Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 63 of 186
Found at i:19754434 original size:27 final size:27
Alignment explanation
Indices: 19754400--19754597 Score: 252
Period size: 27 Copynumber: 7.3 Consensus size: 27
19754390 GTAATTTCAC
* *
19754400 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTATA
* * *
19754427 AATTGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTATA
* *
19754454 AATTGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTATA
* *
19754481 AATCAAGGGTGAAACGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTTTATA
*
19754508 AATCGAGGGTAAAATGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTTTATA
* * *
19754535 AATAGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTATA
* * *
19754562 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGGTAATTTTATA
19754589 AATCGAGGG
1 AATCGAGGG
19754598 CATTTCAGTA
Statistics
Matches: 152, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 152 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTATA
Found at i:19754516 original size:81 final size:81
Alignment explanation
Indices: 19754400--19754597 Score: 279
Period size: 81 Copynumber: 2.4 Consensus size: 81
19754390 GTAATTTCAC
* * * * *
19754400 AATCGAGGGTAAAACGATAATTTTGTAAATTGAGGGTAAAATGGTAATTTTGTAAATTGAGGGTA
1 AATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTATAAATAGAGGGTA
* *
19754465 AAACGGTAATTTTGTA
66 AAACGGTAATTCTATA
* * *
19754481 AATCAAGGGTGAAACGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTATAAATAGAGGGTG
1 AATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTATAAATAGAGGGTA
19754546 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
* * *
19754562 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAACGGTAATTTTATAAATCGAGGG
19754598 CATTTCAGTA
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 102 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (81 bp):
AATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTATAAATAGAGGGTA
AAACGGTAATTCTATA
Found at i:19768495 original size:16 final size:17
Alignment explanation
Indices: 19768474--19768506 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19768464 CACATTGAAG
19768474 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
19768490 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
19768507 CTTTTTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:19772021 original size:55 final size:55
Alignment explanation
Indices: 19771962--19772073 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
19771952 CTAATAATAA
19771962 AATTTTCAAATATCAATAATACAGTAAATAACAATAATTTTCATAAAAATTTTTC
1 AATTTTCAAATATCAATAATACAGTAAATAACAATAATTTTCATAAAAATTTTTC
* *
19772017 AATTTTCAAATATCAATAATACAGTAAATAATAATAATTTTCATAAAATTTTTTC
1 AATTTTCAAATATCAATAATACAGTAAATAACAATAATTTTCATAAAAATTTTTC
19772072 AA
1 AA
19772074 ACATACATAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (55 bp):
AATTTTCAAATATCAATAATACAGTAAATAACAATAATTTTCATAAAAATTTTTC
Found at i:19773912 original size:25 final size:25
Alignment explanation
Indices: 19773884--19774102 Score: 296
Period size: 25 Copynumber: 8.8 Consensus size: 25
19773874 AACTTATTCA
* * *
19773884 GAAATAATAAGGGAAAATTTAACCG
1 GAAATATTAAGAGCAAATTTAACCG
19773909 GAAATATTAAGAGCAAATTTAACCG
1 GAAATATTAAGAGCAAATTTAACCG
*
19773934 AAAATATTAAGAGCAAATTTAACCG
1 GAAATATTAAGAGCAAATTTAACCG
* *
19773959 GAATTATTAAGAACAAATTTAACCG
1 GAAATATTAAGAGCAAATTTAACCG
* *
19773984 GAATTATTAAGAGCAAATTTAACTG
1 GAAATATTAAGAGCAAATTTAACCG
19774009 GAAATATTAAGAGCAAATTTAACCG
1 GAAATATTAAGAGCAAATTTAACCG
* * *
19774034 GAATTATTAAGAACAAATTTAACCA
1 GAAATATTAAGAGCAAATTTAACCG
*
19774059 GAATTATTAAGAGCAAATTTAACC-
1 GAAATATTAAGAGCAAATTTAACCG
* *
19774083 AAAATTATTAAGAACAAATT
1 GAAA-TATTAAGAGCAAATT
19774103 AACAAGCTTA
Statistics
Matches: 175, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
24 2 0.01
25 173 0.99
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (25 bp):
GAAATATTAAGAGCAAATTTAACCG
Found at i:19773977 original size:75 final size:75
Alignment explanation
Indices: 19773898--19774102 Score: 349
Period size: 75 Copynumber: 2.7 Consensus size: 75
19773888 TAATAAGGGA
*
19773898 AAATTTAACCGGAAATATTAAGAGCAAATTTAACCGAAAATATTAAGAGCAAATTTAACCGGAAT
1 AAATTTAACCGGAATTATTAAGAGCAAATTTAACCGAAAATATTAAGAGCAAATTTAACCGGAAT
19773963 TATTAAGAAC
66 TATTAAGAAC
* *
19773973 AAATTTAACCGGAATTATTAAGAGCAAATTTAACTGGAAATATTAAGAGCAAATTTAACCGGAAT
1 AAATTTAACCGGAATTATTAAGAGCAAATTTAACCGAAAATATTAAGAGCAAATTTAACCGGAAT
19774038 TATTAAGAAC
66 TATTAAGAAC
* *
19774048 AAATTTAACCAGAATTATTAAGAGCAAATTTAACC-AAAATTATTAAGAACAAATT
1 AAATTTAACCGGAATTATTAAGAGCAAATTTAACCGAAAA-TATTAAGAGCAAATT
19774103 AACAAGCTTA
Statistics
Matches: 122, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
74 3 0.02
75 119 0.98
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.27
Consensus pattern (75 bp):
AAATTTAACCGGAATTATTAAGAGCAAATTTAACCGAAAATATTAAGAGCAAATTTAACCGGAAT
TATTAAGAAC
Found at i:19774691 original size:21 final size:21
Alignment explanation
Indices: 19774652--19774691 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19774642 TAAAGCCATC
*
19774652 AAATTTAATAATGCTAATTTA
1 AAATTTAATAATCCTAATTTA
19774673 AAATTTAAT-ATCCTGAATT
1 AAATTTAATAATCCT-AATT
19774692 AGGGCTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
AAATTTAATAATCCTAATTTA
Found at i:19776022 original size:46 final size:46
Alignment explanation
Indices: 19775972--19776095 Score: 230
Period size: 46 Copynumber: 2.7 Consensus size: 46
19775962 GTTGAGCATT
*
19775972 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCC
19776018 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCC
*
19776064 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
19776096 GGGGAGGGTT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCC
Found at i:19779143 original size:20 final size:20
Alignment explanation
Indices: 19779120--19779158 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19779110 TCTAGCATAA
19779120 TTCAGCTCATTTGAGCTCAT
1 TTCAGCTCATTTGAGCTCAT
**
19779140 TTCAGCTTGTTTGAGCTCA
1 TTCAGCTCATTTGAGCTCA
19779159 ACCGAGCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (20 bp):
TTCAGCTCATTTGAGCTCAT
Found at i:19781738 original size:79 final size:81
Alignment explanation
Indices: 19781627--19781809 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
19781617 GCTACTCGTT
* * *
19781627 CAAATGCCTTCGGGTCATAGCCCGATTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
19781691 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
19781707 CAAATGCCTTCGGG-CTTAGCCCAGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
19781770 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
19781787 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
19781810 GACATCATTC
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 33 0.37
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:19781748 original size:39 final size:39
Alignment explanation
Indices: 19781627--19781809 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 39
19781617 GCTACTCGTT
* *
19781627 CAAATGCCTTCGGGTCATAGCCCGATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCA
*
19781667 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCA
* *
19781707 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCA
* * * * *
19781746 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAG-CCCGATTTAGTAAC-TCGCA
19781787 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
19781810 GACATCATTC
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
38 2 0.02
39 35 0.29
40 68 0.56
41 17 0.14
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCA
Found at i:19783302 original size:56 final size:56
Alignment explanation
Indices: 19783235--19783522 Score: 567
Period size: 56 Copynumber: 5.1 Consensus size: 56
19783225 TATTAGTTTA
*
19783235 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
19783291 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
19783347 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
19783403 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
19783459 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
19783515 TTGCCCAT
1 TTGCCCAT
19783523 CATCCCTTGT
Statistics
Matches: 231, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 231 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:19784630 original size:41 final size:40
Alignment explanation
Indices: 19784563--19784671 Score: 146
Period size: 41 Copynumber: 2.7 Consensus size: 40
19784553 TAGACGGAGT
* ** *
19784563 TTTAGCGGCGTTTTTCAAAAAACGCCGCAATAGTTCGACC
1 TTTAGCGGTGTTTTTTGAAAAACGCCGCAATAGGTCGACC
* *
19784603 TTTAGCGGTGTTTTTTGAAAAAGCGCCGCTATAGGTCGGCC
1 TTTAGCGGTGTTTTTTGAAAAA-CGCCGCAATAGGTCGACC
*
19784644 TTTACCGGTGTTTTTTGAAAAACGCCGC
1 TTTAGCGGTGTTTTTTGAAAAACGCCGC
19784672 TAAAAGGTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 25 0.41
41 36 0.59
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (40 bp):
TTTAGCGGTGTTTTTTGAAAAACGCCGCAATAGGTCGACC
Found at i:19785008 original size:114 final size:114
Alignment explanation
Indices: 19784799--19785355 Score: 796
Period size: 114 Copynumber: 4.9 Consensus size: 114
19784789 GGAGGACCTC
* * * *
19784799 TAGCGGCGTTTCTT-AGAAAAACGCCACTAAAATGTTAAGGAGAACGACGTCATTTTATATGAGC
1 TAGCGGCGTTT-TTGA-AAAAACGCCACTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGC
* * * * * * *
19784863 TTCATTGTCAGTAGCGGCGTTTTCACGAAAACACCGCA-ATAGATC-AACTT
64 TCCTTTGGCAATAGCGGCGTTTTCCCAAAAACGCCGCAGA-AGATCAAACTT
* *
19784913 TCGCGGCGTTTTTCAACAAAACGCCACTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCT
1 TAGCGGCGTTTTTGAA-AAAACGCCACTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCT
* *
19784978 CCTTTGGCAATAGCGGCGTTTTCCTAAAAACGCCGCAAAAGATCAAACTT
65 CCTTTGGCAATAGCGGCGTTTTCCCAAAAACGCCGCAGAAGATCAAACTT
*
19785028 TAGCGGCGTTTTTGAAAAAACGCCGCTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
1 TAGCGGCGTTTTTGAAAAAACGCCACTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
* *
19785093 CTTTGGTAATAGCGGCGTTTTCCCAAAAACGCCGTAGAAGATCAAACTT
66 CTTTGGCAATAGCGGCGTTTTCCCAAAAACGCCGCAGAAGATCAAACTT
* **
19785142 TAGCGGCGTTTTTGAAAAAACACTGCTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
1 TAGCGGCGTTTTTGAAAAAACGCCACTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
* *
19785207 CTTTGGCAATAACAGCGTTTTCCCAAAAACGCCGCAGAAGATCAAACTT
66 CTTTGGCAATAGCGGCGTTTTCCCAAAAACGCCGCAGAAGATCAAACTT
*
19785256 TAGCGGCGTTTTTGAAAAAACGCCACTAAAATGTTGAGGAAAACGGCGTCGTTTTATATGTGCTC
1 TAGCGGCGTTTTTGAAAAAACGCCACTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
* * ***
19785321 CTTTGGCAGTAGCGGTGTTTTTGAAAAAACGCCGC
66 CTTTGGCAATAGCGGCGTTTTCCCAAAAACGCCGC
