Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 92 of 120
Found at i:27334784 original size:45 final size:44
Alignment explanation
Indices: 27334718--27334872 Score: 220
Period size: 45 Copynumber: 3.4 Consensus size: 44
27334708 AGTATACAGT
* * * **
27334718 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTA
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
27334763 AATCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
27334808 AATCGATAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCG-TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
27334853 AATCAGTAACAGTAACAGTA
1 AATC-GTAACAGTAACAGTA
27334873 GTCGGCACAT
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 1 0.01
45 98 0.98
46 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (44 bp):
AATCGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
Found at i:27334823 original size:39 final size:41
Alignment explanation
Indices: 27334733--27334894 Score: 159
Period size: 45 Copynumber: 3.8 Consensus size: 41
27334723 GTAACGGTAG
* **
27334733 CAGTAACAGTATTCAACACACAAAGTGCTAAATCTGTAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATC-G--A-AGTAA
*
27334778 CGGTAACAGTATTCGACACACAAAGTGCCGAATCGATAACAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCG---A-AGTAA
27334823 CAGTAACAGTATTCGACACACAAAGTGCCGAATC--AGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATCGAAGTAA
* * * *
27334862 CAGTAACAGTAGTCGGCACA-TAAGTGCCTAATC
1 CAGTAACAGTATTCGACACACAAAGTGCCGAATC
27334895 AGTAAGCCGA
Statistics
Matches: 107, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
38 11 0.10
39 23 0.21
44 1 0.01
45 72 0.67
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (41 bp):
CAGTAACAGTATTCGACACACAAAGTGCCGAATCGAAGTAA
Found at i:27337010 original size:21 final size:21
Alignment explanation
Indices: 27336986--27337027 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
27336976 CTTTTTGTTC
27336986 AATTAATT-ATCGAAACTTTAA
1 AATTAATTGA-CGAAACTTTAA
**
27337007 AATTTCTTGACGAAACTTTAA
1 AATTAATTGACGAAACTTTAA
27337028 TACTAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (21 bp):
AATTAATTGACGAAACTTTAA
Found at i:27339488 original size:5 final size:5
Alignment explanation
Indices: 27339455--27339486 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
27339445 TTCCCGTCCC
*
27339455 CCCCA CCCCA CCCCA CCCCA CCCCA CCTCA CC
1 CCCCA CCCCA CCCCA CCCCA CCCCA CCCCA CC
27339487 TCCTATCGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.78, G:0.00, T:0.03
Consensus pattern (5 bp):
CCCCA
Found at i:27339884 original size:25 final size:23
Alignment explanation
Indices: 27339841--27339887 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
27339831 GGAATTTTTT
*
27339841 TTATTTTTTTAATATTAATATAG
1 TTATTTTTTTAATAATAATATAG
27339864 TTATTTTTAATTAATAATAATATA
1 TTATTTTT--TTAATAATAATATA
27339888 AAATTATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTATTTTTTTAATAATAATATAG
Found at i:27350808 original size:16 final size:17
Alignment explanation
Indices: 27350783--27350822 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
27350773 GCCCAAATGC
27350783 CAAA-CCCAAAT-AAAA
1 CAAAGCCCAAATCAAAA
*
27350798 CAAAGCCCAAATCCAAA
1 CAAAGCCCAAATCAAAA
27350815 C-AAGCCCA
1 CAAAGCCCA
27350823 TTACAGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.55, C:0.35, G:0.05, T:0.05
Consensus pattern (17 bp):
CAAAGCCCAAATCAAAA
Found at i:27352020 original size:3 final size:3
Alignment explanation
Indices: 27352012--27352074 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
27352002 CTATTACAAC
27352012 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27352059 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
27352075 TACTCATTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:27359841 original size:16 final size:17
Alignment explanation
Indices: 27359820--27359854 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
27359810 AATTGAAATA
*
27359820 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
27359836 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
27359853 AA
1 AA
27359855 CCCGATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:27363320 original size:31 final size:31
Alignment explanation
Indices: 27363278--27363351 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
27363268 GTCATCTCGA
* * *
27363278 ATTGCCTGACAACAATAACTTACCA-CCCTGG
1 ATTGCCCGACAAAAATAACTTACCATCCC-AG
** *
27363309 ATTGCCCGACAAAAATGGCTTACCATGCCAG
1 ATTGCCCGACAAAAATAACTTACCATCCCAG
27363340 ATTGCCCGACAA
1 ATTGCCCGACAA
27363352 TGATGGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.20
Consensus pattern (31 bp):
ATTGCCCGACAAAAATAACTTACCATCCCAG
Found at i:27364792 original size:23 final size:23
Alignment explanation
Indices: 27364766--27364830 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
27364756 AAAAATGTTT
*
27364766 CAGAATATGTCACAAAGACATTA
1 CAGAATATGACACAAAGACATTA
* * *
27364789 CAGAAT-TCGCCACTAAGGCATTA
1 CAGAATAT-GACACAAAGACATTA
* *
27364812 CGGAATACGACACAAAGAC
1 CAGAATATGACACAAAGAC
27364831 TCTATTTGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (23 bp):
CAGAATATGACACAAAGACATTA
Found at i:27366327 original size:41 final size:41
Alignment explanation
Indices: 27366269--27366476 Score: 344
Period size: 41 Copynumber: 5.0 Consensus size: 41
27366259 CTTAATTTAA
* *
27366269 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
27366311 CAGATCACCGGCACTTAACCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
27366352 TAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
27366393 CAGATCACCAGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
* *
27366434 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
27366475 CA
1 CA
27366477 AATCGCATAA
Statistics
Matches: 156, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 152 0.97
42 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:27367171 original size:2 final size:2
Alignment explanation
Indices: 27367164--27367209 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
27367154 TTTGATACAC
* *
27367164 AT AT AT AT AT AT CT TT 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
27367206 AT AT
1 AT AT
27367210 CTATTCGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:27380917 original size:2 final size:2
Alignment explanation
Indices: 27380906--27380935 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27380896 TCGGTTACTT
27380906 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27380936 TGAAAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27389066 original size:20 final size:22
Alignment explanation
Indices: 27389023--27389070 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
27389013 TTTCTTTTTT
* *
27389023 AATTTTATTTAAATTTGAGGTA
1 AATTATATTTAAATTTGAGATA
27389045 AATTATATTTAAATTT-A-ATA
1 AATTATATTTAAATTTGAGATA
27389065 AATTAT
1 AATTAT
27389071 TCGTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
AATTATATTTAAATTTGAGATA
Found at i:27390638 original size:16 final size:16
Alignment explanation
Indices: 27390617--27390647 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27390607 AAGAGACATA
*
27390617 TAACCATGTCTTAATG
1 TAACCATCTCTTAATG
27390633 TAACCATCTCTTAAT
1 TAACCATCTCTTAAT
27390648 ACTCTAATTG
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:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (16 bp):
TAACCATCTCTTAATG
Found at i:27391339 original size:11 final size:11
Alignment explanation
Indices: 27391323--27391362 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
27391313 TTCAAAAATT
27391323 CTCTTAAGTTA
1 CTCTTAAGTTA
*
27391334 CTCTTAAGTTC
1 CTCTTAAGTTA
*
27391345 CTCTTAAGTTT
1 CTCTTAAGTTA
27391356 CTCTTAA
1 CTCTTAA
27391363 CTCTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (11 bp):
CTCTTAAGTTA
Found at i:27391389 original size:12 final size:12
Alignment explanation
Indices: 27391369--27391411 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
27391359 TTAACTCTCT
27391369 TTTTTAAAATAA
1 TTTTTAAAATAA
* *
27391381 TTTTAAAAATAT
1 TTTTTAAAATAA
*
27391393 TTTTTAAAAT-T
1 TTTTTAAAATAA
27391404 TTTTTAAA
1 TTTTTAAA
27391412 CCGTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTTAAAATAA
Found at i:27392525 original size:7 final size:7
Alignment explanation
Indices: 27392513--27392537 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27392503 AGTCGATTGA
27392513 TATTTAG
1 TATTTAG
27392520 TATTTAG
1 TATTTAG
27392527 TATTTAG
1 TATTTAG
27392534 TATT
1 TATT
27392538 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:27393341 original size:23 final size:23
Alignment explanation
Indices: 27393311--27393572 Score: 233
Period size: 23 Copynumber: 11.6 Consensus size: 23
27393301 NNNNNNNNNN
*
27393311 TAACCTAATTTAATTAAAAACTC
1 TAACCTAATTTAATTAAAAACCC
*
27393334 TAACCTAATTAAATTAAAAACCC
1 TAACCTAATTTAATTAAAAACCC
*
27393357 TAACCTAATTTAATTAAAAACTC
1 TAACCTAATTTAATTAAAAACCC
* *
27393380 TAAACCCTAA---ACTTAAAAAGCC
1 T-AA-CCTAATTTAATTAAAAACCC
*
27393402 TAACCTAATTTAATTAAAAA-CT
1 TAACCTAATTTAATTAAAAACCC
* *
27393424 TAAACCCTAA---ACTTAAAAACTC
1 T-AA-CCTAATTTAATTAAAAACCC
***
27393446 TAACC-CCCTTAACTTAAAAACCC
1 TAACCTAATTTAA-TTAAAAACCC
*
27393469 TAACCTAATTAAATTAAAAACCC
1 TAACCTAATTTAATTAAAAACCC
27393492 TAACCTAATTTAATT-AAAACCC
1 TAACCTAATTTAATTAAAAACCC
*
27393514 TAAACCTTAA---ACTTAAAAACCC
1 T-AACC-TAATTTAATTAAAAACCC
*
27393536 TAACCCAATTTAATTAAAAACCC
1 TAACCTAATTTAATTAAAAACCC
* *
27393559 TAAACTAAATTAAT
1 TAACCTAATTTAAT
27393573 AATTTTACTT
Statistics
Matches: 193, Mismatches: 27, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
20 9 0.05
21 19 0.10
22 30 0.16
23 117 0.61
24 13 0.07
25 5 0.03
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (23 bp):
TAACCTAATTTAATTAAAAACCC
Found at i:27393449 original size:44 final size:44
