Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 127 of 187
Found at i:38536975 original size:26 final size:26
Alignment explanation
Indices: 38536946--38536995 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
38536936 ACACAATATC
38536946 GTAGCAAAGCTGCCAGTAATAGTATT
1 GTAGCAAAGCTGCCAGTAATAGTATT
38536972 GTAGCAAAGCTGCCAGTAATAGTA
1 GTAGCAAAGCTGCCAGTAATAGTA
38536996 AATGCGACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (26 bp):
GTAGCAAAGCTGCCAGTAATAGTATT
Found at i:38537200 original size:27 final size:27
Alignment explanation
Indices: 38537170--38537230 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
38537160 TCATCTCTTA
*
38537170 AGGGTATAATAGTTATTTTACCCTATG
1 AGGGTATAATAGTCATTTTACCCTATG
** * *
38537197 AGGGTATTTTGGTCATTTTACCTTATG
1 AGGGTATAATAGTCATTTTACCCTATG
38537224 AGGGTAT
1 AGGGTAT
38537231 TTCGATCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.43
Consensus pattern (27 bp):
AGGGTATAATAGTCATTTTACCCTATG
Found at i:38537231 original size:27 final size:27
Alignment explanation
Indices: 38537184--38537300 Score: 128
Period size: 27 Copynumber: 4.1 Consensus size: 27
38537174 TATAATAGTT
*
38537184 ATTTTACCCTATGAGGGTATTTTGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTC
* *
38537211 ATTTTACCTTATGAGGGTATTTCGATC
1 ATTTTACCCTATGAGGGTATTTCGGTC
*
38537238 ATTTCACCCTATG-GAGGTATTTCGGTC
1 ATTTTACCCTATGAG-GGTATTTCGGTC
*
38537265 ATTTTACCTTATACTATGAGGGTATTTCGATC
1 ATTTTACC-----CTATGAGGGTATTTCGGTC
38537297 ATTT
1 ATTT
38537301 ATTGACCTCT
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
26 1 0.01
27 53 0.71
32 20 0.27
33 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTATGAGGGTATTTCGGTC
Found at i:38537247 original size:54 final size:56
Alignment explanation
Indices: 38537184--38537300 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 56
38537174 TATAATAGTT
* *
38537184 ATTTTACCCTAT-GAGGGTATTTTGGTCATTTTACC-T-TATGAGGGTATTTCGATC
1 ATTTCACCCTATGGA-GGTATTTCGGTCATTTTACCTTATATGAGGGTATTTCGATC
38537238 ATTTCACCCTATGGAGGTATTTCGGTCATTTTACCTTATACTATGAGGGTATTTCGATC
1 ATTTCACCCTATGGAGGTATTTCGGTCATTTTACC-T-TA-TATGAGGGTATTTCGATC
38537297 ATTT
1 ATTT
38537301 ATTGACCTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
54 30 0.55
55 2 0.04
57 1 0.02
59 22 0.40
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (56 bp):
ATTTCACCCTATGGAGGTATTTCGGTCATTTTACCTTATATGAGGGTATTTCGATC
Found at i:38549348 original size:6 final size:6
Alignment explanation
Indices: 38549334--38549372 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
38549324 TGGGAAAAAT
*
38549334 AAATGA AAATTA AAA-TA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAAT
38549373 GATCCCCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (6 bp):
AAATTA
Found at i:38549863 original size:30 final size:31
Alignment explanation
Indices: 38549829--38549886 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
38549819 AACAGTTCGA
*
38549829 TGACTTAAAT-AAAACTTTTGAATAGTTTAG
1 TGACTTAAATGAAAACTTTTAAATAGTTTAG
38549859 TGACTTAAATGAAAACTTTTAAATAGTT
1 TGACTTAAATGAAAACTTTTAAATAGTT
38549887 CAACTATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTTAAATAGTTTAG
Found at i:38550323 original size:41 final size:39
Alignment explanation
Indices: 38550276--38550377 Score: 111
Period size: 41 Copynumber: 2.6 Consensus size: 39
38550266 TATTAAATTT
*
38550276 ATATTAGAAAAATTATTTATTTGATAAATTAGTGAATAT-A
1 ATATTAGAAAAATTATTTATTTGATAAA--AGTAAATATCA
*
38550316 AGTATTAGATATAATTATATTATTTGATAAAAGTAAATATCA
1 A-TATTAGA-AAAATTAT-TTATTTGATAAAAGTAAATATCA
*
38550358 ATTTTA-AAAAA-TATTTATTT
1 ATATTAGAAAAATTATTTATTT
38550378 TTTAAATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
37 6 0.11
38 3 0.06
39 3 0.06
40 2 0.04
41 19 0.35
42 9 0.17
43 12 0.22
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (39 bp):
ATATTAGAAAAATTATTTATTTGATAAAAGTAAATATCA
Found at i:38550595 original size:7 final size:7
Alignment explanation
Indices: 38550583--38550619 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
38550573 AACTCATTTA
38550583 AAATATT
1 AAATATT
38550590 AAATATTT
1 AAATA-TT
38550598 AAAATATT
1 -AAATATT
38550606 AAATATT
1 AAATATT
38550613 AAATATT
1 AAATATT
38550620 TTAAACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 19 0.68
8 4 0.14
9 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATATT
Found at i:38550624 original size:16 final size:16
Alignment explanation
Indices: 38550578--38550612 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
38550568 TATCAAACTC
38550578 ATTTAAAATATTAAAT
1 ATTTAAAATATTAAAT
38550594 ATTTAAAATATTAAAT
1 ATTTAAAATATTAAAT
38550610 ATT
1 ATT
38550613 AAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTAAAATATTAAAT
Found at i:38551714 original size:21 final size:21
Alignment explanation
Indices: 38551679--38551728 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
38551669 CATTGTTTCT
*
38551679 AATCTCACCACTACAATATCC
1 AATCTCACCACTACAATAACC
** * *
38551700 AATCTCACCTTTACAGTAACT
1 AATCTCACCACTACAATAACC
38551721 AATCTCAC
1 AATCTCAC
38551729 TGTCACCGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.34, G:0.02, T:0.28
Consensus pattern (21 bp):
AATCTCACCACTACAATAACC
Found at i:38554952 original size:19 final size:20
Alignment explanation
Indices: 38554900--38554953 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
38554890 AGTTTATAAA
*
38554900 AATAAAAAATAATAAATTTT
1 AATAAAAAATATTAAATTTT
* *
38554920 -AGAAAAATTATTAAATTTT
1 AATAAAAAATATTAAATTTT
38554939 AATAAAAAAT-TTAAA
1 AATAAAAAATATTAAA
38554954 ACTATTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AATAAAAAATATTAAATTTT
Found at i:38555258 original size:19 final size:19
Alignment explanation
Indices: 38555230--38555292 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 19
38555220 TTAATATTTC
*
38555230 TATATATTTTACAATTTTT
1 TATATTTTTTACAATTTTT
38555249 TATATTTTTTTACAA-TTTT
1 TATA-TTTTTTACAATTTTT
* *
38555268 TATATTTATT-CTATTTTT
1 TATATTTTTTACAATTTTT
*
38555286 AATATTT
1 TATATTT
38555293 AATTTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 2 0.05
18 15 0.39
19 12 0.32
20 9 0.24
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTTTTTACAATTTTT
Found at i:38555261 original size:20 final size:19
Alignment explanation
Indices: 38555236--38555274 Score: 69
Period size: 19 Copynumber: 2.0 Consensus size: 19
38555226 TTTCTATATA
38555236 TTTTACAATTTTTTATATTT
1 TTTTACAA-TTTTTATATTT
38555256 TTTTACAATTTTTATATTT
1 TTTTACAATTTTTATATTT
38555275 ATTCTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTACAATTTTTATATTT
Found at i:38555300 original size:16 final size:16
Alignment explanation
Indices: 38555281--38555311 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38555271 ATTTATTCTA
*
38555281 TTTTTAATATTTAATT
1 TTTTTAAAATTTAATT
38555297 TTTTTAAAATTTAAT
1 TTTTTAAAATTTAAT
38555312 AATATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAAAATTTAATT
Found at i:38555569 original size:90 final size:91
Alignment explanation
Indices: 38555398--38555588 Score: 233
Period size: 90 Copynumber: 2.1 Consensus size: 91
38555388 TTTTTTTTTT
* * *
38555398 AAGTTTGAAGGT-CTTTTTTATACATTTTGAAAGTTCAAGTACCCAATTGAATGCCAAAAAAAAG
1 AAGTTTGAAGGTATTTTTTTATACATTTTGAAAGTTCAAGTACCCAAATGAATGCAAAAAAAAAG
* * *
38555462 TAGGGGGTTAATTGCTTTTTCTGAAA
66 TAAGGGGTTAATTGCTTTTCCTAAAA
* * * * ** *
38555488 AGGTTTTAAGGTATTTTTTTATGCATTTTGAAAGTTTAAGTATTCAAATGATTG-AAAAAAAAAG
1 AAGTTTGAAGGTATTTTTTTATACATTTTGAAAGTTCAAGTACCCAAATGAATGCAAAAAAAAAG
* *
38555552 TAATGGTTTAATTGCTTTTCCTAAAA
66 TAAGGGGTTAATTGCTTTTCCTAAAA
38555578 AAGTTTGAAGG
1 AAGTTTGAAGG
38555589 CTTTTTGTAC
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
90 49 0.59
91 34 0.41
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (91 bp):
AAGTTTGAAGGTATTTTTTTATACATTTTGAAAGTTCAAGTACCCAAATGAATGCAAAAAAAAAG
TAAGGGGTTAATTGCTTTTCCTAAAA
Found at i:38555796 original size:21 final size:21
Alignment explanation
Indices: 38555749--38555797 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
38555739 TGATAATCTA
*
38555749 AAAAATATATTAAAAATTAAT
1 AAAAATATATTAAAAAATAAT
*
38555770 AAAAATATTTTAAAAAATAA-
1 AAAAATATATTAAAAAATAAT
38555790 AACAAATA
1 AA-AAATA
38555798 CAAACAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATATATTAAAAAATAAT
Found at i:38562651 original size:25 final size:27
Alignment explanation
Indices: 38562623--38562702 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
38562613 ACAGTCATAC
*
38562623 ATAACATTAA-GCAT-ACAGTTATTTT
1 ATAACATTAAGGCATAACAGTCATTTT
*
38562648 ATAACA-TAAGGGCATAATAGTCATTTT
1 ATAACATTAA-GGCATAACAGTCATTTT
* *
38562675 ATAACA-TAGGGGCATAATAGTCATTTT
1 ATAACATTA-AGGCATAACAGTCATTTT
38562702 A
1 A
38562703 GTCATTTTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 3 0.06
25 6 0.12
26 4 0.08
27 35 0.73
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (27 bp):
ATAACATTAAGGCATAACAGTCATTTT
Found at i:38562662 original size:26 final size:26
Alignment explanation
Indices: 38562633--38562702 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
38562623 ATAACATTAA
*
38562633 GCATACAGTTATTTTATAACATAAGG
1 GCATACAGTCATTTTATAACATAAGG
* *
38562659 GCATAATAGTCATTTTATAACATAGGG
1 GCAT-ACAGTCATTTTATAACATAAGG
*
38562686 GCATAATAGTCATTTTA
1 GCAT-ACAGTCATTTTA
38562703 GTCATTTTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 4 0.10
27 36 0.90
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (26 bp):
GCATACAGTCATTTTATAACATAAGG
Found at i:38562676 original size:27 final size:27
