Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 5 of 438
Found at i:1373980 original size:21 final size:20
Alignment explanation
Indices: 1373947--1373990 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1373937 TATTTTGAAA
* *
1373947 TTTATTTTACGTTTTAATCAT
1 TTTAGTTTACGTTATAAT-AT
*
1373968 TTTAGTTTGCGTTATAATAT
1 TTTAGTTTACGTTATAATAT
1373988 TTT
1 TTT
1373991 TAATTCACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.61
Consensus pattern (20 bp):
TTTAGTTTACGTTATAATAT
Found at i:1382713 original size:16 final size:16
Alignment explanation
Indices: 1382689--1382719 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1382679 GACCTATTAA
*
1382689 CCCCTCCCCCCCAAAC
1 CCCCCCCCCCCCAAAC
1382705 CCCCCCCCCCCCAAA
1 CCCCCCCCCCCCAAA
1382720 AAAAACCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.77, G:0.00, T:0.03
Consensus pattern (16 bp):
CCCCCCCCCCCCAAAC
Found at i:1384479 original size:2 final size:2
Alignment explanation
Indices: 1384472--1384498 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1384462 AACAAGTGTA
1384472 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 A
1384499 AATCCTGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1394697 original size:13 final size:14
Alignment explanation
Indices: 1394674--1394716 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1394664 AATATTTAAA
1394674 AATATTAAAATATT
1 AATATTAAAATATT
1394688 AATA-TAAAATATT
1 AATATTAAAATATT
* *
1394701 ATATTTTTAAATATT
1 A-ATATTAAAATATT
1394716 A
1 A
1394717 TTAAACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 6 0.24
15 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTAAAATATT
Found at i:1394775 original size:29 final size:28
Alignment explanation
Indices: 1394733--1394804 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
1394723 ATAAATATTT
1394733 AATTATTT-AT-ATTTAGTCA-TATAATA
1 AATTATTTAATAATTTA-TCATTATAATA
* *
1394759 AATTATATTAATAATTTATTATTTTAATA
1 AATTAT-TTAATAATTTATCATTATAATA
*
1394788 AATTATTTAATATTTTA
1 AATTATTTAATAATTTA
1394805 ATTTTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 6 0.15
27 2 0.05
28 14 0.36
29 17 0.44
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
AATTATTTAATAATTTATCATTATAATA
Found at i:1394779 original size:16 final size:16
Alignment explanation
Indices: 1394760--1394794 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1394750 CATATAATAA
*
1394760 ATTATATTAATAATTT
1 ATTATATTAATAAATT
*
1394776 ATTATTTTAATAAATT
1 ATTATATTAATAAATT
1394792 ATT
1 ATT
1394795 TAATATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATATTAATAAATT
Found at i:1394934 original size:15 final size:15
Alignment explanation
Indices: 1394883--1394935 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1394873 ATTCAATATT
*
1394883 AATATCTTAATAATA
1 AATATATTAATAATA
*
1394898 AATATTCATTACAATTATA
1 AATA-T-ATT--AATAATA
1394917 AATATATTAATAATA
1 AATATATTAATAATA
1394932 AATA
1 AATA
1394936 CTTTGTAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.45
16 1 0.03
17 5 0.16
18 1 0.03
19 10 0.32
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:1396703 original size:14 final size:14
Alignment explanation
Indices: 1396686--1396713 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1396676 AAATATTAAA
1396686 AATATTTTTATATT
1 AATATTTTTATATT
1396700 AATATTTTTATATT
1 AATATTTTTATATT
1396714 TTATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:1400320 original size:2 final size:2
Alignment explanation
Indices: 1400313--1400357 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1400303 TCGAAATCTT
1400313 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
1400355 TA T
1 TA T
1400358 TAAAAAACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1405515 original size:263 final size:263
Alignment explanation
Indices: 1405041--1405538 Score: 718
Period size: 263 Copynumber: 1.9 Consensus size: 263
1405031 ATCGAAAATA
* * *
1405041 TTTTTGGGTAAACTATATTTACGGTTACTAAATTATTAATAAGTTTACGTTTTAGTCACTCAATT
1 TTTTTGGGTAAACTACATTTAAGGTTACTAAATTATTAATAAGTTTACGTTTTAGTCACTCAACT
* * * *
1405106 TTAGAAAGTAACAAAATGGTTACTGAACTATTCGAAAGTTTTCATTTAAGTCATTGATTGTTAAT
66 TCAGAAAGTAACAAAATAGTTACTGAACTATTCGAAAATTTTCATTTAAGTCATTGATCGTTAAT
* * * * * * *
1405171 TTTTTTTTAATTGTCTAGCTTGCAGCTCCAAGCTATAAATTGTAGATTGGTATGGTGGATTAATA
131 GTTTTTTTAATTGTCTAGCTAGCAGCTCCAAGATACAAATTGTAGATTGGTACGATAGATTAATA
* *
1405236 CCTATTGACAAGTAGAAAAATATACCTTAGGGCTTAGATCAATACCCATTGACGAGTAGAAAATA
196 CCTATTGACAAGTAGAAAAACATACCTTAGAGCTTAGATCAATACCCATTGACGAGTAGAAAATA
1405301 GTT
261 GTT
*
1405304 TTTTTGGGTAAACTACATTTAAGGTTACTAAATTATTAGTAAGTTTACGTTTTAGTCACTCAACT
1 TTTTTGGGTAAACTACATTTAAGGTTACTAAATTATTAATAAGTTTACGTTTTAGTCACTCAACT
* *
1405369 TCA-AAAGGTTACAAAATAGTTGCTGAACTATTCGAAAATTTTCATTTAAGTCATTGAATCGTTA
66 TCAGAAA-GTAACAAAATAGTTACTGAACTATTCGAAAATTTTCATTTAAGTCATTG-ATCGTTA
* *
1405433 A-GTTTTTTTAATTGTTTAGCTAGCAGTTCCAA-ATGACAAATTG-ATGATTGGTACGATAGATT
129 ATGTTTTTTTAATTGTCTAGCTAGCAGCTCCAAGAT-ACAAATTGTA-GATTGGTACGATAGATT
*
1405495 AATATCC-ATTGACGAGTAGAAAAACATACCTTAGAGCTTAGATC
192 AATA-CCTATTGACAAGTAGAAAAACATACCTTAGAGCTTAGATC
1405539 CAAGTCGAAG
Statistics
Matches: 208, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
262 5 0.02
263 194 0.93
264 9 0.04
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (263 bp):
TTTTTGGGTAAACTACATTTAAGGTTACTAAATTATTAATAAGTTTACGTTTTAGTCACTCAACT
TCAGAAAGTAACAAAATAGTTACTGAACTATTCGAAAATTTTCATTTAAGTCATTGATCGTTAAT
GTTTTTTTAATTGTCTAGCTAGCAGCTCCAAGATACAAATTGTAGATTGGTACGATAGATTAATA
CCTATTGACAAGTAGAAAAACATACCTTAGAGCTTAGATCAATACCCATTGACGAGTAGAAAATA
GTT
Found at i:1415703 original size:48 final size:48
Alignment explanation
Indices: 1415630--1415757 Score: 166
Period size: 48 Copynumber: 2.7 Consensus size: 48
1415620 ATCACCTCCT
* * * * *
1415630 CCGCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTATCCACCA
* *
1415678 CCGCCTTATGTGTATAAATCTCCACCACCACCTTCACCTTATCCTCCA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTATCCACCA
* * *
1415726 CCTCCGTATGTGTACAAGTCTCCACCACCACC
1 CCGCCTTATGTGTATAAGTCTCCACCACCACC
1415758 ACCTAAACAT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.22, C:0.43, G:0.09, T:0.26
Consensus pattern (48 bp):
CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTATCCACCA
Found at i:1415790 original size:48 final size:42
Alignment explanation
Indices: 1415738--1415848 Score: 150
Period size: 42 Copynumber: 2.5 Consensus size: 42
1415728 TCCGTATGTG
1415738 TACAAGTCTCCACCACCACCACCTAAACATGAGGAGAAGCCTTATGAA
1 TACAAGTCTCCACCACCACCACC---A-A--AGGAGAAGCCTTATGAA
*
1415786 TACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAG
1 TACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAA
*
1415828 TACAAGTCTCCACCCCCACCA
1 TACAAGTCTCCACCACCACCA
1415849 TCACCTTCTC
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
42 36 0.59
44 1 0.02
45 1 0.02
48 23 0.38
ACGTcount: A:0.35, C:0.36, G:0.14, T:0.15
Consensus pattern (42 bp):
TACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAA
Found at i:1415815 original size:42 final size:45
Alignment explanation
Indices: 1415738--1416072 Score: 193
Period size: 48 Copynumber: 7.4 Consensus size: 45
1415728 TCCGTATGTG
1415738 TACAAGTCTCCACCACCACCACCTAAACATGAGGAGAAGCCTTATGAA
1 TACAAGTCTCCACCACCACCACC--AACA-GAGGAGAAGCCTTATGAA
*
1415786 TACAAGTCTCCACCACCACCACC-A-A-AGGAGAAGCCTTATGAG
1 TACAAGTCTCCACCACCACCACCAACAGAGGAGAAGCCTTATGAA
* * * ******* ** *
1415828 TACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAG
1 TACAAGTCTCCACCACCACCACCAAC--AGAGGAGA-AGCCTTATGAA
* * * * ***** * ** * **
1415876 TACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTACGTG
1 TACAAGTCTCCACCACCACCACCAAC-AGAGGA-GA-AGCCTTATGAA
* *
1415924 TACAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAAGCCGTATGAA
1 TACAAGTCTCCACCACCACCACC-AA-CA-GAGGAGAAGCCTTATGAA
* *
1415972 TACAAGTCTCCACCACCACCACC--GA-AGGAGAAGCCTTATGAG
1 TACAAGTCTCCACCACCACCACCAACAGAGGAGAAGCCTTATGAA
*
1416014 TACAAGTCTCCACCACCACCACC--GA-AGGAGAAGCCTTATGAA
1 TACAAGTCTCCACCACCACCACCAACAGAGGAGAAGCCTTATGAA
1416056 TACAAGTCTCCACCACC
1 TACAAGTCTCCACCACC
1416073 TCCATCGCCT
Statistics
Matches: 235, Mismatches: 42, Indels: 26
0.78 0.14 0.09
Matches are distributed among these distances:
42 110 0.47
44 2 0.01
45 1 0.00
47 3 0.01
48 115 0.49
49 2 0.01
50 2 0.01
ACGTcount: A:0.31, C:0.38, G:0.13, T:0.18
Consensus pattern (45 bp):
TACAAGTCTCCACCACCACCACCAACAGAGGAGAAGCCTTATGAA
Found at i:1415893 original size:27 final size:26
Alignment explanation
Indices: 1415855--1415943 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
1415845 ACCATCACCT
*
1415855 TCTCCTCCACCTCCTTATGAGTACAAA
1 TCTCCACCACCTCCTTATG-GTACAAA
* **
1415882 TCTCCACCACCTCC--AT--CAC-CT
1 TCTCCACCACCTCCTTATGGTACAAA
* *
1415903 TCTCCACCACCTCCTTACGTGTACAAG
1 TCTCCACCACCTCCTTATG-GTACAAA
1415930 TCTCCACCACCTCC
1 TCTCCACCACCTCC
1415944 ACCAAAGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
21 14 0.29
22 2 0.04
23 1 0.02
25 2 0.04
26 2 0.04
27 27 0.56
ACGTcount: A:0.21, C:0.47, G:0.06, T:0.26
Consensus pattern (26 bp):
TCTCCACCACCTCCTTATGGTACAAA
Found at i:1415957 original size:186 final size:186
Alignment explanation
Indices: 1415632--1416034 Score: 619
Period size: 186 Copynumber: 2.2 Consensus size: 186
1415622 CACCTCCTCC
* * * * * * *
1415632 GCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCACCGCCTTATGTGTATAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCACCATCACCTTCTCCACCACCGCCTTATGAGTACAAAT
* * *
1415697 CTCCACCACCACCTTCACCTTATCCTCCACCTCCGTATGTGTACAAGTCTCCACCACCACCACCT
66 CTCCACCACCACCATCACCTTATCCACCACCTCCGTACGTGTACAAGTCTCCACCACCACCACCT
*
1415762 AAACATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
131 AAACATGAGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
* * *
1415818 GCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCACCATCACCTTCTCCACCACCGCCTTATGAGTACAAAT
* * * *
1415883 CTCCACCACCTCCATCACCTTCTCCACCACCTCCTTACGTGTACAAGTCTCCACCACCTCCACC-
66 CTCCACCACCACCATCACCTTATCCACCACCTCCGTACGTGTACAAGTCTCCACCACCACCACCT
*
1415947 AAAGCATGAGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCGAAGGAGAA
131 AAA-CATGAGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
1416004 GCCTTATGAGTACAAGTCTCCACCACCACCA
1 GCCTTATGAGTACAAGTCTCCACCACCACCA
1416035 CCGAAGGAGA
Statistics
Matches: 196, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
185 3 0.02
186 193 0.98
ACGTcount: A:0.28, C:0.39, G:0.12, T:0.21
Consensus pattern (186 bp):
GCCTTATGAGTACAAGTCTCCACCACCACCATCACCTTCTCCACCACCGCCTTATGAGTACAAAT
CTCCACCACCACCATCACCTTATCCACCACCTCCGTACGTGTACAAGTCTCCACCACCACCACCT
AAACATGAGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
Found at i:1415976 original size:48 final size:42
Alignment explanation
Indices: 1415955--1416072 Score: 218
Period size: 42 Copynumber: 2.8 Consensus size: 42
1415945 CCAAAGCATG
*
1415955 AGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
*
1415997 AGGAGAAGCCTTATGAGTACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1416039 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
1416073 TCCATCGCCT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.35, C:0.32, G:0.19, T:0.14
Consensus pattern (42 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
Found at i:1416050 original size:228 final size:228
Alignment explanation
Indices: 1415769--1416183 Score: 697
Period size: 228 Copynumber: 1.8 Consensus size: 228
1415759 CCTAAACATG
*
1415769 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAGTACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
*
1415834 TCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
66 TCTCCACCACCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
* * * * * *
1415899 ACCTTCTCCACCACCTCCTTACGT-GTACAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAAG
131 ACCATCACCACCACCTCCATAC-TACTACAAGTCGCCACCACCACCACCAAAGCATGAGGAGAAG
1415963 CCGTATGAATACAAGTCTCCACCACCACCACCGA
195 CCGTATGAATACAAGTCTCCACCACCACCACCGA
* *
1415997 AGGAGAAGCCTTATGAGTACAAGTCTCCACCACCACCACCGAAGGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
* * *
1416062 TCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTATGAGTATAAATCTCCACCACCTCCATC
66 TCTCCACCACCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
1416127 ACCATCACCACCACCTCCATACTACTACAAGTCGCCACCACCACCACCAAAGCATGA
131 ACCATCACCACCACCTCCATACTACTACAAGTCGCCACCACCACCACCAAAGCATGA
1416184 AGAACAACCA
Statistics
Matches: 173, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
227 1 0.01
228 172 0.99
ACGTcount: A:0.30, C:0.39, G:0.12, T:0.19
Consensus pattern (228 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
TCTCCACCACCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
ACCATCACCACCACCTCCATACTACTACAAGTCGCCACCACCACCACCAAAGCATGAGGAGAAGC
CGTATGAATACAAGTCTCCACCACCACCACCGA
Found at i:1416415 original size:27 final size:26
Alignment explanation
Indices: 1416378--1416462 Score: 81
Period size: 27 Copynumber: 3.4 Consensus size: 26
1416368 CCATCACCCT
1416378 CACCACCACCTTACTACTATAAATCTC
1 CACCACCACCTTACTACTA-AAATCTC
*
1416405 CACCACCACCTT-C-AC---CATCTC
1 CACCACCACCTTACTACTAAAATCTC
* * *
1416426 CACCACCTCCTTACTACTACAAGTCCC
1 CACCACCACCTTACTACTA-AAATCTC
1416453 CACCACCACC
1 CACCACCACC
1416463 ACCAAAGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
21 16 0.35
22 1 0.02
23 2 0.04
25 2 0.04
26 1 0.02
27 24 0.52
ACGTcount: A:0.28, C:0.51, G:0.01, T:0.20
Consensus pattern (26 bp):
CACCACCACCTTACTACTAAAATCTC
Found at i:1416554 original size:24 final size:24
Alignment explanation
Indices: 1416527--1416606 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
1416517 ACCCTCACCA
*
1416527 CCACCACCTTACTATTACAAGTCT
1 CCACCACCTTACTATTACAAATCT
* **
1416551 CCACCACC--ACCT-TCACCATCTCCT
1 CCACCACCTTA-CTATTA-CAAAT-CT
*
1416575 CCACCACCTTACTACTACAAATCT
1 CCACCACCTTACTATTACAAATCT
1416599 CCACCACC
1 CCACCACC
1416607 ACCCCCACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
22 3 0.07
23 5 0.12
24 28 0.65
25 5 0.12
26 2 0.05
ACGTcount: A:0.28, C:0.49, G:0.01, T:0.23
Consensus pattern (24 bp):
CCACCACCTTACTATTACAAATCT
Found at i:1416554 original size:27 final size:27
Alignment explanation
Indices: 1416524--1416657 Score: 105
Period size: 27 Copynumber: 5.4 Consensus size: 27
1416514 ATCACCCTCA
* *
1416524 CCACCACCACCTTACTATTACAAGTCT
1 CCACCACCACCTTACTACTACAAATCT
1416551 CCACCACCACCTT-C-AC--C--ATCT
1 CCACCACCACCTTACTACTACAAATCT
*
1416572 CCTCCACCACCTTACTACTACAAATCT
1 CCACCACCACCTTACTACTACAAATCT
** * *
1416599 CCACCACCACCCCCAC-ATTAC--GTCT
1 CCACCACCA-CCTTACTACTACAAATCT
1416624 -CACCACCA---TACTACTACAAATCT
1 CCACCACCACCTTACTACTACAAATCT
1416647 CCACCACCACC
1 CCACCACCACC
1416658 AGTGAAATCT
Statistics
Matches: 83, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.02
21 19 0.23
22 1 0.01
23 6 0.07
24 16 0.19
25 5 0.06
26 1 0.01
27 29 0.35
28 4 0.05
ACGTcount: A:0.29, C:0.49, G:0.01, T:0.20
Consensus pattern (27 bp):
CCACCACCACCTTACTACTACAAATCT
Found at i:1416607 original size:48 final size:48
Alignment explanation
Indices: 1416056--1416658 Score: 381
Period size: 48 Copynumber: 12.4 Consensus size: 48
1416046 GCCTTATGAA
* * * * * *
1416056 TACAAGTCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTA-TGAG
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACT-AC
* * * * * *
1416104 TATAAATCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * **** * *
1416152 TACAAGTCGCCACCACCACCACCAAAGCATGAAGAACAACCACCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CTCCACCACCACCTTACTAC
* * * * * * * *
1416203 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * * * * * *
1416251 TACAAGTCCCCACCACCTCCGTCTCCATCACCACCTCCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * **** * * *
1416299 TACAAATCTCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CTCCACCACCACCTTACTAC
*
1416350 TACAAGTCTCCACCACCTCCATCACC--CT-CACCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * *
1416395 TATAAATCTCCACCACCACCTTCACCATCTCCACCACCTCCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * **** * * *
1416443 TACAAGTCCCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CTCCACCACCACCTTACTAC
* * * *
1416494 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTAT
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* *
1416542 TACAAGTCTCCACCACCACCTTCACCATCTCCTCCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* ** ** *
1416590 TACAAATCTCCACCACCACCCCCA-CAT-TACGTCTCACCACCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCT-CCAC-CACCACCTTACTAC
*
1416638 TACAAATCTCCACCACCACCA
1 TACAAGTCTCCACCACCACCA
1416659 GTGAAATCTC
Statistics
Matches: 437, Mismatches: 103, Indels: 30
0.77 0.18 0.05
Matches are distributed among these distances:
45 35 0.08
46 1 0.00
47 8 0.02
48 273 0.62
49 9 0.02
50 11 0.03
51 100 0.23
ACGTcount: A:0.30, C:0.47, G:0.04, T:0.19
Consensus pattern (48 bp):
TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
Found at i:1416640 original size:147 final size:147
Alignment explanation
Indices: 1416056--1416609 Score: 747
Period size: 147 Copynumber: 3.8 Consensus size: 147
1416046 GCCTTATGAA
* * * * * * *
1416056 TACAAGTCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTA-TGAGTATAAATCTCCACCAC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACT-ACTACAAATCTCCACCAC
* * * *
1416120 CTCCATCACCATCACCACCACCTCCATACTACTACAAGTCGCCACCACCACCACCAAAGCATGAA
65 CACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAA
*
1416185 GAACAACCACCATACTAC
130 GAACAACCCCCATACTAC
* * * * * * * * *
1416203 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCTTACTACTACAAGTCCCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
* * * *
1416268 TCCGTCTCCATCACCACCTCCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAAG
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAAG
1416333 AACAACCCCCATACTAC
131 AACAACCCCCATACTAC
*
1416350 TACAAGTCTCCACCACCTCCATCACCCT---CACCACCACCTTACTACTATAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
* * * *
1416412 ACCTTCACCATCTCCACCACCTCCTTACTACTACAAGTCCCCACCACCACCACCAAAGCATGAAG
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAAG
1416477 AACAACCCCCATACTAC
131 AACAACCCCCATACTAC
* *
1416494 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTATTACAAGTCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
* * * *
1416559 ACCTTCACCATCTCCTCCACCACCTTACTACTACAAATCTCCACCACCACC
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACC
1416610 CCCACATTAC
Statistics
Matches: 360, Mismatches: 43, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
144 131 0.36
147 228 0.63
148 1 0.00
ACGTcount: A:0.30, C:0.47, G:0.04, T:0.19
Consensus pattern (147 bp):
TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
ACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAAG
AACAACCCCCATACTAC
Found at i:1416651 original size:24 final size:24
Alignment explanation
Indices: 1416573--1416655 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
1416563 TCACCATCTC
*
1416573 CTCCACCACCTTACTACTACAAAT
1 CTCCACCACCATACTACTACAAAT
** * *
1416597 CTCCACCACC--ACCCCCAC-ATT
1 CTCCACCACCATACTACTACAAAT
1416618 ACGTCTCACCACCATACTACTACAAAT
1 -C-TC-CACCACCATACTACTACAAAT
1416645 CTCCACCACCA
1 CTCCACCACCA
1416656 CCAGTGAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
21 2 0.04
22 6 0.13
23 2 0.04
24 25 0.56
25 2 0.04
26 6 0.13
27 2 0.04
ACGTcount: A:0.31, C:0.48, G:0.01, T:0.19
Consensus pattern (24 bp):
CTCCACCACCATACTACTACAAAT
Found at i:1416723 original size:6 final size:6
Alignment explanation
Indices: 1416712--1416755 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
1416702 CTCCTTACTA
* * *
1416712 CCCCAC CCCCAC CCTCAC CCCCAG CCCCAC CCCCAC CCACAC CC
1 CCCCAC CCCCAC CCCCAC CCCCAC CCCCAC CCCCAC CCCCAC CC
1416756 GCTCATAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.77, G:0.02, T:0.02
Consensus pattern (6 bp):
CCCCAC
Found at i:1417867 original size:36 final size:36
Alignment explanation
Indices: 1417820--1417899 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
1417810 GTACTATTAT
* * *
1417820 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCGGCACCAACTTATGTTTAC
*
1417856 AAGTCACCACCTCCACCGTCACCAACTTATGTTTAC
1 AAGTCACCACCTCCACCGGCACCAACTTATGTTTAC
1417892 AAGTCACC
1 AAGTCACC
1417900 TCCACCTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.25, C:0.40, G:0.10, T:0.25
Consensus pattern (36 bp):
AAGTCACCACCTCCACCGGCACCAACTTATGTTTAC
Found at i:1418007 original size:114 final size:113
Alignment explanation
Indices: 1417856--1418127 Score: 456
Period size: 114 Copynumber: 2.4 Consensus size: 113
1417846 TTATGTTTAC
* *
1417856 AAGTCACCACCTCCACCG-TCACCAACTTATGTTTACAAGTCACCTCCACCTCCTGCGTACTACT
1 AAGTCTCCACCTCCACCGCTC-CC-ACTTATGTTTACAAGTCACCTCCACCTCCTACGTACTACT
* *
1417920 ACAAGTCTCCACCACCACCAAAGCATGTGGAACAGCCTCCATACTACTAT
64 ACAAGTCTCCACCACCACCAAAGCATGTGGAACAACCACCATACTACTAT
*
1417970 AAGTCTCCACCTCCACCAGCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTATGTACTACTA
1 AAGTCTCCACCTCCACC-GCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTACGTACTACTA
1418035 CAAGTCTCCACCACCACCAAAGCATGTGGAACAACCACCATACTACTAT
65 CAAGTCTCCACCACCACCAAAGCATGTGGAACAACCACCATACTACTAT
1418084 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACC
1 AAGTCTCCACCTCCACC-GCTCCCACTTATGTTTACAAGTCACC
1418128 GCCTCCACCA
Statistics
Matches: 150, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
114 145 0.97
115 3 0.02
116 2 0.01
ACGTcount: A:0.28, C:0.39, G:0.10, T:0.23
Consensus pattern (113 bp):
AAGTCTCCACCTCCACCGCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTACGTACTACTAC
AAGTCTCCACCACCACCAAAGCATGTGGAACAACCACCATACTACTAT
Found at i:1418133 original size:36 final size:36
Alignment explanation
Indices: 1418084--1418172 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 36
1418074 ATACTACTAT
* * *
1418084 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* * *
1418120 AAGTCACCGCCTCCACCATCGCCGACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1418156 AAGTCACCTCCACCACC
1 AAGTCACCACCTCCACC
1418173 TGTGTACTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.22, C:0.43, G:0.11, T:0.24
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
Found at i:1418307 original size:48 final size:48
Alignment explanation
Indices: 1418255--1419749 Score: 908
Period size: 48 Copynumber: 31.2 Consensus size: 48
1418245 GCAGCCCCCG
* * *
1418255 TACTACTACAAGTCTCCTCCACCACCATCACCATCTCCTCCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* *
1418303 TACTATTACAAGTCCCCACCACCACCAGTTCA-C-TCTCCACCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA--TCACCATCTCCACCTCCACCA
* * **** ** *
1418351 TACTACTACAAGTCCCCACCACCACCA-AAACATGAGGAACAACCTCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCAT-CTCCACCTCCACCA
* * * * * * *
1418399 TACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * ** * ** *** *
1418447 TACTACTACAAATCCCCACCACCACCA-AAATATGTAGAAGAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCT-CCACCTCCACCA
* * * *
1418495 TACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * *
1418543 TACTACTACAAGTCCCCACCACCACCATCTCCATCACCACCCCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * * *
1418591 TACTATTACAAATCACCC-CCACCACCATCGCCATCTCCTCATCCACCA
1 TACTACTACAAGTC-CCCACCACCACCATCACCATCTCCACCTCCACCA
* * ** *** *
1418639 TACTACTACAAGTCCCCACCACCACCGA--AACATGTAGAGGAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACC-ATCACCATCTCCA-CCTCCACCA
*
1418687 TACTACTACAAGTCTCCC-CCACCACCATCGA-CATCTCCTCCTCCACCA
1 TACTACTACAAGTC-CCCACCACCACCATC-ACCATCTCCACCTCCACCA
* * * * * *
1418735 TACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCACCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * ** *** *
1418783 TACTACTACAAGTCCCCACCACCACCGA--AACATGTAGAGGAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACC-ATCACCATCTCCA-CCTCCACCA
* * * * * *
1418831 TAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCACCACCA
1 TACTA-CTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * *
1418879 TACTATTACAAGTCCCCACCACCACCAGTTCA--TTCTCCATCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA--TCACCATCTCCACCTCCACCA
* * *
1418927 TACTACTACAAGTCTCCACCACCACCAGT--CCACTCCCCACCCCCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
* * * * *
1418975 TACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * * ** ***
1419023 TACTATTACAAGTCTCCACCACCACCA-AAACA-CGTAGAGGAGCC-CCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATC-TCCA-CCTCCACCA
* * * * * *
1419070 TAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCACCACCA
1 TACTA-CTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * *
1419118 TACTATTACAAGTCCCCACCACCACCAGT--TCAT-TCCCACCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCATCT-CCACCTCCACCA
* * * * *
1419165 TACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * ** *** *
1419213 TACTATTACAAGTCCCCACCACCACCA-AAACA-CGTAGAGAAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATC-TCCA-CCTCCACCA
* * * *
1419261 TACATA-TACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCA
1 TAC-TACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * *
1419309 TATTATTACAAGTCCCCACCACCACCAGT--CCACTTTCCACCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
* * * * * *
1419357 TACTATTACAAGTCCCCTCCTCCACCATCGCCATCTCCTCCTCTACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * *
1419405 TACTATTACAAATCCCCACCACCACCAGT--CCACTCTCCACCCCCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
*
1419453 TACTACTACAAATCCCCACCACCACCAGT--CCACTCTCCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
* * *
1419501 TACTACTACAAATCCCCACCACCACCATC-TCATTCACCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCA-TCTCCACCTCCACCA
* * * * * * * *
1419549 TACTATTACAAATCACCC-CCACCTCCAGTGA-AAGCTCCAGCACCTACC-
1 TACTACTACAAGTC-CCCACCACCACCA-TCACCATCTCCACCTCC-ACCA
* * * * * * *
1419597 TACCATTACAACTCCCCTCCTCCACCATCACCATCTCCTCCTCCCCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * *
1419645 TACTACTACAAATCTCCC-CCACCACCAGT--CCACTCTCCCCCACCACCA
1 TACTACTACAAGTC-CCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
* * * * * * * *
1419693 TACTACTACAAATCTCCACCTCCTCCATCTCCCTCACCACCTCCTCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
1419741 TACTACTAC
1 TACTACTAC
1419750 CACTCACCTC
Statistics
Matches: 1119, Mismatches: 259, Indels: 138
0.74 0.17 0.09
Matches are distributed among these distances:
45 1 0.00
46 6 0.01
47 116 0.10
48 934 0.83
49 55 0.05
50 7 0.01
ACGTcount: A:0.29, C:0.48, G:0.04, T:0.19
Consensus pattern (48 bp):
TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
Found at i:1418377 original size:144 final size:144
Alignment explanation
Indices: 1418212--1419527 Score: 1014
Period size: 144 Copynumber: 9.2 Consensus size: 144
1418202 CCACTTATGT
* * *
1418212 CTACAAGTCTCCACCACCACCAAAGCATGTAGAGCAGCCCCCGTACTACTACAAGTCTCCTCCAC
1 CTACAAGTCCCCACCACCACCAAAGCATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCAC
1418277 CACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
66 CACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
1418342 CCACCACCATACTA
131 CCACCACCATACTA
* * * * * * *
1418356 CTACAAGTCCCCACCACCACCAAAACATG-AGGAACAACCTCCATACTACTACAAATCTCCTCCT
1 CTACAAGTCCCCACCACCACCAAAGCATGTA-GAGCAGCCCCCATACTACTACAAGTCTCCACCA
* * * * ** * *
1418420 CCACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAAAAT-A-TGTA
65 CCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACC-AGTTCACTCTC
* ** *
1418483 GAAGAGCCCCCATACTA
129 CACCA-CCACCATACTA
* * * * * * *** ** * *
1418500 CTACAAATCTCCTCCACCACCATCACCATCT-CCTCCTCCACCATACTACTACAAGTCCCCACCA
1 CTACAAGTCCCCACCACCACCA-AAGCATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCA
* * * * * *
1418564 CCACCATCTCCATCACCACCCCCACCATACTATTACAAATCACCC-CCACCACCA--TCGCCATC
65 CCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTC-CCCACCACCACCAGTTC-AC-TC
*
1418626 TCC-TCATCCACCATACTA
127 TCCACCA-CCACCATACTA
* *
1418644 CTACAAGTCCCCACCACCACCGAAA-CATGTAGAGGAGCCCCCATACTACTACAAGTCTCCCCCA
1 CTACAAGTCCCCACCACCACC-AAAGCATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCA
* * *
1418708 CCACCATCGA-CATCTCCTCCTCCACCATACTATTACAAATCTCCTCCACCACCA--TCACCATC
65 CCACCATC-ACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCA-C-TC
*
1418770 TCCTCCACCACCATACTA
127 TCCACCACCACCATACTA
* * *
1418788 CTACAAGTCCCCACCACCACCGAAA-CATGTAGAGGAGCCCCCATAC-ATCTACAAATCTCCTCC
1 CTACAAGTCCCCACCACCACC-AAAGCATGTAGAGCAGCCCCCATACTA-CTACAAGTCTCCACC
* * *
1418851 ACCACCATCGCCATCTCCTCCACCACCATACTATTACAAGTCCCCACCACCACCAGTTCATTCTC
64 ACCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTC
*
1418916 CATCACCACCATACTA
129 CACCACCACCATACTA
* *** * *** *
1418932 CTACAAGTCTCCACCACCACCAGTCCA-CT-CCCCACCCCCACCATACTACTACAAGTCTCCACC
1 CTACAAGTCCCCACCACCACCAAAGCATGTAGAGCA-GCCC-CCATACTACTACAAGTCTCCACC
* * * * * * *** * *
1418995 ACCACCTTCTCCCTCACCACCTCCACCATACTATTACAAGTCTCCACCACCACCAAAACAC-GTA
64 ACCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTC
* **
1419059 GAGGAGCC-CCATAC-A
129 CACCA-CCACCATACTA
* * * ** * **** * * *
1419074 TCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCA-CCACCATACTATTACAAGTCCCCACC
1 -CTACAAGTCCCCACCACCACCAAAG-CATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACC
* * * * * * *
1419138 ACCACCAGT--TCAT-TCCCACCACCACCATACTACTACAAGTCTCCACCACCACC-TTCTCCCT
64 ACCACCA-TCACCATCT-CCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGT-TCACT
* *
1419199 CACCACCTCCACCATACTA
126 CTCCACCACCACCATACTA
* * * * * *
1419218 TTACAAGTCCCCACCACCACCAAAACACGTAGAGAAGCCCCCATACATA-TACAAATCTCCTCCA
1 CTACAAGTCCCCACCACCACCAAAGCATGTAGAGCAGCCCCCATAC-TACTACAAGTCTCCACCA
* * *
1419282 CCACCATCACCATCTCCTCCTCCACCATATTATTACAAGTCCCCACCACCACCAGTCCACTTTCC
65 CCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCC
1419347 ACCACCACCATACTA
130 ACCACCACCATACTA
* * * ** * *** ** ** * * *
1419362 TTACAAGTCCCCTCCTCCACCATCGCCATCT-CCTCCTCTACCATACTATTACAAATCCCCACCA
1 CTACAAGTCCCCACCACCACCAAAG-CATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCA
* * * * *
1419426 CCACCAGT--CCACTCTCCACCCCCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
65 CCACCA-TCACCA-TCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCT
*
1419489 CCACCTCCACCATACTA
128 CCACCACCACCATACTA
*
1419506 CTACAAATCCCCACCACCACCA
1 CTACAAGTCCCCACCACCACCA
1419528 TCTCATTCAC
Statistics
Matches: 936, Mismatches: 191, Indels: 90
0.77 0.16 0.07
Matches are distributed among these distances:
141 1 0.00
142 49 0.05
143 130 0.14
144 726 0.78
145 23 0.02
146 7 0.01
ACGTcount: A:0.30, C:0.47, G:0.05, T:0.19
Consensus pattern (144 bp):
CTACAAGTCCCCACCACCACCAAAGCATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCAC
CACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
CCACCACCATACTA
Found at i:1418905 original size:27 final size:27
Alignment explanation
Indices: 1418864--1419049 Score: 113
Period size: 27 Copynumber: 7.6 Consensus size: 27
1418854 ACCATCGCCA
* *
1418864 TCTCCTCCACCACCATACTATTACAAG
1 TCTCCACCACCACCATACTACTACAAG
* * *
1418891 TCCCCACCACCACC--AGT--T-C-AT
1 TCTCCACCACCACCATACTACTACAAG
*
1418912 TCTCCATCACCACCATACTACTACAAG
1 TCTCCACCACCACCATACTACTACAAG
1418939 TCTCCACCACCACCAGT-C--C-AC---
1 TCTCCACCACCACCA-TACTACTACAAG
* *
1418960 TCCCCACCCCCACCATACTACTACAAG
1 TCTCCACCACCACCATACTACTACAAG
**
1418987 TCTCCACCACCACC-T--T-CT-C-CC
1 TCTCCACCACCACCATACTACTACAAG
* * *
1419008 TCACCACCTCCACCATACTATTACAAG
1 TCTCCACCACCACCATACTACTACAAG
1419035 TCTCCACCACCACCA
1 TCTCCACCACCACCA
1419050 AAACACGTAG
Statistics
Matches: 117, Mismatches: 22, Indels: 40
0.65 0.12 0.22
Matches are distributed among these distances:
20 1 0.01
21 39 0.33
22 3 0.03
23 6 0.05
24 6 0.05
25 5 0.04
26 3 0.03
27 53 0.45
28 1 0.01
ACGTcount: A:0.27, C:0.49, G:0.03, T:0.20
Consensus pattern (27 bp):
TCTCCACCACCACCATACTACTACAAG
Found at i:1419144 original size:27 final size:27
Alignment explanation
