Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009744.1 Kokia drynarioides strain JFW-HI SEQ_124463, 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: 48963
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:321 original size:17 final size:17
Alignment explanation
Indices: 286--324 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
276 AGGTGGAGAA
** *
286 CTTGTTTGTTGAGAGTT
1 CTTGTTTGTAAAGAATT
303 CTTGTTTGTAAAGAATT
1 CTTGTTTGTAAAGAATT
320 CTTGT
1 CTTGT
325 CAAGATGTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.51
Consensus pattern (17 bp):
CTTGTTTGTAAAGAATT
Found at i:4702 original size:17 final size:17
Alignment explanation
Indices: 4649--4702 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
4639 TTATTTGAAA
4649 ATAC-ATTATATACTT-T
1 ATACTATTATATA-TTAT
*
4665 ATAATATTAT-TATCTAT
1 ATACTATTATATAT-TAT
4682 ATACTATTATATATTAT
1 ATACTATTATATATTAT
4699 ATAC
1 ATAC
4703 AACTTTTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 22 0.69
18 3 0.09
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
ATACTATTATATATTAT
Found at i:10262 original size:17 final size:17
Alignment explanation
Indices: 10242--10307 Score: 78
Period size: 17 Copynumber: 3.7 Consensus size: 17
10232 CTCTTGACTT
* *
10242 TTAACATTTCATCTTCC
1 TTAACCTTTCATCTTTC
*
10259 TTAACCTCTTTTGATCTTTC
1 TTAA-C-C-TTTCATCTTTC
10279 TTAACCTTTCATCTTTC
1 TTAACCTTTCATCTTTC
10296 TTAACCTTTCAT
1 TTAACCTTTCAT
10308 ATTCTTGTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
17 26 0.62
18 2 0.05
19 1 0.02
20 13 0.31
ACGTcount: A:0.20, C:0.27, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAACCTTTCATCTTTC
Found at i:10289 original size:37 final size:34
Alignment explanation
Indices: 10225--10302 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 34
10215 TGTTCAACCT
10225 TTAACCTCTCTTGACTTTTAACATTTCATCTTCC
1 TTAACCTCTCTTGACTTTTAACATTTCATCTTCC
* * *
10259 TTAACCTCTTTTGATCTTTCTTAACCTTTCATCTTTC
1 TTAACCTCTCTTGA-C-TT-TTAACATTTCATCTTCC
10296 TTAACCT
1 TTAACCT
10303 TTCATATTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 13 0.34
35 1 0.03
36 2 0.05
37 22 0.58
ACGTcount: A:0.19, C:0.28, G:0.03, T:0.50
Consensus pattern (34 bp):
TTAACCTCTCTTGACTTTTAACATTTCATCTTCC
Found at i:15700 original size:17 final size:17
Alignment explanation
Indices: 15680--15738 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
15670 CCCTTGATTT
15680 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
15697 TTAACC-TCC-T-TTGACC
1 TTAACCTTCCATCTT--CC
* *
15713 TTTAACCTTTCATCTTCT
1 -TTAACCTTCCATCTTCC
15731 TTAACCTT
1 TTAACCTT
15739 TCATATTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 2 0.06
15 1 0.03
16 5 0.15
17 20 0.59
18 3 0.09
19 1 0.03
20 2 0.06
ACGTcount: A:0.19, C:0.34, G:0.02, T:0.46
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:15717 original size:34 final size:34
