Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000524.1 Hibiscus syriacus cultivar Beakdansim tig00001006_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: 146533
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:996 original size:20 final size:22
Alignment explanation
Indices: 946--999 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
936 ATACCGGAAG
946 GGGGTATCGATACCATAGTATA
1 GGGGTATCGATACCATAGTATA
** *
968 GTAGTATCGATACCAT-G-GTA
1 GGGGTATCGATACCATAGTATA
988 GGGGTATCGATA
1 GGGGTATCGATA
1000 ATGAAGAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 12 0.44
21 1 0.04
22 14 0.52
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.28
Consensus pattern (22 bp):
GGGGTATCGATACCATAGTATA
Found at i:1504 original size:34 final size:34
Alignment explanation
Indices: 1466--1600 Score: 126
Period size: 34 Copynumber: 3.6 Consensus size: 34
1456 TCATAGCTGA
*
1466 AATGCATATGGATGCATTATCAGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCAGCATAAAAGAAT
**
1500 AATGCATATGGGTGCATTATTGGCATGAAATGATGTTATAGCT
1 AATGCATATGGGTGCATTATCAGCAT-AAA--A-G--A-A--T
1543 GAAATGCATATGGGTGTGCATTATCAGCATAAAAGAAT
1 --AATGCATAT-GG-GTGCATTATCAGCATAAAAGAAT
1581 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
1601 TTGCATGAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
34 32 0.39
35 5 0.06
36 9 0.11
37 1 0.01
38 2 0.02
40 2 0.02
41 2 0.02
43 2 0.02
44 1 0.01
45 9 0.11
46 5 0.06
47 13 0.16
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.30
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCAGCATAAAAGAAT
Found at i:1551 original size:45 final size:40
Alignment explanation
Indices: 1432--1882 Score: 242
Period size: 45 Copynumber: 11.2 Consensus size: 40
1422 GGCACTGTGT
*
1432 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGG
1 GTGCATTATTAGCATGAAA-GATG-CA-AG-T-AAATGCATATGG
* *
1477 ATGCATTATCAGCAT-AAA-A-G-AA-T-AATGCATATGG
1 GTGCATTATTAGCATGAAAGATGCAAGTAAATGCATATGG
* *
1511 GTGCATTATTGGCATGAAATGATGTTATAGCTGAAATGCATATGGG
1 GTGCATTATTAGCATGAAA-GATG-CA-AG-T-AAATGCATAT-GG
*
1557 TGTGCATTATCAGCAT-AAA-A-G-AA-T-AATGCATATGG
1 -GTGCATTATTAGCATGAAAGATGCAAGTAAATGCATATGG
* *
1592 GTGCATTATTTGCATGAAAGGATGTCATAGCTAAAATGTATATGG
1 GTGCATTATTAGCATGAAA-GATG-CA-AG-T-AAATGCATATGG
*
1637 GTGCATTATCAGCAT-AAA-A-G-AA-T-AATGCATATGG
1 GTGCATTATTAGCATGAAAGATGCAAGTAAATGCATATGG
* * *
1671 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCGTACGG
1 GTGCATTATTAGCATGAAA-GATG-CA-AG-T-AAATGCATATGG
* *
1716 GTGCATTATCAGCAT-AAA-A-G-AA-T-AATGCATATGT
1 GTGCATTATTAGCATGAAAGATGCAAGTAAATGCATATGG
* *
1750 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGC
1 GTGCATTATTAGCATGAAA-GATG-CA-AG-T-AAATGCATATGG
*
1795 GTGCATTATCAGCAT-AAA-AT--AA-T-AATGCATATGG
1 GTGCATTATTAGCATGAAAGATGCAAGTAAATGCATATGG
*
1829 GTGCATTATTGGCATGACAAGATGCCAACGTTGAAATGCATATGG
1 GTGCATTATTAGCATGA-AAGATG-CAA-G-T-AAATGCATATGG
1874 GTGCATTAT
1 GTGCATTAT
1883 CAACCTAAAA
Statistics
Matches: 318, Mismatches: 31, Indels: 114
0.69 0.07 0.25
Matches are distributed among these distances:
34 103 0.32
35 15 0.05
36 15 0.05
37 6 0.02
38 9 0.03
39 4 0.01
40 7 0.02
41 8 0.03
42 5 0.02
43 6 0.02
44 13 0.04
45 109 0.34
46 5 0.02
47 13 0.04
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (40 bp):
GTGCATTATTAGCATGAAAGATGCAAGTAAATGCATATGG
Found at i:1686 original size:79 final size:79
Alignment explanation
Indices: 1432--1896 Score: 736
Period size: 79 Copynumber: 5.9 Consensus size: 79
1422 GGCACTGTGT
*
1432 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGATGCATTATCAGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAG
1497 AATAATGCATATGG
66 AATAATGCATATGG
* *
1511 GTGCATTATTGGCATGAAATGATGTTATAGCTGAAATGCATATGGGTGTGCATTATCAGCATAAA
1 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATAT-GG-GTGCATTATCAGCATAAA
1576 AGAATAATGCATATGG
64 AGAATAATGCATATGG
* * *
1592 GTGCATTATTTGCATGAAAGGATGTCATAGCTAAAATGTATATGGGTGCATTATCAGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAG
1657 AATAATGCATATGG
66 AATAATGCATATGG
* *
1671 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCGTACGGGTGCATTATCAGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAG
*
1736 AATAATGCATATGT
66 AATAATGCATATGG
* * *
1750 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGCGTGCATTATCAGCATAAAAT
1 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAG
1815 AATAATGCATATGG
66 AATAATGCATATGG
* * * *
1829 GTGCATTATTGGCATGACAA-GATGCCA-ACGTTGAAATGCATATGGGTGCATTATCAACCTAAA
1 GTGCATTATTGGCATGA-AAGGATGTCATA-GCTGAAATGCATATGGGTGCATTATCAGCATAAA
1892 AGAAT
64 AGAAT
1897 GCTATAATTG
Statistics
Matches: 357, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
78 1 0.00
79 279 0.78
80 6 0.02
81 71 0.20
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (79 bp):
GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAG
AATAATGCATATGG
Found at i:1754 original size:34 final size:34
Alignment explanation
Indices: 1716--1837 Score: 100
Period size: 34 Copynumber: 3.3 Consensus size: 34
1706 ATGCGTACGG
*
1716 GTGCATTATCAGCATAAAAGAATAATGCATATGT
1 GTGCATTATCAGCATAAAAGAATAATGCATATGC
**
1750 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGC
1 GTGCATTATCAGCAT-AAA--A-G--A-A--T--AATGCATATGC
* *
1795 GTGCATTATCAGCATAAAATAATAATGCATATGG
1 GTGCATTATCAGCATAAAAGAATAATGCATATGC
1829 GTGCATTAT
1 GTGCATTAT
1838 TGGCATGACA
Statistics
Matches: 70, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
34 32 0.46
35 3 0.04
36 1 0.01
37 1 0.01
38 2 0.03
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 3 0.04
45 23 0.33
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (34 bp):
GTGCATTATCAGCATAAAAGAATAATGCATATGC
Found at i:2215 original size:29 final size:29
Alignment explanation
Indices: 2182--2300 Score: 202
Period size: 29 Copynumber: 4.1 Consensus size: 29
2172 TATGCCAGTT
* *
2182 AGATGAATGGTTAAATATTGTTGAGTAAA
1 AGATGAAAGGTTAAATACTGTTGAGTAAA
*
2211 AGATGAAAGGTTAAATATTGTTGAGTAAA
1 AGATGAAAGGTTAAATACTGTTGAGTAAA
2240 AGATGAAAGGTTAAATACTGTTGAGTAAA
1 AGATGAAAGGTTAAATACTGTTGAGTAAA
*
2269 AGATGAAAGGTTAAACACTGTTGAGTAAA
1 AGATGAAAGGTTAAATACTGTTGAGTAAA
2298 AGA
1 AGA
2301 ATAATGGACT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 87 1.00
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.29
Consensus pattern (29 bp):
AGATGAAAGGTTAAATACTGTTGAGTAAA
Found at i:2444 original size:2 final size:2
Alignment explanation
Indices: 2437--2469 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2427 TGAAGGGATG
*
2437 AT AT AT AT TT 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 AT AT A
2470 ATGTACAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3719 original size:32 final size:32
Alignment explanation
Indices: 3659--3896 Score: 271
Period size: 32 Copynumber: 7.4 Consensus size: 32
3649 TTGTGCTTAG
* * * * *
3659 GAGCCAACCTAAGGGAATATCTTGGGGCCTAA
1 GAGCCTACCCAAGGAAATACCTTGGGGCCTCA
* * *
3691 GAGCCTACCCAATGG-AGTACCTTAGGGCCTAA
1 GAGCCTACCCAA-GGAAATACCTTGGGGCCTCA
* *
3723 GAGTCTACCCAAGGAAATACCTTGGGGCCTTA
1 GAGCCTACCCAAGGAAATACCTTGGGGCCTCA
*
3755 GAGCCTACCCAAGGAAATGCCTTGGGGCCTCA
1 GAGCCTACCCAAGGAAATACCTTGGGGCCTCA
* * *
3787 GAGTCTGCCCAAGGAAATGCCTTGGGGCCTCA
1 GAGCCTACCCAAGGAAATACCTTGGGGCCTCA
* * *
3819 GAGTCTGCCCAAGGAAATACCTTGGGGCCTTA
1 GAGCCTACCCAAGGAAATACCTTGGGGCCTCA
** *
3851 GAGCCTACCCAAGGAAATGTCTTAGGGCCTCA
1 GAGCCTACCCAAGGAAATACCTTGGGGCCTCA
*
3883 GAGCCTACTCAAGG
1 GAGCCTACCCAAGG
3897 TCACCTTAGT
Statistics
Matches: 181, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
31 2 0.01
32 177 0.98
33 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (32 bp):
GAGCCTACCCAAGGAAATACCTTGGGGCCTCA
Found at i:3896 original size:96 final size:95
Alignment explanation
Indices: 3654--3896 Score: 324
Period size: 96 Copynumber: 2.5 Consensus size: 95
3644 ACCCATTGTG
* * * * * *
3654 CTTAGGAGCCAACCTAAGGGAATATCTTGGGGCCTAAGAGCCTACCCAATGGAGTACCTTAGGGC
1 CTTA-GAGCCTACCCAAGGAAATGTCTTGGGGCCTCAGAGCCTACCCAA-GGAATACCTTAGGGC
3719 CTAAGAGTCTACCCAAGGAAATACCTTGGGGC
64 CTAAGAGTCTACCCAAGGAAATACCTTGGGGC
* * * * *
3751 CTTAGAGCCTACCCAAGGAAATGCCTTGGGGCCTCAGAGTCTGCCCAAGGAAATGCCTTGGGGCC
1 CTTAGAGCCTACCCAAGGAAATGTCTTGGGGCCTCAGAGCCTACCCAAGG-AATACCTTAGGGCC
* *
3816 TCAGAGTCTGCCCAAGGAAATACCTTGGGGC
65 TAAGAGTCTACCCAAGGAAATACCTTGGGGC
* *
3847 CTTAGAGCCTACCCAAGGAAATGTCTTAGGGCCTCAGAGCCTACTCAAGG
1 CTTAGAGCCTACCCAAGGAAATGTCTTGGGGCCTCAGAGCCTACCCAAGG
3897 TCACCTTAGT
Statistics
Matches: 127, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
95 2 0.02
96 121 0.95
97 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (95 bp):
CTTAGAGCCTACCCAAGGAAATGTCTTGGGGCCTCAGAGCCTACCCAAGGAATACCTTAGGGCCT
AAGAGTCTACCCAAGGAAATACCTTGGGGC
Found at i:9703 original size:27 final size:24
Alignment explanation
Indices: 9673--9721 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
9663 AACCCACATA
9673 ATAAATATAGATATTTGAAATAAAATC
1 ATAAATA-A-ATATTTGAAA-AAAATC
*
9700 ATAAATAAATATTTTAAAAAAA
1 ATAAATAAATATTTGAAAAAAA
9722 CCTCAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 9 0.43
26 1 0.05
27 7 0.33
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAAATAAATATTTGAAAAAAATC
Found at i:15726 original size:60 final size:60
Alignment explanation
Indices: 15659--15786 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