Indices: 1419109--1419239 Score: 90
Period size: 27 Copynumber: 5.3 Consensus size: 27
1419099 GCCATCTCCT
1419109 CCACCACCATACTATTACAAGTCCCCA
1 CCACCACCATACTATTACAAGTCCCCA
* *
1419136 CCACCACC--A--GTT-C-A-TTCCCA
1 CCACCACCATACTATTACAAGTCCCCA
* *
1419156 CCACCACCATACTACTACAAGTCTCCA
1 CCACCACCATACTATTACAAGTCCCCA
* ** *
1419183 CCACCACC-T--T-CT-C-CCTCACCA
1 CCACCACCATACTATTACAAGTCCCCA
*
1419204 CCTCCACCATACTATTACAAGTCCCCA
1 CCACCACCATACTATTACAAGTCCCCA
1419231 CCACCACCA
1 CCACCACCA
1419240 AAACACGTAG
Statistics
Matches: 76, Mismatches: 15, Indels: 26
0.65 0.13 0.22
Matches are distributed among these distances:
20 13 0.17
21 13 0.17
22 4 0.05
23 4 0.05
24 3 0.04
25 3 0.04
26 3 0.04
27 33 0.43
ACGTcount: A:0.29, C:0.50, G:0.03, T:0.18
Consensus pattern (27 bp):
CCACCACCATACTATTACAAGTCCCCA
Found at i:1419444 original size:21 final size:21
Alignment explanation
Indices: 1419420--1419500 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 21
1419410 TTACAAATCC
1419420 CCACCACCACCAGTCCACTCT
1 CCACCACCACCAGTCCACTCT
* *
1419441 CCACCCCCACCA-TACTACTACAAATCC
1 CCACCACCACCAGT-C--C-AC---TCT
1419468 CCACCACCACCAGTCCACTCT
1 CCACCACCACCAGTCCACTCT
*
1419489 CCACCTCCACCA
1 CCACCACCACCA
1419501 TACTACTACA
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
20 1 0.02
21 25 0.53
23 1 0.02
24 4 0.09
25 1 0.02
27 14 0.30
28 1 0.02
ACGTcount: A:0.27, C:0.57, G:0.02, T:0.14
Consensus pattern (21 bp):
CCACCACCACCAGTCCACTCT
Found at i:1419471 original size:27 final size:27
Alignment explanation
Indices: 1419401--1419528 Score: 95
Period size: 27 Copynumber: 5.2 Consensus size: 27
1419391 CTCCTCCTCT
*
1419401 ACCATACTATTACAAATCCCCACCACC
1 ACCATACTACTACAAATCCCCACCACC
* *
1419428 ACCAGT-C--C-AC---TCTCCACCCCC
1 ACCA-TACTACTACAAATCCCCACCACC
1419449 ACCATACTACTACAAATCCCCACCACC
1 ACCATACTACTACAAATCCCCACCACC
* *
1419476 ACCAGT-C--C-AC---TCTCCACCTCC
1 ACCA-TACTACTACAAATCCCCACCACC
1419497 ACCATACTACTACAAATCCCCACCACC
1 ACCATACTACTACAAATCCCCACCACC
1419524 ACCAT
1 ACCAT
1419529 CTCATTCACC
Statistics
Matches: 76, Mismatches: 9, Indels: 32
0.65 0.08 0.27
Matches are distributed among these distances:
20 2 0.03
21 28 0.37
23 2 0.03
24 8 0.11
25 1 0.01
27 33 0.43
28 2 0.03
ACGTcount: A:0.31, C:0.51, G:0.02, T:0.16
Consensus pattern (27 bp):
ACCATACTACTACAAATCCCCACCACC
Found at i:1419564 original size:27 final size:26
Alignment explanation
Indices: 1419489--1419565 Score: 74
Period size: 27 Copynumber: 3.1 Consensus size: 26
1419479 AGTCCACTCT
*
1419489 CCACCTCCACCATACTACTACAAATCC
1 CCACCTCCACCATACTA-TACAAATCA
* *
1419516 CCACCACCACCAT-C--T-C-ATTCA
1 CCACCTCCACCATACTATACAAATCA
1419537 CCACCTCCACCATACTATTACAAATCA
1 CCACCTCCACCATACTA-TACAAATCA
1419564 CC
1 CC
1419566 CCCACCTCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 15 0.38
22 2 0.05
23 1 0.03
25 1 0.03
26 2 0.05
27 18 0.46
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.19
Consensus pattern (26 bp):
CCACCTCCACCATACTATACAAATCA
Found at i:1444769 original size:9 final size:9
Alignment explanation
Indices: 1444757--1444876 Score: 50
Period size: 9 Copynumber: 13.0 Consensus size: 9
1444747 ACAATAATTT
1444757 TTATAAAAA
1 TTATAAAAA
*
1444766 TTAT-TAAA
1 TTATAAAAA
*
1444774 TTTTAATAAA
1 TTATAA-AAA
*
1444784 -AATAAAAA
1 TTATAAAAA
*
1444792 -TATAAAAT
1 TTATAAAAA
1444800 TTATTAAAAA
1 TTA-TAAAAA
* *
1444810 TTACAAACATTT
1 TTATAAA-A--A
1444822 TTATAAAAA
1 TTATAAAAA
*
1444831 TCATAAAAA
1 TTATAAAAA
*
1444840 -AATAAAATA
1 TTATAAAA-A
* *
1444849 TTGTAAAATT
1 TTATAAAA-A
1444859 TTATAAAAA
1 TTATAAAAA
*
1444868 TCATAAAAA
1 TTATAAAAA
1444877 AAATCAACGA
Statistics
Matches: 82, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
8 21 0.26
9 29 0.35
10 25 0.30
11 1 0.01
12 6 0.07
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:1444802 original size:24 final size:26
Alignment explanation
Indices: 1444759--1444810 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1444749 AATAATTTTT
*
1444759 ATAAAAATTATTAAATTTTAATAAAA
1 ATAAAAATTATTAAAATTTAATAAAA
*
1444785 ATAAAAA-TA-TAAAATTTATTAAAA
1 ATAAAAATTATTAAAATTTAATAAAA
1444809 AT
1 AT
1444811 TACAAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 15 0.62
25 2 0.08
26 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAAAAATTATTAAAATTTAATAAAA
Found at i:1445099 original size:19 final size:20
Alignment explanation
Indices: 1445077--1445122 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
1445067 TTCTTACGAC
*
1445077 TTTATAAAATTTTAT-GATT
1 TTTATAAAATTTTATAAATT
1445096 TTTATAAAATTTTATAAATT
1 TTTATAAAATTTTATAAATT
1445116 TTTATAA
1 TTTATAA
1445123 TTTTTTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTATAAAATTTTATAAATT
Found at i:1445109 original size:29 final size:28
Alignment explanation
Indices: 1445077--1445175 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
1445067 TTCTTACGAC
1445077 TTTATAAAATTTTATGATTTTTATAAAAT
1 TTTATAAAATTTTAT-ATTTTTATAAAAT
* * **
1445106 TTTATAAATTTTTATAATTTTTTTCTAAT
1 TTTATAAAATTTTAT-ATTTTTATAAAAT
* *
1445135 TTT-TAATATTTTAATTTTTTTATTAAAAT
1 TTTATAAAATTTT-ATATTTTTA-TAAAAT
* *
1445164 TTAATAATATTT
1 TTTATAAAATTT
1445176 ATAGCTTTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
28 12 0.22
29 35 0.64
30 8 0.15
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTATAAAATTTTATATTTTTATAAAAT
Found at i:1445118 original size:20 final size:19
Alignment explanation
Indices: 1445077--1445178 Score: 75
Period size: 20 Copynumber: 5.3 Consensus size: 19
1445067 TTCTTACGAC
*
1445077 TTTATAAAATTTTATGATT
1 TTTATAAAATTTTATAATT
1445096 TTTATAAAATTTTATAAATT
1 TTTATAAAATTTTAT-AATT
** *
1445116 TTTATAATTTTTTTCTAA-T
1 TTTATAA-AATTTTATAATT
* *
1445135 TTT-TAATATTTTA-ATTTT
1 TTTATAAAATTTTATA-ATT
* *
1445153 TTTATTAAAATTTAATAATA
1 TTTA-TAAAATTTTATAATT
1445173 TTTATA
1 TTTATA
1445179 GCTTTTATTG
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
16 1 0.02
17 5 0.08
18 7 0.11
19 21 0.32
20 25 0.38
21 6 0.09
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTATAAAATTTTATAATT
Found at i:1445128 original size:10 final size:10
Alignment explanation
Indices: 1445077--1445127 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
1445067 TTCTTACGAC
*
1445077 TTTATAAAAT
1 TTTATAAATT
*
1445087 TTTAT-GATT
1 TTTATAAATT
*
1445096 TTTATAAAAT
1 TTTATAAATT
1445106 TTTATAAATT
1 TTTATAAATT
1445116 TTTAT-AATT
1 TTTATAAATT
1445125 TTT
1 TTT
1445128 TTCTAATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 14 0.40
10 21 0.60
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
TTTATAAATT
Found at i:1449911 original size:14 final size:13
Alignment explanation
Indices: 1449877--1449901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1449867 AAATCGATCT
1449877 ATTTTTTAAAATA
1 ATTTTTTAAAATA
1449890 ATTTTTTAAAAT
1 ATTTTTTAAAAT
1449902 GGTCTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTTTAAAATA
Found at i:1453563 original size:32 final size:34
Alignment explanation
Indices: 1453527--1453597 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 34
1453517 AAGAAAATAC
*
1453527 GTTTTTTAGAAAGTATGTTTT-A-TTGAAAACAT
1 GTTTTTTAGAAAGTACGTTTTCAGTTGAAAACAT
* * *
1453559 G--TTTTATAAGGTGCGTTTTCAGTTGAAAACAT
1 GTTTTTTAGAAAGTACGTTTTCAGTTGAAAACAT
1453591 GTTTTTT
1 GTTTTTT
1453598 CTCTCTCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
30 14 0.45
31 1 0.03
32 12 0.39
34 4 0.13
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (34 bp):
GTTTTTTAGAAAGTACGTTTTCAGTTGAAAACAT
Found at i:1459133 original size:20 final size:20
Alignment explanation
Indices: 1459100--1459161 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
1459090 GAAAAAAATC
1459100 AAATTCAA-ATTAAAATACTA
1 AAATTCAAGA-TAAAATACTA
*
1459120 AAATTCAAGATAAAAT-CTTG
1 AAATTCAAGATAAAATAC-TA
*
1459140 AAATTCAGGATAAGAATACTA
1 AAATTCAAGATAA-AATACTA
1459161 A
1 A
1459162 TGTGGCATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 1 0.03
20 27 0.77
21 6 0.17
22 1 0.03
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (20 bp):
AAATTCAAGATAAAATACTA
Found at i:1462360 original size:13 final size:13
Alignment explanation
Indices: 1462342--1462380 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1462332 AGAAGCATAA
1462342 GCTATTTTTGTTG
1 GCTATTTTTGTTG
1462355 GCTATTTTTGTTG
1 GCTATTTTTGTTG
* *
1462368 GTTAGTTTTGTTG
1 GCTATTTTTGTTG
1462381 CTGCAAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.08, C:0.05, G:0.26, T:0.62
Consensus pattern (13 bp):
GCTATTTTTGTTG
Found at i:1467964 original size:27 final size:27
Alignment explanation
Indices: 1467926--1467981 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1467916 CACCATCTTC
1467926 CATTATTTATTTATTTTTATAATAACA
1 CATTATTTATTTATTTTTATAATAACA
1467953 CATTATTTATTTATTTTTATAATAACA
1 CATTATTTATTTATTTTTATAATAACA
1467980 CA
1 CA
1467982 CTAGCTGACT
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:0.38, C:0.09, G:0.00, T:0.54
Consensus pattern (27 bp):
CATTATTTATTTATTTTTATAATAACA
Found at i:1468965 original size:19 final size:17
Alignment explanation
Indices: 1468941--1468995 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 17
1468931 TTTTTTTTCC
1468941 AATTTAAGTTTTCAATTT
1 AATTT-AGTTTTCAATTT
*
1468959 AAATTTAGTTGTTTAATTT
1 -AATTTAGTT-TTCAATTT
*
1468978 AATTTCAGTTTTCTATTT
1 AATTT-AGTTTTCAATTT
1468996 CATAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.58
Consensus pattern (17 bp):
AATTTAGTTTTCAATTT
Found at i:1469652 original size:16 final size:17
Alignment explanation
Indices: 1469633--1469664 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1469623 AAGTTATATA
1469633 TATTT-GAAAATTTTAT
1 TATTTAGAAAATTTTAT
1469649 TATTTAGAAAATTTTA
1 TATTTAGAAAATTTTA
1469665 ATTTTAATTT
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:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTTAGAAAATTTTAT
Found at i:1475109 original size:23 final size:23
Alignment explanation
Indices: 1475083--1475126 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1475073 AAACCATTTT
1475083 ATCCAAATAGAAGGTAAATTTGG
1 ATCCAAATAGAAGGTAAATTTGG
1475106 ATCCAAATAGAAGGTAAATTT
1 ATCCAAATAGAAGGTAAATTT
1475127 AGATAGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (23 bp):
ATCCAAATAGAAGGTAAATTTGG
Found at i:1478286 original size:22 final size:24
Alignment explanation
Indices: 1478259--1478308 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
1478249 AAGAATTAAA
*
1478259 TAATATTAACT-TTTAAAAGA-GT
1 TAATATTAACTATTTAAAAAATGT
*
1478281 TAATATTTACTATTTAAAAAATGT
1 TAATATTAACTATTTAAAAAATGT
1478305 TAAT
1 TAAT
1478309 TATTGTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.42
23 8 0.33
