Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014865.1 Kokia drynarioides strain JFW-HI SEQ_129908, 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: 238142
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 243 characters in sequence are not A, C, G, or T
Found at i:93 original size:2 final size:2
Alignment explanation
Indices: 88--113 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78 AAAAAAAAAA
88 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
114 TTATTCAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7848 original size:102 final size:102
Alignment explanation
Indices: 7667--7877 Score: 415
Period size: 102 Copynumber: 2.1 Consensus size: 102
7657 CAATCCACAT
7667 TAGAG-TTTTATATCTTTAGAAGGTAAAACACCATCTGACAGCCTTAATGCTCAACATGTTAAAA
1 TAGAGCTTTTATATCTTTAGAAGGTAAAACACCATCTGACAGCCTTAATGCTCAACATGTTAAAA
7731 CCCATCTTTCTTTTCCAAGTAACATTGATAGGTAAAC
66 CCCATCTTTCTTTTCCAAGTAACATTGATAGGTAAAC
7768 TAGAGCTTTTATATCTTTAGAAGGTAAAACACCATCTGACAGCCTTAATGCTCAACATGTTAAAA
1 TAGAGCTTTTATATCTTTAGAAGGTAAAACACCATCTGACAGCCTTAATGCTCAACATGTTAAAA
7833 CCCATCTTTCTTTTCCAAGTAACATTGATAGGTAAAC
66 CCCATCTTTCTTTTCCAAGTAACATTGATAGGTAAAC
7870 TAGAGCTT
1 TAGAGCTT
7878 ACAAAATTTT
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 5 0.05
102 104 0.95
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (102 bp):
TAGAGCTTTTATATCTTTAGAAGGTAAAACACCATCTGACAGCCTTAATGCTCAACATGTTAAAA
CCCATCTTTCTTTTCCAAGTAACATTGATAGGTAAAC
Found at i:21785 original size:22 final size:20
Alignment explanation
Indices: 21742--21785 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
21732 TATCAAGATT
*
21742 TAATTATATGTGTTTAAATA
1 TAATTATATGTATTTAAATA
*
21762 TAATTATATTTGTATTTAATTA
1 TAATTATA--TGTATTTAAATA
21784 TA
1 TA
21786 TGTGTTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TAATTATATGTATTTAAATA
Found at i:26331 original size:35 final size:35
Alignment explanation
Indices: 26249--26378 Score: 206
Period size: 35 Copynumber: 3.7 Consensus size: 35
26239 AATACTCTGA
* * * * *
26249 AGCATTTTGATTGCTATCAGATATGTTAAAAGGATA
1 AGCATTTTCATTGCTATCAGATAAGCTAAAA-TATT
26285 AGCATTTTCATTGCTATCAGATAAGCTAAAATATT
1 AGCATTTTCATTGCTATCAGATAAGCTAAAATATT
26320 AGCATTTTCATTGCTATCAGATAAGCTAAAATATT
1 AGCATTTTCATTGCTATCAGATAAGCTAAAATATT
26355 AGCATTTTCATTGCTATCAGATAA
1 AGCATTTTCATTGCTATCAGATAA
26379 ATGAGTGGAA
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 61 0.69
36 28 0.31
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (35 bp):
AGCATTTTCATTGCTATCAGATAAGCTAAAATATT
Found at i:28210 original size:2 final size:2
Alignment explanation
Indices: 28205--28230 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28195 AAAAAAATAA
28205 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28231 TTATTTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36892 original size:25 final size:25
Alignment explanation
Indices: 36845--36892 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
36835 TAGATTGCAC
* *
36845 ATATATAAATAATTATATTTATTCA
1 ATATAAAAATAATTATATGTATTCA
36870 ATATAAAAATAAATTA-ATGTATT
1 ATATAAAAAT-AATTATATGTATT
36893 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
ATATAAAAATAATTATATGTATTCA
Found at i:38581 original size:6 final size:7
Alignment explanation
Indices: 38566--38590 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38556 GACTTGGTTC
38566 AAAATAA
1 AAAATAA
38573 AAAATAA
1 AAAATAA
38580 AAAATAA
1 AAAATAA
38587 AAAA
1 AAAA
38591 GCGGCATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:43090 original size:32 final size:34
Alignment explanation
Indices: 43032--43110 Score: 135
Period size: 32 Copynumber: 2.4 Consensus size: 34
43022 TCACTTAATT
43032 AAATTATCTTTTATTTATTATTATTATTTTAAATG
1 AAATTATCTTTTA-TTATTATTATTATTTTAAATG
43067 AAATTATCTTTTA-T-TTATTATTATTTTAAATG
1 AAATTATCTTTTATTATTATTATTATTTTAAATG
43099 AAATTATCTTTT
1 AAATTATCTTTT
43111 GTTTGCTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
32 30 0.68
33 1 0.02
35 13 0.30
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (34 bp):
AAATTATCTTTTATTATTATTATTATTTTAAATG
Found at i:43104 original size:15 final size:15
Alignment explanation
Indices: 43054--43105 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
43044 ATTTATTATT
43054 ATTATTTTAAATGAA
1 ATTATTTTAAATGAA
* * * *
43069 ATTATCTTTTATTTATT
1 ATTAT-TTTAAATGA-A
43086 ATTATTTTAAATGAA
1 ATTATTTTAAATGAA
43101 ATTAT
1 ATTAT
43106 CTTTTGTTTG
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 10 0.37
16 12 0.44
17 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (15 bp):
ATTATTTTAAATGAA
Found at i:43492 original size:22 final size:22
Alignment explanation
Indices: 43464--43510 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
43454 GCTTGCATTT
*
43464 TTAAATTTGAAAAGTA-GAGAGA
1 TTAAATTTCAAAAGTACGA-AGA
*
43486 TTAAATTTCAAATGTACGAAGA
1 TTAAATTTCAAAAGTACGAAGA
43508 TTA
1 TTA
43511 CATAAGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.32
Consensus pattern (22 bp):
TTAAATTTCAAAAGTACGAAGA
Found at i:61691 original size:6 final size:6
Alignment explanation
Indices: 61667--61705 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
61657 GATTTATTTC
* *
61667 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
61706 ATCAATTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:61692 original size:17 final size:18
