Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold376
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: 580560
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 34811 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5981 original size:43 final size:43
Alignment explanation
Indices: 5933--6203 Score: 308
Period size: 43 Copynumber: 6.3 Consensus size: 43
5923 GAATCGTGCT
* *** *
5933 TTTAGCGGCGTTTATGACAAAAGCGCCGCTAAAGCTCATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
* ** * *
5976 TTTAGCGGCGTTTGTGGGTAAAGTGCAACTAAAGGTCATGCTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
* *
6019 TTTAGCGACGTTTGTAGGTAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
* * * * *
6062 TTTAGCTGCGCTTGTGGGTGAAGCGCCGCTAAAGGTTATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
* *
6105 TTTAGCCGCGTTTGCGGGTAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
* ** * * *
6148 TTTAGCCGCGTTTGTTTGTAGAGCGCCGCTAAAGATCATATTT
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
*
6191 TTTAACGGCGTTT
1 TTTAGCGGCGTTT
6204 TTTCACATAA
Statistics
Matches: 191, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 191 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTC
Found at i:6150 original size:129 final size:129
Alignment explanation
Indices: 5953--6186 Score: 344
Period size: 129 Copynumber: 1.8 Consensus size: 129
5943 TTTATGACAA
* * * *
5953 AAGCGCCGCTAAAGCTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGTGCAACTAAAGGTCATGCT
1 AAGCGCCGCTAAAGCTCATGTTCTTTAGCCGCGTTTGCGGGTAAAGCGCAACTAAAGATCATGCT
6018 CTTTAG-CGACGTTTGTAGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCTGCGCTTGTGGGTG
66 CTTTAGCCG-CGTTTGTAGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCTGCGCTTGTGGGTG
* * ** *
6082 AAGCGCCGCTAAAGGTTATGTTCTTTAGCCGCGTTTGCGGGTAAAGCGCCGCTAAAGATCATGTT
1 AAGCGCCGCTAAAGCTCATGTTCTTTAGCCGCGTTTGCGGGTAAAGCGCAACTAAAGATCATGCT
** *
6147 CTTTAGCCGCGTTTGTTTGTAGAGCGCCGCTAAAGATCAT
66 CTTTAGCCGCGTTTGTAGGTAAAGCGCCGCTAAAGATCAT
6187 ATTTTTTAAC
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
129 90 0.98
130 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (129 bp):
AAGCGCCGCTAAAGCTCATGTTCTTTAGCCGCGTTTGCGGGTAAAGCGCAACTAAAGATCATGCT
CTTTAGCCGCGTTTGTAGGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCTGCGCTTGTGGGTG
Found at i:9312 original size:27 final size:27
Alignment explanation
Indices: 9272--9691 Score: 275
Period size: 27 Copynumber: 15.6 Consensus size: 27
9262 GTAATGGGTC
* *
9272 TAAAATGACCGAAACAACCC-CGAAGGG
1 TAAAATGACTGAAA-TACCCTCGAAGGG
* * *
9299 TAAAATAACTGAAATGCCCTCGAAGGA
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
9326 TAAAATCACTGAAACACCCT-TAGAGGG
1 TAAAATGACTGAAATACCCTCGA-AGGG
9353 TAAAATGA-TCGAAATACCCTCGAAGGG
1 TAAAATGACT-GAAATACCCTCGAAGGG
** * *
9380 TAAAATGACAAAAATATCCTCAAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
9407 TAACATGA-TCGAAATACCCTCGAAGGG
1 TAAAATGACT-GAAATACCCTCGAAGGG
**
9434 TAAAATGACCAAAATACCCTCAGAA-GG
1 TAAAATGACTGAAATACCCTC-GAAGGG
* *
9461 TAAAATAACCGAAATACCC-C-AGAGGG
1 TAAAATGACTGAAATACCCTCGA-AGGG
9487 TAAAATGAGC-GAAATACCCTCGAAGGG
1 TAAAATGA-CTGAAATACCCTCGAAGGG
*
9514 TAAAATGACCGAAATACTCC-C-ATAGGG
1 TAAAATGACTGAAATAC-CCTCGA-AGGG
* *
9541 TAGAATGA-TCGAAATACCC-CCATAGGG
1 TAAAATGACT-GAAATACCCTCGA-AGGG
* * * *
9568 TAGAATGTC-GGAATACCC-CCATAGGG
1 TAAAATGACTGAAATACCCTCGA-AGGG
* * * *
9594 TAGAATAACCGAAATACCC-CCATAGGG
1 TAAAATGACTGAAATACCCTCGA-AGGG
9621 TAAAATGACTGAAATACCCTC-ATAGGG
1 TAAAATGACTGAAATACCCTCGA-AGGG
* * *
9648 TAGAATGA-TCAAAATACTCCT--ATAGGA
1 TAAAATGACT-GAAATAC-CCTCGA-AGGG
9675 TAAAATGACTGAAATAC
1 TAAAATGACTGAAATAC
9692 TTCTTCTAGT
Statistics
Matches: 326, Mismatches: 43, Indels: 48
0.78 0.10 0.12
Matches are distributed among these distances:
24 1 0.00
25 1 0.00
26 53 0.16
27 259 0.79
28 12 0.04
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCGAAGGG
Found at i:9522 original size:80 final size:81
Alignment explanation
Indices: 9349--9691 Score: 331
Period size: 80 Copynumber: 4.3 Consensus size: 81
9339 ACACCCTTAG
* ** * * * *
9349 AGGGTAAAATGATCGAAATACCCTC-GAAGGGTAAAATGACAAAAATATCCTCAAAGGGTAACAT
1 AGGGTAAAATGACCGAAATACCCTCAGAA-GGTAAAATGACCGAAATACCCCCATAGGGTAAAAT
9413 GATCGAAATACCCTCGA
65 GATCGAAATACCCTCGA
* * *
9430 AGGGTAAAATGACCAAAATACCCTCAGAAGGTAAAATAACCGAAATA-CCCCAGAGGGTAAAATG
1 AGGGTAAAATGACCGAAATACCCTCAGAAGGTAAAATGACCGAAATACCCCCATAGGGTAAAATG
*
9494 AGCGAAATACCCTCGA
66 ATCGAAATACCCTCGA
* * * * *
9510 AGGGTAAAATGACCGAAATACTCC-CATAGGGTAGAATGATCGAAATACCCCCATAGGGTAGAAT
1 AGGGTAAAATGACCGAAATAC-CCTCAGAAGGTAAAATGACCGAAATACCCCCATAGGGTAAAAT
* *
9574 G-TCGGAATACCC-CCA
65 GATCGAAATACCCTCGA
* * * * * * * *
9589 TAGGGTAGAATAACCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGGTAGAAT
1 -AGGGTAAAATGACCGAAATACCCTCAGAAGGTAAAATGACCGAAATACCCCCATAGGGTAAAAT
*
9654 GATCAAAATACTCCT--A
65 GATCGAAATAC-CCTCGA
* *
9670 TAGGATAAAATGACTGAAATAC
1 -AGGGTAAAATGACCGAAATAC
9692 TTCTTCTAGT
Statistics
Matches: 222, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
79 4 0.02
80 132 0.59
81 81 0.36
82 5 0.02
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (81 bp):
AGGGTAAAATGACCGAAATACCCTCAGAAGGTAAAATGACCGAAATACCCCCATAGGGTAAAATG
ATCGAAATACCCTCGA
Found at i:9663 original size:54 final size:54
Alignment explanation
Indices: 9272--9691 Score: 313
Period size: 54 Copynumber: 7.8 Consensus size: 54
9262 GTAATGGGTC
* * * *
9272 TAAAATGACCGAAACA-ACCCCGA-AGGGTAAAATAACTGAAATGCCCTCGA-AGGA
1 TAAAATGACC-AAA-ATACCCCCATAGGGTAAAATGACTGAAATACCCTC-ATAGGG
* ** * ** *
9326 TAAAATCACTGAAACACCCTTAGAGGGTAAAATGA-TCGAAATACCCTCGA-AGGG
1 TAAAATGACCAAAATACCCCCATAGGGTAAAATGACT-GAAATACCCTC-ATAGGG
* * * * *
9380 TAAAATGACAAAAATATCCTCAAAGGGTAACATGA-TCGAAATACCCTCGA-AGGG
1 TAAAATGACCAAAATACCCCCATAGGGTAAAATGACT-GAAATACCCTC-ATAGGG
* * * * * *
9434 TAAAATGACCAAAATACCCTCAGAAGGTAAAATAACCGAAATACCC-CAGAGGG
1 TAAAATGACCAAAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGG
* * * *
9487 TAAAATGAGCGAAATACCCTCGA-AGGGTAAAATGACCGAAATACTCC-CATAGGG
1 TAAAATGACCAAAATACCC-CCATAGGGTAAAATGACTGAAATAC-CCTCATAGGG
* * * * * * *
9541 TAGAATGATCGAAATACCCCCATAGGGTAGAATGTC-GGAATACCCCCATAGGG
1 TAAAATGACCAAAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGG
* * *
9594 TAGAATAACCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGG
1 TAAAATGACCAAAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGG
* * * * *
9648 TAGAATGATCAAAATACTCCTATAGGATAAAATGACTGAAATAC
1 TAAAATGACCAAAATACCCCCATAGGGTAAAATGACTGAAATAC
9692 TTCTTCTAGT
Statistics
Matches: 308, Mismatches: 48, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
52 4 0.01
53 96 0.31
54 208 0.68
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (54 bp):
TAAAATGACCAAAATACCCCCATAGGGTAAAATGACTGAAATACCCTCATAGGG
Found at i:9663 original size:134 final size:132
Alignment explanation
Indices: 9294--9691 Score: 389
Period size: 134 Copynumber: 3.0 Consensus size: 132
9284 AACAACCCCG
* ** * * * * * *
9294 AAGGGTAAAATAACTGAAATGCCCTC-GAAGGATAAAATCACTGAAACACCCTTAGAGGGTAAAA
1 AAGGGTAAAATGACCAAAATACCCCCAGAAGG-TAAAATAACCGAAATACCC-CAGAGGGTAAAA
*
9358 TGA-TCGAAATACCCTCGAAGGGTAAAATGACAAAAATA-TCCTCAAAGGGTAACATGATCGAAA
64 TGACT-GAAATACCCTCGAAGGGTAAAATGAC-AAAATACTCC-CATAGGGTAA-ATGATCGAAA
*
9421 TACCCTCG
125 TACCCTCC
*
9429 AAGGGTAAAATGACCAAAATACCCTCAGAAGGTAAAATAACCGAAATACCCCAGAGGGTAAAATG
1 AAGGGTAAAATGACCAAAATACCCCCAGAAGGTAAAATAACCGAAATACCCCAGAGGGTAAAATG
*
9494 AGC-GAAATACCCTCGAAGGGTAAAATGACCGAAATACTCCCATAGGGTAGAATGATCGAAATAC
66 A-CTGAAATACCCTCGAAGGGTAAAATGA-CAAAATACTCCCATAGGGTA-AATGATCGAAATAC
9558 CC-CC
128 CCTCC
* * ** * * * *
9562 ATAGGGTAGAATG-TCGGAATACCCCCATAGGGTAGAATAACCGAAATACCCCCATAGGGTAAAA
1 A-AGGGTAAAATGACCAAAATACCCCCAGAAGGTAAAATAACCGAAATA-CCCCAGAGGGTAAAA
* * *
9626 TGACTGAAATACCCTC-ATAGGGTAGAATGATCAAAATACTCCTATAGGATAAAATGA-CTGAAA
64 TGACTGAAATACCCTCGA-AGGGTAAAATGA-CAAAATACTCCCATAGGGT-AAATGATC-GAAA
9689 TAC
125 TAC
9692 TTCTTCTAGT
Statistics
Matches: 226, Mismatches: 25, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
133 33 0.15
134 144 0.64
135 44 0.19
136 5 0.02
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (132 bp):
AAGGGTAAAATGACCAAAATACCCCCAGAAGGTAAAATAACCGAAATACCCCAGAGGGTAAAATG
ACTGAAATACCCTCGAAGGGTAAAATGACAAAATACTCCCATAGGGTAAATGATCGAAATACCCT
CC
Found at i:9673 original size:107 final size:106
Alignment explanation
Indices: 9349--9691 Score: 311
Period size: 107 Copynumber: 3.2 Consensus size: 106
9339 ACACCCTTAG
* * * ** * * *
9349 AGGGTAAAATGATCGAAATACCCTC-GAAGGGTAAAATGACAAAAATATCCTCAAAGGGTAACAT
1 AGGGTAAAATAACCGAAATACCC-CAG-AGGGTAAAATAACCGAAATACCCTCCAAGGGTAAAAT
* * *
9413 GA-TCGAAATACCCTCGA-AGGGTAAAATGACCAAAATACCCTCAG
64 GACT-GAAATACCCTC-ATAGGGTAGAATGATCAAAATACCCT-AT
* * * *
9457 AAGGTAAAATAACCGAAATACCCCAGAGGGTAAAATGAGCGAAATACCCTCGAAGGGTAAAATGA
1 AGGGTAAAATAACCGAAATACCCCAGAGGGTAAAATAACCGAAATACCCTCCAAGGGTAAAATGA
* * *
9522 CCGAAATACTCC-CATAGGGTAGAATGATCGAAATACCCCCAT
66 CTGAAATAC-CCTCATAGGGTAGAATGATCAAAATA-CCCTAT
* ** * * *
9564 AGGGTAGAAT-GTCGGAATACCCCCATAGGGTAGAATAACCGAAATACCC-CCATAGGGTAAAAT
1 AGGGTAAAATAACCGAAATA-CCCCAGAGGGTAAAATAACCGAAATACCCTCCA-AGGGTAAAAT
9627 GACTGAAATACCCTCATAGGGTAGAATGATCAAAATACTCCTAT
64 GACTGAAATACCCTCATAGGGTAGAATGATCAAAATAC-CCTAT
* * *
9671 AGGATAAAATGACTGAAATAC
1 AGGGTAAAATAACCGAAATAC
9692 TTCTTCTAGT
Statistics
Matches: 191, Mismatches: 34, Indels: 21
0.78 0.14 0.09
Matches are distributed among these distances:
106 12 0.06
107 148 0.77
108 31 0.16
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (106 bp):
AGGGTAAAATAACCGAAATACCCCAGAGGGTAAAATAACCGAAATACCCTCCAAGGGTAAAATGA
CTGAAATACCCTCATAGGGTAGAATGATCAAAATACCCTAT
Found at i:19845 original size:29 final size:30
Alignment explanation
Indices: 19789--19845 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
19779 ATTTTGAAAA
* * *
19789 TATTTACAAAAAGAGACATCTAATTTTTAG
1 TATTTACAAAAAGAGACAACCAAATTTTAG
*
19819 TATTTACAAAAGGAG-CAACCAAATTTT
1 TATTTACAAAAAGAGACAACCAAATTTT
19846 GAAAATAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 9 0.39
30 14 0.61
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (30 bp):
TATTTACAAAAAGAGACAACCAAATTTTAG
Found at i:27311 original size:32 final size:33
Alignment explanation
Indices: 27247--27322 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 33
27237 ATACAATATG
* * *
27247 CAGTAACAGTCTGGGCCTGAGCCCTATTCAGTAA
1 CAGT-ACAGTGTGGGCCTGAGCCCAATACAGTAA
* *
27281 CAGTACAGTGTGGG-CTTAGCCCAATACAGTAT
1 CAGTACAGTGTGGGCCTGAGCCCAATACAGTAA
*
27313 TAGTACAGTG
1 CAGTACAGTG
27323 CAATAATGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 23 0.64
33 9 0.25
34 4 0.11
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (33 bp):
CAGTACAGTGTGGGCCTGAGCCCAATACAGTAA
Found at i:30778 original size:158 final size:157
Alignment explanation
Indices: 30490--30806 Score: 571
Period size: 158 Copynumber: 2.0 Consensus size: 157
30480 AAATTAATGA
* *
30490 TTAAATGTTAATTTCATGAATTATATAATGTATGATGAGATATATTTATTGTTGAAATGAGAATA
1 TTAAATGTTAATTTCATGAATTATATAATGTATGATGAAATATATTTAGTGTTGAAATGAGAATA
30555 AAATAAAAATGCGAAAACCGAATAAATGATCAAATTGAGCGGAACGCCGGATTTGAGTACTTCTG
66 AAATAAAAATGCGAAAACCGAATAAATGATCAAATTGAGCGGAACGCCGGATTTGAGTACTTCTG
30620 ATCAAGTGACAAAGTGATAAGTGGTAGC
131 ATC-AGTGACAAAGTGATAAGTGGTAGC
* *
30648 TTAAATGTTAATTTCATGAATTATATAATGTATGATGAAATGTATTTAGTGTTGAAATGAGAGTA
1 TTAAATGTTAATTTCATGAATTATATAATGTATGATGAAATATATTTAGTGTTGAAATGAGAATA
* *
30713 AAATAAAAATGCGAAAATCGAATAAATGATCAAATTGAGTGGAACGCCGGATTTGAGTACTTCTG
66 AAATAAAAATGCGAAAACCGAATAAATGATCAAATTGAGCGGAACGCCGGATTTGAGTACTTCTG
30778 ATCAGTGACAAAGTGATAAGTGGTAGC
131 ATCAGTGACAAAGTGATAAGTGGTAGC
30805 TT
1 TT
30807 TAGCTACACT
Statistics
