Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002854.1 Kokia drynarioides strain JFW-HI SEQ_115248, 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: 59149
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:941 original size:20 final size:20
Alignment explanation
Indices: 896--941 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
886 GACCAACACC
*
896 CAAAAATGTAATTTTTTTAT
1 CAAAAATGCAATTTTTTTAT
* *
916 CCAAAATGCAATTTTTTTCT
1 CAAAAATGCAATTTTTTTAT
936 CAAAAA
1 CAAAAA
942 GATGGTGTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.41
Consensus pattern (20 bp):
CAAAAATGCAATTTTTTTAT
Found at i:1034 original size:60 final size:57
Alignment explanation
Indices: 983--1212 Score: 175
Period size: 60 Copynumber: 3.9 Consensus size: 57
973 AAAAAATTTG
* * * *
983 AAATTTTTTTAT-TTGAAAAAGGGGTGT-GGCCATTGTATGGCCAACACCCAAAAAT
1 AAATTTTTTTATCTTAAAAAAGGGGTGTAGACCATTGAATGGCCAACACCAAAAAAT
* * *
1038 GCAATTTTTTTATCATTAAAAAAGAGGGTGTCGACCA-TGCAATGGCCAACACCTAAAAAT
1 -AAATTTTTTTATC-TTAAAAAAG-GGGTGTAGACCATTG-AATGGCCAACACCAAAAAAT
* * * *
1098 ACAATTTTTTT-TCTCAAAAAAGGGGTGTAGACCATTGCATGGCCCACACAAAAAAAATTT
1 A-AATTTTTTTATCTTAAAAAAGGGGTGTAGACCATTGAATGGCCAACAC-CAAAAAA--T
* * **
1158 AAATTTTTTT-TCTGACAAAAAAGGGGTGTCGGTCA-TGCAATGGCCAACATCCAAA
1 AAATTTTTTTATCT--TAAAAAAGGGGTGTAGACCATTG-AATGGCCAACA-CCAAA
1213 TTTTTTTTTT
Statistics
Matches: 142, Mismatches: 18, Indels: 23
0.78 0.10 0.13
Matches are distributed among these distances:
56 11 0.08
57 21 0.15
58 23 0.16
59 22 0.15
60 35 0.25
61 29 0.20
62 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (57 bp):
AAATTTTTTTATCTTAAAAAAGGGGTGTAGACCATTGAATGGCCAACACCAAAAAAT
Found at i:3016 original size:9 final size:9
Alignment explanation
Indices: 3002--3031 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2992 ATTTTGAAAA
3002 TATATAAAT
1 TATATAAAT
3011 TATATAAAT
1 TATATAAAT
3020 TATA-AAAT
1 TATATAAAT
3028 TATA
1 TATA
3032 AATATATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TATATAAAT
Found at i:3025 original size:16 final size:17
Alignment explanation
Indices: 2999--3045 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
2989 ATTATTTTGA
2999 AAATATATAAATTATAT
1 AAATATATAAATTATAT
*
3016 AAAT-TATAAAAT-TAT
1 AAATATATAAATTATAT
3031 AAATATATACAATTA
1 AAATATATA-AATTA
3046 AAATGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 7 0.28
16 11 0.44
17 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATATAAATTATAT
Found at i:3039 original size:8 final size:8
Alignment explanation
Indices: 2999--3039 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
2989 ATTATTTTGA
2999 AAATATAT
1 AAATATAT
3007 AAATTATAT
1 AAA-TATAT
3016 AAAT-TAT
1 AAATATAT
3023 AAA-ATTAT
1 AAATA-TAT
3031 AAATATAT
1 AAATATAT
3039 A
1 A
3040 CAATTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 6 0.21
8 14 0.48
9 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATATAT
Found at i:3252 original size:24 final size:23
Alignment explanation
Indices: 3225--3295 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
3215 ACTTAAGTTC
*
3225 ATTTTTTATATACTTTTTAAATTT
1 ATTTTTTATATA-TTTTTAATTTT
*
3249 A-TTTATATAT-TTATTTAATTTT
1 ATTTTTTATATATT-TTTAATTTT
*
3271 TTATTTTTATATATTTTTAATTTT
1 AT-TTTTTATATATTTTTAATTTT
3295 A
1 A
3296 AAATAATCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
21 2 0.05
22 8 0.21
23 8 0.21
24 18 0.47
25 2 0.05
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTTTTATATATTTTTAATTTT
Found at i:3253 original size:21 final size:20
Alignment explanation
Indices: 3225--3274 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
3215 ACTTAAGTTC
3225 ATTTTTTATATACTTT-TTAA
1 ATTTTTTATATA-TTTATTAA
*
3245 ATTTATTTATATATTTATTTA
1 ATTT-TTTATATATTTATTAA
3266 ATTTTTTAT
1 ATTTTTTAT
3275 TTTTATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTTTATATATTTATTAA
Found at i:15400 original size:52 final size:52
