Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001614.1 Kokia drynarioides strain JFW-HI SEQ_113247, 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: 52986
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 131 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 AT AT AT AT AT 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 AT AT AT AT AT
37 GCATGAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18775 original size:15 final size:16
Alignment explanation
Indices: 18755--18784 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18745 AACTTGGAAT
18755 TTTGGATTTT-AAAAC
1 TTTGGATTTTCAAAAC
18770 TTTGGATTTTCAAAA
1 TTTGGATTTTCAAAA
18785 TCAAAGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (16 bp):
TTTGGATTTTCAAAAC
Found at i:24156 original size:49 final size:49
Alignment explanation
Indices: 24084--24197 Score: 228
Period size: 49 Copynumber: 2.3 Consensus size: 49
24074 AAGCTAAATT
24084 CTCTATTCCCATATTACAACTTCCCTTTCAAAACAAGACACCATCAATC
1 CTCTATTCCCATATTACAACTTCCCTTTCAAAACAAGACACCATCAATC
24133 CTCTATTCCCATATTACAACTTCCCTTTCAAAACAAGACACCATCAATC
1 CTCTATTCCCATATTACAACTTCCCTTTCAAAACAAGACACCATCAATC
24182 CTCTATTCCCATATTA
1 CTCTATTCCCATATTA
24198 AGACCTCCTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.33, C:0.34, G:0.02, T:0.31
Consensus pattern (49 bp):
CTCTATTCCCATATTACAACTTCCCTTTCAAAACAAGACACCATCAATC
Found at i:25262 original size:12 final size:12
Alignment explanation
Indices: 25247--25322 Score: 71
Period size: 12 Copynumber: 6.3 Consensus size: 12
25237 TTTTAAACTG
* *
25247 TTTTGGTGTTGT
1 TTTTGCTGTTAT
25259 TTTTGCTGTTAT
1 TTTTGCTGTTAT
* *
25271 TTTCGTTGTTAT
1 TTTTGCTGTTAT
*
25283 TTTTGCGGTTAT
1 TTTTGCTGTTAT
**
25295 TTTTGCTACTAT
1 TTTTGCTGTTAT
* *
25307 TTTGGTTGTTAT
1 TTTTGCTGTTAT
25319 TTTT
1 TTTT
25323 TTTGTTTGGA
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.08, C:0.07, G:0.20, T:0.66
Consensus pattern (12 bp):
TTTTGCTGTTAT
Found at i:25336 original size:20 final size:20
Alignment explanation
Indices: 25307--25344 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25297 TTGCTACTAT
*
25307 TTTGGTTGTTATTTTTTTTG
1 TTTGGATGTTATTTTTTTTG
25327 TTTGGATGTTATTTTTTT
1 TTTGGATGTTATTTTTTT
25345 GCGTTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.18, T:0.74
Consensus pattern (20 bp):
TTTGGATGTTATTTTTTTTG
Found at i:25350 original size:21 final size:20
Alignment explanation
Indices: 25307--25350 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
25297 TTGCTACTAT
* *
25307 TTTGGTTGTTATTTTTTTTG
1 TTTGGATGTTATTTTTTTCG
25327 TTTGGATGTTATTTTTTTGCG
1 TTTGGATGTTATTTTTTT-CG
25348 TTT
1 TTT
25351 TTACTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.07, C:0.02, G:0.20, T:0.70
Consensus pattern (20 bp):
TTTGGATGTTATTTTTTTCG
Found at i:31978 original size:11 final size:11
Alignment explanation
Indices: 31964--32017 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
31954 TGATATTAAG
31964 TTTAAATTTAT
1 TTTAAATTTAT
31975 TTTAAATTTAT
1 TTTAAATTTAT
* * *
31986 TCTGAATTTAAA
1 TTTAAATTT-AT
* *
31998 TTTAAAGTTGT
1 TTTAAATTTAT
32009 TTTAAATTT
1 TTTAAATTT
32018 GAAATATCCA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
11 26 0.79
12 7 0.21
