Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005207.1 Kokia drynarioides strain JFW-HI SEQ_119075, 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: 21497
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Found at i:476 original size:6 final size:6
Alignment explanation
Indices: 432--478 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
422 TAATGGACTT
*
432 TTTAAT TTTAAA TTTAAA TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
479 ATAAATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
4 1 0.03
5 3 0.08
6 32 0.86
7 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:485 original size:17 final size:17
Alignment explanation
Indices: 432--485 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
422 TAATGGACTT
* *
432 TTTAATTTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
* *
450 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATAAA
467 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
484 TT
1 TT
486 AAAAAGGGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 20 0.67
18 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:13344 original size:13 final size:13
Alignment explanation
Indices: 13326--13351 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13316 CAAGCAAGAT
13326 GTAAGCTTCATTA
1 GTAAGCTTCATTA
13339 GTAAGCTTCATTA
1 GTAAGCTTCATTA
13352 CCCGTAGCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GTAAGCTTCATTA
Found at i:18279 original size:98 final size:97
Alignment explanation
Indices: 18111--18562 Score: 532
Period size: 98 Copynumber: 4.6 Consensus size: 97
18101 AGGAAACATT
* * * * *
18111 GAACCTTATACATTAGAGATGTGATGGGAAAGATTGAAGCCGCAACGACGATTCTTGTACCATGG
1 GAACCTTATACCTTAGAGATGTGATGGGAAAGATTGAAGCTGCAACGGC-AATCTTATACCATGG
**
18176 AGATATGGAGGGAAAGGTTGAAGCCGCGACGGT
65 AGATATGGAGGGAAAGGTTGAAGCCGCGACGAC
** * *
18209 GAACCTTATACCTTAGAGATGTGATACGAAAGATTGAAGCTGTAACGGCAAGTCTTGTACCATGG
1 GAACCTTATACCTTAGAGATGTGATGGGAAAGATTGAAGCTGCAACGGCAA-TCTTATACCATGG
* *
18274 AGATATGGAAGGAAAGGTT-AACGCCGCGA-TAGC
65 AGATATGGAGGGAAAGGTTGAA-GCCGCGACGA-C
* * * * * *
18307 AAACCTTATACCTTAGAGATATGATGGGAAAGATTGAGGCCGCAACGATG-AATCTTATACCTTA
1 GAACCTTATACCTTAGAGATGTGATGGGAAAGATTGAAGCTGCAACG--GCAATCTTATACCATG
* *
18371 GAAATATGGAGGGAAAGGTTGAAGTCGCGACGAC
64 GAGATATGGAGGGAAAGGTTGAAGCCGCGACGAC
* * * *
18405 GAACCTTATACCTTAGAAATATGATGGGAAAGATTGAAGCTGCAATGGCCAATCTAATACCATGG
1 GAACCTTATACCTTAGAGATGTGATGGGAAAGATTGAAGCTGCAACGG-CAATCTTATACCATGG
* *
18470 AGATATGGAGGGAAAAGTTGAAGCCACGACGAC
65 AGATATGGAGGGAAAGGTTGAAGCCGCGACGAC
* * * *
18503 GATCCTTATACCTTAGAGATGTGATGGGAAAGATTAAAGCTGTAACGGTGAATCTTATAC
1 GAACCTTATACCTTAGAGATGTGATGGGAAAGATTGAAGCTGCAACGG-CAATCTTATAC
18563 TCTAAAGTTG
Statistics
Matches: 299, Mismatches: 46, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
96 1 0.00
97 3 0.01
98 289 0.97
99 5 0.02
100 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (97 bp):
GAACCTTATACCTTAGAGATGTGATGGGAAAGATTGAAGCTGCAACGGCAATCTTATACCATGGA
GATATGGAGGGAAAGGTTGAAGCCGCGACGAC
Found at i:18560 original size:49 final size:49
Alignment explanation
Indices: 18115--18613 Score: 338
Period size: 49 Copynumber: 10.2 Consensus size: 49
18105 AACATTGAAC
* * * *
18115 CTTATACATTAGAGATGTGATGGGAAAGATTGAAGCCGCAACGACGATT
1 CTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGGCGAAT
* * * * * * *
18164 CTTGTACCATGGAGATATGGA-GGGAAAGGTTGAAGCCGCGACGGTGAAC
1 CTTATACCTTAGAGATAT-GATGGGAAAGATTGAAGCCGCAACGGCGAAT
* ** * *
