Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008620.1 Kokia drynarioides strain JFW-HI SEQ_123299, 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: 30879
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:473 original size:30 final size:30
Alignment explanation
Indices: 401--762 Score: 201
Period size: 29 Copynumber: 12.4 Consensus size: 30
391 AAGGTCCCTG
* * * *
401 AACTATCCAAAAATCACGTTTTCA-CCTCTA
1 AACTTTCCAAAAATTACATTTTGACCCTC-A
431 AACATTT-CAAAAATTACATTTTGACCCTCA
1 AAC-TTTCCAAAAATTACATTTTGACCCTCA
** *
461 AACTTTAAAAAAAATACATTTTGACCC-CTA
1 AACTTTCCAAAAATTACATTTTGACCCTC-A
* *
491 AACTTTCTAAAAATTACATTTTGACCCT-G
1 AACTTTCCAAAAATTACATTTTGACCCTCA
* * *
520 AAC-TT-CACAAACTTACATTTTGACCAT-G
1 AACTTTCCA-AAAATTACATTTTGACCCTCA
548 AACTTTCCAAAAATTACCATTTT-ACCC-CTA
1 AACTTTCCAAAAATTA-CATTTTGACCCTC-A
* *
578 AAC-TTCCAAAAATCACATTTTTG-CCCTCG
1 AACTTTCCAAAAATTACA-TTTTGACCCTCA
*
607 AAC-ATCCAAAAATTACCATTTTGACCCT-A
1 AACTTTCCAAAAATTA-CATTTTGACCCTCA
* * *
636 AACTTTTC-AAAATTACCATTTTG-CCCCCG
1 AACTTTCCAAAAATTA-CATTTTGACCCTCA
* *
665 AGC-ATCCAAAAATTACCATTTTG-CCC-CA
1 AACTTTCCAAAAATTA-CATTTTGACCCTCA
* * *
693 ATC-ATCCAAAAATTATCATTTTG-CCC-CT
1 AACTTTCCAAAAATTA-CATTTTGACCCTCA
* * * *
721 AAGTATCCAAAAAGTACCA-TTTCACCCTCA
1 AACTTTCCAAAAATTA-CATTTTGACCCTCA
* *
751 AATTTTTCAAAA
1 AACTTTCCAAAA
763 GTTTGATTTT
Statistics
Matches: 269, Mismatches: 41, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
27 1 0.00
28 60 0.22
29 108 0.40
30 94 0.35
31 6 0.02
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTGACCCTCA
Found at i:518 original size:29 final size:29
Alignment explanation
Indices: 396--722 Score: 226
Period size: 29 Copynumber: 11.2 Consensus size: 29
386 CCCAAAAGGT
* * * * *
396 CCCTGAACTATCCAAAAATCACGTTTTCA
1 CCCTAAACTTTCCAAAAATTACATTTTGA
425 CCTCTAAACATTT-CAAAAATTACATTTTGA
1 CC-CTAAAC-TTTCCAAAAATTACATTTTGA
** *
455 CCCTCAAACTTTAAAAAAAATACATTTTGA
1 CCCT-AAACTTTCCAAAAATTACATTTTGA
*
485 CCCCTAAACTTTCTAAAAATTACATTTTGA
1 -CCCTAAACTTTCCAAAAATTACATTTTGA
* *
515 CCCTGAAC-TT-CACAAACTTACATTTTGA
1 CCCTAAACTTTCCA-AAAATTACATTTTGA
* *
543 CCATGAACTTTCCAAAAATTACCATTTT-A
1 CCCTAAACTTTCCAAAAATTA-CATTTTGA
*
572 CCCCTAAAC-TTCCAAAAATCACATTTTTG-
1 -CCCTAAACTTTCCAAAAATTACA-TTTTGA
* *
601 CCCTCGAAC-ATCCAAAAATTACCATTTTGA
1 CCCT-AAACTTTCCAAAAATTA-CATTTTGA
* *
631 CCCTAAACTTTTC-AAAATTACCATTTTGC
1 CCCTAAACTTTCCAAAAATTA-CATTTTGA
** * *
660 CCCCGAGC-ATCCAAAAATTACCATTTTG-
1 CCCTAAACTTTCCAAAAATTA-CATTTTGA
* * * *
688 CCCCAATC-ATCCAAAAATTATCATTTTGC
1 CCCTAAACTTTCCAAAAATTA-CATTTTGA
717 CCCTAA
1 CCCTAA
723 GTATCCAAAA
Statistics
Matches: 246, Mismatches: 34, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.00
28 56 0.23
29 99 0.40
30 84 0.34
31 6 0.02
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATTACATTTTGA
Found at i:4778 original size:23 final size:23
Alignment explanation
Indices: 4735--4778 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
4725 ACATTGTTCG
* *
4735 TGAACATATTTGATTAAATTAAA
1 TGAACATATTTCATGAAATTAAA
4758 TGAACATA-TTCATGAACATTA
1 TGAACATATTTCATGAA-ATTA
4779 GACAAACGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (23 bp):
TGAACATATTTCATGAAATTAAA
Found at i:5308 original size:2 final size:2
Alignment explanation
Indices: 5301--5350 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
5291 CATTTAAATG
* * *
5301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA TT TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5342 TA TA T- TA TA
1 TA TA TA TA TA
5351 ATTTTTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:6215 original size:2 final size:2
Alignment explanation
Indices: 6208--6233 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6198 TAAGAAACCA
6208 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6234 TAAATTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6995 original size:15 final size:14
Alignment explanation
Indices: 6980--7035 Score: 64
Period size: 15 Copynumber: 4.0 Consensus size: 14
6970 GTTTACTGGT
6980 GGTGGAGGTGGC--
1 GGTGGAGGTGGCGG
6992 GGTGGAGGTTGTG-GG
1 GGTGGAGG-TG-GCGG
7007 GGTGGAGGTGGCGG
1 GGTGGAGGTGGCGG
7021 CGGTGGAGGTGGCGG
1 -GGTGGAGGTGGCGG
7036 CGGTTGCTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.21
13 3 0.08
14 5 0.13
15 22 0.58
