Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 136 of 150
Found at i:40916580 original size:114 final size:114
Alignment explanation
Indices: 40916417--40916666 Score: 369
Period size: 114 Copynumber: 2.2 Consensus size: 114
40916407 ACCTCTATCT
* * *
40916417 CCAACAAACACATCTCCACCAATATCTACACCTTTAACATCACCTATGATACCAT-TTCCACCTC
1 CCAACAAACTCACCTCCACCAATATCTACACCTTTAAAATCACCTATGATACCATCTT-CACCTC
* * *
40916481 CAAGGAACTTGCGACCACCTTCACCTCTAAGAAACTCATCTTTTCCA-TCA
65 CAAGGAACTTGCGACCACCTCCACCTCTAAGAAACTCACCTTCTCCACT-A
* *
40916531 CCAACAAACTCACCTCCACCAATATCTACTCCTTTAAAATCACCTATGATACTATCTTCACCTCC
1 CCAACAAACTCACCTCCACCAATATCTACACCTTTAAAATCACCTATGATACCATCTTCACCTCC
*
40916596 AAGGAACTTGCGACCACCTCCACCTCTAAGAAACTCGCCTTCTCCACTA
66 AAGGAACTTGCGACCACCTCCACCTCTAAGAAACTCACCTTCTCCACTA
* *
40916645 CTAACAAACTCACATCCACCAA
1 CCAACAAACTCACCTCCACCAA
40916667 GATCATTGTC
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
114 120 0.98
115 3 0.02
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.24
Consensus pattern (114 bp):
CCAACAAACTCACCTCCACCAATATCTACACCTTTAAAATCACCTATGATACCATCTTCACCTCC
AAGGAACTTGCGACCACCTCCACCTCTAAGAAACTCACCTTCTCCACTA
Found at i:40918626 original size:33 final size:33
Alignment explanation
Indices: 40918589--40918666 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
40918579 TGGCCCTGCC
* **
40918589 ATGGTCTTACACTCGTA-ATGCCATAACCCAGTT
1 ATGGTCTTACACTC-AAGATGCCATAACCCAACT
*
40918622 ATGGTCTTATCA-TCAAGATGCCATAGCCCAACT
1 ATGGTCTTA-CACTCAAGATGCCATAACCCAACT
40918655 ATGGTCTTACAC
1 ATGGTCTTACAC
40918667 GTATACATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 3 0.08
33 33 0.87
34 2 0.05
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (33 bp):
ATGGTCTTACACTCAAGATGCCATAACCCAACT
Found at i:40920797 original size:34 final size:35
Alignment explanation
Indices: 40920753--40920819 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
40920743 CAGTAAAATA
*
40920753 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
40920787 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
40920820 CTGGTTTTTG
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:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:40922746 original size:17 final size:17
Alignment explanation
Indices: 40922709--40922747 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
40922699 GGAAATCATG
*
40922709 TTATAAGTGTAATATGG
1 TTATAAGTGTAATATGA
*
40922726 TTATAAGTGTAATCTGA
1 TTATAAGTGTAATATGA
40922743 TTATA
1 TTATA
40922748 TTGTGAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.44
Consensus pattern (17 bp):
TTATAAGTGTAATATGA
Found at i:40924715 original size:5 final size:5
Alignment explanation
Indices: 40924705--40924731 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
40924695 GTCTCCTACC
40924705 TTGCT TTGCT TTGCT TTGCT TTGCT TT
1 TTGCT TTGCT TTGCT TTGCT TTGCT TT
40924732 TCCATCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.19, T:0.63
Consensus pattern (5 bp):
TTGCT
Found at i:40945873 original size:22 final size:22
Alignment explanation
Indices: 40945821--40945874 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
40945811 CAATTCAATA
*
40945821 ATATAAATAATATAAAATGTTT
1 ATATAAATAATATAAAATGTAT
*
40945843 A-ATTTAATAATAT-AAATAGTAT
1 ATA-TAAATAATATAAAAT-GTAT
40945865 ATATAAATAA
1 ATATAAATAA
40945875 AATTATTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.19
22 20 0.77
23 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (22 bp):
ATATAAATAATATAAAATGTAT
Found at i:40946374 original size:9 final size:9
Alignment explanation
Indices: 40946360--40946396 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40946350 TATAGTTTGA
40946360 TATTCGAAT
1 TATTCGAAT
40946369 TATTCGAAT
1 TATTCGAAT
*
40946378 TATTCGAGT
1 TATTCGAAT
*
40946387 TATTCAAAT
1 TATTCGAAT
40946396 T
1 T
40946397 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40950468 original size:37 final size:40
Alignment explanation
Indices: 40950372--40950511 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
40950362 AACACACCAG
* **
40950372 TTTGGCACCCAATGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
* ** *
40950412 TTTGACACCCAGTATCTCATCGGTTAAACCGAAGT-A-AA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
* * *
40950450 -TTGGCACCCAGTGCCTCATCGAATTAATA-TGAAGTAGTAA
1 TTTGGCACCCAGTGCCTCATCGGA-TAA-ACCGAAGTAATAA
* * *
40950490 ATTGACACCCAGTGTCTCATCG
1 TTTGGCACCCAGTGCCTCATCG
40950512 ACTCGAAGTC
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 18 0.23
38 10 0.13
39 2 0.03
40 30 0.38
41 19 0.24
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (40 bp):
TTTGGCACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
Found at i:40950668 original size:19 final size:19
Alignment explanation
Indices: 40950643--40950695 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
40950633 CAATTAAAAT
40950643 AATCAATATATTCAATATA
1 AATCAATATATTCAATATA
* *
40950662 TATCAAT-TAAATCAATATA
1 AATCAATAT-ATTCAATATA
*
40950681 AATTCAATAAATTCA
1 AA-TCAATATATTCA
40950696 TTACACACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (19 bp):
AATCAATATATTCAATATA
Found at i:40951401 original size:11 final size:11
Alignment explanation
Indices: 40951387--40951454 Score: 68
Period size: 11 Copynumber: 6.2 Consensus size: 11
40951377 TTCTCCTTCA
*
40951387 TTTCTTTCCTT
1 TTTCTTTCTTT
40951398 TTTCTTT-TTT
1 TTTCTTTCTTT
*
40951408 TTTCTTTTTTT
1 TTTCTTTCTTT
*
40951419 TTTCTTTC-TG
1 TTTCTTTCTTT
*
40951429 TTTCGTTTCTATC
1 TTTC-TTTCT-TT
40951442 TTTCTTTCTTT
1 TTTCTTTCTTT
40951453 TT
1 TT
40951455 ATTTGTTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 14 0.29
11 24 0.50
12 5 0.10
13 5 0.10
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:40951426 original size:4 final size:4
Alignment explanation
Indices: 40951387--40951452 Score: 50
Period size: 4 Copynumber: 16.8 Consensus size: 4
40951377 TTCTCCTTCA
* *
40951387 TTTC TTTC CTT- TTTC TTT- TTT- TTTC TTT- TTTT TTTC TTTC TGTTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC --TTTC
*
40951433 GTTTC TATC TTTC TTTC TTT
1 -TTTC TTTC TTTC TTTC TTT
40951453 TTATTTGTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
3 11 0.21
4 32 0.62
5 5 0.10
6 4 0.08
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:40954400 original size:17 final size:17
Alignment explanation
Indices: 40954380--40954413 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40954370 GATATTTGTT
40954380 ATTAAAATAAACAAATA
1 ATTAAAATAAACAAATA
*
40954397 ATTAAAATAAATAAATA
1 ATTAAAATAAACAAATA
40954414 TTATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
ATTAAAATAAACAAATA
Found at i:40955176 original size:16 final size:17
Alignment explanation
Indices: 40955152--40955184 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40955142 TATGGTAAGC
40955152 AAATAATAAGGTAAGTG
1 AAATAATAAGGTAAGTG
*
40955169 AAAT-ATAAGTTAAGTG
1 AAATAATAAGGTAAGTG
40955185 TTATTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (17 bp):
AAATAATAAGGTAAGTG
Found at i:40955293 original size:36 final size:36
Alignment explanation
Indices: 40955253--40955324 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
40955243 GAATATTGAC
* *
40955253 TTGAAAATGGAAAAGT-AAATTTGAATTGAATTGTGA
1 TTGAAAATGAAAAAGTGAAA-TTGAATTGAAATGTGA
*
40955289 TTGAAAGTGAAAAAGTGAAATTGAATTGAAATGTGA
1 TTGAAAATGAAAAAGTGAAATTGAATTGAAATGTGA
40955325 ATTTGAGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 29 0.91
37 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.31
Consensus pattern (36 bp):
TTGAAAATGAAAAAGTGAAATTGAATTGAAATGTGA
Found at i:40955552 original size:23 final size:22
Alignment explanation
Indices: 40955524--40955633 Score: 127
Period size: 23 Copynumber: 5.0 Consensus size: 22
40955514 CGGCTTTGCC
40955524 AATCAGGCACTTTATGTGTCGT
1 AATCAGGCACTTTATGTGTCGT
40955546 ACATCAGGCACTTTATGTGTCGT
1 A-ATCAGGCACTTTATGTGTCGT
* *
40955569 ATCTCAGGCACTGTATGTGTCGT
