Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009465.1 Kokia drynarioides strain JFW-HI SEQ_124172, 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: 42559
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--33 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 TA
3 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34 GAAAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2932 original size:10 final size:10
Alignment explanation
Indices: 2913--2965 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
2903 GGGAGGGATG
*
2913 GAGAGTGAAA
1 GAGAGAGAAA
2923 GAGAGAG-AA
1 GAGAGAGAAA
2932 -AGAGAGAAA
1 GAGAGAGAAA
*
2941 GAGAGAG--C
1 GAGAGAGAAA
*
2949 GAGAGATAAA
1 GAGAGAGAAA
2959 GAGAGAG
1 GAGAGAG
2966 CGAGAGCGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
8 12 0.35
9 4 0.12
10 18 0.53
ACGTcount: A:0.53, C:0.02, G:0.42, T:0.04
Consensus pattern (10 bp):
GAGAGAGAAA
Found at i:2966 original size:18 final size:18
Alignment explanation
Indices: 2913--2971 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
2903 GGGAGGGATG
* *
2913 GAGAGTGAAAGAGAGAGA
1 GAGAGAGAAAGAGAGAGC
*
2931 AAGAGAGAAAGAGAGAGC
1 GAGAGAGAAAGAGAGAGC
*
2949 GAGAGATAAAGAGAGAGC
1 GAGAGAGAAAGAGAGAGC
2967 GAGAG
1 GAGAG
2972 CGGGAAGGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.51, C:0.03, G:0.42, T:0.03
Consensus pattern (18 bp):
GAGAGAGAAAGAGAGAGC
Found at i:4294 original size:22 final size:22
Alignment explanation
Indices: 4268--4310 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4258 TCGACTTCCT
4268 TATTTTCTATTT-CTTTTAATTA
1 TATTTTCT-TTTACTTTTAATTA
*
4290 TATTTTCTTTTATTTTTAATT
1 TATTTTCTTTTACTTTTAATT
4311 TTGTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTA
Found at i:7766 original size:22 final size:22
Alignment explanation
Indices: 7740--7784 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
7730 ACTAAAATTT
7740 TAAGTAGATGCATAGAATTTAA
1 TAAGTAGATGCATAGAATTTAA
7762 TAAGTAGATGCATAGAATTTAA
1 TAAGTAGATGCATAGAATTTAA
7784 T
1 T
7785 CTTTTCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.33
Consensus pattern (22 bp):
TAAGTAGATGCATAGAATTTAA
Found at i:8222 original size:22 final size:22
Alignment explanation
Indices: 8196--8238 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8186 TCGACTTCCT
8196 TATTTTCTATTT-CTTTTAATTA
1 TATTTTCT-TTTACTTTTAATTA
*
8218 TATTTTCTTTTATTTTTAATT
1 TATTTTCTTTTACTTTTAATT
8239 TTGTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTA
Found at i:10677 original size:34 final size:34
Alignment explanation
Indices: 10639--10708 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
10629 CGACGAGTGG
*
10639 AAATGCAATAACAATGCAAATGTAGTGACAATTA
1 AAATGCAATAACAAAGCAAATGTAGTGACAATTA
* * * *
10673 AAATGCAATGACAAAGGAAATGTGGTGACAGTTA
1 AAATGCAATAACAAAGCAAATGTAGTGACAATTA
10707 AA
1 AA
10709 TTATAGCTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (34 bp):
AAATGCAATAACAAAGCAAATGTAGTGACAATTA
Found at i:10757 original size:12 final size:13
Alignment explanation
Indices: 10731--10763 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
10721 GATATGCATG
10731 AAAACTAAAACTA
1 AAAACTAAAACTA
*
10744 AAAACTTAAA-TA
1 AAAACTAAAACTA
10756 AAAACTAA
1 AAAACTAA
10764 CTCAATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAACTAAAACTA
Found at i:12817 original size:12 final size:11
Alignment explanation
Indices: 12796--12844 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
12786 AAATAAATGA
12796 AAAATG-AAAT
1 AAAATGAAAAT
*
12806 AAAACTAAAAAT
1 AAAA-TGAAAAT
12818 AAAAATGAAAAT
1 -AAAATGAAAAT
12830 GAAAATGAAAAT
1 -AAAATGAAAAT
12842 AAA
1 AAA
12845 TATATTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 4 0.12
11 4 0.12
12 21 0.64
13 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAATGAAAAT
Found at i:12820 original size:6 final size:6
Alignment explanation
Indices: 12802--12844 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
12792 ATGAAAAATG
* * * *
12802 AAATAA AACTAA AAATAA AAATGA AAATGA AAATGA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
12845 TATATTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:12822 original size:24 final size:24