Alignment explanation
Indices: 27393311--27393556 Score: 259
Period size: 44 Copynumber: 5.5 Consensus size: 44
27393301 NNNNNNNNNN
*
27393311 TAACCTAATTTAATTAAAAACTCT-AA-CCTAATTAAATTAAAAACCC
1 TAACCTAATTTAATTAAAAACT-TAAACCCT-A--AACTTAAAAACCC
*
27393357 TAACCTAATTTAATTAAAAACTCTAAACCCTAAACTTAAAAAGCC
1 TAACCTAATTTAATTAAAAACT-TAAACCCTAAACTTAAAAACCC
*
27393402 TAACCTAATTTAATTAAAAACTTAAACCCTAAACTTAAAAACTC
1 TAACCTAATTTAATTAAAAACTTAAACCCTAAACTTAAAAACCC
*** * *
27393446 TAACC-CCCTTAACTTAAAAACCCT-AA-CCTAATTAAATTAAAAACCC
1 TAACCTAATTTAA-TTAAAAA-CTTAAACCCT-A--AACTTAAAAACCC
* * *
27393492 TAACCTAATTTAATTAAAACCCTAAACCTTAAACTTAAAAACCC
1 TAACCTAATTTAATTAAAAACTTAAACCCTAAACTTAAAAACCC
*
27393536 TAACCCAATTTAATTAAAAAC
1 TAACCTAATTTAATTAAAAAC
27393557 CCTAAACTAA
Statistics
Matches: 172, Mismatches: 18, Indels: 22
0.81 0.08 0.10
Matches are distributed among these distances:
43 7 0.04
44 66 0.38
45 38 0.22
46 49 0.28
47 9 0.05
48 3 0.02
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (44 bp):
TAACCTAATTTAATTAAAAACTTAAACCCTAAACTTAAAAACCC
Found at i:27393504 original size:90 final size:92
Alignment explanation
Indices: 27393387--27393571 Score: 268
Period size: 90 Copynumber: 2.0 Consensus size: 92
27393377 CTCTAAACCC
* * *
27393387 TAAACTTAAAAAGCCTAACCTAATTTAATTAAAAACTTAAACCCTAAACTTAAAAACTCTAACCC
1 TAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCTAAACCCTAAACTTAAAAACCCTAACCC
* *
27393452 -CCTTAACTTAAAAACCCTAACCT-AAT
66 AACTTAA-TTAAAAACCCTAAACTAAAT
* *
27393478 TAAA-TTAAAAACCCTAACCTAATTTAATTAAAACCCTAAACCTTAAACTTAAAAACCCTAACCC
1 TAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCTAAACCCTAAACTTAAAAACCCTAACCC
*
27393542 AATTTAATTAAAAACCCTAAACTAAAT
66 AACTTAATTAAAAACCCTAAACTAAAT
27393569 TAA
1 TAA
27393572 TAATTTTACT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
90 70 0.83
91 14 0.17
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (92 bp):
TAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCTAAACCCTAAACTTAAAAACCCTAACCC
AACTTAATTAAAAACCCTAAACTAAAT
Found at i:27393572 original size:67 final size:67
Alignment explanation
Indices: 27393324--27393572 Score: 292
Period size: 67 Copynumber: 3.7 Consensus size: 67
27393314 CCTAATTTAA
* * * *
27393324 TTAAAAACTCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACTCTAAACCCTA
1 TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACTAAATTAATT-AAAACTCTAAACCTTA
27393389 AAC
65 AAC
* * * *
27393392 TTAAAAAGCCTAACCTAATTTAATTAAAAA-CTTAAACCCTAAACTT-A--AAAACTCTAACCCC
1 TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAA--CTAAA-TTAATTAAAACTCTAA--AC
27393453 CTT-AAC
61 CTTAAAC
* * *
27393459 TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAACCCTAAACCTTAA
1 TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACTAAATTAATTAAAACTCTAAACCTTAA
27393524 AC
66 AC
* *
27393526 TTAAAAACCCTAACCCAATTTAATTAAAAACCCTAAACTAAATTAAT
1 TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACTAAATTAAT
27393573 AATTTTACTT
Statistics
Matches: 152, Mismatches: 19, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
65 2 0.01
66 19 0.12
67 81 0.53
68 43 0.28
69 5 0.03
70 2 0.01
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.27
Consensus pattern (67 bp):
TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACTAAATTAATTAAAACTCTAAACCTTAA
AC
Found at i:27393812 original size:116 final size:116
Alignment explanation
Indices: 27393566--27393926 Score: 625
Period size: 116 Copynumber: 3.1 Consensus size: 116
27393556 CCCTAAACTA
* **
27393566 AATTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTTCCTGGTACTAACAA
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATG--TTTTGACTGGTACTAACAA
* *
27393631 TTAATAATTTTATATAAGTTGATAA-TTTTACTAATCATTAATACAATTTATC
64 TTAATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
* * *
27393683 ATTTACTAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
27393748 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
66 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
27393799 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
27393864 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
66 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
27393915 AATTAATAATTT
1 AATTAATAATTT
27393927 CACAAACTTA
Statistics
Matches: 232, Mismatches: 11, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
115 41 0.18
116 151 0.65
117 40 0.17
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (116 bp):
AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
Found at i:27393873 original size:61 final size:61
Alignment explanation
Indices: 27393689--27393873 Score: 163
Period size: 61 Copynumber: 3.1 Consensus size: 61
27393679 TATCATTTAC
27393689 TAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAA
1 TAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAA
* * * * ** ** ** * *
27393750 TAATTTTATA-T-A-AT-TTGATA-ATTTTTACTAACCAT-TAAT-AC-AAT-TTATCAATTAA
1 TAATTTTACATTCACATAATGTTAGA-TTTGA--AAAAATGTTTTGACTGGTACTAACAATTAA
*
27393805 TAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAA
27393866 TAATTTTA
1 TAATTTTA
27393874 TATAATTTGA
Statistics
Matches: 87, Mismatches: 25, Indels: 24
0.64 0.18 0.18
Matches are distributed among these distances:
55 18 0.21
56 3 0.03
57 15 0.17
58 8 0.09
59 14 0.16
60 3 0.03
61 26 0.30
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (61 bp):
TAATTTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAA
Found at i:27397252 original size:123 final size:123
Alignment explanation
Indices: 27396933--27397307 Score: 590
Period size: 123 Copynumber: 3.0 Consensus size: 123
27396923 GCCCAAAATG
*
27396933 CTACTGTAGCAAAAGCGC-CCACACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTG
27396997 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAATTATTTCTTCCATGAC
* * *
27397057 CGACAGTAGCAAAAGCACGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
*
27397122 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGAC
* * * *
27397180 CTACTGTAGCAAAAACGCGTCCATGAGGGCGCGATTTCAAAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
* ** *
27397245 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA--AAAAATTATTTCTTCCATGAC
27397305 CTA
1 CTA
27397308 AAAACCCTAA
Statistics
Matches: 231, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
123 116 0.50
124 93 0.40
125 22 0.10
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (123 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGAC
Found at i:27398282 original size:6 final size:6
Alignment explanation
Indices: 27398273--27398301 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
27398263 AAATAAAATT
27398273 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
27398302 GTCTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:27398355 original size:9 final size:9
Alignment explanation
Indices: 27398341--27398380 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
27398331 GTAGTGATTC
27398341 AATTCGGTT
1 AATTCGGTT
*
27398350 AATTCGGGT
1 AATTCGGTT
27398359 AATTCGGTT
1 AATTCGGTT
*
27398368 AATTCGATT
1 AATTCGGTT
27398377 AATT
1 AATT
27398381 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:27398379 original size:18 final size:18
Alignment explanation
Indices: 27398336--27398380 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
27398326 ATTATGTAGT
27398336 GATTCAATTCGGTTAATTC
1 GATT-AATTCGGTTAATTC
**
27398355 GGGTAATTCGGTTAATTC
1 GATTAATTCGGTTAATTC
27398373 GATTAATT
1 GATTAATT
27398381 TTTAACCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (18 bp):
GATTAATTCGGTTAATTC
Found at i:27403155 original size:31 final size:33
Alignment explanation
Indices: 27403109--27403169 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
27403099 TTGCAAATAT
27403109 ATATATATATATAAATATTT-ATAACTTTTTAA
1 ATATATATATATAAATATTTAATAACTTTTTAA
* *
27403141 ATATATTTA-ATAAATATTTAATAAGTTTT
1 ATATATATATATAAATATTTAATAACTTTT
27403170 CTAATTTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (33 bp):
ATATATATATATAAATATTTAATAACTTTTTAA
Found at i:27403159 original size:11 final size:11
Alignment explanation
Indices: 27403119--27403164 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
27403109 ATATATATAT
27403119 ATAAATATTT-
1 ATAAATATTTA
* *
27403129 ATAACTTTTTA
1 ATAAATATTTA
*
27403140 A-ATATATTTA
1 ATAAATATTTA
27403150 ATAAATATTTA
1 ATAAATATTTA
27403161 ATAA
1 ATAA
27403165 GTTTTCTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
10 15 0.54
11 13 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
ATAAATATTTA
Found at i:27403160 original size:21 final size:20
Alignment explanation
Indices: 27403123--27403161 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
27403113 ATATATATAA
* *
27403123 ATATTTATAACTTTTTAAAT
1 ATATTTATAAATATTTAAAT
27403143 ATATTTAATAAATATTTAA
1 ATATTT-ATAAATATTTAA
27403162 TAAGTTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTTATAAATATTTAAAT
Found at i:27404526 original size:9 final size:9
Alignment explanation
Indices: 27404512--27404541 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27404502 TTGGTCCTGA
27404512 TTTTATTTT
1 TTTTATTTT
27404521 TTTTA-TTT
1 TTTTATTTT
27404529 TTTTATTTT
1 TTTTATTTT
27404538 TTTT
1 TTTT
27404542 TCTAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTATTTT
Found at i:27414374 original size:27 final size:27
Alignment explanation
Indices: 27414336--27414394 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
27414326 GCGCCAAAGG
27414336 AGAATATATATAAGCGTGCATAGAGAT
1 AGAATATATATAAGCGTGCATAGAGAT
27414363 AGAATATATATAAGCGTGCATAGAGAT
1 AGAATATATATAAGCGTGCATAGAGAT
27414390 AGAAT
1 AGAAT
27414395 TTTCAATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (27 bp):
AGAATATATATAAGCGTGCATAGAGAT
Found at i:27418203 original size:23 final size:22
Alignment explanation
