTTTGAA
61796252 ATTA
1 ATTA
61796256 AGTAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (15 bp):
ATTATATATTTTGAA
Found at i:61797378 original size:31 final size:31
Alignment explanation
Indices: 61797343--61797407 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
61797333 AAAAAACATT
61797343 AATAGCCCAATGACTTAAATAAAAACTTTTG
1 AATAGCCCAATGACTTAAATAAAAACTTTTG
** * *
61797374 AATAGTTCAGTGACTTAAATGAAAACTTTTG
1 AATAGCCCAATGACTTAAATAAAAACTTTTG
61797405 AAT
1 AAT
61797408 CGTTCGTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (31 bp):
AATAGCCCAATGACTTAAATAAAAACTTTTG
Found at i:61800579 original size:3 final size:3
Alignment explanation
Indices: 61800571--61800624 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
61800561 TTACCAACAC
* * *
61800571 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GCT GCT GCT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
*
61800619 GAT GTT
1 GTT GTT
61800625 TTCATCACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.02, C:0.06, G:0.33, T:0.59
Consensus pattern (3 bp):
GTT
Found at i:61800928 original size:2 final size:2
Alignment explanation
Indices: 61800923--61800949 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61800913 AATTGATCTA
61800923 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
61800950 AGAACTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:61802093 original size:9 final size:8
Alignment explanation
Indices: 61802066--61802091 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
61802056 AACCGAATTA
61802066 TTATTTTT
1 TTATTTTT
61802074 TTATTTTT
1 TTATTTTT
61802082 TTATTTTT
1 TTATTTTT
61802090 TT
1 TT
61802092 TAATAATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:61804445 original size:52 final size:49
Alignment explanation
Indices: 61804360--61804726 Score: 431
Period size: 46 Copynumber: 7.6 Consensus size: 49
61804350 TTTGAGTACT
* **
61804360 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
61804406 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
61804458 TCTGATCAAGTG---ATAAAGTGATAAGTTATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
61804504 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
61804550 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
61804602 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
61804654 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
61804700 TCTGATCAAGAGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
61804727 GCTACACTTA
Statistics
Matches: 291, Mismatches: 16, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 133 0.46
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:61804480 original size:98 final size:97
Alignment explanation
Indices: 61804360--61804726 Score: 492
Period size: 98 Copynumber: 3.7 Consensus size: 97
61804350 TTTGAGTACT
* *
61804360 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
61804425 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * *
61804458 TCTGATCAAGTGATAAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
61804518 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
61804550 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
61804615 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
61804654 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
61804719 GATAAGTG
65 GA-AAGTG
61804727 GCTACACTTA
Statistics
Matches: 238, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 143 0.60
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:61804708 original size:196 final size:196
Alignment explanation
Indices: 61804374--61804726 Score: 598
Period size: 196 Copynumber: 1.8 Consensus size: 196
61804364 ATCAAGTGAT
* * *
61804374 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * * *
61804439 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTTATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
61804504 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
61804569 G
196 G
* *
61804570 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
61804635 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
61804700 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTG
61804727 GCTACACTTA