Alignment explanation
Indices: 38562643--38562806 Score: 116
Period size: 27 Copynumber: 6.4 Consensus size: 27
38562633 GCATACAGTT
38562643 ATTTTATAACATAAGGGCATAATAGTC
1 ATTTTATAACATAAGGGCATAATAGTC
*
38562670 ATTTTATAACATAGGGGCATAATAGTC
1 ATTTTATAACATAAGGGCATAATAGTC
*
38562697 ATTTTAGT--CAT-------T-TTAGTC
1 ATTTTA-TAACATAAGGGCATAATAGTC
* * * *
38562715 ATTTTATAGCATATGGGCATAACCA-TT
1 ATTTTATAACATAAGGGCATAA-TAGTC
* *
38562742 ATTTTATAACATAGGGGTATAATAGTC
1 ATTTTATAACATAAGGGCATAATAGTC
** * * *
38562769 ATTTTACCACGTGAGGGCATAACAGTC
1 ATTTTATAACATAAGGGCATAATAGTC
38562796 ATTTTATAACA
1 ATTTTATAACA
38562807 GTTTGGGGGT
Statistics
Matches: 104, Mismatches: 20, Indels: 26
0.69 0.13 0.17
Matches are distributed among these distances:
17 1 0.01
18 11 0.11
19 4 0.04
26 5 0.05
27 81 0.78
28 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (27 bp):
ATTTTATAACATAAGGGCATAATAGTC
Found at i:38562706 original size:9 final size:9
Alignment explanation
Indices: 38562692--38562720 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
38562682 AGGGGCATAA
38562692 TAGTCATTT
1 TAGTCATTT
38562701 TAGTCATTT
1 TAGTCATTT
38562710 TAGTCATTT
1 TAGTCATTT
38562719 TA
1 TA
38562721 TAGCATATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.55
Consensus pattern (9 bp):
TAGTCATTT
Found at i:38574236 original size:33 final size:33
Alignment explanation
Indices: 38574188--38574260 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
38574178 ATACAACATG
* *
38574188 CAGTAACAGTCTGGGCCTGAGCCCTATTCAGTAA
1 CAGT-ACAGTCTGGGCCTGAGCCCAATACAGTAA
* *
38574222 CAGTACAGTGTGGGCCTTAGCCCAATACAGTAA
1 CAGTACAGTCTGGGCCTGAGCCCAATACAGTAA
*
38574255 TAGTAC
1 CAGTAC
38574261 GTGCAATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 30 0.88
34 4 0.12
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (33 bp):
CAGTACAGTCTGGGCCTGAGCCCAATACAGTAA
Found at i:38574390 original size:26 final size:26
Alignment explanation
Indices: 38574360--38574440 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
38574350 AACACACTAA
*
38574360 TATCGCAGCAAACCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* *
38574386 TATCGTAGCGAAGCTGCCAGT-ATCAG
1 TATCGCAGCAAAGCTGCCAGTAAT-AG
*
38574412 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
38574438 TAT
1 TAT
38574441 ATGTGGCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.04
26 44 0.94
27 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:38574465 original size:52 final size:52
Alignment explanation
Indices: 38574360--38574466 Score: 135
Period size: 52 Copynumber: 2.1 Consensus size: 52
38574350 AACACACTAA
* * **
38574360 TATCGCAGCAAACCTGCCAGTAATAGTATCGTAGCGAAGCTGCCAGTATCAG
1 TATCGCAGCAAACCTGCCAGTAACAGTATCGTAGCAAAGCCACCAGTATCAG
* * *
38574412 TATCGCAGCAAAGCTGCCAGTAACAGTATATGTGGCAAAGCCACCAGTA-CAG
1 TATCGCAGCAAACCTGCCAGTAACAGTAT-CGTAGCAAAGCCACCAGTATCAG
38574464 TAT
1 TAT
38574467 ATTTCCTCCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 33 0.70
53 14 0.30
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (52 bp):
TATCGCAGCAAACCTGCCAGTAACAGTATCGTAGCAAAGCCACCAGTATCAG
Found at i:38575607 original size:21 final size:21
Alignment explanation
Indices: 38575581--38575636 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
38575571 AACAGCGGTG
*
38575581 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
38575602 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
38575623 GCCGTGAGATTAGA
1 GCGGTGAGATTAGA
38575637 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:38577105 original size:14 final size:15
Alignment explanation
Indices: 38577088--38577122 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
38577078 ACAATAAAAA
38577088 TTTAATACTT-AATT
1 TTTAATACTTAAATT
*
38577102 TTTAACACTTAAATT
1 TTTAATACTTAAATT
38577117 TTTAAT
1 TTTAAT
38577123 TTATGAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAATACTTAAATT
Found at i:38579384 original size:4 final size:4
Alignment explanation
Indices: 38579372--38579406 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
38579362 TAAAATTAGT
38579372 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
38579407 AAGGATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:38579803 original size:31 final size:31
Alignment explanation
Indices: 38579710--38579805 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
38579700 GACAAATTAC
*
38579710 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
38579741 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
38579773 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
38579804 AA
1 AA
38579806 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:38585657 original size:4 final size:4
Alignment explanation
Indices: 38585645--38585683 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
38585635 TAAAATTAGT
38585645 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
38585684 AAGGATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:38586080 original size:31 final size:31
Alignment explanation
Indices: 38585987--38586082 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
38585977 GGCAAATTAC
*
38585987 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
38586018 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
38586050 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
38586081 AA
1 AA
38586083 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:38587583 original size:50 final size:49
Alignment explanation
Indices: 38587478--38587592 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 49
38587468 GCAAACACAC
* * * *
38587478 CATAGCTCATATGAGCTTACTAATTTCAGCTCGTGAGAGCTTACCGATT
1 CATAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
* * *
38587527 CCTAGCTCGTATGAGCTTACCGATTTATAGCTCGTGAGAGCATACCAATT
1 CATAGCTCGTATGAGCTTACCAATTT-CAGCTCGTGAGAGCATACCAATT
38587577 CATAGCTCGTATGAGC
1 CATAGCTCGTATGAGC
38587593 ATACATGTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 22 0.39
50 35 0.61
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (49 bp):
CATAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
Found at i:38587596 original size:25 final size:25
Alignment explanation
Indices: 38587478--38587592 Score: 112
Period size: 25 Copynumber: 4.6 Consensus size: 25
38587468 GCAAACACAC
* *
38587478 CATAGCTCATATGAGCTTACTAATT
1 CATAGCTCGTATGAGCTTACCAATT
*
38587503 --TCAGCTCGTGA-GAGCTTACCGATT
1 CAT-AGCTCGT-ATGAGCTTACCAATT
* *
38587527 CCTAGCTCGTATGAGCTTACCGATT
1 CATAGCTCGTATGAGCTTACCAATT
* *
38587552 TATAGCTCGTGA-GAGCATACCAATT
1 CATAGCTCGT-ATGAGCTTACCAATT
38587577 CATAGCTCGTATGAGC
1 CATAGCTCGTATGAGC
38587593 ATACATGTAT
Statistics
Matches: 75, Mismatches: 8, Indels: 14
0.77 0.08 0.14
Matches are distributed among these distances:
23 1 0.01
24 19 0.25
25 53 0.71
26 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (25 bp):
CATAGCTCGTATGAGCTTACCAATT
Found at i:38589181 original size:21 final size:21
Alignment explanation
Indices: 38589157--38589198 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
38589147 TTAAAAGGAG
38589157 AGAGTGAGTTTTCGAAACTCA
1 AGAGTGAGTTTTCGAAACTCA
38589178 AGAGTGAGTTTTCGAAACTCA
1 AGAGTGAGTTTTCGAAACTCA
38589199 GTGCGTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (21 bp):
AGAGTGAGTTTTCGAAACTCA
Found at i:38589301 original size:33 final size:32
Alignment explanation
Indices: 38589247--38589338 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 32
38589237 TGTAACAGTC
* * *
38589247 TGGGCCTGAGCCCTATTCAGTAAT-AGTATAGTG
1 TGGGCCTTAGCCC-ATACAGTAATCAGTAT-GAG
38589280 TGGGCCTTAGCCCAGTACAGT-ATCA--ATGAG
1 TGGGCCTTAGCCCA-TACAGTAATCAGTATGAG
38589310 TGGGCCTTAGCCCATTACAGTAATCAGTA
1 TGGGCCTTAGCCCA-TACAGTAATCAGTA
38589339 CAATGCAGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
30 22 0.44
31 6 0.12
32 3 0.06
33 19 0.38
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (32 bp):
TGGGCCTTAGCCCATACAGTAATCAGTATGAG
Found at i:38589497 original size:26 final size:26
Alignment explanation
Indices: 38589448--38589517 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
38589438 AACATCGCAG
* * * * *
38589448 CAAAGCTGTCAGTAATAATGACACAT
1 CAAAGCTGCCAGTAACAGTAACACAA
*
38589474 TAAAGCTGCCAGTAACAGTAACACAA
1 CAAAGCTGCCAGTAACAGTAACACAA
38589500 CAAAGCTGCCAGTAACAG
1 CAAAGCTGCCAGTAACAG
38589518 AAAAGAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (26 bp):
CAAAGCTGCCAGTAACAGTAACACAA
Found at i:38592938 original size:87 final size:87
Alignment explanation
Indices: 38592816--38593146 Score: 493
Period size: 87 Copynumber: 3.8 Consensus size: 87
38592806 TCTAGTGCTG
*
38592816 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGGTGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
38592881 CGATCTGCTTTGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* *
38592903 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGGTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
38592968 CGATCTGCTTCACTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* * * * * **
38592990 AGGAAGGGAAGATCTGTTATCTTTAACTAGCTCCACTACAACCAATGGAGGTGAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
38593055 CGATCTGCTTCGTTGTTAACTC
66 CGATCTGCTTCGCTGTTAACGC
* * * *
38593077 AAGAACGCAAGATCTGCT-CCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGACTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
38593141 CGATCT
66 CGATCT
38593147 ACTGATCTGT
Statistics
Matches: 218, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
86 45 0.21