19785356 TAAAATGTTG
Statistics
Matches: 402, Mismatches: 37, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
113 3 0.01
114 379 0.94
115 20 0.05
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (114 bp):
TAGCGGCGTTTTTGAAAAAACGCCACTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
CTTTGGCAATAGCGGCGTTTTCCCAAAAACGCCGCAGAAGATCAAACTT
Found at i:19785503 original size:74 final size:74
Alignment explanation
Indices: 19785256--19785488 Score: 430
Period size: 74 Copynumber: 3.1 Consensus size: 74
19785246 GATCAAACTT
* * *
19785256 TAGCGGCGTTTTTGAAAAAACGCCACTAAAATGTTGAGGAAAACGGCGTCGTTTTATATGTGCTC
1 TAGCGGTGTTTTTGAAAAAACGCCGCTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
19785321 CTTTGGCAG
66 CTTTGGCAG
19785330 TAGCGGTGTTTTTGAAAAAACGCCGCTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
1 TAGCGGTGTTTTTGAAAAAACGCCGCTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
19785395 CTTTGGCAG
66 CTTTGGCAG
19785404 TAGCGGTGTTTTTGAAAAAACGCCGCTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
1 TAGCGGTGTTTTTGAAAAAACGCCGCTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
19785469 CTTTGGCAG
66 CTTTGGCAG
*
19785478 TAGCGGCGTTT
1 TAGCGGTGTTT
19785489 CCCCAAAAAT
Statistics
Matches: 155, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 155 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (74 bp):
TAGCGGTGTTTTTGAAAAAACGCCGCTAAAATGTTGAGGAAAACGACGTCGTTTTATATGTGCTC
CTTTGGCAG
Found at i:19785641 original size:15 final size:14
Alignment explanation
Indices: 19785623--19785665 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
19785613 CTTAATATTT
19785623 TTATAGGTTTAGGGG
1 TTAT-GGTTTAGGGG
*
19785638 TTATGGGTTTAAGGG
1 TTAT-GGTTTAGGGG
*
19785653 TTATGATTTAGGG
1 TTATGGTTTAGGG
19785666 TTGATGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (14 bp):
TTATGGTTTAGGGG
Found at i:19785672 original size:14 final size:13
Alignment explanation
Indices: 19785630--19785691 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 13
19785620 TTTTTATAGG
*
19785630 TTTAGGGGTTATGGG
1 TTTA-GGGTTAT-GA
19785645 TTTAAGGGTTATGA
1 TTT-AGGGTTATGA
19785659 TTTAGGGTTGATGA
1 TTTAGGGTT-ATGA
**
19785673 TTTATGTTTTATGA
1 TTTA-GGGTTATGA
19785687 TTTAG
1 TTTAG
19785692 AGTTTGAGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
13 7 0.17
14 20 0.49
15 13 0.32
16 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (13 bp):
TTTAGGGTTATGA
Found at i:19785711 original size:28 final size:28
Alignment explanation
Indices: 19785653--19785711 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
19785643 GGTTTAAGGG
**
19785653 TTATGATTTAGGGTTGATGATTTATGTT
1 TTATGATTTAGGGTTGATGATTTATAAT
* *
19785681 TTATGATTTAGAGTTTGA-GGTTTATAAT
1 TTATGATTTAG-GGTTGATGATTTATAAT
19785709 TTA
1 TTA
19785712 AAAGGTTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (28 bp):
TTATGATTTAGGGTTGATGATTTATAAT
Found at i:19786074 original size:7 final size:7
Alignment explanation
Indices: 19786064--19786127 Score: 58
Period size: 7 Copynumber: 9.1 Consensus size: 7
19786054 TAGGGGTTAA
19786064 TTAGGGT
1 TTAGGGT
19786071 TTAGGGT
1 TTAGGGT
* **
19786078 CTAGTAT
1 TTAGGGT
*
19786085 TTGGGGT
1 TTAGGGT
19786092 TTAGGGT
1 TTAGGGT
19786099 TT-GGCGT
1 TTAGG-GT
19786106 TTAGGGT
1 TTAGGGT
*
19786113 TTATGGT
1 TTAGGGT
*
19786120 ATAGGGT
1 TTAGGGT
19786127 T
1 T
19786128 AGAGTCTTAG
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
6 2 0.05
7 39 0.91
8 2 0.05
ACGTcount: A:0.14, C:0.03, G:0.39, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:19786248 original size:21 final size:22
Alignment explanation
Indices: 19786223--19786273 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
19786213 TTTTTAGTGT
19786223 TTTAGGGTTC-AAGG-TATAGGG
1 TTTAGGGTTCTAAGGCT-TAGGG
19786244 TTTAGGG-TCTAAGGCTTAGGG
1 TTTAGGGTTCTAAGGCTTAGGG
19786265 TTTAGGGTT
1 TTTAGGGTT
19786274 TAATTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.20, C:0.06, G:0.37, T:0.37
Consensus pattern (22 bp):
TTTAGGGTTCTAAGGCTTAGGG
Found at i:19786251 original size:7 final size:7
Alignment explanation
Indices: 19786223--19786275 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
19786213 TTTTTAGTGT
19786223 TTTAGGG
1 TTTAGGG
* *
19786230 TTCAAGG
1 TTTAGGG
*
19786237 TATAGGG
1 TTTAGGG
19786244 TTTAGGG
1 TTTAGGG
* *
19786251 TCTAAGG
1 TTTAGGG
*
19786258 CTTAGGG
1 TTTAGGG
19786265 TTTAGGG
1 TTTAGGG
19786272 TTTA
1 TTTA
19786276 ATTTTGAATT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.21, C:0.06, G:0.36, T:0.38
Consensus pattern (7 bp):
TTTAGGG
Found at i:19791582 original size:21 final size:21
Alignment explanation
Indices: 19791556--19791603 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
19791546 TCAACTTAGA
19791556 GCGGAGGCAGCAGT-ACGGGAG
1 GCGGAGGCAGCAGTGA-GGGAG
19791577 GCGGAGGCAGCAGTGAGGGAG
1 GCGGAGGCAGCAGTGAGGGAG
19791598 GCGGAG
1 GCGGAG
19791604 CAGAGCAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.23, C:0.17, G:0.56, T:0.04
Consensus pattern (21 bp):
GCGGAGGCAGCAGTGAGGGAG
Found at i:19791958 original size:43 final size:43
Alignment explanation
Indices: 19791897--19792145 Score: 308
Period size: 43 Copynumber: 5.7 Consensus size: 43
19791887 ACTGGGCAAA
19791897 TTAGCGGCGTTTTTTTTAAAAGCGCCGCTAAAAGCCCTGGTCT
1 TTAGCGGCGTTTTTTTTAAAAGCGCCGCTAAAAGCCCTGGTCT
19791940 TTAGCGG-GATTTTTTTTAAAAGCGCCGCTAAAAGCCCTGGTCT
1 TTAGCGGCG-TTTTTTTTAAAAGCGCCGCTAAAAGCCCTGGTCT
* *
19791983 TTCGCGGCGTTTTTTTTTAAAAGCGCCGCTAAAAGCGC-GGTCT
1 TTAGCGGCG-TTTTTTTTAAAAGCGCCGCTAAAAGCCCTGGTCT
* * *
19792026 TTCGCGGCG-TTTTTTTAAAAGCCGCCACTAAAAGCGCTGGTCT
1 TTAGCGGCGTTTTTTTTAAAAG-CGCCGCTAAAAGCCCTGGTCT
* * *
19792069 TTAGCAGCGTTTTTTTTAAAGGCGCCG-TGAAAAGACCTGGTCT
1 TTAGCGGCGTTTTTTTTAAAAGCGCCGCT-AAAAGCCCTGGTCT
* ** *
19792112 TTAGAGGCGCTTTTTTCAGAAAAACGCCGCTAAA
1 TTAGCGGCG-TTTTTT-TTAAAAGCGCCGCTAAA
19792146 TTTACCGGCG
Statistics
Matches: 181, Mismatches: 16, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
41 12 0.07
42 16 0.09
43 96 0.53
44 45 0.25
45 11 0.06
46 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTTTAAAAGCGCCGCTAAAAGCCCTGGTCT
Found at i:19796226 original size:22 final size:22
Alignment explanation
Indices: 19796201--19796249 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
19796191 CAGTTATATT
*
19796201 TCCTTGTTTGAGTTCCAAAAAC
1 TCCTTCTTTGAGTTCCAAAAAC
19796223 TCCTTCTTTGAGTTCCAAAAAC
1 TCCTTCTTTGAGTTCCAAAAAC
19796245 TCCTT
1 TCCTT
19796250 TCGCTTCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (22 bp):
TCCTTCTTTGAGTTCCAAAAAC
Found at i:19801274 original size:46 final size:46
Alignment explanation
Indices: 19801221--19801385 Score: 174
Period size: 46 Copynumber: 3.6 Consensus size: 46
19801211 TTGGGCATCT
* *
19801221 GAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCAATCATGGATGCAAATGTCC
* * * *
19801267 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCAATCATGGATGCAA--ATG--TCC
* * * *
19801314 GAACTTGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCAATCATGGATGCAAATGTCC
*
19801360 GAGCTCGTTGAGTTGAGTCCGAGTTC
1 GAACTCGTTGAGTTGAGTCCGAGTTC
19801386 GTTTATGGGC
Statistics
Matches: 99, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
43 5 0.05
45 4 0.04
46 52 0.53
47 28 0.28
48 4 0.04
50 6 0.06
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCAATCATGGATGCAAATGTCC
Found at i:19801373 original size:93 final size:93
Alignment explanation
Indices: 19801214--19801387 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
19801204 AGGATGTTTG
* * * * *
19801214 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATCATGGATGCAAACGCCCGAACTCGTTGAG
19801279 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
19801307 GGCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATCATGGATGCAAACGCCCGAACTCGTTGAG
19801372 TTGAGTCCGAGTTCGT
66 TTGAGTCCGAGTTCGT
19801388 TTATGGGCGG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATCATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:19803338 original size:40 final size:40
Alignment explanation
Indices: 19803287--19804004 Score: 1121
Period size: 40 Copynumber: 17.9 Consensus size: 40
19803277 ATTACCACAA
* * * ** *
19803287 GCACAATTGCCTTCGGGTCTTAACCTGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19803327 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19803367 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
19803407 GCACAAAGGCCTGCGGGTCTTAGCTCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19803447 GCACAAAGGCCTGCGGGTCTTAGCCCGGATATATGTCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATA--TCAACTC
*
19803489 CCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19803529 GCACGAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19803569 GCACGAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19803609 GCACAAAGGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19803649 GCACAAATGCCTTCGGGTCTTAGCCCAGATATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCC-G-GATATATCAACTC
* *
19803691 GCACGAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
19803731 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
19803771 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19803811 ACACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
19803851 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19803891 GCACAAAGGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19803931 GCACAAATGCCTTCGGGTCTTAGCCTGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
** *
19803971 GCATGAATGCCTGCGGGTCTTAGCCCGGATATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAT
19804005 TCAAATGCTC
Statistics
Matches: 631, Mismatches: 43, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
40 556 0.88
41 2 0.00
42 73 0.12
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:19803640 original size:202 final size:201
Alignment explanation
Indices: 19803287--19804004 Score: 1152
Period size: 202 Copynumber: 3.6 Consensus size: 201
19803277 ATTACCACAA
* * * * ** * *
19803287 GCACAATTGCCTTCGGGTCTTAACCTGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
* *
19803352 CGGATATATCAACTTGCAC-AATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAAGG
66 CGGATATATCAACTCGCACGAA-TGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAAGG
* * *
19803416 CCTGCGGGTCTTAGCTCGGATATATCAACTCGCACAAAGGCCTGCGGGTCTTAGCCCGGATATAT
130 CCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAT
19803481 GTCAACTC
195 -TCAACTC
* * * *
19803489 CCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACGAATGCCTGCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
19803554 CGGATATATCAACTCGCACGAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAAGGC
66 CGGATATATCAACTCGCACGAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAAGGC
*
19803619 CTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCAGATATATA
131 CTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAT-
19803684 TCAACTC
195 TCAACTC
*
19803691 GCACGAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
* * * *
19803756 CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCACACAAATGC
66 CGGATATATCAACTCGCACGAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAAGGC
*
19803821 CTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA-T
131 CTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATT
19803885 CAACTC
196 CAACTC
*
19803891 GCACAAAGGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
* *
19803956 TGGATATATCAACTCGCATGAATGCCTGCGGGTCTTAGCCCGGATATAT
66 CGGATATATCAACTCGCACGAATGCCTGCGGGTCTTAGCCCGGATATAT
19804005 TCAAATGCTC
Statistics
Matches: 483, Mismatches: 32, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
200 115 0.24
202 366 0.76
203 2 0.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (201 bp):
GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCC
CGGATATATCAACTCGCACGAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAAGGC
CTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATT
CAACTC
Found at i:19811326 original size:40 final size:40
Alignment explanation
Indices: 19811282--19811999 Score: 1175
Period size: 40 Copynumber: 17.9 Consensus size: 40
19811272 ATTACCACAA
* * ** *
19811282 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
19811322 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19811362 GTACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19811402 GTACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19811442 GTACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19811482 GTACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19811522 GCACAAAGGCCTGCGGGTCTTAGCCCGGATATATGTCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATA--TCAACTC
19811564 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19811604 GCACGAATGCCTACGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
19811644 GTACAAAGGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19811684 ACACAAATGCCTTCGGGTCTTAGCCCAGATATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCC-G-GATATATCAACTC
* *
19811726 GCACGAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
19811766 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19811806 GCACCAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19811846 GTACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19811886 GCACCAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
19811926 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19811966 GCACGAATGCCTGCGGGTCTTAGCCCGGATATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAT
19812000 TCAAATGCTC
Statistics
Matches: 638, Mismatches: 36, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
40 563 0.88
41 2 0.00
42 73 0.11
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:19813468 original size:19 final size:20
Alignment explanation
Indices: 19813441--19813480 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
19813431 GGTAACTAAC
19813441 TCAAAAATTAAC-TAAAATT
1 TCAAAAATTAACATAAAATT
*
19813460 TCAAGAATTAACATAAAATT
1 TCAAAAATTAACATAAAATT
19813480 T
1 T
19813481 TTACCTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (20 bp):
TCAAAAATTAACATAAAATT
Found at i:19816404 original size:15 final size:15
Alignment explanation
Indices: 19816384--19816452 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
19816374 ATATCTTGGG
19816384 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
19816399 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
19816414 ATTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
19816429 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
19816444 TTTCTTTAT
1 TTTCTTTAT
19816453 TCGGTTTCCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.14, C:0.17, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:19816453 original size:30 final size:30
Alignment explanation
Indices: 19816375--19816454 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
19816365 CATAGTATCA
* * *
19816375 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* *
19816405 TAT-TCTGGAATTCTTTATTCTGGATTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
19816435 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
19816455 GGTTTCCTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 1 0.02
30 40 0.95
31 1 0.02
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:19818911 original size:46 final size:45
Alignment explanation
Indices: 19818851--19819026 Score: 142
Period size: 46 Copynumber: 3.8 Consensus size: 45
19818841 TGTTTGGGCA
* *
19818851 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AAATG
* * * *
19818897 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AA--ATG
* * * * *
19818942 CATCTGAACTTGTTGAGTTGAGTTCGAGTTCACTCATGGATGAAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AAATG
* * *
19818990 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19819027 GCGGGTTACA
Statistics
Matches: 101, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
43 5 0.05
45 4 0.04
46 57 0.56
47 25 0.25
48 4 0.04
50 6 0.06
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAATG
Found at i:19819006 original size:93 final size:93
Alignment explanation
Indices: 19818847--19819019 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 93
19818837 AGGATGTTTG
* ** * *
19818847 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATGAAAACGCCCGAACTCGTTGAG
*
19818912 TTGAGTCTGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* ** * *
19818940 GGCATCTGAACTTGTTGAGTTGAGTTCGAGTTCACTCATGGATGAAAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATGAAAACGCCCGAACTCGTTGAG
19819005 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
19819020 CTTATGGGCG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTCATGGATGAAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:19825151 original size:10 final size:10
Alignment explanation
Indices: 19825118--19825156 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
19825108 AATGAGCTGG
19825118 AACGAGCTAA
1 AACGAGCTAA
*
19825128 AATCGAGCTCA
1 AA-CGAGCTAA
*
19825139 AACAAGCTAA
1 AACGAGCTAA
19825149 AACGAGCT
1 AACGAGCT
19825157 CAAGTGAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (10 bp):
AACGAGCTAA
Found at i:19825166 original size:20 final size:21
Alignment explanation
Indices: 19825118--19825159 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19825108 AATGAGCTGG
19825118 AACGAGCTAAAATCGAGCTCA
1 AACGAGCTAAAATCGAGCTCA
*
19825139 AACAAGCTAAAA-CGAGCTCA
1 AACGAGCTAAAATCGAGCTCA
19825159 A
1 A
19825160 GTGAGCTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.12
Consensus pattern (21 bp):
AACGAGCTAAAATCGAGCTCA
Found at i:19826642 original size:22 final size:21
Alignment explanation
Indices: 19826609--19826650 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
19826599 TCAAACCTAC
19826609 ACAAGCATACAAAATTTACACA
1 ACAAGCATACAAAA-TTACACA
*
19826631 ACAAGGCA-ACAACATTACAC
1 ACAA-GCATACAAAATTACAC
19826651 CACCATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.14
Consensus pattern (21 bp):
ACAAGCATACAAAATTACACA
Found at i:19827220 original size:42 final size:41
Alignment explanation
Indices: 19827174--19827286 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 41
19827164 TTCTTCATAC
19827174 TCACTCTCTTTTTCAATTTTCTTTTTCTTCTCACATTCTTTT
1 TCACTCTCTTTTTCAA-TTTCTTTTTCTTCTCACATTCTTTT
** * * * ***
19827216 TCACTCTCGATCTCGATCTCTTTTTCCTTCTCTTTTTCTTTT
1 TCACTCTCTTTTTCAATTTCTTTTT-CTTCTCACATTCTTTT
*
19827258 TCACTTTCTTTTTCAATTTCATTTTTCTT
1 TCACTCTCTTTTTCAATTTC-TTTTTCTT
19827287 TTTCTTATTC
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
41 8 0.15
42 42 0.76
43 5 0.09
ACGTcount: A:0.11, C:0.27, G:0.02, T:0.61
Consensus pattern (41 bp):
TCACTCTCTTTTTCAATTTCTTTTTCTTCTCACATTCTTTT
Found at i:19827257 original size:6 final size:6
Alignment explanation
Indices: 19827234--19827308 Score: 60
Period size: 6 Copynumber: 11.8 Consensus size: 6
19827224 GATCTCGATC
* * ** **
19827234 TCTTTT TCCTTC TCTTTT TCTTTT TCACTT TCTTTT TCAATT TCATTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC-TTTT
19827283 TCTTTT TCTTATT CTCTTTT TGCTTT
1 TCTTTT TCTT-TT -TCTTTT T-CTTT
19827309 CTTTCACACT
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
6 37 0.70
7 12 0.23
8 4 0.08
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (6 bp):
TCTTTT
Found at i:19830617 original size:6 final size:6
Alignment explanation
Indices: 19830600--19830645 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
19830590 TTCAACATAT
* * *
19830600 AAATAA AGATAA AAAT-A AAGTAA AAATAA ATA-AA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
19830646 TAGGTGTCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
5 8 0.25
6 24 0.75
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:19830625 original size:11 final size:11
Alignment explanation
Indices: 19830600--19830640 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
19830590 TTCAACATAT
19830600 AAATAAAGATAA
1 AAATAAAG-TAA
19830612 AAATAAAGTAA
1 AAATAAAGTAA
19830623 AAATAAA-TAAA
1 AAATAAAGT-AA
19830634 AAATAAA
1 AAATAAA
19830641 AATAATAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 1 0.04
11 19 0.68
12 8 0.29
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (11 bp):
AAATAAAGTAA
Found at i:19830628 original size:17 final size:17
Alignment explanation
Indices: 19830598--19830645 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
19830588 ATTTCAACAT
*
19830598 ATAAATAAAGATAAA-A
1 ATAAATAAAAATAAATA
19830614 ATAAAGTAAAAATAAATA
1 ATAAA-TAAAAATAAATA
*
19830632 AAAAATAAAAATAA
1 ATAAATAAAAATAA
19830646 TAGGTGTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 5 0.18
17 18 0.64
18 5 0.18
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (17 bp):
ATAAATAAAAATAAATA
Found at i:19831293 original size:57 final size:57
Alignment explanation
Indices: 19831205--19831324 Score: 195
Period size: 57 Copynumber: 2.1 Consensus size: 57
19831195 TTTCAGGGTT
*
19831205 TGACTACTCTAACCTCTGTGTATAACGAATCAGATATCTCTCTATACAGAATTTCAA
1 TGACTACTCTAACCTCTATGTATAACGAATCAGATATCTCTCTATACAGAATTTCAA
* * * *
19831262 TGACTGCTCTGACCTCTATGTATTACGAATCAGATATCTCTCTATACATAATTTCAA
1 TGACTACTCTAACCTCTATGTATAACGAATCAGATATCTCTCTATACAGAATTTCAA
19831319 TGACTA
1 TGACTA
19831325 TGAGGTTTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (57 bp):
TGACTACTCTAACCTCTATGTATAACGAATCAGATATCTCTCTATACAGAATTTCAA
Found at i:19832453 original size:46 final size:47
