Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009371.1 Kokia drynarioides strain JFW-HI SEQ_124078, 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: 30732
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 70 characters in sequence are not A, C, G, or T
Found at i:875 original size:18 final size:18
Alignment explanation
Indices: 849--903 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
839 TCCAAGAATG
849 TAATTTGGACTTTGT-ATT
1 TAATTTGGACTTT-TAATT
*
867 TATTTTGGACTTTTAATT
1 TAATTTGGACTTTTAATT
**
885 TAATTTGGGTTTTTAATT
1 TAATTTGGACTTTTAATT
903 T
1 T
904 TAAATATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.22, C:0.04, G:0.15, T:0.60
Consensus pattern (18 bp):
TAATTTGGACTTTTAATT
Found at i:949 original size:6 final size:6
Alignment explanation
Indices: 938--1020 Score: 62
Period size: 6 Copynumber: 13.8 Consensus size: 6
928 TCAAGTTTGA
** * *
938 TTAAAT TTAAAT TTAAA- ACAAAT TTAAAT TTAAAAAG ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT--AAAT TTAAAT TTAAAT
* * * *
987 TT-AAT ATAAAT TTAAAT TCAAAA ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
1021 CCAATTTAAA
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
5 7 0.12
6 46 0.81
8 4 0.07
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:962 original size:17 final size:17
Alignment explanation
Indices: 939--1020 Score: 101
Period size: 17 Copynumber: 4.6 Consensus size: 17
929 CAAGTTTGAT
939 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
956 CAAATTTAAATTTAAAAAGA
1 TAAATTTAAATTT--AAA-A
*
976 TAAATTTAAATTTAATA
1 TAAATTTAAATTTAAAA
*
993 TAAATTTAAATTCAAAAA
1 TAAATTTAAATT-TAAAA
1011 TAAATTTAAA
1 TAAATTTAAA
1021 CCAATTTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
17 25 0.45
18 15 0.27
19 3 0.05
20 13 0.23
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:982 original size:37 final size:35
Alignment explanation
Indices: 939--1020 Score: 119
Period size: 37 Copynumber: 2.3 Consensus size: 35
929 CAAGTTTGAT
939 TAAATTTAAATTTAAAACAAATTTAAATTTAAAAAGA
1 TAAATTTAAATTTAAAACAAATTTAAA-TTAAAAA-A
* * *
976 TAAATTTAAATTTAATATAAATTTAAATTCAAAAA
1 TAAATTTAAATTTAAAACAAATTTAAATTAAAAAA
1011 TAAATTTAAA
1 TAAATTTAAA
1021 CCAATTTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
35 11 0.26
36 6 0.14
37 25 0.60
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (35 bp):
TAAATTTAAATTTAAAACAAATTTAAATTAAAAAA
Found at i:7578 original size:29 final size:29
Alignment explanation
Indices: 7432--7663 Score: 204
Period size: 30 Copynumber: 7.8 Consensus size: 29
7422 TTGGTTTAAA
*
7432 AAAAATGGAATTTTTAGACA--TTCGGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTC--GGGGT
* *
7462 AAAAATGGAATTTTTGGAAATTTCGGGAT
1 AAAAATGGAATTTTTGGAAGTTTCGGGGT
**
7491 CAAAAATGGTGTTTTTGGAAG-TTCGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTC-GGGGT
* *
7521 AAAAAATAGAATTTTTTGAAGTTTCGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGGGGT
* * *
7551 CGAAAATGGGATTTTTGGAAGTTTGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGGGGT
* *
7581 TAAAATGGAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGGGG-T
* *
7611 GAAAAT-GAGATTTTTGGACG-TTCAGGGGT
1 AAAAATGGA-ATTTTTGGAAGTTTC-GGGGT
7640 AAAAATGGAATTTTTGGATAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
7664 AGGGACCTCC
Statistics
Matches: 166, Mismatches: 25, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
29 52 0.31
