Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003220.1 Kokia drynarioides strain JFW-HI SEQ_115849, 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: 3443
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Found at i:268 original size:49 final size:49
Alignment explanation
Indices: 126--895 Score: 408
Period size: 49 Copynumber: 15.7 Consensus size: 49
116 TAAGACTCGT
* * * *
126 CGTTGCGGCCTCAACCTTTCCCATCATAT-TTCATGGTA-TCAGATTCGT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACT-GGGTTCGC
** * * * *
174 TATTACGGCCTCAATCCTTGT--CATC-CATCTTTTAAGGT-GTCGGGTTCGC
1 CGTTGCGGCCTCAA-CCTT-TCCCATCACATC-TTCATGGTACT-GGGTTCGC
* * * *
223 CATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTTGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACTGGGTTCGC
* * * * * * ** * **
272 CATTGCTGCCTCAACTTTTTCAATCGCATCTTCATGGTACCAGATTTAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACTGGGTTCGC
* *
321 CGTTGCGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTA-TCGGGTTTGC
1 CGTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-ATGGTACT-GGGTTCGC
* * * * * *
371 CGTTGTGGCCTCAACCTTTCCCTTTAAATCTTCATGGTA-TCGAGTTCGT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACT-GGGTTCGC
* * * ** *
420 CATTACGGTCTCAACCTTTCCCATCACAT-TTCATGGTA-TCGAATTCAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACT-GGGTTCGC
* * * *
468 CGTTGCGGCCTTAATCTTTCCCATCACATCTTTTAAGGTAC-GAGGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATC-TTCATGGTACTG-GGTTCGC
* * * * *
518 CGTTGTGGCCTCAATCTTTCCCTTCAAATCTTCATGG-AATCGGGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACT-GGGTTCGC
* * * * * *
567 CATTACGGCCTCAACATTTCCCATCGCATCTTCATGGTACCGGATTCGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACTGGGTTCGC
* * * * * *
616 CGTTGCGACCTTAATCC-TTCCCATCACCTATTCTAAGGTACCT-GGTTCAC
1 CGTTGCGGCCTCAA-CCTTTCCCATCACATCTTC-ATGGTA-CTGGGTTCGC
* * * * *
666 CGTTACAGCCTCAACCTTTTCCCTTTAAATCTTCATGGTA-TCGGGTTCGC
1 CGTTGCGGCCTCAACC-TTTCCCATCACATCTTCATGGTACT-GGGTTCGC
* * ** ** * *
716 CATTGCGACCTCAATATTT-CCATCACAT-TTCATGGTACCAGATTCAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACTGGGTTCGC
* * * * * * **
763 CGTTACGGCCTCAATCTTTTCCATCACATATTCTAAGATACCAGGTTCGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTC-ATGGTACTGGGTTCGC
* * * * * * *
813 CATTACGGCCTCAACCTTTCCCATCACAT-TTAATGATACCGGATTCGT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACTGGGTTCGC
* * * *
861 CGTTGCGGCCTTAGCCTTTCCCTTCAAATCTTCAT
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTCAT
896 ATTTCCTCGG
Statistics
Matches: 546, Mismatches: 144, Indels: 63
0.73 0.19 0.08
Matches are distributed among these distances:
47 32 0.06
48 111 0.20
49 230 0.42
50 161 0.29
51 12 0.02
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (49 bp):
CGTTGCGGCCTCAACCTTTCCCATCACATCTTCATGGTACTGGGTTCGC
Found at i:704 original size:100 final size:97
