Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009812.1 Kokia drynarioides strain JFW-HI SEQ_124533, 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: 61050
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:4281 original size:87 final size:86
Alignment explanation
Indices: 4136--4294 Score: 264
Period size: 87 Copynumber: 1.8 Consensus size: 86
4126 ACACAAGACC
* * *
4136 AAAAAAGCTAGTTAGATGCGGATCCTCTAAGTTCATTTTAGTTTCCTACTATGCACAAGAACAGT
1 AAAAAAGCTAGTTAGAAGCAGACCCTCTAAGTTCATTTTAGTTTCCTACTATGCACAAGAACAGT
4201 CCTTTGTTTCGTGAGATGATA
66 CCTTTGTTTCGTGAGATGATA
* *
4222 AAAAAAGCTAGTTAGAAGCAGACCCTCTTAAGTTCATTTTAGTTTCCTACTATTCACAAGAATAG
1 AAAAAAGCTAGTTAGAAGCAGACCCTC-TAAGTTCATTTTAGTTTCCTACTATGCACAAGAACAG
4287 TCCTTTGT
65 TCCTTTGT
4295 AATATGAGAT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
86 24 0.36
87 43 0.64
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (86 bp):
AAAAAAGCTAGTTAGAAGCAGACCCTCTAAGTTCATTTTAGTTTCCTACTATGCACAAGAACAGT
CCTTTGTTTCGTGAGATGATA
Found at i:10514 original size:10 final size:10
Alignment explanation
Indices: 10499--10523 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10489 TTTAGTGTAT
10499 AATTCATACC
1 AATTCATACC
10509 AATTCATACC
1 AATTCATACC
10519 AATTC
1 AATTC
10524 TAATGCACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTCATACC
Found at i:19554 original size:39 final size:41
Alignment explanation
Indices: 19508--19586 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 41
19498 ATATACAATA
19508 AAATATTTATTATATTTAT-TTGTG-TTTTTTAATATAATT
1 AAATATTTATTATATTTATGTTGTGTTTTTTTAATATAATT
*
19547 AAATATTTATTATGTTTATGGTTGTGTTTTTTTAATATAA
1 AAATATTTATTATATTTAT-GTTGTGTTTTTTTAATATAA
19587 ATATTTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 18 0.50
41 5 0.14
42 13 0.36
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (41 bp):
AAATATTTATTATATTTATGTTGTGTTTTTTTAATATAATT
Found at i:21673 original size:39 final size:40
Alignment explanation
Indices: 21619--21698 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
21609 TATGCACTCA
*
21619 ATGGACACATTTTGAAGAGTCACAACC-CTTTCAAATTGG
1 ATGGACACATATTGAAGAGTCACAACCTCTTTCAAATTGG
* * *
21658 ATGGACACCTATTGAAGAGTCACAACCTTTTTCATATTGG
1 ATGGACACATATTGAAGAGTCACAACCTCTTTCAAATTGG
21698 A
1 A
21699 CATACCTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 25 0.69
40 11 0.31
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (40 bp):
ATGGACACATATTGAAGAGTCACAACCTCTTTCAAATTGG
Found at i:21714 original size:39 final size:38
Alignment explanation
Indices: 21630--21715 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 38
21620 TGGACACATT
*
21630 TTGAAGAGTCACAACCCTTTCAAATTGGATGGACACCTA
1 TTGAAGAGTCACAACCCTTTCAAATTGGA-GCACACCTA
* * * *
21669 TTGAAGAGTCACAACCTTTTTCATATTGGA-CATACCTC
1 TTGAAGAGTCACAACC-CTTTCAAATTGGAGCACACCTA
21707 TTGGAAGAG
1 TT-GAAGAG
21716 ACTTGTCCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 7 0.17
39 22 0.55
40 11 0.28
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (38 bp):
TTGAAGAGTCACAACCCTTTCAAATTGGAGCACACCTA
Found at i:32622 original size:20 final size:19
Alignment explanation
Indices: 32592--32630 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
32582 TAATATTATT
32592 AATAAATATAATTTAATAA
1 AATAAATATAATTTAATAA
32611 AATAATATATAATTTAATAA
1 AATAA-ATATAATTTAATAA
32631 CATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAAATATAATTTAATAA
Found at i:43601 original size:19 final size:19
Alignment explanation
Indices: 43569--43606 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
43559 AAAATGATTT
*
43569 TTAAGAAATGATAATTTAG
1 TTAAGAAATGATAAGTTAG
43588 TTAACGAAAT-ATAAGTTAG
1 TTAA-GAAATGATAAGTTAG
43607 ATATAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (19 bp):
TTAAGAAATGATAAGTTAG
Found at i:53552 original size:6 final size:6
Alignment explanation
Indices: 53527--53581 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
53517 ACAATTCATA
* * * * * *
53527 TCACTT TCAATT CCAATT TCACTT TCACTT TCAATT CCAATT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
53575 TCACTT T
1 TCACTT T
53582 GAGTTTCAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:53593 original size:24 final size:24
Alignment explanation
Indices: 53527--53581 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
53517 ACAATTCATA
53527 TCACTTTCAATTCCAATTTCACTT
1 TCACTTTCAATTCCAATTTCACTT
53551 TCACTTTCAATTCCAATTTCACTT
1 TCACTTTCAATTCCAATTTCACTT
53575 TCACTTT
1 TCACTTT
53582 GAGTTTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (24 bp):
TCACTTTCAATTCCAATTTCACTT
Found at i:55314 original size:44 final size:45
Alignment explanation
Indices: 55253--55340 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 45
55243 AATCCTTGAA
* *
55253 TTTTCTTAACCTTTCTTA-TTTAGACTACACATTCTAATTCTTAAT
1 TTTTCTTAACCTTTCTTATTTTA-ACCACACATTCTAACTCTTAAT
* *
55298 TTTTCTTAATC-TTCTTATTTTAACCACATATTCTAACTCTTAA
1 TTTTCTTAACCTTTCTTATTTTAACCACACATTCTAACTCTTAA
55341 CTCGACACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 24 0.63
45 14 0.37
ACGTcount: A:0.27, C:0.20, G:0.01, T:0.51
Consensus pattern (45 bp):
TTTTCTTAACCTTTCTTATTTTAACCACACATTCTAACTCTTAAT
Found at i:57366 original size:19 final size:19
Alignment explanation
Indices: 57344--57388 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
57334 TTTTATTCGG
57344 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
57363 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
57382 ATTTAAT
1 ATTTAAT
57389 TTATCTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Done.