30 106 0.64
31 8 0.05
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTCGGGGT
Found at i:7609 original size:59 final size:59
Alignment explanation
Indices: 7433--7663 Score: 277
Period size: 59 Copynumber: 3.9 Consensus size: 59
7423 TGGTTTAAAA
* * * * *
7433 AAAATGGAATTTTTAGACA-TTCGGGGGGTAAAAATGGAATTTTTGGAAATTTCGGGATCA
1 AAAATGGGATTTTTGGA-AGTTC-GGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCG
* *
7493 AAAATGGTG-TTTTTGGAAGTTCGGGGGTAAAAAATAGAATTTTTTGAAGTTTCGGGGTCG
1 AAAATGG-GATTTTTGGAAGTTCGGGGGT-AAAAATGGAATTTTTGGAAGTTTCGGGGTCG
* * * *
7553 AAAATGGGATTTTTGGAAGTTTGGGGGTTAAAATGGAATTTTTGGAAGTTTTGGGGTTG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCG
* * *
7612 AAAATGAGATTTTTGGACGTTCAGGGGTAAAAATGGAATTTTTGGATAGTTT
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA-AGTTT
7664 AGGGACCTCC
Statistics
Matches: 148, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
59 75 0.51
60 73 0.49
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.35
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCG
Found at i:9473 original size:20 final size:19
Alignment explanation
Indices: 9450--9488 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9440 AAATCTGTTA
*
9450 AAAAATCATTTGAAAAAAAC
1 AAAAATCA-ATGAAAAAAAC
*
9470 AAAAATTAATGAAAAAAAC
1 AAAAATCAATGAAAAAAAC
9489 TCAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.69, C:0.08, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAAATCAATGAAAAAAAC
Found at i:12339 original size:24 final size:25
Alignment explanation
Indices: 12307--12358 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
12297 ATTGCTACTA
*
12307 TGTATATATATT-ATCAA-AAACATG
1 TGTATATAT-TTCATCAAGAAAAATG
12331 TGTATATATTTCATCAAGAAAAATG
1 TGTATATATTTCATCAAGAAAAATG
12356 TGT
1 TGT
12359 TTGTTATAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 2 0.08
24 14 0.56
25 9 0.36
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (25 bp):
TGTATATATTTCATCAAGAAAAATG
Found at i:15163 original size:65 final size:65
Alignment explanation
Indices: 15093--15225 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 65
15083 TAAAATTCAA
15093 CATATGAAAAGAACAAAAATCAAAATTTGATTAATATTTTCAAAATCTAAATTTCTTTTATCATT
1 CATATGAAAAGAACAAAAATCAAAATTTGATTAATATTTTCAAAATCTAAATTTCTTTTATCATT
*
15158 CATATGAAAAGAACAAAAATCAAAATTTGATTAATATTTTCAAAATCTATATTTCTTTTATCATT
1 CATATGAAAAGAACAAAAATCAAAATTTGATTAATATTTTCAAAATCTAAATTTCTTTTATCATT
15223 CAT
1 CAT
15226 GTCTTTTTCT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (65 bp):
CATATGAAAAGAACAAAAATCAAAATTTGATTAATATTTTCAAAATCTAAATTTCTTTTATCATT
Found at i:19008 original size:19 final size:18
Alignment explanation
Indices: 18962--19008 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
18952 TAATTTGTAT
18962 TTAA-AAAAAAACATTAA
1 TTAATAAAAAAACATTAA
* *
18979 TTACTATAAAAAATATTAA
1 TTAATA-AAAAAACATTAA
18998 TATAATAAAAA
1 T-TAATAAAAA
19009 TATTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 16 0.67
20 4 0.17
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
TTAATAAAAAAACATTAA
Found at i:20833 original size:2 final size:2
Alignment explanation
Indices: 20826--20850 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20816 GAAATTCTTA
20826 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 A
20851 ATTTCTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26898 original size:24 final size:23
Alignment explanation
