Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000381.1 Kokia drynarioides strain JFW-HI SEQ_111181, 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: 119051
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:692 original size:41 final size:41
Alignment explanation
Indices: 620--863 Score: 188
Period size: 41 Copynumber: 6.0 Consensus size: 41
610 TTTGCGGCAT
* * * *
620 TTTTCACATAAGCGCCACTAATGCACCGACCTTTAGCGGCG-
1 TTTT-ACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * * **
661 TTTGTTCATAAGCACCGCTATTGTTCTGACCTTTAGAAGCGC
1 TTT-TACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * * * *
703 TTTCACATAAGCGCCACTATTACTCTGACCTTTAGTGGC-A
1 TTTTACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * * *
743 TTTTCACATAAGCGCTGCTATTGCTCTGACATTTAGTGGTGC
1 TTTT-ACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * *
785 TTTTCCAAAAGCGCCGCTATTGCTCTGACCTTTAGCGGTGC
1 TTTTACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
*** * * * *
826 TTGCCCATAAGTGTCGCTATTGATCT-ACCTTTTGCGGC
1 TTTTACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGC
864 ATTTATGTAA
Statistics
Matches: 161, Mismatches: 38, Indels: 9
0.77 0.18 0.04
Matches are distributed among these distances:
40 13 0.08
41 140 0.87
42 8 0.05
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (41 bp):
TTTTACATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
Found at i:763 original size:82 final size:83
Alignment explanation
Indices: 620--822 Score: 232
Period size: 82 Copynumber: 2.5 Consensus size: 83
610 TTTGCGGCAT
* * * * * *
620 TTTTCACATAAGCGCCACTAATGCACCGACCTTTAGCGGCGTTTGTTCATAAGCACCGCTATTGT
1 TTTTCACATAAGCGCCACTATTGCTCTGACCTTTAGCGGCATTTGTACATAAGCACCGCTATTGC
*
685 TCTGACCTTTAGAAGCGC
66 TCTGACATTTAGAAGCGC
* * * *
703 -TTTCACATAAGCGCCACTATTACTCTGACCTTTAGTGGCATTT-TCACATAAGCGCTGCTATTG
1 TTTTCACATAAGCGCCACTATTGCTCTGACCTTTAGCGGCATTTGT-ACATAAGCACCGCTATTG
** *
766 CTCTGACATTTAGTGGTGC
65 CTCTGACATTTAGAAGCGC
* *
785 TTTTC-CAAAAGCGCCGCTATTGCTCTGACCTTTAGCGG
1 TTTTCACATAAGCGCCACTATTGCTCTGACCTTTAGCGG
823 TGCTTGCCCA
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
81 1 0.01
82 95 0.95
83 4 0.04
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (83 bp):
TTTTCACATAAGCGCCACTATTGCTCTGACCTTTAGCGGCATTTGTACATAAGCACCGCTATTGC
TCTGACATTTAGAAGCGC
Found at i:3073 original size:26 final size:25
Alignment explanation
Indices: 3017--3074 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
3007 AGCATTACGC
* *
3017 CCAGAATTGTCGTTGCAGGAACCTG
1 CCAGAATTATCGTTGCAGGAACATG
* *
3042 CTCAGAATTATCGTTGCATGAATATG
1 C-CAGAATTATCGTTGCAGGAACATG
3068 TCCAGAA
1 -CCAGAA
3075 GTGTTGCCGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 25 0.93
27 1 0.04
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (25 bp):
CCAGAATTATCGTTGCAGGAACATG
Found at i:4822 original size:22 final size:24
Alignment explanation
Indices: 4775--4822 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
4765 AAAAAGTCAA
4775 TTTTGAAAAGCCCAATTTGAGTTG
1 TTTTGAAAAGCCCAATTTGAGTTG
*
4799 TTTTTAAAA-CCCAATTT-AGTTG
1 TTTTGAAAAGCCCAATTTGAGTTG
4821 TT
1 TT
4823 ATTTTCAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.30
23 8 0.35
24 8 0.35
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (24 bp):
TTTTGAAAAGCCCAATTTGAGTTG
Found at i:4827 original size:24 final size:26
Alignment explanation
Indices: 4774--4827 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 26
4764 AAAAAAGTCA
4774 ATTTTGAAAAGCCCAATTTGAGTTGT
1 ATTTTGAAAAGCCCAATTTGAGTTGT
4800 -TTTT-AAAA-CCCAATTT-AGTTGTT
1 ATTTTGAAAAGCCCAATTTGAGTTG-T
4823 ATTTT
1 ATTTT
4828 CAAAGGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 5 0.19
23 9 0.35
24 8 0.31
25 4 0.15
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (26 bp):
ATTTTGAAAAGCCCAATTTGAGTTGT
Found at i:5914 original size:12 final size:12
Alignment explanation
Indices: 5899--5945 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
5889 TTCATTTTTT
5899 TTAAAATTTTAA
1 TTAAAATTTTAA
5911 TTAAAATTTTAA
1 TTAAAATTTTAA
* *
5923 -AAAAATTTAAA
1 TTAAAATTTTAA
*
5934 TTCAAATTTTAA
1 TTAAAATTTTAA
