Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008014.1 Kokia drynarioides strain JFW-HI SEQ_122668, 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: 74293
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 55 characters in sequence are not A, C, G, or T
Found at i:6578 original size:17 final size:17
Alignment explanation
Indices: 6556--6616 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
6546 AACTGTGAAC
6556 TGCGAGCTCATCAAGTG
1 TGCGAGCTCATCAAGTG
* **
6573 TGCGAGCACATCAAGAC
1 TGCGAGCTCATCAAGTG
*
6590 TGCGAACTCATCAAGTG
1 TGCGAGCTCATCAAGTG
6607 TGCGAGCTCA
1 TGCGAGCTCA
6617 CAAAAACTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (17 bp):
TGCGAGCTCATCAAGTG
Found at i:6592 original size:34 final size:33
Alignment explanation
Indices: 6554--6673 Score: 143
Period size: 34 Copynumber: 3.5 Consensus size: 33
6544 CGAACTGTGA
*
6554 ACTGCGAGCTCATCAAGTGTGCGAGCACATCAAG
1 ACTGCGAGCTCATCAAGTGTGCGAGCTCA-CAAG
* *
6588 ACTGCGAACTCATCAAGTGTGCGAGCTCACAAAA
1 ACTGCGAGCTCATCAAGTGTGCGAGCTCAC-AAG
* * *
6622 ACTAG-AAGCACATCAAGTGTGCGAGCTCACCAG
1 ACT-GCGAGCTCATCAAGTGTGCGAGCTCACAAG
6655 ACTGCGAGCTCATCGAAGT
1 ACTGCGAGCTCATC-AAGT
6674 TAGTTTGTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
32 1 0.01
33 12 0.17
34 58 0.81
35 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (33 bp):
ACTGCGAGCTCATCAAGTGTGCGAGCTCACAAG
Found at i:8014 original size:59 final size:57
Alignment explanation
Indices: 7847--8037 Score: 163
Period size: 57 Copynumber: 3.3 Consensus size: 57
7837 TTTATTATAA
* * * ** * *
7847 AATTTGGTACTTTAACTTGACATTTTTTTTTAATTTGGTAGCTAAATTTTTTT-A-CC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAATTT-GTACCTAACTTTTTTTGATCC
* * * * *
7903 TAATTTGGTACCTGAACTTTACACTTTTTCCTAATCTGATACTTAAACTTTTTTGGATCC
1 -AATTTGGTACCTAAACTTGACACTTTTTCCTAATTTG-TACCT-AACTTTTTTTGATCC
*
7963 AATTTGGTACCTAAACTTGACA-TTTTTCCTAATTTAGTACCTAATCTTTTTTTAAGATTC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAATTT-GTACCTAA-CTTTTTTT--GATCC
*
8023 AATTTGGTACTTAAA
1 AATTTGGTACCTAAA
8038 TTTATTAAAT
Statistics
Matches: 108, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
56 1 0.01
57 34 0.31
58 31 0.29
59 22 0.20
60 20 0.19
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (57 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGTACCTAACTTTTTTTGATCC
Found at i:8245 original size:24 final size:24
Alignment explanation
Indices: 8218--8267 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
8208 CAAGTTCAGG
8218 TATTAAATTGGACCCCAAAAAGTT
1 TATTAAATTGGACCCCAAAAAGTT
8242 TATTAAATTGGACCCCAAAAAGTT
1 TATTAAATTGGACCCCAAAAAGTT
8266 TA
1 TA
8268 AGTACCAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (24 bp):
TATTAAATTGGACCCCAAAAAGTT
Found at i:16324 original size:20 final size:20
Alignment explanation
Indices: 16299--16360 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 20
16289 CATTGTTTCG
16299 ATAAAAATATATAATATTTT
1 ATAAAAATATATAATATTTT
* *
16319 ATAAAATTATATATATATAATT
1 ATAAAAATATATA-ATAT-TTT
16341 ATAAAAATATTTATAATATT
1 ATAAAAATA--TATAATATT
16361 ATTAATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 12 0.35
21 4 0.12
22 10 0.29
23 4 0.12
24 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAAAATATATAATATTTT
Found at i:16333 original size:22 final size:22
Alignment explanation
