Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014559.1 Kokia drynarioides strain JFW-HI SEQ_129598, 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: 80590
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 115 characters in sequence are not A, C, G, or T
Found at i:3121 original size:18 final size:19
Alignment explanation
Indices: 3100--3138 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3090 TTTTTAAAAA
3100 TATAAAT-TTTAAAATTTT
1 TATAAATATTTAAAATTTT
**
3118 TATAAATATTTTGAATTTT
1 TATAAATATTTAAAATTTT
3137 TA
1 TA
3139 AAAACTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TATAAATATTTAAAATTTT
Found at i:3777 original size:14 final size:14
Alignment explanation
Indices: 3748--3784 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3738 AAATTATTTT
*
3748 TTATTATTTTTGAAA
1 TTATT-TTTTTAAAA
3763 TTATTTTTTTAAAA
1 TTATTTTTTTAAAA
3777 TTATTTTT
1 TTATTTTT
3785 AGTGAAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TTATTTTTTTAAAA
Found at i:7609 original size:40 final size:41
Alignment explanation
Indices: 7553--7633 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 41
7543 AAAATATAAG
7553 TTTTTAATTTTTATTTAAAATATGAA-AAATAAATTTTAAAA
1 TTTTTAATTTTTATTTAAAATAT-AAGAAATAAATTTTAAAA
* *
7594 TTTTT-ATTTTTATTTAAAGTATAAGAATTAAATTTTAAAA
1 TTTTTAATTTTTATTTAAAATATAAGAAATAAATTTTAAAA
7634 AGTAAGGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 2 0.05
40 30 0.81
41 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (41 bp):
TTTTTAATTTTTATTTAAAATATAAGAAATAAATTTTAAAA
Found at i:8932 original size:9 final size:9
Alignment explanation
Indices: 8918--8996 Score: 70
Period size: 9 Copynumber: 8.6 Consensus size: 9
8908 TTTTGATACA
8918 TTTTATAAT
1 TTTTATAAT
*
8927 TTTTATGAT
1 TTTTATAAT
*
8936 TTTTATAAAA
1 TTTTAT-AAT
*
8946 TTTTACAAT
1 TTTTATAAT
8955 TTTTAT-AT
1 TTTTATAAT
**
8963 TTTTACGAT
1 TTTTATAAT
8972 TTTTATAATT
1 TTTTATAA-T
*
8982 TGTTTCTAAT
1 T-TTTATAAT
8992 TTTTA
1 TTTTA
8997 ATGAGTTTTA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
8 7 0.13
9 32 0.58
10 10 0.18
11 6 0.11
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:9963 original size:22 final size:22
Alignment explanation
Indices: 9937--9978 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9927 GACCTAAATT
9937 TTAAAATCTAAAAAATAAAAAA
1 TTAAAATCTAAAAAATAAAAAA
* *
9959 TTAAATTCTTAAAAATAAAA
1 TTAAAATCTAAAAAATAAAA
9979 GTATAAGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
TTAAAATCTAAAAAATAAAAAA
Found at i:13675 original size:28 final size:29
Alignment explanation
Indices: 13623--13677 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
13613 GGGGGTTTTG
*
13623 GTTCGTGGGTGAAGATGATAATGGTGAAA
1 GTTCATGGGTGAAGATGATAATGGTGAAA
13652 GTTCATGGGTG-AGATGA-AGATGGTGA
1 GTTCATGGGTGAAGATGATA-ATGGTGA
13678 TGAAAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 13 0.54
29 10 0.42
ACGTcount: A:0.29, C:0.04, G:0.40, T:0.27
Consensus pattern (29 bp):
GTTCATGGGTGAAGATGATAATGGTGAAA
Found at i:13744 original size:32 final size:32
Alignment explanation
Indices: 13684--13749 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
13674 GTGATGAAAG
* * *
13684 AAAAAAAGGAAAGGAAAGAATAAGAAATATGA
1 AAAAAAAGGAAAGGAAAAAAGAAGAAATAGGA
*
13716 AAAAGAAAGG-AAGGAAAAAAGAATAAATAGGA
1 AAAA-AAAGGAAAGGAAAAAAGAAGAAATAGGA
13748 AA
1 AA
13750 TAAAGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.08
Consensus pattern (32 bp):
AAAAAAAGGAAAGGAAAAAAGAAGAAATAGGA
Found at i:20252 original size:61 final size:61
Alignment explanation
Indices: 20130--20260 Score: 135
Period size: 61 Copynumber: 2.1 Consensus size: 61
20120 TTGCTGACTC
* * * *
20130 AATTTAAAAAAATTATAAAAATAAATATTAAATTATTCAAAAATTTACATTTTAATTAATT
1 AATTTTAAAAAATTATAAAAATAAATATTAAACTATTCAAAAATTTACATTTAAATCAATT
* * *
20191 AATTTTAAAAAATTAT-AAAAT-AATCGTTAACCTATTCAAAAATCTT-TATTTAAAATCAATT
1 AATTTTAAAAAATTATAAAAATAAAT-ATTAAACTATTCAAAAAT-TTACATTT-AAATCAATT
20252 -ATTATTAAA
1 AATT-TTAAA
20261 TCTTTAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
59 3 0.05
60 27 0.46
61 29 0.49
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (61 bp):
AATTTTAAAAAATTATAAAAATAAATATTAAACTATTCAAAAATTTACATTTAAATCAATT
Found at i:20998 original size:20 final size:21
