Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007968.1 Kokia drynarioides strain JFW-HI SEQ_122616, 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: 8702
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Found at i:5983 original size:149 final size:151
Alignment explanation
Indices: 5704--6004 Score: 464
Period size: 149 Copynumber: 2.0 Consensus size: 151
5694 CTTAGCAAAA
*
5704 TAAAATGTATGCTTTTTTAATGCTTAAATGTATAGCAAAGAATAATTACTTAACTAAAATAAAAT
1 TAAAATGTATGCTTTTTTAATGCTTAAATGTAGAGCAAAGAATAATTACTTAACTAAAATAAAAT
* * * *
5769 GTATGCTATTTGAATGGATTGATTCAGTGATTTGACAGTTGGATAATTTTGATAATGTTTTAAGA
66 GTATGCTATTTGAATGGATTGATTCAGTGATTCGACAGTTGGATAATTCTGATAATATTTCAAGA
5834 TAATACATAACTATCGTGACT
131 TAATACATAACTATCGTGACT
*
5855 TAAAATGTATG-TTGTTTTAATGCTTAAATGT-GA-CAAAGAATAATTACTTAATTAAAATAAAA
1 TAAAATGTATGCTT-TTTTAATGCTTAAATGTAGAGCAAAGAATAATTACTTAACTAAAATAAAA
* * *
5917 TGTATTCTGTTTGAATGGATTGATTCAGTGATTCGACGGTTGGATAATTCTGATAATATTTCAAG
65 TGTATGCTATTTGAATGGATTGATTCAGTGATTCGACAGTTGGATAATTCTGATAATATTTCAAG
* * *
5982 ATAATACATGATTGTCGTGACT
130 ATAATACATAACTATCGTGACT
6004 T
1 T
6005 GTTGTTAGAA
Statistics
Matches: 137, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
149 106 0.77
150 3 0.02
151 28 0.20
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (151 bp):
TAAAATGTATGCTTTTTTAATGCTTAAATGTAGAGCAAAGAATAATTACTTAACTAAAATAAAAT
GTATGCTATTTGAATGGATTGATTCAGTGATTCGACAGTTGGATAATTCTGATAATATTTCAAGA
TAATACATAACTATCGTGACT
Found at i:7578 original size:96 final size:96
Alignment explanation
Indices: 7394--7585 Score: 232
Period size: 96 Copynumber: 2.0 Consensus size: 96
7384 TTCTTGCGAA
** *
7394 AAGGATATTCGATTATCTCGATTTATAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTATAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
7459 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * *
7490 AAGGGTATTCGATTATTTCGATTTGA-AGAAAAATTGCACCTAGTGAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATCTCGATTT-ATAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTT
*
7553 C-GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
64 CAG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
7586 TTAAAACTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
95 3 0.04
96 74 0.89
97 6 0.07
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTATAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:7905 original size:30 final size:29
Alignment explanation
Indices: 7870--8022 Score: 113
Period size: 29 Copynumber: 5.2 Consensus size: 29
7860 GTAAAAGAGT
*
7870 AATTTTGAGAGTTTCGAGGTCGAAAATGG
1 AATTTTGAGAGTTTCGAGGTCAAAAATGG
**
7899 AGATTTT-AGAGGTTT-GAGGGAAAAAATGG
1 A-ATTTTGAGA-GTTTCGAGGTCAAAAATGG
*
7928 AATTTTTG-GAAGTTTCGGGGTCAAAAATGG
1 AA-TTTTGAG-AGTTTCGAGGTCAAAAATGG
* *
7958 AATTTTTG-GAAGTTTGGGGGT-AAAAATGG
1 AA-TTTTGAG-AGTTTCGAGGTCAAAAATGG
7987 AATTTTTG-GAAGTTTCG-GGATCAAAAATGG
1 AA-TTTTGAG-AGTTTCGAGG-TCAAAAATGG
*
8017 GATTTT
1 AATTTT
8023 TGGAAGTTCA
Statistics
Matches: 107, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
28 3 0.03
29 54 0.50
30 50 0.47
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (29 bp):
AATTTTGAGAGTTTCGAGGTCAAAAATGG
Found at i:7942 original size:59 final size:60
Alignment explanation
Indices: 7879--8120 Score: 296
Period size: 59 Copynumber: 4.1 Consensus size: 60
7869 TAATTTTGAG
* * * * *
7879 AGTTTCGAGGTCGAAAATGGAGA-TTTTAGAGGTTTGAGGGAAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGAGATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
*
7938 AGTTTCGGGGTCAAAAATGGA-ATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGAGATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
* * *
7997 AGTTTCGGGATCAAAAATGG-GATTTTTGGAAG-TTCAGGGGTAAAAATGGGATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGAGATTTTTGGAAGTTTGA-GGGTAAAAATGGAATTTTTGGA
* * * ** *
8056 AGTTTTGGGGTCAAAAAT-GAGATTTTTGGAAGTTCGGGGGTAAAAACAGAATTTTTTGA
1 AGTTTCGGGGTCAAAAATGGAGATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
8115 CAGTTT
1 -AGTTT
8121 AGGGACCTTC
Statistics
Matches: 158, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
58 4 0.03
59 148 0.94
60 6 0.04
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (60 bp):
AGTTTCGGGGTCAAAAATGGAGATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
Found at i:8023 original size:30 final size:30
Alignment explanation
Indices: 7920--8120 Score: 252
Period size: 30 Copynumber: 6.8 Consensus size: 30
7910 GTTTGAGGGA
7920 AAAAATGGAATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTC
*
7950 AAAAATGGAATTTTTGGAAGTTTGGGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTC
*
7979 AAAAATGGAATTTTTGGAAGTTTCGGGATC
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTC
*
8009 AAAAATGGGATTTTTGGAAG-TTCAGGGGT-
1 AAAAATGGAATTTTTGGAAGTTTC-GGGGTC
* *
8038 AAAAATGGGATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTC
8068 AAAAAT-GAGATTTTTGGAAG-TTCGGGGGT-
1 AAAAATGGA-ATTTTTGGAAGTTTC-GGGGTC
** *
8097 AAAAACAGAATTTTTTGACAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
8121 AGGGACCTTC
Statistics
Matches: 152, Mismatches: 10, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
29 71 0.47
30 79 0.52
31 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTCGGGGTC
Done.