Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010628.1 Kokia drynarioides strain JFW-HI SEQ_125564, 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: 59230
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 205 characters in sequence are not A, C, G, or T
Found at i:19531 original size:69 final size:69
Alignment explanation
Indices: 19444--19581 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
19434 AGTATTTATT
19444 GCGTAAAATCAAAAATCAAATCACAGAATTCATCCTAGGTTCATCT-TCCCTAGGTATTTAGGAA
1 GCGTAAAATCAAAAATCAAATCACAGAATTCATCCTAGGTTCATCTCT-CCTAGGTATTTAGGAA
19508 TTTAG
65 TTTAG
* *
19513 GCGTAAAATCAGACATCAAATCACAGAATTCATCCTAGGTTCATCTCTCCTAGGTATTTAGGAAT
1 GCGTAAAATCAAAAATCAAATCACAGAATTCATCCTAGGTTCATCTCTCCTAGGTATTTAGGAAT
19578 TTAG
66 TTAG
19582 TTCATACTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 65 0.98
70 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (69 bp):
GCGTAAAATCAAAAATCAAATCACAGAATTCATCCTAGGTTCATCTCTCCTAGGTATTTAGGAAT
TTAG
Found at i:19984 original size:13 final size:13
Alignment explanation
Indices: 19968--20002 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
19958 TAAACAATAT
19968 AATAATAATCCTA
1 AATAATAATCCTA
*
19981 AATATTAATCCTA
1 AATAATAATCCTA
*
19994 AAAAATAAT
1 AATAATAAT
20003 GTTAAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:21875 original size:6 final size:6
Alignment explanation
Indices: 21850--21904 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
21840 ATAATTCATA
* * * *
21850 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCATTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
21898 TCACTT T
1 TCACTT T
21905 TAATTTTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.20, C:0.29, G:0.00, T:0.51
Consensus pattern (6 bp):
TCACTT
Found at i:26154 original size:14 final size:14
Alignment explanation
Indices: 26135--26161 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26125 TGGTCAAAGT
26135 TTTAGAGTTTAGGA
1 TTTAGAGTTTAGGA
26149 TTTAGAGTTTAGG
1 TTTAGAGTTTAGG
26162 GTTCAATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTAGAGTTTAGGA
Found at i:26959 original size:19 final size:18
Alignment explanation
Indices: 26937--26979 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
26927 TTCATGCTAC
26937 TTTTTT-TATTTTTATGAA
1 TTTTTTGTATTTTT-TGAA
26955 TTTTTCTGTATTTTTTGAA
1 TTTTT-TGTATTTTTTGAA
*
26974 TATTTT
1 TTTTTT
26980 AAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.27
19 9 0.41
20 7 0.32
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (18 bp):
TTTTTTGTATTTTTTGAA
Found at i:32409 original size:16 final size:15
Alignment explanation
Indices: 32374--32419 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
32364 GTAATATTTT
32374 AAATATAAATAACTA
1 AAATATAAATAACTA
* *
32389 AAATATAATTTACTAA
1 AAATATAAATAACT-A
*
32405 AAATAAAAATAACTA
1 AAATATAAATAACTA
32420 TTTTAATAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATATAAATAACTA
Found at i:41858 original size:23 final size:22
Alignment explanation
Indices: 41832--41901 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
41822 TTTTAAATAA
41832 TTTTTTTCAATTTTTATGAATTT
1 TTTTTTTCAATTTTTA-GAATTT
* *
41855 TTTTTTAT-AA-TTTTGGAAATTC
1 TTTTTT-TCAATTTTTAG-AATTT
*
41877 TATTTTTCAGATTTTTAGAATTT
1 TTTTTTTCA-ATTTTTAGAATTT
41900 TT
1 TT
41902 AATAATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
21 2 0.06
22 14 0.39
23 14 0.39
24 6 0.17
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTTTTTCAATTTTTAGAATTT
Found at i:41909 original size:19 final size:17
Alignment explanation
Indices: 41887--41927 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
41877 TATTTTTCAG
41887 ATTTTTAGAATTTTTAATA
1 ATTTTTAGAA-TTTTAA-A
*
41906 ATTTTTATAATTTTAAA
1 ATTTTTAGAATTTTAAA
41923 ATTTT
1 ATTTT
41928 GAAAATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
19 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTTTTAGAATTTTAAA
Found at i:41932 original size:9 final size:9
Alignment explanation
Indices: 41887--41961 Score: 57
Period size: 9 Copynumber: 8.3 Consensus size: 9
41877 TATTTTTCAG
*
41887 ATTTTTAGA
1 ATTTTTAAA
41896 ATTTTTAATA
1 ATTTTTAA-A
*
41906 ATTTTTATA
1 ATTTTTAAA
41915 A-TTTTAAA
1 ATTTTTAAA
*
41923 ATTTTGAAA
1 ATTTTTAAA
*
41932 ATTCTATT--T
1 ATT-T-TTAAA
41941 ATTTTTAAA
1 ATTTTTAAA
*
41950 ATTTTCAAA
1 ATTTTTAAA
41959 ATT
1 ATT
41962 CAAAAATTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
7 2 0.04
8 8 0.15
9 32 0.62
10 9 0.17
11 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:46206 original size:7 final size:6
Alignment explanation
Indices: 46184--46224 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
46174 GAGATAAACT
* *
46184 TTTTAA TTTTAA TTTTAA TTTTTA TTATATA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA-A TTTTAA TTTT
46225 GAGATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:47418 original size:21 final size:23
Alignment explanation
Indices: 47376--47418 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47366 GAATTTTTTT
*
47376 AAAATTATATATTTTTGTAATTG
1 AAAAATATATATTTTTGTAATTG
47399 AAAAATATAT-TTTTTG-AATT
1 AAAAATATATATTTTTGTAATT
47419 TTTTTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (23 bp):
AAAAATATATATTTTTGTAATTG
Found at i:47545 original size:20 final size:19
Alignment explanation
Indices: 47506--47543 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
47496 TTTCTTGAAT
47506 TTTTTATATTTATATAATA
1 TTTTTATATTTATATAATA
47525 TTTTTAT-TTTATATAATA
1 TTTTTATATTTATATAATA
47543 T
1 T
47544 ATATTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTATATTTATATAATA
Found at i:48824 original size:27 final size:27
Alignment explanation
Indices: 48773--48824 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
48763 ATTGACAGAA
*
48773 AAAATTTAAATTAATTGAGTTGAGTGT
1 AAAATTTAAATTAATTGAGTCGAGTGT
48800 AAAA-TTAAATTTGAATT-AGTCGAGT
1 AAAATTTAAA-TT-AATTGAGTCGAGT
48825 CAAATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 5 0.23
27 13 0.59
28 4 0.18
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.38
Consensus pattern (27 bp):
AAAATTTAAATTAATTGAGTCGAGTGT
Done.