Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013321.1 Kokia drynarioides strain JFW-HI SEQ_128343, 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: 2818
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1214 original size:96 final size:96
Alignment explanation
Indices: 1030--1221 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
1020 AACTTTGCAA
* *
1030 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGACGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGACACAATATTTCA
*
1095 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * * * * *
1126 AAGGGTATTCGATTATTTCGATTTGAAGGAAA-ATTGCGCCTAGTGAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATCTCGATTTGAA-GAAAGATTGCACCTAGTAAGTTAAGACACAATATTTC
*
1189 AGAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
1222 TTTAAAGCTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 7 0.09
96 66 0.80
97 9 0.11
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGACACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:1596 original size:59 final size:58
Alignment explanation
Indices: 1533--1985 Score: 352
Period size: 59 Copynumber: 7.7 Consensus size: 58
1523 TAAAAGTGAA
*
1533 ATTTTTGGAAGTTTAGGGTCAAAAATGAGATTTTTGGAATTTTCGGGCTCAAAAATGGG
1 ATTTTTGGAAGTTTAGGGTCAAAAATGAGATTTTTGGAAGTTTCGGG-TCAAAAATGGG
* * * * * *
1592 ATTTTTGGAA-ATTCGGGGCTAAAAATGAAATTTTTGGAAGTTTCGAGGACAAAAATGAG
1 ATTTTTGGAAGTTTAGGGTC-AAAAATGAGATTTTTGGAAGTTTCG-GGTCAAAAATGGG
* * * *
1651 ATTTTGGGAAGTTTAGGGTCAAAAATGAGACTTTTGGAAGTTTTTGGGTC-AAAATGGA
1 ATTTTTGGAAGTTTAGGGTCAAAAATGAGATTTTTGGAAG-TTTCGGGTCAAAAATGGG
* * * * *
1709 ATTTTTGGAAATTCAAGG-CTAAAAATG-GAATTTTTAGAGGTTTCGGAGTC-AAAATGGG
1 ATTTTTGGAAGTTTAGGGTC-AAAAATGAG-ATTTTTGGAAGTTTCGG-GTCAAAAATGGG
* * * * * * *
1767 ATTTTTTGAAGTTTCGATGTCAAAAATGAGATTTTTGGAA-ATTCGAGGTTAAAAATTGA
1 ATTTTTGGAAGTTTAG-GGTCAAAAATGAGATTTTTGGAAGTTTCG-GGTCAAAAATGGG
* * * * *
1826 ATTTTTGGAAGTTTTGGGGTTAAAAAT-AGGATTTTTAGAAG-TTCGGGGGT-AAAAACGGA
1 ATTTTTGGAAG-TTTAGGGTCAAAAATGA-GATTTTTGGAAGTTTC--GGGTCAAAAATGGG
* * * * * *
1885 ATTTTT-GAAATTTCGGGTAAAAAATGGGATTTTTGGAAGTTTCAGGTCAAAAATGAG
1 ATTTTTGGAAGTTTAGGGTCAAAAATGAGATTTTTGGAAGTTTCGGGTCAAAAATGGG
* ** *
1942 ATTTTTGGAAATTCGGGGTTAAAAAT-AGAATTTTTGGATAGTTT
1 ATTTTTGGAAGTTTAGGGTCAAAAATGAG-ATTTTTGGA-AGTTT
1986 AGGGACCTCT
Statistics
Matches: 313, Mismatches: 58, Indels: 46
0.75 0.14 0.11
