Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007086.1 Kokia drynarioides strain JFW-HI SEQ_121695, 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: 52126
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:66 original size:17 final size:16
Alignment explanation
Indices: 44--77 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34 TTTTTAAAAA
*
44 AATATTTATATTATTTT
1 AATATTTA-ATAATTTT
61 AATATTTAATAATTTT
1 AATATTTAATAATTTT
77 A
1 A
78 TATCTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATATTTAATAATTTT
Found at i:3400 original size:28 final size:27
Alignment explanation
Indices: 3369--3449 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 27
3359 ATAGCCTTTG
3369 TGGCGAACTCTGAAAAGAAATACCCTT-A
1 TGGCGAACTCTGAAAAGAAA-A-CCTTCA
* * * *
3397 TGGC-ACACACTAAAAAGACAACCTTCG
1 TGGCGA-ACTCTGAAAAGAAAACCTTCA
*
3424 TGGCGAAATCTGAAAAGAATAACCTT
1 TGGCGAACTCTGAAAAGAA-AACCTT
3450 GTGGCATACT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
26 4 0.10
27 15 0.37
28 22 0.54
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (27 bp):
TGGCGAACTCTGAAAAGAAAACCTTCA
Found at i:4544 original size:23 final size:23
Alignment explanation
Indices: 4480--4544 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
4470 AACGCTCTGT
* *
4480 AAAGCCTTTGTGGCATATTTTGT
1 AAAGCCTTTGTGGCATATTTCGC
* * **
4503 GAAG-GTTGTGTGGTGTATTTCGC
1 AAAGCCTT-TGTGGCATATTTCGC
4526 AAAGCCTTTGTGGCATATT
1 AAAGCCTTTGTGGCATATT
4545 CGGTAGTATT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
22 2 0.07
23 26 0.87
24 2 0.07
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (23 bp):
AAAGCCTTTGTGGCATATTTCGC
Found at i:9333 original size:26 final size:26
Alignment explanation
Indices: 9292--9354 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
9282 GTTACTTGAG
9292 TCAA-CTCAAATAAGTAATTCGAATT
1 TCAAGCTCAAATAAGTAATTCGAATT
* * *
9317 TCGAGTTCAAATAAGTAATTCGAGTT
1 TCAAGCTCAAATAAGTAATTCGAATT
9343 TCAAGCTCAAAT
1 TCAAGCTCAAAT
9355 CGAGTTGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 3 0.09
26 29 0.91
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32
Consensus pattern (26 bp):
TCAAGCTCAAATAAGTAATTCGAATT
Found at i:9474 original size:21 final size:21
Alignment explanation
Indices: 9450--9504 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
9440 TCTCTCTCAA
9450 CAAAAATTTCAAAATAATTTT
1 CAAAAATTTCAAAATAATTTT
9471 CAAAAA-TTCAAAATAATTTT
1 CAAAAATTTCAAAATAATTTT
* *
9491 -TAAAATTCCAAAAT
1 CAAAAATTTCAAAAT
9505 TTATATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.13
20 21 0.68
21 6 0.19
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (21 bp):
CAAAAATTTCAAAATAATTTT
Found at i:22022 original size:15 final size:16
Alignment explanation
Indices: 21991--22027 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
21981 TATGGAAGTT
21991 AATTTGATTAATTTTTA
1 AATTTGATT-ATTTTTA
22008 AATTTGATT-TTTTTA
1 AATTTGATTATTTTTA
22023 AATTT
1 AATTT
22028 TTTTAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
17 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
AATTTGATTATTTTTA
Found at i:27171 original size:79 final size:79
Alignment explanation
Indices: 27068--27230 Score: 308
Period size: 79 Copynumber: 2.1 Consensus size: 79
27058 TTATACTATC
*
27068 TTTGAGATGTTTTTATTCAGTAGCATGAACTAATTTCCTAAATACCTAGGGGAGATGAACCTTAT
1 TTTGAGATGTTTTTATTCAGTAGCATGAACTAATTTCCTAAATACCTAGGGGAGATGAACCCTAT
27133 GATGAATTCTGTCA
66 GATGAATTCTGTCA
*
27147 TTTGAGATGTTTTTATTCATTAGCATGAACTAATTTCCTAAATACCTAGGGGAGATGAACCCTAT
1 TTTGAGATGTTTTTATTCAGTAGCATGAACTAATTTCCTAAATACCTAGGGGAGATGAACCCTAT
27212 GATGAATTCTGTCA
66 GATGAATTCTGTCA
27226 TTTGA
1 TTTGA
27231 TTTATGATTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (79 bp):
TTTGAGATGTTTTTATTCAGTAGCATGAACTAATTTCCTAAATACCTAGGGGAGATGAACCCTAT
GATGAATTCTGTCA
Found at i:31124 original size:22 final size:22
Alignment explanation
Indices: 31075--31124 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
31065 CTGTCCTTCC
* * *
31075 TCATTTGTGTTTCTTCTTTTTG
1 TCATTTGTGCTTCCTCTTTTTA
31097 TC-TTTGTGCTTCCTCTTTTTA
1 TCATTTGTGCTTCCTCTTTTTA
31118 TCATTTG
1 TCATTTG
31125 AACCAATCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.06, C:0.18, G:0.12, T:0.64
Consensus pattern (22 bp):
TCATTTGTGCTTCCTCTTTTTA
Found at i:39294 original size:22 final size:23
Alignment explanation
Indices: 39267--39310 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
39257 AGATAGTTAA
*
39267 AATTGTCAATGTAA-TAAAAGTT
1 AATTGTCAATGCAACTAAAAGTT
*
39289 AATTGTCAGTGCAACTAAAAGT
1 AATTGTCAATGCAACTAAAAGT
39311 AAATCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (23 bp):
AATTGTCAATGCAACTAAAAGTT
Done.