Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011638.1 Kokia drynarioides strain JFW-HI SEQ_126629, 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: 3165
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Found at i:547 original size:30 final size:30
Alignment explanation
Indices: 513--943 Score: 213
Period size: 29 Copynumber: 14.6 Consensus size: 30
503 CCCTAAATTA
513 TCCAAAAATTACATTTTTACCCTCGAACTT
1 TCCAAAAATTACATTTTTACCCTCGAACTT
* **
543 TCC-AAAATTCCATTTTTGA-CCTCGATTTTT
1 TCCAAAAATTACATTTTT-ACCCTCGA-ACTT
573 TCCAAAAATTACATTTTTACCCTCGAACTT
1 TCCAAAAATTACATTTTTACCCTCGAACTT
* * * *
603 TCC-AAAATTCCATTTTGA-CCT-TAATTTT
1 TCCAAAAATTACATTTTTACCCTCGAA-CTT
*
631 TCCAAAAATTACATTTTTACCCACGAACTT
1 TCCAAAAATTACATTTTTACCCTCGAACTT
* * * **
661 TCC-AAAATTTCA--TTTAACCTCCATTTTT
1 TCCAAAAATTACATTTTTACCCTCGA-ACTT
* * *
689 TCTAAAAAAATTACCA-TTTTACCCCCAAAC-T
1 TC--CAAAAATTA-CATTTTTACCCTCGAACTT
* * **
720 TCTAAAAATTCCATTTTTGA-CCTCGATTTT
1 TCCAAAAATTACATTTTT-ACCCTCGAACTT
* * *
750 TTCAAAAATGATCA-TTTTACCCTC-AAATT
1 TCCAAAAATTA-CATTTTTACCCTCGAACTT
* **
779 TCCAAAAATGACCATTTTTACCC-CGATTTT
1 TCCAAAAATTA-CATTTTTACCCTCGAACTT
* *
809 TCCAAAAATGACCA-TTTTACCCCCGAAC-T
1 TCCAAAAATTA-CATTTTTACCCTCGAACTT
* * *
838 TCCAAGAATTCCATTTTTGA-CCTCG-ATTCT
1 TCCAAAAATTACATTTTT-ACCCTCGAACT-T
* * *
868 TCCAAAAAGTACCA-TTTTACCCTCGGA-TA
1 TCCAAAAATTA-CATTTTTACCCTCGAACTT
* * * *
897 TCTAAAAATTCCGTTTTTGACCC-CTAAC-T
1 TCCAAAAATTACATTTTT-ACCCTCGAACTT
*
926 TCCCAAAATTACCATTTT
1 TCCAAAAATTA-CATTTT
944 CCCCCGAGTG
Statistics
Matches: 302, Mismatches: 66, Indels: 66
0.70 0.15 0.15
Matches are distributed among these distances:
27 10 0.03
28 18 0.06
29 133 0.44
30 96 0.32
31 35 0.12
32 2 0.01
33 8 0.03
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.38
Consensus pattern (30 bp):
TCCAAAAATTACATTTTTACCCTCGAACTT
Found at i:662 original size:118 final size:117
Alignment explanation
Indices: 513--892 Score: 441
Period size: 118 Copynumber: 3.2 Consensus size: 117
503 CCCTAAATTA
513 TCCAAAAATTA-CATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTTCCA
1 TCCAAAAATTACCA-TTTTACCCTCGAACTTTCCAAAATTCCATTTTT-ACCTCGATTTTTTCCA
* **
577 AAAATTA-CATTTTTACCCTCGAACTTTCCAAAATTCCA-TTTTGACCTTAATTTT
64 AAAATTACCA-TTTTACCCCCGAAC-TTCCAAAATTCCATTTTTGACCTCGATTTT
* * * * *
631 TCCAAAAATTA-CATTTTTACCCACGAACTTTCCAAAATTTCA-TTTAACCTCCATTTTTTCTAA
1 TCCAAAAATTACCA-TTTTACCCTCGAACTTTCCAAAATTCCATTTTTACCTCGATTTTTTC--C
* *
694 AAAAATTACCATTTTACCCCCAAACTTCTAAAAATTCCATTTTTGACCTCGATTTT
63 AAAAATTACCATTTTACCCCCGAACTTC-CAAAATTCCATTTTTGACCTCGATTTT
