Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011438.1 Kokia drynarioides strain JFW-HI SEQ_126422, 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: 86404
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:5406 original size:16 final size:16
Alignment explanation
Indices: 5387--5421 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5377 GAACTCTGAT
5387 TTTGATGAATTCTTGA
1 TTTGATGAATTCTTGA
*
5403 TTTGATGTATTCTTGA
1 TTTGATGAATTCTTGA
5419 TTT
1 TTT
5422 CTTTTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (16 bp):
TTTGATGAATTCTTGA
Found at i:6757 original size:46 final size:46
Alignment explanation
Indices: 6664--6765 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 46
6654 CTATCATATC
* * * *
6664 AGATATATGTGGTCAAGCCACTATATTGCAGCCAAGCTGCCAGAAT
1 AGATATATGTGGTCAAGCCACTAAATTGCAGACAACCTACCAGAAT
* *
6710 AGATATATGTGGTCGAGCCACTACAATTGTAGACAACCTACCA-AAT
1 AGATATATGTGGTCAAGCCACTA-AATTGCAGACAACCTACCAGAAT
6756 AGA-A-ATGTGG
1 AGATATATGTGG
6766 ATAAACCACC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 6 0.12
45 1 0.02
46 28 0.57
47 14 0.29
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (46 bp):
AGATATATGTGGTCAAGCCACTAAATTGCAGACAACCTACCAGAAT
Found at i:7704 original size:68 final size:68
Alignment explanation
Indices: 7552--8134 Score: 326
Period size: 68 Copynumber: 8.6 Consensus size: 68
7542 TAAAGTTGAT
* * * * ** * * * *
7552 TGATTTAAGACCGCAACTTCCAAACAGCTC-TCTAATTTAAGATCG-AACTCATATTATTAAGGT
1 TGATTTAAGATCGCAGCCTCCAAACAGCTCGT-TGATTTAAGATCGCAGTTGATATCACTAAGGC
*
7615 TCGT
65 TCGC
* * * * * * *
7619 TGATTTAATATCCCAGCCTCTAAACAGTTCATTGATTTAAGATCACAGTTGATATCATTAAGGCT
1 TGATTTAAGATCGCAGCCTCCAAACAGCTCGTTGATTTAAGATCGCAGTTGATATCACTAAGGCT
*
7684 CAC
66 CGC
* * * * ** *
7687 TGATTTAAGATCGCAGCCTCTAAACAACTCGCTGATTTAAGATCGCAGCCT--TAGGA-T-A-GA
1 TGATTTAAGATCGCAGCCTCCAAACAGCTCGTTGATTTAAGATCGCAG-TTGATATCACTAAGGC
7747 TCGC
65 TCGC
* * * *
7751 TGGTTTAAGATCGCAGCTGATATCACTAA-AGCTC-TCTGATTTAAGATCGTAGTTGATATCACT
1 TGATTTAAGATCGCAGC----CTC-CAAACAGCTCGT-TGATTTAAGATCGCAGTTGATATCACT
*
7814 AAGGCTCGT
60 AAGGCTCGC
* * * * * ** * * * **
7823 TGCTTTAAGATCGTAGCCTCCATACAGCTCGTTAATTTAAGATCGAAACTAACT-TTATTAAGTT
1 TGATTTAAGATCGCAGCCTCCAAACAGCTCGTTGATTTAAGATCGCAGTTGA-TATCACTAAGGC
7887 TCGC
65 TCGC
* * ** ** * *
7891 TAATTTTAGATCATAGCCTCCAAACAGCTCGTTGATTTAAGATCAAAATTGATATCACTAAAGCT
1 TGATTTAAGATCGCAGCCTCCAAACAGCTCGTTGATTTAAGATCGCAGTTGATATCACTAAGGCT
**
7956 TAC
66 CGC
* * * * * * * *
7959 TAATTTAATATCGCAGCCTCCGAATAGCTCGCTGATATAAGATCGTAGTTGATATCATTAAGGCT
1 TGATTTAAGATCGCAGCCTCCAAACAGCTCGTTGATTTAAGATCGCAGTTGATATCACTAAGGCT
*
8024 -GAT
66 CG-C
* ** * *
8027 TGATTTAAGATCG-AGACCTCCAAATAGCTCACTGATTTAAGATCGCAGCTAATATCACTAAGGC
1 TGATTTAAGATCGCAG-CCTCCAAACAGCTCGTTGATTTAAGATCGCAGTTGATATCACTAAGGC
8091 TCGC
65 TCGC
* * * * * *
8095 TAATTTAAGATTGCAGCCCCCAAATAGCTTGCTGATTTAA
1 TGATTTAAGATCGCAGCCTCCAAACAGCTCGTTGATTTAA
8135 CATAGAACCT
Statistics
Matches: 393, Mismatches: 101, Indels: 43
0.73 0.19 0.08
Matches are distributed among these distances:
64 20 0.05
65 1 0.00
66 1 0.00
67 43 0.11
68 296 0.75
69 11 0.03
70 1 0.00
71 1 0.00
72 19 0.05
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (68 bp):
TGATTTAAGATCGCAGCCTCCAAACAGCTCGTTGATTTAAGATCGCAGTTGATATCACTAAGGCT
CGC
Found at i:7727 original size:32 final size:32
Alignment explanation
Indices: 7686--7767 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
7676 TTAAGGCTCA
7686 CTGATTTAAGATCGCAGCCTCTA-AACA-ACTCG
1 CTGATTTAAGATCGCAGCCT-TAGAACAGA-TCG
* *
7718 CTGATTTAAGATCGCAGCCTTAGGATAGATCG
1 CTGATTTAAGATCGCAGCCTTAGAACAGATCG
*
7750 CTGGTTTAAGATCGCAGC
1 CTGATTTAAGATCGCAGC
7768 TGATATCACT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
31 2 0.04
32 42 0.93
33 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (32 bp):
CTGATTTAAGATCGCAGCCTTAGAACAGATCG
Found at i:7808 original size:36 final size:36
Alignment explanation
Indices: 7754--7839 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
7744 AGATCGCTGG
*
7754 TTTAAGATCGCAGCTGATATCACTAAAGCTC-TCTGA
1 TTTAAGATCGTAGCTGATATCACTAAAGCTCGT-TGA
* * *
7790 TTTAAGATCGTAGTTGATATCACTAAGGCTCGTTGC
1 TTTAAGATCGTAGCTGATATCACTAAAGCTCGTTGA
7826 TTTAAGATCGTAGC
1 TTTAAGATCGTAGC
7840 CTCCATACAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 43 0.98
37 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (36 bp):
TTTAAGATCGTAGCTGATATCACTAAAGCTCGTTGA
Found at i:8147 original size:68 final size:69
Alignment explanation
Indices: 8010--8181 Score: 179
Period size: 68 Copynumber: 2.5 Consensus size: 69
8000 ATCGTAGTTG
* * * * * * *
8010 ATATCATTAAGGCT-GATTGATTTAAGATCGAGACCTCCAAATAGCTCACTGATTTAAGATCGCA
1 ATATCACTAAGGCTCGCTTAATTTAAGATCGAGACCCCCAAATAGCTCACTGATTTAACATAGAA