1 A-ATCAGGCACTTTATGTGTCGT
* **
40955592 -ATCAGGCACCTCGTGTGTCGT
1 AATCAGGCACTTTATGTGTCGT
*
40955613 -TTCAGGCAC-TTATGTGTCGT
1 AATCAGGCACTTTATGTGTCGT
40955633 A
1 A
40955634 TATTGATTAG
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
20 9 0.12
21 24 0.32
22 1 0.01
23 41 0.55
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (22 bp):
AATCAGGCACTTTATGTGTCGT
Found at i:40960151 original size:57 final size:58
Alignment explanation
Indices: 40960046--40960161 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 58
40960036 AACAATTTCT
* *
40960046 ACTTATAGTAATTATACTAAATCATATAATATATACTCTATAGCAAAATTTTAACATA
1 ACTTATAGTAATTATACAAAATCATATAATATATACTCTAGAGCAAAATTTTAACATA
* * * **
40960104 ACTTATGGTAATTATA-AAAATTATATAATATATATTCTAGATTAAAATTTTAACATA
1 ACTTATAGTAATTATACAAAATCATATAATATATACTCTAGAGCAAAATTTTAACATA
40960161 A
1 A
40960162 ACAAAGAACT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 36 0.71
58 15 0.29
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (58 bp):
ACTTATAGTAATTATACAAAATCATATAATATATACTCTAGAGCAAAATTTTAACATA
Found at i:40967292 original size:9 final size:9
Alignment explanation
Indices: 40967275--40967321 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
40967265 TACCTCAATG
*
40967275 ATTTAAAAA
1 ATTTCAAAA
*
40967284 ATTTTAAAA
1 ATTTCAAAA
*
40967293 ATAT-AAAA
1 ATTTCAAAA
40967301 ATTTCAAAA
1 ATTTCAAAA
40967310 ATGTTCAAAA
1 AT-TTCAAAA
40967320 AT
1 AT
40967322 AAAAATTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.21
9 17 0.52
10 9 0.27
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (9 bp):
ATTTCAAAA
Found at i:40968969 original size:19 final size:18
Alignment explanation
Indices: 40968930--40968973 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
40968920 TAAAAACAAA
*
40968930 TTTATAGAAATAAAATGTT
1 TTTATAAAAATAAAA-GTT
40968949 TTTATAAAAATAAGAA-TT
1 TTTATAAAAATAA-AAGTT
40968967 TTTATAA
1 TTTATAA
40968974 TTTTATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 9 0.39
19 12 0.52
20 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (18 bp):
TTTATAAAAATAAAAGTT
Found at i:40971093 original size:4 final size:4
Alignment explanation
Indices: 40971084--40971124 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
40971074 AGAAGAACCC
*
40971084 CATA CATA CATA CGTA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
40971125 CTTCTCTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:40971855 original size:32 final size:32
Alignment explanation
Indices: 40971805--40971868 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
40971795 CCTAAGTTAT
*
40971805 TTGAGTTCGGGTGCGAGTATTGAATATGTATA
1 TTGAGTTCGGGTGCGAGTATTGAAAATGTATA
** *
40971837 TTGAGTTTTGGTGTGAGTATTGAAAATGTATA
1 TTGAGTTCGGGTGCGAGTATTGAAAATGTATA
40971869 CGTGTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.27, C:0.03, G:0.30, T:0.41
Consensus pattern (32 bp):
TTGAGTTCGGGTGCGAGTATTGAAAATGTATA
Found at i:40985100 original size:11 final size:11
Alignment explanation
Indices: 40985084--40985108 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40985074 TTAAATTTTA
40985084 AAAAATTAATT
1 AAAAATTAATT
40985095 AAAAATTAATT
1 AAAAATTAATT
40985106 AAA
1 AAA
40985109 TGATGATGCA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAATTAATT
Found at i:40990194 original size:27 final size:27
Alignment explanation
Indices: 40990153--40990205 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
40990143 TTTTGGTGTA
* *
40990153 TTTCGGATGGATTAGCTCTTATGAGCG
1 TTTCAGATGGATTAGCTCGTATGAGCG
*
40990180 TTTCAGATGGTTTAGCTCGTATGAGC
1 TTTCAGATGGATTAGCTCGTATGAGC
40990206 ATTAGTGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (27 bp):
TTTCAGATGGATTAGCTCGTATGAGCG
Found at i:40990232 original size:35 final size:36
Alignment explanation
Indices: 40990179--40990253 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 36
40990169 TCTTATGAGC
* * *
40990179 GTTTCAGATGGTTTAGCTCGTATGAGCA-TTAGTGT
1 GTTTCAGAGGGATAAGCTCGTATGAGCATTTAGTGT
* * *
40990214 GTTTCAGAGGGATAAGCTCTTATGAGTATTTGGTGT
1 GTTTCAGAGGGATAAGCTCGTATGAGCATTTAGTGT
40990250 GTTT
1 GTTT
40990254 TGGTTGGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.20, C:0.09, G:0.29, T:0.41
Consensus pattern (36 bp):
GTTTCAGAGGGATAAGCTCGTATGAGCATTTAGTGT
Found at i:40991822 original size:81 final size:81
Alignment explanation
Indices: 40991682--40991850 Score: 311
Period size: 81 Copynumber: 2.1 Consensus size: 81
40991672 TTATTTGTGT
* *
40991682 TATTCTTATTCAATCAAGATTCTCCTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTATTA
1 TATTGTTATTCAATCAAGATTCTCCTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTAGTA
40991747 ATAGACAAGTTTCATA
66 ATAGACAAGTTTCATA
*
40991763 TATTGTTATTCAATCAAGATTCTCTTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTAGTA
1 TATTGTTATTCAATCAAGATTCTCCTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTAGTA
40991828 ATAGACAAGTTTCATA
66 ATAGACAAGTTTCATA
40991844 TATTGTT
1 TATTGTT
40991851 TTCTGCCAGA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (81 bp):
TATTGTTATTCAATCAAGATTCTCCTATCTCTCCCTATAAATAGATGATATTGGTAGAGCTAGTA
ATAGACAAGTTTCATA
Found at i:40991900 original size:20 final size:19
Alignment explanation
Indices: 40991871--40991908 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
40991861 AAGTAGTGAG
40991871 AATTTATTTTCTAAGAATA
1 AATTTATTTTCTAAGAATA
*
40991890 AATTCTATTTTCTGAGAAT
1 AATT-TATTTTCTAAGAAT
40991909 TACAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:41000362 original size:25 final size:24
Alignment explanation
Indices: 41000329--41000376 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
41000319 ATATGTTTTG
* *
41000329 TTTATTTATTTATCTATTTATTAT
1 TTTATTTATTTATATATATATTAT
41000353 TTTATATTATTTATATATATATTA
1 TTTAT-TTATTTATATATATATTA
41000377 AAAATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTATTTATTTATATATATATTAT
Found at i:41003992 original size:16 final size:15
Alignment explanation
Indices: 41003969--41003998 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41003959 GCAAAAAAAC
41003969 AAATGGACAAAGGGA
1 AAATGGACAAAGGGA
41003984 AAATAGGACAAAGGG
1 AAAT-GGACAAAGGG
41003999 GAAAGGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.07, G:0.33, T:0.07
Consensus pattern (15 bp):
AAATGGACAAAGGGA
Found at i:41006236 original size:2 final size:2
Alignment explanation
Indices: 41006229--41006259 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41006219 TTTATTTGGT
41006229 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 T
41006260 TTCAGTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41010266 original size:21 final size:20
Alignment explanation
Indices: 41010236--41010275 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41010226 GCGCAAAACA
41010236 AAAACCATGAAAAATGTGGAG
1 AAAACCATG-AAAATGTGGAG
* *
41010257 AAAACTATGATAATGTGGA
1 AAAACCATGAAAATGTGGA
41010276 CTGAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (20 bp):
AAAACCATGAAAATGTGGAG
Found at i:41010886 original size:2 final size:2
Alignment explanation
Indices: 41010879--41010910 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41010869 GTCATCTCTT
41010879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41010911 ATTTTATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41023480 original size:17 final size:16
Alignment explanation
Indices: 41023453--41023484 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41023443 AAACTGTTTG
41023453 TTTTCTTTATTTTTAT
1 TTTTCTTTATTTTTAT
41023469 TTTTCTTTTATTTTTA
1 TTTTC-TTTATTTTTA
41023485 AAATATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTATTTTTAT
Found at i:41024128 original size:3 final size:3
Alignment explanation
Indices: 41024122--41024159 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
41024112 TTATTTAACC
41024122 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT
41024160 TCCTCTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41024492 original size:20 final size:20
Alignment explanation
Indices: 41024467--41024506 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41024457 ATAAATTAAC
41024467 GTATTTATTTGTATACATAT
1 GTATTTATTTGTATACATAT
41024487 GTATTTATTTGTATACATAT
1 GTATTTATTTGTATACATAT
41024507 TTTCTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (20 bp):
GTATTTATTTGTATACATAT
Found at i:41029120 original size:2 final size:2
Alignment explanation
Indices: 41029113--41029147 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41029103 ACCAAAACTA
41029113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41029148 GTTAGAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41039789 original size:15 final size:15
Alignment explanation
Indices: 41039745--41039795 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
41039735 AGAAAACCCG
*
41039745 AATATCTCAAACTCAA
1 AATAT-TCAAACTTAA
*
41039761 AATAATTTAAACTTAA
1 AAT-ATTCAAACTTAA
*
41039777 AATATTCAAACTTGA
1 AATATTCAAACTTAA
41039792 AATA
1 AATA
41039796 ATCCTAACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 14 0.47
16 14 0.47
17 2 0.07
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (15 bp):
AATATTCAAACTTAA
Found at i:41046300 original size:3 final size:3
Alignment explanation
Indices: 41046294--41046340 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
41046284 TATAATTCAG
41046294 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
41046341 GCTTTTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:41046631 original size:21 final size:22
Alignment explanation
Indices: 41046605--41046666 Score: 56
Period size: 27 Copynumber: 2.6 Consensus size: 22
41046595 TTAATAGATC
41046605 CTTCAATTTTTTTTTCTTTCA-
1 CTTCAATTTTTTTTTCTTTCAT
41046626 CTTCAACCTTTCATTTCATTTCTTTCAT
1 CTTCAA--TTT--TTT--TTTCTTTCAT
41046654 CTT-AATTTTTTTT
1 CTTCAATTTTTTTT
41046667 CTCAAAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
21 8 0.24
23 6 0.18
25 6 0.18
27 11 0.32
28 3 0.09
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (22 bp):
CTTCAATTTTTTTTTCTTTCAT
Found at i:41049327 original size:38 final size:38
Alignment explanation
Indices: 41049271--41049343 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
41049261 AGCATGCTTA
* *
41049271 ACCAAAAATAAGTCGAATTCCTTGTCGTCCACCACTGT
1 ACCAAAAATAAGTCGAATTCCTTATCCTCCACCACTGT
*
41049309 ACCAAAAATAAGTGGAATTCCTTATCCTCCACCAC
1 ACCAAAAATAAGTCGAATTCCTTATCCTCCACCAC
41049344 CGTTTGACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (38 bp):
ACCAAAAATAAGTCGAATTCCTTATCCTCCACCACTGT
Found at i:41049645 original size:21 final size:21
Alignment explanation
Indices: 41049623--41049675 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
41049613 ATATATTTTA
41049623 AAAT-TATAGAAAA-TAGAAAT
1 AAATATATA-AAAAGTAGAAAT
41049643 AAATATATAAAAAGTAGAAA-
1 AAATATATAAAAAGTAGAAAT
*
41049663 ATATATTATAAAA
1 AAATA-TATAAAA
41049676 TATAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (21 bp):
AAATATATAAAAAGTAGAAAT
Found at i:41050928 original size:67 final size:68
Alignment explanation
Indices: 41050852--41050989 Score: 197
Period size: 67 Copynumber: 2.0 Consensus size: 68
41050842 TAAATTTATA
* * * *
41050852 AATAAATTAATAAGATAAAAAGATACATATTTTTAGATATAATATAATAAATT-AAAAAGTTAAT
1 AATAAATTAATAAGATAAAAAGATACATACTTTTAAATATAATATAAGAAATTAAAAAAATTAAT
41050916 TTT
66 TTT
* * * *
41050919 AATAAATTAATAGGATAAAAAGATAGATACTTTTAAATTTAATTTAAGAAATTAAAAAAATTAAT
1 AATAAATTAATAAGATAAAAAGATACATACTTTTAAATATAATATAAGAAATTAAAAAAATTAAT
41050984 TTT
66 TTT
41050987 AAT
1 AAT
41050990 TTTACATTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
67 46 0.74
68 16 0.26
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (68 bp):
AATAAATTAATAAGATAAAAAGATACATACTTTTAAATATAATATAAGAAATTAAAAAAATTAAT
TTT
Found at i:41063194 original size:17 final size:17
Alignment explanation
Indices: 41063172--41063205 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41063162 CGGATCATTT
*
41063172 CAAGTTCAAGTTAGTTC
1 CAAGTTCAAGTCAGTTC
*
41063189 CAAGTTCCAGTCAGTTC
1 CAAGTTCAAGTCAGTTC
41063206 GGATTTGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (17 bp):
CAAGTTCAAGTCAGTTC
Found at i:41066802 original size:14 final size:14
Alignment explanation
Indices: 41066783--41066817 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
41066773 TTGACATTTT
*
41066783 TTCTAATGATACTA
1 TTCTAACGATACTA
41066797 TTCTAACGATACTA
1 TTCTAACGATACTA
41066811 TTCTAAC
1 TTCTAAC
41066818 ATGTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:41068105 original size:62 final size:62
Alignment explanation
Indices: 41068021--41068184 Score: 292
Period size: 62 Copynumber: 2.6 Consensus size: 62
41068011 ATTACAACAT
41068021 TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAC
1 TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAC
* * *
41068083 TACAACATTAAAATTTGAAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAT
1 TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAC
*
41068145 TACAACATTAAAACTTGGAACAAACTTTGTAATAGAAATT
1 TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
41068185 AGGTACATTG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 96 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (62 bp):
TACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAATACAC
Found at i:41069516 original size:20 final size:21
Alignment explanation
Indices: 41069490--41069536 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
41069480 AAATAAAAAC
41069490 TTAAACTTAAACTAGCAACAA
1 TTAAACTTAAACTAGCAACAA
*
41069511 -TAAACTTAAGCTAGCAACAA
1 TTAAACTTAAACTAGCAACAA
41069531 TTAAAC
1 TTAAAC
41069537 CAATAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.23
Consensus pattern (21 bp):
TTAAACTTAAACTAGCAACAA
Found at i:41074101 original size:18 final size:18
Alignment explanation
Indices: 41074078--41074113 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41074068 AATAATACAT
41074078 TTTCTTTCTTCTCTTTTC
1 TTTCTTTCTTCTCTTTTC
*
41074096 TTTCTTTCTTCTGTTTTC
1 TTTCTTTCTTCTCTTTTC
41074114 CCTCTCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTCTTTCTTCTCTTTTC
Found at i:41077227 original size:34 final size:34
Alignment explanation
Indices: 41077183--41077255 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
41077173 GTATCTTAAA
*
41077183 AGAATTAGGGATTATATACTTGTGTAATCTAGGC
1 AGAACTAGGGATTATATACTTGTGTAATCTAGGC
*
41077217 AGAACTAGGGATTATATGCTTGTGTAATCTAGGC
1 AGAACTAGGGATTATATACTTGTGTAATCTAGGC
41077251 AGAAC
1 AGAAC
41077256 CTTACTCCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (34 bp):
AGAACTAGGGATTATATACTTGTGTAATCTAGGC
Found at i:41090308 original size:15 final size:14
Alignment explanation
Indices: 41090280--41090306 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41090270 CACATACCTT
41090280 TTTTTTAATATTTA
1 TTTTTTAATATTTA
41090294 TTTTTTAATATTT
1 TTTTTTAATATTT
41090307 TACTATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:41091955 original size:2 final size:2
Alignment explanation
Indices: 41091948--41091972 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41091938 ATTGTAGGGG
41091948 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41091973 ATAAAAGTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41095270 original size:2 final size:2
Alignment explanation
Indices: 41095263--41095290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41095253 CTAACTCAGG
41095263 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41095291 ATCCTACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:41098386 original size:51 final size:51
Alignment explanation
Indices: 41098309--41098421 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
41098299 CTGATTAGTA
41098309 ACAAGTGATAAGTAGTAGTTTCAGCTACACTTATCTGATCAGTGACAAGTG
1 ACAAGTGATAAGTAGTAGTTTCAGCTACACTTATCTGATCAGTGACAAGTG
* *
41098360 ACAAGTGATAAGTGGTAGCTTT-AGCTACACTTATCTTATCAGTGACAAGTG