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:31979 original size:17 final size:17
Alignment explanation
Indices: 31947--32022 Score: 50
Period size: 17 Copynumber: 4.4 Consensus size: 17
31937 GGATCAAACT
*
31947 TTTAAATTGATATTAAG
1 TTTAAATTGATATTAAA
* *
31964 TTTAAATTTATTTTAAA
1 TTTAAATTGATATTAAA
*
31981 TTT-ATTCTGA-ATTTAAA
1 TTTAAAT-TGATA-TTAAA
*
31998 TTTAAAGTTG-TTTTAAA
1 TTTAAA-TTGATATTAAA
32015 TTTGAAAT
1 TTT-AAAT
32023 ATCCAAATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
16 2 0.04
17 36 0.80
18 6 0.13
19 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.53
Consensus pattern (17 bp):
TTTAAATTGATATTAAA
Found at i:32522 original size:3 final size:3
Alignment explanation
Indices: 32508--32571 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
32498 CCATTACCAT
*
32508 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32556 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
32572 ATTTAAGGTA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33377 original size:15 final size:15
Alignment explanation
Indices: 33354--33383 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33344 TCGTTTCATG
33354 CCAAACCAACCCGCC
1 CCAAACCAACCCGCC
*
33369 CCAATCCAACCCGCC
1 CCAAACCAACCCGCC
33384 TCAGGATCCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.60, G:0.07, T:0.03
Consensus pattern (15 bp):
CCAAACCAACCCGCC
Found at i:33856 original size:29 final size:31
Alignment explanation
Indices: 33809--33886 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
33799 CCAATTTTTT
* **
33809 TTCCAAAAATTATCA-TTTTACCCCCAAA-C
1 TTCCAAAAATTACCATTTTTAAACCCAAATC
* *
33838 TTCTAAAAATT-CCATTTTTAAACCCAAATT
1 TTCCAAAAATTACCATTTTTAAACCCAAATC
33868 TTCCAAAAATTACCATTTT
1 TTCCAAAAATTACCATTTT
33887 ATCCCGAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 2 0.05
29 21 0.52
30 10 0.25
31 7 0.17
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.37
Consensus pattern (31 bp):
TTCCAAAAATTACCATTTTTAAACCCAAATC
Found at i:33905 original size:59 final size:59
Alignment explanation
Indices: 33807--34121 Score: 240
Period size: 58 Copynumber: 5.4 Consensus size: 59
33797 CCCCAATTTT
* * *
33807 TTTTCCAAAAATTATCATTTTACCCCCAAACTTCTAAAAATTCCATTTTTAAACC-CAAA
1 TTTTCCAAAAATTACCATTTTACTCCCGAACTTCTAAAAATTCCATTTTT-AACCTCAAA
* * * *
33866 TTTTCCAAAAATTACCATTTTA-TCCCGAAC-TCTCAAAAAATCCATTTTTGACCTTAAT
1 TTTTCCAAAAATTACCATTTTACTCCCGAACTTCT-AAAAATTCCATTTTTAACCTCAAA
* * * * * *
33924 TTTTCCAAAAGTTACCATTTTAAC-CCTGAACTTCCT-AAAATTTCATCTTTAACCTCGAT
1 TTTTCCAAAAATTACCATTTT-ACTCCCGAACTT-CTAAAAATTCCATTTTTAACCTCAAA
* * *
33983 TTTTCC-AAAATTACTATTTTACTCTC-AGA-TGTCTAAAAATTCCATTTTAAACC-CTAAA
1 TTTTCCAAAAATTACCATTTTACTCCCGA-ACT-TCTAAAAATTCCATTTTTAACCTC-AAA
* * * * * *
34041 CTTTCCAAAAATTACCATTTTACCCCCGGATA-AT-TAAAAATTCTAATTTTTGACCTCGAA
1 TTTTCCAAAAATTACCATTTTACTCCC-GA-ACTTCTAAAAATTC-CATTTTTAACCTCAAA
*
34101 CTTTCTC-AAAATTACCATTTT
1 TTTTC-CAAAAATTACCATTTT
34122 GCCCTTGAGT
Statistics
Matches: 205, Mismatches: 34, Indels: 33
0.75 0.12 0.12
Matches are distributed among these distances:
57 13 0.06
58 78 0.38
59 77 0.38
60 31 0.15
61 6 0.03
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (59 bp):
