Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014697.1 Kokia drynarioides strain JFW-HI SEQ_129736, 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: 14921
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:904 original size:30 final size:29
Alignment explanation
Indices: 869--1102 Score: 206
Period size: 29 Copynumber: 7.9 Consensus size: 29
859 TGAAAATCCC
869 ATTTTTGACCTCAAAACTTCCAAAAATTCT
1 ATTTTT-ACCTCAAAACTTCCAAAAATTCT
* * * * *
899 GTTTTTACCCCCAAACTTCCAAAAATCCC
1 ATTTTTACCTCAAAACTTCCAAAAATTCT
*
928 ATTTTTACCTCGAAACTTCCAAAAATTCT
1 ATTTTTACCTCAAAACTTCCAAAAATTCT
*
957 ATTTTTGACCCCAAAACTTCCAAAAATT-T
1 ATTTTT-ACCTCAAAACTTCCAAAAATTCT
* * *
986 CATTTTTACCCTC-GAACTTCCAAAAATCCCA
1 -ATTTTTA-CCTCAAAACTTCCAAAAAT-TCT
* * *
1017 ATTTTAACCTCGAAACTTCCAAAAATTCC
1 ATTTTTACCTCAAAACTTCCAAAAATTCT
* **
1046 GTTTTTA-CTCCCGAACTTCCAAAAATCTCGT
1 ATTTTTACCT-CAAAACTTCCAAAAAT-TC-T
* *
1077 -TTTTGACCCCAAAACTTCCAAAAATT
1 ATTTTTACCTCAAAACTTCCAAAAATT
1103 ACCATTTTAC
Statistics
Matches: 165, Mismatches: 29, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
28 2 0.01
29 89 0.54
30 73 0.44
31 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
ATTTTTACCTCAAAACTTCCAAAAATTCT
Found at i:1069 original size:118 final size:116
Alignment explanation
Indices: 911--1231 Score: 323
Period size: 118 Copynumber: 2.7 Consensus size: 116
901 TTTTACCCCC
* *
911 AAACTTCCAAAAATCCCATTTTTACCTCGAAACTTCCAAAAATTCTATTTTTGACCCCAAAACTT
1 AAACTTCCAAAAATTCC-TTTTTACCCCG-AACTTCCAAAAATTCTATTTTTGACCCCAAAACTT
* *
976 CCAAAAATT-TCATTTTTACCCTCGAA-CTTCCAAAAATCCCAATTTT-AACCTCG
64 CCAAAAATTACCA-TTTTACCCCCGAATCTTCCAAAAAT-CC-ATTTTCAACCTCG
*
1029 AAACTTCCAAAAATTCCGTTTTTACTCCCGAACTTCCAAAAA-TCTCGTTTTTGACCCCAAAACT
1 AAACTTCCAAAAATTCC-TTTTTAC-CCCGAACTTCCAAAAATTCT-ATTTTTGACCCCAAAACT
* * * * *
1093 TCCAAAAATTACCATTTTACCCCCGAATGTTCGAAGACTCCATTTTCGACCTCG
63 TCCAAAAATTACCATTTTACCCCCGAATCTTCCAAAAATCCATTTTCAACCTCG
* * * * **
1147 AAAC-TCTC-AAAATTACCCTTTTACCCCCGAA-TGTCTAAAAATTCTATTTTTAACCCCGAATT
1 AAACTTC-CAAAAATT-CCTTTTTA-CCCCGAACT-TCCAAAAATTCTATTTTTGACCCCAAAAC
* *
1209 TTCCCAAAATTACCATTTCACCC
62 TTCCAAAAATTACCATTTTACCC
1232 TCGAGAATCC
Statistics
Matches: 173, Mismatches: 20, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
116 1 0.01
117 67 0.39
118 93 0.54
119 12 0.07
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (116 bp):
AAACTTCCAAAAATTCCTTTTTACCCCGAACTTCCAAAAATTCTATTTTTGACCCCAAAACTTCC
AAAAATTACCATTTTACCCCCGAATCTTCCAAAAATCCATTTTCAACCTCG
Found at i:1118 original size:59 final size:59
Alignment explanation
Indices: 883--1231 Score: 286
Period size: 59 Copynumber: 5.9 Consensus size: 59
873 TTGACCTCAA
* * * *
883 AACTTCCAAAAATTCTGTTTTT-ACCCCCAAACTTCCAAAAA-TCCCATTTTTA-CCTCG
