Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009486.1 Kokia drynarioides strain JFW-HI SEQ_124195, 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: 28023
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:329 original size:23 final size:23
Alignment explanation
Indices: 277--443 Score: 145
Period size: 23 Copynumber: 7.5 Consensus size: 23
267 TAAACGGAAC
*
277 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
299 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
325 AAACAAAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
345 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
364 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
387 AAACAGAGAGCACGA-GACGTGCT
1 AAACAGAGAGCAC-ACAAAGTGCT
*
410 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
433 AAACAGAGAGC
1 AAACAGAGAGC
444 GCGCTAGTGT
Statistics
Matches: 117, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 78 0.67
24 1 0.01
25 13 0.11
26 7 0.06
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.10
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:352 original size:39 final size:39
Alignment explanation
Indices: 309--383 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
299 GGGCAACAGA
*
309 GAGCACACAAAGTGCTAAACAAAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAAAGAGCACACAAAGTACT
* * *
348 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAAAGAGCACACAAAGT
384 GCTAAACAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAAAGAGCACACAAAGTACT
Found at i:8486 original size:16 final size:16
Alignment explanation
Indices: 8462--8506 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
8452 CATAGAATCT
*
8462 AAAAAGAAATAGA-TA
1 AAAAAGAAATAAAGTA
8477 AAAGAAGAAATAAAGTA
1 AAA-AAGAAATAAAGTA
8494 AAAAAGAAATAAA
1 AAAAAGAAATAAA
8507 CATAAATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 3 0.11
16 19 0.70
17 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (16 bp):
AAAAAGAAATAAAGTA
Found at i:11026 original size:234 final size:234
Alignment explanation
Indices: 10617--11085 Score: 920
Period size: 234 Copynumber: 2.0 Consensus size: 234
10607 TCTCATCTCT
*
10617 TTAATACTTTTGTCAGATTGTCAGCACATTGGTCAAAATTCTGTCAATATACAGAGAAATCGTCC
1 TTAATACTTTTGCCAGATTGTCAGCACATTGGTCAAAATTCTGTCAATATACAGAGAAATCGTCC
10682 ATGAATACCTCTAGTGAATCTTCAATCATATCTGAGAAGATAGCCATCGTAGACCTCTGGAATGT
66 ATGAATACCTCTAGTGAATCTTCAATCATATCTGAGAAGATAGCCATCGTAGACCTCTGGAATGT
10747 GGCTTGTAATAGCTTGATTTTCAGTAGTAACGGAGCAAAGTTTGGAAATTAAATTCCAAGTAGTA
131 GGCTTGTAATAGCTTGATTTTCAGTAGTAACGGAGCAAAGTTTGGAAATTAAATTCCAAGTAGTA
10812 AGTTAATTTTAATATTTAAAATATGCATATAAGATCGTA
196 AGTTAATTTTAATATTTAAAATATGCATATAAGATCGTA
10851 TTAATACTTTTGCCAGATTGTCAGCACATTGGTCAAAATTCTGTCAATATACAGAGAAATCGTCC
1 TTAATACTTTTGCCAGATTGTCAGCACATTGGTCAAAATTCTGTCAATATACAGAGAAATCGTCC
*
10916 ATGAATACCTCTAGTGAATCTTTAATCATATCTGAGAAGATAGCCATCGTAGACCTCTGGAATGT
66 ATGAATACCTCTAGTGAATCTTCAATCATATCTGAGAAGATAGCCATCGTAGACCTCTGGAATGT
10981 GGCTTGTAATAGCTTGATTTTCAGTAGTAACGGAGCAAAGTTTGGAAATTAAATTCCAAGTAGTA
131 GGCTTGTAATAGCTTGATTTTCAGTAGTAACGGAGCAAAGTTTGGAAATTAAATTCCAAGTAGTA
11046 AGTTAATTTTAATATTTAAAATATGCATATAAGATCGTA
