Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 11 of 135
Found at i:4917072 original size:10 final size:10
Alignment explanation
Indices: 4917045--4917082 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
4917035 CATTTATCAT
4917045 ATCACATATTA
1 ATCACAT-TTA
4917056 ATCACATTTA
1 ATCACATTTA
*
4917066 GTCACATTTA
1 ATCACATTTA
4917076 ATCACAT
1 ATCACAT
4917083 GAATATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (10 bp):
ATCACATTTA
Found at i:4917096 original size:24 final size:24
Alignment explanation
Indices: 4917069--4917146 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
4917059 ACATTTAGTC
4917069 ACATTTAATCACATGAATATTTCA
1 ACATTTAATCACATGAATATTTCA
*
4917093 ACATTT-ATCACATCACAT-TTAGTC-
1 ACATTTAATCACATGA-ATATT--TCA
4917117 ACATTTAATCACATGAATATTTCA
1 ACATTTAATCACATGAATATTTCA
*
4917141 GCATTT
1 ACATTT
4917147 GTCATATCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
23 12 0.27
24 21 0.47
25 12 0.27
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.38
Consensus pattern (24 bp):
ACATTTAATCACATGAATATTTCA
Found at i:4917100 original size:59 final size:58
Alignment explanation
Indices: 4917008--4917176 Score: 214
Period size: 59 Copynumber: 3.1 Consensus size: 58
4916998 CACTACATAA
* * *
4917008 TCACACTTAATCATATGAATATTTCATCATTTATCATATCACATATTAATCACATTTAG
1 TCACATTTAATCACATGAATATTTCAACATTT-TCATATCACATATTAATCACATTTAG
4917067 TCACATTTAATCACATGAATATTTCAACA--TT--TATCAC------ATCACATTTAG
1 TCACATTTAATCACATGAATATTTCAACATTTTCATATCACATATTAATCACATTTAG
*
4917115 TCACATTTAATCACATGAATATTTCAGCATTTGTCATATCACATATTAATCACATTTAG
1 TCACATTTAATCACATGAATATTTCAACATTT-TCATATCACATATTAATCACATTTAG
4917174 TCA
1 TCA
4917177 AATTACGTTT
Statistics
Matches: 95, Mismatches: 4, Indels: 22
0.79 0.03 0.18
Matches are distributed among these distances:
48 39 0.41
50 1 0.01
51 1 0.01
53 6 0.06
54 6 0.06
56 1 0.01
57 1 0.01
59 40 0.42
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.39
Consensus pattern (58 bp):
TCACATTTAATCACATGAATATTTCAACATTTTCATATCACATATTAATCACATTTAG
Found at i:4917122 original size:48 final size:48
Alignment explanation
Indices: 4917056--4917172 Score: 189
Period size: 48 Copynumber: 2.4 Consensus size: 48
4917046 TCACATATTA
4917056 ATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCAC
1 ATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCAC
* * *
4917104 ATCACATTTAGTCACATTTAATCACATGAATATTTCAGCATTTGTCAT
1 ATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCAC
*
4917152 ATCACATATTAATCACATTTA
1 ATCACAT-TTAGTCACATTTA
4917173 GTCAAATTAC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
48 52 0.81
49 12 0.19
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (48 bp):
ATCACATTTAGTCACATTTAATCACATGAATATTTCAACATTTATCAC
Found at i:4917687 original size:36 final size:36
Alignment explanation
Indices: 4917641--4917725 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
4917631 TTAGCACAAT
*
4917641 ATATTCACTGTCACATGGCATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
*
4917677 ATATTTACTGTCACATGGCATGGATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
*
4917713 ATATTTACAGTCA
1 ATATTTACTGTCA
4917726 TAACAGTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (36 bp):
ATATTTACTGTCACATGGCATGAATAACATACCCAC
Found at i:4922868 original size:7 final size:7
Alignment explanation
Indices: 4922856--4922880 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4922846 TCCTTGTTTA
4922856 TGGGTTC
1 TGGGTTC
4922863 TGGGTTC
1 TGGGTTC
4922870 TGGGTTC
1 TGGGTTC
4922877 TGGG
1 TGGG
4922881 CTATGGAGCA
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:0.48, T:0.40
Consensus pattern (7 bp):
TGGGTTC
Found at i:4929438 original size:25 final size:26
Alignment explanation
Indices: 4929398--4929465 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
4929388 ATAAAAATAT
4929398 AAATGATATAAA-TATAAAATTT-CAA
1 AAATG-TATAAATTATAAAATTTACAA
* *
4929423 AAATGTATAAATTATAGAATTTATAA
1 AAATGTATAAATTATAAAATTTACAA
*
4929449 AAATAT-TAAATTA-AAAA
1 AAATGTATAAATTATAAAA
4929466 GATTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 9 0.24
25 21 0.57
26 7 0.19
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (26 bp):
AAATGTATAAATTATAAAATTTACAA
Found at i:4934512 original size:35 final size:35
Alignment explanation
Indices: 4934473--4934544 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
4934463 ATATATTTAA
* *
4934473 AAAATATTAT-TTATTTGTATTTTAAATAATATCAT
1 AAAA-ATTATATTAATTATATTTTAAATAATATCAT
4934508 -AAAATTATATTAATTATATTTTAAATAATATCAT
1 AAAAATTATATTAATTATATTTTAAATAATATCAT
4934542 AAA
1 AAA
4934545 TTCGTACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 5 0.15
34 26 0.79
35 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (35 bp):
AAAAATTATATTAATTATATTTTAAATAATATCAT
Found at i:4935454 original size:4 final size:4
Alignment explanation
Indices: 4935445--4935471 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4935435 TTTTAAGAGA
4935445 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
4935472 AGAAGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:4943302 original size:48 final size:48
Alignment explanation
Indices: 4943242--4943385 Score: 279
Period size: 48 Copynumber: 3.0 Consensus size: 48
4943232 TTGATTGAAA
*
4943242 TCAAAGCTCCAATGCTGGTTTGGCTATAAGTTATACTTGTTTGTAAAC
1 TCAAAGCTCCAATGCTAGTTTGGCTATAAGTTATACTTGTTTGTAAAC
4943290 TCAAAGCTCCAATGCTAGTTTGGCTATAAGTTATACTTGTTTGTAAAC
1 TCAAAGCTCCAATGCTAGTTTGGCTATAAGTTATACTTGTTTGTAAAC
4943338 TCAAAGCTCCAATGCTAGTTTGGCTATAAGTTATACTTGTTTGTAAAC
1 TCAAAGCTCCAATGCTAGTTTGGCTATAAGTTATACTTGTTTGTAAAC
4943386 AAGGAACCAC
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 95 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (48 bp):
TCAAAGCTCCAATGCTAGTTTGGCTATAAGTTATACTTGTTTGTAAAC
Found at i:4962329 original size:9 final size:8
Alignment explanation
Indices: 4962304--4962356 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 8
4962294 TTTTGCTTAT
4962304 GAAGAAAA
1 GAAGAAAA
4962312 GGAAGGAAAA
1 -GAA-GAAAA
4962322 GATAGAAAA
1 GA-AGAAAA
*
4962331 GAAGAAAG
1 GAAGAAAA
4962339 GAA-AAAA
1 GAAGAAAA
4962346 GAAGGAAAA
1 GAA-GAAAA
4962355 GA
1 GA
4962357 GTAGCAGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 6 0.16
8 8 0.21
9 18 0.47
10 6 0.16
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (8 bp):
GAAGAAAA
Found at i:4962345 original size:24 final size:26
Alignment explanation
Indices: 4962304--4962356 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
4962294 TTTTGCTTAT
4962304 GAAGAAAAGGAAGGAAAAGATA-GAAAA
1 GAAGAAAAGGAA-GAAAAGA-AGGAAAA
4962331 GAAG-AAAGGAA-AAAAGAAGGAAAA
1 GAAGAAAAGGAAGAAAAGAAGGAAAA
4962355 GA
1 GA
4962357 GTAGCAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 1 0.04
24 13 0.52
26 7 0.28
27 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (26 bp):
GAAGAAAAGGAAGAAAAGAAGGAAAA
Found at i:4972673 original size:26 final size:25
Alignment explanation
Indices: 4972644--4972695 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
4972634 CTTTTTATAA
4972644 ATTTAAAATTTAGTTTTTATATTTTT
1 ATTTAAAATTTAGTTTTT-TATTTTT
* * *
4972670 ATTTAGATTTTAGTTTTTTTTTTTT
1 ATTTAAAATTTAGTTTTTTATTTTT
4972695 A
1 A
4972696 CTTTTTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (25 bp):
ATTTAAAATTTAGTTTTTTATTTTT
Found at i:4988344 original size:22 final size:23
Alignment explanation
Indices: 4988313--4988368 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
4988303 CAAATTAAAT
*
4988313 TATAATTTTTATAATAA-TAAAAA
1 TATAA-TTTTATAAAAAGTAAAAA
* *
4988336 TATAATTTT-TAAAAAGTTAAAT
1 TATAATTTTATAAAAAGTAAAAA
4988358 TATAATTTTAT
1 TATAATTTTAT
4988369 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TATAATTTTATAAAAAGTAAAAA
Found at i:4988396 original size:31 final size:30
Alignment explanation
Indices: 4988340--4988399 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
4988330 TAAAAATATA
* *
4988340 ATTTTTAAAAAGTTAAATTATAATTTTATT
1 ATTTTTAAAAAATTAAAGTATAATTTTATT
*
4988370 ATTTTTAAAAGAATTAGAGTATAATTTTAT
1 ATTTTTAAAA-AATTAAAGTATAATTTTAT
4988400 GTCTATTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (30 bp):
ATTTTTAAAAAATTAAAGTATAATTTTATT
Found at i:4992099 original size:17 final size:17
Alignment explanation
Indices: 4992079--4992144 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 17
4992069 TTTAAAAATT
4992079 ATATTTAATATAATAAA
