Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008606.1 Kokia drynarioides strain JFW-HI SEQ_123284, 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: 14646
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:3652 original size:16 final size:18
Alignment explanation
Indices: 3623--3673 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
3613 AATATTAATT
3623 AATTAAATTAA-TTTTTC
1 AATTAAATTAATTTTTTC
3640 AATTAAA-TAATTTTTTC
1 AATTAAATTAATTTTTTC
*
3657 AATCTAATTCTAATTTT
1 AAT-TAAAT-TAATTTT
3674 ATTAAAGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.10
17 16 0.55
18 3 0.10
20 7 0.24
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTAAATTAATTTTTTC
Found at i:12581 original size:13 final size:12
Alignment explanation
Indices: 12561--12597 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
12551 TGTTTAGTAG
12561 TTAATTATTCAA
1 TTAATTATTCAA
*
12573 TTCAATTATTAAA
1 TT-AATTATTCAA
12586 TTAATTATTCAA
1 TTAATTATTCAA
12598 CTTGTAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (12 bp):
TTAATTATTCAA
Found at i:13071 original size:12 final size:12
Alignment explanation
Indices: 13054--13095 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
13044 GCAAATCCCA
*
13054 AATTAATTAATT
1 AATTAATTGATT
13066 AATTAATTGATT
1 AATTAATTGATT
* *
13078 GATTGATTGATT
1 AATTAATTGATT
13090 AATTAA
1 AATTAA
13096 AAAAATAGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
AATTAATTGATT
Found at i:13541 original size:27 final size:27
Alignment explanation
Indices: 13511--13574 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
13501 TCGAATCTTG
*
13511 AACCCATAACCTCAAA-CTTAAACACTA
1 AACCCA-AACCTCAAATCTCAAACACTA
* *
13538 AACCCAAACTTCAAATCTCAAACCCTA
1 AACCCAAACCTCAAATCTCAAACACTA
*
13565 AACTCAAACC
1 AACCCAAACC
13575 ATTAATATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.17
Consensus pattern (27 bp):
AACCCAAACCTCAAATCTCAAACACTA
Found at i:13620 original size:14 final size:14
Alignment explanation
Indices: 13550--13620 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
13540 CCCAAACTTC
*
13550 AAATCTCAAACCCT
1 AAATCTCAAACCTT
13564 AAA-CTCAAACCATT
1 AAATCTCAAACC-TT
* *
13578 -AATATCAAACCTC
1 AAATCTCAAACCTT
13591 AAATCT-AAATCC-T
1 AAATCTCAAA-CCTT
*
13604 AAATCTTAAACCTT
1 AAATCTCAAACCTT
13618 AAA
1 AAA
13621 CTTGGGTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
13 22 0.48
14 24 0.52
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATCTCAAACCTT
Found at i:14005 original size:17 final size:18
Alignment explanation
Indices: 13982--14081 Score: 100
Period size: 18 Copynumber: 5.7 Consensus size: 18
13972 CAAACTCCCC
13982 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
* * *
14000 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAGA
14017 TTTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
14034 TTTAAATTTAAATTTAAG-
1 TTTAAATTT-ATTTTAAGA
*
14052 TTTAAATTTATTATCAA-A
1 TTTAAATTTATT-TTAAGA
*
14070 TTTAAAATTATT
1 TTTAAATTTATT
14082 ATGAATTTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
17 26 0.38
18 42 0.62
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:14025 original size:6 final size:6
Alignment explanation
Indices: 14014--14061 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
14004 ATTTGTTTAA
* *
14014 AAATTT AAATTT -ATTTT AAATTT AAATTT AAATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
14061 A
1 A
14062 TTATCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:14056 original size:35 final size:34
Alignment explanation
Indices: 13982--14081 Score: 105
Period size: 35 Copynumber: 2.9 Consensus size: 34
13972 CAAACTCCCC
*
13982 TTTAAATTTATTTTAAGA-TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTT-AAAA
*
14017 TTTAAATTTATTTTAAATTTAAATTTAAATTT-AAG
1 TTTAAATTTATTTTAAATTTAAATTT--ATTTAAAA
* *
14052 TTTAAATTTATTATCAAATTTAAAATTATT
1 TTTAAATTTATT-TTAAATTTAAATTTATT
14082 ATGAATTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
34 4 0.07
35 38 0.67
36 12 0.21
37 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAAAA
Found at i:14071 original size:53 final size:52
Alignment explanation
Indices: 13982--14092 Score: 134
Period size: 53 Copynumber: 2.1 Consensus size: 52
13972 CAAACTCCCC
* * * *
13982 TTTAAATTTATTTTAAGATTAAATTTGTTTAAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTAAAAATTTAAAATTATTATAAA
* * *
14034 TTTAAATTTAAATTTAAGTTTAAATTTA-TTATCAAATTTAAAATTATTATGAA
1 TTTAAATTT-AATTTAAGATTAAATTTATTTA-AAAATTTAAAATTATTATAAA
14087 TTTAAA
1 TTTAAA
14093 ATAAATAAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
52 12 0.24
53 38 0.76
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTAAAAATTTAAAATTATTATAAA
Found at i:14090 original size:17 final size:18
Alignment explanation
Indices: 14014--14094 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
14004 ATTTGTTTAA
* *
14014 AAATTTAAATTTATT-TT
1 AAATTTAAAATTATTATC
*
14031 AAATTTAAATTTAAATT-T-
1 AAATTTAAAATT--ATTATC
* *
14049 AAGTTTAAATTTATTATC
1 AAATTTAAAATTATTATC
14067 AAATTTAAAATTATTAT-
1 AAATTTAAAATTATTATC
*
14084 GAATTTAAAAT
1 AAATTTAAAAT
14095 AAATAAAGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.05
17 23 0.41
18 26 0.46
19 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (18 bp):
AAATTTAAAATTATTATC
Done.