Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009077.1 Kokia drynarioides strain JFW-HI SEQ_123777, 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: 4701
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Found at i:1113 original size:49 final size:48
Alignment explanation
Indices: 1006--1417 Score: 203
Period size: 49 Copynumber: 8.4 Consensus size: 48
996 TACCACGAAG
* * ** * * * *
1006 CATGAAGGGAAAGATTTAAGCCGCAGTGGTGAATCTAGTACCCCAAATA
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCAAACCTA-TACCTCAGAGA
* * * *
1055 TATGGAGGGAAAGGTTTAAGTCGTAATGGCAAACCTTATACCTCAGAGA
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCAAACC-TATACCTCAGAGA
* * * *
1104 CATGAAGGGAAAGATTTAAGTCGTAACGGTAAATCC-AGTACCAC-GAAGA
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCAAA-CCTA-TACCTCAG-AGA
* * * * * *
1153 TATGGAGGGAAAGCTTTAAGTCGCAATCGCGAACCTCGTACCTCAGA-A
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCAAACCT-ATACCTCAGAGA
* * * * * *
1201 GCGTGAAGGGAAATATTTAAGCCGCAACGGCGAATCC-AGTACCATGA-AGA
1 -CATGAAGGGAAAGATTTAAGTCGCAATGGC-AAACCTA-TACC-TCAGAGA
* * * * * *
1251 CATAAATGGTAAGGTTTAAGTCGCAATGACGAACCTAATACCTCAGAGA
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCAAACCT-ATACCTCAGAGA
** * *
1300 CATGAAGGGAAAGATTTAAG-CTGCAACAGCGAATCC-AGTACCAC-GAAGA
1 CATGAAGGGAAAGATTTAAGTC-GCAATGGC-AAACCTA-TACCTCAG-AGA
** * * *
1349 CACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTATACCTCAGA-A
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCAAACC-TATACCTCAGAGA
* *
1397 GCATGAAAGGAAAAATTTAAG
1 -CATGAAGGGAAAGATTTAAG
1418 CCGTAACGGG
Statistics
Matches: 263, Mismatches: 76, Indels: 48
0.68 0.20 0.12
Matches are distributed among these distances:
48 17 0.06
49 228 0.87
50 18 0.07
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.19
Consensus pattern (48 bp):
CATGAAGGGAAAGATTTAAGTCGCAATGGCAAACCTATACCTCAGAGA
Found at i:1175 original size:98 final size:98
Alignment explanation
Indices: 1002--1440 Score: 488
Period size: 98 Copynumber: 4.5 Consensus size: 98
992 TCAGTACCAC
** * * * * * * **
1002 GAAGCATGAAGGGAAAGATTTAAGCCGCAGTGGTGAATCTAGTACCCCAAATATATGGAGGGAAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAA
* * *
1067 GGTTTAAGTCGTAATGGCAAACCTTATACCTCA
66 GGTTTAAGTCGCAATGACGAACCTTATACCTCA
* * ** * **
1100 G-AGACATGAAGGGAAAGATTTAAGTCGTAACGGTAAATCCAGTACCACGAAGATATGGAGGGAA
1 GAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAA
* **
1164 AGCTTTAAGTCGCAATCG-CGAACCTCGTACCTCA
65 AGGTTTAAGTCGCAAT-GACGAACCTTATACCTCA
* * * * *
1198 GAAGCGTGAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTACCATGAAGACATAAATGGTAA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAA
*
1263 GGTTTAAGTCGCAATGACGAACCTAATACCTCA
66 GGTTTAAGTCGCAATGACGAACCTTATACCTCA
* * *
