Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006159.1 Kokia drynarioides strain JFW-HI SEQ_120709, 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: 39066
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4591 original size:32 final size:32
Alignment explanation
Indices: 4555--4615 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
4545 TCATAAACTT
4555 ATAAATTAATTACA-TGAATTTAATAACTCGTA
1 ATAAATTAATTA-ATTGAATTTAATAACTCGTA
*
4587 ATAAATTAATTAATTTAATTTAATAACTC
1 ATAAATTAATTAATTGAATTTAATAACTC
4616 AGACTGATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAACTCGTA
Found at i:8095 original size:2 final size:2
Alignment explanation
Indices: 8088--8122 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
8078 AACAACTTTG
*
8088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8123 GGTCCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21988 original size:22 final size:22
Alignment explanation
Indices: 21963--22019 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
21953 AAATCAAAAT
*
21963 TAAATTATAATTTTTATAAT-AG
1 TAAATTATAATTCTTA-AATAAG
* *
21985 TAAAAATATAATTCTTAAATAAT
1 T-AAATTATAATTCTTAAATAAG
*
22008 TAAATTAAAATT
1 TAAATTATAATT
22020 GTATCATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAATTATAATTCTTAAATAAG
Found at i:22011 original size:23 final size:24
Alignment explanation
Indices: 21960--22011 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
21950 TTTAAATCAA
* *
21960 AATT-AAATTATAATTTTTATAAT
1 AATTAAAAATATAATTCTTATAAT
*
21983 -AGTAAAAATATAATTCTTA-AAT
1 AATTAAAAATATAATTCTTATAAT
22005 AATTAAA
1 AATTAAA
22012 TTAAAATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
AATTAAAAATATAATTCTTATAAT
Found at i:24362 original size:50 final size:50
Alignment explanation
Indices: 24287--24384 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
24277 TCGGAATTCT
*
24287 GACTTCTGGTATATAAAACATAAGGAAGAATCCATTTTGTTGGTAAAATG
1 GACTTCTGGTATATAAAACATAAGGAAGAATACATTTTGTTGGTAAAATG
*
24337 GACTTCTGGTATATAAAACATAAGGAAGGATACATTTTGTTGGTAAAA
1 GACTTCTGGTATATAAAACATAAGGAAGAATACATTTTGTTGGTAAAA
24385 AACTGACTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (50 bp):
GACTTCTGGTATATAAAACATAAGGAAGAATACATTTTGTTGGTAAAATG
Found at i:30667 original size:21 final size:20
Alignment explanation
Indices: 30629--30667 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
30619 CAGTAGTAGA
*
30629 CAAAAAATTAACACAAAGTT
1 CAAAAAATTAAAACAAAGTT
*
30649 CAAAAAGATTAAAAGAAAG
1 CAAAAA-ATTAAAACAAAG
30668 AGGCAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.15
Consensus pattern (20 bp):
CAAAAAATTAAAACAAAGTT
Found at i:36400 original size:18 final size:17
Alignment explanation
Indices: 36363--36399 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
36353 ATCGTCGGTA
**
36363 TTTCTATCCCTTTCTTT
1 TTTCTATCCAATTCTTT
36380 TTTCTATCCAATTCTTT
1 TTTCTATCCAATTCTTT
36397 TTT
1 TTT
36400 TATATTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTATCCAATTCTTT
Found at i:36482 original size:23 final size:24
Alignment explanation
Indices: 36421--36484 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
36411 TTTCTTCTAA
*
36421 TTTT-ATCTACCTTCGTGGCACGC
1 TTTTCATCTACCTTTGTGGCACGC
* *
36444 TTTTTC-TCTGCC-TTGTGGCATG-
1 -TTTTCATCTACCTTTGTGGCACGC
36466 TTTTCATCTACCTTTGTGG
1 TTTTCATCTACCTTTGTGG
36485 TAGATCTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 5 0.15
22 5 0.15
23 14 0.42
24 9 0.27
ACGTcount: A:0.09, C:0.25, G:0.19, T:0.47
Consensus pattern (24 bp):
TTTTCATCTACCTTTGTGGCACGC
Found at i:36846 original size:21 final size:20
Alignment explanation
Indices: 36809--36849 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
36799 TGATGTTTCT
* *
36809 TTATTTTTGTCTTTATTTTA
1 TTATTTTTCTCTGTATTTTA
36829 TTATTTTTCTGCTGTATTTTA
1 TTATTTTTCT-CTGTATTTTA
36850 ATTTCATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.71