1 ACAAGTGATAAGTAGTAG-TTTCAGCTACACTTATCTGATCAGTGACAAGTG
41098411 ACAAGTGATAA
1 ACAAGTGATAA
41098422 ATATGATCCG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 56 0.95
52 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (51 bp):
ACAAGTGATAAGTAGTAGTTTCAGCTACACTTATCTGATCAGTGACAAGTG
Found at i:41099015 original size:14 final size:14
Alignment explanation
Indices: 41098996--41099029 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41098986 TTGGTATCAA
41098996 ATTGGTTGAATTGG
1 ATTGGTTGAATTGG
**
41099010 ATTGGTTGGTTTGG
1 ATTGGTTGAATTGG
41099024 ATTGGT
1 ATTGGT
41099030 CTCGGTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (14 bp):
ATTGGTTGAATTGG
Found at i:41109317 original size:14 final size:14
Alignment explanation
Indices: 41109298--41109331 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41109288 TAAGACTGAG
41109298 ACCAATCCAAACCA
1 ACCAATCCAAACCA
**
41109312 ACCAATCCAATTCA
1 ACCAATCCAAACCA
41109326 ACCAAT
1 ACCAAT
41109332 TTGATACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (14 bp):
ACCAATCCAAACCA
Found at i:41110016 original size:33 final size:33
Alignment explanation
Indices: 41109968--41110030 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
41109958 TTGTCACTTG
* *
41109968 TCACTTGTCATTGATCAGATAAGTGTAGCTAAA
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAA
41110001 TCACTTATCACTGATCAGATAAGTGTAGCT
1 TCACTTATCACTGATCAGATAAGTGTAGCT
41110031 GAAGCTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (33 bp):
TCACTTATCACTGATCAGATAAGTGTAGCTAAA
Found at i:41115564 original size:15 final size:15
Alignment explanation
Indices: 41115544--41115572 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41115534 TCGCAGCGGC
41115544 AGCAGCCTTCTTCTG
1 AGCAGCCTTCTTCTG
41115559 AGCAGCCTTCTTCT
1 AGCAGCCTTCTTCT
41115573 TGCTCGCGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.17, T:0.34
Consensus pattern (15 bp):
AGCAGCCTTCTTCTG
Found at i:41117649 original size:25 final size:26
Alignment explanation
Indices: 41117619--41117687 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
41117609 ATTTTGAACT
41117619 TATATTATTTATTTTAAATTGTTCTA
1 TATATTATTTATTTTAAATTGTTCTA
* * * *
41117645 T-TATTATTTACTTTAAGTTTTTTTA
1 TATATTATTTATTTTAAATTGTTCTA
**
41117670 TATATTATGCATTTTAAA
1 TATATTATTTATTTTAAA
41117688 CTATATTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
25 21 0.62
26 13 0.38
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (26 bp):
TATATTATTTATTTTAAATTGTTCTA
Found at i:41123918 original size:15 final size:15
Alignment explanation
Indices: 41123898--41123926 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41123888 TTGCAGCCGC
41123898 AGCAGCCTTCTTCTG
1 AGCAGCCTTCTTCTG
41123913 AGCAGCCTTCTTCT
1 AGCAGCCTTCTTCT
41123927 TGCTTGCGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.17, T:0.34
Consensus pattern (15 bp):
AGCAGCCTTCTTCTG
Found at i:41124815 original size:34 final size:33
Alignment explanation
Indices: 41124743--41124812 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
41124733 ATATGTATAC
* * *
41124743 TAAATAACACTAAAATAAATACAACTTAACAAG
1 TAAATATCTCTAAAATAAATACAAATTAACAAG
41124776 TAAATATCTCTAAAAT-AATAACAAAATTAACAA-
1 TAAATATCTCTAAAATAAAT-AC-AAATTAACAAG
41124809 TAAA
1 TAAA
41124813 ATAAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 3 0.09
33 20 0.62
34 9 0.28
ACGTcount: A:0.61, C:0.13, G:0.01, T:0.24
Consensus pattern (33 bp):
TAAATATCTCTAAAATAAATACAAATTAACAAG
Found at i:41125447 original size:16 final size:16
Alignment explanation
Indices: 41125426--41125494 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
41125416 TTTGGTTCGC
41125426 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41125442 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41125458 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
41125475 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41125491 TGTA
1 TGTA
41125495 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:41125472 original size:33 final size:32
Alignment explanation
Indices: 41125426--41125494 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
41125416 TTTGGTTCGC
41125426 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
41125458 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
41125491 TGTA
1 TGTA
41125495 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:41125559 original size:44 final size:45
Alignment explanation
Indices: 41125475--41125565 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
41125465 GGATTAGAGG
* * *
41125475 TGTATTGGATTAGAGGTGTAATAGCTAATCCATTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCATTGTTTGGTTGAA
*
41125520 TGTAATGGAATAGAGGCGTAATAG-TAAT-CTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCAT-TGTTTGGTTGAA
41125564 TG
1 TG
41125566 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 2 0.05
44 18 0.44
45 21 0.51
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.38
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCATTGTTTGGTTGAA
Found at i:41127587 original size:18 final size:18
Alignment explanation
Indices: 41127564--41127605 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
41127554 AAAAGGGCTT
41127564 TTATTGGTAAATTGCCCG
1 TTATTGGTAAATTGCCCG
41127582 TTATTGGTAAATTGCCCG
1 TTATTGGTAAATTGCCCG
41127600 TTATTG
1 TTATTG
41127606 AAAAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (18 bp):
TTATTGGTAAATTGCCCG
Found at i:41130842 original size:32 final size:32
Alignment explanation
Indices: 41130806--41130870 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
41130796 GAGCTTATTG
41130806 AGATGCTTACATGTAATTCTTGCTTTCTCTTT
1 AGATGCTTACATGTAATTCTTGCTTTCTCTTT
41130838 AGATGCTTACATGTAATTCTTGCTTTCTCTTT
1 AGATGCTTACATGTAATTCTTGCTTTCTCTTT
41130870 A
1 A
41130871 CTTCGTCATT
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:0.20, C:0.18, G:0.12, T:0.49
Consensus pattern (32 bp):
AGATGCTTACATGTAATTCTTGCTTTCTCTTT
Found at i:41136247 original size:16 final size:15
Alignment explanation
Indices: 41136220--41136258 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
41136210 TAATTCCATA
41136220 TTAAAACATATAAAT
1 TTAAAACATATAAAT
*
41136235 TTAAAATCATATATAT
1 TTAAAA-CATATAAAT
41136251 TTGAAAAC
1 TT-AAAAC
41136259 TTTTTCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (15 bp):
TTAAAACATATAAAT
Found at i:41139061 original size:18 final size:18
Alignment explanation
Indices: 41139024--41139062 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
41139014 ACACTCAGAT
*
41139024 TAGTTTATTAAATGAGAA
1 TAGTTTATTAAATGAAAA
*
41139042 TAGTTTATTAAATTAAAA
1 TAGTTTATTAAATGAAAA
41139060 TAG
1 TAG
41139063 AGTTATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (18 bp):
TAGTTTATTAAATGAAAA
Found at i:41139650 original size:27 final size:27
Alignment explanation
Indices: 41139618--41139669 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
41139608 CATTTTAGTC
41139618 CTTTGGCACCATT-GGTGCCGCCAATCT
1 CTTTGGCACC-TTAGGTGCCGCCAATCT
41139645 CTTTGGCACCTTAGGTGCCGCCAAT
1 CTTTGGCACCTTAGGTGCCGCCAAT
41139670 GTGATTGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.15, C:0.33, G:0.23, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCTTAGGTGCCGCCAATCT
Found at i:41139677 original size:27 final size:27
Alignment explanation
Indices: 41139620--41139678 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
41139610 TTTTAGTCCT
*
41139620 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* *
41139647 TTGGCACC-TTAGGTGCCGCCAATGTGA
1 TTGGCACCATT-GGTGCCGCCAATCTCA
41139674 TTGGC
1 TTGGC
41139679 CTGATTAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.29
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:41139782 original size:26 final size:27
Alignment explanation
Indices: 41139731--41139797 Score: 127
Period size: 26 Copynumber: 2.5 Consensus size: 27
