Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009335.1 Kokia drynarioides strain JFW-HI SEQ_124042, 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: 44614
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:19 original size:14 final size:14
Alignment explanation
Indices: 1--27 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1 AAAAAAAAAGAAAA
1 AAAAAAAAAGAAAA
15 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
28 GAATAGAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAA
Found at i:2820 original size:17 final size:17
Alignment explanation
Indices: 2800--2834 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2790 AATAATACTT
2800 TATGTTATATTTATATA
1 TATGTTATATTTATATA
*
2817 TATGTTCTATTTATATA
1 TATGTTATATTTATATA
2834 T
1 T
2835 GCACAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (17 bp):
TATGTTATATTTATATA
Found at i:6600 original size:4 final size:4
Alignment explanation
Indices: 6591--6749 Score: 138
Period size: 4 Copynumber: 39.0 Consensus size: 4
6581 TTAGAAATAT
* * *
6591 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTA ATTA ATTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * * *
6640 GTTA TTTA TTTA TTTTA TTTA GTTA ATTA ATTA ATTA ATTA TTTT TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * *
6689 TTTTA TTTA GTTA TTTA TTTA CTTA TTTA CTTA CTTA TTTA CTTA GTTA
1 -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
6738 TTTA TTTT TTTA
1 TTTA TTTA TTTA
6750 CATCACAAAA
Statistics
Matches: 131, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
4 119 0.91
5 12 0.09
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:6648 original size:41 final size:41
Alignment explanation
Indices: 6591--6729 Score: 178
Period size: 41 Copynumber: 3.5 Consensus size: 41
6581 TTAGAAATAT
*
6591 TTTATTTATTTATTTATTTATTTTATTTAGTTAATTAATTA
1 TTTATTTAATTATTTATTTATTTTATTTAGTTAATTAATTA
*
6632 TTTATTTAGTTATTTATTTATTTTATTTAGTTAATTAATTA
1 TTTATTTAATTATTTATTTATTTTATTTAGTTAATTAATTA
* * *
6673 ---A-TTAATTATTTTTTTATTTTATTTAGTTATTTATTTA
1 TTTATTTAATTATTTATTTATTTTATTTAGTTAATTAATTA
* * *
6710 CTTATTTACTTACTTATTTA
1 TTTATTTAATTATTTATTTA
6730 CTTAGTTATT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
37 32 0.37
38 1 0.01
40 1 0.01
41 52 0.60
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (41 bp):
TTTATTTAATTATTTATTTATTTTATTTAGTTAATTAATTA
Found at i:8826 original size:12 final size:11
Alignment explanation
Indices: 8789--8952 Score: 66
Period size: 12 Copynumber: 14.5 Consensus size: 11
8779 AACGCATAAA
*
8789 AAAATAACACC
1 AAAATAACAAC
*
8800 CAAATAAC-A-
1 AAAATAACAAC
8809 AAAATAACAATC
1 AAAATAACAA-C
*
8821 AAAATAGCAAC
1 AAAATAACAAC
8832 AAAAATAACAAC
1 -AAAATAACAAC
** *
8844 AAAAATAGTAGC
1 -AAAATAACAAC
* *
8856 AAAAACAATATA-
1 -AAAATAACA-AC
8868 AAAATAACAAC
1 AAAATAACAAC
* *
8879 AAAAGTAGCACC
1 AAAA-TAACAAC
* *
8891 AAAACAATAA-
1 AAAATAACAAC
*
8901 AAAATAGCAATC
1 AAAATAACAA-C
*
8913 AAAACAACAAC
1 AAAATAACAAC
* *
8924 AAAAAAACATC
1 AAAATAACAAC
* *
8935 AGAAACAACAAA
1 A-AAATAACAAC
8947 AAAATA
1 AAAATA
8953 GTAATATATT
Statistics
Matches: 113, Mismatches: 30, Indels: 20
