Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 50 of 97
Found at i:20175015 original size:503 final size:504
Alignment explanation
Indices: 20174040--20175139 Score: 1853
Period size: 503 Copynumber: 2.2 Consensus size: 504
20174030 NNNNNNNNNN
* * *
20174040 AAATATTTAAATTTATATTCTCGGATTAAAAGTGTTTAATGTTGTACAAATTTTAATTTTTAAAT
1 AAATATTTAAATTTATATTCTTGGATTAAAAGTGTTTAACGATGTACAAATTTTAATTTTTAAAT
*
20174105 AAAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTGACATGGAAAAGCCTTGATGTAAAAA
66 AAAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTGACATGGAAAAGCCTTGACGTAAAAA
*
20174170 TGCAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACATAAATAT
131 CGCAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACATAAATAT
* *
20174235 GTAAGAGTTAACGTAACAAGGCAATTAAGTAAAAACAATCTATATTTAATGAAAAATAAATATTT
196 GTAACAGTTAACGTAACAAGGCAATTAAGTAAAAACAATCTACATTTAATGAAAAATAAATATTT
*
20174300 AAATTTATATTCTCGAGTTAAAAGTGTTTAACGAGATACAAATTTTAATTTTTAAATAATAAATA
261 AAATTTATATTCTCGAGTTAAAAGTGTTTAACGAGATACAAATTTTAATTTTTAAATAACAAATA
20174365 ATAAGGATAAAAATAATTATAGTTCAAAGTTAACATGGAAAAGCCTTGACATAAAACTATAAGAA
326 ATAAGGATAAAAATAATTATAGTTCAAAGTTAACATGGAAAAGCCTTGACATAAAACTATAAGAA
* **
20174430 TTGACGTAAAAACTTGTAAAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTGTGTAAGAGT
391 TTGACGTAAAAACTTGTAAAGGTGAAATAATTAAATTTTAAATCTTAACGTAAGCATGTAAGAGT
**
20174495 TAACGTAACAAGTCAATTAAGTAAAAATGATTTAAATTTAATAAAAAAT
456 TAACGTAACAAGTCAATTAAGTAAAAACAATTTAAATTTAATAAAAAAT
20174544 AAATATTTAAATTTATATTCTTGGATT-AAAGTGTTTAACGATGTACAAATTTTAATTTTTAAAT
1 AAATATTTAAATTTATATTCTTGGATTAAAAGTGTTTAACGATGTACAAATTTTAATTTTTAAAT
* **
20174608 AAAGAATAATAAAGATAAAAATAATTATAATTCAAAGTTGACATGGAAAAGCCTTGACGTAAAGC
66 AAAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTGACATGGAAAAGCCTTGACGTAAAAA
* * **
20174673 CGTAAGAGTTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAATGTAAATAT
131 CGCAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACATAAATAT
* * **
20174738 GTGACAGTTAACTTAACAATTCAATTAAGTAAAAACAATCTACATTTAATGAAAAATAAATATTT
196 GTAACAGTTAACGTAACAAGGCAATTAAGTAAAAACAATCTACATTTAATGAAAAATAAATATTT
* * *
20174803 AAATTTATATTCTCGGGTTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAACGAATA
261 AAATTTATATTCTCGAGTTAAAAGTGTTTAACGAGATACAAATTTTAATTTTTAAATAACAAATA
20174868 ATAAGGATAAAAATAATTATAGTTCAAAGTTAACATGGAAAAGCCTTGACATAAAACTATAAGAA
326 ATAAGGATAAAAATAATTATAGTTCAAAGTTAACATGGAAAAGCCTTGACATAAAACTATAAGAA
* * * *
20174933 TTGATGTAAAAACTTGTAAATGTGAAATAATTAAATTTTAAATCTTAACGTAAGCATTTAGGAGT
391 TTGACGTAAAAACTTGTAAAGGTGAAATAATTAAATTTTAAATCTTAACGTAAGCATGTAAGAGT
*
20174998 TAACGTAACAAGTCAATTAAGTAAAAACAATTTAAATTTAATGAAAAAT
456 TAACGTAACAAGTCAATTAAGTAAAAACAATTTAAATTTAATAAAAAAT
* * *
20175047 AAATATTTAAATTTATATTCTTAGG-TTAAAAGTATTTAACGATATACAAATTTTAATTTTAAAA
1 AAATATTTAAATTTATATTCTT-GGATTAAAAGTGTTTAACGATGTACAAATTTTAATTTTTAAA
*
20175111 TAAAGAATAATAAGGATAAAAACAATTAT
65 TAAAGAATAATAAGGATAAAAATAATTAT
20175140 TGAAATGCCC
Statistics
Matches: 557, Mismatches: 37, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
503 469 0.84
504 88 0.16
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (504 bp):
AAATATTTAAATTTATATTCTTGGATTAAAAGTGTTTAACGATGTACAAATTTTAATTTTTAAAT
AAAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTGACATGGAAAAGCCTTGACGTAAAAA
CGCAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACATAAATAT
GTAACAGTTAACGTAACAAGGCAATTAAGTAAAAACAATCTACATTTAATGAAAAATAAATATTT
AAATTTATATTCTCGAGTTAAAAGTGTTTAACGAGATACAAATTTTAATTTTTAAATAACAAATA
ATAAGGATAAAAATAATTATAGTTCAAAGTTAACATGGAAAAGCCTTGACATAAAACTATAAGAA
TTGACGTAAAAACTTGTAAAGGTGAAATAATTAAATTTTAAATCTTAACGTAAGCATGTAAGAGT
TAACGTAACAAGTCAATTAAGTAAAAACAATTTAAATTTAATAAAAAAT
Found at i:20176547 original size:11 final size:11
Alignment explanation
Indices: 20176516--20176553 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
20176506 TGTGGCTGAA
20176516 TTTGATGATAT
1 TTTGATGATAT
20176527 TTT-ATGATAT
1 TTTGATGATAT
*
20176537 TTTGGTGATA-
1 TTTGATGATAT
20176547 TTTGATG
1 TTTGATG
20176554 TTTGGTGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (11 bp):
TTTGATGATAT
Found at i:20177948 original size:20 final size:20
Alignment explanation
Indices: 20177923--20177968 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
20177913 TTTTGGCCCC
* *
20177923 ATTTGACTTATTGGAGTATG
1 ATTTGACTAATTGAAGTATG
*
20177943 ATTTGAGTAATTGAAGTATG
1 ATTTGACTAATTGAAGTATG
20177963 ATTTGA
1 ATTTGA
20177969 GGTTTAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (20 bp):
ATTTGACTAATTGAAGTATG
Found at i:20177969 original size:20 final size:20
Alignment explanation
Indices: 20177932--20177969 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20177922 CATTTGACTT
*
20177932 ATTGGAGTATGATTTGAGTA
1 ATTGAAGTATGATTTGAGTA
20177952 ATTGAAGTATGATTTGAG
1 ATTGAAGTATGATTTGAG
20177970 GTTTAGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (20 bp):
ATTGAAGTATGATTTGAGTA
Found at i:20182369 original size:15 final size:15
Alignment explanation
Indices: 20182344--20182383 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
20182334 GATCAGAGAT
*
20182344 TTTGG-TTTTAAAGC
1 TTTGGATTTTAAAGA
20182358 TTTGGATTTTAAAGA
1 TTTGGATTTTAAAGA
*
20182373 TTTTGATTTTA
1 TTTGGATTTTA
20182384 TGGTTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.55
Consensus pattern (15 bp):
TTTGGATTTTAAAGA
Found at i:20186156 original size:19 final size:20
Alignment explanation
Indices: 20186129--20186174 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
20186119 AGGAGACAAG
*
20186129 ATAAAATTTTTA-AAATAAA
1 ATAATATTTTTATAAATAAA
*
20186148 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATAAATAAA
20186167 ATAATATT
1 ATAATATT
20186175 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATAAATAAA
Found at i:20191544 original size:24 final size:25
Alignment explanation
Indices: 20191500--20191550 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
20191490 ACATAACAAG
*
20191500 TTAATTAAATAAAAAAAATTTTAAT
1 TTAATTAAATAAAAAAAATTTAAAT
*
20191525 TTAA-TAAA-AAATAAATATTTAAAT
1 TTAATTAAATAAA-AAAAATTTAAAT
20191549 TT
1 TT
20191551 CTATTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 3 0.13
24 16 0.70
25 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TTAATTAAATAAAAAAAATTTAAAT
Found at i:20191752 original size:20 final size:20
Alignment explanation
Indices: 20191729--20191766 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20191719 TGTATAAAAG
20191729 TTAACGTAAATA-AATTTTAT
1 TTAA-GTAAATATAATTTTAT
*
20191749 TTAATTAAATATAATTTT
1 TTAAGTAAATATAATTTT
20191767 CATATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TTAAGTAAATATAATTTTAT
Found at i:20191819 original size:17 final size:17
Alignment explanation
Indices: 20191799--20191832 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20191789 TATAATTTAT
20191799 AATAAAAAATAAAATAA
1 AATAAAAAATAAAATAA
* *
20191816 AATAAAACATTAAATAA
1 AATAAAAAATAAAATAA
20191833 CTTAAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAAAAATAAAATAA
Found at i:20199922 original size:19 final size:20
Alignment explanation
Indices: 20199900--20199939 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
20199890 CAAGATAAAG
20199900 TTTTTA-GAATAAAATAATA
1 TTTTTATGAATAAAATAATA
*
20199919 -TTTTATTAATAAAATAATA
1 TTTTTATGAATAAAATAATA
20199938 TT
1 TT
20199940 AAAATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
18 5 0.28
19 12 0.67
20 1 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTTTATGAATAAAATAATA
Found at i:20200915 original size:94 final size:93
Alignment explanation
Indices: 20200750--20200936 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 93
20200740 ATTTTCAAGG
20200750 AAATTAAGTGAAAAAGGTGAGATTTTTTCTATTAAGCTTGAGTTTTCTTATTCCCAAGCATTTCT
1 AAATTAAGTGAAAAAGGTGAGATTTTTTCTATTAAGCTTGAGTTTTCTTATTCCCAAGCATTTCT
*
20200815 CTTTATTTTCCATGATTAAATTACATGT
66 CCTTATTTTCCATGATTAAATTACATGT
20200843 NAAATTAAGT-AGAAAAGGTGAGATTTTTTCTATTAAGCTTGAGTTTTCTTATTCCCAAGCATTT
1 -AAATTAAGTGA-AAAAGGTGAGATTTTTTCTATTAAGCTTGAGTTTTCTTATTCCCAAGCATTT
20200907 CTCCTTATTTTCCATGATTAAATTACATGT
64 CTCCTTATTTTCCATGATTAAATTACATGT
20200937 TTTCATGATT
Statistics
Matches: 91, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
93 1 0.01
94 90 0.99
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (93 bp):
AAATTAAGTGAAAAAGGTGAGATTTTTTCTATTAAGCTTGAGTTTTCTTATTCCCAAGCATTTCT
CCTTATTTTCCATGATTAAATTACATGT
Found at i:20201700 original size:13 final size:13
Alignment explanation
Indices: 20201682--20201706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20201672 AGAGAAATTG
20201682 TGATTTTATAAAA
1 TGATTTTATAAAA
20201695 TGATTTTATAAA
1 TGATTTTATAAA
20201707 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:20203769 original size:54 final size:54
Alignment explanation
Indices: 20203687--20203791 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
20203677 TCATCACGTG
* *
20203687 CATCTCACCCAACTTATGTGCATCCCACCACACCATGCACATAGCCGGACATCC
1 CATCTCACCCAACTCATGTGCATCCCACCACACCATGCACATAACCGGACATCC
* * * *
20203741 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCATATAACCGGACA
