Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 72 of 135
Found at i:21618470 original size:15 final size:15
Alignment explanation
Indices: 21618436--21618474 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
21618426 GCATCTTCCA
*
21618436 AGCTCGCATTATTAG
1 AGCTCGCATTACTAG
*
21618451 AGCTCGCATTACTCG
1 AGCTCGCATTACTAG
*
21618466 TGCTCGCAT
1 AGCTCGCAT
21618475 CAGTTCCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (15 bp):
AGCTCGCATTACTAG
Found at i:21621850 original size:25 final size:24
Alignment explanation
Indices: 21621814--21621865 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
21621804 AAACAACTTC
*
21621814 TAAAAAAAACTC-AAGAGCAATTCT
1 TAAAAAAAACTCAAAGAG-AATTAT
*
21621838 TAAAGAAATACTCAAAGAGAATTAT
1 TAAA-AAAAACTCAAAGAGAATTAT
21621863 TAA
1 TAA
21621866 CTCAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.17
25 15 0.62
26 5 0.21
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.23
Consensus pattern (24 bp):
TAAAAAAAACTCAAAGAGAATTAT
Found at i:21624603 original size:17 final size:17
Alignment explanation
Indices: 21624581--21624624 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
21624571 ACCCACAGAA
* *
21624581 TATTTTTTTTATTTTTT
1 TATTTTTTTCATATTTT
*
21624598 TATTTTTCTCATATTTT
1 TATTTTTTTCATATTTT
*
21624615 TCTTTTTTTC
1 TATTTTTTTC
21624625 TCGATTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (17 bp):
TATTTTTTTCATATTTT
Found at i:21624614 original size:19 final size:19
Alignment explanation
Indices: 21624590--21624626 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21624580 ATATTTTTTT
21624590 TATTTTT-TTATTTTTCTCA
1 TATTTTTCTT-TTTTTCTCA
21624609 TATTTTTCTTTTTTTCTC
1 TATTTTTCTTTTTTTCTC
21624627 GATTTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTTCTTTTTTTCTCA
Found at i:21624631 original size:18 final size:19
Alignment explanation
Indices: 21624591--21624634 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
21624581 TATTTTTTTT
*
21624591 ATTTTTTTATTTTTCTCAT
1 ATTTTTTTATTTTTCTCAG
21624610 ATTTTTCTT-TTTTTCTC-G
1 ATTTTT-TTATTTTTCTCAG
21624628 ATTTTTT
1 ATTTTTT
21624635 GATCACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 6 0.26
19 14 0.61
20 2 0.09
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.75
Consensus pattern (19 bp):
ATTTTTTTATTTTTCTCAG
Found at i:21624633 original size:19 final size:17
Alignment explanation
Indices: 21624581--21624634 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 17
21624571 ACCCACAGAA
* *
21624581 TATTTTTTTTATTTTTT
1 TATTTTTCTCATTTTTT
21624598 TATTTTTCTCATATTTTT
1 TATTTTTCTCAT-TTTTT
*
21624616 CTTTTTTTCTCGATTTTTT
1 -TATTTTTCTC-ATTTTTT
21624635 GATCACTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 10 0.32
18 5 0.16
19 14 0.45
20 2 0.06
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (17 bp):
TATTTTTCTCATTTTTT
Found at i:21624831 original size:9 final size:9
Alignment explanation
Indices: 21624817--21624845 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
21624807 AGCAATGAAG
21624817 AACACCCAA
1 AACACCCAA
21624826 AACACCCAA
1 AACACCCAA
21624835 AACACCCAA
1 AACACCCAA
21624844 AA
1 AA
21624846 TTTGATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (9 bp):
AACACCCAA
Found at i:21634827 original size:18 final size:18
Alignment explanation
Indices: 21634804--21634978 Score: 224
Period size: 18 Copynumber: 9.7 Consensus size: 18
21634794 CGCAAAAGGA
21634804 AGAGCATACTGGCTCGTT
1 AGAGCATACTGGCTCGTT
*
21634822 AGAGCATGCTGGCTCGTT
1 AGAGCATACTGGCTCGTT
21634840 AGAGCATACTGGCTCGTT
1 AGAGCATACTGGCTCGTT
*
21634858 TGAGCATACTGGCTCGTT
1 AGAGCATACTGGCTCGTT
21634876 AGAGCATACTGGCTCGTT
1 AGAGCATACTGGCTCGTT
* *
21634894 AGAGCATACTGGTTCATT
1 AGAGCATACTGGCTCGTT
* *
21634912 AGAGCATACTAGCTCATT
1 AGAGCATACTGGCTCGTT
* **
21634930 AGAGCATACTAGCTATTT
1 AGAGCATACTGGCTCGTT
* * * *
21634948 TGAGCATATTGGCTCATA
1 AGAGCATACTGGCTCGTT
21634966 AGAGCATTACTGG
1 AGAGCA-TACTGG
21634979 ATCGCAAGAG
Statistics
Matches: 138, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
18 133 0.96
19 5 0.04
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (18 bp):
AGAGCATACTGGCTCGTT
Found at i:21636345 original size:11 final size:11
Alignment explanation
Indices: 21636329--21636385 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
21636319 AACATCCATT
21636329 ATAAAGACAAC
1 ATAAAGACAAC
21636340 ATAAAG-CAAAC
1 ATAAAGAC-AAC
* *
21636351 ATAAAGTCATC
1 ATAAAGACAAC
*
21636362 ATAAAGCCAAC
1 ATAAAGACAAC
*
21636373 A-AAACACAAC
1 ATAAAGACAAC
21636383 ATA
1 ATA
21636386 CAAGTCAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 9 0.24
11 28 0.74
12 1 0.03
ACGTcount: A:0.60, C:0.21, G:0.07, T:0.12
Consensus pattern (11 bp):
ATAAAGACAAC
Found at i:21636364 original size:22 final size:22
Alignment explanation
Indices: 21636329--21636385 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
21636319 AACATCCATT
21636329 ATAAAGACAACATAAAGCAAAC
1 ATAAAGACAACATAAAGCAAAC
* * *
21636351 ATAAAGTCATCATAAAGCCAAC
1 ATAAAGACAACATAAAGCAAAC
*
21636373 A-AAACACAACATA
1 ATAAAGACAACATA
21636386 CAAGTCAGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.60, C:0.21, G:0.07, T:0.12
Consensus pattern (22 bp):
ATAAAGACAACATAAAGCAAAC
Found at i:21636367 original size:33 final size:33
Alignment explanation
Indices: 21636329--21636392 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
21636319 AACATCCATT
21636329 ATAAAGACAACATAAAGCA-AACATA-AAGTCATC
1 ATAAAGACAACA-AAA-CACAACATACAAGTCATC
*
21636362 ATAAAGCCAACAAAACACAACATACAAGTCA
1 ATAAAGACAACAAAACACAACATACAAGTCA
21636393 GAATAGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 2 0.07
32 9 0.32
33 17 0.61
ACGTcount: A:0.58, C:0.22, G:0.08, T:0.12
Consensus pattern (33 bp):
ATAAAGACAACAAAACACAACATACAAGTCATC
Found at i:21638138 original size:52 final size:52
Alignment explanation
Indices: 21638060--21638356 Score: 398
Period size: 52 Copynumber: 5.7 Consensus size: 52
21638050 ATAAACGAAG
21638060 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
* *
21638112 AGGTCCGATGACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTAAA
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
* *
21638164 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
* * * * * * * *
21638216 AGGTTCAATGACTAAGTGTCATCCTGAGTGTAGGGATCCTTTACAGATTAAG
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
** * * *
21638268 AGGTCCAATGACTCCGTGTCATCGTGAGTATATGAATTGC-TTGCGGATTATA
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAA-TCCTTTACGGATTAAA
** *
21638320 AGGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAAT
21638357 GAAGTGAAAT
Statistics
Matches: 215, Mismatches: 29, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
51 1 0.00
52 212 0.99
53 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (52 bp):
AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAA
Found at i:21641162 original size:52 final size:52
Alignment explanation
Indices: 21641057--21641503 Score: 610
Period size: 52 Copynumber: 8.6 Consensus size: 52
21641047 TTCCCATTTA
** * * * *
21641057 ATACTCATAATGACACAAAGTCATCGAACCTTA-AATCCGTAATAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAA-AGGATTCAT
* * * *
21641109 ATACTCACGATGACACATTGTCATTGGACGTCATAATCCGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
21641161 ATACTCACGATTACACATAATCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
21641213 ATACTCATGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
21641265 ATACTCACGATGACACATACTAATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
** * ** * *
21641317 ATACTCACGATGACACATAGAAATTGGACCTTTTAATCCATAAAGCATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
21641369 ATACTCACGATGACACATAGTCATCGGACCAT-ATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACC-TCATAATCCGTAAAGGATTCAT
* * *
21641421 ATACTCACGATGACACATATTCACCGGACCTCATAATCCGTAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
21641473 ATACTCACCATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
21641504 TTTTCATTTA
Statistics
Matches: 349, Mismatches: 43, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
51 1 0.00
52 338 0.97
53 10 0.03
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:21641219 original size:26 final size:26
Alignment explanation
Indices: 21641190--21641271 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
21641180 ATCATCGGAC
21641190 CTCATAATCCGTAAAGGATTCATATA
1 CTCATAATCCGTAAAGGATTCATATA
* * * *
21641216 CTCATGAT--G-ACACA-TAGTCATCAGA
1 CTCATAATCCGTA-A-AGGATTCAT-ATA
21641241 CCTCATAATCCGTAAAGGATTCATATA
1 -CTCATAATCCGTAAAGGATTCATATA
21641268 CTCA
1 CTCA
21641272 CGATGACACA
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
23 1 0.03
24 7 0.17
25 3 0.08
26 18 0.45
27 3 0.08
28 7 0.17
29 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (26 bp):
CTCATAATCCGTAAAGGATTCATATA
Found at i:21641760 original size:26 final size:26
Alignment explanation
Indices: 21641684--21641761 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 26
21641674 TTCAGGGGCA
21641684 AATCCGTAAAGGATTCATATACTCAC
1 AATCCGTAAAGGATTCATATACTCAC
* * * * *
21641710 AATGACATATA-G--TCATCAGACCTCAT
1 AAT-CCGTAAAGGATTCAT-ATA-CTCAC
21641736 AATCCGTAAAGGATTCATATACTCAC
1 AATCCGTAAAGGATTCATATACTCAC
21641762 GATGACACAT
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
24 4 0.11
25 6 0.17
26 16 0.44
27 6 0.17
28 4 0.11
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (26 bp):
AATCCGTAAAGGATTCATATACTCAC
Found at i:21641767 original size:52 final size:52
Alignment explanation
Indices: 21641684--21641940 Score: 433
Period size: 52 Copynumber: 4.9 Consensus size: 52
21641674 TTCAGGGGCA
* *
21641684 AATCCGTAAAGGATTCATATACTCACAATGACATATAGTCATCAGACCTCAT
1 AATCCGTAAAGGATTCATATACTCACGATGACACATAGTCATCAGACCTCAT
*
21641736 AATCCGTAAAGGATTCATATACTCACGATGACACATAGTTATCAGACCTCAT
1 AATCCGTAAAGGATTCATATACTCACGATGACACATAGTCATCAGACCTCAT
* * *
21641788 AATCCGTAAATGATTCATATACTCACGATGACACACAGTCATCGGACCTCAT
1 AATCCGTAAAGGATTCATATACTCACGATGACACATAGTCATCAGACCTCAT
*
21641840 AATCCGTAAAGGATTCATATACTCACGATGACACATAGTCACCAGACCTCAT
1 AATCCGTAAAGGATTCATATACTCACGATGACACATAGTCATCAGACCTCAT
* *
21641892 AATCCGTAAAGGATTCATATACTCATGATGACACATAGTCATCGGACCT
1 AATCCGTAAAGGATTCATATACTCACGATGACACATAGTCATCAGACCT
21641941 TTTTCATTTA
Statistics
Matches: 191, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 191 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.26
Consensus pattern (52 bp):
AATCCGTAAAGGATTCATATACTCACGATGACACATAGTCATCAGACCTCAT
Found at i:21646576 original size:98 final size:97
Alignment explanation
Indices: 21646407--21646769 Score: 469
Period size: 98 Copynumber: 3.7 Consensus size: 97
21646397 GGGAGGAGTA
* *
21646407 AAACAAGTAGCATATCTCAATCTCCACTGAAGTTACAGTGGAATGGAGTGAAGCCACATTCAAAT
1 AAACAAGTAGCAGATCTCAATCTCCACTGAAGTTACAGTGGAATGGAGTGAAGCCACACTCAAAT
* *
21646472 CATATATCCTTGAAGATGTAATGGATCGGATT
66 CCTATATCCTTGAAGATGCAATGGATCGGATT
* * *
21646504 GAAACAAGTAGCAGATCTTAATCTCCATTGAAGTTACAGTGGAATGGAGTGAAGTCACACTCAAA
1 -AAACAAGTAGCAGATCTCAATCTCCACTGAAGTTACAGTGGAATGGAGTGAAGCCACACTCAAA
* *
21646569 TCCTATATCCCTGAAGATGCAATGGGTCGGATT
65 TCCTATATCCTTGAAGATGCAATGGATCGGATT
* * * * ** *
21646602 AAAAAAAGTAGTAGATCTCAATCTCCACTGAAATTGCAGTGGAATGGAGCAAAGCCACCCTCAAA
1 -AAACAAGTAGCAGATCTCAATCTCCACTGAAGTTACAGTGGAATGGAGTGAAGCCACACTCAAA
