Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013063.1 Kokia drynarioides strain JFW-HI SEQ_128081, 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: 40542
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:509 original size:23 final size:23
Alignment explanation
Indices: 483--630 Score: 181
Period size: 23 Copynumber: 6.3 Consensus size: 23
473 ACACTAGCGC
483 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
506 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
*
529 GCTCTCTGTTATTAGCATTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
554 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
577 GCTCTCTGACTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
600 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
623 GCTCTCTG
1 GCTCTCTG
631 TTGCCCAGCA
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
22 3 0.03
23 84 0.79
25 16 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:551 original size:46 final size:47
Alignment explanation
Indices: 483--658 Score: 164
Period size: 48 Copynumber: 3.8 Consensus size: 47
473 ACACTAGCGC
483 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCT-GT
* * * *
529 GCTCTCTGTTATTAGCATTGTGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTTAGCAC-GTCTGT
* * * * *
577 GCTCTCTG--ACTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTTAGCAC-GTCTGT
*** *
623 GCTCTCTGTTGCCCAGCACT-TATGTGCTCTCTGTTT
1 GCTCTCTGTT-ATTAGCACTGTGTGTGCTCTCTGTTT
659 GTTCCGTATA
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
46 47 0.44
48 53 0.49
49 8 0.07
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (47 bp):
GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTGT
Found at i:631 original size:23 final size:23
Alignment explanation
Indices: 483--658 Score: 176
Period size: 23 Copynumber: 7.5 Consensus size: 23
473 ACACTAGCGC
*
483 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
506 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
*
529 GCTCTCTGTTATTAGCATTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* *
554 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
** * *
577 GCTCTCTGACTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
600 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
623 GCTCTCTGTTGCCCAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
648 GCTCTCTGTTT
1 GCTCTCTGTTT
659 GTTCCGTATA
Statistics
Matches: 128, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.02
23 85 0.66
24 1 0.01
25 30 0.23
26 9 0.07
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:3441 original size:17 final size:18
Alignment explanation
Indices: 3432--3466 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3422 ATTTTAATAG
3432 ATTTAATA-TTAAATTAA
1 ATTTAATATTTAAATTAA
*
3449 ATTTAATATTTATATTAA
1 ATTTAATATTTAAATTAA
3467 TAGTATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAATATTTAAATTAA
Found at i:7779 original size:17 final size:17
Alignment explanation
Indices: 7757--7804 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
7747 AATGCACTAA
*
7757 AATGCAATGACAATGGG
1 AATGCAATGACAATGCG
*
7774 AATGCAATGGCAATGCG
1 AATGCAATGACAATGCG
**
7791 AATATAATGACAAT
1 AATGCAATGACAAT
7805 ACTTACTAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (17 bp):
AATGCAATGACAATGCG
Found at i:7951 original size:15 final size:17
Alignment explanation
Indices: 7921--7953 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7911 TGGTGCTTTT
7921 TCTTCCTTCTCTTATTC
1 TCTTCCTTCTCTTATTC
7938 TCTTCCTT-TC-TATTC
1 TCTTCCTTCTCTTATTC
7953 T
1 T
7954 TCTTATCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (17 bp):
TCTTCCTTCTCTTATTC
Found at i:27577 original size:64 final size:65
Alignment explanation
Indices: 27462--27583 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 65
27452 ACTCAAAATC
* * * * *
27462 CTTTTGGTTTCAAGACGCCCTTTGCGGGTTTTCGTCTTGACCTCTCATTTTTCTTTTTCTTTTTT
1 CTTTGGGTTTCAAGACGCCCTTTACGGGTTTTCATCTCGACCTCTCATTTTTATTTTTCTTTTTT
* * *
27527 CTTTGGGTTTCAAGATGCCTTTTATGGGTTTTCATCTCGACC-C-CATTTTTTATTTTT
1 CTTTGGGTTTCAAGACGCCCTTTACGGGTTTTCATCTCGACCTCTCA-TTTTTATTTTT
27584 TTAGGCAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 2 0.04
64 11 0.23
65 35 0.73
ACGTcount: A:0.11, C:0.21, G:0.16, T:0.52
Consensus pattern (65 bp):
CTTTGGGTTTCAAGACGCCCTTTACGGGTTTTCATCTCGACCTCTCATTTTTATTTTTCTTTTTT
Found at i:28839 original size:3 final size:3
Alignment explanation
Indices: 28831--28863 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28821 GGTCATCCCT
28831 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
28864 AATGTCATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Done.