Alignment explanation
Indices: 15301--15645 Score: 460
Period size: 52 Copynumber: 6.6 Consensus size: 52
15291 GTAAATGCAA
* * *
15301 AAGGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCTTTTACGGATTTCT
1 AAGGTCCGATGACTATGTGTCATCGTGAG-TATATGAATCTTTTACGGA-TTAT
* * * *
15355 AA-GTCAGATGACTATGAGTCATCATGAGTATATGAATCTTTTACGGATTGT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
* * * *
15406 AAGGTCCGATGACTATGTGTCATCTTGAGTATATGAATCCTTTATGGATTAA
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
** * *
15458 AAGGTTTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
* **
15510 GAGGTTTGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTA-
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
*
15561 AGAGGTCCGATGACTATGCGTCATCGTGAGTATATGAATCTTTTACGGATTAT
1 A-AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
* *
15614 AAGGTTCGATGACTATGTGTTATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
15646 TAAATGAGAA
Statistics
Matches: 259, Mismatches: 29, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
51 5 0.02
52 230 0.89
53 22 0.08
54 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
Found at i:15695 original size:62 final size:63
Alignment explanation
Indices: 15594--15714 Score: 165
Period size: 62 Copynumber: 1.9 Consensus size: 63
15584 TCGTGAGTAT
* * * *
15594 ATGAATCTTTTACGGATTATAAGGTTCGATGACTATGTGTTATCGTGAG-TATTAAATGAGAA
1 ATGAATCTATTACGAATTATAAGGTTCGATGACTATGTGTCATCGTGAGATACTAAATGAGAA
* *
15656 ATGAATCCTATTACGAATTA-AATGTTCGATGACTCTGTGTCATCGTGAGATACTAAATG
1 ATGAAT-CTATTACGAATTATAAGGTTCGATGACTATGTGTCATCGTGAGATACTAAATG
15715 CAAATTGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 32 0.63
63 19 0.37
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (63 bp):
ATGAATCTATTACGAATTATAAGGTTCGATGACTATGTGTCATCGTGAGATACTAAATGAGAA
Found at i:20387 original size:16 final size:16
Alignment explanation
Indices: 20366--20398 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20356 CGCAATCCAA
20366 GTAGAATTAAATTCAT
1 GTAGAATTAAATTCAT
20382 GTAGAATTAAATTCAT
1 GTAGAATTAAATTCAT
20398 G
1 G
20399 AAATTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (16 bp):
GTAGAATTAAATTCAT
Found at i:26597 original size:3 final size:3
Alignment explanation
Indices: 26589--26613 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
26579 CATTTGACTT
26589 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
26614 CTTTCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:32564 original size:20 final size:22
Alignment explanation
Indices: 32541--32585 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
32531 TTTTAAATTT
*
32541 TAAAAATTATTAA-AAAATC-A
1 TAAAAATTATAAACAAAATCTA
32561 TAAAAATTATAAACAAAATCTA
1 TAAAAATTATAAACAAAATCTA
32583 TAA
1 TAA
32586 GAAAAAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 6 0.27
22 4 0.18
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAATTATAAACAAAATCTA
Found at i:32739 original size:13 final size:12
Alignment explanation
Indices: 32722--32772 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
32712 AATTTTATAA
32722 TTTTTATAACTT
1 TTTTTATAACTT
*
32734 ATTTTTATAAATT
1 -TTTTTATAACTT
32747 TTGTTTATAACTT
1 TT-TTTATAACTT
*
32760 TTTTAATAA-TT
1 TTTTTATAACTT
32771 TT
1 TT
32773 AAATTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 4 0.12
12 8 0.24
13 22 0.65
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (12 bp):
TTTTTATAACTT
Found at i:32739 original size:22 final size:21
Alignment explanation
Indices: 32714--32772 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 21
32704 TTAATAAGAA
32714 TTTTATAATTTTTATAACTTAT
1 TTTTATAATTTTTATAACTT-T
32736 TTTTATAAATTTTGTTTATAACTTT
1 TTTTAT-AA--TT-TTTATAACTTT
*
32761 TTTAATAATTTT
1 TTTTATAATTTT
32773 AAATTTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 2 0.06
22 8 0.25
23 2 0.06
24 2 0.06
