Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004153.1 Kokia drynarioides strain JFW-HI SEQ_117358, 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: 9369
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--28 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29 TAATTGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6651 original size:29 final size:30
Alignment explanation
Indices: 6619--6691 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
6609 AAAACGTAAT
*
6619 TTTTGGAAAATTT-AGGAT-TAAAATCAAAC
1 TTTTGGAAAATTTGAGG-TCGAAAATCAAAC
* **
6648 TTTTGGAACATTTGAGGTCGAAAATGTAAC
1 TTTTGGAAAATTTGAGGTCGAAAATCAAAC
*
6678 TTTTGGAAATTTTG
1 TTTTGGAAAATTTG
6692 GGGTAAAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 13 0.36
30 23 0.64
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (30 bp):
TTTTGGAAAATTTGAGGTCGAAAATCAAAC
Found at i:6711 original size:29 final size:29
Alignment explanation
Indices: 6668--6738 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
6658 TTTGAGGTCG
*
6668 AAAAT-GTAACTTTTGGAAATTTT-GGGGT
1 AAAATGGTAATTTTTGG-AATTTTAGGGGT
* *
6696 AAAATGGTGATTTTTGGATTTTTAGGGGT
1 AAAATGGTAATTTTTGGAATTTTAGGGGT
6725 AAAATGGTAATTTT
1 AAAATGGTAATTTT
6739 GGGGGAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 10 0.27
29 27 0.73
ACGTcount: A:0.31, C:0.01, G:0.25, T:0.42
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAATTTTAGGGGT
Found at i:6739 original size:28 final size:28
Alignment explanation
Indices: 6668--6801 Score: 91
Period size: 28 Copynumber: 4.7 Consensus size: 28
6658 TTTGAGGTCG
6668 AAAAT-GTAACTTTTGGAAATTTTGGGGT
1 AAAATGGTAA-TTTTGGAAATTTTGGGGT
* *
6696 AAAATGGTGATTTTTGG-ATTTTTAGGGGT
1 AAAATGGT-AATTTTGGAAATTTT-GGGGT
** *
6725 AAAATGGTAATTTTGGGGGAGTTT-GGGT
1 AAAATGGTAATTTT-GGAAATTTTGGGGT
*
6753 CAAAA-GGTAATTTTGGGAAA-GTTGGGAGT
1 -AAAATGGTAATTTT-GGAAATTTTGGG-GT
6782 CAAAAAT-GTAATTTTGGAAA
1 --AAAATGGTAATTTTGGAAA
6802 ACTTCGAGGT
Statistics
Matches: 86, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
27 2 0.02
28 34 0.40
29 34 0.40
30 16 0.19
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (28 bp):
AAAATGGTAATTTTGGAAATTTTGGGGT
Found at i:6757 original size:29 final size:29
Alignment explanation
Indices: 6720--6798 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 29
6710 TGGATTTTTA
**
6720 GGGGT-AAAATGGTAATTTTGGGGGAGTT
1 GGGGTCAAAATGGTAATTTTGGGAAAGTT
*
6748 TGGGTCAAAA-GGTAATTTTGGGAAAGTT
1 GGGGTCAAAATGGTAATTTTGGGAAAGTT
6776 GGGAGTCAAAAAT-GTAATTTTGG
1 GGG-GTC-AAAATGGTAATTTTGG
6799 AAAACTTCGA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
28 22 0.51
29 7 0.16
30 14 0.33
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.32
Consensus pattern (29 bp):
GGGGTCAAAATGGTAATTTTGGGAAAGTT
Found at i:6795 original size:30 final size:28
Alignment explanation
Indices: 6663--7066 Score: 142
Period size: 30 Copynumber: 13.8 Consensus size: 28
6653 GAACATTTGA
*
6663 GGTCGAAAATGTAACTTTT-GGAAATTTTGG
1 GGTC-AAAATGTAA-TTTTGGGAAA-GTTGG
* * ***
6693 GGT-AAAATGGTGATTTTTGGATTTTTAGG
1 GGTCAAAAT-GTAATTTTGGGAAAGTT-GG
** *
6722 GGT-AAAATGGTAATTTTGGGGGAGTTTG
1 GGTCAAAAT-GTAATTTTGGGAAAGTTGG
*
6750 GGTCAAAAGGTAATTTTGGGAAAGTTGG
1 GGTCAAAATGTAATTTTGGGAAAGTTGG
* * *
6778 GAGTCAAAAATGTAATTTTGGAAAACTTCGA
1 G-GTC-AAAATGTAATTTTGGGAAAGTT-GG
* * **
6809 GGTTAAAATGTGATTTTCATG-AAGTTTAGG
1 GGTCAAAATGTAATTTT-GGGAAAG-TT-GG
* * *
6839 GGTCAAAATGTTATTTT-AGAAAGTTCGA
