Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010853.1 Kokia drynarioides strain JFW-HI SEQ_125821, 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: 40831
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:599 original size:6 final size:6
Alignment explanation
Indices: 588--620 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
578 TGATCAAAAT
*
588 TGAAAG TGAAAG TGAAAG TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
621 TATGAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:824 original size:37 final size:38
Alignment explanation
Indices: 724--826 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
714 GACCTCGAGT
* **
724 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGAGC
** * ** *
765 CGATGAGGTACTAGGTACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
802 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
827 TTGCTTCGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 20 0.42
38 14 0.29
41 14 0.29
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
Found at i:6779 original size:63 final size:63
Alignment explanation
Indices: 6680--6806 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
6670 GAATAATATC
6680 GAAAAGAATCCTTCAACCGTGTGAGAAATTGAAGTTACAATCTCCAGATTTATTTATCTCAAT
1 GAAAAGAATCCTTCAACCGTGTGAGAAATTGAAGTTACAATCTCCAGATTTATTTATCTCAAT
6743 GAAAAGAATCCTTCAACCGTGTGAGAAATTGAAGTTACAATCTCCAGATTTATTTATCTCAAT
1 GAAAAGAATCCTTCAACCGTGTGAGAAATTGAAGTTACAATCTCCAGATTTATTTATCTCAAT
6806 G
1 G
6807 CTTCTACTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (63 bp):
GAAAAGAATCCTTCAACCGTGTGAGAAATTGAAGTTACAATCTCCAGATTTATTTATCTCAAT
Found at i:8600 original size:191 final size:192
Alignment explanation
Indices: 8267--8662 Score: 555
Period size: 191 Copynumber: 2.1 Consensus size: 192
8257 TTACGCATTT
* * * * * * * *
8267 GCATGCTCTGTGTTGATCGATGCAGTTACTGGTTCAATTTTTCAACAATTCTTCTCGTACCGAAA
1 GCATGCTCAGTGTAGGTCGATACAGTCACTGATTCAATTTTTCAACAATTCCTCTCATACCGAAA
* * * * *
8332 CAAAAAATGCATCAAAGTAAAAAGTTTCGGACTCTTCAAATCATAATGAATAACATCATTCACGC
66 CAAAAAATGCATCAAACTAAAAAGTTTCCGACGCATCAAATCATAATCAATAACATCATTCACGC
*
8397 ATCGATTTACAATCACGATTCCAGTGAACAGATCGGATCATTG-TTAATTGAACTAACAAGTA
131 ATCGATTTACAATCAAGATTCCAGTGAACAGATCGGATCATTGATTAA-TGAACTAACAAGTA
* *
8459 GCATGCTGAGTGTAGGTCGATACAGTCACTGATTCAGTTTTTCAACAATTCCTCTCATACCGAAA
1 GCATGCTCAGTGTAGGTCGATACAGTCACTGATTCAATTTTTCAACAATTCCTCTCATACCGAAA
** * *
8524 CAGACTAA-GCATCAAACTACAGAGTTTCCGACGCATC-AATCATAATCAATAACATCATTCACG
66 CA-AAAAATGCATCAAACTAAAAAGTTTCCGACGCATCAAATCATAATCAATAACATCATTCACG
* *
8587 CATCGATTTACAATCAAGATTCTAGTGAACAGATCGGATCATTGATTAATGAACTAGCAAGTA
130 CATCGATTTACAATCAAGATTCCAGTGAACAGATCGGATCATTGATTAATGAACTAACAAGTA
8650 GCATGCTCAGTGT
1 GCATGCTCAGTGT
8663 TGAGCAAGGT
Statistics
Matches: 179, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
191 92 0.51
192 84 0.47
193 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (192 bp):
GCATGCTCAGTGTAGGTCGATACAGTCACTGATTCAATTTTTCAACAATTCCTCTCATACCGAAA
CAAAAAATGCATCAAACTAAAAAGTTTCCGACGCATCAAATCATAATCAATAACATCATTCACGC
ATCGATTTACAATCAAGATTCCAGTGAACAGATCGGATCATTGATTAATGAACTAACAAGTA
Found at i:10783 original size:21 final size:21
Alignment explanation
Indices: 10758--10806 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
10748 GTTTGGTGAC
10758 GTGTGACTCAAAAATTGTACT
1 GTGTGACTCAAAAATTGTACT