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 145 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:61804734 original size:37 final size:37
Alignment explanation
Indices: 61804690--61804799 Score: 195
Period size: 37 Copynumber: 3.0 Consensus size: 37
61804680 GATAGCTTTA
61804690 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
61804727 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
61804764 GCTACACTTATCTGATCAAGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
61804800 ATCATACGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 12 0.17
37 58 0.83
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:61804763 original size:150 final size:149
Alignment explanation
Indices: 61804360--61804715 Score: 458
Period size: 150 Copynumber: 2.4 Consensus size: 149
61804350 TTTGAGTACT
* * * * *
61804360 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * *
61804425 GAAAGTGATAAGTAATAGCTTC-G---GCTATACTTATC---TGATCAAGTGATAAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGCAAACTAAACTGATCAAGTGA-CAAGTGATAAAGTGATAAG
*
61804483 TTATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
* *
61804504 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * * *
61804569 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA-AAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAG
61804633 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
*
61804654 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAA
61804716 AGTGATAAGT
Statistics
Matches: 191, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
144 83 0.43
145 1 0.01
149 7 0.04
150 90 0.47
151 7 0.04
152 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (149 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAGTG
ATAGCTTCGGCTATACTTA
Found at i:61823159 original size:34 final size:35
Alignment explanation
Indices: 61823104--61823170 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
61823094 CAAACACTAG
*
61823104 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
61823139 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
61823171 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:61827362 original size:17 final size:16
Alignment explanation
Indices: 61827329--61827376 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
61827319 TGCTTTAAAC
*
61827329 CTATATTTATTATTATA
1 CTATATTTA-TAATATA
61827346 CTATATTTATGAATATA
1 CTATATTTAT-AATATA
* *
61827363 TTATAATTATAATA
1 CTATATTTATAATA
61827377 GTGATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
CTATATTTATAATATA
Found at i:61827409 original size:21 final size:21
Alignment explanation
Indices: 61827383--61827422 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
61827373 AATAGTGATT
*
61827383 TTTTTAAAAAAATATATAACA
1 TTTTTAAAAAAATAAATAACA
*
61827404 TTTTTAAAAGAATAAATAA
1 TTTTTAAAAAAATAAATAA
61827423 AATTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TTTTTAAAAAAATAAATAACA
Found at i:61828732 original size:17 final size:18
Alignment explanation
Indices: 61828690--61828734 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
61828680 GTAAGAAAAA
61828690 ATGAATTTTTTATTTTTC
1 ATGAATTTTTTATTTTTC
61828708 AT-AA-TTTTTATTTTT-
1 ATGAATTTTTTATTTTTC
*
61828723 TTGAATTTTTTA
1 ATGAATTTTTTA
61828735 AACAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 13 0.54
17 8 0.33
18 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (18 bp):
ATGAATTTTTTATTTTTC
Found at i:61830229 original size:50 final size:50
Alignment explanation
Indices: 61830147--61830272 Score: 146
Period size: 50 Copynumber: 2.5 Consensus size: 50
61830137 GTGTACCAAT
* * * *
61830147 AAATTTAGCCCTCAA-AGTTTACGCATTCTGTCAATTCCGTCTTGATTTAAC
1 AAATTTA-CCTTCAACA-TTTACACATTCTGTCAATTCAGTCTTAATTTAAC
* *
61830198 AAATTTACCTTCAACATTTACACATTTTGTCAATTTAGTCTTAATTTAAC
1 AAATTTACCTTCAACATTTACACATTCTGTCAATTCAGTCTTAATTTAAC
* *
61830248 AAATTTAGCTCACAACATTTACACA
1 AAATTTACCT-TCAACATTTACACA
61830273 CTATACCAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
50 44 0.68
51 21 0.32
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.38
Consensus pattern (50 bp):
AAATTTACCTTCAACATTTACACATTCTGTCAATTCAGTCTTAATTTAAC
Found at i:61832110 original size:23 final size:24
Alignment explanation
Indices: 61832070--61832116 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
