Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_pilon, whole genome shotgun sequence
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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 51
Found at i:5805508 original size:28 final size:28
Alignment explanation
Indices: 5805476--5805532 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
5805466 TTTGGTTTCT
*
5805476 GTTTGCTCCGATGAACCCGACTTCGATG
1 GTTTGCTCCGATGAACCCAACTTCGATG
5805504 GTTTGCTCCGATGAACCCAACTTCGATG
1 GTTTGCTCCGATGAACCCAACTTCGATG
5805532 G
1 G
5805533 GAAGCTCCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (28 bp):
GTTTGCTCCGATGAACCCAACTTCGATG
Found at i:5805539 original size:28 final size:28
Alignment explanation
Indices: 5805480--5805545 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
5805470 GTTTCTGTTT
* ***
5805480 GCTCCGATGAACCCGACTTCGATGGTTT
1 GCTCCGATGAACCCAACTTCGATGGGAA
5805508 GCTCCGATGAACCCAACTTCGATGGGAA
1 GCTCCGATGAACCCAACTTCGATGGGAA
5805536 GCTCCGATGA
1 GCTCCGATGA
5805546 CTCACAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.23
Consensus pattern (28 bp):
GCTCCGATGAACCCAACTTCGATGGGAA
Found at i:5808465 original size:20 final size:22
Alignment explanation
Indices: 5808440--5808479 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5808430 AAACCTAAAG
*
5808440 ACAAA-TAAA-TTGTATAATGC
1 ACAAATTAAACTTATATAATGC
5808460 ACAAATTAAACTTATATAAT
1 ACAAATTAAACTTATATAAT
5808480 AAAGTTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 4 0.24
22 8 0.47
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (22 bp):
ACAAATTAAACTTATATAATGC
Found at i:5809920 original size:3 final size:3
Alignment explanation
Indices: 5809912--5809947 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5809902 AATTTAATTA
5809912 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5809948 GATTAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5811515 original size:75 final size:72
Alignment explanation
Indices: 5811409--5811636 Score: 269
Period size: 71 Copynumber: 3.1 Consensus size: 72
5811399 TATGATCAGT
* * * *
5811409 AAGTATCGATACTTTTCCACAAGTATAGATACTTACGAATTTAAAAAAATATATATGAAAAATGA
1 AAGTATCAATATTTTTCCACAAATATAGATACTTTCGAATTTAAAAAAA-A-ATAT-AAAAATGA
*
5811474 GAAGGCTACA
63 GAATGCTACA
* * **
5811484 AAGTATCAATATTTTTCCACAAATATCGATACTTTCAAATTTTTAAAAAAATA-AAAAATGAGAA
1 AAGTATCAATATTTTTCCACAAATATAGATACTTTCGAATTTAAAAAAAAATATAAAAATGAGAA
5811548 TGCTACA
66 TGCTACA
* * * * *
5811555 AAGTTTCAATATTTTTCTACAAATATAAATACTTTTGAATTTAAAAAAAAACATATAAAATGAGA
1 AAGTATCAATATTTTTCCACAAATATAGATACTTTCGAATTTAAAAAAAAATATA-AAAATGAGA
* *
5811620 ATGTTGCA
65 ATGCTACA
5811628 AAGTATCAA
1 AAGTATCAA
5811637 ACTTTTTTTA
Statistics
Matches: 130, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
71 61 0.47
72 1 0.01
73 26 0.20
74 1 0.01
75 41 0.32
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.32
Consensus pattern (72 bp):
AAGTATCAATATTTTTCCACAAATATAGATACTTTCGAATTTAAAAAAAAATATAAAAATGAGAA
TGCTACA
Found at i:5812049 original size:100 final size:92
Alignment explanation
Indices: 5811870--5812071 Score: 233
Period size: 100 Copynumber: 2.1 Consensus size: 92
5811860 TATCGATATT
* *
5811870 GTAATAATAATTACAACTTAACCGGTTAAAATAAAATACCTATTACGTTAAACTAGCTACTGTTT
1 GTAA-AATAATTACAACTTAACCGGTTAAAATAAAATACCTATTACGTTAAACTAACTACGGTTT
* * *
5811935 TTTTAAAGGTATAATAATAATGTAAGCG
65 GTTTAAAAGTATAATAATAATGTAAACG
* * **
5811963 GTAAAATATTTACAACTTAACTGGTTAAAATAAAATAGGCGATACTTATTATTTTAAACTAACTA
1 GTAAAATAATTACAACTTAACCGGTTAAAATAAAATA--C----C-TATTACGTTAAACTAACTA
5812028 CCGGTTTGTTTAAAAGTATAATAATAATGTAAACG
59 -CGGTTTGTTTAAAAGTATAATAATAATGTAAACG
*
5812063 ATAAAATAA
1 GTAAAATAA
5812072 AATAGGCGCT
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
92 31 0.34
93 4 0.04
94 1 0.01
98 1 0.01
99 16 0.18
100 37 0.41
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (92 bp):
GTAAAATAATTACAACTTAACCGGTTAAAATAAAATACCTATTACGTTAAACTAACTACGGTTTG
TTTAAAAGTATAATAATAATGTAAACG
Found at i:5812076 original size:76 final size:76
Alignment explanation
Indices: 5811988--5812146 Score: 203
Period size: 76 Copynumber: 2.1 Consensus size: 76
5811978 CTTAACTGGT
* ** *
5811988 TAAAATAAAATAGGCGATACTTATTATTTTAAACTAACTACCGGTTTGTTTAAA-AGTATAATAA
1 TAAAATAAAATAGGCGATACATATTACGTTAAACTAACTACCAGTTTGTTTAAAGA-TATAATAA
* *
5812052 TAATGTAAACGA
65 AAATGCAAACGA
* * *
5812064 TAAAATAAAATAGGCGCTACATATTACGTTAAACTAGCTATCAGTTTGTTTAAAGATATAATAAA
1 TAAAATAAAATAGGCGATACATATTACGTTAAACTAACTACCAGTTTGTTTAAAGATATAATAAA
* *
5812129 AATGCAAATGG
66 AATGCAAACGA
5812140 TAAAATA
1 TAAAATA
5812147 TTTACAACTT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
76 70 0.99
77 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (76 bp):
TAAAATAAAATAGGCGATACATATTACGTTAAACTAACTACCAGTTTGTTTAAAGATATAATAAA
AATGCAAACGA
Found at i:5812168 original size:176 final size:175
Alignment explanation
Indices: 5811910--5812231 Score: 482
Period size: 176 Copynumber: 1.8 Consensus size: 175
5811900 ATAAAATACC
* * * * * *
5811910 TATTACGTTAAACTAGCTACTGTTTTTTTAAAGGTATAATAATAATGTAAGCGGTAAAATATTTA
1 TATTACGTTAAACTAGCTACAGTTTGTTTAAAGATATAATAAAAATGCAAACGGTAAAATATTTA
** * ** *
5811975 CAACTTAACTGGTTAAAATAAAATAGGCGATACTTATTATTTTAAACTAACTACCGGTTTGTTTA
66 CAACTTAACCAGTTAAAATAAAATAGGCGATACCTATTACGTTAAACTAACTACCGGTTTATTTA
5812040 AAAGTATAATAATAATGTAAACGATAAAATAAAATAGGCGCTACA
131 AAAGTATAATAATAATGTAAACGATAAAATAAAATAGGCGCTACA
*
5812085 TATTACGTTAAACTAGCTATCAGTTTGTTTAAAGATATAATAAAAATGCAAATGGTAAAATATTT
1 TATTACGTTAAACTAGCTA-CAGTTTGTTTAAAGATATAATAAAAATGCAAACGGTAAAATATTT
* * *
5812150 ACAACTTAACCAGTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTAACTACTGTTTTATTT
65 ACAACTTAACCAGTTAAAATAAAATAGGCGATACCTATTACGTTAAACTAACTACCGGTTTATTT
*
5812215 AAAGGTATAATAATAAT
130 AAAAGTATAATAATAAT
5812232 AATAATAATA
Statistics
Matches: 129, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
175 19 0.15
176 110 0.85
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (175 bp):
TATTACGTTAAACTAGCTACAGTTTGTTTAAAGATATAATAAAAATGCAAACGGTAAAATATTTA
CAACTTAACCAGTTAAAATAAAATAGGCGATACCTATTACGTTAAACTAACTACCGGTTTATTTA
AAAGTATAATAATAATGTAAACGATAAAATAAAATAGGCGCTACA
Found at i:5812229 original size:3 final size:3
Alignment explanation
Indices: 5812221--5812276 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
5812211 ATTTAAAGGT
5812221 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5812269 ATA ATA AT
1 ATA ATA AT
5812277 GTAAACGGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5812291 original size:221 final size:221
Alignment explanation
Indices: 5812045--5812452 Score: 631
Period size: 221 Copynumber: 1.8 Consensus size: 221
5812035 GTTTAAAAGT
5812045 ATAATAATAATGTAAACGATAAAATAAAATAGGCGCTACATATTACGTTAAACTAGCTATCAG-T
1 ATAATAATAATGTAAACGATAAAATAAAATAGGCGCTACATATTACGTTAAACTAGCTAT-AGAT
* *
5812109 TTGTTTAAAGATATAATAAAAATGCAAATGGTAAAATATTTACAACTTAACCAGTTAAAATAAAA
65 TTGTTTAAAGATATAATAAAAATGCAAACGATAAAATATTTACAACTTAACCAGTTAAAATAAAA
* *
5812174 TAGGC-GCTACCTATTACGTTAAACTAACTACTGTTTTATTTAAAGGTATAATAATAATAATAAT
130 TA-GCTGCTACCTATTACGTTAAACTAACTACCGGTTTATTTAAAGGTATAATAATAATAATAAT
5812238 AATAATAATAATAATAATAATAATAATA
194 AATAATAATAATAATAATAATAATAATA
* * * * * *
5812266 ATAATAATAATGTAAACGGTAAAATAAAATAGGTGCTGCCTATTACGTTAAACTAGTTATTGATT
1 ATAATAATAATGTAAACGATAAAATAAAATAGGCGCTACATATTACGTTAAACTAGCTATAGATT
* * *
5812331 TGTTTAAAGATATAATAATAATGTAAACGATAAAATATTTACAACTTAACCGGTTAAAATAAAAT
66 TGTTTAAAGATATAATAAAAATGCAAACGATAAAATATTTACAACTTAACCAGTTAAAATAAAAT
* * * *
5812396 AGCTGTTACCTATTACGTTAAACTAATTACCGGTTTGTTTAGAGGTATAATAATAAT
131 AGCTGCTACCTATTACGTTAAACTAACTACCGGTTTATTTAAAGGTATAATAATAAT
5812453 GAAAACGGTA
Statistics
Matches: 168, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
220 3 0.02
221 165 0.98
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (221 bp):
ATAATAATAATGTAAACGATAAAATAAAATAGGCGCTACATATTACGTTAAACTAGCTATAGATT
TGTTTAAAGATATAATAAAAATGCAAACGATAAAATATTTACAACTTAACCAGTTAAAATAAAAT
AGCTGCTACCTATTACGTTAAACTAACTACCGGTTTATTTAAAGGTATAATAATAATAATAATAA
TAATAATAATAATAATAATAATAATA
Found at i:5812348 original size:100 final size:99
Alignment explanation
Indices: 5812242--5812552 Score: 337
Period size: 100 Copynumber: 3.1 Consensus size: 99
5812232 AATAATAATA
* * * * *
5812242 ATAATAATAATAATAATAATAATAATAATAATAA-TGTAAACGG-TAAAATAAAATAGGTGCTGC
1 ATAATAATAATAATAA-AATAA-AATATTTACAACT-TAACCGGTTAAAATAAAATAGGTGCTAC
* **
5812305 CTATTACGTTAAACTAGTTATTGATTTGTTTAAAGAT
63 CTATTACGTTAAACTAATTACCGATTTGTTTAAAGAT
* * *
5812342 ATAATAATAAT-GTAAACGATAAAATATTTACAACTTAACCGGTTAAAATAAAATAGCTGTTACC
1 ATAATAATAATAATAAA--ATAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACC
* * *
5812406 TATTACGTTAAACTAATTACCGGTTTGTTTAGAGGT
64 TATTACGTTAAACTAATTACCGATTTGTTTAAAGAT
**
5812442 ATAATAATAATGAA-AACGGTAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACC
1 ATAATAATAAT-AATAA-AATAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACC
**
5812506 TATTACGTTAAACTACCTACC-AGTTTGTTTAAATG-T
64 TATTACGTTAAACTAATTACCGA-TTTGTTTAAA-GAT