*
8074 GCTA
66 CCTA
* **
8078 ATATCACTAAGGCTCGC-TAATTTAAGATTGCAG-CCCCCAAATAGCTTGCTGATTTAACATAGA
1 ATATCACTAAGGCTCGCTTAATTTAAGATCG-AGACCCCCAAATAGCTCACTGATTTAACATAGA
8141 ACCTA
65 ACCTA
* * * *
8146 ATATTATTAAGGTTCGCTTGATTTAAGATCGAGACC
1 ATATCACTAAGGCTCGCTTAATTTAAGATCGAGACC
8182 TTTAGTATTC
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
68 68 0.81
69 16 0.19
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (69 bp):
ATATCACTAAGGCTCGCTTAATTTAAGATCGAGACCCCCAAATAGCTCACTGATTTAACATAGAA
CCTA
Found at i:8907 original size:31 final size:31
Alignment explanation
Indices: 8867--8937 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
8857 ATTATTTTTT
* *
8867 GAGTTAAATTTGACTCACAACATTTT-AAAAG
1 GAGTCAAATTT-ACCCACAACATTTTGAAAAG
* * *
8898 GAGTCAAA-TTACCCTCAACTTTTTGAAAAT
1 GAGTCAAATTTACCCACAACATTTTGAAAAG
8928 GAGTCAAATT
1 GAGTCAAATT
8938 GATTTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 11 0.33
30 14 0.42
31 8 0.24
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.32
Consensus pattern (31 bp):
GAGTCAAATTTACCCACAACATTTTGAAAAG
Found at i:10264 original size:11 final size:12
Alignment explanation
Indices: 10228--10264 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
10218 TAGCATAAAT
10228 AATAAATAAT-A
1 AATAAATAATAA
10239 AATAAATATATAA
1 AATAAATA-ATAA
10252 AATAAA-AATAA
1 AATAAATAATAA
10263 AA
1 AA
10265 ACACGGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.58
12 3 0.12
13 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:20467 original size:39 final size:35
Alignment explanation
Indices: 20389--20467 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 35
20379 ATTTTGGGGG
* **
20389 ATTAAAAAGGAAAATATATTTTAATTAAGTGGAGG
1 ATTAAAAAGAAAAATATATTTTAATTAAGTGGACA
*
20424 ATTAAAAAGAAAAATATACTTTATTGTATTAAGTGGACA
1 ATTAAAAAGAAAAATATA--TT-TT-AATTAAGTGGACA
20463 ATTAA
1 ATTAA
20468 GTCTATGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
35 17 0.47
37 2 0.06
38 2 0.06
39 15 0.42
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (35 bp):
ATTAAAAAGAAAAATATATTTTAATTAAGTGGACA
Found at i:27080 original size:23 final size:23
Alignment explanation
Indices: 27052--27106 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
27042 AAACACCATT
27052 GAAGAGAAAGGAGGGTTTGGTTG
1 GAAGAGAAAGGAGGGTTTGGTTG
27075 GAAGAGAAAGGAGGGTTTGGTTG
1 GAAGAGAAAGGAGGGTTTGGTTG
*
27098 GAAAAGAAA
1 GAAGAGAAA
27107 ACCCCTTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.44, T:0.18
Consensus pattern (23 bp):
GAAGAGAAAGGAGGGTTTGGTTG
Found at i:37653 original size:52 final size:51
Alignment explanation
Indices: 37575--37755 Score: 211
Period size: 52 Copynumber: 3.5 Consensus size: 51
37565 TGCATATTCG
* * * * *
37575 ATACTCATGATGACATAGAGTAATCAGACCTTTAATCCGTATTGGGAATT-AT
1 ATACTCACGATGACACAAAGTCATCAGACCTTTAATCCGTA-AGGG-ATTCAT
* * * *
37627 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACAAAGTCATCAGACCT-TTAATCCGTAAGGGATTCAT
* * *
37679 ATACTCACGATAACACAAAGTCATCAAACCTTATAATTCGTAAGGGATTCAT
1 ATACTCACGATGACACAAAGTCATCAGACCTT-TAATCCGTAAGGGATTCAT
37731 ATACTCACGATGACACAAAGTCATC
1 ATACTCACGATGACACAAAGTCATC
37756 GAACCTATTT
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
51 3 0.03
52 99 0.90
53 8 0.07
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (51 bp):
ATACTCACGATGACACAAAGTCATCAGACCTTTAATCCGTAAGGGATTCAT
Found at i:39509 original size:48 final size:48
Alignment explanation
Indices: 39418--39509 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
39408 TTTAGTGTCA
* *
39418 TGACTTCAATGTACCCCTATGGATTTAGGGGTATATGATTTGATTTGG
1 TGACTTCAATGTACCCCTATGGATTTAGGGGTATAAGACTTGATTTGG
* * * *
39466 TGACTTCAATTTGCCCCTCTGGATTTAGGGGTCTAAGACTTGAT
1 TGACTTCAATGTACCCCTATGGATTTAGGGGTATAAGACTTGAT
39510 GTGATGGCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (48 bp):
TGACTTCAATGTACCCCTATGGATTTAGGGGTATAAGACTTGATTTGG
Found at i:39529 original size:48 final size:46
Alignment explanation
Indices: 39417--39690 Score: 203
Period size: 47 Copynumber: 5.8 Consensus size: 46
39407 ATTTAGTGTC
* * * *
39417 ATGACTTCAATGTACCCCTATGGATTTAGGGGTATATGATTTGATTTG
1 ATGACTTCAATCTGCCCCTATGGATTT-GGGGTATAAGA-TTGATGTG
* * * *
39465 GTGACTTCAATTTGCCCCTCTGGATTTAGGGGTCTAAGACTTGATGTG
1 ATGACTTCAATCTGCCCCTATGGATTT-GGGGTATAAGA-TTGATGTG
* * * * * *
39513 ATGGCTTAAATCTG-CCCTTTAGGATTTGAGATATAAGATAGATGTG
1 ATGACTTCAATCTGCCCCTAT-GGATTTGGGGTATAAGATTGATGTG
* * * *
39559 ATGACTTCAATCTGCCCTTATAGATTTGGGGTATAATATTATATGTG
1 ATGACTTCAATCTGCCCCTATGGATTTGGGGTATAAGATT-GATGTG
* * * * *
39606 AT-AGCTTCAATCTGTCCCTTTAGATTTTGGGTATAAGACTGTATGTG
1 ATGA-CTTCAATCTGCCCCTATGGATTTGGGGTATAAGATTG-ATGTG
* * * *
39653 ATGACTTTAATCTACCCCTCTAGACTTT-GGGTATAAGA
1 ATGACTTCAATCTGCCCCTATGGA-TTTGGGGTATAAGA