Matches are distributed among these distances:
56 3 0.01
57 44 0.14
58 100 0.32
59 144 0.46
60 21 0.07
61 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (58 bp):
ATTTTTGGAAGTTTAGGGTCAAAAATGAGATTTTTGGAAGTTTCGGGTCAAAAATGGG
Found at i:1621 original size:88 final size:86
Alignment explanation
Indices: 1497--1989 Score: 406
Period size: 88 Copynumber: 5.6 Consensus size: 86
1487 TTTGGGGTTT
* * * *
1497 AAATGGAATTTTTAGAAGTTCAGGGGTAAAAGTGAAATTTTTGGAAGTTTAGGGTCAAAAATGAG
1 AAATGGGATTTTTGGAAATTC-GGGGTAAAAATGAAATTTTTGGAAGTTTAGGGTCAAAAATGAG
*
1562 ATTTTTGGAATTTTCGGGCTCAA
65 ATTTTTGGAAGTTTCGGG-TCAA
* *
1585 AAATGGGATTTTTGGAAATTCGGGGCTAAAAATGAAATTTTTGGAAGTTTCGAGGACAAAAATGA
1 AAATGGGATTTTTGGAAATTCGGGG-TAAAAATGAAATTTTTGGAAGTTTAG-GGTCAAAAATGA
* *
1650 GATTTTGGGAAGTTTAGGGTCAA
64 GATTTTTGGAAGTTTCGGGTCAA
* * * ** * * * * *
1673 AAATGAGACTTTTGGAAGTTTTTGGGTCAAAATGGAATTTTTGGAAATTCAAGG-CTAAAAATG-
1 AAATGGGATTTTTGGAA-ATTCGGGGTAAAAATGAAATTTTTGGAAGTTTAGGGTC-AAAAATGA
* *
1736 GAATTTTTAGAGGTTTCGGAGTC-A
64 G-ATTTTTGGAAGTTTCGG-GTCAA
* * ** * * * *
1760 AAATGGGATTTTTTGAAGTTTCGATGTCAAAAATGAGATTTTTGGAA-ATTCGAGGTTAAAAATT
1 AAATGGGATTTTTGGAA-ATTCGGGGT-AAAAATGAAATTTTTGGAAGTTTAG-GGTCAAAAA-T
* *
1824 GA-ATTTTTGGAAGTTTTGGGGTTAA
62 GAGATTTTTGGAAG-TTTCGGGTCAA
* * * * * * * * *
1849 AAATAGGATTTTTAGAAGTTCGGGGGTAAAAACGGAATTTTT-GAAATTTCGGGTAAAAAATGGG
1 AAATGGGATTTTTGGAAATTC-GGGGTAAAAATGAAATTTTTGGAAGTTTAGGGTCAAAAATGAG
*
1913 ATTTTTGGAAGTTTCAGGTCAA
65 ATTTTTGGAAGTTTCGGGTCAA
*
1935 AAATGAGATTTTTGGAAATTCGGGGTTAAAAAT-AGAATTTTTGGATAGTTTAGGG
1 AAATGGGATTTTTGGAAATTCGGGG-TAAAAATGA-AATTTTTGGA-AGTTTAGGG
1990 ACCTCTAGGG
Statistics
Matches: 320, Mismatches: 65, Indels: 40
0.75 0.15 0.09
Matches are distributed among these distances:
85 4 0.01
86 42 0.13
87 72 0.22
88 144 0.45
89 58 0.18
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (86 bp):
AAATGGGATTTTTGGAAATTCGGGGTAAAAATGAAATTTTTGGAAGTTTAGGGTCAAAAATGAGA
TTTTTGGAAGTTTCGGGTCAA
Found at i:1645 original size:29 final size:29
Alignment explanation
Indices: 1520--1985 Score: 345
Period size: 29 Copynumber: 16.0 Consensus size: 29
1510 AGAAGTTCAG
* * *
1520 GGGT-AAAAGTGAAATTTTTGGAAGTTTA
1 GGGTCAAAAATGAGATTTTTGGAAGTTTC
*
1548 GGGTCAAAAATGAGATTTTTGGAATTTTC
1 GGGTCAAAAATGAGATTTTTGGAAGTTTC
* *
1577 GGGCTCAAAAATGGGATTTTTGGAA-ATTC
1 GGG-TCAAAAATGAGATTTTTGGAAGTTTC
* *
