Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015359.1 Kokia drynarioides strain JFW-HI SEQ_130406, 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: 556503
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 929 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:552954 original size:39 final size:40
Alignment explanation
Indices: 552872--552971 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 40
552862 ATCTTTAATT
* * *
552872 AAATTTA-TTTAAATTTAAATTTATTTTAAGTCTAACTTT
1 AAATTTATTTTAAATTTAAATTAAATTTAAGTCTAACTTA
*
552911 AAATTTATTTTAAATTTAAATTAAATTTAA-TTTAAAC-TA
1 AAATTTATTTTAAATTTAAATTAAATTTAAGTCT-AACTTA
552950 AAATTTATTTTTAAA-TTAAATT
1 AAATTTA-TTTTAAATTTAAATT
552972 TTAAATTGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
39 24 0.44
40 30 0.56
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (40 bp):
AAATTTATTTTAAATTTAAATTAAATTTAAGTCTAACTTA
Found at i:552965 original size:12 final size:12
Alignment explanation
Indices: 552920--552978 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 12
552910 TAAATTTATT
552920 TTAAA-TTTAAA
1 TTAAATTTTAAA
*
552931 TTAAA-TTTAAT
1 TTAAATTTTAAA
* *
552942 TTAAA-CTAAAA
1 TTAAATTTTAAA
* *
552953 TTTATTTTTAAA
1 TTAAATTTTAAA
552965 TTAAATTTTAAA
1 TTAAATTTTAAA
552977 TT
1 TT
552979 GAGTTTAAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
11 21 0.57
12 16 0.43
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAAATTTTAAA
Found at i:553678 original size:17 final size:16
Alignment explanation
Indices: 553633--553685 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
553623 AATTGTATTA
*
553633 AATATAATTAATAAAT
1 AATATAATTATTAAAT
553649 -ATATATATATATTAAAT
1 AATATA-AT-TATTAAAT
553666 AATATTAATTATT-AAT
1 AATA-TAATTATTAAAT
553682 AATA
1 AATA
553686 AATAAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 5 0.16
16 9 0.28
17 11 0.34
18 5 0.16
19 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATAATTATTAAAT
Found at i:554925 original size:29 final size:29
Alignment explanation
Indices: 554857--555210 Score: 170
Period size: 30 Copynumber: 12.1 Consensus size: 29
554847 CCTCAAAACT
* * *
554857 TTTCGAAAATTCCATTTTTGA-TCTCGAA-
1 TTTCCAAAATTACATTTTT-ACCCTCGAAC
*
554885 TCTTCCAAAAATTATATTTTTACCCTCGAAC
1 T-TTCC-AAAATTACATTTTTACCCTCGAAC
* * *
554916 TTTCCAAAATTCCA-TTTTA-ACTCAGAATT
1 TTTCCAAAATTACATTTTTACCCTC-GAA-C
* * ** *
554945 TTTCAAAAATTACATTTTTTACCGTTAAAT
1 TTTCCAAAATTACA-TTTTTACCCTCGAAC
*
554975 TTTTCAAAATT-CTATTTTTGACCCT-GAAC
1 TTTCCAAAATTAC-ATTTTT-ACCCTCGAAC
*
555004 TTTCCAAAATTACCA-TTTTACCCCCGAAC
1 TTTCCAAAATTA-CATTTTTACCCTCGAAC
*
555033 -TTCCTAAAAATTACCA-TTTTACCCTCAAAC
1 TTTCC--AAAATTA-CATTTTTACCCTCGAAC
*
555063 -TTCCAAAAATTACATTTTGT--CGTCGAAC
1 TTTCC-AAAATTACATTTT-TACCCTCGAAC
*
555091 TTCCCAAAAGTTACCA-TTTTACCC-CTGAAC
1 TTTCCAAAA-TTA-CATTTTTACCCTC-GAAC
* *
555121 -TTCCAAAAATTCCATTTTTAACCC-CAAAC
1 TTTCC-AAAATTACATTTTT-ACCCTCGAAC
*
555150 TTCTCAAAAATTAC-TATTTTACCCTCGAAC
1 TT-TCCAAAATTACAT-TTTTACCCTCGAAC
* *
555180 TTTCAAAAAATT-CTATTTTGA-CCTCGAAC
1 TTTC-CAAAATTAC-ATTTTTACCCTCGAAC
555209 TT
1 TT
555211 AGATTCTAAT
Statistics
Matches: 258, Mismatches: 34, Indels: 67
0.72 0.09 0.19
Matches are distributed among these distances:
27 3 0.01
28 32 0.12
29 100 0.39
30 110 0.43
31 12 0.05
32 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (29 bp):
TTTCCAAAATTACATTTTTACCCTCGAAC
Found at i:554933 original size:59 final size:61
Alignment explanation
Indices: 554847--555161 Score: 157
