Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009721.1 Kokia drynarioides strain JFW-HI SEQ_124440, 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: 197705
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 134 characters in sequence are not A, C, G, or T
Found at i:3031 original size:17 final size:18
Alignment explanation
Indices: 3011--3044 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3001 GGATGGTGAA
3011 TTTAAAGGTTA-TGGGTC
1 TTTAAAGGTTATTGGGTC
*
3028 TTTAATGGTTATTGGGT
1 TTTAAAGGTTATTGGGT
3045 TTTCTTGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.47
Consensus pattern (18 bp):
TTTAAAGGTTATTGGGTC
Found at i:18857 original size:16 final size:16
Alignment explanation
Indices: 18826--18864 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18816 TGTTCAACTA
**
18826 ATAATAAATATTTATT
1 ATAATAAATAAATATT
18842 ATAATAAATAAATATT
1 ATAATAAATAAATATT
*
18858 AAAATAA
1 ATAATAA
18865 GCTAACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATAAATAAATATT
Found at i:19829 original size:9 final size:9
Alignment explanation
Indices: 19810--19877 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
19800 TATTATTCTA
19810 TAAAA-TTT
1 TAAAATTTT
19818 TAAAATTTT
1 TAAAATTTT
**
19827 TAATTTTTT
1 TAAAATTTT
*
19836 TATATATTTTT
1 TA-A-AATTTT
*
19847 TAGAATTTTT
1 TA-AAATTTT
19857 TAAAATTTT
1 TAAAATTTT
*
19866 TATAATTTT
1 TAAAATTTT
19875 TAA
1 TAA
19878 TTTTAAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
8 5 0.10
9 28 0.56
10 9 0.18
11 8 0.16
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (9 bp):
TAAAATTTT
Found at i:19889 original size:19 final size:19
Alignment explanation
Indices: 19867--19918 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
19857 TAAAATTTTT
*
19867 ATAATTTTTAATTTTAAAA
1 ATAATTTTAAATTTTAAAA
* * *
19886 ATAAATTTGAACTTTTGAAA
1 AT-AATTTTAAATTTTAAAA
*
19906 ATTATTTTAAATT
1 ATAATTTTAAATT
19919 ATTTTGTAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (19 bp):
ATAATTTTAAATTTTAAAA
Found at i:20755 original size:18 final size:18
Alignment explanation
Indices: 20732--20766 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20722 TTTTACAGTT
*
20732 TATATTAGAGTTATATGA
1 TATATTAGAGGTATATGA
20750 TATATTAGAGGTATATG
1 TATATTAGAGGTATATG
20767 GTTGCTCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (18 bp):
TATATTAGAGGTATATGA
Found at i:21744 original size:164 final size:164
Alignment explanation
Indices: 21473--21803 Score: 484
Period size: 164 Copynumber: 2.0 Consensus size: 164
21463 AACTAATTTA
* ** * * *
21473 AAAAATCAAATATAAGTAGGTCGAGTCTGGTTCAAGATTATCTTTCTTAATTTTGATCAGGTTTG
1 AAAAATCAAATATAAGTAGGTCGACTCTGGCCCAAGATTATCTTTCTTAATTTGGATCAAGCTTG
* * * *
21538 GGCAAAAAATAAGCTCATTTTTAGGGTTGTGCCAGACTCGAGCTTAGAAAATTTATCTAAATACC
66 GGCAAAAAATAAGCCCATTTTTAGGGTTGTGCCAGACTCGAGCTTAAAAAATTGATCTAAATACA
* * *
21603 TTGCATGAGCTTGACACAACCCACGGGATCCTCT
131 TTGCATGAGCTCGACACAACCCACGAGAACCTCT
*
21637 AAAAATCAAATATAAGTAGGTCGACTCTGGCCCAATATTA-CTTTTCTTAATTTGGATCAAGCTT
1 AAAAATCAAATATAAGTAGGTCGACTCTGGCCCAAGATTATC-TTTCTTAATTTGGATCAAGCTT
* * *
21701 GGGTAAAAAATAAGCCCATTTTTTGGGTTGTGCCAGACTCGAGCTTAAAAAATTGATCTAGATAC
65 GGGCAAAAAATAAGCCCATTTTTAGGGTTGTGCCAGACTCGAGCTTAAAAAATTGATCTAAATAC
*
21766 ATTGCATGGGCTCGACACAACCCACGAGAACCTCT
130 ATTGCATGAGCTCGACACAACCCACGAGAACCTCT
21801 AAA
1 AAA
21804 TTTGACCATC
Statistics
Matches: 148, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
163 1 0.01
164 147 0.99
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (164 bp):
AAAAATCAAATATAAGTAGGTCGACTCTGGCCCAAGATTATCTTTCTTAATTTGGATCAAGCTTG
GGCAAAAAATAAGCCCATTTTTAGGGTTGTGCCAGACTCGAGCTTAAAAAATTGATCTAAATACA
TTGCATGAGCTCGACACAACCCACGAGAACCTCT
Found at i:26161 original size:36 final size:37
Alignment explanation
Indices: 26105--26179 Score: 134
Period size: 36 Copynumber: 2.0 Consensus size: 37
26095 AATGCATATG
26105 ATAGTTTTTTTTTTGAAAAATCTCATTATTATAAGTTT
1 ATAGTTTTTTTTTT-AAAAATCTCATTATTATAAGTTT
26143 ATAGTTTTTTTTTT-AAAATCTCATTATTATAAGTTT
1 ATAGTTTTTTTTTTAAAAATCTCATTATTATAAGTTT
26179 A
1 A
26180 GATAATATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 23 0.62
38 14 0.38
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (37 bp):
ATAGTTTTTTTTTTAAAAATCTCATTATTATAAGTTT
Found at i:26616 original size:22 final size:21
Alignment explanation
Indices: 26591--26632 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
26581 AAGTGAATCA
*
26591 GAAAATCTTGAAATAAAAAAAG
1 GAAAATATT-AAATAAAAAAAG
*
26613 GAAAATATTAGATAAAAAAA
1 GAAAATATTAAATAAAAAAA
26633 ACAGAATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.67, C:0.02, G:0.12, T:0.19
Consensus pattern (21 bp):
GAAAATATTAAATAAAAAAAG
Found at i:28547 original size:28 final size:26
Alignment explanation
Indices: 28511--28568 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
28501 TTTTAGGTTA
* *
28511 AATTAATTATATATGCTGTATTTTTTTT
1 AATTAATTAAATAAG-T-TATTTTTTTT
* *
28539 AATTGATTAAATAAGTTTTTTTTTTT
1 AATTAATTAAATAAGTTATTTTTTTT
28565 AATT
1 AATT
28569 TAAGAGAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 13 0.50
27 1 0.04
28 12 0.46
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (26 bp):
AATTAATTAAATAAGTTATTTTTTTT
Found at i:28839 original size:2 final size:2
Alignment explanation
Indices: 28834--28866 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28824 CTTAAAAAAG
28834 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 A
28867 CACACGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32905 original size:25 final size:25
Alignment explanation
Indices: 32877--32925 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
32867 TTAACGGTAG
32877 AAATAGATAGAAATTTTAACAGAAA