1 ATATTTAATATAATAAA
* * **
4992096 ATATTTATTATATTTATTT
1 ATATTTAATATA-ATA-AA
*
4992115 ATATTTTAATATGATAAA
1 ATA-TTTAATATAATAAA
*
4992133 ATATTTATTATA
1 ATATTTAATATA
4992145 TTTAAGTTAG
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
17 18 0.51
18 5 0.14
19 5 0.14
20 7 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATATTTAATATAATAAA
Found at i:4992132 original size:37 final size:36
Alignment explanation
Indices: 4992077--4992148 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
4992067 ATTTTAAAAA
4992077 TTATATTTAATATAATAAAATATTTATTATATTTAT
1 TTATATTTAATATAATAAAATATTTATTATATTTAT
*
4992113 TTATATTTTAATATGATAAAATATTTATTATATTTA
1 TTATA-TTTAATATAATAAAATATTTATTATATTTA
4992149 AGTTAGTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 5 0.15
37 29 0.85
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (36 bp):
TTATATTTAATATAATAAAATATTTATTATATTTAT
Found at i:4995580 original size:32 final size:32
Alignment explanation
Indices: 4995534--4995631 Score: 178
Period size: 32 Copynumber: 3.1 Consensus size: 32
4995524 ATGACAACAA
4995534 AAGCTTCTATTAATCCTAATGTAAATGAAGGT
1 AAGCTTCTATTAATCCTAATGTAAATGAAGGT
* *
4995566 AAGCTTCTAGTAATCCTAATGTAAGTGAAGGT
1 AAGCTTCTATTAATCCTAATGTAAATGAAGGT
4995598 AAGCTTCTATTAATCCTAATGTAAATGAAGGT
1 AAGCTTCTATTAATCCTAATGTAAATGAAGGT
4995630 AA
1 AA
4995632 CTATGGCTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (32 bp):
AAGCTTCTATTAATCCTAATGTAAATGAAGGT
Found at i:5002439 original size:110 final size:111
Alignment explanation
Indices: 5002316--5002527 Score: 399
Period size: 111 Copynumber: 1.9 Consensus size: 111
5002306 ATAGAAACTC
5002316 TTTTTTTTAAGATTCTATTTGATACCTAAATTTATTAAATATTAT-AAAAAGTATGCAAAACAAT
1 TTTTTTTTAAGATTCTATTTGATACCTAAATTTATTAAATATTATAAAAAAGTATGCAAAACAAT
5002380 AAGGTGTTGAAATTTATACATAAATTTTATTAAACATATATAAGCT
66 AAGGTGTTGAAATTTATACATAAATTTTATTAAACATATATAAGCT
* *
5002426 TTTTTTTTAAGATTCTATTTGGTACCTAAATTTATTAAATATTATAAAAAATTATGCAAAACAAT
1 TTTTTTTTAAGATTCTATTTGATACCTAAATTTATTAAATATTATAAAAAAGTATGCAAAACAAT
5002491 AAGGTGTTGAAATTTATACATAAATTTTATTAAACAT
66 AAGGTGTTGAAATTTATACATAAATTTTATTAAACAT
5002528 TTGTTTACTT
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 44 0.44
111 55 0.56
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (111 bp):
TTTTTTTTAAGATTCTATTTGATACCTAAATTTATTAAATATTATAAAAAAGTATGCAAAACAAT
AAGGTGTTGAAATTTATACATAAATTTTATTAAACATATATAAGCT
Found at i:5029691 original size:58 final size:57
Alignment explanation
Indices: 5029616--5029808 Score: 160
Period size: 58 Copynumber: 3.3 Consensus size: 57
5029606 ATCAGAGTTG
* * *
5029616 AAAATGAGACTTTTTGGATACACGGGGGTAAAATGGTAATTTTAAGAAAGTTTGGGGTTA
1 AAAAT-AGAATTTTTGGACAC-CGAGGGTAAAATGGTAATTTT-AGAAAGTTTGGGGTTA
* * ** * * *
5029676 AAAAT-GACA-TTTTGGACATCCGAGAGTAAAACGGTAATTTTTAGAAAAATCGGGATCA
1 AAAATAGA-ATTTTTGGACA-CCGAGGGTAAAATGGTAA-TTTTAGAAAGTTTGGGGTTA
* *
5029734 AAAATAGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTAGGGG-T-
1 AAAATAGAATTTTTGGACA-CCGAGGGTAAAATGGTAATTTTAGAAAGTTT-GGGGTTA
*
5029791 AAAATTGTAATTTTTGGA
1 AAAATAG-AATTTTTGGA
5029809 AGTTTAGGGG
Statistics
Matches: 106, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
57 6 0.06
58 60 0.57
59 35 0.33
60 5 0.05
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (57 bp):
AAAATAGAATTTTTGGACACCGAGGGTAAAATGGTAATTTTAGAAAGTTTGGGGTTA
Found at i:5029764 original size:59 final size:58
Alignment explanation
Indices: 5029641--5029780 Score: 167
Period size: 58 Copynumber: 2.4 Consensus size: 58
5029631 GGATACACGG
* ** * * *
5029641 GGGTAAAATGGTAATTTTAAGAAAGTTTGGGGTTAAAAATGACATTTTGGACATCCGA
1 GGGTAAAATGGTAATTTTTAGAAAAATCGGGATCAAAAATGACATTTTGGACATCCGA
* * *
5029699 GAGTAAAACGGTAATTTTTAGAAAAATCGGGATCAAAAATAGA-ATTTTTGGACATTCGA
1 GGGTAAAATGGTAATTTTTAGAAAAATCGGGATCAAAAAT-GACA-TTTTGGACATCCGA
5029758 GGGTAAAATGGTAATTTTT-GAAA
1 GGGTAAAATGGTAATTTTTAGAAA
5029781 GTTTAGGGGT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 37 0.54
59 32 0.46
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTAGAAAAATCGGGATCAAAAATGACATTTTGGACATCCGA
Found at i:5029773 original size:29 final size:28
Alignment explanation
Indices: 5029758--5030013 Score: 190
Period size: 29 Copynumber: 9.1 Consensus size: 28
5029748 GGACATTCGA
*
5029758 GGGTAAAATGGTAATTTTTGAAAGTTTAG
1 GGGTAAAAT-GTAATTTTTGGAAGTTTAG
5029787 GGGTAAAATTGTAATTTTTGGAAGTTTAG
1 GGGTAAAA-TGTAATTTTTGGAAGTTTAG
* *
5029816 GGGTAAAATGTAATTTTTGGTAGTTTTG
1 GGGTAAAATGTAATTTTTGGAAGTTTAG
* * ** *
5029844 AGGT-CAA---AA--TCGGGAAG-TTCG
1 GGGTAAAATGTAATTTTTGGAAGTTTAG
*
5029865 AGGGTAAAAAT-TAAAATTTTGGAAGTTT-G
1 -GGGT-AAAATGT-AATTTTTGGAAGTTTAG
5029894 GAGGTAAAAATGTAATTTTTGGAAGTTTTAG
1 G-GGT-AAAATGTAATTTTTGGAAG-TTTAG
* * *
5029925 GGTTAAAAATGAAATTTTTGGAAGTTCA-
1 GGGT-AAAATGTAATTTTTGGAAGTTTAG
*
5029953 GGGTAAAAATGTAATTTTTGGAAGTTTCAA
1 GGGT-AAAATGTAATTTTTGGAAGTTT-AG
* * *
5029983 GGTTAATATATAATTTTTGGACAGTTTAG
1 GGGTAAAATGTAATTTTTGGA-AGTTTAG
5030012 GG
1 GG
5030014 ACCTTCAGGG
Statistics
Matches: 186, Mismatches: 24, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.02
22 8 0.04
24 4 0.02
27 4 0.02
28 46 0.25
29 83 0.45
30 36 0.19
31 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTGGAAGTTTAG
Found at i:5031865 original size:17 final size:17
Alignment explanation
Indices: 5031843--5031946 Score: 127
Period size: 17 Copynumber: 6.1 Consensus size: 17
5031833 TTTTAATATT
* *
5031843 AATAAATTTTAATTCAA
1 AATAAATTTAAATTTAA
5031860 AATAAATTTAAATTTAA
1 AATAAATTTAAATTTAA
* *
5031877 AATAAATTTAAACTCAA
1 AATAAATTTAAATTTAA
* **
5031894 CATGGATTTAAATTTAA
1 AATAAATTTAAATTTAA
5031911 AATAAATTTAAATTTAA
1 AATAAATTTAAATTTAA
**
5031928 AATAAATCAAAATTTAA
1 AATAAATTTAAATTTAA
5031945 AA
1 AA
5031947 ATTAAAAGTT
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 73 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:5033933 original size:15 final size:15
Alignment explanation
Indices: 5033913--5033942 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5033903 ATATTAATGT
*
5033913 TATTTAATTTTAAAA
1 TATTTAATATTAAAA
5033928 TATTTAATATTAAAA
1 TATTTAATATTAAAA
5033943 CAATATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTAATATTAAAA
Found at i:5036834 original size:11 final size:11
Alignment explanation
Indices: 5036818--5036843 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5036808 TTTTAGTTTT
5036818 ATGGATTCTCA
1 ATGGATTCTCA
5036829 ATGGATTCTCA
1 ATGGATTCTCA
5036840 ATGG
1 ATGG
5036844 TGTCAGTTGC
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:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (11 bp):
ATGGATTCTCA
Found at i:5055408 original size:3 final size:3
Alignment explanation
Indices: 5055402--5055433 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5055392 TATTATTATT
*
5055402 ATC ATC ACC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
5055434 TATTATCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:5059548 original size:12 final size:12
Alignment explanation
Indices: 5059531--5059556 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5059521 CCTGATTATT
5059531 CTTCAGCTTCTC
1 CTTCAGCTTCTC
5059543 CTTCAGCTTCTC
1 CTTCAGCTTCTC
5059555 CT
1 CT
5059557 GGTTCAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.42, G:0.08, T:0.42
Consensus pattern (12 bp):
CTTCAGCTTCTC
Found at i:5066494 original size:9 final size:9
Alignment explanation
Indices: 5066480--5066691 Score: 87
Period size: 9 Copynumber: 22.8 Consensus size: 9
5066470 GTCCAATTCA
5066480 AATTTTTAT
1 AATTTTTAT
5066489 AATTTTTAT
1 AATTTTTAT
*
5066498 AAATTTATAT
1 -AATTTTTAT
5066508 CAA-TTTTAT
1 -AATTTTTAT
*
5066517 TATTTTTAT
1 AATTTTTAT
* *
5066526 TATTTTTAAG
1 AATTTTT-AT
* * *
5066536 AAGTCTAAT
1 AATTTTTAT
5066545 ACATTTTT-T
1 A-ATTTTTAT
*
5066554 AATTTTAAAT
1 AATTTT-TAT
*
5066564 AAGTTTTATT
1 AATTTTTA-T
5066574 AA-TTTTAT
1 AATTTTTAT
*
5066582 AATTTTTTAC
1 AA-TTTTTAT
5066592 AATTTAGTT-T
1 AATTT--TTAT
*
5066602 -TTTTTTAT
1 AATTTTTAT
*
5066610 -ATTTGTAT
1 AATTTTTAT
**
5066618 AATACTTAT
1 AATTTTTAT
*
5066627 AAGTTTCTAT
1 AA-TTTTTAT
5066637 AATTTTTTAT
1 AA-TTTTTAT
5066647 AATTTTTAT
1 AATTTTTAT
*
5066656 AAGTTTATAT
1 AA-TTTTTAT
*
5066666 CATTTTTA-
1 AATTTTTAT
*
5066674 ATATTTTAAT
1 A-ATTTTTAT
5066684 AATCTTTT
1 AAT-TTTT
5066692 TTTGTTTTTT
Statistics
Matches: 150, Mismatches: 35, Indels: 35
0.68 0.16 0.16
Matches are distributed among these distances:
