Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008705.1 Kokia drynarioides strain JFW-HI SEQ_123387, 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: 33840
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2125 original size:52 final size:52
Alignment explanation
Indices: 2042--2254 Score: 238
Period size: 51 Copynumber: 4.2 Consensus size: 52
2032 ATAGCCACCA
* *
2042 GACCTCATAATCCGT-AAGGATCCGTATACTCACGATGACACAGAGTCATCG
1 GACCTCTTAATCCGTAAAGGATCCATATACTCACGATGACACAGAGTCATCG
* * **
2093 GACCTCTTAATCTGTAAAGGATCCATACACTCACGATGACACTTA-TCATCG
1 GACCTCTTAATCCGTAAAGGATCCATATACTCACGATGACACAGAGTCATCG
* ** *
2144 GACCGT-TTAATCTGTAAAGGATTTATATACTCACGATGACATAGAGTCATCG
1 GACC-TCTTAATCCGTAAAGGATCCATATACTCACGATGACACAGAGTCATCG
* * ** *
2196 GA-CTGTTTAATCCGTAAAGGATTCATATACTCACGA-GACACTTAGTCATTG
1 GACCT-CTTAATCCGTAAAGGATCCATATACTCACGATGACACAGAGTCATCG
2247 GACCTCTT
1 GACCTCTT
2255 CGTTTATGGC
Statistics
Matches: 137, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
50 1 0.01
51 72 0.53
52 64 0.47
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (52 bp):
GACCTCTTAATCCGTAAAGGATCCATATACTCACGATGACACAGAGTCATCG
Found at i:8228 original size:23 final size:22
Alignment explanation
Indices: 8192--8235 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
8182 TAAATATTTC
*
8192 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
8215 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
8236 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:17164 original size:880 final size:880
Alignment explanation
Indices: 15461--17214 Score: 3287
Period size: 880 Copynumber: 2.0 Consensus size: 880
15451 ATAAATAATT
*
15461 AAAGGGAATTGTAAAGGAATGATCATGAGAAATATTATTTGAGTATCCTTTCTACTTTTCTCTCT
1 AAAGGGAATTGTAAAGGAATGATCATGAGAAATATTATTTGAGTATCCTTTATACTTTTCTCTCT
15526 ATTTCTTTCTATTCCTTCCTTTTTTTATTCTGTAAATTCTATGTTGTCCGGATTACACCTAACAA
66 ATTTCTTTCTATTCCTTCCTTTTTTTATTCTGTAAATTCTATGTTGTCCGGATTACACCTAACAA
15591 TTTGTGCTTTCATTGAAAGTCGACGACCATGGTTAAAAATACATAAACCATCCGCTCTTTGCAGG
131 TTTGTGCTTTCATTGAAAGTCGACGACCATGGTTAAAAATACATAAACCATCCGCTCTTTGCAGG
* *
15656 AGACACCAACGAAGCATGACCAACTCTTGGGCTCCCTTATATCCAATGTCCAAGAACAAAAGACA
196 AGACACCAACGAAGCATGACCAACTCTTGAGCTACCTTATATCCAATGTCCAAGAACAAAAGACA
15721 GCTGATGGTATTACAACTGACATATATTTTCTCCCTAATTTAGTGCTTTTATTGTCTCTTTTGTA
261 GCTGATGGTATTACAACTGACATATATTTTCTCCCTAATTTAGTGCTTTTATTGTCTCTTTTGTA
15786 TCTCATTTAGTATGCATCATAAGCATTTTATAATTAGTTTTTATATTTTCTAATACATTACTAGT
326 TCTCATTTAGTATGCATCATAAGCATTTTATAATTAGTTTTTATATTTTCTAATACATTACTAGT
*
15851 TAGTTTAAACTCTTGTTATTTCTATATATTTTGTACTAATGTCGACACAAGCAGTTGGTATATTG
391 TAGTTTAAACTCTTGTTATTTCTATATATTTTGTACTAATGTCGACACAAACAGTTGGTATATTG
*
15916 CATATTAAGATTGCTCGCACAGGAACTCAGTTCAGAAGATCAACATTGACAGAATGCAGCACAAA