39691 CTGTCCTCTA
Statistics
Matches: 181, Mismatches: 38, Indels: 15
0.77 0.16 0.06
Matches are distributed among these distances:
46 34 0.19
47 87 0.48
48 60 0.33
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (46 bp):
ATGACTTCAATCTGCCCCTATGGATTTGGGGTATAAGATTGATGTG
Found at i:39585 original size:94 final size:94
Alignment explanation
Indices: 39466--39690 Score: 237
Period size: 94 Copynumber: 2.4 Consensus size: 94
39456 TTTGATTTGG
* * * * *
39466 TGACTTCAATTTGCCCCTCTGGATTTAGGGGTCTAAGACTT-GATGTGATGGCTTAAATCTG-CC
1 TGACTTCAATCTGCCCCTATAGATTT-GGGGTATAAGA-TTAGATGTGATAGCTTAAATCTGTCC
39529 CTTTAGGA-TTTGAGATATAAGA-TAG-ATGTGA
64 CTTTA-GATTTTG-GATATAAGACT-GTATGTGA
* * * *
39560 TGACTTCAATCTGCCCTTATAGATTTGGGGTATAATATTATATGTGATAGCTTCAATCTGTCCCT
1 TGACTTCAATCTGCCCCTATAGATTTGGGGTATAAGATTAGATGTGATAGCTTAAATCTGTCCCT
*
39625 TTAGATTTTGGGTATAAGACTGTATGTGA
66 TTAGATTTTGGATATAAGACTGTATGTGA
* * *
39654 TGACTTTAATCTACCCCTCTAGACTTT-GGGTATAAGA
1 TGACTTCAATCTGCCCCTATAGA-TTTGGGGTATAAGA
39691 CTGTCCTCTA
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
92 2 0.02
93 37 0.34
94 68 0.62
95 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (94 bp):
TGACTTCAATCTGCCCCTATAGATTTGGGGTATAAGATTAGATGTGATAGCTTAAATCTGTCCCT
TTAGATTTTGGATATAAGACTGTATGTGA
Found at i:39829 original size:167 final size:166
Alignment explanation
Indices: 39544--39857 Score: 404
Period size: 167 Copynumber: 1.9 Consensus size: 166
39534 GGATTTGAGA
* * *
39544 TATAAGATAGATGTGATGACTTCAATCTGCCCTTATAGATTTGGGGTATAATATTATATGTGATA
1 TATAAGATAGATGTGATGACTTCAATCTGCCCTTAGAGATTTGGGGTATAAGATTAGATGTGATA
*
39609 GCTTCAATCTGTCCCTTTAGATTTTGGGTATAAGACTGTATGTGATGACTTTAATCTACCCCTCT
66 GCTTCAATCTGTCCCTTTAGATTTTGGGTATAAGACTGGATGTGATGACTTTAATCTACCCCTCT
39674 AGACTTTGG-GTATAAGACTGTCCTCTAGACTTGGGG
131 AGA-TTTGGAGTATAAGACTGTCCTCTAGACTTGGGG
* * *
39710 TATAAGATTGGATGTGATGGCTTCAATCTTTCCCTCT-GA-ATTTGGGGTATAAGATTAGATGTG
1 TATAAGA-TAGATGTGATGACTTCAATC-TGCCCT-TAGAGATTTGGGGTATAAGATTAGATGTG
* * * * * *
39773 ATGGTTTCAATCTG-CCTTTTTGGA-TTTGAGGTATAAGACTGGATGTGATGACTTTAATTTGCC
63 ATAGCTTCAATCTGTCC-CTTTAGATTTTG-GGTATAAGACTGGATGTGATGACTTTAATCTACC
* *
39836 TCTCTGGATTTGGAGTATAAGA
126 CCTCTAGATTTGGAGTATAAGA
39858 TTGGATGAGA
Statistics
Matches: 127, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
166 18 0.14
167 102 0.80
168 6 0.05
169 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (166 bp):
TATAAGATAGATGTGATGACTTCAATCTGCCCTTAGAGATTTGGGGTATAAGATTAGATGTGATA
GCTTCAATCTGTCCCTTTAGATTTTGGGTATAAGACTGGATGTGATGACTTTAATCTACCCCTCT
AGATTTGGAGTATAAGACTGTCCTCTAGACTTGGGG
Found at i:39876 original size:94 final size:92
Alignment explanation
Indices: 39695--40005 Score: 336
Period size: 94 Copynumber: 3.3 Consensus size: 92
39685 ATAAGACTGT
* * * * * *
39695 CCTCTAGACTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTTTCCCTCTGAATTTGGGGTAT
1 CCTCTAGATTTGAGGTATAAGACTGGATGTGATGGCTTCAAT-TTGCCCTCTGGATTTGGAGTAT
* *
39760 AAGATTAGATGTGATGGTTTCAATCTGCC
65 AAGATT-GATGAGATGATTTCAATCTGCC
** * * * *
39789 TTTTTGGATTTGAGGTATAAGACTGGATGTGATGACTTTAATTTGCCTCTCTGGATTTGGAGTAT
1 CCTCTAGATTTGAGGTATAAGACTGGATGTGATGGCTTCAATTTGCC-CTCTGGATTTGGAGTAT
* *
39854 AAGATTGGATGAGATGACTTCAATTTGCC
65 AAGATT-GATGAGATGATTTCAATCTGCC
* * * * * *
39883 CCTCTAGATTTAAGGTATAAGACTTGATGCGATGGCTTCAATCTGCCCTTTTGGATTTGGTGTAT
1 CCTCTAGATTTGAGGTATAAGACTGGATGTGATGGCTTCAATTTGCCC-TCTGGATTTGGAGTAT
* *
39948 AAAATTCAGTGTA-ATGATTTCAATCTGCC
65 AAGATTGA-TG-AGATGATTTCAATCTGCC
39977 CCTCTAGATTTGAGGTATAAGACTGGATG
1 CCTCTAGATTTGAGGTATAAGACTGGATG
40006 GACGTTTCAA
Statistics
Matches: 178, Mismatches: 35, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
93 6 0.03
94 171 0.96
95 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (92 bp):
CCTCTAGATTTGAGGTATAAGACTGGATGTGATGGCTTCAATTTGCCCTCTGGATTTGGAGTATA
AGATTGATGAGATGATTTCAATCTGCC
Found at i:39930 original size:47 final size:46
Alignment explanation
Indices: 39708--39998 Score: 253
Period size: 47 Copynumber: 6.2 Consensus size: 46
39698 CTAGACTTGG
* ** * *
39708 GGTATAAGATTGGATGTGATGGCTTCAATCTTTCCCTCTGAATTTGG
1 GGTATAAGATT-GATGTGATGACTTCAATCTGCCCCTCTGGATTTGA
** ** *
39755 GGTATAAGATTAGATGTGATGGTTTCAATCTGCCTTTTTGGATTTGA
1 GGTATAAGATT-GATGTGATGACTTCAATCTGCCCCTCTGGATTTGA
* * * *
39802 GGTATAAGACTGGATGTGATGACTTTAATTTGCCTCTCTGGATTTG-
1 GGTATAAGA-TTGATGTGATGACTTCAATCTGCCCCTCTGGATTTGA
* * * *
39848 GAGTATAAGATTGGATGAGATGACTTCAATTTGCCCCTCTAGATTTAA
1 G-GTATAAGATT-GATGTGATGACTTCAATCTGCCCCTCTGGATTTGA
* * * *
39896 GGTATAAGACTTGATGCGATGGCTTCAATCTGCCCTTTTGGATTTG-
1 GGTATAAGA-TTGATGTGATGACTTCAATCTGCCCCTCTGGATTTGA
* * * * *
39942 GTGTATAAAATTCAGTGTAATGATTTCAATCTGCCCCTCTAGATTTGA
1 G-GTATAAGATTGA-TGTGATGACTTCAATCTGCCCCTCTGGATTTGA
39990 GGTATAAGA
