Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000157.1 Kokia drynarioides strain JFW-HI SEQ_110819, 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: 70618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2792 original size:43 final size:43
Alignment explanation
Indices: 2646--2946 Score: 219
Period size: 43 Copynumber: 7.0 Consensus size: 43
2636 TTTATTAATG
* * * *
2646 TTAGCGGCGTTTGTGAGAAAAGCGTCGTTAAAGA-CTAAGTTCT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGTTAAAGATC-ATGTTCT
** * * ** ** * * *
2689 TTAACGGTGTTTATATGAAAAATGCTGTTAAAAATCAAGTTCT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGTTAAAGATCATGTTCT
** * * *
2732 TTAACGGCATTTGTGGGAAAAGCGTCATTAAAGATCATGTTCT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGTTAAAGATCATGTTCT
* ** ** *
2775 TTAGTGGGGTTAATGGGAAAAGCATCGTTAAAGATCATGTTTT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGTTAAAGATCATGTTCT
* * *
2818 TTAGTGGCATTTTTTGGG-AAAGCGCTGTTAAAGATCATGTTCT
1 TTAGTGGC-GTTTGTGGGAAAAGCGCCGTTAAAGATCATGTTCT
* * ** ** * *
2861 TTAGCGGCGTTTGTGGGGAAAGTACCACTAAAGATAATGTTTT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGTTAAAGATCATGTTCT
* *
2904 TTAGTGGCGTTTGTGTGAAAAGCGCCGTTAAAGACCATGTTCT
1 TTAGTGGCGTTTGTGGGAAAAGCGCCGTTAAAGATCATGTTCT
2947 ATAGCGGTAT
Statistics
Matches: 196, Mismatches: 59, Indels: 6
0.75 0.23 0.02
Matches are distributed among these distances:
42 7 0.04
43 182 0.93
44 7 0.04
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (43 bp):
TTAGTGGCGTTTGTGGGAAAAGCGCCGTTAAAGATCATGTTCT
Found at i:2959 original size:129 final size:128
Alignment explanation
Indices: 2646--2961 Score: 326
Period size: 129 Copynumber: 2.5 Consensus size: 128
2636 TTTATTAATG
* * * * * *
2646 TTAGCGGCGTTTGTGAGAAAAGCGTCGTTAAAGACTAAGTTCTTTAACGGTGTTTATATGAAAAA
1 TTAGTGGCGTTTGTGAGAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGGTATTT-TTTGAAAAA
* ** * *
2711 TGCTGTTAAAAATCAAGTTCTTTAACGGCATTTGTGGGAAAAGCGTCATTAAAGATCATGTTCT
65 CGCTGTTAAAAATCAAGTTCTTTAACGGCATTTGTGGGAAAAGCACCACTAAAGATAATGTTCT
* ** * * * * * * * *
2775 TTAGTGGGGTTAATGGGAAAAGCATCGTTAAAGATCATGTTTTTTAGTGGCATTTTTTGGGAAAG
1 TTAGTGGCGTTTGTGAGAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGGTATTTTTT-GAAAAA
* * * * * * *
2840 CGCTGTTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGGAAAGTACCACTAAAGATAATGTTTT
65 CGCTGTTAAAAATCAAGTTCTTTAACGGCATTTGTGGGAAAAGCACCACTAAAGATAATGTTCT
* * *
2904 TTAGTGGCGTTTGTGTGAAAAGCGCCGTTAAAGACCATGTTCTATAGCGGTATTTTTT
1 TTAGTGGCGTTTGTGAGAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGGTATTTTTT
2962 TTAATAAATG
Statistics
Matches: 146, Mismatches: 40, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
128 2 0.01
129 144 0.99
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (128 bp):
TTAGTGGCGTTTGTGAGAAAAGCGTCGTTAAAGACCATGTTCTTTAGCGGTATTTTTTGAAAAAC
GCTGTTAAAAATCAAGTTCTTTAACGGCATTTGTGGGAAAAGCACCACTAAAGATAATGTTCT
Found at i:16110 original size:11 final size:11
Alignment explanation
Indices: 16087--16123 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16077 AGCATTATAA
16087 TTTTT-TTTCTC
1 TTTTTCTTT-TC
16098 TTTTTCTTTTC
1 TTTTTCTTTTC
16109 TTTTTC-TTTC
1 TTTTTCTTTTC
16119 TTTTT
1 TTTTT
16124 ATGTGACAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.36
