Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012812.1 Kokia drynarioides strain JFW-HI SEQ_127825, 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: 2710
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Found at i:432 original size:139 final size:139
Alignment explanation
Indices: 182--869 Score: 1187
Period size: 139 Copynumber: 4.9 Consensus size: 139
172 TCCACAAAGT
*
182 AGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTTCTGAT
1 AGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGAT
*
247 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAACAAATCTTCCTGATGAGATACGGAG
66 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAG
312 AAGTGAGCC
131 AAGTGAGCC
* * *
321 AGATTCGTATTCCTAATGAGATACAGAGAAACGGATCAAAACAATGATGGGATCATTTTCCTGAT
1 AGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGAT
*
386 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACAGAG
66 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAG
451 AAGTGAGCC
131 AAGTGAGCC
* * *
460 AGATTCGTATTCCTGATAAGATATAGAGAAACGGATCGAAACAATGATGGGATCATCTTCTTGAT
1 AGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGAT
525 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAG
66 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAG
*
590 AAGTGAGTC
131 AAGTGAGCC
* *
599 AAATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGAACATCTTCCTGAT
1 AGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGAT
*
664 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACAAGCAAATCTTCCTGATGAGATACGGAG
66 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAG
*
729 AAGTGAACC
131 AAGTGAGCC
* **
738 AGATTCGTATTCCTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGAT
1 AGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGAT
* * * *
803 GAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGTAAATCTTCCTGATAAGATACAGAG
66 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAG
868 AA
131 AA
870 ACGGATCGAA
Statistics
Matches: 517, Mismatches: 32, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
139 517 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (139 bp):
AGATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGAT
GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAG
AAGTGAGCC
Found at i:851 original size:54 final size:53
Alignment explanation
Indices: 792--972 Score: 158
Period size: 54 Copynumber: 3.5 Consensus size: 53
782 CGATGGGATC
792 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGTAA
1 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAAC-AGGCTCGAAACGAGTAA
* * * ** * * * *** *
846 ATCTTCCTGATAAGATACAGAGAA-ACGGATCGAAACA--AT-GATGGGA-T-C
1 ATCTTCCTGATGAGACACTGAGAAGA-AAACCCAAACAGGCTCGAAACGAGTAA
*
894 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACGAGCAA
1 ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAAC-AGGCTCGAAACGAGTAA
* *
948 ATCTTCCTGATGAGATACGGAGAAG
1 ATCTTCCTGATGAGACACTGAGAAG
973 TGAACCAGAT
Statistics
Matches: 92, Mismatches: 27, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
48 27 0.29
49 3 0.03
50 4 0.04
51 2 0.02
52 4 0.04
53 2 0.02
54 50 0.54
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (53 bp):
ATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAGGCTCGAAACGAGTAA
Found at i:907 original size:241 final size:241
Alignment explanation
Indices: 608--1110 Score: 916
Period size: 241 Copynumber: 2.1 Consensus size: 241
598 CAAATTCGTA
608 TTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGAACATCTTCCTGATGAGACACTG
1 TTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGAACATCTTCCTGATGAGACACTG
673 AGAAGAAAACCCAAACAAGGCTCGAAACAAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
66 AGAAGAAAACCCAAACAAGGCTCGAAACAAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
*
738 AGATTCGTATTCCTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGAT
131 AGATTCGTATTCCTGATGAGATACAGAGAAACGGGTCGAAACAGCGATAGGATCATCTTCCTGAT
*
803 GAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGTAAATC
196 GAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
* *
849 TTCCTGATAAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTG
1 TTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGAACATCTTCCTGATGAGACACTG
*
914 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
66 AGAAGAAAACCCAAACAAGGCTCGAAACAAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
*
979 AGATTCGTATTCCTGATGAGATACAGAGAAACGGGTTGAAACAGCGATAGGATCATCTTCCTGAT