1606 GGGGCTAAAAATGAAATTTTTGGAAGTTTC
1 GGGTC-AAAAATGAGATTTTTGGAAGTTTC
* * *
1636 GAGGACAAAAATGAGATTTTGGGAAGTTTA
1 G-GGTCAAAAATGAGATTTTTGGAAGTTTC
* *
1666 GGGTCAAAAATGAGACTTTTGGAAGTTTTT
1 GGGTCAAAAATGAGATTTTTGGAAG-TTTC
*
1696 GGGTC-AAAATG-GAATTTTTGGAA-ATTC
1 GGGTCAAAAATGAG-ATTTTTGGAAGTTTC
* * *
1723 AAGG-CTAAAAATG-GAATTTTTAGAGGTTTC
1 -GGGTC-AAAAATGAG-ATTTTTGGAAGTTTC
* *
1753 GGAGTC-AAAATGGGATTTTTTGAAGTTTC
1 GG-GTCAAAAATGAGATTTTTGGAAGTTTC
* *
1782 GATGTCAAAAATGAGATTTTTGGAA-ATTC
1 G-GGTCAAAAATGAGATTTTTGGAAGTTTC
* *
1811 GAGGTTAAAAATTGA-ATTTTTGGAAGTTTTG
1 G-GGTCAAAAA-TGAGATTTTTGGAAG-TTTC
* *
1842 GGGTTAAAAAT-AGGATTTTTAGAAG-TTC
1 GGGTCAAAAATGA-GATTTTTGGAAGTTTC
* *
1870 GGGGGT-AAAAACG-GAATTTTT-GAAATTTC
1 --GGGTCAAAAATGAG-ATTTTTGGAAGTTTC
* *
1899 GGGTAAAAAATGGGATTTTTGGAAGTTTC
1 GGGTCAAAAATGAGATTTTTGGAAGTTTC
* *
1928 AGGTCAAAAATGAGATTTTTGGAA-ATTC
1 GGGTCAAAAATGAGATTTTTGGAAGTTTC
*
1956 GGGGTTAAAAAT-AGAATTTTTGGATAGTTT
1 -GGGTCAAAAATGAG-ATTTTTGGA-AGTTT
1986 AGGGACCTCT
Statistics
Matches: 356, Mismatches: 49, Indels: 63
0.76 0.10 0.13
Matches are distributed among these distances:
27 7 0.02
28 32 0.09
29 206 0.58
30 102 0.29
31 9 0.03
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGTCAAAAATGAGATTTTTGGAAGTTTC
Found at i:1908 original size:28 final size:28
Alignment explanation
Indices: 1467--1979 Score: 260
Period size: 29 Copynumber: 17.6 Consensus size: 28
1457 ACCCGAGGAT
* * **
1467 AAATGGTAATTTTGGGAAAATTTGGGGTTT
1 AAATGG-AATTTTTGG-AAATTTCGGGTAA
* *
1497 AAATGGAATTTTTAG-AAGTTCAGGGGTAA
1 AAATGGAATTTTTGGAAATTTC--GGGTAA
* * * *
1526 AAGTGAAATTTTTGGAAGTTTAGGGTCAA
1 AAATGGAATTTTTGGAAATTTCGGGT-AA
*
1555 AAAT-GAGATTTTTGGAATTTTCGGGCTCAA
1 AAATGGA-ATTTTTGGAAATTTCGGG-T-AA
*
1585 AAATGGGATTTTTGGAAA-TTCGGGGCTAA
1 AAATGGAATTTTTGGAAATTTC-GGG-TAA
* * *
1614 AAATGAAATTTTTGGAAGTTTCGAGGACAA
1 AAATGGAATTTTTGGAAATTTCG-GG-TAA
* * *
1644 AAAT-GAGATTTTGGGAAGTTTAGGGTCAA
1 AAATGGA-ATTTTTGGAAATTTCGGGT-AA
* * * *
1673 AAAT-GAGACTTTTGGAAGTTTTTGGGTCA
1 AAATGGA-ATTTTTGGAA-ATTTCGGGTAA
*
1702 AAATGGAATTTTTGGAAA-TTCAAGGCTAA
1 AAATGGAATTTTTGGAAATTTC--GGGTAA
* ** *
1731 AAATGGAATTTTTAGAGGTTTCGGAGTCA
1 AAATGGAATTTTTGGAAATTTCGG-GTAA
* * * *
1760 AAATGGGATTTTTTGAAGTTTCGATGTCAA
1 AAATGGAATTTTTGGAAATTTCG-GGT-AA
1790 AAAT-GAGATTTTTGGAAA-TTCGAGGTTAA
1 AAATGGA-ATTTTTGGAAATTTCG-GG-TAA
* * *
1819 AAATTGAATTTTTGGAAGTTTTGGGGTTAA
