Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006741.1 Hibiscus syriacus cultivar Beakdansim tig00016922_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 80390
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2742 original size:28 final size:28
Alignment explanation
Indices: 2680--2768 Score: 110
Period size: 28 Copynumber: 3.1 Consensus size: 28
2670 AATTATTCGA
* *
2680 AATACTTATTATTATG-GTTTAGATTTTCT
1 AATATTTATTATTATGAGTTT--ATTTTTT
2709 AATATTTATTATTATGAGTTTATTTTTT
1 AATATTTATTATTATGAGTTTATTTTTT
2737 AATATTTATTATTA-GAAGTTTATTTTTAT
1 AATATTTATTATTATG-AGTTTATTTTT-T
2766 AAT
1 AAT
2769 TTATTTTTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
27 1 0.02
28 31 0.56
29 19 0.35
30 4 0.07
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.58
Consensus pattern (28 bp):
AATATTTATTATTATGAGTTTATTTTTT
Found at i:5893 original size:18 final size:18
Alignment explanation
Indices: 5847--5882 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5837 AGGGTTCTAC
*
5847 GTGGTCCTATGGGACATA
1 GTGGTCCTACGGGACATA
5865 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
5883 TGTGTTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (18 bp):
GTGGTCCTACGGGACATA
Found at i:5920 original size:28 final size:28
Alignment explanation
Indices: 5865--5921 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
5855 ATGGGACATA
* *
5865 GTGGTCCTACGGGACATATGTGTTCTAC
1 GTGGTCCTACAGGACATATGTGTCCTAC
*
5893 GTGGTCTTACAGGACATA-GTGGTCCTAC
1 GTGGTCCTACAGGACATATGT-GTCCTAC
5921 G
1 G
5922 GGACAAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (28 bp):
GTGGTCCTACAGGACATATGTGTCCTAC
Found at i:8602 original size:23 final size:24
Alignment explanation
Indices: 8576--8621 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
8566 TTAAAATCTA
*
8576 ATAATCAATTTT-ATTTAAAAATC
1 ATAATCAATTTTCAATTAAAAATC
**
8599 ATAATTTATTTTCAATTAAAAAT
1 ATAATCAATTTTCAATTAAAAAT
8622 TGAATAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAATCAATTTTCAATTAAAAATC
Found at i:8928 original size:19 final size:20
Alignment explanation
Indices: 8904--8945 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
8894 TAATAGAATG
8904 TTAC-AAAGTAT-TGATATTT
1 TTACAAAAGTATAT-ATATTT
8923 TTACAAAAGTATATATATTT
1 TTACAAAAGTATATATATTT
8943 TTA
1 TTA
8946 AAATTGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 16 0.76
21 1 0.05
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (20 bp):
TTACAAAAGTATATATATTT
Found at i:9960 original size:44 final size:44
Alignment explanation
Indices: 9867--9961 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 44
9857 CACGTAGGAG
* *
9867 TATAGCACGGGGCAGGGGTCGCGCCTTACCTTTAATTCTGATTTATA
1 TATAGCACGGGGCAGGGGT--CGCCATACCTTTAA-TCTGATTAATA
*
9914 TATAGCGCGGGGCAGGGGT-GCCATACCTTTAA-CTGATATAATTA
1 TATAGCACGGGGCAGGGGTCGCCATACCTTTAATCTGAT-TAA-TA
9958 TATA
1 TATA
9962 AGGCACGGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
42 5 0.12
43 2 0.05
44 18 0.42
47 18 0.42
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (44 bp):
TATAGCACGGGGCAGGGGTCGCCATACCTTTAATCTGATTAATA
Found at i:13607 original size:35 final size:34
Alignment explanation
Indices: 13522--13608 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
13512 AAAATAATTT
* *
13522 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGA
* *
13556 TAAATGATAACCAAATTACAATAATTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGA
13594 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
13609 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGA
Found at i:14208 original size:27 final size:27
Alignment explanation
Indices: 14178--14235 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
14168 GCAGCAGCGG
*
14178 CATCGGGTAAGGGAATGGCGGCGGCGA
1 CATCGGGTAAGGGAAAGGCGGCGGCGA
* * * *
14205 CATCTGGTAATGGAAAGGCGGTGGCGG
1 CATCGGGTAAGGGAAAGGCGGCGGCGA
14232 CATC
1 CATC
14236 ATATATGGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.19, G:0.43, T:0.16
Consensus pattern (27 bp):
CATCGGGTAAGGGAAAGGCGGCGGCGA
Found at i:16161 original size:30 final size:30
Alignment explanation
Indices: 16109--16199 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
16099 CTACGGAACA
* * *
16109 TATGGACAATTTACCTAGGTTCTTTGGGACC
1 TATGGAC-AGTTACCGAGGTTCTTTGTGACC
* *
16140 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* *
16170 TATGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
16199 T
1 T
16200 CTAGATAGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.25
30 31 0.61
31 7 0.14
