Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014446.1 Kokia drynarioides strain JFW-HI SEQ_129485, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 684930
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 166 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:3370 original size:16 final size:16
Alignment explanation
Indices: 3337--3371 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3327 CTTTGAAAAA
*
3337 GTTTTCAAATATATAT
1 GTTTTCAAATATAAAT
*
3353 GTTTTCAAATTTAAAT
1 GTTTTCAAATATAAAT
3369 GTT
1 GTT
3372 CTAACATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (16 bp):
GTTTTCAAATATAAAT
Found at i:13877 original size:22 final size:22
Alignment explanation
Indices: 13849--13890 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
13839 ACTATTTTCA
13849 TTAAAAAGCTAATTTTAATCTT
1 TTAAAAAGCTAATTTTAATCTT
13871 TTAAAAAGCTAATTTTAATC
1 TTAAAAAGCTAATTTTAATC
13891 ACATATTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (22 bp):
TTAAAAAGCTAATTTTAATCTT
Found at i:27715 original size:12 final size:13
Alignment explanation
Indices: 27694--27736 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
27684 TTCAAATGAA
27694 TTTAATATTT-TAT
1 TTTAA-ATTTATAT
*
27707 TTTAAATTTATTT
1 TTTAAATTTATAT
27720 TTTAAATTTAATAT
1 TTTAAATTT-ATAT
27734 TTT
1 TTT
27737 TATTAAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 16 0.62
14 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTAAATTTATAT
Found at i:31584 original size:22 final size:22
Alignment explanation
Indices: 31559--31601 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
31549 TGATAAAGTA
31559 TTTTGATATAAAAATTAAAATGT
1 TTTTGA-ATAAAAATTAAAATGT
* *
31582 TTTTGAATATAAGTTAAAAT
1 TTTTGAATAAAAATTAAAAT
31602 TGACAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTTGAATAAAAATTAAAATGT
Found at i:35272 original size:24 final size:23
Alignment explanation
Indices: 35245--35301 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
35235 ACATTTTTCG
*
35245 TGAACATGTTCAATTATATGTT-CA
1 TGAACATGTTCAATTA-A-GTTAAA
*
35269 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCAATTAAGTTAAA
35292 TGAACATGTT
1 TGAACATGTT
35302 AGTGAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 3 0.10
23 12 0.40
24 15 0.50
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (23 bp):
TGAACATGTTCAATTAAGTTAAA
Found at i:40535 original size:30 final size:30
Alignment explanation
Indices: 40471--40717 Score: 227
Period size: 30 Copynumber: 8.4 Consensus size: 30
40461 TCCTCATGTT
* * *
40471 TTTTTCAAAATTACATTTTGACCCTC-AA-
1 TTTTCCAAAATCACATTTTAACCCTCAAAC
* * *
40499 -TTTCCAAAATTACATTTTGACCCTTAAAC
1 TTTTCCAAAATCACATTTTAACCCTCAAAC
* * *
40528 TTTTCCAAAATCATATTTTAACCCCCAAAT
1 TTTTCCAAAATCACATTTTAACCCTCAAAC
* * *
40558 TTTTCCAAAACCATATTTTGACCCTCAAAC
1 TTTTCCAAAATCACATTTTAACCCTCAAAC
* *
40588 TTTTCCAAAATTACATTTTAA-CCTCTAAAA
1 TTTTCCAAAATCACATTTTAACCCTC-AAAC
** * * * *
40618 TTTTTAAAAAACATAGTTT-ACCCCCAAAC
1 TTTTCCAAAATCACATTTTAACCCTCAAAC
40647 TTTTCCAAAATCACATTTTAATCCC-CAAAC
1 TTTTCCAAAATCACATTTTAA-CCCTCAAAC
*
40677 TTTTCCAAAATCACATTTTAACCCTCGAAC
1 TTTTCCAAAATCACATTTTAACCCTCAAAC
* *
40707 TTCTCTAAAAT
1 TTTTCCAAAAT
40718 TTCATTTTCA
Statistics
Matches: 178, Mismatches: 33, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
27 23 0.13
28 2 0.01
29 25 0.14
30 125 0.70
31 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (30 bp):
TTTTCCAAAATCACATTTTAACCCTCAAAC
Found at i:40655 original size:89 final size:90
Alignment explanation
Indices: 40483--40701 Score: 279
Period size: 89 Copynumber: 2.5 Consensus size: 90
40473 TTTCAAAATT
* * * * *
40483 ACATTTTGACCCTC-AA--TTTCCAAAATTACATTTTGACCCTTAAACTTTTCCAAAATCATATT
1 ACATTTTGACCCTCAAACTTTTCCAAAATTACATTTTAACCCTTAAAATTTTCAAAAAACATAGT
*
40545 TTAACCCCCAAATTTTTCCAAAACC
66 TTAACCCCCAAACTTTTCCAAAACC
* *
40570 ATATTTTGACCCTCAAACTTTTCCAAAATTACATTTTAA-CCTCTAAAATTTTTAAAAAACATAG
1 ACATTTTGACCCTCAAACTTTTCCAAAATTACATTTTAACCCT-TAAAATTTTCAAAAAACATAG
*
40634 TTT-ACCCCCAAACTTTTCCAAAATC
65 TTTAACCCCCAAACTTTTCCAAAACC
* *
40659 ACATTTTAATCCC-CAAACTTTTCCAAAATCACATTTTAACCCT
1 ACATTTTGA-CCCTCAAACTTTTCCAAAATTACATTTTAACCCT
40702 CGAACTTCTC
Statistics
Matches: 114, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
87 13 0.11
88 2 0.02
89 55 0.48
90 44 0.39
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (90 bp):
ACATTTTGACCCTCAAACTTTTCCAAAATTACATTTTAACCCTTAAAATTTTCAAAAAACATAGT
TTAACCCCCAAACTTTTCCAAAACC
Found at i:44902 original size:13 final size:14
Alignment explanation
Indices: 44884--44915 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
44874 TTATAATAAA
44884 GAAAATC-AAAAAT
1 GAAAATCAAAAAAT
44897 GAAAATCAAAAAAT
1 GAAAATCAAAAAAT
44911 GAAAA
1 GAAAA
44916 ATGAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.12
Consensus pattern (14 bp):
GAAAATCAAAAAAT
Found at i:44992 original size:12 final size:11
Alignment explanation
Indices: 44967--44991 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44957 TCAAAACCCT
44967 AAATACAAAAA
1 AAATACAAAAA
44978 AAATACAAAAA
1 AAATACAAAAA
44989 AAA
1 AAA
44992 AAAAAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAATACAAAAA
Found at i:45075 original size:16 final size:15
Alignment explanation
Indices: 45046--45093 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
45036 ATATTTTTTT
45046 AAAAAGAA-AAAAGA
1 AAAAAGAAGAAAAGA
45060 AAAGAAGAAGAAAAGA
1 AAA-AAGAAGAAAAGA
*
45076 AAAAGGAAGAAAAAGA
1 AAAAAGAAG-AAAAGA
45092 AA
1 AA
45094 GTCAATATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 17 0.57
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAAAGA
Found at i:45219 original size:37 final size:37
Alignment explanation
Indices: 45169--45241 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
45159 TCATGGCTTC
*
45169 TTTTTATGTGGGGCATGGACGTCACCGAGCCAAATTA
1 TTTTTATATGGGGCATGGACGTCACCGAGCCAAATTA
*
45206 TTTTTATATGGGGCATGGACGTCACTGAGCCAAATT
1 TTTTTATATGGGGCATGGACGTCACCGAGCCAAATT
45242 CATCAAAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (37 bp):
TTTTTATATGGGGCATGGACGTCACCGAGCCAAATTA
Found at i:45387 original size:46 final size:46
Alignment explanation
Indices: 45320--45413 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
45310 ATCAACGTTT
*
45320 AAGTAGATTCTTGAAAAAGAGAGATTATATGTTGATTTGGAATGCC
1 AAGTAGATTCTTGAAAAAGAGAGATTATATGTCGATTTGGAATGCC
45366 AAGTAGATTCTTGAAAAAGAGAGATTATATGTCGATTTGGAATGCC
1 AAGTAGATTCTTGAAAAAGAGAGATTATATGTCGATTTGGAATGCC
45412 AA
1 AA
45414 AAAGGATTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.31
Consensus pattern (46 bp):
AAGTAGATTCTTGAAAAAGAGAGATTATATGTCGATTTGGAATGCC
Found at i:47094 original size:49 final size:49
Alignment explanation
Indices: 46980--47153 Score: 201
Period size: 49 Copynumber: 3.6 Consensus size: 49
46970 TTTCATTACC
* * * * * * *
46980 ACGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACCT
1 ACGAAGATATGGAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTA-CT
* *
47030 -CGGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTA-T
1 AC-GAAGATATGGAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACT
*
47077 CATGAAGATATGGAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACT
1 -ACGAAGATATGGAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACT
*
47127 ACGAAGATATGGAGGGAAAGGTTTAAG
1 ACGAAGATATGGAGGGAAAGATTTAAG
47154 TCATATTGGC
Statistics
Matches: 105, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.01
48 4 0.04
49 95 0.90
50 5 0.05
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (49 bp):
ACGAAGATATGGAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACT
Found at i:48560 original size:49 final size:49
Alignment explanation
Indices: 47507--48649 Score: 323
Period size: 49 Copynumber: 23.3 Consensus size: 49
47497 AAGCATGAAG
* * * * * * * * *
47507 GGAAAGATTTAAGCCACAACGGTGAATCTAGTACCACAAAGATATGGAG
1 GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* ** * *
47556 GGAAAGGTTTAAGTCGCAA-GGACGAATCTTGTACCTTAA-AAGCAT-GAA
1 GGAAAGGTTTAAGTCGCAATGG-TGAATCCAGTACCATAAGGA-CATGGAA
* * ** ** * * *
47604 GGGAAAGATTTAAGTCGCAACGACGAATCCAGTATTAGAAGGATATGGAG
1 -GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* * * ** * * *
47654 GGAAAAGTTTAAGTCACAACGACGAA-CCTTGTACC-TCAGAAGCAT-GAA
1 GGAAAGGTTTAAGTCGCAATGGTGAATCC-AGTACCATAAGGA-CATGGAA
** * * ** *
47702 GGGAAATATTTAAGTCGCAACGGCGAATCCAGTACCACGAGGACATGGAG
1 -GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* * ** * * *
47752 GGAATGGTTTAAGTCGCAACGACGAA-CCTTGTACC-TCAGAAGCAT-GAA
1 GGAAAGGTTTAAGTCGCAATGGTGAATCC-AGTACCATAAGGA-CATGGAA
* * * * *
47800 GGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCATAAGGATATAG-A
1 -GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* * * * *
47849 GAGAAAGATTTAAGTTGCAACGGTGAA-CCTTA-TACC-TCAGAAGCAT-GAA
1 G-GAAAGGTTTAAGTCGCAATGGTGAATCC--AGTACCATAAGGA-CATGGAA
* * * * * * *
47898 GGGAAAGATTTAAGCCACAACGATGAATCCAGTACCACAAGGACATGGAG
1 -GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* * * * * *
47948 GGAATGGTTTAAGTCACAACGGT-AAACCTTA-TACC-TCAAAAGA-A-CGAA
1 GGAAAGGTTTAAGTCGCAATGGTGAATCC--AGTACCAT--AAGGACATGGAA
* * * * * * *
47996 GGGAAAGATTTATGTCGCAACGGCGAATCCAGTACCATAAGGATATAGAG
1 -GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* * * ** * *
48046 GGAAAGGTTTAAGTCGCAACGATGAAACTTGTACC-TCAA-AAGC-TTGAA
1 GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCAT-AAGGA-CATGGAA
* * * * *
48094 GAGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACAAGGACATGGAG
1 G-GAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* * * *
48144 GGAAAGGTTTCAGTTGCAATGGTGAA-CCTTGTACC-TCAA-AAGCAT-GAA
1 GGAAAGGTTTAAGTCGCAATGGTGAATCC-AGTACCAT-AAGGA-CATGGAA
* * * * ** *
48192 GGGAAAGATTTAAGTCGCAACGATGAATCTAGTACCACGAGGACATGGAG
1 -GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* * * *
48242 GGAAAGGTTTAAGTCGCAACGGTGAA-CCTTGTACC-TCAGAAGCAT-GAA
1 GGAAAGGTTTAAGTCGCAATGGTGAATCC-AGTACCATAAGGA-CATGGAA
** * ** * ** * *
48290 GGGAAATATTTAAGCCGCAATGGCAAATTCAGTACCACCAGGATATAGAA
1 -GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* ** * * * *
48340 GGAAAGGTTTAAGTCGCAACGACG-AGCCTTGTACC-TCAGAAGCAT-GAA
1 GGAAAGGTTTAAGTCGCAATGGTGAATCC-AGTACCATAAGGA-CATGGAA
* * ** ** * *
48388 GAGAAAGATTTAAGCCGCAACAGCAAATCCAGTACCACAAGGACATGGAG
1 G-GAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* * * * *
48438 GGAAAGGTTTAAGTCGCAATGGCG-AGCCTTGTACC-TCAGAATCAT-GAA
1 GGAAAGGTTTAAGTCGCAATGGTGAATCC-AGTACCATAAGGA-CATGGAA
* * * * *
48486 GGGAAAGATTTAAGTCGTAACGGTGAATCCAATACCATAAGGATATGGAA
1 -GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
* * * *
48536 GGAAAGGTTTAAGTTGCAATGGTGAA-CCTTGTACC-TCAGAAGCAT-GAA
1 GGAAAGGTTTAAGTCGCAATGGTGAATCC-AGTACCATAAGGA-CATGGAA
* ** * **
48584 GGGAAAGATTTAAG-CTGCAATATTGAATCCAATACCACGAGGACATGG-A
1 -GGAAAGGTTTAAGTC-GCAATGGTGAATCCAGTACCATAAGGACATGGAA
48633 GAGAAAGGTTTAAGTCG
1 G-GAAAGGTTTAAGTCG
48650 TAACGATAAA
Statistics
Matches: 800, Mismatches: 215, Indels: 158
0.68 0.18 0.13
Matches are distributed among these distances:
48 84 0.10
49 634 0.79
50 82 0.10
