Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001571.1 Kokia drynarioides strain JFW-HI SEQ_113174, 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: 44185
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:7172 original size:20 final size:18
Alignment explanation
Indices: 7132--7172 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
7122 TTTTAGAAAA
*
7132 TTTTTAAAATTTTAATTT
1 TTTTTAAAATTTTAATCT
7150 TTTTTAAAATATTATAATCT
1 TTTTTAAAAT-TT-TAATCT
7170 TTT
1 TTT
7173 AAAAGATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 2 0.10
20 8 0.40
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAAATTTTAATCT
Found at i:9169 original size:29 final size:29
Alignment explanation
Indices: 9137--9199 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
9127 GAAAATGGAG
9137 TTTTTGGACA-TCTGGGGGCAAAAATGACA
1 TTTTTGGACATTC-GGGGGCAAAAATGACA
** * *
9166 TTTTTGGAGGTTCGGGGGTAAAAATGAGA
1 TTTTTGGACATTCGGGGGCAAAAATGACA
9195 TTTTT
1 TTTTT
9200 TGGAAGTTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.27, C:0.08, G:0.30, T:0.35
Consensus pattern (29 bp):
TTTTTGGACATTCGGGGGCAAAAATGACA
Found at i:9218 original size:29 final size:28
Alignment explanation
Indices: 9128--9397 Score: 224
Period size: 30 Copynumber: 9.1 Consensus size: 28
9118 TTATTGGTCG
* * *
9128 AAAATGGAGTTTTTGGACA-TCTGGGGGCA
1 AAAATGGAATTTTTGGA-AGT-TTGGGGTA
* *
9157 AAAAT-GACATTTTTGGAGGTTCGGGGGTA
1 AAAATGGA-ATTTTTGGAAGTT-TGGGGTA
* *
9186 AAAATGAGATTTTTTGGAAGTTCGAGGGTAAA
1 AAAATG-GAATTTTTGGAAGTTTG-GGGT--A
* *
9218 AAAATGAAATTTTTGGGAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTGGGGT-A
*
9248 AAAATGGAATTTATGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-GGGGTA
9277 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTGGGGT-A
* *
9307 ATAATGGGATTTTTGGAAGTTTGGGGGT-
1 AAAATGGAATTTTTGGAAGTTT-GGGGTA
*
9335 AAAATGGAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTGGGGT-A
*
9365 AAAATTGG-ATTTTTGGAAGTTCGAGGGTA
1 AAAA-TGGAATTTTTGGAAGTTTG-GGGTA
9394 AAAA
1 AAAA
9398 CAAAATTTTA
Statistics
Matches: 201, Mismatches: 22, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
28 24 0.12
29 67 0.33
30 81 0.40
31 19 0.09
32 10 0.05
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTA
Found at i:9219 original size:59 final size:58
Alignment explanation
Indices: 9156--9397 Score: 276
Period size: 59 Copynumber: 4.1 Consensus size: 58
9146 ATCTGGGGGC
* **
9156 AAAAAT-GACATTTTTGGAGGTTCGGGGGT-AAAAATGAGATTTTTTGGAAGTTCGAGGGT
1 AAAAATGGA-ATTTTTGGAAGTTTTGGGGTCAAAAATG-GA-TTTTTGGAAGTTCGAGGGT
* * * *
9215 AAAAAAATGAAATTTTTGGGAGTTTTGGGGTCAAAAATGGAATTTATGGAAGTT-TAGGGGT
1 --AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGG-ATTTTTGGAAGTTCGA-GGGT
* * *
9276 AAAAATGGAATTTTTGGAAGTTTTGGGGTCAATAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAAT-GGATTTTTGGAAGTTCGAGGGT
*
9335 -AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATTGGATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAA-TGGATTTTTGGAAGTTCGAGGGT
9393 AAAAA