61832060 TATTTTCATT
*
61832070 TTTTATAAAATTTAAATAATTTTA
1 TTTTATAAAATTTAAATAAATTTA
* *
61832094 TTTT-TAAATTTTTAATAAATTTA
1 TTTTATAAAATTTAAATAAATTTA
61832117 AATCAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATAAAATTTAAATAAATTTA
Found at i:61833110 original size:21 final size:19
Alignment explanation
Indices: 61833086--61833129 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
61833076 AATTTTGTGA
61833086 TTTTTAATTAAATTTTAATAT
1 TTTTTAA-TAAATTTTAA-AT
*
61833107 TTTTTTATAAATTTTAAAT
1 TTTTTAATAAATTTTAAAT
61833126 TTTT
1 TTTT
61833130 CATAGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTAATAAATTTTAAAT
Found at i:61843869 original size:19 final size:19
Alignment explanation
Indices: 61843831--61843869 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
61843821 TTATTGAAAA
*
61843831 TTTAAATTTATATATATAT
1 TTTAAATTTATAAATATAT
61843850 TTTAAATTTTATAAAT-TAT
1 TTTAAA-TTTATAAATATAT
61843869 T
1 T
61843870 AAATCAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAAATTTATAAATATAT
Found at i:61848281 original size:2 final size:2
Alignment explanation
Indices: 61848274--61848300 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61848264 TGTGGTTTGA
61848274 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
61848301 TATATATGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:61849290 original size:22 final size:22
Alignment explanation
Indices: 61849265--61849306 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
61849255 AAGGTTGTTG
61849265 TTTGATAAATTGAAAAGTTATA
1 TTTGATAAATTGAAAAGTTATA
*
61849287 TTTGATAAATTGAAAGGTTA
1 TTTGATAAATTGAAAAGTTA
61849307 AGTATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (22 bp):
TTTGATAAATTGAAAAGTTATA
Found at i:61851285 original size:22 final size:19
Alignment explanation
Indices: 61851260--61851301 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
61851250 TTTATAAAAT
61851260 AGTTAATTATTATTAAATTATA
1 AGTTAATT-TT-TTAAA-TATA
61851282 AGTTAATTTTTTAAATATA
1 AGTTAATTTTTTAAATATA
61851301 A
1 A
61851302 TCATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 2 0.10
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AGTTAATTTTTTAAATATA
Found at i:61851651 original size:14 final size:14
Alignment explanation
Indices: 61851629--61851659 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
61851619 TATTATAATT
*
61851629 AATTTAAATTTAAC
1 AATTAAAATTTAAC
61851643 AATTAAAATTTAAC
1 AATTAAAATTTAAC
61851657 AAT
1 AAT
61851660 ATTAACAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTAAAATTTAAC
Found at i:61856482 original size:10 final size:10
Alignment explanation
Indices: 61856467--61856507 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
61856457 CTCTCCATAC
61856467 ATACATATAT
1 ATACATATAT
61856477 ATACATATAT
1 ATACATATAT
61856487 ATACATACATGAT
1 ATACAT--AT-AT
61856500 ATACATAT
1 ATACATAT
61856508 CACTATGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 16 0.57
11 2 0.07
12 2 0.07
13 8 0.29
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (10 bp):
ATACATATAT
Found at i:61856482 original size:14 final size:14
Alignment explanation
Indices: 61856462--61856506 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
61856452 TTCATCTCTC
61856462 CATACATACATATA
1 CATACATACATATA
* *
61856476 TATACATATATATA
1 CATACATACATATA
*
61856490 CATACAT-GATATA
1 CATACATACATATA
61856503 CATA
1 CATA
61856507 TCACTATGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (14 bp):
CATACATACATATA
Found at i:61859573 original size:6 final size:6
Alignment explanation
Indices: 61859556--61859616 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
61859546 AATATATATA
* ** * *
61859556 TGTATG TG-ATG TGTATG TGTATG TGTCTG TACATG TATATG TATATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
* *
61859603 TATATG TATATG TG
1 TGTATG TGTATG TG
61859617 AATGAAGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
5 5 0.10
6 43 0.90
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.48
Consensus pattern (6 bp):
TGTATG
Found at i:61859581 original size:12 final size:12
Alignment explanation
Indices: 61859550--61859616 Score: 64
Period size: 12 Copynumber: 5.7 Consensus size: 12
61859540 AAGTATAATA
*
61859550 TATATATGTATG
