Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003822.1 Kokia drynarioides strain JFW-HI SEQ_116824, 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: 163945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:16109 original size:18 final size:18
Alignment explanation
Indices: 16078--16119 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
16068 TCAGTCATTT
*
16078 GAAAAA-GAAAAAAATGA
1 GAAAAAGGAAAAAAAAGA
*
16095 GAAAAAGGAAGAAAAAGA
1 GAAAAAGGAAAAAAAAGA
*
16113 AAAAAAG
1 GAAAAAG
16120 AAATTTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
GAAAAAGGAAAAAAAAGA
Found at i:28601 original size:18 final size:18
Alignment explanation
Indices: 28574--28620 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28564 AGAAGATTGA
* *
28574 ACTTTAATTTTTTTTAAG
1 ACTTTAATTTATTTCAAG
*
28592 ACTTTGATTTATTTCAAG
1 ACTTTAATTTATTTCAAG
28610 ACTTGTAATTT
1 ACTT-TAATTT
28621 TTGGAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.55
Consensus pattern (18 bp):
ACTTTAATTTATTTCAAG
Found at i:35196 original size:37 final size:38
Alignment explanation
Indices: 35114--35203 Score: 130
Period size: 37 Copynumber: 2.4 Consensus size: 38
35104 AAACACCACT
35114 CCATCCACCCTACACACCACAATTGGGCTCAGGTAAGC
1 CCATCCACCCTACACACCACAATTGGGCTCAGGTAAGC
* *
35152 CCATCCACCCTGCACACCACAA-TGGGCT-ATGGTAGGC
1 CCATCCACCCTACACACCACAATTGGGCTCA-GGTAAGC
*
35189 CCGTCCACCCTACAC
1 CCATCCACCCTACAC
35204 TCAAATAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
36 1 0.02
37 25 0.53
38 21 0.45
ACGTcount: A:0.26, C:0.42, G:0.17, T:0.16
Consensus pattern (38 bp):
CCATCCACCCTACACACCACAATTGGGCTCAGGTAAGC
Found at i:40858 original size:26 final size:25
Alignment explanation
Indices: 40810--40858 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
40800 TTATCTTAAC
* *
40810 TAGAGTGACTAAATTGAAAAAAATT
1 TAGAGTGACAAAATAGAAAAAAATT
*
40835 TAGAGTGATCAAAATAGAACAAAA
1 TAGAGTGA-CAAAATAGAAAAAAA
40859 GTTATTTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.22
Consensus pattern (25 bp):
TAGAGTGACAAAATAGAAAAAAATT
Found at i:41763 original size:32 final size:32
Alignment explanation
Indices: 41725--41820 Score: 192
Period size: 32 Copynumber: 3.0 Consensus size: 32
41715 GCTCTCTAGG
41725 AATGTGTCTTAGCATCTTTTGCTTTCCTTTTC
1 AATGTGTCTTAGCATCTTTTGCTTTCCTTTTC
41757 AATGTGTCTTAGCATCTTTTGCTTTCCTTTTC
1 AATGTGTCTTAGCATCTTTTGCTTTCCTTTTC
41789 AATGTGTCTTAGCATCTTTTGCTTTCCTTTTC
1 AATGTGTCTTAGCATCTTTTGCTTTCCTTTTC
41821 TTTTTGTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.53
Consensus pattern (32 bp):
AATGTGTCTTAGCATCTTTTGCTTTCCTTTTC
Found at i:47731 original size:20 final size:19
Alignment explanation
Indices: 47667--47732 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
47657 GGCCTGGAGT
*
47667 TATTTTGACTTATTTGAAAAA
1 TATTTTGACTTGTTT--AAAA
** *
47688 TATTTTGAAGTG-TTCAAA
1 TATTTTGACTTGTTTAAAA
47706 TGATTTTGACTTGTTTAAAA
1 T-ATTTTGACTTGTTTAAAA
47726 TCATTTT
1 T-ATTTT
47733 AGCTTGATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
18 4 0.11
19 9 0.26
20 13 0.37
21 9 0.26
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (19 bp):
TATTTTGACTTGTTTAAAA
Found at i:50228 original size:2 final size:2
Alignment explanation
Indices: 50221--50245 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50211 GGTGGCTAAT
50221 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
50246 GAGAGCAACA
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:56160 original size:19 final size:19
Alignment explanation
Indices: 56136--56173 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
56126 ATCTAAATCA
56136 ATAACTTTAAGATTTTCTT
