Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004753.1 Kokia drynarioides strain JFW-HI SEQ_118344, 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: 2166
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:880 original size:30 final size:28
Alignment explanation
Indices: 826--911 Score: 75
Period size: 30 Copynumber: 3.0 Consensus size: 28
816 TTTATCATTT
* * *
826 AATAATTTATATTTCTATAATTTTTATAAA
1 AATAAATTA-ATTTTTATTATTTTTA-AAA
*
856 ATTAAATTAAATTTTTATTATTTTTAAAA
1 AATAAATT-AATTTTTATTATTTTTAAAA
* * *
885 AATCAATTTATTTTTATTA-ATTTAAAA
1 AATAAATTAATTTTTATTATTTTTAAAA
912 TTTTAAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
27 7 0.15
28 10 0.21
29 9 0.19
30 20 0.43
31 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
AATAAATTAATTTTTATTATTTTTAAAA
Found at i:897 original size:28 final size:28
Alignment explanation
Indices: 829--911 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
819 ATCATTTAAT
* *
829 AATTTATATTTCTATAATTTTTATAAAATTA
1 AATTTAT-TTT-TATTATTTTTA-AAAAATA
* *
860 AATTAAATTTTTATTATTTTTAAAAAATC
1 AATT-TATTTTTATTATTTTTAAAAAATA
*
889 AATTTATTTTTATTA-ATTTAAAA
1 AATTTATTTTTATTATTTTTAAAA
912 TTTTAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
27 7 0.16
28 10 0.22
29 9 0.20
30 10 0.22
31 7 0.16
32 2 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
AATTTATTTTTATTATTTTTAAAAAATA
Found at i:1481 original size:40 final size:40
Alignment explanation
Indices: 1426--1529 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
1416 TATTAGCAGC
*
1426 AAAGGTAAAGTAATAGTGGCGTTTTTCCATAAACACCGCA
1 AAAGGTAAAGCAATAGTGGCGTTTTTCCATAAACACCGCA
* * * *
1466 AAAGGTAAAGCAATAGCGG-TTCTTTTCCATAAACGCTGCA
1 AAAGGTAAAGCAATAGTGGCGT-TTTTCCATAAACACCGCA
1506 AAAGGTAAAGCAATAGCT-GCGTTT
1 AAAGGTAAAGCAATAG-TGGCGTTT
1530 ATAGGAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.02
40 52 0.96
41 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (40 bp):
AAAGGTAAAGCAATAGTGGCGTTTTTCCATAAACACCGCA
Found at i:1618 original size:38 final size:39
Alignment explanation
Indices: 1556--1631 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
1546 TAAAGGTCAA
*
1556 AGCATTAGCGGTATTTATGGGAAAGCGCCGCTAAAGGTT
1 AGCATTAGCGGTAGTTATGGGAAAGCGCCGCTAAAGGTT
*
1595 AGCATTAGCGG-CGTTATGGGAAAGCGCCGCTAAAGGT
1 AGCATTAGCGGTAGTTATGGGAAAGCGCCGCTAAAGGT
1632 CAGAGCATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 24 0.69
39 11 0.31
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (39 bp):
AGCATTAGCGGTAGTTATGGGAAAGCGCCGCTAAAGGTT
Found at i:1680 original size:49 final size:49
Alignment explanation
Indices: 1608--1787 Score: 288
Period size: 49 Copynumber: 3.7 Consensus size: 49
1598 ATTAGCGGCG
*
1608 TTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTGCCGGCGCTTTAGTGT
1 TTATGGGAAAGCACCGCTAAAGGTCAGAGCATTGCCGGCGCTTTAGTGT
* **
1657 TTATGGGAAAGCATCGCTAAAGGTCAGAGCATTGCTAGCGCTTTAGTGT
1 TTATGGGAAAGCACCGCTAAAGGTCAGAGCATTGCCGGCGCTTTAGTGT
* *
1706 TTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTGCCGACGCTTTAGTGT
1 TTATGGGAAAGCACCGCTAAAGGTCAGAGCATTGCCGGCGCTTTAGTGT
* *
1755 TTATGGGAAAGCACCGCTAAATGTAAGAGCATT
1 TTATGGGAAAGCACCGCTAAAGGTCAGAGCATT
1788 AGTGGCGTTT
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 119 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (49 bp):
TTATGGGAAAGCACCGCTAAAGGTCAGAGCATTGCCGGCGCTTTAGTGT
Found at i:1784 original size:98 final size:98
Alignment explanation
Indices: 1608--1787 Score: 324
Period size: 98 Copynumber: 1.8 Consensus size: 98
1598 ATTAGCGGCG
* *
1608 TTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTGCCGGCGCTTTAGTGTTTATGGGAAAGCATCG
1 TTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTGCCGACGCTTTAGTGTTTATGGGAAAGCACCG
*
1673 CTAAAGGTCAGAGCATTGCTAGCGCTTTAGTGT
66 CTAAAGGTAAGAGCATTGCTAGCGCTTTAGTGT
1706 TTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTGCCGACGCTTTAGTGTTTATGGGAAAGCACCG
1 TTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTGCCGACGCTTTAGTGTTTATGGGAAAGCACCG
*
1771 CTAAATGTAAGAGCATT
66 CTAAAGGTAAGAGCATT
1788 AGTGGCGTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 78 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (98 bp):
TTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTGCCGACGCTTTAGTGTTTATGGGAAAGCACCG
CTAAAGGTAAGAGCATTGCTAGCGCTTTAGTGT
Done.