*
10779 GTGTGACTCAAAGATTGTACT
1 GTGTGACTCAAAAATTGTACT
*
10800 ATGTGAC
1 GTGTGAC
10807 ACAATTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (21 bp):
GTGTGACTCAAAAATTGTACT
Found at i:11841 original size:18 final size:18
Alignment explanation
Indices: 11820--11856 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11810 GATATTTTAG
11820 TATGATAAACTTGAATCA
1 TATGATAAACTTGAATCA
11838 TATGATAAACTTGAATCA
1 TATGATAAACTTGAATCA
11856 T
1 T
11857 TAATCACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (18 bp):
TATGATAAACTTGAATCA
Found at i:11919 original size:19 final size:20
Alignment explanation
Indices: 11897--11938 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
11887 TTTTATAAAA
11897 TTTTTAAATTTTTA-ACTTT
1 TTTTTAAATTTTTAGACTTT
*
11916 TTTTTATATTTTTAGACTTT
1 TTTTTAAATTTTTAGACTTT
11936 TTT
1 TTT
11939 AAAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTAAATTTTTAGACTTT
Found at i:11998 original size:19 final size:20
Alignment explanation
Indices: 11974--12034 Score: 81
Period size: 21 Copynumber: 3.1 Consensus size: 20
11964 ACAAAACTTA
*
11974 GAATTTTTATAAA-TATTTT
1 GAATTTTTAAAAATTATTTT
11993 GAA-TTTTAAAAATTATTTT
1 GAATTTTTAAAAATTATTTT
*
12012 CAATTTTTTAAAAATTATTTT
1 GAA-TTTTTAAAAATTATTTT
12033 GA
1 GA
12035 TTATTTTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 8 0.22
19 11 0.31
21 17 0.47
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
GAATTTTTAAAAATTATTTT
Found at i:12041 original size:21 final size:21
Alignment explanation
Indices: 11978--12041 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
11968 AACTTAGAAT
*
11978 TTTTATAAA-TATTTTGA--A
1 TTTTAAAAATTATTTTGATTA
*
11996 TTTTAAAAATTATTTTCAATT-
1 TTTTAAAAATTATTTT-GATTA
12017 TTTTAAAAATTATTTTGATTA
1 TTTTAAAAATTATTTTGATTA
12038 TTTT
1 TTTT
12042 GTAATTTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.21
19 6 0.16
20 4 0.11
21 20 0.53
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (21 bp):
TTTTAAAAATTATTTTGATTA
Found at i:12849 original size:8 final size:8
Alignment explanation
Indices: 12836--12864 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12826 TAAAGAATTA
12836 TATAAAAT
1 TATAAAAT
12844 TATAAAAT
1 TATAAAAT
12852 TATAAAAT
1 TATAAAAT
12860 TATAA
1 TATAA
12865 TTTTTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TATAAAAT
Found at i:34696 original size:9 final size:9
Alignment explanation
Indices: 34621--34761 Score: 80
Period size: 9 Copynumber: 15.3 Consensus size: 9
34611 TTATATATTT
34621 ATTATAAAA
1 ATTATAAAA
*
34630 ATCATTAAAA
1 ATTA-TAAAA
* *
34640 ACTATTAAAT
1 ATTA-TAAAA
34650 ATTATAAAA
1 ATTATAAAA
34659 A-TATTAAAA
1 ATTA-TAAAA
34668 A--ATAAAA
1 ATTATAAAA
34675 A--A-AACAA
1 ATTATAA-AA
34682 ACTTATAAAA
1 A-TTATAAAA
34692 ATTATAGAAAA
1 ATTAT--AAAA
34703 ATTATAAAA
1 ATTATAAAA
* *
34712 ATCACAAAA
1 ATTATAAAA
34721 ACTTATAAAA
1 A-TTATAAAA
*
34731 ATCTA-ATAA
1 AT-TATAAAA
34740 ATTATAAAA
1 ATTATAAAA
*
34749 GTTATAATAA
1 ATTATAA-AA
34759 ATT
1 ATT
34762 CAAAGCAAGT
Statistics
Matches: 105, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
6 2 0.02
7 10 0.10
8 5 0.05
9 45 0.43
10 32 0.30
11 11 0.10
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (9 bp):
ATTATAAAA
Found at i:34710 original size:37 final size:36
Alignment explanation
Indices: 34651--34748 Score: 105
Period size: 39 Copynumber: 2.7 Consensus size: 36