5946 ATTTAGTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
TTAAAATTTTAA
Found at i:5920 original size:23 final size:23
Alignment explanation
Indices: 5901--5946 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5891 CATTTTTTTT
*
5901 AAAATTTTAATTAAAATTTTAAA
1 AAAATTTAAATTAAAATTTTAAA
*
5924 AAAATTTAAATTCAAATTTTAAA
1 AAAATTTAAATTAAAATTTTAAA
5947 TTTAGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATTTAAATTAAAATTTTAAA
Found at i:11259 original size:22 final size:24
Alignment explanation
Indices: 11225--11270 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
11215 AAAATATATA
11225 AAAATATTAAAATAAATTTG-AATT
1 AAAATATTAAAAT-AATTTGTAATT
11249 AAAATA-T-AAATAATTTGTAATT
1 AAAATATTAAAATAATTTGTAATT
11271 TTTTAAAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.29
22 8 0.38
23 1 0.05
24 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
AAAATATTAAAATAATTTGTAATT
Found at i:21058 original size:3 final size:3
Alignment explanation
Indices: 21050--21074 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21040 TGCACTTAAG
21050 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
21075 AACACTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:23508 original size:25 final size:25
Alignment explanation
Indices: 23480--23533 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
23470 CTAAACAATG
* *
23480 AAATAACACAAATTGAAATAAAACC
1 AAATAAAACAAAGTGAAATAAAACC
** *
23505 AAATAAAATGAAGTGAAATAAAATC
1 AAATAAAACAAAGTGAAATAAAACC
23530 AAAT
1 AAAT
23534 GCAATAAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.65, C:0.09, G:0.07, T:0.19
Consensus pattern (25 bp):
AAATAAAACAAAGTGAAATAAAACC
Found at i:25196 original size:37 final size:37
Alignment explanation
Indices: 25155--25229 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
25145 TGTTGGAGTA
*
25155 AGGGTTGTTGTTGCAATTGAAGTTGCTTATTTAACAC
1 AGGGTTGTTGTTGCAATTGAAGTTGCTTATATAACAC
25192 AGGGTTGTTGTTGCAATTGAAGTTGCTTATATAACAC
1 AGGGTTGTTGTTGCAATTGAAGTTGCTTATATAACAC
25229 A
1 A
25230 CTGATTCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.39
Consensus pattern (37 bp):
AGGGTTGTTGTTGCAATTGAAGTTGCTTATATAACAC
Found at i:26341 original size:15 final size:15
Alignment explanation
Indices: 26321--26351 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
26311 AATTGCCTAT
26321 CCCTAGCAACGACAC
1 CCCTAGCAACGACAC
26336 CCCTAGCAACGACAC
1 CCCTAGCAACGACAC
26351 C
1 C
26352 AAAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.48, G:0.13, T:0.06
Consensus pattern (15 bp):
CCCTAGCAACGACAC
Found at i:33629 original size:40 final size:40
Alignment explanation
Indices: 33574--33652 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
33564 ATTGAGCCTT
* *
33574 GTGCCTAGCAGGCTTCCTGTCGGTGTATTTATCGGGCTTA
1 GTGCCTAGCAGGCTTCCTGTCAGTGTATTTATCAGGCTTA
* *
33614 GTGCCTAGTAGGCTTCGTGTCAGTGTATTTATCAGGCTT
1 GTGCCTAGCAGGCTTCCTGTCAGTGTATTTATCAGGCTT
33653 CGTGTCGACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.14, C:0.20, G:0.29, T:0.37
Consensus pattern (40 bp):
GTGCCTAGCAGGCTTCCTGTCAGTGTATTTATCAGGCTTA
Found at i:38009 original size:16 final size:16
Alignment explanation
Indices: 37985--38029 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
37975 TAAAAGAAAC
37985 AAAATTAAAAATAAAAG
1 AAAA-TAAAAATAAAAG
*
38002 AAAATAAAATTAAAAG
1 AAAATAAAAATAAAAG
38018 -AAATAGAAAATA
1 AAAATA-AAAATA
38030 GGGAAGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.18
Consensus pattern (16 bp):
AAAATAAAAATAAAAG
Found at i:38010 original size:22 final size:22
Alignment explanation
Indices: 37970--38029 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
37960 CGGTCTAAGG
*
37970 AAAAATAAAAG-AAACAAAATT
1 AAAAATAAAAGAAAATAAAATT
37991 AAAAATAAAAGAAAATAAAATT
1 AAAAATAAAAGAAAATAAAATT
*
38013 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
38030 GGGAAGTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAAAATT
Found at i:38852 original size:19 final size:19
Alignment explanation
Indices: 38828--38870 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
38818 AAACATAAAT
