Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013499.1 Kokia drynarioides strain JFW-HI SEQ_128525, 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: 21088
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:5664 original size:25 final size:23
Alignment explanation
Indices: 5630--5685 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
5620 ACCCTAGCGC
5630 GCTCTCCGTTTATTAGCACGTTAGT
1 GCTCTCCG-TT-TTAGCACGTTAGT
*
5655 GCTCTCCG-TTTAGCACGTTTGT
1 GCTCTCCGTTTTAGCACGTTAGT
5677 GCTCTCCGT
1 GCTCTCCGT
5686 CTAGCACCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 20 0.69
23 1 0.03
25 8 0.28
ACGTcount: A:0.11, C:0.29, G:0.21, T:0.39
Consensus pattern (23 bp):
GCTCTCCGTTTTAGCACGTTAGT
Found at i:5670 original size:22 final size:22
Alignment explanation
Indices: 5642--5705 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
5632 TCTCCGTTTA
5642 TTAGCACGTTAGTGCTCTCCGT
1 TTAGCACGTTAGTGCTCTCCGT
*
5664 TTAGCACGTTTGTGCTCTCCGT
1 TTAGCACGTTAGTGCTCTCCGT
* *
5686 CTAGCACCTTTA-TGCTCTCC
1 TTAGCA-CGTTAGTGCTCTCC
5706 ATTCATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 34 0.92
23 3 0.08
ACGTcount: A:0.12, C:0.31, G:0.19, T:0.38
Consensus pattern (22 bp):
TTAGCACGTTAGTGCTCTCCGT
Found at i:5844 original size:21 final size:18
Alignment explanation
Indices: 5820--5871 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 18
5810 ATCATCATAG
5820 TATTAAGGTGAGCTTAATAAT
1 TATTAAGGTGAG-TTAAT--T
*
5841 TATTAAAGGTAAGTTAATT
1 TATT-AAGGTGAGTTAATT
5860 TATTTAAGGTGA
1 TA-TTAAGGTGA
5872 ACTTTAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 9 0.33
22 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (18 bp):
TATTAAGGTGAGTTAATT
Found at i:9965 original size:16 final size:17
Alignment explanation
Indices: 9934--9968 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
9924 AATTTCTTTG
*
9934 TTCAAAAGTAATTTTTA
1 TTCAAAAATAATTTTTA
9951 TTCAAAAAT-ATTTTTA
1 TTCAAAAATAATTTTTA
9967 TT
1 TT
9969 TGTTATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (17 bp):
TTCAAAAATAATTTTTA
Found at i:10819 original size:21 final size:22
Alignment explanation
Indices: 10784--10825 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
10774 ATCTGCATGC
10784 TTTTGTATATATTATTATGATA
1 TTTTGTATATATTATTATGATA
* *
10806 TTTTTTAT-TATTATTGTGAT
1 TTTTGTATATATTATTATGAT
10826 TTTCATGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (22 bp):
TTTTGTATATATTATTATGATA
Found at i:12046 original size:18 final size:20
Alignment explanation
Indices: 12022--12072 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
12012 ATGAGCAGTT
*
12022 TTGGTATCGATAGAAA-ATA
1 TTGGTATCGATAAAAACATA
12041 -TGGTATCGATAAAAATCATA
1 TTGGTATCGATAAAAA-CATA
12061 TTGGTATCGATA
1 TTGGTATCGATA
12073 CTTCTTGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 14 0.50
20 3 0.11
21 11 0.39
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGGTATCGATAAAAACATA
Found at i:12254 original size:16 final size:17
Alignment explanation
Indices: 12234--12274 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