1 AAAAA
9398 CAAAATTTTA
Statistics
Matches: 156, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
58 52 0.33
59 54 0.35
60 3 0.02
61 38 0.24
62 9 0.06
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.34
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGATTTTTGGAAGTTCGAGGGT
Found at i:9375 original size:58 final size:58
Alignment explanation
Indices: 9123--9396 Score: 254
Period size: 59 Copynumber: 4.6 Consensus size: 58
9113 AGAGTTTATT
* * * * **
9123 GGTCGAAAA-TGGAGTTTTTGGACA-TCTGGGGGCAAAAAT-GACATTTTTGGAGGTTCGGG
1 GGTCAAAAATTGGA-TTTTTGGA-AGTTTGGGGG-TAAAATGGA-ATTTTTGGAAGTTTTGG
* * * *
9182 GGT-AAAAA-TGAGATTTTTTGGAAGTTCGAGGGTAAAAAAATGAAATTTTTGGGAGTTTTGG
1 GGTCAAAAATTG-GA-TTTTTGGAAGTTTGGGGGT---AAAATGGAATTTTTGGAAGTTTTGG
* *
9243 GGTCAAAAA-TGGAATTTATGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGG
1 GGTCAAAAATTGG-ATTTTTGGAAGTTTGGGGGT-AAAATGGAATTTTTGGAAGTTTTGG
* * *
9302 GGTCAATAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGAATTTTTAGAAGTTTTGG
1 GGTCAAAAATTGGATTTTTGGAAGTTTGGGGGTAAAATGGAATTTTTGGAAGTTTTGG
* *
9360 GGTCAAAAATTGGATTTTTGGAAGTTCGAGGGTAAAA
1 GGTCAAAAATTGGATTTTTGGAAGTTTGGGGGTAAAA
9397 ACAAAATTTT
Statistics
Matches: 180, Mismatches: 26, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
58 64 0.36
59 68 0.38
60 2 0.01
61 37 0.21
62 9 0.05
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33
Consensus pattern (58 bp):
GGTCAAAAATTGGATTTTTGGAAGTTTGGGGGTAAAATGGAATTTTTGGAAGTTTTGG
Found at i:9407 original size:58 final size:57
Alignment explanation
Indices: 9180--9415 Score: 224
Period size: 58 Copynumber: 4.0 Consensus size: 57
9170 TGGAGGTTCG
* * *
9180 GGGGT-AAAAATGAGATTTTTTGGAAGTTCGAGGGTAAAAAAATGAAATTTTTGGGAGTTTT
1 GGGGTCAAAAATG-GA-TTTTTGGAAGTTCGAGGGT--AAAAA-GAAAATTTTAGAAGTTTT
* * * * *
9241 GGGGTCAAAAATGGAATTTATGGAAGTT-TAGGGGTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTCAAAAATGG-ATTTTTGGAAGTTCGA-GGGTAAAAA-GAAAATTTTAGAAGTTTT
* * * * * *
9300 GGGGTCAATAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGAATTTTTAGAAGTTTT
1 GGGGTCAAAAAT-GGATTTTTGGAAGTTCGAGGGTAAAAAGAAAATTTTAGAAGTTTT
*
9358 GGGGTCAAAAATTGGATTTTTGGAAGTTCGAGGGTAAAAACAAAATTTTAGATAGTTT
1 GGGGTCAAAAA-TGGATTTTTGGAAGTTCGAGGGTAAAAAGAAAATTTTAGA-AGTTT
9416 AGGGACCTCC
Statistics
Matches: 151, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
58 60 0.40
59 59 0.39
60 3 0.02
61 21 0.14
62 8 0.05
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (57 bp):
GGGGTCAAAAATGGATTTTTGGAAGTTCGAGGGTAAAAAGAAAATTTTAGAAGTTTT
Found at i:10586 original size:9 final size:9
Alignment explanation
Indices: 10574--10616 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
10564 TACTGCTATT
10574 TATTATTAA
1 TATTATTAA
*
10583 TATTATTAT
1 TATTATTAA
10592 TATTTATTAA
1 TA-TTATTAA
*
10602 CTATTATTAC
1 -TATTATTAA
10612 TATTA
1 TATTA
10617 ATGTTACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 15 0.52
10 12 0.41
11 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATTAA
Found at i:10600 original size:13 final size:13
