Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 41 of 211
Found at i:10828785 original size:16 final size:17
Alignment explanation
Indices: 10828766--10828797 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
10828756 TTATTTTCAA
10828766 TTTTT-AAATT-TAAAC
1 TTTTTCAAATTCTAAAC
10828781 TTTTTCAAATTCTAAAC
1 TTTTTCAAATTCTAAAC
10828798 ATTAAGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTTCAAATTCTAAAC
Found at i:10828938 original size:28 final size:28
Alignment explanation
Indices: 10828910--10828962 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
10828900 TTTTTTAATT
*
10828910 TTTTTTA-ATTTTAT-AAAATTTAAATA
1 TTTTTTATTTTTTATAAAAATTTAAATA
10828936 TTTTTTCATTTTTTATAAAAATTTAAA
1 TTTTTT-ATTTTTTATAAAAATTTAAA
10828963 ATTATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 1 0.04
28 6 0.26
29 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTTTATTTTTTATAAAAATTTAAATA
Found at i:10828963 original size:36 final size:36
Alignment explanation
Indices: 10828897--10828965 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
10828887 TGTACAATAT
* **
10828897 ATATTTTTTAATTTTTTTTAATTTTATAAAATTTAA
1 ATATTTTTTAATTTTTTTAAAAATTATAAAATTTAA
*
10828933 ATATTTTTTCATTTTTTATAAAAATT-TAAAATT
1 ATATTTTTTAATTTTTT-TAAAAATTATAAAATT
10828966 ATATATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 23 0.82
37 5 0.18
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (36 bp):
ATATTTTTTAATTTTTTTAAAAATTATAAAATTTAA
Found at i:10829007 original size:23 final size:25
Alignment explanation
Indices: 10828964--10829034 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 25
10828954 AAATTTAAAA
10828964 TTATATATTATTATGACTTTTTAA-CAT
1 TTATATATTATT-T--CTTTTTAATCAT
*
10828991 TTATAT-TTATATT-TTTTTAATTAT
1 TTATATATTAT-TTCTTTTTAATCAT
10829015 TTATATATTATTTCTTTTTA
1 TTATATATTATTTCTTTTTA
10829035 CTTTTTAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
23 7 0.18
24 10 0.26
25 10 0.26
26 5 0.13
27 7 0.18
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (25 bp):
TTATATATTATTTCTTTTTAATCAT
Found at i:10830873 original size:28 final size:27
Alignment explanation
Indices: 10830813--10830873 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
10830803 TAACAAAGGC
* *
10830813 TTAT-TTTGGTAATTAATTTTATTTTA
1 TTATATTTGGTAATTAATTATAATTTA
*
10830839 TTCTATTTGAGTAATTAATTAATAATTT-
1 TTATATTTG-GTAATTAATT-ATAATTTA
10830867 TTATATT
1 TTATATT
10830874 ATTTAGGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.11
27 4 0.14
28 16 0.57
29 5 0.18
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (27 bp):
TTATATTTGGTAATTAATTATAATTTA
Found at i:10831905 original size:13 final size:13
Alignment explanation
Indices: 10831887--10831912 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10831877 TCCTTCTAAC
10831887 TTTTAAATTTTTA
1 TTTTAAATTTTTA
10831900 TTTTAAATTTTTA
1 TTTTAAATTTTTA
10831913 GATTATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTTA
Found at i:10834018 original size:21 final size:23
Alignment explanation
Indices: 10833987--10834028 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
10833977 AGCTTTATTT
10833987 TTCACCCATTTGTTC-TTTTAAC
1 TTCACCCATTTGTTCATTTTAAC
10834009 TTCA-CCATTTGTTCATTTTA
1 TTCACCCATTTGTTCATTTTA
10834029 TAGCTATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.52
Consensus pattern (23 bp):
TTCACCCATTTGTTCATTTTAAC
Found at i:10835543 original size:91 final size:91
Alignment explanation
Indices: 10835391--10835734 Score: 559
Period size: 91 Copynumber: 3.8 Consensus size: 91
10835381 TACGTATGAT
* *
10835391 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTT
**
10835454 GATCAGATAAGTGTAGCT-CGGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
* *
10835479 CACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCCACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACT
*
10835544 TGATCAGATAAGTGTAGCTAAAGCTAT
65 TGATCAGATAAGTGTAGCTAAAGCTAC
* * *
10835571 CACTTATCACTTTGTCACTTGATTAGATAAGTGTAGCTAGGCTACCACTTATCATTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTT
10835636 GATCAGATAAGTGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
10835662 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACT
10835727 TGATCAGA
65 TGATCAGA
10835735 AGTACTCAAA
Statistics
Matches: 235, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
88 10 0.04
89 5 0.02
90 19 0.08
91 129 0.55
92 72 0.31
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (91 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTT
GATCAGATAAGTGTAGCTAAAGCTAC
Found at i:10835544 original size:46 final size:46
Alignment explanation
Indices: 10835391--10835734 Score: 563
Period size: 46 Copynumber: 7.6 Consensus size: 46
10835381 TACGTATGAT
* *
10835391 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
**
10835434 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-CGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
10835479 CACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAAGCCAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
10835525 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
10835571 CACTTATCACTTTGTCACTTGATTAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
10835616 CACTTATCATTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
10835662 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
10835708 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
10835735 AGTACTCAAA
Statistics
Matches: 281, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
43 10 0.04
44 5 0.02
45 104 0.37
46 162 0.58
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:10835653 original size:137 final size:137
Alignment explanation
Indices: 10835391--10835734 Score: 595
Period size: 137 Copynumber: 2.5 Consensus size: 137
10835381 TACGTATGAT
* *
10835391 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
*
10835453 TGATCAGATAAGTGTAGCTCGGCTACCACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTA
66 TGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTA
10835518 AAGCCAC
131 AAGCCAC
*
10835525 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
* * *
10835590 TGATTAGATAAGTGTAGCTAGGCTACCACTTATCATTTTGTCACTTGATCAGATAAGTGTAGCTA
66 TGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTA
*
10835655 AAGCTAC
131 AAGCCAC
10835662 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
10835727 TGATCAGA
66 TGATCAGA
10835735 AGTACTCAAA
Statistics
Matches: 197, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
134 10 0.05
135 5 0.03
136 20 0.10
137 162 0.82
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (137 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
TGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTA
AAGCCAC
Found at i:10840428 original size:20 final size:21
Alignment explanation
Indices: 10840403--10840443 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
10840393 GTTGAGAAAA
10840403 TTATTT-AATTAAAAAATAAT
1 TTATTTAAATTAAAAAATAAT
*
10840423 TTATTTAAATTAATAAATAAT
1 TTATTTAAATTAAAAAATAAT
10840444 ATTTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATTTAAATTAAAAAATAAT
Found at i:10850512 original size:19 final size:20
Alignment explanation
Indices: 10850490--10850530 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
10850480 TTTTTTATTA
10850490 TTATA-ACATTTTTAAATTT
1 TTATATACATTTTTAAATTT
**
10850509 TTATATATTTTTTTAAATTT
1 TTATATACATTTTTAAATTT
10850529 TT
1 TT
10850531 TAAATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATATACATTTTTAAATTT
Found at i:10850529 original size:9 final size:9
Alignment explanation
Indices: 10850498--10850537 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
10850488 TATTATAACA
10850498 TTTTTAAAT
1 TTTTTAAAT
*
10850507 TTTTATATATT
1 TTTT-TA-AAT
10850518 TTTTTAAAT
1 TTTTTAAAT
10850527 TTTTTAAAT
1 TTTTTAAAT
10850536 TT
1 TT
10850538 ATAATTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 17 0.63
10 4 0.15
11 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:10857573 original size:12 final size:12
Alignment explanation
Indices: 10857544--10857595 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
10857534 AATATTAATT
10857544 TTAATTTTTAAA
1 TTAATTTTTAAA
*
10857556 AT-ATTTTTAAA
1 TTAATTTTTAAA
10857567 TTAATTTTTTAAA
1 TTAA-TTTTTAAA
* *
10857580 CTATATATTTAAA
1 TTA-ATTTTTAAA
10857593 TTA
1 TTA
10857596 TATATAGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 10 0.31
12 2 0.06
13 19 0.59
14 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
TTAATTTTTAAA
Found at i:10857591 original size:26 final size:23
Alignment explanation
Indices: 10857544--10857595 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
10857534 AATATTAATT
*
10857544 TTAATTTTTAAAATATTTTTAAA
1 TTAATTTTTAAAATATATTTAAA
10857567 TTAATTTTTTAAACTATATATTTAAA
1 TTAA-TTTTTAAA--ATATATTTAAA
10857593 TTA
1 TTA
10857596 TATATAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.16
24 8 0.32
26 13 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATTTTTAAAATATATTTAAA
Found at i:10857606 original size:16 final size:17
Alignment explanation
Indices: 10857581--10857625 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
10857571 TTTTTTAAAC
10857581 TATATATTTAA-AT-TA
1 TATATATTTAATATATA
10857596 TATATAGTTTAATATATA
1 TATATA-TTTAATATATA
10857614 TATATATATTAA
1 TATATAT-TTAA
10857626 AAATTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.23
16 5 0.19
17 3 0.12
18 12 0.46
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TATATATTTAATATATA
Found at i:10862049 original size:42 final size:41
Alignment explanation
Indices: 10861962--10862090 Score: 134
Period size: 42 Copynumber: 3.1 Consensus size: 41
10861952 ATGTGTTTAC
* * *
10861962 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAA-CTTATATGAG
1 TTTCCG-TTAGCTCTTATGAGCTTCTGTTTAACCTT-TATGGG
* * *
10862004 TTTCCGCTTAGCTCTTTTGAGCTTCTATTTAACCCTTATGGG
1 TTTCCG-TTAGCTCTTATGAGCTTCTGTTTAACCTTTATGGG
* * *
10862046 TTTCCGTTCAACTCTTATGAGCTTCCGTTCAACCTTTATGGG
1 TTTCCGTT-AGCTCTTATGAGCTTCTGTTTAACCTTTATGGG
10862088 TTT
1 TTT
10862091 TTGTTTAGCA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 2 0.03
