Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003611.1 Kokia drynarioides strain JFW-HI SEQ_116498, 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: 19477
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:1065 original size:39 final size:39
Alignment explanation
Indices: 1016--1379 Score: 119
Period size: 39 Copynumber: 9.3 Consensus size: 39
1006 GTTTTTTTTC
*
1016 ATGATTGGGGTAAGAGATTGGCTGACAGTGATCTGCCCT
1 ATGATCGGGGTAAGAGATTGGCTGACAGTGATCTGCCCT
* * * *** **
1055 ATGATCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCT
1 ATGATCGGGGTAAGAGATTGGCTGACAGTGATCTG-CCCT
* * *
1095 ATCG--CGGGATAAGAGATTGGCTGAC-GATAATCTGCCCC
1 AT-GATCGGGGTAAGAGATTGGCTGACAG-TGATCTGCCCT
* * * *
1133 ATGATCGGGGTGAA-AGATCGAACGGTTACA---ATCTACCCCT
1 ATGATCGGGGT-AAGAGATTG---GCTGACAGTGATCT-GCCCT
* * * *
1173 AT-CTCGGGGTAAGAGATTGACTGATAGTGATCTGCCCC
1 ATGATCGGGGTAAGAGATTGGCTGACAGTGATCTGCCCT
* * * ** **
1211 ATGATCGGGGTAAAAGATCGAACTG-TTGCAATCTG-CCT
1 ATGATCGGGGTAAGAGATTG-GCTGACAGTGATCTGCCCT
* * * ** *
1249 CTGTCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCC
1 ATG-ATCGGGGTAAGAGATTGGCTGACAGTGATCTGCCCT
* * * *
1289 ATGATCGGGGTAAAAGA-TAG--AACGGTTGCAATCTGCCC-
1 ATGATCGGGGTAAGAGATTGGCTGACAG-TG--ATCTGCCCT
* * *
1327 CTG-TCGCGGGGTAAGAGATTGGCTAACTGTGATCTGCCCT
1 ATGAT--CGGGGTAAGAGATTGGCTGACAGTGATCTGCCCT
*
1367 ATGATCGAGGTAA
1 ATGATCGGGGTAA
1380 AATATCGGAT
Statistics
Matches: 235, Mismatches: 60, Indels: 60
0.66 0.17 0.17
Matches are distributed among these distances:
36 6 0.03
37 4 0.02
38 23 0.10
39 165 0.70
40 25 0.11
41 4 0.02
42 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (39 bp):
ATGATCGGGGTAAGAGATTGGCTGACAGTGATCTGCCCT
Found at i:1165 original size:78 final size:78
Alignment explanation
Indices: 1022--1437 Score: 532
Period size: 78 Copynumber: 5.3 Consensus size: 78
1012 TTTCATGATT
* * *
1022 GGGGTAAGAGATTGGCTGAC-AGTGATCTGCCCTATGATCGGGGTAAAAGATCGGATGGTTGCAA
1 GGGGTAAGAGATTGGCTGACGA-TGATCTGCCCCATGATCGGGGTAAAAGATCGAACGGTTGCAA
*
1086 TCTGCCCCTATCGC
65 TCTGCCCCTGTCGC
* * * *
1100 GGGATAAGAGATTGGCTGACGATAATCTGCCCCATGATCGGGGTGAAAGATCGAACGGTTACAAT
1 GGGGTAAGAGATTGGCTGACGATGATCTGCCCCATGATCGGGGTAAAAGATCGAACGGTTGCAAT
* * *
1165 CTACCCCTATCTC
66 CTGCCCCTGTCGC
* * *
1178 GGGGTAAGAGATTGACTGA-TAGTGATCTGCCCCATGATCGGGGTAAAAGATCGAACTGTTGCAA
1 GGGGTAAGAGATTGGCTGACGA-TGATCTGCCCCATGATCGGGGTAAAAGATCGAACGGTTGCAA
* *
1242 TCTGCCTCTGTCTC
65 TCTGCCCCTGTCGC
* * * *
1256 GGGGTAAGAGATTGGTTGATGGTGATCTGCCCCATGATCGGGGTAAAAGATAGAACGGTTGCAAT
1 GGGGTAAGAGATTGGCTGACGATGATCTGCCCCATGATCGGGGTAAAAGATCGAACGGTTGCAAT
1321 CTGCCCCTGTCGC
66 CTGCCCCTGTCGC
* * * * * *
1334 GGGGTAAGAGATTGGCTAACTG-TGATCTGCCCTATGATCGAGGTAAAATATCGGATGGTTGCAA
1 GGGGTAAGAGATTGGCTGAC-GATGATCTGCCCCATGATCGGGGTAAAAGATCGAACGGTTGCAA
1398 TCTGCCCCTGTCGC
65 TCTGCCCCTGTCGC
* *
1412 GGGGTAAGAGATTGGTTGACGGTGAT