1 CATCTCACCCAACTCATGTGCATCCCACCACACCATGCACATAACCGGACA
20203792 ACATCACCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.28, C:0.41, G:0.12, T:0.19
Consensus pattern (54 bp):
CATCTCACCCAACTCATGTGCATCCCACCACACCATGCACATAACCGGACATCC
Found at i:20212511 original size:28 final size:27
Alignment explanation
Indices: 20212467--20212519 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
20212457 TGTCTTGGTA
* *
20212467 GTGGAAAATTATAATTTTGCCCCTAGG
1 GTGGAAAATTACAATTTTACCCCTAGG
*
20212494 GTGGCAAAATTACCATTTTACCCCTA
1 GTGG-AAAATTACAATTTTACCCCTA
20212520 TGCTCTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (27 bp):
GTGGAAAATTACAATTTTACCCCTAGG
Found at i:20213404 original size:99 final size:98
Alignment explanation
Indices: 20213285--20213483 Score: 389
Period size: 99 Copynumber: 2.0 Consensus size: 98
20213275 CCAAGCAACA
20213285 AACCCATTTGGCTAACTACTCCAATTTAAAATTTCGTTACCTGGATGAGCTTGGAGGCATGAAGA
1 AACCCATTTGGCTAACTACTCCAATTTAAAATTTCGTTACCTGGATGAGCTTGGAGGCATGAAGA
20213350 TCAACAAAAAAACCTAATCTTTCCAAGAAAAAT
66 TCAACAAAAAAACCTAATCTTTCCAAGAAAAAT
20213383 AANCCCATTTGGCTAACTACTCCAATTTAAAATTTCGTTACCTGGATGAGCTTGGAGGCATGAAG
1 AA-CCCATTTGGCTAACTACTCCAATTTAAAATTTCGTTACCTGGATGAGCTTGGAGGCATGAAG
20213448 ATCAACAAAAAAACCTAATCTTTCCAAGAAAAAT
65 ATCAACAAAAAAACCTAATCTTTCCAAGAAAAAT
20213482 AA
1 AA
20213484 TTTGAAGAAA
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 2 0.02
99 98 0.98
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (98 bp):
AACCCATTTGGCTAACTACTCCAATTTAAAATTTCGTTACCTGGATGAGCTTGGAGGCATGAAGA
TCAACAAAAAAACCTAATCTTTCCAAGAAAAAT
Found at i:20216314 original size:34 final size:34
Alignment explanation
Indices: 20216271--20216343 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
20216261 AATAGTGGAA
* *
20216271 TTCACAAGCTT-CCACCAAGCTTTTACAATGGCTT
1 TTCACAAGCTTACCA-CAACCTTTAACAATGGCTT
*
20216305 TTCACAAGCTTAGCCACAACCTTTAACAATGGTTT
1 TTCACAAGCTTA-CCACAACCTTTAACAATGGCTT
20216340 TTCA
1 TTCA
20216344 AGGGATCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 11 0.32
35 20 0.59
36 3 0.09
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (34 bp):
TTCACAAGCTTACCACAACCTTTAACAATGGCTT
Found at i:20216371 original size:32 final size:31
Alignment explanation
Indices: 20216332--20216431 Score: 110
Period size: 32 Copynumber: 3.0 Consensus size: 31
20216322 AACCTTTAAC
20216332 AATGGTTTTTCAAGGGATCAACCAAAACTCAA
1 AATGGTTTTTCAA-GGATCAACCAAAACTCAA
* * *
20216364 AGTGGTTTTTCAAAGGCTCAACCACAACCTACAA
1 AATGGTTTTTC-AAGGATCAACCA-AAACT-CAA
*
20216398 TAATGGTTTTTCATAGGATCAACCAAAACCCAA
1 -AATGGTTTTTCA-AGGATCAACCAAAACTCAA
20216431 A
1 A
20216432 CTAACTTTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
32 20 0.36
33 9 0.16
34 7 0.12
35 20 0.36
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (31 bp):
AATGGTTTTTCAAGGATCAACCAAAACTCAA
Found at i:20216408 original size:35 final size:33
Alignment explanation
Indices: 20216318--20216431 Score: 115
Period size: 35 Copynumber: 3.4 Consensus size: 33
20216308 ACAAGCTTAG
* *
20216318 CCACAACCTTTAACAATGGTTTTTCAAGGGATCAA
1 CCACAACC-TCAA-AATGGTTTTTCAAAGGATCAA
* * *
20216353 CCA-AAACTCAAAGTGGTTTTTCAAAGGCTCAA
1 CCACAACCTCAAAATGGTTTTTCAAAGGATCAA
*
20216385 CCACAACCTACAATAATGGTTTTTCATAGGATCAA
1 CCACAACCT-CAA-AATGGTTTTTCAAAGGATCAA
*
20216420 CCAAAACC-CAAA
1 CCACAACCTCAAA
20216432 CTAACTTTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
32 22 0.33
33 10 0.15
34 6 0.09
35 28 0.42
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (33 bp):
CCACAACCTCAAAATGGTTTTTCAAAGGATCAA
Found at i:20224311 original size:43 final size:43
Alignment explanation
Indices: 20224254--20224368 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
20224244 GTAATGATAT
* *
20224254 TGACTCGGCTATGTGCGAGTAGGGAGTGCACATAAGCCGATGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCACATAACCCGATGA
* * *
20224297 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCACATAACCCGATGA
** *
20224340 TGACCTAGCCATGTGCGAGTAGGGAGTGC
1 TGACCCGGCTATGTGCGAGTAGGGAGTGC
20224369 GCATGAGCTA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCACATAACCCGATGA
Found at i:20224685 original size:21 final size:22
Alignment explanation
Indices: 20224655--20224714 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
20224645 CAGAATTGGT
* *
20224655 TCTCACTGCAGTGAGAATG-AA
1 TCTCGCTGCAGTGAGAAAGAAA
* *
20224676 TCTCGTTGCAGCGA-AAAGAAA
1 TCTCGCTGCAGTGAGAAAGAAA
*
20224697 TCTCGCTACAGTGAGAAA
1 TCTCGCTGCAGTGAGAAA
20224715 CTCTCTATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (22 bp):
TCTCGCTGCAGTGAGAAAGAAA
Found at i:20226221 original size:77 final size:75
Alignment explanation
Indices: 20226115--20226276 Score: 193
Period size: 77 Copynumber: 2.1 Consensus size: 75
20226105 AATTTCTCAC
* * * *****
20226115 ATTAAAATATTATCCTTAATTTTTAGAATTTCTTTTAAAGTAGGAAACAATTTCCTATTCTTTAT
1 ATTAAAATATTATCCTTAATTTTCAGAATTACTTTTAAAATA-GAAA-AAAAAAATATTCTTTAT
20226180 GAATCACCCAAA
64 GAATCACCCAAA
*
20226192 ATTAAAAT-TCTATCCTTAA-TTTCAGGAATTACTTTTAAAATAGAAAAAAAAAATATTTTTTAT
1 ATTAAAATAT-TATCCTTAATTTTCA-GAATTACTTTTAAAATAGAAAAAAAAAATATTCTTTAT
20226255 GAATCACCCAAA
64 GAATCACCCAAA
20226267 ATTAAAATAT
1 ATTAAAATAT
20226277 ATGGCATTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
75 31 0.42
76 10 0.14
77 32 0.44
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (75 bp):
ATTAAAATATTATCCTTAATTTTCAGAATTACTTTTAAAATAGAAAAAAAAAATATTCTTTATGA
ATCACCCAAA
Found at i:20229213 original size:34 final size:36
Alignment explanation
Indices: 20229138--20229239 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 36
20229128 CACACCCAGC
20229138 TCATGTGCATCCCCCCACATCGTGCACATAGCCGGCACCA
1 TCATGTGCATCCCCCCACATCGTGCACATA--C-G-ACCA
*
20229178 TCATGTGCATCCCCCCACATTGTGCACATA-G-CCA
1 TCATGTGCATCCCCCCACATCGTGCACATACGACCA
* *
20229212 TCATGTACATCCCCCCACATCATGCACA
1 TCATGTGCATCCCCCCACATCGTGCACA
20229240 ATGGCACTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
34 28 0.48
36 1 0.02
40 29 0.50
ACGTcount: A:0.25, C:0.41, G:0.14, T:0.21
Consensus pattern (36 bp):
TCATGTGCATCCCCCCACATCGTGCACATACGACCA
Found at i:20229364 original size:2 final size:2
Alignment explanation
Indices: 20229357--20229384 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20229347 CATGCACAAC
20229357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20229385 TATCATAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20233044 original size:3 final size:3
Alignment explanation
Indices: 20233036--20233094 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
20233026 CGTATATACC
* * * * *
20233036 CAT CAT CAT CAT C-T CAC CAA C-C CAT CAT CAT CAT CAC CAG C-T CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
20233081 CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CA
20233095 CCAGCTCATG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.32, C:0.41, G:0.02, T:0.25
Consensus pattern (3 bp):
CAT
Found at i:20233088 original size:23 final size:23
Alignment explanation
Indices: 20233036--20233103 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
20233026 CGTATATACC
*
20233036 CATCATCATCATC-TCACCAAC-
1 CATCATCATCATCATCACCAGCT
20233057 C--CATCATCATCATCACCAGCT
1 CATCATCATCATCATCACCAGCT
20233078 CATCATCATCATCATCACCAGCT
1 CATCATCATCATCATCACCAGCT
20233101 CAT
1 CAT
20233104 GCGCACTCCC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
19 10 0.24
20 7 0.17
21 2 0.05
23 23 0.55
ACGTcount: A:0.31, C:0.41, G:0.03, T:0.25
Consensus pattern (23 bp):
CATCATCATCATCATCACCAGCT
Found at i:20233103 original size:20 final size:20
Alignment explanation
Indices: 20233038--20233091 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
20233028 TATATACCCA
20233038 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAAC
* *
20233057 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAAC
20233077 TCATCATCATCATCA
1 TCATCATCATCATCA
20233092 TCACCAGCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.31, C:0.41, G:0.02, T:0.26
Consensus pattern (20 bp):
TCATCATCATCATCACCAAC
Found at i:20233136 original size:43 final size:43
Alignment explanation
Indices: 20233089--20233220 Score: 167
Period size: 43 Copynumber: 3.1 Consensus size: 43
20233079 ATCATCATCA
* * ** *
20233089 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATGGCTGGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAACCGGG
*
20233132 TCATCACCGGATTATGCGCACTCCCTACTCGCACATAACCGGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAACCGGG
* * *
20233175 TCATC-CTCGGCTTATGCACACTCCCTACTCGCACATAGCCGAG
1 TCATCAC-CGGCTTATGCGCACTCCCTACTCGCACATAACCGGG
20233218 TCA
1 TCA
20233221 ACATAATTAC
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 1 0.01
43 77 0.99
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.22
Consensus pattern (43 bp):
TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAACCGGG
Found at i:20238519 original size:43 final size:43
Alignment explanation
Indices: 20238461--20238585 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
20238451 TCATCATCAC
* * * *
20238461 CAGCTCATGCACACTCCTTACTCGCACATGGCTGGGTCATCAC-
1 CAGCTTATGCGCACTCCCTACTCGCACATAGCTGGGTCATC-CT
* * * *