Alignment explanation
Indices: 19832290--19832601 Score: 320
Period size: 46 Copynumber: 6.7 Consensus size: 47
19832280 AACCCGCCCC
* * * **
19832290 TAAGTGAACTTGGACTCAACTCAACGAGCTCGG-GCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTACATCCA
* * *
19832336 TAAATGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-ATTTACATCCA
* * * *
19832384 TCA-CGAACTCGAACTCAACTCAACGAGTTCGGA-CATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTACATCCA
* * **
19832429 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTACATCCA
* *
19832475 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-ATTTACATCCA
* *
19832523 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTTACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTACATCCA
19832568 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
19832602 TGCTCAACCA
Statistics
Matches: 220, Mismatches: 31, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
43 13 0.06
44 4 0.02
45 6 0.03
46 121 0.55
47 58 0.26
48 6 0.03
49 4 0.02
50 8 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTACATCCA
Found at i:19832534 original size:93 final size:93
Alignment explanation
Indices: 19832434--19832604 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
19832424 ATCCATAAGT
* *
19832434 GAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAATGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGA-CATTCACATCCATAAATGAACTCGGACTCAACTCA
19832498 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
19832527 GAACTCGGACTCAACTCAACGAGTTCGGACATTTACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
19832592 CGAGTTCGGATGC
66 CGAGTTCGGATGC
19832605 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 70 0.97
94 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:19832540 original size:139 final size:139
Alignment explanation
Indices: 19832290--19832595 Score: 567
Period size: 139 Copynumber: 2.2 Consensus size: 139
19832280 AACCCGCCCC
* *
19832290 TAAGTGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAATGAACTCGGACTCAA
*
19832355 CTCAATGAGTTCGGATGCCTAGTTACATCTCACGAACTCGAACTCAACTCAACGAGTTCGGACAT
66 CTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTCGAACTCAACTCAACGAGTTCGGACAT
*
19832420 TTGCATCCA
131 TTACATCCA
19832429 TAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAATGAACTCGGACTCAA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAATGAACTCGGACTCAA
*
19832494 CTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACAT
66 CTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTCGAACTCAACTCAACGAGTTCGGACAT
19832559 TTACATCCA
131 TTACATCCA
19832568 TAAGTGAACTCGGACTCAACTCAACGAG
1 TAAGTGAACTCGGACTCAACTCAACGAG
19832596 TTCGGATGCT
Statistics
Matches: 162, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 162 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (139 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAAATGAACTCGGACTCAA
CTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTCGAACTCAACTCAACGAGTTCGGACAT
TTACATCCA
Found at i:19840215 original size:46 final size:46
Alignment explanation
Indices: 19840148--19840362 Score: 229
Period size: 46 Copynumber: 4.7 Consensus size: 46
19840138 CGCCCCTAAG
* * *** *
19840148 TGAACTCGGACTCAACTCAATGAGCTCGGGTGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
* * * *
19840194 TGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCATAAA
* * * *
19840241 CGAACTCGGACTCAACTTAACGAGTTCGAACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
*
19840287 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
*
19840333 TGAACTCGAACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA
19840363 TGCTCAACCA
Statistics
Matches: 142, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
43 6 0.04
44 2 0.01
45 1 0.01
46 100 0.70
47 27 0.19
48 1 0.01
49 1 0.01
50 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAA
Found at i:19850876 original size:46 final size:46
Alignment explanation
Indices: 19850791--19850908 Score: 112
Period size: 46 Copynumber: 2.5 Consensus size: 46
19850781 ATCTCGCAGT
* * * * * **
19850791 CGATGCATGTCCTAGACATGTCTTACACTGGCTTACGTCTTGAGGC
1 CGATGCATGTCCCAAACATGTCTTAAACTGCCCTACGTCTCAAGGC
*
19850837 CGATGCATGTCCCAAACATGTCTTAAACTAGCCCT-CGTCTCAATGC
1 CGATGCATGTCCCAAACATGTCTTAAACT-GCCCTACGTCTCAAGGC
* *
19850883 TGATGCCATGTCCCAAAAATGGTCTT
1 CGATG-CATGTCCCAAACAT-GTCTT
19850909 GCACTGGCTC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
46 38 0.64
47 16 0.27
48 5 0.08
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (46 bp):
CGATGCATGTCCCAAACATGTCTTAAACTGCCCTACGTCTCAAGGC
Found at i:19856704 original size:18 final size:18
Alignment explanation
Indices: 19856681--19856717 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
19856671 GAAGATGAGT
19856681 TCTCTATATAATGTTAAG
1 TCTCTATATAATGTTAAG
*
19856699 TCTCTATGTAATGTTAAG
1 TCTCTATATAATGTTAAG
19856717 T
1 T
19856718 TGGTCTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
TCTCTATATAATGTTAAG
Found at i:19867738 original size:21 final size:20
Alignment explanation
Indices: 19867714--19867757 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
19867704 TCTTTTTCAG
*
19867714 TCTCAATCTCGTTTTGTTGTT
1 TCTCAATCTCGTTTTCTT-TT
* *
19867735 TCTCACTCTCTTTTTCTTTT
1 TCTCAATCTCGTTTTCTTTT
19867755 TCT
1 TCT
19867758 ATTTCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.07, C:0.25, G:0.07, T:0.61
Consensus pattern (20 bp):
TCTCAATCTCGTTTTCTTTT
Found at i:19870574 original size:25 final size:25
Alignment explanation
Indices: 19870513--19870586 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
19870503 TGAGCTTTCC
* * *
19870513 AATGTGTAAGCTGCAAGCTCAGTAAA
1 AATGTGCAAGCTGCAAGCTTAG-CAA
19870539 AATGTGCAAGCTGCAAGCTTAGCAA
1 AATGTGCAAGCTGCAAGCTTAGCAA
*
19870564 GATGT-CAAAGCTGCAAGCTTAGC
1 AATGTGC-AAGCTGCAAGCTTAGC
19870587 GAGAAGTGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 1 0.02
25 22 0.51
26 20 0.47
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (25 bp):
AATGTGCAAGCTGCAAGCTTAGCAA
Found at i:19870659 original size:13 final size:13
Alignment explanation
Indices: 19870641--19870666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19870631 TAGTTGCGAG
19870641 CCTGTTGAAGACA
1 CCTGTTGAAGACA
19870654 CCTGTTGAAGACA
1 CCTGTTGAAGACA
19870667 GTATGCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CCTGTTGAAGACA
Found at i:19881160 original size:40 final size:40
Alignment explanation
Indices: 19881101--19881288 Score: 313
Period size: 40 Copynumber: 4.7 Consensus size: 40
19881091 GAGCATTGGA
* *
19881101 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
19881141 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
*
19881181 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAATTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
19881221 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
19881261 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
19881289 ATGTGTTTGC
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 140 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:19886467 original size:40 final size:40
Alignment explanation
Indices: 19886422--19886841 Score: 644
Period size: 40 Copynumber: 10.5 Consensus size: 40
19886412 CAAGCTCAAT
* * * * *
19886422 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
19886462 TGCCTTCGGGTCTTAGCCCGGATATATCAACTT-GCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAA-TTCGCACAAA
*
19886502 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCGCAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* * ** *
19886542 CGCCGTCAAGTCTTAGCCCGGATATATCAGTTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* *
19886582 TGCCTTCGGGTCTTATCCTGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
19886622 CGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
19886662 TGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
19886702 CGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
19886742 TGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* *
19886782 TGCCTTCGGGTCTTAGCCAGGATATATGAATTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
19886822 TGCCTTCGGGTCTTAGCCCG
1 TGCCTTCGGGTCTTAGCCCG
19886842 CACAAATGCC
Statistics
Matches: 344, Mismatches: 34, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
39 2 0.01
40 341 0.99
41 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
Found at i:19886619 original size:120 final size:120
Alignment explanation
Indices: 19886422--19886952 Score: 750
Period size: 120 Copynumber: 4.5 Consensus size: 120
19886412 CAAGCTCAAT
* * * * *
19886422 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
* *
19886487 ATCAACTT-GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCGCAAA
66 ATCAA-TTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* * ** * * *
19886542 CGCCGTCAAGTCTTAGCCCGGATATATCAGTTCGCACAAATGCCTTCGGGTCTTATCCTGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
*
19886607 ATCAATTCGCACAAACGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
66 ATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* *
19886662 TGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAACGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
*
19886727 ATCAATTCGCACAAATGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAA
66 ATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
* *
19886782 TGCCTTCGGGTCTTAGCCAGGATATATGAATTCGCACAAATGCCTTCGGGTCTTAG--C------
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
*
19886839 --C----CGCACAAATGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAA
66 ATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
*
19886888 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGTTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
19886953 CATTCAAATG
Statistics
Matches: 368, Mismatches: 34, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
106 100 0.27
108 1 0.00
110 1 0.00
118 1 0.00
119 2 0.01
120 263 0.71
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (120 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
ATCAATTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTCGCACAAA
Found at i:19886850 original size:26 final size:26
Alignment explanation
Indices: 19886814--19886867 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
19886804 TATATGAATT
*
19886814 CGCACAAATGCCTTCGGGTCTTAGCC
1 CGCACAAATGCCTTCGGGTCTTAACC
19886840 CGCACAAATGCCTTCGGGTCTTAACC
1 CGCACAAATGCCTTCGGGTCTTAACC
19886866 CG
1 CG
19886868 GATATATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.22
Consensus pattern (26 bp):
CGCACAAATGCCTTCGGGTCTTAACC
Found at i:19886880 original size:66 final size:66
Alignment explanation