1 TATATGTGTATG
*
61859562 T-GATGTGTATG
1 TATATGTGTATG
* *
61859573 TGTATGTGTCTG
1 TATATGTGTATG
* *
61859585 TACATGTATATG
1 TATATGTGTATG
*
61859597 TATATGTATATG
1 TATATGTGTATG
61859609 TATATGTG
1 TATATGTG
61859617 AATGAAGTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
11 9 0.20
12 35 0.80
ACGTcount: A:0.25, C:0.03, G:0.24, T:0.48
Consensus pattern (12 bp):
TATATGTGTATG
Found at i:61859596 original size:18 final size:18
Alignment explanation
Indices: 61859570--61859616 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
61859560 TGTGATGTGT
* *
61859570 ATGTGTATGTGTCTGTAC
1 ATGTATATGTGTATGTAC
* *
61859588 ATGTATATGTATATGTAT
1 ATGTATATGTGTATGTAC
61859606 ATGTATATGTG
1 ATGTATATGTG
61859617 AATGAAGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (18 bp):
ATGTATATGTGTATGTAC
Found at i:61861896 original size:15 final size:16
Alignment explanation
Indices: 61861871--61861900 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61861861 TAAAACCTAA
61861871 ATTTATTACAATATTT
1 ATTTATTACAATATTT
61861887 ATTT-TTACAATATT
1 ATTTATTACAATATT
61861901 CGTTTCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATTACAATATTT
Found at i:61866293 original size:15 final size:16
Alignment explanation
Indices: 61866268--61866297 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61866258 AATATTAATT
61866268 GTATATTAAATATATA
1 GTATATTAAATATATA
61866284 GTAT-TTAAATATAT
1 GTATATTAAATATAT
61866298 CATAATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (16 bp):
GTATATTAAATATATA
Found at i:61867941 original size:31 final size:31
Alignment explanation
Indices: 61867905--61867971 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
61867895 TTAACAGCTT
*
61867905 AGTGACTTAAATAAAA-ACTTTTGAATAGTTA
1 AGTGACTTAAATAAAACA-TTTCGAATAGTTA
* *
61867936 AGTGACTTAAATGAAACATTTCGAATAGTTT
1 AGTGACTTAAATAAAACATTTCGAATAGTTA
61867967 AGTGA
1 AGTGA
61867972 TTATTTTGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATAAAACATTTCGAATAGTTA
Found at i:61868096 original size:6 final size:7
Alignment explanation
Indices: 61868081--61868105 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61868071 CTAAAAGTCA
61868081 TTTTCTT
1 TTTTCTT
61868088 TTTTCTT
1 TTTTCTT
61868095 TTTTCTT
1 TTTTCTT
61868102 TTTT
1 TTTT
61868106 TAAAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:61869687 original size:30 final size:30
Alignment explanation
Indices: 61869634--61869718 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
61869624 TCTTCAATGT
* * *
61869634 CGTTTGTTCCCTTGTCATCTGTGTCCCTGC
1 CGTTAGTTTCCTTGTCATTTGTGTCCCTGC
* *
61869664 CGTTCAG-TTCCTTCTCATTTGTGTCCTTGC
1 CGTT-AGTTTCCTTGTCATTTGTGTCCCTGC
*
61869694 CGTTTGTTTCCTTGTCATTTGTGTC
1 CGTTAGTTTCCTTGTCATTTGTGTC
61869719 TTTCTGCTGG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 1 0.02
30 44 0.96
31 1 0.02
ACGTcount: A:0.05, C:0.28, G:0.19, T:0.48
Consensus pattern (30 bp):
CGTTAGTTTCCTTGTCATTTGTGTCCCTGC
Found at i:61869699 original size:15 final size:15
Alignment explanation
Indices: 61869679--61869718 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
61869669 AGTTCCTTCT
61869679 CATTTGTGTCCTTGC
1 CATTTGTGTCCTTGC
* * *
61869694 CGTTTGTTTCCTTGT
1 CATTTGTGTCCTTGC
61869709 CATTTGTGTC
1 CATTTGTGTC
61869719 TTTCTGCTGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.23, G:0.20, T:0.53
Consensus pattern (15 bp):
CATTTGTGTCCTTGC
Found at i:61872365 original size:34 final size:36
Alignment explanation
Indices: 61872289--61872366 Score: 94
Period size: 34 Copynumber: 2.3 Consensus size: 36
61872279 TTTATTAAAA
* *
61872289 TAATAA-ATTATATTAATTATATATATTTGATTTAT
1 TAATAATATTATATTAAATATAAATATTTGATTTAT
*
61872324 T-AT-ATATTATTTTAAATATAAATATTT-ATTT-T
1 TAATAATATTATATTAAATATAAATATTTGATTTAT
61872356 TAATAATATTA
1 TAATAATATTA
61872367 AAAATAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
32 2 0.05
33 7 0.19
34 27 0.73
35 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (36 bp):
TAATAATATTATATTAAATATAAATATTTGATTTAT
Found at i:61872367 original size:29 final size:32
Alignment explanation
Indices: 61872297--61872382 Score: 79
Period size: 34 Copynumber: 2.7 Consensus size: 32
61872287 AATAATAAAT
* *
61872297 TATATTAATTATATATATTTGATTTATTATATA