1 AAATAGATAGAAATTTTAACAGAAA
*
32902 AAATAGATAGAATTTTTAACAGAA
1 AAATAGATAGAAATTTTAACAGAA
32926 GGTTTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.12, T:0.27
Consensus pattern (25 bp):
AAATAGATAGAAATTTTAACAGAAA
Found at i:36376 original size:24 final size:25
Alignment explanation
Indices: 36348--36397 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
36338 TGATAATATA
36348 TATAACTAATATTT-AA-AATATTTT
1 TATAACTAA-ATTTAAATAATATTTT
*
36372 TATAATTAAATTTAAATAATATTTT
1 TATAACTAAATTTAAATAATATTTT
36397 T
1 T
36398 TTCCATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 10 0.43
25 9 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATAACTAAATTTAAATAATATTTT
Found at i:38977 original size:21 final size:21
Alignment explanation
Indices: 38951--38990 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38941 GGCCTTAAAA
38951 GTCTCATACCAATCGTGACAT
1 GTCTCATACCAATCGTGACAT
*
38972 GTCTCATACCAATCTTGAC
1 GTCTCATACCAATCGTGAC
38991 GTGCTTGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (21 bp):
GTCTCATACCAATCGTGACAT
Found at i:46292 original size:16 final size:16
Alignment explanation
Indices: 46271--46301 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46261 TCGACTTGCT
46271 TGAGAAAAAAAAACGC
1 TGAGAAAAAAAAACGC
*
46287 TGAGAAAATAAAACG
1 TGAGAAAAAAAAACG
46302 GTGTTTGTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.10, G:0.19, T:0.10
Consensus pattern (16 bp):
TGAGAAAAAAAAACGC
Found at i:51984 original size:16 final size:15
Alignment explanation
Indices: 51963--51994 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
51953 TGTCTTCGTT
51963 GCATTGTTCTTCTTCA
1 GCATTGTTCTT-TTCA
51979 GCATTGTTCTTTTCA
1 GCATTGTTCTTTTCA
51994 G
1 G
51995 TAAACGCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.12, C:0.22, G:0.16, T:0.50
Consensus pattern (15 bp):
GCATTGTTCTTTTCA
Found at i:62762 original size:18 final size:17
Alignment explanation
Indices: 62749--62800 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
62739 TTTATTATAG
*
62749 ATTTTAATAATATTTAT
1 ATTTTAATAATATTTAA
*
62766 TTTTTACATAATATTTTAA
1 ATTTTA-ATAATA-TTTAA
*
62785 ATTATTTATAATATTT
1 ATT-TTAATAATATTT
62801 CTCTAACTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 5 0.18
18 9 0.32
19 12 0.43
20 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTAATAATATTTAA
Found at i:63489 original size:29 final size:29
Alignment explanation
Indices: 63432--63489 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
63422 TTTAATTAAG
* *
63432 ATCTCAAAAAATTTTGAAAATTCTCATTA
1 ATCTCAAAAAATTTTAAAAATTCTAATTA
*
63461 ATCTCACAAAATTTTAAAAAATTC-AATTA
1 ATCTCAAAAAATTTT-AAAAATTCTAATTA
63490 GACATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (29 bp):
ATCTCAAAAAATTTTAAAAATTCTAATTA
Found at i:79891 original size:13 final size:13
Alignment explanation
Indices: 79873--79904 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
79863 CTTGGTGCTA
79873 CGTTGTTTTATCT
1 CGTTGTTTTATCT
79886 CGTTGTTTTATCT
1 CGTTGTTTTATCT
79899 CGTTGT
1 CGTTGT
79905 GCAGGCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.16, G:0.19, T:0.59
Consensus pattern (13 bp):
CGTTGTTTTATCT
Found at i:82884 original size:22 final size:22
Alignment explanation
Indices: 82859--82901 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
82849 TGGAGTTTAA
82859 GGTTTATAGTTTTGAGGATTAG
1 GGTTTATAGTTTTGAGGATTAG
82881 GGTTTATAGTTTTGAGGATTA
1 GGTTTATAGTTTTGAGGATTA
82902 ATGATTTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (22 bp):
GGTTTATAGTTTTGAGGATTAG
Found at i:84074 original size:14 final size:15
Alignment explanation
Indices: 84050--84078 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
84040 ACGGCGAATG
84050 ATTTTTGAGTTTTTT
1 ATTTTTGAGTTTTTT
84065 ATTTTT-AGTTTTTT
1 ATTTTTGAGTTTTTT
84079 GAAGAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (15 bp):
ATTTTTGAGTTTTTT
Found at i:84779 original size:27 final size:29
Alignment explanation
Indices: 84739--84793 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
84729 GATGATTTGG
84739 AAGAGTTTAGATATAATACT-ATTTTAATT
1 AAGAGTTTAGATATAATA-TAATTTTAATT
84768 AAGA-TTTA-ATATAATATAATTTTAAT
1 AAGAGTTTAGATATAATATAATTTTAAT
84794 ATATATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.04
27 16 0.64
28 4 0.16
29 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (29 bp):
AAGAGTTTAGATATAATATAATTTTAATT
Found at i:88054 original size:18 final size:20
Alignment explanation
Indices: 88019--88056 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
88009 GCCTAATTTC
88019 TTTCACTATTGTTTTGTTGT
1 TTTCACTATTGTTTTGTTGT
88039 TTTC-CTATTG-TTTGTTGT
1 TTTCACTATTGTTTTGTTGT
88057 CATTTTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.08, C:0.11, G:0.16, T:0.66
Consensus pattern (20 bp):
TTTCACTATTGTTTTGTTGT
Found at i:90780 original size:36 final size:36
Alignment explanation
Indices: 90729--90802 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
90719 GCGGGTGTTT
* *
90729 TGGGAGGGGCAGGGGAAGGGGCGGGGGATTGGGTTG
1 TGGGAAGGGCAGGGGAAGGGGCGGAGGATTGGGTTG
*
90765 TGGGAAGGGCGGGGGAAGGGGCGGAGGATTGGGTTG
1 TGGGAAGGGCAGGGGAAGGGGCGGAGGATTGGGTTG
90801 TG
1 TG
90803 AGTGGGGAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.15, C:0.05, G:0.65, T:0.15
Consensus pattern (36 bp):
TGGGAAGGGCAGGGGAAGGGGCGGAGGATTGGGTTG
Found at i:90788 original size:12 final size:12
Alignment explanation
Indices: 90733--90788 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
90723 GTGTTTTGGG
*
90733 AGGGGCAGGGGA
1 AGGGGCGGGGGA
90745 AGGGGCGGGGGA
1 AGGGGCGGGGGA
* ** *
90757 TTGGGTTGTGGGA
1 -AGGGGCGGGGGA
90770 A-GGGCGGGGGA
1 AGGGGCGGGGGA
90781 AGGGGCGG
1 AGGGGCGG