1 AACTTCCAAAAATTCTATTTTTGACCCCGAAACTTCCAAAAATTACCA-TTTTACCCCCG
* * *
940 AAACTTCCAAAAATTCTATTTTTGACCCCAAAACTTCCAAAAATT-TCATTTTTACCCTCG
1 -AACTTCCAAAAATTCTATTTTTGACCCCGAAACTTCCAAAAATTACCA-TTTTACCCCCG
* * * * * * *
1000 AACTTCCAAAAATCCCAATTTTAACCTCGAAACTTCCAAAAATT-CCGTTTTTACTCCCG
1 AACTTCCAAAAATTCTATTTTTGACCCCGAAACTTCCAAAAATTACC-ATTTTACCCCCG
* *
1059 AACTTCCAAAAA-TCTCGTTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATTCT-ATTTTTGACCCCGAAACTTCCAAAAATTACCATTTTACCCCCG
* * * * * * * *
1118 AA-TGTTCGAAGACTCCATTTTCGACCTCGAAAC-TCTC-AAAATTACCCTTTTACCCCCG
1 AACT-TCCAAAAATTCTATTTTTGACCCCGAAACTTC-CAAAAATTACCATTTTACCCCCG
* * ** * *
1176 AA-TGTCTAAAAATTCTATTTTTAACCCCGAATTTTCCCAAAATTACCATTTCACCC
1 AACT-TCCAAAAATTCTATTTTTGACCCCGAAACTTCCAAAAATTACCATTTTACCC
1232 TCGAGAATCC
Statistics
Matches: 236, Mismatches: 44, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
58 68 0.29
59 158 0.67
60 10 0.04
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (59 bp):
AACTTCCAAAAATTCTATTTTTGACCCCGAAACTTCCAAAAATTACCATTTTACCCCCG
Found at i:5169 original size:27 final size:27
Alignment explanation
Indices: 5139--5194 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5129 AATATATTAA
5139 TTAAATTACAAATTATGTCGACATTTT
1 TTAAATTACAAATTATGTCGACATTTT
5166 TTAAATTACAAATTATGTCGACATTTT
1 TTAAATTACAAATTATGTCGACATTTT
5193 TT
1 TT
5195 GGTCAAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (27 bp):
TTAAATTACAAATTATGTCGACATTTT
Found at i:5632 original size:2 final size:2
Alignment explanation
Indices: 5620--5683 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
5610 CAACTTAATC
* * *
5620 TA TA AA TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5662 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
5684 AATGGAAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7978 original size:28 final size:29
Alignment explanation
Indices: 7937--7992 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
7927 AAGATTTTTC
* *
7937 ATAATTTAAGTTATTA-TTAATTAATATA
1 ATAATATAAATTATTATTTAATTAATATA
*
7965 ATAATATAAATTATTATTTAATTGATAT
1 ATAATATAAATTATTATTTAATTAATAT
7993 TATTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
ATAATATAAATTATTATTTAATTAATATA
Found at i:9729 original size:46 final size:45
Alignment explanation
Indices: 9639--9729 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 45
9629 ATTAGTTTAA
* * * *
9639 AAAAATGGTAAAGTGTATTATAAAATTTGACATTATGTTTGAATG
1 AAAAATGATAAAGTGTATTATAAAATTTGACATAATATTAGAATG
9684 AAAAATGAATAAAGT-TATTAGTAAAATTTGA-ATAATATTAAGAATG
1 AAAAATG-ATAAAGTGTATTA-TAAAATTTGACATAATATT-AGAATG
9730 TTTAATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
45 18 0.46
46 21 0.54
ACGTcount: A:0.48, C:0.01, G:0.15, T:0.35
Consensus pattern (45 bp):
AAAAATGATAAAGTGTATTATAAAATTTGACATAATATTAGAATG
Done.