Alignment explanation
Indices: 61653--61697 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
61643 TTAGATGGAT
* *
61653 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
61671 ATTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
61688 TTTAAATTTA
1 TTTAAATTTA
61698 AATTTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:63655 original size:30 final size:30
Alignment explanation
Indices: 63611--63746 Score: 138
Period size: 30 Copynumber: 4.6 Consensus size: 30
63601 CCTTAAAAGT
*
63611 CCCT-AAACTATCCAAAAATTATA-TTTGA
1 CCCTCAAACTTTCCAAAAATTATATTTTGA
*
63639 CCCTCAAACTTCTCC-AAAATCATATTTTGA
1 CCCTCAAACTT-TCCAAAAATTATATTTTGA
63669 CACCT-AAACTTCTCC-AAAATTATATTTTGA
1 C-CCTCAAACTT-TCCAAAAATTATATTTTGA
* * * * * *
63699 CCCCCGAACTTTCTAAAAAATACATTTTTA
1 CCCTCAAACTTTCCAAAAATTATATTTTGA
63729 CCCTCAAACTTTCCAAAA
1 CCCTCAAACTTTCCAAAA
63747 TTCCATTTTT
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.04
29 17 0.19
30 66 0.73
31 3 0.03
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (30 bp):
CCCTCAAACTTTCCAAAAATTATATTTTGA
Found at i:63746 original size:59 final size:57
Alignment explanation
Indices: 63611--63748 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 57
63601 CCTTAAAAGT
* * **
63611 CCCTAAACTATCCAAAAATTATATTTGACCCTCAAACTTCTCCAAAATCATATTTTGA
1 CCCTAAACTTTCC-AAAATTATATTTGACCCCCAAACTTCTAAAAAATCATATTTTGA
*
63669 CACCTAAACTTCTCCAAAATTATATTTTGACCCCCGAACTTTCTAAAAAATACAT-TTTT-A
1 C-CCTAAACTT-TCCAAAATTATA-TTTGACCCCCAAAC-TTCTAAAAAAT-CATATTTTGA
63729 CCCTCAAACTTTCCAAAATT
1 CCCT-AAACTTTCCAAAATT
63749 CCATTTTTGA
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
58 1 0.01
59 29 0.42
60 23 0.33
61 13 0.19
62 3 0.04
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (57 bp):
CCCTAAACTTTCCAAAATTATATTTGACCCCCAAACTTCTAAAAAATCATATTTTGA
Found at i:63755 original size:89 final size:88
Alignment explanation
Indices: 63638--63846 Score: 203
Period size: 89 Copynumber: 2.3 Consensus size: 88
63628 ATTATATTTG
* * * *
63638 ACCCTCAAACTTCTCCAAAA-TCATATTTTGA-CACCTAAACTTCTCCAAAATTATAT-TTTGAC
1 ACCCTCAAACTT-TCCAAAATTC-CATTTTGATC-CCGAAACTT-TCAAAAAGTAT-TGTTTGAC
*
63700 CCCCGAACTTTCTAAAAAATACATTTTT-
61 CCCCGAAC-TTCCAAAAAATACATTTTTA
* * *
63728 ACCCTCAAACTTTCCAAAATTCCATTTTTGATCTCGAAACTTTCAAAAAGTATTGTTTTACCCTC
1 ACCCTCAAACTTTCCAAAATTCCA-TTTTGATCCCGAAACTTTCAAAAAGTATTGTTTGACCCCC
* *
63793 GATCTTCCAAAAAATCCATTTTTA
65 GAACTTCCAAAAAATACATTTTTA
*
63817 ACCC-CAAATTTTCCTAAAATTACCATTTTG
1 ACCCTCAAACTTTCC-AAAATT-CCATTTTG
63847 CCCCTAAGAG
Statistics
Matches: 101, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
88 27 0.27
89 43 0.43
90 30 0.30
91 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (88 bp):
ACCCTCAAACTTTCCAAAATTCCATTTTGATCCCGAAACTTTCAAAAAGTATTGTTTGACCCCCG
AACTTCCAAAAAATACATTTTTA
Found at i:66074 original size:19 final size:19
Alignment explanation
Indices: 66050--66113 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
66040 TAAAAGTATC
66050 ATATAATAAATAATGAAAT
1 ATATAATAAATAATGAAAT
*
66069 ATATAATTTAAAATTAAT-TAAT
1 ATATAA--T-AAA-TAATGAAAT
66091 -TATAAT-AATACATGAAAT
1 ATATAATAAATA-ATGAAAT
66109 ATATA
1 ATATA
66114 TAATATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 2 0.06
17 4 0.11
18 3 0.08
19 11 0.31
21 6 0.17
22 6 0.17
23 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (19 bp):
ATATAATAAATAATGAAAT
Found at i:66078 original size:37 final size:40
Alignment explanation
Indices: 66035--66113 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
66025 ATATAAATGT
*
66035 TAATTTAAAAGT-A-TCA-TATAATAAATA-ATGAAATATA
1 TAATTTAAAAGTAATTAATTATAAT-AATACATGAAATATA
*
66072 TAATTTAAAATTAATTAATTATAATAATACATGAAATATA
1 TAATTTAAAAGTAATTAATTATAATAATACATGAAATATA
66112 TA
1 TA
66114 TAATATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
37 11 0.31
38 1 0.03
39 6 0.17
40 18 0.50
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.38
Consensus pattern (40 bp):
TAATTTAAAAGTAATTAATTATAATAATACATGAAATATA
Found at i:66134 original size:42 final size:40
Alignment explanation
Indices: 66051--66147 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 40
66041 AAAAGTATCA
**
66051 TATAATAAATAATGAAATATATAATTTAAAATTAATTAAT
1 TATAATAAATAATGAAATATATAATTTAAAATTAAAAAAT
66091 TATAAT-AATACATGAAATATATATAATATTAAAA-TAAAAAAT
1 TATAATAAATA-ATG-AA-ATATATAAT-TTAAAATTAAAAAAT
*
66133 TA-AATTAAATTATGA
1 TATAA-TAAATAATGA
66148 GTAAAATGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
39 4 0.08
40 9 0.19
41 5 0.10
42 21 0.44
43 9 0.19
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (40 bp):
TATAATAAATAATGAAATATATAATTTAAAATTAAAAAAT
Found at i:67126 original size:18 final size:20
Alignment explanation
Indices: 67087--67126 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
67077 TTTCACCAAA
*
67087 CATTCTTAAATTATGTTCTT
1 CATTCTTAAATTATGCTCTT
67107 CATTC-TAAATTA-GCTCTT
1 CATTCTTAAATTATGCTCTT
67125 CA
1 CA
67127 ACTTCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (20 bp):
CATTCTTAAATTATGCTCTT
Found at i:72529 original size:62 final size:55
Alignment explanation
Indices: 72438--72587 Score: 203
Period size: 62 Copynumber: 2.6 Consensus size: 55
72428 TGGTTTGTTA
72438 TTTATTTATTTATTTATATTCATAAAATAATAAATAAATAATAATAATAATTAATATTAT
