Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000935.1 Kokia drynarioides strain JFW-HI SEQ_112091, 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: 13872
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1348 original size:96 final size:96
Alignment explanation
Indices: 1164--1351 Score: 265
Period size: 96 Copynumber: 2.0 Consensus size: 96
1154 TTTTTGGGAA
*
1164 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
1229 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * * *
1260 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
1324 GAAACTCGAA-ATAAA-AGAATATTGCCTC
66 G-AA-TCGAAGATAAAGA-AACATTGCCTC
1352 AATTTTAAAG
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
95 7 0.09
96 70 0.85
97 5 0.06
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:1634 original size:28 final size:29
Alignment explanation
Indices: 1566--1639 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
1556 ATCGGAGTTC
* *
1566 AAAATGAGACTTTTCGGATTCTCGGGGGCA
1 AAAATGATAATTTT-GGATTCTCGGGGGCA
*
1596 AAAATGATAATTTTGGATTCTCGGGGGTA
1 AAAATGATAATTTTGGATTCTCGGGGGCA
*
1625 AAACTG-TAATTTTGG
1 AAAATGATAATTTTGG
1640 GAAATTTTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 9 0.22
29 19 0.47
30 12 0.30
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (29 bp):
AAAATGATAATTTTGGATTCTCGGGGGCA
Found at i:1677 original size:29 final size:29
Alignment explanation
Indices: 1645--1910 Score: 301
Period size: 29 Copynumber: 9.1 Consensus size: 29
1635 TTTGGGAAAT
**
1645 TTTGGGGTCAAAAATGGGATTTTTTAAAG
1 TTTGGGGTCAAAAATGGGATTTTTGGAAG
*
1674 TTTGGGGGTC-AAAACGGGATTTTTGGAAG
1 TTT-GGGGTCAAAAATGGGATTTTTGGAAG
*
1703 TTTTGAGGTCAAAAATGGGATTTTTGGAAG
1 -TTTGGGGTCAAAAATGGGATTTTTGGAAG
*
1733 TTTGGTGGT-AAAAATGGGATTTTTGGAAT
1 TTTGG-GGTCAAAAATGGGATTTTTGGAAG
*
1762 TTTGGGGTC-AAAATGAGATTTTTGGAAG
1 TTTGGGGTCAAAAATGGGATTTTTGGAAG
1790 TTTTGGGGTCAAAAATGGGATTTTTGGAAG
1 -TTTGGGGTCAAAAATGGGATTTTTGGAAG
* * *
1820 TTTGAGGGT-GAAAACGGAATTTTTGGAAG
1 TTTG-GGGTCAAAAATGGGATTTTTGGAAG
1849 TTTTGGGGTC-AAAATGGGATTTTTGGAAG
1 -TTTGGGGTCAAAAATGGGATTTTTGGAAG
* ***
1878 TTCGGGGGT-AAAAATAAAATTTTTGGACAG
1 TT-TGGGGTCAAAAATGGGATTTTTGGA-AG
1908 TTT
1 TTT
1911 AGGGACCTCT
Statistics
Matches: 204, Mismatches: 20, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
28 22 0.11
29 122 0.60
30 60 0.29
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.36
Consensus pattern (29 bp):
TTTGGGGTCAAAAATGGGATTTTTGGAAG
Found at i:1696 original size:59 final size:59
Alignment explanation
Indices: 1633--1876 Score: 307
Period size: 59 Copynumber: 4.2 Consensus size: 59
1623 TAAAACTGTA
* ** *
1633 ATTTTGGGAAATTTTGGGGTCAAAAATGGGATTTTTTAAAGTTTGGGGGTCAAAACGGG
1 ATTTTTGGAAATTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTCAAAATGGG
* * * *
1692 ATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTTGGTGGTAAAAATGGG
1 ATTTTTGGAAATTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTCAAAATGGG
* *
1751 ATTTTTGG-AATTTTGGGGTC-AAAATGAGATTTTTGGAAGTTTTGGGGTCAAAAATGGG
1 ATTTTTGGAAATTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTC-AAAATGGG
* * * * *
1809 ATTTTTGG-AAGTTTGAGGGT-GAAAACGGAATTTTTGGAAGTTTTGGGGTCAAAATGGG
1 ATTTTTGGAAATTTTG-GGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTCAAAATGGG
1867 ATTTTTGGAA
1 ATTTTTGGAA
1877 GTTCGGGGGT
Statistics
Matches: 163, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
57 25 0.15
58 48 0.29
59 90 0.55
ACGTcount: A:0.28, C:0.03, G:0.32, T:0.36
Consensus pattern (59 bp):
ATTTTTGGAAATTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTCAAAATGGG
Found at i:1792 original size:87 final size:87
Alignment explanation