41139721 TTTTTTTGCT
41139731 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
41139758 ATATTTTGGTAAAT-AAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
41139784 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
41139798 TTTCTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 26 0.65
27 14 0.35
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:41154156 original size:42 final size:42
Alignment explanation
Indices: 41154110--41154322 Score: 273
Period size: 42 Copynumber: 4.9 Consensus size: 42
41154100 ATTTAACCAA
*
41154110 TATGGGTTTCTGTTCAGCTTTTACGAGCTTCTGTTCAACCCT
1 TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
*
41154152 TATGGGTTTCTGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACTCT
1 TA--------TGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
*
41154202 TATGGGTTTCCGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
1 TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
*
41154244 TATGGGTTTCCGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
1 TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
* * * * *
41154286 TATAGGTTTCTATTTAGCTCTCATGAGCTTCTGTTCA
1 TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCA
41154323 GCTTTCGAGC
Statistics
Matches: 153, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
42 113 0.74
50 40 0.26
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (42 bp):
TATGGGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACCCT
Found at i:41154162 original size:21 final size:21
Alignment explanation
Indices: 41154110--41154163 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
41154100 ATTTAACCAA
* **
41154110 TATGGGTTTCTGTTCAGCTTT
1 TATGGGTTTCTGTTCAACCCT
* * *
41154131 TACGAGCTTCTGTTCAACCCT
1 TATGGGTTTCTGTTCAACCCT
41154152 TATGGGTTTCTG
1 TATGGGTTTCTG
41154164 GGTTTCTGTT
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.44
Consensus pattern (21 bp):
TATGGGTTTCTGTTCAACCCT
Found at i:41154193 original size:21 final size:21
Alignment explanation
Indices: 41154167--41154339 Score: 145
Period size: 21 Copynumber: 8.3 Consensus size: 21
41154157 GTTTCTGGGT
41154167 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * *
41154188 TTCTGTTCAACTCTTATGGGT
1 TTCTGTTCAGCTCTTACGAGC
*
41154209 TTCCGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * * *
41154230 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTCAGCTCTTACGAGC
*
41154251 TTCCGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACGAGC
* * * *
41154272 TTCTGTTCAACCCTTA-TAGGT
1 TTCTGTTCAGCTCTTACGA-GC
* * * *
41154293 TTCTATTTAGCTCTCATGAGC
1 TTCTGTTCAGCTCTTACGAGC
41154314 TTCTGTTCAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTACGAGC
41154333 TTCTGTT
1 TTCTGTT
41154340 AACGATGTAC
Statistics
Matches: 113, Mismatches: 37, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
19 11 0.10
20 2 0.02
21 99 0.88
22 1 0.01
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.42
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACGAGC
Found at i:41156736 original size:30 final size:31
Alignment explanation
Indices: 41156671--41156728 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
41156661 TACCAAGTGT
41156671 TATTAATTTGATAATAATAATTATTAAATTA
1 TATTAATTTGATAATAATAATTATTAAATTA
*
41156702 -ATTAATTT-A-AATAATATTTA-TAAATTA
1 TATTAATTTGATAATAATAATTATTAAATTA
41156729 CATATTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 7 0.27
28 10 0.38
29 1 0.04
30 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
TATTAATTTGATAATAATAATTATTAAATTA
Found at i:41166682 original size:34 final size:34
Alignment explanation
Indices: 41166643--41166709 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
41166633 GGTAAAAAGT
41166643 TATATTTATATATTTATTTTAACATAAATAATTA
1 TATATTTATATATTTATTTTAACATAAATAATTA
* * * *
41166677 TATATTTATTTGTTTATTTTAATATAACTAATT
1 TATATTTATATATTTATTTTAACATAAATAATT
41166710 TTATTCATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (34 bp):
TATATTTATATATTTATTTTAACATAAATAATTA
Found at i:41171902 original size:18 final size:17
Alignment explanation
Indices: 41171881--41171926 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
41171871 TTACTTTTGT
41171881 TTTCTTTAAATATTTTA
1 TTTCTTTAAATATTTTA
*
41171898 GTTTCTTTAATATGTTTTA
1 -TTTCTTTAA-ATATTTTA
41171917 TTTCTTTAAA
1 TTTCTTTAAA
41171927 AATATTGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 18 0.69
19 7 0.27
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTCTTTAAATATTTTA
Found at i:41172758 original size:2 final size:2
Alignment explanation
Indices: 41172751--41172784 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
41172741 AAGTTAGAAT
*
41172751 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41172785 AAGAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:41174563 original size:6 final size:7
Alignment explanation
Indices: 41174541--41174570 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
41174531 GGATCTTGAC
41174541 TTTAAAA
1 TTTAAAA
41174548 TTTAAAA
1 TTTAAAA
*
41174555 TTTAAAT
1 TTTAAAA
41174562 TTTAAAA
1 TTTAAAA
41174569 TT
1 TT
41174571 ATTAGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
TTTAAAA
Found at i:41187899 original size:34 final size:34
Alignment explanation
Indices: 41187860--41187924 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
41187850 AAAATTTATA
41187860 TTTAATACAAT-AAA-ATGCTTATTATATTTATTTT
1 TTTAATACAATGAAACATGC--ATTATATTTATTTT
41187894 TTTAATACAATGAAACATGCATTATATTTAT
1 TTTAATACAATGAAACATGCATTATATTTAT
41187925 AGTGTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 22 0.76
35 3 0.10
36 4 0.14
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.48
Consensus pattern (34 bp):
TTTAATACAATGAAACATGCATTATATTTATTTT
Found at i:41188026 original size:17 final size:17
Alignment explanation
Indices: 41188006--41188041 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41187996 ATATTTTTAA
*
41188006 AAAAATTAATTTAAAAT
1 AAAAATTAATCTAAAAT
41188023 AAAAATTAATCTAAAAT
1 AAAAATTAATCTAAAAT
41188040 AA
1 AA
41188042 GCACATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTAATCTAAAAT
Found at i:41190657 original size:2 final size:2
Alignment explanation
Indices: 41190650--41190674 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41190640 GGCTAGTTTC
41190650 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
41190675 GGCATCACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:41194888 original size:2 final size:2
Alignment explanation
Indices: 41194881--41194920 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
41194871 CTAGTTGCAC
41194881 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41194921 TTCAACAGCA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:41213235 original size:7 final size:7
Alignment explanation
Indices: 41213214--41213248 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
41213204 ATTTTTTTAA
41213214 TTTAA-T
1 TTTAATT
41213220 TTT-ATT
1 TTTAATT
41213226 TTTAATT
1 TTTAATT
41213233 TTTAATT
1 TTTAATT
41213240 TTTAATT
1 TTTAATT
41213247 TT
1 TT
41213249 AAAATTCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 1 0.04
6 7 0.26
7 19 0.70
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTAATT
Found at i:41213250 original size:6 final size:6
Alignment explanation
Indices: 41213208--41213250 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
41213198 TTCACTATTT
*
41213208 TTTTAA -TTTAA TTTTAT TTTTAA TTTTTAA TTTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA -TTTTAA TTTTAA
41213251 AATTCATGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 15 0.45
7 13 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:41214873 original size:2 final size:2
Alignment explanation
Indices: 41214866--41214921 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
41214856 AATTAATTTT
41214866 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41214908 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