7 2 0.01
8 16 0.11
9 72 0.48
10 58 0.39
11 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (9 bp):
AATTTTTAT
Found at i:5066578 original size:28 final size:29
Alignment explanation
Indices: 5066483--5066587 Score: 87
Period size: 28 Copynumber: 3.8 Consensus size: 29
5066473 CAATTCAAAT
* *
5066483 TTTTA-TAATTTTTATAAATTTATATCAA-
1 TTTTATTAATTTTTATAATTTTAAAT-AAG
* * *
5066511 TTTTATT-ATTTTTATTATTTTTAAGAAG
1 TTTTATTAATTTTTATAATTTTAAATAAG
* *
5066539 -TCTAATACATTTTT-TAATTTTAAATAAG
1 TTTTATTA-ATTTTTATAATTTTAAATAAG
5066567 TTTTATTAA-TTTTATAATTTT
1 TTTTATTAATTTTTATAATTTT
5066588 TTACAATTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
27 10 0.17
28 37 0.63
29 12 0.20
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTTATTAATTTTTATAATTTTAAATAAG
Found at i:5066647 original size:10 final size:10
Alignment explanation
Indices: 5066623--5066661 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5066613 TGTATAATAC
5066623 TTATAAGTTT
1 TTATAAGTTT
* *
5066633 CTATAATTTT
1 TTATAAGTTT
5066643 TTATAA-TTT
1 TTATAAGTTT
5066652 TTATAAGTTT
1 TTATAAGTTT
5066662 ATATCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (10 bp):
TTATAAGTTT
Found at i:5066648 original size:29 final size:29
Alignment explanation
Indices: 5066615--5066672 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5066605 TTTATATTTG
*
5066615 TATAATACTTATAAGTTTCTATAATTTTT
1 TATAATACTTATAAGTTTATATAATTTTT
** *
5066644 TATAATTTTTATAAGTTTATATCATTTTT
1 TATAATACTTATAAGTTTATATAATTTTT
5066673 AATATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (29 bp):
TATAATACTTATAAGTTTATATAATTTTT
Found at i:5066670 original size:19 final size:19
Alignment explanation
Indices: 5066624--5066673 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5066614 GTATAATACT
* * *
5066624 TATAAGTTTCTATAATTTTT
1 TATAA-TTTTTATAAGTTTA
5066644 TATAATTTTTATAAGTTTA
1 TATAATTTTTATAAGTTTA
*
5066663 TATCATTTTTA
1 TATAATTTTTA
5066674 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (19 bp):
TATAATTTTTATAAGTTTA
Found at i:5071142 original size:33 final size:33
Alignment explanation
Indices: 5071100--5071165 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
5071090 TTCGCAAAAT
**
5071100 GAATCCGACAGATGGGCAGGATGGTGACAAGGA
1 GAATCCGACAGATGGGCAGGATAATGACAAGGA
5071133 GAATCCGACAGATGGGCAGGATAATGACAAGGA
1 GAATCCGACAGATGGGCAGGATAATGACAAGGA
5071166 ATTGAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.36, T:0.12
Consensus pattern (33 bp):
GAATCCGACAGATGGGCAGGATAATGACAAGGA
Found at i:5076582 original size:17 final size:17
Alignment explanation
Indices: 5076546--5076579 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5076536 TAAAAAATTG
*
5076546 TATACATTTTATATTTT
1 TATAAATTTTATATTTT
5076563 TATAAATTTTA-ATTTT
1 TATAAATTTTATATTTT
5076579 T
1 T
5076580 TATGTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TATAAATTTTATATTTT
Found at i:5076691 original size:2 final size:2
Alignment explanation
Indices: 5076686--5076721 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5076676 TTTTTTATCA
5076686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5076722 TAAAGATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5078838 original size:13 final size:13
Alignment explanation
Indices: 5078820--5078858 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5078810 TCGTGGATAA
*
5078820 TAAAAATGTTATT
1 TAAAAATATTATT
*
5078833 TAAAAA-ATCATT
1 TAAAAATATTATT
5078845 TAAAAATATTATT
1 TAAAAATATTATT
5078858 T
1 T
5078859 CAAATGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (13 bp):
TAAAAATATTATT
Found at i:5079218 original size:92 final size:92
Alignment explanation
Indices: 5079059--5079248 Score: 285
Period size: 92 Copynumber: 2.1 Consensus size: 92
5079049 TTAACATCAT
*
5079059 GTACCATAATAAAACACATATTGATAGTTTAGGTACCACATTGGATATTTTCAAAGTACAAGCAC
1 GTACCATAATAAAACACATATTGATAGTTTAGGTACCACATTGAATATTTTCAAAGTACAAGCAC
*
5079124 CACTTTGAACATTAT-ATGAAAGTACAA
66 CACATTGAACATT-TCATGAAAGTACAA
* *
5079151 GTACCATAATAAAACACATATT-ATTAGTTTAGGTACCACATTGAATATTTTCAAAGTATAAGTA
1 GTACCATAATAAAACACATATTGA-TAGTTTAGGTACCACATTGAATATTTTCAAAGTACAAGCA
* * *
5079215 CCACATTGGATATTTCATGAAAGTACAG
65 CCACATTGAACATTTCATGAAAGTACAA
5079243 GTACCA
1 GTACCA
5079249 AATGTGACAT
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
91 2 0.02
92 87 0.98
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.31
Consensus pattern (92 bp):
GTACCATAATAAAACACATATTGATAGTTTAGGTACCACATTGAATATTTTCAAAGTACAAGCAC
CACATTGAACATTTCATGAAAGTACAA
Found at i:5079247 original size:31 final size:29
Alignment explanation
Indices: 5079181--5079248 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
5079171 TTATTAGTTT
*
5079181 AGGTACCACATTGAATATTTTCAAAGTAT
1 AGGTACCACATTGAATATTTTCAAAGTAC
* * *
5079210 AAGTACCACATTGGATATTTCATGAAAGTAC
1 AGGTACCACATTGAATATTT--TCAAAGTAC
5079241 AGGTACCA
1 AGGTACCA
5079249 AATGTGACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 18 0.56
31 14 0.44
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (29 bp):
AGGTACCACATTGAATATTTTCAAAGTAC
Found at i:5083038 original size:18 final size:18
Alignment explanation
Indices: 5083011--5083051 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
5083001 GGTAAATTAA
*
5083011 TTGCATTTGAATCTGTTT
1 TTGCACTTGAATCTGTTT
*
5083029 TTGCACTTGAATTTGTTT
1 TTGCACTTGAATCTGTTT
5083047 TTGCA
1 TTGCA
5083052 TCTGATATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (18 bp):
TTGCACTTGAATCTGTTT
Found at i:5088168 original size:42 final size:42
Alignment explanation
Indices: 5088121--5088205 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
5088111 ATTTTAGGCA
* *
5088121 AGATATTAGCTTTTCACAGTACTGGCCTTCCTTCTTTACATC
1 AGATATTAGCTTTTCACAGTACTCGCCTTCCTCCTTTACATC
* * *
5088163 AGATATTGGCTTTTCATAGTACTCGTCTTCCTCCTTTACATC
1 AGATATTAGCTTTTCACAGTACTCGCCTTCCTCCTTTACATC
5088205 A
1 A
5088206 TCAAGCACGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (42 bp):
AGATATTAGCTTTTCACAGTACTCGCCTTCCTCCTTTACATC
Found at i:5090570 original size:30 final size:31
Alignment explanation
Indices: 5090530--5090592 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
5090520 AACTTATATC
*
5090530 TTTATAATTTTTAAAGAAT-TAAATAAAATT
1 TTTATAATTTTTAAAGAATAAAAATAAAATT
* *
5090560 TTTATTATTTTTAAAGAATAAAAATATAATT
1 TTTATAATTTTTAAAGAATAAAAATAAAATT
5090591 TT
1 TT
5090593 ATTTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (31 bp):
TTTATAATTTTTAAAGAATAAAAATAAAATT
Found at i:5095463 original size:100 final size:101
Alignment explanation
Indices: 5095289--5095485 Score: 335
Period size: 100 Copynumber: 2.0 Consensus size: 101
5095279 GGAACAGTTT
* *
5095289 ACAAGTAGGTTACGTTAAAGAGATTCCATTCTTGATTTATTTCATGAGTTAATGCATGATTGGTA
1 ACAAGTAGGTTACATTAAAGAGATTCCATTCTTGATTTATTTCATGAGTTAATGCATGATTGCTA
*
5095354 CTGAAAAAAAGTTGTAAAGATTATCCTAGGTTCTCC
66 CTGAAAAAAAGTTGTAAAGATTATCCAAGGTTCTCC
*
5095390 ACAAGTAGGTTACATTAAAGA-ATTTCATTCTTGATTTATTTCATGAGTTAATGCA-GTATTGCT
1 ACAAGTAGGTTACATTAAAGAGATTCCATTCTTGATTTATTTCATGAGTTAATGCATG-ATTGCT
5095453 ACTGAAAAAAAGTTGTAAAGATTATCCAAGGTT
65 ACTGAAAAAAAGTTGTAAAGATTATCCAAGGTT
5095486 TCCCTAGAAG
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
99 1 0.01
100 70 0.77
101 20 0.22
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (101 bp):
ACAAGTAGGTTACATTAAAGAGATTCCATTCTTGATTTATTTCATGAGTTAATGCATGATTGCTA
CTGAAAAAAAGTTGTAAAGATTATCCAAGGTTCTCC
Found at i:5103329 original size:20 final size:21
Alignment explanation
Indices: 5103285--5103329 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
5103275 AATACTAATT
*
5103285 TTGA-ATTTAAATATTTTTTA
1 TTGATATTTAAATATTATTTA
5103305 -T-ATATTTAAA-ATTATTTA
1 TTGATATTTAAATATTATTTA
5103323 TTGATAT
1 TTGATAT
5103330 GATATCTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TTGATATTTAAATATTATTTA
Found at i:5106763 original size:22 final size:22
Alignment explanation
Indices: 5106696--5106763 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
5106686 ATATATGTAA
5106696 AAACAATATAAAAT-ATAAATT
1 AAACAATATAAAATAATAAATT
* * *
5106717 TAATAGATATAAAATAAATTCAATT
1 AAACA-ATATAAAAT-AA-TAAATT
*
5106742 AAACAATAAAAAATAATAAATT
1 AAACAATATAAAATAATAAATT
5106764 CTTAATTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
21 3 0.08
22 14 0.39
23 2 0.06
24 9 0.25
25 8 0.22
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (22 bp):