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (49 bp):
GGAAAGGTTTAAGTCGCAATGGTGAATCCAGTACCATAAGGACATGGAA
Found at i:48799 original size:49 final size:49
Alignment explanation
Indices: 48746--48863 Score: 121
Period size: 49 Copynumber: 2.4 Consensus size: 49
48736 AGGTTTTAGT
* * *
48746 CGCAACGGCGAACCTTGTACCTTAGAAG-CATGAAGGGAAAATTTTAAGC
1 CGCAACGGCGAACCTTGTACCAT-GAAGACATGAAGGGAAAAGTTTAAAC
* * * * * * *
48795 CGCAACAGTGAATCTAGTACCATGAAGATATGAAGGGAAAGGTTTAAAT
1 CGCAACGGCGAACCTTGTACCATGAAGACATGAAGGGAAAAGTTTAAAC
*
48844 CGCTACGGCGAACCTTGTAC
1 CGCAACGGCGAACCTTGTAC
48864 TTCAAAAACA
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
48 4 0.08
49 49 0.92
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (49 bp):
CGCAACGGCGAACCTTGTACCATGAAGACATGAAGGGAAAAGTTTAAAC
Found at i:48897 original size:98 final size:98
Alignment explanation
Indices: 47282--48884 Score: 1752
Period size: 98 Copynumber: 16.4 Consensus size: 98
47272 NAGTCATATT
* * * * *
47282 GGCGAACCTTGTACCTCAAAAGCATAAAGGGAAAGATTTAAGCCGTAACGACGAATCTAGTACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* *
47347 CAAAGATATGGAGGGAAAGATTTAAGTCGCAAC
66 CGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
* * * * * *
47380 GGCGAACCTTGTACCTGAGAAGCATAAAGGGAAAGATTTAAGCCACAACGGTGAATCTAGTAACA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* * *
47445 CGAAGATATGGAGGAAAATGTTTAAGTTGCAAC
66 CGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
* * * * *
47478 GGTGAACCTTGTACTTC-GAAAGCATGAAGGGAAAGATTTAAGCCACAACGGTGAATCTAGTACC
1 GGCGAACCTTGTACCTCAG-AAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACC
*
47542 ACAAAGATATGGAGGGAAAGGTTTAAGTCGCAA-
65 ACGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
* * * * * **
47575 GGACGAATCTTGTACCTTAAAAGCATGAAGGGAAAGATTTAAGTCGCAACGACGAATCCAGTATT
1 GG-CGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACC
* *
47640 A-GAAGGATATGGAGGGAAAAGTTTAAGTCACAAC
65 ACGAA-GATATGGAGGGAAAGGTTTAAGTCGCAAC
* * *
47674 GACGAACCTTGTACCTCAGAAGCATGAAGGGAAATATTTAAGTCGCAACGGCGAATCCAGTACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* * *
47739 CGAGGACATGGAGGGAATGGTTTAAGTCGCAAC
66 CGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
* *
47772 GACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* * * * *
47837 -TAAGGATATAGAGAGAAAGATTTAAGTTGCAAC
66 CGAA-GATATGGAGGGAAAGGTTTAAGTCGCAAC
* * * **
47870 GGTGAACCTTATACCTCAGAAGCATGAAGGGAAAGATTTAAGCCACAACGATGAATCCAGTACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* * *
47935 C-AAGGACATGGAGGGAATGGTTTAAGTCACAAC
66 CGAA-GATATGGAGGGAAAGGTTTAAGTCGCAAC
** * * * * * *
47968 GGTAAACCTTATACCTCAAAAGAACGAAGGGAAAGATTTATGTCGCAACGGCGAATCCAGTACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* *
48033 -TAAGGATATAGAGGGAAAGGTTTAAGTCGCAAC
66 CGAA-GATATGGAGGGAAAGGTTTAAGTCGCAAC
** * * * * *
48066 GATGAAACTTGTACCTCAAAAGCTTGAAGAGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* * * *
48131 C-AAGGACATGGAGGGAAAGGTTTCAGTTGCAAT
66 CGAA-GATATGGAGGGAAAGGTTTAAGTCGCAAC
* * * ** *
48164 GGTGAACCTTGTACCTCAAAAGCATGAAGGGAAAGATTTAAGTCGCAACGATGAATCTAGTACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* *
48229 CGAGGACATGGAGGGAAAGGTTTAAGTCGCAAC
66 CGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
* * * * *
48262 GGTGAACCTTGTACCTCAGAAGCATGAAGGGAAATATTTAAGCCGCAATGGCAAATTCAGTACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* * * *
48327 CCAGGATATAGAAGGAAAGGTTTAAGTCGCAAC
66 CGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
* * * * *
48360 GACGAGCCTTGTACCTCAGAAGCATGAAGAGAAAGATTTAAGCCGCAACAGCAAATCCAGTACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* *
48425 C-AAGGACATGGAGGGAAAGGTTTAAGTCGCAAT
66 CGAA-GATATGGAGGGAAAGGTTTAAGTCGCAAC
* * * * * *
48458 GGCGAGCCTTGTACCTCAGAATCATGAAGGGAAAGATTTAAGTCGTAACGGTGAATCCAATACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* * * *
48523 -TAAGGATATGGAAGGAAAGGTTTAAGTTGCAAT
66 CGAA-GATATGGAGGGAAAGGTTTAAGTCGCAAC
* * **** *
48556 GGTGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCTGCAATATTGAATCCAATACCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* * * *
48621 CGAGGACATGGAGAGAAAGGTTTAAGTCGTAAC
66 CGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
*** * * * * *
48654 GATAAACCTTGTACCTCAAAAGCCTGAAAGGAAAGATTTAAGCCACAACGGCGAATCCAGTGCCA
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
* * * *
48719 CGAGGACT-TGGAAGGAGAGGTTTTAGTCGCAAC
66 CGAAGA-TATGGAGGGAAAGGTTTAAGTCGCAAC
* * * *
48752 GGCGAACCTTGTACCTTAGAAGCATGAAGGGAAA-ATTTTAAGCCGCAACAGTGAATCTAGTACC
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGA-TTTAAGCCGCAACGGCGAATCCAGTACC
* * * *
48816 ATGAAGATATGAAGGGAAAGGTTTAAATCGCTAC
65 ACGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
* * * *
48850 GGCGAACCTTGTACTTCAAAAACATAAAGGGAAAG
1 GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAG
48885 GTTTCGACCG
Statistics
Matches: 1276, Mismatches: 211, Indels: 35
0.84 0.14 0.02
Matches are distributed among these distances:
97 9 0.01
98 1262 0.99
99 5 0.00
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (98 bp):
GGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
CGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC
Found at i:49249 original size:229 final size:229
Alignment explanation
Indices: 48848--49306 Score: 891
Period size: 229 Copynumber: 2.0 Consensus size: 229
48838 TTAAATCGCT
*
48848 ACGGCGAACCTTGTACTTCAAAAACATAAAGGGAAAGGTTTCGACCGCAATGAAAAACCCAGTAC
1 ACGGCGAACCTTGTACTTCAAAAACATAAAGGGAAAGGTTTCGACCGCAACGAAAAACCCAGTAC
48913 TTTAGAAGCATGACAGAAAAGATTAAAGTCGCAACATCAAATCTTATACCCTAAAGCCGAAAAGG
66 TTTAGAAGCATGACAGAAAAGATTAAAGTCGCAACATCAAATCTTATACCCTAAAGCCGAAAAGG
48978 AGCAGATTAAAGTTGTAAAGGTGAATCTTCTACCTCAAAGGTACAATAAATCAAATCAAAATTAA
131 AGCAGATTAAAGTTGTAAAGGTGAATCTTCTACCTCAAAGGTACAATAAATCAAATCAAAATTAA
*
49043 AATAACAAGTCTTTATCTTTCGGAAGTTGTAGTA
196 AATAACAAGTCTTTATCTCTCGGAAGTTGTAGTA
*
49077 ACGGCGAACCTTGTACTTCAGAAACATAAAGGGAAAGGTTTCGACCGCAACGAAAAACCCAGTAC
1 ACGGCGAACCTTGTACTTCAAAAACATAAAGGGAAAGGTTTCGACCGCAACGAAAAACCCAGTAC
49142 TTTAGAAGCATGACAGAAAAGATTAAAGTCGCAACATCAAATCTTATACCCTAAAGCCGAAAAGG
66 TTTAGAAGCATGACAGAAAAGATTAAAGTCGCAACATCAAATCTTATACCCTAAAGCCGAAAAGG
49207 AGCAGATTAAAGTTGTAAAGGTGAATCTTCTACCTCAAAGGTACAATAAATCAAATCAAAATTAA
131 AGCAGATTAAAGTTGTAAAGGTGAATCTTCTACCTCAAAGGTACAATAAATCAAATCAAAATTAA
49272 AATAACAAGTCTTTATCTCTCGGAAGTTGTAGTA
196 AATAACAAGTCTTTATCTCTCGGAAGTTGTAGTA
49306 A
1 A
49307 GAGAAAGATA
Statistics
Matches: 227, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 227 1.00
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (229 bp):
ACGGCGAACCTTGTACTTCAAAAACATAAAGGGAAAGGTTTCGACCGCAACGAAAAACCCAGTAC
TTTAGAAGCATGACAGAAAAGATTAAAGTCGCAACATCAAATCTTATACCCTAAAGCCGAAAAGG
AGCAGATTAAAGTTGTAAAGGTGAATCTTCTACCTCAAAGGTACAATAAATCAAATCAAAATTAA
AATAACAAGTCTTTATCTCTCGGAAGTTGTAGTA
Found at i:49622 original size:153 final size:153
Alignment explanation
Indices: 49344--49660 Score: 510
Period size: 153 Copynumber: 2.1 Consensus size: 153
49334 CCTATCTTCT
*
49344 TGAAGTTACAACGAAGTTGGATTAAAACTACAGTAGTAGATCTCAATCTCCATGAAGTTGAAGTG
1 TGAAGTTACAACGAAGTTAGATTAAAACTACAGTAGTAGATCTCAATCTCCATGAAGTTGAAGTG
* * * * *
49409 GAATGGAGGGAAGCTTCAATACCAAAATTCTTATCCCTAAAGTGTTAGTGGATTGAACAAAGACT
66 GAATGGAGGGAAGCTTCAACACCAAAATTATTAACCCTAAAGTGTCAATGGATTGAACAAAGACT
49474 ACAATAGCGAATCTCAATCTCCC
131 ACAATAGCGAATCTCAATCTCCC
* * * *
49497 TGAAGTTGCAGCGAAGTTAGATTAAAACTACAGTAGTGGATCTCAATCTTCATGAAGTT-ACAGT
1 TGAAGTTACAACGAAGTTAGATTAAAACTACAGTAGTAGATCTCAATCTCCATGAAGTTGA-AGT
* *
49561 GGAATGGAGTGAAGCTTCAACACCAAAATTATTAACCCTGAAGTGTCAATGGATTGAACAAAGAC
65 GGAATGGAGGGAAGCTTCAACACCAAAATTATTAACCCTAAAGTGTCAATGGATTGAACAAAGAC
49626 TACAATAGCGAATCTCAATCTCCC
130 TACAATAGCGAATCTCAATCTCCC
49650 TGAAGTTACAA
1 TGAAGTTACAA
49661 TGGAATGGAG
Statistics
Matches: 149, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
152 1 0.01
153 148 0.99
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (153 bp):
TGAAGTTACAACGAAGTTAGATTAAAACTACAGTAGTAGATCTCAATCTCCATGAAGTTGAAGTG
GAATGGAGGGAAGCTTCAACACCAAAATTATTAACCCTAAAGTGTCAATGGATTGAACAAAGACT
ACAATAGCGAATCTCAATCTCCC
Found at i:52607 original size:15 final size:15
Alignment explanation
Indices: 52589--52618 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52579 AAGAAAATTG
52589 AATGTTATAAAAATA
1 AATGTTATAAAAATA
*
52604 AATGTTTTAAAAATA
1 AATGTTATAAAAATA
52619 TTAGTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
AATGTTATAAAAATA
Found at i:52818 original size:12 final size:12
Alignment explanation
Indices: 52801--52826 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52791 TAATTTAGGG
52801 ATGTTTAGTGTA
1 ATGTTTAGTGTA
52813 ATGTTTAGTGTA
1 ATGTTTAGTGTA
52825 AT
1 AT
52827 TAATTTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (12 bp):
ATGTTTAGTGTA
Found at i:54160 original size:28 final size:29
Alignment explanation
Indices: 54122--54179 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
54112 CATTGTTTAA
* * *
54122 ATATATTTTTTAGGGTATATTA-AAAAAT
1 ATATATATTTTAGGATAAATTATAAAAAT
54150 ATATATATTTTAGGATAAATTATAAAAAT
1 ATATATATTTTAGGATAAATTATAAAAAT
54179 A
1 A
54180 GTCACTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (29 bp):
ATATATATTTTAGGATAAATTATAAAAAT
Found at i:54213 original size:31 final size:31
Alignment explanation
Indices: 54178--54287 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 31
54168 ATTATAAAAA
*
54178 TAGTCACTTTTATTTGCTTCAGGTTACATTT
1 TAGTCACTTTTGTTTGCTTCAGGTTACATTT
* ** * ***
54209 TAGTCACTTATGTTTG--AAATGTTACGTAAAAA
1 TAGTCACTTTTGTTTGCTTCAGGTTAC---ATTT
54241 TAGTCACTTTTGTTTGCTTCAGGTTACATTT
1 TAGTCACTTTTGTTTGCTTCAGGTTACATTT
*
54272 TAGTCACTTATGTTTG
1 TAGTCACTTTTGTTTG
54288 AAATGTTACG
Statistics
Matches: 58, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
29 6 0.10
31 30 0.52
32 16 0.28
34 6 0.10
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (31 bp):
TAGTCACTTTTGTTTGCTTCAGGTTACATTT
Found at i:54233 original size:29 final size:29
Alignment explanation
Indices: 54200--54310 Score: 96
Period size: 29 Copynumber: 3.7 Consensus size: 29
54190 TTTGCTTCAG
54200 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACATTTTAGTCACTTATGTTTGAAAT
*** * ** *
54229 GTTACGTAAAAATAGTCACTTTTGTTTGCTTCAG
1 GTTAC---ATTTTAGTCACTTATGTTTG--AAAT
54263 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACATTTTAGTCACTTATGTTTGAAAT
* *
54292 GTTACGTTTTAATCACTTA
1 GTTACATTTTAGTCACTTA
54311 CGTTATCGTT
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
29 23 0.38
31 16 0.26
32 16 0.26
34 6 0.10
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (29 bp):
GTTACATTTTAGTCACTTATGTTTGAAAT
Found at i:54240 original size:63 final size:63
Alignment explanation
Indices: 54172--54298 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
54162 GGATAAATTA
54172 TAAAAATAGTCACTTTTATTTGCTTCAGGTTACATTTTAGTCACTTATGTTTGAAATGTTACG
1 TAAAAATAGTCACTTTTATTTGCTTCAGGTTACATTTTAGTCACTTATGTTTGAAATGTTACG
*
54235 TAAAAATAGTCACTTTTGTTTGCTTCAGGTTACATTTTAGTCACTTATGTTTGAAATGTTACG