25 8 0.25
26 10 0.31
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATAATTTTTATAACTTT
Found at i:32770 original size:24 final size:26
Alignment explanation
Indices: 32724--32772 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
32714 TTTTATAATT
*
32724 TTTATAACTTATTTTTATAAATTTTG
1 TTTATAACTTATTTTAATAAATTTTG
32750 TTTATAACTT-TTTTAAT-AATTTT
1 TTTATAACTTATTTTAATAAATTTT
32773 AAATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 6 0.27
26 10 0.45
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTATAACTTATTTTAATAAATTTTG
Found at i:34388 original size:42 final size:42
Alignment explanation
Indices: 34342--34545 Score: 194
Period size: 42 Copynumber: 4.8 Consensus size: 42
34332 TTCAGTATAG
* *
34342 CCGATGATGCACTTATGTGTCAATATATTTGCTTCGATTTAT
1 CCGATGATGCACTTATGTGCCAATATAATTGCTTCGATTTAT
* * *
34384 CCGATGATGCACTTATGTGCCAATATAATTGCTTTGGTATAT
1 CCGATGATGCACTTATGTGCCAATATAATTGCTTCGATTTAT
* * * *
34426 CCAATGATGCACTTATGTGCCAACATGATTGCTTCGGTTTAT
1 CCGATGATGCACTTATGTGCCAATATAATTGCTTCGATTTAT
* * * * **
34468 CCGATGATACAC-TATGCGTGTCATTATAATTGCTTTGATTCGT
1 CCGATGATGCACTTAT--GTGCCAATATAATTGCTTCGATTTAT
* ** * *
34511 TCGATGATGCACCTCGTGTGCTAGTATAATTGCTT
1 CCGATGATGCA-CTTATGTGCCAATATAATTGCTT
34546 TGACTTGCCC
Statistics
Matches: 131, Mismatches: 27, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
41 3 0.02
42 84 0.64
43 42 0.32
44 1 0.01
45 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (42 bp):
CCGATGATGCACTTATGTGCCAATATAATTGCTTCGATTTAT
Found at i:34470 original size:84 final size:84
Alignment explanation
Indices: 34336--34504 Score: 225
Period size: 84 Copynumber: 2.0 Consensus size: 84
34326 TTATGCTTCA
* * * *
34336 GTATAGCCGATGATGCACTTATGTGTCAATATATTTGCTTCGATTTATCCGATGATGCACTTAT-
1 GTATAGCCAATGATGCACTTATGTGCCAACATATTTGCTTCGATTTATCCGATGATACAC-TATC
34400 GTGCCAATATAATTGCTTTG
65 GTGCCAATATAATTGCTTTG
* *
34420 GTATATCCAATGATGCACTTATGTGCCAACATGA-TTGCTTCGGTTTATCCGATGATACACTATG
1 GTATAGCCAATGATGCACTTATGTGCCAACAT-ATTTGCTTCGATTTATCCGATGATACACTAT-
* *
34484 CGTGTCATTATAATTGCTTTG
64 CGTGCCAATATAATTGCTTTG
34505 ATTCGTTCGA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
83 3 0.04
84 52 0.70
85 19 0.26
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (84 bp):
GTATAGCCAATGATGCACTTATGTGCCAACATATTTGCTTCGATTTATCCGATGATACACTATCG
TGCCAATATAATTGCTTTG
Found at i:34579 original size:43 final size:43
Alignment explanation
Indices: 34468--34590 Score: 115
Period size: 43 Copynumber: 2.9 Consensus size: 43
34458 TTCGGTTTAT
* * * *
34468 CCGATGATACACTATGCGTGTCATTATAATTGCTTTGATTCGT
1 CCGATGATACACTATGTGTGTTAGTATAATTGCTTTGATTCGC
* * * *
34511 TCGATGATGCACCT-CGTGTGCTAGTATAATTGCTTTGACTT-GC
1 CCGATGATACA-CTATGTGTGTTAGTATAATTGCTTTGA-TTCGC
* * *
34554 CCGATGATACACTATGTATGTTAGTATATTTCCTTTG
1 CCGATGATACACTATGTGTGTTAGTATAATTGCTTTG
34591 GTATATTCGA
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
42 2 0.03
43 56 0.90
44 4 0.06
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (43 bp):
CCGATGATACACTATGTGTGTTAGTATAATTGCTTTGATTCGC
Found at i:37195 original size:21 final size:21
Alignment explanation
Indices: 37166--37217 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
37156 TGGAAAATAA
* *
37166 TAAAATAAATAAATAATTCAT
1 TAAAATAAAAAAATAACTCAT
*
37187 TAAATTAAAAAAATAACTCAT
1 TAAAATAAAAAAATAACTCAT
*
37208 TTAAA-AAAAA
1 TAAAATAAAAA
37218 TCATAGTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAATAAAAAAATAACTCAT
Found at i:51801 original size:19 final size:19
Alignment explanation
Indices: 51777--51819 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
51767 TGGGGCGGGT
51777 TTCGCGAGGCCCGCCTCAC
1 TTCGCGAGGCCCGCCTCAC
51796 TTCGCGAGGCCCGCCTCAC
1 TTCGCGAGGCCCGCCTCAC
51815 TTCGC
1 TTCGC
51820 ACCCAATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.47, G:0.26, T:0.19
Consensus pattern (19 bp):
TTCGCGAGGCCCGCCTCAC
Done.