Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015176.1 Kokia drynarioides strain JFW-HI SEQ_130220, 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: 26892
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3684 original size:27 final size:27
Alignment explanation
Indices: 3651--3703 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3641 TCAGCAAGTT
*
3651 TCAGCTTGCTTT-TTGTTTCGGATTTCC
1 TCAGCTTGCTTTGTTG-CTCGGATTTCC
*
3678 TCAGCTTTCTTTGTTGCTCGGATTTC
1 TCAGCTTGCTTTGTTGCTCGGATTTC
3704 AACTCCCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.51
Consensus pattern (27 bp):
TCAGCTTGCTTTGTTGCTCGGATTTCC
Found at i:5946 original size:6 final size:6
Alignment explanation
Indices: 5935--5964 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5925 CTTTTGTTTT
*
5935 AGTCAC AGTCAC AGTCAC AGTCAC ACTCAC
1 AGTCAC AGTCAC AGTCAC AGTCAC AGTCAC
5965 TTTGCAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.37, G:0.13, T:0.17
Consensus pattern (6 bp):
AGTCAC
Found at i:8732 original size:11 final size:11
Alignment explanation
Indices: 8706--8747 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
8696 TAAGATTTAT
* *
8706 ATTTTTTTATC
1 ATTTTTATATA
8717 ATTTTTA-ATA
1 ATTTTTATATA
8727 ATTTTTATATA
1 ATTTTTATATA
8738 ATTTTGTATA
1 ATTTT-TATA
8748 GAAGGAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 9 0.33
11 14 0.52
12 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (11 bp):
ATTTTTATATA
Found at i:9090 original size:29 final size:30
Alignment explanation
Indices: 9058--9116 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
9048 TATAGTTTAA
* *
9058 TGTGTAATTGTATATATG-AATTTTTATTT
1 TGTGTAATTGTATACATGAAATTTTGATTT
*
9087 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTGTATACATGAAATTTTGATTT
9117 GATCAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.56
Consensus pattern (30 bp):
TGTGTAATTGTATACATGAAATTTTGATTT
Found at i:9229 original size:25 final size:24
Alignment explanation
Indices: 9169--9229 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
9159 ATAATTTTAT
*
9169 ATTTATATATTGCAATAATAAATA
1 ATTTATATATTGCAATAAAAAATA
*
9193 ATTATATTTATT-CAATATAAAAATAA
1 ATT-TATATATTGCAATA-AAAAAT-A
*
9219 ATTTATGTATT
1 ATTTATATATT
9230 TTTTAAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 8 0.26
25 19 0.61
26 4 0.13
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (24 bp):
ATTTATATATTGCAATAAAAAATA
Found at i:9322 original size:30 final size:30
Alignment explanation
Indices: 9254--9325 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
9244 GATTAAATCA
* * *
9254 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAAATTTCAAGTACATAATTGAACC
* * *
9284 ATAATTAAAATTTCACGTGCATAATTGCACC
1 A-AATTAAAATTTCAAGTACATAATTGAACC
9315 AAATTAAAATT
1 AAATTAAAATT
9326 CATGTATACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (30 bp):
AAATTAAAATTTCAAGTACATAATTGAACC
Found at i:9339 original size:29 final size:30
Alignment explanation
Indices: 9306--9364 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
9296 TCACGTGCAT
*
9306 AATTGCAC-CAAATTAAAATTCATGTATAC
1 AATTGCACACAAATCAAAATTCATGTATAC
*
9335 AATTGCACATTAAATCAAAATTCATGTATA
1 AATTGCACA-CAAATCAAAATTCATGTATA
9365 ATTTTAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (30 bp):
AATTGCACACAAATCAAAATTCATGTATAC
Found at i:9922 original size:17 final size:18
Alignment explanation
Indices: 9897--9933 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
9887 TGAACTAATC
9897 TTTTCTATTTTA-AATTT
1 TTTTCTATTTTATAATTT
*
9914 TTTTTTATTTTATAATTT
1 TTTTCTATTTTATAATTT
