Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 129 of 193
Found at i:40764009 original size:12 final size:12
Alignment explanation
Indices: 40763994--40764018 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40763984 ACAATTCATA
40763994 TCACTTTCAATT
1 TCACTTTCAATT
40764006 TCACTTTCAATT
1 TCACTTTCAATT
40764018 T
1 T
40764019 TGATCACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:40766584 original size:98 final size:98
Alignment explanation
Indices: 40766409--40766941 Score: 583
Period size: 98 Copynumber: 5.4 Consensus size: 98
40766399 CAGGTTTCAT
* * *
40766409 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCGATGGCGAACCTTGTACCTCAAAAGCATGA
1 TACCACGAAGACATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* *
40766474 A-AGGAAAGATTTAACCCGCAACAGCGAATCTAG
66 AGA-GAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * *
40766507 TACCACGAAAATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACTTTGTACCTCAAAAACATGA
1 TACCACGAAGACATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * * *
40766572 AGAGAAAAATTTAAACCGTAACGGCGAATCCAA
66 AGAGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * * * *
40766605 TACCATGAGGACATGGAGGGAATGGTTTAAGTCGCAATGGCGAAGCTTGTACCTTAGAAGCATGA
1 TACCACGAAGACATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* *
40766670 AG-GTAAATATTTAAGCTGCAACGGCGAATCTAG
66 AGAG-AAAGATTTAAGCCGCAACGGCGAATCTAG
* *
40766703 TACCAC-AAGGATATAGAGGG-AAGGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAA-CA
1 TACCACGAA-GACATGGAGGGAAAGG-TTTAAGTCGCAACGGCGAACCTTGTACCTCA-AAAGCA
* * * *
40766765 TGAAGGGAAAGATTTAAGCCACAACGGCGAATCCAA
63 TGAAGAGAAAGATTTAAGCCGCAACGGCGAATCTAG
* ** * *
40766801 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAAAAGCGAACCTTATACCTCATAAGCATGA
1 TACCACGAAGACATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
* * * * *
40766866 AGGGAAATATTTAAGCCGCAATGAC-ACTCTAG
66 AGAGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * *
40766898 TAACACGAGGACATGGAGGGAATGATTTAAGTCACAACGGCGAA
1 TACCACGAAGACATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA
40766942 TCCAGTACCA
Statistics
Matches: 364, Mismatches: 62, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
97 49 0.13
98 306 0.84
99 9 0.02
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (98 bp):
TACCACGAAGACATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAGCATGA
AGAGAAAGATTTAAGCCGCAACGGCGAATCTAG
Found at i:40766755 original size:196 final size:195
Alignment explanation
Indices: 40766409--40766941 Score: 703
Period size: 196 Copynumber: 2.7 Consensus size: 195
40766399 CAGGTTTCAT
* * *
40766409 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCGATGGCGAACCTTGTACCTCAAAAGCATGA
1 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAGCATG-
* * * *
40766474 AAGGAAAGATTTAACCCGCAACAGCGAATCTAGTACCACGAA-AATATGGAGGGAAAGG-TTTAA
65 AAGGAAATATTTAAGCCGCAACGGCGAATCTAGTACCAC-AAGGATATGGAGGG-AAGGATTTAA
* **
40766537 GTCGCAACGGCGAACTTTGTACCTCAAAAACATGAAGAGAAAAATTTAAACCGTAACGGCGAATC
128 GTCGCAACGGCGAACCTTGTACCTCAAAAACATGAAGAGAAAAATTTAAACCACAACGGCGAATC
40766602 CAA
193 CAA
* * * * *
40766605 TACCATGAGGACATGGAGGGAATGGTTTAAGTCGCAATGGCGAAGCTTGTACCTTAGAAGCATGA
1 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAGCATGA
* *
40766670 AGGTAAATATTTAAGCTGCAACGGCGAATCTAGTACCACAAGGATATAGAGGGAAGGATTTAAGT
66 AGG-AAATATTTAAGCCGCAACGGCGAATCTAGTACCACAAGGATATGGAGGGAAGGATTTAAGT
* * * *
40766735 CGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCA
130 CGCAACGGCGAACCTTGTACCTCAAAAACATGAAGAGAAAAATTTAAACCACAACGGCGAATCCA
40766800 A
195 A
** * *
40766801 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAAAAGCGAACCTTATACCTCATAAGCATGA
1 TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAGCATGA
* * * * * * *
40766866 AGGGAAATATTTAAGCCGCAATGAC-ACTCTAGTAACACGAGGACATGGAGGGAATGATTTAAGT
66 A-GGAAATATTTAAGCCGCAACGGCGAATCTAGTACCACAAGGATATGGAGGGAAGGATTTAAGT
*
40766930 CACAACGGCGAA
130 CGCAACGGCGAA
40766942 TCCAGTACCA
Statistics
Matches: 294, Mismatches: 39, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
195 54 0.18
196 238 0.81
197 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (195 bp):
TACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAGCATGA
AGGAAATATTTAAGCCGCAACGGCGAATCTAGTACCACAAGGATATGGAGGGAAGGATTTAAGTC
GCAACGGCGAACCTTGTACCTCAAAAACATGAAGAGAAAAATTTAAACCACAACGGCGAATCCAA
Found at i:40766815 original size:49 final size:49
Alignment explanation
Indices: 40766469--40767068 Score: 317
Period size: 49 Copynumber: 12.3 Consensus size: 49
40766459 ACCTCAAAAG
* * * * **
40766469 CATGAAAGGAAAGATTTAACCCGCAACAGCGAATCTAGTACCACGAAAA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAGGA
* * * * ** * * **
40766518 TATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA-CTTTGTACCTCAAAAA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC-CAGTACCACGAGGA
* * * * * *
40766567 CATGAAGAGAAAAATTTAAACCGTAACGGCGAATCCAATACCATGAGGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAGGA
* * * * * * ** *
40766616 CATGGAGGGAATGGTTTAAGTCGCAATGGCGAAGCTTGTACCTTA-GAAG-
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACC--ACGAGGA
* * * * *
40766665 CATGAAGGTAAATATTTAAGCTGCAACGGCGAATCTAGTACCACAAGGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAGGA
* * * * * *
40766714 TAT-AGAGGGAAGGATTTAAGTCGCAACGGCGAA-CCTTGTACCTC-AGAAA
1 CATGA-AGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACGAG-GA
* *
40766763 CATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCAATACCACGAGGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAGGA
* * * ** * **
40766812 CATGGAGGGAAAGGTTTAAGTCGCAAAAGCGAA-CCTTA-TACCTC-ATAA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC--AGTACCACGAGGA
* * * * * *
40766860 GCATGAAGGGAAATATTTAAGCCGCAATGAC-ACTCTAGTAACACGAGGA
1 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAGGA
* * * * *
40766909 CATGGAGGGAATGATTTAAGTCACAACGGCGAATCCAGTACCACGAAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAGGA
* * * * * * *
40766958 TATGGAA-GGAAAGGTTTAAGTCGCAACGACGAA-CCTTGTACCTCG-GAA
1 CAT-GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACGAGGA
* * * *
40767006 GCATGAAAGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGA
1 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAGGA
* *
40767056 TATGGAGGGAAAG
1 CATGAAGGGAAAG
40767069 GTTACTACCG
Statistics
Matches: 402, Mismatches: 124, Indels: 50
0.70 0.22 0.09
Matches are distributed among these distances:
47 2 0.00
48 45 0.11
49 340 0.85
50 14 0.03
51 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (49 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAGGA
Found at i:40766944 original size:146 final size:147
Alignment explanation
Indices: 40766721--40767068 Score: 432
Period size: 146 Copynumber: 2.4 Consensus size: 147
40766711 GGATATAGAG
* * * * * * * *
40766721 GGAAGGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACATGAAGGGAAAGATTTAAGCC
1 GGAAAGATTTAAGCCGCAACGACGAATCTAGTAACAC-GAAGACATGGAGGGAAAGATTTAAGCC
* *
40766785 ACAACGGCGAATCCAATACCACGAGGACATGGAGGGAAAGGTTTAAGTCGCAAA-AGCGAACCTT
65 ACAACGGCGAATCCAATACCACGAAGACATGGAAGGAAAGGTTTAAGTCGCAAAGA-CGAACCTT
* *
40766849 ATACCTCATAAGCATGAAG
129 ATACCTCAGAAGCATGAAA
* * * * * *
40766868 GGAAATATTTAAGCCGCAATGAC-ACTCTAGTAACACGAGGACATGGAGGGAATGATTTAAGTCA
1 GGAAAGATTTAAGCCGCAACGACGAATCTAGTAACACGAAGACATGGAGGGAAAGATTTAAGCCA
* * * *
40766932 CAACGGCGAATCCAGTACCACGAAGATATGGAAGGAAAGGTTTAAGTCGCAACGACGAACCTTGT
66 CAACGGCGAATCCAATACCACGAAGACATGGAAGGAAAGGTTTAAGTCGCAAAGACGAACCTTAT
*
40766997 ACCTCGGAAGCATGAAA
131 ACCTCAGAAGCATGAAA
* *
40767014 GGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGGAGGGAAAG
1 GGAAAGATTTAAGCCGCAACGACGAATCTAGTAACACGAAGACATGGAGGGAAAG
40767069 GTTACTACCG
Statistics
Matches: 168, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
145 2 0.01
146 121 0.72
147 45 0.27
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (147 bp):
GGAAAGATTTAAGCCGCAACGACGAATCTAGTAACACGAAGACATGGAGGGAAAGATTTAAGCCA
CAACGGCGAATCCAATACCACGAAGACATGGAAGGAAAGGTTTAAGTCGCAAAGACGAACCTTAT
ACCTCAGAAGCATGAAA
Found at i:40767097 original size:98 final size:98
Alignment explanation
Indices: 40766916--40767098 Score: 228
Period size: 98 Copynumber: 1.9 Consensus size: 98
40766906 GGACATGGAG
* * * *
40766916 GGAATGATTTAAGTCACAACGGCGAATCCAGTACCACGAAGATATGGAAGGAAAGGTTTAAGTCG
1 GGAAAGATTTAAGCCACAACGACGAATCCAGTACCACGAAGATATGGAAGGAAAGGTTTAAGCCG
* **
40766981 CAACGACGAACCTTGTACCTCGGAAGCATGAAA
66 CAACGACAAACCCGGTACCTCGGAAGCATGAAA
* * *
40767014 GGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGGAGGGAAAGG-TTACTA-C
1 GGAAAGATTTAAGCCACAACGACGAATCCAGTACCACGAAGATATGGAAGGAAAGGTTTA--AGC
40767077 CGCAAC-AGCAAACCCGGTACCT
64 CGCAACGA-CAAACCCGGTACCT
40767099 TAGAAACATG
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
97 4 0.06
98 67 0.93
99 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (98 bp):
GGAAAGATTTAAGCCACAACGACGAATCCAGTACCACGAAGATATGGAAGGAAAGGTTTAAGCCG
CAACGACAAACCCGGTACCTCGGAAGCATGAAA
Found at i:40768126 original size:11 final size:10
Alignment explanation
Indices: 40768099--40768133 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
40768089 TTTACCCACG
40768099 AAAAATACAA
1 AAAAATACAA
40768109 AAAAATACAA
1 AAAAATACAA
*
40768119 AATCAATACAA
1 AA-AAATACAA
40768130 AAAA
1 AAAA
40768134 GGAGCATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAATACAA
Found at i:40768406 original size:29 final size:29
Alignment explanation
Indices: 40768369--40768434 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
40768359 AAATTTTTTT
40768369 ATTTC-TTTGAAAATTCCTTATTAATTTC
1 ATTTCATTTGAAAATTCCTTATTAATTTC
40768397 ATTTCATTTGAAAATTCCTTATTAATTTC
1 ATTTCATTTGAAAATTCCTTATTAATTTC
40768426 ATTTCATTT
1 ATTTCATTT
40768435 TCAATTTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.14
29 32 0.86
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTCATTTGAAAATTCCTTATTAATTTC
Found at i:40768781 original size:30 final size:30
Alignment explanation
Indices: 40768674--40768971 Score: 331
Period size: 30 Copynumber: 10.1 Consensus size: 30
40768664 CTCAAGAGGT
*
40768674 CCCTAAACTTTTCAAAAATTACATTTTAA-
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
*
40768703 CCCTAAACTTATCCAAAATTACATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
40768733 CCC-AAACTTTTCCAAAATTACATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* *
40768762 CCCTAAAGTTTTTCAAAATTACATTTTAA-
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* *
40768791 CCCTCAAACTTTTCCAAAATTATA-TTTGAC
1 CCCT-AAACTTTTCCAAAATTACATTTTAAC
* * *