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:18419 original size:16 final size:16
Alignment explanation
Indices: 18394--18441 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
18384 TTTTATATTG
18394 TAAAAAATTAAATAAT
1 TAAAAAATTAAATAAT
*
18410 TAAAATATTAAATAAAT
1 TAAAAAATTAAAT-AAT
18427 TAAATAAATTAAATA
1 TAAA-AAATTAAATA
18442 CAAACTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 12 0.43
17 8 0.29
18 8 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAAATTAAATAAT
Found at i:18428 original size:9 final size:9
Alignment explanation
Indices: 18394--18441 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
18384 TTTTATATTG
18394 TAAA-AAAT
1 TAAATAAAT
18402 TAAAT-AAT
1 TAAATAAAT
*
18410 TAAA-ATAT
1 TAAATAAAT
18418 TAAATAAAT
1 TAAATAAAT
18427 TAAATAAAT
1 TAAATAAAT
18436 TAAATA
1 TAAATA
18442 CAAACTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 17 0.49
9 18 0.51
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAATAAAT
Found at i:19069 original size:17 final size:17
Alignment explanation
Indices: 19047--19087 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
19037 TCAATTTACT
*
19047 TTTAGATCACTTTTTA-G
1 TTTAGATCA-TTTTAAGG
19064 TTTAGATCATTTTAAGG
1 TTTAGATCATTTTAAGG
19081 TTTAGAT
1 TTTAGAT
19088 TTATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (17 bp):
TTTAGATCATTTTAAGG
Found at i:19552 original size:77 final size:76
Alignment explanation
Indices: 19434--19856 Score: 515
Period size: 77 Copynumber: 5.5 Consensus size: 76
19424 ATTCTAGTGT
* * * * * *
19434 GCAACCCATTTTATTAATAAAAATATTAACATTCTAAATCACAACTTATTTATTCGTGAACTATG
1 GCAA-CCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATG
*
19499 ATATTCTTGGGC
65 ACATTCTTGGGC
* *
19511 GCAACTCATTTTATTAATAAAAATATTAACATTCCAGATCACAATCTATTTCTTAGTGAAACATG
1 GCAAC-CATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATG
*
19576 ACATTCTTGAGC
65 ACATTCTTGGGC
* ** * * *
19588 GAAACTCATTTTATTAATAAAAATATTAACATTATAGATCGCAACATATTTCTTAGTGAATCATG
1 GCAAC-CATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATG
*
19653 ACATTCTTTGG-
65 ACATTCTTGGGC
* * * ** *
19664 TCAACCAATTTTATTAATAAAAATATTAAAATTTCAGATCGTAACCTATTTCTTAGTGAACCACG
1 GCAACC-ATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATG
*
19729 ACATTCTTAGGC
65 ACATTCTTGGGC
* * * * *
19741 GAAACCCATTTTATTAATAAGAATATGAACATTACATATCACAACCTATTTCTTAGTGAACCATG
1 GCAA-CCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATG
19806 ACATTCTTGGGC
65 ACATTCTTGGGC
*
19818 GCAACCTATTTTATTAATGAAAATATTAACATTCCAGAT
1 GCAACC-ATTTTATTAATAAAAATATTAACATTCCAGAT
19857 TGCAACATGT
Statistics
Matches: 295, Mismatches: 46, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
75 1 0.00
76 67 0.23
77 225 0.76
78 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (76 bp):
GCAACCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGTGAACCATGA
CATTCTTGGGC
Found at i:19734 original size:153 final size:152
Alignment explanation
Indices: 19436--19856 Score: 558
Period size: 153 Copynumber: 2.7 Consensus size: 152
19426 TCTAGTGTGC
* * * * *
19436 AACCCATTTTATTAATAAAAATATTAACATTCTAAATCACAACTTATTTATTCGTGAACTATGAT
1 AACCCATTTTATTAATAAAAATATTAACATTATAAATCACAACATATTTCTTAGTGAAC-ATGAC
*
19501 ATTCTTGGGCGCAACTCATTTTATTAATAAAAATATTAACATTCCAGATCACAATCTATTTCTTA
65 ATTCTTGGGCGCAAC-CATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTA
*
19566 GTGAAACATGACATTCTT-GAGCGA
129 GTGAAACACGACATTCTTAG-GCGA
* * *
19590 AACTCATTTTATTAATAAAAATATTAACATTATAGATCGCAACATATTTCTTAGTGAATCATGAC
1 AACCCATTTTATTAATAAAAATATTAACATTATAAATCACAACATATTTCTTAGTGAA-CATGAC
* * * * **
19655 ATTCTTTGG-TCAACCAATTTTATTAATAAAAATATTAAAATTTCAGATCGTAACCTATTTCTTA
65 ATTCTTGGGCGCAACC-ATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTA
*
19719 GTGAACCACGACATTCTTAGGCGA
129 GTGAAACACGACATTCTTAGGCGA
* * * * *
19743 AACCCATTTTATTAATAAGAATATGAACATTACATATCACAACCTATTTCTTAGTGAACCATGAC
1 AACCCATTTTATTAATAAAAATATTAACATTATAAATCACAACATATTTCTTAGTGAA-CATGAC
*
19808 ATTCTTGGGCGCAACCTATTTTATTAATGAAAATATTAACATTCCAGAT
65 ATTCTTGGGCGCAACC-ATTTTATTAATAAAAATATTAACATTCCAGAT
19857 TGCAACATGT
Statistics
Matches: 232, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
152 1 0.00
153 132 0.57
154 98 0.42
155 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (152 bp):
AACCCATTTTATTAATAAAAATATTAACATTATAAATCACAACATATTTCTTAGTGAACATGACA
TTCTTGGGCGCAACCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATTTCTTAGT
GAAACACGACATTCTTAGGCGA
Found at i:19844 original size:230 final size:230
Alignment explanation
Indices: 19435--19869 Score: 595