* *
21646667 TCCTATATCCTTGAAGTTGCAA-GGATCGGAGT
65 TCCTATATCCTTGAAGATGCAATGGATCGGATT
* * * * *
21646699 AAGATAAGTAGCAGACCTTAATCTCCA-TAGAAGTTGCATTGGAATGGAGTGAAGCCACACTCAA
1 AA-ACAAGTAGCAGATCTCAATCTCCACT-GAAGTTACAGTGGAATGGAGTGAAGCCACACTCAA
21646763 ATCCTAT
64 ATCCTAT
21646770 CTTCCTGAAG
Statistics
Matches: 230, Mismatches: 33, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
96 3 0.01
97 65 0.28
98 162 0.70
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (97 bp):
AAACAAGTAGCAGATCTCAATCTCCACTGAAGTTACAGTGGAATGGAGTGAAGCCACACTCAAAT
CCTATATCCTTGAAGATGCAATGGATCGGATT
Found at i:21646779 original size:195 final size:196
Alignment explanation
Indices: 21646405--21646784 Score: 539
Period size: 195 Copynumber: 1.9 Consensus size: 196
21646395 AAGGGAGGAG
* * * ** *
21646405 TAAAACAAGTAGCATATCTCAATCTCCACTGAAGTTACAGTGGAATGGAGTGAAGCCACATTCAA
1 TAAAAAAAGTAGCAGATCTCAATCTCCACTGAAATTACAGTGGAATGGAGCAAAGCCACACTCAA
* * * *
21646470 ATCATATATCCTTGAAGATGTAATGGATCGGATTGAAACAAGTAGCAGATCTTAATCTCCATTGA
66 ATCATATATCCTTGAAGATGCAATGGATCGGAGTGAAACAAGTAGCAGACCTTAATCTCCATAGA
*
21646535 AGTTACAGTGGAATGGAGTGAAGTCACACTCAAATCCTATATCCCTGAAGATGCAATGGGTCGGA
131 AGTTACAGTGGAATGGAGTGAAGCCACACTCAAATCCTATATCCCTGAAGATGCAATGGGTCGGA
21646600 T
196 T
* * *
21646601 TAAAAAAAGTAGTAGATCTCAATCTCCACTGAAATTGCAGTGGAATGGAGCAAAGCCACCCTCAA
1 TAAAAAAAGTAGCAGATCTCAATCTCCACTGAAATTACAGTGGAATGGAGCAAAGCCACACTCAA
* * *
21646666 ATCCTATATCCTTGAAGTTGCAA-GGATCGGAGT-AAGATAAGTAGCAGACCTTAATCTCCATAG
66 ATCATATATCCTTGAAGATGCAATGGATCGGAGTGAA-ACAAGTAGCAGACCTTAATCTCCATAG
* * * * *
21646729 AAGTTGCATTGGAATGGAGTGAAGCCACACTCAAATCCTATCTTCCTGAAGTTGCA
130 AAGTTACAGTGGAATGGAGTGAAGCCACACTCAAATCCTATATCCCTGAAGATGCA
21646785 GTGAAGTGGA
Statistics
Matches: 161, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
194 2 0.01
195 83 0.52
196 76 0.47
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (196 bp):
TAAAAAAAGTAGCAGATCTCAATCTCCACTGAAATTACAGTGGAATGGAGCAAAGCCACACTCAA
ATCATATATCCTTGAAGATGCAATGGATCGGAGTGAAACAAGTAGCAGACCTTAATCTCCATAGA
AGTTACAGTGGAATGGAGTGAAGCCACACTCAAATCCTATATCCCTGAAGATGCAATGGGTCGGA
T
Found at i:21648338 original size:21 final size:22
Alignment explanation
Indices: 21648292--21648341 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
21648282 GTCCTTGAAA
*
21648292 TTTTTATTTTATTTTAATTTCG
1 TTTTAATTTTATTTTAATTTCG
* *
21648314 -TTTAATTTTA-TTTATTTTTG
1 TTTTAATTTTATTTTAATTTCG
21648334 TTTTAATT
1 TTTTAATT
21648342 CGCACCTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTAATTTTATTTTAATTTCG
Found at i:21648477 original size:14 final size:17
Alignment explanation
Indices: 21648458--21648496 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 17
21648448 GATCCCATTT
21648458 TTTTATTTG-TA-TT-A
1 TTTTATTTGTTATTTAA
21648472 TTTTATTTGTTATTTAA
1 TTTTATTTGTTATTTAA
21648489 TTTTATTT
1 TTTTATTT
21648497 ACTGTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.41
15 2 0.09
16 2 0.09
17 9 0.41
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTATTTAA
Found at i:21648507 original size:13 final size:15
Alignment explanation
Indices: 21648489--21648525 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
21648479 TGTTATTTAA
21648489 TTTTATTTACTG-T-
1 TTTTATTTACTGTTC
*
21648502 TTTTATTTATTGTTC
1 TTTTATTTACTGTTC
21648517 TTTTATTTA
1 TTTTATTTA
21648526 TTTTTATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.52
14 1 0.05
15 9 0.43
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (15 bp):
TTTTATTTACTGTTC
Found at i:21648522 original size:15 final size:14
Alignment explanation
Indices: 21648489--21648541 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
21648479 TGTTATTTAA
*
21648489 TTTTATTTACTG-T
1 TTTTATTTATTGTT
21648502 TTTTATTTATTGTT
1 TTTTATTTATTGTT
21648516 CTTTTATTTATT-TT
1 -TTTTATTTATTGTT
21648530 TATGTTATTTAT
1 T-T-TTATTTAT
21648542 ATTCCTGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
13 12 0.34
14 4 0.11
15 19 0.54
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTTATTTATTGTT
Found at i:21648638 original size:28 final size:28
Alignment explanation
Indices: 21648584--21648638 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
21648574 TGTTTTTATG
* *
21648584 TGTTTTATTTATTTGTTAATTTTTTTAA
1 TGTTTTATTTATTTATTAATTTATTTAA
*
21648612 TGTTTT-TCTTATTTATTTATTTATTTA
1 TGTTTTAT-TTATTTATTAATTTATTTA
21648639 TTTATCACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (28 bp):
TGTTTTATTTATTTATTAATTTATTTAA
Found at i:21650578 original size:58 final size:58
Alignment explanation
Indices: 21650471--21650585 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
21650461 ATCAACAAAC
* *
21650471 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTATTCAAAAACACTTATAAAT
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTACTCAAAAACACTCATAAAT
* * *
21650529 TAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCT-AAATAACACTCATAAA
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTACTCAAA-AACACTCATAAA
21650586 CAACTCCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 3 0.06
58 48 0.94
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (58 bp):
TAAACCCAAATATTTTTAAACCCAAATATAATTTCATTACTCAAAAACACTCATAAAT
Found at i:21654339 original size:83 final size:83
Alignment explanation
Indices: 21654200--21654365 Score: 287
Period size: 83 Copynumber: 2.0 Consensus size: 83
21654190 GTAGGTGACC
21654200 TGTAACACCCCTACACCCAGTTCATACGTATAAACCCGGTATAAGAGTATTACATACAGTGCCAG
1 TGTAACACCCCTACACCCAGTTCATACGTATAAACCCGGTATAAGAGTATTACATACAGTGCCAG
21654265 AAAATTAAAAACGAGTAT
66 AAAATTAAAAACGAGTAT
* * *
21654283 TGTAACACCCTTACACCCGGTTTATACGTATAAACCCGGTATAAGAGTATTACATACAGTGCCAG
1 TGTAACACCCCTACACCCAGTTCATACGTATAAACCCGGTATAAGAGTATTACATACAGTGCCAG
* *
21654348 AGAATTAAAAATGAGTAT
66 AAAATTAAAAACGAGTAT
21654366 AACAAAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (83 bp):
TGTAACACCCCTACACCCAGTTCATACGTATAAACCCGGTATAAGAGTATTACATACAGTGCCAG
AAAATTAAAAACGAGTAT
Found at i:21655419 original size:22 final size:22
Alignment explanation
Indices: 21655393--21655457 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
21655383 GCAATAGTAG
*
21655393 GCACACAAAGTGCTAAACAGAA
1 GCACACACAGTGCTAAACAGAA
21655415 GCACACACAGTGCTAAACAGAA
1 GCACACACAGTGCTAAACAGAA
*
21655437 GCACACACAGTGCTGAACAGA
1 GCACACACAGTGCTAAACAGA
21655458 GGGCACAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.45, C:0.26, G:0.20, T:0.09
Consensus pattern (22 bp):
GCACACACAGTGCTAAACAGAA
Found at i:21655577 original size:24 final size:26
Alignment explanation
Indices: 21655539--21655586 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
21655529 TCTACATGGG
21655539 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
21655565 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
21655587 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:21660070 original size:23 final size:23
Alignment explanation
Indices: 21660015--21660087 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
21660005 GGCAACAGTA
* *
21660015 GGCACACAAAGTGCTAAACAAA-
1 GGCACACACAGTGCTGAACAAAG
*
21660037 -ACAACACACAGTGCTGAACAAAG
1 GGC-ACACACAGTGCTGAACAAAG
*
21660060 GGCACACACAGTGCTGAACAGAG
1 GGCACACACAGTGCTGAACAAAG
21660083 GGCAC
1 GGCAC
21660088 GAAATGTGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.02
22 17 0.40
23 24 0.56
24 1 0.02
ACGTcount: A:0.42, C:0.26, G:0.23, T:0.08
Consensus pattern (23 bp):
GGCACACACAGTGCTGAACAAAG
Found at i:21660207 original size:24 final size:26
Alignment explanation
Indices: 21660169--21660216 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
21660159 TCTACATGAG
21660169 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
21660195 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
21660217 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:21664889 original size:18 final size:19
Alignment explanation
Indices: 21664866--21664903 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
21664856 TCACATGCAA
*
21664866 AAGTG-AAAATTGATTTTT
1 AAGTGAAAAAGTGATTTTT
21664884 AAGTGAAAAAGTGATTTTT
1 AAGTGAAAAAGTGATTTTT
21664903 A
1 A
21664904 TGGTCATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (19 bp):
AAGTGAAAAAGTGATTTTT
Found at i:21666668 original size:21 final size:20
Alignment explanation
Indices: 21666631--21666673 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
21666621 AAAATTGAAT
*
21666631 AGAAAAACTAAAGAAAACATA
1 AGAAAAACTAAACAAAAC-TA
*
21666652 AGAAAAACTAACCAAAACTA
1 AGAAAAACTAAACAAAACTA
21666672 AG
1 AG
21666674 CCTAAGTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.67, C:0.14, G:0.09, T:0.09
Consensus pattern (20 bp):
AGAAAAACTAAACAAAACTA
Found at i:21673755 original size:20 final size:20
Alignment explanation
Indices: 21673727--21673769 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
21673717 GGTCGAAGTT
*
21673727 AAGTGATGCACTGATCTTAA
1 AAGTCATGCACTGATCTTAA
21673747 AAGTCATGCACTGATCTTAA
1 AAGTCATGCACTGATCTTAA
21673767 AAG
1 AAG
21673770 AAAGGATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (20 bp):
AAGTCATGCACTGATCTTAA
Found at i:21675362 original size:2 final size:2
Alignment explanation
Indices: 21675355--21675382 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21675345 CTACATGTTT
21675355 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
21675383 CAATTTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21690334 original size:24 final size:24
Alignment explanation
Indices: 21690307--21690354 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
21690297 ATTGTCTAAT
21690307 TTAAAAAAAATAAAAATTTAACCC
1 TTAAAAAAAATAAAAATTTAACCC
21690331 TTAAAAAAAATAAAAATTTAACCC
1 TTAAAAAAAATAAAAATTTAACCC
21690355 CAGGATGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (24 bp):
TTAAAAAAAATAAAAATTTAACCC
Found at i:21696513 original size:21 final size:21
Alignment explanation
Indices: 21696489--21696542 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
21696479 GGAGTTTTTA
* *
21696489 GTATCAGTAGAAGAGTCTCTT
1 GTATCAGTAGAACAGTCACTT
*
21696510 GTATCAGTAGAACTGTCACTT
1 GTATCAGTAGAACAGTCACTT
*
21696531 GTATCGGTAGAA
1 GTATCAGTAGAA
21696543 ATCTGCACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (21 bp):
GTATCAGTAGAACAGTCACTT
Found at i:21696586 original size:15 final size:17
Alignment explanation
Indices: 21696555--21696586 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
21696545 CTGCACTATT
21696555 CTTGAACTACTCACTGA
1 CTTGAACTACTCACTGA
21696572 CTTG-ACTAC-CACTGA
1 CTTGAACTACTCACTGA
21696587 TAGTTGTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.28, C:0.31, G:0.12, T:0.28
Consensus pattern (17 bp):
CTTGAACTACTCACTGA
Found at i:21697946 original size:3 final size:3
Alignment explanation
Indices: 21697938--21697982 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
21697928 TAGTCTAGAA
21697938 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21697983 TATTATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21702035 original size:28 final size:28
Alignment explanation
Indices: 21701978--21702038 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
21701968 TTTGAATAGC
*
21701978 CCACTAAGGGAGAAGGAGCTCAAATCGT
1 CCACTAAGGGAGAAGGAGCCCAAATCGT
*
21702006 CCACTAAGGGAGGAAGGAGCCCAACT-GT
1 CCACTAAGGGA-GAAGGAGCCCAAATCGT
21702034 CCACT
1 CCACT