0.69 0.18 0.12
Matches are distributed among these distances:
9 7 0.06
10 9 0.08
11 36 0.32
12 61 0.54
ACGTcount: A:0.68, C:0.17, G:0.04, T:0.10
Consensus pattern (11 bp):
AAAATAACAAC
Found at i:8850 original size:45 final size:46
Alignment explanation
Indices: 8820--8932 Score: 90
Period size: 47 Copynumber: 2.5 Consensus size: 46
8810 AAATAACAAT
* * *
8820 CAAAATAGCAACAAAAATAACAACAAAAATAGTAGCAAAAACAA-TAT
1 CAAAATAACAACAAAAATAACAACAAAAATA-TA-CAAAAATAACAAT
* * * * *
8867 AAAAATAACAACAAAAGTAGCACCAAAACA-ATA-AAAAATAGCAAT
1 CAAAATAACAACAAAAATAACAACAAAA-ATATACAAAAATAACAAT
*
8912 CAAAACAACAACAAAAA-AACA
1 CAAAATAACAACAAAAATAACA
8933 TCAGAAACAA
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
44 9 0.17
45 16 0.31
46 2 0.04
47 24 0.46
48 1 0.02
ACGTcount: A:0.68, C:0.17, G:0.05, T:0.10
Consensus pattern (46 bp):
CAAAATAACAACAAAAATAACAACAAAAATATACAAAAATAACAAT
Found at i:8855 original size:27 final size:24
Alignment explanation
Indices: 8805--8882 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
8795 ACACCCAAAT
8805 AACAAAAATAACAATCAAAATAGC
1 AACAAAAATAACAATCAAAATAGC
*
8829 AACAAAAATAACAA-CAAAAATAGT
1 AACAAAAATAACAATC-AAAATAGC
* * * * *
8853 AGCAAAAACAA-TATAAAAATAAC
1 AACAAAAATAACAATCAAAATAGC
8876 AACAAAA
1 AACAAAA
8883 GTAGCACCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
23 14 0.32
24 30 0.68
ACGTcount: A:0.71, C:0.14, G:0.04, T:0.12
Consensus pattern (24 bp):
AACAAAAATAACAATCAAAATAGC
Found at i:8871 original size:35 final size:33
Alignment explanation
Indices: 8832--8916 Score: 107
Period size: 35 Copynumber: 2.5 Consensus size: 33
8822 AAATAGCAAC
*
8832 AAAAATAACAACAAAAATAGTAGCAAAAACAATA
1 AAAAATAACAACAAAAATAGCA-CAAAAACAATA
* *
8866 TAAAAATAACAACAAAAGTAGCACCAAAACAATA
1 -AAAAATAACAACAAAAATAGCACAAAAACAATA
*
8900 AAAAATAGCAATCAAAA
1 AAAAATAACAA-CAAAA
8917 CAACAACAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 10 0.22
34 15 0.33
35 20 0.44
ACGTcount: A:0.68, C:0.14, G:0.06, T:0.12
Consensus pattern (33 bp):
AAAAATAACAACAAAAATAGCACAAAAACAATA
Found at i:8908 original size:21 final size:22
Alignment explanation
Indices: 8879--8919 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
8869 AAATAACAAC
*
8879 AAAAGTAGC-ACCAAAACAATA
1 AAAAATAGCAACCAAAACAATA
*
8900 AAAAATAGCAATCAAAACAA
1 AAAAATAGCAACCAAAACAA
8920 CAACAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.66, C:0.17, G:0.07, T:0.10
Consensus pattern (22 bp):
AAAAATAGCAACCAAAACAATA
Found at i:8916 original size:34 final size:32
Alignment explanation
Indices: 8832--8916 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 32
8822 AAATAGCAAC
8832 AAAAATAACAACAAAAATAGTAGCAAAAACAATAT
1 AAAAATAACAAC--AAA-AGTAGCAAAAACAATAT
8867 AAAAATAACAACAAAAGTAGCACCAAAACAATA-
1 AAAAATAACAACAAAAGTAGCA--AAAACAATAT
*
8900 AAAAATAGCAATCAAAA
1 AAAAATAACAA-CAAAA
8917 CAACAACAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
32 7 0.15
33 13 0.28
34 14 0.30
35 12 0.26
ACGTcount: A:0.68, C:0.14, G:0.06, T:0.12
Consensus pattern (32 bp):
AAAAATAACAACAAAAGTAGCAAAAACAATAT
Found at i:8927 original size:33 final size:34
Alignment explanation
