Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold173
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: 1189743
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 33358 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:320606 original size:21 final size:21
Alignment explanation
Indices: 320561--320657 Score: 135
Period size: 21 Copynumber: 4.7 Consensus size: 21
320551 ATTTTCGAGA
*
320561 ATATTCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
320580 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
320601 ATATGCAATCTTAGATTTGAT
1 ATATGCAATCTTAGATATGAT
* *
320622 ATATGCAATCTTAGATATAAC
1 ATATGCAATCTTAGATATGAT
*
320643 ATATACAATCTTAGA
1 ATATGCAATCTTAGA
320658 AGATATGATT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
19 18 0.26
21 52 0.74
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:320693 original size:21 final size:23
Alignment explanation
Indices: 320649--320693 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
320639 TAACATATAC
*
320649 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATATGAATTTGT
*
320672 AATCTTA-AAGAT-TTAATTTGT
1 AATCTTAGAAGATATGAATTTGT
320693 A
1 A
320694 GATACCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
AATCTTAGAAGATATGAATTTGT
Found at i:327553 original size:6 final size:6
Alignment explanation
Indices: 327542--327575 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
327532 AAAAAGTGAT
* *
327542 AAAAAG AAAAAG AAAAGG AAAAGG AAAAGG AAAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAA
327576 TGGAGAGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:328851 original size:44 final size:44
Alignment explanation
Indices: 328803--328987 Score: 112
Period size: 44 Copynumber: 4.2 Consensus size: 44
328793 AAGATTATAG
328803 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
* * ** **
328847 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCATATTTAAGA-CACTAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGC-AA
** * * * * * * * * * *
328891 GCCTTGTCTCCTTGAGCAG-ACGCGGAGTAG-GCTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTA-GTGGAGCAGATC-AAAGATGGCAA
328935 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
328979 ATCTTATCT
1 ATCTTATCT
328988 TTCCAAGATA
Statistics
Matches: 95, Mismatches: 34, Indels: 24
0.62 0.22 0.16
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
44 75 0.79
45 9 0.09
46 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
Found at i:328989 original size:132 final size:132
Alignment explanation
Indices: 328757--329407 Score: 1043
Period size: 132 Copynumber: 4.9 Consensus size: 132
328747 GTGAAACACT
* * *
328757 AAGCCTTGTCTCCCTGAGCAGCAACGGAGTAGGCTGAAGATTATAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGCTGAAAATTGTAGATCTTATCTCCCTAAGCAG
* *
328822 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCATATTTAAGACA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
*
328887 CT
131 CC
* *
328889 AAGCCTTGTCTCCTTGAGCAG-ACGCGGAGTAGGCTGAAGATTGTAGATCTTATCTCCCTAAGCA
1 AAGCCTTGTCTCCCTGAGCAGCA-GCGGAGTAGGCTGAAAATTGTAGATCTTATCTCCCTAAGCA
328953 GTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
65 GTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCC
329018 ACC
130 ACC
*
329021 AAGCCTTGTCTCCCTGAGCAGCAGCGAAGTAGGCTGAAAATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGCTGAAAATTGTAGATCTTATCTCCCTAAGCAG
* * *
329086 TAGTGGAGTAGATCAATGATGCCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
329151 CC
131 CC
* * * * *
329153 AAGCATTGTCTCCCTGAACAGCAGCGGAGTAGGTTGAAAATTTTAGATCTTATCTCCTTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGCTGAAAATTGTAGATCTTATCTCCCTAAGCAG
* * *
329218 TAGTGGAGCAGATCACAGACGGCAAATCTTATCTTTCCAAGATAGTAGGAAGCAGATTTAAGCCA
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
329283 CC
131 CC
** *
329285 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGTTTGAAAATTTTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGCTGAAAATTGTAGATCTTATCTCCCTAAGCAG
* * * *
329350 TAATGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATT
66 TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATT
329408 NNNNNNNNNN
Statistics
Matches: 484, Mismatches: 33, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 482 1.00
133 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (132 bp):
AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGCTGAAAATTGTAGATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
CC
Found at i:329543 original size:44 final size:43
Alignment explanation
Indices: 329493--329872 Score: 233
Period size: 44 Copynumber: 8.7 Consensus size: 43
329483 GATCGCATCT
*
329493 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
*
329537 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * *
329582 AATCTTATATCCCTGAAGTTGCCGTGGAGCAGA-TTA-AAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * * * * *
329625 TAATCCTATCTTCTTGAAGTTGCAGTTGAGCGGATTAA-AACCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * * * * * * *
329669 GGATCTTATCTCTCTAAAGTTGCAG-AGAGCAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
329710 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * * * *
329754 AGTCTTATCTTCCTGAAGTTGTAGT-GAGGTAGACTGAAGATGGAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * *
329799 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-TTAG-AGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
*
329842 TAATCTTATCTCCCTGAAGTTGCAGTGGAGC
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGC
329873 GGATTAAAAC
Statistics
Matches: 262, Mismatches: 51, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
40 20 0.08
41 11 0.04
42 6 0.02
43 17 0.06
44 137 0.52
45 66 0.25
46 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:329601 original size:45 final size:43
Alignment explanation
Indices: 329495--329612 Score: 123
Period size: 45 Copynumber: 2.7 Consensus size: 43
329485 TCGCATCTAG
*
329495 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAG
1 TCTTAT-TCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAA
* * *
329539 TCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAG-ATGGCAAA
1 TCTTATTC-CCTGAAGTTGCAGTGGA-GCAAACT-AAGTA-AGCAAA
*
329584 TCTTATATCCCTGAAGTTGCCGTGGAGCA
1 TCTTAT-TCCCTGAAGTTGCAGTGGAGCA
329613 GATTAAAGCC
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
43 3 0.05
44 27 0.44
45 29 0.47
46 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (43 bp):
TCTTATTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAA
Found at i:329862 original size:217 final size:217
Alignment explanation
Indices: 329477--329882 Score: 677
Period size: 217 Copynumber: 1.9 Consensus size: 217
329467 NNNNNNNNNN
*
329477 AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGTCT
1 AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGCAAGCAAGTCT
* *
329542 TATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATATCCCTGAAGTTGCCGT
66 TATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATATCCCTGAAGTTGCAGT
* * *
329607 GGAGCAGATTAAAGCCGATAATCCTATCTTCTTGAAGTTGCAGTTGAGCGGATTAAAACCTTGGA
131 GGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGA
329672 TCTTATCTCTCTAAAGTTGCAG
196 TCTTATCTCTCTAAAGTTGCAG
* *
329694 AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAGCAAGCAAGTCT
1 AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGCAAGCAAGTCT
* * * *
329759 TATCTTCCTGAAGTTGTAGTGAGGTAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGT
66 TATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATATCCCTGAAGTTGCAGT
* * *
329824 GGAGTAGATTAGAGCCGATAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAC
131 GGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAC
329883 NNNNNNNNNN
Statistics
Matches: 174, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
217 174 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (217 bp):
AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGCAAGCAAGTCT
TATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATATCCCTGAAGTTGCAGT
GGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGA
TCTTATCTCTCTAAAGTTGCAG
Found at i:330380 original size:19 final size:19
Alignment explanation
Indices: 330353--330415 Score: 99
Period size: 19 Copynumber: 3.2 Consensus size: 19
330343 ATTTTCGAGA
*
330353 ATATCCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
330372 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
330391 ATATATGCAATCTTAGATATG
1 --ATATGCAATCTTAGATATG
330412 ATAT
1 ATAT
330416 ATACAATCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 22 0.54
21 19 0.46
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:330433 original size:19 final size:21
Alignment explanation
Indices: 330353--330435 Score: 120
Period size: 21 Copynumber: 4.1 Consensus size: 21
330343 ATTTTCGAGA
*
330353 ATATCCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
330372 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
330393 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
330414 ATATACAATCTTAGA-A-GAT
1 ATATGCAATCTTAGATATGAT
330433 ATA
1 ATA
330436 ATTTTGTAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
19 24 0.40
20 1 0.02
21 35 0.58
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:330434 original size:40 final size:40
Alignment explanation
Indices: 330353--330435 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
330343 ATTTTCGAGA
*
330353 ATATCCAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATCCAATCTTAGATATGATATACAATCTTAGATATGAT
*
330393 ATATGCAATCTTAGATATGATATATACAATCTTAGA-A-GAT
1 ATATCCAATCTTAGATATG--ATATACAATCTTAGATATGAT
330433 ATA
1 ATA
