Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011798.1 Kokia drynarioides strain JFW-HI SEQ_126793, 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: 32152
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:778 original size:33 final size:33
Alignment explanation
Indices: 736--799 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
726 CAAACTTCAA
736 AAAATTACATAATAATCATTTACATTATCGAGT
1 AAAATTACATAATAATCATTTACATTATCGAGT
* *
769 AAAATTACATAATAATTATTTATATTATCGA
1 AAAATTACATAATAATCATTTACATTATCGA
800 ATTATTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (33 bp):
AAAATTACATAATAATCATTTACATTATCGAGT
Found at i:10712 original size:21 final size:21
Alignment explanation
Indices: 10661--10717 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
10651 ATAATAATAA
*
10661 TTTTGTTTTTT-AAAATGATT
1 TTTTTTTTTTTGAAAATGATT
* *
10681 CTTTTTATTTTGAAAATGATT
1 TTTTTTTTTTTGAAAATGATT
10702 TTTTTTTTTTTGAAAA
1 TTTTTTTTTTTGAAAA
10718 GGTCTCTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 8 0.26
21 23 0.74
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.63
Consensus pattern (21 bp):
TTTTTTTTTTTGAAAATGATT
Found at i:15315 original size:58 final size:58
Alignment explanation
Indices: 15253--15383 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 58
15243 TTCGAGGTTA
* * *
15253 AAAATGGACTTTTTAGACATTCGAGGGTAAAA-GCATAATTTTT-GAGAGTTTCGAAGTC
1 AAAATGGAATTTTTAGACATCCGAGGGCAAAATG-ATAATTTTTGGA-AGTTTCGAAGTC
* * * * *
15311 AAAATGGAATTTTTGGACATCCGGGGGCAAAATGGTAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTAGACATCCGAGGGCAAAATGATAATTTTTGGAAGTTTCGAAG-TC
*
15370 AAAATGAAATTTTT
1 AAAATGGAATTTTT
15384 GGAAGATTCT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 44 0.72
59 17 0.28
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTAGACATCCGAGGGCAAAATGATAATTTTTGGAAGTTTCGAAGTC
Found at i:15382 original size:29 final size:30
Alignment explanation
Indices: 15347--15597 Score: 232
Period size: 29 Copynumber: 8.5 Consensus size: 30
15337 GCAAAATGGT
*
15347 AATTTTTGGAAGTTTCGAGGTTAAAAAT-G
1 AATTTTTGGAAGTTTCGAGGGTAAAAATAG
* * *
15376 AAATTTTTGGAAGATTCTAGGTTAAAAATAG
1 -AATTTTTGGAAGTTTCGAGGGTAAAAATAG
* * *
15407 AATTTTTGAAAG-CTCGAGGGCAAAAAT-G
1 AATTTTTGGAAGTTTCGAGGGTAAAAATAG
* * *
15435 TAATTTTGGGAAGTTT-GGGGGTAAAAATGG
1 -AATTTTTGGAAGTTTCGAGGGTAAAAATAG
* *
15465 GATTTTTGGAAGTTT-GAGGGTAAAAATGG
1 AATTTTTGGAAGTTTCGAGGGTAAAAATAG
* * *
15494 ATTTTTTGGAAGTTTTG-GGGTCAAAAATGG
1 AATTTTTGGAAGTTTCGAGGGT-AAAAATAG
* *
15524 AATTTTGGGAAG-TTCGGGGGTAAAAAT-G
1 AATTTTTGGAAGTTTCGAGGGTAAAAATAG
*
15552 TGATTTTTGGAAG-TTCGAGGGTAAAAATAG
1 -AATTTTTGGAAGTTTCGAGGGTAAAAATAG
15582 AATTTTTGGATAGTTT
1 AATTTTTGGA-AGTTT
15598 AGGGACCTCC
Statistics
Matches: 186, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
28 2 0.01
29 116 0.62
30 65 0.35
31 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAGTTTCGAGGGTAAAAATAG
Found at i:15424 original size:59 final size:59
Alignment explanation
Indices: 15347--15596 Score: 274
Period size: 59 Copynumber: 4.2 Consensus size: 59
15337 GCAAAATGGT
* * *
15347 AATTTTTGGAAGTTTCGAGGTTAAAAATGAAATTTTTGGAAGATTCT-AGGTTAAAAATAG
1 AATTTTTGGAAG-TTCGAGGGTAAAAATGTAATTTTTGGAAG-TTCTGAGGGTAAAAATAG
* * * * * *
15407 AATTTTTGAAAGCTCGAGGGCAAAAATGTAATTTTGGGAAGTT-TGGGGGTAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTCTGAGGGTAAAAATAG
