Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012392.1 Kokia drynarioides strain JFW-HI SEQ_127396, 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: 19527
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:648 original size:36 final size:37
Alignment explanation
Indices: 575--663 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 37
565 TGATCGTTAT
*
575 TCGTTTTACTCCCTGTTGACCCCAAAGGTCATGATGC
1 TCGTTTTACTCCCTGTTGACCCCAAAGGTAATGATGC
* * *
612 TCGTTTTACTCCTTGTTGA-CCTAAAGGTAATTATGC
1 TCGTTTTACTCCCTGTTGACCCCAAAGGTAATGATGC
* *
648 TCATTTTTCTCCCTGT
1 TCGTTTTACTCCCTGT
664 ACATCCAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 27 0.60
37 18 0.40
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.40
Consensus pattern (37 bp):
TCGTTTTACTCCCTGTTGACCCCAAAGGTAATGATGC
Found at i:2198 original size:31 final size:31
Alignment explanation
Indices: 2163--2255 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 31
2153 AAAATCAAAT
2163 ATAAACAACTATTGATAAAACTAAATTACAC
1 ATAAACAACTATTGATAAAACTAAATTACAC
* ** *
2194 ATAAATTGAA-TATCCA-AAAAC--CA--A-AC
1 ATAAA--CAACTATTGATAAAACTAAATTACAC
*
2220 ATAAACAACTATTGATAAAACTAGATTACAC
1 ATAAACAACTATTGATAAAACTAAATTACAC
2251 ATAAA
1 ATAAA
2256 TAAGTAGAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 18
0.63 0.11 0.25
Matches are distributed among these distances:
24 2 0.04
25 4 0.09
26 12 0.27
27 1 0.02
28 1 0.02
29 1 0.02
30 1 0.02
31 17 0.38
32 4 0.09
33 2 0.04
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (31 bp):
ATAAACAACTATTGATAAAACTAAATTACAC
Found at i:2234 original size:57 final size:56
Alignment explanation
Indices: 2147--2256 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 56
2137 AACAAATTTT
* *
2147 ATATCCAAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATTGA
1 ATATCCAAAACCAAACATAAACAACTATTGATAAAACTAAATTACACATAAATTGA
*
2203 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAAT
1 ATATCC-AAAACCAAACATAAACAACTATTGATAAAACTAAATTACACATAAAT
2257 AAGTAGAACA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
56 6 0.12
57 44 0.88
ACGTcount: A:0.55, C:0.16, G:0.04, T:0.25
Consensus pattern (56 bp):
ATATCCAAAACCAAACATAAACAACTATTGATAAAACTAAATTACACATAAATTGA
Found at i:5292 original size:31 final size:32
Alignment explanation
Indices: 5257--5321 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
5247 TAACGTCGAC
*
5257 AGCTAAAATGGAAG-GGGAAAAAATGGAAAAT
1 AGCTAAAATGGAAGAGGGAAAAAATGAAAAAT
5288 AGCTAAAATGGAAGAAGGGAAAAAATGAAAAAT
1 AGCTAAAATGGAAG-AGGGAAAAAATGAAAAAT
5321 A
1 A
5322 ACTCCGACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 14 0.45
33 17 0.55
ACGTcount: A:0.58, C:0.03, G:0.26, T:0.12
Consensus pattern (32 bp):
AGCTAAAATGGAAGAGGGAAAAAATGAAAAAT
Found at i:6180 original size:70 final size:67
Alignment explanation
Indices: 6097--6229 Score: 162
Period size: 70 Copynumber: 1.9 Consensus size: 67
6087 TCCGAATAAG
* * *
6097 AAAAGGCAAAACTACGTCGTTTTGATAAATATTTA-TCTATTCTAAAGTTAAA-AGTCAAAACCA
1 AAAAGGAAAAACTACGTCGTGTTCATAAATATTTACTC-A-T-T-AAGTTAAAGAG-CAAAACCA
6160 TTAAGTT
61 TTAAGTT
* *
6167 AAAAGGAAAAACTATGTCGTGTTCATAAATGTTTACTCATTAAGTTAAAGAGCAAAACCATTA
1 AAAAGGAAAAACTACGTCGTGTTCATAAATATTTACTCATTAAGTTAAAGAGCAAAACCATTA
6230 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
67 19 0.34
68 3 0.05
69 1 0.02
70 31 0.55
71 2 0.04
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (67 bp):
AAAAGGAAAAACTACGTCGTGTTCATAAATATTTACTCATTAAGTTAAAGAGCAAAACCATTAAG
TT
Found at i:8607 original size:39 final size:39
Alignment explanation
Indices: 8564--8790 Score: 167
Period size: 39 Copynumber: 5.8 Consensus size: 39
8554 ATGTTGGAAA
*
8564 TATACTGAACCGACAGTGACACTGTAAACACTGCAATGT
1 TATACTGAACCGACAGTGACACTGTAAACACTGCAATGC
* * *
8603 TATACTGAACCAGTA-A-TGACACTGTAAACATTACAAAGC
1 TATACTGAACC-G-ACAGTGACACTGTAAACACTGCAATGC
* * * * * **
8642 TATACGGAACTGGCGGTGACACTGAAAACACTGCAATAA
1 TATACTGAACCGACAGTGACACTGTAAACACTGCAATGC
** * *
8681 TATACTGAACTAACAGTGACATTATAAACACTGCAATGC
1 TATACTGAACCGACAGTGACACTGTAAACACTGCAATGC
* ** * * * *
8720 TATACTGAA-CTAGTGGTAACATTGTAAACACCGCAACGC
