Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008786.1 Kokia drynarioides strain JFW-HI SEQ_123469, 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: 54025
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:8053 original size:6 final size:6
Alignment explanation
Indices: 8042--8067 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
8032 TTTCATTTTG
8042 TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TT
8068 GTTATGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:25161 original size:34 final size:34
Alignment explanation
Indices: 25123--25191 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
25113 TAGGCATCCT
25123 TAGCACATATTTTAGCATTTTTTAGTTTAGTTTA
1 TAGCACATATTTTAGCATTTTTTAGTTTAGTTTA
25157 TAGCACATATTTTAGCATTTTTTAGTTTAGTTTA
1 TAGCACATATTTTAGCATTTTTTAGTTTAGTTTA
25191 T
1 T
25192 TGCATTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.54
Consensus pattern (34 bp):
TAGCACATATTTTAGCATTTTTTAGTTTAGTTTA
Found at i:35371 original size:16 final size:15
Alignment explanation
Indices: 35350--35379 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35340 TGATTTGAGC
35350 ATGTGAATAATGTGAA
1 ATGTGAAT-ATGTGAA
35366 ATGTGAATATGTGA
1 ATGTGAATATGTGA
35380 TTATCAAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
ATGTGAATATGTGAA
Found at i:36028 original size:18 final size:19
Alignment explanation
Indices: 36005--36044 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
35995 ATATTTATTA
36005 TTTTTATGA-ATTATGGAC
1 TTTTTATGATATTATGGAC
* *
36023 TTTTTATTATATTTTGGAC
1 TTTTTATGATATTATGGAC
36042 TTT
1 TTT
36045 GAGGACTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (19 bp):
TTTTTATGATATTATGGAC
Found at i:40827 original size:54 final size:53
Alignment explanation
Indices: 40726--40989 Score: 343
Period size: 54 Copynumber: 4.9 Consensus size: 53
40716 CTCCATTATC
*
40726 GAACCTTTAATCTGTAATAGGA-TTCATATTACTCATGATGACATAGAGTCAT
1 GAACCTTTAATCTGTAATAGGATTTCATATAACTCATGATGACATAGAGTCAT
*
40778 GGAACCTTTAATCTGTAATAGGATTTCATATAACTCACGATGACATAGAGTCATT
1 -GAACCTTTAATCTGTAATAGGATTTCATATAACTCATGATGACATAGAGTCA-T
* * * ** *
40833 GGACCTTTAATCCGTAATAGGATTTCATATAATTCACAATGACACAGAGTCAT
1 GAACCTTTAATCTGTAATAGGATTTCATATAACTCATGATGACATAGAGTCAT
* *
40886 CAGACTTTTAAT-TCGTAATAGGATTTCATATAACTCATGATGACATAGAGTCAT
1 GA-ACCTTTAATCT-GTAATAGGATTTCATATAACTCATGATGACATAGAGTCAT
* ** *
40940 CAGACCTTTAATCCATAATAGGATTTCATATAACTCATGATGACACAGAG
1 GA-ACCTTTAATCTGTAATAGGATTTCATATAACTCATGATGACATAGAG
40990 ATTCATGTAA
Statistics
Matches: 187, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
53 23 0.12
54 163 0.87
55 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (53 bp):
GAACCTTTAATCTGTAATAGGATTTCATATAACTCATGATGACATAGAGTCAT
Found at i:45844 original size:54 final size:54
Alignment explanation
Indices: 45737--46013 Score: 382
Period size: 54 Copynumber: 5.2 Consensus size: 54
45727 AGGAGCTCCA
* * * * *
45737 TCATTGGACCATTAAT-TAGTAATAGGA-TTCATATGACTCACAATGACATAGAG
1 TCATCGGACCTTTAATCT-GTAATAGGATTTCATATAACTCACGATGACACAGAG
* *
45790 TCATCGGATCTTTAATCTGTAATAGGATTTCATATAACTCACGATAACACAGAG
1 TCATCGGACCTTTAATCTGTAATAGGATTTCATATAACTCACGATGACACAGAG
* *
45844 TCATCGGACCTTTAATCTGTAATAGGATTTCTTACAACTCACGATGACACAGAG
1 TCATCGGACCTTTAATCTGTAATAGGATTTCATATAACTCACGATGACACAGAG
* *
45898 TCATTGGACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGAG
1 TCATCGGACCTTTAATCTGTAATAGGATTTCATATAACTCACGATGACACAGAG
* * *
45952 TCATCGGATCTTTAAT-TCGTAATAGGA-TTCATATAACTCATGATGACACAAAG
1 TCATCGGACCTTTAATCT-GTAATAGGATTTCATATAACTCACGATGACACAGAG
46005 TCATCGGAC
1 TCATCGGAC
46014 TTTTTTGCAT
Statistics
Matches: 200, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
53 54 0.27
54 146 0.73
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (54 bp):
TCATCGGACCTTTAATCTGTAATAGGATTTCATATAACTCACGATGACACAGAG