38828 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
38847 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
38866 TAAAT
1 TAAAT
38871 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:41460 original size:21 final size:21
Alignment explanation
Indices: 41434--41473 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41424 ATAGATGCCT
*
41434 CAGTTTTCTTTTGAAAATCCA
1 CAGTTTGCTTTTGAAAATCCA
41455 CAGTTTGCTTTTGAAAATC
1 CAGTTTGCTTTTGAAAATC
41474 TATAAATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCCA
Found at i:41483 original size:21 final size:21
Alignment explanation
Indices: 41441--41484 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41431 CCTCAGTTTT
**
41441 CTTTTGAAAATCCACAGTTTG
1 CTTTTGAAAATCCACAAATTG
* *
41462 CTTTTGAAAATCTATAAATTG
1 CTTTTGAAAATCCACAAATTG
41483 CT
1 CT
41485 GCTAAAATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (21 bp):
CTTTTGAAAATCCACAAATTG
Found at i:42806 original size:21 final size:22
Alignment explanation
Indices: 42782--42828 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
42772 TGATCTAAGG
42782 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
42803 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
42825 AAAA
1 AAAA
42829 GAAATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:42839 original size:22 final size:21
Alignment explanation
Indices: 42782--42843 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 21
42772 TGATCTAAGG
42782 AAAAATAAAAGAAATAGAATTAA
1 AAAAAT-AAA-AAATAGAATTAA
42805 AAATAA-AAGAAAATAGAATTAA
1 AAA-AATAA-AAAATAGAATTAA
42827 AAGAAATAAAAAATAGA
1 AA-AAATAAAAAATAGA
42844 GGTCGAAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
22 26 0.74
23 7 0.20
24 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAAATAGAATTAA
Found at i:43647 original size:19 final size:19
Alignment explanation
Indices: 43623--43665 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
43613 AAACATAAAT
43623 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
43642 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
43661 TAAAT
1 TAAAT
43666 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:45469 original size:54 final size:54
Alignment explanation
Indices: 45387--45489 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
45377 TTTGTATTAC
*
45387 AAATCCATATATGCAAATAGATTTTCAAAGCAGTTGGCAAGTTGAAACAAGAGT
1 AAATCCATATAAGCAAATAGATTTTCAAAGCAGTTGGCAAGTTGAAACAAGAGT
45441 AAATCCATATAAGCAAATAGATTTTCAAAGCAGTTGGCAAGTTGAAACA
1 AAATCCATATAAGCAAATAGATTTTCAAAGCAGTTGGCAAGTTGAAACA
45490 GGAGCAATTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (54 bp):
AAATCCATATAAGCAAATAGATTTTCAAAGCAGTTGGCAAGTTGAAACAAGAGT
Found at i:45782 original size:12 final size:12
Alignment explanation
Indices: 45757--45816 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
45747 AGTTATAACC
*
45757 TAATAAATATTAT
1 TAAT-AATAATAT
45770 TAATAATAATAT
1 TAATAATAATAT
* * *
45782 TATTAATAACAG
1 TAATAATAATAT
45794 TAATAATGAAT-T
1 TAATAAT-AATAT
*
45806 TACTAATAATA
1 TAATAATAATA
45817 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
11 3 0.08
12 28 0.76
13 6 0.16
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:45782 original size:15 final size:16
Alignment explanation
Indices: 45757--45790 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
45747 AGTTATAACC
45757 TAATAAATATTATTAA
1 TAATAAATATTATTAA
45773 TAAT-AATATTATTAA
1 TAATAAATATTATTAA
45788 TAA
1 TAA
45791 CAGTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAAATATTATTAA
Found at i:45830 original size:24 final size:23
Alignment explanation
Indices: 45803--45848 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
45793 GTAATAATGA
* *
45803 ATTTACTAATAATAATAAATAAAT
1 ATTTAATAATAAAAAT-AATAAAT
*
45827 ATTTAATATTAAAAATAATAAA
1 ATTTAATAATAAAAATAATAAA
45849 AATAAAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTTAATAATAAAAATAATAAAT
Found at i:46947 original size:30 final size:29
Alignment explanation
Indices: 46872--47043 Score: 159
Period size: 29 Copynumber: 5.8 Consensus size: 29
46862 CCCTAGAGAT
* *
46872 CCCCAAACTATCCAAAAATTATATTTTTAC
