Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009514.1 Kokia drynarioides strain JFW-HI SEQ_124225, 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: 302545
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:5145 original size:16 final size:17
Alignment explanation
Indices: 5124--5158 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5114 TTTTTTATAC
5124 ATTTTTATATA-TATTA
1 ATTTTTATATATTATTA
*
5140 ATTTTTATTTATTATTA
1 ATTTTTATATATTATTA
5157 AT
1 AT
5159 ATTTCTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTATATATTATTA
Found at i:6018 original size:17 final size:17
Alignment explanation
Indices: 5984--6088 Score: 95
Period size: 17 Copynumber: 6.1 Consensus size: 17
5974 TGGACTCTCT
*
5984 TTTAATATTT-AATTAAA
1 TTTAA-ATTTAAAATAAA
*
6001 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
* *
6018 TTTAAATTTAGAATGAA
1 TTTAAATTTAAAATAAA
* *
6035 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
* *
6052 TTTAAATTTATACTAAA
1 TTTAAATTTAAAATAAA
* *
6069 ATTAAAATTAAAATTAAA
1 TTTAAATTTAAAA-TAAA
6087 TT
1 TT
6089 AACAACTAAA
Statistics
Matches: 68, Mismatches: 18, Indels: 3
0.76 0.20 0.03
Matches are distributed among these distances:
16 4 0.06
17 59 0.87
18 5 0.07
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:6059 original size:23 final size:23
Alignment explanation
Indices: 6033--6080 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6023 ATTTAGAATG
* *
6033 AATTTATATTCAAAA-TAAATTTA
1 AATTTATACT-AAAATTAAAATTA
6056 AATTTATACTAAAATTAAAATTA
1 AATTTATACTAAAATTAAAATTA
6079 AA
1 AA
6081 ATTAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTTATACTAAAATTAAAATTA
Found at i:6586 original size:39 final size:39
Alignment explanation
Indices: 6543--6862 Score: 207
Period size: 39 Copynumber: 8.3 Consensus size: 39
6533 CCATGATCGA
* *
6543 GGTAAGAGATTGACTGATGATGATCTACCCCAAGCTCGG
1 GGTAAAAGATTGACTGATGGTGATCTACCCCAAGCTCGG
* * * * *
6582 GGTAAAAGATCGAATGACT-GTAATCTACCCTAGGCTCGG
1 GGTAAAAGATTGACTGA-TGGTGATCTACCCCAAGCTCGG
* **
6621 GGAAAAAGATTGGTTGATGGTGATCTA-CCCAAGCTCGG
1 GGTAAAAGATTGACTGATGGTGATCTACCCCAAGCTCGG
** *
6659 GGTAAAAGATT---T-ATGGTGATCTGTCCCACA-CTCGA
1 GGTAAAAGATTGACTGATGGTGATCTACCCCA-AGCTCGG
* *
6694 GGTAAAAGA-T--CGGATGGCTGCAATCTACCCCAAGCTTGG
1 GGTAAAAGATTGACTGATGG-TG--ATCTACCCCAAGCTCGG
** * * *
6733 GGTAAAAGATCAAATGATGGTGATCTGCCCCAAGCTTGG
1 GGTAAAAGATTGACTGATGGTGATCTACCCCAAGCTCGG
* * ** *
6772 GGTAAAAGA-T--CGGATGGCTATAGTCTACCTTAGGCTCGG
1 GGTAAAAGATTGACTGATGG-T-GA-TCTACCCCAAGCTCGG
** *
6811 GGTAAGGGATTGACTGATGGTGATCTGCCCCAAGCTCGG
1 GGTAAAAGATTGACTGATGGTGATCTACCCCAAGCTCGG
* *
6850 GATAAGAGATTGA
1 GGTAAAAGATTGA
6863 ATCTTCAATT
Statistics
Matches: 217, Mismatches: 45, Indels: 38
0.72 0.15 0.13
Matches are distributed among these distances:
34 11 0.05
35 18 0.08
36 10 0.05
37 3 0.01
38 22 0.10
39 136 0.63
40 3 0.01
41 3 0.01
42 11 0.05
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (39 bp):
GGTAAAAGATTGACTGATGGTGATCTACCCCAAGCTCGG
Found at i:6703 original size:35 final size:34
Alignment explanation
Indices: 6637--6703 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
6627 AGATTGGTTG
*
6637 ATGGTGATCTACCCAAGCTCGGGGTAAAAGATTT
1 ATGGTGATCTACCCAAGCTCGAGGTAAAAGATTT
*
6671 ATGGTGATCTGTCCCACA-CTCGAGGTAAAAGAT
1 ATGGTGATCT-ACCCA-AGCTCGAGGTAAAAGAT
6704 CGGATGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 10 0.34
35 18 0.62
36 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (34 bp):
ATGGTGATCTACCCAAGCTCGAGGTAAAAGATTT
Found at i:6780 original size:78 final size:77
Alignment explanation
Indices: 6565--6859 Score: 259
Period size: 78 Copynumber: 3.9 Consensus size: 77
6555 ACTGATGATG
* * * * *
6565 ATCTACCCCAAGCTCGGGGTAAAAGATCGAATGACT-GTAATCTACCCTAGGCTCGGGGAAAAAG
1 ATCTACCCCAAGCTCGGGGTAAAAGATCGAATGA-TGGTGATCTGCCCCAAGCTCGGGGTAAAAG
*
6629 ATTGGTTGATGG-TG-
65 A-TCG--GATGGCTGA
* * *
6643 ATCTA-CCCAAGCTCGGGGTAAAAGAT----TTATGGTGATCTGTCCCACA-CTCGAGGTAAAAG
1 ATCTACCCCAAGCTCGGGGTAAAAGATCGAATGATGGTGATCTGCCCCA-AGCTCGGGGTAAAAG
6702 ATCGGATGGCTGCA
65 ATCGGATGGCTG-A
* * *
6716 ATCTACCCCAAGCTTGGGGTAAAAGATCAAATGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGA
1 ATCTACCCCAAGCTCGGGGTAAAAGATCGAATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
6781 TCGGATGGCT-A
66 TCGGATGGCTGA
** * ** * * * *
6792 TAGTCTACCTTAGGCTCGGGGTAAGGGATTGACTGATGGTGATCTGCCCCAAGCTCGGGATAAGA
1 -A-TCTACCCCAAGCTCGGGGTAAAAGATCGAATGATGGTGATCTGCCCCAAGCTCGGGGTAAAA
6857 GAT
64 GAT
6860 TGAATCTTCA
Statistics
Matches: 178, Mismatches: 26, Indels: 26
0.77 0.11 0.11
Matches are distributed among these distances:
70 5 0.03
71 2 0.01
72 3 0.02
73 28 0.16
74 20 0.11
76 1 0.01
77 23 0.13
78 96 0.54
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (77 bp):
ATCTACCCCAAGCTCGGGGTAAAAGATCGAATGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
TCGGATGGCTGA
Found at i:10858 original size:18 final size:18
Alignment explanation
Indices: 10835--10872 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
10825 AATATCGGCT
10835 ACCCATTCTAAGTATTTA
1 ACCCATTCTAAGTATTTA
10853 ACCCATTCTAAGTATTTA
1 ACCCATTCTAAGTATTTA
10871 AC
1 AC
10873 TACTTGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (18 bp):
ACCCATTCTAAGTATTTA
Found at i:13231 original size:26 final size:26
Alignment explanation
Indices: 13195--13246 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
13185 TATTATGGGA
13195 GCAACTCTTGCTTTAGTTTCATCCTT
1 GCAACTCTTGCTTTAGTTTCATCCTT
13221 GCAACTCTTGCTTTAGTTTCATCCTT
1 GCAACTCTTGCTTTAGTTTCATCCTT
13247 CTTTGGTCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.12, T:0.46
Consensus pattern (26 bp):
GCAACTCTTGCTTTAGTTTCATCCTT
Found at i:19071 original size:29 final size:28
Alignment explanation
Indices: 19039--19236 Score: 128
Period size: 30 Copynumber: 6.8 Consensus size: 28
19029 AGTTCAAAGT
* *
19039 AAAAATGTAATTTTTGAAAAATTCGAGGC
1 AAAAATGTAATTTTTG-GAAGTTCGAGGC
* * *
19068 -AAAATGTGATTTTTGGAAGTTCGGGGG
1 AAAAATGTAATTTTTGGAAGTTCGAGGC
* *
19095 TAAAATGTGATTTTTGTGAAGTTCGAGGGC
1 AAAAATGTAATTTTTG-GAAGTTCGA-GGC
* * * * *
19125 AAAAATGTATTTTTTTAGAAGTTTAGGGGT
1 AAAAATGTA-ATTTTTGGAAG-TTCGAGGC
* * **
19155 AAAAATGTGATTTTTGAAAGTTCAGAGAT
1 AAAAATGTAATTTTTGGAAGTTC-GAGGC
* * *
19184 AAAAATATAATTTTTGAGAAGTTATGAGGGT
1 AAAAATGTAATTTTTG-GAAGTT-CGA-GGC
*
19215 AAAAATGTGATTTTTGGAAGTT
1 AAAAATGTAATTTTTGGAAGTT
19237 TGGGGGCATT
Statistics
