Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013411.1 Kokia drynarioides strain JFW-HI SEQ_128436, 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: 3475
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Found at i:870 original size:49 final size:49
Alignment explanation
Indices: 795--1263 Score: 313
Period size: 49 Copynumber: 9.6 Consensus size: 49
785 CATGAAGATT
* *
795 TGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACA
1 TGAAGGGAAAGATCTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACA
* * *
844 TGAAGGGAAAGATCTAAGTCGGAATGGCGGATCC-AATA--TCACGATGACA
1 TGAAGGGAAAGATCTAAGTCGCAATGGC-GAACCTAGTACCTCA-GA-GACA
* * * *
893 T-AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAAATACA
1 TGAAGGGAAAGATCTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACA
* * * *
941 TGAAGGGAAAGATCTAAGCCGCAACGGCGGATCC-AATACCTC-GAAGACA
1 TGAAGGGAAAGATCTAAGTCGCAATGGC-GAACCTAGTACCTCAG-AGACA
* *
990 TGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGA-AGCA
1 TGAAGGGAAAGATCTAAGTCGCAATGGCGAACCTAGTACCTCAGAGA-CA
* * *** * *
1039 TAAAAGGGAAAGATCTAAGCCGCAAAAACGGATCC-AGTACCAC-GAAGACA
1 T-GAAGGGAAAGATCTAAGTCGCAATGGC-GAACCTAGTACCTCAG-AGACA
* * * * * * * *
1089 CG-AGGGAAAGATCTAAGCCGTAACGGTGGATCC-AATACCAC-GAAGACA
1 TGAAGGGAAAGATCTAAGTCGCAATGG-CGAACCTAGTACCTCAG-AGACA
* * * * * *
1137 -CAAGGGAAGGATCTAAGCCGCAACGGC-AGATCTAGTACCATGA-AGACA
1 TGAAGGGAAAGATCTAAGTCGCAATGGCGA-ACCTAGTACC-TCAGAGACA
* * * * *
1185 -CAGAGGGAAAGGTTTAAGTCGCAATGACGAACCTAGTACTTCAGAGACA
1 TGA-AGGGAAAGATCTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACA
* *
1234 TGAAGGGAAAGGTTTAAGTCGCAATGGCGA
1 TGAAGGGAAAGATCTAAGTCGCAATGGCGA
1264 GCCCGGTACC
Statistics
Matches: 331, Mismatches: 63, Indels: 52
0.74 0.14 0.12
Matches are distributed among these distances:
46 1 0.00
47 8 0.02
48 112 0.34
49 161 0.49
50 44 0.13
51 5 0.02
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (49 bp):
TGAAGGGAAAGATCTAAGTCGCAATGGCGAACCTAGTACCTCAGAGACA
Found at i:1078 original size:50 final size:49
Alignment explanation
Indices: 846--1175 Score: 190
Period size: 48 Copynumber: 6.8 Consensus size: 49
836 CAGAGACATG
* * * * * * *
846 AAGGGAAAGATCTAAGTCGGAATGGCGGATCCAATATCACGATGACAT--
1 AAGGGAAAGATCTAAGCCGCAAAGGCGGATCCAGTACCTCGAAG-CATAA
* * * * * * * *
894 AAGGGAAAGGTTTAAGTCGCAATGGC-GAACCTAGTACCTCAAATACAT-G
1 AAGGGAAAGATCTAAGCCGCAAAGGCGGATCC-AGTACCTCGAA-GCATAA
* * *
943 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAATACCTCGAAGACAT-G
1 AAGGGAAAGATCTAAGCCGCAAAGGCGGATCCAGTACCTCGAAG-CATAA
* * * * *
992 AAGGGAAAGGTTTAAGTCGCAATGGC-GAACCTAGTACCTCAGAAGCATAA
1 AAGGGAAAGATCTAAGCCGCAAAGGCGGATCC-AGTACCTC-GAAGCATAA
** * * *
1042 AAGGGAAAGATCTAAGCCGCAAAAACGGATCCAGTACCACGAAG-ACAC
1 AAGGGAAAGATCTAAGCCGCAAAGGCGGATCCAGTACCTCGAAGCATAA
* * * * * * * *
1090 GAGGGAAAGATCTAAGCCGTAACGGTGGATCCAATACCACGAAG-ACAC
