Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 95 of 206
Found at i:27627200 original size:17 final size:17
Alignment explanation
Indices: 27627147--27627204 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
27627137 TAATCACTTT
*
27627147 AATATTAAATT-AATAA
1 AATATTAAATTAAATTA
*
27627163 AATACT--ATTAAGA-TA
1 AATATTAAATTAA-ATTA
*
27627178 AGTATTAAATTAAATTA
1 AATATTAAATTAAATTA
27627195 AATATTAAAT
1 AATATTAAAT
27627205 CTATTCAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
14 3 0.09
15 6 0.19
16 7 0.22
17 16 0.50
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (17 bp):
AATATTAAATTAAATTA
Found at i:27636792 original size:26 final size:26
Alignment explanation
Indices: 27636763--27636825 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
27636753 CTACCTACAA
27636763 CAGTTTCAGAATATCATAACATATAT
1 CAGTTTCAGAATATCATAACATATAT
* *
27636789 CAGTTTCAGAATATCATAGCATGTAT
1 CAGTTTCAGAATATCATAACATATAT
27636815 CAGTTTCAGAA
1 CAGTTTCAGAA
27636826 CACTTACAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (26 bp):
CAGTTTCAGAATATCATAACATATAT
Found at i:27643971 original size:467 final size:465
Alignment explanation
Indices: 27643096--27644916 Score: 2782
Period size: 455 Copynumber: 3.9 Consensus size: 465
27643086 GCTCAAATCC
27643096 CCTCTCTTATTATTTTTATTTTTAATGTCGGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
1 CCTCTCTTATTATTTTTATTTTTAATGTCGGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
*
27643161 CAAAAATTCTTACCATGCAAGAGAGATTCTGTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
66 CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
* * * *
27643226 CCCCTATTTCACTTCCTTTGTTCCCACTCCTTTCCTTTTCTTTCCCATGTCTCACTCCTTGCAAT
131 CCCCTTTTTCACTCCCTTTGTTCCCACTCATTTCCTTTTCTTTTCCATGTCTCACTCCTTGCAAT
27643291 TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTCT
196 TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTCT
* *
27643356 CTTCTCATCCACTTGTTTCTCTCATCATTTTCTCTTCTCTTCCAATAGCCACCACTATTTTCACA
261 CTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTCTCTTTCAATAGCCACCACT-TTTTCACA
*
27643421 TTTTAGCCATCTTATCACCACCTTCGACCATCATTGCAACACCAAATCACCACCCATACACCACC
325 TTTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCACC
* * * *
27643486 GTCACTCCTCTTTCACCCTTTTCTTGCCATTTTTGCACCACCGCTTGACCTCTAATTTGCTGACG
390 GTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGCTTGACCTCTAATTTGCTGTCG
*
27643551 TCATCTCACAG
455 TCATCTCACCG
* * * * * *
27643562 CCTCTCTTATTATTTTTATTTTTAATTTTGGCATTAAAGGCTTGGTCAAACCCCTCATTGCCACT
1 CCTCTCTTATTATTTTTATTTTTAATGTCGGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
* *
27643627 AAAAAATTCTTACCATGCCAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
66 CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
27643692 CCCCTTTTTCACTCCCTTCT-TATCCC-CTTCATTTCCTTTTC-TTTCCAATGTCTCACTCCTTG
131 CCCCTTTTTCACTCCCTT-TGT-TCCCAC-TCATTTCCTTTTCTTTTCC-ATGTCTCACTCCTTG
* *
27643754 CAATTTTTTCCCTTCACCCATTGACTTTTGCCATCCCATGCACCCAGACAAAATAAAATTTTTGT
192 CAATTTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGT
* * * *
27643819 GTCTCTTCTCATCCACTTTTTTTCTCTTATTATTTTCTCTTCTCTTTCAATACCCACCACTTTTT
257 TTCTCTTCTCATCCAC-TTTTTTCTCTCATCATTTTCTCTTCTCTTTCAATAGCCACCACTTTTT
*
27643884 CACATTTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCTATACAC
321 CACATTTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACAC
* *
27643949 CACTGTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGCTTGACCTC-CATTATCG
386 CACCGTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGCTTGACCTCTAATT-T-G
* * *
27644013 CCGTTGTCGTCTCACCG
449 CTGTCGTCATCTCACCG
* * *
27644030 CCTCTCTTAGTATTTTTATTTTTAATGTTGGCATTAAAAGCTTGGTCAAACCCCTCCTTGCTG--
1 CCTCTCTTATTATTTTTATTTTTAATGTCGGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
*
27644093 CAAAAATTCTTACCATGCAAGAGAGATTCTTTGCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
66 CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
27644158 CCCCTTTTTCACTCCCTTTGTTCCCACTCATTTCCTTTTCTTTTCCATGTCTCACTCCTTGCAA-
131 CCCCTTTTTCACTCCCTTTGTTCCCACTCATTTCCTTTTCTTTTCCATGTCTCACTCCTTGCAAT
* * * * **
27644222 TTTTTCCCTGCACCTATTGAACTTTGCCGTCTTATGCACCTAGACAAAATAAAATTTTTGTTTCT
196 TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTCT
* * *
27644287 CTTCTCATCCACTTTTTTCTCTCATCATTTTCCCTTCAC-TTCTAATAGCCACTACTTTTTCACA
261 CTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTCTCTTTC-AATAGCCACCACTTTTTCACA
* *
27644351 TTTTAGCCATCTTATCACCACCTTCGACCACCATT--------AAATCACCACCCATACACTACT
325 TTTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCACC
* ** * *
27644408 GTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTACACCACCTATTGGCCTCTACTGTTGCTGTC
390 GTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGCTTGACCTCTAAT-TTGCTGTC
*
27644473 GTCATCTCGCCG
454 GTCATCTCACCG
* * *
27644485 CCTCTCTTATTATTTTTATTTTTAATGTCAGCATTAAAAGCTTGGTCAAACCTCTCCTTGCTGCC
1 CCTCTCTTATTATTTTTATTTTTAATGTCGGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
*
27644550 CAAAAATTCTTACCATGCAAAAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
66 CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
*
27644615 CCCCTTTTTCACTCCCTTTGTTCCCCCTTC-TTTCCTTTTCTTTTCCATGTCTCACTCCTTGCAA
131 CCCCTTTTTCACTCCCTTTGTTCCCAC-TCATTTCCTTTTCTTTTCCATGTCTCACTCCTTGCAA
*
27644679 TTTTTTCCCTTCACCCATTGACCTTTGCCATCCCATACACCTAGACAAAAT-AAA-TTTT-TTTC
195 TTTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTC
* * *
27644741 TCTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTATCTTTCAATAGCCACCAGTTTTTCAAA
260 TCTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTCTCTTTCAATAGCCACCACTTTTTCACA
* *
27644806 TTTTAGCCATCTGATCACCACCTTCGACCATCATTGCAACACCAAATCACCACCCATACACCACC
325 TTTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCACC
* * * *
27644871 ATCACTCCCCTTTCACCCTTTTCTTACCATTTTTGCACCACCGCTT
390 GTCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGCTT
27644917 AACCGCTACT
Statistics
Matches: 1229, Mismatches: 100, Indels: 55
0.89 0.07 0.04
Matches are distributed among these distances:
455 233 0.19
456 9 0.01
457 127 0.10
458 45 0.04
462 3 0.00
463 136 0.11
464 68 0.06
465 36 0.03
466 233 0.19
467 230 0.19
468 109 0.09
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.39
Consensus pattern (465 bp):
CCTCTCTTATTATTTTTATTTTTAATGTCGGCATTAAAAGCTTGGTCAAACCCCTCCTTGCCGCC
CAAAAATTCTTACCATGCAAGAGAGATTCTTTCCTCCCATACCTTTCTTTTATTTCCCTTCTTAT
CCCCTTTTTCACTCCCTTTGTTCCCACTCATTTCCTTTTCTTTTCCATGTCTCACTCCTTGCAAT
TTTTTCCCTTCACCCATTGACCTTTGCCATCCCATGCACCTAGACAAAATAAAATTTTTGTTTCT
CTTCTCATCCACTTTTTTCTCTCATCATTTTCTCTTCTCTTTCAATAGCCACCACTTTTTCACAT
TTTAGCCATCTTATCACCACCTTCGACCACCATTGCAACACCAAATCACCACCCATACACCACCG
TCACTCCCCTCTCACCCTCTTCTTGCCATTTTTGCACCACCGCTTGACCTCTAATTTGCTGTCGT
CATCTCACCG
Found at i:27645362 original size:20 final size:20
Alignment explanation
Indices: 27645339--27645417 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
27645329 AATGAAGTTT
*
27645339 AAATGATTTTAACCAAGTCA
1 AAATGATTTCAACCAAGTCA
* *
27645359 AAATGACTTCAACCAAGTTA
1 AAATGATTTCAACCAAGTCA
* *
27645379 AAATCATTTTAA-CACA-TCA
1 AAATGATTTCAACCA-AGTCA
* *
27645398 AAATTATTTCAAACAAGTCA
1 AAATGATTTCAACCAAGTCA
27645418 GAATTGCTCT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
19 15 0.32
20 32 0.68
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (20 bp):
AAATGATTTCAACCAAGTCA
Found at i:27645399 original size:39 final size:40
Alignment explanation
Indices: 27645333--27645415 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 40
27645323 TTTTAAAATG
* * *
27645333 AAGTTTAAATGATTTTAACCAAGTCAAAATGACTTCAACC
1 AAGTTAAAATCATTTTAACCAAGTCAAAATGACTTCAAAC
* *
27645373 AAGTTAAAATCATTTTAA-CACA-TCAAAATTATTTCAAAC
1 AAGTTAAAATCATTTTAACCA-AGTCAAAATGACTTCAAAC
27645412 AAGT
1 AAGT
27645416 CAGAATTGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 20 0.54
40 17 0.46
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (40 bp):
AAGTTAAAATCATTTTAACCAAGTCAAAATGACTTCAAAC
Found at i:27653728 original size:20 final size:20
Alignment explanation
Indices: 27653703--27653787 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
27653693 AAGTTAAGTT
27653703 AAAATGATTTTAACCAAGAC
1 AAAATGATTTTAACCAAGAC
* **
27653723 AAAATGATTTCAACCAAGTT
1 AAAATGATTTTAACCAAGAC
* *
27653743 AAAATCATTTT-AGCACA-AC
1 AAAATGATTTTAACCA-AGAC
* *
27653762 AAAATGATTTTCAAACAAGTC
1 AAAATGATTTT-AACCAAGAC
27653783 AAAAT
1 AAAAT
27653788 TGCTCCAGTC
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 13 0.26
20 28 0.56
21 9 0.18
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.27
Consensus pattern (20 bp):
AAAATGATTTTAACCAAGAC
Found at i:27653742 original size:40 final size:40
Alignment explanation
Indices: 27653698--27653787 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 40
27653688 TTTTAAAGTT
* *
27653698 AAGTTAAAATGATTTTAACCA-AGACAAAATGA-TTTCAACC
1 AAGTTAAAATCATTTT-ACCACA-ACAAAATGATTTTCAAAC
*
27653738 AAGTTAAAATCATTTTAGCACAACAAAATGATTTTCAAAC
1 AAGTTAAAATCATTTTACCACAACAAAATGATTTTCAAAC
*
27653778 AAGTCAAAAT
1 AAGTTAAAAT
27653788 TGCTCCAGTC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 12 0.27
40 32 0.73
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (40 bp):
AAGTTAAAATCATTTTACCACAACAAAATGATTTTCAAAC
Found at i:27654258 original size:23 final size:23
Alignment explanation
Indices: 27654191--27654258 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
27654181 GCCAAGATTA
* *
27654191 TTACCATATTGATTTTGATACAG
1 TTACCAAATTGATTTTGATACTG
* **
27654214 TTACTAAACGGATTTTGATACTG
1 TTACCAAATTGATTTTGATACTG
27654237 TTACCAAATTGATTTTGATACT
1 TTACCAAATTGATTTTGATACT
27654259 AAAATGCATG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (23 bp):
TTACCAAATTGATTTTGATACTG
Found at i:27667190 original size:29 final size:29
Alignment explanation
Indices: 27667157--27667220 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
27667147 TAATCCACCA
27667157 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
27667186 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
27667216 CCCAA
1 CCCAA
27667221 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:27667194 original size:30 final size:30
Alignment explanation
Indices: 27667164--27667220 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27667154 CCACCCAACT
27667164 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
27667193 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
27667221 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:27673057 original size:103 final size:104
Alignment explanation
Indices: 27672878--27673141 Score: 415
Period size: 103 Copynumber: 2.5 Consensus size: 104
27672868 GACGTGATTA
* * *
27672878 GTGGATCCCGCACTTAGCACCTCCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
1 GTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
**
27672943 TCAGCACATAGCAACCCCCTTT-TTATTTCAAAGATATG
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATG
27672981 GTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GTGGATCA-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
27673045 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATG
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATG
* * * **
