Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009617.1 Kokia drynarioides strain JFW-HI SEQ_124333, 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: 20037
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:948 original size:29 final size:29
Alignment explanation
Indices: 916--1348 Score: 326
Period size: 29 Copynumber: 14.8 Consensus size: 29
906 CCCTAAATTA
916 TCCAAAAATTACCATTTTACCCTCAAACT
1 TCCAAAAATTACCATTTTACCCTCAAACT
*
945 TCCAAAAATT--CATTTTTGACCC-CGAACCT
1 TCCAAAAATTACCA-TTTT-ACCCTC-AAACT
974 TCCAAAAATTACCATTTTA-CCTCTAAACT
1 TCCAAAAATTACCATTTTACCCTC-AAACT
*
1003 TCCAAAAATT-TCATTTTGACCC-CAAAGCT
1 TCCAAAAATTACCATTTT-ACCCTCAAA-CT
* **
1032 TCCAAAAATTACTATTTTACCCTTGAACT
1 TCCAAAAATTACCATTTTACCCTCAAACT
* * * *
1061 TCCAAAAA-TCCCATTTTTGACCTTGAACCT
1 TCCAAAAATTACCA-TTTT-ACCCTCAAACT
* *
1091 TCCAAAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATTACCATTTTACCCTCAAACT
*
1120 TCCAAAAA-T-CTCATTTTTGA-CCTCGAACCT
1 TCCAAAAATTAC-CA-TTTT-ACCCTC-AAACT
* *
1150 TCC-AAAATTACCATTTTATCCTCGAACT
1 TCCAAAAATTACCATTTTACCCTCAAACT
* * *
1178 TCCAAAAA-TCCCATTTTTGACCCTGAACCT
1 TCCAAAAATTACCA-TTTT-ACCCTCAAACT
*
1208 TCCAAAAATTACCATTTTACCCCCAAACT
1 TCCAAAAATTACCATTTTACCCTCAAACT
* *
1237 TCCAAAAA-TCCCATTTTTAACCCTAAAACT
1 TCCAAAAATTACCA-TTTT-ACCCTCAAACT
** *
1267 T-TTATAATTACCATTTTACCCTCAAAC-
1 TCCAAAAATTACCATTTTACCCTCAAACT
1294 TCTCAAAAA-T-CTCATTTTTAACCC-CAAAACT
1 TC-CAAAAATTAC-CA-TTTT-ACCCTC-AAACT
* *
1325 TCTAAAAATTATCATTTTACCCTC
1 TCCAAAAATTACCATTTTACCCTC
1349 GAACCCTGAA
Statistics
Matches: 319, Mismatches: 47, Indels: 75
0.72 0.11 0.17
Matches are distributed among these distances:
27 5 0.02
28 49 0.15
29 156 0.49
30 93 0.29
31 16 0.05
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTCAAACT
Found at i:986 original size:58 final size:59
Alignment explanation
Indices: 916--1348 Score: 536
Period size: 58 Copynumber: 7.4 Consensus size: 59
906 CCCTAAATTA
916 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAAT-TCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCGAACCT
* * *
974 TCCAAAAATTACCATTTTA-CCTCTAAACTTCCAAAAATTTCA-TTTTGACCCCAAAGCT
1 TCCAAAAATTACCATTTTACCCTC-AAACTTCCAAAAATCTCATTTTTGACCCCGAACCT
* ** * **
1032 TCCAAAAATTACTATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCTTGAACCT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCGAACCT
* * *
1091 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCGAACCT
* * * *
1150 TCC-AAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCATTTTTGACCCTGAACCT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCGAACCT
* * * ** *
1208 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTAAAACT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCGAACCT
** * * * *
1267 T-TTATAATTACCATTTTACCCTCAAAC-TCTCAAAAATCTCATTTTTAACCCCAAAACT
1 TCCAAAAATTACCATTTTACCCTCAAACTTC-CAAAAATCTCATTTTTGACCCCGAACCT
* *
1325 TCTAAAAATTATCATTTTACCCTC
1 TCCAAAAATTACCATTTTACCCTC
1349 GAACCCTGAA
Statistics
Matches: 332, Mismatches: 36, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
57 6 0.02
58 182 0.55
59 144 0.43
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCTCATTTTTGACCCCGAACCT
Found at i:1121 original size:117 final size:118
Alignment explanation
Indices: 916--1346 Score: 557
Period size: 117 Copynumber: 3.7 Consensus size: 118
906 CCCTAAATTA
*