AAACAATATAAAATAATAAATT
Found at i:5109249 original size:31 final size:31
Alignment explanation
Indices: 5109212--5109292 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
5109202 TTTTTTGATC
5109212 TAATTTGGTACTCAAACTTGACA-TTTTTTCT
1 TAATTTGGTACTCAAACTTGACACTTTTTT-T
5109243 TAATTTGGTAC-CTAAACTTGACACTTTTTTT
1 TAATTTGGTACTC-AAACTTGACACTTTTTTT
* * *
5109274 TAAGTTAGTACTTAAACTT
1 TAATTTGGTACTCAAACTT
5109293 TTTAGGATCC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 1 0.02
31 37 0.84
32 6 0.14
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (31 bp):
TAATTTGGTACTCAAACTTGACACTTTTTTT
Found at i:5109539 original size:27 final size:28
Alignment explanation
Indices: 5109482--5109540 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5109472 AATTGAATCT
*
5109482 AAAAAAAGTTTAGGTACCAAATTGGATA
1 AAAAAAAGTTTAGGTACCAAATTAGATA
* * *
5109510 AAAAAAAGTTTATGTATCTAATTAGA-A
1 AAAAAAAGTTTAGGTACCAAATTAGATA
5109537 AAAA
1 AAAA
5109541 GTGTCAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (28 bp):
AAAAAAAGTTTAGGTACCAAATTAGATA
Found at i:5111235 original size:24 final size:24
Alignment explanation
Indices: 5111172--5111254 Score: 68
Period size: 24 Copynumber: 3.6 Consensus size: 24
5111162 AACAACCAAC
* *
5111172 ATAACAACCAAAATAGCAGCAAAA
1 ATAACAACAAAAATAGCAACAAAA
* *
5111196 ATAATAGC--AAA-A-CAACAATAA
1 ATAACAACAAAAATAGCAACAA-AA
5111217 A-AACAACAAAAATAGCAACAAAA
1 ATAACAACAAAAATAGCAACAAAA
**
5111240 ATAACAGTAAAAATA
1 ATAACAACAAAAATA
5111255 ACACTAAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 9 0.20
21 4 0.09
22 6 0.13
23 4 0.09
24 23 0.50
ACGTcount: A:0.67, C:0.16, G:0.06, T:0.11
Consensus pattern (24 bp):
ATAACAACAAAAATAGCAACAAAA
Found at i:5111236 original size:15 final size:15
Alignment explanation
Indices: 5111174--5111237 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
5111164 CAACCAACAT
*
5111174 AACAACCAAAATAGC
1 AACAACAAAAATAGC
*
5111189 AGCAA-AAATAATAGC
1 AACAACAAA-AATAGC
* **
5111204 AA-AACAACAATAAA
1 AACAACAAAAATAGC
5111218 AACAACAAAAATAGC
1 AACAACAAAAATAGC
5111233 AACAA
1 AACAA
5111238 AAATAACAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
14 10 0.27
15 27 0.73
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.08
Consensus pattern (15 bp):
AACAACAAAAATAGC
Found at i:5111264 original size:44 final size:44
Alignment explanation
Indices: 5111174--5111272 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
5111164 CAACCAACAT
* * * *
5111174 AACAACCAAAATAGCAGCAAAAATAATAGCAAAACAACAATAAA
1 AACAACAAAAATAGCAACAAAAATAACAGAAAAACAACAATAAA
* *
5111218 AACAACAAAAATAGCAACAAAAATAACAGTAAAAATAACACT-AA
1 AACAACAAAAATAGCAACAAAAATAACAG-AAAAACAACAATAAA
*
5111262 AACAATAAAAA
1 AACAACAAAAA
5111273 ATTCACAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 38 0.81
45 9 0.19
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.10
Consensus pattern (44 bp):
AACAACAAAAATAGCAACAAAAATAACAGAAAAACAACAATAAA
Found at i:5111264 original size:56 final size:56
Alignment explanation
Indices: 5111161--5111266 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 56
5111151 AATAACATCC
* * * * *
5111161 AAACAACCAACATAACAACCAAAATAGCAGCAAAAATAATAGCAAAACAACAATAA
1 AAACAACAAAAATAACAACAAAAATAACAGCAAAAATAACAGCAAAACAACAATAA
* *
5111217 AAACAACAAAAATAGCAACAAAAATAACAGTAAAAATAACA-CTAAAACAA
1 AAACAACAAAAATAACAACAAAAATAACAGCAAAAATAACAGC-AAAACAA
5111267 TAAAAAATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
55 1 0.02
56 41 0.98
ACGTcount: A:0.67, C:0.19, G:0.05, T:0.09
Consensus pattern (56 bp):
AAACAACAAAAATAACAACAAAAATAACAGCAAAAATAACAGCAAAACAACAATAA
Found at i:5113448 original size:27 final size:32
Alignment explanation
Indices: 5113419--5113486 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
5113409 GTTTATATAT
5113419 TTATAATTTAAA-AAAT-AAAATA-AATTTTTA
1 TTAT-ATTTAAAGAAATCAAAATACAATTTTTA
* *
5113449 TTATTTTTAAAGAAATCAAAATACAA-TTTCA
1 TTATATTTAAAGAAATCAAAATACAATTTTTA
5113480 TTATATT
1 TTATATT
5113487 AATTTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 6 0.19
30 8 0.25
31 16 0.50
32 2 0.06
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (32 bp):
TTATATTTAAAGAAATCAAAATACAATTTTTA
Found at i:5118697 original size:5 final size:5
Alignment explanation
Indices: 5118687--5118727 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
5118677 CCCCATGCTC
5118687 CTCAT CTCAT CTCAT CTCAT CTCAT CTCAT CTCAT CTCAT C
1 CTCAT CTCAT CTCAT CTCAT CTCAT CTCAT CTCAT CTCAT C
5118728 AACAATCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (5 bp):
CTCAT
Found at i:5126133 original size:30 final size:30
Alignment explanation
Indices: 5126099--5126155 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5126089 GTGGTGGGCT
*
5126099 GATGATA-GCTATGGTGAGGGGGGGAGGTTG
1 GATGATATGC-ATGATGAGGGGGGGAGGTTG
*
5126129 GATGATATGCATGATGAGGTGGGGAGG
1 GATGATATGCATGATGAGGGGGGGAGG
5126156 GGGAACTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.23, C:0.04, G:0.51, T:0.23
Consensus pattern (30 bp):
GATGATATGCATGATGAGGGGGGGAGGTTG
Found at i:5132702 original size:18 final size:18
Alignment explanation
Indices: 5132676--5132710 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5132666 CTTTAAATAT
*
5132676 TATGTTAAAAATAATAAA
1 TATGATAAAAATAATAAA
*
5132694 TATGATAAAAATTATAA
1 TATGATAAAAATAATAA
5132711 TAAATTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TATGATAAAAATAATAAA
Found at i:5132723 original size:21 final size:22
Alignment explanation
Indices: 5132685--5132735 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
5132675 TTATGTTAAA
5132685 AATAATAAATATGAT-AAAAAT
1 AATAATAAATATGATAAAAAAT
* *
5132706 TATAATAAATTAT-TTAAAAAAT
1 AATAATAAA-TATGATAAAAAAT
5132728 AATAATAA
1 AATAATAA
5132736 TATAAACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AATAATAAATATGATAAAAAAT
Found at i:5138329 original size:19 final size:19
Alignment explanation
Indices: 5138302--5138339 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5138292 AATTTTATGC
*
5138302 ATATTAAAATGCTTT-TTTT
1 ATATAAAAAT-CTTTATTTT
5138321 ATATAAAAATCTTTATTTT
1 ATATAAAAATCTTTATTTT
5138340 TTTTAATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATAAAAATCTTTATTTT
Found at i:5140179 original size:28 final size:28
Alignment explanation
Indices: 5140126--5140179 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5140116 TTTAGTGTTT
*
5140126 TTTTTTACTATTTTGGTTGCTGTTTTTG
1 TTTTTTACTATTTTGGATGCTGTTTTTG
* *
5140154 TTTTTTACTGTTTT-GATGCTTTTTTT
1 TTTTTTACTATTTTGGATGCTGTTTTT
5140180 ATTGTTTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.07, C:0.07, G:0.15, T:0.70
Consensus pattern (28 bp):
TTTTTTACTATTTTGGATGCTGTTTTTG
Found at i:5140187 original size:28 final size:28
Alignment explanation
Indices: 5140126--5140187 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
5140116 TTTAGTGTTT
* *
5140126 TTTTTTACTATTTTGGTTGCTGTTTTTG
1 TTTTTTACTATTTTGGATGCTGTTTTTA
* *
5140154 TTTTTTACTGTTTT-GATGCTTTTTTTA
1 TTTTTTACTATTTTGGATGCTGTTTTTA
5140181 TTGTTTT
1 TT-TTTT
5140188 GGTTGTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.08, C:0.06, G:0.15, T:0.71
Consensus pattern (28 bp):
TTTTTTACTATTTTGGATGCTGTTTTTA
Found at i:5140288 original size:24 final size:23
Alignment explanation
Indices: 5140182--5140294 Score: 83
Period size: 21 Copynumber: 5.0 Consensus size: 23
5140172 CTTTTTTTAT
*
5140182 TGTTTTGGTTGTTATTTTCGTGTT-A
1 TGTTTT-GTTGTTATTTT--TGTTGC
*
5140207 T-TTTTGCTGTTATTTTTGTTGC
1 TGTTTTGTTGTTATTTTTGTTGC
* ** *
5140229 T-ATTT-TTGTTATTTTTAATGT
1 TGTTTTGTTGTTATTTTTGTTGC
**
5140250 TG-TTTACTGTTATTTTTGTTGC
1 TGTTTTGTTGTTATTTTTGTTGC
5140272 TGTTTTGGTTGTTATTTTTGTTG
1 TGTTTT-GTTGTTATTTTTGTTG
5140295 TTTGGATGTT
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
21 20 0.29
22 18 0.26
23 13 0.19
24 18 0.26
25 1 0.01
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.67
Consensus pattern (23 bp):
TGTTTTGTTGTTATTTTTGTTGC
Found at i:5140289 original size:12 final size:12
Alignment explanation
Indices: 5140184--5140296 Score: 76
Period size: 12 Copynumber: 9.9 Consensus size: 12
5140174 TTTTTTATTG
*
5140184 TTTTGGTTGTTA
1 TTTTTGTTGTTA
*
5140196 TTTTCG-TGTTA
1 TTTTTGTTGTTA
*
5140207 TTTTTGCTGTTA
1 TTTTTGTTGTTA
*
5140219 TTTTTGTTGCTA
1 TTTTTGTTGTTA
5140231 --TTT-TTGTTA
1 TTTTTGTTGTTA
**
5140240 TTTTTAATG-T-
1 TTTTTGTTGTTA
* **
5140250 TGTTTACTGTTA
1 TTTTTGTTGTTA
* *