42 68 0.94
43 2 0.03
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.44
Consensus pattern (41 bp):
TTTCCGTTAGCTCTTATGAGCTTCTGTTTAACCTTTATGGG
Found at i:10862064 original size:21 final size:20
Alignment explanation
Indices: 10862037--10862090 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
10862027 TCTATTTAAC
10862037 CCTTATGGGTTTCCGTTCAA
1 CCTTATGGGTTTCCGTTCAA
* *
10862057 CTCTTATGAGCTTCCGTTCAA
1 C-CTTATGGGTTTCCGTTCAA
10862078 CCTTTATGGGTTT
1 CC-TTATGGGTTT
10862091 TTGTTTAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CCTTATGGGTTTCCGTTCAA
Found at i:10866069 original size:24 final size:24
Alignment explanation
Indices: 10866037--10866121 Score: 109
Period size: 24 Copynumber: 3.5 Consensus size: 24
10866027 ACAGCCTCGT
* *
10866037 CCATTCCCTCCTCGCCCACCAAGA
1 CCATTCCCTCCTCACCCACCACGA
* *
10866061 CCATTCCCTCCTCACCCGCCGCGA
1 CCATTCCCTCCTCACCCACCACGA
*
10866085 CCGA-TCCCTCCTCATCCACCACGA
1 CC-ATTCCCTCCTCACCCACCACGA
10866109 CCATTCCCTCCTC
1 CCATTCCCTCCTC
10866122 CTCATCCTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.96
25 1 0.02
ACGTcount: A:0.16, C:0.56, G:0.08, T:0.19
Consensus pattern (24 bp):
CCATTCCCTCCTCACCCACCACGA
Found at i:10872764 original size:4 final size:4
Alignment explanation
Indices: 10872755--10872780 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
10872745 CAAACTAAAC
10872755 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
10872781 GTCCATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:10874259 original size:5 final size:5
Alignment explanation
Indices: 10874249--10874317 Score: 138
Period size: 5 Copynumber: 13.8 Consensus size: 5
10874239 TGGACCTTTT
10874249 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
10874299 TTATA TTATA TTATA TTAT
1 TTATA TTATA TTATA TTAT
10874318 TTCCTTACTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 64 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:10885549 original size:63 final size:63
Alignment explanation
Indices: 10885450--10885575 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
10885440 AAGAAGTTAG
10885450 TGTAGAAAAGCTTATGCTGCGATATTTGGGGCACCTAATTTCATCTTACTCATTGTGTATTTT
1 TGTAGAAAAGCTTATGCTGCGATATTTGGGGCACCTAATTTCATCTTACTCATTGTGTATTTT
10885513 TGTAGAAAAGCTTATGCTGCGATATTTGGGGCACCTAATTTCATCTTACTCATTGTGTATTTT
1 TGTAGAAAAGCTTATGCTGCGATATTTGGGGCACCTAATTTCATCTTACTCATTGTGTATTTT
10885576 AGCAACGTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (63 bp):
TGTAGAAAAGCTTATGCTGCGATATTTGGGGCACCTAATTTCATCTTACTCATTGTGTATTTT
Found at i:10886266 original size:44 final size:44
Alignment explanation
Indices: 10886186--10886431 Score: 275
Period size: 44 Copynumber: 5.6 Consensus size: 44
10886176 TACCATAGCG
* * *
10886186 AATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGTAGATTGAAGCTACA
* * * *
10886230 AATCTTATCTCGCTGAAGCTGCAATGAAGTAGATTGAAGCGACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGTAGATTGAAGCTACA
* * *
10886274 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGTAGATTGAAGCTACA
* ** *
10886318 AATCTTATCTCCCTAAAGTTATAGTGGAA-CAGATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGT-GAAGTAGATTGAAGCTACA
*
10886362 AATCTTATCTCGCTGAAGTTGCAGTGGAA-TAGATTGAAG-TGACA
1 AATCTTATCTCCCTGAAGTTGCAGT-GAAGTAGATTGAAGCT-ACA
* *
10886406 AATCCTATAC-CTCTGAAGTTGCAGTG
1 AATCTTAT-CTCCCTGAAGTTGCAGTG
10886432 GGTTGGATTA
Statistics
Matches: 171, Mismatches: 28, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
43 2 0.01
44 166 0.97
45 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGAAGTAGATTGAAGCTACA
Found at i:10886443 original size:132 final size:132
Alignment explanation
Indices: 10886186--10886432 Score: 372
Period size: 132 Copynumber: 1.9 Consensus size: 132
10886176 TACCATAGCG
* * * *
10886186 AATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGCTACAAATCTTATCTCGCTGAAGCTG
1 AATCTTATCTCCCTAAAGTTACAGTGGAACAGATTGAAGCTACAAATCTTATCTCGCTGAAGCTG
*
10886251 CAATGAAGTAGATTGAAGCGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGTTA
66 CAATGAAGTAGATTGAAGCGACAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGTTA
10886316 CA
131 CA
* *
10886318 AATCTTATCTCCCTAAAGTTATAGTGGAACAGATTGAAGCTACAAATCTTATCTCGCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTACAGTGGAACAGATTGAAGCTACAAATCTTATCTCGCTGAAGCTG
* * *
10886383 CAGTGGAA-TAGATTGAAGTGACAAATCCTATAC-CTCTGAAGTTGCAGTGG
66 CAAT-GAAGTAGATTGAAGCGACAAATCCTAT-CTCCCTGAAGTTGCAGTGG
10886433 GTTGGATTAA
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
132 99 0.96
133 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (132 bp):
AATCTTATCTCCCTAAAGTTACAGTGGAACAGATTGAAGCTACAAATCTTATCTCGCTGAAGCTG
CAATGAAGTAGATTGAAGCGACAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGTTA
CA
Found at i:10890417 original size:13 final size:13
Alignment explanation
Indices: 10890399--10890437 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
10890389 CATTTGATAA
10890399 ATAAGCTATTGTC
1 ATAAGCTATTGTC
10890412 ATAAGCTATTGTC
1 ATAAGCTATTGTC
10890425 ATAAGCTAATTGT
1 ATAAGCT-ATTGT
10890438 AGGGATGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (13 bp):
ATAAGCTATTGTC
Found at i:10894832 original size:42 final size:42
Alignment explanation
Indices: 10894734--10894836 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
10894724 GTGCTAAATG
* * * *
10894734 AAAACCCACAAGGGTTAAACTGAACCTCAAAAGAGCTTAACA
1 AAAACCCATAAGGGTTAAACTGAACCTCAAAAAAACTGAACA
* *
10894776 AAAACCCATAAGGGTTAAACTGAAGCTCAAAAAAACTGAACT
1 AAAACCCATAAGGGTTAAACTGAACCTCAAAAAAACTGAACA
* * *
10894818 GAAACTCATTAGGGTTAAA
1 AAAACCCATAAGGGTTAAA
10894837 TGGAAACTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.17
Consensus pattern (42 bp):
AAAACCCATAAGGGTTAAACTGAACCTCAAAAAAACTGAACA
Found at i:10898832 original size:3 final size:3
Alignment explanation
Indices: 10898824--10898849 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10898814 ACATGGTTGG
10898824 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
10898850 GGGAATGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:10908783 original size:16 final size:13
Alignment explanation
Indices: 10908750--10908775 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10908740 CTCTATTGTG
10908750 GTGGGAGCTGCCC
1 GTGGGAGCTGCCC
10908763 GTGGGAGCTGCCC
1 GTGGGAGCTGCCC
10908776 AGGCTGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.46, T:0.15
Consensus pattern (13 bp):
GTGGGAGCTGCCC
Found at i:10909047 original size:12 final size:11
Alignment explanation
Indices: 10908994--10909045 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
10908984 AATTTTATGA
10908994 TTTTTAATTAAT
1 TTTTTAA-TAAT
* *
10909006 TTCTTAACAAT
1 TTTTTAATAAT
*
10909017 TTTTATACATGAT
1 TTTT-TA-ATAAT
10909030 TTTTTAATAAT
1 TTTTTAATAAT
10909041 TTTTT
1 TTTTT
10909046 TATGGTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
11 15 0.47
12 10 0.31
13 7 0.22
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:10910001 original size:200 final size:200
Alignment explanation
Indices: 10909658--10910054 Score: 749
Period size: 200 Copynumber: 2.0 Consensus size: 200
10909648 GTTGATTGCA
* *
10909658 AGGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATTCCTTTCTCATCGTCTTAAAAGGTATTT
1 AGGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCATCTTAAAAGGTATTT
*
10909723 ATAGGAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAGAAGTTGTCATCAT
66 ATAGGAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAAAAGTTGTCATCAT
10909788 TGAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTA
131 TGAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTA
10909853 TTTAT
196 TTTAT
10909858 AGGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCATCTTAAAAGGTATTT
1 AGGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCATCTTAAAAGGTATTT
10909923 ATAGGAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAAAAGTTGTCATCAT
66 ATAGGAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAAAAGTTGTCATCAT
* *
10909988 TGAGTAGGTGAGGACGTATAAGGTAGGGCCCATTCTATTATTCCTTTTGAGAGAGTACGAGATTA
131 TGAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTA
10910053 TT
196 TT
10910055 ATGTTTATTT
Statistics
Matches: 192, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
200 192 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (200 bp):
AGGAGTAGTGCTCAAGGTTGCTAATGAGGAAGAAGATCCCTTTCTCATCATCTTAAAAGGTATTT
ATAGGAGAAGTCCTCTTGTCTAGTAGTGGTGACATGGTAGGTTGTTATAAAAAAGTTGTCATCAT
TGAGTAGGTGAGGACATATAAGGTAGGGCCCATTCTATTATTCCTTTTGAAAGAGTACGAGATTA
TTTAT
Found at i:10911128 original size:8 final size:8
Alignment explanation
Indices: 10911117--10911156 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
10911107 TATGTTTTTA
10911117 TATTATAT
1 TATTATAT
10911125 TATTA-AT
1 TATTATAT
10911132 ATATTATAT
1 -TATTATAT
10911141 TATTATAT
1 TATTATAT
10911149 TATTATAT
1 TATTATAT
10911157 ATATGACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 2 0.07
8 26 0.87
9 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:10912561 original size:24 final size:24
Alignment explanation
Indices: 10912519--10912650 Score: 171
Period size: 24 Copynumber: 5.5 Consensus size: 24
10912509 ACTTTAGCGC
10912519 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
*
10912544 GCTCTTTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
*
10912568 GCTCTTTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
**
10912592 GCTCTCTGATATTTAGCACGTCAGT
1 GCTCTCTGATA-TTAGCACGTTGGT
* *
10912617 GCTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
10912639 GCTCTCTG-TATT
1 GCTCTCTGATATT
10912651 TGTTCCGTAT
Statistics
Matches: 98, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
22 19 0.19
23 2 0.02
24 50 0.51
25 27 0.28
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:10918068 original size:32 final size:33
Alignment explanation
Indices: 10918027--10918091 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
10918017 TTGAGGGTAT
* *
10918027 TTTAGTTTTTTCATTT-AAAACAAAACAACAAA
1 TTTAATTTTTTCATTTAAAAAAAAAACAACAAA
10918059 TTTAATTTTTTCATTTAAAAAAAAAACAACAAA
1 TTTAATTTTTTCATTTAAAAAAAAAACAACAAA