18213 CTTATACCTTAGAGATGTGATACGAAAGATTGAAGCTGTAACGGC-AAGT
1 CTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGGCGAA-T
* * * * * * ** * *
18262 CTTGTACCATGGAGATATGGA-AGGAAAGGTT-AACGCCGCGATAGCAAAC
1 CTTATACCTTAGAGATAT-GATGGGAAAGATTGAA-GCCGCAACGGCGAAT
* **
18311 CTTATACCTTAGAGATATGATGGGAAAGATTGAGGCCGCAACGATGAAT
1 CTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGGCGAAT
* * * * * *
18360 CTTATACCTTAGAAATATGGA-GGGAAAGGTTGAAGTCGCGACGACGAAC
1 CTTATACCTTAGAGATAT-GATGGGAAAGATTGAAGCCGCAACGGCGAAT
* * * *
18409 CTTATACCTTAGAAATATGATGGGAAAGATTGAAGCTGCAATGGCCAAT
1 CTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGGCGAAT
* * * * * *
18458 CTAATACCATGGAGATATGGA-GGGAAA-AGTTGAAGCCACGACGACG-AT
1 CTTATACCTTAGAGATAT-GATGGGAAAGA-TTGAAGCCGCAACGGCGAAT
* * * * *
18506 CCTTATACCTTAGAGATGTGATGGGAAAGATTAAAGCTGTAACGGTGAAT
1 -CTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGGCGAAT
* *
18556 CTTATA-CTCTAAAG-T-TGAAGAGGAGCAA-ATTGAAGCCGCAACGGCGAAT
1 CTTATACCT-TAGAGATATGATG-GGA--AAGATTGAAGCCGCAACGGCGAAT
18605 CTTATACCT
1 CTTATACCT
18614 CGAAGTTACG
Statistics
Matches: 339, Mismatches: 90, Indels: 41
0.72 0.19 0.09
Matches are distributed among these distances:
47 4 0.01
48 21 0.06
49 296 0.87
50 18 0.05
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (49 bp):
CTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGGCGAAT
Found at i:18589 original size:98 final size:96
Alignment explanation
Indices: 18111--18613 Score: 406
Period size: 98 Copynumber: 5.1 Consensus size: 96
18101 AGGAAACATT
* * * ** * * **
18111 GAACCTTATACATTAGAGATGTGATGGGAAAGATTGAAGCCGCAACGACGATTCTTGTACCATGG
1 GAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCTGCAACGGTGAATCTTATACCATAA
* **
18176 AGATATGGAGGGAAAGGTTGAAGCCGCGACGGT
66 AG-TATGGAGGGAAA-GTTGAAGCCACGACGAC
* ** * * * *
18209 GAACCTTATACCTTAGAGATGTGATACGAAAGATTGAAGCTGTAACGG-CAAGTCTTGTACCATG
1 GAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCTGCAACGGTGAA-TCTTATACCATA
* * * *
18273 GAGATATGGAAGGAAAGGTT-AACGCCGCGA-TAGC
65 AAG-TATGGAGGGAAA-GTTGAA-GCCACGACGA-C
* * * * *
18307 AAACCTTATACCTTAGAGATATGATGGGAAAGATTGAGGCCGCAACGATGAATCTTATACCTTAG
1 GAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCTGCAACGGTGAATCTTATACCATA-
* * *
18372 AAATATGGAGGGAAAGGTTGAAGTCGCGACGAC
65 AAGTATGGAGGGAAA-GTTGAAGCCACGACGAC
* * ** * **
18405 GAACCTTATACCTTAGAAATATGATGGGAAAGATTGAAGCTGCAATGGCCAATCTAATACCATGG
1 GAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCTGCAACGGTGAATCTTATACCATAA
18470 AGATATGGAGGGAAAAGTTGAAGCCACGACGAC
66 AG-TATGGAGGG-AAAGTTGAAGCCACGACGAC
* * * *
18503 GATCCTTATACCTTAGAGATGTGATGGGAAAGATTAAAGCTGTAACGGTGAATCTTATACTC-TA
1 GAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCTGCAACGGTGAATCTTATAC-CATA
* * *
18567 AAGT-TGAAGAGGAGCAAA-TTGAAGCCGCAACGGC
65 AAGTATG--GAGG-G-AAAGTTGAAGCCACGACGAC
*
18601 GAATCTTATACCT
1 GAACCTTATACCT
18614 CGAAGTTACG
Statistics
Matches: 331, Mismatches: 61, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
96 2 0.01
97 5 0.02
98 310 0.94
99 14 0.04
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.23
Consensus pattern (96 bp):
GAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCTGCAACGGTGAATCTTATACCATAA
AGTATGGAGGGAAAGTTGAAGCCACGACGAC
Found at i:18611 original size:196 final size:195
Alignment explanation
Indices: 18112--18613 Score: 550
Period size: 196 Copynumber: 2.6 Consensus size: 195
18102 GGAAACATTG
* * * * * * * *