87 173 0.79
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTGCTTCGCTGTTAACGC
Found at i:38618781 original size:22 final size:22
Alignment explanation
Indices: 38618751--38618793 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38618741 TACGTGCAAC
38618751 AAAATAAAACAA-TACAAAAAG
1 AAAATAAAACAAGTACAAAAAG
*
38618772 AAAATCAAAACAAGTAGAAAAA
1 AAAAT-AAAACAAGTACAAAAA
38618794 TACTTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.09
Consensus pattern (22 bp):
AAAATAAAACAAGTACAAAAAG
Found at i:38620641 original size:24 final size:24
Alignment explanation
Indices: 38620609--38620655 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38620599 CTAAATTTAT
*
38620609 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
38620633 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
38620656 ATTTACCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:38622763 original size:49 final size:49
Alignment explanation
Indices: 38622678--38622778 Score: 114
Period size: 49 Copynumber: 2.1 Consensus size: 49
38622668 CTCGTTTTCT
** * * * *
38622678 CGATGCCATAGTTCAACTATGGTCTTACATGTAATCACCTATCA-TATAC
1 CGATGCCATAGCCCAACTATGGTCCTACAAGGAATCACATATCACT-TAC
* *
38622727 CGATGCCATAGCCCAGCTATGGTCCTATAAGGAATCACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCCTACAAGGAATCACATATCACTTAC
38622776 CGA
1 CGA
38622779 AAGTACTCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 42 0.98
50 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (49 bp):
CGATGCCATAGCCCAACTATGGTCCTACAAGGAATCACATATCACTTAC
Found at i:38623703 original size:27 final size:28
Alignment explanation
Indices: 38623663--38623715 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
38623653 CAATGATTCC
*
38623663 GGGAATCAACACTTAGTAA-CCCCTTGG
1 GGGAATCAACACTTAGCAATCCCCTTGG
**
38623690 GGGAATCAGTACTTAGCAATCCCCTT
1 GGGAATCAACACTTAGCAATCCCCTT
38623716 TATATTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (28 bp):
GGGAATCAACACTTAGCAATCCCCTTGG
Found at i:38623816 original size:51 final size:51
Alignment explanation
Indices: 38623730--38624032 Score: 339
Period size: 51 Copynumber: 6.0 Consensus size: 51
38623720 TTCAAAGATA
* * *
38623730 CTGGTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTAT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
* * * *
38623781 CTGATACACGTAGTAGCCTGCACATAGTAGTACACACGTGATCGA--AGCTAT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CTAT
* * * *
38623832 TTGGTACGCATAGTAGCCTGCACATAGTACTACACATGTGACCATCATTAT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
* * * *
38623883 CCGATACACGTAGTAGCCTGCACATAGTACTACGCATGTGATCGA--AGCTAT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CTAT
* * * *
38623934 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTAT
*
38623984 CTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACT
38624033 TTCACTTTTA
Statistics
Matches: 208, Mismatches: 34, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
49 4 0.02
50 45 0.22
51 153 0.74
52 5 0.02
53 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (51 bp):
CTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
Found at i:38623924 original size:102 final size:101
Alignment explanation
Indices: 38623738--38624024 Score: 459
Period size: 102 Copynumber: 2.8 Consensus size: 101
38623728 TACTGGTTCA
*
38623738 CATAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCA-TATCTGATACACGTAGTAGCCTGCA
* **
38623803 CATAGTAGTACACACGTGATCGAAGCTATTTGGTACG
65 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
*
38623840 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCATTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCA-TATCTGATACACGTAGTAGCCTGCA
* *
38623905 CATAGTACTACGCATGTGATCGAAGCTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* *
38623942 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCAT-TCTGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACC-ATCATATCTGATACACGTAGTAGCCTGCA
38624006 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
38624025 CCATCACTTT
Statistics
Matches: 171, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 38 0.22
102 129 0.75
103 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATCATATCTGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:38624298 original size:31 final size:29
Alignment explanation
Indices: 38624258--38624316 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
38624248 AAAATCACAC
38624258 TTTGAAAAATT-TACATTTTTGCCCCTAGAG
1 TTTGAAAAATTAT-CA-TTTTGCCCCTAGAG
*
38624288 TTTGACAAAATTATGATTTTGCCCCTAGA
1 TTTGA-AAAATTATCATTTTGCCCCTAGA
38624317 CTCGTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 18 0.69
31 7 0.27
32 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (29 bp):
TTTGAAAAATTATCATTTTGCCCCTAGAG
Found at i:38630186 original size:61 final size:61
Alignment explanation
Indices: 38630090--38630318 Score: 278
Period size: 61 Copynumber: 3.8 Consensus size: 61
38630080 TTGACAGAAA
* * * *
38630090 TCACCACAAAGGCTTACCTTTCAAGAGTTTTGCCACAAAGGCTATCCTTTACATCCAGTAC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
* * * * * *
38630151 TCTCTACAATGGCTTTCCTGTCCAGAGTTTAGCCACAAAGGTTGTCCTTTACATCTAGTAC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
* * * * * * *
38630212 TCACCACAAAGGCTTTTCTGTCCAGAGTGTTGCCACAAATGTTGTACTTTATATCTAGTAC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
* * *
38630273 TCGCCACAAAGGCTTTCCTATCAAAAGTTTTGCCACAAAGGTTATC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATC
38630319 TTTCTCCTGG
Statistics
Matches: 140, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 140 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (61 bp):
TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
Found at i:38630572 original size:18 final size:19
Alignment explanation
Indices: 38630537--38630572 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38630527 TGGGACATTG
*
38630537 ATTTTGGATTTTACTTTGT
1 ATTTTGGATTTGACTTTGT
38630556 ATTTTGG-TTTGACTTTG
1 ATTTTGGATTTGACTTTG
38630573 CATGATTGGG
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:0.14, C:0.06, G:0.19, T:0.61
Consensus pattern (19 bp):
ATTTTGGATTTGACTTTGT
Found at i:38631460 original size:20 final size:20
Alignment explanation
Indices: 38631389--38631461 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
38631379 CCAATTTGGG
* * *
38631389 GACAAGCCACCAGTATTGCA
1 GACAAGCTACCAGTAATGTA
* * * *
38631409 GATAAACTGCCAGTAATGTG
1 GACAAGCTACCAGTAATGTA
38631429 GACAAG-TCACCAGTAATGTA
1 GACAAGCT-ACCAGTAATGTA
38631449 GACAAGCTACCAG
1 GACAAGCTACCAG
38631462 ATTTGTGGAC
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
GACAAGCTACCAGTAATGTA
Found at i:38635827 original size:22 final size:22
Alignment explanation
Indices: 38635793--38635835 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38635783 TACACCAAAA
* *
38635793 TAGGCTTTTAGCGGCATTTTTT
1 TAGGCCTTCAGCGGCATTTTTT
*
38635815 TAGGCCTTCAGCGGCGTTTTT
1 TAGGCCTTCAGCGGCATTTTT
38635836 AAGCGCCACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (22 bp):
TAGGCCTTCAGCGGCATTTTTT
Found at i:38635970 original size:43 final size:43
Alignment explanation
Indices: 38635921--38636163 Score: 312
Period size: 43 Copynumber: 5.7 Consensus size: 43
38635911 AAAAATGCCA
* *
38635921 CTAAAGATCATGGCCTTTAGCGACGCTTTTATCACAAACGTCG
1 CTAAAGATCATGACCTTTAGCGACGCTTTTATCACAAACGCCG
* *
38635964 CTAAAGATCATGACCTTTAGCGACGCTTTTACCACAAACGCCA
1 CTAAAGATCATGACCTTTAGCGACGCTTTTATCACAAACGCCG
*
38636007 CTAAAGATCATGACCTTTAGC-AGCTCTTTTATCACAAACGCCG
1 CTAAAGATCATGACCTTTAGCGA-CGCTTTTATCACAAACGCCG
* * * * * *
38636050 CTAAAGGTCATGATCTTCAGCAACGCTTTTGTCACAAATGCCG
1 CTAAAGATCATGACCTTTAGCGACGCTTTTATCACAAACGCCG
*
38636093 CTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCG
1 CTAAAGATCATGACCTTTAGCGACGC-TTTTATCACAAACGCCG
* *
38636137 CTATAA-AACA-AACCTTTAGCGACGCTT
1 CTA-AAGATCATGACCTTTAGCGACGCTT
38636164 CTCACAAAAA
Statistics
Matches: 175, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
42 3 0.02
43 147 0.84
44 23 0.13
45 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
CTAAAGATCATGACCTTTAGCGACGCTTTTATCACAAACGCCG
Found at i:38636162 original size:86 final size:87
Alignment explanation
Indices: 38635913--38636188 Score: 321
Period size: 86 Copynumber: 3.2 Consensus size: 87
38635903 TTATGTGAAA
* * *
38635913 AAATGCCACTAAAGATCATGGCCTTTAGCGACGC-TTTTATCACAAACGTCGCTAAAGATCATGA
1 AAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCGCTAAAGATCATGA
*
38635977 CCTTTAGCGACGCTTTTACCAC
66 CCTTTAGCGACGCTTTTAACAC
* * *
38635999 AAACGCCACTAAAGATCATGACCTTTAGC-A-GCTCTTTTATCACAAACGCCGCTAAAGGTCATG
1 AAATGCCACTAAAGAACATGACCTTTAGCGACGCT-TTTTATCACAAACGCCGCTAAAGATCATG
* * * **
38636062 ATCTTCAGCAACGCTTTTGTCAC
65 ACCTTTAGCGACGCTTTTAACAC
* * *
38636085 AAATGCCGCTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCGCTATAA-AACA-A
1 AAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCGCTA-AAGATCATG
* * *
38636148 ACCTTTAGCGACGCTTCTCACAA
65 ACCTTTAGCGACGCTTTTAACAC
*
38636171 AAATGCCGCTAAA-AACAT
1 AAATGCCACTAAAGAACAT
38636189 AACATTTAAA
Statistics
Matches: 163, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
84 2 0.01
85 6 0.04
86 127 0.78
87 23 0.14
88 5 0.03
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (87 bp):
AAATGCCACTAAAGAACATGACCTTTAGCGACGCTTTTTATCACAAACGCCGCTAAAGATCATGA
CCTTTAGCGACGCTTTTAACAC
Found at i:38636179 original size:129 final size:129
Alignment explanation
Indices: 38635911--38636183 Score: 320