11 13 0.52
12 3 0.12
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:29478 original size:37 final size:37
Alignment explanation
Indices: 29421--29500 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
29411 TAATGGCGAT
* * *
29421 GCATGAGCACTTCTAGATTGCGCCCAAAACTGTCGCC
1 GCATGAGCACTTCCAAATTGCACCCAAAACTGTCGCC
*
29458 GCATGAGCACTTCCAAATTGCACCCAAAAGTGTCGCC
1 GCATGAGCACTTCCAAATTGCACCCAAAACTGTCGCC
*
29495 GTATGA
1 GCATGA
29501 ATATTTTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (37 bp):
GCATGAGCACTTCCAAATTGCACCCAAAACTGTCGCC
Found at i:29574 original size:38 final size:37
Alignment explanation
Indices: 29531--29610 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
29521 AGACTGTTGT
*
29531 TGCATAAATATTCTTCAAATTGCATCC-AGAACTATCAC
1 TGCATAAATATTCTTC-AATTGCACCCAAGAA-TATCAC
* * *
29569 TGCATAAGTATTTTTCAATTGCACCCAAGAATGTCAC
1 TGCATAAATATTCTTCAATTGCACCCAAGAATATCAC
29606 TGCAT
1 TGCAT
29611 GAAAATATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 19 0.51
38 18 0.49
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.33
Consensus pattern (37 bp):
TGCATAAATATTCTTCAATTGCACCCAAGAATATCAC
Found at i:29606 original size:37 final size:38
Alignment explanation
Indices: 29513--29610 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
29503 ATTTTTGGAA
* ***
29513 TGCACCCAAGACTGTTGTTGCATAAATATTCTTCAAAT
1 TGCACCCAAGAATGTCACTGCATAAATATTCTTCAAAT
* * * *
29551 TGCATCC-AGAACTATCACTGCATAAGTATTTTTC-AAT
1 TGCACCCAAGAA-TGTCACTGCATAAATATTCTTCAAAT
29588 TGCACCCAAGAATGTCACTGCAT
1 TGCACCCAAGAATGTCACTGCAT
29611 GAAAATATAC
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
37 22 0.46
38 26 0.54
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (38 bp):
TGCACCCAAGAATGTCACTGCATAAATATTCTTCAAAT
Found at i:32614 original size:44 final size:44
Alignment explanation
Indices: 32564--32676 Score: 217
Period size: 44 Copynumber: 2.6 Consensus size: 44
32554 GTTATGGTGC
32564 CATAGTATCTTTCAACTATGGTCTTTTACACTTTTGGTTTGATG
1 CATAGTATCTTTCAACTATGGTCTTTTACACTTTTGGTTTGATG
*
32608 CGTAGTATCTTTCAACTATGGTCTTTTACACTTTTGGTTTGATG
1 CATAGTATCTTTCAACTATGGTCTTTTACACTTTTGGTTTGATG
32652 CATAGTATCTTTCAACTATGGTCTT
1 CATAGTATCTTTCAACTATGGTCTT
32677 ATATATTTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (44 bp):
CATAGTATCTTTCAACTATGGTCTTTTACACTTTTGGTTTGATG
Found at i:35812 original size:17 final size:17
Alignment explanation
Indices: 35792--35824 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35782 TTTGGGTGTT
*
35792 GGGTCACTTTGGCCCTC
1 GGGTCACTTTGACCCTC
35809 GGGTCACTTTGACCCT
1 GGGTCACTTTGACCCT
35825 TAATGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.33, G:0.27, T:0.30
Consensus pattern (17 bp):
GGGTCACTTTGACCCTC
Found at i:36313 original size:11 final size:11
Alignment explanation
Indices: 36297--36321 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
36287 TAATATCATA
36297 ATTTAATAATT
1 ATTTAATAATT
36308 ATTTAATAATT
1 ATTTAATAATT
36319 ATT
1 ATT
36322 ATTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:36346 original size:9 final size:9
Alignment explanation
Indices: 36332--36360 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
36322 ATTTCAAAAA
36332 AATAATTTT
1 AATAATTTT
36341 AATAATTTT
1 AATAATTTT
36350 AATAATTTT