Alignment explanation
Indices: 594--784 Score: 247
Period size: 97 Copynumber: 1.9 Consensus size: 97
584 TTCCCATCGC
* * * * *
594 ATCTTCATGGTACCGGATTCGCCGTTGCGACCTTAATCCTTCCCATCACCTATTCTAAGGTACCT
1 ATCTTCATGGTACCGGATTCGCCATTGCGACCTCAAT-ATTCCCATCACAT-TTC-AAGGTACCA
*
659 GGTTCACCGTTACAGCCTCAACCTTTTCCCTTTAA
63 GATTCACCGTTACAGCCTCAACCTTTTCCCTTTAA
* * * *
694 ATCTTCATGGTATCGGGTTCGCCATTGCGACCTCAATATTTCCATCACATTTCATGGTACCAGAT
1 ATCTTCATGGTACCGGATTCGCCATTGCGACCTCAATATTCCCATCACATTTCAAGGTACCAGAT
* *
759 TCACCGTTACGGCCTCAATCTTTTCC
66 TCACCGTTACAGCCTCAACCTTTTCC
785 ATCACATATT
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
97 33 0.42
98 3 0.04
99 10 0.13
100 33 0.42
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.34
Consensus pattern (97 bp):
ATCTTCATGGTACCGGATTCGCCATTGCGACCTCAATATTCCCATCACATTTCAAGGTACCAGAT
TCACCGTTACAGCCTCAACCTTTTCCCTTTAA
Found at i:741 original size:295 final size:295
Alignment explanation
Indices: 134--834 Score: 872
Period size: 295 Copynumber: 2.4 Consensus size: 295
124 GTCGTTGCGG
* * * **** * **
134 CCTCAACCTTTCCCATCATATTTCATGGTATCAGATTCGTTATTACGGCCTCAATCCTTGTCATC
1 CCTCAACATTTCCCATCACATTTCATGGTACCAGATTCACCGTTACGGCCTCAATCTTTCCCATC
* *
199 -CATCTTTTAAGGTGTCG-GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTA
66 ACATCTTTTAAGGT-ACGAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGAA
* * * * * *
262 CTGGGTTTGCCATTGCTGCCTCAACTTTTTCAATCGCATCTTCATGGTACCAGATTTACCGTTGC
130 CTGGGTTCGCCATTACGGCCTCAACATTTCCAATCGCATCTTCATGGTACCAGATTCACCGTTGC
* * * ** ***
327 GGCCTCAATCCTTCCCATCACATCTTCTAAGGTATCGGGTTTGCCGTTGTGGCCTCAACCTTTCC
195 GACCTCAATCCTTCCCATCACATATTCTAAGGTACCGGGTTCACCGTTACAGCCTCAACCTTTCC
* *
392 CTTTAAATCTTCATGGTATCGAGTTCGTCATTACGG
260 CTTTAAATCTTCATGGTATCGAGTTCGCCATTACGA
* * * * *
428 TCTCAACCTTTCCCATCACATTTCATGGTATC-GAATTCACCGTTGCGGCCTTAATCTTTCCCAT
1 CCTCAACATTTCCCATCACATTTCATGGTACCAG-ATTCACCGTTACGGCCTCAATCTTTCCCAT
* * *
492 CACATCTTTTAAGGTACGAGGTTCGCCGTTGTGGCCTCAATCTTTCCCTTCAAATCTTCATGGAA
65 CACATCTTTTAAGGTACGAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGAA
* * *
557 -TCGGGTTCGCCATTACGGCCTCAACATTTCCCATCGCATCTTCATGGTACCGGATTCGCCGTTG
130 CT-GGGTTCGCCATTACGGCCTCAACATTTCCAATCGCATCTTCATGGTACCAGATTCACCGTTG
* * *
621 CGACCTTAATCCTTCCCATCACCTATTCTAAGGTACCTGGTTCACCGTTACAGCCTCAACCTTTT
194 CGACCTCAATCCTTCCCATCACATATTCTAAGGTACCGGGTTCACCGTTACAGCCTCAACC-TTT
* *
686 CCCTTTAAATCTTCATGGTATCGGGTTCGCCATTGCGA
258 CCCTTTAAATCTTCATGGTATCGAGTTCGCCATTACGA
* *
724 CCTCAATATTT-CCATCACATTTCATGGTACCAGATTCACCGTTACGGCCTCAATCTTTTCCATC
1 CCTCAACATTTCCCATCACATTTCATGGTACCAGATTCACCGTTACGGCCTCAATCTTTCCCATC
* * * * *
788 ACATATTCTAAGATACCAGGTTCGCCATTACGGCCTCAACCTTTCCC
66 ACATCTTTTAAGGTACGAGGTTCGCCATTGCGGCCTCAACCTTTCCC
835 ATCACATTTA
Statistics
Matches: 346, Mismatches: 55, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
293 1 0.00