15649 AATATTCTCT
* * * *
15659 AAACTTTTAAACATTCCAATTTCATCCCTAAACTATGA-CTATCAATCTAAATTAG-TCCTC
1 AAACTTTTAAACATTCCAATTCCATCCCCAAAATATAATCT-TCAATCT-AATTAGATCCTC
* * * *
15719 AAACTTTTGAACATTTCAATTCCATCCCCAAAATATAATCTTCACTCTAATTTGATCCTC
1 AAACTTTTAAACATTCCAATTCCATCCCCAAAATATAATCTTCAATCTAATTAGATCCTC
15779 AAACTTTT
1 AAACTTTT
15787 TGAACATTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 5 0.09
60 51 0.88
61 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (60 bp):
AAACTTTTAAACATTCCAATTCCATCCCCAAAATATAATCTTCAATCTAATTAGATCCTC
Found at i:17088 original size:2 final size:2
Alignment explanation
Indices: 17081--17106 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17071 AAAAAGAGTA
17081 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
17107 TAATACTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17588 original size:39 final size:39
Alignment explanation
Indices: 17495--17609 Score: 139
Period size: 37 Copynumber: 3.0 Consensus size: 39
17485 CATAATTCCC
* **
17495 AAATTATTTCACCCTAACATTCTAAATTCCTA-ATTTT-
1 AAATTATTTCACCATAACATTCTAAATTATTATATTTTA
* *
17532 AAATTATTTCACTATAACATTCTAAATTATTATTTTTTA
1 AAATTATTTCACCATAACATTCTAAATTATTATATTTTA
*
17571 AAATTATTTCACCATAAC-TATCTAAATTATT-TCTTTTA
1 AAATTATTTCACCATAACAT-TCTAAATTATTATATTTTA
17609 A
1 A
17610 CTTCAAAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
37 28 0.41
38 12 0.18
39 28 0.41
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (39 bp):
AAATTATTTCACCATAACATTCTAAATTATTATATTTTA
Found at i:18300 original size:27 final size:27
Alignment explanation
Indices: 18269--18335 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
18259 ATATGAAAAT
*
18269 TGCATTAGATAATTACAATGTATGTGC
1 TGCATTAGATAATTACAATGTATGTGA
18296 TGCATTAGATAATTACAATGTATGTGA
1 TGCATTAGATAATTACAATGTATGTGA
18323 TGCATTAGATAAT
1 TGCATTAGATAAT
18336 AAAAAAATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (27 bp):
TGCATTAGATAATTACAATGTATGTGA
Found at i:23064 original size:64 final size:63
Alignment explanation
Indices: 22979--23139 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
22969 TTGTTTAAGG
* *
22979 TGCATCGATGCACATAC-AGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATA-ACGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTT
23042 A
63 A
* * *
23043 TGCATCGATGCATAACGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAACGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
***
23107 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAACG-AGTGCATCGATGCAT
23140 ACCTCCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.02
64 61 0.72
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAACGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:23784 original size:103 final size:103
Alignment explanation
Indices: 23600--23817 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
23590 GTAGAGGGTC
*
23600 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATAC
* *
23665 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* * *
23703 TATGTGGTTCTTTGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATAC
*
23768 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
23806 TATGTGGTCCTT
1 TATGTGGTCCTT
23818 ATGGACATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:23891 original size:23 final size:22
Alignment explanation
Indices: 23841--23896 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
23831 TATGGCAATA
*
23841 CGGTGCAATTCTACGCGGTACT
1 CGGTGCAATTCTACGCGGCACT
*
23863 CTGGTGCAATTCTACGTGGCACTT
1 C-GGTGCAATTCTACGCGGCAC-T
*
23887 CGGTGTAATT
1 CGGTGCAATT
23897 ATATGAGCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 26 0.90
24 2 0.07
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (22 bp):
CGGTGCAATTCTACGCGGCACT
Found at i:28540 original size:2 final size:2
Alignment explanation
Indices: 28533--28557 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28523 AAATAAATAA
28533 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 A
28558 AAGAGTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28922 original size:20 final size:20
Alignment explanation
Indices: 28828--29196 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
28818 GATTTTCCAT
* ** *
28828 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
28848 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
28868 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28888 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
28908 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
28928 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28948 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28968 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28988 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
29008 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29028 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
29048 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29068 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
29088 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29108 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
29128 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
29148 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
29168 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
29188 AATCACAAC
1 AATCGCAAC
29197 ACTTAAATTT
Statistics
Matches: 303, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 295 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:29916 original size:24 final size:24
Alignment explanation
Indices: 29877--29923 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29867 AAATTTGGTC
29877 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
29901 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
29924 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:30115 original size:12 final size:12
Alignment explanation
Indices: 30098--30122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30088 ATATAATCCT
30098 GAAGAAGAAAAA
1 GAAGAAGAAAAA
30110 GAAGAAGAAAAA
1 GAAGAAGAAAAA
30122 G
1 G
30123 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:32427 original size:19 final size:19
Alignment explanation
Indices: 32405--32678 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
32395 CGGAAAATAC
*
32405 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32424 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
32438 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
32458 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
32472 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32491 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
32510 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
32524 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
32543 AATCGCAATGCGGAATGAA
1 AATCGCAATGCGAAATGAA
32562 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32581 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32600 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32619 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
32633 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32652 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
32671 AATCGCAA
1 AATCGCAA
32679 CGAGATAATC
Statistics
Matches: 224, Mismatches: 10, Indels: 42
0.81 0.04 0.15
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 144 0.64
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:32560 original size:71 final size:74
Alignment explanation
Indices: 32433--32678 Score: 293
Period size: 71 Copynumber: 3.4 Consensus size: 74
32423 AAATCCCAAC
* *
32433 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAA-GC-GAAATG-AAATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAA
32493 TCGCAATGCGAA
63 TCGCAATGCGAA
* *
32505 ATGAAAATCGCAA-CGACA-G-AATCGCAATGCGAAATTAAAATCGCAATGCGGAATGAAAATCG
1 ATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAATCG
32567 CAATGCGAA
66 CAATGCGAA
*
32576 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-GAA--AGAAT
1 ATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAAT
32636 CGCAATGCGAA
64 CGCAATGCGAA
32647 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAA-GCGAAATG-AAATCGCAA
32679 CGAGATAATC
Statistics
Matches: 157, Mismatches: 7, Indels: 21
0.85 0.04 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 3 0.02
70 2 0.01
71 93 0.59
72 13 0.08
73 7 0.04
74 2 0.01
76 26 0.17
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (74 bp):
ATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAATCG
CAATGCGAA
Found at i:32607 original size:109 final size:104
Alignment explanation
Indices: 32433--32700 Score: 437
Period size: 109 Copynumber: 2.5 Consensus size: 104
32423 AAATCCCAAC
*
32433 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGG-AATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
32498 ATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
32538 ATTAAAATCGCAATGCGGAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGGAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
32603 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
* *
32647 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGGAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
32701 TATAAACGCA
Statistics