1 ATAACTTTAAGATTTTCTT
*
56155 ATAACTTTAGGATTTTCTT
1 ATAACTTTAAGATTTTCTT
56174 TCACGTATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (19 bp):
ATAACTTTAAGATTTTCTT
Found at i:65880 original size:20 final size:20
Alignment explanation
Indices: 65818--65897 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
65808 GCCTGGAGCT
*
65818 ATTTTGACTTGTTTGAAAAAC
1 ATTTTGACTTGTTT-AAAATC
** *
65839 ATTTTGAAGTG-TT-AAATG
1 ATTTTGACTTGTTTAAAATC
65857 ATTTTGACTTGTTTAAAATC
1 ATTTTGACTTGTTTAAAATC
*
65877 ATTTTAACTTGATTTTAAAAT
1 ATTTTGACTTG--TTTAAAAT
65898 AGTTTCAAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
18 12 0.26
19 2 0.04
20 16 0.34
21 9 0.19
22 8 0.17
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTTTGACTTGTTTAAAATC
Found at i:69509 original size:122 final size:122
Alignment explanation
Indices: 69352--69721 Score: 535
Period size: 122 Copynumber: 3.0 Consensus size: 122
69342 AATGATTTTG
*
69352 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATTATGTTTTAATAAACCTTCC
1 TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
* *
69417 ATATATTTCTTTAAAGGAATATTTCCATTTTCATATGAGATATTATATAAAAGGAAA
66 ATATATTTCTCTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
* * * *
69474 TTAAATATTAAAAGCATGGAAGTTAATAT-CGTTTGGGAAGGATATAATGATTTAATAAACTTTC
1 TTAAATATTAAAA-CATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTC
* * *
69538 CATATATTTCTCTAAAGGAATATTTCTATTTTAATATGAGATATTATATGAAAGAAAA
65 CATATATTTCTCTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
* * * * *
69596 TTGAATATTAGAAAATATGAAAGTTAATATCCTTTTCGAAATGATATAATGTTTTAATAAACCTT
1 TTAAATATT--AAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTT
* * *
69661 CCATATATTTCTCTAATGGAATATTTCCATTTTAATAAGAGATATTAAATAAAAAGGAAA
64 CCATATATTTCTCTAAAGGAATATTTCCATTTTAATATGAGATATTATAT-AAAAGGAAA
69721 T
1 T
69722 ATAGCAGAAT
Statistics
Matches: 218, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
122 104 0.48
123 28 0.13
124 78 0.36
125 8 0.04
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (122 bp):
TTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
ATATATTTCTCTAAAGGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAA
Found at i:78323 original size:21 final size:21
Alignment explanation
Indices: 78297--78352 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
78287 CTAGAAGTCA
*
78297 TTGTATCGATAGAAGG-ATAGG
1 TTGTATCGATAGAAGGCAGA-G
*
78318 TTGTATC-AGTAGATGGCAGAG
1 TTGTATCGA-TAGAAGGCAGAG
78339 TTGTATCGATAGAA
1 TTGTATCGATAGAA
78353 CTTTCACAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.03
21 25 0.86
22 3 0.10
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGTATCGATAGAAGGCAGAG
Found at i:79624 original size:25 final size:25
Alignment explanation
Indices: 79596--79647 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
79586 GCCAAGCATG
79596 ATTAAATTAAATAATAAATTATAAA
1 ATTAAATTAAATAATAAATTATAAA
* * **
79621 ATTATATTTAATAATTTATTATAAA
1 ATTAAATTAAATAATAAATTATAAA
79646 AT
1 AT
79648 ATTTCATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTAAATTAAATAATAAATTATAAA
Found at i:86861 original size:18 final size:18
Alignment explanation
Indices: 86838--86881 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
86828 TCTTTAGGAT
86838 CTTCTTCAAGATCTTCTA
1 CTTCTTCAAGATCTTCTA
*** *
86856 CTTCTTTGGGATCTTCTT
1 CTTCTTCAAGATCTTCTA
86874 CTTCTTCA
1 CTTCTTCA
86882 GCTTGCTATT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.14, C:0.27, G:0.09, T:0.50
Consensus pattern (18 bp):
CTTCTTCAAGATCTTCTA
Found at i:92607 original size:46 final size:45
Alignment explanation
Indices: 92537--92640 Score: 145
