Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005844.1 Kokia drynarioides strain JFW-HI SEQ_120142, 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: 38295
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Found at i:7926 original size:8 final size:8
Alignment explanation
Indices: 7913--7972 Score: 66
Period size: 8 Copynumber: 7.4 Consensus size: 8
7903 TGATTGCGTA
7913 TGTATGTG
1 TGTATGTG
7921 TGTATGTG
1 TGTATGTG
*
7929 TGTATGTA
1 TGTATGTG
* *
7937 TGTGTGTA
1 TGTATGTG
*
7945 TGTGTGTG
1 TGTATGTG
*
7953 TGTATATG
1 TGTATGTG
7961 TGTTATGTG
1 TG-TATGTG
7970 TGT
1 TGT
7973 GAGAGGAGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
8 38 0.84
9 7 0.16
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (8 bp):
TGTATGTG
Found at i:7927 original size:12 final size:12
Alignment explanation
Indices: 7910--7973 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 12
7900 ATATGATTGC
* *
7910 GTATGTATGTGT
1 GTATGTGTGTAT
7922 GTATGTGTGTAT
1 GTATGTGTGTAT
7934 GTATGTGTGTAT
1 GTATGTGTGTAT
*
7946 GTGTGTGTGTA-
1 GTATGTGTGTAT
7957 -TATGTGT-TAT
1 GTATGTGTGTAT
*
7967 GTGTGTG
1 GTATGTG
7974 AGAGGAGGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
9 2 0.04
10 6 0.13
11 5 0.11
12 32 0.71
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (12 bp):
GTATGTGTGTAT
Found at i:7935 original size:20 final size:20
Alignment explanation
Indices: 7910--7972 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
7900 ATATGATTGC
7910 GTATGTATGTGTGTATGTGT
1 GTATGTATGTGTGTATGTGT
7930 GTATGTATGTGTGTATGTGT
1 GTATGTATGTGTGTATGTGT
* *
7950 GTGTGTATATGTGTTATGTGT
1 GTATGTATGTGTG-TATGTGT
7971 GT
1 GT
7973 GAGAGGAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 31 0.77
21 9 0.22
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (20 bp):
GTATGTATGTGTGTATGTGT
Found at i:11503 original size:26 final size:25
Alignment explanation
Indices: 11473--11533 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 25
11463 TTTAATTTTT
11473 TTTTTTTTTAATTTTTAAAGGTTTCAA
1 TTTTTTTTTAATTTTTAAAGG--TCAA
*
11500 TTTTTTTTTAAATTTTTATAGGTCAA
1 TTTTTTTTT-AATTTTTAAAGGTCAA
11526 TTTTTTTT
1 TTTTTTTT
11534 ACCAATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 12 0.38
27 9 0.28
28 11 0.34
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (25 bp):
TTTTTTTTTAATTTTTAAAGGTCAA
Found at i:11544 original size:27 final size:27
Alignment explanation
Indices: 11472--11533 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 27
11462 GTTTAATTTT
*
11472 TTTTTTTTTTAATTTTTAAAGGTTTCAA
1 TTTTTTTTTAAATTTTTAAAGG-TTCAA
*
11500 TTTTTTTTTAAATTTTTATAGG-TCAA
1 TTTTTTTTTAAATTTTTAAAGGTTCAA
11526 TTTTTTTT
1 TTTTTTTT
11534 ACCAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 12 0.38
28 20 0.62
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (27 bp):
TTTTTTTTTAAATTTTTAAAGGTTCAA
Found at i:21551 original size:16 final size:17
Alignment explanation
Indices: 21501--21549 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
21491 CTTCGGTTCA
*
21501 GATCAATTTCATGTTTGG
1 GATCAATTTTATGTTT-G
**
21519 GATC-ATTTTGGGTTTG
1 GATCAATTTTATGTTTG
21535 GATCAATTTTATGTT
1 GATCAATTTTATGTT
21550 GGGGTTGTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 5 0.20
17 16 0.64
18 4 0.16
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.49
Consensus pattern (17 bp):
GATCAATTTTATGTTTG
Found at i:21649 original size:22 final size:23
Alignment explanation
Indices: 21624--21666 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
21614 GAGTCGGATT
* *
21624 ATTTTCT-GTTTGGGTTGTTTCA
