Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011277.1 Kokia drynarioides strain JFW-HI SEQ_126256, 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: 33089
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:412 original size:18 final size:18
Alignment explanation
Indices: 389--425 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
379 ACAATTCATA
389 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
407 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
425 T
1 T
426 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:3116 original size:193 final size:195
Alignment explanation
Indices: 2862--3215 Score: 523
Period size: 193 Copynumber: 1.8 Consensus size: 195
2852 TCCCCTAATT
* * **
2862 ATGCTGCTCACACGAGTTGTCGAGAATATGCATTTAAGCATAAATCCCAGTTATCGTAAGGCCTA
1 ATGCTGCTCACACGAGCTGTCGAGAATATGCACTTAAGCATAAATCCCAACTATCGTAAGGCCTA
** * *
2927 TAATCCATT-TAGGATTCATATCTC-TTTTTCGACTCACGATGCTGCTTACACGAGCTGTCGAGG
66 TAATCCATTATAGGATTCATATCTCATTTCCCGACTCACGATGCTGCTCACACGAGCTGTCAAGG
*
2990 ACTCGCAACATATGCGGTACCTCAGCCATCGATATGGTATCTGTGCATATAACTGTTTCCTAACG
131 ACTCGCAACATATGCGGTACCTCAACCATCGATATGGTATCTGTGCATATAACTGTTTCCTAACG
* * * *
3055 ATGCTGCTCATACGAGCTGTCGAGAATATGCACTTATGCATAAATCTCAACTATTGTAAGGCCTA
1 ATGCTGCTCACACGAGCTGTCGAGAATATGCACTTAAGCATAAATCCCAACTATCGTAAGGCCTA
* * * * *
3120 TAATCCATTATTGGATTCTTTTCTCATTTCCCGACTCACGATGCTGCTCATATGAGCTGTCAAGG
66 TAATCCATTATAGGATTCATATCTCATTTCCCGACTCACGATGCTGCTCACACGAGCTGTCAAGG
*
3185 ACTCGCAACATATGTGGTACCTCAACCATCG
131 ACTCGCAACATATGCGGTACCTCAACCATCG
3216 TATCAGTTTC
Statistics
Matches: 140, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
193 66 0.47
194 12 0.09
195 62 0.44
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (195 bp):
ATGCTGCTCACACGAGCTGTCGAGAATATGCACTTAAGCATAAATCCCAACTATCGTAAGGCCTA
TAATCCATTATAGGATTCATATCTCATTTCCCGACTCACGATGCTGCTCACACGAGCTGTCAAGG
ACTCGCAACATATGCGGTACCTCAACCATCGATATGGTATCTGTGCATATAACTGTTTCCTAACG
Found at i:8385 original size:22 final size:22
Alignment explanation
Indices: 8360--8433 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
8350 AAAAAACAAT
8360 TAAAAAAAAGCAACCAAAACAG
1 TAAAAAAAAGCAACCAAAACAG
*
8382 TAAAAAAATAGC-ACTAAAACAG
1 TAAAAAAA-AGCAACCAAAACAG
* * *
8404 CAAAAAAAA-TAATCAAAACAG
1 TAAAAAAAAGCAACCAAAACAG
8425 TAAAAAAAA
1 TAAAAAAAA
8434 CCAAAATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 17 0.39
22 24 0.55
23 3 0.07
ACGTcount: A:0.70, C:0.14, G:0.07, T:0.09
Consensus pattern (22 bp):
TAAAAAAAAGCAACCAAAACAG
Found at i:8388 original size:21 final size:21
Alignment explanation
Indices: 8362--8432 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
8352 AAAACAATTA
8362 AAAAAAAGCAACCAAAACAGT
1 AAAAAAAGCAACCAAAACAGT
* *
8383 AAAAAAATAGC-ACTAAAACAGC
1 -AAAAAA-AGCAACCAAAACAGT
** *
8405 AAAAAAAATAATCAAAACAGT
1 AAAAAAAGCAACCAAAACAGT
8426 AAAAAAA
1 AAAAAAA
8433 ACCAAAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.03
21 21 0.52
22 15 0.38
23 3 0.08
ACGTcount: A:0.70, C:0.14, G:0.07, T:0.08
Consensus pattern (21 bp):
AAAAAAAGCAACCAAAACAGT
