Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 90 of 132
Found at i:27636886 original size:60 final size:59
Alignment explanation
Indices: 27636750--27636902 Score: 182
Period size: 60 Copynumber: 2.6 Consensus size: 59
27636740 CATTAAAACC
* * * *
27636750 GGGTCAATTTTGAATTTTTAGAAACTTTAGAGGTCAAATCAGAATTTTTGGAAAGTTCGA
1 GGGTCAAATTCGAATTTTTAGAAAATTTAG-GGTCAAATCAGAATTTTTGGAAAATTCGA
* * * **
27636810 GAGTCAAA-TCAAAATTTTTAGAAAGTTTAAGGGTCAAATTTGAATTTTTGGAAAATTCGA
1 GGGTCAAATTC-GAATTTTTAGAAAATTT-AGGGTCAAATCAGAATTTTTGGAAAATTCGA
*
27636870 GGGTCAAATTCGAATTTTTGGAAAATTTAGGGT
1 GGGTCAAATTCGAATTTTTAGAAAATTTAGGGT
27636903 TTAGGATTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
59 6 0.08
60 68 0.87
61 4 0.05
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (59 bp):
GGGTCAAATTCGAATTTTTAGAAAATTTAGGGTCAAATCAGAATTTTTGGAAAATTCGA
Found at i:27637931 original size:16 final size:16
Alignment explanation
Indices: 27637910--27637942 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27637900 ATTTATTTTT
27637910 ATAAAATAAT-AAATAA
1 ATAAAA-AATAAAATAA
27637926 ATAAAAAATAAAATAA
1 ATAAAAAATAAAATAA
27637942 A
1 A
27637943 AATTGGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
ATAAAAAATAAAATAA
Found at i:27638536 original size:40 final size:40
Alignment explanation
Indices: 27638491--27638699 Score: 162
Period size: 40 Copynumber: 5.3 Consensus size: 40
27638481 ATTGGATTGT
*
27638491 TTCAATTTGCCCCATGGTCAGGGTAAGAGATCTGATGGTC
1 TTCAATCTGCCCCATGGTCAGGGTAAGAGATCTGATGGTC
* ** * *
27638531 TTCAATCTGCCCTC-TGGTTAGTATAAAAGAT-TGAATTG-C
1 TTCAATCTGCCC-CATGGTCAGGGTAAGAGATCTG-ATGGTC
** * * * *
27638570 TTCAATCTAACCTATGGTC-GAGGTAAGGGATCGGATGATC
1 TTCAATCTGCCCCATGGTCAG-GGTAAGAGATCTGATGGTC
* * * *
27638610 TTCAATCTGCCCTC-TTGTTAGGGTAAAAGAT-TGGATTG-C
1 TTCAATCTGCCC-CATGGTCAGGGTAAGAGATCT-GATGGTC
* *
27638649 TTCAATCTGCCCCATGGTCGGGGTAAGAGATCTGATGGTG
1 TTCAATCTGCCCCATGGTCAGGGTAAGAGATCTGATGGTC
27638689 TTCAATCTGCC
1 TTCAATCTGCC
27638700 TTTTAGTTAG
Statistics
Matches: 124, Mismatches: 33, Indels: 24
0.69 0.18 0.13
Matches are distributed among these distances:
38 2 0.02
39 55 0.44
40 65 0.52
41 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (40 bp):
TTCAATCTGCCCCATGGTCAGGGTAAGAGATCTGATGGTC
Found at i:27638576 original size:39 final size:38
Alignment explanation
Indices: 27638473--27638735 Score: 160
Period size: 40 Copynumber: 6.7 Consensus size: 38
27638463 TACCTTTAGG
* * *
27638473 GGTAAAAGATTGGATTGTTTCAATTTGCCC-CATGGTCA
1 GGTAAAAGATTGGATTGCTTCAATCTGCCCTC-TGGTTA
* *
27638511 GGGTAAGAGATCT-GATGGTCTTCAATCTGCCCTCTGGTTA
1 -GGTAAAAGAT-TGGATTG-CTTCAATCTGCCCTCTGGTTA
* * ** * *
27638551 GTATAAAAGATTGAATTGCTTCAATCTAACCTATGGTCGA
1 G-GTAAAAGATTGGATTGCTTCAATCTGCCCTCTGGT-TA
** * *
27638591 GGTAAGGGATCGGA-TGATCTTCAATCTGCCCTCTTGTTA
1 GGTAAAAGATTGGATTG--CTTCAATCTGCCCTCTGGTTA
**
27638630 GGGTAAAAGATTGGATTGCTTCAATCTGCCC-CATGGTCGG
1 -GGTAAAAGATTGGATTGCTTCAATCTGCCCTC-TGGT-TA
* * * *
27638670 GGTAAGAGATCT-GATGGTG-TTCAATCTGCCTTTTAGTTA
1 GGTAAAAGAT-TGGAT--TGCTTCAATCTGCCCTCTGGTTA
27638709 GGGTAAAAGATTGGATTGCTTCAATCT
1 -GGTAAAAGATTGGATTGCTTCAATCT
27638736 TTCTCATGAT
Statistics
Matches: 169, Mismatches: 36, Indels: 38
0.70 0.15 0.16
Matches are distributed among these distances:
38 5 0.03
39 77 0.46
40 82 0.49
41 5 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (38 bp):
GGTAAAAGATTGGATTGCTTCAATCTGCCCTCTGGTTA
Found at i:27638612 original size:79 final size:79
Alignment explanation
Indices: 27638472--27638735 Score: 359
Period size: 79 Copynumber: 3.3 Consensus size: 79
27638462 ATACCTTTAG
* *
27638472 GGGTAAAAGATTGGATTGTTTCAATTTGCCCCATGGTC-AGGGTAAGAGATCTGATGGTCTTCAA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGA-GGTAAGAGATCTGATGGTCTTCAA
*
27638536 TCTGCCCTCTGGTTA
65 TCTGCCCTCTAGTTA
** * ** * * * *
27638551 GTATAAAAGATTGAATTGCTTCAATCTAACCTATGGTCGAGGTAAGGGATCGGATGATCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCTGATGGTCTTCAAT
*
27638616 CTGCCCTCTTGTTA
66 CTGCCCTCTAGTTA
* *
27638630 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCTGATGGTGTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCTGATGGTCTTCAAT
* *
27638695 CTGCCTTTTAGTTA
66 CTGCCCTCTAGTTA
27638709 GGGTAAAAGATTGGATTGCTTCAATCT
1 GGGTAAAAGATTGGATTGCTTCAATCT
27638736 TTCTCATGAT
Statistics
Matches: 158, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
79 157 0.99
80 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGAGGTAAGAGATCTGATGGTCTTCAAT
CTGCCCTCTAGTTA
Found at i:27638854 original size:50 final size:50
Alignment explanation
Indices: 27638800--27638911 Score: 129
Period size: 50 Copynumber: 2.2 Consensus size: 50
27638790 TAGAAGTATA
* *
27638800 AGATTCGTCC-TTGC-GACTTCAATCTGCCCCTCCATAGCTTTAGGTGAATG
1 AGATTCG-CCATTGCAG-CTTCAATCTACCCCTCCACAGCTTTAGGTGAATG
** * *
27638850 AGATTCGCCATTGCAGCTTCAATCTACCTTTCTACAGCTTTAGGTGTATG
1 AGATTCGCCATTGCAGCTTCAATCTACCCCTCCACAGCTTTAGGTGAATG
*
27638900 AGATTTGCCATT
1 AGATTCGCCATT
27638912 ATGGTCTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.04
50 50 0.94
51 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (50 bp):
AGATTCGCCATTGCAGCTTCAATCTACCCCTCCACAGCTTTAGGTGAATG
Found at i:27641858 original size:2 final size:2
Alignment explanation
Indices: 27641851--27641881 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27641841 CGAGTATAAA
27641851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27641882 CATAAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27642091 original size:60 final size:59
Alignment explanation
Indices: 27642014--27642230 Score: 226
Period size: 60 Copynumber: 3.6 Consensus size: 59
27642004 CATTAAAATT
* * * *
27642014 GGGTCAATTTTGAATTTTTGGAAACTT-TAGGGGTCAAATCGAAATTTTTAGATAGTT-TG
1 GGGTCAAATTTGAATTTTTGGAAAATTCGA-GGGTCAAATC-AAATTTTTAGATAGTTCAG
* * * *
27642073 AGGGTCAAATTAGAATTTTTGTAAAATTCGAGAGTCAAATCAGAATTTTTAG-TAAGTTCAT
1 -GGGTCAAATTTGAATTTTTGGAAAATTCGAGGGTCAAATCA-AATTTTTAGAT-AGTTCAG
* * * *
27642134 GGGTCAAATTTGTATTTTTGGAAAATTCGAGGGTCAAATTCAAATTTTTGGAAAATTCAG
1 GGGTCAAATTTGAATTTTTGGAAAATTCGAGGGTCAAA-TCAAATTTTTAGATAGTTCAG
* *
27642194 GGGTCAATTTTGAATTTTTGGAAAATTCTA-GGTCAAA
1 GGGTCAAATTTGAATTTTTGGAAAATTCGAGGGTCAAA
27642231 AATAGTTTTA
Statistics
Matches: 132, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
59 9 0.07
60 119 0.90
61 4 0.03
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (59 bp):
GGGTCAAATTTGAATTTTTGGAAAATTCGAGGGTCAAATCAAATTTTTAGATAGTTCAG
Found at i:27642209 original size:90 final size:90
Alignment explanation
Indices: 27642014--27642217 Score: 207
Period size: 90 Copynumber: 2.3 Consensus size: 90
27642004 CATTAAAATT
* * * * *
27642014 GGGTCAATTTTGAATTTTTGGAAACTTTAGGGGTCAAATCGAAATTTTTAGATAGTTTGAGGGTC
1 GGGTCAATTTTGAATTTTTAGAAACTTCAGGGGTCAAATCGAAATTTTTAGAAAATTCGAGGGTC
*
27642079 AAATTAGAATTTTTGTAAAATTCGA
66 AAATTAGAATTTTTGGAAAATTCGA
* * ** * * * * * *
27642104 GAGTCAAATCAGAATTTTTAGTAAGTTCATGGGTCAAATTTG-TATTTTTGGAAAATTCGAGGGT
1 GGGTCAATTTTGAATTTTTAGAAACTTCAGGGGTCAAA-TCGAAATTTTTAGAAAATTCGAGGGT
27642168 CAAATTCA-AATTTTTGGAAAATTC-A
65 CAAATT-AGAATTTTTGGAAAATTCGA
*
27642193 GGGGTCAATTTTGAATTTTTGGAAA
1 -GGGTCAATTTTGAATTTTTAGAAA
27642218 ATTCTAGGTC
Statistics
Matches: 89, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
89 1 0.01
90 85 0.96
91 3 0.03
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (90 bp):
GGGTCAATTTTGAATTTTTAGAAACTTCAGGGGTCAAATCGAAATTTTTAGAAAATTCGAGGGTC
AAATTAGAATTTTTGGAAAATTCGA
Found at i:27642218 original size:30 final size:31
Alignment explanation
Indices: 27642014--27642221 Score: 169
Period size: 30 Copynumber: 6.9 Consensus size: 31
27642004 CATTAAAATT
* * *
27642014 GGGTCAATTTTGAATTTTTGGAAACTTTAG-
1 GGGTCAAATTTGAATTTTTGGAAAATTCAGA
* * * * *
27642044 GGGTCAAA-TCGAAATTTTTAGATAGTT-TGA
1 GGGTCAAATTTG-AATTTTTGGAAAATTCAGA
* *
27642074 GGGTCAAATTAGAATTTTTGTAAAATTC-GA
1 GGGTCAAATTTGAATTTTTGGAAAATTCAGA
* ** * * * *
27642104 GAGTCAAATCAGAATTTTTAGTAAGTTCA-T
1 GGGTCAAATTTGAATTTTTGGAAAATTCAGA
*
27642134 GGGTCAAATTTGTATTTTTGGAAAATTC-GA
1 GGGTCAAATTTGAATTTTTGGAAAATTCAGA
**
27642164 GGGTCAAATTCAAATTTTTGGAAAATTCAG-
1 GGGTCAAATTTGAATTTTTGGAAAATTCAGA
*
27642194 GGGTCAATTTTGAATTTTTGGAAAATTC
1 GGGTCAAATTTGAATTTTTGGAAAATTC
27642222 TAGGTCAAAA
Statistics
Matches: 139, Mismatches: 32, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
29 3 0.02
30 133 0.96
31 3 0.02
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (31 bp):
GGGTCAAATTTGAATTTTTGGAAAATTCAGA
Found at i:27647913 original size:12 final size:12
Alignment explanation
Indices: 27647896--27647920 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27647886 CTAACAACGC
27647896 TGTAACACCCTT
1 TGTAACACCCTT
27647908 TGTAACACCCTT
1 TGTAACACCCTT
27647920 T
1 T
27647921 TTGGAGAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (12 bp):
TGTAACACCCTT
Found at i:27649741 original size:33 final size:32
Alignment explanation
Indices: 27649676--27649747 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
27649666 TAGAAAAGCT
*
27649676 AATATTTTCTGGTGTTTGGATGAATCTATGTA
1 AATATTTTCTGGTGTTTGGAAGAATCTATGTA
*
27649708 AGATATTTTCTGGTGTTT-GACAGATTTCT-TGTA
1 A-ATATTTTCTGGTGTTTGGA-AGA-ATCTATGTA
27649741 AATATTT
1 AATATTT
27649748 CATAAAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
32 9 0.26
33 23 0.66
34 3 0.09
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.49
Consensus pattern (32 bp):
AATATTTTCTGGTGTTTGGAAGAATCTATGTA
Found at i:27652437 original size:98 final size:98
Alignment explanation
Indices: 27652267--27652600 Score: 268
Period size: 98 Copynumber: 3.4 Consensus size: 98
27652257 GCTTTTTTTA
*
27652267 GCTTTAATATGCCCCTTTCCATCTTTAGGGTATAAGATTCACCTTTGTGGCTTCAATTTACCCTT
1 GCTTTAATATGCCCCTTTCCATCTTTAGGGTATAAGATTCACCTTTGCGGCTTCAATTTACCCTT
* *
27652332 TTTCATCTTTAAGGTATAAGATTCGCCTTTGTG
66 TTACATCTCTAAGGTATAAGATTCGCCTTTGTG
* * *
27652365 GCTTTAATTTGCCCCTGTT-CAT-TGTTAGGGTATAAGATTCTCCTTTGCGGCTTCAATCTTTCC
1 GCTTTAATATGCCCCT-TTCCATCT-TTAGGGTATAAGATTCACCTTTGCGGCTTCAAT-TTACC
* * *
27652428 C-TTTACATCTCTAGGGTATAATATTCGCCTTTACT-
63 CTTTTACATCTCTAAGGTATAAGATTCGCCTTT-GTG
* ** * * * * ** *
27652463 GCTTCAATAT-TTCCTTCCACATCTCTATGGTAT-AGATTCACCTTTACAACTTCAATCTTTCCC
1 GCTTTAATATGCCCCTTTC-CATCTTTAGGGTATAAGATTCACCTTTGCGGCTTCAAT-TTACCC
** * ** *
27652526 -TCCACATCTCTAGGGTATAAGATTCATCTTTGCG
64 TTTTACATCTCTAAGGTATAAGATTCGCCTTTGTG
* * ** * * * *
27652560 TCTTCAATATTTCCCTCTACGTCTTTAGGGTATAGGATTCA
1 GCTTTAATATGCCCCTTTCCATCTTTAGGGTATAAGATTCA
27652601 ATGTTTCCTC
Statistics
Matches: 190, Mismatches: 36, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
96 1 0.01
97 76 0.40
98 104 0.55
99 9 0.05
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (98 bp):
GCTTTAATATGCCCCTTTCCATCTTTAGGGTATAAGATTCACCTTTGCGGCTTCAATTTACCCTT
TTACATCTCTAAGGTATAAGATTCGCCTTTGTG
Found at i:27652467 original size:49 final size:47
Alignment explanation
Indices: 27652279--27652600 Score: 231
Period size: 49 Copynumber: 6.6 Consensus size: 47
27652269 TTTAATATGC
* * *
27652279 CCCTTTCCATCTTTAGGGTATAAGATTCACCTTTGTGGCTTCAATTTA
1 CCCTTTACATCTTTAGGGTATAAGATTCACCTTTCT-GCTTCAATTTT
* * * * * *
27652327 CCCTTTTTCATCTTTAAGGTATAAGATTCGCCTTTGTGGCTTTAATTTGC
1 CCC-TTTACATCTTTAGGGTATAAGATTCACCTTTCT-GCTTCAATTT-T
* *
27652377 CCCTGTT-CAT-TGTTAGGGTATAAGATTCTCCTTTGCGGCTTCAATCTTT
1 CCCT-TTACATCT-TTAGGGTATAAGATTCACCTTT-CTGCTTCAAT-TTT
* * *
