Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009601.1 Kokia drynarioides strain JFW-HI SEQ_124317, 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: 54826
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:983 original size:4 final size:4
Alignment explanation
Indices: 964--1028 Score: 51
Period size: 4 Copynumber: 16.0 Consensus size: 4
954 ACACATTACA
* * * * *
964 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTCC TTTC TTTC TTTAT
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTT-C
*
1013 TTTC TTGC TTTC TTTC
1 TTTC TTTC TTTC TTTC
1029 CCGTTTATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
3 3 0.06
4 38 0.81
5 6 0.13
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:997 original size:17 final size:15
Alignment explanation
Indices: 964--1009 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
954 ACACATTACA
964 TTTCTTTCCTTCTTC
1 TTTCTTTCCTTCTTC
979 TTTCTTTCCTCTCCTTC
1 TTTCTTTCCT-T-CTTC
* *
996 TTCCTTTCTTTCTT
1 TTTCTTTCCTTCTT
1010 TATTTTCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 13 0.48
16 2 0.07
17 12 0.44
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCTTTCCTTCTTC
Found at i:7344 original size:28 final size:27
Alignment explanation
Indices: 7290--7342 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 27
7280 TATAGAGTCT
7290 TATAAAATTCATAATTTATAATTAAATA
1 TATAAAATT-ATAATTTATAATTAAATA
7318 TATAAAATT-TAATTATATAATTAAA
1 TATAAAATTATAATT-TATAATTAAA
7343 ATGACGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.21
27 10 0.42
28 9 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
TATAAAATTATAATTTATAATTAAATA
Found at i:9255 original size:13 final size:13
Alignment explanation
Indices: 9239--9263 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9229 TTCAAAGCAG
9239 TTTTTAAAAACAT
1 TTTTTAAAAACAT
9252 TTTTTAAAAACA
1 TTTTTAAAAACA
9264 ATGTTAAACT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTTAAAAACAT
Found at i:11055 original size:16 final size:17
Alignment explanation
Indices: 11029--11067 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
11019 GCAGGGAAAC
11029 AAAAAGCAAAAAAAAGA
1 AAAAAGCAAAAAAAAGA
*
11046 AAAAAG-AAAAATAAGA
1 AAAAAGCAAAAAAAAGA
11062 AGAAAA
1 A-AAAA
11068 TATAAACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAAGCAAAAAAAAGA
Found at i:12374 original size:23 final size:24
Alignment explanation
Indices: 12344--12388 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
12334 AGAGACTGCT
12344 GTTATCTA-TTCTAAGTTGTTTAA
1 GTTATCTATTTCTAAGTTGTTTAA
12367 GTTATCTATTTCTAAGTTGTTT
1 GTTATCTATTTCTAAGTTGTTT
12389 GAATCATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.56
Consensus pattern (24 bp):
GTTATCTATTTCTAAGTTGTTTAA
Found at i:13998 original size:96 final size:98
Alignment explanation
Indices: 13833--14024 Score: 309
Period size: 96 Copynumber: 2.0 Consensus size: 98
13823 ACTTTGTAAG
* * *
13833 AGTCATATGCATTTCTTTTAAAATCTCGAGGTTGACTGAGCAATATAACTCTGGTTATATACGAA
1 AGTCATATGCATTTCTTTTAAAATCTCGAAGTTGACAGAGCAATATAACTCTGGTTATACACGAA
*
13898 G-AAAAGAG-ACAAAAAGAAAAAGAATCTTAAT
66 GAAAAAGAGAAAAAAAAGAAAAAGAATCTTAAT
*
13929 AGTCATATGCATTTCTTTTAAAATCTCGAAGTTGACAGAGCAATATGACTCTGGTTATACAC-AA
1 AGTCATATGCATTTCTTTTAAAATCTCGAAGTTGACAGAGCAATATAACTCTGGTTATACACGAA
13993 TGAAAAAGAGAAAAAAAAGAAAAAGAATCTTA
66 -GAAAAAGAGAAAAAAAAGAAAAAGAATCTTA
14025 TGCCAAGCTG
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
95 2 0.02
96 59 0.67
97 7 0.08
98 20 0.23
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (98 bp):
AGTCATATGCATTTCTTTTAAAATCTCGAAGTTGACAGAGCAATATAACTCTGGTTATACACGAA
GAAAAAGAGAAAAAAAAGAAAAAGAATCTTAAT
Found at i:28259 original size:104 final size:105
Alignment explanation
Indices: 28060--28264 Score: 290
Period size: 104 Copynumber: 2.0 Consensus size: 105
28050 AACGAAGAGC
* * * * * *
28060 TTTCTTTCAAAGGTGTATTTTTGTGCTGGTCATTTTAGCTCATTTCATTTTTAAGTTCCTTCTCG
1 TTTCATTCAAAGGTGTATCTTTGTGCTGATCATTTCAGCTCATTTCATGTTTAAGTTCCTCCTCG
28125 GCTTCTTGATTTTACTTTGTGATTGTTGAGATGCTTGAGT
66 GCTTCTTGATTTTACTTTGTGATTGTTGAGATGCTTGAGT
28165 TTTCATTCAAAGGTGTATCCTTT-TGCTGATCATTTCAGCTCATTTCA-GTTT-AGATTCCTCCT
1 TTTCATTCAAAGGTGTAT-CTTTGTGCTGATCATTTCAGCTCATTTCATGTTTAAG-TTCCTCCT
* * *
28227 TGGCTTCTTGCTTTTATTTTGTGATTGTTGAGATGCTT
64 CGGCTTCTTGATTTTACTTTGTGATTGTTGAGATGCTT
28265 TCAATCTGTT
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
103 2 0.02
104 45 0.51
105 39 0.44
106 3 0.03
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50
Consensus pattern (105 bp):
TTTCATTCAAAGGTGTATCTTTGTGCTGATCATTTCAGCTCATTTCATGTTTAAGTTCCTCCTCG
GCTTCTTGATTTTACTTTGTGATTGTTGAGATGCTTGAGT
Found at i:38622 original size:2 final size:2
Alignment explanation
Indices: 38617--38642 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38607 CACACACACA
38617 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
38643 TTCATCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:53748 original size:23 final size:23
Alignment explanation
Indices: 53722--53766 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
53712 TGCAATCACT
53722 AGGCGCACATAGCGCAAATCAGG
1 AGGCGCACATAGCGCAAATCAGG
53745 AGGCGCACATAGCGCAAATCAG
1 AGGCGCACATAGCGCAAATCAG
53767 TAAGCACACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.27, G:0.29, T:0.09
Consensus pattern (23 bp):
AGGCGCACATAGCGCAAATCAGG
Found at i:53791 original size:23 final size:23
Alignment explanation
Indices: 53764--53842 Score: 149
Period size: 23 Copynumber: 3.4 Consensus size: 23
53754 TAGCGCAAAT
53764 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
53787 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
53810 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
53833 TAGTAAGCAC
1 CAGTAAGCAC
53843 GCTAGCGTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Done.