34641 CTATTAAATA
*
34651 TTATAAAAATATTAAAAAA-TA-AAAAA-A-ACAAAC
1 TTATAAAAATA-TAAAAAATTATAAAAACACAAAAAC
34684 TTATAAAAATTATAGAAAAATTATAAAAATCACAAAAAC
1 TTATAAAAA-TATA-AAAAATTATAAAAA-CACAAAAAC
* *
34723 TTATAAAAATCTAATAAATTATAAAA
1 TTATAAAAATATAAAAAATTATAAAA
34749 GTTATAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
33 11 0.20
34 7 0.13
35 2 0.04
36 5 0.09
37 12 0.22
38 4 0.07
39 14 0.25
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (36 bp):
TTATAAAAATATAAAAAATTATAAAAACACAAAAAC
Found at i:34712 original size:10 final size:10
Alignment explanation
Indices: 34621--34761 Score: 53
Period size: 10 Copynumber: 14.3 Consensus size: 10
34611 TTATATATTT
34621 ATTAT-AAAA
1 ATTATAAAAA
* *
34630 ATCATTAAAA
1 ATTATAAAAA
* * *
34640 ACTATTAAAT
1 ATTATAAAAA
34650 ATTATAAAAA
1 ATTATAAAAA
34660 TATTA-AAAAA
1 -ATTATAAAAA
** *
34670 TAAAAAAAACAA
1 -ATTATAAA-AA
34682 ACTTAT-AAAA
1 A-TTATAAAAA
34692 ATTATAGAAAA
1 ATTATA-AAAA
34703 ATTAT-AAAA
1 ATTATAAAAA
* *
34712 ATCACAAAAA
1 ATTATAAAAA
*
34722 CTTAT-AAAA
1 ATTATAAAAA
* *
34731 A-TCTAATAA
1 ATTATAAAAA
34740 ATTAT-AAAA
1 ATTATAAAAA
* *
34749 GTTATAATAA
1 ATTATAAAAA
34759 ATT
1 ATT
34762 CAAAGCAAGT
Statistics
Matches: 96, Mismatches: 25, Indels: 21
0.68 0.18 0.15
Matches are distributed among these distances:
8 2 0.02
9 30 0.31
10 42 0.44
11 19 0.20
12 3 0.03
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:34721 original size:19 final size:19
Alignment explanation
Indices: 34621--34748 Score: 89
Period size: 20 Copynumber: 6.5 Consensus size: 19
34611 TTATATATTT
*
34621 ATTATAAAAATCATTAAAA
1 ATTATAAAAATCATAAAAA
* * *
34640 ACTATTAAATATTATAAAAA
1 ATTA-TAAAAATCATAAAAA
* *
34660 TATTA-AAAAATAAAAAAAACAA
1 -ATTATAAAAAT--CATAAA-AA
*
34682 ACTTATAAAAATTATAGAAAA
1 A-TTATAAAAATCATA-AAAA
*
34703 ATTATAAAAATCACAAAAA
1 ATTATAAAAATCATAAAAA
* *
34722 CTTATAAAAATC-TAATAA
1 ATTATAAAAATCATAAAAA
34740 ATTATAAAA
1 ATTATAAAA
34749 GTTATAATAA
Statistics
Matches: 85, Mismatches: 16, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
18 12 0.14
19 23 0.27
20 24 0.28
21 13 0.15
22 7 0.08
23 6 0.07
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.28
Consensus pattern (19 bp):
ATTATAAAAATCATAAAAA
Found at i:34758 original size:19 final size:19
Alignment explanation
Indices: 34684--34761 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
34674 AAAAACAAAC
*
34684 TTATAAAAATTATAGAAAAA
1 TTATAAAAATTATA-ATAAA
* *
34704 TTATAAAAATCACAA-AAA
1 TTATAAAAATTATAATAAA
*
34722 CTTATAAAAA-TCTAATAAA
1 -TTATAAAAATTATAATAAA
*
34741 TTATAAAAGTTATAATAAA
1 TTATAAAAATTATAATAAA
34760 TT
1 TT
34762 CAAAGCAAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
18 13 0.27
19 23 0.48
20 12 0.25
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (19 bp):
TTATAAAAATTATAATAAA
Found at i:38361 original size:30 final size:33
Alignment explanation
Indices: 38303--38363 Score: 83
Period size: 30 Copynumber: 1.9 Consensus size: 33
38293 GAAGGTACGA
*
38303 TAAAAAAAAGAAGAAGAGGGAAAATAAACAAAT
1 TAAAAAAAAGAAGAAGAGAGAAAATAAACAAAT
*
38336 TAAAAAAAA-AAGAA-A-AGAAATTAAACAA
1 TAAAAAAAAGAAGAAGAGAGAAAATAAACAA
38364 CTTTACCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 1 0.04
32 5 0.19
33 9 0.35
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (33 bp):
TAAAAAAAAGAAGAAGAGAGAAAATAAACAAAT
Done.