Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006833.1 Kokia drynarioides strain JFW-HI SEQ_121432, 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: 7510
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:4648 original size:29 final size:29
Alignment explanation
Indices: 4601--4936 Score: 243
Period size: 30 Copynumber: 11.4 Consensus size: 29
4591 TAGTTTTGAA
*
4601 AAAGTTTAGGGGTAAAAATGT-ATTTTTGGG
1 AAAGTTTA-GGGTTAAAATGTGA-TTTTGGG
4631 AAAGTTTAGGGTTAAAATGTGATTTTGGG
1 AAAGTTTAGGGTTAAAATGTGATTTTGGG
* * *
4660 GAAGTTT-GGGCTCAAAATGTGATTTTAGG
1 AAAGTTTAGGG-TTAAAATGTGATTTTGGG
* * * *
4689 AAGGTTTAATGGTCAAAATGTGATTTT-AG
1 AAAGTTT-AGGGTTAAAATGTGATTTTGGG
* * *
4718 AGAAGTTTAGGGGTCAAAATGTAATTTTGGA
1 A-AAGTTTA-GGGTTAAAATGTGATTTTGGG
* * *
4749 AAAGTGTAAGGGTCAAAATGTGATTTTAGG
1 AAAGT-TTAGGGTTAAAATGTGATTTTGGG
** *
4779 AAAGCTTTAGGGTTAAAACATGATTTTGGA
1 AAAG-TTTAGGGTTAAAATGTGATTTTGGG
* * ** *
4809 AAAGTTTAGGGGT-GAATGAAATTTT-AG
1 AAAGTTTAGGGTTAAAATGTGATTTTGGG
* * *
4836 AAAATGTTAGGGGTTAAAATG-GAATTTTAGA
1 AAAGT-TTA-GGGTTAAAATGTG-ATTTTGGG
* * *
4867 AAAGTTTGGGGTTAAAATATGATTTTTGG
1 AAAGTTTAGGGTTAAAATGTGATTTTGGG
* * *
4896 AAAGTTTAGGGACTAAAATATGATTTTTGG
1 AAAGTTTAGGG-TTAAAATGTGATTTTGGG
4926 AAAGTTTAGGG
1 AAAGTTTAGGG
4937 ACCTACTAGG
Statistics
Matches: 246, Mismatches: 44, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
27 4 0.02
28 13 0.05
29 86 0.35
30 133 0.54
31 10 0.04
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAGTTTAGGGTTAAAATGTGATTTTGGG
Found at i:4657 original size:59 final size:58
Alignment explanation
Indices: 4576--4936 Score: 231
Period size: 59 Copynumber: 6.1 Consensus size: 58
4566 TTTTAGAGAA
** *
4576 TTTAGGGTTAAAACAT-AGTTTTGAAAAAGTTTAGGGGTAAAAATGTATTTTTGGGAAAG
1 TTTAGGGTTAAAATGTGA-TTTTGAAAAAGTTTAGGGGTAAAAATGTA-TTTTGGAAAAG
*** * * *
4635 TTTAGGGTTAAAATGTGATTTTGGGGAAGTTT-GGGCTCAAAATGTGATTTTAGG-AAGG
1 TTTAGGGTTAAAATGTGATTTTGAAAAAGTTTAGGGGTAAAAATGT-ATTTT-GGAAAAG
* * * *
4693 TTTAATGGTCAAAATGTGATTTT-AGAGAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAG
1 TTT-AGGGTTAAAATGTGATTTTGA-AAAAGTTTAGGGGTAAAAATGT-ATTTTGGAAAAG
* * * *
4753 TGTAAGGGTCAAAATGTGATTTT-AGGAAAGCTTTAGGGTTAAAACATG-ATTTTGGAAAAG
1 T-TTAGGGTTAAAATGTGATTTTGA-AAAAG-TTTAGGGGTAAAA-ATGTATTTTGGAAAAG
* * ** * * * *
4813 TTTAGGGGT-GAATGAAATTTTAGAAAATG-TTAGGGGTTAAAATGGAATTTTAGAAAAG
1 TTTAGGGTTAAAATGTGATTTT-GAAAAAGTTTAGGGGTAAAAAT-GTATTTTGGAAAAG
* * * *