Indices: 1645--1879 Score: 355
Period size: 87 Copynumber: 2.7 Consensus size: 87
1635 TTTGGGAAAT
** * *
1645 TTTGGGGTCAAAAATGGGATTTTTTAAAGTTTGGGGGTCAAAACGGGATTTTTGGAAGTTTTGAG
1 TTTGGGGT-AAAAATGGGATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTTGAG
1710 GTCAAAAATGGGATTTTTGGAAG
65 GTCAAAAATGGGATTTTTGGAAG
* *
1733 TTTGGTGGTAAAAATGGGATTTTTGGAA-TTTTGGGGTCAAAATGAGATTTTTGGAAGTTTTGGG
1 TTTGG-GGTAAAAATGGGATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTTGAG
1797 GTCAAAAATGGGATTTTTGGAAG
65 GTCAAAAATGGGATTTTTGGAAG
* * *
1820 TTTGAGGGTGAAAACGGAATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTT
1 TTTG-GGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTT
1880 CGGGGGTAAA
Statistics
Matches: 134, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
87 78 0.58
88 53 0.40
89 3 0.02
ACGTcount: A:0.28, C:0.03, G:0.32, T:0.37
Consensus pattern (87 bp):
TTTGGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTTGAGG
TCAAAAATGGGATTTTTGGAAG
Found at i:1891 original size:87 final size:88
Alignment explanation
Indices: 1645--1914 Score: 334
Period size: 87 Copynumber: 3.1 Consensus size: 88
1635 TTTGGGAAAT
* * ** * * *
1645 TTTG-GGGTCAAAAATGGGATTTTTTAAAGTTTGGGGGTCAAAACGGGATTTTTGGAAGTTTTGA
1 TTTGAGGGT-AAAAACGGAATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTTGG
1709 GGTCAAAAATGGGATTTTTGGAAG
65 GGTCAAAAATGGGATTTTTGGAAG
* * *
1733 TTTG-GTGGTAAAAATGGGATTTTTGGAA-TTTTGGGGTCAAAATGAGATTTTTGGAAGTTTTGG
1 TTTGAG-GGTAAAAACGGAATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTTGG
1796 GGTCAAAAATGGGATTTTTGGAAG
65 GGTCAAAAATGGGATTTTTGGAAG
* **
1820 TTTGAGGGTGAAAACGGAATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTCGGGG
1 TTTGAGGGTAAAAACGGAATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTTGGG
***
1885 GT-AAAAATAAAATTTTTGGACAG
66 GTCAAAAATGGGATTTTTGGA-AG
1908 TTT-AGGG
1 TTTGAGGG
1915 ACCTCTAGGG
Statistics
Matches: 163, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
87 97 0.60
88 63 0.39
89 3 0.02
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.36
Consensus pattern (88 bp):
TTTGAGGGTAAAAACGGAATTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTGGAAGTTTTGGG
GTCAAAAATGGGATTTTTGGAAG
Found at i:1899 original size:58 final size:58
Alignment explanation
Indices: 1633--1910 Score: 290
Period size: 59 Copynumber: 4.7 Consensus size: 58
1623 TAAAACTGTA
* * * ** ** * *
1633 ATTTTGGGAAATTTTGGGGTCAAAAATGGGATTTTTTAAAGTTTGGGGGTCAAAACGGG
1 ATTTTTGGAAGTTTGGGGGT-AAAAATGAAATTTTTGGAAGTTTTGGGGTCAAAATGGG
* * ** *
1692 ATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAG-TTTGGTGGTAAAAATGGG
1 ATTTTTGGAAGTTTGGGGGT-AAAAATGAAATTTTTGGAAGTTTTGG-GGTCAAAATGGG
* * *
1751 ATTTTTGGAA-TTTTGGGGTCAAAATGAGATTTTTGGAAGTTTTGGGGTCAAAAATGGG
1 ATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGTC-AAAATGGG
* * * *
1809 ATTTTTGGAAGTTTGAGGGTGAAAACGGAATTTTTGGAAGTTTTGGGGTCAAAATGGG
1 ATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGTCAAAATGGG
* *
1867 ATTTTTGGAAGTTCGGGGGTAAAAATAAAATTTTTGGACAGTTT
1 ATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGGA-AGTTT
1911 AGGGACCTCT
Statistics
Matches: 190, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
57 21 0.11
58 75 0.39
59 94 0.49
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (58 bp):
ATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGGAAGTTTTGGGGTCAAAATGGG
Found at i:3785 original size:18 final size:17
Alignment explanation
Indices: 3748--3852 Score: 84
Period size: 17 Copynumber: 6.1 Consensus size: 17
3738 GGCTTTATTT
**
3748 ATTTTAAATTTATGATA
1 ATTTTAAATTTAAAATA
3765 ATTTTAAATTTGAAAATA
1 ATTTTAAATTT-AAAATA