ACGTcount: A:0.07, C:0.07, G:0.68, T:0.18
Consensus pattern (14 bp):
GGTGGAGGTGGCGG
Found at i:7010 original size:21 final size:21
Alignment explanation
Indices: 6980--7035 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
6970 GTTTACTGGT
*
6980 GGTGGAGGTGGCGGTGGAGGT
1 GGTGGAGGTGGCGGTGGAGGC
* * * *
7001 TGTGGGGGTGGAGGTGGCGGC
1 GGTGGAGGTGGCGGTGGAGGC
7022 GGTGGAGGTGGCGG
1 GGTGGAGGTGGCGG
7036 CGGTTGCTGA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.07, C:0.07, G:0.68, T:0.18
Consensus pattern (21 bp):
GGTGGAGGTGGCGGTGGAGGC
Found at i:7032 original size:27 final size:27
Alignment explanation
Indices: 6980--7032 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
6970 GTTTACTGGT
* **
6980 GGTGGAGGTGGCGGTGGAGGTTGTGGG
1 GGTGGAGGTGGCGGCGGAGGAGGTGGG
*
7007 GGTGGAGGTGGCGGCGGTGGAGGTGG
1 GGTGGAGGTGGCGGCGGAGGAGGTGG
7033 CGGCGGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.08, C:0.06, G:0.68, T:0.19
Consensus pattern (27 bp):
GGTGGAGGTGGCGGCGGAGGAGGTGGG
Found at i:7036 original size:15 final size:15
Alignment explanation
Indices: 6989--7039 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
6979 TGGTGGAGGT
* *
6989 GGCGGTGGAGGTTGT
1 GGCGGTGGAGGTGGC
*
7004 GGGGGTGGAGGTGGC
1 GGCGGTGGAGGTGGC
7019 GGCGGTGGAGGTGGC
1 GGCGGTGGAGGTGGC
7034 GGCGGT
1 GGCGGT
7040 TGCTGATGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.06, C:0.10, G:0.67, T:0.18
Consensus pattern (15 bp):
GGCGGTGGAGGTGGC
Found at i:8365 original size:20 final size:20
Alignment explanation
Indices: 8290--8366 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
8280 AACATTATAG
*
8290 AAAATTATTTAAAAACTATT
1 AAAATTATTTAAAAATTATT
* *
8310 AAAGTT-TATAAGAAATTA-T
1 AAAATTATTTAA-AAATTATT
* *
8329 ATATATATATTT-GAAATTATT
1 A-AAAT-TATTTAAAAATTATT
8350 AAAATTATTTAAAAATT
1 AAAATTATTTAAAAATT
8367 GTAAAAAGCA
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
19 11 0.26
20 26 0.62
21 3 0.07
22 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (20 bp):
AAAATTATTTAAAAATTATT
Found at i:16006 original size:11 final size:11
Alignment explanation
Indices: 15990--16016 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
15980 GTCTTGTTCT
15990 AAAAAAAATAA
1 AAAAAAAATAA
16001 AAAAAAAATAA
1 AAAAAAAATAA
16012 AAAAA
1 AAAAA
16017 TTATATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:23323 original size:17 final size:17
Alignment explanation
Indices: 23283--23322 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
23273 TGGTTATTAG
23283 AAAAATATAAAACGTTTT
1 AAAAATATAAAAC-TTTT
*
23301 AAAAATATAAAATTTATT
1 AAAAATATAAAACTT-TT
23319 AAAA
1 AAAA
23323 TTGGTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAAATATAAAACTTTT
Found at i:24755 original size:25 final size:24
Alignment explanation
Indices: 24723--24770 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
24713 ATTGGAATTA
24723 TATATTAATATTAAATAAATATAAT
1 TATATTAATATTAAATAAA-ATAAT
*
24748 TATATTAATATTGAATAAAATAA
1 TATATTAATATTAAATAAAATAA
24771 AAATCCCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TATATTAATATTAAATAAAATAAT
Found at i:25606 original size:26 final size:26
Alignment explanation
Indices: 25577--25632 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
25567 TTTATAGAAT
* *
25577 ATAAGAATAGGGTAAAGTCAGAAATA
1 ATAAGAATAAGATAAAGTCAGAAATA
25603 ATAAGAATAAGATAAAGTCAGAAATA
1 ATAAGAATAAGATAAAGTCAGAAATA
25629 ATAA
1 ATAA
25633 ATGTGATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.59, C:0.04, G:0.18, T:0.20
Consensus pattern (26 bp):
ATAAGAATAAGATAAAGTCAGAAATA
Found at i:25745 original size:3 final size:3
Alignment explanation
Indices: 25737--25761 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25727 TTAAGGTTGA
25737 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
25762 AGGTTGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:28175 original size:15 final size:18
Alignment explanation
Indices: 28157--28195 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
28147 TAAGATACAT
28157 TAAAATAA-AA-AT-ATA
1 TAAAATAATAATATAATA
28172 TAAAA-AATAATATAATA
1 TAAAATAATAATATAATA
28189 TAAAATA
1 TAAAATA
28196 TTATAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.10
15 7 0.35
16 2 0.10
17 8 0.40
18 1 0.05
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAATAATAATATAATA
Done.