Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014903.1 Kokia drynarioides strain JFW-HI SEQ_129946, 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: 5116
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.30
Warning! 250 characters in sequence are not A, C, G, or T
Found at i:1831 original size:58 final size:58
Alignment explanation
Indices: 1769--1904 Score: 195
Period size: 58 Copynumber: 2.3 Consensus size: 58
1759 CTTCGGGAAC
* *
1769 AAAATGGTAATTTTTGAAAGGTTCGGGGTTAAAAATGGAA-TTTTAGACATTCAACGGT-
1 AAAATGGTAATTTTTGAAAGGTTAGGGGTT-AAAATGAAATTTTTAGACATTCAA-GGTA
* *
1827 AAAATGGTAATTTTTGGAAGGTTAGGGGTTAAAATGAAATTTTTAGACATTCGAGGTA
1 AAAATGGTAATTTTTGAAAGGTTAGGGGTTAAAATGAAATTTTTAGACATTCAAGGTA
*
1885 AAAATGGTAATTTTGGAAAG
1 AAAATGGTAATTTTTGAAAG
1905 TTCAGGTTCA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
57 11 0.16
58 59 0.84
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTTGAAAGGTTAGGGGTTAAAATGAAATTTTTAGACATTCAAGGTA
Found at i:1896 original size:29 final size:30
Alignment explanation
Indices: 1769--1898 Score: 96
Period size: 29 Copynumber: 4.5 Consensus size: 30
1759 CTTCGGGAAC
* *
1769 AAAATGGTAATTTTT-GAAAGGTTCGGGGTTA
1 AAAATGGTAATTTTTAGACA-GTTCGAGG-TA
*
1800 AAAATGG-AA-TTTTAGACA-TTCAACGGT-
1 AAAATGGTAATTTTTAGACAGTTCGA-GGTA
* * * *
1827 AAAATGGTAATTTTTGGA-AGGTTAGGGGTT
1 AAAATGGTAATTTTTAGACA-GTTCGAGGTA
*
1857 AAAAT-GAAATTTTTAGACA-TTCGAGGTA
1 AAAATGGTAATTTTTAGACAGTTCGAGGTA
1885 AAAATGGTAATTTT
1 AAAATGGTAATTTT
1899 GGAAAGTTCA
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
27 7 0.09
28 18 0.23
29 32 0.42
30 13 0.17
31 7 0.09
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATGGTAATTTTTAGACAGTTCGAGGTA
Found at i:1898 original size:28 final size:29
Alignment explanation
Indices: 1769--1911 Score: 84
Period size: 28 Copynumber: 5.0 Consensus size: 29
1759 CTTCGGGAAC
* * *
1769 AAAATGGTAATTTTTGAAAGGTTCGGGGTTA
1 AAAATGGTAATTTTAGACA-GTTCGAGG-TA
*
1800 AAAATGG-AATTTTAGACA-TTCAACGGT-
1 AAAATGGTAATTTTAGACAGTTCGA-GGTA
* * * *
1827 AAAATGGTAATTTTTGGA-AGGTTAGGGGTT
1 AAAATGGTAA-TTTTAGACA-GTTCGAGGTA
*
1857 AAAAT-GAAATTTTTAGACA-TTCGAGGTA
1 AAAATGGTAA-TTTTAGACAGTTCGAGGTA
* *
1885 AAAATGGTAATTTTGGAAAGTTC-AGGT
1 AAAATGGTAATTTTAGACAGTTCGAGGT
1912 TCAGAAACGG
Statistics
Matches: 87, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
27 7 0.08
28 29 0.33
29 27 0.31
30 17 0.20
31 7 0.08
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTAGACAGTTCGAGGTA
Found at i:1995 original size:29 final size:29
Alignment explanation
Indices: 1883--2167 Score: 200
Period size: 30 Copynumber: 9.7 Consensus size: 29
1873 ACATTCGAGG
*
1883 TAAAAATGGTAATTTTGGAAAGTTCA-GGT
1 TAAAAATGG-AATTTTGGAAAGTTTAGGGT
* * * * *