41214922 CAGATTTGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41215272 original size:3 final size:3
Alignment explanation
Indices: 41215264--41215329 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
41215254 GATTCGCATC
41215264 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41215312 ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
41215330 TTAGTATTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41215347 original size:9 final size:8
Alignment explanation
Indices: 41215335--41215384 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
41215325 TTATTTTAGT
41215335 ATTTTAATA
1 ATTTTAA-A
41215344 ATTTTTAAA
1 A-TTTTAAA
*
41215353 TTTTTAAA
1 ATTTTAAA
*
41215361 TTTTTAAA
1 ATTTTAAA
*
41215369 TTTTTAAA
1 ATTTTAAA
41215377 ATTTTAAA
1 ATTTTAAA
41215385 TTATATCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 30 0.79
9 2 0.05
10 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATTTTAAA
Found at i:41215405 original size:7 final size:8
Alignment explanation
Indices: 41215343--41215386 Score: 79
Period size: 8 Copynumber: 5.5 Consensus size: 8
41215333 GTATTTTAAT
41215343 AATTTTTA
1 AATTTTTA
41215351 AATTTTTA
1 AATTTTTA
41215359 AATTTTTA
1 AATTTTTA
41215367 AATTTTTA
1 AATTTTTA
*
41215375 AAATTTTA
1 AATTTTTA
41215383 AATT
1 AATT
41215387 ATATCTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
AATTTTTA
Found at i:41215954 original size:2 final size:2
Alignment explanation
Indices: 41215947--41215996 Score: 66
Period size: 2 Copynumber: 24.5 Consensus size: 2
41215937 ATTACTCTTT
*
41215947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CT- TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
41215989 CTA TA TA T
1 -TA TA TA T
41215997 TAAGCACTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 1 0.02
2 39 0.91
3 3 0.07
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41219839 original size:11 final size:11
Alignment explanation
Indices: 41219823--41219860 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
41219813 TTTTTTTTAA
41219823 TTTTAAAATAT
1 TTTTAAAATAT
41219834 TTTTAAAATAT
1 TTTTAAAATAT
41219845 TTTTAAAATAT
1 TTTTAAAATAT
41219856 TTTTA
1 TTTTA
41219861 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:41220510 original size:21 final size:20
Alignment explanation
Indices: 41220470--41220511 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
41220460 TTTAATAATT
*
41220470 TTTAAACCTAAATCTTAAAC
1 TTTAAACCTAAATATTAAAC
*
41220490 TTTAAATCCTGAATATTAAAC
1 TTTAAA-CCTAAATATTAAAC
41220511 T
1 T
41220512 CTGAACCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAAACCTAAATATTAAAC
Found at i:41221624 original size:19 final size:20
Alignment explanation
Indices: 41221600--41221639 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
41221590 AATTTTAAAA
41221600 TATTTTTAAAAT-AATTTTT
1 TATTTTTAAAATAAATTTTT
41221619 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAATAAATTTTT
41221639 T
1 T
41221640 GTGTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTAAAATAAATTTTT
Found at i:41221646 original size:20 final size:19
Alignment explanation
Indices: 41221604--41221646 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
41221594 TTAAAATATT
*
41221604 TTTAAAATAATTTTTTATT
1 TTTAAAATAATTTTTTATG
*
41221623 TTTAAAATAAATTTTTTGTG
1 TTTAAAAT-AATTTTTTATG
41221643 TTTA
1 TTTA
41221647 TTAAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTAAAATAATTTTTTATG
Found at i:41227420 original size:19 final size:20
Alignment explanation
Indices: 41227396--41227447 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
41227386 AGGGTCGTAG
41227396 AAAATAAACAA-AAAATAAA
1 AAAATAAACAATAAAATAAA
41227415 AAAAT--ACAATAAAATAAA
1 AAAATAAACAATAAAATAAA
*
41227433 AAAAAAACACAATAA
1 AAAATAA-ACAATAA
41227448 CAAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 4 0.14
18 12 0.43
19 5 0.18
21 7 0.25
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAATAAACAATAAAATAAA
Found at i:41227438 original size:21 final size:20
Alignment explanation
Indices: 41227396--41227460 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
41227386 AGGGTCGTAG
* *
41227396 AAAATA-AACAAAAAATAAA
1 AAAATACAATAAAAAAAAAA
41227415 AAAATACAATAAAATAAAAAA
1 AAAATACAATAAAA-AAAAAA
* *
41227436 AAAACACAATAACAAAGAAAA
1 AAAATACAATAA-AAAAAAAA
41227457 AAAA
1 AAAA
41227461 GAAAAGAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.15
20 6 0.15
21 25 0.64
22 2 0.05
ACGTcount: A:0.82, C:0.08, G:0.02, T:0.09
Consensus pattern (20 bp):
AAAATACAATAAAAAAAAAA
Found at i:41228053 original size:16 final size:16
Alignment explanation
Indices: 41228013--41228053 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
41228003 TAACAATTTA
* *
41228013 AACCCTAAAATAATAT
1 AACCCTAAACTAAAAT
41228029 AA-CCT-AACTAAAAT
1 AACCCTAAACTAAAAT
41228043 AACCCTAAACT
1 AACCCTAAACT
41228054 TTAAAACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 9 0.43
15 6 0.29
16 6 0.29
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (16 bp):
AACCCTAAACTAAAAT
Found at i:41235560 original size:16 final size:17
Alignment explanation
Indices: 41235528--41235560 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41235518 ATCTCTTTTT
*
41235528 CCGTAAGTTTGATTGAA
1 CCGTAAGATTGATTGAA
41235545 CCGTAAGATT-ATTGAA
1 CCGTAAGATTGATTGAA
41235561 TTGAGTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (17 bp):
CCGTAAGATTGATTGAA
Found at i:41247615 original size:14 final size:14
Alignment explanation
Indices: 41247579--41247635 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
41247569 TATATAGTCT
41247579 ATTATAAAAATATA
1 ATTATAAAAATATA
*
41247593 GACTATAAAAATATA
1 -ATTATAAAAATATA
* *
41247608 ATTTTAAAAAAATA
1 ATTATAAAAATATA
*
41247622 ATCATAAAAATATA
1 ATTATAAAAATATA
41247636 TAATTTAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
14 22 0.63
15 13 0.37
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (14 bp):
ATTATAAAAATATA
Found at i:41249312 original size:6 final size:6
Alignment explanation
Indices: 41249289--41249347 Score: 64
Period size: 6 Copynumber: 9.5 Consensus size: 6
41249279 TTAGTTCATC
** * *
41249289 TTTATT TTTCCT TTTATT TCTATT TGTAGTGT TTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTA-T-T TTTATT TTTATT TTTATT
41249339 TTTATT TTT
1 TTTATT TTT
41249348 TTAATTTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 38 0.86
7 2 0.05
8 4 0.09
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:41249382 original size:3 final size:3
Alignment explanation
Indices: 41249374--41249416 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
41249364 TTTTTAATCC
41249374 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41249417 TCTCCTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41250898 original size:7 final size:7
Alignment explanation
Indices: 41250886--41250915 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
41250876 GATGCATGCA
41250886 TGCATGT
1 TGCATGT
41250893 TGCATGT
1 TGCATGT
41250900 TGCATGT
1 TGCATGT
41250907 TGCATGT
1 TGCATGT
41250914 TG
1 TG
41250916 AGGGGATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.43
Consensus pattern (7 bp):
TGCATGT
Found at i:41251478 original size:12 final size:12
Alignment explanation
Indices: 41251458--41251500 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
41251448 TTAACTCCCT
41251458 TTTTTAAAATAA
1 TTTTTAAAATAA
* *
41251470 TTTTAAAAATAT
1 TTTTTAAAATAA
*
41251482 TTTTTAAAAT-T
1 TTTTTAAAATAA
41251493 TTTTTAAA
1 TTTTTAAA
41251501 CCGTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTTAAAATAA
Found at i:41252614 original size:7 final size:7
Alignment explanation
Indices: 41252602--41252626 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41252592 AGTCGATTGA
41252602 TATTTAG
1 TATTTAG
41252609 TATTTAG
1 TATTTAG
41252616 TATTTAG
1 TATTTAG
41252623 TATT
1 TATT