40768821 CCTTAAACTTTTCCAAAATCATATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
** * *
40768851 ATCTAAACTTTTCAAAAATTATATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* * * *
40768881 CCCCAAACTTTTCCAAAATCATATTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* *
40768911 CTCC-AAACTTTTCTAAAATCACA-TTTAAC
1 C-CCTAAACTTTTCCAAAATTACATTTTAAC
* *
40768940 CCAC-AAACTTTTCCAAAATCACATTTTGAC
1 CC-CTAAACTTTTCCAAAATTACATTTTAAC
40768970 CC
1 CC
40768972 TCGAGCTTCT
Statistics
Matches: 233, Mismatches: 28, Indels: 15
0.84 0.10 0.05
Matches are distributed among these distances:
28 1 0.00
29 106 0.45
30 124 0.53
31 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTACATTTTAAC
Found at i:40768829 original size:89 final size:90
Alignment explanation
Indices: 40768674--40768973 Score: 380
Period size: 89 Copynumber: 3.4 Consensus size: 90
40768664 CTCAAGAGGT
* * *
40768674 CCCTAAACTTTTCAAAAATTACATTTTAACCCT-AAACTTATCCAAAATTACATTTTAACCC-CA
1 CCCTAAACTTTTCAAAAATTACATTTTAACCCTCAAACTTTTCCAAAATTATATTTTGACCCTCA
*
40768737 AACTTTTCCAAAATTACATTTTAAC
66 AACTTTTCCAAAATCACATTTTAAC
* *
40768762 CCCTAAAGTTTTTC-AAAATTACATTTTAACCCTCAAACTTTTCCAAAATTATA-TTTGACCCTT
1 CCCTAAA-CTTTTCAAAAATTACATTTTAACCCTCAAACTTTTCCAAAATTATATTTTGACCCTC
*
40768825 AAACTTTTCCAAAATCATATTTTAAC
65 AAACTTTTCCAAAATCACATTTTAAC
** * * *
40768851 ATCTAAACTTTTCAAAAATTATATTTTAACCCCCAAACTTTTCCAAAATCATATTTTGA-CCTCC
1 CCCTAAACTTTTCAAAAATTACATTTTAACCCTCAAACTTTTCCAAAATTATATTTTGACCCT-C
*
40768915 AAACTTTTCTAAAATCACA-TTTAAC
65 AAACTTTTCCAAAATCACATTTTAAC
* * *
40768940 CCAC-AAACTTTTCCAAAATCACATTTTGACCCTC
1 CC-CTAAACTTTTCAAAAATTACATTTTAACCCTC
40768974 GAGCTTCTTT
Statistics
Matches: 182, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
88 38 0.21
89 121 0.66
90 23 0.13
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.36
Consensus pattern (90 bp):
CCCTAAACTTTTCAAAAATTACATTTTAACCCTCAAACTTTTCCAAAATTATATTTTGACCCTCA
AACTTTTCCAAAATCACATTTTAAC
Found at i:40768995 original size:59 final size:59
Alignment explanation
Indices: 40768678--40768970 Score: 270
Period size: 59 Copynumber: 4.9 Consensus size: 59
40768668 AGAGGTCCCT
* * * * * *
40768678 AAACTTTTCAAAAATTACATTTTAACCC-TAAACTTATCCAAAATTACATTTTAACC-CC
1 AAACTTTTCTAAAATCACA-TTTAACCCACAAACTTTTCCAAAATCACATTTTGACCTCC
* * * * * *
40768736 AAACTTTTCCAAAATTACATTTTAACCC-CTAAAGTTTTTCAAAATTACATTTTAACC-CTC
1 AAACTTTTCTAAAATCACA-TTTAACCCAC-AAACTTTTCCAAAATCACATTTTGACCTC-C
* * * * ** * * * *
40768796 AAACTTTTCCAAAATTATATTTGACCCTTAAACTTTTCCAAAATCATATTTTAACATCT
1 AAACTTTTCTAAAATCACATTTAACCCACAAACTTTTCCAAAATCACATTTTGACCTCC
* * * * *
40768855 AAACTTTTCAAAAATTATATTTTAACCCCCAAACTTTTCCAAAATCATATTTTGACCTCC
1 AAACTTTTCTAAAATCACA-TTTAACCCACAAACTTTTCCAAAATCACATTTTGACCTCC
40768915 AAACTTTTCTAAAATCACATTTAACCCACAAACTTTTCCAAAATCACATTTTGACC
1 AAACTTTTCTAAAATCACATTTAACCCACAAACTTTTCCAAAATCACATTTTGACC
40768971 CTCGAGCTTC
Statistics
Matches: 204, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
58 27 0.13
59 107 0.52
60 70 0.34
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (59 bp):
AAACTTTTCTAAAATCACATTTAACCCACAAACTTTTCCAAAATCACATTTTGACCTCC
Found at i:40769885 original size:14 final size:15
Alignment explanation
Indices: 40769866--40769911 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
40769856 AACTTAGCTA
40769866 ATTAATTACCAAAAT
1 ATTAATTACCAAAAT
*
40769881 A-TAATATA-AAAAAT
1 ATTAAT-TACCAAAAT
40769895 AATTAATTACCAAAAT
1 -ATTAATTACCAAAAT
40769911 A
1 A
40769912 ATATCCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAATTACCAAAAT
Found at i:40769909 original size:16 final size:16
Alignment explanation
Indices: 40769864--40769913 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
40769854 TAAACTTAGC
40769864 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
40769880 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
40769894 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
40769910 TAAT
1 TAAT
40769914 ATCCTCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:40769980 original size:30 final size:29
Alignment explanation
Indices: 40769946--40770040 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
40769936 AAATGGTACA
40769946 AAATAAATATTTATTTTGTACCATTTTGGT
1 AAATAAATA-TTATTTTGTACCATTTTGGT
* * *
40769976 AAAT-AATGA-TGTGTGGATACCATTTTGGT
1 AAATAAAT-ATTATTTTG-TACCATTTTGGT
* *
40770005 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATAT-TATTTTGTACCATTTTGGT
40770035 AAATAA
1 AAATAA
40770041 CCCATTTTGA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 4 0.08
29 19 0.37
30 24 0.47
31 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (29 bp):
AAATAAATATTATTTTGTACCATTTTGGT
Found at i:40771313 original size:43 final size:43
Alignment explanation
Indices: 40771231--40771313 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
40771221 ATTAACATGT
* *
40771231 TAAATTATATTATTTGACTCGTGTTAATATGGTTGCATGTCAC
1 TAAATTATATTATTTGACTCGTATTAATATGCTTGCATGTCAC
*
40771274 TAAATTATATTACTTT-ACTCTTATTAATAT-CTTGACATGT
1 TAAATTATATTA-TTTGACTCGTATTAATATGCTTG-CATGT
40771314 TATTAATTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 3 0.09
43 29 0.83
44 3 0.09
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTATTTGACTCGTATTAATATGCTTGCATGTCAC
Found at i:40771936 original size:45 final size:45
Alignment explanation
Indices: 40771863--40771954 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
40771853 TCCTAGCTCA
* * *
40771863 TCAAGCCAAGGATATTAGCCTTAGTTTGACGAGCCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCACAATAC
* *
40771908 TCAAGCCAAGGATATCAGGCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCACAATAC
40771953 TC
1 TC
40771955 TACTCCTCCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCACAATAC
Found at i:40772244 original size:14 final size:14
Alignment explanation
Indices: 40772227--40772294 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
40772217 CCTTAAACAA
40772227 TAAACCCTAAATTT
1 TAAACCCTAAATTT
* **
40772241 TAAAACACTAAACAT
1 T-AAACCCTAAATTT
* *
40772256 T-AACCATAAATCT
1 TAAACCCTAAATTT
40772269 TAAACCCTAAATTT
1 TAAACCCTAAATTT
* *
40772283 GATACCCTAAAT
1 TAAACCCTAAAT
40772295 AGATAAAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
13 9 0.22
14 21 0.51
15 11 0.27
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.29
Consensus pattern (14 bp):
TAAACCCTAAATTT
Found at i:40775497 original size:19 final size:19
Alignment explanation
Indices: 40775459--40775497 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
40775449 TTTACAATCA
* **
40775459 AAATAAAATTAACATGCAC
1 AAATAAAATAAACACACAC
40775478 AAATAAAATAAACACACAC
1 AAATAAAATAAACACACAC
40775497 A
1 A
40775498 CACACACACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.64, C:0.18, G:0.03, T:0.15
Consensus pattern (19 bp):
AAATAAAATAAACACACAC
Found at i:40777617 original size:33 final size:33
Alignment explanation
Indices: 40777554--40777628 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 33
40777544 GGAGTTCAAG
*
40777554 GAAAAAAATTACCAAAATTATATATCAATAATAT
1 GAAAAAAATTACCAAAATTATATATAAATAAT-T
**
40777588 GAAAAAAATTATTAAAA-TATA-ATTAAATAATT
1 GAAAAAAATTACCAAAATTATATA-TAAATAATT
*
40777620 AAAAAAAAT
1 GAAAAAAAT
40777629 CATAAATGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 10 0.28
33 11 0.31
34 15 0.42
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (33 bp):
GAAAAAAATTACCAAAATTATATATAAATAATT
Found at i:40783232 original size:24 final size:24
Alignment explanation
Indices: 40783204--40783262 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
40783194 TAGAGTAATA
*
40783204 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
40783228 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
40783252 AGAGTTTAACT
1 AGAGTTTAACT
40783263 AAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:40783638 original size:24 final size:24
Alignment explanation
Indices: 40783577--40783639 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
40783567 TAGAGTAATA
* *
40783577 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
40783601 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
40783625 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
40783640 GATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:40783656 original size:373 final size:371
Alignment explanation
Indices: 40782932--40783677 Score: 1255
Period size: 373 Copynumber: 2.0 Consensus size: 371
40782922 AACGTGAAAA
* *
40782932 AACCCCTCCGAAGAGGATAAAAAACCACGGGCAAAGATAATTTTACTATAATGGTAAAGAACGAA
1 AACCCCTCCGAAGAGGATAAAAAACCACGGGAAAAGATAATTTTACTATAATGGAAAAGAACGAA
* * *
40782997 GAGTATAAAAGATGGAGATAAAAAACTAAACCCCAAAAACCCGAAAATAAAGAACTCTCAAAACG
66 GAGTACAAAAGATGGAGATAAAAAACTAAACCCCAAAAACCCGAAAATAAAGAACGCTCAAAACA
*
40783062 TAAACACTAAATTCTCCAAAAGTGTTAGAGTTCTAAACTATAATGGGTATGTCTAAAATGAGTAT
131 TAAACACTAAATTCTACAAAAGTGTTAGAGTTCTAAACTATAATGGGTATGTCTAAAATGAGTAT
*
40783127 ATTTTTAAGGTTGTAAAAGAGCCTATTTATAAGCTAAATTTCTAAGTCAAATAATAATAAAATAA
196 ATTTTTAAGGTTGTAAAAGAGCCTATTTATAAGCTAAATTTCTAAATCAAATAATAATAAAATAA
*
40783192 TCTAGAGTAATAAGAGTTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAATAGAGT
261 TCTAGAGTAATAAGAGTTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAACAGAGT
*
40783257 TTAACTAAAAGATTATTTTTCAAATTTGACTTGAAATAGGAGTCAT
326 TTAACTAAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCAT
* * *
40783303 AACCCCTCCGAAGAGGATAAAAAACTA-GGGAAAAATATAATTTTTACTATAATGGCAAAAGAAT
1 AACCCCTCCGAAGAGGATAAAAAACCACGGG-AAAAGATAA-TTTTACTATAATGG-AAAAGAAC
* *
40783367 GAAGAGTACAAAAGATGGAGA-AAAAAACTAAACCCTAAAAATCCGAAAATAAAGAACGCTCAAA
63 GAAGAGTACAAAAGATGGAGATAAAAAACTAAACCCCAAAAACCCGAAAATAAAGAACGCTCAAA
*
40783431 ACATAAACACTAAATTCTACAAAAGTGTTAGGAGTTCTAAACTATAATGGGTATGTCTAAAATGG
128 ACATAAACACTAAATTCTACAAAAGTGTTA-GAGTTCTAAACTATAATGGGTATGTCTAAAATGA
* * *
40783496 GTAT-TTATTTAAGGTTGTAAAAGAGCTTATTTATAGGTTAAATTTCTAAATCAAATAATAATAA
192 GTATATT-TTTAAGGTTGTAAAAGAGCCTATTTATAAGCTAAATTTCTAAATCAAATAATAATAA
40783560 AATAATCTAGAGTAATAAGAGTTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAAC
256 AATAATCTAGAGTAATAAGAGTTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAAC
*
40783625 AGAGTTTAACTGAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCAT
321 AGAGTTTAACTAAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCAT
40783676 AA
1 AA
40783678 TTCAACAAAT
Statistics
Matches: 351, Mismatches: 19, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
370 3 0.01
371 33 0.09
372 84 0.24
373 231 0.66
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.27
Consensus pattern (371 bp):
