Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006395.1 Kokia drynarioides strain JFW-HI SEQ_120972, 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: 1986
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Found at i:851 original size:49 final size:49
Alignment explanation
Indices: 793--1002 Score: 176
Period size: 49 Copynumber: 4.5 Consensus size: 49
783 ACCAAATTCG
* *
793 TCTTCCTGATGAGGTACAGAGAAGTAGATTAAAACAAGTGATA-CGGTCA
1 TCTTCCTGATGAGATACAGAGAAGTAGATTAAAACAAATGA-AGCGGTCA
* **
842 TCTTCCTGATGAGATACGGAGAAGCGGATTAAAACAAATGAAGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGTAGATTAAAACAAATGAAGCGGTCA
* * *
891 TCTTCCTAATGAGATACAGAGAAGT-G----GACCAAAT----C--T-A
1 TCTTCCTGATGAGATACAGAGAAGTAGATTAAAACAAATGAAGCGGTCA
* *** * **
928 TCTTCTTGATGAGATACAGAGAAACGGATTAAAACAACTGAAGCAATCA
1 TCTTCCTGATGAGATACAGAGAAGTAGATTAAAACAAATGAAGCGGTCA
*
977 TCTTCCTAATGAGATACAGAGAAGTA
1 TCTTCCTGATGAGATACAGAGAAGTA
1003 AACCAAATCA
Statistics
Matches: 126, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
37 22 0.17
38 2 0.02
40 1 0.01
42 5 0.04
44 6 0.05
46 1 0.01
48 3 0.02
49 86 0.68
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (49 bp):
TCTTCCTGATGAGATACAGAGAAGTAGATTAAAACAAATGAAGCGGTCA
Found at i:932 original size:135 final size:133
Alignment explanation
Indices: 708--1000 Score: 320
Period size: 135 Copynumber: 2.2 Consensus size: 133
698 ATCAAATCCT
* * ** * * * * *
708 ATCTTCCTGATGGGATACAGAGAAGTGGGTCGAACCAATAAGTGGTCATCTTCTTGACGAGATGC
1 ATCTTCCTGATGAGATACAGAGAAGCGGGTAAAACAAATAAGCGGTCATCTTCCTAACGAGATAC
* * ** *
773 AGAAAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGTAGATTAAAACAAGTGATA-C
66 AGAAAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAACAGATTAAAACAACTGA-AGC
**
837 GGTC
130 AATC
* * *
841 ATCTTCCTGATGAGATACGGAGAAGCGGATTAAAACAAATGAAGCGGTCATCTTCCTAATGAGAT
1 ATCTTCCTGATGAGATACAGAGAAGCGG-GTAAAACAAAT-AAGCGGTCATCTTCCTAACGAGAT
* * * *
906 ACAGAGAAGTGGACCAAA-TCTATCTTCTTGATGAGATACAGAGAAACGGATTAAAACAACTGAA
64 ACAGAAAAGTGAACCAAATTC-ATCTTCCTGATGAGATACAGAGAAACAGATTAAAACAACTGAA
970 GCAATC
128 GCAATC
*
976 ATCTTCCTAATGAGATACAGAGAAG
1 ATCTTCCTGATGAGATACAGAGAAG
1001 TAAACCAAAT
Statistics
Matches: 131, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
133 25 0.19
134 10 0.08
135 96 0.73
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (133 bp):
ATCTTCCTGATGAGATACAGAGAAGCGGGTAAAACAAATAAGCGGTCATCTTCCTAACGAGATAC
AGAAAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAACAGATTAAAACAACTGAAGCA
ATC
Found at i:986 original size:86 final size:86
Alignment explanation
Indices: 841--1011 Score: 270
Period size: 86 Copynumber: 2.0 Consensus size: 86
831 TGATACGGTC
* * **
841 ATCTTCCTGATGAGATACGGAGAAGCGGATTAAAACAAATGAAGCGGTCATCTTCCTAATGAGAT
1 ATCTTCCTGATGAGATACAGAGAAACGGATTAAAACAAATGAAGCAATCATCTTCCTAATGAGAT
**
906 ACAGAGAAGTGGACCAAATCT
66 ACAGAGAAGTAAACCAAATCT
* *
927 ATCTTCTTGATGAGATACAGAGAAACGGATTAAAACAACTGAAGCAATCATCTTCCTAATGAGAT
1 ATCTTCCTGATGAGATACAGAGAAACGGATTAAAACAAATGAAGCAATCATCTTCCTAATGAGAT
992 ACAGAGAAGTAAACCAAATC
66 ACAGAGAAGTAAACCAAATC
1012 AATTAAGCGA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (86 bp):
