Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009579.1 Kokia drynarioides strain JFW-HI SEQ_124293, 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: 18265
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:301 original size:29 final size:27
Alignment explanation
Indices: 267--538 Score: 107
Period size: 29 Copynumber: 9.4 Consensus size: 27
257 TCCCTGAACC
267 TTCCAAAAATTATCGTTTTACCCTCGAA
1 TTCCAAAAATTATCGTTTTACCC-CGAA
*
295 TTCCCAAAAATCCCAT--TTTTAACCCCGAA
1 TT-CCAAAAAT--TATCGTTTT-ACCCCGAA
* *
324 GCTTCC-AAAATTACCGTTTTACCCCTAAA
1 --TTCCAAAAATTATCGTTTTACCCC-GAA
*
353 TTCCCAAAAATCCCAT--TTTTGACCCCGAA
1 TT-CCAAAAAT--TATCGTTTT-ACCCCGAA
* *
382 GCTTCC-AAAATTACCGTTTTACCCTCAAA
1 --TTCCAAAAATTATCGTTTTACCC-CGAA
*
411 TTCCCAAAAATCCCAT--TTTTGACCCCGAA
1 TT-CCAAAAAT--TATCGTTTT-ACCCCGAA
*
440 GCTTCCAAAAATTACCGTTTTACCCCTGAA
1 --TTCCAAAAATTATCGTTTTACCCC-GAA
470 TTTCCAAAAATCTCAT--TTTTAACCCCGAA
1 -TTCCAAAAAT-T-ATCGTTTT-ACCCCGAA
* *
499 GCTT-CTAAAATTACCGTTTTACCCTCGAA
1 --TTCCAAAAATTATCGTTTTACCC-CGAA
528 TTCCCAAAAAT
1 TT-CCAAAAAT
539 CCCATTTTTT
Statistics
Matches: 185, Mismatches: 21, Indels: 75
0.66 0.07 0.27
Matches are distributed among these distances:
27 9 0.05
28 21 0.11
29 104 0.56
30 40 0.22
31 11 0.06
ACGTcount: A:0.32, C:0.31, G:0.07, T:0.31
Consensus pattern (27 bp):
TTCCAAAAATTATCGTTTTACCCCGAA
Found at i:495 original size:117 final size:117
Alignment explanation
Indices: 266--664 Score: 572
Period size: 117 Copynumber: 3.4 Consensus size: 117
256 GTCCCTGAAC
* *
266 CTTCCAAAAATTATCGTTTTACCCTCGAATTCCCAAAAATCCCATTTTTAACCCCGAAGCTTCCA
1 CTTCCAAAAATTACCGTTTTACCCTCGAATTCCCAAAAATCCCATTTTTGACCCCGAAGCTTCCA
* * *
331 AAATTACCGTTTTACCCCTAAATTCCCAAAAATCCCATTTTTGACCCCGAAG
66 AAATTACCGTTTTACCCCTGAATTTCCAAAAATCCCATTTTTAACCCCGAAG
*
383 CTTCC-AAAATTACCGTTTTACCCTCAAATTCCCAAAAATCCCATTTTTGACCCCGAAGCTTCCA
1 CTTCCAAAAATTACCGTTTTACCCTCGAATTCCCAAAAATCCCATTTTTGACCCCGAAGCTTCC-
*
447 AAAATTACCGTTTTACCCCTGAATTTCCAAAAATCTCATTTTTAACCCCGAAG
65 AAAATTACCGTTTTACCCCTGAATTTCCAAAAATCCCATTTTTAACCCCGAAG
* *
500 CTT-CTAAAATTACCGTTTTACCCTCGAATTCCCAAAAATCCCATTTTTTGACCTCGAAGCTTCC
1 CTTCCAAAAATTACCGTTTTACCCTCGAATTCCCAAAAATCCCA-TTTTTGACCCCGAAGCTTCC
* * * * * *
564 AAAATTACCGTCTTACCCCCGGACTTCCAAAAATCCCATTTTAAACCCCGAAT
65 AAAATTACCGTTTTACCCCTGAATTTCCAAAAATCCCATTTTTAACCCCGAAG
* * *
617 CTTCCAAAAATTACCATTTTATCCC-CGAACTT-CCAAAATTACCATTTT
1 CTTCCAAAAATTACCGTTTTA-CCCTCGAA-TTCCCAAAAATCCCATTTT
665 ACCCTCAAGT
Statistics
Matches: 256, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
116 56 0.22
117 147 0.57
118 48 0.19
119 5 0.02
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (117 bp):
CTTCCAAAAATTACCGTTTTACCCTCGAATTCCCAAAAATCCCATTTTTGACCCCGAAGCTTCCA
AAATTACCGTTTTACCCCTGAATTTCCAAAAATCCCATTTTTAACCCCGAAG
Found at i:665 original size:59 final size:57
Alignment explanation
Indices: 266--664 Score: 514
