Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013086.1 Kokia drynarioides strain JFW-HI SEQ_128104, 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: 48121
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 140 characters in sequence are not A, C, G, or T
Found at i:3168 original size:24 final size:24
Alignment explanation
Indices: 3124--3169 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3114 TAAATTAATT
* *
3124 TTTACTTTATTTTTATGATTTTGA
1 TTTAATTTATTTTTATAATTTTGA
3148 TTTAATTT-TTTTTAATAATTTT
1 TTTAATTTATTTTT-ATAATTTT
3170 ACTCTTCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTAATTTATTTTTATAATTTTGA
Found at i:14815 original size:28 final size:28
Alignment explanation
Indices: 14782--14837 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
14772 TAAAAATATA
14782 AACTAT-TAAAATAATAAAATTATATTTT
1 AACTATATAAAATAATAAAATTA-ATTTT
* *
14810 AACTATCATAAAATTATACAATTAATTT
1 AACTAT-ATAAAATAATAAAATTAATTT
14838 CGACCCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 4 0.17
30 14 0.58
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (28 bp):
AACTATATAAAATAATAAAATTAATTTT
Found at i:17887 original size:29 final size:30
Alignment explanation
Indices: 17839--17909 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
17829 TTAAATTTTT
* *
17839 AATAAT-AAAATTGTATTTTAGTTTTTTAA
1 AATAATAAAAATTGTAATTTAATTTTTTAA
17868 AATAATAAAAATT-TAATTTAATTTTTTAA
1 AATAATAAAAATTGTAATTTAATTTTTTAA
*
17897 AATTTATAAAAAT
1 AA-TAATAAAAAT
17910 ATAAATTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AATAATAAAAATTGTAATTTAATTTTTTAA
Found at i:17922 original size:25 final size:25
Alignment explanation
Indices: 17887--17945 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
17877 AATTTAATTT
* *
17887 AATTTTTTAAAATTTATAAAAATATA
1 AATTTATTAAAA-TGATAAAAATATA
*
17913 AA-TTATTAAAATGATAAAATTATA
1 AATTTATTAAAATGATAAAAATATA
17937 AATTTATTA
1 AATTTATTA
17946 TCGGAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.45
25 14 0.48
26 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
AATTTATTAAAATGATAAAAATATA
Found at i:17932 original size:17 final size:16
Alignment explanation
Indices: 17894--17938 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
17884 TTTAATTTTT
17894 TAAAATTTATAAAAATA
1 TAAAA-TTATAAAAATA
*
17911 T-AAATTATTAAAATGA
1 TAAAATTATAAAAAT-A
17927 TAAAATTATAAA
1 TAAAATTATAAA
17939 TTTATTATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 9 0.38
16 5 0.21
17 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAAATTATAAAAATA
Found at i:27038 original size:63 final size:62
Alignment explanation
Indices: 26924--27052 Score: 179
Period size: 63 Copynumber: 2.1 Consensus size: 62
26914 GGCTAGGCTT
** * *
26924 AAGCTTGAACATTCAAGATCCGAGCTTTACCTATATATTAACCAAACTTAATTTTTTTACCTC
1 AAGCTTGAACATTCAAGATCCGAGCTCGACCCATATATTAAACAAACTTAATTTTTTTACC-C
* *
26987 AAGCTTGAACATTCAA-AGTCCGAGCTCGACCCATATTTTAAACAAATTTAATTTTTTTACCC
1 AAGCTTGAACATTCAAGA-TCCGAGCTCGACCCATATATTAAACAAACTTAATTTTTTTACCC
27049 AAGC
1 AAGC
27053 CCAATTTTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
62 6 0.10
63 53 0.90
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (62 bp):
AAGCTTGAACATTCAAGATCCGAGCTCGACCCATATATTAAACAAACTTAATTTTTTTACCC
Found at i:34627 original size:22 final size:22
Alignment explanation
Indices: 34596--34637 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34586 CTTTTTTCTT
*
34596 AACTTCTATGGATAAAATAAAC
1 AACTTCTATGCATAAAATAAAC
*
34618 AACTTTTATGCATAAAATAA
1 AACTTCTATGCATAAAATAA
34638 GTGCCCCTAA
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:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (22 bp):
AACTTCTATGCATAAAATAAAC
Found at i:42658 original size:19 final size:19
Alignment explanation
Indices: 42618--42662 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42608 TTGTATTAGG
42618 ATTTAATATTTAAGATATT
1 ATTTAATATTTAAGATATT
* *
42637 ATTTATTATTTAA-ATTTGT
1 ATTTAATATTTAAGATAT-T
42656 ATTTAAT
1 ATTTAAT
42663 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAGATATT
Found at i:42685 original size:14 final size:14
Alignment explanation
Indices: 42662--42691 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42652 TTGTATTTAA
*
42662 TTTATGTTTATCTT
1 TTTATATTTATCTT
42676 TTTATATTTATCTT
1 TTTATATTTATCTT
42690 TT
1 TT
42692 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:43486 original size:22 final size:22
Alignment explanation
Indices: 43461--43506 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
