Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015221.1 Kokia drynarioides strain JFW-HI SEQ_130265, 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: 81301
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 292 characters in sequence are not A, C, G, or T
Found at i:11858 original size:20 final size:19
Alignment explanation
Indices: 11833--11885 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
11823 TTTTTTTTAT
11833 TTTTAAAAATATTTATATAA
1 TTTTAAAAATATTTA-ATAA
*
11853 TTTTAATTCAATATTTAATAA
1 TTTTAA--AAATATTTAATAA
11874 -TTT-AAAATATTT
1 TTTTAAAAATATTT
11886 TTATTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 7 0.24
19 1 0.03
20 9 0.31
21 4 0.14
22 8 0.28
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAAAATATTTAATAA
Found at i:28173 original size:20 final size:19
Alignment explanation
Indices: 28148--28186 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
28138 TAAGAGAGTT
28148 TTTTTCAGAAAATCAATTCA
1 TTTTTC-GAAAATCAATTCA
* *
28168 TTTTTCGTAAATCATTTCA
1 TTTTTCGAAAATCAATTCA
28187 CGAAAGTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (19 bp):
TTTTTCGAAAATCAATTCA
Found at i:29165 original size:2 final size:2
Alignment explanation
Indices: 29158--29193 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29148 ACTTATAATT
29158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29194 AAGAATAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43786 original size:23 final size:23
Alignment explanation
Indices: 43727--43856 Score: 105
Period size: 23 Copynumber: 5.9 Consensus size: 23
43717 GAGAGTACTG
* *
43727 AAGTACTAAACAGAGAGCACA-T
1 AAGTGCTAAACAGAGAGCACACA
*
43749 AAGTGCTGGGCAACAGAGAGCACACA
1 AAGTGCT---AAACAGAGAGCACACA
*
43775 AAGTGCTAAACAGAGAGTACACA
1 AAGTGCTAAACAGAGAGCACACA
*
43798 AA--G-T--AC--TGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
*
43814 AAGTGCTAATCAGAGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
43837 CAGTGCTAATCAGAGAGCAC
1 AAGTGCTAAACAGAGAGCAC
43857 GAGACATGTT
Statistics
Matches: 87, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
16 10 0.11
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 6 0.07
23 44 0.51
25 13 0.15
26 7 0.08
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AAGTGCTAAACAGAGAGCACACA
Found at i:43873 original size:23 final size:23
Alignment explanation
Indices: 43805--43877 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
43795 ACAAAGTACT
* *
43805 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAAACAGA
*
43828 GAGCACACACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAAACAGA
* *
43851 GAGCACGAGACA-TGTTAAACAGA
1 GAGCAC-ACACAGTGCTAAACAGA
43874 GAGC
1 GAGC
43878 GCGCTAGTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (23 bp):
GAGCACACACAGTGCTAAACAGA
Found at i:56372 original size:21 final size:21
Alignment explanation
Indices: 56348--56391 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56338 TTATATATGT
*
56348 TTAATTAAGC-TTTAGTTAATC
1 TTAATTAA-CTTTTAATTAATC
56369 TTAATTAACTTTTAATTAATC
1 TTAATTAACTTTTAATTAATC
56390 TT
1 TT
56392 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (21 bp):
TTAATTAACTTTTAATTAATC
Found at i:64828 original size:16 final size:16
Alignment explanation
Indices: 64808--64839 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
64798 TGAAAAAATG
64808 AAAAATCAAAAATACAT
1 AAAAA-CAAAAATACAT
64825 AAAAACAAAAATACA
1 AAAAACAAAAATACA
64840 CACATGCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAACAAAAATACAT
Found at i:71564 original size:54 final size:54
Alignment explanation
Indices: 71447--71592 Score: 276
Period size: 54 Copynumber: 2.7 Consensus size: 54
71437 TCAAATCTAT
*
71447 TTAACGATTTGAGTTTAATTAAGAAGAAATACTTG-AAAAAACACACACACGAA
1 TTAATGATTTGAGTTTAATTAAGAAGAAATACTTGAAAAAAACACACACACGAA
71500 TTAATGATTTGAGTTTAATTAAGAAGAAATACTTGAAAAAAACACACACACGAA
1 TTAATGATTTGAGTTTAATTAAGAAGAAATACTTGAAAAAAACACACACACGAA
71554 TTAATGATTTGAGTTTAATTAAGAAGAAATACTTGAAAA
1 TTAATGATTTGAGTTTAATTAAGAAGAAATACTTGAAAA
71593 GAAAAAACAA
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
53 34 0.37
54 57 0.63
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.28
Consensus pattern (54 bp):
TTAATGATTTGAGTTTAATTAAGAAGAAATACTTGAAAAAAACACACACACGAA
Done.