Matches: 132, Mismatches: 28, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
27 8 0.06
28 31 0.23
29 33 0.25
30 36 0.27
31 24 0.18
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
AAAAATGTAATTTTTGGAAGTTCGAGGC
Found at i:19079 original size:28 final size:27
Alignment explanation
Indices: 19040--19236 Score: 108
Period size: 28 Copynumber: 6.8 Consensus size: 27
19030 GTTCAAAGTA
* * *
19040 AAAATGTAATTTTTGAAAAATTCGAGGC
1 AAAATGTGATTTTTG-GAAGTTCGAGGC
* *
19068 AAAATGTGATTTTTGGAAGTTCGGGGGT
1 AAAATGTGATTTTTGGAAGTTC-GAGGC
19096 AAAATGTGATTTTTGTGAAGTTCGAGGGC
1 AAAATGTGATTTTTG-GAAGTTCGA-GGC
* * * *
19125 AAAAATGT-ATTTTTTTAGAAGTTTAGGGGTA
1 -AAAATGTGA--TTTTTGGAAG-TTCGAGG-C
* **
19156 AAAATGTGATTTTTGAAAGTTCAGAGATA
1 AAAATGTGATTTTTGGAAGTTC-GAG-GC
* * * *
19185 AAAATATAATTTTTGAGAAGTTATGAGGGTA
1 AAAATGTGATTTTTG-GAAGTT-CGA-GG-C
19216 AAAATGTGATTTTTGGAAGTT
1 AAAATGTGATTTTTGGAAGTT
19237 TGGGGGCATT
Statistics
Matches: 131, Mismatches: 23, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
27 5 0.04
28 35 0.27
29 34 0.26
30 33 0.25
31 24 0.18
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (27 bp):
AAAATGTGATTTTTGGAAGTTCGAGGC
Found at i:19132 original size:30 final size:29
Alignment explanation
Indices: 19006--19236 Score: 170
Period size: 29 Copynumber: 7.9 Consensus size: 29
18996 AAAGTTTTTG
** *
19006 GGGTAAAAATGACATTTTGGGAGAGTTC-A
1 GGGTAAAAATGTGATTTTTGGA-AGTTCGA
** * * *
19035 AAGTAAAAATGTAATTTTTGAAAAATTCGA
1 GGGTAAAAATGTGATTTTTG-GAAGTTCGA
* *
19065 -GG-CAAAATGTGATTTTTGGAAGTTCGG
1 GGGTAAAAATGTGATTTTTGGAAGTTCGA
19092 GGGT-AAAATGTGATTTTTGTGAAGTTCGA
1 GGGTAAAAATGTGATTTTTG-GAAGTTCGA
* * *
19121 GGGCAAAAATGT-ATTTTTTTAGAAGTT-TA
1 GGGTAAAAATGTGA--TTTTTGGAAGTTCGA
*
19150 GGGGTAAAAATGTGATTTTTGAAAGTTC-A
1 -GGGTAAAAATGTGATTTTTGGAAGTTCGA
* * * *
19179 GAGATAAAAATATAATTTTTGAGAAGTTATGA
1 G-GGTAAAAATGTGATTTTTG-GAAGTT-CGA
19211 GGGTAAAAATGTGATTTTTGGAAGTT
1 GGGTAAAAATGTGATTTTTGGAAGTT
19237 TGGGGGCATT
Statistics
Matches: 159, Mismatches: 28, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
27 6 0.04
28 32 0.20
29 60 0.38
30 37 0.23
31 22 0.14
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTGATTTTTGGAAGTTCGA
Found at i:19197 original size:60 final size:58
Alignment explanation
Indices: 19037--19236 Score: 178
Period size: 59 Copynumber: 3.4 Consensus size: 58
19027 AGAGTTCAAA
* * * * * **
19037 GTAAAAATGTAATTTTTGAAAAATTCGAGG-C-AAAATGTGA-TTTTTGGAAGTTCGGGG
1 GTAAAAATGTGATTTTTG-GAAGTTCGAGGACAAAAATAT-ATTTTTTAGAAGTTTAGGG
* *
19094 GT-AAAATGTGATTTTTGTGAAGTTCGAGGGCAAAAATGTATTTTTTTAGAAGTTTAGGG
1 GTAAAAATGTGATTTTTG-GAAGTTCGAGGACAAAAATATA-TTTTTTAGAAGTTTAGGG
* * *
19153 GTAAAAATGTGATTTTTGAAAGTTC-AGAGATAAAAATATAATTTTTGAGAAG-TTATGAGG
1 GTAAAAATGTGATTTTTGGAAGTTCGAG-GACAAAAATAT-ATTTTTTAGAAGTTTA-G-GG
19213 GTAAAAATGTGATTTTTGGAAGTT
1 GTAAAAATGTGATTTTTGGAAGTT
19237 TGGGGGCATT
Statistics
Matches: 121, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
56 23 0.19
57 4 0.03
58 12 0.10
59 41 0.34
60 41 0.34
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
GTAAAAATGTGATTTTTGGAAGTTCGAGGACAAAAATATATTTTTTAGAAGTTTAGGG
Found at i:20219 original size:17 final size:16
Alignment explanation
Indices: 20189--20227 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
20179 TTTTTATACG
20189 TTTTTATATATATTAA
1 TTTTTATATATATTAA
*
20205 TTTTTATTTATTATTAA
1 TTTTTATATA-TATTAA
20222 TATTTT
1 T-TTTT
20228 TTGATCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 7 0.35
18 4 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTATATATATTAA
Found at i:20495 original size:23 final size:22
Alignment explanation
Indices: 20447--20495 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
20437 TGGTAAAATT
* **
20447 AATATAGTAAATAATATATATT
1 AATATAGTAAATAATAAATAAC
*
20469 AATATATTATAATAATAAATAAC
1 AATATAGTA-AATAATAAATAAC
20492 AATA
1 AATA
20496 AATAAAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AATATAGTAAATAATAAATAAC
Found at i:21056 original size:6 final size:6
Alignment explanation
Indices: 21047--21131 Score: 54
Period size: 6 Copynumber: 14.8 Consensus size: 6
21037 TAATTTTTAA
** *
21047 TTAAAT TTAAAT TTAAA- ACAAAT TTAAAT TTAGAA- -TGAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT TTAAAT
* * * * *
21093 TCAAA- ATAAAT TTAAAT TTATA- CTAAAT TTAAAC TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
21132 AATAAATTAA
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
4 2 0.03
5 10 0.17
6 44 0.76
7 2 0.03
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:21069 original size:17 final size:17
Alignment explanation
Indices: 21049--21132 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
21039 ATTTTTAATT
21049 AAATTTAAATTTAAAAC
1 AAATTTAAATTTAAAAC
* *
21066 AAATTTAAATTTAGAAT
1 AAATTTAAATTTAAAAC
* * *
21083 GAATTTAAATTCAAAAT
1 AAATTTAAATTTAAAAC
*
21100 AAATTTAAATTT-ATAC
1 AAATTTAAATTTAAAAC
*
21116 TAAATTTAAACTTAAAA
1 -AAATTTAAATTTAAAA
21133 ATAAATTAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
16 2 0.04
17 50 0.93
18 2 0.04
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTTAAAAC
Found at i:21073 original size:34 final size:34
Alignment explanation
Indices: 21048--21132 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 34
21038 AATTTTTAAT
21048 TAAATTTAAATTTAAAACAAATTTAAATTTAGAA
1 TAAATTTAAATTTAAAACAAATTTAAATTTAGAA
* * * * *
21082 TGAATTTAAATTCAAAATAAATTTAAATTTATAC
1 TAAATTTAAATTTAAAACAAATTTAAATTTAGAA
*
21116 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
21133 ATAAATTAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (34 bp):
TAAATTTAAATTTAAAACAAATTTAAATTTAGAA
Found at i:23807 original size:13 final size:13
Alignment explanation
Indices: 23789--23813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23779 ATTTGAAGTA
23789 AATCATAGTATGT
1 AATCATAGTATGT
23802 AATCATAGTATG
1 AATCATAGTATG
23814 CAATTTAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATCATAGTATGT
Found at i:26637 original size:45 final size:45
Alignment explanation
Indices: 26585--26674 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
26575 ATTTAATATA
26585 GCTATATGTTTGATTTCACAATAACATGGCATATTTTAGAGTATC
1 GCTATATGTTTGATTTCACAATAACATGGCATATTTTAGAGTATC
26630 GCTATATGTTTGATTTCACAATAACATGGCATATTTTAGAGTATC
1 GCTATATGTTTGATTTCACAATAACATGGCATATTTTAGAGTATC
26675 TTCAAAACCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (45 bp):
GCTATATGTTTGATTTCACAATAACATGGCATATTTTAGAGTATC