27652426 CCCTTTACATCTCTAGGGTATAATATTCGCCTTTACTGCTTCAATATTT
1 CCCTTTACATCTTTAGGGTATAAGATTCACCTTT-CTGCTTCAAT-TTT
* * * **
27652475 -CCTTCCACATCTCTATGGTAT-AGATTCACCTTTACAACTTCAATCTTT
1 CCCTT-TACATCTTTAGGGTATAAGATTCACCTTT-CTGCTTCAAT-TTT
** * *
27652523 CCCTCCACATCTCTAGGGTATAAGATTCATCTTTGC-GTCTTCAATATTT
1 CCCTTTACATCTTTAGGGTATAAGATTCACCTTT-CTG-CTTCAAT-TTT
* * *
27652572 CCCTCTACGTCTTTAGGGTATAGGATTCA
1 CCCTTTACATCTTTAGGGTATAAGATTCA
27652601 ATGTTTCCTC
Statistics
Matches: 228, Mismatches: 34, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
48 47 0.21
49 173 0.76
50 8 0.04
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (47 bp):
CCCTTTACATCTTTAGGGTATAAGATTCACCTTTCTGCTTCAATTTT
Found at i:27652533 original size:97 final size:98
Alignment explanation
Indices: 27652390--27652600 Score: 255
Period size: 97 Copynumber: 2.2 Consensus size: 98
27652380 TGTTCATTGT
* * * ** ** * *
27652390 TAGGGTATAAGATTCTCCTTTGCGGCTTCAATCTTTCCCTTTACATCTCTAGGGTATAATATTCG
1 TAGGGTATAGGATTCACCTTTACAACTTCAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCA
*
27652455 CCTTTAC-TGCTTCAATATTTCCTTCCACATCTC
66 CCTTTACGT-CTTCAATATTTCCCTCCACATCTC
*
27652488 TATGGTATA-GATTCACCTTTACAACTTCAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCA
1 TAGGGTATAGGATTCACCTTTACAACTTCAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCA
* * * * *
27652552 TCTTTGCGTCTTCAATATTTCCCTCTACGTCTT
66 CCTTTACGTCTTCAATATTTCCCTCCACATCTC
27652585 TAGGGTATAGGATTCA
1 TAGGGTATAGGATTCA
27652601 ATGTTTCCTC
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
97 80 0.84
98 15 0.16
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (98 bp):
TAGGGTATAGGATTCACCTTTACAACTTCAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCA
CCTTTACGTCTTCAATATTTCCCTCCACATCTC
Found at i:27680506 original size:25 final size:25
Alignment explanation
Indices: 27680474--27680522 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
27680464 CTATTCTCTC
* *
27680474 AGAGATGAAGGCTCTTGAAAAAAAG
1 AGAGATGAACGCTCATGAAAAAAAG
*
27680499 AGAGATGAACTCTCATGAAAAAAA
1 AGAGATGAACGCTCATGAAAAAAA
27680523 CAATAAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.16
Consensus pattern (25 bp):
AGAGATGAACGCTCATGAAAAAAAG
Found at i:27682406 original size:257 final size:258
Alignment explanation
Indices: 27681941--27682455 Score: 722
Period size: 258 Copynumber: 2.0 Consensus size: 258
27681931 AAAGTCATCT
* * *
27681941 ATTTAGAGATTATAGACAAGATTATGCAACAACTAAGATCTGGGGTAACCTTATTGGTACCATAT
1 ATTTAGAGATTATAGACAAGATTATGCAACAACTAAGATCTGGGGCAACCTTATTGATACCATAA
* * * *
27682006 TTTTACAAATTTTTCCATTTAGCAGAGTTATATCTCTAAAAATAATAATCCTGAAGCCAATAAGA
66 ATTTACAAATTGTGCCATTTAGCAGAGTTATATCCCTAAAAATAATAATCCTGAAGCCAATAAGA
*
27682071 AAAGATATAGTACATCCTAAAGATCAAAATTTCCAACTAGAAGCAACCAGTGGCCTATATATAAA
131 AAAGATATAGTACATCCTAAAGATCAAAATTTCCAACTAGAAGCAACCAGTAGCCTATATATAAA
*
27682136 AATATTATCAACAAGATG-GATGGAAATCCCA-TGTGCA-CTTTCCGGGTTTAATGAGAAGCACC
196 AATATTATCAACAAGATGAAATGGAAATCCCACT-TGCACCTTT-CGGGTTTAATGAGAAGCACC
* * * *
27682198 ATTTAGAGATTATATG-CATGATTGTGCAACAAC-AGTGATTTGGGGCAACCTTATTGATACCAT
1 ATTTAGAGATTATA-GACAAGATTATGCAACAACTA-AGATCTGGGGCAACCTTATTGATACCAT
*
27682261 AAATTTACAACTTGTGCCATTTAGCAGAGTTATATCCCTAATAAATAATAATCCTGAAGCCAATA
64 AAATTTACAAATTGTGCCATTTAGCAGAGTTATATCCCTAA-AAATAATAATCCTGAAGCCAATA
* * **
27682326 AGAAAATATATAGTACATCCTAAAGATCAAAATTTCCGACTAGAAGTGACC-GATAGCCTAGT-T
128 AGAAAAGATATAGTACATCCTAAAGATCAAAATTTCCAACTAGAAGCAACCAG-TAGCCTA-TAT
* * *
27682389 AT-AAGATATTCTCAACAAGATGAAATGGAAATCCCACTTGCACCTTTTGGGTTTAATGAGAAGC
191 ATAAAAATATTATCAACAAGATGAAATGGAAATCCCACTTGCACCTTTCGGGTTTAATGAGAAGC
27682453 ACC
256 ACC
27682456 GTATAAGTTG
Statistics
Matches: 229, Mismatches: 21, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
256 1 0.00
257 107 0.47
258 115 0.50
259 6 0.03
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (258 bp):
ATTTAGAGATTATAGACAAGATTATGCAACAACTAAGATCTGGGGCAACCTTATTGATACCATAA
ATTTACAAATTGTGCCATTTAGCAGAGTTATATCCCTAAAAATAATAATCCTGAAGCCAATAAGA
AAAGATATAGTACATCCTAAAGATCAAAATTTCCAACTAGAAGCAACCAGTAGCCTATATATAAA
AATATTATCAACAAGATGAAATGGAAATCCCACTTGCACCTTTCGGGTTTAATGAGAAGCACC
Found at i:27686123 original size:25 final size:25
Alignment explanation
Indices: 27686085--27686132 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
27686075 CTAGGAATAA
* *
27686085 AACTTTATTTGCAA-GAAAGCCTAGT
1 AACTTTACTGGCAAGGAAA-CCTAGT
27686110 AACTTTACTGGCAAGGAAACCTA
1 AACTTTACTGGCAAGGAAACCTA
27686133 TTATGAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (25 bp):
AACTTTACTGGCAAGGAAACCTAGT
Found at i:27688452 original size:83 final size:83
Alignment explanation
Indices: 27688355--27688522 Score: 336
Period size: 83 Copynumber: 2.0 Consensus size: 83
27688345 GAAACTCTAA
27688355 TTGTGGTTCAAATATATACTTGAAACTTTAATTTTGATTTAATCATACACATTTAAATAAATAAA
1 TTGTGGTTCAAATATATACTTGAAACTTTAATTTTGATTTAATCATACACATTTAAATAAATAAA
27688420 TAAATACATCAATTTATT
66 TAAATACATCAATTTATT
27688438 TTGTGGTTCAAATATATACTTGAAACTTTAATTTTGATTTAATCATACACATTTAAATAAATAAA
1 TTGTGGTTCAAATATATACTTGAAACTTTAATTTTGATTTAATCATACACATTTAAATAAATAAA
27688503 TAAATACATCAATTTATT
66 TAAATACATCAATTTATT
27688521 TT
1 TT
27688523 TATATTGGAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.43
Consensus pattern (83 bp):
TTGTGGTTCAAATATATACTTGAAACTTTAATTTTGATTTAATCATACACATTTAAATAAATAAA
TAAATACATCAATTTATT
Found at i:27689211 original size:5 final size:5
Alignment explanation
Indices: 27689201--27689244 Score: 79
Period size: 5 Copynumber: 8.6 Consensus size: 5
27689191 TCTTTCTTGT
27689201 TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTTCCC TTC
1 TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC -TTCCC TTC
27689245 GCAGTTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 33 0.87
6 5 0.13
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (5 bp):
TTCCC
Found at i:27689593 original size:15 final size:15
Alignment explanation
Indices: 27689561--27689593 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
27689551 AAAATCAATC
27689561 AATAATTTTTTATAT
1 AATAATTTTTTATAT
27689576 AATAGATTTTTTAT-T
1 AATA-ATTTTTTATAT
27689591 AAT
1 AAT
27689594 TTGAACTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
AATAATTTTTTATAT
Found at i:27690783 original size:15 final size:16
Alignment explanation
Indices: 27690755--27690797 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27690745 ATAATGTGTA
* *
27690755 AAAAGTAAAGTAAAGT
1 AAAAGTAAAATAAAAT
27690771 AAAA-TAAAATAAAAT
1 AAAAGTAAAATAAAAT
27690786 AAATAGTAAAAT
1 AAA-AGTAAAAT
27690798 GAATGCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
16 5 0.22
17 6 0.26
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAAGTAAAATAAAAT
Found at i:27692757 original size:24 final size:24
Alignment explanation
Indices: 27692725--27692799 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
27692715 GTTTAGTGCA
* * * *
27692725 TTTACGCTCGCCAGCTAATGTACG
1 TTTATGCTCGTCAGCCACTGTACG
*
27692749 TTTATGCTCATCAGCCACTGTACG
1 TTTATGCTCGTCAGCCACTGTACG
27692773 TTTATGCTCGTCAGCCACTGTACG
1 TTTATGCTCGTCAGCCACTGTACG
27692797 TTT
1 TTT
27692800 GATACTTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (24 bp):
TTTATGCTCGTCAGCCACTGTACG
Found at i:27696587 original size:21 final size:22
Alignment explanation
Indices: 27696561--27696605 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
27696551 ACCCTGCAAC
* *
27696561 TTCTACCGATACATGTATG-AG
1 TTCTACCGAAACAAGTATGTAG
27696582 TTCTACCGAAACAAGTATGTAG
1 TTCTACCGAAACAAGTATGTAG
27696604 TT
1 TT
27696606 TTCAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (22 bp):
TTCTACCGAAACAAGTATGTAG
Found at i:27697196 original size:26 final size:26
Alignment explanation
Indices: 27697142--27697216 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
27697132 TAGCTCATAT
* * **
27697142 GAGCTAGTTCAGCATATCGCTTTTTC
1 GAGCTAGTTCAGTATATCGCTCTACC
*
27697168 GAGCTAGTGCAGTATATCGCTCTACC
1 GAGCTAGTTCAGTATATCGCTCTACC
* *
27697194 GAGCCAATTCAGTATATCGCTCT
1 GAGCTAGTTCAGTATATCGCTCT
27697217 TATGAGGCAG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (26 bp):
GAGCTAGTTCAGTATATCGCTCTACC
Found at i:27697409 original size:24 final size:24
Alignment explanation
Indices: 27697380--27697604 Score: 342
Period size: 24 Copynumber: 9.4 Consensus size: 24
27697370 TGCCAGCTAA
* * *
27697380 TGTACGTTTATGCTCATTAGTCAC
1 TGTACGTTTATGCTCGTCAGCCAC
*
27697404 TATACGTTTATGCTCGTCAGCCAC
1 TGTACGTTTATGCTCGTCAGCCAC
*
27697428 TGTACGTTTATACTCGTCAGCCAC
1 TGTACGTTTATGCTCGTCAGCCAC
27697452 TGTACGTTTATGCTCGTCAGCCAC
1 TGTACGTTTATGCTCGTCAGCCAC
**
27697476 TGTACGTTTATGCAAGTCAGCCAC
1 TGTACGTTTATGCTCGTCAGCCAC
**
27697500 TGTACGTTTATGCAAGTCAGCCAC
1 TGTACGTTTATGCTCGTCAGCCAC
*
27697524 TGTACGTTTATGCTCGTTAGCCAC
1 TGTACGTTTATGCTCGTCAGCCAC
**
27697548 TGTACGTTTATGCTAATCAGCCAC
1 TGTACGTTTATGCTCGTCAGCCAC
27697572 TGTACGTTTATGCTCGTCAGCCAC
1 TGTACGTTTATGCTCGTCAGCCAC
27697596 TGTACGTTT
1 TGTACGTTT
27697605 GATACTTTTA
Statistics
Matches: 184, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 184 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (24 bp):
TGTACGTTTATGCTCGTCAGCCAC
Found at i:27698733 original size:3 final size:3
Alignment explanation
Indices: 27698725--27698784 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
27698715 GCCAAAGATT
27698725 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
27698773 GAA GAA GAA GAA
1 GAA GAA GAA GAA
27698785 TGATTTTCTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:27700841 original size:26 final size:26
Alignment explanation
Indices: 27700812--27700902 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
27700802 ATATATTGGC
27700812 AATTTGTGAATGTGAAACATAATCAT
1 AATTTGTGAATGTGAAACATAATCAT
* * ***
27700838 AATTTGTATGCAT-TGGAAAGTGATATATTGGC
1 AATTTG--TGAATGT-GAAA--CATA-A-TCAT
27700870 AATTTGTGAATGTGAAACATAATCAT
1 AATTTGTGAATGTGAAACATAATCAT
27700896 AATTTGT
1 AATTTGT
27700903 ATGCATTGGA
Statistics
Matches: 47, Mismatches: 10, Indels: 16
0.64 0.14 0.22
Matches are distributed among these distances:
26 14 0.30
27 2 0.04
28 11 0.23
30 11 0.23
31 2 0.04
32 7 0.15
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (26 bp):
AATTTGTGAATGTGAAACATAATCAT
Found at i:27700867 original size:58 final size:58
Alignment explanation
Indices: 27700798--27700912 Score: 230
Period size: 58 Copynumber: 2.0 Consensus size: 58
27700788 TACACAACAT
27700798 AGTGATATATTGGCAATTTGTGAATGTGAAACATAATCATAATTTGTATGCATTGGAA
1 AGTGATATATTGGCAATTTGTGAATGTGAAACATAATCATAATTTGTATGCATTGGAA
27700856 AGTGATATATTGGCAATTTGTGAATGTGAAACATAATCATAATTTGTATGCATTGGA
1 AGTGATATATTGGCAATTTGTGAATGTGAAACATAATCATAATTTGTATGCATTGGA
27700913 TAAACGAATC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.37
Consensus pattern (58 bp):
AGTGATATATTGGCAATTTGTGAATGTGAAACATAATCATAATTTGTATGCATTGGAA
Found at i:27702654 original size:23 final size:24
Alignment explanation
Indices: 27702628--27702674 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27702618 AACTATTCAT
27702628 TTTATCTTA-ATTTGCTCTGACAA
1 TTTATCTTATATTTGCTCTGACAA
* *
27702651 TTTATTTTATATTTGCTTTGACAA
1 TTTATCTTATATTTGCTCTGACAA
27702675 ACTAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTATCTTATATTTGCTCTGACAA
Found at i:27702690 original size:26 final size:26
Alignment explanation
Indices: 27702654--27702705 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
27702644 CTGACAATTT
