Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001814.1 Kokia drynarioides strain JFW-HI SEQ_113553, 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: 10426
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Found at i:647 original size:24 final size:23
Alignment explanation
Indices: 616--663 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
606 ACTTGGACAT
*
616 TTTAAATAAATTTTAAATTT-AAA
1 TTTAAATAAA-CTTAAATTTCAAA
639 TTTATAATAAACTTAAATTTCAAA
1 TTTA-AATAAACTTAAATTTCAAA
663 T
1 T
664 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAATAAACTTAAATTTCAAA
Found at i:649 original size:17 final size:17
Alignment explanation
Indices: 629--705 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
619 AAATAAATTT
*
629 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
646 TAAACTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
663 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
** *
680 TAAACCTAATTTTAAAA
1 TAAATTTAAATTTAAAA
697 TAAATTTAA
1 TAAATTTAA
706 GTTTGTTGGG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:667 original size:34 final size:34
Alignment explanation
Indices: 629--705 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 34
619 AAATAAATTT
* * * *
629 TAAATTTAAATTTATAATAAACTTAAATTTCAAA
1 TAAATTTAAATTCAAAATAAACCTAAATTTAAAA
*
663 TAAATTTAAATTCAAAATAAACCTAATTTTAAAA
1 TAAATTTAAATTCAAAATAAACCTAAATTTAAAA
697 TAAATTTAA
1 TAAATTTAA
706 GTTTGTTGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (34 bp):
TAAATTTAAATTCAAAATAAACCTAAATTTAAAA
Found at i:2718 original size:27 final size:28
Alignment explanation
Indices: 2688--2778 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 28
2678 CCGCTAAAGG
2688 TGTGTCTT-TGTCTGTGCTACATGTTGT
1 TGTGTCTTCTGTCTGTGCTACATGTTGT
* * * * *
2715 TGTGTGTTTCTATTTGTGGTACATATTTGT
1 TGTGT-CTTCTGTCTGTGCTACAT-GTTGT
* * *
2745 TGTGTGTTCTGTCTGTGTTATATGATTGT
1 TGTGTCTTCTGTCTGTGCTACATG-TTGT
2774 TGTGT
1 TGTGT
2779 GATGTTATCT
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
27 5 0.10
28 2 0.04
29 33 0.67
30 9 0.18
ACGTcount: A:0.10, C:0.09, G:0.26, T:0.55
Consensus pattern (28 bp):
TGTGTCTTCTGTCTGTGCTACATGTTGT
Found at i:2732 original size:29 final size:28
Alignment explanation
Indices: 2698--2779 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
2688 TGTGTCTTTG
2698 TCTGTGCTACATGTTGTTGTGTGTTTCTA
1 TCTGTGCTACATGTTGTTGTGTG-TTCTA
* * * *
2727 TTTGTGGTACATATTTGTTGTGTGTTCTG
1 TCTGTGCTACAT-GTTGTTGTGTGTTCTA
* *
2756 TCTGTGTTATATGATTGTTGTGTG
1 TCTGTGCTACATG-TTGTTGTGTG
2780 ATGTTATCTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 33 0.77
30 10 0.23
ACGTcount: A:0.11, C:0.09, G:0.27, T:0.54
Consensus pattern (28 bp):
TCTGTGCTACATGTTGTTGTGTGTTCTA
Found at i:5290 original size:27 final size:27
Alignment explanation
Indices: 5248--5331 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
5238 GTTTGGCTTA
* *
5248 AATGAGCAATACTCTGAACTCTA-CTCG
1 AATGAGCATTATTCTG-ACTCTAGCTCG
** *
5275 AATGAGCATTATTCTGTGTTTAGCTCG
1 AATGAGCATTATTCTGACTCTAGCTCG
* *
5302 AAAGAGCATTATTCTGTACT-TGGCTCG
1 AATGAGCATTATTCTG-ACTCTAGCTCG
5329 AAT
1 AAT
5332 AAGTCATTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
