Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008752.1 Kokia drynarioides strain JFW-HI SEQ_123434, 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: 24518
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5135 original size:96 final size:98
Alignment explanation
Indices: 4971--5246 Score: 272
Period size: 96 Copynumber: 2.8 Consensus size: 98
4961 CTAGGAAGCT
* * * * ** * **
4971 TGAGGCCTGGTCTTGACAGACAATTGGTAGAGATGCTGAGAACCTTGAATGGTAACTTGCCTTAC
1 TGAGGCATAGTCTTGACAGACAAATGGTAGAGGTGCCAAGAACC-TAAATGGTAACTTGTATTAC
* *
5036 ATGCATGAGCACGAGC-AT-A-AGTATGAACGAG
65 ATGCATGAGCACGAGCAATCAGAGCATAAACGAG
* * * *
5067 TGAGGCATAGTCTTCACAGACAAGTGGTAGAGGTCCCAAGAACCATAAATGATAACTTGTATTAC
1 TGAGGCATAGTCTTGACAGACAAATGGTAGAGGTGCCAAGAACC-TAAATGGTAACTTGTATTAC
5132 ATGCATGAGCATGAACGAGCAATGCATGAGCATAAACGAG
65 ATGCATGAGC----ACGAGCAAT-CA-GAGCATAAACGAG
* * **
5172 CGAGGCATAGTCTTGACAGACAAAAGGTAGAGGTGCCAAGAA-CTAAACTGGTAACTCATATTAC
1 TGAGGCATAGTCTTGACAGACAAATGGTAGAGGTGCCAAGAACCTAAA-TGGTAACTTGTATTAC
5236 ATGCATGAGCA
65 ATGCATGAGCA
5247 GAAGCCAGCA
Statistics
Matches: 147, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
96 62 0.42
100 7 0.05
101 2 0.01
103 5 0.03
104 24 0.16
105 47 0.32
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (98 bp):
TGAGGCATAGTCTTGACAGACAAATGGTAGAGGTGCCAAGAACCTAAATGGTAACTTGTATTACA
TGCATGAGCACGAGCAATCAGAGCATAAACGAG
Found at i:5156 original size:21 final size:21
Alignment explanation
Indices: 5132--5172 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5122 CTTGTATTAC
*
5132 ATGCATGAGCATGAACGAGCA
1 ATGCATGAGCATAAACGAGCA
5153 ATGCATGAGCATAAACGAGC
1 ATGCATGAGCATAAACGAGC
5173 GAGGCATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.15
Consensus pattern (21 bp):
ATGCATGAGCATAAACGAGCA
Found at i:5179 original size:21 final size:21
Alignment explanation
Indices: 5134--5179 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5124 TGTATTACAT
* *
5134 GCATGAGCATGAACGAGCAAT
1 GCATGAGCATAAACGAGCAAG
*
5155 GCATGAGCATAAACGAGCGAG
1 GCATGAGCATAAACGAGCAAG
5176 GCAT
1 GCAT
5180 AGTCTTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (21 bp):
GCATGAGCATAAACGAGCAAG
Found at i:5754 original size:78 final size:78
Alignment explanation
Indices: 5625--5785 Score: 277
Period size: 78 Copynumber: 2.1 Consensus size: 78
5615 CATCTTTGGT
* * * *
5625 TGCTTTGCTTTACTTGATGTTTAGTGCCTAACTAATTCTAAATTCTTATGATTATTGACTACTTC
1 TGCTTTGCTTTACTAGATCTTTAGTGCCTAACTAATTCTAAATTCATATGATTATTGACTACATC
5690 TAAACAAGTTGCA
66 TAAACAAGTTGCA
*
5703 TGCTTTGCTTTACTAGATCTTTAGTGCCTAACTAATTCTAAATTCATATGATTATTGATTACATC
1 TGCTTTGCTTTACTAGATCTTTAGTGCCTAACTAATTCTAAATTCATATGATTATTGACTACATC
5768 TAAACAAGTTGCA
66 TAAACAAGTTGCA
5781 TGCTT
1 TGCTT
5786 ACATGGATAC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (78 bp):
TGCTTTGCTTTACTAGATCTTTAGTGCCTAACTAATTCTAAATTCATATGATTATTGACTACATC
TAAACAAGTTGCA
Found at i:6738 original size:21 final size:21
Alignment explanation
Indices: 6712--6755 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
6702 TGTCAAGACT
6712 ATGCCTCGCTCGTTCATGCTC
1 ATGCCTCGCTCGTTCATGCTC
*
6733 ATGCCTTGCTCGTTCATGCTC
1 ATGCCTCGCTCGTTCATGCTC
6754 AT
1 AT
6756 ACATGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.34, G:0.18, T:0.36
Consensus pattern (21 bp):
ATGCCTCGCTCGTTCATGCTC
Found at i:6834 original size:105 final size:96
Alignment explanation
Indices: 6652--6911 Score: 306
Period size: 105 Copynumber: 2.6 Consensus size: 96
6642 CTATCATTTG
* **
6652 CATGTAATACAAGTTACCATGTAAGGTTCTTGGCACCTCTACCTTTTGTCTGTCAAGACTATGCC
1 CATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCAATTGTCTGTCAAGACTATGCC
* *
6717 TCGCTCGTTCATGCTCATGCCT-TGCTCGTTCATGCTCATA
66 TCACTCGGTCATG-T--T---TATGCTCG----TGCTCATA
* * * *
6757 CATGTAATACAAGTTATCATTTATGGTTCTTGGCACCTCTACCACTTGTCTGTGAAGACTATGCC
1 CATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCAATTGTCTGTCAAGACTATGCC
*
6822 TCACTCGGTCATGTTTATGCTCGTGCTCATG
66 TCACTCGGTCATGTTTATGCTCGTGCTCATA
* * *
6853 CATGTAAGACAAGTTACCATTCAAGGTTCTCGGCACCTCTACCAATTGTCTGTCAAGAC
1 CATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCAATTGTCTGTCAAGAC
6912 ACTCAAGACC
Statistics
Matches: 138, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
96 59 0.43
99 1 0.01
100 6 0.04
102 1 0.01
104 1 0.01
105 70 0.51
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (96 bp):
CATGTAATACAAGTTACCATTTAAGGTTCTTGGCACCTCTACCAATTGTCTGTCAAGACTATGCC
TCACTCGGTCATGTTTATGCTCGTGCTCATA
Found at i:9756 original size:45 final size:45
Alignment explanation
Indices: 9692--9782 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
9682 CTTCTAAAGC
9692 TAAGGGTAAAGGTAAAGTGGTGGAGAGCTAGGCAAGAAGCTTTGT
1 TAAGGGTAAAGGTAAAGTGGTGGAGAGCTAGGCAAGAAGCTTTGT
9737 TAAGGGTAAAGGTAAAGTGGTGGAGAGCTAGGCAAGAAGCTTTGT
1 TAAGGGTAAAGGTAAAGTGGTGGAGAGCTAGGCAAGAAGCTTTGT
9782 T
1 T
9783 GGTGTTCTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.07, G:0.37, T:0.23
Consensus pattern (45 bp):
TAAGGGTAAAGGTAAAGTGGTGGAGAGCTAGGCAAGAAGCTTTGT
Found at i:15114 original size:17 final size:17
Alignment explanation
Indices: 15092--15126 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
15082 TATAGACTCG
*
15092 TTTAGATATACTTAGTA
1 TTTAGATATAATTAGTA
15109 TTTAGATATAATTAGTA
1 TTTAGATATAATTAGTA
15126 T
1 T
15127 AATAAACGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (17 bp):
TTTAGATATAATTAGTA
Found at i:15640 original size:12 final size:12
Alignment explanation
Indices: 15623--15649 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15613 ATTCCTTCTA
15623 AAAGTTCATATC
1 AAAGTTCATATC
15635 AAAGTTCATATC
1 AAAGTTCATATC
15647 AAA
1 AAA
15650 ATAGTACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (12 bp):
AAAGTTCATATC
Found at i:18245 original size:20 final size:21
Alignment explanation
Indices: 18179--18247 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
18169 TCACTTCGTT
18179 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
18200 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
* * *
18221 TCTTTTTGTCTAACTCACTTC
1 TCTTTTTGTCCAAGTTACTTC
18242 -CTTTTT
1 TCTTTTT
18248 TCTTTGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:18931 original size:13 final size:13
Alignment explanation
Indices: 18913--18937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18903 AAACTTGATC
18913 GTTATAATAAAAT
1 GTTATAATAAAAT
18926 GTTATAATAAAA
1 GTTATAATAAAA
18938 GGATGGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
GTTATAATAAAAT
Found at i:19146 original size:23 final size:21
Alignment explanation
Indices: 19091--19133 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
19081 ATTTATAAAA
19091 TTTTATAATTCTT-TAAATTTT
1 TTTTATAATT-TTATAAATTTT
19112 TTTTATAATTTTATAAATTTT
1 TTTTATAATTTTATAAATTTT
19133 T
1 T
19134 ATTTTTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATAATTTTATAAATTTT
Found at i:20153 original size:18 final size:18
Alignment explanation
Indices: 20127--20165 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
20117 TGACGTACAT
* *
20127 AAATTTAAAATATTTTTA
1 AAATATAAAATAATTTTA
*
20145 AAATATAAACTAATTTTA
1 AAATATAAAATAATTTTA
20163 AAA
1 AAA
20166 AGTATAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATAAAATAATTTTA
Done.