1 GGTATAAGA
39999 CTGGATGGAC
Statistics
Matches: 197, Mismatches: 39, Indels: 16
0.78 0.15 0.06
Matches are distributed among these distances:
46 6 0.03
47 186 0.94
48 5 0.03
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (46 bp):
GGTATAAGATTGATGTGATGACTTCAATCTGCCCCTCTGGATTTGA
Found at i:39987 original size:141 final size:141
Alignment explanation
Indices: 39695--40005 Score: 348
Period size: 141 Copynumber: 2.2 Consensus size: 141
39685 ATAAGACTGT
* * * * * **
39695 CCTCTAGACTTGGGGTATAAGATTGGATGTGATGGCTTCAATCTTTCCCTCTGAATTTGGGGTAT
1 CCTCTAGATTTGGAGTATAAGATTGGATGAGATGACTTCAATCTTCCCCTCTGAATTTAAGGTAT
* * * * * *
39760 AAGATTAGATGTGATGGTTTCAATCTGCCTTTTTGGATTTGAGGTATAAGACTGGATGTGATGAC
66 AAGATTAGATGCGATGGCTTCAATCTGCCCTTTTGGATTTGAGGTATAAAACTAGATGTAATGAC
*
39825 TTTAATTTGCC
131 TTTAATCTGCC
* *
39836 TCTCTGGATTTGGAGTATAAGATTGGATGAGATGACTTCAAT-TTGCCCCTCT-AGATTTAAGGT
1 CCTCTAGATTTGGAGTATAAGATTGGATGAGATGACTTCAATCTT-CCCCTCTGA-ATTTAAGGT
*
39899 ATAAGACTT-GATGCGATGGCTTCAATCTGCCCTTTTGGATTTG-GTGTATAAAATTCAG-TGTA
64 ATAAGA-TTAGATGCGATGGCTTCAATCTGCCCTTTTGGATTTGAG-GTATAAAACT-AGATGTA
39961 ATGA-TTTCAATCTGCC
126 ATGACTTT-AATCTGCC
*
39977 CCTCTAGATTT-GAGGTATAAGACTGGATG
1 CCTCTAGATTTGGA-GTATAAGATTGGATG
40006 GACGTTTCAA
Statistics
Matches: 143, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
140 9 0.06
141 131 0.92
142 3 0.02
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (141 bp):
CCTCTAGATTTGGAGTATAAGATTGGATGAGATGACTTCAATCTTCCCCTCTGAATTTAAGGTAT
AAGATTAGATGCGATGGCTTCAATCTGCCCTTTTGGATTTGAGGTATAAAACTAGATGTAATGAC
TTTAATCTGCC
Found at i:40097 original size:84 final size:84
Alignment explanation
Indices: 39965--40176 Score: 201
Period size: 84 Copynumber: 2.5 Consensus size: 84
39955 AGTGTAATGA
* * * * ** * *
39965 TTTCAATCTGCCCCTCTAGATTTGAGGTATAAGACTGGATGGACGTTTCAATCTGCTCGCTAGTT
1 TTTCAATCT-ACCCTCTAGA--TGGGGTAAAAGATTGGATGGTGGTTTCAATCTGCCCACTAGTT
40030 AGGGTAAAAAATTGGATGGTACC
63 AGGGTAAAAAATTGGATGG-ACC
* * * * *
40053 TTT-AATTTTCCCTCTAGATGGGGTAAAAGATTGGATGGTGGTTTCAATCTGCCCATTGGTTGGG
1 TTTCAATCTACCCTCTAGATGGGGTAAAAGATTGGATGGTGGTTTCAATCTGCCCACTAGTTAGG
* **
40117 GTAAAAGATTGGATGGAGG
66 GTAAAAAATTGGATGGACC
* * * *
40136 TTTCAATCTACCCACTGGTTGGGGTAAAATATTGGATGGTG
1 TTTCAATCTACCCTCTAGATGGGGTAAAAGATTGGATGGTG
40177 ATGTAACTTC
Statistics
Matches: 102, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
83 4 0.04
84 82 0.80
86 9 0.09
87 4 0.04
88 3 0.03
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (84 bp):
TTTCAATCTACCCTCTAGATGGGGTAAAAGATTGGATGGTGGTTTCAATCTGCCCACTAGTTAGG
GTAAAAAATTGGATGGACC
Found at i:40117 original size:42 final size:42
Alignment explanation
Indices: 40071--40176 Score: 176
Period size: 42 Copynumber: 2.5 Consensus size: 42
40061 TCCCTCTAGA
* *
40071 TGGGGTAAAAGATTGGATGGTGGTTTCAATCTGCCCATTGGT
1 TGGGGTAAAAGATTGGATGGTGGTTTCAATCTACCCACTGGT
*
40113 TGGGGTAAAAGATTGGATGGAGGTTTCAATCTACCCACTGGT
1 TGGGGTAAAAGATTGGATGGTGGTTTCAATCTACCCACTGGT
*
40155 TGGGGTAAAATATTGGATGGTG
1 TGGGGTAAAAGATTGGATGGTG
40177 ATGTAACTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.25, C:0.10, G:0.34, T:0.31
Consensus pattern (42 bp):
TGGGGTAAAAGATTGGATGGTGGTTTCAATCTACCCACTGGT
Found at i:42213 original size:15 final size:14
Alignment explanation
Indices: 42195--42226 Score: 55
Period size: 14 Copynumber: 2.2 Consensus size: 14
42185 CATCTCGACT
42195 TTTTTCTTCTTTTTC
1 TTTTTCTT-TTTTTC
42210 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
42224 TTT
1 TTT
42227 CTTTGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:42218 original size:12 final size:12
Alignment explanation
Indices: 42194--42230 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42184 TCATCTCGAC
42194 TTTTTTC-TTCT
1 TTTTTTCTTTCT
42205 TTTTCTT-TTTCT
1 TTTT-TTCTTTCT
42217 TTTTTTCTTTCT
1 TTTTTTCTTTCT
42229 TT
1 TT
42231 GGGTTTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTCTTTCT
Found at i:43125 original size:16 final size:16
Alignment explanation
Indices: 43098--43131 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
43088 GATTTTTTTT
43098 AATGCGTAATGAAATGC
1 AATGCGTAATG-AATGC
43115 AATGC-TAATGAATGC
1 AATGCGTAATGAATGC
43130 AA
1 AA
43132 GAAATGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (16 bp):
AATGCGTAATGAATGC
Found at i:47217 original size:56 final size:56
Alignment explanation
Indices: 47151--47265 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
47141 CACCATAATC
*
47151 TTTAATCCTTTTATTTTACCAATTTGATTAAATCTTTATTTAATTTGTATATAAAT
1 TTTAATCCTTTTATTTTACCAATTTGACTAAATCTTTATTTAATTTGTATATAAAT
*
47207 TTTAATCCTTTTATTTTACGAATTTGACTAAATCTTTATTTAATTTGTATATAAAT
1 TTTAATCCTTTTATTTTACCAATTTGACTAAATCTTTATTTAATTTGTATATAAAT
47263 TTT
1 TTT