Matches: 153, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
157 26 0.17
158 127 0.83
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (157 bp):
TTAAATGTTAATTTCATGAATTATATAATGTATGATGAAATATATTTAGTGTTGAAATGAGAATA
AAATAAAAATGCGAAAACCGAATAAATGATCAAATTGAGCGGAACGCCGGATTTGAGTACTTCTG
ATCAGTGACAAAGTGATAAGTGGTAGC
Found at i:30834 original size:46 final size:46
Alignment explanation
Indices: 30774--31025 Score: 354
Period size: 46 Copynumber: 5.6 Consensus size: 46
30764 TTTGAGTACT
*
30774 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
30819 TCTGACCAAGAGACAAAGTGATAAGTGG-AGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
30864 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAACTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* **
30910 TCTGATCAAGTA-ATAAAGTGATAAGTAATAGCTTTAGCTACACTTA
1 TCTGATCAAG-AGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
30956 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
31001 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTG
31026 ATCATACGTA
Statistics
Matches: 187, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
43 12 0.06
44 5 0.03
45 67 0.36
46 103 0.55
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:30999 original size:91 final size:91
Alignment explanation
Indices: 30774--31024 Score: 377
Period size: 91 Copynumber: 2.8 Consensus size: 91
30764 TTTGAGTACT
*
30774 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGACCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
*
30838 GATAAGTGGAGCTTTAGCTACACTTA
66 GATAAGTAGAGCTTTAGCTACACTTA
* * *
30864 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAACTACACTTATCTGATCAAGTA-ATAAAG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAG-AGACAAAG
*
30928 TGATAAGTAATAGCTTTAGCTACACTTA
65 TGATAAGT-AGAGCTTTAGCTACACTTA
* *
30956 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AGGGAC-AAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
31018 GATAAGT
66 GATAAGT
31025 GATCATACGT
Statistics
Matches: 146, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
89 11 0.08
90 10 0.07
91 76 0.52
92 49 0.34
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (91 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
GATAAGTAGAGCTTTAGCTACACTTA
Found at i:31073 original size:137 final size:135
Alignment explanation
Indices: 30774--31041 Score: 328
Period size: 137 Copynumber: 2.0 Consensus size: 135
30764 TTTGAGTACT
* **
30774 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGACCAAGAGACAAAGT
1 TCTGATCAAGT-AGAAAGTGA-AAGTAATAGCTTTAGCTACACTTATCTGACCAAGAGACAAAGT
* * * * * *
30838 GATAAGTGGAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAACT
64 GATAAGTGGAGCTCTAGCTACACTTATCTGATCAAGGGACAAAGTGATAAGTGATAACGTAAACC
30903 ACACTTA
129 ACACTTA
* * *
30910 TCTGATCAAGTAATAAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGT-AGAAAGTGA-AAGTAATAGCTTTAGCTACACTTATCTGACCAAGAGACAAAGT
30975 GATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTGATCATACGTAA
64 GATAAGTGG-AGCTCTAGCTACACTTATCTGATCAAGGGACAAAGTGATAAGTGAT-A-ACGTAA
31037 GACCA
126 -ACCA
31042 TAGTTATACT
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
135 14 0.12
136 13 0.11
137 82 0.71
138 6 0.05
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (135 bp):
TCTGATCAAGTAGAAAGTGAAAGTAATAGCTTTAGCTACACTTATCTGACCAAGAGACAAAGTGA
TAAGTGGAGCTCTAGCTACACTTATCTGATCAAGGGACAAAGTGATAAGTGATAACGTAAACCAC
ACTTA
Found at i:31311 original size:82 final size:84
Alignment explanation
Indices: 31198--31363 Score: 309
Period size: 82 Copynumber: 2.0 Consensus size: 84
31188 TTATTTTAAA
31198 GTGACATTTTCATTGCAAAAATTGAGAATTTCATAAATGTGTTATTGAATGGTATAATCGATAAA
1 GTGACATTTTCATTGCAAAAATTGAGAATTTCATAAATGTGTTATTGAATGGTATAATCGATAAA
31263 CGTTGAGTTAAATGGTAAG
66 CGTTGAGTTAAATGGTAAG
*
31282 GTGAC-TTTTCATTGC-AAAATTGGGAATTTCATAAATGTGTTATTGAATGGTATAATCGATAAA
1 GTGACATTTTCATTGCAAAAATTGAGAATTTCATAAATGTGTTATTGAATGGTATAATCGATAAA
31345 CGTTGAGTTAAATGGTAAG
66 CGTTGAGTTAAATGGTAAG
31364 TATGTATTAG
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
82 66 0.81
83 10 0.12
84 5 0.06
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (84 bp):
GTGACATTTTCATTGCAAAAATTGAGAATTTCATAAATGTGTTATTGAATGGTATAATCGATAAA
CGTTGAGTTAAATGGTAAG
Found at i:33430 original size:21 final size:21
Alignment explanation
Indices: 33401--33440 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33391 TTTTAATTTG
33401 ATTTCTTAT-ATAGAATTTATA
1 ATTTCTTATAATA-AATTTATA
*
33422 ATTTTTTATAATAAATTTA
1 ATTTCTTATAATAAATTTA
33441 GTAACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTCTTATAATAAATTTATA
Found at i:35657 original size:139 final size:140
Alignment explanation
Indices: 35476--35728 Score: 377
Period size: 139 Copynumber: 1.8 Consensus size: 140
35466 GCCACAAATT
* * *
35476 TTATGGTAAATTATAATATATACAATTAGCATTATATAATTAAGGTAGATTATTAATGATATGTA
1 TTATGGTAAATTATAATATATACAATTAACATGATATAATTAAAGTAGATTATTAATGATATGTA
* * *
35541 ATCCTATATATAACTATGTTATTA-AAATGTACA-TTTTATATTAATGATATGTGAGCTTAAACC
66 A-CCCATATACAACTATGATATTATAAA-GTACATTTTTATATTAATGATATGTGAGCTTAAACC
35604 CTACCCTTAATC
129 CTACCCTTAATC
* *
35616 TTATGGTAGA-TATAATATATACAATTAACATGATATTATTAAAGTAGATTATTAATGATATGTA
1 TTATGGTAAATTATAATATATACAATTAACATGATATAATTAAAGTAGATTATTAATGATATGTA
* *
35680 ACCCATATACAATTATGATATTATAAAGTGCATTTTTATATTAATGATA
66 ACCCATATACAACTATGATATTATAAAGTACATTTTTATATTAATGATA
35729 CTTAACCTTA
Statistics
Matches: 101, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
138 22 0.22
139 70 0.69
140 9 0.09
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (140 bp):
TTATGGTAAATTATAATATATACAATTAACATGATATAATTAAAGTAGATTATTAATGATATGTA
ACCCATATACAACTATGATATTATAAAGTACATTTTTATATTAATGATATGTGAGCTTAAACCCT
ACCCTTAATC
Found at i:37271 original size:77 final size:77
Alignment explanation
Indices: 36998--37269 Score: 298
Period size: 76 Copynumber: 3.5 Consensus size: 77
36988 GGAAATTAAA
* * * * *
36998 AGTAAAAT-AAAATCGTTTTGGCATTGATTCCCACAGTTCAACAATTTTATTCCAAATTTGTTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCACCGTTCAACGATTTTATTCC-AATTTTTTTT
*
37062 ATTTCCAAAAATG
65 ATTTCCAAAAACG
* * * * *
37075 AGTAAAATAAAAATTGTTTTGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTGTTT-
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCACCGTTCAACGATTTTATTCCAATTTTTTTTA
37139 TTTCCAAAAACG
66 TTTCCAAAAACG
* * * *** * *
37151 AGTAAAATAAAAATCATTTCGAGAGTGATTCTTGCCATTCAATGATTTTATTCCAATTTTTTTTA
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCACCGTTCAACGATTTTATTCCAATTTTTTTTA
37216 TTTCCAAAAACG
66 TTTCCAAAAACG
* * * *
37228 AGTAACAT-AAAATCTGTTTCGGGATTTATTCCTATCGTTCAA
1 AGTAAAATAAAAATC-GTTTCGGGATTGATTCCCACCGTTCAA
37270 TGGATTTATT
Statistics
Matches: 163, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
76 70 0.43
77 53 0.33
78 40 0.25
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (77 bp):
AGTAAAATAAAAATCGTTTCGGGATTGATTCCCACCGTTCAACGATTTTATTCCAATTTTTTTTA
TTTCCAAAAACG
Found at i:41545 original size:16 final size:15
Alignment explanation
Indices: 41515--41544 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41505 GTTAATCCCA
41515 AAAATTATTTGTTTT
1 AAAATTATTTGTTTT
41530 AAAATTATTTGTTTT
1 AAAATTATTTGTTTT
41545 TGTTATAATA
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:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
AAAATTATTTGTTTT
Found at i:43430 original size:22 final size:24
Alignment explanation
Indices: 43405--43457 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
43395 ATTTTTTTAA
*
43405 ATAAAATACA-CAT-AATTTTTTC
1 ATAAAATAAACCATAAATTTTTTC
43427 AT-AAATAAACCATAGAATTTTTTC
1 ATAAAATAAACCATA-AATTTTTTC
43451 A-AAAATA
1 ATAAAATA
43458 TGTTCTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 6 0.23
22 5 0.19
24 15 0.58
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAAAATAAACCATAAATTTTTTC
Found at i:43666 original size:24 final size:25
Alignment explanation
Indices: 43626--43673 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
43616 TTCGATCGAG
43626 TCGAGTTGAATCGAGTTAAAGAATT
1 TCGAGTTGAATCGAGTTAAAGAATT
* *
43651 TCGAGTT-AGTCGAGTTGAAGAAT
1 TCGAGTTGAATCGAGTTAAAGAAT
43674 CCTATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.31
Consensus pattern (25 bp):
TCGAGTTGAATCGAGTTAAAGAATT
Found at i:45669 original size:41 final size:41
Alignment explanation
Indices: 45604--45878 Score: 410
Period size: 41 Copynumber: 6.7 Consensus size: 41
45594 CCTTTCAGGG
** * * * *
45604 CTTTAGCGGCGTTTTTATAAAAGCGCCGCTAGTTCTCGGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
45645 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
*
45686 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCT-TAGGG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCT-GGT
45727 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
* *
45768 CTTTAGCAGCGTTTTCTGG-GAAGCGCCGCTAATGCTCAGGT
1 CTTTAGCGGCGTTTT-TGGAGAAGCGCCGCTAATGCTCTGGT
*
45809 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
* *
45850 CTTTAGCGGCGTTTTTGGAAAATCGCCGC
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGC
45879 AAAAACATTT
Statistics
Matches: 216, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
40 4 0.02
41 208 0.96
42 4 0.02
ACGTcount: A:0.16, C:0.22, G:0.30, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
Found at i:47335 original size:161 final size:161
Alignment explanation
Indices: 47070--47394 Score: 650
Period size: 161 Copynumber: 2.0 Consensus size: 161
47060 AACATAATTT
47070 TTTATGGCGTTTTCTTAAAAAACGCTGCAATAGATAAGCAATAGCGACGTTTTTAATAAAAACAC
1 TTTATGGCGTTTTCTTAAAAAACGCTGCAATAGATAAGCAATAGCGACGTTTTTAATAAAAACAC
47135 CGCAAAAATCATTTAAAAAAAAAGGCGCGTTTTATTTCCAAATTTCTCCGCCTAAGATCTCCAAA
66 CGCAAAAATCATTTAAAAAAAAAGGCGCGTTTTATTTCCAAATTTCTCCGCCTAAGATCTCCAAA
47200 TTAAAGGAGCTCCCCTACTAAAGCAGAAAGG
131 TTAAAGGAGCTCCCCTACTAAAGCAGAAAGG
47231 TTTATGGCGTTTTCTTAAAAAACGCTGCAATAGATAAGCAATAGCGACGTTTTTAATAAAAACAC
1 TTTATGGCGTTTTCTTAAAAAACGCTGCAATAGATAAGCAATAGCGACGTTTTTAATAAAAACAC
47296 CGCAAAAATCATTTAAAAAAAAAGGCGCGTTTTATTTCCAAATTTCTCCGCCTAAGATCTCCAAA
66 CGCAAAAATCATTTAAAAAAAAAGGCGCGTTTTATTTCCAAATTTCTCCGCCTAAGATCTCCAAA
47361 TTAAAGGAGCTCCCCTACTAAAGCAGAAAGG
131 TTAAAGGAGCTCCCCTACTAAAGCAGAAAGG
47392 TTT
1 TTT
47395 TTGAAATTCC
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 164 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (161 bp):
TTTATGGCGTTTTCTTAAAAAACGCTGCAATAGATAAGCAATAGCGACGTTTTTAATAAAAACAC
CGCAAAAATCATTTAAAAAAAAAGGCGCGTTTTATTTCCAAATTTCTCCGCCTAAGATCTCCAAA
TTAAAGGAGCTCCCCTACTAAAGCAGAAAGG
Found at i:50588 original size:42 final size:43
Alignment explanation
Indices: 50418--50664 Score: 349
Period size: 43 Copynumber: 5.8 Consensus size: 43
50408 AAGGTGCACC
* * * *
50418 TTAGCAGCGTTTGCGGGAAAAAGTGCTGCTAAAGGT-CATGGTCT
1 TTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTAC-TGGTCT
* *
50462 ATAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTACTGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTACTGGTCT
*
50505 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTATTGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTACTGGTCT
50548 TTAGCGGCGTTTGTGGGAAAA-CGCCGCTAAAGGTACTGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTACTGGTCT
*
50590 ATAGCGGCGTTTGT--GAAATAGCGCCGCTAAAGGTACTGGTCT
1 TTAGCGGCGTTTGTGGGAAA-AGCGCCGCTAAAGGTACTGGTCT
* *
50632 TTAGCGACGTTTGTGGGAAAAGCGCCGCAAAAG
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
50665 TTAGCGACAC
Statistics
Matches: 184, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
40 4 0.02
41 1 0.01
42 66 0.36
43 94 0.51
44 19 0.10
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTACTGGTCT
Found at i:50634 original size:127 final size:129
Alignment explanation
Indices: 50418--50664 Score: 376