5812542 ATAATAATAAT
1 ATAATAATAAT
5812553 GTAAACGGTA
Statistics
Matches: 179, Mismatches: 23, Indels: 18
0.81 0.10 0.08
Matches are distributed among these distances:
98 1 0.01
99 17 0.09
100 158 0.88
101 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (99 bp):
ATAATAATAATAATAAAATAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACCTA
TTACGTTAAACTAATTACCGATTTGTTTAAAGAT
Found at i:5812553 original size:100 final size:99
Alignment explanation
Indices: 5812285--5812567 Score: 415
Period size: 100 Copynumber: 2.8 Consensus size: 99
5812275 ATGTAAACGG
* * **
5812285 TAAAATAAAATAGGTGCTGCCTATTACGTTAAACTAGTTA-TTGATTTGTTTAAAGATATAATAA
1 TAAAATAAAATAGGTGCTACCTATTACGTTAAACTAATTACCAG-TTTGTTTAAAG-TATAATAA
*
5812349 TAATGTAAACGATAAAATATTTACAACTTAACCGGT
64 TAATGTAAACGGTAAAATATTTACAACTTAACCGGT
* * * *
5812385 TAAAATAAAATAGCTGTTACCTATTACGTTAAACTAATTACCGGTTTGTTTAGAGGTATAATAAT
1 TAAAATAAAATAGGTGCTACCTATTACGTTAAACTAATTACCAGTTTGTTTA-AAGTATAATAAT
*
5812450 AATGAAAACGGTAAAATATTTACAACTTAACCGGT
65 AATGTAAACGGTAAAATATTTACAACTTAACCGGT
**
5812485 TAAAATAAAATAGGTGCTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAATGTATAATAAT
1 TAAAATAAAATAGGTGCTACCTATTACGTTAAACTAATTACCAGTTTGTTTAAA-GTATAATAAT
5812550 AATGTAAACGGTAAAATA
65 AATGTAAACGGTAAAATA
5812568 AAATAGATGC
Statistics
Matches: 164, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
99 1 0.01
100 160 0.98
101 3 0.02
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (99 bp):
TAAAATAAAATAGGTGCTACCTATTACGTTAAACTAATTACCAGTTTGTTTAAAGTATAATAATA
ATGTAAACGGTAAAATATTTACAACTTAACCGGT
Found at i:5812611 original size:76 final size:79
Alignment explanation
Indices: 5812485--5812646 Score: 258
Period size: 76 Copynumber: 2.1 Consensus size: 79
5812475 CTTAACCGGT
* * *
5812485 TAAAATAAAATAGGTGCTACCTATTACGTTAAACTACCTACCAGTTTGTTT-AAA-TGT-ATAAT
1 TAAAATAAAATAGATGCTACCTATTACGTTAAACTACCTACCAATTTGTTTAAAAGTATAATAAT
5812547 AATAATGTAAACGG
66 AATAATGTAAACGG
* *
5812561 TAAAATAAAATAGATGCTACGTATTACGTTAAACTATCTACCAATTTGTTTAAAAGTATAATAAT
1 TAAAATAAAATAGATGCTACCTATTACGTTAAACTACCTACCAATTTGTTTAAAAGTATAATAAT
5812626 AATAATGTAAACGG
66 AATAATGTAAACGG
5812640 TAAAATA
1 TAAAATA
5812647 TTTACAACTT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
76 47 0.60
77 3 0.04
78 2 0.03
79 26 0.33
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (79 bp):
TAAAATAAAATAGATGCTACCTATTACGTTAAACTACCTACCAATTTGTTTAAAAGTATAATAAT
AATAATGTAAACGG
Found at i:5812685 original size:179 final size:176
Alignment explanation
Indices: 5812385--5812746 Score: 539
Period size: 179 Copynumber: 2.0 Consensus size: 176
5812375 CTTAACCGGT
* * ** * *
5812385 TAAAATAAAATAGCTGTTACCTATTACGTTAAACTAATTACCGGTTTGTTTAGAGGTATAATAAT
1 TAAAATAAAATAGATGCTACCTATTACGTTAAACTAATTACCAATTTGTTTAAAGATATAATAAT
**
5812450 AATGAAAACGGTAAAATATTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACCTATTACGTT
66 AATGAAAACGGTAAAATATTTACAACTTAACCGGTTAAAATAAAATAGACGCTACCTATTACGTT
* *
5812515 AAACTACCTACC-AGTTTGTTTAAATGTATAATAATAATGTAAACGG
131 AAACTACCTACCGA-TTTGTTTAAAGGAATAATAATAATGTAAACGG
*
5812561 TAAAATAAAATAGATGCTACGTATTACGTTAAACT-ATCTACCAATTTGTTTAAAAGTATAATAA
1 TAAAATAAAATAGATGCTACCTATTACGTTAAACTAAT-TACCAATTTGTTT-AAAG-AT-ATAA
* *
5812625 TAATAATGTAAACGGTAAAATATTTACAACTTAACCGGTTAAAATAAAATATACGCTACCTATTA
62 TAATAATGAAAACGGTAAAATATTTACAACTTAACCGGTTAAAATAAAATAGACGCTACCTATTA
*
5812690 CGTTAAACTACCTACCGATTTGTTTAAAGGAATAATCATAATGTAAACGG
127 CGTTAAACTACCTACCGATTTGTTTAAAGGAATAATAATAATGTAAACGG
5812740 TAAAATA
1 TAAAATA
5812747 TTTACAACTT
Statistics
Matches: 167, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
175 2 0.01
176 43 0.26
177 3 0.02
178 1 0.01
179 117 0.70
180 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (176 bp):
TAAAATAAAATAGATGCTACCTATTACGTTAAACTAATTACCAATTTGTTTAAAGATATAATAAT
AATGAAAACGGTAAAATATTTACAACTTAACCGGTTAAAATAAAATAGACGCTACCTATTACGTT
AAACTACCTACCGATTTGTTTAAAGGAATAATAATAATGTAAACGG
Found at i:5812690 original size:103 final size:100
Alignment explanation
Indices: 5812561--5812770 Score: 312
Period size: 100 Copynumber: 2.1 Consensus size: 100
5812551 ATGTAAACGG
* * * *
5812561 TAAAATAAAATAGATGCTACGTATTACGTTAAACTATCTACCAATTTGTTTAAAAGTATAATAAT
1 TAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACCAATTTGTTT-AAAG--GAATAAT
5812626 AATAATGTAAACGGTAAAATATTTACAACTTAACCGGT
63 AATAATGTAAACGGTAAAATATTTACAACTTAACCGGT
* * *
5812664 TAAAATAAAATATACGCTACCTATTACGTTAAACTACCTACCGATTTGTTTAAAGGAATAATCAT
1 TAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACCAATTTGTTTAAAGGAATAATAAT
*
5812729 AATGTAAACGGTAAAATATTTACAACTTAACCGTT
66 AATGTAAACGGTAAAATATTTACAACTTAACCGGT
*
5812764 TGAAATA
1 TAAAATA
5812771 TTTTTTTTAA
Statistics
Matches: 98, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
100 48 0.49
102 4 0.04
103 46 0.47
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.32
Consensus pattern (100 bp):
TAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACCAATTTGTTTAAAGGAATAATAAT
AATGTAAACGGTAAAATATTTACAACTTAACCGGT
Found at i:5813789 original size:108 final size:107
Alignment explanation
Indices: 5813467--5813797 Score: 412
Period size: 108 Copynumber: 3.0 Consensus size: 107
5813457 CGAAGTCAAC
* * * * * *
5813467 TTAAACTTTGTTAACATATTAGGCGCAACCTAAATATGTTGATAATATTTATAAAAAAATAAGTA
1 TTAAACTTTGATAACATTTTAGGCGCTACCT-AATATGTTGATAATATTAATAACAAAATAAATA
* ** * * *
5813532 ATTAACCTATTTTGTTATCATGTGATTTATAATGCTTCGTCAGC
65 ATTAACCTATTTTGTTATCGTAAGATTTATAAGGC-TCATCAGT
*
5813576 TTAAACTTTGATAACATTTTAGGCACTACCTAATATGTTGATAATATTAATAACAAAATAAATAA
1 TTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAATAA
* ** * *
5813641 TTAATCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGT
66 TTAACCTATTTTGTTATCGTAAGATTTATAAGG-CTCATCAGT
* * *
5813684 TTAAACTTTTG-TAACATTTTAGGCGTTACATAATATGTTGGTAATATTAATAACAAAATAAATA
1 TTAAAC-TTTGATAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAATA
5813748 ATTAACCTATTTTGTTATCGTAAGATTTATAAGGTCTCATCAGCT
65 ATTAACCTATTTTGTTATCGTAAGATTTATAAGG-CTCATCAG-T
5813793 TTAAA
1 TTAAA
5813798 TAAGCGCAAT
Statistics
Matches: 193, Mismatches: 26, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
108 155 0.80
109 38 0.20
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39
Consensus pattern (107 bp):
TTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAATAA
TTAACCTATTTTGTTATCGTAAGATTTATAAGGCTCATCAGT
Found at i:5813835 original size:23 final size:23
Alignment explanation
Indices: 5813791--5813836 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5813781 GTCTCATCAG
* *
5813791 CTTTAAATAAGCGCAATATGTTA
1 CTTTAAATAAGCACAACATGTTA
* *
5813814 CTTTAAATAGGCACAACCTGTTA
1 CTTTAAATAAGCACAACATGTTA
5813837 TGTTATTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (23 bp):
CTTTAAATAAGCACAACATGTTA
Found at i:5820859 original size:2 final size:2
Alignment explanation
Indices: 5820854--5820923 Score: 97
Period size: 2 Copynumber: 35.5 Consensus size: 2
5820844 TTTTAAAAAA
* * * *
5820854 AT AT AT AT AT AT TT TT AT AT TT TT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5820895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5820924 GTGATGCGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:5821260 original size:16 final size:17
Alignment explanation
Indices: 5821239--5821283 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
5821229 CAACATACCC
*
5821239 AATATACTT-GCTCAAA
1 AATATACTTCGATCAAA
*
5821255 AATATAGTTCGATCAAA
1 AATATACTTCGATCAAA
*
5821272 AATATAGTTCGA
1 AATATACTTCGA
5821284 CGAGTATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (17 bp):
AATATACTTCGATCAAA
Found at i:5821272 original size:17 final size:17
Alignment explanation
Indices: 5821250--5821283 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5821240 ATATACTTGC
5821250 TCAAAAATATAGTTCGA
1 TCAAAAATATAGTTCGA
5821267 TCAAAAATATAGTTCGA
1 TCAAAAATATAGTTCGA
5821284 CGAGTATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
TCAAAAATATAGTTCGA
Found at i:5822962 original size:20 final size:20
Alignment explanation
Indices: 5822939--5822990 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5822929 AACGCGATCC
5822939 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
5822959 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
5822979 CCAAAATCGCAA
1 CCAGAATCGCAA
5822991 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:5823007 original size:21 final size:20
Alignment explanation
Indices: 5822980--5823078 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
5822970 AATCAGTTTC
5822980 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
5823001 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
5823022 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5823042 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5823063 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
5823079 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5823107 original size:20 final size:20
Alignment explanation
Indices: 5823045--5823238 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