27673085 GTGGATCACGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 GTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
27673142 TTTATATACA
Statistics
Matches: 148, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 83 0.56
104 64 0.43
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (104 bp):
GTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATG
Found at i:27673503 original size:29 final size:29
Alignment explanation
Indices: 27673470--27673533 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
27673460 TAATCCACCA
27673470 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
27673499 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
27673529 CCCAA
1 CCCAA
27673534 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:27673507 original size:30 final size:30
Alignment explanation
Indices: 27673477--27673533 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27673467 CCACCCAACT
27673477 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
27673506 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
27673534 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:27676461 original size:21 final size:22
Alignment explanation
Indices: 27676420--27676461 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
27676410 GCTTGTTTTC
*
27676420 TATGTTATTTAGTATTTAGTAT
1 TATGTTATTTAGTATTAAGTAT
*
27676442 TATGTT-TTTGGTATTAAGTA
1 TATGTTATTTAGTATTAAGTA
27676462 CTTAGGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (22 bp):
TATGTTATTTAGTATTAAGTAT
Found at i:27679151 original size:35 final size:37
Alignment explanation
Indices: 27679082--27679151 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
27679072 TCATGATTGG
***
27679082 TACATATTATACAATTATTTTTCAAACCGTAATGGTA
1 TACATATTATACAATTATTTTTCAAACAAAAATGGTA
27679119 TACATATTATACAATTATTTTT-AAA-AAAAATGG
1 TACATATTATACAATTATTTTTCAAACAAAAATGG
27679152 GGATGCCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 5 0.17
36 3 0.10
37 22 0.73
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (37 bp):
TACATATTATACAATTATTTTTCAAACAAAAATGGTA
Found at i:27683168 original size:14 final size:14
Alignment explanation
Indices: 27683149--27683176 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27683139 TATATATTTC
27683149 ATTCCATCACATAT
1 ATTCCATCACATAT
27683163 ATTCCATCACATAT
1 ATTCCATCACATAT
27683177 CCAACTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTCCATCACATAT
Found at i:27685990 original size:21 final size:21
Alignment explanation
Indices: 27685964--27686006 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
27685954 GTTTTAGAAA
*
27685964 TTGTTAGATTTCATGACGTAT
1 TTGTTAGATTTAATGACGTAT
27685985 TTGTTAGATTTAATGACGTAT
1 TTGTTAGATTTAATGACGTAT
27686006 T
1 T
27686007 GCTATCGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.49
Consensus pattern (21 bp):
TTGTTAGATTTAATGACGTAT
Found at i:27689581 original size:27 final size:27
Alignment explanation
Indices: 27689551--27689714 Score: 166
Period size: 27 Copynumber: 6.1 Consensus size: 27
27689541 AGGTAGTCCA
* * * *
27689551 TTCAAAGTTCGCCACAAAGACGATTCT
1 TTCAGAGTTCTCCACAAAGGCTATTCT
* * *
27689578 TTCAGATTTTTCCACAAAGGTTATTCT
1 TTCAGAGTTCTCCACAAAGGCTATTCT
* *
27689605 TTCAGATTTTTCCACAAAGGCTATTCT
1 TTCAGAGTTCTCCACAAAGGCTATTCT
* * *
27689632 TTCAAAGTTCACCATAAAGGCTATTCT
1 TTCAGAGTTCTCCACAAAGGCTATTCT
* * **
27689659 TTTAGGGTTCTCCACAAAGATTATTCT
1 TTCAGAGTTCTCCACAAAGGCTATTCT
* *
27689686 TTTAGAGTTCGCCACAAAGGCTATTCT
1 TTCAGAGTTCTCCACAAAGGCTATTCT
27689713 TT
1 TT
27689715 GTTGTCGTGT
Statistics
Matches: 113, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 113 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (27 bp):
TTCAGAGTTCTCCACAAAGGCTATTCT
Found at i:27689675 original size:81 final size:81
Alignment explanation
Indices: 27689551--27689714 Score: 211
Period size: 81 Copynumber: 2.0 Consensus size: 81
27689541 AGGTAGTCCA
* * * * * **
27689551 TTCAAAGTTCGCCACAAAGACGATTCTTTCAGATTTTTCCACAAAGGTTATTCTTTCAGATTTTT
1 TTCAAAGTTCACCACAAAGACGATTCTTTCAGAGTTCTCCACAAAGATTATTCTTTCAGAGTTCG
27689616 CCACAAAGGCTATTCT
66 CCACAAAGGCTATTCT
* * * * * *
27689632 TTCAAAGTTCACCATAAAGGCTATTCTTTTAGGGTTCTCCACAAAGATTATTCTTTTAGAGTTCG
1 TTCAAAGTTCACCACAAAGACGATTCTTTCAGAGTTCTCCACAAAGATTATTCTTTCAGAGTTCG
27689697 CCACAAAGGCTATTCT
66 CCACAAAGGCTATTCT
27689713 TT
1 TT
27689715 GTTGTCGTGT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (81 bp):
TTCAAAGTTCACCACAAAGACGATTCTTTCAGAGTTCTCCACAAAGATTATTCTTTCAGAGTTCG
CCACAAAGGCTATTCT
Found at i:27690078 original size:22 final size:22
Alignment explanation
Indices: 27690053--27690096 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
27690043 CATATACAAC
*
27690053 CATACTCCAA-CATTTCAGTACT
1 CATACACCAATCATTTCA-TACT
27690075 CATACACCAATCATTTCATACT
1 CATACACCAATCATTTCATACT
27690097 TCAATTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (22 bp):
CATACACCAATCATTTCATACT
Found at i:27698148 original size:10 final size:10
Alignment explanation
Indices: 27698133--27698157 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27698123 CGCGTCAAGC
27698133 CCTTTTTTTT
1 CCTTTTTTTT
27698143 CCTTTTTTTT
1 CCTTTTTTTT
27698153 CCTTT
1 CCTTT
27698158 CTCTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
CCTTTTTTTT
Found at i:27701108 original size:6 final size:6
Alignment explanation
Indices: 27701099--27701148 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
27701089 CACGCCTTTG
27701099 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA
1 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA
27701147 CC
1 CC
27701149 CATTGCTACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTTCA
Found at i:27704347 original size:50 final size:50
Alignment explanation
Indices: 27704272--27704565 Score: 444
Period size: 50 Copynumber: 5.9 Consensus size: 50
27704262 CGTTTGGGTA
* *
27704272 GAGAGGTCCTATGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
27704322 GAGAGGTCCCATGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
27704372 GAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
27704422 GAGAGGTCCCATGTAAGATCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** * * *
27704472 GTGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** *
27704522 AAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
27704566 TGTTATGATC
Statistics
Matches: 223, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
50 189 0.85
51 34 0.15
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (50 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:27704915 original size:12 final size:12
Alignment explanation
Indices: 27704898--27704927 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27704888 TTTATGCTTA
27704898 CTTCTTTTATTT
1 CTTCTTTTATTT
27704910 CTTCTTTTATTT
1 CTTCTTTTATTT
27704922 C-TCTTT
1 CTTCTTT
27704928 CTCTTATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTCTTTTATTT
Found at i:27713276 original size:2 final size:2
Alignment explanation
Indices: 27713269--27713316 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
27713259 ACTCTACTAT
*
27713269 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
27713311 TG TG TG
1 TG TG TG
27713317 GAGGAGGAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:27714089 original size:23 final size:19
Alignment explanation
Indices: 27714018--27714074 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
27714008 ATAGATAATA
*
27714018 TATCTTAGTTAATTAATTATT
1 TATCTTTGTTAATT-ATT-TT
* *
27714039 TTTCTTT-CTAATTATTTT
1 TATCTTTGTTAATTATTTT
27714057 TATCTTTGTTAATTATTT
1 TATCTTTGTTAATTATTT
27714075 GTTCAGTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 8 0.27
19 12 0.40
20 5 0.17
21 5 0.17
ACGTcount: A:0.25, C:0.07, G:0.04, T:0.65
Consensus pattern (19 bp):
TATCTTTGTTAATTATTTT
Found at i:27718173 original size:57 final size:57
Alignment explanation
Indices: 27718063--27718173 Score: 204
Period size: 57 Copynumber: 1.9 Consensus size: 57
27718053 AATCTATATC
* *
27718063 TAGTGTCGCGACATTGAAGTCAATGGGGTAATTTGTTTGCAGTGTCGCGACATTCGT
1 TAGTGTCGCGACATTGAAGTCAATGGGGTAATTTGTTTGCAGTGTCACAACATTCGT
27718120 TAGTGTCGCGACATTGAAGTCAATGGGGTAATTTGTTTGCAGTGTCACAACATT
1 TAGTGTCGCGACATTGAAGTCAATGGGGTAATTTGTTTGCAGTGTCACAACATT
27718174 GGCCCTATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (57 bp):
TAGTGTCGCGACATTGAAGTCAATGGGGTAATTTGTTTGCAGTGTCACAACATTCGT
Found at i:27727149 original size:27 final size:26
Alignment explanation
Indices: 27727110--27727163 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
27727100 TGGATCCGTA
* *
27727110 TGTTACTTGTTTTTGTTAATTTTAATT
1 TGTTACTTGTTTTT-TAAATTTCAATT
* *
27727137 TGTTTCTTTTTTTTTAAATTTCAATT
1 TGTTACTTGTTTTTTAAATTTCAATT
27727163 T
1 T
27727164 ACTAAGCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.19, C:0.06, G:0.07, T:0.69
Consensus pattern (26 bp):
TGTTACTTGTTTTTTAAATTTCAATT
Found at i:27728408 original size:30 final size:30
Alignment explanation
Indices: 27728372--27728436 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
27728362 CTGTACGTGA
* *
27728372 GTTTGGCATCGATCTTAATTTTTCACATGT
1 GTTTGGCATCGATCTTAATTCTCCACATGT
27728402 GTTTGGCATCGATCTTAATTCTCCACATGT
1 GTTTGGCATCGATCTTAATTCTCCACATGT
27728432 GTTTG
1 GTTTG
27728437 AGAACCTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (30 bp):
GTTTGGCATCGATCTTAATTCTCCACATGT
Found at i:27733357 original size:21 final size:21
Alignment explanation
Indices: 27733333--27733383 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
27733323 AAAAAATACA
27733333 AAAAAAAATTAAAATATTT-AT
1 AAAAAAAATTAAAAT-TTTCAT
**
27733354 -AAAAAAATCCAAATTTTCAT
1 AAAAAAAATTAAAATTTTCAT
27733374 AAAAAAAATT
1 AAAAAAAATT
27733384 TCACTCGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 8 0.32
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAAAATTAAAATTTTCAT
Found at i:27735115 original size:22 final size:21
Alignment explanation
Indices: 27735090--27735137 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
27735080 AATTATATTT
27735090 TAAAA-TTCAAAAAATAAATGAA
1 TAAAATTTCAAAAAATAAA--AA
*
27735112 TAAAATTTCTAAAAATAAAAA
1 TAAAATTTCAAAAAATAAAAA
27735133 TAAAA
1 TAAAA
27735138 GTTTGGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 5 0.21
23 12 0.50
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (21 bp):
TAAAATTTCAAAAAATAAAAA
Found at i:27741894 original size:43 final size:43
Alignment explanation
Indices: 27741846--27741932 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
27741836 ATAATGTCAT
27741846 TAGTTAGTCTAAATATTTAATATTATTAACTATTTCAATAAAA
1 TAGTTAGTCTAAATATTTAATATTATTAACTATTTCAATAAAA
* * *
27741889 TAGTTAGTCTAAATATTTAATATTGTTAACTGTTTTAATAAAA
1 TAGTTAGTCTAAATATTTAATATTATTAACTATTTCAATAAAA
27741932 T
1 T
27741933 TGCTTATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (43 bp):
TAGTTAGTCTAAATATTTAATATTATTAACTATTTCAATAAAA
Found at i:27742831 original size:44 final size:44
Alignment explanation
Indices: 27742764--27742999 Score: 176
Period size: 44 Copynumber: 5.4 Consensus size: 44
27742754 GGTCTCCAAT
* * *
27742764 CCCATCTTATGTGTATACGATGTGTGGATTTTATCCCGTTTTTC
1 CCCATCTTATGTGTATGCTATGTGTGGATTTTATCCAGTTTTTC
* * * *
27742808 CCCATCTTATATGTATGCTATGTGTGGGTTTT-TCTAGTTCTTC
1 CCCATCTTATGTGTATGCTATGTGTGGATTTTATCCAGTTTTTC
* * * * *
27742851 CCTATCTTGTGTGTATG-TCATGTATGGGTTTTATCCAATTCTTT-