5140262 TTTTTGTTGCTG
1 TTTTTGTTGTTA
*
5140274 TTTTGGTTGTTA
1 TTTTTGTTGTTA
5140286 TTTTTGTTGTT
1 TTTTTGTTGTT
5140297 TGGATGTTAT
Statistics
Matches: 78, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
9 5 0.06
10 10 0.13
11 15 0.19
12 48 0.62
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.68
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:5140294 original size:43 final size:43
Alignment explanation
Indices: 5140182--5140310 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 43
5140172 CTTTTTTTAT
* *
5140182 TGTTTTGGTTGTTATTTTCGTGTTATTTTTGCTGTTATTTTTGTTGC
1 TGTTTTGGTTGTTATTTT--TG-T-TGTTTACTGTTATTTTTGTTGC
* * * *
5140229 TATTTTTGTTATT-TTTAATGTTGTTTACTGTTATTTTTGTTGC
1 TGTTTTGGTTGTTATTT-TTGTTGTTTACTGTTATTTTTGTTGC
5140272 TGTTTTGGTTGTTATTTTTGTTGTTTGGA-TGTTATTTTT
1 TGTTTTGGTTGTTATTTTTGTTGTTT--ACTGTTATTTTT
5140311 TTATGCGTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
43 38 0.56
44 14 0.21
45 3 0.04
46 3 0.04
47 10 0.15
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.67
Consensus pattern (43 bp):
TGTTTTGGTTGTTATTTTTGTTGTTTACTGTTATTTTTGTTGC
Found at i:5143360 original size:15 final size:17
Alignment explanation
Indices: 5143341--5143382 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
5143331 TTAATTTTTA
5143341 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
5143357 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
5143373 AAAATTATAA
1 AAAATTATAA
5143383 TTTTATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 2 0.09
17 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:5149051 original size:32 final size:32
Alignment explanation
Indices: 5149002--5149065 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
5148992 TTTTAATGCA
5149002 ATCAAATTCCATCCTCCCATGTGGATTACAAT
1 ATCAAATTCCATCCTCCCATGTGGATTACAAT
*
5149034 ATCAGATTCCAAT-CTCCCATGTGGATTACAAT
1 ATCAAATTCC-ATCCTCCCATGTGGATTACAAT
5149066 GTTCACGGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (32 bp):
ATCAAATTCCATCCTCCCATGTGGATTACAAT
Found at i:5150690 original size:21 final size:21
Alignment explanation
Indices: 5150666--5150707 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5150656 TATTGGCACA
5150666 ACCAAGGAATTCACATAGAGC
1 ACCAAGGAATTCACATAGAGC
5150687 ACCAAGGAATTCACATAGAGC
1 ACCAAGGAATTCACATAGAGC
5150708 TTACTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14
Consensus pattern (21 bp):
ACCAAGGAATTCACATAGAGC
Found at i:5167680 original size:338 final size:338
Alignment explanation
Indices: 5166825--5168139 Score: 2212
Period size: 338 Copynumber: 3.9 Consensus size: 338
5166815 ACTAGCTACA
* * *
5166825 TTATATAATTACCTGGATAATATGGCACAGATTTACTACTTCATTTCATTCTAATTATAGGTTTT
1 TTATATAATTACCTGGTTAATATGGCACAGATTTACTACTTCATTCCATTCTAATTATAAGTTTT
* *
5166890 TAAAACTTGTTTTCCTGCATTAACTCTGAAATCTGAAGTTGGGCTTTTACTTTCTAGATCTCCAG
66 TAAAACCTGTTTTCCTGCATTAACTCTGAAATCTGAAGTTGGGTTTTTACTTTCTAGATCTCCAG
*
5166955 AAAAAAAGGTTCTCTACAAAAGCCATAAGAACAACAAAGTATTATTGAAATTAAAACACACACAC
131 AAAAAAAGGTTCTCTACAAAAGCCATAAGAACAACAAAATATTATTGAAATTAAAACACACACAC
* ** * * *
5167020 ACAGAGTCTACCTTCAATGTCTTCTTCATTGATGTCATTGGTATTGCCTTGATTGTGTTCTCCAC
196 AGAGACACTACCTTCAGTGTCTTCTTCATTGATGCCATTGGTACTGCCTTGATTGTGTTCTCCAC
* * *
5167085 TGGTATAATCTTCTTGGTTATTACCTCCATTGGATCCTTCATCGTCTTCATGGGTGTTACCTACA
261 TGG--T-ATCTTCTTGGTTATTCCCTCCATTGGATCCTTCACCGTCTTCGTGGGTGTTACCTACA
5167150 TTGGGTTCTTCACTGG
323 TTGGGTTCTTCACTGG
* * * *
5167166 TTAAACAATTACCTAGTTAATATGGCACAGATTTACTACTTCATTCCATTCTAATTAT-AGGTTT
1 TTATATAATTACCTGGTTAATATGGCACAGATTTACTACTTCATTCCATTCTAATTATAAGTTTT
* *
5167230 TAAAA-CTAGTTTTCCTGCATTGACTCTGAAATCTGAAGTTGGGTTTTTACTTTTTAGATCTCCA
66 TAAAACCT-GTTTTCCTGCATTAACTCTGAAATCTGAAGTTGGGTTTTTACTTTCTAGATCTCCA
5167294 GGAAAAAAA-GTTCTCTACAAAAGCCATAAGAACAACAAAATATTATTGAAATTAAAACACACAC
130 -GAAAAAAAGGTTCTCTACAAAAGCCATAAGAACAACAAAATATTATTGAAATTAAAACACACAC
5167358 ACAGAGACACTACCTTCAGTGTCTTCTTCATTGATGCCATTGGTACTGCCTTGATTGTGTTCTCC
194 ACAGAGACACTACCTTCAGTGTCTTCTTCATTGATGCCATTGGTACTGCCTTGATTGTGTTCTCC
5167423 ACTGGTATCTTCTTGGTTATTCCCTCCATTGGATCCTTCACCGTCTTCGTGGGTGTTACCTACAT
259 ACTGGTATCTTCTTGGTTATTCCCTCCATTGGATCCTTCACCGTCTTCGTGGGTGTTACCTACAT
5167488 TGGGTTCTTCACTGG
324 TGGGTTCTTCACTGG
* *
5167503 TTATATAATTACCTGGTTAATAGGGCACAGATTTACTACTTCATTCCATTCTAAGTATAAGTTTT
1 TTATATAATTACCTGGTTAATATGGCACAGATTTACTACTTCATTCCATTCTAATTATAAGTTTT
* * *
5167568 TAAAACCTGTTTTCCTGCATTGACTCTGGAATCTGAAATTGGGTTTTTACTTTCTAGATCTCCAG
66 TAAAACCTGTTTTCCTGCATTAACTCTGAAATCTGAAGTTGGGTTTTTACTTTCTAGATCTCCAG
* *
5167633 AAAAAAAGGTTCTCTACAAAAGCCATAACAACAGCAAAATATTATTGAAATTAAAACACACACAC
131 AAAAAAAGGTTCTCTACAAAAGCCATAAGAACAACAAAATATTATTGAAATTAAAACACACACAC
5167698 AGAGACACTACCTTCAGTGTCTTCTTCATTGATGCCATTGGTACTGCCTTGATTGTGTTCTCCAC
196 AGAGACACTACCTTCAGTGTCTTCTTCATTGATGCCATTGGTACTGCCTTGATTGTGTTCTCCAC
* * *
5167763 TGGTACCTTCTTGGTTATTCCCTCCATTGGATCCTTCACTGTCTTTGTGGGTGTTACCTACATTG
261 TGGTATCTTCTTGGTTATTCCCTCCATTGGATCCTTCACCGTCTTCGTGGGTGTTACCTACATTG
*
5167828 TGTTCTTCACTGG
326 GGTTCTTCACTGG
*
5167841 TTATATAATTACCTGGTTAATATGGCACAGATTTACTACTTCATTTCATTCTAATTATAAGTTTT
1 TTATATAATTACCTGGTTAATATGGCACAGATTTACTACTTCATTCCATTCTAATTATAAGTTTT
*
5167906 TAAAACTTGTTTTCCTGCATTAACTCTGAAATCTGAAGTTGGGTTTTTACTTTCTAGATCTCCAG
66 TAAAACCTGTTTTCCTGCATTAACTCTGAAATCTGAAGTTGGGTTTTTACTTTCTAGATCTCCAG
*
5167971 --AAAAAGGTTCTCTACAAAAGGCATAAGAACAACAAAATATTATTGAAATTAAAACACACACAC
131 AAAAAAAGGTTCTCTACAAAAGCCATAAGAACAACAAAATATTATTGAAATTAAAACACACACAC
*
5168034 AGAG--ACTACCTTCAGTGTCTTCTTCATTGATGTCATTGGTACTGCCTTGATTGTGTTCTCCAC
196 AGAGACACTACCTTCAGTGTCTTCTTCATTGATGCCATTGGTACTGCCTTGATTGTGTTCTCCAC
5168097 TGGTATCTTCTTGGTTATTCCCTCCATTGGATCCTTCACCGTC
261 TGGTATCTTCTTGGTTATTCCCTCCATTGGATCCTTCACCGTC
5168140 AGTATTACCT
Statistics
Matches: 920, Mismatches: 49, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
334 99 0.11
336 64 0.07
337 132 0.14
338 381 0.41
339 3 0.00
340 180 0.20
341 61 0.07
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (338 bp):
TTATATAATTACCTGGTTAATATGGCACAGATTTACTACTTCATTCCATTCTAATTATAAGTTTT
TAAAACCTGTTTTCCTGCATTAACTCTGAAATCTGAAGTTGGGTTTTTACTTTCTAGATCTCCAG
AAAAAAAGGTTCTCTACAAAAGCCATAAGAACAACAAAATATTATTGAAATTAAAACACACACAC
AGAGACACTACCTTCAGTGTCTTCTTCATTGATGCCATTGGTACTGCCTTGATTGTGTTCTCCAC
TGGTATCTTCTTGGTTATTCCCTCCATTGGATCCTTCACCGTCTTCGTGGGTGTTACCTACATTG
GGTTCTTCACTGG
Found at i:5168444 original size:7 final size:8
Alignment explanation
Indices: 5168427--5168451 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5168417 AGAAGGTACC
5168427 AAAAAGAA
1 AAAAAGAA
5168435 AAAAAGAA
1 AAAAAGAA
5168443 AAAAAGAA
1 AAAAAGAA
5168451 A
1 A
5168452 TATATAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:5169775 original size:20 final size:20
Alignment explanation
Indices: 5169740--5169798 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
5169730 ATTATATTCT
5169740 TGTTTTGGTT-TTTTTTTAC
1 TGTTTTGGTTATTTTTTTAC
*
5169759 TGTTTTGGTTATTTTTTTGC
1 TGTTTTGGTTATTTTTTTAC
*
5169779 TATTTTGGTGTTATTTTTTT
1 TGTTTT-G-GTTATTTTTTT
5169799 TACTATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 10 0.29
20 13 0.37
21 1 0.03
22 11 0.31
ACGTcount: A:0.07, C:0.03, G:0.17, T:0.73
Consensus pattern (20 bp):
TGTTTTGGTTATTTTTTTAC
Found at i:5169796 original size:23 final size:22
Alignment explanation
Indices: 5169749--5169818 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
5169739 TTGTTTTGGT
*
5169749 TTTTTTTTACTGTTTTG-GTTA
1 TTTTTTTTACTATTTTGTGTTA
*
5169770 -TTTTTTTGCTATTTTGGTGTTA
1 TTTTTTTTACTATTTT-GTGTTA
*
5169792 TTTTTTTTACTATTTTAGTGTTG
1 TTTTTTTTACTATTTT-GTGTTA
5169815 TTTT
1 TTTT
5169819 GCTATTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 13 0.32
21 1 0.02
22 4 0.10
23 23 0.56
ACGTcount: A:0.10, C:0.04, G:0.14, T:0.71
Consensus pattern (22 bp):
TTTTTTTTACTATTTTGTGTTA
Found at i:5169841 original size:12 final size:12
Alignment explanation
Indices: 5169766--5169872 Score: 78
Period size: 12 Copynumber: 9.2 Consensus size: 12
5169756 TACTGTTTTG
5169766 GTTATTTTT-TT
1 GTTATTTTTGTT
* *
5169777 GCTA-TTTTGGT
1 GTTATTTTTGTT
*
5169788 GTTATTTTTTTT
1 GTTATTTTTGTT
** *
5169800 ACTATTTTAG-T
1 GTTATTTTTGTT
* *
5169811 GTT-GTTTTGCT
1 GTTATTTTTGTT
*
5169822 ATTATTTTTGTT
1 GTTATTTTTGTT
* *
5169834 GTTCTTTTGGTT
1 GTTATTTTTGTT
*
5169846 GCTATTTTTGTT
1 GTTATTTTTGTT
5169858 GTTATTTTTGTT
1 GTTATTTTTGTT
5169870 GTT
1 GTT