47266 TAATATATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (56 bp):
TTTAATCCTTTTATTTTACCAATTTGACTAAATCTTTATTTAATTTGTATATAAAT
Found at i:48754 original size:28 final size:28
Alignment explanation
Indices: 48714--48901 Score: 148
Period size: 28 Copynumber: 6.8 Consensus size: 28
48704 AGAAAAGGAA
48714 AAAACTGTAAAATCTGAAAAACATGGGC
1 AAAACTGTAAAATCTGAAAAACATGGGC
* * *
48742 AAAATTGTAAAATCTGAATAACAAGGG-
1 AAAACTGTAAAATCTGAAAAACATGGGC
* *
48769 AAAACTATAAAATCTGAATAAA-ATGGGT
1 AAAACTGTAAAATCTGAA-AAACATGGGC
* * * * *
48797 AAAATTGTAAAATATGATAAATAGGGGC
1 AAAACTGTAAAATCTGAAAAACATGGGC
* * * * *
48825 AAAACTATAAAATTTGGAAACCAAT-GGA
1 AAAACTGTAAAATCTGAAAAAC-ATGGGC
* * * *
48853 AAAACTATAAAATCTGAAAAATAGGGGT
1 AAAACTGTAAAATCTGAAAAACATGGGC
* *
48881 AAAACTGTAAATTTTGAAAAA
1 AAAACTGTAAAATCTGAAAAA
48902 TAGGAGACAC
Statistics
Matches: 124, Mismatches: 31, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
27 24 0.19
28 99 0.80
29 1 0.01
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAACTGTAAAATCTGAAAAACATGGGC
Found at i:48795 original size:55 final size:56
Alignment explanation
Indices: 48714--48901 Score: 170
Period size: 56 Copynumber: 3.4 Consensus size: 56
48704 AGAAAAGGAA
* *
48714 AAAACTGTAAAATCTGAAAAACATGGGCAAAATTGTAAAATCTGAATAACA-A-GGG-
1 AAAACTATAAAATCTGAAAAACATGGGCAAAATTGTAAAATATG-ATAA-ATAGGGGC
*
48769 AAAACTATAAAATCTGAATAAA-ATGGGTAAAATTGTAAAATATGATAAATAGGGGC
1 AAAACTATAAAATCTGAA-AAACATGGGCAAAATTGTAAAATATGATAAATAGGGGC
* * * * * * * * *
48825 AAAACTATAAAATTTGGAAACCAAT-GGAAAAACTATAAAATCTGAAAAATAGGGGT
1 AAAACTATAAAATCTGAAAAAC-ATGGGCAAAATTGTAAAATATGATAAATAGGGGC
* * *
48881 AAAACTGTAAATTTTGAAAAA
1 AAAACTATAAAATCTGAAAAA
48902 TAGGAGACAC
Statistics
Matches: 111, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
53 1 0.01
54 5 0.05
55 42 0.38
56 61 0.55
57 2 0.02
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.23
Consensus pattern (56 bp):
AAAACTATAAAATCTGAAAAACATGGGCAAAATTGTAAAATATGATAAATAGGGGC
Found at i:59729 original size:87 final size:87
Alignment explanation
Indices: 59620--59813 Score: 259
Period size: 87 Copynumber: 2.2 Consensus size: 87
59610 AAATTTAGGG
* * *
59620 GGAAAGTTTTAGGGTGAAAACATAACTTTAGGAAGTTT-GAGGGTTAAAATGTAATTTTGGAAAA
1 GGAAAGTTTT-GGGTCAAAACATAACTTTAGAAAGTTTAG-GGGTTAAAATATAATTTTGG-AAA
* * *
59684 GTT-TAGGGTAAAAGTGTAATTTTA
63 GTTCGAGGGTAAAAATATAATTTTA
*
59708 GG-AAGTTTTGGGTTCAAAACATAATTTTAGAAAGTTTAGGGGTTAAAATATAATTTTGGAAAGT
1 GGAAAGTTTTGGG-TCAAAACATAACTTTAGAAAGTTTAGGGGTTAAAATATAATTTTGGAAAGT
*
59772 TCGAGGGTAAAAATATAATTTTT
65 TCGAGGGTAAAAATATAATTTTA
59795 GGAAAGTTTTGGGTCAAAA
1 GGAAAGTTTTGGGTCAAAA
59814 TGTGATTTTG
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
86 9 0.10
87 72 0.77
88 13 0.14
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (87 bp):
GGAAAGTTTTGGGTCAAAACATAACTTTAGAAAGTTTAGGGGTTAAAATATAATTTTGGAAAGTT
CGAGGGTAAAAATATAATTTTA
Found at i:59814 original size:29 final size:29
Alignment explanation
Indices: 59620--59864 Score: 187
Period size: 29 Copynumber: 8.4 Consensus size: 29
59610 AAATTTAGGG
* * * *
59620 GGAAAGTTTTAGGGTGAAAACATAACTTTA
1 GGAAAG-TTTAGGGTCAAAATATAATTTTT
* *
59650 GG-AAGTTTGAGGGTTAAAATGTAA-TTTT
1 GGAAAGTTT-AGGGTCAAAATATAATTTTT
* *
59678 GGAAAAGTTTAGGGT-AAAAGTGTAATTTTA
1 GG-AAAGTTTAGGGTCAAAA-TATAATTTTT
* *
59708 GG-AAGTTTTGGGTTCAAAACATAA-TTTT
1 GGAAAGTTTAGGG-TCAAAATATAATTTTT
* *
59736 AGAAAGTTTAGGGGTTAAAATATAA-TTTT
1 GGAAAGTTTA-GGGTCAAAATATAATTTTT
* *
59765 GGAAAGTTCGAGGGTAAAAATATAATTTTT
1 GGAAAGTT-TAGGGTCAAAATATAATTTTT
* * * *
59795 GGAAAGTTTTGGGTCAAAATGTGATTTTG
1 GGAAAGTTTAGGGTCAAAATATAATTTTT
* * *
59824 GGAAAGTTTGGGGACCAAAATATGATTTTT
1 GGAAAGTTTAGGG-TCAAAATATAATTTTT
59854 GGAAAGTTTAG
1 GGAAAGTTTAG
59865 TGACCTATTG
Statistics
Matches: 176, Mismatches: 27, Indels: 24
0.78 0.12 0.11
Matches are distributed among these distances:
28 25 0.14
29 95 0.54
30 56 0.32
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
GGAAAGTTTAGGGTCAAAATATAATTTTT
Found at i:59822 original size:87 final size:85
Alignment explanation
Indices: 59623--59861 Score: 248
Period size: 87 Copynumber: 2.7 Consensus size: 85
59613 TTTAGGGGGA
* * * *
59623 AAGTTTTAGGG-TGAAAACATAACTTTAGGAAGTTTGAGGGTTAAAATGTAATTTTGGAAAAGTT
1 AAGTTTT-GGGTTCAAAACATAATTTTAGAAAGTTTG-GGGTTAAAATATAATTTTGG-AAAGTT
* * *
59687 TAGGGTAAAAGTGTAATTTTAGG
63 GAGGGTAAAAATATAATTTTAGG
59710 AAGTTTTGGGTTCAAAACATAATTTTAGAAAGTTTAGGGGTTAAAATATAATTTTGGAAAGTTCG
1 AAGTTTTGGGTTCAAAACATAATTTTAGAAAGTTT-GGGGTTAAAATATAATTTTGGAAAGTT-G
*
59775 AGGGTAAAAATATAATTTTTGG
64 AGGGTAAAAATATAATTTTAGG
** * * ** *
59797 AAAGTTTTGGG-TCAAAATGTGATTTTGGGAAAGTTTGGGGACCAAAATATGATTTTTGGAAAGT
1 -AAGTTTTGGGTTCAAAACATAATTTT-AGAAAGTTTGGGG-TTAAAATAT-AATTTTGGAAAGT
59861 T
62 T
59862 TAGTGACCTA