20238504 CGGGTTATGCGCACTCCCTACTCGCACATAACCGGGTCATCCT
1 CAGCTTATGCGCACTCCCTACTCGCACATAGCTGGGTCATCCT
* *
20238547 CAGCTTATGTGCACTCCCTACTCGCACATAGCTGAGTCA
1 CAGCTTATGCGCACTCCCTACTCGCACATAGCTGGGTCA
20238586 ATGTCATTTC
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 1 0.01
43 66 0.99
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
CAGCTTATGCGCACTCCCTACTCGCACATAGCTGGGTCATCCT
Found at i:20247545 original size:29 final size:29
Alignment explanation
Indices: 20247496--20247753 Score: 276
Period size: 29 Copynumber: 9.0 Consensus size: 29
20247486 TTAAGACAAG
* * *
20247496 TCTTGTCTTTAATTAATACAAAACATGTTA
1 TCTTGTC-TAAATTAAGACAAAACATGTTT
* *
20247526 TCTTGTCTAAATTGAGAC-AAATATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
* * * *
20247554 TATTATCTAGATTAAGACAAAACATATTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
* * *
20247583 T-TTTTCTTAAATTAAGAC-AAGCATACTTT
1 TCTTGTC-TAAATTAAGACAAAACAT-GTTT
*
20247612 T-TTCGTCTAAATTAAGGCAAAACATGTTT
1 TCTT-GTCTAAATTAAGACAAAACATGTTT
*
20247641 TCTTGTTTAAATTAAGAC-AAACATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
20247669 TCTTGTCTAAATTAAGACAAAACATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
*
20247698 TCTTGTCTAAATTAAGAC-AAACATTTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
* * *
20247726 TCTTATCTAAATTAGGACAAAAAATGTT
1 TCTTGTCTAAATTAAGACAAAACATGTT
20247754 AAAGCTACCA
Statistics
Matches: 193, Mismatches: 27, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
28 83 0.43
29 94 0.49
30 16 0.08
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAACATGTTT
Found at i:20247595 original size:57 final size:57
Alignment explanation
Indices: 20247506--20247753 Score: 302
Period size: 57 Copynumber: 4.3 Consensus size: 57
20247496 TCTTGTCTTT
* * * * *
20247506 AATTAATACAAAACATGTTATCTTGTCTAAATTGAGACAAATATGTTTTATTATCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTA
* * * * * *
20247563 GATTAAGACAAAACATATTTT-TTTTCTTAAATTAAGACAAGCATACTTTT-TTCGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTC-TAAATTAAGACAAACAT-GTTTTCTT-ATCTA
* * *
20247621 AATTAAGGCAAAACATGTTTTCTTGTTTAAATTAAGACAAACATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTA
*
20247678 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATTTTTTCTTATCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTA
* *
20247735 AATTAGGACAAAAAATGTT
1 AATTAAGACAAAACATGTT
20247754 AAAGCTACCA
Statistics
Matches: 163, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
56 4 0.02
57 112 0.69
58 44 0.27
59 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (57 bp):
AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTATCTA
Found at i:20251419 original size:20 final size:20
Alignment explanation
Indices: 20251394--20251448 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
20251384 TTCTAATTGC
20251394 TATCTATCGATAGATCTGGA
1 TATCTATCGATAGATCTGGA
* * *
20251414 TATCTATGGTTAGATCTGGC
1 TATCTATCGATAGATCTGGA
* *
20251434 CATCTATCCATAGAT
1 TATCTATCGATAGAT
20251449 GTTCTTCAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
TATCTATCGATAGATCTGGA
Found at i:20252662 original size:31 final size:30
Alignment explanation
Indices: 20252624--20252714 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
20252614 ACATAGAACT
* **
20252624 TTTATCTACCCTTTTTTATAAAGGTATAACC
1 TTTATCTA-CCTTTTCTATGGAGGTATAACC
*
20252655 TTTATCTACCTTTTCCATGGAGGTATAACC
1 TTTATCTACCTTTTCTATGGAGGTATAACC
20252685 TTTATCTACCTTTTCTATGGAGGTATAACC
1 TTTATCTACCTTTTCTATGGAGGTATAACC
20252715 AACAACAGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 47 0.85
31 8 0.15
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (30 bp):
TTTATCTACCTTTTCTATGGAGGTATAACC
Found at i:20266536 original size:34 final size:34
Alignment explanation
Indices: 20266493--20266569 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
20266483 CCGAGGCTTG
20266493 CAGGGCAGCTGTTGCTTACCATTGGCAACAGTGC
1 CAGGGCAGCTGTTGCTTACCATTGGCAACAGTGC
20266527 CAGGGCAGCTGTTGCTTACCATTGGCAACAGTGC
1 CAGGGCAGCTGTTGCTTACCATTGGCAACAGTGC
20266561 CAGGGCAGC
1 CAGGGCAGC
20266570 ATCAGAGGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (34 bp):
CAGGGCAGCTGTTGCTTACCATTGGCAACAGTGC
Found at i:20267022 original size:39 final size:39
Alignment explanation
Indices: 20266929--20267034 Score: 137
Period size: 38 Copynumber: 2.7 Consensus size: 39
20266919 GATAGTGCCC
** *
20266929 ATGTGCACGATGTGGGGGGATGTACACAATGGCACTGGT
1 ATGTGCACGATGTGGGGGGATGTACATGATGGCACTGCT
*
20266968 -TGTGCACGATGT-GGGGGATGCACATGATGGTGC-CTGCT
1 ATGTGCACGATGTGGGGGGATGTACATGAT-G-GCACTGCT
20267006 ATGTGCACGATGTGGGGGGATGTACATGA
1 ATGTGCACGATGTGGGGGGATGTACATGA
20267035 GCCAGGAGTG
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
37 13 0.22
38 17 0.29
39 14 0.24
40 14 0.24
ACGTcount: A:0.21, C:0.15, G:0.40, T:0.25
Consensus pattern (39 bp):
ATGTGCACGATGTGGGGGGATGTACATGATGGCACTGCT
Found at i:20276960 original size:43 final size:43
Alignment explanation
Indices: 20276890--20277017 Score: 157
Period size: 43 Copynumber: 3.0 Consensus size: 43
20276880 TATATGGACT
* *
20276890 CAGCTATGTGCGAGTAGGGAGTACGCATAAGCCGATGATGATC
1 CAGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGATC
* * * * *
20276933 CTGTTATGTGCGAGTAGGGACTGCGCATAAACCGGTGATGACC
1 CAGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGATC
* * * *
20276976 CAGCCATGTTCGAGTAGGGAGTGCGCATGAGCTGGTGATGAT
1 CAGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGAT
20277018 GGGATGGTGT
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (43 bp):
CAGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGATC
Found at i:20287278 original size:42 final size:36
Alignment explanation
Indices: 20287186--20287396 Score: 162
Period size: 36 Copynumber: 5.7 Consensus size: 36
20287176 GCAACTCAGC
*
20287186 TCATGTGCACTCCCACACCACACATGGCAAATATCA
1 TCATGTGCACTCCCACACCGCACATGGCAAATATCA
* *
20287222 TCGTGTGCATTCCCACACCGCACATGGCAAATATCATCATCA
1 TCATGTGCACTCCCACACCGCACATGGC--A-A--AT-ATCA
* * **
20287264 TCATATGCACTCCCACACCGCACA--CCACGT-TCCCA
1 TCATGTGCACTCCCACACCGCACATGGCAAATAT--CA
* *
20287299 TAATGTGCACTCCCACACCACACATGGCAATATCATCA
1 TCATGTGCACTCCCACACCGCACATGGCAA-AT-ATCA
* * **
20287337 TCATGTGCACTCCCACACTGCACA--CCACCCTCATCA
1 TCATGTGCACTCCCACACCGCACATGGCA-AAT-ATCA
20287373 TCATGTGCACTCCCACACCGCACA
1 TCATGTGCACTCCCACACCGCACA
20287397 CGCACGATTA
Statistics
Matches: 139, Mismatches: 22, Indels: 28
0.74 0.12 0.15
Matches are distributed among these distances:
33 1 0.01
35 24 0.17
36 56 0.40
37 2 0.01
38 26 0.19
39 1 0.01
40 2 0.01
41 2 0.01
42 25 0.18
ACGTcount: A:0.29, C:0.40, G:0.11, T:0.20
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACATGGCAAATATCA
Found at i:20287349 original size:73 final size:77
Alignment explanation
Indices: 20287225--20287396 Score: 235
Period size: 73 Copynumber: 2.3 Consensus size: 77
20287215 AATATCATCG
*
20287225 TGTGCATTCCCACACCGCACATGGCAAATATCATCATCATCATATGCACTCCCACACCGCACACC
1 TGTGCACTCCCACACCGCACATGGC-AATATCATCATCATCATATGCACTCCCACACCGCACACC
**
20287290 ACGTTC-CCATAA
65 ACCCTCACCATAA
* * *
20287302 TGTGCACTCCCACACCACACATGGC-A-AT-ATCATCATCATGTGCACTCCCACACTGCACACCA
1 TGTGCACTCCCACACCGCACATGGCAATATCATCATCATCATATGCACTCCCACACCGCACACCA
* *
20287364 CCCTCATCATCA
66 CCCTCACCATAA
20287376 TGTGCACTCCCACACCGCACA
1 TGTGCACTCCCACACCGCACA
20287397 CGCACGATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
73 35 0.41
74 26 0.31
75 1 0.01
77 23 0.27
ACGTcount: A:0.28, C:0.41, G:0.10, T:0.20
Consensus pattern (77 bp):
TGTGCACTCCCACACCGCACATGGCAATATCATCATCATCATATGCACTCCCACACCGCACACCA
CCCTCACCATAA
Found at i:20287401 original size:115 final size:109
Alignment explanation
Indices: 20287188--20287402 Score: 290
Period size: 109 Copynumber: 1.9 Consensus size: 109
20287178 AACTCAGCTC
* *
20287188 ATGTGCACTCCCACACCACACATGGCAAATATCATCGTGTGCATTCCCACACCGCACATGGCAAA
1 ATGTGCACTCCCACACCACACATGGCAAATATCATCATGTGCACTCCCACACCGCACA--GC--A
* *
20287253 TATCATCATCATCATATGCACTCCCACACCGCACACCACGTTCCCATA
62 CACCATCATCATCATATGCACTCCCACACCGCACACCACGTTCCCATA
*
20287301 ATGTGCACTCCCACACCACACATGGCAATATCATCATCATGTGCACTCCCACACTGCACA-C-CA
1 ATGTGCACTCCCACACCACACATGGCAA-AT-ATCATCATGTGCACTCCCACACCGCACAGCACA
* *
20287364 CCCTCATCATCATGTGCACTCCCACACCGCACACGCACG
64 CCATCATCATCATATGCACTCCCACACCGCACAC-CACG
20287403 ATTATAATTA
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
109 32 0.35
110 4 0.04
112 1 0.01
113 28 0.30
114 2 0.02
115 25 0.27
ACGTcount: A:0.29, C:0.40, G:0.12, T:0.19
Consensus pattern (109 bp):
ATGTGCACTCCCACACCACACATGGCAAATATCATCATGTGCACTCCCACACCGCACAGCACACC
ATCATCATCATATGCACTCCCACACCGCACACCACGTTCCCATA
Found at i:20289266 original size:20 final size:18
Alignment explanation
Indices: 20289216--20289263 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
20289206 GCTATAAATA
*
20289216 TCTTGTTCTTCCAGCAGCT
1 TCTTCTTCTT-CAGCAGCT
20289235 TCTTCATTCTTCAGCAGCT
1 TCTTC-TTCTTCAGCAGCT
20289254 T-TTCTTCTTC
1 TCTTCTTCTTC
20289264 TTCTTCTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 6 0.22
18 3 0.11
19 13 0.48
20 5 0.19
ACGTcount: A:0.10, C:0.31, G:0.10, T:0.48
Consensus pattern (18 bp):
TCTTCTTCTTCAGCAGCT
