Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005922.1 Kokia drynarioides strain JFW-HI SEQ_120292, 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: 30342
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1968 original size:22 final size:22
Alignment explanation
Indices: 1938--2019 Score: 128
Period size: 22 Copynumber: 3.7 Consensus size: 22
1928 AAAAACAAAA
1938 TGAACAGTGAGATTCTTTGACG
1 TGAACAGTGAGATTCTTTGACG
* * *
1960 TGAATAGTGAGATTCTCTAACG
1 TGAACAGTGAGATTCTTTGACG
*
1982 TGAACAGTAAGATTCTTTGACG
1 TGAACAGTGAGATTCTTTGACG
2004 TGAACAGTGAGATTCT
1 TGAACAGTGAGATTCT
2020 ATGGCAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.32
Consensus pattern (22 bp):
TGAACAGTGAGATTCTTTGACG
Found at i:2298 original size:14 final size:14
Alignment explanation
Indices: 2279--2333 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
2269 CAAAGTTTTT
*
2279 AGTTTTCAAATTTA
1 AGTTTTAAAATTTA
*
2293 AGTTTTAAAATTCA
1 AGTTTTAAAATTTA
*
2307 AATTTTAAAATTTA
1 AGTTTTAAAATTTA
*
2321 AGTTTTCAAATTT
1 AGTTTTAAAATTT
2334 TAATTACATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (14 bp):
AGTTTTAAAATTTA
Found at i:2338 original size:28 final size:28
Alignment explanation
Indices: 2275--2338 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
2265 TTACCAAAGT
* *
2275 TTTTAGTTTTCAAATTTAAGTTTTAAAA
1 TTTTAATTTTAAAATTTAAGTTTTAAAA
** *
2303 TTCAAATTTTAAAATTTAAGTTTTCAAA
1 TTTTAATTTTAAAATTTAAGTTTTAAAA
2331 TTTTAATT
1 TTTTAATT
2339 ACATTATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (28 bp):
TTTTAATTTTAAAATTTAAGTTTTAAAA
Found at i:4657 original size:35 final size:34
Alignment explanation
Indices: 4570--4661 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 34
4560 TATTCTGTTA
*
4570 TTTTTGTTCTTTATATATATAT-TTACAATACTT
1 TTTTTATTCTTTATATATATATATTACAATACTT
** * *
4603 AGTTTATT-TTTACTTTATATATATATT-CAGTATTT
1 TTTTTATTCTTTA---TATATATATATTACAATACTT
4638 TTTTTATTCTTTATATATATATAT
1 TTTTTATTCTTTATATATATATAT
4662 CTAATACGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
32 4 0.09
33 16 0.34
35 21 0.45
36 6 0.13
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (34 bp):
TTTTTATTCTTTATATATATATATTACAATACTT
Found at i:4673 original size:37 final size:36
Alignment explanation
Indices: 4567--4673 Score: 102
Period size: 37 Copynumber: 3.0 Consensus size: 36
4557 CAGTATTCTG
* *
4567 TTATTTTTGTTCTTTATATATATATTTACAATACTTAGT
1 TTATTTTTATTCTTTATATATATA-TT-CAATACGTA-T
4606 TTATTTTTA--CTTTATATATATATTC---A-GTAT
1 TTATTTTTATTCTTTATATATATATTCAATACGTAT
4636 TT-TTTTTATTCTTTATATATATATATCTAATACGTAT
1 TTATTTTTATTCTTTATATATATAT-TC-AATACGTAT
4673 T
1 T
4674 ATTCTATCTA
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
29 6 0.10
30 3 0.05
31 16 0.28
32 3 0.05
35 1 0.02
36 3 0.05
37 18 0.31
39 8 0.14
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (36 bp):
TTATTTTTATTCTTTATATATATATTCAATACGTAT
Found at i:18338 original size:27 final size:27
Alignment explanation
Indices: 18298--18358 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
18288 TGAGGAGTAA
18298 TCTGATTCTAGCTCGAAAGAGCGTTAT
1 TCTGATTCTAGCTCGAAAGAGCGTTAT
* *
18325 TTTGATTCTGGCTCGAAAGAGCGTTAT
1 TCTGATTCTAGCTCGAAAGAGCGTTAT
18352 TCTGATT
1 TCTGATT
18359 AGCGTTATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (27 bp):
TCTGATTCTAGCTCGAAAGAGCGTTAT
