Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012093.1 Kokia drynarioides strain JFW-HI SEQ_127092, 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: 30886
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Found at i:816 original size:19 final size:20
Alignment explanation
Indices: 777--816 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
767 GAAGAAAAGA
* *
777 TGATATTTTCATCTTTTAAT
1 TGATATTTTCATCTCTAAAT
797 TGAT-TTTTCATCTCTAAAT
1 TGATATTTTCATCTCTAAAT
816 T
1 T
817 TCTCTAGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.57
Consensus pattern (20 bp):
TGATATTTTCATCTCTAAAT
Found at i:13740 original size:26 final size:25
Alignment explanation
Indices: 13679--13740 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
13669 TTTAATCAAT
*
13679 AGCAATTAA-C-TTTTACCTCATTT
1 AGCAATTAATCATTTTACCTCATTA
* *
13702 A-CAATTTACTCATTTTTCCTTCATTA
1 AGCAA-TTAATCATTTTACC-TCATTA
13728 AGCAATTAATCAT
1 AGCAATTAATCAT
13741 AAAAGTTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
22 3 0.10
23 4 0.13
24 1 0.03
25 6 0.20
26 13 0.43
27 3 0.10
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (25 bp):
AGCAATTAATCATTTTACCTCATTA
Found at i:15132 original size:3 final size:3
Alignment explanation
Indices: 15124--15149 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15114 GGATTAAATC
15124 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
15150 ACAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:15318 original size:30 final size:30
Alignment explanation
Indices: 15223--15332 Score: 132
Period size: 30 Copynumber: 3.7 Consensus size: 30
15213 ACATTAAACC
*
15223 AGGGTCAAATTGGAATTTTTGGAAAGTTTA
1 AGGGTCAAATTGGAATTTTTGGAAAGTTTG
15253 AGGGTCAAATTGGAATTTTTGG-AAGATTTG
1 AGGGTCAAATTGGAATTTTTGGAAAG-TTTG
* * *
15283 AGGGTTAAATTTGAATTTTTGGAAAGTCTG
1 AGGGTCAAATTGGAATTTTTGGAAAGTTTG
* * **
15313 GGGGTTAAATTCAAATTTTT
1 AGGGTCAAATTGGAATTTTT
15333 AAAAAATTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
29 3 0.04
30 65 0.92
31 3 0.04
ACGTcount: A:0.31, C:0.04, G:0.26, T:0.39
Consensus pattern (30 bp):
AGGGTCAAATTGGAATTTTTGGAAAGTTTG
Found at i:15353 original size:60 final size:60
Alignment explanation
Indices: 15225--15362 Score: 141
Period size: 60 Copynumber: 2.3 Consensus size: 60
15215 ATTAAACCAG
* * ** ** * * *
15225 GGTCAAATTGGAATTTTTGGAAAGTTTAAGGGTCAAATTGGAATTTTTGGAAGATTTGAG
1 GGTCAAATTCGAATTTTTGGAAAGTCTAAGGGTCAAATTCAAATTTTTAAAAAATTTAAC
* * ** *
15285 GGTTAAATTTGAATTTTTGGAAAGTCTGGGGGTTAAATTCAAATTTTTAAAAAATTTAAC
1 GGTCAAATTCGAATTTTTGGAAAGTCTAAGGGTCAAATTCAAATTTTTAAAAAATTTAAC
*
15345 GGTCAAATTCAAATTTTT
1 GGTCAAATTCGAATTTTT
15363 AAAAGTTCAA
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (60 bp):
GGTCAAATTCGAATTTTTGGAAAGTCTAAGGGTCAAATTCAAATTTTTAAAAAATTTAAC
Found at i:22249 original size:20 final size:21
Alignment explanation
Indices: 22172--22257 Score: 81
Period size: 20 Copynumber: 4.1 Consensus size: 21
22162 TATATTGTTG
22172 TTTTGATGCTATTTTTTACTG-
1 TTTTGATGCT-TTTTTTACTGT
* *
22193 TTTTGATTACTTTTTTATGCTG-
1 TTTTGA-TGCTTTTTT-TACTGT
* *
22215 TTTTGGTG-TTGTTTTACTGT
1 TTTTGATGCTTTTTTTACTGT
22235 TTTTG-TGCTTTTTTTACTGT
1 TTTTGATGCTTTTTTTACTGT
22255 TTT
1 TTT
22258 GGTTGTTGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.11