5823035 CGATTTTCCA
* ** *
5823045 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
5823065 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
5823085 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5823105 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
5823125 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
5823145 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5823165 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
5823185 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
5823205 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
5823226 AAATCGCAACGCG
1 AAATCGCAACGCG
5823239 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:5823129 original size:60 final size:60
Alignment explanation
Indices: 5823045--5823238 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
5823035 CGATTTTCCA
* ** * *
5823045 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
5823105 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
5823165 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
5823226 AAATCGCAACGCG
1 AAATCGCAACGCG
5823239 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:5823659 original size:33 final size:33
Alignment explanation
Indices: 5823620--5823690 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
5823610 TTCACTTAGA
5823620 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
5823653 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
5823686 TTTCA
1 TTTCA
5823691 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:5823830 original size:14 final size:14
Alignment explanation
Indices: 5823811--5823865 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5823801 AGAATGACTG
5823811 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
5823825 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
5823844 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
5823858 TCGCAACG
1 TCGCAACG
5823866 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:5823878 original size:33 final size:33
Alignment explanation
Indices: 5823811--5823881 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5823801 AGAATGACTG
***
5823811 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
5823844 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
5823877 TCGCA
1 TCGCA
5823882 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:5823899 original size:19 final size:19
Alignment explanation
Indices: 5823877--5823974 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
5823867 GAAACCAAAA
*
5823877 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5823896 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5823910 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5823929 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
5823943 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
5823962 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5823975 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5823918 original size:14 final size:14
Alignment explanation
Indices: 5823899--5823988 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5823889 TTTCATTTCG
5823899 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5823913 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5823932 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5823946 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
5823963 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
5823979 CGTTGCGATT
1 CGTTGCGATT
5823989 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5823924 original size:33 final size:33
Alignment explanation
Indices: 5823882--5823996 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5823872 CAAAATCGCA
5823882 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5823915 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
5823948 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5823981 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
5823997 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:5826353 original size:12 final size:12
Alignment explanation
Indices: 5826336--5826360 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5826326 TCTTCGGGGA
5826336 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5826348 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5826360 C
1 C
5826361 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5826569 original size:24 final size:24
Alignment explanation
Indices: 5826535--5826581 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5826525 CTGAAACATC
5826535 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5826559 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5826582 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:5827285 original size:20 final size:20
Alignment explanation
Indices: 5827276--5827623 Score: 452
Period size: 20 Copynumber: 17.4 Consensus size: 20
5827266 CAGATTCTCA
*
5827276 TTGCGATTTACGGATTA-TCG
1 TTGCGATTTACGGA-TACGCG
* * *
5827296 TTGCGATTTACAGATTCTCG
1 TTGCGATTTACGGATACGCG
*
5827316 TTGCGATTTACGGATTA-TCG
1 TTGCGATTTACGGA-TACGCG
5827336 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
*
5827356 TTGCGATTTACGGATTA-TCG
1 TTGCGATTTACGGA-TACGCG
5827376 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
*
5827396 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGGATACGCG
5827416 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
*
5827436 TTGCGATTTACGGATACACG
1 TTGCGATTTACGGATACGCG
*
5827456 TTGCGGTTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
5827476 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
5827496 TTGCGATATACGGATACGCA
1 TTGCGATTTACGGATACGCG
**
5827516 TTGCGATTTACCCATACGCG
1 TTGCGATTTACGGATACGCG
*
5827536 TTGCGATTTACGGATACACG
1 TTGCGATTTACGGATACGCG
5827556 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
5827576 TTGCGATTTATGTG-TTCGCG
1 TTGCGATTTACG-GATACGCG
* ** *
5827596 TTGCGATTTTCATATTCGCG
1 TTGCGATTTACGGATACGCG
5827616 TTGCGATT
1 TTGCGATT
5827624 ATGGAAAATC
Statistics
Matches: 292, Mismatches: 29, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 283 0.97
21 4 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:5844291 original size:20 final size:20
Alignment explanation
Indices: 5844266--5844304 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5844256 TAAATTAAAT
*
5844266 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
5844286 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
5844305 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:5844351 original size:20 final size:21
Alignment explanation
Indices: 5844318--5844357 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5844308 TCTATTAGTT
5844318 ATTAGATATGATCA-TTTTTA
1 ATTAGATATGATCAGTTTTTA
5844338 ATTAGATA-GAATCAGTTTTT
1 ATTAGATATG-ATCAGTTTTT
5844358 TATTCTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 12 0.67
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (21 bp):
ATTAGATATGATCAGTTTTTA
Found at i:5844384 original size:53 final size:52
Alignment explanation
Indices: 5844265--5844414 Score: 266
Period size: 53 Copynumber: 2.9 Consensus size: 52
5844255 CTAAATTAAA
*
5844265 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
*
5844317 TATTAGATATGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
5844370 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
5844415 GTTGCTAATT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 10 0.11
52 34 0.36
53 50 0.53
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.49
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:5844396 original size:20 final size:20
Alignment explanation
Indices: 5844371--5844410 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5844361 TCTATTAGTT
*
5844371 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
5844391 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
5844411 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:5848940 original size:20 final size:20
Alignment explanation
Indices: 5848915--5848953 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5848905 TAAATTAAAT
*
5848915 ATTAGATAGGATCAATTTTA
1 ATTAGATAGAATCAATTTTA
*
5848935 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAATTTT
5848954 TATTCTATTA
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:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAATTTTA
Found at i:5849000 original size:20 final size:21
Alignment explanation
Indices: 5848967--5849006 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5848957 TCTATTAGTT
5848967 ATTAGATATGATCA-TTTTTA
1 ATTAGATATGATCAGTTTTTA
5848987 ATTAGATA-GAATCAGTTTTT
1 ATTAGATATG-ATCAGTTTTT
5849007 TATTCTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 12 0.67
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (21 bp):
ATTAGATATGATCAGTTTTTA
Found at i:5849035 original size:53 final size:52
Alignment explanation
Indices: 5848914--5849063 Score: 257
Period size: 53 Copynumber: 2.9 Consensus size: 52
5848904 ATAAATTAAA
*
5848914 TATTAGATAGGATCAATTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
*
5848966 TATTAGATATGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
*
5849019 TATTAGATAGGGTCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
5849064 GTTGCTAATT
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
51 10 0.11
52 34 0.37
53 49 0.53
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.49
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:5849045 original size:20 final size:20
Alignment explanation
Indices: 5849020--5849059 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5849010 TCTATTAGTT
**
5849020 ATTAGATAGGGTCATTTTTA
1 ATTAGATAGAATCATTTTTA
5849040 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
5849060 TTCTGTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:5851961 original size:10 final size:10
Alignment explanation
Indices: 5851946--5851975 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5851936 AAATTTATTA
5851946 AAAAATGAAG
1 AAAAATGAAG
5851956 AAAAATGAAG
1 AAAAATGAAG
*
5851966 AAAAAAGAAG
1 AAAAATGAAG
5851976 GAAGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (10 bp):
AAAAATGAAG
Found at i:5852335 original size:24 final size:24
Alignment explanation
Indices: 5852299--5852357 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
5852289 AGAATGGATT
* *
5852299 TTTTTTTATATATATTTCTA-TGA
1 TTTTTTAAAATATATTTCTATTGA
*
5852322 TTTTTATAAAATATATTTTTATTTGA
1 TTTTT-TAAAATATATTTCTA-TTGA
5852348 TTTTTTAAAA
1 TTTTTTAAAA
5852358 AATAAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.17
24 12 0.40
25 5 0.17
26 8 0.27
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (24 bp):
TTTTTTAAAATATATTTCTATTGA
Found at i:5852335 original size:26 final size:27
Alignment explanation
Indices: 5852306--5852368 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
5852296 ATTTTTTTTT
* *
5852306 ATATATATTTCTATGA-TTTTTATAAA
1 ATATATATTTATATGATTTTTTAAAAA
* *
5852332 ATATATTTTTATTTGATTTTTTAAAAA
1 ATATATATTTATATGATTTTTTAAAAA
*
5852359 ATAAATATTT
1 ATATATATTT
5852369 TCAGTTAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (27 bp):
ATATATATTTATATGATTTTTTAAAAA
Found at i:5852994 original size:16 final size:18
Alignment explanation
Indices: 5852962--5852995 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5852952 TATTAATGTA
5852962 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
5852980 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
5852996 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:5853663 original size:130 final size:130
Alignment explanation
Indices: 5853459--5853706 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
5853449 AATTTTCTTC
* *
5853459 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
5853524 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
5853589 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
5853654 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
5853707 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:5854154 original size:35 final size:35
Alignment explanation
Indices: 5854104--5854179 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
5854094 AATTGAATTT
* *
5854104 AATTGAATTATTTTGGAATTTAGGGTTTAAAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAAAATGA
* *
5854139 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAAAATGA
5854174 AATTGA
1 AATTGA
5854180 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAAAATGA
Found at i:5855192 original size:15 final size:15
Alignment explanation
Indices: 5855172--5855203 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5855162 TTAATAAGTC
5855172 ATGTTATTGCATTTT
1 ATGTTATTGCATTTT
*
5855187 ATGTTATTGTATTTT
1 ATGTTATTGCATTTT
5855202 AT
1 AT
5855204 CCTACTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (15 bp):
ATGTTATTGCATTTT
Found at i:5855226 original size:29 final size:30
Alignment explanation
Indices: 5855182--5855244 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
5855172 ATGTTATTGC
*
5855182 ATTTTATGTTATTGTATTTTATCCTACTCT
1 ATTTTATGATATTGTATTTTATCCTACTCT
* *
5855212 ATTTTAT-ATATTGTATTTTCTCCTATTCT
1 ATTTTATGATATTGTATTTTATCCTACTCT
5855241 ATTT
1 ATTT
5855245 ATTATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (30 bp):
ATTTTATGATATTGTATTTTATCCTACTCT
Found at i:5855243 original size:15 final size:15
Alignment explanation
Indices: 5855191--5855244 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
5855181 CATTTTATGT
*
5855191 TATTGTATTTTATCC
1 TATTCTATTTTATCC
* *
5855206 TACTCTATTTTAT-A
1 TATTCTATTTTATCC
* *
5855220 TATTGTATTTTCTCC
1 TATTCTATTTTATCC
5855235 TATTCTATTT
1 TATTCTATTT
5855245 ATTATTTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.20, C:0.15, G:0.04, T:0.61
Consensus pattern (15 bp):
TATTCTATTTTATCC
Found at i:5857763 original size:3 final size:3
Alignment explanation
Indices: 5857755--5857783 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5857745 GAATTGGGTT
5857755 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
5857784 CTCCTTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:5860871 original size:2 final size:2
Alignment explanation
Indices: 5860860--5860888 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5860850 TCATTATCAT
5860860 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5860889 ACCTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5865920 original size:22 final size:21
Alignment explanation
Indices: 5865889--5865954 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 21
5865879 TTAGTCATTT
5865889 GGGACATATCCAGTGGTCCTTC
1 GGGAC-TATCCAGTGGTCCTTC
**
5865911 GGGACGTATCCAGTGGTTATTC
1 GGGAC-TATCCAGTGGTCCTTC
5865933 GGGAC-AT--AGTGGTCCTTC
1 GGGACTATCCAGTGGTCCTTC
5865951 GGGA
1 GGGA
5865955 TAAATACTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 13 0.33
20 2 0.05
22 24 0.62
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.27
Consensus pattern (21 bp):
GGGACTATCCAGTGGTCCTTC
Found at i:5870086 original size:22 final size:22
Alignment explanation
Indices: 5870061--5870115 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
5870051 GGGTATATTA
*
5870061 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAATG
5870083 GTCCTTCGGGACGTATCCAATG
1 GTCCTTCGGGACGTATCCAATG
5870105 GTCCTTCGGGA
1 GTCCTTCGGGA
5870116 TAAATACTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.27
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAATG
Found at i:5871293 original size:20 final size:19
Alignment explanation
Indices: 5871253--5871296 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5871243 GATAAAAAAT
*
5871253 AAAAGTTAAAATGAAATAG
1 AAAAGTTAAAATGAAAGAG
5871272 AAAAGTTAAGGAA-GAAAGAG
1 AAAAGTTAA--AATGAAAGAG
5871292 AAAAG
1 AAAAG
5871297 AAAAAGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 11 0.50
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.14
Consensus pattern (19 bp):
AAAAGTTAAAATGAAAGAG
Found at i:5886019 original size:24 final size:24
Alignment explanation
Indices: 5885970--5886019 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
5885960 TGTCTAAGTT
*
5885970 TTATTTTTAATGAATGTTTTCTTTA
1 TTATTTTTAAT-AATGTTTTCATTA
*
5885995 TTATGTTTTAAT-ATGTTTTGATTA
1 TTAT-TTTTAATAATGTTTTCATTA
5886019 T
1 T
5886020 GAAACTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 11 0.50
25 4 0.18
26 7 0.32
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (24 bp):
TTATTTTTAATAATGTTTTCATTA
Found at i:5890072 original size:23 final size:23
Alignment explanation
Indices: 5890046--5890094 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
5890036 ATAAAGAACC
5890046 AAAATAAACT-TAAACATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
5890069 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
5890092 AAA
1 AAA
5890095 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:5891903 original size:54 final size:54
Alignment explanation
Indices: 5891840--5891984 Score: 175
Period size: 54 Copynumber: 2.6 Consensus size: 54
5891830 TCATACTTGG
* * * *
5891840 GGGTATCGATATGCTCTCTAATGTACCAATACACAAATAGCACTCGATG-TTTGA
1 GGGTATCGATATACTC-CTAGTGTACCGATACACAAATAGAACTCGATGTTTTGA
* * * * *
5891894 GGGTATCGATACACTCCTCAGTGTACTGATACATAAATGGAATTCGATGTTTTGA
1 GGGTATCGATATACTCCT-AGTGTACCGATACACAAATAGAACTCGATGTTTTGA
5891949 GGGTATCGATATACTCCTTAGTGTACCGATACACAA
1 GGGTATCGATATACTCC-TAGTGTACCGATACACAA
5891985 TCATACAATT
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
53 2 0.03
54 37 0.49
55 36 0.47
56 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (54 bp):
GGGTATCGATATACTCCTAGTGTACCGATACACAAATAGAACTCGATGTTTTGA
Found at i:5895017 original size:2 final size:2
Alignment explanation
Indices: 5895005--5895038 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
5894995 CATCATAATC
5895005 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5895039 ACCTTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5895511 original size:29 final size:29
Alignment explanation
Indices: 5895469--5895535 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