24 6 0.25
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (24 bp):
TAATATTAACTATTTAAAAAATGT
Found at i:1478889 original size:20 final size:20
Alignment explanation
Indices: 1478864--1478908 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1478854 ATTCTCCAAT
1478864 TACAATAAATTCTAGATTCA
1 TACAATAAATTCTAGATTCA
1478884 TACAATAAATTCTAGATTCA
1 TACAATAAATTCTAGATTCA
1478904 -ACAAT
1 TACAAT
1478909 CAAACATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (20 bp):
TACAATAAATTCTAGATTCA
Found at i:1483094 original size:36 final size:36
Alignment explanation
Indices: 1483019--1483102 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
1483009 AGTATGCATT
** * *
1483019 TCTTACATTGCATATTACCAATGAATGTGTTGCATC
1 TCTTACATTTTATATTACCAATGAATGTGTTGAACC
*
1483055 TCTTACATTTTATATTACCAATGGATG-GCTTGAACC
1 TCTTACATTTTATATTACCAATGAATGTG-TTGAACC
1483091 TCTT-CTATTTTA
1 TCTTAC-ATTTTA
1483103 CATTTTCAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.05
36 39 0.95
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (36 bp):
TCTTACATTTTATATTACCAATGAATGTGTTGAACC
Found at i:1483567 original size:27 final size:27
Alignment explanation
Indices: 1483537--1483588 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
1483527 AAATATAAAT
1483537 TTTGAAATTTTT-ATAAA-TATTTTGAAA
1 TTTG-AATTTTTGA-AAATTATTTTGAAA
1483564 TTTGAATTTTTGAAAATTATTTTGA
1 TTTGAATTTTTGAAAATTATTTTGA
1483589 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (27 bp):
TTTGAATTTTTGAAAATTATTTTGAAA
Found at i:1485342 original size:25 final size:23
Alignment explanation
Indices: 1485309--1485367 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
1485299 TGCTAGTTAT
*
1485309 TAATATCATAATTTAAATGATTAAA
1 TAATATCATAATCTAAA--ATTAAA
*
1485334 TAATATCAT-ATCTCAAATTAAA
1 TAATATCATAATCTAAAATTAAA
1485356 TATATATCATAA
1 TA-ATATCATAA
1485368 AAATGAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 8 0.27
23 7 0.23
24 6 0.20
25 9 0.30
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATATCATAATCTAAAATTAAA
Found at i:1496157 original size:2 final size:2
Alignment explanation
Indices: 1496150--1496187 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1496140 AAGTACAATA
1496150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1496188 GAATTCAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1501717 original size:21 final size:21
Alignment explanation
Indices: 1501691--1501731 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1501681 ATCTGCTCAA
* *
1501691 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1501712 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1501732 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1505494 original size:25 final size:26
Alignment explanation
Indices: 1505439--1505526 Score: 92
Period size: 25 Copynumber: 3.4 Consensus size: 26
1505429 CTTTATAAAA
*
1505439 TTTTAT-ATTTTTTTATATTTCTATATA
1 TTTTATAATTTTTTTATATTT-TAT-TT
1505466 TTTTATAATTTTTTTAT-TTTTATTT
1 TTTTATAATTTTTTTATATTTTATTT
* * *
1505491 TTTTCTAA-TTTTTAATATTTAATTT
1 TTTTATAATTTTTTTATATTTTATTT
*
1505516 TTTTAAAATTT
1 TTTTATAATTT
1505527 AATAATATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
24 7 0.13
25 21 0.40
26 5 0.10
27 9 0.17
28 10 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTATAATTTTTTTATATTTTATTT
Found at i:1505518 original size:16 final size:16
Alignment explanation
Indices: 1505499--1505529 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1505489 TTTTTTCTAA
*
1505499 TTTTTAATATTTAATT
1 TTTTTAAAATTTAATT
1505515 TTTTTAAAATTTAAT
1 TTTTTAAAATTTAAT
1505530 AATATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAAAATTTAATT
Found at i:1507896 original size:32 final size:34
Alignment explanation
Indices: 1507860--1507930 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 34
1507850 AAGAAAATAC
*
1507860 GTTTTTTAGAAAGTATGTTTT-A-TTGAAAACAT
1 GTTTTTTAGAAAGTACGTTTTCAGTTGAAAACAT
* * *
1507892 G--TTTTATAAGGTGCGTTTTCAGTTGAAAACAT
1 GTTTTTTAGAAAGTACGTTTTCAGTTGAAAACAT
1507924 GTTTTTT
1 GTTTTTT
1507931 CTCTCTCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
30 14 0.45
31 1 0.03
32 12 0.39
34 4 0.13
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (34 bp):
GTTTTTTAGAAAGTACGTTTTCAGTTGAAAACAT
Found at i:1515590 original size:22 final size:20
Alignment explanation
Indices: 1515535--1515591 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
1515525 AACAATAGTA
1515535 ATAAAGATAAAAAT-ATATAC
1 ATAAA-ATAAAAATAATATAC
** *
1515555 ATAAAATAGTAATAATATAT
1 ATAAAATAAAAATAATATAC
1515575 ATAACTAATAAAAATAA
1 ATAA--AATAAAAATAA
1515592 AAATAAGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 6 0.21
20 14 0.48
22 9 0.31
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (20 bp):
ATAAAATAAAAATAATATAC
Found at i:1523041 original size:14 final size:14
Alignment explanation
Indices: 1523022--1523063 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1523012 AAAAATATAA
1523022 TAATAATATAATAG
1 TAATAATATAATAG
* *
1523036 TAATAATACAATGG
1 TAATAATATAATAG
1523050 TAATAATACTAATA
1 TAATAATA-TAATA
1523064 AAAGTTAGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (14 bp):
TAATAATATAATAG
Found at i:1523435 original size:3 final size:3
Alignment explanation
Indices: 1523427--1523522 Score: 53
Period size: 3 Copynumber: 34.0 Consensus size: 3
1523417 GTTAGTAACG
* * *
1523427 ATA ATA ATA ATA TATA AAA ATA A-A A-A ATA ATA AT- ATG GTA A-A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
1523469 ATA TTA AT- ATA TTA ATA AGA ATA ATA GTA ATA A-A ATA A-G ATT ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1523514 ATA ATA ATA
1 ATA ATA ATA
1523523 TTAACAAGAA
Statistics
Matches: 70, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
2 13 0.19
3 54 0.77
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1523520 original size:19 final size:20
Alignment explanation
Indices: 1523429--1523522 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
1523419 TAGTAACGAT
1523429 AATAATAATATATAAAAATAA-
1 AATAATAATA-AT-AAAATAAG
***
1523450 AA-AATAATAATATGGTAA-
1 AATAATAATAATAAAATAAG
* *
1523468 AATATTAAT-ATATTAATAAG
1 AATAATAATAATA-AAATAAG
*
1523488 AATAATAGTAATAAAATAAG
1 AATAATAATAATAAAATAAG
1523508 ATTATAATAATAATA
1 A--ATAATAATAATA
1523523 TTAACAAGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
18 9 0.16
19 11 0.19
20 21 0.37
21 5 0.09
22 11 0.19
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
AATAATAATAATAAAATAAG
Found at i:1548367 original size:27 final size:27
Alignment explanation
Indices: 1548350--1548408 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
1548340 AATGCGGTAG
1548350 AACTGTTGTAACTGAATATTGCAGTAA
1 AACTGTTGTAACTGAATATTGCAGTAA
1548377 AACTGTTGTAACTGAATATTGCAGTAA
1 AACTGTTGTAACTGAATATTGCAGTAA
1548404 AACTG
1 AACTG
1548409 CCAAATCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (27 bp):
AACTGTTGTAACTGAATATTGCAGTAA
Found at i:1553654 original size:14 final size:13
Alignment explanation
Indices: 1553627--1553651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1553617 TTTTTTTTAT
1553627 TTATTTTTGGTTC
1 TTATTTTTGGTTC
1553640 TTATTTTTGGTT
1 TTATTTTTGGTT
1553652 TCTGTTTAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.04, G:0.16, T:0.72
Consensus pattern (13 bp):
TTATTTTTGGTTC
Found at i:1558753 original size:12 final size:12
Alignment explanation
Indices: 1558736--1558765 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1558726 ACAAAATCCG
1558736 AATTTAATTTCC
1 AATTTAATTTCC
*
1558748 AATTTAATTTCT
1 AATTTAATTTCC
1558760 AATTTA
1 AATTTA
1558766 TTTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:1563218 original size:13 final size:13
Alignment explanation
Indices: 1563200--1563225 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1563190 ATGAAGTGTT
1563200 GAAGATCAAGCTG
1 GAAGATCAAGCTG
1563213 GAAGATCAAGCTG
1 GAAGATCAAGCTG
1563226 CTGGAATATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (13 bp):
GAAGATCAAGCTG
Found at i:1582354 original size:3 final size:3
Alignment explanation
Indices: 1582341--1582388 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
1582331 TACACAGTTA
*
1582341 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1582388 A
1 A
1582389 GTGGAGGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1585158 original size:7 final size:7
Alignment explanation
Indices: 1585146--1585170 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1585136 ACGGCTTGTA
1585146 TGCATGC
1 TGCATGC
1585153 TGCATGC
1 TGCATGC
1585160 TGCATGC
1 TGCATGC
1585167 TGCA
1 TGCA
1585171 GCAACATGTT
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:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (7 bp):
TGCATGC
Found at i:1604319 original size:3 final size:3
Alignment explanation
Indices: 1604311--1604339 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1604301 ATGATAGTAA
1604311 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1604340 ATGAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1609967 original size:24 final size:24
Alignment explanation
Indices: 1609935--1609980 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1609925 ATTGATGATG
*
1609935 TATTGATATTATATTCATCATAAT
1 TATTCATATTATATTCATCATAAT
1609959 TATTCATATTATATTCATCATA
1 TATTCATATTATATTCATCATA
1609981 TAGATTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTCATATTATATTCATCATAAT
Found at i:1610316 original size:18 final size:18
Alignment explanation
Indices: 1610290--1610324 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1610280 GAGTGTGATC
1610290 GGAAGATATGTTGTCCTT
1 GGAAGATATGTTGTCCTT
* *
1610308 GGAATATATGTTTTCCT
1 GGAAGATATGTTGTCCT
1610325 ATCAACGGGT
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:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (18 bp):
GGAAGATATGTTGTCCTT
Found at i:1612118 original size:18 final size:20
Alignment explanation
Indices: 1612095--1612132 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1612085 CGGTTTGTGT
1612095 GAAGCT-TCG-CTTTTTGAA
1 GAAGCTATCGACTTTTTGAA
*
1612113 GAAGCTATGGACTTTTTGAA
1 GAAGCTATCGACTTTTTGAA
1612133 TAGAATGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAGCTATCGACTTTTTGAA
Found at i:1619137 original size:14 final size:14
Alignment explanation
Indices: 1619118--1619149 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1619108 CCCACATCTC
1619118 ATATACATATATAT
1 ATATACATATATAT
1619132 ATATACATATATAT
1 ATATACATATATAT
1619146 ATAT
1 ATAT
1619150 TCGAATCAAT
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:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATACATATATAT
Found at i:1620206 original size:21 final size:20
Alignment explanation
Indices: 1620182--1620276 Score: 68
Period size: 22 Copynumber: 4.5 Consensus size: 20
1620172 AGAATTTGAG
1620182 TTAAATTTAAATAAATATTTT
1 TTAAATTTAAATAAA-ATTTT
* *
1620203 TTAATTTTAAATTTAAAATATT
1 TTAAATTTAAA--TAAAATTTT
*
1620225 TAAAATTTAAAATAAAATATTT
1 TTAAATTT-AAATAAAAT-TTT
* *
1620247 TTAATATTTTAAT--TATTTT
1 TTAA-ATTTAAATAAAATTTT
1620266 TTAAATATTAA
1 TTAAAT-TTAA
1620277 TTTTTGGGGA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
18 2 0.03
19 10 0.17
20 2 0.03
21 16 0.27
22 18 0.31
23 11 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAATTTAAATAAAATTTT
Found at i:1620219 original size:23 final size:23
Alignment explanation
Indices: 1620182--1620258 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 23
1620172 AGAATTTGAG
1620182 TTAAA-TTT-AAA-TAAATATTT
1 TTAAATTTTAAAATTAAATATTT
* * *
1620202 TTTAATTTTAAATTTAAA-ATAT
1 TTAAATTTTAAAATTAAATATTT
* *
1620224 TTAAAATTTAAAATAAAATATTT
1 TTAAATTTTAAAATTAAATATTT
1620247 TTAATATTTTAA
1 TTAA-ATTTTAA
1620259 TTATTTTTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 4 0.09
21 3 0.07
22 19 0.44
23 11 0.26
24 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAATTTTAAAATTAAATATTT
Found at i:1620230 original size:16 final size:16
Alignment explanation
Indices: 1620206--1620238 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1620196 ATATTTTTTA
*
1620206 ATTTTAAATTTAAAAT
1 ATTTAAAATTTAAAAT
1620222 ATTTAAAATTTAAAAT
1 ATTTAAAATTTAAAAT
1620238 A
1 A
1620239 AAATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAAAATTTAAAAT
Found at i:1621788 original size:3 final size:3
Alignment explanation
Indices: 1621780--1621811 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1621770 AATTTTTACT
1621780 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1621812 TTTTGTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1622336 original size:21 final size:21
Alignment explanation
Indices: 1622290--1622336 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1622280 TCGGAATTGG
1622290 GGTTTAATTTTTTTGGGTTGT
1 GGTTTAATTTTTTTGGGTTGT
* * *
1622311 TGTTTGATTTTTGTTTGGTT-T
1 GGTTTAATTTTT-TTGGGTTGT
1622332 GGTTT
1 GGTTT
1622337 TTGATCTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.06, C:0.00, G:0.28, T:0.66
Consensus pattern (21 bp):
GGTTTAATTTTTTTGGGTTGT
Found at i:1622339 original size:23 final size:22
Alignment explanation
Indices: 1622297--1622341 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1622287 TGGGGTTTAA
1622297 TTTTTTTGGGTTGTTGTTTGAT
1 TTTTTTTGGGTTGTTGTTTGAT
*
1622319 TTTTGTTTGGTTTGGTT-TTTGAT
1 TTTT-TTTGGGTT-GTTGTTTGAT
1622342 CTTTAATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.04, C:0.00, G:0.27, T:0.69
Consensus pattern (22 bp):
TTTTTTTGGGTTGTTGTTTGAT
Found at i:1631076 original size:13 final size:13
Alignment explanation
Indices: 1631059--1631095 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1631049 GAAATTTTTA
*
1631059 ACTTTTCAAAAGT
1 ACTTTTGAAAAGT
*
1631072 GCTTTTGAAAAGT
1 ACTTTTGAAAAGT
1631085 ACTTTTGAAAA
1 ACTTTTGAAAA
1631096 TGAGAAGCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (13 bp):
ACTTTTGAAAAGT
Found at i:1631835 original size:138 final size:138
Alignment explanation
Indices: 1631676--1632097 Score: 589
Period size: 138 Copynumber: 3.1 Consensus size: 138
1631666 GAGAACATAT
*
1631676 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATTGAATTTATT
*
1631741 AATATAAACAACTATATTAATTAATTTCGGTCAAAATATAAAAGATATGAAAATTAATATTATTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGATATGAAAATTAATATTATTT
*
1631806 TGGAAATA
131 TGGAAAAA
* **
1631814 ATATAATTAATATATAAATTTGACCCATACAAAATATTAATTGTATATATTTTATTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATTGAATTTATT
* * ** ** *
1631879 AATATAAATC-GTTATATTAATTAATATCACTCAAAGCATAAAAGATATGAAAAATAATATTCA-
66 AATATAAA-CAATTATATTAATTAATTTCGGTCAAAATATAAAAGATATGAAAATTAATATT-AT
**
1631942 TTACGAAAAA
129 TTTGGAAAAA
* *
1631952 ATATAATTAATATATGAATTTGATTCATGCAAAATGTTAATTGTATATATTTTATTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATTGAATTTATT
* * * * * *
1632017 AATATAAATAATTATATTAATTAATTTCGGTCAAAATATAAAATACATAAAAATTAATGTTCTTT
66 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGATATGAAAATTAATATTATTT
1632082 T-GAAAAGA
131 TGGAAAA-A
1632090 ATATAATT
1 ATATAATT
1632098 CTTCTTTTTT
Statistics
Matches: 245, Mismatches: 34, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
137 5 0.02
138 238 0.97
139 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATTGAATTTATT
AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGATATGAAAATTAATATTATTT
TGGAAAAA
Found at i:1640251 original size:6 final size:6
Alignment explanation
Indices: 1640235--1640269 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1640225 TTTTGATGTA
*
1640235 TATATC GATATC TATATC TATATC TATATC TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT
1640270 AATATATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (6 bp):
TATATC
Found at i:1645947 original size:43 final size:43
Alignment explanation
Indices: 1645894--1646033 Score: 176
Period size: 43 Copynumber: 3.3 Consensus size: 43
1645884 TTTTTTAAAA
* *
1645894 AAACGTCGCTAAAGACCAGGACCTTTAGCGGCGTTTTTCTCGC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGTTTTTCTCGC
* *
1645937 AAAGGCCGCTAAAGACCATGACCTTGAGCGGCGCTTTTTC-CGC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCG-TTTTTCTCGC
* * * *
1645980 AAACGCCGCTAAAGACCATGACTTTTAGTGGCACTTTTT-TCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGC-GTTTTTCTCGC
1646023 AAACGCCGCTA
1 AAACGCCGCTA
1646034 TAGAATAGAC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
43 78 0.93
44 6 0.07
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGTTTTTCTCGC
Found at i:1651558 original size:41 final size:39
Alignment explanation
Indices: 1651485--1651562 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
1651475 CCACTTTTTT
**
1651485 TATTGCATTTTTTTGTGGCGATTTTATAAAAAAACGCCGC
1 TATTGCATTTTTTTGCAGCGATTTTAT-AAAAAACGCCGC
*
1651525 TATTGCATATTTTTTGCAGCGTTTTTCAT-AAAAACGCC
1 TATTGCAT-TTTTTTGCAGCGATTTT-ATAAAAAACGCC
1651563 ACTAATCTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.52
41 14 0.42
42 2 0.06
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (39 bp):
TATTGCATTTTTTTGCAGCGATTTTATAAAAAACGCCGC
Found at i:1651937 original size:22 final size:22
Alignment explanation
Indices: 1651912--1651976 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
1651902 CACTAATTAA
1651912 TCTAAACCCTTAATCCCTAAAC
1 TCTAAACCCTTAATCCCTAAAC
* * *
1651934 TCTAAACTCTAAAAT-CCTAAAA
1 TCTAAACCCT-TAATCCCTAAAC
* *
1651956 TATAAACCATTAA-CCCTAAAC
1 TCTAAACCCTTAATCCCTAAAC
1651977 CCATAACCCA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 8 0.24
22 22 0.67
23 3 0.09
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (22 bp):
TCTAAACCCTTAATCCCTAAAC
Found at i:1651982 original size:22 final size:21
Alignment explanation
Indices: 1651957--1652031 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
1651947 ATCCTAAAAT
1651957 ATAAACCATTAA-CCCTAAACCC
1 ATAAACCA-TAACCCCT-AACCC
*
1651979 ATAACCCATAACCCCTAACCC
1 ATAAACCATAACCCCTAACCC
* **
1652000 TTAAACTTTAAACCCC-AACCC
1 ATAAACCAT-AACCCCTAACCC
*
1652021 TTAAACCATAA
1 ATAAACCATAA
1652032 TACATAAACC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 2 0.05
21 25 0.57
22 17 0.39
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (21 bp):
ATAAACCATAACCCCTAACCC
Found at i:1652109 original size:14 final size:14
Alignment explanation
Indices: 1652065--1652103 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1652055 TCATAAACCT
*
1652065 TAAACCCTTAATCA
1 TAAACCCTAAATCA
*
1652079 TATACCCTAAATCA
1 TAAACCCTAAATCA
1652093 TAAACCCTAAA
1 TAAACCCTAAA
1652104 CTATAATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:1652682 original size:40 final size:41
Alignment explanation
Indices: 1652586--1652704 Score: 186
Period size: 41 Copynumber: 2.9 Consensus size: 41
1652576 GGGTTTAGAC
1652586 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* **
1652627 TTTTAACGGCGTTTTACCAAAAGCGTGGCTAATGCTCTGG-
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
1652667 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT
1652705 TTGTTTTACA
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 33 0.47
41 37 0.53
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.33
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:1652751 original size:12 final size:12
Alignment explanation
Indices: 1652736--1652761 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1652726 GTTTTTTGAT
1652736 AAAACGCCGCTA
1 AAAACGCCGCTA
1652748 AAAACGCCGCTA
1 AAAACGCCGCTA
1652760 AA
1 AA
1652762 GCCCTGTTTT
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:1654906 original size:30 final size:31
Alignment explanation
Indices: 1654866--1654928 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
1654856 GCATTAAGTT
1654866 TTGAGGGATCTAATTAAAATTTTTAA-AAAAA
1 TTGAGGGATCTAATTAAAA-TTTTAAGAAAAA
1654897 TTGA-GGATCTAATTAAAATTTTAAGAAAAA
1 TTGAGGGATCTAATTAAAATTTTAAGAAAAA
1654927 TT
1 TT
1654929 AGTGAGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 6 0.19
30 21 0.68
31 4 0.13
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.37
Consensus pattern (31 bp):
TTGAGGGATCTAATTAAAATTTTAAGAAAAA
Found at i:1659583 original size:30 final size:31
Alignment explanation
Indices: 1659518--1659575 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1659508 AACAATCCAA
*
1659518 TGACTTAAATGAAAACTTCTGAATAGTTCAG
1 TGACTTAAATGAAAACTTCTAAATAGTTCAG
1659549 TGACTT-AATGAAAACTT-TAAAATAGTT
1 TGACTTAAATGAAAACTTCT-AAATAGTT
1659576 TGGTGACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
30 18 0.72
31 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTCTAAATAGTTCAG
Found at i:1673007 original size:22 final size:22
Alignment explanation
Indices: 1672956--1673016 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
1672946 ATAAGTAAAT
* *
1672956 ACAAAAATAA-AGGAAAATATA
1 ACAAAAATAATAGAAAAATACA
* *
1672977 ATAACAATAATAGAAAAATACA
1 ACAAAAATAATAGAAAAATACA
* *
1672999 ACAATAATAATAGTAAAA
1 ACAAAAATAATAGAAAAA
1673017 GATATAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (22 bp):
ACAAAAATAATAGAAAAATACA
Found at i:1673116 original size:3 final size:3
Alignment explanation
Indices: 1673108--1673174 Score: 89
Period size: 3 Copynumber: 21.7 Consensus size: 3
1673098 AAAGTAGTGC
1673108 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* * *
1673154 CAA TGA TAAA TTA TAA TAA TA
1 TAA TAA T-AA TAA TAA TAA TA
