Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005134.1 Kokia drynarioides strain JFW-HI SEQ_118970, 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: 4527
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:653 original size:59 final size:58
Alignment explanation
Indices: 590--869 Score: 343
Period size: 59 Copynumber: 4.8 Consensus size: 58
580 CGAACCTTTT
*
590 AAAAATTACCA-TTTTACCCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCC
1 AAAAA-TACCATTTTTA-CCCCGAACCTTCTAAAAATTACCATTTTACCCTCAAACTTCC
* * *
649 AAAAATCCCATTTTTTACGCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCC
1 AAAAATACCA-TTTTTACCCCGAACCTTCTAAAAATTACCATTTTACCCTCAAACTTCC
** *
708 AAAAATACCATTTTTGACCTTGAACATTCTAAAAATTACCATTTTATCCC-CAAACTTCC
1 AAAAATACCATTTTT-ACCCCGAACCTTCTAAAAATTACCATTTTA-CCCTCAAACTTCC
* *
767 AAAAATCCCATTTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCC
1 AAAAATACCATTTTT-ACCCCGAACCTTCTAAAAATTACCATTTTACCCTCAAACTTCC
* * * *
826 AAAAAT-CTTATTTTTGACTCCGAACCTTC-CAAAACTACCATTTT
1 AAAAATAC-CATTTTT-ACCCCGAACCTTCTAAAAATTACCATTTT
870 GCCCCCGTGC
Statistics
Matches: 197, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
58 26 0.13
59 163 0.83
60 8 0.04
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (58 bp):
AAAAATACCATTTTTACCCCGAACCTTCTAAAAATTACCATTTTACCCTCAAACTTCC
Found at i:656 original size:89 final size:89
Alignment explanation
Indices: 536--876 Score: 367
Period size: 89 Copynumber: 3.9 Consensus size: 89
526 TTTTCGAAAT
**
536 TTACCATTTTACCC-CTAAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTTTAAAAATTACC
1 TTACCATTTTACCCTC-AAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCCAAAAATTACC
600 ATTTTACCCCCGAACCTTCTAAAAA
65 ATTTTACCCCCGAACCTTCTAAAAA
* * * *
625 TTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACGCCGAACCTTCTAAAAATTACCA
1 TTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCCAAAAATTACCA
* *
690 TTTTACCCTCGAA-CTTCCAAAAA
66 TTTTACCCCCGAACCTTCTAAAAA
** * * * *
713 -TACCATTTTTGA-CCTTGAACATTCTAAAAATTACCA-TTTT-A-TCCCCAAACTTCCAAAAA-
1 TTACCA-TTTT-ACCCTCAAAC-TTCCAAAAA-TCCCATTTTTGACT-CCGAACCTTCCAAAAAT
* *
772 TCCCATTTTTAACCCCGAACCTTCTAAAAA
61 TACCA-TTTTACCCCCGAACCTTCTAAAAA
* ** *
802 TTACCATTTTACCCCCAAACTTCCAAAAATCTTATTTTTGACTCCGAACCTTCC-AAAACTACCA
1 TTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCCAAAAATTACCA
*
866 TTTTGCCCCCG
66 TTTTACCCCCG
877 TGCATCCGAA
Statistics
Matches: 209, Mismatches: 29, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
87 11 0.05
88 71 0.34
89 116 0.56
90 11 0.05
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (89 bp):
TTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCCAAAAATTACCA
TTTTACCCCCGAACCTTCTAAAAA
Found at i:869 original size:30 final size:29
Alignment explanation
Indices: 537--869 Score: 263
Period size: 30 Copynumber: 11.3 Consensus size: 29
527 TTTCGAAATT
* *
537 TACCA-TTTTACCCCTAAACTTCCAAAAA
1 TACCATTTTTACCCCGAACCTTCCAAAAA
* * **
565 TCCCATTTTTGACTCCGAACCTTTTAAAAA
1 TACCATTTTT-ACCCCGAACCTTCCAAAAA
*
595 TTACCA-TTTTACCCCCGAACCTTCTAAAAA
1 -TACCATTTTTA-CCCCGAACCTTCCAAAAA
625 TTACCA-TTTTACCCTCGAA-CTTCCAAAAA
1 -TACCATTTTTACCC-CGAACCTTCCAAAAA
* * *
654 TCCCATTTTTTACGCCGAACCTTCTAAAAA