Period size: 230 Copynumber: 1.9 Consensus size: 230
19425 TTCTAGTGTG
* * * * * *
19435 CAACCCATTTTATTAATAAAAATATTAACATTCTAAATCACAACTTATTTATTCGTGAACTATGA
1 CAACCAATTTTATTAATAAAAATATTAAAATTCTAAATCACAACCTATTTATTAGTGAACCACGA
* * * * * * *
19500 TATTCTTGGGCGCAACTCATTTTATTAATAAAAATATTAACATTCCAGATCACAATCTATTTCTT
66 CATTCTTAGGCGAAACCCATTTTATTAATAAAAATATGAACATTACAGATCACAACCTATTTCTT
*
19565 AGTGAAACATGACATTCTTGAGCGAAACTCATTTTATTAATAAAAATATTAACATTATAGATCGC
131 AGTGAAACATGACATTCTTGAGCGAAACTCATTTTATTAATAAAAATATTAACATTACAGATCGC
19630 AACATATTTCTTAGTGAATCATGACATTCTTTGGT
196 AACATATTTCTTAGTGAATCATGACATTCTTTGGT
* ** *
19665 CAACCAATTTTATTAATAAAAATATTAAAATT-TCAGATCGTAACCTATTTCTTAGTGAACCACG
1 CAACCAATTTTATTAATAAAAATATTAAAATTCT-AAATCACAACCTATTTATTAGTGAACCACG
* *
19729 ACATTCTTAGGCGAAACCCATTTTATTAATAAGAATATGAACATTACATATCACAACCTATTTCT
65 ACATTCTTAGGCGAAACCCATTTTATTAATAAAAATATGAACATTACAGATCACAACCTATTTCT
* * * * * *
19794 TAGTGAACCATGACATTCTTGGGCGCAAC-CTATTTTATTAATGAAAATATTAACATTCCAGATT
130 TAGTGAAACATGACATTCTTGAGCGAAACTC-ATTTTATTAATAAAAATATTAACATTACAGATC
*
19858 GCAACATGTTTC
194 GCAACATATTTC
19870 CTAATAAGCC
Statistics
Matches: 176, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
229 2 0.01
230 174 0.99
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (230 bp):
CAACCAATTTTATTAATAAAAATATTAAAATTCTAAATCACAACCTATTTATTAGTGAACCACGA
CATTCTTAGGCGAAACCCATTTTATTAATAAAAATATGAACATTACAGATCACAACCTATTTCTT
AGTGAAACATGACATTCTTGAGCGAAACTCATTTTATTAATAAAAATATTAACATTACAGATCGC
AACATATTTCTTAGTGAATCATGACATTCTTTGGT
Found at i:19882 original size:77 final size:77
Alignment explanation
Indices: 19434--19906 Score: 490
Period size: 77 Copynumber: 6.1 Consensus size: 77
19424 ATTCTAGTGT
* * * * * * *
19434 GCAACCCATTTTATTAATAAAAATATTAACATT-CTAAATCACAACTTATTTATTCGTGAACTAT
1 GCAACCTATTTTATTAATAAAAATATTAACATTAC-AGATCGCAACATATTTCTTAGTGAACCAT
*
19498 GATATTCTTGGGC
65 GACATTCTTGGGC
* * *
19511 GCAA-CTCATTTTATTAATAAAAATATTAACATTCCAGATCACAATC-TATTTCTTAGTGAAACA
1 GCAACCT-ATTTTATTAATAAAAATATTAACATTACAGATCGCAA-CATATTTCTTAGTGAACCA
*
19574 TGACATTCTTGAGC
64 TGACATTCTTGGGC
* * *
19588 G-AAACTCATTTTATTAATAAAAATATTAACATTATAGATCGCAACATATTTCTTAGTGAATCAT
1 GCAACCT-ATTTTATTAATAAAAATATTAACATTACAGATCGCAACATATTTCTTAGTGAACCAT
*
19652 GACATTCTTTGG-
65 GACATTCTTGGGC
* * * * * * *
19664 TCAACCAATTTTATTAATAAAAATATTAAAATTTCAGATCGTAACCTATTTCTTAGTGAACCACG
1 GCAACCTATTTTATTAATAAAAATATTAACATTACAGATCGCAACATATTTCTTAGTGAACCATG
*
19729 ACATTCTTAGGC
66 ACATTCTTGGGC
* * * * * * *
19741 GAAACCCATTTTATTAATAAGAATATGAACATTACATATCACAACCTATTTCTTAGTGAACCATG
1 GCAACCTATTTTATTAATAAAAATATTAACATTACAGATCGCAACATATTTCTTAGTGAACCATG
19806 ACATTCTTGGGC
66 ACATTCTTGGGC
* * * * * *
19818 GCAACCTATTTTATTAATGAAAATATTAACATTCCAGATTGCAACATGTTTCCTAAT-AAGCCAT
1 GCAACCTATTTTATTAATAAAAATATTAACATTACAGATCGCAACATATTTCTTAGTGAA-CCAT
* * *
19882 GATATTTTTAGGC
65 GACATTCTTGGGC
19895 GCAACCGTATTT
1 GCAACC-TATTT
19907 CTTATATATA
Statistics
Matches: 334, Mismatches: 53, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
76 67 0.20
77 260 0.78
78 7 0.02
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (77 bp):
GCAACCTATTTTATTAATAAAAATATTAACATTACAGATCGCAACATATTTCTTAGTGAACCATG
ACATTCTTGGGC
Found at i:20094 original size:40 final size:40
Alignment explanation
Indices: 20005--20094 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 40
19995 ATTTTAGGCA
* * * * *
20005 CAACCTATTTTATTATTAAAAATATTAAGATTCTAGATTG
1 CAACATATTTTATCAATAAAAATATTAACATTCTAGATCG
* *
20045 CAACCTATTTTATCAATAAAAATATTAACATTAC-ATATCG
1 CAACATATTTTATCAATAAAAATATTAACATT-CTAGATCG
*
20085 TAACATATTT
1 CAACATATTT
20095 CTTAGTGAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 41 0.98
41 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (40 bp):
CAACATATTTTATCAATAAAAATATTAACATTCTAGATCG
Found at i:20538 original size:22 final size:21
Alignment explanation
Indices: 20513--20555 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20503 TTTTTCAAAA
20513 TAATATATAATTTTTAAAATTT
1 TAATATAT-ATTTTTAAAATTT
* *
20535 TAATTTATTTTTTTAAAATTT
1 TAATATATATTTTTAAAATTT
20556 AAATTTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATATATATTTTTAAAATTT
Found at i:31072 original size:18 final size:18
Alignment explanation
Indices: 31049--31084 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31039 CGAAAATTTT
31049 AAGGATGTTAGAAAATGG
1 AAGGATGTTAGAAAATGG
31067 AAGGATGTTAGAAAATGG
1 AAGGATGTTAGAAAATGG
31085 TTGAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (18 bp):
AAGGATGTTAGAAAATGG