Indices: 19886774--19886907 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
19886764 TATATCAATT
* *
19886774 CGCACAAATGCCTTCGGGTCTTAGCCAGGATATATGAATTCGCACAAATGCCTTCGGGTCTTAGC
1 CGCACAAATGCCTTCGGGTCTTAACCAGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGC
19886839 C
66 C
*
19886840 CGCACAAATGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGC
1 CGCACAAATGCCTTCGGGTCTTAACCAGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGC
19886905 C
66 C
19886906 CG
1 CG
19886908 GATATATCAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (66 bp):
CGCACAAATGCCTTCGGGTCTTAACCAGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGC
C
Found at i:19886895 original size:40 final size:40
Alignment explanation
Indices: 19886840--19886952 Score: 208
Period size: 40 Copynumber: 2.8 Consensus size: 40
19886830 GGTCTTAGCC
*
19886840 CGCACAAATGCCTTCGGGTCTTAACCCGGATATATCAATT
1 CGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATT
19886880 CGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATT
1 CGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATT
*
19886920 CGCACAAATGCCTTCGGTTCTTAGCCCGGATAT
1 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
19886953 CATTCAAATG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (40 bp):
CGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATT
Found at i:19886920 original size:106 final size:106
Alignment explanation
Indices: 19886734--19886947 Score: 392
Period size: 106 Copynumber: 2.0 Consensus size: 106
19886724 TATATCAATT
*
19886734 CGCACAAATGCCTTCGGGTCTTATCCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGC
1 CGCACAAATGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGC
*
19886799 CAGGATATATGAATTCGCACAAATGCCTTCGGGTCTTAGCC
66 CAGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCC
19886840 CGCACAAATGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGC
1 CGCACAAATGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGC
* *
19886905 CCGGATATATCAATTCGCACAAATGCCTTCGGTTCTTAGCC
66 CAGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCC
19886946 CG
1 CG
19886948 GATATCATTC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (106 bp):
CGCACAAATGCCTTCGGGTCTTAACCCGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGC
CAGGATATATCAATTCGCACAAATGCCTTCGGGTCTTAGCC
Found at i:19892390 original size:28 final size:28
Alignment explanation
Indices: 19892327--19893292 Score: 1853
Period size: 28 Copynumber: 34.5 Consensus size: 28
19892317 ATATTAAGTC
*
19892327 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
19892354 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
19892382 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892410 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892438 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892466 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892494 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892522 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892550 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892578 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892606 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892634 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892662 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892690 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892718 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892746 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892774 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892802 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892830 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892858 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892886 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892914 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892942 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892970 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19892998 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19893026 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19893054 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19893082 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19893110 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19893138 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19893166 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19893194 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
19893222 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
19893250 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
19893279 CGCACACTTAGTGC
1 CGCACACTTAGTGC
19893293 CAATCTCATG
Statistics
Matches: 928, Mismatches: 9, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
27 21 0.02
28 888 0.96
29 19 0.02
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:19899753 original size:23 final size:23
Alignment explanation
Indices: 19899725--19899774 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
19899715 GGGTGTTACA
19899725 TTTACTATATATTAAATTAAGAT
1 TTTACTATATATTAAATTAAGAT
*
19899748 TTTACTATATATTAACTTAAGAT
1 TTTACTATATATTAAATTAAGAT
19899771 TTTA
1 TTTA
19899775 TAAATTTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTACTATATATTAAATTAAGAT
Found at i:19901640 original size:114 final size:119
Alignment explanation
Indices: 19901461--19901682 Score: 269
Period size: 114 Copynumber: 1.9 Consensus size: 119
19901451 AATTAATAGT
* * *
19901461 TATTTAGACTTCTTTTTCATTATATTAACTTTATTTTATGCAACAACAAAATATCACTACCATAG
1 TATTTAGACTTCTTTTTCATAATATTAAC-TTATTATAAGCAACAACAAAATATCACTACCATAG
* * * *
19901526 AGTTATTTTCA-TAGTATAATTTATGTAAAAAATATTTTAATTATCAAGAAAATTTA
65 AATTATTATCATTA-CATAATTTATGT-AAAAATATTATAATTATCAAGAAAATTTA
* * *
19901582 TATTTAGACTT-TTTTTCATAATA-TAAC-TATTATAAGTAA-AA-AAAA-ATCATTACTATAGA
1 TATTTAGACTTCTTTTTCATAATATTAACTTATTATAAGCAACAACAAAATATCACTACCATAGA
*
19901641 ATTATTATCATTACATATTTTATGTAAAAATATTATAATTAT
66 ATTATTATCATTACATAATTTATGTAAAAATATTATAATTAT
19901683 TTTAAAATGT
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
113 16 0.18
114 30 0.34
115 6 0.07
116 2 0.02
117 9 0.10
119 4 0.04
120 11 0.12
121 11 0.12
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (119 bp):
TATTTAGACTTCTTTTTCATAATATTAACTTATTATAAGCAACAACAAAATATCACTACCATAGA
ATTATTATCATTACATAATTTATGTAAAAATATTATAATTATCAAGAAAATTTA
Found at i:19901859 original size:17 final size:15
Alignment explanation
Indices: 19901840--19901878 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
19901830 TTGTTTGATA
*
19901840 AAAATAATATAATCAT
1 AAAATAATATAA-AAT
19901856 AAAATAA-ATAAAAT
1 AAAATAATATAAAAT
19901870 AAAATAATA
1 AAAATAATA
19901879 ATTGGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 5 0.24
16 7 0.33
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAATATAAAAT
Found at i:19901870 original size:22 final size:22
Alignment explanation
Indices: 19901837--19901879 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
19901827 AGATTGTTTG
* *
19901837 ATAAAAATAATATAATCATAAA
1 ATAAAAATAATAAAATAATAAA
19901859 ATAAATAA-AATAAAATAATAA
1 ATAAA-AATAATAAAATAATAA
19901880 TTGGATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAAAAATAATAAAATAATAAA
Found at i:19907168 original size:9 final size:9
Alignment explanation
Indices: 19907154--19907179 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19907144 GTTATATATA
19907154 TATAATAAC
1 TATAATAAC
19907163 TATAATAAC
1 TATAATAAC
19907172 TATAATAA
1 TATAATAA
19907180 AAATCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (9 bp):
TATAATAAC
Found at i:19907564 original size:16 final size:17
Alignment explanation
Indices: 19907545--19907577 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19907535 AATTTATTTC
19907545 ATAAATAATA-TTAATA
1 ATAAATAATATTTAATA
*
19907561 ATAATTAATATTTAATA
1 ATAAATAATATTTAATA
19907578 TATATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATAATATTTAATA
Found at i:19910695 original size:4 final size:4
Alignment explanation
Indices: 19910686--19910719 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
19910676 GAGCAAACGT
19910686 GAAA GAAA G-AA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
19910720 GGGAAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:19912731 original size:2 final size:2
Alignment explanation
Indices: 19912724--19912749 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19912714 ACCATTTAAA
19912724 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19912750 TTCTTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19915118 original size:23 final size:23
Alignment explanation
Indices: 19915092--19915143 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
19915082 AATTAAAAAG
19915092 ATGAAAGCAT-TATAGCTATCATT
1 ATGAAAGCATAT-TAGCTATCATT
*
19915115 ATGAAAGCATATTAGCTATTATT
1 ATGAAAGCATATTAGCTATCATT
19915138 ATGAAA
1 ATGAAA
19915144 CCAAGTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:19915206 original size:9 final size:9
Alignment explanation
Indices: 19915194--19915225 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
19915184 ACAAATATTA
19915194 AAAATAAAC
1 AAAATAAAC
19915203 AAAATAAAC
1 AAAATAAAC
19915212 AAAATAAAC
1 AAAATAAAC
19915221 AAAAT
1 AAAAT
19915226 GCACCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAC
Found at i:19919581 original size:23 final size:23
Alignment explanation
Indices: 19919555--19919606 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
19919545 AATTAAAAAG
19919555 ATGAAAGCAT-TATAGCTATCATT
1 ATGAAAGCATAT-TAGCTATCATT
*
19919578 ATGAAAGCATATTAGCTATTATT
1 ATGAAAGCATATTAGCTATCATT
19919601 ATGAAA
1 ATGAAA
19919607 CCAAGTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:19919669 original size:9 final size:9
Alignment explanation
Indices: 19919657--19919688 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
19919647 ACAAATATTA
19919657 AAAATAAAC
1 AAAATAAAC
19919666 AAAATAAAC
1 AAAATAAAC
19919675 AAAATAAAC
1 AAAATAAAC
19919684 AAAAT
1 AAAAT
19919689 GCACCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAC
Found at i:19925210 original size:28 final size:28
Alignment explanation
Indices: 19925170--19925228 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
19925160 ATTTAAGCTT
*
19925170 TAAAGCTT-TTTAAAAAATGAATAAAAAA
1 TAAAGCTTCTTAAAAAAAT-AATAAAAAA
19925198 TAAAGCTTCTTAAAAAAATAATAAAAAA
1 TAAAGCTTCTTAAAAAAATAATAAAAAA
19925226 TAA
1 TAA
19925229 GATTCGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (28 bp):
TAAAGCTTCTTAAAAAAATAATAAAAAA
Found at i:19925825 original size:25 final size:24
Alignment explanation
Indices: 19925797--19925879 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 24