10918092 ATTTTGCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.37
Consensus pattern (33 bp):
TTTAATTTTTTCATTTAAAAAAAAAACAACAAA
Found at i:10921144 original size:9 final size:9
Alignment explanation
Indices: 10921079--10921146 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
10921069 TTAAAGGGTT
10921079 TTTTTATACA
1 TTTTTATA-A
*
10921089 -TTTTATATT
1 TTTTTATA-A
*
10921098 TTTTTATGA
1 TTTTTATAA
10921107 TTTTTATAAA
1 TTTTTAT-AA
* *
10921117 ATTTTACAA
1 TTTTTATAA
10921126 TTTTTATAA
1 TTTTTATAA
*
10921135 TTTTTCTAA
1 TTTTTATAA
10921144 TTT
1 TTT
10921147 CAAAAAAATT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
9 34 0.74
10 12 0.26
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:10921704 original size:3 final size:3
Alignment explanation
Indices: 10921698--10921747 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
10921688 TCATCATATC
10921698 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10921746 AT
1 AT
10921748 CTTGCAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:10924323 original size:13 final size:12
Alignment explanation
Indices: 10924307--10924361 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
10924297 CTTTATTCTA
10924307 TTTTTTTCATTTC
1 TTTTTTTC-TTTC
10924320 TTTTTCTT-TATTC
1 TTTTT-TTCT-TTC
10924333 TTTTTTT-TTAT-
1 TTTTTTTCTT-TC
10924344 TTTTTTTCTTTC
1 TTTTTTTCTTTC
10924356 TTTTTT
1 TTTTTT
10924362 CTGTTTAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
11 9 0.24
12 13 0.35
13 13 0.35
14 2 0.05
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:10924328 original size:28 final size:27
Alignment explanation
Indices: 10924288--10924354 Score: 100
Period size: 28 Copynumber: 2.5 Consensus size: 27
10924278 ACGTTCCCAC
*
10924288 TTTCTTTGTCTTTATTCTATTTTTTTCA
1 TTTCTTTTTCTTTATTCT-TTTTTTTCA
*
10924316 TTTCTTTTTCTTTATTCTTTTTTTTTA
1 TTTCTTTTTCTTTATTCTTTTTTTTCA
10924343 TTT-TTTTTCTTT
1 TTTCTTTTTCTTT
10924355 CTTTTTTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 9 0.24
27 11 0.30
28 17 0.46
ACGTcount: A:0.07, C:0.12, G:0.01, T:0.79
Consensus pattern (27 bp):
TTTCTTTTTCTTTATTCTTTTTTTTCA
Found at i:10924368 original size:26 final size:27
Alignment explanation
Indices: 10924288--10924368 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
10924278 ACGTTCCCAC
*
10924288 TTTCTTTGTCTTTATTCTATTTT-TTTCA
1 TTTCTTTTTCTTTATTCT-TTTTGTTT-A
*
10924316 TTTCTTTTTCTTTATTCTTTTTTTTTA
1 TTTCTTTTTCTTTATTCTTTTTGTTTA
*
10924343 TTT-TTTTTCTTTCTT-TTTTCTGTTTA
1 TTTCTTTTTCTTTATTCTTTT-TGTTTA
10924369 GATTTGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 4 0.08
26 16 0.33
27 8 0.17
28 20 0.42
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.78
Consensus pattern (27 bp):
TTTCTTTTTCTTTATTCTTTTTGTTTA
Found at i:10925011 original size:41 final size:41
Alignment explanation
Indices: 10924921--10924999 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
10924911 TAATCTACAT
* ** *
10924921 CACACGGACGTGTGGTTAGTCGTGTGTCAGGCCGTGTGCGC
1 CACACGGACGTGTGGTCAACCGTGTGCCAGGCCGTGTGCGC
*
10924962 CACACGGACGTGTGGTCAACCGTGTGCCAGGTCGTGTG
1 CACACGGACGTGTGGTCAACCGTGTGCCAGGCCGTGTG
10925000 GAGCACACGG
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:0.14, C:0.25, G:0.38, T:0.23
Consensus pattern (41 bp):
CACACGGACGTGTGGTCAACCGTGTGCCAGGCCGTGTGCGC
Found at i:10926642 original size:53 final size:52
Alignment explanation
Indices: 10926562--10926720 Score: 194
Period size: 53 Copynumber: 3.0 Consensus size: 52
10926552 CCATGGCACT
* * *
10926562 GAAGACTATATTCTGTAAGACCGTAACTGGTTGGTTATGGAATCATATGGAAA
1 GAAGACAATA-TCTGTAAGACCATAACTGGTGGGTTATGGAATCATATGGAAA
* *
10926615 GAAGACAATATCGTGTAAGACCATAACTGGTGGGTCATGAAATCATATGGAAA
1 GAAGACAATATC-TGTAAGACCATAACTGGTGGGTTATGGAATCATATGGAAA
* * * *
10926668 GAATACCATATCATGTAAGACCATAATTGATGGGTTAT-GACATCATATGGAAA
1 GAAGACAATATC-TGTAAGACCATAACTGGTGGGTTATGGA-ATCATATGGAAA
10926721 ATTTAAGAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
52 3 0.03
53 89 0.97
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (52 bp):
GAAGACAATATCTGTAAGACCATAACTGGTGGGTTATGGAATCATATGGAAA
Found at i:10926914 original size:27 final size:29
Alignment explanation
Indices: 10926871--10926937 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
10926861 AAGGATACGT
* *
10926871 CTTTGTGGCGA-ACCTCTTA-AAGG-ATGC
1 CTTTGTAGCGAGACCTC-TAGAAGGAAAGC
*
10926898 CTTTGTTGCGAGA-CTCTAGAAGGAAAGC
1 CTTTGTAGCGAGACCTCTAGAAGGAAAGC
10926926 CTTTGTAGCGAG
1 CTTTGTAGCGAG
10926938 TACTTAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 17 0.50
28 15 0.44
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (29 bp):
CTTTGTAGCGAGACCTCTAGAAGGAAAGC
Found at i:10930976 original size:16 final size:17
Alignment explanation
Indices: 10930946--10930978 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10930936 TTTTTTATTA
*
10930946 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
10930963 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
10930979 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:10938366 original size:21 final size:22
Alignment explanation
Indices: 10938328--10938370 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
10938318 AGTATGTTAT
10938328 GTCGTGACGAGAAACCCCCAAC
1 GTCGTGACGAGAAACCCCCAAC
*
10938350 GTCGTGATGAG-AACCCCCAAC
1 GTCGTGACGAGAAACCCCCAAC
10938371 ATCCTGACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.35, G:0.23, T:0.12
Consensus pattern (22 bp):
GTCGTGACGAGAAACCCCCAAC
Found at i:10946651 original size:37 final size:37
Alignment explanation
Indices: 10946601--10946676 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
10946591 TCACGAGTTC
10946601 CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
1 CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
*
10946638 CTTTAGCTGATTCTATGGAAGAGGTGGTGAAGCTTAA
1 CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
10946675 CT
1 CT
10946677 CTTCTAAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (37 bp):
CTTTAGCTGATTCTATGAAAGAGGTGGTGAAGCTTAA
Found at i:10948465 original size:228 final size:228
Alignment explanation
Indices: 10948068--10948517 Score: 686
Period size: 228 Copynumber: 2.0 Consensus size: 228
10948058 AAGAGTGGCC
* *
10948068 ACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGATCCGGGTAGTAATGA
1 ACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGATCCGGGCAGTAATAA
* * * * * * *
10948133 CTTTTATGCCCTCTTTTTCCAGGAGCAGTGGGGTACAATGGGCCCAGCTGTTTGTTATTAGGTGA
66 CTTTCATGCCCTCTTCTTCCAGAAACAGTAGGGTACAATGGGCCCAGCTATTTGTGATTAGGTGA
*
10948198 AAATGGTATTTAATGGAGGCATTATTGATACTAAGCTTAATAACACATTGATTATTCTTATTCCC
131 AAATGGTATTTAATGGAGGCATTATTGATAATAAGCTTAATAACACATTGATTATTCTTATTCCC
10948263 AAGTTTTAGAGTCATGAA-GGGTTTTCTGTGGTT
196 AAGTTTTAGAGTCAT-AAGGGGTTTTCTGTGGTT
* * * * *
10948296 ACTGATGAATAAATTAAAAAGGTTTTGTTTGACATGGCTCCTCTAAAAGCTCTGGGCAGTAGTAA
1 ACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGATCCGGGCAGTAATAA
* * *
10948361 CTTTCATGCCCTCTTCTTCTAGAAACAGTAGGGTACAGTGGGCCCAGCTATTTGTGATTGGGTGA
66 CTTTCATGCCCTCTTCTTCCAGAAACAGTAGGGTACAATGGGCCCAGCTATTTGTGATTAGGTGA
* * *
10948426 AAATGGTATTTAATGGAGGCGTTATTGATAATGAGCTTAATAACACATTGATTGTTCTTATTCCC
131 AAATGGTATTTAATGGAGGCATTATTGATAATAAGCTTAATAACACATTGATTATTCTTATTCCC
*
10948491 AAGTTTTAGAGTCCTAAGGGGTTTTCT
196 AAGTTTTAGAGTCATAAGGGGTTTTCT
10948518 TAGTTTTTCC
Statistics
Matches: 199, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
227 2 0.01
228 197 0.99
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (228 bp):
ACTGATGAATAAATTAAAAAGGCTTTGTTTGACATGGCTCCTCCAAAAGATCCGGGCAGTAATAA
CTTTCATGCCCTCTTCTTCCAGAAACAGTAGGGTACAATGGGCCCAGCTATTTGTGATTAGGTGA
AAATGGTATTTAATGGAGGCATTATTGATAATAAGCTTAATAACACATTGATTATTCTTATTCCC
AAGTTTTAGAGTCATAAGGGGTTTTCTGTGGTT
Found at i:10950428 original size:17 final size:17
Alignment explanation
Indices: 10950406--10950438 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10950396 ATATTTAATA
10950406 TATATTTTATTAAAAAG
1 TATATTTTATTAAAAAG
10950423 TATATTTTATTAAAAA
1 TATATTTTATTAAAAA
10950439 TAAAAAATAT
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATTTTATTAAAAAG
Found at i:10952288 original size:17 final size:18
Alignment explanation
Indices: 10952268--10952309 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
10952258 CATAATTTTT
10952268 AAATATAAAATATTTA-A
1 AAATATAAAATATTTATA
*
10952285 AAAT-TGAAAATGTTTATA
1 AAATAT-AAAATATTTATA
10952303 AAATATA
1 AAATATA
10952310 TTTATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 6 0.29
19 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
AAATATAAAATATTTATA
Found at i:10961028 original size:24 final size:25
Alignment explanation
Indices: 10961000--10961046 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
10960990 TTTAATTAAG
*
10961000 TTTTTAAAATTAGATCC-TAATATT
1 TTTTTAAAATTAAATCCTTAATATT
10961024 TTTTTAAAATTAAATCCTTAATA
1 TTTTTAAAATTAAATCCTTAATA
10961047 CCACGCCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTTAAAATTAAATCCTTAATATT
Found at i:10986284 original size:46 final size:46
Alignment explanation
Indices: 10986231--10986322 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
10986221 ATATTTGAAA
10986231 AGAAAAATGCCATTTCTTTCGATTTACAAAGACTTGTTGAAAATTT
1 AGAAAAATGCCATTTCTTTCGATTTACAAAGACTTGTTGAAAATTT
10986277 AGAAAAATGCCATTTCTTTCGATTTACAAAGACTTGTTGAAAATTT
1 AGAAAAATGCCATTTCTTTCGATTTACAAAGACTTGTTGAAAATTT
10986323 CTGGCATTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (46 bp):
AGAAAAATGCCATTTCTTTCGATTTACAAAGACTTGTTGAAAATTT
Found at i:10987680 original size:41 final size:41
Alignment explanation
Indices: 10987623--10987703 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
10987613 ACCTAATTGT
*
10987623 GAAAATAATTCCCTTATTCTGATAAACTACTAAAAGATAAG
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
10987664 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
10987704 AATAAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (41 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
Found at i:10990833 original size:17 final size:18
Alignment explanation
Indices: 10990800--10990833 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10990790 CAGATTGTTA