196 AGTTAATTTTAATATTTAAAATATGCATATAAGATCGTA
11085 T
1 T
11086 AAAGCATCTA
Statistics
Matches: 233, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
234 233 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (234 bp):
TTAATACTTTTGCCAGATTGTCAGCACATTGGTCAAAATTCTGTCAATATACAGAGAAATCGTCC
ATGAATACCTCTAGTGAATCTTCAATCATATCTGAGAAGATAGCCATCGTAGACCTCTGGAATGT
GGCTTGTAATAGCTTGATTTTCAGTAGTAACGGAGCAAAGTTTGGAAATTAAATTCCAAGTAGTA
AGTTAATTTTAATATTTAAAATATGCATATAAGATCGTA
Found at i:11175 original size:21 final size:21
Alignment explanation
Indices: 11115--11175 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
11105 AATTTATGGT
*
11115 TGCCGGTGTATTCAGGCTAAG
1 TGCCGGTGTATTCAGGCTATG
*
11136 TGCC----TA-GCAGGCT-TCG
1 TGCCGGTGTATTCAGGCTAT-G
11152 TGCCGGTGTATTCAGGCTATG
1 TGCCGGTGTATTCAGGCTATG
11173 TGC
1 TGC
11176 TTAGCAGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
16 11 0.37
17 2 0.07
20 2 0.07
21 14 0.47
22 1 0.03
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.30
Consensus pattern (21 bp):
TGCCGGTGTATTCAGGCTATG
Found at i:11301 original size:37 final size:37
Alignment explanation
Indices: 11115--11293 Score: 250
Period size: 37 Copynumber: 4.8 Consensus size: 37
11105 AATTTATGGT
* *
11115 TGCCGGTGTATTCAGGCTAAGTGCCTAGCAGGCTTCG
1 TGCCAGTGTATTCAGGCTATGTGCCTAGCAGGCTTCG
* * *
11152 TGCCGGTGTATTCAGGCTATGTGCTTAGCAGGCTTCA
1 TGCCAGTGTATTCAGGCTATGTGCCTAGCAGGCTTCG
*
11189 TGCCAGTGTATTCAGGCTATGTGCCTAGCAGGCTTCA
1 TGCCAGTGTATTCAGGCTATGTGCCTAGCAGGCTTCG
* * * *
11226 TGCTAGTGTATTCAGCCTATGTGTCTAGCAGGCTTTG
1 TGCCAGTGTATTCAGGCTATGTGCCTAGCAGGCTTCG
* *
11263 TGCAAGTGTATTCAAGCTATGTGCCTAGCAG
1 TGCCAGTGTATTCAGGCTATGTGCCTAGCAG
11294 ACTTTGTGTC
Statistics
Matches: 128, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 128 1.00
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.31
Consensus pattern (37 bp):
TGCCAGTGTATTCAGGCTATGTGCCTAGCAGGCTTCG
Found at i:13116 original size:148 final size:148
Alignment explanation
Indices: 12848--13137 Score: 499
Period size: 148 Copynumber: 2.0 Consensus size: 148
12838 AATGGACTGT
* *
12848 TTCCCTTCATCTTCCAGTCTGATTTTGTGCATGCAAAAAGTAGGACTAATACCTCTGATGTCTGC
1 TTCCCTTCATCTTCCAATCTGATTTTATGCATGCAAAAAGTAGGACTAATACCTCTGATGTCTGC
* * *
12913 AATACTCCATGCAATGACTCTTTTGTGCTCCTTTAAAAATGCGATGAGCTTTTCTTCTTGAATTG
66 AATACTCCATGCAATGACTCTGTTGTGCTCATTTAAAAATACGATGAGCTTTTCTTCTTGAATTG
12978 CGTCGAGGCTTGCACTAC
131 CGTCGAGGCTTGCACTAC
* *
12996 TTCCCTTCATCTTCCAATCTGATTTTATGCATGCAAAAAGTATGACTAATGCCTCTGATGTCTGC
1 TTCCCTTCATCTTCCAATCTGATTTTATGCATGCAAAAAGTAGGACTAATACCTCTGATGTCTGC
* *
13061 AATATTCCATGCAATGACTCTGTTGTGCTCATTTAAAATTACGATGAGCTTTTCTTCTTGAATTG
66 AATACTCCATGCAATGACTCTGTTGTGCTCATTTAAAAATACGATGAGCTTTTCTTCTTGAATTG
13126 CGTCGAGGCTTG
131 CGTCGAGGCTTG
13138 TGCTGACAAT
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
148 133 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (148 bp):
TTCCCTTCATCTTCCAATCTGATTTTATGCATGCAAAAAGTAGGACTAATACCTCTGATGTCTGC
AATACTCCATGCAATGACTCTGTTGTGCTCATTTAAAAATACGATGAGCTTTTCTTCTTGAATTG
CGTCGAGGCTTGCACTAC
Found at i:14639 original size:17 final size:18
Alignment explanation
