Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011114.1 Kokia drynarioides strain JFW-HI SEQ_126087, 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: 23174
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:136 original size:24 final size:25
Alignment explanation
Indices: 104--150 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
94 AGTTAAATTG
*
104 AAATTTTT-GAAGGTTCGAGGGTCA
1 AAATTTTTGGAAAGTTCGAGGGTCA
128 AAATTTTTGGAAAGTTCGAGGGT
1 AAATTTTTGGAAAGTTCGAGGGT
151 TAAATTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.34
Consensus pattern (25 bp):
AAATTTTTGGAAAGTTCGAGGGTCA
Found at i:165 original size:30 final size:29
Alignment explanation
Indices: 63--173 Score: 108
Period size: 30 Copynumber: 3.9 Consensus size: 29
53 CATTAAAATC
*
63 GGGTCAAATTTGAATTTTTGGAAAGTAT-GA
1 GGGTTAAA-TTGAATTTTTGGAAAGT-TCGA
* *
93 GAGTTAAATTGAAATTTTT-GAAGGTTCGA
1 GGGTTAAATTG-AATTTTTGGAAAGTTCGA
*
122 GGG-TCAA---AATTTTTGGAAAGTTCGA
1 GGGTTAAATTGAATTTTTGGAAAGTTCGA
147 GGGTTAAATTTGAATTTTTGGAAAGTT
1 GGGTTAAA-TTGAATTTTTGGAAAGTT
174 TAAGGGCTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
24 7 0.11
25 12 0.18
26 3 0.05
28 4 0.06
29 12 0.18
30 28 0.42
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (29 bp):
GGGTTAAATTGAATTTTTGGAAAGTTCGA
Found at i:2205 original size:44 final size:44
Alignment explanation
Indices: 2142--2276 Score: 153
Period size: 50 Copynumber: 2.9 Consensus size: 44
2132 CCCTTTTATA
* *
2142 GCTTTAGAGGTATAGGATTTGTCGTTTTATCGTCATTCTCTACG
1 GCTTTAGAGGTATAGGATTTGTCATTCTATCGTCATTCTCTACG
* * *
2186 GCTTTAGAGGTATAGGATTTGTCATTACAACTTCAATTCGTTCCTCTACG
1 GCTTTAGAGGTATAGGATTTGTCATT-CTA--TC--GTCATT-CTCTACG
* *
2236 GCTTTAGAGGTATAGGATTCGTCATTCTATCGCCATTCTCT
1 GCTTTAGAGGTATAGGATTTGTCATTCTATCGTCATTCTCT
2277 GAGTATATGA
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
44 29 0.39
45 4 0.05
47 4 0.05
49 6 0.08
50 32 0.43
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (44 bp):
GCTTTAGAGGTATAGGATTTGTCATTCTATCGTCATTCTCTACG
Found at i:10910 original size:18 final size:19
Alignment explanation
Indices: 10884--10921 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
10874 CAGTTGGTTC
*
10884 GAGGGACAA-GAAAAGAAA
1 GAGGCACAAGGAAAAGAAA
*
10902 GAGGCACAAGGGAAAGAAA
1 GAGGCACAAGGAAAAGAAA
10921 G
1 G
10922 TGAAGAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.37, T:0.00
Consensus pattern (19 bp):
GAGGCACAAGGAAAAGAAA
Found at i:13312 original size:20 final size:20
Alignment explanation
Indices: 13287--13324 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13277 TATCAACTAT
13287 ACTTGCATCAA-CGTGTGTAC
1 ACTTGCA-CAATCGTGTGTAC
13307 ACTTGCACAATCGTGTGT
1 ACTTGCACAATCGTGTGT
13325 CGTAAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
ACTTGCACAATCGTGTGTAC
Found at i:14595 original size:24 final size:21
Alignment explanation
Indices: 14547--14598 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
14537 CTCTGAACCT
* *
14547 CTCCTCTAACCATTTACAATG
1 CTCCTCCAACCATTTACAATC
*
14568 CTCCTCCAACCATTTACAACC
1 CTCCTCCAACCATTTACAATC
14589 CTCCTCCAAC
1 CTCCTCCAAC
14599 TAGTTAGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.44, G:0.02, T:0.27
Consensus pattern (21 bp):
CTCCTCCAACCATTTACAATC
Found at i:18712 original size:23 final size:23