Period size: 46 Copynumber: 2.3 Consensus size: 45
92527 AGATGGTAGT
* *
92537 TTCAATATGCCCCTCTTGATTTAGGCGTAAAAGATTGAATAGAGGC
1 TTCAATCTGCCCCTCTTGACTTAGGCGTAAAAGATTGAAT-GAGGC
* * *
92583 TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGTGGC
1 TTCAATCTGCCCCTCTTGACTTAGGCGTAAAAGATTGAATGAGGC
*
92628 TTCAATCTTCCCC
1 TTCAATCTGCCCC
92641 ATTACTGGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 16 0.31
46 36 0.69
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (45 bp):
TTCAATCTGCCCCTCTTGACTTAGGCGTAAAAGATTGAATGAGGC
Found at i:92894 original size:78 final size:78
Alignment explanation
Indices: 92606--93093 Score: 469
Period size: 78 Copynumber: 6.2 Consensus size: 78
92596 TCTTGACTTA
* * * * * * *
92606 GGGGTAAAAGATTGGATGTGGCTTCAATCTTCCC-CATTACTGGGGTAAGAGATTGGATGACTTC
1 GGGGTAAGAGATTGG-TGTGTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTGGATG-CTTC
*
92670 AA-CATGCCTCATGATC
63 AATC-TGCCCCATGATC
* * *** * * *
92686 GGGGCAAAAGATCAATGTGTCTTCACTCTGCCCTCTGATTAGGGTAAAATATTGGATGCTTCGAT
1 GGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAAT
* * * *
92751 CTGTCCTATGGTT
66 CTGCCCCATGATC
* * * *
92764 GGGGTAAGATATTGGATGATGTCTTCAATCTGCCCTCTGATTAGTGTAAAAGATCGGATGCTTCG
1 GGGGTAAGAGATTGG-TG-TGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCA
* * *
92829 ATTTGGCCTATGATC
64 ATCTGCCCCATGATC
*
92844 GGGGTAACG-GATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATGCTTCAA
1 GGGGTAA-GAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAA
* *
92908 TCTACCCCATGGTC
65 TCTGCCCCATGATC
* * * * * *
92922 GGGGTAAGTGATTGAATGATGTCTTCAATCTGCCATCTAATTAGGGTAAAAGATCGGCTGCTTCA
1 GGGGTAAGAGATTG-GTG-TGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCA
92987 ATCTGCCCCATGATC
64 ATCTGCCCCATGATC
* * * * * *
93002 AGGGTAAGAGATTAGTGTGTTTTCAATTTGCCCTCTGATTAGAGTAAAAGATTAGATGCTTCAAT
1 GGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAAT
*
93067 CTACCCCATGATC
66 CTGCCCCATGATC
* *
93080 AGGGTATGAGATTG
1 GGGGTAAGAGATTG
93094 AATGGTAGCT
Statistics
Matches: 337, Mismatches: 63, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
77 1 0.00
78 149 0.44
79 42 0.12
80 144 0.43
81 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (78 bp):
GGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAAT
CTGCCCCATGATC
Found at i:92898 original size:158 final size:158
Alignment explanation
Indices: 92648--93097 Score: 528
Period size: 158 Copynumber: 2.8 Consensus size: 158
92638 CCCATTACTG
* * * * * * * * *
92648 GGGTAAGAGATTGGATGACTTCAA-CATGCCTCATGATCGGGGCAAAAGATCAATGTGTCTTCAC
1 GGGTAAAAGATCGGATG-CTTCAATC-TGCCCCATGATCAGGGTAAGAGATTAGTGTGTCTTCAA
* * ** * *
92712 TCTGCCCTCTGATTAGGGTAAAATATTGGATGCTTCGATCTGTCCTATGGTTGGGGTAAGAT-AT
64 TCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTACCCCATGGTCGGGGTAAG-TGAT
* * *
92776 TGGATGATGTCTTCAATCTGCCCTCTGATTA
128 TGAATGATGTCTTCAATCTGCCATCTAATTA
* * * * * * *
92807 GTGTAAAAGATCGGATGCTTCGATTTGGCCTATGATCGGGGTAACG-GATTGGTGTGTCTTCAAT
1 GGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCAGGGTAA-GAGATTAGTGTGTCTTCAAT
*
92871 CTGCCCTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTACCCCATGGTCGGGGTAAGTGATTG
65 CTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTACCCCATGGTCGGGGTAAGTGATTG
92936 AATGATGTCTTCAATCTGCCATCTAATTA
130 AATGATGTCTTCAATCTGCCATCTAATTA
* * *
92965 GGGTAAAAGATCGGCTGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTAGTGTGTTTTCAATT
1 GGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTAGTGTGTCTTCAATC
* * * * * *
93030 TGCCCTCTGATTAGAGTAAAAGATTAGATGCTTCAATCTACCCCATGATCAGGGTATGAGATTGA
