Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013769.1 Kokia drynarioides strain JFW-HI SEQ_128797, 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: 50968
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 149 characters in sequence are not A, C, G, or T
Found at i:106 original size:19 final size:19
Alignment explanation
Indices: 78--118 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
68 AATAAAATAA
78 TTTCTAAATT-ATATTAAT
1 TTTCTAAATTGATATTAAT
*
96 TTTCTTAAATTGATATTTAT
1 TTTC-TAAATTGATATTAAT
116 TTT
1 TTT
119 TTTTAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
20 10 0.50
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTCTAAATTGATATTAAT
Found at i:16332 original size:21 final size:22
Alignment explanation
Indices: 16286--16337 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
16276 GACATATATA
*
16286 AAAT-ATTTTTAAATTTTTTTT
1 AAATAATTTCTAAATTTTTTTT
16307 AAATAATTTCTAAA-TTTTTTT
1 AAATAATTTCTAAATTTTTTTT
*
16328 GAATAATTTC
1 AAATAATTTC
16338 ATTATAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
AAATAATTTCTAAATTTTTTTT
Found at i:16498 original size:22 final size:23
Alignment explanation
Indices: 16439--16500 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
16429 GGAAGACCAA
* *
16439 AATTAAATCATAATTTTTAAAAT
1 AATTAAATCAAAATTTTTAAAAG
*
16462 AATTAAAAT-ACAATTTTT-AAAG
1 AATT-AAATCAAAATTTTTAAAAG
*
16484 AGTTAAATCAAAATTTT
1 AATTAAATCAAAATTTT
16501 ATCATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
23 12 0.36
24 4 0.12
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (23 bp):
AATTAAATCAAAATTTTTAAAAG
Found at i:21303 original size:26 final size:26
Alignment explanation
Indices: 21249--21303 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
21239 AAATTTAGTC
* *
21249 TTTAATATTTATATTTTTTTATTATT
1 TTTAATATTTATATTTTTTAATTAAT
21275 TTTAAT-TTT-TATTTTTTAAGTTAAAT
1 TTTAATATTTATATTTTTTAA-TT-AAT
21301 TTT
1 TTT
21304 GGCTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 9 0.36
25 5 0.20
26 11 0.44
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTAATATTTATATTTTTTAATTAAT
Found at i:24960 original size:12 final size:13
Alignment explanation
Indices: 24934--24962 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
24924 TTTTTTTTAG
24934 AAATATTTATGAA
1 AAATATTTATGAA
24947 AAATATTT-TGAA
1 AAATATTTATGAA
24959 AAAT
1 AAAT
24963 TGTCAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
AAATATTTATGAA
Found at i:36816 original size:4 final size:4
Alignment explanation
Indices: 36807--36832 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
36797 TAGGCTTGGA
36807 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
36833 CGAGGAGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:46728 original size:20 final size:19
Alignment explanation
Indices: 46672--46737 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
46662 CAAATAAAAG
*
46672 GGAAAAAAAAAAAGAA-AA
1 GGAAAGAAAAAAAGAAGAA
*
46690 -GAAAGAAAGAAAGGAAGAA
1 GGAAAGAAA-AAAAGAAGAA
*
46709 GGAGATGAAAAAAAGAAGAA
1 GGA-AAGAAAAAAAGAAGAA
46729 GGAAAGAAA
1 GGAAAGAAA
46738 TGTAATGTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 7 0.18
18 6 0.15
19 7 0.18
20 14 0.36
21 5 0.13
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (19 bp):
GGAAAGAAAAAAAGAAGAA
Found at i:46823 original size:19 final size:19
Alignment explanation
Indices: 46778--46823 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
46768 ATATGATATC
*
46778 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
**
46797 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCGTATTTAA
46817 TTTTTAA
1 TTTTTAA
46824 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Found at i:49916 original size:28 final size:28
Alignment explanation
Indices: 49877--49947 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
49867 CCCTCTTTAA
49877 TCAA-TCTAGTGTTTACGATTTAGAGTT
1 TCAAGTCTAGTGTTTACGATTTAGAGTT
*
49904 TCAAGTCTAGTGTTTACGGTTTAGAGTT
1 TCAAGTCTAGTGTTTACGATTTAGAGTT
* *
49932 TCAAGTTTAGGGTTTA
1 TCAAGTCTAGTGTTTA
49948 TAATTTAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 4 0.10
28 36 0.90
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.44
Consensus pattern (28 bp):
TCAAGTCTAGTGTTTACGATTTAGAGTT
Found at i:49939 original size:14 final size:14
Alignment explanation
Indices: 49895--49946 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
49885 GTGTTTACGA
49895 TTTAGAGTTTCAAG
1 TTTAGAGTTTCAAG
* * *
49909 TCTAGTGTTT-ACGG
1 TTTAGAGTTTCA-AG
49923 TTTAGAGTTTCAAG
1 TTTAGAGTTTCAAG
*
49937 TTTAGGGTTT
1 TTTAGAGTTT
49947 ATAATTTAGG
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.46
Consensus pattern (14 bp):
TTTAGAGTTTCAAG
Found at i:49954 original size:28 final size:28
Alignment explanation
Indices: 49877--49959 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 28
49867 CCCTCTTTAA
* *
49877 TCAA-TCTAGTGTTTACGATTTAGAGTT
1 TCAAGTCTAGGGTTTACAATTTAGAGTT
* **
49904 TCAAGTCTAGTGTTTACGGTTTAGAGTT
1 TCAAGTCTAGGGTTTACAATTTAGAGTT
* *
49932 TCAAGTTTAGGGTTTATAATTTAG-GTT
1 TCAAGTCTAGGGTTTACAATTTAGAGTT
49959 T
1 T
49960 TAGGGTTTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.16
28 41 0.84
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (28 bp):
TCAAGTCTAGGGTTTACAATTTAGAGTT
Found at i:50289 original size:45 final size:45
Alignment explanation
Indices: 50225--50361 Score: 177
Period size: 45 Copynumber: 3.0 Consensus size: 45
50215 GGGAGGAATA
* * * **
50225 GAGTATCGTGGTGGCTCGTCAAACTCAGCTTGATATCCTTCTCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGCTTGATATCCTTAGCTT
* *
50270 GAGTATTGCGGTGGCTCGTCAAATTGAGGTTGATATCCTTAGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGCTTGATATCCTTAGCTT
* *
50315 GAGTATTACGGTGGCTCGTCAAACTGAGGC-TGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGA-GCTTGATATCCTTAGCTT
50360 GA
1 GA
50362 TGAGCTATGC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 79 0.99
46 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTGAGCTTGATATCCTTAGCTT
Done.