Alignment explanation
Indices: 15663--15737 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
15653 TGTTCAACCT
**
15663 TTAACCTCCCTTGATTTTTAACCTTCCATCTTCC
1 TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
* * *
15697 TTAACCTCCTTTGACCTTTAACCTTTCATCTTCT
1 TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
15731 TTAACCT
1 TTAACCT
15738 TTCATATTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.19, C:0.33, G:0.03, T:0.45
Consensus pattern (34 bp):
TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
Found at i:15739 original size:17 final size:17
Alignment explanation
Indices: 15712--15753 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
15702 CTCCTTTGAC
*
15712 CTTTAACCTTTCATCTT
1 CTTTAACCTTTCATATT
15729 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
15746 CTTGTAAC
1 CTT-TAAC
15754 TACTTTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:18293 original size:53 final size:53
Alignment explanation
Indices: 18210--18340 Score: 149
Period size: 53 Copynumber: 2.5 Consensus size: 53
18200 GTGTGTCTTA
*
18210 AACAATATACACACACCCAGACACACGCCCATGTGTCAGCCTATGTGGCCC-AG
1 AACAATATACACACACCCAGACACACGCCCATGTGTCAGCCCATGT-GCCCTAG
* * * * *
18263 AATAATATACACACACCTTA-ACATATGCCCATGTGTCAGCCCGTGTGCCCTAG
1 AACAATATACACACACC-CAGACACACGCCCATGTGTCAGCCCATGTGCCCTAG
* * *
18316 AACAGTATACACACACACTGACACA
1 AACAATATACACACACCCAGACACA
18341 AGTCCGTGTG
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
52 4 0.06
53 58 0.92
54 1 0.02
ACGTcount: A:0.34, C:0.33, G:0.15, T:0.18
Consensus pattern (53 bp):
AACAATATACACACACCCAGACACACGCCCATGTGTCAGCCCATGTGCCCTAG
Found at i:21758 original size:27 final size:27
Alignment explanation
Indices: 21720--21830 Score: 170
Period size: 27 Copynumber: 4.1 Consensus size: 27
21710 ATTTTGAGCA
21720 TCTCTAACTCCAATCTCAGCTTCTCAT
1 TCTCTAACTCCAATCTCAGCTTCTCAT
* *
21747 TCTCTATCTCCAATCTCAGCTTTTCAT
1 TCTCTAACTCCAATCTCAGCTTCTCAT
*
21774 TCTCTAACTCCAGTCTCAGCTTCTCAT
1 TCTCTAACTCCAATCTCAGCTTCTCAT
*
21801 AT-TCTAACTCCAATCTCAGCCTCTCAT
1 -TCTCTAACTCCAATCTCAGCTTCTCAT
21828 TCT
1 TCT
21831 GGTGCAACAA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 1 0.01
27 73 0.97
28 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.05, T:0.39
Consensus pattern (27 bp):
TCTCTAACTCCAATCTCAGCTTCTCAT
Found at i:21965 original size:93 final size:93
Alignment explanation
Indices: 21806--22015 Score: 357
Period size: 93 Copynumber: 2.3 Consensus size: 93
21796 CTCATATTCT
* * *
21806 AACTCCAATCTCAGCCTCTCATTCTGGTGCAACAATTGATCTCCTTTGTTGATCACTTGAATCAA
1 AACTCCAATCTCAGCCTCTCATTCCGGTGCAACAATTGATCTCCTTCGTTGACCACTTGAATCAA
*
21871 TTTCAAGTTCTGTTCCCTTTCACGTTCA
66 TTTCAAGTTCTGTTCCCTTTCACGCTCA
*
21899 AACTCCAATCTCAGCCTCTCATTCCGGTGCAACAATTGATCTTCTTCGTTGACCACTTGAATCAA
1 AACTCCAATCTCAGCCTCTCATTCCGGTGCAACAATTGATCTCCTTCGTTGACCACTTGAATCAA