456 CATATTAAGATTGCTAGCACAGGAACTCAGTTCAGAAGATCAACATTGACAGAATGCAGCACAAA
*
15981 ACTAGCTTGGAATTGCGACCAGAGATGTCACTGCATTGAAGTTGAACCTCAAATGAGTAGAGTTA
521 ACTAGCTTGGAATTGCAACCAGAGATGTCACTGCATTGAAGTTGAACCTCAAATGAGTAGAGTTA
16046 AGCTGAGTTTACACTAGAAGCATCAGTGCAAGAATATCACAGATGTCGCTATAATTACAACATCA
586 AGCTGAGTTTACACTAGAAGCATCAGTGCAAGAATATCACAGATGTCGCTATAATTACAACATCA
*
16111 GAATGCGTCTAATAGTACAGCGACAATCTACAGATCTTTAAAGAAAACATGTAATCTGCGTGAGT
651 GAATGCGTCTAATAGTACAGCGACAATCTACAGATCCTTAAAGAAAACATGTAATCTGCGTGAGT
* * * * *
16176 GCATAGTTGTACTCTAACTAATTTTGATAGCTACAAAAATCCAAATCTGAATCTGAGAATGAAGG
716 GCACAGCTGTACTCTAACTAACTTTGACAACTACAAAAATCCAAATCTGAATCTGAGAATGAAGG
*
16241 ATGAAATATGCAAATATTTAGGTATTATAAATAGACGAAAAAGAAGGAAAAACATCATCAAGAAC
781 ATGAAATATGCAAATATTTAGGTATTATAAATAGACAAAAAAGAAGGAAAAACATCATCAAGAAC
16306 AAGGGGATTAAATTTTAAAAATTCTTTGTCAAATG
846 AAGGGGATTAAATTTTAAAAATTCTTTGTCAAATG
16341 AAAGGGAATTGTAAAGGAATGATCATGAGAAATATTATTTGAGTATCCTTTATACTTTTCTCTCT
1 AAAGGGAATTGTAAAGGAATGATCATGAGAAATATTATTTGAGTATCCTTTATACTTTTCTCTCT
*
16406 ATTTCTTTCTATTCCTTCCTTTTTTTATTCTGTAAATTCTGTGTTGTCCGGATTACACCTAACAA
66 ATTTCTTTCTATTCCTTCCTTTTTTTATTCTGTAAATTCTATGTTGTCCGGATTACACCTAACAA
* *
16471 TTTGTGCTTTCATTGAGAGTCGACGACCATGGTTAAAAATACATAAACCATCCGCTCTTTGTAGG
131 TTTGTGCTTTCATTGAAAGTCGACGACCATGGTTAAAAATACATAAACCATCCGCTCTTTGCAGG
*
16536 AGGCACCAAC-AAGGCATGACCAACTCTTGAGCTACCTTATATCCAATGTCCAAGAACAAAAGAC
196 AGACACCAACGAA-GCATGACCAACTCTTGAGCTACCTTATATCCAATGTCCAAGAACAAAAGAC
*
16600 AGTTGATGGTATTACAACTGACATATA-TTTCTCCCTAATTTAGTGCTTTTATTGTCTCTTTTGT
260 AGCTGATGGTATTACAACTGACATATATTTTCTCCCTAATTTAGTGCTTTTATTGTCTCTTTTGT
16664 ATCTCATTTAGTATGCATCATAAGCATTTTATAATTAGTTTTTATATTTTCTAATACATTACTAG
325 ATCTCATTTAGTATGCATCATAAGCATTTTATAATTAGTTTTTATATTTTCTAATACATTACTAG
16729 TTAGTTTAAACTCTTGTTATTTCTATATATTTTGTACTAATGTCGACACAAACAGTTGGTATATT
390 TTAGTTTAAACTCTTGTTATTTCTATATATTTTGTACTAATGTCGACACAAACAGTTGGTATATT
*
16794 GCATATTAAGATTGCTAGCACAGGAACTCAGTTCAGAAGATCAACATTGATAGAATGCAGCCACA
455 GCATATTAAGATTGCTAGCACAGGAACTCAGTTCAGAAGATCAACATTGACAGAATGCAG-CACA
16859 AAACTAGCTTGGAATTGCAACCAGAGATGTCACTGCATTGAAGTTGAACCTCAAATGAGTAGAGT
519 AAACTAGCTTGGAATTGCAACCAGAGATGTCACTGCATTGAAGTTGAACCTCAAATGAGTAGAGT
16924 TAAGCTGAGTTTACACTAGAAGCATCAGTGCAAGAATATCACAGATGTCGCTATAATTACAACAT
584 TAAGCTGAGTTTACACTAGAAGCATCAGTGCAAGAATATCACAGATGTCGCTATAATTACAACAT
16989 CAGAATGCGTCTAATAGTACAGCGACAATCTACAGATCCTTAAAGAAAACATGTAATCTGCGTGA
649 CAGAATGCGTCTAATAGTACAGCGACAATCTACAGATCCTTAAAGAAAACATGTAATCTGCGTGA
*
17054 GTGCACAGCTGTACTCTAACTAACTTTGACAACTACAAAAATCCAGATCTGAATCTGAGAATGAA
714 GTGCACAGCTGTACTCTAACTAACTTTGACAACTACAAAAATCCAAATCTGAATCTGAGAATGAA
17119 GGATGAAATATGCAAATATTTAGGTATTATAAATAGACAAAAAAGAAGGAAAAACATCATCAAGA
