Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012783.1 Kokia drynarioides strain JFW-HI SEQ_127795, 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: 22596
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:798 original size:15 final size:16
Alignment explanation
Indices: 778--807 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
768 CTTCCATATT
778 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
793 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
808 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:802 original size:22 final size:22
Alignment explanation
Indices: 774--833 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
764 TTGACTTCCA
774 TATTTTCTATTT-CTTTTAATTC
1 TATTTTCT-TTTACTTTTAATTC
*
796 TATTTTCTTTTATTTTTAATTC
1 TATTTTCTTTTACTTTTAATTC
* *
818 T-GTTTCTTTTATTTTT
1 TATTTTCTTTTACTTTT
834 CCTTAGATCG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTC
Found at i:823 original size:21 final size:22
Alignment explanation
Indices: 787--833 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
777 TTTCTATTTC
*
787 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
809 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
830 TTTT
1 TTTT
834 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:7370 original size:105 final size:103
Alignment explanation
Indices: 7194--7396 Score: 237
Period size: 105 Copynumber: 2.0 Consensus size: 103
7184 ATTTGGAATG
* * * *
7194 TGTTAGACTGAGTAACCGGGTTGGAGTGATTGGTTGTCATTTCACTTCGCGTCAAAATGACTAAC
1 TGTTAGACTGAGTAACCGGGATGGAGTGATTGGGTGTCATTTCACTTCGCGTCAAAAGGACCAAC
7259 ACATTC-TACAAAAAAAAAAGAGAAGAAAAAATTGAGAGCA
66 ACATTCTTA-AAAAAAAAAA-A-AAGAAAAAATTGAGAGCA
* * ** * * *
7299 TGTTAGGCTGAGTAATCGGGATGGAGTTCTTGGGTGTCATTTCATTTCGCGTCAAAAGGTCCAAT
1 TGTTAGACTGAGTAACCGGGATGGAGTGATTGGGTGTCATTTCACTTCGCGTCAAAAGGACCAAC
** * *
7364 GTATTCTTAAAGAAAAAAAAAAGAAAAATTTGA
66 ACATTCTTAAAAAAAAAAAAAAGAAAAAATTGA
7397 CAAAATAAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
103 12 0.15
104 1 0.01
105 67 0.82
106 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (103 bp):
TGTTAGACTGAGTAACCGGGATGGAGTGATTGGGTGTCATTTCACTTCGCGTCAAAAGGACCAAC
ACATTCTTAAAAAAAAAAAAAAGAAAAAATTGAGAGCA
Found at i:7984 original size:19 final size:19
Alignment explanation
Indices: 7962--8006 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
7952 TTATATTAGG
7962 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
7981 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
8000 ATTTAAT
1 ATTTAAT
8007 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:11343 original size:91 final size:90
Alignment explanation
Indices: 11188--11370 Score: 348
Period size: 91 Copynumber: 2.0 Consensus size: 90
11178 AAGCAGAGAG
*
11188 AGAAGATTTCAAGATTTTTAGGAAGAAGAATCTTATTAGAACATTCTCAATGCCACCACCGAAGA
1 AGAAGATTTCAAGATTTTTAGAAAGAAGAATCTTATTAGAACATTCTCAATGCCACCACCGAAGA
11253 AATTTATAGATAGTGAAGTCTGAGT
66 AATTTATAGATAGTGAAGTCTGAGT
11278 NAGAAGATTTCAAGATTTTTAGAAAGAAGAATCTTATTAGAACATTCTCAATGCCACCACCGAAG
1 -AGAAGATTTCAAGATTTTTAGAAAGAAGAATCTTATTAGAACATTCTCAATGCCACCACCGAAG
11343 AAATTTATAGATAGTGAAGTCTGAGT
65 AAATTTATAGATAGTGAAGTCTGAGT
11369 AG
1 AG
11371 CAGTCTCTTC
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
90 2 0.02
91 89 0.98
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (90 bp):
AGAAGATTTCAAGATTTTTAGAAAGAAGAATCTTATTAGAACATTCTCAATGCCACCACCGAAGA
AATTTATAGATAGTGAAGTCTGAGT
