Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003960.1 Hibiscus syriacus cultivar Beakdansim tig00008572_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: 70540
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:2937 original size:84 final size:83
Alignment explanation
Indices: 2785--3881 Score: 957
Period size: 84 Copynumber: 13.3 Consensus size: 83
2775 AAAACAAACT
* * * * ** *
2785 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGTTATCTACCACC-AAGACCTTTAAGTTCGACTACGC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACAC
*
2849 TCAGCTCGAGGGCACATC
66 TCAGCTCGAAGGCACATC
* *
2867 ATTTGAAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAGCCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA-CCAAAGACCTTCGAGTTCGACTACA
* *
2932 CTCAGCTCCAAGGCACATA
65 CTCAGCTCGAAGGCACATC
* * * * *
2951 ATTTGCAGCATAACTTAA-GTTGATAAGGGATATATGCCA--AAAGACCTTCGAGTTCGACTACA
1 ATTTGCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACA
*
3013 CTCAGCTCGAGGGCACATC
65 CTCAGCTCGAAGGCACATC
* * * *
3032 ATTTGTAGCATAATTCAAGGCTAGAAGGGTTATCTGCCAGCCAAAGACCTTCGAGATCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA-CCAAAGACCTTCGAGTTCGACTACA
*
3097 CTCAGCTCCAAGGCACATC
65 CTCAGCTCGAAGGCACATC
** * * * * * * ** * *
3116 ATTTGCAATATAGCTTAAGTCGAGAATGGCTATCTGCCA--AAAGACCCCCGAGTTTGATTACAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACAC
*
3179 TCAGCTTCGAAGGCATATC
66 TCAGC-TCGAAGGCACATC
* *
3198 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACA
*
3263 CTCAGCTCCAAGGCACATC
65 CTCAGCTCGAAGGCACATC
* * * * * * ** * * * *
3282 ATTTGCAGCATAGCTTAAGTCGAGAAGAGCTAT-T--TTCCAAAGACCCTCAAGTTCGATTACGC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACAC
* *
3344 TCAACTTCGAGGGCACATC
66 TCAGC-TCGAAGGCACATC
* * **
3363 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAGACCTTTAAGTTCGA-TCACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACT-ACA
*
3427 CTCAGCTC-AATAGCACATC
65 CTCAGCTCGAA-GGCACATC
* * * * * * *
3446 ATTTAC-GTTATAGCTCAAGGCTAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTTGATTACA
1 ATTTGCAG-CATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACA
*
3507 CTCAGCTTCGAGGGCACATC
65 CTCAGC-TCGAAGGCACATC
* * * * *
3527 ATTTTCAGCATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAGACCTTTGAGTTCGATTACAC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACAC
3592 TCAGCTC-AATGGCACATC
66 TCAGCTCGAA-GGCACATC
* * * * * * * *
3610 ATTTGCGGTATAGCTCAAGGCTAAAAGGGCTATCTG---CCAAAGACC-CCGAGTTTGA-TTCTA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTAC-A
* *
3670 CTCAGCTTCGAGGGTACATC
65 CTCAGC-TCGAAGGCACATC
* ** * * * *
3690 ATTTGCAGCATAACTAAAGGCTAGAAGGGTTATCTGCCAAAAAAGGCCTTTTGAGTCCGATTACA
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACC-TTCGAGTTCGACTACA
* **
3755 CTCAACTC-AATGGCATGTC
65 CTCAGCTCGAA-GGCACATC
* * * * * *
3774 ATTTGCGGTATAGCTCAAGGCTAGAAGGGCTATCTG---CCAAAGACATTCGAGTTCGACTACGC
1 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACAC
* * *
3836 TCAGCTCCAAGGTACAAC
66 TCAGCTCGAAGGCACATC
* * *
3854 ATTTACAGTATAACTCAAGGCAAGAAGG
1 ATTTGCAGCATAACTCAAGGCTAGAAGG
3882 ACTATCTGTC
Statistics
Matches: 807, Mismatches: 171, Indels: 76
0.77 0.16 0.07
Matches are distributed among these distances:
78 2 0.00
79 14 0.02
80 145 0.18
81 175 0.22
82 82 0.10
83 91 0.11
84 260 0.32
85 36 0.04
86 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (83 bp):
ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACAC
TCAGCTCGAAGGCACATC
Found at i:3489 original size:164 final size:163
Alignment explanation
Indices: 2795--3881 Score: 1204
Period size: 164 Copynumber: 6.6 Consensus size: 163
2785 ATTTGCAGCT
* * * * ** * *
2795 TAGCTCAAGGCCAGAAGGGTTATCTACCACCAAGACCTTTAAGTTCGACTACGCTCAGC-TCGAG
1 TAGCTCAAGGCTAGAAGGGCTATCTGCCA--AAGACCCTCGAGTTCGATTACACTCAGCTTCGAG
* *
2859 GGCACATCATTTGAAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAGCCAAAGACCTTCGAGTT
64 GGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA-ACAAAGACCTTCGAGTT
* * *
2924 CGACTACGCTCAGCTCCAAGGCACATAATTTGCAGCA
128 CGACTACACTCAGCTCCAAGGCACATCATTTGC-GTA
* * * * * * * *
2961 TAACTTAA-GTTGATAAGGGATATATGCCAAAAGACCTTCGAGTTCGACTACACTCAGC-TCGAG
1 TAGCTCAAGGCT-AGAAGGGCTATCTGCC-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAG
* * * *
3024 GGCACATCATTTGTAGCATAATTCAAGGCTAGAAGGGTTATCTGCCAGCCAAAGACCTTCGAGAT
64 GGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA-ACAAAGACCTTCGAGTT
* *
3089 CGACTACGCTCAGCTCCAAGGCACATCATTTGCAATA
128 CGACTACACTCAGCTCCAAGGCACATCATTTGC-GTA
* * * * * * *
3126 TAGCTTAAGTCGAGAATGGCTATCTGCCAAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAAG
1 TAGCTCAAGGCTAGAAGGGCTATCTGCC-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGG
* *
3191 GCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTC
65 GCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTC
* *
3256 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGCA
129 GACTACACTCAGCTCCAAGGCACATCATTTGC-GTA
* * * * * * * * *
3292 TAGCTTAAGTCGAGAAGAGCTATTTTCCAAAGACCCTCAAGTTCGATTACGCTCAACTTCGAGGG
1 TAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGG
* **
3357 CACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAGACCTTTAAGTTCGA
66 CACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGA
* *
3422 -TCACACTCAGCT-CAATAGCACATCATTTACGTTA
131 CT-ACACTCAGCTCCAA-GGCACATCATTTGCG-TA
*
3456 TAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGG
1 TAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGG
* * *
3521 CACATCATTTTCAGCATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAGACCTTTGAGTTCGA
66 CACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGA
*
3586 TTACACTCAGCT-CAATGGCACATCATTTGCGGTA
131 CTACACTCAGCTCCAA-GGCACATCATTTGC-GTA
* *
3620 TAGCTCAAGGCTAAAAGGGCTATCTGCCAAAGACCC-CGAGTTTGATT-CTACTCAGCTTCGAGG