Period size: 129 Copynumber: 2.1 Consensus size: 129
38635901 GTTTATGTGA
* * * * * *
38635911 AAAAATGCCACTAAAGATCATGGCCTTTAGCGACGCTTTTATCACAAACGTCGCTAAAGATCATG
1 AAAAATGCCGCTAAAGATCATGACCTTCAGCAACGCTTTTATCACAAACGCCGCTAAAGAACATG
* * * *
38635976 ACCTTTAGCGACGCTTTTACCACAAACGCCACTAAAGATCATGACCTTTAGCAGCTCTTTTATC
66 ACCTTTAGCGACGCTTTTACCACAAACGCCACTAAAGAACATAACCTTTAGCAGCTCTCTCATC
* * * * * *
38636040 ACAAACGCCGCTAAAGGTCATGATCTTCAGCAACGCTTTTGTCACAAATGCCGCTAAAGAACATG
1 AAAAATGCCGCTAAAGATCATGACCTTCAGCAACGCTTTTATCACAAACGCCGCTAAAGAACATG
* *
38636105 ACCTTTAGCGACGCTTTTTATCACAAACGCCGCTATAA-AACA-AACCTTTAGCGACGCT-TCTC
66 ACCTTTAGCGACGC-TTTTACCACAAACGCCACTA-AAGAACATAACCTTTAGC-A-GCTCTCTC
38636167 A-C
127 ATC
38636169 AAAAATGCCGCTAAA
1 AAAAATGCCGCTAAA
38636184 AACATAACAT
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
129 90 0.75
130 25 0.21
131 5 0.04
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (129 bp):
AAAAATGCCGCTAAAGATCATGACCTTCAGCAACGCTTTTATCACAAACGCCGCTAAAGAACATG
ACCTTTAGCGACGCTTTTACCACAAACGCCACTAAAGAACATAACCTTTAGCAGCTCTCTCATC
Found at i:38637372 original size:16 final size:16
Alignment explanation
Indices: 38637351--38637381 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
38637341 AGTCCCAAAC
38637351 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
38637367 TATTGTAAACATCAG
1 TATTGTAAACATCAG
38637382 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:38640555 original size:41 final size:42
Alignment explanation
Indices: 38640526--38640811 Score: 279
Period size: 41 Copynumber: 7.0 Consensus size: 42
38640516 GCCACTATCG
38640526 CCCTGAACATTAGCGGCGCTTTTTC-AAAAACGCCGCTAAAGA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAA-A
* * *
38640568 CCC--AATCATTAGTGACGCTTTCT-AAAAAACGCCGCTAAAA
1 CCCTGAA-CATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
* * * * *
38640608 CCATGAGCATTAGCGGCGC-TTCTCCAAAAACACCGCTAAAGA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAA-A
* * **
38640650 CCC-GATCATTAGCGGCGCTTTTT-AAAAAACACCATTAAAA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
* * *
38640690 CCCT-AAGCATTAGCGGCGCCTATTC-AAAAACGCCGCTAAAT
1 CCCTGAA-CATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
* *
38640731 CCCTGAGCATTAGCGGCGC-TTTACAAAAAACGCCGCTAAAA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
* * *
38640772 CCCTGAGCATTAGCGGTGCTTTTT-AAAAAACGCCACTAAA
1 CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAA
38640812 GCCCCAAAAA
Statistics
Matches: 202, Mismatches: 29, Indels: 27
0.78 0.11 0.10
Matches are distributed among these distances:
40 17 0.08
41 171 0.85
42 14 0.07
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (42 bp):
CCCTGAACATTAGCGGCGCTTTTTCAAAAAACGCCGCTAAAA
Found at i:38640621 original size:82 final size:82
Alignment explanation
Indices: 38640526--38640818 Score: 356
Period size: 82 Copynumber: 3.6 Consensus size: 82
38640516 GCCACTATCG
* * *
38640526 CCCTGAACATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCAATCATTAGTGACGCTTTCT
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCAATCATTAGCGGCGCTTTCT
38640591 AAAAAACGCCGCTAAAA
66 AAAAAACGCCGCTAAAA
* * * * * *
38640608 CCATGAGCATTAGCGGCGCTTCTCCAAAAACACCGCTAAAGACCCGATCATTAGCGGCGCTTTTT
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCAATCATTAGCGGCGCTTTCT
* **
38640673 AAAAAACACCATTAAAA
66 AAAAAACGCCGCTAAAA
* * * * * *
38640690 CCCTAAGCATTAGCGGCGCCTATTCAAAAACGCCGCTAAA-TCCCTGAGCATTAGCGGCGCTTTA
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCC-AATCATTAGCGGCGCTTT-
38640754 C-AAAAAACGCCGCTAAAA
64 CTAAAAAACGCCGCTAAAA
* * * *
38640772 CCCTGAGCATTAGCGGTGCTTTTTAAAAAACGCCACTAAAGCCCCAA
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCAA
38640819 AAACTAAAAA
Statistics
Matches: 176, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
81 3 0.02
82 170 0.97
83 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (82 bp):
CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCAATCATTAGCGGCGCTTTCT
AAAAAACGCCGCTAAAA
Found at i:38640701 original size:123 final size:123
Alignment explanation
Indices: 38640526--38640818 Score: 371
Period size: 123 Copynumber: 2.4 Consensus size: 123
38640516 GCCACTATCG
* * * * *
38640526 CCCTGAACATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCAATCATTAGTGACG-CT-TT
1 CCCTGAGCATTAGCGGCGCTTTTTAAAAAACGCCACTAAAGACCCAAGCATTAGCGACGCCTATT
*
38640589 CTAAAAAACGCCGCTAAAACCATGAGCATTAGCGGCGCTTCT-CCAAAAACACCGCTAAAGA
66 C--AAAAACGCCGCTAAAACCATGAGCATTAGCGGCGCTT-TACAAAAAACACCGCTAAA-A
* * * *
38640650 CCC-GATCATTAGCGGCGCTTTTTAAAAAACACCATTAAA-ACCCTAAGCATTAGCGGCGCCTAT
1 CCCTGAGCATTAGCGGCGCTTTTTAAAAAACGCCACTAAAGACCC-AAGCATTAGCGACGCCTAT
* * *
38640713 TCAAAAACGCCGCTAAATCCCTGAGCATTAGCGGCGCTTTACAAAAAACGCCGCTAAAA
65 TCAAAAACGCCGCTAAAACCATGAGCATTAGCGGCGCTTTACAAAAAACACCGCTAAAA
* *
38640772 CCCTGAGCATTAGCGGTGCTTTTTAAAAAACGCCACTAAAGCCCCAA
1 CCCTGAGCATTAGCGGCGCTTTTTAAAAAACGCCACTAAAGACCCAA
38640819 AAACTAAAAA
Statistics
Matches: 146, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
122 9 0.06
123 126 0.86
124 8 0.05
125 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (123 bp):
CCCTGAGCATTAGCGGCGCTTTTTAAAAAACGCCACTAAAGACCCAAGCATTAGCGACGCCTATT
CAAAAACGCCGCTAAAACCATGAGCATTAGCGGCGCTTTACAAAAAACACCGCTAAAA
Found at i:38640860 original size:13 final size:13
Alignment explanation
Indices: 38640842--38640867 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38640832 GACGTCGTTG
38640842 GCGGCATTTTTTA
1 GCGGCATTTTTTA
38640855 GCGGCATTTTTTA
1 GCGGCATTTTTTA
38640868 AAAGCGCCAC
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:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
GCGGCATTTTTTA
Found at i:38643896 original size:28 final size:28
Alignment explanation
Indices: 38643823--38643938 Score: 124
Period size: 30 Copynumber: 3.9 Consensus size: 28
38643813 ATACAATATG
* *
38643823 TAGTAACAGTCTGGGCCTGAGCCCTATTCA
1 TAGTAACAGTGTGGGCCTTAGCCC-ATT-A
*
38643853 GTAGTAGTATAGTGTGGGCCTTAGCCCATTA
1 -TAGTA--ACAGTGTGGGCCTTAGCCCATTA
*
38643884 TAGTAACAGTGTGTGGGCCTTAGCCCAATA
1 TAGTAACA--GTGTGGGCCTTAGCCCATTA
*
38643914 CAGTAACAGTGTGGGCCTTAGCCCA
1 TAGTAACAGTGTGGGCCTTAGCCCA
38643939 ATGCAGCAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
28 19 0.25
30 31 0.41
31 6 0.08
32 3 0.04
33 16 0.21
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (28 bp):
TAGTAACAGTGTGGGCCTTAGCCCATTA
Found at i:38644104 original size:26 final size:25
Alignment explanation
Indices: 38644038--38644111 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 25
38644028 AACACACCAA
*
38644038 TATCGCAGCAAAGTTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGT-ATAG
* * * *
38644064 GATCACAGTAGAGCTGCCAGTATCAG
1 TATCGCAGCAAAGCTGCCAGTAT-AG
*
38644090 TATCGCAGCAAAGCTACCAGTA
1 TATCGCAGCAAAGCTGCCAGTA
38644112 ACAGCATATG
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 2 0.05
26 35 0.95
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (25 bp):
TATCGCAGCAAAGCTGCCAGTATAG
Found at i:38644371 original size:27 final size:27
Alignment explanation
Indices: 38644341--38644736 Score: 426
Period size: 27 Copynumber: 14.7 Consensus size: 27
38644331 TTATCTCCTA
** *
38644341 GGGGTATAACAGTCATTTTACCCTAAG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
38644368 GGGGTATTTCGGTCATTTTATCTTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
38644395 GAGGTATTTCAGTCATTCTACCCTGTG
1 GGGGTATTTCAGTCATTTTACCCTATG
38644422 GGGGTATTT-AGGTCATTTTACCCTATG
1 GGGGTATTTCA-GTCATTTTACCCTATG
* * *
38644449 AGGGTATTTTAGTCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
38644476 AGGGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* *
38644503 GGGGTATTTCGGTCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
38644530 GGGGTATTTCGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
38644557 GGGGTATTTC-GATCATTTTAGCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
38644584 GGGGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* *
38644611 GGGATATTTC-GATCATTTTACCCTATA
1 GGGGTATTTCAG-TCATTTTACCCTATG
* *
38644638 GGGGTATTTAAGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
*
38644665 AGGGTATTTCAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
** * *
38644692 GGATTAATTT-GGTCATTTTACCCTGTG
1 GGGGT-ATTTCAGTCATTTTACCCTATG
* * *
38644719 GGGCTAATTCGGTCATTT
1 GGGGTATTTCAGTCATTT
38644737 ATTGACCTCT
Statistics
Matches: 320, Mismatches: 41, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
26 6 0.02
27 307 0.96
28 7 0.02
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:38647105 original size:34 final size:35
Alignment explanation
Indices: 38647037--38647109 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
38647027 TAGCCTTCGG
* * * * *
38647037 TTCTTTCTTCTTTTCTTTGTGGTCGAATATTGCCT
1 TTCTTTATTCTTCTCATTGTGGCCGAATACTGCCT
38647072 TTCTTTATTCTTCTCATT-TGGCCGAATACTGCCT
1 TTCTTTATTCTTCTCATTGTGGCCGAATACTGCCT
38647106 TTCT
1 TTCT
38647110 CTCCCTTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.11, C:0.23, G:0.12, T:0.53
Consensus pattern (35 bp):
TTCTTTATTCTTCTCATTGTGGCCGAATACTGCCT
Found at i:38647938 original size:27 final size:27
Alignment explanation
Indices: 38647739--38647936 Score: 256
Period size: 27 Copynumber: 7.3 Consensus size: 27
38647729 GTAATGGGCA
38647739 TAAAATGACCGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
**
38647766 TAAAATGACTAAAATACCC-CTGAAGGG
1 TAAAATGACCGAAATACCCTC-GAAGGG
**
38647793 TAAAATGAGGGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
38647820 TAAAATGACCGAAATACCC-CTGAAGGG