1 TATATTAAATATAAATATTT-ATTTATTATATA
*
61872330 TTATTTTAAATATAAATATTTATTT-TTA-ATA
1 -TATATTAAATATAAATATTTATTTATTATATA
*
61872361 -ATATTAAAAATAATTATATTTA
1 TATATTAAATATAA--ATATTTA
61872383 AAATCAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 11 0.24
31 10 0.22
32 3 0.07
33 4 0.09
34 17 0.38
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
TATATTAAATATAAATATTTATTTATTATATA
Found at i:61878951 original size:19 final size:19
Alignment explanation
Indices: 61878927--61878963 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
61878917 TAAGGTTAAT
61878927 AAGAATTTGGGTCACATAC
1 AAGAATTTGGGTCACATAC
61878946 AAGAATTTGGGTCACATA
1 AAGAATTTGGGTCACATA
61878964 TCTTTAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (19 bp):
AAGAATTTGGGTCACATAC
Found at i:61882080 original size:24 final size:24
Alignment explanation
Indices: 61882053--61882104 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
61882043 ATAGTAAGTC
*
61882053 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
61882077 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
61882101 AAAT
1 AAAT
61882105 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:61883010 original size:20 final size:20
Alignment explanation
Indices: 61882968--61883010 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
61882958 AACATTATAT
*
61882968 AAGTTATTTAAAATATTAAA
1 AAGTTATTTAAAAGATTAAA
*
61882988 AAGTTA-TTGAAAGATTAATA
1 AAGTTATTTAAAAGATTAA-A
61883008 AAG
1 AAG
61883011 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (20 bp):
AAGTTATTTAAAAGATTAAA
Found at i:61883997 original size:16 final size:18
Alignment explanation
Indices: 61883965--61883997 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
61883955 CACTATATTT
61883965 TTACTTCACATATTCACC
1 TTACTTCACATATTCACC
61883983 TTAC-TCACA-ATTCAC
1 TTACTTCACATATTCAC
61883998 AAAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (18 bp):
TTACTTCACATATTCACC
Found at i:61898347 original size:7 final size:7
Alignment explanation
Indices: 61898335--61898363 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
61898325 AAAATAAATG
61898335 TATTAAA
1 TATTAAA
61898342 TATTAAA
1 TATTAAA
61898349 TATTAAA
1 TATTAAA
61898356 TATTAAA
1 TATTAAA
61898363 T
1 T
61898364 TAAAAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TATTAAA
Found at i:61902351 original size:111 final size:111
Alignment explanation
Indices: 61902157--61902380 Score: 430
Period size: 111 Copynumber: 2.0 Consensus size: 111
61902147 CCGTGATTCA
*
61902157 TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGACGTGGTCTGCATGCATAT
1 TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGAAGTGGTCTGCATGCATAT
61902222 CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
66 CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
*
61902268 TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGAAGTGGTTTGCATGCATAT
1 TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGAAGTGGTCTGCATGCATAT
61902333 CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
66 CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
61902379 TT
1 TT
61902381 ATCTTGTTAA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.42
Consensus pattern (111 bp):
TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGAAGTGGTCTGCATGCATAT
CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
Found at i:61924678 original size:31 final size:31
Alignment explanation
Indices: 61924642--61924708 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
61924632 AACAGCCCAG
* * *
61924642 ATGACTTCAATAAAAACTTTTGAATAGTTTA
1 ATGACTTAAATAAAAACTTTCGAATAGTTCA
*
61924673 ATGACTTAAATGAAAACTTTCGAATAGTTCA
1 ATGACTTAAATAAAAACTTTCGAATAGTTCA
61924704 ATGAC
1 ATGAC
61924709 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (31 bp):
ATGACTTAAATAAAAACTTTCGAATAGTTCA
Found at i:61941882 original size:25 final size:25
Alignment explanation
Indices: 61941854--61941910 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
61941844 ATGCTCTCAT
61941854 GAGCTGTAAATTAAG-AAGCTAATAC
1 GAGCTGTAAA-TAAGTAAGCTAATAC
** * *
61941879 GAGCTACAAATCAGTAAGCTCATAC
1 GAGCTGTAAATAAGTAAGCTAATAC
61941904 GAGCTGT
1 GAGCTGT
61941911 GGTGTGTCCG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (25 bp):