* * * * * *
750 TTCAAAAATGATCATTTTACCCTC-AAATTTCCAAAAATGACCATTTTTACCCCGA-TTTTTCCA
1 TCCAAAAATTACCATTTTACCCTCGAACTTTCC-AAAAT-TCCATTTTTACCTCGATTTTTTCCA
* *
813 AAAATGACCATTTTACCCCCGAACTTCCAAGAATTCCATTTTTGACCTCGATTCT
64 AAAATTACCATTTTACCCCCGAACTTCCAA-AATTCCATTTTTGACCTCGATTTT
*
868 TCCAAAAAGTACCATTTTACCCTCG
1 TCCAAAAATTACCATTTTACCCTCG
893 GATATCTAAA
Statistics
Matches: 223, Mismatches: 28, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
116 13 0.06
117 8 0.04
118 145 0.65
119 39 0.17
120 10 0.04
121 8 0.04
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.38
Consensus pattern (117 bp):
TCCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTACCTCGATTTTTTCCAAA
AATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTGACCTCGATTTT
Found at i:756 original size:29 final size:29
Alignment explanation
Indices: 724--943 Score: 59
Period size: 30 Copynumber: 7.4 Consensus size: 29
714 CAAACTTCTA
** *
724 AAAATTCCATTTTTGA-CCTCGATTTTTTCA
1 AAAATTCCATTTTT-ACCCTCGA-ACTTTCC
*
754 AAAATGATC-ATTT-TACCCTC-AAATTTCC
1 AAAAT--TCCATTTTTACCCTCGAACTTTCC
* **
782 AAAAATGACCATTTTTACCC-CGATTTTTCC
1 -AAAAT-TCCATTTTTACCCTCGAACTTTCC
* *
812 AAAAATGACCA-TTTTACCCCCGAAC-TTCC
1 -AAAAT-TCCATTTTTACCCTCGAACTTTCC
*
841 AAGAATTCCATTTTTGA-CCTCG-ATTCTTCC
1 AA-AATTCCATTTTT-ACCCTCGAACT-TTCC
* * * *
871 AAAAAGTACCA-TTTTACCCTCGGA-TATCTA
1 -AAAA-TTCCATTTTTACCCTCGAACTTTC-C
* * *
901 AAAATTCCGTTTTTGACCC-CTAACTTCCC
1 AAAATTCCATTTTT-ACCCTCGAACTTTCC
930 AAAATTACCATTTT
1 AAAATT-CCATTTT
944 CCCCCGAGTG
Statistics
Matches: 145, Mismatches: 23, Indels: 44
0.68 0.11 0.21
Matches are distributed among these distances:
28 14 0.10
29 54 0.37
30 64 0.44
31 11 0.08
32 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCGAACTTTCC
Found at i:786 original size:59 final size:59
Alignment explanation
Indices: 513--918 Score: 348
Period size: 59 Copynumber: 6.9 Consensus size: 59
503 CCCTAAATTA
* *
513 TCCAAAAATTA-CATTTTTACCCTCGAACTTTCC-AAAATTCCATTTTTGACCTCGATTTTT
1 TCCAAAAATGACCA-TTTTACCCTC-AAATTTCCAAAAATTCCATTTTTGACCTCGA-TTTT
* * **
573 TCCAAAAATTA-CATTTTTACCCTCGAACTTTCC-AAAATTCCA-TTTTGACCTTAATTTT
1 TCCAAAAATGACCA-TTTTACCCTC-AAATTTCCAAAAATTCCATTTTTGACCTCGATTTT
* * * * * *
631 TCCAAAAATTA-CATTTTTACCCACGAACTTTCC-AAAATTTCA--TTTAACCTCCATTTTT
1 TCCAAAAATGACCA-TTTTACCCTC-AAATTTCCAAAAATTCCATTTTTGACCTCGA-TTTT
* * * * *
689 TCTAAAAAAATTACCATTTTACCCCCAAACTTCTAAAAATTCCATTTTTGACCTCGATTTT
1 TC--CAAAAATGACCATTTTACCCTCAAATTTCCAAAAATTCCATTTTTGACCTCGATTTT
* * * *
750 TTCAAAAATGATCATTTTACCCTCAAATTTCCAAAAATGACCATTTTT-ACCCCGATTTT
