Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007002.1 Kokia drynarioides strain JFW-HI SEQ_121608, 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: 21173
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2003 original size:2 final size:2
Alignment explanation
Indices: 1996--2020 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1986 TTTTAAACTT
1996 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 T
2021 GGCATAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4443 original size:21 final size:21
Alignment explanation
Indices: 4418--4466 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4408 ATAAATATAT
4418 AAATAAATCATGAAGTTAAA-A
1 AAATAAATC-TGAAGTTAAAGA
* * *
4439 AAATAACTCTTAATTTAAAGA
1 AAATAAATCTGAAGTTAAAGA
4460 AAATAAA
1 AAATAAA
4467 CTAACTATCC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (21 bp):
AAATAAATCTGAAGTTAAAGA
Found at i:7010 original size:18 final size:16
Alignment explanation
Indices: 6987--7020 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
6977 TAAAAGAAGT
6987 TTAAAATTGAAATGAAAA
1 TTAAAATT-AAAT-AAAA
7005 TTAAAATTAAATAAAA
1 TTAAAATTAAATAAAA
7021 AGAGATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
TTAAAATTAAATAAAA
Found at i:7453 original size:14 final size:14
Alignment explanation
Indices: 7434--7460 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7424 ATCCCCAATT
7434 TACTAACTCGATTC
1 TACTAACTCGATTC
7448 TACTAACTCGATT
1 TACTAACTCGATT
7461 TTTGGGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (14 bp):
TACTAACTCGATTC
Found at i:20751 original size:304 final size:299
Alignment explanation
Indices: 20207--20770 Score: 898
Period size: 304 Copynumber: 1.9 Consensus size: 299
20197 AACAAGTCTC
*
20207 GATTTATAATTTGGAAAATGAAAATGGAGTCGCCAATAAATTTTTTAAAACAGGTGTAATTGGGT
1 GATTTATAATTTGGAAAATGAAAATGGAGTCGCCAATAAATTTTTTAAAACAGGTGTAATTGGAT
* *
20272 CACCTTTCGAGATTTTTTTAAAAATCATTAAAATAATTTTGGTATTTGAAACCATAAAACGAGTT
66 CACATTTCGAGATTTTTTTAAAAATCATTAAAATAATTTTGGTATTTGAAACCATAAAACGAGCT
* * * * *
20337 TGAGAGTCGGTTACGAATAAGGAATGATTAGCACCCTTACATGCTTAAAATTGGTACCTAATCGA
131 CGAGAGTCGGTTACGAATAAGGAATGATTAACACCCTTACACGCTCAAAATTGATACCTAATCGA
* *
20402 TTATTCAAAATCTTATTTGTTGAAAACTAAAAATTTGAGAAAAATTTAAATCGCAATCCTTAAAT
196 TTATTCAAAATCTTATTTATTGAAAACTAAAAATTCGAGAAAAATTTAAATCGCAATCCTTAAAT
20467 ACATGTGTCGAAACCATTTTTTTTGAAAAAAAAAGTTTT
261 ACATGTGTCGAAACCATTTTTTTTGAAAAAAAAAGTTTT
* *
20506 GATTTATATTTTGGAAAATGAAAATGGAGTCGCCACCAATAAATTTTTTTAAAATAGGTGTAATT
1 GATTTATAATTTGGAAAATGAAAATGGAGTCG---CCAATAAA-TTTTTTAAAACAGGTGTAATT
* * * *
20571 GGATCATATTTCGAGATTTTTTTAAAAAATCATTAAAATAATTTTGTTCTTTGAAACCATAAAAT
62 GGATCACATTTCGAGATTTTTTT-AAAAATCATTAAAATAATTTTGGTATTTGAAACCATAAAAC
20636 GAGCTCGAGAGTCGGTTAC-ACATAAGGAATGATTAACACCCTTACACG-TCCAAAATTGATACC
126 GAGCTCGAGAGTCGGTTACGA-ATAAGGAATGATTAACACCCTTACACGCT-CAAAATTGATACC
*
20699 TAATCGATTATTCAAAATCTTATTTATTGAAAACTAAAAATTCGAGAAAAATTTAAATCGCGATC
189 TAATCGATTATTCAAAATCTTATTTATTGAAAACTAAAAATTCGAGAAAAATTTAAATCGCAATC
20764 CTTAAAT
254 CTTAAAT
20771 GTATGAACGT
Statistics
Matches: 241, Mismatches: 17, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
299 31 0.13
302 8 0.03
303 42 0.17
304 160 0.66
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (299 bp):
GATTTATAATTTGGAAAATGAAAATGGAGTCGCCAATAAATTTTTTAAAACAGGTGTAATTGGAT
CACATTTCGAGATTTTTTTAAAAATCATTAAAATAATTTTGGTATTTGAAACCATAAAACGAGCT
CGAGAGTCGGTTACGAATAAGGAATGATTAACACCCTTACACGCTCAAAATTGATACCTAATCGA
TTATTCAAAATCTTATTTATTGAAAACTAAAAATTCGAGAAAAATTTAAATCGCAATCCTTAAAT
ACATGTGTCGAAACCATTTTTTTTGAAAAAAAAAGTTTT
Found at i:21155 original size:18 final size:17
Alignment explanation
Indices: 21108--21156 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
21098 ATTTACAGGT
21108 ATAAATAATAAAAAAACA
1 ATAAATAAT-AAAAAACA
* *
21126 ATATATACATAAAATACA
1 ATAAATA-ATAAAAAACA
21144 ATAAGATAATAAA
1 ATAA-ATAATAAA
21157 TTGAGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (17 bp):
ATAAATAATAAAAAACA
Done.