AACCCCTCCGAAGAGGATAAAAAACCACGGGAAAAGATAATTTTACTATAATGGAAAAGAACGAA
GAGTACAAAAGATGGAGATAAAAAACTAAACCCCAAAAACCCGAAAATAAAGAACGCTCAAAACA
TAAACACTAAATTCTACAAAAGTGTTAGAGTTCTAAACTATAATGGGTATGTCTAAAATGAGTAT
ATTTTTAAGGTTGTAAAAGAGCCTATTTATAAGCTAAATTTCTAAATCAAATAATAATAAAATAA
TCTAGAGTAATAAGAGTTTGACTCAAACAAATAAACAGAGTTTAATTGAAACAAATAAACAGAGT
TTAACTAAAAGATTATTTCTCAAATTTGACTTGAAATAGGAGTCAT
Found at i:40785426 original size:24 final size:24
Alignment explanation
Indices: 40785410--40785484 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
40785400 AGTTTGACTC
40785410 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
40785434 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
40785458 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
40785482 AAA
1 AAA
40785485 GATTATTTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:40787414 original size:24 final size:24
Alignment explanation
Indices: 40787386--40787442 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
40787376 TAGATTAATA
* *
40787386 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
* * *
40787410 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
40787434 AGAGTTTAA
1 AGAGTTTAA
40787443 TTGAAAGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:40787443 original size:24 final size:24
Alignment explanation
Indices: 40787398--40787448 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
40787388 AGTTTGACTC
*
40787398 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
40787422 AAACAATTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
40787446 AAA
1 AAA
40787449 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:40798643 original size:268 final size:268
Alignment explanation
Indices: 40797996--40799011 Score: 1698
Period size: 268 Copynumber: 3.8 Consensus size: 268
40797986 TATATGTGTG
* * *
40797996 TGCTATGTTCTTACTGTTGATCGAATCATTAGCCCCTTATCTGCATGCATT-TTTCCTAGCAGGT
1 TGCTATGTTCTTAGTGTTGATCGAATCATTAGCCCCTGATCTCCATGC-TTCTTTCCTAGCAGGT
* * *
40798060 GGTGTTGTACTTTAGCCTCTTAAACTGCTATCCCTATTCCTCTGAATCCGGCTTTCTTTGGACCG
65 GGTGTTGTACTTTAGTCTCTTAAACTGCTATCCCTATTCCTCCGAATCCGGCTTTCATTGGACCG
* * *
40798125 ATTTCTGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAATTATTATTACATTGACAAATGCTT
130 ATTTCGGCCATGAATCGGAACTCTTTGTTACCTTGAAAAATTTATTATTACATTGACAAATGCTT
40798190 TAAATGTGATATGTACATTCAGCTGTGAGAATGCATACATTTATATTTTATATATGTGTGTGTGT
195 TAAATGTGATATGTACATTCAGCTGTGAGAATGCATACA-TT-TATTTT-TATA--TGTGTGTGT
40798255 GTATGATGCAATGC
255 GTATGATGCAATGC
* *
40798269 TGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTCTTTCCTAGCCGGTG
1 TGCTATGTTCTTAGTGTTGATCGAATCATTAGCCCCTGATCTCCATGCTTCTTTCCTAGCAGGTG
* *
40798334 GTGTTGTACTTTAGTCTCTTAAACTGCTATCCCTATTTCC-CCGAATCCGGTTTTCATTGGACTG
66 GTGTTGTACTTTAGTCTCTTAAACTGCTATCCCTA-TTCCTCCGAATCCGGCTTTCATTGGACCG
40798398 ATTTCGGCCATGAATCGGAACTCTTTGTTACCTTGAAAAATTTATTATTACATTGACAAATGCTT
130 ATTTCGGCCATGAATCGGAACTCTTTGTTACCTTGAAAAATTTATTATTACATTGACAAATGCTT
*
40798463 TAAATATGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTTTATATGTGTGTGTGTATG
195 TAAATGTGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTTTATATGTGTGTGTGTATG
*
40798528 ATGCTATGC
260 ATGCAATGC
40798537 TGCTATGTTCTTAGTGTTGATCGAATCATTAGCCCCTGATCTCCATGCTTCTTTCCTAGCAGGTG
1 TGCTATGTTCTTAGTGTTGATCGAATCATTAGCCCCTGATCTCCATGCTTCTTTCCTAGCAGGTG
* *
40798602 GTGTTGTACTTTAGTCTCTTAAACTGCTATCCCTATTTCC-CCGAATCCGGTTTTCATTGGACTG
66 GTGTTGTACTTTAGTCTCTTAAACTGCTATCCCTA-TTCCTCCGAATCCGGCTTTCATTGGACCG
*
40798666 ATTTCGGCCATGAATCGGAACTCTTTGTTACCTTGAAAATTTTATTATTACATTGACAAATGCTT
130 ATTTCGGCCATGAATCGGAACTCTTTGTTACCTTGAAAAATTTATTATTACATTGACAAATGCTT
40798731 TAAATGTGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTTTATATGTGTGTGTGTATG
195 TAAATGTGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTTTATATGTGTGTGTGTATG
40798796 ATGCAATGC
260 ATGCAATGC
* *
40798805 TGCTATGTTCTTAGTGTTGATCGAATCATTAGCCCCTGATCTTCATGCTTCTTTCCTAGCCGGTG
1 TGCTATGTTCTTAGTGTTGATCGAATCATTAGCCCCTGATCTCCATGCTTCTTTCCTAGCAGGTG
* *
40798870 GTGTTGTACTTTAGTCTCTTAAACTGCTATCCCTATTCCTCTGAATCCGGCTTTCTTTGGACCGA
66 GTGTTGTACTTTAGTCTCTTAAACTGCTATCCCTATTCCTCCGAATCCGGCTTTCATTGGACCGA
* * *
40798935 TTTCGGCCATGAATCGGAACTCTTTGTTACCTTGAAAATTTTATTATTACACTAACAAATGCTTT
131 TTTCGGCCATGAATCGGAACTCTTTGTTACCTTGAAAAATTTATTATTACATTGACAAATGCTTT
40799000 AAAT-TGGATATG
196 AAATGT-GATATG
40799012 CTTGTTTTCT
Statistics
Matches: 711, Mismatches: 28, Indels: 13
0.95 0.04 0.02
Matches are distributed among these distances:
267 5 0.01
268 477 0.67
270 4 0.01
271 6 0.01
272 4 0.01
273 211 0.30
274 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (268 bp):
TGCTATGTTCTTAGTGTTGATCGAATCATTAGCCCCTGATCTCCATGCTTCTTTCCTAGCAGGTG
GTGTTGTACTTTAGTCTCTTAAACTGCTATCCCTATTCCTCCGAATCCGGCTTTCATTGGACCGA
TTTCGGCCATGAATCGGAACTCTTTGTTACCTTGAAAAATTTATTATTACATTGACAAATGCTTT
AAATGTGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTTTATATGTGTGTGTGTATGA
TGCAATGC
Found at i:40799865 original size:11 final size:10
Alignment explanation
Indices: 40799838--40799868 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
40799828 ATACAAGTTT
40799838 TAAATATTTA
1 TAAATATTTA
40799848 TAAATATTTA
1 TAAATATTTA
40799858 TAAAATATTTA
1 T-AAATATTTA
40799869 ATATATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAAATATTTA
Found at i:40800620 original size:11 final size:11
Alignment explanation
Indices: 40800600--40800629 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40800590 TATTTAAGTA
40800600 TAATTT-TTTT
1 TAATTTATTTT
40800610 TAATTTATTTT
1 TAATTTATTTT
40800621 TAATTTATT
1 TAATTTATT
40800630 GAGAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TAATTTATTTT
Found at i:40802522 original size:98 final size:98
Alignment explanation
Indices: 40802345--40802548 Score: 309
Period size: 98 Copynumber: 2.1 Consensus size: 98
40802335 TGAACATTCA
* * * *
40802345 AGGATATGCGAACTAGGCTCGCGACGCGAGCTTTCCCTGCGAACCTTTAACGTATCCACTTGATA
1 AGGATATGCGAACTAGGCTCGCGACACGAGCTCTCCCTGCAAACCCTTAACGTATCCACTTGATA
*
40802410 AGGCCTAAACTCGGATCGCAAATTGATAGTCCG
66 AGGCCCAAACTCGGATCGCAAATTGATAGTCCG
* * *
40802443 AGGATATGCGAACTAGGCTCGCGACATGAGCTCTCCTTGTAAACCCTTAACGTATCCACTTGATA
1 AGGATATGCGAACTAGGCTCGCGACACGAGCTCTCCCTGCAAACCCTTAACGTATCCACTTGATA
* *
40802508 AGGCCCAAATTCGGATCGCAAATTGATAGTTCG
66 AGGCCCAAACTCGGATCGCAAATTGATAGTCCG
40802541 AGGTATAT
1 AGG-ATAT
40802549 TTAAGTTTCG
Statistics
Matches: 95, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
98 91 0.96
99 4 0.04
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (98 bp):
AGGATATGCGAACTAGGCTCGCGACACGAGCTCTCCCTGCAAACCCTTAACGTATCCACTTGATA
AGGCCCAAACTCGGATCGCAAATTGATAGTCCG
Found at i:40803667 original size:50 final size:52
Alignment explanation
Indices: 40803567--40803668 Score: 118
Period size: 50 Copynumber: 2.0 Consensus size: 52
40803557 CCAGATACCC
* * *
40803567 AAAAATATATTTTTTGGGTGTTTGTCAACCCATGACCAACATCCAAAAATAA
1 AAAAATATATATTTTGGGTGTTTGTCAACCAATGACCAACACCCAAAAATAA
* * * * *
40803619 AAAAAT-TATATTTT-GGTGTTTGTCATCTAATGATCGACACCCACAAATAA
1 AAAAATATATATTTTGGGTGTTTGTCAACCAATGACCAACACCCAAAAATAA
40803669 TACGAATAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 29 0.69
51 7 0.17
52 6 0.14
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (52 bp):
AAAAATATATATTTTGGGTGTTTGTCAACCAATGACCAACACCCAAAAATAA
Found at i:40803771 original size:59 final size:61
Alignment explanation
Indices: 40803647--40803779 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 61
40803637 TTTGTCATCT
* ** * *
40803647 AATGATCGACACCCACAAATAATACGAATAAAAATAATAATTTTTTTGATGTTCGACAAGC
1 AATGGTCGACACCCACAAATAATAAAAATAAAAATAATAATTTTTTTGATGTTAGACAACC
* * *
40803708 AATGG-CTGACACCCATAAA-AATAAAAATTAAAA-AATAATTTTTTTGGTGTTTAG-CAACC
1 AATGGTC-GACACCCACAAATAATAAAAATAAAAATAATAATTTTTTTGATG-TTAGACAACC
40803767 AATGGTCGACACC
1 AATGGTCGACACC
40803780 AACTTTTCCT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
59 30 0.49
60 16 0.26
61 15 0.25
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (61 bp):
AATGGTCGACACCCACAAATAATAAAAATAAAAATAATAATTTTTTTGATGTTAGACAACC
Found at i:40803982 original size:31 final size:31
Alignment explanation
Indices: 40803944--40804019 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
40803934 AATTTCGGGG
*
40803944 ATATACTGTAATGTATTGCCGAAGTTGAATT
1 ATATACTGTAATGTATTACCGAAGTTGAATT
* *
40803975 ATTTACTGTAATGCATTACCGAAGTTGAATT
1 ATATACTGTAATGTATTACCGAAGTTGAATT
*
40804006 ATATACTGTCATGT
1 ATATACTGTAATGT
40804020 GAAGCAGCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (31 bp):
ATATACTGTAATGTATTACCGAAGTTGAATT
Found at i:40804213 original size:60 final size:61
Alignment explanation
Indices: 40804089--40804224 Score: 150
Period size: 60 Copynumber: 2.2 Consensus size: 61
40804079 CGAGATGTCC
* * * ** * *
40804089 AAAAAATATATATTTTGGTATCTGAAAAAGGGGGTGTCGGGAATGAGTTGGCAGCCACCC-
1 AAAAAATATTTTTTTTGGTATCTAAAAAAAAGGGTGTCGGGAATGAGTTGACAGACACCCA
** *
40804149 AAAAAATATTTTTTTTGGTATCTAAAAAAAAGGGTGTCGGTCATG-GCTTGACAGACACCTA
1 AAAAAATATTTTTTTTGGTATCTAAAAAAAAGGGTGTCGGGAATGAG-TTGACAGACACCCA
*
40804210 AAAAAATAATTTTTT
1 AAAAAATATTTTTTT
40804225 ATTCGTATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.76
61 14 0.22
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (61 bp):
AAAAAATATTTTTTTTGGTATCTAAAAAAAAGGGTGTCGGGAATGAGTTGACAGACACCCA
Found at i:40807058 original size:39 final size:41
Alignment explanation
Indices: 40807008--40807107 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 41
40806998 TTAGGATTCT
*
40807008 ATAAATATTTACATATTTTTTTCTATATTTCTATAT-ATTTT-
1 ATAAAT-TTTACATATTTTTTTATA-ATTTCTATATAATTTTA
* * *
40807049 AT-AATTTTACA-ATTTTTTTATAATTTTTTTCTAATTTTA
1 ATAAATTTTACATATTTTTTTATAATTTCTATATAATTTTA
*
40807088 ATAAATTTTAAATATTTTTT
1 ATAAATTTTACATATTTTTT
40807108 ATATTTTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
37 7 0.14
38 15 0.30
39 8 0.16
40 11 0.22
41 9 0.18
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (41 bp):
ATAAATTTTACATATTTTTTTATAATTTCTATATAATTTTA
Found at i:40807086 original size:10 final size:11
Alignment explanation
Indices: 40807053--40807086 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40807043 TATTTTATAA
*
40807053 TTTTACAATTT
1 TTTTATAATTT
40807064 TTTTATAATTT
1 TTTTATAATTT
*
40807075 TTTTCTAATTT
1 TTTTATAATTT
40807086 T
1 T
40807087 AATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:40807096 original size:29 final size:29
Alignment explanation
Indices: 40807064--40807127 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
40807054 TTTACAATTT
*
40807064 TTTTATAAT-TTTTTTCTAATTTTAATAAA
1 TTTTA-AATATTTTTTATAATTTTAATAAA