5895459 TATAGAGTTT
*
5895469 CATATTCTCTTATCATGTATTTCATCTCA
1 CATATTCTTTTATCATGTATTTCATCTCA
5895498 CATATTCTTTTATCATGTATTTCATCTCA
1 CATATTCTTTTATCATGTATTTCATCTCA
5895527 CATATTCTT
1 CATATTCTT
5895536 GATTTCATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.03, T:0.51
Consensus pattern (29 bp):
CATATTCTTTTATCATGTATTTCATCTCA
Found at i:5895542 original size:21 final size:21
Alignment explanation
Indices: 5895516--5895566 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5895506 TTTATCATGT
*
5895516 ATTTCATCTCACATATTCTTG
1 ATTTCATATCACATATTCTTG
5895537 ATTTCATATCACATATTCTTG
1 ATTTCATATCACATATTCTTG
5895558 ATTTCATAT
1 ATTTCATAT
5895567 GATCACATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTTCATATCACATATTCTTG
Found at i:5897238 original size:8 final size:7
Alignment explanation
Indices: 5897218--5897284 Score: 59
Period size: 8 Copynumber: 9.4 Consensus size: 7
5897208 ACAAAAACAT
5897218 TTTATTA
1 TTTATTA
5897225 TATTATATA
1 T-TTAT-TA
5897234 TTTATTTA
1 TTTA-TTA
5897242 TTTATT-
1 TTTATTA
5897248 TTTATTA
1 TTTATTA
5897255 -TTATTA
1 TTTATTA
* *
5897261 -GTAATA
1 TTTATTA
5897267 TTTATTA
1 TTTATTA
5897274 TTTTATTA
1 -TTTATTA
5897282 TTT
1 TTT
5897285 TTGTAGGCCC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
6 16 0.32
7 10 0.20
8 20 0.40
9 4 0.08
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:5897280 original size:33 final size:30
Alignment explanation
Indices: 5897217--5897276 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 30
5897207 TACAAAAACA
5897217 TTTTATTATATTATATATTTATTTATTTAT
1 TTTTATTATATTATATATTTATTTATTTAT
5897247 TTTTATTATTATTAGTAATATTTA-TTATTT
1 TTTTATTA-TATTA-T-ATATTTATTTATTT
5897277 TATTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 8 0.30
31 5 0.19
32 7 0.26
33 7 0.26
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (30 bp):
TTTTATTATATTATATATTTATTTATTTAT
Found at i:5900834 original size:21 final size:21
Alignment explanation
Indices: 5900823--5900883 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
5900813 AAAAACAAAG
5900823 AAAAAAGCAAAAACAAAATAA
1 AAAAAAGCAAAAACAAAATAA
**
5900844 AAAAAAGCAAAAACAAAGGAA
1 AAAAAAGCAAAAACAAAATAA
* *
5900865 AAATAAAGAAAAAAGAAAA
1 AAA-AAAGCAAAAACAAAA
5900884 CAAGACGCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 22 0.65
22 12 0.35
ACGTcount: A:0.80, C:0.07, G:0.10, T:0.03
Consensus pattern (21 bp):
AAAAAAGCAAAAACAAAATAA
Found at i:5900856 original size:11 final size:11
Alignment explanation
Indices: 5900809--5900878 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
5900799 CAAAAAAATT
5900809 AAAAAAAAA-C
1 AAAAAAAAAGC
5900819 AAAGAAAAAAGC
1 AAA-AAAAAAGC
5900831 AAAAACAAAA--
1 AAAAA-AAAAGC
*
5900841 TAAAAAAAAGC
1 AAAAAAAAAGC
* *
5900852 AAAAACAAAGG
1 AAAAAAAAAGC
*
5900863 AAAAATAAAG-
1 AAAAAAAAAGC
5900873 AAAAAA
1 AAAAAA
5900879 GAAAACAAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
9 4 0.08
10 12 0.24
11 25 0.51
12 8 0.16
ACGTcount: A:0.81, C:0.07, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:5902736 original size:36 final size:33
Alignment explanation
Indices: 5902689--5902816 Score: 130
Period size: 36 Copynumber: 3.6 Consensus size: 33
5902679 ACAAGGGGTC
* * *
5902689 GTCTCACTTGAGACTAATTTACTCAAAACAAAGTTT
1 GTCTCTCTTGAGAC-AGTTT-CTCGAAACAAA-TTT
5902725 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATCTT
1 GTCTCTCTTGAGACAGTTTCTC--GAAACAAAT-TT
* *
5902761 ATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAGTTT--CTCGAAACAAA-TTT
5902797 GTCTCTCTTGAGACAGTTTC
1 GTCTCTCTTGAGACAGTTTC
5902817 CATTGAAACA
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
34 4 0.05
35 5 0.06
36 68 0.85
37 1 0.01
38 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (33 bp):
GTCTCTCTTGAGACAGTTTCTCGAAACAAATTT
Found at i:5902817 original size:36 final size:36
Alignment explanation
Indices: 5902714--5903164 Score: 315
Period size: 36 Copynumber: 12.6 Consensus size: 36
5902704 AATTTACTCA
* *
5902714 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
5902750 AAACAAATCTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
5902786 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCATTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * *
5902822 AAACAAA------ATCT-TTGAATATATTTTTACATT-
1 AAACAAATTTTGTCTCTCTTG-AGACA-GTTTCCCTTG
* * ** *
5902852 AAATAAATTTTGTCTCCCTTGAGACAGTTTCTTTTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * *
5902888 TAACTAAGTTTTGTCTCTTTTGAGACAATTTCTCTTT
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
5902925 AAACAAATTTTGTCTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-----T-TTTGTCTCTCTTGAGACAGTTTCCCTTG
5902967 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
5903003 AAACAAA------ATCT-TTGA-ATATGTTTTCTTTG
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCCCTTG
* * * **
5903032 AAA-AACAATTCGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * *
5903068 GAACTAAGTTTTGTCTCTATTAAGACAGATTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
5903105 AAACAAATTTTGGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTG
5903142 AAACAAAGTTTTGTCTCTCTTGA
1 AAACAAA-TTTTGTCTCTCTTGA
5903165 AACAAAAAAA
Statistics
Matches: 326, Mismatches: 58, Indels: 61
0.73 0.13 0.14
Matches are distributed among these distances:
28 4 0.01
29 19 0.06
30 15 0.05
31 7 0.02
35 7 0.02
36 135 0.41
37 100 0.31
38 6 0.02
41 1 0.00
42 32 0.10
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:5902944 original size:42 final size:42
Alignment explanation
Indices: 5902897--5902981 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
5902887 TTAACTAAGT
* *
5902897 TTTGTCTCTTTTGAGACAATTTCTCTTTAAACAAATTTTGTC
1 TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTC
*
5902939 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
1 TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTC
5902981 T
1 T
5902982 CTCTTGAGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (42 bp):
TTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAATTTTGTC
Found at i:5903007 original size:78 final size:79
Alignment explanation
Indices: 5902860--5903009 Score: 212
Period size: 78 Copynumber: 1.9 Consensus size: 79
5902850 TTAAATAAAT
* ** * * * *
5902860 TTTGTCTCCCTTGAGACAGTTTCTTTTTTAACTAAGTTTTGTCTCTTTTGAGACAATTTCTCTTT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
5902925 AAACAAATTTTGTC
66 AAACAAATTTTGTC
* *
5902939 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
5903003 AAACAAA
66 AAACAAA
5903010 ATCTTTGAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
78 34 0.55
79 28 0.45
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (79 bp):
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
AAACAAATTTTGTC
Found at i:5903124 original size:22 final size:21
Alignment explanation
Indices: 5903098--5903170 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
5903088 TAAGACAGAT
5903098 TCTCTTGAAACAAATTTTGGTC
1 TCTCTTGAAACAAATTTT-GTC
* *
5903120 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
5903137 -C-CTTGAAACAAAGTTTTGTC
1 TCTCTTGAAACAAA-TTTTGTC
5903157 TCTCTTGAAACAAA
1 TCTCTTGAAACAAA
5903171 AAAAAACCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
15 7 0.17
16 1 0.03
17 3 0.08
19 4 0.10
20 3 0.08
21 1 0.03
22 21 0.52
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:5903160 original size:37 final size:37
Alignment explanation
Indices: 5903043--5903164 Score: 156
Period size: 37 Copynumber: 3.3 Consensus size: 37
5903033 AAAACAATTC
* * * *
5903043 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTT
* * *
5903080 GTCTCTATTAAGACAGATTCTCTTGAAACAAA-TTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTT
*
5903116 GGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTT
1 -GTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTT
5903154 GTCTCTCTTGA
1 GTCTCTCTTGA
5903165 AACAAAAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
36 4 0.06
37 64 0.89
38 4 0.06
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (37 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTT
Found at i:5903355 original size:84 final size:84
Alignment explanation
Indices: 5903210--5903378 Score: 196
Period size: 84 Copynumber: 2.0 Consensus size: 84
5903200 ACACCAAACT
* *
5903210 TTCGAGTTCGATTACACTCAGCTCCAAGGCACACCATTTACAACATAGCTCAAGGTAAGAAGGGC
1 TTCGAGTTCGACTACACTCAGCTCCAAGGAACACCATTTACAACATAGCTCAAGGTAAGAAGGGC
* * * *
5903275 TTTTTGTCAACTAAAGACC
66 TATCTGCCAACCAAAGACC
* * * * ** * *
5903294 TTCGAGTTCGACTACGCTCAGCTTCAAGGAACATCATTTGCTGCATAGCTTAA-GTCGAGAAGGG
1 TTCGAGTTCGACTACACTCAGCTCCAAGGAACACCATTTACAACATAGCTCAAGGT-AAGAAGGG
5903358 CTATCTGCCAACCAAAGACC
65 CTATCTGCCAACCAAAGACC
5903378 T
1 T
5903379 GAAGAGTTCG
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
83 2 0.03
84 68 0.97
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (84 bp):
TTCGAGTTCGACTACACTCAGCTCCAAGGAACACCATTTACAACATAGCTCAAGGTAAGAAGGGC
TATCTGCCAACCAAAGACC
Found at i:5903659 original size:30 final size:30
Alignment explanation