1 TAAAAATAGTCACTTTTATTTGCTTCAGGTTACATTTTAGTCACTTATGTTTGAAATGTTACG
54298 T
1 T
54299 TTTAATCACT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.45
Consensus pattern (63 bp):
TAAAAATAGTCACTTTTATTTGCTTCAGGTTACATTTTAGTCACTTATGTTTGAAATGTTACG
Found at i:54465 original size:18 final size:18
Alignment explanation
Indices: 54442--54484 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
54432 GAATAATTTT
54442 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
54460 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
54478 TTAATTA
1 TTAATTA
54485 CAACTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:57132 original size:3 final size:3
Alignment explanation
Indices: 57124--57160 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
57114 AATAAGGCTT
57124 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
57161 TATTATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:57165 original size:3 final size:3
Alignment explanation
Indices: 57159--57195 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
57149 AATAATAATA
57159 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
57196 CTAATATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:58430 original size:29 final size:29
Alignment explanation
Indices: 58319--58429 Score: 136
Period size: 29 Copynumber: 3.8 Consensus size: 29
58309 AAACTGTCTG
58319 AAAATTCCATTTTT-ACCCTCGAACTTCCA
1 AAAATTCCATTTTTAACCC-CGAACTTCCA
* *
58348 AAAATTCCATTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTTAACCCC-GAACTTCCA
* *
58378 AAAATTCCATTTTTAACCTCGAA-TGTCTA
1 AAAATTCCATTTTTAACCCCGAACT-TCCA
*
58407 AAAATTCCATTTTAAACCCCGAA
1 AAAATTCCATTTTTAACCCCGAA
58430 TTTTTCCAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
28 1 0.01
29 41 0.57
30 30 0.42
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTCCATTTTTAACCCCGAACTTCCA
Found at i:70520 original size:205 final size:205
Alignment explanation
Indices: 70156--70939 Score: 1207
Period size: 205 Copynumber: 3.8 Consensus size: 205
70146 GCGATTACCC
* *
70156 ACAAACGACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACA-TTCG
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTT-G
* * * *
70220 ATGTAAGCAAATCTTCGAACCCTAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
65 ATGTGAGCAAATCTTCAAACCCTAGCTTCCTAATGAGACACTGAGAAGCAAGTCGAAGCAATAAA
70285 AGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAA
130 AGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAA
70350 AGCGAATTGAA
195 AGCGAATTGAA
* *
70361 ACAAACAACGCAGTCATCTTCCTGATGAGATACTGGGAAGAAGACCAAATCAAACCCACACTTGA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTTGA
* * *
70426 TGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
66 TGTGAGCAAATCTTCAAACCCTAGCTTCCTAATGAGACACTGAGAAGCAAGTCGAAGCAATAAAA
*
70491 GGCTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAAA
70556 GCGAATTGAA
196 GCGAATTGAA
** **
70566 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTTACGTTTGA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTTGA
*
70631 TGTGAGCAAATCTTCAAACCCTAGCTTCCTAATGAGACACTGAGAGGCAAGTCGAAGCAATAAAA
66 TGTGAGCAAATCTTCAAACCCTAGCTTCCTAATGAGACACTGAGAAGCAAGTCGAAGCAATAAAA
70696 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGA-AA
70761 A-CGAATTGAA
195 AGCGAATTGAA
* * * * * *
70771 ACAAACGACGCGGTCATCTTCCTAATGAGACA-T-AGAAGAGAAGACAAAATCAAACCCACGCTC
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAG-A-AGAAGACCAAATCAAACCCACACTT
* * * * *
70834 GACGTGAGCAAATCTTCAAACCCCAGCTTCTTAATGAGATACTGAGAAGCAAGTCGAAGTAATAA
64 GATGTGAGCAAATCTTCAAACCCTAGCTTCCTAATGAGACACTGAGAAGCAAGTCGAAGCAATAA
* * * *
70899 AACGGTTAGCTTCCTGATGAAATACGGGGAAGTGAACCAAA
129 AA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAA
70940 ACCATTTTCC
Statistics
Matches: 539, Mismatches: 35, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
203 2 0.00
204 2 0.00
205 496 0.92
206 39 0.07
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (205 bp):
ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACACTTGA
TGTGAGCAAATCTTCAAACCCTAGCTTCCTAATGAGACACTGAGAAGCAAGTCGAAGCAATAAAA
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAAA
GCGAATTGAA
Found at i:72142 original size:3 final size:3
Alignment explanation
Indices: 72134--72195 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
72124 AATAAGACTT
** *
72134 TAA TAA TAA TAA TGG TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
72182 TAA TAA TAC TAA TA
1 TAA TAA TAA TAA TA
72196 TCATTAATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:73359 original size:29 final size:29
Alignment explanation
Indices: 73326--73477 Score: 141
Period size: 29 Copynumber: 5.2 Consensus size: 29
73316 TGAAAATTAT
*
73326 ATTTTTACCCCATAACTTTCAAAAATTCC
1 ATTTTTACCCCAGAACTTTCAAAAATTCC
* *
73355 ATTTTTGACCCCAAAACTTCCAAAAATTCC
1 ATTTTT-ACCCCAGAACTTTCAAAAATTCC
*
73385 ATTTTTACCCCCGAAC-TTCTAAAAATTCC
1 ATTTTTACCCCAGAACTTTC-AAAAATTCC
* ** *
73414 ATTTTGA-CCTTGAAACTTTCAAAAATTTC
1 ATTTTTACCCCAG-AACTTTCAAAAATTCC
* * *
73443 ATTTTGAACCC-GAA-TGTCTAAAAATTCC
1 ATTTTTACCCCAGAACTTTC-AAAAATTCC
73471 ATTTTTA
1 ATTTTTA
73478 ATCCCGAATT
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
27 3 0.03
28 21 0.20
29 48 0.46
30 32 0.31
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (29 bp):
ATTTTTACCCCAGAACTTTCAAAAATTCC
Found at i:73410 original size:59 final size:59
Alignment explanation
Indices: 73326--73476 Score: 175
Period size: 58 Copynumber: 2.6 Consensus size: 59
73316 TGAAAATTAT
**
73326 ATTTTTACCCCATAACTT-TCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCC
1 ATTTTTACCCCCGAACTTCT-AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCC
*** * *
73385 ATTTTTACCCCCGAACTTCTAAAAATTCCA-TTTTGACCTTGAAACTTTCAAAAATTTC
1 ATTTTTACCCCCGAACTTCTAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCC
* *
73443 ATTTTGA-ACCCGAA-TGTCTAAAAATTCCATTTTT
1 ATTTTTACCCCCGAACT-TCTAAAAATTCCATTTTT
73477 AATCCCGAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
56 1 0.01
57 19 0.24
58 33 0.41
59 26 0.32
60 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (59 bp):
ATTTTTACCCCCGAACTTCTAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCC
Found at i:77838 original size:30 final size:32
Alignment explanation
Indices: 77793--77852 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
77783 CTATAATGTA
77793 TTATTTTTGAAGGGATAAAACTG-ATTTTTTT
1 TTATTTTTGAAGGGATAAAACTGCATTTTTTT
* *
77824 TTATTTTT-AAGGGATCAAATTGCATTTTT
1 TTATTTTTGAAGGGATAAAACTGCATTTTT
77853 ACTATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.52
Consensus pattern (32 bp):
TTATTTTTGAAGGGATAAAACTGCATTTTTTT
Found at i:82418 original size:18 final size:17
Alignment explanation
Indices: 82393--82428 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
82383 ATATCATAAT
*
82393 TTAATATTTTTTATCAA
1 TTAATATTTTTTAACAA
82410 TTAACTATTTTTTAACAA
1 TTAA-TATTTTTTAACAA
82428 T
1 T
82429 CTCCTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATATTTTTTAACAA
Found at i:85629 original size:11 final size:10
Alignment explanation
Indices: 85615--85723 Score: 64
Period size: 11 Copynumber: 10.3 Consensus size: 10
85605 AAAATTATTG
85615 TTTTAGAATAT
1 TTTTA-AATAT
85626 TTTTAAA-AT
1 TTTTAAATAT
*
85635 TTTTAACT-T
1 TTTTAAATAT
85644 TTTTAATATAT
1 TTTTAA-ATAT
85655 TTTTAGAAT-T
1 TTTTA-AATAT
*
85665 TTTTAAAAATT
1 TTTTAAATA-T
* *
85676 TTTTAATTCT
1 TTTTAAATAT
85686 TTTTAAAATAT
1 TTTT-AAATAT
85697 AAATTTTGAAA-AT
1 ---TTTT-AAATAT
85710 TTTATAAATAT
1 TTT-TAAATAT
85721 TTT
1 TTT
85724 GAAAATTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
9 17 0.22
10 20 0.26
11 30 0.39
12 1 0.01
13 2 0.03
14 7 0.09
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTAAATAT
Found at i:85729 original size:35 final size:34
Alignment explanation
Indices: 85665--85733 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
85655 TTTTAGAATT
* * * *
85665 TTTTAAAAATTTTTTAATTCTTTTTAAAATATAAA
1 TTTTAAAAATTTTATAAATATTTTGAAAAT-TAAA
*
85700 TTTTGAAAATTTTATAAATATTTTGAAAATTAAA
1 TTTTAAAAATTTTATAAATATTTTGAAAATTAAA
85734 AATTATTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (34 bp):
TTTTAAAAATTTTATAAATATTTTGAAAATTAAA
Found at i:85735 original size:27 final size:27
Alignment explanation
Indices: 85705--85758 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
85695 ATAAATTTTG
85705 AAAATT-TTAT-AAATATTTTGAAAATTA
1 AAAATTATTATGAAA-A-TTTGAAAATTA
*
85732 AAAATTATTTTGAAAATTTGAAAATTA
1 AAAATTATTATGAAAATTTGAAAATTA
85759 TTTTGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 17 0.71
28 4 0.17
29 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (27 bp):
AAAATTATTATGAAAATTTGAAAATTA
Found at i:85742 original size:19 final size:20
Alignment explanation
Indices: 85699--85764 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
85689 TAAAATATAA
*
85699 ATTTTGAAAATTTTATAAA-T
1 ATTTTGAAAA-TTTAAAAATT
85719 ATTTTGAAAA-TTAAAAATT
1 ATTTTGAAAATTTAAAAATT
*
85738 ATTTTGAAAATTTGAAAATT
1 ATTTTGAAAATTTAAAAATT
85758 ATTTTGA
1 ATTTTGA
85765 TTTTTTTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.14
19 11 0.26
20 25 0.60
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
ATTTTGAAAATTTAAAAATT
Found at i:92304 original size:25 final size:25
Alignment explanation
Indices: 92250--92307 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
92240 GATATAAATG
*
92250 TTAAAAAT-TTTATATTATGCTCTA
1 TTAAAAATATTTATATTATGCACTA
**
92274 CCAAAAATATTTATATTAT-CACTAA
1 TTAAAAATATTTATATTATGCACT-A
92299 TTAAAAATA
1 TTAAAAATA
92308 AAATAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (25 bp):
TTAAAAATATTTATATTATGCACTA
Found at i:97700 original size:29 final size:28
Alignment explanation
Indices: 97662--97902 Score: 114
Period size: 29 Copynumber: 8.3 Consensus size: 28
97652 CAAAAATGAA
97662 AATTTTGGAAATTTAGGGGTAAAATGGT
1 AATTTTGGAAATTTAGGGGTAAAATGGT
* * * *
97690 AATTTTAGGAAGAATCAAGGGTAAAAAT-GA
1 AATTTT-GGAA-ATTTAGGGGT-AAAATGGT
* * * *
97720 AATTTTGGATAGTTCGAGGTTAAAATGGT
1 AATTTTGGAAATTTAG-GGGTAAAATGGT
** *
97749 AATTTTTGGGAAA-AAAGGGTTAAAATGG-
1 AA-TTTT-GGAAATTTAGGGGTAAAATGGT
** **
97777 AATTTTTAAAAGTTTAGGGGTAAAATAAT
1 AATTTTGGAAA-TTTAGGGGTAAAATGGT
* * * *
97806 AATTTTGGAAAAATCAAGGTTAAAAATGG-
1 AATTTTGG-AAATTTAGGGGT-AAAATGGT
* *
97835 AATTTTTAGAAGTTTAGGGGTAAAATGGT
1 AA-TTTTGGAAATTTAGGGGTAAAATGGT
** *
97864 AATTTTTGGAAAAATCGGGGCTAAAAAT-GT
1 AA-TTTTGGAAATTTAGGGG-T-AAAATGGT
97894 AATTTTGGA
1 AATTTTGGA
97903 GAAGTTTGGA
Statistics
Matches: 156, Mismatches: 41, Indels: 31
0.68 0.18 0.14
Matches are distributed among these distances:
26 3 0.02
27 4 0.03
28 32 0.21
29 66 0.42
30 37 0.24
31 14 0.09
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (28 bp):
AATTTTGGAAATTTAGGGGTAAAATGGT
Found at i:97849 original size:58 final size:60
Alignment explanation
Indices: 97618--97909 Score: 244
Period size: 58 Copynumber: 5.0 Consensus size: 60
97608 TAGGATCCGA
* * * * ** * * * *
97618 GGGTAAAATAGTAATTTCTAGAAAAAAT-TAGGACCAAAAATGAAAATTTTGGAAATTTAG
1 GGGTAAAATGGTAATTTTTAGGAAAAATCAAGG-TTAAAAATGGAATTTTTAGAAGTTTAG