1673175 GTGATGAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 51 0.91
4 5 0.09
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1673337 original size:16 final size:15
Alignment explanation
Indices: 1673308--1673350 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
1673298 TATACGTATG
*
1673308 AAAAATAATGATAGT
1 AAAAATAATAATAGT
1673323 AAAATATAATAATAGT
1 AAAA-ATAATAATAGT
*
1673339 AATAATAATAAT
1 AAAAATAATAAT
1673351 GGAATGAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAAATAATAATAGT
Found at i:1673455 original size:3 final size:3
Alignment explanation
Indices: 1673447--1673482 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1673437 ACTACCATAT
1673447 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1673483 TAGAAATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1673568 original size:14 final size:14
Alignment explanation
Indices: 1673518--1673569 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1673508 TAAATTTAAA
*
1673518 AAAAATACTATATAT
1 AAAAATA-TATACAT
*
1673533 AAAAGTATATACAT
1 AAAAATATATACAT
* * *
1673547 ACATATATGTACAT
1 AAAAATATATACAT
1673561 AAAAATATA
1 AAAAATATA
1673570 CACTAATATA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
14 22 0.79
15 6 0.21
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.31
Consensus pattern (14 bp):
AAAAATATATACAT
Found at i:1673591 original size:3 final size:3
Alignment explanation
Indices: 1673573--1673640 Score: 120
Period size: 3 Copynumber: 22.7 Consensus size: 3
1673563 AAATATACAC
1673573 TAA TATA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1673618 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
1673641 TTAAAATGCA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1674137 original size:28 final size:29
Alignment explanation
Indices: 1674097--1674172 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 29
1674087 GATTTTTTGT
* *
1674097 TCTTAAATCTCAAAAAAAGAAAAATC-CC
1 TCTTGAATCTCAAAAAAAAAAAAATCTCC
*
1674125 TCTTGAATCTCAAAAAAAAAAAAATCTCT
1 TCTTGAATCTCAAAAAAAAAAAAATCTCC
*
1674154 TCTTGAATTTCAAAAAAAA
1 TCTTGAATCTCAAAAAAAA
1674173 TCTCCTCTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 24 0.56
29 19 0.44
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.26
Consensus pattern (29 bp):
TCTTGAATCTCAAAAAAAAAAAAATCTCC
Found at i:1679252 original size:19 final size:18
Alignment explanation
Indices: 1679228--1679264 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
1679218 TTATGTTTCA
1679228 TATTATTATATTATTTATT
1 TATTATTATA-TATTTATT
1679247 TATTATTATATATTTATT
1 TATTATTATATATTTATT
1679265 ATGTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTATTATATATTTATT
Found at i:1679276 original size:17 final size:14
Alignment explanation
Indices: 1679236--1679266 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1679226 CATATTATTA
*
1679236 TATTATTTATTTAT
1 TATTATATATTTAT
1679250 TATTATATATTTAT
1 TATTATATATTTAT
1679264 TAT
1 TAT
1679267 GTAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATATATTTAT
Found at i:1679686 original size:26 final size:26
Alignment explanation
Indices: 1679657--1679706 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1679647 AGCCCTCCCC
1679657 AAAAAAAAAG-AAAAAACCTAACCCA
1 AAAAAAAAAGAAAAAAACCTAACCCA
1679682 AAAAAAAAAGAAAAAAACCTAACCC
1 AAAAAAAAAGAAAAAAACCTAACCC
1679707 CCCAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.72, C:0.20, G:0.04, T:0.04
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAACCTAACCCA
Found at i:1679713 original size:26 final size:27
Alignment explanation
Indices: 1679653--1679717 Score: 98
Period size: 25 Copynumber: 2.4 Consensus size: 27
1679643 ATTAAGCCCT
1679653 CCCCAAAAAAAAAGAAAAAACCTAA--
1 CCCCAAAAAAAAAGAAAAAACCTAACC
*
1679678 CCCAAAAAAAAAAGAAAAAAACCTAACC
1 CCCCAAAAAAAAAG-AAAAAACCTAACC
1679706 CCCCAAAAAAAA
1 CCCCAAAAAAAA
1679718 CCAAGAAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 13 0.37
26 11 0.31
28 11 0.31
ACGTcount: A:0.68, C:0.26, G:0.03, T:0.03
Consensus pattern (27 bp):
CCCCAAAAAAAAAGAAAAAACCTAACC
Found at i:1680259 original size:39 final size:36
Alignment explanation
Indices: 1680200--1680304 Score: 113
Period size: 39 Copynumber: 2.9 Consensus size: 36
1680190 TTTTTTTAGG
* *
1680200 TATTTTATATATA-TTATGTATATATTTTTTAATGC
1 TATTATATATATATTTATGTATATATTTTTTAATAC
* * *
1680235 TATTAGTTATATATTTCTTATGTATATATTCTTAAATAC
1 TATTA--TATATATAT-TTATGTATATATTTTTTAATAC
* *
1680274 TATTATATATATATATATATATATATTTTTT
1 TATTATATATATATTTATGTATATATTTTTT
1680305 TTAAATACCA
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
35 4 0.07
36 13 0.23
37 15 0.27
39 24 0.43
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (36 bp):
TATTATATATATATTTATGTATATATTTTTTAATAC
Found at i:1680309 original size:39 final size:38
Alignment explanation
Indices: 1680204--1680334 Score: 99
Period size: 39 Copynumber: 3.3 Consensus size: 38
1680194 TTTAGGTATT
* * *
1680204 TTATATATATTATGTATATATTTTTT-AATGCTATTAG
1 TTATATATATTATATATATTTTTTTTAAATACTATTAG
* * * *
1680241 TTATATAT-TTCTTATGTATATATTCTTAAATACTATTA-
1 TTATATATATT-ATATATAT-TTTTTTTAAATACTATTAG
1680279 TATATATATATATATATATATTTTTTTTAAATACCATATT-G
1 T-TATATATAT-TATATATATTTTTTTTAAATA-C-TATTAG
1680320 TGTATATATTATTAT
1 T-TATATA-TATTAT
1680335 TACAAATTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
36 2 0.03
37 13 0.18
38 5 0.07
39 26 0.36
40 8 0.11
41 15 0.21
42 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (38 bp):
TTATATATATTATATATATTTTTTTTAAATACTATTAG
Found at i:1680411 original size:2 final size:2
Alignment explanation
Indices: 1680399--1680432 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1680389 TTTTATGTAC
* *
1680399 AT AT GT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1680433 TTTGTACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1680485 original size:15 final size:15
Alignment explanation
Indices: 1680465--1680494 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1680455 ATTATTGTTG
1680465 TATATTTTTTATGTA
1 TATATTTTTTATGTA
1680480 TATATTTTTTATGTA
1 TATATTTTTTATGTA
1680495 CGTTTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TATATTTTTTATGTA
Found at i:1682328 original size:12 final size:12
Alignment explanation
Indices: 1682311--1682346 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1682301 ATTCATTTGA
*
1682311 CATTCATGCATT
1 CATTCATACATT
1682323 CATTCATACATT
1 CATTCATACATT
1682335 CATTCATACATT
1 CATTCATACATT
1682347 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.42
Consensus pattern (12 bp):
CATTCATACATT
Found at i:1687585 original size:71 final size:69
Alignment explanation
Indices: 1687487--1687661 Score: 226
Period size: 71 Copynumber: 2.5 Consensus size: 69
1687477 TTTTCAAGGG
* *
1687487 AAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTAT
1687551 GTTTT
65 GTTTT
** * *
1687556 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTA
1 --AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTA
1687621 TGTTTT
64 TGTTTT
** * *
1687627 AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1687662 TTTAATTTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
69 31 0.33
71 60 0.65
72 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (69 bp):
AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTATG
TTTT
Found at i:1687782 original size:72 final size:71
Alignment explanation
Indices: 1687661--1687826 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
1687651 GAGTTAAGCC
** * *
1687661 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTGTTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1687725 TGAGGTA
65 TGAGGTA
*
1687732 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAATTTTTGT-TTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1687797 TGAGGTA
65 TGAGGTA
* *
1687804 TTTTCAATTTCTGTTTTCAATTT
1 TTTTCAATTTTTGTTTTTAATTT
1687827 ACGTTGTTCA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT
GAGGTA
Found at i:1687922 original size:140 final size:140
Alignment explanation
Indices: 1687759--1688387 Score: 1195
Period size: 140 Copynumber: 4.5 Consensus size: 140
1687749 TTAATTTCAA
1687759 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
1687824 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTTTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
1687889 TCAAAATCAG
131 TCAAAATCAG
1687899 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1687964 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
1688029 TCAAAATCAG
131 TCAAAATCAG
1688039 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
1688104 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTAC-TTT
1688169 TTCAAAATCAG
130 TTCAAAATCAG
1688180 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1688245 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
1688310 TCAAAATCAG
131 TCAAAATCAG
*
1688320 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCTGAGGTATTTTCAATTTCTATCTTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC--GCTGAGGTATTTTCAATTTCTGT-TTT
1688385 CAA
63 CAA
1688388 AAAAAAATTC
Statistics
Matches: 481, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
140 314 0.65
141 139 0.29
142 22 0.05
143 6 0.01
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (140 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAG
Found at i:1688294 original size:281 final size:280
Alignment explanation
Indices: 1687759--1688387 Score: 1195
Period size: 281 Copynumber: 2.2 Consensus size: 280
1687749 TTAATTTCAA
1687759 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
1687824 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTTTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
1687889 TCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
131 TCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
1687954 CTGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAAT
196 CTGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAAT
1688019 TTCTACTTTTTCAAAATCAG
261 TTCTACTTTTTCAAAATCAG
1688039 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1688104 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTAC-TTT
1688169 TTCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATT
130 TTCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATT
1688234 TCTGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAA
195 TCTGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAA
1688299 TTTCTACTTTTTCAAAATCAG
260 TTTCTACTTTTTCAAAATCAG
*
1688320 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCTGAGGTATTTTCAATTTCTATCTTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC--GCTGAGGTATTTTCAATTTCTGT-TTT
1688385 CAA