1 CCCCGAACT-TCCAAAAATTACATTTTTAC
* *
46902 CCCCGAACTTCCAAAAACTCCATTTTTGAC
1 CCCCGAACTTCCAAAAATTACATTTTT-AC
*
46932 CCCCAAACCTT-CAAAAATTACATTTTTAC
1 CCCCGAA-CTTCCAAAAATTACATTTTTAC
*
46961 CCCCGAACTTCCAAAAATTTCATTTTTTA-
1 CCCCGAACTTCCAAAAATTACA-TTTTTAC
* * * *
46990 TCTCGAAACATCCAAAAATTATATTTTTAC
1 CCCCG-AACTTCCAAAAATTACATTTTTAC
** * *
47020 CCTTGAACCTCCAAAAATTTCATT
1 CCCCGAACTTCCAAAAATTACATT
47044 ATTAACCTAA
Statistics
Matches: 117, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
28 3 0.03
29 58 0.50
30 53 0.45
31 3 0.03
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCCGAACTTCCAAAAATTACATTTTTAC
Found at i:46965 original size:59 final size:58
Alignment explanation
Indices: 46884--47165 Score: 232
Period size: 59 Copynumber: 4.8 Consensus size: 58
46874 CCAAACTATC
* * * *
46884 CAAAAATTATATTTTTACCCCCGAACTTCCAAAAACTCCATTTTTGACCCCCAAACCTT
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT-ACCCCAAAACCTT
* * * * * * *
46943 CAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTTCATTTTTTATCTCGAAACATC
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTTACCCCAAAACCTT
* * * * * ** *
47002 CAAAAATTATATTTTTACCCTTGAACCTCCAAAAATTTCATTATTAACCTAAAAACTTT
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATT-TTTACCCCAAAACCTT
* * * *
47061 CAAAAATTACCA-TTTTACCCTC-AAATATCAAAAAACTCCATTTTTAACCCTAAAA-CTCT
1 CAAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTT-ACCCCAAAACCT-T
*
47120 CAAAAATTACCA-TTTTATCCTCGAA-TGTCCAAAAATTCCATTTTTA
1 CAAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTA
47166 TCTCGATTTT
Statistics
Matches: 183, Mismatches: 33, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
58 8 0.04
59 167 0.91
60 8 0.04
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (58 bp):
CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCCCAAAACCTT
Found at i:47125 original size:30 final size:31
Alignment explanation
Indices: 47031--47135 Score: 96
Period size: 30 Copynumber: 3.5 Consensus size: 31
47021 CTTGAACCTC
* * *
47031 CAAAAATT-TCATTATTAA-CCTAAAAACTTT
1 CAAAAATTACCATTTTTAACCCT-AAAACTAT
*
47061 CAAAAATTACCA-TTTT-ACCCTCAAA-TAT
1 CAAAAATTACCATTTTTAACCCTAAAACTAT
* *
47089 CAAAAAACT-CCATTTTTAACCCTAAAACTCT
1 C-AAAAATTACCATTTTTAACCCTAAAACTAT
47120 CAAAAATTACCATTTT
1 CAAAAATTACCATTTT
47136 ATCCTCGAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
28 6 0.10
29 14 0.23
30 28 0.47
31 12 0.20
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (31 bp):
CAAAAATTACCATTTTTAACCCTAAAACTAT
Found at i:47167 original size:29 final size:28
Alignment explanation
Indices: 46882--47165 Score: 135
Period size: 29 Copynumber: 9.7 Consensus size: 28
46872 CCCCAAACTA
** *
46882 TCCAAAAATTATATTTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCTCGAA-T
* * *
46911 TCCAAAAACTCCATTTTTGACCCCCAAACCT
1 TCCAAAAATTCCATTTTT-ACCCTCGAA--T
* *
46942 T-CAAAAATTACATTTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCTCGAA-T
* * *
46970 TCCAAAAATTTCATTTTTTA-TCTCGAAACA
1 TCCAAAAATTCCA-TTTTTACCCTCG-AA-T
** * *
47000 TCCAAAAATTATATTTTTACCCTTGAACC
1 TCCAAAAATTCCATTTTTACCCTCGAA-T
* * * **
47029 TCCAAAAATTTCATTATTAACCTAAAAACT
1 TCCAAAAATTCCATTTTTACCCT-CGAA-T
* *
47059 TTCAAAAATTACCA-TTTTACCCTCAAAT
1 TCCAAAAATT-CCATTTTTACCCTCGAAT
* * ** *
47087 ATCAAAAAACTCCATTTTTAACCCTAAAAC
1 -TCCAAAAATTCCATTTTT-ACCCTCGAAT
*
47117 TCTCAAAAATTACCA-TTTTATCCTCGAAT
1 TC-CAAAAATT-CCATTTTTACCCTCGAAT
47146 GTCCAAAAATTCCATTTTTA
1 -TCCAAAAATTCCATTTTTA
47166 TCTCGATTTT
Statistics
Matches: 201, Mismatches: 39, Indels: 30
0.74 0.14 0.11
Matches are distributed among these distances:
28 10 0.05
29 99 0.49
30 84 0.42
31 8 0.04
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (28 bp):
TCCAAAAATTCCATTTTTACCCTCGAAT
Found at i:59071 original size:115 final size:114
Alignment explanation
Indices: 58897--59103 Score: 297
Period size: 115 Copynumber: 1.8 Consensus size: 114
58887 CGCTCAACGC
* * * ** *
58897 GAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAATGG
1 GAGCAAATATTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCAATAAAA-GG
*