1 GGTCAAAATGTAATTTTGGGAAAGTT-GG
* * * * *
6867 AGTTAAAATGTGATTTTCGTG-AAGTTAGA
1 GGTCAAAATGTAATTTT-GGGAAAGTT-GG
* **
6896 AGTCAAAATGTAATTGTTATG-AAGTTTGG
1 GGTCAAAATGTAATT-TTGGGAAAG-TTGG
*
6925 AGGTCAAAATATAATTTT-GGAAAGTTAGAG
1 -GGTCAAAATGTAATTTTGGGAAAGTT-G-G
* * *
6955 GGT-AAAATGTAATTTTTGAAAAGTTAAAG
1 GGTCAAAATGTAATTTTGGGAAAGTT--GG
* * * *
6984 GGTTAAAATGTAATTTTTGTAAAGTTTAAG
1 GGTCAAAATGTAATTTTGGGAAAG-TT-GG
* * * *
7014 GTTTAAAATGTAATTTTAGAAAAGTTTGGG
1 GGTCAAAATGTAATTTTGGGAAAG-TT-GG
*
7044 GGTTAAAATGTAATTTTGGGAAA
1 GGTCAAAATGTAATTTTGGGAAA
7067 TTTAAGGGGT
Statistics
Matches: 297, Mismatches: 55, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
28 66 0.22
29 98 0.33
30 129 0.43
31 4 0.01
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
GGTCAAAATGTAATTTTGGGAAAGTTGG
Found at i:6816 original size:29 final size:29
Alignment explanation
Indices: 6784--7095 Score: 177
Period size: 30 Copynumber: 10.6 Consensus size: 29
6774 TTGGGAGTCA
* *
6784 AAAATGTAATTTTGGAAAACTTCGAGGTT
1 AAAATGTAATTTTGGAAAAGTTAGAGGTT
* * * * *
6813 AAAATGTGATTTT-CATGAAGTTTAGGGGTC
1 AAAATGTAATTTTGGA-AAAG-TTAGAGGTT
* * * *
6843 AAAATGTTATTTTAG-AAAGTTCGAAGTT
1 AAAATGTAATTTTGGAAAAGTTAGAGGTT
* * ** * *
6871 AAAATGTGATTTTCGTGAAGTTAGAAGTC
1 AAAATGTAATTTTGGAAAAGTTAGAGGTT
* * *
6900 AAAATGTAATTGTT--ATGAAGTTTGGAGGTC
1 AAAATGTAATT-TTGGA-AAAG-TTAGAGGTT
* *
6930 AAAATATAATTTTGG-AAAGTTAGAGGGT
1 AAAATGTAATTTTGGAAAAGTTAGAGGTT
* *
6958 AAAATGTAATTTTTGAAAAGTTAAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTAGA-GGTT
* *
6988 AAAATGTAATTTTTGTAAAGTTTA-AGGTTT
1 AAAATGTAATTTTGGAAAAG-TTAGAGG-TT
* * *
7018 AAAATGTAATTTTAGAAAAGTTTGGGGGTT
1 AAAATGTAATTTTGGAAAAG-TTAGAGGTT
* * *
7048 AAAATGTAATTTTGGGAAATTTAAGGGGTT
1 AAAATGTAATTTTGGAAAAGTT-AGAGGTT
*
7078 AAAAAATGCAATTTTGGA
1 --AAAATGTAATTTTGGA
7096 TAAGATTATG
Statistics
Matches: 223, Mismatches: 43, Indels: 31
0.75 0.14 0.10
Matches are distributed among these distances:
28 38 0.17
29 58 0.26
30 108 0.48
31 5 0.02
32 14 0.06
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTAGAGGTT
Found at i:6921 original size:58 final size:58
Alignment explanation
Indices: 6779--6910 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
6769 GAAAGTTGGG
* * * *
6779 AGTCAAAAATGTAATTTTGGAAAACTTCGAGGTTAAAATGTGATTTTCATGAAGTTTAGG
1 AGTC-AAAATGTAATTTTAG-AAAGTTCGAAGTTAAAATGTGATTTTCATGAAGTTTAGA
* * *
6839 GGTCAAAATGTTATTTTAGAAAGTTCGAAGTTAAAATGTGATTTTCGTGAAG-TTAGA
1 AGTCAAAATGTAATTTTAGAAAGTTCGAAGTTAAAATGTGATTTTCATGAAGTTTAGA
6896 AGTCAAAATGTAATT
1 AGTCAAAATGTAATT
6911 GTTATGAAGT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 17 0.27
58 30 0.48
59 13 0.21
60 3 0.05
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.36
Consensus pattern (58 bp):
AGTCAAAATGTAATTTTAGAAAGTTCGAAGTTAAAATGTGATTTTCATGAAGTTTAGA
Found at i:8155 original size:30 final size:32
Alignment explanation
Indices: 8097--8176 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 32
8087 TTTGCAAGCA
*
8097 ATAATAAATAGAAATTAATGAGTATATTAATGT
1 ATAATAAATAGAAATTAA-GAGTATATTAATAT
8130 ATAATAAATA-AATATTAA-A-TATATTAATAT
1 ATAATAAATAGAA-ATTAAGAGTATATTAATAT
8160 ATATACTTAAATAGAAA
1 ATA-A--TAAATAGAAA
8177 ATGCTTCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
30 13 0.32
31 2 0.05
32 2 0.05
33 22 0.54
34 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (32 bp):
ATAATAAATAGAAATTAAGAGTATATTAATAT
Done.