1 TAAAATGACCGAAATACCCTC-GAAGGG
* *
38647847 TAAAATTACCGAAATACCCTCGAAGAG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
38647874 TAAACTGACCAAAATACCCTCGAAAGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
38647901 TAAAATGACTGAAATACCCTTGATGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
38647928 TAAAATGAC
1 TAAAATGAC
38647937 TGTTATACCC
Statistics
Matches: 147, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.01
27 143 0.97
28 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAGGG
Found at i:38648338 original size:28 final size:28
Alignment explanation
Indices: 38648298--38648372 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
38648288 ATTGTACTTT
38648298 TACTATATTGGGCTAAGGCCCACACTGC
1 TACTATATTGGGCTAAGGCCCACACTGC
* * *
38648326 TACTGTATTGGGCTAATGCCCACACTGT
1 TACTATATTGGGCTAAGGCCCACACTGC
* * *
38648354 TGCTATATAGGGCTCAGGC
1 TACTATATTGGGCTAAGGC
38648373 TTAGACTGCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (28 bp):
TACTATATTGGGCTAAGGCCCACACTGC
Found at i:38654629 original size:34 final size:35
Alignment explanation
Indices: 38654570--38654652 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
38654560 TAGCCTTTGG
* * *
38654570 TTCTTTCCTCTTTTCTTTGTGGCCGAATATTGCCT
1 TTCTTTCCTCTTCTCTCTGTGGCCGAATACTGCCT
*
38654605 TTCTTTCTTCTTCTCTCT-TGGCCGAATACTGCCT
1 TTCTTTCCTCTTCTCTCTGTGGCCGAATACTGCCT
*
38654639 TTCTCTCCCTCTTC
1 TTCT-TTCCTCTTC
38654653 ATCTATTCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 19 0.46
35 22 0.54
ACGTcount: A:0.07, C:0.33, G:0.11, T:0.49
Consensus pattern (35 bp):
TTCTTTCCTCTTCTCTCTGTGGCCGAATACTGCCT
Found at i:38655541 original size:27 final size:27
Alignment explanation
Indices: 38655280--38655533 Score: 280
Period size: 27 Copynumber: 9.4 Consensus size: 27
38655270 GTAATGGGCC
** *
38655280 TAAAATGACCAAAATACCCTTGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
38655307 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
** *
38655334 TAAAATGACTTCAATACCCCCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
** *
38655361 TAAAATGACCAAAATACCCTCAAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
38655388 TAAAATGACTAAAATGCCCTAGAAAGGG
1 TAAAATGACTGAAATACCCTCG-AAGGG
* * *
38655416 TAAAAT-AATCGAAATACCCCCGAAGGA
1 TAAAATGACT-GAAATACCCTCGAAGGG
*
38655443 TAAAATTACTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* *
38655470 TAAACTGACCG-AATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* *
38655496 TAAAATTA-TCAAAATACCCTCGAAGGG
1 TAAAATGACT-GAAATACCCTCGAAGGG
38655523 TAAAATGACTG
1 TAAAATGACTG
38655534 TTATACCCCT
Statistics
Matches: 188, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
26 21 0.11
27 145 0.77
28 22 0.12
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.19
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCGAAGGG
Found at i:38655749 original size:26 final size:26
Alignment explanation
Indices: 38655720--38655782 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
38655710 GATACTGGCT
*
38655720 GCTTTGCTGCGTTACTGTTACTAGTA
1 GCTTTGCTGCGTTACTATTACTAGTA
** * * *
38655746 GCTTAACTGCATTACTATTATTGGTA
1 GCTTTGCTGCGTTACTATTACTAGTA
*
38655772 ACTTTGCTGCG
1 GCTTTGCTGCG
38655783 ATATTGGTGT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (26 bp):
GCTTTGCTGCGTTACTATTACTAGTA
Found at i:38666232 original size:21 final size:21
Alignment explanation
Indices: 38666208--38666249 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38666198 AGTCGTTTTC
*
38666208 AATTAATTAACTAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
38666229 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
38666250 TACAACCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:38672326 original size:21 final size:23
Alignment explanation
Indices: 38672302--38672361 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
38672292 TTATAATGGT
38672302 TATTGTATTAT-TATTCA-AATG
1 TATTGTATTATGTATTCATAATG
*
38672323 TATTTTATTATGTATTCATAATG
1 TATTGTATTATGTATTCATAATG
38672346 TAATTG-ATTGATGTAT
1 T-ATTGTATT-ATGTAT
38672362 ATCCAAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 10 0.30
22 6 0.18
23 8 0.24
24 9 0.27
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (23 bp):
TATTGTATTATGTATTCATAATG
Found at i:38672361 original size:24 final size:22
Alignment explanation
Indices: 38672303--38672361 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
38672293 TATAATGGTT
38672303 ATTGTATTAT-TATTCAAATGTA
1 ATTG-ATTATGTATTCAAATGTA
* *
38672325 TTTTATTATGTATTCATAATGTA
1 ATTGATTATGTATTCA-AATGTA
38672348 ATTGATTGATGTAT
1 ATTGATT-ATGTAT
38672362 ATCCAAATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 8 0.27
23 11 0.37
24 6 0.20
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (22 bp):
ATTGATTATGTATTCAAATGTA
Found at i:38675904 original size:24 final size:24
Alignment explanation
Indices: 38675880--38675926 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
38675870 AAACTACTTC
38675880 TAAAGAAAACTCAAGAGAGAATTCT
1 TAAAGAAAACTCAA-AGAGAATTCT
**
38675905 TGGAGAAAACTCAAAGAGAATT
1 TAAAGAAAACTCAAAGAGAATT
38675927 TTTCACTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (24 bp):
TAAAGAAAACTCAAAGAGAATTCT
Found at i:38685713 original size:33 final size:33
Alignment explanation
Indices: 38685641--38685717 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
38685631 GTGTATATAT
* * * *
38685641 GTAAGACCATAGTTGGGCTTATGGCATTCTGAT
1 GTAAGACCATAGCTGGGCTTATGGCACTATGAC
38685674 GATAAGACCATAGCTGGG-TTATGGCACTATGGAC
1 G-TAAGACCATAGCTGGGCTTATGGCACTAT-GAC
38685708 GTAAGACCAT
1 GTAAGACCAT
38685718 GGTTGGACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 20 0.53
34 18 0.47
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (33 bp):
GTAAGACCATAGCTGGGCTTATGGCACTATGAC
Found at i:38685817 original size:101 final size:102
Alignment explanation
Indices: 38685607--38685866 Score: 323
Period size: 101 Copynumber: 2.6 Consensus size: 102
38685597 TATTCAAACG
* * *
38685607 TAAGACCATGGTTGGACCATGGTAGTGTATATATGTAAGACCATAGTTGGGCTTATGGCATTCTG
1 TAAGACCATGGTTGGACCATGGCAATGTATATATATAAGACCATAGTTGGGCTTATGGCATTCTG
* * *
38685672 ATGATAAGACCATAGCTGGGTTATGGCACTATGGACG
66 ATGATAAGACCATAACTGGGTTATGGCACTATGAACA
* * *
38685709 TAAGACCATGGTTGGACCATGGCAATGTTTATATATAAGATCATAGTTGGG-TTGTGGCATTCTG
1 TAAGACCATGGTTGGACCATGGCAATGTATATATATAAGACCATAGTTGGGCTTATGGCATTCTG
* *
38685773 ATGATAAGACTATAATTGGGTTATGGCACTATGAACA
66 ATGATAAGACCATAACTGGGTTATGGCACTATGAACA
** * * * *
38685810 TAAGACCATGGCAAGG-CCATGGCAAT-T-CATATGTAAGACTATAGTTGGAC-TATGGCA
1 TAAGACCATGG-TTGGACCATGGCAATGTATATATATAAGACCATAGTTGGGCTTATGGCA
38685867 CAATAAGAAA
Statistics
Matches: 137, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
99 23 0.17
100 1 0.01
101 65 0.47
102 48 0.35
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (102 bp):
TAAGACCATGGTTGGACCATGGCAATGTATATATATAAGACCATAGTTGGGCTTATGGCATTCTG
ATGATAAGACCATAACTGGGTTATGGCACTATGAACA
Found at i:38687613 original size:13 final size:13
Alignment explanation
Indices: 38687595--38687624 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38687585 GTTGTATGAA
*
38687595 ATCAAGAGATTGG
1 ATCAAGAAATTGG
38687608 ATCAAGAAATTGG
1 ATCAAGAAATTGG
38687621 ATCA
1 ATCA
38687625 GCTCAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (13 bp):
ATCAAGAAATTGG
Found at i:38690472 original size:17 final size:18
Alignment explanation
Indices: 38690430--38690472 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
38690420 CTTTATTTTC
38690430 TTATTTATTATTCTAGTTT
1 TTATTTATTATTCTAG-TT
38690449 TTGATTTATTATTCTA-TT
1 TT-ATTTATTATTCTAGTT
38690467 TTATTT
1 TTATTT
38690473 TATTTATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 2 0.09
20 13 0.57
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (18 bp):
TTATTTATTATTCTAGTT
Found at i:38690494 original size:27 final size:26
Alignment explanation
Indices: 38690421--38690496 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 26
38690411 ATATATCTTC
*
38690421 TTTATTT-TCTTATT-TATTATTCTAG
1 TTTATTTATCTTATTAT-TTATTTTAG
* *
38690446 TTT-TTGAT-TTATTATTCTATTTTAT
1 TTTATTTATCTTATTATT-TATTTTAG
38690471 TTTATTTATCTTAGTTATTTATTTTA
1 TTTATTTATCTTA-TTATTTATTTTA
38690497 ATTGTTTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 8 0.20
25 14 0.34
26 4 0.10
27 10 0.24
28 5 0.12
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTATTTATCTTATTATTTATTTTAG
Found at i:38698849 original size:43 final size:41
Alignment explanation
Indices: 38698765--38698905 Score: 142
Period size: 43 Copynumber: 3.4 Consensus size: 41
38698755 CTCGAGGGAC
* ** *
38698765 CTAAGTGTTGATTCCCCGAATTATTGATTCTAAAGGTGGTTG
1 CTAAGTGTTGATTCCCCGTATCCTTGATTATAAAGG-GGTTG
*
38698807 CTAAGTGTTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTG
1 CTAAGTGTTGATTCC-CCGTATCCTTGATTAT-AAAGGGGTTG
* * *
38698850 CTATGTGTTGATTCCCCGTATCAC-TGAATAT-AAGTTGGTTG
1 CTAAGTGTTGATTCCCCGTATC-CTTGATTATAAAG-GGGTTG
*
38698891 CTAAGTGTTGGTTCC
1 CTAAGTGTTGATTCC
38698906 ACCGAGTAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
40 3 0.04
41 18 0.21
42 27 0.32
43 32 0.38
44 5 0.06
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (41 bp):
CTAAGTGTTGATTCCCCGTATCCTTGATTATAAAGGGGTTG
Found at i:38706304 original size:17 final size:18
Alignment explanation
Indices: 38706282--38706315 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38706272 ATATTAGGGG
*
38706282 AAAAAGTGT-AATTTTGC
1 AAAAAGTATGAATTTTGC
38706299 AAAAAGTATGAATTTTG
1 AAAAAGTATGAATTTTG
