Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002648.1 Kokia drynarioides strain JFW-HI SEQ_114884, 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: 14344
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:1809 original size:30 final size:29
Alignment explanation
Indices: 1746--2019 Score: 306
Period size: 29 Copynumber: 9.3 Consensus size: 29
1736 CCCTAATCTA
** *
1746 TCCAAAAATTCCATTTTT-ACCTTTTACCT
1 TCCAAAAATTCCATTTTTGACC-TCAAACT
1775 TCCAAAAATTCCATTTTTGACCTCAAAACT
1 TCCAAAAATTCCATTTTTGACCTC-AAACT
* *
1805 TCCAAAAATTCCATTTTT-ACCCCTGAACT
1 TCCAAAAATTCCATTTTTGACCTC-AAACT
*
1834 TACAAAAATTCCATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTTGACCTC-AAACT
* *
1864 TCCAAAAATTCCATTTTT-ACCCTCGAATT
1 TCCAAAAATTCCATTTTTGA-CCTCAAACT
* *
1893 TCCAAAATTTCCATTTTTGACC-CCAACT
1 TCCAAAAATTCCATTTTTGACCTCAAACT
* * *
1921 TCCAAAAATTACATCTTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTTGACCTC-AAACT
*
1951 TCCAAAAATTCCATTTTT-ACCTCCGAACT
1 TCCAAAAATTCCATTTTTGACCT-CAAACT
1980 TCCAAAAATTCCATTTTTGACCTCAAAACT
1 TCCAAAAATTCCATTTTTGACCTC-AAACT
*
2010 TTCAAAAATT
1 TCCAAAAATT
2020 ACCCTTTTAC
Statistics
Matches: 209, Mismatches: 26, Indels: 19
0.82 0.10 0.07
Matches are distributed among these distances:
28 23 0.11
29 94 0.45
30 92 0.44
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTGACCTCAAACT
Found at i:2001 original size:59 final size:58
Alignment explanation
Indices: 1746--1997 Score: 323
Period size: 59 Copynumber: 4.3 Consensus size: 58
1736 CCCTAATCTA
*** * **
1746 TCCAAAAATTCCATTTTTACCTTTTACCTTCCAAAAATTCCATTTTTGACCTCAAAACT
1 TCCAAAAATTCCATTTTTACC-CCGAACTTCCAAAAATTCCATTTTTGACCTCCGAACT
*
1805 TCCAAAAATTCCATTTTTACCCCTGAACTTACAAAAATTCCATTTTTGACCT-CGAAACT
1 TCCAAAAATTCCATTTTTACCCC-GAACTTCCAAAAATTCCATTTTTGACCTCCG-AACT
* *
1864 TCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAATTTCCATTTTTGACC-CC-AACT
1 TCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATTCCATTTTTGACCTCCGAACT
* *
1921 TCCAAAAATTACATCTTTGACCCCGAAACTTCCAAAAATTCCATTTTT-ACCTCCGAACT
1 TCCAAAAATTCCAT-TTTTACCCCG-AACTTCCAAAAATTCCATTTTTGACCTCCGAACT
1980 TCCAAAAATTCCATTTTT
1 TCCAAAAATTCCATTTTT
1998 GACCTCAAAA
Statistics
Matches: 169, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
57 22 0.13
58 32 0.19
59 114 0.67
60 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.36
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCTCCGAACT
Found at i:2016 original size:146 final size:146
Alignment explanation
Indices: 1773--2060 Score: 418
Period size: 146 Copynumber: 2.0 Consensus size: 146
1763 TACCTTTTAC
* * *
1773 CTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTACA
1 CTTCCAAAAATTACATCTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTACA
* * * **
1838 AAAATTCCATTTTTGACCTCGAAACTTCCAAAAATT-CCATTTTTACCCTCGAATTTCCAAAATT
66 AAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACC-CTTTTACCCTCGAATGTCCAAAAAC
*
1902 TCCATTTTTGACCCCAA
130 TCCATTTTCGACCCCAA
* *
1919 CTTCCAAAAATTACATCTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCTCC-GAACTTCC
1 CTTCCAAAAATTACATCTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACC-CCTGAACTTAC