41252627 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:41254053 original size:68 final size:68
Alignment explanation
Indices: 41253790--41254254 Score: 338
Period size: 68 Copynumber: 6.8 Consensus size: 68
41253780 AACCATTAAT
* *
41253790 ACCCTTAAA-TTAAAAACCCTAACCTAATTTAATTAAAAAC-CTTAAACCCT-A--AACTTAAAA
1 ACCC-TAAACTTAAAAACCCTAACCTAATTAAATTAAAAACTC-T-AA-CCTAATTAAATTAAAA
41253850 ACCCTAA
62 ACCCTAA
* * * * *
41253857 CCCCCTTAACTTAGAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACC
1 -ACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACTCTAACCTAATTAAATTAAAAACC
41253922 CT-A
65 CTAA
* * ** * * *
41253925 A-CCTAATTTAATAAAAAAACTTTAAACCCT-A--AACTTAAAAACCCCTAACCTAATTTAATTA
1 ACCCTAA---ACT-TAAAAACCCT-AA-CCTAATTAAATTAAAAA-CTCTAACCTAATTAAATTA
41253986 AAAACCCTAA
59 AAAACCCTAA
*
41253996 ACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAATTCTAACCTAATTAAATTAAAAACCC
1 ACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACTCTAACCTAATTAAATTAAAAACCC
41254061 TAA
66 TAA
*** *
41254064 ACCCTAAACTT-AAAACCCTAACCCCCTTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCC
1 ACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACTCTAACCTAATTAAATTAAAAACCC
41254128 T-A
66 TAA
* * * * *
41254130 A-CCTAATTAAATTAAAAACCCTAAACCCT-A--AACTTAAAAACCCTAACCCT-CTTAACTTAA
1 ACCCT-A--AACTTAAAAACCCT-AA-CCTAATTAAATTAAAAACTCTAA-CCTAATTAAATTAA
41254190 AAACCCT-A
60 AAACCCTAA
* ** * *
41254198 A-CCTAATTAAATTAAAAACCCTAACCTAATTTTATTAAAAACCCTAAACTAAATTAA
1 ACCCT-A--AACTTAAAAACCCTAACCTAATTAAATTAAAAACTCTAACCT-AATTAA
41254255 TAATTTTACT
Statistics
Matches: 330, Mismatches: 38, Indels: 56
0.78 0.09 0.13
Matches are distributed among these distances:
65 3 0.01
66 16 0.05
67 61 0.18
68 138 0.42
69 59 0.18
70 38 0.12
71 7 0.02
72 8 0.02
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.26
Consensus pattern (68 bp):
ACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACTCTAACCTAATTAAATTAAAAACCC
TAA
Found at i:41254202 original size:28 final size:23
Alignment explanation
Indices: 41253794--41254254 Score: 407
Period size: 23 Copynumber: 20.2 Consensus size: 23
41253784 ATTAATACCC
41253794 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
41253817 TTTAATTAAAAACCTTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
* ***
41253841 --AACTTAAAAACCCTAACCCCC
1 TTAAATTAAAAACCCTAACCTAA
* *
41253862 TTAACTTAGAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
41253885 TTTAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
41253908 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* * **
41253931 TTTAATAAAAAAACTTTAAACCCT-A
1 TTAAAT-TAAAAACCCT-AA-CCTAA
*
41253956 --AACTTAAAAACCCCTAACCTAA
1 TTAAATTAAAAA-CCCTAACCTAA
*
41253978 TTTAATTAAAAACCCTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
*
41254002 --AACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
**
41254023 TTAAATTAAAAATTCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
41254046 TTAAATTAAAAACCCTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
* ***
41254070 --AACTT-AAAACCCTAACCCCC
1 TTAAATTAAAAACCCTAACCTAA
* *
41254090 TTAACTTAAAAACTCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
41254113 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
41254136 TTAAATTAAAAACCCTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
* *
41254160 --AACTTAAAAACCCTAACCCT-C
1 TTAAATTAAAAACCCTAA-CCTAA
*
41254181 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
41254204 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
** *
41254227 TTTTATTAAAAACCCTAAACTAAA
1 TTAAATTAAAAACCCTAACCT-AA
41254251 TTAA
1 TTAA
41254255 TAATTTTACT
Statistics
Matches: 358, Mismatches: 51, Indels: 57
0.77 0.11 0.12
Matches are distributed among these distances:
19 2 0.01
20 7 0.02
21 22 0.06
22 56 0.16
23 222 0.62
24 31 0.09
25 15 0.04
26 3 0.01
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (23 bp):
TTAAATTAAAAACCCTAACCTAA
Found at i:41254214 original size:91 final size:91
Alignment explanation
Indices: 41253890--41254246 Score: 442
Period size: 91 Copynumber: 3.9 Consensus size: 91
41253880 CCTAATTTAA
* * * * **
41253890 TTAAAAACCCTAA-CCTAATTAAATTAAAAACCCTAACCTAATTTAATAAAAAAACTTTAAACCC
1 TTAAAAACCCTAACCCT-CTTAACTTAAAAACCCTAACCTAATTAAAT-TAAAAACCCT-AA-CC
* *
41253954 T-A--AACTTAAAAACCCCT-AA-CCTAATTTAA
62 TAATTAAATTAAAAA-CCCTAAACCCTAA---AC
* * **
41253983 TTAAAAACCCTAAACC-CTAAACTTAAAAACCCTAACCTAATTAAATTAAAAATTCTAACCTAAT
1 TTAAAAACCCTAACCCTCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
41254047 TAAATTAAAAACCCTAAACCCTAAAC
66 TAAATTAAAAACCCTAAACCCTAAAC
* *
41254073 TT-AAAACCCTAACCCCCTTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCCTAACCTAAT
1 TTAAAAACCCTAACCCTCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
41254137 TAAATTAAAAACCCTAAACCCTAAAC
66 TAAATTAAAAACCCTAAACCCTAAAC
41254163 TTAAAAACCCTAACCCTCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
1 TTAAAAACCCTAACCCTCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
**
41254228 TTTATTAAAAACCCTAAAC
66 TAAATTAAAAACCCTAAAC
41254247 TAAATTAATA
Statistics
Matches: 238, Mismatches: 18, Indels: 18
0.87 0.07 0.07
Matches are distributed among these distances:
89 15 0.06
90 78 0.33
91 88 0.37
92 37 0.16
93 18 0.08
94 2 0.01
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (91 bp):
TTAAAAACCCTAACCCTCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAAT
TAAATTAAAAACCCTAAACCCTAAAC
Found at i:41254394 original size:116 final size:116
Alignment explanation
Indices: 41254249--41254492 Score: 418
Period size: 116 Copynumber: 2.1 Consensus size: 116
41254239 CCCTAAACTA
* * **
41254249 AATTAATAATTTTACTTTTACATAATGTTAGATTTGGAAAAATGTTTTTTCCTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATG-TTTTGACTGGTACTAACAAT
* *
41254314 TAATAATTTTATATAATTTGAT-ATTTTTACTAATCATTAATACAATTTATC
65 TAACAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
41254365 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
41254430 AACAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
66 AACAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
41254481 AATTAATAATTT
1 AATTAATAATTT
41254493 CACAAACTTA
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
115 39 0.32
116 82 0.68
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (116 bp):
AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
AACAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
Found at i:41257757 original size:124 final size:125
Alignment explanation
Indices: 41257535--41257907 Score: 563
Period size: 124 Copynumber: 3.0 Consensus size: 125
41257525 CAAACATGCT
* *
41257535 ACTGTAGCAAAAGCGCGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGC-AATTTCACAAATTCTTCTCAAATAGCATCCTGCT
*
41257600 ATAAGCGAA-TTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACCG
65 AGAAGC-AATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACCG
*
41257661 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTT-ACAAATTCTTCTCAAATAGTATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
*
41257725 GAAGCAATTTTATACTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTTCCATGACCT
66 GAAGCAATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACCG
* * *
41257784 ACTGTAGCAAAAGCACGTCCACAAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
** * **** *
41257849 GAAGTGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACC
66 GAAGCAATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACC
41257908 TAAAAACCCT
Statistics
Matches: 227, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
123 59 0.26
124 115 0.51
125 24 0.11
126 29 0.13
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (125 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
GAAGCAATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGACCG
Found at i:41271693 original size:12 final size:12
Alignment explanation