1 TATACTGAACCGA-CAGTGACACTGTAAACACTGCAATGC
*
8759 TATACTGAA--GTAGTAGTGACACTGTAAACACT
1 TATACTGAACCG-A-CAGTGACACTGTAAACACT
8791 ACTAGACTAT
Statistics
Matches: 146, Mismatches: 36, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
38 2 0.01
39 141 0.97
40 2 0.01
41 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (39 bp):
TATACTGAACCGACAGTGACACTGTAAACACTGCAATGC
Found at i:8701 original size:78 final size:78
Alignment explanation
Indices: 8579--8792 Score: 239
Period size: 78 Copynumber: 2.7 Consensus size: 78
8569 TGAACCGACA
* * * *
8579 GTGACACTGTAAACACTGCAATGTTATACTGAACCAGTAATGACACTGTAAACATTACAAAGCTA
1 GTGACACTGTAAACACTGCAATGATATACTGAACTAGTAGTGACACTGTAAACACTACAAAGCTA
*
8644 TACGGAACTGGCG
66 TACGGAACTAGCG
* * ** * * * *
8657 GTGACACTGAAAACACTGCAATAATATACTGAACTAACAGTGACATTATAAACACTGCAATGCTA
1 GTGACACTGTAAACACTGCAATGATATACTGAACTAGTAGTGACACTGTAAACACTACAAAGCTA
* *
8722 TACTGAACTAGTG
66 TACGGAACTAGCG
* * * * * *
8735 GTAACATTGTAAACACCGCAACGCTATACTGAAGTAGTAGTGACACTGTAAACACTAC
1 GTGACACTGTAAACACTGCAATGATATACTGAACTAGTAGTGACACTGTAAACACTAC
8793 TAGACTATTA
Statistics
Matches: 108, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
78 108 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (78 bp):
GTGACACTGTAAACACTGCAATGATATACTGAACTAGTAGTGACACTGTAAACACTACAAAGCTA
TACGGAACTAGCG
Found at i:8778 original size:117 final size:117
Alignment explanation
Indices: 8562--8790 Score: 278
Period size: 117 Copynumber: 2.0 Consensus size: 117
8552 CCATGTTGGA
* * * *
8562 AATATACTGAACCGACAGTGACACTGTAAACACTGCAATGTTATACTGAACCAGTAATGACACTG
1 AATATACTGAACCAACAGTGACACTATAAACACTGCAATGCTATACTGAACCAGTAATAACACTG
** * *
8627 TAAACATTACAAAGCTATACGGAACTGGCGGTGACACTGAAAACACTGCAAT
66 TAAACACCACAAAGCTATACGGAACTAGCAGTGACACTGAAAACACTGCAAT
* * * ** *
8679 AATATACTGAACTAACAGTGACATTATAAACACTGCAATGCTATACTGAACTAGTGGTAACATTG
1 AATATACTGAACCAACAGTGACACTATAAACACTGCAATGCTATACTGAACCAGTAATAACACTG
* * * * * *
8744 TAAACACCGCAACGCTATACTGAAGTAGTAGTGACACTGTAAACACT
66 TAAACACCACAAAGCTATACGGAACTAGCAGTGACACTGAAAACACT
8791 ACTAGACTAT
Statistics
Matches: 92, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
117 92 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (117 bp):
AATATACTGAACCAACAGTGACACTATAAACACTGCAATGCTATACTGAACCAGTAATAACACTG
TAAACACCACAAAGCTATACGGAACTAGCAGTGACACTGAAAACACTGCAAT
Found at i:9341 original size:26 final size:26
Alignment explanation
Indices: 9320--9370 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
9310 GTACTGTGTT
9320 TAATTGATCTATGATTGAACTGTTAC
1 TAATTGATCTATGATTGAACTGTTAC
* * *
9346 TAGTTGATCTTTGACTGAACTGTTA
1 TAATTGATCTATGATTGAACTGTTA
9371 TCAGTTGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (26 bp):
TAATTGATCTATGATTGAACTGTTAC
Found at i:10943 original size:26 final size:26
Alignment explanation
Indices: 10914--10965 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
10904 TATTTATAGT
10914 TATGTTTATCTTAACATTAATATATA
1 TATGTTTATCTTAACATTAATATATA
10940 TATGTTTATCTTAACATTAATATATA
1 TATGTTTATCTTAACATTAATATATA
10966 AACTTTCTAT
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:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (26 bp):
TATGTTTATCTTAACATTAATATATA
Found at i:13241 original size:44 final size:44
Alignment explanation
Indices: 13178--13281 Score: 181
Period size: 44 Copynumber: 2.4 Consensus size: 44
13168 GCTATAATGT
* *
13178 TAGTGTTTTTCAACTATGGTCTTTTCATTTCTGGAATATTATTG
1 TAGTGTCTTTCAACTATGGTCTTTTCATTTCTGGAATATTATCG
13222 TAGTGTCTTTCAACTATGGTCTTTTCATTTCTGGAATATTATCG
1 TAGTGTCTTTCAACTATGGTCTTTTCATTTCTGGAATATTATCG
*
13266 TAGTATCTTTCAACTA
1 TAGTGTCTTTCAACTA
13282 AGGTTTTATT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (44 bp):
TAGTGTCTTTCAACTATGGTCTTTTCATTTCTGGAATATTATCG
Found at i:17943 original size:22 final size:21
Alignment explanation
Indices: 17918--17959 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17908 ACCATTCCAT
*
17918 AACTTAAGATAACATAAAAAAA
1 AACTT-AGATAAAATAAAAAAA
*
17940 AACTTGGATAAAATAAAAAA
1 AACTTAGATAAAATAAAAAA
17960 TCATTCTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (21 bp):
AACTTAGATAAAATAAAAAAA
Done.