1 CCCATCTTATGTGTATGCT-ATGTGTGGATTTTATCCAGTT-TTTC
* * * * *
27742895 CCTATCTTGTGTATATGCTATGTGTGGATTTTATCTAGTTCTTC
1 CCCATCTTATGTGTATGCTATGTGTGGATTTTATCCAGTTTTTC
* * * * * * *
27742939 CCTATCTTGTGTGTACGCCATGTAT-GAGTTTTATCTAGTTCTTC
1 CCCATCTTATGTGTATGCTATGTGTGGA-TTTTATCCAGTTTTTC
*
27742983 TCTC-TCTTATGTGTATG
1 -CCCATCTTATGTGTATG
27743000 TCCGTTGTGC
Statistics
Matches: 157, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
42 1 0.01
43 38 0.24
44 114 0.73
45 4 0.03
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.48
Consensus pattern (44 bp):
CCCATCTTATGTGTATGCTATGTGTGGATTTTATCCAGTTTTTC
Found at i:27745013 original size:6 final size:7
Alignment explanation
Indices: 27744994--27745019 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27744984 ATATTATAAT
27744994 TTAAAAA
1 TTAAAAA
27745001 TTAAAAA
1 TTAAAAA
27745008 TTAAAAA
1 TTAAAAA
27745015 TTAAA
1 TTAAA
27745020 TTCGGTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:27746055 original size:14 final size:14
Alignment explanation
Indices: 27746036--27746069 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
27746026 GCCCTCCTGT
27746036 AGCAACAATTCAAA
1 AGCAACAATTCAAA
27746050 AGCAACAATTCAAA
1 AGCAACAATTCAAA
27746064 AGCAAC
1 AGCAAC
27746070 CAATAGCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.24, G:0.09, T:0.12
Consensus pattern (14 bp):
AGCAACAATTCAAA
Found at i:27746354 original size:21 final size:21
Alignment explanation
Indices: 27746290--27746356 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
27746280 GCTCTGCTCC
* *
27746290 GCTTCTCTCGCTGCAGCCTCC
1 GCTTCCCTCGCTGCAGCCTCT
*
27746311 GCTTCCCTCGCTGCAGCCGCT
1 GCTTCCCTCGCTGCAGCCTCT
* *
27746332 GCTTCCCTCGCTTCCGCCTCT
1 GCTTCCCTCGCTGCAGCCTCT
27746353 GCTT
1 GCTT
27746357 TAAGTTATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.48, G:0.19, T:0.30
Consensus pattern (21 bp):
GCTTCCCTCGCTGCAGCCTCT
Found at i:27750996 original size:9 final size:9
Alignment explanation
Indices: 27750982--27751493 Score: 265
Period size: 9 Copynumber: 58.9 Consensus size: 9
27750972 TATCTATGAA
27750982 TTATGTAAG
1 TTATGTAAG
*
27750991 TTATGTACG
1 TTATGTAAG
27751000 TGTA--TAAG
1 T-TATGTAAG
*
27751008 TTAAGTAAG
1 TTATGTAAG
27751017 TTATGT-A-
1 TTATGTAAG
*
27751024 TTAAGTAAG
1 TTATGTAAG
27751033 TTATGTAAG
1 TTATGTAAG
*
27751042 TTATGAAAG
1 TTATGTAAG
* *
27751051 TAATGTATG
1 TTATGTAAG
*
27751060 TAATGTAAG
1 TTATGTAAG
27751069 -T-TGTAAG
1 TTATGTAAG
*
27751076 TTAT-TATG
1 TTATGTAAG
27751084 TATTATGTAAG
1 --TTATGTAAG
27751095 TTATGTAAG
1 TTATGTAAG
* *
27751104 TTATATATAT
1 TTATGTA-AG
27751114 TTATGT-A-
1 TTATGTAAG
* *
27751121 TTAAGTAAA
1 TTATGTAAG
27751130 TTATGTAAG
1 TTATGTAAG
*
27751139 TTATGTACG
1 TTATGTAAG
27751148 TGTA--TAAG
1 T-TATGTAAG
*
27751156 TTAAGTAAG
1 TTATGTAAG
27751165 TTATGT-A-
1 TTATGTAAG
*
27751172 TTAAGTAAG
1 TTATGTAAG
27751181 TTATGTAAG
1 TTATGTAAG
*
27751190 TTATGAAAG
1 TTATGTAAG
* *
27751199 TAATGTATG
1 TTATGTAAG
*
27751208 TAATGTAAG
1 TTATGTAAG
27751217 -T-TGTAAG
1 TTATGTAAG
*
27751224 TTAT-TATG
1 TTATGTAAG
27751232 TATTATGTAAG
1 --TTATGTAAG
27751243 TTATGTAAG
1 TTATGTAAG
27751252 TTATGTAAG
1 TTATGTAAG
27751261 TTAAATGT-A-
1 TT--ATGTAAG
27751270 TTATGTAAG
1 TTATGTAAG
27751279 -T-TGTAAG
1 TTATGTAAG
27751286 TTAAATGT-A-
1 TT--ATGTAAG
*
27751295 TTAAGTAAG
1 TTATGTAAG
27751304 -T-TGTAAG
1 TTATGTAAG
27751311 TTAAGTGT-A-
1 TT-A-TGTAAG
27751320 TTATGTAAG
1 TTATGTAAG
27751329 -T-TGTAAG
1 TTATGTAAG
*
27751336 TTAT-TATG
1 TTATGTAAG
27751344 TATTATGTAAG
1 --TTATGTAAG
27751355 -T-TGTAAG
1 TTATGTAAG
27751362 TTAAATGT-A-
1 TT--ATGTAAG
*
27751371 TTGTG-AAG
1 TTATGTAAG
27751379 -T-TGTAAG
1 TTATGTAAG
*
27751386 TTAT-TATG
1 TTATGTAAG
27751394 TATTATGTAAG
1 --TTATGTAAG
27751405 TTATGTAAG
1 TTATGTAAG
27751414 TTAAATGT-A-
1 TT--ATGTAAG
*
27751423 TTATGTAGG
1 TTATGTAAG
27751432 TTATGTAAG
1 TTATGTAAG
*
27751441 TTGTGTAAG
1 TTATGTAAG
** *
27751450 AGATTTAAG
1 TTATGTAAG
*
27751459 TTATGTAGG
1 TTATGTAAG
* *
27751468 TTATTTAGG
1 TTATGTAAG
27751477 TTATGTAAG
1 TTATGTAAG
*
27751486 TTTTGTAA
1 TTATGTAA
27751494 TGTGCAAGTG
Statistics
Matches: 389, Mismatches: 54, Indels: 120
0.69 0.10 0.21
Matches are distributed among these distances:
6 2 0.01
7 75 0.19
8 41 0.11
9 211 0.54
10 31 0.08
11 29 0.07
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:27751021 original size:35 final size:35
Alignment explanation
Indices: 27750982--27751252 Score: 125
Period size: 35 Copynumber: 7.5 Consensus size: 35
27750972 TATCTATGAA
*
27750982 TTATGTAAGTTATGTACGTGTATAAGTTAAGTAAG
1 TTATGTAAGTTATGTAAGTGTATAAGTTAAGTAAG
* * *
27751017 TTATGT-A-TTAAGTAAGT-TATGTAAGTTATGAAAG
1 TTATGTAAGTTATGTAAGTGTA--TAAGTTAAGTAAG
* * * *
27751051 TAATGTATGTAATGTAAGT-TGTAAGTTATTATGT-A-
1 TTATGTAAGTTATGTAAGTGTATAAGTTA--A-GTAAG
* *
27751086 TTATGTAAGTTATGTAAGTTATATATATTTATGTATTAAGTAAA
1 TTATGTAAGTTATGTAAG---TGTATA---A-G--TTAAGTAAG
*
27751130 TTATGTAAGTTATGTACGTGTATAAGTTAAGTAAG
1 TTATGTAAGTTATGTAAGTGTATAAGTTAAGTAAG
* * *
27751165 TTATGT-A-TTAAGTAAGT-TATGTAAGTTATGAAAG
1 TTATGTAAGTTATGTAAGTGTA--TAAGTTAAGTAAG
* * * *
27751199 TAATGTATGTAATGTAAGT-TGTAAGTTATTATGT-A-
1 TTATGTAAGTTATGTAAGTGTATAAGTTA--A-GTAAG
27751234 TTATGTAAGTTATGTAAGT
1 TTATGTAAGTTATGTAAGT
27751253 TATGTAAGTT
Statistics
Matches: 178, Mismatches: 32, Indels: 52
0.68 0.12 0.20
Matches are distributed among these distances:
32 4 0.02
33 16 0.09
34 48 0.27
35 51 0.29
36 20 0.11
37 3 0.02
38 2 0.01
39 3 0.02
41 5 0.03
42 3 0.02
43 3 0.02
44 17 0.10
45 3 0.02
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.44
Consensus pattern (35 bp):
TTATGTAAGTTATGTAAGTGTATAAGTTAAGTAAG
Found at i:27751040 original size:25 final size:25
Alignment explanation
Indices: 27750982--27751447 Score: 226
Period size: 25 Copynumber: 18.6 Consensus size: 25
27750972 TATCTATGAA
27750982 TTATGTAAGTTATGTACGTGT-A-TAAG
1 TTATGTAAGTTATGTA--T-TAAGTAAG
*
27751008 TTAAGTAAGTTATGTATTAAGTAAG
1 TTATGTAAGTTATGTATTAAGTAAG
27751033 TTATGTAAGTTATG-A--AAGTAA-
1 TTATGTAAGTTATGTATTAAGTAAG
* *
27751054 TGTATGTAA-TGTAAGT-TGTAAGTTA-
1 T-TATGTAAGT-TATGTAT-TAAGTAAG
*
27751079 TTATGT-A-TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-A-TTAAGTAAG
* * *
27751104 TTATATATATTTATGTATTAAGTAAA
1 TTATGTA-AGTTATGTATTAAGTAAG
27751130 TTATGTAAGTTATGTACGTGT-A-TAAG
1 TTATGTAAGTTATGTA--T-TAAGTAAG
*
27751156 TTAAGTAAGTTATGTATTAAGTAAG
1 TTATGTAAGTTATGTATTAAGTAAG
27751181 TTATGTAAGTTATG-A--AAGTAA-
1 TTATGTAAGTTATGTATTAAGTAAG
* *
27751202 TGTATGTAA-TGTAAGT-TGTAAGTTA-
1 T-TATGTAAGT-TATGTAT-TAAGTAAG
*
27751227 TTATGT-A-TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-A-TTAAGTAAG
*
27751252 TTATGTAAGTTAAATGTATTATGTAAG
1 TTATGTAAGTT--ATGTATTAAGTAAG
27751279 -T-TGTAAGTTAAATGTATTAAGTAAG
1 TTATGTAAGTT--ATGTATTAAGTAAG
*
27751304 -T-TGTAAGTTAAGTGTATTATGTAAG
1 TTATGTAAGTT-A-TGTATTAAGTAAG
*
27751329 -T-TGTAAGTTATTATGTATTATGTAAG
1 TTATGTAAG---TTATGTATTAAGTAAG
27751355 -T-TGTAAGTTAAATGTATT--GTGAAG
1 TTATGTAAGTT--ATGTATTAAGT-AAG
*
27751379 -T-TGTAAGTTATTATGTATTATGTAAG
1 TTATGTAAG---TTATGTATTAAGTAAG
* *
27751405 TTATGTAAGTTAAATGTATTATGTAGG
1 TTATGTAAGTT--ATGTATTAAGTAAG
*
27751432 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
27751448 AGAGATTTAA
Statistics
Matches: 366, Mismatches: 24, Indels: 101
0.75 0.05 0.21
Matches are distributed among these distances:
21 4 0.01
22 40 0.11
23 10 0.03
24 38 0.10
25 138 0.38
26 71 0.19
27 45 0.12
28 16 0.04
29 4 0.01
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTAAGTAAG
Found at i:27751191 original size:148 final size:149
Alignment explanation
Indices: 27750956--27751255 Score: 566
Period size: 148 Copynumber: 2.0 Consensus size: 149
27750946 ATATCATATG
*
27750956 ATATATATTTATGTATTATCTATGAATTATGTAAGTTATGTACGTGTATAAGTTAAGTAAGTTAT
1 ATATATATTTATGTATTAACTA-GAATTATGTAAGTTATGTACGTGTATAAGTTAAGTAAGTTAT
27751021 GTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAGTTGTAAGTTATTATGTA
65 GTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAGTTGTAAGTTATTATGTA
27751086 TTATGTAAGTTATGTAAGTT
130 TTATGTAAGTTATGTAAGTT
*
27751106 ATATATATTTATGTATTAAGTA-AATTATGTAAGTTATGTACGTGTATAAGTTAAGTAAGTTATG
1 ATATATATTTATGTATTAACTAGAATTATGTAAGTTATGTACGTGTATAAGTTAAGTAAGTTATG
27751170 TATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAGTTGTAAGTTATTATGTAT
66 TATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAGTTGTAAGTTATTATGTAT
27751235 TATGTAAGTTATGTAAGTT
131 TATGTAAGTTATGTAAGTT
27751254 AT
1 AT
27751256 GTAAGTTAAA
Statistics
Matches: 148, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
148 128 0.86
150 20 0.14
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (149 bp):
ATATATATTTATGTATTAACTAGAATTATGTAAGTTATGTACGTGTATAAGTTAAGTAAGTTATG
TATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAGTTGTAAGTTATTATGTAT
TATGTAAGTTATGTAAGTT
Found at i:27751210 original size:22 final size:24
Alignment explanation
Indices: 27750982--27751112 Score: 72
Period size: 22 Copynumber: 5.8 Consensus size: 24
27750972 TATCTATGAA
*
27750982 TTATGTAAGTTATGTACGTGTA-TAAG
1 TTATGTAAGTTATGTA--T-AAGTAAG
*
27751008 TTAAGTAAGTTATGTATTAAGTAAG
1 TTATGTAAGTTATGTA-TAAGTAAG
27751033 TTATGTAAGTTATG-A-AAGTAA-
1 TTATGTAAGTTATGTATAAGTAAG
*
27751054 TGTATGTAA-TGTAAGT-T--GTAAG
1 T-TATGTAAGT-TATGTATAAGTAAG
*
27751076 TTAT-TATG-TAT-TAT--GTAAG
1 TTATGTAAGTTATGTATAAGTAAG
*
27751095 TTATGTAAGTTATATATA
1 TTATGTAAGTTATGTATA
27751113 TTTATGTATT
Statistics
Matches: 85, Mismatches: 8, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
18 1 0.01
19 12 0.14
20 5 0.06
21 12 0.14
22 20 0.24
24 2 0.02
25 18 0.21
26 15 0.18
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.44
Consensus pattern (24 bp):
TTATGTAAGTTATGTATAAGTAAG
Found at i:27751304 original size:148 final size:145
Alignment explanation
Indices: 27751004--27751447 Score: 506
Period size: 148 Copynumber: 3.1 Consensus size: 145
27750994 TGTACGTGTA
27751004 TAAGTTAAGTAAGTTATGTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAG
1 TAAGTTAAGTAAGTTATGTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAG
* *
27751069 TTGTAAGTTATTATGTATTATGTAAGTTATGTAAGTTATATATATTTATGTATTAAGTAAATTAT
66 TTGTAAGTTATTATGTATTATGTAAGTTATGTAAGTTAT-TA-A-TTATGTATTATGT-AAGTAT
27751134 GTAAGTT--ATGTACGTGT-A-
127 GTAAGTTAAATGTA--T-TAAG
27751152 TAAGTTAAGTAAGTTATGTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAG
1 TAAGTTAAGTAAGTTATGTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAG
27751217 TTGTAAGTTATTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGT-T
66 TTGTAAGTTATTATGTATTATGTAAGTTATGTAAGTTAT-TAA-TT--ATGTATTATGTAAGTAT
27751281 GTAAGTTAAATGTATTAAG
127 GTAAGTTAAATGTATTAAG
*
27751300 TAAGTT--GTAAGTTAAGTGTATTATGTAAG-T-TGTAAGTTAT-----T-ATGTAT-T-ATGTA
1 TAAGTTAAGTAAGTT-A-TGTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTA
* *
27751353 AGTTGTAAGTTA-AATGTATTGTG-AAG-T-TGTAAG---TT-ATTATGTATTATGTAAGTTATG
64 AGTTGTAAGTTATTATGTATTATGTAAGTTATGTAAGTTATTAATTATGTATTATGTAAG-TATG
*
27751410 TAAGTTAAATGTATTATG
128 TAAGTTAAATGTATTAAG
* * *
27751428 TAGGTTATGTAAGTTGTGTA
1 TAAGTTAAGTAAGTTATGTA
27751448 AGAGATTTAA
Statistics
Matches: 274, Mismatches: 10, Indels: 44
0.84 0.03 0.13
Matches are distributed among these distances:
126 14 0.05
127 1 0.00
128 30 0.11
