Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 2 of 144
Found at i:385344 original size:98 final size:98
Alignment explanation
Indices: 385171--385816 Score: 896
Period size: 98 Copynumber: 6.6 Consensus size: 98
385161 GTTTCATTAG
** * *
385171 CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACAACGAACCTTGTACCTAAAAAACATGAAGG
1 CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGG
* * *
385236 GAAATATTTAAGTCGCAACGGCGAATCCAATAC
66 GAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
** * ** * * * * *
385269 TGCAAAGATATGGAGGGAAAGGTTTAAGTCGTGATGGTGAACCTTTTACCTCATAAGCATGAAGG
1 CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGG
385334 GAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
66 GAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
* * *
385367 CACAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAACTTTGTACCTCAGAAACATGAAGG
1 CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGG
* * *
385432 GAAAGATTTAAGTCGCAATGGTGAATCCAGTAC
66 GAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
* * * * * *
385465 CACGAGGATATAGAGGGAAAGGTTTAAGTTGCAATGGCGAACCTTGTACCTCAGAAGCATAAAGG
1 CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGG
* * * *
385530 GAAAGATTTAAGTCGCAATGGTGAATCTAGTAC
66 GAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
* *
385563 CACGAAGATATTGAGGGAAAGGTTTAAGTCGCAACGGCGAGCCTTGTACCTCAGAAACATGAAGG
1 CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGG
385628 GAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
66 GAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
* * * * *
385661 CACGAGGATATAGAGGGAAAGATTTAAGTCGCAACAGTGAACCTTGTACCTCAGAAACATGAAGG
1 CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGG
* *
385726 GAAAGATTTAAGCCGCAACGTCGAATCCAATAC
66 GAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
* *
385759 CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCAAACCTTGTACCTCAAAAAC
1 CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
385817 GTAAAAGAAA
Statistics
Matches: 484, Mismatches: 64, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 484 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (98 bp):
CACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGG
GAAAGATTTAAGCCGCAACGGCGAATCCAGTAC
Found at i:386191 original size:40 final size:39
Alignment explanation
Indices: 386145--386223 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
386135 AGTTACATCA
*
386145 CCAATCTCTTACCCCGATCATGGGGCTGATTGAAAACCAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATT-AAAACCAT
386185 CCAATCTCTTACCCCGATCATGGGGCAGATTAAAACCAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATTAAAACCAT
386224 TATCCAATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 8 0.21
40 30 0.79
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (39 bp):
CCAATCTCTTACCCCGATCATGGGGCAGATTAAAACCAT
Found at i:392863 original size:59 final size:57
Alignment explanation
Indices: 392798--393020 Score: 295
Period size: 59 Copynumber: 3.8 Consensus size: 57
392788 AAAAAATTTG
*
392798 GGGTTAAAAATGGAATTTTAGAAAGTTTAAGGGTAAAATGGTAATTTTAGGTGAAATC
1 GGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTT-GGTGAAATC
** **
392856 GGCGTTAAAAATAAAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTT-GTGAAATC
1 GG-GTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTGGTGAAATC
* * * * *
392913 GAGGTCAAAAATGGAATTTTGAAAAGCTCAAGGGTAAAATGGTAATTTTGGGTGAAATTG
1 G-GGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTT-GGTGAAA-TC
*
392973 GGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTT
1 GGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTT
393021 TGAAAGTTTT
Statistics
Matches: 141, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
57 47 0.33
58 3 0.02
59 89 0.63
60 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (57 bp):
GGGTTAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTGGTGAAATC
Found at i:392902 original size:29 final size:29
Alignment explanation
Indices: 392870--393029 Score: 125
Period size: 29 Copynumber: 5.5 Consensus size: 29
392860 TTAAAAATAA
*
392870 AATTTTGGAAAGTTTGGGGGTAAAATGGT
1 AATTTTGGAAAGTTTAGGGGTAAAATGGT
** ***
392899 AATTTTGTGAAA-TCGAGGTCAAAAATGG-
1 AATTTTG-GAAAGTTTAGGGGTAAAATGGT
* * * *
392927 AATTTTGAAAAGCTCAAGGGTAAAATGGT
1 AATTTTGGAAAGTTTAGGGGTAAAATGGT
392956 AATTTTGGGTGAAA--TT-GGGGTTAAAAATGG-
1 AATTTT--G-GAAAGTTTAGGGG-T-AAAATGGT
392986 AATTTTGGAAAGTTTAGGGGTAAAATGGT
1 AATTTTGGAAAGTTTAGGGGTAAAATGGT
*
393015 AATTTTTGAAAGTTT
1 AATTTTGGAAAGTTT
393030 TAAGGTCAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 24
0.71 0.13 0.17
Matches are distributed among these distances:
27 7 0.07
28 24 0.24
29 43 0.43
30 16 0.16
31 8 0.08
32 3 0.03
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
AATTTTGGAAAGTTTAGGGGTAAAATGGT
Found at i:392931 original size:116 final size:115
Alignment explanation
Indices: 392803--393025 Score: 349
Period size: 116 Copynumber: 1.9 Consensus size: 115
392793 ATTTGGGGTT
* *
392803 AAAAATGGAATTTT-AGAAAGTTTAAGGGTAAAATGGTAATTTTAGGTGAAATCGGCGTTAAAAA
1 AAAAATGGAATTTTGA-AAAGCTCAAGGGTAAAATGGTAATTTTAGGTGAAATCGGCGTTAAAAA
*
392867 TAAAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTGTGAAATCGAGGTC
65 TAAAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTT-TGAAATCGAGGTC
* * *
392919 AAAAATGGAATTTTGAAAAGCTCAAGGGTAAAATGGTAATTTTGGGTGAAATTGGGGTTAAAAAT
1 AAAAATGGAATTTTGAAAAGCTCAAGGGTAAAATGGTAATTTTAGGTGAAATCGGCGTTAAAAAT
**
392984 GGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGAAA
66 AAAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGAAA
393026 GTTTTAAGGT
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
115 5 0.05
116 92 0.94
117 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (115 bp):
AAAAATGGAATTTTGAAAAGCTCAAGGGTAAAATGGTAATTTTAGGTGAAATCGGCGTTAAAAAT
AAAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGAAATCGAGGTC
Found at i:393041 original size:30 final size:29
Alignment explanation
Indices: 392986--393093 Score: 100
Period size: 29 Copynumber: 3.7 Consensus size: 29
392976 TTAAAAATGG
* *
392986 AATTTTGGAAAG-TTTAGGGGT-AAAATGGT
1 AATTTTTGAAAGTTTTA-GGGTCAAAAT-AT
*
393015 AATTTTTGAAAGTTTTAAGGTCAAAATAT
1 AATTTTTGAAAGTTTTAGGGTCAAAATAT
393044 AATTTTCT-AAAGTTTT-GGGATCACAAATAT
1 AATTTT-TGAAAGTTTTAGGG-TCA-AAATAT
393074 AATTTTTGAATAG-TTTAGGG
1 AATTTTTGAA-AGTTTTAGGG
393094 ACCTATAAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.03
29 33 0.49
30 27 0.40
31 5 0.07
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (29 bp):
AATTTTTGAAAGTTTTAGGGTCAAAATAT
Found at i:395598 original size:14 final size:14
Alignment explanation
Indices: 395566--395607 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
395556 GATTTCACCC
395566 AAAA-AAAAAG-AA
1 AAAATAAAAAGAAA
* *
395578 AATATAAAGAGAAA
1 AAAATAAAAAGAAA
395592 AAAATAAAAAGAAA
1 AAAATAAAAAGAAA
395606 AA
1 AA
395608 GGAGAGGTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 3 0.12
13 5 0.21
14 16 0.67
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (14 bp):
AAAATAAAAAGAAA
Found at i:396860 original size:49 final size:49
Alignment explanation
Indices: 396742--397256 Score: 328
Period size: 49 Copynumber: 10.5 Consensus size: 49
396732 CAAGTTTCAT
* * * ** * *
396742 TACCACGAAGATATAGAGGGAAAGGTTTAAGTTGCAACGGTGAA-CCTTG
1 TACCACAAAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AG
* * * * * *
396791 TACCTCAAAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAA
1 TACCACAAAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* * * * * * *
396840 TACCGCAAAGATATGGAGGGAAAGGTTTAAGTCGCGATGGC-AAACCTTG
1 TACCACAAAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AG
* * * *
396889 TACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAA
1 TACCACA-AAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
** * *
396938 TACCACAAAGATATGGAGGGAAAGGCTTAAGTCGCAACGGCGAA-CCTTG
1 TACCACAAAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AG
** * * * *
396987 TACCTTAGAA-ACATGAAGGGAAAGATTTAAGCCGCAGCGACGAATCCAG
1 TACCACA-AAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* * * * * * * *
397036 TACCACGAGGATATTGAGGGAAAGGTTTAAGTCGCAATGGTGAA-CCTTG
1 TACCACAAAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AG
* * * * *
397085 TACCTCAGAA-ACATGAAGGGAAATATTTAAGCCGCAACGACGAATCCAG
1 TACCACA-AAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* * * * * *
397134 TGCCAATAAAGATATGGAGGGAAAGGTATAGGTCGCAACGGCGAA-CCATG
1 TACC-ACAAAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCCA-G
** * * * *
397184 TACCTTATAA-ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAA
1 TACCACA-AAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* *
397233 AACCACGAAGATATGGAGGGAAAG
1 TACCACAAAGATATGGAGGGAAAG
397257 GGTTGAGTCG
Statistics
Matches: 341, Mismatches: 107, Indels: 36
0.70 0.22 0.07
Matches are distributed among these distances:
48 14 0.04
49 275 0.81
50 52 0.15
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (49 bp):
TACCACAAAGATATGGAGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
Found at i:397325 original size:98 final size:98
Alignment explanation
Indices: 396742--397293 Score: 762
Period size: 98 Copynumber: 5.6 Consensus size: 98
396732 CAAGTTTCAT
* * * * *
396742 TACCACGAAGATATAGAGGGAAAGGTTTAAGTTGCAACGGTGAACCTTGTACCTCAAAAACATGA
1 TACCACAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
396807 AGGGAAAGATTTAAGCCGCAACGACGAATCCAA
66 AGGGAAAGATTTAAGCCGCAACGACGAATCCAA
* * * * *
396840 TACCGCAAAGATATGGAGGGAAAGGTTTAAGTCGCGATGGCAAACCTTGTACCTCAGAAGCATGA
1 TACCACAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
*
396905 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAA
66 AGGGAAAGATTTAAGCCGCAACGACGAATCCAA
* *
396938 TACCACAAAGATATGGAGGGAAAGGCTTAAGTCGCAACGGCGAACCTTGTACCTTAGAAACATGA
1 TACCACAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* *
397003 AGGGAAAGATTTAAGCCGCAGCGACGAATCCAG
66 AGGGAAAGATTTAAGCCGCAACGACGAATCCAA
* * * * *
397036 TACCACGAGGATATTGAGGGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTCAGAAACATGA
1 TACCACAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* *
397101 AGGGAAATATTTAAGCCGCAACGACGAATCCAG
66 AGGGAAAGATTTAAGCCGCAACGACGAATCCAA
* * * * * * *
397134 TGCCAATAAAGATATGGAGGGAAAGGTATAGGTCGCAACGGCGAACCATGTACCTTATAAACATG
1 TACC-ACAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATG
* *
397199 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAA
65 AAGGGAAAGATTTAAGCCGCAACGACGAATCCAA
* * * * * *
397233 AACCACGAAGATATGGAGGGAAAGGGTTGAGTCGCATCGGCGAACCTTGTACCTCAAAAAC
1 TACCACAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
397294 GTAAAAGGAA
Statistics
Matches: 395, Mismatches: 58, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
98 314 0.79
99 81 0.21
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (98 bp):
TACCACAAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
AGGGAAAGATTTAAGCCGCAACGACGAATCCAA
Found at i:398375 original size:28 final size:31
Alignment explanation
Indices: 398305--398383 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 31
398295 TTTTGGGGAC
* *
398305 AAAATGGTAATTTTGAGAAAATTTCGGGTTA
1 AAAATGGTAATTTTGAGAAAATTTAGGGGTA
*
398336 AAAAT-G-ACATTTT-AG-ACATTTAGGGGT-
1 AAAATGGTA-ATTTTGAGAAAATTTAGGGGTA
*
398363 AAAATGGTAATTTTTAGAAAA
1 AAAATGGTAATTTTGAGAAAA
398384 ATCAGGATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
27 5 0.13
28 15 0.38
29 6 0.15
30 8 0.21
31 5 0.13