1 AATAATTTT
36359 AA
1 AA
36361 AATCATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AATAATTTT
Found at i:38150 original size:29 final size:31
Alignment explanation
Indices: 38097--38156 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
38087 GTATCCATTG
*
38097 GATGATAAATCATCATTTTATTAAATTTGAAA
1 GATGATAAATCATCA-TCTATTAAATTTGAAA
38129 GATGATAAATCATCA-CT-TTAAATTTGAA
1 GATGATAAATCATCATCTATTAAATTTGAA
38157 TAGTGCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.41
30 1 0.04
32 15 0.56
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (31 bp):
GATGATAAATCATCATCTATTAAATTTGAAA
Found at i:42930 original size:16 final size:16
Alignment explanation
Indices: 42909--42942 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
42899 TCTATAAATT
42909 TCCAACAAAAATAGGA
1 TCCAACAAAAATAGGA
42925 TCCAACAAAAATAGGA
1 TCCAACAAAAATAGGA
42941 TC
1 TC
42943 AAGGTTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.21, G:0.12, T:0.15
Consensus pattern (16 bp):
TCCAACAAAAATAGGA
Found at i:53328 original size:18 final size:17
Alignment explanation
Indices: 53303--53336 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
53293 TATTCCTTTT
53303 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
53320 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
53337 TTCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:64060 original size:26 final size:26
Alignment explanation
Indices: 64024--64081 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
64014 AATTGCACCT
*
64024 AGAAATATCGCTGCATGAACATGTCC
1 AGAATTATCGCTGCATGAACATGTCC
*
64050 AGAATTATCGCTGCATGAACGTGTCC
1 AGAATTATCGCTGCATGAACATGTCC
*
64076 AAAATT
1 AGAATT
64082 GCGCCCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (26 bp):
AGAATTATCGCTGCATGAACATGTCC
Found at i:67807 original size:5 final size:5
Alignment explanation
Indices: 67785--67828 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
67775 TCAATCACAT
67785 AAAA- AAAAG AAGAAG AAAAG AAAAG AAAAG AAAAG AAAAAG AAA
1 AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAA
67829 TATATTTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.11
5 23 0.62
6 10 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:67815 original size:15 final size:15
Alignment explanation
Indices: 67785--67828 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
67775 TCAATCACAT
67785 AAAA-AAAAGAAGAAG
1 AAAAGAAAAGAA-AAG
67800 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
67815 AAAAGAAAAAGAAA
1 AAAAG-AAAAGAAA
67829 TATATTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:68331 original size:37 final size:37
Alignment explanation
Indices: 68261--68338 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
68251 TTACTACTAA
* * * *
68261 TGTCGTTGCATGAGCACTTCTAGATTGAGCCCAAAAT
1 TGTCGCTGCATGAGCACTTCCAAATTGAGCCCAAAAC
68298 TGTCGCTGCATGAGCACTTCCAAATTGCA-CCCAAAAC
1 TGTCGCTGCATGAGCACTTCCAAATTG-AGCCCAAAAC
68335 TGTC
1 TGTC
68339 ATCGCAGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (37 bp):
TGTCGCTGCATGAGCACTTCCAAATTGAGCCCAAAAC
Found at i:68453 original size:37 final size:38
Alignment explanation
Indices: 68377--68457 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 38
68367 AAGACAATCA
* *
68377 CTGCATAAATATTCTACAAATTGCATCCATAACTATCG
