Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009026.1 Kokia drynarioides strain JFW-HI SEQ_123724, 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: 5106
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:661 original size:20 final size:20
Alignment explanation
Indices: 636--687 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
626 ATGGGAATAA
636 AAAATA-AAAGCCAGTCAAAT
1 AAAATATAAA-CCAGTCAAAT
**
656 AAAATATAAACCTTTCAAAT
1 AAAATATAAACCAGTCAAAT
676 AAAATATAAACC
1 AAAATATAAACC
688 TTATAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.60, C:0.15, G:0.04, T:0.21
Consensus pattern (20 bp):
AAAATATAAACCAGTCAAAT
Found at i:688 original size:20 final size:20
Alignment explanation
Indices: 650--689 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
640 TAAAAGCCAG
650 TCAAATAAAATATAAACCTT
1 TCAAATAAAATATAAACCTT
670 TCAAATAAAATATAAACCTT
1 TCAAATAAAATATAAACCTT
690 ATAACTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (20 bp):
TCAAATAAAATATAAACCTT
Found at i:3153 original size:14 final size:15
Alignment explanation
Indices: 3136--3165 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3126 TTTCCATTCC
3136 TTTTTC-TTTTTCTT
1 TTTTTCTTTTTTCTT
3150 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTCTT
3165 T
1 T
3166 AAAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTCTTTTTTCTT
Found at i:4715 original size:49 final size:49
Alignment explanation
Indices: 4657--4897 Score: 189
Period size: 49 Copynumber: 4.9 Consensus size: 49
4647 CATCCGTGCT
* * * *
4657 TTCGAGGTACTAGG-TTCGTCGTTGCGGCTTAAACCATTCCCTTTGTATC
1 TTCGTGGTACT-GGATTCGTCGTTACGACTTAAACCTTTCCCTTTGTATC
* * * *
4706 TTCGTGGTACTGGATTTGTCGTTACGACTTAAATCTTTCCCTCTGTATT
1 TTCGTGGTACTGGATTCGTCGTTACGACTTAAACCTTTCCCTTTGTATC
* * * * * *
4755 TTCTGAGGT-GTGAGGTTCGTCGATACGACTTAAACCTTTCTCTTTTGTGTC
1 TTC-GTGGTACTG-GATTCGTCGTTACGACTTAAACCTTTC-CCTTTGTATC
* * * * **
4806 TTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATATC
1 TTCGTGGTACTGGATTCGTCGTTACGACTTAAACCTTTCCCTTTGTATC
* * ** * * *
4855 TTCGTGGTATTGAATTTTTCGTTGCGACTTAAATCTTTTCCTT
1 TTCGTGGTACTGGATTCGTCGTTACGACTTAAACCTTTCCCTT
4898 CGTCCTTTCA
Statistics
Matches: 150, Mismatches: 37, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
48 2 0.01
49 85 0.57
50 52 0.35
51 11 0.07
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (49 bp):
TTCGTGGTACTGGATTCGTCGTTACGACTTAAACCTTTCCCTTTGTATC
Found at i:4821 original size:100 final size:99
Alignment explanation
Indices: 4606--4847 Score: 263
Period size: 100 Copynumber: 2.4 Consensus size: 99
4596 GGCTATAATG
* * * * * * * * ** *
4606 TCTTCGCGATACTAGATTCGCCGTTGCGGCTTAAATCTTTTCATCCGTGCTTTC-GAGGTACT-A
1 TCTTCGTGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCCTCTGTATTTTCTGAGGT-GTGA
* * *
4669 GGTTCGTCGTTGCGGCTTAAACCATTCCCTTTGTA
65 GGTTCGTCGATACGACTTAAACCATTCCCTTTGTA
* *
4704 TCTTCGTGGTACTGGATTTGTCGTTACGACTTAAATCTTTCCCTCTGTATTTTCTGAGGTGTGAG
1 TCTTCGTGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCCTCTGTATTTTCTGAGGTGTGAG
* * *
4769 GTTCGTCGATACGACTTAAACCTTTCTCTTTTGTG
66 GTTCGTCGATACGACTTAAACCATTC-CCTTTGTA
* *
4804 TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
1 TCTTCGTGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCCT
4848 TCATATCTTC
Statistics
Matches: 118, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
98 43 0.36
99 29 0.25
100 46 0.39
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (99 bp):
TCTTCGTGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCCTCTGTATTTTCTGAGGTGTGAG
GTTCGTCGATACGACTTAAACCATTCCCTTTGTA
Found at i:4837 original size:50 final size:49
Alignment explanation
Indices: 4604--4892 Score: 181
Period size: 49 Copynumber: 5.9 Consensus size: 49
4594 GTGGCTATAA
* * * * * * *
4604 TGTCTTCGCGATACTAGATTCGCCGTTGCGGCTTAAATCTTTTCATCCG
1 TGTCTTCGAGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTCTG
* * *
4653 TG-CTTTCGAGGTACTAGG-TTCGTCGTTGCGGCTTAAACCATTCCCTTTG
1 TGTC-TTCGAGGTACT-GGATTCGTCGTTGCGGCTTAAATCTTTCCCTCTG
* * * * *
4702 TATCTTCGTGGTACTGGATTTGTCGTTACGACTTAAATCTTTCCCTCTG
1 TGTCTTCGAGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTCTG
* * * * * * * * * *
4751 TATTTTCTGAGGT-GTGAGGTTCGTCGATACGACTTAAACCTTTCTCTTTTG
1 TGTCTTC-GAGGTACTG-GATTCGTCGTTGCGGCTTAAATCTTTC-CCTCTG
* * *
4802 TGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT-TCA
1 TGTCTTCGAGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTCT-G
* * * * ** *
4851 TATCTTCGTGGTATTGAATTTTTCGTTGCGACTTAAATCTTT
1 TGTCTTCGAGGTACTGGATTCGTCGTTGCGGCTTAAATCTTT
4893 TCCTTCGTCC
Statistics
Matches: 185, Mismatches: 46, Indels: 18
0.74 0.18 0.07
Matches are distributed among these distances:
48 4 0.02
49 116 0.63
50 54 0.29
51 11 0.06
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (49 bp):
TGTCTTCGAGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTCTG
Found at i:4912 original size:49 final size:48
Alignment explanation
Indices: 4825--4949 Score: 137
Period size: 49 Copynumber: 2.6 Consensus size: 48
4815 CTGGATTCGC
* *
4825 CGTTGCGGCTTAAATCTTTCCCTTCATATCTTCGTGGTATT-GAATTTTT
1 CGTTGCGGCTTAAATCTTTCCCTTCATATCTTCATGGTATTAG-A-TTTG
* * * *
4874 CGTTGCGACTTAAATCTTTTCCTTCGT-CCTTTCATGGTATTAGATTTG
1 CGTTGCGGCTTAAATCTTTCCCTTCATATC-TTCATGGTATTAGATTTG
*
4922 CTGTTGCGGCTTAAATCTTTCCCATCAT
1 C-GTTGCGGCTTAAATCTTTCCCTTCAT
4950 GGTAATGAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
48 5 0.08
49 57 0.90
50 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (48 bp):
CGTTGCGGCTTAAATCTTTCCCTTCATATCTTCATGGTATTAGATTTG
Done.