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (31 bp):
AAAATGGTAATTTTGAGAAAATTTAGGGGTA
Found at i:400319 original size:12 final size:12
Alignment explanation
Indices: 400304--400336 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
400294 AATTGGACTT
400304 TTAATTTTAATA
1 TTAATTTTAATA
*
400316 TTAAGTTTAATA
1 TTAATTTTAATA
400328 TT-ATTTTAA
1 TTAATTTTAA
400337 ATTTAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:400341 original size:17 final size:17
Alignment explanation
Indices: 400332--400371 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
400322 TTAATATTAT
400332 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
400349 TTTAAATTTAAAATCAA
1 TTTAAATTTAAAATAAA
400366 TTTAAA
1 TTTAAA
400372 CTCTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:400969 original size:134 final size:135
Alignment explanation
Indices: 400725--401016 Score: 480
Period size: 134 Copynumber: 2.2 Consensus size: 135
400715 ATCTGGTCTT
* *
400725 CTTCTCTGTGTCTCATCAGGAAGATGACCGCAATTGTCTGTTTTAATTCGCTTCTCTGAATCTCT
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCAATTGTCTGTTTTAATTCGCTTCTCTGAATCTCC
* * *
400790 TCAGGAAGACGAATTTAGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCA
66 TCAAGAAGACGAATTTAGTCCACTTCTCTGTGTCTCATCAAGAAGCTAACCATTTTATTGCCTCA
400855 ACCTG
131 ACCTG
* *
400860 CTTCTCAGTGTCTCATCAGGAAGATGACCGC-CTTG-CTTGTTTTAATTCGCTTCTCTGGATCTC
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCAATTGTC-TGTTTTAATTCGCTTCTCTGAATCTC
*
400923 CTCAAGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAAGAAGCTAACCATTTTATTGCCTC
65 CTCAAGAAGACGAATTTAGTCCACTTCTCTGTGTCTCATCAAGAAGCTAACCATTTTATTGCCTC
*
400988 GACCTG
130 AACCTG
400994 CTTCTCAGTGTCTCATCAGGAAG
1 CTTCTCAGTGTCTCATCAGGAAG
401017 CTAAGGTTCG
Statistics
Matches: 147, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
133 1 0.01
134 116 0.79
135 30 0.20
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.35
Consensus pattern (135 bp):
CTTCTCAGTGTCTCATCAGGAAGATGACCGCAATTGTCTGTTTTAATTCGCTTCTCTGAATCTCC
TCAAGAAGACGAATTTAGTCCACTTCTCTGTGTCTCATCAAGAAGCTAACCATTTTATTGCCTCA
ACCTG
Found at i:401294 original size:205 final size:205
Alignment explanation
Indices: 400860--401509 Score: 1041
Period size: 205 Copynumber: 3.2 Consensus size: 205
400850 CTTCAACCTG
* ** *
400860 CTTCTCAGTGTCTCATCAGGAAGATGACCGCCTTGCTTGTTTTAATTCGCTTCTCTGGATCTCCT
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTAGATCTCCT
* * * *
400925 CAAGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAAGAAGCTAACCATTTTATTGCCTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
*
400990 CCTGCTTCTCAGTGTCTCATCAGGAAGCTAAGGTTCGAAGATTTGCTCGTATTGAGCCTGGGTTT
131 CCTGCTTCTCAGTGTCTCATCAGGAAGCT-AGGTTCGAAGATTTGCTCATATTGAGCCTGGGTTT
401055 GATTTGGTCTT
195 GATTTGGTCTT
* *
401066 CTTCTCAGTGTCTCATCAGGAAGATGATCGCATCATTTGTTTTAATTCGCTTCTCTAGATCTCCT
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTAGATCTCCT
*
401131 CAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCAGGAAGCTAACCA-TTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * * *
401195 CCTGATTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGCCTAGGTTT
131 CCTGCTTCTCAGTGTCTCATCAGGAAGCT-AGGTTCGAAGATTTGCTCATATTGAGCCTGGGTTT
401260 GATTTGGTCTT
195 GATTTGGTCTT
* * **
401271 CTTCTCAGTGTCTCATTAGGAAGATGACCGCATCACTTATTTTAATTCATTTCTCTAGATCTCCT
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTAGATCTCCT
401336 CAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * **
401401 CCTGCTTCTCAGTATCTCATCAGGAAGCTAGGTTCGAAGATTTGCTCATATCGAGTGTGGGTTTG
131 CCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTTCGAAGATTTGCTCATATTGAGCCTGGGTTTG
*
401466 ATTTGATCTT
196 ATTTGGTCTT
*
401476 CTTCTCAGTATCTCATCAGGAAGATGACCGCATC
1 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATC
401510 GTTTGTTTCA
Statistics
Matches: 408, Mismatches: 35, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
205 262 0.64
206 146 0.36
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (205 bp):
CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTAGATCTCCT
CAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTTCGAAGATTTGCTCATATTGAGCCTGGGTTTG
ATTTGGTCTT
Found at i:401657 original size:78 final size:78
Alignment explanation
Indices: 401552--401772 Score: 264
Period size: 78 Copynumber: 2.8 Consensus size: 78
401542 TTGGGGTAGA
* * * * * * *
401552 AGATTGGTTGATGATGATCTGCTCCAAGTTCGGAGTAAAAGGTCAGATGGTTATAATCTGGCCCT
1 AGATTGGTTGATGATGATCTGCCCCAAGCTCGGAGTAAAAGATCAAATGGCTACAATCTGCCCCT
*
401617 AGCCCGAGATAAG
66 AGCCCAAGATAAG
* * *
401630 AGATTGATTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCAATCTGCCCCT
1 AGATTGGTTGATGATGATCTGCCCCAAGCTCGGAGTAAAAGATCAAATGGCTACAATCTGCCCCT
* * *
401695 GGCTCAAGGTAAG
66 AGCCCAAGATAAG
* * * *
401708 AGATTGGTTGATGATGATCTACCCCAGGCTC-GAGGTAAGAGATCAAATGGCTTCAATCTGCCCC
1 AGATTGGTTGATGATGATCTGCCCCAAGCTCGGA-GTAAAAGATCAAATGGCTACAATCTGCCCC
401772 T
65 T
401773 GGCTCGGGGC
Statistics
Matches: 122, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
77 1 0.01
78 121 0.99
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (78 bp):
AGATTGGTTGATGATGATCTGCCCCAAGCTCGGAGTAAAAGATCAAATGGCTACAATCTGCCCCT
AGCCCAAGATAAG
Found at i:401706 original size:39 final size:39
Alignment explanation
Indices: 401663--401791 Score: 109
Period size: 39 Copynumber: 3.3 Consensus size: 39
401653 CCAAGCTCGG
*
401663 GGTAAAAGATCAAATGGCTGCAATCTGCCCCTGGCTCAA
1 GGTAAGAGATCAAATGGCTGCAATCTGCCCCTGGCTCAA
*** * * * * *
401702 GGTAAGAGAT-TGGTTGATG-ATGATCTACCCCAGGCTCGA
1 GGTAAGAGATCAAATGGCTGCA--ATCTGCCCCTGGCTCAA
* **
401741 GGTAAGAGATCAAATGGCTTCAATCTGCCCCTGGCTCGG
1 GGTAAGAGATCAAATGGCTGCAATCTGCCCCTGGCTCAA
*
401780 GGCAAGAGATCA
1 GGTAAGAGATCA
401792 GAATCTTCAT
Statistics
Matches: 67, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
37 1 0.01
38 4 0.06
39 58 0.87
40 3 0.04
41 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (39 bp):
GGTAAGAGATCAAATGGCTGCAATCTGCCCCTGGCTCAA
Found at i:401787 original size:78 final size:78
Alignment explanation
Indices: 401627--401789 Score: 245
Period size: 78 Copynumber: 2.1 Consensus size: 78
401617 AGCCCGAGAT
* *
401627 AAGAGATTGATTGATGATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGGCTGCAATCTGCC
1 AAGAGATTGATTGATGATGATCTACCCCAAGCTCGAGGTAAAAGATCAAATGGCTGCAATCTGCC
*
401692 CCTGGCTCAAGGT
66 CCTGGCTCAAGGC
* * * *
401705 AAGAGATTGGTTGATGATGATCTACCCCAGGCTCGAGGTAAGAGATCAAATGGCTTCAATCTGCC
1 AAGAGATTGATTGATGATGATCTACCCCAAGCTCGAGGTAAAAGATCAAATGGCTGCAATCTGCC
**
401770 CCTGGCTCGGGGC
66 CCTGGCTCAAGGC
401783 AAGAGAT
1 AAGAGAT
401790 CAGAATCTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (78 bp):
AAGAGATTGATTGATGATGATCTACCCCAAGCTCGAGGTAAAAGATCAAATGGCTGCAATCTGCC
CCTGGCTCAAGGC
Found at i:402307 original size:50 final size:50
Alignment explanation
Indices: 402121--402308 Score: 159
Period size: 50 Copynumber: 3.7 Consensus size: 50
402111 CTGTCTTCGT
* *
402121 GGTACTGGATCCACCGTCGCGG-CTTAGATCTTTCCCTTTTGTCTTTTTGC
1 GGTACTGGATCCGCCATCGCGGTCTTAGATCTTT-CCTTTTGTCTTTTTGC
* * * * * *
402171 GGTACTGGATTCGTCATTGCGGTCTTAGATCTTTCCTGTCGTGTC-TTCTGA
1 GGTACTGGATCCGCCATCGCGGTCTTAGATCTTTCCT-T-TTGTCTTTTTGC
* * * * * * *
402222 GGTACACGG-TCTGCCGTTGC-GACATAGACCTTTTCCTTTTGTCTTTTTGC
1 GGTAC-TGGATCCGCCATCGCGGTCTTAGATC-TTTCCTTTTGTCTTTTTGC
*
402272 GGTACTGGATCCGCCATCGCGGTCTTAAATCTTTCCT
1 GGTACTGGATCCGCCATCGCGGTCTTAGATCTTTCCT
402309 ATCGTGTCTT
Statistics
Matches: 103, Mismatches: 27, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
49 6 0.06
50 51 0.50
51 40 0.39
52 6 0.06
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (50 bp):
GGTACTGGATCCGCCATCGCGGTCTTAGATCTTTCCTTTTGTCTTTTTGC
Found at i:402366 original size:101 final size:96
Alignment explanation
Indices: 402094--402359 Score: 282
Period size: 101 Copynumber: 2.6 Consensus size: 96
402084 ACCATTGCAA
* ** *
402094 CTTAGATCTTTCTCTTCCTGTCTTCGTGGTACTGGATCCACCGTCGCGGCTTAGATCTTTCCCTT
1 CTTAGATCTTTC-CTTCGTGTCTTC-TGGTACTGGATCTGCCGTTGC-GC-TAGATCTTTCCCTT
* * *
402159 TTGTCTTTTTGCGGTACTGGATTCGTCATTGCGGT
62 TTGTCTTTTTGCGGTACTGGATCCGCCATCGCGGT
* * *
402194 CTTAGATCTTTCCTGTCGTGTCTTCTGAGGTACACGG-TCTGCCGTTGCGACATAGACCTTTTCC
1 CTTAGATCTTTCCT-TCGTGTCTTCT--GGTAC-TGGATCTGCCGTTGCG-C-TAGATCTTTCCC
402258 TTTTGTCTTTTTGCGGTACTGGATCCGCCATCGCGGT
60 TTTTGTCTTTTTGCGGTACTGGATCCGCCATCGCGGT
* * *
402295 CTTAAATCTTTCCTATCGTGTCTTCATGGTACTGGATCTGCCATTGCAGCTGAAATCTTTCCCTT
1 CTTAGATCTTTCCT-TCGTGTCTTC-TGGTACTGGATCTGCCGTTGC-GCT-AGATCTTTCCCTT
402360 CATGTCTCTA
Statistics
Matches: 139, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
99 6 0.04
100 48 0.35
101 82 0.59
102 3 0.02
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.40
Consensus pattern (96 bp):
CTTAGATCTTTCCTTCGTGTCTTCTGGTACTGGATCTGCCGTTGCGCTAGATCTTTCCCTTTTGT
CTTTTTGCGGTACTGGATCCGCCATCGCGGT
Found at i:404464 original size:12 final size:12
Alignment explanation
Indices: 404427--404465 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
404417 TTTGTGATCA
404427 AAATTGGAAGTG
1 AAATTGGAAGTG
* *
404439 AAAGTGAAAGTG
1 AAATTGGAAGTG
*
404451 AAATTGGAATTG
1 AAATTGGAAGTG
404463 AAA
1 AAA
404466 ATGATATGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (12 bp):
AAATTGGAAGTG
Found at i:406017 original size:7 final size:6
Alignment explanation
Indices: 406000--406059 Score: 68
Period size: 6 Copynumber: 9.5 Consensus size: 6
405990 CAACCTCTCC
*
406000 TTTTCT TTTTCTT TTTTCTGT TTTTCT TTTTCT TTTTGT TTTTCAT TTTTC-
1 TTTTCT TTTTC-T TTTTC--T TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT
406051 TTTTCT TTT
1 TTTTCT TTT
406060 ATTCATTGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
5 5 0.11
6 24 0.51
7 12 0.26
8 6 0.13
ACGTcount: A:0.02, C:0.13, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:406041 original size:12 final size:11
Alignment explanation
Indices: 405999--406059 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
405989 TCAACCTCTC
*
405999 CTTTTCTTTTT
1 CTTTTTTTTTT
* *
406010 CTTTTTTCTGT
1 CTTTTTTTTTT
*
406021 -TTTTCTTTTT
1 CTTTTTTTTTT
406031 CTTTTTGTTTTT
1 CTTTTT-TTTTT
*
406043 CATTTTTCTTTT
1 C-TTTTTTTTTT
406055 CTTTT
1 CTTTT
406060 ATTCATTGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
10 7 0.18
11 16 0.41
12 11 0.28
13 5 0.13
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:412049 original size:6 final size:6
Alignment explanation
Indices: 412024--412070 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
412014 AAAGCCACGG
* *
412024 TTTCTT TTCTTTT CTTTCTT TTTCTT TTTCTT TTTCTT TTTATT TTT
1 TTTCTT TT-TCTT -TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
412071 TATAAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 28 0.78
7 6 0.17
8 2 0.06
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:413187 original size:12 final size:12
Alignment explanation
Indices: 413172--413204 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
413162 AATTGGACTT
413172 TTAATTTTAATA
1 TTAATTTTAATA
*
413184 TTAAGTTTAATA
1 TTAATTTTAATA
413196 TT-ATTTTAA
1 TTAATTTTAA
413205 ATTTGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:413564 original size:40 final size:39
Alignment explanation
Indices: 413518--413596 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
413508 AGTTACATCA
413518 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAAACCAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATT-AAAACCAT
*
413558 CCAATCTCTTACCCCGATCATGGGGTAGATTAAAACCAT