Found at i:32024 original size:19 final size:19
Alignment explanation
Indices: 32000--32038 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31990 TTCTTCCTTC
32000 ATACGTGAGAGCCAAAGCA
1 ATACGTGAGAGCCAAAGCA
32019 ATACGTGAGAGCCAAAGCA
1 ATACGTGAGAGCCAAAGCA
32038 A
1 A
32039 ATGTGAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.10
Consensus pattern (19 bp):
ATACGTGAGAGCCAAAGCA
Found at i:38674 original size:3 final size:3
Alignment explanation
Indices: 38666--38694 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38656 TCCAGAGTTC
38666 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
38695 ATACGTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:39776 original size:18 final size:18
Alignment explanation
Indices: 39753--39805 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
39743 ATGGATTATC
39753 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
39771 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
*
39789 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
39806 AATTTTAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:40727 original size:45 final size:45
Alignment explanation
Indices: 40631--41352 Score: 1179
Period size: 45 Copynumber: 16.2 Consensus size: 45
40621 ATCAATAAAT
* * * * *
40631 TTACCATTTATCCCATAGGCTCGTAAACTTATTTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTA-TTTTACCAATATAC
* * *
40677 TTACCATTTATTCCATAAGCTCTTAAGCCTATTTTACTAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
40722 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
* *
40767 TTACCA-TTATTCCATAAGCTCGTAAGCCTATGTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
40811 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
*
40856 TTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
40900 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
*
40945 TTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
40989 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
*
41034 TTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
*
41078 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
*
41123 TTACCA-TTATTCCATAAGCTCGTAAGCCTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
* *
41167 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
*
41212 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
*
41257 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
** * *
41302 TTGTCA-TTATTCCATAAGCTCGTAAGCTTAATTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
41346 TT-CCATT
1 TTACCATT
41353 AACCTCATTT
Statistics
Matches: 642, Mismatches: 28, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
43 2 0.00
44 253 0.39
45 361 0.56
46 26 0.04
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATAC
Found at i:40809 original size:89 final size:89
Alignment explanation
Indices: 40631--41352 Score: 1203
Period size: 89 Copynumber: 8.1 Consensus size: 89
40621 ATCAATAAAT
* * * * *
40631 TTACCATTTATCCCATAGGCTCGTAAACTTATTTTTACCAACATACTTACCATTTATTCCATAAG
1 TTACCATTTATTCCATAAGCTCGTAAGCCTA-TTTTACCAATATACTTACCA-TTATTCCATAAG
* *
40696 CTCTTAAGCCTATTTTACTAACATAC
64 CTCGTAAGCCTATTTTACCAACATAC
40722 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
*
40787 CGTAAGCCTATGTTACCAACATAC
66 CGTAAGCCTATTTTACCAACATAC
40811 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
* *
40876 CGTAAGCTTATTTTACCAATATAC
66 CGTAAGCCTATTTTACCAACATAC
40900 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
* *
40965 CGTAAGCTTATTTTACCAATATAC
66 CGTAAGCCTATTTTACCAACATAC
40989 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
* *
41054 CGTAAGCTTATTTTACCAATATAC
66 CGTAAGCCTATTTTACCAACATAC
*
41078 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGCT
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
41143 CGTAAGCCTATTTTACCAACATAC
66 CGTAAGCCTATTTTACCAACATAC
* *
41167 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATTCCATAAGC
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCA-TTATTCCATAAGC
41232 TCGTAAGCCTATTTTACCAACATAC
65 TCGTAAGCCTATTTTACCAACATAC
* **
41257 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGTCATTATTCCATAAGCT
1 TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
* * *
41322 CGTAAGCTTAATTTACCAATATAC
66 CGTAAGCCTATTTTACCAACATAC
41346 TT-CCATT
1 TTACCATT
41353 AACCTCATTT
Statistics
Matches: 609, Mismatches: 21, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
88 5 0.01
89 472 0.78
90 105 0.17
91 27 0.04
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (89 bp):
TTACCATTTATTCCATAAGCTCGTAAGCCTATTTTACCAATATACTTACCATTATTCCATAAGCT