90789 AGGATTGGGT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
11 8 0.24
12 17 0.52
13 8 0.24
ACGTcount: A:0.16, C:0.07, G:0.68, T:0.09
Consensus pattern (12 bp):
AGGGGCGGGGGA
Found at i:91489 original size:33 final size:32
Alignment explanation
Indices: 91450--91543 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 32
91440 TTAATAATAG
*
91450 TAAAATTATATTTTAATTCTTTTAAAAATTTGA
1 TAAAATTATAATTTAATT-TTTTAAAAATTTGA
*
91483 TAAAATTTTAATTTAATTTTTTAAAAA-TT-A
1 TAAAATTATAATTTAATTTTTTAAAAATTTGA
* * * *
91513 TAAAAATATAAATTATTATTTTTAATAATTT
1 TAAAATTATAATTTAAT-TTTTTAAAAATTT
91544 ATATTTTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
30 14 0.27
31 11 0.21
32 11 0.21
33 16 0.31
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (32 bp):
TAAAATTATAATTTAATTTTTTAAAAATTTGA
Found at i:91535 original size:31 final size:31
Alignment explanation
Indices: 91462--91542 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 31
91452 AAATTATATT
* * *
91462 TTAATTCTTTTAAAAATTTGATAAAATTTTAAT
1 TTAATT-TTTTAAAAA-TTGATAAAAATATAAA
91495 TTAATTTTTTAAAAATT-ATAAAAATATAAA
1 TTAATTTTTTAAAAATTGATAAAAATATAAA
* *
91525 TTATTATTTTTAATAATT
1 TTAAT-TTTTTAAAAATT
91543 TATATTTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 14 0.33
31 13 0.31
32 9 0.21
33 6 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (31 bp):
TTAATTTTTTAAAAATTGATAAAAATATAAA
Found at i:93791 original size:20 final size:20
Alignment explanation
Indices: 93763--93814 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
93753 AAATATATTA
**
93763 TAAAAATATATATTTAAA-T
1 TAAAAATATATATAAAAATT
93782 TAACAAATAT-TATAAAAATT
1 TAA-AAATATATATAAAAATT
93802 TAAAAATATATAT
1 TAAAAATATATAT
93815 GAATTTCAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATATATATAAAAATT
Found at i:93819 original size:18 final size:18
Alignment explanation
Indices: 93763--93820 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
93753 AAATATATTA
93763 TAAAAATATATATTTAAA-T
1 TAAAAATATATA--TAAATT
*
93782 TAACAAATATTATAAAAATT
1 TAA-AAATA-TATATAAATT
*
93802 TAAAAATATATATGAATT
1 TAAAAATATATATAAATT
93820 T
1 T
93821 CAAGTAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 9 0.27
19 11 0.33
20 9 0.27
21 4 0.12
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAAAATATATATAAATT
Found at i:93916 original size:23 final size:22
Alignment explanation
Indices: 93866--93947 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
93856 AATAGTTTTT
* *
93866 TTTTTAGAA-TTTTAGAATTATA
1 TTTTTAAAATTTTTA-AAATATA
93888 TATTTTAAAATTTTATAAAA-AGTA
1 T-TTTTAAAATTTT-TAAAATA-TA
* *
93912 TTTTTAAACTTTTTAAAATATT
1 TTTTTAAAATTTTTAAAATATA
*
93934 TTTTTACAATTTTT
1 TTTTTAAAATTTTT
93948 GTAATAATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
22 19 0.39
23 20 0.41
24 8 0.16
25 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTTAAAATTTTTAAAATATA
Found at i:93937 original size:22 final size:21
Alignment explanation
Indices: 93888--93947 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
93878 TAGAATTATA
*
93888 TATTTTAAAATTTTATAAAAAG
1 TATTTTTAAATTTT-TAAAAAG
93910 TATTTTTAAACTTTTTAAAATA-
1 TATTTTTAAA-TTTTTAAAA-AG
*
93932 TTTTTTTACAATTTTT
1 TATTTTTA-AATTTTT
93948 GTAATAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTTTTAAATTTTTAAAAAG
Found at i:94059 original size:20 final size:20
Alignment explanation
Indices: 94034--94074 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
94024 AGATTATAAA
94034 ATTTGAATTTTTATATATTT
1 ATTTGAATTTTTATATATTT
*
94054 ATTTGAATTTTTATATTTTT
1 ATTTGAATTTTTATATATTT
94074 A
1 A
94075 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTGAATTTTTATATATTT
Found at i:94576 original size:21 final size:21
Alignment explanation
Indices: 94543--94584 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
94533 TAACATGAAA
* *
94543 TAAATTACTATAGTGATAAAAT
1 TAAATTACGATAG-CATAAAAT
94565 TAAA-TACGATAGCATAAAAT
1 TAAATTACGATAGCATAAAAT
94585 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (21 bp):
TAAATTACGATAGCATAAAAT
Found at i:94727 original size:5 final size:5
Alignment explanation
Indices: 94717--94749 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
94707 TTAATGCCTA
94717 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
94750 GAATAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:94768 original size:10 final size:10
Alignment explanation
Indices: 94717--94768 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
94707 TTAATGCCTA
*
94717 AAAATAAAAT
1 AAAAGAAAAT
*
94727 AAAATAAAAT
1 AAAAGAAAAT
*
94737 AAAATAAAAT
1 AAAAGAAAAT
94747 -AAAGAATAAT
1 AAAAGAA-AAT
*
94757 AAAAGAATAT
1 AAAAGAAAAT
94767 AA
1 AA
94769 TTACAGTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 5 0.13
10 27 0.71
11 6 0.16
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:94873 original size:15 final size:12
Alignment explanation
Indices: 94841--94865 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
94831 TATAATTTTT
94841 TTTATTATAACA
1 TTTATTATAACA
94853 TTTATTATAACA
1 TTTATTATAACA
94865 T
1 T
94866 AACTTATTTT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTATTATAACA
Found at i:105102 original size:49 final size:49
Alignment explanation
Indices: 105047--105142 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
105037 AATACAAAGA
105047 TAAACTTAACAAACTATCTGCCTACTCATTTGAATTCCAACAAAAGGCC
1 TAAACTTAACAAACTATCTGCCTACTCATTTGAATTCCAACAAAAGGCC
* *
105096 TAAACTTAACAAATTATCTGCCTACTCATTTGAATTCCAGCAAAAGG
1 TAAACTTAACAAACTATCTGCCTACTCATTTGAATTCCAACAAAAGG
105143 TCTTCCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (49 bp):
TAAACTTAACAAACTATCTGCCTACTCATTTGAATTCCAACAAAAGGCC
Found at i:105399 original size:14 final size:14