294 55 0.16
295 244 0.71
296 46 0.13
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.34
Consensus pattern (295 bp):
CCTCAACATTTCCCATCACATTTCATGGTACCAGATTCACCGTTACGGCCTCAATCTTTCCCATC
ACATCTTTTAAGGTACGAGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGAAC
TGGGTTCGCCATTACGGCCTCAACATTTCCAATCGCATCTTCATGGTACCAGATTCACCGTTGCG
ACCTCAATCCTTCCCATCACATATTCTAAGGTACCGGGTTCACCGTTACAGCCTCAACCTTTCCC
TTTAAATCTTCATGGTATCGAGTTCGCCATTACGA
Found at i:895 original size:147 final size:147
Alignment explanation
Indices: 128--834 Score: 774
Period size: 147 Copynumber: 4.8 Consensus size: 147
118 AGACTCGTCG
* * **** * *
128 TTGCGGCCTCAACCTTTCCCATCATATTTCATGGTATCAGATTCGTTATTACGGCCTCAATCCTT
1 TTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCAGATTCACCGTTGCGGCCTCAATCTTT
** * ** * *
193 GTCATC-CATCTTTTAAGGTGTCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCAAATCTTCA
66 CCCATCACATCTTCTAAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCA
*
257 TGGTA-CTGGGTTTGCCA
131 TGGTATC-GGGTTCGCCA
* * * * * * *
274 TTGCTGCCTCAACTTTTTCAATCGCATCTTCATGGTACCAGATTTACCGTTGCGGCCTCAATCCT
1 TTGCGGCCTCAACCTTTCCCATCACAT-TTCATGGTACCAGATTCACCGTTGCGGCCTCAATCTT
* * * * *
339 TCCCATCACATCTTCTAAGGTATCGGGTTTGCCGTTGTGGCCTCAACCTTTCCCTTTAAATCTTC
65 TCCCATCACATCTTCTAAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTC
* *
404 ATGGTATCGAGTTCGTCA
130 ATGGTATCGGGTTCGCCA
* * * *
422 TTACGGTCTCAACCTTTCCCATCACATTTCATGGTATC-GAATTCACCGTTGCGGCCTTAATCTT
1 TTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCAG-ATTCACCGTTGCGGCCTCAATCTT
* * * *
486 TCCCATCACATCTTTTAAGGTACGAGGTTCGCCGTTGTGGCCTCAATCTTTCCCTTCAAATCTTC
65 TCCCATCACATCTTCTAAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTC
*
551 ATGGAATCGGGTTCGCCA
130 ATGGTATCGGGTTCGCCA
* * * * * * * *
569 TTACGGCCTCAACATTTCCCATCGCATCTTCATGGTACCGGATTCGCCGTTGCGACCTTAATCCT
1 TTGCGGCCTCAACCTTTCCCATCACAT-TTCATGGTACCAGATTCACCGTTGCGGCCTCAATCTT
* * * * * * *
634 TCCCATCACCTATTCTAAGGTACCTGGTTCACCGTTACAGCCTCAACCTTTTCCCTTTAAATCTT
65 TCCCATCACATCTTCTAAGGTACCAGGTTCGCCGTTGCGGCCTCAACC-TTTCCCTTCAAATCTT
699 CATGGTATCGGGTTCGCCA
129 CATGGTATCGGGTTCGCCA
* ** *
718 TTGCGACCTCAATATTT-CCATCACATTTCATGGTACCAGATTCACCGTTACGGCCTCAATCTTT
1 TTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCAGATTCACCGTTGCGGCCTCAATCTTT
* * * * *
782 TCCATCACATATTCTAAGATACCAGGTTCGCCATTACGGCCTCAACCTTTCCC
66 CCCATCACATCTTCTAAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCC
835 ATCACATTTA
Statistics
Matches: 473, Mismatches: 81, Indels: 14
0.83 0.14 0.02
Matches are distributed among these distances:
146 28 0.06
147 235 0.50
148 161 0.34
149 49 0.10
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (147 bp):
TTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCAGATTCACCGTTGCGGCCTCAATCTTT
CCCATCACATCTTCTAAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCA
TGGTATCGGGTTCGCCA
Done.