Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012459.1 Kokia drynarioides strain JFW-HI SEQ_127463, 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: 4736
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:321 original size:17 final size:17
Alignment explanation
Indices: 301--412 Score: 116
Period size: 17 Copynumber: 6.5 Consensus size: 17
291 GGCTTTATTT
**
301 ATTTTAAATTTATGATA
1 ATTTTAAATTTAAAATA
318 ATTTTAAATTTGAAAATA
1 ATTTTAAATTT-AAAATA
*
336 ATTTTAAACTTAAAATA
1 ATTTTAAATTTAAAATA
*
353 AATTTAAATTTAAAATA
1 ATTTTAAATTTAAAATA
* * *
370 AATTTAAATTTTTAAACA
1 ATTTTAAA-TTTAAAATA
* *
388 AATTTAATTTTAAAATA
1 ATTTTAAATTTAAAATA
*
405 AATTTAAA
1 ATTTTAAA
413 GGGAGTTTGG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
17 54 0.66
18 28 0.34
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:359 original size:35 final size:34
Alignment explanation
Indices: 303--412 Score: 130
Period size: 35 Copynumber: 3.2 Consensus size: 34
293 CTTTATTTAT
** * *
303 TTTAAATTTATGATAATTTTAAATTTGAAAATAAT
1 TTTAAATTTAAAATAAATTTAAATTT-AAAATAAA
*
338 TTTAAACTTAAAATAAATTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
* * *
372 TTTAAATTTTTAAACAAATTTAATTTTAAAATAAA
1 TTTAAA-TTTAAAATAAATTTAAATTTAAAATAAA
407 TTTAAA
1 TTTAAA
413 GGGAGTTTGG
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
34 13 0.20
35 52 0.80
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
Found at i:376 original size:52 final size:52
Alignment explanation
Indices: 303--412 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
293 CTTTATTTAT
** * * *
303 TTTAAATTTATGATAATTTTAAATTTGAAAATAATTTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
** **
355 TTTAAATTTAAAATAAATTTAAATTTTTAAACAAATTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
407 TTTAAA
1 TTTAAA
413 GGGAGTTTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
Found at i:728 original size:6 final size:5
Alignment explanation
Indices: 704--766 Score: 54
Period size: 5 Copynumber: 11.6 Consensus size: 5
694 CGGCCCCCTT
* * *
704 TTTAA TTTAT TTTAAA TTTAGA TTTAT TTTAAA TTTAA ATTAA TTTAAA
1 TTTAA TTTAA TTT-AA TTTA-A TTTAA TTT-AA TTTAA TTTAA TTT-AA
753 TTTAAA TTTAA TTT
1 TTT-AA TTTAA TTT
767 CAAAATTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 24 0.50
6 24 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
TTTAA
Found at i:763 original size:17 final size:17
Alignment explanation
Indices: 707--776 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
697 CCCCCTTTTT
*
707 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
* *
724 GATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
741 AA-TTAATTTAAATTTA
1 AATTTAATTTAAATTTA
*
757 AATTTAATTTCAAAATTA
1 AATTTAATTT-AAATTTA
775 AA
1 AA
777 AGAAAAGAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
16 15 0.32
17 24 0.51
18 8 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:765 original size:11 final size:11
Alignment explanation
Indices: 704--766 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
694 CGGCCCCCTT
*
704 TTTAATTT-AT
1 TTTAATTTAAA
*
714 TTTAAATTTAGA
1 TTT-AATTTAAA
*
726 TTTATTTTAAA
1 TTTAATTTAAA
*
737 TTTAAATT-AA
1 TTTAATTTAAA
747 TTTAAATTTAAA
1 TTT-AATTTAAA
759 TTTAATTT
1 TTTAATTT
767 CAAAATTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.19