Matches: 152, Mismatches: 6, Indels: 11
0.90 0.04 0.07
Matches are distributed among these distances:
104 32 0.21
105 18 0.12
106 2 0.01
107 2 0.01
108 1 0.01
109 97 0.64
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGGAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:32648 original size:161 final size:157
Alignment explanation
Indices: 32405--32715 Score: 500
Period size: 161 Copynumber: 2.0 Consensus size: 157
32395 CGGAAAATAC
*
32405 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
32470 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
32535 GAAATTA-AAATCGCAATGCGGAATGAA
131 GAAATTATAAA-CGCAATGCGGAATGAA
* *
32562 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
32626 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
32691 AATGCGAAATTATAAACGCATTGCG
126 AATGCGAAATTATAAACGCAATGCG
32716 ATTTTCATTT
Statistics
Matches: 142, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
157 25 0.18
159 1 0.01
161 97 0.68
162 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (157 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGGAATGAA
Found at i:32716 original size:52 final size:52
Alignment explanation
Indices: 32433--32700 Score: 428
Period size: 52 Copynumber: 5.0 Consensus size: 52
32423 AAATCCCAAC
32433 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
32486 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * *
32538 ATTAAAATCGCAATGCGGAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
32595 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
32647 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
32699 AT
1 AT
32701 TATAAACGCA
Statistics
Matches: 199, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
52 132 0.66
53 17 0.09
54 2 0.01
55 2 0.01
56 1 0.01
57 45 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:32815 original size:19 final size:19
Alignment explanation
Indices: 32707--32807 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
32697 AAATTATAAA
32707 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
32726 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
32746 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
32762 CG--TTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
32778 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
32797 CGCATTGCGAT
1 CGCATTGCGAT
32808 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 8 0.11
17 3 0.04
18 6 0.08
19 29 0.39
20 19 0.26
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:32933 original size:14 final size:14
Alignment explanation
Indices: 32914--32950 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
32904 CATCAATTAC
32914 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
32928 ACAAATCATCTTTT
1 ACAAATCAACTTTT
32942 ACAAATCAA
1 ACAAATCAA
32951 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:34878 original size:20 final size:20
Alignment explanation
Indices: 34853--34918 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
34843 TAGTTTACTT
* *
34853 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
34873 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
34892 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
34911 TCGCAACG
1 TCGCAACG
34919 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:34928 original size:14 final size:14
Alignment explanation
Indices: 34909--34965 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
34899 GCGAAATGAA
*
34909 AATCGCAACGACAG
1 AATCGCAACGAAAG
34923 AATCGCAAAGCGAAATG
1 AATCGC-AA-CGAAA-G
34940 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
34956 AATCGCAACG
1 AATCGCAACG
34966 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
15 2 0.05
16 5 0.14
17 6 0.16
18 2 0.05
19 6 0.16
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:34936 original size:33 final size:33
Alignment explanation
Indices: 34890--34982 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
34880 GCGAAACCAA
*
34890 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
34923 AATCGCAAAGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
34956 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
34983 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:34947 original size:19 final size:19
Alignment explanation
Indices: 34869--34987 Score: 105
Period size: 19 Copynumber: 6.8 Consensus size: 19
34859 CACGAAACTT
* **
34869 AAAATCGCAACGCGAAACC
1 AAAATCGCAAAGCGAAATG
*
34888 AAAATCGCAACGCGAAATG
1 AAAATCGCAAAGCGAAATG
*
34907 AAAATCGC-AA-CGACA-G
1 AAAATCGCAAAGCGAAATG
34923 --AATCGCAAAGCGAAATG
1 AAAATCGCAAAGCGAAATG
34940 AAAATCGC-AA-CGAAA-G
1 AAAATCGCAAAGCGAAATG
*
34956 --AATCGCAACGCGAAATG
1 AAAATCGCAAAGCGAAATG
*
34973 AAAATCGCAATGCGA
1 AAAATCGCAAAGCGA
34988 TTTTGGTTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 12 0.14
15 3 0.04
16 11 0.13
17 11 0.13
18 3 0.04
19 43 0.52
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.09
Consensus pattern (19 bp):
AAAATCGCAAAGCGAAATG
Found at i:35005 original size:19 final size:19
Alignment explanation
Indices: 34983--35111 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
34973 AAAATCGCAA
34983 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
35002 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
35016 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
35035 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
35049 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
35068 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
35087 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
35107 TGCGA
1 TGCGA
35112 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:35025 original size:33 final size:33
Alignment explanation
Indices: 34983--35074 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
34973 AAAATCGCAA
34983 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
35016 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
35049 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
35075 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:35446 original size:93 final size:93
Alignment explanation
Indices: 35155--35626 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
35145 TTGAATGGAT
35155 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
35220 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
35248 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
35312 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
35340 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
35405 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
35433 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
35497 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
35525 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
35590 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
35618 AAATTTACT
1 AAATTTACT
35627 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 191 0.51
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:35467 original size:185 final size:185
Alignment explanation
Indices: 35155--35626 Score: 926
Period size: 185 Copynumber: 2.6 Consensus size: 185
35145 TTGAATGGAT
35155 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
35220 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
35285 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
35340 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
35405 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
35470 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
35525 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
35590 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
35627 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 285 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:37350 original size:14 final size:14
Alignment explanation
Indices: 37331--37420 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
37321 TTGAAATGAA
37331 AATCGCAACGAGAG
1 AATCGCAACGAGAG
37345 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
37362 ACAATCGCAACGAGAT
1 --AATCGCAACGAGAG
*
37378 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
37397 AATCGCAACGAGAG
1 AATCGCAACGAGAG
37411 AATCGCAACG
1 AATCGCAACG
37421 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 20
0.73 0.03 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 7 0.11
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:37368 original size:33 final size:33
Alignment explanation
Indices: 37323--37437 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
37313 GTCTTTGGTT
37323 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
37356 GAGATGACAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
37389 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
37422 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
37438 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:37369 original size:19 final size:18
Alignment explanation
Indices: 37330--37442 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
37320 GTTGAAATGA
37330 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
37345 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
37362 ACAATCGCAA--CGAGAT-
1 A-AATCGCAACGCGAGATG
*
37378 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
