Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003460.1 Kokia drynarioides strain JFW-HI SEQ_116258, 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: 2807
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:670 original size:15 final size:14
Alignment explanation
Indices: 623--674 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 14
613 TTTCAGGAAT
623 AACTATGTTTAGAAC
1 AACT-TGTTTAGAAC
*
638 AATCATTGTTTGGAAC
1 AA-C-TTGTTTAGAAC
654 AACTTGTATTAGAAC
1 AACTTGT-TTAGAAC
669 AA-TTGT
1 AACTTGT
675 GTTATTCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
16 12 0.38
17 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (14 bp):
AACTTGTTTAGAAC
Found at i:1598 original size:39 final size:40
Alignment explanation
Indices: 1555--1637 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
1545 AGTAACAGCG
* *
1555 TTTTTCCATAAACGCCGCAAAAGGTAAAGCAATAGCTGCT
1 TTTTTCCAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCT
**
1595 TTTTTTTAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCT
1 TTTTTCCAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCT
1635 TTT
1 TTT
1638 GTAGGAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (40 bp):
TTTTTCCAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCT
Found at i:1704 original size:41 final size:40
Alignment explanation
Indices: 1604--1838 Score: 177
Period size: 41 Copynumber: 5.8 Consensus size: 40
1594 TTTTTTTTAA
* * * * **
1604 AAACGCCGCAAAAGGT-AAAGCAATAGCGGCTTTTGTAGG
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAATAGG
* *
1643 AAAAATGCCGCTAAAAGTCAGAGCATTAGCGGCGTTAATGAGG
1 --AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAAT-AGG
** *
1686 AAACGCCGCTAAAGGTCAGAGCATTAGCAACGTTTATGAGG
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAAT-AGG
* * * * *
1727 AAACACCACTAAAGGTCAGAGCATTAGCGACGTTTACTAGA
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCG-TTAATAGG
* * * * *
1768 AAACGCTGCTAAAGGTAAGAGCATTAGTGGTGTTTATAGG
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAATAGG
* * *
1808 AAAAACACCGCTAAAGGTTA-AGCAATAGCGG
1 --AAACGCCGCTAAAGGTCAGAGCATTAGCGG
1839 GATTTTCCCA
Statistics
Matches: 155, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
40 5 0.03
41 114 0.74
42 33 0.21
43 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (40 bp):
AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGTTAATAGG
Found at i:1837 original size:82 final size:83
Alignment explanation
Indices: 1603--1825 Score: 240
Period size: 82 Copynumber: 2.7 Consensus size: 83
1593 CTTTTTTTTA
* * * ** *
1603 AAAACGCCGCAAAAGGTAA-AGCAATAGCGGCT-TTTGTAGGAAAAATGCCGCTAAAAGTCAGAG
1 AAAACGCCGCTAAAGGTAAGAGCATTAGCGG-TGTTTATAGGAAAAACACCGCTAAAGGTCAGAG
*
1666 CATTAGCGGCGTTAATGAG
65 CATTAGCGACGTTAATGAG
* * *** *
1685 GAAACGCCGCTAAAGGTCAGAGCATTAGCAACGTTTATGAGG--AAACACCACTAAAGGTCAGAG
1 AAAACGCCGCTAAAGGTAAGAGCATTAGCGGTGTTTAT-AGGAAAAACACCGCTAAAGGTCAGAG
*
1748 CATTAGCGACGTTTACT-AG
65 CATTAGCGACG-TTAATGAG
* *
1767 AAAACGCTGCTAAAGGTAAGAGCATTAGTGGTGTTTATAGGAAAAACACCGCTAAAGGT
1 AAAACGCCGCTAAAGGTAAGAGCATTAGCGGTGTTTATAGGAAAAACACCGCTAAAGGT
1826 TAAGCAATAG
Statistics
Matches: 113, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
81 3 0.03
82 76 0.67
83 31 0.27
84 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (83 bp):
AAAACGCCGCTAAAGGTAAGAGCATTAGCGGTGTTTATAGGAAAAACACCGCTAAAGGTCAGAGC
ATTAGCGACGTTAATGAG
Found at i:2168 original size:31 final size:28
Alignment explanation
Indices: 2132--2211 Score: 72
Period size: 31 Copynumber: 2.7 Consensus size: 28
2122 AATTAAATCA
2132 AAATTAAAGTTTCGTGTATACATGTGAACC
1 AAATTAAAGTTTCGTGTATA-AT-TGAACC
* * *
2162 ATAATTAGAAATTCACGTGTATAATTGCACC
1 A-AATTA-AAGTT-TCGTGTATAATTGAACC
*
2193 AAATTAAAG-TTCATGTATA
1 AAATTAAAGTTTCGTGTATA
2212 TAATTGCACA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
27 7 0.17
28 1 0.02
29 2 0.05
30 6 0.15
31 11 0.27
32 6 0.15
33 8 0.20
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (28 bp):
AAATTAAAGTTTCGTGTATAATTGAACC
Found at i:2213 original size:29 final size:29
Alignment explanation
Indices: 2132--2220 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
2122 AATTAAATCA
* * *
2132 AAATTAAAGTTTCGTGTATA-CATGTGAACC
1 AAATTAAAG-TTCATGTATATAAT-TGCACC
* * *
2162 ATAATTAGAAATTCACGTGTATAATTGCACC
1 A-AATTA-AAGTTCATGTATATAATTGCACC
2193 AAATTAAAGTTCATGTATATAATTGCAC
1 AAATTAAAGTTCATGTATATAATTGCAC
2221 ATTAAATCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
29 19 0.40
30 6 0.13
31 18 0.38
32 4 0.09
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (29 bp):
AAATTAAAGTTCATGTATATAATTGCACC
Found at i:2242 original size:29 final size:27
Alignment explanation
Indices: 2179--2244 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
2169 GAAATTCACG
*
2179 TGTATAATTGCACCAAATTAAAGTTCA
1 TGTATAATTGCACCAAATCAAAGTTCA
* *
2206 TGTATATAATTGCACATTAAATCAATGTTCA
1 TG--TATAATTGCAC--CAAATCAAAGTTCA
2237 TGTATAAT
1 TGTATAAT
2245 ATTGAGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 2 0.06
29 17 0.53
31 13 0.41
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAGTTCA
Done.