1 TAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAC-ACTCAGCTTCGAGG
* * * * * *
3683 GTACATCATTTGCAGCATAACTAAAGGCTAGAAGGGTTATCTGCCAAAAAAGGCCTTTTGAGTCC
65 GCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACC-TTCGAGTTC
* * **
3748 GATTACACTCAACT-CAATGGCATGTCATTTGCGGTA
129 GACTACACTCAGCTCCAA-GGCACATCATTTGC-GTA
** * * * *
3784 TAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACATTCGAGTTCGACTACGCTCAGC-TCCAAGG
1 TAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGG
* * * * *
3848 TACAACATTTACAGTATAACTCAAGGCAAGAAGG
66 CACATCATTTGCAGCATAACTCAAGGCTAGAAGG
3882 ACTATCTGTC
Statistics
Matches: 812, Mismatches: 95, Indels: 30
0.87 0.10 0.03
Matches are distributed among these distances:
162 1 0.00
163 79 0.10
164 328 0.40
165 263 0.32
166 140 0.17
167 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (163 bp):
TAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGG
CACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGA
CTACACTCAGCTCCAAGGCACATCATTTGCGTA
Found at i:4424 original size:2 final size:2
Alignment explanation
Indices: 4417--4457 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
4407 TCGTCCCATT
* * *
4417 TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4458 GGTTTAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:4493 original size:39 final size:38
Alignment explanation
Indices: 4450--4867 Score: 372
Period size: 39 Copynumber: 11.3 Consensus size: 38
4440 ACATACATAC
* *
4450 ATATATATGGTTTAAAAACATTTTTAAAACATATATATA
1 ATATATA-GTTTTTAAAACATTTTTAAAACATATATATA
* *
4489 ATATATAGTTTTGAAAAC-TTGTTTGAAAACATTTATATA
1 ATATATAGTTTTTAAAACATT-TTT-AAAACATATATATA
*
4528 TTATATAGTTTTTAAAACATTTTTTAAAACATATATATA
1 ATATATAGTTTTTAAAACA-TTTTTAAAACATATATATA
* * * *
4567 TTATATAGCTTTTAAAACA-TTTTGAAA-ATATGTATA
1 ATATATAGTTTTTAAAACATTTTTAAAACATATATATA
* * *
4603 ATATATAGTTTTTAAAATA-TTTGAAAA-TTATATATA
1 ATATATAGTTTTTAAAACATTTTTAAAACATATATATA
*
4639 ATATATAGTTTTTTAAAAACATTTTT----GA-AT-TAT-
1 ATATATAG-TTTTT-AAAACATTTTTAAAACATATATATA
*
4672 -TATATAG-TTTTAAAACATTTTGAAAACATATATATA
1 ATATATAGTTTTTAAAACATTTTTAAAACATATATATA
* * *
4708 TTATATAGTTTTTAAAACATTTTAAAAACATATATACA
1 ATATATAGTTTTTAAAACATTTTTAAAACATATATATA
* * * *
4746 TTATATAATTTTTAAAACGTTTTTGAAA-ATATATATA
1 ATATATAGTTTTTAAAACATTTTTAAAACATATATATA
* *
4783 ATATATAAGTTTTTAAAATAATTTTTGAAA-ATATATAT-
1 ATATAT-AGTTTTTAAAA-CATTTTTAAAACATATATATA
* * * *
4821 -TATATAGTTTTGAAAATTATTTTTTAAACATATATGT-
1 ATATATAGTTTTTAAAA-CATTTTTAAAACATATATATA
4858 -TATATAGTTT
1 ATATATAGTTT
4868 AAAAAATGTT
Statistics
Matches: 323, Mismatches: 36, Indels: 42
0.81 0.09 0.10
Matches are distributed among these distances:
29 10 0.03
30 4 0.01
32 7 0.02
33 1 0.00
34 5 0.02
35 5 0.02
36 65 0.20
37 56 0.17
38 78 0.24
39 87 0.27
40 3 0.01
41 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (38 bp):
ATATATAGTTTTTAAAACATTTTTAAAACATATATATA
Found at i:4717 original size:37 final size:36
Alignment explanation
Indices: 4669--4872 Score: 168
Period size: 37 Copynumber: 5.5 Consensus size: 36
4659 ATTTTTGAAT
4669 TATTATATAGTTTTAAAACATTTTGAAAACATATATA
1 TATTATATAGTTTTAAAACATTTTG-AAACATATATA
*
4706 TATTATATAGTTTTTAAAACATTTTAAAAACATATATA
1 TATTATATAG-TTTTAAAACATTTT-GAAACATATATA
* * *
4744 CATTATATAATTTTTAAAACGTTTTTGAAA-ATATATA
1 TATTATAT-AGTTTTAAAAC-ATTTTGAAACATATATA
* *
4781 TAATATATAAGTTTTTAAAATAATTTTTG-AA-A-ATATA
1 TATTATAT-AG-TTTTAAAA-CA-TTTTGAAACATATATA
* *
4818 TATTATATAGTTTTGAAAATTATTTTTTAAAC--ATATA
1 TATTATATAGTTTT-AAAA-CA-TTTTGAAACATATATA
* *
4855 TGTTATATAGTTTAAAAA
1 TATTATATAGTTTTAAAA
4873 ATGTTTTTTT
Statistics
Matches: 142, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
35 4 0.03
36 17 0.12
37 56 0.39
38 55 0.39
39 10 0.07
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
TATTATATAGTTTTAAAACATTTTGAAACATATATA
Found at i:4728 original size:67 final size:68
Alignment explanation
Indices: 4604--4730 Score: 188
Period size: 68 Copynumber: 1.9 Consensus size: 68
4594 ATATGTATAA
* *
4604 TATATAGTTTTTAAAATATTTGAAAATTATATATAATATATAGTTTTTTAAAAACATTTTTGAAT
1 TATATAGTTTTAAAAATATTTGAAAAATATATATAATATATAGTTTTTTAAAAACATTTTTGAAT
4669 TAT
66 TAT
*
4672 TATATAGTTTTAAAACAT-TTTGAAAACATATATATATTATATAG-TTTTT-AAAACATTTT
1 TATATAGTTTTAAAA-ATATTTGAAAA-ATATATATAATATATAGTTTTTTAAAAACATTTT
4731 AAAAACATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
67 10 0.19
68 27 0.50
69 17 0.31
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (68 bp):
TATATAGTTTTAAAAATATTTGAAAAATATATATAATATATAGTTTTTTAAAAACATTTTTGAAT
TAT
Found at i:4763 original size:105 final size:104
Alignment explanation
Indices: 4565--4772 Score: 287
Period size: 105 Copynumber: 2.0 Consensus size: 104
4555 AACATATATA
* *
4565 TATTATATAGCTTTTAAAACATTTTGAAAATATGTATAATATATAGTTTTTAAAATATTTGAAAA
1 TATTATATAGCTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAACATTTGAAAA
** *
4630 TTATATATAATATATAGTTTTTTAAAAACATTTTTGAAT
66 ACATATATAATATATAGATTTTTAAAAACATTTTTGAAT
* *
4669 TATTATATAG-TTTTAAAACATTTTGAAAACATATATATATTATATAGTTTTTAAAACATTTTAA
1 TATTATATAGCTTTTAAAACATTTTG-AAA-ATATATATAATATATAGTTTTTAAAACATTTGAA
*
4733 AAACATATATACATTATATA-ATTTTT-AAAACGTTTTTGAA
64 AAACATATATA-A-TATATAGATTTTTAAAAACATTTTTGAA
4773 AATATATATA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
103 15 0.16
104 13 0.14
105 52 0.57
106 6 0.07
107 6 0.07
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (104 bp):
TATTATATAGCTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAACATTTGAAAA
ACATATATAATATATAGATTTTTAAAAACATTTTTGAAT
Found at i:4880 original size:35 final size:35
Alignment explanation
Indices: 4522--4880 Score: 158
Period size: 36 Copynumber: 9.9 Consensus size: 35
4512 TGAAAACATT
*
4522 TATATATTATATAGTTTTTAAAA-CATTTTTTAAAACATA
1 TATATATTATATAG-TTTTAAAATAATTTTTT--AA-A-A