Found at i:20290167 original size:19 final size:19
Alignment explanation
Indices: 20290143--20290206 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
20290133 TGCTCGTGTG
20290143 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
20290162 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
20290181 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
20290200 CACGATG
1 CACGATG
20290207 ACTTCGACTA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 3 0.09
19 26 0.81
20 3 0.09
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:20291764 original size:20 final size:20
Alignment explanation
Indices: 20291739--20291790 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
20291729 TTATAAATCA
20291739 TTTTGAAATTGAATGATGAT
1 TTTTGAAATTGAATGATGAT
20291759 TTTTGAAATTGAATGATGAT
1 TTTTGAAATTGAATGATGAT
*
20291779 TTTAGAAATTGA
1 TTTTGAAATTGA
20291791 GTAATTGGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTTGAAATTGAATGATGAT
Found at i:20295347 original size:3 final size:3
Alignment explanation
Indices: 20295339--20295363 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20295329 CTAGTAGCTT
20295339 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
20295364 CTTTCACGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:20296253 original size:2 final size:2
Alignment explanation
Indices: 20296246--20296281 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
20296236 ATGATGATTG
* *
20296246 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20296282 GGTATATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20305663 original size:76 final size:75
Alignment explanation
Indices: 20305536--20305688 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 75
20305526 ATTAAGCTTG
*
20305536 GTTTTTAGCTGTAGAAAATGGCTAGTAATTGGGATTTATGAGCTGTTTTATTGTTGAGTATGTTC
1 GTTTTTAGCTGCAGAAAATGGCTAGTAATTGGGATTTATGAGCTGTTTTATTGTTGAGTATGTTC
20305601 ATTACTTTTA
66 ATTACTTTTA
20305611 GNTTTTTAGCTGCAGAAAATGGCTAGTAATTGGGATTTATGAGCTGTTTTATTGTTGAGTATGTT
1 G-TTTTTAGCTGCAGAAAATGGCTAGTAATTGGGATTTATGAGCTGTTTTATTGTTGAGTATGTT
20305676 CATTACTTTTA
65 CATTACTTTTA
20305687 GT
1 GT
20305689 GATTAAGATA
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
75 2 0.03
76 74 0.97
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (75 bp):
GTTTTTAGCTGCAGAAAATGGCTAGTAATTGGGATTTATGAGCTGTTTTATTGTTGAGTATGTTC
ATTACTTTTA
Found at i:20306182 original size:43 final size:42
Alignment explanation
Indices: 20306101--20306212 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 42
20306091 TATTGACTCG
* *
20306101 GCTATGTGCGAGTAGGGAGTGAGCATAAGTCGAGGATGA-CA
1 GCTATGTGCAAGTAGGGAGTGCGCATAAGTCGAGGATGACCA
* *
20306142 TGTTTATGTGCAAGTAGGGAGTGCGCATAATTCG-GTGATGACCCA
1 -G-CTATGTGCAAGTAGGGAGTGCGCATAAGTCGAG-GATGA-CCA
*
20306187 GCCATGTGCAAGTAGGGAGTGCGCAT
1 GCTATGTGCAAGTAGGGAGTGCGCAT
20306213 GAACTGGTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
42 2 0.03
43 55 0.92
44 1 0.02
45 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (42 bp):
GCTATGTGCAAGTAGGGAGTGCGCATAAGTCGAGGATGACCA
Found at i:20310430 original size:2 final size:2
Alignment explanation
Indices: 20310423--20310465 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
20310413 GGGCATATGC
20310423 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20310465 A
1 A
20310466 NATGGGATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20310817 original size:21 final size:21
Alignment explanation
Indices: 20310793--20310838 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
20310783 ACACTACAGC
20310793 TTCTCGCTGCAGCGA-AATACA
1 TTCTCGCTGCAGCGAGAA-ACA
20310814 TTCTCGCTGCAGCGAGAAACA
1 TTCTCGCTGCAGCGAGAAACA
20310835 TTCT
1 TTCT
20310839 GTTTTCTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (21 bp):
TTCTCGCTGCAGCGAGAAACA
Found at i:20318724 original size:43 final size:43
Alignment explanation
Indices: 20318676--20318856 Score: 226
Period size: 43 Copynumber: 4.2 Consensus size: 43
20318666 TGTTGTGTGA
*
20318676 TGATGATTACCCAGA-TATGTGCGATGTCA-GAGTGCACATAAGC
1 TGATGATGACCC-GACTATGTGCGATGT-AGGAGTGCACATAAGC
* *
20318719 TGATGATGACCCGACTATGTGCGATGTGGGAGTGCACATGAGC
1 TGATGATGACCCGACTATGTGCGATGTAGGAGTGCACATAAGC
*
20318762 TGATGATGACCCGACTATGTGC-AAGTAAGGAGTGCACATAAGC
1 TGATGATGACCCGACTATGTGCGATGT-AGGAGTGCACATAAGC
** * *
20318805 CAATGATGACTCGGCTATGTGCGA-GTAGGGAGTGCACATAAGC
1 TGATGATGACCCGACTATGTGCGATGTA-GGAGTGCACATAAGC
20318848 TGATGATGA
1 TGATGATGA
20318857 TGACCCGGCT
Statistics
Matches: 121, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
42 6 0.05
43 114 0.94
44 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (43 bp):
TGATGATGACCCGACTATGTGCGATGTAGGAGTGCACATAAGC
Found at i:20338729 original size:46 final size:43
Alignment explanation
Indices: 20338679--20338833 Score: 188
Period size: 43 Copynumber: 3.6 Consensus size: 43
20338669 TGTTGTGTGA
* * * *
20338679 TGATGATGACCCAGCTATGTACGATGT-GAGAGTTCACATGAGC
1 TGATGATGACCCAGCTATGTACGA-GTAGGGAGTGCGCATAAGC
* *
20338722 TGATGATGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGC
1 TGATGATGACCCAGCTATGTACGAGTAGGGAGTGCGCATAAGC
* *
20338765 TGATGATGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCC
1 TGATGATGACCCAGCTATGTACGAGTAGGGAGTGCGCATAAG-C
20338809 GATGATGATGACCCAGCTATG-ACGA
1 --TGATGATGACCCAGCTATGTACGA
20338834 TGAATGAAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
42 2 0.02
43 76 0.76
44 1 0.01
45 3 0.03
46 18 0.18
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (43 bp):
TGATGATGACCCAGCTATGTACGAGTAGGGAGTGCGCATAAGC
Found at i:20339111 original size:22 final size:22
Alignment explanation
Indices: 20339080--20339138 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
20339070 CCAGTCCTGT
*
20339080 TTCTCACTGCAGC-AAAAAAGAA
1 TTCTCGCTGCAGCGAAAAAAG-A
*
20339102 TTCTCGCTGCAGCGAAAATAGA
1 TTCTCGCTGCAGCGAAAAAAGA
20339124 TTCTCGCTGCAGCGA
1 TTCTCGCTGCAGCGA
20339139 GAAACTCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 28 0.82
23 6 0.18
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (22 bp):
TTCTCGCTGCAGCGAAAAAAGA
Found at i:20339962 original size:13 final size:13
Alignment explanation
Indices: 20339944--20339970 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20339934 AATATATGGT
20339944 TTAGAAATGATGA
1 TTAGAAATGATGA
20339957 TTAGAAATGATGA
1 TTAGAAATGATGA
20339970 T
1 T
20339971 CGGGATTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (13 bp):
TTAGAAATGATGA
Found at i:20340503 original size:25 final size:25
Alignment explanation
Indices: 20340475--20340529 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
20340465 CACAACCACA
* *
20340475 TATATCAACTCGTGGCCTAGCCATG
1 TATATCAACCCATGGCCTAGCCATG
*
20340500 TATATCAACCCATGGCCTTGCCATG
1 TATATCAACCCATGGCCTAGCCATG
20340525 TATAT
1 TATAT
20340530 ATATCACAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (25 bp):
TATATCAACCCATGGCCTAGCCATG
Found at i:20342063 original size:19 final size:19
Alignment explanation
Indices: 20342041--20342080 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20342031 CTCTCCTTTC
*
20342041 TCTTTCATTCTTTTTCCTT
1 TCTTCCATTCTTTTTCCTT
* *
20342060 TCTTCCCTTTTTTTTCCTT
1 TCTTCCATTCTTTTTCCTT
20342079 TC
1 TC
20342081 AAAATCGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (19 bp):
TCTTCCATTCTTTTTCCTT
Found at i:20342323 original size:15 final size:15
Alignment explanation
Indices: 20342303--20342333 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20342293 ACCTTCACTA
*
20342303 CCTCATTCTTTCTTT
1 CCTCATTCTTTATTT
20342318 CCTCATTCTTTATTT
1 CCTCATTCTTTATTT
20342333 C
1 C
20342334 ATGCACCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.32, G:0.00, T:0.58
Consensus pattern (15 bp):
CCTCATTCTTTATTT
Found at i:20345893 original size:13 final size:13
Alignment explanation
Indices: 20345875--20345900 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20345865 AAGAGAAATT
20345875 ATGATTTTATAAA
1 ATGATTTTATAAA
20345888 ATGATTTTATAAA
1 ATGATTTTATAAA
20345901 TTTCCTAAAA
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATGATTTTATAAA
Found at i:20347120 original size:15 final size:16
Alignment explanation
Indices: 20347100--20347140 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
20347090 CAGAGATTTT
20347100 GATTTTAAAG-CTTTG
1 GATTTTAAAGTCTTTG
*
20347115 GATTTTAAAGTTTTTG
1 GATTTTAAAGTCTTTG
20347131 G-TTTTAAAGT
1 GATTTTAAAGT
20347141 TGTTTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (16 bp):
GATTTTAAAGTCTTTG
Found at i:20347141 original size:15 final size:15
Alignment explanation
Indices: 20347096--20347141 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
20347086 AGATCAGAGA
*
20347096 TTTTGATTTTAAAG-
1 TTTTGGTTTTAAAGT
*
20347110 CTTTGGATTTTAAAGT
1 TTTTGG-TTTTAAAGT
20347126 TTTTGGTTTTAAAGT
1 TTTTGGTTTTAAAGT
20347141 T
1 T
20347142 GTTTTAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 18 0.67
16 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (15 bp):
TTTTGGTTTTAAAGT
Found at i:20347186 original size:5 final size:5
Alignment explanation
Indices: 20347176--20347210 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