1 CCAATCTCTTACCCCGATCATGGGGCAGATTAAAACCAT
413597 TGTCCAATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 8 0.21
40 30 0.79
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (39 bp):
CCAATCTCTTACCCCGATCATGGGGCAGATTAAAACCAT
Found at i:414090 original size:22 final size:21
Alignment explanation
Indices: 414042--414096 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
414032 AGCCCAAAGA
414042 TAAAAACTAAAAAAAATAAATC
1 TAAAAA-TAAAAAAAATAAATC
* *
414064 CAAAAATAAAATAAAAT-AATT
1 TAAAAATAAAA-AAAATAAATC
*
414085 TTAAAATAAAAA
1 TAAAAATAAAAA
414097 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
22 10 0.36
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAAAATAAAAAAAATAAATC
Found at i:414236 original size:35 final size:35
Alignment explanation
Indices: 414160--414228 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
414150 AACTCAAACC
*
414160 AACCCAAATCCTAAAACTACCCAAAACCCATTACA
1 AACCCAAATCCTAAAACTACCCAAAACCCATAACA
*
414195 AACCCAAA-CCTAAACCTAGCCCAAATACCC-TAAC
1 AACCCAAATCCTAAAACTA-CCCAAA-ACCCATAAC
414229 TACCCCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 9 0.30
35 17 0.57
36 4 0.13
ACGTcount: A:0.46, C:0.39, G:0.01, T:0.13
Consensus pattern (35 bp):
AACCCAAATCCTAAAACTACCCAAAACCCATAACA
Found at i:415874 original size:19 final size:20
Alignment explanation
Indices: 415830--415873 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
415820 TTCAATTACA
*
415830 ATTTTGTGTATTTTTATATT
1 ATTTTATGTATTTTTATATT
415850 ATTTTATGTATTTTT-TATTT
1 ATTTTATGTATTTTTATA-TT
415870 ATTT
1 ATTT
415874 ACTTGTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (20 bp):
ATTTTATGTATTTTTATATT
Found at i:433475 original size:19 final size:19
Alignment explanation
Indices: 433443--433480 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
433433 AAAGAGAAAT
433443 TAAAAAAAAATAGAAAAAC
1 TAAAAAAAAATAGAAAAAC
* *
433462 TAAAACAAATTAGAAAAAC
1 TAAAAAAAAATAGAAAAAC
433481 AAATTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (19 bp):
TAAAAAAAAATAGAAAAAC
Found at i:433851 original size:23 final size:23
Alignment explanation
Indices: 433808--433876 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 23
433798 AGACAGAAGC
*
433808 GTTCCACAAGGGCAGAGAAAAAGT
1 GTTCCACAA-GGTAGAGAAAAAGT
433832 GTTCCACAAGGTAGAGAAAAAGT
1 GTTCCACAAGGTAGAGAAAAAGT
* *
433855 GTGCCACAAAGGTAGATAAAAA
1 GTTCCAC-AAGGTAGAGAAAAA
433877 CTAGAGGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.46
24 22 0.54
ACGTcount: A:0.45, C:0.14, G:0.26, T:0.14
Consensus pattern (23 bp):
GTTCCACAAGGTAGAGAAAAAGT
Found at i:433866 original size:24 final size:24
Alignment explanation
Indices: 433811--433876 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
433801 CAGAAGCGTT
* * *
433811 CCACAAGGGCAGAGAAAAAGTGTT
1 CCACAAAGGTAGAGAAAAAGTGTG
433835 CCAC-AAGGTAGAGAAAAAGTGTG
1 CCACAAAGGTAGAGAAAAAGTGTG
*
433858 CCACAAAGGTAGATAAAAA
1 CCACAAAGGTAGAGAAAAA
433877 CTAGAGGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.47, C:0.15, G:0.26, T:0.12
Consensus pattern (24 bp):
CCACAAAGGTAGAGAAAAAGTGTG
Found at i:435231 original size:2 final size:2
Alignment explanation
Indices: 435224--435272 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
435214 ACATATACAA
435224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
435266 AT AT AT A
1 AT AT AT A
435273 ATTTATAATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:436015 original size:13 final size:13
Alignment explanation
Indices: 435997--436044 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
435987 TCCATTTACA
435997 AAGGCCCAAATTG
1 AAGGCCCAAATTG
*
436010 AAGGCCC-AATTACA
1 AAGGCCCAAATT--G
436024 AAGGCCCAAATTG
1 AAGGCCCAAATTG
*
436037 AGGGCCCA
1 AAGGCCCA
436045 TTTACGATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 14 0.48
14 7 0.24
15 4 0.14
ACGTcount: A:0.38, C:0.27, G:0.23, T:0.12
Consensus pattern (13 bp):
AAGGCCCAAATTG
Found at i:436029 original size:14 final size:14
Alignment explanation
Indices: 435992--436032 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
435982 CCAAGTCCAT
435992 TTACAAAGGCCCAAA
1 TTACAAAGGCCC-AA
*
436007 TT--GAAGGCCCAA
1 TTACAAAGGCCCAA
436019 TTACAAAGGCCCAA
1 TTACAAAGGCCCAA
436033 ATTGAGGGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 9 0.41
15 2 0.09
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (14 bp):
TTACAAAGGCCCAA
Found at i:436056 original size:27 final size:27
Alignment explanation
Indices: 435988--436049 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
435978 ATAACCAAGT
435988 CCATTTACAAAGGCCCAAATTGAAGGC
1 CCATTTACAAAGGCCCAAATTGAAGGC
* *
436015 CCAATTACAAAGGCCCAAATTGAGGGC
1 CCATTTACAAAGGCCCAAATTGAAGGC
436042 CCATTTAC
1 CCATTTAC
436050 GATGGCCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.19
Consensus pattern (27 bp):
CCATTTACAAAGGCCCAAATTGAAGGC
Found at i:436371 original size:25 final size:24
Alignment explanation
Indices: 436337--436385 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
436327 TGTAAGGGGT
*
436337 TACAAACCCTGTTCTGGAAAATCAA
1 TACAAACCCTATTCTGG-AAATCAA
*
436362 TACAAACCCTATTCTTGAAATCAA
1 TACAAACCCTATTCTGGAAATCAA
436386 AGAAACAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (24 bp):
TACAAACCCTATTCTGGAAATCAA
Found at i:437557 original size:32 final size:33
Alignment explanation
Indices: 437520--437583 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
437510 TGCGCGTTTG
**
437520 GTCCTTCT-ATATTTTTTAATTA-TTTTAATTTA
1 GTCCTTCTCATACCTTTT-ATTATTTTTAATTTA
*
437552 GTCCTTTTCATACCTTTTATTATTTTTAATTT
1 GTCCTTCTCATACCTTTTATTATTTTTAATTT
437584 GGCCCGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.22, C:0.12, G:0.03, T:0.62
Consensus pattern (33 bp):
GTCCTTCTCATACCTTTTATTATTTTTAATTTA
Found at i:438021 original size:60 final size:59
Alignment explanation
Indices: 437862--438059 Score: 210
Period size: 58 Copynumber: 3.4 Consensus size: 59
437852 TAGACTGTTC
* * *
437862 AAAAATTACCATTTTACCCCCGAACTTTCC-AAAATTCCATTTTTAACCCTGA-TTT-CA
1 AAAAATTACCATTTTACCCCCGAA-TTTCCTAAAATCCCATTTTCAACCCCGATTTTCCA
* * * *
437919 TCAAAATTACCATTTTACCCTCGAATTT-TTGAAAATCTCATTTTCAACCCCGATTTTGCCA
1 -AAAAATTACCATTTTACCCCCGAATTTCCT-AAAATCCCATTTTCAACCCCGATTTT-CCA
* * *
437980 AAAAATTACCATTTTACCCCCGAATTTCCTAATATCCCATTTTCAACCCC-AATTTCACC
1 AAAAATTACCATTTTACCCCCGAATTTCCTAAAATCCCATTTTCAACCCCGATTTTC-CA
438039 AAAAATTA-CATTTTTACCCCC
1 AAAAATTACCA-TTTTACCCCC
438060 AAAAGTCAAA
Statistics
Matches: 118, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
57 3 0.03
58 43 0.36
59 26 0.22
60 43 0.36
61 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAATTTCCTAAAATCCCATTTTCAACCCCGATTTTCCA
Found at i:440488 original size:21 final size:21
Alignment explanation
Indices: 440464--440518 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
440454 TACAGATTTC
* *
440464 TACCGATACAAGTGATTGTTA
1 TACCGATACAAGTGACTCTTA
*
440485 TACCGATACAAGTGACTCTTC
1 TACCGATACAAGTGACTCTTA
440506 TACCGATACAAGT
1 TACCGATACAAGT
440519 TTCACCTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (21 bp):
TACCGATACAAGTGACTCTTA
Found at i:450045 original size:22 final size:23
Alignment explanation
Indices: 450008--450052 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
449998 AAATAATATT
450008 ATTTTAATAAATTTAATATTAAA
1 ATTTTAATAAATTTAATATTAAA
*
450031 ATTTT-ATTAATTTAATATTAAA
1 ATTTTAATAAATTTAATATTAAA
450053 GTGATTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTAATAAATTTAATATTAAA
Found at i:450084 original size:17 final size:19
Alignment explanation
Indices: 450038--450086 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
450028 AAAATTTTAT
450038 TAATTTAATATTAAAGTGA
1 TAATTTAATATTAAAGTGA
*
450057 TTATCTTAATATTAAA-T-A
1 TAAT-TTAATATTAAAGTGA
450075 TAATTTAATATT
1 TAATTTAATATT
450087 TATCTGATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 8 0.30
18 4 0.15
19 4 0.15
20 11 0.41
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TAATTTAATATTAAAGTGA
Found at i:450132 original size:35 final size:35
Alignment explanation
Indices: 450075--450252 Score: 131
Period size: 35 Copynumber: 5.3 Consensus size: 35
450065 ATATTAAATA
* * * *
450075 TAATTTAATATTTATCTGATAGATAAATATTCTAT
1 TAATTTAATAATTATATTATAGATAAATATTTTAT
450110 TAATTTAATAATTATATTATAGATAAATATTTTAT
1 TAATTTAATAATTATATTATAGATAAATATTTTAT
** * **
450145 TAAACTAATAA--A-ATT-TA-AT-ATTA-AATA-
1 TAATTTAATAATTATATTATAGATAAATATTTTAT
* * **
450172 TAATTTAAT-ATTGATCTTGTAGATAAATATGGTAT
1 TAATTTAATAATT-ATATTATAGATAAATATTTTAT
* * *
450207 TAATTTAATAATTATTTTGTACATAAATATTTTAT
1 TAATTTAATAATTATATTATAGATAAATATTTTAT
*
450242 TAAATTAATAA
1 TAATTTAATAA
450253 AATTTAATAT
Statistics
Matches: 113, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.01
27 7 0.06
28 2 0.02
29 4 0.04
30 4 0.04
31 4 0.04
32 5 0.04
33 4 0.04
34 2 0.02
35 77 0.68
36 3 0.03
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (35 bp):
TAATTTAATAATTATATTATAGATAAATATTTTAT
Found at i:450171 original size:97 final size:97
Alignment explanation
Indices: 450062--450282 Score: 338
Period size: 97 Copynumber: 2.3 Consensus size: 97
450052 AGTGATTATC
*
450062 TTAATATTAAATATAATTTAATATTTATC-TGATAGATAAATATTCTATTAATTTAATAATTATA
1 TTAATATTAAATATAATTTAATATTTATCTTG-TAGATAAATATGCTATTAATTTAATAATTATA
*
450126 TTATAGATAAATATTTTATTAAACTAATAAAAT
65 TTATACATAAATATTTTATTAAACTAATAAAAT
* * *
450159 TTAATATTAAATATAATTTAATATTGATCTTGTAGATAAATATGGTATTAATTTAATAATTATTT
1 TTAATATTAAATATAATTTAATATTTATCTTGTAGATAAATATGCTATTAATTTAATAATTATAT
* *
450224 TGTACATAAATATTTTATTAAATTAATAAAAT
66 TATACATAAATATTTTATTAAACTAATAAAAT
* *
450256 TTAATATTATAT-TAATATAATATTTAT
1 TTAATATTAAATATAATTTAATATTTAT
450283 AAATAGAGGC
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
96 13 0.12
97 98 0.87
98 2 0.02
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (97 bp):
TTAATATTAAATATAATTTAATATTTATCTTGTAGATAAATATGCTATTAATTTAATAATTATAT
TATACATAAATATTTTATTAAACTAATAAAAT
Found at i:450176 original size:17 final size:17
Alignment explanation
Indices: 450151--450183 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
450141 TTATTAAACT
450151 AATAAAATTTAATATTA
1 AATAAAATTTAATATTA
*
450168 AATATAATTTAATATT
1 AATAAAATTTAATATT
450184 GATCTTGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAAAATTTAATATTA
Found at i:450263 original size:21 final size:23
Alignment explanation
Indices: 450232--450281 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
450222 TTTGTACATA
450232 AATATTT--TATTAAATTAATA-
1 AATATTTAATATTAAATTAATAT
*
450252 AA-ATTTAATATTATATTAATAT
1 AATATTTAATATTAAATTAATAT
450274 AATATTTA
1 AATATTTA
450282 TAAATAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 2 0.08
21 12 0.48
22 2 0.08
23 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATTTAATATTAAATTAATAT
Found at i:454837 original size:29 final size:30
Alignment explanation
Indices: 454795--454875 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
454785 TAATTTGATC
*
454795 AAATCAAAATTTCATGTATAAAATTGCACA-
1 AAATC-AAAGTTCATGTATAAAATTGCACAT
** *
454825 AAATCAAAGTTCATACATACAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTGCACA-T
* *
454856 AAACCATAGTTCATGTATAA
1 AAATCAAAGTTCATGTATAA
454876 TTTTGGTATT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 20 0.50
30 5 0.12
31 15 0.38
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGCACAT
Found at i:467598 original size:145 final size:145
Alignment explanation
Indices: 467335--467622 Score: 522