129 1 0.00
130 8 0.03
131 1 0.00
134 6 0.02
135 1 0.00
136 3 0.01
137 9 0.03
138 17 0.06
139 1 0.00
140 6 0.02
141 1 0.00
146 18 0.07
147 15 0.05
148 127 0.46
149 15 0.05
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.44
Consensus pattern (145 bp):
TAAGTTAAGTAAGTTATGTATTAAGTAAGTTATGTAAGTTATGAAAGTAATGTATGTAATGTAAG
TTGTAAGTTATTATGTATTATGTAAGTTATGTAAGTTATTAATTATGTATTATGTAAGTATGTAA
GTTAAATGTATTAAG
Found at i:27751354 original size:19 final size:19
Alignment explanation
Indices: 27751210--27751345 Score: 74
Period size: 19 Copynumber: 7.3 Consensus size: 19
27751200 AATGTATGTA
27751210 ATGTAAGTTGTAAGTTATT
1 ATGTAAGTTGTAAGTTATT
*
27751229 ATGT-ATTATGTAAGTTATGT
1 ATGTAAGT-TGTAAGTTAT-T
* * * *
27751249 AAGTTATGTAAGTTAAATGTATT
1 ATG-TAAGT-TG-TAAGT-TATT
*
27751272 ATGTAAGTTGTAAGTTA-A
1 ATGTAAGTTGTAAGTTATT
* *
27751290 ATGT-A--T-TAAGTAAGT
1 ATGTAAGTTGTAAGTTATT
27751305 -TGTAAG-T-TAAGTGTATT
1 ATGTAAGTTGTAAGT-TATT
27751322 ATGTAAGTTGTAAGTTATT
1 ATGTAAGTTGTAAGTTATT
27751341 ATGTA
1 ATGTA
27751346 TTATGTAAGT
Statistics
Matches: 89, Mismatches: 15, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
14 9 0.10
15 2 0.02
16 6 0.07
17 3 0.03
18 12 0.13
19 26 0.29
20 12 0.13
21 2 0.02
22 7 0.08
23 7 0.08
24 3 0.03
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.45
Consensus pattern (19 bp):
ATGTAAGTTGTAAGTTATT
Found at i:27753007 original size:16 final size:17
Alignment explanation
Indices: 27752986--27753017 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27752976 CATCAATAAA
27752986 TAACAAACA-AAAAAAT
1 TAACAAACACAAAAAAT
27753002 TAACAAACACAAAAAA
1 TAACAAACACAAAAAA
27753018 ACCCAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.16, G:0.00, T:0.09
Consensus pattern (17 bp):
TAACAAACACAAAAAAT
Found at i:27753142 original size:19 final size:19
Alignment explanation
Indices: 27753115--27753156 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
27753105 TCTCTGTCTG
*
27753115 GAAATCGGGAAATCGGGAA
1 GAAACCGGGAAATCGGGAA
27753134 GAAACCGGGAAATCGGGAA
1 GAAACCGGGAAATCGGGAA
27753153 GAAA
1 GAAA
27753157 TCAGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.36, T:0.07
Consensus pattern (19 bp):
GAAACCGGGAAATCGGGAA
Found at i:27753165 original size:19 final size:19
Alignment explanation
Indices: 27753124--27753166 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
27753114 GGAAATCGGG
* *
27753124 AAATCGGGAAGAAACCGGG
1 AAATCGGGAAGAAACCAGA
*
27753143 AAATCGGGAAGAAATCAGA
1 AAATCGGGAAGAAACCAGA
27753162 AAATC
1 AAATC
27753167 CGAACCTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.28, T:0.09
Consensus pattern (19 bp):
AAATCGGGAAGAAACCAGA
Found at i:27754124 original size:83 final size:80
Alignment explanation
Indices: 27754032--27754195 Score: 256
Period size: 83 Copynumber: 2.0 Consensus size: 80
27754022 AAATCTTACA
* * * *
27754032 AATTTCATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCTTTTTTTA
1 AATTTCATTTCACGAAACGGCTCCGTTTTACTCAATTTTCCAAATATTATTTGC-G--TTTGTTA
27754097 CAAAAACGCCACTAAATT
63 CAAAAACGCCACTAAATT
*
27754115 AATTTCATTTCACGAAACGGCTCCGTTTTACTCAATTTTTCAAATATTATTTGCGTTTGTTACAA
1 AATTTCATTTCACGAAACGGCTCCGTTTTACTCAATTTTCCAAATATTATTTGCGTTTGTTACAA
27754180 AAACGCCACTAAATT
66 AAACGCCACTAAATT
27754195 A
1 A
27754196 TTTATATTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
80 25 0.33
82 1 0.01
83 50 0.66
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (80 bp):
AATTTCATTTCACGAAACGGCTCCGTTTTACTCAATTTTCCAAATATTATTTGCGTTTGTTACAA
AAACGCCACTAAATT
Found at i:27754654 original size:39 final size:40
Alignment explanation
Indices: 27754577--27754665 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 40
27754567 CCCAAATTCC
* **
27754577 TAACCCAT-AACCCCTAAATCCCCCTTAACCTTTAAAGCA
1 TAACCCCTAAACCCCTAAATCCCCCTTAACCCCTAAAGCA
* *
27754616 TAAGCCCTAAACCCCTAAATCTCCC-TAACCCCTAAAGCA
1 TAACCCCTAAACCCCTAAATCCCCCTTAACCCCTAAAGCA
27754655 TAACCCCTAAA
1 TAACCCCTAAA
27754666 TAATTTTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 28 0.65
40 15 0.35
ACGTcount: A:0.37, C:0.39, G:0.03, T:0.20
Consensus pattern (40 bp):
TAACCCCTAAACCCCTAAATCCCCCTTAACCCCTAAAGCA
Found at i:27755411 original size:115 final size:115
Alignment explanation
Indices: 27755152--27755378 Score: 408
Period size: 115 Copynumber: 2.0 Consensus size: 115
27755142 AAATTAGTCT
*
27755152 AAGTATGACCAAAAAAGT----AAAAAAAAAAAATCAGATACGGAGATGAGAAAAACGTAGAGTT
1 AAGTATGACCAAAAAAGTAAAAAAAAAAAAAAAATCAGATACCGAGATGAGAAAAACGTAGAGTT
27755213 TAAGTTCCCTATGTGGATTAAGGAAAAAACAGAAGGAAAGGAACAAAGAA
66 TAAGTTCCCTATGTGGATTAAGGAAAAAACAGAAGGAAAGGAACAAAGAA
*
27755263 AAGTATGACCAAAAAAGTAAAAAAAAAAAAAAAATCAGATACCGAGATGAGAATAACGTAGAGTT
1 AAGTATGACCAAAAAAGTAAAAAAAAAAAAAAAATCAGATACCGAGATGAGAAAAACGTAGAGTT
27755328 TAAGTTCCCTATGTGGATTAAGGAAAAAACAGAAGGAAAGGAACAAAGAA
66 TAAGTTCCCTATGTGGATTAAGGAAAAAACAGAAGGAAAGGAACAAAGAA
27755378 A
1 A
27755379 TTTACTAATA
Statistics
Matches: 110, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
111 18 0.16
115 92 0.84
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.15
Consensus pattern (115 bp):
AAGTATGACCAAAAAAGTAAAAAAAAAAAAAAAATCAGATACCGAGATGAGAAAAACGTAGAGTT
TAAGTTCCCTATGTGGATTAAGGAAAAAACAGAAGGAAAGGAACAAAGAA
Found at i:27757715 original size:3 final size:3
Alignment explanation
Indices: 27757707--27757745 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
27757697 CTCCATTAGT
*
27757707 TTC TTC TTC TTC TTC TTC TTC CTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
27757746 GCCATTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:27763496 original size:11 final size:12
Alignment explanation
Indices: 27763480--27763512 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
27763470 ATTTCACTGA
27763480 AAAATTTCG-TG
1 AAAATTTCGTTG
27763491 AAAATTTCGTTTG
1 AAAATTTCG-TTG
27763504 AAAATTTCG
1 AAAATTTCG
27763513 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
13 11 0.55
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (12 bp):
AAAATTTCGTTG
Found at i:27764628 original size:42 final size:43
Alignment explanation
Indices: 27764577--27764817 Score: 221
Period size: 42 Copynumber: 5.7 Consensus size: 43
27764567 ATTGAATAAG
* *
27764577 AAGG-GGTTGCTAAGTGCTGATTCC-CCGAATTATTGACTTTA
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATTATTGAATTTA
27764618 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCT-TTG-ATTGTGA
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTAT-TATTGAATT-T-A
* * *
27764662 AAGG-GGTTGCTATGTGCTGATTCC-CCGTATTACTGAATATA
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATTATTGAATTTA
* * * * *
27764703 AAGGTGGTTGCTAAGTGTTCATTCCACTGTATCT-TTGACTGTGA
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTAT-TATTGAAT-TTA
* * * * *
27764747 AAGGGGGGTTGCTATGTGCTGATTCC-TCGTATCACTGAATTT-
1 AA-GGTGGTTGCTAAGTGCTGATTCCACCGTATTATTGAATTTA
*
27764789 AAGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGTGGTTGCTAAGTGCTGATTCCACCG
27764818 AGTAACGGAT
Statistics
Matches: 159, Mismatches: 27, Indels: 27
0.75 0.13 0.13
Matches are distributed among these distances:
41 30 0.19
42 52 0.33
43 40 0.25
44 18 0.11
45 19 0.12
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (43 bp):
AAGGTGGTTGCTAAGTGCTGATTCCACCGTATTATTGAATTTA
Found at i:27764727 original size:85 final size:84
Alignment explanation
Indices: 27764577--27764817 Score: 329
Period size: 85 Copynumber: 2.8 Consensus size: 84
27764567 ATTGAATAAG
* * * * *
27764577 AAGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGACTTTAAAGGTGGTTGCTAAGTGCTGATTC
1 AAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGA-ATTAAAGGTGGTTGCTAAGTGCTCATTC
*
27764642 CACCGTATCTTTGATTGTGA
65 CACCGTATCTTTGACTGTGA
*
27764662 AAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATATAAAGGTGGTTGCTAAGTGTTCATTC
1 AAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAAT-TAAAGGTGGTTGCTAAGTGCTCATTC
*
27764727 CACTGTATCTTTGACTGTGA
65 CACCGTATCTTTGACTGTGA
* * * * *
27764747 AAGGGGGGTTGCTATGTGCTGATTCCTCGTATCACTGAATTTAAGGTGGTTGCTAAGTGCTGAAT
1 AA--GGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGCTCATT
27764812 CCACCG
64 CCACCG
27764818 AGTAACGGAT
Statistics
Matches: 138, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
84 1 0.01
85 77 0.56
86 26 0.19
87 34 0.25
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (84 bp):
AAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGCTCATTCC
ACCGTATCTTTGACTGTGA
Found at i:27767608 original size:103 final size:104
Alignment explanation
Indices: 27767468--27767678 Score: 311
Period size: 103 Copynumber: 2.0 Consensus size: 104
27767458 GCCAAAATAA
* * *
27767468 TATCGATTTTCAATTGAGTATCGATACTTTTTGGTAAAATATCGATACCATCAACTAATTATTGA
1 TATCAATTTTCAATTGAGTATCAATACTTTTTGGTAAAATATCGATACCATCAACTAATTATCGA
*
27767533 TACCA-TTGTTTTACAAAGAAAACA-AAGTTGAATTTTTG
66 TACCATTTGTTTTACAAAGAAAACATAA-TTGAATTTTGG
*
27767571 TATCAATTTTCAATTGAGTATTAATACATTTTT-GTAAAATATCGATACCATCAACTAATTATCG
1 TATCAATTTTCAATTGAGTATCAATAC-TTTTTGGTAAAATATCGATACCATCAACTAATTATCG
* *
27767635 ATACCATTTTTTTTTACAAAGAAAATATAATTGAATTTTGG
65 ATACCA-TTTGTTTTACAAAGAAAACATAATTGAATTTTGG
27767676 TAT
1 TAT
27767679 TGATTTTTCT
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
103 60 0.62
104 5 0.05
105 30 0.31
106 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (104 bp):
TATCAATTTTCAATTGAGTATCAATACTTTTTGGTAAAATATCGATACCATCAACTAATTATCGA
TACCATTTGTTTTACAAAGAAAACATAATTGAATTTTGG
Found at i:27786356 original size:30 final size:29
Alignment explanation
Indices: 27786320--27786482 Score: 134
Period size: 30 Copynumber: 5.4 Consensus size: 29
27786310 AGCTATCGAT
* *
27786320 TATGAAAAGGGATGGTGACGACCATGGAAC
1 TATGAAAAGGGATGATGACGACCAT-CAAC
* ** * *
27786350 TATGAAAAGGGATGGCT-TTGGCTATCAATC
1 TATGAAAAGGGAT-GATGACGACCATCAA-C
* *
27786380 TATGAAAAGGGATGACT-TC-AGCTATCAATC
1 TATGAAAAGGGATGA-TGACGA-CCATCAA-C
27786410 TATGAAAAGGGATGATGACGACCATCGAAC
1 TATGAAAAGGGATGATGACGACCATC-AAC
* *
27786440 TATGAAAAGGGATGATGACGACAATCAAAT
1 TATGAAAAGGGATGATGACGACCATC-AAC
27786470 TATGAAAAGGGAT
1 TATGAAAAGGGAT
27786483 AGCTTCAGTT
Statistics
Matches: 112, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.04
30 103 0.92
31 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (29 bp):
TATGAAAAGGGATGATGACGACCATCAAC
Found at i:27786467 original size:90 final size:90
Alignment explanation
Indices: 27786292--27786511 Score: 261
Period size: 90 Copynumber: 2.5 Consensus size: 90
27786282 TTATCAACGA
* * * * *
27786292 ATGAAAAGGAATAGCTTTAGCTATCGAT-TATGAAAAGGGATGGTGACGACCATGGAACTATGAA
1 ATGAAAAGGGATAGCTTCAGCTATCAATCTATGAAAAGGGATGATGACGACCATCGAACTATGAA
* ** * *
27786356 AAGGGATGGCTTTGGCTATC-AATCT
66 AAGGGATGGATACGACAATCAAAT-T
27786381 ATGAAAAGGGAT-GACTTCAGCTATCAATCTATGAAAAGGGATGATGACGACCATCGAACTATGA
1 ATGAAAAGGGATAG-CTTCAGCTATCAATCTATGAAAAGGGATGATGACGACCATCGAACTATGA
27786445 AAAGGGAT-GATGACGACAATCAAATT
65 AAAGGGATGGAT-ACGACAATCAAATT
* *
27786471 ATGAAAAGGGATAGCTTCAGTTGTCTAA-CTATGAAAAGGGA
1 ATGAAAAGGGATAGCTTCAGCTATC-AATCTATGAAAAGGGA
27786512 AAACTTCGGT
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
88 1 0.01
89 25 0.22
90 81 0.72
91 6 0.05
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (90 bp):
ATGAAAAGGGATAGCTTCAGCTATCAATCTATGAAAAGGGATGATGACGACCATCGAACTATGAA