Indices: 5903623--5903684 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
5903613 CAAAAACATT
5903623 TTATTA-TATTA-T-ATATTTATTTA-TTTA
1 TTATTATTATTAGTAATATTT-TTTATTTTA
5903650 TTATTATTATTAGTAATATTTTTTATTTTA
1 TTATTATTATTAGTAATATTTTTTATTTTA
5903680 TTATT
1 TTATT
5903685 TTTTCATGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.19
28 5 0.16
29 5 0.16
30 15 0.48
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (30 bp):
TTATTATTATTAGTAATATTTTTTATTTTA
Found at i:5904159 original size:23 final size:24
Alignment explanation
Indices: 5904131--5904175 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5904121 AATGCTTTAT
5904131 TTATTATTATT-ATTTTTACATTC
1 TTATTATTATTCATTTTTACATTC
* *
5904154 TTATTATTTTTCTTTTTTACAT
1 TTATTATTATTCATTTTTACAT
5904176 GATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATTATTATTCATTTTTACATTC
Found at i:5906715 original size:24 final size:24
Alignment explanation
Indices: 5906683--5906733 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
5906673 TGGTGCTTCC
5906683 TCATCGGCT-GACTGGTGAATC-TCT
1 TCATCGGCTAG-CTGGTGAA-CATCT
*
5906707 TCATTGGCTAGCTGGTGAACATCT
1 TCATCGGCTAGCTGGTGAACATCT
5906731 TCA
1 TCA
5906734 CATGCTTCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 1 0.04
24 22 0.92
25 1 0.04
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (24 bp):
TCATCGGCTAGCTGGTGAACATCT
Found at i:5911614 original size:23 final size:23
Alignment explanation
Indices: 5911587--5911650 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
5911577 CAGCTTGTAT
*
5911587 AATTGCACCAAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
5911610 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
*
5911633 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
5911651 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:5913171 original size:21 final size:21
Alignment explanation
Indices: 5913129--5913210 Score: 128
Period size: 21 Copynumber: 3.9 Consensus size: 21
5913119 TTCGCTTGAG
*
5913129 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
*
5913151 GGGTATCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
5913172 GGGTACCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
*
5913193 GGGTACCGATTTCCCTTG
1 GGGTACCGATTCCCCTTG
5913211 CCCAGAAATC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
21 43 0.74
22 15 0.26
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:5914138 original size:16 final size:16
Alignment explanation
Indices: 5914099--5914141 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5914089 AGCATCAGTT
*
5914099 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
5914115 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
5914132 CTTATCAATC
1 CTTATCAATC
5914142 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:5916954 original size:23 final size:23
Alignment explanation
Indices: 5916923--5916991 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
5916913 CACCACAACT
* *
5916923 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
5916946 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
5916969 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
5916992 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:5918518 original size:21 final size:21
Alignment explanation
Indices: 5918476--5918557 Score: 146
Period size: 21 Copynumber: 3.9 Consensus size: 21
5918466 TTCGCTTGAG
*
5918476 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
5918498 GGGTACCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
5918519 GGGTACCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
5918540 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
5918558 CCCAGAAATC
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
21 45 0.76
22 14 0.24
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.29
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:5922975 original size:2 final size:2
Alignment explanation
Indices: 5922968--5922999 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5922958 ATGTCTTATC
5922968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5923000 TCACATGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5923075 original size:2 final size:2
Alignment explanation
Indices: 5923062--5923116 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
5923052 TTCATCTTCC
*
5923062 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5923104 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
5923117 TTCCTATACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5924251 original size:20 final size:20
Alignment explanation
Indices: 5924226--5924263 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5924216 TTCCCCTTGA
5924226 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
*
5924246 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
5924264 TTAACATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:5928428 original size:2 final size:2
Alignment explanation
Indices: 5928415--5928461 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
5928405 TTCATCTTCC
* * *
5928415 TA TA TT TA TA TA TA TA AA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5928457 TA TA T
1 TA TA T
5928462 CATCTTTACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5930488 original size:12 final size:12
Alignment explanation
Indices: 5930471--5930495 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5930461 TAGGGTTTTG
5930471 TTGTTGTTGTTA
1 TTGTTGTTGTTA
5930483 TTGTTGTTGTTA
1 TTGTTGTTGTTA
5930495 T
1 T
5930496 AAACTCTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (12 bp):
TTGTTGTTGTTA
Found at i:5933102 original size:20 final size:20
Alignment explanation
Indices: 5933073--5933115 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5933063 ATTCCACCAC
5933073 ATGCAACTATAT-ATTCCTAA
1 ATGCAACTATATGA-TCCTAA
*
5933093 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
5933113 ATG
1 ATG
5933116 GGCTCTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:5935307 original size:13 final size:13
Alignment explanation
Indices: 5935289--5935331 Score: 77
Period size: 13 Copynumber: 3.2 Consensus size: 13
5935279 AAAGTCAACA
5935289 GTCAACGGTCACG
1 GTCAACGGTCACG
5935302 GTCAACGGTCACG
1 GTCAACGGTCACG
5935315 GTCAACGGTCAACG
1 GTCAACGGTC-ACG
5935329 GTC
1 GTC
5935332 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCACG
Found at i:5935328 original size:20 final size:20
Alignment explanation
Indices: 5935282--5935331 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
5935272 GTCAAAGAAA
*
5935282 GTCAACAGTCAACGGTCACG
1 GTCAACGGTCAACGGTCACG
5935302 GTCAACGGTC-ACGGTCAACG
1 GTCAACGGTCAACGGTC-ACG
5935322 GTCAACGGTC
1 GTCAACGGTC
5935332 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCACG
Found at i:5935343 original size:17 final size:17
Alignment explanation
Indices: 5935321--5935378 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
5935311 CACGGTCAAC
5935321 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5935338 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
5935355 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5935372 GGTCAAC
1 GGTCAAC
5935379 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:5935348 original size:7 final size:7
Alignment explanation
Indices: 5935282--5935331 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
5935272 GTCAAAGAAA
*
5935282 GTCAACA
1 GTCAACG
5935289 GTCAACG
1 GTCAACG
5935296 GTC-ACG
1 GTCAACG
5935302 GTCAACG
1 GTCAACG
5935309 GTC-ACG
1 GTCAACG
5935315 GTCAACG
1 GTCAACG
5935322 GTCAACG
1 GTCAACG
5935329 GTC
1 GTC
5935332 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 12 0.30
7 28 0.70
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:5935411 original size:10 final size:10
Alignment explanation
Indices: 5935379--5935423 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
5935369 TCGGGTCAAC
5935379 CCGGTTCAGA
1 CCGGTTCAGA
5935389 CCGG-TCA-A
1 CCGGTTCAGA
5935397 CCCGGTTCAGA
1 -CCGGTTCAGA
*
5935408 CCGG-TCAAA
1 CCGGTTCAGA
5935417 CCGGTTC
1 CCGGTTC
5935424 GAACCGGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
8 1 0.03
9 15 0.50
10 13 0.43
11 1 0.03
ACGTcount: A:0.20, C:0.36, G:0.27, T:0.18
Consensus pattern (10 bp):
CCGGTTCAGA
Found at i:5935435 original size:19 final size:19
Alignment explanation
Indices: 5935372--5935461 Score: 110
Period size: 19 Copynumber: 4.7 Consensus size: 19
5935362 AGTCGGGTCG
*
5935372 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
5935391 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
5935410 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* * *
5935429 GGTCAAACCAGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
5935449 GGTCAAACCGGTT
1 GGTCAAACCGGTT
5935462 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 48 0.76
20 14 0.22
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:5942666 original size:13 final size:13
Alignment explanation
Indices: 5942648--5942690 Score: 77
Period size: 13 Copynumber: 3.2 Consensus size: 13
5942638 GTCAAAGAAA
