Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005035.1 Kokia drynarioides strain JFW-HI SEQ_118800, 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: 36953
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:319 original size:23 final size:23
Alignment explanation
Indices: 287--340 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
277 ACGCTAGAGC
287 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
*
310 GCTTATTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTTGTGT
333 GCTTACTG
1 GCTTACTG
341 ATTTGCGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.09, C:0.20, G:0.22, T:0.48
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTTGTGT
Found at i:907 original size:20 final size:21
Alignment explanation
Indices: 869--907 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
859 TTTGTACTAA
**
869 AAATCATATTTTATTTCTTTT
1 AAATCATATTTTAAGTCTTTT
890 AAATCA-ATTTTAAGTCTT
1 AAATCATATTTTAAGTCTT
908 GATTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (21 bp):
AAATCATATTTTAAGTCTTTT
Found at i:3564 original size:15 final size:14
Alignment explanation
Indices: 3535--3574 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
3525 TAATATGTTT
3535 ATAATTAAATTTAA
1 ATAATTAAATTTAA
*
3549 ATAATTATATTTTAA
1 ATAATTA-AATTTAA
3564 ATAATTTAAAT
1 ATAA-TTAAAT
3575 AGTTAGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 7 0.32
15 12 0.55
16 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTAAATTTAA
Found at i:7044 original size:66 final size:66
Alignment explanation
Indices: 6929--7121 Score: 269
Period size: 66 Copynumber: 2.9 Consensus size: 66
6919 CGACGACAAC
* * * *
6929 GATTCTGCATCCATGAATGCTGAAAGAGCAAAGGGAGAAGTGAAAGAAGAGGAAAAGGAAGAAGA
1 GATTCTGAATCCTTGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGAAGA
6994 T
66 T
* * * *
6995 GTTTCTGTATCCTTGAATGCTGAAAGTGCGAAGGGAGAAGAGAACGAAGAGGAAAAGGAAGAAGA
1 GATTCTGAATCCTTGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGAAGA
7060 T
66 T
* * * * *
7061 GATTCTGAATCTTTAAATGCTGAAAGTTCAAAAGAAGAAGAGAAAGAAGAGGAAAAGGAAG
1 GATTCTGAATCCTTGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAG
7122 GGGAGCAGGA
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 111 1.00
ACGTcount: A:0.45, C:0.08, G:0.31, T:0.17
Consensus pattern (66 bp):
GATTCTGAATCCTTGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGAAGA
T
Found at i:10846 original size:29 final size:31
Alignment explanation
Indices: 10804--10862 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
10794 CATTTTACCA
* *
10804 ACTTCAT-ATTTAAAT-TATGTATATTAATT
1 ACTTCATAATTAAAATATAAGTATATTAATT
*
10833 ACTTGATAATTAAAATATAAGTATATTAAT
1 ACTTCATAATTAAAATATAAGTATATTAAT
10863 AATCGCTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 7 0.28
31 12 0.48
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (31 bp):
ACTTCATAATTAAAATATAAGTATATTAATT
Found at i:11261 original size:24 final size:24
Alignment explanation
Indices: 11234--11304 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
11224 GGGGGCGATG
11234 GAGTGAGGAACAATACATATGGGC
1 GAGTGAGGAACAATACATATGGGC
**
11258 GAGT-AGGGAAC-GGAC----GGTG-
1 GAGTGA-GGAACAATACATATGG-GC
11277 GAGTGAGGAACAATACATATGGGC
1 GAGTGAGGAACAATACATATGGGC
11301 GAGT
1 GAGT
11305 AGGGAACGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 18
0.61 0.07 0.32
Matches are distributed among these distances:
19 11 0.32
20 4 0.12
23 4 0.12
24 15 0.44
ACGTcount: A:0.34, C:0.11, G:0.39, T:0.15
Consensus pattern (24 bp):
GAGTGAGGAACAATACATATGGGC
Found at i:11293 original size:43 final size:43
Alignment explanation
Indices: 11232--11319 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
11222 GTGGGGGCGA