CGTAAGCCTATTTTACCAACATAC
Found at i:41614 original size:59 final size:56
Alignment explanation
Indices: 41449--42202 Score: 397
Period size: 59 Copynumber: 12.9 Consensus size: 56
41439 TCTCAGTGCT
* * * *
41449 CTATCTGGAAAAT-CATACGCTTAGTATGCTTCCCCTT-TCATTTTAGCACACAAAGTGCC
1 CTATCTGG-AAATCCATAC-ATTAGTATGATT-TCCTTATC-TTTTAGCACATAAA-TGCC
** * * ** *
41508 CTAT-TCAAAAATTCATACCATTAGTATAATTTTGTTACCATTTTAGCACATGAAATGCC
1 CTATCT-GGAAATCCATA-CATTAGTATGATTTCCTTATC-TTTTAGCACAT-AAATGCC
* * * * * * *
41567 CTATGTGAAAATCCATACCATTAGTATGATTTCCTTATCTTTGTAGCACCCTTAGTACT
1 CTATCTGGAAATCCATA-CATTAGTATGATTTCCTTATCTTT-TAGCA-CATAAATGCC
* * * * * *
41626 TTATTTGGAAATTCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAAAATGCC
1 CTATCTGGAAATCCATACA-TTAGTATGATTTCCTTATC-TTTTAGCACAT-AAATGCC
** * * * * * *
41685 CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGAACAGTCAGTGCT
1 CTATCTGGAAATCCATACATT-AGTATGATTTCCTTATCTTTTAGCACA-TAAATGCC
* * * * *
41743 CTATATGGAAATCTATACACTCAATATGATTTCCTTACCATTTTAGCACATAAAATGCC
1 CTATCTGGAAATCCATACA-TTAGTATGATTTCCTTATC-TTTTAGCACAT-AAATGCC
* ** * * * *
41802 CTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTC
1 CTATCTGGAAATCCATACATT-AGTATGATTTCCTTATCTTTTAGCACA-TAAATGC-C
* * * *
41861 C-ATATGGAAATCTATACACTCAGTATGATTTCCTTACCATTTTAGCACATAAAATGCC
1 CTATCTGGAAATCCATACA-TTAGTATGATTTCCTTATC-TTTTAGCACAT-AAATGCC
* * ** * * * *
41919 TTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCTC
1 CTATCTGGAAATCCATACATT-AGTATGATTTCCTTATCTTTTAGCACA-TAAATGC-C
* * * * * * * *
41978 C-ATATGGAAATCTATACACTCAGTATGATTTCCTTATCTTTGTAGCACCCTTAGTACT
1 CTATCTGGAAATCCATACA-TTAGTATGATTTCCTTATCTTT-TAGCA-CATAAATGCC
* * * * *
42036 TTATCTGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTATCACATAAAATGCC
1 CTATCTGGAAATCCATACA-TTAGTATGATTTCCTTATC-TTTTAGCACAT-AAATGCC
** * *
42095 CTATCTGGAAATCCATATTTTCAGTATGATTTCCTTATCATTTAGCACA-ACTAGTGCTC
1 CTATCTGGAAATCCATACATT-AGTATGATTTCCTTATCTTTTAGCACATA--AATGC-C
* * * *
42154 C-ATATGGAAATCTATACACTCAGTATGATTTCCTTATCATTTTACCACA
1 CTATCTGGAAATCCATACA-TTAGTATGATTTCCTTATC-TTTTAGCACA
42203 AAAGGTGTCA
Statistics
Matches: 530, Mismatches: 127, Indels: 76
0.72 0.17 0.10
Matches are distributed among these distances:
56 1 0.00
58 193 0.36
59 322 0.61
60 14 0.03
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (56 bp):
CTATCTGGAAATCCATACATTAGTATGATTTCCTTATCTTTTAGCACATAAATGCC
Found at i:41930 original size:176 final size:175
Alignment explanation
Indices: 41542--42195 Score: 608
Period size: 176 Copynumber: 3.7 Consensus size: 175
41532 TATAATTTTG
* * * ** *
41542 TTACCATTTTAGCACATGAAATGCCCTATGTGAAAATCCATACCATT-AGTATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATA-TTTTCAATATGATTTCCTTATC
* * * * ** * * *
41606 TTTGTAGCACCCT-TAGTACTTTATTTGGAAAT-TCATACACTCAGTATGATTCCCTTACCATTT
65 ATT-TAGCA-CATAAAGTGCTCCATATGGAAATCT-ATACACTCAGTATGATTTCCTTATCA-TT
* * * * *** * *
41669 TAGCACA-TAAAATGC-CCTATCTGGAAATCCATATTTTCAATATGATTTCC
126 TAGCACACT-CAGTACTCC-ATATGGAAATCCATACACTCAGTATGATTCCC
* * * * * * * *** *
41719 TTATCA-TTTAGAACAGT-CAGTGCTCTATATGGAAATCTATACACTCAATATGATTTCCTTACC
1 TTACCATTTTAGCACA-TAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATC
* * * *** *
41782 ATTTTAGCACATAAAATGC-CCTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTA
65 A-TTTAGCACATAAAGTGCTCC-ATATGGAAATCTATACACTCAGTATGATTTCCTTATCATTTA
* * *
41846 GCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
128 GCACACTCAGTACTCCATATGGAAATCCATACACTCAGTATGATTCCC
* *
41894 TTACCATTTTAGCACATAAAATGCCTTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
* *
41959 TTTAGCACACT-CAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCTTATCTTTGTAG
66 TTTAGCACA-TAAAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCTTATCATT-TAG
* * ** *
42023 CACCCTTAGTACTTTATCTGGAAATCCATACACTCAGTATGATTCCC
129 CACACTCAGTACTCCATATGGAAATCCATACACTCAGTATGATTCCC
* *
42070 TTACCATTTTATCACATAAAATGCCCTATCTGGAAATCCATATTTTCAGTATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
*
42135 TTTAGCACA-ACTAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCTTATCATTT
66 TTTAGCACATA-AAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCTTATCATTT
42196 TACCACAAAA
Statistics
Matches: 394, Mismatches: 68, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
175 97 0.25
176 289 0.73
177 8 0.02
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (175 bp):
TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
TTTAGCACATAAAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCTTATCATTTAGCA
CACTCAGTACTCCATATGGAAATCCATACACTCAGTATGATTCCC
Found at i:42025 original size:117 final size:117
Alignment explanation
Indices: 41542--42013 Score: 723
Period size: 117 Copynumber: 4.0 Consensus size: 117
41532 TATAATTTTG
* * * ** *
41542 TTACCATTTTAGCACATGAAATGCCCTATGTGAAAATCCATACCATT-AGTATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTATTTGGAAATCCATA-TTTTCAATATGATTTCCTTATC
* * * * ** * *
41606 TTTGTAGCACCCTTAGTACTTTATTTGGAAAT-TCATACACTCAGTATGATTCCC
65 ATT-TAGCACACTCAGTGCTCCATATGGAAATCT-ATACACTCAGTATGATTTCC
*
41660 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA
* * * *
41725 TTTAGAACAGTCAGTGCTCTATATGGAAATCTATACACTCAATATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
41777 TTACCATTTTAGCACATAAAATGCCCTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA
41842 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
*
41894 TTACCATTTTAGCACATAAAATGCCTTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA
41959 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
42011 TTA
1 TTA
42014 TCTTTGTAGC
Statistics
Matches: 330, Mismatches: 22, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
117 272 0.82
118 58 0.18
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (117 bp):
TTACCATTTTAGCACATAAAATGCCCTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
Found at i:42064 original size:117 final size:117
Alignment explanation
Indices: 41542--42195 Score: 687
Period size: 117 Copynumber: 5.6 Consensus size: 117
41532 TATAATTTTG
* * * * *
41542 TTACCATTTTAGCACATGAAATGCCCTATGTGAAAATCCATAC-CATTAGTATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATACTC-TCAATATGATTTCCTTATC
* * * * ** * *
41606 TTTGTAGCACCCTTAGTACTTTATTTGGAAAT-TCATACACTCAGTATGATTCCC
65 ATT-TAGCACACTCAGTGCTCCATATGGAAATCT-ATACACTCAGTATGATTTCC
* *
41660 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATACTCTCAATATGATTTCCTTATCA
* * * *
41725 TTTAGAACAGTCAGTGCTCTATATGGAAATCTATACACTCAATATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
* * *
41777 TTACCATTTTAGCACATAAAATGCCCTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATACTCTCAATATGATTTCCTTATCA
41842 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
* * * *
41894 TTACCATTTTAGCACATAAAATGCCTTATTTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATACTCTCAATATGATTTCCTTATCA
41959 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
* * * * * ** * * * *
42011 TTATC-TTTGTAGCACCCT-TAGTACTTTATCTGGAAATCCATACACTCAGTATGATTCCCTTAC
1 TTACCATTT-TAGCA-CATAAAATGCCCTATCTGGAAATCCATACTCTCAATATGATTTCCTTAT
* * * * * ***
42074 CATTTTATCACA-TAAAATGC-CCTATCTGGAAATCCATATTTTCAGTATGATTTCC
64 CA-TTTAGCACACT-CAGTGCTCC-ATATGGAAATCTATACACTCAGTATGATTTCC
* * * * * * *
42129 TTATCA-TTTAGCACA-ACTAGTGCTCC-ATATGGAAATCTATACACTCAGTATGATTTCCTTAT
1 TTACCATTTTAGCACATA-AAATGC-CCTATCTGGAAATCCATACTCTCAATATGATTTCCTTAT
42191 CATTT
64 CATTT
42196 TACCACAAAA
Statistics
Matches: 473, Mismatches: 52, Indels: 24
0.86 0.09 0.04
Matches are distributed among these distances:
116 7 0.01
117 359 0.76
118 107 0.23
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (117 bp):
TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATACTCTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
Found at i:53995 original size:14 final size:14
Alignment explanation
Indices: 53975--54008 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
53965 ATTCGGCCAT
53975 AGGGAAGAAAATTG
1 AGGGAAGAAAATTG
*
53989 GGGGAAGAAAATTG
1 AGGGAAGAAAATTG
54003 AGGGAA
1 AGGGAA
54009 AATGTTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.41, T:0.12
Consensus pattern (14 bp):
AGGGAAGAAAATTG
Found at i:56484 original size:20 final size:21
Alignment explanation
Indices: 56453--56498 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
56443 GATGGTATTA
*
56453 ATACTGAACCCATCAGTATCG
1 ATACTGAACCCAACAGTATCG
*
56474 ATACT-AACCCAAGAGTATCG
1 ATACTGAACCCAACAGTATCG
56494 ATACT
1 ATACT
56499 CCTATTAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (21 bp):
ATACTGAACCCAACAGTATCG
Found at i:57667 original size:64 final size:62
Alignment explanation
Indices: 57598--57776 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 62
57588 TGGGACACTT
*
57598 AGTGCATCGGTGCACTAAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAA-ATAGCCT
1 AGTGCATCGATGCA-T-AGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAT-GCC-
57662 G
62 G
* * *
57663 -GTGCATCGATGCATTGCTTG-TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCCG
1 AGTGCATCGATGCATAG---GATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCG
* * *
57726 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAG-GA-TGCATCGATGCATAAAATGCATTCGATGTT
57777 CAATTAAATC
Statistics
Matches: 99, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 92 0.93
65 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCG
Found at i:57795 original size:64 final size:61
Alignment explanation
Indices: 57619--57806 Score: 180
Period size: 64 Copynumber: 2.9 Consensus size: 61
57609 GCACTAAGGA
* * * ***
57619 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATTGCTTG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAAAT--CATGGTGCATCGATGCATGGAGAG
* * *
57683 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTC-CGAGTGCATCGATGCATGGAGAG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAA-A-TCATG-GTGCATCGATGCATGGAGAG
* *
57747 TGCATCGGTGCATGAAATGCATTCGATGTTCAATTAAATCATAGGTGCATCGATGCATGG
1 TGCATCGATGCATAAAATGCATTCGATGTTCAA--AAATCAT-GGTGCATCGATGCATGG
57807 TTTGATGCAT
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
63 7 0.07
64 95 0.89
65 4 0.04
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (61 bp):
TGCATCGATGCATAAAATGCATTCGATGTTCAAAAATCATGGTGCATCGATGCATGGAGAG
Found at i:65255 original size:64 final size:62
Alignment explanation
Indices: 65186--65364 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 62
65176 TGGGACACTT
*
65186 AGTGCATCGGTGCACTAAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAA-ATAGCCT
1 AGTGCATCGATGCA-T-AGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAT-GCC-
65250 G
62 G
* * *
65251 -GTGCATCGATGCATTGCTTG-TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCCG
1 AGTGCATCGATGCATAG---GATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCG
* * *
65314 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAG-GA-TGCATCGATGCATAAAATGCATTCGATGTT
65365 CAATTAAATC
Statistics
Matches: 99, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 92 0.93
65 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCG
Found at i:65383 original size:64 final size:61
Alignment explanation
Indices: 65207--65393 Score: 178
Period size: 64 Copynumber: 2.9 Consensus size: 61
65197 GCACTAAGGA
* * * ***
65207 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATTGCTTG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAAAT--CATGGTGCATCGATGCATGGAGAG
* * *
65271 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTC-CGAGTGCATCGATGCATGGAGAG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAA-A-TCATG-GTGCATCGATGCATGGAGAG
* *
65335 TGCATCGGTGCATGAAATGCATTCGATGTTCAATTAAATCATAGGTGCATCGATGCATG
1 TGCATCGATGCATAAAATGCATTCGATGTTCAA--AAATCAT-GGTGCATCGATGCATG
65394 ATTTGATTCA
Statistics
Matches: 106, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
63 7 0.07
64 94 0.89
65 4 0.04
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (61 bp):
TGCATCGATGCATAAAATGCATTCGATGTTCAAAAATCATGGTGCATCGATGCATGGAGAG
Found at i:72024 original size:15 final size:15
Alignment explanation
Indices: 71999--72034 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
71989 TTTTTTTTAG
71999 TTTAA-TTATTAATA
1 TTTAATTTATTAATA
72013 TTTAATTTATTAATA
1 TTTAATTTATTAATA
*
72028 ATTAATT
1 TTTAATT
72035 CATATTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATTTATTAATA
Found at i:73581 original size:44 final size:43
Alignment explanation
Indices: 73508--73606 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 43
73498 TGTATTAAAA
*
73508 TAAT-AATTACTAATTAATAATTTAGTATTTTTAATTAT-TCAT
1 TAATAAATTAATAATTAATAATTTAGTATTTTTAATTATCT-AT
* * *
73550 TAGA-AAATTAATAGATTAGTAATTTATTATTTTTTATTATCTAT
1 TA-ATAAATTAATA-ATTAATAATTTAGTATTTTTAATTATCTAT
73594 TAATAAATTAATA
1 TAATAAATTAATA
73607 TTTTTTAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.04
43 9 0.19
44 36 0.75
45 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (43 bp):
TAATAAATTAATAATTAATAATTTAGTATTTTTAATTATCTAT
Found at i:74869 original size:20 final size:20
Alignment explanation
Indices: 74825--74863 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
74815 TGTTATTGTG
*
74825 GTTTATGTTCATTTATGTTA
1 GTTTACGTTCATTTATGTTA
74845 GTTTACGTTCATTTATGTT
1 GTTTACGTTCATTTATGTT
74864 TATTTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.08, G:0.15, T:0.59
Consensus pattern (20 bp):
GTTTACGTTCATTTATGTTA
Found at i:74886 original size:10 final size:10
Alignment explanation
Indices: 74826--74870 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
74816 GTTATTGTGG
74826 TTTATGTTCA
1 TTTATGTTCA
74836 TTTATGTT-A
1 TTTATGTTCA
*
74845 GTTTACGTTCA
