Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011339.1 Kokia drynarioides strain JFW-HI SEQ_126319, 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: 41786
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:807 original size:14 final size:14
Alignment explanation
Indices: 788--830 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
778 TTGCATAATT
**
788 AAAATAAAATTTAA
1 AAAATAAAATAAAA
802 AAAATAAAATAAAA
1 AAAATAAAATAAAA
816 ATAAATAAAAATAAA
1 A-AAAT-AAAATAAA
831 TATGAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 4 0.16
16 8 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATAAAATAAAA
Found at i:821 original size:10 final size:10
Alignment explanation
Indices: 801--844 Score: 61
Period size: 10 Copynumber: 4.1 Consensus size: 10
791 ATAAAATTTA
801 AAAAATAAAAT
1 AAAAAT-AAAT
812 AAAAATAAAT
1 AAAAATAAAT
822 AAAAATAAAT
1 AAAAATAAAT
832 ATGAAAATAAAT
1 A--AAAATAAAT
844 A
1 A
845 TACTAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 15 0.48
11 6 0.19
12 10 0.32
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:838 original size:22 final size:21
Alignment explanation
Indices: 801--844 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
791 ATAAAATTTA
801 AAAAATAAAATAAAAATAAAT
1 AAAAATAAAATAAAAATAAAT
*
822 AAAAATAAATATGAAAATAAAT
1 AAAAATAAA-ATAAAAATAAAT
844 A
1 A
845 TACTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAATAAAATAAAAATAAAT
Found at i:1891 original size:18 final size:18
Alignment explanation
Indices: 1868--1905 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1858 ACATGTAAAC
1868 TACCAATGAGACAAGGAA
1 TACCAATGAGACAAGGAA
1886 TACCAATGAGACAAGGAA
1 TACCAATGAGACAAGGAA
1904 TA
1 TA
1906 GTAAAACTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.16, G:0.21, T:0.13
Consensus pattern (18 bp):
TACCAATGAGACAAGGAA
Found at i:3753 original size:14 final size:13
Alignment explanation
Indices: 3733--3788 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
3723 ATAAAAGGGA
3733 AAAAAATTAAAAT
1 AAAAAATTAAAAT
3746 AGAAAAATT-AAAT
1 A-AAAAATTAAAAT
* *
3759 TAAAAATGAAAAT
1 AAAAAATTAAAAT
*
3772 AATAAAATAAAAAT
1 AA-AAAATTAAAAT
3786 AAA
1 AAA
3789 TAATAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 6 0.17
13 11 0.31
14 19 0.53
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (13 bp):
AAAAAATTAAAAT
Found at i:3778 original size:26 final size:26
Alignment explanation
Indices: 3734--3788 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3724 TAAAAGGGAA
* * *
3734 AAAAATTAAAATAGAAAAATTAAATT
1 AAAAATGAAAATAGAAAAATAAAAAT
3760 AAAAATGAAAATA-ATAAAATAAAAAT
1 AAAAATGAAAATAGA-AAAATAAAAAT
3786 AAA
1 AAA
3789 TAATAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (26 bp):
AAAAATGAAAATAGAAAAATAAAAAT
Found at i:3784 original size:21 final size:21
Alignment explanation
Indices: 3754--3800 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
3744 ATAGAAAAAT
* *
3754 TAAATTAAAAATGAA-AATAA
1 TAAAATAAAAATAAATAATAA
3774 TAAAATAAAAATAAATAATAA
1 TAAAATAAAAATAAATAATAA
3795 TAAAAT
1 TAAAAT
3801 GGCTAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAATAAAAATAAATAATAA
Found at i:4453 original size:15 final size:15
Alignment explanation
Indices: 4432--4473 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
4422 TAAGCACATC
4432 AATCAAGAATTAATA
1 AATCAAGAATTAATA
* *
4447 TATCAAGAA-TACTA
1 AATCAAGAATTAATA
4461 AATCAAGAATTAA
1 AATCAAGAATTAA
4474 GTACACATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (15 bp):
AATCAAGAATTAATA
Found at i:4882 original size:25 final size:23