10990800 AGATAATCAAGGAAATGG
1 AGATAATCAAGGAAATGG
*
10990818 AGATAA-CAAGGGAATG
1 AGATAATCAAGGAAATG
10990834 CAGGTTACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.29, T:0.15
Consensus pattern (18 bp):
AGATAATCAAGGAAATGG
Found at i:10991643 original size:34 final size:34
Alignment explanation
Indices: 10991581--10991651 Score: 124
Period size: 35 Copynumber: 2.1 Consensus size: 34
10991571 GAGAAAACAG
*
10991581 AAAGAAAATGGATCTTAGCACTTAAAAAAGCACA
1 AAAGAAAAGGGATCTTAGCACTTAAAAAAGCACA
10991615 AAAGAAAAAGGGATCTTAGCACTTAAAAAAGCACA
1 AAAG-AAAAGGGATCTTAGCACTTAAAAAAGCACA
10991650 AA
1 AA
10991652 TGGCACAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 4 0.11
35 31 0.89
ACGTcount: A:0.55, C:0.14, G:0.15, T:0.15
Consensus pattern (34 bp):
AAAGAAAAGGGATCTTAGCACTTAAAAAAGCACA
Found at i:10997783 original size:27 final size:23
Alignment explanation
Indices: 10997753--10997805 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
10997743 TTTTTTAAGT
10997753 TAAAAAAGTAGAATTATAATATAAT-
1 TAAAAAA-TAGAATTA-AAT-TAATA
*
10997778 TATAAAATAGAATTAAATTAATA
1 TAAAAAATAGAATTAAATTAATA
10997801 TAAAA
1 TAAAA
10997806 TAGACGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.16
23 7 0.28
24 8 0.32
25 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (23 bp):
TAAAAAATAGAATTAAATTAATA
Found at i:10997804 original size:21 final size:24
Alignment explanation
Indices: 10997756--10997809 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 24
10997746 TTTAAGTTAA
10997756 AAAAGTAGAATTATAATATAATTAT
1 AAAA-TAGAATTATAATATAATTAT
10997781 AAAATAGAATTA-AAT-TAA-TAT
1 AAAATAGAATTATAATATAATTAT
10997802 AAAATAGA
1 AAAATAGA
10997810 CGGATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.38
22 3 0.10
23 3 0.10
24 8 0.28
25 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAATAGAATTATAATATAATTAT
Found at i:11006668 original size:2 final size:2
Alignment explanation
Indices: 11006661--11006687 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11006651 GGTCTGTTCT
11006661 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
11006688 TTAATGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11030131 original size:13 final size:13
Alignment explanation
Indices: 11030109--11030141 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
11030099 TGTTTCGTTA
11030109 TTTATCTTTATTT
1 TTTATCTTTATTT
*
11030122 TTTATTTTTATTT
1 TTTATCTTTATTT
11030135 TTT-TCTT
1 TTTATCTT
11030142 ACAAACGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 3 0.17
13 15 0.83
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATCTTTATTT
Found at i:11031806 original size:218 final size:215
Alignment explanation
Indices: 11031450--11031869 Score: 651
Period size: 218 Copynumber: 1.9 Consensus size: 215
11031440 AAAAAAATTT
* * * *
11031450 AAAATAAGGTAATGTTTTGGGTTTGAAAATTCGAGGAAACGTGCCCTAATGTGTTGGGTTTCGAT
1 AAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
* * *
11031515 TTTCTCGTTCGATCAAATAGCCAAATATCCTTTTAAAATTTCAAAATAAGGTAATGTTTTGCGTT
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAATAAGGCAATGTTTTGAGTT
* *
11031580 TGGAAATTCGAGAAAACGTGCCCTAATGTGCCGGGTTTCGATTTTTCTCGTTCGATCAAATAGCC
131 TGGAAATTCGAGAAAACGTGCCCTAATGTGCCGGGTTTC-A-ATTTCTCGTTCGACCAAATAGCC
11031645 AAATATCCTTTTAAAATTTTCA
194 AAATATCCTTTTAAAATTTTCA
*
11031667 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
1 AAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-
* * *
11031732 TTTTCTCGTTTGACCAAATAGCCGAATATCCTTTTAAAATTTTAAAATAAGGCAATGTTTTGAGT
65 TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAATAAGGCAATGTTTTGAGT
* * ** *
11031797 TTGGAAATTCGAGGAAATGTGCCCTAATGTGTTGGGTTTCAATTTCTCGTTGGACCAAATAGCCA
130 TTGGAAATTCGAGAAAACGTGCCCTAATGTGCCGGGTTTCAATTTCTCGTTCGACCAAATAGCCA
11031862 AATATCCT
195 AATATCCT
11031870 CTTATATTTT
Statistics
Matches: 184, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
216 29 0.16
217 60 0.33
218 95 0.52
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (215 bp):
AAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAATAAGGCAATGTTTTGAGTT
TGGAAATTCGAGAAAACGTGCCCTAATGTGCCGGGTTTCAATTTCTCGTTCGACCAAATAGCCAA
ATATCCTTTTAAAATTTTCA
Found at i:11031833 original size:108 final size:107
Alignment explanation
Indices: 11031428--11031869 Score: 643
Period size: 110 Copynumber: 4.1 Consensus size: 107
11031418 TACGCATTTT
* * * * *
11031428 AATATCCTTTTAAAAAAAATTTAAAATAAGGTAATGTTTTGGGTTTGAAAATTCGAGGAAACGTG
1 AATATCCTTTT---AAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTG
* *
11031493 CCCTAATGTGTTGGGTTTCGATTTTCTCGTTCGATCAAATAGCCA
63 CCCTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
* *
11031538 AATATCCTTTTAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCC
1 AATATCCTTTTAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCC
* *
11031603 TAATGTGCCGGGTTTCGATTTTTCTCGTTCGATCAAATAGCCA
66 TAATGTGCTGGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCA
11031646 AATATCCTTTTAAAATTTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGC
1 AATATCCTTTTAAAATTTT--AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGC
* *
11031711 CCTAATGTGCTGGGTTTCGATTTTTCTCGTTTGACCAAATAGCCG
64 CCTAATGTGCTGGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCA
* * *
11031756 AATATCCTTTTAAAATTTTAAAATAAGGCAATGTTTTGAGTTTGGAAATTCGAGGAAATGTGCCC
1 AATATCCTTTTAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCC
* * *
11031821 TAATGTGTTGGGTTTC-AATTTCTCGTTGGACCAAATAGCCA
66 TAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
11031862 AATATCCT
1 AATATCCT
11031870 CTTATATTTT
Statistics
Matches: 309, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
106 29 0.09
107 66 0.21
108 100 0.32
110 114 0.37
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (107 bp):
AATATCCTTTTAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCC
TAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
Found at i:11032818 original size:16 final size:16
Alignment explanation
Indices: 11032797--11032831 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11032787 TGTTGTTTTG
* *
11032797 TTTTGACTGCATGGCA
1 TTTTGACTACATGACA
11032813 TTTTGACTACATGACA
1 TTTTGACTACATGACA
11032829 TTT
1 TTT
11032832 CATTAAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (16 bp):
TTTTGACTACATGACA
Found at i:11043321 original size:44 final size:45
Alignment explanation
Indices: 11043264--11043390 Score: 134
Period size: 44 Copynumber: 2.9 Consensus size: 45
11043254 CAGCTTCGAA
* * *
11043264 TCCTATTTTCCTGAAATTGCAATGGAGCAGGTTGAAGAT-ACAAG
1 TCCTATTTCCCTGAAATTGCAGTGGAGTAGGTTGAAGATAACAAG
* ** *
11043308 TCTTATTTCCCTGAAGA-TGCAGTGGAGTAGACTGAAAATAACAAG
1 TCCTATTTCCCTGAA-ATTGCAGTGGAGTAGGTTGAAGATAACAAG
* * *
11043353 TCCTATCTCCCT-AAATAGTAGTGGAGTAGGTTGAAGAT
1 TCCTATTTCCCTGAAATTGCAGTGGAGTAGGTTGAAGAT
11043391 TGTAGATCTT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
43 1 0.02
44 49 0.74
45 16 0.24
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (45 bp):
TCCTATTTCCCTGAAATTGCAGTGGAGTAGGTTGAAGATAACAAG
Found at i:11046029 original size:17 final size:18
Alignment explanation
Indices: 11046007--11046043 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
11045997 ATGAAGTGTA
11046007 AAGTATATATATC-ATAT
1 AAGTATATATATCTATAT
*
11046024 AAGTATTTATATCTATAT
1 AAGTATATATATCTATAT
11046042 AA
1 AA
11046044 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
AAGTATATATATCTATAT
Found at i:11047231 original size:14 final size:13
Alignment explanation
Indices: 11047207--11047242 Score: 63
Period size: 14 Copynumber: 2.7 Consensus size: 13
11047197 GCTATTGTCC
11047207 TCTGTTTTTTGCT
1 TCTGTTTTTTGCT
11047220 TCTGTCTTTTTGCT
1 TCTGT-TTTTTGCT
11047234 TCTGTTTTT
1 TCTGTTTTT
11047243 GCAGGAGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.00, C:0.17, G:0.14, T:0.69
Consensus pattern (13 bp):
TCTGTTTTTTGCT
Found at i:11048855 original size:218 final size:215
Alignment explanation
Indices: 11048488--11048907 Score: 671
Period size: 218 Copynumber: 1.9 Consensus size: 215
11048478 AAAAAAATTT
* * *
11048488 AAAATAAGGCAATTTTTTGGGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
1 AAAATAAGGCAATGTTCTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
*
11048553 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAATAAGGTAATGTTTTGCGTT
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAATAAGGCAATGTTTTGCGTT
** * *
11048618 TGGAAATTTTAGAAAACGTGCCCTAATGTG-TCGGGTTTCGATTTTTCTCGTTCGACCAAATAGC
131 TGGAAATTCGAGAAAACGTGCCCTAATGTGCT-GGGTTTC-A-ATTTCTCGATCGACCAAATAGC
11048682 CAAATATCCTTTTAAAAGTTTCA
193 CAAATATCCTTTTAAAAGTTTCA
*
11048705 AAAATAAGGCAATGTTCTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTTCGAT
1 AAAATAAGGCAATGTTCTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-
*
11048770 TTTTCTCGTTCGACCAAATAGCCGAATATCCTTTTAAAATTTCAAAATAAGGCAATGTTTTGCGT
65 TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAATAAGGCAATGTTTTGCGT
* ** *
11048835 TTGGAAATTCGAGGAAACGTGCGTTAATGTGCTGGGTTTCAATTTCTCGATGGACCAAATAGCCA
130 TTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAATTTCTCGATCGACCAAATAGCCA
11048900 AATATCCT
195 AATATCCT
11048908 CTTATATCTT
Statistics
Matches: 187, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
216 29 0.16
217 61 0.33
218 96 0.51
219 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (215 bp):
AAAATAAGGCAATGTTCTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGAT
TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAATAAGGCAATGTTTTGCGTT
TGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCAATTTCTCGATCGACCAAATAGCCAA
ATATCCTTTTAAAAGTTTCA
Found at i:11048938 original size:108 final size:108
Alignment explanation
Indices: 11048481--11048907 Score: 666
Period size: 110 Copynumber: 4.0 Consensus size: 108
11048471 CTTTTTAAAA
* *
11048481 AAAATTT-AAAATAAGGCAATTTTTTGGGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGG
1 AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGG
11048545 GTTTCGA-TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
66 GTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* **