1296 G-AGACATGAAGGGAAAGATTTAAGCTGCAACAGCGAATCCAGTACCACGAAGACACAAAGGGAA
1 GAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAA
1360 AGGTTTAAGTCGCAATGACGAACCTTATACCTCA
65 AGGTTTAAGTCGCAATGACGAACCTTATACCTCA
* * * * **
1394 GAAGCATGAAAGGAAAAATTTAAGCCGTAACGGGGAATTTAGTACCA
1 GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
1441 TGCAGATTAA
Statistics
Matches: 289, Mismatches: 46, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
97 5 0.02
98 279 0.97
99 5 0.02
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (98 bp):
GAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACATAAAGGGAAA
GGTTTAAGTCGCAATGACGAACCTTATACCTCA
Found at i:1873 original size:6 final size:6
Alignment explanation
Indices: 1851--1925 Score: 52
Period size: 6 Copynumber: 13.0 Consensus size: 6
1841 GGCCTAACAT
* * *
1851 AATTTG AATTT- ATTTTA AATTTA AATTT- -ATTGGA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA
* *
1897 AATTT- -ATCATA AATTTA GATTTA AATTTA
1 AATTTA AAT-TTA AATTTA AATTTA AATTTA
1926 TTTAAATGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
4 5 0.09
5 5 0.09
6 39 0.72
7 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:1877 original size:17 final size:17
Alignment explanation
Indices: 1851--1896 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1841 GGCCTAACAT
* **
1851 AATTTGAATTTATTTTA
1 AATTTAAATTTATTGGA
1868 AATTTAAATTTATTGGA
1 AATTTAAATTTATTGGA
1885 AATTTAAATTTA
1 AATTTAAATTTA
1897 AATTTATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTGGA
Found at i:1890 original size:23 final size:23
Alignment explanation
Indices: 1864--1927 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1854 TTGAATTTAT
*
1864 TTTAAATTTAAATTTATTGGAAA
1 TTTAAATTTAAATTTATTAGAAA
* *
1887 TTTAAATTTAAATTTATCATAAA
1 TTTAAATTTAAATTTATTAGAAA
*
1910 TTTAGATTTAAATTTATT
1 TTTAAATTTAAATTTATT
1928 TAAATGATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
TTTAAATTTAAATTTATTAGAAA
Found at i:3797 original size:29 final size:30
Alignment explanation
Indices: 3752--4057 Score: 204
Period size: 29 Copynumber: 10.4 Consensus size: 30
3742 ACCCCAAATC
*
3752 TTTTCT-AAAATTCCA-TTTTAACCTCAAA
1 TTTTCTAAAAATTACATTTTTAACCTCAAA
* *
3780 CTTTCTAAAAATTACATTTTT-ACCCCTAAA
1 TTTTCTAAAAATTACATTTTTAACCTC-AAA
* *
3810 TTTTC-CAAAATCACATTTTTAAACC-CAAA
1 TTTTCTAAAAATTACATTTTT-AACCTCAAA
* * ** *
3839 TTTTCTAAAAAATACATTTTTATCCTTGAG
1 TTTTCTAAAAATTACATTTTTAACCTCAAA
* * *
3869 TTTTC-AAAAATTCCATTTTTGACCTTAAA
1 TTTTCTAAAAATTACATTTTTAACCTCAAA
* *
3898 TTTTCAAAAAATTACATTTTT-ACCCCTAAA
1 TTTTCTAAAAATTACATTTTTAACCTC-AAA
* * * * *
3928 CTTTCT-AATATTCCATTTTTTACC-CTGAA
1 TTTTCTAAAAATTACATTTTTAACCTC-AAA
* *
3957 TTTTCTAAAAATTACATTTTTACCCTTAAA
1 TTTTCTAAAAATTACATTTTTAACCTCAAA
* * * *
3987 -TATCTAAAAATTCCTTTTTTAAACTCAAA