20 24 0.44
21 12 0.22
22 12 0.22
ACGTcount: A:0.09, C:0.08, G:0.16, T:0.66
Consensus pattern (21 bp):
TTTTGATGCTTTTTTTACTGT
Found at i:22269 original size:20 final size:19
Alignment explanation
Indices: 22212--22269 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
22202 CTTTTTTATG
22212 CTGTTTTGGTGTTGTTTTA
1 CTGTTTTGGTGTTGTTTTA
* *
22231 CTGTTTTTGTGCTTTTTTTA
1 CTGTTTTGGTG-TTGTTTTA
22251 CTGTTTTGGTTGTTGTTTT
1 CTGTTTTGG-TGTTGTTTT
22270 GGTGTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 10 0.30
20 21 0.64
21 2 0.06
ACGTcount: A:0.03, C:0.07, G:0.22, T:0.67
Consensus pattern (19 bp):
CTGTTTTGGTGTTGTTTTA
Found at i:22310 original size:12 final size:12
Alignment explanation
Indices: 22295--22393 Score: 100
Period size: 12 Copynumber: 8.6 Consensus size: 12
22285 ACTATTTTGA
*
22295 TGTTGTTAATTT
1 TGTTGTTATTTT
22307 TGTTGTTATTTT
1 TGTTGTTATTTT
**
22319 TACTGTTATTTT
1 TGTTGTTATTTT
22331 TGTT-TCTATTTT
1 TGTTGT-TATTTT
22343 TGTTG---TTTT
1 TGTTGTTATTTT
*
22352 TGTTGTT-GTTT
1 TGTTGTTATTTT
*
22363 TGCTGTTATTTT
1 TGTTGTTATTTT
22375 TGTTGTTATTTT
1 TGTTGTTATTTT
*
22387 GGTTGTT
1 TGTTGTT
22394 TGTATGTTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
9 9 0.12
11 10 0.14
12 53 0.74
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.71
Consensus pattern (12 bp):
TGTTGTTATTTT
Found at i:22363 original size:20 final size:20
Alignment explanation
Indices: 22340--22381 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
22330 TTGTTTCTAT
*
22340 TTTTGTTGTT-TTTGTTGTTG
1 TTTTGCTGTTATTT-TTGTTG
22360 TTTTGCTGTTATTTTTGTTG
1 TTTTGCTGTTATTTTTGTTG
22380 TT
1 TT
22382 ATTTTGGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.02, C:0.02, G:0.21, T:0.74
Consensus pattern (20 bp):
TTTTGCTGTTATTTTTGTTG
Found at i:22373 original size:32 final size:32
Alignment explanation
Indices: 22337--22407 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
22327 TTTTTGTTTC
* *
22337 TATTTTTGTTGTT-TTTGTTGTTGTTT-TGCTGT
1 TATTTTTGTTGTTATTT-TGGTTGTTTGT-ATGT
22369 TATTTTTGTTGTTATTTTGGTTGTTTGTATGT
1 TATTTTTGTTGTTATTTTGGTTGTTTGTATGT
22401 TATTTTT
1 TATTTTT
22408 ATGCGTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.07, C:0.01, G:0.20, T:0.72
Consensus pattern (32 bp):
TATTTTTGTTGTTATTTTGGTTGTTTGTATGT
Found at i:22385 original size:44 final size:43
Alignment explanation
Indices: 22252--22394 Score: 135
Period size: 44 Copynumber: 3.1 Consensus size: 43
22242 CTTTTTTTAC
* * *
22252 TGTTTTGGTTGTTGTTTTGGTGTCATTTTT-TTTACTATTTTGATGT
1 TGTTTTTGTTGTTGTTTTGCTGTTATTTTTGTTT--TATTTT--TGT
* *
22298 TGTTAATTTTGTTGTTATTTTTACTGTTATTTTTGTTTCTATTTTTGT
1 TG-T--TTTTGTTGTT-GTTTTGCTGTTATTTTTGTTT-TATTTTTGT
*
22346 TGTTTTTGTTGTTGTTTTGCTGTTATTTTTGTTGTTATTTTGGT
1 TGTTTTTGTTGTTGTTTTGCTGTTATTTTTGTT-TTATTTTTGT
22390 TGTTT
1 TGTTT
22395 GTATGTTATT
Statistics
Matches: 83, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
44 31 0.37
45 11 0.13
46 2 0.02
47 2 0.02
48 5 0.06
49 9 0.11
50 20 0.24
51 3 0.04
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.69
Consensus pattern (43 bp):
TGTTTTTGTTGTTGTTTTGCTGTTATTTTTGTTTTATTTTTGT
Found at i:22401 original size:23 final size:21
Alignment explanation
Indices: 22304--22406 Score: 77
Period size: 23 Copynumber: 4.7 Consensus size: 21