38706316 GACCAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (18 bp):
AAAAAGTATGAATTTTGC
Found at i:38710862 original size:9 final size:9
Alignment explanation
Indices: 38710848--38710873 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
38710838 CCGTACACCT
38710848 GCAACAAAC
1 GCAACAAAC
38710857 GCAACAAAC
1 GCAACAAAC
38710866 GCAACAAA
1 GCAACAAA
38710874 GGCAGCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.31, G:0.12, T:0.00
Consensus pattern (9 bp):
GCAACAAAC
Found at i:38711891 original size:3 final size:3
Alignment explanation
Indices: 38711883--38711941 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
38711873 TATAATCATA
* * *
38711883 TAT TAT TAT TTT TAT TTT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38711931 TAT TAT TAT TA
1 TAT TAT TAT TA
38711942 CTTTTTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:38712917 original size:27 final size:25
Alignment explanation
Indices: 38712887--38712936 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
38712877 GGGTACATTA
38712887 TCATATTCAAATTTTCTTTTTAAAAGG
1 TCATATTCAAA-TTT-TTTTTAAAAGG
**
38712914 TCATATTTTAATTTTTTTTAAAA
1 TCATATTCAAATTTTTTTTAAAA
38712937 TTTCGACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 3 0.14
27 9 0.43
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (25 bp):
TCATATTCAAATTTTTTTTAAAAGG
Found at i:38718846 original size:29 final size:29
Alignment explanation
Indices: 38718804--38718881 Score: 112
Period size: 24 Copynumber: 2.9 Consensus size: 29
38718794 GGGGGACTGG
38718804 CATCTAGAAAGTATTATGTATGGATCCGC
1 CATCTAGAAAGTATTATGTATGGATCCGC
*
38718833 CATCTAGAAAG---TAT-TAT-CATCCGC
1 CATCTAGAAAGTATTATGTATGGATCCGC
38718857 CATCTAGAAAGTATTATGTATGGAT
1 CATCTAGAAAGTATTATGTATGGAT
38718882 GTAACATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
24 17 0.40
25 3 0.07
26 3 0.07
27 3 0.07
28 3 0.07
29 13 0.31
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (29 bp):
CATCTAGAAAGTATTATGTATGGATCCGC
Found at i:38725724 original size:16 final size:16
Alignment explanation
Indices: 38725703--38725755 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
38725693 GAATAAAGGG
38725703 GTAATGGATTAGAGGC
1 GTAATGGATTAGAGGC
*
38725719 GTAATGGATCAGA-GC
1 GTAATGGATTAGAGGC
*
38725734 TGTAATGGAATAGAGGC
1 -GTAATGGATTAGAGGC
38725751 GTAAT
1 GTAAT
38725756 AGTAAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 28 0.88
17 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.34, T:0.25
Consensus pattern (16 bp):
GTAATGGATTAGAGGC
Found at i:38726006 original size:16 final size:16
Alignment explanation
Indices: 38725969--38726010 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38725959 TTAATCATAT
*
38725969 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
38725985 TT-AAATATATTATAA
1 TTAAAATATATTATAA
38726000 TTAAAATATAT
1 TTAAAATATAT
38726011 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:38726017 original size:14 final size:15
Alignment explanation
Indices: 38725978--38726019 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38725968 TTTAAACATA
*
38725978 ATTATTATTAAATAT
1 ATTATAATTAAATAT
38725993 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
38726007 A-TATAATTTAATA
1 ATTATAATTAAATA
38726020 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:38726337 original size:23 final size:21
Alignment explanation
Indices: 38726293--38726333 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
38726283 TATATGAATT
38726293 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATATAA
38726314 TACTAAAATCATAATATATA
1 TACTAAAATCATAATATATA
38726334 TAATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TACTAAAATCATAATATATAA
Found at i:38734350 original size:11 final size:11
Alignment explanation
Indices: 38734334--38734376 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
38734324 ACGAGATTGT
38734334 AAAAAAAATTC
1 AAAAAAAATTC
38734345 AAAAAAAATTC
1 AAAAAAAATTC
*
38734356 GAAAAAAATTC
1 AAAAAAAATTC
*
38734367 GAAAAAAATT
1 AAAAAAAATT
38734377 ATTATTTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:38734363 original size:22 final size:22
Alignment explanation
Indices: 38734335--38734376 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
38734325 CGAGATTGTA
38734335 AAAAAAATTCAAAAAAAATTCG
1 AAAAAAATTCAAAAAAAATTCG
*
38734357 AAAAAAATTCGAAAAAAATT
1 AAAAAAATTCAAAAAAAATT
38734377 ATTATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.07, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAAAATTCAAAAAAAATTCG
Found at i:38735278 original size:21 final size:21
Alignment explanation
Indices: 38735254--38735296 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
38735244 GAGGGAAGAA
* *
38735254 AAAAAGAAATGAGAGAAAAAG
1 AAAAAGAAATAAAAGAAAAAG
38735275 AAAAAGAAATAAAAGAAAAAG
1 AAAAAGAAATAAAAGAAAAAG
38735296 A
1 A
38735297 TATCAAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (21 bp):
AAAAAGAAATAAAAGAAAAAG
Found at i:38735288 original size:15 final size:14
Alignment explanation
Indices: 38735249--38735296 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
38735239 AAATTGAGGG
38735249 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
38735263 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
38735278 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
38735293 AAGA
1 AAGA
38735297 TATCAAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:38735347 original size:41 final size:41
Alignment explanation
Indices: 38735301--38735403 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
38735291 AAAAGATATC
*
38735301 AAAAGGATAACAAAT-AAAGAGATTGAAAATGATGTTATCCA
1 AAAAGGATAACAAATGAAA-AGATTGAAAAGGATGTTATCCA
* * *
38735342 GAAAGGATATCAAATGAAAAGGTTGAAAAGGATGTTATCCA
1 AAAAGGATAACAAATGAAAAGATTGAAAAGGATGTTATCCA
* *
38735383 AAAATGACAACAAATGAAAAG
1 AAAAGGATAACAAATGAAAAG
38735404 GAAACCATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 50 0.94
42 3 0.06
ACGTcount: A:0.53, C:0.08, G:0.19, T:0.19
Consensus pattern (41 bp):
AAAAGGATAACAAATGAAAAGATTGAAAAGGATGTTATCCA
Found at i:38746213 original size:16 final size:16
Alignment explanation
Indices: 38746194--38746227 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
38746184 TACTAAAATA
38746194 TTTAGAAACATTTACT
1 TTTAGAAACATTTACT
*
38746210 TTTAGGAACATTTACT
1 TTTAGAAACATTTACT
38746226 TT
1 TT
38746228 GTTTCAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (16 bp):
TTTAGAAACATTTACT
Found at i:38752154 original size:33 final size:33
Alignment explanation
Indices: 38752117--38752181 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
38752107 GGCCTGAGCC
38752117 CTATGAAGTGACAGTACAGTGTAGACCTTAGCT
1 CTATGAAGTGACAGTACAGTGTAGACCTTAGCT
* *
38752150 CTATGAAGTGACAGTACAGTGTGGGCCTTAGC
1 CTATGAAGTGACAGTACAGTGTAGACCTTAGC
38752182 CCAATACAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (33 bp):
CTATGAAGTGACAGTACAGTGTAGACCTTAGCT
Found at i:38752373 original size:27 final size:26
Alignment explanation
Indices: 38752299--38752373 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
38752289 AATACACTAA
* *
38752299 TATCGCAGCAAAGCTACCAGTATCAG
1 TATCGTAGCAAAGCTACCAGTAACAG
* *
38752325 TATCGTAGCAAAGCTGCTAGTAACAG
1 TATCGTAGCAAAGCTACCAGTAACAG
* * *
38752351 TATATGTGGCAAAGCCACCAGTA
1 TAT-CGTAGCAAAGCTACCAGTA
38752374 GGTCCACAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
26 25 0.64
27 14 0.36
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (26 bp):
TATCGTAGCAAAGCTACCAGTAACAG
Found at i:38752617 original size:27 final size:27
Alignment explanation
Indices: 38752587--38752810 Score: 304
Period size: 27 Copynumber: 8.3 Consensus size: 27
38752577 GGGTATAACA
* *
38752587 GTCATTTTACCCTATAAGGTTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
*
38752614 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
*
38752641 ATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* * *
38752668 ATCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTCG
38752695 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* * *
38752722 ATCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
** * *
38752749 GTCATTTTACATTATGGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTCG
**
38752776 GTCATTTTACCCTATAGGGGTATTTTA
1 GTCATTTTACCCTATAGGGGTATTTCG
38752803 GTCATTTT
1 GTCATTTT
38752811 CATCTATTAG
Statistics
Matches: 177, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 177 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTCG
Found at i:38752618 original size:54 final size:53
Alignment explanation
Indices: 38752561--38752810 Score: 299
Period size: 54 Copynumber: 4.6 Consensus size: 53
38752551 GCCATAACAG
** * * *
38752561 TCATTTTATCTCCTA-GGGGTATAACAGTCATTTTACCCTATAAGGTTATTTCGG
1 TCATTTTA-C-CCTAGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGA
38752615 TCATTTTACCCTATGGGGGTATTTC-GATCATTTTACCCTATAGGGGTATTTCGA
1 TCATTTTACCCTA-GGGGGTATTTCAG-TCATTTTACCCTATAGGGGTATTTCGA
38752669 TCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGA
1 TCATTTTACCCTA-GGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGA
* * ** *
38752723 TCATTTTACCTTATGGGGGTATTTCGGTCATTTTACATTATGGGGGTATTTC-A
1 TCATTTTACCCTA-GGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGA
* *
38752776 GTCATTTTACCCTATAGGGGTATTTTAGTCATTTT
1 -TCATTTTACCCTA-GGGGGTATTTCAGTCATTTT
38752811 CATCTATTAG
Statistics
Matches: 177, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
52 4 0.02
53 3 0.02
54 169 0.95
55 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.43