Alignment explanation
Indices: 10521--10593 Score: 69
Period size: 13 Copynumber: 5.8 Consensus size: 13
10511 CCCTTTTTAT
10521 TTTATTATTAATA
1 TTTATTATTAATA
10534 TTT-TTATTAATA
1 TTTATTATTAATA
* * **
10546 ATTATTAATGCTA
1 TTTATTATTAATA
* **
10559 TTTATTACTGCTA
1 TTTATTATTAATA
10572 TTTATTATTAATA
1 TTTATTATTAATA
10585 -TTATTATTA
1 TTTATTATTA
10594 TTTATTAACT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
12 20 0.40
13 30 0.60
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:10628 original size:51 final size:50
Alignment explanation
Indices: 10522--10628 Score: 110
Period size: 51 Copynumber: 2.1 Consensus size: 50
10512 CCTTTTTATT
* * * *
10522 TTATTATTAATATTTTTATTAATAATTATTAATGCTATTTATTACTGCTAT
1 TTATTATTAATATTATTATTAAT-ATTATTAATACTATTTATTAATGCTAC
* *
10573 TTATTATTAATATTATTATT-AT-TTATTAACTATTATTACTATTAATGTTAC
1 TTATTATTAATATTATTATTAATATTATTAA-TACTATT--TATTAATGCTAC
10624 TTATT
1 TTATT
10629 GCTGTAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
48 7 0.15
49 5 0.11
50 2 0.04
51 33 0.70
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.58
Consensus pattern (50 bp):
TTATTATTAATATTATTATTAATATTATTAATACTATTTATTAATGCTAC
Found at i:12148 original size:23 final size:23
Alignment explanation
Indices: 12105--12148 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12095 GAAAGAATAT
*
12105 AGATATATAAATATATTGGATGA
1 AGATATATAAATATATAGGATGA
*
12128 AGATAT-TTAATAGTATAGGAT
1 AGATATATAAATA-TATAGGAT
12149 AATTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (23 bp):
AGATATATAAATATATAGGATGA
Found at i:18077 original size:18 final size:18
Alignment explanation
Indices: 18054--18096 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
18044 GAATAGATTT
18054 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
**
18072 TTAATTGGAAAATTTAAA
1 TTAATTAAAAAATTTAAA
18090 TTAATTA
1 TTAATTA
18097 CACCTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:38719 original size:16 final size:16
Alignment explanation
Indices: 38695--38783 Score: 67
Period size: 15 Copynumber: 5.5 Consensus size: 16
38685 ATTTTGGATT
38695 TTTTATATTTTCAAAATA
1 TTTTAT-TTTT-AAAATA
* *
38713 TTTTATTTTT-AAGTT
1 TTTTATTTTTAAAATA
* *
38728 TTTTGTATTTTAAACAGA
1 TTTTAT-TTTTAAA-ATA
38746 TTTTATTTTTAAAA-A
1 TTTTATTTTTAAAATA
* *
38761 TATAATTTTTAAAAT-
1 TTTTATTTTTAAAATA
38776 TTTTATTT
1 TTTTATTT
38784 AAAATATGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
15 27 0.48
16 5 0.09
17 13 0.23
18 11 0.20
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTATTTTTAAAATA
Found at i:38737 original size:33 final size:33
Alignment explanation
Indices: 38693--38757 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
38683 GAATTTTGGA
*
38693 TTTTTTATATTTTCAAA-ATATTTTATTTTTAAG
1 TTTTTTATATTTT-AAACAGATTTTATTTTTAAG
*
38726 TTTTTTGTATTTTAAACAGATTTTATTTTTAA
1 TTTTTTATATTTTAAACAGATTTTATTTTTAA
38758 AAATATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (33 bp):
TTTTTTATATTTTAAACAGATTTTATTTTTAAG
Done.