Alignment explanation
Indices: 105382--105410 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
105372 AGCCCTTTCA
105382 CCTTCATCATCACC
1 CCTTCATCATCACC
105396 CCTTCATCATCACC
1 CCTTCATCATCACC
105410 C
1 C
105411 AAATGAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.52, G:0.00, T:0.28
Consensus pattern (14 bp):
CCTTCATCATCACC
Found at i:108279 original size:26 final size:26
Alignment explanation
Indices: 108250--108317 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
108240 CAAGGATTTG
108250 ATTTGTGTATTGATTTTATTACTTTT
1 ATTTGTGTATTGATTTTATTACTTTT
108276 ATTTGTGTATTGATTTTATTACTTTT
1 ATTTGTGTATTGATTTTATTACTTTT
108302 ATTTGTGTATTGATTT
1 ATTTGTGTATTGATTT
108318 GGGCAATGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.19, C:0.03, G:0.13, T:0.65
Consensus pattern (26 bp):
ATTTGTGTATTGATTTTATTACTTTT
Found at i:121317 original size:22 final size:23
Alignment explanation
Indices: 121272--121317 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
121262 TATTTTTGAT
*
121272 AAAATTGATATTTATATAATATA
1 AAAATTGATATTTATATAACATA
121295 AAAATT-ATATTTACTA-AACATA
1 AAAATTGATATTTA-TATAACATA
121317 A
1 A
121318 CGATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAATTGATATTTATATAACATA
Found at i:121372 original size:7 final size:7
Alignment explanation
Indices: 121362--121420 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
121352 ATTAAAAAAT
121362 AAATTAA
1 AAATTAA
121369 AAATTAA
1 AAATTAA
121376 AAA-TAA
1 AAATTAA
121382 AAA-TAA
1 AAATTAA
*
121388 TATATTTAA
1 -A-AATTAA
*
121397 TAATTAA
1 AAATTAA
*
121404 AAATAAA
1 AAATTAA
121411 AAACTTAA
1 AAA-TTAA
121419 AA
1 AA
121421 TAATATGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
6 9 0.21
7 24 0.57
8 6 0.14
9 3 0.07
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATTAA
Found at i:128322 original size:39 final size:39
Alignment explanation
Indices: 128279--128358 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
128269 CTAAATGCAA
* *
128279 ACATGTTATGATGCATGGGCCTATGATATAAATTCTATG
1 ACATGTTATGATGCATAGGCCTATGATATAAATTCAATG
* * *
128318 ACATGTTATGATGGATAGGCCTTTGGTATAAATTCAATG
1 ACATGTTATGATGCATAGGCCTATGATATAAATTCAATG
128357 AC
1 AC
128359 TGACTGTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (39 bp):
ACATGTTATGATGCATAGGCCTATGATATAAATTCAATG
Found at i:132220 original size:44 final size:45
Alignment explanation
Indices: 132134--132221 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
132124 CAATTAAGAC
*
132134 TTCTTTTTTCTTTATGTTCACTCTAGAGTGCTCAAGTATATATGAT
1 TTCTTTTTTCTTTATGTTCACTCTAGAGTACTCAAG-ATATATGAT
*
132180 TTCTTTTCTTC-TTATGTTCACTCTAGAGTACTTAAG-TATATG
1 TTCTTTT-TTCTTTATGTTCACTCTAGAGTACTCAAGATATATG
132222 TGTTTTCGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 6 0.15
46 30 0.77
47 3 0.08
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (45 bp):
TTCTTTTTTCTTTATGTTCACTCTAGAGTACTCAAGATATATGAT
Found at i:140341 original size:15 final size:15
Alignment explanation
Indices: 140321--140351 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
140311 AATTAAATCC
*
140321 AAATATTAAAATAAA
1 AAATATAAAAATAAA
140336 AAATATAAAAATAAA
1 AAATATAAAAATAAA
140351 A
1 A
140352 TCGAATCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATATAAAAATAAA
Found at i:143002 original size:2 final size:2
Alignment explanation
Indices: 142995--143021 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
142985 TCTTCATGAA
142995 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
143022 ATACATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:145032 original size:102 final size:102
Alignment explanation
Indices: 144856--145060 Score: 410
Period size: 102 Copynumber: 2.0 Consensus size: 102
144846 CAACATCCCA
144856 AAACAAATAGGAATAAGAATAATTTGTTTTTGTTGAGAGATTTTGTAACACCTTGAGAGAAGTCT
1 AAACAAATAGGAATAAGAATAATTTGTTTTTGTTGAGAGATTTTGTAACACCTTGAGAGAAGTCT
144921 TTTAAGTATTGTCCACCTAGATCGCGGACTTCTTGAC
66 TTTAAGTATTGTCCACCTAGATCGCGGACTTCTTGAC
144958 AAACAAATAGGAATAAGAATAATTTGTTTTTGTTGAGAGATTTTGTAACACCTTGAGAGAAGTCT
1 AAACAAATAGGAATAAGAATAATTTGTTTTTGTTGAGAGATTTTGTAACACCTTGAGAGAAGTCT
145023 TTTAAGTATTGTCCACCTAGATCGCGGACTTCTTGAC
66 TTTAAGTATTGTCCACCTAGATCGCGGACTTCTTGAC
145060 A
1 A
145061 TGTTTGGTAT
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (102 bp):
AAACAAATAGGAATAAGAATAATTTGTTTTTGTTGAGAGATTTTGTAACACCTTGAGAGAAGTCT
TTTAAGTATTGTCCACCTAGATCGCGGACTTCTTGAC
Found at i:147876 original size:32 final size:32
Alignment explanation
Indices: 147835--147896 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
147825 TTCAGGTCAA
*
147835 TTCATGTTCATGTTGTTTCGGGTTAGGGTCCT
1 TTCATGTTCAGGTTGTTTCGGGTTAGGGTCCT
* *
147867 TTCATGTTCAGGTTGTTTTGGTTTAGGGTC
1 TTCATGTTCAGGTTGTTTCGGGTTAGGGTC
147897 ATTTGAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.13, G:0.29, T:0.48
Consensus pattern (32 bp):
TTCATGTTCAGGTTGTTTCGGGTTAGGGTCCT
Found at i:151003 original size:48 final size:48
Alignment explanation
Indices: 150703--151852 Score: 376
Period size: 48 Copynumber: 24.0 Consensus size: 48
150693 CTGTTGCTGC
* * * * *
150703 TGCAGCAGGTGCAGCAGGAGGTGGTGCTCCTATCGGTTTGCCTGTTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* ** ** * * * * ** *
150751 TGCAGTTGAAGCATTAGGAGGTGGTGCTCGTATAGATGCGTGTGGTTT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* ** * * * * *
150799 TGCATCTCTTGCACCATGAGGTGGTGATCCTATTGGTGTCCCTGATGC
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* * * * *
150847 TACAGCTGGTGCACCAGGAAGTGGTGCTCCAATTGGCT-TTCCTAGTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGG-TGTGCCTGGTGT
* * *
150895 TGCAGCTGGTGCATTCA-GAGGTGGTGCTCCTATTGGCGTGCTTGGTGT