Consensus pattern (53 bp):
TCATTTTACCCTAGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGA
Found at i:38752699 original size:81 final size:81
Alignment explanation
Indices: 38752588--38752800 Score: 336
Period size: 81 Copynumber: 2.6 Consensus size: 81
38752578 GGTATAACAG
** * * *
38752588 TCATTTTACCCTATAAGGTTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCC
38752653 TATAGGGGTATTTCGA
66 TATAGGGGTATTTCGA
*
38752669 TCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCT
1 TCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCC
* *
38752734 TATGGGGGTATTTCGG
66 TATAGGGGTATTTCGA
**
38752750 TCATTTTACATTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTT
1 TCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTT
38752801 TAGTCATTTT
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 122 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCC
TATAGGGGTATTTCGA
Found at i:38752817 original size:27 final size:26
Alignment explanation
Indices: 38752559--38752871 Score: 211
Period size: 27 Copynumber: 11.6 Consensus size: 26
38752549 AGGCCATAAC
* * ***
38752559 AGTCATTTTATCTCCTAGGGGTATAAC
1 AGTCATTTTACCT-ATAGGGGTATTTT
* * *
38752586 AGTCATTTTACCCTATAAGGTTATTTC
1 AGTCATTTTA-CCTATAGGGGTATTTT
* *
38752613 GGTCATTTTACCCTATGGGGGTA-TTT
1 AGTCATTTTA-CCTATAGGGGTATTTT
*
38752639 CGATCATTTTACCCTATAGGGGTA-TTT
1 AG-TCATTTTA-CCTATAGGGGTATTTT
* * *
38752666 CGATCATTTTACCCTATGGGGGTATTTC
1 AG-TCATTTTA-CCTATAGGGGTATTTT
38752694 AGTCATTTTACCCTATAGGGGTA-TTT
1 AGTCATTTTA-CCTATAGGGGTATTTT
* * *
38752720 CGATCATTTTACCTTATGGGGGTATTTC
1 AG-TCATTTTACC-TATAGGGGTATTTT
* * * *
38752748 GGTCATTTTACATTATGGGGGTATTTC
1 AGTCATTTTAC-CTATAGGGGTATTTT
38752775 AGTCATTTTACCCTATAGGGGTATTTT
1 AGTCATTTTA-CCTATAGGGGTATTTT
* ***
38752802 AGTCATTTTCATCTATTAGGGGTAAAAT
1 AGTCATTTT-ACCTA-TAGGGGTATTTT
*
38752830 AGTTATTTTATCCT-TCAGGGGTATTTT
1 AGTCATTTTA-CCTAT-AGGGGTATTTT
*
38752857 GGTCATTTTACCTAT
1 AGTCATTTTACCTAT
38752872 TTTGGAGTCT
Statistics
Matches: 235, Mismatches: 38, Indels: 26
0.79 0.13 0.09
Matches are distributed among these distances:
26 12 0.05
27 194 0.83
28 29 0.12
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (26 bp):
AGTCATTTTACCTATAGGGGTATTTT
Found at i:38753138 original size:19 final size:19
Alignment explanation
Indices: 38753099--38753158 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
38753089 ATCCGTGTAG
* *
38753099 GGCCCACA-AG-CCAATTA
1 GGCCCACACAGCCCATTTC
38753116 GGCCCACACAGCCCATTTC
1 GGCCCACACAGCCCATTTC
*
38753135 GGCCCA-ACGTGGCCCATTTC
1 GGCCCACAC--AGCCCATTTC
38753155 GGCC
1 GGCC
38753159 TAAGCCCATG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.22
18 4 0.11
19 11 0.31
20 13 0.36
ACGTcount: A:0.22, C:0.42, G:0.22, T:0.15
Consensus pattern (19 bp):
GGCCCACACAGCCCATTTC
Found at i:38758348 original size:18 final size:17
Alignment explanation
Indices: 38758325--38758361 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
38758315 GGATGAAAAC
38758325 ATTAAGGGTAAAATTATA
1 ATTAA-GGTAAAATTATA
*
38758343 ATTAAGTTAAAATTATA
1 ATTAAGGTAAAATTATA
38758360 AT
1 AT
38758362 AAAATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (17 bp):
ATTAAGGTAAAATTATA
Found at i:38762524 original size:20 final size:20
Alignment explanation
Indices: 38762501--38762547 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
38762491 TAAATTAAAC
38762501 TATTTTTTATTAAAATTTCA
1 TATTTTTTATTAAAATTTCA
*
38762521 TA--TTTTATTGAAATTTCA
1 TATTTTTTATTAAAATTTCA
38762539 TATTCTTTT
1 TATT-TTTT
38762548 GAATGACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 17 0.74
20 2 0.09
21 4 0.17
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTTTATTAAAATTTCA
Found at i:38762550 original size:18 final size:18
Alignment explanation
Indices: 38762505--38762542 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
38762495 TTAAACTATT
*
38762505 TTTTATTAAAATTTCATA
1 TTTTATTGAAATTTCATA
38762523 TTTTATTGAAATTTCATA
1 TTTTATTGAAATTTCATA
38762541 TT
1 TT
38762543 CTTTTGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTATTGAAATTTCATA
Found at i:38763007 original size:14 final size:14
Alignment explanation
Indices: 38762985--38763017 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
38762975 TTGTGTTAAA
38762985 CTATA-TGTGAGCT
1 CTATATTGTGAGCT
38762998 CTATATTGTGAGCT
1 CTATATTGTGAGCT
*
38763012 ATATAT
1 CTATAT
38763018 GAATAGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (14 bp):
CTATATTGTGAGCT
Found at i:38764695 original size:24 final size:24
Alignment explanation
Indices: 38764663--38764709 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38764653 GCAAGCCCAT
* *
38764663 TTCATAGCTCGTGTGAGCATTATA
1 TTCATAGCTCATATGAGCATTATA
38764687 TTCATAGCTCATATGAGCATTAT
1 TTCATAGCTCATATGAGCATTAT
38764710 TATCCTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TTCATAGCTCATATGAGCATTATA
Found at i:38776758 original size:6 final size:6
Alignment explanation
Indices: 38776743--38776781 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
38776733 GGTTTTCTTG
*
38776743 AAATGA AAATGG AAATGA AAATGA AAATGA AAACTGA AA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAA-TGA AA
38776782 GATGGTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.64, C:0.03, G:0.18, T:0.15
Consensus pattern (6 bp):
AAATGA
Found at i:38777403 original size:6 final size:6
Alignment explanation
Indices: 38777392--38777434 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
38777382 GGTTTTCTTG
*
38777392 AAATGA AAATGA AAATGA AAATGA AAATGA GAATGA GAAATGA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA -AAATGA
38777435 TTCATTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (6 bp):
AAATGA
Found at i:38782875 original size:36 final size:36
Alignment explanation
Indices: 38782828--38782934 Score: 135
Period size: 36 Copynumber: 3.0 Consensus size: 36
38782818 GACAATCCCA
* *
38782828 CCAAAACACACCAGATGCTCATAAGAGCTAGTCCAT
1 CCAAAACACACCAAATGCTCATAAGAGCTAATCCAT
*
38782864 CCAAAACACACCAAATGCTCATATGAGCTAATCCAT
1 CCAAAACACACCAAATGCTCATAAGAGCTAATCCAT
* * **
38782900 CAAAAACACA-CTAATGGCTCGGAAGAGCTAATCCA
1 CCAAAACACACCAAAT-GCTCATAAGAGCTAATCCA
38782935 ATCGAAACAC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.06
36 58 0.94
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.17
Consensus pattern (36 bp):
CCAAAACACACCAAATGCTCATAAGAGCTAATCCAT
Found at i:38792995 original size:20 final size:21
Alignment explanation
Indices: 38792955--38792995 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38792945 TATTAAATTC
*
38792955 AATATAATATTTATCTTGATA
1 AATATAATATTAATCTTGATA
*
38792976 AATATTATATTAAT-TTGATA
1 AATATAATATTAATCTTGATA
38792996 TTAAAGTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (21 bp):
AATATAATATTAATCTTGATA
Found at i:38797584 original size:27 final size:27
Alignment explanation
Indices: 38797529--38797585 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
38797519 GTAATTCTTG
**
38797529 ATAGTTTGAAAGCTGCTTCAGATTGAC
1 ATAGTTTGAAAGCTGCTTCAGATCAAC
38797556 ATAGTTTGAAAGCTGCTTCAGATCAAC
1 ATAGTTTGAAAGCTGCTTCAGATCAAC
38797583 ATA
1 ATA
38797586 AATCGTATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (27 bp):
ATAGTTTGAAAGCTGCTTCAGATCAAC
Found at i:38800263 original size:20 final size:20
Alignment explanation
Indices: 38800228--38800276 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
38800218 ATCATGGTCT
*
38800228 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
38800247 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
38800267 TTGCTTACTT
1 TTGCTTACTT
38800277 TAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:38800596 original size:50 final size:50
Alignment explanation
Indices: 38800528--38800720 Score: 188
Period size: 50 Copynumber: 3.7 Consensus size: 50
38800518 TTTCCTGTAC
* * *
38800528 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTAATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTAATATTGG
* ** * * * *
38800578 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTAATATTGG
** * * **
38800628 TGCCAACACCATGTCCCAGAAATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CT-TC-TAA--T-ATTGG
38800684 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
38800721 TCTCATTCCT
Statistics
Matches: 111, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
50 71 0.64
51 1 0.01
52 2 0.02
53 2 0.02
55 1 0.01
56 34 0.31
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTAATATTGG
Found at i:38811914 original size:48 final size:48
Alignment explanation
Indices: 38811843--38811939 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
38811833 CAAAAATGTT
38811843 AGTCTAGCTTTCAACTCAATTAAAATCAAACCATCATCAGTCAACGTC
1 AGTCTAGCTTTCAACTCAATTAAAATCAAACCATCATCAGTCAACGTC
38811891 AGTCTAGCTTTCAACTCAATTAAAATCAAACCATCATCAGTCAACGTC
1 AGTCTAGCTTTCAACTCAATTAAAATCAAACCATCATCAGTCAACGTC
38811939 A
1 A
38811940 ACCGCGTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (48 bp):
AGTCTAGCTTTCAACTCAATTAAAATCAAACCATCATCAGTCAACGTC
Found at i:38817796 original size:164 final size:164
Alignment explanation
Indices: 38817612--38817939 Score: 638
Period size: 164 Copynumber: 2.0 Consensus size: 164
38817602 GCATGTAAAC
38817612 ATCAAAATTTCGTAACGAAATTTTTATACGACCTTTCCAATAAACCATAGGCATTAAAAAATAAT
1 ATCAAAATTTCGTAACGAAATTTTTATACGACCTTTCCAATAAACCATAGGCATTAAAAAATAAT
*
38817677 AAAATAAATATTTACTAATCAAATTTGTGGCCCTAAAACCACTATTTACACCTGAGACCCCGCCT
66 AAAATAAATATTTACTAATCAAATTTGTGGCCCTAAAACCACTATTTACACCTGAAACCCCGCCT
