Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014190.1 Kokia drynarioides strain JFW-HI SEQ_129223, 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: 50015
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:6968 original size:41 final size:40
Alignment explanation
Indices: 6923--7126 Score: 160
Period size: 41 Copynumber: 5.0 Consensus size: 40
6913 GCTCCGGCCT
*
6923 TTAGTAGCGTTTATGAGGAAGCGCCACTAAAGGTCAGAGCA
1 TTAGTAGCGTTTATGA-TAAGCGCCACTAAAGGTCAGAGCA
* * * *
6964 TTAGTGATGC-TTTATCATAAACGCTACTAAAAGTCAGAGCA
1 TTAGT-A-GCGTTTATGATAAGCGCCACTAAAGGTCAGAGCA
* * ** *
7005 TTAGCT-GCATTTTTGTCATAAGCGCCGTTAAAGGTCAAAGCA
1 TTAG-TAGCGTTTATG--ATAAGCGCCACTAAAGGTCAGAGCA
* * * *
7047 TTAGTGGCACTTTATCATAAACGCCACTAAAGGTCAGAGCA
1 TTAGTAGC-GTTTATGATAAGCGCCACTAAAGGTCAGAGCA
* * * *
7088 TTAGCAGCGTTTATGGTGAAGTGCCGCTAAAGGTCAGAG
1 TTAGTAGCGTTTATGAT-AAGCGCCACTAAAGGTCAGAG
7127 TAATACAACA
Statistics
Matches: 126, Mismatches: 28, Indels: 18
0.73 0.16 0.10
Matches are distributed among these distances:
39 2 0.02
40 10 0.08
41 75 0.60
42 33 0.26
43 6 0.05
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (40 bp):
TTAGTAGCGTTTATGATAAGCGCCACTAAAGGTCAGAGCA
Found at i:7047 original size:42 final size:42
Alignment explanation
Indices: 6944--7092 Score: 169
Period size: 41 Copynumber: 3.6 Consensus size: 42
6934 TATGAGGAAG
***
6944 CGCCACTAAAGGTCAGAGCATTAG-TGATGCTTTATCATAAA
1 CGCCACTAAAGGTCAGAGCATTAGCTGGCACTTTATCATAAA
* * * * *
6985 CGCTACTAAAAGTCAGAGCATTAGCT-GCATTTTTGTCATAAG
1 CGCCACTAAAGGTCAGAGCATTAGCTGGCA-CTTTATCATAAA
** *
7027 CGCCGTTAAAGGTCAAAGCATTAG-TGGCACTTTATCATAAA
1 CGCCACTAAAGGTCAGAGCATTAGCTGGCACTTTATCATAAA
7068 CGCCACTAAAGGTCAGAGCATTAGC
1 CGCCACTAAAGGTCAGAGCATTAGC
7093 AGCGTTTATG
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
41 53 0.62
42 32 0.38
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (42 bp):
CGCCACTAAAGGTCAGAGCATTAGCTGGCACTTTATCATAAA
Found at i:7189 original size:41 final size:41
Alignment explanation
Indices: 7065--7221 Score: 122
Period size: 41 Copynumber: 3.8 Consensus size: 41
7055 ACTTTATCAT
* * * **
7065 AAACGCCACTAAAGGTCAGAGCATTAGCAGCGTTTATG-GTG
1 AAACGCCGCTAAAGGTCA-AGCAATAGCGGCGTTTATGAGAA
** * ** *
7106 AAGTGCCGCTAAAGGTCAGAGTAATA-CAACATTTATGAG-A
1 AAACGCCGCTAAAGGTCA-AGCAATAGCGGCGTTTATGAGAA
* * *
7146 AAACGCCGCTAAATGTCAACGCATTAGCGGCGTTTATGGGAA
1 AAACGCCGCTAAAGGTCAA-GCAATAGCGGCGTTTATGAGAA
* *
7188 AAACGCTGCTAAAGGTTAAGCAATAGCGGCGTTT
1 AAACGCCGCTAAAGGTCAAGCAATAGCGGCGTTT
7222 TCAATTTATT
Statistics
Matches: 91, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
39 1 0.01
40 28 0.31
41 45 0.49
42 17 0.19
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (41 bp):
AAACGCCGCTAAAGGTCAAGCAATAGCGGCGTTTATGAGAA
Found at i:7899 original size:18 final size:19
Alignment explanation
