Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014035.1 Kokia drynarioides strain JFW-HI SEQ_129066, 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: 45931
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 132 characters in sequence are not A, C, G, or T
Found at i:1861 original size:25 final size:23
Alignment explanation
Indices: 1827--1874 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1817 GCTAGGGAAA
1827 CAGTAAGCACACACACAGTGCAATC
1 CAGTAAG--CACACACAGTGCAATC
*
1852 CAGTAGGCACACACAGTGCAATC
1 CAGTAAGCACACACAGTGCAATC
1875 AATAGGCGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.73
25 6 0.27
ACGTcount: A:0.38, C:0.31, G:0.19, T:0.12
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAATC
Found at i:1866 original size:23 final size:22
Alignment explanation
Indices: 1836--1908 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
1826 ACAGTAAGCA
1836 CACACACAGTGCAATCCAGTAGG
1 CACACACAGTGCAAT-CAGTAGG
*
1859 CACACACAGTGCAATCAATAGG
1 CACACACAGTGCAATCAGTAGG
* * * *
1881 CGCACATAGCGTAAATCAGTAGG
1 CACACACAGTG-CAATCAGTAGG
1904 CACAC
1 CACAC
1909 GAGGTGCGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 14 0.33
23 28 0.67
ACGTcount: A:0.37, C:0.29, G:0.21, T:0.14
Consensus pattern (22 bp):
CACACACAGTGCAATCAGTAGG
Found at i:3271 original size:14 final size:13
Alignment explanation
Indices: 3247--3276 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3237 TCAAATTCTC
3247 TAAAAATCTCACT
1 TAAAAATCTCACT
3260 TAAAATATCTCACT
1 TAAAA-ATCTCACT
3274 TAA
1 TAA
3277 TAGAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAAATCTCACT
Found at i:4347 original size:17 final size:18
Alignment explanation
Indices: 4320--4353 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
4310 AGTTATCATC
4320 ATATCAATTTTTTTTATA
1 ATATCAATTTTTTTTATA
4338 ATAT-AATTTTTTTTAT
1 ATATCAATTTTTTTTAT
4354 CAAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATCAATTTTTTTTATA
Found at i:5705 original size:3 final size:3
Alignment explanation
Indices: 5697--5734 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
5687 AAGAGTAGGG
* *
5697 ATA ATA ATA ATA ATA ATA GTA ATA GTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5735 GTGTTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7924 original size:17 final size:17
Alignment explanation
Indices: 7904--7938 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
7894 ATTTTTGTCA
7904 TTTATTGAATTT-TGAAT
1 TTTA-TGAATTTGTGAAT
7921 TTTATGAATTTGTGAAT
1 TTTATGAATTTGTGAAT
7938 T
1 T
7939 AAAATCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (17 bp):
TTTATGAATTTGTGAAT
Found at i:27830 original size:14 final size:15
Alignment explanation
Indices: 27801--27830 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27791 CAATTATTAA
27801 AATTTTATATTTCAT
1 AATTTTATATTTCAT
27816 AATTTTATA-TTCAT
1 AATTTTATATTTCAT
27830 A
1 A
27831 TATACACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTTATATTTCAT
Found at i:29197 original size:2 final size:2
Alignment explanation
Indices: 29190--29214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29180 GCTACTGTTT
29190 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
29215 TAGCATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44609 original size:30 final size:30
Alignment explanation
Indices: 44575--44662 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
44565 AAATGTAAAA
44575 AAATCATTAGAGTCTGAAATTTATATGGAT
1 AAATCATTAGAGTCTGAAATTTATATGGAT
* * *
44605 AAATCCTTA-A---TGAGAATGTA-A---AA
1 AAATCATTAGAGTCTGA-AATTTATATGGAT
44628 AAATCATTAGAGTCTGAAATTTATATGGAT
1 AAATCATTAGAGTCTGAAATTTATATGGAT
44658 AAATC
1 AAATC
44663 CTTAATGAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
23 9 0.21
24 1 0.02
26 9 0.21
27 9 0.21
29 1 0.02
30 14 0.33
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (30 bp):
AAATCATTAGAGTCTGAAATTTATATGGAT
Found at i:44625 original size:53 final size:53
Alignment explanation
Indices: 44566--44671 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
44556 ATCATAGAAA
44566 AATGTAAAAAAATCATTAGAGTCTGAAATTTATATGGATAAATCCTTAATGAG
1 AATGTAAAAAAATCATTAGAGTCTGAAATTTATATGGATAAATCCTTAATGAG
44619 AATGTAAAAAAATCATTAGAGTCTGAAATTTATATGGATAAATCCTTAATGAG
1 AATGTAAAAAAATCATTAGAGTCTGAAATTTATATGGATAAATCCTTAATGAG
44672 TCTATTTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (53 bp):
AATGTAAAAAAATCATTAGAGTCTGAAATTTATATGGATAAATCCTTAATGAG
Found at i:45071 original size:23 final size:23
Alignment explanation
Indices: 45041--45094 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
45031 ACGCTAGCGC
*
45041 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACCTCGTGT
*
45064 GCTTACTGTTTCGTACCTCGTGT
1 GCTTACTGTTTCGCACCTCGTGT
*
45087 GCCTACTG
1 GCTTACTG
45095 ATTTGTGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.09, C:0.28, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTTCGCACCTCGTGT
Found at i:45157 original size:26 final size:26
Alignment explanation
Indices: 45121--45193 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
45111 CCTACTGATT
*
45121 GCACTGTGTGTGCTTATTGTTTCCCTA
1 GCACT-TGTGTGCTTATTGTTTCCCCA
45148 GCACTTGTGTGCTTATTGTTTCCCCA
1 GCACTTGTGTGCTTATTGTTTCCCCA
*
45174 GCACTTGTGTGCTTACTGTT
1 GCACTTGTGTGCTTATTGTT
45194 AAGTACTTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 39 0.89
27 5 0.11
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (26 bp):
GCACTTGTGTGCTTATTGTTTCCCCA
Done.