* * *
1983 AAAAATTCCATTTTTGACCTCAAAACTTTCAAAAATTACCCTTTTACGCTCGGATGTCCAAAAAC
65 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACCCTTTTACCCTCGAATGTCCAAAAAC
2048 TCCATTTTCGACC
130 TCCATTTTCGACC
2061 TCAAAACTCT
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
146 122 0.97
147 4 0.03
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (146 bp):
CTTCCAAAAATTACATCTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTACA
AAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACCCTTTTACCCTCGAATGTCCAAAAACT
CCATTTTCGACCCCAA
Found at i:2028 original size:59 final size:59
Alignment explanation
Indices: 1746--2115 Score: 300
Period size: 59 Copynumber: 6.3 Consensus size: 59
1736 CCCTAATCTA
*** * * **
1746 TCCAAAAATTCCATTTTTACCTTTTACCTTCCAAAAATTCCATTTTTGACCTCAAAACT
1 TCCAAAAATTCCATTTTTACCTCAAAACTTTCAAAAATTCCATTTTTGACCTCCGAACT
* ** *
1805 TCCAAAAATTCCATTTTTACCCCTGAACTTACAAAAATTCCATTTTTGACCT-CGAAACT
1 TCCAAAAATTCCATTTTTACCTCAAAACTTTCAAAAATTCCATTTTTGACCTCCG-AACT
* *
1864 TCCAAAAATTCCATTTTTACCCTC-GAA-TTTCCAAAATTTCCATTTTTGACC-CC-AACT
1 TCCAAAAATTCCATTTTTA-CCTCAAAACTTT-CAAAAATTCCATTTTTGACCTCCGAACT
* * * * *
1921 TCCAAAAATTACATCTTTGACCCCGAAACTTCCAAAAATTCCATTTTT-ACCTCCGAACT
1 TCCAAAAATTCCAT-TTTTACCTCAAAACTTTCAAAAATTCCATTTTTGACCTCCGAACT
* *
1980 TCCAAAAATTCCATTTTTGACCTCAAAACTTTCAAAAATTACC-CTTTT-ACGCT-CGGA-T
1 TCCAAAAATTCCATTTTT-ACCTCAAAACTTTCAAAAATT-CCATTTTTGAC-CTCCGAACT
* * * * * *
2038 GTCCAAAAACTCCATTTTCGACCTCAAAACTCTC-GAAATTACC-CTTTT-ACCCCCGAA-T
1 -TCCAAAAATTCCATTTT-TACCTCAAAACTTTCAAAAATT-CCATTTTTGACCTCCGAACT
*
2096 GTCAAAAAATTCCATTTTTA
1 -TCCAAAAATTCCATTTTTA
2116 ACCCTAAATT
Statistics
Matches: 264, Mismatches: 32, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
57 25 0.09
58 64 0.24
59 168 0.64
60 7 0.03
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTACCTCAAAACTTTCAAAAATTCCATTTTTGACCTCCGAACT
Found at i:2090 original size:146 final size:147
Alignment explanation
Indices: 1773--2120 Score: 390
Period size: 146 Copynumber: 2.4 Consensus size: 147
1763 TACCTTTTAC
* ** * *
1773 CTTCCAAAAATTCCATTTTTGA-CCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTAC
1 CTTCCAAAAATTACACCTTTGACCCCCGAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTAC
* * * **
1837 AAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAATT
66 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCACTTTTACCCTCGAATGTCCAAAAAC
* *
1902 TCCATTTTTGACCCCAA
131 TCCATTTTCGACCCAAA
* *
1919 CTTCCAAAAATTACATCTTTGA-CCCCGAAACTTCCAAAAATTCCATTTTTACCTCC-GAACTTC
1 CTTCCAAAAATTACACCTTTGACCCCCGAAACTTCCAAAAATTCCATTTTTACC-CCTGAACTTA
* * *
1982 CAAAAATTCCATTTTTGACCTCAAAACTTTCAAAAATTACC-CTTTTACGCTCGGATGTCCAAAA
65 CAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATT-CCACTTTTACCCTCGAATGTCCAAAA
2046 ACTCCATTTTCGACCTCAAAA
129 ACTCCATTTTCGACC-C-AAA
* * * *
2067 C-TCTC-GAAATTAC-CCTTTTACCCCCG-AA-TGTCAAAAAATTCCATTTTTAACCCT
1 CTTC-CAAAAATTACACCTTTGACCCCCGAAACT-TCCAAAAATTCCATTTTTACCCCT
2121 AAATTTTCCC
Statistics
Matches: 174, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
145 3 0.02
146 148 0.85
147 19 0.11