* * * * *
97678 GGGTAAAATGGTAA-TTTTAGGAAGAATCAAGGGTAAAAAT-GAAATTTTGGATAG-TTCG
1 GGGTAAAATGGTAATTTTTAGGAAAAATCAAGGTTAAAAATGGAATTTTTAGA-AGTTTAG
* * * *
97736 AGGTTAAAATGGTAATTTTTGGGAAAAA--AGGGTT-AAAATGGAATTTTTAAAAGTTTAG
1 -GGGTAAAATGGTAATTTTTAGGAAAAATCAAGGTTAAAAATGGAATTTTTAGAAGTTTAG
**
97794 GGGTAAAATAATAA-TTTT-GGAAAAATCAAGGTTAAAAATGGAATTTTTAGAAGTTTAG
1 GGGTAAAATGGTAATTTTTAGGAAAAATCAAGGTTAAAAATGGAATTTTTAGAAGTTTAG
** * * *
97852 GGGTAAAATGGTAATTTTT-GGAAAAATCGGGGCTAAAAATGTAATTTTGGAGAAGTTT
1 GGGTAAAATGGTAATTTTTAGGAAAAATCAAGGTTAAAAATGGAATTTT-TAGAAGTTT
97910 GGAGGTTAAA
Statistics
Matches: 190, Mismatches: 31, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
55 7 0.04
56 4 0.02
57 23 0.12
58 63 0.33
59 59 0.31
60 34 0.18
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.32
Consensus pattern (60 bp):
GGGTAAAATGGTAATTTTTAGGAAAAATCAAGGTTAAAAATGGAATTTTTAGAAGTTTAG
Found at i:99094 original size:3 final size:3
Alignment explanation
Indices: 99086--99131 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
99076 ACTTTTTTAT
* *
99086 TTA TTA TTA TTCA TTA GTG TTA TTA TTA TTA TTA -TA TT- TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
99130 TT
1 TT
99132 TAAAAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:99127 original size:16 final size:19
Alignment explanation
Indices: 99086--99131 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
99076 ACTTTTTTAT
*
99086 TTATTATTATTCATTAGTG
1 TTATTATTATTCATTAGTA
99105 TTATTATTATT-ATTA-TA
1 TTATTATTATTCATTAGTA
99122 TT-TTATTATT
1 TTATTATTATT
99132 TAAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.31
17 3 0.12
18 4 0.15
19 11 0.42
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TTATTATTATTCATTAGTA
Found at i:99639 original size:22 final size:22
Alignment explanation
Indices: 99609--99651 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
99599 TGGTTGGGGC
* *
99609 AGCTGGTGGCAGTGCAAGTTGA
1 AGCTAGTGGCAGGGCAAGTTGA
99631 AGCTAGTGGCAGGGCAAGTTG
1 AGCTAGTGGCAGGGCAAGTTG
99652 CAAGGTGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.42, T:0.21
Consensus pattern (22 bp):
AGCTAGTGGCAGGGCAAGTTGA
Found at i:99898 original size:17 final size:17
Alignment explanation
Indices: 99872--99943 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
99862 CCTTTAATTT
*
99872 AATTTTAATTTAAAATA
1 AATTTAAATTTAAAATA
*
99889 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAATA
* * * *
99906 AATTCAAACTCAAAATG
1 AATTTAAATTTAAAATA
*
99923 AATTTGAATTTAAAATA
1 AATTTAAATTTAAAATA
99940 AATT
1 AATT
99944 CAAACTTATT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:99921 original size:34 final size:34
Alignment explanation
Indices: 99883--99949 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
99873 ATTTTAATTT
*
99883 AAAATAAATTTAAATTTAAAGTAAATTCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATTCAAACTC
* *
99917 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
99950 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTC
Found at i:117080 original size:17 final size:19
Alignment explanation
Indices: 117060--117094 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
117050 CATCATCTAG
117060 TACCA-TCAAA-AATCTTT
1 TACCATTCAAACAATCTTT
117077 TACCATTCAAACAATCTT
1 TACCATTCAAACAATCTT
117095 GCAAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (19 bp):
TACCATTCAAACAATCTTT
Found at i:126395 original size:2 final size:2
Alignment explanation
Indices: 126388--126416 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
126378 TTTTATTCCA
126388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
126417 AAGTTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127151 original size:48 final size:47
Alignment explanation
Indices: 127099--127226 Score: 161
Period size: 48 Copynumber: 2.7 Consensus size: 47
127089 AAGTGTTGGG
* * * *
127099 TAACAAAGGGCACACAAAGTACTAATCAGAGGGCAC-ACAAAGTGCTAA
1 TAACAGAGGGCACACACAGTGCTAATCAGAGAGCACGA-AAAGTGCT-A
* *
127147 TAACAGAGGGCACACACAGTGCTAAACAGAGAGCACGAAACGTGCTA
1 TAACAGAGGGCACACACAGTGCTAATCAGAGAGCACGAAAAGTGCTA
*
127194 -AACAGAGAGCACACACAGTGCTAATCAGAGAGC
1 TAACAGAGGGCACACACAGTGCTAATCAGAGAGC
127227 GCGCTAGTGT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
46 31 0.44
47 1 0.01
48 38 0.54
49 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (47 bp):
TAACAGAGGGCACACACAGTGCTAATCAGAGAGCACGAAAAGTGCTA
Found at i:127224 original size:23 final size:23
Alignment explanation
Indices: 127108--127226 Score: 132
Period size: 23 Copynumber: 5.1 Consensus size: 23
127098 GTAACAAAGG
* * *
127108 GCACACAAAGTACTAATCAGAGG
1 GCACACACAGTGCTAATCAGAGA
* *
127131 GCACACAAAGTGCTAATAACAGAGG
1 GCACACACAGTGCTAAT--CAGAGA
*
127156 GCACACACAGTGCTAAACAGAGA
1 GCACACACAGTGCTAATCAGAGA
* *
127179 GCACGAAAC-GTGCTAAACAGAGA
1 GCAC-ACACAGTGCTAATCAGAGA
127202 GCACACACAGTGCTAATCAGAGA
1 GCACACACAGTGCTAATCAGAGA
127225 GC
1 GC
127227 GCGCTAGTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
22 3 0.04
23 58 0.68
24 3 0.04
25 21 0.25
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (23 bp):
GCACACACAGTGCTAATCAGAGA
Found at i:127327 original size:24 final size:26
Alignment explanation
Indices: 127289--127336 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
127279 TCTACATGGG
127289 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
127315 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
127337 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:129882 original size:13 final size:15
Alignment explanation
Indices: 129864--129895 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
129854 TTATAGCCTT
129864 AAATA-TTTTA-AAA
1 AAATATTTTTATAAA
129877 AAATATTTTTATAAA
1 AAATATTTTTATAAA
129892 AAAT
1 AAAT
129896 TTAATTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 5 0.29
15 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATATTTTTATAAA
Found at i:129952 original size:14 final size:14
Alignment explanation
Indices: 129935--129978 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
129925 AAAAAAAATA
129935 TTAAAAAAATATTT
1 TTAAAAAAATATTT
129949 TTAATAAAAA-ATTT
1 TTAA-AAAAATATTT
* *
129963 TCACAAAAATATTT
1 TTAAAAAAATATTT
129977 TT
1 TT
129979 TTATAGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 5 0.20
14 15 0.60
15 5 0.20
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAAAATATTT
Found at i:131271 original size:29 final size:30
Alignment explanation
Indices: 131227--131283 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
131217 AAATTGAATC
131227 AAATCAAAATGTCATGTATAAAATTACACA
1 AAATCAAAATGTCATGTATAAAATTACACA
*
131257 AAATCAAAAT-TCATGTATAATATTACA
1 AAATCAAAATGTCATGTATAAAATTACA
131284 AATTTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATCAAAATGTCATGTATAAAATTACACA
Found at i:136367 original size:30 final size:29
Alignment explanation
Indices: 136317--136595 Score: 222
Period size: 30 Copynumber: 9.6 Consensus size: 29
136307 TTCGAGGTCA
*
136317 AAAATGG-AATCTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTCGAGGGT
*
136345 AAAATGGTAATTTTTAGGAAGTTTGAGGGT
1 AAAATGGTAATTTTT-GGAAGTTCGAGGGT
*
136375 AAAATGGTAATTTTTGGAAAATT-GA-GGT
1 AAAATGGTAATTTTTGG-AAGTTCGAGGGT
* * *
136403 CAAAAATGG-AATTTTTAGATGTTCGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTCGAGGGT
* **
136433 AAAATGGTAATTTTTGAAAAATC-AGGGT
1 AAAATGGTAATTTTTGGAAGTTCGAGGGT
136461 AAAAATGG-AATTTTTGGATA-TTCG-GAGGT
1 -AAAATGGTAATTTTTGGA-AGTTCGAG-GGT
**
136490 AAAATGGTAA-TTTTGGAAAGTTTAAGGGTT
1 AAAATGGTAATTTTTGG-AAGTTCGAGGG-T
* **
136520 AAAAT-GTATTTTTTGGAAAGTTAAAGGGTT
1 AAAATGGTAATTTTTGG-AAGTTCGAGGG-T
136550 AAAAT-GTAATTTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGG-AAGTTCGAGGGT
136579 CAAAAT-GTAATGTTTTG
1 -AAAATGGTAAT-TTTTG
136596 ACAGTTTAAG
Statistics
Matches: 209, Mismatches: 22, Indels: 37
0.78 0.08 0.14
Matches are distributed among these distances:
28 50 0.24
29 51 0.24
30 103 0.49
31 5 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTCGAGGGT
Found at i:136379 original size:58 final size:61
Alignment explanation
Indices: 136317--136594 Score: 250
Period size: 57 Copynumber: 4.8 Consensus size: 61
136307 TTCGAGGTCA
* *
136317 AAAATGG-AATCTTTGG-AAGTTCGAGGGT-AAAATGGTAATTTTTAGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTAAAAATGGTAATTTTTAGGAAGTTCGAGGGT
* * *
136375 AAAATGGTAATTTTTGGAAAATT-GA-GGTCAAAAATGG-AATTTTTA-GATGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGT-AAAAATGGTAATTTTTAGGAAGTTCGAGGGT
**
136433 AAAATGGTAATTTTT-GAAAAATC-AGGGTAAAAATGG-AATTTTT-GGATA-TTCG-GAGGT
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTAAAAATGGTAATTTTTAGGA-AGTTCGAG-GGT
** * * **
136490 AAAATGGTAA-TTTTGGAAAGTTTAAGGGTTAAAAT-GT-ATTTTTTGGAAAGTTAAAGGGTT
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTAAAAATGGTAATTTTTAGG-AAGTTCGAGGG-T
*
136550 AAAAT-GTAATTTTTGGAAAGTTCGAGGGTCAAAAT-GTAATGTTTT
1 AAAATGGTAATTTTTGGAAAGTTCGAGGGTAAAAATGGTAAT-TTTT
136595 GACAGTTTAA
Statistics
Matches: 184, Mismatches: 16, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
56 5 0.03
57 53 0.29
58 51 0.28
59 27 0.15
60 42 0.23
61 2 0.01
62 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (61 bp):
AAAATGGTAATTTTTGGAAAGTTCGAGGGTAAAAATGGTAATTTTTAGGAAGTTCGAGGGT
Found at i:136402 original size:88 final size:87
Alignment explanation
Indices: 136307--136583 Score: 273
Period size: 88 Copynumber: 3.1 Consensus size: 87
136297 TTTTGAACAC
*
136307 TTCGAGGTCAAAAATGGAATCTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGGAAGTTTGAG
1 TTCGAGGTCAAAAATGGAAT-TTTGGAAGTTCGAGGGTAAAATGGTAATTTTT-GGAAGTTTAAG
136372 GGTAAAATGGTAATTTTTGGAAAA
64 GGTAAAATGGTAATTTTTGGAAAA
* * * *** *
136396 TT-GAGGTCAAAAATGGAATTTTTAGATGTTCGGGGGTAAAATGGTAATTTTT-GAAAAATCAGG
1 TTCGAGGTCAAAAATGGAA-TTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTAAGG
*
136459 GTAAAAATGG-AATTTTTGG-ATA
65 GT-AAAATGGTAATTTTTGGAAAA
** * *
136481 TTCGGAGGT--AAAATGGTAATTTTGGAAAGTTTAAGGGTTAAAAT-GTATTTTTTGGAAAGTTA
1 TTC-GAGGTCAAAAATGG-AATTTTGG-AAGTTCGAGGG-TAAAATGGTAATTTTTGG-AAGTTT
*
136543 AAGGGTTAAAAT-GTAATTTTTGGAAAG
61 AAGGG-TAAAATGGTAATTTTTGGAAAA
136570 TTCGAGGGTCAAAA
1 TTCGA-GGTCAAAA
136584 TGTAATGTTT
Statistics
Matches: 152, Mismatches: 21, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
85 16 0.11
86 35 0.23
87 20 0.13
88 67 0.44
89 11 0.07
91 3 0.02
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (87 bp):
TTCGAGGTCAAAAATGGAATTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTAAGGG
TAAAATGGTAATTTTTGGAAAA
Found at i:137678 original size:11 final size:11
Alignment explanation
Indices: 137652--137701 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 11
137642 TGATGTTATT
*
137652 TAATATTA-AC
1 TAATATTATAA
*
137662 TAATATTATTA
1 TAATATTATAA
137673 TAATATTATAA
1 TAATATTATAA
* *
137684 TAAT-TAATAT
1 TAATATTATAA
137694 TAATATTA
1 TAATATTA
137702 ATGATATCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 16 0.50
11 16 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATATTATAA
Found at i:139044 original size:50 final size:49