37395 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
37411 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
37428 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
37443 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:37473 original size:14 final size:14
Alignment explanation
Indices: 37454--37508 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
37444 TTTGGTTTCG
37454 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
37468 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
37487 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
37501 CGTTGCGA
1 CGTTGCGA
37509 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:37486 original size:33 final size:33
Alignment explanation
Indices: 37438--37508 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
37428 AAAATCGCAA
**
37438 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
37471 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
37504 TGCGA
1 TGCGA
37509 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:37516 original size:33 final size:33
Alignment explanation
Indices: 37449--37530 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
37439 GCGATTTTGG
***
37449 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
37482 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
37515 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
37531 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:37535 original size:20 final size:20
Alignment explanation
Indices: 37461--37549 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
37451 TCGCGTTGCG
37461 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
37481 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
37494 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
37514 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
37534 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
37550 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:37671 original size:33 final size:33
Alignment explanation
Indices: 37629--37699 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
37619 AATACTAACT
*
37629 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
37662 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
37695 TGAAA
1 TGAAA
37700 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:37933 original size:22 final size:22
Alignment explanation
Indices: 37881--37935 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
37871 TGGTTGTGAG
*
37881 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
37903 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
37925 GGATTTCTTCG
1 GGATTTCTTCG
37936 CCGTAGAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:38106 original size:20 final size:20
Alignment explanation
Indices: 38081--38254 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
38071 CTTTAAATAT
38081 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
38101 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
38123 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
38142 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
38162 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
38182 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
38202 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
38222 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
38242 CGCGTTGCGATTT
1 CGCGTTGCGATTT
38255 TCATATTCGC
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 113 0.86
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:38263 original size:20 final size:20
Alignment explanation
Indices: 38080--38273 Score: 66
Period size: 20 Copynumber: 9.7 Consensus size: 20
38070 GCTTTAAATA
***
38080 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* *
38100 ACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGA-TTTATATAT
** ***
38121 TATCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
38141 ACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
38161 ACGCATTGCGATTTACCCAT
1 TCGCGTTGCGATTTATATAT
* ***
38181 ACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
38201 ACACGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * *
38221 ACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTATATAT
38241 TCGCGTTGCGATTT-TCATAT
1 TCGCGTTGCGATTTAT-ATAT
*
38261 TCGCATTGCGATT
1 TCGCGTTGCGATT
38274 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
19 1 0.01
20 128 0.89
21 15 0.10
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATTTATATAT
Found at i:38273 original size:60 final size:60
Alignment explanation
Indices: 38081--38254 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
38071 CTTTAAATAT
**
38081 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
38142 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* *
38202 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
38255 TCATATTCGC
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.71
61 28 0.29
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:38354 original size:20 final size:20
Alignment explanation
Indices: 38329--38380 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
38319 AAGAATCGCG
*
38329 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
38349 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
38369 TTGCGATTCTGG
1 TTGCGATTCTGG
38381 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:40394 original size:3 final size:3
Alignment explanation
Indices: 40388--40420 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
40378 TATGTAACAT
*
40388 TAA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
40421 TTTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:40403 original size:6 final size:6
Alignment explanation
Indices: 40375--40434 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
40365 GTAAAAAAAA
* * * * *
40375 TAATAT GTAACAT TAATAA TAATAT TAATAA TAATAA TAATA- TAATTT
1 TAATAT -TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
40423 TAATA- TAATAT T
1 TAATAT TAATAT T
40435 TATAATCCGG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
5 9 0.20
6 30 0.68
7 5 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TAATAT
Found at i:42951 original size:64 final size:64
Alignment explanation
Indices: 42883--43026 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 64
42873 ATGTACATGC
42883 AGTGCATCGATGCATTG-ATTTAAAAAGAAAACATCGAATAGGATTTATGCATCAATACATAAG-
1 AGTGCATCGATGCATTGCA-TTAAAAA-AAAACATCGAATAGGATTTATGCATCAATACAT-AGT
42946 G-
63 GT
* * * * *
42947 AGTGCATCGATGCA-TGCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTG
1 AGTGCATCGATGCATTG--CATTAAAAAAAAACATCGAATAGGATTTATGCATCAATACATAGTG
43011 T
64 T
43012 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
43027 ATCTCCATTA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
63 3 0.04
64 45 0.65
65 20 0.29
66 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (64 bp):
AGTGCATCGATGCATTGCATTAAAAAAAAACATCGAATAGGATTTATGCATCAATACATAGTGT
Found at i:43674 original size:103 final size:103
Alignment explanation
Indices: 43487--43701 Score: 358
Period size: 103 Copynumber: 2.1 Consensus size: 103
43477 GTAGAGGGTC
*
43487 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGGGTGAGACACATAC
* * *
43552 TTGATCCTTGGCATGTGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
* *
43590 TATGTGGTCATTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGGGTGAGACACATAC
* *
43655 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
43693 TATGTGGTC
1 TATGTGGTC
43702 CTTATGGACA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
Found at i:43783 original size:23 final size:23
Alignment explanation
Indices: 43720--43783 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
43710 CATTATTATA
* *
43720 TGGCACTACGGTGCAATACTACG
1 TGGCACTTCGGTGCAATTCTACG
*
43743 CGGCAC-TCTGGTGCAATTCTACG
1 TGGCACTTC-GGTGCAATTCTACG
*
43766 TGGCACTTCGGTGTAATT
1 TGGCACTTCGGTGCAATT
43784 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.91
24 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:47961 original size:12 final size:12
Alignment explanation
Indices: 47944--47969 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47934 AACCAATTAC
47944 ATATTTGGATGA
1 ATATTTGGATGA
47956 ATATTTGGATGA
1 ATATTTGGATGA
47968 AT
1 AT
47970 TTAGGGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (12 bp):
ATATTTGGATGA
Found at i:49068 original size:42 final size:40
Alignment explanation
Indices: 48976--49095 Score: 152
Period size: 42 Copynumber: 2.9 Consensus size: 40
48966 CATAATTCCC
* ** *
48976 AAATTATTTCACCCTTAACATTCTAAATTCCTAATTTTTTT
1 AAATTATTTCA-CCATAACATTCTAAATTATTAATTTTTTA
49017 AAATTATTTCACCATAACATTCTAAATTATTATTATTTTTTA
1 AAATTATTTCACCATAACATTCTAAATTATTA--ATTTTTTA
*
49059 AAATTATTTCACCATAAC-TATCTAAATTATTTATTTT
1 AAATTATTTCACCATAACAT-TCTAAATTATTAATTTT
49096 AACTTCAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
40 23 0.32
41 12 0.17
42 36 0.51
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (40 bp):
AAATTATTTCACCATAACATTCTAAATTATTAATTTTTTA
Found at i:49662 original size:3 final size:3
Alignment explanation
Indices: 49654--49679 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49644 AAGGAGTTTG
49654 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