66 TGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTACCCCATGGTCGGGGTAAGTGATTGA
93095 ATG
131 ATG
93098 GTAGCTTTGA
Statistics
Matches: 246, Mismatches: 41, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
157 2 0.01
158 230 0.93
159 14 0.06
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (158 bp):
GGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGATTAGTGTGTCTTCAATC
TGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTACCCCATGGTCGGGGTAAGTGATTGA
ATGATGTCTTCAATCTGCCATCTAATTA
Found at i:93006 original size:38 final size:37
Alignment explanation
Indices: 92706--93085 Score: 177
Period size: 38 Copynumber: 9.7 Consensus size: 37
92696 ATCAATGTGT
* * *
92706 CTTCACTCTGCCCTCTGATTAGGGTAAAATATTGGATG
1 CTTCAATCTGCCC-CTGATCAGGGTAAAAGATTGGATG
* ** * ** * *
92744 CTTCGATCTGTCCTATGGTTGGGGTAAGATATTGGATGATG
1 CTTCAATCTG-CCCCTGATCAGGGTAAAAGATT-G--GATG
* * *
92785 TCTTCAATCTGCCCTCTGATTAGTGTAAAAGATCGGATG
1 -CTTCAATCTGCCC-CTGATCAGGGTAAAAGATTGGATG
* * ** * ** *
92824 CTTCGATTTGGCCTATGATCGGGGTAACGGATTGGTGTG
1 CTTCAATCT-GCCCCTGATCAGGGTAAAAGATTGG-ATG
* *
92863 TCTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGATG
1 -CTTCAATCTGCCC-CTGATCAGGGTAAAAGATTGGATG
* * * **
92902 CTTCAATCTACCCCATGGTCGGGGTAAGTGATTGAATGATG
1 CTTCAATCTGCCCC-TGATCAGGGTAAAAGATTG---GATG
* * * * *
92943 TCTTCAATCTGCCATCTAATTAGGGTAAAAGATCGGCTG
1 -CTTCAATCTGCC-CCTGATCAGGGTAAAAGATTGGATG
*
92982 CTTCAATCTGCCCCATGATCAGGGTAAGAGATTAGTG-TG
1 CTTCAATCTGCCCC-TGATCAGGGTAAAAGATT-G-GATG
* * * * *
93021 TTTTCAATTTGCCCTCTGATTAGAGTAAAAGATTAGATG
1 -CTTCAATCTGCCC-CTGATCAGGGTAAAAGATTGGATG
*
93060 CTTCAATCTACCCCATGATCAGGGTA
1 CTTCAATCTGCCCC-TGATCAGGGTA
93086 TGAGATTGAA
Statistics
Matches: 249, Mismatches: 70, Indels: 46
0.68 0.19 0.13
Matches are distributed among these distances:
37 3 0.01
38 115 0.46
39 25 0.10
40 49 0.20
41 12 0.05
42 44 0.18
43 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (37 bp):
CTTCAATCTGCCCCTGATCAGGGTAAAAGATTGGATG
Found at i:93034 original size:40 final size:38
Alignment explanation
Indices: 92626--93092 Score: 151
Period size: 38 Copynumber: 11.9 Consensus size: 38
92616 ATTGGATGTG
* * * *
92626 GCTTCAATCTTCCCCATTA-CTGGGGTAAGAGATTGGAT
1 GCTTCAATCTGCCCCATGATC-AGGGTAAGAGATTAGAT
* * * * *
92664 GACTTCAA-CATGCCTCATGATCGGGGCAAAAGATCA-ATGT
1 G-CTTCAATC-TGCCCCATGATCAGGGTAAGAGATTAGA--T
* * * * *
92704 GTCTTCACTCTGCCCTC-TGATTAGGGTAAAATATTGGAT
1 G-CTTCAATCTGCCC-CATGATCAGGGTAAGAGATTAGAT
* * * * ** *
92743 GCTTCGATCTGTCCTATGGTTGGGGTAAGATATTGGATGAT
1 GCTTCAATCTGCCCCATGATCAGGGTAAGAGATT--A-GAT
* * * **
92784 GTCTTCAATCTGCCCTC-TGATTAGTGTAAAAGATCGGAT
1 G-CTTCAATCTGCCC-CATGATCAGGGTAAGAGATTAGAT
* * * * * * *
92823 GCTTCGATTTGGCCTATGATCGGGGTAACG-GATTGGTGT
1 GCTTCAATCTGCCCCATGATCAGGGTAA-GAGATTAG-AT
* * * *
92862 GTCTTCAATCTGCCCTC-TAATTAGGGTAAAAGATTGGAT
1 G-CTTCAATCTGCCC-CATGATCAGGGTAAGAGATTAGAT
* * * *
92901 GCTTCAATCTACCCCATGGTCGGGGTAAGTGATTGAATGAT
1 GCTTCAATCTGCCCCATGATCAGGGTAAGAGATT--A-GAT
* * * * ** *
92942 GTCTTCAATCTGCCATC-TAATTAGGGTAAAAGATCGGCT
1 G-CTTCAATCTGCC-CCATGATCAGGGTAAGAGATTAGAT
*
92981 GCTTCAATCTGCCCCATGATCAGGGTAAGAGATTAGTGT
1 GCTTCAATCTGCCCCATGATCAGGGTAAGAGATTAG-AT
* * * * *
93020 GTTTTCAATTTGCCCTC-TGATTAGAGTAAAAGATTAGAT
1 G-CTTCAATCTGCCC-CATGATCAGGGTAAGAGATTAGAT
* *
93059 GCTTCAATCTACCCCATGATCAGGGTATGAGATT
1 GCTTCAATCTGCCCCATGATCAGGGTAAGAGATT
93093 GAATGGTAGC
Statistics
Matches: 306, Mismatches: 92, Indels: 62
0.67 0.20 0.13
Matches are distributed among these distances:
37 3 0.01
38 127 0.42
39 40 0.13
40 78 0.25
41 12 0.04
42 45 0.15
43 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (38 bp):