Alignment explanation
Indices: 138886--139062 Score: 132
Period size: 49 Copynumber: 3.6 Consensus size: 49
138876 TGGTACTAAA
* * * * * * *
138886 TTCGCCATTGCGGCTTAAA-TTTTCTTTTCATGCTTCTGAGGCATAAAG
1 TTCGCCATTGCGACTTAAACCTTCCCTTTCATGCTTTTGAGTCATAAGG
* * * *
138934 TTTGCCATTGCGACTTAAACCTTTCCCCTT-GTG-TCTTCGCAGT-ACT--GG
1 TTCGCCATTGCGACTTAAACC-TTCCCTTTCATGCT-TTTG-AGTCA-TAAGG
* *
138982 ATTCGCTATTGCGGCTTAAATCCTTCCCTTTCATGCTTTTGAGTCATAAGG
1 -TTCGCCATTGCGACTTAAA-CCTTCCCTTTCATGCTTTTGAGTCATAAGG
*
139033 TTCGCCATTGCGACTTAAACCTTTCCTTTC
1 TTCGCCATTGCGACTTAAACCTTCCCTTTC
139063 GTGTCTTCGT
Statistics
Matches: 97, Mismatches: 20, Indels: 23
0.69 0.14 0.16
Matches are distributed among these distances:
48 19 0.20
49 42 0.43
50 33 0.34
51 3 0.03
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.39
Consensus pattern (49 bp):
TTCGCCATTGCGACTTAAACCTTCCCTTTCATGCTTTTGAGTCATAAGG
Found at i:139047 original size:99 final size:97
Alignment explanation
Indices: 138885--139087 Score: 273
Period size: 99 Copynumber: 2.1 Consensus size: 97
138875 ATGGTACTAA
* * *
138885 ATTCGCCATTGCGGCTTAAATTTTCTTTTCATGCTTCTGAGGCATAAAGTTTGCCATTGCGACTT
1 ATTCGCCATTGCGGCTTAAATTTCCCTTTCATGCTTCTGAGGCATAAAGTTCGCCATTGCGACTT
*
138950 AAACCTTTCCCCTT-GTGTCTTCGCAGTACTGG
66 AAACCTTT-CCCTTCGTGTCTTCGCAGTACAGG
* * * *
138982 ATTCGCTATTGCGGCTTAAATCCTTCCCTTTCATGCTTTTGAGTCATAAGGTTCGCCATTGCGAC
1 ATTCGCCATTGCGGCTTAAAT--TTCCCTTTCATGCTTCTGAGGCATAAAGTTCGCCATTGCGAC
* **
139047 TTAAACCTTTCCTTTCGTGTCTTCGTGGTACAGG
64 TTAAACCTTTCCCTTCGTGTCTTCGCAGTACAGG
139081 ATTCGCC
1 ATTCGCC
139088 GTTACGAATT
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
97 20 0.22
98 4 0.04
99 67 0.74
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.38
Consensus pattern (97 bp):
ATTCGCCATTGCGGCTTAAATTTCCCTTTCATGCTTCTGAGGCATAAAGTTCGCCATTGCGACTT
AAACCTTTCCCTTCGTGTCTTCGCAGTACAGG
Found at i:139087 original size:49 final size:49
Alignment explanation
Indices: 138941--139914 Score: 635
Period size: 49 Copynumber: 19.8 Consensus size: 49
138931 AAGTTTGCCA
* ** **
138941 TTGCGACTTAAACCTTTCCCCTT-GTGTCTTCGCAGTACTGGATTCGCTA
1 TTGCGACTTAAACCTTT-CCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* * *
138990 TTGCGGCTTAAATCC-TTCCCTTTCATG-CTT-TTGAGT-CATAAGG-TTCGCCA
1 TTGCGACTTAAA-CCTTTCCC-TTCATGTCTTCGTG-GTAC-T--GGATTCGCCG
* * *
139040 TTGCGACTTAAACCTTTCCTTTCGTGTCTTCGTGGTACAGGATTCGCCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* * * * * * *
139089 TTACGAATTAAATCTTTTCCTTCATGTTTTTGTGGTACTGGATTCGTCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* * * * *
139138 TTACGGCTTAAATCTTTCCCTTCGTGTCTTCGTGGTATTGGATTCGCCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* *
139187 TTGC-AGCTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATTTGCCG
1 TTGCGA-CTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* * * * * * *
139236 TTGCGGCTTAAATCTTTCCATTCATG-CTTCTGAAGGATA-AGG-TTCACCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTC-G-TGG-TACTGGATTCGCCG
* * *
139285 TTGCGACTTAAACCTTTCCCCTCGTGTCTTCGTGGTATTGGATTCGCCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* * *
139334 TTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTA-TAAGG-TTCGCCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTC-GTGGTACT--GGATTCGCCG
* *
139383 TTGTGACTTAAACCTTTCCCTTTATGTCTTCGTGGTACTGGATTCGCCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* * * *
139432 TTGCGGA-TTAAATCTTTCCCTTCATATC-TCTGAGGTA-TAAGG-TTCGCCA
1 TTGC-GACTTAAACCTTTCCCTTCATGTCTTC-GTGGTACT--GGATTCGCCG
* * * *
139481 TTACGACTTAAACCTTTCCCTTCGTGTCTTCGTGGTATTGGATTCACCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* * * * *
139530 TTACGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTA-TAAGG-TTAGCCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTC-GTGGTACT--GGATTCGCCG
* * *
139579 TTGC-AGCTTAAACCTTTCCCTTCGTATCTTTGTGGTACTGGATTCGCCG
1 TTGCGA-CTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* ** * * * *
139628 TTGAGGTTTAAATCTTTCCTTTCATGTC-TCTGAGGTA-TAAGG-TTCGCCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTC-GTGGTACT--GGATTCGCCG
* * * * *
139677 TTGCGGCTTAAACCTTTCCCTTCGTATCTTTGTGGTACTGGATTCACCG
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
* * * ** *
139726 TTGTGGCTTAAATCTTTCCCTTCACATC-TC-TAAGGTA-TAAGG-TTCGCCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTCGT--GGTACT--GGATTCGCCG
* * **
139775 TTGCAACTTAAACCTTTCCCTTTTC-TATCTTCGTGGTACTGGATTCATCG
1 TTGCGACTTAAACCTTTCCC--TTCATGTCTTCGTGGTACTGGATTCGCCG
* * * * *
139825 TTGCGGCTTAAATCTTTCCCTTCATGT-ATCTGAGGTA-TAAGG-TTCGCCA
1 TTGCGACTTAAACCTTTCCCTTCATGTCTTC-GTGGTACT--GGATTCGCCG
** *
139874 TTGCGACTTAAACCTTTCCCTTTTGTGTTTTCGTGGTACTG
1 TTGCGACTTAAACCTTTCCC-TTCATGTCTTCGTGGTACTG
139915 AGACCTGTAG
Statistics
Matches: 722, Mismatches: 138, Indels: 130
0.73 0.14 0.13
Matches are distributed among these distances:
47 3 0.00
48 43 0.06
49 559 0.77
50 100 0.14
51 16 0.02
52 1 0.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (49 bp):
TTGCGACTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCGCCG
Found at i:139100 original size:99 final size:99
Alignment explanation
Indices: 138911--139188 Score: 278
Period size: 99 Copynumber: 2.8 Consensus size: 99
138901 TAAATTTTCT
* * * * **
138911 TTTCATGCTTCTGAGGCATAAAGTTTGCCATTGCGACTTAAACCTTTCCCCTT-GTGTCTTCGCA
1 TTTCATGCTTTTGAGTCATAAGGTTCGCCATTGCGACTTAAACCTTT-CCCTTCGTGTCTTCGTG
** * **
138975 GTACTGGATTCGCTATTGCGGCTTAAATCCTTCCC
65 GTACTGGATTCGCCGTTACGAATTAAATCCTTCCC
*
139010 TTTCATGCTTTTGAGTCATAAGGTTCGCCATTGCGACTTAAACCTTTCCTTTCGTGTCTTCGTGG
1 TTTCATGCTTTTGAGTCATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTGTCTTCGTGG
* * *
139075 TACAGGATTCGCCGTTACGAATTAAATCTTTTCC
66 TACTGGATTCGCCGTTACGAATTAAATCCTTCCC
* * * * * * *
139109 -TTCATGTTTTTGTGGT-ACT--GGATTCGTCGTTACGGCTTAAATCTTTCCCTTCGTGTCTTCG
1 TTTCATGCTTTTG-AGTCA-TAAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTCGTGTCTTCG
*
139170 TGGTATTGGATTCGCCGTT
63 TGGTACTGGATTCGCCGTT
139189 GCAGCTTAAA
Statistics
Matches: 150, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
97 2 0.01
98 66 0.44
99 82 0.55
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.40
Consensus pattern (99 bp):
TTTCATGCTTTTGAGTCATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTGTCTTCGTGG
TACTGGATTCGCCGTTACGAATTAAATCCTTCCC
Found at i:139162 original size:98 final size:98
Alignment explanation
Indices: 139033--139914 Score: 1053
Period size: 98 Copynumber: 9.0 Consensus size: 98
139023 AGTCATAAGG
* * * * * * * * *
139033 TTCGCCATTGCGACTTAAACCTTTCCTTTCGTGTCT-TCGTGGTA-CAGGATTCGCCGTTACGAA
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT-GAGGTATAAGG-TTCGCCGTTGCGAC
* * * * *
139096 TTAAATCTTTTCCTTCATGTTTTTGTGGTACTGGA
64 TTAAACCTTTCCCTTCGTGTCTTCGTGGTACTGGA
* * * * *
139131 TTCGTCGTTACGGCTTAAATCTTTCCCTTCGTGTCT-TCGTGGTAT-TGGATTCGCCGTTGC-AG
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT-GAGGTATAAGG-TTCGCCGTTGCGA-
* *
139193 CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGA
63 CTTAAACCTTTCCCTTCGTGTCTTCGTGGTACTGGA
* * * *
139229 TTTGCCGTTGCGGCTTAAATCTTTCCATTCATG-CTTCTGAAGG-ATAAGGTTCACCATTGCGAC
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTG-AGGTATAAGGTTCGCCGTTGCGAC
* *
139292 TTAAACCTTTCCCCTCGTGTCTTCGTGGTATTGGA
64 TTAAACCTTTCCCTTCGTGTCTTCGTGGTACTGGA
*
139327 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCGTTGTGACTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTT
**
139392 AAACCTTTCCCTTTATGTCTTCGTGGTACTGGA
66 AAACCTTTCCCTTCGTGTCTTCGTGGTACTGGA
* * * *
139425 TTCGCCGTTGCGGATTAAATCTTTCCCTTCATATCTCTGAGGTATAAGGTTCGCCATTACGACTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTT
*
139490 AAACCTTTCCCTTCGTGTCTTCGTGGTATTGGA
66 AAACCTTTCCCTTCGTGTCTTCGTGGTACTGGA
* * *
139523 TTCACCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTAGCCGTTGC-AGCT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGA-CT
* *
139587 TAAACCTTTCCCTTCGTATCTTTGTGGTACTGGA
65 TAAACCTTTCCCTTCGTGTCTTCGTGGTACTGGA
* * * * *
139621 TTCGCCGTTGAGGTTTAAATCTTTCCTTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCGGCTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTT
* *
139686 AAACCTTTCCCTTCGTATCTTTGTGGTACTGGA
66 AAACCTTTCCCTTCGTGTCTTCGTGGTACTGGA
* * ** * * *
139719 TTCACCGTTGTGGCTTAAATCTTTCCCTTCACATCTCTAAGGTATAAGGTTCGCCATTGCAACTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTT
*
139784 AAACCTTTCCCTTTTC-TATCTTCGTGGTACTGGA
66 AAACCTTTCCC--TTCGTGTCTTCGTGGTACTGGA
** * *
139818 TTCATCGTTGCGGCTTAAATCTTTCCCTTCATGTATCTGAGGTATAAGGTTCGCCATTGCGACTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTT
* *
139883 AAACCTTTCCCTTTTGTGTTTTCGTGGTACTG
66 AAACCTTTCCC-TTCGTGTCTTCGTGGTACTG
139915 AGACCTGTAG
Statistics
Matches: 690, Mismatches: 80, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
97 6 0.01
98 574 0.83
99 107 0.16
100 3 0.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (98 bp):
TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCGTTGCGACTT
AAACCTTTCCCTTCGTGTCTTCGTGGTACTGGA
Found at i:149125 original size:109 final size:109
Alignment explanation
Indices: 148861--149178 Score: 361
Period size: 109 Copynumber: 2.9 Consensus size: 109
148851 TTGTCAATTA
* * *
148861 ATCTGACTAGTGTTGGGCACATAAATTGTCGATTTAACCGACTAGCACAGGGCGCAACATCGTTG
1 ATCTGACTAGTGTTGGGCACACAAATTGTCGGTTTAACCGACTAGCGCAGGGCGCAACATCGTTG
* *
148926 GTTTATCCAACTAGAGCTAGGCTCATCCTTTATATCATCAGTAT
66 GCTTATCCAACTAGAGCTAGGCTCACCCTTTATATCATCAGTAT
* * * * * *
148970 ATTTGACTAGTGCTGGGCACACAAATTATCGGTTTAACCGACTAGCGCGGGGTGCAACATTGTTG
1 ATCTGACTAGTGTTGGGCACACAAATTGTCGGTTTAACCGACTAGCGCAGGGCGCAACATCGTTG
* *
149035 GCTTATCCAACTAGCGCTAGGCTCACCCTTTATATCGTCAGTAT
66 GCTTATCCAACTAGAGCTAGGCTCACCCTTTATATCATCAGTAT
* * * * * * ** * ** *
149079 ATCTGACTAGTGTTGGACACACCATTTGTTGGTTTAACCAAATAGCG-TTGGCGTAGTATTTGTT
1 ATCTGACTAGTGTTGGGCACACAAATTGTCGGTTTAACCGACTAGCGCAGGGCGCAACA-TCGTT
* *
149143 GG-TATATCCAACTAGAGCTGGGCTCACCTTTTATAT
65 GGCT-TATCCAACTAGAGCTAGGCTCACCCTTTATAT
149179 TGTCGGTTTA
Statistics
Matches: 176, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
108 6 0.03
109 170 0.97
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (109 bp):
ATCTGACTAGTGTTGGGCACACAAATTGTCGGTTTAACCGACTAGCGCAGGGCGCAACATCGTTG
GCTTATCCAACTAGAGCTAGGCTCACCCTTTATATCATCAGTAT
Found at i:149331 original size:2 final size:2
Alignment explanation
Indices: 149324--149363 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
149314 TGAAAGAATT
149324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
149364 CTTATTCGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:151203 original size:86 final size:85
Alignment explanation
Indices: 150934--151312 Score: 355
Period size: 86 Copynumber: 4.5 Consensus size: 85
150924 TAACTAGTAT
* * *
150934 ACGATGCTGCTCACACAAGATGTTAAGAATCCGCAACATATGCAGGATCTCAA-CCATCGATA-C
1 ACGATGCTGCTCACACAAGCTGTCAAGAATCCGCAACATATGCAGGATCT-AAGCCATCGA-AGG
* * *
150997 GATCTATAT-T---A-CCACAC
64 GTTCTAAATGTAACACCCACTC
* * * * * *