Indices: 26871--26926 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
26861 CCAAACTCCC
*
26871 TTTAAATTTGTTTAAAATTTTAAA
1 TTTAAATTTATTTAAAA-TTTAAA
**
26895 TTTAAATTTATTTTGAATTTAAA
1 TTTAAATTTATTTAAAATTTAAA
26918 TTT-AATTTA
1 TTTAAATTTA
26927 AGTTTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 6 0.21
23 9 0.31
24 14 0.48
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTAAATTTATTTAAAATTTAAA
Found at i:26900 original size:6 final size:6
Alignment explanation
Indices: 26889--26952 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
26879 TGTTTAAAAT
* * *
26889 TTTAAA TTTAAA TTT-AT TTTGAA TTTAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
26935 TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA
26953 ATTACTATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
5 13 0.28
6 30 0.64
7 4 0.09
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:26913 original size:17 final size:17
Alignment explanation
Indices: 26887--26952 Score: 96
Period size: 17 Copynumber: 3.8 Consensus size: 17
26877 TTTGTTTAAA
26887 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
26904 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
* *
26921 AATTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
26938 ATTTTCAAATTTAAA
1 ATTTT-AAATTTAAA
26953 ATTACTATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 34 0.81
18 8 0.19
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:26936 original size:23 final size:23
Alignment explanation
Indices: 26871--26938 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
26861 CCAAACTCCC
26871 TTTAAATTT-GTTTAAAATTTTAAA
1 TTTAAATTTAGTTT-AAA-TTTAAA
* *
26895 TTTAAATTTATTTTGAATTTAAA
1 TTTAAATTTAGTTTAAATTTAAA
26918 TTT-AATTTAAGTTTAAATTTA
1 TTTAAATTT-AGTTTAAATTTA
26939 TTTTCAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 5 0.13
23 19 0.50
24 11 0.29
25 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAGTTTAAATTTAAA
Found at i:28932 original size:30 final size:29
Alignment explanation
Indices: 28884--29224 Score: 123
Period size: 30 Copynumber: 11.6 Consensus size: 29
28874 CCCTGGATTG
*
28884 TCCAAAAATCA-CATTTTTAATCTCGAAACTT
1 TCCAAAAATCACCA-TTTTAACCTCG-AA-TT
*
28915 T-CAAAAATCACCATTTTACCCTCGAATT
1 TCCAAAAATCACCATTTTAACCTCGAATT
* **
28943 TCCAAAAATC-CCATTTTAACCTTGAACCC
1 TCCAAAAATCACCATTTTAACCTCGAA-TT
* * * *
28972 TCTAAAAATC-CCAATTTTAACCCCAAAAGT
1 TCCAAAAATCACC-ATTTTAACCTC-GAATT
* **
29002 TCCAAAAATC-CCATTTTAACCCCGAACCC
1 TCCAAAAATCACCATTTTAACCTCGAA-TT
* * * * *
29031 TCTAAAAATC-CTAATTTTAACCCCAAAACT
1 TCCAAAAATCAC-CATTTTAACCTC-GAATT
* * *
29061 TCCAAAAATC-CAAATTTGACC-CTGAACCTT
1 TCCAAAAATCACCATTTTAACCTC-GAA--TT
* * * *
29091 T-TAAAAATTACCATTTT-ACCACTAAATT
1 TCCAAAAATCACCATTTTAACCTC-GAATT
* *
29119 CCCAAAAATC-CCATTTTTGACCTCGAACTT
1 TCCAAAAATCACCA-TTTTAACCTCGAA-TT
* * * * *
29149 TCTAAAAATTACCATTTTACCCCCCAAATT
1 TCCAAAAATCACCATTTTA-ACCTCGAATT
* * **
29179 CCCAAAAATC-CCAATTTTAACCCCGAAAG
1 TCCAAAAATCACC-ATTTTAACCTCGAATT
29208 TCCAAAAATC-CCATTTT
1 TCCAAAAATCACCATTTT
29225 TGACCCTAAG
Statistics
Matches: 240, Mismatches: 51, Indels: 41
0.72 0.15 0.12
Matches are distributed among these distances:
28 32 0.13
29 90 0.38
30 103 0.43
31 15 0.06
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.29
Consensus pattern (29 bp):
TCCAAAAATCACCATTTTAACCTCGAATT
Found at i:29005 original size:59 final size:58