131 AGATTCGTATTCCTGATGAGATACAGAGAAACGGGTCGAAACAGCGATAGGATCATCTTCCTGAT
* * *
1044 GATATACTGAGAAGAAAACCCAAACGAGGCTCGAAGCGAGCAAATC
196 GAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
*
1090 TTCCTGATGAGATACTGAGAA
1 TTCCTGATGAGATACAGAGAA
1111 GTGAACCAAA
Statistics
Matches: 251, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
241 251 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.18
Consensus pattern (241 bp):
TTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGAACATCTTCCTGATGAGACACTG
AGAAGAAAACCCAAACAAGGCTCGAAACAAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
AGATTCGTATTCCTGATGAGATACAGAGAAACGGGTCGAAACAGCGATAGGATCATCTTCCTGAT
GAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATC
Found at i:923 original size:102 final size:102
Alignment explanation
Indices: 747--971 Score: 387
Period size: 102 Copynumber: 2.2 Consensus size: 102
737 CAGATTCGTA
* *
747 TTCCTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCATCTTCCTGATGAGACACTG
1 TTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
* *
812 AGAAGAAAACCCAAACGAGGCTCGAAACGAGTAAATC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATC
* *
849 TTCCTGATAAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTG
1 TTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
914 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATC
*
951 TTCCTGATGAGATACGGAGAA
1 TTCCTGATGAGATACAGAGAA
972 GTGAACCAGA
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 115 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (102 bp):
TTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATGGGATCATCTTCCTGATGAGACACTG
AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATC
Found at i:930 original size:48 final size:49
Alignment explanation
Indices: 782--931 Score: 124
Period size: 48 Copynumber: 3.0 Consensus size: 49
772 GTCGAAACAG
*
782 CGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCT
1 CGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAAC-A--AT
*** * * * * ** * *
834 CGAAACGAGTAAATCTTCCTGATAAGATACAGAGAA-ACGGATCGAAACAAT
1 CGATGGGA-T-CATCTTCCTGATGAGACACTGAGAAGA-AAACCCAAACAAT
885 -GATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAA
1 CGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAA
932 GGCTCGAAAC
Statistics
Matches: 71, Mismatches: 23, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
48 29 0.41
49 2 0.03
50 4 0.06
51 1 0.01
52 5 0.07
53 3 0.04
54 27 0.38
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (49 bp):
CGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACAAT
Found at i:1099 original size:139 final size:139
Alignment explanation
Indices: 849--1123 Score: 442
Period size: 139 Copynumber: 2.0 Consensus size: 139
839 CGAGTAAATC
* *
849 TTCCTGATAAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTG
1 TTCCTGATAAGATACAGAGAAACGGATCGAAACAACGATAGGATCATCTTCCTGATGAGACACTG
914 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
*
979 AGATTCGTA
131 AAATTCGTA
* * * * * *
988 TTCCTGATGAGATACAGAGAAACGGGTTGAAACAGCGATAGGATCATCTTCCTGATGATATACTG
1 TTCCTGATAAGATACAGAGAAACGGATCGAAACAACGATAGGATCATCTTCCTGATGAGACACTG
* * *
1053 AGAAGAAAACCCAAACGAGGCTCGAAGCGAGCAAATCTTCCTGATGAGATACTGAGAAGTGAACC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
1118 AAATTC
131 AAATTC
1124 ATAAGCGAAT
Statistics
Matches: 124, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
139 124 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (139 bp):
TTCCTGATAAGATACAGAGAAACGGATCGAAACAACGATAGGATCATCTTCCTGATGAGACACTG
AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
AAATTCGTA
Found at i:1236 original size:380 final size:372
Alignment explanation
Indices: 469--1202 Score: 986
Period size: 380 Copynumber: 2.0 Consensus size: 372
459 CAGATTCGTA
* *
469 TTCCTGATAAGATATAGAGAAACGGATCGAAACAATGATGGGATCATCTTCTTGATGAGACACTG
1 TTCCTGATAAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTG
**
534 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAGTC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
* *
599 AAATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAATGATGGGAACATCTTCCTGAT
131 AAATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATAGGAACATCTTCCTGAT
664 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACAAGCAAATCTTCCTGATGAGATACGGAG
196 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACAAGCAAATCTTCCTGATGAGATACGGAG
* * * *