58962 TTTGCTTCCTCATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGT
65 TTAGCTTCCTCATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGT
*
59012 GAGCAAATATTCGAATCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCAATAAAAGGT
1 GAGCAAATATTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCAATAAAAGGT
** **
59077 TAGCTTCCTGGTGAGATATTGAGAAGT
66 TAGCTTCCTCATGAGATACAGAGAAGT
59104 GGACCAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
114 25 0.31
115 55 0.69
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (114 bp):
GAGCAAATATTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCAATAAAAGGT
TAGCTTCCTCATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGT
Found at i:59367 original size:206 final size:205
Alignment explanation
Indices: 59003--59603 Score: 873
Period size: 206 Copynumber: 2.9 Consensus size: 205
58993 CCAACTCAGG
* * * * * *
59003 GCTCGATGTGAGCAAATATTCGAATCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCA
1 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAAGTCGAAGCA
* * *
59068 ATAAAA-GGTTAGCTTCCTGGTGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* *
59132 TAGAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
131 CAGAGAAGCGGATTGAAA-AAAGGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
59197 ATCAAACCCAC
195 ATCAAACCCAC
* *
59208 GCTTGATATGAGCAAATCTTCGAACCCCAGCTTTCTAATGAGATACTAAGAAGCAAGTCGAAGCA
1 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAAGTCGAAGCA
59273 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* * * *
59338 CAGAGAAGCGAATTGAAATAAAGGATGCGGTCATCTTTCTAATGAGATACTGAGAAGAAGACTAA
131 CAGAGAAGCGGATTGAAA-AAAGGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
59403 ATCAAACCCAC
195 ATCAAACCCAC
* * * *
59414 GCTCGATATGAGAAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCATGTTGAAGCA
1 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAAGTCGAAGCA
* * * *
59479 ATAAGATGATTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGACA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
* * * ** *
59544 CAAAGAAGTGGA-TCAAAACAAGTGATATGGTCGTCTTCCTGATGAGATACTGAGAAGAAG
131 CAGAGAAGCGGATTGAAAA-AAG-GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAG
59604 GTCAAGTCAA
Statistics
Matches: 356, Mismatches: 37, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
204 1 0.00
205 70 0.20
206 285 0.80
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (205 bp):
GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAAGTCGAAGCA
ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
CAGAGAAGCGGATTGAAAAAAGGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
TCAAACCCAC
Found at i:59979 original size:22 final size:22
Alignment explanation
Indices: 59951--59992 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
59941 AAGCTTTGAT
59951 TTTAAAATTAGGTTTAAATTGG
1 TTTAAAATTAGGTTTAAATTGG
**
59973 TTTAAAATTATTTTTAAATT
1 TTTAAAATTAGGTTTAAATT
59993 TAAATTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTAAAATTAGGTTTAAATTGG
Found at i:59980 original size:11 final size:12
Alignment explanation
Indices: 59951--59982 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
59941 AAGCTTTGAT
59951 TTTAAAATTAGG
1 TTTAAAATTAGG
59963 TTT-AAATT-GG
1 TTTAAAATTAGG
59973 TTTAAAATTA
1 TTTAAAATTA
59983 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.28
11 10 0.56
12 3 0.17
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (12 bp):
TTTAAAATTAGG
Found at i:59996 original size:6 final size:6
Alignment explanation
Indices: 59985--60018 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
59975 TAAAATTATT
*
59985 TTTAAA TTTAAA TTT-GA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
60019 TCAAATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:60916 original size:29 final size:30
Alignment explanation
Indices: 60862--60977 Score: 100
Period size: 30 Copynumber: 3.9 Consensus size: 30
60852 AATATTATCC
* * *
60862 ATTTTTGCCCTTAAACTGTCCAAAAATTAT
1 ATTTTTACCCCTAAACTGTCTAAAAATTAT
*
60892 ATTTTTACCCCTAAACT-TCTAAAAATTAC
1 ATTTTTACCCCTAAACTGTCTAAAAATTAT
60921 ATTTTTGA-CCCTAAAAC--TCTAAAAATT-T