Period size: 145 Copynumber: 2.0 Consensus size: 145
467325 TGCTGAATAT
* *
467335 ATATCTGTATCCAAAGTCCTGAAAGAAATACATTCAACAATTTTTATTATTTTTTGGCAAAATTA
1 ATATCTGTATCCAAAGTCCTGAAAGAAATACATTCAACAATTTTTATTATATTTTGACAAAATTA
467400 TTCAATTTTATCACTTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGAATA
66 TTCAATTTTATCACTTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGAATA
*
467465 CATGAGGTTGGTGAA
131 CACGAGGTTGGTGAA
*
467480 ATATCTGTATCCAAAGTCCTGAAAGAAATACATTCAACATTTTTTATTATATTTTGACAAAATTA
1 ATATCTGTATCCAAAGTCCTGAAAGAAATACATTCAACAATTTTTATTATATTTTGACAAAATTA
* *
467545 TTTAATTTTATCACTTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGCATA
66 TTCAATTTTATCACTTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGAATA
467610 CACGAGGTTGGTG
131 CACGAGGTTGGTG
467623 TACGTGAGAC
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
145 137 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (145 bp):
ATATCTGTATCCAAAGTCCTGAAAGAAATACATTCAACAATTTTTATTATATTTTGACAAAATTA
TTCAATTTTATCACTTCTTTTTGAGACAATATGGTGAAATACTTGTAGAAACATCTTGAGGAATA
CACGAGGTTGGTGAA
Found at i:471914 original size:13 final size:13
Alignment explanation
Indices: 471896--471920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
471886 CAAATAAACG
471896 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
471909 AGAAAGAAAGAA
1 AGAAAGAAAGAA
471921 GGAAGAAGGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:471926 original size:24 final size:24
Alignment explanation
Indices: 471899--471945 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
471889 ATAAACGAGA
471899 AAGAAAGAAAAGAAAGAAAGAAGG
1 AAGAAAGAAAAGAAAGAAAGAAGG
* * *
471923 AAGAAGGAGATGAAAGAAAGAAG
1 AAGAAAGAAAAGAAAGAAAGAAG
471946 AAGGTGAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (24 bp):
AAGAAAGAAAAGAAAGAAAGAAGG
Found at i:471958 original size:20 final size:20
Alignment explanation
Indices: 471897--471949 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
471887 AAATAAACGA
*
471897 GAAAGAAAGAA-AA-GA-AA
1 GAAAGAAAGAAGAAGGAGAT
*
471914 GAAAGAAGGAAGAAGGAGAT
1 GAAAGAAAGAAGAAGGAGAT
471934 GAAAGAAAGAAGAAGG
1 GAAAGAAAGAAGAAGG
471950 TGAGAAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.33
18 2 0.07
19 2 0.07
20 16 0.53
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (20 bp):
GAAAGAAAGAAGAAGGAGAT
Found at i:475340 original size:45 final size:45
Alignment explanation
Indices: 475274--475365 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
475264 GGGAGGAGTA
* *
475274 GAGTATTGCGGTGGCTCGTCAAACTAAGTCTGATATCCTTGGCTT
1 GAGTATTGCAGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTT
*
475319 GAGTATTGCAGTGGCTTGTCAAACTAAGGCTGATATCCTTGGCTT
1 GAGTATTGCAGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTT
475364 GA
1 GA
475366 TGAGCTAGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (45 bp):
GAGTATTGCAGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTT
Found at i:477250 original size:30 final size:30
Alignment explanation
Indices: 477206--477300 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
477196 CCAAAATGGG
* *
477206 TTATTTACTAAAATGGTACAAAATATATAT
1 TTATTTACCAAAATGGTACAAAATAAATAT
* * **
477236 TTATATACCAAAATGGTATC--CATACACCA-
1 TTATTTACCAAAATGGTA-CAAAATA-AATAT
477265 TTATTTACCAAAATGGTACAAAATAAATAT
1 TTATTTACCAAAATGGTACAAAATAAATAT
477295 TTATTT
1 TTATTT
477301 TGTACCATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
28 1 0.02
29 22 0.44
30 26 0.52
31 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (30 bp):
TTATTTACCAAAATGGTACAAAATAAATAT
Found at i:480843 original size:22 final size:21
Alignment explanation
Indices: 480793--480843 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
480783 TTAAATAACA
* *
480793 AATC-AATTAAAAATTAAATT
1 AATCAAATAAAAAATTAAAAT
*
480813 AAACAAAATAAAAAACTTAAAAT
1 AATC-AAATAAAAAA-TTAAAAT
480836 AATCAAAT
1 AATCAAAT
480844 TAACTAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
22 12 0.50
23 9 0.38
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (21 bp):
AATCAAATAAAAAATTAAAAT
Found at i:481128 original size:14 final size:14
Alignment explanation
Indices: 481076--481127 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
481066 TTCCTTCTTC
481076 TCCTTCTTCCTTAT
1 TCCTTCTTCCTTAT
481090 TCCTTCTTCCTTAT
1 TCCTTCTTCCTTAT
* *
481104 TCCTTCTTTCTTTTT
1 TCCTTC-TTCCTTAT
481119 TCCTTCTTC
1 TCCTTCTTC
481128 TCATGTTGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.62
Consensus pattern (14 bp):
TCCTTCTTCCTTAT
Found at i:486242 original size:65 final size:64
Alignment explanation
Indices: 486118--486249 Score: 237
Period size: 65 Copynumber: 2.0 Consensus size: 64
486108 GGAGGAGAAA
* *
486118 TGTAATGACCTAAATTCACGGGCACCGGAAAAGTGAGTTATAGGGCCTCCGTCTTAGTAAACCG
1 TGTAATGACCTAAATTCACGGGCACCGAAAAAATGAGTTATAGGGCCTCCGTCTTAGTAAACCG
486182 TGTAATGACCTAAATTCACGGGCACCGAAAAAAATGAGTTATAGGGCCTCCGTCTTAGTAAACCG
1 TGTAATGACCTAAATTCACGGGCACCG-AAAAAATGAGTTATAGGGCCTCCGTCTTAGTAAACCG
486247 TGT
1 TGT
486250 TCGTAAATAA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 27 0.42
65 38 0.58
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (64 bp):
TGTAATGACCTAAATTCACGGGCACCGAAAAAATGAGTTATAGGGCCTCCGTCTTAGTAAACCG
Found at i:486549 original size:48 final size:52
Alignment explanation
Indices: 486473--486568 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 52
486463 AAGATTTTTC
486473 ATTATTTAATCTATTATTAATTAATATT-A-TAATATA-ATA-ATATAAATT
1 ATTATTTAATCTATTATTAATTAATATTAACTAATATATATATATATAAATT
* *
486521 ATTATTTAAT-TATTATTATTTTATTATTAACTAATATATATATATATA
1 ATTATTTAATCTATTATTA-ATTAATATTAACTAATATATATATATATA
486569 TATAATAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
47 8 0.20
48 17 0.41
49 1 0.02
50 7 0.17
51 3 0.07
52 5 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (52 bp):
ATTATTTAATCTATTATTAATTAATATTAACTAATATATATATATATAAATT
Found at i:486668 original size:17 final size:17
Alignment explanation
Indices: 486643--486676 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
486633 ACGAAACAGG
* *
486643 GGAAGAAGAAAAGGGAA
1 GGAAAAAGAAAAAGGAA
486660 GGAAAAAGAAAAAGGAA
1 GGAAAAAGAAAAAGGAA
486677 AAATTAGGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
GGAAAAAGAAAAAGGAA
Found at i:490875 original size:31 final size:31
Alignment explanation
Indices: 490838--490899 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
490828 AATTGACCCA
* *
490838 ACTTAAAATTGGCGTGACCTCAAATTGAATT
1 ACTTAAAATTAGCATGACCTCAAATTGAATT
* *
490869 ACTTAAAATTAGCATGATCTTAAATTGAATT
1 ACTTAAAATTAGCATGACCTCAAATTGAATT
490900 GAACTCGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (31 bp):
ACTTAAAATTAGCATGACCTCAAATTGAATT
Found at i:491646 original size:28 final size:28
Alignment explanation
Indices: 491591--491648 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
491581 TTTAAATTTT
***
491591 AATCTAATTACTTTTTTTTTTGTCAAAA
1 AATCTAATTACTTTTTTTTAAATCAAAA
*
491619 AATCTAATTACTTTTTTTTAAATTAAAA
1 AATCTAATTACTTTTTTTTAAATCAAAA
491647 AA
1 AA
491649 AAGTTAATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.50
Consensus pattern (28 bp):
AATCTAATTACTTTTTTTTAAATCAAAA
Found at i:492092 original size:16 final size:17
Alignment explanation
Indices: 492068--492100 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
492058 AATTTCAATT
492068 TTAAATTTT-AATTAAA
1 TTAAATTTTAAATTAAA
*
492084 TTAATTTTTAAATTAAA
1 TTAAATTTTAAATTAAA
492101 AAAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATTTTAAATTAAA
Found at i:493716 original size:28 final size:29
Alignment explanation
Indices: 493666--493721 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
493656 TAAACCATAA
* *
493666 TTATTGGATTAGGTCAGTTTTTGCAAAAT
1 TTATCGGATTAGGTCAGATTTTGCAAAAT
* *
493695 TTATCGGATTAGGT-TGATTTTGGAAAA
1 TTATCGGATTAGGTCAGATTTTGCAAAA
493722 ACTCATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.29, C:0.05, G:0.23, T:0.43
Consensus pattern (29 bp):
TTATCGGATTAGGTCAGATTTTGCAAAAT
Found at i:494062 original size:138 final size:139
Alignment explanation
Indices: 493883--494136 Score: 386
Period size: 140 Copynumber: 1.8 Consensus size: 139
493873 ATTTGTTTTT
* * *
493883 TTTTATTTCATGTTACTTCAAGCTTTTTAAAATTTTTATTAA-TTTTTTAACACATTAGTTCTTT
1 TTTTATTTCATGTTACTTCAAGATTTTTAAAATTTTTATTAAGTTTTTTAACACATTAGTCCTTA
493947 GGTTAGATGGTCAGATAGTTGCAATTACATCTTTGAGTCTCGAGTTTGATAACTCTTCTACTCAT
66 GGTTAGATGGTCAGATAGTTGCAATTACATCTTTGAGTCTCGAGTTTGATAACTCTTCTACTCAT
494012 ATTTGTATA
131 ATTTGTATA
* * ** *
494021 TTTTATTTCATGTTGCTTTAAGATTTTT-AAATTTTTAATTAATGTTTTTTAACATTTTTGTCCT
1 TTTTATTTCATGTTACTTCAAGATTTTTAAAATTTTT-ATTAA-GTTTTTTAACACATTAGTCCT
* *
494085 TAGGTTAGATGGTTAGATAGTTGTAATTACATCTTTGAGTCTCGAGTTTGAT
64 TAGGTTAGATGGTCAGATAGTTGCAATTACATCTTTGAGTCTCGAGTTTGAT
494137 TCATCTACTA
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
137 8 0.08
138 30 0.29
140 65 0.63
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (139 bp):
TTTTATTTCATGTTACTTCAAGATTTTTAAAATTTTTATTAAGTTTTTTAACACATTAGTCCTTA
GGTTAGATGGTCAGATAGTTGCAATTACATCTTTGAGTCTCGAGTTTGATAACTCTTCTACTCAT
ATTTGTATA
Found at i:494992 original size:1 final size:1
Alignment explanation
Indices: 494986--495010 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
494976 GTAAATTCTC
494986 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
495011 CACAACCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:498200 original size:29 final size:30
Alignment explanation
Indices: 498158--498224 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
498148 TCAAAATTTT
*
498158 ATGTATAAAATTG-CATAAAATCAAAGTTC
1 ATGTATAAAATTGACATAAAACCAAAGTTC
* * *
498187 ATGTATACAATTGCACATTAAACCATAGTTC
1 ATGTATAAAATTG-ACATAAAACCAAAGTTC
498218 ATGTATA
1 ATGTATA
498225 GTTTTGGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.38
31 20 0.62
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (30 bp):
ATGTATAAAATTGACATAAAACCAAAGTTC
Found at i:501245 original size:17 final size:17
Alignment explanation
Indices: 501220--501254 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
501210 GTTTCTCCAC
*
501220 AATTTAAAAAATTATAA
1 AATTAAAAAAATTATAA
*
501237 AATTAAAAAAATTCTAA
1 AATTAAAAAAATTATAA
501254 A
1 A
501255 GAAAGTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAAAAAATTATAA
Found at i:504892 original size:20 final size:20
Alignment explanation
Indices: 504867--504925 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
504857 TTTGTTATAA
504867 AAACTTGTGGTACAAGAAAC
1 AAACTTGTGGTACAAGAAAC
* *
504887 AAACTTATGGTGA-AAGAAAG
1 AAACTTGTGGT-ACAAGAAAC
504907 AAACTTGTGGTACAAGAAA
1 AAACTTGTGGTACAAGAAA
504926 TAATCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.20
Consensus pattern (20 bp):
AAACTTGTGGTACAAGAAAC
Found at i:505354 original size:18 final size:19
Alignment explanation
Indices: 505317--505354 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
505307 TATTTATATT
*
505317 TAAATAAAGTTATCAGTTA
1 TAAATAAAGTTATCAATTA
*
505336 TAAAT-AAGTTCTCAATTA
1 TAAATAAAGTTATCAATTA
505354 T
1 T
505355 CTTTTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (19 bp):
TAAATAAAGTTATCAATTA
Found at i:507213 original size:30 final size:30
Alignment explanation
Indices: 507174--507299 Score: 157
Period size: 30 Copynumber: 4.3 Consensus size: 30
507164 AGGAGATCCC
* *
507174 TAAACTTTTCAAAAATCATATTTTAACCCT
1 TAAACTTTTCCAAAATCACATTTTAACCCT
* *
507204 TAAAATTTTCCAAAATTACATTTTAACCCT
1 TAAACTTTTCCAAAATCACATTTTAACCCT
*
