Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009375.1 Kokia drynarioides strain JFW-HI SEQ_124082, 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: 16963
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:11836 original size:16 final size:16
Alignment explanation
Indices: 11805--11849 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
11795 ACTTTTAACT
11805 TTTATTTATT-TATTTA
1 TTTATTTATTAT-TTTA
11821 TTTATTTATTATTTTA
1 TTTATTTATTATTTTA
**
11837 AATATTTATTATT
1 TTTATTTATTATT
11850 AGTGTTTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATTTATTATTTTA
Found at i:11846 original size:4 final size:4
Alignment explanation
Indices: 11805--11834 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
11795 ACTTTTAACT
11805 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
11835 TAAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:12759 original size:96 final size:96
Alignment explanation
Indices: 12582--12766 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
12572 GAAAAGGATG
* **
12582 TTCGATTATCTTGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
1 TTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
*
12647 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAGAAACATTGCCTCGATTAAGGGTA
* *
12678 TTCGATTATTTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTC
1 TTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TC
*
12742 GAA-ATAAA-AGAATATTGCCTCGATT
64 GAAGATAAAGA-AACATTGCCTCGATT
12767 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
95 2 0.03
96 72 0.91
97 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
AGATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:13131 original size:29 final size:29
Alignment explanation
Indices: 13099--13405 Score: 297
Period size: 29 Copynumber: 10.4 Consensus size: 29
13089 AAAATAGAGT
13099 TTTTTGGACA-TTCGAGGGT-AAAATGGTAA
1 TTTTTGGA-AGTTCGAGGGTAAAAATGG-AA
*
13128 TTTTTGAAAGTTTCGA-GGTCAAAAATGGAA
1 TTTTTGGAAG-TTCGAGGGT-AAAAATGGAA
* *
13158 ATTTTGGAGGTTCGAGGGTAAAAAT--AA
1 TTTTTGGAAGTTCGAGGGTAAAAATGGAA
** *
13185 TTTTTTTGGAAGTTTTAGGATCAAAAATGGAA
1 --TTTTTGGAAGTTCGAGGGT-AAAAATGGAA
* * *
13217 TTTTTGGAAGTTTGGGGGTGAAAATGGAA
1 TTTTTGGAAGTTCGAGGGTAAAAATGGAA
* *
13246 TTTTTGGAAGTTCGAGGGTGAAAATTGAA
1 TTTTTGGAAGTTCGAGGGTAAAAATGGAA
*
13275 TTTTTGGAAGTTTCG-GGGTTAAAAATGAAA
1 TTTTTGGAAG-TTCGAGGG-TAAAAATGGAA
13305 TTTTTGGAAGTTCGAGGGTAAAAATGGAA
1 TTTTTGGAAGTTCGAGGGTAAAAATGGAA
* * *
13334 TTTTAGTAAGTTC-AGTGGTGAAAATGGAA
1 TTTTTGGAAGTTCGAG-GGTAAAAATGGAA
*
13363 TTTTTGAAAGTTTCGA-GGTCAAAGAATGGAA
1 TTTTTGGAAG-TTCGAGGGT-AAA-AATGGAA
13394 TTTTTGGAAGTT
1 TTTTTGGAAGTT
13406 TAGGGACCTC
Statistics
Matches: 233, Mismatches: 27, Indels: 35
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.01
28 3 0.01
29 131 0.56
30 71 0.30
31 24 0.10
32 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
TTTTTGGAAGTTCGAGGGTAAAAATGGAA
Found at i:13163 original size:59 final size:59
Alignment explanation
Indices: 13099--13405 Score: 312
Period size: 59 Copynumber: 5.2 Consensus size: 59
13089 AAAATAGAGT
*
13099 TTTTTGGACA-TTCGAGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAA
1 TTTTTGGA-AGTTCGAGGGTGAAAATGG-AATTTTTGGAAGTTTCGAGGTCAAAAATGGAA
* * * *
13158 ATTTTGGAGGTTCGAGGGTAAAAAT--AATTTTTTTGGAAGTTT-TAGGATCAAAAATGGAA
1 TTTTTGGAAGTTCGAGGGTGAAAATGGAA--TTTTTGGAAGTTTCGAGG-TCAAAAATGGAA
* * * *
13217 TTTTTGGAAGTTTGGGGGTGAAAATGGAATTTTTGGAAG-TTCGAGGGT-GAAAATTGAA
1 TTTTTGGAAGTTCGAGGGTGAAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAAATGGAA
* *
13275 TTTTTGGAAGTTTCG-GGGTTAAAAATGAAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAA
1 TTTTTGGAAG-TTCGAGGG-TGAAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAAATGGAA
* * *
