Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009700.1 Kokia drynarioides strain JFW-HI SEQ_124419, 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: 10038
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:6877 original size:30 final size:29
Alignment explanation
Indices: 6844--7248 Score: 265
Period size: 29 Copynumber: 13.8 Consensus size: 29
6834 AGAGGTCCCT
**
6844 AAACTTCCTAAAAATTACATTTTTACCCTT
1 AAACTTCC-AAAAATTACATTTTTACCCCC
* * * *
6874 AAACTTTCTAAAATTCCATTTTTGA-CCTC
1 AAACTTCCAAAAATTACATTTTT-ACCCCC
* ** *
6903 GATTTTCCAAAAATTACATTTTTACCCTC
1 AAACTTCCAAAAATTACATTTTTACCCCC
* * *
6932 GAACTTTCC-AAAATT-CTATTTTGA-CCCA
1 AAAC-TTCCAAAAATTAC-ATTTTTACCCCC
* *
6960 AAACTTTCAAAAATTACCATTTTT-CCCCT
1 AAACTTCCAAAAATTA-CATTTTTACCCCC
* * *
6989 GAACTTCCAAAAATTCCATTTTTACCCCG
1 AAACTTCCAAAAATTACATTTTTACCCCC
*
7018 AAACTTTCAAAAATTACATTTTTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCC
*
7047 AAACTTCCAAAAATT-CTATTTTTGACCTCCG
1 AAACTTCCAAAAATTAC-ATTTTT-ACC-CCC
* * **
7078 AAACTTCTAAACATTACATTTTTACCAAC
1 AAACTTCCAAAAATTACATTTTTACCCCC
* * *
7107 AAACCTT-TAAAAATTCCATTTTTGACCCCA
1 AAA-CTTCCAAAAATTACATTTTT-ACCCCC
*
7137 AAACTTCTAAAAATTACATTTTTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCC
** * * *
7166 GGA-TGTCCAAAAACTACATTTTTGACCTCG
1 AAACT-TCCAAAAATTACATTTTT-ACCCCC
*
7196 AAAC-TCTCAAAAATTATC-GTTTTACCCCC
1 AAACTTC-CAAAAATTA-CATTTTTACCCCC
* * *
7225 GAA-TGTCCAAAAATTCCTTTTTTA
1 AAACT-TCCAAAAATTACATTTTTA
7249 AACTCGATTT
Statistics
Matches: 295, Mismatches: 56, Indels: 49
0.74 0.14 0.12
Matches are distributed among these distances:
27 3 0.01
28 23 0.08
29 184 0.62
30 62 0.21
31 22 0.07
32 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCC
Found at i:6945 original size:58 final size:59
Alignment explanation
Indices: 6848--7282 Score: 306
Period size: 58 Copynumber: 7.4 Consensus size: 59
6838 GTCCCTAAAC
** * *
6848 TTCCTAAAAATTACATTTTTACCCTTAAACTTT-CTAAAATTCCATTTTTGACCTCGATT
1 TTCC-AAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCTCGAAT
* *
6907 TTCCAAAAATTACATTTTTACCCTCGAACTTTCC-AAAATTCTA-TTTTGACC-CAAAACT
1 TTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCTC-GAA-T
* *
6965 TT-CAAAAATTACCATTTTTCCCCT-GAAC-TTCCAAAAATTCCATTTTT-ACCCCGAAACT
1 TTCCAAAAATTA-CATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCTCG-AA-T
* * * *
7023 TT-CAAAAATTACATTTTTACCCCCAAAC-TTCCAAAAATTCTATTTTTGACCTCCGAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCT-CG-AAT
* * ** * * * *
7082 TTCTAAACATTACATTTTTACCAACAAACCTTT--AAAAATTCCATTTTTGACCCCAAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAA-CTTTCCAAAAATTCCATTTTTGACCTC-GAAT
* * * * * * *
7141 TTCTAAAAATTACATTTTTACCCCCGGA-TGTCCAAAAACTACATTTTTGACCTCGAAA
1 TTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCTCGAAT
* * * * * * * *
7199 CTCTCAAAAATTATC-GTTTTACCCCCGAA-TGTCCAAAAATTCCTTTTTTAAACTCGATT
1 TTC-CAAAAATTA-CATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCTCGAAT
** **
7258 TTTTAAAAATTACCGTTTTACCCTC
1 TTCCAAAAATTACATTTTTACCCTC
7283 TGATGTCTAA
Statistics
Matches: 309, Mismatches: 47, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
56 5 0.02
57 46 0.15
58 111 0.36
59 99 0.32
60 45 0.15
61 1 0.00
62 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (59 bp):
TTCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTCCATTTTTGACCTCGAAT
Found at i:7178 original size:59 final size:60
Alignment explanation
Indices: 6844--7247 Score: 383
Period size: 59 Copynumber: 6.9 Consensus size: 60
6834 AGAGGTCCCT
*** * * *
6844 AAACTTC-CTAAAAATTACATTTTTACCCTTAAACTTTCTAAAATTCCATTTTTGACCTCG
1 AAACTTCTC-AAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCG
** * * *
6904 -ATTTTC-CAAAAATTACATTTTTACCCTCGAACTTTCC-AAAATTCTA-TTTTGA-CCCA