Indices: 14605--14640 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
14595 GTGCAGTCTG
14605 TTGTGGTTGCATTCTAGC
1 TTGTGGTTGCATTCTAGC
14623 TTGTGGTTGCA-TCTAGC
1 TTGTGGTTGCATTCTAGC
14640 T
1 T
14641 ATGTACCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.44
Consensus pattern (18 bp):
TTGTGGTTGCATTCTAGC
Found at i:20768 original size:14 final size:14
Alignment explanation
Indices: 20749--20777 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20739 AAAAGAATTG
20749 TATAACAGTATATA
1 TATAACAGTATATA
20763 TATAACAGTATATA
1 TATAACAGTATATA
20777 T
1 T
20778 GTAAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (14 bp):
TATAACAGTATATA
Found at i:20836 original size:35 final size:37
Alignment explanation
Indices: 20760--20861 Score: 99
Period size: 37 Copynumber: 2.9 Consensus size: 37
20750 ATAACAGTAT
* *
20760 ATATATAACAGTATATATGTAAAAACAATATATGTAA
1 ATATAAAATAGTATATATGTAAAAACAATATATGTAA
**
20797 ATATAAAATAGTATATATGTATAAAA-AA-A-ATGTGG
1 ATATAAAATAGTATATATGTA-AAAACAATATATGTAA
* *
20832 ATATAACATTGTATATA--T-AAAACAATATAT
1 ATATAAAATAGTATATATGTAAAAACAATATAT
20862 ATGTATAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
31 4 0.07
32 2 0.04
33 2 0.04
34 2 0.04
35 19 0.35
36 1 0.02
37 21 0.38
38 4 0.07
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (37 bp):
ATATAAAATAGTATATATGTAAAAACAATATATGTAA
Found at i:20877 original size:14 final size:14
Alignment explanation
Indices: 20860--20914 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
20850 AAAACAATAT
20860 ATATGTATAAAAAA
1 ATATGTATAAAAAA
*
20874 ATATGTAT-AAAAT
1 ATATGTATAAAAAA
* * *
20887 ATACAGTTTAAAGAA
1 ATA-TGTATAAAAAA
20902 ATATGTATAAAAA
1 ATATGTATAAAAA
20915 TTACTAATCT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
13 7 0.23
14 18 0.58
15 6 0.19
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (14 bp):
ATATGTATAAAAAA
Found at i:21521 original size:2 final size:2
Alignment explanation
Indices: 21516--21540 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21506 ATATATAGAT
21516 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
21541 AAACATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27704 original size:115 final size:115
Alignment explanation
Indices: 27501--27739 Score: 338
Period size: 115 Copynumber: 2.1 Consensus size: 115
27491 TAGACGATGC
* * * * *
27501 TGCTCACACGAGCTGTGGAGAATCCGCAACATATGCTTGATCTCAGCTATCGATAGGTCATCTAT
1 TGCTCACACAAGCTATGGAGAATCCGCAACATATGCTTGATCTCAACCATCGATAGGACATCTAT
**
27566 GACCAGTACCCATCTAACATGTAATGCTCACATGAGCTGTGAAGTGGGCA
66 GACCAGTACCCATCTAACATGTAATGCTCACACAAGCTGTGAAGTGGGCA
*
27616 TGCTCACACAAGCTATGGAGAATCCGTAACATATG-TTGGATCTCAACCATCGATAGGACATCTA
1 TGCTCACACAAGCTATGGAGAATCCGCAACATATGCTT-GATCTCAACCATCGATAGGACATCT-
* * * *
27680 AT-ACCAGTACCCATCTAACGTGTAATGCTTACACAAGTTGTGAAGTGGGCC
64 ATGACCAGTACCCATCTAACATGTAATGCTCACACAAGCTGTGAAGTGGGCA
27731 TGCTCACAC
1 TGCTCACAC
27740 GAGTTGTGGG
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
114 2 0.02
115 106 0.96
116 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (115 bp):
TGCTCACACAAGCTATGGAGAATCCGCAACATATGCTTGATCTCAACCATCGATAGGACATCTAT
GACCAGTACCCATCTAACATGTAATGCTCACACAAGCTGTGAAGTGGGCA
Done.