ATCTTCCTGATGAGATACAGAGAAACGGATTAAAACAAATGAAGCAATCATCTTCCTAATGAGAT
ACAGAGAAGTAAACCAAATCT
Found at i:1405 original size:124 final size:124
Alignment explanation
Indices: 1185--1457 Score: 438
Period size: 124 Copynumber: 2.2 Consensus size: 124
1175 GATGCAGTCA
1185 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATATGAGTGAAACT
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATATGAGTGAAACT
* * * * * *
1250 TCGAACCCCCATCTTCTTAATGATATACTAAGAAGTGCGTCAAAGTAATAAAACGGTCG
66 TCAAACCCCCATCTTCCTAATAAGATACTAAGAAGTGCGTCAAAGCAATAAAACGATCG
*
1309 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACT
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATATGAGTGAAACT
* * * *
1374 TCAAACCCCCATCTTCCTGATAAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATTG
66 TCAAACCCCCATCTTCCTAATAAGATACTAAGAAGTGCGTCAAAGCAATAAAACGATCG
*
1433 TCTTCCTGATAAGATACAGAGAAGT
1 TCTTCCTGATGAGATACAGAGAAGT
1458 GGATTAAATA
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 137 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (124 bp):
TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATATGAGTGAAACT
TCAAACCCCCATCTTCCTAATAAGATACTAAGAAGTGCGTCAAAGCAATAAAACGATCG
Found at i:1452 original size:334 final size:332
Alignment explanation
Indices: 973--1676 Score: 1113
Period size: 334 Copynumber: 2.1 Consensus size: 332
963 AACTGAAGCA
* * * * *
973 ATCATCTTCCTAATGAGATACAGAGAAGTAAACCAAATCAATTAAGCGAATCTCAATACGATGAG
1 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGATGAA
*
1038 ATTCCAAACCCCATCTTCCTGATCAGATACTAAGAAGTGGATCAAAGCAATAAAGCGATCGTCTT
66 ATTCCAAACCCCATCTTCCTGATAAGATACTAAGAAGTGGATCAAAGCAATAAAGCGATCGTCTT
* *
1103 CCTGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGGATTAA
131 CCTGATAAGATACAGAGAAGTGGACCAAATATGTCTTCCTGATGAGATACAGAGAAGCGGATTAA
1168 AACAAGTGATGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGC
196 AACAAGTGATGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGC
* * *
1233 TCAATATGAGTGAAACTTCGAACCCCCATCTTCTTAATGATATACTAAGAAGTGCGTCAAAGTAA
261 TCAATATGAGTGAAACTTCGAACACCCATCTTCTTAATGAGATACTAAGAAGTGCGTCAAAGCAA
1298 TAAAACG
326 TAAAACG
* * * **
1305 GTCGTCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGA
1 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGA-TGA
* *
1370 AACTT-CAAACCCCCATCTTCCTGATAAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATTGT
65 AA-TTCCAAA-CCCCATCTTCCTGATAAGATACTAAGAAGTGGATCAAAGCAATAAAGCGATCGT
** *
1434 CTTCCTGATAAGATACAGAGAAGTGGATTAAATATGTCTTCCTGATGAGATACAGAGAAGTGGAT
128 CTTCCTGATAAGATACAGAGAAGTGGACCAAATATGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * *
1499 TAAAATAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATTGATGAAGCGA
193 TAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGA
* * *
1564 AGCTCAATGTGAGTGAAACTTCGAACACCCATCTTCTTGATGAGATACTAAGAAGTGGGTCAAAG
258 AGCTCAATATGAGTGAAACTTCGAACACCCATCTTCTTAATGAGATACTAAGAAGTGCGTCAAAG
*
1629 CCATAAAACG
323 CAATAAAACG
*
1639 ATCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAT
1 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAT
1677 TCGTCTTCCT
Statistics
