Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013113.1 Kokia drynarioides strain JFW-HI SEQ_128132, 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: 28111
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 39 characters in sequence are not A, C, G, or T
Found at i:10488 original size:57 final size:56
Alignment explanation
Indices: 10427--10704 Score: 198
Period size: 58 Copynumber: 5.0 Consensus size: 56
10417 TTCTAGACAC
** * *
10427 TCGAGGGAAAAATGGTAATTTTGGAAAAATAGGGGTTAAAATGGAATTTTAGGACGA
1 TCGAGGGAAAAATGGTAATTTTGGTGAAATCGGGGTTAAAATGGAATTTT-GGAAGA
* * *
10484 TCGAGGG---TAT--T--TTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGT
1 TCGAGGGAAAAATGGTAATTTTGGTGAAATCGGGGT-TAAAATGGAATTTTGG-AAGA
* * * *
10535 TCGAGGGTAAAATGGTAATTTTCGTGAAATCGGGGTTAAAATGGAATTTTAGAAAGT
1 TCGAGGGAAAAATGGTAATTTTGGTGAAATCGGGGTTAAAATGGAATTTT-GGAAGA
** * *
10592 TTAAGGGTAAAAT-ATAATTTTTGGTGAAAT-GAGGGTTAAAAATGGAATTTTGGAA-A
1 TCGAGGGAAAAATGGTAA-TTTTGGTGAAATCG-GGGTT-AAAATGGAATTTTGGAAGA
* * * ** * *
10648 TTTGAGGGTAAAAATGTTATTTTTGGAAAAATCGAGGTTAAAAATAGAATTTTGGAA
1 -TCGAGGG-AAAAATGGTAATTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAA
10705 AGTTTAGGGG
Statistics
Matches: 179, Mismatches: 25, Indels: 33
0.76 0.11 0.14
Matches are distributed among these distances:
50 17 0.09
51 22 0.12
52 1 0.01
54 4 0.02
56 5 0.03
57 60 0.34
58 67 0.37
59 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.32
Consensus pattern (56 bp):
TCGAGGGAAAAATGGTAATTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAGA
Found at i:10546 original size:29 final size:28
Alignment explanation
Indices: 10502--10705 Score: 138
Period size: 29 Copynumber: 7.1 Consensus size: 28
10492 ATTTTTTGGT
10502 GAAA-TCG-GGGTCAAAAATGGAATTTTG
1 GAAATTCGAGGGT-AAAAATGGAATTTTG
10529 GAAAGTTCGAGGGT-AAAATGGTAATTTTCG
1 GAAA-TTCGAGGGTAAAAATGG-AATTTT-G
* *
10559 TGAAA-TCG-GGGTTAAAATGGAATTTTA
1 -GAAATTCGAGGGTAAAAATGGAATTTTG
**
10586 GAAAGTTTAAGGGTAAAATAT--AATTTTTGG
1 GAAA-TTCGAGGGTAAAA-ATGGAA-TTTT-G
10616 TGAAA-T-GAGGGTTAAAAATGGAATTTTG
1 -GAAATTCGAGGG-TAAAAATGGAATTTTG
* * *
10644 GAAATTTGAGGGTAAAAATGTTATTTTTG
1 GAAATTCGAGGGTAAAAATG-GAATTTTG
* * *
10673 GAAAAATCGAGGTTAAAAATAGAATTTTG
1 G-AAATTCGAGGGTAAAAATGGAATTTTG
10702 GAAA
1 GAAA
10706 GTTTAGGGGT
Statistics
Matches: 142, Mismatches: 14, Indels: 41
0.72 0.07 0.21
Matches are distributed among these distances:
26 4 0.03
27 8 0.06
28 39 0.27
29 59 0.42
30 24 0.17
31 8 0.06
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (28 bp):
GAAATTCGAGGGTAAAAATGGAATTTTG
Found at i:10563 original size:58 final size:58
Alignment explanation
Indices: 10495--10729 Score: 275
Period size: 58 Copynumber: 4.1 Consensus size: 58
10485 CGAGGGTATT
* * *
10495 TTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAA
1 TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGATAA
* * *
10553 TTTTCGTGAAATCGGGGTT-AAAATGGAATTTTAGAAAGTTTAAGGGTAAAAT-ATAA
1 TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGATAA
* *
10609 TTTTTGGTGAAAT-GAGGGTTAAAAATGGAATTTTGGAAA-TTTGAGGGTAAAAATGTTAT
1 -TTTTGGTGAAATCG-GGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT-AAAATGATAA
** * *
10668 TTTTGGAAAAATCGAGGTTAAAAATAGAATTTTGGAAAGTTT-AGGGGTAAAAAT-ATAA
1 TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGA-GGGT-AAAATGATAA
10726 TTTT
1 TTTT
10730 CAAAAAGTTT
Statistics
Matches: 152, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
56 4 0.03
57 54 0.36
58 78 0.51
59 16 0.11
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.34
Consensus pattern (58 bp):
TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGATAA
Found at i:10602 original size:28 final size:28
Alignment explanation