Found at i:28316 original size:20 final size:20
Alignment explanation
Indices: 28293--28332 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28283 GTATTGATAC
*
28293 TTTTTGTCAAGTATCAATAG
1 TTTTTATCAAGTATCAATAG
**
28313 TTTTTATTGAGTATCAATAG
1 TTTTTATCAAGTATCAATAG
28333 AACCAAGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTTTATCAAGTATCAATAG
Found at i:32351 original size:7 final size:7
Alignment explanation
Indices: 32339--32370 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
32329 CTTATTTTAT
32339 TTTATTA
1 TTTATTA
32346 TTTATTA
1 TTTATTA
32353 TTTATTA
1 TTTATTA
32360 TTTATCTA
1 TTTAT-TA
32368 TTT
1 TTT
32371 GTGATTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:32509 original size:22 final size:25
Alignment explanation
Indices: 32484--32538 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 25
32474 TTGTTTGTTT
32484 TTTAATTTAT-TATTATTT-AT-TA
1 TTTAATTTATGTATTATTTAATATA
*
32506 TTT-ATTTTTGTATTATTTAATGATA
1 TTTAATTTATGTATTATTTAAT-ATA
32531 TTTAATTT
1 TTTAATTT
32539 TATTGATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.19
22 11 0.41
23 2 0.07
25 5 0.19
26 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTAATTTATGTATTATTTAATATA
Found at i:38071 original size:48 final size:48
Alignment explanation
Indices: 38009--38108 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
37999 CAAGGACATA
* * * *
38009 TGTGGACAAAGCCACTAAATTTGTAGACAAGCTGCCAATACACATGGT
1 TGTGAACAAAGCCACTAAAATTGTAGACAAACTACCAATACACATGGT
38057 TGTGAACAAAGCCACTAAAATTGTAGACAAACTACCAATACACATGGT
1 TGTGAACAAAGCCACTAAAATTGTAGACAAACTACCAATACACATGGT
38105 TGTG
1 TGTG
38109 GATAAACCAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (48 bp):
TGTGAACAAAGCCACTAAAATTGTAGACAAACTACCAATACACATGGT
Found at i:38129 original size:48 final size:48
Alignment explanation
Indices: 38009--38131 Score: 149
Period size: 48 Copynumber: 2.6 Consensus size: 48
37999 CAAGGACATA
* * * * *
38009 TGTGGACAAAGCCACTAAATTTGTAGACAAGCTGCCAATACACATGGT
1 TGTGAACAAAGCCACCAAAATTGTAGACAAACTACCAATACACATGGT
*
38057 TGTGAACAAAGCCACTAAAATTGTAGACAAACTACCAATACACATGGT
1 TGTGAACAAAGCCACCAAAATTGTAGACAAACTACCAATACACATGGT
* * *
38105 TGTGGATAAA-CCACCAATAGTTGTAGA
1 TGTGAACAAAGCCACCAA-AATTGTAGA
38132 TTATTAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
47 6 0.09
48 60 0.91
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (48 bp):
TGTGAACAAAGCCACCAAAATTGTAGACAAACTACCAATACACATGGT
Found at i:39658 original size:24 final size:21
Alignment explanation
Indices: 39610--39658 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
39600 AATCAATGGT
* *
39610 TTCAAAATAAAAAGAAAATAC
1 TTCAAAATAAAAAGAAAACAA
39631 TTCAAAATTAAAAGATGAAAACAA
1 TTCAAAA-TAAAA-A-GAAAACAA
39655 TTCA
1 TTCA
39659 CTCTATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 5 0.22
23 1 0.04
24 10 0.43
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.22
Consensus pattern (21 bp):
TTCAAAATAAAAAGAAAACAA
Found at i:41631 original size:2 final size:2
Alignment explanation
Indices: 41624--41657 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41614 CTTATCACTT
41624 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
41658 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:41858 original size:21 final size:21
Alignment explanation
Indices: 41834--41880 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
41824 AAACTCTATT
41834 GATACAAGT-ATG-AATTCTACC
1 GATACAAGTCATGCAA--CTACC
41855 GATACAAGTCATGCAACTACC
1 GATACAAGTCATGCAACTACC
41876 GATAC
1 GATAC
41881 CAAAAACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 19 0.79
22 3 0.12
23 2 0.08
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (21 bp):
GATACAAGTCATGCAACTACC
Found at i:42569 original size:35 final size:35
Alignment explanation
Indices: 42525--42610 Score: 154
Period size: 35 Copynumber: 2.5 Consensus size: 35
42515 TCGTTATTTG
42525 TTTACTCCCTATTGACTCAAAAGTCATGATGCATA
1 TTTACTCCCTATTGACTCAAAAGTCATGATGCATA
* *
42560 TTTACTCCCTATTGACTCCAAAGTCATGATGCGTA
1 TTTACTCCCTATTGACTCAAAAGTCATGATGCATA
42595 TTTACTCCCTATTGAC
1 TTTACTCCCTATTGAC
42611 CTAGATGTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (35 bp):
TTTACTCCCTATTGACTCAAAAGTCATGATGCATA
Found at i:42621 original size:35 final size:34
Alignment explanation
Indices: 42525--42622 Score: 133
Period size: 35 Copynumber: 2.8 Consensus size: 34
42515 TCGTTATTTG
*
42525 TTTACTCCCTATTGACTCAAAAGTCATGATGCATA
1 TTTACTCCCTATTGAC-CTAAAGTCATGATGCATA
* *
42560 TTTACTCCCTATTGACTCCAAAGTCATGATGCGTA
1 TTTACTCCCTATTGAC-CTAAAGTCATGATGCATA
*
42595 TTTACTCCCTATTGACCTAGATGTCATG
1 TTTACTCCCTATTGACCTA-AAGTCATG
42623 CTTGTTACCA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
34 2 0.03
35 56 0.97
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (34 bp):
TTTACTCCCTATTGACCTAAAGTCATGATGCATA
Found at i:49736 original size:35 final size:35
Alignment explanation
Indices: 49697--49782 Score: 127
Period size: 35 Copynumber: 2.5 Consensus size: 35
49687 TCGTTATTCG
*
49697 TTTACTCCCTATTGACTTAAAAGTCATGATGCACA
1 TTTACTCCCTATTGACTCAAAAGTCATGATGCACA
* **
49732 TTTACTCCCTATTAACTCAAAAGTCATGATGCGTA
1 TTTACTCCCTATTGACTCAAAAGTCATGATGCACA
*
49767 TTTACTCCTTATTGAC
1 TTTACTCCCTATTGAC
49783 CTAGATGTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.37
Consensus pattern (35 bp):
TTTACTCCCTATTGACTCAAAAGTCATGATGCACA
Found at i:49793 original size:35 final size:35
Alignment explanation
Indices: 49697--49794 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
49687 TCGTTATTCG
*
49697 TTTACTCCCTATTGACTTAAAAGTCATGATGCACA
1 TTTACTCCCTATTGACCTAAAAGTCATGATGCACA
* **
49732 TTTACTCCCTATT-AACTCAAAAGTCATGATGCGTA
1 TTTACTCCCTATTGACCT-AAAAGTCATGATGCACA
* * *
49767 TTTACTCCTTATTGACCTAGATGTCATG
1 TTTACTCCCTATTGACCTAAAAGTCATG
49795 CTTGTTACCA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.04
35 48 0.91
36 3 0.06
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (35 bp):
TTTACTCCCTATTGACCTAAAAGTCATGATGCACA
Found at i:56237 original size:26 final size:24
Alignment explanation
Indices: 56208--56256 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
56198 TTATTTTCCT
*
56208 ATTAAAGAATAAGATAATTTTTTATA
1 ATTAAAG-ATAA-ATAATTTATTATA
*
56234 ATTAAAGTTAAATAATTTATTAT
1 ATTAAAGATAAATAATTTATTAT
56257 TAAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 3 0.14
26 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