AAGGGATGGATACGACAATCAAATT
Found at i:27793408 original size:29 final size:30
Alignment explanation
Indices: 27793314--27793531 Score: 180
Period size: 29 Copynumber: 7.4 Consensus size: 30
27793304 TCATTGACGA
*
27793314 ATGAAAAGGAATAGCTTCGGCTATCGAA-T
1 ATGAAAAGGGATAGCTTCGGCTATCGAATT
* *
27793343 ACGGAAAGGGATAGCTTCGGCTATCGAA-T
1 ATGAAAAGGGATAGCTTCGGCTATCGAATT
* * *
27793372 ACGGAAAGGGATAGCTTCAGCTATC-AATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATT
* * * * *
27793401 ATGAAAAGGGAT-GGTGACGACCATCGAACT
1 ATGAAAAGGGATAGCT-TCGGCTATCGAATT
* * ** * * *
27793431 ATGAAAAGGGAT-GGTGACAACCATCAAACT
1 ATGAAAAGGGATAGCT-TCGGCTATCGAATT
*
27793461 ATGAAAAGGGATGGCTTCGGCTATC-AATCT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT-T
*
27793491 ATGAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATT
27793521 AT-AAAAGGGAT
1 ATGAAAAGGGAT
27793532 GGTGACAACC
Statistics
Matches: 162, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.02
29 77 0.48
30 76 0.47
31 5 0.03
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAATT
Found at i:27793436 original size:30 final size:30
Alignment explanation
Indices: 27793400--27793591 Score: 183
Period size: 30 Copynumber: 6.4 Consensus size: 30
27793390 AGCTATCAAT
*
27793400 TATGAAAAGGGATGGTGACGACCATCGAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
*
27793430 TATGAAAAGGGATGGTGACAACCATCAAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
* * * *
27793460 TATGAAAAGGGATGGCT-TCGGCTATCAATC
1 TATGAAAAGGGATGG-TGACGACCATCAAAC
* * * * *
27793490 TATGAAAAGGGATAGCT-TCGGCTATCAAAT
1 TATGAAAAGGGAT-GGTGACGACCATCAAAC
* *
27793520 TAT-AAAAGGGATGGTGACAACCATCGAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
* * * *
27793549 TATGAAAAAGGATGGTAATGACCATCAAAT
1 TATGAAAAGGGATGGTGACGACCATCAAAC
*
27793579 TATAAAAAGGGAT
1 TATGAAAAGGGAT
27793592 AGCTTTGGCA
Statistics
Matches: 133, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
28 2 0.02
29 19 0.14
30 110 0.83
31 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (30 bp):
TATGAAAAGGGATGGTGACGACCATCAAAC
Found at i:27793484 original size:89 final size:89
Alignment explanation
Indices: 27793376--27793563 Score: 254
Period size: 89 Copynumber: 2.1 Consensus size: 89
27793366 TCGAATACGG
* * *
27793376 AAAGGGATAGCTTCAGCTATCAAT-TATGAAAAGGGAT-GGTGACGACCATCGAACTATGAAAAG
1 AAAGGGATGGCTTCAGCTATCAATCTATGAAAAGGGATAGCT-ACGACCATCAAACTAT-AAAAG
27793439 GGATGGTGACAACCATCAAACTATGA
64 GGATGGTGACAACCATCAAACTATGA
* * * * *
27793465 AAAGGGATGGCTTCGGCTATCAATCTATGAAAAGGGATAGCTTCGGCTATCAAATTATAAAAGGG
1 AAAGGGATGGCTTCAGCTATCAATCTATGAAAAGGGATAGCTACGACCATCAAACTATAAAAGGG
*
27793530 ATGGTGACAACCATCGAACTATGA
66 ATGGTGACAACCATCAAACTATGA
*
27793554 AAAAGGATGG
1 AAAGGGATGG
27793564 TAATGACCAT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
89 61 0.70
90 24 0.28
91 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (89 bp):
AAAGGGATGGCTTCAGCTATCAATCTATGAAAAGGGATAGCTACGACCATCAAACTATAAAAGGG
ATGGTGACAACCATCAAACTATGA
Found at i:27793515 original size:119 final size:119
Alignment explanation
Indices: 27793347--27793652 Score: 404
Period size: 119 Copynumber: 2.6 Consensus size: 119
27793337 TCGAATACGG
* * *
27793347 AAAGGGATAGCTTCGGCTATCGAA-TACGGAAAGGGATAGCTTCAGCTATC-AATTATGAAAAGG
1 AAAGGGATAGCTTCGGCTATC-AACTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGG
* * * *
27793410 GATGGTGACGACCATCGAACTATGAAAAGGGATGGTGACAACCATCAAACTATGA
65 GATGGTGACAACCATCGAACTATGAAAAAGGATGGTAACAACCATCAAACTATAA
*
27793465 AAAGGGATGGCTTCGGCTATCAATCTATGAAAAGGGATAGCTTCGGCTATCAAATTAT-AAAAGG
1 AAAGGGATAGCTTCGGCTATCAA-CTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGG
** *
27793529 GATGGTGACAACCATCGAACTATGAAAAAGGATGGTAATGACCATCAAATTATAA
65 GATGGTGACAACCATCGAACTATGAAAAAGGATGGTAACAACCATCAAACTATAA
* * ** *
27793584 AAAGGGATAGCTTTGGC-AGTCAAACTATGAAAAGGGATAACTTCGATTATCAAATTATGAAAAT
1 AAAGGGATAGCTTCGGCTA-TC-AACTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAG
27793648 GGATG
64 GGATG
27793653 TGTCAATCAT
Statistics
Matches: 165, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
117 2 0.01
118 21 0.13
119 125 0.76
120 17 0.10
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (119 bp):
AAAGGGATAGCTTCGGCTATCAACTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGG
ATGGTGACAACCATCGAACTATGAAAAAGGATGGTAACAACCATCAAACTATAA
Found at i:27793576 original size:89 final size:90
Alignment explanation
Indices: 27793427--27793621 Score: 256
Period size: 89 Copynumber: 2.2 Consensus size: 90
27793417 ACGACCATCG
* * *
27793427 AACTATGAAAAGGGATGGTGACAACCATCAAACTATGAAAAGGGATGGCTTCGGCTATC-AATCT
1 AACTATGAAAAGGGATGGTGACAACCATCAAACTATGAAAAAGGATGGCTTCGACCATCAAAT-T
*
27793491 ATGAAAAGGGATAGCTTCGGCTA-TCA
65 ATAAAAAGGGATAGCTTCGGC-AGTCA
* *
27793517 AATTAT-AAAAGGGATGGTGACAACCATCGAACTATGAAAAAGGATGG-TAAT-GACCATCAAAT
1 AACTATGAAAAGGGATGGTGACAACCATCAAACTATGAAAAAGGATGGCT--TCGACCATCAAAT
*
27793579 TATAAAAAGGGATAGCTTTGGCAGTCA
64 TATAAAAAGGGATAGCTTCGGCAGTCA
27793606 AACTATGAAAAGGGAT
1 AACTATGAAAAGGGAT
27793622 AACTTCGATT
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
88 2 0.02
89 72 0.78
90 18 0.20
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (90 bp):
AACTATGAAAAGGGATGGTGACAACCATCAAACTATGAAAAAGGATGGCTTCGACCATCAAATTA
TAAAAAGGGATAGCTTCGGCAGTCA
Found at i:27793617 original size:30 final size:30
Alignment explanation
Indices: 27793572--27793651 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 30
27793562 GGTAATGACC
* *
27793572 ATCAAATTATAAAAAGGGATAGCTTTGGC-
1 ATCAAACTATGAAAAGGGATAGCTTTGGCT
* * **
27793601 AGTCAAACTATGAAAAGGGATAACTTCGATT
1 A-TCAAACTATGAAAAGGGATAGCTTTGGCT
* *
27793632 ATCAAATTATGAAAATGGAT
1 ATCAAACTATGAAAAGGGAT
27793652 GTGTCAATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.28
Consensus pattern (30 bp):
ATCAAACTATGAAAAGGGATAGCTTTGGCT
Found at i:27805849 original size:27 final size:27
Alignment explanation
Indices: 27805807--27805859 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
27805797 AGTATGATCC
27805807 TAGTCTCAATGATAATCCAAATGGTTT
1 TAGTCTCAATGATAATCCAAATGGTTT
* *
27805834 TAGTCTTAATGTTAATCCAAATGGTT
1 TAGTCTCAATGATAATCCAAATGGTT
27805860 AAGATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (27 bp):
TAGTCTCAATGATAATCCAAATGGTTT
Found at i:27816528 original size:19 final size:19
Alignment explanation
Indices: 27816504--27816552 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
27816494 AGTCGTGTGG
27816504 CCAGGCTATGTGAGAAAGC
1 CCAGGCTATGTGAGAAAGC
*
27816523 CCAGGCTATGTGATAAAGC
1 CCAGGCTATGTGAGAAAGC
27816542 CCAGGCTATGT
1 CCAGGCTATGT
27816553 AACATTCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (19 bp):
CCAGGCTATGTGAGAAAGC
Found at i:27817404 original size:38 final size:38
Alignment explanation
Indices: 27817351--27817470 Score: 188
Period size: 38 Copynumber: 3.2 Consensus size: 38
27817341 AACATTTATT
* *
27817351 ACACCGGCA-TCAAGCCTGCTAGGCATTAAGCCTAAATA
1 ACACCGGCACT-AAGCCTGCTAGGCATTAAGCATGAATA
27817389 ACACCGGCACTAAGCCTGCTAGGCATTAAGCATGAATA
1 ACACCGGCACTAAGCCTGCTAGGCATTAAGCATGAATA
* *
27817427 ACACCGACACTAAGCCTGCTAGGCACTAAGCATGAATA
1 ACACCGGCACTAAGCCTGCTAGGCATTAAGCATGAATA
27817465 ACACCG
1 ACACCG
27817471 CATTTGACTA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 76 0.99
39 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (38 bp):
ACACCGGCACTAAGCCTGCTAGGCATTAAGCATGAATA
Found at i:27821930 original size:381 final size:381
Alignment explanation
Indices: 27821228--27822374 Score: 1861
Period size: 381 Copynumber: 3.0 Consensus size: 381
27821218 CTGGAGCTCC
* * *
27821228 CCAAGAAGATATACTCGGTCGAATGAAACCTCTATCTAGTAATTCTTGCAATTGTGCTTTAAGTT
1 CCAAGAAGATATACTCGGTCAAAAGAAACCTCTATCTAGTAATTCTTGCAACTGTGCTTTAAGTT
* ** * * * * *
27821293 CTTTTAACTCAGTTGGTGCCCTTTTATA-CAGCAGAATCGATATCGATGT-GT-CTCGGTTATTA
66 CTTTTAACTAAGTCAGTGCCATTCTATATGA-CAGAATCGATATAGGTGTAGTCCT-GGTTATTA
* * * * * * * * *
27821355 AATCAATAGAAAATTCAACTTTCTGCTCTGCCGGTAATC-CAGATAGCTCTTCAAGAAATACGTA
129 AATCAATAGCAAATTCAAATTCCTGCTTTGGCGGCAATCTC-GGTAGCTCTTCAGGAAATACGTT
* * * * * * *
27821419 TAAGAATTCACTTACTGTTGGTACGTGATCCACTTTCTTCTCTGGCACTCTGGAGTCCAGAATGT
193 TGAGAATTCACATACTGTTGGTACTTGGTCCACCTTCTTCGCTGGCACTTTGGAGTCCAGAATGT
27821484 AAGCTAAAAATGCATCACAACCTTTTCGTACTAGTTTTGCGCTTTTATTACCGAGATGAAACTCG
258 AAGCTAAAAATGCATCACAACCTTTTCGTACTAGTTTTGCGCTTTTATTACCGAGATGAAACTCG
27821549 AAATACTATCGGTTTTATCAAATCTAAAAGAAACTATCCTACCATCGAGACATCTCAAA
323 AAATACTATCGGTTTTATCAAATCTAAAAGAAACTATCCTACCATCGAGACATCTCAAA
27821608 CCAAGAAGATATACTCGGTCAAAAGAAACCTCTATCTAGTAATTCTTGCAACTGTGCTTTAAGTT
1 CCAAGAAGATATACTCGGTCAAAAGAAACCTCTATCTAGTAATTCTTGCAACTGTGCTTTAAGTT
27821673 CTTTTAACTAAGTCAGTGCCATTCTATATGACAGAATCGATATAGGTGTAGTCCTGGTTATTAAA
66 CTTTTAACTAAGTCAGTGCCATTCTATATGACAGAATCGATATAGGTGTAGTCCTGGTTATTAAA
*
27821738 TCAATAGCAAATTCAAATTCCTACTTTGGCGGCAATCTCGGTAGCTCTTCAGGAAATACGTTTGA
131 TCAATAGCAAATTCAAATTCCTGCTTTGGCGGCAATCTCGGTAGCTCTTCAGGAAATACGTTTGA
27821803 GAATTCACATACTGTTGGTACTTGGTCCACCTTCTTCGCTGGCACTTTGGAGTCCAGAATGTAAG
196 GAATTCACATACTGTTGGTACTTGGTCCACCTTCTTCGCTGGCACTTTGGAGTCCAGAATGTAAG
27821868 CTAAAAATGCATCACAACCTTTTCGTACTAGTTTTGCGCTTTTATTACCGAGATGAAACTCGAAA
261 CTAAAAATGCATCACAACCTTTTCGTACTAGTTTTGCGCTTTTATTACCGAGATGAAACTCGAAA
27821933 TACTATCGGTTTTATCAAATCTAAAAGAAACTATCCTACCATCGAGACATCTCAAA
326 TACTATCGGTTTTATCAAATCTAAAAGAAACTATCCTACCATCGAGACATCTCAAA
27821989 CCAAGAAGATATACTCGGTCAAAAGAAACCTCTATCTAGTAATTCTTGCAACTGTGCTTTAAGTT
1 CCAAGAAGATATACTCGGTCAAAAGAAACCTCTATCTAGTAATTCTTGCAACTGTGCTTTAAGTT
27822054 CTTTTAACTAAGTCAGTGCCATTCTATATGACAGAATCGATATAGGTGTAGTCCTGGTTATTAAA
66 CTTTTAACTAAGTCAGTGCCATTCTATATGACAGAATCGATATAGGTGTAGTCCTGGTTATTAAA
27822119 TCAATAGCAAATTCAAATTCCTGCTTTGGCGGCAATCTCGGTAGCTCTTCAGGAAATACGTTTGA
131 TCAATAGCAAATTCAAATTCCTGCTTTGGCGGCAATCTCGGTAGCTCTTCAGGAAATACGTTTGA
*
27822184 GAATTCACATACTGTTGGTACTTGGTCCACCTTCTTCGCTGGCACTTTGGAGTCCAAAATGTAAG
196 GAATTCACATACTGTTGGTACTTGGTCCACCTTCTTCGCTGGCACTTTGGAGTCCAGAATGTAAG
** * * *
27822249 CTAAAAATGCATCACAACCTTTTCGTACTAGTTTCTGCGCTTTTATTGTCGAGTTAAAACTTGAA
261 CTAAAAATGCATCACAACCTTTTCGTACTAGTTT-TGCGCTTTTATTACCGAGATGAAACTCGAA
* ** * * * *
27822314 ATACCATAAGTTCTATCAAATCTAAAAGAAATTATCCTACCATCGGGATATCTCAAA
325 ATACTATCGGTTTTATCAAATCTAAAAGAAACTATCCTACCATCGAGACATCTCAAA
27822371 CCAA
1 CCAA
27822375 CTCTTTTTCA
Statistics
Matches: 720, Mismatches: 42, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
380 101 0.14
381 537 0.75
382 82 0.11
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (381 bp):
CCAAGAAGATATACTCGGTCAAAAGAAACCTCTATCTAGTAATTCTTGCAACTGTGCTTTAAGTT
CTTTTAACTAAGTCAGTGCCATTCTATATGACAGAATCGATATAGGTGTAGTCCTGGTTATTAAA
TCAATAGCAAATTCAAATTCCTGCTTTGGCGGCAATCTCGGTAGCTCTTCAGGAAATACGTTTGA
GAATTCACATACTGTTGGTACTTGGTCCACCTTCTTCGCTGGCACTTTGGAGTCCAGAATGTAAG
CTAAAAATGCATCACAACCTTTTCGTACTAGTTTTGCGCTTTTATTACCGAGATGAAACTCGAAA
TACTATCGGTTTTATCAAATCTAAAAGAAACTATCCTACCATCGAGACATCTCAAA
Found at i:27830408 original size:130 final size:130
Alignment explanation
Indices: 27830252--27830507 Score: 503
Period size: 130 Copynumber: 2.0 Consensus size: 130
27830242 TGTTACATGG
27830252 ACAAAAATAGTCTACACAGCCGTGTAACATGACCGTGTGACACACACAGCCTGGACACACGGGCG
1 ACAAAAATAGTCTACACAGCCGTGTAACATGACCGTGTGACACACACAGCCTGGACACACGGGCG