Indices: 10515--10604 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
10505 ATCGGGGTCA
* **
10515 AAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGAATTTTAGAAAGTTTAAGGGT
* **
10543 AAAATGGTAATTTTCGTGAAA---TCGGGGTT
1 AAAATGG-AATTTT--AGAAAGTTTAAGGG-T
10572 AAAATGGAATTTTAGAAAGTTTAAGGGT
1 AAAATGGAATTTTAGAAAGTTTAAGGGT
10600 AAAAT
1 AAAAT
10605 ATAATTTTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
26 4 0.08
28 22 0.46
29 18 0.38
31 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (28 bp):
AAAATGGAATTTTAGAAAGTTTAAGGGT
Found at i:10718 original size:29 final size:29
Alignment explanation
Indices: 10508--10829 Score: 150
Period size: 30 Copynumber: 11.0 Consensus size: 29
10498 TGGTGAAATC
* *
10508 GGGGTCAAAAATGGAATTTTGGAAAG-TTC
1 GGGGT-AAAAATAGAATTTTGGAAAGTTTA
* *
10537 GAGGGT-AAAATGGTAATTTTCGTGAAA---TC
1 G-GGGTAAAAATAG-AATTTT-G-GAAAGTTTA
* * *
10566 GGGGTTAAAATGGAATTTTAGAAAGTTTA
1 GGGGTAAAAATAGAATTTTGGAAAGTTTA
* * *
10595 AGGGTAAAATATA-ATTTTTGGTGAAA--TGA
1 GGGGTAAAA-ATAGAATTTT-G-GAAAGTTTA
* *
10624 GGGTTAAAAATGGAATTTTGGAAA-TTT-
1 GGGGTAAAAATAGAATTTTGGAAAGTTTA
* ** *
10651 GAGGGTAAAAAT-GTTATTTTTGGAAA-AATC
1 G-GGGTAAAAATAG--AATTTTGGAAAGTTTA
*
10681 GAGGTTAAAAATAGAATTTTGGAAAGTTTA
1 G-GGGTAAAAATAGAATTTTGGAAAGTTTA
* **
10711 GGGGTAAAAATATAATTTTCAAAAAGTTTA
1 GGGGTAAAAATAGAATTTT-GGAAAGTTTA
**
10741 GGGGTAAAAAT-GTAATTTTCAAAAAGTTTA
1 GGGGTAAAAATAG-AATTTT-GGAAAGTTTA
* *
10771 GGGGTCAAAATATAATTTTGGAGAAGTTTA
1 GGGGTAAAAATAGAATTTTGGA-AAGTTTA
* * *
10801 GGGTTAAAATATA-ATTTTTGGACAGTTTA
1 GGGGTAAAA-ATAGAATTTTGGAAAGTTTA
10830 AGGACCTTTA
Statistics
Matches: 234, Mismatches: 35, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
26 4 0.02
27 6 0.03
28 30 0.13
29 88 0.38
30 94 0.40
31 12 0.05
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATAGAATTTTGGAAAGTTTA
Found at i:10739 original size:30 final size:30
Alignment explanation
Indices: 10686--10818 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
10676 AAATCGAGGT
* **
10686 TAAAAATAGAATTTT-GGAAAGTTTAGGGG
1 TAAAAATATAATTTTCAAAAAGTTTAGGGG
10715 TAAAAATATAATTTTCAAAAAGTTTAGGGG
1 TAAAAATATAATTTTCAAAAAGTTTAGGGG
*
10745 TAAAAATGTAATTTTCAAAAAGTTTAGGGG
1 TAAAAATATAATTTTCAAAAAGTTTAGGGG
* ** *
10775 TCAAAATATAATTTTGGAGAAGTTTA-GGG
1 TAAAAATATAATTTTCAAAAAGTTTAGGGG
*
10804 TTAAAATATAATTTT
1 TAAAAATATAATTTT
10819 TGGACAGTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
29 31 0.33
30 62 0.67
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (30 bp):
TAAAAATATAATTTTCAAAAAGTTTAGGGG
Found at i:10820 original size:30 final size:28
Alignment explanation
Indices: 10567--10829 Score: 151
Period size: 29 Copynumber: 9.0 Consensus size: 28
10557 CGTGAAATCG
** *
10567 GGGTTAAAATGGAATTTTAGAAAGTTTAA
1 GGGTTAAAATATAATTTTGGAAAGTTT-A
*
10596 GGG-TAAAATATAATTTTTGGTGAAA--TGA
1 GGGTTAAAATATAA-TTTT-G-GAAAGTTTA
10624 GGGTTAAAA-ATGGAATTTTGGAAA-TTTGA
1 GGGTTAAAATAT--AATTTTGGAAAGTTT-A
* * * ** *
10653 GGGTAAAAATGTTATTTTTGGAAA-AATC
1 GGGTTAAAAT-ATAATTTTGGAAAGTTTA
*
10681 GAGGTTAAAAATAGAATTTTGGAAAGTTTA
1 G-GGTT-AAAATATAATTTTGGAAAGTTTA
* **
10711 GGGGTAAAAATATAATTTTCAAAAAGTTTA
1 -GGGTTAAAATATAATTTT-GGAAAGTTTA
* * **
10741 GGGGTAAAAATGTAATTTTCAAAAAGTTTA
1 -GGGTTAAAATATAATTTT-GGAAAGTTTA
*
10771 GGGGTCAAAATATAATTTTGGAGAAGTTTA
1 -GGGTTAAAATATAATTTTGGA-AAGTTTA
*
10801 GGGTTAAAATATAATTTTTGGACAGTTTA
1 GGGTTAAAATATAA-TTTTGGAAAGTTTA
10830 AGGACCTTTA
Statistics
Matches: 188, Mismatches: 29, Indels: 34
0.75 0.12 0.14
Matches are distributed among these distances:
27 4 0.02
28 17 0.09
29 82 0.44
30 79 0.42
31 6 0.03
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (28 bp):
GGGTTAAAATATAATTTTGGAAAGTTTA
Found at i:11941 original size:21 final size:21
