Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004254.1 Kokia drynarioides strain JFW-HI SEQ_117538, 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: 5936
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:1607 original size:59 final size:57
Alignment explanation
Indices: 1556--2061 Score: 382
Period size: 59 Copynumber: 8.6 Consensus size: 57
1546 TTTAGGAAAA
* *
1556 TTCGGGGATAAAAATGGAATTTTTAGACA-TTCGGGGTTGAAAATGGGATTTTTGGAAG
1 TTCGGGGATAAAAATGGAATTTTTAGA-AGTTTGGGGTTAAAAATGGGA-TTTTGGAAG
* * * *
1614 TTC-AGGAGTAAAAATGAAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAG
1 TTCGGGGA-TAAAAATGGAATTTTTAGAAG-TTTGGGGTTAAAAATGGGA-TTTTGGAAG
* * * *
1673 TTTGGAGATAAAAATTGAATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGAAG
1 TTCGGGGATAAAAATGGAATTTTTAGAAG-TTTGGGGTTAAAAATGGGATTTTGGAAG
* * * * *
1731 TTTGGGGGTAAAAATGAAATTTTTAGAAGTTTTGAGG-TCAAAATGGGAGTTTTGGAAG
1 TTCGGGGATAAAAATGGAATTTTTAGAAG-TTTGGGGTTAAAAATGGGA-TTTTGGAAG
*** * * * * *
1789 TTTAAGG-TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAG
1 TTCGGGGAT-AAAAATGGAATTTTTAGAAGTTTGGGGTTAAAAATGGGA-TTTTGGAAG
* * ** *
1847 TTTCGGGGATAAAAATGGGATTTTTAGAAGTTCGAGGG-TAAAAATGAAGTTTTTTAGAAG
1 -TTCGGGGATAAAAATGGAATTTTTAGAAGTTTG-GGGTTAAAAATG--GGATTTTGGAAG
* * * * * *
1907 TTTCGAGGTTAAAAATGGGATTTTT-GATAGTTCGAGGG-TAAAAATGAGATTTTTAGAAG
1 -TTCGGGGATAAAAATGGAATTTTTAGA-AGTTTG-GGGTTAAAAATGGGA-TTTTGGAAG
* * * * *
1966 TTCAAGGG-TAAAAATAGAATTTTTAAAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAG
1 TTC-GGGGATAAAAATGGAATTTTTAGAAGTTT-GGGGTTAAAAATGGGA-TTTTGGAAG
*
2025 TTCGAGGG-TAAAAATAGAATTTTTAGAAGTTTCGGGG
1 TTCG-GGGATAAAAATGGAATTTTTAGAAGTTT-GGGG
2062 ACCTCCAAGG
Statistics
Matches: 374, Mismatches: 55, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
57 20 0.05
58 131 0.35
59 167 0.45
60 55 0.15
61 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (57 bp):
TTCGGGGATAAAAATGGAATTTTTAGAAGTTTGGGGTTAAAAATGGGATTTTGGAAG
Found at i:1658 original size:30 final size:29
Alignment explanation
Indices: 1556--2061 Score: 433
Period size: 29 Copynumber: 17.2 Consensus size: 29
1546 TTTAGGAAAA
*
1556 TTCGGGGATAAAAATGGAATTTTTAGACA--
1 TTCGGGG-TAAAAATGGGATTTTTAGA-AGT
* *
1585 TTCGGGGTTGAAAATGGGATTTTTGGAAG-
1 TTCGGGG-TAAAAATGGGATTTTTAGAAGT
* ** *
1614 TTCAGGAGTAAAAATGAAATTTTTGGAAGT
1 TTC-GGGGTAAAAATGGGATTTTTAGAAGT
*
1644 TTTGGGGTTAAAAATGGGATTTTTAGAAGT
1 TTCGGGG-TAAAAATGGGATTTTTAGAAGT
* * *
1674 TT-GGAGATAAAAATTGAATTTTTAGAAGT
1 TTCGG-GGTAAAAATGGGATTTTTAGAAGT
*
1703 TTTGGGGTTAAAAATGGGATTTTT-GAAGT
1 TTCGGGG-TAAAAATGGGATTTTTAGAAGT
* **
1732 TTGGGGGTAAAAATGAAATTTTTAGAAGT
1 TTCGGGGTAAAAATGGGATTTTTAGAAGT
* * * * *
1761 TTTGAGGTCAAAATGGGAGTTTTGGAAGT
