Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011665.1 Kokia drynarioides strain JFW-HI SEQ_126657, 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: 38401
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3035 original size:10 final size:10
Alignment explanation
Indices: 3013--3047 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
3003 TAGTTTTCAG
3013 CACATATTAAT
1 CACATA-TAAT
3024 CACATATAAT
1 CACATATAAT
3034 CACATATAAT
1 CACATATAAT
3044 CACA
1 CACA
3048 CTCAGTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.29
Consensus pattern (10 bp):
CACATATAAT
Found at i:3513 original size:36 final size:36
Alignment explanation
Indices: 3485--3741 Score: 354
Period size: 36 Copynumber: 7.1 Consensus size: 36
3475 ATATTCACCA
3485 TCACATGG-AGTGAATAACATACCCACATATTTACTG
1 TCACATGGCA-TGAATAACATACCCACATATTTACTG
*
3521 TCTCATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* *
3557 TCACATGTCATGAATAACATACCCACATATTTACTA
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * * *
3593 TCTCATGACATGAATAACATACCCACACATTTATTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * *
3629 TAACATGGCATGAATAACATACCCACACATTTATTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * *
3665 TAACATGGCATGAATAACATACACACATATTTATTG
1 TCACATGGCATGAATAACATACCCACATATTTACTG
* * *
3701 TCTCATGGCATGAATAACATACTCACATATTTACTT
1 TCACATGGCATGAATAACATACCCACATATTTACTG
3737 TCACA
1 TCACA
3742 ACAGTTATCA
Statistics
Matches: 200, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
36 199 1.00
37 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (36 bp):
TCACATGGCATGAATAACATACCCACATATTTACTG
Found at i:9379 original size:42 final size:42
Alignment explanation
Indices: 9315--9505 Score: 226
Period size: 42 Copynumber: 4.5 Consensus size: 42
9305 ACTTGATATA
* *
9315 TAAATGGAAGACTCATGTCTTGGGATAAGCATGAGATTATGTT
1 TAAA-GGAAGACTCATGACTCGGGATAAGCATGAGATTATGTT
* *
9358 TAAAGGAAGACTCATGACTTGGGATGAGCATGAGATTATGTT
1 TAAAGGAAGACTCATGACTCGGGATAAGCATGAGATTATGTT
* * *
9400 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATGTT
1 TAAAGGAAGACTCATGACTCGGGATAAGCATGAGATTATGTT
* * *
9442 TAAAAGGAAGACTTATGACTCGGTA-AAGCATAAGATT-T-TT
1 T-AAAGGAAGACTCATGACTCGGGATAAGCATGAGATTATGTT
*
9482 TGAAAAGGAAGACTTATGACTCGG
1 T--AAAGGAAGACTCATGACTCGG
9506 TTGGAGCATA
Statistics
Matches: 135, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
40 3 0.02
41 23 0.17
42 86 0.64
43 23 0.17
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.28
Consensus pattern (42 bp):
TAAAGGAAGACTCATGACTCGGGATAAGCATGAGATTATGTT
Found at i:18199 original size:17 final size:17
Alignment explanation
Indices: 18173--18211 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18163 TTAGCATTCT
18173 TGCA-TTTTATTGTGC-C
1 TGCATTTTTATTGT-CAC
18189 TGCATTTTTATTGTCAC
1 TGCATTTTTATTGTCAC
18206 TGCATT
1 TGCATT
18212 CTTCTTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (17 bp):
TGCATTTTTATTGTCAC
Found at i:20340 original size:12 final size:12
Alignment explanation
Indices: 20323--20349 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20313 TTATTTTCAA
20323 TATCTTATTTAG
1 TATCTTATTTAG
20335 TATCTTATTTAG
1 TATCTTATTTAG
20347 TAT
1 TAT
20350 GCATCATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (12 bp):
TATCTTATTTAG
Found at i:22699 original size:39 final size:39
Alignment explanation
Indices: 22653--22751 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
22643 TTAAATAAGG
22653 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
*
22692 TTTTAATGTGTCTTATTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
* *
22731 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
22752 GACAAATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
Found at i:23167 original size:10 final size:10
Alignment explanation
Indices: 23152--23184 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
23142 TCTAGCCTAG
23152 TCCATTCAGC
1 TCCATTCAGC
*
23162 TCCATTCAAC
1 TCCATTCAGC
23172 TCCATTCAGC
1 TCCATTCAGC
23182 TCC
1 TCC
23185 TTACTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.42, G:0.06, T:0.30
Consensus pattern (10 bp):
TCCATTCAGC
Found at i:33398 original size:17 final size:17
Alignment explanation
Indices: 33378--33422 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
33368 AAATGCTAGA
33378 ACAAATAAAATGCAAAG
1 ACAAATAAAATGCAAAG
* *
33395 ACAATAAAAAATGCAATG
1 ACAA-ATAAAATGCAAAG
*
33413 ACAATTAAAA
1 ACAAATAAAA
33423 GAAATGCATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.16
Consensus pattern (17 bp):
ACAAATAAAATGCAAAG
Found at i:33407 original size:18 final size:19
Alignment explanation
Indices: 33384--33422 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
33374 TAGAACAAAT
33384 AAAATGCAAAGACAA-TAA
1 AAAATGCAAAGACAATTAA
*
33402 AAAATGCAATGACAATTAA
1 AAAATGCAAAGACAATTAA
33421 AA
1 AA
33423 GAAATGCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAATGCAAAGACAATTAA
Found at i:33815 original size:3 final size:3
Alignment explanation
Indices: 33807--33861 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
33797 CGGGGCAACA
* *
33807 TCT TCT TCT TTT TCT TCCT TC- TCT TCT TTT TCT TCT TCT T-T TCTT
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TC-T
33852 TCT TCT TCT T
1 TCT TCT TCT T
33862 ATGCCTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:33833 original size:18 final size:18
Alignment explanation
Indices: 33810--33859 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
33800 GGCAACATCT
33810 TCTTCTTTTTCTTCCTTC
1 TCTTCTTTTTCTTCCTTC
33828 TCTTCTTTTTCTT-CTTC
1 TCTTCTTTTTCTTCCTTC
*
33845 TTTTCTTTCTTCTTC
1 TCTTCTTT-TTCTTC
33860 TTATGCCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TCTTCTTTTTCTTCCTTC
Found at i:33860 original size:21 final size:23
Alignment explanation
Indices: 33807--33861 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
33797 CGGGGCAACA
*
33807 TCTTCTTCTTTTTCTTCCTTCTCT
1 TCTTCTTCTTCTTCTT-CTTCTCT
*
33831 TCTTTTTCTTCTTCTT-TTCT-T
1 TCTTCTTCTTCTTCTTCTTCTCT
33852 TCTTCTTCTT
1 TCTTCTTCTT
33862 ATGCCTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.36
22 4 0.14
24 14 0.50
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (23 bp):
TCTTCTTCTTCTTCTTCTTCTCT
Done.