Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012189.1 Kokia drynarioides strain JFW-HI SEQ_127190, 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: 18238
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:109 original size:6 final size:6
Alignment explanation
Indices: 99--151 Score: 74
Period size: 6 Copynumber: 9.0 Consensus size: 6
89 TAATAGACTT
*
99 TTTAAT TTTAAA TTTAAA TTTAAA TTTAAA TTTAAGA -TT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
146 TTTAAA
1 TTTAAA
152 ATAAATTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 38 0.88
7 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:158 original size:17 final size:17
Alignment explanation
Indices: 105--158 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
95 ACTTTTTAAT
*
105 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* *
123 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATAAA
140 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
157 TT
1 TT
159 AAAAAGGGGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 20 0.65
18 11 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:12510 original size:29 final size:28
Alignment explanation
Indices: 12478--12655 Score: 93
Period size: 29 Copynumber: 6.1 Consensus size: 28
12468 TTACACATTC
12478 AGGGGTAAAAGGGTAA-TTTT-GAGAGTTTT
1 AGGGGTAAAAGGG-AATTTTTGGA-AG-TTT
*
12507 AGGGGTAAAAATGGAATTTTTGGAAGTTT
1 AGGGGT-AAAAGGGAATTTTTGGAAGTTT
** *
12536 AGGGGTAAAAATGAGATTTTTGGAAATTT
1 AGGGGTAAAAGGGA-ATTTTTGGAAGTTT
* * *
12565 TGAGGTTAAAATGGG-ATTTTTTGAAGTTCT
1 AG-GGGTAAAA-GGGAATTTTTGGAAGTT-T
12595 A--GGTAAAAATGGG-ATTTTTGGAAG-TT
1 AGGGGT-AAAA-GGGAATTTTTGGAAGTTT
* *
12621 CGAGGTCAAAAATGGG-ATTTTTGGACAGTTT
1 AGGGGT--AAAA-GGGAATTTTTGGA-AGTTT
12652 AGGG
1 AGGG
12656 ACCCCAGGGC
Statistics
Matches: 120, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.01
27 3 0.03
28 27 0.22
29 60 0.50
30 22 0.18
31 7 0.06
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (28 bp):
AGGGGTAAAAGGGAATTTTTGGAAGTTT
Found at i:12555 original size:58 final size:59
Alignment explanation
Indices: 12454--12655 Score: 179
Period size: 58 Copynumber: 3.5 Consensus size: 59
12444 CTTTAGAGTT
** * * * *
12454 TAAAAATGGAATTTTTACACA-TTCAGGGGT-AAAA-GGGTAATTTT-GAGAGTTTTAGGGG
1 TAAAAATGGAATTTTTGGACAGTTTAGGGGTAAAAATGAG-ATTTTTGGA-AGTTTT-GAGG
*
12512 TAAAAATGGAATTTTTGGA-AGTTTAGGGGTAAAAATGAGATTTTTGGAAATTTTGAGG
1 TAAAAATGGAATTTTTGGACAGTTTAGGGGTAAAAATGAGATTTTTGGAAGTTTTGAGG
* * * * *
12570 TTAAAATGGGATTTTTTGA-AGTTCTA--GGTAAAAATGGGATTTTTGGAAG-TTCGAGG
1 TAAAAATGGAATTTTTGGACAGTT-TAGGGGTAAAAATGAGATTTTTGGAAGTTTTGAGG
*
12626 TCAAAAATGGGATTTTTGGACAGTTTAGGG
1 T-AAAAATGGAATTTTTGGACAGTTTAGGG
12656 ACCCCAGGGC
Statistics
Matches: 120, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
56 7 0.06
57 40 0.33
58 52 0.43
59 17 0.14
60 4 0.03
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (59 bp):
TAAAAATGGAATTTTTGGACAGTTTAGGGGTAAAAATGAGATTTTTGGAAGTTTTGAGG
Found at i:12603 original size:28 final size:28
Alignment explanation
Indices: 12510--12654 Score: 168
Period size: 29 Copynumber: 5.1 Consensus size: 28
12500 GAGTTTTAGG
*
12510 GGTAAAAATGGAATTTTTGGAAGTT-TA
1 GGTAAAAATGGGATTTTTGGAAGTTCTA
* * *
12537 GGGGTAAAAATGAGATTTTTGGAAATTTTGA
1 --GGTAAAAATGGGATTTTTGGAAGTTCT-A
* *
12568 GGTTAAAATGGGATTTTTTGAAGTTCTA
1 GGTAAAAATGGGATTTTTGGAAGTTCTA
*
12596 GGTAAAAATGGGATTTTTGGAAGTTCGA
1 GGTAAAAATGGGATTTTTGGAAGTTCTA
12624 GGTCAAAAATGGGATTTTTGGACAGTT-TA
1 GGT-AAAAATGGGATTTTTGGA-AGTTCTA
12653 GG
1 GG
12655 GACCCCAGGG
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
28 29 0.29
29 65 0.65
30 5 0.05
31 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (28 bp):