TTTTCCAAAAATTACCATTTTACTCCCGAACTTCTAAAAATTCCATTTTTAACCTCAAA
Found at i:33932 original size:117 final size:117
Alignment explanation
Indices: 33806--34067 Score: 289
Period size: 117 Copynumber: 2.2 Consensus size: 117
33796 CCCCCAATTT
* *
33806 TTTTTCCAAAAATTATCATTTTACCCCCAAACTT-CTAAAAATTCCATTTTTAAACC-CAAATTT
1 TTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCT-AAAATTCCATCTTT-AACCTCAAATTT
* ** *
33869 TCCAAAAATTACCATTTTA-TC-CCGAACTCTCAAAAAATCCATTTTTGACCTTAA
64 TCC-AAAATTACCATTTTACTCTCAGAACTCT-AAAAAATCCATTTTAAACCCTAA
* * ** * * *
33923 TTTTTCCAAAAGTTACCATTTTAACCCTGAACTTCCTAAAATTTCATCTTTAACCTCGATTTTTC
1 TTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCTAAAATTCCATCTTTAACCTCAAATTTTC
* ** *
33988 CAAAATTACTATTTTACTCTCAGATGTCTAAAAATTCCATTTTAAACCCTAA
66 CAAAATTACCATTTTACTCTCAGAACTCTAAAAAATCCATTTTAAACCCTAA
**
34040 ACTTTCCAAAAATTACCATTTTACCCCC
1 TTTTTCCAAAAATTACCATTTTACCCCC
34068 GGATAATTAA
Statistics
Matches: 119, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
116 18 0.15
117 93 0.78
118 8 0.07
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (117 bp):
TTTTTCCAAAAATTACCATTTTACCCCCAAACTTCCTAAAATTCCATCTTTAACCTCAAATTTTC
CAAAATTACCATTTTACTCTCAGAACTCTAAAAAATCCATTTTAAACCCTAA
Found at i:34003 original size:29 final size:28
Alignment explanation
Indices: 33922--34003 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 28
33912 TTTGACCTTA
33922 ATTTTTCCAAAAGTTACCATTTTAACCCTG
1 ATTTTTCCAAAA-TTA-CATTTTAACCCTG
** *
33952 A-ACTTCCTAAAATTTCATCTTTAA-CCTCG
1 ATTTTTCC-AAAATTACAT-TTTAACCCT-G
33981 ATTTTTCCAAAATTACTATTTTA
1 ATTTTTCCAAAATTAC-ATTTTA
34004 CTCTCAGATG
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
28 6 0.15
29 24 0.59
30 11 0.27
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.43
Consensus pattern (28 bp):
ATTTTTCCAAAATTACATTTTAACCCTG
Found at i:34168 original size:28 final size:28
Alignment explanation
Indices: 34107--34166 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
34097 CGAACTTTCT
** *
34107 CAAAATTACCATTTTGCCCTTGAGTGTC
1 CAAAATTACCATTTTGCCCCCGAGTATC
34135 CAAAATTACCATTTTGCCCCCG-GTATC
1 CAAAATTACCATTTTGCCCCCGAGTATC
34162 CAAAA
1 CAAAA
34167 ATCTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 9 0.31
28 20 0.69
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (28 bp):
CAAAATTACCATTTTGCCCCCGAGTATC
Found at i:35222 original size:2 final size:2
Alignment explanation
Indices: 35215--35242 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35205 TGGTTTCGAC
35215 AT 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 AT
35243 CCATGGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51462 original size:22 final size:22
Alignment explanation
Indices: 51406--51481 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 22
51396 CTGGGGAAAT
* *
51406 AGTAAGCATACACAGCGCAATCC
1 AGTAGGCACACACAGCGCAAT-C
* *
51429 AATAGGCACACACAGTGCAATC
1 AGTAGGCACACACAGCGCAATC
* *
51451 AGTAGGCGCACATAGCGCAAATC
1 AGTAGGCACACACAGCGC-AATC
51474 AGTAGGCA
1 AGTAGGCA
51482 TACGAGGTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
22 15 0.35
23 28 0.65
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.13
Consensus pattern (22 bp):
AGTAGGCACACACAGCGCAATC
Done.