1 TACCA-TTTTTACCCCGAACCTTCCAAAAA
684 TTACCA-TTTTACCCTCGAA-CTTCCAAAAA
1 -TACCATTTTTACCC-CGAACCTTCCAAAAA
** * *
713 TACCATTTTTGACCTTGAACATTCTAAAAA
1 TACCATTTTT-ACCCCGAACCTTCCAAAAA
*
743 TTACCA-TTTTATCCCC-AAACTTCCAAAAA
1 -TACCATTTTTA-CCCCGAACCTTCCAAAAA
* *
772 TCCCATTTTTAACCCCGAACCTTCTAAAAA
1 TACCATTTTT-ACCCCGAACCTTCCAAAAA
* *
802 TTACCA-TTTTACCCCCAAACTTCCAAAAA
1 -TACCATTTTTACCCCGAACCTTCCAAAAA
* * *
831 T-CTTATTTTTGACTCCGAACCTTCCAAAAC
1 TAC-CATTTTT-ACCCCGAACCTTCCAAAAA
861 TACCATTTT
1 TACCATTTT
870 GCCCCCGTGC
Statistics
Matches: 244, Mismatches: 38, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.00
28 19 0.08
29 83 0.34
30 123 0.50
31 18 0.07
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
TACCATTTTTACCCCGAACCTTCCAAAAA
Found at i:889 original size:59 final size:59
Alignment explanation
Indices: 609--908 Score: 284
Period size: 59 Copynumber: 5.1 Consensus size: 59
599 CATTTTACCC
* * * * * * *
609 CCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACG
1 CCGAACCTTCTAAAAACTACCATTTTACCCCCAAACATCCAAAAATCTCATTTTTGACT
* * * *
668 CCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATAC-CATTTTTGAC-
1 CCGAACCTTCTAAAAACTACCATTTTACCCCCAAACATCCAAAAAT-CTCATTTTTGACT
* * * * * * * *
726 CTTGAACATTCTAAAAATTACCATTTTATCCCCAAACTTCCAAAAATCCCATTTTTAACC
1 C-CGAACCTTCTAAAAACTACCATTTTACCCCCAAACATCCAAAAATCTCATTTTTGACT
* * *
786 CCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTTATTTTTGACT
1 CCGAACCTTCTAAAAACTACCATTTTACCCCCAAACATCCAAAAATCTCATTTTTGACT
* * ***
845 CCGAACCTTC-CAAAACTACCATTTTGCCCCCGTGCATCCGAAAAAGTCTCA-TTTTGTACT
1 CCGAACCTTCTAAAAACTACCATTTTACCCCCAAACATCC-AAAAA-TCTCATTTTTG-ACT
905 CCGA
1 CCGA
909 TTACATCATT
Statistics
Matches: 212, Mismatches: 22, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
58 24 0.11
59 175 0.83
60 13 0.06
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (59 bp):
CCGAACCTTCTAAAAACTACCATTTTACCCCCAAACATCCAAAAATCTCATTTTTGACT
Found at i:889 original size:118 final size:117
Alignment explanation
Indices: 590--876 Score: 380
Period size: 118 Copynumber: 2.4 Consensus size: 117
580 CGAACCTTTT
*** *
590 AAAAATTACCATTTTACCCCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAAT
1 AAAAA-TACCATTTTTGACCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT
* * * *
655 CCCATTTTTTACGCCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCC
65 CCCATTTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCC
* * * *
708 AAAAATACCATTTTTGACCTTGAACATTCTAAAAATTACCATTTTATCCCCAAACTTCCAAAAAT
1 AAAAATACCATTTTTGACC-CGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT
773 CCCATTTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCC
65 CCCATTTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCC
* * * *
826 AAAAAT-CTTATTTTTGACTCCGAACCTTC-CAAAACTACCATTTTGCCCCCG
1 AAAAATAC-CATTTTTGAC-CCGAACCTTCTAAAAATTACCATTTTACCCCCG
877 TGCATCCGAA
Statistics
Matches: 146, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
117 29 0.20
118 116 0.79
119 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (117 bp):
AAAAATACCATTTTTGACCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATC
CCATTTTTAACCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCC
Done.