Indices: 27418164--27418206 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
27418154 TAATTAAATG
27418164 AAAAAAAATAATGAGAAAATAT
1 AAAAAAAATAATGAGAAAATAT
27418186 AAAAACAATATAAT-AGAAAAT
1 AAAAA-AA-ATAATGAGAAAAT
27418207 CAAAATAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAAAAAATAATGAGAAAATAT
Found at i:27418648 original size:22 final size:23
Alignment explanation
Indices: 27418609--27418669 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
27418599 AATATCCAAA
27418609 CAATAATAATAATAAAAT-AGTAG
1 CAATAATAATAATAAAATGA-TAG
* *
27418632 CAAT-ATAATAGTGAAATGATAG
1 CAATAATAATAATAAAATGATAG
* *
27418654 CAA-AACAATAAAAAAA
1 CAATAATAATAATAAAA
27418670 AGTACAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
22 25 0.83
23 5 0.17
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (23 bp):
CAATAATAATAATAAAATGATAG
Found at i:27419402 original size:36 final size:36
Alignment explanation
Indices: 27419320--27419404 Score: 86
Period size: 38 Copynumber: 2.3 Consensus size: 36
27419310 CTTGTTATTT
*
27419320 TAAAATTTTAAAGTAAAATATAAAATAAATTTATTGAA
1 TAAAATTTTAAAGTAAAATATAAAATAAA--TATTCAA
*
27419358 -AAATATTTTAAATTAAAAT-TGAATAATAAA-ATTCAA
1 TAAA-ATTTTAAAGTAAAATAT-AA-AATAAATATTCAA
27419394 TAAAATTTTAA
1 TAAAATTTTAA
27419405 TTTTAGTAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
36 12 0.29
37 7 0.17
38 16 0.39
39 6 0.15
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.38
Consensus pattern (36 bp):
TAAAATTTTAAAGTAAAATATAAAATAAATATTCAA
Found at i:27426281 original size:17 final size:15
Alignment explanation
Indices: 27426259--27426293 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
27426249 ACCAAATTAC
27426259 AAAAAAGAAACAGAAAA
1 AAAAAAGAAA-A-AAAA
27426276 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
27426291 AAA
1 AAA
27426294 GAGTTACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 1 0.06
17 10 0.56
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAA
Found at i:27426284 original size:11 final size:11
Alignment explanation
Indices: 27426259--27426292 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
27426249 ACCAAATTAC
27426259 AAAAAAGAAACAG
1 AAAAAA-AAA-AG
27426272 AAAAAAAAAAG
1 AAAAAAAAAAG
27426283 AAAAAAAAAA
1 AAAAAAAAAA
27426293 AGAGTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 3 0.14
13 6 0.29
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:27431354 original size:6 final size:6
Alignment explanation
Indices: 27431343--27431367 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27431333 TTGTATTACA
27431343 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
27431368 CAATTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:27439407 original size:4 final size:4
Alignment explanation
Indices: 27439398--27439438 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
27439388 ACGTATGTTG
*
27439398 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA AGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
27439439 AGCGTATACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:27440275 original size:29 final size:29
Alignment explanation
Indices: 27440241--27440304 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
27440231 AGTAAAACAT
*
27440241 GTCCAGCTCAACGCGCTGA-GGAAAAACGC
1 GTCCAGCTCAACGAG-TGAGGGAAAAACGC
* * *
27440270 GTCCAGTTCAGCGAGTTAGGGAAAAACGC
1 GTCCAGCTCAACGAGTGAGGGAAAAACGC
27440299 GTCCAG
1 GTCCAG
27440305 ATTAGTGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.30, C:0.27, G:0.30, T:0.14
Consensus pattern (29 bp):
GTCCAGCTCAACGAGTGAGGGAAAAACGC
Found at i:27442311 original size:50 final size:49
Alignment explanation
Indices: 27442246--27442443 Score: 184
Period size: 51 Copynumber: 4.0 Consensus size: 49
27442236 AAAGTGAAAG
* *
27442246 TGAT-GGTCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTACCGGAA
1 TGATAGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGG-A
* * * * *
27442295 TGATAGGTCGCATGTGTAGTATTATGTGCAGGCTACTATGCGTACCGGA
1 TGATAGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGA
* * * * *
27442344 TAGTTTCGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGA
1 T-G-ATAGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGA
* * * *
27442395 TTATAATGGTCACATGTGTAGTACTCTGTGCAAGG-TACTATGTGAACCG
1 TGAT-A-GGTCACATGTGTAGTACTATGTG-AAGGCTACTACGTGTACCG
27442444 AACATCATTG
Statistics
Matches: 118, Mismatches: 25, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
49 7 0.06
50 38 0.32
51 69 0.58
52 4 0.03
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (49 bp):
TGATAGGTCACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGA
Found at i:27442372 original size:101 final size:102
Alignment explanation
Indices: 27442252--27442436 Score: 277
Period size: 101 Copynumber: 1.8 Consensus size: 102
27442242 AAAGTGATGG
* *
27442252 TCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGG-ATGATAATGGTCACATGTGTAGT
*
27442315 ATTATGTGC-AGGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAAGG-TACTATGCGTACCGGATAGTTTCGA
* *
27442353 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGATTATAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGATGATAATGGTCACATGTGTAGTA
*
27442418 CTCTGTGCAAGGTACTATG
66 CTATGTGCAAGGTACTATG
27442437 TGAACCGAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 4 0.05
101 40 0.53
102 28 0.37
103 3 0.04
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGATGATAATGGTCACATGTGTAGTA
CTATGTGCAAGGTACTATGCGTACCGGATAGTTTCGA
Found at i:27442491 original size:45 final size:45
Alignment explanation
Indices: 27442440--27442532 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
27442430 TACTATGTGA
* * *
27442440 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTCGCTATGTGCTGAATCC
27442485 ACCGAACATCATTGATTAATAAGGTGGTCGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTCGCTATGTGCTGAATCC
27442530 ACC
1 ACC
27442533 AAGTATCTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTCGCTATGTGCTGAATCC
Found at i:27446773 original size:20 final size:20
Alignment explanation
Indices: 27446716--27446786 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
27446706 TTCAATTATA
*
27446716 ATTAAACTTAATTACTTTAAT
1 ATTAAA-TTAATAACTTTAAT
27446737 ATTAAATT--TAA-TTTAAT
1 ATTAAATTAATAACTTTAAT
* *
27446754 ATCAACTTAATAACTTTAAT
1 ATTAAATTAATAACTTTAAT
27446774 ATTAAATTAATAA
1 ATTAAATTAATAA
27446787 AATACTATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
17 12 0.29
18 2 0.05
19 3 0.07
20 19 0.45
21 6 0.14
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAATTAATAACTTTAAT
Found at i:27448338 original size:14 final size:15
Alignment explanation
Indices: 27448305--27448336 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27448295 TATGCATGCA
*
27448305 AAATATAAAAGACAT
1 AAATAAAAAAGACAT
27448320 AAATAAAAAAGACAT
1 AAATAAAAAAGACAT
27448335 AA
1 AA
27448337 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATAAAAAAGACAT
Found at i:27452211 original size:16 final size:16
Alignment explanation
Indices: 27452190--27452230 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
27452180 ATATTTTATA
*
27452190 TAATTTTAATAATAAT
1 TAATTTTAATAACAAT
27452206 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
27452222 TAGTTTTAA
1 TAATTTTAA
27452231 GTTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:27457200 original size:41 final size:41
Alignment explanation
Indices: 27457142--27457224 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
27457132 CGCTGCGATG
*
27457142 ACCATCGCTTGATGTCACGATGTGGACTCTGTTTTTGGCAC
1 ACCATCGCTTGACGTCACGATGTGGACTCTGTTTTTGGCAC
27457183 ACCATCGCTTGACGTCACGATGTGGACTCTGTTTTTGGCAC
1 ACCATCGCTTGACGTCACGATGTGGACTCTGTTTTTGGCAC
27457224 A
1 A
27457225 AATTAAGCCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (41 bp):
ACCATCGCTTGACGTCACGATGTGGACTCTGTTTTTGGCAC
Found at i:27457993 original size:17 final size:19
Alignment explanation
Indices: 27457960--27457994 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
27457950 AATATTTGGA
27457960 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
27457979 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
27457995 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:27466296 original size:20 final size:21
Alignment explanation
Indices: 27466270--27466311 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
27466260 AGAGCTAATT
27466270 AAAACACTAACTCATTCATTA
1 AAAACACTAACTCATTCATTA
* *
27466291 ATACACACTAACTTATTCATT
1 A-AAACACTAACTCATTCATT
27466312 TATTCATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAACACTAACTCATTCATTA
Found at i:27468713 original size:50 final size:50
Alignment explanation
Indices: 27468650--27468754 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
27468640 TATGAAAAAT
* *
27468650 TAATAATGTTAACAACATAATAATTAACTATTTAACATTAAATAATATAA
1 TAATAATGTTAACAACATAATAATTAACTAATTAAAATTAAATAATATAA
* * *
27468700 TAATAATGTTAACAGCATAATAATTAACTAATTAAAATTTAATAATTTAA
1 TAATAATGTTAACAACATAATAATTAACTAATTAAAATTAAATAATATAA
27468750 TAATA
1 TAATA
27468755 TTTTCCTATC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (50 bp):
TAATAATGTTAACAACATAATAATTAACTAATTAAAATTAAATAATATAA
Found at i:27468950 original size:28 final size:28
Alignment explanation
Indices: 27468884--27468950 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
27468874 AAATAATAAT
* * *
27468884 AATTTAGAATTTAGAATAAAAAATCGAG
1 AATTAAGAATTGAGAATAAAAAATCAAG
* * *
27468912 AATTAATAATTGAGAATAAAAATTTAAG
1 AATTAAGAATTGAGAATAAAAAATCAAG
*
27468940 AATTGAGAATT
1 AATTAAGAATT
27468951 AAGTTGAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.54, C:0.01, G:0.13, T:0.31
Consensus pattern (28 bp):
AATTAAGAATTGAGAATAAAAAATCAAG
Found at i:27469667 original size:44 final size:45
Alignment explanation
Indices: 27469604--27469699 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 45