11048587 AAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTTTAGAAAACGTGCCCTAATGTG-TCG
1 AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCT-G
11048651 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
65 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* *
11048695 AAAAGTTTCAAAAATAAGGCAATGTTCTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTT
1 AAAA-TTTC-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCT
*
11048760 GGGTTTCGATTTTTCTCGTTCGACCAAATAGCCGAATATCCTTTT
64 GGGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
* **
11048805 AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCGTTAATGTGCTGG
1 AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGG
* * *
11048870 GTTTC-A-ATTTCTCGATGGACCAAATAGCCAAATATCCT
66 GTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCT
11048908 CTTATATCTT
Statistics
Matches: 296, Mismatches: 19, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
106 36 0.12
107 58 0.20
108 96 0.32
109 8 0.03
110 97 0.33
111 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (108 bp):
AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGG
GTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
Found at i:11049696 original size:34 final size:35
Alignment explanation
Indices: 11049637--11049717 Score: 139
Period size: 34 Copynumber: 2.3 Consensus size: 35
11049627 TTTATTTATA
11049637 ATTT-TAATTTTTTCTAAATATTTTTTTATTAATTT
1 ATTTGTAA-TTTTTCTAAATATTTTTTTATTAATTT
11049672 ATTTGTAATTTTTCTAAATA-TTTTTTATTAATTT
1 ATTTGTAATTTTTCTAAATATTTTTTTATTAATTT
11049706 ATTTGTAATTTT
1 ATTTGTAATTTT
11049718 ACTTATTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
34 26 0.58
35 16 0.36
36 3 0.07
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (35 bp):
ATTTGTAATTTTTCTAAATATTTTTTTATTAATTT
Found at i:11049733 original size:34 final size:34
Alignment explanation
Indices: 11049637--11049733 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
11049627 TTTATTTATA
*
11049637 ATTT-TAATTTTTTCTAAATATTTTTTTATTAATTT
1 ATTTGTAA-TTTTACTAAAT-TTTTTTTATTAATTT
* *
11049672 ATTTGTAATTTTTCTAAATATTTTTTATTAATTT
1 ATTTGTAATTTTACTAAATTTTTTTTATTAATTT
*
11049706 ATTTGTAATTTTACT-TATTTTTATTTAT
1 ATTTGTAATTTTACTAAATTTTT-TTTAT
11049734 ACACTATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
33 5 0.09
34 33 0.59
35 15 0.27
36 3 0.05
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (34 bp):
ATTTGTAATTTTACTAAATTTTTTTTATTAATTT
Found at i:11064693 original size:13 final size:13
Alignment explanation
Indices: 11064675--11064709 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
11064665 GCCCAGCCCA
11064675 GCCTGAAATATGG
1 GCCTGAAATATGG
11064688 GCCTGAAATATGG
1 GCCTGAAATATGG
*
11064701 GCCTAAAAT
1 GCCTGAAAT
11064710 TTTGTCCAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (13 bp):
GCCTGAAATATGG
Found at i:11076135 original size:31 final size:30
Alignment explanation
Indices: 11076071--11076139 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
11076061 CGATTTCGCG
11076071 AAAAAT-GGCCCATTCCGGTAAATAATAAA
1 AAAAATCGGCCCATTCCGGTAAATAATAAA
* **
11076100 AAAAATCGGCCCATTTCGGTAAATTTTAAA
1 AAAAATCGGCCCATTCCGGTAAATAATAAA
*
11076130 AAAAAACGGC
1 AAAAATCGGC
11076140 TTTTTTTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 6 0.17
30 29 0.83
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.22
Consensus pattern (30 bp):
AAAAATCGGCCCATTCCGGTAAATAATAAA
Found at i:11077101 original size:34 final size:31
Alignment explanation
Indices: 11077030--11077145 Score: 117
Period size: 34 Copynumber: 3.5 Consensus size: 31
11077020 GTTTAATATT
* *
11077030 TTTTTAAAAATTAATTAAATTAGATTTTAAGG
1 TTTTTAAAAAATAATTAAATTAGAGTTTAA-G
* *
11077062 GTTTTAAATAAATAAGTTAAATTAGGGTTTAGAG
1 TTTTTAAA-AAATAA-TTAAATTAGAGTTTA-AG
11077096 TTTTTAAGAAAATTAATTAAATTAGAGTTT-AG
1 TTTTTAA-AAAA-TAATTAAATTAGAGTTTAAG
11077128 TTTTTAAAAGAAATAATT
1 TTTTT-AAA-AAATAATT
11077146 TTGTGTTTAG
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
32 20 0.28
33 10 0.14
34 36 0.51
35 5 0.07
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (31 bp):
TTTTTAAAAAATAATTAAATTAGAGTTTAAG
Found at i:11077367 original size:126 final size:125
Alignment explanation
Indices: 11077208--11077601 Score: 508
Period size: 126 Copynumber: 3.1 Consensus size: 125
11077198 ATTTTGTTTT
* * * * *
11077208 TTTTTCTACAGTATTTTC-AGGAAAATTAATTTTGAGAAGATGATTCTGAAAAGATAATGTCAAA
1 TTTTTCTACAGTAGTTTCTTGAAAAAATAATTTTGAGAAGATG-TTCTGAAAA-ATAGTGTCAAA
* *
11077272 AACGCTTCAAGCAGAATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCTACGTGGACGCTA
64 AACGCTTCAAGCAGAATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCTACATGGACGCTC
* * * * *
11077334 TTTTTTTATAGTAGTTTC-TGAAAAAATAATTTTGAAAAGACGGTTCTAAATAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTTCTTGAAAAAATAATTTTGAGAAGA-TGTTCTGAA-AAATAGTGTCAAA
* * *
11077398 AATGCTTCAAGCAGAATGCACTGTCAGCAAAATTGATGAAAAGAGCTCCTACTTGGACGCTC
64 AACGCTTCAAGCAGAATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCTACATGGACGCTC
* *
11077460 TTTTTCTACAATA-ATTCTTGAAAAAATAATTTTGAGAAGACTGTTCTGAACAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTTCTTGAAAAAATAATTTTGAGAAGA-TGTTCTGAA-AAATAGTGTCAAA
* * * *
11077524 AACGCTTCAAGCAGGATTCACTGTCAGCAAAATTGATGAAAAAAGCTTCTACATGGACACTC
64 AACGCTTCAAGCAGAATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCTACATGGACGCTC
11077586 TTTTTCTACAGTAGTT
1 TTTTTCTACAGTAGTT
11077602 CATGTTTGGC
Statistics
Matches: 232, Mismatches: 31, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
125 3 0.01
126 224 0.97
127 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTTCTTGAAAAAATAATTTTGAGAAGATGTTCTGAAAAATAGTGTCAAAAA
CGCTTCAAGCAGAATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCTACATGGACGCTC
Found at i:11085599 original size:25 final size:25
Alignment explanation
Indices: 11085565--11085614 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
11085555 TTGGATAAAA
11085565 AAGGGTTGCTAAGTGCAGATTCCCC
1 AAGGGTTGCTAAGTGCAGATTCCCC
*
11085590 AAGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGTTGCTAAGTGCAGATTCCCC
11085615 GAATTATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (25 bp):
AAGGGTTGCTAAGTGCAGATTCCCC
Found at i:11085695 original size:43 final size:44
Alignment explanation
Indices: 11085593--11085827 Score: 188
Period size: 42 Copynumber: 5.5 Consensus size: 44
11085583 ATTCCCCAAG
* * *
11085593 GGTTGCTAAGTGCTGATTCC-CCGAAT-TATTGACTCT-AAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCT-TTGATTGTGAAAGGT
* *
11085635 GGTTGCTAAGTGTTGATTCCACGGTATCTTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGT
** * * *
11085678 GGTTGC-AATGTGCTGATTCC-CCGTATCACTCAATAT-AAAGGT
1 GGTTGCTAA-GTGCTGATTCCACCGTATCTTTGATTGTGAAAGGT
* *
11085720 GGTTGCTAAGTGCTGATTTCACTGTATCTTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGT
* * **
11085763 GGTTGCTATGTGTTGATTCC-CCGTATCACTGAATT-T--AAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTG-ATTGTGAAAGGT
* * *
11085804 GGTTACTAAGTGTTGAATCCACCG
1 GGTTGCTAAGTGCTGATTCCACCG
11085828 AGTAATGGAT
Statistics
Matches: 154, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
40 4 0.03
41 22 0.14
42 59 0.38
43 58 0.38
44 11 0.07
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (44 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGT
Found at i:11085737 original size:85 final size:84
Alignment explanation
Indices: 11085592--11085825 Score: 317
Period size: 85 Copynumber: 2.8 Consensus size: 84
11085582 GATTCCCCAA
* * * *
11085592 GGGTTGCTAA-GTGCTGATTCCCCGAATTATTGACTCTAAAGGTGGTTGCTAAGTGTTGATTCCA
1 GGGTTGC-AATGTGCTGATTCCCCGTATCACTGAAT-TAAAGGTGGTTGCTAAGTGTTGATTCCA
11085656 CGGTATCTTTGATTGTGAAAG
64 CGGTATCTTTGATTGTGAAAG
* * *
11085677 GGGTTGCAATGTGCTGATTCCCCGTATCACTCAATATAAAGGTGGTTGCTAAGTGCTGATTTCAC
1 GGGTTGCAATGTGCTGATTCCCCGTATCACTGAAT-TAAAGGTGGTTGCTAAGTGTTGATTCCAC
*
11085742 TGTATCTTTGATTGTGAAAG
65 GGTATCTTTGATTGTGAAAG
* * * * *
11085762 GGGTTGCTATGTGTTGATTCCCCGTATCACTGAATTTAAGGTGGTTACTAAGTGTTGAATCCAC
1 GGGTTGCAATGTGCTGATTCCCCGTATCACTGAATTAAAGGTGGTTGCTAAGTGTTGATTCCAC
11085826 CGAGTAATGG
Statistics
Matches: 131, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
84 26 0.20
85 105 0.80
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (84 bp):
GGGTTGCAATGTGCTGATTCCCCGTATCACTGAATTAAAGGTGGTTGCTAAGTGTTGATTCCACG
GTATCTTTGATTGTGAAAG
Found at i:11088912 original size:397 final size:396
Alignment explanation
Indices: 11088172--11088939 Score: 942
Period size: 397 Copynumber: 1.9 Consensus size: 396
11088162 TCTAGTGTCT
* *
11088172 TAAGTGTAGTATTTTCGTCTATATACAATTGTATTTTTTCAAACATATTAGCTAATAAAATTATT
1 TAAGTGTAGTATTTTCGTCAATATACAATTGTATTTTTTCAAACAGATTAGCTAATAAAATTATT
* **
11088237 CATGAATTACATTAATATCCTTTGTATATTATCCTCAATGGTTTTTGTATGCAAAGCAAAATGAA
66 CATGAATTACATTAATA-CCTTTGTATAATATCCTCAATGGTTTTTGTACACAAAGCAAAATGAA
* * * *
11088302 AGCAAATATTAGCTCATTGGTTGTCTAATGTTTAACTAATACTAAACGGTATTATGTGATTAGAT
130 AGCAAATATTAGCTCACTGGTTGTCTAATGTTTAACTAATACTAAACGATATTATATGATCAGAT
* * * * * *
11088367 CGTAATACAGAAAGATAGTTTATATTAGTAGATGAACCTAAAGATATCCTTAATTTGATATAAAA
195 CGTAATACAGAAAGATAATTTATATTAGTAGACGAACCTAAAGATATCCCTAATCTAATAGAAAA
** * *
11088432 TGAGCAAACTGATTAAAAGACTAATATGTCATCTATCAAGTTCAATTGGGGAGATGCTTTATCTT
260 TGAGCAAACCAATTAAAAGACTAATATGTCATCTATCAAGTCCAATTAGGGAGATGCTTTATCTT
* *
11088497 GGGCATCAGAGCGGATGACTCCTAGAAGATAGAGACATAGATGTGATTGACCGGCTATTGGATCA
325 AGGCATCAGAGCGGATGACTCCTAAAAGATAGAGACATAGATGTGATTGACCGGCTATTGGATCA
11088562 GGTGCCC
390 GGTGCCC
* * * * *
11088569 TAAGTGTAGTATTTTCGTCAATGTACACTTGTAAATTTTTT-GAACAGGTT-GATTAATAAAATT
1 TAAGTGTAGTATTTTCGTCAATATACAATTGT--ATTTTTTCAAACAGATTAG-CTAATAAAATT
* * *
11088632 ATTCATGAATTACATTAATA-CTTTGTATAATGTCCTCATGTGGTTTTTGTACACAAAGTAAAAT
63 ATTCATGAATTACATTAATACCTTTGTATAATATCCTCA-ATGGTTTTTGTACACAAAGCAAAAT
* * * ** *
11088696 -AGGAGCAAATGTT-GCTCACTGGTTGTTTAATGTTTAAACTAATACTAAGTGATATTATATGGT
127 GA-AAGCAAATATTAGCTCACTGGTTGTCTAATGTTT-AACTAATACTAAACGATATTATATGAT
* * * * *
11088759 CGGATTGTAATAC-GAAA-ATACATCTTATATTAGTAGACGAACCTAAATATGTCCCTAGTCTAA
190 CAGATCGTAATACAGAAAGATA-AT-TTATATTAGTAGACGAACCTAAAGATATCCCTAATCTAA
* * * **