Statistics
Matches: 130, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
86 9 0.07
87 82 0.63
88 26 0.20
89 13 0.10
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (85 bp):
AAGTTTTGGGTTCAAAACATAATTTTAGAAAGTTTGGGGTTAAAATATAATTTTGGAAAGTTGAG
GGTAAAAATATAATTTTAGG
Found at i:62058 original size:76 final size:76
Alignment explanation
Indices: 61966--62117 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
61956 TTAAACCCAG
61966 CCAAGTGTACTTTTGGAGTCACTTTGGGCAAGCTGTTAGGCTTTATGGTCAGCAAAAAGGTGATT
1 CCAAGTGTACTTTTGGAGTCACTTTGGGCAAGCTGTTAGGCTTTATGGTCAGCAAAAAGGTGATT
62031 GAAATTGATTT
66 GAAATTGATTT
*
62042 CCAAGTGTACTTTTGGAGTCACTTTGGGCAAGCTGTTAGGCTTTGTGGTCAGCAAAAAGGTGATT
1 CCAAGTGTACTTTTGGAGTCACTTTGGGCAAGCTGTTAGGCTTTATGGTCAGCAAAAAGGTGATT
62107 GAAATTGATTT
66 GAAATTGATTT
62118 AGATAAAGTC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (76 bp):
CCAAGTGTACTTTTGGAGTCACTTTGGGCAAGCTGTTAGGCTTTATGGTCAGCAAAAAGGTGATT
GAAATTGATTT
Found at i:65670 original size:85 final size:85
Alignment explanation
Indices: 65509--65671 Score: 211
Period size: 84 Copynumber: 1.9 Consensus size: 85
65499 CGATCTCTTA
* * *
65509 TCCTGATGAGATACAAAGAAGTGGATCAAAGCAATAAAGTGTTCATCTTCTTGATGAGATACAGA
1 TCCTGATGAGATACAAAGAAGTGGATCAAAGCAATAAAGTGGTCATCTTCCTAATGAGATACAGA
**
65574 GAAGTGGACCAAATCCATCT
66 GAAGTAAACCAAATCCATCT
* * * * * *
65594 TCCTGATGAGATACAGAGAAGTGGTTGAAA-CAATGAGGTGGTCATCTTCCTAATGAGATATAGA
1 TCCTGATGAGATACAAAGAAGTGGATCAAAGCAATAAAGTGGTCATCTTCCTAATGAGATACAGA
65658 GAAGTAAAACCAAA
66 GAAGT-AAACCAAA
65672 ATCAAATGAA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 33 0.50
85 33 0.50
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (85 bp):
TCCTGATGAGATACAAAGAAGTGGATCAAAGCAATAAAGTGGTCATCTTCCTAATGAGATACAGA
GAAGTAAACCAAATCCATCT
Found at i:65889 original size:48 final size:48
Alignment explanation
Indices: 65800--65891 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
65790 GGACCGAATC
* * ** *
65800 CATCTTCTTGATGAGATAAAGAAAAGTGGATTAAATTAATGAAGTGAT
1 CATCTTCCTGATGAGATAAAGAAAAGTAGACCAAATCAATGAAGTGAT
* *
65848 CATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAG
1 CATCTTCCTGATGAGATAAAGAAAAGTAGACCAAATCAATGAAG
65892 CAAAGCTCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (48 bp):
CATCTTCCTGATGAGATAAAGAAAAGTAGACCAAATCAATGAAGTGAT
Found at i:65957 original size:209 final size:208
Alignment explanation
Indices: 65509--66212 Score: 843
Period size: 209 Copynumber: 3.4 Consensus size: 208
65499 CGATCTCTTA
* * *
65509 TCCTGATGAGATACA-AAGAAGTGGATCAAAGCAATAAAG-TGTTCATCTTCTTGATGAGATACA
1 TCCTGATGAGATACAGAA-AAGTGGGTCAAAGCAATAAAGCGGTT-ATCTTCCTGATGAGATACA
*
65572 GAGAAGTGGACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGG-TTGAAA-CAATGAGGTGG
64 GAGAAGTGGACCAAATCCATCTTCTTGATGAGATACAGAGAAGTGGATT-AAATCAATGAGGTGG
* * *
65635 TCATCTTCCTAATGAGATATAGAGAAGTAAAACCAAAATCAAATGAAGTGAAGCTCAATGTGAGT
128 TCATCTTCCTGATGAGATATAGAGAAGT-AAACC-AAATC-AATGAAG-AAAGCTCAATGAGAGT
* *
65700 GAAACTTCGAACCCCCATCT
189 GAAACTTCCAAACCCCATCT
* *
65720 TCCTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTTATCTTCCTGATGAGATACAGA
1 TCCTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGGTTATCTTCCTGATGAGATACAGA
* * * * * *
65785 GAAGTGGACCGAATCCATCTTCTTGATGAGATAAAGAAAAGTGGATTAAATTAATGAAGTGATCA
66 GAAGTGGACCAAATCCATCTTCTTGATGAGATACAGAGAAGTGGATTAAATCAATGAGGTGGTCA
* *
65850 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGAGAGTGAAACT
131 TCTTCCTGATGAGATATAGAGAAGTAAACCAAATCAATGAAG-AAAGCTCAATGAGAGTGAAACT
65915 TCCAAACCCCATCT
195 TCCAAACCCCATCT
* * *
65929 T-TTAGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGATCATCTTCCTGATGAGATACAG
1 TCCT-GATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGGTTATCTTCCTGATGAGATACAG
* ** * ** * *
65993 AAAAGCAGACCAAATTCGCCTTCTTGATGAGATACTGAGAAGTGGATTAAATCAATGAGGCGGTC
65 AGAAGTGGACCAAATCCATCTTCTTGATGAGATACAGAGAAGTGGATTAAATCAATGAGGTGGTC
* * * * * * *
66058 ATTTTCCTGAT-AAAAATAGAGAAATAAACTAAATCAATGAAGAGAAGCTCAAAT-ACGAATGAG
130 ATCTTCCTGATGAGATATAGAGAAGTAAACCAAATCAATGAAGA-AAGCTC-AATGA-GAGTGAA
*
66121 ACTT-CAAACACCATCT
192 ACTTCCAAACCCCATCT
* * * *
66137 TCCTGATGAAATACAGAGAAA-TGGGTCAAA-CAATGAAGTGGTTATCTTCCTGATGAGATACAA
1 TCCTGATGAGATACAGA-AAAGTGGGTCAAAGCAATAAAGCGGTTATCTTCCTGATGAGATACAG
66200 AGAAGTGGACCAA
65 AGAAGTGGACCAA
66213 GATATGAAGC
Statistics
Matches: 424, Mismatches: 59, Indels: 24
0.84 0.12 0.05
Matches are distributed among these distances:
207 39 0.09
208 66 0.16
209 173 0.41
210 5 0.01
211 101 0.24
212 40 0.09
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (208 bp):
TCCTGATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGGTTATCTTCCTGATGAGATACAGA
GAAGTGGACCAAATCCATCTTCTTGATGAGATACAGAGAAGTGGATTAAATCAATGAGGTGGTCA
