Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011878.1 Kokia drynarioides strain JFW-HI SEQ_126875, 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: 3528
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Found at i:486 original size:3 final size:3
Alignment explanation
Indices: 465--523 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
455 GTATTAACTG
* * *
465 AAT ATT AAT AA- AA- AAT AAT AAT ATT AAT -AT AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
510 AAT AAT AGT AAT AA
1 AAT AAT AAT AAT AA
524 CAACAAAAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 6 0.13
3 40 0.87
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1707 original size:29 final size:30
Alignment explanation
Indices: 1595--1712 Score: 91
Period size: 30 Copynumber: 3.9 Consensus size: 30
1585 AAATGTCCCT
* * *
1595 AAACTATCCAAAAATTAGA-TTTTAACCCCT
1 AAACT-TCCAAAAATTACATTTTTGACCCCC
* * *
1625 AAATTTTTCC-AAAATTCCATTTTTGA-CCTC
1 AAA--CTTCCAAAAATTACATTTTTGACCCCC
* *
1655 AAACTTTCCAAAAATTATAATTTT-ACCCCC
1 AAAC-TTCCAAAAATTACATTTTTGACCCCC
*
1685 AAACTTCCAAAAATTCCATTTTTGACCC
1 AAACTTCCAAAAATTACATTTTTGACCC
1713 TAATTTTTTT
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
29 21 0.31
30 37 0.55
31 8 0.12
32 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTGACCCCC
Found at i:1856 original size:59 final size:59
Alignment explanation
Indices: 1601--1974 Score: 366
Period size: 59 Copynumber: 6.3 Consensus size: 59
1591 CCCTAAACTA
* * * **
1601 TCCAAAAATTA-GATTTTAACCCCTAAATTTTTCC-AAAATTCCATTTTTGACCTCAAACTT
1 TCCAAAAATTACCATTTT-ACCCCTGAA--TTTCCAAAAATTCCATTTTTGACCTTAATTTT
** ** * *
1661 TCCAAAAATTATAATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCTAATTTTTT
1 TCCAAAAATTACCATTTTACCCCTGAATTTCCAAAAATTCCATTTTTGACCTTAA--TTTT
* * * * *
1722 TCTAAAAGTTACCAATTTA-CCCTCGAATTTCCAAAAATTCCATTTTTTACCTTGATTTT
1 TCCAAAAATTACCATTTTACCCCT-GAATTTCCAAAAATTCCATTTTTGACCTTAATTTT
* * *
1781 TCC-AAAATTACCATTTTACCCCTGAATTTCCAAAAGTCCCATTTTTTACCTTAATTTT
1 TCCAAAAATTACCATTTTACCCCTGAATTTCCAAAAATTCCATTTTTGACCTTAATTTT
* * *
1839 TCCAAAAATTACCATTTTACCCGTGAATTTTCAAAAATTCCATTTTTAACCTTGAA-TTT
1 TCCAAAAATTACCATTTTACCCCTGAATTTCCAAAAATTCCATTTTTGACCTT-AATTTT
* * * *
1898 TCCAAAAATTACCATTTTA-CCCTCGAATGTCTAAAAATTCCATTTTTGATCCTCAA-CTT
1 TCCAAAAATTACCATTTTACCCCT-GAATTTCCAAAAATTCCATTTTTGA-CCTTAATTTT
* *
1957 TCCCAAAATAACCATTTT
1 TCCAAAAATTACCATTTT
1975 GCTTGTTATC
Statistics
Matches: 266, Mismatches: 38, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
58 55 0.21
59 137 0.52
60 27 0.10
61 47 0.18
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.40
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCTGAATTTCCAAAAATTCCATTTTTGACCTTAATTTT
Found at i:1916 original size:30 final size:30
Alignment explanation
Indices: 1719--1943 Score: 195
Period size: 29 Copynumber: 7.7 Consensus size: 30
1709 ACCCTAATTT
* * * *
1719 TTTTCTAAAAGTTACCAATTTACCCTCGAA
1 TTTTCCAAAAATTACCATTTTACCCTTGAA
*
1749 -TTTCCAAAAATT-CCATTTTTTA-CCTTGAT
1 TTTTCCAAAAATTACCA--TTTTACCCTTGAA
*
1778 TTTTCC-AAAATTACCATTTTACCCCTGAA
1 TTTTCCAAAAATTACCATTTTACCCTTGAA
* *
1807 -TTTCC-AAAAGTCCCATTTTTTA-CCTT-AA
1 TTTTCCAAAAATTACCA--TTTTACCCTTGAA
*
1835 TTTTTCCAAAAATTACCATTTTACCCGTGAA
1 -TTTTCCAAAAATTACCATTTTACCCTTGAA
*
1866 TTTT-CAAAAATT-CCATTTTTAACCTTGAA
1 TTTTCCAAAAATTACCA-TTTTACCCTTGAA
*
1895 TTTTCCAAAAATTACCATTTTACCCTCGAA
1 TTTTCCAAAAATTACCATTTTACCCTTGAA
* *
1925 -TGTCTAAAAATT-CCATTTT
1 TTTTCCAAAAATTACCATTTT
1944 TGATCCTCAA
Statistics
Matches: 161, Mismatches: 19, Indels: 32
0.76 0.09 0.15
Matches are distributed among these distances:
28 33 0.20
29 67 0.42
30 48 0.30
31 13 0.08
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (30 bp):
TTTTCCAAAAATTACCATTTTACCCTTGAA
Found at i:3213 original size:24 final size:24
Alignment explanation
Indices: 3185--3242 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3175 ACAGTCCGCA
*
3185 ACACTTCTCAACTGCTCGAAGTTC
1 ACACTTCTCAACTGCTCGAAGTCC
* * * *
3209 GCACTTCACAATTGCTCGTAGTCC
1 ACACTTCTCAACTGCTCGAAGTCC
3233 ACACTTCTCA
1 ACACTTCTCA
3243 GTTCAAATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.34, G:0.12, T:0.29
Consensus pattern (24 bp):
ACACTTCTCAACTGCTCGAAGTCC
Found at i:3272 original size:30 final size:30
Alignment explanation
Indices: 3233--3298 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3223 CTCGTAGTCC
* *
3233 ACACTTCTCAGTTCAAATTTCACAGCTGCGA
1 ACAC-TCTCAGTTCAAACTTCACAACTGCGA
***
3264 ACACTCTCAGTTTGCACTTCACAACTGCGA
1 ACACTCTCAGTTCAAACTTCACAACTGCGA
3294 ACACT
1 ACACT
3299 TCTAACAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.27
Consensus pattern (30 bp):
ACACTCTCAGTTCAAACTTCACAACTGCGA
Done.