11088822 TCGAAAATGAGTAAACCAATTGAAAGACTAATATGTTGTCTATCAAGTCCAATTAGGGAGATG-T
253 TAGAAAATGAGCAAACCAATTAAAAGACTAATATGTCATCTATCAAGTCCAATTAGGGAGATGCT
* * *
11088886 TTCGTCTTAGGCATC-GAAGTGGATGACTCCTAAAAGATAGAGACATGGATGTGA
318 TT-ATCTTAGGCATCAG-AGCGGATGACTCCTAAAAGATAGAGACATAGATGTGA
11088940 CTGGCTAGAT
Statistics
Matches: 313, Mismatches: 48, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
395 3 0.01
396 46 0.15
397 221 0.71
398 36 0.12
399 7 0.02
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (396 bp):
TAAGTGTAGTATTTTCGTCAATATACAATTGTATTTTTTCAAACAGATTAGCTAATAAAATTATT
CATGAATTACATTAATACCTTTGTATAATATCCTCAATGGTTTTTGTACACAAAGCAAAATGAAA
GCAAATATTAGCTCACTGGTTGTCTAATGTTTAACTAATACTAAACGATATTATATGATCAGATC
GTAATACAGAAAGATAATTTATATTAGTAGACGAACCTAAAGATATCCCTAATCTAATAGAAAAT
GAGCAAACCAATTAAAAGACTAATATGTCATCTATCAAGTCCAATTAGGGAGATGCTTTATCTTA
GGCATCAGAGCGGATGACTCCTAAAAGATAGAGACATAGATGTGATTGACCGGCTATTGGATCAG
GTGCCC
Found at i:11089768 original size:57 final size:57
Alignment explanation
Indices: 11089674--11089854 Score: 236
Period size: 51 Copynumber: 3.3 Consensus size: 57
11089664 ATAGAAATTG
11089674 TGAAAATGGAGAAATTGAAATCATTTGGAAATT-ATTATGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAA-TGAAATCATTTGG-AATTGATTATGGTTTTCTCCAAAATGAAAA
* *
11089732 TGAAAATGGAGAAATGAAAACATTTGGAATTGATTATGGTTTTTTCC------AAAA
1 TGAAAATGGAGAAATGAAATCATTTGGAATTGATTATGGTTTTCTCCAAAATGAAAA
* * *
11089783 TGAAAATGGAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGAAATCATTTGGAATTGATTATGGTTTTCTCCAAAATGAAAA
11089840 TGAAAAT-GA-AAATGA
1 TGAAAATGGAGAAATGA
11089855 CCTGAAAAAT
Statistics
Matches: 109, Mismatches: 7, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
51 46 0.42
55 6 0.06
56 6 0.06
57 37 0.34
58 14 0.13
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.30
Consensus pattern (57 bp):
TGAAAATGGAGAAATGAAATCATTTGGAATTGATTATGGTTTTCTCCAAAATGAAAA
Found at i:11089841 original size:6 final size:6
Alignment explanation
Indices: 11089830--11089854 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11089820 GGTTTTCTCC
11089830 AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG A
11089855 CCTGAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:11092231 original size:19 final size:21
Alignment explanation
Indices: 11092189--11092232 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
11092179 ATGTTTCCTT
*
11092189 CTTTCTCTATTTTTTTTTCAA
1 CTTTCTCTATTTCTTTTTCAA
11092210 CTTTCTCT-TTTCTTTTTC-A
1 CTTTCTCTATTTCTTTTTCAA
11092229 CTTT
1 CTTT
11092233 TGATACTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 9 0.41
21 8 0.36
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.68
Consensus pattern (21 bp):
CTTTCTCTATTTCTTTTTCAA
Found at i:11098063 original size:2 final size:2
Alignment explanation
Indices: 11098056--11098184 Score: 226
Period size: 2 Copynumber: 65.5 Consensus size: 2
11098046 CGGTTGCCAT
*
11098056 TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
11098098 TC TC TC TC -C CC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11098138 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11098180 TC TC T
1 TC TC T
11098185 TTTGAACTCT
Statistics
Matches: 122, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
1 2 0.02
2 120 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:11098705 original size:37 final size:37
Alignment explanation
Indices: 11098642--11098722 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 37
11098632 AAATTTTAAT
11098642 AAATAA-A-AAATATATAAAATTATTAACTATTAAATTA
1 AAATAATATAAATATATAAAATTATTAACTATTAAA--A
* * *
11098679 AAATAATATAAATATAT-ATATT-TTAACTTTTTAAA
1 AAATAATATAAATATATAAAATTATTAACTATTAAAA
11098714 AAATAATAT
1 AAATAATAT
11098723 GTGCAGGTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
35 10 0.26
37 16 0.41
38 5 0.13
39 8 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (37 bp):
AAATAATATAAATATATAAAATTATTAACTATTAAAA
Found at i:11098937 original size:23 final size:22
Alignment explanation
Indices: 11098872--11098937 Score: 53
Period size: 24 Copynumber: 2.9 Consensus size: 22
11098862 AATTATTTTA
* *
11098872 ATATTTTTTATCAAATAAAATTT
1 ATATTTTTTAACAAA-AAAATAT
*
11098895 A-AGTTTATTTAAAAACAAAAATAT
1 ATA-TTT-TTTAACAA-AAAAATAT
*
11098919 ATATTTTTTAACAATAAAA
1 ATATTTTTTAACAAAAAAA
11098938 CAATAAATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
22 5 0.15
23 11 0.32
24 16 0.47
25 2 0.06
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATTTTTTAACAAAAAAATAT
Found at i:11103340 original size:41 final size:41
Alignment explanation
Indices: 11103133--11103329 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
11103123 TTTATCGTTA
* * * *
11103133 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
11103174 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
11103215 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
11103256 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
11103297 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
11103330 AAGAGCCGGT
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 143 0.97
42 2 0.01
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:11103600 original size:33 final size:33
Alignment explanation
Indices: 11103544--11103641 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
11103534 ATAGATATGT
*
11103544 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
11103576 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
11103609 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
11103642 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Found at i:11111829 original size:37 final size:37
Alignment explanation
Indices: 11111780--11111874 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 37
11111770 CTCAACTAGA
*
11111780 TTTATTAAATAAAAAATTGATATGTTTAGTAAATAA-
1 TTTATTTAATAAAAAATTGATATGTTTAGTAAATAAC
11111816 TTATATTTAATAAACATAAATTTGATATGTTTAGTAAATAAC
1 TT-TATTTAAT-AA-A-AAA-TTGATATGTTTAGTAAATAAC
*
11111858 TTTATTTAATTAAAAAT
1 TTTATTTAATAAAAAAT
11111875 CTCAATTCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
36 2 0.04
37 8 0.16
38 5 0.10
39 2 0.04
40 4 0.08
41 28 0.55
42 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTATTTAATAAAAAATTGATATGTTTAGTAAATAAC
Found at i:11113684 original size:150 final size:148
Alignment explanation
Indices: 11113328--11113913 Score: 849
Period size: 150 Copynumber: 4.0 Consensus size: 148
11113318 TAGGCGATCT
* * *
11113328 GGAGGCACATTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGCGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
* * * * * *
11113393 CACTGTATGTCTCACTTCTAGTAGTCCTTCCACC-CT-TCTTATTAGTTTTCCTTCCAAGATTTT
66 CACTATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTTTATCAGTTTTCCTTCCAAGATTTT
11113456 CTTCACTGTGCAATTT--
131 CTTCACTGTGCAATTTGG
* * *
11113472 GGAGGCACCTTCCACTGAGGATCTACTACTCCCCATCACGTTGGACGGAGAAGAGTGGGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
*
11113537 CACTGTGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCATTTTATCAGTTTTCCTTCCAAGATTT
66 CACTATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGATTT
11113602 TCTTCACTGTGCAATTTGGG
130 TCTTCACTGTGCAATTT-GG
* * *
11113622 GGAGGCACCTTTCACTGAGGATCTACTACTACCGATCACATTGGACGGAGAAGGGTGAGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
** * * * *
11113687 CACTATGCATCTCACTTCTAGGAATCCTTCCCCCACCCTTTATATCAGTTTTCCTTACAAGATTT
66 CACTATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTT-TATCAGTTTTCCTTCCAAGATTT
11113752 TCTTCACTGTGCAATTTGG
130 TCTTCACTGTGCAATTTGG
*
11113771 AGGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGATGGAGAAGAGTGAGGAATT
1 -GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATT
* **
11113836 CCA-TCATGTGTCTCACTTCTAGGAGTCCGTCCTCCACTCTTTTTATCAGTTTTCCTTCCATTAT
65 CCACT-ATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGAT
11113900 TTTCTTCACTGTGC
128 TTTCTTCACTGTGC
11113914 TTTCTCTTCT
Statistics
Matches: 396, Mismatches: 36, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
144 91 0.23
145 2 0.01
147 41 0.10
149 6 0.02
150 253 0.64
151 3 0.01
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (148 bp):
GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
CACTATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTTTATCAGTTTTCCTTCCAAGATTTT
CTTCACTGTGCAATTTGG
Found at i:11115622 original size:30 final size:29
Alignment explanation
Indices: 11115581--11115637 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 29
11115571 ATATAAAAGC
11115581 AAAAGAAGAAAACATAAGAGGG-GAGAGAGGT
1 AAAAGAAG-AAA-A-AAGAGGGAGAGAGAGGT
11115612 AAAA-AAGAAAAAAGAGGGAGAGAGAG
1 AAAAGAAGAAAAAAGAGGGAGAGAGAG
11115638 AGAAGAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 7 0.28
28 8 0.32
29 3 0.12
30 3 0.12
31 4 0.16
ACGTcount: A:0.60, C:0.02, G:0.35, T:0.04
Consensus pattern (29 bp):
AAAAGAAGAAAAAAGAGGGAGAGAGAGGT
Found at i:11119820 original size:137 final size:136
Alignment explanation
Indices: 11119571--11119820 Score: 308
Period size: 137 Copynumber: 1.8 Consensus size: 136
11119561 CCTCTTCTTC
* *
11119571 TTCATCATCAGAAAACGCCATTACCACTCTGATAGTATTGACAACAATGAAAGAAATAACTAACT
1 TTCATCATCAGAAAACGCCAGTACCACTCTGATAGTATTAACAACAATGAAAGAAATAACTAACT
* * * * * *
11119636 AGATTTTACTAAAAAAAATGCAATTAACAATATAAGAAATTGCAACAACATTAACAAAACCACTT
66 AAAGTTTAATAAAAAAAATGCAATTAACAATAAAAGAAACTGAAACAACATTAACAAAACCACTT
11119701 CCCTTT
131 CCCTTT
* * * *
11119707 TTCATCATTAGAAAACGCGAGTACCACTAC-GATCA-TATTAAACAACAATG-ACGAAAATAATT
1 TTCATCATCAGAAAACGCCAGTACCACT-CTGAT-AGTATT-AACAACAATGAAAG-AAATAACT
* * *
11119769 AACTAAAGTTTAATAAGAATAATGCAATTAACACTAAAAGAAACTGAAACAA
62 AACTAAAGTTTAATAAAAAAAATGCAATTAACAATAAAAGAAACTGAAACAA
11119821 TAATTACAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
136 34 0.36
137 61 0.64
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.24
Consensus pattern (136 bp):
TTCATCATCAGAAAACGCCAGTACCACTCTGATAGTATTAACAACAATGAAAGAAATAACTAACT
AAAGTTTAATAAAAAAAATGCAATTAACAATAAAAGAAACTGAAACAACATTAACAAAACCACTT
CCCTTT
Found at i:11133468 original size:50 final size:49
Alignment explanation
Indices: 11133406--11133668 Score: 211
Period size: 50 Copynumber: 5.3 Consensus size: 49