27830317 TGTCCTAGGCCATGTGAAACCTGTAGCTATTTTTTTCAACTTTAAAACAAGTCAGAGAGTTGTCT
66 TGTCCTAGGCCATGTGAAACCTGTAGCTATTTTTTTCAACTTTAAAACAAGTCAGAGAGTTGTCT
*
27830382 ACAAAAATAGTCTACACAGCCGTGTAACATGACCGTGTGACACACACGGCCTGGACACACGGGCG
1 ACAAAAATAGTCTACACAGCCGTGTAACATGACCGTGTGACACACACAGCCTGGACACACGGGCG
27830447 TGTCCTAGGCCATGTGAAACCTGTAGCTATTTTTTTCAACTTTAAAACAAGTCAGAGAGTT
66 TGTCCTAGGCCATGTGAAACCTGTAGCTATTTTTTTCAACTTTAAAACAAGTCAGAGAGTT
27830508 ACACAGGCAA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 125 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (130 bp):
ACAAAAATAGTCTACACAGCCGTGTAACATGACCGTGTGACACACACAGCCTGGACACACGGGCG
TGTCCTAGGCCATGTGAAACCTGTAGCTATTTTTTTCAACTTTAAAACAAGTCAGAGAGTTGTCT
Found at i:27831027 original size:17 final size:18
Alignment explanation
Indices: 27830994--27831027 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27830984 CTTTGGTCAA
27830994 CATCACACCTGCTCACCT
1 CATCACACCTGCTCACCT
*
27831012 CATCACCCCT-CTCACC
1 CATCACACCTGCTCACC
27831028 AAGTGAGCCA
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:0.21, C:0.56, G:0.03, T:0.21
Consensus pattern (18 bp):
CATCACACCTGCTCACCT
Found at i:27831286 original size:18 final size:19
Alignment explanation
Indices: 27831260--27831328 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 19
27831250 AATTATTTAA
27831260 TTTATTTTTTATTCTATTT
1 TTTATTTTTTATTCTATTT
*
27831279 TTTATTTTTT-TTCTCTTTT
1 TTTATTTTTTATTCT-ATTT
27831298 CTTTAATGTTATTTATT-TA-TT
1 -TTT-AT-TT-TTTATTCTATTT
27831319 TTTATTTTTT
1 TTTATTTTTT
27831329 TCCTGCTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
17 3 0.07
18 6 0.14
19 15 0.36
20 6 0.14
21 4 0.10
22 2 0.05
23 4 0.10
24 2 0.05
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (19 bp):
TTTATTTTTTATTCTATTT
Found at i:27831353 original size:40 final size:39
Alignment explanation
Indices: 27831265--27831358 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 39
27831255 TTTAATTTAT
* *
27831265 TTTTTATTCTATTTTTTATTTTTTTTCTCTTTTCTTTAATG
1 TTTTTATT-TA-TTTTTATTTTTTTCCTCTTTTCTTTAATA
*
27831306 TTATTTATTTATTTTTATTTTTTTCCTGCTTATT-TTTATTA
1 TT-TTTATTTATTTTTATTTTTTTCCT-CTT-TTCTTTAATA
27831347 TTTTTATTTATT
1 TTTTTATTTATT
27831359 CTCTTTAGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
40 25 0.53
41 14 0.30
42 8 0.17
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (39 bp):
TTTTTATTTATTTTTATTTTTTTCCTCTTTTCTTTAATA
Found at i:27853131 original size:35 final size:35
Alignment explanation
Indices: 27853092--27853161 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
27853082 AATGAAACAA
27853092 GAATGTCATGACAAAGCCACTACAGAAAAGAAGAT
1 GAATGTCATGACAAAGCCACTACAGAAAAGAAGAT
27853127 GAATGTCATGACAAAGCCACTACAGAAAAGAAGAT
1 GAATGTCATGACAAAGCCACTACAGAAAAGAAGAT
27853162 TAAGGAACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.14
Consensus pattern (35 bp):
GAATGTCATGACAAAGCCACTACAGAAAAGAAGAT
Found at i:27854869 original size:18 final size:19
Alignment explanation
Indices: 27854841--27854877 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
27854831 GCATTCACAT
27854841 CTTTCCTCTCTTCTCTCCA
1 CTTTCCTCTCTTCTCTCCA
*
27854860 CTTT-CTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTCTCCA
27854878 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTCTCCA
Found at i:27856711 original size:38 final size:38
Alignment explanation
Indices: 27856640--27856712 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
27856630 TGAATCGTAT
*
27856640 TGTTATTCAGGCTTAGTGCCTAACATGCCTAGTGCTGG
1 TGTTATTCAGGCTTAGTGCCTAACAGGCCTAGTGCTGG
* *
27856678 TGTTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGC
1 TGTTATTCAGGCTTAGTGCCTAACAGGCCTAGTGC
27856713 CAATGCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (38 bp):
TGTTATTCAGGCTTAGTGCCTAACAGGCCTAGTGCTGG
Found at i:27856723 original size:38 final size:38
Alignment explanation
Indices: 27856643--27856729 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 38
27856633 ATCGTATTGT
* *** *
27856643 TATTCAGGCTTAGTGCCTAACATGCCTAGTGCTGGTGT
1 TATTCAGGCTTAGTGCCTAACAGGCCTAGTGCCAATGC
* *
27856681 TATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCAATGC
1 TATTCAGGCTTAGTGCCTAACAGGCCTAGTGCCAATGC
*
27856719 TATTCATGCTT
1 TATTCAGGCTT
27856730 GGTGTTGGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (38 bp):
TATTCAGGCTTAGTGCCTAACAGGCCTAGTGCCAATGC
Found at i:27856787 original size:38 final size:38
Alignment explanation
Indices: 27856736--27856831 Score: 131
Period size: 38 Copynumber: 2.5 Consensus size: 38
27856726 GCTTGGTGTT
*
27856736 GGTGTTTTTCAGGCTTATTGCCTAGC-AGGCTTAGTGCC
1 GGTGTTATTCAGGCTTATTGCCTAGCGA-GCTTAGTGCC
* *
27856774 GGTGTTATTCAGGCATAGTGCCTAGCGAGCTTAGTGCC
1 GGTGTTATTCAGGCTTATTGCCTAGCGAGCTTAGTGCC
**
27856812 AATGTTATTCAGGCTTATTG
1 GGTGTTATTCAGGCTTATTG
27856832 TCGGTGTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 49 0.98
39 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (38 bp):
GGTGTTATTCAGGCTTATTGCCTAGCGAGCTTAGTGCC
Found at i:27856814 original size:98 final size:98
Alignment explanation
Indices: 27856640--27856827 Score: 279
Period size: 98 Copynumber: 1.9 Consensus size: 98
27856630 TGAATCGTAT
* * *
27856640 TGTTATTCAGGCTTAGTGCCTAACATGCCTAGTGCTGGTGTTATTCAGGCTTAGTGCCTAGCAGG
1 TGTTATTCAGGCTTAGTGCCTAACAGGCCTAGTGCCGGTGTTATTCAGGCATAGTGCCTAGCAGG
*
27856705 CTTAGTGCCAATGCTATTCATGCTTGGTGTTGG
66 CTTAGTGCCAATGCTATTCAGGCTTGGTGTTGG
* * * *
27856738 TGTTTTTCAGGCTTATTGCCTAGCAGGCTTAGTGCCGGTGTTATTCAGGCATAGTGCCTAGC-GA
1 TGTTATTCAGGCTTAGTGCCTAACAGGCCTAGTGCCGGTGTTATTCAGGCATAGTGCCTAGCAG-
*
27856802 GCTTAGTGCCAATGTTATTCAGGCTT
65 GCTTAGTGCCAATGCTATTCAGGCTT
27856828 ATTGTCGGTG
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
97 1 0.01
98 79 0.99
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (98 bp):
TGTTATTCAGGCTTAGTGCCTAACAGGCCTAGTGCCGGTGTTATTCAGGCATAGTGCCTAGCAGG
CTTAGTGCCAATGCTATTCAGGCTTGGTGTTGG
Found at i:27865159 original size:335 final size:335
Alignment explanation
Indices: 27864549--27865218 Score: 1115
Period size: 335 Copynumber: 2.0 Consensus size: 335
27864539 AGTATTTGAT
* * * *
27864549 GACATAGAGGGAACTGAATCTGAGACAGTAACGGTGGTTAGAGCTATTGAAAGATTATGACCTTG
1 GACATAGAAGGAACTGAATCTGAGACAGCAACAGTGGTTAGAGCTATTGAAAGATTATGACCTCG
* *
27864614 TGATTGATTACCATCCTGGGAAGGTAAATGTTGTTGCAAATGATTTAAGCCACAAATCATTGTTT
66 TGATTAATTACCATCCTAGGAAGGTAAATGTTGTTGCAAATGATTTAAGCCACAAATCATTGTTT
27864679 ACTTTAAAAACAATGAACGCACATTTATCCCTAGAGAGTGATGGTTCTGTTATAGCTAAGCTTAG
131 ACTTTAAAAACAATGAACGCACATTTATCCCTAGAGAGTGATGGTTCTGTTATAGCTAAGCTTAG
***
27864744 GGCTAGGCCGTTATTTCTTCAGCGAATTTGGGAATTACAAAGTGATGACCTGAAGTTAGTAGCCA
196 GGCTAGGCCGTTATTTCTTCAGCGAATTCAAGAATTACAAAGTGATGACCTGAAGTTAGTAGCCA
*
27864809 AACGAGAGCTGATCCAGAGTGATTCGACTATGGGATTCATTATGAGTGACAATGGTATGATGTAT
261 AACGAGAGCTGATCCAGAGTGATTCGACTAAGGGATTCATTATGAGTGACAATGGTATGATGTAT
27864874 TTTCATAATC
326 TTTCATAATC
* * *
27864884 GACATAGAAGGAACTGAATCTGAGACAGCGATAGTGGTTAGAGCTATTGAAAGATTATGGCCTCG
1 GACATAGAAGGAACTGAATCTGAGACAGCAACAGTGGTTAGAGCTATTGAAAGATTATGACCTCG
* * ** *
27864949 TGATTAATTACCATCCTAGGAAGGTAAATGTTGTTGCAGATGCTTTAAGCTGCAAATGATTGTTT
66 TGATTAATTACCATCCTAGGAAGGTAAATGTTGTTGCAAATGATTTAAGCCACAAATCATTGTTT
* * * *
27865014 GCTTTAAGAACAATGAACGCACATTTATCCTTGGAGAGTGATGGTTCTGTTATAGCTAAGCTTAG
131 ACTTTAAAAACAATGAACGCACATTTATCCCTAGAGAGTGATGGTTCTGTTATAGCTAAGCTTAG
*
27865079 GGCTAGGTCGTTATTTCTTCAGCGAATTCAAGAATTACAAAGTGATGACCTGAAGTTAGTAGCCA
196 GGCTAGGCCGTTATTTCTTCAGCGAATTCAAGAATTACAAAGTGATGACCTGAAGTTAGTAGCCA
*
27865144 AACGAGAGCTGATCCAGAGTGATTCGACTAAGGGATTCATTATTAGTGACAATGGTATGATGTAT
261 AACGAGAGCTGATCCAGAGTGATTCGACTAAGGGATTCATTATGAGTGACAATGGTATGATGTAT
*
27865209 TTTGATAATC
326 TTTCATAATC
27865219 AACTGTGTAT
Statistics
Matches: 310, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
335 310 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (335 bp):
GACATAGAAGGAACTGAATCTGAGACAGCAACAGTGGTTAGAGCTATTGAAAGATTATGACCTCG
TGATTAATTACCATCCTAGGAAGGTAAATGTTGTTGCAAATGATTTAAGCCACAAATCATTGTTT
ACTTTAAAAACAATGAACGCACATTTATCCCTAGAGAGTGATGGTTCTGTTATAGCTAAGCTTAG
GGCTAGGCCGTTATTTCTTCAGCGAATTCAAGAATTACAAAGTGATGACCTGAAGTTAGTAGCCA
AACGAGAGCTGATCCAGAGTGATTCGACTAAGGGATTCATTATGAGTGACAATGGTATGATGTAT
TTTCATAATC
Found at i:27867750 original size:22 final size:21
Alignment explanation
Indices: 27867677--27867751 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 21
27867667 TGAATCGTAT
27867677 TGTTATTCAGGCTTAGTGCCA
1 TGTTATTCAGGCTTAGTGCCA
27867698 GTGTTATTCAGGCTTAGTGCC-
1 -TGTTATTCAGGCTTAGTGCCA
*
27867719 ---TA-GCAGGCTTAGTGCCGA
1 TGTTATTCAGGCTTAGTGCC-A
27867737 TGTTATTCAGGCTTA
1 TGTTATTCAGGCTTA
27867752 TTGTCGGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
16 13 0.29
17 2 0.04
21 2 0.04
22 28 0.62
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (21 bp):
TGTTATTCAGGCTTAGTGCCA
Found at i:27869271 original size:21 final size:20
Alignment explanation
Indices: 27869247--27869292 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
27869237 TGAAATACAA
27869247 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
27869268 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
27869288 T-AACC
1 TCAACC
27869293 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:27873521 original size:22 final size:22
Alignment explanation
Indices: 27873493--27873623 Score: 190
Period size: 22 Copynumber: 6.0 Consensus size: 22
27873483 TTTATTGTTC
*
27873493 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
27873515 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
27873537 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
27873559 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
27873581 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
27873603 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
27873624 GAAATATTAT
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 98 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:27873784 original size:31 final size:30
Alignment explanation
Indices: 27873726--27873788 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
27873716 GCTTTTTGAA
* *
27873726 AATATTTAAAAAAAGAGGCATCTAATTTTT
1 AATATTTAAAAAAAGAGGCACCAAATTTTT
27873756 AATATTTACAAAAAAGA-GCAACCAAATTTTT
1 AATATTTA-AAAAAAGAGGC-ACCAAATTTTT
27873787 AA
1 AA
27873789 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTAAAAAAAGAGGCACCAAATTTTT
Found at i:27878035 original size:50 final size:50
Alignment explanation
Indices: 27877955--27878195 Score: 272
Period size: 50 Copynumber: 4.8 Consensus size: 50
27877945 ATTTGGGTAA
* * *
27877955 AGAAATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCTCCGAGACG
1 AGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
27878005 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
27878055 AGAAGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * *
27878105 AGAACTCCCATATAAGTCCATATCTGGGATATGGCATTGGCA--GTACATG
1 AGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
27878154 A-AACATCCCATGTAAAACCATGTCTGGGACATGGCTTTGGCA
1 AGAA-GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
27878196 TGTTATTATC
Statistics
Matches: 160, Mismatches: 29, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
48 3 0.02
49 36 0.22
50 121 0.76
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
AGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:27881381 original size:13 final size:13
Alignment explanation
Indices: 27881363--27881389 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27881353 GCGAGTGAAG
27881363 TAAAAGCGTCTAC
1 TAAAAGCGTCTAC
27881376 TAAAAGCGTCTAC
1 TAAAAGCGTCTAC
27881389 T
1 T
27881390 TCATGTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (13 bp):
TAAAAGCGTCTAC
Found at i:27883252 original size:21 final size:20
Alignment explanation
Indices: 27883223--27883268 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
27883213 CGAAATAGAA
27883223 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
27883244 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
27883264 T-AACC
1 TCAACC
27883269 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:27889859 original size:12 final size:12
Alignment explanation
Indices: 27889842--27889867 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27889832 TTGAAGGTGA
27889842 TCTACTGATCAT
1 TCTACTGATCAT
27889854 TCTACTGATCAT
1 TCTACTGATCAT
27889866 TC
1 TC
27889868 ATCCTCATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.08, T:0.42
Consensus pattern (12 bp):
TCTACTGATCAT
Found at i:27897165 original size:30 final size:29
Alignment explanation
Indices: 27897123--27897179 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
27897113 CCAAACTTTG
27897123 GGGAAAAATGTAAATATG-CAAAAGTTTA
1 GGGAAAAATGTAAATATGTCAAAAGTTTA
* *
27897151 GGGACAAAATTGTAATTTTGTCAAAAGTT
1 GGGA-AAAA-TGTAAATATGTCAAAAGTT
27897180 GAGTCGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 8 0.33
31 8 0.33
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (29 bp):
GGGAAAAATGTAAATATGTCAAAAGTTTA
Found at i:27908821 original size:25 final size:25
Alignment explanation
Indices: 27908793--27908875 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
27908783 TGATGATAAG
27908793 ATGTTGTCCATTTTTTAGTATATTA
1 ATGTTGTCCATTTTTTAGTATATTA
** *
27908818 ATGTTGTCCA--CATT-G-ATGCTTA
1 ATGTTGTCCATTTTTTAGTAT-ATTA
* *
27908840 ATTGCTGTCCATTTTTGAGTATATTA
1 A-TGTTGTCCATTTTTTAGTATATTA
27908866 ATGTTGTCCA
1 ATGTTGTCCA
27908876 AATTGATGCT
Statistics
Matches: 43, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
21 2 0.05
22 5 0.12
23 10 0.23
25 19 0.44
26 5 0.12
27 2 0.05
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (25 bp):
ATGTTGTCCATTTTTTAGTATATTA
Found at i:27908854 original size:48 final size:48
Alignment explanation
Indices: 27908797--27908951 Score: 238
Period size: 48 Copynumber: 3.2 Consensus size: 48
27908787 GATAAGATGT
*
27908797 TGTCCATTTTTTAGTATATTAATGTTGTCCACATTGATGCTTAATTGC
1 TGTCCATTTTTTAGTATATTAATGTTGTCCAAATTGATGCTTAATTGC
*
27908845 TGTCCATTTTTGAGTATATTAATGTTGTCCAAATTGATGCTTAATTGC
1 TGTCCATTTTTTAGTATATTAATGTTGTCCAAATTGATGCTTAATTGC
* * * * * *
27908893 TGCCCATTTTTTAGTTTATTAATGCTGTCCAAATTGGTGCTTAAATGT
1 TGTCCATTTTTTAGTATATTAATGTTGTCCAAATTGATGCTTAATTGC
27908941 TGTCCATTTTT
1 TGTCCATTTTT
27908952 GTACAAATCA
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (48 bp):
TGTCCATTTTTTAGTATATTAATGTTGTCCAAATTGATGCTTAATTGC
Found at i:27908888 original size:22 final size:22
Alignment explanation
Indices: 27908815--27908889 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
27908805 TTTTAGTATA
*
27908815 TTAATGTTGTCCACATTGATGC
1 TTAATGTTGTCCAAATTGATGC
* ** **
27908837 TTAATTGCTGTCCATTTTTGAGTATA
1 TTAA-TGTTGTCCA-AATTGA-T-GC
27908863 TTAATGTTGTCCAAATTGATGC
1 TTAATGTTGTCCAAATTGATGC
27908885 TTAAT
1 TTAAT
27908890 TGCTGCCCAT
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
22 9 0.23
23 9 0.23
24 8 0.21
25 9 0.23
26 4 0.10
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (22 bp):
TTAATGTTGTCCAAATTGATGC
Found at i:27926133 original size:104 final size:104
Alignment explanation
Indices: 27925953--27926155 Score: 379
Period size: 104 Copynumber: 2.0 Consensus size: 104
27925943 AAGCTTTTAC
*
27925953 TTACATCAAAGTATACAAGTCATGCATACATAGCCTGTCATTCAGTTAGGATTTAAGTATGCCAC
1 TTACATCAAAGTATACAAGTCATGCATACATAGCCCGTCATTCAGTTAGGATTTAAGTATGCCAC
27926018 ACTATGAACGTCACAAGTGAATAAATCCATAAACAAATT
66 ACTATGAACGTCACAAGTGAATAAATCCATAAACAAATT
**
27926057 TTACATCAAAGTATATGAGTCATGCATACATAGCCCGTCATTCAGTTAGGATTTAAGTATGCCAC
1 TTACATCAAAGTATACAAGTCATGCATACATAGCCCGTCATTCAGTTAGGATTTAAGTATGCCAC
27926122 ACTATGAACGTCACAAGTGAATAAATCCATAAAC
66 ACTATGAACGTCACAAGTGAATAAATCCATAAAC
27926156 GGATTTAGGA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (104 bp):
TTACATCAAAGTATACAAGTCATGCATACATAGCCCGTCATTCAGTTAGGATTTAAGTATGCCAC
ACTATGAACGTCACAAGTGAATAAATCCATAAACAAATT
Found at i:27928163 original size:53 final size:53
Alignment explanation
Indices: 27928088--27928190 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
27928078 TGCTTATAAA
*
27928088 ATTTTGAGTCTGTTGAATATAGGAATATGTGAAATAGGTTTAGTAATTAATTT
1 ATTTTGAGTCTGTTGAACATAGGAATATGTGAAATAGGTTTAGTAATTAATTT
*
27928141 ATTTTGAGTCTGTTGAACATAGGAATATGTGAAATATGTTTAGTAATTAA
1 ATTTTGAGTCTGTTGAACATAGGAATATGTGAAATAGGTTTAGTAATTAA
27928191 GTAAGTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (53 bp):
ATTTTGAGTCTGTTGAACATAGGAATATGTGAAATAGGTTTAGTAATTAATTT
Found at i:27930179 original size:21 final size:20
Alignment explanation
Indices: 27930158--27930196 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27930148 AAACCTAAGA
27930158 AACCAAAAGAACA-AATCTAG
1 AACCAAAAGAA-AGAATCTAG
*
27930178 AACCTAAAGAAAGAATCTA
1 AACCAAAAGAAAGAATCTA
27930197 AGCCAATGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.13
Consensus pattern (20 bp):
AACCAAAAGAAAGAATCTAG
Found at i:27930790 original size:13 final size:13
Alignment explanation
Indices: 27930772--27930801 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27930762 CTCAAGCAAC
*
27930772 ATAAATAAAGATG
1 ATAAATAAAAATG
27930785 ATAAATAAAAATG
1 ATAAATAAAAATG
27930798 ATAA
1 ATAA
27930802 CCCTTGAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
ATAAATAAAAATG
Found at i:27936126 original size:20 final size:20
Alignment explanation
Indices: 27936103--27936145 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27936093 TACACTTCGA
*
27936103 TGCCCCTGTTCGCACATTGG
1 TGCCCCTATTCGCACATTGG
* *
27936123 TGCCCCTATTTGCACTTTGG
1 TGCCCCTATTCGCACATTGG
27936143 TGC
1 TGC
27936146 TTCTTACTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.09, C:0.33, G:0.23, T:0.35
Consensus pattern (20 bp):
TGCCCCTATTCGCACATTGG
Found at i:27944084 original size:40 final size:40
Alignment explanation
Indices: 27944040--27944117 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
27944030 AAATTGTTGT
27944040 ATGAATGCACATACATGCCCCTATTGGTACTTAAGTACCC
1 ATGAATGCACATACATGCCCCTATTGGTACTTAAGTACCC
* * * *
27944080 ATGAATGCACATACCTGCCCCTGTTTGTACTTCAGTAC
1 ATGAATGCACATACATGCCCCTATTGGTACTTAAGTAC
27944118 TTTGAATGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (40 bp):
ATGAATGCACATACATGCCCCTATTGGTACTTAAGTACCC
Found at i:27949687 original size:45 final size:45
Alignment explanation
Indices: 27949619--27949712 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
27949609 AACAGATACT
* * * *
27949619 CGGTGGATTCAGCACATAACAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAACAACCACCTTACTAATAAATGATGTC
* * *
27949664 CGGTGGAATCAACACATAGCAACCACTTTACTAATAAATGATGTT
1 CGGTGGAATCAACACATAACAACCACCTTACTAATAAATGATGTC
27949709 CGGT
1 CGGT
27949713 TCACATAGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAACACATAACAACCACCTTACTAATAAATGATGTC
Found at i:27949796 original size:51 final size:50
Alignment explanation
Indices: 27949714--27949850 Score: 141
Period size: 50 Copynumber: 2.7 Consensus size: 50
27949704 ATGTTCGGTT
* ** *
27949714 CACATAGTAGCCTGCACATAGTATTGTACATGTGATCAAAAC-TATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CAAAACAT-TCCGATA
* * ** * *
27949765 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACAAAACATTCCGATA
* *
27949815 CACGTAGTAGCCTGCACATAGTACTACACACGTGAC
1 CACATAGTAGCCTGCACATAGTACTACACATGTGAC
27949851 CATCACTTTC
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
50 40 0.56
51 31 0.44
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACAAAACATTCCGATA
Found at i:27957840 original size:30 final size:30
Alignment explanation
Indices: 27957806--27958083 Score: 192
Period size: 30 Copynumber: 9.3 Consensus size: 30
27957796 TCGATAAATA
*
27957806 AAAAGGGATAGCTTCGACTATCGATCAATG
1 AAAAGGGATAGCTTCGACTATCGATCTATG
* * *
27957836 AAAAGGGATAGCTTTGACTATCGACCAATG
1 AAAAGGGATAGCTTCGACTATCGATCTATG
* * *
27957866 AAAAGGGGTAGCTTTGACTATCGAACTATG
1 AAAAGGGATAGCTTCGACTATCGATCTATG
* ** *
27957896 AAAAGAGATAGCTTCGGTTATCAAAT-TATG
1 AAAAGGGATAGCTTCGACTATC-GATCTATG
* * * * * *
27957926 AAAGGGGAT-GGTGACGACCATC-AACAATG
1 AAAAGGGATAGCT-TCGACTATCGATCTATG
* * * * * * *
27957955 AAAAGCGAT-GGTGACAACCATCAAACTATG
1 AAAAGGGATAGCT-TCGACTATCGATCTATG
27957985 AAAAGGGATAGCTTCGACTATCGAAT-TATG
1 AAAAGGGATAGCTTCGACTATCG-ATCTATG
* * *
27958015 AAAAAGGATAGCTTCGGCTATCAAAT-TATG
1 AAAAGGGATAGCTTCGACTATC-GATCTATG
* *
27958045 AAAAGGGATAGCTTCGGCTATCAAAT-TATG
1 AAAAGGGATAGCTTCGACTATC-GATCTATG
27958075 AAAAGGGAT
1 AAAAGGGAT
27958084 GGTGACAACC
Statistics
Matches: 205, Mismatches: 36, Indels: 14
0.80 0.14 0.05
Matches are distributed among these distances:
28 1 0.00
29 24 0.12
30 176 0.86
31 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (30 bp):
AAAAGGGATAGCTTCGACTATCGATCTATG
Found at i:27957927 original size:60 final size:60
Alignment explanation
Indices: 27957806--27958139 Score: 248
Period size: 60 Copynumber: 5.6 Consensus size: 60
27957796 TCGATAAATA
* * * * * * *
27957806 AAAAGGGATAGCTTCGACTATCGATCAATGAAAAGGGATAGCTTTGACTATCGACCAATG
1 AAAAGGGATAGCTTCGACTATCGAACTATGAAAAGAGATAGCTTCGACTATCAAACTATG
* * ** *
27957866 AAAAGGGGTAGCTTTGACTATCGAACTATGAAAAGAGATAGCTTCGGTTATCAAATTATG
1 AAAAGGGATAGCTTCGACTATCGAACTATGAAAAGAGATAGCTTCGACTATCAAACTATG
* * * * * * * * * *
27957926 AAAGGGGAT-GGTGACGACCATC-AACAATGAAAAGCGAT-GGTGACAACCATCAAACTATG
1 AAAAGGGATAGCT-TCGACTATCGAACTATGAAAAGAGATAGCT-TCGACTATCAAACTATG
* * *
27957985 AAAAGGGATAGCTTCGACTATCGAATTATGAAAA-AGGATAGCTTCGGCTATCAAATTATG
1 AAAAGGGATAGCTTCGACTATCGAACTATGAAAAGA-GATAGCTTCGACTATCAAACTATG
* * * * * * * * * *
27958045 AAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGAT-GGTGACAACCATCAAAATAAG
1 AAAAGGGATAGCTTCGACTATCGAACTATGAAAAGAGATAGCT-TCGACTATCAAACTATG
*
27958105 AAAAGGGATAGCTTC-AGCTATCGAACAATGGAAAA
1 AAAAGGGATAGCTTCGA-CTATCGAACTAT-GAAAA
27958140 TGATGGTGAC
Statistics
Matches: 210, Mismatches: 54, Indels: 19
0.74 0.19 0.07
Matches are distributed among these distances:
58 2 0.01
59 44 0.21
60 157 0.75
61 7 0.03
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (60 bp):
AAAAGGGATAGCTTCGACTATCGAACTATGAAAAGAGATAGCTTCGACTATCAAACTATG
Found at i:27957956 original size:29 final size:30
Alignment explanation
Indices: 27957923--27957993 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
27957913 TTATCAAATT
* *
27957923 ATGAAAGGGGATGGTGACGACCATC-AACA
1 ATGAAAAGGGATGGTGACAACCATCAAACA
* *
27957952 ATGAAAAGCGATGGTGACAACCATCAAACT
1 ATGAAAAGGGATGGTGACAACCATCAAACA
27957982 ATGAAAAGGGAT
1 ATGAAAAGGGAT
27957994 AGCTTCGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (30 bp):
ATGAAAAGGGATGGTGACAACCATCAAACA
Found at i:27958098 original size:30 final size:30