19925787 CCTAAAACAT
19925797 TATTTTTAGTATATTTAATTTATTA
1 TATTTTTA-TATATTTAATTTATTA
* ** **
19925822 TATTTTTA-AAATTTGTTTTTAACA
1 TATTTTTATATATTT-AATTTATTA
19925846 TTATTTTTACTATATTTAATTTATTA
1 -TATTTTTA-TATATTTAATTTATTA
19925872 TATTTTTA
1 TATTTTTA
19925880 AAATTTGTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
23 5 0.11
24 5 0.11
25 24 0.55
26 5 0.11
27 5 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTTTTATATATTTAATTTATTA
Found at i:19925846 original size:50 final size:50
Alignment explanation
Indices: 19925792--19925892 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
19925782 CCATTCCTAA
*
19925792 AACATTATTTTTAGTATATTTAATTTATTATATTTTTAAAATTTGTTTTT
1 AACATTATTTTTACTATATTTAATTTATTATATTTTTAAAATTTGTTTTT
19925842 AACATTATTTTTACTATATTTAATTTATTATATTTTTAAAATTTGTTTTT
1 AACATTATTTTTACTATATTTAATTTATTATATTTTTAAAATTTGTTTTT
19925892 A
1 A
19925893 TATAAAAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (50 bp):
AACATTATTTTTACTATATTTAATTTATTATATTTTTAAAATTTGTTTTT
Found at i:19925915 original size:50 final size:50
Alignment explanation
Indices: 19925811--19925915 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 50
19925801 TTTAGTATAT
** ** * * *
19925811 TTAATTTATTATATTTTTAAAATTTGTTTTTAACATTATTTTTACTATAT
1 TTAATTTATTATATTTTTAAAATTTGTTTTTAACAAAAAATTTACAAAAA
*
19925861 TTAATTTATTATATTTTTAAAATTTGTTTTTATATAAAAAATTTA-AAAAA
1 TTAATTTATTATATTTTTAAAATTTGTTTTTA-ACAAAAAATTTACAAAAA
19925911 TTAAT
1 TTAAT
19925916 ATGAGTGGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 39 0.85
51 7 0.15
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (50 bp):
TTAATTTATTATATTTTTAAAATTTGTTTTTAACAAAAAATTTACAAAAA
Found at i:19926899 original size:21 final size:20
Alignment explanation
Indices: 19926873--19926912 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19926863 GTAAAAAATG
*
19926873 TTTATTGTATAAAAATGAAAC
1 TTTATT-TACAAAAATGAAAC
*
19926894 TTTATTTCCAAAAATGAAA
1 TTTATTTACAAAAATGAAA
19926913 ATATGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (20 bp):
TTTATTTACAAAAATGAAAC
Found at i:19927620 original size:16 final size:16
Alignment explanation
Indices: 19927595--19927625 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19927585 TATACAAAAA
*
19927595 AAAACTAAATTCAATC
1 AAAACGAAATTCAATC
19927611 AAAACGAAATTCAAT
1 AAAACGAAATTCAAT
19927626 TATATAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAACGAAATTCAATC
Found at i:19928975 original size:17 final size:19
Alignment explanation
Indices: 19928955--19928992 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
19928945 AAGTGAATTG
19928955 AAATTGC-GAAATT-AAAT
1 AAATTGCAGAAATTGAAAT
19928972 AAATTGCAGAAATTGAAAT
1 AAATTGCAGAAATTGAAAT
19928991 AA
1 AA
19928993 GAAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.26
Consensus pattern (19 bp):
AAATTGCAGAAATTGAAAT
Found at i:19929711 original size:20 final size:20
Alignment explanation
Indices: 19929688--19929735 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
19929678 TAAATTCTAA
*
19929688 AAAGATAAATACAA-TTAATT
1 AAAGATAAATA-AAGATAATT
19929708 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
19929728 AAA-ATAAA
1 AAAGATAAA
19929736 ATCCTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:19929746 original size:19 final size:18
Alignment explanation
Indices: 19929722--19929765 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
19929712 ATAAATAAAG
19929722 ATAATTAAAATAAAATCCTA
1 ATAATTAAAAT--AATCCTA
*
19929742 A-AATTTAAATAATCCTA
1 ATAATTAAAATAATCCTA
19929759 ATAATTA
1 ATAATTA
19929766 TCCTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 8 0.38
20 1 0.05
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATTAAAATAATCCTA
Found at i:19929780 original size:15 final size:15
Alignment explanation
Indices: 19929760--19929789 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19929750 ATAATCCTAA
19929760 TAATTATCCTAATAT
1 TAATTATCCTAATAT
19929775 TAATTATCCTAATAT
1 TAATTATCCTAATAT
19929790 AAATAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:19932727 original size:21 final size:21
Alignment explanation
Indices: 19932701--19932743 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
19932691 ATTTAACCAT
*
19932701 AAACCAGTATAAATACGAAAA
1 AAACCAATATAAATACGAAAA
19932722 AAACCAATATAAATACGAAAA
1 AAACCAATATAAATACGAAAA
19932743 A
1 A
19932744 GCTCTGAATA
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:0.65, C:0.14, G:0.07, T:0.14
Consensus pattern (21 bp):
AAACCAATATAAATACGAAAA
Found at i:19941923 original size:28 final size:30
Alignment explanation
Indices: 19941891--19941947 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
19941881 AATAGGAGTT
* *
19941891 AATTTTAATT-TTTTAAA-TATAAGGATTA
1 AATTTCAATTGTTGTAAAGTATAAGGATTA
*
19941919 AATTTCAATTGTTGTAAAGTATAATGATT
1 AATTTCAATTGTTGTAAAGTATAAGGATT
19941948 GATAACATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.38
29 6 0.25
30 9 0.38
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (30 bp):
AATTTCAATTGTTGTAAAGTATAAGGATTA
Found at i:19942982 original size:22 final size:22
Alignment explanation
Indices: 19942957--19943001 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19942947 TTAAAAGGTT
* *
19942957 TAAAAAAGTTGCCAAAATTATA
1 TAAAAAAGTTACCAAAATAATA
*
19942979 TAAAGAAGTTACCAAAATAATA
1 TAAAAAAGTTACCAAAATAATA
19943001 T
1 T
19943002 CGTGCGGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (22 bp):
TAAAAAAGTTACCAAAATAATA
Found at i:19949485 original size:24 final size:24
Alignment explanation
Indices: 19949451--19949518 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
19949441 TATATAACGG
*
19949451 GAAGCTTATAAGAGCCATAATCAA
1 GAAGCTCATAAGAGCCATAATCAA
* *
19949475 GAAGTTCATAAAGAACCAT-ATCAA
1 GAAGCTCAT-AAGAGCCATAATCAA
*
19949499 GAAGCTCACAAAGAGCCATA
1 GAAGCTCA-TAAGAGCCATA
19949519 TAATGGGAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 27 0.77
25 8 0.23
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCATAATCAA
Found at i:19949519 original size:24 final size:24
Alignment explanation
Indices: 19949460--19949519 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
19949450 GGAAGCTTAT
* *
19949460 AAGAGCCATAATCAAGAAGTTCATA
1 AAGAGCCAT-ATCAAGAAGCTCACA
*
19949485 AAGAACCATATCAAGAAGCTCACA
1 AAGAGCCATATCAAGAAGCTCACA
19949509 AAGAGCCATAT
1 AAGAGCCATAT
19949520 AATGGGAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 23 0.74
25 8 0.26
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (24 bp):
AAGAGCCATATCAAGAAGCTCACA
Found at i:19960326 original size:44 final size:44
Alignment explanation
Indices: 19960259--19960835 Score: 498
Period size: 44 Copynumber: 13.1 Consensus size: 44
19960249 CGCCATTGTC
* * *
19960259 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAA
1 GATCTGC-ATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
* * * * *
19960304 GATCTGCATCGTCGATCCACTTC-CTACCAATATAGGAAGATAG
1 GATCTGCATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
* * *
19960347 GATCTGC-TACATTCGATCTACTTCA-CGCCAATACATGAAGACAA
1 GATCTGCAT-C-TTCGATCTACTTCACCACCAATATAGGAAGACAA
* * *
19960391 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGC-ATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
* * * *
19960436 GATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGATAG
1 GATCTGCATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
* * *
19960479 GATCTGC-TACATTCGATCTACTTCA-CGCCAATACATGAAGACAA
1 GATCTGCAT-C-TTCGATCTACTTCACCACCAATATAGGAAGACAA
* * *
19960523 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGC-ATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
* * * *
19960568 GATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGATAG
1 GATCTGCATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
* * *
19960611 GATCTGC-TACATTCGATCTACTTCA-CGCCAATACATGAAGACAA
1 GATCTGCAT-C-TTCGATCTACTTCACCACCAATATAGGAAGACAA
** * * * *
19960655 GATCTGTTTTCTTCGATCCACTTC-CTACCAATATAGGAAGATAG
1 GATCTG-CATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
** * *
19960699 GATCTGCTATCTTCGATCTACTTCA-TGCCAATACATGAAGACAA
1 GATCTGC-ATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
* * * *
19960743 GATCTGCTTTCTTCGATCTACTTC-CTACCAATATAGGAAGATAG
1 GATCTGC-ATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
* * *
19960787 GATCTGC-TACATTCGATCTACTTCA-CGCCAATACATGAAGACAA
1 GATCTGCAT-C-TTCGATCTACTTCACCACCAATATAGGAAGACAA
19960831 GATCT
1 GATCT
19960836 ACTTTAATGA
Statistics
Matches: 428, Mismatches: 80, Indels: 49
0.77 0.14 0.09
Matches are distributed among these distances:
42 4 0.01
43 72 0.17
44 295 0.69
45 54 0.13
46 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (44 bp):
GATCTGCATCTTCGATCTACTTCACCACCAATATAGGAAGACAA
Found at i:19960408 original size:88 final size:87
Alignment explanation
Indices: 19960259--19960840 Score: 672
Period size: 88 Copynumber: 6.6 Consensus size: 87
19960249 CGCCATTGTC
* * * *** * *
19960259 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC-ATCGTCGATCCA
1 GATCTGC-TACTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCCA
19960323 CTTCCTACCAATATAGGAAGATAG
64 CTTCCTACCAATATAGGAAGATAG
*
19960347 GATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
1 GATCTGCTAC-TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCCAC
* * * *
19960412 TTCGCCACCAATATGGGAAGACAA
65 TTC-CTACCAATATAGGAAGATAG
* * * * * * * *
19960436 GATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGATAGGATCTGC-TACATTCGATCT
1 GATCTGCTA-CTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTC-TTCGATCC
* * * * *
19960498 ACTTCAC-GCCAATACATGAAGACAA
63 ACTTC-CTACCAATATAGGAAGATAG
* * * *** *
19960523 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCA
1 GATCTGC-TACTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCCA
19960587 CTTCCTACCAATATAGGAAGATAG
64 CTTCCTACCAATATAGGAAGATAG
*
19960611 GATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCCAC
1 GATCTGCTAC-TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCCAC
19960676 TTCCTACCAATATAGGAAGATAG
65 TTCCTACCAATATAGGAAGATAG
* *
19960699 GATCTGCTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
1 GATCTGCTA-CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCCAC
19960764 TTCCTACCAATATAGGAAGATAG
65 TTCCTACCAATATAGGAAGATAG
*
19960787 GATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTT
1 GATCTGCTAC-TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
19960841 AATGACTTTA
Statistics
Matches: 428, Mismatches: 51, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
87 72 0.17
88 307 0.72
89 48 0.11
90 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (87 bp):
GATCTGCTACTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCCACT
TCCTACCAATATAGGAAGATAG
Found at i:19960496 original size:132 final size:132
Alignment explanation
Indices: 19960259--19960810 Score: 833
Period size: 132 Copynumber: 4.2 Consensus size: 132
19960249 CGCCATTGTC
* * *
19960259 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCGTCGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
19960324 TTCCTACCAATATAGGAAGATAGGATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTACCAATATAGGAAGATAGGATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGAC
19960389 AA
131 AA
19960391 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
19960456 TTCCTACCAATATAGGAAGATAGGATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTACCAATATAGGAAGATAGGATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGAC
19960521 AA
131 AA
19960523 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
19960588 TTCCTACCAATATAGGAAGATAGGATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTACCAATATAGGAAGATAGGATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGAC
19960653 AA
131 AA
* * * * * * *
19960655 GATCTGTTTTCTTCGATCCACTTC-CTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTA
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCA
* * * * * * * * * *
19960719 CTTCATGCCAATACATGAAGACAAGATCTGCTTTC-TTCGATCTACTTC-CTACCAATATAGGAA
65 CTTCCTACCAATATAGGAAGATAGGATCTGC-TACATTCGATCTACTTCAC-GCCAATACATGAA
* *
19960782 GATAG
128 GACAA
*
19960787 GATCTGC-TACATTCGATCTACTTC
1 GATCTGCTTTC-TTCGATCTACTTC
19960811 ACGCCAATAC
Statistics
Matches: 391, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
131 26 0.07
132 363 0.93
133 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (132 bp):
GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
TTCCTACCAATATAGGAAGATAGGATCTGCTACATTCGATCTACTTCACGCCAATACATGAAGAC
AA
Found at i:19976535 original size:129 final size:129
Alignment explanation
Indices: 19976305--19976562 Score: 489
Period size: 129 Copynumber: 2.0 Consensus size: 129
19976295 GTACGACCCC
*
19976305 TAATTATCTCTGGTTAATTTATAATGAATTTCTAAAGTCGGAGTAGGGAATCCAGAAACCGTTCT
1 TAATTATCTCTGGTTAATTTATAATGAATTTCTAAAGTCGGAGCAGGGAATCCAGAAACCGTTCT
*
19976370 GGCCCTGTCCCACAAAAATCTGATTATCTCTTAATATACTGCCCATATGATCTTTTCGTTACTT
66 GGCCCTGTCCCACAAAAATCTGATTATCTCTTAATATAATGCCCATATGATCTTTTCGTTACTT
*
19976434 TAATTATCTCTGGTTAATTTATAATGAATTTCTAAAGTCGGAGCAGGGAATCCAGAAATCGTTCT
1 TAATTATCTCTGGTTAATTTATAATGAATTTCTAAAGTCGGAGCAGGGAATCCAGAAACCGTTCT
19976499 GGCCCTGTCCCACAAAAATCTGATTATCTCTTAATATAATGCCCATATGATCTTTTCGTTACTT
66 GGCCCTGTCCCACAAAAATCTGATTATCTCTTAATATAATGCCCATATGATCTTTTCGTTACTT
19976563 CCTCATGAAA
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 126 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (129 bp):
TAATTATCTCTGGTTAATTTATAATGAATTTCTAAAGTCGGAGCAGGGAATCCAGAAACCGTTCT
GGCCCTGTCCCACAAAAATCTGATTATCTCTTAATATAATGCCCATATGATCTTTTCGTTACTT
Found at i:19977208 original size:79 final size:79
Alignment explanation
Indices: 19977075--19977232 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
19977065 AACCTATCGA
*
19977075 TTCAATTTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAGGACATTGAAGCATTT
1 TTCAATTTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAAGACATTGAAGCATTT
19977140 TCATAAATCAATTT
66 TCATAAATCAATTT
19977154 TTCAATTTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAAGACATTGAAGCATTT
1 TTCAATTTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAAGACATTGAAGCATTT
19977219 TCATAAATCAATTT
66 TCATAAATCAATTT
19977233 ATTTTCGTTA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (79 bp):
TTCAATTTCATATCAATTCATGCATTCACATTCCATATACTCATCAATAAGACATTGAAGCATTT
TCATAAATCAATTT
Found at i:19977503 original size:27 final size:27
Alignment explanation
Indices: 19977473--19977646 Score: 179
Period size: 27 Copynumber: 6.4 Consensus size: 27
19977463 TGAGTCCGCT
* * *
19977473 CACTCAGTGCTATATAATCAACTCGCA
1 CACTTAGTGCTACATAGTCAACTCGCA
** * *
19977500 CACTTAGTGCTATGTAATCAAATCGCA
1 CACTTAGTGCTACATAGTCAACTCGCA
19977527 CACTTAGTGCTACATAGTCAAACTCGCA
1 CACTTAGTGCTACATAGTC-AACTCGCA
** *
19977555 CACTTAGTGCCGCATGGTCAACTCGCA
1 CACTTAGTGCTACATAGTCAACTCGCA
* **
19977582 CACTTAGTGC-ATCATATTCATTTCGCA
1 CACTTAGTGCTA-CATAGTCAACTCGCA
* * *
19977609 CACTTAGTGCAACATAGTTAAATCGCA
1 CACTTAGTGCTACATAGTCAACTCGCA
19977636 CACTTAGTGCT
1 CACTTAGTGCT
19977647 GTACAATTTA
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 100 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
CACTTAGTGCTACATAGTCAACTCGCA
Found at i:19977615 original size:82 final size:81
Alignment explanation
Indices: 19977490--19977645 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19977480 TGCTATATAA
* *
19977490 TCAACTCGCACACTTAGTGCTATGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTATATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
19977555 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* ** *
19977572 TCAACTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTTAAATCGCA
1 TCAACTCGCACACTTAGTGCTAT-ATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
19977636 CACTTAGTGC
65 CACTTAGTGC
19977646 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 17 0.25
82 50 0.75
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTATATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:19978146 original size:12 final size:12
Alignment explanation
Indices: 19978129--19978154 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19978119 ATGGCATACT
19978129 TATGTATATATA
1 TATGTATATATA
19978141 TATGTATATATA
1 TATGTATATATA
19978153 TA
1 TA
19978155 CTTCGGAATG
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:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:19984588 original size:49 final size:49
Alignment explanation
Indices: 19984462--19985460 Score: 1833
Period size: 49 Copynumber: 20.6 Consensus size: 49
19984452 CCCTTCGGGA
* * * * *
19984462 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984509 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984556 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984605 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984654 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984703 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984752 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984801 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984850 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984899 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984948 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19984997 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19985046 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19985095 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19985144 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19985193 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19985242 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19985291 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTATCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA--GGC
**
19985340 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAAAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19985387 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19985434 CTTATCAC--ATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
19985461 TATTCAAATA
Statistics
Matches: 937, Mismatches: 9, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
46 1 0.00
47 156 0.17
49 780 0.83
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19987607 original size:161 final size:161
Alignment explanation
Indices: 19987342--19987662 Score: 579
Period size: 161 Copynumber: 2.0 Consensus size: 161
19987332 CATTGTTGCT
*
19987342 ATTATTGTCTTCTTCAAGCATCCACAAAGAGATTTCTAAGCGTTTCTTAACCCTATTCTTATGCT
1 ATTATTGTCTTCTTCAAGCATCCACAAAGAGATTTCTAAGCGTTTCTTAACCCTATTCTCATGCT
* *
19987407 TATTTTGATGTATGATTTGAGTATATGTTTGGTTGTTGTGTGCATGAAAATGATGATTTGTAACT
66 TATTTTAATGTATGATTTAAGTATATGTTTGGTTGTTGTGTGCATGAAAATGATGATTTGTAACT
19987472 AAATTTATCGTGGTTGATTGATGTAAATATA
131 AAATTTATCGTGGTTGATTGATGTAAATATA
* * *
19987503 ATTATTGTCTTCTTCAAGCATCCATAAAGAGATTTCTAAGCTTTTGTTAACCCTATTCTCATGCT
1 ATTATTGTCTTCTTCAAGCATCCACAAAGAGATTTCTAAGCGTTTCTTAACCCTATTCTCATGCT
19987568 TATTTTAATGTATGATTTAAGTATATGTTTGGTTGTTGTGTGCATGAAAATGATGATTTGTAACT
66 TATTTTAATGTATGATTTAAGTATATGTTTGGTTGTTGTGTGCATGAAAATGATGATTTGTAACT
*
19987633 AAATTTATCGTGGTTGGTTGATGTAAATAT
131 AAATTTATCGTGGTTGATTGATGTAAATAT
19987663 TATTTGGTTA
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
161 153 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (161 bp):
ATTATTGTCTTCTTCAAGCATCCACAAAGAGATTTCTAAGCGTTTCTTAACCCTATTCTCATGCT
TATTTTAATGTATGATTTAAGTATATGTTTGGTTGTTGTGTGCATGAAAATGATGATTTGTAACT
AAATTTATCGTGGTTGATTGATGTAAATATA
Found at i:19990911 original size:43 final size:43
Alignment explanation
Indices: 19990847--19990943 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 43
19990837 CGTTTTTAAG
*
19990847 CGCCGCTAAAGACCAGAACTTTTAGCGACGCTTTTCTAAAAAA
1 CGCCGCTAAAGACCAGAACTTTTAGCGACGCTTTTCCAAAAAA
* * * * ***
19990890 CGCCGCTAAAGTCCAGGACTTTTTGCGGCGCTTTTCCCGCAAA
1 CGCCGCTAAAGACCAGAACTTTTAGCGACGCTTTTCCAAAAAA
19990933 CGCCGCTAAAG
1 CGCCGCTAAAG
19990944 GTCATAAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (43 bp):
CGCCGCTAAAGACCAGAACTTTTAGCGACGCTTTTCCAAAAAA
Found at i:19994727 original size:16 final size:16
Alignment explanation
Indices: 19994706--19994737 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19994696 AAATATTAAA
*
19994706 TTTTTAAGTTTTTTAT
1 TTTTTAAATTTTTTAT
19994722 TTTTTAAATTTTTTAT
1 TTTTTAAATTTTTTAT
19994738 GAAAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTAAATTTTTTAT
Found at i:19994763 original size:21 final size:21
Alignment explanation
Indices: 19994722--19994764 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
19994712 AGTTTTTTAT
**
19994722 TTTTTAAATTTTTTATGAAAA
1 TTTTTAAATTTCATATGAAAA
19994743 TTTTTAAATTATCATAT-AAAA
1 TTTTTAAATT-TCATATGAAAA
19994764 T
1 T
19994765 ACAAAAGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTTAAATTTCATATGAAAA
Found at i:19995354 original size:7 final size:7
Alignment explanation
Indices: 19995342--19995412 Score: 70
Period size: 7 Copynumber: 10.0 Consensus size: 7
19995332 GTTAACTAAT
19995342 CTAAACC
1 CTAAACC
19995349 CTAAACTC
1 CTAAAC-C
*
19995357 CTAATCC
1 CTAAACC
*
19995364 CTAAACA
1 CTAAACC
*
19995371 TTAAACC
1 CTAAACC
*
19995378 CTAAAAC
1 CTAAACC
*
19995385 ATAAACC
1 CTAAACC
*
19995392 CTGAACC
1 CTAAACC
*
19995399 CTGAACC
1 CTAAACC
19995406 CTAAACC
1 CTAAACC
19995413 ATGAACCATG
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