* *
40807093 TTTTAAATATTTTTTATATTTTTATTAAA
1 TTTTAAATATTTTTTATAATTTTAATAAA
*
40807122 ATTTAA
1 TTTTAA
40807128 CAGTTTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTAAATATTTTTTATAATTTTAATAAA
Found at i:40807125 original size:40 final size:38
Alignment explanation
Indices: 40806944--40807125 Score: 97
Period size: 40 Copynumber: 4.6 Consensus size: 38
40806934 GGTATGATAA
*
40806944 TTTTTATATATATTTTTTACAAA-TTTATATTTCTTTAC-A-T
1 TTTTTATA-AT-TTTTTTA-AAATTTTATA-AT-TTTACAATT
* * ** *
40806984 TTTTTAGAATTTTCTTAGGATTCTATAAATATTTACATATT
1 TTTTTATAATTTTTTTAAAATTTTAT-AAT-TTTACA-ATT
* * * *
40807025 TTTTTCT-ATATTTCTATATATTTTATAATTTTACAATT
1 TTTTTATAATTTTTTTA-AAATTTTATAATTTTACAATT
**
40807063 TTTTTATAATTTTTTTCTAATTTTAATAAATTTTA-AATAT
1 TTTTTATAATTTTTTTAAAATTTT-AT-AATTTTACAAT-T
40807103 TTTTTAT-ATTTTTATTAAAATTT
1 TTTTTATAATTTTT-TTAAAATTT
40807126 AACAGTTTTA
Statistics
Matches: 108, Mismatches: 23, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
37 1 0.01
38 30 0.28
39 26 0.24
40 39 0.36
41 12 0.11
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (38 bp):
TTTTTATAATTTTTTTAAAATTTTATAATTTTACAATT
Found at i:40807922 original size:2 final size:2
Alignment explanation
Indices: 40807915--40807954 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
40807905 CTAATGTTTC
*
40807915 CT CT CT CT CT CT CT CT CT CG CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
40807955 GTTTTACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:40808621 original size:210 final size:208
Alignment explanation
Indices: 40808232--40808650 Score: 515
Period size: 210 Copynumber: 2.0 Consensus size: 208
40808222 AGTTTTTTTA
** * **
40808232 GTTAATTCAACTAGTTCCAGTTCTTTATACAATGACGATTCCGAACGATTTTTTCAAAATCCAAT
1 GTTAATTCAACTAGTTCCAGTTCTCGATACAATGACGATTCCGAACAATTTACTCAAAATCCAAT
* * *
40808297 TCAATGTCTCTATTCGGACCACTACACCTATCAATTCTCAATTCAATTGATTGGATCATTCAATC
66 TCAATATCTCTATTCAGACCACTACACCCATCAATTCTCAATTCAATTGATTGGATCATTCAATC
* *
40808362 CAATCAGGTTCCAACAACATCAAATTAATAACTAATCCACACATTGGGTTTGTTTGAAAGATAGT
131 CAATCAGATTCCAACAACATCAAATTAATAACTAAT-C-CACATTGGGTTTGTTTGAAAGATAAT
40808427 GAAGTCC-TCAAAATC
194 GAAG-CCTTCAAAATC
* * ** * *
40808442 GTTACTTCAACTAGTTCCAGTTCTCGATACAATGACGGTTTTGAATAATTTACTCAAAATTCAAT
1 GTTAATTCAACTAGTTCCAGTTCTCGATACAATGACGATTCCGAACAATTTACTCAAAATCCAAT
* * * *
40808507 TCAATATTTTTA-TCTAGACCAGTACACCCATCAATTCTCAATTGAATTGATTGGATCAATCAAT
66 TCAATATCTCTATTC-AGACCACTACACCCATCAATTCTCAATTCAATTGATTGG----ATC-AT
* * *
40808571 TCAATCTAATCTGATTCCAACAACATTAAATTAATAACTAAT-C-C-TTGGGTTTGTTTGAAAGA
125 TCAATCCAATCAGATTCCAACAACATCAAATTAATAACTAATCCACATTGGGTTTGTTTGAAAGA
40808633 TAATGAAGCCTTCAAAAT
190 TAATGAAGCCTTCAAAAT
40808651 ATTTACTTTG
Statistics
Matches: 179, Mismatches: 23, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
209 4 0.02
210 130 0.73
211 1 0.01
212 1 0.01
214 3 0.02
215 40 0.22
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (208 bp):
GTTAATTCAACTAGTTCCAGTTCTCGATACAATGACGATTCCGAACAATTTACTCAAAATCCAAT
TCAATATCTCTATTCAGACCACTACACCCATCAATTCTCAATTCAATTGATTGGATCATTCAATC
CAATCAGATTCCAACAACATCAAATTAATAACTAATCCACATTGGGTTTGTTTGAAAGATAATGA
AGCCTTCAAAATC
Found at i:40817192 original size:49 final size:49
Alignment explanation
Indices: 40817113--40817428 Score: 162
Period size: 49 Copynumber: 6.4 Consensus size: 49
40817103 AGATTTATCG
* * * ** * *
40817113 TTGCGGCTTCAATCTTTCCCCTTATGTCTTCGCGGTACTAGATTCGTCA
1 TTGCAGCTTAAATCTTTCCCTTTACATCTTCGAGGTACTAGATTCGCCA
* *
40817162 TTGCAGCTTAAATTTTTCCCTTTACATCTTCGAGGTACTAGATTCGCCG
1 TTGCAGCTTAAATCTTTCCCTTTACATCTTCGAGGTACTAGATTCGCCA
* * * * **
40817211 TTGCGGCTTAAATCTTTCCC-TT-CATGCTTTTGAGGTACAAGGTTCATCA
1 TTGCAGCTTAAATCTTTCCCTTTACAT-C-TTCGAGGTACTAGATTCGCCA
* ** ** * * * *
40817260 TTGC-GACTTAAACCTTTCCCTCCATTGTCTTCGTGGTACTGGATTTGCCG
1 TTGCAG-CTTAAATCTTTCCCTTTA-CATCTTCGAGGTACTAGATTCGCCA
** * * *
40817310 TTGTGGCTTAAATCTTTCCC-TT-CATGCTTCTGAGGTACAAGGTTCGCCG
1 TTGCAGCTTAAATCTTTCCCTTTACAT-CTTC-GAGGTACTAGATTCGCCA
* * * * * * * *
40817359 TTGCAACTTAAACCTTT--CTTTTCATGCTTTTGACGTACAAGGTTCGTCA
1 TTGCAGCTTAAATCTTTCCCTTTACAT-C-TTCGAGGTACTAGATTCGCCA
40817408 TTGC-GACTTAAATCTTTCCCT
1 TTGCAG-CTTAAATCTTTCCCT
40817429 CCATGTCTTC
Statistics
Matches: 200, Mismatches: 52, Indels: 28
0.71 0.19 0.10
Matches are distributed among these distances:
47 5 0.03
48 10 0.05
49 150 0.75
50 30 0.15
51 4 0.02
52 1 0.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (49 bp):
TTGCAGCTTAAATCTTTCCCTTTACATCTTCGAGGTACTAGATTCGCCA
Found at i:40817226 original size:98 final size:100
Alignment explanation
Indices: 40817111--40817376 Score: 267
Period size: 99 Copynumber: 2.7 Consensus size: 100
40817101 TAAGATTTAT
* * * *
40817111 CGTTGCGGCTTCAATCTTTCCCCTT-ATG-TCTTCGCGGTACTAGATTCGTCATTGC-AGCTTAA
1 CGTTGCGGCTTAAATCTTTCCCCTTCATGCT-TTCGAGGTACAAGATTCATCATTGCGA-CTTAA
** **
40817173 ATTTTTCCCTTTA-CATCTTCGAGGTACTAGATTCGC
64 ACCTTTCCCTCCATCATCTTCGAGGTACTAGATTCGC
* *
40817209 CGTTGCGGCTTAAATCTTT-CCCTTCATGCTTTTGAGGTACAAGGTTCATCATTGCGACTTAAAC
1 CGTTGCGGCTTAAATCTTTCCCCTTCATGCTTTCGAGGTACAAGATTCATCATTGCGACTTAAAC
** * * *
40817273 CTTTCCCTCCATTGTCTTCGTGGTACTGGATTTGC
66 CTTTCCCTCCATCATCTTCGAGGTACTAGATTCGC
* * ** * *
40817308 CGTTGTGGCTTAAATCTTT-CCCTTCATGC-TTCTGAGGTACAAGGTTCGCCGTTGCAACTTAAA
1 CGTTGCGGCTTAAATCTTTCCCCTTCATGCTTTC-GAGGTACAAGATTCATCATTGCGACTTAAA
40817371 CCTTTC
65 CCTTTC
40817377 TTTTCATGCT
Statistics
Matches: 142, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
97 5 0.04
98 57 0.40
99 80 0.56
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (100 bp):
CGTTGCGGCTTAAATCTTTCCCCTTCATGCTTTCGAGGTACAAGATTCATCATTGCGACTTAAAC
CTTTCCCTCCATCATCTTCGAGGTACTAGATTCGC
Found at i:40817328 original size:99 final size:99
Alignment explanation
Indices: 40817188--40817376 Score: 297
Period size: 99 Copynumber: 1.9 Consensus size: 99
40817178 TCCCTTTACA
*
40817188 TCTTCGAGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGG
1 TCTTCGAGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* *
40817253 TTCATCATTGCGACTTAAACCTTTCCCTCCATTG
66 TTCACCATTGCAACTTAAACCTTTCCCTCCATTG
* * * *
40817287 TCTTCGTGGTACTGGATTTGCCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
1 TCTTCGAGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* *
40817352 TTCGCCGTTGCAACTTAAACCTTTC
66 TTCACCATTGCAACTTAAACCTTTC
40817377 TTTTCATGCT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 81 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (99 bp):
TCTTCGAGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
TTCACCATTGCAACTTAAACCTTTCCCTCCATTG
Found at i:40817331 original size:148 final size:147
Alignment explanation
Indices: 40817167--40817444 Score: 407
Period size: 148 Copynumber: 1.9 Consensus size: 147
40817157 CGTCATTGCA
* * ** *
40817167 GCTTAAATTTTTCCCTTTACAT-CTTC-GAGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCC
1 GCTTAAATCTTTCCC-TT-CATGCTTCTGAGGTACAAGATTCGCCGTTGCAACTTAAACCTTTCC
* *
40817230 CTTCATGCTTTTGAGGTACAAGGTTCATCATTGCGACTTAAACCTTTCCCTCCATTGTCTTCGTG
64 CTTCATGCTTTTGACGTACAAGGTTCATCATTGCGACTTAAACCTTTCCCTCCA-TGTCTTCATG
40817295 GTACTGGATTTGCCGTTGTG
128 GTACTGGATTTGCCGTTGTG
* **
40817315 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCAACTTAAACCTTTCTTT
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGATTCGCCGTTGCAACTTAAACCTTTCCCT
* *
40817380 TCATGCTTTTGACGTACAAGGTTCGTCATTGCGACTTAAATCTTTCCCTCCATGTCTTCATGGTA
66 TCATGCTTTTGACGTACAAGGTTCATCATTGCGACTTAAACCTTTCCCTCCATGTCTTCATGGTA
40817445 ATGAGACTTG
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
146 3 0.03
147 18 0.16
148 95 0.82
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (147 bp):
GCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGATTCGCCGTTGCAACTTAAACCTTTCCCT
TCATGCTTTTGACGTACAAGGTTCATCATTGCGACTTAAACCTTTCCCTCCATGTCTTCATGGTA
CTGGATTTGCCGTTGTG
Found at i:40818611 original size:12 final size:13
Alignment explanation
Indices: 40818578--40818612 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
40818568 GTTGCCCCAG
40818578 TAGAAGTTCTGAC
1 TAGAAGTTCTGAC
40818591 TAGAAGTTCTGAC
1 TAGAAGTTCTGAC
40818604 TA-AAGTTCT
1 TAGAAGTTCT
40818613 ATAAGCAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (13 bp):
TAGAAGTTCTGAC
Found at i:40825480 original size:29 final size:29
Alignment explanation
Indices: 40825359--40825613 Score: 156
Period size: 29 Copynumber: 8.8 Consensus size: 29
40825349 TTTTGGATAC
* **
40825359 TCGGAGGTAAAATGGTAATTTT-G-GACT
1 TCGGGGGTAAAATGGTAATTTTGGTGAAA
*
40825386 TGCGGGGGCAAAATGGTAATTTTCGGTGAAA
1 T-CGGGGGTAAAATGGTAATTTT-GGTGAAA
* *
40825417 TC-AGGGTCGAAAATGG-AATTTTGG-AAAA
1 TCGGGGGT--AAAATGGTAATTTTGGTGAAA
* *
40825445 TTTGGGGGTAAAATGGTGATTTTGGTGAAA
1 -TCGGGGGTAAAATGGTAATTTTGGTGAAA
* *
40825475 TCGGGGTTAAAAATAG-AATTTT-G-GAAA
1 TCGGGGGT-AAAATGGTAATTTTGGTGAAA
*** *
40825502 GTTTAAGGGTAAAATGGTAATTTTAGTGAAA
1 --TCGGGGGTAAAATGGTAATTTTGGTGAAA
* *
40825533 TCAGGGTTAAAGATGG-AATTTT-G-GAAA
1 TCGGGGGTAAA-ATGGTAATTTTGGTGAAA
*
40825560 GTTCGAGGGTAAAATGGTAATTTTTGGTGAAA
1 --TCGGGGGTAAAATGGTAA-TTTTGGTGAAA
*
40825592 TCGGGGTTAAAATGGT-ATTTTG
1 TCGGGGGTAAAATGGTAATTTTG
40825614 CAAAGTTTAG
Statistics
Matches: 177, Mismatches: 28, Indels: 45
0.71 0.11 0.18
Matches are distributed among these distances:
27 9 0.05
28 46 0.26
29 59 0.33
30 44 0.25
31 15 0.08
32 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTTGGTGAAA
Found at i:40825537 original size:116 final size:117
Alignment explanation
Indices: 40825395--40825641 Score: 365
Period size: 116 Copynumber: 2.1 Consensus size: 117
40825385 TTGCGGGGGC
* * *
40825395 AAAATGGTAATTTTCGGTGAAATCAGGGTCGAAA-ATGGAATTTTGGAAAATTTGGGGGTAAAAT
1 AAAATGGTAATTTTCAGTGAAATCAGGGT-GAAAGATGGAATTTTGGAAAATTCGAGGGTAAAAT
* *
40825459 GGTGA-TTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAAGGGT
65 GGTAATTTTTGGTGAAATCGGGGTT-AAAATAGAATTTTGCAAAGTTTAAGGGT
* *
40825512 AAAATGGTAATTTT-AGTGAAATCAGGGTTAAAGATGGAATTTTGGAAAGTTCGAGGGTAAAATG
1 AAAATGGTAATTTTCAGTGAAATCAGGGTGAAAGATGGAATTTTGGAAAATTCGAGGGTAAAATG
* * *
40825576 GTAATTTTTGGTGAAATCGGGGTTAAAATGGTATTTTGCAAAGTTTAGGGGT
66 GTAATTTTTGGTGAAATCGGGGTTAAAATAGAATTTTGCAAAGTTTAAGGGT
40825628 AAAATGGTAATTTT
1 AAAATGGTAATTTT
40825642 TGGATAGTTC
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
115 3 0.03
116 82 0.69
117 33 0.28
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (117 bp):
AAAATGGTAATTTTCAGTGAAATCAGGGTGAAAGATGGAATTTTGGAAAATTCGAGGGTAAAATG
GTAATTTTTGGTGAAATCGGGGTTAAAATAGAATTTTGCAAAGTTTAAGGGT
Found at i:40825642 original size:58 final size:58
Alignment explanation
Indices: 40825390--40825644 Score: 327