49680 TCCTAACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:53628 original size:15 final size:15
Alignment explanation
Indices: 53608--53639 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
53598 AACCTATTAA
53608 AAGAACAAAGTCTCG
1 AAGAACAAAGTCTCG
53623 AAGAACAAAGTCTCG
1 AAGAACAAAGTCTCG
53638 AA
1 AA
53640 AATTCAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (15 bp):
AAGAACAAAGTCTCG
Found at i:54910 original size:30 final size:30
Alignment explanation
Indices: 54862--54933 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
54852 TAAGTGTATG
*
54862 CTCATAATAACAA-ATATTGAAAAAAATGGA
1 CTCATAATAA-AATGTATTGAAAAAAATGGA
* *
54892 CCTC-TAATAAAATGTATTGAAAAAATTGTA
1 -CTCATAATAAAATGTATTGAAAAAAATGGA
54922 CTCATAATAAAA
1 CTCATAATAAAA
54934 AATAAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 5 0.14
30 28 0.78
31 3 0.08
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.28
Consensus pattern (30 bp):
CTCATAATAAAATGTATTGAAAAAAATGGA
Found at i:55053 original size:29 final size:30
Alignment explanation
Indices: 54976--55054 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
54966 AACATGTCTC
*
54976 TAATAACAAATATT-GAAAAATTAGGCCCT
1 TAATAACAAATATTAGAAAAATGAGGCCCT
* *
55005 TAATAATAAATATTAAAAAAATGA-GCCCT
1 TAATAACAAATATTAGAAAAATGAGGCCCT
* *
55034 TAATAACAAGTGTTAGAAAAA
1 TAATAACAAATATTAGAAAAA
55055 AATATTGACA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 35 0.83
30 7 0.17
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (30 bp):
TAATAACAAATATTAGAAAAATGAGGCCCT
Found at i:56355 original size:75 final size:74
Alignment explanation
Indices: 56276--56576 Score: 350
Period size: 75 Copynumber: 4.1 Consensus size: 74
56266 CGAAGTTTTT
** * *
56276 TATATAATATATAGTTTTGAAAACGGTTTTCGAAAATATATATATTATATAG-CTTTG-AAATTT
1 TATATAATATATAGTTTTGAAAA-TATTTTTGAAAATATATATATTATATAGTTTTTGAAAATTT
56339 TTTGAAAACATA
65 TTTG-AAA-ATA
* * * **
56351 TATATAATATTTAGTTTTTGAAAATATTTTTAAAAATATATATAATATATAGTTTTTGAAAACAT
1 TATATAATATATAG-TTTTGAAAATATTTTTGAAAATATATATATTATATAGTTTTTGAAAATTT
56416 TTTGAAAATA
65 TTTGAAAATA
*
56426 TATATAATATATAGGTTTTGAAAACA-TTTTGAAAATATATATATAATATATAGTTTTTGAAAAT
1 TATATAATATATA-GTTTTGAAAATATTTTTGAAAATATATATAT--TATATAGTTTTTGAAAAT
*
56490 ATTTTTGAAAATG
63 -TTTTTGAAAATA
**
56503 TATATAATATATAGTTTTGAAAATATTTTTG--AA-A-ATATA-TATATAG-TTTTGAAAACATT
1 TATATAATATATAGTTTTGAAAATATTTTTGAAAATATATATATTATATAGTTTTTGAAAATTTT
56562 TTGAAAATA
66 TTGAAAATA
56571 TATATA
1 TATATA
56577 TATGGTTTTG
Statistics
Matches: 198, Mismatches: 20, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
68 16 0.08
69 9 0.05
70 7 0.04
73 5 0.03
74 17 0.09
75 63 0.32
76 45 0.23
77 36 0.18
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (74 bp):
TATATAATATATAGTTTTGAAAATATTTTTGAAAATATATATATTATATAGTTTTTGAAAATTTT
TTGAAAATA
Found at i:56433 original size:37 final size:36
Alignment explanation
Indices: 56276--56592 Score: 346
Period size: 37 Copynumber: 8.7 Consensus size: 36
56266 CGAAGTTTTT
*
56276 TATATAATATATAGTTTTGAAAACGGTTTTCGAAAATA
1 TATATAATATATAGTTTTGAAAAC-ATTTT-GAAAATA
* * **
56314 TATATATTATATAGCTTTG-AAATTTTTTGAAAACATA
1 TATATAATATATAGTTTTGAAAACATTTTG-AAA-ATA
* * *
56351 TATATAATATTTAGTTTTTGAAAATATTTTTAAAAATA
1 TATATAATATATAG-TTTTGAAAACA-TTTTGAAAATA
56389 TATATAATATATAGTTTTTGAAAACATTTTGAAAATA
1 TATATAATATATAG-TTTTGAAAACATTTTGAAAATA
56426 TATATAATATATAGGTTTTGAAAACATTTTGAAAATATA
1 TATATAATATATA-GTTTTGAAAACATTTTG-AAA-ATA
* *
56465 TATATAATATATAGTTTTTGAAAATATTTTTGAAAATG
1 TATATAATATATAG-TTTTGAAAACA-TTTTGAAAATA
*
56503 TATATAATATATAGTTTTGAAAATATTTTTG--AA-A
1 TATATAATATATAGTTTTGAAAACA-TTTTGAAAATA
56537 -ATAT-ATATATAGTTTTGAAAACATTTTG-AAA-A
1 TATATAATATATAGTTTTGAAAACATTTTGAAAATA
*
56569 TATAT-ATATATGGTTTTGAAAACA
1 TATATAATATATAGTTTTGAAAACA
56593 CATATAATAT
Statistics
Matches: 250, Mismatches: 17, Indels: 29
0.84 0.06 0.10
Matches are distributed among these distances:
31 5 0.02
32 21 0.08
33 26 0.10
35 3 0.01
36 7 0.03
37 74 0.30
38 69 0.28
39 36 0.14
40 9 0.04
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (36 bp):
TATATAATATATAGTTTTGAAAACATTTTGAAAATA
Found at i:56466 original size:114 final size:112
Alignment explanation
Indices: 56276--56578 Score: 429
Period size: 114 Copynumber: 2.7 Consensus size: 112
56266 CGAAGTTTTT
* * * **
56276 TATATAATATATAGTTTTGAAAACGGTTTTCGAAAATATATATATTATATAGCTTTG-AAATTTT
1 TATATAATATATAGTTTTGAAAAC-ATTTT-GAAAATATATATAATATATAGTTTTGAAAACATT
* *
56340 TTGAAAACATATATATAATATTTAGTTTTTGAAAATATTTTTAAAAATA
64 TTGAAAATATATATATAATATATAGTTTTTGAAAATATTTTTAAAAATA
56389 TATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGGTTTTGAAAACATT
1 TATATAATATATAG-TTTTGAAAACATTTTGAAAATATATATAATATATA-GTTTTGAAAACATT
* *
56454 TTGAAAATATATATATAATATATAGTTTTTGAAAATATTTTTGAAAATG
64 TTGAAAATATATATATAATATATAGTTTTTGAAAATATTTTTAAAAATA
*
56503 TATATAATATATAGTTTTGAAAATATTTTTG--AA-A-ATAT-ATATATAGTTTTGAAAACATTT
1 TATATAATATATAGTTTTGAAAACA-TTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
56563 TGAAAATATATATATA
65 TGAAAATATATATATA
56579 TGGTTTTGAA
Statistics
Matches: 176, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
108 31 0.18
109 7 0.04
110 4 0.02
111 1 0.01
112 21 0.12
113 33 0.19
114 79 0.45
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (112 bp):
TATATAATATATAGTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTTT
GAAAATATATATATAATATATAGTTTTTGAAAATATTTTTAAAAATA
Found at i:56567 original size:31 final size:31
Alignment explanation
Indices: 56466--56636 Score: 147
Period size: 31 Copynumber: 5.4 Consensus size: 31
56456 GAAAATATAT
56466 ATATAATATATAGTTTTTGAAAATATTTTTGAAAA
1 ATAT-ATATATAG-TTTTGAAAATA-TTTTG-AAA
56501 TGTATATAATATATAGTTTTGAAAATATTTTTGAAA
1 ---ATAT-ATATATAGTTTTGAAAATA-TTTTGAAA
*
56537 ATATATATATAGTTTTGAAAACATTTTGAAA
1 ATATATATATAGTTTTGAAAATATTTTGAAA
* * *
56568 ATATATATATATGGTTTTGAAAACA-----CAT
1 ATATATATATA--GTTTTGAAAATATTTTGAAA
*
56596 ATA-ATATATAGTTTTGAAAATATTTTAAAA
1 ATATATATATAGTTTTGAAAATATTTTGAAA
*
56626 ATAAATATATA
1 ATATATATATA
56637 ACATATAATT
Statistics
Matches: 119, Mismatches: 6, Indels: 23
0.80 0.04 0.16
Matches are distributed among these distances:
25 11 0.09
27 7 0.06
28 4 0.03
30 4 0.03
31 26 0.22
32 18 0.15
33 16 0.13
36 3 0.03
37 17 0.14
38 13 0.11
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (31 bp):
ATATATATATAGTTTTGAAAATATTTTGAAA
Found at i:56672 original size:38 final size:36
Alignment explanation
Indices: 56582--56672 Score: 92
Period size: 38 Copynumber: 2.4 Consensus size: 36
56572 ATATATATGG
* * * *
56582 TTTTGAAAACACATATAATATATAGTTTTGAAAATA
1 TTTTGAAAATATATATAACATATAATTTTGAAAATA
* *
56618 TTTTAAAAATAAATATATAACATATAATTTTGGAAAATCT
1 TTTTGAAAAT--ATATATAACATATAATTTT-GAAAAT-A
56658 TTTTGAAAATATATA
1 TTTTGAAAATATATA
56673 ATATTTTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
36 8 0.18
38 21 0.48
39 6 0.14
40 9 0.20
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (36 bp):
TTTTGAAAATATATATAACATATAATTTTGAAAATA
Found at i:56818 original size:12 final size:12
Alignment explanation
Indices: 56789--56825 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
56779 ATTTACTTAC
*
56789 TTTTTAATTTAA
1 TTTTTATTTTAA
56801 --TTTATTTTAA
1 TTTTTATTTTAA
56811 TTTTTATTTTAA
1 TTTTTATTTTAA
56823 TTT
1 TTT
56826 GGTCTATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATTTTAA
Found at i:57631 original size:177 final size:177
Alignment explanation
Indices: 57335--57692 Score: 680
Period size: 177 Copynumber: 2.0 Consensus size: 177
57325 AAGAGACATC
57335 GGTTTCAAGGTAAAAAATCGAAACTTTGGGCACAGATCTACACCTATAAGGTTTTTTTAGGACGA
1 GGTTTCAAGGTAAAAAATCGAAACTTTGGGCACAGATCTACACCTATAAGGTTTTTTTAGGACGA
57400 ATAGGCTTCGGTTTTGTGATTATCGTGTTAAGGTGAGCATTTTAGTAAGTTTGGATTTTTTTCAA
66 ATAGGCTTCGGTTTTGTGATTATCGTGTTAAGGTGAGCATTTTAGTAAGTTTGGATTTTTTTCAA
*
57465 CCACCGGAGGCGGTGGTCGGAGCGGTAGCCGGCGGCGTCCGAGCAGT
131 CCACCGGAGGCGGTGGTCGGAGCGGTAGACGGCGGCGTCCGAGCAGT
* *
57512 GGTTTCAAGGTAAAAAATTGAAACTTTGGGCACAGATCTACACCTATAGGGTTTTTTTAGGACGA
1 GGTTTCAAGGTAAAAAATCGAAACTTTGGGCACAGATCTACACCTATAAGGTTTTTTTAGGACGA
57577 ATAGGCTTCGGTTTTGTGATTATCGTGTTAAGGTGAGCATTTTAGTAAGTTTGGATTTTTTTCAA
66 ATAGGCTTCGGTTTTGTGATTATCGTGTTAAGGTGAGCATTTTAGTAAGTTTGGATTTTTTTCAA
*
57642 CCACCGGAGGCGGTGGTCGGAGCGGTAGACGGTGGCGTCCGAGCAGT
131 CCACCGGAGGCGGTGGTCGGAGCGGTAGACGGCGGCGTCCGAGCAGT
57689 GGTT
1 GGTT
57693 GGTCACCGTA
Statistics
Matches: 177, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 177 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.31
Consensus pattern (177 bp):
GGTTTCAAGGTAAAAAATCGAAACTTTGGGCACAGATCTACACCTATAAGGTTTTTTTAGGACGA
ATAGGCTTCGGTTTTGTGATTATCGTGTTAAGGTGAGCATTTTAGTAAGTTTGGATTTTTTTCAA
CCACCGGAGGCGGTGGTCGGAGCGGTAGACGGCGGCGTCCGAGCAGT
Found at i:58331 original size:2 final size:2
Alignment explanation
Indices: 58326--58381 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
58316 TGTTTAATAA
58326 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
58368 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
58382 TTATTTTACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65166 original size:39 final size:38
Alignment explanation
Indices: 65123--65435 Score: 289
Period size: 39 Copynumber: 8.4 Consensus size: 38
65113 TTTTAATTTT
65123 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTGAAAACA
* *
65162 TTTTG-AAAATATATATAATATATAATTTTTGAAAAAAA
1 TTTTGAAAAATATATATAATATATAGTTTTTG-AAAACA
* * *
65200 ATTGGAAAAA-ATATATATATAATATAGTTTTTGAAAATA
1 TTTTGAAAAATATATATA-AT-ATATAGTTTTTGAAAACA
* * *
65239 TTGTTG-AAAATGTATATAATATATAG-TTTTAAAAATA
1 TT-TTGAAAAATATATATAATATATAGTTTTTGAAAACA
*
65276 TTTTTG----A-A-A-AT-ATATATAG-TTTTGCAAACA
1 -TTTTGAAAAATATATATAATATATAGTTTTTGAAAACA
*
65306 TTTTG-AAAATATATATAATATAT-GGTTTTGAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTGAAAACA
*
65342 TTTTGAAAACACATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTGAAAACA
* * * * *
65381 TTTTGAAAATAAATATATAACATATAATTTTGGAAAACCT
1 TTTTGAAAA-ATATATATAATATATAGTTTTTGAAAA-CA
65421 TTTTG-AAAATATATA
1 TTTTGAAAAATATATA
65436 ATATTTTTAA
Statistics
Matches: 231, Mismatches: 24, Indels: 39
0.79 0.08 0.13
Matches are distributed among these distances:
29 5 0.02
30 16 0.07
31 2 0.01
32 2 0.01
33 1 0.00
34 2 0.01
35 3 0.01
36 21 0.09
37 38 0.16
38 46 0.20
39 70 0.30
40 25 0.11
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.41
Consensus pattern (38 bp):
TTTTGAAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:65172 original size:28 final size:28
Alignment explanation
Indices: 65122--65176 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
65112 GTTTTAATTT
*
65122 TTTTTGAAAACATATATATAATATATAG
1 TTTTTGAAAACATATATAAAATATATAG
*
65150 TTTTTGAAAACAT-TTTGAAAATATATA
1 TTTTTGAAAACATATAT-AAAATATATA
65177 TAATATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTTTGAAAACATATATAAAATATATAG
Found at i:65225 original size:40 final size:40
Alignment explanation
Indices: 65128--65236 Score: 125
Period size: 38 Copynumber: 2.8 Consensus size: 40
65118 ATTTTTTTTG
* * * *
65128 AAAACATATATATAATATATAGTTTTTG-AAAACATTTTGAA
1 AAAATATATATATAATATA-A-TTTTTGAAAAAAAATTGGAA
*
65169 AATATATATA-AT-ATATAATTTTTGAAAAAAAATTGGAA
1 AAAATATATATATAATATAATTTTTGAAAAAAAATTGGAA
*
65207 AAAATATATATATAATATAGTTTTTGAAAA
1 AAAATATATATATAATATAATTTTTGAAAA
65237 TATTGTTGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
37 6 0.10
38 20 0.34
39 7 0.12
40 17 0.29
41 8 0.14
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (40 bp):
AAAATATATATATAATATAATTTTTGAAAAAAAATTGGAA
Found at i:65291 original size:66 final size:64
Alignment explanation
Indices: 65228--65447 Score: 170
Period size: 66 Copynumber: 3.1 Consensus size: 64
65218 ATAATATAGT
* * *
65228 TTTTGAAAATATTGTTGAAAATGTATATAATATATAGTTTTAAAAATATTTTTGAAAATATATAT
1 TTTTGAAAACATT-TTGAAAATATATATAATATATAGTTTTAAAAACA-TTTTGAAAATATATAT
65293 A
64 A
* * *
65294 GTTTTGCAAACATTTTGAAAATATATATAATATATGGTTTTGAAAACATTTTGAAAACACATATA
1 -TTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTAAAAACATTTTG-----A-A-A-A
65359 TAATATATA
57 T-ATATATA
* * * *
65368 GTTTTTGAAAACATTTTGAAAATAAATATATAACATATAATTTTGGAAAACCTTTTTGAAAATAT
1 --TTTTGAAAACATTTTGAAAAT--ATATATAATATATAGTTTT--AAAAACATTTTGAAAATAT
65433 ATAATA
60 AT-ATA
*
65439 TTTTTAAAA
1 TTTTGAAAA
65448 TGTTTTTAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
65 5 0.04
66 30 0.24
67 11 0.09
69 8 0.07
70 5 0.04
71 6 0.05
72 2 0.02
73 3 0.02
74 8 0.07
75 20 0.16
77 16 0.13
79 9 0.07
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (64 bp):
TTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTAAAAACATTTTGAAAATATATATA
Found at i:65319 original size:29 final size:30
Alignment explanation
Indices: 65257--65322 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
65247 AATGTATATA
*
65257 ATATATAGTTTTAAAAATATTTTTGAAAAT
1 ATATATAGTTTTAAAAACATTTTTGAAAAT
**
65287 ATATATAGTTTTGCAAACA-TTTTGAAAAT
1 ATATATAGTTTTAAAAACATTTTTGAAAAT
65316 ATATATA
1 ATATATA
65323 ATATATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (30 bp):
ATATATAGTTTTAAAAACATTTTTGAAAAT
Found at i:65328 original size:144 final size:144
Alignment explanation
Indices: 65142--65447 Score: 383
Period size: 144 Copynumber: 2.1 Consensus size: 144
65132 CATATATATA
*
65142 ATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAATTTTTGAAAAAAAATTGGAA
1 ATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATAT-AGTTTTG-AAAAAAATTGGAA
* * * *
65207 AA-A-ATATATATATAATATAGTTTTTGAAAATATTGTTGAAAAT-GTATATAATATATAGTTTT
64 AACACATATATA-AT-ATATAGTTTTTGAAAACATT-TTGAAAATAATATATAACATATAATTTT
*
65269 -AAAAATATTTTTGAAAAT
126 GAAAAACATTTTTGAAAAT
* * * * *
65287 ATATATAG-TTTTGCAAACATTTTGAAAATATATATAATATATGGTTTTGAAAACATTTTGAAAA
1 ATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAAAAATTGGAAAA
*
65351 CACATATATAATATATAGTTTTTGAAAACATTTTGAAAATAAATATATAACATATAATTTTGGAA
66 CACATATATAATATATAGTTTTTGAAAACATTTTGAAAAT-AATATATAACATATAATTTTGAAA
*
65416 AACCTTTTTGAAAAT
130 AACATTTTTGAAAAT
65431 ATATAATA-TTTTT-AAAA
1 ATAT-ATAGTTTTTGAAAA
65448 TGTTTTTAAA
Statistics
Matches: 140, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
141 8 0.06
142 31 0.22
143 24 0.17
144 62 0.44
145 15 0.11
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.41
Consensus pattern (144 bp):
ATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAAAAATTGGAAAA
CACATATATAATATATAGTTTTTGAAAACATTTTGAAAATAATATATAACATATAATTTTGAAAA
ACATTTTTGAAAAT
Found at i:65359 original size:104 final size:102
Alignment explanation
Indices: 65212--65397 Score: 259
Period size: 104 Copynumber: 1.8 Consensus size: 102
65202 TGGAAAAAAT
* * ** *
65212 ATATATATAATATAGTTTTTGAAAATATTGTTGAAAATGTATATAATATATAG-TTTTAAAAATA
1 ATATATATAATATAGGTTTTGAAAACATTGTTGAAAACATATATAATATATAGTTTTTAAAAACA
*
65276 TTTTTGAAAATATATATAGTTTTGCAAACATTTTGAAA
66 -TTTTGAAAATAAATATAGTTTTGCAAACATTTTGAAA
*
65314 ATATATATAATATATGGTTTTGAAAACATT-TTGAAAACACATATATAATATATAGTTTTTGAAA
1 ATATATATAATATA-GGTTTTGAAAACATTGTTG-AAA-ACATATATAATATATAGTTTTTAAAA
65378 ACATTTTGAAAATAAATATA
63 ACATTTTGAAAATAAATATA
65398 TAACATATAA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
102 17 0.23
103 16 0.22
104 31 0.42
105 9 0.12
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (102 bp):
ATATATATAATATAGGTTTTGAAAACATTGTTGAAAACATATATAATATATAGTTTTTAAAAACA
TTTTGAAAATAAATATAGTTTTGCAAACATTTTGAAA
Found at i:66219 original size:8 final size:8
Alignment explanation
Indices: 66206--66232 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
66196 TCAACCGGAT
66206 GAGGGAGA
1 GAGGGAGA
66214 GAGGGAGA
1 GAGGGAGA
66222 GAGGGAGA
1 GAGGGAGA
66230 GAG
1 GAG
66233 AAGGGAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (8 bp):
GAGGGAGA
Found at i:66666 original size:7 final size:7
Alignment explanation
Indices: 66656--66707 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
66646 TTTTATTTTT
66656 TTTAAAA
1 TTTAAAA
66663 TTTAAAA
1 TTTAAAA
66670 TTTAAAA
1 TTTAAAA
66677 TTTAAAA
1 TTTAAAA
*
66684 TTTAACA
1 TTTAAAA
*
66691 TTTAACA
1 TTTAAAA
*
66698 TTTAACA
1 TTTAAAA
66705 TTT
1 TTT
66708 TTTTATTTCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:68665 original size:35 final size:36
Alignment explanation
Indices: 68619--68697 Score: 133
Period size: 35 Copynumber: 2.2 Consensus size: 36
68609 CACAATCATT
*
68619 AATTACATTCTAAACCCCAAATT-CTAAAATACTTC
1 AATTACATTCTAAACCCCAAATTCCAAAAATACTTC
*
68654 AATTACATTCTAAACCTCAAATTCCAAAAATACTTC
1 AATTACATTCTAAACCCCAAATTCCAAAAATACTTC
68690 AATTACAT
1 AATTACAT
68698 GCCCAAACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 22 0.54
36 19 0.46
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (36 bp):
AATTACATTCTAAACCCCAAATTCCAAAAATACTTC
Found at i:68691 original size:36 final size:35
Alignment explanation
Indices: 68619--68714 Score: 131
Period size: 36 Copynumber: 2.7 Consensus size: 35
68609 CACAATCATT
*
68619 AATTACATTCTAAACCCCAAATTCTAAAATACTTC
1 AATTACATTCTAAACCCCAAATTCAAAAATACTTC
*
68654 AATTACATTCTAAACCTCAAATTCCAAAAATACTTC
1 AATTACATTCTAAACCCCAAATT-CAAAAATACTTC
* *
68690 AATTACATGCCCAAA-CCCAAATTCA
1 AATTACAT-TCTAAACCCCAAATTCA
68715 TAATTCATTC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 24 0.44
36 26 0.48
37 4 0.07
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.28
Consensus pattern (35 bp):
AATTACATTCTAAACCCCAAATTCAAAAATACTTC
Found at i:69357 original size:148 final size:148
Alignment explanation
Indices: 69188--69474 Score: 470
Period size: 148 Copynumber: 1.9 Consensus size: 148
69178 AAACTGTTTA
* * *
69188 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTAAAA
*
69253 AATTCAATTCAATTAGACTTGATTTAAATTTTATAAACTCAAA-T-AAAAAATATTTCAAGCCAA
66 AATTCAATTCAATTAGAATTGATTTAAATTTTATAAACTCAAATTGAAAAAA-A-TTCAAGCCAA
*
69316 TTATTTTATAAGTTGAACTG
129 ATATTTTATAAGTTGAACTG
69336 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTAAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTAAAA
* * *
69401 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATTGAAAAAAATTCGAGTCAAAT
66 AATTCAATTCAATTAGAATTGATTTAAATTTTATAAACTCAAATTGAAAAAAATTCAAGCCAAAT
69466 ATTTTATAA
131 ATTTTATAA
69475 ACTGAATTGA
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
148 121 0.94
149 2 0.02
150 6 0.05
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTAAAA
AATTCAATTCAATTAGAATTGATTTAAATTTTATAAACTCAAATTGAAAAAAATTCAAGCCAAAT
ATTTTATAAGTTGAACTG
Found at i:69693 original size:35 final size:35
Alignment explanation
Indices: 69654--69730 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
69644 ATTAGGTATG
**
69654 TAATTGAAGTATTTTGGAATTTGA-GGTTTAGAATA