7 45 0.88
8 6 0.12
ACGTcount: A:0.42, C:0.37, G:0.03, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:19995381 original size:14 final size:14
Alignment explanation
Indices: 19995343--19995393 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
19995333 TTAACTAATC
19995343 TAAACCCTAAAC-T
1 TAAACCCTAAACAT
*
19995356 CCTAATCCCTAAACAT
1 --TAAACCCTAAACAT
19995372 TAAACCCTAAAACA-
1 TAAACCCT-AAACAT
19995386 TAAACCCT
1 TAAACCCT
19995394 GAACCCTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 15 0.47
15 16 0.50
16 1 0.03
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACAT
Found at i:19995398 original size:21 final size:21
Alignment explanation
Indices: 19995374--19995419 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
19995364 CTAAACATTA
*
19995374 AACCCTAAAACATAAACCCTG
1 AACCCTAAAACATAAACCATG
* * *
19995395 AACCCTGAACCCTAAACCATG
1 AACCCTAAAACATAAACCATG
19995416 AACC
1 AACC
19995420 ATGAACCCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.37, G:0.07, T:0.13
Consensus pattern (21 bp):
AACCCTAAAACATAAACCATG
Found at i:19995419 original size:7 final size:7
Alignment explanation
Indices: 19995388--19995427 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
19995378 CTAAAACATA
19995388 AACCCTG
1 AACCCTG
19995395 AACCCTG
1 AACCCTG
*
19995402 AACCCTA
1 AACCCTG
*
19995409 AACCATG
1 AACCCTG
*
19995416 AACCATG
1 AACCCTG
19995423 AACCC
1 AACCC
19995428 CTAACCCCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (7 bp):
AACCCTG
Found at i:19995433 original size:21 final size:21
Alignment explanation
Indices: 19995386--19995427 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19995376 CCCTAAAACA
* *
19995386 TAAACCCTGAACCCTGAACCC
1 TAAACCATGAACCATGAACCC
19995407 TAAACCATGAACCATGAACCC
1 TAAACCATGAACCATGAACCC
19995428 CTAACCCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.14
Consensus pattern (21 bp):
TAAACCATGAACCATGAACCC
Found at i:19995602 original size:41 final size:40
Alignment explanation
Indices: 19995545--19995681 Score: 175
Period size: 41 Copynumber: 3.4 Consensus size: 40
19995535 CTAGTTGGTA
*
19995545 TCTTTAGCGGCATTTCACCAAAAGCGCCGCTAATGCTCTGG
1 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCT-G
19995586 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTG
1 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTG
* * * * * * *
19995626 TTTTTAGTGGCGTTTTAACAAAAAACGCCGCTATTGCTCAG
1 TCTTTAGCGGCG-TTTCACCAAAAGCGCCGCTAATGCTCTG
*
19995667 TTTTTAGCGGCGTTT
1 TCTTTAGCGGCGTTT
19995682 TTGTCAAAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
40 14 0.16
41 72 0.84
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (40 bp):
TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTG
Found at i:19995682 original size:41 final size:41
Alignment explanation
Indices: 19995547--19995699 Score: 168
Period size: 41 Copynumber: 3.8 Consensus size: 41
19995537 AGTTGGTATC
* * *
19995547 TTTAGCGGC-ATTTCACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTCACCAAAAGCGCCGCTAATGCTC-AGTT
*
19995588 TTTAGCGGCG-TTTCACCAAAAGCGCCGCTAATGCTCTGTT
1 TTTAGCGGCGTTTTCACCAAAAGCGCCGCTAATGCTCAGTT
* * * * *
19995628 TTTAGTGGCGTTTTAACAAAAAACGCCGCTATTGCTCAGTT
1 TTTAGCGGCGTTTTCACCAAAAGCGCCGCTAATGCTCAGTT
***
19995669 TTTAGCGGCGTTTTTGTCAAAA-CGCCGCTAA
1 TTTAGCGGCGTTTTCACCAAAAGCGCCGCTAA
19995700 AGCCCTATTT
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
40 19 0.20
41 77 0.80
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTCACCAAAAGCGCCGCTAATGCTCAGTT
Found at i:20009228 original size:61 final size:60
Alignment explanation
Indices: 20009156--20009283 Score: 136
Period size: 61 Copynumber: 2.1 Consensus size: 60
20009146 GTATAATAAG
* * * * *
20009156 AATTTTT-AAAAATTTGAAGAGTTTAATTCAAATTTTTTAAAAACTTCAAGAGAAAAAT-A-
1 AATTTTTAAAAAAGTTGAACA-CTTAATTAAAATTTTCTAAAAACTTCAA-AGAAAAATCAT
* *
20009215 AATTTTTACAAAAAAGTTGAACACTTAATTAAAATTTTCTAAAAATTTCAATGAAAAATCAT
1 AATTTTT--AAAAAAGTTGAACACTTAATTAAAATTTTCTAAAAACTTCAAAGAAAAATCAT
20009277 AATTTTT
1 AATTTTT
20009284 CAATTTCTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
59 7 0.12
60 7 0.12
61 25 0.44
62 18 0.32
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.38
Consensus pattern (60 bp):
AATTTTTAAAAAAGTTGAACACTTAATTAAAATTTTCTAAAAACTTCAAAGAAAAATCAT
Found at i:20011319 original size:70 final size:69
Alignment explanation
Indices: 20011245--20011390 Score: 152
Period size: 71 Copynumber: 2.1 Consensus size: 69
20011235 GAACTCCAGT
* * * * * *
20011245 CTAAATAATT-TTACTTTTTTTTAACT-TTTAGTATTAGAATTAAATTGAAAACTTTTGTAAATA
1 CTAAATAATTATTA-TTATTATT-ACTATTTAGAATTAGAACTAAATGGAAAA-TTTTATAAATA
*
20011308 TTTAGGG
63 TTGAGGG
* * *
20011315 CTAAATTTATTATTATTATTATTATTATTTAGAATTAGAACTAGATGGAAAATTTTATAAATATT
1 CTAAA-TAATTATTATTATTATTACTATTTAGAATTAGAACTAAATGGAAAATTTTATAAATATT
20011380 GAGGG
65 GAGGG
20011385 CTAAAT
1 CTAAAT
20011391 TTGTTGAATT
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
69 1 0.02
70 28 0.44
71 31 0.49
72 3 0.05
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (69 bp):
CTAAATAATTATTATTATTATTACTATTTAGAATTAGAACTAAATGGAAAATTTTATAAATATTG
AGGG
Found at i:20012302 original size:7 final size:7
Alignment explanation
Indices: 20012290--20012315 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20012280 TAATTATAAA
20012290 AAAAAAC
1 AAAAAAC
20012297 AAAAAAC
1 AAAAAAC
20012304 AAAAAAC
1 AAAAAAC
20012311 AAAAA
1 AAAAA
20012316 TCTATCTTCT
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:20029638 original size:38 final size:38
Alignment explanation
Indices: 20029596--20029671 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
20029586 TTGTTTCTTA
*
20029596 ACTCTTTCATTTCCCGTGCAAGAATTTTGATTGGTTTT
1 ACTCTTTCATTTCCCGTGCAAGAATTTTGATCGGTTTT
*
20029634 ACTCTTTCGTTTCCCGTGCAAGAATTTTGATCGGTTTT
1 ACTCTTTCATTTCCCGTGCAAGAATTTTGATCGGTTTT
20029672 TCACTGTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (38 bp):
ACTCTTTCATTTCCCGTGCAAGAATTTTGATCGGTTTT
Found at i:20035970 original size:25 final size:24
Alignment explanation
Indices: 20035932--20035984 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
20035922 AAGTTCAAGT
*
20035932 GAGCCATATCAGGAAGCTCACAAA
1 GAGCCATAGCAGGAAGCTCACAAA
* * *
20035956 GAGCCTATAGCAGGACGCTTATAAA
1 GAGCC-ATAGCAGGAAGCTCACAAA
20035981 GAGC
1 GAGC
20035985 TACGTTTGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (24 bp):
GAGCCATAGCAGGAAGCTCACAAA
Found at i:20036339 original size:20 final size:20
Alignment explanation
Indices: 20036290--20036339 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
20036280 ACATGACAAT
20036290 CATACATTTCAAAATCATAA
1 CATACATTTCAAAATCATAA
*
20036310 CATTCAATTT-AAACAT-ATAAA
1 CATAC-ATTTCAAA-ATCAT-AA
20036331 CATACATTT
1 CATACATTT
20036340 TAGTTACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (20 bp):
CATACATTTCAAAATCATAA
Found at i:20036341 original size:21 final size:20
Alignment explanation
Indices: 20036290--20036341 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
20036280 ACATGACAAT
*
20036290 CATACATTTCAAAATCATAA
1 CATACATTTTAAAATCATAA
* *
20036310 CATTCAATTTAAACAT-ATAAA
1 CATACATTTTAAA-ATCAT-AA
20036331 CATACATTTTA
1 CATACATTTTA
20036342 GTTACACAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (20 bp):
CATACATTTTAAAATCATAA
Found at i:20043522 original size:27 final size:27
Alignment explanation
Indices: 20043484--20043570 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
20043474 GCGAGGCTGC
20043484 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGTCACCAGATA
20043511 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGTCACCAGATA
* * * *
20043538 CAGATATTGTGGCTAGGCCACCAGA-A
1 CAGATATTGTGACGAAGTCACCAGATA
20043564 CAGATAT
1 CAGATAT
20043571 ATATATATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
26 8 0.14
27 48 0.86
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (27 bp):
CAGATATTGTGACGAAGTCACCAGATA
Found at i:20043838 original size:22 final size:18
Alignment explanation
Indices: 20043796--20043832 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
20043786 ACCCTAGGGG
20043796 TAAAATTGTAATTTTGCA
1 TAAAATTGTAATTTTGCA
20043814 TAAAATTGTAATTTTGCA
1 TAAAATTGTAATTTTGCA
20043832 T
1 T
20043833 GCATAAGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (18 bp):
TAAAATTGTAATTTTGCA
Found at i:20045698 original size:23 final size:22
Alignment explanation
Indices: 20045670--20045716 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
20045660 AATTATAAAT
*
20045670 TTATAATTGTAAACATCTA-TCAA
1 TTATAATT-CAAA-ATCTAGTCAA
20045693 TTATAATTCAAAATCTAGTCAA
1 TTATAATTCAAAATCTAGTCAA
20045715 TT
1 TT
20045717 TTATGAGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 9 0.41
23 8 0.36
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (22 bp):
TTATAATTCAAAATCTAGTCAA
Found at i:20050382 original size:27 final size:27
Alignment explanation
Indices: 20050325--20050397 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
20050315 ATATGCCATG
*
20050325 AAGGTGTTCC-TTTCCATAGATCACCACA
1 AAGGT-TTCCATTT-CATAGATCACCAAA
**
20050353 AAGGTTTCCATTTCATAGATTGCCAAA
1 AAGGTTTCCATTTCATAGATCACCAAA
* * *
20050380 AAGGCTTCGATTGCATAG
1 AAGGTTTCCATTTCATAG
20050398 GTTATCACAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 30 0.79
28 8 0.21
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (27 bp):
AAGGTTTCCATTTCATAGATCACCAAA
Found at i:20050963 original size:15 final size:16
Alignment explanation
Indices: 20050943--20050979 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
20050933 AATTGGAAAG
20050943 ATGAAAAGTT-ATTAA
1 ATGAAAAGTTAATTAA
*
20050958 ATG-AAATTTAATTAA
1 ATGAAAAGTTAATTAA
20050973 ATGAAAA
1 ATGAAAA
20050980 ATAAAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 11 0.58
16 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (16 bp):
ATGAAAAGTTAATTAA
Found at i:20058628 original size:48 final size:48
Alignment explanation
Indices: 20058501--20058638 Score: 163
Period size: 49 Copynumber: 2.9 Consensus size: 48
20058491 TGAAATCGAG
* *
20058501 GCCGACACCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATTT
1 GCCGATACCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATAT
* * * *
20058549 GTGCGATGCCATGTCCCAGGCATGGTCTTACACTAGCTCTCGTC-TCA-AT
1 G-CCGATACCATGTCCCAGACATGGTCTTACACTAGCTCTC-ACAT-ATAT
* *
20058598 GCCGATACCATGTCCTAGACATGGTCTTACACTGGCTCTCA
1 GCCGATACCATGTCCCAGACATGGTCTTACACTAGCTCTCA
20058639 TAGACATGTC
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
48 35 0.47
49 38 0.51
50 2 0.03
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.28
Consensus pattern (48 bp):
GCCGATACCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATAT
Done.