1 ATTTTT-ACCCCT-AAACTGTCTAAAAATTAT
* *
60949 ACCATTTTACCCCCAAA-TGTCTAAAAATT
1 A--TTTTTACCCCTAAACTGTCTAAAAATT
60978 CCATTTTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.01
29 34 0.47
30 37 0.51
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (30 bp):
ATTTTTACCCCTAAACTGTCTAAAAATTAT
Found at i:60925 original size:59 final size:58
Alignment explanation
Indices: 60861--60985 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 58
60851 AAATATTATC
* * *
60861 CATTTTTG-CCCTTAAACTGTCCAAAAATTATA-TTTTTACCCCTAAACT-TCTAAAAATTA
1 CATTTTTGACCCTAAAAC--TCCAAAAATT-TACATTTTACCCCCAAA-TGTCTAAAAATTA
* *
60920 CATTTTTGACCCTAAAACTCTAAAAATTTACCATTTTACCCCCAAATGTCTAAAAATTC
1 CATTTTTGACCCTAAAACTCCAAAAATTTA-CATTTTACCCCCAAATGTCTAAAAATTA
60979 CATTTTT
1 CATTTTT
60986 TATCTCGATT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
57 2 0.04
58 10 0.18
59 37 0.65
60 8 0.14
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.38
Consensus pattern (58 bp):
CATTTTTGACCCTAAAACTCCAAAAATTTACATTTTACCCCCAAATGTCTAAAAATTA
Found at i:60985 original size:29 final size:30
Alignment explanation
Indices: 60859--60985 Score: 113
Period size: 29 Copynumber: 4.3 Consensus size: 30
60849 ATAAATATTA
* * *
60859 TCCATTTTTGCCCTTAAACTGTCCAAAAAT
1 TCCATTTTTACCCCTAAACTGTCTAAAAAT
**
60889 TATATTTTTACCCCTAAACT-TCTAAAAAT
1 TCCATTTTTACCCCTAAACTGTCTAAAAAT
*
60918 TACATTTTTGA-CCCTAAAAC--TCTAAAAATT
1 TCCATTTTT-ACCCCT-AAACTGTCTAAAAA-T
*
60948 TACCA-TTTTACCCCCAAA-TGTCTAAAAAT
1 T-CCATTTTTACCCCTAAACTGTCTAAAAAT
60977 TCCATTTTT
1 TCCATTTTT
60986 TATCTCGATT
Statistics
Matches: 81, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
28 3 0.04
29 38 0.47
30 38 0.47
31 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
TCCATTTTTACCCCTAAACTGTCTAAAAAT
Found at i:60987 original size:30 final size:29
Alignment explanation
Indices: 60893--60987 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
60883 AAAAATTATA
*
60893 TTTTTACCCCTAAACTTCTAAAAATTACAT
1 TTTTTACCCCTAAA-TTCTAAAAATTCCAT
* *
60923 TTTTGA-CCCTAAAACTCTAAAAATTTACCA-
1 TTTTTACCCCT-AAATTCTAAAAA-TT-CCAT
*
60953 -TTTTACCCCCAAATGTCTAAAAATTCCAT
1 TTTTTACCCCTAAAT-TCTAAAAATTCCAT
60982 TTTTTA
1 TTTTTA
60988 TCTCGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
28 3 0.06
29 21 0.40
30 26 0.50
31 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (29 bp):
TTTTTACCCCTAAATTCTAAAAATTCCAT
Found at i:61076 original size:58 final size:59
Alignment explanation
Indices: 60939--61079 Score: 151
Period size: 58 Copynumber: 2.4 Consensus size: 59
60929 CCCTAAAACT
** * ** *
60939 CTAAAAATTTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTTTATCTCGATTTTT
1 CTAAAAA-TTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTAAACCTAAATTTTC
* * * *
60999 CTAAAAATTATCGTTTTACCCTCGAATGTCT-AAAATTCCATTTTAAACCCTAAATTTTC
1 CTAAAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTAAA-CCTAAATTTTC
*
61058 CT-AAAATTACCATATTACCCCC
1 CTAAAAATTACCATTTTACCCCC
61080 GAGAATCCAA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
58 30 0.45
59 29 0.44
60 7 0.11
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (59 bp):
CTAAAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTAAACCTAAATTTTC
Found at i:61110 original size:28 final size:28
Alignment explanation
Indices: 61060--61119 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
61050 AAATTTTCCT
61060 AAAATTACCATATTACCCCCGAGAATCC
1 AAAATTACCATATTACCCCCGAGAATCC
* * * * *
61088 AAAATTATCATTTTGCCCTCGAGTATCC
1 AAAATTACCATATTACCCCCGAGAATCC
61116 AAAA
1 AAAA
61120 AATCTCATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (28 bp):
AAAATTACCATATTACCCCCGAGAATCC
Found at i:63484 original size:2 final size:2
Alignment explanation
Indices: 63479--63505 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63469 TATATATATA
63479 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
63506 CTTGGATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:67855 original size:56 final size:57
Alignment explanation
Indices: 67721--67878 Score: 180
Period size: 56 Copynumber: 2.8 Consensus size: 57
67711 TCTATTATAT