Indices: 8857--8927 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
8847 AATAGTAGCA
* * *
8857 AAAACAATATAAAAATAACAACAAAAGTAGCACC
1 AAAACAATATAAAAATAACAACAAAAGCAACAAC
*
8891 AAAACAATA-AAAAATAGCAATCAAAA-CAACAAC
1 AAAACAATATAAAAATAACAA-CAAAAGCAACAAC
8924 AAAA
1 AAAA
8928 AAACATCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 18 0.56
34 14 0.44
ACGTcount: A:0.69, C:0.17, G:0.04, T:0.10
Consensus pattern (34 bp):
AAAACAATATAAAAATAACAACAAAAGCAACAAC
Found at i:10079 original size:23 final size:23
Alignment explanation
Indices: 10049--10177 Score: 143
Period size: 23 Copynumber: 5.5 Consensus size: 23
10039 GCTGGACAAT
*
10049 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACAAAGTGCTAAAC
* *
10072 AGAGAGCACACAAAGTACTAATC
1 AGAGAGCACACAAAGTGCTAAAC
*
10095 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAAAC
* * *
10118 AGAGAGCACATACAGTGTTAATAAC
1 AGAGAGCACACAAAGTGCT-A-AAC
*
10143 AGAGAGCACA-AGACGTGCTAAAC
1 AGAGAGCACACA-AAGTGCTAAAC
*
10166 AGAGAGCGCACA
1 AGAGAGCACACA
10178 GTGTTCCTTA
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
23 70 0.78
24 4 0.04
25 16 0.18
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAAAC
Found at i:10081 original size:48 final size:44
Alignment explanation
Indices: 10003--10181 Score: 121
Period size: 46 Copynumber: 3.9 Consensus size: 44
9993 CGGAACAAAC
* * *
10003 AGAGAGTAC-CAAAGTACT-AACAAAGAGCACATAGGTGCTGGACAAT
1 AGAGAGCACACAAAGTGCTAAACAGAGAGCACATA-GTG-T--ACAAT
* * **
10049 AGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
1 AGAGAGCACACAAAGTGCTAAACAGAGAGCACATAGTGTAC-AAT
* * *
10094 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACATACAGTGTTAATAAC
1 -AGAGAGCACACAAAGTGCTAAACAGAGAGCACAT--AGTG-T-ACAAT
* * *
10143 AGAGAGCACA-AGACGTGCTAAACAGAGAGCGCACAGTGT
1 AGAGAGCACACA-AAGTGCTAAACAGAGAGCACATAGTGT
10182 TCCTTAATGA
Statistics
Matches: 106, Mismatches: 18, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
44 2 0.02
45 4 0.04
46 44 0.42
47 9 0.08
48 43 0.41
49 3 0.03
50 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (44 bp):
AGAGAGCACACAAAGTGCTAAACAGAGAGCACATAGTGTACAAT
Found at i:10122 original size:69 final size:68
Alignment explanation
Indices: 9999--10152 Score: 170
Period size: 69 Copynumber: 2.2 Consensus size: 68
9989 TATACGGAAC
* * *
9999 AAACAGAGAGTAC-CAAAGTACTAACAAAGAGCACATAGGTGCTGGACAATAGAGAGCACACACA
1 AAACAGAGAGCACACAAAGTACTAACAAAGAGCACAAAAGTGCT-G--AATAGAGAGCACACACA
10063 GTGCT-
63 GTGCTA
* *
10068 AAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACATACA
1 AAACAGAGAGCACACAAAGTACTAA-CAAAGAGCACA-AAAGTGCTGAAT-AGAGAGCACACACA
*
10132 GTGTTA
63 GTGCTA
10138 ATAACAGAGAGCACA
1 A-AACAGAGAGCACA
10153 AGACGTGCTA
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
68 3 0.04
69 29 0.40
70 12 0.16
71 23 0.32
72 6 0.08
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.13
Consensus pattern (68 bp):
AAACAGAGAGCACACAAAGTACTAACAAAGAGCACAAAAGTGCTGAATAGAGAGCACACACAGTG
CTA
Found at i:11913 original size:16 final size:16
Alignment explanation
Indices: 11892--11929 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
11882 TTATTGAAAA
*
