Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013958.1 Kokia drynarioides strain JFW-HI SEQ_128988, 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: 5053
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Found at i:3660 original size:29 final size:30
Alignment explanation
Indices: 3614--3694 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
3604 CGGATCTTCG
*
3614 GGGGT-AAAATGGTAATTTTGGGAAAATTC
1 GGGGTAAAAATGGTGATTTTGGGAAAATTC
* **
3643 GGGGTAAAAATGG-GATTTTTGGAAGTTTC
1 GGGGTAAAAATGGTGATTTTGGGAAAATTC
* *
3672 GAGGTCAAAAATGGTGTTTTTGG
1 GGGGT-AAAAATGGTGATTTTGG
3695 AAGTTTAGGG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 21 0.50
30 15 0.36
31 6 0.14
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.33
Consensus pattern (30 bp):
GGGGTAAAAATGGTGATTTTGGGAAAATTC
Found at i:3762 original size:29 final size:29
Alignment explanation
Indices: 3640--3927 Score: 241
Period size: 30 Copynumber: 9.9 Consensus size: 29
3630 TTTGGGAAAA
*
3640 TTCGGGGTAAAAATGGGATTTTTGGAAGT
1 TTCGGGGTAAAAATAGGATTTTTGGAAGT
* *
3669 TTCGAGGTCAAAAAT-GGTGTTTTTGGAAGT
1 TTCGGGGT-AAAAATAGG-ATTTTTGGAAGT
* * *
3699 TTAGGGAT-AAAATAGAATTTTTGGAAGT
1 TTCGGGGTAAAAATAGGATTTTTGGAAGT
3727 TTCGGGGTAAAAAATAGGATTTTTGGAAGT
1 TTCGGGGT-AAAAATAGGATTTTTGGAAGT
* * * *
3757 TTGGGGGT----ATAGAATTTTTAGAATT
1 TTCGGGGTAAAAATAGGATTTTTGGAAGT
* * *
3782 TTTGAGGTTAAAAATGGGATTTTTGGAAGT
1 TTCG-GGGTAAAAATAGGATTTTTGGAAGT
* * *
3812 TTGGGGGTAAAAAT-GAAATTTTTGAAAGT
1 TTCGGGGTAAAAATAG-GATTTTTGGAAGT
* * * *
3841 TTCGAGGTCAAAAATAAGATTTTTAGAAAT
1 TTCGGGGT-AAAAATAGGATTTTTGGAAGT
*
3871 TTGGGGGTAAAAAT-GAGATTTTTGGAAGT
1 TTCGGGGTAAAAATAG-GATTTTTGGAAGT
*
3900 TTCGAGGTTAAAAAATAGGATTTTTGGA
1 TTCG-GGGT-AAAAATAGGATTTTTGGA
3928 CAATCTAGGG
Statistics
Matches: 204, Mismatches: 38, Indels: 32
0.74 0.14 0.12
Matches are distributed among these distances:
25 17 0.08
26 3 0.01
28 23 0.11
29 56 0.27
30 88 0.43
31 16 0.08
32 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
TTCGGGGTAAAAATAGGATTTTTGGAAGT
Found at i:3862 original size:59 final size:59
Alignment explanation
Indices: 3643--3927 Score: 323
Period size: 59 Copynumber: 4.9 Consensus size: 59
3633 GGGAAAATTC
** * * *
3643 GGGGTAAAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAAT-GGTGTTTTTGGAAGTTTA
1 GGGGTAAAAATGAAATTTTTGGAAGTTTCGAGGTAAAAAATAGG-ATTTTTGGAAGTTTG
* *
3702 GGGAT-AAAAT-AGAATTTTTGGAAGTTTCGGGGTAAAAAATAGGATTTTTGGAAGTTTG
1 GGGGTAAAAATGA-AATTTTTGGAAGTTTCGAGGTAAAAAATAGGATTTTTGGAAGTTTG
* * * * * *
3760 GGGGT--ATA-G-AATTTTTAGAATTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTG
1 GGGGTAAAAATGAAATTTTTGGAAGTTTCGAGGTAAAAAATAGGATTTTTGGAAGTTTG
* * * * *
3815 GGGGTAAAAATGAAATTTTTGAAAGTTTCGAGGTCAAAAATAAGATTTTTAGAAATTTG
1 GGGGTAAAAATGAAATTTTTGGAAGTTTCGAGGTAAAAAATAGGATTTTTGGAAGTTTG
*
3874 GGGGTAAAAATGAGATTTTTGGAAGTTTCGAGGTTAAAAAATAGGATTTTTGGA
1 GGGGTAAAAATGAAATTTTTGGAAGTTTCGAGG-TAAAAAATAGGATTTTTGGA
3928 CAATCTAGGG
Statistics
Matches: 188, Mismatches: 30, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
55 45 0.24
57 4 0.02
58 48 0.26
59 74 0.39
60 17 0.09
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (59 bp):
GGGGTAAAAATGAAATTTTTGGAAGTTTCGAGGTAAAAAATAGGATTTTTGGAAGTTTG
Found at i:4976 original size:3 final size:3
Alignment explanation
Indices: 4970--5033 Score: 67
Period size: 3 Copynumber: 21.3 Consensus size: 3
4960 ATTATTAAAA
* * *
4970 ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
* *
5016 ATT A-T ATA AAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
5034 ATAATATAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:4997 original size:34 final size:34
Alignment explanation
Indices: 4919--5000 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
4909 TTATTAAGGA
**
4919 AATATTTATTATTAATAAATATTACTCTTGTCATT
1 AATA-TTATTATTAATAAATATTACTAGTGTCATT
** *
4954 AATGCTATTATTAA-AAATTATTATTAGTGTCATT
1 AATATTATTATTAATAAA-TATTACTAGTGTCATT
*
4988 ATTATTATTATTA
1 AATATTATTATTA
5001 TTATTATTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
33 3 0.08
34 32 0.84
35 3 0.08
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (34 bp):
AATATTATTATTAATAAATATTACTAGTGTCATT
Found at i:5051 original size:24 final size:24
Alignment explanation
Indices: 5002--5053 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4992 TTATTATTAT
* *
5002 TATTATTAATTATTATTATATAAA
1 TATTATTAATAATTAATATATAAA
*
5026 TATTATTAATAATATAATA-ATCAA
1 TATTATTAATAAT-TAATATATAAA
5050 TATT
1 TATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTATTAATAATTAATATATAAA
Done.