Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003013.1 Kokia drynarioides strain JFW-HI SEQ_115525, 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: 34627
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:5870 original size:22 final size:22
Alignment explanation
Indices: 5829--5871 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5819 AAGTTTCTGT
**
5829 ATTTTTTTAGTTTTGGAATTTA
1 ATTTTTTTAGTTTTCAAATTTA
5851 ATTTTTTTAGTTTTCAAATTT
1 ATTTTTTTAGTTTTCAAATTT
5872 CAAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.65
Consensus pattern (22 bp):
ATTTTTTTAGTTTTCAAATTTA
Found at i:7901 original size:2 final size:2
Alignment explanation
Indices: 7894--7926 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7884 TGACTTTTAT
7894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7927 TATTTTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17342 original size:16 final size:17
Alignment explanation
Indices: 17308--17342 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17298 ATTAATTCTA
*
17308 AAAAATATTTTTGAGAT
1 AAAAATATTTTTGAAAT
17325 AAAAATATTTTT-AAAT
1 AAAAATATTTTTGAAAT
17341 AA
1 AA
17343 GTTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (17 bp):
AAAAATATTTTTGAAAT
Found at i:17684 original size:6 final size:7
Alignment explanation
Indices: 17668--17696 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
17658 AAACAATCCC
17668 AAAAAGA
1 AAAAAGA
17675 AAAAAGA
1 AAAAAGA
17682 AAAAAGA
1 AAAAAGA
17689 AAAAAGA
1 AAAAAGA
17696 A
1 A
17697 TTGACCTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:18582 original size:2 final size:2
Alignment explanation
Indices: 18575--18600 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18565 ACCATTGAAC
18575 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
18601 GATGTCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18797 original size:43 final size:42
Alignment explanation
Indices: 18743--18872 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 42
18733 TTTTTCTATC
* *
18743 CACGGGATTTGAACTCAAGATTTTAGTAGAGGTATATTAAACT
1 CACGAGATTTGAACTCGAGATTTTAGTAGAGG-ATATTAAACT
* *
18786 CACGAGATTTGAACTTGAGATTTTAGTAAAGAGATATTAAACT
1 CACGAGATTTGAACTCGAGATTTTAGTAGAG-GATATTAAACT
* * * *
18829 CATGTGATTTGAACCCGAGTTTTTAGT-GAAGGGATATTAAACT
1 CACGAGATTTGAACTCGAGATTTTAGTAG-A-GGATATTAAACT
18872 C
1 C
18873 CTTACCGCTT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 72 0.97
44 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (42 bp):
CACGAGATTTGAACTCGAGATTTTAGTAGAGGATATTAAACT
Found at i:23545 original size:158 final size:159
Alignment explanation
Indices: 23257--23575 Score: 622
Period size: 158 Copynumber: 2.0 Consensus size: 159
23247 TCATGGCAGG
23257 CAAACTAATTTTGTAAATCCAGTCCCATAAATTTGAAACTTACTAAGAAAAAATCCAATAAAGGG
1 CAAACTAATTTTGTAAATCCAGTCCCATAAATTTGAAACTTACTAAGAAAAAATCCAATAAAGGG
23322 ACTAAAATAAGACGAAATAATAAAAATTTTACTCCCATTGAACTGATGCCACAAATTTACAAACA
66 ACTAAAATAAGACGAAATAATAAAAATTTTACTCCCATTGAACTGATGCCACAAATTTACAAACA
*
23387 AAA-CCATCCTCCGGATAATCAAAATTAC
131 AAACCCATCCTCCAGATAATCAAAATTAC
23415 CAAACTAATTTTGTAAATCCAGTCCCATAAATTTGAAACTTACTAAGAAAAAATCCAATAAAGGG
1 CAAACTAATTTTGTAAATCCAGTCCCATAAATTTGAAACTTACTAAGAAAAAATCCAATAAAGGG
23480 ACTAAAATAAGACGAAATAATAAAAATTTTACTCCCATTGAACTGATGCCACAAATTTACAAACA
66 ACTAAAATAAGACGAAATAATAAAAATTTTACTCCCATTGAACTGATGCCACAAATTTACAAACA
23545 AAACCCATCCTCCAGATAATCAAAATTAC
131 AAACCCATCCTCCAGATAATCAAAATTAC
23574 CA
1 CA
23576 CCTAACTGCT
Statistics
Matches: 159, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
158 133 0.84
159 26 0.16
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (159 bp):
CAAACTAATTTTGTAAATCCAGTCCCATAAATTTGAAACTTACTAAGAAAAAATCCAATAAAGGG
ACTAAAATAAGACGAAATAATAAAAATTTTACTCCCATTGAACTGATGCCACAAATTTACAAACA
AAACCCATCCTCCAGATAATCAAAATTAC
Done.