Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008805.1 Kokia drynarioides strain JFW-HI SEQ_123488, 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: 21688
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:3711 original size:58 final size:58
Alignment explanation
Indices: 3550--3716 Score: 205
Period size: 58 Copynumber: 2.9 Consensus size: 58
3540 ATATTATATA
* * *
3550 TTATAATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAT
* * * *
3610 ATATTA-TTTTATTAAATTGTGTTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
*
3667 TTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
3717 AACAATAATC
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
57 21 0.23
58 54 0.59
59 9 0.10
60 8 0.09
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:6664 original size:212 final size:212
Alignment explanation
Indices: 6297--6729 Score: 794
Period size: 212 Copynumber: 2.0 Consensus size: 212
6287 TTAGGGTTTC
*
6297 TTTCTTAGTCTTCCTTCTCCAAACAATTGATACGTTGAAAATCCCTACAAAATAATTAAATCATC
1 TTTCTTAGTCTGCCTTCTCCAAACAATTGATACGTTGAAAATCCCTACAAAATAATTAAATCATC
*
6362 ATACCTCCACTCCCAAATCTCCCATAAAAGGGATTAGTTCCTCATGGTTTCATGAGATATTATAA
66 ATACCTCCACTCCCAAATCCCCCATAAAAGGGATTAGTTCCTCATGGTTTCATGAGATATTATAA
* * *
6427 TTTCAATATAAATAATAAACTTAAAGAATTGTATTGAAAATATAAGTAGAAAGAAACTTAGGGTA
131 TTTCAATATAAATAATAAACTTAAAGAATTGAATGGAAAATATAACTAGAAAGAAACTTAGGGTA
6492 GCATTCTGATGATCGTT
196 GCATTCTGATGATCGTT
6509 TTTCTTAGTCTGCCTTCTCCAAACAATTGATACGTTGAAAATCCCTACAAAATAATTAAATCATC
1 TTTCTTAGTCTGCCTTCTCCAAACAATTGATACGTTGAAAATCCCTACAAAATAATTAAATCATC
*
6574 ATACCTCCACTCCCTAATCCCCCATAAAAGGGATTAGTTCCTCATGGTTTCATGAGATATTATAA
66 ATACCTCCACTCCCAAATCCCCCATAAAAGGGATTAGTTCCTCATGGTTTCATGAGATATTATAA
6639 TTTCAATATAAATAATAAACTTAAAGAATTGAATGGAAAATATAACTAGAAAGAAACTTAGGGTA
131 TTTCAATATAAATAATAAACTTAAAGAATTGAATGGAAAATATAACTAGAAAGAAACTTAGGGTA
*
6704 GCATTCTGATGGTCGTT
196 GCATTCTGATGATCGTT
6721 TTTCCTTAG
1 TTT-CTTAG
6730 CCTTAGGTCA
Statistics
Matches: 213, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
212 208 0.98
213 5 0.02
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (212 bp):
TTTCTTAGTCTGCCTTCTCCAAACAATTGATACGTTGAAAATCCCTACAAAATAATTAAATCATC
ATACCTCCACTCCCAAATCCCCCATAAAAGGGATTAGTTCCTCATGGTTTCATGAGATATTATAA
TTTCAATATAAATAATAAACTTAAAGAATTGAATGGAAAATATAACTAGAAAGAAACTTAGGGTA
GCATTCTGATGATCGTT
Found at i:9078 original size:17 final size:18
Alignment explanation
Indices: 9048--9081 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9038 TCCCCATTGT
9048 TAAAAACAATAGAGAATG
1 TAAAAACAATAGAGAATG
*
9066 TAAAAATAA-AGAGAAT
1 TAAAAACAATAGAGAAT
9082 AAATACTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (18 bp):
TAAAAACAATAGAGAATG
Found at i:9785 original size:18 final size:18
Alignment explanation
Indices: 9744--9787 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
9734 TTCCATAAGA
* *
9744 TCTTCCTCAGGATCTTCT
1 TCTTCTTCAAGATCTTCT
9762 TCTTCTTCAAGATCTTCT