151014 ACGATGCTGCTCACACAAACTATCAAGAATCCACAACATATGTAAGATCTCAGCCAT-GAAGGGT
1 ACGATGCTGCTCACACAAGCTGTCAAGAATCCGCAACATATGCAGGATCTAAGCCATCGAAGGGT
* *
151078 CCATAAATGTAACACCTACTC
66 TC-TAAATGTAACACCCACTC
* * * *
151099 TCGATGCTGCTCACACAAGTTGTTAAGAATCCGCAACATATGCAGGATCTAAGTCATCGAAGGGT
1 ACGATGCTGCTCACACAAGCTGTCAAGAATCCGCAACATATGCAGGATCTAAGCCATCGAAGGGT
151164 TCGTAAATGTAACACCCACTC
66 TC-TAAATGTAACACCCACTC
* * *
151185 AAGATGCTGCTCATACAAGCTGTCACGAATCCGCAACATATGCAGGATCTCAA-CCATC-AGAGG
1 ACGATGCTGCTCACACAAGCTGTCAAGAATCCGCAACATATGCAGGATCT-AAGCCATCGA-AGG
* **
151248 GTCTATAAATGTATGACCCACTC
64 GT-TCTAAATGTAACACCCACTC
* * * * **
151271 TCGATGTTACTCACACAAGCTTTCAAGAATCCATAACATATG
1 ACGATGCTGCTCACACAAGCTGTCAAGAATCCGCAACATATG
151313 TAGAATATCA
Statistics
Matches: 241, Mismatches: 46, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
78 1 0.00
79 5 0.02
80 51 0.21
81 1 0.00
84 1 0.00
85 52 0.22
86 127 0.53
87 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (85 bp):
ACGATGCTGCTCACACAAGCTGTCAAGAATCCGCAACATATGCAGGATCTAAGCCATCGAAGGGT
TCTAAATGTAACACCCACTC
Found at i:153791 original size:54 final size:54
Alignment explanation
Indices: 153727--153835 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
153717 ACCAATTAAT
153727 TCGAATATAGAGGATAACAATCTCATAATAATCTCGAATGACATGAAATTTATC
1 TCGAATATAGAGGATAACAATCTCATAATAATCTCGAATGACATGAAATTTATC
153781 TCGAATATAGAGGATAACAATCTCATAATAATCTCGAATGACATGAAATTTATC
1 TCGAATATAGAGGATAACAATCTCATAATAATCTCGAATGACATGAAATTTATC
153835 T
1 T
153836 TGGCTTCCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (54 bp):
TCGAATATAGAGGATAACAATCTCATAATAATCTCGAATGACATGAAATTTATC
Found at i:155927 original size:20 final size:21
Alignment explanation
Indices: 155902--155940 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
155892 TTTCATAGCT
*
155902 TCAAAA-TCTAACAATTTCTA
1 TCAAAACTCAAACAATTTCTA
155922 TCAAAACTCAAACAATTTC
1 TCAAAACTCAAACAATTTC
155941 ACTCTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (21 bp):
TCAAAACTCAAACAATTTCTA
Found at i:156397 original size:3 final size:3
Alignment explanation
Indices: 156389--156473 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
156379 ATTTTCTCTT
156389 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
156437 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
156474 ATTGCACACC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:159044 original size:2 final size:2
Alignment explanation
Indices: 159039--159072 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
159029 GCTATATATA
*
159039 TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
159073 CGATTTATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:165190 original size:27 final size:27
Alignment explanation
Indices: 165152--165207 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
165142 TTGTGTTGAG
165152 ATATGAAAATGGTATGTTTGAAACTGA
1 ATATGAAAATGGTATGTTTGAAACTGA
165179 ATATGAAAATGGTATGTTTGAAACTGA
1 ATATGAAAATGGTATGTTTGAAACTGA
165206 AT
1 AT
165208 TGAGTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (27 bp):
ATATGAAAATGGTATGTTTGAAACTGA
Found at i:166133 original size:35 final size:34
Alignment explanation
Indices: 166094--166172 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
166084 ATAATATCTA
*
166094 AACAACCAAAACAGCAGCAAAAATAATAAAAAAAT
1 AACAACCAAAACAACA-CAAAAATAATAAAAAAAT
** * *
166129 AACAATAAAAACAACACCAAAATAGTAAAAAAAT
1 AACAACCAAAACAACACAAAAATAATAAAAAAAT
*
166163 AGC-ACCAAAA
1 AACAACCAAAA
166173 TAGTAAAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
33 5 0.14
34 18 0.50
35 13 0.36
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.09
Consensus pattern (34 bp):
AACAACCAAAACAACACAAAAATAATAAAAAAAT
Found at i:166209 original size:22 final size:21
Alignment explanation
Indices: 166135--166256 Score: 99
Period size: 22 Copynumber: 5.8 Consensus size: 21
166125 AAATAACAAT
*
166135 AAAAACAACACCAAAATAGTA
1 AAAAACAACACCAAAACAGTA
*
166156 AAAAA-ATAGCACCAAAATAGT-
1 AAAAACA-A-CACCAAAACAGTA
166177 AAAAA-AA-ACCAAAACAGTA
1 AAAAACAACACCAAAACAGTA
* *
166196 AAAACACAATACCAAAACAGCA
1 AAAA-ACAACACCAAAACAGTA
* * * *
166218 AAAAATAGCAACTAAAACAGCAA
1 AAAAACAAC-ACCAAAACAG-TA
166241 AAAAACAACACCAAAA
1 AAAAACAACACCAAAA
166257 TAACAATATA
Statistics
Matches: 83, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
18 10 0.12
19 4 0.05
20 3 0.04
21 16 0.19
22 42 0.51
23 8 0.10
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (21 bp):
AAAAACAACACCAAAACAGTA
Found at i:166696 original size:6 final size:6
Alignment explanation
Indices: 166685--166711 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
166675 CTTTATAATA
166685 TATATT TATATT TATATT TATATT TAT
1 TATATT TATATT TATATT TATATT TAT
166712 TTTTTTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:170286 original size:2 final size:2
Alignment explanation
Indices: 170279--170308 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
170269 TAATTAATTA
170279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
170309 GTTGGATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180849 original size:20 final size:21
Alignment explanation
Indices: 180824--180862 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
180814 CGATTCAAAT
180824 TTAAAT-AATATTTAAAATGA
1 TTAAATAAATATTTAAAATGA
*
180844 TTAAATAAATATTTTAAAT
1 TTAAATAAATATTTAAAAT
180863 TCAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
TTAAATAAATATTTAAAATGA
Found at i:186281 original size:21 final size:23
Alignment explanation
Indices: 186222--186285 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
186212 ATGTAATCTT
*
186222 AGATATGATATGTAGATATTAGA
1 AGATATGATTTGTAGATATTAGA
186245 AGATATGATTTTTGTA-ATATTAG-
1 AGATATGA--TTTGTAGATATTAGA
*
186268 AGATTTGATTTGTAGATA
1 AGATATGATTTGTAGATA
186286 GTTTTAGCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 6 0.17
22 3 0.08
23 15 0.42
24 7 0.19
25 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (23 bp):
AGATATGATTTGTAGATATTAGA
Found at i:194764 original size:128 final size:128
Alignment explanation
Indices: 194536--194793 Score: 453
Period size: 128 Copynumber: 2.0 Consensus size: 128
194526 AGTACTATCA
*
194536 TTTGTTTGCAACAATTATAATAAGGGTACAAGTAATGAGCAATTTAAATACAAAATTTACATTAC
1 TTTGTTTGCAACAATTATAATAAGGGTACAAGTAATGAGAAATTTAAATACAAAATTTACATTAC
194601 GAACTTATCGGACTGAATTATAGTTTCGGATAGGCTTCAGGGACTATTCTGCTAATTTCTTTT
66 GAACTTATCGGACTGAATTATAGTTTCGGATAGGCTTCAGGGACTATTCTGCTAATTTCTTTT
* *
194664 TTTGTTTGCAATAATTATAATAAGGGTACAAGTAATGAGAAATTTAAATACAAAATTTACATTAT
1 TTTGTTTGCAACAATTATAATAAGGGTACAAGTAATGAGAAATTTAAATACAAAATTTACATTAC
* * * *
194729 GAACTTATTGGATTGAATTGTAGTTTCGGATAGGCTTTAGGGACTATTCTGCTAATTTCTTTT
66 GAACTTATCGGACTGAATTATAGTTTCGGATAGGCTTCAGGGACTATTCTGCTAATTTCTTTT
194792 TT
1 TT
194794 ACTCGATTCG
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 123 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (128 bp):
TTTGTTTGCAACAATTATAATAAGGGTACAAGTAATGAGAAATTTAAATACAAAATTTACATTAC
GAACTTATCGGACTGAATTATAGTTTCGGATAGGCTTCAGGGACTATTCTGCTAATTTCTTTT
Found at i:199656 original size:25 final size:25
Alignment explanation
Indices: 199600--199689 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
199590 CTCTAAACTC
* *
199600 TGGCTCATAAGAGCGATATTCTGTT
1 TGGCTCGTAGGAGCGATATTCTGTT
*
199625 TGGCTCGTAGGAGCGATATTTTGTT
1 TGGCTCGTAGGAGCGATATTCTGTT
199650 TGGCTCGTAGGAGC-ATTATTCT-TT
1 TGGCTCGTAGGAGCGA-TATTCTGTT
*
199674 CTGGGCTCGTATGAGC
1 -T-GGCTCGTAGGAGC
199690 TAAATATTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.05
25 42 0.74
26 12 0.21
ACGTcount: A:0.18, C:0.17, G:0.29, T:0.37
Consensus pattern (25 bp):
TGGCTCGTAGGAGCGATATTCTGTT
Found at i:201828 original size:22 final size:24
Alignment explanation
Indices: 201803--201853 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
201793 GAGTTTTGCA
201803 TGATTTATAAAATGTG-AAATAT-
1 TGATTTATAAAATGTGTAAATATG
* * *
201825 TGATATATATATTGTGTAAATATG
1 TGATTTATAAAATGTGTAAATATG
201849 TGATT
1 TGATT
201854 GGCATGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 13 0.57
23 6 0.26
24 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (24 bp):
TGATTTATAAAATGTGTAAATATG
Found at i:202075 original size:47 final size:47
Alignment explanation
Indices: 202007--202118 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
201997 AAGGAGGAAG
* * *
202007 AAGTGGC-AGTTATCTGCAAAAGTGGTGATTTGTCCACAATTTTATT
1 AAGTGGCAATTTATCTGCAAAAGTGGTGACTTGTCCACAATTTTACT
* * * *
202053 AAGTGGTAATTTATCTGCAAAAGTGGTGGCTTGTTCACAATTTTGCT
1 AAGTGGCAATTTATCTGCAAAAGTGGTGACTTGTCCACAATTTTACT
202100 AAGTGGCAATTTATCTGCA
1 AAGTGGCAATTTATCTGCA
202119 TTACTGTGAT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 6 0.11
47 51 0.89
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (47 bp):
AAGTGGCAATTTATCTGCAAAAGTGGTGACTTGTCCACAATTTTACT
Found at i:202668 original size:24 final size:24
Alignment explanation
Indices: 202635--202697 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
202625 AGAAATAATC
202635 TTTAAGTTAAACTCTATTTATTTG
1 TTTAAGTTAAACTCTATTTATTTG
*
202659 TTTAAATTAAACTCTATTTATTTG
1 TTTAAGTTAAACTCTATTTATTTG
*
202683 TTTGAGTTAAACTCT
1 TTTAAGTTAAACTCT
202698 TATTACTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTAAGTTAAACTCTATTTATTTG
Found at i:202733 original size:56 final size:56
Alignment explanation
Indices: 202664--202779 Score: 214
Period size: 56 Copynumber: 2.1 Consensus size: 56
202654 ATTTGTTTAA
* *
202664 ATTAAACTCTATTTATTTGTTTGAGTTAAACTCTTATTACTCTAAATTATTTTATT
1 ATTAAACTATATTTATTTATTTGAGTTAAACTCTTATTACTCTAAATTATTTTATT
202720 ATTAAACTATATTTATTTATTTGAGTTAAACTCTTATTACTCTAAATTATTTTATT
1 ATTAAACTATATTTATTTATTTGAGTTAAACTCTTATTACTCTAAATTATTTTATT
202776 ATTA
1 ATTA
202780 TTTGACTTGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.53
Consensus pattern (56 bp):
ATTAAACTATATTTATTTATTTGAGTTAAACTCTTATTACTCTAAATTATTTTATT
Found at i:204680 original size:24 final size:24
Alignment explanation
Indices: 204651--204701 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
204641 AGAAATAATC
* *
204651 TTTCAATTAAATTATGTTTATTTG
1 TTTCAATTAAACTATATTTATTTG
*
204675 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTATATTTATTTG
204699 TTT
1 TTT
204702 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.59
Consensus pattern (24 bp):
TTTCAATTAAACTATATTTATTTG
Found at i:204720 original size:24 final size:24
Alignment explanation
Indices: 204667--204713 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
204657 TTAAATTATG
*
204667 TTTATTTGTTTCAATTAAACTCTA
1 TTTATTTGTTTCAATCAAACTCTA
* *
204691 TTTATTTGTTTGAGTCAAACTCT
1 TTTATTTGTTTCAATCAAACTCT
204714 TATTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTATTTGTTTCAATCAAACTCTA
Found at i:208445 original size:43 final size:43
Alignment explanation
Indices: 208364--208451 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
208354 TATCAGCACC
* *** * *
208364 ATCTTGCTTAAAGTGATAGTTCCTTTTATCGACGATCAAATTT
1 ATCTTGCTCAAAGTGATAAAACCTGTTATCGACAATCAAATTT
*
208407 ATCTTGCTCAAAGTGATAAAACCTGTTATTGACAATCAAATTT