11892 TAAATTTAACAATATT
1 TAAATTTAACAAAATT
11908 TAAA-TTAACAAAATT
1 TAAATTTAACAAAATT
11923 TAAATTT
1 TAAATTT
11930 TCGTATTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTAACAAAATT
Found at i:12134 original size:9 final size:9
Alignment explanation
Indices: 12111--12161 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
12101 ATTTGAGTGT
*
12111 TTGAAAGAG
1 TTGAGAGAG
*
12120 TCGAGAGAG
1 TTGAGAGAG
*
12129 TTGAGAGAA
1 TTGAGAGAG
12138 TTGAGAGAG
1 TTGAGAGAG
12147 TTAGGAGAGAG
1 TT--GAGAGAG
12158 TTGA
1 TTGA
12162 ATGAAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 26 0.74
11 9 0.26
ACGTcount: A:0.37, C:0.02, G:0.39, T:0.22
Consensus pattern (9 bp):
TTGAGAGAG
Found at i:13358 original size:19 final size:19
Alignment explanation
Indices: 13321--13366 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
13311 TATTTAAGAG
13321 TCTATTTA--AAAATAAAA
1 TCTATTTATTAAAATAAAA
13338 TCTATTATATTAAAA-AAAA
1 TCTATT-TATTAAAATAAAA
13357 TCTATTTATT
1 TCTATTTATT
13367 TAGGCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.23
18 6 0.23
19 10 0.38
20 4 0.15
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (19 bp):
TCTATTTATTAAAATAAAA
Found at i:16609 original size:24 final size:24
Alignment explanation
Indices: 16593--16661 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
16583 AGTTTGACTC
16593 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
16617 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
16641 AAATAATTAAACAGAGTTTAA
1 AAACAAATAAACAGAGTTTAA
16662 CTAAAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.28
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:16669 original size:24 final size:24
Alignment explanation
Indices: 16581--16663 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
16571 TAGACTAATA
* *
16581 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
16605 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* * *
16629 AGAGTTTAATTGAAATAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
16653 AGAGTTTAACT
1 AGAGTTTAACT
16664 AAAATATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:16990 original size:50 final size:50
Alignment explanation
Indices: 16936--17037 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
16926 GAGAACCTCT
16936 CTTCAACGAAATAATCATACATTTTCCCTCCTATGACCAAGCTGCCTTTG
1 CTTCAACGAAATAATCATACATTTTCCCTCCTATGACCAAGCTGCCTTTG
* *
16986 CTTCAACGAAATAGTCATACATTTTCCCTCTTATGACCAAGCTGCCTTTG
1 CTTCAACGAAATAATCATACATTTTCCCTCCTATGACCAAGCTGCCTTTG
17036 CT
1 CT
17038 CCAAACGAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (50 bp):
CTTCAACGAAATAATCATACATTTTCCCTCCTATGACCAAGCTGCCTTTG
Found at i:17643 original size:14 final size:14
Alignment explanation
Indices: 17607--17634 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17597 TTACAATAGC
17607 GACATCTTTTGTCT
1 GACATCTTTTGTCT
17621 GACATCTTTTGTCT
1 GACATCTTTTGTCT
17635 CGCTTCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GACATCTTTTGTCT
Found at i:18708 original size:24 final size:24
Alignment explanation
Indices: 18649--18710 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
18639 TAGACTAATA