Period size: 58 Copynumber: 4.4 Consensus size: 58
40825380 TGGACTTGCG
* * * * *
40825390 GGGGCAAAATGGTAATTTTCGGTGAAATCAGGGTCGAAAATGGAATTTTGGAAAATTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGT-TAAAATGGAATTTTGGAAAGTTTA
* * *
40825449 GGGGTAAAATGGTGA-TTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTT-AAAATGGAATTTTGGAAAGTTTA
* * *
40825507 AGGGTAAAATGGTAA-TTTTAGTGAAATCAGGGTTAAAGATGGAATTTTGGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAA-ATGGAATTTTGGAAAGTTTA
* * *
40825564 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGTATTTTGCAAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGAATTTTGGAAAGTTTA
40825623 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
40825645 ATAGTTCAGG
Statistics
Matches: 171, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
57 5 0.03
58 130 0.76
59 36 0.21
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGAATTTTGGAAAGTTTA
Found at i:40825921 original size:162 final size:162
Alignment explanation
Indices: 40825716--40826053 Score: 496
Period size: 162 Copynumber: 2.1 Consensus size: 162
40825706 GGCATCCAGA
** * * *
40825716 AGTCAAAGGACGAATTTGTAAATCTTAAAAAATTCTCGGGCCAATTTTGTAATTAAGCAGAAGTT
1 AGTCAAAGGATTAATTTATAAATCTTAAAAAATTCTCGGGCCAATTTTGTAATTAAACAAAAGTT
* * * * *
40825781 GATTTGAAGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAATCAAAAA
66 GATTTGAAGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACATAAATAAACCAAAAA
* * * *
40825846 GTGACATATGGCGGCCTCTGGTGCAGTCAAAC
131 GTGACACATGGCAGCCTCCGATGCAGTCAAAC
* *
40825878 AGTCAAAGGATTAATTTATAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAACAAAAGTT
1 AGTCAAAGGATTAATTTATAAATCTTAAAAAATTCTCGGGCCAATTTTGTAATTAAACAAAAGTT
* *
40825943 GATTTGAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAACCAAAAA
66 GATTTGAAGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACATAAATAAACCAAAAA
* *
40826008 GTGACACGTGGCAGCCTCCGATGCAGTCCAAC
131 GTGACACATGGCAGCCTCCGATGCAGTCAAAC
40826040 AGTCAAAGGATTAA
1 AGTCAAAGGATTAA
40826054 ATTCAAAACC
Statistics
Matches: 156, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
162 156 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (162 bp):
AGTCAAAGGATTAATTTATAAATCTTAAAAAATTCTCGGGCCAATTTTGTAATTAAACAAAAGTT
GATTTGAAGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATACATAAATAAACCAAAAA
GTGACACATGGCAGCCTCCGATGCAGTCAAAC
Found at i:40826594 original size:14 final size:14
Alignment explanation
Indices: 40826575--40826601 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40826565 TGAGCCAAAA
40826575 CCAGATCTGGAAAC
1 CCAGATCTGGAAAC
40826589 CCAGATCTGGAAA
1 CCAGATCTGGAAA
40826602 TTTCCAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (14 bp):
CCAGATCTGGAAAC
Found at i:40826865 original size:20 final size:20
Alignment explanation
Indices: 40826840--40826923 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
40826830 CTTTTTTATT
40826840 TTATTATAAATTAATATTTA
1 TTATTATAAATTAATATTTA
** *
40826860 TTATTA-AAACCAAAACTTTA
1 TTATTATAAATTAATA-TTTA
**
40826880 TTATTATTTAAAAAATATATTTA
1 TTATTA--TAAATTA-ATATTTA
*
40826903 TTATTAT-TATTAATA-TTA
1 TTATTATAAATTAATATTTA
40826921 TTA
1 TTA
40826924 ATGTTATTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
18 6 0.12
19 9 0.18
20 18 0.36
21 1 0.02
23 14 0.28
24 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTATAAATTAATATTTA
Found at i:40826914 original size:9 final size:9
Alignment explanation
Indices: 40826900--40826934 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
40826890 AAAAATATAT
*
40826900 TTATTATTA
1 TTATTAATA
40826909 TTATTAATA
1 TTATTAATA
*
40826918 TTATTAATG
1 TTATTAATA
40826927 TTATTAAT
1 TTATTAAT
40826935 GCTTCTGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (9 bp):
TTATTAATA
Found at i:40827709 original size:6 final size:6
Alignment explanation
Indices: 40827698--40827791 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
40827688 TTAAATTTGA
* * *
40827698 TTAAAT TTAAAT CTAAA- ATAAAT TTAAAT AAGTAAAT TTAAAT TTAAGA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAA-AT
** *
40827747 -TAAAT TTAAAT TTAAA- ACAAAT TTAAAA TT-AAT TTAAACT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAA
40827792 AGCCCAAGCC
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
4 1 0.01
5 14 0.21
6 41 0.60
7 7 0.10
8 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:40827719 original size:17 final size:17
Alignment explanation
Indices: 40827699--40827778 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
40827689 TAAATTTGAT
*
40827699 TAAATTTAAATCTAAAA
1 TAAATTTAAATTTAAAA
*
40827716 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAA
*
40827730 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAA
40827747 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
40827764 CAAATTTAAAATTAA
1 TAAATTTAAATTTAA
40827779 TTTAAACTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.22
15 1 0.02
16 1 0.02
17 40 0.74
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:40827725 original size:11 final size:11
Alignment explanation
Indices: 40827705--40827784 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 11
40827695 TGATTAAATT
*
40827705 TAAATCTAAAA
1 TAAATTTAAAA
40827716 TAAATTTAAATAA
1 TAAATTT-AA-AA
*
40827729 GTAAATTTAAAT
1 -TAAATTTAAAA
* ** *
40827741 TTAAGATAAATT
1 TAAATTTAAA-A
40827753 TAAATTTAAAA
1 TAAATTTAAAA
*
40827764 CAAATTTAAAA
1 TAAATTTAAAA
*
40827775 TTAATTTAAA
1 TAAATTTAAA
40827785 CTTTAAAAGC
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 31 0.58
12 11 0.21
13 4 0.08
14 7 0.13
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:40827736 original size:31 final size:31
Alignment explanation
Indices: 40827699--40827757 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
40827689 TAAATTTGAT
40827699 TAAATTTAAATCTAAAATAAATTTAAATAAG
1 TAAATTTAAATCTAAAATAAATTTAAATAAG
* *
40827730 TAAATTTAAATTTAAGATAAATTTAAAT
1 TAAATTTAAATCTAAAATAAATTTAAAT
40827758 TTAAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAATTTAAATCTAAAATAAATTTAAATAAG
Found at i:40827780 original size:28 final size:29
Alignment explanation
Indices: 40827737--40827792 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
40827727 AAGTAAATTT
*
40827737 AAATTTAAGATAAATTTAAA-TTTAAAAC
1 AAATTTAAAATAAATTTAAACTTTAAAAC
*
40827765 AAATTTAAAATTAATTTAAACTTTAAAA
1 AAATTTAAAATAAATTTAAACTTTAAAA
40827793 GCCCAAGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (29 bp):
AAATTTAAAATAAATTTAAACTTTAAAAC
Found at i:40834287 original size:17 final size:17
Alignment explanation
Indices: 40834252--40834287 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40834242 AGAGAGACAG
*
40834252 TCTCGGGAGCTGAGCAA
1 TCTCGGGAGCCGAGCAA
*
40834269 TCTCGGGAGCCGAGGAA
1 TCTCGGGAGCCGAGCAA
40834286 TC
1 TC
40834288 AACGGTCAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.25, G:0.36, T:0.17
Consensus pattern (17 bp):
TCTCGGGAGCCGAGCAA
Found at i:40834798 original size:17 final size:17
Alignment explanation
Indices: 40834760--40834811 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
40834750 TCAGATCAAT
40834760 AAATAATTTAAAAATTATAA
1 AAAT-ATTTAAAAA--ATAA
40834780 AAATATTTAAAAAATAA
1 AAATATTTAAAAAATAA
*
40834797 AAAAATTTAAAAAAT
1 AAATATTTAAAAAAT
40834812 TAGCATGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 18 0.58
19 9 0.29
20 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATTTAAAAAATAA
Found at i:40834810 original size:9 final size:9
Alignment explanation
Indices: 40834759--40834812 Score: 58
Period size: 8 Copynumber: 6.0 Consensus size: 9
40834749 ATCAGATCAA
*
40834759 TAAATAATT
1 TAAAAAATT
40834768 T-AAAAATT
1 TAAAAAATT
40834776 ATAAAAATATT
1 -TAAAAA-ATT
40834787 TAAAAAA-T
1 TAAAAAATT
*
40834795 AAAAAAATT
1 TAAAAAATT
40834804 TAAAAAATT
1 TAAAAAATT
40834813 AGCATGAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 13 0.34
9 12 0.32
10 10 0.26
11 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAAAATT
Found at i:40834956 original size:31 final size:31
Alignment explanation
Indices: 40834903--40834962 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
40834893 ATAATTCGAC
* * *
40834903 TTTTTTAAAAGATTGATAACCAACTTTAATT
1 TTTTTTAAAAGATTAAGAACCAAATTTAATT
* *
40834934 TTTTTTAAAAGGTTAAGGACCAAATTTAA
1 TTTTTTAAAAGATTAAGAACCAAATTTAA
40834963 CTTAAAAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (31 bp):
TTTTTTAAAAGATTAAGAACCAAATTTAATT
Found at i:40838062 original size:16 final size:17
Alignment explanation
Indices: 40838029--40838071 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
40838019 TAATTATTTC
40838029 TTTTTTAAATATGAATA
1 TTTTTTAAATATGAATA
* *
40838046 TTTTTTAATTTTG-ATA
1 TTTTTTAAATATGAATA
*
40838062 TTTTTAAAAT
1 TTTTTTAAAT
40838072 CATAATTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTTTTAAATATGAATA
Found at i:40839252 original size:11 final size:11
Alignment explanation
Indices: 40839235--40839264 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
40839225 ATGGAAATTT
40839235 AAAAAAATATAG
1 AAAAAAATA-AG
40839247 AAAAAAATAAG
1 AAAAAAATAAG
40839258 AAAAAAA
1 AAAAAAA
40839265 GATAGGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (11 bp):
AAAAAAATAAG
Found at i:40839252 original size:12 final size:12
Alignment explanation
Indices: 40839235--40839269 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
40839225 ATGGAAATTT
40839235 AAAAAAATATAG
1 AAAAAAATATAG
40839247 AAAAAAATA-AG
1 AAAAAAATATAG
*
40839258 AAAAAAAGATAG
1 AAAAAAATATAG
40839270 GTTCAGCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (12 bp):
AAAAAAATATAG
Found at i:40840064 original size:77 final size:77
Alignment explanation
Indices: 40839966--40840116 Score: 248
Period size: 77 Copynumber: 2.0 Consensus size: 77
40839956 GATTTGATTG
*
40839966 GGGAATTAGGGTTTGTGATTGGAGTTCAATTTGTGTAATGATATTGACCAAAGGAATAGCCTTTG
1 GGGAATTAGGGTTTGTGATTGGAGTTCAATTTGTGTAATGATATTGACCAAAGGAATAGCCATTG
40840031 ATAAGGATAATT
66 ATAAGGATAATT
* * * **
40840043 GGGAATTAGGGTTTTTTATTGGAGTTCAATTTGTTTAATTTTATTGACCAAAGGAATAGCCATTG
1 GGGAATTAGGGTTTGTGATTGGAGTTCAATTTGTGTAATGATATTGACCAAAGGAATAGCCATTG
40840108 ATAAGGATA
66 ATAAGGATA
40840117 GACTTTAAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.37
Consensus pattern (77 bp):
GGGAATTAGGGTTTGTGATTGGAGTTCAATTTGTGTAATGATATTGACCAAAGGAATAGCCATTG
ATAAGGATAATT
Found at i:40844306 original size:15 final size:16
Alignment explanation
Indices: 40844284--40844320 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
40844274 TTTTAAATGA
40844284 ATTTTTTTAATCAAAT
1 ATTTTTTTAATCAAAT
*
40844300 ATTTTTTTAATCTAAT
