Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008011.1 Kokia drynarioides strain JFW-HI SEQ_122665, 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: 35950
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:7383 original size:21 final size:20
Alignment explanation
Indices: 7357--7435 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 20
7347 ATTAAAAAAT
*
7357 AATTGAGGATTGAAAATGCGA
1 AATTGAGGATTGAAAAT-TGA
** *
7378 AATTGAAAATTGAAAATATAA
1 AATTGAGGATTGAAAAT-TGA
7399 AATTGCAAAGGATTGAAAATTGA
1 AATTG---AGGATTGAAAATTGA
7422 GAATTGAGGATTGA
1 -AATTGAGGATTGA
7436 GATTTTTGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
21 29 0.63
23 2 0.04
24 15 0.33
ACGTcount: A:0.48, C:0.03, G:0.23, T:0.27
Consensus pattern (20 bp):
AATTGAGGATTGAAAATTGA
Found at i:7387 original size:7 final size:7
Alignment explanation
Indices: 7377--7428 Score: 52
Period size: 7 Copynumber: 7.0 Consensus size: 7
7367 TGAAAATGCG
7377 AAATTGA
1 AAATTGA
7384 AAATTGA
1 AAATTGA
7391 AAATAT-A
1 AAAT-TGA
7398 AAATTGCA
1 AAATTG-A
7406 AAGGATTGA
1 AA--ATTGA
7415 AAATTGA
1 AAATTGA
*
7422 GAATTGA
1 AAATTGA
7429 GGATTGAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
6 1 0.03
7 27 0.69
8 4 0.10
9 3 0.08
10 4 0.10
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (7 bp):
AAATTGA
Found at i:16275 original size:34 final size:34
Alignment explanation
Indices: 16212--16320 Score: 148
Period size: 34 Copynumber: 3.2 Consensus size: 34
16202 AAATACATGT
* * * *
16212 TAAGCATGACT-TTGCTACCGTACTAATTTGTTA
1 TAAGCATGTCTATTGCTACTGTATTGATTTGTTA
16245 TAAGCATGTCTATTGCTACTGTATTGATTTGTTA
1 TAAGCATGTCTATTGCTACTGTATTGATTTGTTA
* * *
16279 TAAGCATGTCCATTGCTACTGAATTGATCTGTTA
1 TAAGCATGTCTATTGCTACTGTATTGATTTGTTA
16313 TAAGCATG
1 TAAGCATG
16321 AATACTGTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
33 10 0.15
34 58 0.85
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (34 bp):
TAAGCATGTCTATTGCTACTGTATTGATTTGTTA
Found at i:23344 original size:22 final size:23
Alignment explanation
Indices: 23312--23355 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
23302 TAGAAAGTTA
*
23312 TAAAAATTATT-TAAAAATTTTG
1 TAAAAAATATTATAAAAATTTTG
*
23334 TAAAAAATATTATAAAACTTTT
1 TAAAAAATATTATAAAAATTTT
23356 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAAAAATATTATAAAAATTTTG
Found at i:23360 original size:22 final size:22
Alignment explanation
Indices: 23313--23360 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
23303 AGAAAGTTAT
* *
23313 AAAAATTATTTAAAAATTTTGT
1 AAAAAATATTTAAAAATTTTGA
*
23335 AAAAAATATTATAAAACTTTT-A
1 AAAAAATATT-TAAAAATTTTGA
23357 AAAA
1 AAAA
23361 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAATATTTAAAAATTTTGA
Found at i:24499 original size:18 final size:18
Alignment explanation
Indices: 24450--24499 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
24440 TTAAATAATC
24450 AAAA-TATTTTAAAAGTT
1 AAAACTATTTTAAAAGTT
* *
24467 AAAACTACTTAAAAAGTT
1 AAAACTATTTTAAAAGTT
*
24485 ATGAACT-TTTTAAAA
1 A-AAACTATTTTAAAA
24500 TGTGAAATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (18 bp):
AAAACTATTTTAAAAGTT