Period size: 127 Copynumber: 1.9 Consensus size: 129
50408 AAGGTGCACC
* *
50418 TTAGCAGCGTTTGCGGGAAAAAGTGCTGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAA
1 TTAGCAGCGTTTGCGGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGT-GGAAAA
* * *
50483 GCGCCGTTAAAGGTACTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTATTGGTCT
65 GCGCCGCTAAAGGTACTGGTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCAAAAGGTATTGGTCT
* *
50548 TTAGCGGCGTTTGTGGG-AAAA-CGCCGCTAAAGGT-ACTGGTCTATAGCGGCGTTTGT-GAAAT
1 TTAGCAGCGTTTGCGGGAAAAAGCGCCGCTAAAGGTCA-TGGTCTATAGCGGCGTTTGTGGAAA-
50609 AGCGCCGCTAAAGGTACTGGTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCAAAAG
64 AGCGCCGCTAAAGGTACTGGTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCAAAAG
50665 TTAGCGACAC
Statistics
Matches: 108, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
126 4 0.04
127 54 0.50
128 31 0.29
129 4 0.04
130 15 0.14
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (129 bp):
TTAGCAGCGTTTGCGGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAG
CGCCGCTAAAGGTACTGGTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCAAAAGGTATTGGTCT
Found at i:52281 original size:26 final size:26
Alignment explanation
Indices: 52245--52301 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
52235 TTTTAGAATG
* *
52245 TTTTATAATTTTTTTAAAAATATAAA
1 TTTTAGAATTTTTATAAAAATATAAA
* *
52271 TTTTAGAATTTTTATAAAAATTTGAA
1 TTTTAGAATTTTTATAAAAATATAAA
52297 TTTTA
1 TTTTA
52302 TTGAATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TTTTAGAATTTTTATAAAAATATAAA
Found at i:52407 original size:9 final size:9
Alignment explanation
Indices: 52393--52422 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
52383 ACATCAATCT
52393 ATTATTCGA
1 ATTATTCGA
*
52402 ATTATTTGA
1 ATTATTCGA
52411 ATTATTCGA
1 ATTATTCGA
52420 ATT
1 ATT
52423 GTAAAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (9 bp):
ATTATTCGA
Found at i:53616 original size:11 final size:11
Alignment explanation
Indices: 53600--53633 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
53590 GTTGGTGTTA
53600 GTAATGTCTTT
1 GTAATGTCTTT
53611 GTAATGTCTTT
1 GTAATGTCTTT
* *
53622 ATAATGTGTTT
1 GTAATGTCTTT
53633 G
1 G
53634 ATGTGTATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.21, C:0.06, G:0.21, T:0.53
Consensus pattern (11 bp):
GTAATGTCTTT
Found at i:54434 original size:29 final size:30
Alignment explanation
Indices: 54389--54458 Score: 106
Period size: 29 Copynumber: 2.3 Consensus size: 30
54379 CAGAATACCT
* *
54389 ATATATGCATGGGTTTTGTTATATATAT-A
1 ATATATGCGTGGATTTTGTTATATATATAA
54418 ATATATGCGTGGATTTTGTTATATATATAAA
1 ATATATGCGTGGATTTTGTTATATATAT-AA
54449 ATATATGCGT
1 ATATATGCGT
54459 ATATGGTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 26 0.70
31 11 0.30
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (30 bp):
ATATATGCGTGGATTTTGTTATATATATAA
Found at i:54443 original size:31 final size:29
Alignment explanation
Indices: 54389--54458 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 29
54379 CAGAATACCT
* * *
54389 ATATATGCATGGGTTTTGTTATATATATA
1 ATATATGCGTGGATTTTGTTATATATAAA
54418 ATATATGCGTGGATTTTGTTATATATATAAA
1 ATATATGCGTGGATTTTG-T-TATATATAAA
54449 ATATATGCGT
1 ATATATGCGT
54459 ATATGGTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 16 0.44
30 1 0.03
31 19 0.53
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (29 bp):
ATATATGCGTGGATTTTGTTATATATAAA
Found at i:54477 original size:34 final size:32
Alignment explanation
Indices: 54403--54488 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 32
54393 ATGCATGGGT
*
54403 TTTGTTATATATAT-AATATATGCGTGGAT--
1 TTTGTTATATATATAAATATATGCGTAGATGG
*
54432 TTTGTTATATATATAAAATATATGCGTATATGG
1 TTTGTTATATATAT-AAATATATGCGTAGATGG
*
54465 TTCTGTTATATATACACAATATAT
1 TT-TGTTATATATATA-AATATAT
54489 ATGTGTGTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 14 0.29
31 13 0.27
33 3 0.06
34 18 0.38
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.47
Consensus pattern (32 bp):
TTTGTTATATATATAAATATATGCGTAGATGG
Found at i:55718 original size:17 final size:17
Alignment explanation
Indices: 55685--55736 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
55675 TATGATGTGG
* *
55685 TATGAATGAATTATTA-
1 TATGAATGAACTGTTAT
55701 TATTGAATGAACTGTTAT
1 TA-TGAATGAACTGTTAT
*
55719 TATGCATGAACTGTTAT
1 TATGAATGAACTGTTAT
55736 T
1 T
55737 TCATATGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 2 0.06
17 27 0.87
18 2 0.06
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (17 bp):
TATGAATGAACTGTTAT
Found at i:55744 original size:17 final size:16
Alignment explanation
Indices: 55707--55740 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
55697 ATTATATTGA
55707 ATGAACTGTTATTATGC
1 ATGAACTGTTATTAT-C
55724 ATGAACTGTTATT-TC
1 ATGAACTGTTATTATC
55739 AT
1 AT
55741 ATGATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 1 0.06
17 13 0.76
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (16 bp):
ATGAACTGTTATTATC
Found at i:61175 original size:44 final size:42
Alignment explanation
Indices: 61108--61220 Score: 156
Period size: 44 Copynumber: 2.6 Consensus size: 42
61098 TTCTGATATG
* * *
61108 TGATTTTGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATT
1 TGATTTTGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
61149 TGAGATTTATGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
1 T--GATTT-TGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
*
61194 TGATTTCGTGTAAGACCATGTCTGGGA
1 TGATTTTGTGTAAGACCATGTCTGGGA
61221 TAGCGGCATT
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
41 1 0.02
42 20 0.31
43 10 0.16
44 30 0.47
45 3 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (42 bp):
TGATTTTGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
Found at i:61229 original size:42 final size:43
Alignment explanation
Indices: 61115--61253 Score: 131
Period size: 42 Copynumber: 3.2 Consensus size: 43
61105 ATGTGATTTT
* * * *
61115 GTGTAAGACCACGTCTGGGAC-GTTGGCATCGATTTGA-GATTTAT
1 GTGTAAGACCATGTCTGGGACAG-CGGCATCGATAT-ATGA-TTAC
** *
61159 GTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTTC
1 GTGTAAGACCATGTCTGGGACAGCGGCATCGATATATGATTAC
* * *
61201 GTGTAAGACCATGTCTGGGATAGCGGCATTGATATTTGATTAC
1 GTGTAAGACCATGTCTGGGACAGCGGCATCGATATATGATTAC
*
61244 ATGTAAGACC
1 GTGTAAGACC
61254 TCATCTGGGA
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
42 30 0.38
43 22 0.28
44 28 0.35
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACAGCGGCATCGATATATGATTAC
Found at i:61274 original size:43 final size:43
Alignment explanation
Indices: 61115--61272 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 43
61105 ATGTGATTTT
* * *
61115 GTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTAT
1 GTGTAAGACCATGTCTGGGACGTTGGCATCGATATT-TGA-TTAC
* * *
61159 GTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTTC
1 GTGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGATTAC
* * *
61201 GTGTAAGACCATGTCTGGGATAG-CGGCATTGATATTTGATTAC
1 GTGTAAGACCATGTCTGGGA-CGTTGGCATCGATATTTGATTAC
* *
61244 ATGTAAGACC-TCATCTGGGACGTTGGCAT
1 GTGTAAGACCAT-GTCTGGGACGTTGGCAT
61273 TGTACGAGTT
Statistics
Matches: 93, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
42 30 0.32
43 33 0.35
44 30 0.32
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGATTAC
Found at i:64759 original size:17 final size:17
Alignment explanation
Indices: 64737--64770 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
64727 CAAGTGTTGG
64737 AAATGTTCGATCCGATC
1 AAATGTTCGATCCGATC
64754 AAATGTTCGATCCGATC
1 AAATGTTCGATCCGATC
64771 GACCTGAGTG
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:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
AAATGTTCGATCCGATC
Found at i:83116 original size:17 final size:18
Alignment explanation
Indices: 83089--83122 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
83079 TTTATTGGCT
83089 TTTTCTTTTTGTATTTTG
1 TTTTCTTTTTGTATTTTG
*
83107 TTTT-TTTTTGTGTTTT
1 TTTTCTTTTTGTATTTT
83123 TTTAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTGTATTTTG
Found at i:83133 original size:3 final size:3
Alignment explanation
Indices: 83127--83156 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
83117 TGTTTTTTTA
83127 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
83157 CCTATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:93132 original size:17 final size:18
Alignment explanation
Indices: 93105--93138 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
93095 ATTTTTGGCT
93105 TTTTCTTTTTGTATTTTG
1 TTTTCTTTTTGTATTTTG
*
93123 TTTT-TTTTTGTGTTTT
1 TTTTCTTTTTGTATTTT
93139 TTTAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTGTATTTTG
Found at i:93149 original size:3 final size:3
Alignment explanation
Indices: 93143--93172 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
93133 TGTTTTTTTA
93143 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
93173 CCTATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:104128 original size:11 final size:11
Alignment explanation
Indices: 104093--104129 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
104083 TATTTATGAT
104093 TATGATATGTA
1 TATGATATGTA
**
104104 TAAAATATGTA
1 TATGATATGTA
104115 TATGATATGTA
1 TATGATATGTA
104126 TATG
1 TATG
104130 TGTGGGGTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (11 bp):
TATGATATGTA
Found at i:113147 original size:47 final size:47
Alignment explanation
Indices: 113091--113184 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
113081 GCAAATTGAT
*
113091 TTTAAATTAGGTTCGATTGCTTCCAATTACCTATTTTATTTAATAGA
1 TTTAAATTAGGTTAGATTGCTTCCAATTACCTATTTTATTTAATAGA
*
113138 TTTAAATTAGGTTAGATTGCTTCCAATTACCTGTTTTATTTAATAGA
1 TTTAAATTAGGTTAGATTGCTTCCAATTACCTATTTTATTTAATAGA
113185 GTTAGATTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (47 bp):
TTTAAATTAGGTTAGATTGCTTCCAATTACCTATTTTATTTAATAGA
Found at i:113190 original size:37 final size:37
Alignment explanation
Indices: 113148--113225 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
113138 TTTAAATTAG
113148 GTTAGATTGCTTCCAATTACCTGTTTTATTTAATAGA
1 GTTAGATTGCTTCCAATTACCTGTTTTATTTAATAGA
* *
113185 GTTAGATTGCTTCGAATTACCTGTTTTATTTAATAGT
1 GTTAGATTGCTTCCAATTACCTGTTTTATTTAATAGA
113222 GTTA
1 GTTA
113226 AGGTCAGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (37 bp):
GTTAGATTGCTTCCAATTACCTGTTTTATTTAATAGA
Found at i:118374 original size:19 final size:19
Alignment explanation
Indices: 118350--118386 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
118340 GTTTTTGGGG
*
118350 TTTGGGGGGAAGTAAAAGT
1 TTTGGGGGAAAGTAAAAGT
118369 TTTGGGGGAAAGTAAAAG
1 TTTGGGGGAAAGTAAAAG
118387 GAAAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.41, T:0.24
Consensus pattern (19 bp):
TTTGGGGGAAAGTAAAAGT
Found at i:118375 original size:18 final size:19
Alignment explanation
Indices: 118349--118386 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
118339 AGTTTTTGGG
118349 GTTTGGGGGG-AAGTAAAA
1 GTTTGGGGGGAAAGTAAAA
*
118367 GTTTTGGGGGAAAGTAAAA
1 GTTTGGGGGGAAAGTAAAA
118386 G
1 G
118387 GAAAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.42, T:0.24
Consensus pattern (19 bp):
GTTTGGGGGGAAAGTAAAA
Found at i:125138 original size:24 final size:24
Alignment explanation
Indices: 125100--125154 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
125090 TAAGACATGA
* * *
125100 CCGTGTGATAGCTCGTGTCCTAGG
1 CCGTGTGACAACTCGTGTCCCAGG
125124 CCGTGTGACAACTCGTGTCCCAGG
1 CCGTGTGACAACTCGTGTCCCAGG
125148 CCGTGTG
1 CCGTGTG
125155 CACCATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.29, G:0.33, T:0.25
Consensus pattern (24 bp):
CCGTGTGACAACTCGTGTCCCAGG
Found at i:127934 original size:30 final size:30
