Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013937.1 Kokia drynarioides strain JFW-HI SEQ_128967, 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: 51972
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:9578 original size:21 final size:21
Alignment explanation
Indices: 9554--9598 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
9544 GAACCTCTTC
9554 AAATA-ACATTAAAAACATTAA
1 AAATATACATTAAAAA-ATTAA
* *
9575 AAATATATATTATAAAATTAA
1 AAATATACATTAAAAAATTAA
9596 AAA
1 AAA
9599 CATATCAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATATACATTAAAAAATTAA
Found at i:9603 original size:21 final size:22
Alignment explanation
Indices: 9561--9603 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
9551 TTCAAATAAC
*
9561 ATTAAAAACATTAAAAATATAT
1 ATTAAAAACATTAAAAACATAT
*
9583 ATTATAAA-ATTAAAAACATAT
1 ATTAAAAACATTAAAAACATAT
9604 CAACATCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
ATTAAAAACATTAAAAACATAT
Found at i:10119 original size:13 final size:13
Alignment explanation
Indices: 10103--10127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10093 TTTTTTTATC
10103 AATTTGATACTTA
1 AATTTGATACTTA
10116 AATTTGATACTT
1 AATTTGATACTT
10128 TTTGAGGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTTGATACTTA
Found at i:10361 original size:28 final size:29
Alignment explanation
Indices: 10329--10399 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 29
10319 TTTAATAAAT
*
10329 TTAGGTACCAAATTGAATATAAAAAAA-C
1 TTAGGTACCAAATTGAATACAAAAAAAGC
** * *
10357 TTAGGTACCAAATTGGGTCCAAAAAAAGT
1 TTAGGTACCAAATTGAATACAAAAAAAGC
10386 TTAGGTACCAAATT
1 TTAGGTACCAAATT
10400 AGAAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 23 0.62
29 14 0.38
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (29 bp):
TTAGGTACCAAATTGAATACAAAAAAAGC
Found at i:12762 original size:23 final size:22
Alignment explanation
Indices: 12736--12845 Score: 107
Period size: 23 Copynumber: 4.9 Consensus size: 22
12726 TTACTGTTCA
*
12736 GCACTGTGTGTGCTTACT-ATTT
1 GCACTGTGTGTGCCTACTGA-TT
12758 CGCACT-TCGTGTGCCTACTGATTT
1 -GCACTGT-GTGTGCCTACTGA-TT
** * *
12782 GCGTTATGTGCGCCTACTGATT
1 GCACTGTGTGTGCCTACTGATT
12804 GCACTGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCCTACT-GATT
*
12827 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCCTACTG
12846 TTAAGTACTT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
22 18 0.24
23 51 0.69
24 5 0.07
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (22 bp):
GCACTGTGTGTGCCTACTGATT
Found at i:12845 original size:45 final size:47
Alignment explanation
Indices: 12736--12845 Score: 122
Period size: 45 Copynumber: 2.4 Consensus size: 47
12726 TTACTGTTCA
12736 GCACTGTGTGTGCTTACT-ATTTCGCACTTCGTGTGCCTACTGATTT
1 GCACTGTGTGTGCTTACTGATTTCGCACTTCGTGTGCCTACTGATTT
** * * *
12782 GCGTTATGTGCGCCTACTGA-TT-GCACTGT-GTGTGCCTACTGGA-TT
1 GCACTGTGTGTGCTTACTGATTTCGCACT-TCGTGTGCCTACT-GATTT
12827 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCTTACTG
12846 TTAAGTACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
45 32 0.63
46 18 0.35
47 1 0.02
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (47 bp):
GCACTGTGTGTGCTTACTGATTTCGCACTTCGTGTGCCTACTGATTT
Found at i:17268 original size:180 final size:180
Alignment explanation
Indices: 16960--17322 Score: 620
Period size: 180 Copynumber: 2.0 Consensus size: 180
16950 CACTTTTGAA
* *
16960 AGAAAATCGTCGCAATAAGATGATGAAAGAGAATAAGAGAAAGAAAAGAGATAAAAGAAGAGAGT
1 AGAAAATCGTCGCAATAAGATGATAAAAGAGAATAAGAGAAAGAAAAGAGAGAAAAGAAGAGAGT
* *
17025 TTATATATGAGATATAGGAATTGCCATGTGTAAGCATTTTGTTGGTAGTAGAGTCACATCCTATT
66 TTATATATGAGACATAGGAATTGCCATGTGTAAGCATTTTGTTGATAGTAGAGTCACATCCTATT
*
17090 CCATTGTAGAGATGGTGATATGA-TCTTATGGATTAGTAACGTGACAATAT
131 CCATTGTAGAGACGGTGATATGACT-TTATGGATTAGTAACGTGACAATAT
* * * *
17140 AGAAAGTCGTCGCGATAAGGTGATAAAAGAGAATAAGAGAAAGAAAAGAGAGAAAGGAAGAGAGT
1 AGAAAATCGTCGCAATAAGATGATAAAAGAGAATAAGAGAAAGAAAAGAGAGAAAAGAAGAGAGT
*
17205 TTATATATGAGACATAGGAATTGTCATGTGTAAGCATTTTGTTGATAGTAGAGTCACATCCTATT
66 TTATATATGAGACATAGGAATTGCCATGTGTAAGCATTTTGTTGATAGTAGAGTCACATCCTATT
17270 CCATTGTAGAGACGGTGATATGACTTTATGGATTAGTAACGTGACAATAT
131 CCATTGTAGAGACGGTGATATGACTTTATGGATTAGTAACGTGACAATAT