TCTTCCTGATGAGATATAGAGAAGTAAACCAAATCAATGAAGAAAGCTCAATGAGAGTGAAACTT
CCAAACCCCATCT
Found at i:66550 original size:14 final size:15
Alignment explanation
Indices: 66528--66561 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
66518 AATATTTAAC
*
66528 ACAAAGTCCAA-ATT
1 ACAATGTCCAAGATT
66542 ACAATGTCCAAGATT
1 ACAATGTCCAAGATT
66557 ACAAT
1 ACAAT
66562 ATAGCCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.24
Consensus pattern (15 bp):
ACAATGTCCAAGATT
Found at i:68195 original size:28 final size:29
Alignment explanation
Indices: 68156--68344 Score: 119
Period size: 30 Copynumber: 6.4 Consensus size: 29
68146 TGATCCTAAC
* *
68156 CTTTTCAAAAACACATTTCGACCCCCAAA
1 CTTTTCAAAATCACATTTCAACCCCCAAA
* * * *
68185 CTTTTCCAAA-CACATTTCGACCCTCGAA
1 CTTTTCAAAATCACATTTCAACCCCCAAA
* * *
68213 CTCTTACAAAATTACATTTCAACCCCTAAA
1 CT-TTTCAAAATCACATTTCAACCCCCAAA
* * *
68243 CTTTTTCAAAATTACATTTTAACCCCTAAA
1 C-TTTTCAAAATCACATTTCAACCCCCAAA
* * ** *
68273 CTTTTCCAAAATTACCTTTTGACCCCTAAA
1 CTTTT-CAAAATCACATTTCAACCCCCAAA
* * * * *
68303 CTTCTCCAAAATTATATTTTAACCCTCAAA
1 CTT-TTCAAAATCACATTTCAACCCCCAAA
*
68333 CTTCTCCAAAAT
1 CTT-TTCAAAAT
68345 TATATTTTGA
Statistics
Matches: 135, Mismatches: 20, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
28 18 0.13
29 19 0.14
30 96 0.71
31 2 0.01
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (29 bp):
CTTTTCAAAATCACATTTCAACCCCCAAA
Found at i:68298 original size:60 final size:60
Alignment explanation
Indices: 68168--68413 Score: 254
Period size: 60 Copynumber: 4.2 Consensus size: 60
68158 TTTCAAAAAC
* * * ** * * *
68168 ACATTTCGACCCCCAAACTTTTCC-AAA-CACATTTCGACCCTCGAACTCTTACAAAATT
1 ACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTCAAACTTTTCCAAAATT
** *
68226 ACATTTCAACCCCTAAACTTTTTCAAAATTACATTTTAACCC-CTAAACTTTTCCAAAATT
1 ACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTC-AAACTTTTCCAAAATT
* * * *
68286 ACCTTTTGACCCCTAAACTTCTCCAAAATTATATTTTAACCCTCAAACTTCTCCAAAATT
1 ACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTCAAACTTTTCCAAAATT
* * * * *
68346 ATATTTTGA-CCCTAAAC-TTCCCAAAATTACACTTT--CTCTCAAACTTTTCCAAACTT
1 ACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTCAAACTTTTCCAAAATT
68402 ACATTTTGACCC
1 ACATTTTGACCC
68414 TGTGTTCTCT
Statistics
Matches: 157, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
56 26 0.17
57 2 0.01
58 35 0.22
59 12 0.08
60 81 0.52
61 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.34
Consensus pattern (60 bp):
ACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCTCAAACTTTTCCAAAATT
Found at i:68334 original size:30 final size:31
Alignment explanation
Indices: 68219--68414 Score: 196
Period size: 30 Copynumber: 6.6 Consensus size: 31
68209 CGAACTCTTA
* * *
68219 CAAAATTACATTTCAACCC-CTAAACTTTTT
1 CAAAATTACATTTTAACCCTCTAAACTTCTC
*
68249 CAAAATTACATTTTAACCC-CTAAACTTTTC
1 CAAAATTACATTTTAACCCTCTAAACTTCTC
* *
68279 CAAAATTACCTTTTGACCC-CTAAACTTCTC
1 CAAAATTACATTTTAACCCTCTAAACTTCTC
*
68309 CAAAATTATATTTTAACCCTC-AAACTTCTC
1 CAAAATTACATTTTAACCCTCTAAACTTCTC
* *
68339 CAAAATTATATTTTGA-CC-CTAAACTTC-C
1 CAAAATTACATTTTAACCCTCTAAACTTCTC
* * *
68367 CAAAATTACACTTT--CTCTC-AAACTTTTC
1 CAAAATTACATTTTAACCCTCTAAACTTCTC
* *
68395 CAAACTTACATTTTGACCCT
1 CAAAATTACATTTTAACCCT
68415 GTGTTCTCTA
Statistics
Matches: 143, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
27 7 0.05
28 28 0.20
29 9 0.06
30 98 0.69
31 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (31 bp):
CAAAATTACATTTTAACCCTCTAAACTTCTC
Found at i:71599 original size:28 final size:29
Alignment explanation
Indices: 71575--71763 Score: 160
Period size: 29 Copynumber: 6.5 Consensus size: 29
71565 TCAAAAATAG
*
71575 AATTTTGGAAAGTTTGAGGGTAAAATGGT
1 AATTTTGGAAAGTTCGAGGGTAAAATGGT
**
71604 AATTTTTGGTGAAA--TCGAGGCCAAAAATGG-
1 AA-TTTT-G-GAAAGTTCGAGG-GTAAAATGGT
* *
71634 AATTTTGGAAACTTCGAGGGTAAAACGGT
1 AATTTTGGAAAGTTCGAGGGTAAAATGGT
* *
71663 AATTTTTGGTGAAA--TCAAGGTTAAAAATGG-
1 AA-TTTT-G-GAAAGTTCGAGGGT-AAAATGGT
*
71693 AATTTTGGAAAGTTC-AGGTGTAAAATTGT
1 AATTTTGGAAAGTTCGAGG-GTAAAATGGT
*
71722 AATTTTGGAAAGTTCGGGGGT-AAATGGT
1 AATTTTGGAAAGTTCGAGGGTAAAATGGT
71750 AATTTTGGAAAGTT
1 AATTTTGGAAAGTT
71764 TAGGGGTAAA
Statistics
Matches: 131, Mismatches: 13, Indels: 33
0.74 0.07 0.19
Matches are distributed among these distances:
27 8 0.06
28 37 0.28
29 38 0.29
30 25 0.19
31 15 0.11
32 8 0.06
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (29 bp):
AATTTTGGAAAGTTCGAGGGTAAAATGGT
Found at i:71638 original size:30 final size:30
Alignment explanation
Indices: 71538--71698 Score: 99
Period size: 30 Copynumber: 5.5 Consensus size: 30
71528 ATCCAGGGGT
*
71538 AAAATGGTAATTTTTGGTGGAA-CGAGGTCA
1 AAAATGGTAATTTTTGGTGAAATCGAGG-CA
* * **