Alignment explanation
Indices: 127898--127976 Score: 124
Period size: 30 Copynumber: 2.6 Consensus size: 30
127888 CCCACATGAC
127898 CGTGTGGCCCACACTGCCCAAATGGCGAGA-
1 CGTGTGGCCCACA-TGCCCAAATGGCGAGAT
127928 CGTGTGGCCCACATTGCCCAAATGGCGAGAT
1 CGTGTGGCCCACA-TGCCCAAATGGCGAGAT
*
127959 CGTATGGCCCACATGCCC
1 CGTGTGGCCCACATGCCC
127977 TACTTGATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 34 0.74
31 12 0.26
ACGTcount: A:0.22, C:0.34, G:0.28, T:0.16
Consensus pattern (30 bp):
CGTGTGGCCCACATGCCCAAATGGCGAGAT
Found at i:130540 original size:34 final size:34
Alignment explanation
Indices: 130497--130609 Score: 145
Period size: 34 Copynumber: 3.3 Consensus size: 34
130487 AATGCTATAT
* **
130497 GACATGCTTATAACAGATCAATACGGTAGCAAGG
1 GACATGCTTATAACAAATCAATACGGTAGCAAAA
* * ** *
130531 GACATGCTTATAACATATTAATACTATAGCAATA
1 GACATGCTTATAACAAATCAATACGGTAGCAAAA
*
130565 GACATGCTTATATCAAATCAATACGGTAGCAAAA
1 GACATGCTTATAACAAATCAATACGGTAGCAAAA
130599 GACATGCTTAT
1 GACATGCTTAT
130610 CATGTATTCG
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (34 bp):
GACATGCTTATAACAAATCAATACGGTAGCAAAA
Found at i:139630 original size:30 final size:30
Alignment explanation
Indices: 139594--139654 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
139584 TTTTTTTGAA
139594 TTTTGAGTTAAACAAATCGAGTTATTCGAG
1 TTTTGAGTTAAACAAATCGAGTTATTCGAG
139624 TTTTGAGTTAAACAAATCGAGTTATTCGAG
1 TTTTGAGTTAAACAAATCGAGTTATTCGAG
139654 T
1 T
139655 CAACTCGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (30 bp):
TTTTGAGTTAAACAAATCGAGTTATTCGAG
Found at i:140369 original size:125 final size:125
Alignment explanation
Indices: 140147--140663 Score: 761
Period size: 125 Copynumber: 4.1 Consensus size: 125
140137 TGTGTAAGCA
* * * * * *
140147 CTTTTGCTATAGTAGGTCCT-GAAAAAATAATTTTGAGTTTACGTTTCTGAGCACATAGTATAAA
1 CTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAA
* * * *
140211 ATCGCTTCTAGCAGGATGCTGTGTGATAAGAATTTGTGAAATCGCGCCCTCGTGGATGCG
66 ATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCG
* * *
140271 GTTTTGCTACAGTAGGTCCTGGAAGAAATAACTTCGACTTGATGTTTCTGAGCAAATAGTATAAA
1 CTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAA
*
140336 ATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCG
66 ATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCG
* *
140396 CTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTTGACTTGACGTTTCTAAGCAAATAGTATAAA
1 CTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAA
* *
140461 ATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAATCGCGCCTTCGTGGACGCG
66 ATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCG
* *
140521 CTTTTGCTACAGTAGGTCCTGGAAAAATAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTT
1 CTTTTGCTACAGTAGGTCCTGG---AAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAG--T
* * *
140586 AAAAAAT-GCTTCAAACAGGA-GCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCG
61 ATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCG
140649 CTTTTGCTACAGTAG
1 CTTTTGCTACAGTAG
140664 CATGTTTGGG
Statistics
Matches: 356, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
124 18 0.05
125 231 0.65
128 89 0.25
129 11 0.03
130 7 0.02
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (125 bp):
CTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAA
ATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCG
Found at i:145754 original size:50 final size:49
Alignment explanation
Indices: 145674--145823 Score: 141
Period size: 49 Copynumber: 3.0 Consensus size: 49
145664 TTTATGCTAA
*
145674 GGGTTAGTGA-TTTTAATTTATGGGTTAGGGTTTTTAATTAA-GGTTTAGG
1 GGGTTAG-GATTTTTAATTTA-AGGTTAGGGTTTTTAATTAAGGGTTTAGG
* *
145723 GGGTTTATGG-TTTTTAATTTAAGGTTAAGGGTTTTTATTTTAATGG-TTA--
1 GGG-TTA-GGATTTTTAATTTAAGGTT-AGGGTTTTTA-ATTAAGGGTTTAGG
*
145772 GGGTTAGGATTTTTAACTTTAAGGTTTATGGTTTTTAAGTTAAGGGTTTAGG
1 GGGTTAGGATTTTTAA-TTTAAGG-TTAGGGTTTTTAA-TTAAGGGTTTAGG
145824 ATTATTAATT
Statistics
Matches: 83, Mismatches: 5, Indels: 23
0.75 0.05 0.21
Matches are distributed among these distances:
47 2 0.02
48 10 0.12
49 32 0.39
50 29 0.35
51 8 0.10
52 2 0.02
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.49
Consensus pattern (49 bp):
GGGTTAGGATTTTTAATTTAAGGTTAGGGTTTTTAATTAAGGGTTTAGG
Found at i:145934 original size:22 final size:22
Alignment explanation
Indices: 143755--145905 Score: 2039
Period size: 21 Copynumber: 99.9 Consensus size: 22
143745 AAAACCTTAA
143755 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
143777 GG-TTTTAAGTTAATGTTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
143798 GG-TTTTAAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
143818 GGTTATTAAGTTAA-TGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
143839 GGTCTTTAATTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
143860 GGTTTTTAAGTTAAGTG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
143881 GGTTTTTAATTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
143902 GGTTTTTAATTTAATGGTTAGGGTTAG
1 GGTTTTTAAGTTAA--G---GGTTTAG
* *
143929 GGTTTTTAAGTTAAAGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAG
143951 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* * * *
143973 GCTTATTAATTTAA-GG-TGAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
143993 GGTTTTTAATTTAATGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144015 GGTTTTTAAGTTAA-GGTTTA-
1 GGTTTTTAAGTTAAGGGTTTAG
*
144035 GGTTTTTAATTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144056 GGTTTTTTAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144077 GGTTTTTAAGCTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144098 GGTTTTTAATTTAA-GGCTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144119 GGTTTTTAATTTAATGGTTAGGGTTAG
1 GGTTTTTAAGTTAA--G---GGTTTAG
* * *
144146 GGTTTTTAAGTTAAAGATTTAA
1 GGTTTTTAAGTTAAGGGTTTAG
144168 GGTATAATTGT-A-TTAAGGGTTTAG
1 GGT-T--TT-TAAGTTAAGGGTTTAG
* *
144192 GGTTTTAAATTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144213 GGTTTTTAA-TTAA-GGATTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144233 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144255 GGTTTTTAAGTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144276 GGTTATTAAGTTAAGGG-TTAC
1 GGTTTTTAAGTTAAGGGTTTAG
**
144297 AATTTTTAAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144318 GGTTTTTAAGTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144339 GGTTTTTAAGTTAA-GGTTTAC
1 GGTTTTTAAGTTAAGGGTTTAG
**
144360 AATTTTTAAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144381 GGTTTTTAAGTTAA-AGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144402 GGTTTTTAATTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144423 GGTTTTTAA-TTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144443 GGTTTTTAAGTTTA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* * *
144464 GATTTTTAAGTTAAAGGTTTAA
1 GGTTTTTAAGTTAAGGGTTTAG
*
144486 GGTTTTTAAGTTAA-GATTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144507 GGTTTTTAAGTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144528 GGTTTTTAAGTTTAA-GG-TTAG
1 GGTTTTTAAG-TTAAGGGTTTAG
** *
144549 CATTTTTAAGTTAAAGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144571 GGTTTTTAATTTAA-GGTTTAA
1 GGTTTTTAAGTTAAGGGTTTAG
* * *
144592 TGTTTTTAATTTAATGGTTAGGGTTAG
1 GGTTTTTAAGTTAA--G---GGTTTAG
*
144619 GGTTTTTAAGTTGAA-GGTTTAT
1 GGTTTTTAAGTT-AAGGGTTTAG
144641 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144663 GGTTATTAATTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144684 GGTTTTTAAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144705 GGTTTTTAAGTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144726 GGTTTTTAAGTTAAGGGTTTTG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144748 GGTTTTTAAGTTAA-GGTTTAA
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144769 GGTTATTAGGTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
144790 GGTTTTTAAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144811 GGTCTTTAAGTTAAGGG-TTAA
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144832 GGTTTCTAATTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144853 GGTTTTTAATTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144874 GGTTTTTAA-TTAA-GGTTTAA
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144894 GGTTTTTAAGTT-TGGGGTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
144915 GGTTTTTAAGTTAAGGGTTTAA
1 GGTTTTTAAGTTAAGGGTTTAG
*
144937 GGTTTTTAAGTGAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
144958 GGTTATTAAGTTAAGGG-TTAC
1 GGTTTTTAAGTTAAGGGTTTAG
*
144979 GATTTTTAAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
145000 GGTTTCTAATTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145021 GGTTTTTAATTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
145042 GGTTTTTAA-TT-ATGGTTTAA
1 GGTTTTTAAGTTAAGGGTTTAG
* *
145062 GGTTTTTAAGTT-TGGGGTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145083 GTTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145105 GGTTTTTAAGTTAA-AGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145126 GGTTATTAAGTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145147 GGTTTTTAAGTTAAGGG-TTAC
1 GGTTTTTAAGTTAAGGGTTTAG
** *
145168 AATTTTTAAGATAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145189 GGTTATTAAGTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
145210 GGTTTTTAATTTAAGAG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
145231 TGTTTTTAA-TT-AGGGGTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
145251 GGTTTTGAAGTTAAGGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAG
145273 GGTTTTTAAGTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145294 GGTTATTAAGTTAA-GGTTTA-
1 GGTTTTTAAGTTAAGGGTTTAG
145314 GGTTTTTAAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
145335 GGGTTTTAAGTTAAAGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* **
145357 GGTTTTTAATTTAA-ATTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145378 GG-TTTTAATTTATTGGTTAGGG-TTAG
1 GGTTTTTAAGTTA------AGGGTTTAG
* *
145404 GGTTTTTAAGTTAAAGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAG
145426 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
145448 GGTTATTAATTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145469 GGTTATTAAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145490 GGTTTTTGAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
145511 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145533 GGTTATTAAGTTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* *
145554 GGTTATTAAGCTAA-GGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* * *
145575 GGCTTTTAATTTAAGGG-TTAA
1 GGTTTTTAAGTTAAGGGTTTAG
145596 GGTTTTTAAGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145617 GGTTTTTATGTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* * *
145638 GGTTTTAAATTTAAGGGATTAG
1 GGTTTTTAAGTTAAGGGTTTAG
** * *
145660 CATTTTTATGCTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* * * *
145681 TGATTTTAATTTATGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
145702 GGTTTTTAA-TTAA-GGTTTAGGGGG
1 GGTTTTTAAGTTAAGGGTTTA----G
* *
145726 TTTATGGTTTTTAATTTAA-GGTTAAG
1 -----GGTTTTTAAGTTAAGGGTTTAG
** *
145752 GGTTTTTATTTTAATGGTTAGGGTTAG
1 GGTTTTTAAGTTAA--G---GGTTTAG
* * *
145779 GATTTTTAACTTTAA-GGTTTAT
1 GGTTTTTAA-GTTAAGGGTTTAG
145801 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* * *
145823 GATTATTAATTTAAGGG-TTAG
1 GGTTTTTAAGTTAAGGGTTTAG
* * *
145844 GGTTATTAAGTTAAGGATTAAG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145866 GG-TTTTAAGTTAAGGGTTTTG
1 GGTTTTTAAGTTAAGGGTTTAG
*
145887 GGTTTTTAATTTAAGGGTT
1 GGTTTTTAAGTTAAGGGTT
145906 ATGTTTAGGG
Statistics
Matches: 1789, Mismatches: 234, Indels: 212
