Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014888.1 Kokia drynarioides strain JFW-HI SEQ_129931, 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: 32994
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2388 original size:26 final size:26
Alignment explanation
Indices: 2359--2410 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2349 AAAGAGTGTG
2359 ATTAGCAGTCAAATGGATGCTTTAAT
1 ATTAGCAGTCAAATGGATGCTTTAAT
2385 ATTAGCAGTCAAATGGATGCTTTAAT
1 ATTAGCAGTCAAATGGATGCTTTAAT
2411 GGGGTTGTCA
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:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (26 bp):
ATTAGCAGTCAAATGGATGCTTTAAT
Found at i:3516 original size:14 final size:13
Alignment explanation
Indices: 3491--3524 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
3481 AAATTATATT
3491 AAATTA-AAATAA
1 AAATTATAAATAA
3503 AAATATATAAATAA
1 AAAT-TATAAATAA
3517 AAATTATA
1 AAATTATA
3525 TTTCCTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 6 0.30
14 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATTATAAATAA
Found at i:5469 original size:11 final size:10
Alignment explanation
Indices: 5440--5469 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
5430 AATAATTTAT
5440 AAATTATAAA
1 AAATTATAAA
5450 AAATTATAAA
1 AAATTATAAA
5460 AAATTGATAA
1 AAATT-ATAA
5470 TAATTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (10 bp):
AAATTATAAA
Found at i:7997 original size:145 final size:143
Alignment explanation
Indices: 7721--8131 Score: 477
Period size: 145 Copynumber: 2.8 Consensus size: 143
7711 TTCGGTTAAT
* *
7721 AGTTTTCTGGTTAGTTCATTAGCTCTTGGTTAGACTGTGTAATCAAATGTTGACTTTAACTCGAA
1 AGTTTTCGGGTTAGTT-AATAGCT-TTGGTTAGACTGTGTAATCAAATGTT-ACTTTAACTCGAA
* * * * * ** * * *
7786 CACAATCGTTATAGGATGTATGAAAAAGAGTTGTTTGTGTGATACATCCGGTTGATGAACTTTGT
63 CACGATCGTTCTAGGATCTATGAACAAGAGTTGTTCGCATGATAGATTCGGTTGATGAACTCTGT
7851 TTGGTGTATGTAATGA
128 TTGGTGTATGTAATGA
* *
7867 AGTTTTCGGGTTAGTTAAGTAGCTTTTGGTTAGACTGTGTTATCAAATGTTTCTTTAACTCGAAC
1 AGTTTTCGGGTTAGTTAA-TAGC-TTTGGTTAGACTGTGTAATCAAATGTTACTTTAACTCGAAC
* * * * *
7932 ATGATCATTCTAGGTTCTTTGAACAAGAGTTGTTCGCATGATAGATTTGGTTGATGAACTCTGTT
64 ACGATCGTTCTAGGATCTATGAACAAGAGTTGTTCGCATGATAGATTCGGTTGATGAACTCTGTT
7997 TGGTGTATGTAATGA
129 TGGTGTATGTAATGA
* * * * *
8012 AGTTTTCGGGTTAGTTCAATAGC--T-CTTAGACTATGTAATCAAATGTTGCTTTAACCCAAACA
1 AGTTTTCGGGTTAGTT-AATAGCTTTGGTTAGACTGTGTAATCAAATGTTACTTTAACTCGAACA
* * * * *
8074 CGATTGTTCTAGGCTCTGTGAAACAAGAGTTGTTCACATGATAGATTCAGTTGATGAA
65 CGATCGTTCTAGGATCTATG-AACAAGAGTTGTTCGCATGATAGATTCGGTTGATGAA
8132 GTTTTTCGGG
Statistics
Matches: 228, Mismatches: 33, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
141 47 0.21
142 35 0.15
145 99 0.43
146 46 0.20
147 1 0.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (143 bp):
AGTTTTCGGGTTAGTTAATAGCTTTGGTTAGACTGTGTAATCAAATGTTACTTTAACTCGAACAC
GATCGTTCTAGGATCTATGAACAAGAGTTGTTCGCATGATAGATTCGGTTGATGAACTCTGTTTG
GTGTATGTAATGA
Found at i:9773 original size:148 final size:149
Alignment explanation
Indices: 9504--9799 Score: 443
Period size: 148 Copynumber: 2.0 Consensus size: 149
9494 GATGGATGGA
* *
9504 TATGCATTCTCCAAATTAGAATTTGTAAAACAACCCTTGCTTTGTTTGCATGATACTACATGTTG
1 TATGCATTCTCCAAATTAGAATTTGTAAAACAACCCTTGCTTTGCTTCCATGATACTACATGTTG
* * * * *
9569 ATGTGCTTTTGATGTTTGCCTTGCTTTAAAGCTCCTCTCATCTTCATTTTCATGTATATTTATAT
66 ATGTACTTTTCATGTTTGCCTTGCTTTAAAGCTCCTCTAATCTTCATTTTCATGTATATGTATAG
9634 ATCTATGCATGCATGTATG
131 ATCTATGCATGCATGTATG
* * *
9653 TATGCGTTCTCCTAATTAGAATTTGTAAAACATCCCTTGC-TTGCTTCCATGATAC-ATCATGTT
1 TATGCATTCTCCAAATTAGAATTTGTAAAACAACCCTTGCTTTGCTTCCATGATACTA-CATGTT
* *
9716 GATGTACTTTTCATGTTTGCCTTGCTTTAAAGTTCCTCTAATCTTCATTTTCATGTATATGTATG
65 GATGTACTTTTCATGTTTGCCTTGCTTTAAAGCTCCTCTAATCTTCATTTTCATGTATATGTATA
* *
9781 GATCTATGTATGTATGTAT
130 GATCTATGCATGCATGTAT
9800 CATGCATGCA