330436 ATTTTGTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 24 0.62
41 1 0.03
42 14 0.36
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (40 bp):
ATATCCAATCTTAGATATGATATACAATCTTAGATATGAT
Found at i:330854 original size:14 final size:15
Alignment explanation
Indices: 330825--330853 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
330815 AATTTTTAGG
330825 ATGTAATTATTTTTT
1 ATGTAATTATTTTTT
330840 ATGTAATTATTTTT
1 ATGTAATTATTTTT
330854 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
ATGTAATTATTTTTT
Found at i:334378 original size:50 final size:49
Alignment explanation
Indices: 334320--334432 Score: 127
Period size: 49 Copynumber: 2.3 Consensus size: 49
334310 AAAGCTTGAG
* * * *
334320 GTCTCGAGACAATGATCCTTTAAAGCAAACCTTAGCTTTGATGTTGGCTA
1 GTCTCGAGACAAGGATCCCTTAAAGC-AACCTTAGCTTTAATGTAGGCTA
* * ** * *
334370 GTCTCGAGACAAGGTTCCCTTGAAGCAATTTTAGCTTTAATGTAGGTTT
1 GTCTCGAGACAAGGATCCCTTAAAGCAACCTTAGCTTTAATGTAGGCTA
334419 GTCTCGAGACAAGG
1 GTCTCGAGACAAGG
334433 TTGGGAACCT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
49 31 0.58
50 22 0.42
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (49 bp):
GTCTCGAGACAAGGATCCCTTAAAGCAACCTTAGCTTTAATGTAGGCTA
Found at i:335409 original size:13 final size:13
Alignment explanation
Indices: 335391--335415 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
335381 ATGTCCATTT
335391 CAGATACAGATAA
1 CAGATACAGATAA
335404 CAGATACAGATA
1 CAGATACAGATA
335416 TGAAGATCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (13 bp):
CAGATACAGATAA
Found at i:336837 original size:9 final size:9
Alignment explanation
Indices: 336819--336865 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
336809 AGGCTTGAAC
*
336819 CAAAAATAA
1 CAAAATTAA
336828 CAAAATTAA
1 CAAAATTAA
*
336837 CAAAATTAC
1 CAAAATTAA
*
336846 CAAAAATAA
1 CAAAATTAA
336855 CAAAATTAA
1 CAAAATTAA
336864 CA
1 CA
336866 GCTGTGTCAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (9 bp):
CAAAATTAA
Found at i:348148 original size:12 final size:12
Alignment explanation
Indices: 348131--348183 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
348121 ACTAATCCTC
348131 TCTCAAATTTCT
1 TCTCAAATTTCT
*
348143 TCTC-AATTTCC
1 TCTCAAATTTCT
348154 TCTC-AATTTCCT
1 TCTCAAATTT-CT
*
348166 TCT-AAAATTC-
1 TCTCAAATTTCT
348176 TCTCAAAT
1 TCTCAAAT
348184 CCATATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 3 0.09
11 19 0.56
12 12 0.35
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.45
Consensus pattern (12 bp):
TCTCAAATTTCT
Found at i:348178 original size:22 final size:21
Alignment explanation
Indices: 348129--348181 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
348119 AAACTAATCC
* *
348129 TCTCTCAAATTTCTTCTCAATT
1 TCTCTC-AATTTCTTCTAAAAT
348151 TCCTCTCAATTTCCTTCTAAAAT
1 T-CTCTCAATTT-CTTCTAAAAT
348174 TCTCTCAA
1 TCTCTCAA
348182 ATCCATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (21 bp):
TCTCTCAATTTCTTCTAAAAT
Found at i:348260 original size:12 final size:12
Alignment explanation
Indices: 348245--348269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
348235 CCCTTTTTTT
348245 AAATAATTTTAA
1 AAATAATTTTAA
348257 AAATAATTTTAA
1 AAATAATTTTAA
348269 A
1 A
348270 TTTTTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAATTTTAA
Found at i:350775 original size:123 final size:123
Alignment explanation
Indices: 350555--350779 Score: 405
Period size: 123 Copynumber: 1.8 Consensus size: 123
350545 CCCAAACATG
*
350555 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGAATCCTGC
** *
350620 TAGAAGCGATTTTATACTATTTTCTCAGAAACGTCAAAAAAAATATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGATCACAAACGTCAAAAAAAATATTTCTTCCATGAC
350678 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGAATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGAATCCTGC
*
350743 TAGAAGCGATTTTGTACTATTTGATCACAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGATCACAAACGTCAA
350780 CTCGAAATTA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 97 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (123 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGAATCCTGC
TAGAAGCGATTTTATACTATTTGATCACAAACGTCAAAAAAAATATTTCTTCCATGAC
Found at i:354073 original size:256 final size:255
Alignment explanation
Indices: 353619--354130 Score: 907
Period size: 256 Copynumber: 2.0 Consensus size: 255
353609 AAACTATCAT
* *
353619 TTCATATCTTTCAGTGATTTTTTACAATCTTTGGATTTTGCAGAGTTAGTGCTTGGAAAATCAAA
1 TTCATATCTTTCAGTGATTTTTTACAATATTTGGATTTTCCAGAGTTAGTGCTTGGAAAATCAAA
* * *
353684 GATAGAAATGGTAAGAAGTTTCTATGTTGGATCTGATGCCCTGAGTGTAGTATTTTTGTTTGTAA
66 GATAGAAATGGTAAGAAGTTTCTATGTTGGATCTAATGCCCTGAGTGTAATATTTTTGTTTGAAA
*
353749 ACTTGTAATTTTTTTGAATATATTGATTAATAAAATAATTCATGGATTACATTAATTATACTTTA
131 ACTTGTAATTTTTTTGAATAGATTGATTAATAAAATAATTCATGGATTACATTAATTATACTTTA
* *
353814 TATAATTGTCCTTATGTGGTTTTTGCATGCAAAGCAAAATAGAAGTAAATATTGGCTTAC
196 TATAATTGTCCTCATGTGGTTTTTGCATGCAAAGCAAAATAGAAGCAAATATTGGCTTAC
353874 TTCATATCTTTCAGTGATTTTTTACAATATTTGGATTTTCCAGAGTTAGTGCTTGGAAAATCAAA
1 TTCATATCTTTCAGTGATTTTTTACAATATTTGGATTTTCCAGAGTTAGTGCTTGGAAAATCAAA
* *
353939 GATAGAAATGGTAAGAGGTTTCTAGTGTTGGATCTAATGCCCTGAGTGTAATATTTTTTTTTGAA
66 GATAGAAATGGTAAGAAGTTTCTA-TGTTGGATCTAATGCCCTGAGTGTAATATTTTTGTTTGAA
* *
354004 AACTTGTAATTTTTTTGAATAGATTGGTTAATAAAATAATTCATGGATTATATTAATTATACTTT
130 AACTTGTAATTTTTTTGAATAGATTGATTAATAAAATAATTCATGGATTACATTAATTATACTTT
354069 ATATAATTGTCCTCATGTGGTTTTTGCATGCAAAGCAAAATAGAAGCAAATATTGGCTTAC
195 ATATAATTGTCCTCATGTGGTTTTTGCATGCAAAGCAAAATAGAAGCAAATATTGGCTTAC
354130 T
1 T
354131 GGTTGTCTAA
Statistics
Matches: 244, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
255 86 0.35
256 158 0.65
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.42
Consensus pattern (255 bp):
TTCATATCTTTCAGTGATTTTTTACAATATTTGGATTTTCCAGAGTTAGTGCTTGGAAAATCAAA
GATAGAAATGGTAAGAAGTTTCTATGTTGGATCTAATGCCCTGAGTGTAATATTTTTGTTTGAAA
ACTTGTAATTTTTTTGAATAGATTGATTAATAAAATAATTCATGGATTACATTAATTATACTTTA
TATAATTGTCCTCATGTGGTTTTTGCATGCAAAGCAAAATAGAAGCAAATATTGGCTTAC
Found at i:355400 original size:13 final size:13
Alignment explanation
Indices: 355366--355456 Score: 85
Period size: 13 Copynumber: 7.1 Consensus size: 13
355356 TCTATTTCCT
*
355366 TATAATCAATTCA
1 TATAATCATTTCA
355379 TATAA-CATTTCA
1 TATAATCATTTCA
*
355391 TGTAATCATTTCA
1 TATAATCATTTCA
* **
355404 TATAACCATTTTG
1 TATAATCATTTCA
*
355417 TATAACCATTTCA
1 TATAATCATTTCA
* *
355430 TCTAAACATTTCA
1 TATAATCATTTCA
* *
355443 TTTTATCATTTCA
1 TATAATCATTTCA
355456 T
1 T
355457 TTACACATTT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
12 10 0.16
13 54 0.84
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (13 bp):
TATAATCATTTCA
Found at i:355413 original size:26 final size:25
Alignment explanation
Indices: 355366--355466 Score: 94
Period size: 26 Copynumber: 3.9 Consensus size: 25
355356 TCTATTTCCT
*
355366 TATAATCAATTCATATAACATTTCA
1 TATAATCATTTCATATAACATTTCA
* **
355391 TGTAATCATTTCATATAACCATTTTG
1 TATAATCATTTCATATAA-CATTTCA
* *
355417 TATAACCATTTCATCTAAACATTTCA
1 TATAATCATTTCATAT-AACATTTCA
* * *
355443 TTTTATCATTTCATTTACACATTT
1 TATAATCATTTCATATA-ACATTT
355467 AGCACAGAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
25 17 0.28
26 41 0.68
27 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.46
Consensus pattern (25 bp):
TATAATCATTTCATATAACATTTCA
Found at i:355465 original size:13 final size:12
Alignment explanation
Indices: 355375--355466 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
355365 TTATAATCAA
*
355375 TTCATATAACAT
1 TTCATTTAACAT
*
355387 TTCATGTAATCAT
1 TTCATTTAA-CAT
*
355400 TTCATATAACCAT
1 TTCATTTAA-CAT
** *
355413 TTTGTATAACCAT
1 TTCATTTAA-CAT
*
355426 TTCATCTAAACAT
1 TTCAT-TTAACAT
*
355439 TTCATTTTATCAT
1 TTCA-TTTAACAT
355452 TTCATTTACACAT
1 TTCATTTA-ACAT
355465 TT
1 TT
355467 AGCACAGAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
12 12 0.19
13 49 0.77
14 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (12 bp):
TTCATTTAACAT
Found at i:355690 original size:25 final size:25
Alignment explanation
Indices: 355626--355690 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
355616 CACGGGAAAG
* *
355626 ATGCTCATACAAGCTGTAACTGTAA
1 ATGCTCACACAAGCTATAACTGTAA
* * *
355651 TTGCTCTCA-AGAGCTATATCTGTAA
1 ATGCTCACACA-AGCTATAACTGTAA
355676 ATGCTCACACAAGCT
1 ATGCTCACACAAGCT
355691 GCGAAATGGG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
24 1 0.03
25 29 0.94
26 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (25 bp):
ATGCTCACACAAGCTATAACTGTAA
Found at i:375282 original size:21 final size:21
Alignment explanation
Indices: 375236--375283 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
375226 TAATTTTGTG
*
375236 ATATTTTTATAAATTAGCTTT
1 ATATTTTTATAAATTAGATTT
*
375257 ATATTTTTACTAAATTATATTT
1 ATATTTTTA-TAAATTAGATTT
375279 -TATTT
1 ATATTT
375284 ATTTCCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATTTTTATAAATTAGATTT
Found at i:380437 original size:546 final size:547
Alignment explanation
Indices: 379395--380487 Score: 1715
Period size: 546 Copynumber: 2.0 Consensus size: 547
379385 CGAACGACGA
* * *
379395 AAGCCAAAAATGGGGCTGTCGATGCCACACGTCCGTGTACCAGGCCGTGTGGCAGGCCGTGTGTG
1 AAGCCAAAAATGGGGCTATCGACGCCACACGTCCGTGTACCAGGCCGTGTGGCAGACCGTGTGTG
* **
379460 ACACATAATTGTGTAAGTCACTAACTTGGGTCACACGGGCATGTGCCCAGACTGTGCAAAGGACT
66 ACACATAATCGTGTAAGTCACTAACTTGGGTCACACGAACATGTGCCCAGACTGTGCAAAGGACT
* * *
379525 GATTTTTTATTAGAGTTACGCGGGAGTGTGACACAACCGTGTGGGCCACACGGGCCAGCCATTTA
131 GATTTTTTATTAGAGTTACACAGGAGTGTGACACAACCATGTGGGCCACACGGGCCAGCCATTTA
* ** *