21702039 TGAGGTGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.13
Consensus pattern (28 bp):
CCACTAAGGGAGAAGGAGCCCAAATCGT
Found at i:21704793 original size:19 final size:19
Alignment explanation
Indices: 21704759--21704795 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21704749 TAAAAATTAA
21704759 TAAAAAATAAATAAAAGGT
1 TAAAAAATAAATAAAAGGT
21704778 TAAATAAATAAA-AAAAGG
1 TAAA-AAATAAATAAAAGG
21704796 AGCAAAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (19 bp):
TAAAAAATAAATAAAAGGT
Found at i:21706124 original size:11 final size:11
Alignment explanation
Indices: 21706093--21706134 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
21706083 CCCAACTTGG
21706093 ATTTTAAATTA
1 ATTTTAAATTA
* *
21706104 AGTTTGAATTA
1 ATTTTAAATTA
*
21706115 ATTTTAAATTT
1 ATTTTAAATTA
21706126 A-TTTAAATT
1 ATTTTAAATT
21706135 TAAATTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:21706134 original size:17 final size:17
Alignment explanation
Indices: 21706095--21706156 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
21706085 CAACTTGGAT
*
21706095 TTTAAA-TTAAGTTTGA
1 TTTAAATTTAAATTTGA
* *
21706111 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
21706127 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
21706144 TTTAAATTTAAAT
1 TTTAAATTTAAAT
21706157 ACATTTAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:21706137 original size:22 final size:22
Alignment explanation
Indices: 21706093--21706134 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
21706083 CCCAACTTGG
*
21706093 ATTTTAAATTAAGTTTGAATTA
1 ATTTTAAATTAAGTTTAAATTA
*
21706115 ATTTTAAATTTA-TTTAAATT
1 ATTTTAAATTAAGTTTAAATT
21706135 TAAATTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAAATTAAGTTTAAATTA
Found at i:21706140 original size:27 final size:27
Alignment explanation
Indices: 21706101--21706153 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
21706091 GGATTTTAAA
* *
21706101 TTAAGTTTGAATTAATTTTAAATTTAT
1 TTAAATTTAAATTAATTTTAAATTTAT
**
21706128 TTAAATTTAAATTTGTTTTAAATTTA
1 TTAAATTTAAATTAATTTTAAATTTA
21706154 AATACATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (27 bp):
TTAAATTTAAATTAATTTTAAATTTAT
Found at i:21706942 original size:10 final size:10
Alignment explanation
Indices: 21706919--21706958 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
21706909 TAATAAAGGC
21706919 ATTAATAA-T
1 ATTAATAATT
*
21706928 ATTAATATTT
1 ATTAATAATT
21706938 ATTAATAATT
1 ATTAATAATT
*
21706948 AATAATAATT
1 ATTAATAATT
21706958 A
1 A
21706959 ATATTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTAATAATT
Found at i:21706959 original size:10 final size:10
Alignment explanation
Indices: 21706919--21706973 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
21706909 TAATAAAGGC
21706919 ATTAATAAT-
1 ATTAATAATA
21706928 ATTAAT-AT-
1 ATTAATAATA
*
21706936 -TTATTAATA
1 ATTAATAATA
21706945 ATTAATAATA
1 ATTAATAATA
*
21706955 ATTAAT-ATT
1 ATTAATAATA
21706964 A-TAATAATA
1 ATTAATAATA
21706973 A
1 A
21706974 AAAATAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 4 0.11
8 8 0.21
9 12 0.32
10 14 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTAATAATA
Found at i:21707341 original size:14 final size:14
Alignment explanation
Indices: 21707322--21707352 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21707312 ATTGTTTTTT
21707322 AAAAGAAAAAAAGA
1 AAAAGAAAAAAAGA
*
21707336 AAAAGAAGAAAAGA
1 AAAAGAAAAAAAGA
21707350 AAA
1 AAA
21707353 GGGTAAGAAG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAGA
Found at i:21708268 original size:59 final size:59
Alignment explanation
Indices: 21708092--21708504 Score: 480
Period size: 59 Copynumber: 7.0 Consensus size: 59
21708082 GCTCTCTAGT
* *
21708092 CCTCGAACTTTTCAAAATTCCATTTTTGACCCCAATTTCACCAAAAATTACCATTTTAC
1 CCTCAAACTTTTCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
* * * * * *
21708151 CCCCGAAC-TTTCTAAAATTCTA-TTTTGACCTCAGTTTCACCAAAAATTACCATTTTAC
1 CCTCAAACTTTTC-AAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
* *
21708209 CCTCAAACTTTTCAACATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
1 CCTCAAACTTTTCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
* * *
21708268 CC-CTAAAC-TTTCTAAAATCCCA-TTTTAACCCCAATTTCACTAAAAATTTCCATTTTAC
1 CCTC-AAACTTTTC-AAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
* * *
21708326 CCTCAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCGTTTTAC
1 CCTCAAACTTTTCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
** ** * * *
21708385 CCTTTAAC-TTTCTAAAACCCCATTTTTAGCCCCGATTTCACCAAAAATTACCGTTTTAC
1 CCTCAAACTTTTC-AAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
** * * *
21708444 CCTTGAACTTTCCAAAATTCCATTTTTGACCCTAATTTCACCAAAAATTA-CATTTTCAC
1 CCTCAAACTTTTCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTT-AC
21708503 CC
1 CC
21708505 CCGAAAGTCA
Statistics
Matches: 307, Mismatches: 36, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
58 112 0.36
59 192 0.63
60 3 0.01
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (59 bp):
CCTCAAACTTTTCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
Found at i:21708291 original size:28 final size:28
Alignment explanation
Indices: 21708259--21708351 Score: 86
Period size: 28 Copynumber: 3.2 Consensus size: 28
21708249 CCAAAAATTA
21708259 CCATTTTACCCCTAAACTTTCTAAAATC
1 CCATTTTACCCCTAAACTTTCTAAAATC
*
21708287 CCATTTTAACCCC--AA-TTTCACTAAAAATTT
1 CCATTTT-ACCCCTAAACTTT--CT-AAAA-TC
*
21708317 CCATTTTA-CCCTCAAACTTTCCAAAATC
1 CCATTTTACCCCT-AAACTTTCTAAAATC
21708345 CCATTTT
1 CCATTTT
21708352 TAACCCCAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
26 3 0.06
27 2 0.04
28 20 0.38
29 14 0.26
30 9 0.17
31 2 0.04
32 3 0.06
ACGTcount: A:0.32, C:0.31, G:0.00, T:0.37
Consensus pattern (28 bp):
CCATTTTACCCCTAAACTTTCTAAAATC
Found at i:21708306 original size:117 final size:117
Alignment explanation
Indices: 21708092--21708505 Score: 560
Period size: 117 Copynumber: 3.5 Consensus size: 117
21708082 GCTCTCTAGT
* * * **
21708092 CCTCGAACTTTTCAAAATTCCATTTTTGACCCCAATTTCACCAAAAATTACCATTTTACCCCCGA
1 CCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAA
* * * * *
21708157 ACTTTCTAAAATTCTATTTTGACCTCAGTTTCACCAAAAATTACCATTTTAC
66 ACTTTCTAAAATCCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
* * *
21708209 CCTCAAACTTTTCAACATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTAA
1 CCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAA
* *
21708274 ACTTTCTAAAATCCCATTTTAACCCCAATTTCACTAAAAATTTCCATTTTAC
66 ACTTTCTAAAATCCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
* * * *
21708326 CCTCAAACTTTCCAAAATCCCATTTTTAACCCCAATTTCACCAAAAATTACCGTTTTACCCTTTA
1 CCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAA
* * * *
21708391 ACTTTCTAAAACCCCATTTTTAGCCCCGATTTCACCAAAAATTACCGTTTTAC
66 ACTTTCTAAAATCCCA-TTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
** * *
21708444 CCTTGAACTTTCCAAAATTCCATTTTTGACCCTAATTTCACCAAAAATTA-CATTTTCACCCC
1 CCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTT-ACCCC
21708506 CGAAAGTCAA
Statistics
Matches: 262, Mismatches: 33, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
117 182 0.69
118 80 0.31
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (117 bp):
CCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAA
ACTTTCTAAAATCCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTAC
Found at i:21711616 original size:39 final size:40
Alignment explanation
Indices: 21711554--21711644 Score: 141
Period size: 39 Copynumber: 2.3 Consensus size: 40
21711544 TCGGATGGTG
*
21711554 TCTTCAATCTG-CCTTCTGGTTAGGGTAAGAAATTGGATA
1 TCTTCAATCTGCCCTTCTGCTTAGGGTAAGAAATTGGATA
* *
21711593 TCTTCAATCTGCCCTT-TGCTTAGGGTAAGAGATTGGATG
1 TCTTCAATCTGCCCTTCTGCTTAGGGTAAGAAATTGGATA
21711632 TCTTCAATCTGCC
1 TCTTCAATCTGCC
21711645 TCATGATCGG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
39 44 0.92
40 4 0.08
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (40 bp):
TCTTCAATCTGCCCTTCTGCTTAGGGTAAGAAATTGGATA
Found at i:21711736 original size:42 final size:42
Alignment explanation
Indices: 21711541--21712240 Score: 721
Period size: 42 Copynumber: 17.2 Consensus size: 42
21711531 CGTTCGAAAA
* * * * **
21711541 AGATCGGATGGTGTCTTCAATCTGCCTTC-TGGTTAGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCC-CCATGATCGGGGTAAG
* ** * **
21711583 AAATTGGAT-A--TCTTCAATCTGCCCTTTGCTTAGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * *
21711622 AGATT-G--GATGTCTTCAATCTGCCTCATGATCGGTGTCAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * *
21711661 AGATTGGATGA---CTTCAATTTGCCCTATGGTCGGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * *
21711700 AGATTGGATGATATCTTCAATCTGCCTCATGATCGGGGTAAA
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
*
21711742 AGATTGGATGATGTCTTCAATCTGCCCTATGATCGGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
*
21711784 AGATTGGATGATGTCTTCACTCTGCCCCATGATCGGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * **
21711826 AGATTGGATG--G-CTTCAATCTACCCCATGGTCCAGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * ** *
21711865 AGATTGGATGGTGTCTTCAATCTGCCTCATGATCTAGTTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* *
21711907 AGATTGGATGA---C-TC---C--CCCCATGGTCGGGGTAAA
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * *
21711940 AGATTGGATAATGTCTTCAATCTGCGCCATGATCGAGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * *
21711982 AGATTGGATGA---CTTCAATTTGCCCCATGGTCGAGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * *
21712021 AGATTGGATGATGTTTTCAATTTGCCCCATGATCGGGGTAAA
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * * * *
21712063 AGATTGGATGATGTGTTCAATTTTCCCCATGATTGAGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* * * *
21712105 AGATTGGATGGTTTCTTCAATCTGCCCCATGGTAGGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
* *
21712147 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCAGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
21712189 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
1 AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
*
21712231 AGATTTGATG
1 AGATTGGATG
21712241 GCTTCAATGA
Statistics
Matches: 551, Mismatches: 82, Indels: 50
0.81 0.12 0.07
Matches are distributed among these distances:
33 22 0.04
35 1 0.00
36 1 0.00
37 3 0.01
38 3 0.01
39 158 0.29
40 3 0.01
41 1 0.00
42 359 0.65
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (42 bp):
AGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAG
Found at i:21712174 original size:126 final size:124
Alignment explanation
Indices: 21711541--21712248 Score: 656
Period size: 123 Copynumber: 5.8 Consensus size: 124
21711531 CGTTCGAAAA
* * * **
21711541 AGATCGGATGGTGTCTTCAATCTGCCTTC-TGGTTAGGGTAAGAA-ATTGGAT-A--TCTTCAAT
1 AGATTGGATGATGTCTTCAATCTGCC-CCATGGTCGGGGTAA-AAGATTGGATGATGTCTTCAAT
** * * * * * * *
21711601 CTGCCCTTTGCT-TAGGGTAAGAGATTGGAT-GTCTTCAATCTGCCTCATGATCG-GTGTCAG
64 CTGCCCCATGATCGA-GGTAAGAGATTGGATGGACTTCAATCTGCCCCATGGTAGAG-GTAAG
* * * *
21711661 AGATTGGATGA---CTTCAATTTGCCCTATGGTCGGGGTAAGAGATTGGATGATATCTTCAATCT
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTGGATGATGTCTTCAATCT
* * * * * * * *
21711723 GCCTCATGATCGGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCTATGATCGGGGTAAG
66 GCCCCATGATCGAGGTAAGAGATTGGATG--GACTTCAATCTGCCCCATGGTAGAGGTAAG