1 ATTTTTTTAATCAAAT
40844316 ATTTT
1 ATTTT
40844321 AATTCAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTTTAATCAAAT
Found at i:40850026 original size:51 final size:51
Alignment explanation
Indices: 40849908--40850192 Score: 285
Period size: 51 Copynumber: 5.6 Consensus size: 51
40849898 TTTCATTTAA
* ** * * *
40849908 TACTCACGATGAC-GTATAGTCATCGGACCCCTTGTTCCGTATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGA-CCCTTAATCCGTAAAAG-ATTCATT
* * * * **
40849961 TACTCACGATGACACTGAGTCATCGGACCCTTAATTCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATCCGTAAAAGATTCATT
* *
40850012 TACTCACGATGACACTTAGTCATCAGA-ACTGTAATCCGTAAAAGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCT-TAATCCGTAAAAGATTCATT
* * *
40850063 TACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATCCGTAAAAGATTCATT
* * * * **
40850114 TACTCATGACGACTCTTCGTCATCGGACGTTTAATCCGTAAAAGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATCCGTAAAAGATTCATT
40850165 TACTCACGATG--AC--AGTCATCGGACCCTT
1 TACTCACGATGACACTTAGTCATCGGACCCTT
40850193 TCGTTTATAG
Statistics
Matches: 195, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
47 12 0.06
49 1 0.01
50 2 0.01
51 145 0.74
52 11 0.06
53 23 0.12
54 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCCTTAATCCGTAAAAGATTCATT
Found at i:40852236 original size:17 final size:17
Alignment explanation
Indices: 40852214--40852246 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40852204 GAGAAATAAT
40852214 AAATGATATAAAAATAC
1 AAATGATATAAAAATAC
40852231 AAATGATATAAAAATA
1 AAATGATATAAAAATA
40852247 ATAAATTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (17 bp):
AAATGATATAAAAATAC
Found at i:40852383 original size:21 final size:22
Alignment explanation
Indices: 40852359--40852404 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
40852349 AAAACAAAAA
40852359 AAAATATA-ATAACA-TACAAAT
1 AAAATATATA-AACACTACAAAT
*
40852380 AAAATATATAAACACTATAAAT
1 AAAATATATAAACACTACAAAT
40852402 AAA
1 AAA
40852405 GATTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATATATAAACACTACAAAT
Found at i:40853041 original size:21 final size:22
Alignment explanation
Indices: 40853007--40853051 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
40852997 TAAATGAAAA
40853007 AAAATATAATAACA-TACAAAT
1 AAAATATAATAACACTACAAAT
*
40853028 AAAATAT-ATAAACACTATAAAT
1 AAAATATAAT-AACACTACAAAT
40853050 AA
1 AA
40853052 GGATTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 11 0.52
22 8 0.38
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATATAATAACACTACAAAT
Found at i:40854567 original size:24 final size:24
Alignment explanation
Indices: 40854540--40854585 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40854530 TTAAAATAAT
* *
40854540 ATTTGGTACATGATTTTTTTTTTA
1 ATTTGATACATGAATTTTTTTTTA
*
40854564 ATTTGATACTTGAATTTTTTTT
1 ATTTGATACATGAATTTTTTTT
40854586 GTTCCAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.63
Consensus pattern (24 bp):
ATTTGATACATGAATTTTTTTTTA
Found at i:40856542 original size:32 final size:32
Alignment explanation
Indices: 40856506--40856566 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
40856496 TTCACTCTTA
* *
40856506 AATTTT-GTGAAAAATTTTAATTAGACCCTTTG
1 AATTTTAGTG-AAAATTTTAAGTAAACCCTTTG
*
40856538 AATTTTATTGAAAATTTTAAGTAAACCCT
1 AATTTTAGTGAAAATTTTAAGTAAACCCT
40856567 CAAACTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 23 0.92
33 2 0.08
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (32 bp):
AATTTTAGTGAAAATTTTAAGTAAACCCTTTG
Found at i:40862335 original size:8 final size:8
Alignment explanation
Indices: 40862322--40862355 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
40862312 CTCTTTCTAT
40862322 ATGTATGC
1 ATGTATGC
*
40862330 ATGTATGT
1 ATGTATGC
40862338 ATGTATGC
1 ATGTATGC
*
40862346 ATGCATGC
1 ATGTATGC
40862354 AT
1 AT
40862356 AGTTTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (8 bp):
ATGTATGC
Found at i:40864138 original size:20 final size:20
Alignment explanation
Indices: 40864115--40864162 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
40864105 TTGAGTCTCC
* *
40864115 TTTTATTTTCTTTT-TTTACA
1 TTTTATTCTCTTTTCTCTA-A
40864135 TTTTGATTCTCTTTTCTCTAA
1 TTTT-ATTCTCTTTTCTCTAA
40864156 TTTTATT
1 TTTTATT
40864163 GTCCCTTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 14 0.58
22 3 0.12
ACGTcount: A:0.15, C:0.12, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTATTCTCTTTTCTCTAA
Found at i:40872562 original size:16 final size:17
Alignment explanation
Indices: 40872541--40872575 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
40872531 TGCCAATATC
40872541 AAATCAAAT-GAAATTT
1 AAATCAAATCGAAATTT
40872557 AAATCAAATCGAAATTT
1 AAATCAAATCGAAATTT
40872574 AA
1 AA
40872576 GAAGATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (17 bp):
AAATCAAATCGAAATTT
Found at i:40874247 original size:15 final size:15
Alignment explanation
Indices: 40874224--40874257 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40874214 CCCACCAAAT
*
40874224 CACCTCCACCGACAC
1 CACCACCACCGACAC
*
40874239 CACCACCACCGTCAC
1 CACCACCACCGACAC
40874254 CACC
1 CACC
40874258 TCTTCCTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.62, G:0.06, T:0.06
Consensus pattern (15 bp):
CACCACCACCGACAC
Found at i:40878367 original size:12 final size:12
Alignment explanation
Indices: 40878350--40878385 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
40878340 GGTTTTTCAT
*
40878350 TAATTAATTAAC
1 TAATTAATTAAA
40878362 TAATTAATTAAA
1 TAATTAATTAAA
*
40878374 TAATTAAGTAAA
1 TAATTAATTAAA
40878386 GTAGGTAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (12 bp):
TAATTAATTAAA
Found at i:40879449 original size:2 final size:2
Alignment explanation
Indices: 40879442--40879482 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
40879432 AACTCTTTGC
40879442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40879483 TATGAATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40881101 original size:6 final size:6
Alignment explanation
Indices: 40881090--40881120 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
40881080 CAAAAATCCA
40881090 CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC C
1 CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC C
40881121 ATCTCTACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00
Consensus pattern (6 bp):
CCCAGC
Found at i:40889029 original size:25 final size:25
Alignment explanation
Indices: 40888978--40889034 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
40888968 TTTAAGTTCT
*
40888978 CAAAAAAGTGTAAACATCATATCTACC
1 CAAAAAAGTGTAAACAT-ATATATA-C
* *
40889005 CAAAAAAGTGTTAAGAT-TATATAC
1 CAAAAAAGTGTAAACATATATATAC
40889029 CAAAAA
1 CAAAAA
40889035 TGGGTTAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 7 0.26
25 5 0.19
27 15 0.56
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.23
Consensus pattern (25 bp):
CAAAAAAGTGTAAACATATATATAC
Found at i:40897060 original size:18 final size:18
Alignment explanation
Indices: 40897037--40897073 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40897027 TGAGTTTTCG
40897037 AATTCAAAT-AACTCGAAT
1 AATTCAAATGAA-TCGAAT
40897055 AATTCAAATGAATCGAAT
1 AATTCAAATGAATCGAAT
40897073 A
1 A
40897074 TCAAACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTCAAATGAATCGAAT
Found at i:40897158 original size:27 final size:27
Alignment explanation
Indices: 40897121--40897172 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40897111 AAATCTTTTT
* *
40897121 ACTTTTTCCCCAAAACTTTTACTCCTC
1 ACTTTTCCCCCAAAACTTTCACTCCTC
40897148 ACTTTTCCCCCAAAACTTTCACTCC
1 ACTTTTCCCCCAAAACTTTCACTCC
40897173 CTTCCCATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (27 bp):
ACTTTTCCCCCAAAACTTTCACTCCTC
Found at i:40909247 original size:24 final size:23
Alignment explanation
Indices: 40909199--40909247 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
40909189 CATAAGGCAG
* *
40909199 AAGCGTGCCACAAGGCAAAGGAA
1 AAGCATGCCACAAGGCAAAGAAA
*
40909222 AAGCATGCCACAAAGGCAAATAAA
1 AAGCATGCCAC-AAGGCAAAGAAA
40909246 AA
1 AA
40909248 CTAGAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.51, C:0.20, G:0.22, T:0.06
Consensus pattern (23 bp):
AAGCATGCCACAAGGCAAAGAAA
Found at i:40912928 original size:14 final size:15
Alignment explanation
Indices: 40912900--40912928 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40912890 TCACTGCTAC
40912900 AAAGGAGAGGAAAGA
1 AAAGGAGAGGAAAGA
40912915 AAAGGAGA-GAAAGA
1 AAAGGAGAGGAAAGA
40912929 GACGACAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
AAAGGAGAGGAAAGA
Found at i:40915768 original size:6 final size:6
Alignment explanation
Indices: 40915757--40915785 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40915747 AAAGAAACAA
40915757 CTGGTG CTGGTG CTGGTG CTGGTG CTGGT
1 CTGGTG CTGGTG CTGGTG CTGGTG CTGGT
40915786 TATGGTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.48, T:0.34
Consensus pattern (6 bp):
CTGGTG
Found at i:40915791 original size:18 final size:18
Alignment explanation
Indices: 40915757--40915791 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40915747 AAAGAAACAA
*
40915757 CTGGTGCTGGTGCTGGTG
1 CTGGTGCTGGTGATGGTG
*
40915775 CTGGTGCTGGTTATGGT
1 CTGGTGCTGGTGATGGT
40915792 TATGGTTATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.14, G:0.46, T:0.37
Consensus pattern (18 bp):
CTGGTGCTGGTGATGGTG
Found at i:40916468 original size:24 final size:24
Alignment explanation
Indices: 40916441--40916495 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
40916431 GGGTTAAAAG
**
40916441 TTAAATTATATTTTAATTTTTTAT
1 TTAAATTATAAATTAATTTTTTAT
**
40916465 TTAAAAAATAAATTAATTTTTTAT
1 TTAAATTATAAATTAATTTTTTAT
*
40916489 TAAAATT
1 TTAAATT
40916496 TTATCCATTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAAATTATAAATTAATTTTTTAT
Found at i:40916992 original size:12 final size:12
Alignment explanation
Indices: 40916975--40916999 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40916965 ATCATTAAGG
40916975 TGTTAAATCACT
1 TGTTAAATCACT
40916987 TGTTAAATCACT
1 TGTTAAATCACT
40916999 T
1 T
40917000 ACTTTTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTAAATCACT
Found at i:40926237 original size:37 final size:37
Alignment explanation
Indices: 40926193--40926269 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
40926183 GTAAAGAACC
40926193 TAAAAATTTCTTCATCAAACAACAACAAATAAGAGGG
1 TAAAAATTTCTTCATCAAACAACAACAAATAAGAGGG
40926230 TAAAAATTTCTTCATCAAACAACAACAAATAAGAGGG
1 TAAAAATTTCTTCATCAAACAACAACAAATAAGAGGG
40926267 TAA
1 TAA
40926270 GAAAGATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (37 bp):