* * * * * *
15465 GATTTTTGGAAGTTTGAGGGTAAAAATGGATTTTTTGGAAGTTTTG-GGGTCAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTCTGAGGGT-AAAAATAG
* * *
15524 AATTTTGGGAAGTTCGGGGGTAAAAATGTGATTTTTGGAAGTTC-GAGGGTAAAAATAG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTCTGAGGGTAAAAATAG
15582 AATTTTTGGATAGTT
1 AATTTTTGGA-AGTT
15597 TAGGGACCTC
Statistics
Matches: 158, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
57 1 0.01
58 68 0.43
59 78 0.49
60 11 0.07
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (59 bp):
AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTCTGAGGGTAAAAATAG
Found at i:15519 original size:88 final size:88
Alignment explanation
Indices: 15335--15597 Score: 309
Period size: 88 Copynumber: 3.0 Consensus size: 88
15325 GGACATCCGG
* * * * *
15335 GGGC-AAAATGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGAAATTTTTGGAAGATTCT-AGGT
1 GGGCAAAAAT-GTAATTTTGGGAAGTTT-GGGGGTAAAAATGAGATTTTTGGAAG-TT-TGAGGG
* *
15398 TAAAAATAGAATTTTTGAAAG-CTCGA
62 TAAAAATAGAATTTTTGGAAGTTTCGA
*
15424 GGGCAAAAATGTAATTTTGGGAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAA
1 GGGCAAAAATGTAATTTTGGGAAGTTTGGGGGTAAAAATGAGATTTTTGGAAGTTTGAGGGTAAA
* * *
15489 AATGGATTTTTTGGAAGTTTTG-
66 AATAGAATTTTTGGAAGTTTCGA
* * * *
15511 GGGTCAAAAATGGAATTTTGGGAAGTTCGGGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGTAA
1 GGG-CAAAAATGTAATTTTGGGAAGTTTGGGGGTAAAAATGAGATTTTTGGAAGTTTGAGGGTAA
15576 AAATAGAATTTTTGGATAGTTT
65 AAATAGAATTTTTGGA-AGTTT
15598 AGGGACCTCC
Statistics
Matches: 152, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
86 1 0.01
87 26 0.17
88 95 0.62
89 25 0.16
90 5 0.03
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (88 bp):
GGGCAAAAATGTAATTTTGGGAAGTTTGGGGGTAAAAATGAGATTTTTGGAAGTTTGAGGGTAAA
AATAGAATTTTTGGAAGTTTCGA
Found at i:16711 original size:3 final size:3
Alignment explanation
Indices: 16705--16752 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
16695 AGAAAACTGT
* * * * *
16705 TTA TTA TTA TTA ATG TCA TTA ATA TTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16753 AAACAGTTAT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:16734 original size:9 final size:9
Alignment explanation
Indices: 16709--16782 Score: 58
Period size: 9 Copynumber: 7.8 Consensus size: 9
16699 AACTGTTTAT
16709 TATTATTAA
1 TATTATTAA
* *
16718 TGTCATTAA
1 TATTATTAA
*
16727 TATTATTAT
1 TATTATTAA
**
16736 TATTATTGT
1 TATTATTAA
16745 TATTATTAAAA
1 TATTATT--AA
*
16756 CAGTTATTAA
1 TA-TTATTAA
16766 TATTATTAA
1 TATTATTAA
16775 TAGTTATT
1 TA-TTATT
16783 GAAACGTTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
9 37 0.73
10 8 0.16
11 1 0.02
12 5 0.10
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (9 bp):
TATTATTAA
Found at i:17465 original size:18 final size:17
Alignment explanation
Indices: 17436--17516 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
17426 TAAATAGATT
*
17436 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
17454 TAAATTTAAAATTTTAAG
1 TAAATTT-AAATTTAAAA
*
17472 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
17489 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
17506 TGAATTTAAAT
1 TAAATTTAAAT
17517 CCTGTTGGGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
17 34 0.65