27702654 ATTTTATATTTGCTTTGACAAACTAA
1 ATTTTATATTTGCTTTGACAAACTAA
*
27702680 ATTTTATATTTGTTTTGACAAACTAA
1 ATTTTATATTTGCTTTGACAAACTAA
27702706 CTCTTTTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (26 bp):
ATTTTATATTTGCTTTGACAAACTAA
Found at i:27710573 original size:20 final size:18
Alignment explanation
Indices: 27710536--27710578 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
27710526 AATCCTTGAG
27710536 GAAGAGAAAGGAACTGAA
1 GAAGAGAAAGGAACTGAA
*
27710554 GAAGAGAAGGAGGAAGTGAA
1 GAAGAGAA--AGGAACTGAA
27710574 GAAGA
1 GAAGA
27710579 ATGAAGAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.53, C:0.02, G:0.40, T:0.05
Consensus pattern (18 bp):
GAAGAGAAAGGAACTGAA
Found at i:27711012 original size:17 final size:17
Alignment explanation
Indices: 27710987--27711029 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
27710977 ATGCATCTCA
27710987 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
* *
27711004 TTTAGTTGTCGTTGCAT
1 TTTAATTGTCATTGCAT
*
27711021 TTTACTTGT
1 TTTAATTGT
27711030 TAGTTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:27713163 original size:24 final size:23
Alignment explanation
Indices: 27713126--27713172 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
27713116 ACTATTCATT
27713126 TTTATCTTAATTTGC-TCTGACAA
1 TTTATCTTAATTTGCGT-TGACAA
*
27713149 TTTATTTTATATTTGCGTTGACAA
1 TTTATCTTA-ATTTGCGTTGACAA
27713173 ACTAACTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.51
Consensus pattern (23 bp):
TTTATCTTAATTTGCGTTGACAA
Found at i:27713424 original size:34 final size:34
Alignment explanation
Indices: 27713386--27713467 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 34
27713376 CCAATTAGGT
27713386 TCACACAACATG-AGGCTTGTACATAAT-TTAGGGC
1 TCACACAACATGTAGGCTTG--CATAATATTAGGGC
* *
27713420 TCACAC-ACATCGTAGGCTTGCATGATATTAGGGT
1 TCACACAACAT-GTAGGCTTGCATAATATTAGGGC
*
27713454 TCGCACAACATGTA
1 TCACACAACATGTA
27713468 TAAGTTTGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
33 9 0.22
34 21 0.51
35 11 0.27
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (34 bp):
TCACACAACATGTAGGCTTGCATAATATTAGGGC
Found at i:27732931 original size:14 final size:14
Alignment explanation
Indices: 27732912--27732943 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
27732902 ATCACATTTA
*
27732912 AAAATAAAAATAAT
1 AAAATAAAAAAAAT
27732926 AAAATAAAAAAAAT
1 AAAATAAAAAAAAT
27732940 AAAA
1 AAAA
27732944 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:27746900 original size:15 final size:15
Alignment explanation
Indices: 27746857--27746894 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
27746847 GGTGAATGAT
*
27746857 ATTAATCTAAAGT--
1 ATTAATCTAAACTAA
27746870 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
27746885 ATTAATCTAA
1 ATTAATCTAA
27746895 GTTAAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:27746911 original size:26 final size:28
Alignment explanation
Indices: 27746857--27746913 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
27746847 GGTGAATGAT
* *
27746857 ATTAATCTAAAGTATTAATCTAAACTAA
1 ATTAATCTAAAGTATAAAGCTAAACTAA
27746885 ATTAATCT-AAGT-TAAAGCTAAACTAA
1 ATTAATCTAAAGTATAAAGCTAAACTAA
27746911 ATT
1 ATT
27746914 TCCAATGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 15 0.56
27 4 0.15
28 8 0.30
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (28 bp):
ATTAATCTAAAGTATAAAGCTAAACTAA
Found at i:27749811 original size:15 final size:15
Alignment explanation
Indices: 27749768--27749805 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
27749758 GGTGAATGAT
*
27749768 ATTAATCTAAAGT--
1 ATTAATCTAAACTAA
27749781 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
27749796 ATTAATCTAA
1 ATTAATCTAA
27749806 GTTAAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:27749822 original size:26 final size:28
Alignment explanation
Indices: 27749768--27749824 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
27749758 GGTGAATGAT
* *
27749768 ATTAATCTAAAGTATTAATCTAAACTAA
1 ATTAATCTAAAGTATAAAGCTAAACTAA
27749796 ATTAATCT-AAGT-TAAAGCTAAACTAA
1 ATTAATCTAAAGTATAAAGCTAAACTAA
27749822 ATT
1 ATT
27749825 TCCAATGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 15 0.56
27 4 0.15
28 8 0.30
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (28 bp):
ATTAATCTAAAGTATAAAGCTAAACTAA
Found at i:27759650 original size:12 final size:12
Alignment explanation
Indices: 27759636--27759699 Score: 67
Period size: 12 Copynumber: 5.3 Consensus size: 12
27759626 CCAAACAATC
*
27759636 AAAATAACAACC
1 AAAATAACAACA
*
27759648 AAAATAGCAACA
1 AAAATAACAACA
*
27759660 AAAATAATAGA-A
1 AAAATAACA-ACA
*
27759672 AAAATAGCAACA
1 AAAATAACAACA
*
27759684 AAAATAACAATA
1 AAAATAACAACA
27759696 AAAA
1 AAAA
27759700 CAGCACCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 1 0.02
12 40 0.95
13 1 0.02
ACGTcount: A:0.72, C:0.12, G:0.05, T:0.11
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:27759664 original size:24 final size:23
Alignment explanation
Indices: 27759636--27759732 Score: 97
Period size: 24 Copynumber: 4.1 Consensus size: 23
27759626 CCAAACAATC
*
27759636 AAAATAACAACCAAAATAGCAACA
1 AAAATAACAA-AAAAATAGCAACA
*
27759660 AAAATAATAGAAAAAATAGCAACA
1 AAAATAACA-AAAAAATAGCAACA
* *
27759684 AAAATAACAATAAAAACAGC-ACC
1 AAAATAACAA-AAAAATAGCAACA
** *
27759707 AAAATAGTAAAAAAATAGCACCA
1 AAAATAACAAAAAAATAGCAACA
27759730 AAA
1 AAA
27759733 CAGTAACCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
22 8 0.13
23 15 0.25
24 36 0.60
25 1 0.02
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.10
Consensus pattern (23 bp):
AAAATAACAAAAAAATAGCAACA
Found at i:27759726 original size:22 final size:23
Alignment explanation
Indices: 27759648--27759732 Score: 100
Period size: 24 Copynumber: 3.7 Consensus size: 23
27759638 AATAACAACC
27759648 AAAATAGCAACAAAAATAATAGAA
1 AAAATAGCAACAAAAATAATA-AA
*
27759672 AAAATAGCAACAAAAATAACAATA
1 AAAATAGCAACAAAAATAATAA-A
* * *
27759696 AAAACAGC-ACCAAAATAGTAAA
1 AAAATAGCAACAAAAATAATAAA
*
27759718 AAAATAGCACCAAAA
1 AAAATAGCAACAAAA
27759733 CAGTAACCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 8 0.16
23 15 0.29
24 28 0.55
ACGTcount: A:0.68, C:0.14, G:0.07, T:0.11
Consensus pattern (23 bp):
AAAATAGCAACAAAAATAATAAA
Found at i:27759737 original size:22 final size:22
Alignment explanation
Indices: 27759695--27759747 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
27759685 AAATAACAAT
*
27759695 AAAAACAGCACCAAAATAGTAA
1 AAAAACAGCACCAAAACAGTAA
*
27759717 AAAAATAGCACCAAAACAGTAA
1 AAAAACAGCACCAAAACAGTAA
*
27759739 CCAAAACAG
1 -AAAAACAG
27759748 TAAAAACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.62, C:0.21, G:0.09, T:0.08
Consensus pattern (22 bp):
AAAAACAGCACCAAAACAGTAA
Found at i:27759754 original size:21 final size:21
Alignment explanation
Indices: 27759729--27759797 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 21
27759719 AAATAGCACC
*
27759729 AAAACAGTAACCAAAACAGTA
1 AAAACAGAAACCAAAACAGTA
* *
27759750 AAAACACAACACCAAAACAATAA
1 AAAACAGAA-ACCAAAACAGT-A
* *
27759773 AAAATAGCAACCAAAACAGTA
1 AAAACAGAAACCAAAACAGTA
27759794 AAAA
1 AAAA
27759798 ACTGCATCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 12 0.31
22 20 0.51
23 7 0.18
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (21 bp):
AAAACAGAAACCAAAACAGTA
Found at i:27759765 original size:22 final size:22
Alignment explanation
Indices: 27759737--27759799 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
27759727 CCAAAACAGT
27759737 AACCAAAACAGTAAAAACACAAC
1 AACCAAAACAGTAAAAA-ACAAC
* * *
27759760 -ACCAAAACAATAAAAAATAGC
1 AACCAAAACAGTAAAAAACAAC
27759781 AACCAAAACAGTAAAAAAC
1 AACCAAAACAGTAAAAAAC
27759800 TGCATCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 3 0.09
22 31 0.91
ACGTcount: A:0.67, C:0.22, G:0.05, T:0.06
Consensus pattern (22 bp):
AACCAAAACAGTAAAAAACAAC
Found at i:27759808 original size:21 final size:21
Alignment explanation
Indices: 27759738--27759811 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
27759728 CAAAACAGTA
**
27759738 ACCAAAACAGTAAAAACACAAC
1 ACCAAAACAGTAAAAA-ACTGC
*
27759760 ACCAAAACAATAAAAAA-TAGC
1 ACCAAAACAGTAAAAAACT-GC
27759781 AACCAAAACAGTAAAAAACTGC
1 -ACCAAAACAGTAAAAAACTGC
*
27759803 ATCAAAACA
1 ACCAAAACA
27759812 ACAATATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 10 0.23
22 33 0.75
23 1 0.02
ACGTcount: A:0.64, C:0.23, G:0.05, T:0.08
Consensus pattern (21 bp):
ACCAAAACAGTAAAAAACTGC
Found at i:27762178 original size:69 final size:69
Alignment explanation
Indices: 27762051--27762304 Score: 233
Period size: 69 Copynumber: 3.7 Consensus size: 69
27762041 GCAGCATTTG
** * ** * * *
27762051 TGTCATTTTAAGGTTCGCAAGTAAAGAGTCGTAACCTCCAGCATC-GTTAGCAAAAGCAAAGCTC
1 TGTCATTTTAAGGTTCGCAAGCGAAGAGCCACAACCTCCAACA-CAGTTAGCGAGAGCAAAGCTC
**
27762115 TTAAT
65 TTAGC
* * *
27762120 TGTCATTTTAAGGTTCGCAAGCGAAGAGCCACAACATCCAACACAGTTAACGAGAGCAAAGCTCC
1 TGTCATTTTAAGGTTCGCAAGCGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAAAGCTCT
* *
27762185 CAGG
66 TAGC
** * * * *** * *
27762189 TACCATTTTAAGGTTAGTAGGCGAAGAGCTGTAACCTCCAACATAGTTAGTGAGAGCAAAGCTCT
1 TGTCATTTTAAGGTTCGCAAGCGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAAAGCTCT
27762254 TAGC
66 TAGC
** *
27762258 TG-CATTTTAAGGTTCATAGGCGAAGAGCCACAACCTCCAACACAGTT
1 TGTCATTTTAAGGTTCGCAAGCGAAGAGCCACAACCTCCAACACAGTT
27762305 TTTGAGATCA
Statistics
Matches: 148, Mismatches: 36, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
68 40 0.27
69 108 0.73
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (69 bp):
TGTCATTTTAAGGTTCGCAAGCGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAAAGCTCT
TAGC
Found at i:27762333 original size:137 final size:137
Alignment explanation
Indices: 27762081--27762337 Score: 329
Period size: 137 Copynumber: 1.9 Consensus size: 137
27762071 GTAAAGAGTC
* * * *
27762081 GTAACCTCCAGCATCGTTAGCAAAAGCAAAGCTCTTAATTGTCATTTTAAGGTTCGCAAGCGAAG
1 GTAACCTCCAACATAGTTAGCAAAAGCAAAGCTCTTAACTGTCATTTTAAGGTTCACAAGCGAAG
*
27762146 AGCCACAACATCCAACACAGTTAACGAGAGCAAAGCTCCCAGGTACCATTTTAAGGTTAGTAGGC
66 AGCCACAACATCCAACACAGTTAACGAGAGCAAAACTCCCAGGTA-CATTTTAAGGTTAGTAGGC
27762211 GAAGAGCT
130 GAAGAGCT
** * * * *
27762219 GTAACCTCCAACATAGTTAGTGAGAGCAAAGCTCTTAGCTG-CATTTTAAGGTTCATAGGCGAAG
1 GTAACCTCCAACATAGTTAGCAAAAGCAAAGCTCTTAACTGTCATTTTAAGGTTCACAAGCGAAG
* *** *
27762283 AGCCACAACCTCCAACACAGTTTTTGAGATCAAAACTCCCAGCAGT-CATTTTAAG
66 AGCCACAACATCCAACACAGTTAACGAGAGCAAAACTCCCAG--GTACATTTTAAG
27762338 TTTGAGATAG
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
137 65 0.64
138 34 0.34
139 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (137 bp):
GTAACCTCCAACATAGTTAGCAAAAGCAAAGCTCTTAACTGTCATTTTAAGGTTCACAAGCGAAG
AGCCACAACATCCAACACAGTTAACGAGAGCAAAACTCCCAGGTACATTTTAAGGTTAGTAGGCG
AAGAGCT
Found at i:27762475 original size:58 final size:58
Alignment explanation
Indices: 27762413--27762523 Score: 186
Period size: 58 Copynumber: 1.9 Consensus size: 58
27762403 CAACTCGCAA
*
27762413 ATTCACATCCCAACTTATTATTTTTAAGAAAAATTTCTAAGTTTAAAATAGCTTAGGG
1 ATTCACATCCCAACTTATTAATTTTAAGAAAAATTTCTAAGTTTAAAATAGCTTAGGG
* * *
27762471 ATTCACATCCCAACTTATTAATTTTAAGAAAATTTTCTAAGTTTGAGATAGCT
1 ATTCACATCCCAACTTATTAATTTTAAGAAAAATTTCTAAGTTTAAAATAGCT
27762524 CGCATATGCA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (58 bp):
ATTCACATCCCAACTTATTAATTTTAAGAAAAATTTCTAAGTTTAAAATAGCTTAGGG