1 TAATTGAAACATTTTGG-ATTTGAGGGTTTAGAATA
* *
69689 TAATTGAAACATTTTGGATTTTAGGGTTTAGAATG
1 TAATTGAAACATTTTGGATTTGAGGGTTTAGAATA
69724 TAATTGA
1 TAATTGA
69731 TGATTGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.14
35 32 0.86
ACGTcount: A:0.34, C:0.01, G:0.22, T:0.43
Consensus pattern (35 bp):
TAATTGAAACATTTTGGATTTGAGGGTTTAGAATA
Found at i:75545 original size:20 final size:20
Alignment explanation
Indices: 75517--75554 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
75507 CTTCCATTAT
* *
75517 TTTTCTTTTCTACCTTTTCC
1 TTTTATTTTCAACCTTTTCC
75537 TTTTATTTTCAACCTTTT
1 TTTTATTTTCAACCTTTT
75555 TAGGCAAAAA
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:0.11, C:0.24, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATTTTCAACCTTTTCC
Found at i:76539 original size:70 final size:70
Alignment explanation
Indices: 76422--76564 Score: 259
Period size: 70 Copynumber: 2.0 Consensus size: 70
76412 TTTTTCCTTC
*
76422 TTGCCTGTAGTATGTTGAATAGTTGACATTTAGATTTTAGACTTCAAAAAGAAAAATTGAATTAT
1 TTGCCTGTAGTATGTTGAATAGTTGACATTTAGATTTTAGACCTCAAAAAGAAAAATTGAATTAT
76487 AGATG
66 AGATG
* *
76492 TTGCCTGTGGTATGTTGAATAGTTGACATTTAGATTTTAGACCTCAAAAAGCAAAATTGAATTAT
1 TTGCCTGTAGTATGTTGAATAGTTGACATTTAGATTTTAGACCTCAAAAAGAAAAATTGAATTAT
76557 AGATG
66 AGATG
76562 TTG
1 TTG
76565 TCTGCGAACT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (70 bp):
TTGCCTGTAGTATGTTGAATAGTTGACATTTAGATTTTAGACCTCAAAAAGAAAAATTGAATTAT
AGATG
Found at i:81614 original size:35 final size:35
Alignment explanation
Indices: 81567--81646 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
81557 AACACAATCA
* *
81567 TCAATTATATTCTAAACCCCAAAATCCAAAATATT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* *
81602 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
81637 TCAATTACAT
1 TCAATTACAT
81647 GTCCAATCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATACT
Found at i:81660 original size:35 final size:34
Alignment explanation
Indices: 81567--81662 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 34
81557 AACACAATCA
* * * *
81567 TCAATTATATTCTAAACCCCAAAATCCAAAATATT
1 TCAATTACATTCCAAA-CCCAAATTCCAAAATACT
*
81602 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCCAAACC-CAAATTCCAAAATACT
*
81637 TCAATTACATGTCCAATCCCAAATTC
1 TCAATTACAT-TCCAAACCCAAATTC
81663 ATAATCAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
34 2 0.04
35 46 0.85
36 6 0.11
ACGTcount: A:0.42, C:0.26, G:0.01, T:0.31
Consensus pattern (34 bp):
TCAATTACATTCCAAACCCAAATTCCAAAATACT
Found at i:88563 original size:81 final size:81
Alignment explanation
Indices: 88444--88593 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 81
88434 ATACAAACAC
** * * * *
88444 CAAACGCTGCTAAAGTACTTCTCTGTTGCAATGTTTGTTGTAAAAATGCCACTATATATAAACCC
1 CAAACGCCACTAAAGTACTTCTCTGTTGCAACGTTTGTT-AAAAAACGCAACTATATATAAACCC
88509 TATTGTGCATTTTTATA
65 TATTGTGCATTTTTATA
** * *
88526 CAAACGCCACTAAAGTAC-TCTCTGTTGCGGCGTTTGTTAAAAAACGCAACTATATATGAATCCT
1 CAAACGCCACTAAAGTACTTCTCTGTTGCAACGTTTGTTAAAAAACGCAACTATATATAAACCCT
88590 ATTG
66 ATTG
88594 CAGCGTAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 25 0.43
81 17 0.29
82 16 0.28
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (81 bp):
CAAACGCCACTAAAGTACTTCTCTGTTGCAACGTTTGTTAAAAAACGCAACTATATATAAACCCT
ATTGTGCATTTTTATA
Found at i:88764 original size:13 final size:13
Alignment explanation
Indices: 88730--88765 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
88720 GCACAATCTT
*
88730 AGAAACAACTTTG
1 AGAAACAATTTTG
88743 AGAAACAATTTTG
1 AGAAACAATTTTG
*
88756 AGACACAATT
1 AGAAACAATT
88766 CACAAAGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (13 bp):
AGAAACAATTTTG
Found at i:91955 original size:35 final size:35
Alignment explanation
Indices: 91915--91986 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
91905 TTGATGCTAT
*
91915 TTATAATAAGTCATGTCACTTGGTGAATAGACTTA
1 TTATAATAAGTCATATCACTTGGTGAATAGACTTA
*
91950 TTATAATAAGTCATATCACTTGGTGAATGGACTTA
1 TTATAATAAGTCATATCACTTGGTGAATAGACTTA
91985 TT
1 TT
91987 TTTTAGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (35 bp):
TTATAATAAGTCATATCACTTGGTGAATAGACTTA
Found at i:92153 original size:13 final size:13
Alignment explanation
Indices: 92135--92181 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
92125 GCACAATCTT
92135 AGAAACAACTTTG
1 AGAAACAACTTTG
92148 AGAAACAACTTTG
1 AGAAACAACTTTG
*
92161 AGAGACAACTTTG
1 AGAAACAACTTTG
*
92174 AGACACAA
1 AGAAACAA
92182 TTCACAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (13 bp):
AGAAACAACTTTG
Found at i:97270 original size:15 final size:16
Alignment explanation
Indices: 97250--97282 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
97240 CACCATCCAC
97250 TTTAGTAATT-TTTAT
1 TTTAGTAATTCTTTAT
*
97265 TTTAGTATTTCTTTAT
1 TTTAGTAATTCTTTAT
97281 TT
1 TT
97283 CCTTTTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTAGTAATTCTTTAT
Found at i:101250 original size:10 final size:10
Alignment explanation
Indices: 101220--101272 Score: 54
Period size: 11 Copynumber: 5.0 Consensus size: 10
101210 TATCCACTTA
101220 ATTTTATTCTT
1 ATTTTATT-TT
*
101231 TTTCTTATTTT
1 ATT-TTATTTT
101242 ATTTTATTTT
1 ATTTTATTTT
101252 A-TTTATTTT
1 ATTTTATTTT
101261 ACTTTTACTTTT
1 A-TTTTA-TTTT
101273 TTAATTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 9 0.25
10 8 0.22
11 10 0.28
12 9 0.25
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (10 bp):
ATTTTATTTT
Found at i:101256 original size:14 final size:14
Alignment explanation
Indices: 101239--101280 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
101229 TTTTTCTTAT
101239 TTTATTTTATTTTA
1 TTTATTTTATTTTA
101253 TTTATTTTACTTTTA
1 TTTATTTTA-TTTTA
* *
101268 CTT-TTTTAATTTA
1 TTTATTTTATTTTA
101281 GTCATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 14 0.56
15 7 0.28
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:101268 original size:6 final size:5
Alignment explanation
Indices: 101220--101272 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
101210 TATCCACTTA
*
101220 ATTTT ATTCTT TTTCTT ATTTT ATTTT ATTTT A-TTT ATTTT ACTTTT
1 ATTTT ATT-TT ATT-TT ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT
101267 ACTTTT
1 A-TTTT
101273 TTAATTTAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
4 4 0.09
5 20 0.47
6 19 0.44
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:101275 original size:19 final size:18
Alignment explanation
Indices: 101230--101280 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
101220 ATTTTATTCT
*
101230 TTTTCTTATTTTATTTTAT
1 TTTT-TTATTTTATTTTAC
101249 TTTATTTATTTTACTTTTAC
1 TTT-TTTATTTTA-TTTTAC
*
101269 TTTTTTAATTTA
1 TTTTTTATTTTA
101281 GTCATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTATTTTATTTTAC
Found at i:103974 original size:29 final size:29
Alignment explanation
Indices: 103940--103998 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
103930 CCTAAATTAA
103940 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
103969 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
103998 T
1 T
103999 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:108642 original size:29 final size:29
Alignment explanation
Indices: 108609--108680 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
108599 GCCTATATGT
108609 TTACACCTAAATTA-ATTTGATGTCATTGC
1 TTACACC-AAATTAGATTTGATGTCATTGC
* * *
108638 TTACATCAATTTAGTTTTGATGTCATTGC
1 TTACACCAAATTAGATTTGATGTCATTGC
* *
108667 TTACATCAATTTAG
1 TTACACCAAATTAG
108681 TTAGGTGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44
Consensus pattern (29 bp):
TTACACCAAATTAGATTTGATGTCATTGC
Found at i:108681 original size:29 final size:29
Alignment explanation
Indices: 108624--108682 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
108614 CCTAAATTAA
108624 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
108653 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
108682 T
1 T
108683 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:111601 original size:12 final size:12
Alignment explanation
Indices: 111584--111608 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
111574 TGTTGCTCAG
111584 GGGTTTTCACAA
1 GGGTTTTCACAA
111596 GGGTTTTCACAA
1 GGGTTTTCACAA
111608 G
1 G
111609 TTCCAGGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (12 bp):
GGGTTTTCACAA
Found at i:118542 original size:74 final size:76
Alignment explanation
Indices: 118453--118605 Score: 229
Period size: 74 Copynumber: 2.0 Consensus size: 76
118443 CAACAGATTG
* *
118453 ATACATTTGTACTTTTTAAAATTTCAAATTATCGTATAATTTAAATATTTTT-T-TATATATTTT
1 ATACAGTTGTACTTTTTAAAATTTCAAATTATCGCATAATTTAAATATTTTTCTATATATATTTT
118516 TTGTTTATCCA
66 TTGTTTATCCA
* * * *
118527 ATACAGTTGTACTTTTTAAAATTTTAAATTCTCGCATAATTTAAATATTTTTCGTATATTTTTTT
1 ATACAGTTGTACTTTTTAAAATTTCAAATTATCGCATAATTTAAATATTTTTC-TATATATATTT
118592 TTTGTTTATCCA
65 TTTGTTTATCCA
118604 AT
1 AT
118606 TTTGCATCTT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
74 48 0.69
76 1 0.01
77 21 0.30
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (76 bp):
ATACAGTTGTACTTTTTAAAATTTCAAATTATCGCATAATTTAAATATTTTTCTATATATATTTT
TTGTTTATCCA
Found at i:122453 original size:16 final size:16
Alignment explanation
Indices: 122428--122470 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
122418 CATTTAATAA
