Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008162.1 Kokia drynarioides strain JFW-HI SEQ_122821, 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: 55069
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2173 original size:22 final size:23
Alignment explanation
Indices: 2147--2189 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2137 CATGAATCTT
2147 TAAATTTAAAAAATA-GAAAAAC
1 TAAATTTAAAAAATATGAAAAAC
* *
2169 TAAATTTTAAATATATGAAAA
1 TAAATTTAAAAAATATGAAAA
2190 TTACATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
TAAATTTAAAAAATATGAAAAAC
Found at i:4092 original size:31 final size:31
Alignment explanation
Indices: 4048--4116 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
4038 AAAAGCATAC
4048 TAAACT-TTTTTTTAGAAGTATTATAAATTA
1 TAAACTATTTTTTTAGAAGTATTATAAATTA
4078 TAAACTATTTTTTTAGAAGTATTATAAATTA
1 TAAACTATTTTTTTAGAAGTATTATAAATTA
4109 TAAACTAT
1 TAAACTAT
4117 AAGTAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (31 bp):
TAAACTATTTTTTTAGAAGTATTATAAATTA
Found at i:20730 original size:18 final size:17
Alignment explanation
Indices: 20709--20742 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20699 TGGTAAATGT
20709 TTGTAATAAGATTTTATA
1 TTGT-ATAAGATTTTATA
*
20727 TTGTATACGATTTTAT
1 TTGTATAAGATTTTAT
20743 TTTTTTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (17 bp):
TTGTATAAGATTTTATA
Found at i:31597 original size:31 final size:31
Alignment explanation
Indices: 31562--31651 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 31
31552 TCGTTTGAAT
*
31562 AATCAATATTTTTATAAATTTTAAAAGATT-A
1 AATCAATATTTTTAT-AATTTTAAAAAATTAA
* *
31593 AATCAA-AATTTTATTATTTTAAAAAAATTAA
1 AATCAATATTTTTATAATTTT-AAAAAATTAA
31624 AATACAATTTATTTTTATTAA-TTTAAAA
1 AAT-CAA--TATTTTTA-TAATTTTAAAA
31652 TTTTAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
29 5 0.11
30 14 0.30
31 10 0.21
32 3 0.06
34 4 0.09
35 9 0.19
36 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (31 bp):
AATCAATATTTTTATAATTTTAAAAAATTAA
Found at i:36423 original size:90 final size:90
Alignment explanation
Indices: 36270--36542 Score: 483
Period size: 90 Copynumber: 3.0 Consensus size: 90
36260 TTTAGGGATA
** *
36270 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATGGATGTAAAGTCTACA
1 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
*
36335 TCATTCAGCAAGGAGAATAGCAGCC
66 TCATTCAGCAAGGGGAATAGCAGCC
36360 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
1 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
*
36425 TCATCCAGCAAGGGGAATAGCAGCC
66 TCATTCAGCAAGGGGAATAGCAGCC
* *
36450 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGAACTCAAAGGAGATAAATGTGAAGTCTACG
1 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
36515 TCATTCAGCAAGGGGAATAGCAGCC
66 TCATTCAGCAAGGGGAATAGCAGCC
36540 AAA
1 AAA
36543 GACCTGGAGA
Statistics
Matches: 175, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 175 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.16
Consensus pattern (90 bp):
AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
TCATTCAGCAAGGGGAATAGCAGCC
Found at i:42260 original size:21 final size:20
Alignment explanation
Indices: 42236--42289 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
42226 AATGGAGGTG
42236 AAAACAACAAATAAGTCGTTA
1 AAAACAACAAATAAGTC-TTA
* *
42257 AAAAC-ACTACATAAGTCTTG
1 AAAACAAC-AAATAAGTCTTA
*
42277 AAGACAACAAATA
1 AAAACAACAAATA
42290 TTTTGTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.56, C:0.17, G:0.09, T:0.19
Consensus pattern (20 bp):
AAAACAACAAATAAGTCTTA
Found at i:44421 original size:2 final size:2
Alignment explanation
Indices: 44414--44474 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
44404 TCAAACCAAC
* * * *
44414 AT AT AT AT AT AT AT AT AT AC AC AT AT AT AC AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
44456 AC AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
44475 CCAGAAAAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (2 bp):
AT
Found at i:44429 original size:10 final size:10
Alignment explanation
Indices: 44412--44475 Score: 83
Period size: 10 Copynumber: 6.2 Consensus size: 10
44402 TCTCAAACCA
44412 ACATATATAT
1 ACATATATAT
*
44422 ATATATATAT
1 ACATATATAT
*
44432 ACACATATAT
1 ACATATATAT
44442 ACATATATATAT
1 AC--ATATATAT
*
44454 ACACATATAT
1 ACATATATAT
44464 ACATATATAT
1 ACATATATAT
44474 AC
1 AC
44476 CAGAAAAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
10 37 0.80
12 9 0.20
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (10 bp):
ACATATATAT
Found at i:44440 original size:22 final size:22
Alignment explanation
Indices: 44412--44474 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
44402 TCTCAAACCA
*
44412 ACATATATATATATATATATAC
1 ACATATATACATATATATATAC
44434 ACATATATACATATATATATAC
1 ACATATATACATATATATATAC
44456 ACATATATACATATATATA
1 ACATATATACATATATATA
44475 CCAGAAAAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
ACATATATACATATATATATAC
Found at i:45721 original size:3 final size:3
Alignment explanation
Indices: 45713--45737 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45703 TTAATGCACT
45713 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
45738 GGATAGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.