1 ATCTTGCTCAAAGTGATAAAACCTGTTATCGACAATCAAATTT
208450 AT
1 AT
208452 TCTCCATGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (43 bp):
ATCTTGCTCAAAGTGATAAAACCTGTTATCGACAATCAAATTT
Found at i:208564 original size:21 final size:19
Alignment explanation
Indices: 208524--208572 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
208514 ATGTTTTATA
* *
208524 TTTGATTATTTTTAGCTAT
1 TTTGATTAATTTTAACTAT
*
208543 TTCATGATTAATTTTAATTAT
1 TT--TGATTAATTTTAACTAT
208564 TTTGATTAA
1 TTTGATTAA
208573 CTTATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 9 0.36
21 16 0.64
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.59
Consensus pattern (19 bp):
TTTGATTAATTTTAACTAT
Found at i:212311 original size:16 final size:17
Alignment explanation
Indices: 212285--212316 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
212275 TGAATTAGTT
212285 TTTTATTTATTTTTAAA
1 TTTTATTTATTTTTAAA
212302 TTTT-TTTATTTTTAA
1 TTTTATTTATTTTTAA
212317 TAATTTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATTTATTTTTAAA
Found at i:219035 original size:125 final size:125
Alignment explanation
Indices: 218870--219122 Score: 497
Period size: 125 Copynumber: 2.0 Consensus size: 125
218860 GAAGAGAGCA
218870 ATGCATCTCTTGAAGACAGCCTTGGTAAATACTTCCTTCTAATTGTCTTGCAAAATTTCATCATT
1 ATGCATCTCTTGAAGACAGCCTTGGTAAATACTTCCTTCTAATTGTCTTGCAAAATTTCATCATT
218935 TCCTTTTTTACATGGTTAGCACCTCTCCTCTGATTAATGGCTATGGATGATGGCTTTGCC
66 TCCTTTTTTACATGGTTAGCACCTCTCCTCTGATTAATGGCTATGGATGATGGCTTTGCC
218995 ATGCATCTCTTGAAGACAGCCTTGGTAAATACTTCCTTCTAATTGTCTTGCAAAATTTCATCATT
1 ATGCATCTCTTGAAGACAGCCTTGGTAAATACTTCCTTCTAATTGTCTTGCAAAATTTCATCATT
*
219060 TCCTTTTTTACATGGTTAGCACCTCTCCTCTGATTAATGGCTATGGATGATGGTTTTGCC
66 TCCTTTTTTACATGGTTAGCACCTCTCCTCTGATTAATGGCTATGGATGATGGCTTTGCC
219120 ATG
1 ATG
219123 AATACTCATT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 127 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.40
Consensus pattern (125 bp):
ATGCATCTCTTGAAGACAGCCTTGGTAAATACTTCCTTCTAATTGTCTTGCAAAATTTCATCATT
TCCTTTTTTACATGGTTAGCACCTCTCCTCTGATTAATGGCTATGGATGATGGCTTTGCC
Found at i:222578 original size:28 final size:29
Alignment explanation
Indices: 222538--222595 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
222528 CTTTTAGGGT
*
222538 TTTAGGGTTTTTTAGGGTTTATTTTTTTA
1 TTTAGGGTTTTTTAGGGTTTATTTATTTA
*
222567 TTTAGGG-TTTTTAGGTTTTATTTATTTA
1 TTTAGGGTTTTTTAGGGTTTATTTATTTA
222595 T
1 T
222596 AAAATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.66
Consensus pattern (29 bp):
TTTAGGGTTTTTTAGGGTTTATTTATTTA
Found at i:224864 original size:18 final size:19
Alignment explanation
Indices: 224841--224876 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
224831 ATTAGAAGGA
224841 CAAAATA-AATAAATTAGC
1 CAAAATAGAATAAATTAGC
*
224859 CAAAATAGATTAAATTAG
1 CAAAATAGAATAAATTAG
224877 TGGAATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.25
Consensus pattern (19 bp):
CAAAATAGAATAAATTAGC
Found at i:227459 original size:10 final size:10
Alignment explanation
Indices: 227444--227472 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
227434 TGGTAGTGGA
227444 TTTGAGAGAG
1 TTTGAGAGAG
227454 TTTGAGAGAG
1 TTTGAGAGAG
227464 -TTGAGAGAG
1 TTTGAGAGAG
227473 ATTTTGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (10 bp):
TTTGAGAGAG
Found at i:228509 original size:27 final size:27
Alignment explanation
Indices: 228441--228510 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
228431 ACTCGGGGGT
* *
228441 AAAATGGTAATTTTAGACTTATAGGGC
1 AAAATGGGAATTTTGGACTTATAGGGC
228468 AAAATGGGAATTTTGGACTTATAGGGC
1 AAAATGGGAATTTTGGACTTATAGGGC
228495 AAAATGGGAATTTTGG
1 AAAATGGGAATTTTGG
228511 GAAAGTTCGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (27 bp):
AAAATGGGAATTTTGGACTTATAGGGC
Found at i:228649 original size:59 final size:59
Alignment explanation
Indices: 228582--229041 Score: 350
Period size: 59 Copynumber: 7.8 Consensus size: 59
228572 ATAATCAGGA
* * *
228582 TCAAAAATGGAATTTTTGGATA-TTCGAGGGTAAAAGGGTAATTTTTGAAAGTTTTTGGG
1 TCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTAGGG
* * ** * *
228641 TCAAAAATGGAA-TTTTGGAAGTTTGGGGGTAAAATAATAATTTTT-AAGAGTTTTGGGG
1 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGA-AGTTTTAGGG
* * * * * *
228699 TTAAAAATGGAATTTTT-AAAGGTT-TAGGGGTAAAATGATAA-TTTTAGAAG-TTTCGAGG
1 TCAAAAATGGAATTTTTGGAA-GTTCGA-GGGTAAAATGGTAATTTTTGGAAGTTTTAG-GG
* * * *
228757 TC-AAAATCAAGATTTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGG
1 TCAAAAAT--GGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTAGGG
** * *
228817 TC-AAAATCAAGATTTTTGGAGGTTCAAGGGTAAAATGGTAATTTTTGGAAGTTTTAGGG
1 TCAAAAATGGA-ATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTAGGG
* * * * * * *
228876 TTAAAATTGAGATTTTTTGGAATTTTGAGGATAAAATGGTAATTTTTGGAAGTTTCAGGG
1 TCAAAAATG-GAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTAGGG
** * * * * *
228936 TCAAATCTAG-ATTTTTGGAAGTTCGAGGATAAAAAT-ATAATTTTTGGAAGTTTCAAGG
1 TCAAAAATGGAATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTGGAAGTTTTAGGG
* * * * *
228994 TCAAAAGTGGAATTTTGGAGAAGTTTGGGGGTCAAAAT-ATAATTTTTG
1 TCAAAAATGGAATTTTTG-GAAGTTCGAGGGT-AAAATGGTAATTTTTG
229042 AACACTTTAG
Statistics
Matches: 326, Mismatches: 56, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
57 12 0.04
58 102 0.31
59 112 0.34
60 95 0.29
61 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.37
Consensus pattern (59 bp):
TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTAGGG
Found at i:228656 original size:29 final size:29
Alignment explanation
Indices: 228624--228733 Score: 107
Period size: 29 Copynumber: 3.8 Consensus size: 29
228614 AAAGGGTAAT
* *
228624 TTTTGAAAGTTTTTGGGTCAAAAATGGAA
1 TTTTGAAAGTTTTGGGGTAAAAAATGGAA
* *
228653 TTTTGGAAGTTTGGGGGTAAAATAAT--AA
1 TTTTGAAAGTTTTGGGGTAAAA-AATGGAA
* *
228681 TTTTTAAGAGTTTTGGGGTTAAAAATGGAA
1 TTTTGAA-AGTTTTGGGGTAAAAAATGGAA
* *
228711 TTTTTAAAGGTTTAGGGGTAAAA
1 TTTTGAAA-GTTTTGGGGTAAAA
228734 TGATAATTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
28 10 0.15
29 32 0.48
30 24 0.36
ACGTcount: A:0.35, C:0.01, G:0.26, T:0.38
Consensus pattern (29 bp):
TTTTGAAAGTTTTGGGGTAAAAAATGGAA
Found at i:228741 original size:29 final size:29
Alignment explanation
Indices: 228660--228743 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 29
228650 GAATTTTGGA
* *
228660 AGTTTGGGGGTAAAATAATAATTTTTAAG
1 AGTTTAGGGGTAAAATGATAATTTTTAAG
* *
228689 AGTTTTGGGGTTAAAAATG-GAATTTTTAA-
1 AGTTTAGGGG-T-AAAATGATAATTTTTAAG
228718 AGGTTTAGGGGTAAAATGATAATTTT
1 A-GTTTAGGGGTAAAATGATAATTTT
228744 AGAAGTTTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
28 6 0.13
29 17 0.37
30 18 0.39
31 5 0.11
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (29 bp):
AGTTTAGGGGTAAAATGATAATTTTTAAG
Found at i:228762 original size:29 final size:28
Alignment explanation
Indices: 228730--229039 Score: 118
Period size: 29 Copynumber: 10.5 Consensus size: 28
228720 GTTTAGGGGT
*
228730 AAAATGATAATTTTAGAAGTTTCGAGGTC
1 AAAATGATAATTTTGGAAGTTT-GAGGTC
*
228759 AAAATCAAGAT-TTTTTGGAAGTTTGAGGGT-
1 AAAAT---GATAATTTTGGAAGTTTGA-GGTC
* *
228789 AAAATGGTAATTTTTGGAAGTTTTGGGGTC
1 AAAATGATAA-TTTTGGAAG-TTTGAGGTC
* * **
228819 AAAATCA-AGATTTTTGGAGGTTCAAGGGT-
1 AAAATGATA-A-TTTTGGAAGTTTGA-GGTC
* * *
228848 AAAATGGTAATTTTTGGAAGTTTTAGGGTT
1 AAAATGATAA-TTTTGGAAGTTTGA-GGTC
* * *
228878 AAAATTGAGATTTTTTGGAATTTTGAGGAT-
1 AAAA-TGATA-ATTTTGGAAGTTTGAGG-TC
* *
228908 AAAATGGTAATTTTTGGAAGTTTCAGGGTC
1 AAAATGATAA-TTTTGGAAGTTTGA-GGTC
* * *
228938 -AAAT-CTAGATTTTTGGAAGTTCGAGGATA
1 AAAATGATA-A-TTTTGGAAGTTTGAGG-TC
*
228967 AAAAT-ATAATTTTTGGAAGTTTCAAGGTC
1 AAAATGATAA-TTTTGGAAGTTT-GAGGTC
* *
228996 AAAAGTG-GAATTTTGGAGAAGTTTGGGGGTC
1 AAAA-TGATAATTTT-G-GAAGTTT-GAGGTC
229027 AAAAT-ATAATTTT
1 AAAATGATAATTTT
229040 TGAACACTTT
Statistics
Matches: 215, Mismatches: 39, Indels: 53
0.70 0.13 0.17
Matches are distributed among these distances:
27 2 0.01
28 4 0.02
29 99 0.46
30 62 0.29
31 45 0.21
32 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (28 bp):
AAAATGATAATTTTGGAAGTTTGAGGTC
Found at i:230945 original size:18 final size:17
Alignment explanation
Indices: 230924--230978 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
230914 TGTTTTGGAC
* *
230924 TTTTAATTTAATATTAAG
1 TTTTAATTCAAT-TTAAA
*
230942 TTTTAAATCAATTTAAA
1 TTTTAATTCAATTTAAA
*
230959 TTTTAATTAAATTTAAA
1 TTTTAATTCAATTTAAA
230976 TTT
1 TTT
230979 AAAAGATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 22 0.69
18 10 0.31
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTAATTCAATTTAAA
Found at i:230970 original size:11 final size:11
Alignment explanation
Indices: 230954--231022 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
230944 TTAAATCAAT
*
230954 TTAAATTTTAA
1 TTAAATTTAAA
230965 TTAAATTTAAA
1 TTAAATTTAAA
**
230976 TTTAAAAGATAAA
1 -TT-AAATTTAAA
230989 TTTAAATTTAAAA
1 -TTAAATTT-AAA
*
231002 ATAAATTTAAA
1 TTAAATTTAAA
231013 -TAAATTTAAA
1 TTAAATTTAAA
231023 CCCAATCTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
10 10 0.20
11 13 0.27
12 13 0.27
13 13 0.27
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:230974 original size:6 final size:6
Alignment explanation
Indices: 230951--231022 Score: 69
Period size: 6 Copynumber: 12.3 Consensus size: 6
230941 GTTTTAAATC
* **
230951 AATTTA AATTTT AA-TTA AATTTA AATTTAA AAGATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA AATTTA
**
230999 AAAATA AATTTA AA--TA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AA
231023 CCCAATCTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
4 4 0.08
5 4 0.08
6 40 0.77
7 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:231007 original size:18 final size:18
Alignment explanation
Indices: 230946--231013 Score: 93
Period size: 19 Copynumber: 3.8 Consensus size: 18
230936 ATTAAGTTTT
* *
230946 AAATCAATTTAAATTT-T
1 AAATAAATTTAAATTTAA
*
230963 AATTAAATTTAAATTTAA
1 AAATAAATTTAAATTTAA
230981 AAGATAAATTTAAATTTAA
1 AA-ATAAATTTAAATTTAA
231000 AAATAAATTTAAAT
1 AAATAAATTTAAAT
231014 AAATTTAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
17 14 0.31
18 14 0.31
19 17 0.38
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (18 bp):
AAATAAATTTAAATTTAA
Found at i:234202 original size:29 final size:30
Alignment explanation
Indices: 234165--234222 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
234155 TCCAAAAATT
*
234165 TTTTGACCCC-AAACTATCT-AAAAATTATA
1 TTTTAACCCCTAAACT-TCTCAAAAATTATA
*
234194 TTTTAACCCCTAAACTTTTCAAAAATTAT
1 TTTTAACCCCTAAACTTCTCAAAAATTAT
234223 GTTTGACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTTAACCCCTAAACTTCTCAAAAATTATA
Found at i:234236 original size:29 final size:29
Alignment explanation
Indices: 234184--234406 Score: 131
Period size: 29 Copynumber: 7.6 Consensus size: 29
234174 CAAACTATCT
* *
234184 AAAAATTATATTTTAACCCCTAAACTTTTC
1 AAAAATTATA-TTTGACCTCTAAACTTTTC
*
234214 AAAAATTATGTTTGACCTCTAAA-TTTTC
1 AAAAATTATATTTGACCTCTAAACTTTTC
* * * *
234242 AAAAAATTCAAATTT-ACCCCCAAACTTTCC
1 -AAAAATT-ATATTTGACCTCTAAACTTTTC