1 TTTATTTATTTATTTATATTCATAAAATAATAAATAAAT-A-AAT-AT--TTAATATTAT
*
72498 TTTACATTTATTTATTTATATTCATACAATAATAAATAAATAAATATTTAATATTAT
1 TTT--ATTTATTTATTTATATTCATAAAATAATAAATAAATAAATATTTAATATTAT
*
72555 TTTA-TTATTTATTTATATTTATAAAAATAATAA
1 TTTATTTATTTATTTATATTCAT-AAAATAATAA
72588 GAAAAATGGA
Statistics
Matches: 84, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
54 17 0.20
55 10 0.12
57 13 0.15
59 2 0.02
60 6 0.07
61 1 0.01
62 35 0.42
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (55 bp):
TTTATTTATTTATTTATATTCATAAAATAATAAATAAATAAATATTTAATATTAT
Found at i:73251 original size:58 final size:58
Alignment explanation
Indices: 73161--73271 Score: 186
Period size: 58 Copynumber: 1.9 Consensus size: 58
73151 AAGAGATCTA
*
73161 ATGGTCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCAG
1 ATGGTCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTAGATTGCTTCAATCTGCCAG
* * *
73219 ATGGTTTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTAGATTGCTTCAATCT
1 ATGGTCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTAGATTGCTTCAATCT
73272 ACCCCATAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (58 bp):
ATGGTCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTAGATTGCTTCAATCTGCCAG
Found at i:73288 original size:39 final size:39
Alignment explanation
Indices: 73245--73413 Score: 153
Period size: 39 Copynumber: 4.3 Consensus size: 39
73235 CCTCTGGTTA
*
73245 GGGTAAAAGATTAGATTGCTTCAATCTACCCCATAGTCG
1 GGGTAAAAGATTAGATTGCTTCAATCTGCCCCATAGTCG
** * *
73284 GGGTAAAAGATTAGATTTTTTCAATTTGCCTCAT-GATCG
1 GGGTAAAAGATTAGATTGCTTCAATCTGCCCCATAG-TCG
* * * * ** **
73323 GGGTAAGAGATCAAATGGTCTTCAATCTTGCCCTTTAGTTA
1 GGGTAAAAGATTAGATTG-CTTCAATC-TGCCCCATAGTCG
* *
73364 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCAT-GATCG
1 GGGTAAAAGATTAGATTGCTTCAATCTGCCCCATAG-TCG
73403 GGGTAAAAGAT
1 GGGTAAAAGAT
73414 CGGATGGTCT
Statistics
Matches: 98, Mismatches: 27, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
38 2 0.02
39 63 0.64
40 14 0.14
41 18 0.18
42 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (39 bp):
GGGTAAAAGATTAGATTGCTTCAATCTGCCCCATAGTCG
Found at i:73368 original size:41 final size:41
Alignment explanation
Indices: 73323--73514 Score: 144
Period size: 39 Copynumber: 4.8 Consensus size: 41
73313 CTCATGATCG
* ** *
73323 GGGTAAGAGATCAAATGGTCTTCAATCTTGCCCTTTAGTTA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTATAGTTA
* * * **
73364 GGGTAAAAGATTGGAT-TTCTTCAATC-TGCCCCAT-GATCG
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTATAG-TTA
* *
73403 GGGTAAAAGATCGGATGGTCTTCAATCTTACCCTCTAGTTA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTATAGTTA
* * * * * *
73444 GGGTAAAAGATTGAAT-TTCTTTAATC-AGCCCCAT-GATTA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTATAG-TTA
* * *
73483 TGGTAAAAGATTGGATAGTCTTCAATCTTGCC
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCC
73515 TTCTGGTTAG
Statistics
Matches: 115, Mismatches: 29, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
38 2 0.02
39 43 0.37
40 34 0.30
41 35 0.30
42 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (41 bp):
GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTATAGTTA
Found at i:73381 original size:80 final size:80
Alignment explanation
Indices: 73245--73480 Score: 289
Period size: 80 Copynumber: 3.0 Consensus size: 80
73235 CCTCTGGTTA
* * * ** * *
73245 GGGTAAAAGATTAGATTG-CTTCAATC-TACCC-CATAGTCGGGGTAAAAGATTAGATTTTTTCA
1 GGGTAAAAGATCAAATGGTCTTCAATCTTACCCTC-TAGTTAGGGTAAAAGATTGGATTTCTTCA
* *
73307 ATTTGCCTCATGATCG
65 ATCTGCCCCATGATCG
* * *
73323 GGGTAAGAGATCAAATGGTCTTCAATCTTGCCCTTTAGTTAGGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATCAAATGGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTGGATTTCTTCAA
73388 TCTGCCCCATGATCG
66 TCTGCCCCATGATCG
** * *
73403 GGGTAAAAGATCGGATGGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTGAATTTCTTTAA
1 GGGTAAAAGATCAAATGGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTGGATTTCTTCAA
*
73468 TCAGCCCCATGAT
66 TCTGCCCCATGAT
73481 TATGGTAAAA
Statistics
Matches: 135, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
78 14 0.10
79 8 0.06
80 113 0.84
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (80 bp):
GGGTAAAAGATCAAATGGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTGGATTTCTTCAA
TCTGCCCCATGATCG
Found at i:73488 original size:80 final size:80
Alignment explanation
Indices: 73244--73511 Score: 283
Period size: 80 Copynumber: 3.4 Consensus size: 80
73234 CCCTCTGGTT
** * ** *
73244 AGGGTAAAAGATTAGATTG-CTTCAATC-TACCC-CATAGTCGGGGTAAAAGATT-AGATTTTTT
1 AGGGTAAAAGATCGGATGGTCTTCAATCTTACCCTC-TAGTTAGGGTAAAAGATTGA-ATTTCTT
** *
73305 CAATTTGCCTCATGATC
64 CAATCAGCCCCATGATC
* * ** * * *
73322 GGGGTAAGAGATCAAATGGTCTTCAATCTTGCCCTTTAGTTAGGGTAAAAGATTGGATTTCTTCA
1 AGGGTAAAAGATCGGATGGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTGAATTTCTTCA
*
73387 ATCTGCCCCATGATC
66 ATCAGCCCCATGATC
* *
73402 GGGGTAAAAGATCGGATGGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTGAATTTCTTTA
1 AGGGTAAAAGATCGGATGGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTGAATTTCTTCA
*
73467 ATCAGCCCCATGATT
66 ATCAGCCCCATGATC
* * *
73482 ATGGTAAAAGATTGGATAGTCTTCAATCTT
1 AGGGTAAAAGATCGGATGGTCTTCAATCTT
73512 GCCTTCTGGT
Statistics