11232 TGGAGTGAGGAACAATACATATGGGCGAGTAGGGAACGGACGG
1 TGGAGTGAGGAACAATACATATGGGCGAGTAGGGAACGGACGG
11275 TGGAGTGAGGAACAATACATATGGGCGAGTAGGGAACGGACGG
1 TGGAGTGAGGAACAATACATATGGGCGAGTAGGGAACGGACGG
11318 TG
1 TG
11320 ATGAGTATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.32, C:0.11, G:0.42, T:0.15
Consensus pattern (43 bp):
TGGAGTGAGGAACAATACATATGGGCGAGTAGGGAACGGACGG
Found at i:11985 original size:20 final size:20
Alignment explanation
Indices: 11962--12014 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
11952 AAGAACAAAA
*
11962 AATAAAATATGCATAAAAGC
1 AATAAAACATGCATAAAAGC
*
11982 AATAATACATGCATAAAAGC
1 AATAAAACATGCATAAAAGC
*
12002 AATAATACATGCA
1 AATAAAACATGCA
12015 CCTATTACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.21
Consensus pattern (20 bp):
AATAAAACATGCATAAAAGC
Found at i:16669 original size:11 final size:12
Alignment explanation
Indices: 16648--16673 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16638 ATTATTTTCA
16648 TTTTCATTTTTT
1 TTTTCATTTTTT
16660 TTTTCATTTTTT
1 TTTTCATTTTTT
16672 TT
1 TT
16674 CTTGTCTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTCATTTTTT
Found at i:20460 original size:22 final size:22
Alignment explanation
Indices: 20417--20465 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
20407 TGCCTTAGTC
**
20417 TACAAAAATTAAGAAAGTAATA
1 TACAAAAATTAAGAAAAAAATA
20439 TACAAAATATT-AGAAAAAAATA
1 TACAAAA-ATTAAGAAAAAAATA
*
20461 AACAA
1 TACAA
20466 TTTAACAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.20
Consensus pattern (22 bp):
TACAAAAATTAAGAAAAAAATA
Found at i:28226 original size:21 final size:21
Alignment explanation
Indices: 28202--28264 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
28192 TAACCAAAAA
28202 AAATTAATATTATTAACAATT
1 AAATTAATATTATTAACAATT
*
28223 AAATTTGA-ATT-TT-A-AA--
1 AAA-TTAATATTATTAACAATT
28239 AAATTAATATTATTAACAATT
1 AAATTAATATTATTAACAATT
*
28260 GAATT
1 AAATT
28265 TGAATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
15 3 0.09
16 6 0.19
17 2 0.06
18 3 0.09
19 3 0.09
20 2 0.06
21 10 0.31
22 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (21 bp):
AAATTAATATTATTAACAATT
Found at i:28245 original size:37 final size:37
Alignment explanation
Indices: 28199--28276 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
28189 ATTTAACCAA
28199 AAAAAATTAATATTATTAACAATTAAATTTGAATTTT
1 AAAAAATTAATATTATTAACAATTAAATTTGAATTTT
*
28236 AAAAAATTAATATTATTAACAATTGAATTTGAATTTT
1 AAAAAATTAATATTATTAACAATTAAATTTGAATTTT
28273 AAAA
1 AAAA
28277 TCTAAAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (37 bp):
AAAAAATTAATATTATTAACAATTAAATTTGAATTTT
Found at i:28298 original size:30 final size:31
Alignment explanation
Indices: 28264--28323 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
28254 ACAATTGAAT
*
28264 TTGAATT-TTAAAATCT-AAAATGTAGAGATA
1 TTGAATTCTTAAAA-CTGAAAATATAGAGATA
*
28294 TTGAATTCTTATAACTGAAAATATAGAGAT
1 TTGAATTCTTAAAACTGAAAATATAGAGAT
28324 TAAATTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (31 bp):
TTGAATTCTTAAAACTGAAAATATAGAGATA
Found at i:35005 original size:50 final size:50
Alignment explanation
Indices: 34950--35058 Score: 166
Period size: 50 Copynumber: 2.2 Consensus size: 50
34940 AATTGCGATG
*
34950 GTTTCAATAGAATCACATCATTCACGATC-CTTTTTCAATTATTTAAATAC
1 GTTTCAATAGAATCACATCATTCACGATCTC-TTTACAATTATTTAAATAC
* *
35000 GTTTCAATATAATCACATCGTTCACGATCTCTTTACAATTATTTAAATAC
1 GTTTCAATAGAATCACATCATTCACGATCTCTTTACAATTATTTAAATAC
*
35050 ATTTCAATA
1 GTTTCAATA
35059 ATTTTTTTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 53 0.98
51 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (50 bp):
GTTTCAATAGAATCACATCATTCACGATCTCTTTACAATTATTTAAATAC
Done.