Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009822.1 Kokia drynarioides strain JFW-HI SEQ_124543, 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: 35516
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:14093 original size:26 final size:27
Alignment explanation
Indices: 14057--14110 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
14047 TGAGAATATT
*
14057 TCTCATGTT-AAAAAAATTCAACTTGG
1 TCTCATGTTAAAAAAAAATCAACTTGG
14083 TCTCATGTTAAAAAAAAATCAACTTGG
1 TCTCATGTTAAAAAAAAATCAACTTGG
14110 T
1 T
14111 TTTATTTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (27 bp):
TCTCATGTTAAAAAAAAATCAACTTGG
Found at i:17572 original size:45 final size:45
Alignment explanation
Indices: 17498--17656 Score: 178
Period size: 45 Copynumber: 3.5 Consensus size: 45
17488 GTTCAATACC
* *
17498 TCATAATGTCTTTCAACTATGATCTTATTCATTTCGGATATAGTG
1 TCATAATGTCTTTCAACTATGGTCTTATTCATTTCGAATATAGTG
* * *
17543 CCATAGTGTCTTTCAACTATGGTCGTATTCATTTTC-AATATAGTG
1 TCATAATGTCTTTCAACTATGGTCTTATTCA-TTTCGAATATAGTG
* * *
17588 TCATAATG-CTTTCAACAATGGTCTTATTAATTTCCGATATATAATG
1 TCATAATGTCTTTCAACTATGGTCTTATTCATTT-CGA-ATATAGTG
* * *
17634 TCATAGTGCCTTTTAACTATGGT
1 TCATAATGTCTTTCAACTATGGT
17657 TTTTTTCGTT
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
43 3 0.03
44 20 0.21
45 42 0.44
46 18 0.19
47 12 0.13
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (45 bp):
TCATAATGTCTTTCAACTATGGTCTTATTCATTTCGAATATAGTG
Found at i:24600 original size:39 final size:40
Alignment explanation
Indices: 24546--24621 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
24536 CACTCAATGG
*
24546 ACATCTTTTGAAGAGTCACAACCC-TTTCAAATTGGATGA
1 ACATCTTTCGAAGAGTCACAACCCTTTTCAAATTGGATGA
*
24585 ACATCTTTCGAAGAGTCACAACCCTTTTCATATTGGA
1 ACATCTTTCGAAGAGTCACAACCCTTTTCAAATTGGA
24622 CGTACCCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 23 0.68
40 11 0.32
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (40 bp):
ACATCTTTCGAAGAGTCACAACCCTTTTCAAATTGGATGA
Found at i:24638 original size:39 final size:39
Alignment explanation
Indices: 24555--24631 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
24545 GACATCTTTT
* * *
24555 GAAGAGTCACAACCCTTTCAAATTGGATGAACATCTTTC
1 GAAGAGTCACAACCCTTTCAAATTGGACGAACACCCTTC
* *
24594 GAAGAGTCACAACCCTTTTCATATTGGACGTAC-CCCTT
1 GAAGAGTCACAACCC-TTTCAAATTGGACGAACACCCTT
24632 GAAAGAGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 18 0.56
40 14 0.44
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (39 bp):
GAAGAGTCACAACCCTTTCAAATTGGACGAACACCCTTC
Found at i:29496 original size:39 final size:40
Alignment explanation
Indices: 29442--29521 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
29432 TATGCATTCA
29442 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
* *
29481 ATGGACACCTTTTGAAGAGTCATAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
29521 A
1 A
29522 CATACCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:29537 original size:39 final size:38
Alignment explanation
Indices: 29446--29538 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 38
29436 CATTCAATGG
* *
29446 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGG
1 ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGA-GC
* * *
29485 ACACCTTTTGAAGAGTCATAACCCTTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACCC-TTTCAAATTGGAGC
*
29523 ATACCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
29539 ACTTGTCCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 5 0.11
39 31 0.66
40 11 0.23
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:30651 original size:17 final size:18
Alignment explanation
Indices: 30619--30661 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
30609 AAAATAAAAT
*
30619 ATATATTTTATATTTTAA
1 ATATTTTTTATATTTTAA
30637 ATATTTTTTAT-TTTTAA
1 ATATTTTTTATATTTTAA
*
30654 AAATTTTT
1 ATATTTTT
30662 GCCACGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTTTTTATATTTTAA
Found at i:31851 original size:25 final size:25
Alignment explanation
Indices: 31819--31878 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
31809 TCACTAAGTT
31819 AAAAATAAAATATTTATTTTCCCTA
1 AAAAATAAAATATTTATTTTCCCTA
31844 AAAAATAAAATATTTATTTTCCCTA
1 AAAAATAAAATATTTATTTTCCCTA
31869 AAAAATAAAA
1 AAAAATAAAA
31879 CACATAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAAATAAAATATTTATTTTCCCTA
Found at i:34518 original size:3 final size:3
Alignment explanation
Indices: 34510--34539 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
34500 CTACAATCTC
34510 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
34540 TCTTAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.