* *
4561 TATATATTATATAGCTTTTAAAA-CA-TTTTGAAAA
1 TATATATTATATAG-TTTTAAAATAATTTTTTAAAA
* *
4595 TATGTATAATATATAGTTTTTAAAAT-A--TTTGAAAA
1 TA--TATATTATATAG-TTTTAAAATAATTTTTTAAAA
*
4630 TTATATATAATATATAGTTTTTTAAAA-ACA-TTTTT--GA
1 -TATATAT--TATATAG--TTTTAAAATA-ATTTTTTAAAA
* **
4667 -AT-TATTATATAGTTTTAAAA-CATTTTGAAAACATA
1 TATATATTATATAGTTTTAAAATAATTTT-TTAA-A-A
* **
4702 TATATATTATATAGTTTTTAAAA-CATTTTAAAAACA
1 TATATATTATATAG-TTTTAAAATAATTTTTTAAA-A
* ** *
4738 TATATACATTATATAATTTTTAAAA-CGTTTTTGAAAA
1 TATAT--ATTATAT-AGTTTTAAAATAATTTTTTAAAA
*
4775 TATATATAATATATAAGTTTTTAAAATAATTTTTGAAAA
1 TATATAT--TATAT-AG-TTTTAAAATAATTTTTTAAAA
*
4814 TATATATTATATAGTTTTGAAAATTATTTTTTAAACA
1 TATATATTATATAGTTTT-AAAATAATTTTTTAAA-A
*
4851 TATATGTTATATAG-TTTAAAA-AATGTTTTT
1 TATATATTATATAGTTTTAAAATAAT-TTTTT
4881 TTTATTATAT
Statistics
Matches: 268, Mismatches: 23, Indels: 62
0.76 0.07 0.18
Matches are distributed among these distances:
29 1 0.00
30 11 0.04
32 7 0.03
34 12 0.04
35 27 0.10
36 59 0.22
37 56 0.21
38 50 0.19
39 45 0.17
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (35 bp):
TATATATTATATAGTTTTAAAATAATTTTTTAAAA
Found at i:4923 original size:31 final size:30
Alignment explanation
Indices: 4879--4936 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
4869 AAAAATGTTT
4879 TTTTTATTATATTTATTATTA-TTATTTACC
1 TTTTTATTATATTTATT-TTATTTATTTACC
*
4909 TTTTTATTTTTATTTATTTTATTTATTT
1 TTTTTA-TTATATTTATTTTATTTATTT
4937 TGTTTATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTTTATTATATTTATTTTATTTATTTACC
Found at i:4930 original size:9 final size:9
Alignment explanation
Indices: 4880--4944 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
4870 AAAATGTTTT
4880 TTTTA-TTA
1 TTTTATTTA
4888 TATTTA-TTA
1 T-TTTATTTA
4897 TTATTATTTA
1 TT-TTATTTA
**
4907 CCTT-TTTA
1 TTTTATTTA
4915 TTTTTATTTA
1 -TTTTATTTA
4925 TTTTATTTA
1 TTTTATTTA
*
4934 TTTTGTTTA
1 TTTTATTTA
4943 TT
1 TT
4945 ACTTTTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
8 6 0.13
9 34 0.72
10 7 0.15
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:4944 original size:40 final size:36
Alignment explanation
Indices: 4876--4955 Score: 90
Period size: 40 Copynumber: 2.1 Consensus size: 36
4866 TTAAAAAATG
4876 TTTTTTTTATTATATTTATTATTATTATTTACCTTTTT
1 TTTTTTTTATTATATTTATTATTATTA-TTA-CTTTTT
* *
4914 ATTTTTATTTATTTTATTTATT-TTGTTTATTACTTTTT
1 -TTTTT-TTTATTATATTTATTATT-ATTATTACTTTTT
4952 TTTT
1 TTTT
4956 CTTTCTTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 4 0.11
38 6 0.16
39 10 0.27
40 17 0.46
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (36 bp):
TTTTTTTTATTATATTTATTATTATTATTACTTTTT
Found at i:4955 original size:18 final size:17
Alignment explanation
Indices: 4910--4969 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
4900 TTATTTACCT
*
4910 TTTTATTTTTATTTATT-
1 TTTT-TTTTTCTTTATTC
*
4927 TTATTTATTTTGTTTATTAC
1 TT-TTT-TTTTCTTTATT-C
*
4947 TTTTTTTTTCTTTCTTC
1 TTTTTTTTTCTTTATTC
4964 TTTTTT
1 TTTTTT
4970 CGTTTTGTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 10 0.28
18 21 0.58
19 3 0.08
20 2 0.06
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTTTTTTCTTTATTC
Found at i:6932 original size:2 final size:2
Alignment explanation
Indices: 6925--6953 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6915 ACACGTGTGC
6925 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
6954 ATTTGCACCA
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:8200 original size:4 final size:4
Alignment explanation
Indices: 8191--8230 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
8181 ATTTTCTTCC
8191 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
8231 CTTCTATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:8605 original size:27 final size:26
Alignment explanation
Indices: 8585--8674 Score: 153
Period size: 27 Copynumber: 3.3 Consensus size: 26
8575 ATCATAAGGA
8585 GAAGATGAATGGATCACATCAAGCATG
1 GAAGATGAATGGATCACATCAAGCA-G
8612 GAAGATGAATGGATCACATCAAGCATG
1 GAAGATGAATGGATCACATCAAGCA-G
8639 GAAGATGAATGGATCACATCAAGCATG
1 GAAGATGAATGGATCACATCAAGCA-G
8666 GAAGATGAA
1 GAAGATGAA
8675 GAGGAAAGCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.42, C:0.13, G:0.27, T:0.18
Consensus pattern (26 bp):
GAAGATGAATGGATCACATCAAGCAG
Found at i:8718 original size:18 final size:18
Alignment explanation
Indices: 8695--8747 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
8685 GCAACACCAA
8695 CGGAGTAAGAAGAAGAAT
1 CGGAGTAAGAAGAAGAAT
*
8713 CGGAGTAAGAAGAAAAAT
1 CGGAGTAAGAAGAAGAAT
*
8731 CAGAGTAAGAAGAAGAA
1 CGGAGTAAGAAGAAGAA
8748 GAAAAAGAAG
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:0.55, C:0.06, G:0.30, T:0.09
Consensus pattern (18 bp):
CGGAGTAAGAAGAAGAAT
Found at i:10417 original size:2 final size:2
Alignment explanation
Indices: 10410--10466 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
10400 CCAATTAATC
10410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10452 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
10467 AACATGTTAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12261 original size:17 final size:16
Alignment explanation
Indices: 12243--12311 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 16
12233 TTATTTAATA
12243 AAATTTTATATTTTTT
1 AAATTTTATATTTTTT
*
12259 AAATGATTA-ATTATTTAAT
1 AAAT-TTTATATT-TTT--T
12278 AAAATTTTATATTTTTT
1 -AAATTTTATATTTTTT
*
12295 AAATTTAAATATTTTTT
1 AAATTT-TATATTTTTT
12312 TACATGAACC
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
16 13 0.30
17 16 0.37
19 7 0.16
20 7 0.16
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
AAATTTTATATTTTTT
Found at i:12273 original size:36 final size:36
Alignment explanation
Indices: 12226--12298 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
12216 AACCCCTACT