Found at i:27765636 original size:26 final size:26
Alignment explanation
Indices: 27765584--27765636 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
27765574 ATTTGTTAAT
* * *
27765584 AAAACTTTGATTATTGTTGAAGAAAA
1 AAAACTTTGATTATTCTTAAACAAAA
*
27765610 AAAACTTTGATTA-TCTTAAACATAA
1 AAAACTTTGATTATTCTTAAACAAAA
27765635 AA
1 AA
27765637 CAGGGTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (26 bp):
AAAACTTTGATTATTCTTAAACAAAA
Found at i:27769240 original size:40 final size:40
Alignment explanation
Indices: 27769189--27769270 Score: 130
Period size: 40 Copynumber: 2.0 Consensus size: 40
27769179 AGTATTAATA
*
27769189 TTGTTACCTATACA-TAAGAGCATGAGTAAATGCATTTATC
1 TTGTTACCTATACAGAAAGA-CATGAGTAAATGCATTTATC
*
27769229 TTGTTATCTATACAGAAAGACATGAGTAAATGCATTTATC
1 TTGTTACCTATACAGAAAGACATGAGTAAATGCATTTATC
27769269 TT
1 TT
27769271 CCTATTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (40 bp):
TTGTTACCTATACAGAAAGACATGAGTAAATGCATTTATC
Found at i:27772688 original size:27 final size:27
Alignment explanation
Indices: 27772636--27772690 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
27772626 CACTCATGAA
* *
27772636 TTTTCTTCTTTTGTTTCTACTCATTTC
1 TTTTCTTCTTATCTTTCTACTCATTTC
*
27772663 TTTTCTTCTTGATCTTTTTACT-ATTTC
1 TTTTCTTCTT-ATCTTTCTACTCATTTC
27772690 T
1 T
27772691 CTCTTTTGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.09, C:0.20, G:0.04, T:0.67
Consensus pattern (27 bp):
TTTTCTTCTTATCTTTCTACTCATTTC
Found at i:27788373 original size:24 final size:25
Alignment explanation
Indices: 27788323--27788373 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
27788313 AGTTAATAAT
27788323 AATTCTCTTTGAGTTTTTCTTCAAG
1 AATTCTCTTTGAGTTTTTCTTCAAG
*
27788348 AATTGCTC-TTGAGTTTTT-TTCTAG
1 AATT-CTCTTTGAGTTTTTCTTCAAG
27788372 AA
1 AA
27788374 GTTGATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 14 0.58
26 3 0.12
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (25 bp):
AATTCTCTTTGAGTTTTTCTTCAAG
Found at i:27790303 original size:55 final size:55
Alignment explanation
Indices: 27790239--27790393 Score: 195
Period size: 55 Copynumber: 2.8 Consensus size: 55
27790229 GATAGCTATA
* * * *
27790239 AGATGCGACGATAATTCTGGGTGCAATTCTGGATCTACTCATGTAACGAGCTGTC
1 AGATGCGACGATAATTCTGGGCGCAATTCTAGATATACTCATGCAACGAGCTGTC
* *
27790294 AGATGCGACGATAATTTTGGGCGCAATTCTAGATATGCTCATGCAACGAGCTGTC
1 AGATGCGACGATAATTCTGGGCGCAATTCTAGATATACTCATGCAACGAGCTGTC
** * * *
27790349 AGATGCGGTGATAATTCTAGGCGCAATT-TTGTATATGCTCATGCA
1 AGATGCGACGATAATTCTGGGCGCAATTCTAG-ATATACTCATGCA
27790394 GCGACATTAG
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 2 0.02
55 86 0.98
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (55 bp):
AGATGCGACGATAATTCTGGGCGCAATTCTAGATATACTCATGCAACGAGCTGTC
Found at i:27799196 original size:21 final size:20
Alignment explanation
Indices: 27799152--27799196 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
27799142 CTTGGGAAAG
* *
27799152 TTCTACCGATACAGTGTAAC
1 TTCTACCGAAACAGTCTAAC
*
27799172 TTCTACCGAAACAAGTCTTAC
1 TTCTACCGAAAC-AGTCTAAC
27799193 TTCT
1 TTCT
27799197 TCTGATACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (20 bp):
TTCTACCGAAACAGTCTAAC
Found at i:27805418 original size:21 final size:21
Alignment explanation
Indices: 27805377--27805433 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
27805367 AGAGAAATGG
*
27805377 AGAAAAAT-A-TA-AAAGAAA
1 AGAAAAATGAGTAGAAACAAA
27805395 AGAAAAATGAGTAGAAACAAA
1 AGAAAAATGAGTAGAAACAAA
**
27805416 AGAATCATGAGTAAGAAA
1 AGAAAAATGAGT-AGAAA
27805434 ACATGTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 8 0.25
19 1 0.03
20 2 0.06
21 16 0.50
22 5 0.16
ACGTcount: A:0.67, C:0.04, G:0.18, T:0.12
Consensus pattern (21 bp):
AGAAAAATGAGTAGAAACAAA
Found at i:27822340 original size:15 final size:15
Alignment explanation
Indices: 27822320--27822359 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
27822310 GGATTACGAT
27822320 TATGATGATGACATC
1 TATGATGATGACATC
* *
27822335 TATGATGATGATATT
1 TATGATGATGACATC
*
27822350 TATGAAGATG
1 TATGATGATG
27822360 GATACAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (15 bp):
TATGATGATGACATC
Found at i:27830765 original size:25 final size:26
Alignment explanation
Indices: 27830736--27830784 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
27830726 ACACCAATGA
*
27830736 TTTAGATTA-ATTTTTCTCTTTTTAG
1 TTTAGATTAGACTTTTCTCTTTTTAG
* *
27830761 TTTAGTTTAGGCTTTTCTCTTTTT
1 TTTAGATTAGACTTTTCTCTTTTT
27830785 CTTAGGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.65
Consensus pattern (26 bp):
TTTAGATTAGACTTTTCTCTTTTTAG
Found at i:27835375 original size:9 final size:10
Alignment explanation
Indices: 27835360--27835403 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
27835350 TAGGTTATTT
27835360 TTCTTCTTTC
1 TTCTTCTTTC
27835370 -TCTTCTTTC
1 TTCTTCTTTC
*
27835379 -T-TTCCTTC
1 TTCTTCTTTC
27835387 TTCTTC-TTC
1 TTCTTCTTTC
27835396 TTCTTCTT
1 TTCTTCTT
27835404 GATCCTTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
8 6 0.20
9 20 0.67
10 4 0.13
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:27835401 original size:12 final size:11
Alignment explanation
Indices: 27835360--27835403 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
27835350 TAGGTTATTT
27835360 TTCTTCTTTCTC
1 TTCTTCTTT-TC
*
27835372 TTCTTTCTTTCC
1 TTC-TTCTTTTC
27835384 TTCTTCTTCTTC
1 TTCTTCTT-TTC
27835396 TTCTTCTT
1 TTCTTCTT
27835404 GATCCTTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 5 0.18
12 17 0.61
13 6 0.21
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (11 bp):
TTCTTCTTTTC
Found at i:27837290 original size:14 final size:15
Alignment explanation
Indices: 27837256--27837293 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
27837246 CTGAAACAAC
*
27837256 ACAACTAAAAGTGAA
1 ACAAATAAAAGTGAA
27837271 ACAAATAAAAG-GAA
1 ACAAATAAAAGTGAA
*
27837285 ATAAATAAA
1 ACAAATAAA
27837294 TGCGTCGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.68, C:0.08, G:0.11, T:0.13
Consensus pattern (15 bp):
ACAAATAAAAGTGAA
Found at i:27847163 original size:37 final size:38
Alignment explanation
Indices: 27847091--27847169 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
27847081 GACTGTCGCA
* * *
27847091 GCATAAATATTCTTCAAATTGCGTCCAGAACTATCGTT
1 GCATAAATATTCTTCAAATTGCGACCAAAAATATCGTT
*
27847129 GCATAAGTATTCTTC-AATTGC-ACCTAAAAATATCGTT
1 GCATAAATATTCTTCAAATTGCGACC-AAAAATATCGTT
27847166 GCAT
1 GCAT
27847170 GAACATGTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 2 0.06
37 20 0.56
38 14 0.39
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (38 bp):
GCATAAATATTCTTCAAATTGCGACCAAAAATATCGTT
Found at i:27850709 original size:5 final size:5
Alignment explanation
Indices: 27850693--27850725 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
27850683 ACTATAAATA
27850693 TTATT ATTATT TTATT TTATT TTATT TTATT TT
1 TTATT -TTATT TTATT TTATT TTATT TTATT TT
27850726 TTTACTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:27855680 original size:36 final size:36
Alignment explanation
Indices: 27855640--27855752 Score: 156
Period size: 36 Copynumber: 3.1 Consensus size: 36
27855630 AAATAAGTCA
* * *
27855640 ATAAATGATCTTATAAACGAGTTTTTAAATGAGTTT
1 ATAAACGATCTTATAAACGAGTTTATAAATGAGCTT
*
27855676 ATAAACGAGCTTATAAACGA-TCTTATAAATGAGCTT
1 ATAAACGATCTTATAAACGAGT-TTATAAATGAGCTT
* *
27855712 ATAAACGATCTTATAAATGAGTTTATAAACGAGCTT
1 ATAAACGATCTTATAAACGAGTTTATAAATGAGCTT
27855748 ATAAA
1 ATAAA
27855753 TGAGCCATAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 1 0.01
36 66 0.97
37 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (36 bp):
ATAAACGATCTTATAAACGAGTTTATAAATGAGCTT
Found at i:27855757 original size:12 final size:12
Alignment explanation
Indices: 27855640--27855770 Score: 138
Period size: 12 Copynumber: 11.0 Consensus size: 12
27855630 AAATAAGTCA
*
27855640 ATAAATGATCTT
1 ATAAATGAGCTT
* *
27855652 ATAAACGAGTTT
1 ATAAATGAGCTT
* *
27855664 TTAAATGAGTTT
1 ATAAATGAGCTT
*
27855676 ATAAACGAGCTT
1 ATAAATGAGCTT
* *
27855688 ATAAACGATCTT
1 ATAAATGAGCTT
27855700 ATAAATGAGCTT
1 ATAAATGAGCTT
* *
27855712 ATAAACGATCTT
1 ATAAATGAGCTT
*
27855724 ATAAATGAGTTT
1 ATAAATGAGCTT
*
27855736 ATAAACGAGCTT
1 ATAAATGAGCTT
*
27855748 ATAAATGAGC-C
1 ATAAATGAGCTT
27855759 ATAAATGAGCTT
1 ATAAATGAGCTT
27855771 GTTCGTGAAC
Statistics
Matches: 97, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
11 10 0.10
12 87 0.90
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (12 bp):
ATAAATGAGCTT
Found at i:27859404 original size:2 final size:2
Alignment explanation
Indices: 27859397--27859447 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
27859387 TCGTTTGCTT
27859397 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
27859439 TC TC TC TC T
1 TC TC TC TC T
27859448 TTTCTCCATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:27860570 original size:49 final size:49
Alignment explanation
Indices: 27860419--27860737 Score: 168
Period size: 49 Copynumber: 6.5 Consensus size: 49
27860409 GTCGTTGCGG
*
27860419 CTTAAACCTTTCCCTTCATGTC-CTGAGGTACAAGGTTCGCCGTTGTGA
1 CTTAAACCTTTCCCTTCATGTCTTTGAGGTACAAGGTTCGCCGTTGTGA
* * * * * * ** * *
27860467 CTTAAACCCTTCTCTCCATTTTCTTCGTGGTA-TTGGATTCGCCGTTGCGG
1 CTTAAACCTTTCCCTTCA-TGTCTTTGAGGTACAAGG-TTCGCCGTTGTGA
* * * * *
27860517 CTTAAATCTTTCACTTCATGTCTTTGTGGTACAAGGTTCACCATTGTGA
1 CTTAAACCTTTCCCTTCATGTCTTTGAGGTACAAGGTTCGCCGTTGTGA
* * *** *
27860566 CTTAAACCTTTCCCTTCATG-CTTCTGAGGTATAAGGTACGTTATTGCGA
1 CTTAAACCTTTCCCTTCATGTCTT-TGAGGTACAAGGTTCGCCGTTGTGA
* * * * * *
27860615 CTTAAACCTTACCC-TCTAT-TATATTCGTA-GTACTAGATTCGCCGTTGCGG
1 CTTAAACCTTTCCCTTC-ATGTCT-TT-G-AGGTACAAGGTTCGCCGTTGTGA
* ** * * * *
27860665 CTTAAACCTTTCCCTTAACATC-TTCATGGTTC-TGGATTCGCCGTTGTGG
1 CTTAAACCTTTCCCTTCATGTCTTTGA-GGTACAAGG-TTCGCCGTTGTGA
* *
27860714 CTTAAATCTTTACCTTCATGTCTT
1 CTTAAACCTTTCCCTTCATGTCTT
27860738 CATGATAAAC
Statistics
Matches: 199, Mismatches: 56, Indels: 30
0.70 0.20 0.11
Matches are distributed among these distances:
47 1 0.01
48 21 0.11
49 112 0.56
50 62 0.31
51 3 0.02
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (49 bp):
CTTAAACCTTTCCCTTCATGTCTTTGAGGTACAAGGTTCGCCGTTGTGA
Found at i:27860597 original size:98 final size:98
Alignment explanation
Indices: 27860405--27860597 Score: 246
Period size: 98 Copynumber: 2.0 Consensus size: 98
27860395 GTAGTACTAA
* * * *
27860405 ATTCGTCGTTGCGGCTTAAACCTTTCCCTTCATGTCCTGAGGTACAAGGTTCGCCGTTGTGACTT
1 ATTCGCCGTTGCGGCTTAAACCTTTCACTTCATGTCCTGAGGTACAAGGTTCACCATTGTGACTT
* * *
27860470 AAACCCTTCTCTCCATTTTCTTCGTGGTATTGG
66 AAACCCTTCCCTCCATCTTCTTCGAGGTATTGG
* * *
27860503 ATTCGCCGTTGCGGCTTAAATCTTTCACTTCATGTCTTTGTGGTACAAGGTTCACCATTGTGACT
1 ATTCGCCGTTGCGGCTTAAACCTTTCACTTCATGTC-CTGAGGTACAAGGTTCACCATTGTGACT
* *
27860568 TAAACCTTTCCCTTCATGCTTC-T-GAGGTAT
65 TAAACCCTTCCCTCCAT-CTTCTTCGAGGTAT
27860598 AAGGTACGTT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
98 39 0.48
99 39 0.48
100 3 0.04
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (98 bp):
ATTCGCCGTTGCGGCTTAAACCTTTCACTTCATGTCCTGAGGTACAAGGTTCACCATTGTGACTT
AAACCCTTCCCTCCATCTTCTTCGAGGTATTGG
Found at i:27860613 original size:98 final size:98
Alignment explanation
Indices: 27860413--27860624 Score: 223
Period size: 98 Copynumber: 2.2 Consensus size: 98
27860403 AAATTCGTCG
* * *
27860413 TTGCGGCTTAAACCTTTCCCTTCATGTCCTGAGGTACAAGGTTCGCCGTTGTGACTTAAACCCTT