9932 TT
1 TT
9934 AATAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCTATTTTATAATTT
Found at i:16210 original size:25 final size:25
Alignment explanation
Indices: 16158--16238 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 25
16148 ACACTAGCGC
* *
16158 GCTCTCTG--ATTAGTATTGTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGT
* *
16181 GCTCTTTG-T-TTAGCAC-GTCTTGT
1 GCTCTCTGTTATTAGCACTGT-GTGT
16204 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGT
16229 GCTCTCTGTT
1 GCTCTCTGTT
16239 GCCCAGCACT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 2 0.04
23 22 0.47
24 1 0.02
25 20 0.43
26 2 0.04
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (25 bp):
GCTCTCTGTTATTAGCACTGTGTGT
Found at i:18000 original size:24 final size:23
Alignment explanation
Indices: 17951--18000 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
17941 TAAAATAGGT
* *
17951 TATATATTATTTTTCTAATATTA
1 TATATATGATTTTTCTAATATCA
17974 TATATTATGATTTTTACTAAT-TCA
1 TATA-TATGATTTTT-CTAATATCA
17998 TAT
1 TAT
18001 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TATATATGATTTTTCTAATATCA
Found at i:18051 original size:32 final size:31
Alignment explanation
Indices: 18015--18121 Score: 89
Period size: 32 Copynumber: 3.5 Consensus size: 31
18005 ATAATAATTA
18015 TATTAAAAATATAATTAAATTATTTATTATTT
1 TATT-AAAATATAATTAAATTATTTATTATTT
* * * * *
18047 TATT-AAAT-T--TT-ATTTAATAATAATTA
1 TATTAAAATATAATTAAATTATTTATTATTT
*
18073 TGTTAAAATATAATTAAATTATTTATTATTTT
1 TATTAAAATATAATTAAATTATTTATTA-TTT
* *
18105 TATTAAATTATATTTAA
1 TATTAAAATATAATTAA
18122 TAATAATCTT
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
26 13 0.24
27 6 0.11
28 1 0.02
29 1 0.02
30 6 0.11
31 8 0.15
32 20 0.36
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TATTAAAATATAATTAAATTATTTATTATTT
Found at i:18139 original size:58 final size:58
Alignment explanation
Indices: 17978--18144 Score: 232
Period size: 58 Copynumber: 2.9 Consensus size: 58
17968 ATATTATATA
* *
17978 TTATGATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAT
* *
18038 TTATTA-TTTTATTAAATTTTATTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
*
18095 TTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
18145 AATAATAATT
Statistics
Matches: 97, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
57 24 0.25
58 55 0.57
59 9 0.09
60 9 0.09
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:18321 original size:16 final size:16
Alignment explanation
Indices: 18300--18339 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
18290 TGAATTACTG
18300 ATTACAG-TCTTATTCC
1 ATTACAGTTC-TATTCC
*
18316 ATTACAATTCTATTCC
1 ATTACAGTTCTATTCC
18332 ATTACAGT
1 ATTACAGT
18340 GAATCAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:22637 original size:27 final size:27
Alignment explanation
Indices: 22604--22656 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
22594 TCAGCAAGTT
*
22604 TCAGCTTGCTTT-TTGTTTCGGATTTCC
1 TCAGCTTGCTTTGTTG-CTCGGATTTCC
*
22631 TCAGCTTTCTTTGTTGCTCGGATTTC
1 TCAGCTTGCTTTGTTGCTCGGATTTC
22657 AACTCCCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.51
Consensus pattern (27 bp):
TCAGCTTGCTTTGTTGCTCGGATTTCC
Found at i:24899 original size:6 final size:6
Alignment explanation
Indices: 24888--24917 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
24878 CTTTTGTTTT
*
24888 AGTCAC AGTCAC AGTCAC AGTCAC ACTCAC
1 AGTCAC AGTCAC AGTCAC AGTCAC AGTCAC
24918 TTTGCAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.37, G:0.13, T:0.17
Consensus pattern (6 bp):
AGTCAC
Done.