148 4 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (147 bp):
CTTCCAAAAATTACACCTTTGACCCCCGAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTAC
AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCACTTTTACCCTCGAATGTCCAAAAAC
TCCATTTTCGACCCAAA
Found at i:6379 original size:22 final size:21
Alignment explanation
Indices: 6338--6380 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
6328 CCTAGACAAA
*
6338 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
6359 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
6381 GCAAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Found at i:14245 original size:11 final size:11
Alignment explanation
Indices: 14231--14278 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
14221 TATAAAATTT
14231 AATTTATTTTA
1 AATTTATTTTA
*
14242 AATTTAAATTTA
1 AATTT-ATTTTA
* *
14254 AATTAAGTTTA
1 AATTTATTTTA
14265 AATTTACTTTTA
1 AATTTA-TTTTA
14277 AA
1 AA
14279 ATTAAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 15 0.50
12 15 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:14249 original size:6 final size:6
Alignment explanation
Indices: 14225--14301 Score: 63
Period size: 6 Copynumber: 13.5 Consensus size: 6
14215 ATTTATTATA
* *
14225 AAATTT -AATTT -ATTTT AAATTT AAATTT AAA-TT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
** * * *
14270 ACTTTT AAAATT AAAATT -ATTTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAA
14302 AGTCTCATTA
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
5 16 0.29
6 40 0.71
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:14249 original size:23 final size:24
Alignment explanation
Indices: 14223--14270 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
14213 AAATTTATTA
* *
14223 TAAAATTT-AATTTATTTTAAATT
1 TAAAATTTAAATTAAGTTTAAATT
14246 T-AAATTTAAATTAAGTTTAAATT
1 TAAAATTTAAATTAAGTTTAAATT
14269 TA
1 TA
14271 CTTTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TAAAATTTAAATTAAGTTTAAATT
Found at i:14276 original size:23 final size:24
Alignment explanation
Indices: 14238--14302 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
14228 TTTAATTTAT
14238 TTTAAATTTAAATTT-AAATTAAG
1 TTTAAATTTAAATTTAAAATTAAG
** *
14261 TTTAAATTTACTTTTAAAATTAAA
1 TTTAAATTTAAATTTAAAATTAAG
* *
14285 ATT-ATTTTAAATTTAAAA
1 TTTAAATTTAAATTTAAAA
14303 GTCTCATTAC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 25 0.74
24 9 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTAAATTTAAATTTAAAATTAAG
Found at i:14302 original size:17 final size:17
Alignment explanation
Indices: 14210--14301 Score: 105
Period size: 17 Copynumber: 5.4 Consensus size: 17
14200 TAAATTCCTT
*
14210 TTTAAATTTATTATAAAA
1 TTTAAATTTATT-TTAAA
14228 TTT-AATTTATTTTAAA
1 TTTAAATTTATTTTAAA
** *
14244 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
14261 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
14279 ATTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
14296 TTTAAA
1 TTTAAA
14302 AGTCTCATTA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
16 7 0.11
17 40 0.65
18 15 0.24
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Done.