27469594 TTTATAACCC
27469604 AATAAAAGGTAAATAATGTCCTTTCATTGGCATTA-ATGATAGAT
1 AATAAAAGGTAAATAATGTCCTTTCATTGGCATTAGATGATAGAT
* * * *
27469648 AATAAATGGTAAATGATGTCTTTTCATTGGTATTAGATGATAGAT
1 AATAAAAGGTAAATAATGTCCTTTCATTGGCATTAGATGATAGAT
27469693 AA-AAAAG
1 AATAAAAG
27469700 TAACGTGATT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 35 0.76
45 11 0.24
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (45 bp):
AATAAAAGGTAAATAATGTCCTTTCATTGGCATTAGATGATAGAT
Found at i:27480066 original size:127 final size:126
Alignment explanation
Indices: 27479784--27480246 Score: 626
Period size: 126 Copynumber: 3.7 Consensus size: 126
27479774 GATAAAATCA
* * * * * * * *
27479784 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCACACCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGT
*
27479849 AGGTCCTGGAAAAATAATTTCGACTTGACGTTTATGAGCAAATAGTTT-AAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTATGAGCAAATAGTTTAAAAAAACGCTTC
* *
27479909 AAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCTCGTGGATGCGCTTTTGCTACAGT
1 AAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGT
* * *
27479974 TGGTCCTGGAAGAAATAATTTCGAGTTAACGTTTTTGAGCAAATAGTTTAAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTATGAGCAAATAGTTTAAAAAAACGCTTC
* * * *
27480036 AAGCAAGATGCTTTATAAGAGGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGT
* * * * * *
27480101 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTATGAGCAAATAGTTTAAAAAAACGCTTC
* * *
27480162 AAGC-AGCATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTAGCTACA
1 AAGCAAG-ATGCT-TTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACA
*
27480225 GTAGGTCCTAGAAAAATAATTT
64 GTAGGTCCTGGAAAAATAATTT
27480247 ACAGTAGGTC
Statistics
Matches: 299, Mismatches: 35, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
125 67 0.22
126 150 0.50
127 82 0.27
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (126 bp):
AAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTATGAGCAAATAGTTTAAAAAAACGCTTC
Found at i:27486544 original size:30 final size:31
Alignment explanation
Indices: 27486508--27486575 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
27486498 AGTCTGCATG
* *
27486508 TATGAATTCACTATGATCATGAAG-TTCTTT
1 TATGAATTCACTATGATCATAAAGTTTCTTC
** *
27486538 TATGAATTTGCTATGTTCATAAAGTTTCTTC
1 TATGAATTCACTATGATCATAAAGTTTCTTC
27486569 TATGAAT
1 TATGAAT
27486576 CCGCCTGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (31 bp):
TATGAATTCACTATGATCATAAAGTTTCTTC
Found at i:27486650 original size:45 final size:45
Alignment explanation
Indices: 27486596--27486704 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
27486586 GAATCTACTT
* * * * *
27486596 TATCCATGAAGT-TTCTTCTATGAATTTGCATGTATGAGTTTTCCA
1 TATCCATGAA-TCTTCTTCTATAAATCTACATGTATGAGTCTACCA
* * *
27486641 TATCTATGAATCATCTTCAATAAATCTACATGTATGAGTCTACCA
1 TATCCATGAATCTTCTTCTATAAATCTACATGTATGAGTCTACCA
27486686 TATCCATGAATCTTCTTCT
1 TATCCATGAATCTTCTTCT
27486705 TTTGCATGTA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
44 1 0.02
45 51 0.98
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (45 bp):
TATCCATGAATCTTCTTCTATAAATCTACATGTATGAGTCTACCA
Found at i:27489552 original size:20 final size:19
Alignment explanation
Indices: 27489513--27489557 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
27489503 GGTAACAATT
27489513 AATATGCTTATAACATATC
1 AATATGCTTATAACATATC
27489532 AAATATGCTTATAACGA-ATC
1 -AATATGCTTATAAC-ATATC
27489552 AATATG
1 AATATG
27489558 GTAACAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.25
20 17 0.71
21 1 0.04
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (19 bp):
AATATGCTTATAACATATC
Found at i:27489587 original size:54 final size:54
Alignment explanation
Indices: 27489482--27489587 Score: 140
Period size: 54 Copynumber: 2.0 Consensus size: 54
27489472 GCAATATGGC
* * *
27489482 ATGCTTTTAACAAACCAATACGGTAACAATTAATATGCTTATAACATATCAAAT
1 ATGCTTATAACAAACCAATACGGTAACAATTAATATGCTTATAAAAAATCAAAT
* * * * *
27489536 ATGCTTATAACGAATCAATATGGTAACAATTAATATGTTTGTAAAAAATCAA
1 ATGCTTATAACAAACCAATACGGTAACAATTAATATGCTTATAAAAAATCAA
27489588 TACAAGAGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (54 bp):
ATGCTTATAACAAACCAATACGGTAACAATTAATATGCTTATAAAAAATCAAAT
Found at i:27492547 original size:18 final size:18
Alignment explanation
Indices: 27492505--27492550 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
27492495 CTTTCTATAT
* **
27492505 ATATGTATATTTATTTTT
1 ATATATATATTTATTTCC
*
27492523 ATGTATATATTTATTTCC
1 ATATATATATTTATTTCC
27492541 ATATATATAT
1 ATATATATAT
27492551 ACGCATATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (18 bp):
ATATATATATTTATTTCC
Found at i:27494457 original size:23 final size:24
Alignment explanation
Indices: 27494404--27494457 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
27494394 CATGTGTTGC
*
27494404 ATATAAATATACATATTTAATTATTT
1 ATAT-AATAAACATATTT-ATTATTT
27494430 -T-TAATAAACATATTT-TTATTT
1 ATATAATAAACATATTTATTATTT
27494451 ATATAAT
1 ATATAAT
27494458 TAATGTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 6 0.24
22 1 0.04
23 16 0.64
24 1 0.04
25 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATAATAAACATATTTATTATTT
Found at i:27499234 original size:43 final size:44
Alignment explanation
Indices: 27499121--27499235 Score: 103
Period size: 44 Copynumber: 2.6 Consensus size: 44
27499111 GGAGATTTTG
* * * **
27499121 TGTAAGACCATGTCTGGGACGTTGGCATTATTTTGAGATTTATG
1 TGTAAGACCACGTCTGGGACTTTGGCATCATTTTGAGATTTACA
* * *
27499165 TGTAAGACC-CTGTCTGGGA-TAATGGCATCGTTATT-TGA-TTACA
1 TGTAAGACCAC-GTCTGGGACT-TTGGCATCATT-TTGAGATTTACA
27499208 TGTAAGACCACGTCTGGGACTTTGGCAT
1 TGTAAGACCACGTCTGGGACTTTGGCAT
27499236 TGTACGAGCT
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
43 26 0.46
44 29 0.51
45 2 0.04
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACTTTGGCATCATTTTGAGATTTACA
Found at i:27516211 original size:15 final size:14
Alignment explanation
Indices: 27516186--27516223 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
27516176 GTTTGCCAGT
27516186 AAAAT-ATTTTTCGG
1 AAAATGATTTTT-GG
27516200 AAAATGATTTTTGG
1 AAAATGATTTTTGG
27516214 AAAATGATTT
1 AAAATGATTT
27516224 ACTTTTCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (14 bp):
AAAATGATTTTTGG
Found at i:27516237 original size:19 final size:19
Alignment explanation
Indices: 27516215--27516252 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
27516205 GATTTTTGGA
27516215 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
27516234 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
27516253 TGTTTGGATG
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:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTGG
Found at i:27516354 original size:18 final size:18
Alignment explanation
Indices: 27516328--27516370 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
27516318 AAAAGCTGTT
*
27516328 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
27516346 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
27516364 TTTATAT
1 TTTATAT
27516371 TTTAAATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:27517583 original size:32 final size:32
Alignment explanation
Indices: 27517537--27517597 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
27517527 TATCAATCAT
27517537 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
* *
27517569 TTCAATATCTAACAAGCTTAAAGCATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
27517598 CAATATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:27517622 original size:27 final size:27
Alignment explanation
Indices: 27517570--27517624 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
27517560 CATAATAAAT
*
27517570 TCAATATCTAACAAGCTTAAAGCATAA
1 TCAATATCTAACAAGATTAAAGCATAA
*
27517597 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATTAAAG-CATAA
27517624 T
1 T
27517625 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.27
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAGCATAA
Found at i:27520798 original size:16 final size:16
Alignment explanation
Indices: 27520774--27520808 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27520764 AAAACTTTCT
27520774 TCACAACAACTACACA
1 TCACAACAACTACACA
*
27520790 TCACCACAACTACACA
1 TCACAACAACTACACA
27520806 TCA
1 TCA
27520809 AGATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (16 bp):
TCACAACAACTACACA
Found at i:27521748 original size:2 final size:2
Alignment explanation
Indices: 27521741--27521789 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
27521731 AATCCATGTT
27521741 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27521783 TA TA TA T
1 TA TA TA T
27521790 TAATTTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27521941 original size:28 final size:28
Alignment explanation
Indices: 27521899--27521953 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
27521889 ATATTATAAT
* *
27521899 AAAAATCCTAATTATTTTTAAAGTATTA
1 AAAAATCATAATTATTATTAAAGTATTA
*
27521927 AAAAATCATATTTATTATTAAAGTATT
1 AAAAATCATAATTATTATTAAAGTATT
27521954 TGTACAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (28 bp):
AAAAATCATAATTATTATTAAAGTATTA
Found at i:27522263 original size:17 final size:17
Alignment explanation
Indices: 27522241--27522280 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
27522231 AATTCTATCA
*
27522241 AAAAAATATTTAAAAAT
1 AAAAAATATATAAAAAT
*
27522258 AAAAAATATATAAAATT
1 AAAAAATATATAAAAAT
27522275 AAAAAA
1 AAAAAA
27522281 ATCTAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAAAATATATAAAAAT
Found at i:27522272 original size:16 final size:16
Alignment explanation
Indices: 27522241--27522305 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 16
27522231 AATTCTATCA
*
27522241 AAAAAATATTTAAAAAT
1 AAAAAATATAT-AAAAT