* * *
21711784 AGATTGGATGATGTCTTCACTCTGCCCCATGATCGGGGTAAGAGATTGGATG--G-CTTCAATCT
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTGGATGATGTCTTCAATCT
* * * * * * ** *
21711846 ACCCCATGGTCCAGGTAAGAGATTGGATGGTGTCTTCAATCTGCCTCATGATCTAGTTAAG
66 GCCCCATGATCGAGGTAAGAGATTGGAT-G-GACTTCAATCTGCCCCATGGTAGAGGTAAG
*
21711907 AGATTGGATGA---C-TC---C--CCCCATGGTCGGGGTAAAAGATTGGATAATGTCTTCAATCT
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTGGATGATGTCTTCAATCT
* * *
21711963 GCGCCATGATCGAGGTAAGAGATTGGAT-GACTTCAATTTGCCCCATGGTCGAGGTAAG
66 GCCCCATGATCGAGGTAAGAGATTGGATGGACTTCAATCTGCCCCATGGTAGAGGTAAG
* * * * *
21712021 AGATTGGATGATGTTTTCAATTTGCCCCATGATCGGGGTAAAAGATTGGATGATGTGTTCAATTT
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTGGATGATGTCTTCAATCT
* * * *
21712086 TCCCCATGATTGAGGTAAGAGATTGGATGGTTTCTTCAATCTGCCCCATGGTAGGGGTAAG
66 GCCCCATGATCGAGGTAAGAGATTGGATGG--ACTTCAATCTGCCCCATGGTAGAGGTAAG
* *
21712147 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGATGTCTTCAATCT
1 AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTGGATGATGTCTTCAATCT
* *
21712212 GCCCCATGATCGGGGTAAGAGATTTGATGG-CTTCAAT
66 GCCCCATGATCGAGGTAAGAGATTGGATGGACTTCAAT
21712249 GATACGAGTC
Statistics
Matches: 488, Mismatches: 71, Indels: 55
0.79 0.12 0.09
Matches are distributed among these distances:
114 60 0.12
116 3 0.01
117 61 0.12
118 3 0.01
119 2 0.00
120 40 0.08
123 173 0.35
124 3 0.01
126 143 0.29
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (124 bp):
AGATTGGATGATGTCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTGGATGATGTCTTCAATCT
GCCCCATGATCGAGGTAAGAGATTGGATGGACTTCAATCTGCCCCATGGTAGAGGTAAG
Found at i:21724672 original size:39 final size:39
Alignment explanation
Indices: 21724613--21724739 Score: 209
Period size: 39 Copynumber: 3.3 Consensus size: 39
21724603 AAACAGAACC
* * * * *
21724613 TTGGCTTTGCGGAGGAATGTATATGCCTAAATTTCGAAG
1 TTGGCTTTGCGGAGGGATGTATATGCTTTATTTTCGAAA
21724652 TTGGCTTTGCGGAGGGATGTATATGCTTTATTTTCGAAA
1 TTGGCTTTGCGGAGGGATGTATATGCTTTATTTTCGAAA
21724691 TTGGCTTTGCGGAGGGATGTATATGCTTTATTTTCGAAA
1 TTGGCTTTGCGGAGGGATGTATATGCTTTATTTTCGAAA
21724730 TTGGCTTTGC
1 TTGGCTTTGC
21724740 ATTACAATGC
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.39
Consensus pattern (39 bp):
TTGGCTTTGCGGAGGGATGTATATGCTTTATTTTCGAAA
Found at i:21724775 original size:26 final size:26
Alignment explanation
Indices: 21724739--21724824 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
21724729 ATTGGCTTTG
21724739 CATTACAATGCATGTCTGCGAGCTAT
1 CATTACAATGCATGTCTGCGAGCTAT
* * *
21724765 CATTGCAATGCATGTGTGCGAGCTGT
1 CATTACAATGCATGTCTGCGAGCTAT
* * *
21724791 TATTACCATACATGTGC-GCGAGCTAT
1 CATTACAATGCATGT-CTGCGAGCTAT
*
21724817 TATTACAA
1 CATTACAA
21724825 ATTTTGGTAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (26 bp):
CATTACAATGCATGTCTGCGAGCTAT
Found at i:21725670 original size:21 final size:21
Alignment explanation
Indices: 21725633--21725672 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21725623 AAATCTAATT
*
21725633 TCTGTTCATCTTTTTTTTATG
1 TCTGTTCATCTTCTTTTTATG
21725654 TCTGATTCAT-TTCTTTTTA
1 TCTG-TTCATCTTCTTTTTA
21725673 CTTTAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.12, C:0.15, G:0.07, T:0.65
Consensus pattern (21 bp):
TCTGTTCATCTTCTTTTTATG
Found at i:21732502 original size:19 final size:19
Alignment explanation
Indices: 21732478--21732543 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
21732468 TGTGTGTATA
21732478 TATGTATAATTATGTATGT
1 TATGTATAATTATGTATGT
*
21732497 TATGTACT-GTTATGTATGTTATT
1 TATGTA-TAATTATGTATG----T
21732520 TATGTATAATTATGTATGT
1 TATGTATAATTATGTATGT
21732539 TATGT
1 TATGT
21732544 TTACTGTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
19 21 0.54
20 1 0.03
22 1 0.03
23 16 0.41
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.55
Consensus pattern (19 bp):
TATGTATAATTATGTATGT
Found at i:21732522 original size:23 final size:23
Alignment explanation
Indices: 21732488--21732555 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
21732478 TATGTATAAT
21732488 TATG-TATGTTATGTACTGTTATG
1 TATGTTAT-TTATGTACTGTTATG
*
21732511 TATGTTATTTATGTA-TAATTATG
1 TATGTTATTTATGTACT-GTTATG
*
21732534 TATGTTATGT-T-TACTGTTATG
1 TATGTTATTTATGTACTGTTATG
21732555 T
1 T
21732556 TTCTATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 8 0.21
22 3 0.08
23 25 0.64
24 3 0.08
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.56
Consensus pattern (23 bp):
TATGTTATTTATGTACTGTTATG
Found at i:21732553 original size:12 final size:12
Alignment explanation
Indices: 21732536--21732594 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
21732526 TAATTATGTA
21732536 TGTTATGTTTAC
1 TGTTATGTTTAC
21732548 TGTTATGTTT-C
1 TGTTATGTTTAC
* *
21732559 TATATTTGTATGTA-
1 TGT-TATGT-T-TAC
21732573 TGTTATGTTTAC
1 TGTTATGTTTAC
*
21732585 TGCTATGTTT
1 TGTTATGTTT
21732595 GTATGTCTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
11 5 0.14
12 24 0.65
13 5 0.14
14 3 0.08
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.59
Consensus pattern (12 bp):
TGTTATGTTTAC
Found at i:21735938 original size:23 final size:23
Alignment explanation
Indices: 21735872--21735930 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
21735862 GATAGTTTTG
*
21735872 TTAACATACGATGGATGATTTTAT
1 TTAA-ATACGATGGATTATTTTAT
* *
21735896 TTAGATACGATGGATTATTTTTT
1 TTAAATACGATGGATTATTTTAT
21735919 TTAAATACGATG
1 TTAAATACGATG
21735931 TTTAATTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 28 0.90
24 3 0.10
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (23 bp):
TTAAATACGATGGATTATTTTAT
Found at i:21739775 original size:16 final size:16
Alignment explanation
Indices: 21739754--21739794 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
21739744 AGAAAATGAT
*
21739754 AAATGATGGTGAGGGA
1 AAATGATGGTCAGGGA
*
21739770 AAATGATAGTCAGGGA
1 AAATGATGGTCAGGGA
*
21739786 AAACGATGG
1 AAATGATGG
21739795 AGAAATCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.37, T:0.17
Consensus pattern (16 bp):
AAATGATGGTCAGGGA
Found at i:21739849 original size:74 final size:74
Alignment explanation
Indices: 21739765--21739912 Score: 197
Period size: 74 Copynumber: 2.0 Consensus size: 74
21739755 AATGATGGTG
* * * * * *
21739765 AGGGAAAATGATAGTCAGGGAAAACGATGGAGAAATCAAAAGAAAAAAAGGGTTTATATTTCTTT
1 AGGGAAAATGATAGTCAGAGAAAACAATGGAGAAAACAAAAGAAAAAAAGGGTTAAAATTTATTT
21739830 GAAGAAAAA
66 GAAGAAAAA
* * * * *
21739839 AGGGAAAATGATGGTGAGAGAAAACAATGGTGAAAACGAAAGAAAAAACGGGTTAAAATTTATTT
1 AGGGAAAATGATAGTCAGAGAAAACAATGGAGAAAACAAAAGAAAAAAAGGGTTAAAATTTATTT
21739904 GAAGAAAAA
66 GAAGAAAAA
21739913 TGAGAACATG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.51, C:0.05, G:0.25, T:0.19
Consensus pattern (74 bp):
AGGGAAAATGATAGTCAGAGAAAACAATGGAGAAAACAAAAGAAAAAAAGGGTTAAAATTTATTT
GAAGAAAAA
Found at i:21741527 original size:29 final size:30
Alignment explanation
Indices: 21741465--21741528 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
21741455 TATATGTCGT
** * *
21741465 TTTTAATAAATAATTAGGGATATGTGCTGG
1 TTTTAATAAATAATTAGGGATATAAGCCGA
21741495 TTTTAA-AAATAATTAGGGATATAAGCCGA
1 TTTTAATAAATAATTAGGGATATAAGCCGA
21741524 TTTTA
1 TTTTA
21741529 GGTTAGGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.39
Consensus pattern (30 bp):
TTTTAATAAATAATTAGGGATATAAGCCGA
Found at i:21743117 original size:46 final size:46
Alignment explanation
Indices: 21743048--21743196 Score: 181
Period size: 46 Copynumber: 3.2 Consensus size: 46
21743038 TTACTTGCAG
* * * **
21743048 AGGCAAAGAATATGTGTGTAGAAAAAATTACTTGCATGAATAATAT
1 AGGCAAAGAATACGTGTGCAGAAAAAATAACTTGCACAAATAATAT
* * *
21743094 AGGCAAAGAATACGTGTGCAGAAAAAATAACTTGTACCAATAATGT
1 AGGCAAAGAATACGTGTGCAGAAAAAATAACTTGCACAAATAATAT
** * * *
21743140 AGGCAAAGAATACACGTGCAGAAAAAATGACTTGCACAAAAAAAAT
1 AGGCAAAGAATACGTGTGCAGAAAAAATAACTTGCACAAATAATAT
21743186 AGGCAAAGAAT
1 AGGCAAAGAAT
21743197 GTGTGGATTC
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.20
Consensus pattern (46 bp):
AGGCAAAGAATACGTGTGCAGAAAAAATAACTTGCACAAATAATAT
Found at i:21745854 original size:2 final size:2
Alignment explanation
Indices: 21745849--21745878 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21745839 ACTTATTTTA
21745849 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21745879 AGTGTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21746700 original size:17 final size:19
Alignment explanation
Indices: 21746680--21746716 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
21746670 TGTTTATTAA
*
21746680 ATTTTGTAT-ATTA-TGCT
1 ATTTTATATCATTATTGCT
21746697 ATTTTATATCATTATTGCT
1 ATTTTATATCATTATTGCT
21746716 A
1 A
21746717 CAGTCTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (19 bp):
ATTTTATATCATTATTGCT
Found at i:21747782 original size:38 final size:38
Alignment explanation
Indices: 21747717--21747801 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
21747707 AGCAGGCTAT
* * * **
21747717 GTGCTGGTGTTTATCGAGCTTAGTGTCTAGTAAGCTTC
1 GTGCAGGTGGTTATCGAGCTTAATGTCTAACAAGCTTC
*
21747755 GTGCCGGTGGTTATCGAGCTTAATGTCTAACAAGCTTC
1 GTGCAGGTGGTTATCGAGCTTAATGTCTAACAAGCTTC
*
21747793 TTGCAGGTG
1 GTGCAGGTG
21747802 TATTGAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (38 bp):
GTGCAGGTGGTTATCGAGCTTAATGTCTAACAAGCTTC
Found at i:21752863 original size:21 final size:23
Alignment explanation
Indices: 21752839--21752895 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
21752829 AACCCTATAT
*
21752839 CCTAATATCAAAATC-CTAAA-C
1 CCTAATATCAAAATCACCAAACC
*
21752860 CCTAATATGAAAA-CACCAAACC
1 CCTAATATCAAAATCACCAAACC
*
21752882 CCTAATATTAAAAT
1 CCTAATATCAAAAT
21752896 AAAATTAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 16 0.53
22 13 0.43
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (23 bp):
CCTAATATCAAAATCACCAAACC
Found at i:21753327 original size:20 final size:22
Alignment explanation
Indices: 21753299--21753347 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
21753289 ATTTATAGGA
*
21753299 AAAAAATTCAAAA-AAA-TTAT
1 AAAATATTCAAAATAAAGTTAT
21753319 AAAATATTCAAAATAAAGTTAT
1 AAAATATTCAAAATAAAGTTAT
*
21753341 TAAATAT
1 AAAATAT
21753348 ATTATTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.48
21 3 0.12
22 10 0.40
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATATTCAAAATAAAGTTAT
Found at i:21755005 original size:25 final size:25
Alignment explanation
Indices: 21754976--21755024 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
21754966 AATAATAATG
* *
21754976 CAATAATAAAAATGATAACAAATAA
1 CAATAATAAAAATGACAAAAAATAA
*
21755001 CAATAATAATAATGACAAAAAATA
1 CAATAATAAAAATGACAAAAAATA
21755025 TGATAAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.20
Consensus pattern (25 bp):
CAATAATAAAAATGACAAAAAATAA
Found at i:21755177 original size:20 final size:20
Alignment explanation
Indices: 21755154--21755192 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21755144 TAAATATACT
21755154 AGACA-AAAAATAAAATAAAA
1 AGACAGAAAAAT-AAATAAAA
*
21755174 AGACAGATAAATAAATAAA
1 AGACAGAAAAATAAATAAA
21755193 TAAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (20 bp):
AGACAGAAAAATAAATAAAA
Found at i:21755205 original size:14 final size:15
Alignment explanation
Indices: 21755186--21755221 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