4871 TTTGGGGTTAAAATATGATTTTTG-GAAAGTTTAGGGACTAAAATATG-ATTTTTGG-AAAG
1 TTTAGGGTTAAAATGTGA-TTTTGAAAAAGTTTAGGG-GTAAAA-ATGTA-TTTTGGAAAAG
4930 TTTAGGG
1 TTTAGGG
4937 ACCTACTAGG
Statistics
Matches: 238, Mismatches: 44, Indels: 40
0.74 0.14 0.12
Matches are distributed among these distances:
56 2 0.01
57 11 0.05
58 51 0.21
59 84 0.35
60 73 0.31
61 14 0.06
62 3 0.01
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.35
Consensus pattern (58 bp):
TTTAGGGTTAAAATGTGATTTTGAAAAAGTTTAGGGGTAAAAATGTATTTTGGAAAAG
Found at i:4839 original size:28 final size:29
Alignment explanation
Indices: 4557--4906 Score: 153
Period size: 30 Copynumber: 11.9 Consensus size: 29
4547 AATAGGGTAA
* * *
4557 AAAATGAAGTTTTAGAGAA-TTTAGGGTT
1 AAAATGAAATTTTAGAAAAGTTTAGGGGT
* *
4585 AAAA-CATAGTTTT-GAAAAAGTTTAGGGGT
1 AAAATGA-AATTTTAG-AAAAGTTTAGGGGT
* * * * *
4614 AAAAATGTATTTTTGGGAAAGTTTAGGGTT
1 -AAAATGAAATTTTAGAAAAGTTTAGGGGT
** * ** *
4644 AAAATGTGATTTTGGGGAAGTTT-GGGCT
1 AAAATGAAATTTTAGAAAAGTTTAGGGGT
** * * **
4672 CAAAATGTGATTTTAGGAAGGTTTAATGGT
1 -AAAATGAAATTTTAGAAAAGTTTAGGGGT
** *
4702 CAAAATGTGATTTTAGAGAAGTTTAGGGGT
1 -AAAATGAAATTTTAGAAAAGTTTAGGGGT
* * * *
4732 CAAAATGTAATTTTGGAAAAGTGTAAGGGT
1 -AAAATGAAATTTTAGAAAAGTTTAGGGGT
** * *
4762 CAAAATGTGATTTTAGGAAAGCTTTAGGGTT
1 -AAAATGAAATTTTAGAAAAG-TTTAGGGGT
*
4793 AAAACATG--ATTTTGGAAAAGTTTAGGGGT
1 -AAA-ATGAAATTTTAGAAAAGTTTAGGGGT
*
4822 -GAATGAAATTTTAGAAAA-TGTTAGGGGTT
1 AAAATGAAATTTTAGAAAAGT-TTAGGGG-T
*
4851 AAAATGGAATTTTAGAAAAGTTT-GGGGTT
1 AAAATGAAATTTTAGAAAAGTTTAGGGG-T
* * *
4880 AAAAT-ATGATTTTTGGAAAGTTTAGGG
1 AAAATGA-AATTTTAGAAAAGTTTAGGG
4907 ACTAAAATAT
Statistics
Matches: 258, Mismatches: 46, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
26 3 0.01
27 4 0.02
28 34 0.13
29 81 0.31
30 122 0.47
31 11 0.04
32 3 0.01
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGAAATTTTAGAAAAGTTTAGGGGT
Found at i:6531 original size:30 final size:29
Alignment explanation
Indices: 6422--6854 Score: 315
Period size: 30 Copynumber: 14.7 Consensus size: 29
6412 TTCGGAGTCA
6422 AAAAT-GAGATTTTTGGAA-GTTC-AGGGGT
1 AAAATGGA-ATTTTTGGAAGGTTCGA-GGGT
*
6450 AAAATGGTAA-TTTTGGAAGGTTC--GGAT
1 AAAATGG-AATTTTTGGAAGGTTCGAGGGT
*
6477 AAAAAAT-GAGATTTTTAGAA-GTTCGAGGGT
1 --AAAATGGA-ATTTTTGGAAGGTTCGAGGGT
*
6507 AAAATGGTAATTTTTGGAAGGTTCG-GGAT
1 AAAATGG-AATTTTTGGAAGGTTCGAGGGT
* *
6536 AAAAAATGAGACTTTTTGG-AGGTTCGGGGGT
1 --AAAATG-GAATTTTTGGAAGGTTCGAGGGT
* * *
6567 AAAATGGTAAATTTTGGAAGGTTTGAGGTT
1 AAAATGG-AATTTTTGGAAGGTTCGAGGGT