GGTAAAAATGGGATTTTTGGAAGTTCTA
Found at i:12615 original size:57 final size:57
Alignment explanation
Indices: 12513--12655 Score: 182
Period size: 57 Copynumber: 2.5 Consensus size: 57
12503 TTTTAGGGGT
* * *
12513 AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGAGATTTTTGGAAATTTTGAGGT-
1 AAAAATGGGATTTTTGGAAGTTTA-GGGTAAAAATGAGATTTTTGG-AAGTTCGAGGTC
* * *
12571 TAAAATGGGATTTTTTGAAGTTCTA-GGTAAAAATGGGATTTTTGGAAGTTCGAGGTC
1 AAAAATGGGATTTTTGGAAGTT-TAGGGTAAAAATGAGATTTTTGGAAGTTCGAGGTC
12628 AAAAATGGGATTTTTGGACAGTTTAGGG
1 AAAAATGGGATTTTTGGA-AGTTTAGGG
12656 ACCCCAGGGC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
56 9 0.12
57 37 0.51
58 25 0.34
59 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.36
Consensus pattern (57 bp):
AAAAATGGGATTTTTGGAAGTTTAGGGTAAAAATGAGATTTTTGGAAGTTCGAGGTC
Found at i:13816 original size:3 final size:3
Alignment explanation
Indices: 13716--13798 Score: 103
Period size: 3 Copynumber: 26.3 Consensus size: 3
13706 TTTATTTTTA
* * *
13716 ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT AATG AGGT AGTT ATT ACTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT A-TT A-TT ATT A-TT
13765 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
13799 ATAGCACATT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
3 62 0.87
4 9 0.13
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:13825 original size:52 final size:52
Alignment explanation
Indices: 13716--13827 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 52
13706 TTTATTTTTA
** *
13716 ATTATTAATATTATTATTATTATTATTATTAATGAGGTAGTTATTACTTATT
1 ATTATTAATATTATTATTATTATTATTATTAATGAGACAGTTATTACTTATG
* *
13768 ATTATTATTATTATTATTATTATTATTATTAAT-AGCACATTTATTA-TTAATG
1 ATTATTAATATTATTATTATTATTATTATTAATGAG-ACAGTTATTACTT-ATG
*
13820 GTTATTAA
1 ATTATTAA
13828 ATAAATTGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
51 4 0.08
52 47 0.92
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (52 bp):
ATTATTAATATTATTATTATTATTATTATTAATGAGACAGTTATTACTTATG
Found at i:14583 original size:6 final size:6
Alignment explanation
Indices: 14573--14636 Score: 80
Period size: 6 Copynumber: 11.0 Consensus size: 6
14563 TTATGGACTT
* *
14573 TTTAAT TTTAAA ATTAAA TTTAAA TTTAAA -TTAAA TTTAAA TTTAAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
14621 -TT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
14637 ATAAATTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
4 1 0.02
5 8 0.16
6 41 0.80
7 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:14605 original size:17 final size:17
Alignment explanation
Indices: 14573--14643 Score: 99
Period size: 17 Copynumber: 4.1 Consensus size: 17
14563 TTATGGACTT
*
14573 TTTAATTTTAAAATTAAA
1 TTTAAATTT-AAATTAAA
14591 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
14608 TTTAAATTTAAGATT-AA
1 TTTAAATTTAA-ATTAAA
*
14625 TTTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
14642 TT
1 TT
14644 AAAAAGGGCT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
16 2 0.04
17 36 0.73
18 11 0.22
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:14606 original size:11 final size:11
Alignment explanation
Indices: 14580--14643 Score: 67
Period size: 11 Copynumber: 5.6 Consensus size: 11
14570 CTTTTTAATT
*
14580 TTAAAATTAAA
1 TTAAATTTAAA
14591 TTTAAATTTAAA
1 -TTAAATTTAAA
14603 TTAAATTTAAA
1 TTAAATTTAAA
*
14614 TTTAAGA-TTAAT
1 -TTAA-ATTTAAA
14626 TTAAATTTAAA
1 TTAAATTTAAA
*
14637 ATAAATT
1 TTAAATT
14644 AAAAAGGGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
10 1 0.02
11 25 0.56
12 18 0.40
13 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TTAAATTTAAA
Done.