0.80 0.10 0.09
Matches are distributed among these distances:
19 12 0.01
20 170 0.10
21 1078 0.60
22 403 0.23
23 2 0.00
24 13 0.01
25 3 0.00
26 9 0.01
27 74 0.04
28 7 0.00
29 9 0.01
30 9 0.01
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.46
Consensus pattern (22 bp):
GGTTTTTAAGTTAAGGGTTTAG
Found at i:145979 original size:10 final size:12
Alignment explanation
Indices: 145949--145979 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
145939 TTGTCAATTA
145949 AATTATATATTT
1 AATTATATATTT
145961 AATTATATATTT
1 AATTATATATTT
145973 AATTATA
1 AATTATA
145980 AATTATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATTATATATTT
Found at i:147188 original size:7 final size:7
Alignment explanation
Indices: 147178--147203 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
147168 TTATATACAT
147178 AATACTA
1 AATACTA
147185 AATACTA
1 AATACTA
147192 AATACTA
1 AATACTA
147199 AATAC
1 AATAC
147204 CAATCGACTA
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:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:147397 original size:20 final size:20
Alignment explanation
Indices: 147372--147409 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
147362 TTTATTTTTA
147372 AAAATCTAA-ATAATAATTGT
1 AAAATCTAATATAA-AATTGT
147392 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
147410 TACCTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:157575 original size:19 final size:20
Alignment explanation
Indices: 157533--157572 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
157523 ACTCATCGTA
*
157533 TTCAAATAATTATTAGAAGT
1 TTCAAATAATTATCAGAAGT
157553 TTCAAA-AATT-TCAGAAGT
1 TTCAAATAATTATCAGAAGT
157571 TT
1 TT
157573 TCAGTCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (20 bp):
TTCAAATAATTATCAGAAGT
Found at i:158198 original size:25 final size:25
Alignment explanation
Indices: 158169--158218 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
158159 AATTTAAGTA
158169 AGGCAAATTAAAGTAAAAATAGTTT
1 AGGCAAATTAAAGTAAAAATAGTTT
158194 AGGCAAATTAAAGTAAAAATAGTTT
1 AGGCAAATTAAAGTAAAAATAGTTT
158219 TATGGCATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.28
Consensus pattern (25 bp):
AGGCAAATTAAAGTAAAAATAGTTT
Found at i:167116 original size:13 final size:13
Alignment explanation
Indices: 167098--167122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
167088 GAGGTTTGAT
167098 TTATTTTGAACTC
1 TTATTTTGAACTC
167111 TTATTTTGAACT
1 TTATTTTGAACT
167123 ATTGTTAGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (13 bp):
TTATTTTGAACTC
Found at i:171163 original size:25 final size:25
Alignment explanation
Indices: 171135--171217 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
171125 TAGGATCATC
**
171135 ATGACATTTCATCGTCAAAATCAAA
1 ATGACATTTCATTTTCAAAATCAAA
* * *
171160 ATGACATGTCATTTTTAGAATCAAA
1 ATGACATTTCATTTTCAAAATCAAA
*
171185 ATGAC-TTGTCATTTTCAAGAT-AAA
1 ATGACATT-TCATTTTCAAAATCAAA
171209 ATGACATTT
1 ATGACATTT
171218 GATTATAAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 10 0.21
25 37 0.79
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (25 bp):
ATGACATTTCATTTTCAAAATCAAA
Found at i:171246 original size:49 final size:49
Alignment explanation
Indices: 171111--171265 Score: 125
Period size: 49 Copynumber: 3.1 Consensus size: 49
171101 CATAATAAGG
** * *
171111 ATGACATTTGATTATAGGATCATCATGACATTTCATCGTCAAAATCAAA
1 ATGACATTTGATTATAGGATCAAAATGACCTTTCATTGTCAAAATCAAA
* * * * * *
171160 ATGACATGTCATTTTTAGAATCAAAATGA-CTTGTCATTTTCAAGAT-AAA
1 ATGACATTTGA-TTATAGGATCAAAATGACCTT-TCATTGTCAAAATCAAA
* * ** *
171209 ATGACATTTGATTATAAGGATCAGAATAACCTTTCATTACCAAAATCAGA
1 ATGACATTTGATTAT-AGGATCAAAATGACCTTTCATTGTCAAAATCAAA
*
171259 ATAACAT
1 ATGACAT
171266 ATGTTTATTT
Statistics
Matches: 80, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
48 3 0.04
49 43 0.54
50 34 0.43
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (49 bp):
ATGACATTTGATTATAGGATCAAAATGACCTTTCATTGTCAAAATCAAA
Found at i:172960 original size:23 final size:23
Alignment explanation
Indices: 172934--172979 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
172924 TCTACAGATG
*
172934 AATCGCACTGAAGTACCAGAATA
1 AATCACACTGAAGTACCAGAATA
* * *
172957 AATCATATTGAAGTGCCAGAATA
1 AATCACACTGAAGTACCAGAATA
172980 CTCCTACTAA
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:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (23 bp):
AATCACACTGAAGTACCAGAATA
Found at i:174320 original size:79 final size:79
Alignment explanation
Indices: 173963--174297 Score: 670
Period size: 79 Copynumber: 4.2 Consensus size: 79
173953 TTTCCCTTCC
173963 AGATTTCTACTTCTTCTTCTGGTACAATACGCTTCTTTTCTTCTCACATTTCTTTTCTTTTATCC
1 AGATTTCTACTTCTTCTTCTGGTACAATACGCTTCTTTTCTTCTCACATTTCTTTTCTTTTATCC
174028 ATTTTCTTTTCTCT
66 ATTTTCTTTTCTCT
174042 AGATTTCTACTTCTTCTTCTGGTACAATACGCTTCTTTTCTTCTCACATTTCTTTTCTTTTATCC
1 AGATTTCTACTTCTTCTTCTGGTACAATACGCTTCTTTTCTTCTCACATTTCTTTTCTTTTATCC
174107 ATTTTCTTTTCTCT
66 ATTTTCTTTTCTCT
174121 AGATTTCTACTTCTTCTTCTGGTACAATACGCTTCTTTTCTTCTCACATTTCTTTTCTTTTATCC
1 AGATTTCTACTTCTTCTTCTGGTACAATACGCTTCTTTTCTTCTCACATTTCTTTTCTTTTATCC
174186 ATTTTCTTTTCTCT
66 ATTTTCTTTTCTCT
174200 AGATTTCTACTTCTTCTTCTGGTACAATACGCTTCTTTTCTTCTCACATTTCTTTTCTTTTATCC
1 AGATTTCTACTTCTTCTTCTGGTACAATACGCTTCTTTTCTTCTCACATTTCTTTTCTTTTATCC
174265 ATTTTCTTTTCTCT
66 ATTTTCTTTTCTCT
174279 AGATTTCTACTTCTTCTTC
1 AGATTTCTACTTCTTCTTC
174298 CAAATTTTTT
Statistics
Matches: 256, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 256 1.00
ACGTcount: A:0.14, C:0.25, G:0.05, T:0.56
Consensus pattern (79 bp):
AGATTTCTACTTCTTCTTCTGGTACAATACGCTTCTTTTCTTCTCACATTTCTTTTCTTTTATCC
ATTTTCTTTTCTCT
Found at i:177317 original size:61 final size:61
Alignment explanation
Indices: 177252--177444 Score: 232
Period size: 61 Copynumber: 3.2 Consensus size: 61
177242 ATTTTATAGT
177252 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAA
* ** * * * * * * * * *
177313 ATTATATATTATTATTAAATTATATTTA-ATAATAATTATTTTA-AATTA-TATTTTA-TAGT
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TATTTCATACTAAGAATTTTATTA-A
177372 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAA
177433 ATTATATATTAT
1 ATTATATATTAT
177445 TATTAAATTA
Statistics
Matches: 102, Mismatches: 24, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
58 2 0.02
59 34 0.33
60 18 0.18
61 46 0.45
62 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (61 bp):
ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAA
Found at i:177319 original size:59 final size:59
Alignment explanation
Indices: 177256--177439 Score: 182
Period size: 59 Copynumber: 3.1 Consensus size: 59
177246 TATAGTATTA
177256 TATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAAAT
1 TATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAAAT
* * * * ** * *
177315 TATA-TAT--TATTATTAAATT-ATATTTAATAATAATT-ATTTTAAATTATATTTTA-TAGTAT
1 TATATTATGATTTTAGTAAATTCATA--TAAGAATATTTCATACT-AA-GA-ATTTTATTA--AA
177374 T
59 T
177375 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAAAT
1 -TATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAAAT
177435 TATAT
1 TATAT
177440 ATTATTATTA
Statistics
Matches: 95, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
55 3 0.03
56 13 0.14
57 11 0.12
58 6 0.06
59 15 0.16
60 4 0.04
61 10 0.11
62 6 0.06
63 11 0.12
64 13 0.14
65 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (59 bp):
TATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTAAAT
Found at i:177362 original size:26 final size:28
Alignment explanation
Indices: 177302--177482 Score: 102
Period size: 28 Copynumber: 6.2 Consensus size: 28
177292 TCATACTAAG
* * *
177302 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
177330 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
* *
177356 AATTATATTTTATAGTATTATATATTATGATTT
1 AATTATA-TTTA-A-TA--ATATATTATTATTA
* * * * * *
177389 TAGTAAATTCATATAAGAATATT-TCATACTAA
1 AATTATATTTA-ATAA-TATATTAT--TA-TTA
* * *
177421 GAATTTTATTAAATTATATATTATTATTA
1 -AATTATATTTAATAATATATTATTATTA
177450 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
177476 AATTATA
1 AATTATA
177483 CAAATTCATA
Statistics
Matches: 116, Mismatches: 24, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
26 20 0.17
27 16 0.14
28 29 0.25
29 6 0.05
30 7 0.06
31 11 0.09
32 15 0.13
33 12 0.10
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:177371 original size:120 final size:120
Alignment explanation
Indices: 177227--177482 Score: 512
Period size: 120 Copynumber: 2.1 Consensus size: 120
177217 TTCAAATTTT
177227 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
177292 TCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATA
66 TCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATA
177347 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
1 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
177412 TCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATA
66 TCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATA
177467 ATTATTTTAAATTATA
1 ATTATTTTAAATTATA
177483 CAAATTCATA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 136 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (120 bp):
ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
TCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATA
Found at i:177473 original size:61 final size:61
Alignment explanation
Indices: 177288--177473 Score: 218
Period size: 61 Copynumber: 3.1 Consensus size: 61
177278 CATATAAGAA
177288 TATTTCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATAAT
1 TATTTCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATAAT
* * * * * * ** * * * *
177349 TATTTTA-AATTA-TATTTTA-TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAA-
1 TATTTCATACTAAGAATTTTATTA-AATTATATATTATTATTAAATTATATTTA-ATAATAAT
177408 TATTTCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATAAT
1 TATTTCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATAAT
177469 TATTT
1 TATTT
177474 TAAATTATAC
Statistics
Matches: 95, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
58 2 0.02
59 34 0.36
60 18 0.19
61 39 0.41
62 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (61 bp):
TATTTCATACTAAGAATTTTATTAAATTATATATTATTATTAAATTATATTTAATAATAAT
Found at i:177524 original size:91 final size:90
Alignment explanation
Indices: 177321--177526 Score: 201
Period size: 91 Copynumber: 2.3 Consensus size: 90
177311 AAATTATATA
* * * *
177321 TTATTATTAAATTATATTT-AATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATG
1 TTATTATTAAATTAT-TTTAAATTATAATTATTTTAAATTATATTTAATAATATTATATATTATA
* * *
177385 ATTTTAGTAAATTCATATAAGAATAT
65 ATTATAGCAAATTCATATAAGAAAAT
*
177411 TTCA-TACTAAGAATT-TTATTAAATTATATATTATTATTAAATTATATTTAATAATAATTAT-T
1 TT-ATTA-TTA-AATTATT-TTAAATTATA-ATTATT-TTAAATTATATTTAATAAT-ATTATAT
177473 -TTA-AATTATA-CAAATTCATATAAGAAAAT
59 ATTATAATTATAGCAAATTCATATAAGAAAAT
177502 TTATTAGTTATAATTATTTTAAATT
1 TTATTA-TTA-AATTATTTTAAATT
177527 TTATTAAATC
Statistics
Matches: 95, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
90 6 0.06
91 40 0.42
92 17 0.18
93 9 0.09
94 18 0.19
95 5 0.05
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (90 bp):
TTATTATTAAATTATTTTAAATTATAATTATTTTAAATTATATTTAATAATATTATATATTATAA
TTATAGCAAATTCATATAAGAAAAT
Found at i:177597 original size:28 final size:27
Alignment explanation
Indices: 177510--177597 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 27
177500 ATTTATTAGT
* *
177510 TATAATTATTTTAAATTTTATTAAATCA
1 TATAATTA-TTTAAATTATATTAAATTA
* * * *
177538 TATATTTTAATTAAAATATATTTAA-TA
1 TATA-ATTATTTAAATTATATTAAATTA
177565 T-TAATTATTTCAAATTATATTAAATTA
1 TATAATTATTT-AAATTATATTAAATTA
177592 TATAAT
1 TATAAT