Found at i:25897 original size:28 final size:28
Alignment explanation
Indices: 25866--25919 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
25856 GATAAATTAT
25866 ATGCA-AA-AATTAAAAATACTAAATACGA
1 ATGCATAATAATT-AAAA-ACTAAATACGA
*
25894 ATGCATAATGATTAAAAACTAAATAC
1 ATGCATAATAATTAAAAACTAAATAC
25920 AAATATTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 14 0.61
29 6 0.26
30 3 0.13
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.24
Consensus pattern (28 bp):
ATGCATAATAATTAAAAACTAAATACGA
Found at i:26017 original size:28 final size:27
Alignment explanation
Indices: 25957--26028 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
25947 CAATCGGAGT
* *
25957 TAAAATTGTGATTTTGGATACCGGGGG
1 TAAAATGGTAATTTTGGATACCGGGGG
*
25984 CAAAATGGTAATTTTGG-TCACTCGGGGG
1 TAAAATGGTAATTTTGGAT-AC-CGGGGG
26012 TAAAATGGTAATTTTGG
1 TAAAATGGTAATTTTGG
26029 GAAAGTTGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 16 0.41
28 22 0.56
ACGTcount: A:0.28, C:0.08, G:0.31, T:0.33
Consensus pattern (27 bp):
TAAAATGGTAATTTTGGATACCGGGGG
Found at i:26083 original size:29 final size:29
Alignment explanation
Indices: 25979--26323 Score: 90
Period size: 29 Copynumber: 11.9 Consensus size: 29
25969 TTTGGATACC
* ** * *
25979 GGGGGCAAAATGGTAATTTT-GGTCACTC
1 GGGGGTAAAATGGTAATTTTGGGAAAGTT
26007 GGGGGTAAAATGGTAATTTTGGGAAAGTT
1 GGGGGTAAAATGGTAATTTTGGGAAAGTT
* * * *
26036 -GGGGTCAAAACGG-AATTTTTGGATATTT
1 GGGGGT-AAAATGGTAATTTTGGGAAAGTT
* ** *
26064 GGGGGTAAAATGGTACTTTT-CAAAAGAAT
1 GGGGGTAAAATGGTAATTTTGGGAAAG-TT
* * *
26093 CGGGATCAAAAATGG-AATTTTTGG-AAGTT
1 GGGGGT--AAAATGGTAATTTTGGGAAAGTT
* * **
26122 CGAGGGTAAAATGGTAATTTT-GAAAAAAT
1 -GGGGGTAAAATGGTAATTTTGGGAAAGTT
** *
26151 CAGGGTCAAAAATGG-AATTTTTGG-AAGTT
1 GGGGGT--AAAATGGTAATTTTGGGAAAGTT
* **
26180 CGAGGGTAAAAATGGTAATTTT-GGAAAAAT
1 -GGGGGT-AAAATGGTAATTTTGGGAAAGTT
** ** *
26210 CAGGGTCAAAAATGG-AATTTT-TAAAACTT
1 GGGGGT--AAAATGGTAATTTTGGGAAAGTT
** **
26239 CAAGGGTAAAATGGTAATTTT-GGAAAAAT
1 -GGGGGTAAAATGGTAATTTTGGGAAAGTT
* * *
26268 CGGGGTCAAGAAT-GAAATTTTTGG-AAGTT
1 GGGGGT-AA-AATGGTAATTTTGGGAAAGTT
* *
26297 CGAGGGTAAAATGGTAATTTTTGGAAA
1 -GGGGGTAAAATGGTAATTTTGGGAAA
26324 AATTAAGGTT
Statistics
Matches: 238, Mismatches: 53, Indels: 50
0.70 0.16 0.15
Matches are distributed among these distances:
28 71 0.30
29 103 0.43
30 57 0.24
31 7 0.03
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (29 bp):
GGGGGTAAAATGGTAATTTTGGGAAAGTT
Found at i:26228 original size:117 final size:116
Alignment explanation
Indices: 26009--26376 Score: 463
Period size: 117 Copynumber: 3.2 Consensus size: 116
25999 GGTCACTCGG
* * * * * *
26009 GGGTAAAATGGTAATTTTGGGAAAGTTGGGGTC-AAAACGGAATTTTTGGATA-TTTGGGGGTAA
1 GGGTAAAATGGTAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAA
* **
26072 AATGGTACTTTTCAAAAGAATC-GGGATCAAAAATGGAATTTTTGGAAGTTCGA
65 AATGGTAATTTTGGAAA-AATCAGGG-TCAAAAATGGAATTTTTGGAAGTTCGA
* *
26125 GGGTAAAATGGTAATTTTGAAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
1 GGGTAAAATGGTAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT-AA
** * *
26190 AATGGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTAAAACTTCAA
65 AATGGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
* *
26242 GGGTAAAATGGTAATTTTGGAAAAATCGGGGTCAAGAATGAAATTTTTGGAAGTTCGAGGGTAAA
1 GGGTAAAATGGTAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
* * * *
26307 ATGGTAATTTTTGGAAAAATTAAGGTTAAAAATGGAATTTTTGGAAGTTTGA
66 ATGGTAA-TTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
* *
26359 GGGTAAAAAGATAATTTT
1 GGGTAAAATGGTAATTTT
26377 TTAATAGTTT
Statistics
Matches: 218, Mismatches: 29, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
116 39 0.18
117 160 0.73
118 19 0.09
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (116 bp):
GGGTAAAATGGTAATTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
ATGGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
Found at i:26377 original size:59 final size:58
Alignment explanation
Indices: 26009--26376 Score: 454
Period size: 59 Copynumber: 6.3 Consensus size: 58
25999 GGTCACTCGG
* * ** * * *
26009 GGGTAAAATGGTAATTTTGGGAAAGTTGGGGTC-AAAACGGAATTTTTGGATA-TTTGG
1 GGGTAAAATGGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGA-AGTTCGA
* **
26066 GGGTAAAATGGTACTTTTCAAAAGAATC-GGGATCAAAAATGGAATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTGGAAA-AATCAGGG-TCAAAAATGGAATTTTTGGAAGTTCGA
*
26125 GGGTAAAATGGTAATTTTGAAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
** * *
26183 GGGTAAAAATGGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTAAAACTTCAA
1 GGGT-AAAATGGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
* * *
26242 GGGTAAAATGGTAATTTTGGAAAAATCGGGGTCAAGAATGAAATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
* * * *
26300 GGGTAAAATGGTAATTTTTGGAAAAATTAAGGTTAAAAATGGAATTTTTGGAAGTTTGA
1 GGGTAAAATGGTAA-TTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
* *
26359 GGGTAAAAAGATAATTTT
1 GGGTAAAATGGTAATTTT
26377 TTAATAGTTT
Statistics
Matches: 272, Mismatches: 32, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
57 22 0.08
58 105 0.39
59 145 0.53
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
Found at i:26378 original size:30 final size:28
Alignment explanation
Indices: 26283--26377 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
26273 TCAAGAATGA
* *
26283 AATTTTTGGAAGTTCGAGGGTAAAATGGT
1 AATTTTTGGAAGTTTGAGGGTAAAA-AGT
** * * *
26312 AATTTTTGGAAAAATTAAGGTTAAAAATGG
1 AATTTTTGG-AAGTTTGAGGGTAAAAA-GT
26342 AATTTTTGGAAGTTTGAGGGTAAAAAGAT
1 AATTTTTGGAAGTTTGAGGGTAAAAAG-T
26371 AATTTTT
1 AATTTTT
26378 TAATAGTTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
28 1 0.02
29 29 0.57
30 21 0.41
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (28 bp):
AATTTTTGGAAGTTTGAGGGTAAAAAGT
Found at i:28262 original size:17 final size:17
Alignment explanation
Indices: 28232--28318 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
28222 TTTTAATATT
* * *
28232 AATAATTTTTAATTCAA
1 AATAAATTTAAATTTAA
* *
28249 AATACATTCAAATTTAA
1 AATAAATTTAAATTTAA
* *
28266 AATAAATTTAAACTCAA
1 AATAAATTTAAATTTAA
* *
28283 CATGAATTTAAATTTAA
1 AATAAATTTAAATTTAA
*
28300 AATAAATTAAAATTTAA
1 AATAAATTTAAATTTAA
28317 AA
1 AA
28319 ATTAAAAGTT
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Done.