1 AAATGGAATTTTTGGAA-ATTTCGGG-TAA
* *
1849 AAATAGG-ATTTTTAG-AAGTTCGGGGGTAA
1 AAAT-GGAATTTTTGGAAATTTC--GGGTAA
*
1878 AAACGGAATTTTT-GAAATTTCGGGTAAA
1 AAATGGAATTTTTGGAAATTTCGGGT-AA
* * *
1906 AAATGGGATTTTTGGAAGTTTCAGGTCAA
1 AAATGGAATTTTTGGAAATTTCGGGT-AA
1935 AAAT-GAGATTTTTGGAAA-TTCGGGGTTAA
1 AAATGGA-ATTTTTGGAAATTTC-GGG-TAA
*
1964 AAATAGAATTTTTGGA
1 AAATGGAATTTTTGGA
1980 TAGTTTAGGG
Statistics
Matches: 379, Mismatches: 68, Indels: 73
0.73 0.13 0.14
Matches are distributed among these distances:
27 10 0.03
28 29 0.08
29 226 0.60
30 109 0.29
31 5 0.01
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AAATGGAATTTTTGGAAATTTCGGGTAA
Found at i:2335 original size:108 final size:108
Alignment explanation
Indices: 2138--2360 Score: 387
Period size: 108 Copynumber: 2.0 Consensus size: 108
2128 ATTAAAACAA
2138 ATTA-AAAAAAAAAGGGACCGTTTGTAGAAATAAACCTAAATAATGACACGTGGCAGCCCCTGGT
1 ATTAGAAAAAAAAAGGGACC---TGTAGAAATAAACCTAAATAATGACACGTGGCAGCCCCTGGT
*
2202 GGCTTCAAAAGGGGTCCAAGGATTAAATTGAAAAGCATTGAAAAAT
63 GCCTTCAAAAGGGGTCCAAGGATTAAATTGAAAAGCATTGAAAAAT
2248 ATTAGNAAAAAAAAAGGGACC-GTAGAAATAAACCTAAATAATGACACGTGGCAGCCCCTGGTGC
1 ATTAG-AAAAAAAAAGGGACCTGTAGAAATAAACCTAAATAATGACACGTGGCAGCCCCTGGTGC
2312 CTTCAAAAGGGGTCCAAGGATTAAATTGAAAAGCATTGAAAAAT
65 CTTCAAAAGGGGTCCAAGGATTAAATTGAAAAGCATTGAAAAAT
2356 ATTAG
1 ATTAG
2361 GCCAATTTAA
Statistics
Matches: 110, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
108 91 0.83
110 4 0.04
112 15 0.14
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (108 bp):
ATTAGAAAAAAAAAGGGACCTGTAGAAATAAACCTAAATAATGACACGTGGCAGCCCCTGGTGCC
TTCAAAAGGGGTCCAAGGATTAAATTGAAAAGCATTGAAAAAT
Found at i:2479 original size:70 final size:69
Alignment explanation
Indices: 2400--2540 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 69
2390 AAGGACCTGA
*
2400 TTAAAATTTTGAGAAAAAGCGGAACGACCAAACGCATAAATATCTCTTTTCTTGAAAACACGCGG
1 TTAAAATTTTGAGAAAAAGCGGAACGACCAAACGCATAAATATCTCTTTTCTCGAAAACACGCGG
2465 ACCC
66 ACCC
2469 TTNAAAATTTTGAGAAAAAGCGGAACGACCAAACGCATAAATATCTCTTTTCTCGAAAACACGCG
1 TT-AAAATTTTGAGAAAAAGCGGAACGACCAAACGCATAAATATCTCTTTTCTCGAAAACACGCG
2534 GACCC
65 GACCC
2539 TT
1 TT
2541 TAGGCGGGTC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 2 0.03
70 68 0.97
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (69 bp):
TTAAAATTTTGAGAAAAAGCGGAACGACCAAACGCATAAATATCTCTTTTCTCGAAAACACGCGG
ACCC
Done.