1 TTGCGGCTTAAACCTTTCACTTCATGTCCTGAGGTACAAGGTTCACCATTGTGACTTAAACCCTT
* * * * * *
27860478 CTCTCCATTTTCTTCGTGGTATTGGATTCGCCG
66 CCCTCCATCTTCTTCGAGGTATAGGATACGCCA
* * * *
27860511 TTGCGGCTTAAATCTTTCACTTCATGTCTTTGTGGTACAAGGTTCACCATTGTGACTTAAACCTT
1 TTGCGGCTTAAACCTTTCACTTCATGTC-CTGAGGTACAAGGTTCACCATTGTGACTTAAACCCT
* **
27860576 TCCCTTCATGCTTC-T-GAGGTATAAGG-TACGTTA
65 TCCCTCCAT-CTTCTTCGAGGTAT-AGGATACGCCA
*
27860609 TTGCGACTTAAACCTT
1 TTGCGGCTTAAACCTT
27860625 ACCCTCTATT
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
98 49 0.53
99 41 0.44
100 3 0.03
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (98 bp):
TTGCGGCTTAAACCTTTCACTTCATGTCCTGAGGTACAAGGTTCACCATTGTGACTTAAACCCTT
CCCTCCATCTTCTTCGAGGTATAGGATACGCCA
Found at i:27860712 original size:148 final size:149
Alignment explanation
Indices: 27860405--27860738 Score: 352
Period size: 148 Copynumber: 2.3 Consensus size: 149
27860395 GTAGTACTAA
* * * * * *
27860405 ATTCGTCGTTGCGGCTTAAACCTTTCCCTTCATG-TCCTGAGGTACAAGGTTCGCCGTTGTGACT
1 ATTCGCCGTTGTGGCTTAAACCTTTCCCTTCATGCTTCTGAGGTACAAGGTACGCCATTGCGACT
* * * * * * * *
27860469 TAAACCCTTCTCTCCATTTTCTTCGTGGTATTGGATTCGCCGTTGCGGCTTAAATCTTTCACTTC
66 TAAACCCTTCCCTCCATTATATTCGTAGTACTAGATTCGCCGTTGCGGCTTAAACCTTTCACTTA
** **
27860534 ATGTCTTTGTGGTACAAGG
131 ACATCTTCATGGTACAAGG
* * * * **
27860553 -TTCACCATTGTGACTTAAACCTTTCCCTTCATGCTTCTGAGGTATAAGGTACGTTATTGCGACT
1 ATTCGCCGTTGTGGCTTAAACCTTTCCCTTCATGCTTCTGAGGTACAAGGTACGCCATTGCGACT
* *
27860617 TAAA-CCTTACCCTCTATTATATTCGTAGTACTAGATTCGCCGTTGCGGCTTAAACCTTTCCCTT
66 TAAACCCTT-CCCTCCATTATATTCGTAGTACTAGATTCGCCGTTGCGGCTTAAACCTTTCACTT
* *
27860681 AACATCTTCATGGTTC-TGG
130 AACATCTTCATGGTACAAGG
* *
27860700 ATTCGCCGTTGTGGCTTAAATCTTTACCTTCATGTCTTC
1 ATTCGCCGTTGTGGCTTAAACCTTTCCCTTCATG-CTTC
27860739 ATGATAAACC
Statistics
Matches: 149, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
147 34 0.23
148 111 0.74
149 4 0.03
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (149 bp):
ATTCGCCGTTGTGGCTTAAACCTTTCCCTTCATGCTTCTGAGGTACAAGGTACGCCATTGCGACT
TAAACCCTTCCCTCCATTATATTCGTAGTACTAGATTCGCCGTTGCGGCTTAAACCTTTCACTTA
ACATCTTCATGGTACAAGG
Found at i:27861127 original size:60 final size:60
Alignment explanation
Indices: 27861034--27861155 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
27861024 CGCAGATCCT
27861034 TGCATTTTCGTGTGATATTAGTCTATTATCCATTATCTTATTATGAAAATACTTGGTCAG
1 TGCATTTTCGTGTGATATTAGTCTATTATCCATTATCTTATTATGAAAATACTTGGTCAG
*
27861094 TGCATTTTCGTGTGATATTAGTCTATTATCCATTATCTTGTTATGAAAATACTTGGTCAG
1 TGCATTTTCGTGTGATATTAGTCTATTATCCATTATCTTATTATGAAAATACTTGGTCAG
27861154 TG
1 TG
27861156 TGGCAAATGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (60 bp):
TGCATTTTCGTGTGATATTAGTCTATTATCCATTATCTTATTATGAAAATACTTGGTCAG
Found at i:27872754 original size:2 final size:2
Alignment explanation
Indices: 27872747--27872782 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27872737 TTCTTTTGCG
27872747 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
27872783 TTTCTCTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:27873066 original size:14 final size:14
Alignment explanation
Indices: 27873042--27873077 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
27873032 TAGCGTTGAT
27873042 GTGGC-ATGCTGAC
1 GTGGCAATGCTGAC
*
27873055 GTGGCAATGCTGAT
1 GTGGCAATGCTGAC
27873069 GTGGCAATG
1 GTGGCAATG
27873078 GCTACTGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.19, C:0.17, G:0.39, T:0.25
Consensus pattern (14 bp):
GTGGCAATGCTGAC
Found at i:27875648 original size:47 final size:47
Alignment explanation
Indices: 27875597--27875729 Score: 167
Period size: 47 Copynumber: 2.8 Consensus size: 47
27875587 ATGCAAATAA
* * * *
27875597 ACTGCCAATAATCAAAATTGTGGAGAAGCCACCAAAGTCGCAGATAT
1 ACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCACAGATAT
* *
27875644 ACTGCCAATAATCAATATCGTGGACAAGTCACCAAAATCACAGATAT
1 ACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCACAGATAT
* * * * *
27875691 ACTACAAATAATCAATATCATGGACAAGGCACCAAAATC
1 ACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATC
27875730 GTAAAAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 76 1.00
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.20
Consensus pattern (47 bp):
ACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCACAGATAT
Found at i:27875748 original size:47 final size:47
Alignment explanation
Indices: 27875590--27875748 Score: 129
Period size: 47 Copynumber: 3.4 Consensus size: 47
27875580 CGCACTAATG
* * ** * * * *
27875590 CAAATAAACTGCCAATAATCAAAATTGTGGAGAAGCCACCAAAGTCG
1 CAAAAAAACTGCCAATAATCAATATCATGGACAAGGCACCAAAATCA
* * * * *
27875637 CAGATATACTGCCAATAATCAATATCGTGGACAAGTCACCAAAATCA
1 CAAAAAAACTGCCAATAATCAATATCATGGACAAGGCACCAAAATCA
* * * * * *
27875684 CAGATATACTACAAATAATCAATATCATGGACAAGGCACCAAAATCG
1 CAAAAAAACTGCCAATAATCAATATCATGGACAAGGCACCAAAATCA
* *
27875731 TAAAAAAATTGCCAATAA
1 CAAAAAAACTGCCAATAA
27875749 CTTCCACCTT
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 92 1.00
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (47 bp):
CAAAAAAACTGCCAATAATCAATATCATGGACAAGGCACCAAAATCA
Found at i:27879673 original size:2 final size:2
Alignment explanation
Indices: 27879666--27879693 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27879656 TAAATTTTTA
27879666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27879694 TGATTTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27886469 original size:51 final size:51
Alignment explanation
Indices: 27886399--27886626 Score: 393
Period size: 51 Copynumber: 4.5 Consensus size: 51
27886389 TTTCATTTAA
*
27886399 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
* *
27886450 TACTCACGACGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
* *
27886501 TACTCACGATGACACTTAGTCACCGAACCTTTAATCCTTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
* *
27886552 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
27886603 TACTCACGATGACACTTAGTCATC
1 TACTCACGATGACACTTAGTCATC
27886627 AGACTCTTTC
Statistics
Matches: 165, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 165 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
Found at i:27890361 original size:49 final size:48
Alignment explanation
Indices: 27890308--27890860 Score: 622
Period size: 49 Copynumber: 11.3 Consensus size: 48
27890298 GAAGGCGTGA
* * *
27890308 AGGGAAAGATTGAAGCCGCAACAGCGAATCTTGTACCCTAGAGATATAG
1 AGGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGT-G
* *
27890357 AGGGAAAGATTGAAGCCGCAATGATGAATCTTGTACCCTAGAGATGTG
1 AGGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGTG
* * * * * *
27890405 AAGGGAAAGATTGAAGCTGCCACAGCGAATCTTGTACCTTACAGATGTG
1 -AGGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGTG
* *
27890454 ATGGGAAATATTGAAGCCGCAACGGTGAATCTTGTACCTTAGAGATGTGG
1 A-GGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGT-G
* *
27890504 AGGGAAAGATTGAAGTCGCAATGGTGAATCTTGTACCCTAGAGATGTG
1 AGGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGTG
* * * *
27890552 AAGGGAAAGATTGAAGCCGCAATGGTGAACCTTGTACCTTAGAGATATG
1 -AGGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGTG
* * * *
27890601 ATGAGAAACATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGATTTGG
1 A-GGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGT-G
* * *
27890651 AGGGAAAGATTGAAGCTGCAATGGTGAATCTTGTACCCTAGATATGTG
1 AGGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGTG
* * * *
27890699 AAGGGAAAGATTGAAGCTGCAACGGTGAATCTTATACCTTACAGATGTG
1 -AGGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGTG
*
27890748 ATGGGAAAGATTGAAGCCGCAATC-GTGAATCTTGTACCTTAGAGATGTG
1 A-GGGAAAGATTGAAGCCGCAA-CGGTGAATCTTGTACCCTAGAGATGTG
* * * ** * * *
27890797 ATGGGAAATATTGAAGTCGTAATAGCGAATCTTGTACCCTAAAAGGTGTG
1 A-GGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCT-AGAGATGTG
*
27890847 AAAGGAAAGATTGA
1 -AGGGAAAGATTGA
27890861 GCCCACAACG
Statistics
Matches: 433, Mismatches: 59, Indels: 23
0.84 0.11 0.04
Matches are distributed among these distances:
48 6 0.01
49 404 0.93
50 22 0.05
51 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (48 bp):
AGGGAAAGATTGAAGCCGCAACGGTGAATCTTGTACCCTAGAGATGTG
Found at i:27890461 original size:98 final size:97
Alignment explanation
Indices: 27890304--27890860 Score: 686
Period size: 98 Copynumber: 5.7 Consensus size: 97
27890294 CCCTGAAGGC
* *
27890304 GTGAAGGGAAAGATTGAAGCCGCAACAGCGAATCTTGTACCCTAGAGATATAGAGGGAAAGATTG
1 GTGAAGGGAAAGATTGAAGCTGCAACAGCGAATCTTGTACCCTAGAGATGT-GAGGGAAAGATTG
* *
27890369 AAGCCGCAATGATGAATCTTGTACCCTAGAGAT
65 AAGCCGCAATGGTGAATCTTGTACCTTAGAGAT
* * * *
27890402 GTGAAGGGAAAGATTGAAGCTGCCACAGCGAATCTTGTACCTTACAGATGTGATGGGAAATATTG
1 GTGAAGGGAAAGATTGAAGCTGCAACAGCGAATCTTGTACCCTAGAGATGTGA-GGGAAAGATTG
*
27890467 AAGCCGCAACGGTGAATCTTGTACCTTAGAGAT
65 AAGCCGCAATGGTGAATCTTGTACCTTAGAGAT
* ** *
27890500 GTGGAGGGAAAGATTGAAG-TCGCAATGGTGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATT
1 GTGAAGGGAAAGATTGAAGCT-GCAACAGCGAATCTTGTACCCTAGAGATGTG-AGGGAAAGATT
*
27890564 GAAGCCGCAATGGTGAACCTTGTACCTTAGAGAT
64 GAAGCCGCAATGGTGAATCTTGTACCTTAGAGAT
* * * * * * *
27890598 ATGATGAGAAACATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGATTTGGAGGGAAAGATTG
1 GTGAAGGGAAAGATTGAAGCTGCAACAGCGAATCTTGTACCCTAGAGATGT-GAGGGAAAGATTG
* * *
27890663 AAGCTGCAATGGTGAATCTTGTACCCTAGATAT
65 AAGCCGCAATGGTGAATCTTGTACCTTAGAGAT
* * * * *
27890696 GTGAAGGGAAAGATTGAAGCTGCAACGGTGAATCTTATACCTTACAGATGTGATGGGAAAGATTG
1 GTGAAGGGAAAGATTGAAGCTGCAACAGCGAATCTTGTACCCTAGAGATGTGA-GGGAAAGATTG
*
27890761 AAGCCGCAATCGTGAATCTTGTACCTTAGAGAT
65 AAGCCGCAATGGTGAATCTTGTACCTTAGAGAT
* * * * * * *
27890794 GTGATGGGAAATATTGAAG-TCGTAATAGCGAATCTTGTACCCTAAAAGGTGTGAAAGGAAAGAT
1 GTGAAGGGAAAGATTGAAGCT-GCAACAGCGAATCTTGTACCCT-AGAGATGTG-AGGGAAAGAT
27890858 TGA
63 TGA
27890861 GCCCACAACG
Statistics
Matches: 393, Mismatches: 57, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
97 6 0.02
98 366 0.93
99 20 0.05
100 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (97 bp):
GTGAAGGGAAAGATTGAAGCTGCAACAGCGAATCTTGTACCCTAGAGATGTGAGGGAAAGATTGA
AGCCGCAATGGTGAATCTTGTACCTTAGAGAT
Found at i:27890586 original size:147 final size:147
Alignment explanation
Indices: 27890304--27890860 Score: 778
Period size: 147 Copynumber: 3.8 Consensus size: 147
27890294 CCCTGAAGGC
* * * *
27890304 GTGAAGGGAAAGATTGAAGCCGCAACAGCGAATCTTGTACCCTAGAGATATAGAGGGAAAGATTG
1 GTGATGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGATGTGGAGGGAAAGATTG
* * * * *
27890369 AAGCCGCAATGATGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCTGCCACAGCGAA
66 AAGTCGCAATGGTGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCTGCAACGGTGAA
27890434 TCTTGTACCTTACAGAT
131 TCTTGTACCTTACAGAT
* * *
27890451 GTGATGGGAAATATTGAAGCCGCAACGGTGAATCTTGTACCTTAGAGATGTGGAGGGAAAGATTG
1 GTGATGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGATGTGGAGGGAAAGATTG
* *
27890516 AAGTCGCAATGGTGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAATGGTGAA
66 AAGTCGCAATGGTGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCTGCAACGGTGAA
* *
27890581 CCTTGTACCTTAGAGAT
131 TCTTGTACCTTACAGAT
* * * *
27890598 ATGATGAGAAACATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGATTTGGAGGGAAAGATTG
1 GTGATGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGATGTGGAGGGAAAGATTG
*
27890663 AAG-CTGCAATGGTGAATCTTGTACCCTAGATATGTGAAGGGAAAGATTGAAGCTGCAACGGTGA
66 AAGTC-GCAATGGTGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCTGCAACGGTGA
*
27890727 ATCTTATACCTTACAGAT
130 ATCTTGTACCTTACAGAT
* * *
27890745 GTGATGGGAAAGATTGAAGCCGCAATC-GTGAATCTTGTACCTTAGAGATGT-GATGGGAAATAT
1 GTGATGGGAAAGATTGAAGCCGCAA-CGGCGAATCTTGTACCCTAGAGATGTGGA-GGGAAAGAT
* * * * * *
27890808 TGAAGTCGTAATAGCGAATCTTGTACCCTAAAAGGTGTGAAAGGAAAGATTGA
64 TGAAGTCGCAATGGTGAATCTTGTACCCT-AGAGATGTGAAGGGAAAGATTGA
27890861 GCCCACAACG
Statistics
Matches: 363, Mismatches: 42, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
146 3 0.01
147 339 0.93
148 21 0.06
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (147 bp):
GTGATGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGATGTGGAGGGAAAGATTG
AAGTCGCAATGGTGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCTGCAACGGTGAA
TCTTGTACCTTACAGAT
Found at i:27892828 original size:2 final size:2
Alignment explanation
Indices: 27892821--27892846 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27892811 AAATATTTTA
27892821 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
27892847 TAGTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27895285 original size:23 final size:23
Alignment explanation
Indices: 27895252--27895299 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
27895242 ACATTAACTG
*
27895252 ATAAAACCCCTTTTTGTATTCCC
1 ATAAAAACCCTTTTTGTATTCCC
27895275 ATAAAAACCCTTTTTGTATTCCC
1 ATAAAAACCCTTTTTGTATTCCC
27895298 AT
1 AT
27895300 TTTCATCGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40
Consensus pattern (23 bp):
ATAAAAACCCTTTTTGTATTCCC
Found at i:27901000 original size:6 final size:6
Alignment explanation
Indices: 27900989--27901015 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27900979 AAAAATTATA
27900989 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
27901016 TAAAAGTTAT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:27901030 original size:10 final size:9
Alignment explanation
Indices: 27900979--27901146 Score: 62
Period size: 10 Copynumber: 18.4 Consensus size: 9
27900969 ACATGTGGTA
27900979 AAAAATTAT
1 AAAAATTAT
* *
27900988 AAAAAATAA
1 AAAAATTAT
**
27900997 AAATAAAAAT
1 AAA-AATTAT
*
27901007 AAAAATAAAT
1 AAAAAT-TAT
*
27901017 AAAAGTTAT
1 AAAAATTAT
27901026 AAAAATTATT
1 AAAAATTA-T
* **
27901036 AGATTTTAAT
1 AAAAATT-AT
*
27901046 AAAAATATTT
1 AAAAAT-TAT
*
27901056 TAAAA-TATT
1 AAAAATTA-T
*
27901065 AAAAATTAG
1 AAAAATTAT
27901074 AAAAA--A-
1 AAAAATTAT
*
27901080 AAAGA-TA-
1 AAAAATTAT
*
27901087 AAAATATAAT
1 AAAA-ATTAT
27901097 AA-AATTAT
1 AAAAATTAT
27901105 AAAATATTAT
1 AAAA-ATTAT
*
27901115 AAAATTTTAT
1 AAAA-ATTAT
*
27901125 AAAAATAAT
1 AAAAATTAT
27901134 AAAAATTAT
1 AAAAATTAT
27901143 AAAA
1 AAAA
27901147 TGTATCAAAA
Statistics
Matches: 119, Mismatches: 27, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
6 4 0.03
7 5 0.04
8 8 0.07
9 49 0.41
10 51 0.43
11 2 0.02
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:27901106 original size:19 final size:19
Alignment explanation
Indices: 27900980--27901146 Score: 87
Period size: 19 Copynumber: 8.6 Consensus size: 19
27900970 CATGTGGTAA
*
27900980 AAAATTATAAAAAATAAAAAT
1 AAAATTAT-AAAAAT-ATAAT
27901001 AAAA--ATAAAAATA-AAT
1 AAAATTATAAAAATATAAT
*
27901017 AAAAGTTATAAAAAT-TATT
1 AAAA-TTATAAAAATATAAT
** **
27901036 AGATTTTAATAAAAATATTTT
1 A-AAATT-ATAAAAATATAAT
* *
27901057 AAAA-TATTAAAAATTAGAAAA
1 AAAATTA-TAAAAA-TA-TAAT
**
27901078 AAAAAGATAAAAATATAAT
1 AAAATTATAAAAATATAAT
*
27901097 AAAATTAT-AAAATATTAT
1 AAAATTATAAAAATATAAT
*
27901115 AAAATTTTATAAAA-ATAAT
1 AAAATTATA-AAAATATAAT
27901134 AAAAATTATAAAA
1 -AAAATTATAAAA
27901147 TGTATCAAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 30
0.70 0.12 0.19
Matches are distributed among these distances:
16 7 0.06
17 1 0.01
18 23 0.20
19 37 0.33
20 26 0.23
21 18 0.16
22 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAAAATATAAT
Found at i:27901108 original size:18 final size:18
Alignment explanation
Indices: 27901087--27901147 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
27901077 AAAAAAGATA
27901087 AAAATATAATAAAATTAT
1 AAAATATAATAAAATTAT
*
27901105 AAAATATTATAAAATTTTAT
1 AAAATATAATAAAA--TTAT
27901125 AAAA-ATAATAAAAATTAT
1 AAAATATAAT-AAAATTAT
27901143 AAAAT
1 AAAAT
27901148 GTATCAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 21 0.57
19 4 0.11
20 12 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATATAATAAAATTAT
Found at i:27901119 original size:28 final size:28
Alignment explanation
Indices: 27901087--27901147 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
27901077 AAAAAAGATA
*
27901087 AAAATATAAT-AAAATTATAAAATATTAT
1 AAAATATAATAAAAATAATAAAA-ATTAT
* *
27901115 AAAATTTTATAAAAATAATAAAAATTAT
1 AAAATATAATAAAAATAATAAAAATTAT
27901143 AAAAT
1 AAAAT
27901148 GTATCAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
AAAATATAATAAAAATAATAAAAATTAT
Found at i:27901157 original size:79 final size:78
Alignment explanation
Indices: 27900979--27901158 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 78
27900969 ACATGTGGTA
* * *
27900979 AAAAATTATAAAA-AATAAAAATAAAAATAAAAATAAATAAAAGTTATAAAAATTATTAGATTTT
1 AAAAATTATAAAATTATAAAAATAAAAATAAAAATAAATAAAAGTTATAAAAATTATAAAATTTT
*
27901043 AATAAAAATATTTT
66 AATAAAAATA-TAT
*
27901057 AAAATATTA-AAAATTAGAAAAA-AAAAGATAAAAATATAATAAAA-TTATAAAATATTATAAAA
1 AAAA-ATTATAAAATTATAAAAATAAAA-ATAAAAATA-AATAAAAGTTATAAAA-ATTATAAAA
27901119 TTTT-ATAAAAATA-AT
62 TTTTAATAAAAATATAT
27901134 AAAAATTATAAAATGTATCAAAAAT
1 AAAAATTATAAAAT-TAT-AAAAAT
27901159 CTCTTTAATC
Statistics
Matches: 87, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
76 4 0.05
77 10 0.11
78 14 0.16
79 41 0.47
80 18 0.21
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (78 bp):
AAAAATTATAAAATTATAAAAATAAAAATAAAAATAAATAAAAGTTATAAAAATTATAAAATTTT
AATAAAAATATAT
Found at i:27901408 original size:18 final size:18
Alignment explanation
Indices: 27901387--27901437 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
27901377 TTTTATAAAA
27901387 TTTTATAATTTTTAAGAT
1 TTTTATAATTTTTAAGAT
*
27901405 TTTTATAATTTTTAATAT
1 TTTTATAATTTTTAAGAT
*
27901423 TCTTTATATTTTTTA
1 T-TTTATAATTTTTA
27901438 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATAATTTTTAAGAT
Found at i:27911066 original size:38 final size:38
Alignment explanation
Indices: 27910996--27911264 Score: 173
Period size: 36 Copynumber: 7.2 Consensus size: 38
27910986 AAGGCCGACC
* ** *
27910996 TTTAAAAAAGGTTGGGATAAGTTTTGTCTAAGGGAACCT
1 TTTAAAAAAAGTTGGGATAA-ACTTGTCTAAGGCAACCT
* *
27911035 TTTAAAAAAAGTTGGGATAAACTCGTTTAAGGCAACC-
1 TTTAAAAAAAGTTGGGATAAACTTGTCTAAGGCAACCT
* * * *
27911072 -TTAAAAAGA-TTAGGATAGACATTGTCTAAGACAACCT
1 TTTAAAAAAAGTTGGGATAAAC-TTGTCTAAGGCAACCT
* * **
27911109 TTT-AAAAAAGTTGAGATAAACCTTATCTAAAACAACC-
1 TTTAAAAAAAGTTGGGATAAA-CTTGTCTAAGGCAACCT
* * *
27911146 -TTAAAAAAA-TTGGGATATACCTTATCTAAAGCAACC-
1 TTTAAAAAAAGTTGGGATA-AACTTGTCTAAGGCAACCT
* * *
27911182 TTT--AAAAGGTTAGGATAAATCTTGTCTAAGACAACCT
1 TTTAAAAAAAGTTGGGATAAA-CTTGTCTAAGGCAACCT
* * * * * *
27911219 TATAAAAAGA-TTGGAATAAATCTTATCTAAAGCAACAT
1 TTTAAAAAAAGTTGGGATAAA-CTTGTCTAAGGCAACCT
27911257 TTTAAAAA
1 TTTAAAAA
27911265 GATTGAGATA
Statistics
Matches: 180, Mismatches: 37, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
35 14 0.08
36 64 0.36
37 16 0.09
38 63 0.35
39 23 0.13
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (38 bp):
TTTAAAAAAAGTTGGGATAAACTTGTCTAAGGCAACCT
Found at i:27911145 original size:74 final size:72
Alignment explanation
Indices: 27911067--27911346 Score: 241
Period size: 74 Copynumber: 3.8 Consensus size: 72
27911057 TCGTTTAAGG
* *
27911067 CAACC-TTAAAAAGATTAGGATAGACATTGTCT-AAGACAACCTTTTAAAAAAGTTGAGATAAAC
1 CAACCTTTAAAAAGATT-GGATAAAC-TTATCTAAAG-CAACCTTTT-AAAAAGTTGAGATAAAC
27911130 CTTATCTAAAA
62 CTTATCTAAAA
* * * *
27911141 CAACC-TTAAAAAAATTGGGATATACCTTATCTAAAGCAACC-TTTAAAAGGTT-AGGATAAATC
1 CAACCTTTAAAAAGATT-GGATA-AACTTATCTAAAGCAACCTTTTAAAAAGTTGA-GATAAACC
* *
27911203 TTGTCTAAGA
63 TTATCTAAAA
* *
27911213 CAACCTTATAAAAAGATTGGAATAAATCTTATCTAAAGCAACATTTTAAAAAGATTGAGATAGAC
1 CAACCTT-TAAAAAGATTGG-ATAAA-CTTATCTAAAGCAACCTTTTAAAAAG-TTGAGATAAAC
*
27911278 CTTATCTAAAG
62 CTTATCTAAAA
* * * ** *
27911289 TAACCTTTAAAAAAGATTGAAATAGACAGATCTAAAGCAACC--TTAAAAGGTTGAGATA
1 CAACCTTT-AAAAAGATTG-GATAAACTTATCTAAAGCAACCTTTTAAAAAGTTGAGATA
27911347 GACACATGTA
Statistics
Matches: 169, Mismatches: 25, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
71 1 0.01
72 35 0.21
73 14 0.08
74 57 0.34
75 26 0.15
76 35 0.21
77 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (72 bp):
CAACCTTTAAAAAGATTGGATAAACTTATCTAAAGCAACCTTTTAAAAAGTTGAGATAAACCTTA
TCTAAAA
Found at i:27911207 original size:110 final size:111
Alignment explanation
Indices: 27911036--27911300 Score: 308
Period size: 110 Copynumber: 2.4 Consensus size: 111
27911026 AGGGAACCTT
* * * *
27911036 TTAAAAAAAGTTGGGATAAACTCGT-T-TAAGGCAACCTTAAAAAGATTAGGATAGACATTGTCT
1 TTAAAAAAA-TTGGGATAAAC-CTTATCTAAAGCAACCTTTAAAAGATTAGGATAAACATTGTCT
*
27911099 AAGACAACCTTTTAAAAA-AGTT-GAGATAAACCTTATCTAAAACAAC-C
64 AAGACAACCTTATAAAAAGA-TTGGA-ATAAACCTTATCTAAAACAACAC
* *
27911146 TTAAAAAAATTGGGATATACCTTATCTAAAGCAACCTTTAAAAGGTTAGGATAAATC-TTGTCTA
1 TTAAAAAAATTGGGATAAACCTTATCTAAAGCAACCTTTAAAAGATTAGGATAAA-CATTGTCTA
* * *
27911210 AGACAACCTTATAAAAAGATTGGAATAAATCTTATCTAAAGCAACATT
65 AGACAACCTTATAAAAAGATTGGAATAAACCTTATCTAAAACAACA-C
* * * *
27911258 TTAAAAAGATTGAGATAGACCTTATCTAAAGTAACCTTTAAAA
1 TTAAAAAAATTGGGATAAACCTTATCTAAAGCAACCTTTAAAA
27911301 AAGATTGAAA
Statistics
Matches: 134, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
108 2 0.01
109 11 0.08
110 78 0.58
111 4 0.03
112 39 0.29
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.29
Consensus pattern (111 bp):
TTAAAAAAATTGGGATAAACCTTATCTAAAGCAACCTTTAAAAGATTAGGATAAACATTGTCTAA
GACAACCTTATAAAAAGATTGGAATAAACCTTATCTAAAACAACAC
Found at i:27911265 original size:38 final size:38
Alignment explanation
Indices: 27911030--27911332 Score: 197
Period size: 38 Copynumber: 8.2 Consensus size: 38
27911020 TGTCTAAGGG
* * * *
27911030 AACCTTTTAAAAAAAGTTGGGATAAACTCGT-T-TAAGGC
1 AACCTTTTAAAAAGA-TTGGAATAAAC-CTTATCTAAAGC
* * *
27911068 AACC--TTAAAAAGATTAGG-ATAGACATTGTCT-AAGAC
1 AACCTTTTAAAAAGATT-GGAATAAACCTTATCTAAAG-C
*
27911104 AACCTTTTAAAAA-AGTT-GAGATAAACCTTATCTAAAAC
1 AACCTTTTAAAAAGA-TTGGA-ATAAACCTTATCTAAAGC
* * *
27911142 AACC--TTAAAAAAATTGGGATATACCTTATCTAAAGC
1 AACCTTTTAAAAAGATTGGAATAAACCTTATCTAAAGC
* * *
27911178 AACC-TTT-AAAAGGTTAGG-ATAAATCTTGTCT-AAGAC
1 AACCTTTTAAAAAGATT-GGAATAAACCTTATCTAAAG-C
* *
27911214 AACCTTATAAAAAGATTGGAATAAATCTTATCTAAAGC
1 AACCTTTTAAAAAGATTGGAATAAACCTTATCTAAAGC
* * *
27911252 AACATTTTAAAAAGATT-GAGATAGACCTTATCTAAAGT
1 AACCTTTTAAAAAGATTGGA-ATAAACCTTATCTAAAGC
* * * **
27911290 AACCTTTAAAAAAGATTGAAATAGA-CAGATCTAAAGC
1 AACCTTTTAAAAAGATTGGAATAAACCTTATCTAAAGC
27911327 AACCTT
1 AACCTT
27911333 AAAAGGTTGA
Statistics
Matches: 213, Mismatches: 31, Indels: 43
0.74 0.11 0.15
Matches are distributed among these distances:
34 1 0.00
35 13 0.06
36 67 0.31
37 28 0.13
38 98 0.46
39 6 0.03
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (38 bp):
AACCTTTTAAAAAGATTGGAATAAACCTTATCTAAAGC
Found at i:27911348 original size:34 final size:35
Alignment explanation
Indices: 27911066--27911362 Score: 119
Period size: 38 Copynumber: 8.1 Consensus size: 35
27911056 CTCGTTTAAG
**
27911066 GCAACCTTAAAAAGATT-AGGATAGACATTGTCT-AA