Matches: 160, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
78 14 0.09
79 8 0.05
80 138 0.86
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (80 bp):
AGGGTAAAAGATCGGATGGTCTTCAATCTTACCCTCTAGTTAGGGTAAAAGATTGAATTTCTTCA
ATCAGCCCCATGATC
Found at i:78230 original size:63 final size:65
Alignment explanation
Indices: 78143--78280 Score: 208
Period size: 67 Copynumber: 2.1 Consensus size: 65
78133 TTTTGGTTTG
* *
78143 TTATTTATTTATATTCAT-AAAAT-AATAAATAAATAATAACACAAAATTAATATTATTTTACAT
1 TTATTTATTTAAATTCATAAAAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACAT
* *
78206 TTATTTATTTAAATTCATACAATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTTAT
1 TTATTTATTTAAATTCATA-AA-AATAAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
78271 AT
64 AT
78273 TTATTTAT
1 TTATTTAT
78281 ATTTATAATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
63 17 0.25
65 2 0.03
66 3 0.04
67 45 0.67
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (65 bp):
TTATTTATTTAAATTCATAAAAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACAT
Found at i:78256 original size:67 final size:63
Alignment explanation
Indices: 78143--78307 Score: 205
Period size: 67 Copynumber: 2.6 Consensus size: 63
78133 TTTTGGTTTG
* *
78143 TTATTTATTTATATTCATAAAATAATAAATAAATAATAACACAAAATTAATATTATTTTACAT
1 TTATTTATTTAAATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACAT
*
78206 TTATTTATTTAAATTCATACAATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTT--
1 TTATTTATTTAAATTCAT--AA-AAT-AATAAATAAATAATAAAACAAAATTAATATTATTTTAC
78269 A-
62 AT
* *
78270 -TATTTATTTATATTTATAATAATAATAAAT-AATAATAA
1 TTATTTATTTAAATTCATAA-AATAATAAATAAATAATAA
78308 TAATAATAAT
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
59 8 0.09
60 7 0.08
61 6 0.06
63 32 0.34
65 3 0.03
66 3 0.03
67 34 0.37
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (63 bp):
TTATTTATTTAAATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACAT
Found at i:78293 original size:3 final size:3
Alignment explanation
Indices: 78285--78319 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
78275 ATTTATATTT
78285 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA A
78320 GAAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:78694 original size:20 final size:20
Alignment explanation
Indices: 78639--78694 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
78629 AAAACAAATG
*
78639 AAAATATTATTAAAATTATA
1 AAAATATTATAAAAATTATA
* *
78659 AAAATAATAGTAAAAATTATT
1 AAAATATTA-TAAAAATTATA
*
78680 AAAAGATTATAAAAA
1 AAAATATTATAAAAA
78695 AATTAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
AAAATATTATAAAAATTATA
Found at i:78841 original size:20 final size:18
Alignment explanation
Indices: 78818--78857 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
78808 TAGCATTAAT
*
78818 AATTATTAAAATGTTCTAAA
1 AATTA-TAAAAT-TCCTAAA
78838 AATTATAAAATTCCTAAA
1 AATTATAAAATTCCTAAA
78856 AA
1 AA
78858 ATAAAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTATAAAATTCCTAAA
Found at i:82453 original size:78 final size:78
Alignment explanation
Indices: 82324--82484 Score: 295
Period size: 78 Copynumber: 2.1 Consensus size: 78
82314 GCTCACAATA
*
82324 TCAACTTGCACGGGCCAAGCGGAGCTTGTAGGAGGGAGACCGCGAGCTCTGACAAACAACCCATA
1 TCAACTTGCACGGGCCAAGCGGAGCTTGTAGGAGGGAGACCGCGAGCTCTGACAAACAACCCAGA
*
82389 ATGGATCACGTGT
66 ATGGAACACGTGT
*
82402 TCAACTTGCATGGGCCAAGCGGAGCTTGTAGGAGGGAGACCGCGAGCTCTGACAAACAACCCAGA
1 TCAACTTGCACGGGCCAAGCGGAGCTTGTAGGAGGGAGACCGCGAGCTCTGACAAACAACCCAGA
82467 ATGGAACACGTGT
66 ATGGAACACGTGT
82480 TCAAC
1 TCAAC
82485 ATGCTCGAAC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.29, C:0.25, G:0.29, T:0.16
Consensus pattern (78 bp):
TCAACTTGCACGGGCCAAGCGGAGCTTGTAGGAGGGAGACCGCGAGCTCTGACAAACAACCCAGA
ATGGAACACGTGT
Found at i:88701 original size:5 final size:5
Alignment explanation
Indices: 88691--88716 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
88681 AAGAAATTCG
88691 TGTTT TGTTT TGTTT TGTTT TGTTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT T
88717 TGGAATGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TGTTT
Found at i:89653 original size:2 final size:2
Alignment explanation
Indices: 89646--89671 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89636 AAGTGAATAC
89646 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
89672 TAATTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92465 original size:3 final size:3
Alignment explanation
Indices: 92452--92491 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
92442 CCCAATTTTC
*
92452 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
92492 TTATTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:96478 original size:5 final size:5
Alignment explanation
Indices: 96468--96497 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
96458 GTATTTGATT
*
96468 GAGTC GAGTC GAGTC GAGTC GAATC GAGTC
1 GAGTC GAGTC GAGTC GAGTC GAGTC GAGTC
96498 AATAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (5 bp):
GAGTC
Found at i:111884 original size:3 final size:3
Alignment explanation
Indices: 111872--111904 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
111862 GAATAACAAG
111872 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
111905 ATCATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:120995 original size:63 final size:63