779 GGATGAAATATGCAAATATTTAGGTATTATAAATAGACAAAAAAGAAGGAAAAACATCATCAAGA
*
17184 ATAAGGGGATTAAATTTTAAAAATTCTTTGT
844 ACAAGGGGATTAAATTTTAAAAATTCTTTGT
17215 GAATCAAATA
Statistics
Matches: 851, Mismatches: 21, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
879 226 0.27
880 625 0.73
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (880 bp):
AAAGGGAATTGTAAAGGAATGATCATGAGAAATATTATTTGAGTATCCTTTATACTTTTCTCTCT
ATTTCTTTCTATTCCTTCCTTTTTTTATTCTGTAAATTCTATGTTGTCCGGATTACACCTAACAA
TTTGTGCTTTCATTGAAAGTCGACGACCATGGTTAAAAATACATAAACCATCCGCTCTTTGCAGG
AGACACCAACGAAGCATGACCAACTCTTGAGCTACCTTATATCCAATGTCCAAGAACAAAAGACA
GCTGATGGTATTACAACTGACATATATTTTCTCCCTAATTTAGTGCTTTTATTGTCTCTTTTGTA
TCTCATTTAGTATGCATCATAAGCATTTTATAATTAGTTTTTATATTTTCTAATACATTACTAGT
TAGTTTAAACTCTTGTTATTTCTATATATTTTGTACTAATGTCGACACAAACAGTTGGTATATTG
CATATTAAGATTGCTAGCACAGGAACTCAGTTCAGAAGATCAACATTGACAGAATGCAGCACAAA
ACTAGCTTGGAATTGCAACCAGAGATGTCACTGCATTGAAGTTGAACCTCAAATGAGTAGAGTTA
AGCTGAGTTTACACTAGAAGCATCAGTGCAAGAATATCACAGATGTCGCTATAATTACAACATCA
GAATGCGTCTAATAGTACAGCGACAATCTACAGATCCTTAAAGAAAACATGTAATCTGCGTGAGT
GCACAGCTGTACTCTAACTAACTTTGACAACTACAAAAATCCAAATCTGAATCTGAGAATGAAGG
ATGAAATATGCAAATATTTAGGTATTATAAATAGACAAAAAAGAAGGAAAAACATCATCAAGAAC
AAGGGGATTAAATTTTAAAAATTCTTTGTCAAATG
Found at i:21929 original size:18 final size:19
Alignment explanation
Indices: 21903--21940 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21893 CGGTTGGTTT
*
21903 GAGGGACAA-GAAAAGAAA
1 GAGGCACAAGGAAAAGAAA
*
21921 GAGGCACAAGGGAAAGAAA
1 GAGGCACAAGGAAAAGAAA
21940 G
1 G
21941 TGAAGAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.37, T:0.00
Consensus pattern (19 bp):
GAGGCACAAGGAAAAGAAA
Found at i:22683 original size:3 final size:3
Alignment explanation
Indices: 22675--22716 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
22665 ATAGTGGTAG
22675 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
22717 ATGTTGAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:29255 original size:43 final size:43
Alignment explanation
Indices: 29151--29310 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 43
29141 TTGTATTAAC
* * *
29151 CTTATGCTCCAACCGAGTCATAAGTTCTTCCATTTACAAATAA-
1 CTTATGCTCTAACCGAGACATAAG-TCTTCCATTTATAAATAAT
*** * * *
29194 CTTTATGCTCTTGTCGAGACATAAGTATTCCGTTTATAAACAAT
1 C-TTATGCTCTAACCGAGACATAAGTCTTCCATTTATAAATAAT
* * *
29238 CTTATGCTCTAACCGAGACAAAAGTCTTCCATTTATGATTAAT
1 CTTATGCTCTAACCGAGACATAAGTCTTCCATTTATAAATAAT
* *
29281 CTCATGCTCTAGCCGAGACA-AGAGTCTTCC
1 CTTATGCTCTAACCGAGACATA-AGTCTTCC
29311 TTTTTGTAAC
Statistics
Matches: 94, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
42 1 0.01
43 74 0.79
44 19 0.20
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (43 bp):
CTTATGCTCTAACCGAGACATAAGTCTTCCATTTATAAATAAT
Done.