Consensus pattern (20 bp):
TTATTTTTCTCTGTATTTTA
Found at i:37930 original size:27 final size:30
Alignment explanation
Indices: 37864--37945 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 30
37854 TTCGGATACA
* * *
37864 CGGGGGTAAAATGGTAATTTTGGGAATATT
1 CGGGGGTAAAATAGTAATTTTGAGAACATT
*
37894 CGGGGTTAAAATAG-AATTTT-AG-ACATT
1 CGGGGGTAAAATAGTAATTTTGAGAACATT
** *
37921 CGGGGGTAAAAGGGTAAGTTTGAGA
1 CGGGGGTAAAATAGTAATTTTGAGA
37946 GTTTCGAGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
27 15 0.37
28 6 0.15
29 8 0.20
30 12 0.29
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.29
Consensus pattern (30 bp):
CGGGGGTAAAATAGTAATTTTGAGAACATT
Found at i:38067 original size:29 final size:29
Alignment explanation
Indices: 37984--38366 Score: 348
Period size: 29 Copynumber: 13.0 Consensus size: 29
37974 ACATTCGAGA
*
37984 GTAAAATGATAATTTTTGGAAGTTTCG-GG
1 GTAAAATGGTAATTTTTGGAAGTTT-GAGG
* *
38013 GTCAAAAAATGTGT--TTTTTGGAAGTTCGAGT
1 GT---AAAATG-GTAATTTTTGGAAGTTTGAGG
* *
38044 GTAACATGGTAATTTTTGGAAGTTTTAGG
1 GTAAAATGGTAATTTTTGGAAGTTTGAGG
*
38073 GTCAAAAATGG-GATTTTTGGAAGTTTGAGG
1 GT--AAAATGGTAATTTTTGGAAGTTTGAGG
*
38103 GTAAAAT-GTAATTTTTGGAAGTTTTA-G
1 GTAAAATGGTAATTTTTGGAAGTTTGAGG
* *
38130 GTCAAAAATGG-GATTTTTGGAAGTTCGAGG
1 GT--AAAATGGTAATTTTTGGAAGTTTGAGG
38160 G-AAAATTGGTAATTTTTGGAAGTTTTG-GG
1 GTAAAA-TGGTAATTTTTGGAAG-TTTGAGG
*
38189 GTTAAGAATGG-GATTTTTGGAAGTTT-AGGG
1 G-TAA-AATGGTAATTTTTGGAAGTTTGA-GG
*
38219 GTAAAATGGTAATTTTTGGAAGTTTTAGG
1 GTAAAATGGTAATTTTTGGAAGTTTGAGG
*
38248 GTCAAGAAT-G-AGATTTTTGGAAGTTCGAGG
1 GT-AA-AATGGTA-ATTTTTGGAAGTTTGAGG
38278 GTAAAATGGTAATTTTTGGAAGTTTTG-GG
1 GTAAAATGGTAATTTTTGGAAG-TTTGAGG
*
38307 GTTAAAAATGG-GATTTTTGGAAGTTTGAGG
1 G-T-AAAATGGTAATTTTTGGAAGTTTGAGG
38337 GTAAAATGGTAATTTTTGGATAGTTT-AGG
1 GTAAAATGGTAATTTTTGGA-AGTTTGAGG
38366 G
1 G
38367 ACCTCCGAGG
Statistics
Matches: 295, Mismatches: 24, Indels: 70
0.76 0.06 0.18
Matches are distributed among these distances:
27 10 0.03
28 43 0.15
29 111 0.38
30 86 0.29
31 36 0.12
32 8 0.03
33 1 0.00
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.38
Consensus pattern (29 bp):
GTAAAATGGTAATTTTTGGAAGTTTGAGG
Found at i:38212 original size:59 final size:59
Alignment explanation
Indices: 37977--38362 Score: 546
Period size: 59 Copynumber: 6.5 Consensus size: 59
37967 TCTTCGGACA
* * * * *
37977 TTCGAGAGTAAAATGATAATTTTTGGAAGTTTCGGGGTCAAAAAATGTGTTTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTC-AAAAATGGGATTTTTGGAAG
* * *
38037 TTCGAGTGTAACATGGTAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* *
38096 TTTGAGGGTAAAAT-GTAATTTTTGGAAGTTTT-AGGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* *
38153 TTCGAGGG-AAAATTGGTAATTTTTGGAAGTTTTGGGGTTAAGAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAA-TGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* * * *
38212 TT-TAGGGGTAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAGAATGAGATTTTTGGAAG
1 TTCGA-GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
*
38271 TTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
*
38330 TTTGAGGGTAAAATGGTAATTTTTGGATAGTTT
1 TTCGAGGGTAAAATGGTAATTTTTGGA-AGTTT
38363 AGGGACCTCC
Statistics
Matches: 294, Mismatches: 25, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
56 4 0.01
57 32 0.11
58 37 0.13
59 177 0.60
60 44 0.15
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.38
Consensus pattern (59 bp):
TTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
Found at i:38785 original size:5 final size:5
Alignment explanation
Indices: 38740--38774 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
38730 CGGATCCTAA
38740 GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG
1 GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG
38775 ATTCGAGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
GTCGG
Done.