Alignment explanation
Indices: 18680--18809 Score: 129
Period size: 23 Copynumber: 5.7 Consensus size: 23
18670 GCTGAGGAAA
*
18680 CAGTAAGCACACACAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
* **
18703 CAGTAGGCACACGTAGTGCAAAAT
1 CAGTAAGCACACACAGTGC-AAAT
*
18727 -ACTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
18749 CAATAAGCACATATAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
18772 CAATAACCACACACAGTGCTGAA-
1 CAGTAAGCACACACAGTGC-AAAT
18795 CAGTAAGCACACACA
1 CAGTAAGCACACACA
18810 CAGTGCTGAA
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
22 4 0.05
23 78 0.90
24 5 0.06
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.15
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:18733 original size:46 final size:46
Alignment explanation
Indices: 18683--18807 Score: 155
Period size: 46 Copynumber: 2.7 Consensus size: 46
18673 GAGGAAACAG
* * *
18683 TAAGCACACACAGTGCGAATCAGTAGGCACACGTAGTGCAAAAT-AC
1 TAAGCACACACAGTGCGAATCAGTAAGCACACATAGTGC-AAATCAA
* * *
18729 TAAGCACACACAGTGCAAATCAATAAGCACATATAGTGCAAATCAA
1 TAAGCACACACAGTGCGAATCAGTAAGCACACATAGTGCAAATCAA
*
18775 TAACCACACACAGTGCTGAA-CAGTAAGCACACA
1 TAAGCACACACAGTGC-GAATCAGTAAGCACACA
18808 CACAGTGCTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 4 0.06
46 61 0.91
47 2 0.03
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.15
Consensus pattern (46 bp):
TAAGCACACACAGTGCGAATCAGTAAGCACACATAGTGCAAATCAA
Found at i:18807 original size:25 final size:25
Alignment explanation
Indices: 18779--18826 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
18769 AATCAATAAC
18779 CACACACAGTGCTGAACAGTAAGCA
1 CACACACAGTGCTGAACAGTAAGCA
*
18804 CACACACAGTGCTGAATAGTAAG
1 CACACACAGTGCTGAACAGTAAG
18827 AGCGCTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (25 bp):
CACACACAGTGCTGAACAGTAAGCA
Found at i:22589 original size:29 final size:28
Alignment explanation
Indices: 22557--22788 Score: 98
Period size: 29 Copynumber: 7.9 Consensus size: 28
22547 TAGACATCCG
22557 AAGGT-AAAATGGTAATTTTTGGAAAAATC
1 AAGGTAAAAATGG-AA-TTTTGGAAAAATC
* * **
22586 AAGGCTAAAAATGGAATTTTTGTAAGTTC
1 AAGG-TAAAAATGGAATTTTGGAAAAATC
** *
22615 GGGGGT-AAAATGGTAATTTTGGAAAAATT
1 -AAGGTAAAAATGG-AATTTTGGAAAAATC
* ** *
22644 AGGGTTAAAAATGGAATTTT-GAGAAGTTT
1 AAGG-TAAAAATGGAATTTTGGA-AAAATC
* *
22673 AAGGGT-AAAATGTTATTTTTTTTGGAAAAATC
1 AA-GGTAAAAATG-GA---ATTTTGGAAAAATC
** **
22705 GCGGTCAAAAATGGAATTTTTGG-AAGTTC
1 AAGGT-AAAAATGGAA-TTTTGGAAAAATC
* *
22734 GAGGGT-AAAATGGTAATTTTGGAAAAATT
1 -AAGGTAAAAATGG-AATTTTGGAAAAATC
22763 AAGGTTAAAAATGGAATTTTGGAAAA
1 AAGG-TAAAAATGGAATTTTGGAAAA
22789 GTTCAAGGGT
Statistics
Matches: 150, Mismatches: 32, Indels: 42
0.67 0.14 0.19
Matches are distributed among these distances:
28 34 0.23
29 60 0.40
30 30 0.20
31 10 0.07
32 8 0.05
33 8 0.05
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.33
Consensus pattern (28 bp):
AAGGTAAAAATGGAATTTTGGAAAAATC
Found at i:22663 original size:58 final size:58
Alignment explanation
Indices: 22506--22804 Score: 309
Period size: 58 Copynumber: 5.0 Consensus size: 58
22496 CAAGGACAAT
** * * *
22506 ATGGTAATTTTGGGAAAGTTTAGGGTTAAAAATGGAATTTTTAGACA-TCCGAAGGTAAA
1 ATGGTAATTTT-GGAAAAATTAGGGTTAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAA
* * * * *