Indices: 7876--7919 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
7866 GAAAAATAAA
7876 AAAATTATTAAT-ATTTCT
1 AAAATTATTAATAATTTCT
* **
7894 AAAATTTTTGGTAATTTCT
1 AAAATTATTAATAATTTCT
7913 AAAATTA
1 AAAATTA
7920 ACATTATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (19 bp):
AAAATTATTAATAATTTCT
Found at i:8726 original size:24 final size:24
Alignment explanation
Indices: 8688--8737 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
8678 CCATAAACAC
* *
8688 CGCTAAAGGTTAGAGCACTAGCGG
1 CGCTAAAGATCAGAGCACTAGCGG
* *
8712 CGCTAAAGATCAGAGCATTAGTGG
1 CGCTAAAGATCAGAGCACTAGCGG
8736 CG
1 CG
8738 TTTATGAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.32, T:0.18
Consensus pattern (24 bp):
CGCTAAAGATCAGAGCACTAGCGG
Found at i:9009 original size:27 final size:27
Alignment explanation
Indices: 8979--9056 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
8969 ACAATTATTT
8979 TAAAATTTATATAAACTAAAAAAATTC
1 TAAAATTTATATAAACTAAAAAAATTC
* *
9006 TAAAATTT-T-TAAA-AAAATCTAAAATTT
1 TAAAATTTATATAAACTAAA---AAAATTC
*
9033 TAAAACTTATATAAACTAAAAAAA
1 TAAAATTTATATAAACTAAAAAAA
9057 AATAAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
24 3 0.07
25 4 0.10
26 1 0.02
27 25 0.61
28 1 0.02
29 4 0.10
30 3 0.07
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAAATTTATATAAACTAAAAAAATTC
Found at i:9020 original size:20 final size:18
Alignment explanation
Indices: 8995--9037 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
8985 TTATATAAAC
8995 TAAAAAAATTCTAAAATTTT
1 TAAAAAAA-TCTAAAA-TTT
9015 TAAAAAAATCTAAAATTT
1 TAAAAAAATCTAAAATTT
9033 TAAAA
1 TAAAA
9038 CTTATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
20 8 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAAAATCTAAAATTT
Found at i:9225 original size:75 final size:76
Alignment explanation
Indices: 9089--9239 Score: 218
Period size: 75 Copynumber: 2.0 Consensus size: 76
9079 TTTTTCCCCG
9089 AATCCTTTCTTTCCCCCAAAATCCCCAAATCAATAACCCATCACTATTATGTCTTCCCATAAAAC
1 AATCCTTTCTTTCCCCCAAAATCCCCAAATCAATAACCCATCACTATTATGTCTTCCCATAAAAC
*
9154 AGAGCAGAGAA
66 AAAGCAGAGAA
* * * *
9165 AATCTTTTCTTTCCTCCCAAAA-CTCCAAATCAA-AATCCATTC-TTATTATGTCTTCCCATAAA
1 AATCCTTTCTTTCC-CCCAAAATCCCCAAATCAATAACCCA-TCACTATTATGTCTTCCCATAAA
9227 ACAAAGCAGAGAA
64 ACAAAGCAGAGAA
9240 GGTAAAACCC
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
75 36 0.53
76 25 0.37
77 7 0.10
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.28
Consensus pattern (76 bp):
AATCCTTTCTTTCCCCCAAAATCCCCAAATCAATAACCCATCACTATTATGTCTTCCCATAAAAC
AAAGCAGAGAA
Found at i:13320 original size:43 final size:43
Alignment explanation
Indices: 13242--13341 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
13232 TATTAGCGAT
*** * * *
13242 GTTTGTAGGAAAAGCGTTGTTAAAGATTTTTTTTTTTAACGGC
1 GTTTGTAGGAAAAGCACCGTTAAAGACTATGTTTTTTAACGGC
** *
13285 GTTTGTAGGAAAAGCACCGTTAAAGACTATGTTTTTTAGTGGT
