Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000500.1 Kokia drynarioides strain JFW-HI SEQ_111377, 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: 44171
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:823 original size:31 final size:31
Alignment explanation
Indices: 785--844 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
775 AAAATAGTCA
*
785 CTAAATTATTCGAAAGTTTTCATTTAAGTTG
1 CTAAATTATTCAAAAGTTTTCATTTAAGTTG
* *
816 CTAAATTATTTAAAAGTTTTTATTTAAGT
1 CTAAATTATTCAAAAGTTTTCATTTAAGT
845 CATTGGGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (31 bp):
CTAAATTATTCAAAAGTTTTCATTTAAGTTG
Found at i:1304 original size:9 final size:9
Alignment explanation
Indices: 1290--1314 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1280 ATACTCAACC
1290 TACATGACT
1 TACATGACT
1299 TACATGACT
1 TACATGACT
1308 TACATGA
1 TACATGA
1315 ATGTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (9 bp):
TACATGACT
Found at i:6875 original size:93 final size:93
Alignment explanation
Indices: 6764--6956 Score: 386
Period size: 93 Copynumber: 2.1 Consensus size: 93
6754 TAAATAAAAA
6764 CTTTTAAATAATACAATATTTTATATTTTTTTTCGAAATTGAGTAACCAAAACTACACTTTCTAA
1 CTTTTAAATAATACAATATTTTATATTTTTTTTCGAAATTGAGTAACCAAAACTACACTTTCTAA
6829 CAATTTAGTAACCTTAGGTATAATTTAC
66 CAATTTAGTAACCTTAGGTATAATTTAC
6857 CTTTTAAATAATACAATATTTTATATTTTTTTTCGAAATTGAGTAACCAAAACTACACTTTCTAA
1 CTTTTAAATAATACAATATTTTATATTTTTTTTCGAAATTGAGTAACCAAAACTACACTTTCTAA
6922 CAATTTAGTAACCTTAGGTATAATTTAC
66 CAATTTAGTAACCTTAGGTATAATTTAC
6950 CTTTTAA
1 CTTTTAA
6957 TATTTTATAC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 100 1.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.42
Consensus pattern (93 bp):
CTTTTAAATAATACAATATTTTATATTTTTTTTCGAAATTGAGTAACCAAAACTACACTTTCTAA
CAATTTAGTAACCTTAGGTATAATTTAC
Found at i:7069 original size:16 final size:16
Alignment explanation
Indices: 7050--7083 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
7040 CTTTTTGTTT
*
7050 AAGATCAATTTTTTTA
1 AAGATCAATTTATTTA
7066 AAGATCAATTTATTTA
1 AAGATCAATTTATTTA
7082 AA
1 AA
7084 ATTATGTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
AAGATCAATTTATTTA
Found at i:11757 original size:31 final size:28
Alignment explanation
Indices: 11698--11762 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
11688 TCGAAAGTTT
*
11698 AAAATTTAATCTCTATACTTTTATTTTC
1 AAAATTTAATCTCTATACTTTTAATTTC
* *
11726 AAGAATTTAATCTCTCTATTTTTCAAATTTC
1 AA-AATTTAATCTCTATACTTTT--AATTTC
11757 AAAATT
1 AAAATT
11763 GAAGTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 2 0.06
29 18 0.58
30 4 0.13
31 7 0.23
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (28 bp):
AAAATTTAATCTCTATACTTTTAATTTC
Found at i:24124 original size:63 final size:63
Alignment explanation
Indices: 24025--24159 Score: 234
Period size: 63 Copynumber: 2.1 Consensus size: 63
24015 GGTTGTCGTT
24025 GATGGAAACGATGTGATTGATAGCGTAGAATCGAAGGAAGCCAATGAAGAAACAAGCGAACCC
1 GATGGAAACGATGTGATTGATAGCGTAGAATCGAAGGAAGCCAATGAAGAAACAAGCGAACCC
* * * *
24088 GATGGAAACGTTGTGATTGATAGCGTAGAATCGAAGGAAGCTATTGCAGAAACAAGCGAACCC
1 GATGGAAACGATGTGATTGATAGCGTAGAATCGAAGGAAGCCAATGAAGAAACAAGCGAACCC
24151 GATGGAAAC
1 GATGGAAAC
24160 ATGGGCTCGT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.16
Consensus pattern (63 bp):
GATGGAAACGATGTGATTGATAGCGTAGAATCGAAGGAAGCCAATGAAGAAACAAGCGAACCC
