Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000254.1 Kokia drynarioides strain JFW-HI SEQ_110991, 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: 38667
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:14492 original size:16 final size:16
Alignment explanation
Indices: 14471--14504 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
14461 ACTTAAGAAT
14471 ATTTATAATATTATTC
1 ATTTATAATATTATTC
*
14487 ATTTATAGTATTATTC
1 ATTTATAATATTATTC
14503 AT
1 AT
14505 ATCGATGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTTATAATATTATTC
Found at i:18560 original size:22 final size:22
Alignment explanation
Indices: 18532--18578 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
18522 TTTTTTGAAT
18532 TTTTTAA-AAAATATTTATATAA
1 TTTTTAATAAAATATTTA-ATAA
**
18554 TTTTTAATTTAATATTTAATAA
1 TTTTTAATAAAATATTTAATAA
18576 TTT
1 TTT
18579 AACTTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTAATAAAATATTTAATAA
Found at i:20613 original size:10 final size:11
Alignment explanation
Indices: 20591--20625 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
20581 TAAAACATGG
*
20591 TTGTTTGAATT
1 TTGTTTAAATT
20602 TTGTTT-AATT
1 TTGTTTAAATT
20612 TTGTTTAAATT
1 TTGTTTAAATT
20623 TTG
1 TTG
20626 ATGTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (11 bp):
TTGTTTAAATT
Found at i:21362 original size:29 final size:28
Alignment explanation
Indices: 21293--21369 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
21283 TTGATTAAAT
* *
21293 AAAAAAAATT-AGAGATTAAATGTAGAG
1 AAAAAAAATTAAGACATTAAAGGTAGAG
*** *
21320 AAAAAGTGTTAAGATATTAAAGGTAGAG
1 AAAAAAAATTAAGACATTAAAGGTAGAG
21348 AAAAAAACATTAAGACATTAAA
1 AAAAAAA-ATTAAGACATTAAA
21370 TGTGAGGAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 7 0.18
28 20 0.51
29 12 0.31
ACGTcount: A:0.58, C:0.03, G:0.17, T:0.22
Consensus pattern (28 bp):
AAAAAAAATTAAGACATTAAAGGTAGAG
Found at i:25669 original size:21 final size:20
Alignment explanation
Indices: 25645--25695 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
25635 GCAGTGTCAA
*
25645 TGAAATTAATTACTGTAACAG
1 TGAAATTAA-TACTATAACAG
* *
25666 TGAAATTGAATATTATAATAG
1 TGAAATT-AATACTATAACAG
25687 TGAAATTAA
1 TGAAATTAA
25696 AACCAAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAATTAATACTATAACAG
Found at i:27132 original size:7 final size:7
Alignment explanation
Indices: 27120--27158 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
27110 GTATTGAATC
27120 GAATCGT
1 GAATCGT
27127 GAATCGT
1 GAATCGT
27134 GAATCGT
1 GAATCGT
27141 GAATCGT
1 GAATCGT
27148 GAATCGT
1 GAATCGT
27155 GAAT
1 GAAT
27159 GCTAATATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (7 bp):
GAATCGT
Found at i:33477 original size:3 final size:3
Alignment explanation
Indices: 33469--33509 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
33459 GCTAATCTGC
*
33469 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT ATT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
33510 ATTTTTGTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:37640 original size:8 final size:8
Alignment explanation
Indices: 37629--37668 Score: 71
Period size: 8 Copynumber: 5.0 Consensus size: 8
37619 AGGGTTATAT
37629 AATGAGTG
1 AATGAGTG
37637 AATGAGTG
1 AATGAGTG
37645 AATGAGTG
1 AATGAGTG
37653 AATGAGTG
1 AATGAGTG
*
37661 AAGGAGTG
1 AATGAGTG
37669 TCGGTGCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.23
Consensus pattern (8 bp):
AATGAGTG
Found at i:38460 original size:11 final size:11
Alignment explanation
Indices: 38444--38477 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
38434 GGGGGGGACC
*
38444 AAGGAAAAATG
1 AAGGAAAAAAG
38455 AAGGAAAAAAG
1 AAGGAAAAAAG
*
38466 AAAGAAAAAAG
1 AAGGAAAAAAG
38477 A
1 A
38478 GAAAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (11 bp):
AAGGAAAAAAG
Found at i:38473 original size:21 final size:21
Alignment explanation
Indices: 38449--38508 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 21
38439 GGACCAAGGA
38449 AAAATGAAGGAAA-AAAGAAAG
1 AAAA-GAAGGAAAGAAAGAAAG
38470 AAAA-AAGAGAAAGAAAGAAAG
1 AAAAGAAG-GAAAGAAAGAAAG
38491 AAGAAGGAAGGAGAAGAA
1 AA-AA-GAAGGA-AAGAA
38509 GGGGAAGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 14 0.42
22 2 0.06
23 2 0.06
24 8 0.24
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (21 bp):
AAAAGAAGGAAAGAAAGAAAG
Found at i:38484 original size:17 final size:17
Alignment explanation
Indices: 38462--38494 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38452 ATGAAGGAAA
38462 AAAGAAAGAAAAAAGAG
1 AAAGAAAGAAAAAAGAG
*
38479 AAAGAAAGAAAGAAGA
1 AAAGAAAGAAAAAAGA
38495 AGGAAGGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAG
Done.