* * *
67721 ATTA-TTA-TTTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGTTATTAA
1 ATTATTTATTTTTTATTAAATT-ATA-TTTAATAATAATCATATTAAGAATATGATTAA
* * * *
67777 ATTATATACTATTTTATTAAATTGTATTTAATAATAATCATGTTAA-AATATGATTAA
1 ATTATTTA-TTTTTTATTAAATTATATTTAATAATAATCATATTAAGAATATGATTAA
* *
67834 ATTATTTATTTTTTATTAAATTATATTTAACAATAATCTTATTAA
1 ATTATTTATTTTTTATTAAATTATATTTAATAATAATCATATTAA
67879 ATTTTAATAA
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
56 36 0.42
57 18 0.21
58 18 0.21
59 9 0.11
60 4 0.05
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (57 bp):
ATTATTTATTTTTTATTAAATTATATTTAATAATAATCATATTAAGAATATGATTAA
Found at i:67875 original size:26 final size:25
Alignment explanation
Indices: 67846--67894 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
67836 TATTTATTTT
*
67846 TTATTAAATTATATTTAACAATAATC
1 TTATTAAATTATA-ATAACAATAATC
*
67872 TTATTAAATTTTAATAACAATAA
1 TTATTAAATTATAATAACAATAA
67895 CAATAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (25 bp):
TTATTAAATTATAATAACAATAATC
Found at i:69381 original size:18 final size:19
Alignment explanation
Indices: 69355--69391 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
69345 AGTTATTCTT
69355 ATGAATTATAAAAT-TATA
1 ATGAATTATAAAATATATA
*
69373 ATGATTTATAAAATATATA
1 ATGAATTATAAAATATATA
69392 TTTAATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
ATGAATTATAAAATATATA
Found at i:78440 original size:17 final size:19
Alignment explanation
Indices: 78404--78445 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
78394 TTTTTAAATC
*
78404 TATAAAATCAATAATATAA-
1 TATAAAAACAAT-ATATAAT
78423 TATAAAAACAAT-TATAAT
1 TATAAAAACAATATATAAT
78441 TATAA
1 TATAA
78446 TTATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 11 0.52
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
TATAAAAACAATATATAAT
Found at i:80785 original size:16 final size:16
Alignment explanation
Indices: 80764--80795 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
80754 ACAAAATAGT
80764 CCTTAGTATCTAAAGC
1 CCTTAGTATCTAAAGC
80780 CCTTAGTATCTAAAGC
1 CCTTAGTATCTAAAGC
80796 GTTACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (16 bp):
CCTTAGTATCTAAAGC
Found at i:91511 original size:79 final size:79
Alignment explanation
Indices: 91348--91495 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 79
91338 TACCATTAAC
* *
91348 AACA-AAAATTGAATAAATTCTGTTGAACGACACGAATAGAATCCTGAAATAGAATTGTTCAATT
1 AACAGAAAATTGAATAAATTCTGTTGAACGACACGAATAAAATCCTGAAATAGAATTATTCAATT
*
91412 GATTTCTATTTGCA
66 AATTTCTATTTGCA
* ** * *
91426 AACAGAAAATTGAATAAATTTTGTTGAACGGTAGGAATAAAATCGTGAAATAGAATTATTCAATT
1 AACAGAAAATTGAATAAATTCTGTTGAACGACACGAATAAAATCCTGAAATAGAATTATTCAATT
91491 AATTT
66 AATTT
91496 TTGTTCTCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
78 4 0.07
79 57 0.93
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (79 bp):
AACAGAAAATTGAATAAATTCTGTTGAACGACACGAATAAAATCCTGAAATAGAATTATTCAATT
AATTTCTATTTGCA
Found at i:92023 original size:24 final size:24
Alignment explanation
Indices: 91964--92024 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
91954 TTTGACTAAT
91964 AGAGCCATTAACGTCTATGAATTAA
1 AGAGCCATTAACGTC-ATGAATTAA
*
91989 A-ATCCAAATTAACGTC-TGAATTAA
1 AGAGCC--ATTAACGTCATGAATTAA
92013 AGGAGCCATTAA
1 A-GAGCCATTAA
92025 ATTCAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
24 17 0.57
25 1 0.03
26 12 0.40
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (24 bp):
AGAGCCATTAACGTCATGAATTAA
Found at i:96235 original size:52 final size:52
Alignment explanation
Indices: 95893--96228 Score: 437
Period size: 52 Copynumber: 6.5 Consensus size: 52
95883 ATTTCATTTA
* * * * ** * *
95893 ATACTCACAATGACTCATAGTTATCGGACCTCTTGTTC-CGTAAAGGAATCGT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCAC-TAAAGGATTCAT
* * * *
95945 ACACTCACGATTG-CACATAGTCATTGAACCTCATAATC-CGTAAAGGATTCGT
1 ATACTCACGA-TGACACATAGTCATCGGACCTCATAATCAC-TAAAGGATTCAT
* *
95997 ATACTCATGATGACACATAGTCATCGAACCTCATAATC-CGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCAC-TAAAGGATTCAT
* *