379590 GGCAATGCGAATCCATACGGGTGTGTGGGCCAAAATTCTAAAATTTTCCCTAGGGCCATAAATGT
196 GGCAATGCGAATCCACACGGACGTGTGGGCCAAAATTCTAAAATTTTCCCTAGGGCCATAAACGT
*
379655 TTTTTGGATCAAACGCAAGCCTTCCATAGGGTCTGTATGATATGGATTAAGTTATAAAACTCGAA
261 TGTTTGGATCAAACGCAAGCCTTCCATAGGGTCTGTATGATATGGATTAAGTTATAAAACTCGAA
* * * * *
379720 ATCTGGTTATCTGTTAGTGTGTAATTTGTTATTTATACGTATGTGTAATATGACATAAGTTAAGT
326 ACCTGGTGATCTGTTAGTGTATAATTTGTTATCTATACGTATGTCTAATATGACATAAGTTAAGT
* * *
379785 AGTATGATTTGTTAGCGTATAATGTGCTTTTGCTTGGGGTGTGTTTAAGGTATGTGATTTATTCA
391 AGTATGATTTGTTAGCATATAATGTGCTTTTGCTTGGGATGTGTCTAAGGTATGTGATTTATTCA
379850 GGTATGACCCGTGTTCTATTAATTTTGATAGTACATTTTTGTGTTACTTTGTTGGATGAGAACAT
456 GGTATGACCCGTGTTCTATTAATTTTGATAGTACATTTTTGTGTTACTTTGTTGGATGAGAACAT
379915 GCAATATCTGAATATGTTGATTTGTCT
521 GCAATATCTGAATATGTTGATTTGTCT
* *
379942 AAGCCAAAAATGGGGCTATCGACGCCACACAG-CCGTGTACTAGGCCGTGTGGTAGACCGTGTGT
1 AAGCCAAAAATGGGGCTATCGACGCCACAC-GTCCGTGTACCAGGCCGTGTGGCAGACCGTGTGT
* * * * * * *
380006 GACACATAGTCGTGTGAGTCACTAATTTGGGTCACACGAACGTGTGCCTAGACTGTGCAAGGGAT
65 GACACATAATCGTGTAAGTCACTAACTTGGGTCACACGAACATGTGCCCAGACTGTGCAAAGGAC
* * * *
380071 TGATTTTTTATTAGAGTTACACAGGCGTGTGACACGACTATGTGGGCTACAC-GGCCAGCCATTT
130 TGATTTTTTATTAGAGTTACACAGGAGTGTGACACAACCATGTGGGCCACACGGGCCAGCCATTT
** * * *
380135 AGGCTGTGTGAATTCACACGGACGTGTGGGCCGAAAA-TCTAAAATTTTCCCTAGGGCTATAAAC
195 AGGCAATGCGAATCCACACGGACGTGTGGGCC-AAAATTCTAAAATTTTCCCTAGGGCCATAAAC
* * * *
380199 GTTGTTTGGATCGAACGCAAGCTTTCCGTAGGGTCTGTATGATATGTATTAAGTTATAAAACTCG
259 GTTGTTTGGATCAAACGCAAGCCTTCCATAGGGTCTGTATGATATGGATTAAGTTATAAAACTCG
*
380264 AAACCTGGTGATCTGTTAGTGTATAATTTGTTATCTGTACGTATGTCTAATATGACATAAGTTAA
324 AAACCTGGTGATCTGTTAGTGTATAATTTGTTATCTATACGTATGTCTAATATGACATAAGTTAA
380329 GTAGTATGATTTGTTAGCATATAATGTGCTTTTGCTTGGGATGTGTCTAAGGTATGTGATTTATT
389 GTAGTATGATTTGTTAGCATATAATGTGCTTTTGCTTGGGATGTGTCTAAGGTATGTGATTTATT
* * *
380394 CAGGTATGACCCGTGTTCTGTTAATTTTGATGGTACGTTTTTGTGTTACTTTGTTGGATGAGAAC
454 CAGGTATGACCCGTGTTCTATTAATTTTGATAGTACATTTTTGTGTTACTTTGTTGGATGAGAAC
380459 ATGCAATATCTGAATATGTTGATTTGTCT
519 ATGCAATATCTGAATATGTTGATTTGTCT
380488 GATATTGATT
Statistics
Matches: 496, Mismatches: 48, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
546 334 0.67
547 161 0.32
548 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (547 bp):
AAGCCAAAAATGGGGCTATCGACGCCACACGTCCGTGTACCAGGCCGTGTGGCAGACCGTGTGTG
ACACATAATCGTGTAAGTCACTAACTTGGGTCACACGAACATGTGCCCAGACTGTGCAAAGGACT
GATTTTTTATTAGAGTTACACAGGAGTGTGACACAACCATGTGGGCCACACGGGCCAGCCATTTA
GGCAATGCGAATCCACACGGACGTGTGGGCCAAAATTCTAAAATTTTCCCTAGGGCCATAAACGT
TGTTTGGATCAAACGCAAGCCTTCCATAGGGTCTGTATGATATGGATTAAGTTATAAAACTCGAA
ACCTGGTGATCTGTTAGTGTATAATTTGTTATCTATACGTATGTCTAATATGACATAAGTTAAGT
AGTATGATTTGTTAGCATATAATGTGCTTTTGCTTGGGATGTGTCTAAGGTATGTGATTTATTCA
GGTATGACCCGTGTTCTATTAATTTTGATAGTACATTTTTGTGTTACTTTGTTGGATGAGAACAT
GCAATATCTGAATATGTTGATTTGTCT
Found at i:386813 original size:18 final size:17
Alignment explanation
Indices: 386743--386813 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 17
386733 CCACATCAGC
* *
386743 AATTAATTAATTTTTAA
1 AATTAAATAATTTTAAA
386760 AATTAAAT-ATTATTGAAA
1 AATTAAATAATT-TT-AAA
*
386778 AATATAAAAAAATTTTAAA
1 AAT-T-AAATAATTTTAAA
*
386797 AATTAATTAATTGTTAA
1 AATTAAATAATT-TTAA
386814 TGTGGCAGCC
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
16 3 0.07
17 15 0.35
18 10 0.23
19 7 0.16
20 5 0.12
21 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AATTAAATAATTTTAAA
Found at i:388779 original size:5 final size:5
Alignment explanation
Indices: 388769--388813 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
388759 TGTATTAAGG
388769 ATATA ATATA ATATA ATATA ATATA ATATA ATATA A-A-A ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
388814 TAAATTGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 34 0.89
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:404433 original size:24 final size:23
Alignment explanation
Indices: 404397--404447 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
404387 TTTAAGGGTT
* *
404397 TTTTTTATCATTTTGTTTAAAAATA
1 TTTTTAATCA-TTT-TTTAAAAAAA
404422 TTTTTAAT-ATTTTTTAAAAAAA
1 TTTTTAATCATTTTTTAAAAAAA
404444 TTTT
1 TTTT
404448 AGAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.54
23 3 0.12
24 1 0.04
25 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTTAATCATTTTTTAAAAAAA
Found at i:412155 original size:22 final size:22
Alignment explanation
Indices: 412108--412161 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
412098 ATATGCTAGC
**
412108 ATTTTAATTTAGTATTTCTATC
1 ATTTTAATTTAGTATTTCTAAA
*
412130 ATTTTCAATTTGGT-TTTCTAAA
1 ATTTT-AATTTAGTATTTCTAAA
412152 A-TTTAATTTA
1 ATTTTAATTTA
412162 TCTTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 5 0.19
21 3 0.11
22 12 0.44
23 7 0.26
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.57
Consensus pattern (22 bp):
ATTTTAATTTAGTATTTCTAAA
Found at i:415403 original size:21 final size:20
Alignment explanation
Indices: 415365--415422 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
415355 GGTTATCCCG
* *
415365 GCCCTGTGGGTGGAGGCACAT
1 GCCCTGTGGAT-GAGGCACAC
415386 GCCTCTGTGGATGAGGCACAC
1 GCC-CTGTGGATGAGGCACAC
*
415407 GCCCATGCGGATGAGG
1 GCCC-TGTGGATGAGG
415423 GATATGGTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 24 0.75
22 7 0.22
ACGTcount: A:0.17, C:0.26, G:0.40, T:0.17
Consensus pattern (20 bp):
GCCCTGTGGATGAGGCACAC
Found at i:423162 original size:16 final size:18
Alignment explanation
Indices: 423129--423162 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
423119 TCAAGTTGTA
423129 TCAGAACAAGAGCTTGAG
1 TCAGAACAAGAGCTTGAG
423147 TCAGAAC-AGA-CTTGAG
1 TCAGAACAAGAGCTTGAG
423163 CTTCTTGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (18 bp):
TCAGAACAAGAGCTTGAG
Found at i:428458 original size:2 final size:2
Alignment explanation
Indices: 428451--428475 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
428441 TGGAATGGGT
428451 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
428476 TGTAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:432662 original size:55 final size:55
Alignment explanation
Indices: 432578--432708 Score: 181
Period size: 55 Copynumber: 2.4 Consensus size: 55
432568 TTAATGAAAG
* *
432578 CAAGTTAATGAGTTACACGGGCTAGTCACAAAGGCGTGTTGCTGGCCGTGTGACC
1 CAAGTCAATGAGTTACACGGGCTAGTCACAAAGGCGTGTGGCTGGCCGTGTGACC
* * * ** * *
432633 CAAGTCAGTGAGTTACATGGGTTAGTCACACGGGGGTGTGGTTGGCCGTGTGACC
1 CAAGTCAATGAGTTACACGGGCTAGTCACAAAGGCGTGTGGCTGGCCGTGTGACC
432688 CAAGTCAATGAGTTACACGGG
1 CAAGTCAATGAGTTACACGGG
432709 GTCAGACATG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.24
Consensus pattern (55 bp):
CAAGTCAATGAGTTACACGGGCTAGTCACAAAGGCGTGTGGCTGGCCGTGTGACC
Found at i:435587 original size:34 final size:31
Alignment explanation
Indices: 435531--435598 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 31
435521 CAATTCAATA
* * *
435531 ACAGTTCAGTTCAGTTGTGCCTTTGCTCATT
1 ACAGTTCAGTTCAGTTGGGCCTTAGCCCATT
435562 ACAGTATCAGTATCAGTGTGGGCCTTAGCCCATT
1 ACAGT-TCAGT-TCAGT-TGGGCCTTAGCCCATT
435596 ACA
1 ACA
435599 CTGACAGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 5 0.16
32 5 0.16
33 5 0.16
34 16 0.52
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (31 bp):
ACAGTTCAGTTCAGTTGGGCCTTAGCCCATT
Found at i:435921 original size:27 final size:27
Alignment explanation
Indices: 435887--435950 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
435877 AATCATACAA
435887 TCATTTTATAACATAGGGGCATAACAG
1 TCATTTTATAACATAGGGGCATAACAG
** ** *
435914 TCATTTTACCATGTGGGGGCATAACAG
1 TCATTTTATAACATAGGGGCATAACAG
*
435941 TCAGTTTATA
1 TCATTTTATA
435951 TCAGTTTGGG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (27 bp):
TCATTTTATAACATAGGGGCATAACAG
Found at i:437028 original size:44 final size:44
Alignment explanation
Indices: 436965--437053 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
436955 TGCCACCAAT
*
436965 CGGGATAACCTCTCCAATCCCATAATCTTCTCCTAAAATGACTC
1 CGGGATAACCTCTCCAATCCCATAATCTTCTCCTAAAATCACTC
437009 CGGGATAACCTC-CCTAATCCCATAATCTTCTCCTAAAATCACTC
1 CGGGATAACCTCTCC-AATCCCATAATCTTCTCCTAAAATCACTC
437053 C
1 C
437054 AACCTTCCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
43 2 0.05
44 41 0.95
ACGTcount: A:0.29, C:0.36, G:0.08, T:0.27
Consensus pattern (44 bp):
CGGGATAACCTCTCCAATCCCATAATCTTCTCCTAAAATCACTC
Found at i:444814 original size:23 final size:23
Alignment explanation
Indices: 444788--444840 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
444778 AAGAAAGGTG
**
444788 ACTGTAATATGCCGAAAATTACT
1 ACTGTAATACCCCGAAAATTACT
*
444811 ACTGCAATACCCCGAAAATTACT
1 ACTGTAATACCCCGAAAATTACT
*
444834 ACAGTAA
1 ACTGTAA
444841 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.25
Consensus pattern (23 bp):
ACTGTAATACCCCGAAAATTACT
Found at i:454853 original size:44 final size:44
Alignment explanation
Indices: 454439--454826 Score: 614
Period size: 44 Copynumber: 8.8 Consensus size: 44
454429 TAAGTTCTAT
* *
454439 CTCCCTGAACAGTAGTGGAATAGGTGGAAGATTGTAAGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTATGTCCTAG
*
454483 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTAAGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTATGTCCTAG
*
454527 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTATGTCCTAG
* * * *
454571 CTCTCTGAACAGTAGTGGAATAGGTGGAAGACTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTATGTCCTAG
* *
454615 CTCCCTGAACAGCAGTGGAATAGGTGGAAAATTGTATGTCCTAT
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTATGTCCTAG
* *
454659 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTATAAGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTATGTCCTAG
** *
454703 CTCCCTGAACAGCAGTGGAATAGGTCAAAGATTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTATGTCCTAG
*
454747 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTATGTCCTAG
* *
454791 CTCCCTGAATAGTAGTGGAATAGGTGGAAGATTGTA
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTA
454827 GATCCTGTCT
Statistics
Matches: 318, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 318 1.00
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (44 bp):
CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGTATGTCCTAG
Found at i:455302 original size:21 final size:21
Alignment explanation
Indices: 455276--455320 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
455266 ATCGGGCAAA
455276 ATTGGCCTTTTTTAGTCTTTG
1 ATTGGCCTTTTTTAGTCTTTG
455297 ATTGGCCTTTTTTAGTCTTTG
1 ATTGGCCTTTTTTAGTCTTTG
455318 ATT
1 ATT
455321 CATTCCCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.11, C:0.13, G:0.18, T:0.58
Consensus pattern (21 bp):
ATTGGCCTTTTTTAGTCTTTG
Found at i:462329 original size:34 final size:34
Alignment explanation
Indices: 462268--462334 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
462258 TCAGTTCAAT
*
462268 TGGGCCTTTACCAATTACAGTATCAGTATCAGTG
1 TGGGCCTTTACCAATTACAGTATCAGTAACAGTG
*
462302 TGGGCC-TTAGCCCATTACAGTGA-CAGTAACAGT
1 TGGGCCTTTA-CCAATTACAGT-ATCAGTAACAGT
462335 TCAGACATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 3 0.10
34 25 0.86
35 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (34 bp):
TGGGCCTTTACCAATTACAGTATCAGTAACAGTG
Found at i:462623 original size:27 final size:27
Alignment explanation
Indices: 462571--462652 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
462561 ACAGTCATAC
* *
462571 ATAACATAA-AGCAT-ACAATCATTTT
1 ATAACATAAGGGCATAACAGTCATTTT
*
462596 ATAACATAGGGGCATAACAGTCATTTT
1 ATAACATAAGGGCATAACAGTCATTTT
** *
462623 ACCACGTAAGGGCATAACAGTCATTTT
1 ATAACATAAGGGCATAACAGTCATTTT
462650 ATA
1 ATA
462653 TCAGTTTCAG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
25 8 0.17
26 4 0.09
27 34 0.74
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (27 bp):
ATAACATAAGGGCATAACAGTCATTTT
Found at i:463739 original size:44 final size:44
Alignment explanation
Indices: 463676--463764 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
463666 CCCACCAAAT
*
463676 CGGGATAACCTCCCCAATCCCATAATCTTCT-CTTAAATGCACTC
1 CGGGATAACCTCCCCAATCCCATAATCTTCTCCTAAAAT-CACTC
463720 CGGGATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTC
1 CGGGATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTC
463764 C
1 C
463765 AACCTTTCCA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 37 0.86
45 6 0.14
ACGTcount: A:0.28, C:0.38, G:0.08, T:0.26
Consensus pattern (44 bp):
CGGGATAACCTCCCCAATCCCATAATCTTCTCCTAAAATCACTC
Found at i:465829 original size:16 final size:16
Alignment explanation
Indices: 465810--465840 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
465800 TTGAAAGAGT
465810 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
465826 TTTCAAATTTATATG
1 TTTCAAATATATATG
465841 CTCCAAGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:465917 original size:23 final size:23
Alignment explanation
Indices: 465874--465920 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
465864 GGTAAGAAAA
**
465874 TTTTAATTTAACATGTTTAATTT
1 TTTTAATTTAACATGAATAATTT
*
465897 TTTTAATTTAACTTGAATAATTT
1 TTTTAATTTAACATGAATAATTT
465920 T
1 T
465921 ATTCTATTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTAATTTAACATGAATAATTT
Found at i:474067 original size:22 final size:22
Alignment explanation
Indices: 474039--474082 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
474029 GCCTGTCGAT
474039 ACAAATTTCAACAAAAGAAGAG
1 ACAAATTTCAACAAAAGAAGAG
474061 ACAAATTTCAACAAAAGAAGAG
1 ACAAATTTCAACAAAAGAAGAG
474083 TTAGGGAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (22 bp):
ACAAATTTCAACAAAAGAAGAG
Found at i:474205 original size:23 final size:23
Alignment explanation
Indices: 474143--474207 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
474133 ATAGGATTTA
*
474143 CTTGTTTGGTAGTGGTGATGCGT
1 CTTGTTTGGTAGTGGTGATACGT
* * *
474166 C-TGTTAT-TTATGGGGTGATACTT
1 CTTGTT-TGGTA-GTGGTGATACGT
474189 CTTGTTTGGTAGTGGTGAT
1 CTTGTTTGGTAGTGGTGAT
474208 GTGGCAAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
22 6 0.19
23 20 0.62
24 6 0.19
ACGTcount: A:0.12, C:0.08, G:0.34, T:0.46
Consensus pattern (23 bp):
CTTGTTTGGTAGTGGTGATACGT
Found at i:493232 original size:33 final size:30
Alignment explanation
Indices: 493184--493297 Score: 85
Period size: 33 Copynumber: 3.7 Consensus size: 30
493174 TAACAACACA
*
493184 TAATAACAATGAATAAGACATCAATAAATAACG
1 TAATAACAATAAATAA-A-A-CAATAAATAACG
*
493217 TAATAACGATAAATAAAACAATAAATAAC-
1 TAATAACAATAAATAAAACAATAAATAACG
*
493246 -AAT-A-AATAACA-ACAACAATAAATAACAACG
1 TAATAACAATAA-ATAAAACAATAAAT---AACG
*
493276 ATAATAACAATAAATAATACAA
1 -TAATAACAATAAATAAAACAA
493298 CACATAATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
26 15 0.23
27 2 0.03
28 3 0.05
29 3 0.05
30 11 0.17
31 1 0.02
32 4 0.06
33 16 0.25
34 10 0.15
ACGTcount: A:0.64, C:0.12, G:0.04, T:0.19
Consensus pattern (30 bp):
TAATAACAATAAATAAAACAATAAATAACG
Found at i:493243 original size:22 final size:23
Alignment explanation
Indices: 493218--493292 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
493208 TAAATAACGT
*
493218 AATAACGATAAATAA-AACAATA
1 AATAACAATAAATAACAACAATA
493240 AATAACAATAAATAACAACAACAATA
1 AATAACAATAAAT---AACAACAATA
** *
493266 AATAACAA-CGATAATAACAATA
1 AATAACAATAAATAACAACAATA
493288 AATAA
1 AATAA
493293 TACAACACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 26 0.58
25 4 0.09
26 15 0.33
ACGTcount: A:0.68, C:0.12, G:0.03, T:0.17
Consensus pattern (23 bp):
AATAACAATAAATAACAACAATA
Found at i:493254 original size:26 final size:27
Alignment explanation
Indices: 493205--493273 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 27
493195 AATAAGACAT
493205 CAATAAATAACGTAATAACGATAA-ATAAAA
1 CAATAAATAAC--AATAAC-ATAACA-AAAA
*
493235 CAATAAATAACAATAA-ATAACAACAA
1 CAATAAATAACAATAACATAACAAAAA
493261 CAATAAATAACAA
1 CAATAAATAACAA
493274 CGATAATAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 20 0.54
27 1 0.03
28 5 0.14
30 11 0.30
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.17
Consensus pattern (27 bp):
CAATAAATAACAATAACATAACAAAAA
Found at i:493281 original size:12 final size:12
Alignment explanation
Indices: 493228--493307 Score: 65
Period size: 12 Copynumber: 6.4 Consensus size: 12
493218 AATAACGATA
493228 AATAA-AACAAT
1 AATAACAACAAT
*
493239 AAATAACAATAAAT
1 -AATAACAA-CAAT
*
493253 AACAACAACAAT
1 AATAACAACAAT
*
493265 AAATAACAACGAT
1 -AATAACAACAAT
*
493278 AATAACAATAAAT
1 AATAACAA-CAAT
493291 AAT-ACAACACAT
1 AATAACAACA-AT
493303 AATAA
1 AATAA
493308 GACAATATTA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
11 1 0.02
12 25 0.46
13 25 0.46
14 3 0.06
ACGTcount: A:0.68, C:0.14, G:0.01, T:0.17
Consensus pattern (12 bp):
AATAACAACAAT
Found at i:493282 original size:16 final size:16
Alignment explanation
Indices: 493243--493274 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
493233 AACAATAAAT
493243 AACAATAAATAACAAC
1 AACAATAAATAACAAC
493259 AACAATAAATAACAAC
1 AACAATAAATAACAAC
493275 GATAATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.19, G:0.00, T:0.12
Consensus pattern (16 bp):
AACAATAAATAACAAC
Found at i:493449 original size:15 final size:15
Alignment explanation
Indices: 493429--493460 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
493419 ACAAGGTTGT
*
493429 AATAATAGTAATAAC
1 AATAATAATAATAAC
493444 AATAATAATAATAAC
1 AATAATAATAATAAC
493459 AA
1 AA
493461 CAACAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:495172 original size:132 final size:132
Alignment explanation
Indices: 494956--495428 Score: 741
Period size: 132 Copynumber: 3.6 Consensus size: 132
494946 GCTGCCTTCT
*
494956 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTACTG-CCTA
1 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCC-A
* * *
495020 GGGAGATAGGACTGGTGGCTTAAATCAGCTTCCTTACTACCTTGGGAAGATAAGATTCACCGTAT
65 GGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCT
495085 TTG
130 TTG
* * *
495088 ATCTGCTCCACTACTATTTAAGGAGACAAGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
1 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
* * *
495153 GGAGATAGGACCGGCGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATCTT
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTT
495218 TG
131 TG
* * * * *
495220 ATCTGCTCCACTAATGCTTAGGGAGACAGGATGTACAATCTTCAACCTAATCCACTGTTGTCCAG
1 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
*
495285 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTTACCGTCTT
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTT
495350 TG
131 TG
* * * * *
495352 ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGTTGTACAA
1 ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
495417 GGAGATAGGACT
66 GGAGATAGGACT
495429 TACAATCTTC
Statistics
Matches: 312, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
132 310 0.99
133 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
ATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCAACCTATTCCACTGCTGTCCAG
GGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTT
TG
Found at i:495406 original size:44 final size:45
Alignment explanation
Indices: 495358--495471 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 45
495348 TTTGATCTAC
* * *
495358 TCCACTACTGCTTAGGGAGACAGGATC-TACAATCTTCAACCTAT
1 TCCACTGCTGCTTAAGGAGATAGGATCTTACAATCTTCAACCTAT