ATTAAAGATAAATAATTTATTATA
Found at i:57211 original size:21 final size:22
Alignment explanation
Indices: 57185--57235 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
57175 ATTGGTGAAT
57185 TCTTTTATATATT-TTTTTATA
1 TCTTTTATATATTGTTTTTATA
*
57206 TCTTTTCA-A-ATTGTTTTTTTA
1 TCTTTT-ATATATTGTTTTTATA
57227 T-TTTTATAT
1 TCTTTTATAT
57236 TACAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
19 1 0.04
20 8 0.32
21 15 0.60
22 1 0.04
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.71
Consensus pattern (22 bp):
TCTTTTATATATTGTTTTTATA
Found at i:67212 original size:18 final size:18
Alignment explanation
Indices: 67189--67303 Score: 112
Period size: 18 Copynumber: 6.4 Consensus size: 18
67179 GAAGGAATTT
*
67189 CATACTCGCTCATTTA-AG
1 CATACTGGCTC-TTTAGAG
*
67207 CATACTGGCTCGTTAGAG
1 CATACTGGCTCTTTAGAG
*
67225 CATACTAGCTCTTTAGAG
1 CATACTGGCTCTTTAGAG
* *
67243 CATATTGGCTAATTTA-AG
1 CATACTGGCT-CTTTAGAG
*
67261 CATACTAGCT-TGTTAGAG
1 CATACTGGCTCT-TTAGAG
67279 CATACTGGCTCGTTT-GAG
1 CATACTGGCTC-TTTAGAG
67297 CATACTG
1 CATACTG
67304 ACTCGAAAGA
Statistics
Matches: 81, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
16 1 0.01
17 6 0.07
18 67 0.83
19 6 0.07
20 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (18 bp):
CATACTGGCTCTTTAGAG
Found at i:67245 original size:36 final size:36
Alignment explanation
Indices: 67189--67302 Score: 135
Period size: 36 Copynumber: 3.2 Consensus size: 36
67179 GAAGGAATTT
*
67189 CATACTCGCTCATTTA-AGCATACTGGCTCGTTAGAG
1 CATACTAGCTC-TTTAGAGCATACTGGCTCGTTAGAG
* **
67225 CATACTAGCTCTTTAGAGCATATTGGCTAATTTA-AG
1 CATACTAGCTCTTTAGAGCATACTGGCT-CGTTAGAG
*
67261 CATACTAGCT-TGTTAGAGCATACTGGCTCGTTTGAG
1 CATACTAGCTCT-TTAGAGCATACTGGCTCGTTAGAG
67297 CATACT
1 CATACT
67303 GACTCGAAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
35 7 0.11
36 56 0.85
37 3 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (36 bp):
CATACTAGCTCTTTAGAGCATACTGGCTCGTTAGAG
Found at i:67315 original size:18 final size:18
Alignment explanation
Indices: 67275--67317 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
67265 CTAGCTTGTT
* **
67275 AGAGCATACTGGCTCGTT
1 AGAGCATACTGACTCGAA
*
67293 TGAGCATACTGACTCGAA
1 AGAGCATACTGACTCGAA
67311 AGAGCAT
1 AGAGCAT
67318 TACCGGATCG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (18 bp):
AGAGCATACTGACTCGAA
Found at i:74322 original size:18 final size:18
Alignment explanation
Indices: 74301--74396 Score: 140
Period size: 18 Copynumber: 5.3 Consensus size: 18
74291 TAGCATGCTC
74301 GCTCGTTTGAGCATACTG
1 GCTCGTTTGAGCATACTG
* *
74319 GCTCGTTAGAGCATACTA
1 GCTCGTTTGAGCATACTG
74337 GCTCGTTTTG-GCATACTG
1 GCTCG-TTTGAGCATACTG
* *
74355 GCTCGTTCGAGCATACTA
1 GCTCGTTTGAGCATACTG
74373 GCTCGTTTGAGCATACTG
1 GCTCGTTTGAGCATACTG
74391 GCTCGT
1 GCTCGT
74397 AAGAGCATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
17 3 0.04
18 62 0.91
19 3 0.04
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (18 bp):
GCTCGTTTGAGCATACTG
Found at i:74341 original size:36 final size:36
Alignment explanation
Indices: 74292--74410 Score: 177
Period size: 36 Copynumber: 3.3 Consensus size: 36
74282 GGGAAGGAAT
* *
74292 AGCATGCTCGCTCGTTTGAGCATACTGGCTCGTTAG
1 AGCATACTAGCTCGTTTGAGCATACTGGCTCGTTAG
*
74328 AGCATACTAGCTCGTTTTG-GCATACTGGCTCGTTCG
1 AGCATACTAGCTCG-TTTGAGCATACTGGCTCGTTAG
*
74364 AGCATACTAGCTCGTTTGAGCATACTGGCTCGTAAG
1 AGCATACTAGCTCGTTTGAGCATACTGGCTCGTTAG
74400 AGCATTACTAG
1 AGCA-TACTAG
74411 ATCGCATGAG
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 4 0.05
36 61 0.81
37 10 0.13
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (36 bp):
AGCATACTAGCTCGTTTGAGCATACTGGCTCGTTAG
Found at i:81230 original size:18 final size:18
Alignment explanation
Indices: 81207--81255 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
81197 GGGAAGGAAG
81207 AGCATACTGGCTCATTTA
1 AGCATACTGGCTCATTTA
*
81225 AGCATACTGGCTCGTTTA
1 AGCATACTGGCTCATTTA
* *
81243 AGCGTATTGGCTC
1 AGCATACTGGCTC
81256 GTTAGAGCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (18 bp):
AGCATACTGGCTCATTTA
Found at i:81256 original size:18 final size:19
Alignment explanation
Indices: 81214--81293 Score: 105
Period size: 18 Copynumber: 4.4 Consensus size: 19
81204 AAGAGCATAC
* * *
81214 TGGCTCATTTA-AGCATAC
1 TGGCTCGTTTAGAGCGTAT
81232 TGGCTCGTTTA-AGCGTAT
1 TGGCTCGTTTAGAGCGTAT
81250 TGGCTCG-TTAGAGCGTAT
1 TGGCTCGTTTAGAGCGTAT
81268 TGGCTCG-TTAGAGCGTAT
1 TGGCTCGTTTAGAGCGTAT
81286 TGGCTCGT
1 TGGCTCGT
81294 AAGAGCATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
17 3 0.05
18 54 0.95
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (19 bp):
TGGCTCGTTTAGAGCGTAT
Found at i:81298 original size:18 final size:18
Alignment explanation
Indices: 81232--81299 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
81222 TTAAGCATAC
81232 TGGCTCGTTTA-AGCGTAT
1 TGGCTCG-TTAGAGCGTAT
81250 TGGCTCGTTAGAGCGTAT
1 TGGCTCGTTAGAGCGTAT
81268 TGGCTCGTTAGAGCGTAT
1 TGGCTCGTTAGAGCGTAT
*
81286 TGGCTCGTAAGAGC
1 TGGCTCGTTAGAGC
81300 ATTACTGGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
17 3 0.06
18 45 0.94
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (18 bp):
TGGCTCGTTAGAGCGTAT
Found at i:86273 original size:49 final size:49
Alignment explanation
Indices: 86170--86275 Score: 124
Period size: 49 Copynumber: 2.2 Consensus size: 49
86160 TTCATGTTCG
* * * *
86170 GGTTTTGGATTTGAGGTTCAAGGTTCAAGGTTTAGGGTTTAAGGTTTTA
1 GGTTTGGGATTTAAGGTTCAAGGTTCAAGGTTAAGGGTTTAAGGTTATA
* * **
86219 TGTTTGGGATTTAAGGTTC-GGGTTCAAGGTTCAAGGGTTTGTGGTTATA
1 GGTTTGGGATTTAAGGTTCAAGGTTCAAGGTT-AAGGGTTTAAGGTTATA
86268 GGTTTGGG
1 GGTTTGGG
86276 GTTCATGGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 11 0.23
49 36 0.77
ACGTcount: A:0.18, C:0.05, G:0.36, T:0.42
Consensus pattern (49 bp):
GGTTTGGGATTTAAGGTTCAAGGTTCAAGGTTAAGGGTTTAAGGTTATA
Found at i:86309 original size:36 final size:36
Alignment explanation
Indices: 86238--86312 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
86228 TTTAAGGTTC
* *
86238 GGGTTCAAGGTTCAAGGGTTTGTGGTTATAGGTTTG
1 GGGTTCAAGGTTCAAGGGTTCGAGGTTATAGGTTTG
* * *
86274 GGGTTCATGGTTTAAGGGTTCGAGTTTAT-GTGTTTG
1 GGGTTCAAGGTTCAAGGGTTCGAGGTTATAG-GTTTG
86310 GGG
1 GGG
86313 CTTTTGGTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 1 0.03
36 32 0.97
ACGTcount: A:0.15, C:0.05, G:0.40, T:0.40
Consensus pattern (36 bp):
GGGTTCAAGGTTCAAGGGTTCGAGGTTATAGGTTTG