27522258 AAAAAATATATAAAATT
1 AAAAAATATATAAAA-T
*
27522275 AAAAAA-ATCTAAATAT
1 AAAAAATATATAAA-AT
*
27522291 ATAAAAT-TA-AAAAT
1 AAAAAATATATAAAAT
27522305 A
1 A
27522306 TATTTAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 17 0.41
17 18 0.44
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAATATATAAAAT
Found at i:27522279 original size:24 final size:24
Alignment explanation
Indices: 27522252--27522303 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
27522242 AAAAATATTT
27522252 AAAAATAAAAAATATATAAAATTAA
1 AAAAAT-AAAAATATATAAAATTAA
**
27522277 AAAAATCTAAATATATAAAATTAA
1 AAAAATAAAAATATATAAAATTAA
27522301 AAA
1 AAA
27522304 TATATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAATAAAAATATATAAAATTAA
Found at i:27527286 original size:23 final size:23
Alignment explanation
Indices: 27527256--27527304 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
27527246 ATTGCAAAGA
27527256 TCAAATTCGAATCGAGTAATAGG
1 TCAAATTCGAATCGAGTAATAGG
27527279 TCAAATTCGAATCGAGTAATAGG
1 TCAAATTCGAATCGAGTAATAGG
27527302 TCA
1 TCA
27527305 TGATTACCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (23 bp):
TCAAATTCGAATCGAGTAATAGG
Found at i:27532935 original size:19 final size:20
Alignment explanation
Indices: 27532902--27532939 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
27532892 TTGTTAAAAG
*
27532902 TAAAAATCATTAAAATTATT
1 TAAAAATCATAAAAATTATT
27532922 TAAAAAT-ATAAAAATTAT
1 TAAAAATCATAAAAATTAT
27532940 AAAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATCATAAAAATTATT
Found at i:27538241 original size:16 final size:15
Alignment explanation
Indices: 27538222--27538251 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
27538212 TTCATTAAAA
27538222 AAATTATTTAGATTTT
1 AAATTATTTA-ATTTT
27538238 AAATTATTTAATTT
1 AAATTATTTAATTT
27538252 CTTTTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
AAATTATTTAATTTT
Found at i:27547779 original size:5 final size:5
Alignment explanation
Indices: 27547763--27547801 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
27547753 GCCTAAGATG
* *
27547763 TGAAT TGGAT TGAAT TGAAT ATGAAT TGTAT TGAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
27547802 GCTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:27551487 original size:25 final size:25
Alignment explanation
Indices: 27551449--27551496 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
27551439 TACAGCCCGA
27551449 ATAAGCTTTCCATTAAATGGCTCAT
1 ATAAGCTTTCCATTAAATGGCTCAT
*
27551474 ATAAGC-TTCTCATTATATGGCTC
1 ATAAGCTTTC-CATTAAATGGCTC
27551497 GAGAGATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (25 bp):
ATAAGCTTTCCATTAAATGGCTCAT
Found at i:27556020 original size:31 final size:32
Alignment explanation
Indices: 27555964--27556024 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
27555954 TATAAAATGA
*
27555964 TCACACAACTATTTGACTTTTTTCTTTTTTGG
1 TCACACAACTATTTGACATTTTTCTTTTTTGG
*
27555996 TCACCCAACTATTTGA-ATTTTTCTTTTTT
1 TCACACAACTATTTGACATTTTTCTTTTTT
27556025 AGTTATCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.54
Consensus pattern (32 bp):
TCACACAACTATTTGACATTTTTCTTTTTTGG
Found at i:27564479 original size:18 final size:20
Alignment explanation
Indices: 27564456--27564499 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
27564446 TACTTTAATA
27564456 TTTATGCAA-ATAATTG-TT
1 TTTATGCAATATAATTGATT
* *
27564474 TTTATGGAATATTATTGATT
1 TTTATGCAATATAATTGATT
27564494 TTTATG
1 TTTATG
27564500 AAGCAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTATGCAATATAATTGATT
Found at i:27575486 original size:30 final size:30
Alignment explanation
Indices: 27575452--27575514 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
27575442 GTAAGGAAAG
*
27575452 TAGTGGAGGATGATAATCGATGGGCTGAGA
1 TAGTGGAGGATGATAATCGATAGGCTGAGA
27575482 TAGTGGAGGATGATAATCGATAGGCTGAGA
1 TAGTGGAGGATGATAATCGATAGGCTGAGA
27575512 TAG
1 TAG
27575515 GGCATCTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.38, T:0.24
Consensus pattern (30 bp):
TAGTGGAGGATGATAATCGATAGGCTGAGA
Found at i:27577508 original size:29 final size:28
Alignment explanation
Indices: 27577462--27577518 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
27577452 TTCTCGTAAA
* * *
27577462 TTAAAAAAAAGTCTATTTTTGTAATATTT
1 TTAAAAAAAAGACCATTTTT-TAAAATTT
*
27577491 TTAAAAAAATGACCATTTTTTAAAATTT
1 TTAAAAAAAAGACCATTTTTTAAAATTT
27577519 AATCAGAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (28 bp):
TTAAAAAAAAGACCATTTTTTAAAATTT
Found at i:27579301 original size:43 final size:43
Alignment explanation
Indices: 27579149--27579344 Score: 265
Period size: 42 Copynumber: 4.6 Consensus size: 43
27579139 AAACGTTTGT
* *
27579149 GGCG-TTTTTTCCTACAAACGCCGCTATAGATCATGAACTTTAGC
1 GGCGCTTTTTT-C-ACAAACGCCGCTATAGATCAAGACCTTTAGC
* * * * *
27579193 GGCGC-TTTTACACAAACCCCGCTATAGCTCAGGATCTTTAGC
1 GGCGCTTTTTTCACAAACGCCGCTATAGATCAAGACCTTTAGC
27579235 GGCGCTTTTTT-ACAAACGCCGCTATAGATCAAGACCTTTAGC
1 GGCGCTTTTTTCACAAACGCCGCTATAGATCAAGACCTTTAGC
27579277 GGCGCTTTTTTCACAAACGCCGCTATAGATCAAGACCTTTAGC
1 GGCGCTTTTTTCACAAACGCCGCTATAGATCAAGACCTTTAGC
*
27579320 GGCGCTTTGATT-ACAAACGCCGCTA
1 GGCGCTTT-TTTCACAAACGCCGCTA
27579345 AAAGTACCGT
Statistics
Matches: 137, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
42 70 0.51
43 57 0.42
44 10 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (43 bp):
GGCGCTTTTTTCACAAACGCCGCTATAGATCAAGACCTTTAGC
Found at i:27585092 original size:16 final size:17
Alignment explanation
Indices: 27585056--27585097 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
27585046 CACTATAATC
27585056 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
27585074 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
27585090 ATTATTTA
1 ATTATTTA
27585098 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:27585221 original size:14 final size:14
Alignment explanation
Indices: 27585204--27585419 Score: 107
Period size: 14 Copynumber: 15.4 Consensus size: 14
27585194 ACTAATTAAT
*
27585204 CTAAACCCTAAATC
1 CTAAACCCTAAACC
*
27585218 CTAAATCCTAAACCC
1 CTAAACCCTAAA-CC
* *
27585233 CT-AACTCTTAACC
1 CTAAACCCTAAACC
* *
27585246 CTCAACCCCTAACCC
1 CT-AAACCCTAAACC
27585261 CT-AACTCCTAAACC
1 CTAAAC-CCTAAACC
* *
27585275 TTAAACCC-CAACC
1 CTAAACCCTAAACC
* *
27585288 CTTAA-TCTATAACC
1 CTAAACCCTA-AACC
* *
27585302 TTAAACCATAAACC
1 CTAAACCCTAAACC
* *
27585316 GTAACCCCTAAACC
1 CTAAACCCTAAACC
27585330 CTAAACCCTAAACC
1 CTAAACCCTAAACC
* * *
27585344 TTAAACCATAAACT
1 CTAAACCCTAAACC
* * *
27585358 GTAAACCATAACCC
1 CTAAACCCTAAACC
* *
27585372 CTAAAACCATAATCC
1 CT-AAACCCTAAACC
* * *
27585387 ATAAACCTTAAACT
1 CTAAACCCTAAACC
* * *
27585401 CTATACCATATACC
1 CTAAACCCTAAACC
27585415 CTAAA
1 CTAAA
27585420 TCAAAAACCT
Statistics
Matches: 149, Mismatches: 44, Indels: 18
0.71 0.21 0.09
Matches are distributed among these distances:
12 1 0.01
13 13 0.09
14 106 0.71
15 29 0.19
ACGTcount: A:0.41, C:0.37, G:0.01, T:0.22
Consensus pattern (14 bp):
CTAAACCCTAAACC
Found at i:27585279 original size:7 final size:7
Alignment explanation
Indices: 27585269--27585399 Score: 61
Period size: 7 Copynumber: 18.7 Consensus size: 7
27585259 CCCTAACTCC
27585269 TAAACCT
1 TAAACCT
*
27585276 TAAACCC
1 TAAACCT
* *
27585283 CAACCCT
1 TAAACCT
*
27585290 T-AATCT
1 TAAACCT
27585296 ATA-ACCT
1 -TAAACCT
*
27585303 TAAACCA
1 TAAACCT
*
27585310 TAAACCG
1 TAAACCT
* *
27585317 TAACCCC
1 TAAACCT
*
27585324 TAAACCC
1 TAAACCT
*
27585331 TAAACCC
1 TAAACCT
27585338 TAAACCT
1 TAAACCT
*
27585345 TAAACCA
1 TAAACCT
27585352 TAAA-CT
1 TAAACCT
*
27585358 GTAAACCA
1 -TAAACCT
*
27585366 TAACCCCT
1 TAA-ACCT
* *
27585374 AAAACCA
1 TAAACCT
* *
27585381 TAATCCA
1 TAAACCT
27585388 TAAACCT
1 TAAACCT
27585395 TAAAC
1 TAAAC
27585400 TCTATACCAT
Statistics
Matches: 92, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
6 6 0.07
7 81 0.88
8 5 0.05
ACGTcount: A:0.44, C:0.34, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAACCT
Found at i:27585409 original size:21 final size:21
Alignment explanation
Indices: 27585284--27585419 Score: 89
Period size: 21 Copynumber: 6.4 Consensus size: 21
27585274 CTTAAACCCC
* *
27585284 AACCCTTAA-TCTATAACCTTA
1 AACCCTAAACTCTA-AACCATA
* * *
27585305 AACCATAAAC-CGTAACCCCTA
1 AACCCTAAACTC-TAAACCATA
* *
27585326 AACCCTAAACCCTAAACCTTA
1 AACCCTAAACTCTAAACCATA
* *
27585347 AACCATAAACTGTAAACCATA
1 AACCCTAAACTCTAAACCATA
* *
27585368 ACCCCTAAAAC-CATAATCCATA
1 AACCCT-AAACTC-TAAACCATA
* *
27585390 AACCTTAAACTCTATACCATA
1 AACCCTAAACTCTAAACCATA
*
27585411 TACCCTAAA
1 AACCCTAAA
27585420 TCAAAAACCT
Statistics
Matches: 88, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
21 68 0.77
22 20 0.23
ACGTcount: A:0.44, C:0.32, G:0.01, T:0.22
Consensus pattern (21 bp):
AACCCTAAACTCTAAACCATA
Found at i:27585828 original size:41 final size:41
Alignment explanation
Indices: 27585741--27585858 Score: 209
Period size: 41 Copynumber: 2.9 Consensus size: 41
27585731 AAATGTTTTT
*
27585741 GCGGCGCTTTTACAAAAACGCCGCTAAAGCCCCTGAGCATTA
1 GCGGCGCTTCTACAAAAACGCCGCTAAAG-CCCTGAGCATTA
*
27585783 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGAGCATTA
27585824 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGA
1 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGA
27585859 AAGGTGAGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 46 0.63
42 27 0.37
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (41 bp):
GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:27585986 original size:40 final size:40
Alignment explanation
Indices: 27585950--27586026 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
27585940 GCGTTTTCCT
*
27585950 TAAAGCGCCGCTAGTGCTCGATCTTTAGCGGCGTTTTATA
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTATA
*
27585990 TAAAGCGCCGCTAATGCTCGATTTTTAGCGGCGTTTT