Alignment explanation
Indices: 4854--4899 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
4844 GTTGGATCCA
4854 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
4879 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
4900 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:8591 original size:11 final size:11
Alignment explanation
Indices: 8575--8603 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
8565 TGATAAAACA
8575 CACACACCTTG
1 CACACACCTTG
8586 CACACACCTTG
1 CACACACCTTG
8597 CACACAC
1 CACACAC
8604 AAGTGCTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.48, G:0.07, T:0.14
Consensus pattern (11 bp):
CACACACCTTG
Found at i:9617 original size:23 final size:22
Alignment explanation
Indices: 9562--9619 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
9552 ATGAGTCAGA
*
9562 ATTAAATTATAAATTTTAATAT
1 ATTAAATTATAATTTTTAATAT
*
9584 ATTAACA-TATAATTTTATAATGT
1 ATTAA-ATTATAATTTT-TAATAT
*
9607 ATTAATTTATAAT
1 ATTAAATTATAAT
9620 ATCATCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAAATTATAATTTTTAATAT
Found at i:14404 original size:27 final size:27
Alignment explanation
Indices: 14365--14491 Score: 164
Period size: 27 Copynumber: 4.7 Consensus size: 27
14355 CATGTCGAAA
* *
14365 AAATGAAAGCCTTTGTGGCGATTTAAG
1 AAATGGAAGCCTTTGTGGCGATCTAAG
* *
14392 TAATGGAAGCCTTTGCGGCGATCTAAG
1 AAATGGAAGCCTTTGTGGCGATCTAAG
* * * * *
14419 AAATGAAAGTCTTTATGACAATCTAAG
1 AAATGGAAGCCTTTGTGGCGATCTAAG
14446 AAATGGAAGCCTTTGTGGCGATCTAAG
1 AAATGGAAGCCTTTGTGGCGATCTAAG
*
14473 AAATGGAAGCTTTTGTGGC
1 AAATGGAAGCCTTTGTGGC
14492 AAATCTTATA
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGGCGATCTAAG
Found at i:20874 original size:22 final size:22
Alignment explanation
Indices: 20830--20875 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
20820 TCACTATTTT
*
20830 ATATTTTATTTAATGATGTTGC
1 ATATTTTATTTAATGATGATGC
*
20852 ATATTATTATTTACT-ATGATGC
1 ATATT-TTATTTAATGATGATGC
20874 AT
1 AT
20876 GAAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (22 bp):
ATATTTTATTTAATGATGATGC
Found at i:34160 original size:40 final size:40
Alignment explanation
Indices: 34095--34181 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
34085 ACATTTTATC
* *
34095 CATCCTTACGAATTTTCTTTCTAAAAAAGGATAAAATGTA
1 CATCATTACAAATTTTCTTTCTAAAAAAGGATAAAATGTA
34135 CATCATTACAAATTTTCTTTCTAAAAAAGGATAAAATGTA
1 CATCATTACAAATTTTCTTTCTAAAAAAGGATAAAATGTA
34175 CATCATT
1 CATCATT
34182 TTTTTATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (40 bp):
CATCATTACAAATTTTCTTTCTAAAAAAGGATAAAATGTA
Found at i:35843 original size:60 final size:59
Alignment explanation
Indices: 35750--35868 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 59
35740 AATGTCCCGA
35750 CCCTTTTGAAGAGGTTGATAAATATAATCGGGATAAGTGAACAGTGAGTGACATCTAGG
1 CCCTTTTGAAGAGGTTGATAAATATAATCGGGATAAGTGAACAGTGAGTGACATCTAGG
*
35809 NCCCTTTTGAATAGGTTGATAAATATAATCGGGATAAGTGAACAGTGAGTGACATCTAGG
1 -CCCTTTTGAAGAGGTTGATAAATATAATCGGGATAAGTGAACAGTGAGTGACATCTAGG
35869 ATCAAGGTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (59 bp):
CCCTTTTGAAGAGGTTGATAAATATAATCGGGATAAGTGAACAGTGAGTGACATCTAGG
Found at i:36761 original size:13 final size:13
Alignment explanation
Indices: 36743--36767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36733 GGATAGAAGT
36743 CTTACGATTAATG
1 CTTACGATTAATG
36756 CTTACGATTAAT
1 CTTACGATTAAT
36768 TCCATCAGAG
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:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
CTTACGATTAATG
Done.