1 GGGGTAAGAGATTGGCTGACGATGAT
1438 GTAGCTTCAC
Statistics
Matches: 295, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
77 2 0.01
78 291 0.99
79 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (78 bp):
GGGGTAAGAGATTGGCTGACGATGATCTGCCCCATGATCGGGGTAAAAGATCGAACGGTTGCAAT
CTGCCCCTGTCGC
Found at i:1306 original size:156 final size:156
Alignment explanation
Indices: 1022--1437 Score: 611
Period size: 156 Copynumber: 2.7 Consensus size: 156
1012 TTTCATGATT
*
1022 GGGGTAAGAGATTGGCTGACAGTGATCTGCCCTATGATCGGGGTAAAAGATCGGATGGTTGCAAT
1 GGGGTAAGAGATTGGCTGATAGTGATCTGCCCTATGATCGGGGTAAAAGATCGGATGGTTGCAAT
* * * * * * *
1087 CTGCCCCTATCGCGGGATAAGAGATTGGCTGACGATAATCTGCCCCATGATCGGGGTGAAAGATC
66 CTGCCCCTGTCGCGGGGTAAGAGATTGGTTGACGGTGATCTGCCCCATGATCGGGGTAAAAGATA
*
1152 GAACGGTTACAATCTACCCCTATCTC
131 GAACGGTTACAATCTACCCCTATCGC
* * *
1178 GGGGTAAGAGATTGACTGATAGTGATCTGCCCCATGATCGGGGTAAAAGATCGAACT-GTTGCAA
1 GGGGTAAGAGATTGGCTGATAGTGATCTGCCCTATGATCGGGGTAAAAGATCGGA-TGGTTGCAA
* * *
1242 TCTGCCTCTGTCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCATGATCGGGGTAAAAGAT
65 TCTGCCCCTGTCGCGGGGTAAGAGATTGGTTGACGGTGATCTGCCCCATGATCGGGGTAAAAGAT
* * *
1307 AGAACGGTTGCAATCTGCCCCTGTCGC
130 AGAACGGTTACAATCTACCCCTATCGC
* * *
1334 GGGGTAAGAGATTGGCTAACT-GTGATCTGCCCTATGATCGAGGTAAAATATCGGATGGTTGCAA
1 GGGGTAAGAGATTGGCTGA-TAGTGATCTGCCCTATGATCGGGGTAAAAGATCGGATGGTTGCAA
1398 TCTGCCCCTGTCGCGGGGTAAGAGATTGGTTGACGGTGAT
65 TCTGCCCCTGTCGCGGGGTAAGAGATTGGTTGACGGTGAT
1438 GTAGCTTCAC
Statistics
Matches: 230, Mismatches: 27, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
155 1 0.00
156 227 0.99
157 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (156 bp):
GGGGTAAGAGATTGGCTGATAGTGATCTGCCCTATGATCGGGGTAAAAGATCGGATGGTTGCAAT
CTGCCCCTGTCGCGGGGTAAGAGATTGGTTGACGGTGATCTGCCCCATGATCGGGGTAAAAGATA
GAACGGTTACAATCTACCCCTATCGC
Found at i:13651 original size:60 final size:60
Alignment explanation
Indices: 13460--13862 Score: 362
Period size: 60 Copynumber: 6.8 Consensus size: 60
13450 GAATTTGGGG
* * * * *
13460 TAAAAATGTAATTTTGGAAAAGTTTAA-GGTCAAAATATGATTTTAGGAAAGTTTGGGGT
1 TAAAAATGTAATTTTAGAAAAGTTTAAGGGTCAAAATATAATTTTAGAAAAGTTTAGAGT
* * * * * *
13519 CAAAAATGTAATTTTGGAAAA-TTT-TGGGATCAAAATGTAATTTTAG-GAAGTTTA-AGGG
1 TAAAAATGTAATTTTAGAAAAGTTTAAGGG-TCAAAATATAATTTTAGAAAAGTTTAGA-GT
* * * * *
13577 TCAAAATGTGATTTTATAAAAGTTTAAGGGTCAAAATGTGATTTTAGAAAAGTTTAGAGT
1 TAAAAATGTAATTTTAGAAAAGTTTAAGGGTCAAAATATAATTTTAGAAAAGTTTAGAGT
* * * * * * *
13637 TTAAAATATAATTTTAGAGAAGTTTGAGGGTTAAAATATAATTTTAGGAAAGTTTAGGGGT
1 TAAAAATGTAATTTTAGAAAAGTTTAAGGGTCAAAATATAATTTTAGAAAAGTTTA-GAGT
* *
13698 TAAAAATGTAATTTTAGAAAAATTTAA-GGTCAAAATATAATTTT-GAAAAAGTTTAGGGGT
1 TAAAAATGTAATTTTAGAAAAGTTTAAGGGTCAAAATATAATTTTAG-AAAAGTTTA-GAGT
*
13758 T-AAAATGT-ATTTGTA-AAGAAGTTT-AGGGGCTAAAATATAATTTTAGAAAAGTTTAGA-T