Alignment explanation
Indices: 27957863--27958117 Score: 160
Period size: 30 Copynumber: 8.5 Consensus size: 30
27957853 CTATCGACCA
* ** * * *
27957863 ATGAAAAGGGGTAGCTTTGACTATCGAACT
1 ATGAAAAGGGATAGCTACGACCATCAAATT
* * ***
27957893 ATGAAAAGAGATAGCTTCGGTTATCAAATT
1 ATGAAAAGGGATAGCTACGACCATCAAATT
* *
27957923 ATGAAAGGGGAT-GGTGACGACCATCAACA--
1 ATGAAAAGGGATAGCT-ACGACCATCAA-ATT
* * * *
27957952 ATGAAAAGCGAT-GGTGACAACCATCAAACT
1 ATGAAAAGGGATAGCT-ACGACCATCAAATT
* * *
27957982 ATGAAAAGGGATAGCTTCGACTATCGAATT
1 ATGAAAAGGGATAGCTACGACCATCAAATT
* * * *
27958012 ATGAAAAAGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATAGCTACGACCATCAAATT
* * *
27958042 ATGAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATAGCTACGACCATCAAATT
* * *
27958072 ATGAAAAGGGAT-GGTGACAACCATCAAAAT
1 ATGAAAAGGGATAGCT-ACGACCATCAAATT
*
27958102 AAGAAAAGGGATAGCT
1 ATGAAAAGGGATAGCT
27958118 TCAGCTATCG
Statistics
Matches: 182, Mismatches: 36, Indels: 13
0.79 0.16 0.06
Matches are distributed among these distances:
28 1 0.01
29 28 0.15
30 148 0.81
31 5 0.03
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTACGACCATCAAATT
Found at i:27965086 original size:12 final size:12
Alignment explanation
Indices: 27965077--27965101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27965067 TAAGAACAGG
27965077 GGCTAGAACACA
1 GGCTAGAACACA
27965089 GGCTAGAACACA
1 GGCTAGAACACA
27965101 G
1 G
27965102 ATGTGTGTCC
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:0.40, C:0.24, G:0.28, T:0.08
Consensus pattern (12 bp):
GGCTAGAACACA
Found at i:27969661 original size:19 final size:19
Alignment explanation
Indices: 27969633--27969671 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
27969623 TAATATTTAG
*
27969633 TTTAGGTATTAAATGTGTC
1 TTTAGGTATTAAATATGTC
* *
27969652 TTTAGTTATTTAATATGTC
1 TTTAGGTATTAAATATGTC
27969671 T
1 T
27969672 AAGTATCTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTAGGTATTAAATATGTC
Found at i:27971931 original size:17 final size:16
Alignment explanation
Indices: 27971909--27971966 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 16
27971899 AAACGAGTGC
27971909 AAAAGAAAGAGAGCCTG
1 AAAAGAAAGAGAG-CTG
27971926 AAAAGAAA-ACGAG-TG
1 AAAAGAAAGA-GAGCTG
27971941 AAAAAGAAAGAGAGCTTG
1 -AAAAGAAAGAGAGC-TG
27971959 AAAAGAAA
1 AAAAGAAA
27971967 ACAAGTGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.06
16 12 0.33
17 20 0.56
18 2 0.06
ACGTcount: A:0.60, C:0.07, G:0.26, T:0.07
Consensus pattern (16 bp):
AAAAGAAAGAGAGCTG
Found at i:27971936 original size:33 final size:33
Alignment explanation
Indices: 27971899--27972000 Score: 159
Period size: 33 Copynumber: 3.1 Consensus size: 33
27971889 AATATGAATG
* *
27971899 AAACGAGTGCAAAAGAAAGAGAGCCTGAAAAGA
1 AAACGAGTGAAAAAGAAAGAGAGCTTGAAAAGA
27971932 AAACGAGTGAAAAAGAAAGAGAGCTTGAAAAGA
1 AAACGAGTGAAAAAGAAAGAGAGCTTGAAAAGA
* *
27971965 AAACAAGTGAAAAAGAGAGAGAGCTTGAAAATGA
1 AAACGAGTGAAAAAGAAAGAGAGCTTGAAAA-GA
27971999 AA
1 AA
27972001 CGTGCGAAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 60 0.94
34 4 0.06
ACGTcount: A:0.57, C:0.08, G:0.26, T:0.09
Consensus pattern (33 bp):
AAACGAGTGAAAAAGAAAGAGAGCTTGAAAAGA
Found at i:27971947 original size:16 final size:15
Alignment explanation
Indices: 27971899--27971977 Score: 63
Period size: 17 Copynumber: 4.9 Consensus size: 15
27971889 AATATGAATG
27971899 AAACGAGTGCAAAAGA
1 AAACGAGTG-AAAAGA
27971915 AAGA-GAGCCTGAAAAGA
1 AA-ACGAG--TGAAAAGA
27971932 AAACGAGTGAAAAAGA
1 AAACGAGTG-AAAAGA
27971948 AAGA-GAGCTTGAAAAGA
1 AA-ACGAG--TGAAAAGA
*
27971965 AAACAAGTGAAAA
1 AAACGAGTGAAAA
27971978 AGAGAGAGAG
Statistics
Matches: 53, Mismatches: 1, Indels: 19
0.73 0.01 0.26
Matches are distributed among these distances:
15 8 0.15
16 18 0.34
17 23 0.43
18 4 0.08
ACGTcount: A:0.58, C:0.09, G:0.25, T:0.08
Consensus pattern (15 bp):
AAACGAGTGAAAAGA
Found at i:27971980 original size:16 final size:16
Alignment explanation
Indices: 27971899--27971980 Score: 64
Period size: 16 Copynumber: 5.0 Consensus size: 16
27971889 AATATGAATG
*
27971899 AAACGAGTGCAAAAGA
1 AAACGAGTGAAAAAGA
27971915 AAGA-GAGCCTG-AAAAGA
1 AA-ACGAG--TGAAAAAGA
27971932 AAACGAGTGAAAAAGA
1 AAACGAGTGAAAAAGA
27971948 AAGA-GAGCTTG-AAAAGA
1 AA-ACGAG--TGAAAAAGA
*
27971965 AAACAAGTGAAAAAGA
1 AAACGAGTGAAAAAGA
27971981 GAGAGAGCTT
Statistics
Matches: 55, Mismatches: 1, Indels: 20
0.72 0.01 0.26
Matches are distributed among these distances:
15 4 0.07
16 24 0.44
17 23 0.42
18 4 0.07
ACGTcount: A:0.59, C:0.09, G:0.26, T:0.07
Consensus pattern (16 bp):
AAACGAGTGAAAAAGA
Found at i:27973359 original size:27 final size:27
Alignment explanation
Indices: 27973326--27973380 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
27973316 AGATAATATC
*
27973326 ATAAATTAGGTGTAGCTTTGGAGGCTA
1 ATAAATTAAGTGTAGCTTTGGAGGCTA
27973353 ATAAATTAAGTGTAGCTTTGGAGGCTA
1 ATAAATTAAGTGTAGCTTTGGAGGCTA
27973380 A
1 A
27973381 GTATTTGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (27 bp):
ATAAATTAAGTGTAGCTTTGGAGGCTA
Found at i:27974475 original size:16 final size:16
Alignment explanation
Indices: 27974437--27974476 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
27974427 GGTAAATGTT
* *
27974437 GAAATGGCGGGATACC
1 GAAATGTCGGAATACC
*
27974453 GAAATGTCGGAATGCC
1 GAAATGTCGGAATACC
27974469 GAAATGTC
1 GAAATGTC
27974477 AGAAAGCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (16 bp):
GAAATGTCGGAATACC
Found at i:27975266 original size:27 final size:27
Alignment explanation
Indices: 27975235--27975323 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 27
27975225 CCTAATATTT
*
27975235 GTAAAATGACCGTAATGCCCCTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* *
27975262 GTAAAATGACTGTAATTCCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* *
27975289 GTAAAATGATCGTGATGCCCCTGTA-G
1 GTAAAATGACCGTAATGCCCCTGTAGG
27975315 GTAAAATGA
1 GTAAAATGA
27975324 TTGTAATACC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 10 0.18
27 45 0.82
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (27 bp):
GTAAAATGACCGTAATGCCCCTGTAGG
Found at i:27975338 original size:26 final size:26
Alignment explanation
Indices: 27975235--27975343 Score: 101
Period size: 27 Copynumber: 4.1 Consensus size: 26
27975225 CCTAATATTT
** * *
27975235 GTAAAATGACCGTAATGCCCCTATAGG
1 GTAAAATGATTGTAATACCCCTGTA-G
* *
27975262 GTAAAATGACTGTAATTCCCCTGTAGG
1 GTAAAATGATTGTAATACCCCTGTA-G
* * *
27975289 GTAAAATGATCGTGATGCCCCTGTAG
1 GTAAAATGATTGTAATACCCCTGTAG
*
27975315 GTAAAATGATTGTAATACCTCTGTTAG
1 GTAAAATGATTGTAATACCCCTG-TAG
27975342 GT
1 GT
27975344 GAATTGAACG
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
26 20 0.29
27 50 0.71
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (26 bp):
GTAAAATGATTGTAATACCCCTGTAG
Found at i:27975429 original size:24 final size:24
Alignment explanation
Indices: 27975397--27975491 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 24
27975387 CCCTCGAGGT
*
27975397 TAAATGATTGATTTGTCTGTGATG
1 TAAATGACTGATTTGTCTGTGATG
* * * *
27975421 TAAGTGATTGATTTGTCCGAGATG
1 TAAATGACTGATTTGTCTGTGATG
*
27975445 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATG
*
27975469 TAAATGACTGATTTTTCTGTGAT
1 TAAATGACTGATTTGTCTGTGAT
27975492 AGGTATGACT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.44
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATG
Found at i:27975499 original size:24 final size:24
Alignment explanation
Indices: 27975448--27975529 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
27975438 CGAGATGTAA
* * **
27975448 ATGACTGATTTGTCTGTGATTTAA
1 ATGACTGATTTTTCTGTGATATGT
*
27975472 ATGACTGATTTTTCTGTGATAGGT
1 ATGACTGATTTTTCTGTGATATGT
*
27975496 ATGACTAATTTTTCTGTGA-ATTGT
1 ATGACTGATTTTTCTGTGATA-TGT
27975520 ATGACTGATT
1 ATGACTGATT
27975530 CTGAGCATGG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 1 0.02
24 48 0.98
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.46
Consensus pattern (24 bp):
ATGACTGATTTTTCTGTGATATGT
Found at i:27975654 original size:27 final size:27
Alignment explanation
Indices: 27975598--27975657 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
27975588 GGAAATATTG
*
27975598 TACTGGTGGCTTTGCCACAATCACTAT
1 TACTGGTGGCTTAGCCACAATCACTAT
* *
27975625 TACTGGTGGCTTAGCTACATAT-ACTGT
1 TACTGGTGGCTTAGCCACA-ATCACTAT
27975652 TACTGG
1 TACTGG
27975658 CAGCTTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (27 bp):
TACTGGTGGCTTAGCCACAATCACTAT
Found at i:27975690 original size:26 final size:26
Alignment explanation
Indices: 27975646--27975696 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
27975636 TAGCTACATA
* * *
27975646 TACTGTTACTGGCAGCTTTGTTGCGG
1 TACTGTTACTGGAAACTTTGCTGCGG
*
27975672 TACTGTTGCTGGAAACTTTGCTGCG
1 TACTGTTACTGGAAACTTTGCTGCG
27975697 ATGCTGCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.29, T:0.37
Consensus pattern (26 bp):
TACTGTTACTGGAAACTTTGCTGCGG
Found at i:27975787 original size:32 final size:32
Alignment explanation
Indices: 27975698--27975826 Score: 143
Period size: 32 Copynumber: 4.0 Consensus size: 32
27975688 TTTGCTGCGA
* *
27975698 TGCTGCTGATGGCTTTGTGTCGATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
* * * * * *
27975730 TGTTACTG-TAGGGTGTGTACCGATCATATCAT
1 TGCTACTGAT-GGCTTTGTGCCGATCATATTAC
*
27975762 TGCTACTGATGGCTTTGTGCTGATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
* *
27975794 TACTACTGATGGCTTTGTGCCAATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
27975826 T
1 T
27975827 ATAATTATGG
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
31 1 0.01
32 75 0.97
33 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (32 bp):
TGCTACTGATGGCTTTGTGCCGATCATATTAC
Found at i:27982439 original size:15 final size:14
Alignment explanation
Indices: 27982419--27982448 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
27982409 TAGTCATACA
27982419 TCTACTATAATAGGT
1 TCTACTATAA-AGGT
27982434 TCTACTATAAAGGT
1 TCTACTATAAAGGT
27982448 T
1 T
27982449 GTTGTCGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (14 bp):
TCTACTATAAAGGT
Found at i:27985535 original size:19 final size:19
Alignment explanation
Indices: 27985511--27985555 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
27985501 ACTTGGATTT
27985511 CCACTGAGCCAAGAGTTAG
1 CCACTGAGCCAAGAGTTAG
*
27985530 CCACTGAGCCAAGAGTTGG
1 CCACTGAGCCAAGAGTTAG
27985549 CCACTGA
1 CCACTGA
27985556 TGTTATTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (19 bp):
CCACTGAGCCAAGAGTTAG
Found at i:27991288 original size:22 final size:23
Alignment explanation
Indices: 27991244--27991289 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
27991234 TAAAGTTCTC
*
27991244 ATCTTTAGTGTTCTTATTTATTT
1 ATCTTTAGTGTTCTTATTCATTT
27991267 ATCTTT-GTGTTGCTT-TTCATTT
1 ATCTTTAGTGTT-CTTATTCATTT
27991289 A
1 A
27991290 ATTTTATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.63
Consensus pattern (23 bp):
ATCTTTAGTGTTCTTATTCATTT
Found at i:27995025 original size:19 final size:19
Alignment explanation
Indices: 27995001--27995037 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
27994991 TTATTCTAAG
27995001 ATTTATCTACCTAAATAAT
1 ATTTATCTACCTAAATAAT
27995020 ATTTATCTACCTAAATAA
1 ATTTATCTACCTAAATAA
27995038 CTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTATCTACCTAAATAAT
Done.