1 GTTTGTAGGAAAAGCACCGTTAAAGACTATGTTTTTTAACGGC
*
13328 GTTTGTGGGAAAAG
1 GTTTGTAGGAAAAG
13342 TGTTGTCAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.39
Consensus pattern (43 bp):
GTTTGTAGGAAAAGCACCGTTAAAGACTATGTTTTTTAACGGC
Found at i:13422 original size:42 final size:42
Alignment explanation
Indices: 13304--13425 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
13294 AAAAGCACCG
* ***
13304 TTAAAGA-CTATGTTTTTTAGTGGTGTTTGTGGGAAAAGTGTTG
1 TTAAAGATC-ATGTTTTTTAGTGGTGTTTGT-GGAAAAATGCCA
* * * * * *
13347 TCAAAGATCATGATCTTTAGTAGAGTTTATGGAAAAATGCCA
1 TTAAAGATCATGTTTTTTAGTGGTGTTTGTGGAAAAATGCCA
*
13389 TTAAAGATCATGTTTTTTAGCGGTGTTTGTGGAAAAA
1 TTAAAGATCATGTTTTTTAGTGGTGTTTGTGGAAAAA
13426 GCGTCGTTAA
Statistics
Matches: 61, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
42 38 0.62
43 22 0.36
44 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.39
Consensus pattern (42 bp):
TTAAAGATCATGTTTTTTAGTGGTGTTTGTGGAAAAATGCCA
Found at i:13479 original size:85 final size:84
Alignment explanation
Indices: 13234--13487 Score: 233
Period size: 85 Copynumber: 3.0 Consensus size: 84
13224 TCTATTAATA
* * * * ** *
13234 TTAGCGATGTTTGTAGGAAAAGCGTTGTTAAAGATTTTTTTTTTTAACGGCGTTTGTAGGAAAAG
1 TTAGCGGTGTTTGT-GGAAAAGCGTTGTTAAAGATTATATTATTTAGTGGCGTTTAT-GGAAAAG
*
13299 CACCGTTAAAGA-CTATGTTTT
64 TACCGTTAAAGATC-ATGTTTT
* * * * * * * *
13320 TTAGTGGTGTTTGTGGGAAAAGTGTTGTCAAAGATCATGA-TCTTTAGTAGAGTTTATGGAAAAA
1 TTAGCGGTGTTTGT-GGAAAAGCGTTGTTAAAGATTAT-ATTATTTAGTGGCGTTTATGGAAAAG
* *
13384 TGCCATTAAAGATCATGTTTT
64 TACCGTTAAAGATCATGTTTT
* *
13405 TTAGCGGTGTTTGTGGAAAAAGCGTCGTTAAATATTATATTATTTAGTGGCGTTTATGGAAAAGT
1 TTAGCGGTGTTTGTGG-AAAAGCGTTGTTAAAGATTATATTATTTAGTGGCGTTTATGGAAAAGT
** *
13470 TTCGCTAAAGATCATGTT
65 ACCGTTAAAGATCATGTT
13488 CTATAGCAAT
Statistics
Matches: 132, Mismatches: 32, Indels: 9
0.76 0.18 0.05
Matches are distributed among these distances:
84 3 0.02
85 86 0.65
86 43 0.33
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (84 bp):
TTAGCGGTGTTTGTGGAAAAGCGTTGTTAAAGATTATATTATTTAGTGGCGTTTATGGAAAAGTA
CCGTTAAAGATCATGTTTT
Found at i:16361 original size:2 final size:2
Alignment explanation
Indices: 16354--16380 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16344 ACATTTTAGA
16354 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
16381 ATTTTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23721 original size:21 final size:23
Alignment explanation
Indices: 23697--23747 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
23687 GAAAAAAAAA
23697 ATTTAAATCTA-AAATAT-TTAT
1 ATTTAAATCTATAAATATATTAT
* *
23718 ATTTATATCTATATATATATTAT
1 ATTTAAATCTATAAATATATTAT
*
23741 AGTTAAA
1 ATTTAAA
23748 CATTTTCTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 9 0.38
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTAAATCTATAAATATATTAT
Found at i:34461 original size:16 final size:17
Alignment explanation
Indices: 34420--34464 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
34410 TTTTTTGTTT
34420 GTTTTATATTGTTTAATAA
1 GTTTT-TATT-TTTAATAA
*
34439 GTATTTATTTTTAA-AA
1 GTTTTTATTTTTAATAA
34455 GTTTTTATTT
1 GTTTTTATTT
34465 GCTCATGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.46
17 5 0.21
18 4 0.17
19 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
GTTTTTATTTTTAATAA
Found at i:46569 original size:23 final size:22
Alignment explanation
Indices: 46539--46665 Score: 110
Period size: 23 Copynumber: 5.5 Consensus size: 22
46529 ACACTACCGC
46539 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCACGTCT-GT
**
46562 GCTCTCTGTTATTAGCACTGTGAGT
1 GCTCTCTG-T-TTAGCAC-GTCTGT
* *
46587 GCTCTCTGATTAGCACTTCATGT
1 GCTCTCTGTTTAGCACGTC-TGT
* * *
46610 GTTCTCTGATTAGCACTTCGTGT
1 GCTCTCTGTTTAGCACGTC-TGT
*
46633 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCAC-GTCTGT
*
46656 GCTATCTGTT
1 GCTCTCTGTT
46666 GCCCAGCACT
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.01
23 64 0.74
24 2 0.02
25 17 0.20
26 2 0.02
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.42
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACGTCTGT
Found at i:46639 original size:46 final size:47
Alignment explanation
Indices: 46539--46649 Score: 138
Period size: 46 Copynumber: 2.4 Consensus size: 47
46529 ACACTACCGC
*
46539 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGAGT
1 GCTCTCTGTTTAGCACTTCTCGTGCTCTCTG-TATTAGCACTGTGAGT
* * *
46587 GCTCTCTGATTAGCACTTCAT-GTGTTCTCTG-ATTAGCACT-TCGTGT
1 GCTCTCTGTTTAGCACTTC-TCGTGCTCTCTGTATTAGCACTGT-GAGT
46633 GCTCTCTGTTTAGCACT
1 GCTCTCTGTTTAGCACT
46650 GTGTGTGCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
45 1 0.02
46 28 0.50
48 26 0.46
49 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.41
Consensus pattern (47 bp):
GCTCTCTGTTTAGCACTTCTCGTGCTCTCTGTATTAGCACTGTGAGT
Found at i:46681 original size:71 final size:68
Alignment explanation
Indices: 46539--46712 Score: 176
Period size: 71 Copynumber: 2.5 Consensus size: 68
46529 ACACTACCGC
* *
46539 GCTCTCTGTTTAGCACGTC-TCGTGCTCTCTGTTATTAGCACTGTGAGTGCTCTCTGATTAGCAC
1 GCTCTCTG-TTAGCACTTCGT-GTGCTCTCTG-T-TTAGCACTGTGAGTGCTATCTGATTAGCAC
46603 TTCATGT
62 TTCATGT
* *
46610 GTTCTCTGATTAGCACTTCGTGTGCTCTCTGTTTAGCACTGTGTGTGCTATCTG-TTGCCCAGCA
1 GCTCTCTG-TTAGCACTTCGTGTGCTCTCTGTTTAGCACTGTGAGTGCTATCTGATT----AGCA
46674 CTT-ATGT
61 CTTCATGT
* * *
46681 GCTCTCTGTTAGTACTTTG-GTACTCTCTGTTT
1 GCTCTCTGTTAGCACTTCGTGTGCTCTCTGTTT
46713 GTCCCACGGT
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
68 2 0.02
69 32 0.36
70 10 0.11
71 37 0.42
72 8 0.09
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (68 bp):
GCTCTCTGTTAGCACTTCGTGTGCTCTCTGTTTAGCACTGTGAGTGCTATCTGATTAGCACTTCA
TGT
Done.