63 CAA
1688388 AAAAAAATTC
Statistics
Matches: 342, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
280 124 0.36
281 190 0.56
283 22 0.06
284 6 0.02
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (280 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
CTGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAAT
TTCTACTTTTTCAAAATCAG
Found at i:1688487 original size:72 final size:72
Alignment explanation
Indices: 1688297--1688528 Score: 277
Period size: 72 Copynumber: 3.1 Consensus size: 72
1688287 TGAACCTTTT
* ** * * *
1688297 AATTTCTACTTTTTCAAAA-TCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCT
1 AATTTCTA--TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG--ACACGTT
*
1688361 GAGGTATTTTC
62 GAGGTAATTTC
*
1688372 AATTTCTATCTTTCAAAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCATCAAGACACG
1 AATTTCTAT-TTTC-----AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
1688437 TTGAGGTAATTTC
60 TTGAGGTAATTTC
*
1688450 AATTTCTATTTTCAAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
1688515 TAATTTT
66 TAATTTC
1688522 AATTTCT
1 AATTTCT
1688529 GTTCAAAATG
Statistics
Matches: 139, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
72 63 0.45
73 1 0.01
74 4 0.03
75 8 0.06
77 4 0.03
78 24 0.17
79 4 0.03
80 31 0.22
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (72 bp):
AATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTC
Found at i:1688557 original size:49 final size:49
Alignment explanation
Indices: 1688485--1688580 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
1688475 ATATTGCAAG
* *
1688485 AAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTTAATTTCTGTTCA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTCA
1688534 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTT
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTT
1688581 TTCAAAATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (49 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTCA
Found at i:1688627 original size:121 final size:121
Alignment explanation
Indices: 1688413--1688652 Score: 410
Period size: 121 Copynumber: 2.0 Consensus size: 121
1688403 ATATTGCGAG
*
1688413 AAATGAGTTGAGCATCAAGACACGTTGAGGTAATTTCAATTTCTATTTTCAAAATTCAACTCATA
1 AAATGAGTTGAGCATCAAGACACGCTGAGGTAATTTCAATTTCTATTTTCAAAATTCAACTCATA
*
1688478 TTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTT-AATTTCTGTTCA
66 TTGCAAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTTCAATTTCTGTTCA
* *
1688534 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
1 AAATGAGTTGAGCATCAAGACACGCTGAGGTAATTTCAATTTCTATTTTCAAAATTCAACTCATA
* *
1688599 TTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTT
66 TTGCAAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTT
1688653 TTTCAAAAAA
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
120 5 0.04
121 107 0.96
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (121 bp):
AAATGAGTTGAGCATCAAGACACGCTGAGGTAATTTCAATTTCTATTTTCAAAATTCAACTCATA
TTGCAAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTCA
Found at i:1688772 original size:74 final size:74
Alignment explanation
Indices: 1688537--1688798 Score: 384
Period size: 75 Copynumber: 3.5 Consensus size: 74
1688527 CTGTTCAAAA
*
1688537 TGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTC--AAAATTCAACTCATAT
1 TGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAAAATCAACTCATAT
**
1688600 TGCGAGAAA
66 TGCGAGAGG
* *
1688609 TGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATA
1 TGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTG-TTTTCAAAAAAATCAACTCATA
1688674 TTGCGAGAGG
65 TTGCGAGAGG
* * *
1688684 TGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAAAATCAACTCATAT
1688749 TGCGAGAGG
66 TGCGAGAGG
* * *
1688758 CGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATTT
1 TGAGTTGAGCCTCAAG--ACACGCTGAGGTAATTTCAATTT
1688799 TCGTTTTTCA
Statistics
Matches: 173, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
72 40 0.23
73 5 0.03
74 45 0.26
75 61 0.35
76 22 0.13
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (74 bp):
TGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAAAATCAACTCATAT
TGCGAGAGG
Found at i:1689026 original size:79 final size:78
Alignment explanation
Indices: 1688802--1689026 Score: 281
Period size: 78 Copynumber: 2.9 Consensus size: 78
1688792 TCAATTTTCG
* * * *
1688802 TTTTTCAATTTCTACCTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGCTC
1 TTTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATC
* *
1688867 ACGCACTGAGCTA
66 ACACACTAAGCTA
* * *
1688880 -TTTTCAATTTCTATCTTTCAGAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
1 TTTTTCAATTTCTATCTTTCA-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAT
*
1688944 CACACACTAAGGTA
65 CACACACTAAGCTA
* * * * * *
1688958 TTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGCGAGTTGAGCCTCGGGT
1 -TTTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAT
1689023 CACA
65 CACA
1689027 TGTCGAGGTA
Statistics
Matches: 125, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
77 19 0.15
78 48 0.38
79 40 0.32
80 18 0.14
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (78 bp):
TTTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATC
ACACACTAAGCTA
Found at i:1689036 original size:79 final size:79
Alignment explanation
Indices: 1688802--1689040 Score: 270
Period size: 79 Copynumber: 3.0 Consensus size: 79
1688792 TCAATTTTCG
* * * *
1688802 TTTTTCAATTTCTACCTTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGCTC
1 TTTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATC
*
1688867 AC-GCACTGAGCTA-
66 ACAG-ACTGAGGTAT
* * *
1688880 -TTTTCAATTTCTATCTTTCAGAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
1 TTTTTCAATTTCTATCTTTCA-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAT
* *
1688944 CACACACTAAGGTAT
65 CACAGACTGAGGTAT
* * * * * *
1688959 TTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGCGAGTTGAGCCTCGGGTC
1 TTTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATC
*
1689024 ACATGTC-GAGGTAT
66 ACA-GACTGAGGTAT
1689038 TTT
1 TTT
1689041 CAAAATCTGT
Statistics
Matches: 134, Mismatches: 22, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
77 19 0.14
78 47 0.35
79 49 0.37
80 19 0.14
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (79 bp):
TTTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGATC
ACAGACTGAGGTAT
Found at i:1689311 original size:254 final size:247
Alignment explanation
Indices: 1688580--1689396 Score: 739
Period size: 254 Copynumber: 3.3 Consensus size: 247
1688570 CAATTTCTGT
* ** ** * * *
1688580 TTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACATG--CTGAGGTATTT
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGCACTGAGCTATTT
*
1688641 TCAATTTCTG---TT-TTTCA-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--
65 TCAATTT-TGTTTTTCTTTCAGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
* * * * * * * **
1688699 GACACGCTGAGGTA--ATTTCAATTTCT-GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGCGA
129 CACACACTAAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGCGA
* ** * * * * **
1688761 GTTGAGCCT-CAGGTCACA-CGCTGAGGTATTTTC-AATTTTCGTTTTTCAATTTCTACC
193 GTTGAACCTCCA-GTCACATATC-GAGGTATTTTCAAAATCT-GCTTTTCAA-AT-TAAG
*
1688818 TTTCAAAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTGGCTCACGCACTGAGCTATTT
1 TTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTT
* * *
1688883 TCAA--TT-TCTATCTTTCAGAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
65 TCAATTTTGTTTTTCTTTCAGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
* *
1688945 ACACACTAAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGCGAG
130 ACACACTAAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGCGAG
* ** * * **
1689010 TTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATTTTG
194 TTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAG
* * *
1689064 TTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAACCTTGGCTCACGTACTGAGCTATTT
1 -TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTT
* * *
1689128 TCAATTCTTGTTTTTTTTTCA-AAAAAATTCAACTCATATTGCGAGATGTGAGTTGAGCTTTTTA
65 TCAATT-TTGTTTTTCTTTCAGAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCA
* * * * * * *
1689192 -ATTTCTACAAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGC
126 GA--TC-AC-ACA-CTAAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGC
* * *
1689254 GAGAGGTGAGTTGAACCTCCAGTTACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAAG
184 GAGAGGCGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAG
*
1689318 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTT
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTTT
1689383 CAATTTCTGTTTTT
66 CAATTT-TGTTTTT
1689397 AATGTCTGTT
Statistics
Matches: 479, Mismatches: 65, Indels: 54
0.80 0.11 0.09
Matches are distributed among these distances:
238 4 0.01
239 2 0.00
240 37 0.08
241 1 0.00
242 19 0.04
243 39 0.08
245 70 0.15
246 1 0.00
247 15 0.03
248 74 0.15
249 41 0.09
250 1 0.00
251 3 0.01
252 2 0.00
253 7 0.01
254 141 0.29
255 4 0.01
256 13 0.03
257 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (247 bp):
TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCACTGAGCTATTTT
CAATTTTGTTTTTCTTTCAGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCA
CACACTAAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGCGAGTT
GAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAG
Found at i:1692592 original size:26 final size:26
Alignment explanation
Indices: 1692529--1692602 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
1692519 CTCCCCCAAA
1692529 AAAAAACCTAA--CCAAAAAAAAAAG
1 AAAAAACCTAACCCCAAAAAAAAAAG
*
1692553 AAAAAACCTAACCCCAAAAAAAAAGG
1 AAAAAACCTAACCCCAAAAAAAAAAG
*
1692579 AAAAAACCTAACCCCCAAAAAAAA
1 AAAAAACCTAACCCCAAAAAAAAA
1692603 CCAAGAAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.24
26 35 0.76
ACGTcount: A:0.69, C:0.23, G:0.04, T:0.04
Consensus pattern (26 bp):
AAAAAACCTAACCCCAAAAAAAAAAG
Found at i:1692615 original size:27 final size:26
Alignment explanation
Indices: 1692529--1692612 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 26
1692519 CTCCCCCAAA
**
1692529 AAAAAACCTAA--CCAAAAAAAAAAG
1 AAAAAACCTAACCCCAAAAAAAAACC
**
1692553 AAAAAACCTAACCCCAAAAAAAAAGG
1 AAAAAACCTAACCCCAAAAAAAAACC
*
1692579 AAAAAACCTAACCCCCAAAAAAAACC
1 AAAAAACCTAACCCCAAAAAAAAACC
*
1692605 AAGAAACC
1 AAAAAACC
1692613 CTAGCCACTT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
24 11 0.21
26 42 0.79
ACGTcount: A:0.67, C:0.25, G:0.05, T:0.04
Consensus pattern (26 bp):
AAAAAACCTAACCCCAAAAAAAAACC
Done.