Found at i:12665 original size:2 final size:2
Alignment explanation
Indices: 12658--12694 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12648 GTCAGTCACT
12658 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12695 TCCGAAGTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:14640 original size:20 final size:20
Alignment explanation
Indices: 14615--14653 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
14605 TATGCTTCAG
14615 CTTATCACATACTTTGATTT
1 CTTATCACATACTTTGATTT
14635 CTTATCACATACTTTGATT
1 CTTATCACATACTTTGATT
14654 AGCACCAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (20 bp):
CTTATCACATACTTTGATTT
Found at i:15405 original size:2 final size:2
Alignment explanation
Indices: 15394--15422 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
15384 GCAGCCTTAA
15394 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15423 GCTTTGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:18039 original size:27 final size:27
Alignment explanation
Indices: 18001--18054 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
17991 CGGTGTAAAA
*
18001 ATAAATAAATTTCTTATTGAGATTGTG
1 ATAAATAAATTTCTTAATGAGATTGTG
*
18028 ATAAATAAATTTGTTAATGAGATTGTG
1 ATAAATAAATTTCTTAATGAGATTGTG
18055 GGGATGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.43
Consensus pattern (27 bp):
ATAAATAAATTTCTTAATGAGATTGTG
Found at i:22449 original size:22 final size:21
Alignment explanation
Indices: 22418--22458 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
22408 CTCTTTATTC
22418 TTTTTATTTTATTTTAATTGT
1 TTTTTATTTTATTTTAATTGT
*
22439 TTTTTAGTTTTGTTTTAATT
1 TTTTTA-TTTTATTTTAATT
22459 CAACCCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTTTATTTTATTTTAATTGT
Found at i:25167 original size:22 final size:22
Alignment explanation
Indices: 25140--25191 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
25130 CAAATGAACG
*
25140 GAGAGCACCAAGGTGCTAAACA
1 GAGAGCACAAAGGTGCTAAACA
*
25162 GAGAGCACAAATGTGCTAAACA
1 GAGAGCACAAAGGTGCTAAACA
*
25184 AAGAGCAC
1 GAGAGCAC
25192 TTTATGTGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (22 bp):
GAGAGCACAAAGGTGCTAAACA
Found at i:30891 original size:29 final size:28
Alignment explanation
Indices: 30858--31228 Score: 229
Period size: 30 Copynumber: 12.6 Consensus size: 28
30848 GAAACTCTCT
30858 AAAAATTACCATTTTACCCTCGAACCTCC
1 AAAAA-TACCATTTTACCCTCGAACCTCC
*
30887 AAAAATCCCATTTTGA-CCTCGAACTCTCC
1 AAAAATACCATTTT-ACCCTCGAAC-CTCC
* * *
30916 AAAAATTACAATTTTACCCCCGAACTTCC
1 AAAAA-TACCATTTTACCCTCGAACCTCC
* *
30945 AAAAA-CCCATTTTTGA-CCTCGAATTCTCC
1 AAAAATACCA-TTTT-ACCCTCGAA-CCTCC
** *
30974 AAAAATTACCATTTTACCCTTAAACTTCC
1 AAAAA-TACCATTTTACCCTCGAACCTCC
* * *
31003 AAAAATCCCATTTTTAACCC-CAAACTCTAC
1 AAAAATACCA-TTTT-ACCCTCGAAC-CTCC
31033 AAAAATTACCATTTTACCCTCGAA-CTACC
1 AAAAA-TACCATTTTACCCTCGAACCT-CC
* * *
31062 AAAAATCCCATTTTTGACCC-CAAACCTTCT
1 AAAAATACCA-TTTT-ACCCTCGAACC-TCC
* * *
31092 AAAAATTACCATTTTTACCCCCAAACTTCC
1 AAAAA-TACCA-TTTTACCCTCGAACCTCC
*
31122 AAAAAT-CTCATTTTTGACCC-CGAACCTTTC
1 AAAAATAC-CA-TTTT-ACCCTCGAACC-TCC
*
31152 AAAAATTACCATTTTACCCTCGAACTTCC