12224 AACTTAATTT
*
12234 TTTTTGTTCAAAAGCAA
1 TTTTTGTTCAAAAACAA
*
12251 TTTTTATTCAAAAAC-A
1 TTTTTGTTCAAAAACAA
12267 TTTTTGTT
1 TTTTTGTT
12275 TGTTATATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (17 bp):
TTTTTGTTCAAAAACAA
Found at i:15687 original size:30 final size:30
Alignment explanation
Indices: 15651--15863 Score: 153
Period size: 30 Copynumber: 7.1 Consensus size: 30
15641 GAGTTCGAGA
*
15651 TCAAAATATGATTTTTAAAAAGTTTAAGGG
1 TCAAAATATAATTTTTAAAAAGTTTAAGGG
* * * *
15681 TCAAAATCA-AAGTTTTCAATAGTTTGAGGG
1 TCAAAAT-ATAATTTTTAAAAAGTTTAAGGG
* * **
15711 TCAAATTTTAATTTTTGGAAAGTTTAAGGG
1 TCAAAATATAATTTTTAAAAAGTTTAAGGG
* * *
15741 TCAAAAAATAATTTTTGAAAAGTTTAGGGG
1 TCAAAATATAATTTTTAAAAAGTTTAAGGG
* * * *
15771 TTAAAATATGATTTTTGGAAAA-TTTAGGGG
1 TCAAAATATAATTTTT-AAAAAGTTTAAGGG
* ** * * *
15801 TTAAAATGCAATTTTTAGAGAGTTCAA-GG
1 TCAAAATATAATTTTTAAAAAGTTTAAGGG
* * * *
15830 TTAAAATGTGATTTTTAGAAAGTTTAAGGG
1 TCAAAATATAATTTTTAAAAAGTTTAAGGG
15860 TCAA
1 TCAA
15864 GTCTAAGTTT
Statistics
Matches: 145, Mismatches: 33, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
29 27 0.19
30 112 0.77
31 6 0.04
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.37
Consensus pattern (30 bp):
TCAAAATATAATTTTTAAAAAGTTTAAGGG
Found at i:15814 original size:60 final size:59
Alignment explanation
Indices: 15606--15863 Score: 166
Period size: 60 Copynumber: 4.4 Consensus size: 59
15596 AAAATGTAAA
* * * * * * *
15606 TTTGGAAAGTTT-GGGGTTAAAATGA-AATTTTTAGAGAGTTCGAGATCAAAATATGATT
1 TTTGGAAAGTTTAAGGGTCAAAA-AACAATTTTTAGAAAGTTCAAGGTTAAAATATGATT
** * * * * * * * * *
15664 TTTAAAAAGTTTAAGGGTCAAAATCAA-AGTTTTCA-ATAGTTTGAGGGTCAAATTTTAATT
1 TTTGGAAAGTTTAAGGGTCAAAA--AACAATTTTTAGAAAG-TTCAAGGTTAAAATATGATT
* * *
15724 TTTGGAAAGTTTAAGGGTCAAAAAATAATTTTT-GAAAAGTTTAGGGGTTAAAATATGATT
1 TTTGGAAAGTTTAAGGGTCAAAAAACAATTTTTAG-AAAGTTCA-AGGTTAAAATATGATT
* * * ** * *
15784 TTTGGAAAATTTAGGGGTTAAAATGCAATTTTTAGAGAGTTCAAGGTTAAAATGTGATT
1 TTTGGAAAGTTTAAGGGTCAAAAAACAATTTTTAGAAAGTTCAAGGTTAAAATATGATT
*
15843 TTTAGAAAGTTTAAGGGTCAA
1 TTTGGAAAGTTTAAGGGTCAA
15864 GTCTAAGTTT
Statistics
Matches: 152, Mismatches: 40, Indels: 15
0.73 0.19 0.07
Matches are distributed among these distances:
58 12 0.08
59 50 0.33
60 89 0.59
61 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.37
Consensus pattern (59 bp):
TTTGGAAAGTTTAAGGGTCAAAAAACAATTTTTAGAAAGTTCAAGGTTAAAATATGATT
Found at i:15832 original size:29 final size:29
Alignment explanation
Indices: 15799--15858 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
15789 AAAATTTAGG
*
15799 GGTTAAAATGCAATTTTTAGAGAGTTCAA
1 GGTTAAAATGCAATTTTTAGAAAGTTCAA
** *
15828 GGTTAAAATGTGATTTTTAGAAAGTTTAA
1 GGTTAAAATGCAATTTTTAGAAAGTTCAA
15857 GG
1 GG
15859 GTCAAGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
GGTTAAAATGCAATTTTTAGAAAGTTCAA
Found at i:16988 original size:17 final size:15
Alignment explanation
Indices: 16963--17004 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
16953 TTGATTATTG
16963 TTCTT-TATTGTTTC