12226 TGATTAATTATTTAATAAAATTTTATATTTTTTAAA
1 TGATTAATTATTTAATAAAATTTTATATTTTTTAAA
12262 TGATTAATTATTTAATAAAATTTTATATTTTTTAAA
1 TGATTAATTATTTAATAAAATTTTATATTTTTTAAA
12298 T
1 T
12299 TTAAATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (36 bp):
TGATTAATTATTTAATAAAATTTTATATTTTTTAAA
Found at i:12280 original size:19 final size:19
Alignment explanation
Indices: 12226--12280 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
12216 AACCCCTACT
12226 TGATTAATTATTTAATAAAA
1 TGATTAATTATTTAAT-AAA
*
12246 T-TTTATATT-TTT--TAAA
1 TGATTA-ATTATTTAATAAA
12262 TGATTAATTATTTAATAAA
1 TGATTAATTATTTAATAAA
12281 ATTTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
16 7 0.25
17 7 0.25
19 10 0.36
20 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TGATTAATTATTTAATAAA
Found at i:13071 original size:31 final size:31
Alignment explanation
Indices: 13000--13073 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
12990 ATATTTTTAT
**
13000 TTCGGGTCGATTCAGGTTTCTCTGTCATATA
1 TTCGGGTCGGGTCAGGTTTCTCTGTCATATA
*
13031 TTCGGGTCGGGTCGGGTTTCTCTGTCATATA
1 TTCGGGTCGGGTCAGGTTTCTCTGTCATATA
13062 TTCGGGTCGGGT
1 TTCGGGTCGGGT
13074 GAAAACTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.11, C:0.19, G:0.31, T:0.39
Consensus pattern (31 bp):
TTCGGGTCGGGTCAGGTTTCTCTGTCATATA
Found at i:13556 original size:45 final size:45
Alignment explanation
Indices: 13491--13583 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
13481 TTATTGGTTC
*
13491 ATCGAGCATATTTAAAGATAAGAGATTTTAAAGAATGCTTTTGCA
1 ATCGAGCATATTTAAAGATAAAAGATTTTAAAGAATGCTTTTGCA
*
13536 ATCGAGCATATTTAAGGATAAAAGATTTTAAAGAATGCTTTTGCA
1 ATCGAGCATATTTAAAGATAAAAGATTTTAAAGAATGCTTTTGCA
13581 ATC
1 ATC
13584 AATATTTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (45 bp):
ATCGAGCATATTTAAAGATAAAAGATTTTAAAGAATGCTTTTGCA
Found at i:15529 original size:19 final size:20
Alignment explanation
Indices: 15485--15538 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
15475 CTTGACAACG
*
15485 TAGAAAAATAAAATAAAAAA
1 TAGAAAAATAAAACAAAAAA
*
15505 TAAGAAAAA-AAAACAAACAA
1 T-AGAAAAATAAAACAAAAAA
15525 TAGAAAAATTAAAA
1 TAGAAAAA-TAAAA
15539 ATGGTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 7 0.24
20 11 0.38
21 11 0.38
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.13
Consensus pattern (20 bp):
TAGAAAAATAAAACAAAAAA
Found at i:15865 original size:28 final size:28
Alignment explanation
Indices: 15792--15871 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 28
15782 GTATTTGTAA
** *
15792 TAAACCCTAAATTTTAAAATCAAAAACC
1 TAAACCCTAAATTTTAATCTCTAAAACC
* *
15820 TAAACCCTAACTTTTAATCTCTAAACCC
1 TAAACCCTAAATTTTAATCTCTAAAACC
* *
15848 TAAACCCTAAATATTAATCCCTAA
1 TAAACCCTAAATTTTAATCTCTAA
15872 TCCATAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (28 bp):
TAAACCCTAAATTTTAATCTCTAAAACC
Found at i:15869 original size:21 final size:21
Alignment explanation
Indices: 15840--15955 Score: 84
Period size: 21 Copynumber: 5.9 Consensus size: 21
15830 CTTTTAATCT
15840 CTAAACCCTAAACCCTAAATA
1 CTAAACCCTAAACCCTAAATA
* * * *
15861 TTAATCCCTAATCCATAAATA
1 CTAAACCCTAAACCCTAAATA
*
15882 CTAAACCATAAACCCT-AAT-
1 CTAAACCCTAAACCCTAAATA
** * *
15901 -T----CCTGTACACTAAGTA
1 CTAAACCCTAAACCCTAAATA
*
15917 CTAAACCCTAAACCATAAATA
1 CTAAACCCTAAACCCTAAATA
*
15938 CTAAACCCTAATCCCTAA
1 CTAAACCCTAAACCCTAA
15956 GCCCTTAATT
Statistics
Matches: 67, Mismatches: 21, Indels: 14
0.66 0.21 0.14
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
17 1 0.01
18 1 0.01
20 3 0.04
21 54 0.81
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.24
Consensus pattern (21 bp):
CTAAACCCTAAACCCTAAATA
Found at i:15879 original size:28 final size:28
Alignment explanation
Indices: 15815--15879 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
15805 TTAAAATCAA
* * *
15815 AAACC-TAAACCCTAACTTTTAATCTCT
1 AAACCATAAACCCTAAATATTAATCCCT
*
15842 AAACCCTAAACCCTAAATATTAATCCCT
1 AAACCATAAACCCTAAATATTAATCCCT
*
15870 AATCCATAAA
1 AAACCATAAA
15880 TACTAAACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.28
Consensus pattern (28 bp):
AAACCATAAACCCTAAATATTAATCCCT
Found at i:23244 original size:28 final size:28
Alignment explanation
Indices: 23204--23262 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
23194 CTACACGCAT
23204 ATGGGCAGAATTTGAGGGTGAGTGGAGC
1 ATGGGCAGAATTTGAGGGTGAGTGGAGC
23232 ATGGGCAGAATTTGAGGGTGAGTGGAGC
1 ATGGGCAGAATTTGAGGGTGAGTGGAGC
23260 ATG
1 ATG
23263 AGTGGAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.46, T:0.22
Consensus pattern (28 bp):
ATGGGCAGAATTTGAGGGTGAGTGGAGC
Found at i:23274 original size:28 final size:28
Alignment explanation
Indices: 23208--23274 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
23198 ACGCATATGG
* *
23208 GCAGAATTTGAGGGTGAGTGGAGCATGG
1 GCAGAACTTGAGGGTGAGTGGAGCATGA
*
23236 GCAGAATTTGAGGGTGAGTGGAGCATGA
1 GCAGAACTTGAGGGTGAGTGGAGCATGA
**
23264 GTGGAACTTGA
1 GCAGAACTTGA
23275 TATGTATGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.07, G:0.43, T:0.22
Consensus pattern (28 bp):
GCAGAACTTGAGGGTGAGTGGAGCATGA
Found at i:23716 original size:3 final size:3
Alignment explanation
Indices: 23710--23745 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
23700 ACATTATTAT
23710 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
23746 TCCCGGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:23992 original size:55 final size:54
Alignment explanation
Indices: 23933--24257 Score: 398
Period size: 55 Copynumber: 5.9 Consensus size: 54
23923 AACATGTTAA
* * * *
23933 CTCCCTATTCCTTCAGAGAGTATGAGACCGGAATAATCTTCAATAAACGTATCTG
1 CTCCCTATTCCTTCAGAGAGTATGAGACC-GAACAATCTTCAACAATCGTGTCTG
*
23988 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATGAGAC-CGAACAATCTTCAACAATCGTGTCTG
* * **