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTT
27586027 TTATGCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (40 bp):
TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTATA
Found at i:27587172 original size:24 final size:24
Alignment explanation
Indices: 27587127--27587173 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
27587117 TATTTATACC
27587127 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
27587151 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
27587174 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:27587893 original size:14 final size:15
Alignment explanation
Indices: 27587876--27587905 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27587866 GCTCTGTTTC
27587876 TTTC-TTTATTTCTT
1 TTTCTTTTATTTCTT
27587890 TTTCTTTTATTTCTT
1 TTTCTTTTATTTCTT
27587905 T
1 T
27587906 GTTTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTATTTCTT
Found at i:27589841 original size:2 final size:2
Alignment explanation
Indices: 27589834--27589901 Score: 120
Period size: 2 Copynumber: 34.0 Consensus size: 2
27589824 NNNNNNNNNN
27589834 AT AT AT AT AT AT AT AT AT AT -T AGT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
27589876 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
27589902 TATTAGATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 61 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27589911 original size:14 final size:13
Alignment explanation
Indices: 27589834--27589911 Score: 101
Period size: 12 Copynumber: 6.2 Consensus size: 13
27589824 NNNNNNNNNN
27589834 ATATATA-TATAT
1 ATATATATTATAT
27589846 ATATATATTAGTAT
1 ATATATATTA-TAT
27589860 ATATATA-TATAT
1 ATATATATTATAT
27589872 ATATATA-TATAT
1 ATATATATTATAT
27589884 ATATATA-TATAT
1 ATATATATTATAT
*
27589896 ATATATTATTAGAT
1 ATATA-TATTATAT
27589910 AT
1 AT
27589912 TCAAACTATT
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
12 39 0.64
13 6 0.10
14 16 0.26
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:27590705 original size:6 final size:6
Alignment explanation
Indices: 27590694--27590720 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27590684 CAAATCCAGT
27590694 AATTAA AATTAA AATTAA AATTAA AAT
1 AATTAA AATTAA AATTAA AATTAA AAT
27590721 CTGAATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTAA
Found at i:27591008 original size:34 final size:35
Alignment explanation
Indices: 27590940--27591009 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
27590930 AAGCCTAAAT
* *
27590940 ATGCCCGGGCCCAAATAAATATACAAAACCCAATA
1 ATGCCCGGGCCCAAACAAATAAACAAAACCCAATA
*
27590975 ATGCCCGGGCCCAAACCAATAAAC-AAACCCAATA
1 ATGCCCGGGCCCAAACAAATAAACAAAACCCAATA
27591009 A
1 A
27591010 CATCCTGGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.46, C:0.31, G:0.11, T:0.11
Consensus pattern (35 bp):
ATGCCCGGGCCCAAACAAATAAACAAAACCCAATA
Found at i:27592291 original size:24 final size:24
Alignment explanation
Indices: 27592253--27592301 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
27592243 CACACGCATC
*
27592253 TTTTTTATAGTATACCTATACATA
1 TTTTTTATAGTATACATATACATA
*
27592277 TTTTTTAT-GTAATACATATATATA
1 TTTTTTATAGT-ATACATATACATA
27592301 T
1 T
27592302 ATATCCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTTTTATAGTATACATATACATA
Found at i:27594256 original size:13 final size:13
Alignment explanation
Indices: 27594238--27594263 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27594228 AAAGAGATTT
27594238 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
27594251 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
27594264 AATTGAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:27594332 original size:19 final size:20
Alignment explanation
Indices: 27594295--27594334 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
27594285 TCTTTTCGCA
* *
27594295 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
27594315 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
27594334 T
1 T
27594335 AAACACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:27597160 original size:7 final size:7
Alignment explanation
Indices: 27597148--27597210 Score: 91
Period size: 7 Copynumber: 9.7 Consensus size: 7
27597138 AAGTGATGTA
27597148 GAAAAAT
1 GAAAAAT
27597155 G-AAAA-
1 GAAAAAT
27597160 -AAAAAT
1 GAAAAAT
27597166 G-AAAAT
1 GAAAAAT
27597172 GAAAAAT
1 GAAAAAT
27597179 GAAAAAT
1 GAAAAAT
27597186 GAAAAAT
1 GAAAAAT
27597193 GAAAAAT
1 GAAAAAT
27597200 GAAAAAT
1 GAAAAAT
27597207 -AAAA
1 GAAAA
27597211 TGGAGAGGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
5 4 0.08
6 14 0.27
7 34 0.65
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
GAAAAAT
Found at i:27598637 original size:89 final size:89
Alignment explanation
Indices: 27598466--27599422 Score: 1237
Period size: 89 Copynumber: 10.7 Consensus size: 89
27598456 GAGCAGGTTG
* * * * *
27598466 AAAGATAACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATCAGAGAT-ACAGGTCTTGCCTT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGTCTT
*
27598530 CCCATACTGGTGGCGAAGCAGATC
66 CCCATACTGGTGGCGAAGTAGATC
** * *
27598554 AAAGAAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACATATCTTGCCTT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGTCTT
* *
27598619 CCCATACTGGTGGCGAAGCAGATT
66 CCCATACTGGTGGCGAAGTAGATC
* * *
27598643 GAAGAAAACAGATCTTGTCTTTATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGTCTT
*
27598708 CCCATACTGGTGGCGAAGTATATC
66 CCCATACTGGTGGCGAAGTAGATC
* * * * * *
27598732 GAAGGAAAAAACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATCAAAGAT-ACAGGTCTTGC
1 -AA--AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGT
*
27598796 CTTCCCATACTGGTGGCGAAGCAGATC
63 CTTCCCATACTGGTGGCGAAGTAGATC
* * *
27598823 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACATATCTTGCCTT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGTCTT
*
27598888 CCCATACTGGTGGCGAAGCAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* * *
27598912 GAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGTCTT
*
27598977 CCCATACTGGTGGCGAAGTAGATTG
66 CCCATACTGGTGGCGAAGTAGA-TC
* * * *
27599002 AAGGAAAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTATC
1 AA--AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGTC
27599067 TTCCCATACTGGTGGCGAAGTAGATC
64 TTCCCATACTGGTGGCGAAGTAGATC
* * *
27599093 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGTCTT
27599158 CCCATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* * *
27599182 GAAGAAAACAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATC-GAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAG-AGATAACAGATCTTGTCT
*** *
27599246 TCATGTACTGGT-GTGAAGTAGATC
65 TCCCATACTGGTGGCGAAGTAGATC
*** * * * *
27599270 AAAGAAAACAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATC-GA-AGAACAGATCTTATCT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAGAGATAACAGATCTTGTCT
*** * * *
27599333 TCATGTATTGG-CGTGAAGTAGATC
65 TCCCATACTGGTGGCGAAGTAGATC
* *
27599357 AAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGAAAACAGATCTTGTCT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAG-AGATAACAGATCTTGTCT
27599421 TC
65 TC
27599423 ATGTATTGGC
Statistics
Matches: 784, Mismatches: 72, Indels: 26
0.89 0.08 0.03
Matches are distributed among these distances:
86 13 0.02
87 65 0.08
88 142 0.18
89 396 0.51
90 5 0.01
91 36 0.05
92 127 0.16
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (89 bp):
AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGTCTT
CCCATACTGGTGGCGAAGTAGATC
Found at i:27598951 original size:269 final size:269
Alignment explanation
Indices: 27598472--27599422 Score: 1358
Period size: 269 Copynumber: 3.6 Consensus size: 269
27598462 GTTGAAAGAT
* * *
27598472 AACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATCAGAGATACAGGTCTTGCCTTCCCATAC
1 AACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATCAAAGATACAGATCTTACCTTCCCATAC
**
27598537 TGGTGGCGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAG
66 TGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAG
* * * *
27598602 ATAACATATCTTGCCTTCCCATACTGGTGGCGAAGCAGATTGAAGAAAACAGATCTTGTCTTTAT
131 AAAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCAT
*
27598667 GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTATATC
196 GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
27598732 GAAGGAAAA
261 GAAGGAAAA
* *
27598741 AACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATCAAAGATACAGGTCTTGCCTTCCCATAC
1 AACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATCAAAGATACAGATCTTACCTTCCCATAC
*
27598806 TGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAG
66 TGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAG
* * *
27598871 ATAACATATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAATAGATCTTGTCTTCAT
131 AAAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCAT
*
27598936 GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATT
196 GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
27599001 GAAGGAAAA
261 GAAGGAAAA
* * * *
27599010 AATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTATCTTCCCATA
1 AACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATCAAAGAT-ACAGATCTTACCTTCCCATA
* * *
27599075 CTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAA
65 CTGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGA
* *
27599140 GAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCA
130 GAAAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCA
* * * *** *
27599205 TGTACTGGTGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGT-GTGAAGTAGAT
195 TGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
*
27599269 C-AA--AGAA
260 CGAAGGAAAA
*** * ** * * * ***
27599276 AACAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGA-ACAGATCTTATCTTCATGTA
1 AACAGATCTTGTCTTCATGTACT-GACGTAAAGTAGATCAAAGATACAGATCTTACCTTCCCATA