GAGCTGTAAATAAGTAAGCTAATAC
Found at i:61958931 original size:19 final size:19
Alignment explanation
Indices: 61958907--61958946 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
61958897 ACAACAAAAT
*
61958907 AATAGTAACATAATAGTGA
1 AATAGTAACAAAATAGTGA
*
61958926 AATAGTAGCAAAATAGTGA
1 AATAGTAACAAAATAGTGA
61958945 AA
1 AA
61958947 AAACAAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.23
Consensus pattern (19 bp):
AATAGTAACAAAATAGTGA
Found at i:61959320 original size:20 final size:19
Alignment explanation
Indices: 61959284--61959323 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
61959274 TTTTAAATTT
61959284 TTTTATCTATTTTTTTTTA
1 TTTTATCTATTTTTTTTTA
61959303 TTTT-TCTATGTTTCTTTTTA
1 TTTTATCTAT-TTT-TTTTTA
61959323 T
1 T
61959324 GATTTAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTATCTATTTTTTTTTA
Found at i:61972782 original size:20 final size:20
Alignment explanation
Indices: 61972757--61972796 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61972747 CGTAAAATGA
*
61972757 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
61972777 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
61972797 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:61972786 original size:34 final size:35
Alignment explanation
Indices: 61972742--61972808 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
61972732 CAGTAAAATA
*
61972742 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
61972776 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
61972809 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:61975254 original size:22 final size:22
Alignment explanation
Indices: 61975203--61975256 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
61975193 TGCAAAAAAA
* *
61975203 ATTGTTTTACTGTTGTTTTTCC
1 ATTGTTTTGCAGTTGTTTTTCC
* *
61975225 ACTATTTTGCAGTTG-TTTTCC
1 ATTGTTTTGCAGTTGTTTTTCC
61975246 TATTGTTTTGC
1 -ATTGTTTTGC
61975257 TATCATTCCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59
Consensus pattern (22 bp):
ATTGTTTTGCAGTTGTTTTTCC
Found at i:61977865 original size:12 final size:13
Alignment explanation
Indices: 61977838--61977867 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
61977828 ATTTTGGAGC
*
61977838 TTTTTGCTTGATT
1 TTTTTGCTCGATT
61977851 TTTTTGCTCGATT
1 TTTTTGCTCGATT
61977864 TTTT
1 TTTT
61977868 CTTTTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.10, G:0.13, T:0.70
Consensus pattern (13 bp):
TTTTTGCTCGATT
Found at i:61978180 original size:28 final size:28
Alignment explanation
Indices: 61978140--61978198 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
61978130 AATATAATTT
* *
61978140 TTTTGAAAGATTAGGGTTCAAAATGTAA
1 TTTTGAAAAATTAGGGGTCAAAATGTAA
61978168 TTTTGAAAAATTAGGGGTCAAAATGTAA
1 TTTTGAAAAATTAGGGGTCAAAATGTAA
61978196 TTT
1 TTT
61978199 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.37
Consensus pattern (28 bp):
TTTTGAAAAATTAGGGGTCAAAATGTAA
Found at i:61978645 original size:75 final size:75
Alignment explanation
Indices: 61978553--61978834 Score: 411
Period size: 75 Copynumber: 3.8 Consensus size: 75
61978543 GCTCGGCATA
* * * * *
61978553 CGACCCGAAGCTTAACTCACCTCTTGGATTATGAGTTGATCTTTGAAAAATGGAAATTGAAAATA
1 CGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAATAGAAATTGAAAATA
*
61978618 CATTAGCGCG
66 CATTAGCGTG
* * *
61978628 CGACCCGAGGCTCAACTCACCTCTCAGTTTATGAGTTGATTTTTAAAAAATAGAAATTGAAAATA
1 CGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAATAGAAATTGAAAATA
* *
61978693 CCTCAGCGTG
66 CATTAGCGTG
*
61978703 CGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATA
1 CGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAATAGAAATTGAAAATA
*
61978768 CTTTAGCGTG
66 CATTAGCGTG
* * * *
61978778 CGACCCGAGACTCAACTCACCTCTCGGGTTATGAGTTAATTTTTGAAAAACAGAAAT
1 CGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAATAGAAAT
61978835 AAAAATATGT
Statistics
Matches: 187, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 187 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (75 bp):
CGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAATAGAAATTGAAAATA
CATTAGCGTG
Found at i:61983623 original size:27 final size:28
Alignment explanation
Indices: 61983592--61983644 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