Found at i:86748 original size:22 final size:22
Alignment explanation
Indices: 86722--86767 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
86712 TTGACATTGT
*
86722 TAGATATATAATACAAACATTA
1 TAGATACATAATACAAACATTA
* *
86744 TAGATACGTAATGCAAACATTA
1 TAGATACATAATACAAACATTA
86766 TA
1 TA
86768 CTGCAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (22 bp):
TAGATACATAATACAAACATTA
Found at i:89595 original size:21 final size:21
Alignment explanation
Indices: 89571--89613 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
89561 TAATAGCAAG
* *
89571 ATTTTACCATTAAATAAAATT
1 ATTTTAACAATAAATAAAATT
89592 ATTTTAACAATAAATAAAATT
1 ATTTTAACAATAAATAAAATT
89613 A
1 A
89614 AATCGATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTTAACAATAAATAAAATT
Found at i:91314 original size:15 final size:15
Alignment explanation
Indices: 91282--91310 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
91272 AAAATGAAAT
91282 TTTATCATTTTAATA
1 TTTATCATTTTAATA
91297 TTTAT-ATTTTAATA
1 TTTATCATTTTAATA
91311 ATTTTTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATCATTTTAATA
Found at i:91815 original size:52 final size:52
Alignment explanation
Indices: 91736--91911 Score: 259
Period size: 52 Copynumber: 3.4 Consensus size: 52
91726 GGAAGCCACA
* *
91736 AAAACCCACCTTTAGAGAAAATCTTGTCTGAAAACCTTAATTTCAACGGAAA-
1 AAAACTCACCTTTAGAGAAAATCTTGTCTGAAAA-CTTAATTTCAACGAAAAC
* * *
91788 AAAACTCACCTTTAGAGAAAATTTTGTCTGAAAATATTAATTTCAATGAAAAC
1 AAAACTCACCTTTAGAGAAAATCTTGTCTGAAAA-CTTAATTTCAACGAAAAC
*
91841 AAAACTCACCTTTAGAAAAAATCTTGTCTGAAAAC--AATTTCAACGAAAAC
1 AAAACTCACCTTTAGAGAAAATCTTGTCTGAAAACTTAATTTCAACGAAAAC
91891 AAAACTCACCTTTAGAGAAAA
1 AAAACTCACCTTTAGAGAAAA
91912 CCCTAGTTTT
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
50 34 0.30
52 46 0.41
53 32 0.29
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (52 bp):
AAAACTCACCTTTAGAGAAAATCTTGTCTGAAAACTTAATTTCAACGAAAAC
Found at i:93695 original size:10 final size:9
Alignment explanation
Indices: 93673--93724 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
93663 TGAACCAACT
93673 GCATCAGTGA
1 GCATCAGT-A
93683 GCATCGAGTA
1 GCATC-AGTA
*
93693 GCATCAGCAA
1 GCATCAG-TA
*
93703 GCATCGAGCA
1 GCATC-AGTA
93713 GCATCAGTA
1 GCATCAGTA
93722 GCA
1 GCA
93725 GTTGGCAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 8 0.22
10 23 0.64
11 5 0.14
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (9 bp):
GCATCAGTA
Found at i:93698 original size:20 final size:19
Alignment explanation
Indices: 93673--93724 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
93663 TGAACCAACT
*
93673 GCATCAGTGAGCATCGAGTA
1 GCATCAGT-AGCATCGAGCA
*
93693 GCATCAGCAAGCATCGAGCA
1 GCATCAG-TAGCATCGAGCA
93713 GCATCAGTAGCA
1 GCATCAGTAGCA
93725 GTTGGCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (19 bp):
GCATCAGTAGCATCGAGCA
Found at i:107979 original size:21 final size:21
Alignment explanation
Indices: 107955--108032 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
107945 TAGTGCAGAC
107955 TTCTACCAATACAAGAGATAG
1 TTCTACCAATACAAGAGATAG
* * *
107976 TTCTACCGATACAAGTG-TCAC
1 TTCTACCAATACAAGAGAT-AG
* * *
107997 TTCTATCGATGCAAGAGATAG
1 TTCTACCAATACAAGAGATAG
108018 TTCTTA-CAATACAAG
1 TTC-TACCAATACAAG
108033 TGTCACTTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.02
21 41 0.91
22 3 0.07
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCTACCAATACAAGAGATAG
Found at i:108012 original size:42 final size:42
Alignment explanation
Indices: 107966--108047 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
107956 TCTACCAATA
* *
107966 CAAGAGATAGTTC-TACCGATACAAGTGTCACTTCTATCGATG
1 CAAGAGATAGTTCTTA-CAATACAAGTGTCACTTATATCGATG
108008 CAAGAGATAGTTCTTACAATACAAGTGTCACTTATATCGA
1 CAAGAGATAGTTCTTACAATACAAGTGTCACTTATATCGA
108048 CACAAGTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (42 bp):
CAAGAGATAGTTCTTACAATACAAGTGTCACTTATATCGATG
Found at i:116864 original size:58 final size:59
Alignment explanation
Indices: 116800--116937 Score: 192
Period size: 58 Copynumber: 2.4 Consensus size: 59
116790 TAATTCATTT
* * * *
116800 TTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA-TTTTATTAAATTGTA
1 TTTAATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTTATCAAATTATA
* *
116858 TTTAATAATAATTATGTT-AAAATATAATTAAATTATTTATTATTTTTATCAAATTATA
1 TTTAATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTTATCAAATTATA
116916 TTTAATAATAATCT-TATTAAAA
1 TTTAATAATAAT-TATATTAAAA
116938 TTTAATAACA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 21 0.30
58 45 0.64
59 4 0.06
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (59 bp):
TTTAATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTTATCAAATTATA
Found at i:136065 original size:19 final size:20
Alignment explanation
Indices: 136024--136070 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
136014 TTTCAGAGGT
*
136024 ATCGATAATTTTCGTTAAAA
1 ATCGATACTTTTCGTTAAAA
*
136044 ATCGATACTTTTC-TTTAAA
1 ATCGATACTTTTCGTTAAAA
136063 ATCGATAC
1 ATCGATAC
136071 CACGGACCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (20 bp):
ATCGATACTTTTCGTTAAAA
Found at i:142934 original size:26 final size:26
Alignment explanation
Indices: 142899--142951 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
142889 ATTGGTATTA
*
142899 AAAGTGATTATTTCTTAATAAAACTT
1 AAAGTAATTATTTCTTAATAAAACTT
142925 AAAGTAATTATTTCTTAATAAAACTT
1 AAAGTAATTATTTCTTAATAAAACTT
142951 A
1 A
142952 GGTTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (26 bp):
AAAGTAATTATTTCTTAATAAAACTT
Found at i:150727 original size:49 final size:49
Alignment explanation
Indices: 150661--150765 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 49
150651 GGGTTTGCAA
* *
150661 TTGGATTTAGGATAGTTTAGGATTTGATTTTGGGCATTTGGCTTGTAAT
1 TTGGATTTAGGATAGTTTAGGATTTGATTTTGGGCATTGGGCTCGTAAT
* * *
150710 TTGGGTTTGGGATAGTTTAGGATTTGATTTTGGGTATTGGGCTCGTAAT
1 TTGGATTTAGGATAGTTTAGGATTTGATTTTGGGCATTGGGCTCGTAAT
150759 TTGGATT
1 TTGGATT
150766 AAGGGTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.18, C:0.04, G:0.31, T:0.47
Consensus pattern (49 bp):
TTGGATTTAGGATAGTTTAGGATTTGATTTTGGGCATTGGGCTCGTAAT
Found at i:152821 original size:28 final size:27
Alignment explanation
Indices: 152789--152852 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 27
152779 TGAAAAAAAG
*
152789 GATAAGCACCAAAGTGCAAAATAATAAC
1 GATAAGCACCAAAGTACAAAATAAT-AC
* *
152817 GATAAGCACCGAAGTACGAAATAATAC