22294 ATGTTGTTAA
* *
22304 TTTTGTTGTTATTTTTACTGTTAT
1 TTTTGTTGTTA-TTTT--GGTTGT
*
22328 TTTTGTT-TCTATTTTTGTTGT
1 TTTTGTTGT-TATTTTGGTTGT
* *
22349 TTTTGTTGTTGTTTTGCTGTTAT
1 TTTTGTTGTTATTTTG--GTTGT
22372 TTTTGTTGTTATTTTGGTTG-
1 TTTTGTTGTTATTTTGGTTGT
22392 -TTTGTATGTTATTTT
1 TTTTGT-TGTTATTTT
22407 TATGCGTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
19 5 0.07
20 9 0.13
21 20 0.29
22 1 0.01
23 24 0.35
24 9 0.13
ACGTcount: A:0.08, C:0.03, G:0.17, T:0.72
Consensus pattern (21 bp):
TTTTGTTGTTATTTTGGTTGT
Found at i:22555 original size:26 final size:27
Alignment explanation
Indices: 22524--22604 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 27
22514 TAATATAAAT
22524 ATTTTTTAATGTTTTTTAAATTTGTTT-
1 ATTTTTTAAT-TTTTTTAAATTTGTTTG
* * *
22551 ATTTTTTAATATTTTTAAGTTTATTTG
1 ATTTTTTAATTTTTTTAAATTTGTTTG
* *
22578 ATATATTATATATTTTTTAAATTTGTT
1 ATTTTTTA-AT-TTTTTTAAATTTGTT
22605 GTATATAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 13 0.30
27 16 0.37
28 2 0.05
29 12 0.28
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (27 bp):
ATTTTTTAATTTTTTTAAATTTGTTTG
Found at i:22563 original size:10 final size:10
Alignment explanation
Indices: 22521--22566 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
22511 TTTTAATATA
22521 AATATTTTTT
1 AATATTTTTT
*
22531 AATGTTTTTT
1 AATATTTTTT
*
22541 AA-ATTTGTT
1 AATATTTTTT
22550 --TATTTTTT
1 AATATTTTTT
22558 AATATTTTT
1 AATATTTTT
22567 AAGTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
8 6 0.21
9 5 0.17
10 18 0.62
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (10 bp):
AATATTTTTT
Found at i:22610 original size:29 final size:27
Alignment explanation
Indices: 22529--22611 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 27
22519 TAAATATTTT
* * *
22529 TTAATGTTTTTTAAATTTGTTTATTTT
1 TTAATATTTTTTAAATTTGTTTATATA
* *
22556 TTAATA-TTTTTAAGTTTATTTGATATA
1 TTAATATTTTTTAAATTTGTTT-ATATA
22583 TTATATATTTTTTAAATTTGTTGTATATA
1 TTA-ATATTTTTTAAATTTGTT-TATATA
22612 ATAAAATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
26 13 0.29
27 11 0.24
28 3 0.07
29 17 0.38
30 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (27 bp):
TTAATATTTTTTAAATTTGTTTATATA
Found at i:24486 original size:26 final size:26
Alignment explanation
Indices: 24447--24499 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
24437 TTTTGGGAAG
*
24447 AACTCAGATAACTTCACCCAACTCCA
1 AACTCAAATAACTTCACCCAACTCCA
* *
24473 AACTCAAATGACTTTACCCAACTCCA
1 AACTCAAATAACTTCACCCAACTCCA
24499 A
1 A
24500 TCTCCTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.36, G:0.04, T:0.21
Consensus pattern (26 bp):
AACTCAAATAACTTCACCCAACTCCA
Found at i:27175 original size:57 final size:57
Alignment explanation
Indices: 27101--27215 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
27091 GAACGAACTG
27101 CACATTATTAACATCCACAACCACATCAACAGTGTCCTTCCATAGCACCCAAATTCC
1 CACATTATTAACATCCACAACCACATCAACAGTGTCCTTCCATAGCACCCAAATTCC
* * *
27158 CACATTATTAACGTCCACAACGACATCAACAGTGTCCTTCCATAGCACCCGAATTCC
1 CACATTATTAACATCCACAACCACATCAACAGTGTCCTTCCATAGCACCCAAATTCC
27215 C
1 C
27216 CCAGTGAACC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.33, C:0.37, G:0.08, T:0.23
Consensus pattern (57 bp):
CACATTATTAACATCCACAACCACATCAACAGTGTCCTTCCATAGCACCCAAATTCC
Done.