1912 TCAGAAACGGAATTCTAGAAAGTTT-GGTGG
1 T-AAAAATGGAATTTTGGAAAGTTTAGG-GT
* **
1942 TAAAAATGTAATTTTTAAAGAGTTTAGGGT
1 TAAAAATGGAATTTTGGAA-AGTTTAGGGT
* * *
1972 TAAATATGGAAGTTTGGAAAGTTTAGGGA
1 TAAAAATGGAATTTTGGAAAGTTTAGGGT
** ** *
2001 TAAAAATGTTATTTTCTAAGAGTTTAAGGT
1 TAAAAATGGAATTTTGGAA-AGTTTAGGGT
* * * *
2031 TAAAAGTGGAATTTTAGAAAGTTTGGGGG
1 TAAAAATGGAATTTTGGAAAGTTTAGGGT
* *
2060 TAAAAATGTAACTTTTGGAAAATTTAGGGT
1 TAAAAATGGAA-TTTTGGAAAGTTTAGGGT
* *
2090 T-AAAATGAAATTTTGAAAAGTTTATGGG-
1 TAAAAATGGAATTTTGGAAAGTTTA-GGGT
* *
2118 TAAAAATGTAAGTTTTGGAAAATTTAGTGGT
1 TAAAAATGGAA-TTTTGGAAAGTTTAG-GGT
* *
2149 CAAAAATAGAATTTTGGAA
1 TAAAAATGGAATTTTGGAA
2168 TGTCTTCTGC
Statistics
Matches: 194, Mismatches: 50, Indels: 23
0.73 0.19 0.09
Matches are distributed among these distances:
28 13 0.07
29 84 0.43
30 87 0.45
31 10 0.05
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTGGAAAGTTTAGGGT
Found at i:2035 original size:30 final size:29
Alignment explanation
Indices: 1942--2133 Score: 124
Period size: 29 Copynumber: 6.6 Consensus size: 29
1932 AGTTTGGTGG
1942 TAAAAATGTAATTTTTAAAGAGTTTAGGGT
1 TAAAAATGTAATTTTT-AAGAGTTTAGGGT
* * ** *
1972 TAAATATGGAAGTTTGGAA-AGTTTAGGGA
1 TAAAAATGTAA-TTTTTAAGAGTTTAGGGT
* *
2001 TAAAAATGTTATTTTCTAAGAGTTTAAGGT
1 TAAAAATGTAATTTT-TAAGAGTTTAGGGT
* * * * *
2031 TAAAAGTGGAA-TTTTAGAAAGTTTGGGGG
1 TAAAAATGTAATTTTTA-AGAGTTTAGGGT
* *
2060 TAAAAATGTAACTTTTGGAA-AATTTAGGGT
1 TAAAAATGTAA-TTTT-TAAGAGTTTAGGGT
* * *
2090 T-AAAATGAAATTTTGAAAAGTTTATGGG-
1 TAAAAATGTAATTTTTAAGAGTTTA-GGGT
*
2118 TAAAAATGTAAGTTTT
1 TAAAAATGTAATTTTT
2134 GGAAAATTTA
Statistics
Matches: 122, Mismatches: 30, Indels: 21
0.71 0.17 0.12
Matches are distributed among these distances:
27 3 0.02
28 15 0.12
29 61 0.50
30 35 0.29
31 7 0.06
32 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (29 bp):
TAAAAATGTAATTTTTAAGAGTTTAGGGT
Found at i:2119 original size:58 final size:56
Alignment explanation
Indices: 1881--2164 Score: 225
Period size: 59 Copynumber: 4.8 Consensus size: 56
1871 AGACATTCGA
* * * * *
1881 GGTAAAAATGGTAATTTTGGAAAGTTCA-GGTTCAGAAACGGAATTCT-AGAAAGTTTGG
1 GGTAAAAAT-GTAATTTTGGAAAATTTAGGGTT-A-AAATGGAATTTTGA-AAAGTTTAG
* * *
1939 TGGTAAAAATGTAATTTT-TAAAGAGTTTAGGGTTAAATATGGAAGTTTGGAAAGTTTAG
1 -GGTAAAAATGTAATTTTGGAAA-A-TTTAGGGTTAAA-ATGGAATTTTGAAAAGTTTAG
* ** * * *
1998 GGATAAAAATGTTATTTTCTAAGAGTTTAAGGTTAAAAGTGGAATTTT-AGAAAGTTTGGG
1 GG-TAAAAATGTAATTTTGGAA-AATTTAGGGTTAAAA-TGGAATTTTGA-AAAGTTT-AG
*
2058 GGTAAAAATGTAACTTTTGGAAAATTTAGGGTTAAAATGAAATTTTGAAAAGTTTATG
1 GGTAAAAATGTAA-TTTTGGAAAATTTAGGGTTAAAATGGAATTTTGAAAAGTTTA-G
* *
2116 GGTAAAAATGTAAGTTTTGGAAAATTTAGTGGTCAAAAATAGAATTTTG
1 GGTAAAAATGTAA-TTTTGGAAAATTTAG-GGT-TAAAATGGAATTTTG
2165 GAATGTCTTC