177598 ATAGTATCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
25 5 0.11
26 13 0.28
27 5 0.11
28 20 0.43
29 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
TATAATTATTTAAATTATATTAAATTA
Found at i:177684 original size:14 final size:15
Alignment explanation
Indices: 177663--177711 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
177653 AATTTTATTA
177663 AATT-ATATAT-TTT
1 AATTAATATATGTTT
177676 AATTAATATATGTTT
1 AATTAATATATGTTT
*
177691 AA-TAATAATTATGTTA
1 AATTAAT-A-TATGTTT
177707 AATTA
1 AATTA
177712 TCTTAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.13
14 10 0.33
15 6 0.20
16 8 0.27
17 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
AATTAATATATGTTT
Found at i:177855 original size:39 final size:41
Alignment explanation
Indices: 177799--177904 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
177789 TTTCCTTATG
* *
177799 CTATTACACCTTTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACACCTCTATTCCATTCAACCAAACAAAAGAATTAC
*
177839 C-ATTACGCCTCTATTCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACACCTC---T--ATTCCATTCAACCAAACAAAAGAATTAC
177884 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
177905 ACGCATCTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 8 0.15
40 1 0.02
41 8 0.15
42 1 0.02
43 1 0.02
44 23 0.42
45 4 0.07
46 9 0.16
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.30
Consensus pattern (41 bp):
CTATTACACCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:177879 original size:44 final size:46
Alignment explanation
Indices: 177812--177904 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
177802 TTACACCTTT
* *
177812 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCC
177856 ATTCCATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCC
177902 ATT
1 ATT
177905 ACGCATCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 4 0.09
46 18 0.40
ACGTcount: A:0.38, C:0.31, G:0.03, T:0.28
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACACCTCTATTCC
Found at i:177932 original size:16 final size:16
Alignment explanation
Indices: 177886--177939 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
177876 AGAATTACCT
177886 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* *
177902 ATTACGCATCTATTCC
1 ATTACACCTCTATTCC
*
177918 ATTACACCTCAATTCC
1 ATTACACCTCTATTCC
*
177934 AATACA
1 ATTACA
177940 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:181065 original size:51 final size:51
Alignment explanation
Indices: 180989--181093 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
180979 GTAAGGGGGG
180989 ATTTTGGAATGTAAAGAAAAAATACAGAGACAAAGAAAATAGAAAAAAAAT
1 ATTTTGGAATGTAAAGAAAAAATACAGAGACAAAGAAAATAGAAAAAAAAT
181040 ATTTTGGAATGTAAAGAAAAAATACAGAGACAAAGAAAATAGAAAAAAAAT
1 ATTTTGGAATGTAAAGAAAAAATACAGAGACAAAGAAAATAGAAAAAAAAT
181091 ATT
1 ATT
181094 GATAGGAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.62, C:0.04, G:0.15, T:0.19
Consensus pattern (51 bp):
ATTTTGGAATGTAAAGAAAAAATACAGAGACAAAGAAAATAGAAAAAAAAT
Found at i:181083 original size:26 final size:26
Alignment explanation
Indices: 181003--181087 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
180993 TGGAATGTAA
181003 AGAAAAAATACAGAGACAAAGAAAAT
1 AGAAAAAATACAGAGACAAAGAAAAT
**** * * *
181029 AGAAAAAAAATATTTTG-GAATG-TAA-
1 AG--AAAAAATACAGAGACAAAGAAAAT
181054 AGAAAAAATACAGAGACAAAGAAAAT
1 AGAAAAAATACAGAGACAAAGAAAAT
181080 AGAAAAAA
1 AGAAAAAA
181088 AATATTGATA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
23 9 0.22
24 3 0.08
25 4 0.10
26 12 0.30
27 3 0.08
28 9 0.22
ACGTcount: A:0.67, C:0.05, G:0.15, T:0.13
Consensus pattern (26 bp):
AGAAAAAATACAGAGACAAAGAAAAT
Found at i:185621 original size:19 final size:20
Alignment explanation
Indices: 185576--185621 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
185566 AATTTATAAA
185576 AAAAAATCATAATAAATATT
1 AAAAAATCATAATAAATATT
*
185596 ATAAAAA-CA-AATAAATTTGT
1 A-AAAAATCATAATAAATAT-T
185616 AAAAAA
1 AAAAAA
185622 ACATGAGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 13 0.57
20 5 0.22
21 5 0.22
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAAATCATAATAAATATT
Found at i:185623 original size:20 final size:20
Alignment explanation
Indices: 185575--185625 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
185565 AAATTTATAA
185575 AAAAAAATCATAATAAATATT
1 AAAAAAA-CATAATAAATATT
* *
185596 ATAAAAACA-AATAAATTTGT
1 AAAAAAACATAATAAATAT-T
185616 AAAAAAACAT
1 AAAAAAACAT
185626 GAGCAAGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 8 0.32
20 11 0.44
21 6 0.24
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAAACATAATAAATATT
Found at i:185843 original size:9 final size:9
Alignment explanation
Indices: 185829--185905 Score: 55
Period size: 10 Copynumber: 7.9 Consensus size: 9
185819 ATTCCATATG
*
185829 TTTTATTAT
1 TTTTATAAT
185838 TTTTATAAT
1 TTTTATAAT
*
185847 TTATTAGAACT
1 TT-TTATAA-T
185858 TTTTATAAGT
1 TTTTATAA-T
*
185868 TTTTATGACT
1 TTTTAT-AAT
*
185878 TATTTATAAG
1 T-TTTATAAT
185888 TTTTATAAGT
1 TTTTATAA-T
*
185898 TTATATAA
1 TTTTATAA
185906 ATTCCATGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
9 17 0.31
10 28 0.52
11 9 0.17
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (9 bp):
TTTTATAAT
Found at i:185873 original size:30 final size:30
Alignment explanation
Indices: 185828--185905 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
185818 TATTCCATAT
* *
185828 GTTTTATTA-TTTTTATAATTTA-TTAGAA
1 GTTTTATAAGTTTTTATAACTTATTTAGAA
* * *
185856 CTTTTTATAAGTTTTTATGACTTATTTATAA
1 -GTTTTATAAGTTTTTATAACTTATTTAGAA
*
185887 GTTTTATAAGTTTATATAA
1 GTTTTATAAGTTTTTATAA
185906 ATTCCATGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 7 0.18
30 27 0.69
31 5 0.13
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.58
Consensus pattern (30 bp):
GTTTTATAAGTTTTTATAACTTATTTAGAA
Found at i:185893 original size:20 final size:20
Alignment explanation
Indices: 185837--185891 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
185827 TGTTTTATTA
185837 TTTTTATAA-TTTATTA-GAAC
1 TTTTTATAAGTTT-TTATG-AC
185857 TTTTTATAAGTTTTTATGAC
1 TTTTTATAAGTTTTTATGAC
185877 TTATTTATAAGTTTT
1 TT-TTTATAAGTTTT
185892 ATAAGTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTTATAAGTTTTTATGAC
Found at i:185901 original size:21 final size:21
Alignment explanation
Indices: 185839--185896 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
185829 TTTTATTATT
185839 TTTATAA-TTTATT-AGAACTT-
1 TTTATAAGTTT-TTAAG-ACTTA
*
185859 TTTATAAGTTTTTATGACTTA
1 TTTATAAGTTTTTAAGACTTA
185880 TTTATAAGTTTTATAAG
1 TTTATAAGTTTT-TAAG
185897 TTTATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 13 0.41
21 16 0.50
22 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (21 bp):
TTTATAAGTTTTTAAGACTTA
Found at i:188211 original size:43 final size:42
Alignment explanation
Indices: 188158--188356 Score: 206
Period size: 43 Copynumber: 4.7 Consensus size: 42
188148 GTTTTTAGAA
188158 ACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCTC
1 ACAAACGCCGCTAAAGAACAA-ACCTTTAGCGGCGCTTTTCTC
* *
188201 ACAAACGCCGCTAAAG-ACAAAGGCCTTTAGCGGCGCTTTCCCC
1 ACAAACGCCGCTAAAGAACAAA--CCTTTAGCGGCGCTTTTCTC
* * * *
188244 ACAAACGCCGCTAAAGACCATAACCTTTAGCGACGTTTTTTGTC
1 ACAAACGCCGCTAAAGAACA-AACCTTTAGCGGCG-CTTTTCTC
* * * * *
188288 ACAAATGCCGCT-AAGATCAAACCTTTAGCAGCGCTTCTCGC
1 ACAAACGCCGCTAAAGAACAAACCTTTAGCGGCGCTTTTCTC
* *
188329 AAAAACGCCACTAAA-AACATAACCTTTA
1 ACAAACGCCGCTAAAGAACA-AACCTTTA
188357 AAAAAAATTA
Statistics
Matches: 129, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
41 17 0.13
42 26 0.20
43 67 0.52
44 17 0.13
45 2 0.02
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (42 bp):
ACAAACGCCGCTAAAGAACAAACCTTTAGCGGCGCTTTTCTC
Found at i:188270 original size:86 final size:85
Alignment explanation
Indices: 188158--188356 Score: 237
Period size: 86 Copynumber: 2.3 Consensus size: 85
188148 GTTTTTAGAA
*
188158 ACAAACGCCGCTAAAGAACA-AGACCTTTAGCGGCG-CTTTTCTCACAAACGCCGCTAAAGA-CA
1 ACAAACGCCGCTAAAGAACATA-ACCTTTAGCGACGTCTTTTCTCACAAACGCCGCT-AAGATCA
*
188220 AAGGCCTTTAGCGGCGCTT-TCCCC
64 AA--CCTTTAGCAGCGCTTCT-CCC
* * * *
188244 ACAAACGCCGCTAAAGACCATAACCTTTAGCGACGTTTTTTGTCACAAATGCCGCTAAGATCAAA
1 ACAAACGCCGCTAAAGAACATAACCTTTAGCGACGTCTTTTCTCACAAACGCCGCTAAGATCAAA
*
188309 CCTTTAGCAGCGCTTCTCGC
66 CCTTTAGCAGCGCTTCTCCC
* *
188329 AAAAACGCCACTAAA-AACATAACCTTTA
1 ACAAACGCCGCTAAAGAACATAACCTTTA
188357 AAAAAAATTA
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
84 12 0.12
85 29 0.29
86 36 0.36
87 22 0.22
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (85 bp):
ACAAACGCCGCTAAAGAACATAACCTTTAGCGACGTCTTTTCTCACAAACGCCGCTAAGATCAAA
CCTTTAGCAGCGCTTCTCCC
Found at i:192818 original size:145 final size:146
Alignment explanation
Indices: 192548--192887 Score: 479
Period size: 146 Copynumber: 2.3 Consensus size: 146
192538 TTTAAAAGTA
* * * *
192548 ATTTTTTGTGGCGTTTTATATGAAAATGCCGCTATTGCTTATCTATTGCGGCGTTTTTTATAAAA
1 ATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTTATAAAA
* * * * *
192613 ATGCCGCAAAAAATTATTTTATTTGGAATAAAACGACGCTGTTTGTTATATAAAATGGCGCTA-T
66 ACGCCGCAAAAAATTATTTTATTTAGAATAAAACGACACTGTTTGCTATATAAAAGGGCGCTATT
192677 TTTTTAAAATAAAATT
131 TTTTTAAAATAAAATT
* * *
192693 ATTTTTTGTGGCGTTTTTTAAAAAAACGCCGCTATTGATTAACTTTTGCGGCG-TTTTTA-AAAA
1 ATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTTATAAAA
* * * *
192756 ACGCCGTAAAAAATTATTTTATTTAGAATAAAACGACACTATTTTGCTATGCTAAGAGGGCGCTA
66 ACGCCGCAAAAAATTATTTTATTTAGAATAAAACGACACT-GTTTGCTAT-ATAAAAGGGCGCTA
* *
192821 TTTTTTTTAAGTAAAATT
129 TTTTTTTAAAATAAAATT
192839 ATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTATCTTTTGC
1 ATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTATCTTTTGC
192888 TAAAAATCTT
Statistics
Matches: 171, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
143 40 0.23
144 13 0.08
145 57 0.33
146 61 0.36
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (146 bp):
ATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTATCTTTTGCGGCGTTTTTTATAAAA
ACGCCGCAAAAAATTATTTTATTTAGAATAAAACGACACTGTTTGCTATATAAAAGGGCGCTATT
TTTTTAAAATAAAATT
Found at i:194880 original size:41 final size:41
Alignment explanation
Indices: 194818--195018 Score: 285
Period size: 41 Copynumber: 4.9 Consensus size: 41
194808 AGATTTTATT
* **
194818 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
194859 ATCAGCGGCACTTCTTAAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
194900 ATTAGCGGTGCTTATTCGAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
194941 ATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
*
194982 ATTAGTGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
195019 CAAAAACTCA
Statistics
Matches: 139, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 139 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:195178 original size:40 final size:40
Alignment explanation
Indices: 195054--195189 Score: 163
Period size: 40 Copynumber: 3.5 Consensus size: 40
195044 GGGCTTAGGC
* *
195054 TTTTT-GCGGCGCTTTTCAAAAAACGCCGCTAATGCT-TA
1 TTTTTAGCGGCGCTTTTTAAAAAGCGCCGCTAATGCTCTA
*
195092 TTTTTAGCGGCG-TTTTCTAAAAAGCACCGCTAATGCTCTA
1 TTTTTAGCGGCGCTTTT-TAAAAAGCGCCGCTAATGCTCTA
** *
195132 CCTTTAGCGGCG-TTTTTATAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGCTTTTTA-AAAAGCGCCGCTAATGCTCTA
*
195172 TTTTTAGTGGCGCTTTTT
1 TTTTTAGCGGCGCTTTTT
195190 GTCCAAACGC
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
38 9 0.11
39 25 0.30
40 44 0.53
41 5 0.06
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGCTTTTTAAAAAGCGCCGCTAATGCTCTA
Found at i:195211 original size:12 final size:12
Alignment explanation
Indices: 195194--195219 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
195184 CTTTTTGTCC
195194 AAACGCCGCTAA