Statistics
Matches: 132, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
147 1 0.01
148 94 0.71
149 37 0.28
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (149 bp):
TATGCATTCTCCAAATTAGAATTTGTAAAACAACCCTTGCTTTGCTTCCATGATACTACATGTTG
ATGTACTTTTCATGTTTGCCTTGCTTTAAAGCTCCTCTAATCTTCATTTTCATGTATATGTATAG
ATCTATGCATGCATGTATG
Found at i:17853 original size:30 final size:30
Alignment explanation
Indices: 17786--17858 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
17776 TATTGGGACT
* * *
17786 GAATCAAATTAGTCCTTCTACTATTAAAGA
1 GAATCAAATTAGTCCCTATACTATTAAAAA
*
17816 G-ATCAAATTAGTCCCTATATTATTAAAAA
1 GAATCAAATTAGTCCCTATACTATTAAAAA
*
17845 GAATCAAATAAGTC
1 GAATCAAATTAGTC
17859 TAGATTGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (30 bp):
GAATCAAATTAGTCCCTATACTATTAAAAA
Found at i:21920 original size:22 final size:21
Alignment explanation
Indices: 21895--21935 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21885 TTAAAAAAAA
*
21895 CTCTAACATTAAAAAGAATTCC
1 CTCTAACA-AAAAAAGAATTCC
*
21917 CTCTTACAAAAAAAGAATT
1 CTCTAACAAAAAAAGAATT
21936 TGGAATTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.27
Consensus pattern (21 bp):
CTCTAACAAAAAAAGAATTCC
Found at i:23384 original size:15 final size:17
Alignment explanation
Indices: 23356--23387 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
23346 TAAAAAATTA
23356 AAAAAATATAAATCAAT
1 AAAAAATATAAATCAAT
23373 AAAAAA-AT-AATCAAT
1 AAAAAATATAAATCAAT
23388 CAATGAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAAATATAAATCAAT
Found at i:23388 original size:19 final size:18
Alignment explanation
Indices: 23354--23391 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23344 AATAAAAAAT
23354 TAAAAAAATATAAATCAA
1 TAAAAAAATATAAATCAA
*
23372 TAAAAAAATAATCAATCAA
1 TAAAAAAAT-ATAAATCAA
23391 T
1 T
23392 GAAATGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAAAAATATAAATCAA
Found at i:29090 original size:70 final size:70
Alignment explanation
Indices: 28988--29136 Score: 262
Period size: 70 Copynumber: 2.1 Consensus size: 70
28978 TAACCAATAA
* * *
28988 TAACAAGCCACCTAAGGCTTCTTCTTGACATTTCTACTATTATCATCCATCAAGCCAAATTAACC
1 TAACAAGCCACCTAAGACTTCTTCTAGACATTTCTACCATTATCATCCATCAAGCCAAATTAACC
29053 ACAAT
66 ACAAT
*
29058 TAACAAGTCACCTAAGACTTCTTCTAGACATTTCTACCATTATCATCCATCAAGCCAAATTAACC
1 TAACAAGCCACCTAAGACTTCTTCTAGACATTTCTACCATTATCATCCATCAAGCCAAATTAACC
29123 ACAAT
66 ACAAT
29128 TAACAAGCC
1 TAACAAGCC
29137 GGACATTTCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.28
Consensus pattern (70 bp):
TAACAAGCCACCTAAGACTTCTTCTAGACATTTCTACCATTATCATCCATCAAGCCAAATTAACC
ACAAT
Found at i:31931 original size:157 final size:157
Alignment explanation
Indices: 31645--31963 Score: 620
Period size: 157 Copynumber: 2.0 Consensus size: 157
31635 GAATTAAACA
31645 ATAATTTCAACGAATTCTGGGAATTCTCTTGAGCAGGATATAATCTCGTGCCTACCTGTATTTCG
1 ATAATTTCAACGAATTCTGGGAATTCTCTTGAGCAGGATATAATCTCGTGCCTACCTGTATTTCG
*
31710 GGAAGCATTCCGGTATTGAATGCAAAAACGAGATTTGCAGATGCCCTGATGGTTGAAAAAATCCG
66 GGAAGCATTCCGGTATTGAATGCAAAAACGAGATTTGCAGATGCCCTGATGGTGGAAAAAATCCG
31775 GTTGGCGGTTGATGTCCAGTGTATGGT
131 GTTGGCGGTTGATGTCCAGTGTATGGT
31802 ATAATTTCAACGAATTCTGGGAATTCTCTTGAGCAGGATATAATCTCGTGCCTACCTGTATTTCG
1 ATAATTTCAACGAATTCTGGGAATTCTCTTGAGCAGGATATAATCTCGTGCCTACCTGTATTTCG
31867 GGAAGCATTCCGGTATTGAATGCAAAAACGAGATTTGCAGATGCCCTGATGGTGGAAAAAATCCG
66 GGAAGCATTCCGGTATTGAATGCAAAAACGAGATTTGCAGATGCCCTGATGGTGGAAAAAATCCG
*
31932 GTTGGTGGTTGATGTCCAGTGTATGGT
131 GTTGGCGGTTGATGTCCAGTGTATGGT
31959 ATAAT
1 ATAAT
31964 CTCTAGGCGA
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 160 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (157 bp):
ATAATTTCAACGAATTCTGGGAATTCTCTTGAGCAGGATATAATCTCGTGCCTACCTGTATTTCG
GGAAGCATTCCGGTATTGAATGCAAAAACGAGATTTGCAGATGCCCTGATGGTGGAAAAAATCCG
GTTGGCGGTTGATGTCCAGTGTATGGT
Done.