18112 AACCTTATACATTAGAGATGTGATGGGAAAGATTGAAGCCGCAACGACGATTCTTGTACCATGGA
1 AACCTTATACCTTAGAGATATGATGGGAAAGATTAAAGCCGCAACGATGAATCTTATACCTTAGA
* * * *
18177 GATATGGAGGGAAAGGTTGAAGCCGCGACGGTGAACCTTATACCTTAGAGATGTGATACGAAAGA
66 AATATGGAGGGAAA-GTTGAAGCCGCGACGGCGAACCTTATACCTTAGAAATATGATACGAAAGA
* ** * * *
18242 TTGAAGCTGTAACGGCAAGTCTTGTACCATGGAGATATGGAAGGAAAGGTTAACGCCGCGATAGC
130 TTGAAGCTGCAACGGCAAGTCTAATACCATGGAGATATGGAAGGAAAAGTTAACGCCACGAGAGC
18307 A
195 A
* *
18308 AACCTTATACCTTAGAGATATGATGGGAAAGATTGAGGCCGCAACGATGAATCTTATACCTTAGA
1 AACCTTATACCTTAGAGATATGATGGGAAAGATTAAAGCCGCAACGATGAATCTTATACCTTAGA
* * **
18373 AATATGGAGGGAAAGGTTGAAGTCGCGACGACGAACCTTATACCTTAGAAATATGATGGGAAAGA
66 AATATGGAGGGAAA-GTTGAAGCCGCGACGGCGAACCTTATACCTTAGAAATATGATACGAAAGA
* *
18438 TTGAAGCTGCAATGGCCAA-TCTAATACCATGGAGATATGGAGGGAAAAGTTGAA-GCCACGACG
130 TTGAAGCTGCAACGG-CAAGTCTAATACCATGGAGATATGGAAGGAAAAGTT-AACGCCACGA-G
*
18501 A-CG
192 AGCA
* * * * *
18504 ATCCTTATACCTTAGAGATGTGATGGGAAAGATTAAAGCTGTAACGGTGAATCTTATA-CTCTA-
1 AACCTTATACCTTAGAGATATGATGGGAAAGATTAAAGCCGCAACGATGAATCTTATACCT-TAG
* * *
18567 AAGT-TGAAGAGGAGCAAA-TTGAAGCCGCAACGGCGAATCTTATACCT
65 AAATATG--GAGG-G-AAAGTTGAAGCCGCGACGGCGAACCTTATACCT
18614 CGAAGTTACG
Statistics
Matches: 261, Mismatches: 37, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
194 2 0.01
195 5 0.02
196 244 0.93
197 7 0.03
198 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.23
Consensus pattern (195 bp):
AACCTTATACCTTAGAGATATGATGGGAAAGATTAAAGCCGCAACGATGAATCTTATACCTTAGA
AATATGGAGGGAAAGTTGAAGCCGCGACGGCGAACCTTATACCTTAGAAATATGATACGAAAGAT
TGAAGCTGCAACGGCAAGTCTAATACCATGGAGATATGGAAGGAAAAGTTAACGCCACGAGAGCA
Found at i:19205 original size:11 final size:12
Alignment explanation
Indices: 19191--19234 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
19181 CACATCAACG
19191 CCACGTCA-CTA
1 CCACGTCAGCTA
*
19202 CCACATCAGC-A
1 CCACGTCAGCTA
*
19213 CCATGTCAGCTA
1 CCACGTCAGCTA
19225 CCACGTCAGC
1 CCACGTCAGC
19235 CACTCAACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.27, C:0.43, G:0.14, T:0.16
Consensus pattern (12 bp):
CCACGTCAGCTA
Found at i:19205 original size:22 final size:23
Alignment explanation
Indices: 19180--19228 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
19170 TTCACCATGG
*
19180 CCACATCAACGCCACGTCA-CTA
1 CCACATCAACACCACGTCAGCTA
* *
19202 CCACATCAGCACCATGTCAGCTA
1 CCACATCAACACCACGTCAGCTA
19225 CCAC
1 CCAC
19229 GTCAGCCACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.31, C:0.45, G:0.10, T:0.14
Consensus pattern (23 bp):
CCACATCAACACCACGTCAGCTA
Found at i:19558 original size:18 final size:18
Alignment explanation
Indices: 19535--19569 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19525 ACTTTGAAAA
19535 AAATAAACTAAA-ATAAAT
1 AAATAAA-TAAATATAAAT
19553 AAATAAATAAATATAAA
1 AAATAAATAAATATAAA
19570 AGAAAAAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAATAAATATAAAT
Found at i:20470 original size:28 final size:29
Alignment explanation
Indices: 20427--20507 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
20417 TTTTCTTTCC
*
20427 TTGTAAATTGAACCCCT-TTATTCAGTT-TT
1 TTGTAAATTAAACCCCTCTTATT--GTTCTT
*
20456 TT-TAAATTAAACCCCTCTTATTTTTCTT
1 TTGTAAATTAAACCCCTCTTATTGTTCTT
*
20484 TTGTCAAATTAAACCCCTGTTATT
1 TTGT-AAATTAAACCCCTCTTATT
20508 TTTTATTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
27 2 0.04
28 17 0.38
29 8 0.18
30 18 0.40
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (29 bp):
TTGTAAATTAAACCCCTCTTATTGTTCTT
Done.