1 CTGCATAAATATTCTACAAATTGCACCCAGAACTATCG
* * *
68415 CTGCATAAGTATTCTTC-AATTGCACCCAGGAA-TGTCG
1 CTGCATAAATATTCTACAAATTGCACCCA-GAACTATCG
68452 CTGCAT
1 CTGCAT
68458 GAACGGGTCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 20 0.54
38 17 0.46
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (38 bp):
CTGCATAAATATTCTACAAATTGCACCCAGAACTATCG
Found at i:69281 original size:35 final size:35
Alignment explanation
Indices: 69166--69340 Score: 143
Period size: 35 Copynumber: 5.1 Consensus size: 35
69156 ATCTACCGTT
*
69166 CAAGAATTTCAATTCATTCATATATTATAAACAAT-
1 CAAGAATTT-AATTCATTCATATATCATAAACAATA
* * **
69201 CAATAACTTAATTCATTCATATATCGCAAACAATCA
1 CAAGAATTTAATTCATTCATATATCATAAACAAT-A
* * *
69237 CAA-ATTTTAATTCTTTCATATATCATAATCAATA
1 CAAGAATTTAATTCATTCATATATCATAAACAATA
* *
69271 AAAGAATTTAATCCATTCATATAT--TAATAGCAA-A
1 CAAGAATTTAATTCATTCATATATCATAA-A-CAATA
*
69305 -AAGATTTTCAATTCATTCATATAT--TAAACAAT-
1 CAAGAATTT-AATTCATTCATATATCATAAACAATA
69337 CAAG
1 CAAG
69341 GAAGTAAAAC
Statistics
Matches: 114, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
32 3 0.03
33 14 0.12
34 43 0.38
35 51 0.45
36 3 0.03
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36
Consensus pattern (35 bp):
CAAGAATTTAATTCATTCATATATCATAAACAATA
Found at i:69324 original size:69 final size:69
Alignment explanation
Indices: 69166--69336 Score: 167
Period size: 69 Copynumber: 2.5 Consensus size: 69
69156 ATCTACCGTT
* * * * *
69166 CAAGAATTTCAATTCATTCATATATTATAAACAATCAATAACTTAATTCATTCATATATCGCAAA
1 CAAGATTTTCAATTCATTCATATATCATAAACAATAAAGAACTTAATCCATTCATATATC-CAAA
69231 CAATCA
65 CAA-CA
* * * *
69237 CAA-ATTTT-AATTCTTTCATATATCATAATCAATAAAAGAATTTAATCCATTCATATAT-TAAT
1 CAAGATTTTCAATTCATTCATATATCATAAACAAT-AAAGAACTTAATCCATTCATATATCCAA-
69299 AGCAA-A
64 A-CAACA
69305 -AAGATTTTCAATTCATTCATATAT--TAAACAAT
1 CAAGATTTTCAATTCATTCATATATCATAAACAAT
69337 CAAGGAAGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
67 9 0.11
68 8 0.10
69 37 0.44
70 27 0.32
71 3 0.04
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (69 bp):
CAAGATTTTCAATTCATTCATATATCATAAACAATAAAGAACTTAATCCATTCATATATCCAAAC
AACA
Found at i:70565 original size:126 final size:127
Alignment explanation
Indices: 70340--70588 Score: 329
Period size: 126 Copynumber: 2.0 Consensus size: 127
70330 TACATACAGG
* * *
70340 TGCAAACGAGCTACCATATGGTTGAGGATCCACAACCCCTAGCAGATAAAAGCTGTCAGAAAAAG
1 TGCAAACAAGCTACCATATGGTTCAGGATCCACAACCCCTAGCAGATAAAAGCTATCAGAAAAAG
* * ** *
70405 TTGTGAATACTCCGTATAAAAGTCGCTGTTGGAATCTAC-TAAGTTATGAATACACAAAGGA
66 TCGTGAATACTACGTATAAAAGTCGCAATTGGAATCTACTTAAGCTATGAATACACAAAGGA
* * * * * * *
70466 TGCAAACAAGCTACCGTATGGTTCAGGATCCACAACTCCTCGCATATAAAATCTATTAGAGAAAG
1 TGCAAACAAGCTACCATATGGTTCAGGATCCACAACCCCTAGCAGATAAAAGCTATCAGAAAAAG
* * *
70531 TCGTGAATACTATGTATAAAGGTTGCAATTGGAATCTACTTAAGCTATGAATACACAA
66 TCGTGAATACTACGTATAAAAGTCGCAATTGGAATCTACTTAAGCTATGAATACACAA
70589 CGGTAAAACA
Statistics
Matches: 104, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
126 87 0.84
127 17 0.16
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (127 bp):
TGCAAACAAGCTACCATATGGTTCAGGATCCACAACCCCTAGCAGATAAAAGCTATCAGAAAAAG
TCGTGAATACTACGTATAAAAGTCGCAATTGGAATCTACTTAAGCTATGAATACACAAAGGA
Done.