Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008640.1 Kokia drynarioides strain JFW-HI SEQ_123320, 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: 30929
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4208 original size:17 final size:17
Alignment explanation
Indices: 4186--4235 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
4176 TTAAACAAAT
4186 CTGCGAGCTCATTAAAG
1 CTGCGAGCTCATTAAAG
*
4203 CTGCGAGCTCAATT-TAG
1 CTGCGAGCTC-ATTAAAG
*
4220 TTGCGAGCTCATTAAA
1 CTGCGAGCTCATTAAA
4236 ATGTGAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.11
17 22 0.79
18 3 0.11
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (17 bp):
CTGCGAGCTCATTAAAG
Found at i:5852 original size:15 final size:15
Alignment explanation
Indices: 5811--5856 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5801 CATTTTTATA
*
5811 TGAATGTAAATTTTT
1 TGAATTTAAATTTTT
* *
5826 TTAATTT-TATTTTT
1 TGAATTTAAATTTTT
5840 TGAATTTAAATTTTT
1 TGAATTTAAATTTTT
5855 TG
1 TG
5857 TTTAAACATG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (15 bp):
TGAATTTAAATTTTT
Found at i:9753 original size:41 final size:41
Alignment explanation
Indices: 9699--9802 Score: 140
Period size: 41 Copynumber: 2.5 Consensus size: 41
9689 GCACCTGAAT
* * *
9699 ATCAGGCCTTGAGCTTAGCAGGCTTTGAGT-CGA-TGTATTGA
1 ATCAAGCCTTGAGCCTAGCAGGC-TTCA-TACGAGTGTATTGA
*
9740 ATCAAGCCTTGAGCCTAGCAGGCTTCATACTAGTGTATTGA
1 ATCAAGCCTTGAGCCTAGCAGGCTTCATACGAGTGTATTGA
9781 ATCAAGCCTTGAGCCTAGCAGG
1 ATCAAGCCTTGAGCCTAGCAGG
9803 TTTATTGTCG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
39 1 0.02
40 5 0.09
41 51 0.89
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (41 bp):
ATCAAGCCTTGAGCCTAGCAGGCTTCATACGAGTGTATTGA
Found at i:11839 original size:26 final size:25
Alignment explanation
Indices: 11792--12045 Score: 215
Period size: 26 Copynumber: 9.8 Consensus size: 25
11782 CATTCGCCAC
*
11792 CATGATTATTAGTTTACGCTCGTCAG
1 CATGATTA-TACTTTACGCTCGTCAG
*
11818 CATGATTATACTTTCACACTCGTCAG
1 CATGATTATACTTT-ACGCTCGTCAG
** *
11844 CATGATTATGTGTTTATGCTCGTCAG
1 CATGATTAT-ACTTTACGCTCGTCAG
*
11870 CATGATTATACGTTTATGCTCGTCAG
1 CATGATTATAC-TTTACGCTCGTCAG
11896 CATGATTATACATTTACGCTCGTCAG
1 CATGATTATAC-TTTACGCTCGTCAG
* * * *
11922 CATGATTATGCATTTATGCTCGCCAT
1 CATGATTATAC-TTTACGCTCGTCAG
* * * *
11948 CATGATTATGCGTCTATGCTCGCCAG
1 CATGATTATAC-TTTACGCTCGTCAG
** * **
11974 CATGATTATGTGTTTATGCTCACCAG
1 CATGATTAT-ACTTTACGCTCGTCAG
12000 CATGGA-TATACGTTTACGCTCGTCAG
1 CAT-GATTATAC-TTTACGCTCGTCAG
12026 CATGGA-TATACGTTTACGCT
1 CAT-GATTATAC-TTTACGCT
12046 ACTAGAGCTC
Statistics
Matches: 196, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
25 5 0.03
26 186 0.95
27 5 0.03
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (25 bp):
CATGATTATACTTTACGCTCGTCAG
Found at i:11921 original size:78 final size:77
Alignment explanation
Indices: 11792--12041 Score: 281
Period size: 78 Copynumber: 3.2 Consensus size: 77
11782 CATTCGCCAC
* * *
11792 CATGATTATTA-GTTTACGCTCGTCAGCATGATTATACTTTCACACTCGTCAGCATGATTATGTG
1 CATGATTA-TACGTTTATGCTCGTCAGCATGATTATACTTT-ACGCTCGTCAGCATGATTATGCG
11856 TTTATGCTCGTCAG