Found at i:49452 original size:19 final size:18
Alignment explanation
Indices: 49430--49465 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
49420 TGCTCTTACG
49430 AGCCAATATTGCTCAAACA
1 AGCCAATA-TGCTCAAACA
*
49449 AGCCAGTATGCTCAAAC
1 AGCCAATATGCTCAAAC
49466 GAGCATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19
Consensus pattern (18 bp):
AGCCAATATGCTCAAACA
Found at i:51689 original size:26 final size:25
Alignment explanation
Indices: 51652--51734 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 25
51642 TTGATTTTGA
51652 TTTTTTTT-AATTTAGTATTTAAAT
1 TTTTTTTTCAATTTAGTATTTAAAT
*
51676 TTTTTTATTCAATTTAGTACTTAAAGTT
1 TTTTTT-TTCAATTTAGTATTTAAA--T
*
51704 GATTTTTTTTCTTAATTTGGTATTTAAAT
1 --TTTTTTTTC--AATTTAGTATTTAAAT
51733 TT
1 TT
51735 AACATTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
24 6 0.12
25 2 0.04
26 14 0.29
27 2 0.04
28 1 0.02
29 4 0.08
30 6 0.12
31 13 0.27
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.63
Consensus pattern (25 bp):
TTTTTTTTCAATTTAGTATTTAAAT
Found at i:51712 original size:31 final size:30
Alignment explanation
Indices: 51673--51765 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 30
51663 TTAGTATTTA
*
51673 AATTTTTTTATTCAATTTAGTACTTAAAGTT
1 AATTTTTTT-TTCAATTTGGTACTTAAAGTT
* * * *
51704 GATTTTTTTTCTTAATTTGGTATTTAAATTT
1 AATTTTTTTT-TCAATTTGGTACTTAAAGTT
*
51735 AACATTTTTTTTCAATTTGGTACTTAAAGTT
1 AA-TTTTTTTTTCAATTTGGTACTTAAAGTT
51766 TTTGAGGTCC
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.02
31 42 0.84
32 7 0.14
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (30 bp):
AATTTTTTTTTCAATTTGGTACTTAAAGTT
Found at i:52964 original size:16 final size:16
Alignment explanation
Indices: 52943--52974 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52933 CAAAATCGAT
52943 CGGCTAACCGAATTAA
1 CGGCTAACCGAATTAA
*
52959 CGGCTAACTGAATTAA
1 CGGCTAACCGAATTAA
52975 TCAAACGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (16 bp):
CGGCTAACCGAATTAA
Found at i:53594 original size:30 final size:28
Alignment explanation
Indices: 53560--53655 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 28
53550 TTTATTTTCA
* *
53560 TTAAAAGTCAAAGAAAAAATTTTAAAATCC
1 TTAAAAGT-AAAAAAAAAATTTT-AAACCC
53590 TTAAAAGTTAATAAAAAAAAATTTTAAACCC
1 TTAAAAG-T-A-AAAAAAAAATTTTAAACCC
* *
53621 TTAAAAGT-TAAAAAAAA-TTTGAACCTC
1 TTAAAAGTAAAAAAAAAATTTTAAACC-C
53648 TTAAAAGT
1 TTAAAAGT
53656 TAGTAAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 7 0.12
27 17 0.29
30 8 0.14
31 14 0.24
32 12 0.21
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.29
Consensus pattern (28 bp):
TTAAAAGTAAAAAAAAAATTTTAAACCC
Found at i:53623 original size:31 final size:31
Alignment explanation
Indices: 53560--53637 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
53550 TTTATTTTCA
* * *
53560 TTAAAAG-TCAAAGAAAAAATTTTAAAATCC
1 TTAAAAGTTAAAAAAAAAAATTTTAAAACCC
53590 TTAAAAGTTAATAAAAAAAAATTTT-AAACCC
1 TTAAAAGTTAA-AAAAAAAAATTTTAAAACCC
53621 TTAAAAGTTAAAAAAAA
1 TTAAAAGTTAAAAAAAA
53638 TTTGAACCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 13 0.30
31 18 0.42
32 12 0.28
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (31 bp):
TTAAAAGTTAAAAAAAAAAATTTTAAAACCC
Found at i:53663 original size:27 final size:27
Alignment explanation
Indices: 53573--53657 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 27
53563 AAAGTCAAAG
*
53573 AAAAAATTTTAAAATCCTTAAAAGTTAATAAA
1 AAAAAATTTT-AAACCCTTAAAAG-T--T-AA
53605 AAAAAATTTTAAACCCTTAAAAGTTAA
1 AAAAAATTTTAAACCCTTAAAAGTTAA
*
53632 AAAAAA-TTTGAACCTCTTAAAAGTTA
1 AAAAAATTTTAAACC-CTTAAAAGTTA
53658 GTAAAATTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.14
27 19 0.38
28 1 0.02
30 1 0.02
31 12 0.24
32 10 0.20
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (27 bp):
AAAAAATTTTAAACCCTTAAAAGTTAA
Done.