11133396 GATCTGTAAT
* *
11133406 CTTCAATTTGTTCAACTGCAATTTCGGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGC-ATTTCAGGGAAACCAGATCCGCCGTCGTAG
* * * * * **** * *
11133456 CTTCAATCTGTTCCACCGCACTGCTAAGGACGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCATTTC-AGGGAAACCAGATCCGCCGTCGTAG
* * *
11133506 CTTCAATTTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGC-ATTTCAGGGAAACCAGATCCGCCGTCGTAG
** * * * *** * *
11133556 CTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCATTTC-AGGGAAACCAGATCCGCCGTCGTAG
* * * *
11133606 CTTCAATCTTTTTAATTGCTATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGC-ATTTCAGGGAAACCAGATCCGCCGTCGTAG
11133656 CTTCAATCTGTTC
1 CTTCAATCTGTTC
11133669 TGCTGCACTG
Statistics
Matches: 153, Mismatches: 56, Indels: 8
0.71 0.26 0.04
Matches are distributed among these distances:
49 5 0.03
50 144 0.94
51 4 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (49 bp):
CTTCAATCTGTTCAACTGCATTTCAGGGAAACCAGATCCGCCGTCGTAG
Found at i:11133516 original size:100 final size:100
Alignment explanation
Indices: 11133406--11133714 Score: 512
Period size: 100 Copynumber: 3.1 Consensus size: 100
11133396 GATCTGTAAT
* *
11133406 CTTCAATTTGTTCAACTGCAATTTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATTTGTTCAACTGCAATATCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCG
* *
11133471 CCGCACTGCTAAGGACGTAAGATCCGCCGTTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
*
11133506 CTTCAATTTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCG
1 CTTCAATTTGTTCAACTGCAATATCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCG
11133571 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
66 CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
* * * * *
11133606 CTTCAATCTT-TTTAATTGCTATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCT
1 CTTCAAT-TTGTTCAACTGCAATATCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
11133670 GCTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
65 GCTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
11133706 CTTCAATTT
1 CTTCAATTT
11133715 TTTTACTTTT
Statistics
Matches: 198, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
99 2 0.01
100 194 0.98
101 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (100 bp):
CTTCAATTTGTTCAACTGCAATATCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCG
CTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGG
Found at i:11133694 original size:50 final size:50
Alignment explanation
Indices: 11133440--11133712 Score: 246
Period size: 50 Copynumber: 5.5 Consensus size: 50
11133430 CGGGGAAACC
* *
11133440 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACTGCTAAGGACGTA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
* * * * * ** ***
11133490 AGATCCGCCGTTGTGGCTTCAATTTGTTCAACTGCAATG-TCGGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCT-AAGGAAGTA
*
11133540 AGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
* * * ** * * * ***
11133590 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCTA-T-ATCAGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGC-ACTGCT-AAGGAAGTA
**
11133640 AGATCCGCCGTCGTAGCTTCAATCTGTTCTGCTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
* *
11133690 AGATCCGCCGTTGTGGCTTCAAT
1 AGATCCGCCGTCGTAGCTTCAAT
11133713 TTTTTTACTT
Statistics
Matches: 168, Mismatches: 49, Indels: 12
0.73 0.21 0.05
Matches are distributed among these distances:
49 3 0.02
50 162 0.96
51 3 0.02
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.28
Consensus pattern (50 bp):
AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
Found at i:11145910 original size:8 final size:8
Alignment explanation
Indices: 11145897--11145922 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11145887 CCGAATTTAG
11145897 AAAAATAA
1 AAAAATAA
11145905 AAAAATAA
1 AAAAATAA
11145913 AAAAATAA
1 AAAAATAA
11145921 AA
1 AA
11145923 TCAGGACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:11149563 original size:27 final size:27
Alignment explanation
Indices: 11149533--11149591 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
11149523 TTTAAATATC
*
11149533 CGTGGGACATTTCGCAATATAGGTGTT
1 CGTGGGACATTCCGCAATATAGGTGTT
* *
11149560 CGTGGGACATTCCGTAATATATGTGTT
1 CGTGGGACATTCCGCAATATAGGTGTT
11149587 CGTGG
1 CGTGG
11149592 AAAAGTCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.20, C:0.15, G:0.31, T:0.34
Consensus pattern (27 bp):
CGTGGGACATTCCGCAATATAGGTGTT
Found at i:11153033 original size:13 final size:13
Alignment explanation
Indices: 11153015--11153039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11153005 CAAAACGATA
11153015 AAATTTTCACACG
1 AAATTTTCACACG
11153028 AAATTTTCACAC
1 AAATTTTCACAC
11153040 AAGTAAATTC
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:11159838 original size:68 final size:72
Alignment explanation
Indices: 11159755--11159885 Score: 198
Period size: 68 Copynumber: 1.9 Consensus size: 72
11159745 TAATAATATT
* *
11159755 TTAATATTAAATTTAATTTAATACTTATC-T-T-AAT-AGTATTTTATTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATTTAATACTTATCTTGTGAATAAATATTATATTAATTTAATATTAAAGT
11159816 GATTATC
66 GATTATC
* *
11159823 TTAATATTAAATTTAATTTAATATTTATCTTGTGGATAAATATTATATTAATTTAATATTAAA
1 TTAATATTAAATTTAATTTAATACTTATCTTGTGAATAAATATTATATTAATTTAATATTAAA
11159886 TAATATTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
68 28 0.51
69 1 0.02
70 1 0.02
71 2 0.04
72 23 0.42
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (72 bp):
TTAATATTAAATTTAATTTAATACTTATCTTGTGAATAAATATTATATTAATTTAATATTAAAGT
GATTATC
Found at i:11159891 original size:10 final size:11
Alignment explanation
Indices: 11159867--11159902 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
11159857 GATAAATATT
*
11159867 ATATTAATTTA
1 ATATTAAATTA
11159878 ATATTAAA-TA
1 ATATTAAATTA
11159888 ATATTAAATTA
1 ATATTAAATTA
11159899 ATAT
1 ATAT
11159903 AATATTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAAATTA
Found at i:11159926 original size:5 final size:6
Alignment explanation
Indices: 11159861--11159908 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 6
11159851 CTTGTGGATA
11159861 AATATT -ATATT AAT-TT AATATT AA-A-T AATATT AA-ATT AATA-T
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
11159903 AATATT
1 AATATT
11159909 TATCTTGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
4 3 0.08
5 22 0.61
6 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:11163136 original size:19 final size:19
Alignment explanation
Indices: 11163090--11163137 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
11163080 GTATACATTT
11163090 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
11163108 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
11163127 TAAATTTTATT
1 TAAATTTTATT
11163138 CATATTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:11168412 original size:21 final size:21
Alignment explanation
Indices: 11168364--11168412 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
11168354 TTGTTAAATA
* *
11168364 TAAATTATTAAAAATTATATT
1 TAAATTTTTAAAAAATATATT
*
11168385 TATATTTTTAATAAAATATA-T
1 TAAATTTTTAA-AAAATATATT
11168406 TAAATTT
1 TAAATTT
11168413 ATTTTAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATTTTTAAAAAATATATT
Found at i:11168868 original size:42 final size:42
Alignment explanation
Indices: 11168816--11168899 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
11168806 TATCTAAAAT
*
11168816 AATATAAAATATTATATTAATAAGATTCAAATTAGAAATAAA
1 AATATAAAATATTATATTAATAAGATCCAAATTAGAAATAAA
* *
11168858 AATATAAAATATTATATTATTAAGATCCTAATTAGAAATAAA
1 AATATAAAATATTATATTAATAAGATCCAAATTAGAAATAAA
11168900 TAATCTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.35
Consensus pattern (42 bp):
AATATAAAATATTATATTAATAAGATCCAAATTAGAAATAAA
Found at i:11181179 original size:24 final size:24
Alignment explanation
Indices: 11181138--11181187 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
11181128 CTACAGAAGA
* *
11181138 AAATAACAAAGATTTTATGCTAAT
1 AAATAACAAAGATGTTATACTAAT
11181162 AAATAACAAATG-TGTTATACTAAT
1 AAATAACAAA-GATGTTATACTAAT
11181186 AA
1 AA
11181188 TTTCTAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (24 bp):
AAATAACAAAGATGTTATACTAAT
Found at i:11188996 original size:18 final size:19
Alignment explanation
Indices: 11188967--11189004 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
11188957 TAAATGAATA
*
11188967 ATTATATATTTTTAAAGAC
1 ATTATATATTTTGAAAGAC
11188986 ATTAT-TATTTTGAAAGAC
1 ATTATATATTTTGAAAGAC
11189004 A
1 A
11189005 CCTATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (19 bp):
ATTATATATTTTGAAAGAC
Found at i:11189621 original size:29 final size:30
Alignment explanation
Indices: 11189567--11189720 Score: 172
Period size: 30 Copynumber: 5.2 Consensus size: 30
11189557 AAAAAAACTG
* *
11189567 CATTTTTACCTCTAAACTTT-TCTAAAATTA
1 CATTTTGACCCCTAAACTTTCT-TAAAATTA
* *
11189597 CATTTTGACTCCT-AATTTTCTTAAAATTA
1 CATTTTGACCCCTAAACTTTCTTAAAATTA
**
11189626 CATTTCAACCCCTAAA-TTT-TTATAAATTA
1 CATTTTGACCCCTAAACTTTCTTA-AAATTA
* *
11189655 CATTTTGACTCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTTAAAATTA
* *
11189685 TATTTTGACCCCTAAACTTTCTTGAAATTA
1 CATTTTGACCCCTAAACTTTCTTAAAATTA
11189715 CATTTT
1 CATTTT
11189721 AGTCCCAAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.03
29 45 0.44
30 53 0.51
31 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTTAAAATTA
Found at i:11189682 original size:59 final size:58
Alignment explanation
Indices: 11189578--11189720 Score: 189
Period size: 59 Copynumber: 2.4 Consensus size: 58
11189568 ATTTTTACCT
* *
11189578 CTAAACTTTTCTAAAATTACATTTTGACTCCTAATTTTCTTAAAATTACATTTCAACCC
1 CTAAACTTTT-TAAAATTACATTTTGACTCCTAACTTTCTCAAAATTACATTTCAACCC
* **
11189637 CTAAA-TTTTTATAAATTACATTTTGACTCCTAAACTTTCTCAAAATTATATTTTGACCC
1 CTAAACTTTTTA-AAATTACATTTTGACTCCT-AACTTTCTCAAAATTACATTTCAACCC
*
11189696 CTAAACTTTCTTGAAATTACATTTT
1 CTAAACTTT-TTAAAATTACATTTT
11189721 AGTCCCAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
57 2 0.03
58 23 0.31
59 32 0.43
60 15 0.20
61 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.44