1 ATTTTCTAATTTGAGTTGTTTCA
21646 ATTTTCTAATTTGAGTTGTTT
1 ATTTTCTAATTTGAGTTGTTT
21667 TAGGTTCAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.14, C:0.07, G:0.19, T:0.60
Consensus pattern (23 bp):
ATTTTCTAATTTGAGTTGTTTCA
Found at i:21886 original size:53 final size:53
Alignment explanation
Indices: 21801--21906 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
21791 ATGTGCCTTC
21801 CCATGTCATTCTTACTCATAGAACCTCATCTTTGCCGGTGTTTTTGGTCCATA
1 CCATGTCATTCTTACTCATAGAACCTCATCTTTGCCGGTGTTTTTGGTCCATA
* *
21854 CCATGTCATTCTTACTCATAGAACCTCTTCTTTTCCGGTGTTTTTGGTCCATA
1 CCATGTCATTCTTACTCATAGAACCTCATCTTTGCCGGTGTTTTTGGTCCATA
21907 TCTTGGGGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (53 bp):
CCATGTCATTCTTACTCATAGAACCTCATCTTTGCCGGTGTTTTTGGTCCATA
Found at i:23196 original size:6 final size:6
Alignment explanation
Indices: 23185--23225 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
23175 ACATTGATTC
*
23185 TTTTTG TTTTTG TTTTTG TTTTT- TTGTTTT TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TT-TTTG TTTTTG TTTTT
23226 TGTCTAGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 2 0.06
6 28 0.88
7 2 0.06
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:23210 original size:14 final size:13
Alignment explanation
Indices: 23185--23219 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
23175 ACATTGATTC
*
23185 TTTTTGTTTTTGT
1 TTTTTTTTTTTGT
23198 TTTTGTTTTTTTGT
1 TTTT-TTTTTTTGT
23212 TTTTTTTT
1 TTTTTTTT
23220 GTTTTTTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTGT
Found at i:23218 original size:18 final size:20
Alignment explanation
Indices: 23185--23226 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
23175 ACATTGATTC
23185 TTTTTGTTTTTGTTTTTGTT
1 TTTTTGTTTTTGTTTTTGTT
23205 TTTTTG-TTTT-TTTTTGTT
1 TTTTTGTTTTTGTTTTTGTT
23223 TTTT
1 TTTT
23227 GTCTAGTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 12 0.55
19 4 0.18
20 6 0.27
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (20 bp):
TTTTTGTTTTTGTTTTTGTT
Found at i:28424 original size:68 final size:70
Alignment explanation
Indices: 28320--28451 Score: 178
Period size: 68 Copynumber: 1.9 Consensus size: 70
28310 GCTTGCTAAG
* * * *
28320 AAGGTAGCAGCAACTCAACTCTATGAGACTCCCAAACAAGC-T-ATAAGCTGAAGGAGGAGTTCC
1 AAGGCAGCAGCAACTCAACCCTATAAAACTCCCAAACAAGCTTGATAAGCTGAAGGAGGAGTTCC
28383 AAGGT
66 AAGGT
* * *
28388 AAGGCAGCAGCAACTCACCCCTGTAAAACTCTCAAACAAGCTTGGATAAGCTGAAGGAGGAGTT
1 AAGGCAGCAGCAACTCAACCCTATAAAACTCCCAAACAAGCTT-GATAAGCTGAAGGAGGAGTT
28452 GATGAAACAT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
68 34 0.63
69 1 0.02
71 19 0.35
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (70 bp):
AAGGCAGCAGCAACTCAACCCTATAAAACTCCCAAACAAGCTTGATAAGCTGAAGGAGGAGTTCC
AAGGT
Found at i:32075 original size:15 final size:16
Alignment explanation
Indices: 32049--32085 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
32039 TTGAATCAAT
32049 TTTTTATCTTTTAAT-A
1 TTTTTATCTTTT-ATGA
32065 TTTTTAT-TTTTATGA
1 TTTTTATCTTTTATGA
32080 TTTTTA
1 TTTTTA
32086 ATGATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 11 0.55
16 7 0.35
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTTATCTTTTATGA
Found at i:32478 original size:17 final size:17
Alignment explanation
Indices: 32453--32486 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32443 ATTGAACAAA
32453 TTTTATTTAATTTTAAT
1 TTTTATTTAATTTTAAT
* *
32470 TTTTTTTTATTTTTAAT
1 TTTTATTTAATTTTAAT
32487 AATTTATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTAATTTTAAT
Done.