96049 ATACTCACGATGACACATAGTCATCGGACCTCATAATCAGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCACTAAAGGATTCAT
*
96101 ATACTCACGATGACACATAGTCATCGGACCTCATAATCAGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCACTAAAGGATTCAT
*
96153 ATACTCAAGATGACACATAGTCATCGGACCTCATAATCACTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCACTAAAGGATTCAT
*
96205 ATGCTCACGATGACACATAGTCAT
1 ATACTCACGATGACACATAGTCAT
96229 TAGACCTTTT
Statistics
Matches: 258, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
51 2 0.01
52 254 0.98
53 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCACTAAAGGATTCAT
Found at i:102839 original size:19 final size:17
Alignment explanation
Indices: 102817--102860 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
102807 AACTTGAGAT
*
102817 AGAAAAAAGTAAAAGGTAA
1 AGAAAAAA-TAAAA-GAAA
102836 AGAAAGAAATAAAAGAAA
1 AGAAA-AAATAAAAGAAA
102854 AGAAAAA
1 AGAAAAA
102861 GAGAGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 2 0.09
18 8 0.35
19 10 0.43
20 3 0.13
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (17 bp):
AGAAAAAATAAAAGAAA
Found at i:106319 original size:22 final size:22
Alignment explanation
Indices: 106301--106349 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
106291 ATTTGATGTG
106301 CTCTGCATCTGAATCTGATATC
1 CTCTGCATCTGAATCTGATATC
* * * *
106323 CTTTGCATCTGCATCTGTTATA
1 CTCTGCATCTGAATCTGATATC
106345 CTCTG
1 CTCTG
106350 TTCTATTTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (22 bp):
CTCTGCATCTGAATCTGATATC
Found at i:109607 original size:20 final size:20
Alignment explanation
Indices: 109564--109607 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
109554 ATGACACATA
109564 AATAATATAATTTTTTTATG
1 AATAATATAATTTTTTTATG
109584 AATAAGTAT-ATTATTTTTAT-
1 AATAA-TATAATT-TTTTTATG
109604 AATA
1 AATA
109608 TATCATGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
AATAATATAATTTTTTTATG
Found at i:112175 original size:16 final size:16
Alignment explanation
Indices: 112156--112221 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
112146 TGTTAATGTC
112156 ATAACTAATTAACATA
1 ATAACTAATTAACATA
112172 ATAACTAA-TAAC-TA
1 ATAACTAATTAACATA
*
112186 AT---T-ATTCAAAATA
1 ATAACTAATT-AACATA
*
112199 ATAATTAATTAACATA
1 ATAACTAATTAACATA
112215 ATTAACT
1 A-TAACT
112222 TTAGTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
10 1 0.03
11 2 0.05
12 2 0.05
13 4 0.10
14 4 0.10
15 4 0.10
16 15 0.38
17 7 0.18
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAACTAATTAACATA
Found at i:112476 original size:18 final size:16
Alignment explanation
Indices: 112445--112481 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
112435 CTAATAATTG
112445 TATTTTAAATTTTAAT
1 TATTTTAAATTTTAAT
112461 TATTATTAAATGTTTAAT
1 TATT-TTAAAT-TTTAAT
112479 TAT
1 TAT
112482 CACAACTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TATTTTAAATTTTAAT
Found at i:112497 original size:44 final size:44
Alignment explanation
Indices: 112449--112538 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
112439 TAATTGTATT
* * *
112449 TTAAATTTTAATTATTATTAAATGTTTAATTATCACAACTTCTA
1 TTAAATTATAATTATTATTAAATGTATAATTATCAAAACTTCTA
* *
112493 TTAAATTATATTTATTTTTAAATGTATAATTATCAAAACTTCTA
1 TTAAATTATAATTATTATTAAATGTATAATTATCAAAACTTCTA
112537 TT
1 TT
112539 TTATTTCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (44 bp):
TTAAATTATAATTATTATTAAATGTATAATTATCAAAACTTCTA
Found at i:112828 original size:20 final size:20
Alignment explanation
Indices: 112803--112843 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
112793 AAACTGAATG
112803 AAAATAAAATTAAAATATAA
1 AAAATAAAATTAAAATATAA
**
112823 AAAATAACTTTAAAATATAA
1 AAAATAAAATTAAAATATAA
112843 A
1 A
112844 TTCAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATAAAATTAAAATATAA
Found at i:118916 original size:18 final size:19
Alignment explanation
Indices: 118893--118928 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
118883 ATTATATAAT
118893 ATTTAAATATATA-ATTTA
1 ATTTAAATATATATATTTA
*
118911 ATTTAAATGTATATATTT
1 ATTTAAATATATATATTT
118929 TTTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTAAATATATATATTTA
Done.