507234 TAAACTTTTCCAAAATCACATTTTGACCC-
1 TAAACTTTTCCAAAATCACATTTTAACCCT
** *
507263 TAAACTTCCCCAAAATCACATTTTGACCC-
1 TAAACTTTTCCAAAATCACATTTTAACCCT
*
507292 CAAACTTT
1 TAAACTTT
507300 CATAAAAATT
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
29 33 0.39
30 52 0.61
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
TAAACTTTTCCAAAATCACATTTTAACCCT
Found at i:507276 original size:29 final size:29
Alignment explanation
Indices: 507171--507346 Score: 149
Period size: 30 Copynumber: 5.9 Consensus size: 29
507161 CTCAGGAGAT
* * * *
507171 CCCTAAACTTTTCAAAAATCATATTTTAA
1 CCCTAAACTTCTCCAAAATCACATTTTGA
* * * *
507200 CCCTTAAAATTTTCCAAAATTACATTTTAA
1 CCC-TAAACTTCTCCAAAATCACATTTTGA
*
507230 CCCTTAAACTTTTCCAAAATCACATTTTGA
1 CCC-TAAACTTCTCCAAAATCACATTTTGA
*
507260 CCCTAAACTTCCCCAAAATCACATTTTGA
1 CCCTAAACTTCTCCAAAATCACATTTTGA
* * * *
507289 CCCCAAACTT-TCATAAAAATTACCTTTTGA
1 CCCTAAACTTCTC--CAAAATCACATTTTGA
*
507319 CCCCTAAA-TTCTCCCAAAATTACATTTT
1 -CCCTAAACTTCT-CCAAAATCACATTTT
507347 AACCTCAAAT
Statistics
Matches: 124, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.01
29 36 0.29
30 79 0.64
31 7 0.06
32 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCTCCAAAATCACATTTTGA
Found at i:509966 original size:29 final size:29
Alignment explanation
Indices: 509924--509984 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
509914 ACCTTAAATG
*
509924 GAACTGTGCCAAACCTTTAGTGGTTACCC
1 GAACTATGCCAAACCTTTAGTGGTTACCC
*
509953 GAACTATGCCAAACCTTTAGTGGTTACTC
1 GAACTATGCCAAACCTTTAGTGGTTACCC
509982 GAA
1 GAA
509985 TAAGGTAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (29 bp):
GAACTATGCCAAACCTTTAGTGGTTACCC
Found at i:512018 original size:18 final size:19
Alignment explanation
Indices: 511992--512032 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
511982 TTATCAAAAG
*
511992 AAAATAAAAAAAGAG-AAA
1 AAAAGAAAAAAAGAGTAAA
*
512010 AAAAGAAAAAAAGGGTAAA
1 AAAAGAAAAAAAGAGTAAA
512029 AAAA
1 AAAA
512033 TCCGTAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAAGAAAAAAAGAGTAAA
Found at i:512921 original size:9 final size:9
Alignment explanation
Indices: 512889--512929 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
512879 AGATTCGATG
512889 AAGAAAAAT
1 AAGAAAAAT
*
512898 AA-AAGAAAG
1 AAGAA-AAAT
512907 AA-AAAAAT
1 AAGAAAAAT
512915 AAGAAAAAT
1 AAGAAAAAT
512924 AAGAAA
1 AAGAAA
512930 TAAAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (9 bp):
AAGAAAAAT
Found at i:512925 original size:26 final size:22
Alignment explanation
Indices: 512889--512965 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 22
512879 AGATTCGATG
512889 AAGAAAAATAAAAGAAAGAAAAAAA
1 AAGAAAAAT--AAGAAA-AAAAAAA
*
512914 TAAGAAAAATAAGAAATAAAAAA
1 -AAGAAAAATAAGAAAAAAAAAA
* *
512937 AAGAAAAA-AGGAAAAAAGGAAA
1 AAGAAAAATAAGAAAAAA-AAAA
512959 AAGAAAA
1 AAGAAAA
512966 GGAGAGGTCG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.15
22 18 0.39
23 6 0.13
24 6 0.13
26 9 0.20
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (22 bp):
AAGAAAAATAAGAAAAAAAAAA
Found at i:512930 original size:16 final size:15
Alignment explanation
Indices: 512900--512965 Score: 59
Period size: 16 Copynumber: 4.5 Consensus size: 15
512890 AGAAAAATAA
512900 AAGAAAGAAAA-AAAT
1 AAGAAA-AAAAGAAAT
512915 AAGAAAAATAAGAAAT
1 AAGAAAAA-AAGAAAT
*
512931 -A-AAAAAAAGAAAA
1 AAGAAAAAAAGAAAT
*
512944 AAGGAAAAAAGGAAA-
1 AA-GAAAAAAAGAAAT
512959 AAGAAAA
1 AAGAAAA
512966 GGAGAGGTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
13 6 0.14
14 13 0.30
15 11 0.25
16 14 0.32
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (15 bp):
AAGAAAAAAAGAAAT
Found at i:512932 original size:7 final size:7
Alignment explanation
Indices: 512898--512965 Score: 59
Period size: 7 Copynumber: 9.3 Consensus size: 7
512888 GAAGAAAAAT
512898 AAAAGAA
1 AAAAGAA
512905 AGAAA-AA
1 A-AAAGAA
512912 AATAAGAAA
1 AA-AAG-AA
512921 AATAAGAA
1 AA-AAGAA
*
512929 ATAA-AA
1 AAAAGAA
512935 AAAAGAA
1 AAAAGAA
512942 AAAAGGAA
1 AAAA-GAA
*
512950 AAAAGGA
1 AAAAGAA
512957 AAAAGAA
1 AAAAGAA
512964 AA
1 AA
512966 GGAGAGGTCG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
6 6 0.12
7 24 0.47
8 13 0.25
9 8 0.16
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:512945 original size:8 final size:8
Alignment explanation
Indices: 512892--512960 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
512882 TTCGATGAAG
*
512892 AAAAATAA
1 AAAAAGAA
512900 AAGAAAGAA
1 AA-AAAGAA
*
512909 AAAAATAA
1 AAAAAGAA
*
512917 GAAAAATAA
1 -AAAAAGAA
*
512926 GAAATA-AA
1 -AAAAAGAA
512934 AAAAAGAA
1 AAAAAGAA
*
512942 AAAAGGAA
1 AAAAAGAA
*
512950 AAAAGGAA
1 AAAAAGAA
512958 AAA
1 AAA
512961 GAAAAGGAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
7 4 0.08
8 29 0.55
9 20 0.38
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (8 bp):
AAAAAGAA
Found at i:512951 original size:15 final size:14
Alignment explanation
Indices: 512898--512965 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 14
512888 GAAGAAAAAT
512898 AAAAGAAAGAAA-AA
1 AAAAGAAA-AAAGAA
512912 AATAAGAAAAATAAGAA
1 AA-AAG-AAAA-AAGAA
*
512929 ATAA-AAAAAAGAA
1 AAAAGAAAAAAGAA
*
512942 AAAAGGAAAAAAGGA
1 AAAA-GAAAAAAGAA
512957 AAAAGAAAA
1 AAAAGAAAA
512966 GGAGAGGTCG
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 8 0.18
14 11 0.24
15 16 0.36
16 7 0.16
17 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:514334 original size:40 final size:39
Alignment explanation
Indices: 514283--514433 Score: 187
Period size: 40 Copynumber: 3.7 Consensus size: 39
514273 AATTGCACTC
514283 ATTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAT
1 ATTCC-ATCTTTTACCCCTAATCAAGAGGGGCAAATTGAT
*
514323 CA-TCCGATCTTTTACCCCTAATCAAGAGGGGCAAATTGAAG
1 -ATTCC-ATCTTTTACCCCTAATCAAGAGGGGCAAATTG-AT
* * *
514364 ATTCCAGTCTTTTACCCCTAATCAAGAGGGGGAGATTTAAT
1 ATTCCA-TCTTTTACCCCTAATCAAGAGGGGCA-AATTGAT
514405 ATTCCAAATCTTTTACCCCTAATCAAGAG
1 ATTCC--ATCTTTTACCCCTAATCAAGAG
514434 AAGCAGATTG
Statistics
Matches: 98, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
40 37 0.38
41 36 0.37
42 24 0.24
43 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (39 bp):
ATTCCATCTTTTACCCCTAATCAAGAGGGGCAAATTGAT
Found at i:514382 original size:81 final size:83
Alignment explanation
Indices: 514283--514433 Score: 227
Period size: 81 Copynumber: 1.8 Consensus size: 83
514273 AATTGCACTC
* *
514283 ATTCCAATCTTTTACCCCTAATCAAGAGGGGCA-AATTGATCA-TCC-GATCTTTTACCCCTAAT
1 ATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGAATTAAT-ATTCCAAATCTTTTACCCCTAAT
514345 CAAGAGGGGCAAATTGAAG
65 CAAGAGGGGCAAATTGAAG
* * *
514364 ATTCCAGTCTTTTACCCCTAATCAAGAGGGGGAGATTTAATATTCCAAATCTTTTACCCCTAATC
1 ATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGAATTAATATTCCAAATCTTTTACCCCTAATC
514429 AAGAG
66 AAGAG
514434 AAGCAGATTG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
81 32 0.52
82 8 0.13
83 22 0.35
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (83 bp):
ATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGAATTAATATTCCAAATCTTTTACCCCTAATC
AAGAGGGGCAAATTGAAG
Found at i:514387 original size:41 final size:41
Alignment explanation
Indices: 514282--514472 Score: 222
Period size: 41 Copynumber: 4.6 Consensus size: 41
514272 AAATTGCACT
*
514282 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAT
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAA
*
514323 CA-TCCGATCTTTTACCCCTAATCAAGAGGGGCAAATTGAA
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAA
* * * * *
514363 GATTCCAGTCTTTTACCCCTAATCAAGAGGGGGAGATTTAA
1 CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAA
* ** *
514404 TATTCCAAATCTTTTACCCCTAATCAAGAGAAGCAGATTGAGGA
1 CATTCC-AATCTTTTACCCCTAATCAAGAGGGGCAAATTGA--A
** *
514448 CACACCAATCTCTTACCCCTAATCA
1 CATTCCAATCTTTTACCCCTAATCA
514473 TGGGGTAGAT
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 37 0.29
41 40 0.31
42 29 0.23
43 18 0.14
44 4 0.03
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (41 bp):
CATTCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAA
Found at i:514483 original size:83 final size:83
Alignment explanation
Indices: 514286--514472 Score: 209
Period size: 83 Copynumber: 2.3 Consensus size: 83
514276 TGCACTCATT
* * * * *
514286 CCAATCTTTTACCCCTAATCAAGAGGGGCA-AATTGATCA-TCC-GATCTTTTACCCCTAATCAA
1 CCAATCTCTTACCCCTAATCAAGAGGGGGAGATTTAAT-ATTCCAAATCTTTTACCCCTAATCAA
** * **
514348 GAGGGGCAAATTGAAGATT
65 GAGAAGCAAATTGAACACA
* *
514367 CCAGTCTTTTACCCCTAATCAAGAGGGGGAGATTTAATATTCCAAATCTTTTACCCCTAATCAAG
1 CCAATCTCTTACCCCTAATCAAGAGGGGGAGATTTAATATTCCAAATCTTTTACCCCTAATCAAG
*
514432 AGAAGCAGATTGAGGACACA
66 AGAAGCAAATTGA--ACACA
514452 CCAATCTCTTACCCCTAATCA
1 CCAATCTCTTACCCCTAATCA
514473 TGGGGTAGAT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
81 29 0.33
82 8 0.09
83 30 0.34
85 21 0.24
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (83 bp):
CCAATCTCTTACCCCTAATCAAGAGGGGGAGATTTAATATTCCAAATCTTTTACCCCTAATCAAG
AGAAGCAAATTGAACACA
Found at i:514529 original size:45 final size:43
Alignment explanation
Indices: 514452--514578 Score: 141
Period size: 42 Copynumber: 2.9 Consensus size: 43
514442 TGAGGACACA
*
514452 CCAATCTCTTACCCCTAATCATGGGGTAGATTGCAGCCATTATCAT
1 CCAATCTCTTA-CCCTGATCAT-GGGTAGATTGCAGCCA-TATCAT
* *
514498 CCAATCTCTTACCCTGATCATGGGACAGATTGCA-ACA-ATCAT
1 CCAATCTCTTACCCTGATCATGGG-TAGATTGCAGCCATATCAT
* * *
514540 CCGATCTTTTACCCCGATCATAGGGTAGATTGCAGCCAT
1 CCAATCTCTTACCCTGATCAT-GGGTAGATTGCAGCCAT
514579 CCAATCTCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
42 31 0.45
43 5 0.07
44 5 0.07
45 17 0.25
46 11 0.16
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (43 bp):
CCAATCTCTTACCCTGATCATGGGTAGATTGCAGCCATATCAT
Found at i:514552 original size:42 final size:42
Alignment explanation
Indices: 514452--514610 Score: 137
Period size: 42 Copynumber: 3.8 Consensus size: 42
514442 TGAGGACACA
* * * *
514452 CCAATCTCTTACCCCTAATCATGGGGTAGATTGCAGCCATTATCAT
1 CCAATCTCTTACCCC-GATCATAGGGCAGATTGCA-ACA--ATCAT
*
514498 CCAATCTCTTACCCTGATCAT-GGGACAGATTGCAACAATCAT
1 CCAATCTCTTACCCCGATCATAGGG-CAGATTGCAACAATCAT
* * * *
514540 CCGATCTTTTACCCCGATCATAGGGTAGATTGCAGC---CAT
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGCAACAATCAT
* * *
514579 CCAATCTCTTATCCTGATCATAGGGCATATTG
1 CCAATCTCTTACCCCGATCATAGGGCAGATTG
514611 TAGTCATCCG
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
39 29 0.30
42 32 0.33
43 3 0.03
44 5 0.05
45 13 0.14
46 14 0.15
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (42 bp):
CCAATCTCTTACCCCGATCATAGGGCAGATTGCAACAATCAT
Found at i:514619 original size:39 final size:39
Alignment explanation
Indices: 514494--514619 Score: 128
Period size: 39 Copynumber: 3.2 Consensus size: 39
514484 GCAGCCATTA
*
514494 TCATCCAATCTCTTACCCTGATCAT-GGGACAGATTGCAACAA
1 TCATCCAATCTCTTACCCTGATCATAGGG-CAGATTG---CAG
* * * *
514536 TCATCCGATCTTTTACCCCGATCATAGGGTAGATTGCAG
1 TCATCCAATCTCTTACCCTGATCATAGGGCAGATTGCAG
* * * *
514575 CCATCCAATCTCTTATCCTGATCATAGGGCATATTGTAG
1 TCATCCAATCTCTTACCCTGATCATAGGGCAGATTGCAG
514614 TCATCC
1 TCATCC
514620 GAACCAATAA
Statistics
Matches: 69, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
39 38 0.55
42 28 0.41
43 3 0.04
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (39 bp):
TCATCCAATCTCTTACCCTGATCATAGGGCAGATTGCAG
Found at i:515013 original size:208 final size:208
Alignment explanation
Indices: 514624--515477 Score: 1140
Period size: 208 Copynumber: 4.1 Consensus size: 208
514614 TCATCCGAAC
* * ** ** * * *