5942648 GTCAACGGTCACG
1 GTCAACGGTCACG
5942661 GTCAACGGTCACG
1 GTCAACGGTCACG
5942674 GTCAACGGTCAACG
1 GTCAACGGTC-ACG
5942688 GTC
1 GTC
5942691 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCACG
Found at i:5942668 original size:7 final size:7
Alignment explanation
Indices: 5942648--5942702 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
5942638 GTCAAAGAAA
5942648 GTCAACG
1 GTCAACG
5942655 GTC-ACG
1 GTCAACG
5942661 GTCAACG
1 GTCAACG
5942668 GTC-ACG
1 GTCAACG
5942674 GTCAACG
1 GTCAACG
5942681 GTCAACG
1 GTCAACG
*
5942688 GTC--GG
1 GTCAACG
5942693 GTCAACG
1 GTCAACG
5942700 GTC
1 GTC
5942703 GGGTCGGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 4 0.10
6 12 0.29
7 26 0.62
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:5942697 original size:12 final size:12
Alignment explanation
Indices: 5942680--5942707 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5942670 CACGGTCAAC
5942680 GGTCAACGGTCG
1 GGTCAACGGTCG
5942692 GGTCAACGGTCG
1 GGTCAACGGTCG
5942704 GGTC
1 GGTC
5942708 GGGTCAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:5942709 original size:17 final size:17
Alignment explanation
Indices: 5942673--5942728 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
5942663 CAACGGTCAC
*
5942673 GGTCAACGGTCAACGGTCG
1 GGTCAACGGTC--GGGTCG
5942692 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
5942709 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5942726 GGT
1 GGT
5942729 TAACCCGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 24 0.69
19 11 0.31
ACGTcount: A:0.16, C:0.23, G:0.43, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:5942757 original size:19 final size:19
Alignment explanation
Indices: 5942733--5942796 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
5942723 TCGGGTTAAC
5942733 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGGTCAAA
*
5942752 CCGGTTCAGACCGATCAAA
1 CCGGTTCAGACCGGTCAAA
* * *
5942771 CCAGTTCAAAACTGGTCAAA
1 CCGGTTC-AGACCGGTCAAA
5942791 CCGGTT
1 CCGGTT
5942797 TTCCAGCAGC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
19 24 0.63
20 14 0.37
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (19 bp):
CCGGTTCAGACCGGTCAAA
Found at i:5947259 original size:23 final size:23
Alignment explanation
Indices: 5947232--5947277 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
5947222 AATGGAAACT
5947232 GAAATTTAATGGTAAATTTTTTA
1 GAAATTTAATGGTAAATTTTTTA
*
5947255 GAAATTTAATGGTAATTTTTTTA
1 GAAATTTAATGGTAAATTTTTTA
5947278 AAAAGTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (23 bp):
GAAATTTAATGGTAAATTTTTTA
Found at i:5952184 original size:2 final size:2
Alignment explanation
Indices: 5952177--5952223 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5952167 TGACATATGA
5952177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5952219 AT AT A
1 AT AT A
5952224 CATCAACATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5953947 original size:15 final size:15
Alignment explanation
Indices: 5953927--5953957 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5953917 ATACCACGTC
5953927 AGCATTCTATTACCT
1 AGCATTCTATTACCT
5953942 AGCATTCTATTACCT
1 AGCATTCTATTACCT
5953957 A
1 A
5953958 AATAATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
AGCATTCTATTACCT
Found at i:5954999 original size:26 final size:27
Alignment explanation
Indices: 5954941--5954999 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
5954931 TATAATTTTA
*
5954941 TTTAATATATCATATACAATATAAAAT
1 TTTAAAATATCATATACAATATAAAAT
* * * *
5954968 TATAAAATAT-ATTTACAATATTATAT
1 TTTAAAATATCATATACAATATAAAAT
5954994 TTTAAA
1 TTTAAA
5955000 GAAGTTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (27 bp):
TTTAAAATATCATATACAATATAAAAT
Found at i:5962177 original size:2 final size:2
Alignment explanation
Indices: 5962170--5962243 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
5962160 TTATCCTTTA
5962170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5962212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5962244 CCTTTGTTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5966878 original size:50 final size:50
Alignment explanation
Indices: 5966803--5966898 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 50
5966793 CCAGTAATTC
5966803 GAGTAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACATCT
1 GAGTAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACATCT
* *
5966853 GAGTAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAGTAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATATTTTAC
5966899 GAACCAGTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (50 bp):
GAGTAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACATCT
Found at i:5968109 original size:76 final size:76
Alignment explanation
Indices: 5967978--5968158 Score: 274
Period size: 76 Copynumber: 2.4 Consensus size: 76
5967968 TATTTCCCAT
*
5967978 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
* *
5968043 GCCTTAGGGTC
66 ACCTTAGAGTC
* *
5968054 ATCTATAAGTCCTACATTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
5968119 ACCTTCGAGTC
66 ACCTTAGAGTC
* *
5968130 AGCTGTAAGCCCTACAGTGCA-GAATGTTT
1 ATCTGTAAGTCCTACAGTGCATG-ATGTTT
5968159 TTTTTTCTTA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 1 0.01
76 93 0.99
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (76 bp):
ATCTGTAAGTCCTACAGTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
ACCTTAGAGTC
Found at i:5968371 original size:113 final size:113
Alignment explanation
Indices: 5968170--5968695 Score: 806
Period size: 113 Copynumber: 4.7 Consensus size: 113
5968160 TTTTTCTTAA
* *
5968170 AACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAA
1 AACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
* * *
5968234 TGAGAAGAACTTGTTTAACCTTTTGTTCGAATCCATCACTTGATGGATC
65 TGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
* *
5968283 AACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAA
1 AACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
* * * *
5968347 TGAGAAGAACTTGTTCAACTTTTTGCCCGAATTCATCACTTGATGGATC
65 TGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
* * *
5968396 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-ATGAAGAAGAAATTCATAAT
1 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
5968460 GAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACATAATGGATC
66 GAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
* *
5968508 AACTTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
5968573 GAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGGTGGATC
66 GAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
*
5968621 AACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
5968686 GAGAAGAACT
66 GAGAAGAACT
5968696 CATCTGAAGA
Statistics
Matches: 378, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
112 98 0.26
113 279 0.74
114 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
Found at i:5968565 original size:225 final size:226
Alignment explanation
Indices: 5968170--5968695 Score: 824
Period size: 225 Copynumber: 2.3 Consensus size: 226
5968160 TTTTTCTTAA
* *
5968170 AACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAA
1 AACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
* * * * *
5968234 TGAGAAGAACTTGTTTAACCTTTTGTTCGAATCCATCACTTGATGGATCAACATTTCCAGGTAGA
65 TGAGAAGAACTTGTTTAACCTTTTGCTCAAATCCATCACATAATGGATCAACATTTCCAGGTAAA
5968299 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCA
130 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
5968364 ACTTTTTGCCCGAATTCATCACTTGATGGATC
195 ACCTTTTGCCCAAATCCATCACTTGATGGATC
* * *
5968396 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-ATGAAGAAGAAATTCATAAT
1 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
5968460 GAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACATAATGGATCAACTTTTCCAGAG-AAA
66 GAGAAGAACTTGTTTAACCTTTTGCTCAAATCCATCACATAATGGATCAACATTTCCAG-GTAAA
* * *
5968524 GTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
130 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
5968589 ACCTTTTGCTCAAATCCATCACTTGGTGGATC
195 ACCTTTTGCCCAAATCCATCACTTGATGGATC
*
5968621 AACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
5968686 GAGAAGAACT
66 GAGAAGAACT
5968696 CATCTGAAGA
Statistics
Matches: 272, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
225 203 0.75
226 68 0.25
227 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (226 bp):
AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTTAACCTTTTGCTCAAATCCATCACATAATGGATCAACATTTCCAGGTAAAG
TTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTTGCCCAAATCCATCACTTGATGGATC
Found at i:5968577 original size:24 final size:23
Alignment explanation
Indices: 5968534--5968578 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
5968524 GTTCATAATG
*
5968534 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
5968557 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
5968579 AGCTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:5968690 original size:40 final size:40