* *
495402 TCCACTGTTG-TACAAGGAGATAGGA-CTTACAATCTTCAACCTAT
1 TCCACTGCTGCT-TAAGGAGATAGGATCTTACAATCTTCAACCTAT
*
495446 TCCACTGCTGCCTAAGGAGATAGGAT
1 TCCACTGCTGCTTAAGGAGATAGGAT
495472 TTGCTATCTT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
43 2 0.03
44 56 0.97
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (45 bp):
TCCACTGCTGCTTAAGGAGATAGGATCTTACAATCTTCAACCTAT
Found at i:496773 original size:43 final size:44
Alignment explanation
Indices: 496733--496821 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
496723 ATTTTTCATT
*
496733 TTCATC-ATTTTTCGACTCAAAGCGCCCTTTGCGGGTTTTCACC
1 TTCATCTATTTTTCGACTCAAAGCGCCCTTTGCAGGTTTTCACC
* * *
496776 TTGATCTTTTTTTTGACTCAAAGCGCCCTTTGCAGGTTTTCACC
1 TTCATCTATTTTTCGACTCAAAGCGCCCTTTGCAGGTTTTCACC
496820 TT
1 TT
496822 GGTCTCTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 5 0.12
44 36 0.88
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.42
Consensus pattern (44 bp):
TTCATCTATTTTTCGACTCAAAGCGCCCTTTGCAGGTTTTCACC
Found at i:507910 original size:15 final size:15
Alignment explanation
Indices: 507890--507921 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
507880 ACAAGGTTGT
*
507890 AATAATAGTAATAAC
1 AATAATAATAATAAC
507905 AATAATAATAATAAC
1 AATAATAATAATAAC
507920 AA
1 AA
507922 CAACAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:510593 original size:26 final size:27
Alignment explanation
Indices: 510531--510611 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 27
510521 GAAGCACGTT
*
510531 AGGACAATCTAATGTGGGAAGTCCGCA
1 AGGACAATCTAATGTGGGAAGTCCACA
* * *
510558 AGAACCATCTATTGT-GGAAGTCCACA
1 AGGACAATCTAATGTGGGAAGTCCACA
* * *
510584 AGGACTATCTGATATATGGGAAATCCAC
1 AGGACAATCT-A-ATGTGGGAAGTCCAC
510612 CGGGGCTATC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
26 18 0.43
27 13 0.31
28 2 0.05
29 9 0.21
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (27 bp):
AGGACAATCTAATGTGGGAAGTCCACA
Found at i:518603 original size:16 final size:16
Alignment explanation
Indices: 518582--518630 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
518572 TTCGCTGTAT
*
518582 TGGAATAGAGGCGTAA
1 TGGAATAGAGGAGTAA
*
518598 TGGAATAGAGGTGTAA
1 TGGAATAGAGGAGTAA
518614 TGGAATAGAGGAGTAA
1 TGGAATAGAGGAGTAA
518630 T
1 T
518631 AGCAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGAGTAA
Found at i:518660 original size:45 final size:44
Alignment explanation
Indices: 518609--518699 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 44
518599 GGAATAGAGG
518609 TGTAATGGAATAGAGGAGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGAGTAATAG-AAATC-ATGTGTTTGGTTGAA
* * *
518654 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGAGTAATAGAAATCATGTGTTTGGTTGAA
518698 TG
1 TG
518700 GNNNNNNNNN
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.43
45 23 0.55
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGAGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:520254 original size:6 final size:6
Alignment explanation
Indices: 520243--520268 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
520233 TAGTTTGAAC
520243 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
520269 AATTTCGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:520676 original size:13 final size:13
Alignment explanation
Indices: 520658--520682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
520648 ATCAAATTTG
520658 TATGTACTCTTTA
1 TATGTACTCTTTA
520671 TATGTACTCTTT
1 TATGTACTCTTT
520683 CACTAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:520837 original size:21 final size:21
Alignment explanation
Indices: 520811--520870 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
520801 TTTCTATTAA
520811 AAAAACATATAACCTATTAGT
1 AAAAACATATAACCTATTAGT
520832 AAAAACATATAACCTATTAGT
1 AAAAACATATAACCTATTAGT
*
520853 AAAAACATATAACATATT
1 AAAAACATATAACCTATT
520871 TTAAATTCCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAAACATATAACCTATTAGT
Found at i:521223 original size:29 final size:29
Alignment explanation
Indices: 521189--521257 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
521179 AAACAAATGC
521189 AACAATTTCCAGTTTCATTGAAAACAACA
1 AACAATTTCCAGTTTCATTGAAAACAACA
**
521218 AACAATTTCCAGTTTCATTGAAAACTGCA
1 AACAATTTCCAGTTTCATTGAAAACAACA
*
521247 GACAATTTCCA
1 AACAATTTCCA
521258 TTGCAACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.29
Consensus pattern (29 bp):
AACAATTTCCAGTTTCATTGAAAACAACA
Found at i:531158 original size:11 final size:11
Alignment explanation
Indices: 531137--531173 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
531127 TAAGTAGATT
531137 AATAT-ATAAA
1 AATATAATAAA
531147 AATATAATAAA
1 AATATAATAAA
531158 AATATAATAAA
1 AATATAATAAA
531169 AATAT
1 AATAT
531174 TAAACTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATATAATAAA
Found at i:531170 original size:22 final size:23
Alignment explanation
Indices: 531137--531197 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
531127 TAAGTAGATT
531137 AATAT-ATAAAAATATAATAAA-
1 AATATAATAAAAATATAATAAAC
531158 AATATAATAAAAATAT--TAAAC
1 AATATAATAAAAATATAATAAAC
531179 TAAT-TAATAAAAAATATAA
1 -AATATAAT-AAAAATATAA
531198 ACCGTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.12
21 9 0.26
22 21 0.62
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AATATAATAAAAATATAATAAAC
Found at i:533738 original size:20 final size:18
Alignment explanation
Indices: 533693--533741 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
533683 TATAATTCTT
*
533693 AAATTTTTAGTAAATTTA
1 AAATTTTTATTAAATTTA
*
533711 AATTTTTTTATTAAAGTTTA
1 AA-ATTTTTATTAAA-TTTA
533731 ATAATTTTTAT
1 A-AATTTTTAT
533742 AATTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 10 0.40
20 12 0.48
21 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
AAATTTTTATTAAATTTA
Found at i:533745 original size:9 final size:9
Alignment explanation
Indices: 533731--533774 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
533721 TTAAAGTTTA
533731 ATAATTTTT
1 ATAATTTTT
533740 ATAATTTTT
1 ATAATTTTT
*
533749 ATTGATTTTT
1 A-TAATTTTT
533759 AT--TTTTT
1 ATAATTTTT
533766 ATAATTTTT
1 ATAATTTTT
533775 TTGTCACATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
7 7 0.23
9 16 0.52
10 8 0.26
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (9 bp):
ATAATTTTT
Found at i:537789 original size:3 final size:3
Alignment explanation
Indices: 537781--537817 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
537771 AGTATGGGTG
* *
537781 TGA TGA TGA TGA TGA TGA TGA TGA CGA CGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
537818 AGCGATGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:548871 original size:28 final size:28
Alignment explanation
Indices: 548801--548873 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
548791 CGACATACAT
* *
548801 TAACAATCTGGGCCTGAGCTCTAAGCAG
1 TAACAGTCTGGGCCTTAGCTCTAAGCAG
**
548829 TAACAGTCTAAGCCTTAGC-CTAAAGCAG
1 TAACAGTCTGGGCCTTAGCTCT-AAGCAG
*
548857 TAACAGTGTGGGCCTTA
1 TAACAGTCTGGGCCTTA
548874 ACCCAATACA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
27 2 0.05
28 35 0.95
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (28 bp):
TAACAGTCTGGGCCTTAGCTCTAAGCAG
Found at i:549241 original size:27 final size:27
Alignment explanation
Indices: 549212--549444 Score: 290
Period size: 27 Copynumber: 8.6 Consensus size: 27
549202 CAACTCCTAG
* * * * *
549212 GGGTATTTCAATTATTTTACCTTTTGG
1 GGGTATTTCGATCATTTTACCCTTCGA
*
549239 GGGTATCTC-AGTCATTTTACCCTTCGA
1 GGGTATTTCGA-TCATTTTACCCTTCGA
* *
549266 GGGTATTTCGATCCTTTTACCCTTTGA
1 GGGTATTTCGATCATTTTACCCTTCGA
* *
549293 GGGTATTTTGGTCATTTTACCCTTCGA
1 GGGTATTTCGATCATTTTACCCTTCGA
*
549320 GGGAATTTCGATCATTTTACCCTTCGA
1 GGGTATTTCGATCATTTTACCCTTCGA
*
549347 GGGTATTTCGATGATTTTACCCTTCGA
1 GGGTATTTCGATCATTTTACCCTTCGA
*
549374 GGGTATTTCGGTCATTTTACCCTTCGA
1 GGGTATTTCGATCATTTTACCCTTCGA
* *
549401 GGGCATTT-TAGTCATTTTACCCTTCGA
1 GGGTATTTCGA-TCATTTTACCCTTCGA
*
549428 GGGCATTTCGATCATTT
1 GGGTATTTCGATCATTT
549445 GAAGCCCATT
Statistics
Matches: 179, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 176 0.98
28 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGTATTTCGATCATTTTACCCTTCGA
Found at i:553359 original size:16 final size:17
Alignment explanation
Indices: 553338--553370 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
553328 AAATTTGATC
553338 GTATTT-TATTTAATAA
1 GTATTTATATTTAATAA
*
553354 GTATTTATCTTTAATAA
1 GTATTTATATTTAATAA
553371 ATTAATAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (17 bp):
GTATTTATATTTAATAA
Found at i:553986 original size:25 final size:25
Alignment explanation
Indices: 553948--554003 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 25
553938 TTTCTCCTAA
553948 ATTTTAATTGTATTGAATTAATTAAT
1 ATTTTAATTGTATTGAATT-ATTAAT
553974 -TTTTCAATT-TATTGAATTATTAAT
1 ATTTT-AATTGTATTGAATTATTAAT
553998 ATTTTA
1 ATTTTA
554004 TACTGATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.25
25 17 0.61
26 4 0.14
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (25 bp):
ATTTTAATTGTATTGAATTATTAAT
Found at i:556094 original size:27 final size:27
Alignment explanation
Indices: 556056--556109 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
556046 TGTCCCAAAC
556056 ACTAGATTCAGTACTATTCAAAATGTT
1 ACTAGATTCAGTACTATTCAAAATGTT
556083 ACTAGATTCAGTACTATTCAAAATGTT
1 ACTAGATTCAGTACTATTCAAAATGTT
556110 CCTTGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (27 bp):
ACTAGATTCAGTACTATTCAAAATGTT
Found at i:557498 original size:19 final size:20
Alignment explanation
Indices: 557474--557515 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