916 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAAT-TCATTTTTGACCCCGAACCTTCCAAA
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAA
* * * *
980 AATTACCATTTTACCTCTAAACTTCCAAAAATTTCA-TTTTGACCCCAAAGCT
66 AATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAACT
* ** **
1032 TCCAAAAATTACTATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCTTGAACCTTCCAAA
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAA
* * * *
1097 AATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCT
66 AATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAACT
* * *
1150 TCC-AAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCATTTTTGACCCTGAACCTTCCAAA
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAA
* * *
1214 AATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTAAAACT
66 AATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAACT
** * * * * * *
1267 T-TTATAATTACCATTTTACCCTCAAAC-TCTCAAAAATCTCATTTTTAACCCCAAAACTTCTAA
1 TCCAAAAATTACCATTTTACCCTCAAACTTC-CAAAAATCCCATTTTTGACCCCGAACCTTCCAA
*
1330 AAATTATCATTTTACCC
65 AAATTACCATTTTACCC
1347 TCGAACCCTG
Statistics
Matches: 276, Mismatches: 35, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
116 37 0.13
117 223 0.81
118 16 0.06
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (118 bp):
TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAA
AATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCAAAACT
Found at i:10886 original size:31 final size:31
Alignment explanation
Indices: 10831--10889 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
10821 AAAAATGAAA
*
10831 TTTTAAAAAAATTAAATCAAAATTTTATAAT
1 TTTTAAAAAAATAAAATCAAAATTTTATAAT
*
10862 TTTTAAAAAAATCAAAAT-ATAATTTTAT
1 TTTTAAAAAAAT-AAAATCAAAATTTTAT
10890 TTTAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTAAAAAAATAAAATCAAAATTTTATAAT
Found at i:11467 original size:25 final size:27
Alignment explanation
Indices: 11413--11478 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
11403 CAATGCTAAA
*
11413 AAAACTCTT-TATTATTTTGATTTAATT
1 AAAA-TCTTATATTATTTTGATCTAATT
*
11440 AAAGTCTTATATTATTTTGATCT-A-T
1 AAAATCTTATATTATTTTGATCTAATT
*
11465 AAAATTTTATATTA
1 AAAATCTTATATTA
11479 GTGCGCAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 13 0.38
26 5 0.15
27 16 0.47
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (27 bp):
AAAATCTTATATTATTTTGATCTAATT
Found at i:16981 original size:115 final size:114
Alignment explanation
Indices: 16794--17010 Score: 317
Period size: 115 Copynumber: 1.9 Consensus size: 114
16784 TGTTCGTATA
* * ** *
16794 AGCTAGTTCAACCAACACACTAAATGTTGTAACATATCTCGTTAGTCCGTAATAGATGCAGGACC
1 AGCTAGTCCAACCAACACACAAAATACTGTAACATATCTCGTTAGTCCGCAATAGATGCAGGACC
*
16859 TTAATATATTCAATGAACATATAATCTACTGTAATCAAATGTCTGTAAG
66 TCAATATATTCAATGAACATATAATCTACTGTAATCAAATGTCTGTAAG
* * *
16908 AGCTAGTCCATCCAACACACCAAAATACTGTAACATATCTCGTTAGTCTGCAATAGATGTAGGAC
1 AGCTAGTCCAACCAACACA-CAAAATACTGTAACATATCTCGTTAGTCCGCAATAGATGCAGGAC
* **
16973 CTCAATATATTCAGTGAACATATAATCTGTTGTAATCA
65 CTCAATATATTCAATGAACATATAATCTACTGTAATCA
17011 TCTTCACTAC
Statistics
Matches: 90, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
114 17 0.19
115 73 0.81
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (114 bp):
AGCTAGTCCAACCAACACACAAAATACTGTAACATATCTCGTTAGTCCGCAATAGATGCAGGACC
TCAATATATTCAATGAACATATAATCTACTGTAATCAAATGTCTGTAAG
Done.