** *
3783 ATTTTAAACATAAATTA
1 ATTTTAAATTTAAAATA
*
3800 AATTTAAATTTAAAATA
1 ATTTTAAATTTAAAATA
** * *
3817 AAATTAAATTTTTAAACA
1 ATTTTAAA-TTTAAAATA
* *
3835 AATTTAATTTTAAAATA
1 ATTTTAAATTTAAAATA
3852 A
1 A
3853 ATTCAAAGGG
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
17 44 0.63
18 26 0.37
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:6600 original size:52 final size:52
Alignment explanation
Indices: 6526--6868 Score: 517
Period size: 52 Copynumber: 6.6 Consensus size: 52
6516 TTCCCATTTA
* * * * *
6526 ATACTCACGATGACACAAAGTCATCGAACCTTA-AATCTGTAAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAGGATTCAT
* *
6578 ATGCTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * * *
6630 ATACTCATGATGACAAATAGCCATCGGGCCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
6682 ATACTCACGATGACACATAGCCATCGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
6734 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGGTTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
6786 ATACTCACGATGACACATTGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
6838 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
6869 TTTTCATTTA
Statistics
Matches: 265, Mismatches: 25, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
52 259 0.98
53 6 0.02
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:8430 original size:20 final size:20
Alignment explanation
Indices: 8379--8482 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
8369 AGTGCATTCT
* *
8379 ATGTACCAGGCTTTGTGTCG
1 ATGTATCAGGCTTTGTGCCG
8399 ATGTA--A-GCTTTGTGCCG
1 ATGTATCAGGCTTTGTGCCG
*
8416 GTGTATCAGGCTTTGTGCCG
1 ATGTATCAGGCTTTGTGCCG
*
8436 GTGTATCAGGCTTTGTGCCG
1 ATGTATCAGGCTTTGTGCCG
*
8456 ATGTATCAGGCTTTATGCCG
1 ATGTATCAGGCTTTGTGCCG
8476 ATGTATC
1 ATGTATC
8483 GGACATTGTG
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
17 14 0.18
18 1 0.01
19 1 0.01
20 61 0.79
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.36
Consensus pattern (20 bp):
ATGTATCAGGCTTTGTGCCG
Found at i:8505 original size:40 final size:40
Alignment explanation
Indices: 8408--8498 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
8398 GATGTAAGCT
* * *
8408 TTGTGCCGGTGTATCAGGCTTTGTGCCGGTGTATCAGGCT
1 TTGTGCCGGTGTATCAGGCTTTATGCCGATGTATCAGGCA
*
8448 TTGTGCCGATGTATCAGGCTTTATGCCGATGTATC-GGACA
1 TTGTGCCGGTGTATCAGGCTTTATGCCGATGTATCAGG-CA
*
8488 TTGTGTCGGTG
1 TTGTGCCGGTG
8499 ATTCAGGAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
39 2 0.05
40 42 0.95
ACGTcount: A:0.13, C:0.19, G:0.33, T:0.35
Consensus pattern (40 bp):
TTGTGCCGGTGTATCAGGCTTTATGCCGATGTATCAGGCA
Found at i:8505 original size:60 final size:57
Alignment explanation
Indices: 8380--8498 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 57
8370 GTGCATTCTA
* * * * *
8380 TGTACCAGGCTTTGTGTCGATGTAAGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGG
1 TGTATCAGGCTTTGTGCCGATGTAAGCTTTATGCCGATGTATCAGGCATTGTGCCGG
*
8437 TGTATCAGGCTTTGTGCCGATGTATCAGGCTTTATGCCGATGTATC-GGACATTGTGTCGG
1 TGTATCAGGCTTTGTGCCGATGTA--A-GCTTTATGCCGATGTATCAGG-CATTGTGCCGG
8497 TG
1 TG
8499 ATTCAGGAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
57 22 0.42
59 3 0.06
60 27 0.52
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.35
Consensus pattern (57 bp):
TGTATCAGGCTTTGTGCCGATGTAAGCTTTATGCCGATGTATCAGGCATTGTGCCGG
Found at i:13029 original size:18 final size:18
Alignment explanation
Indices: 13008--13042 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12998 AATGATATAT
*
13008 TAATTAATAATAATATTA
1 TAATAAATAATAATATTA
13026 TAATAAATAATAATATT
1 TAATAAATAATAATATT
13043 TTATTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Done.