Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008682.1 Kokia drynarioides strain JFW-HI SEQ_123364, 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: 25209
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:3526 original size:30 final size:29
Alignment explanation
Indices: 3462--3594 Score: 167
Period size: 30 Copynumber: 4.5 Consensus size: 29
3452 CAAGCCATCA
*
3462 AAAGTGCGAGCCTGTTGAAGACAGCAAGC
1 AAAGTGCGAGCCTGTTAAAGACAGCAAGC
* * *
3491 AAAGTGTGAGCCTGTCAAAGACAGTAAGTC
1 AAAGTGCGAGCCTGTTAAAGACAGCAAG-C
*
3521 AAAGTGCGAGCCTGTTAAAGACAGTAAGCC
1 AAAGTGCGAGCCTGTTAAAGACAGCAAG-C
* * *
3551 AAAGTGCGAGCCTATTGAAGATAGCAAGC
1 AAAGTGCGAGCCTGTTAAAGACAGCAAGC
*
3580 AAAGTGTGAGCCTGT
1 AAAGTGCGAGCCTGT
3595 CGAATTGCAA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 38 0.42
30 52 0.58
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (29 bp):
AAAGTGCGAGCCTGTTAAAGACAGCAAGC
Found at i:3528 original size:59 final size:59
Alignment explanation
Indices: 3462--3594 Score: 169
Period size: 59 Copynumber: 2.3 Consensus size: 59
3452 CAAGCCATCA
* * * *
3462 AAAGTGCGAGCCTGTTGAAGACAGCAAG-CAAAGTGTGAGCCTGTCAAAGACAGTAAGTC
1 AAAGTGCGAGCCTGTTAAAGACAGCAAGCCAAAGTGCGAGCCTATCAAAGACAGCAAG-C
* ** *
3521 AAAGTGCGAGCCTGTTAAAGACAGTAAGCCAAAGTGCGAGCCTATTGAAGATAGCAAGC
1 AAAGTGCGAGCCTGTTAAAGACAGCAAGCCAAAGTGCGAGCCTATCAAAGACAGCAAGC
*
3580 AAAGTGTGAGCCTGT
1 AAAGTGCGAGCCTGT
3595 CGAATTGCAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 41 0.64
60 23 0.36
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (59 bp):
AAAGTGCGAGCCTGTTAAAGACAGCAAGCCAAAGTGCGAGCCTATCAAAGACAGCAAGC
Found at i:3663 original size:44 final size:44
Alignment explanation
Indices: 3600--3695 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
3590 CCTGTCGAAT
* * * *
3600 TGCAAGCCGAGGTGGCGGACGGTCTAAATGCAA-ACCCGAGTGGG
1 TGCAAGCCGAAGCGACGGACAGTCTAAATGCAAGA-CCGAGTGGG
*
3644 TGCAAGCCGAAGCGACGGACAGTCTAAATGCAAGATCGAGTGGG
1 TGCAAGCCGAAGCGACGGACAGTCTAAATGCAAGACCGAGTGGG
3688 TGCAAGCC
1 TGCAAGCC
3696 AAAATGGCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 45 0.98
45 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.35, T:0.14
Consensus pattern (44 bp):
TGCAAGCCGAAGCGACGGACAGTCTAAATGCAAGACCGAGTGGG
Found at i:7113 original size:33 final size:33
Alignment explanation
Indices: 7028--7105 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
7018 AATGCCCCAC
7028 CACATGTCGAATCTACTTTATGTAACCCACCAA
1 CACATGTCGAATCTACTTTATGTAACCCACCAA
*
7061 CACATGTCGAATCTACTTTATGTAACTCACCAA
1 CACATGTCGAATCTACTTTATGTAACCCACCAA
7094 CACATGTCGAAT
1 CACATGTCGAAT
7106 ATGCTTTACC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (33 bp):
CACATGTCGAATCTACTTTATGTAACCCACCAA
Found at i:8902 original size:9 final size:10
Alignment explanation
Indices: 8888--8932 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
8878 ACTGTTATAT
*
8888 GCAGTTA-AG
1 GCAGTTAGAA
8897 GCAGTTAGAA
1 GCAGTTAGAA
*
8907 GCAGTTA-AG
1 GCAGTTAGAA
8916 GCAGTTAGAA
1 GCAGTTAGAA
8926 GCAGTTA
1 GCAGTTA
8933 CTGCTGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.22
Consensus pattern (10 bp):
GCAGTTAGAA
Found at i:8950 original size:19 final size:19
Alignment explanation
Indices: 8888--8932 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
8878 ACTGTTATAT
8888 GCAGTTAAGGCAGTTAGAA
1 GCAGTTAAGGCAGTTAGAA
8907 GCAGTTAAGGCAGTTAGAA
1 GCAGTTAAGGCAGTTAGAA
8926 GCAGTTA
1 GCAGTTA
8933 CTGCTGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.22
Consensus pattern (19 bp):
GCAGTTAAGGCAGTTAGAA
Found at i:14334 original size:28 final size:28
Alignment explanation