26 3 0.07
27 41 0.91
28 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
AATGAGCATTATTCTGACTCTAGCTCG
Found at i:6392 original size:18 final size:17
Alignment explanation
Indices: 6345--6393 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
6335 ATTTACAAGT
6345 ATAAATAATAAGAAAACA
1 ATAAATAATAA-AAAACA
* *
6363 ATATATACATAAAATACA
1 ATAAATA-ATAAAAAACA
6381 ATAAGATAATAAA
1 ATAA-ATAATAAA
6394 TTGAGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.22
Consensus pattern (17 bp):
ATAAATAATAAAAAACA
Found at i:6488 original size:3 final size:3
Alignment explanation
Indices: 6480--6520 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
6470 GGATTAACTC
6480 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6521 AAGAGATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6631 original size:30 final size:31
Alignment explanation
Indices: 6595--6769 Score: 164
Period size: 30 Copynumber: 5.8 Consensus size: 31
6585 AATTAAAATC
*
6595 GGGTCAAATTTGAA-TTTTAGGAAAGTTTGG
1 GGGTCAAATTCGAATTTTTAGGAAAGTTTGG
* * *
6625 GGGTCAAATTAGAATTTTT-GGAAAATTTAG
1 GGGTCAAATTCGAATTTTTAGGAAAGTTTGG
* * *
6655 GGGTCAAATTGGAACTTTT-GGAAGGTTTGG
1 GGGTCAAATTCGAATTTTTAGGAAAGTTTGG
* *
6685 GGGTTAAATTCAAATTTTTA-GAAAGTTTGG
1 GGGTCAAATTCGAATTTTTAGGAAAGTTTGG
* * * * *
6715 GGATTAAATTCAAATTTTTAGG-AAGTTCGA
1 GGGTCAAATTCGAATTTTTAGGAAAGTTTGG
* *
6745 GGGTTAAATTTGAATTTTT-GGAAAG
1 GGGTCAAATTCGAATTTTTAGGAAAG
6770 ATCAATGGTT
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
29 2 0.02
30 115 0.94
31 5 0.04
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (31 bp):
GGGTCAAATTCGAATTTTTAGGAAAGTTTGG
Found at i:6683 original size:60 final size:58
Alignment explanation
Indices: 6595--6768 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 58
6585 AATTAAAATC
* *
6595 GGGTCAAATTTGAATTTTAGGAAAGTTTGGGGGTCAAATTAGAATTTTTGGAAAATTTAG
1 GGGTCAAATTCGAATTTTAGG-AAGTTTGGGGGTTAAATTAGAATTTTTGGAAAATTT-G
* * *
6655 GGGTCAAATTGGAACTTTT-GGAAGGTTTGGGGGTTAAATTCA-AATTTTTAGAAAGTTTG
1 GGGTCAAATTCGAA-TTTTAGGAA-GTTTGGGGGTTAAATT-AGAATTTTTGGAAAATTTG
* * * * *
6714 GGGATTAAATTCAAATTTTTAGGAAGTTCGAGGGTTAAATTTGAATTTTTGGAAA
1 GGG-TCAAATTCGAA-TTTTAGGAAGTTTGGGGGTTAAATTAGAATTTTTGGAAA
6769 GATCAATGGT
Statistics
Matches: 96, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
59 6 0.06
60 81 0.84
61 9 0.09
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.37
Consensus pattern (58 bp):
GGGTCAAATTCGAATTTTAGGAAGTTTGGGGGTTAAATTAGAATTTTTGGAAAATTTG
Found at i:8556 original size:40 final size:40
Alignment explanation
Indices: 8489--8781 Score: 212
Period size: 39 Copynumber: 7.4 Consensus size: 40
8479 ATAGCTTTAG
*
8489 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCCATGGTCA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCA
* * * *
8528 GGGTAAGAGATCGGATGGTCTTTAATCTGCCCTC-TGGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCC-CATGGTCA
* * * *
8568 GGGTAAAAGATTGGAT--TACTTCAATTTTCCCGATGATCA
1 GGGTAAAAGATTGGATGGT-CTTCAATCTGCCCCATGGTCA
* * * * * * *
8607 AGGTAAGAGATCGAATGGTTTTCAATCTGCCCTC-TGATTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCC-CATGGTCA
* *
8647 GGGTAAAAGATT-GACTGGTCCTT-AATCTACCCTATGGTC-