Consensus pattern (58 bp):
CTAAACTTTTTAAAATTACATTTTGACTCCTAACTTTCTCAAAATTACATTTCAACCC
Found at i:11190088 original size:5 final size:5
Alignment explanation
Indices: 11190079--11190131 Score: 67
Period size: 5 Copynumber: 11.2 Consensus size: 5
11190069 AAAAAATAAA
* *
11190079 AAAAG CAAAG -AAAG AAAAG AAAAG AAAAG -AAAG AAAAG AAAA- AGAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
11190126 AAAAG A
1 AAAAG A
11190132 GGGGAGAGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 11 0.26
5 31 0.74
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:11190092 original size:9 final size:9
Alignment explanation
Indices: 11190076--11190128 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
11190066 AATAAAAAAT
11190076 AAAA-AAAG
1 AAAAGAAAG
*
11190084 CAAAGAAAG
1 AAAAGAAAG
11190093 AAAAGAAAAG
1 AAAAG-AAAG
11190103 AAAAGAAAG
1 AAAAGAAAG
11190112 AAAAGAAA-
1 AAAAGAAAG
11190120 AAGAAGAAA
1 AA-AAGAAA
11190129 AGAGGGGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
8 5 0.12
9 26 0.65
10 9 0.22
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:11190096 original size:14 final size:13
Alignment explanation
Indices: 11190071--11190131 Score: 77
Period size: 14 Copynumber: 4.5 Consensus size: 13
11190061 ACAAAAATAA
*
11190071 AAAATAAAAAAAG
1 AAAAGAAAAAAAG
*
11190084 CAAAGAAAGAAAAG
1 AAAAGAAA-AAAAG
11190098 AAAAGAAAAGAAAG
1 AAAAGAAAA-AAAG
11190112 AAAAGAAAAAGAAG
1 AAAAGAAAAA-AAG
11190126 AAAAGA
1 AAAAGA
11190132 GGGGAGAGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
13 8 0.19
14 34 0.81
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:11190107 original size:19 final size:19
Alignment explanation
Indices: 11190079--11190120 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
11190069 AAAAAATAAA
*
11190079 AAAAGCAAAGAAAGAAAAG
1 AAAAGAAAAGAAAGAAAAG
11190098 AAAAGAAAAGAAAGAAAAG
1 AAAAGAAAAGAAAGAAAAG
11190117 AAAA
1 AAAA
11190121 AGAAGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAGAAAGAAAAG
Found at i:11190129 original size:9 final size:8
Alignment explanation
Indices: 11190069--11190129 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 8
11190059 ACACAAAAAT
*
11190069 AAAAAATA
1 AAAAAAGA
11190077 AAAAAAGCA
1 AAAAAAG-A
*
11190086 AAGAAAGA
1 AAAAAAGA
*
11190094 AAAGAA-A
1 AAAAAAGA
*
11190101 AGAAAAGA
1 AAAAAAGA
11190109 AAGAAAAGA
1 AA-AAAAGA
11190118 AAAAGAAGA
1 AAAA-AAGA
11190127 AAA
1 AAA
11190130 GAGGGGAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
7 5 0.12
8 15 0.36
9 22 0.52
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:11190232 original size:7 final size:7
Alignment explanation
Indices: 11190220--11190286 Score: 64
Period size: 7 Copynumber: 9.0 Consensus size: 7
11190210 GAAGGAAAGG
11190220 AAGAAAA
1 AAGAAAA
11190227 AAGAAAAA
1 AAG-AAAA
11190235 AAGAAGAAGA
1 AAG-A-AA-A
*
11190245 AAGAAAG
1 AAGAAAA
*
11190252 AAGAAAG
1 AAGAAAA
11190259 AAGAAAA
1 AAGAAAA
11190266 AA-AGAAA
1 AAGA-AAA
11190273 AAGAAAA
1 AAGAAAA
11190280 AAGAAAA
1 AAGAAAA
11190287 TAATTTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
6 1 0.02
7 33 0.62
8 12 0.23
9 3 0.06
10 4 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:11190241 original size:11 final size:11
Alignment explanation
Indices: 11190223--11190286 Score: 57
Period size: 11 Copynumber: 6.1 Consensus size: 11
11190213 GGAAAGGAAG
11190223 AAAA-AAGAAA
1 AAAAGAAGAAA
11190233 AAAAGAAG-AA
1 AAAAGAAGAAA
*
11190243 GAAAGAA-AGAA
1 AAAAGAAGA-AA
*
11190254 GAAAGAAGAAA
1 AAAAGAAGAAA
11190265 AAAAGAA-AAA
1 AAAAGAAGAAA
11190275 GAAAA-AAGAAA
1 -AAAAGAAGAAA
11190286 A
1 A
11190287 TAATTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
10 18 0.39
11 27 0.59
12 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:11190242 original size:18 final size:18
Alignment explanation
Indices: 11190219--11190286 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
11190209 AGAAGGAAAG
11190219 GAAGAAAAAAGAAAAAAA
1 GAAGAAAAAAGAAAAAAA
* *
11190237 GAAGAAGAAAG-AAAGAA
1 GAAGAAAAAAGAAAAAAA
*
11190254 GAAAGAAGAAAA-AAAGAAA
1 G-AAGAA-AAAAGAAAAAAA
11190273 -AAGAAAAAAGAAAA
1 GAAGAAAAAAGAAAA
11190287 TAATTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.10
17 14 0.35
18 15 0.38
19 7 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
GAAGAAAAAAGAAAAAAA
Found at i:11190245 original size:21 final size:21
Alignment explanation
Indices: 11190219--11190286 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
11190209 AGAAGGAAAG
11190219 GAAGAAAAAAGAAAAAAAGAA
1 GAAGAAAAAAGAAAAAAAGAA
*
11190240 GAAGAAAGAAAG-AAGAAAGAA
1 GAAGAAA-AAAGAAAAAAAGAA
11190261 G-A-AAAAAAGAAAAAGAA-AA
1 GAAGAAAAAAGAAAAA-AAGAA
11190280 -AAGAAAA
1 GAAGAAAA
11190287 TAATTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 4 0.10
19 9 0.22
20 7 0.17
21 16 0.40
22 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
GAAGAAAAAAGAAAAAAAGAA
Found at i:11190569 original size:15 final size:15
Alignment explanation
Indices: 11190541--11190587 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
11190531 GAGGTAGGCC
11190541 AGAAAAAAAGAAAGGA
1 AGAAAAAAA-AAAGGA
*
11190557 AGAGAAAAAAAA-GA
1 AGAAAAAAAAAAGGA
11190571 GAGAAAAAAAAAAGGA
1 -AGAAAAAAAAAAGGA
11190587 A
1 A
11190588 AAAGAAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 2 0.07
15 15 0.56
16 10 0.37
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAAGGA
Found at i:11190575 original size:13 final size:13
Alignment explanation
Indices: 11190557--11190607 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
11190547 AAAGAAAGGA
11190557 AGAGAAAAAAAAG
1 AGAGAAAAAAAAG
*
11190570 AGAGAAAAAAAAA
1 AGAGAAAAAAAAG
11190583 AG-GAAAAAGAAAG
1 AGAGAAAAA-AAAG
11190596 AGA-AAAAGAAAA
1 AGAGAAAA-AAAA
11190608 AAGGTTCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 6 0.18
13 26 0.79
14 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AGAGAAAAAAAAG
Found at i:11190589 original size:6 final size:6
Alignment explanation
Indices: 11190541--11190608 Score: 52
Period size: 6 Copynumber: 11.2 Consensus size: 6
11190531 GAGGTAGGCC
* *
11190541 AGAAAA A-AAGAA AGGAAG AGAAAA A-AAAGA GAGAAAA A-AAAA AGGAAAA
1 AGAAAA AGAA-AA AGAAAA AGAAAA AGAAA-A -AGAAAA AGAAAA A-GAAAA
*
11190590 AGAAAG AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA A
11190609 AGGTTCAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
5 10 0.20
6 28 0.57
7 8 0.16
8 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:11190597 original size:26 final size:25
Alignment explanation
Indices: 11190545--11190611 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
11190535 TAGGCCAGAA
*
11190545 AAAAAGAAAGGAAGAGAAAAAAAAGAG
1 AAAAAGAAA-AAAG-GAAAAAAAAGAG
11190572 AGAAAA-AAAAAAGGAAAAAGAAAGAG
1 A-AAAAGAAAAAAGGAAAAA-AAAGAG
11190598 AAAAAGAAAAAAGG
1 AAAAAGAAAAAAGG
11190612 TTCAATTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 10 0.28
26 18 0.50
27 4 0.11
28 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (25 bp):
AAAAAGAAAAAAGGAAAAAAAAGAG
Found at i:11190603 original size:12 final size:12
Alignment explanation
Indices: 11190551--11190606 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
11190541 AGAAAAAAAG
*
11190551 AAAGGAAGAGAA
1 AAAGAAAGAGAA
11190563 AAA-AAAGAGAGA
1 AAAGAAAGAGA-A
* *
11190575 AAAAAAAAAGGAA
1 AAAGAAAGA-GAA
11190588 AAAGAAAGAGAA
1 AAAGAAAGAGAA
11190600 AAAGAAA
1 AAAGAAA
11190607 AAAGGTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 6 0.16
12 17 0.46
13 12 0.32
14 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAGAA
Found at i:11190946 original size:19 final size:20
Alignment explanation
Indices: 11190924--11190965 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
11190914 GAAAATATTC
11190924 AAAAAAATT-T-GTGTTTTCG
1 AAAAAAATTCTCGT-TTTTCG
11190943 AAAAAAATTCTCGTTTTTCG
1 AAAAAAATTCTCGTTTTTCG
11190963 AAA
1 AAA
11190966 TTTTTGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 10 0.48
21 2 0.10
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (20 bp):
AAAAAAATTCTCGTTTTTCG
Found at i:11191013 original size:17 final size:18
Alignment explanation
Indices: 11190991--11191024 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11190981 AATTTTTTTC
11190991 TCGTG-TTTCAAAAATAT
1 TCGTGTTTTCAAAAATAT
11191008 TCGTGTTTTCAAAAATA
1 TCGTGTTTTCAAAAATA
11191025 AGGCAACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATAT
Found at i:11191181 original size:18 final size:18
Alignment explanation
Indices: 11191140--11191181 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11191130 ATTTGTGTAA
*
11191140 AAAAAATCTTCGTGGTTT
1 AAAAAATATTCGTGGTTT
* *
11191158 CAAAAATATTCGTGTTTT
1 AAAAAATATTCGTGGTTT
11191176 AAAAAA
1 AAAAAA
11191182 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (18 bp):
AAAAAATATTCGTGGTTT
Found at i:11191231 original size:18 final size:18
Alignment explanation
Indices: 11191210--11191488 Score: 143
Period size: 17 Copynumber: 15.6 Consensus size: 18
11191200 AAGAATCCGT
* *
11191210 TTTTTAAAATTTTTCGTG
1 TTTTCAAAAATTTTCGTG
* * *
11191228 TTTTCAAAAA-ATTCCTA
1 TTTTCAAAAATTTTCGTG
*
11191245 TGTTTCAAAAATCTTCGTG
1 T-TTTCAAAAATTTTCGTG
*
11191264 TTTTC-AAAAGTTTCGGTG
1 TTTTCAAAAATTTTC-GTG
*
11191282 TTTTCAAAAATTTTCATG
1 TTTTCAAAAATTTTCGTG
**
11191300 TTTTCAAAAATTCCCGTG
1 TTTTCAAAAATTTTCGTG
* *
11191318 TTTT-AAAAATTTCCATG
1 TTTTCAAAAATTTTCGTG
*
11191335 TTTT-AAAAAATTT-GTG
1 TTTTCAAAAATTTTCGTG
*
11191351 TTTT-AAAATTTTTCGTG
1 TTTTCAAAAATTTTCGTG
* **
11191368 -CTTCAAAAAGAAAATTCGTG
1 TTTTC--AAA-AATTTTCGTG
*
11191388 TTTTCAAAAAAAAATTCTCGTG
1 TTTTC----AAAAATTTTCGTG
11191410 -TTTC-AAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
* **
11191426 TTTTTTTAAAAAAATTCGTG
1 --TTTTCAAAAATTTTCGTG
* *
11191446 -TTTCTAAAATTCT-GTTG
1 TTTTCAAAAATTTTCG-TG
*
11191463 TTTT-AAAAAGTTTCGTG
1 TTTTCAAAAATTTTCGTG
11191480 TTTT-AAAAA
1 TTTTCAAAAA
11191489 AAAAGGTTGC
Statistics
Matches: 200, Mismatches: 42, Indels: 39
0.71 0.15 0.14
Matches are distributed among these distances:
16 27 0.14
17 64 0.32
18 54 0.27
19 19 0.09
20 17 0.09
21 7 0.04
22 7 0.04
23 5 0.03
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Done.