Indices: 14267--14339 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
14257 ACTTCAATTT
* * *
14267 CTTCGCGACTTCACCGTGACAACTTGCA
1 CTTCGCAACTTCACTGTAACAACTTGCA
* * * *
14295 GTTTGTAGCTTCACTGTAACAACTTGCA
1 CTTCGCAACTTCACTGTAACAACTTGCA
14323 CTTCGCAACTTCACTGT
1 CTTCGCAACTTCACTGT
14340 TCGCCAAAAT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (28 bp):
CTTCGCAACTTCACTGTAACAACTTGCA
Found at i:19661 original size:21 final size:21
Alignment explanation
Indices: 19635--19688 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
19625 GGAGATTTTA
*
19635 GTATCGGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTC-TCACTT
*
19656 GTATCGGTAGATGTCTCACTT
1 GTATCGGTAGAAGTCTCACTT
19677 GTATCGGTAGAA
1 GTATCGGTAGAA
19689 CTATCATAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCTCACTT
Found at i:21783 original size:36 final size:37
Alignment explanation
Indices: 21737--21836 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 37
21727 AAATTCAGGC
**
21737 TGTGCCTAGTAGGCTTTGTGCCGGTG-TTTC-AGTCTG
1 TGTGCCTAGTAGGCTTTGTGCCGGTGAAATCGAG-CTG
* * * *
21773 TGTGCTTAGTAAGCTTCGTGCCGGTGAAATCGAGCTT
1 TGTGCCTAGTAGGCTTTGTGCCGGTGAAATCGAGCTG
*
21810 TGTGCCTAGTAGACTTTGTGCCGGTGA
1 TGTGCCTAGTAGGCTTTGTGCCGGTGA
21837 CCAAAGATTA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
36 23 0.44
37 27 0.52
38 2 0.04
ACGTcount: A:0.14, C:0.19, G:0.32, T:0.35
Consensus pattern (37 bp):
TGTGCCTAGTAGGCTTTGTGCCGGTGAAATCGAGCTG
Found at i:24222 original size:37 final size:37
Alignment explanation
Indices: 24164--24370 Score: 263
Period size: 37 Copynumber: 5.6 Consensus size: 37
24154 GGGTTATGTA
* **
24164 CCTAGTAGGCTTTGTGCCGGTGTTTTCAAG-TTGTGTG
1 CCTAGTAGGCTTCGTGCCGGTGTAATCAAGCTT-TGTG
* * * * *
24201 CTTAGTAGGCTTCGGGTCGGTGAAATCGAGCTTTGTG
1 CCTAGTAGGCTTCGTGCCGGTGTAATCAAGCTTTGTG
24238 CCTAGTAGGCTTCGTGCCGGTGTAATCAAGCTTTGTG
1 CCTAGTAGGCTTCGTGCCGGTGTAATCAAGCTTTGTG
** * *
24275 CCTAGTAGGCTTCGTGCCTATGTAATCAGGCTTTGTC
1 CCTAGTAGGCTTCGTGCCGGTGTAATCAAGCTTTGTG
*
24312 CCTAGTAGGCTTCGTGCCGGTGTAATCGAGCTTTGTG
1 CCTAGTAGGCTTCGTGCCGGTGTAATCAAGCTTTGTG
* *
24349 CCTAGTTGGCTTTGTGCCGGTG
1 CCTAGTAGGCTTCGTGCCGGTG
24371 ACCAAAGATT
Statistics
Matches: 145, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
37 143 0.99
38 2 0.01
ACGTcount: A:0.14, C:0.20, G:0.31, T:0.35
Consensus pattern (37 bp):
CCTAGTAGGCTTCGTGCCGGTGTAATCAAGCTTTGTG
Found at i:24254 original size:16 final size:16
Alignment explanation
Indices: 24230--24329 Score: 56
Period size: 16 Copynumber: 5.6 Consensus size: 16
24220 GTGAAATCGA
*
24230 GCTTTGTGCCTAGTAG
1 GCTTCGTGCCTAGTAG
* *
24246 GCTTCGTGCCGGTGTAATCAA
1 GCTTCGTGCC----TAGT-AG
*
24267 GCTTTGTGCCTAGTAG
1 GCTTCGTGCCTAGTAG
24283 GCTTCGTGCCTATGTAATCAG
1 GCTTCGTGCCTA-G---T-AG
* *
24304 GCTTTGTCCCTAGTAG
1 GCTTCGTGCCTAGTAG
24320 GCTTCGTGCC
1 GCTTCGTGCC
24330 GGTGTAATCG
Statistics
Matches: 63, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
16 31 0.49
17 5 0.08
20 5 0.08
21 22 0.35
ACGTcount: A:0.14, C:0.24, G:0.28, T:0.34
Consensus pattern (16 bp):
GCTTCGTGCCTAGTAG
Found at i:24307 original size:21 final size:21
Alignment explanation
Indices: 24244--24307 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
24234 TGTGCCTAGT
**
24244 AGGCTTCGTGCCGGTGTAATC
1 AGGCTTCGTGCCTATGTAATC
* *
24265 AAGCTTTGTGCCTA-G---T-
1 AGGCTTCGTGCCTATGTAATC
24281 AGGCTTCGTGCCTATGTAATC
1 AGGCTTCGTGCCTATGTAATC
24302 AGGCTT
1 AGGCTT
24308 TGTCCCTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 12 0.38
17 2 0.06
20 2 0.06
21 16 0.50
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (21 bp):
AGGCTTCGTGCCTATGTAATC
Done.