* *
18649 AGAGTTTGATTCAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
18673 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAATTGAAACAAATAAAC
18697 AGAGTTTAATTGAA
1 AGAGTTTAATTGAA
18711 TGATTATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:23739 original size:41 final size:41
Alignment explanation
Indices: 23677--23759 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
23667 CAATTGTTGC
* *
23677 ATATCCTTGAGAGAAAAATGATAAGTTTGAGTTGAAATTTA
1 ATATCCTCGAGAGAAAAATGATAAGTTTGAGCTGAAATTTA
**
23718 ATATCCTCGAGAGAAGGATGATAAGTTTGAGCTGAAATTTA
1 ATATCCTCGAGAGAAAAATGATAAGTTTGAGCTGAAATTTA
23759 A
1 A
23760 GCTTTCATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (41 bp):
ATATCCTCGAGAGAAAAATGATAAGTTTGAGCTGAAATTTA
Found at i:24686 original size:13 final size:13
Alignment explanation
Indices: 24668--24692 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24658 TAGATTGGAT
24668 TTGATTATGTAAA
1 TTGATTATGTAAA
24681 TTGATTATGTAA
1 TTGATTATGTAA
24693 TCTTCTAAAT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:25294 original size:3 final size:3
Alignment explanation
Indices: 25282--25315 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
25272 GTTTTGATGC
25282 TAT T-T TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25316 ATAACTCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:42830 original size:96 final size:95
Alignment explanation
Indices: 42646--42837 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 95
42636 TCTTTGGGAA
* * *
42646 AAGGATATTCGATTATCTTGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAGTATTTCA
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATCGCACCTAGTAAGGTAAGGCACAATATTTCA
*
42711 GAATCAAATATAAGGAAACATTGCCTCGATT
66 GAATCAAATAAAAGG-AACATTGCCTCGATT
* * *
42742 AAGGGTATTCGATTAT-TTCGATTTGAGGAAAAATTGCACCTAGTAAGGTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATCTT-GATTTGAAGAAAAATCGCACCTAGTAAGGTAAGGCACAATA-TTT
* *
42805 CGGAACTCGAAATAAAAGG-ATATTGCCTCGATT
64 CAGAA-TC-AAATAAAAGGAACATTGCCTCGATT
42838 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
95 3 0.04
96 69 0.83
97 2 0.02
98 9 0.11
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.29
Consensus pattern (95 bp):
AAGGATATTCGATTATCTTGATTTGAAGAAAAATCGCACCTAGTAAGGTAAGGCACAATATTTCA
GAATCAAATAAAAGGAACATTGCCTCGATT
Found at i:43339 original size:117 final size:117
Alignment explanation
Indices: 43169--43548 Score: 579
Period size: 117 Copynumber: 3.2 Consensus size: 117
43159 GTCTTCGGAC
* * * * * *
43169 GTTCGGGAGTAAAATAGTAATTTTAAGG-TGTTTCGGGGTCGAAAA-GGTGATTTTTAGG-AGTT
1 GTTCGGGGGTAAAATGGTAATTTT-TGGAAGGTTCGGGGTCAAAAATGG-GATTTTT-GGAAGTT
43231 CGGGGGTAAAATGGTAA-TTTTGGAAGGTTCAGGGTCAAAAGTGGGATTTTTGGAA
63 CGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAA-TGGGATTTTTGGAA
* * *
43286 GTTCGAGGGTAAAATGGTAACTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGG
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
43351 GGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAATGGGATTTTTGGAA
66 GGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAATGGGATTTTTGGAA
* *