1 GGGTAAAAGATTGGA-TGGT-CTTCAATCTGCCCCATGGTCA
* * *
8686 GAGGTAAAATATTGGATTG-CTTCAATCTGCCCCATGGTCG
1 G-GGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCA
* * * *
8726 GGGTAAAATATTGGATTG-CTTCAATTTTCCCCATGGTC-
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCA
*
8764 GAGGTAAAATATTGGATG
1 G-GGTAAAAGATTGGATG
8782 TGGTGACTTC
Statistics
Matches: 201, Mismatches: 38, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
38 5 0.02
39 107 0.53
40 83 0.41
41 6 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (40 bp):
GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGGTCA
Found at i:8612 original size:79 final size:79
Alignment explanation
Indices: 8489--8659 Score: 254
Period size: 79 Copynumber: 2.2 Consensus size: 79
8479 ATAGCTTTAG
* * * *
8489 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATGGTCTTT-AA
1 GGGTAAAAGATTGGATTACTTCAATCTGCCCCATGATCAAGGTAAGAGATCGAATGGT-TTTCAA
*
8553 TCTGCCCTCTGGTTA
65 TCTGCCCTCTGATTA
* * *
8568 GGGTAAAAGATTGGATTACTTCAATTTTCCCGATGATCAAGGTAAGAGATCGAATGGTTTTCAAT
1 GGGTAAAAGATTGGATTACTTCAATCTGCCCCATGATCAAGGTAAGAGATCGAATGGTTTTCAAT
8633 CTGCCCTCTGATTA
66 CTGCCCTCTGATTA
8647 GGGTAAAAGATTG
1 GGGTAAAAGATTG
8660 ACTGGTCCTT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 3 0.04
79 80 0.96
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTACTTCAATCTGCCCCATGATCAAGGTAAGAGATCGAATGGTTTTCAAT
CTGCCCTCTGATTA
Found at i:9080 original size:132 final size:132
Alignment explanation
Indices: 8843--9106 Score: 528
Period size: 132 Copynumber: 2.0 Consensus size: 132
8833 ACTCCATTCC
8843 ACTACAACTTTAGTGGAGATCGAAGCTTGTTACTGTGAGTTTTAATCTGTCCCGTCATAGCTTTA
1 ACTACAACTTTAGTGGAGATCGAAGCTTGTTACTGTGAGTTTTAATCTGTCCCGTCATAGCTTTA
8908 GGGGTATAAGATCTGCTCTTGTAGCTTCAATTTACCCTTTTTCAGCTTCAGGAGTATAAGATTCG
66 GGGGTATAAGATCTGCTCTTGTAGCTTCAATTTACCCTTTTTCAGCTTCAGGAGTATAAGATTCG
8973 CT
131 CT
8975 ACTACAACTTTAGTGGAGATCGAAGCTTGTTACTGTGAGTTTTAATCTGTCCCGTCATAGCTTTA
1 ACTACAACTTTAGTGGAGATCGAAGCTTGTTACTGTGAGTTTTAATCTGTCCCGTCATAGCTTTA
9040 GGGGTATAAGATCTGCTCTTGTAGCTTCAATTTACCCTTTTTCAGCTTCAGGAGTATAAGATTCG
66 GGGGTATAAGATCTGCTCTTGTAGCTTCAATTTACCCTTTTTCAGCTTCAGGAGTATAAGATTCG
9105 CT
131 CT
9107 CTTGTAGCTT
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 132 1.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (132 bp):
ACTACAACTTTAGTGGAGATCGAAGCTTGTTACTGTGAGTTTTAATCTGTCCCGTCATAGCTTTA
GGGGTATAAGATCTGCTCTTGTAGCTTCAATTTACCCTTTTTCAGCTTCAGGAGTATAAGATTCG
CT
Found at i:9217 original size:50 final size:49
Alignment explanation
Indices: 9112--9246 Score: 135
Period size: 50 Copynumber: 2.7 Consensus size: 49
9102 TCGCTCTTGT
* * * *
9112 AGCTTCAATATGCCCCTCTACAGTTTTAGGTGAATGAGATTCAACATTGC
1 AGCTTCAAT-TGCTCCTCTACAGCTTTAGGTGTATGAGATTCAACATTAC
***
9162 AGCTTCAATCTGCTCCTCTACAGCTTTAGGTGTATGAGATTTGTCATTAC
1 AGCTTCAAT-TGCTCCTCTACAGCTTTAGGTGTATGAGATTCAACATTAC
* * * * *
9212 GGCTTCAATTCGATCCTTTATAGCTTTAGGGGTAT
1 AGCTTCAATT-GCTCCTCTACAGCTTTAGGTGTAT
9247 AGGATTCGTC
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 1 0.01
50 70 0.99
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (49 bp):
AGCTTCAATTGCTCCTCTACAGCTTTAGGTGTATGAGATTCAACATTAC
Done.