18 18 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:18567 original size:206 final size:206
Alignment explanation
Indices: 17943--18693 Score: 992
Period size: 206 Copynumber: 3.7 Consensus size: 206
17933 TCCCTGTACT
** *
17943 TCATCAAGG-AGCTAACTGTTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGG
1 TCATC-AGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGG
* *
18007 GTTCGAAGATTTGCTCATATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTACCTTATCAGGA
65 GTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTACCTCATCAGGA
* * * * *
18072 AGATGGCCGTGTCGTTTGTTTCAATCCGTTTTTCTGTATCTCATCAGGAAAACAAATTTGGTTGA
130 AGATGACCGTGTCATTTGTTTCAATCCGTTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCGA
18137 CTTCTCAGTATC
195 CTTCTCAGTATC
* *
18149 TCATCAGGAAGCTAACCATTTTATTGCTTTGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGG
1 TCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGG
* * * * * * * * * *
18214 TTCGAAGATTTGCTCGCGTTGAGC-----CTCGAGTTGGTATACTTCTCTGTATCTCATCAGGAA
66 TTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAA
*** * * * * * *
18274 GATGACCACCTCACTTGTTTTAATCCGCTTCTCTATACCTCATCAGGAAGACAAATTTGGTCCAC
131 GATGACCGTGTCATTTGTTTCAATCCGTTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCGAC
18339 TTCTCAGTATC
196 TTCTCAGTATC
* * * *
18350 TCATCAGGAAGCTAACCTTTTTATTACTTCGACCTACTTCTCAGTGTCTCATCAAGAAGATGGGG
1 TCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGG
* *
18415 TTCGAAGATTTGCTCATATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTACCTCATCAAGAA
66 TTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAA
* * *
18480 GATGACCGTGTCATTTGTTTCAATCCATTTCTCTGTATCTCATTAGGAAGACGAATTTGGTCGAC
131 GATGACCGTGTCATTTGTTTCAATCCGTTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCGAC
18545 TTCTCAGTATC
196 TTCTCAGTATC
* *
18556 TCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGG
1 TCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGG
* ** * * *
18621 TTCGAAGATTTGCTCACATCGAGCCTCGTTTCATTGATTCGGTCTTTTTCTCAGTATCTCATCAG
66 TTCGAAGATTTGCTCACATCGAGCGT-GGGT--TTGATTTGGTCTTCTTCTCAGTACCTCATCAG
18686 GAAGATGA
128 GAAGATGA
18694 TCGCATCGCT
Statistics
Matches: 461, Mismatches: 75, Indels: 15
0.84 0.14 0.03
Matches are distributed among these distances:
201 169 0.37
205 3 0.01
206 251 0.54
207 2 0.00
209 36 0.08
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (206 bp):
TCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGG
TTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAA
GATGACCGTGTCATTTGTTTCAATCCGTTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCGAC
TTCTCAGTATC
Found at i:30241 original size:96 final size:96
Alignment explanation
Indices: 30053--30242 Score: 215
Period size: 96 Copynumber: 2.0 Consensus size: 96
30043 ATTTTGGGAA
** * **
30053 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACCAAATATTTCA
* *
30118 GAATCGAAGATAAATAAACATTGCCTCGATT
66 GAATCGAAGACAAATAAACATTACCTCGATT
* * * * *
30149 AAGGGTATTCGATTATTTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAAATTTTTG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGAC-CAAATATTTC
*
30214 A-AACTCGAA-ACAAA-AGAATATTACCTCGA
65 AGAA-TCGAAGACAAATA-AACATTACCTCGA
30243 CTTTAAAATC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
95 1 0.01
96 65 0.83
97 12 0.15
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACCAAATATTTCA
GAATCGAAGACAAATAAACATTACCTCGATT
Found at i:30642 original size:59 final size:58
Alignment explanation
Indices: 30518--30652 Score: 184
Period size: 59 Copynumber: 2.3 Consensus size: 58
30508 ATTAGGGGTT
* * *
30518 AAAAATGGACTTTTTAGACATTCGGGGGTAAAAGGGTAATTTTGAGGGTTTCAAGGTA
1 AAAAATGGAATTTTTGGACATTCGGGGGTAAAAGGGTAATTTTGAGAGTTTCAAGGTA
* *
30576 AAAAATGGAATTTTTGGACATTCGAGGGG-AAAATGGTAATTTTTG-GAAGTTTCAAGGTC
1 AAAAATGGAATTTTTGGACATTCG-GGGGTAAAAGGGTAA-TTTTGAG-AGTTTCAAGGTA
30635 AAAAATGGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
30653 AGTTTTAGGG
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
58 32 0.46
59 37 0.54
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGACATTCGGGGGTAAAAGGGTAATTTTGAGAGTTTCAAGGTA
Found at i:30649 original size:30 final size:29
Alignment explanation
Indices: 30565--30881 Score: 255
Period size: 29 Copynumber: 10.9 Consensus size: 29
30555 AATTTTGAGG
*
30565 GTTTCAAGGTAAAAAATGGAATTTTTGGACA
1 GTTTCAGGGT-AAAAATGGAATTTTTGGA-A
*
30596 --TTCGAGGG-GAAAATGGTAATTTTTGGAA
1 GTTTC-AGGGTAAAAATGG-AATTTTTGGAA
*
30624 GTTTCAAGGTCAAAAATGGAATTTTTGGAA
1 GTTTCAGGGT-AAAAATGGAATTTTTGGAA
*
30654 GTTTTAGGGTCAAAAATGGAATTTTTGGAA
1 GTTTCAGGGT-AAAAATGGAATTTTTGGAA
* *
30684 G-CTCGAGGGTAAAAATAGAATTTTT-GAA
1 GTTTC-AGGGTAAAAATGGAATTTTTGGAA
* * *
30712 GTTTTAAGGTCAAAAATGGAATTTTGGGAA
1 GTTTCAGGGT-AAAAATGGAATTTTTGGAA
30742 GTTT-AGGGGTAAAAATGGGAA-TTTTGGAA
1 GTTTCA-GGGTAAAAAT-GGAATTTTTGGAA
***
30771 G-TTCGAGGGTAAAAATGGAATTTTCAAAA
1 GTTTC-AGGGTAAAAATGGAATTTTTGGAA
** *
30800 GTTTTGGGGTTAAAAATGGAATTTTGGGAA
1 GTTTCAGGG-TAAAAATGGAATTTTTGGAA
*
30830 G-TTCGGGGGTAAAAATAGG-ATTTTTGGAA
1 GTTTC-AGGGTAAAAAT-GGAATTTTTGGAA
*
30859 G-TTCGGGGGTAAAAAT--AATTTTT
1 GTTTC-AGGGTAAAAATGGAATTTTT
30882 TTTGACAATT
Statistics
Matches: 240, Mismatches: 26, Indels: 44
0.77 0.08 0.14
Matches are distributed among these distances:
27 6 0.03
28 22 0.09
29 113 0.47
30 92 0.38
31 7 0.03
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (29 bp):
GTTTCAGGGTAAAAATGGAATTTTTGGAA
Found at i:30743 original size:88 final size:88
Alignment explanation
Indices: 30576--30875 Score: 353
Period size: 88 Copynumber: 3.4 Consensus size: 88
30566 TTTCAAGGTA
* * *
30576 AAAAAT-GGAATTTTTGGACA-TTCGAGGG-GAAAATGGTAATTTTTGGAAGTTTCAAGGTCAAA
1 AAAAATAGGAATTTTTGGA-AGTTCGAGGGTAAAAATAG-AATTTTT-GAAGTTTTAAGGTCAAA
*
30638 AATGGAATTTTTGGAAGTTTTAGGGT
63 AATGGAATTTTGGGAAGTTTTAGGGT
*
30664 CAAAAAT-GGAATTTTTGGAAGCTCGAGGGTAAAAATAGAATTTTTGAAGTTTTAAGGTCAAAAA
1 -AAAAATAGGAATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGAAGTTTTAAGGTCAAAAA
30728 TGGAATTTTGGGAAG-TTTAGGGGT
65 TGGAATTTTGGGAAGTTTTA-GGGT
* * ** ** *
30752 AAAAATGGGAA-TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTCAAAAGTTTTGGGGTTAAAAA
1 AAAAATAGGAATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTT-TGAAGTTTTAAGGTCAAAAA
***
30816 TGGAATTTTGGGAAGTTCGGGGGT
65 TGGAATTTTGGGAAGTTTTAGGGT
*
30840 AAAAATAGG-ATTTTTGGAAGTTCGGGGGTAAAAATA
1 AAAAATAGGAATTTTTGGAAGTTCGAGGGTAAAAATA
30876 ATTTTTTTTG
Statistics
Matches: 186, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
87 41 0.22
88 106 0.57
89 33 0.18
90 6 0.03
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.32
Consensus pattern (88 bp):
AAAAATAGGAATTTTTGGAAGTTCGAGGGTAAAAATAGAATTTTTGAAGTTTTAAGGTCAAAAAT
GGAATTTTGGGAAGTTTTAGGGT
Done.