Alignment explanation
Indices: 12790--12844 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
12780 TAATTAAAAT
12790 AAATGAAAAATG-AAAT-AAAACTAA
1 AAAT-AAAAATGAAAATGAAAA-TAA
*
12814 AAATAAAAATGAAAATGAAAATGA
1 AAATAAAAATGAAAATGAAAATAA
12838 AAATAAA
1 AAATAAA
12845 TATATTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.25
24 17 0.61
25 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (24 bp):
AAATAAAAATGAAAATGAAAATAA
Found at i:12823 original size:18 final size:17
Alignment explanation
Indices: 12785--12844 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
12775 CTACATAATT
12785 AAAAT-AAATGAAAAAT-
1 AAAATAAAAT-AAAAATA
*
12801 GAAATAAAACTAAAAATA
1 AAAATAAAA-TAAAAATA
* *
12819 AAAATGAAAATGAAAATG
1 AAAAT-AAAATAAAAATA
12837 AAAATAAA
1 AAAATAAA
12845 TATATTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 4 0.11
17 12 0.33
18 16 0.44
19 4 0.11
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:12868 original size:10 final size:10
Alignment explanation
Indices: 12853--12878 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12843 AATATATTAA
12853 TTTTTTTCAT
1 TTTTTTTCAT
12863 TTTTTTTCAT
1 TTTTTTTCAT
12873 TTTTTT
1 TTTTTT
12879 AAAAACATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCAT
Found at i:16466 original size:25 final size:23
Alignment explanation
Indices: 16437--16482 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
16427 GTTGGATTCA
16437 AATTAAACTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
16462 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
16483 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:16590 original size:16 final size:13
Alignment explanation
Indices: 16559--16591 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
16549 GTAATATAAT
16559 AATAATAATCCTA
1 AATAATAATCCTA
16572 AATAATAATCCTA
1 AATAATAATCCTA
*
16585 AAAAATA
1 AATAATA
16592 GAGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:18714 original size:3 final size:3
Alignment explanation
Indices: 18708--18734 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18698 ACTACTACTA
18708 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
18735 TGAGACTACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:19709 original size:42 final size:40
Alignment explanation
Indices: 19631--19728 Score: 124
Period size: 42 Copynumber: 2.4 Consensus size: 40
19621 TAATATATAC
* * * *
19631 GGAGAGTGAGAGTGAAGGAGAAAAGGGAGGAGGGAGGGAG
1 GGAGAGAGAGAGAGAGGGACAAAAGGGAGGAGGGAGGGAG
*
19671 GGAGAGAGAGAGAGAGGGACAAAGAGGGATGGATGGAGGGAG
1 GGAGAGAGAGAGAGAGGGACAAA-AGGGA-GGAGGGAGGGAG
*
19713 GGAGAGAGAAAGAGAG
1 GGAGAGAGAGAGAGAG
19729 AGAGATGGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 19 0.38
41 5 0.10
42 26 0.52
ACGTcount: A:0.40, C:0.01, G:0.55, T:0.04
Consensus pattern (40 bp):
GGAGAGAGAGAGAGAGGGACAAAAGGGAGGAGGGAGGGAG
Found at i:22778 original size:41 final size:41
Alignment explanation
Indices: 22716--22793 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
22706 GGCAAAAGGT
* *
22716 TAATATATATGGAGAGTGAGAGATTAGATGAAGATTACTGC
1 TAATATATATGGAGAGGGAGAGATTAAATGAAGATTACTGC
22757 TAATATATATGGAGAGGGAGAGATTAAATGAAGATTA
1 TAATATATATGGAGAGGGAGAGATTAAATGAAGATTA
22794 GATACACCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.42, C:0.03, G:0.27, T:0.28
Consensus pattern (41 bp):
TAATATATATGGAGAGGGAGAGATTAAATGAAGATTACTGC
Found at i:26086 original size:41 final size:41
Alignment explanation
Indices: 26041--26132 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 41
26031 TAGTGAGAGG
* *
26041 GTGAGAGATTAGATGAAGACTATGATTAATATATATGAAGA
1 GTGAGAGAGTAGATGAAGACTATGACTAATATATATGAAGA
*
26082 GTGAGAGAGTAGATGAAGACTATGACTAATATATATGGAGA
1 GTGAGAGAGTAGATGAAGACTATGACTAATATATATGAAGA
*
26123 GTCAGAGAGT
1 GTGAGAGAGT
26133 GAAAGATTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.41, C:0.04, G:0.28, T:0.26
Consensus pattern (41 bp):
GTGAGAGAGTAGATGAAGACTATGACTAATATATATGAAGA
Found at i:27420 original size:49 final size:50
Alignment explanation
Indices: 27349--27521 Score: 205
Period size: 49 Copynumber: 3.5 Consensus size: 50
27339 AATATATATG