Alignment explanation
Indices: 120891--121009 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 63
120881 CACAAAATGT
* * * * ** * *
120891 ACCAGTTTATTTTACACCAGTACCACAGCATGTGCATTCATTCTCTAG-ACCAACACAGTCATC
1 ACCAATTTATTTTACACAAGCACCACAGCACGCACAATCATTCCCT-GCACCAACACAGTCATC
120954 ACCAATTTATTTTACACAAGCACCACAGCACGCACAATCATTCCCTGCACCAACAC
1 ACCAATTTATTTTACACAAGCACCACAGCACGCACAATCATTCCCTGCACCAACAC
121010 CTTCTCCAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
62 1 0.02
63 46 0.98
ACGTcount: A:0.33, C:0.34, G:0.09, T:0.24
Consensus pattern (63 bp):
ACCAATTTATTTTACACAAGCACCACAGCACGCACAATCATTCCCTGCACCAACACAGTCATC
Found at i:122998 original size:27 final size:28
Alignment explanation
Indices: 122968--123022 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
122958 ATTACAAAAT
122968 AATACAAA-AATTAAAAAAATGGTATGG
1 AATACAAATAATTAAAAAAATGGTATGG
**
122995 AATACAAATTAATTACCAAAATGGTATG
1 AATACAAA-TAATTAAAAAAATGGTATG
123023 TTTTGGGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
29 16 0.67
ACGTcount: A:0.55, C:0.07, G:0.13, T:0.25
Consensus pattern (28 bp):
AATACAAATAATTAAAAAAATGGTATGG
Found at i:124747 original size:86 final size:86
Alignment explanation
Indices: 124613--124770 Score: 271
Period size: 86 Copynumber: 1.8 Consensus size: 86
124603 CAAGTTGACC
* *
124613 CAATGTTAGACTTTTTGCCTATACTTGTTACCAAGTTCTATACCAAGTAAAAATTATCCTCAACA
1 CAATGTTAGACTTTATGCCTATACCTGTTACCAAGTTCTATACCAAGTAAAAATTATCCTCAACA
124678 AAGAAAAGGTACAACCCTTAT
66 AAGAAAAGGTACAACCCTTAT
* * *
124699 CAATGTTAGACTTTATGCCTATACCTGTTACCAAGTTCTATACTAAGTAAAAATTGTCCTCAGCA
1 CAATGTTAGACTTTATGCCTATACCTGTTACCAAGTTCTATACCAAGTAAAAATTATCCTCAACA
124764 AAGAAAA
66 AAGAAAA
124771 TGGTCAAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 67 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (86 bp):
CAATGTTAGACTTTATGCCTATACCTGTTACCAAGTTCTATACCAAGTAAAAATTATCCTCAACA
AAGAAAAGGTACAACCCTTAT
Found at i:126858 original size:19 final size:18
Alignment explanation
Indices: 126836--126875 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
126826 AATTAATTTG
126836 AATTTCATATTATTTTCAT
1 AATTTCATATTATTTT-AT
**
126855 AATTTTGTATTATTTTAT
1 AATTTCATATTATTTTAT
126873 AAT
1 AAT
126876 ATTTAGGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (18 bp):
AATTTCATATTATTTTAT
Found at i:127279 original size:21 final size:22
Alignment explanation
Indices: 127254--127301 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
127244 TTTATTAAGT
127254 TTAATTAATTCG-ATT-AATCGA
1 TTAATTAA-TCGAATTCAATCGA
*
127275 TTAATTAATCGAATTCGATCGA
1 TTAATTAATCGAATTCAATCGA
127297 TTAAT
1 TTAAT
127302 CAAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 11 0.46
22 10 0.42
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (22 bp):
TTAATTAATCGAATTCAATCGA
Found at i:128328 original size:25 final size:24
Alignment explanation
Indices: 128293--128350 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
128283 TAAGTTTGAA
128293 TATATTA-TAATTATTAATTC-GAT
1 TATATTATTAA-TATTAATTCTGAT
128316 TATATTATGTAATATTAATTCTGAT
1 TATATTAT-TAATATTAATTCTGAT
128341 TATAATTATT
1 TAT-ATTATT
128351 TTAATATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.23
24 9 0.29
25 10 0.32
26 5 0.16
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (24 bp):
TATATTATTAATATTAATTCTGAT
Found at i:128899 original size:21 final size:22
Alignment explanation
Indices: 128859--128900 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
128849 AATAAAACCT
*
128859 TAAAAATAAAAAAGGGTAAAAG
1 TAAAAATAAAAAAGGATAAAAG
*
128881 TAAAAA-AAAAAATGATAAAA
1 TAAAAATAAAAAAGGATAAAA
128901 TTGGTAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (22 bp):
TAAAAATAAAAAAGGATAAAAG
Found at i:132088 original size:20 final size:21
Alignment explanation
Indices: 132043--132099 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
132033 CACACGAGTT
*
132043 TTAAA-TT-AATAATTTTATA
1 TTAAATTTAAATATTTTTATA
*
132062 TTGAATTTCAAA-ATTTTTAT-
1 TTAAATTT-AAATATTTTTATA
132082 TTAAATTTAAATATTTTT
1 TTAAATTTAAATATTTTT
132100 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 7 0.23
20 15 0.48
21 7 0.23
22 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTAAATTTAAATATTTTTATA
Found at i:132361 original size:2 final size:2
Alignment explanation
Indices: 132354--132389 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
132344 AAAATTTTAT
132354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
132390 AAATAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:132411 original size:17 final size:16
Alignment explanation
Indices: 132389--132423 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
132379 ATATATATAT
132389 AAAATAATAATTAAATA
1 AAAATAATAATT-AATA
132406 AAAATAATAATTAATA
1 AAAATAATAATTAATA
132422 AA
1 AA
132424 TTTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAATAATTAATA
Found at i:133224 original size:19 final size:19
Alignment explanation
Indices: 133202--133251 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
133192 AAAATGAAAA
133202 TAAAAATATTTTAAAAATT
1 TAAAAATATTTTAAAAATT
**
133221 T-AAAATGATTAAAAAAATT
1 TAAAAAT-ATTTTAAAAATT
*
133240 AAAAAATATTTT
1 TAAAAATATTTT
133252 TTTGATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
18 5 0.21
19 14 0.58