Alignment explanation
Indices: 11886--11942 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
11876 TTCCTTTTTT
* *
11886 TTATTAATTAT-TTATTATTA
1 TTATTAATAATATTATTACTA
* *
11906 TTATTAA-ATTCATTATTACTG
1 TTATTAATAAT-ATTATTACTA
11927 TTATTAATAATATTAT
1 TTATTAATAATATTAT
11943 CATTAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.03
20 7 0.24
21 19 0.66
22 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTAATAATATTATTACTA
Found at i:12803 original size:14 final size:14
Alignment explanation
Indices: 12784--12813 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12774 AAATTATCTT
*
12784 AATTAAAATAACTA
1 AATTAAAAAAACTA
12798 AATTAAAAAAACTA
1 AATTAAAAAAACTA
12812 AA
1 AA
12814 ATAACCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
AATTAAAAAAACTA
Found at i:13144 original size:3 final size:3
Alignment explanation
Indices: 13136--13165 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
13126 TATTGAAAAT
*
13136 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13166 GATCCTACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:14030 original size:3 final size:3
Alignment explanation
Indices: 14022--14051 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
14012 AAAATCGAAA
14022 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14052 ATAATCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:14289 original size:21 final size:20
Alignment explanation
Indices: 14231--14290 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 20
14221 TGATTGAAAG
14231 TAAATAAATTATTAAAAATTTT
1 TAAAT-AATTA-TAAAAATTTT
* **
14253 AAAATTAAAAAT-AAAATTATT
1 TAAA-TAATTATAAAAATT-TT
14274 TAAATAATTATAAAAAT
1 TAAATAATTATAAAAAT
14291 ATGTTCAACC
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
20 11 0.38
21 11 0.38
22 6 0.21
23 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATAATTATAAAAATTTT
Found at i:16182 original size:32 final size:32
Alignment explanation
Indices: 16145--16205 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
16135 AGTGTCAAGG
16145 ACTTGAAGCTAGTTTAGTCCTTGTTACTAAGA
1 ACTTGAAGCTAGTTTAGTCCTTGTTACTAAGA
16177 ACTTGAAGCTAGTTTAGTCCTTGTTACTA
1 ACTTGAAGCTAGTTTAGTCCTTGTTACTA
16206 GTCTATGCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (32 bp):
ACTTGAAGCTAGTTTAGTCCTTGTTACTAAGA
Found at i:16963 original size:20 final size:19
Alignment explanation
Indices: 16933--16974 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
16923 CTAATACAAG
16933 TTTAGGACAATTAAAAGTC
1 TTTAGGACAATTAAAAGTC
* *
16952 TTTAGAGACAATTTAAGGTC
1 TTTAG-GACAATTAAAAGTC
16972 TTT
1 TTT
16975 TTTAAGTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (19 bp):
TTTAGGACAATTAAAAGTC
Found at i:19669 original size:25 final size:25
Alignment explanation
Indices: 19653--19714 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
19643 AAAAATATAC
19653 AAAAATCAACACGCAAATATTACAA
1 AAAAATCAACACGCAAATATTACAA
19678 AAAAATCAACACGCAAATATTACAA
1 AAAAATCAACACGCAAATATTACAA
19703 AAAAATCAACAC
1 AAAAATCAACAC
19715 AAAGAGAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.61, C:0.21, G:0.03, T:0.15
Consensus pattern (25 bp):
AAAAATCAACACGCAAATATTACAA
Found at i:19676 original size:23 final size:24
Alignment explanation
Indices: 19645--19714 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 24
19635 GGGATACAAA
19645 AAATA-TAC-AAAAATCAACACGC
1 AAATATTACAAAAAATCAACACGC
19667 AAATATTACAAAAAAATCAACACGC
1 AAATATTAC-AAAAAATCAACACGC
19692 AAATATTACAAAAAAATCAACAC
1 AAATATTAC-AAAAAATCAACAC
19715 AAAGAGAGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
22 5 0.11
23 3 0.07
25 37 0.82
ACGTcount: A:0.61, C:0.20, G:0.03, T:0.16
Consensus pattern (24 bp):
AAATATTACAAAAAATCAACACGC
Done.