21755176 ACAGATAAAT
21755186 AAATAAATA-AATAA
1 AAATAAATACAATAA
*
21755200 AAATAAATACATTAA
1 AAATAAATACAATAA
21755215 AAATAAA
1 AAATAAA
21755222 GAAACATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATAAATACAATAA
Found at i:21755353 original size:18 final size:18
Alignment explanation
Indices: 21755326--21755364 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
21755316 TAAAAACAGA
21755326 AAATAAAAGG-CTAAATT
1 AAATAAAAGGACTAAATT
21755343 AAATAAAAAGGACTAAATT
1 AAAT-AAAAGGACTAAATT
21755362 AAA
1 AAA
21755365 ACCTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (18 bp):
AAATAAAAGGACTAAATT
Found at i:21758599 original size:21 final size:20
Alignment explanation
Indices: 21758573--21758611 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21758563 TTGACATGTT
*
21758573 CGTCGCGACACAGCTAACCGA
1 CGTCGCGACAAAGC-AACCGA
21758594 CGTCGCGACAAAGCAACC
1 CGTCGCGACAAAGCAACC
21758612 AAACTACCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.38, G:0.23, T:0.08
Consensus pattern (20 bp):
CGTCGCGACAAAGCAACCGA
Found at i:21764923 original size:26 final size:26
Alignment explanation
Indices: 21764894--21765020 Score: 191
Period size: 26 Copynumber: 4.9 Consensus size: 26
21764884 CCCAGTTAGG
* *
21764894 ATATCGGTCTTACGAGCTAGTTCACT
1 ATATCGCTCTTACGAGCTAGTTCAGT
*
21764920 ATATCGCTCTTACGAGCCAGTTCAGT
1 ATATCGCTCTTACGAGCTAGTTCAGT
* * *
21764946 ATATCGCTTTTACGAGCCAGCTCAGT
1 ATATCGCTCTTACGAGCTAGTTCAGT
*
21764972 ATATTGCTCTTACGAGCTAGTTCAGT
1 ATATCGCTCTTACGAGCTAGTTCAGT
21764998 ATATCGCTCTTACGAGCTAGTTC
1 ATATCGCTCTTACGAGCTAGTTC
21765021 CATATTGTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 91 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (26 bp):
ATATCGCTCTTACGAGCTAGTTCAGT
Found at i:21764959 original size:52 final size:52
Alignment explanation
Indices: 21764873--21765020 Score: 199
Period size: 52 Copynumber: 2.8 Consensus size: 52
21764863 TAAAAATTTA
* * *
21764873 GCTCATACGAGCCCAGTT-AGGATATCGGTCTTACGAGCTAGTTCACTATATC
1 GCTCTTACGAG-CCAGTTCAGTATATCGCTCTTACGAGCTAGTTCACTATATC
* * * * *
21764925 GCTCTTACGAGCCAGTTCAGTATATCGCTTTTACGAGCCAGCTCAGTATATT
1 GCTCTTACGAGCCAGTTCAGTATATCGCTCTTACGAGCTAGTTCACTATATC
*
21764977 GCTCTTACGAGCTAGTTCAGTATATCGCTCTTACGAGCTAGTTC
1 GCTCTTACGAGCCAGTTCAGTATATCGCTCTTACGAGCTAGTTC
21765021 CATATTGTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
51 6 0.07
52 77 0.93
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (52 bp):
GCTCTTACGAGCCAGTTCAGTATATCGCTCTTACGAGCTAGTTCACTATATC
Found at i:21765557 original size:189 final size:189
Alignment explanation
Indices: 21765237--21765605 Score: 738
Period size: 189 Copynumber: 2.0 Consensus size: 189
21765227 CTAATGCAAA
21765237 TTAACCTAAGTATGCAAACTATATGTATGAAATAGATTTTAGCATAAATTAAACACAATTCACAA
1 TTAACCTAAGTATGCAAACTATATGTATGAAATAGATTTTAGCATAAATTAAACACAATTCACAA
21765302 CAAGTATAACATAAATAAACTAGGACAATTACTTTAATTAAACTCAATTCATTATCAACATGCTT
66 CAAGTATAACATAAATAAACTAGGACAATTACTTTAATTAAACTCAATTCATTATCAACATGCTT
21765367 AATAACATTTGGAAAAACATTCCATGGCAACTCGACCTTTCATGAGTTTGAAATAGATT
131 AATAACATTTGGAAAAACATTCCATGGCAACTCGACCTTTCATGAGTTTGAAATAGATT
21765426 TTAACCTAAGTATGCAAACTATATGTATGAAATAGATTTTAGCATAAATTAAACACAATTCACAA
1 TTAACCTAAGTATGCAAACTATATGTATGAAATAGATTTTAGCATAAATTAAACACAATTCACAA
21765491 CAAGTATAACATAAATAAACTAGGACAATTACTTTAATTAAACTCAATTCATTATCAACATGCTT
66 CAAGTATAACATAAATAAACTAGGACAATTACTTTAATTAAACTCAATTCATTATCAACATGCTT
21765556 AATAACATTTGGAAAAACATTCCATGGCAACTCGACCTTTCATGAGTTTG
131 AATAACATTTGGAAAAACATTCCATGGCAACTCGACCTTTCATGAGTTTG
21765606 GAAACCACAT
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 180 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (189 bp):
TTAACCTAAGTATGCAAACTATATGTATGAAATAGATTTTAGCATAAATTAAACACAATTCACAA
CAAGTATAACATAAATAAACTAGGACAATTACTTTAATTAAACTCAATTCATTATCAACATGCTT
AATAACATTTGGAAAAACATTCCATGGCAACTCGACCTTTCATGAGTTTGAAATAGATT
Found at i:21774886 original size:18 final size:18
Alignment explanation
Indices: 21774859--21774897 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
21774849 GATAGTAAAA
*
21774859 AATGATAACAAATATAAT
1 AATGACAACAAATATAAT
*
21774877 AATGACAACAAATATGAT
1 AATGACAACAAATATAAT
21774895 AAT
1 AAT
21774898 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.26
Consensus pattern (18 bp):
AATGACAACAAATATAAT
Found at i:21775036 original size:18 final size:19
Alignment explanation
Indices: 21775013--21775057 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
21775003 ATAGTAGACA
21775013 ACAAATAAAATAAA-AAAG
1 ACAAATAAAATAAACAAAG
*
21775031 ACAAAT-AAATAAACAAAT
1 ACAAATAAAATAAACAAAG
*
21775049 AAAAATAAA
1 ACAAATAAA
21775058 TACATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.30
18 14 0.61
19 2 0.09
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (19 bp):
ACAAATAAAATAAACAAAG
Found at i:21775086 original size:22 final size:20
Alignment explanation
Indices: 21775015--21775082 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 20
21775005 AGTAGACAAC
*
21775015 AAATAAAATAAAAAAGACAAAT
1 AAATAAAA-AATAAAGA-AAAT
*
21775037 AAATAAACAAATAAAAATAAAT
1 AAATAAA-AAATAAAGA-AAAT
*
21775059 ACATAAAAAATAAAGAAACAT
1 AAATAAAAAATAAAGAAA-AT
21775080 AAA
1 AAA
21775083 ATAAGGGATC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 23 0.61
23 1 0.03
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (20 bp):
AAATAAAAAATAAAGAAAAT
Found at i:21775196 original size:18 final size:18
Alignment explanation
Indices: 21775169--21775207 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
21775159 CAAAAATAGA
21775169 AAATAAAAGG-CTAAATT
1 AAATAAAAGGACTAAATT
21775186 AAATAAAAAGGACTAAATT
1 AAAT-AAAAGGACTAAATT
21775205 AAA
1 AAA
21775208 ACCTAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (18 bp):
AAATAAAAGGACTAAATT
Found at i:21776968 original size:100 final size:100
Alignment explanation
Indices: 21776821--21777215 Score: 393
Period size: 100 Copynumber: 4.0 Consensus size: 100
21776811 GACTTGCTAA
* * * * * *
21776821 TGTAGTTTCAATTTGATCCACT-ACAATTTCAAGGATATAAGATTTGATGCCGTAACTTCATCTT
1 TGTAGCTTCAATTCGACCCACTGA-AACTTCAAGGATATAGGATTTGATGTCGTAACTTCATCTT
* *
21776885 GCTTCACTGCATCTTCAGGGAGAAAAGATTTGCTTT
65 GCTCCACTGCAACTTCAGGGAGAAAAGATTTGCTTT
* * * * * *
21776921 TGTAGCTTCAATTCGACCCACTGAAACTTTAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTT
1 TGTAGCTTCAATTCGACCCACTGAAACTTCAAGGATATAGGATTTGATGTCGTAACTTCATCTTG
* * * * *
21776986 CTCTACTGCAACTTTAGAGAGATAAAGCTTTGCTAT
66 CTCCACTGCAACTTCAGGGAGA-AAAGATTTGCTTT
* * *
21777022 TGTAGTTTTAA-TCTGACCC-CTGCAACTTCAAGGATATAGGATTTGATGTCGTAACTTCATCTT
1 TGTAGCTTCAATTC-GACCCACTGAAACTTCAAGGATATAGGATTTGATGTCGTAACTTCATCTT
* * * * * *
21777085 TCTCCCCTACATCTTCAGGGAGATAAGATTTGCTTC
65 GCTCCACTGCAACTTCAGGGAGAAAAGATTTGCTTT
* * * * * * *
21777121 TGTAGCTTCAATCCAATCCACT-ACAACTTCAAGGATATAGGATTTGGTGTTGTAGCTCCATCTT
1 TGTAGCTTCAATTCGACCCACTGA-AACTTCAAGGATATAGGATTTGATGTCGTAACTTCATCTT
* *
21777185 GCTCCACTGCAACTTTAGGGAGATAAGATTT
65 GCTCCACTGCAACTTCAGGGAGAAAAGATTT
21777216 TTTGTTTGTA
Statistics
Matches: 237, Mismatches: 52, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
99 21 0.09
100 190 0.80
101 26 0.11
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (100 bp):
TGTAGCTTCAATTCGACCCACTGAAACTTCAAGGATATAGGATTTGATGTCGTAACTTCATCTTG
CTCCACTGCAACTTCAGGGAGAAAAGATTTGCTTT
Found at i:21777196 original size:200 final size:201
Alignment explanation
Indices: 21776814--21777210 Score: 546
Period size: 200 Copynumber: 2.0 Consensus size: 201
21776804 GGGATAGGAC
* *
21776814 TTGCTAATGTAGTTTCAATTTGATCCACTACAATTTCAAGGATATAAGATTTGATGCCGTAACTT
1 TTGCTAATGTAGTTTCAATCTGATCCACTACAACTTCAAGGATATAAGATTTGATGCCGTAACTT
* * * * *
21776879 CATCTTGCTTCACTGCATCTTCAGGGAGAAAAGATTTGCTTTTGTAGCTTCAATTCGACCCACTG
66 CATCTTGCTCCACTACATCTTCAGGGAGAAAAGATTTGCTTCTGTAGCTTCAATCCAACCCACTG
* * * * * *
21776944 AAACTTTAGGGGTATAGGATTTGATGTTGTAGCTTCATCTTTCTCTACTGCAACTTTAGAGAGAT
131 AAACTTCAAGGATATAGGATTTGATGTTGTAGCTCCATCTTGCTCCACTGCAACTTTAGAGAGAT
21777009 AAAGCT
196 AAAGCT
* * * * * *
21777015 TTGCTATTGTAGTTTTAATCTGA-CCCCTGCAACTTCAAGGATATAGGATTTGATGTCGTAACTT
1 TTGCTAATGTAGTTTCAATCTGATCCACTACAACTTCAAGGATATAAGATTTGATGCCGTAACTT
* * * *
21777079 CATCTTTCTCCCCTACATCTTCAGGGAGATAAGATTTGCTTCTGTAGCTTCAATCCAATCCACT-
66 CATCTTGCTCCACTACATCTTCAGGGAGAAAAGATTTGCTTCTGTAGCTTCAATCCAACCCACTG
* *
21777143 ACAACTTCAAGGATATAGGATTTGGTGTTGTAGCTCCATCTTGCTCCACTGCAACTTTAGGGAGA
131 A-AACTTCAAGGATATAGGATTTGATGTTGTAGCTCCATCTTGCTCCACTGCAACTTTAGAGAGA
21777208 TAA
195 TAA
21777211 GATTTTTTGT
Statistics
Matches: 170, Mismatches: 25, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
199 1 0.01
200 149 0.88
201 20 0.12
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (201 bp):
TTGCTAATGTAGTTTCAATCTGATCCACTACAACTTCAAGGATATAAGATTTGATGCCGTAACTT
CATCTTGCTCCACTACATCTTCAGGGAGAAAAGATTTGCTTCTGTAGCTTCAATCCAACCCACTG
AAACTTCAAGGATATAGGATTTGATGTTGTAGCTCCATCTTGCTCCACTGCAACTTTAGAGAGAT
AAAGCT
Found at i:21777215 original size:50 final size:50
Alignment explanation
Indices: 21776837--21777215 Score: 180
Period size: 50 Copynumber: 7.6 Consensus size: 50
21776827 TTCAATTTGA
* * * * * ** * *
21776837 TCCACTACAATTTCAAGGATATAAGATTTGATGCCGTAACTTCATCTTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTGTTGTAGCTCCATCTTGC
* * * * * *
21776887 TTCACTGCATCTTCAGGGAGAAAAGATTTGCTTTTGTAGCTTCAAT-TCGAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTGTTGTAGC-TCCATCTTG-C
* * * * * *
21776938 -CCACTGAAACTTTAGGG-GTATAGGATTTGATGTTGTAGCTTCATCTTTC
1 TCCACTGCAACTTCAGGGAG-ATAAGATTTGCTGTTGTAGCTCCATCTTGC
* * * * * * **
21776987 TCTACTGCAACTTTAGAGAGATAAAGCTTTGCTATTGTAGTTTTAATC-TGAC
1 TCCACTGCAACTTCAGGGAGAT-AAGATTTGCTGTTGTAG-CTCCATCTTG-C
* * * * * * * *
21777039 -CC-CTGCAACTTCAAGGATATAGGATTTGATGTCGTAACTTCATCTTTC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTGTTGTAGCTCCATCTTGC
* * * * ***
21777087 TCCCCTACATCTTCAGGGAGATAAGATTTGCT-TCTGTAGCTTCAATC-CAA
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTGT-TGTAGC-TCCATCTTGC
* * * * *
21777137 TCCACTACAACTTCAAGGATATAGGATTTGGTGTTGTAGCTCCATCTTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTGCTGTTGTAGCTCCATCTTGC
*
21777187 TCCACTGCAACTTTAGGGAGATAAGATTT
1 TCCACTGCAACTTCAGGGAGATAAGATTT
21777216 TTTGTTTGTA
Statistics
Matches: 234, Mismatches: 79, Indels: 32
0.68 0.23 0.09
Matches are distributed among these distances:
48 6 0.03
49 25 0.11
50 172 0.74
51 25 0.11
52 6 0.03
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (50 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGCTGTTGTAGCTCCATCTTGC
Found at i:21778364 original size:129 final size:129
Alignment explanation
Indices: 21778087--21778346 Score: 303
Period size: 130 Copynumber: 2.0 Consensus size: 129
21778077 TGAGAGATAA
* * * * * *
21778087 GACCATTTCATGCCCATCCTTTGATCCAAATTTGAGCCGCCCTTTCAAGTTTTCAACTCAAATCT
1 GACCATTACATG-CAATTCTTTGATCCAAATTTGAACCACCATTTCAAGTTTTCAACTCAAATCT
* * *
21778152 CCTTTGGTTTCGAGCTGCCCTTTACGGGTTTTCATCTTGACCTCTCCCTTTTTTTAGGGTGAAGC
65 CCTTTGGTTTCGAACTGCCCTTTACGAGTTTTCATCTCGACCTCTCCCTTTTTTTAGGGTGAAGC
* ** *
21778217 GACCATTACATGCCAATTCTTTGGTCCAAATTTGAACCACCATTTCGGGTTTTCGACTCAAA-CT
1 GACCATTACATG-CAATTCTTTGATCCAAATTTGAACCACCATTTCAAGTTTTCAACTCAAATCT
*
21778281 -CTTTAGGTTTCGAAAC-GTCCTTTACGAGTTTTCATCTCGACCTCTTCCCCTTTGTTTTA-GGT