* * * * *
27599340 TTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GA
65 CTGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAG-
*
27599403 AGAAAACAGATCTTGTCTTC
129 AGAAAACAGATCTTGCCTTC
27599423 ATGTATTGGC
Statistics
Matches: 631, Mismatches: 48, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
264 73 0.12
265 20 0.03
266 21 0.03
267 17 0.03
268 2 0.00
269 313 0.50
270 185 0.29
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (269 bp):
AACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATCAAAGATACAGATCTTACCTTCCCATAC
TGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAG
AAAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATCTTGTCTTCAT
GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
GAAGGAAAA
Found at i:27599069 original size:44 final size:44
Alignment explanation
Indices: 27598466--27599460 Score: 927
Period size: 44 Copynumber: 22.4 Consensus size: 44
27598456 GAGCAGGTTG
* * *
27598466 AAAGATAACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * * * *** * * *
27598510 AGAG-ATACAGGTCTTGCCTTCCCATACTGGTGGCGAAGCAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
**
27598554 AAAGAAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * * * *** * * * *
27598598 AGAGATAACATATCTTGCCTTCCCATACTGGTGGCGAAGCAGATT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
* *
27598643 GAAGAAAACAGATCTTGTCTTTATGTACTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* *** * * *
27598687 AAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTATATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
* * *
27598732 GAAGGAAAAAACAGATCTTGTCTTCATGTACTGACGTAAAGTAGATC
1 -AA--AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * * *** * * *
27598779 AAAG-ATACAGGTCTTGCCTTCCCATACTGGTGGCGAAGCAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
*
27598823 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * * * *** * * *
27598867 AGAGATAACATATCTTGCCTTCCCATACTGGTGGCGAAGCAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
* *
27598912 GAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* *** * * *
27598956 AAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTG
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGA-TC
* *
27599002 AAGGAAAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
1 AA--AGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* * *** * *
27599048 AAAGATAACAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
*
27599093 GAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
*** * *
27599137 AAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
* *
27599182 GAAGAAAACAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* *
27599226 GAAGAAAACAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
*** * *
27599270 AAAGAAAACAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
* * *
27599315 GAAG--AACAGATCTTATCTTCATGTATTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
*
27599357 AAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* *
27599401 GAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
* **
27599445 GAAGATTACAGATCTT
1 AAAGAAAACAGATCTT
27599461 ATCTCCCTAA
Statistics
Matches: 753, Mismatches: 179, Indels: 38
0.78 0.18 0.04
Matches are distributed among these distances:
42 15 0.02
43 58 0.08
44 398 0.53
45 208 0.28
46 10 0.01
47 18 0.02
48 46 0.06
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (44 bp):
AAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
Found at i:27599488 original size:44 final size:44
Alignment explanation
Indices: 27599437--27599908 Score: 243
Period size: 44 Copynumber: 10.7 Consensus size: 44
27599427 ATTGGCGTGA
*
27599437 AGTAGATCGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* * ** * * *
27599481 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGAG--GTTACAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG-T--AGTGG
* * * * ** *
27599526 AGTACATTGAAG-CTAGTA-AT-TCTATCTTCCTGGGCAGCAGTGG
1 AGTAGATTGAAGATTA-CAGATCT-TATCTCCCTAAGCAGTAGTGG
* *
27599569 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* * ** * * * **
27599613 AGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGGTAACAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAA-GCAGTAGTGG
* * * ** *
27599658 AGTACATTGAAGCCATTA-A-TTC-TATTTCCCTGGGCAGCAGTGG
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAGTAGTGG
*
27599701 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* * * * * * **
27599745 AGCAGATCGAAGATGGA-GGATTTTACCTCCCT--GTGGTTACAGTGG
1 AGTAGATTGAAGAT-TACAGATCTTATCTCCCTAAGCAG-T--AGTGG
* * * * *
27599790 AGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTAGGCAGCAGTGG
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* * *
27599833 AATAGATTGAAGATTATAGATCTTATCTCCCTAGGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* * * *
27599877 AGTAGATCGAAGATGACAGATTTTACCTCCCT
1 AGTAGATTGAAGATTACAGATCTTATCTCCCT
27599909 GAGGTTACAG
Statistics
Matches: 314, Mismatches: 87, Indels: 54
0.69 0.19 0.12
Matches are distributed among these distances:
41 7 0.02
42 5 0.02
43 56 0.18
44 188 0.60
45 50 0.16
46 5 0.02
47 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
Found at i:27599951 original size:44 final size:45
Alignment explanation
Indices: 27599771--27599967 Score: 126
Period size: 44 Copynumber: 4.5 Consensus size: 45
27599761 AGGATTTTAC
* *
27599771 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA-AT-TCTAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGCAGATCT-TAT
* * * ** *
27599815 CTCCCT-AGG-CAGCAGTGGAATAGATTGAAGATTA-TAGATCTTAT
1 CTCCCTGAGGTTA-CAGTGGAGTACATTGAAG-CCAGCAGATCTTAT
* * * * * *
27599859 CTCCCT-AGG-CAGTAGTGGAGTAGATCGAAG--ATGACAGATTTTAC
1 CTCCCTGAGGTTA-CAGTGGAGTACATTGAAGCCA-G-CAGATCTTAT
27599903 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGCAG-TCTTAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGCAGATCTTAT
* *
27599947 CTCCCTGAAGTTGCAGTGGAG
1 CTCCCTGAGGTTACAGTGGAG
27599968 CAGATTAAAG
Statistics
Matches: 122, Mismatches: 20, Indels: 22
0.74 0.12 0.13
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 20 0.16
44 75 0.61
45 22 0.18
46 2 0.02
47 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (45 bp):
CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGCAGATCTTAT
Found at i:27599952 original size:132 final size:132
Alignment explanation
Indices: 27599439--27599937 Score: 838
Period size: 132 Copynumber: 3.8 Consensus size: 132
27599429 TGGCGTGAAG
* *
27599439 TAGATCGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATTT
* *
27599504 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTATCTTCCTGGGCAGCAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
27599569 AA
131 AA
* *
27599571 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATTT
* * * *
27599636 TACCTCCCTAAGGTAACAGTGGAGTACATTGAAGCCATTAATTCTATTTCCCTGGGCAGCAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
27599701 AA
131 AA
*
27599703 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGA-GGATT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT-GACAGATT
* *
27599767 TTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAGCAGTG
65 TTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTG
27599832 GAA
130 GAA
* * *
27599835 TAGATTGAAGATTATAGATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGACAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATTT
27599900 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAG
27599938 CAGTCTTATC
Statistics
Matches: 343, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 2 0.01
132 340 0.99
133 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATTT
TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
AA
Found at i:27600294 original size:34 final size:35
Alignment explanation
Indices: 27600226--27600295 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
27600216 AAGTCCAAAT
* *
27600226 ATGCCCGGGCCCAAATAAATATACAAAACCCAATA
1 ATGCCCGGGCCCAAACAAATAAACAAAACCCAATA
*
27600261 ATGCCCGGGCCCAAACCAATAAAC-AAACCCAATA
1 ATGCCCGGGCCCAAACAAATAAACAAAACCCAATA
27600295 A
1 A
27600296 CATCCTGGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.46, C:0.31, G:0.11, T:0.11
Consensus pattern (35 bp):
ATGCCCGGGCCCAAACAAATAAACAAAACCCAATA
Found at i:27601496 original size:24 final size:24
Alignment explanation
Indices: 27601458--27601506 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
27601448 CACACGCATC
*
27601458 TTTTTTATAGTATACCTATACATA
1 TTTTTTATAGTATACATATACATA
*
27601482 TTTTTTAT-GTAATACATATATATA
1 TTTTTTATAGT-ATACATATACATA
27601506 T
1 T
27601507 ATCCATAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTTTTATAGTATACATATACATA
Found at i:27601644 original size:34 final size:35
Alignment explanation
Indices: 27601591--27601680 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 35
27601581 CTTTTATATA
* * *
27601591 TTTTATATTTTATAGATATATACATATACA-TTTC
1 TTTTATATTGTAAATATATATACATATACATTTTC
* *
27601625 TTTTATATTGTAAATATATATACTTATACATTTTT
1 TTTTATATTGTAAATATATATACATATACATTTTC
*
27601660 TTTCTATTTTGTAAATATATA
1 TTT-TATATTGTAAATATATA
27601681 CCCATGTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
34 26 0.54
35 6 0.12
36 16 0.33
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (35 bp):
TTTTATATTGTAAATATATATACATATACATTTTC
Found at i:27608877 original size:154 final size:149
Alignment explanation
Indices: 27608688--27609003 Score: 455
Period size: 149 Copynumber: 2.1 Consensus size: 149
27608678 TAGTGTGTTT
* *
27608688 AAAAAATACAAACAAAAGGCCGAAATAAGGATTTTTTTTAAATTTATTTAAAAAACACATTAAAT
1 AAAAAATACAAACAAAAAGCCGAAATAAGGA---TTTTT-AATTTATTTAAAAAA-ACACTAAAT
*
27608753 TAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATATGAAAATAATATATTT
61 TAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATATGAAAATAATATATTT
27608818 TTATTGAAAATAATAAAATTCGGA
126 TTATTGAAAATAATAAAATTCGGA
* * * *
27608842 AAAAAATACGAATAAAAAGTCGAAATAAGGGTTTTTAATTTATTTAAAAAAACACTAAATTAATA
1 AAAAAATACAAACAAAAAGCCGAAATAAGGATTTTTAATTTATTTAAAAAAACACTAAATTAATA
27608907 CATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATATGAAAATAATATATTTGTTA-
66 CATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATATGAAAATAATATATTT-TTAT
*
27608971 --AAAGTAATAAAATT---A
130 TGAAAATAATAAAATTCGGA
*
27608986 AAAAAATGCAAACAAAAA
1 AAAAAATACAAACAAAAA
27609004 ATCAAAATAG
Statistics
Matches: 150, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
144 16 0.11
147 13 0.09
149 72 0.48
150 18 0.12
151 5 0.03
154 26 0.17
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (149 bp):
AAAAAATACAAACAAAAAGCCGAAATAAGGATTTTTAATTTATTTAAAAAAACACTAAATTAATA
CATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATATGAAAATAATATATTTTTATT
GAAAATAATAAAATTCGGA
Found at i:27608958 original size:16 final size:15
Alignment explanation
Indices: 27608932--27608961 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
27608922 GTACTAAAAT
27608932 AATATAAAATAATAA
1 AATATAAAATAATAA
27608947 AATATGAAAATAATA
1 AATAT-AAAATAATA
27608962 TATTTGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:27609257 original size:30 final size:30
Alignment explanation
Indices: 27609217--27609284 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
27609207 ACCAATAAAA
*
27609217 GCCG-TTTTTTTCAAAATTTATCGAAATGG
1 GCCGATTTTTTTCAAAATTTACCGAAATGG
* ** *
27609246 GCCGATTTTTTTTATTATTTACCGGAATGG
1 GCCGATTTTTTTCAAAATTTACCGAAATGG
27609276 GCC-ATTTTT
1 GCCGATTTTT
27609285 CGCGAAATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.46
Consensus pattern (30 bp):
GCCGATTTTTTTCAAAATTTACCGAAATGG
Found at i:27612286 original size:15 final size:15
Alignment explanation
Indices: 27612268--27612297 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27612258 TCCTTTTATT
27612268 TATTTATGGGTTAGA
1 TATTTATGGGTTAGA
27612283 TATTTATGGGTTAGA
1 TATTTATGGGTTAGA
27612298 AGGAGTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (15 bp):
TATTTATGGGTTAGA
Found at i:27614585 original size:44 final size:44
Alignment explanation
Indices: 27614356--27614596 Score: 200
Period size: 43 Copynumber: 5.6 Consensus size: 44
27614346 AATGCTATAT
* * **
27614356 CCAGATATGGTCTTACATGTTATCAC--ATATCGATGCCAATAGC
1 CCAGCTATGGTCTTACACGAAATCACATATATCGATGCC-ATAGC
27614399 CCAGCTATGGTCTTACACG-AAT--CATATATCGATGCCA-ATGTC
1 CCAGCTATGGTCTTACACGAAATCACATATATCGATGCCATA-G-C
* *
27614441 CCAGAC-ATAGTCTTACACGAAATCACATA-A-AGATGCCA-ATGTC
1 CCAG-CTATGGTCTTACACGAAATCACATATATCGATGCCATA-G-C
* * *
27614484 CTAGAC-ATGGTCTTACACGTAATCACATATATCGATGCCATATC
1 CCAG-CTATGGTCTTACACGAAATCACATATATCGATGCCATAGC
** * *
27614528 CCATATATAGTCTTACAC-AAAGTCTCATATATCGATGCCATAGC
1 CCAGCTATGGTCTTACACGAAA-TCACATATATCGATGCCATAGC
*
27614572 CCAGCTATGGTCTTATACGAAATCA
1 CCAGCTATGGTCTTACACGAAATCA
27614597 TGTAATGCCA
Statistics
Matches: 162, Mismatches: 22, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 30 0.19
43 61 0.38
44 52 0.32
45 14 0.09
46 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (44 bp):
CCAGCTATGGTCTTACACGAAATCACATATATCGATGCCATAGC
Found at i:27618624 original size:32 final size:32
Alignment explanation
Indices: 27618588--27618651 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
27618578 AACGTCATGT
27618588 TTATCACGGATGTAATGCAATGTTATCAAAAC
1 TTATCACGGATGTAATGCAATGTTATCAAAAC
27618620 TTATCACGGATGTAATGCAATGTTATCAAAAC
1 TTATCACGGATGTAATGCAATGTTATCAAAAC
27618652 AGTCTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (32 bp):
TTATCACGGATGTAATGCAATGTTATCAAAAC
Found at i:27619399 original size:18 final size:17
Alignment explanation
Indices: 27619373--27619425 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
27619363 TGGGTAATTT
27619373 TCGGGTAATTCGGTTAA
1 TCGGGTAATTCGGTTAA
*
27619390 CTCGGTTAATTCGGTTAA
1 -TCGGGTAATTCGGTTAA
*
27619408 TCGGGTAATTCGGGTAA
1 TCGGGTAATTCGGTTAA
27619425 T
1 T
27619426 TTGAGTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 16 0.50
18 16 0.50
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (17 bp):
TCGGGTAATTCGGTTAA
Found at i:27619420 original size:9 final size:9
Alignment explanation
Indices: 27619372--27619426 Score: 67
Period size: 9 Copynumber: 6.2 Consensus size: 9
27619362 TTGGGTAATT
27619372 TTCGGGTAA
1 TTCGGGTAA
*
27619381 TTCGGTTAA
1 TTCGGGTAA
* *
27619390 CTCGGTTAA
1 TTCGGGTAA
*
27619399 TTCGGTTAA
1 TTCGGGTAA
27619408 -TCGGGTAA
1 TTCGGGTAA
27619416 TTCGGGTAA
1 TTCGGGTAA
27619425 TT
1 TT
27619427 TGAGTAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
8 7 0.17
9 34 0.83
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:27621383 original size:15 final size:16
Alignment explanation
Indices: 27621363--27621400 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
27621353 TTTTAAACCT
27621363 ATAATTTAA-TAAAAA
1 ATAATTTAACTAAAAA
*
27621378 ATAA-TTAACTCAAAA
1 ATAATTTAACTAAAAA
27621393 ATAATTTA
1 ATAATTTA
27621401 TGCTTATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 4 0.20
15 13 0.65
16 3 0.15
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATTTAACTAAAAA
Found at i:27622639 original size:127 final size:125
Alignment explanation
Indices: 27622341--27622908 Score: 721
Period size: 126 Copynumber: 4.5 Consensus size: 125
27622331 GATAAAATCA
* * * ** * * *
27622341 AAGCAGGATGATTTATCAAAAGGCTTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
27622406 AGATCTTGGAAAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCTTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAATGCTTC
* * * * * *
27622466 AAGCATGATGCTTTATGAGAAGAACTTATGAAATCGCGTCCTCGTGGACGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
27622531 TGGTCTTGGAAAAAATAATTTCGAATTGACGTTTCTGAGCAAATAGTTTAAAAAAATGCTTC
66 AGGTCTTGG-AAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTT-AAAAAATGCTTC
*
27622593 AAGCAGGACGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
27622658 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATAATGCTGC
66 AGGTCTTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAA-AATGCTTC
* * * * *
27622719 AAGTAGAATGCTATT-TGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAA
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * *
27622783 TAGGTCTTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAATAG--TATAAAATCGCTTC
65 TAGGTCTTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAT-GCTTC
* * * * * *
27622843 TAGTAGGATGTTTTATGAGAAGAATTTGTGAAATCACGCCCACGTGGA-GCGATTTTGCTATAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
27622907 AG
66 AG
27622909 CATGTTTGGG
Statistics
Matches: 387, Mismatches: 50, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
123 20 0.05
124 49 0.13
125 63 0.16
126 178 0.46
127 77 0.20
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCTTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAATGCTTC
Found at i:27626133 original size:16 final size:17
Alignment explanation
Indices: 27626112--27626149 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
27626102 GGGTTTTTAA
27626112 TTTAAGG-GTTAGGGTT
1 TTTAAGGTGTTAGGGTT
*
27626128 TTTAAGGTTTTAGGGTT
1 TTTAAGGTGTTAGGGTT
27626145 TTTAA
1 TTTAA
27626150 TTTAAGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (17 bp):
TTTAAGGTGTTAGGGTT
Found at i:27626143 original size:38 final size:38
Alignment explanation
Indices: 27626023--27626183 Score: 160
Period size: 38 Copynumber: 4.0 Consensus size: 38
27626013 TCAAATTATA
* *
27626023 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGTGTTAGGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAG----GTTTTAGGGTT
* * ** *
27626065 TTTTATTTAATGGTTACAGTTTTAAAGTAAGGGTTTAGGGTT
1 TTTAATTTAAGGGTTAGGGTTTT----TAAGGTTTTAGGGTT
27626107 TTTAATTTAAGGGTTAGGGTTTTTAAGGTTTTAGGGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGGTTTTAGGGTT
* * *
27626145 TTTAATTTAAGGATTAAGGTTTTTAAGGTTTTAGAGTT
1 TTTAATTTAAGGGTTAGGGTTTTTAAGGTTTTAGGGTT
27626183 T
1 T
27626184 AAGGTTTTTA
Statistics
Matches: 100, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
38 50 0.50
42 46 0.46
46 4 0.04
ACGTcount: A:0.25, C:0.01, G:0.26, T:0.48
Consensus pattern (38 bp):
TTTAATTTAAGGGTTAGGGTTTTTAAGGTTTTAGGGTT
Found at i:27626190 original size:7 final size:7
Alignment explanation
Indices: 27626150--27626414 Score: 52
Period size: 8 Copynumber: 35.9 Consensus size: 7
27626140 GGGTTTTTAA
27626150 TTTAAGG
1 TTTAAGG
*
27626157 ATTAAGG
1 TTTAAGG
27626164 TTTTTAAGG
1 --TTTAAGG
*
27626173 TTTTAGAG
1 TTTAAG-G
27626181 TTTAAGG
1 TTTAAGG
27626188 TTTTTAA--
1 --TTTAAGG
27626195 TTTAAGGG
1 TTTAA-GG
*
27626203 TTTATGGGG
1 TTTA--AGG
27626212 TTTTAA-G
1 -TTTAAGG
27626219 -TTAAGAG
1 TTTAAG-G
*
27626226 TTTAAGAT
1 TTTAAG-G
27626234 TTTAAGG
1 TTTAAGG
*
27626241 TTTTATGG
1 -TTTAAGG
*
27626249 TTTAGGG
1 TTTAAGG
27626256 TTATTAA--
1 -T-TTAAGG
27626263 TTTAAGG
1 TTTAAGG
*
27626270 ATTTAGGG
1 -TTTAAGG
27626278 TTTTAA-G
1 -TTTAAGG
27626285 -TTAATGG
1 TTTAA-GG
*
27626292 TTTAGGG
1 TTTAAGG
*
27626299 TTTTAGGG
1 -TTTAAGG
27626307 TTT-AGAG
1 TTTAAG-G
27626314 TTT-AGAG
1 TTTAAG-G
27626321 TTTAAGG
1 TTTAAGG
27626328 TTTTTAA-G
1 --TTTAAGG
*
27626336 TTAAAGG
1 TTTAAGG
*
27626343 TTTAGGG
1 TTTAAGG
27626350 TTT-AGG
1 TTTAAGG
*
27626356 GTTAAGG
1 TTTAAGG
27626363 TTTATAGG
1 TTTA-AGG
27626371 -TTAAGGG
1 TTTAA-GG
*
27626378 TTTATGTG
1 TTTAAG-G
*
27626386 TTTAGGG
1 TTTAAGG
*
27626393 TTTTAAAGT
1 -TTT-AAGG
*
27626402 TTTAGGG
1 TTTAAGG
27626409 TTTAAG
1 TTTAAG
27626415 ATTTTTAAGT
Statistics
Matches: 193, Mismatches: 29, Indels: 72
0.66 0.10 0.24
Matches are distributed among these distances:
5 17 0.09
6 11 0.06
7 68 0.35
8 70 0.36
9 23 0.12
10 4 0.02
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (7 bp):
TTTAAGG
Done.