1 AAACGCCGCTAA
195206 AAACGCCGCTAA
1 AAACGCCGCTAA
195218 AA
1 AA
195220 GCCTGTTTTG
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:202402 original size:25 final size:25
Alignment explanation
Indices: 202362--202409 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
202352 CTTAGTTTCG
*
202362 TTTTGTTATTTTTTTTTCTTTTAGC
1 TTTTGTTATTTTTTTTTCATTTAGC
202387 TTTT-TTATTTTATTTTTCATTTA
1 TTTTGTTATTTT-TTTTTCATTTA
202410 AAATATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTTGTTATTTTTTTTTCATTTAGC
Found at i:203069 original size:25 final size:27
Alignment explanation
Indices: 203026--203093 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
203016 TTGTATTTTC
* * * *
203026 TATACATATAAATACGCAT-TTTTTTA
1 TATATATATATATAAGCATATTTTTAA
203052 TATATA-ATATATAAGCATATTTTTAA
1 TATATATATATATAAGCATATTTTTAA
*
203078 TATATATATTTATAAG
1 TATATATATATATAAG
203094 TACGCATCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 10 0.29
26 17 0.49
27 8 0.23
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (27 bp):
TATATATATATATAAGCATATTTTTAA
Found at i:203132 original size:6 final size:6
Alignment explanation
Indices: 203121--203147 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
203111 CATACATACT
203121 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
203148 CCTAACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:208235 original size:7 final size:7
Alignment explanation
Indices: 208210--208253 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
208200 AGTGATGTGA
208210 AAAAATG
1 AAAAATG
208217 AAAAGATG
1 AAAA-ATG
208225 -AAAATG
1 AAAAATG
208231 AAAAATG
1 AAAAATG
208238 AAAAA-G
1 AAAAATG
208244 TAAAAATG
1 -AAAAATG
208252 AA
1 AA
208254 GAGGCTAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 4 0.12
7 25 0.76
8 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:208249 original size:21 final size:21
Alignment explanation
Indices: 208210--208253 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
208200 AGTGATGTGA
*
208210 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
208231 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
208252 AA
1 AA
208254 GAGGCTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:209610 original size:44 final size:44
Alignment explanation
Indices: 209555--210498 Score: 956
Period size: 44 Copynumber: 21.4 Consensus size: 44
209545 CATACTGGTG
**
209555 ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGAT
1 ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGGC
*** * * *
209599 ATGAAGTAGATC-AGAGATAGCAGATCTTATCTTCATGTGTTGAC
1 ATGAAGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGGC
*
209643 ATGAAGTAGATCGAA-AGTAATGGATCTTGTCTTCATGTATTGAC
1 ATGAAGTAGATCGAAGA-TAATGGATCTTGTCTTCATGTATTGGC
*** * *
209687 ATGAAGTAGATC-AGAGATAGCAGATCTTATCTTCATGTATTGAC
1 ATGAAGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGGC
* * * *
209731 ATGAAGTAGATCGAAGGTAATGAATTTTGTCTTCATGTATTGAC
1 ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGGC
*** * * * *
209775 ATGAAGTAGATC-AGAGATAGCAGATCTTGTCTTCCTATACTGGTG
1 ATGAAGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGG-C
* * * *
209820 GTGAAGTAGATCGAAGGTAATTGATCTTGTCTTCATGTATTGAC
1 ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGGC
* * * * *
209864 ATGAAGTAGATC-AGAGATAGTAGATCTTATCTTCTTGTATTGAC
1 ATGAAGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGGC
*
209908 ATGAAGTAGATCGAA-AGTAATGGATCTTGTCTTCATGTATTGAC
1 ATGAAGTAGATCGAAGA-TAATGGATCTTGTCTTCATGTATTGGC
***
209952 ATGAAGTAGATC-AGAGATAGCAGATCTTGTCTTCATGTATTGGC
1 ATGAAGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGGC
209996 ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGGC
1 ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGGC
* ** *
210040 GTGACA-TAGATC-AGAGATAACAGATCTTGTCTTCATGTATTGGT
1 ATGA-AGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGGC
*
210084 ATGAAGTAGATCGGAGATAATGGATCTTGTCTTCATGTATTGGC
1 ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGGC
* ** *
210128 GTGACA-TAGATC-AGAGATAACAGATCTTGTCTTCATGTATTGGT
1 ATGA-AGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGGC
* *
210172 ATGAAGTAGATCGGAGATAATGGATCTTGTCTTCATGTATTGAC
1 ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGGC
***
210216 ATGAAGTAGATC-AGAGATAGCAGATCTTGTCTTCATGTATTGGC
1 ATGAAGTAGATCGA-AGATAATGGATCTTGTCTTCATGTATTGGC
* * *
210260 GTGAAGAAGATCGAAGA-AA-GCAGATCTTGTCTTCATGTACTGGC
1 ATGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATGTATTGGC
* *
210304 GTGAAGTAGATCGAAGA-AA-GCAGATCTTGTCTTCATGTACTGGC
1 ATGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATGTATTGGC
* *
210348 GTGAAGTAGATCGAAGA-AA-GCAGATCTTGTCTTCATGTACTGGC
1 ATGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATGTATTGGC
* *
210392 GTGAAGTAGATCGAAGA-AA-GCAGATCTTGTCTTCATGTACTGGC
1 ATGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATGTATTGGC
* *** * *
210436 GTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGCATTGAC
1 ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGGC
210480 ATGAAGTAGATCGAAGATA
1 ATGAAGTAGATCGAAGATA
210499 CCAGTCTTAT
Statistics
Matches: 774, Mismatches: 97, Indels: 58
0.83 0.10 0.06
Matches are distributed among these distances:
43 11 0.01
44 720 0.93
45 42 0.05
46 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (44 bp):
ATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGGC
Found at i:210496 original size:88 final size:88
Alignment explanation
Indices: 209528--210491 Score: 1273
Period size: 88 Copynumber: 10.9 Consensus size: 88
209518 GCTAAAAAGC
*** * *
209528 AGCAGATCTTGTCTTCCCATACTGGTGATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTATTGG-CATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
*
209593 ATTGATATGAAGTAGATCAGAGAT
65 ATTGACATGAAGTAGATCAGAGAT
* * *
209617 AGCAGATCTTATCTTCATGTGTTGACATGAAGTAGATCGAA-AGTAATGGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGA-TAATGGATCTTGTCTTCATGT
209681 ATTGACATGAAGTAGATCAGAGAT
65 ATTGACATGAAGTAGATCAGAGAT
* * * * *
209705 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGGTAATGAATTTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
209770 TTGACATGAAGTAGATCAGAGAT
66 TTGACATGAAGTAGATCAGAGAT
* * * ** * *
209793 AGCAGATCTTGTCTTCCTATACTGGTGGTGAAGTAGATCGAAGGTAATTGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTATTGG-CATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
209858 ATTGACATGAAGTAGATCAGAGAT
65 ATTGACATGAAGTAGATCAGAGAT
* * * *
209882 AGTAGATCTTATCTTCTTGTATTGACATGAAGTAGATCGAA-AGTAATGGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGA-TAATGGATCTTGTCTTCATGT
209946 ATTGACATGAAGTAGATCAGAGAT
65 ATTGACATGAAGTAGATCAGAGAT
209970 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
* *
210035 TTGGCGTGACA-TAGATCAGAGAT
66 TTGACATGA-AGTAGATCAGAGAT
* * *
210058 AACAGATCTTGTCTTCATGTATTGGTATGAAGTAGATCGGAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
* *
210123 TTGGCGTGACA-TAGATCAGAGAT
66 TTGACATGA-AGTAGATCAGAGAT
* * *
210146 AACAGATCTTGTCTTCATGTATTGGTATGAAGTAGATCGGAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
210211 TTGACATGAAGTAGATCAGAGAT
66 TTGACATGAAGTAGATCAGAGAT
* *
210234 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGAAGATCGAAGA-AA-GCAGATCTTGTCTTCATG
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATG
* * * *
210297 TACTGGCGTGAAGTAGATC-GAAGAA
64 TATTGACATGAAGTAGATCAG-AGAT
* *
210322 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGA-AA-GCAGATCTTGTCTTCATG
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATG
* * * *
210385 TACTGGCGTGAAGTAGATC-GAAGAA
64 TATTGACATGAAGTAGATCAG-AGAT
* * *** *
210410 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGCA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
210475 TTGACATGAAGTAGATC
66 TTGACATGAAGTAGATC
210492 GAAGATACCA
Statistics
Matches: 802, Mismatches: 61, Indels: 25
0.90 0.07 0.03
Matches are distributed among these distances:
86 1 0.00
87 5 0.01
88 698 0.87
89 98 0.12
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.32
Consensus pattern (88 bp):
AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
TTGACATGAAGTAGATCAGAGAT
Found at i:212700 original size:2 final size:2
Alignment explanation
Indices: 212693--212717 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
212683 NNNNATCTTC
212693 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 T
212718 CTTTTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:213790 original size:20 final size:19
Alignment explanation
Indices: 213762--213799 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
213752 GAAATTTAAA
213762 ATATTTTTTAAATTTTTAT
1 ATATTTTTTAAATTTTTAT
*
213781 ATATTATTTTGAATTTTTA
1 ATATT-TTTTAAATTTTTA
213800 AATTTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
ATATTTTTTAAATTTTTAT
Found at i:215318 original size:20 final size:19
Alignment explanation
Indices: 215280--215323 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
215270 TTATATTTAT
*
215280 AATATTTACTATAAATAAA
1 AATATTTACAATAAATAAA
*
215299 AATATTCTACAATTAATAAA
1 AATATT-TACAATAAATAAA
*
215319 TATAT
1 AATAT
215324 ATTTGCTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATTTACAATAAATAAA
Found at i:221995 original size:29 final size:29
Alignment explanation
Indices: 221953--222014 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
221943 AGACTGTATC
*
221953 ACACGGCTGTGTGGCAAA-CTGTGTGGGTT
1 ACACGGCTATGTGGCAAATC-GTGTGGGTT
**
221982 ACACGGCTATGTGGCTGATCGTGTGGGTT
1 ACACGGCTATGTGGCAAATCGTGTGGGTT
222011 ACAC
1 ACAC
222015 AGTTGTGTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.27
Consensus pattern (29 bp):
ACACGGCTATGTGGCAAATCGTGTGGGTT
Found at i:222023 original size:29 final size:29
Alignment explanation
Indices: 221973--222043 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
221963 GTGGCAAACT
* *
221973 GTGTGGGTTACACGGCTATGTGGCT-GATC
1 GTGTGGGTTACACAGCTATGTGG-TAGACC
* *
222002 GTGTGGGTTACACAGTTGTGTGGTAGACC
1 GTGTGGGTTACACAGCTATGTGGTAGACC
*
222031 GTGTGGGTCACAC
1 GTGTGGGTTACAC
222044 GACTGTGTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 1 0.03
29 35 0.97
ACGTcount: A:0.15, C:0.17, G:0.38, T:0.30
Consensus pattern (29 bp):
GTGTGGGTTACACAGCTATGTGGTAGACC
Found at i:222050 original size:29 final size:29
Alignment explanation
Indices: 221951--222051 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 29
221941 GTAGACTGTA
* * * *
221951 TCACACGGCTGTGTGGCAAACTGTGTGGG
1 TCACACGACTGTGTGGTAGACCGTGTGGG
* * * *
221980 TTACACGGCTATGTGGCT-GATCGTGTGGG
1 TCACACGACTGTGTGG-TAGACCGTGTGGG
* *
222009 TTACAC-AGTTGTGTGGTAGACCGTGTGGG
1 TCACACGA-CTGTGTGGTAGACCGTGTGGG
222038 TCACACGACTGTGT
1 TCACACGACTGTGT
222052 CGTTGGCTAT
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
28 1 0.02
29 54 0.96
30 1 0.02
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.29
Consensus pattern (29 bp):
TCACACGACTGTGTGGTAGACCGTGTGGG
Found at i:237048 original size:26 final size:26
Alignment explanation
Indices: 237019--237073 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
237009 AATTTTCTCC
237019 AAATTTTA-TCGAGGGTAAAATTGTCA
1 AAATTTTACT-GAGGGTAAAATTGTCA
*
237045 AAATTTTACTGAGGGTAAAATTGTTA
1 AAATTTTACTGAGGGTAAAATTGTCA
237071 AAA
1 AAA
237074 AATTTATTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (26 bp):
AAATTTTACTGAGGGTAAAATTGTCA
Found at i:237086 original size:26 final size:26
Alignment explanation
Indices: 237029--237089 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
237019 AAATTTTATC
* *
237029 GAGGGTAAAATTGTCAAAATTTTACT
1 GAGGGTAAAATTGTAAAAAATTTACT
*
237055 GAGGGTAAAATTGTTAAAAAATTTATT
1 GAGGGTAAAATTG-TAAAAAATTTACT
237082 G-GGGTAAA
1 GAGGGTAAA
237090 TTTTGGATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (26 bp):