Statistics
Matches: 184, Mismatches: 25, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
57 3 0.02
58 57 0.31
59 95 0.52
60 28 0.15
61 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (56 bp):
GGTAAAAATGTAATTTTGGAAAATTTAGGGTTAAAATGGAATTTTGAAAAGTTTAG
Found at i:2161 original size:118 final size:116
Alignment explanation
Indices: 1881--2163 Score: 311
Period size: 118 Copynumber: 2.4 Consensus size: 116
1871 AGACATTCGA
* * * * * *
1881 GGTAAAAATGGTAATTTTGGAAAGTTCAGGTTCAGAAACGGAATTCTAGAAAGTTTGGTGGTAAA
1 GGTAAAAAT-GTAATTTTGGAAAGTTTAGGGTCAAAAATGGAATTTTAGAAAGTTTGGGGGTAAA
* * *
1946 AATGTAATTTTTAAAGAGTTTAGGGTTAAATATGGAAGTTTGGAAAGTTTAG
65 AATGTAATTTTGAAAGAGTTTAGGGTTAAATATGAAAGTTTGAAAAGTTTAG
* ** * * *
1998 GGATAAAAATGTTATTTTCTAAGAGTTTAAGGTTAAAAGTGGAATTTTAGAAAGTTTGGGGGTAA
1 GG-TAAAAATGTAATTTTGGAA-AGTTTAGGGTCAAAAATGGAATTTTAGAAAGTTTGGGGGTAA
*
2063 AAATGTAACTTTTGGAAA-A-TTTAGGGTTAAA-ATGAAATTTTGAAAAGTTTATG
64 AAATGTAA-TTTT-GAAAGAGTTTAGGGTTAAATATGAAAGTTTGAAAAGTTTA-G
* *
2116 GGTAAAAATGTAAGTTTTGGAAAATTTAGTGGTCAAAAATAGAATTTT
1 GGTAAAAATGTAA-TTTTGGAAAGTTTAG-GGTCAAAAATGGAATTTT
2164 GGAATGTCTT
Statistics
Matches: 135, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
117 43 0.32
118 84 0.62
119 5 0.04
120 3 0.02
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (116 bp):
GGTAAAAATGTAATTTTGGAAAGTTTAGGGTCAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAA
ATGTAATTTTGAAAGAGTTTAGGGTTAAATATGAAAGTTTGAAAAGTTTAG
Found at i:4513 original size:72 final size:72
Alignment explanation
Indices: 4396--4603 Score: 292
Period size: 72 Copynumber: 2.9 Consensus size: 72
4386 ATGCAATGGG
* * * *
4396 AACATCTAATAAATCTGCGAGATCTTTCTCTCAAGAATTTTCCCAATTTAGCATCGCTTCCGGAG
1 AACATCTAATAAATCTGCAAGATCTTTCTCTCGAGAATTTGCCCAATTTAACATCGCTTCCGGAG
4461 GGGATTC
66 GGGATTC
* *
4468 AACATCTAATAAATCTGCAAGATCTTTCTCTCGCGAATTTGCCCAAGTTAACATCGCTTCCGGAG
1 AACATCTAATAAATCTGCAAGATCTTTCTCTCGAGAATTTGCCCAATTTAACATCGCTTCCGGAG
*
4533 TGGATTC
66 GGGATTC
* ** **
4540 AACATCTAATAAATCTGCAA-AGGCTTTCTCTCGTTAATTTGCCCAATTTAATGTCGCTTCCGGA
1 AACATCTAATAAATCTGCAAGA-TCTTTCTCTCGAGAATTTGCCCAATTTAACATCGCTTCCGGA
4604 TGAGATGCGT
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
71 1 0.01
72 121 0.99
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (72 bp):
AACATCTAATAAATCTGCAAGATCTTTCTCTCGAGAATTTGCCCAATTTAACATCGCTTCCGGAG
GGGATTC
Found at i:4767 original size:6 final size:6
Alignment explanation
Indices: 4756--4784 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4746 TATTGAAAAA
4756 CTACTC CTACTC CTACTC CTACTC CTACT
1 CTACTC CTACTC CTACTC CTACTC CTACT
4785 AATTCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.34
Consensus pattern (6 bp):
CTACTC
Done.