514624 CAATAAAGCGGTCATATTCCTGATTAGATACAGAGAAGTGGACCAAATCTATCTTCTTGATAAGA
1 CAATAAAGTGGTCATCTTCCTGACGAGATGTAGAGAAGTGAACCAAATCTGTCTTCCTGATAAGA
* * * * *
514689 TACAAATAAGTGGATTGAAACAATGAGGCGGCCATCTTCCTAATGAGATACAGAGAAGTAAACCA
66 TACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCA
* * * *
514754 AATTAATGAGGCGAAGCTCAATACGAATGAGACTTCAAATCCTATCTTCCTGATGAGATACAAAG
131 AATCAATAAGGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAAAG
514819 AAGTAGGTCAAAG
196 AAGTAGGTCAAAG
* * * *
514832 TAATAAAATGGTCATCTTCTTGACGAGATGTAGAGAAGTGAACCAAATCTGTCTTCCTGATGAGA
1 CAATAAAGTGGTCATCTTCCTGACGAGATGTAGAGAAGTGAACCAAATCTGTCTTCCTGATAAGA
* * *
514897 TACAGAGAAGTGGATTGAAACAATGAGGCGGTCATTTTCTTGATGAGATACAGAGAAGTAGATCA
66 TACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCA
* *
514962 AATCAATAAGGCGAAGCTCAATACGAATGAGACTTCAAACCTCATCTTCCTGATGAGATACAGAG
131 AATCAATAAGGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAAAG
* * *
515027 AAATGGGTTAAAG
196 AAGTAGGTCAAAG
* * * *
515040 CAATAAAGTGGTCATCTTCCTGACGAGATGTAGAGAATTGAATCAAAT-TCGTCTTCTTAATAAG
1 CAATAAAGTGGTCATCTTCCTGACGAGATGTAGAGAAGTGAACCAAATCT-GTCTTCCTGATAAG
*
515104 ATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACA-AGAAGTAGTCC
65 ATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACC
* * *
515168 AAATCAATGAGGCGAAGCTCAATACGAATGTGACTTCAAACCCCATCTT-CTGATGAGATACAGA
130 AAATCAATAAGGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAAA
515232 GAAGTAGGTCAAAG
195 GAAGTAGGTCAAAG
* * *
515246 CAATAAAGTGGTCATATTCCTGATGAGATGTAGAGAAGTGAACCAAATCTGTCTTCCT-ACTGAG
1 CAATAAAGTGGTCATCTTCCTGACGAGATGTAGAGAAGTGAACCAAATCTGTCTTCCTGA-TAAG
* * * * * *
515310 ATACAGAGAAGTGGATTAAAACAATAAGACGGTCATCTTCTTGATAAGATACAGAGAAGTAGGCC
65 ATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACC
* * ** * * * *
515375 AAATCAATAAAGCGAAACTCAATGTGAGTGAAACTTCGAACCCCCATCTTCCTGATGAGATACTA
130 AAATCAATAAGGCGAAGCTCAATACGAATGAGACTTC-AAACCCCATCTTCCTGATGAGATACAA
515440 AGAAGTAGGTCAAAG
194 AGAAGTAGGTCAAAG
* *
515455 CAATAAAGCGGTCGTCTTCCTGA
1 CAATAAAGTGGTCATCTTCCTGA
515478 TAAGATACAG
Statistics
Matches: 566, Mismatches: 74, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
205 1 0.00
206 128 0.23
207 96 0.17
208 294 0.52
209 47 0.08
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (208 bp):
CAATAAAGTGGTCATCTTCCTGACGAGATGTAGAGAAGTGAACCAAATCTGTCTTCCTGATAAGA
TACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCA
AATCAATAAGGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAAAG
AAGTAGGTCAAAG
Found at i:515556 original size:48 final size:48
Alignment explanation
Indices: 515419--515558 Score: 147
Period size: 48 Copynumber: 2.9 Consensus size: 48
515409 TTCGAACCCC
* * * *
515419 CATCTTCCTGATGAGATACTAAGAAGTAGGTCAAAGCAATAAAGCGGT
1 CATCTTCCTGATGAGATACAAAGAAGTAGATCAAATCAATGAAGCGGT
* * * * *
515467 CGTCTTCCTGATAAGATACAGAGAAGTAGATTGAAAT-AATGAGGCGGT
1 CATCTTCCTGATGAGATACAAAGAAGTAGA-TCAAATCAATGAAGCGGT
** * *
515515 CATCTTTTTGATGAGACACAAAGAAGTAGACCAAATCAATGAAG
1 CATCTTCCTGATGAGATACAAAGAAGTAGATCAAATCAATGAAG
515559 TGAAGCTCAA
Statistics
Matches: 72, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
47 4 0.06
48 64 0.89
49 4 0.06
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAAAGAAGTAGATCAAATCAATGAAGCGGT
Found at i:515678 original size:48 final size:48
Alignment explanation
Indices: 515590--515684 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
515580 CTTCAAACCT
* **
515590 CATCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAATGAGGCGAC
1 CATCTTCCTGATGAGATACAAAGAAGTAGATCCAAACAATGAGGCGAC
* * *
515638 CATCTTCCTTATGAGATACAGAGAAGTAGA-CCAAATCAATGTGGCGA
1 CATCTTCCTGATGAGATACAAAGAAGTAGATCCAAA-CAATGAGGCGA
515685 AGCTCAATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 3 0.08
48 37 0.93
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAAAGAAGTAGATCCAAACAATGAGGCGAC
Found at i:515688 original size:123 final size:122
Alignment explanation
Indices: 515469--515797 Score: 383
Period size: 123 Copynumber: 2.7 Consensus size: 122
515459 AAAGCGGTCG
* * * * * * *
515469 TCTTCCTGATAAGATACAGAGAAGTAGATTGAAATAATGAGGCGGTCATCTTTTTGATGAGACAC
1 TCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAATGAGGCGATCATCTTCTT-ATGAGATAC
* * * * *
515534 AAAGAAGTAGACCAAATCAATGAAGTGAAGCTCAATATGAATGAGACTTCAAACCTCA
65 AGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAAGGAGACTTCAAACCCCA
*
515592 TCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAATGAGGCGACCATCTTCCTTATGAGATAC
1 TCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAATGAGGCGATCATCTT-CTTATGAGATAC
** *
515657 AGAGAAGTAGACCAAATCAATGTGGCGAAGCTCAATACGAAGGAGACTTTAAACCCCA
65 AGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAAGGAGACTTCAAACCCCA
* * * * * * *
515715 TATTCCTGATGAGATAAAAAGAAGTGG-GTCAAAGCAATAAAGC-AGTCATCTTTCTGATGAGAT
1 TCTTCCTGATGAGATACAAAGAAGTGGATTGAAA-CAATGAGGCGA-TCATC-TTCTTATGAGAT
*
515778 ACAGAGAAGTGGACCAAATC
63 ACAGAGAAGTAGACCAAATC
515798 CGTCTTCTTG
Statistics
Matches: 177, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
122 5 0.03
123 168 0.95
124 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.23
Consensus pattern (122 bp):
TCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAATGAGGCGATCATCTTCTTATGAGATACA
GAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAAGGAGACTTCAAACCCCA
Found at i:515957 original size:208 final size:208
Alignment explanation
Indices: 515592--516575 Score: 1375
Period size: 208 Copynumber: 4.7 Consensus size: 208
515582 TCAAACCTCA
* * **
515592 TCTTCCTGATGAGATACAAAGAAGTGGATTGAAACAATGAGGCGACCATCTTCCTT-ATGAGATA
1 TCTTCTTGATGAGATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTT-CTTGATGAGATA
** ** * *
515656 CAGAGAAGTAGACCAAATCAATGTGGCGAAGCTCAATACGAAGGAGACTTTAAACCCCATATTCC
65 CAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATAAGACTTCAAACCCCATCTTCC
* * ** *
515721 TGATGAGATAAAAAGAAGTGGGTCAAAGCAATAAAGCAGTCATCTTTCTGATGAGATACAGAGAA
130 TGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCTGATGAGATACAGAGAA
*
515786 GTGGACCAAATCCG
195 GTGAACCAAATCCG
*
515800 TCTTCTTGATGAGATACAGAGAAGTGGATTGAACCAATGAGGCGGTCATCTTCTTGATGAGATAC
1 TCTTCTTGATGAGATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCTTGATGAGATAC
515865 AGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATAAGACTTCAAACCCCATCTTCCT
66 AGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATAAGACTTCAAACCCCATCTTCCT
* * *
515930 GATGAGATACAGAGAAATCGATCAAAGCAATAAAGTGGTCATCTTCCTGATGAGATACAGAGAAG
131 GATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCTGATGAGATACAGAGAAG
515995 T-AGACCAAATCCG
196 TGA-ACCAAATCCG
* * * *
516008 TCTTCCTGATGAGATACAGAGAAGTGGATTGAAATAATGAGGCAGTCATCTTCCTT-ATAAGATA
1 TCTTCTTGATGAGATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTT-CTTGATGAGATA
* * *
516072 CAAAGAAGTAGACCAAATCAAT-AAGGTGAAGCTCAATACGAATTAGACTTCAAACCCCATCTTC
65 CAGAGAAGTAGACCAAATCAATGAA-GCGAAGCTCAATACGAATAAGACTTCAAACCCCATCTTC
* * * *
516136 CTGATGAGATATAAAGAAGTGGGTCAAAGCAATAAAGTGGTTATCTTCCTGATGAGATGCAGAGA
129 CTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCTGATGAGATACAGAGA
*
516201 AGTGAACTAAATCCG
194 AGTGAACCAAATCCG
* *
516216 TCTTCTTAATGAGATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCTTGATAAGATAC
1 TCTTCTTGATGAGATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCTTGATGAGATAC
* * * * *
516281 AGAGAAGTGGACCAAATCATTGAGGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTTCT
66 AGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATAAGACTTCAAACCCCATCTTCCT
* * * **
516346 GATGAGATACAGAGAAGTGGGTTAAAGCAATAAAGTGGTCATCTTCCTTACGAGATGGAGAGAAG
131 GATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCTGATGAGATACAGAGAAG
*
516411 TGAACCAAATTCG
196 TGAACCAAATCCG
* * * ** *
516424 TCTTCTTGATGAGATACAGAGAAGTAGATTAAAATAATGAAACGGTCATCTTCCTGATGAGATAC
1 TCTTCTTGATGAGATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCTTGATGAGATAC
* * * *
516489 AGAGAAGTAGACCAAATCAATGAAGCGAAACTTAATACGAATGAA-ACTTCAAAACACTCATCCT
66 AGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAAT-AAGACTTC-AAAC-CCCATCTT
516553 CCTGATGAGATACAGAGAAGTGG
128 CCTGATGAGATACAGAGAAGTGG
516576 ACCGAAAGAT
Statistics
Matches: 693, Mismatches: 73, Indels: 18
0.88 0.09 0.02
Matches are distributed among these distances:
207 8 0.01
208 647 0.93
209 10 0.01
210 28 0.04
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (208 bp):
TCTTCTTGATGAGATACAGAGAAGTGGATTGAAACAATGAGGCGGTCATCTTCTTGATGAGATAC
AGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATAAGACTTCAAACCCCATCTTCCT
GATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGTGGTCATCTTCCTGATGAGATACAGAGAAG
TGAACCAAATCCG
Found at i:516071 original size:85 final size:85
Alignment explanation
Indices: 515923--516090 Score: 221
Period size: 85 Copynumber: 2.0 Consensus size: 85
515913 TCAAACCCCA
** *
515923 TCTTCCTGATGAGATACAGAGAAATCGATCAAAGCAATAAAGTGGTCATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAATCGATCAAAGCAATAAAGCAGTCATCTTCCTGATAAGATAC
*
515988 AGAGAAGTAGACCAAATCCG
66 AAAGAAGTAGACCAAATCCG
* * * * * * *
516008 TCTTCCTGATGAGATACAGAGAAGTGGATTGAAA-TAATGAGGCAGTCATCTTCCTTATAAGATA
1 TCTTCCTGATGAGATACAGAGAAATCGA-TCAAAGCAATAAAGCAGTCATCTTCCTGATAAGATA
516072 CAAAGAAGTAGACCAAATC
65 CAAAGAAGTAGACCAAATC
516091 AATAAGGTGA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 67 0.94
86 4 0.06
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAATCGATCAAAGCAATAAAGCAGTCATCTTCCTGATAAGATAC
AAAGAAGTAGACCAAATCCG
Found at i:516305 original size:48 final size:48
Alignment explanation
Indices: 516216--516307 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
516206 ACTAAATCCG
* **
516216 TCTTCTTAATGAGATACAGAGAAGTGGATTGAAACAATGAGGCGGTCA
1 TCTTCTTAATAAGATACAGAGAAGTGGATCCAAACAATGAGGCGGTCA
* *
516264 TCTTCTTGATAAGATACAGAGAAGTGGA-CCAAATCATTGAGGCG
1 TCTTCTTAATAAGATACAGAGAAGTGGATCCAAA-CAATGAGGCG
516308 AAGCTCAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 3 0.08
48 35 0.92
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (48 bp):
TCTTCTTAATAAGATACAGAGAAGTGGATCCAAACAATGAGGCGGTCA
Found at i:516493 original size:85 final size:85
Alignment explanation
Indices: 516345--516505 Score: 209
Period size: 85 Copynumber: 1.9 Consensus size: 85
516335 CCCATCTTTC
* * * * * **
516345 TGATGAGATACAGAGAAGTGGGTTAAAGCAATAAAGTGGTCATCTTCCTTACGAGATGGAGAGAA
1 TGATGAGATACAGAGAAGTAGATTAAAACAATAAAGCGGTCATCTTCCTGACGAGATACAGAGAA
516410 GT-GAACCAAATTCGTCTTCT
66 GTAG-ACCAAATTCGTCTTCT
* *
516430 TGATGAGATACAGAGAAGTAGATTAAAATAATGAAA-CGGTCATCTTCCTGATGAGATACAGAGA
1 TGATGAGATACAGAGAAGTAGATTAAAACAAT-AAAGCGGTCATCTTCCTGACGAGATACAGAGA
516494 AGTAGACCAAAT
65 AGTAGACCAAAT
516506 CAATGAAGCG
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
85 61 0.94
86 4 0.06
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (85 bp):
TGATGAGATACAGAGAAGTAGATTAAAACAATAAAGCGGTCATCTTCCTGACGAGATACAGAGAA
GTAGACCAAATTCGTCTTCT
Found at i:518324 original size:30 final size:30
Alignment explanation
Indices: 518285--518439 Score: 197
Period size: 30 Copynumber: 5.2 Consensus size: 30
518275 CTCAGGAAGT
* *
518285 CCCTAAACTTTTCAAAAATCATATTTTGAC
1 CCCTAAACTTTTCCAAAATTATATTTTGAC
** *
518315 CATTAAACTTTTCCAAAATTACATTTTGA-
1 CCCTAAACTTTTCCAAAATTATATTTTGAC
* *
518344 CCCTAAACTTTTTCAAAATTATATTTTAAC
1 CCCTAAACTTTTCCAAAATTATATTTTGAC
* *
518374 CCCTTAACTTTTCTAAAATTATATTTTGAC
1 CCCTAAACTTTTCCAAAATTATATTTTGAC
* *
518404 CCCTAAACTTTTCCAAAATCACATTTTGA-
1 CCCTAAACTTTTCCAAAATTATATTTTGAC