1 TGCAGCTGGTGCA-CCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* ** * *
150943 TGCGGCCAGTGCACCAGGAGGTGGTGCTCCTATTGATGTGCTTGGTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* * * * * * *
150991 TGTAGCTGGTGCACTAGGAGTTGATGTTGCTATCT-GTGTGCCAGAG-GT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTAT-TGGTGTGCCTG-GTGT
* * * *
151039 TGCAGCTGGTGCTCCAATTGACATTCCAGGTGTTGCTGCTGGTGCTCCTATTGGTGAGCCTTGTC
1 TGCAGCT-G-G-------TG-CA--CCAGGAG-----G-TGGTGCTCCTATTGGTGTGCCTGGTG
151104 T
48 T
* * * * ** * * ** * * *
151105 TGCATCGGGTGCAGCGGGACATGGTGCTTCAATTGGCATGCTTTGTTT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* * ** * * * *
151153 TCCGGCCAGTGCA-CTGGTAGGTGGTGCTCCTACTGGCGTGCCTGTTGT
1 TGCAGCTGGTGCACCAGG-AGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* * * ** * * *
151201 TGCAGCTGGCGCAGCAGGAGGTAGTGAACCTATTGGCGTACCTGGTCT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* *
151249 TGCAGCTGGTGCACCAGGAGGTGGTGCTTCTATTGGCT-TGCCAGGTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGG-TGTGCCTGGTGT
* * * * * * *
151297 TGCATCTGGTGCATCAGGAGTTGGTGCTCTTGTT-GTCATGCCTGATGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGT-GTGCCTGGTGT
* * * * *
151345 T-----T-CTG---CTGGAGGTGATGCTCCTGTTGTTGTGCC---T-T
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* ** * * * *** * *
151380 T----CT-TTGCTGCTGGAGGTGGTGCTCCTGTCGCCATCCCTGGAGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* * * * * * * *
151423 TGTAGCTGGTGCATCAGTAGGTGGTCCTCTTGA-CGGCGTTG-CTGATGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCT-ATTGGTG-TGCCTGGTGT
* * * * * * ** *
151471 TTCAGCTTGAGCGCCAGGTGGTGGTGCTTCTACAGGTGTGCCTGGTGC
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* ** * * * ** *
151519 TGCAGCTGCTGCACTGGGAGGAGTTGCTCCAATTGGCATGTCTGGTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* * * ** * * **
151567 TGCAACTGATGTACTGGGAGGTGATACTCCTATTGGCATGCCTGGTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* * * * * ***
151615 TCCAGCTGATGTACCAAGAGATGGTGCTCCTATTGCCATGCCTGGTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* ** *
151663 TGCAGCTGCTGTGCCAGGAGGTGGTGCTCCTATT-GTCATGCCTGGTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGT-GTGCCTGGTGT
* * *
151711 TGCAGTTGGTGCGCCAGGAGGTGGTGCTCCTACTGGTGTGCCTGGTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* ** * *
151759 TGCAGCTGCTGTGCCAGGAGGTGGTGCTCCTATTGGTGTACCTTGTGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
* ** ** *
151807 TGCAGCCGGTGCACTTGGATTTGGTGCTCCTATTGGAGTGCCTGGT
1 TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGT
151853 ACTACGGCTG
Statistics
Matches: 800, Mismatches: 251, Indels: 102
0.69 0.22 0.09
Matches are distributed among these distances:
35 2 0.00
36 4 0.00
39 42 0.05
40 1 0.00
42 2 0.00
43 3 0.00
46 1 0.00
47 11 0.01
48 680 0.85
49 12 0.01
50 1 0.00
54 3 0.00
56 2 0.00
57 4 0.00
58 2 0.00
60 5 0.01
64 1 0.00
65 3 0.00
66 21 0.03
ACGTcount: A:0.13, C:0.21, G:0.34, T:0.32
Consensus pattern (48 bp):
TGCAGCTGGTGCACCAGGAGGTGGTGCTCCTATTGGTGTGCCTGGTGT
Found at i:151378 original size:39 final size:39
Alignment explanation
Indices: 151321--151407 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
151311 CAGGAGTTGG
* *
151321 TGCTCTTGTTGTCATGCCTGATGTTT-CTGCTGGAGGTGA
1 TGCTCCTGTTGTCATGCCT-ATCTTTGCTGCTGGAGGTGA
** * *
151360 TGCTCCTGTTGTTGTGCCTTTCTTTGCTGCTGGAGGTGG
1 TGCTCCTGTTGTCATGCCTATCTTTGCTGCTGGAGGTGA
151399 TGCTCCTGT
1 TGCTCCTGT
151408 CGCCATCCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 4 0.10
39 37 0.90
ACGTcount: A:0.06, C:0.21, G:0.31, T:0.43
Consensus pattern (39 bp):
TGCTCCTGTTGTCATGCCTATCTTTGCTGCTGGAGGTGA
Found at i:162148 original size:3 final size:3
Alignment explanation
Indices: 162140--162175 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
162130 TGGATAACGC
162140 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
162176 ATACACCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:183527 original size:22 final size:22
Alignment explanation
Indices: 183502--183558 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
183492 ATATTGAACT
183502 TTGTCTCGAGACAGAAG-CCTCA
1 TTGTCTCGAGACAGAAGCCCT-A
** *
183524 TTGTCTCGAGACCTACGCCCTA
1 TTGTCTCGAGACAGAAGCCCTA
183546 TTGTCTCGAGACA
1 TTGTCTCGAGACA
183559 AGTAATTTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (22 bp):
TTGTCTCGAGACAGAAGCCCTA
Found at i:183754 original size:23 final size:24
Alignment explanation
Indices: 183708--183755 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
183698 TATGCTCCTA
183708 AAAGCATAATAAGGATCTAAAATC
1 AAAGCATAATAAGGATCTAAAATC
183732 AAAGCATAATAAGGA-CTAAAATC
1 AAAGCATAATAAGGATCTAAAATC
183755 A
1 A
183756 TTCATAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (24 bp):
AAAGCATAATAAGGATCTAAAATC
Found at i:184987 original size:16 final size:16
Alignment explanation
Indices: 184966--184999 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
184956 TTTAGTAAAT
184966 ATAGAGAAAGTTAGGC
1 ATAGAGAAAGTTAGGC
*
184982 ATAGAGAAATTTAGGC
1 ATAGAGAAAGTTAGGC
184998 AT
1 AT
185000 TACACCTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (16 bp):
ATAGAGAAAGTTAGGC
Found at i:187690 original size:57 final size:56
Alignment explanation
Indices: 187621--188024 Score: 286
Period size: 57 Copynumber: 7.1 Consensus size: 56
187611 AAATACGAAT
* *
187621 AAAATTTTTTTTTTGGTGTTTGCCACCCAATGACATACACCACTTTTCCCAGATTTA
1 AAAATATTTTTTTTGGTGTTTGCCACCCAATGACATACACCA-TTTTCTCAGATTTA
* * ** * *
187678 AAAATATTTTTTTGGGTGTTTGTCACTTAATAGCCTATAC-CTCATTTTC-CAAATTTA
1 AAAATATTTTTTTTGGTGTTTGCCACCCAAT-GAC-ATACAC-CATTTTCTCAGATTTA
** * * *
187735 AAAATATTTTTTTT-GTGTTTTTCACCCAATAGTC-TACATCATCTTTCTTAGATTTA