Found at i:18364 original size:15 final size:15
Alignment explanation
Indices: 18344--18373 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18334 GGCTCGAAAG
18344 AGCGTTATTCTGATT
1 AGCGTTATTCTGATT
18359 AGCGTTATTCTGATT
1 AGCGTTATTCTGATT
18374 CTGGCTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
AGCGTTATTCTGATT
Found at i:18376 original size:42 final size:42
Alignment explanation
Indices: 18317--18400 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
18307 AGCTCGAAAG
*
18317 AGCGTTATTTTGATTCTGGCTCGAAAGAGCGTTATTCTGATT
1 AGCGTTATTCTGATTCTGGCTCGAAAGAGCGTTATTCTGATT
* *
18359 AGCGTTATTCTGATTCTGGCTCGATAGAGCTTTATTCTGATT
1 AGCGTTATTCTGATTCTGGCTCGAAAGAGCGTTATTCTGATT
18401 CTGGGCTCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (42 bp):
AGCGTTATTCTGATTCTGGCTCGAAAGAGCGTTATTCTGATT
Found at i:18401 original size:27 final size:28
Alignment explanation
Indices: 18363--18417 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
18353 CTGATTAGCG
18363 TTATTCTGATTCT-GGCTCG-ATAGAGCT
1 TTATTCTGATTCTGGGCTCGTA-AGAGCT
18390 TTATTCTGATTCTGGGCTCGTAAGAGCT
1 TTATTCTGATTCTGGGCTCGTAAGAGCT
18418 AACTATTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 13 0.50
28 12 0.46
29 1 0.04
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (28 bp):
TTATTCTGATTCTGGGCTCGTAAGAGCT
Found at i:18431 original size:24 final size:24
Alignment explanation
Indices: 18398--18556 Score: 230
Period size: 24 Copynumber: 6.6 Consensus size: 24
18388 CTTTATTCTG
*
18398 ATTCTGGGCTCGTAAGAGCTAACT
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
18422 ATTCTAGGCTCGTAAGATG-TAACT
1 ATTCTGGGCTCGTAAGA-GCTAACC
* * *
18446 ATTCTAGGCTTGTAAGAGCTAACT
1 ATTCTGGGCTCGTAAGAGCTAACC
18470 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
18494 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
18518 ATTTTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
18542 ATTCTGTGCTCGTAA
1 ATTCTGGGCTCGTAA
18557 TGAGTTAAAA
Statistics
Matches: 125, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 1 0.01
24 123 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:18662 original size:23 final size:23
Alignment explanation
Indices: 18627--18672 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
18617 ATACATACTC
18627 GTTATCATCTTTTAACTGATTTG
1 GTTATCATCTTTTAACTGATTTG
* *
18650 GTTATTATGTTTTAACTGATTTG
1 GTTATCATCTTTTAACTGATTTG
18673 TCTATTTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.54
Consensus pattern (23 bp):
GTTATCATCTTTTAACTGATTTG
Found at i:20211 original size:14 final size:14
Alignment explanation
Indices: 20188--20225 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20178 CATTTTTGCA
20188 TTTCCTTTTATCT-
1 TTTCCTTTTATCTG
*
20201 TTTCACTTTTATTTG
1 TTTC-CTTTTATCTG
20216 TTTCCTTTTA
1 TTTCCTTTTA
20226 AGTTCTATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTCCTTTTATCTG
Found at i:20569 original size:20 final size:20
Alignment explanation
Indices: 20541--20583 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
20531 CTTTGTTGTT
20541 TTTACTCTTACTCTCT-CAAG
1 TTTACTCTT-CTCTCTACAAG
* *
20561 TTTATTCTTTTCTCTACAAG
1 TTTACTCTTCTCTCTACAAG
20581 TTT
1 TTT
20584 CTTTTAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.19, C:0.23, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTACTCTTCTCTCTACAAG
Done.