Indices: 16301--16360 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
16291 TTGTTTCGAT
16301 AAAA-ATATATAATATTTTATA
1 AAAATATATATAATATTTTATA
* *
16322 AAATTATATAT-ATATAATTATA
1 AAAATATATATAATAT-TTTATA
*
16344 AAAATATTTATAATATT
1 AAAATATATATAATATT
16361 ATTAATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.23
22 20 0.65
23 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATATATATAATATTTTATA
Found at i:27901 original size:11 final size:11
Alignment explanation
Indices: 27887--27920 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
27877 TATTTTTTGC
27887 TATTATTTTAT
1 TATTATTTTAT
* *
27898 TATTATGTTGT
1 TATTATTTTAT
27909 TATTATTTTAT
1 TATTATTTTAT
27920 T
1 T
27921 GTTAATGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:27937 original size:22 final size:22
Alignment explanation
Indices: 27890--27937 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
27880 TTTTTGCTAT
* *
27890 TATTTTATTATTATGTTGTTAT
1 TATTTTATTATTATGTTGTGAA
*
27912 TATTTTATTGTTAATGTT-TGAA
1 TATTTTATTATT-ATGTTGTGAA
27934 TATT
1 TATT
27938 GTATAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (22 bp):
TATTTTATTATTATGTTGTGAA
Found at i:27973 original size:18 final size:19
Alignment explanation
Indices: 27916--27978 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
27906 TGTTATTATT
*
27916 TTATTGTTAATGTTTG--A
1 TTATTGTTAATATTTGTTA
* *
27933 ATATTGTATAATATTTATT-
1 TTATTGT-TAATATTTGTTA
27952 TTATTGTTAAT-TTTGTTA
1 TTATTGTTAATATTTGTTA
27970 TTATT-TTAA
1 TTATTGTTAA
27979 AGATATTTAC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
17 15 0.41
18 16 0.43
19 6 0.16
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (19 bp):
TTATTGTTAATATTTGTTA
Found at i:35272 original size:21 final size:21
Alignment explanation
Indices: 35253--35293 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
35243 CTTTTTTTTC
35253 TATTTTGATTGTTGTTTTTTGA
1 TATTTTGA-TGTTGTTTTTTGA
*
35275 TGTTTTGATGTTGTTTTTT
1 TATTTTGATGTTGTTTTTT
35294 TTACTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.71
Consensus pattern (21 bp):
TATTTTGATGTTGTTTTTTGA
Found at i:35335 original size:12 final size:12
Alignment explanation
Indices: 35311--35451 Score: 149
Period size: 12 Copynumber: 11.8 Consensus size: 12
35301 TTTGGTGCTA
*
35311 TTTTGCTGTTAT
1 TTTTGTTGTTAT
*
35323 TTTTGTTGCTAT
1 TTTTGTTGTTAT
**
35335 TTTTACTGTTAT
1 TTTTGTTGTTAT
*
35347 TTTTGTTGCTAT
1 TTTTGTTGTTAT
35359 TTTTGTTGTTAT
1 TTTTGTTGTTAT
*
35371 TTTTGTTGTTGT
1 TTTTGTTGTTAT
*
35383 TTTTGTTGCTAT
1 TTTTGTTGTTAT
*
35395 TTTTGTTGTT-G
1 TTTTGTTGTTAT
*
35406 TTTTGCTGTTAT
1 TTTTGTTGTTAT
* * *
35418 TTTTGCTGCTGT
1 TTTTGTTGTTAT
*
35430 TTTGGTTGTTAT
1 TTTTGTTGTTAT
*
35442 TTTGGTTGTT
1 TTTTGTTGTT
35452 TGAATGTTAT
Statistics
Matches: 106, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
11 9 0.08
12 97 0.92
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.68
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:35360 original size:36 final size:36
Alignment explanation
Indices: 35311--35444 Score: 171
Period size: 36 Copynumber: 3.8 Consensus size: 36
35301 TTTGGTGCTA
* * *
35311 TTTTGCTGTTATTTTTGTTGCTATTTTTACTGTTAT
1 TTTTGCTGCTATTTTTGTTGTTATTTTTGCTGTTAT
* * *
35347 TTTTGTTGCTATTTTTGTTGTTATTTTTGTTGTTGT
1 TTTTGCTGCTATTTTTGTTGTTATTTTTGCTGTTAT
* *
35383 TTTTGTTGCTATTTTTGTTGTT-GTTTTGCTGTTAT
1 TTTTGCTGCTATTTTTGTTGTTATTTTTGCTGTTAT
* *