Alignment explanation
Indices: 28917--29205 Score: 273
Period size: 59 Copynumber: 4.9 Consensus size: 58
28907 CGAAACTTTC
* * * **
28917 AAAAATCACCATTTT-ACCCTCGAATTTCCAAAAATCCCATTTTAACCTTGAACCCTCT
1 AAAAATTACCATTTTAACCC-CAAAATTCCAAAAATCCCATTTTAACCCCGAACCCTCT
*
28975 AAAAA-TCCCAATTTTAACCCCAAAAGTTCCAAAAATCCCATTTTAACCCCGAACCCTCT
1 AAAAATTACC-ATTTTAACCCCAAAA-TTCCAAAAATCCCATTTTAACCCCGAACCCTCT
* * * * * *
29034 AAAAA-T-CCTAATTTTAACCCCAAAACTTCCAAAAATCCAAATTTGACCCTGAACCTTTT
1 AAAAATTACC--ATTTTAACCCCAAAA-TTCCAAAAATCCCATTTTAACCCCGAACCCTCT
* * * * **
29093 AAAAATTACCATTTT-ACCACTAAATTCCCAAAAATCCCATTTTTGACCTCGAACTTTCT
1 AAAAATTACCATTTTAACCCCAAAATT-CCAAAAATCCCA-TTTTAACCCCGAACCCTCT
* *
29152 AAAAATTACCATTTTACCCCCCAAATTCCCAAAAATCCCAATTTTAACCCCGAA
1 AAAAATTACCATTTTAACCCCAAAATT-CCAAAAATCCC-ATTTTAACCCCGAA
29206 AGTCCAAAAA
Statistics
Matches: 195, Mismatches: 26, Indels: 18
0.82 0.11 0.08
Matches are distributed among these distances:
57 4 0.02
58 33 0.17
59 123 0.63
60 32 0.16
61 3 0.02
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.28
Consensus pattern (58 bp):
AAAAATTACCATTTTAACCCCAAAATTCCAAAAATCCCATTTTAACCCCGAACCCTCT
Found at i:29225 original size:29 final size:28
Alignment explanation
Indices: 28884--29281 Score: 201
Period size: 29 Copynumber: 13.6 Consensus size: 28
28874 CCCTGGATTG
* * *
28884 TCCAAAAATCACATTTTTAATCTCGAAACT
1 TCCAAAAATCCCA-TTTTAACCCCGAAA-T
* *
28914 TTCAAAAATCACCATTTT-ACCCTCGAATT
1 TCCAAAAATC-CCATTTTAACCC-CGAAAT
** **
28943 TCCAAAAATCCCATTTTAACCTTGAACCC
1 TCCAAAAATCCCATTTTAACCCCGAA-AT
* *
28972 TCTAAAAATCCCAATTTTAACCCCAAAAGT
1 TCCAAAAATCCC-ATTTTAACCCCGAAA-T
**
29002 TCCAAAAATCCCATTTTAACCCCGAACCC
1 TCCAAAAATCCCATTTTAACCCCGAA-AT
* * *
29031 TCTAAAAATCCTAATTTTAACCCCAAAACT
1 TCCAAAAATCC-CATTTTAACCCCGAAA-T
* * * * *
29061 TCCAAAAATCCAAATTTGACCCTGAACCT
1 TCCAAAAATCCCATTTTAACCCCGAA-AT
** * * *
29090 TTTAAAAATTACCATTTT-ACCACTAAAT
1 TCCAAAAA-TCCCATTTTAACCCCGAAAT
* * *
29118 TCCCAAAAATCCCATTTTTGACCTCGAACTT
1 T-CCAAAAATCCCA-TTTTAACCCCGAA-AT
* * * *
29149 TCTAAAAATTACCATTTTACCCCCCAAAT
1 TCCAAAAA-TCCCATTTTAACCCCGAAAT
*
29178 TCCCAAAAATCCCAATTTTAACCCCGAAAG
1 T-CCAAAAATCCC-ATTTTAACCCCGAAAT
* * *
29208 TCCAAAAATCCCATTTTTGA-CCCTAAGCT
1 TCCAAAAATCCCA-TTTTAACCCCGAA-AT
* * * *
29237 TCTAAAATTACCATTTT-ACCGCCGAACT
1 TCCAAAAATCCCATTTTAACC-CCGAAAT
*
29265 TCCAAAAATCTCATTTT
1 TCCAAAAATCCCATTTT
29282 TGATTCTGAA
Statistics
Matches: 276, Mismatches: 70, Indels: 46
0.70 0.18 0.12
Matches are distributed among these distances:
27 1 0.00
28 42 0.15
29 116 0.42
30 109 0.39
31 8 0.03
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (28 bp):
TCCAAAAATCCCATTTTAACCCCGAAAT
Found at i:29253 original size:57 final size:58
Alignment explanation
Indices: 29192--29311 Score: 145
Period size: 57 Copynumber: 2.1 Consensus size: 58
29182 AAAAATCCCA
* * *
29192 ATTTTAACC-CCGAAAGTCCAAAAATCCCATTTTTGACCCT-AAGCTTCTAAAATTACC
1 ATTTT-ACCGCCGAAAGTCCAAAAATCCCATTTTTGACCCTGAACCTTCCAAAACTACC
** * **
29249 ATTTTACCGCCGAACTTCCAAAAATCTCATTTTTGATTCTGAACCTTCCAAAACTACC
1 ATTTTACCGCCGAAAGTCCAAAAATCCCATTTTTGACCCTGAACCTTCCAAAACTACC
29307 ATTTT
1 ATTTT
29312 GCCCCTTTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
56 3 0.06
57 31 0.58
58 19 0.36
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.33
Consensus pattern (58 bp):
ATTTTACCGCCGAAAGTCCAAAAATCCCATTTTTGACCCTGAACCTTCCAAAACTACC
Done.