*
21964 TTTCAAGTTCTGTTCCCTTTCACGCTCT
66 TTTCAAGTTCTGTTCCCTTTCACGCTCA
*
21992 AACTCCAATCTCAGCCTCACATTC
1 AACTCCAATCTCAGCCTCTCATTC
22016 TCCTTCTCCA
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 110 1.00
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.35
Consensus pattern (93 bp):
AACTCCAATCTCAGCCTCTCATTCCGGTGCAACAATTGATCTCCTTCGTTGACCACTTGAATCAA
TTTCAAGTTCTGTTCCCTTTCACGCTCA
Found at i:27608 original size:22 final size:23
Alignment explanation
Indices: 27576--27620 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
27566 ATGAACTTAC
27576 CTAATTACATAA-TCAACAATTT
1 CTAATTACATAATTCAACAATTT
* *
27598 CTAATTTCATAATTCAACCATTT
1 CTAATTACATAATTCAACAATTT
27621 GGCAACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (23 bp):
CTAATTACATAATTCAACAATTT
Found at i:29623 original size:17 final size:17
Alignment explanation
Indices: 29601--29640 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
29591 CCAACATATG
29601 ATATTTGGATGATTAAA
1 ATATTTGGATGATTAAA
*
29618 ATATTTTTGATGATTAAA
1 ATA-TTTGGATGATTAAA
*
29636 TTATT
1 ATATT
29641 GTTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (17 bp):
ATATTTGGATGATTAAA
Found at i:30179 original size:46 final size:45
Alignment explanation
Indices: 30127--30398 Score: 228
Period size: 46 Copynumber: 6.0 Consensus size: 45
30117 GTTATAAAAG
* *
30127 TGGCTTCAATTTGCCCCTCTGGATTTAGGGTTAAAAGATTGGATGA
1 TGGCTTCAATCTGCCCCTCTAGATTTAGGG-TAAAAGATTGGATGA
* * * *
30173 TGGCTTCAATTTGCTCCTCTAGATTTAGGGGTAAAATATCGGATGA
1 TGGCTTCAATCTGCCCCTCTAGATTTA-GGGTAAAAGATTGGATGA
* *
30219 TGGCTTCAATCTGCCCCTTTGGATTTAGGCGTAAAAGATT-G--GA
1 TGGCTTCAATCTGCCCCTCTAGATTTAGG-GTAAAAGATTGGATGA
* * * ** * *
30262 T-GCTTCAGTTTGCCCCTCTAGATTTGGGGTATCAGACTGAATGTGA
1 TGGCTTCAATCTGCCCCTCTAGATTTAGGGTAAAAGATTGGA--TGA
** ** * * * * *
30308 TGATTTCAATCTGCCATTTTGGATTTAGAGTATAAGATTGGATGTGG
1 TGGCTTCAATCTGCCCCTCTAGATTTAGGGTAAAAGATTGGA--TGA
*
30355 TGGCTTCAATCTGCCCCTCTAGATTTAGGGTATAAGATTGGATG
1 TGGCTTCAATCTGCCCCTCTAGATTTAGGGTAAAAGATTGGATG
30399 CTTTAGTTTG
Statistics
Matches: 178, Mismatches: 40, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
41 7 0.04
42 22 0.12
43 3 0.02
45 5 0.03
46 72 0.40
47 69 0.39
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (45 bp):
TGGCTTCAATCTGCCCCTCTAGATTTAGGGTAAAAGATTGGATGA
Found at i:30432 original size:40 final size:41
Alignment explanation
Indices: 30221--30523 Score: 178
Period size: 47 Copynumber: 7.0 Consensus size: 41
30211 TCGGATGATG
* * * *
30221 GCTTCAATCTGCCCCTTTGGATTTAGGCGTAAAAGATTGGAT
1 GCTTTAATTTGCCCTTTTGGATTTAGG-GTATAAGATTGGAT
* * * * * * *
30263 GCTTCAGTTTGCCCCTCTAGATTTGGGGTATCAGACTGAATGTGAT
1 GCTTTAATTTGCCCTTTTGGATTTAGGGTAT-A-A--GATTG-GAT
* * * *
30309 GATTTCAATCTGCCATTTTGGATTTAGAGTATAAGATTGGATGTGGT
1 GCTTT-AATTTGCCCTTTTGGATTTAGGGTATAAGATTGGA-----T
* * * * *