GCTTCAATCTGCCCCATGATCAGGGTAAGAGATTAGAT
Found at i:93296 original size:42 final size:42
Alignment explanation
Indices: 93236--93342 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
93226 TAAGGACGTA
* * *
93236 AGATTCACCTTTGTAGCTTCAATCTAGCCTTT-TACAACTTTG
1 AGATTCGCCTTTGCAGCTTCAATAT-GCCTTTATACAACTTTG
* **
93278 AGATTCGCCTTTGCAGCTTCAATATGCTTTTATACAGTTTTG
1 AGATTCGCCTTTGCAGCTTCAATATGCCTTTATACAACTTTG
* *
93320 AGATTCGTCTTTGCATCTTCAAT
1 AGATTCGCCTTTGCAGCTTCAAT
93343 TTGCTTTTCC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 5 0.09
42 51 0.91
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.42
Consensus pattern (42 bp):
AGATTCGCCTTTGCAGCTTCAATATGCCTTTATACAACTTTG
Found at i:93432 original size:49 final size:49
Alignment explanation
Indices: 93379--93513 Score: 123
Period size: 49 Copynumber: 2.8 Consensus size: 49
93369 ATATTTGTTG
* * * *
93379 TTGCAGCCTT-AACCTTTCCCTTCACATCTCTACTGTATATGGTTCACCA
1 TTGCAGACTTCAACCTTTCCC-TCACATCTCTACGGTATAAGATTCACCA
* * *
93428 TTGCA-ACTTCAACCTTTTCCTCTACATCTTTAGGGTATAAGATTCACCA
1 TTGCAGACTTCAACCTTTCCCTC-ACATCTCTACGGTATAAGATTCACCA
* * * *
93477 TTGC-GGCTTCAATCTTTCCCATCACGTCTCTAAGGTA
1 TTGCAGACTTCAACCTTTCCC-TCACATCTCTACGGTA
93514 CGAGGTTCGT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
48 5 0.07
49 62 0.90
50 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (49 bp):
TTGCAGACTTCAACCTTTCCCTCACATCTCTACGGTATAAGATTCACCA
Found at i:93530 original size:49 final size:49
Alignment explanation
Indices: 93481--93934 Score: 285
Period size: 49 Copynumber: 9.3 Consensus size: 49
93471 TCACCATTGC
** * * *
93481 GGCTTCAATCTTTCCCATCACGTCTCTAAGGTACGAGGTTCGTTGTTGC
1 GGCTTCAATCTTTCCCATCATATCTCTAAGGTACAAGGTTCGTCGTTGT
** * ** * *
93530 GAATTCAACCTTTCCTTTCATATCTCCGT-A-GTACAAGATTCGTCGTTGC
1 GGCTTCAATCTTTCCCATCATATCT-C-TAAGGTACAAGGTTCGTCGTTGT
* * * * * * * *
93579 GGCTTCCATCTTTCCCATCACATATCTAAGATACAAGGTTTGCCATTAT
1 GGCTTCAATCTTTCCCATCATATCTCTAAGGTACAAGGTTCGTCGTTGT
* * * *
93628 GGCTTTAATCTTTCCC-TCCATATCTCCATGGTACAAGATTCGTCGTTGT
1 GGCTTCAATCTTTCCCAT-CATATCTCTAAGGTACAAGGTTCGTCGTTGT
* * ** *
93677 GGCTTCAATCTCTCCCATCACATCGT-TAAGGTACAAGGTTCACCATTGT
1 GGCTTCAATCTTTCCCATCATATC-TCTAAGGTACAAGGTTCGTCGTTGT
** * * * * *
93726 GGCTTCACCCTTTCCC-TCCATATCTC-AGTGGTACAAGATTTGCCGTTGC
1 GGCTTCAATCTTTCCCAT-CATATCTCTA-AGGTACAAGGTTCGTCGTTGT
* * * * * * *
93775 AGCTTCAATTTTTACCATCATGTCTCTAAGGTACAATGTTTGTTGTTGT
1 GGCTTCAATCTTTCCCATCATATCTCTAAGGTACAAGGTTCGTCGTTGT
* * ** *
93824 GGCTTCAACCTTTCCC-TCCATATCTCTAGGGTATTAGAGTT-GTCGTTAT
1 GGCTTCAATCTTTCCCAT-CATATCTCTAAGGTACAAG-GTTCGTCGTTGT
* * * **
93873 GGCTTCAATCTTTCCCTTCATGTCTTTAAGGTACAAGGTTTTTCGTTGT
1 GGCTTCAATCTTTCCCATCATATCTCTAAGGTACAAGGTTCGTCGTTGT
* *
93922 GGGTTCAACCTTT
1 GGCTTCAATCTTT
93935 TCCTCCGTAT
Statistics
Matches: 300, Mismatches: 89, Indels: 32
0.71 0.21 0.08
Matches are distributed among these distances:
47 1 0.00
48 10 0.03
49 278 0.93
50 10 0.03
51 1 0.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (49 bp):
GGCTTCAATCTTTCCCATCATATCTCTAAGGTACAAGGTTCGTCGTTGT
Found at i:93568 original size:98 final size:98
Alignment explanation
Indices: 93461--93947 Score: 413
Period size: 98 Copynumber: 5.0 Consensus size: 98
93451 ACATCTTTAG
* * * * * ***
93461 GGTATAAGATTCACCATTGCGGCTTCAATCTTTCCCATCACGTCTCTAAGGTACGAGGTTCGTTG
1 GGTACAAGATTCGCCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCA
* ** * *
93526 TTGCGAATTCAACCTTTCCTTTCATATCTCCGT
66 TTGTGGCTTCAACCTTTCCCTCCATATCTCCGT
* * * * * *
93559 AGTACAAGATTCGTCGTTGCGGCTTCCATCTTTCCCATCACATATCTAAGATACAAGGTTTGCCA
1 GGTACAAGATTCGCCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCA
* * * *
93624 TTATGGCTTTAATCTTTCCCTCCATATCTCCAT
66 TTGTGGCTTCAACCTTTCCCTCCATATCTCCGT
* * * *
93657 GGTACAAGATTCGTCGTTGTGGCTTCAATCTCTCCCATCACATCGT-TAAGGTACAAGGTTCACC
1 GGTACAAGATTCGCCGTTGCGGCTTCAATCTTTCCCATCACATC-TCTAAGGTACAAGGTTCGCC
* *
93721 ATTGTGGCTTCACCCTTTCCCTCCATATCTCAGT
65 ATTGTGGCTTCAACCTTTCCCTCCATATCTCCGT
* * * * ** * * ***
93755 GGTACAAGATTTGCCGTTGCAGCTTCAATTTTTACCATCATGTCTCTAAGGTACAATGTTTGTTG
1 GGTACAAGATTCGCCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCA
*
93820 TTGTGGCTTCAACCTTTCCCTCCATATCTCTAG-
66 TTGTGGCTTCAACCTTTCCCTCCATATCTC-CGT
** * ** * ** * ***
93853 GGTATTAGAGTT-GTCGTTATGGCTTCAATCTTTCCCTTCATGTCTTTAAGGTACAAGGTTTTTC
1 GGTACAAGA-TTCGCCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCC
* * * *
93917 GTTGTGGGTTCAACCTTTTCCTCCGTATCTC
65 ATTGTGGCTTCAACCTTTCCCTCCATATCTC
93948 TAGGGAATTA
Statistics
Matches: 316, Mismatches: 69, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
97 1 0.00
98 310 0.98
99 5 0.02
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (98 bp):
GGTACAAGATTCGCCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCA
TTGTGGCTTCAACCTTTCCCTCCATATCTCCGT
Found at i:93750 original size:196 final size:196
Alignment explanation
Indices: 93533--93947 Score: 463
Period size: 196 Copynumber: 2.1 Consensus size: 196
93523 TTGTTGCGAA
* * * * * * *
93533 TTCAACCTTTCCTTTCATATCTCCGTAGTACAAGATTCGTCGTTGCGGCTTCCATCTTTCCCATC
1 TTCAACCTTTCCCTCCATATCTCAGTAGTACAAGATTCGCCGTTGCAGCTTCAATCTTTACCATC
* * *
93598 ACATATCTAAGATACAAGGTTTGCCATTATGGCTTTAATCTTTCCCTCCATATCTCCATGGTACA
66 ACATATCTAAGATACAAGGTTTGCCATTATGGCTTCAACCTTTCCCTCCATATCTCCAGGGTACA
*
93663 AGA-TTCGTCGTTGTGGCTTCAATCTCTCCCATCACATCGTTAAGGTACAAGGTTCACCATTGTG
131 AGAGTT-GTCGTTATGGCTTCAATCTCTCCCATCACATCGTTAAGGTACAAGGTTCACCATTGTG
93727 GC
195 GC
* * * *
93729 TTCACCCTTTCCCTCCATATCTCAGTGGTACAAGATTTGCCGTTGCAGCTTCAATTTTTACCATC
1 TTCAACCTTTCCCTCCATATCTCAGTAGTACAAGATTCGCCGTTGCAGCTTCAATCTTTACCATC
** * * * *** * * **
93794 ATGTCTCTAAGGTACAATGTTTGTTGTTGTGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATT
66 ACATATCTAAGATACAAGGTTTGCCATTATGGCTTCAACCTTTCCCTCCATATCTCCAGGGTACA
* * ** * *** *
93859 AGAGTTGTCGTTATGGCTTCAATCTTTCCCTTCATGTCTTTAAGGTACAAGGTTTTTCGTTGTGG
131 AGAGTTGTCGTTATGGCTTCAATCTCTCCCATCACATCGTTAAGGTACAAGGTTCACCATTGTGG
*
93924 G
196 C
* *
93925 TTCAACCTTTTCCTCCGTATCTC
1 TTCAACCTTTCCCTCCATATCTC
93948 TAGGGAATTA
Statistics
Matches: 178, Mismatches: 40, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
196 176 0.99
197 2 0.01
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (196 bp):
TTCAACCTTTCCCTCCATATCTCAGTAGTACAAGATTCGCCGTTGCAGCTTCAATCTTTACCATC
ACATATCTAAGATACAAGGTTTGCCATTATGGCTTCAACCTTTCCCTCCATATCTCCAGGGTACA
AGAGTTGTCGTTATGGCTTCAATCTCTCCCATCACATCGTTAAGGTACAAGGTTCACCATTGTGG
C
Found at i:93990 original size:98 final size:98
Alignment explanation
Indices: 93434--93986 Score: 378
Period size: 98 Copynumber: 5.6 Consensus size: 98
93424 ACCATTGCAA
* * * * * ** * * *
93434 CTTCAACCTTTTCCTCTACATCTTTAGGGTATAAGATTCACCATTGCGGCTTCAATCTTTCCCAT
1 CTTCAACCTTTCCCTCCATATCTCTAGGGTATTAGATTTGCCGTTACAGCTTCAATCTTTCCCAT
* * * * * *
93499 CACGTCTCTAAGGTACGAGGTTCGTT-GTTGCGA
66 CATGTCTTTAAGGTACAAGGTT-TTTCGTTGTGG
* * * ** * * * * *
93532 ATTCAACCTTTCCTTTCATATCTCCGTA--GTACAAGATTCGTCGTTGCGGCTTCCATCTTTCCC
1 CTTCAACCTTTCCCTCCATATCT-C-TAGGGTATTAGATTTGCCGTTACAGCTTCAATCTTTCCC
** * * * ** * *
93595 ATCACATATCTAAGATACAAGGTTTGCCATTATGG
64 ATCATGTCTTTAAGGTACAAGGTTTTTCGTTGTGG
* * * * ** * * *** *
93630 CTTTAATCTTTCCCTCCATATCTCCATGGTACAAGATTCGTCGTTGTGGCTTCAATCTCTCCCAT