24043 CTCCCTATTTCTTCAGAGAGTATAAGATTTGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATGAGA-CCGAACAATCTTCAACAATCGTGTCTG
* * *
24098 CTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAAACAATCGTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATGAGAC-CGAACAATCTTC-AACAATCGTGTCTG
* * * * *
24154 CTCCCTATTCCTTCAGGGAGTATGAAACTCGAACAATCTTTAATAATCGTGTCTA
1 CTCCCTATTCCTTCAGAGAGTATGAGAC-CGAACAATCTTCAACAATCGTGTCTG
* * * *
24209 CTCCCTATTTCTTCAGAGAGTATAAGATTCGAACAATCTTCAACCATCG
1 CTCCCTATTCCTTCAGAGAGTATGAGA-CCGAACAATCTTCAACAATCG
24258 GGTTCGCTCC
Statistics
Matches: 238, Mismatches: 27, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
55 188 0.79
56 50 0.21
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (54 bp):
CTCCCTATTCCTTCAGAGAGTATGAGACCGAACAATCTTCAACAATCGTGTCTG
Found at i:24206 original size:166 final size:165
Alignment explanation
Indices: 23933--24257 Score: 499
Period size: 166 Copynumber: 2.0 Consensus size: 165
23923 AACATGTTAA
* * * *
23933 CTCCCTATTCCTTCAGAGAGTATGAGACCGGAATAATCTTCAATAAACGTATCTGCTCCCTATTT
1 CTCCCTATTCCTTCAGAGAGTATAAGACCGGAACAATCTTCAATAAACGTATCCGCTCCCTATTC
* *
23998 CTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAG
66 CTTCAGAGAGTATGAAACTCGAACAATCTTCAACAATCGTGTCTACTCCCTATTTCTTCAGAGAG
*
24063 TATAAGATTTGAACAATCTTCAACAATCGTGTCTG
131 TATAAGATTCGAACAATCTTCAACAATCGTGTCTG
** *
24098 CTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAA-ACAATCGTGTCCGCTCCCTAT
1 CTCCCTATTCCTTCAGAGAGTATAAGACCGGAACAATCTTCAATA-AA-CGTATCCGCTCCCTAT
* * *
24162 TCCTTCAGGGAGTATGAAACTCGAACAATCTTTAATAATCGTGTCTACTCCCTATTTCTTCAGAG
64 TCCTTCAGAGAGTATGAAACTCGAACAATCTTCAACAATCGTGTCTACTCCCTATTTCTTCAGAG
*
24227 AGTATAAGATTCGAACAATCTTCAACCATCG
129 AGTATAAGATTCGAACAATCTTCAACAATCG
24258 GGTTCGCTCC
Statistics
Matches: 144, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
164 1 0.01
165 41 0.28
166 102 0.71
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (165 bp):
CTCCCTATTCCTTCAGAGAGTATAAGACCGGAACAATCTTCAATAAACGTATCCGCTCCCTATTC
CTTCAGAGAGTATGAAACTCGAACAATCTTCAACAATCGTGTCTACTCCCTATTTCTTCAGAGAG
TATAAGATTCGAACAATCTTCAACAATCGTGTCTG
Found at i:24268 original size:55 final size:55
Alignment explanation
Indices: 23933--24995 Score: 476
Period size: 54 Copynumber: 19.8 Consensus size: 55
23923 AACATGTTAA
* * * * *
23933 CTCCCTATTCCTTCAGAGAGTATGAGAC-CGGAATAATCTTCAATAAAC--GTATCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTC-GAACAATCTTCAACAATCGGGT-TC-G
* *
23988 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTG-TCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGTTC-G
* * *
24043 CTCCCTATTTCTTCAGAGAGTATAAGATTTGAACAATCTTCAACAATCGTG-TCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGTTC-G
* * * *
24098 CTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAAACAATCGTGTCCG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC-AACAATCGGGTTCG
* * * * * *
24154 CTCCCTATTCCTTCAGGGAGTATGAA-ACTCGAACAATCTTTAATAATCGTG-TCTA
1 CTCCCTATTTCTTCAGAGAGTAT-AAGACTCGAACAATCTTCAACAATCGGGTTC-G
* *
24209 CTCCCTATTTCTTCAGAGAGTATAAGATTCGAACAATCTTCAACCATCGGGTTCG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGTTCG
* * * * ** *
24264 CTCCCTCTTT-TTTAGGGAGTAT-AGAACTCGAAC-TTCTTCTGCAAACGGGTTCG
1 CTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGGGTTCG
* * * * *
24317 CTCCCTCTTTATT-AGGGAGTATACA-ACTC-AAAAATCTTC-A-AA-CGGGTTTG
1 CTCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGGGTTCG
* * * * ** *
24367 TTCCCTCTTTC-TCTAGGGAGTAT-AGAACTCGGAC-ATCTTCTTCAAACGGGTTCG
1 CTCCCTATTTCTTC-AGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGGGTTCG
*
24421 CTCCCTCTTTCTTCAG-GAAGTAT-AGAACTCGAACAATCTTC-A-AA-CGGGTTCG
1 CTCCCTATTTCTTCAGAG-AGTATAAG-ACTCGAACAATCTTCAACAATCGGGTTCG
* * * ** * *
24473 CTCCC--TCTCTTCAGGGAGTAT-GGAACTCGAAC-ATCTTCTTCTTAT-GGGTTCA
1 CTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAAC-AATCGGGTTCG
* *
24525 CTCCC-ACTTTC-TCTAGGGAGTAT-AGAACTCGGACATATTCTTC-A-AAT-GGGTTCG
1 CTCCCTA-TTTCTTC-AGAGAGTATAAG-ACTCGAACA-A-TCTTCAACAATCGGGTTCG
* * * * * ** *
24579 CTCCCTCTTTC-TCTAGGGAGTAT-AGAACTTGGAC-ATGTTCTTCAAACGGGTTCG
1 CTCCCTATTTCTTC-AGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGGGTTCG
*
24633 CTCCCTCTTTCTTCAG-GAAGTAT-AGAACTCGAACAATCTTC-A-AA-CGGGTTCG
1 CTCCCTATTTCTTCAGAG-AGTATAAG-ACTCGAACAATCTTCAACAATCGGGTTCG
* * * * ** *
24685 CTCCC--TCTCTTTAGGGAGTAT-GGAACTCGAAC-ATCTTCTTC-TTACGGGTTCG
1 CTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAT-CGGGTTCG
* * *
24737 CTCCCTCTTTC-TCTAGGGAGTAT-AGAACTCGGACATATTCTTC-A-AA-CGGGTTCG
1 CTCCCTATTTCTTC-AGAGAGTATAAG-ACTCGAACA-A-TCTTCAACAATCGGGTTCG
* * * * ** *
24791 CTCCCTCTTTC-TCTAGGGAGTAT-AGAACTTGGAC-ATCTTCTTCAAACGGGTTCG
1 CTCCCTATTTCTTC-AGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGGGTTCG
* * * * *
24845 CTCCCTCTTTCTTCAG-GAAT-TATAGAACT-TAGACATCTCTTC-A-AA-CTGGTTCG
1 CTCCCTATTTCTTCAGAGAGTATA-AG-ACTCGA-ACA-ATCTTCAACAATCGGGTTCG
* * * * * * *
24898 CTCCTTCTTCCTTTA-AGGAGAATATA-ACTCGAA-TATCTTCAACAATCGTG-TCTG
1 CTCCCTATTTCTTCAGA-GAGTATA-AGACTCGAACAATCTTCAACAATCGGGTTC-G
* * *
24952 CTCCCTATTTCTTCAGAGAGTATGAGATTCGAACGATCTTCAAC
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
24996 GATTGTTGGG
Statistics
Matches: 830, Mismatches: 103, Indels: 150
0.77 0.10 0.14
Matches are distributed among these distances:
49 14 0.02
50 61 0.07
51 37 0.04
52 58 0.07
53 91 0.11
54 271 0.33
55 228 0.27
56 56 0.07
57 14 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (55 bp):
CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGGGTTCG
Found at i:24429 original size:54 final size:54
Alignment explanation
Indices: 24256--24906 Score: 778
Period size: 54 Copynumber: 12.3 Consensus size: 54
24246 CTTCAACCAT
* * * *
24256 CGGGTTCGCTCCCTCTTT-TTTAGGGAGTATAGAACTCGAACTTCTTCTGCAAA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * ***
