Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007934.1 Kokia drynarioides strain JFW-HI SEQ_122579, 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: 45207
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:10632 original size:2 final size:2
Alignment explanation
Indices: 10625--10649 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10615 CGAAGTTTAC
10625 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10650 AAAGCACTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18030 original size:22 final size:21
Alignment explanation
Indices: 18005--18047 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
17995 TCGGATTTTC
18005 AAAAATCTTAAAATATATATTT
1 AAAAATCTTAAAATATA-ATTT
* *
18027 AAAAATGTTAAATTATAATTT
1 AAAAATCTTAAAATATAATTT
18048 TTGAAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAAATCTTAAAATATAATTT
Found at i:21640 original size:19 final size:19
Alignment explanation
Indices: 21616--21652 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21606 CATGTTTTCT
21616 ATTTTATAATTTTTAAATC
1 ATTTTATAATTTTTAAATC
**
21635 ATTTTATTTTTTTTAAAT
1 ATTTTATAATTTTTAAAT
21653 TTAATCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTATAATTTTTAAATC
Found at i:21760 original size:12 final size:12
Alignment explanation
Indices: 21743--21767 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21733 TAGGTAGGTA
21743 ATTTTTCTTTTT
1 ATTTTTCTTTTT
21755 ATTTTTCTTTTT
1 ATTTTTCTTTTT
21767 A
1 A
21768 ATCAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTCTTTTT
Found at i:24905 original size:31 final size:31
Alignment explanation
Indices: 24870--24932 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
24860 AAGAGCTCAA
*
24870 TAACTTATATAAAAACTTTTAAATAGTTCAG
1 TAACTTAAATAAAAACTTTTAAATAGTTCAG
* * *
24901 TAACTTAAATGAAAATTTTTTAATAGTTCAG
1 TAACTTAAATAAAAACTTTTAAATAGTTCAG
24932 T
1 T
24933 GATAATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (31 bp):
TAACTTAAATAAAAACTTTTAAATAGTTCAG
Found at i:25879 original size:25 final size:26
Alignment explanation
Indices: 25836--25884 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
25826 TTTATTTGGT
* * *
25836 TTTTTAGATTTTTTTTTTATTTATGA
1 TTTTTAGATTATTTATTTAATTATGA
25862 TTTTTA-ATTATTTATTTAATTAT
1 TTTTTAGATTATTTATTTAATTAT
25885 TGTTGATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTTTAGATTATTTATTTAATTATGA
Found at i:31333 original size:3 final size:3
Alignment explanation
Indices: 31325--31351 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31315 GCATGATTAA
31325 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
31352 GATGCAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37154 original size:19 final size:19
Alignment explanation
Indices: 37130--37166 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
37120 TTTCAACATT
*
37130 AAAAAACAA-AAATTAAAA
1 AAAAAAAAAGAAATTAAAA
37148 AAAAAAAAAGAAATTAAAA
1 AAAAAAAAAGAAATTAAAA
37167 GTAAAGATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAGAAATTAAAA
Found at i:42576 original size:21 final size:21
Alignment explanation
Indices: 42537--42577 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42527 ATCAACGAAC
*
42537 GTAAAATAATTTATTTTTTTT
1 GTAAAATAATTTATATTTTTT
* *
42558 GTAAAATGATTTGTATTTTT
1 GTAAAATAATTTATATTTTT
42578 GAAAAACGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (21 bp):
GTAAAATAATTTATATTTTTT
Found at i:42825 original size:12 final size:12
Alignment explanation
Indices: 42784--42825 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
42774 TTTAGTCACA
42784 TAATAAATTATT
1 TAATAAATTATT
**
42796 TAATTTATTATTT
1 TAATAAATTA-TT
42809 TAATAAATTATT
1 TAATAAATTATT
42821 TAATA
1 TAATA
42826 TTTCGATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATAAATTATT
Found at i:42892 original size:20 final size:21
Alignment explanation
Indices: 42864--42906 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
42854 AATAATATTC
* *
42864 TTAACATATTATTAA-AAATA
1 TTAAAATATTAATAATAAATA
42884 TTAAAATATTAATAATAAATA
1 TTAAAATATTAATAATAAATA
42905 TT
1 TT
42907 TTGTAGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATATTAATAATAAATA
Found at i:43681 original size:5 final size:5
Alignment explanation
Indices: 43671--43708 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
43661 ACATGTACGA
43671 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTT
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTT
43709 ACCCAAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
TTTCC
Done.