38817742 ATCGTTTTGGGCAGTCCTTTATCAGGTGTTCCTT
131 ATCGTTTTGGGCAGTCCTTTATCAGGTGTTCCTT
38817776 ATCAAAATTTCGTAACGAAATTTTTATACGACCTTTCCAATAAACCATAGGCATTAAAAAATAAT
1 ATCAAAATTTCGTAACGAAATTTTTATACGACCTTTCCAATAAACCATAGGCATTAAAAAATAAT
*
38817841 AAAATAAATATTTACTAATCAAATTTGTGGCCCTAAAACCACTATTTACACTTGAAACCCCGCCT
66 AAAATAAATATTTACTAATCAAATTTGTGGCCCTAAAACCACTATTTACACCTGAAACCCCGCCT
38817906 ATCGTTTTGGGCAGTCCTTTATCAGGTGTTCCTT
131 ATCGTTTTGGGCAGTCCTTTATCAGGTGTTCCTT
38817940 GGACCCACAC
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 162 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (164 bp):
ATCAAAATTTCGTAACGAAATTTTTATACGACCTTTCCAATAAACCATAGGCATTAAAAAATAAT
AAAATAAATATTTACTAATCAAATTTGTGGCCCTAAAACCACTATTTACACCTGAAACCCCGCCT
ATCGTTTTGGGCAGTCCTTTATCAGGTGTTCCTT
Found at i:38823306 original size:20 final size:20
Alignment explanation
Indices: 38823251--38823309 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
38823241 GATGAATAAT
*
38823251 AGGGGCACCAAAGTGCAGAC
1 AGGGGCACCAAAGTGCAAAC
**
38823271 AGGTTCA-CAAATGTGCAAAC
1 AGGGGCACCAAA-GTGCAAAC
*
38823291 AGGGGCACCGAAGTGCAAA
1 AGGGGCACCAAAGTGCAAA
38823310 TCTTGTACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 4 0.13
20 24 0.77
21 3 0.10
ACGTcount: A:0.37, C:0.22, G:0.31, T:0.10
Consensus pattern (20 bp):
AGGGGCACCAAAGTGCAAAC
Found at i:38827210 original size:29 final size:29
Alignment explanation
Indices: 38827168--38827225 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
38827158 GGAAAGATGA
38827168 TAATTTTTTCATCATCTTTCCTCCGCTTT
1 TAATTTTTTCATCATCTTTCCTCCGCTTT
38827197 TAATTTTTTCATCATCTTTCCTCCGCTTT
1 TAATTTTTTCATCATCTTTCCTCCGCTTT
38827226 ATATTAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.28, G:0.03, T:0.55
Consensus pattern (29 bp):
TAATTTTTTCATCATCTTTCCTCCGCTTT
Found at i:38829310 original size:50 final size:50
Alignment explanation
Indices: 38829242--38829679 Score: 471
Period size: 50 Copynumber: 8.6 Consensus size: 50
38829232 TTTCCTGTAC
* ** ** *
38829242 TGCCAATGCCATATCCCAGGTATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ** *
38829292 TGCCCATGCCATTTCCCAGACATGGTCTTACGGGGGACCTCTAATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
38829342 TGCCAACGCCATGTCCTAGACATGGTCATACATGGGTCCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * *
38829392 TGTCAACGCCATATCTCAAACATGGTCTTACATAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
38829442 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
38829492 TGCCAATACCATGTCCCAGACATGGTCTTATATGGGAGCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * **
38829542 TGCCAATGCCATGTTCCAGACATGGTCTTACGTGAGACCTCTCTTCTTAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * *
38829592 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATAATTTTAGTAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAC--CTC-TCA-TCTCG--G
38829648 TGCCAATGCCATGTCCCAGACATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
38829680 CTGGCTTACA
Statistics
Matches: 320, Mismatches: 62, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
50 283 0.88
52 3 0.01
53 1 0.00
54 2 0.01
56 31 0.10
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:38831977 original size:23 final size:23
Alignment explanation
Indices: 38831944--38831987 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
38831934 CAGTGAAACA
*
38831944 GGGGAGCCTTTAACTAATAAATG
1 GGGGAGACTTTAACTAATAAATG
38831967 GGGGAGACTTTAACTAATAAA
1 GGGGAGACTTTAACTAATAAA
38831988 CTGTACTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (23 bp):
GGGGAGACTTTAACTAATAAATG
Found at i:38837462 original size:50 final size:50
Alignment explanation
Indices: 38837387--38837678 Score: 325
Period size: 50 Copynumber: 5.9 Consensus size: 50
38837377 CATTTGGGTA
*
38837387 AAGAGGTCCCATGTAAGACCATGTCTGGGGCATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
38837437 AAGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * *
38837487 AAGAGGTCCCATGTAAGACCATGTCTGGGAGATGGTGTTGGCATCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** * * *
38837537 GAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** * * * * ** * *
38837587 GAGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA-ATACAA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** * * *
38837636 AAAACATCCCATATAAGACCATGTCTGGGATATGGCTTTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
38837679 TGTTATTATC
Statistics
Matches: 207, Mismatches: 35, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
49 37 0.18
50 170 0.82
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:38840237 original size:50 final size:50
Alignment explanation
Indices: 38840170--38840563 Score: 554
Period size: 50 Copynumber: 7.9 Consensus size: 50
38840160 TTTCCTATAC
* * ** ** ** *
38840170 TGCCAATGCCATATCCCAGGTATGGTCTTACATCAGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ***
38840220 TGCCCATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
38840270 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCCCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
38840320 TGTCAGCGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
38840370 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
38840420 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
38840470 TGCCAATGCCATGTTCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
38840520 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA
38840564 CAATTTCAAT
Statistics
Matches: 311, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 311 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:38851347 original size:53 final size:53
Alignment explanation
Indices: 38851262--38851363 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
38851252 ATGGCACTAC
* *
38851262 AGAAGACGATATCATGTAATACCATAATTGGTGGGTTATGACATCATATTTGA
1 AGAAGACGATATCATGTAAGACCATAACTGGTGGGTTATGACATCATATTTGA
* * **
38851315 AGAAGATC-ATATCGTGTAAGACCGTAACTGGTGGGTTATGGTATCATAT
1 AGAAGA-CGATATCATGTAAGACCATAACTGGTGGGTTATGACATCATAT
38851364 GGAAAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 41 0.98
54 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (53 bp):
AGAAGACGATATCATGTAAGACCATAACTGGTGGGTTATGACATCATATTTGA
Found at i:38851543 original size:28 final size:28
Alignment explanation
Indices: 38851491--38851612 Score: 124
Period size: 29 Copynumber: 4.3 Consensus size: 28
38851481 AGAAGAAAAT
38851491 CCTTTGTGGCAAAACTTTGGAAAGGCAAG
1 CCTTTGTGGCAAAACTTT-GAAAGGCAAG
* *
38851520 CCTTTGTGGCAAACCTATT-AAAGG-ATAA
1 CCTTTGTGGCAAAACT-TTGAAAGGCA-AG
*
38851548 CCTTTGTTGCAAAACTTTAGAAAGGCAAG
1 CCTTTGTGGCAAAACTTT-GAAAGGCAAG
** * *
38851577 CCTTTGTGGTGAAACTCTGAAAGG-ACG
1 CCTTTGTGGCAAAACTTTGAAAGGCAAG
38851604 CCTTTGTGG
1 CCTTTGTGG
38851613 AGAGACTCTG
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
27 14 0.18
28 26 0.33
29 35 0.45
30 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (28 bp):
CCTTTGTGGCAAAACTTTGAAAGGCAAG
Found at i:38851572 original size:29 final size:28
Alignment explanation
Indices: 38851491--38851641 Score: 112
Period size: 28 Copynumber: 5.4 Consensus size: 28
38851481 AGAAGAAAAT
*
38851491 CCTTTGTGGCAAAACTTTGGAAAGGCAAG
1 CCTTTGTGGCAAAACTTT-GAAAGGCAAA
*
38851520 CCTTTGTGGCAAACCTATT-AAAGG-ATAA
1 CCTTTGTGGCAAAACT-TTGAAAGGCA-AA
* *
38851548 CCTTTGTTGCAAAACTTTAGAAAGGCAAG
1 CCTTTGTGGCAAAACTTT-GAAAGGCAAA
** * **
38851577 CCTTTGTGGTGAAACTCTGAAAGG-ACG
1 CCTTTGTGGCAAAACTTTGAAAGGCAAA
* * *
38851604 CCTTTGTGG-AGAGACTCTGAAAGGAAAA
1 CCTTTGTGGCA-AAACTTTGAAAGGCAAA
*
38851632 TCTTTGTGGC
1 CCTTTGTGGC
38851642 CACTACTTAA
Statistics
Matches: 99, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
27 26 0.26
28 35 0.35
29 35 0.35
30 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (28 bp):
CCTTTGTGGCAAAACTTTGAAAGGCAAA
Found at i:38851612 original size:27 final size:27
Alignment explanation
Indices: 38851491--38851629 Score: 95
Period size: 29 Copynumber: 5.0 Consensus size: 27
38851481 AGAAGAAAAT
*
38851491 CCTTTGTGGCA-AAACTTTGGAAAGGCAAG
1 CCTTTGTGG-AGAAACTCT-GAAAGG-AAG
* * * *
38851520 CCTTTGTGGCA-AACCTATTAAAGGATAA
1 CCTTTGTGG-AGAAACTCTGAAAGGA-AG
* *
38851548 CCTTTGTTGCA-AAACTTTAGAAAGGCAAG
1 CCTTTG-TGGAGAAACTCT-GAAAGG-AAG
* *
38851577 CCTTTGTGGTGAAACTCTGAAAGGACG
1 CCTTTGTGGAGAAACTCTGAAAGGAAG
*
38851604 CCTTTGTGGAGAGACTCTGAAAGGAA
1 CCTTTGTGGAGAAACTCTGAAAGGAA
38851630 AATCTTTGTG
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
27 26 0.29
28 26 0.29
29 36 0.40
30 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (27 bp):
CCTTTGTGGAGAAACTCTGAAAGGAAG
Found at i:38860419 original size:48 final size:48
Alignment explanation
Indices: 38860351--38860547 Score: 234
Period size: 48 Copynumber: 4.1 Consensus size: 48
38860341 AATAGATTTC
* * * *
38860351 TCGGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTC
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
* * * *
38860399 TCGGTGGCCTGCACATAGTCCGTGTCACCCTTGTATCTTAACA-AGTTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGA-TTA
* * * * * * *
38860447 TTGGTGGCCTACACATACTCTGTGCCACCCTTGTGTCACAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
*
38860495 TCGGTGGCTTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
38860543 TCGGT
1 TCGGT
38860548 ACGGATAGTA
Statistics
Matches: 122, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
47 1 0.01
48 120 0.98
49 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (48 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
Done.