Alignment explanation
Indices: 20975--21015 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
20965 GGAGGAACAA
20975 ATGGTTAGTTT-CTCGAACGG
1 ATGGTTAGTTTCCTCGAACGG
20995 ATGGTTAGTTTCCTCGAACGG
1 ATGGTTAGTTTCCTCGAACGG
21016 CTACCTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (21 bp):
ATGGTTAGTTTCCTCGAACGG
Found at i:21490 original size:26 final size:26
Alignment explanation
Indices: 21454--21505 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
21444 TTACTAATAA
21454 TTCGGTGACTTTGGATATAGTTTACC
1 TTCGGTGACTTTGGATATAGTTTACC
21480 TTCGGTGACTTTGGATATAGTTTACC
1 TTCGGTGACTTTGGATATAGTTTACC
21506 CTACTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (26 bp):
TTCGGTGACTTTGGATATAGTTTACC
Found at i:44021 original size:25 final size:25
Alignment explanation
Indices: 43987--44038 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
43977 AGTGCATGTT
43987 TTAATTGCAATAAATCTTCAAGTGC
1 TTAATTGCAATAAATCTTCAAGTGC
44012 TTAATTGCAATAAATCTTCAAGTGC
1 TTAATTGCAATAAATCTTCAAGTGC
44037 TT
1 TT
44039 CCTTCCAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (25 bp):
TTAATTGCAATAAATCTTCAAGTGC
Found at i:46009 original size:17 final size:19
Alignment explanation
Indices: 45974--46015 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
45964 AAAAATTATA
45974 TTATATTATTTTAATATTT
1 TTATATTATTTTAATATTT
45993 TTAT-TTATTTTAA-ATTT
1 TTATATTATTTTAATATTT
46010 TTATAT
1 TTATAT
46016 AATCATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 10 0.45
19 4 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATTATTTTAATATTT
Found at i:51530 original size:76 final size:76
Alignment explanation
Indices: 51437--51607 Score: 211
Period size: 76 Copynumber: 2.2 Consensus size: 76
51427 AATTTAGTAA
* * * *
51437 AGATTTAGATTTCTAAGTTTCATTAGATTCAAGATTGGAT-TTAC-ATTTTAAATTTGATTAAAT
1 AGATTTAGATTTTTAAGTTTCACTAGATTCAAGATT--ATGTTACTATTTTAAATTGGATTAAAC
* **
51500 TTAGCTTTAAATG
64 GTAGCCGTAAATG
* * *
51513 AGATTTAGATTTTTAAGTTTCACTAGGTTCAAGATTATGTTTCTATTTTAAATTGGATTAGACGT
1 AGATTTAGATTTTTAAGTTTCACTAGATTCAAGATTATGTTACTATTTTAAATTGGATTAAACGT
51578 AGCCGTAAATG
66 AGCCGTAAATG
*
51589 AGGTTTAGATTTTTAAGTT
1 AGATTTAGATTTTTAAGTT
51608 ACAAAAAAAT
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
74 2 0.02
75 3 0.04
76 77 0.94
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (76 bp):
AGATTTAGATTTTTAAGTTTCACTAGATTCAAGATTATGTTACTATTTTAAATTGGATTAAACGT
AGCCGTAAATG
Found at i:53337 original size:18 final size:19
Alignment explanation
Indices: 53314--53349 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53304 TGTCATGATA
*
53314 CCAATA-TATGTAGGAGAT
1 CCAATATTATGGAGGAGAT
53332 CCAATATTATGGAGGAGA
1 CCAATATTATGGAGGAGA
53350 GTCCCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (19 bp):
CCAATATTATGGAGGAGAT
Found at i:57447 original size:8 final size:9
Alignment explanation
Indices: 57420--57468 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
57410 AAAATATGTC
57420 AATTATAAA
1 AATTATAAA
57429 AATTATAAA
1 AATTATAAA
57438 AATTATAAA
1 AATTATAAA
*
57447 AATGGA-AAGA
1 AAT-TATAA-A
57457 AATTATAAA
1 AATTATAAA
57466 AAT
1 AAT
57469 ATATGTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 28 0.80
10 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (9 bp):
AATTATAAA
Found at i:61342 original size:4 final size:4
Alignment explanation
Indices: 61333--61358 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
61323 TAACCTTTAG
61333 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
61359 AACCCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:72944 original size:3 final size:3
Alignment explanation
Indices: 72938--72975 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
72928 TTATTATTAT
*
72938 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG GAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
72976 AATTGAAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
TAG
Found at i:75363 original size:2 final size:2
Alignment explanation
Indices: 75351--75401 Score: 93
Period size: 2 Copynumber: 25.0 Consensus size: 2
75341 CTAATTTGTA
75351 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75394 AT AT AT AT
1 AT AT AT AT
75402 TGTGATTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.