1 GATAAGCACCAAAGTACAAAATAATAC
152844 GATAAGCAC
1 GATAAGCAC
152853 GCTAATATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 11 0.33
28 22 0.67
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (27 bp):
GATAAGCACCAAAGTACAAAATAATAC
Found at i:154843 original size:17 final size:17
Alignment explanation
Indices: 154821--154856 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
154811 AATTAATTTA
* *
154821 AATTAATTAATTTTTTC
1 AATTAAATAATTTTCTC
154838 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
154855 AA
1 AA
154857 CTCAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:156458 original size:13 final size:13
Alignment explanation
Indices: 156440--156464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
156430 AAAGTTAAAA
156440 TATTAAATTGTGC
1 TATTAAATTGTGC
156453 TATTAAATTGTG
1 TATTAAATTGTG
156465 ATTGCTATGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
TATTAAATTGTGC
Found at i:165276 original size:37 final size:37
Alignment explanation
Indices: 165217--165296 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
165207 TAATGTCTCT
* *
165217 GCATGAGCACTTCTAGATTGCA-CTCAAAATTGTTATC
1 GCATGAGCACTTCTAGAGTGCACCT-AAAATTGTCATC
* *
165254 GCATGAGTACTT-TCAGAGTGCACCTAAAATTGTCATT
1 GCATGAGCACTTCT-AGAGTGCACCTAAAATTGTCATC
165291 GCATGA
1 GCATGA
165297 ATATTTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 1 0.03
37 34 0.92
38 2 0.05
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (37 bp):
GCATGAGCACTTCTAGAGTGCACCTAAAATTGTCATC
Found at i:166287 original size:16 final size:16
Alignment explanation
Indices: 166266--166296 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
166256 TTGTGGATCC
166266 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
166282 CATTTTATCTTTATT
1 CATTTTACCTTTATT
166297 TTTACATTAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:169661 original size:37 final size:37
Alignment explanation
Indices: 169589--169671 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 37
169579 TACTACTAAT
* ** *
169589 GTCGTTGCATGAGCACTTCTAGATCGTGCCTAAAACC
1 GTCGTCGCATGAGCACTTCTAGATCGCACCAAAAACC
* *
169626 GTCGTCGCATGAGCACTT-TCAGATTGCACCAAAAACT
1 GTCGTCGCATGAGCACTTCT-AGATCGCACCAAAAACC
*
169663 GTTGTCGCA
1 GTCGTCGCA
169672 GGAATATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (37 bp):
GTCGTCGCATGAGCACTTCTAGATCGCACCAAAAACC
Found at i:169783 original size:37 final size:38
Alignment explanation
Indices: 169706--169784 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 38
169696 CACTGACGTA
* *
169706 GCATAAATATTCTTTAAATTGCATCCAGAACTATCGCT
1 GCATAAATATTCTTTAAATTGCACCCAGAACTATCACT
* * *
169744 GCATAAGTATTC-TTCAATTGCACCCAAGAA-TGTCACT
1 GCATAAATATTCTTTAAATTGCACCC-AGAACTATCACT
169781 GCAT
1 GCAT
169785 GATCATGTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 20 0.57
38 15 0.43
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (38 bp):
GCATAAATATTCTTTAAATTGCACCCAGAACTATCACT
Found at i:170621 original size:16 final size:16
Alignment explanation
Indices: 170600--170630 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
170590 TTGTGGATCC
170600 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
170616 CATTTTATCTTTATT
1 CATTTTACCTTTATT
170631 TTTACATTAC
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:176592 original size:21 final size:21
Alignment explanation
Indices: 176551--176592 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
176541 TAAGTTTAAT
* *
176551 ATAATATATTTTGATTTTGAG
1 ATAATATATTTTGAATATGAG
176572 ATAA-ATATTTTAGAATATGAG
1 ATAATATATTTT-GAATATGAG
176593 CATTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (21 bp):
ATAATATATTTTGAATATGAG
Found at i:186420 original size:18 final size:18
Alignment explanation
Indices: 186397--186438 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
186387 GAAATTAAAA
186397 ATAAAA-TATTAAAATATT
1 ATAAAATTATT-AAATATT
186415 ATAAAATTATTAAATATT
1 ATAAAATTATTAAATATT
*
186433 ACAAAA
1 ATAAAA
186439 AAATCTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAAATTATTAAATATT
Found at i:186532 original size:11 final size:10
Alignment explanation
Indices: 186507--186571 Score: 53
Period size: 11 Copynumber: 6.3 Consensus size: 10
186497 AAAAACATAT
*
186507 AAAA-TATAG
1 AAAATTATAA
186516 AAAATTATTAA
1 AAAATTA-TAA
*
186527 AAAATTAGTTAT
1 AAAATTA--TAA
186539 AAAATTATAGA
1 AAAATTATA-A
*
186550 AAAAATAT-A
1 AAAATTATAA
186559 AAAATTATAA
1 AAAATTATAA
186569 AAA
1 AAA
186572 TGAGAAATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
9 12 0.26
10 8 0.17
11 16 0.35
12 10 0.22
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:187991 original size:24 final size:24
Alignment explanation
Indices: 187949--187994 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
187939 AATATGTGAC
*
187949 AAAAAATTATAAATATCAATATGA
1 AAAAAATGATAAATATCAATATGA
187973 AAAAAATGGATAAAT-TCAATAT
1 AAAAAAT-GATAAATATCAATAT
187995 CAATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (24 bp):
AAAAAATGATAAATATCAATATGA
Found at i:189835 original size:16 final size:17
Alignment explanation
Indices: 189803--189835 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
189793 CTTATTGTAG
189803 ATTTAAAAATTTAAATAT
1 ATTTAAAAA-TTAAATAT
189821 ATTTAAAAA-TAAATA
1 ATTTAAAAATTAAATA
189836 GAACACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTAAAAATTAAATAT
Found at i:190973 original size:8 final size:8
Alignment explanation
Indices: 190960--191002 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
190950 GGTATCGAAT
190960 TTTAATTC
1 TTTAATTC
190968 TTTAATTC
1 TTTAATTC
190976 TTTAATTC
1 TTTAATTC
190984 --T--TTC
1 TTTAATTC
190988 TTTAATTC
1 TTTAATTC
190996 TTTAATT
1 TTTAATT
191003 TAGTGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 3 0.10
6 2 0.06
8 26 0.84
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTAATTC
Found at i:190988 original size:20 final size:20
Alignment explanation
Indices: 190965--191002 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
190955 CGAATTTTAA
190965 TTCTTTAATTCTTTAATTCT
1 TTCTTTAATTCTTTAATTCT
190985 TTCTTTAATTCTTTAATT
1 TTCTTTAATTCTTTAATT
191003 TAGTGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (20 bp):
TTCTTTAATTCTTTAATTCT
Found at i:190990 original size:12 final size:12
Alignment explanation
Indices: 190973--190998 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
190963 AATTCTTTAA
190973 TTCTTTAATTCT