Period size: 58 Copynumber: 6.8 Consensus size: 57
256 GTCCCTGAAC
*
266 CTTCCAAAAATTATCGTTTTACCCTCGAATTCCCAAAAATCCCATTTTTAACCCCGAAG
1 CTTCC-AAAATTACCGTTTTACCC-CGAATTCCCAAAAATCCCATTTTTAACCCCGAAG
* *
325 CTTCCAAAATTACCGTTTTACCCCTAAATTCCCAAAAATCCCATTTTTGACCCCGAAG
1 CTTCCAAAATTACCGTTTTACCCC-GAATTCCCAAAAATCCCATTTTTAACCCCGAAG
* *
383 CTTCCAAAATTACCGTTTTACCCTCAAATTCCCAAAAATCCCATTTTTGACCCCGAAG
1 CTTCCAAAATTACCGTTTTACCC-CGAATTCCCAAAAATCCCATTTTTAACCCCGAAG
* *
441 CTTCCAAAAATTACCGTTTTACCCCTGAATTTCCAAAAATCTCATTTTTAACCCCGAAG
1 CTTCC-AAAATTACCGTTTTACCCC-GAATTCCCAAAAATCCCATTTTTAACCCCGAAG
* * *
500 CTTCTAAAATTACCGTTTTACCCTCGAATTCCCAAAAATCCCATTTTTTGACCTCGAAG
1 CTTCCAAAATTACCGTTTTACCC-CGAATTCCCAAAAATCCCA-TTTTTAACCCCGAAG
* * * *
559 CTTCCAAAATTACCGTCTTACCCCCGGACTT-CCAAAAATCCCATTTTAAACCCCGAAT
1 CTTCCAAAATTACCGTTTTA-CCCC-GAATTCCCAAAAATCCCATTTTTAACCCCGAAG
* * *
617 CTTCCAAAAATTACCATTTTATCCCCGAACTT-CCAAAATTACCATTTT
1 CTTCC-AAAATTACCGTTTTA-CCCCGAA-TTCCCAAAAATCCCATTTT
665 ACCCTCAAGT
Statistics
Matches: 305, Mismatches: 25, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
57 1 0.00
58 162 0.53
59 135 0.44
60 7 0.02
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (57 bp):
CTTCCAAAATTACCGTTTTACCCCGAATTCCCAAAAATCCCATTTTTAACCCCGAAG
Found at i:2759 original size:21 final size:21
Alignment explanation
Indices: 2735--2777 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2725 TTTTTTCACG
2735 TAATTATATTATTATAATATT
1 TAATTATATTATTATAATATT
* * *
2756 TAATTTTATTGTTATTATATT
1 TAATTATATTATTATAATATT
2777 T
1 T
2778 TTACATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TAATTATATTATTATAATATT
Found at i:5868 original size:22 final size:24
Alignment explanation
Indices: 5838--5884 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
5828 TCTATGATAA
5838 TAAATAGTTAAAAATAT-TTTTTT
1 TAAATAGTTAAAAATATATTTTTT
*
5861 TAAA-AGTTAAAAATTTATTTTTT
1 TAAATAGTTAAAAATATATTTTTT
5884 T
1 T
5885 GGTGAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TAAATAGTTAAAAATATATTTTTT
Found at i:6284 original size:46 final size:46
Alignment explanation
Indices: 6101--6284 Score: 280
Period size: 46 Copynumber: 4.0 Consensus size: 46
6091 AATAGACTAG
** * * * *
6101 AACAAAATACAAACACATTTAAAAG-TTCATTGTGGTTATTAACATG
1 AACAAAATGTAAACACGTTTAAAAGCTT-AATGTGGATATTAACATT
6147 AACAAAATGTAAACACGTTTAAAAGCTTAATGTGGATATTAACATT
1 AACAAAATGTAAACACGTTTAAAAGCTTAATGTGGATATTAACATT
*
6193 AACAAAATGTAATCACGTTTAAAAGCTTAATGTGGATATTAACATT
1 AACAAAATGTAAACACGTTTAAAAGCTTAATGTGGATATTAACATT
*
6239 AACAAAAAGTAAACACGTTTAAAAGCTTAATGTGGATATTAACATT
1 AACAAAATGTAAACACGTTTAAAAGCTTAATGTGGATATTAACATT
6285 TAAGGATTGA
Statistics
Matches: 128, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
46 126 0.98
47 2 0.02
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (46 bp):
AACAAAATGTAAACACGTTTAAAAGCTTAATGTGGATATTAACATT
Done.