1 AAGGGAAAGATCTAAGCCGCAAAGGCGGATCCAGTACCTCGAAGCATAA
* * * *
1138 AAGGGAAGGATCTAAGCCGCAACGGCAGATCTAGTACC
1 AAGGGAAAGATCTAAGCCGCAAAGGCGGATCCAGTACC
1176 ATGAAGACAC
Statistics
Matches: 224, Mismatches: 49, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
47 4 0.02
48 110 0.49
49 71 0.32
50 35 0.16
51 4 0.02
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (49 bp):
AAGGGAAAGATCTAAGCCGCAAAGGCGGATCCAGTACCTCGAAGCATAA
Found at i:1144 original size:195 final size:196
Alignment explanation
Indices: 785--1244 Score: 538
Period size: 195 Copynumber: 2.4 Consensus size: 196
775 TGAGAAAAAA
** *
785 CATGAAGATTTGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAG-AGACATGAAG
1 CATGAAGACATGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAGACATAAAG
* * *** * * * * * *
849 GGAAAGATCTAAGTCGGAATGGCGGATCCAATATCACGATGACATAAGGGAAAGGTTTAAGTCGC
66 GGAAAGATCTAAGCCGCAAAAACGGATCCAATACCACGAAGACACAAGGGAAAGATCTAAGCCGC
* * * * * *
914 AATGGCGAACCTAGTACCTCAAATACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAATA
131 AACGGCGAACCTAATACCACAAAGACATCAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAATA
979 C
196 C
980 C-TCGAAGACATGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAG-CATAAA
1 CAT-GAAGACATGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAGACAT-AA
* *
1043 AGGGAAAGATCTAAGCCGCAAAAACGGATCCAGTACCACGAAGACACGAGGGAAAGATCTAAGCC
64 AGGGAAAGATCTAAGCCGCAAAAACGGATCCAATACCACGAAGACACAAGGGAAAGATCTAAGCC
* * * * * *
1108 GTAACGGTGGATCC-AATACCACGAAGACA-CAAGGGAAGGATCTAAGCCGCAACGGCAGATCTA
129 GCAACGG-CGAACCTAATACCACAAAGACATCAAGGGAAAGATCTAAGCCGCAACGGCAGATCCA
*
1171 GTAC
193 ATAC
* * * *
1175 CATGAAGACA-CAGAGGGAAAGGTTTAAGTCGCAATGACGAACCTAGTACTTCAG-AGACATGAA
1 CATGAAGACATGA-AGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAGACATAAA
1238 GGGAAAG
65 GGGAAAG
1245 GTTTAAGTCG
Statistics
Matches: 225, Mismatches: 33, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
194 13 0.06
195 136 0.60
196 72 0.32
197 4 0.02
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.16
Consensus pattern (196 bp):
CATGAAGACATGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAGAAGACATAAAG
GGAAAGATCTAAGCCGCAAAAACGGATCCAATACCACGAAGACACAAGGGAAAGATCTAAGCCGC
AACGGCGAACCTAATACCACAAAGACATCAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAATA
C
Found at i:1295 original size:49 final size:49
Alignment explanation
Indices: 1191--1295 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
1181 GACACAGAGG
* * *
1191 GAAAGGTTTAAGTCGCAATGACGAACCTAGTACTTCAGAGACATGAAGG
1 GAAAGGTTTAAGTCGCAATGACGAACCCAGTACTTCAGAAACATGAAGA
* * * *
1240 GAAAGGTTTAAGTCGCAATGGCGAGCCCGGTACCTT-AGAAACATGACGA
1 GAAAGGTTTAAGTCGCAATGACGAACCCAGTA-CTTCAGAAACATGAAGA
*
1289 GTAAGGT
1 GAAAGGT
1296 CGAATCCACA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 44 0.94
50 3 0.06