1 TTCTTTAATTCT
190985 TTCTTTAATTCT
1 TTCTTTAATTCT
190997 TT
1 TT
190999 AATTTAGTGG
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:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTTAATTCT
Found at i:203840 original size:33 final size:33
Alignment explanation
Indices: 203801--203905 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 33
203791 TGGAAATAGG
*
203801 TATGATTACAT-TCGTATTCTACATATATGTTAA
1 TATGATTACATCT-GTATTCTGCATATATGTTAA
* * * * *
203834 TATGATTGCATCTGTATTTTGTATATCTATTAA
1 TATGATTACATCTGTATTCTGCATATATGTTAA
* * *
203867 TATGA-TACATCTATATTCCGGATATATGTTAA
1 TATGATTACATCTGTATTCTGCATATATGTTAA
203899 TATGATT
1 TATGATT
203906 GCATGCATTT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 25 0.44
33 31 0.54
34 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.47
Consensus pattern (33 bp):
TATGATTACATCTGTATTCTGCATATATGTTAA
Found at i:203899 original size:32 final size:32
Alignment explanation
Indices: 203823--203904 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
203813 CGTATTCTAC
* * ** *
203823 ATATATGTTAATATGATTGCATCTGTATTTTGT
1 ATATATGTTAATATGA-TACATCTATATTCCGG
* *
203856 ATATCTATTAATATGATACATCTATATTCCGG
1 ATATATGTTAATATGATACATCTATATTCCGG
203888 ATATATGTTAATATGAT
1 ATATATGTTAATATGAT
203905 TGCATGCATT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 26 0.65
33 14 0.35
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (32 bp):
ATATATGTTAATATGATACATCTATATTCCGG
Found at i:212151 original size:13 final size:14
Alignment explanation
Indices: 212133--212161 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
212123 TTGCTTTCTA
212133 TTTTATTTTAT-CT
1 TTTTATTTTATGCT
212146 TTTTATTTTATGCT
1 TTTTATTTTATGCT
212160 TT
1 TT
212162 GAAAGCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTATTTTATGCT
Found at i:217767 original size:91 final size:91
Alignment explanation
Indices: 217612--217793 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
217602 AGGATCATAC
217612 CCAAAGGAGGCGTAAAGCGATAGTAAATTAAATCCCTACAAAGAATAAAAGTAATTAGCACTTAC
1 CCAAAGGAGGCGTAAAGCGATAGTAAATTAAATCCCTACAAAGAATAAAAGTAATTAGCACTTAC
217677 TTTAGGGATTATAGTACGAAGAATAA
66 TTTAGGGATTATAGTACGAAGAATAA
217703 CCAAAGGAGGCGTAAAGCGATAGTAAATTAAATCCCTACAAAGAATAAAAGTAATTAGCACTTAC
1 CCAAAGGAGGCGTAAAGCGATAGTAAATTAAATCCCTACAAAGAATAAAAGTAATTAGCACTTAC
217768 TTTAGGGATTATAGTACGAAGAATAA
66 TTTAGGGATTATAGTACGAAGAATAA
217794 TAAAAGAGTT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (91 bp):
CCAAAGGAGGCGTAAAGCGATAGTAAATTAAATCCCTACAAAGAATAAAAGTAATTAGCACTTAC
TTTAGGGATTATAGTACGAAGAATAA
Found at i:218632 original size:12 final size:11
Alignment explanation
Indices: 218617--218655 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
218607 TTAAAGGCAT
218617 AAAATAAAAGA
1 AAAATAAAAGA
*
218628 TAAAATAAAATA
1 -AAAATAAAAGA
218640 ATAAATAAAAGA
1 A-AAATAAAAGA
218652 AAAA
1 AAAA
218656 GCTTGAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAAAAGA
Found at i:218637 original size:17 final size:17
Alignment explanation
Indices: 218615--218654 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
218605 GTTTAAAGGC
218615 ATAAAATAA-AAGATAAA
1 ATAAAATAATAA-ATAAA
218632 ATAAAATAATAAATAAA
1 ATAAAATAATAAATAAA
*
218649 AGAAAA
1 ATAAAA
218655 AGCTTGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (17 bp):
ATAAAATAATAAATAAA
Found at i:219698 original size:12 final size:12
Alignment explanation
Indices: 219681--219722 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
219671 GTTTGAAGGC
219681 ATAAAATAAAAG
1 ATAAAATAAAAG
*
219693 ATAAAATAAAAT
1 ATAAAATAAAAG
219705 AGTAAAA-AAAAG
1 A-TAAAATAAAAG
*
219717 AGAAAA
1 ATAAAA
219723 AGCTTGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 4 0.15
12 17 0.65
13 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:220763 original size:14 final size:15
Alignment explanation
Indices: 220739--220769 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
220729 GAGTTGTTTG
220739 AAAGCATAAAAATAA
1 AAAGCATAAAAATAA
220754 AAAG-ATAAAAATAA
1 AAAGCATAAAAATAA
220768 AA
1 AA
220770 CAAAGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAGCATAAAAATAA
Found at i:234171 original size:23 final size:23
Alignment explanation
Indices: 234141--234184 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
234131 TAACTAAAGG
*
234141 CCAAACTTCCTTCCACAAAACGA
1 CCAAACTTCCTTCCAAAAAACGA
*
234164 CCAAACTTCCTTTCAAAAAAC
1 CCAAACTTCCTTCCAAAAAAC
234185 CATCATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.36, G:0.02, T:0.20
Consensus pattern (23 bp):
CCAAACTTCCTTCCAAAAAACGA
Found at i:246818 original size:55 final size:55
Alignment explanation
Indices: 246734--246845 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
246724 TGTGCCCTGG
246734 GATGGCGAGGAAGTGTTTGAAAACAAAAGTCCCATCAATGATATATCAGTTGAAA
1 GATGGCGAGGAAGTGTTTGAAAACAAAAGTCCCATCAATGATATATCAGTTGAAA
246789 GATGGCGAGGAAGTGTTTGAAAACAAAAGTCCCATCAATGATATATCAGTTGAAA
1 GATGGCGAGGAAGTGTTTGAAAACAAAAGTCCCATCAATGATATATCAGTTGAAA
246844 GA
1 GA
246846 ATGATTCGAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.23
Consensus pattern (55 bp):
GATGGCGAGGAAGTGTTTGAAAACAAAAGTCCCATCAATGATATATCAGTTGAAA
Found at i:247977 original size:19 final size:17
Alignment explanation
Indices: 247943--247992 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
247933 ATAGTTTGCA
247943 TGCATTTTTATTGTCAT
1 TGCATTTTTATTGTCAT
247960 TGCATTTTTATTTTGTCAT
1 TGCATTTTTA--TTGTCAT
* *
247979 TGTATTTTTTTTGT
1 TGCATTTTTATTGT
247993 TAATTTAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 14 0.48
19 15 0.52
ACGTcount: A:0.14, C:0.08, G:0.12, T:0.66
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:248603 original size:12 final size:12
Alignment explanation
Indices: 248576--248614 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
248566 GAAACTGAGA
248576 AAAAG-AAAGA-
1 AAAAGAAAAGAG
248586 AAAAGAAAAGAG
1 AAAAGAAAAGAG
248598 AAAAGAAAAGAAG
1 AAAAGAAAAG-AG
248611 AAAA
1 AAAA
248615 AATGTGTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
12 10 0.38
13 6 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:258584 original size:6 final size:6
Alignment explanation
Indices: 258573--258597 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
258563 GGAGAACATC
258573 AAGGCT AAGGCT AAGGCT AAGGCT A
1 AAGGCT AAGGCT AAGGCT AAGGCT A
258598 TTTAATTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (6 bp):
AAGGCT