TAAAAATTTCTTCATCAAACAACAACAAATAAGAGGG
Found at i:40933635 original size:16 final size:16
Alignment explanation
Indices: 40933614--40933644 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40933604 TTTGTTAGAG
40933614 CATATATAATTGAAAC
1 CATATATAATTGAAAC
*
40933630 CATATATATTTGAAA
1 CATATATAATTGAAA
40933645 ATTTTTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATATAATTGAAAC
Found at i:40933789 original size:24 final size:25
Alignment explanation
Indices: 40933762--40933809 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
40933752 TATATATTAG
40933762 AATTTTAAATTTTTTTA-AAATATA
1 AATTTTAAATTTTTTTATAAATATA
40933786 AATTTTAAATTTTTTTATAAATAT
1 AATTTTAAATTTTTTTATAAATAT
40933810 TTTGAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AATTTTAAATTTTTTTATAAATATA
Found at i:40949803 original size:12 final size:12
Alignment explanation
Indices: 40949764--40949809 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
40949754 TCCTTCCCCT
40949764 TATTTT-TTTTA
1 TATTTTGTTTTA
* *
40949775 TATTTAGTTCT-
1 TATTTTGTTTTA
40949786 TATTTTGTTTTA
1 TATTTTGTTTTA
40949798 TATTTTGGTTTT
1 TATTTT-GTTTT
40949810 CTTCTAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 14 0.50
12 9 0.32
13 5 0.18
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.74
Consensus pattern (12 bp):
TATTTTGTTTTA
Found at i:40957986 original size:16 final size:17
Alignment explanation
Indices: 40957965--40957997 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40957955 GTGGATAATT
40957965 TTTTTTA-AAAAAAATA
1 TTTTTTATAAAAAAATA
40957981 TTTTTTATTAAAAAAAT
1 TTTTTTA-TAAAAAAAT
40957998 TAAATGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTTATAAAAAAATA
Found at i:40964035 original size:17 final size:17
Alignment explanation
Indices: 40964015--40964047 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40964005 ATTAATTTAA
40964015 TATT-TATATTATAGTAG
1 TATTATATATT-TAGTAG
40964032 TATTATATATTTAGTA
1 TATTATATATTTAGTA
40964048 TAAGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TATTATATATTTAGTAG
Found at i:40964660 original size:22 final size:21
Alignment explanation
Indices: 40964634--40964685 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
40964624 ATATTATTTT
40964634 TTATTTT-TTTCAAATATTTATA
1 TTATTTTATTT-AAATATTTA-A
*
40964656 TTATTTTATTTTAATATTTAA
1 TTATTTTATTTAAATATTTAA
*
40964677 TGATTTTAT
1 TTATTTTAT
40964686 ACAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 9 0.33
22 15 0.56
23 3 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTATTTTATTTAAATATTTAA
Found at i:40971630 original size:49 final size:49
Alignment explanation
Indices: 40971562--40971893 Score: 254
Period size: 49 Copynumber: 6.8 Consensus size: 49
40971552 CGTGGTACTA
* * *
40971562 GATTCGCAGTTGCGGCTTAAATCTTTCCCTCCATGCTTTTGAGGTACAAG
1 GATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTTTGAGGTAC-AG
* * * *
40971612 G-TTCGCCATTGCGACTTAAA-CATTT-CCTT-TTG-TATCTTCGTGGTACTG
1 GATTCGCCGTTGCGACTTAAATC-TTTCCCTTCATGCT-T-TT-GAGGTACAG
* * * *
40971660 GATTCGCCGTTGCGGCTTAAATATTTCCCTTCGTGCTTCTGAGGTACAAG
1 GATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTTTGAGGTAC-AG
* * * * *
40971710 G-TTCGCTGTTGCAACTTAAACCTTTCCCTT--TG-TATCTTCGTGGTACTG
1 GATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCT-T-TT-GAGGTACAG
* *
40971758 GATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAG
1 GATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTTTGAGGTAC-AG
* * ** * * *
40971808 G-TTCGCCGTTGCGACTTAACT-TTTCCCTCCATTATCTTCGTGGTACTG
1 GATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCT-TTTGAGGTACAG
*
40971856 GATTCGCCGTTGTGACTTAAATCTTTCCCTTCATGCTT
1 GATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTT
40971894 CATGGTAATG
Statistics
Matches: 218, Mismatches: 43, Indels: 43
0.72 0.14 0.14
Matches are distributed among these distances:
46 2 0.01
47 6 0.03
48 24 0.11
49 156 0.72
50 22 0.10
51 6 0.03
52 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (49 bp):
GATTCGCCGTTGCGACTTAAATCTTTCCCTTCATGCTTTTGAGGTACAG
Found at i:40971727 original size:98 final size:98
Alignment explanation
Indices: 40971548--40971894 Score: 518
Period size: 98 Copynumber: 3.5 Consensus size: 98
40971538 GGCTTCAATG
* * * *
40971548 TCTTCGTGGTACTAGATTCGCAGTTGCGGCTTAAATCTTTCCCTCCATGCTTTTGAGGTACAAGG
1 TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
*
40971613 TTCGCCATTGCGACTTAAACATTTCCTTTTGTA
66 TTCGCCGTTGCGACTTAAACATTTCCTTTTGTA
* *
40971646 TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATATTTCCCTTCGTGCTTCTGAGGTACAAGG
1 TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* * * *
40971711 TTCGCTGTTGCAACTTAAACCTTTCCCTTTGTA
66 TTCGCCGTTGCGACTTAAACATTTCCTTTTGTA
40971744 TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
1 TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* **
40971809 TTCGCCGTTGCGACTT-AACTTTTCCCTCCAT-TA
66 TTCGCCGTTGCGACTTAAACATTT-CCT-TTTGTA
* *
40971842 TCTTCGTGGTACTGGATTCGCCGTTGTGACTTAAATCTTTCCCTTCATGCTTC
1 TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTC
40971895 ATGGTAATGA
Statistics
Matches: 226, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
97 6 0.03
98 219 0.97
99 1 0.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.38
Consensus pattern (98 bp):
TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
TTCGCCGTTGCGACTTAAACATTTCCTTTTGTA
Found at i:40972352 original size:18 final size:18
Alignment explanation
Indices: 40972325--40972361 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40972315 AATAATTGCC
*
40972325 AAATATTTACAAGGAACA
1 AAATAATTACAAGGAACA
40972343 AAATAATTACAAGGAACA
1 AAATAATTACAAGGAACA
40972361 A
1 A
40972362 TATTAGATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (18 bp):
AAATAATTACAAGGAACA
Found at i:40987519 original size:18 final size:18
Alignment explanation
Indices: 40987496--40987533 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
40987486 TCCTTGTTTT
40987496 TCATTTAGAGTGGTAAAG
1 TCATTTAGAGTGGTAAAG
40987514 TCATTTAGAGTGGTAAAG
1 TCATTTAGAGTGGTAAAG
40987532 TC
1 TC
40987534 CTGTTCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (18 bp):
TCATTTAGAGTGGTAAAG
Found at i:40991353 original size:37 final size:37
Alignment explanation
Indices: 40991312--40991383 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
40991302 CTTCAACAAC
*
40991312 CAGTCCTCAACTTTTAACTTTACCTGGTTTCCAGTGT
1 CAGTCCTCAACTTTTAACTTCACCTGGTTTCCAGTGT
* * *
40991349 CAGTCCTCAATTTTTCACTTCAGCTGGTTTCCAGT
1 CAGTCCTCAACTTTTAACTTCACCTGGTTTCCAGT
40991384 ATCGGCACGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.40
Consensus pattern (37 bp):
CAGTCCTCAACTTTTAACTTCACCTGGTTTCCAGTGT
Found at i:40997056 original size:59 final size:59
Alignment explanation
Indices: 40996972--40997087 Score: 169
Period size: 59 Copynumber: 2.0 Consensus size: 59
40996962 GTTATGGACT
* ** * *
40996972 AACTTGGCAATTGTTCTCACATTAGGGTTTGAATTTTTTTTTGTCCAAGTTAGTCCCTA
1 AACTTGGCAATTGTTCCCACATTAGGACTTGAATTTTTTTTGGTCCAAGTTAATCCCTA
* *
40997031 AACTTGGCTATTGTTCCCACTTTAGGACTTGAATTTTTTTTGGTCCAAGTTAATCCC
1 AACTTGGCAATTGTTCCCACATTAGGACTTGAATTTTTTTTGGTCCAAGTTAATCCC
40997088 CACATTAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (59 bp):
AACTTGGCAATTGTTCCCACATTAGGACTTGAATTTTTTTTGGTCCAAGTTAATCCCTA
Found at i:40997110 original size:99 final size:100
Alignment explanation
Indices: 40997001--40997183 Score: 271
Period size: 99 Copynumber: 1.8 Consensus size: 100
40996991 CATTAGGGTT
* * * * *
40997001 TGAATTTTTTTTTGTCCAAGTTAGTCCCTAAACTTGGCT-ATTGTTCCCACTTTAGGACTTGAA-
1 TGAACTTTTTTTTATCCAAGTTAATCCCTAAACTTGG-TAATTGTTCCCACTTTAAGACCTGAAT
40997064 TTTTTTTTGGTCCAAGTTAATCCCCACATTAAGGCC
65 TTTTTTTTGGTCCAAGTTAATCCCCACATTAAGGCC
* *
40997100 TGAACTTTTTTTTATCTAAGTTAATCCCTGAACTTGGTAATTGTTCCCACTTTAAGACCTGAATT
1 TGAACTTTTTTTTATCCAAGTTAATCCCTAAACTTGGTAATTGTTCCCACTTTAAGACCTGAA-T
40997165 TTTTTTTTGGTCCAAGTTA
65 TTTTTTTTGGTCCAAGTTA
40997184 GTCATTGATA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
98 1 0.01
99 54 0.73
101 19 0.26
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (100 bp):
TGAACTTTTTTTTATCCAAGTTAATCCCTAAACTTGGTAATTGTTCCCACTTTAAGACCTGAATT
TTTTTTTGGTCCAAGTTAATCCCCACATTAAGGCC
Found at i:41005581 original size:29 final size:27
Alignment explanation
Indices: 41005529--41005589 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
41005519 AACTTTTAAG
* *
41005529 TTATTTTTACTATTTTAAATATAATATAT
1 TTATTTTTACTATTTAAAAGATAA-A-AT
41005558 TTATTTTTAC-ATTGTAAAAGATAAAAT
1 TTATTTTTACTATT-TAAAAGATAAAAT
41005585 TTATT
1 TTATT
41005590 ATAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 7 0.24
28 4 0.14
29 18 0.62
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (27 bp):
TTATTTTTACTATTTAAAAGATAAAAT
Found at i:41007325 original size:6 final size:6
Alignment explanation
Indices: 41007286--41007321 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
41007276 AATCAAACTT
* *
41007286 CATAAA CATACA CATACA CATACA CATACA TATACA
1 CATACA CATACA CATACA CATACA CATACA CATACA
41007322 TATATGTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (6 bp):
CATACA
Found at i:41009726 original size:17 final size:17
Alignment explanation
Indices: 41009704--41009763 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
41009694 GTTAAAATGG
*
41009704 ATTTAAATTTATTTTAA
1 ATTTAAATTTAATTTAA
** *
41009721 ATTTAAATTTGCTCTAA
1 ATTTAAATTTAATTTAA
* *
41009738 ATTTAAGTTTAATTGAA
1 ATTTAAATTTAATTTAA
*
41009755 ATATAAATT
1 ATTTAAATT
41009764 GATATTAACC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:41010320 original size:21 final size:22
Alignment explanation
Indices: 41010294--41010335 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
41010284 ATTAGGTATT
41010294 AATGCATGTTT-ACTACCATTC
1 AATGCATGTTTAACTACCATTC
*
41010315 AATGCATGTTTAACTGCCATT
1 AATGCATGTTTAACTACCATT
41010336 TATATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (22 bp):
AATGCATGTTTAACTACCATTC
Found at i:41010531 original size:20 final size:21
Alignment explanation
Indices: 41010487--41010532 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
41010477 TAATAATGGC
*
41010487 AATAATTATTATTAAATATTT
1 AATAATTAATATTAAATATTT
*
41010508 -ATAATTAATATT-AATTTTT
1 AATAATTAATATTAAATATTT
41010527 AATAAT
1 AATAAT
41010533 ATTTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATAATTAATATTAAATATTT
Found at i:41011180 original size:17 final size:16
Alignment explanation
Indices: 41011160--41011218 Score: 82
Period size: 17 Copynumber: 3.6 Consensus size: 16
41011150 TATTTTAAGA
*