* * *
6597 AAAAATGGGATTTTTAGAAGGTTTG-GGGTT
1 -AAAATGGAATTTTTGGAAGGTTCGAGGG-T
*
6627 AAAATAGTAATTTTTGGAAGGTTC-AGGGTT
1 AAAAT-GGAATTTTTGGAAGGTTCGAGGG-T
* * *
6657 AAAAATGGGATTTTTAGAAGGTTCGAGGTT
1 -AAAATGGAATTTTTGGAAGGTTCGAGGGT
6687 AAAATGGTAATTTTTGGAAGGTTC-AGGGTT
1 AAAATGG-AATTTTTGGAAGGTTCGAGGG-T
* * *
6717 AAAAATGGGATTTTTGGAAGTTTAG-GGGT
1 -AAAATGGAATTTTTGGAAGGTTCGAGGGT
*
6746 AAAATGGTAATTTTTGGAAGGTTTG-GGGTTT
1 AAAATGG-AATTTTTGGAAGGTTCGAGGG--T
* *
6777 AAAATGGGATTTTTGGAA-GTTTGAGGGT
1 AAAATGGAATTTTTGGAAGGTTCGAGGGT
* *
6805 TAAATGGTAATTTTTGGAAGGTTCGAGGTT
1 AAAATGG-AATTTTTGGAAGGTTCGAGGGT
6835 AAAAAT-GAGATTTTTGGAAG
1 -AAAATGGA-ATTTTTGGAAG
6855 TTTAGGGACC
Statistics
Matches: 330, Mismatches: 39, Indels: 70
0.75 0.09 0.16
Matches are distributed among these distances:
27 4 0.01
28 39 0.12
29 95 0.29
30 140 0.42
31 51 0.15
32 1 0.00
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGGTTCGAGGGT
Found at i:6781 original size:59 final size:59
Alignment explanation
Indices: 6385--6861 Score: 550
Period size: 60 Copynumber: 8.1 Consensus size: 59
6375 CGGATGCACG
* * * * * *
6385 GGGGTAAAATCGTAGTTTTGGGGAAGGTTCGGAGTCAAAAATGAGATTTTTGGAAGTTCA
1 GGGGTAAAATGGTAATTTT-TGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTTA
* * * *
6445 GGGGTAAAATGGTAA-TTTTGGAAGGTTC-GGATAAAAAATGAGATTTTTAGAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTTA
* * * **
6501 GAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGATAAAAAATGAGACTTTTTGGAGGTTCG
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGA-TTTTTGGAAGTTTA
* * * * *
6562 GGGGTAAAATGGTAAATTTTGGAAGGTTTGAGGTTAAAAATGGGATTTTTAGAAGGTTT-
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAA-GTTTA
* * * * * *
6621 GGGGTTAAAATAGTAATTTTTGGAAGGTTCAGGGTTAAAAATGGGATTTTTAGAAGGTTC
1 GGGG-TAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTTA
* * *
6681 GAGGTTAAAATGGTAATTTTTGGAAGGTTCAGGGTTAAAAATGGGATTTTTGGAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTTA
* * *
6741 GGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTTTAAAATGGGATTTTTGGAAGTTT-
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTTA
* *
6799 GAGGGTTAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTTA
6859 GGG
1 GGG
6862 ACCTTCGAGG
Statistics
Matches: 364, Mismatches: 42, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
56 2 0.01
57 35 0.10
58 23 0.06
59 139 0.38
60 161 0.44
61 4 0.01
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTTA
Done.