1 TTCTTCTATTGTTTC
16977 TTGCTTCGTATTTGTTTC
1 TT-CTTC-TA-TTGTTTC
16995 TTCTTCTATT
1 TTCTTCTATT
17005 CTTCTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.08
15 5 0.21
16 2 0.08
17 6 0.25
18 9 0.38
ACGTcount: A:0.07, C:0.17, G:0.10, T:0.67
Consensus pattern (15 bp):
TTCTTCTATTGTTTC
Found at i:16993 original size:18 final size:16
Alignment explanation
Indices: 16970--17004 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
16960 TTGTTCTTTA
16970 TTGTTTCTTGCTTCGTAT
1 TTGTTTCTT-CTTC-TAT
16988 TTGTTTCTTCTTCTAT
1 TTGTTTCTTCTTCTAT
17004 T
1 T
17005 CTTCTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 4 0.24
18 9 0.53
ACGTcount: A:0.06, C:0.17, G:0.11, T:0.66
Consensus pattern (16 bp):
TTGTTTCTTCTTCTAT
Found at i:17173 original size:11 final size:11
Alignment explanation
Indices: 17157--17201 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
17147 GAGTCACGTG
17157 GCTGACGTGGC
1 GCTGACGTGGC
*
17168 GCTGACGTGGT
1 GCTGACGTGGC
* *
17179 GTTGACATGGC
1 GCTGACGTGGC
17190 TGCTGACGTGGC
1 -GCTGACGTGGC
17202 CACGAGCTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.11, C:0.22, G:0.42, T:0.24
Consensus pattern (11 bp):
GCTGACGTGGC
Found at i:17828 original size:40 final size:38
Alignment explanation
Indices: 17763--18581 Score: 368
Period size: 40 Copynumber: 20.9 Consensus size: 38
17753 TGTGCGTGGC
* *
17763 TTCAATCTGCCCTCTGAT-TGAGGTAAAAAGATTGGACGGT
1 TTCAATCTGCCC-CTGATCAG-GGT-AAAAGATTGGATGGT
* *
17803 TTCAATCTGCCCCATGATCAGGGTAAGAGATTAG-TGTGT
1 TTCAATCTGCCCC-TGATCAGGGTAAAAGATTGGATG-GT
* * * * * *
17842 CTTCACTATGCCCTCTGATTAAGGTAAAAGATTAGAT-GC
1 -TTCAATCTGCCC-CTGATCAGGGTAAAAGATTGGATGGT
* *
17881 TTCAATCTGTCCCATGATCAGGGTAAGAGATTGG-TGCGT
1 TTCAATCTG-CCCCTGATCAGGGTAAAAGATTGGATG-GT
* * * *
17920 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGAT-GC
1 -TTCAATCTGCC-CCTGATCAGGGTAAAAGATTGGATGGT
* *
17959 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-TGCGT
1 TTCAATCTGCCCC-TGATCAGGGTAAAAGATTGGATG-GT
* * * *
17998 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCT
1 -TTCAATCTGCC-CCTGATCAGGGTAAAAGATTGGATGGT
* *
18038 TT-AATCTGCCCCATGATCGGGGTAAGAGATTGG-TGTGT
1 TTCAATCTGCCCC-TGATCAGGGTAAAAGATTGGATG-GT
* * * * * * * *
18076 CTTCAATTTGCCTTCTAATTAAGGTAAAATATTAGAT-GC
1 -TTCAATCTGCC-CCTGATCAGGGTAAAAGATTGGATGGT
* * *
18115 TTCAATATGCCCAATGATC-GAGGTAAGAGATTGG-TGTGT
1 TTCAATCTGCCC-CTGATCAG-GGTAAAAGATTGGATG-GT
* * * * *
18154 CTTCAATCTACCTTCTGATTAAGGTAAAAGATTGGAT-GC
1 -TTCAATCTGCC-CCTGATCAGGGTAAAAGATTGGATGGT
* *
18193 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-TGCGT
1 TTCAATCTGCCCC-TGATCAGGGTAAAAGATTGGATG-GT
* * * *
18232 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGAT-GC
1 -TTCAATCTGCC-CCTGATCAGGGTAAAAGATTGGATGGT
*
18271 TTCAATCTGCCCCATGATC-GAGGTAAGAGATTGG-TGCGT
1 TTCAATCTGCCCC-TGATCAG-GGTAAAAGATTGGATG-GT
* * ** * * * *
18310 CTTTAATCTACCTTTTGATTAAGGTAAAAGATTGAAT-GC
1 -TTCAATCTGCC-CCTGATCAGGGTAAAAGATTGGATGGT
* *
18349 TTCAATCTGCCCCATGATCGGGGTAAGAGATT-GATGTGT
1 TTCAATCTGCCCC-TGATCAGGGTAAAAGATTGGATG-GT