* * *
27349 GAGAGTGAGAGAATAGAA-GAAGATTATGATTAACATATATGGAGAGTGA
1 GAGAGTGTGAGATTAGAATGAAGACTATGATTAACATATATGGAGAGTGA
* * *
27398 GAGAGTGTGCGATTCG-ATGAAGACTATGATTAATATATATGGAGAGTGA
1 GAGAGTGTGAGATTAGAATGAAGACTATGATTAACATATATGGAGAGTGA
*
27447 GAGAGTGTGAGATTAGAAT-AAGACTATGATT-ACTATATATGGAGAGTGC
1 GAGAGTGTGAGATTAGAATGAAGACTATGATTAAC-ATATATGGAGAGTGA
* *
27496 GAG-GCTGAGAGATTAG-ATGAACACTA
1 GAGAG-TGTGAGATTAGAATGAAGACTA
27522 GTAAAAACAT
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
48 5 0.05
49 100 0.93
50 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.30, T:0.25
Consensus pattern (50 bp):
GAGAGTGTGAGATTAGAATGAAGACTATGATTAACATATATGGAGAGTGA
Found at i:29661 original size:23 final size:25
Alignment explanation
Indices: 29635--29680 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29625 CCAATTAGGG
29635 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
29658 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
29681 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:33824 original size:10 final size:10
Alignment explanation
Indices: 33811--33855 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
33801 TTTTCTCAAT
33811 TTTTTTTGAC
1 TTTTTTTGAC
33821 TTTTTTTCGA-
1 TTTTTTT-GAC
33831 TTTTTTT--C
1 TTTTTTTGAC
33839 TTTTTTTGAC
1 TTTTTTTGAC
33849 TTTTTTT
1 TTTTTTT
33856 TTTCTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.23
10 22 0.71
11 2 0.06
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAC
Found at i:33841 original size:18 final size:19
Alignment explanation
Indices: 33820--33865 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
33810 TTTTTTTTGA
33820 CTTTTTTTCGA-TTTTTTT
1 CTTTTTTTCGACTTTTTTT
33838 CTTTTTTT-GACTTTTTTT
1 CTTTTTTTCGACTTTTTTT
*
33856 TTTCTTTTTC
1 CTT-TTTTTC
33866 AGCAATTCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 17 0.71
19 5 0.21
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.78
Consensus pattern (19 bp):
CTTTTTTTCGACTTTTTTT
Found at i:34792 original size:20 final size:19
Alignment explanation
Indices: 34767--34808 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
34757 GTGCATAATT
*
34767 AAAATAAAATTAAAAAATAA
1 AAAATAAAACT-AAAAATAA
34787 AAAATAAAACTAAAAATAA
1 AAAATAAAACTAAAAATAA
34806 AAA
1 AAA
34809 TGAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAATAAAACTAAAAATAA
Found at i:34795 original size:13 final size:13
Alignment explanation
Indices: 34767--34818 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
34757 GTGCATAATT
*
34767 AAAATAAAATTAA
1 AAAATAAAAATAA
34780 AAAATAAAAA-ATA
1 AAAATAAAAATA-A
*
34793 AAACTAAAAAT-A
1 AAAATAAAAATAA
*
34805 AAAATGAAAATAA
1 AAAATAAAAATAA
34818 A
1 A
34819 TATACTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 11 0.34
13 21 0.66
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:34814 original size:7 final size:6
Alignment explanation
Indices: 34767--34818 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
34757 GTGCATAATT
* * *
34767 AAAATA AAATTAA AAAATAA AAAATA AAACTA AAAATA AAAATG AAAATA
1 AAAATA AAAAT-A AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA
34817 AA
1 AA
34819 TATACTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
6 27 0.69
7 12 0.31
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:39471 original size:24 final size:24
Alignment explanation
Indices: 39435--39480 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
39425 CCAATTAGGG
39435 AATTACTGTTTAG-ATTTAATTCT
1 AATTACTGTTTAGAATTTAATTCT
*
39458 AATTATCTTTTTAGAATTTAATT
1 AATTA-CTGTTTAGAATTTAATT
39481 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (24 bp):
AATTACTGTTTAGAATTTAATTCT
Found at i:40579 original size:20 final size:20
Alignment explanation
Indices: 40531--40585 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
40521 TTAGCCATTC
*
40531 TTTTTATTTTTATTTTATTA
1 TTTTTATTTTTATTTAATTA
**
40551 TTTGCATTTTTAATTTAATT-
1 TTTTTATTTTT-ATTTAATTA
40571 TTTTTA-TTTTATTTA
1 TTTTTATTTTTATTTA
40586 TTTCCTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 5 0.17
19 4 0.14
20 13 0.45
21 7 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTTATTTAATTA
Done.