43451 TTCGACTTCC
43461 CTATATTCTATTT-CTTTTAATT
1 CTATATTCT-TTTACTTTTAATT
* *
43483 CTATTTTCTTTTATTTTTAATT
1 CTATATTCTTTTACTTTTAATT
43505 CT
1 CT
43507 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (22 bp):
CTATATTCTTTTACTTTTAATT
Found at i:43492 original size:16 final size:15
Alignment explanation
Indices: 43465--43509 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
43455 ACTTCCCTAT
43465 ATTCTATTTCTTTTA
1 ATTCTATTTCTTTTA
43480 ATTCTATTTTCTTTTA
1 ATTCTA-TTTCTTTTA
* * *
43496 TTTTTAATTCTTTT
1 ATTCTATTTCTTTT
43510 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTCTATTTCTTTTA
Found at i:43511 original size:22 final size:20
Alignment explanation
Indices: 43475--43519 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
43465 ATTCTATTTC
43475 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTATTTT-TTTT-T
43497 TTTTAATTCT-TTTTTTTTT
1 TTTTAATTCTATTTTTTTTT
43516 TTTT
1 TTTT
43520 CTTAGATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.22
20 4 0.17
21 4 0.17
22 10 0.43
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTAATTCTATTTTTTTTT
Found at i:43521 original size:15 final size:15
Alignment explanation
Indices: 43471--43522 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
43461 CTATATTCTA
* *
43471 TTTCTTTTAATTCTAT
1 TTTCTTTT-ATTTTTT
*
43487 TTTCTTTTATTTTTA
1 TTTCTTTTATTTTTT
* *
43502 ATTCTTTTTTTTTTT
1 TTTCTTTTATTTTTT
43517 TTTCTT
1 TTTCTT
43523 AGATTGCGAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 21 0.72
16 8 0.28
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTATTTTTT
Found at i:45871 original size:30 final size:30
Alignment explanation
Indices: 45837--45919 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
45827 GAACTTTCTA
* *
45837 AAAATCATATTTTAACACCTAAACTTTTCC
1 AAAATTATATTTTAACCCCTAAACTTTTCC
*
45867 AAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTATATTTTAACCCCTAAACTTTTCC
* *
45897 AAAATTGTAATTTAACCCCTAAA
1 AAAATTATATTTTAACCCCTAAA
45920 ATTTCTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (30 bp):
AAAATTATATTTTAACCCCTAAACTTTTCC
Found at i:46017 original size:28 final size:29
Alignment explanation
Indices: 45955--46191 Score: 198
Period size: 29 Copynumber: 8.1 Consensus size: 29
45945 TGAACATTCA
* * *
45955 AAAAATCACGTTTTTTTCTCCCAAACTTTC
1 AAAAATCACATTTTTATC-CCCAAACTTCC
*
45985 AAAAATCACATTTTTATCCCTAAACTTCC
1 AAAAATCACATTTTTATCCCCAAACTTCC
* *
46014 AAAAATCACATTTTGACCCCCAAACTTCTC
1 AAAAATCACATTTTTATCCCCAAACTTC-C
* *
46044 AAAAATTACA-TTTT-CCCCCAAACTTCTC
1 AAAAATCACATTTTTATCCCCAAACTTC-C
* *
46072 AAAAATTACA-TTTT-TCCCCAAGCTTCC
1 AAAAATCACATTTTTATCCCCAAACTTCC
* * *
46099 AAAAATTATATTTTT-TCCCTCGAACTTCC
1 AAAAATCACATTTTTATCCC-CAAACTTCC
* *
46128 AAAAATCACATTTTTA-CTCTCGAACTTCTC
1 AAAAATCACATTTTTATC-CCCAAACTTC-C
* * *
46158 AAAAATAACTTTTTTATCCCTAAAACTTTCC
1 AAAAATCACATTTTTATCCC-CAAAC-TTCC
46189 AAA
1 AAA
46192 TTACGTTTTA
Statistics
Matches: 176, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
27 10 0.06
28 46 0.26
29 66 0.38
30 43 0.24
31 8 0.05
32 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAAATCACATTTTTATCCCCAAACTTCC
Found at i:46117 original size:57 final size:56
Alignment explanation
Indices: 45967--46142 Score: 196
Period size: 57 Copynumber: 3.1 Consensus size: 56
45957 AAATCACGTT
* * *
45967 TTTTTCTCCCAAACTTTCAAAAATCACATTTTTAT-CCCTAAACTTCCAAAAATCACA
1 TTTTTC-CCCAAACTTCCAAAAATTACATTTTT-TCCCCCAAACTTCCAAAAATCACA
* *
46024 TTTTGACCCCCAAACTTCTCAAAAATTACA--TTTTCCCCCAAACTTCTCAAAAATTACA
1 TTTT--TCCCCAAACTTC-CAAAAATTACATTTTTTCCCCCAAACTTC-CAAAAATCACA
* * * *
46082 TTTTTCCCCAAGCTTCCAAAAATTATATTTTTTCCCTCGAACTTCCAAAAATCACA
1 TTTTTCCCCAAACTTCCAAAAATTACATTTTTTCCCCCAAACTTCCAAAAATCACA
46138 TTTTT
1 TTTTT
46143 ACTCTCGAAC
Statistics
Matches: 101, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
55 10 0.10
56 26 0.26
57 31 0.31
58 23 0.23
59 11 0.11
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (56 bp):
TTTTTCCCCAAACTTCCAAAAATTACATTTTTTCCCCCAAACTTCCAAAAATCACA
Found at i:46346 original size:15 final size:15
Alignment explanation
Indices: 46326--46370 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
46316 CGATTCATAT
*
46326 TTTATTTTTCTTATA
1 TTTATTTTTCGTATA
46341 TTTA-TTTTCGTATA
1 TTTATTTTTCGTATA
*
46355 TTTATTCATTCGTATA
1 TTTATT-TTTCGTATA
46371 ATTGTTCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 13 0.50
15 5 0.19
16 8 0.31
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.64
Consensus pattern (15 bp):
TTTATTTTTCGTATA
Done.