1 TTTTCTAAAAATTACATTTTTAACCTCAAA
* * * *
4016 ATTTCTAAAATTTACCA-TTTTACCCTCAGA
1 TTTTCTAAAAATTA-CATTTTTAACCTCAAA
*
4046 TGTT-TAAAAATT
1 TTTTCTAAAAATT
4058 CTATTTTCAA
Statistics
Matches: 214, Mismatches: 50, Indels: 27
0.74 0.17 0.09
Matches are distributed among these distances:
28 5 0.02
29 113 0.53
30 92 0.43
31 4 0.02
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (30 bp):
TTTTCTAAAAATTACATTTTTAACCTCAAA
Found at i:3830 original size:59 final size:59
Alignment explanation
Indices: 3752--4040 Score: 293
Period size: 59 Copynumber: 4.9 Consensus size: 59
3742 ACCCCAAATC
* *
3752 TTTTCTAAAATTCCA-TTTTAACCTCAAACTTTCTAAAAATTACATTTTTACCCCTAAA
1 TTTTCAAAAATTCCATTTTTAACCTCAAATTTTCTAAAAATTACATTTTTACCCCTAAA
* * * * * *
3810 TTTTCCAAAA-TCACATTTTTAAACC-CAAATTTTCTAAAAAATACATTTTTATCCTTGAG
1 TTTTCAAAAATTC-CATTTTT-AACCTCAAATTTTCTAAAAATTACATTTTTACCCCTAAA
* * *
3869 TTTTCAAAAATTCCATTTTTGACCTTAAATTTTCAAAAAATTACATTTTTACCCCTAAA
1 TTTTCAAAAATTCCATTTTTAACCTCAAATTTTCTAAAAATTACATTTTTACCCCTAAA
* * * * * *
3928 CTTTCTAATATTCCATTTTTTACC-CTGAATTTTCTAAAAATTACATTTTTACCCTTAAA
1 TTTTCAAAAATTCCATTTTTAACCTC-AAATTTTCTAAAAATTACATTTTTACCCCTAAA
* * * * *
3987 -TATCTAAAAATTCCTTTTTTAAACTCAAAATTTCTAAAATTTACCA-TTTTACCC
1 TTTTC-AAAAATTCCATTTTTAACCTCAAATTTTCTAAAAATTA-CATTTTTACCC
4041 TCAGATGTTT
Statistics
Matches: 189, Mismatches: 33, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
57 2 0.01
58 17 0.09
59 161 0.85
60 9 0.05
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.43
Consensus pattern (59 bp):
TTTTCAAAAATTCCATTTTTAACCTCAAATTTTCTAAAAATTACATTTTTACCCCTAAA
Found at i:3996 original size:118 final size:118
Alignment explanation
Indices: 3758--4040 Score: 324
Period size: 118 Copynumber: 2.4 Consensus size: 118
3748 AATCTTTTCT
* *
3758 AAAATTCCA-TTTTAACCTCAAACTTTCTAAAAATTACATTTTTACCCCTAAATTTTCCAAAATC
1 AAAATTCCATTTTTAACCTCAAACTTTCAAAAAATTACATTTTTACCCCTAAACTTTCCAAAATC
* * * *
3822 ACATTTTTAAACCCAAATTTTCTAAAAAATACATTTTTATCCTTGAGTTTTCA
66 ACATTTTTAAACCCAAATTTTCTAAAAAATACATTTTTACCCTTAAATTCTCA
* * * * *
3875 AAAATTCCATTTTTGACCTTAAATTTTCAAAAAATTACATTTTTACCCCTAAACTTTCTAATATT
1 AAAATTCCATTTTTAACCTCAAACTTTCAAAAAATTACATTTTTACCCCTAAACTTTCCAA-AAT
* * *
3940 C-CATTTTT-TACCCTGAATTTTCTAAAAATTACATTTTTACCCTTAAATATCT-A
65 CACATTTTTAAACCC-AAATTTTCTAAAAAATACATTTTTACCCTTAAAT-TCTCA
* * * * *
3993 AAAATTCCTTTTTTAAACTCAAAATTTCTAAAATTTACCA-TTTTACCC
1 AAAATTCCATTTTTAACCTCAAACTTTCAAAAAATTA-CATTTTTACCC
4041 TCAGATGTTT
Statistics
Matches: 140, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
117 13 0.09
118 120 0.86
119 7 0.05
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.42
Consensus pattern (118 bp):
AAAATTCCATTTTTAACCTCAAACTTTCAAAAAATTACATTTTTACCCCTAAACTTTCCAAAATC
ACATTTTTAAACCCAAATTTTCTAAAAAATACATTTTTACCCTTAAATTCTCA
Done.