1 AAAAA-TACCATTTTACCCTCGAACCTCC
* **
31181 AAAAATCCCATTTTTTA-TTTCGAACCTTCC
1 AAAAATACCA--TTTTACCCTCGAACC-TCC
*
31211 AAAACTACCATTTTACCC
1 AAAAATACCATTTTACCC
31229 CCCGTGCATC
Statistics
Matches: 269, Mismatches: 41, Indels: 64
0.72 0.11 0.17
Matches are distributed among these distances:
27 2 0.01
28 46 0.17
29 96 0.36
30 99 0.37
31 25 0.09
32 1 0.00
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAAATACCATTTTACCCTCGAACCTCC
Found at i:30940 original size:58 final size:59
Alignment explanation
Indices: 30850--31195 Score: 466
Period size: 59 Copynumber: 5.9 Consensus size: 59
30840 GAGGTCCTGA
* * *
30850 AACTCTCTAAAAATTACCATTTTACCCTCGAACCTCCAAAAATCCCA-TTTTGACCTCG
1 AACTCTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
30908 AACTCTCCAAAAATTACAATTTTACCCCCGAACTTCCAAAAA-CCCATTTTTGACCTCG
1 AACTCTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* ** * *
30966 AATTCTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATCCCATTTTTAACCCCA
1 AACTCTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
31025 AACTCTACAAAAATTACCATTTTACCCTCGAACTACCAAAAATCCCATTTTTGACCCCA
1 AACTCTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
31084 AAC-CTTCTAAAAATTACCATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCG
1 AACTC-TCCAAAAATTACCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
*
31144 AAC-CTTTCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTT
1 AACTC-TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTT
31196 TATTTCGAAC
Statistics
Matches: 254, Mismatches: 30, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
57 4 0.02
58 87 0.34
59 111 0.44
60 52 0.20
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (59 bp):
AACTCTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:31197 original size:30 final size:29
Alignment explanation
Indices: 30869--31195 Score: 276
Period size: 29 Copynumber: 11.1 Consensus size: 29
30859 AAAATTACCA
*
30869 TTTTACCCTCGAACCTCCAAAAATCCCAT
1 TTTTACCCTCGAACTTCCAAAAATCCCAT
* ** *
30898 TTTGA-CCTCGAACTCTCCAAAAATTACAA
1 TTTTACCCTCGAACT-TCCAAAAATCCCAT
*
30927 TTTTACCCCCGAACTTCCAAAAA-CCCAT
1 TTTTACCCTCGAACTTCCAAAAATCCCAT
* *
30955 TTTTGA-CCTCGAATTCTCCAAAAATTACCA-
1 TTTT-ACCCTCGAACT-TCCAAAAA-TCCCAT
**
30985 TTTTACCCTTAAACTTCCAAAAATCCCAT
1 TTTTACCCTCGAACTTCCAAAAATCCCAT
* * *
31014 TTTTAACCC-CAAACTCTACAAAAATTACCA-
1 TTTT-ACCCTCGAACT-TCCAAAAA-TCCCAT
*
31044 TTTTACCCTCGAACTACCAAAAATCCCAT
1 TTTTACCCTCGAACTTCCAAAAATCCCAT
* * *
31073 TTTTGACCC-CAAACCTTCTAAAAATTACCAT
1 TTTT-ACCCTCGAA-CTTCCAAAAA-TCCCAT
* * *
31104 TTTTACCCCCAAACTTCCAAAAATCTCAT
1 TTTTACCCTCGAACTTCCAAAAATCCCAT
* *
31133 TTTTGACCC-CGAACCTTTCAAAAATTACCA-
1 TTTT-ACCCTCGAA-CTTCCAAAAA-TCCCAT
31163 TTTTACCCTCGAACTTCCAAAAATCCCAT
1 TTTTACCCTCGAACTTCCAAAAATCCCAT
31192 TTTT
1 TTTT
31196 TATTTCGAAC
Statistics
Matches: 239, Mismatches: 37, Indels: 44
0.75 0.12 0.14
Matches are distributed among these distances:
28 33 0.14
29 99 0.41
30 84 0.35
31 23 0.10
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (29 bp):
TTTTACCCTCGAACTTCCAAAAATCCCAT
Done.