1 TCTTCTTCAAGATCTTCT
9780 TCTTCTTC
1 TCTTCTTC
9788 TTTAGCTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.32, G:0.07, T:0.50
Consensus pattern (18 bp):
TCTTCTTCAAGATCTTCT
Found at i:10697 original size:16 final size:15
Alignment explanation
Indices: 10678--10724 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
10668 AAATAATAAC
*
10678 AATTAAAAAGTTAATA
1 AATTAAAAAATTAA-A
10694 AATTAAATAAATTAAA
1 AATTAAA-AAATTAAA
*
10710 AATTACAAAA-TAAA
1 AATTAAAAAATTAAA
10724 A
1 A
10725 TTTTTTTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 5 0.18
15 3 0.11
16 14 0.50
17 6 0.21
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AATTAAAAAATTAAA
Found at i:11161 original size:13 final size:13
Alignment explanation
Indices: 11143--11170 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11133 TGACTTTCGA
11143 TGGCTACCGATGG
1 TGGCTACCGATGG
11156 TGGCTACCGATGG
1 TGGCTACCGATGG
11169 TG
1 TG
11171 ACTAATTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.39, T:0.25
Consensus pattern (13 bp):
TGGCTACCGATGG
Found at i:15933 original size:28 final size:28
Alignment explanation
Indices: 15895--15950 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
15885 TTCCTTAAAT
15895 TTCTTAGAGTCTCTGTATCACTCGGCAA
1 TTCTTAGAGTCTCTGTATCACTCGGCAA
15923 TTCTTAGAGTCTCTGTATCACTCGGCAA
1 TTCTTAGAGTCTCTGTATCACTCGGCAA
15951 AGCACCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (28 bp):
TTCTTAGAGTCTCTGTATCACTCGGCAA
Found at i:17354 original size:24 final size:24
Alignment explanation
Indices: 17335--17383 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
17325 AGAATAAGTT
17335 AGAAATTAGATAGAAAAATAAATA
1 AGAAATTAGATAGAAAAATAAATA
17359 AGAAATTAGATAGAAAAATAAATA
1 AGAAATTAGATAGAAAAATAAATA
17383 A
1 A
17384 ACCAAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.20
Consensus pattern (24 bp):
AGAAATTAGATAGAAAAATAAATA
Found at i:19742 original size:21 final size:21
Alignment explanation
Indices: 19698--19749 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
19688 CTTGACAGTT
* *
19698 CTACCGATACAAGTGAGGCAA
1 CTACCGATACAAGTCAGACAA
* *
19719 CTACCGATACAAGTCATACTA
1 CTACCGATACAAGTCAGACAA
*
19740 CTACCAATAC
1 CTACCGATAC
19750 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.19
Consensus pattern (21 bp):
CTACCGATACAAGTCAGACAA
Found at i:20457 original size:36 final size:36
Alignment explanation
Indices: 20404--20543 Score: 199
Period size: 36 Copynumber: 3.9 Consensus size: 36
20394 TGATTGATAT
* * *
20404 TCATTTTACTCTCTGTTGACTCAGAGGTCATGATGC
1 TCATTTTACTCCCTGTTGACCCAAAGGTCATGATGC
* *
20440 TCATTTTACTCCTTGTTGACCCAAAGGTCATTATGC
1 TCATTTTACTCCCTGTTGACCCAAAGGTCATGATGC
* *
20476 TCATTTTTCTCCCTGTTGACCCAAAGGTCATTATGC
1 TCATTTTACTCCCTGTTGACCCAAAGGTCATGATGC
* *
20512 TCATTTTTCTCCCTCTTGACCCAAAGGTCATG
1 TCATTTTACTCCCTGTTGACCCAAAGGTCATG
20544 CTTGTTACCT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (36 bp):
TCATTTTACTCCCTGTTGACCCAAAGGTCATGATGC
Done.