1 TAAAAATGTAATTT-TAGAA-AAGTTTAAGGGTC-AAAATATAATTTTAGAAAAGTTTAGAGT
* * * * *
13816 GTAAAAATGTAATATTAGAAAATTTTTAGGGTCAAAACATGATTTTA
1 -TAAAAATGTAATTTTAGAAAAGTTTAAGGGTCAAAATATAATTTTA
13863 AGAAGTTCGA
Statistics
Matches: 282, Mismatches: 43, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
58 36 0.13
59 74 0.26
60 135 0.48
61 37 0.13
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (60 bp):
TAAAAATGTAATTTTAGAAAAGTTTAAGGGTCAAAATATAATTTTAGAAAAGTTTAGAGT
Found at i:13747 original size:29 final size:29
Alignment explanation
Indices: 13462--13852 Score: 297
Period size: 30 Copynumber: 13.1 Consensus size: 29
13452 ATTTGGGGTA
*
13462 AAAATGTAATTTTGGAAAAGTTTAAGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAGGTC
* * * **
13491 AAAATATGATTTTAGGAAAGTTTGGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAGGTC
* **
13520 AAAAATGTAATTTTGGAAAA-TTTTGGGATC
1 -AAAATGTAATTTTAGAAAAGTTTAAGG-TC
*
13550 AAAATGTAATTTTAG-GAAGTTTAAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAA-GGTC
* *
13579 AAAATGTGATTTTATAAAAGTTTAAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAA-GGTC
* * *
13609 AAAATGTGATTTTAGAAAAGTTTAGAGTTT
1 AAAATGTAATTTTAGAAAAGTTTA-AGGTC
* * * *
13639 AAAATATAATTTTAGAGAAGTTTGAGGGTT
1 AAAATGTAATTTTAGAAAAGTTT-AAGGTC
* * * *
13669 AAAATATAATTTTAGGAAAGTTTAGGGGTTA
1 AAAATGTAATTTTAGAAAAGTTTA-AGG-TC
*
13700 AAAATGTAATTTTAGAAAAATTTAAGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAGGTC
* * *
13729 AAAATATAATTTT-GAAAAAGTTTAGGGGTT
1 AAAATGTAATTTTAG-AAAAGTTTA-AGGTC
* *
13759 AAAATGT-ATTTGTA-AAGAAGTTTAGGGGC
1 AAAATGTAATTT-TAGAA-AAGTTTAAGGTC
* * *
13788 TAAAATATAATTTTAGAAAAGTTTAGATGTA
1 -AAAATGTAATTTTAGAAAAGTTTA-AGGTC
* * *
13819 AAAATGTAATATTAGAAAATTTTTAGGGTC
1 AAAATGTAATTTTAGAAAA-GTTTAAGGTC
13849 AAAA
1 AAAA
13853 CATGATTTTA
Statistics
Matches: 291, Mismatches: 52, Indels: 37
0.77 0.14 0.10
Matches are distributed among these distances:
28 3 0.01
29 92 0.32
30 161 0.55
31 35 0.12
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAAGTTTAAGGTC
Found at i:15602 original size:15 final size:16
Alignment explanation
Indices: 15574--15607 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
15564 TGGGTTGTAA
15574 TTTTGTAAAATGGACT
1 TTTTGTAAAATGGACT
*
15590 TTTTGT-AAGTGGACT
1 TTTTGTAAAATGGACT
15605 TTT
1 TTT
15608 AAACTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.50
Consensus pattern (16 bp):
TTTTGTAAAATGGACT
Found at i:17434 original size:11 final size:11
Alignment explanation
Indices: 17406--17439 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
17396 ATTCAATAAT
17406 AATT-TTAAAA
1 AATTATTAAAA
17416 AATATATTAAAA
1 AAT-TATTAAAA
17428 AATTATTAAAA
1 AATTATTAAAA
17439 A
1 A
17440 TCTTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 10 0.45
12 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATTATTAAAA
Done.