Period size: 59 Copynumber: 5.3 Consensus size: 61
554837 CATATTTTGA
* * *
554847 CCTCAAAACTTTTCGAAAATTCCATTTTTGATCTC-GAATCTTCCAAAAATTATA-TTTTTAC
1 CCTC-AAAC-TTTCCAAAATTCCATTTTTGAACTCAGAATCTTCCAAAAATTACATTTTTTAC
* * *
554908 CCTCGAACTTTCCAAAATTCCA-TTTT-AACTCAGAATTTTTCAAAAATTACATTTTTTAC
1 CCTCAAACTTTCCAAAATTCCATTTTTGAACTCAGAATCTTCCAAAAATTACATTTTTTAC
* * * * * * *
554967 CGTTAAATTTTTCAAAATTCTATTTTTG-ACCCTGAA-CTTTCC-AAAATTACCA--TTTTAC
1 CCTCAAACTTTCCAAAATTCCATTTTTGAACTCAGAATC-TTCCAAAAATTA-CATTTTTTAC
* * * *
555025 CCCCGAAC-TTCCTAAAAATTACCA-TTTT-ACCCTCA-AA-CTTCCAAAAATTACATTTTGT--
1 CCTCAAACTTTCC--AAAATT-CCATTTTTGA-ACTCAGAATCTTCCAAAAATTACATTTTTTAC
* * * * * * * *
555083 CGTCGAACTTCCCAAAAGTTACCA-TTTT-ACCCCTGAA-CTTCCAAAAATTCCATTTTTAAC
1 CCTCAAACTTTCCAAAA-TT-CCATTTTTGAACTCAGAATCTTCCAAAAATTACATTTTTTAC
*
555143 CC-CAAACTTCTCAAAAATT
1 CCTCAAACTT-TCCAAAATT
555162 ACTATTTTAC
Statistics
Matches: 195, Mismatches: 39, Indels: 42
0.71 0.14 0.15
Matches are distributed among these distances:
57 14 0.07
58 72 0.37
59 74 0.38
60 31 0.16
61 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.37
Consensus pattern (61 bp):
CCTCAAACTTTCCAAAATTCCATTTTTGAACTCAGAATCTTCCAAAAATTACATTTTTTAC
Found at i:555053 original size:88 final size:89
Alignment explanation
Indices: 554886--555188 Score: 283
Period size: 88 Copynumber: 3.4 Consensus size: 89
554876 GATCTCGAAT
* * * **
554886 CTTCCAAAAATTATATTTTT-ACCCTCGAACTTTCCAAAATT-CCATTTTAACTCAGAA-TTTTT
1 CTTCCAAAAATTCTATTTTTGACCCTCGAACTTTCCAAAATTACCATTTTACCCCAGAACTTCCT
* *
554948 CAAAAATTA-CATTTTTTACCGTTAAA
66 -AAAAATTACCA--TTTTACCCTCAAA
* * *
554974 TTTTTC-AAAATTCTATTTTTGACCCT-GAACTTTCCAAAATTACCATTTTACCCCCGAACTTCC
1 -CTTCCAAAAATTCTATTTTTGACCCTCGAACTTTCCAAAATTACCATTTTACCCCAGAACTTCC
555037 TAAAAATTACCATTTTACCCTCAAA
65 TAAAAATTACCATTTTACCCTCAAA
* * * *
555062 CTTCCAAAAATTAC-A-TTTTG-TCGTCGAACTTCCCAAAAGTTACCATTTTACCCCTGAACTTC
1 CTTCCAAAAATT-CTATTTTTGACCCTCGAACTTTCCAAAA-TTACCATTTTACCCCAGAACTTC
555124 C-AAAAATT-CCATTTTTAACCC-CAAA
64 CTAAAAATTACCA-TTTT-ACCCTCAAA
*
555149 CTTCTCAAAAATTACTA-TTTT-ACCCTCGAACTTTCAAAAA
1 CTTC-CAAAAATT-CTATTTTTGACCCTCGAACTTTCCAAAA
555189 ATTCTATTTT
Statistics
Matches: 181, Mismatches: 20, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
86 5 0.03
87 39 0.22
88 83 0.46
89 49 0.27
90 5 0.03
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (89 bp):
CTTCCAAAAATTCTATTTTTGACCCTCGAACTTTCCAAAATTACCATTTTACCCCAGAACTTCCT
AAAAATTACCATTTTACCCTCAAA
Found at i:555170 original size:30 final size:28
Alignment explanation
Indices: 554990--555210 Score: 189
Period size: 29 Copynumber: 7.5 Consensus size: 28
554980 AAAATTCTAT
*
554990 TTTTGACCCTGAACTTTCC-AAAATTACCA
1 TTTT-ACCCCGAAC-TTCCAAAAATTACCA
555019 TTTTACCCCCGAACTTCCTAAAAATTACCA
1 TTTTA-CCCCGAACTTCC-AAAAATTACCA
*
555049 TTTTACCCTCAAACTTCCAAAAATTA-CA
1 TTTTACCC-CGAACTTCCAAAAATTACCA
* ** *
555077 TTTTGTCGTCGAACTTCCCAAAAGTTACCA
1 TTTT-ACCCCGAACTT-CCAAAAATTACCA
555107 TTTTACCCCTGAACTTCCAAAAATT-CCA
1 TTTTACCCC-GAACTTCCAAAAATTACCA
* *
555135 TTTTTAACCCCAAACTTCTCAAAAATTACTA
1 -TTTT-ACCCCGAACTTC-CAAAAATTACCA
* *
555166 TTTTACCCTCGAACTTTCAAAAAATT-CTA
1 TTTTACCC-CGAAC-TTCCAAAAATTACCA
*
555195 TTTTGACCTCGAACTT
1 TTTT-ACCCCGAACTT
555211 AGATTCTAAT
Statistics
Matches: 161, Mismatches: 16, Indels: 31
0.77 0.08 0.15
Matches are distributed among these distances:
28 22 0.14
29 68 0.42
30 66 0.41
31 5 0.03
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (28 bp):
TTTTACCCCGAACTTCCAAAAATTACCA
Done.