20347166 TGCGTGACCC
*
20347176 AAGTT AAGTT AAGTT AAGTT -AGTT AAGTC AAGTT A
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT A
20347211 GGTAGAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (5 bp):
AAGTT
Found at i:20347201 original size:14 final size:14
Alignment explanation
Indices: 20347175--20347211 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
20347165 CTGCGTGACC
20347175 CAAGTTAAGTTAAGT
1 CAAGTT-AGTTAAGT
*
20347190 TAAGTTAGTTAAGT
1 CAAGTTAGTTAAGT
20347204 CAAGTTAG
1 CAAGTTAG
20347212 GTAGAATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (14 bp):
CAAGTTAGTTAAGT
Found at i:20356995 original size:74 final size:71
Alignment explanation
Indices: 20356906--20357074 Score: 231
Period size: 68 Copynumber: 2.4 Consensus size: 71
20356896 AAGTTTTGAA
*
20356906 CCAACC-CTCCGAGAGTTTCTCGCTGCAACGA-GAATGGAATTTCGCTACAGTGAAATCCCGAAC
1 CCAACCAC-CCGAGAGTTTCTCGCTGCAACGACG-A--G-ATTTCGCTACAGCGAAATCCCGAAC
20356969 AAGCATTTTAC
61 AAGCATTTTAC
* *
20356980 CCAACCACCCTAGAGTTTCTCGCT---ACGACGAGATTTGGCTACAGCGAAATCCCGAACAAGCA
1 CCAACCACCCGAGAGTTTCTCGCTGCAACGACGAGATTTCGCTACAGCGAAATCCCGAACAAGCA
20357042 TTTTAC
66 TTTTAC
20357048 CCAACCACCCGAGAGTTTCTCGCTGCA
1 CCAACCACCCGAGAGTTTCTCGCTGCA
20357075 GCAAAAATCT
Statistics
Matches: 86, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
68 57 0.66
69 1 0.01
71 5 0.06
72 1 0.01
74 21 0.24
75 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (71 bp):
CCAACCACCCGAGAGTTTCTCGCTGCAACGACGAGATTTCGCTACAGCGAAATCCCGAACAAGCA
TTTTAC
Found at i:20359677 original size:55 final size:55
Alignment explanation
Indices: 20359579--20359771 Score: 314
Period size: 55 Copynumber: 3.5 Consensus size: 55
20359569 GTCGTTACAG
* * * * *
20359579 GTCATCAGCTCATGTGCACTCCCACACCACACGCAGCTAGAATCATCATCCACTA
1 GTCATCAGCTCATGTGCACTCCCACACTACACACAGTTGGAATCATCATCCACCA
* *
20359634 GTCTTCAACTCATGTGCACTCCCACACTACACACAGTTGGAATCATCATCCACCA
1 GTCATCAGCTCATGTGCACTCCCACACTACACACAGTTGGAATCATCATCCACCA
*
20359689 GTCATCAGCTCATGTGCACTCCCACACTGCACACAGTTGGAATCATCATCCACCA
1 GTCATCAGCTCATGTGCACTCCCACACTACACACAGTTGGAATCATCATCCACCA
20359744 GTCATCAGCTCATGTGCACTCCCACACT
1 GTCATCAGCTCATGTGCACTCCCACACT
20359772 GCAAATAGCT
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 128 1.00
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.22
Consensus pattern (55 bp):
GTCATCAGCTCATGTGCACTCCCACACTACACACAGTTGGAATCATCATCCACCA
Found at i:20365759 original size:80 final size:80
Alignment explanation
Indices: 20365626--20365796 Score: 299
Period size: 80 Copynumber: 2.1 Consensus size: 80
20365616 ATTCTTGATC
*
20365626 CATTGGATAGATAAGAGAACATGATACAACTTTCATGTTTACCATTTTACATAATTCAGATCTAG
1 CATTGGATAGATAAGAGAACAGGATACAACTTTCATGTTTACCATTTTACATAATTCAGATCTAG
*
20365691 CTAAGGTGAAAATCA
66 CCAAGGTGAAAATCA
*
20365706 CATTGGATAGATAAGAGAACAGGATACAACTTTCATGTTTACCATTTTACATAATTCAGATCTGG
1 CATTGGATAGATAAGAGAACAGGATACAACTTTCATGTTTACCATTTTACATAATTCAGATCTAG
*
20365771 CCAAGGTGAAAATCG
66 CCAAGGTGAAAATCA
20365786 CATTGGA-AGAT
1 CATTGGATAGAT
20365797 GATGGATGTT
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 4 0.05
80 83 0.95
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (80 bp):
CATTGGATAGATAAGAGAACAGGATACAACTTTCATGTTTACCATTTTACATAATTCAGATCTAG
CCAAGGTGAAAATCA
Found at i:20371094 original size:31 final size:29
Alignment explanation
Indices: 20371058--20371124 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
20371048 TGCTAGTTAT
20371058 TATGGATATTCAATATATCTTAGTTAGCTAC
1 TATGGATATT--ATATATCTTAGTTAGCTAC
* *
20371089 TATGGATATTGTATATCTTATTTAGCTAC
1 TATGGATATTATATATCTTAGTTAGCTAC
*
20371118 TGTGGAT
1 TATGGAT
20371125 GTTACAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 23 0.70
31 10 0.30
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.45
Consensus pattern (29 bp):
TATGGATATTATATATCTTAGTTAGCTAC
Found at i:20385459 original size:20 final size:20
Alignment explanation
Indices: 20385425--20385472 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
20385415 TTATAATTAG
*
20385425 GTTACTTTTAAGTTAGTT-AT
1 GTTAATTTTAAGTTA-TTCAT
* *
20385445 TTTAATTTTATGTTATTCAT
1 GTTAATTTTAAGTTATTCAT
20385465 GTTAATTT
1 GTTAATTT
20385473 GGTTATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.60
Consensus pattern (20 bp):
GTTAATTTTAAGTTATTCAT
Found at i:20387332 original size:63 final size:63
Alignment explanation
Indices: 20387255--20387412 Score: 217
Period size: 63 Copynumber: 2.5 Consensus size: 63
20387245 CATAATTACC
* * * *
20387255 GGCATGTGCACTACCCACTCCGCACATGCATGGTAGTAATTATCGCAACATCGTCATTCAACA
1 GGCATGTGCACTACCCACTCCGCACATGCACGGTAGTAACTATCGAAACATCATCATTCAACA
* * * * *
20387318 GGCATGTGCACTACCCACTCTGCACATGCACGGTTGTAACTATCGAAACCTCATCATTTAACC
1 GGCATGTGCACTACCCACTCCGCACATGCACGGTAGTAACTATCGAAACATCATCATTCAACA
* *
20387381 GACATGTGCACTGCCCACTCCGCACATGCACG
1 GGCATGTGCACTACCCACTCCGCACATGCACG
20387413 ATTACATCCA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 83 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.23
Consensus pattern (63 bp):
GGCATGTGCACTACCCACTCCGCACATGCACGGTAGTAACTATCGAAACATCATCATTCAACA
Found at i:20391581 original size:24 final size:24
Alignment explanation
Indices: 20391554--20391618 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
20391544 GCCATTTCCA
*
20391554 TGGGCTCTTCCCATTTCTTCCTAT
1 TGGGCTCTGCCCATTTCTTCCTAT
* *
20391578 TGGGC-CATGCCCATTCTTTTCTTAT
1 TGGGCTC-TGCCCATT-TCTTCCTAT
*
20391603 TGGGCTATGCCCATTT
1 TGGGCTCTGCCCATTT
20391619 TTTTTTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 1 0.03
24 13 0.38
25 20 0.59
ACGTcount: A:0.11, C:0.29, G:0.17, T:0.43
Consensus pattern (24 bp):
TGGGCTCTGCCCATTTCTTCCTAT
Found at i:20391606 original size:25 final size:25
Alignment explanation
Indices: 20391575--20391622 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
20391565 CATTTCTTCC
20391575 TATTGGGCCATGCCCATTCTTTTCT
1 TATTGGGCCATGCCCATTCTTTTCT
* *
20391600 TATTGGGCTATGCCCATTTTTTT
1 TATTGGGCCATGCCCATTCTTTT
20391623 TTCTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (25 bp):
TATTGGGCCATGCCCATTCTTTTCT
Found at i:20391669 original size:19 final size:18
Alignment explanation
Indices: 20391635--20391670 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20391625 CTTTTCTTCC
20391635 TTTCCCTTTCCTTCTCTT
1 TTTCCCTTTCCTTCTCTT
*
20391653 TTTCTCTTTCTCTTCTCT
1 TTTCCCTTTC-CTTCTCT
20391671 CCCGCAGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTCCCTTTCCTTCTCTT
Found at i:20391950 original size:91 final size:90
Alignment explanation
Indices: 20391821--20392054 Score: 299
Period size: 91 Copynumber: 2.6 Consensus size: 90
20391811 CTCCTCATTT
* * * * *
20391821 CAGCCTTAAAAATCAGCAGCCAAAGTTGCTCATTTCACCCTCAAAATCGGCAGCAAAAACCTCAA
1 CAGCCTTCAAAATCAGAAGCTAAAGCTGCTCATCTCACCCTCAAAAT-GGCAGCAAAAACCTCAA
*
20391886 AAATCAGCAGCCAAAGTTGCTCCTTG
65 AAATCAACAGCCAAAGTTGCTCCTTG
* * * * *
20391912 CAGCCTTCAAAATCAGTAGCTAAAGCTACTCCTCTCACCCTCAAAATTGGCAGCCAAAACCTTAA
1 CAGCCTTCAAAATCAGAAGCTAAAGCTGCTCATCTCACCCTCAAAA-TGGCAGCAAAAACCTCAA
* *
20391977 AAATCAATAGCCAAAGTTGCTCCTTT
65 AAATCAACAGCCAAAGTTGCTCCTTG
*
20392003 CAGCCTTCAAAAATCAGCAAG-TAAAGCTGCTCATCTCACCCTTAAAATGGCA
1 CAGCCTTC-AAAATCAG-AAGCTAAAGCTGCTCATCTCACCCTCAAAATGGCA
20392055 AAAAAATAAG
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
91 90 0.73
92 32 0.26
93 2 0.02
ACGTcount: A:0.36, C:0.29, G:0.13, T:0.22
Consensus pattern (90 bp):
CAGCCTTCAAAATCAGAAGCTAAAGCTGCTCATCTCACCCTCAAAATGGCAGCAAAAACCTCAAA
AATCAACAGCCAAAGTTGCTCCTTG
Found at i:20392304 original size:22 final size:22
Alignment explanation
Indices: 20392268--20392313 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 22
20392258 CTTTGACTTC
20392268 TCTTTCTTT-TT-T-TTTTCT-
1 TCTTTCTTTCTTATATTTTCTA
20392286 TCTTTCTTTCTTATATTTTCTA
1 TCTTTCTTTCTTATATTTTCTA
20392308 TCTTTC
1 TCTTTC
20392314 ATCTTTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
19 2 0.08
20 1 0.04
21 6 0.25
22 6 0.25
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.74
Consensus pattern (22 bp):
TCTTTCTTTCTTATATTTTCTA
Found at i:20392321 original size:22 final size:21
Alignment explanation
Indices: 20392280--20392330 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
20392270 TTTCTTTTTT
*
20392280 TTTTCTTCTTTCTTTCTTATA
1 TTTTCTTCTTTCTCTCTTATA
*
20392301 TTTTCTATCTTTCATCT-TTATC
1 TTTTCT-TCTTTC-TCTCTTATA
20392323 TTATTCTT
1 TT-TTCTT
20392331 TCTTACCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 6 0.24
22 13 0.52
23 6 0.24
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTCTTCTTTCTCTCTTATA
Found at i:20400046 original size:19 final size:19
Alignment explanation
Indices: 20400022--20400059 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20400012 CCATTTGACT
20400022 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
20400041 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
20400060 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:20401310 original size:13 final size:13
Alignment explanation
Indices: 20401292--20401316 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20401282 GGAGAAATTG
20401292 TGATTTTATAAAA
1 TGATTTTATAAAA
20401305 TGATTTTATAAA