557464 ATCTCAACCC
557474 TTCTCATCTCT-TCACTTCA
1 TTCTCATCTCTCTCACTTCA
* *
557493 TTCTCATTTCTCTCTCTTCA
1 TTCTCATCTCTCTCACTTCA
557513 TTC
1 TTC
557516 CCTTCCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.12, C:0.36, G:0.00, T:0.52
Consensus pattern (20 bp):
TTCTCATCTCTCTCACTTCA
Found at i:563666 original size:53 final size:53
Alignment explanation
Indices: 563586--563690 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
563576 CACACTTCAC
* * *
563586 CTTTATAAAGCATAAGTATTGACCTCACACGAAATATAAAATAGGAATATTAA
1 CTTTATAAAGCATAAGTACTGACCTCACACAAAATATAAAATAGAAATATTAA
* * *
563639 CTTTATAAAGCATAATTACTGGCCTCACACAAAATATAAACTAGAAATATTA
1 CTTTATAAAGCATAAGTACTGACCTCACACAAAATATAAAATAGAAATATTA
563691 CACACATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.29
Consensus pattern (53 bp):
CTTTATAAAGCATAAGTACTGACCTCACACAAAATATAAAATAGAAATATTAA
Found at i:572547 original size:12 final size:12
Alignment explanation
Indices: 572532--572582 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
572522 AGATTATGTG
572532 AAAAATTAAATA
1 AAAAATTAAATA
572544 AAAAATTAAAT-
1 AAAAATTAAATA
572555 -AAAATTAAATTA
1 AAAAATTAAA-TA
* *
572567 AAAAAATAACTA
1 AAAAATTAAATA
572579 AAAA
1 AAAA
572583 CATGGTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
12 17 0.50
13 7 0.21
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTAAATA
Found at i:572558 original size:22 final size:23
Alignment explanation
Indices: 572533--572581 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
572523 GATTATGTGA
*
572533 AAAATTAAA-TAAAAAATTAAAT
1 AAAATTAAATTAAAAAAATAAAT
*
572555 AAAATTAAATTAAAAAAATAACT
1 AAAATTAAATTAAAAAAATAAAT
572578 AAAA
1 AAAA
572582 ACATGGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATTAAATTAAAAAAATAAAT
Found at i:575875 original size:17 final size:17
Alignment explanation
Indices: 575829--575878 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
575819 TCTCAGATTT
* *
575829 TGATACCCATATATTTC
1 TGATACCTATATCTTTC
*
575846 TAATA-CTCATATCTTTC
1 TGATACCT-ATATCTTTC
575863 TGATACCTATATCTTT
1 TGATACCTATATCTTT
575879 GACTTTCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.04
17 24 0.89
18 2 0.07
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (17 bp):
TGATACCTATATCTTTC
Found at i:580245 original size:17 final size:17
Alignment explanation
Indices: 580223--580255 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
580213 TCTCAAATTT
580223 TGATACCTATATCTTTC
1 TGATACCTATATCTTTC
580240 TGATACCTATATCTTT
1 TGATACCTATATCTTT
580256 GACTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (17 bp):
TGATACCTATATCTTTC
Found at i:586787 original size:23 final size:22
Alignment explanation
Indices: 586734--586794 Score: 90
Period size: 21 Copynumber: 2.8 Consensus size: 22
586724 CGACACATAA
586734 GTGCCTAAA-ACAACACACGAG
1 GTGCCTAAATACAACACACGAG
586755 GTGCCT-AATACAACACACGAG
1 GTGCCTAAATACAACACACGAG
*
586776 GTGCCTGAAATACGACACA
1 GTGCCT-AAATACAACACA
586795 TAAAGTGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 2 0.06
21 24 0.67
23 10 0.28
ACGTcount: A:0.39, C:0.28, G:0.20, T:0.13
Consensus pattern (22 bp):
GTGCCTAAATACAACACACGAG
Found at i:594562 original size:23 final size:23
Alignment explanation
Indices: 594536--594601 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
594526 GGTGGCTGAA
594536 ATACGACACATAAAGTGCCTAAT
1 ATACGACACATAAAGTGCCTAAT
*
594559 ATACGAAACATAAAGTGCCTAAT
1 ATACGACACATAAAGTGCCTAAT
*
594582 ATACGTCACATAAAGTGCCT
1 ATACGACACATAAAGTGCCT
594602 GATCGGCAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTAAT
Found at i:599173 original size:22 final size:21
Alignment explanation
Indices: 599148--599188 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
599138 TTATTCCTAT
*
599148 AGAGAATTTGAGAGTTACAAAA
1 AGAGAA-TTCAGAGTTACAAAA
*
599170 AGAGGATTCAGAGTTACAA
1 AGAGAATTCAGAGTTACAA
599189 GCAAAATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.22
Consensus pattern (21 bp):
AGAGAATTCAGAGTTACAAAA
Found at i:601985 original size:23 final size:23
Alignment explanation
Indices: 601947--601997 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
601937 ACTCAAACGG
* *
601947 TGTAATATCCCTAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
601970 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
601993 AGTAA
1 TGTAA
601998 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:611361 original size:14 final size:15
Alignment explanation
Indices: 611326--611363 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
611316 GCCCATAGTT
*
611326 CGGTTC-ACTAGATT
1 CGGTTCAACTAGATG
611340 CGGTTCAACTA-ATG
1 CGGTTCAACTAGATG
611354 CGGTTCAACT
1 CGGTTCAACT
611364 GGACCCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (15 bp):
CGGTTCAACTAGATG
Found at i:624518 original size:37 final size:37
Alignment explanation
Indices: 624441--624519 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
624431 CTGATCTGGC
* *
624441 GTGTTATCGGTTGGATTAGCTCTTATGAGAGTTTGGT
1 GTGTTATCGGATGGATTAGCTCTTATGAGAGATTGGT
*
624478 GTGTTATCGGATGGATTAGCTCTTATGAGCA-ATTGTT
1 GTGTTATCGGATGGATTAGCTCTTATGAG-AGATTGGT
624515 GTGTT
1 GTGTT
624520 CGGTTGGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.18, C:0.09, G:0.30, T:0.43
Consensus pattern (37 bp):
GTGTTATCGGATGGATTAGCTCTTATGAGAGATTGGT
Found at i:629891 original size:26 final size:25
Alignment explanation
Indices: 629857--629937 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
629847 AATATGTGAT
*
629857 TTAATTTGGTCTTAGTTTAGAACAAA
1 TTAAATTGGTCTTAGTTTAG-ACAAA
* *
629883 TTAAATTGGTCTTA-TTTCGGACACA
1 TTAAATTGGTCTTAGTTT-AGACAAA
629908 TT-AATTGTGT-TTATTGTTTAGACAAA
1 TTAAATTG-GTCTTA--GTTTAGACAAA
629934 TTAA
1 TTAA
629938 TTGTGTCCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
24 8 0.18
25 11 0.25
26 21 0.48
27 4 0.09
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTTAGACAAA
Found at i:638454 original size:64 final size:64
Alignment explanation
Indices: 638376--638634 Score: 518
Period size: 64 Copynumber: 4.0 Consensus size: 64
638366 GCAATATGCC
638376 AAATTAGTGGACAGTCCACATCATTAACATTACATACTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTACATACTGTTTTAAGATGAACAAGAATGGAACT
638440 AAATTAGTGGACAGTCCACATCATTAACATTACATACTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTACATACTGTTTTAAGATGAACAAGAATGGAACT
638504 AAATTAGTGGACAGTCCACATCATTAACATTACATACTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTACATACTGTTTTAAGATGAACAAGAATGGAACT
638568 AAATTAGTGGACAGTCCACATCATTAACATTACATACTGTTTTAAGATGAACAAGAATGGAACT
1 AAATTAGTGGACAGTCCACATCATTAACATTACATACTGTTTTAAGATGAACAAGAATGGAACT
638632 AAA
1 AAA
638635 GTGTCTACCG
Statistics
Matches: 195, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 195 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (64 bp):
AAATTAGTGGACAGTCCACATCATTAACATTACATACTGTTTTAAGATGAACAAGAATGGAACT
Found at i:644579 original size:37 final size:37
Alignment explanation
Indices: 644538--644612 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
644528 TGCACGTACT
644538 TAACCGCTTCAGCGATCTTCGCCTTATCTACCAGAAC
1 TAACCGCTTCAGCGATCTTCGCCTTATCTACCAGAAC
* *
644575 TAACCTCTTCAGCGGTCTTCGCCTTATCTACCAGAAC
1 TAACCGCTTCAGCGATCTTCGCCTTATCTACCAGAAC
644612 T
1 T
644613 GCGAACTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.35, G:0.13, T:0.29
Consensus pattern (37 bp):
TAACCGCTTCAGCGATCTTCGCCTTATCTACCAGAAC
Found at i:656058 original size:19 final size:18
Alignment explanation
Indices: 656036--656077 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
656026 ATAATTTCAG
656036 ATAATATAA-ATTATTTTAA
1 ATAATATAAGA-TATTTT-A
*
656055 ATAAAATAAGATATTTTA
1 ATAATATAAGATATTTTA
656073 ATAAT
1 ATAAT
656078 TTTCCTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.25
19 14 0.70
20 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAATATAAGATATTTTA
Found at i:659368 original size:22 final size:22
Alignment explanation
Indices: 659334--659397 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
659324 AGAACTTTGA
659334 ATCTATATCTGATATGCTCTGC
1 ATCTATATCTGATATGCTCTGC
* *
659356 ATCTGTATTTGATATGCTCTGC
1 ATCTATATCTGATATGCTCTGC
659378 ATCTATATCT-ATGATGCTCT
1 ATCTATATCTGAT-ATGCTCT
659398 ATTTCTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 2 0.05
22 35 0.95
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (22 bp):
ATCTATATCTGATATGCTCTGC
Found at i:669076 original size:71 final size:66
Alignment explanation
Indices: 668999--669146 Score: 188
Period size: 66 Copynumber: 2.2 Consensus size: 66
668989 CAAATAGCAA
* * * * *
668999 AATCTTACATTCTAACCAAATGAAATAAATAAATAAAAAGGTAATGTAATATACTTAGTAATGTG
1 AATCTTACATTCCAACCAAATG----AAACAAA-AAAAAGGTAATATAAAATACCTAGTAATGTG
*
669064 CTAAGT
61 CTAAAT
*
669070 AATCTTATATTCCAACCAAATGAAACAAAAAAAAGGTAATATAAAATACCTAGTAATGTGCTAAA
1 AATCTTACATTCCAACCAAATGAAACAAAAAAAAGGTAATATAAAATACCTAGTAATGTGCTAAA
669135 T
66 T
669136 AATCTTACATT
1 AATCTTACATT
669147 TTGACAATCA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
66 43 0.62
67 6 0.09
71 20 0.29
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (66 bp):
AATCTTACATTCCAACCAAATGAAACAAAAAAAAGGTAATATAAAATACCTAGTAATGTGCTAAA
T
Found at i:672877 original size:22 final size:20
Alignment explanation
Indices: 672834--672872 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
672824 TAATTTAAAA
672834 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
672854 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
672873 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:673017 original size:34 final size:35
Alignment explanation
Indices: 672959--673025 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