1 CTTCAACCTTTCCCTCCATATCTCTAGGGTATTAGATTTGCCGTTACAGCTTCAATCTTTCCCAT
** * *** *
93695 CACATCGTTAAGGTACAAGGTTCACCATTGTGG
66 CATGTCTTTAAGGTACAAGGTTTTTCGTTGTGG
* ** * * *
93728 CTTCACCCTTTCCCTCCATATCTC-AGTGGTACAAGATTTGCCGTTGCAGCTTCAATTTTTACCA
1 CTTCAACCTTTCCCTCCATATCTCTAG-GGTATTAGATTTGCCGTTACAGCTTCAATCTTTCCCA
* *
93792 TCATGTCTCTAAGGTACAATGTTTGTT-GTTGTGG
65 TCATGTCTTTAAGGTACAAGGTTT-TTCGTTGTGG
* * ** *
93826 CTTCAACCTTTCCCTCCATATCTCTAGGGTATTAGAGTTGTCGTTATGGCTTCAATCTTTCCCTT
1 CTTCAACCTTTCCCTCCATATCTCTAGGGTATTAGATTTGCCGTTACAGCTTCAATCTTTCCCAT
93891 CATGTCTTTAAGGTACAAGGTTTTTCGTTGTGG
66 CATGTCTTTAAGGTACAAGGTTTTTCGTTGTGG
* * * * *
93924 GTTCAACCTTTTCCTCCGTATCTCTAGGGAATTAGATTTACCGTTACAGCTTCAATCTTTCCC
1 CTTCAACCTTTCCCTCCATATCTCTAGGGTATTAGATTTGCCGTTACAGCTTCAATCTTTCCC
93987 TTCAAACCTG
Statistics
Matches: 365, Mismatches: 81, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
96 1 0.00
97 4 0.01
98 356 0.98
99 2 0.01
100 2 0.01
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.37
Consensus pattern (98 bp):
CTTCAACCTTTCCCTCCATATCTCTAGGGTATTAGATTTGCCGTTACAGCTTCAATCTTTCCCAT
CATGTCTTTAAGGTACAAGGTTTTTCGTTGTGG
Found at i:95714 original size:10 final size:10
Alignment explanation
Indices: 95659--95714 Score: 58
Period size: 11 Copynumber: 5.3 Consensus size: 10
95649 TCATCTTAAC
95659 TTTCTTTTTT
1 TTTCTTTTTT
*
95669 CTTCCTTTTTCT
1 -TTTCTTTTT-T
*
95681 TTTCTTCTTCT
1 TTTCTT-TTTT
*
95692 TTTCTTTTCT
1 TTTCTTTTTT
95702 TTTCTTTTTT
1 TTTCTTTTTT
95712 TTT
1 TTT
95715 TTCTTAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
10 16 0.41
11 20 0.51
12 3 0.08
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:95715 original size:21 final size:22
Alignment explanation
Indices: 95659--95715 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
95649 TCATCTTAAC
* *
95659 TTTCTTTTTTCTTCCTTTTTCT
1 TTTCTTTTTTTTTTCTTTTTCT
* *
95681 TTTCTTCTTCTTTTC-TTTTCT
1 TTTCTTTTTTTTTTCTTTTTCT
95702 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
95716 TCTTAAAGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTCTTTTTTTTTTCTTTTTCT
Found at i:95716 original size:5 final size:5
Alignment explanation
Indices: 95675--95713 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
95665 TTTTCTTCCT
95675 TTTTC TTTTC TTCTTC TTTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTT
95714 TTTCTTAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:100602 original size:63 final size:63
Alignment explanation
Indices: 100535--100668 Score: 250
Period size: 63 Copynumber: 2.1 Consensus size: 63
100525 AATAAAATAG
*
100535 TGGGGATTGAATTAGAATAAAATAGAAATGAAGGAGTATAATTTCAAAAGAGGAAAAATAACT
1 TGGGGATTGAATTAGAATAAAATAGAAATAAAGGAGTATAATTTCAAAAGAGGAAAAATAACT
100598 TGGGGATTGAATTAGAATAAAATAGAAATAAAGGAGTATAATTTCAAAAGAGGAAAAATAACT
1 TGGGGATTGAATTAGAATAAAATAGAAATAAAGGAGTATAATTTCAAAAGAGGAAAAATAACT
*
100661 TGTGGATT
1 TGGGGATT
100669 AGATTAAAAC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 69 1.00
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.25
Consensus pattern (63 bp):
TGGGGATTGAATTAGAATAAAATAGAAATAAAGGAGTATAATTTCAAAAGAGGAAAAATAACT
Found at i:122638 original size:42 final size:42
Alignment explanation
Indices: 122574--122657 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
122564 ACTCGTGCTA
*
122574 ATAACGTGTTATAAACAAAAATAATGGATAAAGGATGGATAT
1 ATAACGTGTTATAAACAAAAATAATAGATAAAGGATGGATAT
*
122616 ATAATGTGTTATAAACAAAAATAATAGATAAAGGATGGATAT
1 ATAACGTGTTATAAACAAAAATAATAGATAAAGGATGGATAT
122658 GAGAATATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (42 bp):
ATAACGTGTTATAAACAAAAATAATAGATAAAGGATGGATAT