17320 AGA
1 AGA
17323 GTGACTTGAC
Statistics
Matches: 172, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
180 171 0.99
181 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.27
Consensus pattern (180 bp):
AGAAAATCGTCGCAATAAGATGATAAAAGAGAATAAGAGAAAGAAAAGAGAGAAAAGAAGAGAGT
TTATATATGAGACATAGGAATTGCCATGTGTAAGCATTTTGTTGATAGTAGAGTCACATCCTATT
CCATTGTAGAGACGGTGATATGACTTTATGGATTAGTAACGTGACAATAT
Found at i:24952 original size:24 final size:25
Alignment explanation
Indices: 24920--24971 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
24910 AAATAATTAT
24920 ATTAATATT-AAAAATATATTTTTA
1 ATTAATATTCAAAAATATATTTTTA
* *
24944 ATTATTATTCAAATATATATTTTTA
1 ATTAATATTCAAAAATATATTTTTA
24969 ATT
1 ATT
24972 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTAATATTCAAAAATATATTTTTA
Found at i:31444 original size:20 final size:20
Alignment explanation
Indices: 31421--31458 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31411 AATTAACCAA
31421 TTTAAAATAAATAAATTTTT
1 TTTAAAATAAATAAATTTTT
* *
31441 TTTAAAATTAATCAATTT
1 TTTAAAATAAATAAATTT
31459 AAAATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAAATAAATAAATTTTT
Found at i:48708 original size:59 final size:59
Alignment explanation
Indices: 48642--49015 Score: 407
Period size: 59 Copynumber: 6.4 Consensus size: 59
48632 GGATACATGG
* *
48642 GGGT-AAAATGGTAATTTTGGGAAAATTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
1 GGGTAAAAATGG-AATTTTTGGAAATTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
* * * *
48701 GGGTAAAAATGGAATTTTTGGAAGTTTCGGGG-TCAAAATGGGATTTTTAGAAGTT--A
1 GGGTAAAAATGGAATTTTTGGAAATTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
** * * * * **
48757 GGGATAAAAAAAGAATTTTTGTAAGTTTTGGGGTTAAAAATGAGATTTTTTGAAGTTTAA
1 GGG-TAAAAATGGAATTTTTGGAAATTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
* * *
48817 GGGT-AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAATTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
* * * *
48875 GGGTAAAAATAGAATTTTTGGAAGTTTTAGGGTTAAAATTGGGATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAATTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
* ** * * ** * * *
48934 GGGTGAAAATGGGTTTTTTAGAAGTTTCAGGGTTAAAAATGAGATTTTTGGAAGTTTGG
1 GGGTAAAAATGGAATTTTTGGAAATTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
*
48993 GGGTAAAAATGAAATTTTTGGAA
1 GGGTAAAAATGGAATTTTTGGAA
49016 GTTTAGGGAC
Statistics
Matches: 267, Mismatches: 42, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
56 4 0.01
57 25 0.09
58 90 0.34
59 137 0.51
60 11 0.04
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.36
Consensus pattern (59 bp):
GGGTAAAAATGGAATTTTTGGAAATTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
Found at i:49019 original size:29 final size:29
Alignment explanation
Indices: 48639--49019 Score: 327
Period size: 29 Copynumber: 13.0 Consensus size: 29
48629 TTCGGATACA
* * *
48639 TGGGGGT-AAAATGGTAATTTTGGGAAAATT
1 TGGGGGTAAAAATGG-GATTTTTGG-AAGTT
*
48669 TGGGGTTAAAAATGGGATTTTTGGAAGTT
1 TGGGGGTAAAAATGGGATTTTTGGAAGTT
* * *
48698 CGAGGGTAAAAATGGAATTTTTGGAAGTT
1 TGGGGGTAAAAATGGGATTTTTGGAAGTT
* * *
48727 TCGGGGTCAAAATGGGATTTTTAGAAG-T
1 TGGGGGTAAAAATGGGATTTTTGGAAGTT
* * ** * *
48755 TAGGGATAAAAAAAGAATTTTTGTAAGTTT
1 TGGGGGTAAAAATGGGATTTTTGGAAG-TT
* * *
48785 TGGGGTTAAAAATGAGATTTTTTGAAGTT
1 TGGGGGTAAAAATGGGATTTTTGGAAGTT
** *
48814 TAAGGGT-AAAATGGAATTTTTGGAAGTTT
1 TGGGGGTAAAAATGGGATTTTTGGAAG-TT
* *
48843 TGAGGTTAAAAATGGGATTTTTGGAAGTT
1 TGGGGGTAAAAATGGGATTTTTGGAAGTT
* * *
48872 CGGGGGTAAAAATAGAATTTTTGGAAGTTT
1 TGGGGGTAAAAATGGGATTTTTGGAAG-TT
* * *
48902 TAGGGTTAAAATTGGGATTTTTGGAAGTT
1 TGGGGGTAAAAATGGGATTTTTGGAAGTT
* * * * *
48931 CGAGGGTGAAAATGGGTTTTTTAGAAGTT
1 TGGGGGTAAAAATGGGATTTTTGGAAGTT
* * *
48960 TCAGGGTTAAAAATGAGATTTTTGGAAGTT
1 T-GGGGGTAAAAATGGGATTTTTGGAAGTT
**
48990 TGGGGGTAAAAATGAAATTTTTGGAAGTT
1 TGGGGGTAAAAATGGGATTTTTGGAAGTT
49019 T
1 T
49020 AGGGACTTTC
Statistics
Matches: 275, Mismatches: 69, Indels: 15
0.77 0.19 0.04
Matches are distributed among these distances:
28 36 0.13
29 136 0.49
30 96 0.35
31 7 0.03
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (29 bp):
TGGGGGTAAAAATGGGATTTTTGGAAGTT
Done.