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (49 bp):
GAAAGGTTTAAGTCGCAATGACGAACCCAGTACTTCAGAAACATGAAGA
Found at i:1585 original size:39 final size:39
Alignment explanation
Indices: 1537--1758 Score: 152
Period size: 39 Copynumber: 5.7 Consensus size: 39
1527 CAACCGTTTG
* *
1537 ATCTTTTACCCCGAGCTTGGGGCAAATCATCGTCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCGTCAACCA
* * *
1576 ATCTCTTACCCTGAACCTGGGGCAGAT--T-G-CAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCGTCAACCA
* * ** *
1611 TTTGTTCTTTCACCTTGAGCTTGGGGCAGATCATCGTTAACCA
1 -AT-CTC-TT-ACCCCGAGCTTGGGGCAGATCATCGTCAACCA
* * * *
1654 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAAC--CATCCG
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CATCGTCAACCA
* * * *
1693 A-CTTTTTACCCCGAGCTTGGGGTAGATCACCATCAACCA
1 ATC-TCTTACCCCGAGCTTGGGGCAGATCATCGTCAACCA
* *
1732 ATCTCCTACCTCGAGCTTGGGGCAGAT
1 ATCTCTTACCCCGAGCTTGGGGCAGAT
1759 TGTAGTTATC
Statistics
Matches: 139, Mismatches: 30, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
35 6 0.04
36 2 0.01
37 6 0.04
38 4 0.03
39 104 0.75
40 4 0.03
41 6 0.04
42 2 0.01
43 5 0.04
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCATCGTCAACCA
Found at i:1620 original size:78 final size:77
Alignment explanation
Indices: 1486--1760 Score: 334
Period size: 78 Copynumber: 3.5 Consensus size: 77
1476 AATGGAGTTA
* * * * *
1486 CATCGTCAACCAATTTTTTACCCCGAGCCTAGGGCAAATTGCAACCGTTTGATCTTTTACCCCGA
1 CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTTG-TCTTTTACCCCGA
*
1551 GCTTGGGGCAAAT
65 GCTTGGGGCAGAT
* * * **
1564 CATCGTCAACCAATCTCTTACCCTGAACCTGGGGCAGATTGCAACCATTTGTTCTTTCACCTTGA
1 CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTTG-TCTTTTACCCCGA
1629 GCTTGGGGCAGAT
65 GCTTGGGGCAGAT
* ** *
1642 CATCGTTAACCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATCCGACTTTTTACCCCGA
1 CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTTGTC-TTTTACCCCGA
*
1707 GCTTGGGGTAGAT
65 GCTTGGGGCAGAT
* * * * *
1720 CACCATCAACCAATCTCCTACCTCGAGCTTGGGGCAGATTG
1 CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTG
1761 TAGTTATCCA
Statistics
Matches: 168, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
77 1 0.01
78 167 0.99
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (77 bp):
CATCGTCAACCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTTGTCTTTTACCCCGAG
CTTGGGGCAGAT
Found at i:3236 original size:28 final size:29
Alignment explanation
Indices: 3128--3420 Score: 143
Period size: 29 Copynumber: 9.9 Consensus size: 29
3118 GAGGTCCCTA
* * * *
3128 AACTGTCCAAAAATTATATTTTGACCCTTG
1 AACTTTCC-AAAATTACATTTTTACCCTCG
* * * *
3158 ATCTTCTCCAAAATTATATTTTGACCCCCG
1 AACTT-TCCAAAATTACATTTTTACCCTCG
3188 AACTTTCCAAAATTACATTTTTACCCTCG
1 AACTTTCCAAAATTACATTTTTACCCTCG
* * * *
3217 AAC-TTCCCAAATTTCTTTTTTAACCTCG
1 AACTTTCCAAAATTACATTTTTACCCTCG