61983582 TAATTTATGT
*
61983592 AAGATGAACACAATATT-TTTTTTAAAG
1 AAGATGAACACAATATTATTCTTTAAAG
* *
61983619 AAGATGACCACATTATTATTCTTTAA
1 AAGATGAACACAATATTATTCTTTAA
61983645 TTTCTCATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (28 bp):
AAGATGAACACAATATTATTCTTTAAAG
Found at i:61983924 original size:22 final size:21
Alignment explanation
Indices: 61983887--61983948 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
61983877 AAAAGGTTAA
61983887 AAATA-TTTTA-TA-TTTTTT
1 AAATATTTTTATTATTTTTTT
*
61983905 -AATACTTTTTATTATTTTTTAA
1 AAATA-TTTTTATTATTTTTT-T
61983927 AAATATTTTTA-TATTTTTTT
1 AAATATTTTTATTATTTTTTT
61983947 AA
1 AA
61983949 TTTTTGAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 4 0.11
19 5 0.14
20 4 0.11
21 13 0.36
22 6 0.17
23 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
AAATATTTTTATTATTTTTTT
Found at i:61983943 original size:20 final size:20
Alignment explanation
Indices: 61983883--61983944 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 20
61983873 TTAAAAAAGG
61983883 TTAAAAATA-TTTTATATTT
1 TTAAAAATATTTTTATATTT
*
61983902 TT--TAATACTTTTTATTATTTT
1 TTAAAAATA-TTTTTA-TA-TTT
61983923 TTAAAAATATTTTTATATTT
1 TTAAAAATATTTTTATATTT
61983943 TT
1 TT
61983945 TTAATTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
17 4 0.11
19 7 0.20
20 7 0.20
21 7 0.20
22 6 0.17
23 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTAAAAATATTTTTATATTT
Found at i:61990762 original size:51 final size:51
Alignment explanation
Indices: 61990655--61990767 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
61990645 CATCTGTAGG
* * * *
61990655 TTATCCGCAACCCCCGGTAGTGTCACCCGTGGTGGCATATCCGGATCCGCA
1 TTATCCACAAGCCCCGGTAATGTCACCCGTGGTGGCATATCCGGATCCACA
* * * *
61990706 CTATCCCCAAGCCCCGGTAAAT-TCACCTGTGGTGGCATATCCGGATCCATA
1 TTATCCACAAGCCCCGGT-AATGTCACCCGTGGTGGCATATCCGGATCCACA
61990757 TTATCCACAAG
1 TTATCCACAAG
61990768 TAAACACCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 50 0.96
52 2 0.04
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.23
Consensus pattern (51 bp):
TTATCCACAAGCCCCGGTAATGTCACCCGTGGTGGCATATCCGGATCCACA
Found at i:61991562 original size:6 final size:6
Alignment explanation
Indices: 61991555--61991591 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
61991545 GGGCCCTCAC
*
61991555 CATCAC CATCAA CCATCAA CATCAA CATCAA CATCAA
1 CATCAA CATCAA -CATCAA CATCAA CATCAA CATCAA
61991592 TAGGAAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (6 bp):
CATCAA
Found at i:61991583 original size:19 final size:18
Alignment explanation
Indices: 61991555--61991591 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
61991545 GGGCCCTCAC
*
61991555 CATCACCATCAACCATCAA
1 CATCAACATCAA-CATCAA
61991574 CATCAACATCAACATCAA
1 CATCAACATCAACATCAA
61991592 TAGGAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (18 bp):
CATCAACATCAACATCAA
Found at i:61991585 original size:12 final size:13
Alignment explanation
Indices: 61991553--61991591 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
61991543 CAGGGCCCTC
*
61991553 ACCATCACCATCA
1 ACCATCAACATCA
61991566 ACCATCAACATCA
1 ACCATCAACATCA
61991579 A-CATCAACATCA
1 ACCATCAACATCA
61991591 A
1 A
61991592 TAGGAAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (13 bp):
ACCATCAACATCA
Found at i:61992153 original size:16 final size:16
Alignment explanation
Indices: 61992134--61992176 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
61992124 TGTTTGAATA
61992134 AATTTTGAGTTTAAAT
1 AATTTTGAGTTTAAAT
* *
61992150 AATTTTAAATTTAAAT
1 AATTTTGAGTTTAAAT
*
61992166 CATTTTGAGTT
1 AATTTTGAGTT
61992177 CATATTGAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (16 bp):
AATTTTGAGTTTAAAT
Found at i:61992451 original size:21 final size:22
Alignment explanation
Indices: 61992427--61992478 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
61992417 CATGAAGCAA
61992427 CCCCATACC-CCACTACAACAG
1 CCCCATACCTCCACTACAACAG
61992448 CCCCATACCTCCACTACAACAG
1 CCCCATACCTCCACTACAACAG
*
61992470 TCCCATACC
1 CCCCATACC
61992479 GTCTGACACT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.31, C:0.52, G:0.04, T:0.13
Consensus pattern (22 bp):
CCCCATACCTCCACTACAACAG
Found at i:61992948 original size:11 final size:11
Alignment explanation