1 AAAATATTTTTTTTGGTGTTTGCCACCCAAT-GACATACACCAT-TTTCTCAGATTTA
* ** * * *
187791 AAAATA-TTTTTTTGATTGTTTGCCATTCAAT-AGCTTACACCATATTTTTCAAATTTA
1 AAAATATTTTTTTTG-GTGTTTGCCACCCAATGA-CATACACCAT-TTTCTCAGATTTA
* ** *
187848 AAAATA-TTTTTTTGAGTATTTGCCACCCAATGGTTGACAT-CACTTTTTTTTTCAGATTTA
1 AAAATATTTTTTTTG-GTGTTTGCCACCCAA----TGACATACAC-CATTTTCTCAGATTTA
* * * * * *
187908 AAAATATTTTTTTGGGTGTTTGTCACCTAATGACCTACACCATTTTTTTCAAATTTA
1 AAAATATTTTTTTTGGTGTTTGCCACCCAATGACATACACCA-TTTTCTCAGATTTA
* * * *
187965 AAAATA-TTTTTTTGGATATTTACCACCCAATAACATACACCACCTTTCTCAGATTTA
1 AAAATATTTTTTTTGG-TGTTTGCCACCCAATGACATACACCA-TTTTCTCAGATTTA
188022 AAA
1 AAA
188025 TTTTAAAATT
Statistics
Matches: 274, Mismatches: 53, Indels: 40
0.75 0.14 0.11
Matches are distributed among these distances:
54 6 0.02
55 11 0.04
56 42 0.15
57 156 0.57
58 8 0.03
59 6 0.02
60 33 0.12
61 11 0.04
62 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.44
Consensus pattern (56 bp):
AAAATATTTTTTTTGGTGTTTGCCACCCAATGACATACACCATTTTCTCAGATTTA
Found at i:187737 original size:113 final size:113
Alignment explanation
Indices: 187628--188024 Score: 437
Period size: 113 Copynumber: 3.5 Consensus size: 113
187618 AATAAAATTT
* *
187628 TTTTTTTGGTGTTTGCCACCCAATGACATACACCACTTTTCCCAGATTTAAAAATATTTTTTTGG
1 TTTTTTTGGTATTTGCCACCCAATGACATACACCACTTTTCTCAGATTTAAAAATATTTTTTTGG
* *
187693 GTGTTTGTCACTTAATAGCCTATACC-TCATTTTCCAAATTTAAAAATA
66 GTGTTTGTCACTTAATAGCCTACACCAT-ATTTTTCAAATTTAAAAATA
* * ** * * *
187741 TTTTTTTTGTGTTTTTCACCCAATAGTC-TACATCA-TCTTTCTTAGATTTAAAAATATTTTTTT
1 TTTTTTTGGTATTTGCCACCCAAT-GACATACACCACT-TTTCTCAGATTTAAAAATATTTTTTT
** * *
187804 GATTGTTTGCCA-TTCAATAGCTTACACCATATTTTTCAAATTTAAAAATA
64 GGGTGTTTGTCACTT-AATAGCCTACACCATATTTTTCAAATTTAAAAATA
*** *
187854 TTTTTTTGAGTATTTGCCACCCAATGGTTGACAT-CACTTTTTTTTTCAGATTTAAAAATATTTT
1 TTTTTTTG-GTATTTGCCACCCAA----TGACATACACCACTTTTCTCAGATTTAAAAATATTTT
* *
187918 TTTGGGTGTTTGTCACCTAAT-GACCTACACCATTTTTTTCAAATTTAAAAATA
61 TTTGGGTGTTTGTCACTTAATAG-CCTACACCATATTTTTCAAATTTAAAAATA
* * *
187971 TTTTTTTGGATATTTACCACCCAATAACATACACCACCTTTCTCAGATTTAAAA
1 TTTTTTTGG-TATTTGCCACCCAATGACATACACCACTTTTCTCAGATTTAAAA
188025 TTTTAAAATT
Statistics
Matches: 233, Mismatches: 36, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
112 3 0.01
113 102 0.44
114 33 0.14
116 2 0.01
117 89 0.38
118 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (113 bp):
TTTTTTTGGTATTTGCCACCCAATGACATACACCACTTTTCTCAGATTTAAAAATATTTTTTTGG
GTGTTTGTCACTTAATAGCCTACACCATATTTTTCAAATTTAAAAATA
Found at i:187947 original size:117 final size:113
Alignment explanation
Indices: 187628--188024 Score: 402
Period size: 117 Copynumber: 3.5 Consensus size: 113
187618 AATAAAATTT
* * * *
187628 TTTTTTTGGTGTTTGCCACCCAAT-GACATACACCA-CTTT-TCCCAGATTTAAAAATATTTTTT
1 TTTTTTTGGTATTT-CCACCCAATAGTC-TACATCATCTTTCT-TCAGATTTAAAAATATTTTTT
* *
187690 TGGGTGTTTGTCACTTAATAGCCTATACC-TCATTTTCCAAATTTAAAAATA
63 TGGGTGTTTGTCACTTAATAGCCTACACCAT-ATTTTTCAAATTTAAAAATA
*
187741 TTTTTTTTGTGT-TTTTCACCCAATAGTCTACATCATCTTTCTT-AGATTTAAAAATATTTTTTT
1 -TTTTTTTG-GTATTTCCACCCAATAGTCTACATCATCTTTCTTCAGATTTAAAAATATTTTTTT
** * *
187804 GATTGTTTGCCA-TTCAATAGCTTACACCATATTTTTCAAATTTAAAAATA
64 GGGTGTTTGTCACTT-AATAGCCTACACCATATTTTTCAAATTTAAAAATA
* * *
187854 TTTTTTTGAGTATTTGCCACCCAATGGT-TGACATCACTTTTTTTTTCAGATTTAAAAATATTTT
1 TTTTTTTG-GTATTT-CCACCCAATAGTCT-ACATCA--TCTTTCTTCAGATTTAAAAATATTTT
* *
187918 TTTGGGTGTTTGTCACCTAAT-GACCTACACCATTTTTTTCAAATTTAAAAATA
61 TTTGGGTGTTTGTCACTTAATAG-CCTACACCATATTTTTCAAATTTAAAAATA
* * *
187971 TTTTTTTGGATATTTACCACCCAATA-ACATACACCACCTTTC-TCAGATTTAAAA
1 TTTTTTTGG-TATTT-CCACCCAATAGTC-TACATCATCTTTCTTCAGATTTAAAA
188025 TTTTAAAATT
Statistics
Matches: 238, Mismatches: 28, Indels: 34
0.79 0.09 0.11
Matches are distributed among these distances:
112 12 0.05
113 77 0.32
114 46 0.19
115 6 0.03
116 8 0.03
117 87 0.37
118 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (113 bp):
TTTTTTTGGTATTTCCACCCAATAGTCTACATCATCTTTCTTCAGATTTAAAAATATTTTTTTGG
GTGTTTGTCACTTAATAGCCTACACCATATTTTTCAAATTTAAAAATA
Found at i:188301 original size:57 final size:57
Alignment explanation
Indices: 188210--188363 Score: 211
Period size: 57 Copynumber: 2.7 Consensus size: 57
188200 AGATCATTGG
* * *
188210 CAAACATCTAAAAAAAATATTTTTTACATATGAAAAAGGTGGTGTAAACCATAGGATGA
1 CAAACA-CTAAAAAAAATA-TTTTTAAATTTGAAAAAGGTGGTGTAAACAATAGGATGA
** * *
188269 CAAACACTAAAAAAAATATTTTTAAATTTGAAAAAAATGGTGTAGACAATTGGATGA
1 CAAACACTAAAAAAAATATTTTTAAATTTGAAAAAGGTGGTGTAAACAATAGGATGA
*
188326 CAAACACT-AAAAAAATATTTTTAAATTTGAGAAAGGTG
1 CAAACACTAAAAAAAATATTTTTAAATTTGAAAAAGGTG
188364 ATATATGTCA
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
56 27 0.32
57 40 0.47
58 12 0.14
59 6 0.07
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.28
Consensus pattern (57 bp):
CAAACACTAAAAAAAATATTTTTAAATTTGAAAAAGGTGGTGTAAACAATAGGATGA
Found at i:188948 original size:32 final size:34
Alignment explanation
Indices: 188888--188959 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 34
188878 AAATCTTTAT
*
188888 TTTAAATTTATTCTAAGTTTAGAATTATTTTAAA
1 TTTAAATTTATTCTAAGTTCAGAATTATTTTAAA
188922 TTTAAATTTA-T-TAAGTTCA-AATTTATTTTAAA
1 TTTAAATTTATTCTAAGTTCAGAA-TTATTTTAAA
188954 TTTAAA
1 TTTAAA
188960 ATTTGAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 2 0.06
32 23 0.64
33 1 0.03
34 10 0.28
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTCTAAGTTCAGAATTATTTTAAA
Found at i:189751 original size:3 final size:3
Alignment explanation
Indices: 189736--189792 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
189726 TAAATAATTT
* * * *
189736 TAA TAA CAA TAA TAA TAA TGA TAA TAA -ATA TAA TAT TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