1 TGATTTTATAAA
20401317 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:20403934 original size:15 final size:15
Alignment explanation
Indices: 20403900--20403939 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
20403890 AAGATTTTCA
20403900 TTTTCTTTTC-CTTG
1 TTTTCTTTTCTCTTG
20403914 TTTTCTTTTCTCTCT-
1 TTTTCTTTTCTCT-TG
20403929 TTTTCTTTTCT
1 TTTTCTTTTCT
20403940 TACTCCTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 10 0.42
15 13 0.54
16 1 0.04
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTCTTTTCTCTTG
Found at i:20407183 original size:21 final size:21
Alignment explanation
Indices: 20407159--20407198 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20407149 GAGTGTGTGC
*
20407159 ATATATATATATGTACTTTAA
1 ATATAAATATATGTACTTTAA
*
20407180 ATATAAATATATTTACTTT
1 ATATAAATATATGTACTTT
20407199 TTATTTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
ATATAAATATATGTACTTTAA
Found at i:20412968 original size:18 final size:19
Alignment explanation
Indices: 20412930--20412969 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
20412920 TTAATATTTT
20412930 AATATTATTTTATTATTAA
1 AATATTATTTTATTATTAA
*
20412949 AATATTATTTTCTT-TTAA
1 AATATTATTTTATTATTAA
20412967 AAT
1 AAT
20412970 TTTCCACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTATTTTATTATTAA
Found at i:20413081 original size:11 final size:11
Alignment explanation
Indices: 20413065--20413096 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
20413055 CGATAAAAGT
20413065 ATTATTATTTA
1 ATTATTATTTA
*
20413076 ATTATTATTTT
1 ATTATTATTTA
20413087 ATTATTATTT
1 ATTATTATTT
20413097 CCTCATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTATTATTTA
Found at i:20415231 original size:60 final size:60
Alignment explanation
Indices: 20415138--20415304 Score: 205
Period size: 60 Copynumber: 2.8 Consensus size: 60
20415128 TAGGAGACCA
*
20415138 AAACAGAAAGTTTTTCGCTGCAGCGAGATTCTTTCTCGCTGC-GACGAAATTAT-AACCCAG
1 AAACAGAAAGTTTCTCGCTGCAGCGAGATTCTTTCTCGCTGCAG-CGAAATT-TCAACCCAG
* * * * *
20415198 AAACAGAAGGTTTCTCACTGCAGCGAGATTCTTTCTTGCTGCAGTGAAATTTCTACCCAG
1 AAACAGAAAGTTTCTCGCTGCAGCGAGATTCTTTCTCGCTGCAGCGAAATTTCAACCCAG
* * *
20415258 AAATAGAAAGTTTCTCGCTGCAGCGAGAATGTATT-TCGCTGCAGCGA
1 AAACAGAAAGTTTCTCGCTGCAGCGAGATTCT-TTCTCGCTGCAGCGA
20415305 GAAGTTACAG
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 87 0.96
61 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (60 bp):
AAACAGAAAGTTTCTCGCTGCAGCGAGATTCTTTCTCGCTGCAGCGAAATTTCAACCCAG
Found at i:20415286 original size:21 final size:21
Alignment explanation
Indices: 20415262--20415307 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
20415252 ACCCAGAAAT
20415262 AGAAAGT-TTCTCGCTGCAGCG
1 AGAAAGTATT-TCGCTGCAGCG
*
20415283 AGAATGTATTTCGCTGCAGCG
1 AGAAAGTATTTCGCTGCAGCG
20415304 AGAA
1 AGAA
20415308 GTTACAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (21 bp):
AGAAAGTATTTCGCTGCAGCG
Found at i:20415537 original size:2 final size:2
Alignment explanation
Indices: 20415525--20415563 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
20415515 CCATCAATAC
* *
20415525 AT AT CAT AT AT AT TT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20415564 CAACATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20425440 original size:38 final size:38
Alignment explanation
Indices: 20425398--20425578 Score: 182
Period size: 38 Copynumber: 4.7 Consensus size: 38
20425388 ATAATGCCCG
* *
20425398 TGTGCACAATGTGGGGGGATGTACACGATGGCACTGAC
1 TGTGCACGATGTGGGGGGATGCACACGATGGCACTGAC
* * * * *
20425436 TGTGCACGATGTGGGGGGATGCACACAATGACTCCGGC
1 TGTGCACGATGTGGGGGGATGCACACGATGGCACTGAC
* * *
20425474 TATGTGCACTATGTGGGGGGATGTACACGATGGCACTGAT
1 --TGTGCACGATGTGGGGGGATGCACACGATGGCACTGAC
* * * * *
20425514 TGTGCACGATGTGGGGGGATGCACACAATGACTCCGGC
1 TGTGCACGATGTGGGGGGATGCACACGATGGCACTGAC
*
20425552 TATGTGCACTATGTGGGGGGATGCACA
1 --TGTGCACGATGTGGGGGGATGCACA
20425579 TGAGCTGGGT
Statistics
Matches: 115, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
38 61 0.53
40 54 0.47
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGCACACGATGGCACTGAC
Found at i:20425489 original size:40 final size:40
Alignment explanation
Indices: 20425436--20425578 Score: 200
Period size: 40 Copynumber: 3.6 Consensus size: 40
20425426 TGGCACTGAC
20425436 TGTGCACGATGTGGGGGGATGCACACAATGACTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACAATGACTCCGGCTA
* * * * * * *
20425476 TGTGCACTATGTGGGGGGATGTACACGATGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGCACACAATGACTCCGGCTA
20425514 TGTGCACGATGTGGGGGGATGCACACAATGACTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACAATGACTCCGGCTA
*
20425554 TGTGCACTATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
20425579 TGAGCTGGGT
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
38 28 0.33
39 6 0.07
40 52 0.60
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACACAATGACTCCGGCTA
Found at i:20425527 original size:78 final size:78
Alignment explanation
Indices: 20425398--20425574 Score: 336
Period size: 78 Copynumber: 2.3 Consensus size: 78
20425388 ATAATGCCCG
*
20425398 TGTGCACAATGTGGGGGGATGTACACGATGGCACTGACTGTGCACGATGTGGGGGGATGCACACA
1 TGTGCACTATGTGGGGGGATGTACACGATGGCACTGACTGTGCACGATGTGGGGGGATGCACACA
20425463 ATGACTCCGGCTA
66 ATGACTCCGGCTA
*
20425476 TGTGCACTATGTGGGGGGATGTACACGATGGCACTGATTGTGCACGATGTGGGGGGATGCACACA
1 TGTGCACTATGTGGGGGGATGTACACGATGGCACTGACTGTGCACGATGTGGGGGGATGCACACA
20425541 ATGACTCCGGCTA
66 ATGACTCCGGCTA
20425554 TGTGCACTATGTGGGGGGATG
1 TGTGCACTATGTGGGGGGATG
20425575 CACATGAGCT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 97 1.00
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (78 bp):
TGTGCACTATGTGGGGGGATGTACACGATGGCACTGACTGTGCACGATGTGGGGGGATGCACACA
ATGACTCCGGCTA
Found at i:20435696 original size:55 final size:55
Alignment explanation
Indices: 20435601--20435761 Score: 250
Period size: 55 Copynumber: 2.9 Consensus size: 55
20435591 ATGTATATAA
*
20435601 CCACCGGTCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCAT
1 CCACCGGTCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCAC
* * * *
20435656 CCTCCGGTCATCAGCTCATGTGCACTCCCACATTGTACATAGCTAGAATCATCAC
1 CCACCGGTCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCAC
* **
20435711 CCACCAGTCATCAGCTCATGTGCACTCCCACACCACACATAGCTGGAATCA
1 CCACCGGTCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCA
20435762 CCCGTCATCA
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 94 1.00
ACGTcount: A:0.27, C:0.37, G:0.15, T:0.22
Consensus pattern (55 bp):
CCACCGGTCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCAC
Found at i:20442661 original size:42 final size:42
Alignment explanation
Indices: 20442615--20442740 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
20442605 TGTTGATGTG
* *
20442615 GACCCGGCTATATGTGAGTAGGAGTGTACATAAGCCGATGAT
1 GACCCGGCTATATGCGAGTAGGAGTGCACATAAGCCGATGAT
* *
20442657 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGATGAT
1 GACCCGGCTATATGCGAGTAGGAGTGCACATAAGCCGATGAT
* * * * * * *
20442699 GACCCAGCCATATGCTAGTGGGGAGTGCGCATGAGCTGATGA
1 GACCCGGCTATATGCGAGT-AGGAGTGCACATAAGCCGATGA
20442741 CGATGGGAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 53 0.74
43 19 0.26
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (42 bp):
GACCCGGCTATATGCGAGTAGGAGTGCACATAAGCCGATGAT
Found at i:20446426 original size:2 final size:2
Alignment explanation
Indices: 20446419--20446459 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
20446409 AAAGAAACTT
20446419 TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC T
20446460 GCCCCTATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:20457638 original size:115 final size:115
Alignment explanation
Indices: 20457436--20457666 Score: 462
Period size: 115 Copynumber: 2.0 Consensus size: 115
20457426 AAGCAAGTAA
20457436 TGTTTTACTCTTATATCATGCCATCATGTTGAACAGAATTTGTAGGATTTGCAATTTTCATGTTG
1 TGTTTTACTCTTATATCATGCCATCATGTTGAACAGAATTTGTAGGATTTGCAATTTTCATGTTG
20457501 ACAGAAAGAGTGGCACCTATAGAGTTAATTCAGTACAAAAAGAGACTTCT
66 ACAGAAAGAGTGGCACCTATAGAGTTAATTCAGTACAAAAAGAGACTTCT
20457551 TGTTTTACTCTTATATCATGCCATCATGTTGAACAGAATTTGTAGGATTTGCAATTTTCATGTTG
1 TGTTTTACTCTTATATCATGCCATCATGTTGAACAGAATTTGTAGGATTTGCAATTTTCATGTTG
20457616 ACAGAAAGAGTGGCACCTATAGAGTTAATTCAGTACAAAAAGAGACTTCT
66 ACAGAAAGAGTGGCACCTATAGAGTTAATTCAGTACAAAAAGAGACTTCT
20457666 T
1 T
20457667 CCTGATCCAT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (115 bp):
TGTTTTACTCTTATATCATGCCATCATGTTGAACAGAATTTGTAGGATTTGCAATTTTCATGTTG
ACAGAAAGAGTGGCACCTATAGAGTTAATTCAGTACAAAAAGAGACTTCT
Found at i:20467800 original size:67 final size:67
Alignment explanation
Indices: 20467715--20467850 Score: 193
Period size: 67 Copynumber: 2.0 Consensus size: 67
20467705 GAAAAGTTAG
* * * * *
20467715 TTTTGGATTTTGATTGATCTCGTGAAAAACTATTGTTAAAGGTTGTGGTTGAGCCTT-TGAAAAG
1 TTTTGGATTTTGATTGATCCCGTGAAAAACCATTGTTAAAGGTTATGGCTGAG-CTTGTGAAAAA
20467779 CCA
65 CCA
* *
20467782 TTTTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTAAAGGTTATGGCTGAGCTTGTGAAAAAC
1 TTTTGGATTTTGATTGATCCCGTGAAAAACCATTGTTAAAGGTTATGGCTGAGCTTGTGAAAAAC
20467847 CA
66 CA
20467849 TT