20 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAAAATATTTTAAAAATT
Found at i:133416 original size:18 final size:18
Alignment explanation
Indices: 133393--133432 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
133383 TATAAATCCT
133393 AAAATTAAA-AAAAACTTA
1 AAAATTAAAGAAAAA-TTA
133411 AAAATTAAATGAAAAATTA
1 AAAATTAAA-GAAAAATTA
133430 AAA
1 AAA
133433 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 6 0.30
20 5 0.25
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATTAAAGAAAAATTA
Found at i:136714 original size:15 final size:16
Alignment explanation
Indices: 136675--136715 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
136665 ATACAACATA
136675 TATTTCTTTTTTCTTCT
1 TATTTC-TTTTTCTTCT
136692 T-TTCTCTTTTTC-TCT
1 TATT-TCTTTTTCTTCT
136707 TATTTCTTT
1 TATTTCTTT
136716 CTTTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 9 0.41
16 10 0.45
17 3 0.14
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTCTTTTTCTTCT
Found at i:162199 original size:12 final size:12
Alignment explanation
Indices: 162182--162207 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
162172 CCTAACCTGT
162182 TGTGACTATCGA
1 TGTGACTATCGA
162194 TGTGACTATCGA
1 TGTGACTATCGA
162206 TG
1 TG
162208 AGGCCACCAC
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:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (12 bp):
TGTGACTATCGA
Found at i:163044 original size:14 final size:14
Alignment explanation
Indices: 163016--163054 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
163006 CTTGAGTGAC
*
163016 AAAAATGAAAAAAA
1 AAAAAAGAAAAAAA
* *
163030 AAAGAAGAAAGAAA
1 AAAAAAGAAAAAAA
163044 AAAAAAGAAAA
1 AAAAAAGAAAA
163055 TAAGTTGCTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAGAAAAAAA
Found at i:174946 original size:12 final size:12
Alignment explanation
Indices: 174931--174956 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
174921 ATACACTTAA
174931 AAATATTAAAAT
1 AAATATTAAAAT
174943 AAATATTAAAAT
1 AAATATTAAAAT
174955 AA
1 AA
174957 CAAACAAATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATTAAAAT
Found at i:174985 original size:41 final size:43
Alignment explanation
Indices: 174932--175019 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 43
174922 TACACTTAAA
*
174932 AATATTAAAATAAATATTAAAATAACAAACAAATT-AAAA-AC
1 AATATTAAAATAAATAGTAAAATAACAAACAAATTGAAAATAC
* *
174973 AATATTAAAATAATTCGTAAAATAACAAACAAATTGAAAATAC
1 AATATTAAAATAAATAGTAAAATAACAAACAAATTGAAAATAC
175016 AATA
1 AATA
175020 AGCATCCTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
41 32 0.76
42 4 0.10
43 6 0.14
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (43 bp):
AATATTAAAATAAATAGTAAAATAACAAACAAATTGAAAATAC
Found at i:175706 original size:24 final size:23
Alignment explanation
Indices: 175667--175712 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
175657 TATTACAAGC
175667 AAAAAAAATTAGTATTAAAAATA
1 AAAAAAAATTAGTATTAAAAATA
* *
175690 AAAATAAAATTATTATTATAAAT
1 AAAA-AAAATTAGTATTAAAAAT
175713 CTGGGTCGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAAAATTAGTATTAAAAATA
Found at i:178129 original size:24 final size:24
Alignment explanation
Indices: 178101--178163 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
178091 AGAAATAATT
178101 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
178125 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
178149 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
178164 TATTACTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:180106 original size:24 final size:24
Alignment explanation
Indices: 180077--180127 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
180067 AGAAATAATC
* *
180077 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTAGTTG
180101 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAATTAAACTCTATTTAGTTG
180125 TTT
1 TTT
180128 AAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAGTTG
Found at i:180136 original size:24 final size:24
Alignment explanation
Indices: 180077--180139 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
180067 AGAAATAATC
* * *
180077 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTATTTAGTTG
*
180101 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAATCAAACTCTATTTAGTTG
180125 TTT-AAGTCAAACTCT
1 TTTCAA-TCAAACTCT
180140 TATTACTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (24 bp):
TTTCAATCAAACTCTATTTAGTTG
Found at i:184563 original size:9 final size:9
Alignment explanation
Indices: 184535--184576 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
184525 CAACTACGGG
184535 AGAAGAAGAA
1 AGAA-AAGAA
* *
184545 GGAAATGAA
1 AGAAAAGAA
184554 AGAAAAGAA
1 AGAAAAGAA
184563 AG-AAAGAA
1 AGAAAAGAA
184571 AGAAAA
1 AGAAAA
184577 AGGAGAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 8 0.30
9 16 0.59
10 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (9 bp):
AGAAAAGAA
Found at i:184901 original size:24 final size:25
Alignment explanation
Indices: 184848--184902 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
184838 TTATTATAAG
*
184848 TTATTTGTTTTGTTTAATTTAATTT
1 TTATTTGATTTGTTTAATTTAATTT
* *
184873 TTATTTGATTTG-TTATTTTTATTT
1 TTATTTGATTTGTTTAATTTAATTT
184897 TTATTT
1 TTATTT
184903 AGTAGAGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (25 bp):
TTATTTGATTTGTTTAATTTAATTT