189781 TAA TAA TAA TAA
1 TAA TAA TAA TAA
189793 ATAAATAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 42 0.95
4 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:193811 original size:18 final size:18
Alignment explanation
Indices: 193788--193824 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
193778 GCATCTAATA
*
193788 TTGTTCCTTGTAATTATT
1 TTGTTCCTTGTAAATATT
193806 TTGTTCCTTGTAAATATT
1 TTGTTCCTTGTAAATATT
193824 T
1 T
193825 GGCAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (18 bp):
TTGTTCCTTGTAAATATT
Found at i:194312 original size:49 final size:49
Alignment explanation
Indices: 194232--194522 Score: 268
Period size: 49 Copynumber: 6.0 Consensus size: 49
194222 CTGTAGGTCT
* * *
194232 TAGTACCACGAA-ACATGAAGGGAAAGATTTAAGTCGTAACGGTGAATC
1 TAGTACCACGAAGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* ** * * *
194280 TAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACC
1 TAGTACCACGAAGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* *
194329 TTA-TACCTCAAAGACATAAAGGGAAAGATTTAAG-CTGCAACGGCGAATC
1 -TAGTACCACGAAGACATAAAGGGAAAGATTTAAGTC-GCAACGGCGAATC
* ** ** * * *
194378 CAGTACCATAAAGACACGAAGGGAAAGGTTTAAGTCGTAACGGCGAACC
1 TAGTACCACGAAGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * *
194427 TTA-TACCTC-AGAGACATAAAAGGAAAGATTTAAGCCGCAACGGCGAATC
1 -TAGTACCACGA-AGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
* * * * *
194476 CAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTTGCAATGGCGAA
1 TAGTACCACGAAGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAA
194523 CCTTATACTC
Statistics
Matches: 193, Mismatches: 41, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
48 16 0.08
49 172 0.89
50 5 0.03
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.18
Consensus pattern (49 bp):
TAGTACCACGAAGACATAAAGGGAAAGATTTAAGTCGCAACGGCGAATC
Found at i:194425 original size:98 final size:98
Alignment explanation
Indices: 194244--194562 Score: 423
Period size: 98 Copynumber: 3.3 Consensus size: 98
194234 GTACCACGAA
* * * * * * * *
194244 ACATGAAGGGAAAGATTTAAGTCGTAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
1 ACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGT
*
194309 TTAAGTCGCAACGACGAACCTTATACCTCAAAG
66 TTAAGTCGCAACGGCGAACCTTATACCTCAAAG
* **
194342 ACATAAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCATAAAGACACGAAGGGAAAGGT
1 ACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGT
* *
194407 TTAAGTCGTAACGGCGAACCTTATACCTCAGAG
66 TTAAGTCGCAACGGCGAACCTTATACCTCAAAG
* *
194440 ACATAAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACAAAGGGAAAGGT
1 ACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGT
* *
194505 TTAAGTTGCAATGGCGAACCTTATA-CTCAGAAG
66 TTAAGTCGCAACGGCGAACCTTATACCTCA-AAG
194538 -CATGAAA--GAAA-ATTTAAGCCGCAAC
1 ACAT-AAAGGGAAAGATTTAAGCCGCAAC
194563 AGTGAATTTA
Statistics
Matches: 196, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
95 14 0.07
96 4 0.02
97 7 0.04
98 171 0.87
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (98 bp):
ACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGT
TTAAGTCGCAACGGCGAACCTTATACCTCAAAG
Found at i:194515 original size:147 final size:146
Alignment explanation
Indices: 194248--194522 Score: 331
Period size: 147 Copynumber: 1.9 Consensus size: 146
194238 CACGAAACAT
* * * ** * *
194248 GAAGGGAAAGATTTAAGTCGTAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGTCGTAACGGCGAACCTAGTACCACGAAGACATAAAAGGAAAGATTTAA
* * *
194313 GTCGCAACGACGAACCTTATACCTCAAAGACATAAAGGGAAAGATTTAAGCTGCAACGGCGAATC
66 GCCGCAACGACGAACC-TATACCACAAAGACACAAAGGGAAAGATTTAAGCTGCAACGGCGAATC
194378 CAGTACCATAAAGACAC
130 CAGTACCATAAAGACAC
* *
194395 GAAGGGAAAGGTTTAAGTCGTAACGGCGAACCTTA-TACCTC-AGAGACATAAAAGGAAAGATTT
1 GAAGGGAAAGATTTAAGTCGTAACGGCGAACC-TAGTACCACGA-AGACATAAAAGGAAAGATTT
* * * * *
194458 AAGCCGCAACGGCGAATCC-AGTACCACGAAGACACAAAGGGAAAGGTTTAAGTTGCAATGGCGA
64 AAGCCGCAACGACGAA-CCTA-TACCACAAAGACACAAAGGGAAAGATTTAAGCTGCAACGGCGA
194522 A
127 A
194523 CCTTATACTC
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
146 2 0.02
147 101 0.94
148 4 0.04
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (146 bp):
GAAGGGAAAGATTTAAGTCGTAACGGCGAACCTAGTACCACGAAGACATAAAAGGAAAGATTTAA
GCCGCAACGACGAACCTATACCACAAAGACACAAAGGGAAAGATTTAAGCTGCAACGGCGAATCC
AGTACCATAAAGACAC
Found at i:195061 original size:15 final size:16
Alignment explanation
Indices: 195042--195085 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
195032 TTAGAAATAT
195042 TTTAAATTTAAATTTA
1 TTTAAATTTAAATTTA
*
195058 -TTAAGTTTAAATTTA
1 TTTAAATTTAAATTTA
195073 TTTTAAATTTAAA
1 -TTTAAATTTAAA
195086 ATTTGAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 14 0.58
17 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:195075 original size:32 final size:34
Alignment explanation
Indices: 195016--195085 Score: 101
Period size: 32 Copynumber: 2.1 Consensus size: 34
195006 ATCATTATTA
195016 TAAATTTATTCTAAGTTTAGAAATATTTTAAATT
1 TAAATTTATTCTAAGTTTAGAAATATTTTAAATT
*
195050 TAAATTTA-T-TAAGTTTA-AATTTATTTTAAATT
1 TAAATTTATTCTAAGTTTAGAA-ATATTTTAAATT
195082 TAAA
1 TAAA
195086 ATTTGAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 2 0.06
32 23 0.68
33 1 0.03
34 8 0.24
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (34 bp):
TAAATTTATTCTAAGTTTAGAAATATTTTAAATT
Found at i:195405 original size:77 final size:76
Alignment explanation
Indices: 195276--195431 Score: 294
Period size: 77 Copynumber: 2.0 Consensus size: 76
195266 CTAAAGTCAA
195276 ACCCTAAAAAGTAACTACCCCCACTTGCACTGCTACTGCCGTCCACCCTCAGCCACTCAGTGCGT
1 ACCCTAAAAAGTAACTACCCCCACTTGCACTGCTACTGCCGTCCACCCTCAGCCACTCAGTGCGT