Found at i:28149 original size:92 final size:93
Alignment explanation
Indices: 27996--28172 Score: 243
Period size: 92 Copynumber: 1.9 Consensus size: 93
27986 GATAAATAAA
* * * *
27996 AAAAAAACTTTTAAGTACTTAAGTGGAAAAAGTAGTATAGTGTGAGGGCTAATTTTGATTTAAGT
1 AAAAAAAC-TTTAAGTACTTAAATGGAAAAAGTAATATAGTGTGAGGACTAATTTTGATTTAAGC
*
28061 CATTTTGATATTGTGTGGCTTTTGAAAAG
65 CATTTAGATATTGTGTGGCTTTTGAAAAG
* *
28090 AAAAAAA-TTTAAGTACTTAAATGG-AAAAGTAATAT-GATTTGAGGACTGATTTTGTATTTAAG
1 AAAAAAACTTTAAGTACTTAAATGGAAAAAGTAATATAG-TGTGAGGACTAATTTTG-ATTTAAG
28152 CCATTTAGATATTGTGTGGCT
64 CCATTTAGATATTGTGTGGCT
28173 CATATAGAGG
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
90 1 0.01
91 24 0.32
92 42 0.57
94 7 0.09
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (93 bp):
AAAAAAACTTTAAGTACTTAAATGGAAAAAGTAATATAGTGTGAGGACTAATTTTGATTTAAGCC
ATTTAGATATTGTGTGGCTTTTGAAAAG
Found at i:28363 original size:16 final size:16
Alignment explanation
Indices: 28344--28423 Score: 53
Period size: 15 Copynumber: 5.2 Consensus size: 16
28334 ATGATTTAAT
28344 TTTGGTTAATTTCGTA
1 TTTGGTTAATTTCGTA
* *
28360 TTTGGATAATTTAGT-
1 TTTGGTTAATTTCGTA
*
28375 TTTGAGTT-ATTTTG-A
1 TTTG-GTTAATTTCGTA
*
28390 TTTGGATT-ATTTCATA
1 TTTGG-TTAATTTCGTA
* *
28406 TTT-TTTAGTTTCGTA
1 TTTGGTTAATTTCGTA
28421 TTT
1 TTT
28424 AAGTGTTTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
14 3 0.06
15 28 0.56
16 19 0.38
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.60
Consensus pattern (16 bp):
TTTGGTTAATTTCGTA
Found at i:28372 original size:31 final size:31
Alignment explanation
Indices: 28332--28423 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 31
28322 TAAAATTTTC
*
28332 GGATGATTTAATTTTGGTTAATTTCGTATTT
1 GGATAATTTAATTTTGGTTAATTTCGTATTT
* *
28363 GGATAATTTAGTTTTGAGTT-ATTTTG-ATTT
1 GGATAATTTAATTTTG-GTTAATTTCGTATTT
* *
28393 GGATTATTTCATATTTT--TTAGTTTCGTATTT
1 GGATAATTT-A-ATTTTGGTTAATTTCGTATTT
28424 AAGTGTTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
29 2 0.04
30 16 0.33
31 24 0.49
32 7 0.14
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.58
Consensus pattern (31 bp):
GGATAATTTAATTTTGGTTAATTTCGTATTT
Found at i:30241 original size:24 final size:24
Alignment explanation
Indices: 30214--30261 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
30204 AATTTTATCA
**
30214 AATAAAAATGTCACATTAAAAAAT
1 AATAAAAATACCACATTAAAAAAT
* *
30238 AATATAATTACCACATTAAAAAAT
1 AATAAAAATACCACATTAAAAAAT
30262 TGAAAATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.27
Consensus pattern (24 bp):
AATAAAAATACCACATTAAAAAAT
Found at i:41786 original size:17 final size:17
Alignment explanation
Indices: 41766--41799 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41756 AATGATTAAG
41766 CTTGAATAACTTAATCT
1 CTTGAATAACTTAATCT
41783 CTTGAATAACTTAATCT
1 CTTGAATAACTTAATCT
41800 TAAATGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (17 bp):
CTTGAATAACTTAATCT
Found at i:43378 original size:23 final size:24
Alignment explanation
Indices: 43339--43387 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
43329 CAAATATATC
43339 TTTCATAAAATACAA-GGACTAAA
1 TTTCATAAAATACAAGGGACTAAA
* *
43362 TTTCAATAAATTA-AAGGGACTGAA
1 TTTC-ATAAAATACAAGGGACTAAA
43386 TT
1 TT
43388 CCTAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
TTTCATAAAATACAAGGGACTAAA
Done.