1 GCAACCTTAAAAAGATTGA-GATAGACA-CATCTAAA
*
27911101 GACAACCTTTTAAAAA-AGTTGAGATAAAC-CTTATCTAAA
1 G-CAACC--TTAAAAAGA-TTGAGATAGACAC--ATCTAAA
* * * *
27911140 ACAACCTTAAAAAAATTGGGATATAC-CTTATCTAAA
1 GCAACCTTAAAAAGATTGAGATAGACAC--ATCTAAA
* * * ***
27911176 GCAACCTTTAAAAGGTT-AGGATAAATCTTGTCT-AA
1 GCAACCTTAAAAAGATTGA-GATAGA-CACATCTAAA
* **
27911211 GACAACCTTATAAAAAGATTG-GAATAAATCTTATCTAAA
1 G-CAACC-T-TAAAAAGATTGAG-ATAGA-CACATCTAAA
*
27911250 GCAACATTTTAAAAAGATTGAGATAGAC-CTTATCTAAA
1 GCAAC--CTTAAAAAGATTGAGATAGACAC--ATCTAAA
* * *
27911288 GTAACCTTTAAAAAAGATTGAAATAGACAGATCTAAA
1 GCAACC-TT-AAAAAGATTGAGATAGACACATCTAAA
* *
27911325 GCAACCTT-AAAAGGTTGAGATAGACACATGTAAA
1 GCAACCTTAAAAAGATTGAGATAGACACATCTAAA
27911359 GCAA
1 GCAA
27911363 TTTTTTTATT
Statistics
Matches: 207, Mismatches: 29, Indels: 53
0.72 0.10 0.18
Matches are distributed among these distances:
34 26 0.13
35 4 0.02
36 59 0.29
37 20 0.10
38 90 0.43
39 8 0.04
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (35 bp):
GCAACCTTAAAAAGATTGAGATAGACACATCTAAA
Found at i:27911472 original size:17 final size:18
Alignment explanation
Indices: 27911443--27911476 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
27911433 ATACAACTAA
27911443 AAAATATAAAATTAAATT
1 AAAATATAAAATTAAATT
27911461 AAAATA-AAAATTAAAT
1 AAAATATAAAATTAAAT
27911477 ACTACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATATAAAATTAAATT
Found at i:27914173 original size:20 final size:20
Alignment explanation
Indices: 27914148--27914185 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27914138 CGAAACCTAT
27914148 AACCCTAAA-CTTTAAATTCG
1 AACCCTAAATC-TTAAATTCG
27914168 AACCCTAAATCTTAAATT
1 AACCCTAAATCTTAAATT
27914186 TTAAACCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.24, G:0.03, T:0.32
Consensus pattern (20 bp):
AACCCTAAATCTTAAATTCG
Found at i:27914714 original size:22 final size:20
Alignment explanation
Indices: 27914686--27914747 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 20
27914676 GAGATCATGA
27914686 GTTATGAGTTTGAGGTTTAG
1 GTTATGAGTTTGAGGTTTAG
* *
27914706 TGTTTATGATTTTAAGGTTTGAG
1 -G-TTATGAGTTTGAGGTTT-AG
*
27914729 GTTACGAGTTTGAGGTTTA
1 GTTATGAGTTTGAGGTTTA
27914748 AGGATCACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 15 0.44
22 16 0.47
23 2 0.06
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.47
Consensus pattern (20 bp):
GTTATGAGTTTGAGGTTTAG
Found at i:27915264 original size:36 final size:36
Alignment explanation
Indices: 27915206--27915618 Score: 426
Period size: 36 Copynumber: 11.3 Consensus size: 36
27915196 TTTATTGAAG
* *
27915206 GGTTGGGATAGA-CTTATCTAAGGCAAATTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACTTTAAAAA
* *
27915241 GGTTGGGGTAAACCTTGTCTAAGGCAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAA-CTTT-AAAAA
* * *
27915279 GATTGGAATAGA-CTTATCTAAGGCAACTTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAAC-TTT-AAAAA
* *
27915316 AGTTGGGATAGA-CTTGTCTAAGACAA-TCTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACT-TTAAAAA
27915351 GGTTGGGATAGACCTTGTCTAAGGCAACTTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACTTTAAAAA
* * *
27915387 GGTTGGAATAGACATTGT-TGAGGCAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAA-CTTT-AAAAA
* *
27915424 GGTTGGAATAGACCTTGTTTAAGGCAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAA-CTTT-AAAAA
* * *
27915462 GATTGGGATAGACCTTGTCTAAAGCAA-TCTT-AAAC
1 GGTTGGGATAGACCTTGTCTAAGGCAACT-TTAAAAA
* *
27915497 GAGTTGGAATAGACCTTGTCTAAGGCAAAATTTTAAAAA
1 G-GTTGGGATAGACCTTGTCTAAGGC--AACTTTAAAAA
* * *
27915536 GATTGAGATAGACCTTGTCTAAGGCAACCTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACTTTAAAAA
* * *
27915572 GGTTGGGACAGACCTTGTCTAAAGCAACCTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACTTTAAAAA
*
27915608 GGTTGGCATAG
1 GGTTGGGATAG
27915619 TGTTGGATAA
Statistics
Matches: 321, Mismatches: 41, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
35 38 0.12
36 128 0.40
37 71 0.22
38 79 0.25
39 5 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (36 bp):
GGTTGGGATAGACCTTGTCTAAGGCAACTTTAAAAA
Found at i:27915313 original size:74 final size:74
Alignment explanation
Indices: 27915206--27915618 Score: 450
Period size: 74 Copynumber: 5.6 Consensus size: 74
27915196 TTTATTGAAG
* * * * *
27915206 GGTTGGGATAGA-CTTATCTAAGGCAA-ATTTAAAAAGGTTGGGGTAAACCTTGTCTAAGGCAAC
1 GGTTGGAATAGACCTTGTCTAAGGCAACTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
27915269 CTTTAAAAAA
66 C-TTAAAAAA
* * * *
27915279 GATTGGAATAGA-CTTATCTAAGGCAACTTTTAAAAAAAGTTGGGATAGA-CTTGTCTAAGACAA
1 GGTTGGAATAGACCTTGTCTAAGGCAACTTTT-AAAAAGGTTGGGATAGACCTTGTCTAAGGCAA
*
27915342 TCTT-AAAAA
65 CCTTAAAAAA
* * * *
27915351 GGTTGGGATAGACCTTGTCTAAGGCAAC-TTTAAAAAGGTTGGAATAGACATTGT-TGAGGCAAC
1 GGTTGGAATAGACCTTGTCTAAGGCAACTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
27915414 CTTTAAAAAA
66 C-TTAAAAAA
* * * *
27915424 GGTTGGAATAGACCTTGTTTAAGGCAACCTTTAAAAAAGATTGGGATAGACCTTGTCTAAAGCAA
1 GGTTGGAATAGACCTTGTCTAAGGCAA-CTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAA
* **
27915489 TCTTAAACGA
65 CCTTAAAAAA
* * *
27915499 -GTTGGAATAGACCTTGTCTAAGGCAAAATTTTAAAAAGATTGAGATAGACCTTGTCTAAGGCAA
1 GGTTGGAATAGACCTTGTCTAAGGC-AACTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAA
27915563 CCTT-AAAAA
65 CCTTAAAAAA
* * * * *
27915572 GGTTGGGACAGACCTTGTCTAAAGCAAC-CTTAAAAAGGTTGGCATAG
1 GGTTGGAATAGACCTTGTCTAAGGCAACTTTTAAAAAGGTTGGGATAG
27915619 TGTTGGATAA
Statistics
Matches: 285, Mismatches: 44, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
71 22 0.08
72 39 0.14
73 75 0.26
74 98 0.34
75 44 0.15
76 7 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (74 bp):
GGTTGGAATAGACCTTGTCTAAGGCAACTTTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAC
CTTAAAAAA
Found at i:27915325 original size:110 final size:109
Alignment explanation
Indices: 27915207--27915618 Score: 474
Period size: 110 Copynumber: 3.8 Consensus size: 109
27915197 TTATTGAAGG
* * * *
27915207 GTTGGGATAGA-CTTATCTAAGGCAAATTTAAAAAGGTTGGGGTAAACCTTGTCTAAGGCAACCT
1 GTTGGGATAGACCTTGTCTAAGGCAAATTTAAAAAGGTTGGGATAGACCTTGTCTAAAGCAACC-
*
27915271 TTAAAAAAGATTGGAATAGACTTATCTAAGGCAACTTTTAAAAAAA
65 TTAAAAAAG-TTGGAATAGACTTGTCTAAGGCAACTTTTAAAAAAA
* * *
27915317 GTTGGGATAGA-CTTGTCTAAGAC-AATCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACT
1 GTTGGGATAGACCTTGTCTAAGGCAAAT-TTAAAAAGGTTGGGATAGACCTTGTCTAAAGCAACC
* * * *
27915380 TTAAAAAGGTTGGAATAGACATTGT-TGAGGCAACCTTTAAAAAAG
65 TTAAAAAAGTTGGAATAGAC-TTGTCTAAGGCAACTTTTAAAAAAA
* * * * *
27915425 GTTGGAATAGACCTTGTTTAAGGCAACCTTTAAAAAAGATTGGGATAGACCTTGTCTAAAGCAAT
1 GTTGGGATAGACCTTGTCTAAGGCAA-ATTT-AAAAAGGTTGGGATAGACCTTGTCTAAAGCAAC
** * *
27915490 CTTAAACGAGTTGGAATAGACCTTGTCTAAGGCAAAATTTTAAAAAGA
64 CTTAAAAAAGTTGGAATAGA-CTTGTCTAAGGC-AACTTTTAAAAAAA
* ** *
27915538 -TTGAGATAGACCTTGTCTAAGGCAACCTTAAAAAGGTTGGGACAGACCTTGTCTAAAGCAACCT
1 GTTGGGATAGACCTTGTCTAAGGCAAATTTAAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCT
* *
27915602 TAAAAAGGTTGGCATAG
66 TAAAAAAGTTGGAATAG
27915619 TGTTGGATAA
Statistics
Matches: 256, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
108 38 0.15
109 24 0.09
110 102 0.40
111 54 0.21
112 28 0.11
113 10 0.04
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (109 bp):
GTTGGGATAGACCTTGTCTAAGGCAAATTTAAAAAGGTTGGGATAGACCTTGTCTAAAGCAACCT
TAAAAAAGTTGGAATAGACTTGTCTAAGGCAACTTTTAAAAAAA
Found at i:27915910 original size:141 final size:140
Alignment explanation
Indices: 27915604--27915937 Score: 449
Period size: 141 Copynumber: 2.4 Consensus size: 140
27915594 AGCAACCTTA
* * * *
27915604 AAAAG-GTTGGCATAGTGTTGGATAAAGCCAAGTCTTATTTAAGCGTTGCCTTAGGCATGCACAT
1 AAAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCACAT
* * *
27915668 CCCAACCCTTATACAAAGAGTTGACCAAAGCGTATCCCGACAAGTCTATCCCAATACTTAGGAAA
66 CCCAACCCTTATACAAAGAGTTGACAAAAGCGTATCACGACAAGTCTATCCCAACACTTAGGAAA
27915733 GTGTCAGCCC
131 GTGTCAGCCC
* * *
27915743 AAAAGTGTCGCCATAGTATTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATAT
1 AAAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCACAT
* * * * *
27915808 CCCAACCCTTGTACAAAAGAGTTGGCAAAAGCGTATGTACG-CAGGTCTATGCCAACACTTAGGA
66 CCCAACCCTTATAC-AAAGAGTTGACAAAAGCGTAT-CACGACAAGTCTATCCCAACACTTAGGA
*
27915872 AAGTTTC-GCCCC
129 AAGTGTCAG-CCC
* * *
27915884 AAAAGTGTCGGCATAGTGTTGAACAAAGCCAACTTTTATTTAAGTGTTGTCTTA
1 AAAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTA
27915938 AAACTCGAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
139 5 0.03
140 66 0.39
141 97 0.57
142 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (140 bp):
AAAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCACAT
CCCAACCCTTATACAAAGAGTTGACAAAAGCGTATCACGACAAGTCTATCCCAACACTTAGGAAA
GTGTCAGCCC
Found at i:27916511 original size:7 final size:7
Alignment explanation
Indices: 27916501--27916533 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
27916491 ATTCATTATT
27916501 CATTTTG
1 CATTTTG
27916508 CATTTTG
1 CATTTTG
27916515 CATTTTG
1 CATTTTG
27916522 CATTTTG
1 CATTTTG
27916529 CATTT
1 CATTT
27916534 AAGATTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (7 bp):
CATTTTG
Found at i:27917102 original size:224 final size:222
Alignment explanation
Indices: 27916841--27917248 Score: 629
Period size: 227 Copynumber: 1.8 Consensus size: 222
27916831 ATTTTACTTG
* * *
27916841 TAAATTACATGGATTTATCCATCTTTTGCAAAACATTTTTAACAAAATAAA-ATATCGTTTTTTA
1 TAAATTACATGGATTGATCCATCTTTTGCAAAACA-TTTTAACAAAATAAATATATCATTTTTAA
* *
27916905 AATACATAAATTGTTTTAAAAATAAAGGCAATGTTCTTTTATTTTAGGGAATTCGAGAAATTGTG
65 AATACATAAATTGTTTTAAAAATAAAGACAATGTCCTTTTATTTTAGGGAATTCGAGAAATTGTG
* * *
27916970 TCCTAACGTGTTGGGTACAATTTTCCTTTGAACCTAAATATTTGAGTATCCTCCTCGAATCGATA
130 CCCTAACGAGTTGGGTACAATTTTCCTTTGAACCTAAATAATTGAGTATCCTCCTCGAATCGATA
27917035 ATTGCCCTTTTTTGTTTTTGTTTTTATA
195 ATTGCCCTTTTTTGTTTTTGTTTTTATA
*
27917063 TAAATTACATAGTTATTGATCCATCTTTTGCAAAACATTTTAACAAAATAAATTGCATATCATTT
1 TAAATTACAT-G-GATTGATCCATCTTTTGCAAAACATTTTAACAAAATAAA-T--ATATCATTT
*
27917128 TTAAAATACATAAATTGTTTTAAAAATTAAGACAATGTCCTTTTATTTTAGGGAATTCGAGAAAT
61 TTAAAATACATAAATTGTTTTAAAAATAAAGACAATGTCCTTTTATTTTAGGGAATTCGAGAAAT
** * *
27917193 TGTGCCCTAACGAGTTGGGTATGATTTTTCTTTGAACCTAAATAATTGGGTATCCT
126 TGTGCCCTAACGAGTTGGGTACAATTTTCCTTTGAACCTAAATAATTGAGTATCCT
27917249 ACTTAAAATT
Statistics
Matches: 166, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
222 10 0.06
223 16 0.10
224 22 0.13
227 118 0.71
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (222 bp):
TAAATTACATGGATTGATCCATCTTTTGCAAAACATTTTAACAAAATAAATATATCATTTTTAAA
ATACATAAATTGTTTTAAAAATAAAGACAATGTCCTTTTATTTTAGGGAATTCGAGAAATTGTGC
CCTAACGAGTTGGGTACAATTTTCCTTTGAACCTAAATAATTGAGTATCCTCCTCGAATCGATAA
TTGCCCTTTTTTGTTTTTGTTTTTATA
Found at i:27919507 original size:14 final size:14
Alignment explanation
Indices: 27919488--27919516 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27919478 TTAGAGAAAT
27919488 AGCAAGTGCATAGA
1 AGCAAGTGCATAGA
27919502 AGCAAGTGCATAGA
1 AGCAAGTGCATAGA
27919516 A
1 A
27919517 TGAAGGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.28, T:0.14
Consensus pattern (14 bp):
AGCAAGTGCATAGA
Found at i:27924050 original size:6 final size:6
Alignment explanation
Indices: 27924039--27924077 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
27924029 CCATTAATTA
27924039 ATACTC ATACTC ATACTC ATACTC ATACTC ATAC-C ATAC