5169873 TTGCTACTGT
Statistics
Matches: 69, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
10 8 0.12
11 12 0.17
12 49 0.71
ACGTcount: A:0.09, C:0.05, G:0.17, T:0.69
Consensus pattern (12 bp):
GTTATTTTTGTT
Found at i:5169901 original size:56 final size:56
Alignment explanation
Indices: 5169768--5169901 Score: 155
Period size: 56 Copynumber: 2.4 Consensus size: 56
5169758 CTGTTTTGGT
* * * *
5169768 TATTTTTTTGCTATTTTGG-TGTTATTTTTTTTACTATTTTAGTGTTGTTTTGCTAT
1 TATTTTTTTGTTATTTTGGTTGCTATTTTTGTTACTATTTTA-TGTTGTTTTGCTAC
* **
5169824 TATTTTTGTTGTTCTTTTGGTTGCTATTTTTGTTGTTATTTT-TGTTGTTTTGCTAC
1 TATTTTT-TTGTTATTTTGGTTGCTATTTTTGTTACTATTTTATGTTGTTTTGCTAC
*
5169880 TGTTTTTATTGTTATTTTGGTT
1 TATTTTT-TTGTTATTTTGGTT
5169902 ATTTGGATGT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
56 39 0.59
57 10 0.15
58 17 0.26
ACGTcount: A:0.10, C:0.05, G:0.16, T:0.69
Consensus pattern (56 bp):
TATTTTTTTGTTATTTTGGTTGCTATTTTTGTTACTATTTTATGTTGTTTTGCTAC
Found at i:5177908 original size:6 final size:6
Alignment explanation
Indices: 5177897--5177923 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5177887 GTCGTCTCTG
5177897 TTTGCT TTTGCT TTTGCT TTTGCT TTT
1 TTTGCT TTTGCT TTTGCT TTTGCT TTT
5177924 CTGTGGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTGCT
Found at i:5182580 original size:12 final size:13
Alignment explanation
Indices: 5182552--5182579 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5182542 GTTATATATT
5182552 AAATATTTTTTAA
1 AAATATTTTTTAA
5182565 AAATATTTTTTAA
1 AAATATTTTTTAA
5182578 AA
1 AA
5182580 TGAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:5186854 original size:27 final size:27
Alignment explanation
Indices: 5186824--5186886 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
5186814 CTTGATAGAA
*
5186824 AGGCACCATTGGTGCCGCCTGTCAGGT
1 AGGCACCACTGGTGCCGCCTGTCAGGT
5186851 AGGCACCACTGGTGCCGCCTGTCAGGT
1 AGGCACCACTGGTGCCGCCTGTCAGGT
5186878 AGGCACCAC
1 AGGCACCAC
5186887 CCATTTATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.33, G:0.32, T:0.17
Consensus pattern (27 bp):
AGGCACCACTGGTGCCGCCTGTCAGGT
Found at i:5187064 original size:15 final size:15
Alignment explanation
Indices: 5187044--5187085 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
5187034 AACGGGGAGA
5187044 ATATATTATTTTGGT
1 ATATATTATTTTGGT
**
5187059 ATATATATATTTTTTT
1 ATATAT-TATTTTGGT
5187075 A-ATATTATTTT
1 ATATATTATTTT
5187086 AGTAAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.25
15 10 0.42
16 8 0.33
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
ATATATTATTTTGGT
Found at i:5194100 original size:21 final size:21
Alignment explanation
Indices: 5194075--5194117 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5194065 TGCAACTGTA
5194075 TCCTCAGTTTCCTCTACCTCC
1 TCCTCAGTTTCCTCTACCTCC
*
5194096 TCCTCAGTTTCCTCTGCCTCC
1 TCCTCAGTTTCCTCTACCTCC
5194117 T
1 T
5194118 TCCACAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.47, G:0.07, T:0.40
Consensus pattern (21 bp):
TCCTCAGTTTCCTCTACCTCC
Found at i:5227847 original size:23 final size:22
Alignment explanation
Indices: 5227808--5227855 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
5227798 CCCTAAACAT
5227808 GAAAAAGAAAAAGAAAA-AGAGA
1 GAAAAAGAAAAAGAAAATA-AGA
5227830 GAAAAA-AAAAAGGAAAAATAAGA
1 GAAAAAGAAAAA-G-AAAATAAGA
5227853 GAA
1 GAA
5227856 GGTTGTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.22
22 7 0.30
23 10 0.43
24 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (22 bp):
GAAAAAGAAAAAGAAAATAAGA
Found at i:5234623 original size:21 final size:22
Alignment explanation
Indices: 5234580--5234640 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
5234570 ATATTATAAA
*
5234580 AATATTGAATATTAA-TAATTTT
1 AATATT-AATATAAATTAATTTT
5234602 AATATTAATATAAATTAA-TTT
1 AATATTAATATAAATTAATTTT
*
5234623 AACAATT-ATATAAATTAA
1 AA-TATTAATATAAATTAA
5234641 CTGAACTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AATATTAATATAAATTAATTTT
Found at i:5248159 original size:24 final size:24
Alignment explanation
Indices: 5248121--5248212 Score: 114
Period size: 24 Copynumber: 3.9 Consensus size: 24
5248111 ATTTGAGAAA
* *
5248121 TAATT-TTTCAGTTAAACTTTGTT
1 TAATTGTTTCAATTAAACTCTGTT
5248144 TAATTGTTTCAATTAAACTCTGTT
1 TAATTGTTTCAATTAAACTCTGTT
* *
5248168 TATTTGTTTCAATTAAACTCTATT
1 TAATTGTTTCAATTAAACTCTGTT
* * *
5248192 TATTTGTTTGAGTTAAACTCT
1 TAATTGTTTCAATTAAACTCT
5248213 TATTAGTCTA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
23 5 0.08
24 57 0.92
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (24 bp):
TAATTGTTTCAATTAAACTCTGTT
Found at i:5250172 original size:24 final size:24
Alignment explanation
Indices: 5250141--5250225 Score: 134
Period size: 24 Copynumber: 3.5 Consensus size: 24
5250131 AGAAATAATC
5250141 TTTCAATTAAACTTTGTTTAATTG
1 TTTCAATTAAACTTTGTTTAATTG
5250165 TTTCAATTAAACTTTGTTTAATTG
1 TTTCAATTAAACTTTGTTTAATTG
* *
5250189 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTTTGTTTAATTG
* *
5250213 TTTGAGTTAAACT
1 TTTCAATTAAACT
5250226 CTTATTAGTC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTTTGTTTAATTG
Found at i:5253332 original size:1 final size:1
Alignment explanation
Indices: 5253326--5253350 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5253316 TTTTAACTCT
5253326 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
5253351 TCATTTTTAA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5254844 original size:14 final size:14
Alignment explanation
Indices: 5254825--5254851 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5254815 TTATTGAAAG
5254825 CGAATTAATTTGAC
1 CGAATTAATTTGAC
5254839 CGAATTAATTTGA
1 CGAATTAATTTGA
5254852 GTTGATTATG
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:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (14 bp):
CGAATTAATTTGAC
Found at i:5260694 original size:20 final size:18
Alignment explanation
Indices: 5260671--5260719 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
5260661 TGATATTTTA
5260671 TATAAAAATAATTAAAAATT
1 TATAAAAATAA-TAAAAA-T
*
5260691 TATAAAAAATAATAAATAT
1 TAT-AAAAATAATAAAAAT
5260710 TATAAAAATA
1 TATAAAAATA
5260720 CAAAAAGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 7 0.26
19 4 0.15
20 8 0.30
21 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAAAAATAATAAAAAT
Found at i:5260700 original size:21 final size:20
Alignment explanation
Indices: 5260667--5260717 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
5260657 AAATTGATAT
5260667 TTTATATAAAAATAATTAAAAA
1 TTTATA-AAAAATAA-TAAAAA
*
5260689 TTTATAAAAAATAATAAATA
1 TTTATAAAAAATAATAAAAA
5260709 -TTATAAAAA
1 TTTATAAAAA
5260718 TACAAAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 9 0.32
20 5 0.18
21 8 0.29
22 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TTTATAAAAAATAATAAAAA
Found at i:5269246 original size:19 final size:19
Alignment explanation
Indices: 5269204--5269269 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
5269194 GTTTTATATT
5269204 TTTTTAAATATATAATTTTAGAA
1 TTTTTAAA-AT-T-ATTTT-GAA
*
5269227 TTTTTATAATTATTTTGAA
1 TTTTTAAAATTATTTTGAA
*
5269246 TATTTGAAAATTATTTTG-A
1 T-TTTTAAAATTATTTTGAA
5269265 TTTTT
1 TTTTT
5269270 TTATTTTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.08
19 6 0.16
20 19 0.50
21 1 0.03
22 2 0.05
23 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (19 bp):
TTTTTAAAATTATTTTGAA
Found at i:5274225 original size:27 final size:27
Alignment explanation
Indices: 5274195--5274250 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5274185 TGTAAATCTT
5274195 AAACAATAATTTTAATATGTCAAACTG
1 AAACAATAATTTTAATATGTCAAACTG
5274222 AAACAATAATTTTAATATGTCAAACTG
1 AAACAATAATTTTAATATGTCAAACTG
5274249 AA
1 AA
5274251 TATATTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (27 bp):
AAACAATAATTTTAATATGTCAAACTG
Found at i:5280208 original size:20 final size:19
Alignment explanation
Indices: 5280183--5280236 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
5280173 TTTTGATAAT
5280183 TTTTAAACTTGAATTCTGAA
1 TTTTAAACTTGAA-TCTGAA
*
5280203 TTTTAAACTTTGAATCTTAA
1 TTTTAAAC-TTGAATCTGAA
*
5280223 ATTTAAATCTTGAA
1 TTTTAAA-CTTGAA
5280237 CTTAAATCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 24 0.80
21 6 0.20
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.46
Consensus pattern (19 bp):
TTTTAAACTTGAATCTGAA
Found at i:5283859 original size:6 final size:6