71568 AAAATAG-AA-TTTT-G-GAAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGTGAAA--TCGAGGCA
71596 AAAATGGTAATTTTTGGTGAAATCGAGGCCA
1 AAAATGGTAATTTTTGGTGAAATCGAGG-CA
**
71627 AAAATGG-AA-TTTT-G-GAAACTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAA--TCGAGGCA
* * *
71655 AAAACGGTAATTTTTGGTGAAATCAAGGTTA
1 AAAATGGTAATTTTTGGTGAAATCGAGG-CA
71686 AAAATGG-AATTTT
1 AAAATGGTAATTTT
71699 GGAAAGTTCA
Statistics
Matches: 100, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
26 3 0.03
27 5 0.05
28 17 0.17
29 20 0.20
30 32 0.32
31 15 0.15
32 8 0.08
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGCA
Found at i:71643 original size:59 final size:59
Alignment explanation
Indices: 71534--71727 Score: 275
Period size: 59 Copynumber: 3.3 Consensus size: 59
71524 AGACATCCAG
* *
71534 GGGTAAAATGGTAATTTTTGGTGGAA-CGAGGTCAAAAATAGAATTTTGGAAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTGA
* * *
71592 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGCCAAAAATGGAATTTTGGAAACTTCGA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTGA
* * * *
71651 GGGTAAAACGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAAAG-TTCA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTGA
*
71709 GGTGTAAAATTGTAATTTT
1 GG-GTAAAATGGTAATTTT
71728 GGAAAGTTCG
Statistics
Matches: 120, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
58 29 0.24
59 91 0.76
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTGA
Found at i:71769 original size:28 final size:28
Alignment explanation
Indices: 71687--71773 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
71677 TCAAGGTTAA
*
71687 AAATGG-AATTTTGGAAAGTTCAGGTGT
1 AAATGGTAATTTTGGAAAGTTCAGGGGT
* *
71714 AAAATTGTAATTTTGGAAAGTTCGGGGGT
1 -AAATGGTAATTTTGGAAAGTTCAGGGGT
*
71743 AAATGGTAATTTTGGAAAGTTTAGGGGT
1 AAATGGTAATTTTGGAAAGTTCAGGGGT
71771 AAA
1 AAA
71774 AAGATAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 33 0.63
29 19 0.37
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.33
Consensus pattern (28 bp):
AAATGGTAATTTTGGAAAGTTCAGGGGT
Found at i:71782 original size:29 final size:28
Alignment explanation
Indices: 71686--71784 Score: 119
Period size: 29 Copynumber: 3.5 Consensus size: 28
71676 ATCAAGGTTA
* *
71686 AAAATGGAATTTTGGAAAGTTCAGGTGT
1 AAAATGTAATTTTGGAAAGTTCAGGGGT
*
71714 AAAATTGTAATTTTGGAAAGTTCGGGGGT
1 AAAA-TGTAATTTTGGAAAGTTCAGGGGT
*
71743 -AAATGGTAATTTTGGAAAGTTTAGGGGT
1 AAAAT-GTAATTTTGGAAAGTTCAGGGGT
*
71771 AAAAAGATAATTTT
1 AAAATG-TAATTTT
71785 TAGGGAGTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
27 1 0.02
28 29 0.48
29 31 0.51
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAGTTCAGGGGT
Found at i:71822 original size:29 final size:29
Alignment explanation
Indices: 71766--71822 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
71756 GGAAAGTTTA
* **
71766 GGGGTAAAAAGATAATTTTTAGGGAGTTC
1 GGGGTAAAAAGATAATTTCTAGACAGTTC
* *
71795 GGGGTCAAAATATAATTTCTAGACAGTT
1 GGGGTAAAAAGATAATTTCTAGACAGTT
71823 TAGGGACCTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (29 bp):
GGGGTAAAAAGATAATTTCTAGACAGTTC
Found at i:77239 original size:20 final size:20
Alignment explanation
Indices: 77216--77261 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
77206 AATTGCTTGT
77216 TGATGCTGCTCGATGATGCC
1 TGATGCTGCTCGATGATGCC
* * *
77236 TGATGTTGCTCGATGCTGGC
1 TGATGCTGCTCGATGATGCC
77256 TGATGC
1 TGATGC
77262 AGTTGGCTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.33
Consensus pattern (20 bp):
TGATGCTGCTCGATGATGCC
Found at i:84977 original size:40 final size:38
Alignment explanation
Indices: 84922--85022 Score: 107
Period size: 40 Copynumber: 2.6 Consensus size: 38
84912 TGGTAACCTC
* *
84922 AAATTTTATATATATATATAAATAAAATTAAATACGCAAA
1 AAATTATATATATATATATAAAT--AATGAAATACGCAAA
*
84962 AAATTATATATATATATAT--ATAATGAAATAGGCAAA
1 AAATTATATATATATATATAAATAATGAAATACGCAAA
* *
84998 AAAGATATTTTATATATATATAAAT
1 AAA-TTA-TATATATATATATAAAT
85023 TTTACCGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
36 16 0.31
37 2 0.04
38 14 0.27
40 20 0.38
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (38 bp):
AAATTATATATATATATATAAATAATGAAATACGCAAA
Found at i:85012 original size:36 final size:36
Alignment explanation
Indices: 84929--85020 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 36
84919 CTCAAATTTT
* * *
84929 ATATATATATATAAATAAAATTAAATACGCAAAAAA
1 ATATATATATATATATATAATGAAATACGCAAAAAA
* *
84965 TTATATATATATATATATAATGAAATAGGCAAAAAA
1 ATATATATATATATATATAATGAAATACGCAAAAAA
*
85001 GATAT-TTTATATATATATAA
1 -ATATATATATATATATATAA
85021 ATTTTACCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 45 0.94
37 3 0.06
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (36 bp):
ATATATATATATATATATAATGAAATACGCAAAAAA
Done.