672949 CAAACACCAG
672959 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
672994 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
673026 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:674192 original size:11 final size:13
Alignment explanation
Indices: 674176--674208 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
674166 ATTTCATGAA
674176 AAAATTTCG-T-G
1 AAAATTTCGTTCG
674187 AAAATTTCGTTCG
1 AAAATTTCGTTCG
674200 AAAATTTCG
1 AAAATTTCG
674209 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 1 0.05
13 10 0.50
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (13 bp):
AAAATTTCGTTCG
Found at i:675242 original size:51 final size:50
Alignment explanation
Indices: 675173--675804 Score: 526
Period size: 51 Copynumber: 12.5 Consensus size: 50
675163 GTAGCATTGT
*
675173 GTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTGA
1 GTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACATGTGTAGTACTGA
* * * * * * *
675224 GTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGT
1 GTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACATGTGTAGTACTGA
* * *
675275 GTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAA
1 GTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACATGTGTAGTACTGA
* * * * * * *
675326 GTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGT
1 GTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACATGTGTAGTACTGA
**
675377 GTGAAGGCTACTACGTGTTTCGATAAATAATGGTCACATGTGTAGTACTGA
1 GTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACATGTGTAGTACTGA
* * * * * *
675428 GTGAAGGTTACAATGTGTACCGAGAAGCTTTGGTCAC--GTGTAGTACT-A
1 GTGAAGGCTACTACGTGTACCGATAA-ATATGGTCACATGTGTAGTACTGA
* * *
675476 TGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAA
1 -GTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCACATGTGTAGTACTGA
* * *
675528 GTGAAGGCTACTATGTGTACCGA-AAAGCTTTGGTCACGTGTGTAGTACT-A
1 GTGAAGGCTACTACGTGTACCGATAAA--TATGGTCACATGTGTAGTACTGA
* * *
675578 TGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTACT-A
1 -GTGAAGGCTACTACGTGTACCGATAAATA--TGGTCACATGTGTAGTACTGA
* * *
675628 TGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTACT-A
1 -GTGAAGGCTACTACGTGTACCGATAAATA--TGGTCACATGTGTAGTACTGA
* * *
675678 TGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTACT-A
1 -GTGAAGGCTACTACGTGTACCGATAAATA--TGGTCACATGTGTAGTACTGA
* * *
675728 TGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTACT-A
1 -GTGAAGGCTACTACGTGTACCGATAAATA--TGGTCACATGTGTAGTACTGA
*
675778 TGTGAAGGCTACTACGTGAACCG-TAAA
1 -GTGAAGGCTACTACGTGTACCGATAAA
675805 ACTTGATGAT
Statistics
Matches: 503, Mismatches: 62, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
48 2 0.00
49 37 0.07
50 202 0.40
51 257 0.51
52 5 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (50 bp):
GTGAAGGCTACTACGTGTACCGATAAATATGGTCACATGTGTAGTACTGA
Found at i:675332 original size:102 final size:102
Alignment explanation
Indices: 675156--675797 Score: 863
Period size: 100 Copynumber: 6.4 Consensus size: 102
675146 TATCGATGAA
* * * *
675156 CACGTGTGTAGCATTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
*
675221 TGAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* *
675258 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
675323 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* **
675360 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTTTCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
675425 TGAGTGAAGGTTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
*
675462 CAC--GTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
675525 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* * * *
675562 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTA
* * * * * *
675625 CTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGAT
65 CTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
* * * *
675662 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTA
* * * * * *
675725 CTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGAT
65 CTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
675762 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA
675798 CCGTAAAACT
Statistics
Matches: 508, Mismatches: 28, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
100 232 0.46
101 45 0.09
102 231 0.45
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
Found at i:682891 original size:16 final size:18
Alignment explanation
Indices: 682860--682892 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
682850 TTGTTTTATT
682860 TATTTTATCATTAATTAC
1 TATTTTATCATTAATTAC
682878 TATTTTA-C-TTAATTA
1 TATTTTATCATTAATTA
682893 ACCTTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTTATCATTAATTAC
Found at i:683911 original size:219 final size:219
Alignment explanation
Indices: 683532--683970 Score: 808
Period size: 219 Copynumber: 2.0 Consensus size: 219
683522 GAGGCAGCTC
683532 ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTCACAGTCTATCATTAATGATCGAGGG
1 ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTCACAGTCTATCATTAATGATCGAGGG
* *
683597 GTGAGTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATGGGCTTAGACTTGATCTTTTCCA
66 GTGAGTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATAGGCTCAGACTTGATCTTTTCCA
*
683662 CTAGTATACATCCACAAACAGATGGTCAAACATAGTAAGTGAATGCGCTGTCGGGGACGTATCTT
131 CTAGTATACATCCACAAACAGATGGTCAAACATAGCAAGTGAATGCGCTGTCGGGGACGTATCTT
683727 CGGTACTATGTGAGTGCCACACAA
196 CGGTACTATGTGAGTGCCACACAA
683751 ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTCACAGTCTATCATTAATGATCGAGGG
1 ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTCACAGTCTATCATTAATGATCGAGGG
*
683816 GTGATTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATAGGCTCAGACTTGATCTTTTCCA
66 GTGAGTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATAGGCTCAGACTTGATCTTTTCCA
* *
683881 CTAGTATACATCCACAAATC-GATGGTCAAACATAGCAAGTGAATGTGTTGTCGGGGACGTATCT
131 CTAGTATACATCCACAAA-CAGATGGTCAAACATAGCAAGTGAATGCGCTGTCGGGGACGTATCT
683945 TCGGTACTATGTGAGTGCCACACAA
195 TCGGTACTATGTGAGTGCCACACAA
683970 A
1 A
683971 AGGACTGGCC
Statistics
Matches: 213, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
219 212 1.00
220 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (219 bp):
ATTTGTTCCTTAGACATGTGGTGAAATATTGGGGAGTGTCACAGTCTATCATTAATGATCGAGGG
GTGAGTCACGAGCTGGTTCTGGACGGAGTTGTTCAAGTTAATAGGCTCAGACTTGATCTTTTCCA
CTAGTATACATCCACAAACAGATGGTCAAACATAGCAAGTGAATGCGCTGTCGGGGACGTATCTT
CGGTACTATGTGAGTGCCACACAA
Found at i:684898 original size:20 final size:19
Alignment explanation
Indices: 684845--684901 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 19
684835 AGCTTGGCAC
* *
684845 ATATGGAATGTAATCTTTG
1 ATATGAAATGTAATCTTAG
*
684864 A-A-GAAATGCAATCTTAG
1 ATATGAAATGTAATCTTAG
684881 ATATGAAATGTAAATCTTAG
1 ATATGAAATGT-AATCTTAG
684901 A
1 A
684902 AGATATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 13 0.42
18 2 0.06
19 7 0.23
20 9 0.29
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (19 bp):
ATATGAAATGTAATCTTAG
Found at i:686819 original size:14 final size:14
Alignment explanation
Indices: 686800--686828 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
686790 CAATATATAT
686800 ATAAGAATTATACG
1 ATAAGAATTATACG
686814 ATAAGAATTATACG
1 ATAAGAATTATACG
686828 A
1 A
686829 ATCCATCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:689274 original size:18 final size:18
Alignment explanation
Indices: 689248--689282 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
689238 GTGTGAGTTT
*
689248 GTGTTTGTGTGGGTGTGG
1 GTGTGTGTGTGGGTGTGG
689266 GTGTGTGTGTGGGTGTG
1 GTGTGTGTGTGGGTGTG
689283 TGAGAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.43
Consensus pattern (18 bp):
GTGTGTGTGTGGGTGTGG
Found at i:689283 original size:12 final size:12
Alignment explanation
Indices: 689254--689284 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
689244 GTTTGTGTTT
*
689254 GTGTGGGTGTGG
1 GTGTGTGTGTGG
689266 GTGTGTGTGTGG
1 GTGTGTGTGTGG
689278 GTGTGTG
1 GTGTGTG
689285 AGAGAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.61, T:0.39
Consensus pattern (12 bp):
GTGTGTGTGTGG
Found at i:702778 original size:22 final size:23
Alignment explanation
Indices: 702729--702778 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
702719 ACACGCATAG
*
702729 TTTT-TAATATATATGCATATTT
1 TTTTATAATATATATGCATATTA
*
702751 TCTTTATAATATATATGTATA-TA
1 T-TTTATAATATATATGCATATTA
702774 TTTTA
1 TTTTA
702779 AACTTTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 5 0.21
23 5 0.21
24 14 0.58
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTTATAATATATATGCATATTA
Found at i:703090 original size:17 final size:18
Alignment explanation
Indices: 703065--703098 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
703055 TTTTCAAAAT
*
703065 TTATTTATATAT-CATAC
1 TTATATATATATACATAC
703082 TTATATATATATACATA
1 TTATATATATATACATA
703099 TTTTGTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATATATATATACATAC
Found at i:707508 original size:15 final size:15
Alignment explanation
Indices: 707490--707530 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
707480 AAAAAAAATC
707490 AAAATCAAAATCTAA
1 AAAATCAAAATCTAA
707505 AAAATCAAAATCTAA
1 AAAATCAAAATCTAA
*
707520 AAAATGAAAAT
1 AAAATCAAAAT
707531 GATGAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAATCAAAATCTAA
Found at i:707568 original size:11 final size:11
Alignment explanation
Indices: 707534--707566 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
707524 TGAAAATGAT
707534 GAAAAAGGAAAA
1 GAAAAA-GAAAA
707546 GAAAAAGAAAA