24309 CGGGTTCGCTCCCTCTTTAT-TAGGGAGTATACAACTC--A-AAAATCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
* *
24359 CGGGTTTGTTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * *
24413 CGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCGAACA--ATCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * * **
24465 CGGGTTCGCTCCCTCTCT-TC-AGGGAGTATGGAACTCGAACATCTTCTTCTTA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * * *
24517 TGGGTTCACTCCCACTTTCTCTAGGGAGTATAGAACTCGGACATATTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * *
24571 TGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATGTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * *
24625 CGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCGAACA--ATCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * * **
24677 CGGGTTCGCTCCCTC--TCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
*
24729 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATATTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
*
24783 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * **
24837 CGGGTTCGCTCCCTCTTTCT-TCAGGAATTATAGAACTTAGACATC-TCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGGACATCTTCTTCAAA
* *
24890 CTGGTTCGCTCCTTCTT
1 CGGGTTCGCTCCCTCTT
24907 CCTTTAAGGA
Statistics
Matches: 520, Mismatches: 60, Indels: 36
0.84 0.10 0.06
Matches are distributed among these distances:
50 65 0.12
51 19 0.04
52 89 0.17
53 63 0.12
54 284 0.55
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (54 bp):
CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
Found at i:24445 original size:158 final size:159
Alignment explanation
Indices: 24256--24937 Score: 783
Period size: 158 Copynumber: 4.3 Consensus size: 159
24246 CTTCAACCAT
* * *
24256 CGGGTTCGCTCCCTCTTT-TTTAGGGAGTATAGAACTCGAACTTCTTCTGCAAACGGGTTCGCTC
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTC
* * * *
24320 CCTCTTTATTAGGGAGTATACAACTC-AAAAATCTTCAAACGGGTTTGTTCCCTCTTTCTCTAGG
66 CCTCTTTCTTAGGGAGTATAGAACTCGAAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
24384 GAGTATAGAACTCGGACATCTTCTTCAAA
131 GAGTATAGAACTCGGACATCTTCTTCAAA
* *
24413 CGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTCGAACA--ATCTTCAAACGGGTTCGCT
1 CGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCT
* ** ** * * *
24475 CCCTC--TCTTCAGGGAGTATGGAACTCGAACATCTTCTTCTTATGGGTTCACTCCCACTTTCTC
65 CCCTCTTTCTT-AGGGAGTATAGAACTCGAA-A-AATCTTCAAACGGGTTCGCTCCCTCTTTCTC
*
24538 TAGGGAGTATAGAACTCGGACATATTCTTCAAA
127 TAGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * * *
24571 TGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATGTTCTTCAAACGGGTTCGCTC
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTC
* * *
24636 CCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTC--TCTTTAG
66 CCTCTTTCTT-AGGGAGTATAGAACTCGAAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAG
* * **
24699 GGAGTATGGAACTCGAACATCTTCTTCTTA
130 GGAGTATAGAACTCGGACATCTTCTTCAAA
* *
24729 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATATTCTTCAAACGGGTTCGCTC
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTC
* ***
24794 CCTCTTTCTCTAGGGAGTATAGAACTTGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-T
66 CCTCTTTCT-TAGGGAGTATAGAAC-TCGA-AAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * **
24858 CAGGAATTATAGAACTTAGACATC-TCTTCAAA
128 -AGGGAGTATAGAACTCGGACATCTTCTTCAAA
* * * * * * * *
24890 CTGGTTCGCTCCTTCTTCCTTTAAGGAGAATATAACTCGAATATCTTC
1 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTC
24938 AACAATCGTG
Statistics
Matches: 444, Mismatches: 64, Indels: 30
0.83 0.12 0.06
Matches are distributed among these distances:
154 3 0.01
155 14 0.03
156 24 0.05
157 20 0.05
158 226 0.51
159 5 0.01
160 65 0.15
161 45 0.10
162 42 0.09
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (159 bp):
CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTC
CCTCTTTCTTAGGGAGTATAGAACTCGAAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
GAGTATAGAACTCGGACATCTTCTTCAAA
Found at i:24462 original size:212 final size:211
Alignment explanation
Indices: 24209--24937 Score: 1029
Period size: 212 Copynumber: 3.4 Consensus size: 211
24199 ATCGTGTCTA
* *
24209 CTCCCTATTTCTTCA-GAGAGTATA-AGATTCGAACAATCTTCAACCATCGGGTTCGCTCCCTCT
1 CTCCCTCTTTCTTCAGGA-AGTATAGA-ACTCGAACAATCTTCAA--A-CGGGTTCGCTCCCTC-
* * * * ** *
24272 TTTTTAGGGAGTATAGAACTCGAACTTCTTCTGCAAACGGGTTCGCTCCCTCTTTAT-TAGGGAG
60 TCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAG
* * * * * *
24336 TATACAACTC-A-AAAATCTTCAAACGGGTTTGTTCCCTCTTTCTCTAGGGAGTATAGAACTCGG
125 TATAGAACTCGACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGG
24399 ACATCTTCTTCAAACGGGTTCG
190 ACATCTTCTTCAAACGGGTTCG
*
24421 CTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTCTTCA
1 CTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTCTTTA
* * *
24486 GGGAGTATGGAACTCGAACATCTTCTTCTTATGGGTTCACTCCCACTTTCTCTAGGGAGTATAGA
66 GGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGA
* *
24551 ACTCGGACATATTCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATG
131 ACTC-GACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATC
24616 TTCTTCAAACGGGTTCG
195 TTCTTCAAACGGGTTCG
24633 CTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTCTTTA
1 CTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTCTTTA
24698 GGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGA
66 GGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGA
24763 ACTCGGACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATC
131 ACTC-GACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATC
24828 TTCTTCAAACGGGTTCG
195 TTCTTCAAACGGGTTCG
* * * * *
24845 CTCCCTCTTTCTTCAGGAATTATAGAACT-TAGACATCTCTTCAAACTGGTTCGCTCCTTCTTCC
1 CTCCCTCTTTCTTCAGGAAGTATAGAACTCGA-ACA-ATCTTCAAACGGGTTCGCTCCCTC-T-C