41011160 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
41011177 TTAAATTTAAATTTATT
1 TTAAATTTAAATTTA-T
*
41011194 TTAAGTTTAAATTTAT
1 TTAAATTTAAATTTAT
41011210 TTAAATTTA
1 TTAAATTTA
41011219 TTTTAAAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.34
17 25 0.66
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:41011211 original size:27 final size:27
Alignment explanation
Indices: 41011181--41011245 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
41011171 TTTTATTTAA
41011181 ATTTAAATTTATTTT-AAGTTTAAATTT
1 ATTTAAATTTATTTTAAAG-TTAAATTT
41011208 ATTTAAATTTATTTTAAAGTTAAATTT
1 ATTTAAATTTATTTTAAAGTTAAATTT
* *
41011235 AATCAAATTTA
1 ATTTAAATTTA
41011246 AAAATAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (27 bp):
ATTTAAATTTATTTTAAAGTTAAATTT
Found at i:41011218 original size:6 final size:6
Alignment explanation
Indices: 41011160--41011236 Score: 65
Period size: 6 Copynumber: 13.7 Consensus size: 6
41011150 TATTTTAAGA
* * * *
41011160 TTAATT TTAAAT TT-TAT TTAAAT TTAAAT TT-ATT TTAAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
41011206 TT--AT TTAAAT TT-ATT TTAAAG TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
41011237 TCAAATTTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
4 4 0.07
5 12 0.21
6 40 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (6 bp):
TTAAAT
Found at i:41011225 original size:11 final size:11
Alignment explanation
Indices: 41011149--41011225 Score: 61
Period size: 11 Copynumber: 6.9 Consensus size: 11
41011139 TGGATTTCGC
41011149 TTATTTTAAGAT
1 TTATTTTAA-AT
*
41011161 TAATTTTAAAT
1 TTATTTTAAAT
41011172 TT-TATTTAAAT
1 TTAT-TTTAAAT
* *
41011183 TTAAATTT-ATT
1 TT-ATTTTAAAT
*
41011194 TTAAGTTTAAAT
1 TT-ATTTTAAAT
41011206 TTA-TTTAAAT
1 TTATTTTAAAT
41011216 TTATTTTAAA
1 TTATTTTAAA
41011226 GTTAAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
10 11 0.20
11 28 0.52
12 15 0.28
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
TTATTTTAAAT
Found at i:41012811 original size:30 final size:30
Alignment explanation
Indices: 41012775--41012884 Score: 175
Period size: 30 Copynumber: 3.7 Consensus size: 30
41012765 AATTGTCCAG
* *
41012775 AAATTATATTTTGACCCCAAAACTTTTCTA
1 AAATTACATTTTGACCCCAAAACTTTACTA
*
41012805 AAATTATATTTTGACCCCAAAACTTTACTA
1 AAATTACATTTTGACCCCAAAACTTTACTA
* *
41012835 AAATTACATTTTAACCCCAAAACTTTCCTA
1 AAATTACATTTTGACCCCAAAACTTTACTA
41012865 AAATTACATTTTGACCCCAA
1 AAATTACATTTTGACCCCAA
41012885 TAATAATCAT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTACTA
Found at i:41019121 original size:68 final size:68
Alignment explanation
Indices: 41019012--41019917 Score: 1003
Period size: 68 Copynumber: 12.9 Consensus size: 68
41019002 ATCAATGCCA
*
41019012 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41019077 GTC
66 GTC
41019080 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41019145 GTC
66 GTC
*
41019148 ATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41019213 GTC
66 GTC
*
41019216 ATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41019281 GTC
66 GTC
*
41019284 ATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41019349 GTC
66 GTC
* * * **
41019352 ATCC-CTTCGAAATTGAAATAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAATAA
1 ATCCTCTT-GAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAG-AGCA
*
41019416 GATCATTTCC
64 -A-C--GT-C
* * *
41019426 TATCCTCTTGAAATTGAAGTAAAGCTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGTA
1 -ATCCTCTTGAAATTGAAGTAGAG-TGGATAATACGTCTTTATCTCTGAAATTGAAGT-A-AG-A
**
41019491 GCATCATTTCC
61 GCA--ACGT-C
* * * * * *
41019502 TATCCTCTCGAAATTGAAGTAAAGCTGGAT-ATCAAGTTTCTTATCTCCGAAAATGAAGTAAGAG
1 -ATCCTCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCT-TTATCTCTGAAATTGAAGTAAGAG
*
41019566 CGAGATCATTTTC
62 C-A-A-C---GTC
* * *
41019579 TATCCTCTTGAAATTGAAGTAAAGCTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGTA
1 -ATCCTCTTGAAATTGAAGTAGAG-TGGATAATACGTCTTTATCTCTGAAATTGAAGT-A-AG-A
**
41019644 GCATTATTTCC
61 GCA--ACGT-C
* * * * *
41019655 TATCCTCTCGAAATTGAAGTAAAGCTGGAT-ATCAAGTTTCTTATCTCCGAAATTGAAGTAAGAG
1 -ATCCTCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCT-TTATCTCTGAAATTGAAGTAAGAG
41019719 CAACGTC
62 CAACGTC
* *
41019726 ATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41019791 G--
66 GTC
* *
41019792 ----TC-----ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
41019848 GTC
66 GTC
* * *
41019851 ATCCCCTTGAAATTGAAGTAGAGTGGACAACACGTCTTTATCTCTGAAATTGTTGAAGTAAGAGC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAA---TTGAAGTAAGAGC
41019916 AA
63 AA
41019918 GATCATTTTC
Statistics
Matches: 744, Mismatches: 51, Indels: 83
0.85 0.06 0.09
Matches are distributed among these distances:
57 54 0.07
62 1 0.00
63 1 0.00
67 3 0.00
68 385 0.52
69 11 0.01
70 23 0.03
71 17 0.02
72 2 0.00
73 1 0.00
74 9 0.01
75 26 0.03
76 125 0.17
77 71 0.10
78 10 0.01
79 5 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (68 bp):
ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:41019447 original size:38 final size:37
Alignment explanation
Indices: 41019396--41019676 Score: 184
Period size: 38 Copynumber: 7.4 Consensus size: 37
41019386 TCTTTATCTC
*
41019396 TGAAATTGAAGTAAGAATAAGATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGACT-AGATCATTTCCTATCCTCT
* * *
41019434 TGAAATTGAAGTAA-AGCTGGATAACATGTCTTTAT-CTC-
1 TGAAATTGAAGTAAGA-CTAGAT--CATTTC-CTATCCTCT
*
41019472 TGAAATTGAAGTAAGAGTAGCATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGACTAG-ATCATTTCCTATCCTCT
* * *
41019510 CGAAATTGAAGTAA-AGCTGGATATCAAGTTTCTTAT-CTC-
1 TGAAATTGAAGTAAGA-CT--AGATC-A-TTTCCTATCCTCT
* * * *
41019549 CGAAAATGAAGTAAGAGCGAGATCATTTTCTATCCTCT
1 TGAAATTGAAGTAAGA-CTAGATCATTTCCTATCCTCT
* * *
41019587 TGAAATTGAAGTAA-AGCTGGATAACATGTCTTTAT-CTC-
1 TGAAATTGAAGTAAGA-CTAGAT--CATTTC-CTATCCTCT
* *
41019625 TGAAATTGAAGTAAGAGTAGCATTATTTCCTATCCTCT
1 TGAAATTGAAGTAAGACTAG-ATCATTTCCTATCCTCT
*
41019663 CGAAATTGAAGTAA
1 TGAAATTGAAGTAA
41019677 AGCTGGATAT
Statistics
Matches: 190, Mismatches: 30, Indels: 46
0.71 0.11 0.17
Matches are distributed among these distances:
36 12 0.06
37 30 0.16
38 90 0.47
39 37 0.19
40 14 0.07
41 7 0.04
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (37 bp):
TGAAATTGAAGTAAGACTAGATCATTTCCTATCCTCT
Found at i:41019825 original size:57 final size:57
Alignment explanation
Indices: 41019737--41019852 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
41019727 TCCCCTTGAA
*
41019737 ATTGAAGTAGAGTGGATAATACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTC
1 ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTC
41019794 ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTC
1 ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTC
41019851 AT
1 AT
41019853 CCCCTTGAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (57 bp):
ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTC
Found at i:41019899 original size:37 final size:37
Alignment explanation
Indices: 41019794--41019902 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 37
41019784 GAGCAACGTC
*
41019794 ATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAA
1 ATTGAAGTAGAGTGGACAACACGTCTTCATCTCTGAA
* * **
41019831 ATTGAAGTA-AG-AG-C-A-ACGTCATCCCCT-TGAA
1 ATTGAAGTAGAGTGGACAACACGTCTTCATCTCTGAA
*
41019862 ATTGAAGTAGAGTGGACAACACGTCTTTATCTCTGAA
1 ATTGAAGTAGAGTGGACAACACGTCTTCATCTCTGAA
41019899 ATTG
1 ATTG
41019903 TTGAAGTAAG
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
31 13 0.23
32 11 0.20
33 2 0.04
34 1 0.02
35 2 0.04
36 10 0.18
37 17 0.30
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (37 bp):
ATTGAAGTAGAGTGGACAACACGTCTTCATCTCTGAA
Found at i:41020331 original size:6 final size:6
Alignment explanation
Indices: 41020322--41020388 Score: 59
Period size: 6 Copynumber: 11.7 Consensus size: 6
41020312 TATTTTAAGA
* * * * *
41020322 TTAATT TTAAAT TT-TAT TTAAAT TTAAAT TT-ATT TTGAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
41020368 TT-ATT TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
41020389 TCAAATTTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
5 12 0.24
6 37 0.76
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (6 bp):
TTAAAT
Found at i:41020342 original size:17 final size:17
Alignment explanation
Indices: 41020322--41020387 Score: 89
Period size: 17 Copynumber: 3.9 Consensus size: 17
41020312 TATTTTAAGA
*
41020322 TTAATTTTAAATTT-TAT
1 TTAAATTTAAATTTAT-T
41020339 TTAAATTTAAATTTATT
1 TTAAATTTAAATTTATT
* *
41020356 TTGAGTTTAAATTTATT
1 TTAAATTTAAATTTATT
41020373 TTAAATTTAAATTTA
1 TTAAATTTAAATTTA
41020388 ATCAAATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
17 42 0.98
18 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTAAATTTAAATTTATT
Found at i:41020381 original size:11 final size:11
Alignment explanation
Indices: 41020311--41020381 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
41020301 TGGATTTCGC
41020311 TTATTTTAAGAT
1 TTATTTTAA-AT
*
41020323 TAATTTTAAAT
1 TTATTTTAAAT
41020334 TT-TATTTAAAT
1 TTAT-TTTAAAT
* *
41020345 TTAAATTT-ATT
1 TT-ATTTTAAAT
*
41020356 TTGAGTTTAAAT
1 TT-ATTTTAAAT
41020368 TTATTTTAAAT
1 TTATTTTAAAT
41020379 TTA
1 TTA
41020382 AATTTAATCA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
10 1 0.02
11 31 0.66
12 15 0.32
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (11 bp):
TTATTTTAAAT
Found at i:41021323 original size:9 final size:9
Alignment explanation
Indices: 41021309--41021333 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41021299 CGCGTGAGAG
41021309 GGACGGCGA
1 GGACGGCGA
41021318 GGACGGCGA
1 GGACGGCGA
41021327 GGACGGC
1 GGACGGC
41021334 CGGTGATCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.24, G:0.56, T:0.00
Consensus pattern (9 bp):
GGACGGCGA
Found at i:41021917 original size:30 final size:30
Alignment explanation
Indices: 41021881--41022043 Score: 227
Period size: 30 Copynumber: 5.4 Consensus size: 30
41021871 AAATTGTCCA
* *
41021881 AAAATTATATTTTGACCCCAGAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCT
* *
41021911 AAAATTATATTTTGACCCCAGAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCT
* * *
41021941 AAAATTATATTTTGACCCCAAAACTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCT
**
41021971 AAAATTACATTTTGACCTTAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCT
* *
41022001 AAAATTACATTTTAACCCCAAAACTTTCCT
1 AAAATTACATTTTGACCCCAAAACTTTTCT
41022031 AAAATTACATTTT
1 AAAATTACATTTT
41022044 TAACCCCGAT
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 121 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCT
Done.