Alignment explanation
Indices: 5283848--5283885 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
5283838 CTTGAATGCA
5283848 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GG
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GG
5283886 GGGCCACTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:5286760 original size:64 final size:64
Alignment explanation
Indices: 5286659--5286786 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
5286649 GTTTATAAAG
5286659 TATCTTATTCCGGTATCATGAAATTTGAACTCGCGACCGCATAACCACTATCAACTGGGCTCCC
1 TATCTTATTCCGGTATCATGAAATTTGAACTCGCGACCGCATAACCACTATCAACTGGGCTCCC
5286723 TATCTTATTCCGGTATCATGAAATTTGAACTCGCGACCGCATAACCACTATCAACTGGGCTCCC
1 TATCTTATTCCGGTATCATGAAATTTGAACTCGCGACCGCATAACCACTATCAACTGGGCTCCC
5286787 GAGTTATACT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (64 bp):
TATCTTATTCCGGTATCATGAAATTTGAACTCGCGACCGCATAACCACTATCAACTGGGCTCCC
Found at i:5286816 original size:50 final size:49
Alignment explanation
Indices: 5286757--5286859 Score: 138
Period size: 50 Copynumber: 2.1 Consensus size: 49
5286747 TTGAACTCGC
5286757 GACCGCATAACCACTATCAACT-GG-GCTCCCGAGTTATACTTCTAACCCGT
1 GACCGCATAACCACTATCAACTAGGAG-T-CCGAGTTATACTTC-AACCCGT
* * *
5286807 GACCGCATAACCACTATCAATTAGGAGTCCTAGTTATACTTCAACTCGT
1 GACCGCATAACCACTATCAACTAGGAGTCCGAGTTATACTTCAACCCGT
5286856 GACC
1 GACC
5286860 ATATAAGCAC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
49 10 0.21
50 34 0.71
51 3 0.06
52 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (49 bp):
GACCGCATAACCACTATCAACTAGGAGTCCGAGTTATACTTCAACCCGT
Found at i:5287941 original size:18 final size:18
Alignment explanation
Indices: 5287909--5287944 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5287899 ATCGTATTTG
5287909 TTAAAAAATATAAATATT
1 TTAAAAAATATAAATATT
5287927 TTAATAAAATA-AAATATT
1 TTAA-AAAATATAAATATT
5287945 AGAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAAAATATAAATATT
Found at i:5303209 original size:15 final size:15
Alignment explanation
Indices: 5303191--5303221 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5303181 ATGCATATTA
5303191 TAAAAATATATGTTT
1 TAAAAATATATGTTT
*
5303206 TAAAAATATTTGTTT
1 TAAAAATATATGTTT
5303221 T
1 T
5303222 GAAGTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
TAAAAATATATGTTT
Found at i:5316605 original size:2 final size:2
Alignment explanation
Indices: 5316600--5316638 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
5316590 CCCCCCCCCC
*
5316600 CT CT CT CT CT CT CT CT CT CT CT CAT -T CT CT CT CT TT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT C
5316639 AATGGCACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:5321765 original size:18 final size:18
Alignment explanation
Indices: 5321731--5321765 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5321721 GAGTTAAACG
*
5321731 AATCGAGTTGTTCGAGTT
1 AATCGAGTTATTCGAGTT
*
5321749 AATCGAGTTATTTGAGT
1 AATCGAGTTATTCGAGT
5321766 CAACTCGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:5321929 original size:21 final size:21
Alignment explanation
Indices: 5321890--5321930 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5321880 CCCCAACCCC
*
5321890 CAAACATTTTTACTTTTCCCT
1 CAAACATTTTTACTCTTCCCT
5321911 CAAA-ATTTTTACTCCTTCCC
1 CAAACATTTTTACT-CTTCCC
5321931 ACTTTCTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (21 bp):
CAAACATTTTTACTCTTCCCT
Found at i:5322502 original size:18 final size:17
Alignment explanation
Indices: 5322479--5322549 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
5322469 CAATTTCATA
5322479 TTTTATCTTTAAAATAAT
1 TTTTAT-TTTAAAATAAT
**
5322497 TTTTATTAAAAAATCACAT
1 TTTTATTTTAAAAT-A-AT
* * *
5322516 TTTTACATTTAATATATT
1 TTTTA-TTTTAAAATAAT
5322534 TTTTAATTTTAAAATA
1 TTTT-ATTTTAAAATA
5322550 CATTGTGACA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
17 6 0.15
18 20 0.50
19 9 0.22
20 5 0.12
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTATTTTAAAATAAT
Found at i:5322677 original size:19 final size:19
Alignment explanation
Indices: 5322653--5322690 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5322643 GAAAGTTAAT
*
5322653 AACAAATTTGATTACGGTG
1 AACAAATTTAATTACGGTG
5322672 AACAAATTTAATTACGGTG
1 AACAAATTTAATTACGGTG
5322691 GGTGACCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (19 bp):
AACAAATTTAATTACGGTG
Found at i:5330235 original size:91 final size:91
Alignment explanation
Indices: 5330080--5330258 Score: 358
Period size: 91 Copynumber: 2.0 Consensus size: 91
5330070 AAAACTTTAT
5330080 TTGTGATTGTATATGTTAGGGCATGCTGGTTATGGAAAGCAGAATCTGTGGCGATTATCTAAAAC
1 TTGTGATTGTATATGTTAGGGCATGCTGGTTATGGAAAGCAGAATCTGTGGCGATTATCTAAAAC
5330145 TTTATTTGTGATTGTATATGTTAAAG
66 TTTATTTGTGATTGTATATGTTAAAG
5330171 TTGTGATTGTATATGTTAGGGCATGCTGGTTATGGAAAGCAGAATCTGTGGCGATTATCTAAAAC
1 TTGTGATTGTATATGTTAGGGCATGCTGGTTATGGAAAGCAGAATCTGTGGCGATTATCTAAAAC
5330236 TTTATTTGTGATTGTATATGTTA
66 TTTATTTGTGATTGTATATGTTA
5330259 GGGCATGCTG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (91 bp):
TTGTGATTGTATATGTTAGGGCATGCTGGTTATGGAAAGCAGAATCTGTGGCGATTATCTAAAAC
TTTATTTGTGATTGTATATGTTAAAG
Found at i:5332632 original size:21 final size:21
Alignment explanation
Indices: 5332608--5332651 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5332598 TCCACCACCC
5332608 GGAGGATATGCC-CCTCCAGGA
1 GGAGGATAT-CCTCCTCCAGGA
*
5332629 GGAGGATATCCTCCTCCTGGA
1 GGAGGATATCCTCCTCCAGGA
5332650 GG
1 GG
5332652 TTACCCCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
GGAGGATATCCTCCTCCAGGA
Found at i:5334891 original size:6 final size:6
Alignment explanation
Indices: 5334880--5334904 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5334870 GTCCCACATT
5334880 CCCCAA CCCCAA CCCCAA CCCCAA C
1 CCCCAA CCCCAA CCCCAA CCCCAA C
5334905 AATGATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCAA
Found at i:5345762 original size:79 final size:79
Alignment explanation
Indices: 5345631--5345789 Score: 169
Period size: 79 Copynumber: 2.0 Consensus size: 79
5345621 GAACAATCAA
* * *
5345631 AATAATGGTAAGTATCATATAAACAATAAAGGAAGACTTGATCCAGAAAGGAACAATCAAGTAAC
1 AATAATGCTAAGTATCATATAAACAACAAAGGAAGACTTGAACCAGAAAGGAACAATCAAGTAAC
*
5345696 AAACATAGAATAGT
66 AAACACAGAATAGT
** * * * * *
5345710 AATAATGCTAAGTATCATATAAA-AAGCGGAGGAA-AGCTTGAACTAGAGAGGAAGAATTAAGTG
1 AATAATGCTAAGTATCATATAAACAA-CAAAGGAAGA-CTTGAACCAGAAAGGAACAATCAAGTA
**
5345773 ACAGGCACAGAATAGT
64 ACAAACACAGAATAGT
5345789 A
1 A
5345790 CCTTCAACCA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
78 3 0.05
79 62 0.95
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (79 bp):
AATAATGCTAAGTATCATATAAACAACAAAGGAAGACTTGAACCAGAAAGGAACAATCAAGTAAC
AAACACAGAATAGT
Found at i:5357026 original size:80 final size:80
Alignment explanation
Indices: 5356893--5357060 Score: 336
Period size: 80 Copynumber: 2.1 Consensus size: 80
5356883 GTATTATTGT
5356893 AATGTAATCATGATTGATGTTTCAACGCATACAAAAATGATTATTTTATTGTGAATCTGACTATA
1 AATGTAATCATGATTGATGTTTCAACGCATACAAAAATGATTATTTTATTGTGAATCTGACTATA
5356958 ATTACTCCAATAACG
66 ATTACTCCAATAACG
5356973 AATGTAATCATGATTGATGTTTCAACGCATACAAAAATGATTATTTTATTGTGAATCTGACTATA
1 AATGTAATCATGATTGATGTTTCAACGCATACAAAAATGATTATTTTATTGTGAATCTGACTATA
5357038 ATTACTCCAATAACG
66 ATTACTCCAATAACG
5357053 AATGTAAT
1 AATGTAAT
5357061 ATCTTGATGC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 88 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.36
Consensus pattern (80 bp):
AATGTAATCATGATTGATGTTTCAACGCATACAAAAATGATTATTTTATTGTGAATCTGACTATA
ATTACTCCAATAACG
Found at i:5367728 original size:18 final size:18
Alignment explanation
Indices: 5367705--5367740 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5367695 GTGGACCATG
*
5367705 TTTATAACTTAAAATAAA
1 TTTATAAATTAAAATAAA
*
5367723 TTTATAAATTAATATAAA
1 TTTATAAATTAAAATAAA
5367741 ACACATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTATAAATTAAAATAAA
Found at i:5369006 original size:6 final size:6
Alignment explanation
Indices: 5368990--5369030 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
5368980 TGTAAACCAC
* *
5368990 CAACAGG CAACGG CAACGG CAACGG CAACAG CAACAG CAAC
1 CAAC-GG CAACGG CAACGG CAACGG CAACGG CAACGG CAAC
5369031 AGTGAAACTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.41, C:0.34, G:0.24, T:0.00
Consensus pattern (6 bp):
CAACGG
Found at i:5369018 original size:18 final size:19