Found at i:259543 original size:15 final size:15
Alignment explanation
Indices: 259507--259544 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
259497 GTTGTTTTGG
259507 TGCAAGAAAAATAAA
1 TGCAAGAAAAATAAA
**
259522 TGC-AGAAATTTAAA
1 TGCAAGAAAAATAAA
259536 TGCAAGAAA
1 TGCAAGAAA
259545 GTAAATTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.58, C:0.08, G:0.16, T:0.18
Consensus pattern (15 bp):
TGCAAGAAAAATAAA
Found at i:267064 original size:37 final size:37
Alignment explanation
Indices: 267005--267101 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
266995 ATTTATAGAA
* * **
267005 TGCACCTAAGATTGTCGTTGCATAAATATTCTTCAAT
1 TGCACCTAAGAATATCACTGCATAAATATTCTTCAAT
* *
267042 TGCATCC-AAGACTATCACTGCATAAGTATTCTTCAAT
1 TGCA-CCTAAGAATATCACTGCATAAATATTCTTCAAT
*
267079 TGCACCTAGGAATATCACTGCAT
1 TGCACCTAAGAATATCACTGCAT
267102 GAACATGTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
36 2 0.04
37 47 0.92
38 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (37 bp):
TGCACCTAAGAATATCACTGCATAAATATTCTTCAAT
Found at i:270586 original size:5 final size:5
Alignment explanation
Indices: 270573--270606 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
270563 CAATCACATA
*
270573 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAA
270607 TATATTAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:271100 original size:37 final size:37
Alignment explanation
Indices: 271045--271116 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
271035 TATTATTGTT
*
271045 GCATAAGCACTTCTAGATTGCGCCCAAAACTGTCATC
1 GCATAAGCACTTCTAGATTGCACCCAAAACTGTCATC
271082 GCATAAGCACTT-TCAGATTGCACCCAAAACTGTCA
1 GCATAAGCACTTCT-AGATTGCACCCAAAACTGTCA
271117 CCACATGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 1 0.03
37 32 0.97
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (37 bp):
GCATAAGCACTTCTAGATTGCACCCAAAACTGTCATC
Found at i:271183 original size:37 final size:37
Alignment explanation
Indices: 271137--271233 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 37
271127 ATTTCCAGAA
* * *
271137 TGCACCCAAGATTGTCGCTGCATAAATATTTTTCAAT
1 TGCACCCAAGACTATCGCTGCATAAATATTCTTCAAT
* * *
271174 TGCATCCAAGACTATCGTTGCATAAGTATTCTTCAAT
1 TGCACCCAAGACTATCGCTGCATAAATATTCTTCAAT
* * *
271211 TGCACTCAGGAATATCGCTGCAT
1 TGCACCCAAGACTATCGCTGCAT
271234 GAACATGTCT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (37 bp):
TGCACCCAAGACTATCGCTGCATAAATATTCTTCAAT
Found at i:274535 original size:23 final size:25
Alignment explanation
Indices: 274509--274554 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
274499 TCAACTAGGG
274509 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
274532 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
274555 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:278647 original size:12 final size:12
Alignment explanation
Indices: 278632--278662 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
278622 TTAGAAGTAG
278632 TTTTCTTCTCAA
1 TTTTCTTCTCAA
*
278644 TTTTCTTCTCGA
1 TTTTCTTCTCAA
278656 TTTTCTT
1 TTTTCTT
278663 TAAGGAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.03, T:0.65
Consensus pattern (12 bp):
TTTTCTTCTCAA
Found at i:284392 original size:24 final size:24
Alignment explanation
Indices: 284366--284410 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
284356 TTTTATTATT
*
284366 TTTTACTTTAA-ACTTTTTTTTAA
1 TTTTAATTTAACACTTTTTTTTAA
*
284389 TTTTAATTTAACCCTTTTTTTT
1 TTTTAATTTAACACTTTTTTTT
284411 TTTTTATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTAATTTAACACTTTTTTTTAA
Found at i:284415 original size:23 final size:22
Alignment explanation
Indices: 284355--284416 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
284345 GAATATTTCT
*
284355 TTTTTATTATTTTTTACTTTAAAC
1 TTTTT-TT-TTTTTTAATTTAAAC
* *
284379 TTTTTTTTAATTTTAATTTAACCC
1 TTTTTTTT-TTTTTAATTTAA-AC
284403 TTTTTTTTTTTTTA
1 TTTTTTTTTTTTTA
284417 TCTTTTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 17 0.53
24 14 0.44
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTTTTTTTAATTTAAAC
Found at i:285083 original size:109 final size:108
Alignment explanation
Indices: 284926--285140 Score: 263
Period size: 109 Copynumber: 2.0 Consensus size: 108
284916 AAAATCAAGG
* *
284926 CAATATTCTTTTATTTTAGATAAATTGAGAAATTGTACCCTAACGTGTTGGGTACGA-TTTTTCT
1 CAATACTCTTTTATTTTAGAGAAATTGAGAAATTGTACCCTAACGTGTTGGGTACGATTTTTTCT
* **
284990 TTGAACTTAAATAATTGAGTATCCTATTTAAAGTCGATAAATGGT
66 TTGAACATAAATAATT-AACATCCTATTTAAA-TCGATAAATGGT
* * * * * *
285035 CAATACTCTTTTATTTTAGGGGACTTGA-AAACTTGTGCCCTAATGTGTTGGGTATGATTTTTTC
1 CAATACTCTTTTATTTTAGAGAAATTGAGAAA-TTGTACCCTAACGTGTTGGGTACGATTTTTTC
* * *
285099 TTTGAACATAAGTAATTAACATCTTATTTAAATTGATAAATG
65 TTTGAACATAAATAATTAACATCCTATTTAAATCGATAAATG
285141 TTCTTTATTT
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
108 12 0.13
109 57 0.63
110 21 0.23
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (108 bp):
CAATACTCTTTTATTTTAGAGAAATTGAGAAATTGTACCCTAACGTGTTGGGTACGATTTTTTCT
TTGAACATAAATAATTAACATCCTATTTAAATCGATAAATGGT
Found at i:286119 original size:19 final size:18
Alignment explanation
Indices: 286095--286140 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
286085 TTTTTATCTC
286095 TTTTTCTTT-TTTACTTTAT
1 TTTTTCTTTGTTTA-TTT-T
286114 TTTTTCCTTTGTTTATTTT
1 TTTTT-CTTTGTTTATTTT
286133 TTTTTCTT
1 TTTTTCTT
286141 CTTATGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.12
19 11 0.44
20 7 0.28
21 4 0.16
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTGTTTATTTT
Found at i:291362 original size:14 final size:16
Alignment explanation
Indices: 291338--291374 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
291328 GAGACTATTG
*
291338 AGAAGAAAGAAAA-AA
1 AGAAAAAAGAAAATAA
291353 A-AAAAAAGAAAATAA
1 AGAAAAAAGAAAATAA
291368 AGAAAAA
1 AGAAAAA
291375 TAATAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.53
15 4 0.21
16 5 0.26
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AGAAAAAAGAAAATAA
Found at i:300126 original size:27 final size:27
Alignment explanation
Indices: 300088--300142 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
300078 AGGGGAAGAA
300088 GGAAAGAAATAATTAGGTAGGTTATTT
1 GGAAAGAAATAATTAGGTAGGTTATTT
300115 GGAAAGAAATAATTAGGTAGGTTATTT
1 GGAAAGAAATAATTAGGTAGGTTATTT
300142 G
1 G
300143 TAGCAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (27 bp):
GGAAAGAAATAATTAGGTAGGTTATTT
Done.