11 26 0.62
12 8 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:777 original size:6 final size:6
Alignment explanation
Indices: 714--776 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
704 TTTAATTTAT
* *
714 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
759 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
777 AGAAAAGAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 2 0.04
5 12 0.26
6 29 0.62
7 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:884 original size:26 final size:26
Alignment explanation
Indices: 807--886 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
797 AATAATGTTC
* *
807 AATTACAAATGGCCCAAGTCAGCCCA
1 AATTACAAATGGCCCAAGTCAACCTA
* * **
833 AA-TAC--ATGACCCAAATGCCATTCTA
1 AATTACAAATGGCCC-AA-GTCAACCTA
858 AATTACAAATGGCCCAAGTCAACCTA
1 AATTACAAATGGCCCAAGTCAACCTA
884 AAT
1 AAT
887 ACCCTAAGCC
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
23 6 0.15
24 2 0.05
25 10 0.25
26 14 0.35
27 2 0.05
28 6 0.15
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (26 bp):
AATTACAAATGGCCCAAGTCAACCTA
Found at i:1564 original size:21 final size:21
Alignment explanation
Indices: 1516--1567 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1506 TCTTAATATT
**
1516 TATTAATAATAATAAATGTTT
1 TATTAATAATAATAAATGTAC
*
1537 TAATAATAATAAT-AATGATAC
1 TATTAATAATAATAAATG-TAC
1558 TATTAATAAT
1 TATTAATAAT
1568 TATTAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (21 bp):
TATTAATAATAATAAATGTAC
Found at i:2565 original size:21 final size:21
Alignment explanation
Indices: 2539--2588 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2529 CCCTGAACTT
2539 CCAAAAATCTCATTTTTGACC
1 CCAAAAATCTCATTTTTGACC
2560 CCAAAAATCTCATTTTTGACC
1 CCAAAAATCTCATTTTTGACC
2581 CCAAAAAT
1 CCAAAAAT
2589 TCCAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.30
Consensus pattern (21 bp):
CCAAAAATCTCATTTTTGACC
Found at i:2596 original size:30 final size:29
Alignment explanation
Indices: 2560--2931 Score: 356
Period size: 29 Copynumber: 12.6 Consensus size: 29
2550 ATTTTTGACC
*
2560 CCAAAAATCTCATTTTTGACCCCAAAAATT
1 CCAAAAATCTCATTTTT-ACCCCAAAACTT
***
2590 CCAAAAAATC-CATTTTTACCCTTGAACTT
1 CC-AAAAATCTCATTTTTACCCCAAAACTT
*
2619 CCAAAAATCCCATTTTTGACCCCAAAACTT
1 CCAAAAATCTCATTTTT-ACCCCAAAACTT
* * * **
2649 CCAAAAATTTTATTTTAACCCCCGAACTT
1 CCAAAAATCTCATTTTTACCCCAAAACTT
**
2678 CCAAAAAT-TCCATTTTTACCCCCGAACTT
1 CCAAAAATCT-CATTTTTACCCCAAAACTT
2707 CCAAAAATCTCATTTTTGACCCCAAAACTT
1 CCAAAAATCTCATTTTT-ACCCCAAAACTT
2737 CCAAAAAT-TCCATTTTTACCCCCAAAACTT
1 CCAAAAATCT-CATTTTTA-CCCCAAAACTT
* * * ***
2767 CTAAAAATTTTATTTTTACCCTTGAACTT
1 CCAAAAATCTCATTTTTACCCCAAAACTT
* *
2796 CCAAAAAATCCCATTTTTGATCCCGAAAACTT
1 CC-AAAAATCTCATTTTT-A-CCCCAAAACTT
* *
2828 CCAAAAATTTCATTTTTACCCCCAAACTT
1 CCAAAAATCTCATTTTTACCCCAAAACTT
* *
2857 CCCAAAATCTCATTTTTGACCCCGAAACTT
1 CCAAAAATCTCATTTTT-ACCCCAAAACTT
** *
2887 CCAAAAAT-TCTATTTTTACCCCCGAATTT
1 CCAAAAATCTC-ATTTTTACCCCAAAACTT
*
2916 CCAAAAATCCCATTTT
1 CCAAAAATCTCATTTT
2932 CGACCTCGAA
Statistics
Matches: 286, Mismatches: 41, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.03
29 126 0.44
30 120 0.42
31 22 0.08
32 10 0.03
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
CCAAAAATCTCATTTTTACCCCAAAACTT