Indices: 61992919--61992962 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
61992909 CTGGCCGGAT
* *
61992919 TCCCTTCCCCC
1 TCCCTTCTCTC
61992930 TCCCTTCTCTC
1 TCCCTTCTCTC
61992941 TCCCTTCTCTC
1 TCCCTTCTCTC
*
61992952 TTCCCCTCTCT
1 -TCCCTTCTCT
61992963 TCTTTTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (11 bp):
TCCCTTCTCTC
Found at i:61993450 original size:3 final size:3
Alignment explanation
Indices: 61993427--61993496 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
61993417 AATATCCTTG
* * **
61993427 TTA TT- TTA -TA TTA TTA GTA TTA TTA GTA TTA CCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
61993473 TGTA TTA GTA TATA TTT TTA TTA T
1 T-TA TTA TTA T-TA TTA TTA TTA T
61993497 GTACGTGTAT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:61993493 original size:23 final size:22
Alignment explanation
Indices: 61993439--61993499 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
61993429 ATTTTATATT
*
61993439 ATTAGTATTATTA-GTATTACC
1 ATTATTATTATTATGTATTACC
**
61993460 ATTATTATTATTATGTATTAGT
1 ATTATTATTATTATGTATTACC
*
61993482 ATATATTTTTATTATGTA
1 AT-TATTATTATTATGTA
61993500 CGTGTATACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.35
22 8 0.24
23 14 0.41
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (22 bp):
ATTATTATTATTATGTATTACC
Found at i:61993506 original size:23 final size:23
Alignment explanation
Indices: 61993462--61993507 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
61993452 GTATTACCAT
*
61993462 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTAGTAGTATA
*
61993485 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
61993508 CATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:61994075 original size:11 final size:11
Alignment explanation
Indices: 61994059--61994083 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
61994049 GTACGTATTG
61994059 TATATGTTCTA
1 TATATGTTCTA
61994070 TATATGTTCTA
1 TATATGTTCTA
61994081 TAT
1 TAT
61994084 TTTTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
TATATGTTCTA
Found at i:61994151 original size:24 final size:23
Alignment explanation
Indices: 61994113--61994158 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
61994103 TATATAGTTC
*
61994113 TTATACATTTCATGTACATATTT
1 TTATACATCTCATGTACATATTT
*
61994136 TTATACCATCTCATGTATATATT
1 TTATA-CATCTCATGTACATATT
61994159 CATTGTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.50
Consensus pattern (23 bp):
TTATACATCTCATGTACATATTT
Found at i:61994964 original size:1 final size:1
Alignment explanation
Indices: 61994960--61994984 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
61994950 TTTTTTTAGC
61994960 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
61994985 CTTAAACGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:62010456 original size:51 final size:51
Alignment explanation
Indices: 62010349--62010461 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
62010339 CATCTGTAGG
* * * *
62010349 TTATCCGCAACCCCCGGTAGTGTCACCCGTGGTGGCATATCCGGATCCGCA
1 TTATCCACAAGCCCCGGTAATGTCACCCGTGGTGGCATATCCGGATCCACA
* * * *
62010400 CTATCCCCAAGCCCCGGTAAAT-TCACCTGTGGTGGCATATCCGGATCCATA
1 TTATCCACAAGCCCCGGT-AATGTCACCCGTGGTGGCATATCCGGATCCACA
62010451 TTATCCACAAG
1 TTATCCACAAG
62010462 TAAACACCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 50 0.96
52 2 0.04
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.23
Consensus pattern (51 bp):
TTATCCACAAGCCCCGGTAATGTCACCCGTGGTGGCATATCCGGATCCACA
Found at i:62011256 original size:6 final size:6
Alignment explanation
Indices: 62011249--62011285 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
62011239 GGGCCCTCAC
*
62011249 CATCAC CATCAA CCATCAA CATCAA CATCAA CATCAA
1 CATCAA CATCAA -CATCAA CATCAA CATCAA CATCAA
62011286 TAGGAAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (6 bp):
CATCAA
Found at i:62011277 original size:19 final size:18
Alignment explanation
Indices: 62011249--62011285 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
62011239 GGGCCCTCAC
*
62011249 CATCACCATCAACCATCAA
1 CATCAACATCAA-CATCAA
62011268 CATCAACATCAACATCAA
1 CATCAACATCAACATCAA
62011286 TAGGAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (18 bp):
CATCAACATCAACATCAA
Done.