* * * *
234272 AAAAATTCAAAATT-ACCCCCAAAC-TTTC
1 AAAAATT-ATATTTGACCTCTAAACTTTTC
* *
234300 TAAAAATTCAAATTTGACCTC-AAACTTTCC
1 -AAAAATT-ATATTTGACCTCTAAACTTTTC
234330 AAAAATT-TGAATTTGACCTC-AAAC-TTTC
1 AAAAATTAT--ATTTGACCTCTAAACTTTTC
* *
234358 TAAAAATTCTAATTTGA-CTCCTAAACTTTCC
1 -AAAAATTAT-ATTTGACCT-CTAAACTTTTC
*
234389 AAAAATTCAAATTTGACC
1 AAAAATT-ATATTTGACC
234407 CGATTTTAAA
Statistics
Matches: 160, Mismatches: 18, Indels: 29
0.77 0.09 0.14
Matches are distributed among these distances:
28 13 0.08
29 101 0.63
30 42 0.26
31 4 0.03
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTATATTTGACCTCTAAACTTTTC
Found at i:234246 original size:58 final size:58
Alignment explanation
Indices: 234155--234395 Score: 244
Period size: 58 Copynumber: 4.2 Consensus size: 58
234145 CCTCAAGTTG
* * * *
234155 TCCAAAAATT-T-TTTGACCCCAAACTATCTAAAAATT-ATATTTTAACCCCTAAACTT
1 TCCAAAAATTATGTTTGACCTCAAACTTTCTAAAAATTCA-AATTTGACCCCTAAACTT
* * * *
234211 TTCAAAAATTATGTTTGACCTCTAAATTTTCAAAAAATTCAAATTT-ACCCCCAAACTT
1 TCCAAAAATTATGTTTGACCTC-AAACTTTCTAAAAATTCAAATTTGACCCCTAAACTT
*** * *
234269 TCCAAAAATTCAAAATT-ACCCCCAAACTTTCTAAAAATTCAAATTTGACCTC-AAACTT
1 TCCAAAAATT-ATGTTTGA-CCTCAAACTTTCTAAAAATTCAAATTTGACCCCTAAACTT
* *
234327 TCCAAAAATT-TGAATTTGACCTCAAACTTTCTAAAAATTCTAATTTGACTCCTAAACTT
1 TCCAAAAATTATG--TTTGACCTCAAACTTTCTAAAAATTCAAATTTGACCCCTAAACTT
234386 TCCAAAAATT
1 TCCAAAAATT
234396 CAAATTTGAC
Statistics
Matches: 152, Mismatches: 22, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
56 9 0.06
57 1 0.01
58 97 0.64
59 44 0.29
60 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (58 bp):
TCCAAAAATTATGTTTGACCTCAAACTTTCTAAAAATTCAAATTTGACCCCTAAACTT
Found at i:234277 original size:88 final size:87
Alignment explanation
Indices: 234166--234406 Score: 265
Period size: 88 Copynumber: 2.7 Consensus size: 87
234156 CCAAAAATTT
* * **
234166 TTTGACCCCAAACTATCTAAAAATTATATTTTAACCCCTAAACTTTTCAAAAATT-ATGTTTGAC
1 TTTGACCCCAAACTTTCTAAAAATTATAATTT-ACCCCTAAACTTTTCAAAAATTCAAATTTGAC
*
234230 CTCTAAATTTTCAAAAAATTCAAA
65 CTC-AAACTTTCAAAAAATTCAAA
* * *
234254 TTT-ACCCCCAAACTTTCCAAAAATTCA-AAATTACCCCCAAAC-TTTCTAAAAATTCAAATTTG
1 TTTGA-CCCCAAACTTTCTAAAAATT-ATAATTTACCCCTAAACTTTTC-AAAAATTCAAATTTG
* **
234316 ACCTCAAACTTTCCAAAAATTTGAA
63 ACCTCAAACTTTCAAAAAATTCAAA
* * * *
234341 TTTGACCTCAAACTTTCTAAAAATTCTAATTTGACTCCTAAACTTTCCAAAAATTCAAATTTGAC
1 TTTGACCCCAAACTTTCTAAAAATTATAATTT-ACCCCTAAACTTTTCAAAAATTCAAATTTGAC
234406 C
65 C
234407 CGATTTTAAA
Statistics
Matches: 127, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
86 4 0.03
87 58 0.46
88 61 0.48
89 4 0.03
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34
Consensus pattern (87 bp):
TTTGACCCCAAACTTTCTAAAAATTATAATTTACCCCTAAACTTTTCAAAAATTCAAATTTGACC
TCAAACTTTCAAAAAATTCAAA
Found at i:240229 original size:3 final size:3
Alignment explanation
Indices: 240221--240250 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
240211 TTCACATATT
240221 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
240251 ACACGACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:244010 original size:51 final size:51
Alignment explanation
Indices: 243897--244081 Score: 171
Period size: 51 Copynumber: 3.6 Consensus size: 51
243887 TTTCATTTAA
** * * *
243897 TACTCACGATGACA-TATAGTCATCGGACCTCTTGTTCCGTACAGAAATTCA--
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAG-GATTCATT
* * * *
243948 TACTCACGATGACTCTGAGTCATCGGACCTTTAATCCATCATA-TATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCAT-AAAGGATTCATT
* * * * *
243999 TGCTCATGATGACACTTAGTCATCTGATCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
244050 TACTCACGATGACACTTAGTCATCGAACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
244082 TCGTTTATAG
Statistics
Matches: 108, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
49 5 0.05
50 8 0.07
51 94 0.87
52 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:251207 original size:51 final size:50
Alignment explanation
Indices: 251152--251329 Score: 207
Period size: 51 Copynumber: 3.5 Consensus size: 50
251142 TAGAAATTCA
* **
251152 TACTCACGATGACACTGAGTCATC-AGACCTTTAATCTATCATAA-ATTCATT
1 TACTCACGATGACACTTAGTCATCGA-ACCTTTAATCCGT-A-AAGATTCATT
* * * *
251203 TACTCACGATGACACTTAGTTATCGTACTTTTAAACCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAA-GATTCATT
* * *
251254 TACTCACGATGAGACTTAGTCATCGAATCTTTAATCCGTAAAGGATTTATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAA-GATTCATT
251305 TACTCACGATGACACTTAGTCATCG
1 TACTCACGATGACACTTAGTCATCG
251330 GACCCTTTCG
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
49 2 0.02
50 1 0.01
51 106 0.97
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (50 bp):
TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGATTCATT
Found at i:256696 original size:3 final size:3
Alignment explanation
Indices: 256688--256713 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
256678 TTCACATATT
256688 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
256714 TTTCACACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:262398 original size:3 final size:3
Alignment explanation
Indices: 262390--262463 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
262380 AAATTCTTTA
262390 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
262438 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
262464 CACTAATTAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:264896 original size:36 final size:36
Alignment explanation
Indices: 264799--264897 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 36
264789 TGATAACAGG
* * * * *
264799 CATGACCTTTGGGTCAATAGGGAATAAAGTGAGCAT
1 CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAC
* *
264835 CATGACCTTTTGGTCAACAAAGAGTAAAATGAGCAC
1 CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAC
*
264871 CATGACCTTTGGGTAAACAAGGAGTAA
1 CATGACCTTTGGGTCAACAAGGAGTAA
264898 GCATGACCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAC
Found at i:264903 original size:28 final size:28
Alignment explanation
Indices: 264871--264925 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
264861 AAATGAGCAC
264871 CATGACCTTTGGGTAAACAAGGAGTAAG
1 CATGACCTTTGGGTAAACAAGGAGTAAG
* *
264899 CATGACCTTTGGGTCAACAGGGAGTAA
1 CATGACCTTTGGGTAAACAAGGAGTAA
264926 ATCAGACATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (28 bp):
CATGACCTTTGGGTAAACAAGGAGTAAG
Found at i:269993 original size:36 final size:36
Alignment explanation
Indices: 269946--270040 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
269936 TGGTTACAGG
* * * *
269946 CATGACTTTTGGGTTAATATGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAT
269982 CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAT
*
270018 CATGACCTTTAGGTCAACAAGGA
1 CATGACCTTTGGGTCAACAAGGA
270041 ATAAGCATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAAGGAGTAAAATGAGCAT
Found at i:278834 original size:38 final size:39
Alignment explanation
Indices: 278792--278871 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 39
278782 GTGGAAGTAT
278792 GATTATTTAATTGTTCTTTAAAAGGGA-TTTTACATTCG
1 GATTATTTAATTGTTCTTTAAAAGGGATTTTTACATTCG
278830 GATTATTTAATTGTTCTTTAAAAGGGATTTTTACATTCG
1 GATTATTTAATTGTTCTTTAAAAGGGATTTTTACATTCG
278869 GAT
1 GAT
278872 CAGTTTTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 27 0.66
39 14 0.34
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.47
Consensus pattern (39 bp):
GATTATTTAATTGTTCTTTAAAAGGGATTTTTACATTCG
Found at i:288158 original size:18 final size:18
Alignment explanation
Indices: 288135--288171 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
288125 CCAAAACAAG
288135 TATAAAGAATTCTCAAAT
1 TATAAAGAATTCTCAAAT
*
288153 TATAAATAATTCTCAAAT
1 TATAAAGAATTCTCAAAT
288171 T
1 T
288172 CACACAAGTT
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:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (18 bp):
TATAAAGAATTCTCAAAT
Found at i:288721 original size:40 final size:40
Alignment explanation
Indices: 288625--288721 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
288615 CTTCATAGGT
* *
288625 TCATAAGTCTTCCTTTCAATCAATATTATGCTCTATCGAG
1 TCATAAGTCTTCCTTTTAATCAATATTATGCTCTACCGAG
* * * *
288665 TCACAAGTCTTCCTTTTAATCACTCTTATGCTTTACCGAG
1 TCATAAGTCTTCCTTTTAATCAATATTATGCTCTACCGAG
288705 TCATAAGTCTTCCTTTT
1 TCATAAGTCTTCCTTTT
288722 TTTTAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.24, C:0.25, G:0.09, T:0.42
Consensus pattern (40 bp):
TCATAAGTCTTCCTTTTAATCAATATTATGCTCTACCGAG
Found at i:288785 original size:41 final size:41
Alignment explanation
Indices: 288748--288888 Score: 192
Period size: 41 Copynumber: 3.4 Consensus size: 41
288738 CACTCATTTT
* *
288748 GAGACATGATTCTTCCTTTAATATAATCTCATTCTCATCCT
1 GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCC
* *
288789 GAGACATGAGTCTTCCTTTAATATGATCTCATTCTTATCCC
1 GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCC
* * * *
288830 GAGACATGAGTATTCCTTTAATATAAATTCTCATGCTCAACTC
1 GAGACATGAGTCTTCCTTTAATAT-AA-TCTCATTCTCATCCC
288873 GAGACATGAGTCTTCC
1 GAGACATGAGTCTTCC
288889 ATTCAAATAT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 60 0.69
42 1 0.01
43 26 0.30
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (41 bp):
GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCC
Found at i:295884 original size:40 final size:40
Alignment explanation
Indices: 295840--295927 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
295830 TTCATAATTC
* *
295840 TTCCTTTTAATCAATCTTATGCTCTACCGAGTCACAAGTA
1 TTCCTTTTAATCAATATTATGCTCTACCGAATCACAAGTA
* * * * *
295880 TTCCTTTTAGTCACTATTATGCTCTACTGAATCATAAGTG
1 TTCCTTTTAATCAATATTATGCTCTACCGAATCACAAGTA
295920 TTCCTTTT
1 TTCCTTTT
295928 TAAAAACAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.43
Consensus pattern (40 bp):
TTCCTTTTAATCAATATTATGCTCTACCGAATCACAAGTA
Found at i:296084 original size:43 final size:41
Alignment explanation
Indices: 295953--296099 Score: 204
Period size: 41 Copynumber: 3.5 Consensus size: 41
295943 CGCTCATTTT
*
295953 GAGACATGGGTCTTCCTTTAATATAATCTCATTCTCATCCC
1 GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCC
*
295994 GAGACATGAGTCTTCCTTTAATATGATCTCATTCTCATCCC
1 GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCC
* * * * *
296035 GAGACATGAATCTTCCTTTATTATAAATTCCCATGCTCAACCC
1 GAGACATGAGTCTTCCTTTAATAT-AA-TCTCATTCTCATCCC
296078 GAGACATGAGTCTTCCATTTAA
1 GAGACATGAGTCTTCC-TTTAA
296100 AATAGAGTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
41 61 0.66
42 1 0.01
43 27 0.29
44 4 0.04
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (41 bp):
GAGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCC
Found at i:308343 original size:18 final size:18
Alignment explanation
Indices: 308320--308362 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
308310 GTTCAAAGTG
308320 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
308338 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
308356 TAATTAA
1 TAATTAA
308363 AAACATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Done.