GAGGGTAAAATTGTAAAAAATTTACT
Found at i:242864 original size:21 final size:22
Alignment explanation
Indices: 242839--242905 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 22
242829 TCTGTAATTT
242839 AAGGTAATTTTAAATA-TTTTA
1 AAGGTAATTTTAAATATTTTTA
** **
242860 AAGGTGTTTTTCCATATTTTTA
1 AAGGTAATTTTAAATATTTTTA
* *
242882 ATGG-AATTTTAAATCGTTTTTA
1 AAGGTAATTTTAAAT-ATTTTTA
242904 AA
1 AA
242906 TTAGCCCCGA
Statistics
Matches: 33, Mismatches: 11, Indels: 3
0.70 0.23 0.06
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.49
Consensus pattern (22 bp):
AAGGTAATTTTAAATATTTTTA
Found at i:245654 original size:24 final size:24
Alignment explanation
Indices: 245604--245654 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
245594 TAGGAAGAAA
* **
245604 ATGGTTGTTTGATATGTTTTTGAT
1 ATGGTTATTTGATATGTTTAAGAT
* *
245628 ATGGTTATTTGGTATGTTTAAGGT
1 ATGGTTATTTGATATGTTTAAGAT
245652 ATG
1 ATG
245655 TTAAATGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (24 bp):
ATGGTTATTTGATATGTTTAAGAT
Found at i:252624 original size:21 final size:22
Alignment explanation
Indices: 252590--252646 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
252580 TACATGGCCA
252590 TGTGGC-TCCT-CACACACCTG
1 TGTGGCTTCCTCCACACACCTG
* *
252610 TGTGTCTTCC-CCACACGCCTG
1 TGTGGCTTCCTCCACACACCTG
252631 TGTGGCTTCCTCCACA
1 TGTGGCTTCCTCCACA
252647 TGCCCATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 5 0.16
21 21 0.68
22 5 0.16
ACGTcount: A:0.12, C:0.40, G:0.19, T:0.28
Consensus pattern (22 bp):
TGTGGCTTCCTCCACACACCTG
Found at i:257225 original size:2 final size:2
Alignment explanation
Indices: 257218--257242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
257208 TGGTGTGGGA
257218 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 A
257243 ATGGGTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:257824 original size:18 final size:18
Alignment explanation
Indices: 257801--257838 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
257791 ATGTCTAAGA
257801 TTAAATTAAAATTAAAGT
1 TTAAATTAAAATTAAAGT
257819 TTAAATTAAAATTAAAGT
1 TTAAATTAAAATTAAAGT
257837 TT
1 TT
257839 CAAGTATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TTAAATTAAAATTAAAGT
Found at i:275210 original size:7 final size:7
Alignment explanation
Indices: 275198--275254 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
275188 TTTGAGTCAA
275198 AAAAATG
1 AAAAATG
275205 AAAAATG
1 AAAAATG
275212 AAAAAATG
1 -AAAAATG
275220 -AAAATG
1 AAAAATG
*
275226 ATAAATG
1 AAAAATG
275233 AAAAAATG
1 -AAAAATG
275241 AAAAA-G
1 AAAAATG
275247 TAAAAATG
1 -AAAAATG
275255 GAGAGGCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
6 7 0.16
7 22 0.51
8 14 0.33
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (7 bp):
AAAAATG
Found at i:275216 original size:8 final size:8
Alignment explanation
Indices: 275197--275245 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
275187 CTTTGAGTCA
275197 AAAAAATG
1 AAAAAATG
275205 -AAAAATG
1 AAAAAATG
275212 AAAAAATG
1 AAAAAATG
275220 --AAAATG
1 AAAAAATG
*
275226 -ATAAATG
1 AAAAAATG
275233 AAAAAATG
1 AAAAAATG
275241 AAAAA
1 AAAAA
275246 GTAAAAATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 6 0.17
7 12 0.33
8 18 0.50
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.14
Consensus pattern (8 bp):
AAAAAATG
Found at i:275223 original size:21 final size:21
Alignment explanation
Indices: 275199--275254 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
275189 TTGAGTCAAA
275199 AAAATGAAAAATGAAAAAATG
1 AAAATGAAAAATGAAAAAATG
*
275220 AAAATGATAAATGAAAAAATG
1 AAAATGAAAAATGAAAAAATG
*
275241 AAAAAGTAAAAATG
1 AAAATG-AAAAATG
275255 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (21 bp):
AAAATGAAAAATGAAAAAATG
Found at i:275237 original size:14 final size:15
Alignment explanation
Indices: 275197--275254 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
275187 CTTTGAGTCA
275197 AAAAAATGAAAAATG
1 AAAAAATGAAAAATG
275212 AAAAAATG-AAAATG
1 AAAAAATGAAAAATG
*
275226 -ATAAATGAAAAAATG
1 AAAAAATG-AAAAATG
*
275241 AAAAAGT-AAAAATG
1 AAAAAATGAAAAATG
275255 GAGAGGCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 6 0.16
14 13 0.35
15 14 0.38
16 4 0.11
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.16
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:276804 original size:132 final size:132
Alignment explanation
Indices: 276643--277352 Score: 823
Period size: 132 Copynumber: 5.4 Consensus size: 132
276633 GACACCAGCC
** * *
276643 TTACCTCCCTGTGGTTACAATGGAGTACATTGAAGTTAGTAATTCTATCTCCCAGGTTGGCAGTG
1 TTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTAGCAGTG
* * * *
276708 GTATAGATTGAAGATTATAGATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGA
66 GAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCAGA
276773 TT
131 TT
* * *
276775 TTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGTAGTG
1 TTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTAGCAGTG
* * * * * *
276840 GAATAGATTGGAA-ATTACAGATCTTGTCTCCCTAAGCAGTAGCTGAGCAGATCGAAAATGACAA
66 GAATAGATT-GAAGATTATAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCAG
276904 ATT
130 ATT
* * ** * * * * * * * *
276907 TTATCTTCAAG-AG-T--AA-GGAAGCAGATTTAAGCCA-CAAGTCCTATCTCCCTGGTCAACAG
1 TTACCTCCCTGTGGTTACAATGG-AGTACATTGAAGCCAGTAA-TTCTATCTCCCTGGTTAGCAG
* * *
276966 TGGAATAGGTTG-GGATT-TCAGATCTTATCTCCCTAAGCAGTAGCGGAGTAGATCGAAGATGGC
64 TGGAATAGATTGAAGATTAT-AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGC
277029 AGATT
128 AGATT
* *
277034 TTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAATTCTATATCCCTGGGTAGCAGTG
1 TTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTAGCAGTG
*
277099 GAATAGATTGAAGATT-TCAGATCTTATCTCCCTAAGCAGTAGCGGAGTAGATCGAAGATGGCAG
66 GAATAGATTGAAGATTAT-AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCAG
277163 ATT
130 ATT
* * * *
277166 TTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAATAGTTCTA-CTTCCATAGG-CAGCAG
1 TTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAATTCTATC-TCCCT-GGTTAGCAG
* * * * *
277229 TGGAATAGATTGAATATTACAGATCTTATCTCCTTAAGCAATAGCGGAGCAGATCGAAGATGACA
64 TGGAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCA
277294 GATT
129 GATT
** * * * *
277298 TTACCTCCCTAAGGTTACAGTGGAGTATATTGAAGCCACTAATCCTATCTCCCTG
1 TTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAATTCTATCTCCCTG
277353 AAATTACAGT
Statistics
Matches: 488, Mismatches: 74, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
127 58 0.12
128 40 0.08
129 1 0.00
130 1 0.00
131 43 0.09
132 339 0.69
133 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (132 bp):
TTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTAGCAGTG
GAATAGATTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCAGA
TT
Found at i:277604 original size:50 final size:50
Alignment explanation
Indices: 277542--277800 Score: 186
Period size: 50 Copynumber: 5.2 Consensus size: 50
277532 GCAATGGAAC
* * * *
277542 AAGATTAAAGCCACAACGGTGAATCTTGCTTCCTTGACATTGCCGTTAAA
1 AAGATTAAAGCCACAACAGCGAATCTTGCTTCCTCGACATTGCAGTTAAA
* ** * **
277592 AGGATTAAAGCCACAACAGCGAATCTCACTT-CTCAAGCGGTGCAG-TAAA
1 AAGATTAAAGCCACAACAGCGAATCTTGCTTCCTCGA-CATTGCAGTTAAA
* * * * *
277641 ACATATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAA
1 A-AGATTAAAGCCACAACAGCGAATCTTGCTTCCTCGACATTGCAGTTAAA
* * * * **
277692 AAGATTAAAGCTACAACAGCGAATCTT-ATTACCTTGGCGA-TG-AGTGGAA
1 AAGATTAAAGCCACAACAGCGAATCTTGCTT-CCTCGAC-ATTGCAGTTAAA
* * * * * **
277741 CAGATTAACGCCATAACGGCGAACCTTGCTTCCTCGACATCACAGTTAAA
1 AAGATTAAAGCCACAACAGCGAATCTTGCTTCCTCGACATTGCAGTTAAA
*
277791 CAGATTAAAG
1 AAGATTAAAG
277801 TTACGAGTTA
Statistics
Matches: 154, Mismatches: 46, Indels: 18
0.71 0.21 0.08
Matches are distributed among these distances:
48 1 0.01
49 41 0.27
50 103 0.67
51 9 0.06
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (50 bp):
AAGATTAAAGCCACAACAGCGAATCTTGCTTCCTCGACATTGCAGTTAAA
Found at i:277796 original size:99 final size:99
Alignment explanation
Indices: 277530--277800 Score: 296
Period size: 100 Copynumber: 2.7 Consensus size: 99
277520 TTCCCTGAGA
* * *
277530 ATGCAATGGAACAAGATTAAAGCCACAACGGTGAATCTTGCTTCCTTGACATTGCCGTTAAAAGG
1 ATGCAGTGGAAC-AGATTAAAGCCACAACGGTGAATCTTGCTTCCTCGACATTGCAGTTAAAA-G
277595 ATTAAAGCCACAACAGCGAATCTCACTTCTCAAGCG
64 ATTAAAGCCACAACAGCGAATCTCACTTCTCAAGCG
* ** * * *
277631 GTGCAGTAAAACATATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
1 ATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCTCGACATTGCAGTT-AAAAGA
* * **
277696 TTAAAGCTACAACAGCGAATCTTA-TTAC-CTTGGCG
65 TTAAAGCCACAACAGCGAATCTCACTT-CTC-AAGCG
* * * * **
277731 ATG-AGTGGAACAGATTAACGCCATAACGGCGAACCTTGCTTCCTCGACATCACAGTTAAACAGA
1 ATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCTCGACATTGCAGTTAAA-AGA
277795 TTAAAG
65 TTAAAG
277801 TTACGAGTTA
Statistics
Matches: 141, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
98 3 0.02
99 55 0.39
100 71 0.50
101 12 0.09
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (99 bp):
ATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCTCGACATTGCAGTTAAAAGAT
TAAAGCCACAACAGCGAATCTCACTTCTCAAGCG
Found at i:278267 original size:14 final size:15
Alignment explanation
Indices: 278248--278276 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
278238 CGAGTCCAAA
278248 AATAACCC-AATTAC
1 AATAACCCAAATTAC
278262 AATAACCCAAATTAC
1 AATAACCCAAATTAC
278277 CAGCCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAACCCAAATTAC
Found at i:283454 original size:45 final size:45
Alignment explanation
Indices: 283390--283475 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
283380 ATAGATACTT
*
283390 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATATCC
1 GGTGGAATCAGCACATAGCAACCACCTTATTAATCAATGATATCC
283435 GGTGGAATCAGCACATAGCAACCACCTTATTAATCAATGAT
1 GGTGGAATCAGCACATAGCAACCACCTTATTAATCAATGAT
283476 GTTCGGTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTATTAATCAATGATATCC
Found at i:305331 original size:27 final size:27
Alignment explanation
Indices: 305293--305355 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
305283 CGACATCATA
*
305293 GATAGTCCAACAAGACATTAAACACAG
1 GATAGTCCAACAAGACACTAAACACAG
* *
305320 GATAGTTCAACAAGACACTAAACACCG
1 GATAGTCCAACAAGACACTAAACACAG
*
305347 GATGGTCCA
1 GATAGTCCA
305356 TTGATGCGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (27 bp):
GATAGTCCAACAAGACACTAAACACAG
Found at i:305437 original size:21 final size:19
Alignment explanation
Indices: 305392--305429 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
305382 CATGTAAGAC
305392 CATAGTTGAAAGACACTAT
1 CATAGTTGAAAGACACTAT
305411 CATAGTTGAAAGACACTAT
1 CATAGTTGAAAGACACTAT
305430 GACATAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
CATAGTTGAAAGACACTAT
Found at i:312466 original size:23 final size:23
Alignment explanation
Indices: 312436--312479 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
312426 AGCATATGGA
312436 ACGGTTTTGGGCTGCCCAGTGGG
1 ACGGTTTTGGGCTGCCCAGTGGG
*
312459 ACGGTTTTGGGCTGCCTAGTG
1 ACGGTTTTGGGCTGCCCAGTG
312480 CTCAGTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.20, G:0.41, T:0.30
Consensus pattern (23 bp):
ACGGTTTTGGGCTGCCCAGTGGG
Found at i:312747 original size:10 final size:10
Alignment explanation
Indices: 312728--312776 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
312718 AAATCTATCG
312728 AAAA-TAATC
1 AAAATTAATC
312737 AAAATTAATC
1 AAAATTAATC
*
312747 AAAATTTAATAT
1 AAAA-TTAAT-C
*
312759 AAAATTAATT
1 AAAATTAATC
312769 AAAATTAA
1 AAAATTAA
312777 ACATGTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
9 4 0.11
10 18 0.50
11 10 0.28
12 4 0.11
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTAATC
Done.