Found at i:184977 original size:21 final size:20
Alignment explanation
Indices: 184951--184994 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
184941 TCGTTATTTT
184951 TAATTTTATTTTATTAGTAAG
1 TAATTTTATTTTATTAGT-AG
*
184972 TAATTTTATTTTGTTAGTAG
1 TAATTTTATTTTATTAGTAG
184992 TAA
1 TAA
184995 GTAAGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (20 bp):
TAATTTTATTTTATTAGTAG
Found at i:186987 original size:43 final size:43
Alignment explanation
Indices: 186926--187025 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
186916 TGCCATTACT
* *
186926 TGACATGTTATTAAATTATATTAC-TGAACCCGTGTTAATATCG
1 TGACATGTTATTAAATTATATTACTTG-ACCCGTGCTAATACCG
* * *
186969 TGACATGTTATTAAATTATATTACTTGACTCTTGCTAATCCCG
1 TGACATGTTATTAAATTATATTACTTGACCCGTGCTAATACCG
187012 TGACATGTTATTAA
1 TGACATGTTATTAA
187026 TTGTGCAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 49 0.96
44 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (43 bp):
TGACATGTTATTAAATTATATTACTTGACCCGTGCTAATACCG
Found at i:188417 original size:21 final size:21
Alignment explanation
Indices: 188392--188447 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
188382 AAGTATTCGA
188392 ACTACCGATACAACT-ATAACT
1 ACTACCGATACAACTCA-AACT
* * * *
188413 TCTACGGAAACAACTCACACT
1 ACTACCGATACAACTCAAACT
188434 ACTACCGATACAAC
1 ACTACCGATACAAC
188448 AAACTCAAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.41, C:0.32, G:0.07, T:0.20
Consensus pattern (21 bp):
ACTACCGATACAACTCAAACT
Found at i:188459 original size:112 final size:112
Alignment explanation
Indices: 188281--188508 Score: 341
Period size: 112 Copynumber: 2.0 Consensus size: 112
188271 TGTGGAGGTT
* * *
188281 CTACCGATACAACTATGACTTATATCAAAATAACTCACACAACTACCGATACAACAAACTCTAGA
1 CTACCGATACAACTATAACTTATATCAAAACAACTCACACAACTACCGATACAACAAACTCAAGA
* *
188346 GAGCTAAGAAGCTTACCCTGAAACTTCTACCAATACAAGTATTCGAA
66 GAGCTAAGAAGCTTACCCCGAAACTTCTACCAATACAAGTATTAGAA
* * *
188393 CTACCGATACAACTATAACTTCTA-CGGAAACAACTCACACTACTACCGATACAACAAACTCAAG
1 CTACCGATACAACTATAACTTATATC-AAAACAACTCACACAACTACCGATACAACAAACTCAAG
* * *
188457 AGAGCTAGGAAGCTTACCCCGCAACTTCTACCGATACAAGTATTAGAA
65 AGAGCTAAGAAGCTTACCCCGAAACTTCTACCAATACAAGTATTAGAA
188505 CTAC
1 CTAC
188509 AACTATGATC
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
111 1 0.01
112 103 0.99
ACGTcount: A:0.40, C:0.28, G:0.11, T:0.21
Consensus pattern (112 bp):
CTACCGATACAACTATAACTTATATCAAAACAACTCACACAACTACCGATACAACAAACTCAAGA
GAGCTAAGAAGCTTACCCCGAAACTTCTACCAATACAAGTATTAGAA
Found at i:191043 original size:24 final size:24
Alignment explanation
Indices: 190971--191044 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
190961 CACTATACAC
*
190971 GGAGTTGGATCTTTATTTTCTACT
1 GGAGTTGGATCTTCATTTTCTACT
* *
190995 AGAGTTGGATCTTCATTTTTTACT
1 GGAGTTGGATCTTCATTTTCTACT
* *
191019 GGAGTTGGATATTCATTTCCTACT
1 GGAGTTGGATCTTCATTTTCTACT
191043 GG
1 GG
191045 TTCCACATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.46
Consensus pattern (24 bp):
GGAGTTGGATCTTCATTTTCTACT
Found at i:192181 original size:29 final size:31
Alignment explanation
Indices: 192128--192192 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
192118 GATATGGGGA
*
192128 AATTGAATCAAAATTAAAGTTTTATATATAT
1 AATTGAATAAAAATTAAAGTTTTATATATAT
*
192159 AATTGAA-AAAAATTAAAG-TTTATGTATAT
1 AATTGAATAAAAATTAAAGTTTTATATATAT
*
192188 GATTG
1 AATTG
192193 CACATTGGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.45
30 10 0.32
31 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (31 bp):
AATTGAATAAAAATTAAAGTTTTATATATAT
Found at i:194865 original size:23 final size:24
Alignment explanation
Indices: 194837--194884 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
194827 TTTGATAATT
194837 TTAGGTACCAAATTA-AAAAAAAA
1 TTAGGTACCAAATTACAAAAAAAA
* *
194860 TTAGGTATCTAATTAGCAAAAAAAA
1 TTAGGTACCAAATTA-CAAAAAAAA
194885 GAGAGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.25
Consensus pattern (24 bp):
TTAGGTACCAAATTACAAAAAAAA
Found at i:195621 original size:2 final size:2
Alignment explanation
Indices: 195614--195638 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
195604 ATAGTAACTG
195614 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
195639 GTATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:201021 original size:15 final size:15
Alignment explanation
Indices: 201001--201031 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
200991 ATGAGTCTAC
201001 TAGTACTAAACATTA
1 TAGTACTAAACATTA
*
201016 TAGTACTTAACATTA
1 TAGTACTAAACATTA
201031 T
1 T
201032 CTTAGTTTAC
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:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (15 bp):
TAGTACTAAACATTA
Found at i:204631 original size:16 final size:16
Alignment explanation
Indices: 204601--204640 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
204591 ATGTATGTGA
204601 AATGATTATATTATTG
1 AATGATTATATTATTG
*
204617 CATGA-TATATATATTG
1 AATGATTATAT-TATTG
204633 AATGATTA
1 AATGATTA
204641 GGATACGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 5 0.25
16 13 0.65
17 2 0.10
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (16 bp):
AATGATTATATTATTG
Found at i:205038 original size:16 final size:17
Alignment explanation
Indices: 204995--205040 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