1 TTCGGGGTAAAAATGGGATTTTTAGAAGT
** *
1790 TT-AAGGTCAAAAATGGGATTTTTGGAAG-
1 TTCGGGGT-AAAAATGGGATTTTTAGAAGT
* *
1818 TTCGGGGGTAAAAATGGAATTTTTGGAAGT
1 TTC-GGGGTAAAAATGGGATTTTTAGAAGT
1848 TTCGGGGATAAAAATGGGATTTTTAGAAG-
1 TTCGGGG-TAAAAATGGGATTTTTAGAAGT
* *
1877 TTCGAGGGTAAAAATGAAGTTTTTTAGAAGT
1 TTCG-GGGTAAAAATG-GGATTTTTAGAAGT
*
1908 TTCGAGGTTAAAAATGGGATTTTT-GATAG-
1 TTCG-GGGTAAAAATGGGATTTTTAGA-AGT
*
1937 TTCGAGGGTAAAAATGAGATTTTTAGAAG-
1 TTCG-GGGTAAAAATGGGATTTTTAGAAGT
* * * *
1966 TTCAAGGGTAAAAATAGAATTTTTAAAAGT
1 TTC-GGGGTAAAAATGGGATTTTTAGAAGT
* *
1996 TTCGAGGTCAAAAATGGGATTTTTGGAAG-
1 TTCGGGGT-AAAAATGGGATTTTTAGAAGT
* *
2025 TTCGAGGGTAAAAATAGAATTTTTAGAAGT
1 TTCG-GGGTAAAAATGGGATTTTTAGAAGT
2055 TTCGGGG
1 TTCGGGG
2062 ACCTCCAAGG
Statistics
Matches: 395, Mismatches: 59, Indels: 46
0.79 0.12 0.09
Matches are distributed among these distances:
28 21 0.05
29 241 0.61
30 118 0.30
31 15 0.04
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
TTCGGGGTAAAAATGGGATTTTTAGAAGT
Found at i:2027 original size:88 final size:85
Alignment explanation
Indices: 1556--2055 Score: 431
Period size: 88 Copynumber: 5.7 Consensus size: 85
1546 TTTAGGAAAA
* * *
1556 TTCGGGGATAAAAATGGAATTTTTAGACA-TTCGGGGTTGAAAATGGGATTTTTGGAAGTTC-AG
1 TTCGGGG-TAAAAATGGAATTTTTAGA-AGTTCGGGG-TAAAAATGAGATTTTTAGAAGTTCAAG
*
1619 GAGTAAAAATGAAATTTTTGGAAGT
63 G-GTAAAAATG-AATTTTTAGAAGT
* * * * ***
1644 TTTGGGGTTAAAAATGGGATTTTTAGAAGTTTGGAGATAAAAATTGA-ATTTTTAGAAGTTTTGG
1 TTCGGGG-TAAAAATGGAATTTTTAGAAGTTCGG-GGTAAAAA-TGAGATTTTTAGAAGTTCAAG
*
1708 GGTTAAAAATGGGATTTTT-GAAGT
63 GG-TAAAAAT-GAATTTTTAGAAGT
* * * * * * * * *
1732 TTGGGGGTAAAAATGAAATTTTTAGAAGTTTTGAGGTCAAAATGGGAGTTTTGGAAGTTTAA-GG
1 TTCGGGGTAAAAATGGAATTTTTAGAAG-TTCGGGGTAAAAATGAGATTTTTAGAAGTTCAAGGG
* *
1796 TCAAAAATGGGATTTTTGGAAG-
65 T-AAAAAT-GAATTTTTAGAAGT
* * *
1818 TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGATAAAAATGGGATTTTTAGAAGTTCGAG
1 TTC-GGGGTAAAAATGGAATTTTTAGAAG-TTCGGGG-TAAAAATGAGATTTTTAGAAGTTCAAG
1883 GGTAAAAATGAAGTTTTTTAGAAGT
63 GGTAAAAATGAA--TTTTTAGAAGT
* *
1908 TTCGAGGTTAAAAATGGGATTTTT-GATAGTTCGAGGGTAAAAATGAGATTTTTAGAAGTTCAAG
1 TTCG-GGGTAAAAATGGAATTTTTAGA-AGTTCG-GGGTAAAAATGAGATTTTTAGAAGTTCAAG
*
1972 GGTAAAAATAGAATTTTTAAAAGT
63 GGTAAAAAT-GAATTTTTAGAAGT
* * *
1996 TTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAAT-AGAATTTTTAGAAGTT
1 TTCGGGGT-AAAAATGGAATTTTTAGAAGTTCG-GGGTAAAAATGAG-ATTTTTAGAAGTT
2056 TCGGGGACCT
Statistics
Matches: 348, Mismatches: 41, Indels: 46
0.80 0.09 0.11
Matches are distributed among these distances:
85 1 0.00
86 21 0.06
87 77 0.22
88 147 0.42
89 73 0.21
90 29 0.08
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (85 bp):
TTCGGGGTAAAAATGGAATTTTTAGAAGTTCGGGGTAAAAATGAGATTTTTAGAAGTTCAAGGGT