22565 ATGGTAATTTTTGGAAAAATCAAGGCTAAAAATGGAATTTTTGTAAGTTCGGGGGTAAA
1 ATGGTAA-TTTTGGAAAAATTAGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
**
22624 ATGGTAATTTTGGAAAAATTAGGGTTAAAAATGGAA-TTTTGAGAAGTTTAAGGGTAAA
1 ATGGTAATTTTGGAAAAATTAGGGTTAAAAATGGAATTTTTG-GAAGTTCGAGGGTAAA
* * * *
22682 ATGTTATTTTTTTTGGAAAAA-TCGCGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
1 ATGGTA---ATTTTGGAAAAATTAG-GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
* *
22743 ATGGTAATTTTGGAAAAATTAAGGTTAAAAATGGAA-TTTTGGAAAAGTTCAAGGGTCAAA
1 ATGGTAATTTTGGAAAAATTAGGGTTAAAAATGGAATTTTTGG--AAGTTCGAGGGT-AAA
22803 AT
1 AT
22805 ATGATTTTTG
Statistics
Matches: 199, Mismatches: 29, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
57 11 0.06
58 68 0.34
59 61 0.31
60 11 0.06
61 43 0.22
62 5 0.03
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (58 bp):
ATGGTAATTTTGGAAAAATTAGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
Found at i:22740 original size:119 final size:119
Alignment explanation
Indices: 22506--22813 Score: 392
Period size: 119 Copynumber: 2.6 Consensus size: 119
22496 CAAGGACAAT
** * * *
22506 ATGGTAATTTTGGGAAAGTTTAGGGTTAAAAATGGAATTTTTAGACA-TCCGAA-GGTAAAATGG
1 ATGGTAATTTT-GGAAAAATTAGGGTTAAAAATGGAATTTTGAGA-AGTTC-AAGGGTAAAATGT
* * *
22569 TA--ATTTTTGGAAAAATCAAGGCTAAAAATGGAATTTTTGTAAGTTCGGGGGTAAA
63 TATTTTTTTTGGAAAAATCAAGGCTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
*
22624 ATGGTAATTTTGGAAAAATTAGGGTTAAAAATGGAATTTTGAGAAGTTTAAGGGTAAAATGTTAT
1 ATGGTAATTTTGGAAAAATTAGGGTTAAAAATGGAATTTTGAGAAGTTCAAGGGTAAAATGTTAT
**
22689 TTTTTTTGGAAAAATCGCGG-TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
66 TTTTTTTGGAAAAATCAAGGCT-AAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
* * * *
22743 ATGGTAATTTTGGAAAAATTAAGGTTAAAAATGGAATTTTGGAAAAGTTCAAGGGTCAAAATATG
1 ATGGTAATTTTGGAAAAATTAGGGTTAAAAATGGAATTTT-GAGAAGTTCAAGGGT-AAAATGTT
22808 ATTTTT
64 ATTTTT
22814 GGATAGTTTA
Statistics
Matches: 167, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
116 3 0.02
117 42 0.25
118 12 0.07
119 85 0.51
120 13 0.08
121 12 0.07
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (119 bp):
ATGGTAATTTTGGAAAAATTAGGGTTAAAAATGGAATTTTGAGAAGTTCAAGGGTAAAATGTTAT
TTTTTTTGGAAAAATCAAGGCTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAA
Found at i:22812 original size:30 final size:29
Alignment explanation
Indices: 22621--22816 Score: 84
Period size: 30 Copynumber: 6.6 Consensus size: 29
22611 GTTCGGGGGT
* *
22621 AAAATGGTAATTTTGGAAAAATTAGGGTTA
1 AAAATGG-AATTTTGGAAAAATTAAGGTCA
**
22651 AAAATGGAATTTT-GAGAAGTTTAAGGGT--
1 AAAATGGAATTTTGGA-AAAATTAA-GGTCA
* * ***
22679 AAAATGTTATTTTTTTTGGAAAAATCGCGGTCA
1 AAAATG-GA---ATTTTGGAAAAATTAAGGTCA
* *
22712 AAAATGGAATTTTTGG--AAGTTCGAGGGT--
1 AAAATGGAA-TTTTGGAAAAATT--AAGGTCA
*
22740 AAAATGGTAATTTTGGAAAAATTAAGGTTA
1 AAAATGG-AATTTTGGAAAAATTAAGGTCA
*
22770 AAAATGGAATTTTGGAAAAGTTCAAGGGTCA
1 AAAATGGAATTTTGGAAAAATT-AA-GGTCA
*
22801 AAATAT-GATTTTTGGA
1 AAA-ATGGAATTTTGGA
22817 TAGTTTAGGG
Statistics
Matches: 125, Mismatches: 21, Indels: 39
0.68 0.11 0.21
Matches are distributed among these distances:
28 28 0.22
29 28 0.22
30 32 0.26
31 19 0.15
32 10 0.08
33 8 0.06
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTGGAAAAATTAAGGTCA
Done.