204985 GAGCATAATT
204995 TAATA-GTATATG-TTA
1 TAATATGTATATGATTA
*
205010 TAATATG-AAATGATTA
1 TAATATGTATATGATTA
205026 T-ATATGTATATGATT
1 TAATATGTATATGATT
205041 TCGATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (17 bp):
TAATATGTATATGATTA
Found at i:216846 original size:23 final size:23
Alignment explanation
Indices: 216802--216846 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
216792 AGTCTTCGTT
* *
216802 TTGTCTTTTTTCAATACATTCCA
1 TTGTCTTTTTGCAACACATTCCA
216825 TTGTCTTGTTTGCAACAC-TTCC
1 TTGTCTT-TTTGCAACACATTCC
216847 TTTCTCCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.49
Consensus pattern (23 bp):
TTGTCTTTTTGCAACACATTCCA
Found at i:218029 original size:135 final size:135
Alignment explanation
Indices: 217787--218058 Score: 535
Period size: 135 Copynumber: 2.0 Consensus size: 135
217777 CAAGTAACAC
217787 TTCCTCGATGTATCAACTATTGAAGGGTAAGAGGAGTTCTATTAGACAACCTATGCTTTTTTTTT
1 TTCCTCGATGTATCAACTATTGAAGGGTAAGAGGAGTTCTATTAGACAACCTATGCTTTTTTTTT
217852 CCTTTTTTTCTTTTCACATATGGAGAGTTTCAGATACAATCCTCATCCCGCCTAAAATTCTAAGA
66 CCTTTTTTTCTTTTCACATATGGAGAGTTTCAGATACAATCCTCATCCCGCCTAAAATTCTAAGA
217917 ATTTG
131 ATTTG
*
217922 TTCCTCGATGTATCAACTATTGAAGGGTAAGAGGAGTTCTATTAGACAACCTATGTTTTTTTTTT
1 TTCCTCGATGTATCAACTATTGAAGGGTAAGAGGAGTTCTATTAGACAACCTATGCTTTTTTTTT
217987 CCTTTTTTTCTTTTCACATATGGAGAGTTTCAGATACAATCCTCATCCCGCCTAAAATTCTAAGA
66 CCTTTTTTTCTTTTCACATATGGAGAGTTTCAGATACAATCCTCATCCCGCCTAAAATTCTAAGA
218052 ATTTG
131 ATTTG
218057 TT
1 TT
218059 ATAGTTAGAA
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (135 bp):
TTCCTCGATGTATCAACTATTGAAGGGTAAGAGGAGTTCTATTAGACAACCTATGCTTTTTTTTT
CCTTTTTTTCTTTTCACATATGGAGAGTTTCAGATACAATCCTCATCCCGCCTAAAATTCTAAGA
ATTTG
Found at i:219192 original size:29 final size:30
Alignment explanation
Indices: 219134--219192 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
219124 ATCTCATAAT
* *
219134 TATATATGAACTTTGATTTAATGTGTAATTG
1 TATATATGAACTTTAATTTAA-GTGCAATTG
*
219165 TATATATGAACTTTAATTTGA-TGCAATT
1 TATATATGAACTTTAATTTAAGTGCAATT
219193 ATTCACGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
31 19 0.76
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (30 bp):
TATATATGAACTTTAATTTAAGTGCAATTG
Found at i:222807 original size:18 final size:18
Alignment explanation
Indices: 222784--222820 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
222774 CATTTCCAGA
222784 AAACAATGAATTAATAGC
1 AAACAATGAATTAATAGC
222802 AAACAATGAATTAATAGC
1 AAACAATGAATTAATAGC
222820 A
1 A
222821 TATTAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.22
Consensus pattern (18 bp):
AAACAATGAATTAATAGC
Found at i:225294 original size:28 final size:29
Alignment explanation
Indices: 225263--225319 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
225253 TTAACATTTT
*
225263 CCCTCCAAAA-TTTTATTTT-TCTCAAAAA
1 CCCT-CAAAACTTTTATTTTCCCTCAAAAA
225291 CCCTCAAAACTTTTTATTTTCCCTCAAAA
1 CCCTCAAAAC-TTTTATTTTCCCTCAAAA
225320 CTTTTACTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
28 4 0.16
29 9 0.36
30 7 0.28
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (29 bp):
CCCTCAAAACTTTTATTTTCCCTCAAAAA
Found at i:229478 original size:34 final size:34
Alignment explanation
Indices: 229430--229506 Score: 127
Period size: 34 Copynumber: 2.2 Consensus size: 34
229420 TATTTTTCTG
*
229430 TTATGTTATGCTTGAAAGTTTTGTTGAGGGATTAC
1 TTATGTT-TGCTTGAAAGTTTTGTTAAGGGATTAC
229465 TTATGTTTGCTTGAAAGTTTTGTTAAGGGATTAC
1 TTATGTTTGCTTGAAAGTTTTGTTAAGGGATTAC
*
229499 TCATGTTT
1 TTATGTTT
229507 ATATTAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 33 0.82
35 7 0.17
ACGTcount: A:0.22, C:0.06, G:0.23, T:0.48
Consensus pattern (34 bp):
TTATGTTTGCTTGAAAGTTTTGTTAAGGGATTAC
Found at i:234948 original size:27 final size:26
Alignment explanation
Indices: 234898--234961 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
234888 AAATCTTCTC
234898 TAAATTAATAAATATTAATTTATCAA
1 TAAATTAATAAATATTAATTTATCAA
* *
234924 TAAATTAATAAATTATTCATTTATCGA
1 TAAATTAATAAA-TATTAATTTATCAA
*
234951 TAAACTAATAA
1 TAAATTAATAA
234962 CCTTGATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (26 bp):
TAAATTAATAAATATTAATTTATCAA
Found at i:237852 original size:62 final size:63
Alignment explanation
Indices: 237781--237902 Score: 237
Period size: 62 Copynumber: 2.0 Consensus size: 63
237771 GAGGTGCATT
237781 ATTATGCACTAATGAACGGAGAGCACCAAGGTGTTGTACGGA-AGAACAAACGTGCTAAATAA
1 ATTATGCACTAATGAACGGAGAGCACCAAGGTGTTGTACGGAGAGAACAAACGTGCTAAATAA
237843 ATTATGCACTAATGAACGGAGAGCACCAAGGTGTTGTACGGAGAGAACAAACGTGCTAAA
1 ATTATGCACTAATGAACGGAGAGCACCAAGGTGTTGTACGGAGAGAACAAACGTGCTAAA
237903 CGGAGAGCAC
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 42 0.71
63 17 0.29
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.19
Consensus pattern (63 bp):
ATTATGCACTAATGAACGGAGAGCACCAAGGTGTTGTACGGAGAGAACAAACGTGCTAAATAA
Found at i:237905 original size:22 final size:23
Alignment explanation
Indices: 237880--237925 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
237870 AAGGTGTTGT
237880 ACGGAGAGAAC-AAACGTGCTAA
1 ACGGAGAGAACTAAACGTGCTAA
*
237902 ACGGAGAGCACTAAACGTGCTAA
1 ACGGAGAGAACTAAACGTGCTAA
237925 A
1 A
237926 TAATGGAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (23 bp):
ACGGAGAGAACTAAACGTGCTAA
Done.