Matches: 338, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
332 52 0.15
333 8 0.02
334 278 0.82
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (332 bp):
ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGATGAA
ATTCCAAACCCCATCTTCCTGATAAGATACTAAGAAGTGGATCAAAGCAATAAAGCGATCGTCTT
CCTGATAAGATACAGAGAAGTGGACCAAATATGTCTTCCTGATGAGATACAGAGAAGCGGATTAA
AACAAGTGATGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGC
TCAATATGAGTGAAACTTCGAACACCCATCTTCTTAATGAGATACTAAGAAGTGCGTCAAAGCAA
TAAAACG
Found at i:1472 original size:37 final size:37
Alignment explanation
Indices: 1431--1502 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
1421 ATAAAGCGAT
1431 TGTCTTCCTGATAAGATACAGAGAAGTGGATTAAATA
1 TGTCTTCCTGATAAGATACAGAGAAGTGGATTAAATA
*
1468 TGTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
1 TGTCTTCCTGATAAGATACAGAGAAGTGGATTAAA
1503 ATAAGTGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (37 bp):
TGTCTTCCTGATAAGATACAGAGAAGTGGATTAAATA
Found at i:1525 original size:210 final size:209
Alignment explanation
Indices: 1303--1986 Score: 1044
Period size: 210 Copynumber: 3.3 Consensus size: 209
1293 AGTAATAAAA
*
1303 CGGTCGTCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
* * *
1368 GAAACTTCAAACCCCCATCTTCCTGATAAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATTG
66 GAAACTTCGAACCCCCATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATCG
* **
1433 TCTTCCTGATAAGATACAGAGAAGTGGATTAAATATGTCTTCCTGATGAGATACAGAGAAGTGGA
131 TCTTCCTGATGAGATACAGAGAAGTGGACCAAAT-TGTCTTCCTGATGAGATACAGAGAAGTGGA
* * *
1498 TTAAAATAAGTGATG
195 TTAAAACAAATGAGG
*
1513 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATTGATGAAGCGAAGCTCAATGTGAGT
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
* * * * *
1578 GAAACTTCGAACACCCATCTTCTTGATGAGATACTAAGAAGTGGGTCAAAGCCATAAAACGATCA
66 GAAACTTCGAACCCCCATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATCG
*
1643 TCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACGGAGAAGTGGA
131 TCTTCCTGATGAGATACAGAGAAGTGGACCAAATT-GTCTTCCTGATGAGATACAGAGAAGTGGA
1708 TTAAAACAAATGAGG
195 TTAAAACAAATGAGG
* *
1723 CGGTCATCTTCCTGATGAGATAGAGAGAAGTAGACCAAATCGATGAAGCGAAGCTAAATGTGAGT
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
* * * * *
1788 GAAACTTTGAACCCCCATCTTTCTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGTGGTCG
66 GAAACTTCGAACCCCCATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATCG
* * * * *
1853 TCTTCCTGATGAGATATAAAGAAGTGGACCAAATCTGTCTTCCCGATGAGATACAAAAAAGTGGA
131 TCTTCCTGATGAGATACAGAGAAGTGGACCAAAT-TGTCTTCCTGATGAGATACAGAGAAGTGGA
*
1918 TTTTAAACAAATGAGG
195 -TTAAAACAAATGAGG
* *
1934 CGGTCATCTTCCTGATGAGATAGAAAGAAGTAGACCAAATCGATGAAGCGAAG
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAG
Statistics
Matches: 433, Mismatches: 38, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
209 1 0.00
210 365 0.84
211 67 0.15
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (209 bp):
CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
GAAACTTCGAACCCCCATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATCG
TCTTCCTGATGAGATACAGAGAAGTGGACCAAATTGTCTTCCTGATGAGATACAGAGAAGTGGAT
TAAAACAAATGAGG
Done.