1 TT
20467851 GTAAAAGCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 3 0.05
67 58 0.95
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (67 bp):
TTTTGGATTTTGATTGATCCCGTGAAAAACCATTGTTAAAGGTTATGGCTGAGCTTGTGAAAAAC
CA
Found at i:20467842 original size:35 final size:35
Alignment explanation
Indices: 20467736--20467857 Score: 117
Period size: 35 Copynumber: 3.6 Consensus size: 35
20467726 GATTGATCTC
* *
20467736 GTGAAAAACTATTGTTAAAGGTTGTGGTTGAGCCTT
1 GTGAAAAACCATTGTTAAAGGTTATGGTTGAG-CTT
* * * * **
20467772 -TGAAAAGCCATT-TT--GGGTTTTGGTTGATCCC
1 GTGAAAAACCATTGTTAAAGGTTATGGTTGAGCTT
*
20467803 GTGAAAAACCATTGTTAAAGGTTATGGCTGAGCTT
1 GTGAAAAACCATTGTTAAAGGTTATGGTTGAGCTT
*
20467838 GTGAAAAACCATTGTAAAAG
1 GTGAAAAACCATTGTTAAAG
20467858 CTTGGTGGAA
Statistics
Matches: 67, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
31 1 0.01
32 22 0.33
33 2 0.03
34 2 0.03
35 40 0.60
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
GTGAAAAACCATTGTTAAAGGTTATGGTTGAGCTT
Found at i:20470186 original size:34 final size:34
Alignment explanation
Indices: 20470148--20470224 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
20470138 TTAGTATGGG
* *
20470148 TTATGCTTGCTCCCGTAAAAAAGTATTGTGTGGA
1 TTATGCTTGCTCCCATAAAAAAGTATTGTGAGGA
** * *
20470182 TTATGCTTGCTCTTATAAAAAGGTATTGTGAGGG
1 TTATGCTTGCTCCCATAAAAAAGTATTGTGAGGA
20470216 TTATGCTTG
1 TTATGCTTG
20470225 AGCTTGGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.39
Consensus pattern (34 bp):
TTATGCTTGCTCCCATAAAAAAGTATTGTGAGGA
Found at i:20470236 original size:34 final size:34
Alignment explanation
Indices: 20470164--20470253 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
20470154 TTGCTCCCGT
* * * ** *
20470164 AAAAAAGTATTGTGTGGATTATGCTTGCTCTTAT
1 AAAAAGGTATTGTGAGGGTTATGCTTGAGCTTAG
*
20470198 AAAAAGGTATTGTGAGGGTTATGCTTGAGCTTGG
1 AAAAAGGTATTGTGAGGGTTATGCTTGAGCTTAG
* * *
20470232 AAAAAGGCATTGTAAAGGTTAT
1 AAAAAGGTATTGTGAGGGTTAT
20470254 AATTGAGCCT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (34 bp):
AAAAAGGTATTGTGAGGGTTATGCTTGAGCTTAG
Found at i:20471355 original size:18 final size:19
Alignment explanation
Indices: 20471334--20471369 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20471324 TTTATTGCCC
20471334 GCAACACATCTT-TCTCAA
1 GCAACACATCTTGTCTCAA
*
20471352 GCAACCCATCTTGTCTCA
1 GCAACACATCTTGTCTCA
20471370 TTCTCGGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.28
Consensus pattern (19 bp):
GCAACACATCTTGTCTCAA
Found at i:20478016 original size:28 final size:29
Alignment explanation
Indices: 20477975--20478039 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
20477965 GTCTATGGGC
* *
20477975 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
20478003 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
*
20478033 AAATTTT
1 AATTTTT
20478040 AAAAATTACT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 12 0.40
30 18 0.60
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.42
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:20481264 original size:19 final size:19
Alignment explanation
Indices: 20481226--20481264 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20481216 CGGTTGAGGG
* *
20481226 AGAGTAAAGGAAAAATAAA
1 AGAGCAAAGGAAAAAGAAA
*
20481245 AGAGCAAAGGAAGAAGAAA
1 AGAGCAAAGGAAAAAGAAA
20481264 A
1 A
20481265 AACCGAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.26, T:0.05
Consensus pattern (19 bp):
AGAGCAAAGGAAAAAGAAA
Found at i:20481476 original size:34 final size:34
Alignment explanation
Indices: 20481387--20481479 Score: 125
Period size: 34 Copynumber: 2.7 Consensus size: 34
20481377 CCATTTAAGG
* *
20481387 GCTGGTTTTGGAGGTCGAAAAA-TGCCATTTTTTT
1 GCTGGTTTTGGAGG-CCAAAAAGTGCCATTTTTCT
* **
20481421 GCTGGTTTTGGAGACTGAAAAGTGCCATTTTTCT
1 GCTGGTTTTGGAGGCCAAAAAGTGCCATTTTTCT
20481455 GCTGGTTTTGGAGGCCAAAAAGTGC
1 GCTGGTTTTGGAGGCCAAAAAGTGC
20481480 AAAATTTTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 5 0.10
34 46 0.90
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (34 bp):
GCTGGTTTTGGAGGCCAAAAAGTGCCATTTTTCT
Found at i:20481610 original size:35 final size:35
Alignment explanation
Indices: 20481571--20481657 Score: 99
Period size: 34 Copynumber: 2.5 Consensus size: 35
20481561 AGGGAAAGGT
*
20481571 GCAGCTTAGCTGCTGAAATTTT-AAGGAAAAACAAA
1 GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAA-AAA
* *
20481606 GCAGCATAGCTGCTG--ATTTTGAAGCAAAAATAA
1 GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAAAAA
*
20481639 GCAGCCTTAGCTGTTGAAA
1 GCAG-CTTAGCTGCTGAAA
20481658 AATTAAAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
33 11 0.26
34 17 0.40
35 14 0.33
36 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (35 bp):
GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAAAAA
Found at i:20481641 original size:33 final size:34
Alignment explanation
Indices: 20481571--20481643 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
20481561 AGGGAAAGGT
* *
20481571 GCAGCTTAGCTGCTGAAATTTTAAGGAAAAACAAA
1 GCAGCATAGCTGCTG-AATTTTAAGCAAAAACAAA
*
20481606 GCAGCATAGCTGCTG-ATTTTGAAGCAAAAA-TAA
1 GCAGCATAGCTGCTGAATTTT-AAGCAAAAACAAA
20481639 GCAGC
1 GCAGC
20481644 CTTAGCTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 12 0.35
34 8 0.24
35 14 0.41
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (34 bp):
GCAGCATAGCTGCTGAATTTTAAGCAAAAACAAA
Found at i:20481800 original size:5 final size:5
Alignment explanation
Indices: 20481786--20481847 Score: 108
Period size: 5 Copynumber: 12.6 Consensus size: 5
20481776 GGTGGGAGAG
20481786 AAAG- AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
*
20481835 AAGGA AAAGA AAA
1 AAAGA AAAGA AAA
20481848 TAACAAGATA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
4 4 0.07
5 51 0.93
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:20481940 original size:25 final size:24
Alignment explanation
Indices: 20481883--20481942 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 24
20481873 CCAACAAGAT
20481883 AGAAAAATGGACAAGGTCCAATAA
1 AGAAAAATGGACAAGGTCCAATAA
*
20481907 AGGAAAAATGGACATGGTCCAATTAA
1 A-GAAAAATGGACAAGGTCCAA-TAA
20481933 A-AAGAAATGG
1 AGAA-AAATGG
20481943 GAGAAGTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 3 0.09
25 25 0.78
26 4 0.12
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.15
Consensus pattern (24 bp):
AGAAAAATGGACAAGGTCCAATAA
Found at i:20482052 original size:15 final size:15
Alignment explanation
Indices: 20482032--20482063 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20482022 CCTAGCTTAA
20482032 TTGGGTAAAATTTCT
1 TTGGGTAAAATTTCT
20482047 TTGGGTAAAATTTCT
1 TTGGGTAAAATTTCT
20482062 TT
1 TT
20482064 ACTCTTCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (15 bp):
TTGGGTAAAATTTCT
Found at i:20485984 original size:30 final size:30
Alignment explanation
Indices: 20485948--20486005 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
20485938 TTAATCAAGC
20485948 CCTTATACTTTTATTTTGAA-TCAAATAAGT
1 CCTTATACTTTTATTTT-AAGTCAAATAAGT
20485978 CCTTATACTTTTATTTTAAGTCAAATAA
1 CCTTATACTTTTATTTTAAGTCAAATAA
20486006 ACCGTTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (30 bp):
CCTTATACTTTTATTTTAAGTCAAATAAGT
Found at i:20486159 original size:33 final size:33
Alignment explanation
Indices: 20486071--20486146 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
20486061 TGGCATTGAC
*
20486071 GTGACATGCT-ATCATATCACAATTGATGATAAT
1 GTGACATGCTGA-CATATCATAATTGATGATAAT
*
20486104 GTGGCATGCTGACATATCATAATTGATGATAAT
1 GTGACATGCTGACATATCATAATTGATGATAAT
*
20486137 GTGATATGCT
1 GTGACATGCT
20486147 AATTTGGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 37 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (33 bp):
GTGACATGCTGACATATCATAATTGATGATAAT
Found at i:20486345 original size:29 final size:29
Alignment explanation
Indices: 20486271--20486346 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
20486261 ATAATTAGTC
*
20486271 ATAAGGGCTTATTT-AACTCAAAATAAAAAT
1 ATAAGGGCTTATTTGAACT--AAATAAAAAA
20486301 ATAAGGGCTTGA-TTGAACGT-AATAAAAAA
1 ATAAGGGCTT-ATTTGAAC-TAAATAAAAAA
20486330 ATAAGGGCTTATTTGAA
1 ATAAGGGCTTATTTGAA
20486347 TTTTGTTGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 1 0.02
29 23 0.56
30 12 0.29
31 4 0.10
32 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (29 bp):
ATAAGGGCTTATTTGAACTAAATAAAAAA
Found at i:20489827 original size:13 final size:13
Alignment explanation
Indices: 20489809--20489833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20489799 GGCAGAGAGC
20489809 ACTTAGTTGACTG
1 ACTTAGTTGACTG
20489822 ACTTAGTTGACT
1 ACTTAGTTGACT
20489834 AAATTAGTTC
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:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
ACTTAGTTGACTG
Found at i:20503845 original size:23 final size:24
Alignment explanation
Indices: 20503798--20503845 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
20503788 CCTAAAGCAT
* **
20503798 AAATGAGTGATGAAAATAAGGATA
1 AAATGAGTGAAGAAAATAAAAATA
20503822 AAATGA-TGAAGAAAATAAAAATA
1 AAATGAGTGAAGAAAATAAAAATA
20503845 A
1 A
20503846 TGATGATTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (24 bp):