64 TTTATGCTCGTCAG
*
11870 CATGATTATACGTTTATGCTCGTCAGCATGATTATACATTTACGCTCGTCAGCATGATTATGCAT
1 CATGATTATACGTTTATGCTCGTCAGCATGATTATAC-TTTACGCTCGTCAGCATGATTATGCGT
* *
11935 TTATGCTCGCCAT
65 TTATGCTCGTCAG
* * * ** * ** *
11948 CATGATTATGCGTCTATGCTCGCCAGCATGATTATGTGTTTATGCTCACCAGCATGGA-TATACG
1 CATGATTATACGTTTATGCTCGTCAGCATGATTAT-ACTTTACGCTCGTCAGCAT-GATTATGCG
*
12012 TTTACGCTCGTCAG
64 TTTATGCTCGTCAG
12026 CATGGA-TATACGTTTA
1 CAT-GATTATACGTTTA
12042 CGCTACTAGA
Statistics
Matches: 146, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
77 2 0.01
78 137 0.94
79 7 0.05
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (77 bp):
CATGATTATACGTTTATGCTCGTCAGCATGATTATACTTTACGCTCGTCAGCATGATTATGCGTT
TATGCTCGTCAG
Found at i:12041 original size:52 final size:52
Alignment explanation
Indices: 11785--12041 Score: 279
Period size: 52 Copynumber: 4.9 Consensus size: 52
11775 GCAATTTCAT
* **
11785 TCGCCACCATGATTATTA-GTTTACGCTCGTCAGCATGATTATAC-TTTCACAC
1 TCGCCAGCATGATTA-TACGTTTACGCTCGTCAGCATGATTATACGTTT-ATGC
* ** *
11837 TCGTCAGCATGATTATGTGTTTATGCTCGTCAGCATGATTATACGTTTATGC
1 TCGCCAGCATGATTATACGTTTACGCTCGTCAGCATGATTATACGTTTATGC
* * * *
11889 TCGTCAGCATGATTATACATTTACGCTCGTCAGCATGATTATGCATTTATGC
1 TCGCCAGCATGATTATACGTTTACGCTCGTCAGCATGATTATACGTTTATGC
* * * * * **
11941 TCGCCATCATGATTATGCGTCTATGCTCGCCAGCATGATTATGTGTTTATGC
1 TCGCCAGCATGATTATACGTTTACGCTCGTCAGCATGATTATACGTTTATGC
*
11993 TCACCAGCATGGA-TATACGTTTACGCTCGTCAGCATGGA-TATACGTTTA
1 TCGCCAGCAT-GATTATACGTTTACGCTCGTCAGCAT-GATTATACGTTTA
12042 CGCTACTAGA
Statistics
Matches: 172, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
51 1 0.01
52 164 0.95
53 7 0.04
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (52 bp):
TCGCCAGCATGATTATACGTTTACGCTCGTCAGCATGATTATACGTTTATGC
Found at i:18781 original size:4 final size:4
Alignment explanation
Indices: 18761--18807 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
18751 CAAATAGCTG
* * *
18761 AGAA A-AA AAAA ATGAA AGAA AGAA AGAA AGAA AGAA GGAG AGAA AGA
1 AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA
18808 TTTTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.08
4 30 0.83
5 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:19205 original size:12 final size:12
Alignment explanation
Indices: 19179--19212 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
19169 AAATTAATTT
19179 GTTAGT-AGT-A
1 GTTAGTAAGTAA
19189 GTTAGTAAGTAA
1 GTTAGTAAGTAA
19201 GTTAGTAAGTAA
1 GTTAGTAAGTAA
19213 TTTTATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.27
11 3 0.14
12 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (12 bp):
GTTAGTAAGTAA
Found at i:24478 original size:18 final size:17
Alignment explanation
Indices: 24426--24478 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
24416 AAAAAATTAC
24426 CTTTCTTTCT-TCTTCT
1 CTTTCTTTCTCTCTTCT
*
24442 -TTTTTTTCTCTCCTT-T
1 CTTTCTTTCTCT-CTTCT
24458 CTTTCTTTCCTCTCTTCT
1 CTTTCTTT-CTCTCTTCT
24476 CTT
1 CTT
24479 CTCTCTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 8 0.27
16 2 0.07
17 12 0.40
18 8 0.27
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCTTTCTCTCTTCT
Done.