65 CCTTT-GGTTTCG-AACTGCCCTTTACGAGTTTTCATCTCGACCTC-T-CCCTTT-TTTTAGGGT
21778343 GAAG
125 GAAG
21778347 TACTTATTCA
Statistics
Matches: 111, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
128 4 0.04
129 34 0.31
130 55 0.50
131 13 0.12
132 5 0.05
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (129 bp):
GACCATTACATGCAATTCTTTGATCCAAATTTGAACCACCATTTCAAGTTTTCAACTCAAATCTC
CTTTGGTTTCGAACTGCCCTTTACGAGTTTTCATCTCGACCTCTCCCTTTTTTTAGGGTGAAGC
Found at i:21779365 original size:15 final size:16
Alignment explanation
Indices: 21779332--21779394 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
21779322 ACAACAAATA
* *
21779332 AAATAAAAAAGACAGAT
1 AAATAAAAAACATA-AT
*
21779349 AAATAAAATA-ATAAT
1 AAATAAAAAACATAAT
*
21779364 -AATAAAAAACATAAA
1 AAATAAAAAACATAAT
21779379 AAATAAAGAAACATAA
1 AAATAAA-AAACATAA
21779395 AATAAGGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 8 0.21
15 6 0.15
16 8 0.21
17 17 0.44
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (16 bp):
AAATAAAAAACATAAT
Found at i:21779383 original size:16 final size:17
Alignment explanation
Indices: 21779364--21779396 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21779354 AAATAATAAT
21779364 AATAAA-AAACATAAAA
1 AATAAAGAAACATAAAA
21779380 AATAAAGAAACATAAAA
1 AATAAAGAAACATAAAA
21779397 TAAGGGATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (17 bp):
AATAAAGAAACATAAAA
Found at i:21779399 original size:22 final size:21
Alignment explanation
Indices: 21779327--21779399 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
21779317 ACTAGACAAC
* *
21779327 AAATAAAATAAAAAAGACAGA
1 AAATAAAATAAAAAATAAAGA
* *
21779348 TAAATAAAAT-AATAAT-AATA
1 -AAATAAAATAAAAAATAAAGA
*
21779368 AAA-AACATAAAAAATAAAGA
1 AAATAAAATAAAAAATAAAGA
21779388 AACATAAAATAA
1 AA-ATAAAATAA
21779400 GGGATCGAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
18 4 0.10
19 8 0.21
20 7 0.18
21 5 0.13
22 15 0.38
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (21 bp):
AAATAAAATAAAAAATAAAGA
Found at i:21781843 original size:15 final size:15
Alignment explanation
Indices: 21781825--21781860 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21781815 TAGATGACAG
21781825 TTATGATGACGATAT
1 TTATGATGACGATAT
*
21781840 TTATGATGATGATAT
1 TTATGATGACGATAT
*
21781855 CTATGA
1 TTATGA
21781861 AGATAGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (15 bp):
TTATGATGACGATAT
Found at i:21785294 original size:40 final size:40
Alignment explanation
Indices: 21785231--21785418 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
21785221 TGTCTTATAA
* * *
21785231 CCTACTAAGTCGTAGCTTAAGTTTTGACATCGGCTCATAG
1 CCTACTAAGTCGTAGCTTGAGTTTTTACACCGGCTCATAG
* * *
21785271 CTTGCTAAGTCGTAACTTGAGTTTTTTTTACACCGGCTCATAG
1 CCTACTAAGTCGTAGCTTGAG---TTTTTACACCGGCTCATAG
* * * ** *
21785314 CTTGCTATA-CCGTAGCTTGAGTTTTCTTACACTAGCTCACAG
1 CCTACTA-AGTCGTAGCTTGAG-TTT-TTACACCGGCTCATAG
21785356 CCTACTAAGTCGTAGCTTGAGTTTTTACACCGGCTCATAG
1 CCTACTAAGTCGTAGCTTGAGTTTTTACACCGGCTCATAG
*
21785396 CCTACTAAGCCGTAGCTTGAGTT
1 CCTACTAAGTCGTAGCTTGAGTT
21785419 GATTTAAACA
Statistics
Matches: 124, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
40 52 0.42
41 8 0.06
42 29 0.23
43 34 0.27
44 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (40 bp):
CCTACTAAGTCGTAGCTTGAGTTTTTACACCGGCTCATAG
Found at i:21788116 original size:19 final size:19
Alignment explanation
Indices: 21788092--21788150 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
21788082 CTCATGCGTT
21788092 CCAATAATGCTCTTACAAG
1 CCAATAATGCTCTTACAAG
* * ** *
21788111 CCAATAGTGCCCAAACGAG
1 CCAATAATGCTCTTACAAG
21788130 CCAAT-ATGCTCTTACAAG
1 CCAATAATGCTCTTACAAG
21788148 CCA
1 CCA
21788151 GTATGCTCAA
Statistics
Matches: 30, Mismatches: 10, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.20
Consensus pattern (19 bp):
CCAATAATGCTCTTACAAG
Found at i:21788155 original size:18 final size:18
Alignment explanation
Indices: 21788092--21788158 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
21788082 CTCATGCGTT
21788092 CCAATAATGCTCTTACAAG
1 CCAAT-ATGCTCTTACAAG
* ** *
21788111 CCAATAGTGCCCAAACGAG
1 CCAATA-TGCTCTTACAAG
21788130 CCAATATGCTCTTACAAG
1 CCAATATGCTCTTACAAG
*
21788148 CCAGTATGCTC
1 CCAATATGCTC
21788159 AAACGAACCA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
18 19 0.50
19 19 0.50
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (18 bp):
CCAATATGCTCTTACAAG
Found at i:21788174 original size:36 final size:37
Alignment explanation
Indices: 21788092--21788175 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 37
21788082 CTCATGCGTT
*
21788092 CCAATAATGCTCTTACAAGCCAATAGTGCCCAAACGAG
1 CCAAT-ATGCTCTTACAAGCCAATAGTGCCCAAACGAA
* *
21788130 CCAATATGCTCTTACAAGCCAGTA-TGCTCAAACGAA
1 CCAATATGCTCTTACAAGCCAATAGTGCCCAAACGAA
*
21788166 CCAGTATGCT
1 CCAATATGCT
21788176 ATTCCTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 19 0.45
37 18 0.43
38 5 0.12
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (37 bp):
CCAATATGCTCTTACAAGCCAATAGTGCCCAAACGAA
Found at i:21794229 original size:24 final size:23
Alignment explanation
Indices: 21794197--21794241 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
21794187 GTCCAGCTAC
21794197 TACCTGGTTACAATTGAAGTGGG
1 TACCTGGTTACAATTGAAGTGGG
21794220 TACCTTGGTTACAATTGAAGTG
1 TACC-TGGTTACAATTGAAGTG
21794242 AGTATATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (23 bp):
TACCTGGTTACAATTGAAGTGGG
Found at i:21795031 original size:41 final size:41
Alignment explanation
Indices: 21794970--21795048 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
21794960 TTGTATCAGC
*
21794970 CTTGGTTTAGCATCCGTCTTTGCAAAAAAATATCTCAAAGT
1 CTTGGTTTAACATCCGTCTTTGCAAAAAAATATCTCAAAGT
* * * *
21795011 CTTGGTTTAACGTCCTTCTTTGCGAAAAGATATCTCAA
1 CTTGGTTTAACATCCGTCTTTGCAAAAAAATATCTCAA
21795049 CGCTAAATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (41 bp):
CTTGGTTTAACATCCGTCTTTGCAAAAAAATATCTCAAAGT
Found at i:21804295 original size:52 final size:52
Alignment explanation
Indices: 21804216--21804350 Score: 216
Period size: 52 Copynumber: 2.6 Consensus size: 52
21804206 TAAATGAAAA
* * **
21804216 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTGTG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAG
*
21804268 AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACAGATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAG
*
21804320 AGGTTCGATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
21804351 TAAATGAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAG
Found at i:21804398 original size:60 final size:60
Alignment explanation
Indices: 21804299--21804475 Score: 252
Period size: 60 Copynumber: 3.0 Consensus size: 60
21804289 TTGTGAGTAT
* *
21804299 ATGAAT-CCTTTACAGATTAAGAGGT-TCGATGACTATGTGTCATCGTGAGTATTAAATGAA
1 ATGAATCCCATTACAGATTAA-AGGTCT-GATGACTCTGTGTCATCGTGAGTATTAAATGAA
*
21804359 ATGAATCCCATTACAGATTAAAGGTCTGATAACTCTGTGTCATCGTGAGTATTAAATGAA
1 ATGAATCCCATTACAGATTAAAGGTCTGATGACTCTGTGTCATCGTGAGTATTAAATGAA
* * *
21804419 ATGAATCCCATTA-AGGATTAAAGGTCCGATGACTCTGTGTCATCATGAGTATCAAAT
1 ATGAATCCCATTACA-GATTAAAGGTCTGATGACTCTGTGTCATCGTGAGTATTAAAT
21804476 ACAAATTGAA
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
59 1 0.01
60 92 0.86
61 14 0.13
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (60 bp):
ATGAATCCCATTACAGATTAAAGGTCTGATGACTCTGTGTCATCGTGAGTATTAAATGAA
Found at i:21809115 original size:18 final size:18
Alignment explanation
Indices: 21809050--21809115 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
21809040 TGCTCTTACA
*
21809050 AGCCAGTAGTGCCCAAACG
1 AGCCAGTA-TGCTCAAACG
21809069 AGCCAGTATGCTC-AACG
1 AGCCAGTATGCTCAAACG
* *
21809086 A-CTCAATATGCTCAAATG
1 AGC-CAGTATGCTCAAACG
21809104 AGCCAGTATGCT
1 AGCCAGTATGCT
21809116 ATTCCTTTCG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 1 0.03
17 14 0.35
18 16 0.40
19 9 0.22
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (18 bp):
AGCCAGTATGCTCAAACG
Found at i:21810977 original size:21 final size:22
Alignment explanation
Indices: 21810942--21810984 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
21810932 TTGGGATTAT
21810942 GGTCATTTGGGTTTTGTATTTG
1 GGTCATTTGGGTTTTGTATTTG
* *
21810964 GGTC-TTTTGGTTTTTTATTTG
1 GGTCATTTGGGTTTTGTATTTG
21810985 TAAATGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.07, C:0.05, G:0.28, T:0.60
Consensus pattern (22 bp):
GGTCATTTGGGTTTTGTATTTG
Found at i:21813030 original size:25 final size:26
Alignment explanation
Indices: 21812991--21813039 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
21812981 TGTAGAAATA
*
21812991 TTATTGTTAAAATATTTTTTATTATT
1 TTATTGTTAAAATATTTTATATTATT
*
21813017 TTATT-TTAAGATATTTTATATTA
1 TTATTGTTAAAATATTTTATATTA
21813040 ATTAATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (26 bp):
TTATTGTTAAAATATTTTATATTATT
Found at i:21820431 original size:55 final size:55
Alignment explanation
Indices: 21820341--21820449 Score: 123
Period size: 55 Copynumber: 2.0 Consensus size: 55
21820331 AACAAGAGTC
* * *
21820341 ACACGGTCGTGCCTCAGACCATGTGCCAGACCGTGTG-CATACACAAAATACCCAT
1 ACACAGTCGTGCCACAGACCATGTGCAAGACCGTGTGACATACA-AAAATACCCAT
* * *
21820396 ACACAGTCGTGTCACAGACCATGTGACAAG-TCGTGTGAACATGCAAAAATACCC
1 ACACAGTCGTGCCACAGACCATGTG-CAAGACCGTGTG-ACATACAAAAATACCC
21820450 CACACGCCCG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
55 28 0.62
56 12 0.27
57 5 0.11
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.18
Consensus pattern (55 bp):
ACACAGTCGTGCCACAGACCATGTGCAAGACCGTGTGACATACAAAAATACCCAT
Found at i:21821196 original size:26 final size:26
Alignment explanation
Indices: 21821155--21821207 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
21821145 TCTTCCAGAA
*
21821155 TTTAGCTCATACGAGCCCAGACAAAG
1 TTTAGCTCATACGAGCCCAAACAAAG
* *
21821181 TTTAGCTCTTATGAGCCCAAACAAAG
1 TTTAGCTCATACGAGCCCAAACAAAG
21821207 T
1 T
21821208 ATAACCAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (26 bp):
TTTAGCTCATACGAGCCCAAACAAAG
Found at i:21821357 original size:80 final size:80
Alignment explanation
Indices: 21821222--21821456 Score: 231
Period size: 86 Copynumber: 2.9 Consensus size: 80
21821212 CCAGTATACG
* * ** * *
21821222 ATGCTGCTCACACAAGCTGTCAGGAAACTGTAACATATGCAGGATCCCAGA-CATCGATACGGTC
1 ATGCTGCTCACACAAGCTGTCAAGAATCTACAACATATGCAGGATCTCA-ACCATCGA-AGGGTC
21821286 CATATTAC-CACTCACA
64 CATATTACTCACTCACA
* * * *
21821302 ATGCTACTCACACAAGCTATCAAGAATCTACAACCTATGCAGGATCTCAACCATCGGAGGGTCCA
1 ATGCTGCTCACACAAGCTGTCAAGAATCTACAACATATGCAGGATCTCAACCATCGAAGGGTCCA
* * *
21821367 TAAACATAACACTCACTCTCG
66 T----AT--TACTCACTCACA
* * * *
21821388 ATGCTGCTCATACAAGCTGTCAAAAATCCACAACATATGCAGGATCTCAGCCATCGAAGGGTCCA
1 ATGCTGCTCACACAAGCTGTCAAGAATCTACAACATATGCAGGATCTCAACCATCGAAGGGTCCA
21821453 TATT
66 TATT
21821457 TCAATATCCA
Statistics
Matches: 125, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
79 9 0.07
80 46 0.37
82 2 0.02
83 2 0.02
85 2 0.02
86 64 0.51
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.22
Consensus pattern (80 bp):
ATGCTGCTCACACAAGCTGTCAAGAATCTACAACATATGCAGGATCTCAACCATCGAAGGGTCCA
TATTACTCACTCACA
Found at i:21836321 original size:24 final size:24
Alignment explanation
Indices: 21836294--21836348 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
21836284 TTTGGCCCAC
21836294 ACGAGCCCAGAAA-GGTTAGCTCTT