AAAAATGAATTTTTAGAAGT
Found at i:3839 original size:19 final size:19
Alignment explanation
Indices: 3784--3839 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
3774 GGCTTAGGGT
3784 ATTTGGGCTGACTTGGGCC
1 ATTTGGGCTGACTTGGGCC
**
3803 ATTTTAG-T-A--T-GG-C
1 ATTTGGGCTGACTTGGGCC
3816 ATTTGGGCTGACTTGGGCC
1 ATTTGGGCTGACTTGGGCC
3835 ATTTG
1 ATTTG
3840 TAATTTAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 12
0.63 0.09 0.28
Matches are distributed among these distances:
13 6 0.22
14 3 0.11
15 2 0.07
17 2 0.07
18 3 0.11
19 11 0.41
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.38
Consensus pattern (19 bp):
ATTTGGGCTGACTTGGGCC
Found at i:3944 original size:17 final size:17
Alignment explanation
Indices: 3886--3955 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
3876 TTTTGACTTT
* *
3886 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
* *
3904 TTTAAATTT-AGATTAA
1 TTTAAATTTAAAATAAA
3920 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
3937 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
3954 TT
1 TT
3956 AAAAAGGGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
16 13 0.30
17 22 0.51
18 8 0.19
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:3950 original size:7 final size:6
Alignment explanation
Indices: 3886--3948 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
3876 TTTTGACTTT
* *
3886 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
3932 -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
3949 ATAAATTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 1 0.02
5 11 0.24
6 32 0.70
7 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:4834 original size:258 final size:258
Alignment explanation
Indices: 4377--4905 Score: 873
Period size: 258 Copynumber: 2.1 Consensus size: 258
4367 TCCCTGTATT
* * *
4377 TCATCAGAAAGCTAACCGTTTTATTACTTGCTTCGATCGACTTCTCTATATCTTATCAGGAAGAT
1 TCATCAGGAAGCTAACCGTTTTATTACTTGCTTCGACCGACTTCTCGATATCTTATCAGGAAGAT
4442 AGGGTTCGAAGATTTCGCTTGCTTTGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
66 AGGGTTCGAAGATTTCGCTTGCTTTGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
*
4507 AGGAAGATGACCGCATCTCTTGTTTCAATCAGTTTCTCTATATCTCATCAGGAGAACGAATTTGG
131 AGGAAGATGACCGCATCTCTTGTTTCAATCAGCTTCTCTATATCTCATCAGGAGAACGAATTTGG
*
4572 TTCACTTCTCAGTGTCTCATCAGAAAGCTAACCGTTTATTGCTTCAACCTGCTTCTCAGTGTC
196 TTCACTTCTCAGTATCTCATCAGAAAGCTAACCGTTTATTGCTTCAACCTGCTTCTCAGTGTC
* * * * * *
4635 TCATCAGGAAGCTAACTGTTTTATTACTTGCTTTGACCGGCTTCTCGGTGTCTTATCAGGAAGTT
1 TCATCAGGAAGCTAACCGTTTTATTACTTGCTTCGACCGACTTCTCGATATCTTATCAGGAAGAT
* *
4700 GGGGTTCGAAGATTTCGCTTGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCAGT
66 AGGGTTCGAAGATTTCGCTTGCTTTGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCA-T
*
4765 -AGGAAGATGACCGCATCTCTTGTTTCAATTC-GCTTCTCTGTATCTCATCAGGAGAACGAATTT
130 CAGGAAGATGACCGCATCTCTTGTTTCAA-TCAGCTTCTCTATATCTCATCAGGAGAACGAATTT
* * *
4828 GGTTCACTTCTTAGTATCTCATCAGAAAGCTAACCGTTTATTGCTTCGACCTGCTTCTCGGTGTC
194 GGTTCACTTCTCAGTATCTCATCAGAAAGCTAACCGTTTATTGCTTCAACCTGCTTCTCAGTGTC
4893 TCATCAGGAAGCT
1 TCATCAGGAAGCT
4906 GGGGTTCAGA
Statistics
Matches: 252, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
258 249 0.99
259 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (258 bp):
TCATCAGGAAGCTAACCGTTTTATTACTTGCTTCGACCGACTTCTCGATATCTTATCAGGAAGAT
AGGGTTCGAAGATTTCGCTTGCTTTGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
AGGAAGATGACCGCATCTCTTGTTTCAATCAGCTTCTCTATATCTCATCAGGAGAACGAATTTGG
TTCACTTCTCAGTATCTCATCAGAAAGCTAACCGTTTATTGCTTCAACCTGCTTCTCAGTGTC
Found at i:5075 original size:152 final size:152
Alignment explanation
Indices: 4807--5124 Score: 507
Period size: 152 Copynumber: 2.1 Consensus size: 152
4797 CTTCTCTGTA
* *
4807 TCTCATCAGG-AGAACGAATTTGGTTCACTTCTTAGTATCTCATCAGAAAGCTAACCGTTTATTG
1 TCTCACCAGGAAG-ACGAATTTGGTTCACTTCTCAGTATCTCATCAGAAAGCTAACCGTTTATTG
* * * *
4871 CTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCAGAGATTTTGCTCGCTTTGAGCC
65 CTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTAGGATTCAGAGATTTTGCTCACTTTGAGCC
4936 TCGTTTGGGTCTTCTTCTCAATG
130 TCGTTTGGGTCTTCTTCTCAATG
*
4959 TCTCACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATTG
1 TCTCACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGAAAGCTAACCG-TTTATTG
*
5024 CTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTAGGATTC-GAAGA-TTTGCTCATTTTGAGC
65 CTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTAGGATTCAG-AGATTTTGCTCACTTTGAGC
*
5087 CTCGTTTGGGTCTTCTTCTCAGTG
129 CTCGTTTGGGTCTTCTTCTCAATG
5111 TCTCACCAGGAAGA
1 TCTCACCAGGAAGA
5125 TGATCACATT
Statistics
Matches: 154, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
152 103 0.67
153 51 0.33
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (152 bp):
TCTCACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGAAAGCTAACCGTTTATTGC
TTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTAGGATTCAGAGATTTTGCTCACTTTGAGCCT
CGTTTGGGTCTTCTTCTCAATG
Found at i:5649 original size:23 final size:23
Alignment explanation
Indices: 5618--5664 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5608 AGAATTCTAT
* *
5618 TAAATGAGGATAAAAGGAAACAA
1 TAAAAGAGGATAAAAGAAAACAA
*
5641 TAAAAGAGGATCAAAGAAAACAA
1 TAAAAGAGGATAAAAGAAAACAA
5664 T
1 T
5665 TACTAGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.06, G:0.19, T:0.13
Consensus pattern (23 bp):
TAAAAGAGGATAAAAGAAAACAA
Done.