Indices: 41271648--41271694 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
41271638 TAAGAAAATT
41271648 ATTATTAAATATA
1 ATTATT-AATATA
*
41271661 A-T-TTAATAAA
1 ATTATTAATATA
*
41271671 ATTCTTAATATA
1 ATTATTAATATA
41271683 ATTATTAATATA
1 ATTATTAATATA
41271695 TGAATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 6 0.21
11 3 0.10
12 19 0.66
13 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTATTAATATA
Found at i:41274488 original size:14 final size:15
Alignment explanation
Indices: 41274461--41274498 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
41274451 TTAATAGGAC
41274461 TAAAT-TTAAGAAAA
1 TAAATATTAAGAAAA
*
41274475 TAAATATTAAAAAAA
1 TAAATATTAAGAAAA
41274490 T-AATATTAA
1 TAAATATTAA
41274499 TTTCATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
TAAATATTAAGAAAA
Found at i:41275316 original size:10 final size:9
Alignment explanation
Indices: 41275303--41275362 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
41275293 TTTATATTTG
41275303 AAATTATTGA
1 AAATTATT-A
41275313 AAATTAATTA
1 AAATT-ATTA
*
41275323 AAATTATAA
1 AAATTATTA
41275332 AAATTCA-TA
1 AAATT-ATTA
* *
41275341 CAATATATAA
1 AAAT-TATTA
41275351 AAATTATTA
1 AAATTATTA
41275360 AAA
1 AAA
41275363 ACATTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
9 20 0.50
10 17 0.43
11 3 0.08
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (9 bp):
AAATTATTA
Found at i:41275336 original size:9 final size:9
Alignment explanation
Indices: 41275312--41275383 Score: 56
Period size: 9 Copynumber: 7.4 Consensus size: 9
41275302 GAAATTATTG
*
41275312 AAAATTAATT
1 AAAATT-ATA
41275322 AAAATTATA
1 AAAATTATA
41275331 AAAATTCAT-
1 AAAATT-ATA
*
41275340 ACAATATATA
1 AAAAT-TATA
41275350 AAAATTATTAA
1 AAAATTA-T-A
*
41275361 AAACATTTTA
1 AAA-ATTATA
41275371 AAAATTATA
1 AAAATTATA
41275380 AAAA
1 AAAA
41275384 ATAGAAGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
9 25 0.49
10 18 0.35
11 5 0.10
12 3 0.06
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:41275336 original size:19 final size:19
Alignment explanation
Indices: 41275312--41275362 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
41275302 GAAATTATTG
41275312 AAAATTAATTAAAAT-TATA
1 AAAATT-ATTAAAATATATA
*
41275331 AAAATTCA-TACAATATATA
1 AAAATT-ATTAAAATATATA
41275350 AAAATTATTAAAA
1 AAAATTATTAAAA
41275363 ACATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTATTAAAATATATA
Found at i:41275363 original size:10 final size:10
Alignment explanation
Indices: 41275303--41275385 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 10
41275293 TTTATATTTG
*
41275303 AAATTATTGA
1 AAATTATTAA
41275313 AAATTAATT-A
1 AAATT-ATTAA
41275323 AAATTA-TAA
1 AAATTATTAA
41275332 AAATTCA-T-A
1 AAATT-ATTAA
*
41275341 CAA-TATATAA
1 AAATTAT-TAA
41275351 AAATTATTAAA
1 AAATTATT-AA
41275362 AACATT-TTAA
1 AA-ATTATTAA
*
41275372 AAATTATAAA
1 AAATTATTAA
41275382 AAAT
1 AAAT
41275386 AGAAGAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
7 1 0.02
8 2 0.03
9 14 0.23
10 28 0.47
11 12 0.20
12 3 0.05
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (10 bp):
AAATTATTAA
Found at i:41275507 original size:16 final size:15
Alignment explanation
Indices: 41275442--41275519 Score: 57
Period size: 16 Copynumber: 4.5 Consensus size: 15
41275432 AAATTTATTT
41275442 AAAATGATAAAATATAA
1 AAAAT-ATAAAATAT-A
*
41275459 AAAATGGAGAAAAGTATTA
1 AAAAT--ATAAAA-TA-TA
41275478 AAAATTATTAAAATGATA
1 AAAA-TA-TAAAAT-ATA
41275496 AAAATATAAAATATAA
1 AAAATATAAAATAT-A
41275512 AAAATATA
1 AAAATATA
41275520 TGAAAAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
15 2 0.04
16 15 0.29
17 7 0.13
18 14 0.27
19 12 0.23
20 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (15 bp):
AAAATATAAAATATA
Found at i:41275538 original size:18 final size:20
Alignment explanation
Indices: 41275503--41275564 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
41275493 ATAAAAATAT
*
41275503 AAAATA-TAAAAAATATATGA
1 AAAATATTAAAATATATA-GA
*
41275523 AAAATGTTAAAA-ATATAGA
1 AAAATATTAAAATATATAGA
*
41275542 AAATTATTAAAATATATAGA
1 AAAATATTAAAATATATAGA
41275562 AAA
1 AAA
41275565 TTGCCAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 12 0.32
20 20 0.54
21 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAATATTAAAATATATAGA
Found at i:41275545 original size:54 final size:53
Alignment explanation
Indices: 41275442--41275557 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 53
41275432 AAATTTATTT
* * *
41275442 AAAATGATAAAATATAAAAAATGGAGAAAAGTATTAAAAATTATTAAAATGATA
1 AAAAT-ATAAAATATAAAAAATAGAGAAAAATATTAAAAATTATGAAAATGATA
* * * *
41275496 AAAATATAAAATATAAAAAATATATGAAAAATGTTAAAAA-TATAGAAAATTATT
1 AAAATATAAAATATAAAAAATAGA-GAAAAATATTAAAAATTAT-GAAAATGATA
41275550 AAAATATA
1 AAAATATA
41275558 TAGAAAATTG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 20 0.38
54 33 0.62
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.28
Consensus pattern (53 bp):
AAAATATAAAATATAAAAAATAGAGAAAAATATTAAAAATTATGAAAATGATA
Found at i:41275573 original size:20 final size:20
Alignment explanation
Indices: 41275512--41275567 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
41275502 TAAAATATAA
*
41275512 AAAATATAT-GAAAAATGTT
1 AAAATATATAGAAAATTGTT
*
41275531 AAAA-ATATAGAAAATTATT
1 AAAATATATAGAAAATTGTT
41275550 AAAATATATAGAAAATTG
1 AAAATATATAGAAAATTG
41275568 CCAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.12
19 16 0.50
20 12 0.38
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (20 bp):
AAAATATATAGAAAATTGTT
Found at i:41275698 original size:18 final size:18
Alignment explanation
Indices: 41275677--41275714 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41275667 ATGAAATTGC
*
41275677 AATAAAATATTAGAATAT
1 AATAAAATATTAAAATAT
*
41275695 AATAAAGTATTAAAATAT
1 AATAAAATATTAAAATAT
41275713 AA
1 AA
41275715 AACATGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AATAAAATATTAAAATAT
Found at i:41276122 original size:19 final size:19
Alignment explanation
Indices: 41276098--41276143 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
41276088 ACAAGTTATG
41276098 TATTTTTT-AAATTTTAAT
1 TATTTTTTCAAATTTTAAT
*
41276116 ATATTTTTTGCAATTTTTAAT
1 -TATTTTTT-CAAATTTTAAT
41276137 TATTTTT
1 TATTTTT
41276144 AAGAACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 7 0.29
21 9 0.38
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTTCAAATTTTAAT
Found at i:41276130 original size:20 final size:19
Alignment explanation
Indices: 41276098--41276143 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
41276088 ACAAGTTATG
41276098 TATTTTTTAAA-TTTTAAT
1 TATTTTTTAAATTTTTAAT
*
41276116 ATATTTTTTGCAATTTTTAAT
1 -TATTTTTT-AAATTTTTAAT
41276137 TATTTTT
1 TATTTTT
41276144 AAGAACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 9 0.38
21 7 0.29
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTTAAATTTTTAAT
Found at i:41280112 original size:11 final size:11
Alignment explanation
Indices: 41280060--41280132 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
41280050 CACTATTATA
*
41280060 TTATTATTATT
1 TTATTATTGTT
41280071 TTATTATTGTTGT
1 TTATTATTG-T-T
* *
41280084 TTAGGTATTGTA
1 TTA-TTATTGTT
*
41280096 TAATTATTGTT
1 TTATTATTGTT
41280107 TTATTATTAGTT
1 TTATTATT-GTT
* *
41280119 TTACTATTATT
1 TTATTATTGTT
41280130 TTA
1 TTA
41280133 GAAACTTTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
11 26 0.53
12 13 0.27
13 5 0.10
14 5 0.10
ACGTcount: A:0.25, C:0.01, G:0.10, T:0.64
Consensus pattern (11 bp):
TTATTATTGTT
Found at i:41280209 original size:11 final size:12
Alignment explanation
Indices: 41280180--41280212 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41280170 TATTTAAATA
41280180 TAAATATTATTTT
1 TAAAT-TTATTTT
41280193 TAAATTTATTTT
1 TAAATTTATTTT
41280205 T-AATTTAT
1 TAAATTTAT
41280213 CGGGAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 8 0.40
13 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TAAATTTATTTT
Done.