Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003116.1 Kokia drynarioides strain JFW-HI SEQ_115689, 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: 12584
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Found at i:204 original size:12 final size:12
Alignment explanation
Indices: 187--220 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
177 ATAAAAGAAT
187 AAAGAAAGAAAA
1 AAAGAAAGAAAA
*
199 AAAGAAACAAAA
1 AAAGAAAGAAAA
*
211 GAAGAAAGAA
1 AAAGAAAGAA
221 CAGAGGCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:664 original size:17 final size:18
Alignment explanation
Indices: 642--677 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
632 TAAATGAGTT
642 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
659 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
677 A
1 A
678 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:3182 original size:17 final size:18
Alignment explanation
Indices: 3138--3192 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
3128 AACTTCACTC
*
3138 AAATATTTATATATTCTA
1 AAATATTTATATATTATA
3156 AATATATTTATA-ATTATA
1 AA-ATATTTATATATTATA
*
3174 AAATTTTTA-ATA-TATA
1 AAATATTTATATATTATA
3190 AAA
1 AAA
3193 GCAACCCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 8 0.24
17 7 0.21
18 9 0.27
19 9 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATATTTATATATTATA
Found at i:7440 original size:29 final size:30
Alignment explanation
Indices: 7408--7469 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
7398 ATTAACCTTA
* *
7408 TTTCATTCAAAAAA-ATTTCAGCAGCTCTC
1 TTTCAATCAAAAAATATTTCAGCAACTCTC
*
7437 TTTCAATCAAAAAATTTTTCAGCAACTCTC
1 TTTCAATCAAAAAATATTTCAGCAACTCTC
7467 TTT
1 TTT
7470 GCTTAACTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.39
Consensus pattern (30 bp):
TTTCAATCAAAAAATATTTCAGCAACTCTC
Found at i:11175 original size:30 final size:30
Alignment explanation
Indices: 11141--11256 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 30
11131 CTTAGACATC
11141 CGAGGGTAAAATGGTAATTTTGAAAAGATT
1 CGAGGGTAAAATGGTAATTTTGAAAAGATT
* ** * * * * *
11171 CGAGGTTAAAAACGAAATTTT-TAGACATC
1 CGAGGGTAAAATGGTAATTTTGAAAAGATT
*
11200 CGAGGGTAAAATGGTAATTTTTGGAAAG-TT
1 CGAGGGTAAAATGGTAA-TTTTGAAAAGATT
*
11230 TGAGGGTAAAAAT-GTAATTTTAGAAAA
1 CGAGGGT-AAAATGGTAATTTT-GAAAA
11257 TTTAGGTCAA
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
29 21 0.33
30 36 0.56
31 7 0.11
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (30 bp):
CGAGGGTAAAATGGTAATTTTGAAAAGATT
Found at i:11177 original size:59 final size:57
Alignment explanation
Indices: 11027--11253 Score: 274
Period size: 59 Copynumber: 3.9 Consensus size: 57
11017 GGATGCTCGG
* **
11027 GGGTAAAAATGGTAATTTTGGAAAGTTCGAAGTTAAAAACGAAATTTTAGATGTCCGA
1 GGGT-AAAATGGTAATTTTGGAAAGTTCGAGGTTAAAAACGAAATTTTAGACATCCGA
* * * * * *
11085 GGGTATAATGATGATTTTTGGAAAGTTCAAGGTTAAAAACGGAGTTCTTAGACATCCGA
1 GGGTAAAATGGT-AATTTTGGAAAGTTCGAGGTTAAAAACGAAATT-TTAGACATCCGA
*
11144 GGGTAAAATGGTAATTTTGAAAAGATTCGAGGTTAAAAACGAAATTTTTAGACATCCGA
1 GGGTAAAATGGTAATTTTGGAAAG-TTCGAGGTTAAAAACGAAA-TTTTAGACATCCGA
* * * *
11203 GGGTAAAATGGTAATTTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTAGA
1 GGGTAAAATGGTAA-TTTTGGAAAGTTCGAGGTTAAAAACGAAATTTTAGA
11254 AAATTTAGGT
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
57 6 0.04
58 49 0.34
59 77 0.54
60 11 0.08
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.31
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTGGAAAGTTCGAGGTTAAAAACGAAATTTTAGACATCCGA
Found at i:11218 original size:29 final size:29
Alignment explanation
Indices: 11132--11221 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
11122 AACGGAGTTC
11132 TTAGACATCCGAGGGTAAAATGGTAATTT
1 TTAGACATCCGAGGGTAAAATGGTAATTT
* * * * * ** *
11161 TGAAAAGATTCGAGGTTAAAAACGAAATTT
1 T-TAGACATCCGAGGGTAAAATGGTAATTT
11191 TTAGACATCCGAGGGTAAAATGGTAATTT
1 TTAGACATCCGAGGGTAAAATGGTAATTT
11220 TT
1 TT
11222 GGAAAGTTTG
Statistics
Matches: 44, Mismatches: 16, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (29 bp):
TTAGACATCCGAGGGTAAAATGGTAATTT
Found at i:11240 original size:118 final size:117
Alignment explanation
Indices: 11027--11241 Score: 315
Period size: 118 Copynumber: 1.8 Consensus size: 117
11017 GGATGCTCGG
* ** *
11027 GGGTAAAAATGGTAATTTTGGAAAGTTCGAAGTTAAAAACGAAATTTTAGATGTCCGAGGGTATA
1 GGGTAAAAATGGTAATTTTGAAAAGTTCGAAGTTAAAAACGAAATTTTAGACATCCGAGGGTAAA
* *