* * ** *
24909 TTTAAGGAGAATATAACTCGAATATCTTC
62 TTTAGGGAGTATGGAACTCGAACATCTTC
24938 AACAATCGTG
Statistics
Matches: 470, Mismatches: 37, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
208 46 0.10
209 31 0.07
210 1 0.00
211 2 0.00
212 340 0.72
213 24 0.05
214 1 0.00
215 25 0.05
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (211 bp):
CTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTCTTTA
GGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGA
ACTCGACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATCT
TCTTCAAACGGGTTCG
Found at i:25950 original size:17 final size:17
Alignment explanation
Indices: 25930--25968 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
25920 TCTTTTTTCC
25930 ATTTTTATATATTTTTT
1 ATTTTTATATATTTTTT
* *
25947 ATTTTTTTATTTTTTTT
1 ATTTTTATATATTTTTT
25964 ATTTT
1 ATTTT
25969 CACTCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
ATTTTTATATATTTTTT
Found at i:25953 original size:9 final size:9
Alignment explanation
Indices: 25931--25968 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
25921 CTTTTTTCCA
*
25931 TTTTTATAT
1 TTTTTTTAT
*
25940 ATTTTTTA-
1 TTTTTTTAT
25948 TTTTTTTAT
1 TTTTTTTAT
25957 TTTTTTTAT
1 TTTTTTTAT
25966 TTT
1 TTT
25969 CACTCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:36088 original size:1 final size:1
Alignment explanation
Indices: 36084--36115 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
36074 TACTTTTTGC
36084 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
36116 TTCGAGGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38578 original size:28 final size:28
Alignment explanation
Indices: 38538--38596 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
38528 CTACACGCAT
38538 ATGGGCAGAATTTGAGGGTGAGTGGAGC
1 ATGGGCAGAATTTGAGGGTGAGTGGAGC
38566 ATGGGCAGAATTTGAGGGTGAGTGGAGC
1 ATGGGCAGAATTTGAGGGTGAGTGGAGC
38594 ATG
1 ATG
38597 AGTGGAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.46, T:0.22
Consensus pattern (28 bp):
ATGGGCAGAATTTGAGGGTGAGTGGAGC
Found at i:38608 original size:28 final size:28
Alignment explanation
Indices: 38542--38608 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
38532 ACGCATATGG
* *
38542 GCAGAATTTGAGGGTGAGTGGAGCATGG
1 GCAGAACTTGAGGGTGAGTGGAGCATGA
*
38570 GCAGAATTTGAGGGTGAGTGGAGCATGA
1 GCAGAACTTGAGGGTGAGTGGAGCATGA
**
38598 GTGGAACTTGA
1 GCAGAACTTGA
38609 TATGTATGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.07, G:0.43, T:0.22
Consensus pattern (28 bp):
GCAGAACTTGAGGGTGAGTGGAGCATGA
Found at i:39050 original size:3 final size:3
Alignment explanation
Indices: 39044--39076 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
39034 ACATTATTAT
39044 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
39077 TCCCGGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40278 original size:12 final size:12
Alignment explanation
Indices: 40231--40277 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
40221 GAGCTTGAAT
40231 CGAGCTCCAAAC
1 CGAGCTCCAAAC
40243 CGAGCTCCAAAC
1 CGAGCTCCAAAC
*
40255 CGAGCTCCAAAT
1 CGAGCTCCAAAC
*
40267 TGAGCTCCAAA
1 CGAGCTCCAAA
40278 TCAAGCCTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.34, C:0.36, G:0.17, T:0.13
Consensus pattern (12 bp):
CGAGCTCCAAAC
Found at i:40313 original size:23 final size:24
Alignment explanation
Indices: 40287--40340 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
40277 ATCAAGCCTG
40287 AATCGAGTTTGAAATC-GACCTTC
1 AATCGAGTTTGAAATCTGACCTTC
** *
40310 AATCGAGTTTGAGTTCTGAGCTTC
1 AATCGAGTTTGAAATCTGACCTTC
40334 AATCGAG
1 AATCGAG
40341 CTTTTGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (24 bp):
AATCGAGTTTGAAATCTGACCTTC
Found at i:42401 original size:27 final size:28
Alignment explanation
Indices: 42357--42422 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
42347 TTCCAAGTCA
42357 CGAGGGTATTT-AAGTCATTCCAAAACT
1 CGAGGGTATTTCAAGTCATTCCAAAACT
* *
42384 CGAGGGTATTTCTA-TCATTCCAAAGCT
1 CGAGGGTATTTCAAGTCATTCCAAAACT
* *
42411 CAAGGATATTTC
1 CGAGGGTATTTC
42423 GGTCATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 33 0.97
28 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (28 bp):
CGAGGGTATTTCAAGTCATTCCAAAACT
Found at i:42428 original size:27 final size:27
Alignment explanation
Indices: 42370--42429 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
42360 GGGTATTTAA
* * *
42370 GTCATTCCAAAACTCGAGGGTATTTCT
1 GTCATTCCAAAACTCAAGGATATTTCG
* *
42397 ATCATTCCAAAGCTCAAGGATATTTCG
1 GTCATTCCAAAACTCAAGGATATTTCG
42424 GTCATT
1 GTCATT
42430 TTACTCAAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (27 bp):
GTCATTCCAAAACTCAAGGATATTTCG
Found at i:43388 original size:20 final size:20
Alignment explanation
Indices: 43352--43389 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43342 ATCCTATTCC
**
43352 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
43372 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
43390 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:44857 original size:17 final size:17
Alignment explanation
Indices: 44820--44857 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
44810 AATAAATGAA
*
44820 ATATAATTTAATTTTAT
1 ATATAATTTAAATTTAT
*
44837 -TATAGTTTAAATTTAT
1 ATATAATTTAAATTTAT
44853 ATATA
1 ATATA
44858 TCAAATATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATATAATTTAAATTTAT
Found at i:45844 original size:28 final size:28
Alignment explanation
Indices: 45804--45900 Score: 122
Period size: 28 Copynumber: 3.4 Consensus size: 28
45794 AAAAAGTTTG
* *
45804 AATAGTTTAGGTACCTATTTTGACATAA
1 AATACTTTAGGTACCTATTTTGACAAAA
*
45832 AATACTTTAGGTATCTATTTTGACAAAA
1 AATACTTTAGGTACCTATTTTGACAAAA
*
45860 GATATAACTTTAGGTACTTATTTTGACAAAA
1 -A-AT-ACTTTAGGTACCTATTTTGACAAAA
*
45891 AAAACTTTAG
1 AATACTTTAG