Found at i:16915 original size:21 final size:21
Alignment explanation
Indices: 16864--16915 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
16854 TAGAATATAG
*
16864 ACTTGTATCAGTAGAAGAGTC
1 ACTTGTATCGGTAGAAGAGTC
*
16885 ACTTGTATCGGTAGAACTA-TC
1 ACTTGTATCGGTAGAA-GAGTC
16906 ACTTGTATCG
1 ACTTGTATCG
16916 ATAAGAGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGAGTC
Found at i:18902 original size:24 final size:24
Alignment explanation
Indices: 18866--19097 Score: 205
Period size: 24 Copynumber: 9.7 Consensus size: 24
18856 AATAACAATT
*
18866 TTAT-TACGTTTACGCTCGTCAGC
1 TTATATACGTTTACGCTCATCAGC
* *
18889 ATATATACGTTTACGCTCGTCAGC
1 TTATATACGTTTACGCTCATCAGC
** * * *
18913 TTGCACACGTTTTCTCTCATCAGC
1 TTATATACGTTTACGCTCATCAGC
*
18937 TTATATACATTTACGCTCATCAGC
1 TTATATACGTTTACGCTCATCAGC
** * * * *
18961 TTGCACATGTTTATGCTCATCACC
1 TTATATACGTTTACGCTCATCAGC
* * *
18985 TGATATACTTTTATGCTCATCAGC
1 TTATATACGTTTACGCTCATCAGC
**
19009 TTGCATACGTTTACGCTCATCAGC
1 TTATATACGTTTACGCTCATCAGC
* * *
19033 TTATATATGTTTACGCTCGTCAAC
1 TTATATACGTTTACGCTCATCAGC
** * *
19057 TTGCACACGTTTACGCTCGTCAGC
1 TTATATACGTTTACGCTCATCAGC
*
19081 TTATATACATTTACGCT
1 TTATATACGTTTACGCT
19098 ATTATGAAAT
Statistics
Matches: 161, Mismatches: 47, Indels: 1
0.77 0.22 0.00
Matches are distributed among these distances:
23 3 0.02
24 158 0.98
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (24 bp):
TTATATACGTTTACGCTCATCAGC
Found at i:18942 original size:48 final size:48
Alignment explanation
Indices: 18871--19097 Score: 292
Period size: 48 Copynumber: 4.7 Consensus size: 48
18861 CAATTTTATT
* * * *
18871 ACGTTTACGCTCGTCAGCATATATACGTTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCATCAGCTTATATACATTTACGCTCATCAGCTTGCAC
* *
18919 ACGTTTTCTCTCATCAGCTTATATACATTTACGCTCATCAGCTTGCAC
1 ACGTTTACGCTCATCAGCTTATATACATTTACGCTCATCAGCTTGCAC
* * * * * * *
18967 ATGTTTATGCTCATCACCTGATATACTTTTATGCTCATCAGCTTGCAT
1 ACGTTTACGCTCATCAGCTTATATACATTTACGCTCATCAGCTTGCAC
** * *
19015 ACGTTTACGCTCATCAGCTTATATATGTTTACGCTCGTCAACTTGCAC
1 ACGTTTACGCTCATCAGCTTATATACATTTACGCTCATCAGCTTGCAC
*
19063 ACGTTTACGCTCGTCAGCTTATATACATTTACGCT
1 ACGTTTACGCTCATCAGCTTATATACATTTACGCT
19098 ATTATGAAAT
Statistics
Matches: 151, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 151 1.00
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (48 bp):
ACGTTTACGCTCATCAGCTTATATACATTTACGCTCATCAGCTTGCAC
Found at i:18960 original size:72 final size:71
Alignment explanation
Indices: 18866--19097 Score: 243
Period size: 72 Copynumber: 3.2 Consensus size: 71
18856 AATAACAATT
* * * *
18866 TTAT-TACGTTTACGCTCGTCAGCATATATACGTTTACGCTCGTCAGCTTGCACACGTTTTCTCT
1 TTATATACATTTACGCTCATCAGCTTATATATGTTTACGCTCGTCA-CTTGCACACGTTTTCTCT
18930 CATCAGC
65 CATCAGC
** * * * * * * *
18937 TTATATACATTTACGCTCATCAGCTTGCACATGTTTATGCTCATCACCTGATATAC-TTTTATGC
1 TTATATACATTTACGCTCATCAGCTTATATATGTTTACGCTCGTCACTTG-CACACGTTTTCT-C
19001 TCATCAGC
64 TCATCAGC
** * * *
19009 TTGCATACGTTTACGCTCATCAGCTTATATATGTTTACGCTCGTCAACTTGCACACGTTTACGCT
1 TTATATACATTTACGCTCATCAGCTTATATATGTTTACGCTCGTC-ACTTGCACACGTTTTCTCT
*
19074 CGTCAGC
65 CATCAGC
19081 TTATATACATTTACGCT
1 TTATATACATTTACGCT
19098 ATTATGAAAT
Statistics
Matches: 125, Mismatches: 31, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
71 12 0.10
72 106 0.85
73 7 0.06
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (71 bp):
TTATATACATTTACGCTCATCAGCTTATATATGTTTACGCTCGTCACTTGCACACGTTTTCTCTC
ATCAGC
Done.