1 ATACTC ATACTC ATACTC ATACTC ATACTC ATACTC ATAC
27924078 AATCAATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (6 bp):
ATACTC
Found at i:27928583 original size:39 final size:39
Alignment explanation
Indices: 27928528--27928824 Score: 247
Period size: 39 Copynumber: 7.4 Consensus size: 39
27928518 GGTGAAGCTA
* * * *
27928528 CCATTCAATCTCTTACCCCGACCATGGGGTAGATTGAAG
1 CCATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAG
** * *
27928567 TTATCCAATTTTTTACCCCGACCATGGGGCAGATTGAAG
1 CCATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAG
* * *
27928606 TCATCTAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG
1 CCATCCAATCTTTTACCCCAACCATG-GGGCAGATTGAAG
* * *
27928645 ACACTATCTAATCTCTTACCCCAACCATGGGACAGATTGAAG
1 -C-C-ATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAG
* * * *
27928687 CCATCCAATCTTTTACCCTAACTA-GAGAGTAGATTGAAG
1 CCATCCAATCTTTTACCCCAACCATG-GGGCAGATTGAAG
* ** *
27928726 ACACCATCCAATCTCTTACCCTGACCATGGGGCAGATTAAAG
1 ---CCATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAG
* * **
27928768 CCATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAG
1 CCATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAG
* *
27928807 ACCATCTAATTTTTTACC
1 -CCATCCAATCTTTTACC
27928825 TATTCAGATG
Statistics
Matches: 211, Mismatches: 36, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 126 0.60
40 16 0.08
41 2 0.01
42 63 0.30
43 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (39 bp):
CCATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAG
Found at i:27928675 original size:81 final size:80
Alignment explanation
Indices: 27928579--27928816 Score: 352
Period size: 81 Copynumber: 3.0 Consensus size: 80
27928569 ATCCAATTTT
* * *
27928579 TTACCCCGACCATGGGGCAGATTGAAGTCATCTAATCTTTTACCCTAACCAGAGGGCAGATTGAA
1 TTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAA
27928644 GACACTATCTAATCTC
66 GACAC-ATCTAATCTC
* * * *
27928660 TTACCCCAACCATGGGACAGATTGAAGCCATCCAATCTTTTACCCTAACTAGAGAGTAGATTGAA
1 TTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAA
*
27928725 GACACCATCCAATCTC
66 GACA-CATCTAATCTC
* * *
27928741 TTACCCTGACCATGGGGCAGATTAAAGCCATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAA
1 TTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAA
27928806 GAC-CATCTAAT
66 GACACATCTAAT
27928817 TTTTTACCTA
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
79 7 0.05
81 132 0.94
82 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (80 bp):
TTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAA
GACACATCTAATCTC
Found at i:27928778 original size:120 final size:117
Alignment explanation
Indices: 27928527--27928824 Score: 278
Period size: 120 Copynumber: 2.5 Consensus size: 117
27928517 AGGTGAAGCT
* * * ** *
27928527 ACCATTCAATCTCTTACCCCGACCATGGGGTAGATTGAAGTTATCCAATTTTTTACCCCGACCAT
1 ACCATCCAATCTCTTACCCCAACCAT-GGGCAGATTGAAGCCATCCAATTTTTTACCCCAACCAT
* * * * *
27928592 GGGGCAGATTGAAGTCATCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
65 GGAGCAGATTGAAGCCATCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAG
* * * *
27928645 ACACTATCTAATCTCTTACCCCAACCATGGGACAGATTGAAGCCATCCAATCTTTTACCCTAACT
1 AC-C-ATCCAATCTCTTACCCCAACCATGGG-CAGATTGAAGCCATCCAATTTTTTACCCCAACC
* *
27928710 A-GAGAGTAGATTGAAGACACCATCCAATCTCTTACCCTGACCATG-GGGCAGATTAAAG
63 ATG-GAGCAGATTGAAG---CCATCCAATCTCTTACCCTAACCA-GAGGGCAGATTAAAG
* * * * *
27928768 -CCATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGACCATCTAATTTTTTACC
1 ACCATCCAATCTCTTACCCCAAC-CATGGGCAGATTGAAG-CCATCCAATTTTTTACC
27928825 TATTCAGATG
Statistics
Matches: 146, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
118 2 0.01
119 5 0.03
120 85 0.58
121 20 0.14
122 1 0.01
123 32 0.22
124 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (117 bp):
ACCATCCAATCTCTTACCCCAACCATGGGCAGATTGAAGCCATCCAATTTTTTACCCCAACCATG
GAGCAGATTGAAGCCATCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAG
Found at i:27934370 original size:7 final size:7
Alignment explanation
Indices: 27934354--27934398 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
27934344 CAATAAAATT
27934354 ATTT-AA
1 ATTTAAA
27934360 ATTTAAA
1 ATTTAAA
27934367 ATTTAAA
1 ATTTAAA
27934374 ATTTAAA
1 ATTTAAA
27934381 TATATT-AA
1 -AT-TTAAA
27934389 A-TTAAA
1 ATTTAAA
27934395 ATTT
1 ATTT
27934399 TATTACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
5 2 0.06
6 7 0.21
7 19 0.56
8 4 0.12
9 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
ATTTAAA
Found at i:27934460 original size:18 final size:16
Alignment explanation
Indices: 27934424--27934458 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27934414 ATTTTATATT
27934424 AAATATATAAATTTAA
1 AAATATATAAATTTAA
*
27934440 AAATATATATATTTAA
1 AAATATATAAATTTAA
27934456 AAA
1 AAA
27934459 AAATTCAAAG
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATATATAAATTTAA
Found at i:27946483 original size:340 final size:340
Alignment explanation
Indices: 27945863--27946547 Score: 1039
Period size: 340 Copynumber: 2.0 Consensus size: 340
27945853 AAGTTCTAAT
* * **
27945863 GAAATCTCACTGCTATCGACTTCTCTGTTTAACGAAGGCCCAAGTGCTCACAATTACCGCACCTT
1 GAAATCTCACTGCTATCGACTTCTCTGTTTAACAAAGACCCAAGTGCTCACAATTACCAAACCTT
* * * * *
27945928 CCAGTGCTGGCAATATTTCGCACTTAAGAACAAGTGGCCAGAAGTCCTTCTTGCCTTAAGTAACT
66 CCAGTGCTGGCAATACTTCGCACTTAAGAACAAGTGACCAGAAGTCCTTCTTACCTCAAGCAACT
* *
27945993 TCCGTTGTCTTGCTTGTTAATCTAACTTTGTCACCGCACCTTCCAGTGAGTGTGACAGCAATCGC
131 TCCGTTGTCTTGCTTATTAATCTAACTTTGTCACCGCACCTTCCAGTGACTGTGACAGCAATCGC
* * * *
27946058 ACTTTTGTAGTCAAAACAGTTAAATCCAAATATAAATGGATGAGAAGAAATGAGTAGAAATCAAA
196 ACTTTCGTAGTCAAAAAAGTTAAATCCAAATATAAATAGATAAGAAGAAATGAGTAGAAATCAAA
* *
27946123 ATAGATCTAGCATTAATAGGTACTGCCATACACAATTAATAGTTAACAGAATTCATCAACATTCA
261 ATAGATCTAACATTAATAGGTACTGCCATACACAATTAATAGTCAACAGAATTCATCAACATTCA
*
27946188 AGAGGACTTAAAGAC
326 AGAGGACTTAAAGAA
* * *
27946203 GAAATCTTACTGCTATTGACTTCTCTGTTTAATAAAGACCCAAGTGCTCACAATTACCAAACCTT
1 GAAATCTCACTGCTATCGACTTCTCTGTTTAACAAAGACCCAAGTGCTCACAATTACCAAACCTT
* * * * * *
27946268 CTAGTGTTGGCAATGCTTCGCACTTAAGAACAAGTGACTAGAATTCTTTCTTACCTCAAGCAACT
66 CCAGTGCTGGCAATACTTCGCACTTAAGAACAAGTGACCAGAAGTCCTTCTTACCTCAAGCAACT
* * ** *
27946333 TTCGTTGTCTTGCTTATTAATTTAACTTTGTCATTGCACCTTCCAGTGACTGTGACTGCAATCGC
131 TCCGTTGTCTTGCTTATTAATCTAACTTTGTCACCGCACCTTCCAGTGACTGTGACAGCAATCGC
*
27946398 ACTTTCGT-GTTCAAAAAAGTTAAATCCAAATATAAATAGATAAGAAGAATTGAGTAGAAATCAA
196 ACTTTCGTAG-TCAAAAAAGTTAAATCCAAATATAAATAGATAAGAAGAAATGAGTAGAAATCAA
*
27946462 AATAGATCTAACATTAATAGGTACTTCCATACACAATTAATAGTCAACAGAATTCATCAACATTC
260 AATAGATCTAACATTAATAGGTACTGCCATACACAATTAATAGTCAACAGAATTCATCAACATTC
*
27946527 AAGAGGATTTAAAGAA
325 AAGAGGACTTAAAGAA
27946543 GAAAT
1 GAAAT
27946548 TGAATCATGC
Statistics
Matches: 309, Mismatches: 35, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
339 1 0.00
340 308 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (340 bp):
GAAATCTCACTGCTATCGACTTCTCTGTTTAACAAAGACCCAAGTGCTCACAATTACCAAACCTT
CCAGTGCTGGCAATACTTCGCACTTAAGAACAAGTGACCAGAAGTCCTTCTTACCTCAAGCAACT
TCCGTTGTCTTGCTTATTAATCTAACTTTGTCACCGCACCTTCCAGTGACTGTGACAGCAATCGC
ACTTTCGTAGTCAAAAAAGTTAAATCCAAATATAAATAGATAAGAAGAAATGAGTAGAAATCAAA
ATAGATCTAACATTAATAGGTACTGCCATACACAATTAATAGTCAACAGAATTCATCAACATTCA
AGAGGACTTAAAGAA
Found at i:27948240 original size:19 final size:21
Alignment explanation
Indices: 27948205--27948243 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
27948195 GAGACAAACA
27948205 AAATGTAATGACAACTAAATG
1 AAATGTAATGACAACTAAATG
27948226 AAATGT-ATG-CAACTAAAT
1 AAATGTAATGACAACTAAAT
27948244 TAAGTACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (21 bp):
AAATGTAATGACAACTAAATG
Found at i:27948358 original size:18 final size:19
Alignment explanation
Indices: 27948335--27948370 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27948325 GCGCGCTTTT
27948335 TTGCGTTT-CGCCTTTTCC
1 TTGCGTTTGCGCCTTTTCC
*
27948353 TTGCGTTTGCGCTTTTTC
1 TTGCGTTTGCGCCTTTTC
27948371 TCCTTGGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.28, G:0.19, T:0.53
Consensus pattern (19 bp):
TTGCGTTTGCGCCTTTTCC
Found at i:27958534 original size:80 final size:80
Alignment explanation
Indices: 27958393--27958546 Score: 236
Period size: 80 Copynumber: 1.9 Consensus size: 80
27958383 CAACCAAATC
* * * * *
27958393 CGTCAATTCATGGCACCCGGTGCCTAGCGGATAAACCGCGATAAGTGAGCCCAGCTCTAGTTCGA
1 CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCACAATAAATGAGCCCAACTCTAGTTCGA
27958458 TTAACCAATAAATTT
66 TTAACCAATAAATTT
* * *
27958473 CGTCAATTCGTGGCACCCAGTGCCTAGCGGATAAACCACAATAAATGAGCCCAACTTTAGTTGGA
1 CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCACAATAAATGAGCCCAACTCTAGTTCGA
27958538 TTAACCAAT
66 TTAACCAAT
27958547 GGTTTGTGCC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (80 bp):
CGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCACAATAAATGAGCCCAACTCTAGTTCGA
TTAACCAATAAATTT
Found at i:27958727 original size:81 final size:81
Alignment explanation
Indices: 27958585--27958733 Score: 210
Period size: 81 Copynumber: 1.8 Consensus size: 81
27958575 CCAATGATCT
** * ** *
27958585 TGGCACCCAGTGCCTAGCAGTTAAACTGCGAAAGTAAGCCCAGCTCTGGTTGGTTTGACCAATGA
1 TGGCACCCAGTGCCTAGCAGTTAAACCACGAAAGTAAGCCCAGCTCTAGTTGGTTAAACCAACGA
27958650 ATAATCTGTCAAATCC
66 ATAATCTGTCAAATCC
* *
27958666 TGGCACCCAGTGCCTAGCTA-TTTAACCACGAAAGTGAGCCCAGCTCTAGTTGGTTAAACCAACG
1 TGGCACCCAGTGCCTAGC-AGTTAAACCACGAAAGTAAGCCCAGCTCTAGTTGGTTAAACCAACG
27958730 AATA
65 AATA
27958734 TTGTACAGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
81 58 0.98
82 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (81 bp):
TGGCACCCAGTGCCTAGCAGTTAAACCACGAAAGTAAGCCCAGCTCTAGTTGGTTAAACCAACGA
ATAATCTGTCAAATCC
Found at i:27968155 original size:17 final size:18
Alignment explanation
Indices: 27968133--27968166 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27968123 TTACCATATT
27968133 AACCCA-TCTTTCATCAA
1 AACCCATTCTTTCATCAA
*
27968150 AACCCATTTTTTCATCA
1 AACCCATTCTTTCATCA
27968167 TAGCCCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (18 bp):
AACCCATTCTTTCATCAA
Found at i:28000734 original size:4 final size:4
Alignment explanation
Indices: 28000699--28000729 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
28000689 TTATTTATTC
28000699 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
28000730 TATTTTCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
ATTG
Found at i:28000923 original size:20 final size:20
Alignment explanation
Indices: 28000894--28000942 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
28000884 TACAATTTAG
**
28000894 TATCGATACTTTTCTAAAAA
1 TATCGATACTCGTCTAAAAA
* *
28000914 TATTGATACTCGTGTAAAAA
1 TATCGATACTCGTCTAAAAA
28000934 TATCGATAC
1 TATCGATAC
28000943 CACCAGGCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (20 bp):
TATCGATACTCGTCTAAAAA
Found at i:28003980 original size:17 final size:17
Alignment explanation
Indices: 28003947--28004007 Score: 86
Period size: 17 Copynumber: 3.5 Consensus size: 17
28003937 CATTAAATTA
28003947 CAATGACAAATGAAAATG
1 CAATGAC-AATGAAAATG
* *
28003965 TAATGACAATGCAAATG
1 CAATGACAATGAAAATG
*
28003982 CAATGACAATTAAAATG
1 CAATGACAATGAAAATG
28003999 CAATGACAA
1 CAATGACAA
28004008 AGGGAATGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
17 32 0.84
18 6 0.16
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.20
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Done.