Alignment explanation
Indices: 5368990--5369032 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
5368980 TGTAAACCAC
* *
5368990 CAACAGGCAACGGCAACGG
1 CAACAGGCAACAGCAACAG
5369009 CAAC-GGCAACAGCAACAG
1 CAACAGGCAACAGCAACAG
5369027 CAACAG
1 CAACAG
5369033 TGAAACTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.42, C:0.33, G:0.26, T:0.00
Consensus pattern (19 bp):
CAACAGGCAACAGCAACAG
Found at i:5372608 original size:16 final size:16
Alignment explanation
Indices: 5372589--5372639 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
5372579 AAGTTATAAT
5372589 ATATTTAAATAATTTA
1 ATATTTAAATAATTTA
* *
5372605 ATA-TAATAATAAATT-
1 ATATTTA-AATAATTTA
5372620 ATATTTAAATAATTTA
1 ATATTTAAATAATTTA
5372636 ATAT
1 ATAT
5372640 AATAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTTAAATAATTTA
Found at i:5372608 original size:18 final size:18
Alignment explanation
Indices: 5372585--5372640 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
5372575 AGTTAAGTTA
5372585 TAATATATTTAAATAATT
1 TAATATATTTAAATAATT
*
5372603 TAATATA-AT-AATAA--
1 TAATATATTTAAATAATT
*
5372617 -ATTATATTTAAATAATT
1 TAATATATTTAAATAATT
5372634 TAATATA
1 TAATATA
5372641 ATAATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
13 5 0.17
14 1 0.03
15 5 0.17
16 5 0.17
17 1 0.03
18 12 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATATTTAAATAATT
Found at i:5372610 original size:10 final size:9
Alignment explanation
Indices: 5372586--5372642 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 9
5372576 GTTAAGTTAT
5372586 AATATATTTA
1 AATA-ATTTA
5372596 AATAATTTA
1 AATAATTTA
*
5372605 ATATAATAATA
1 A-ATAAT-TTA
5372616 AATTATATTTA
1 AA-TA-ATTTA
5372627 AATAATTTA
1 AATAATTTA
5372636 ATATAAT
1 A-ATAAT
5372643 AATATATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 12 0.30
10 17 0.43
11 9 0.22
12 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AATAATTTA
Found at i:5372623 original size:31 final size:31
Alignment explanation
Indices: 5372588--5372646 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
5372578 TAAGTTATAA
5372588 TATATTTAAATAATTTAATATAATAATAAAT
1 TATATTTAAATAATTTAATATAATAATAAAT
5372619 TATATTTAAATAATTTAATATAATAATA
1 TATATTTAAATAATTTAATATAATAATA
5372647 TATAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TATATTTAAATAATTTAATATAATAATAAAT
Found at i:5381536 original size:15 final size:14
Alignment explanation
Indices: 5381501--5381532 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
5381491 CAATACTCAT
5381501 TTTATTTTTTAAAA
1 TTTATTTTTTAAAA
5381515 TTTATTTTTTAAAA
1 TTTATTTTTTAAAA
5381529 TTTA
1 TTTA
5381533 ATTTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTATTTTTTAAAA
Found at i:5381766 original size:111 final size:111
Alignment explanation
Indices: 5381632--5381913 Score: 269
Period size: 109 Copynumber: 2.5 Consensus size: 111
5381622 TATTTTTTCC
*
5381632 TTTAC-TTTTTTTAGAATTAATTTTAGATTTTTCTAGTAAAAAAGAAAAATATGAGATTTTA-AA
1 TTTACTTTTTTTTAGAATTAATTTTAGATTTTTC-AGTAAAAAAGAAAAATATGAGATTCTACAA
5381695 AAAATTA-TCTAGATTTTTATAG-GCAAAAACCAATTTATCTTTTTAA-
65 AAAATTACT-TAGATTTTTATAGAG-AAAAACCAATTTATCTTTTTAAT
* *
5381741 TTTACTTTATTTTTAGAATTAATTTTA-ATTTTTCCCAAT-AAAAA-AAAACT-TGAGATTCTAC
1 TTTACTTT-TTTTTAGAATTAATTTTAGATTTTT--CAGTAAAAAAGAAAAATATGAGATTCTAC
* * * * *
5381802 AGAAAATTACTTGGATTTTTATCGAGAAAAATCATTTTATCTTTTTAATT
63 AAAAAATTACTTAGATTTTTATAGAGAAAAACCAATTTATCTTTTTAA-T
*
5381852 TCCTTCATTCTCTTTTTTTTAGAATTAATTTTTAG-TTTTTCAGTAAACAAGAAAATATATGA
1 T--TT-A----CTTTTTTTTAGAATTAA-TTTTAGATTTTTCAGTAAAAAAGAAAA-ATATGA
5381914 TTTTCATATT
Statistics
Matches: 140, Mismatches: 11, Indels: 33
0.76 0.06 0.18
Matches are distributed among these distances:
108 9 0.06
109 49 0.35
110 15 0.11
111 21 0.15
112 1 0.01
113 2 0.01
114 1 0.01
116 3 0.02
117 17 0.12
118 18 0.13
119 1 0.01
120 3 0.02
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.46
Consensus pattern (111 bp):
TTTACTTTTTTTTAGAATTAATTTTAGATTTTTCAGTAAAAAAGAAAAATATGAGATTCTACAAA
AAATTACTTAGATTTTTATAGAGAAAAACCAATTTATCTTTTTAAT
Found at i:5382817 original size:14 final size:15
Alignment explanation
Indices: 5382795--5382824 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5382785 AGAAATGTCG
5382795 AAATAAAAATAAATA
1 AAATAAAAATAAATA
5382810 AAAT-AAAATAAATA
1 AAATAAAAATAAATA
5382824 A
1 A
5382825 GTCAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAAAAATAAATA
Found at i:5383494 original size:19 final size:19
Alignment explanation
Indices: 5383470--5383512 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5383460 AAATATAAAT
5383470 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
5383489 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
5383508 TAAAT
1 TAAAT
5383513 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:5404538 original size:6 final size:6
Alignment explanation
Indices: 5404515--5404563 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
5404505 GGGTCGCCGA
* * * * *
5404515 GGCTGA GGCTGG GGCTGG GGCTGG GGTTGG GGTTGG GGTTGG GGTTGG
1 GGCTGG GGCTGG GGCTGG GGCTGG GGCTGG GGCTGG GGCTGG GGCTGG
5404563 G
1 G
5404564 ACTCCATGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.02, C:0.08, G:0.65, T:0.24
Consensus pattern (6 bp):
GGCTGG
Found at i:5404545 original size:18 final size:18
Alignment explanation
Indices: 5404524--5404563 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5404514 AGGCTGAGGC
5404524 TGGGGCTGGGGCTGGGGT
1 TGGGGCTGGGGCTGGGGT
* *
5404542 TGGGGTTGGGGTTGGGGT
1 TGGGGCTGGGGCTGGGGT
5404560 TGGG
1 TGGG
5404564 ACTCCATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.05, G:0.68, T:0.28
Consensus pattern (18 bp):
TGGGGCTGGGGCTGGGGT
Found at i:5404913 original size:17 final size:18
Alignment explanation
Indices: 5404878--5404916 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
5404868 ATTAAAAATG
5404878 TTATTCATTTATATCAAT
1 TTATTCATTTATATCAAT
5404896 TTATTC-TTTAATAT-AAT
1 TTATTCATTT-ATATCAAT
5404913 TTAT
1 TTAT
5404917 ATAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTCATTTATATCAAT
Found at i:5412854 original size:12 final size:12
Alignment explanation
Indices: 5412837--5412864 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5412827 ATTCTCTCAC
5412837 TTATATATATAT
1 TTATATATATAT
5412849 TTATATATATAT
1 TTATATATATAT
5412861 TTAT
1 TTAT
5412865 GTTATCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATATATAT
Found at i:5417167 original size:14 final size:15
Alignment explanation
Indices: 5417148--5417185 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
5417138 TGTTTAACTG
5417148 AAAATGATTTTC-GA
1 AAAATGATTTTCTGA
5417162 AAAATGA-TTTCTGA
1 AAAATGATTTTCTGA
5417176 AAAATGATTT
1 AAAATGATTT
5417186 ACTTTCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 16 0.73
15 2 0.09
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (15 bp):
AAAATGATTTTCTGA
Found at i:5427239 original size:31 final size:32
Alignment explanation
Indices: 5427204--5427264 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
5427194 AACCGTACAC
*
5427204 AAATACAATTAATACAAGA-AAAACCATACGA
1 AAATACAATTAATACAAAATAAAACCATACGA
*
5427235 AAATACAATTAGTACAAAATAAAACCATAC
1 AAATACAATTAATACAAAATAAAACCATAC
5427265 AAACAATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (32 bp):
AAATACAATTAATACAAAATAAAACCATACGA
Found at i:5432370 original size:17 final size:17
Alignment explanation
Indices: 5432350--5432410 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 17
5432340 TATTATTTTG
5432350 AAATTAAAAAATATATA
1 AAATTAAAAAATATATA
5432367 AAATTTCAAAAAATTAAATATA
1 AAA-TT-AAAAAA-T--ATATA
*
5432389 TAAATTAATAAAAAATATA
1 -AAATTAA-AAAATATATA
5432408 AAA
1 AAA
5432411 AAATTACATT
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
17 3 0.08
18 5 0.14
19 11 0.31
20 1 0.03
21 2 0.06
22 11 0.31
23 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATTAAAAAATATATA
Found at i:5432401 original size:24 final size:25
Alignment explanation
Indices: 5432358--5432409 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 25
5432348 TGAAATTAAA
5432358 AAATATATAAAATTTCAAAAAAT-T
1 AAATATATAAAATTTCAAAAAATAT
5432382 AAATATAT-AAATTAAT-AAAAAATAT
1 AAATATATAAAATT--TCAAAAAATAT
5432407 AAA
1 AAA
5432410 AAAATTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.20
24 15 0.60
25 5 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATATATAAAATTTCAAAAAATAT
Done.