Alignment explanation
Indices: 5968635--5968732 Score: 196
Period size: 40 Copynumber: 2.5 Consensus size: 40
5968625 TTTCCAGAGA
5968635 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
5968675 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
5968715 AAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGA
5968733 GCTTGTTCAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.48, C:0.09, G:0.24, T:0.18
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:5968711 original size:153 final size:159
Alignment explanation
Indices: 5968522--5968996 Score: 624
Period size: 163 Copynumber: 3.0 Consensus size: 159
5968512 TTTCCAGAGA
*
5968522 AAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
* * *
5968587 CAACCTTTTGCTCAAATCCATCAC-TTG-G-T-G-G-ATCAACTTTTCCAGAGAAAGTTCATAAT
66 CAACCTTTTGCTCAAATCCATCACAATGAGATAGAGTATCAACATTTCCAGAAAAAGTTCATAAT
* *
5968646 GAGAAGAACTCATCTGAAGAAGGAAGAAG
131 AAGAAGAACTCATCTGAAGAAGGAAAAAG
5968675 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
* ** * * *
5968740 CAACC-TTTGTTTGATTCTATCACAGAATGAGATAGATCAGTATCAACATTTCCATAAAAAGTTC
66 CAACCTTTTGCTCAAATCCATCAC--AATGAGATAG---AGTATCAACATTTCCAGAAAAAGTTC
5968804 ATAATAAGAAGAACTCATCTGAAGAAGGAAAAAG
126 ATAATAAGAAGAACTCATCTGAAGAAGGAAAAAG
*
5968838 AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
* ** * * * *
5968903 CAACC-TTTGTTTGATTCTATCACAGAATGAGATAGATCAGTATCAGCATTTCCATAAAAAGTTC
66 CAACCTTTTGCTCAAATCCATCAC--AATGAGATAG---AGTATCAACATTTCCAGAAAAAGTTC
5968967 ATAATAAGAAGAACTCATCTGAAGAAGGAA
126 ATAATAAGAAGAACTCATCTGAAGAAGGAA
5968997 GAGAATTTGT
Statistics
Matches: 297, Mismatches: 14, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
152 13 0.04
153 69 0.23
155 2 0.01
156 1 0.00
157 1 0.00
158 1 0.00
162 1 0.00
163 209 0.70
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.25
Consensus pattern (159 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
CAACCTTTTGCTCAAATCCATCACAATGAGATAGAGTATCAACATTTCCAGAAAAAGTTCATAAT
AAGAAGAACTCATCTGAAGAAGGAAAAAG
Found at i:5968818 original size:163 final size:163
Alignment explanation
Indices: 5968618--5968998 Score: 699
Period size: 163 Copynumber: 2.3 Consensus size: 163
5968608 CACTTGGTGG
* * * *
5968618 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
5968683 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
66 AATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
5968748 GTTTGATTCTATCACAGAATGAGATAGATCAGT
131 GTTTGATTCTATCACAGAATGAGATAGATCAGT
*
5968781 ATCAACATTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCAT
1 ATCAACATTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
5968846 AATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
66 AATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
5968911 GTTTGATTCTATCACAGAATGAGATAGATCAGT
131 GTTTGATTCTATCACAGAATGAGATAGATCAGT
*
5968944 ATCAGCATTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
1 ATCAACATTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
5968999 GAATTTGTTC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
163 210 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (163 bp):
ATCAACATTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
GTTTGATTCTATCACAGAATGAGATAGATCAGT
Found at i:5968847 original size:40 final size:40
Alignment explanation
Indices: 5968798--5968895 Score: 169
Period size: 40 Copynumber: 2.5 Consensus size: 40
5968788 TTTCCATAAA
* *
5968798 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAAAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAAAAG
*
5968838 AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAAAAG
5968878 AAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGA
5968896 GCTTGTTCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.18
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAAAAG
Found at i:5969197 original size:103 final size:101
Alignment explanation
Indices: 5968897--5969202 Score: 325
Period size: 102 Copynumber: 3.0 Consensus size: 101
5968887 ATGAGAAGAG
* * * *
5968897 CTTGTTCAACC-TTTGTTTGATTCTATCACAGAATGAGATAGATCAGTATCAGCATTTCCATAAA
1 CTTGTTCAACCTTTTGCTTGATTCTATCACAGAA-G-G-TAGATCA-AATCAAC-TTTCCAGAAA
5968961 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
61 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
* * * * * *** **
5969002 TTTGTTCAACTTTTTGCTAGATTAC-ATTACAGAA-GAAGAT-AAATTGTCATCCCCAGCGAAAA
1 CTTGTTCAACCTTTTGCTTGATT-CTATCACAGAAGGTAGATCAAATCAAC-TTTCCA--GAAAA
*
5969064 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGGAGAA
62 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
*
5969104 CTTGTTCAACCTTTTGCTTGATTCTATCACATAAGGTAGATCAACATCAACTTTGCCAGAAAAAG
1 CTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGTAGATCAA-ATCAACTTT-CCAGAAAAAG
*
5969169 TTCATAATGAGAAGAACTCATCTGAAGAA-GAAGA
64 TTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
5969203 AGTTCGTAAT
Statistics
Matches: 165, Mismatches: 27, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
100 8 0.05
101 2 0.01
102 78 0.47
103 41 0.25
104 3 0.02
105 15 0.09
106 17 0.10
107 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (101 bp):
CTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGTAGATCAAATCAACTTTCCAGAAAAAGTT
CATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
Found at i:5973112 original size:2 final size:2
Alignment explanation
Indices: 5973099--5973133 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5973089 TAACTCTATC
*
5973099 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5973134 TGTGTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5973386 original size:32 final size:32
Alignment explanation
Indices: 5973309--5973391 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 32
5973299 GATTACCATG
*
5973309 TCATCACTTTTTGACGA-GTGGCATAAATCACA
1 TCATCACTTTTTGAC-ACATGGCATAAATCACA
* * ** *
5973341 TCAT-ACTTATTGACACATGTCATGTATCATA
1 TCATCACTTTTTGACACATGGCATAAATCACA
5973372 TCATCACTTTTTGACACATG
1 TCATCACTTTTTGACACATG
5973392 ATATGTGCCA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 1 0.02
31 23 0.55
32 18 0.43
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (32 bp):
TCATCACTTTTTGACACATGGCATAAATCACA
Found at i:5973505 original size:32 final size:32
Alignment explanation
Indices: 5973464--5973554 Score: 173
Period size: 32 Copynumber: 2.8 Consensus size: 32
5973454 ATATGCCATC
*
5973464 TTATCACTTTTGACATGTGACATGTGCAACAT
1 TTATCACTTTTGACACGTGACATGTGCAACAT
5973496 TTATCACTTTTGACACGTGACATGTGCAACAT
1 TTATCACTTTTGACACGTGACATGTGCAACAT
5973528 TTATCACTTTTGACACGTGACATGTGC
1 TTATCACTTTTGACACGTGACATGTGC
5973555 CAAATTAGCG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (32 bp):
TTATCACTTTTGACACGTGACATGTGCAACAT
Found at i:5975064 original size:15 final size:15
Alignment explanation
Indices: 5975041--5975070 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5975031 CTGGGAAGGT
*
5975041 GGTATCGATACCATA
1 GGTACCGATACCATA
5975056 GGTACCGATACCATA
1 GGTACCGATACCATA
5975071 AGGGAGGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (15 bp):
GGTACCGATACCATA
Found at i:5978156 original size:3 final size:3
Alignment explanation
Indices: 5978148--5978240 Score: 123
Period size: 3 Copynumber: 31.0 Consensus size: 3
5978138 TTTGATTTAT
* *
5978148 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
5978196 TAA ATA TTA TTA TTA TTA TAA ATA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5978241 AATATATATA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:5980303 original size:21 final size:20
Alignment explanation
Indices: 5980270--5980312 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
5980260 TTTAAATTTT
5980270 TTTTATATATATACATATTA
1 TTTTATATATATACATATTA
* *
5980290 TTTTAGTATTTATATATATTA
1 TTTTA-TATATATACATATTA
5980311 TT
1 TT
5980313 AATATTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTATATATATACATATTA
Found at i:5990958 original size:10 final size:10
Alignment explanation
Indices: 5990943--5991004 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
5990933 TTGAAGAAAA
5990943 AAAAAAGAAG
1 AAAAAAGAAG
5990953 AAAAAA-AGAG
1 AAAAAAGA-AG
5990963 AGAAAAAG-AG
1 A-AAAAAGAAG
5990973 -AAAAAGCAA-
1 AAAAAAG-AAG
*
5990982 AAAAAAAAAG
1 AAAAAAGAAG
5990992 AAAAAAGAA-
1 AAAAAAGAAG
5991001 AAAA
1 AAAA
5991005 GGGGTCAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
8 6 0.14
9 7 0.16
10 25 0.58
11 5 0.12
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:5990961 original size:8 final size:8
Alignment explanation
Indices: 5990939--5991004 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
5990929 ATGCTTGAAG
5990939 AAAAAA-A
1 AAAAAAGA
*
5990946 AAAGAAGA
1 AAAAAAGA
5990954 AAAAAAGA
1 AAAAAAGA
5990962 GAGAAAAAGA
1 -A-AAAAAGA
*
5990972 GAAAAAG-
1 AAAAAAGA
*
5990979 -CAAAA-A
1 AAAAAAGA
5990985 AAAAAAG-
1 AAAAAAGA
5990992 AAAAAAGA
1 AAAAAAGA
5991000 AAAAA
1 AAAAA
5991005 GGGGTCAAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
6 4 0.09
7 16 0.34
8 19 0.40
9 1 0.02
10 7 0.15
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Done.