13334 TTTTAGTAAGTTC-AGTGGTGAAAATGGAATTTTTGAAAGTTTCGAGGTCAAAGAATGGAA
1 TTTTTGGAAGTTCGAG-GGTGAAAATGGAATTTTTGGAAGTTTCGAGGTCAAA-AATGGAA
13394 TTTTTGGAAGTT
1 TTTTTGGAAGTT
13406 TAGGGACCTC
Statistics
Matches: 208, Mismatches: 24, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
57 2 0.01
58 51 0.25
59 129 0.62
60 24 0.12
61 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (59 bp):
TTTTTGGAAGTTCGAGGGTGAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAA
Found at i:13280 original size:88 final size:87
Alignment explanation
Indices: 13118--13406 Score: 323
Period size: 88 Copynumber: 3.3 Consensus size: 87
13108 ATTCGAGGGT
* * * * * *
13118 AAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAAATTTTGGAGGTTCGAGGGT-AAAAA
1 AAAATGG-AATTTTTGGAAGTTTGGGGGT-AAAAATGGAATTTTTGGAAGTTCGAGGGTGAAAAT
*
13182 T-AATTTTTTTGGAAGTTTTAGGATCA
64 TGAA--TTTTTGGAAGTTTCAGG-TCA
*
13208 AAAATGGAATTTTTGGAAGTTTGGGGGTGAAAATGGAATTTTTGGAAGTTCGAGGGTGAAAATTG
1 AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTGAAAATTG
* *
13273 AATTTTTGGAAGTTTCGGGGTTA
66 AATTTTTGGAAGTTTC-AGGTCA
* * * * * *
13296 AAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTAGTAAGTTC-AGTGGTGAAAATG
1 AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTCGAG-GGTGAAAATT
*
13360 GAATTTTTGAAAGTTTCGAGGTCA
65 GAATTTTTGGAAGTTTC-AGGTCA
13384 AAGAATGGAATTTTTGGAAGTTT
1 AA-AATGGAATTTTTGGAAGTTT
13407 AGGGACCTCT
Statistics
Matches: 172, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
87 2 0.01
88 118 0.69
89 43 0.25
90 9 0.05
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (87 bp):
AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTGAAAATTG
AATTTTTGGAAGTTTCAGGTCA
Found at i:14475 original size:15 final size:16
Alignment explanation
Indices: 14449--14478 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14439 AATGTCATTA
14449 TGATTATTATTAATAT
1 TGATTATTATTAATAT
14465 TGATT-TTATTAATA
1 TGATTATTATTAATA
14479 CGTTTTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TGATTATTATTAATAT
Found at i:15159 original size:11 final size:11
Alignment explanation
Indices: 15143--15192 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
15133 TTTAATTTTG
15143 AAATTTAAATT
1 AAATTTAAATT
15154 AAATTTAAATTT
1 AAATTTAAA-TT
*
15166 AAGA-TTAATTT
1 AA-ATTTAAATT
*
15177 AAATTTAAAAT
1 AAATTTAAATT
15188 AAATT
1 AAATT
15193 AAAAAAAGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.03
11 23 0.70
12 8 0.24
13 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:15165 original size:17 final size:17
Alignment explanation
Indices: 15143--15192 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
15133 TTTAATTTTG
15143 AAATTTAAATTAAATTT
1 AAATTTAAATTAAATTT
15160 AAATTTAAGATT-AATTT
1 AAATTTAA-ATTAAATTT
*
15177 AAATTTAAAATAAATT
1 AAATTTAAATTAAATT
15193 AAAAAAAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 2 0.07
17 25 0.83
18 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AAATTTAAATTAAATTT
Found at i:15166 original size:6 final size:6
Alignment explanation
Indices: 15133--15185 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
15123 TATTTGGACT
*
15133 TTTAAT TTTGAAA TTTAAA -TTAAA TTTAAA TTTAAGA -TT-AA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
15180 TTTAAA
1 TTTAAA
15186 ATAAATTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
4 1 0.02
5 8 0.20
6 26 0.63
7 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:16623 original size:23 final size:25
Alignment explanation
Indices: 16597--16642 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16587 CCAATTAGGG
16597 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
16620 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
16643 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Done.