518433 CCCTAAA
1 CCCTAAA
518440 ATTCCCAAAA
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
29 31 0.29
30 75 0.71
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTATATTTTGAC
Found at i:518362 original size:59 final size:59
Alignment explanation
Indices: 518285--518434 Score: 196
Period size: 59 Copynumber: 2.5 Consensus size: 59
518275 CTCAGGAAGT
518285 CCCTAAAC-TTTTCAAAAATCATATTTTGACCATTAAACTTTTCCAAAATTACATTTTGA-
1 CCCTAAACTTTTTC-AAAATCATATTTTGACCATT-AACTTTTCCAAAATTACATTTTGAC
* * * * *
518344 CCCTAAACTTTTTCAAAATTATATTTTAACCCCTTAACTTTTCTAAAATTATATTTTGAC
1 CCCTAAACTTTTTCAAAATCATATTTTGA-CCATTAACTTTTCCAAAATTACATTTTGAC
* *
518404 CCCTAAACTTTTCCAAAATCACATTTTGACC
1 CCCTAAACTTTTTCAAAATCATATTTTGACC
518435 CTAAAATTCC
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
59 45 0.57
60 34 0.43
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (59 bp):
CCCTAAACTTTTTCAAAATCATATTTTGACCATTAACTTTTCCAAAATTACATTTTGAC
Found at i:518450 original size:29 final size:29
Alignment explanation
Indices: 518285--518468 Score: 109
Period size: 30 Copynumber: 6.2 Consensus size: 29
518275 CTCAGGAAGT
* * * *
518285 CCCTAAACTTTTCAAAAATCATATTTTGA
1 CCCTAAACATTCCCAAAATCACATTTTGA
* * * *
518314 CCATTAAACTTTTCCAAAATTACATTTTGA
1 CC-CTAAACATTCCCAAAATCACATTTTGA
* ** * * *
518344 CCCTAAACTTTTTCAAAATTATATTTTAA
1 CCCTAAACATTCCCAAAATCACATTTTGA
* * * * * *
518373 CCCCTTAACTTTTCTAAAATTATATTTTGA
1 -CCCTAAACATTCCCAAAATCACATTTTGA
* *
518403 CCCCTAAACTTTTCCAAAATCACATTTTGA
1 -CCCTAAACATTCCCAAAATCACATTTTGA
* *
518433 CCCTAAA-ATTCCCAAAAATCACGTTTGGA
1 CCCTAAACATTCCC-AAAATCACATTTTGA
518462 CCCTAAA
1 CCCTAAA
518469 TTTTCATAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
28 4 0.03
29 52 0.39
30 76 0.58
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
CCCTAAACATTCCCAAAATCACATTTTGA
Found at i:518451 original size:59 final size:57
Alignment explanation
Indices: 518285--518473 Score: 182
Period size: 59 Copynumber: 3.2 Consensus size: 57
518275 CTCAGGAAGT
* * *
518285 CCCTAAACTTTTCAAAAATCATATTTTGACCATTAAACTTTTCCAAAATTACATTTTGA
1 CCCTAAACTTTTCCAAAATCATATTTTGACC-CTAAA-ATTTCCAAAATTACATTTTGA
* * * ** * *
518344 CCCTAAACTTTTTCAAAATTATATTTTAACCCCTTAACTTTTCTAAAATTATATTTTGA
1 CCCTAAACTTTTCCAAAATCATATTTTGA-CCC-TAAAATTTCCAAAATTACATTTTGA
* * * * *
518403 CCCCTAAACTTTTCCAAAATCACATTTTGACCCTAAAATTCCCAAAAATCACGTTTGGA
1 -CCCTAAACTTTTCCAAAATCATATTTTGACCCTAAAATTTCC-AAAATTACATTTTGA
518462 CCCTAAA-TTTTC
1 CCCTAAACTTTTC
518474 ATAAAATTGC
Statistics
Matches: 106, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
57 5 0.05
58 13 0.12
59 58 0.55
60 30 0.28
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (57 bp):
CCCTAAACTTTTCCAAAATCATATTTTGACCCTAAAATTTCCAAAATTACATTTTGA
Found at i:518451 original size:89 final size:89
Alignment explanation
Indices: 518285--518449 Score: 242
Period size: 89 Copynumber: 1.9 Consensus size: 89
518275 CTCAGGAAGT
* *
518285 CCCTAAACTTTTCAAAAATCATATTTTGACCATTAAACTTTTCCAAAATTACATTTTGACCCTAA
1 CCCTAAACTTTTCAAAAATCATATTTTGACCACTAAACTTTTCCAAAATCACATTTTGACCCTAA
* **
518350 ACTTTTTCAAAATTATATTTTAAC
66 ACATTCCCAAAATTATATTTTAAC
* * * *
518374 CCCTTAACTTTTCTAAAATTATATTTTGACCCCTAAACTTTTCCAAAATCACATTTTGACCCTAA
1 CCCTAAACTTTTCAAAAATCATATTTTGACCACTAAACTTTTCCAAAATCACATTTTGACCCTAA
518439 A-ATTCCCAAAA
66 ACATTCCCAAAA
518450 ATCACGTTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 7 0.10
89 60 0.90
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (89 bp):
CCCTAAACTTTTCAAAAATCATATTTTGACCACTAAACTTTTCCAAAATCACATTTTGACCCTAA
ACATTCCCAAAATTATATTTTAAC
Found at i:518548 original size:29 final size:30
Alignment explanation
Indices: 518327--518532 Score: 95
Period size: 29 Copynumber: 7.0 Consensus size: 30
518317 TTAAACTTTT
* * *
518327 CCAAAATTACATTTTGA-CCCTAAACTT-TT
1 CCAAAATTATATTTTAACCCCTAAA-TTCTC
* * *
518356 TCAAAATTATATTTTAACCCCTTAACTT-TT
1 CCAAAATTATATTTTAACCCC-TAAATTCTC
* * *
518386 CTAAAATTATATTTTGACCCCTAAACTT-TT
1 CCAAAATTATATTTTAACCCCTAAA-TTCTC
* * *
518416 CCAAAATCACATTTTGA-CCCTAAAATTC-C
1 CCAAAATTATATTTTAACCCCT-AAATTCTC
* * ** ** *
518445 CAAAAATCACGTTTGGA-CCCTAAATTTTC
1 CCAAAATTATATTTTAACCCCTAAATTCTC
** ***
518474 ATAAAATTGCCTTTTAACCCTCTAAATTCTC
1 CCAAAATTATATTTTAACCC-CTAAATTCTC
518505 CCAAAATTATATTTTAACCCC-AAATTCT
1 CCAAAATTATATTTTAACCCCTAAATTCT
518533 TCGAAATTTC
Statistics
Matches: 140, Mismatches: 29, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
28 5 0.04
29 59 0.42
30 49 0.35
31 27 0.19
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (30 bp):
CCAAAATTATATTTTAACCCCTAAATTCTC
Found at i:519050 original size:25 final size:25
Alignment explanation
Indices: 519022--519069 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
519012 ATAAATTAAA
519022 TTATCAAAAATAA-TAATTAAAATGT
1 TTAT-AAAAATAAGTAATTAAAATGT
*
519047 TTATTAAAATAAGTAATTAAAAT
1 TTATAAAAATAAGTAATTAAAAT
519070 AATATTTTTA
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:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
TTATAAAAATAAGTAATTAAAATGT
Found at i:520037 original size:30 final size:30
Alignment explanation
Indices: 520001--520073 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
519991 GTTTACACGT
*
520001 ACTTTAATTTTGTGCAATTATATACATGAA
1 ACTTTAATTTTGTGCAAATATATACATGAA
* * * *
520031 ACTTTAATTGTGGTTCAAATGTATACTTGAA
1 ACTTTAATT-TTGTGCAAATATATACATGAA
520062 ACTTTAATTTTG
1 ACTTTAATTTTG
520074 ATTTAATCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 11 0.31
31 25 0.69
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (30 bp):
ACTTTAATTTTGTGCAAATATATACATGAA
Found at i:527045 original size:6 final size:6
Alignment explanation
Indices: 527036--527157 Score: 94
Period size: 6 Copynumber: 21.0 Consensus size: 6
527026 AAATGATTTT
* * *
527036 TTTAAA TTT-AT TTCTAAA ATTAAA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
527083 TTCATT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
527129 TTTGAAA --TAAT TTTAAA ATTAAA ATTAAA
1 TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
527158 AAGCCCAAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
4 2 0.02
5 17 0.19
6 67 0.74
7 5 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:527075 original size:17 final size:17
Alignment explanation
Indices: 527036--527136 Score: 85
Period size: 17 Copynumber: 5.4 Consensus size: 17
527026 AAATGATTTT
*
527036 TTTAAATTTATTTCTAAA
1 TTTAAATTTACTT-TAAA
*
527054 ATTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
527071 TTTAAATTTAAATTCATTTTTAAA
1 TTTAAATTT--A--C---TTTAAA
*
527095 TTTAAATTTATTTTAAA
1 TTTAAATTTACTTTAAA
*
527112 TTTAAATTTAATTTAAA
1 TTTAAATTTACTTTAAA
527129 TTTGAAAT
1 TTT-AAAT
527137 AATTTTAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
17 37 0.53
18 15 0.21
19 1 0.01
21 1 0.01
22 1 0.01
24 15 0.21
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:527100 original size:41 final size:41
Alignment explanation
Indices: 527036--527122 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
527026 AAATGATTTT
*
527036 TTTAAATTTATTTCTAAAATTAAATTTACTTTAAATTTAAA
1 TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
* * *
527077 TTTAAATTCATTTTTAAATTTAAATTTATTTTAAATTTAAA
1 TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
527118 TTTAA
1 TTTAA
527123 TTTAAATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (41 bp):
TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
Found at i:527143 original size:17 final size:17
Alignment explanation
Indices: 527055--527156 Score: 100
Period size: 17 Copynumber: 5.9 Consensus size: 17
527045 ATTTCTAAAA
** *
527055 TTAAATTTACTTTAAAT
1 TTAAATTTAAATTAATT
*
527072 TTAAATTTAAATTCATTT
1 TTAAATTTAAATT-AATT
*
527090 TTAAATTTAAATTTATT
1 TTAAATTTAAATTAATT
527107 TTAAATTTAAATTTAA-T
1 TTAAATTTAAA-TTAATT
527124 TTAAATTTGAAA-TAATT
1 TTAAATTT-AAATTAATT
*
527141 TTAAAATTAAAATTAA
1 TT-AAATTTAAATTAA
527157 AAAGCCCAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.04
17 39 0.55
18 29 0.41
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (17 bp):
TTAAATTTAAATTAATT
Found at i:527599 original size:29 final size:29
Alignment explanation
Indices: 527542--527599 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
527532 AAAGGGTTAC
*
527542 AAACCCGATTATTGAAATCCAAAATACAA
1 AAACCCGATTATTGAAATCCAAAAGACAA
* *
527571 AAACCCTATTCTTGAAAT-CAAAGAGACAA
1 AAACCCGATTATTGAAATCCAAA-AGACAA
527600 CCCCTTTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.50, C:0.21, G:0.09, T:0.21
Consensus pattern (29 bp):
AAACCCGATTATTGAAATCCAAAAGACAA
Found at i:529092 original size:29 final size:29
Alignment explanation
Indices: 529054--529506 Score: 225
Period size: 29 Copynumber: 15.4 Consensus size: 29
529044 AAGATTACCA
*
529054 TTTTACCCCCGAACTTTCCAAAATTCCAT
1 TTTTAACCCCGAACTTTCCAAAATTCCAT
*
529083 TTTTATCCCCG-A-TTTCACCAAAAATTACCA-
1 TTTTAACCCCGAACTTT--CC-AAAATT-CCAT
** *
529113 TTTT-ACCCTTAAACTTCCCAAAATTCCAT
1 TTTTAACCC-CGAACTTTCCAAAATTCCAT
529142 TTTTAACCCCG-A-TTTCATCAAAAAATTACCA-
1 TTTTAACCCCGAACTTTC--C--AAAATT-CCAT
* *
529173 TTTTACCCCCGAACTTCCCAAAATTCCAT
1 TTTTAACCCCGAACTTTCCAAAATTCCAT
* *
529202 TTTTAACCCTG--GTTTCATCAAAAATTACCA-
1 TTTTAACCCCGAACTTTC--C-AAAATT-CCAT
* * * *
529232 TTTTACCCCCGAACTTCCCAAAATTCTAA
1 TTTTAACCCCGAACTTTCCAAAATTCCAT
* *
529261 TTTTAA-CCCTAA-TTTCATCAAAATTAC-T
1 TTTTAACCCCGAACTTTC--CAAAATTCCAT
*
529289 ATTTTACCCCCGAACTTTCCAAAATTCCAT
1 -TTTTAACCCCGAACTTTCCAAAATTCCAT
*
529319 TTTTAACCCC--AGTTTCACCAAAAATTACCA-
1 TTTTAACCCCGAACTTT--CC-AAAATT-CCAT
** *
529349 TTTT-ACCCTTAAACTTTCCAAAATTCCGT
1 TTTTAACCC-CGAACTTTCCAAAATTCCAT
*
529378 TTTTAACCCC--AGTTTCATCAAAAATTACCA-
1 TTTTAACCCCGAACTTTC--C-AAAATT-CCAT
*
529408 TCTT-ACCCTCGAACTTTCCAAAATTCCAT
1 TTTTAACCC-CGAACTTTCCAAAATTCCAT
*
529437 TATTAACCCCG-A-TTTCATCAAAAATTACCA-
1 TTTTAACCCCGAACTTTC--C-AAAATT-CCAT
* * *
529467 TTTTACCCCCTAACTTTCCAAGATTCCAT
1 TTTTAACCCCGAACTTTCCAAAATTCCAT
529496 TTTTAACCCCG
1 TTTTAACCCCG
529507 GTTTCACCAA
Statistics
Matches: 324, Mismatches: 45, Indels: 110
0.68 0.09 0.23
Matches are distributed among these distances:
27 25 0.08
28 24 0.07
29 129 0.40
30 84 0.26
31 37 0.11
32 22 0.07
33 3 0.01
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (29 bp):
TTTTAACCCCGAACTTTCCAAAATTCCAT
Found at i:529119 original size:59 final size:59
Alignment explanation
Indices: 529047--529557 Score: 670
Period size: 59 Copynumber: 8.7 Consensus size: 59
529037 CTGTCCGAAG
*
529047 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTATCCCCGATTTCACCAAAA
1 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
*** * *
529106 ATTACCATTTTACCCTTAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCATCAAAAA
1 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CCAAAA
* * * *
529166 ATTACCATTTTACCCCCGAACTTCCCAAAATTCCATTTTTAACCCTGGTTTCATCAAAA
1 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * * ** *
529225 ATTACCATTTTACCCCCGAACTTCCCAAAATTCTAATTTTAACCCTAATTTCATC-AAA
1 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
*
529283 ATTACTATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCC-AGTTTCACCAAAA
1 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCACCAAAA
*** * *
529342 ATTACCATTTTACCCTTAAACTTTCCAAAATTCCGTTTTTAACCCC-AGTTTCATCAAAA
1 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCACCAAAA
* * * *
529401 ATTACCATCTTACCCTCGAACTTTCCAAAATTCCATTATTAACCCCGATTTCATCAAAA
1 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * *
529460 ATTACCATTTTACCCCCTAACTTTCCAAGATTCCATTTTTAACCCCGGTTTCACCAAAA
1 ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * *
529519 ATTACCATTTTGCCCCCGTAC-GTCCAAAATTACCATTTT
1 ATTACCATTTTACCCCCGAACTTTCCAAAATT-CCATTTT
529558 GCCCCCGGGT
Statistics
Matches: 401, Mismatches: 46, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
57 1 0.00
58 58 0.14
59 288 0.72
60 54 0.13
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (59 bp):
ATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
Found at i:535383 original size:50 final size:51
Alignment explanation
Indices: 535280--535393 Score: 124
Period size: 50 Copynumber: 2.3 Consensus size: 51
535270 GCCCCTGATA
* * * * *
535280 TTACATATTTTGTCAATTTGACATTTATTTAATAAATTTAATTCACGACAT
1 TTACATATTTTGTCAATTAGACATTGATTTAACAAATTTAACTCACAACAT
* * *
535331 TTACATATTTTTTCAATTAGTC-TTGATTTAACAAATTTAAC-CTACAATAT
1 TTACATATTTTGTCAATTAGACATTGATTTAACAAATTTAACTC-ACAACAT
*
535381 TTACACATTTTGT
1 TTACATATTTTGT
535394 TAAATCAAGA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
49 1 0.02
50 32 0.62
51 19 0.37
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (51 bp):
TTACATATTTTGTCAATTAGACATTGATTTAACAAATTTAACTCACAACAT
Found at i:535684 original size:17 final size:17
Alignment explanation
Indices: 535661--535718 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
535651 ATGGATATTC
535661 AACCTTTCATCTCCCTT
1 AACCTTTCATCTCCCTT
* * *
535678 GACCTTT-A--ACCTTT
1 AACCTTTCATCTCCCTT
*
535692 AACCTTTCATCTTCCTT
1 AACCTTTCATCTCCCTT
535709 AACCTTTCAT
1 AACCTTTCAT
535719 ATTCTTGTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 10 0.32
15 1 0.03
16 1 0.03
17 19 0.61
ACGTcount: A:0.21, C:0.34, G:0.02, T:0.43
Consensus pattern (17 bp):
AACCTTTCATCTCCCTT
Found at i:540571 original size:24 final size:24
Alignment explanation
Indices: 540537--540584 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
540527 ATGGATGTTC
* *
540537 AACCTTTCATCTCCCTTGACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
*
540561 AACCTTCCATCTTCCTTAACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
540585 CATATTCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.02, T:0.42
Consensus pattern (24 bp):
AACCTTCCATCTCCCTTAACCTTT
Found at i:541234 original size:19 final size:20
Alignment explanation
Indices: 541197--541239 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
541187 AAAAATAATT
541197 CAAAATAATTTTTAGAAATG
1 CAAAATAATTTTTAGAAATG
*
541217 CAAAATAATTTTTA-AAATT
1 CAAAATAATTTTTAGAAATG
541236 CAAA
1 CAAA
541240 GTATTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (20 bp):
CAAAATAATTTTTAGAAATG
Found at i:545057 original size:461 final size:454
Alignment explanation
Indices: 544189--545102 Score: 1203
Period size: 461 Copynumber: 2.0 Consensus size: 454
544179 AATTAAATTG
* * * *
544189 AAGTTCATTACAATATTATTTTTATTATTACATGATTATTAAGTGGATATTTTCATCATTTCAAA
1 AAGTTCATTACAATATTATTTCTATTATTACATGATTATCAAATGAATATTTTCATCATTTCAAA
* * * *
544254 ATGTTACACTAACTAGGAACGAAACGAAGCTAGGAAATTAATTTAAGGGCTAAAATATGAATAAA
66 ATCTCACACTAACTAGG-A-GAAACGAAGCTAGGAAATTAATTTAAGGGCCAAAATAAGAATAAA
*
544319 AATTTGGGGGAGTCAAAGTGTAAATTTACCATTACACTAACTTGTGATTTTCTAGAGATTATATA
129 AATTTGGGGGAGTCAAAGTGTAAATTTACCATTACACTAACTTGTGAGTTTCTAGAGATTATATA
* ** * * *
544384 AAGAAATTCATGTTTTGGGAGTGGTCAAGGCCACTGCCTGGCCTTCTCTCTCTCTCCACCTTTGA
194 AACAAATTCATGTTTAAGGAGTGGTCAAGGCCAATGCCTGCCCTTCTCTCTCTCTCCACCCTTGA
*
544449 CACCAACATATGAATAGAATAATTTTAAGGATTTTAACAATTATACTTGAATTTTTAAAATCGAA
259 CACCAACATATGAATAG-A-AA--TTAA-GATTTCAACAATTATACTTGAATTTTTAAAATCGAA
* * *
544514 AAATAAAAAGATTAAATTTCAAAAATACAAAAAAGTAAAAAAACTTGTAGCATATTATAATCTAA
319 AAATAAAAAGATTAAACTTCAAAAATACAAAAAAATAAAAAAACTTATAGCATATTATAATCTAA
* * *
544579 TATATAATATACTAGGTAGACAGATATAAAGTCCTAACTATGATATTTATATGAAAAGACATGTT
384 TATACAATATACTAGGTAGACAAATAAAAAGTCCTAACTATGATATTTATATGAAAAGACATGTT
544644 AAGTTA
449 AAGTTA
* * * *
544650 AAGTTTATTACAATGTTATTTCTATTGTTACATGATTATCAAATGAATATTTTTATCATTTCAAA
1 AAGTTCATTACAATATTATTTCTATTATTACATGATTATCAAATGAATATTTTCATCATTTCAAA
* * * *
544715 ATCTCACACTAACTA-G-G-ATCGAAGTTAGGAAATTGATTTAGGGGCCAAAATAAGAATAAAAA
66 ATCTCACACTAACTAGGAGAAACGAAGCTAGGAAATTAATTTAAGGGCCAAAATAAGAATAAAAA
* * * *
544777 TTTTGGGGAGTTAAAGTGTAAATTTACCATTATACTAACTTGTGAGTTTCTAGGGATTATATAAA
131 TTTGGGGGAGTCAAAGTGTAAATTTACCATTACACTAACTTGTGAGTTTCTAGAGATTATATAAA
* *
544842 CAATTTCATGTTTAAGGAGTGGTTAAGGCCAATGCCTGCCCCCCCCCCCCCCCTCTCTCTCTCTC
196 CAAATTCATGTTTAAGGAGTGGTCAAGGCCAATGCCTG------------CCCT-TCTCTCTCTC
*
544907 TCCACCCTTGACACCAACATATTGAATAG-AA-T-A-ATTTCAACAATTGTACTTGAATTTTTAA
248 TCCACCCTTGACACCAACATA-TGAATAGAAATTAAGATTTCAACAATTATACTTGAATTTTTAA
* * ** *
544968 AATCGAAATATAAGAAGATTAAACTTCAAATGTACAAAAAAATACAAAAACTTATAGCATATTAT
312 AATCGAAAAATAAAAAGATTAAACTTCAAAAATACAAAAAAATAAAAAAACTTATAGCATATTAT
*
545033 AATCTATTATACAATATACTAGGTAGACAAATAAAAAGTCCTAACTATGATATTTATATGAAAAG
377 AATCTAATATACAATATACTAGGTAGACAAATAAAAAGTCCTAACTATGATATTTATATGAAAAG
545098 ACATG
442 ACATG
545103 ATACTATTGG
Statistics
Matches: 396, Mismatches: 43, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
456 131 0.33
457 1 0.00
460 1 0.00
461 219 0.55
463 1 0.00
464 1 0.00
467 2 0.01
468 3 0.01
469 30 0.08
470 7 0.02
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (454 bp):
AAGTTCATTACAATATTATTTCTATTATTACATGATTATCAAATGAATATTTTCATCATTTCAAA
ATCTCACACTAACTAGGAGAAACGAAGCTAGGAAATTAATTTAAGGGCCAAAATAAGAATAAAAA
TTTGGGGGAGTCAAAGTGTAAATTTACCATTACACTAACTTGTGAGTTTCTAGAGATTATATAAA
CAAATTCATGTTTAAGGAGTGGTCAAGGCCAATGCCTGCCCTTCTCTCTCTCTCCACCCTTGACA
CCAACATATGAATAGAAATTAAGATTTCAACAATTATACTTGAATTTTTAAAATCGAAAAATAAA
AAGATTAAACTTCAAAAATACAAAAAAATAAAAAAACTTATAGCATATTATAATCTAATATACAA
TATACTAGGTAGACAAATAAAAAGTCCTAACTATGATATTTATATGAAAAGACATGTTAAGTTA
Found at i:546388 original size:13 final size:13
Alignment explanation
Indices: 546370--546394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
546360 TGAAAAGATG
546370 GGGGGTGGGGGGT
1 GGGGGTGGGGGGT
546383 GGGGGTGGGGGG
1 GGGGGTGGGGGG
546395 GACTAGAAGT
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:0.00, C:0.00, G:0.88, T:0.12
Consensus pattern (13 bp):
GGGGGTGGGGGGT
Found at i:550476 original size:168 final size:170
Alignment explanation
Indices: 550173--550668 Score: 572
Period size: 171 Copynumber: 2.9 Consensus size: 170
550163 TTTCGAATGA
* * * *
550173 TTTAAATAAAACTTAACAACCCAATGATTTAAATAAAAAAAAAACC-TTTGAATAGTTCAAT-AA
1 TTTAAAAAAAACTTAACAACCCAATGACTTAAAT------AAAACCATTTAAATAATTCAATGAA
* * * * *
550236 CTTAAATGAAAATTTTCAAATAG--AAGTGACCAAATTGTAACTTTTTTTAGTTAAATGACCAAA
60 -TTAAATGAAAACTTTCAAATAGTTCAGTGATCAAATTATAA-TTTTTTTAGTTAAGTGACCAAA
* *
550299 ACAAAAATTTACCCATAATTTAGTGACAAATGGTGTAGTTTAC-CCTT
123 ACAAAAATTTACCCATAATTTAGTGACAAATGATGCAGTTTACACCTT
* *
550346 TTT-AAGAAAACTTAACAACCCAATGACTTAAATAAAACCATTTAAATAATTCAATGATTTAAAT
1 TTTAAAAAAAACTTAACAACCCAATGACTTAAATAAAACCATTTAAATAATTCAATGAATTAAAT
*
550410 GAAAACTTTCAAATAGTTCAGTGATCAAATTATAATTTTTTTAGTTAAGTGACCAAAACGAAAAT
66 GAAAACTTTCAAATAGTTCAGTGATCAAATTATAATTTTTTTAGTTAAGTGACCAAAACAAAAAT
* **
550475 TTACCCCTAATTTAGTGACAAATGATGCAGTTTACATTTTT
131 TTACCCATAATTTAGTGACAAATGATGCAGTTTACA-CCTT
* ** * * * *
550516 TTTAAAAAAAATTTAACAGTCTAGTGACTTAAATAAAATCATTTAAATAATTCAGTGAATTAAAT
1 TTTAAAAAAAACTTAACAACCCAATGACTTAAATAAAACCATTTAAATAATTCAATGAATTAAAT
* * * * * *
550581 GAAAACTTTCGAATAGTTCAGTGATCAAATAATAATTTTTTTAATCAAGTGATCAAAACAAAAAC
66 GAAAACTTTCAAATAGTTCAGTGATCAAATTATAATTTTTTTAGTTAAGTGACCAAAACAAAAAT
* * *
550646 TCACCTAAAATTTAGTGACAAAT
131 TTACCCATAATTTAGTGACAAAT
550669 AATATAATTT
Statistics
Matches: 280, Mismatches: 36, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
166 6 0.02
167 34 0.12
168 61 0.22
169 14 0.05
170 5 0.02
171 129 0.46
172 28 0.10
173 3 0.01
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (170 bp):
TTTAAAAAAAACTTAACAACCCAATGACTTAAATAAAACCATTTAAATAATTCAATGAATTAAAT
GAAAACTTTCAAATAGTTCAGTGATCAAATTATAATTTTTTTAGTTAAGTGACCAAAACAAAAAT
TTACCCATAATTTAGTGACAAATGATGCAGTTTACACCTT
Found at i:556697 original size:37 final size:37
Alignment explanation
Indices: 556642--556751 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
556632 TAGCCCAAAT
556642 ACACCAGCAT-AAGACCTACTAGGCACAAAGCCTGAAA
1 ACACCAGCATAAAG-CCTACTAGGCACAAAGCCTGAAA
* *
556679 ACACCGGCATAAAGCCTACTAGGCACAAAGCCTAAAA
1 ACACCAGCATAAAGCCTACTAGGCACAAAGCCTGAAA
* *
556716 ACACTAGCATAAAGCCTACTAGGCATAAAGCCTGAA
1 ACACCAGCATAAAGCCTACTAGGCACAAAGCCTGAA
556752 TTTGTGTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 63 0.95
38 3 0.05
ACGTcount: A:0.43, C:0.28, G:0.16, T:0.13
Consensus pattern (37 bp):
ACACCAGCATAAAGCCTACTAGGCACAAAGCCTGAAA
Found at i:556737 original size:74 final size:73
Alignment explanation
Indices: 556607--556751 Score: 186
Period size: 74 Copynumber: 2.0 Consensus size: 73
556597 GTTATTGGAT
* * *
556607 CACCGGCACAAAGCCTGCTAGACTATAGCCCAAATACACCAGCATAAGACCTACTAGGCACAAAG
1 CACCGGCACAAAGCCTACTAGACTAAAGCCCAAAAACACCAGCATAAGACCTACTAGGCACAAAG
556672 CCTGAAAA
66 CCTGAAAA
* * * *
556680 CACCGGCATAAAGCCTACTAGGCAC-AAAGCCTAAAAACACTAGCATAA-AGCCTACTAGGCATA
1 CACCGGCACAAAGCCTACTA-G-ACTAAAGCCCAAAAACACCAGCATAAGA-CCTACTAGGCACA
556743 AAGCCTGAA
63 AAGCCTGAA
556752 TTTGTGTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
73 19 0.31
74 41 0.66
75 2 0.03
ACGTcount: A:0.41, C:0.30, G:0.17, T:0.13
Consensus pattern (73 bp):
CACCGGCACAAAGCCTACTAGACTAAAGCCCAAAAACACCAGCATAAGACCTACTAGGCACAAAG
CCTGAAAA
Found at i:556743 original size:16 final size:16
Alignment explanation
Indices: 556684--556748 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 16
556674 TGAAAACACC
556684 GGCATAAAGCCTACTA
1 GGCATAAAGCCTACTA
*
556700 GGCACAAAGCCTAAAAACACTA
1 GGCATAAAGCCT------ACTA
556722 -GCATAAAGCCTACTA
1 GGCATAAAGCCTACTA
556737 GGCATAAAGCCT
1 GGCATAAAGCCT
556749 GAATTTGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
15 4 0.10
16 22 0.55
21 10 0.25
22 4 0.10
ACGTcount: A:0.42, C:0.26, G:0.17, T:0.15
Consensus pattern (16 bp):
GGCATAAAGCCTACTA
Found at i:559105 original size:25 final size:26
Alignment explanation
Indices: 559066--559115 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
559056 ATACAGATTA
* *
559066 TTTAAAAATTATAATTATTTGTTAAT
1 TTTAAAAAATATAATTAATTGTTAAT
559092 TTTAAAAAAT-TAATTAATTGTTAA
1 TTTAAAAAATATAATTAATTGTTAA
559116 CATGACTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
TTTAAAAAATATAATTAATTGTTAAT
Found at i:559360 original size:43 final size:44
Alignment explanation
Indices: 559285--559369 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 44
559275 GTCTTTTTAA
* *
559285 AATTTGTTGGAAAACATTTGTTTCACTGTTTTTAATGTATTTTC
1 AATTTGTTGGAAAACATTTGTTTCAATATTTTTAATGTATTTTC
* * * *
559329 AATTTGTT-GTAAATATTTGTTTTAATATTTTTAGTGTATTT
1 AATTTGTTGGAAAACATTTGTTTCAATATTTTTAATGTATTT
559370 GATCTATTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
43 27 0.77
44 8 0.23
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (44 bp):
AATTTGTTGGAAAACATTTGTTTCAATATTTTTAATGTATTTTC
Found at i:559514 original size:30 final size:31
Alignment explanation
Indices: 559480--559540 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
559470 GAGCCTGAGT
*
559480 AAAAATTTAA-TCTATTTTTTGAGTCAAGCC
1 AAAAATTTAAGCCTATTTTTTGAGTCAAGCC
559510 AAAAATTTAAGCCTATTTTTTGAGTCAAGCC
1 AAAAATTTAAGCCTATTTTTTGAGTCAAGCC
559541 CGAGCCTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (31 bp):
AAAAATTTAAGCCTATTTTTTGAGTCAAGCC
Done.