35418 TTTTGCTGCTGTTTTGGTTGTTATTTT
1 TTTTGCTGCTATTTTTGTTGTTATTTT
35445 GGTTGTTTGA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 29 0.35
36 55 0.65
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.69
Consensus pattern (36 bp):
TTTTGCTGCTATTTTTGTTGTTATTTTTGCTGTTAT
Found at i:45456 original size:13 final size:14
Alignment explanation
Indices: 45428--45460 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
45418 AATTAATATC
*
45428 TTATTATTTTTAAT
1 TTATTATTTGTAAT
45442 TTATTA-TTGTAAT
1 TTATTATTTGTAAT
45455 TTATTA
1 TTATTA
45461 GTTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
TTATTATTTGTAAT
Found at i:50004 original size:13 final size:13
Alignment explanation
Indices: 49988--50013 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49978 ATGTAATTTC
49988 ATAAAAAAATTAA
1 ATAAAAAAATTAA
50001 ATAAAAAAATTAA
1 ATAAAAAAATTAA
50014 GGGACTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAAAAAATTAA
Found at i:52252 original size:34 final size:34
Alignment explanation
Indices: 52209--52277 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
52199 TTTGGTTTCT
52209 ACAGCATGTGGATGCTGTTGTGTTAATGTGAATA
1 ACAGCATGTGGATGCTGTTGTGTTAATGTGAATA
52243 ACAGCATGTGGATGCTGTTGTGTTAATGTGAATA
1 ACAGCATGTGGATGCTGTTGTGTTAATGTGAATA
52277 A
1 A
52278 TAGTAAGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.35
Consensus pattern (34 bp):
ACAGCATGTGGATGCTGTTGTGTTAATGTGAATA
Found at i:73528 original size:17 final size:17
Alignment explanation
Indices: 73506--73609 Score: 120
Period size: 17 Copynumber: 6.1 Consensus size: 17
73496 CAAACTCCCT
73506 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
73523 TTAAATTT-GTTTAAAA
1 TTAAATTTATTTTAAAA
*
73539 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
*
73557 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAA
* **
73574 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAA
* *
73591 TTAAAATTATTTTCAAA
1 TTAAATTTATTTTAAAA
73608 TT
1 TT
73610 TAAAATTTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
16 7 0.09
17 62 0.83
18 6 0.08
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:73543 original size:34 final size:34
Alignment explanation
Indices: 73505--73618 Score: 138
Period size: 34 Copynumber: 3.3 Consensus size: 34
73495 CCAAACTCCC
*
73505 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAAATTAAATTTATTTAAAA
* *
73539 TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAAATTAAATTTATTTAAAA
* ** * *
73573 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAATTAAATTTA-TTTAAAA
73608 TTTAAAATTTA
1 TTT-AAATTTA
73619 AAATAAAACT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
34 55 0.77
35 9 0.13
36 7 0.10
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAAATTAAATTTATTTAAAA
Found at i:73553 original size:11 final size:11
Alignment explanation
Indices: 73539--73611 Score: 50
Period size: 11 Copynumber: 6.9 Consensus size: 11
73529 TTGTTTAAAA
73539 TTTAAATTTAT
1 TTTAAATTTAT
73550 TTT-AA---AT
1 TTTAAATTTAT
73557 -TTAAATTTAT
1 TTTAAATTTAT
*
73567 TTTAAATTTAAA
1 TTTAAATTT-AT
*
73579 TTT-AATTTAAG
1 TTTAAATTT-AT
*
73590 TTTAAAATTAT
1 TTTAAATTTAT
73601 TTTCAAATTTA
1 TTT-AAATTTA
73612 AAATTTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
6 2 0.04
7 4 0.08
10 4 0.08
11 25 0.51
12 14 0.29
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Done.