30356 GGCTTCAATCTGCCCCTCTAGATTTAGGGTATAAGATTGGAT
1 -GCTTTAATTTGCCCTTTTGGATTTAGGGTATAAGATTGGAT
* *
30398 GCTTTAGTTTGTCCTTTTGGATTT-GGGTATAAGATTGGAT
1 GCTTTAATTTGCCCTTTTGGATTTAGGGTATAAGATTGGAT
* * * *
30438 GCTTTAATCTACCCTTTTGGATTTAGGG-ATAAAACTTGAAGGT
1 GCTTTAATTTGCCCTTTTGGATTTAGGGTATAAGA-TTG--GAT
* * *
30481 GGCTTCAATTTGCCCTTTTGGATTTGGGGTATAATATTGGAT
1 -GCTTTAATTTGCCCTTTTGGATTTAGGGTATAAGATTGGAT
30523 G
1 G
30524 GTCACTAGTC
Statistics
Matches: 199, Mismatches: 44, Indels: 37
0.71 0.16 0.13
Matches are distributed among these distances:
40 41 0.21
41 27 0.14
42 28 0.14
43 7 0.04
44 27 0.14
45 10 0.05
46 7 0.04
47 49 0.25
48 3 0.02
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.38
Consensus pattern (41 bp):
GCTTTAATTTGCCCTTTTGGATTTAGGGTATAAGATTGGAT
Found at i:31310 original size:7 final size:7
Alignment explanation
Indices: 31298--31337 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
31288 CCTCTCTTTC
31298 TTTTCTT
1 TTTTCTT
31305 TTTTCTT
1 TTTTCTT
31312 TTTTCTT
1 TTTTCTT
31319 TCTTT-TT
1 T-TTTCTT
31326 TTTCTCTT
1 TTT-TCTT
31334 TTTT
1 TTTT
31338 TTTGGGTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 2 0.07
7 20 0.67
8 8 0.27
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:31311 original size:12 final size:11
Alignment explanation
Indices: 31294--31340 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
31284 TCGACCTCTC
31294 TTTCTTTTCTTT
1 TTTCTTTT-TTT
*
31306 TTTCTTTTTTC
1 TTTCTTTTTTT
31317 TTTCTTTTTTT
1 TTTCTTTTTTT
*
31328 TCTCTTTTTTT
1 TTTCTTTTTTT
31339 TT
1 TT
31341 GGGTGAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 23 0.74
12 8 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:31338 original size:23 final size:23
Alignment explanation
Indices: 31292--31337 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
31282 TCTCGACCTC
*
31292 TCTTTCTTTTCTTTTTTCTTTTT
1 TCTTTCTTTTCTTTTCTCTTTTT
31315 TCTTTCTTTT-TTTTCTCTTTTT
1 TCTTTCTTTTCTTTTCTCTTTTT
31337 T
1 T
31338 TTTGGGTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (23 bp):
TCTTTCTTTTCTTTTCTCTTTTT
Found at i:35780 original size:18 final size:19
Alignment explanation
Indices: 35757--35794 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35747 ATTAGAAGTA
35757 AAATAA-AT-GCAAATAATT
1 AAATAACATGGCAAA-AATT
35775 AAATAACATGGCAAAAATT
1 AAATAACATGGCAAAAATT
35794 A
1 A
35795 GAATGTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (19 bp):
AAATAACATGGCAAAAATT
Found at i:42970 original size:22 final size:23
Alignment explanation
Indices: 42944--42986 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
42934 AGATGAAAGG
*
42944 TTTAAAAATTAG-AAAAAGGGGT
1 TTTAAAAATAAGCAAAAAGGGGT
*
42966 TTTAAAACTAAGCAAAAAGGG
1 TTTAAAAATAAGCAAAAAGGG
42987 TAATTTATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.23
Consensus pattern (23 bp):
TTTAAAAATAAGCAAAAAGGGGT
Done.