Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005202.1 Kokia drynarioides strain JFW-HI SEQ_119068, 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: 1729
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Found at i:655 original size:30 final size:29
Alignment explanation
Indices: 590--906 Score: 254
Period size: 30 Copynumber: 10.8 Consensus size: 29
580 GGAGGTCCTT
*
590 AAACTTCCAAAAATTACCA-TTTTACCTCC-
1 AAACTTCCAAAAA-TCCCATTTTTACC-CCG
*
619 AAACTTCCAAAGATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
* *
649 AAACTTCCAAAAATTACCA-TTTTACACTCG
1 AAACTTCCAAAAA-TCCCATTTTTAC-CCCG
* * **
679 -AACTCCCGAAAATCCCATTTTTGACCTTG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
*
708 AAACTTCCAAAAATTACCA-TTTTACCCTCG
1 AAACTTCCAAAAA-TCCCATTTTTACCC-CG
* *
738 -AACTTCTAAAAATCCCATTTTTAACCCG
1 AAACTTCCAAAAATCCCATTTTTACCCCG
* * **
766 AAAACTTCCCAAAATTCCATTTTTACCCTT
1 -AAACTTCCAAAAATCCCATTTTTACCCCG
* * *
796 AAACTTCTAAAAATCCCACTTTTGACCCCA
1 AAACTTCCAAAAATCCCA-TTTTTACCCCG
*
826 AAACTTCCAAAAAAT-CCACTTTTACCCTCG
1 AAACTTCC-AAAAATCCCATTTTTACCC-CG
* * *
856 -AACTTTCAAAAATCCCATTTTTAATCCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
*
885 AAACTTCTAAAAATCCCATTTT
1 AAACTTCCAAAAATCCCATTTT
907 CAACCTCAAA
Statistics
Matches: 230, Mismatches: 39, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
28 20 0.09
29 94 0.41
30 102 0.44
31 14 0.06
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCG
Found at i:662 original size:59 final size:59
Alignment explanation
Indices: 590--906 Score: 365
Period size: 59 Copynumber: 5.4 Consensus size: 59
580 GGAGGTCCTT
* *
590 AAACTTCCAAAAATTACCATTTTA-CCTCCAAACTTCCAAAGATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTACCATTTTACCCT-CGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * **
649 AAACTTCCAAAAATTACCATTTTACACTCGAACTCCCGAAAATCCCATTTTTGACCTTG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
708 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTT-AACCCG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* ** * * *
766 AAAACTTCCCAAAATT-CCATTTTTACCCTTAAACTTCTAAAAATCCCACTTTTGACCCCA
1 -AAACTTCCAAAAATTACCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * *
826 AAACTTCCAAAAAAT-CCACTTTTACCCTCGAACTTTCAAAAATCCCATTTTTAATCCCA
1 AAACTTCCAAAAATTACCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
885 AAACTTCTAAAAA-TCCCATTTT
1 AAACTTCCAAAAATTACCATTTT
907 CAACCTCAAA
Statistics
Matches: 222, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
58 11 0.05
59 205 0.92
60 6 0.03
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:927 original size:29 final size:30
Alignment explanation
Indices: 863--927 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
853 TCGAACTTTC
* *
863 AAAAATCCCATTTTTAATCCCAAAACTTCT
1 AAAAATCCCATTTTCAATCCCAAAACTCCT
893 AAAAATCCCATTTTCAA-CCTCAAAAC-CCT
1 AAAAATCCCATTTTCAATCC-CAAAACTCCT
*
922 CAAAAT
1 AAAAAT
928 TACCCTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.28
Consensus pattern (30 bp):
AAAAATCCCATTTTCAATCCCAAAACTCCT
Found at i:1001 original size:59 final size:59
Alignment explanation
Indices: 890--1002 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
880 TCCCAAAACT
*
890 TCTAAAAATCCCATTTTCAACCTCAAAACCCTCAAAATTACCCTTTTACCCCTCGAATG
1 TCTAAAAATCCCATTTTCAACCTCAAAACCCTCAAAATTACCATTTTACCCCTCGAATG
* * **
949 TCTAAAAATTCCATTTTTAACCTCAAATTTTCC-CAAAATTACCATTTT-CCCCTC
1 TCTAAAAATCCCATTTTCAACCTCAAA--ACCCTCAAAATTACCATTTTACCCCTC
1003 TCCGGGTATC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 31 0.66
60 14 0.30
61 2 0.04
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.34
Consensus pattern (59 bp):
TCTAAAAATCCCATTTTCAACCTCAAAACCCTCAAAATTACCATTTTACCCCTCGAATG
Done.