1 ACGAGCCCA-AAATGGTTAGCTCTT
21836318 ACGAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAAAATGGTTAGCTCTT
21836342 ACGAGCC
1 ACGAGCC
21836349 TACACGGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (24 bp):
ACGAGCCCAAAATGGTTAGCTCTT
Found at i:21840269 original size:21 final size:21
Alignment explanation
Indices: 21840245--21840284 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21840235 TACCCTGTAC
* * *
21840245 TTCTATCGATACATGTATGGG
1 TTCTACCGAAACAAGTATGGG
21840266 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
21840285 CAGAATCACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGGG
Found at i:21848359 original size:21 final size:19
Alignment explanation
Indices: 21848322--21848362 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
21848312 ATGAGAAAAA
21848322 GTAAATTAAAGCCGTAAAG
1 GTAAATTAAAGCCGTAAAG
*
21848341 GTAAATCTCAAAGCTGTAAAG
1 GTAAAT-T-AAAGCCGTAAAG
21848362 G
1 G
21848363 GCTAGATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (19 bp):
GTAAATTAAAGCCGTAAAG
Found at i:21848597 original size:38 final size:39
Alignment explanation
Indices: 21848516--21849344 Score: 384
Period size: 38 Copynumber: 21.2 Consensus size: 39
21848506 TACAGTAGAG
*
21848516 CAGATTGAAGACATGCAATCTCTTACCCCGATCATGGGG
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCATGGGA
* * * * **
21848555 CAGATTGAAG-CATTCGATCTTTTACCTCGATTGTGGGA
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCATGGGA
* * *
21848593 CAGATT-ACAGCCTTCCAATCTCTTACCCCGATCATAGGG-
1 CAGATTGA-AGACATGCAATCTCTTACCCCGATCAT-GGGA
* * * ** * *
21848632 CAGAGTGAAG-CATCCAATCTTTTACCCTAATTA-GAGGG
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCATG-GGA
* * * *
21848670 CAGATTGAAGACATCATCCAATCTCTTACCTCAATCATGGGG
1 CAGATTGAAG--A-CATGCAATCTCTTACCCCGATCATGGGA
* * * *
21848712 TAGATTGAAG-CATCCAATCTCATACCCCGATCATGGGG
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCATGGGA
* *
21848750 CAAATTGAAGACACAT-CAATCTCTTACCTCGATCATGAGG-
1 CAGATTGAAG--ACATGCAATCTCTTACCCCGATCATG-GGA
* * ***
21848790 CAGATTAAAG-CATCCAATCTCTTACCTTAATCA-GAAGG-
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCATG--GGA
* *
21848828 CAGATTGAAGACCATCCAATCTTTTACCCCGATCATGAGG-
1 CAGATTGAAGA-CATGCAATCTCTTACCCCGATCATG-GGA
* *** * *
21848868 CAGATTGAA-ACATTCAATCTCTTACCTTAATTA-GAGGG
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCATG-GGA
**
21848906 CAGATTGAAGACAACCAAATCTCTTACCCTCGATCATGGGA
1 CAGATTGAAGACATGC-AATCTCTTACCC-CGATCATGGGA
* * * * *
21848947 CAGATTGAAG-CATCCAATGTTTTA-CCCTAGTTA-GAAGG-
1 CAGATTGAAGACATGCAATCTCTTACCCCGA-TCATG--GGA
* ** *
21848985 TAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGG
1 CAGATTGAAGACA-TGCAATCTCTTACCCCGATCATGGGA
* * * * *
21849025 CAGATTGAAG-CATCCAATCTTTTA-CCCTAGTTA-GAGGG
1 CAGATTGAAGACATGCAATCTCTTACCCCGA-TCATG-GGA
* * *
21849063 CAAATTGAAGACACAT-TAATCTCTTACCCCGATCATGGGG
1 CAGATTGAAG--ACATGCAATCTCTTACCCCGATCATGGGA
* * * * *
21849103 CAAATTGAAG-CATCCAATCCCATACCCCGATCATGGGG
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCATGGGA
* * * **
21849141 TAGATTGAAG-CATCCAATCTCATACCTTGATCATGAGG-
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCATG-GGA
* * **
21849179 CAGATTGAA-ACATCCAATCTTTTACCCTAATCATAGGG-
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCAT-GGGA
* ** * * ** *
21849217 CAGATGGAAGACACACCAATCTATCACCCTAATCATGGGG
1 CAGATTGAAGACA-TGCAATCTCTTACCCCGATCATGGGA
* * ** *
21849257 CAGATTGAAG-CATCCAATCTTTTACCCTAATCA-GAGGG
1 CAGATTGAAGACATGCAATCTCTTACCCCGATCATG-GGA
* *
21849295 CAGATTGAAGACATCATCTAATCTCTTACCCCGATCATGGGG
1 CAGATTGAAGACAT--GC-AATCTCTTACCCCGATCATGGGA
21849337 CAGATTGA
1 CAGATTGA
21849345 CGCCACCATC
Statistics
Matches: 636, Mismatches: 101, Indels: 103
0.76 0.12 0.12
Matches are distributed among these distances:
36 1 0.00
37 23 0.04
38 301 0.47
39 68 0.11
40 148 0.23
41 35 0.06
42 58 0.09
43 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (39 bp):
CAGATTGAAGACATGCAATCTCTTACCCCGATCATGGGA
Found at i:21848806 original size:78 final size:78
Alignment explanation
Indices: 21848515--21849391 Score: 882
Period size: 78 Copynumber: 11.1 Consensus size: 78
21848505 TTACAGTAGA
* *
21848515 GCAGATTGAAG--ACATGCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATTCGATCTTTT
1 GCAGATTGAAGACACAT-CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTT
* * *
21848578 A-CCTCGAT-TGTGG
65 ACCCT-AATCAGAGG
* * *
21848591 GACAGATT-ACAG-C-CTTCCAATCTCTTACCCCGATCATAGGGCAGAGTGAAGCATCCAATCTT
1 G-CAGATTGA-AGACACAT-CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTT
*
21848653 TTACCCTAATTAGAGG
63 TTACCCTAATCAGAGG
* * * **
21848669 GCAGATTGAAGACATCATCCAATCTCTTACCTCAATCATGGGGTAGATTGAAGCATCCAATCTCA
1 GCAGATTGAAGACA-CAT-CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTT
**
21848734 TACCCCGATCATG-GG
64 TACCCTAATCA-GAGG
* * * * *
21848749 GCAAATTGAAGACACATCAATCTCTTACCTCGATCATGAGGCAGATTAAAGCATCCAATCTCTTA
1 GCAGATTGAAGACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
* *
21848814 CCTTAATCAGAAG
66 CCCTAATCAGAGG
* * * * *
21848827 GCAGATTGAAGAC-CATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAACATTCAATCTCTT
1 GCAGATTGAAGACACAT-CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTT
* *
21848891 ACCTTAATTAGAGG
65 ACCCTAATCAGAGG
* * *
21848905 GCAGATTGAAGACA-ACCAAATCTCTTACCCTCGATCATGGGACAGATTGAAGCATCCAATGTTT
1 GCAGATTGAAGACACATC-AATCTCTTACCC-CGATCATGGGGCAGATTGAAGCATCCAATCTTT
* * *
21848969 TACCCTAGTTAGAAG
64 TACCCTAATCAGAGG
* *
21848984 GTAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
1 GCAGATTGAAGACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
* *
21849049 CCCTAGTTAGAGG
66 CCCTAATCAGAGG
* * * ***
21849062 GCAAATTGAAGACACATTAATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCAATCCCATA
1 GCAGATTGAAGACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
**
21849127 CCCCGATCATG-GG
66 CCCTAATCA-GAGG
* * ** * *
21849140 GTAGATTGAAG---CATCCAATCTCATACCTTGATCATGAGGCAGATTGAAACATCCAATCTTTT
1 GCAGATTGAAGACACAT-CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTT
*
21849202 ACCCTAATCATAGG
65 ACCCTAATCAGAGG
* * * * **
21849216 GCAGATGGAAGACACACCAATCTATCACCCTAATCATGGGGCAGATTGAAGCATCCAATCTTTTA
1 GCAGATTGAAGACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
21849281 CCCTAATCAGAGG
66 CCCTAATCAGAGG
*
21849294 GCAGATTGAAGACATCATCTAATCTCTTACCCCGATCATGGGGCAGATTGACGCCACCATCCAAT
1 GCAGATTGAAGACA-CATC-AATCTCTTACCCCGATCATGGGGCAGATTGA----AGCATCCAAT
* *
21849359 CTTTTACCCTTAAACAATAGG
60 CTTTTACCC-TAATC-AGAGG
21849380 GACAGATTGAAG
1 G-CAGATTGAAG
21849392 CTACCATCTC
Statistics
Matches: 670, Mismatches: 100, Indels: 51
0.82 0.12 0.06
Matches are distributed among these distances:
75 3 0.00
76 58 0.09
77 69 0.10
78 334 0.50
79 73 0.11
80 95 0.14
81 1 0.00
84 18 0.03
85 4 0.01
86 5 0.01
87 10 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (78 bp):
GCAGATTGAAGACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
CCCTAATCAGAGG
Found at i:21848837 original size:116 final size:117
Alignment explanation
Indices: 21848515--21849367 Score: 688
Period size: 116 Copynumber: 7.3 Consensus size: 117
21848505 TTACAGTAGA
* * *
21848515 GCAGATTGAAG--ACATGCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATTCGATCTTTT
1 GCAGATTGAAGACACAT-CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTT
** ** * * * *
21848578 ACCTCGATTGTGGGACAGATT-ACAGCCTTCCAATCTCTTACCCCGATCATAGG
65 ACCTTAATCATGGGGCAGATTGA-AGACATCCAATCTCTTACCCCGATCATGGG
* * ** *
21848631 GCAGAGTGAAG---CATCCAATCTTTTACCCTAATTA-GAGGGCAGATTGAAGACATCATCCAAT
1 GCAGATTGAAGACACAT-CAATCTCTTACCCCGATCATG-GGGCAGATTGAAG----CATCCAAT
* * *
21848692 CTCTTACCTCAATCATGGGGTAGATTGAAG-CATCCAATCTCATACCCCGATCATGGG
60 CTCTTACCTTAATCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCGATCATGGG
* * * *
21848749 GCAAATTGAAGACACATCAATCTCTTACCTCGATCATGAGGCAGATTAAAGCATCCAATCTCTTA
1 GCAGATTGAAGACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTA
* * *
21848814 CCTTAATCA-GAAGGCAGATTGAAGACCATCCAATCTTTTACCCCGATCATGAG
66 CCTTAATCATG-GGGCAGATTGAAGA-CATCCAATCTCTTACCCCGATCATGGG
* *** * *
21848867 GCAGATTGAA-ACA-TTCAATCTCTTACCTTAATTA-GAGGGCAGATTGAAGACAACCAAATCTC
1 GCAGATTGAAGACACATCAATCTCTTACCCCGATCATG-GGGCAGATTGAAG-CATCC-AATCTC
** * * * * * *
21848929 TTACCCTCGATCATGGGACAGATTGAAG-CATCCAATGTTTTA-CCCTAGTTA-GAAG
63 TTA-CCTTAATCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCGA-TCATG-GG
* * *
21848984 GTAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
1 GCAGATTGAAGACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTA
* * * * *
21849049 CCCTAGTTA-GAGGGCAAATTGAAGACA-CATTAATCTCTTACCCCGATCATGGG
66 CCTTAATCATG-GGGCAGATTGAAGACATC--CAATCTCTTACCCCGATCATGGG
* * * * *
21849102 GCAAATTGAAG---CATCCAATCCCATACCCCGATCATGGGGTAGATTGAAGCATCCAATCTCAT
1 GCAGATTGAAGACACAT-CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTT
* * * ** *
21849164 ACCTTGATCATGAGGCAGATTGAA-ACATCCAATCTTTTACCCTAATCATAGG
65 ACCTTAATCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCGATCATGGG
* * * * ** *
21849216 GCAGATGGAAGACACACCAATCTATCACCCTAATCATGGGGCAGATTGAAGCATCCAATCTTTTA
1 GCAGATTGAAGACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTA
*
21849281 CCCTAATCA-GAGGGCAGATTGAAGACATCATCTAATCTCTTACCCCGATCATGGG
66 CCTTAATCATG-GGGCAGATTGAAGACATC--C-AATCTCTTACCCCGATCATGGG
* * *
21849336 GCAGATTGACGCCACCATCCAATCTTTTACCC
1 GCAGATTGAAGACA-CAT-CAATCTCTTACCC
21849368 TTAAACAATA
Statistics
Matches: 582, Mismatches: 113, Indels: 78
0.75 0.15 0.10
Matches are distributed among these distances:
114 28 0.05
115 40 0.07
116 208 0.36
117 51 0.09
118 101 0.17
119 80 0.14
120 57 0.10
121 6 0.01
122 11 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (117 bp):
GCAGATTGAAGACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTCTTA
CCTTAATCATGGGGCAGATTGAAGACATCCAATCTCTTACCCCGATCATGGG
Found at i:21848956 original size:235 final size:233
Alignment explanation
Indices: 21848515--21849344 Score: 919
Period size: 235 Copynumber: 3.5 Consensus size: 233
21848505 TTACAGTAGA
** * *
21848515 GCAGATTGAAGACA-TGCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATTCGATCTTTTA
1 GCAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
* * * * *
21848579 -CCTCGAT-TGTGGGACAGATT-ACAG-C-CTTCCAATCTCTTACCCCGATCAT-AGGGCAGAGT
66 CCCT-AATCAGAGGG-CAGATTGA-AGACACATCCAATCTCTTACCCCGATCATGA-GGCAGATT
* *
21848638 GAAGCATCCAATCTTTTACCCTAATTAGAGGGCAGATTGAAGACATCATCCAATCTCTTACCTCA
127 GAAGCATCCAATCTCTTACCCTAATTAGAGGGCAGATTGAAGACA--A-CCAATCTCTTACCTCG
* ** *
21848703 ATCATGGGGTAGATTGAAGCATCCAATCTCATACCCCGATCATGGG
189 ATCAT-GGGCAGATTGAAGCATCCAATCTTTTACCCCAATCATGGG
* * * * * *
21848749 GCAAATTGAAGACACATCAATCTCTTACCTCGATCATGAGGCAGATTAAAGCATCCAATCTCTTA
1 GCAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
* * * *
21848814 CCTTAATCAGAAGGCAGATTGAAGAC-CATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAA
66 CCCTAATCAGAGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* *
21848878 CATTCAATCTCTTACCTTAATTAGAGGGCAGATTGAAGACAACCAAATCTCTTACCCTCGATCAT
131 CATCCAATCTCTTACCCTAATTAGAGGGCAGATTGAAGACAACC-AATCTCTTA-CCTCGATCAT
* * * * *
21848943 GGGACAGATTGAAGCATCCAATGTTTTACCCTAGTTA-GAAG
194 GGG-CAGATTGAAGCATCCAATCTTTTACCCCAATCATG-GG
*
21848984 GTAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
1 GCAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