Found at i:123100 original size:16 final size:15
Alignment explanation
Indices: 123069--123136 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 15
123059 ATTACCATTA
123069 CTTATTATACTTTTATT
1 CTTATTAT--TTTTATT
123086 CTTTATTATTTTTA-T
1 C-TTATTATTTTTATT
* *
123101 CTTATTCTATTTTATA
1 CTTATTAT-TTTTATT
123117 CTTATTATATTTTTATT
1 CTTA-T-TATTTTTATT
123134 CTT
1 CTT
123137 TATATAAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 6 0.14
15 7 0.17
16 9 0.21
17 11 0.26
18 9 0.21
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (15 bp):
CTTATTATTTTTATT
Found at i:123140 original size:24 final size:24
Alignment explanation
Indices: 123067--123140 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
123057 TTATTACCAT
*
123067 TACTTATTATACTTTTATTCTTTA
1 TACTTATTATATTTTTATTCTTTA
* *
123091 TTA-TTTTTATCTTATTCTA-T-TTTA
1 -TACTTATTATATT-TT-TATTCTTTA
123115 TACTTATTATATTTTTATTCTTTA
1 TACTTATTATATTTTTATTCTTTA
123139 TA
1 TA
123141 TAAGTATCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 2 0.05
23 5 0.13
24 25 0.64
25 5 0.13
26 2 0.05
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.66
Consensus pattern (24 bp):
TACTTATTATATTTTTATTCTTTA
Found at i:123141 original size:15 final size:15
Alignment explanation
Indices: 123073--123141 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 15
123063 CCATTACTTA
*
123073 TTATACTTTTATTCT
1 TTATATTTTTATTCT
123088 TTATTATTTTTA-TCTT
1 TTA-TATTTTTATTC-T
* *
123104 ATTCTATTTTATACTT-A
1 -TTATATTTT-TA-TTCT
123121 TTATATTTTTATTCT
1 TTATATTTTTATTCT
123136 TTATAT
1 TTATAT
123142 AAGTATCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
14 2 0.05
15 13 0.31
16 22 0.52
17 4 0.10
19 1 0.02
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATATTTTTATTCT
Found at i:129460 original size:17 final size:17
Alignment explanation
Indices: 129422--129468 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
129412 TCAAAAAAGA
129422 GAAAAGAGAAGAAGAAG
1 GAAAAGAGAAGAAGAAG
129439 G--AAGAGAAG-AGAAG
1 GAAAAGAGAAGAAGAAG
*
129453 GAAAA-AGAAAAAGAAG
1 GAAAAGAGAAGAAGAAG
129469 AAGTTGTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 6 0.23
15 12 0.46
16 7 0.27
17 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAAGAGAAGAAGAAG
Found at i:135206 original size:38 final size:34
Alignment explanation
Indices: 135126--135211 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 34
135116 TTTGTACATG
*
135126 TTTATGCAGCGACATTTATGGGTGCAATTGAATA
1 TTTATGCAGCGACATTTATGGATGCAATTGAATA
* * *
135160 CTTATGCAGTGACATTTCTGGATGCAATTTGAAGAATA
1 TTTATGCAGCGACATTTATGGATGCAA-TT---GAATA
135198 TTTATGCAGCGACA
1 TTTATGCAGCGACA
135212 GTCTTGGGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
34 23 0.55
35 2 0.05
38 17 0.40
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (34 bp):
TTTATGCAGCGACATTTATGGATGCAATTGAATA
Found at i:138678 original size:13 final size:13
Alignment explanation
Indices: 138662--138686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
138652 TCTTATTGTA
138662 CTTTTAGTTTTCC
1 CTTTTAGTTTTCC
138675 CTTTTAGTTTTC
1 CTTTTAGTTTTC
138687 GAAGTTTTTT
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:0.08, C:0.20, G:0.08, T:0.64
Consensus pattern (13 bp):
CTTTTAGTTTTCC
Found at i:150947 original size:18 final size:18
Alignment explanation
Indices: 150924--150958 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
150914 GATCTTTCTC
150924 ATCTTCTTCTTCCTCAGG
1 ATCTTCTTCTTCCTCAGG
*
150942 ATCTTCTTCTTCTTCAG
1 ATCTTCTTCTTCCTCAG
150959 CTTGCTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.31, G:0.09, T:0.49
Consensus pattern (18 bp):
ATCTTCTTCTTCCTCAGG
Done.