1 GAAAAAGAAAA
707557 G-AAAAGAAAA
1 GAAAAAGAAAA
707567 AGGAGAGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
11 6 0.29
12 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:709201 original size:36 final size:36
Alignment explanation
Indices: 709154--709229 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
709144 CTCTTTGGCA
*
709154 TTACAGTGGAATAGATTGAAACCACAATGGCGAATC
1 TTACAGTGGAATAGATTGAAACCACAACGGCGAATC
709190 TTACAGTGGAATAGATTGAAACCACAACGGCGAATC
1 TTACAGTGGAATAGATTGAAACCACAACGGCGAATC
709226 TTAC
1 TTAC
709230 TTCCTTAGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (36 bp):
TTACAGTGGAATAGATTGAAACCACAACGGCGAATC
Found at i:709781 original size:44 final size:44
Alignment explanation
Indices: 709591--709783 Score: 175
Period size: 44 Copynumber: 4.5 Consensus size: 44
709581 CATCCAATCC
*
709591 TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAATCAT-AGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-CATCAGATCT
* * **
709635 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCATCCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACAT-CAGATCT
* ** * *
709675 TATCTCCCTAAAGTTGCAGTGGAGCAGACAGAAAAAAATCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAG--ATTAAAACATCAGATCT
* *
709720 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACTTCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACATCAGATCT
* *
709764 TATCTCTCTGAAATTGCAGT
1 TATCTCCCTGAAGTTGCAGT
709784 AGAATAGATC
Statistics
Matches: 117, Mismatches: 22, Indels: 20
0.74 0.14 0.13
Matches are distributed among these distances:
39 3 0.03
40 20 0.17
41 8 0.07
42 1 0.01
43 16 0.14
44 38 0.32
45 29 0.25
46 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACATCAGATCT
Found at i:713941 original size:25 final size:25
Alignment explanation
Indices: 713913--713966 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
713903 AAATGTGGAC
*
713913 AAAATAAAACCATAAAATTGTAGAT
1 AAAATAAAACCACAAAATTGTAGAT
*
713938 AAAATAAAACCACAAAATTGTGGAT
1 AAAATAAAACCACAAAATTGTAGAT
713963 AAAA
1 AAAA
713967 CCATGATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20
Consensus pattern (25 bp):
AAAATAAAACCACAAAATTGTAGAT
Found at i:716645 original size:50 final size:52
Alignment explanation
Indices: 716520--716650 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 52
716510 TGAACAAATG
* * *
716520 AGTTACTTAATGCA-AGACTTAATTTAATGATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGGA
** * * *
716572 AGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
*
716622 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATAACTTTATTTAATG
716651 CAGAACACAC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
50 31 0.48
51 15 0.23
52 19 0.29
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (52 bp):
AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
Found at i:721163 original size:2 final size:2
Alignment explanation
Indices: 721156--721184 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
721146 TTAGAAGGGG
721156 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
721185 GGGGGTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:750140 original size:35 final size:36
Alignment explanation
Indices: 750093--750165 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 36
750083 CCTAAAGTTT
*
750093 TACATTTCTTAACCCCGTAGTGCCATCATATTCATA
1 TACATTTCTTAACCCCGTAATGCCATCATATTCATA
*
750129 TACA-TTCTTAACCCTGTAATGCCATCATATTCATA
1 TACATTTCTTAACCCCGTAATGCCATCATATTCATA
750164 TA
1 TA
750166 ATCCATCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 31 0.89
36 4 0.11
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (36 bp):
TACATTTCTTAACCCCGTAATGCCATCATATTCATA
Found at i:750522 original size:457 final size:457
Alignment explanation
Indices: 749668--750556 Score: 1679
Period size: 457 Copynumber: 1.9 Consensus size: 457
749658 AATAACAATC
749668 CATATACATTCTTAACCCCGTAATGCCACCATATTCATATAATCCATCTATATATACATTTCAAT
1 CATATACATTCTTAACCCCGTAATGCCACCATATTCATATAATCCATCTATATATACATTTCAAT
749733 TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
66 TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
* *
749798 AGATGCCGATTTCACCAAAATTACATAACAATTTAAACTAATAAGTAAACAATATAATACAAAAA
131 AGATGCCGATTTCACCAAAATTACATAACAATCTAAACTAATAAGTAAAAAATATAATACAAAAA
749863 TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
196 TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
*
749928 TTAGGAACTAATCCGTAATTTTACATTTTCCTCGATTATTATACGATTGATTCAATTCTTGGTGT
261 TCAGGAACTAATCCGTAATTTTACATTTTCCTCGATTATTATACGATTGATTCAATTCTTGGTGT
749993 ATAATAATTTATTTCAATTTATCAATTCAAAATCTCTTATAAAATTCAATTATAAGCATATATCA
326 ATAATAATTTATTTCAATTTATCAATTCAAAATCTCTTATAAAATTCAATTATAAGCATATATCA
750058 ATTCAATTTCATTTAAAAAAAGTTCCCTAAAGTTTTACATTTCTTAACCCCGTAGTGCCATCATA
391 ATTCAATTTCATTTAAAAAAAGTTCCCTAAAGTTTTACATTTCTTAACCCCGTAGTGCCATCATA
750123 TT
456 TT
* *
750125 CATATACATTCTTAACCCTGTAATGCCATCATATTCATATAATCCATCTATATATACATTTCAAT
1 CATATACATTCTTAACCCCGTAATGCCACCATATTCATATAATCCATCTATATATACATTTCAAT
750190 TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
66 TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
750255 AGATGCCGATTTCACCAAAATTACATAACAATCTAAACTAATAAGTAAAAAATATAATACAAAAA
131 AGATGCCGATTTCACCAAAATTACATAACAATCTAAACTAATAAGTAAAAAATATAATACAAAAA
750320 TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
196 TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
* * *
750385 TCAGGAACTAATCTGTAATTTTACATTTTCCTCGATTATTATACGATTGGTTCAATTCTTTGTGT
261 TCAGGAACTAATCCGTAATTTTACATTTTCCTCGATTATTATACGATTGATTCAATTCTTGGTGT
* *
750450 ATAATAATTTATTTCAATTTATCAATTCAAAATCTTTTATAAAATTCTATTATAAGCATATATCA
326 ATAATAATTTATTTCAATTTATCAATTCAAAATCTCTTATAAAATTCAATTATAAGCATATATCA
*
750515 ATTCAATTTCATTTTAAAAAAGTTCCCTAAAGTTTTACATTT
391 ATTCAATTTCATTTAAAAAAAGTTCCCTAAAGTTTTACATTT
750557 TCTTCAATTT
Statistics
Matches: 421, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
457 421 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (457 bp):
CATATACATTCTTAACCCCGTAATGCCACCATATTCATATAATCCATCTATATATACATTTCAAT
TCCATTAAATACATCATACCTATTTGTGGTAATTATATCATTCATTCTTTACGATTTAGTCCTTT
AGATGCCGATTTCACCAAAATTACATAACAATCTAAACTAATAAGTAAAAAATATAATACAAAAA
TATCATGAATTAAATAAGTAAGTCTCATATGTACTTACCTAGCAAAAACAACAATTGATAAGGTG
TCAGGAACTAATCCGTAATTTTACATTTTCCTCGATTATTATACGATTGATTCAATTCTTGGTGT
ATAATAATTTATTTCAATTTATCAATTCAAAATCTCTTATAAAATTCAATTATAAGCATATATCA
ATTCAATTTCATTTAAAAAAAGTTCCCTAAAGTTTTACATTTCTTAACCCCGTAGTGCCATCATA
TT
Found at i:752436 original size:33 final size:29
Alignment explanation
Indices: 752321--752455 Score: 107
Period size: 29 Copynumber: 4.5 Consensus size: 29
752311 AAGTACTGTA
*
752321 ATATAT-ACATATATGAGTTTT-GTTATT-T
1 ATATATAATATATATG-GTTTTGGTT-TTAT
* *
752349 AAATATAATATATATGGGTTTTGGTGTTAT
1 ATATATAATATATAT-GGTTTTGGTTTTAT
* *
752379 ATATATAATATATAT-GTGTGGGTTTTATT
1 ATATATAATATATATGGTTTTGGTTTTA-T
*
752408 ATATATAATATATATGCGTTTATAGGTTTTGT
1 ATATATAATATATATG-GTTT-T-GGTTTTAT
*
752440 ATCATCTAATATATAT
1 AT-ATATAATATATAT
752456 AAATGTATAT
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
28 14 0.16
29 30 0.35
30 18 0.21
31 3 0.03
32 3 0.03
33 18 0.21
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (29 bp):
ATATATAATATATATGGTTTTGGTTTTAT
Found at i:752820 original size:36 final size:36
Alignment explanation
Indices: 752778--752853 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
752768 GTTATATTAT
* *
752778 GAACCATGTTAACTTGGTGAAT-TATATTATTATGGC
1 GAACCATGTTAACTTGGTG-ATGTATATTAATATGAC
*
752814 GAACCATGTTAATTTGGTGATGTATATTAATATGAC
1 GAACCATGTTAACTTGGTGATGTATATTAATATGAC
752850 GAAC
1 GAAC
752854 TATATTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 2 0.06
36 34 0.94
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (36 bp):
GAACCATGTTAACTTGGTGATGTATATTAATATGAC
Found at i:752862 original size:36 final size:36
Alignment explanation
Indices: 752778--752864 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
752768 GTTATATTAT
* * * *
752778 GAACCATGTTAACTTGGTGAATTATATTATTATGGC
1 GAACCATATTAATTTGGTGAATTATATTAATATGAC
*
752814 GAACCATGTTAATTTGGTG-ATGTATATTAATATGAC
1 GAACCATATTAATTTGGTGAAT-TATATTAATATGAC
*
752850 GAACTATATTAATTT
1 GAACCATATTAATTT
752865 TCCAAACTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
35 2 0.04
36 43 0.96
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.40
Consensus pattern (36 bp):
GAACCATATTAATTTGGTGAATTATATTAATATGAC
Found at i:753496 original size:17 final size:17
Alignment explanation
Indices: 753476--753554 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
753466 TTATGATGGA
753476 GCATGAACTGTTATTTT
1 GCATGAACTGTTATTTT
* **
753493 GCATGAATTGTTATTCG
1 GCATGAACTGTTATTTT
* * *
753510 GTATGAATTGGTATTTT
1 GCATGAACTGTTATTTT
** *
753527 ATATGAACTATTATTTT
1 GCATGAACTGTTATTTT
*
753544 GCATGAGCTGT
1 GCATGAACTGT
753555 CCTTTGGCAA
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.25, C:0.09, G:0.20, T:0.46
Consensus pattern (17 bp):
GCATGAACTGTTATTTT
Found at i:755279 original size:14 final size:14
Alignment explanation
Indices: 755257--755290 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
755247 TTTAAAAAAA
* *
755257 ATATGTATATGTGT
1 ATATATATATGTAT
755271 ATATATATATGTAT
1 ATATATATATGTAT
755285 ATATAT
1 ATATAT
755291 GTATATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:755332 original size:2 final size:2
Alignment explanation
Indices: 755325--755349 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
755315 ATAGTAAGAA
755325 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
755350 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.