195341 GCCACATAAAC
66 GCCACATAAAC
*
195352 ACNCCTAAAAAGTAACTACCCCCACTTGCACTGCTGCTGCCGTCCACCCTCAGCCACTCAGTGCG
1 AC-CCTAAAAAGTAACTACCCCCACTTGCACTGCTACTGCCGTCCACCCTCAGCCACTCAGTGCG
195417 TGCCACATAAAC
65 TGCCACATAAAC
195429 ACC
1 ACC
195432 AGCAACACCA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
76 3 0.04
77 75 0.96
ACGTcount: A:0.27, C:0.41, G:0.13, T:0.18
Consensus pattern (76 bp):
ACCCTAAAAAGTAACTACCCCCACTTGCACTGCTACTGCCGTCCACCCTCAGCCACTCAGTGCGT
GCCACATAAAC
Found at i:197117 original size:29 final size:28
Alignment explanation
Indices: 197050--197355 Score: 292
Period size: 29 Copynumber: 10.5 Consensus size: 28
197040 CCCCTAAACT
*
197050 TTTCCAAAATTACATTTTTAACTCGAAC
1 TTTCCAAAATTACATTTTTACCTCGAAC
**
197078 TTTTTTGAAAATTACATTTTTACTCTCGAAC
1 --TTTCCAAAATTACATTTTTAC-CTCGAAC
* * *
197109 TTTCCAAAATTCCATTTTTGACCACGAAT
1 TTTCCAAAATTACATTTTT-ACCTCGAAC
* *
197138 TTTCCAAAAATTACATTTTTACCCCCAAAC
1 TTTCC-AAAATTACATTTTTA-CCTCGAAC
* *
197168 TTTCCAAAATTCCATTTTTAACC-CTGAAT
1 TTTCCAAAATTACATTTTT-ACCTC-GAAC
* * *
197197 TTTCCAAAATTTCATATTTGACCTCGAAT
1 TTTCCAAAATTACAT-TTTTACCTCGAAC
197226 TTTCCAAAAATTACATTTTTATCCTCGAAC
1 TTTCC-AAAATTACATTTTTA-CCTCGAAC
* * *
197256 TTTCCAAAATTCCATTTTTAACCTTGAAT
1 TTTCCAAAATTACATTTTT-ACCTCGAAC
* *
197285 TTTCCAAAAATTACA-TTTTACCTCAAAT
1 TTTCC-AAAATTACATTTTTACCTCGAAC
*
197313 TTTCCAAAAATTACATTTTTACCCCCGAAC
1 TTTCC-AAAATTACATTTTTA-CCTCGAAC
197343 TTTCCAAAATTAC
1 TTTCCAAAATTAC
197356 CCTCGAATGT
Statistics
Matches: 233, Mismatches: 29, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
28 23 0.10
29 115 0.49
30 88 0.38
31 7 0.03
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (28 bp):
TTTCCAAAATTACATTTTTACCTCGAAC
Found at i:197119 original size:59 final size:57
Alignment explanation
Indices: 197050--197355 Score: 287
Period size: 59 Copynumber: 5.2 Consensus size: 57
197040 CCCCTAAACT
* **
197050 TTTCCAAAATTACATTTTTAACTCGAACTTTTTTGAAAATTACATTTTTACTCTCGAAC
1 TTTCCAAAATTACATTTTTACCTCGAA-TTTTTCAAAAATTACATTTTTAC-CTCGAAC
* * * * *
197109 TTTCCAAAATTCCATTTTTGACCACGAATTTTCCAAAAATTACATTTTTACCCCCAAAC
1 TTTCCAAAATTACATTTTT-ACCTCGAATTTTTCAAAAATTACATTTTTA-CCTCGAAC
* * * * *
197168 TTTCCAAAATTCCATTTTTAACC-CTGAA-TTTTCCAAAATTTCATATTTGACCTCGAAT
1 TTTCCAAAATTACATTTTT-ACCTC-GAATTTTTCAAAAATTACAT-TTTTACCTCGAAC
* * * * *
197226 TTTCCAAAAATTACATTTTTATCCTCGAA-CTTTCCAAAATTCCATTTTTAACCTTGAAT
1 TTTCC-AAAATTACATTTTTA-CCTCGAATTTTTCAAAAATTACATTTTT-ACCTCGAAC
* * *
197285 TTTCCAAAAATTACA-TTTTACCTCAAATTTTCCAAAAATTACATTTTTACCCCCGAAC
1 TTTCC-AAAATTACATTTTTACCTCGAATTTTTCAAAAATTACATTTTTA-CCTCGAAC
197343 TTTCCAAAATTAC
1 TTTCCAAAATTAC
197356 CCTCGAATGT
Statistics
Matches: 208, Mismatches: 29, Indels: 22
0.80 0.11 0.08
Matches are distributed among these distances:
57 15 0.07
58 59 0.28
59 126 0.61
60 8 0.04
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (57 bp):
TTTCCAAAATTACATTTTTACCTCGAATTTTTCAAAAATTACATTTTTACCTCGAAC
Found at i:197201 original size:88 final size:88
Alignment explanation
Indices: 197049--197353 Score: 395
Period size: 88 Copynumber: 3.5 Consensus size: 88
197039 ACCCCTAAAC
* * ** * * *
197049 TTTTCC-AAAATTACATTTTTA-ACTCGAACTTTTTTGAAAATTACATTTTT-ACTCTCGAACTT
1 TTTTCCAAAAATTACATTTTTACCCCCGAAC--TTTCCAAAATTCCATTTTTAACCCT-GAATTT
* *
197111 TCCAAAATTCCATTTTTGACCACGAA
63 TCCAAAATTACATTTTTGACCTCGAA
*
197137 TTTTCCAAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTGAATTTTCC
1 TTTTCCAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTGAATTTTCC
* *
197202 AAAATTTCATATTTGACCTCGAA
66 AAAATTACATTTTTGACCTCGAA
* * *
197225 TTTTCCAAAAATTACATTTTTATCCTCGAACTTTCCAAAATTCCATTTTTAACCTTGAATTTTCC
1 TTTTCCAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTGAATTTTCC
*
197290 AAAAATTACA-TTTT-ACCTCAAA
66 -AAAATTACATTTTTGACCTCGAA
197312 TTTTCCAAAAATTACATTTTTACCCCCGAACTTTCCAAAATT
1 TTTTCCAAAAATTACATTTTTACCCCCGAACTTTCCAAAATT
197354 ACCCTCGAAT
Statistics
Matches: 193, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
87 47 0.24
88 114 0.59
89 27 0.14
90 5 0.03
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (88 bp):
TTTTCCAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTGAATTTTCC
AAAATTACATTTTTGACCTCGAA
Found at i:197378 original size:108 final size:108
Alignment explanation
Indices: 197261--197464 Score: 263
Period size: 108 Copynumber: 1.9 Consensus size: 108
197251 CGAACTTTCC
* * *** *
197261 AAAATTCCATTTTTAACCTTGAATTTTCCAAAAATTA-CATTTTA-CCTCAAATTTTCCAAAAAT
1 AAAATTCCATTTTTAACCCTAAACCCTCCAAAAATTACCATTTTACCCTCAAA-TAT-CAAAAAT
*
197324 TA-CATTTTTACCCCCGAA-CTTTCCAAAATTACCCTCGAATGTCTA
64 TACCA-TTTTACCCCCGAAGC-ATCCAAAATTACCCTCGAATGTCTA
* *
197369 AAAATTCCATTTTTGACCCTAAACCCTCCAAAAATTACCATTTTACCCTCAAATATCTAAAATTA
1 AAAATTCCATTTTTAACCCTAAACCCTCCAAAAATTACCATTTTACCCTCAAATATCAAAAATTA
197434 CCATTTTACCCCCGAAGCATCCAAAATTACC
66 CCATTTTACCCCCGAAGCATCCAAAATTACC
197465 ATTTCCCCTG
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
108 64 0.77
109 12 0.14
110 7 0.08
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (108 bp):
AAAATTCCATTTTTAACCCTAAACCCTCCAAAAATTACCATTTTACCCTCAAATATCAAAAATTA
CCATTTTACCCCCGAAGCATCCAAAATTACCCTCGAATGTCTA
Found at i:197435 original size:28 final size:29
Alignment explanation
Indices: 197399--197468 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
197389 AAACCCTCCA
* * *
197399 AAAATTACCATTTTACCCTC-AAATATCT
1 AAAATTACCATTTTACCCCCGAAACATCC
*
197427 AAAATTACCATTTTACCCCCGAAGCATCC
1 AAAATTACCATTTTACCCCCGAAACATCC
197456 AAAATTACCATTT
1 AAAATTACCATTT
197469 CCCCTGGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.39, C:0.27, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAAACATCC
Done.