* * * * * *
21849049 CCCTAGTTAGAGGGCAAATTGAAGACACAT-TAATCTCTTACCCCGATCATGGGGCAAATTGAAG
66 CCCTAATCAGAGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
* * ** * * * * *
21849113 CATCCAATCCCATACCCCGATCATG-GGGTAGATTGAAG-CATCCAATCTCATACCTTGATCATG
131 CATCCAATCTCTTACCCTAATTA-GAGGGCAGATTGAAGACAACCAATCTCTTACCTCGATCATG
* * *
21849176 AGGCAGATTGAAACATCCAATCTTTTACCCTAATCATAGG
195 -GGCAGATTGAAGCATCCAATCTTTTACCCCAATCATGGG
* * * **
21849216 GCAGATGGAAGACACACCAATCTATCACCCTAATCATGGGGCAGATTGAAGCATCCAATCTTTTA
1 GCAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
* *
21849281 CCCTAATCAGAGGGCAGATTGAAGACATCATCTAATCTCTTACCCCGATCATGGGGCAGATTGA
66 CCCTAATCAGAGGGCAGATTGAAGACA-CATCCAATCTCTTACCCCGATCATGAGGCAGATTGA
21849345 CGCCACCATC
Statistics
Matches: 505, Mismatches: 75, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
232 123 0.24
233 15 0.03
234 62 0.12
235 223 0.44
236 81 0.16
237 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (233 bp):
GCAGATTGAAGACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
CCCTAATCAGAGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAG
CATCCAATCTCTTACCCTAATTAGAGGGCAGATTGAAGACAACCAATCTCTTACCTCGATCATGG
GCAGATTGAAGCATCCAATCTTTTACCCCAATCATGGG
Found at i:21851490 original size:16 final size:17
Alignment explanation
Indices: 21851456--21851493 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
21851446 TTTTAATATT
21851456 TTTTGAATTCTTTTATC
1 TTTTGAATTCTTTTATC
*
21851473 TTTTGAATT-TTTTTTC
1 TTTTGAATTCTTTTATC
21851489 TTTTG
1 TTTTG
21851494 TCGCTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.13, C:0.08, G:0.08, T:0.71
Consensus pattern (17 bp):
TTTTGAATTCTTTTATC
Found at i:21852872 original size:24 final size:24
Alignment explanation
Indices: 21852845--21852897 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
21852835 ACAGACAACT
*
21852845 TTAGCCCACACGAGCCTAGAATGG
1 TTAGCCCACACGAGCCCAGAATGG
****
21852869 TTAGCTTTTACGAGCCCAGAATGG
1 TTAGCCCACACGAGCCCAGAATGG
21852893 TTAGC
1 TTAGC
21852898 TCTTACAAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (24 bp):
TTAGCCCACACGAGCCCAGAATGG
Found at i:21852898 original size:24 final size:24
Alignment explanation
Indices: 21852854--21852912 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
21852844 TTTAGCCCAC
* *
21852854 ACGAGCCTAGAATGGTTAGCTTTT
1 ACGAGCCCAGAATGGTTAGCTCTT
21852878 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
21852902 ACAAGCCCAGA
1 ACGAGCCCAGA
21852913 TAAATTAGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:21855607 original size:670 final size:667
Alignment explanation
Indices: 21854327--21855654 Score: 1868
Period size: 670 Copynumber: 2.0 Consensus size: 667
21854317 CCACGCTTCC
* * *
21854327 CGATCATACTAAAAATAGACTAATTAGTAAATTCTCATTTAATTAGGATTTAAATACAATTTATC
1 CGATCATACTAAAAATAAACTAATTAGTAAATCCTCATTTAATTAGGATTTAAATACAATTTACC
* *
21854392 AAAATCTGAAGAGTTTCTCATCATTTCTATTATTAGACCATTTAAAGAGGGTTCAATTTCATAAT
66 AAAATCTAAAGAGTTTCACATCATTTCTATTATTAGACCATTTAAAGAGGGTTCAATTTCATAAT
* * *
21854457 TGGTCCTTCAACTATATTAAATTCCAACTAAATAAACTTTATTTCAATTTAACCTTAAACTACTT
131 TAGTCCTTCAACTATATTAAATTCCAACTAAACAAACTTTATTTCAATTTAACCTTAAACTAATT
*
21854522 AGGACTAAAAAAAATTCCAAAAGTTAGTGGAAGGTAATCATATCCTCCACCGCTTGGACATTTTG
196 AGGACTAAAAAAAATCCCAAAAGTTAGTGGAAGGTAATCATA--CTCCACCGC-TGGACATTTTG
*
21854587 ACCATGGTGCAATTACCACTTTGGTCCCTTTTATTTTTAATCAATAGTAATTAACTTTTACCCCT
258 ACCATGGTGCAATTACCACTTTGGTCCCTTTTATTTTTAATCAATAGCAATTAACTTTTACCCCT
* * *
21854652 TTTACAATTTACTCCTTTTTCCTTAATTAAGCGATTAATCATCAAAATTACCAACCGAACTTCAA
323 TTTACAATTTACTCCTTTTTCCTTAATTAAACAATTAATCATCAAAATTACCAACCAAACTTCAA
* *
21854717 TTCACATATAATAAGACTCTGTAAATATTTAATAAAAATATTTACGGCTCTTAATTTCAAAAAAA
388 TTCACATAAAATAAGACTCTGTAAATATTTAATAAAAATATTTACGGCTCTAAATTTCAAAAAAA
* * * *
21854782 AGGTCCCAATACCTCATTTTCTAAAGCCACTTGACTTTTGAACTAAATCACTTATACTAACTTTT
453 AGGTCCCAATACCTCATTTTCTAAAACCACTTGACTTTTGAACCAAACCACTTATACCAACTTTT
* * *
21854847 AATTCAATAATTAAAATTCTTCGATTCAAAATTCTATATAAAATTATTATTTACTTATTTAATTT
518 AATTCAATAATTAAAATAC-TCCATTCAAAATTCTATATAAAATTATTATTGACTTATTTAATTT
* * * * * *
21854912 AAACACTCATTATAAAAATTTTCTCGTCGGG-TTTGTGGTCCCAAAATCACTGTTTCTGACACCA
582 AAAAACTCATCAGAAAAATTTTCTCGTCGGGTTTTGTGGTCCCAAAACCACTATTTCCGACACCA
21854976 CTGAAAAACAGGCTGTTGCAT
647 CTGAAAAACAGGCTGTTGCAT
* * * *
21854997 CGATCATACTAAAAATAAATTAATTAGTAAATCCTCATTTTATTAGGATTTAATTGCAATTTACC
1 CGATCATACTAAAAATAAACTAATTAGTAAATCCTCATTTAATTAGGATTTAAATACAATTTACC
*
21855062 AAAATCTAAAGAGTTTCACATCATTTCTATTATTAGGA-CATTTAAAGAGGGTT-TATTTCATAA
66 AAAATCTAAAGAGTTTCACATCATTTCTATTATTA-GACCATTTAAAGAGGGTTCAATTTCATAA
* * * **
21855125 TTAGTCCTTCAATTATATTAAATTTCAATTAAACAAACTTGT-TTTCAATTTAGTCTTAAACTAA
130 TTAGTCCTTCAACTATATTAAATTCCAACTAAACAAACTT-TATTTCAATTTAACCTTAAACTAA
* * *
21855189 TTAGGATTAAATAAATAAATAACCCAAAAGTTAGTGGATGGTAATCATA-TCCA-C-C-GGACTT
194 TTAGGACT-AA-AAA-AAAT--CCCAAAAGTTAGTGGAAGGTAATCATACTCCACCGCTGGACAT
** * *
21855250 TTTGACCATGGTTTAATTACCATTTTGGTCCCTTTACTATTTTTTAATCCATAGCAATTAACTTT
254 TTTGACCATGGTGCAATTACCACTTTGGTCCCTTT--TA-TTTTTAATCAATAGCAATTAACTTT
* * *
21855315 TACCTCTTTTACAATTTACTCCTTTTTCGTTAATTAAACAATTAATTATCAAAATTACTCAACCA
316 TACCCCTTTTACAATTTACTCCTTTTTCCTTAATTAAACAATTAATCATCAAAATTAC-CAACCA
21855380 AACTTCAATTCACATAAAATAAGACTCTGTAAATATTTAATAAAAATATTTACGG-TGCTAAATT
380 AACTTCAATTCACATAAAATAAGACTCTGTAAATATTTAATAAAAATATTTACGGCT-CTAAATT
* * * * * * *
21855444 TTATAAATAGGGTCCCGATTCCTCATTTTCTAAAACCACTTGACTTTTGAACCGAACCACTTATA
444 TCAAAAAAAAGGTCCCAATACCTCATTTTCTAAAACCACTTGACTTTTGAACCAAACCACTTATA
* *
21855509 CCAACTTTTAATTCAATAATTAAACTAC-CCATTC-AAATTTTCATATAAAAATTATTATTGACT
509 CCAACTTTTAATTCAATAATTAAAATACTCCATTCAAAATTCT-ATAT-AAAATTATTATTGACT
* * *
21855572 TATTTAATTTAAAAACTCATCAGCAGAATTTTCTCGTCGGGTTTTGTGGTCCTAAAACCACTATT
572 TATTTAATTTAAAAACTCATCAGAAAAATTTTCTCGTCGGGTTTTGTGGTCCCAAAACCACTATT
*
21855637 TCCGACACCATTGAAAAA
637 TCCGACACCACTGAAAAA
21855655 TGGACTGTTA
Statistics
Matches: 582, Mismatches: 61, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
667 37 0.06
668 6 0.01
669 82 0.14
670 238 0.41
671 190 0.33
672 4 0.01
674 25 0.04
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (667 bp):
CGATCATACTAAAAATAAACTAATTAGTAAATCCTCATTTAATTAGGATTTAAATACAATTTACC
AAAATCTAAAGAGTTTCACATCATTTCTATTATTAGACCATTTAAAGAGGGTTCAATTTCATAAT
TAGTCCTTCAACTATATTAAATTCCAACTAAACAAACTTTATTTCAATTTAACCTTAAACTAATT
AGGACTAAAAAAAATCCCAAAAGTTAGTGGAAGGTAATCATACTCCACCGCTGGACATTTTGACC
ATGGTGCAATTACCACTTTGGTCCCTTTTATTTTTAATCAATAGCAATTAACTTTTACCCCTTTT
ACAATTTACTCCTTTTTCCTTAATTAAACAATTAATCATCAAAATTACCAACCAAACTTCAATTC
ACATAAAATAAGACTCTGTAAATATTTAATAAAAATATTTACGGCTCTAAATTTCAAAAAAAAGG
TCCCAATACCTCATTTTCTAAAACCACTTGACTTTTGAACCAAACCACTTATACCAACTTTTAAT
TCAATAATTAAAATACTCCATTCAAAATTCTATATAAAATTATTATTGACTTATTTAATTTAAAA
ACTCATCAGAAAAATTTTCTCGTCGGGTTTTGTGGTCCCAAAACCACTATTTCCGACACCACTGA
AAAACAGGCTGTTGCAT
Found at i:21860643 original size:14 final size:14
Alignment explanation
Indices: 21860626--21860692 Score: 64
Period size: 14 Copynumber: 4.6 Consensus size: 14
21860616 TTGCGCTTTG
21860626 GTAATTTGGGTTGT
1 GTAATTTGGGTTGT
*
21860640 GTAATTTGGGCCTTTGG
1 GTAATTTGGG---TTGT
* *
21860657 GTAATTAGGCTT-T
1 GTAATTTGGGTTGT
21860670 GGTAATTTGGGTTGT
1 -GTAATTTGGGTTGT
21860685 GTAATTTG
1 GTAATTTG
21860693 AGTTTGGGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
14 30 0.71
15 1 0.02
17 11 0.26
ACGTcount: A:0.16, C:0.04, G:0.33, T:0.46
Consensus pattern (14 bp):
GTAATTTGGGTTGT
Found at i:21860660 original size:31 final size:30
Alignment explanation
Indices: 21860621--21860680 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
21860611 GGTAATTGCG
* *
21860621 CTTTGGTAATTTGG-GTTGTGTAATTTGGGC
1 CTTTGGTAATTAGGCTTTG-GTAATTTGGGC
21860651 CTTTGGGTAATTAGGCTTTGGTAATTTGGG
1 CTTT-GGTAATTAGGCTTTGGTAATTTGGG
21860681 TTGTGTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 19 0.73
32 3 0.12
ACGTcount: A:0.15, C:0.07, G:0.33, T:0.45
Consensus pattern (30 bp):
CTTTGGTAATTAGGCTTTGGTAATTTGGGC
Found at i:21860669 original size:45 final size:45
Alignment explanation
Indices: 21860599--21860692 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
21860589 ATTTGGGTTT
21860599 TTTGGGCCTTTGGGTAATTGCGCTTTGGTAATTTGGGTTGTGTAA
1 TTTGGGCCTTTGGGTAATTGCGCTTTGGTAATTTGGGTTGTGTAA
21860644 TTTGGGCCTTTGGGTAATTAG-GCTTTGGTAATTTGGGTTGTGTAA
1 TTTGGGCCTTTGGGTAATT-GCGCTTTGGTAATTTGGGTTGTGTAA
21860689 TTTG
1 TTTG
21860693 AGTTTGGGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 47 0.98
46 1 0.02
ACGTcount: A:0.14, C:0.07, G:0.33, T:0.46
Consensus pattern (45 bp):
TTTGGGCCTTTGGGTAATTGCGCTTTGGTAATTTGGGTTGTGTAA
Found at i:21863627 original size:22 final size:22
Alignment explanation
Indices: 21863599--21863648 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
21863589 ATACAAAATA
21863599 AAAAAT-AA-AAAATGTAATATAT
1 AAAAATAAAGAAAAT-TAATAT-T
21863621 AAAAATAGAAGAAAATTAATATT
1 AAAAATA-AAGAAAATTAATATT
21863644 AAAAA
1 AAAAA
21863649 AAGCCGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.24
23 6 0.24
24 8 0.32
25 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (22 bp):
AAAAATAAAGAAAATTAATATT
Found at i:21867356 original size:50 final size:50
Alignment explanation
Indices: 21867291--21867390 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 50
21867281 AAACGAGTCA
*
21867291 CTGCATGAGTTGATGGAAGCTTGATGAT-TGAAATGATAAAACAAATCTCT
1 CTGCATGAGTTGATGGAAGCTTGAT-ATCTAAAATGATAAAACAAATCTCT
* * *
21867341 CTGCATGAGTTGATGGAAGTTTGATTTCTAAAATGATAAAACAAGTCTCT
1 CTGCATGAGTTGATGGAAGCTTGATATCTAAAATGATAAAACAAATCTCT
21867391 GCACAAATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 1 0.02
50 44 0.98
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (50 bp):
CTGCATGAGTTGATGGAAGCTTGATATCTAAAATGATAAAACAAATCTCT
Found at i:21877628 original size:52 final size:52
Alignment explanation
Indices: 21877540--21877836 Score: 409
Period size: 52 Copynumber: 5.7 Consensus size: 52
21877530 ATTTCACTTC
* * * * *
21877540 ATTCATATATTCACGATGACACATAGCCA-CTGGACCTTATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACATAGTCATC-GGACCTTTTAATCCGTAAAGG
* * * *
21877592 ATTCGTATACTCACGATGACACAGAGTCATCAGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGG
* * *
21877644 ATCCCTATACTCATGATGACACGAT-GTCATCGGACCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACAC-ATAGTCATCGGACCTTTTAATCCGTAAAGG
* *
21877696 ATTCATATACTCACGATGACACTTAGTCATCAGACCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGG
* * *
21877748 ATTCAAATACTCACTATGACACATAGTCATCGGACCTTTTAATCTGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGG
21877800 ATTCATATACTCACGATGACACATAGTCATCGGACCT
1 ATTCATATACTCACGATGACACATAGTCATCGGACCT
21877837 CTTCGTTTAT
Statistics
Matches: 215, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
51 1 0.00
52 212 0.99
53 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGG
Found at i:21882642 original size:21 final size:21
Alignment explanation
Indices: 21882635--21882694 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
21882625 TAGATGCATG
21882635 ACTTGTATCGGTAGAAATTGC
1 ACTTGTATCGGTAGAAATTGC
* *
21882656 ACTTGTATCGGTAGAACTAGC
1 ACTTGTATCGGTAGAAATTGC
** *
21882677 ACAAGTATCAGTAGAAAT
1 ACTTGTATCGGTAGAAAT
21882695 CTATATAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAATTGC
Done.