1 AAACTTCTCAAAAATTACATTTTTACCCCCGAAC-TTCCAAAAATTCCATTTTTGACCCCG
*
6960 AAACTT-TCAAAAATTACCATTTTT-CCCCTGAACTTCCAAAAATTCCATTTTT-ACCCCG
1 AAACTTCTCAAAAATTA-CATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCG
* *
7018 AAACTT-TCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCTATTTTTGACCTCCG
1 AAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACC-CCG
* ** * * *
7078 AAACTTCT-AAACATTACATTTTTACCAACAAACCTT-TAAAAATTCCATTTTTGACCCCA
1 AAACTTCTCAAAAATTACATTTTTACCCCCGAA-CTTCCAAAAATTCCATTTTTGACCCCG
* * * *
7137 AAACTTCT-AAAAATTACATTTTTACCCCCGGA-TGTCCAAAAACTACATTTTTGACCTCG
1 AAACTTCTCAAAAATTACATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTTGACCCCG
* *
7196 AAAC-TCTCAAAAATTATC-GTTTTACCCCCGAA-TGTCCAAAAATTCCTTTTTT
1 AAACTTCTCAAAAATTA-CATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTT
7248 AAACTCGATT
Statistics
Matches: 290, Mismatches: 38, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
56 6 0.02
57 42 0.14
58 90 0.31
59 99 0.34
60 49 0.17
61 4 0.01
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (60 bp):
AAACTTCTCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:8353 original size:96 final size:96
Alignment explanation
Indices: 8165--8356 Score: 210
Period size: 96 Copynumber: 2.0 Consensus size: 96
8155 TCTTTGCGAA
* ** *
8165 AAGGATATTTGATTATCTCGATTTCAAGAAAGGTTGCACCTAGTAAGTTTAGGCGCAATATTTCG
1 AAGGATATTTAATTATCTCGATTTCAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
* * *
8230 GAATCGAAGATAAGGAAACATTACCTCGATT
66 AAACCGAAGATAAAGAAACATTACCTCGATT
* * * * *
8261 AAGGGTATTTAATTATTTTGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTC
1 AAGGATATTTAATTATCTCGATTTCAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTC
* *
8325 GAAACCCGAA-ATGAAAG-AATATTGCCTCGATT
65 GAAA-CCGAAGAT-AAAGAAACATTACCTCGATT
8357 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
95 1 0.01
96 71 0.90
97 7 0.09
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (96 bp):
AAGGATATTTAATTATCTCGATTTCAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
AAACCGAAGATAAAGAAACATTACCTCGATT
Found at i:8655 original size:30 final size:29
Alignment explanation
Indices: 8586--8761 Score: 214
Period size: 29 Copynumber: 6.0 Consensus size: 29
8576 TCGGATTCCC
* *
8586 GGGGGTAAAAATG-GTTTTTTTGGAAGTTC
1 GGGGGTAAAAATGAG-ATTTTTGGAAGTTT
*
8615 GAGGGTAAAAATGAGATTTTTGGAAGTTT
1 GGGGGTAAAAATGAGATTTTTGGAAGTTT
* *
8644 TGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 GGGGGT-AAAAATGAGATTTTTGGAAGTTT
*
8674 GGGGGTAAAATTGAGATTTTTGGAAGTTTT
1 GGGGGTAAAAATGAGATTTTTGGAAG-TTT
*
8704 GGGGTTAAAAAT-AGGATTTTTGGAAGTTT
1 GGGGGTAAAAATGA-GATTTTTGGAAGTTT
8733 GGGGGTAAAAAT-AGAATTTTTGGACAGTT
1 GGGGGTAAAAATGAG-ATTTTTGGA-AGTT
8762 AGGGACCTTC
Statistics
Matches: 129, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
28 1 0.01
29 71 0.55
30 57 0.44
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (29 bp):
GGGGGTAAAAATGAGATTTTTGGAAGTTT
Found at i:8655 original size:59 final size:57
Alignment explanation
Indices: 8587--8761 Score: 244
Period size: 59 Copynumber: 3.0 Consensus size: 57
8577 CGGATTCCCG
* * *
8587 GGGGTAAAAATGGTTTTTTTGGAAGTTCGAGGGTAAAAATGAGATTTTTGGAAGTTTT
1 GGGGTAAAAATGG-ATTTTTGGAAGTTTGGGGGTAAAAATGAGATTTTTGGAAGTTTT
*
8645 GGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATTGAGATTTTTGGAAGTTTT
1 GGGGT-AAAAAT-GGATTTTTGGAAGTTTGGGGGTAAAAATGAGATTTTTGGAAGTTTT
8704 GGGGTTAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAAT-AGAATTTTTGGACAGTT
1 GGGG-TAAAAAT-GGATTTTTGGAAGTTTGGGGGTAAAAATGAG-ATTTTTGGA-AGTT
8762 AGGGACCTTC
Statistics
Matches: 106, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
58 7 0.07
59 92 0.87
60 7 0.07
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.37
Consensus pattern (57 bp):
GGGGTAAAAATGGATTTTTGGAAGTTTGGGGGTAAAAATGAGATTTTTGGAAGTTTT
Done.