Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014241.1 Kokia drynarioides strain JFW-HI SEQ_129274, 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: 43000
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:4115 original size:30 final size:30
Alignment explanation
Indices: 4081--4140 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4071 GTGCTGGTGC
* *
4081 TGGTGGAGGGTTTGGTAAAGGTGGTGGATA
1 TGGTGGAGGGATTGGCAAAGGTGGTGGATA
* *
4111 TGGTGGTGGGATTGGCAAGGGTGGTGGATA
1 TGGTGGAGGGATTGGCAAAGGTGGTGGATA
4141 CGGAGGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.18, C:0.02, G:0.52, T:0.28
Consensus pattern (30 bp):
TGGTGGAGGGATTGGCAAAGGTGGTGGATA
Found at i:4149 original size:30 final size:30
Alignment explanation
Indices: 4100--4197 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 30
4090 GTTTGGTAAA
* * * * *
4100 GGTGGTGGATATGGTGGTGGGATTGGCAAG
1 GGTGGTGGATACGGAGGTGGAATAGGAAAG
4130 GGTGGTGGATACGGAGGTGGAATAGGAAAG
1 GGTGGTGGATACGGAGGTGGAATAGGAAAG
* * *
4160 GGTGGAGGATACGGAGGTGGCATAGGAAAA
1 GGTGGTGGATACGGAGGTGGAATAGGAAAG
4190 GGTGGTGG
1 GGTGGTGG
4198 GATTGGCAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.24, C:0.04, G:0.52, T:0.19
Consensus pattern (30 bp):
GGTGGTGGATACGGAGGTGGAATAGGAAAG
Found at i:4164 original size:78 final size:77
Alignment explanation
Indices: 4112--4323 Score: 300
Period size: 78 Copynumber: 2.7 Consensus size: 77
4102 TGGTGGATAT
* * *
4112 GGTGGTGGGATTGGCAAGGGTGGTGGATACGGAGGTGGAATAGGAAAGGGTGGAGGATACGGAGG
1 GGTGGTGGGATTGGCAAAGGAGGAGGATACGGAGGTGGAATAGGAAAGGGTGGAGGATACGGAGG
4177 TGGCATAGGAAAA
66 TGG-ATAGGAAAA
* * *
4190 GGTGGTGGGATTGGCAAAGGAGGAGG-TGCTGGTGGTGGAATCGGAAAGGGTGGAGGATACGGAG
1 GGTGGTGGGATTGGCAAAGGAGGAGGATAC-GGAGGTGGAATAGGAAAGGGTGGAGGATACGGAG
*
4254 GTGGCATAGGAAAG
65 GTGG-ATAGGAAAA
* * *
4268 GGTGGTGGGATTGGCAAAGGAGGAGGATACGGAGGTGGAATTGGTAAGGGAGGAGG
1 GGTGGTGGGATTGGCAAAGGAGGAGGATACGGAGGTGGAATAGGAAAGGGTGGAGG
4324 CCATGGAATT
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
77 2 0.02
78 116 0.97
79 2 0.02
ACGTcount: A:0.27, C:0.05, G:0.51, T:0.17
Consensus pattern (77 bp):
GGTGGTGGGATTGGCAAAGGAGGAGGATACGGAGGTGGAATAGGAAAGGGTGGAGGATACGGAGG
TGGATAGGAAAA
Found at i:8514 original size:31 final size:32
Alignment explanation
Indices: 8452--8518 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 32
8442 AAAAAAAAAT
8452 TAGATACTAAATTAAGAAAAAAGGGTCAAATTTA
1 TAGATACTAAATTAAGAAAAAA--GTCAAATTTA
*
8486 TAGATACTAAATTAA-AAAAATA-TTAAATTTA
1 TAGATACTAAATTAAGAAAAA-AGTCAAATTTA
8517 TA
1 TA
8519 TACCAAAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 10 0.32
33 5 0.16
34 16 0.52
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.31
Consensus pattern (32 bp):
TAGATACTAAATTAAGAAAAAAGTCAAATTTA
Found at i:17320 original size:153 final size:153
Alignment explanation
Indices: 17042--17350 Score: 582
Period size: 153 Copynumber: 2.0 Consensus size: 153
17032 TGAGTCCATT
*
17042 AGAAGGCCAACTCAAGGCTAGTAACTTAGCGAAGATGCACTGAGGTAATGGGTTTACAAGCATTA
1 AGAAGGCCAACTCAAGGCTAGTAACTTAGCGAAGATGCACTGAGGCAATGGGTTTACAAGCATTA
*
17107 GAATATAGACGATTTCTGTTTTTAAGTTCCCAATGAACAATATTGGCTTCCATTGACATAACATG
66 GAATATAGACGATTTCTGTTTTTAAATTCCCAATGAACAATATTGGCTTCCATTGACATAACATG