** * *
3245 ATTTTTCCAAAAAATACCA-TTTTACCCTCA
1 AACTTTCC-AAAATTA-CATTTTTACCCTCG
* *
3275 AAC-TTCAAAAAATTCCATTTTTGA-CCTC-
1 AACTTTC-CAAAATTACATTTTT-ACCCTCG
* * *
3303 AATTTTTCCAAAAATTACCA-TTTTACCCCCA
1 AA-CTTTCC-AAAATTA-CATTTTTACCCTCG
* **
3334 AAC-TTCCAAAAATTCCATTTTTGTCCTCG
1 AACTTTCC-AAAATTACATTTTTACCCTCG
* * * *
3363 ATTCTTCCCAAAATTACCA-TTTTACCCCCA
1 A-ACTTTCCAAAATTA-CATTTTTACCCTCG
* *
3393 AACTTCCCAAAATTCCATTTTTGACCCT
1 AACTTTCCAAAATTACATTTTT-ACCCT
3421 AATTTTTCCA
Statistics
Matches: 199, Mismatches: 45, Indels: 38
0.71 0.16 0.13
Matches are distributed among these distances:
28 30 0.15
29 80 0.40
30 76 0.38
31 13 0.07
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.37
Consensus pattern (29 bp):
AACTTTCCAAAATTACATTTTTACCCTCG
Found at i:3259 original size:59 final size:58
Alignment explanation
Indices: 3191--3474 Score: 351
Period size: 59 Copynumber: 4.9 Consensus size: 58
3181 ACCCCCGAAC
* * * * * * *
3191 TTTCC-AAAATTA-CATTTTTACCCTCGAACTTCCCAAATTTCTTTTTTAACCTCGATT
1 TTTCCAAAAATTACCA-TTTTACCCCCAAACTTCCAAAATTCCATTTTTGACCTCAATT
* * *
3248 TTTCCAAAAAATACCATTTTACCCTCAAACTTCAAAAAATTCCATTTTTGACCTCAATT
1 TTTCCAAAAATTACCATTTTACCCCCAAACTTC-CAAAATTCCATTTTTGACCTCAATT
* *
3307 TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGTCCTCGATT
1 TTTCCAAAAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTGACCTCAATT
* *
3366 CTTCCCAAAATTACCATTTTACCCCCAAACTTCCCAAAATTCCATTTTTGACC-CTAATT
1 TTTCCAAAAATTACCATTTTACCCCCAAACTT-CCAAAATTCCATTTTTGACCTC-AATT
*
3425 TTTCCAAAAA-TACCATTTTACCCCTAAACTTCCTAAAATTCCATTTTTGA
1 TTTCCAAAAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTGA
3475 A
Statistics
Matches: 200, Mismatches: 20, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
57 7 0.04
58 59 0.29
59 132 0.66
60 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.38
Consensus pattern (58 bp):
TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAATTCCATTTTTGACCTCAATT
Found at i:3431 original size:29 final size:31
Alignment explanation
Indices: 3282--3474 Score: 131
Period size: 29 Copynumber: 6.5 Consensus size: 31
3272 TCAAACTTCA
*
3282 AAAAATTCCATTTTTGACCTC-AATTTTTCC
1 AAAAATTCCATTTTTGACCCCTAATTTTTCC
* **
3312 AAAAATTACCA-TTTT-ACCCCCAA-ACTTCC
1 AAAAATT-CCATTTTTGACCCCTAATTTTTCC
* * * *
3341 AAAAATTCCATTTTTGTCCTC-GATTCTTCC
1 AAAAATTCCATTTTTGACCCCTAATTTTTCC
* * **
3371 CAAAATTACCA-TTTT-ACCCCCAA-ACTTCC
1 AAAAATT-CCATTTTTGACCCCTAATTTTTCC
*
3400 CAAAATTCCATTTTTGA-CCCTAATTTTTCC
1 AAAAATTCCATTTTTGACCCCTAATTTTTCC
* **
3430 AAAAATACCA-TTTT-ACCCCTAA-ACTTCC
1 AAAAATTCCATTTTTGACCCCTAATTTTTCC
*
3458 TAAAATTCCATTTTTGA
1 AAAAATTCCATTTTTGA
3475 A
Statistics
Matches: 129, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
28 19 0.15
29 58 0.45
30 46 0.36
31 6 0.05
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (31 bp):
AAAAATTCCATTTTTGACCCCTAATTTTTCC
Done.