729 AAGTGAACCAGATTCGTATTCCTGATGAGATACAGAGAAACGGGTCGAAACAGCGATGGGATCAT
261 AAGTGAACCAGA----TATTCATGAAGAGATACAGAG-AACAGCTCG--A-AGCGATGGGATCAT
* * * * * *
794 CTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGTAAATC
318 CTTCCTGATGAGACACTAAGAAGAAAAACCAAACCACGCTCGAAACAAGTAAAGC
849 TTCCTGATAAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTG
1 TTCCTGATAAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTG
914 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
66 AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
* * * * *
979 AGATTCGTATTCCTGATGAGATACAGAGAAACGGGTTGAAACAGCGATAGGATCATCTTCCTGAT
131 AAATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATAGGAACATCTTCCTGAT
* * * * * *
1044 GATATACTGAGAAGAAAACCCAAACGAGGCTCGAAGCGAGCAAATCTTCCTGATGAGATACTGAG
196 GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACAAGCAAATCTTCCTGATGAGATACGGAG
* **
1109 AAGTGAACCA-A-ATTCAT-AAGCGA-ATTGAG-ACAGCT-G-A-CG-T-GG-TCATCTTCCTGA
261 AAGTGAACCAGATATTCATGAAGAGATACAGAGAACAGCTCGAAGCGATGGGATCATCTTCCTGA
**
1163 TGAGATGCTAAGAAGAAGGCCAAACCAAACCCACGCTCGA
326 TGAGACACTAAGAAGAA----AAACCAAA-CCACGCTCGA
1203 TGTGAGCAAA
Statistics
Matches: 319, Mismatches: 30, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
361 26 0.08
362 2 0.01
363 1 0.00
364 2 0.01
365 8 0.03
366 8 0.03
369 1 0.00
370 4 0.01
372 4 0.01
373 4 0.01
374 5 0.02
379 1 0.00
380 253 0.79
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.19
Consensus pattern (372 bp):
TTCCTGATAAGATACAGAGAAACGGATCGAAACAATGATGGGATCATCTTCCTGATGAGACACTG
AGAAGAAAACCCAAACAAGGCTCGAAACGAGCAAATCTTCCTGATGAGATACGGAGAAGTGAACC
AAATTCGTATTCCTGATGAGATACAGAGAAACGGATCGAAACAACGATAGGAACATCTTCCTGAT
GAGACACTGAGAAGAAAACCCAAACAAGGCTCGAAACAAGCAAATCTTCCTGATGAGATACGGAG
AAGTGAACCAGATATTCATGAAGAGATACAGAGAACAGCTCGAAGCGATGGGATCATCTTCCTGA
TGAGACACTAAGAAGAAAAACCAAACCACGCTCGAAACAAGTAAAGC
Found at i:1642 original size:17 final size:17
Alignment explanation
Indices: 1620--1682 Score: 92
Period size: 17 Copynumber: 3.7 Consensus size: 17
1610 TTGGAAATTG
*
1620 AATTTAAGTTTATTTGA
1 AATTTAAATTTATTTGA
1637 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTGA
1654 AATTTAAATTTATTAT-A
1 AATTTAAATTTATT-TGA
*
1671 AAATTAAATTTA
1 AATTTAAATTTA
1683 GAAAAGTCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
17 42 0.98
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Found at i:1737 original size:15 final size:15
Alignment explanation
Indices: 1719--1787 Score: 84
Period size: 15 Copynumber: 4.5 Consensus size: 15
1709 AAACAAAAGT
1719 CCCAATTACAAATGG
1 CCCAATTACAAATGG
*
1734 CCCAAATAACAAATGG
1 CCC-AATTACAAATGG
* *
1750 CCCAGTTACAGATGG
1 CCCAATTACAAATGG
*
1765 CCCAAATACAAATGG
1 CCCAATTACAAATGG
*
1780 TCCAATTA
1 CCCAATTA
1788 TAAAGTGCTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 30 0.68
16 14 0.32
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (15 bp):
CCCAATTACAAATGG
Found at i:1747 original size:16 final size:15
Alignment explanation
Indices: 1706--1784 Score: 79
Period size: 15 Copynumber: 5.3 Consensus size: 15
1696 ACAAAAAAAT
* *
1706 CCAAA-ACAAAAGTC
1 CCAAATACAAATGGC
*
1720 CCAATTACAAATGGC
1 CCAAATACAAATGGC
1735 CCAAATAACAAATGGC
1 CCAAAT-ACAAATGGC
** *
1751 CCAGTTACAGATGGC
1 CCAAATACAAATGGC
*
1766 CCAAATACAAATGGT
1 CCAAATACAAATGGC
1781 CCAA
1 CCAA
1785 TTATAAAGTG
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
14 4 0.08
15 35 0.67
16 13 0.25
ACGTcount: A:0.44, C:0.27, G:0.14, T:0.15
Consensus pattern (15 bp):
CCAAATACAAATGGC
Found at i:1759 original size:31 final size:31
Alignment explanation
Indices: 1710--1787 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
1700 AAAAATCCAA
* *
1710 AACAAAAGTCCCAATTACAAATGGCCCAAAT
1 AACAAATGGCCCAATTACAAATGGCCCAAAT
* *
1741 AACAAATGGCCCAGTTACAGATGGCCCAAAT
1 AACAAATGGCCCAATTACAAATGGCCCAAAT
*
1772 -ACAAATGGTCCAATTA
1 AACAAATGGCCCAATTA
1788 TAAAGTGCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 14 0.34
31 27 0.66
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.18
Consensus pattern (31 bp):
AACAAATGGCCCAATTACAAATGGCCCAAAT
Found at i:2396 original size:12 final size:11
Alignment explanation
Indices: 2377--2411 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2367 AAATGTTTTG
2377 ATTTATTAATA
1 ATTTATTAATA
*
2388 ATATTATTAATT
1 AT-TTATTAATA
2400 ATTTATTAATA
1 ATTTATTAATA
2411 A
1 A
2412 AAAAAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTTATTAATA
Done.