AAATGAGTGAAGAAAATAAAAATA
Found at i:20504090 original size:23 final size:23
Alignment explanation
Indices: 20504060--20504103 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
20504050 CCATAAATAT
*
20504060 CATTTTCCAGCAGCTTTTTCTCA
1 CATTTTCCAGCAGCTTCTTCTCA
*
20504083 CATTTTCCAGTAGCTTCTTCT
1 CATTTTCCAGCAGCTTCTTCT
20504104 TCTTCTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.30, G:0.09, T:0.45
Consensus pattern (23 bp):
CATTTTCCAGCAGCTTCTTCTCA
Found at i:20507823 original size:37 final size:38
Alignment explanation
Indices: 20507770--20507978 Score: 205
Period size: 37 Copynumber: 5.3 Consensus size: 38
20507760 TAATGTTGTG
*
20507770 TGATGATG-TTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATAGAAGTGTGCGAGTAGGGAGTGCACACA
20507807 TGATGATGATAG-AGTGTGCGAGTAGGGAGTGCGAGTAGGGAGTGCACA
1 TGATGATGATAGAAGTGTGCGAGTAGGGAGTGC--------A---CACA
20507855 TG-TGATAATGATAG-AGTGTGCGAGTAGGGAGTGCACACA
1 TGATG--A-TGATAGAAGTGTGCGAGTAGGGAGTGCACACA
* *
20507894 TGATGATG-TTGAAGTGTGCGAGTAGCGAGTGCACACA
1 TGATGATGATAGAAGTGTGCGAGTAGGGAGTGCACACA
* *
20507931 TGATGATG-TTGAAGTGTGCGAGTAGAGAGTGCACACA
1 TGATGATGATAGAAGTGTGCGAGTAGGGAGTGCACACA
20507968 TGATGATGATA
1 TGATGATGATA
20507979 TTGCATTAAG
Statistics
Matches: 149, Mismatches: 5, Indels: 35
0.79 0.03 0.19
Matches are distributed among these distances:
36 2 0.01
37 98 0.66
38 4 0.03
39 6 0.04
40 2 0.01
42 1 0.01
45 1 0.01
47 2 0.01
48 6 0.04
49 1 0.01
50 26 0.17
ACGTcount: A:0.29, C:0.10, G:0.37, T:0.24
Consensus pattern (38 bp):
TGATGATGATAGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:20507840 original size:13 final size:13
Alignment explanation
Indices: 20507822--20507851 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
20507812 ATGATAGAGT
20507822 GTGCGAGTAGGGA
1 GTGCGAGTAGGGA
20507835 GTGCGAGTAGGGA
1 GTGCGAGTAGGGA
20507848 GTGC
1 GTGC
20507852 ACATGTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.10, G:0.53, T:0.17
Consensus pattern (13 bp):
GTGCGAGTAGGGA
Found at i:20507840 original size:50 final size:50
Alignment explanation
Indices: 20507785--20507888 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
20507775 ATGTTGAAGT
*
20507785 GTGCGAGTAGGGAGTGCACACATGATGATGATAGAGTGTGCGAGTAGGGA
1 GTGCGAGTAGGGAGTGCACACATGATAATGATAGAGTGTGCGAGTAGGGA
**
20507835 GTGCGAGTAGGGAGTGCACATGTGATAATGATAGAGTGTGCGAGTAGGGA
1 GTGCGAGTAGGGAGTGCACACATGATAATGATAGAGTGTGCGAGTAGGGA
20507885 GTGC
1 GTGC
20507889 ACACATGATG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.27, C:0.10, G:0.42, T:0.21
Consensus pattern (50 bp):
GTGCGAGTAGGGAGTGCACACATGATAATGATAGAGTGTGCGAGTAGGGA
Found at i:20509533 original size:73 final size:74
Alignment explanation
Indices: 20509447--20509633 Score: 227
Period size: 73 Copynumber: 2.6 Consensus size: 74
20509437 AAACAAAGAA
* * ** *
20509447 GACTTAGTCGACTAAGAAGCATGGTTAGTCGACTAAGAGCTTACTGCCAGAAACTGAG-TTTAGA
1 GACTTAATCGACTAAGAAGCATGGTTAGTCGACTAAGAGCTTACTGCCAGAAACGGAGATCAAAA
* *
20509511 GACAGAGAT
66 GACAGAAAC
* * * *
20509520 GACTTAATCGACTACGAAGCATTGTTAGTAGACTAAGAGCTTACTGCCAGAAACGGGGATCAAAA
1 GACTTAATCGACTAAGAAGCATGGTTAGTCGACTAAGAGCTTACTGCCAGAAACGGAGATCAAAA
*
20509585 GATAGAAAC
66 GACAGAAAC
*
20509594 GACTTAATCGACTAAGAAG--TGTGTTAGTCAACTAAGAGCT
1 GACTTAATCGACTAAGAAGCATG-GTTAGTCGACTAAGAGCT
20509634 CTCTATTTGA
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
72 1 0.01
73 68 0.71
74 27 0.28
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (74 bp):
GACTTAATCGACTAAGAAGCATGGTTAGTCGACTAAGAGCTTACTGCCAGAAACGGAGATCAAAA
GACAGAAAC
Found at i:20516906 original size:73 final size:73
Alignment explanation
Indices: 20516827--20516970 Score: 209
Period size: 73 Copynumber: 2.0 Consensus size: 73
20516817 AAGATGGTTG
* * *
20516827 GTTCAGAAACAGAGAAGACTTAGTGGACCAAGGAA-CATGGTTAGTCGACTAAGAGTTTACTGCC
1 GTTCAGAAACAGAGAAGACTTAATCGACCAA-GAAGCATGGTTAGTCGACTAAGAGCTTACTGCC
20516891 AGAAACTGA
65 AGAAACTGA
* * * *
20516900 GTTCAGAGACAGAGACGACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGCTTACTGCCA
1 GTTCAGAAACAGAGAAGACTTAATCGACCAAGAAGCATGGTTAGTCGACTAAGAGCTTACTGCCA
20516965 GAAACT
66 GAAACT
20516971 AGGATCAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
72 3 0.05
73 60 0.95
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (73 bp):
GTTCAGAAACAGAGAAGACTTAATCGACCAAGAAGCATGGTTAGTCGACTAAGAGCTTACTGCCA
GAAACTGA
Found at i:20520501 original size:35 final size:35
Alignment explanation
Indices: 20520457--20520527 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
20520447 GTTAGTTTTG
* * * *
20520457 GGTTTTGGTTGATCTTGGGAAAAACCATTGTTAAA
1 GGTTATGGTTGAGCCTGGGAAAAACCATTGTAAAA
* *
20520492 GGTTATGGTTGAGCCTGTGAAAAGCCATTGTAAAA
1 GGTTATGGTTGAGCCTGGGAAAAACCATTGTAAAA
20520527 G
1 G
20520528 CTTAGTGGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32
Consensus pattern (35 bp):
GGTTATGGTTGAGCCTGGGAAAAACCATTGTAAAA
Found at i:20529716 original size:43 final size:43
Alignment explanation
Indices: 20529628--20529745 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
20529618 GTAATTATGT
* * *
20529628 TGACTCGGCTATGTACGAGTAGGGAGTGTGCATAACCCGAGGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGA
* * * *
20529671 TGACCCGGTTATGTGCGAGTAGGGAATGCGCATTATCCG-GTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGAG-GA
* *
20529714 TGACCCAGCCATGTGCGAGTA-GGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
20529746 GAGCTGGTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 11 0.17
43 52 0.83
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGA
Found at i:20529773 original size:14 final size:17
Alignment explanation
Indices: 20529744--20529823 Score: 112
Period size: 17 Copynumber: 4.8 Consensus size: 17
20529734 AGGAGTGCGC
20529744 ATGAGCTGGTGATGATG
1 ATGAGCTGGTGATGATG
20529761 ATGAGCTGGTGATGATG
1 ATGAGCTGGTGATGATG
20529778 ATGAGCTGGTGATGATG
1 ATGAGCTGGTGATGATG
* *
20529795 ATGATGGTGGTGGTGA-G
1 ATGA-GCTGGTGATGATG
20529812 ATGA--TGGTGATG
1 ATGAGCTGGTGATG
20529824 GGTATATACG
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
14 7 0.12
17 43 0.73
18 9 0.15
ACGTcount: A:0.23, C:0.04, G:0.44, T:0.30
Consensus pattern (17 bp):
ATGAGCTGGTGATGATG
Found at i:20533465 original size:13 final size:13
Alignment explanation
Indices: 20533447--20533472 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20533437 AAACATTTTT
20533447 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
20533460 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
20533473 CTAGCATGAT
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:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGAGAG
Found at i:20544101 original size:40 final size:38
Alignment explanation
Indices: 20544055--20544150 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
20544045 ACCCGGTTCA
*
20544055 TGTGCATCCCCCCACATCGTGCACATACCCGGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACA-A-CCAGTGCCATCG
*
20544095 TGTGCATCCCCCCACATCGTGCACAATCAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACAACCAGTGCCATCG
* *
20544133 TATACATCCCCCCACATC
1 TGTGCATCCCCCCACATC
20544151 AAGCACACAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 26 0.50
39 1 0.02
40 25 0.48
ACGTcount: A:0.21, C:0.43, G:0.16, T:0.21
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAACCAGTGCCATCG
Found at i:20545759 original size:43 final size:43
Alignment explanation
Indices: 20545692--20545804 Score: 131
Period size: 43 Copynumber: 2.6 Consensus size: 43
20545682 GTAATGACAT
*
20545692 TGACTCGGTTATGTGCGAGTAGGGAGTACGCATAAGC-CGAG-GA
1 TGACCCGGTTATGTGCGAGTAGGGAGTACGCATAA-CTCG-GTGA
* **
20545735 TGACCTGGTTATGTGCGAGTAGGGAGTGTGCATAACTCGGTGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTACGCATAACTCGGTGA
* **
20545778 TGACCCAGCCATGTGCGAGTAGGGAGT
1 TGACCCGGTTATGTGCGAGTAGGGAGT
20545805 GCACATGAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 58 0.97
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (43 bp):
TGACCCGGTTATGTGCGAGTAGGGAGTACGCATAACTCGGTGA
Found at i:20546215 original size:21 final size:21
Alignment explanation
Indices: 20546186--20546227 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
20546176 TTCATCAGTT
*
20546186 GAATTTCGCTGCAGAGAGAAA
1 GAATCTCGCTGCAGAGAGAAA
*
20546207 GAATCTCGCTGCAGCGAGAAA
1 GAATCTCGCTGCAGAGAGAAA
20546228 CATTCTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.17
Consensus pattern (21 bp):
GAATCTCGCTGCAGAGAGAAA
Found at i:20550336 original size:25 final size:24
Alignment explanation
Indices: 20550297--20550343 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
20550287 GTTTCACACA
* *
20550297 AGGCCACGGTTGATATGTGTGGCT
1 AGGCCACAGTTGATATATGTGGCT
20550321 AGGCCACTAGTTGATATATGTGG
1 AGGCCAC-AGTTGATATATGTGG
20550344 TTGCGACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (24 bp):
AGGCCACAGTTGATATATGTGGCT
Found at i:20558626 original size:2 final size:2
Alignment explanation
Indices: 20558619--20558659 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
20558609 AAACGTCTAT
20558619 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
20558660 TATATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.