11092 ATGATGATTTTTGGAAAGTTCAAGGTTAAAAACGGAGTTCTTAGACATCCGA
66 ATGATAATTTTTGGAAAGTTCAAGGGTAAAAACGGAGTTCTTAGACATCCGA
*
11144 GGGT-AAAATGGTAATTTTGAAAAGATTCGAGGTTAAAAACGAAATTTTTAGACATCCGAGGGTA
1 GGGTAAAAATGGTAATTTTGAAAAG-TTCGAAGTTAAAAACGAAA-TTTTAGACATCCGAGGGTA
* **
11208 AAATGGTAATTTTTGGAAAGTTTGAGGGTAAAAA
64 AAATGATAATTTTTGGAAAGTTCAAGGGTAAAAA
11242 TGTAATTTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
116 19 0.22
117 22 0.26
118 45 0.52
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (117 bp):
GGGTAAAAATGGTAATTTTGAAAAGTTCGAAGTTAAAAACGAAATTTTAGACATCCGAGGGTAAA
ATGATAATTTTTGGAAAGTTCAAGGGTAAAAACGGAGTTCTTAGACATCCGA
Found at i:11276 original size:28 final size:29
Alignment explanation
Indices: 11237--11341 Score: 108
Period size: 28 Copynumber: 3.7 Consensus size: 29
11227 GTTTGAGGGT
11237 AAAAATGTAATTTTAGAAAATTT-AGGTC
1 AAAAATGTAATTTTAGAAAATTTAAGGTC
* * * *
11265 AACAATGGAATTTTGGAAAGTTTAAGGGT-
1 AAAAATGTAATTTTAGAAAATTTAA-GGTC
* *
11294 AAAAATGTAATTTTTTG-AAATTTGAGGTC
1 AAAAATGTAA-TTTTAGAAAATTTAAGGTC
*
11323 AAAAATGAAATTTTAGAAA
1 AAAAATGTAATTTTAGAAA
11342 GTTCGGGAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 27 0.44
29 26 0.43
30 8 0.13
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (29 bp):
AAAAATGTAATTTTAGAAAATTTAAGGTC
Found at i:11293 original size:57 final size:58
Alignment explanation
Indices: 11207--11344 Score: 190
Period size: 57 Copynumber: 2.4 Consensus size: 58
11197 ATCCGAGGGT
*
11207 AAAATGGTAATTTTTGGAAAGTTTGAGGGTAAAAATGTAA-TTTTAGAAAATTT-AGGTCA
1 AAAATGG-AA-TTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTAG-AAATTTGAGGTCA
* *
11266 ACAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTTGAAATTTGAGGTCA
1 AAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTAGAAATTTGAGGTCA
* *
11324 AAAATGAAATTTTAGAAAGTT
1 AAAATGGAATTTTGGAAAGTT
11345 CGGGAGTCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
57 34 0.48
58 31 0.44
59 6 0.08
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (58 bp):
AAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTAGAAATTTGAGGTCA
Found at i:11306 original size:29 final size:29
Alignment explanation
Indices: 11201--11344 Score: 136
Period size: 29 Copynumber: 5.0 Consensus size: 29
11191 TTAGACATCC
*
11201 GAGGGT-AAAATGGTAATTTTTGGAAAGTTT
1 GAGGGTAAAAAT-GTAA-TTTTAGAAAGTTT
*
11231 GAGGGTAAAAATGTAATTTTAGAAAATTT
1 GAGGGTAAAAATGTAATTTTAGAAAGTTT
* * *
11260 -A-GGTCAACAATGGAATTTTGGAAAGTTT
1 GAGGGT-AAAAATGTAATTTTAGAAAGTTT
* *
11288 AAGGGTAAAAATGTAATTTTTTGAAA-TTT
1 GAGGGTAAAAATGTAA-TTTTAGAAAGTTT
*
11317 GA-GGTCAAAAATGAAATTTTAGAAAGTT
1 GAGGGT-AAAAATGTAATTTTAGAAAGTT
11345 CGGGAGTCAA
Statistics
Matches: 95, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
27 3 0.03
28 31 0.33
29 35 0.37
30 21 0.22
31 5 0.05
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (29 bp):
GAGGGTAAAAATGTAATTTTAGAAAGTTT
Found at i:12428 original size:13 final size:13
Alignment explanation
Indices: 12410--12434 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12400 ATTATTAATA
12410 TTATTAATATTTT
1 TTATTAATATTTT
12423 TTATTAATATTT
1 TTATTAATATTT
12435 ATTAATGCTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTAATATTTT
Found at i:12429 original size:22 final size:24
Alignment explanation
Indices: 12396--12440 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
12386 TTTCGTATTT
12396 TTTTATTATTAATA-TTATTAATA
1 TTTTATTATTAATATTTATTAATA
12419 TTTT-TTATTAATATTTATTAAT
1 TTTTATTATTAATATTTATTAAT
12441 GCTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATTATTAATATTTATTAATA
Found at i:12448 original size:23 final size:22
Alignment explanation
Indices: 12401--12451 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
12391 TATTTTTTTA
* *
12401 TTATTAATATTATTAATATTTT
1 TTATTAATATTATTAATACTAT
*
12423 TTATTAATATTTATTAATGCTAT
1 TTATTAATA-TTATTAATACTAT
12446 TTATTA
1 TTATTA
12452 CTTCTATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTATTAATATTATTAATACTAT
Found at i:12503 original size:15 final size:15
Alignment explanation
Indices: 12456--12505 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12446 TTATTACTTC
* *
12456 TATTCATTATTAACAT
1 TATT-ATTAATAAAAT
**
12472 TATTATTAATATTAT
1 TATTATTAATAAAAT
12487 TATTATTAATAAAAT
1 TATTATTAATAAAAT
12502 TATT
1 TATT
12506 TAATATACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 25 0.86
16 4 0.14
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTATTAATAAAAT
Done.