43403 GTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
*
43468 GGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTAAAAAATGGGATTTTTGGAA
66 GGGTAAAATGGTAATTTTTGGAAGGTTCAGGGT-CAAAATGGGATTTTTGGAA
43521 GTTCGGGGGTAAAATGGTAATTTTTGGA
1 GTTCGGGGGTAAAATGGTAATTTTTGGA
43549 CAGTCTGGGG
Statistics
Matches: 242, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
116 4 0.02
117 168 0.69
118 70 0.29
ACGTcount: A:0.28, C:0.04, G:0.34, T:0.33
Consensus pattern (117 bp):
GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG
GGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAATGGGATTTTTGGAA
Found at i:43430 original size:176 final size:176
Alignment explanation
Indices: 43169--43548 Score: 563
Period size: 176 Copynumber: 2.2 Consensus size: 176
43159 GTCTTCGGAC
* * * * * *
43169 GTTCGGGAGTAAAATAGTAATTTTAAGG-TGTTTCGGGGTCGAAAAGGTGATTTTTAGGAGTTCG
1 GTTCGGGGGTAAAATGGTAATTTT-TGGAAGGTTCAGGGTCGAAAAGGTGATTTTTAGGAGTTCG
*
43233 GGGGTAAAATGGTAATTTTGGAAGGTTCAGGGTCAAAAGTGGGATTTTTGGAAGTTCGAGGGTAA
65 GGGGTAAAATGGTAATTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
*
43298 AATGGTAACTTTTGGAAGGTTC-GAGGTCAAAAATGGGATTTTTGGAA
130 AATGGTAACTTTTGGAAGGTTCAG-GGTAAAAAATGGGATTTTTGGAA
*
43345 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTC-AAAATGG-GATTTTT-GGAAGTTT
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCGAAAA-GGTGATTTTTAGG-AGTTC
** *
43407 GGGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
64 GGGGGTAAAATGGTAA-TTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
*
43472 AAAATGGTAATTTTTGGAAGGTTCAGGGTAAAAAATGGGATTTTTGGAA
128 AAAATGGTAACTTTTGGAAGGTTCAGGGTAAAAAATGGGATTTTTGGAA
43521 GTTCGGGGGTAAAATGGTAATTTTTGGA
1 GTTCGGGGGTAAAATGGTAATTTTTGGA
43549 CAGTCTGGGG
Statistics
Matches: 186, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
174 2 0.01
175 33 0.18
176 150 0.81
177 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.34, T:0.33
Consensus pattern (176 bp):
GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCGAAAAGGTGATTTTTAGGAGTTCGG
GGGTAAAATGGTAATTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAA
ATGGTAACTTTTGGAAGGTTCAGGGTAAAAAATGGGATTTTTGGAA
Found at i:43545 original size:59 final size:59
Alignment explanation
Indices: 43169--43548 Score: 556
Period size: 59 Copynumber: 6.5 Consensus size: 59
43159 GTCTTCGGAC
* * * * * * *
43169 GTTCGGGAGTAAAATAGTAATTTTAAGG-TGTTTCGGGGTCGAAAA-GGTGATTTTTAGG-A
1 GTTCGGGGGTAAAATGGTAATTTT-TGGAAGGTTCAGGGTCAAAAATGG-GATTTTT-GGAA
*
43228 GTTCGGGGGTAAAATGGTAA-TTTTGGAAGGTTCAGGGTCAAAAGTGGGATTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAA
* *
43286 GTTCGAGGGTAAAATGGTAACTTTTGGAAGGTTC-GAGGTCAAAAATGGGATTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAG-GGTCAAAAATGGGATTTTTGGAA
43345 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTC-AAAATGGGATTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAA
* **
43403 GTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAA
*
43462 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTAAAAAATGGGATTTTTGGAA
1 GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAA
43521 GTTCGGGGGTAAAATGGTAATTTTTGGA