1 TCCAAAAATGACCATTTTACCCTCAAATTTCCAAAAAT-TCCATTTTTGACCTCGATTTT
* * * * *
809 TCCAAAAATGACCATTTTACCCCCGAACTTCCAAGAATTCCATTTTTGACCTCGATTCT
1 TCCAAAAATGACCATTTTACCCTCAAATTTCCAAAAATTCCATTTTTGACCTCGATTTT
** * * *
868 TCCAAAAA-GTACCATTTTACCCTCGGATATCTAAAAATTCCGTTTTTGACC
1 TCCAAAAATG-ACCATTTTACCCTCAAATTTCCAAAAATTCCATTTTTGACC
919 CCTAACTTCC
Statistics
Matches: 296, Mismatches: 40, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
57 8 0.03
58 59 0.20
59 138 0.47
60 75 0.25
61 7 0.02
62 9 0.03
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.38
Consensus pattern (59 bp):
TCCAAAAATGACCATTTTACCCTCAAATTTCCAAAAATTCCATTTTTGACCTCGATTTT
Found at i:904 original size:118 final size:114
Alignment explanation
Indices: 513--950 Score: 388
Period size: 118 Copynumber: 3.7 Consensus size: 114
503 CCCTAAATTA
* * *
513 TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTTCCAA
1 TCCAAAAA-TACA-TTTTACCCTCGAA-TTTCAAAAATACCATTTTT-ACCCCGATTTTTTCCAA
* **
578 AAATTA-CATTTTTACCCTCGAACTTTCCAAAATTCCA-TTTTGACCTTAATTTT
62 AAATTACCA-TTTTACCCCCGAAC-TTCCAAAATTCCATTTTTGACCTCGATTTT
* * ** * *
631 TCCAAAAATTACATTTTTACCCACGAACTTTCCAAAATTTCA-TTTAACCTCC-ATTTTTTCTAA
1 TCCAAAAA-TACA-TTTTACCCTCGAA-TTTCAAAAATACCATTTTTACC-CCGATTTTTTC--C
* *
694 AAAAATTACCATTTTACCCCCAAACTTCTAAAAATTCCATTTTTGACCTCGATTTT
60 AAAAATTACCATTTTACCCCCGAACTTC-CAAAATTCCATTTTTGACCTCGATTTT
* *
750 TTCAAAAATGATCATTTTACCCTCAAATTTCCAAAAATGACCATTTTTACCCCGA-TTTTTCCAA
1 TCCAAAAAT-A-CATTTTACCCTCGAATTT-CAAAAAT-ACCATTTTTACCCCGATTTTTTCCAA
* *
814 AAATGACCATTTTACCCCCGAACTTCCAAGAATTCCATTTTTGACCTCGATTCT
62 AAATTACCATTTTACCCCCGAACTTCCAA-AATTCCATTTTTGACCTCGATTTT
* * * * *** *
868 TCCAAAAAGTACCATTTTACCCTCGGATATCTAAAAATTCCGTTTTTGACCCC--TAACTTCCCA
1 TCCAAAAA-TA-CATTTTACCCTCGAATTTC-AAAAATACCATTTTT-ACCCCGATTTTTTCCAA
931 AAATTACCATTTT-CCCCCGA
62 AAATTACCATTTTACCCCCGA
951 GTGACAAATT
Statistics
Matches: 269, Mismatches: 34, Indels: 36
0.79 0.10 0.11
Matches are distributed among these distances:
116 18 0.07
117 34 0.13
118 156 0.58
119 42 0.16
120 12 0.04
121 7 0.03
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (114 bp):
TCCAAAAATACATTTTACCCTCGAATTTCAAAAATACCATTTTTACCCCGATTTTTTCCAAAAAT
TACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTGACCTCGATTTT
Found at i:3132 original size:7 final size:7
Alignment explanation
Indices: 3120--3149 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
3110 AAATGGTCTC
3120 TTTATTA
1 TTTATTA
3127 TTTATTTA
1 TTTA-TTA
3135 TTTATTA
1 TTTATTA
3142 TTTATTA
1 TTTATTA
3149 T
1 T
3150 AAGATGAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Done.