1 -TTTATGTTCA
*
74856 TTTATGTTTA
1 TTTATGTTCA
74866 TTTAT
1 TTTAT
74871 TGTGTTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 1 0.03
10 28 0.93
11 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.11, T:0.62
Consensus pattern (10 bp):
TTTATGTTCA
Found at i:78021 original size:4 final size:4
Alignment explanation
Indices: 78012--78038 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
78002 AACGAAAAGA
78012 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
78039 AAAGACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:78128 original size:4 final size:4
Alignment explanation
Indices: 78119--78143 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
78109 ATATACATAG
78119 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
78144 GCAAGAGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:78180 original size:13 final size:13
Alignment explanation
Indices: 78162--78188 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
78152 GGAAAATATA
78162 AAATAAAATAAAT
1 AAATAAAATAAAT
78175 AAATAAAATAAAT
1 AAATAAAATAAAT
78188 A
1 A
78189 TAAGATAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:78292 original size:39 final size:37
Alignment explanation
Indices: 78213--78298 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 37
78203 TGATAATATG
78213 TATATATA-AAATAAATAAAAACATAAAAAATAGTAAA
1 TATATATATAAATAAATAAAAACATAAAAAATA-TAAA
*
78250 TATATATATAAATTAAT-AAAACATATAATGAAAT-TAACA
1 TATATATATAAATAAATAAAAACATA-AA--AAATATAA-A
78289 TATATATATA
1 TATATATATA
78299 TATATATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
37 16 0.37
38 12 0.28
39 11 0.26
40 4 0.09
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (37 bp):
TATATATATAAATAAATAAAAACATAAAAAATATAAA
Found at i:78295 original size:2 final size:2
Alignment explanation
Indices: 78288--78339 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
78278 TGAAATTAAC
* * * *
78288 AT AT AT AT AT AT AT AT AT AT AT AT GT A- AT CT AA AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78329 AT AT AT AT AT A
1 AT AT AT AT AT A
78340 CTAAAGTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:78352 original size:29 final size:29
Alignment explanation
Indices: 78294--78351 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
78284 TAACATATAT
* *
78294 ATATATATATATATATATGTAATCTAAAA
1 ATATATATATATATATATCTAAACTAAAA
*
78323 ATATATATATATATATA-CTAAAGTAAAA
1 ATATATATATATATATATCTAAACTAAAA
78351 A
1 A
78352 AGAAAATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (29 bp):
ATATATATATATATATATCTAAACTAAAA
Found at i:78712 original size:30 final size:30
Alignment explanation
Indices: 78651--78712 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
78641 TTTTTAGGAG
* *
78651 TTTGAATCATAGTAGAACTCCATCCTATTT
1 TTTGAATCATAGTAAAACTCCATCATATTT
* *
78681 TTTGAATCCTAGTAAAACTCTATCAT-TTT
1 TTTGAATCATAGTAAAACTCCATCATATTT
78710 TTT
1 TTT
78713 AGGAGTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (30 bp):
TTTGAATCATAGTAAAACTCCATCATATTT
Found at i:79463 original size:78 final size:74
Alignment explanation
Indices: 79307--79463 Score: 163
Period size: 78 Copynumber: 2.1 Consensus size: 74
79297 GTAATCGAAC
* * * * *
79307 TCGAAGGTCTTTGATAACTGAAACCTTCTTGCTTGATTATACTACAAATGATGTGCCTTGGAGCT
1 TCGAAGGTCTTTGATAACAGAAACCTTCTAGCTTGATTATACTACAAATGATGTCCCTCGAAGCT
*
79372 GAGCGTAGT
66 GAGCGTAGA
* * * *
79381 TCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACCCTCG
1 TCGAAGGTCTTTGATAACAGA-AA-CCTTCTAG-CTTGA-TTATACTACAAATGATGT-CCCTCG
*
79446 AAGCTGAGTGTA-A
61 AAGCTGAGCGTAGA
79459 TCGAA
1 TCGAA
79464 CTCGAAGGCT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
74 18 0.27
75 2 0.03
76 7 0.10
77 5 0.07
78 21 0.31
79 14 0.21
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (74 bp):
TCGAAGGTCTTTGATAACAGAAACCTTCTAGCTTGATTATACTACAAATGATGTCCCTCGAAGCT
GAGCGTAGA
Found at i:79638 original size:37 final size:36
Alignment explanation
Indices: 79545--79646 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 36
79535 TTTTTTTTGT
* * * *
79545 GTTTCAAGAGAAACTGTCTCAAAAGGGACAAAATTT
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
*
79581 GTTTCAAAAGAAACTATCTCAAGAGAGACAAAACTTA
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTA
*
79618 GTTAT-AAAAGAAACTGTCTCAAGGGAGAC
1 GTT-TCAAAAGAAACTGTCTCAAGAGAGAC
79647 GAATTTTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
36 29 0.51
37 27 0.47
38 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (36 bp):
GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
Done.