17172 CAGTTATCAACATATAAAGGATA
131 CAGTTATCAACATATAAAGGATA
*
17195 AGAAGGCCAACTCAAGGCTAGTAACTTAGCGAAGATGGACTGAGGCAATGGGTTTACAAGCATTA
1 AGAAGGCCAACTCAAGGCTAGTAACTTAGCGAAGATGCACTGAGGCAATGGGTTTACAAGCATTA
17260 GAATATAGACGATTTCTGTTTTTAAATTCCCAATGAACAATATTGGCTTCCATTGACATAACATG
66 GAATATAGACGATTTCTGTTTTTAAATTCCCAATGAACAATATTGGCTTCCATTGACATAACATG
*
17325 CAGTTATCGACATATAAAGGATA
131 CAGTTATCAACATATAAAGGATA
17348 AGA
1 AGA
17351 TAATTGAGAT
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 152 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (153 bp):
AGAAGGCCAACTCAAGGCTAGTAACTTAGCGAAGATGCACTGAGGCAATGGGTTTACAAGCATTA
GAATATAGACGATTTCTGTTTTTAAATTCCCAATGAACAATATTGGCTTCCATTGACATAACATG
CAGTTATCAACATATAAAGGATA
Found at i:26957 original size:18 final size:18
Alignment explanation
Indices: 26934--26972 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
26924 AATTTAATGA
26934 TTTTT-ATTTTTAAATTTT
1 TTTTTAATTTTT-AATTTT
26952 TTTTTAATTTTTAATTTT
1 TTTTTAATTTTTAATTTT
26970 TTT
1 TTT
26973 AAAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTAATTTTTAATTTT
Found at i:27476 original size:14 final size:14
Alignment explanation
Indices: 27457--27492 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
27447 ACGTCCATTG
27457 AGAAAAGGCTTTTA
1 AGAAAAGGCTTTTA
27471 AGAAAAGGCTTTTA
1 AGAAAAGGCTTTTA
27485 AGAAAAGG
1 AGAAAAGG
27493 TTAAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (14 bp):
AGAAAAGGCTTTTA
Found at i:29984 original size:28 final size:30
Alignment explanation
Indices: 29927--29984 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29917 AACATTAAAC
*
29927 AAACGAACATGAAAACACATAATTTTAAAT
1 AAACGAACATGAAAACACATAATTTAAAAT
29957 AAACGAACATGAACAA-A-A-AATTTAAAAT
1 AAACGAACATGAA-AACACATAATTTAAAAT
29985 TTTTAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 9 0.35
29 1 0.04
30 14 0.54
31 2 0.08
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (30 bp):
AAACGAACATGAAAACACATAATTTAAAAT
Found at i:34647 original size:41 final size:41
Alignment explanation
Indices: 34600--34738 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
34590 TAGCGTGCTT
* * *
34600 ATAAGCGTCGCTGTTGCTCTGATATTTAGCGGTGCTTGCCC
1 ATAAGCGTCGCTATTGCTCTGACATTTAGCGGTGCTTTCCC
* * * * *
34641 ATAAGCGTTGCTATTGCTCTGACATTTAGTGGCGTTTTTCC
1 ATAAGCGTCGCTATTGCTCTGACATTTAGCGGTGCTTTCCC
* * *
34682 ATAAACGTCGCTATTGCTCTGACCTTTAACGGTGCTTTCCC
1 ATAAGCGTCGCTATTGCTCTGACATTTAGCGGTGCTTTCCC
* * *
34723 GTAAGCGCCGTTATTG
1 ATAAGCGTCGCTATTG
34739 TTCTACCTTT
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (41 bp):
ATAAGCGTCGCTATTGCTCTGACATTTAGCGGTGCTTTCCC
Found at i:36574 original size:6 final size:6
Alignment explanation
Indices: 36538--36573 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
36528 AGCTTAGTTG
*
36538 AACAAT AACAAT AACAAT AACAAT AACAAT TACAAT
1 AACAAT AACAAT AACAAT AACAAT AACAAT AACAAT
36574 TTTATAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (6 bp):
AACAAT
Found at i:42968 original size:2 final size:2
Alignment explanation
Indices: 42961--43000 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
42951 TATTTTAAGA
42961 AT AT 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
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.