45901 ATACTTAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
28 32 0.53
29 2 0.03
30 3 0.05
31 23 0.38
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (28 bp):
AATACTTTAGGTACCTATTTTGACAAAA
Found at i:46773 original size:21 final size:21
Alignment explanation
Indices: 46741--46793 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
46731 AACAATACTT
* *
46741 TTCATGGAAAAG-TTATGTCC
1 TTCATGAAAAAGATTAAGTCC
*
46761 TTCTATGAAAAAGATTAAGTCT
1 TTC-ATGAAAAAGATTAAGTCC
46783 TTCATGAAAAA
1 TTCATGAAAAA
46794 ATGTTAAGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (21 bp):
TTCATGAAAAAGATTAAGTCC
Found at i:46800 original size:22 final size:21
Alignment explanation
Indices: 46768--46846 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 21
46758 TCCTTCTATG
46768 AAAAAGA-TTAAGTCTTTCAT
1 AAAAAGAGTTAAGTCTTTCAT
*
46788 GAAAAA-ATGTTAAGCCCTTTCAT
1 -AAAAAGA-GTTAAG-TCTTTCAT
* *
46811 AAAAAGAGTAAAGTCTTTTAAT
1 AAAAAGAGTTAAGTC-TTTCAT
*
46833 CAAAAG-GTTAAGTC
1 AAAAAGAGTTAAGTC
46847 ATTTAATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 25 0.53
23 8 0.17
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (21 bp):
AAAAAGAGTTAAGTCTTTCAT
Found at i:46828 original size:21 final size:22
Alignment explanation
Indices: 46751--46828 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
46741 TTCATGGAAA
* *
46751 AGTTATGTCCTTCTATGAAAAAG
1 AGTTAAGTCTTTC-ATGAAAAAG
46774 A-TTAAGTCTTTCATGAAAAA-
1 AGTTAAGTCTTTCATGAAAAAG
*
46794 ATGTTAAGCCCTTTCAT-AAAAAG
1 A-GTTAAG-TCTTTCATGAAAAAG
*
46817 AGTAAAGTCTTT
1 AGTTAAGTCTTT
46829 TAATCAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
20 1 0.02
21 12 0.26
22 24 0.52
23 9 0.20
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (22 bp):
AGTTAAGTCTTTCATGAAAAAG
Found at i:51734 original size:39 final size:38
Alignment explanation
Indices: 51651--51735 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 38
51641 CAACGGTCAA
* *
51651 CGGTCAACGGTCCGGTCGGGTCGGGTCGGGTCAACGGT
1 CGGTCAACAGTCCGGTCGGGTCGGGTCGGGTCAACGAT
*
51689 CGGGTCAACAGTCTGGTCGGGTCAGTCGGTCGGGTC-A-GAT
1 C-GGTCAACAGTCCGGTCGGGTC-G--GGTCGGGTCAACGAT
51729 CGGTCAA
1 CGGTCAA
51736 ACTGGTTCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 1 0.03
39 25 0.62
40 4 0.10
41 1 0.03
42 9 0.22
ACGTcount: A:0.14, C:0.25, G:0.41, T:0.20
Consensus pattern (38 bp):
CGGTCAACAGTCCGGTCGGGTCGGGTCGGGTCAACGAT
Found at i:51751 original size:19 final size:19
Alignment explanation
Indices: 51723--51800 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 19
51713 GTCGGTCGGG
* *
51723 TCAGATCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
51742 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
51761 T-TGAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
51780 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
51800 T
1 T
51801 TCCAGCAGCC
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.06
19 35 0.74
20 9 0.19
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.21
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:51796 original size:10 final size:10
Alignment explanation
Indices: 51729--51799 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
51719 CGGGTCAGAT
51729 CGGTCA-AAC
1 CGGTCAGAAC
*
51738 TGGTTCAG-AC
1 CGG-TCAGAAC
51748 CGGTCA-AAC
1 CGGTCAGAAC
**
51757 CGGTTTGAAC
1 CGGTCAGAAC
*
51767 CGGT-TGAAAC
1 CGGTCAG-AAC
51777 CGGTCA-AAC
1 CGGTCAGAAC
51786 CGGTCAGAAC
1 CGGTCAGAAC
51796 CGGT
1 CGGT
51800 TTCCAGCAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
9 22 0.44
10 28 0.56
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (10 bp):
CGGTCAGAAC
Found at i:59031 original size:22 final size:22
Alignment explanation
Indices: 58977--59037 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
58967 GTCAACGATC
* *
58977 CGGTCGGGTCAGGCCGGGTCAA
1 CGGTCGGGTCGGGTCGGGTCAA
58999 CGGTCGGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCGGGTCAA
* *
59021 CGGTCTGGTCGGTTCGG
1 CGGTCGGGTCGGGTCGG
59038 TCGGGTCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.08, C:0.25, G:0.48, T:0.20
Consensus pattern (22 bp):
CGGTCGGGTCGGGTCGGGTCAA
Found at i:59099 original size:10 final size:10
Alignment explanation
Indices: 59052--59140 Score: 69
Period size: 10 Copynumber: 9.1 Consensus size: 10
59042 GTCAGACCGA
59052 TCAAACCGGT
1 TCAAACCGGT
* *
59062 TCAGACTGG-
1 TCAAACCGGT
* *
59071 TCAAATCGGA
1 TCAAACCGGT
*
59081 TCGAACCGGT
1 TCAAACCGGT
*
59091 TGAAACCGG-
1 TCAAACCGGT
59100 TCAAACCGG-
1 TCAAACCGGT
59109 TCAGAACCGGT
1 TCA-AACCGGT
*
59120 TGAAAACCGGT
1 T-CAAACCGGT
59131 T-AAACCGGT
1 TCAAACCGGT
59140 T
1 T
59141 TCCAGCAGCC
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
9 26 0.41
10 27 0.43
11 9 0.14
12 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:59107 original size:9 final size:9
Alignment explanation
Indices: 59041--59139 Score: 63
Period size: 9 Copynumber: 10.3 Consensus size: 9
59031 GGTTCGGTCG
*
59041 GGTCAGACC
1 GGTCAAACC
*
59050 GATCAAACC
1 GGTCAAACC
* *
59059 GGTTCAGACT
1 GG-TCAAACC
*
59069 GGTCAAATC
1 GGTCAAACC
*
59078 GGATCGAACC
1 GG-TCAAACC
*
59088 GGTTGAAACC
1 GG-TCAAACC
59098 GGTCAAACC
1 GGTCAAACC
59107 GGTCAGAACC
1 GGTCA-AACC
*
59117 GGTTGAAAACC
1 GG-T-CAAACC
*
59128 GGTTAAACC
1 GGTCAAACC
59137 GGT
1 GGT
59140 TTCCAGCAGC
Statistics
Matches: 69, Mismatches: 16, Indels: 10
0.73 0.17 0.11
Matches are distributed among these distances:
9 33 0.48
10 28 0.41
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:65222 original size:15 final size:15
Alignment explanation
Indices: 65204--65233 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
65194 CCACGGTGCT
65204 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
65219 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
65234 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Done.