Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004631.1 Kokia drynarioides strain JFW-HI SEQ_118154, 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: 25966
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:4575 original size:15 final size:15
Alignment explanation
Indices: 4557--4587 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4547 AAAAAAAGAA
*
4557 TAAAAGGGCAAATTT
1 TAAAAGGGAAAATTT
4572 TAAAAGGGAAAATTT
1 TAAAAGGGAAAATTT
4587 T
1 T
4588 GAGGGTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.29
Consensus pattern (15 bp):
TAAAAGGGAAAATTT
Found at i:6389 original size:46 final size:45
Alignment explanation
Indices: 6313--6772 Score: 598
Period size: 46 Copynumber: 10.1 Consensus size: 45
6303 GCTTTTGTGA
* * *
6313 GATGGTAGCTTCAGT-TGCCCCTCTTGATTTAGAGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
* *
6358 GATGGTGACTTCAATCTGCCCCTCTTAATTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
* * * *
6404 GATGGTGGCTTTAATCTACCCCTTTTGACTTAGGGGTAAAAGATTA
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
* * *
6450 GATGGTGGCTTCAATTTTCTCCTCTTGAATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTG-ATTAGGGGTAAAAGATTG
* *
6496 AATGGTGGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAAATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
* ** **
6542 GAAGGTATCTTCAATCTAACCCTCTTGATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * * * * *
6587 GACGGTAGTTTCAATCTGCCTCTCCTGATTAGGGGTAAAAGTTTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
*
6632 GATGGTGGCTTCAATCTGCCCCTATTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
*
6678 GATGGTGGCTTCAATTTGCCCCTCTTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
*
6724 GATGGTGACTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
6769 GATG
1 GATG
6773 TGGTGATGTA
Statistics
Matches: 362, Mismatches: 49, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
45 109 0.30
46 252 0.70
47 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (45 bp):
GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
Found at i:6667 original size:182 final size:182
Alignment explanation
Indices: 6314--6770 Score: 641
Period size: 182 Copynumber: 2.5 Consensus size: 182
6304 CTTTTGTGAG
* * * *
6314 ATGGTAGCTTCAGTTGCCCCTCTTGATTTAGAGGTAAAAGATTGGATGGTGACTTCAATCTGCCC
1 ATGGTGGCTTCAATTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCCC
* * * **
6379 CTCTTAATTTAGGGGTAAAAGATTGGATGGTGGCTTTAATCTACCCCTTTTGACTTAGGGGTAAA
66 CTCTTGA-TTAGGGGTAAAAGATTGGACGGTAGCTTTAATCTACCCCTCCTGACTTAGGGGTAAA
* * * *
6444 AGATTAGATGGTGGCTTCAATTTTCTCCTCTTGAATTAGGGGTAAAAGATTGA
130 AGATTAGATGGTGGCTTCAATCTGCCCCTATTGAATTAGGGGTAAAAGATTGA
* * **
6497 ATGGTGGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAAATTGGAAGGT-ATCTTCAATCTAA
1 ATGGTGGCTTCAAT-TGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGA-CTTCAATCTGC
* *
6561 CCCTCTTGATTAGGGGTAAAAGATTGGACGGTAG-TTTCAATCTGCCTCTCCTGA-TTAGGGGTA
64 CCCTCTTGATTAGGGGTAAAAGATTGGACGGTAGCTTT-AATCTACCCCTCCTGACTTAGGGGTA
* * * *
6624 AAAGTTTGGATGGTGGCTTCAATCTGCCCCTATTGACTTAGGGGTAAAAGATTGG
128 AAAGATTAGATGGTGGCTTCAATCTGCCCCTATTGAATTAGGGGTAAAAGATTGA
6679 ATGGTGGCTTCAATTTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCC
1 ATGGTGGCTTCAA-TTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCC
6744 CCTCTTGATTAGGGGTAAAAGATTGGA
65 CCTCTTGATTAGGGGTAAAAGATTGGA
6771 TGTGGTGATG
Statistics
Matches: 242, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
182 143 0.59
183 50 0.21
184 49 0.20
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (182 bp):
ATGGTGGCTTCAATTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCCC
CTCTTGATTAGGGGTAAAAGATTGGACGGTAGCTTTAATCTACCCCTCCTGACTTAGGGGTAAAA
GATTAGATGGTGGCTTCAATCTGCCCCTATTGAATTAGGGGTAAAAGATTGA
Found at i:8830 original size:16 final size:16
Alignment explanation
Indices: 8811--8843 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
8801 GACTTTTTTC
8811 TTCTTTCCTTTTTCTT
1 TTCTTTCCTTTTTCTT
*
8827 TTCTTTTCTTTTTCTT
1 TTCTTTCCTTTTTCTT
8843 T
1 T
8844 CATTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTCTTTCCTTTTTCTT
Found at i:8849 original size:16 final size:15
Alignment explanation
Indices: 8805--8849 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
8795 CATCTTGACT
*
8805 TTTTTC-TTCTTTCC
1 TTTTTCTTTCTTTTC
8819 TTTTTCTTTTCTTTTC
1 TTTTTC-TTTCTTTTC
8835 TTTTTCTTTCATTTT
1 TTTTTCTTTC-TTTT
8850 TTAGCTCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 17 0.63
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTCTTTTC
Found at i:14207 original size:20 final size:21
Alignment explanation
Indices: 14166--14208 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
14156 TATTTTAGTC
14166 TTAGGCTTAGGTGAGTTTGGG
1 TTAGGCTTAGGTGAGTTTGGG
*
14187 TTAGG-TTAGTTG-GTTTAGGG
1 TTAGGCTTAGGTGAGTTT-GGG
14207 TT
1 TT
14209 TAACAAATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.14, C:0.02, G:0.40, T:0.44
Consensus pattern (21 bp):
TTAGGCTTAGGTGAGTTTGGG
Found at i:17047 original size:17 final size:17
Alignment explanation
Indices: 17025--17064 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
17015 AAACTTGCTT
*
17025 AAAACCATTAATGGGTC
1 AAAACCATCAATGGGTC
17042 AAAACCATCAATGGGTC
1 AAAACCATCAATGGGTC
17059 AAAACC
1 AAAACC
17065 CCTCTCTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (17 bp):
AAAACCATCAATGGGTC
Done.