Found at i:2652 original size:59 final size:59
Alignment explanation
Indices: 2560--3011 Score: 438
Period size: 59 Copynumber: 7.7 Consensus size: 59
2550 ATTTTTGACC
* * * **
2560 CCAAAAATCTCATTTTTGACCCCAAAAATTCCAAAAAATCCATTTTTACCCTTGAACTT
1 CCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
** *
2619 CCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTTTATTTTAACCCCCGAACTT
1 CCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
* ** **
2678 CCAAAAATTCCATTTTT-ACCCCCGAACTTCCAAAAA-TCTCATTTTTGACCCCAAAACTT
1 CCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTC-CATTTTT-ACCCCCGAACTT
* * ** **
2737 CCAAAAATTCCATTTTT-ACCCCCAAAACTTCTAAAAATTTTATTTTTACCCTTGAACTT
1 CCAAAAATCCCATTTTTGA-CCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
* * *
2796 CCAAAAAATCCCATTTTTGATCCCGAAAACTTCCAAAAATTTCATTTTTACCCCCAAACTT
1 CC-AAAAATCCCATTTTTGA-CCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
* * * * *
2857 CCCAAAATCTCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTACCCCCGAATTT
1 CCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
* * *
2916 CCAAAAATCCCATTTTCGACCTCGAAAC-TCTC-AAAATTAACC--TTTTACCCCCCGAA-TAT
1 CCAAAAATCCCATTTTTGACCCCAAAACTTC-CAAAAATT--CCATTTTTA-CCCCCGAACT-T
* * * *
2975 -CAAAAATTCCA-TTTTAACCCCAAAATTTCCCAAAATT
1 CCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATT
3012 ACTATTTCAC
Statistics
Matches: 329, Mismatches: 51, Indels: 27
0.81 0.13 0.07
Matches are distributed among these distances:
57 12 0.04
58 54 0.16
59 174 0.53
60 51 0.16
61 38 0.12
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
CCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
Found at i:3009 original size:29 final size:29
Alignment explanation
Indices: 2560--3011 Score: 272
Period size: 29 Copynumber: 15.3 Consensus size: 29
2550 ATTTTTGACC
* *
2560 CCAAAAA-TCTCATTTTTGACCCCAAAAATT
1 CCAAAAATTC-CA-TTTTAACCCCAAAACTT
* * ***
2590 CCAAAAAATCCATTTTTACCCTTGAACTT
1 CCAAAAATTCCATTTTAACCCCAAAACTT
* *
2619 CCAAAAATCCCATTTTTGACCCCAAAACTT
1 CCAAAAATTCCA-TTTTAACCCCAAAACTT
** **
2649 CCAAAAATTTTATTTTAACCCCCGAACTT
1 CCAAAAATTCCATTTTAACCCCAAAACTT
* **
2678 CCAAAAATTCCATTTTTACCCCCGAACTT
1 CCAAAAATTCCATTTTAACCCCAAAACTT
*
2707 CCAAAAA-TCTCATTTTTGACCCCAAAACTT
1 CCAAAAATTC-CA-TTTTAACCCCAAAACTT
*
2737 CCAAAAATTCCATTTTTACCCCCAAAACTT
1 CCAAAAATTCCA-TTTTAACCCCAAAACTT
* ** * ***
2767 CTAAAAATTTTATTTTTACCCTTGAACTT
1 CCAAAAATTCCATTTTAACCCCAAAACTT
* * *
2796 CCAAAAAATCCCATTTTTGATCCCGAAAACTT
1 CC-AAAAATTCCA-TTTT-AACCCCAAAACTT
* * *
2828 CCAAAAATTTCATTTTTACCCCCAAACTT
1 CCAAAAATTCCATTTTAACCCCAAAACTT
* * *
2857 CCCAAAA-TCTCATTTTTGACCCCGAAACTT
1 CCAAAAATTC-CA-TTTTAACCCCAAAACTT
* * ** *
2887 CCAAAAATTCTATTTTTACCCCCGAATTT
1 CCAAAAATTCCATTTTAACCCCAAAACTT
* * * *
2916 CCAAAAATCCCATTTTCGACCTCGAAAC-T
1 CCAAAAATTCCATTTT-AACCCCAAAACTT
* **
2945 CTC-AAAATTAACC-TTTTACCCCCCGAA-TAT
1 C-CAAAAATT--CCATTTTAACCCCAAAACT-T
*
2975 -CAAAAATTCCATTTTAACCCCAAAATTT
1 CCAAAAATTCCATTTTAACCCCAAAACTT
*
3003 CCCAAAATT
1 CCAAAAATT
3012 ACTATTTCAC
Statistics
Matches: 326, Mismatches: 75, Indels: 43
0.73 0.17 0.10
Matches are distributed among these distances:
27 2 0.01
28 16 0.05
29 154 0.47
30 124 0.38
31 20 0.06
32 10 0.03
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
CCAAAAATTCCATTTTAACCCCAAAACTT
Done.