1 GTTCGGGGGTAAAATGGTAATTTTTGGA
43549 CAGTCTGGGG
Statistics
Matches: 295, Mismatches: 19, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
57 4 0.01
58 98 0.33
59 192 0.65
60 1 0.00
ACGTcount: A:0.28, C:0.04, G:0.34, T:0.33
Consensus pattern (59 bp):
GTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAA
Found at i:43546 original size:29 final size:29
Alignment explanation
Indices: 43210--43548 Score: 326
Period size: 29 Copynumber: 11.6 Consensus size: 29
43200 TTCGGGGTCG
*
43210 AAAA-GGTGATTTTTAGG-AGTTCGGGGGT
1 AAAATGGTAATTTTT-GGAAGTTCGGGGGT
*
43238 AAAATGGTAA-TTTTGGAAGGTTC-AGGGT
1 AAAATGGTAATTTTTGGAA-GTTCGGGGGT
* *
43266 CAAAAGTGG-GATTTTTGGAAGTTCGAGGGT
1 -AAAA-TGGTAATTTTTGGAAGTTCGGGGGT
* *
43296 AAAATGGTAACTTTTGGAAGGTTC-GAGGT
1 AAAATGGTAATTTTTGGAA-GTTCGGGGGT
*
43325 CAAAAATGG-GATTTTTGGAAGTTCGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTCGGGGGT
*
43355 AAAATGGTAATTTTTGGAAGGTTC-AGGGT
1 AAAATGGTAATTTTTGGAA-GTTCGGGGGT
* *
43384 CAAAATGG-GATTTTTGGAAGTTTGGGGGT
1 -AAAATGGTAATTTTTGGAAGTTCGGGGGT
*
43413 AAAATGGTAATTTTTGGAAGGTT-TGGGGT
1 AAAATGGTAATTTTTGGAA-GTTCGGGGGT
*
43442 CAAAAATGG-GATTTTTGGAAGTTCGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTCGGGGGT
*
43472 AAAATGGTAATTTTTGGAAGGTTC-AGGGT
1 AAAATGGTAATTTTTGGAA-GTTCGGGGGT
*
43501 AAAAAATGG-GATTTTTGGAAGTTCGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTCGGGGGT
43531 AAAATGGTAATTTTTGGA
1 AAAATGGTAATTTTTGGA
43549 CAGTCTGGGG
Statistics
Matches: 260, Mismatches: 24, Indels: 53
0.77 0.07 0.16
Matches are distributed among these distances:
27 2 0.01
28 47 0.18
29 110 0.42
30 80 0.31
31 21 0.08
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTCGGGGGT
Found at i:43558 original size:29 final size:28
Alignment explanation
Indices: 43169--43548 Score: 319
Period size: 29 Copynumber: 13.0 Consensus size: 28
43159 GTCTTCGGAC
* * *
43169 GTTCGGGAGTAAAATAGTAATTTTAAGG-T
1 GTTCGGG-GTAAAATGGTAATTTT-TGGAA
*
43198 GTTTCGGGGTCGAAAA-GGTGATTTTTAGG-A
1 G-TTCGGGGT--AAAATGGTAATTTTT-GGAA
43228 GTTCGGGGGTAAAATGGTAA-TTTTGGAA
1 GTTC-GGGGTAAAATGGTAATTTTTGGAA
* *
43256 GGTTCAGGGTCAAAAGTGG-GATTTTTGGAA
1 -GTTCGGGGT-AAAA-TGGTAATTTTTGGAA
*
43286 GTTCGAGGGTAAAATGGTAACTTTTGGAA
1 GTTCG-GGGTAAAATGGTAATTTTTGGAA
* *
43315 GGTTCGAGGTCAAAAATGG-GATTTTTGGAA
1 -GTTCGGGGT--AAAATGGTAATTTTTGGAA
43345 GTTCGGGGGTAAAATGGTAATTTTTGGAA
1 GTTC-GGGGTAAAATGGTAATTTTTGGAA
* *
43374 GGTTCAGGGTCAAAATGG-GATTTTTGGAA
1 -GTTCGGGGT-AAAATGGTAATTTTTGGAA
*
43403 GTTTGGGGGTAAAATGGTAATTTTTGGAA
1 G-TTCGGGGTAAAATGGTAATTTTTGGAA
* *
43432 GGTTTGGGGTCAAAAATGG-GATTTTTGGAA
1 -GTTCGGGGT--AAAATGGTAATTTTTGGAA
43462 GTTCGGGGGTAAAATGGTAATTTTTGGAA
1 GTTC-GGGGTAAAATGGTAATTTTTGGAA
* *
43491 GGTTCAGGGTAAAAAATGG-GATTTTTGGAA
1 -GTTCGGGGT--AAAATGGTAATTTTTGGAA
43521 GTTCGGGGGTAAAATGGTAATTTTTGGA
1 GTTC-GGGGTAAAATGGTAATTTTTGGA
43549 CAGTCTGGGG
Statistics
Matches: 291, Mismatches: 28, Indels: 64
0.76 0.07 0.17
Matches are distributed among these distances:
27 2 0.01
28 45 0.15
29 120 0.41
30 99 0.34
31 25 0.09
ACGTcount: A:0.28, C:0.04, G:0.34, T:0.33
Consensus pattern (28 bp):
GTTCGGGGTAAAATGGTAATTTTTGGAA
Done.