*
122428 ATAAACGAACACGAAC
1 ATAAACGAACACAAAC
*
122444 ATAAATGAACACAAAC
1 ATAAACGAACACAAAC
122460 ATAAACGAACA
1 ATAAACGAACA
122471 TAAAACTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:122483 original size:13 final size:13
Alignment explanation
Indices: 122465--122490 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
122455 CAAACATAAA
122465 CGAACATAAAACT
1 CGAACATAAAACT
122478 CGAACATAAAACT
1 CGAACATAAAACT
122491 ATCAAGCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (13 bp):
CGAACATAAAACT
Found at i:122596 original size:11 final size:11
Alignment explanation
Indices: 122582--122646 Score: 76
Period size: 11 Copynumber: 5.8 Consensus size: 11
122572 ACTCGACTCG
*
122582 AGCTCGATTGA
1 AGCTCGATTCA
*
122593 AGCTTGATTCA
1 AGCTCGATTCA
**
122604 AGCTCGATTTTG
1 AGCTCGA-TTCA
122616 AGCTCGATTCA
1 AGCTCGATTCA
122627 AGCTCGATTCA
1 AGCTCGATTCA
*
122638 AGCGCGATT
1 AGCTCGATT
122647 GACCCAATCC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
11 36 0.80
12 9 0.20
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:122619 original size:34 final size:34
Alignment explanation
Indices: 122581--122646 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
122571 AACTCGACTC
* * *
122581 GAGCTCGATTGAAGCTTGATTCAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGATTCAAGCGCGATTTT
122615 GAGCTCGATTCAAGCTCGATTCAAGCGCGATT
1 GAGCTCGATTCAAGCTCGATTCAAGCGCGATT
122647 GACCCAATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (34 bp):
GAGCTCGATTCAAGCTCGATTCAAGCGCGATTTT
Found at i:123008 original size:14 final size:14
Alignment explanation
Indices: 122991--123022 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
122981 AATGAACATA
*
122991 AACGAACATAATCG
1 AACGAACATAAACG
123005 AACGAACATAAACG
1 AACGAACATAAACG
123019 AACG
1 AACG
123023 TTCACGAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.22, G:0.16, T:0.09
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:123032 original size:24 final size:24
Alignment explanation
Indices: 122971--123021 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
122961 GATTGGGTTA
*
122971 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
122995 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
123019 AAC
1 AAC
123022 GTTCACGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.14
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:125121 original size:2 final size:2
Alignment explanation
Indices: 125114--125167 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
125104 TATAAATTTA
125114 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
125156 AT AT AT AT AT AT
1 AT AT AT AT AT AT
125168 TAAGATAATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:126379 original size:86 final size:86
Alignment explanation
Indices: 126234--126406 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
126224 TTCTTCCCTC
126234 TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTGTTTAATTGTTTAG
1 TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTGTTTAATTGTTTAG
126299 TTTACTGATCTGTGAGGTTTG
66 TTTACTGATCTGTGAGGTTTG
126320 TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTGTTTAATTGTTTAG
1 TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTGTTTAATTGTTTAG
126385 TTTACTGATCTGTGAGGTTTG
66 TTTACTGATCTGTGAGGTTTG
126406 T
1 T
126407 GTTGAGAAAG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.20, C:0.08, G:0.23, T:0.49
Consensus pattern (86 bp):
TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTGTTTAATTGTTTAG
TTTACTGATCTGTGAGGTTTG
Found at i:126896 original size:53 final size:53
Alignment explanation
Indices: 126834--126985 Score: 243
Period size: 53 Copynumber: 2.9 Consensus size: 53
126824 TTCAACCAGT
*
126834 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCTTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTAC
* * *
126887 GGGTTCGCTCCCTCTTGCTTCAAGGAATAGAACTC-AAAATATCTTCTTCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACA-ATCTTCTGCCTAC
*
126940 GGGTTCACTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTC
126986 ATAAAACGGG
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 3 0.03
53 84 0.93
54 3 0.03
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.30
Consensus pattern (53 bp):
GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTAC
Found at i:126995 original size:53 final size:52
Alignment explanation
Indices: 126834--127005 Score: 229
Period size: 53 Copynumber: 3.2 Consensus size: 52
126824 TTCAACCAGT
*
126834 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCTTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCT-CATAC
* * *
126887 GGGTTCGCTCCCTCTTGCTTCAAGGAATAGAACTC-AAAATATCTTCTTCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACA-ATCTTC-TCATAC
* * *
126940 GGGTTCACTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCATAAAAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTC-TCATAC
*
126993 GGGTCCGCTCCCT
1 GGGTTCGCTCCCT
127006 ATCCGTTCAG
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
52 3 0.03
53 97 0.93
54 4 0.04
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (52 bp):
GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTCATAC
Found at i:127050 original size:51 final size:51
Alignment explanation
Indices: 126995--127298 Score: 484
Period size: 51 Copynumber: 5.9 Consensus size: 51
126985 CATAAAACGG
* * * ** *
126995 GTCCGCTCCCTA-TCCGTTCAGGGAGTATAAGACTCGATCTTCAATAAACGT
1 GTCCGCTCCCTATTCC-TTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
127046 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTT
*
127101 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
127152 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
127203 GTCCGCTCCCTATTCCTTCAGAGAGTATATGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
127254 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
127299 AAACGAGTTT
Statistics
Matches: 238, Mismatches: 10, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
51 188 0.79
52 3 0.01
55 47 0.20
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:128693 original size:18 final size:19
Alignment explanation
Indices: 128653--128694 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
128643 TCTTTTTTCA
*
128653 TTTTT-CATTTTTTCTTCC
1 TTTTTCCATTTTTCCTTCC
*
128671 CTTTTCCATTTTTCCTT-C
1 TTTTTCCATTTTTCCTTCC
128689 TTTTTC
1 TTTTTC
128695 TTTCTTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTCCATTTTTCCTTCC
Found at i:132226 original size:2 final size:2
Alignment explanation
Indices: 132219--132258 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
132209 GAAAGAGAAG
*
132219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132259 GGGAGGATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:138468 original size:45 final size:45
Alignment explanation
Indices: 138401--138543 Score: 198
Period size: 45 Copynumber: 3.1 Consensus size: 45
138391 TGTTATCCAC
* * *
138401 AAAAAGAAATCCTAACCTCATGATATCTAATTCGCATGCTTATTC-
1 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTATTCG
*
138446 AGAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTGTTCG
1 A-AAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTATTCG
*
138492 AAAAATAAACCTAACCGCATGATATCTAGTTCGCAAGCATTTATTCG
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC--TTATTCG
138539 AAAAA
1 AAAAA
138544 ATGAAAATAA
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
45 69 0.78
46 8 0.09
47 11 0.12
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (45 bp):
AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTATTCG
Found at i:140196 original size:2 final size:2
Alignment explanation
Indices: 140189--140265 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
140179 TATAAATTTA
140189 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
140231 AT AT AT 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 AT AT AT A
140266 AGATAATGAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:141476 original size:86 final size:86
Alignment explanation
Indices: 141331--141503 Score: 337
Period size: 86 Copynumber: 2.0 Consensus size: 86
141321 TTCTTCCCTC
141331 TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTATTTAATTGTTTAG
1 TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTATTTAATTGTTTAG
141396 TTTACTGATCTGTGAGGTTTG
66 TTTACTGATCTGTGAGGTTTG
*
141417 TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTGTTTAATTGTTTAG
1 TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTATTTAATTGTTTAG
141482 TTTACTGATCTGTGAGGTTTG
66 TTTACTGATCTGTGAGGTTTG
141503 T
1 T
141504 GTTGAGAAAG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.20, C:0.08, G:0.23, T:0.49
Consensus pattern (86 bp):
TTCAATTGAGATGTCGAATGACTGAGGATGATTTTTTTACTGTTTGTTTCTATTTAATTGTTTAG
TTTACTGATCTGTGAGGTTTG
Found at i:145005 original size:31 final size:31
Alignment explanation
Indices: 144941--145006 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
144931 GTTTTTCTGA
* * *
144941 TTCTCAGTCGGTTCTTCCGGTTATTTATCGG
1 TTCTCAGCCGGTTCTTCCGCTTATCTATCGG
*
144972 TTCTCAGCCGGTTCTTCCGCTTCTCTA-CTGG
1 TTCTCAGCCGGTTCTTCCGCTTATCTATC-GG
145003 TTCT
1 TTCT
145007 GTGCTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.08, C:0.29, G:0.20, T:0.44
Consensus pattern (31 bp):
TTCTCAGCCGGTTCTTCCGCTTATCTATCGG
Done.