* * * * * * *
18388 CTTCAATCTTCCTTCTAATTAAGGTAAAAGATTTGAT-GC
1 -TTCAATCTGCC-CCTGATCAGGGTAAAAGATTGGATGGT
* *
18427 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-TGCGT
1 TTCAATCTGCCCC-TGATCAGGGTAAAAGATTGGATG-GT
* * * * * *
18466 ATTCAATCTGCCTTCTGATTAAGATAATAGATTGGAT-GC
1 -TTCAATCTGCC-CCTGATCAGGGTAAAAGATTGGATGGT
* *
18505 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-TGTGT
1 TTCAATCTGCCCC-TGATCAGGGTAAAAGATTGGATG-GT
** * * *
18544 CTTCAATCTGCTTTCTAATTAAGGTAAAAGATTGGATG
1 -TTCAATCTGC-CCCTGATCAGGGTAAAAGATTGGATG
18582 CTTCATCTAC
Statistics
Matches: 570, Mismatches: 145, Indels: 127
0.68 0.17 0.15
Matches are distributed among these distances:
37 17 0.03
38 225 0.39
39 36 0.06
40 270 0.47
41 22 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (38 bp):
TTCAATCTGCCCCTGATCAGGGTAAAAGATTGGATGGT
Found at i:17911 original size:78 final size:78
Alignment explanation
Indices: 17762--18631 Score: 1312
Period size: 78 Copynumber: 11.2 Consensus size: 78
17752 TTGTGCGTGG
* * * * *
17762 CTTCAATCTGCCCTCTGATTGAGGTAAAAAGATTGGACGGTTTCAATCTGCCCCATGATCAGGGT
1 CTTCAATCTGCCTTCTGATTAAGGT-AAAAGATTGGA-TGCTTCAATCTGCCCCATGATCGGGGT
*
17827 AAGAGATTAGTGTGT
64 AAGAGATTGGTGTGT
* * * * * *
17842 CTTCACTATGCCCTCTGATTAAGGTAAAAGATTAGATGCTTCAATCTGTCCCATGATCAGGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
17907 GAGATTGGTGCGT
66 GAGATTGGTGTGT
17920 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
17985 GAGATTGGTGCGT
66 GAGATTGGTGTGT
*
17998 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTTAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
18063 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * * * * * *
18076 CTTCAATTTGCCTTCTAATTAAGGTAAAATATTAGATGCTTCAATATGCCCAATGATCGAGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
18141 GAGATTGGTGTGT
66 GAGATTGGTGTGT
*
18154 CTTCAATCTACCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
18219 GAGATTGGTGCGT
66 GAGATTGGTGTGT
*
18232 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
18297 GAGATTGGTGCGT
66 GAGATTGGTGTGT
* * * *
18310 CTTTAATCTACCTTTTGATTAAGGTAAAAGATTGAATGCTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
18375 GAGATTGATGTGT
66 GAGATTGGTGTGT
* * *
18388 CTTCAATCTTCCTTCTAATTAAGGTAAAAGATTTGATGCTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
18453 GAGATTGGTGCGT
66 GAGATTGGTGTGT
* * *
18466 ATTCAATCTGCCTTCTGATTAAGATAATAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
18531 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * * *
18544 CTTCAATCTGCTTTCTAATTAAGGTAAAAGATTGGATGCTTC-ATCTACCTCATGATCGGGGTAA
1 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
18608 GAGATTAGTGTG-
66 GAGATTGGTGTGT
*
18620 CTTCAATTTGCC
1 CTTCAATCTGCC
18632 CCGTGATCGG
Statistics
Matches: 722, Mismatches: 68, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
76 10 0.01
77 31 0.04
78 649 0.90
79 10 0.01
80 22 0.03
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (78 bp):
CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
GAGATTGGTGTGT
Done.