Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008298.1 Kokia drynarioides strain JFW-HI SEQ_122963, 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: 50119
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 33 characters in sequence are not A, C, G, or T
Found at i:9584 original size:30 final size:29
Alignment explanation
Indices: 9540--9613 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
9530 AATGTTTAAA
* *
9540 TTAATAAA-AATAAAATTATACTTTAACCCT
1 TTAA-AAATAATAAAATT-TAATTTAACCAT
*
9570 TTAAAAATAATAAAAATTTAATTTAATCAT
1 TTAAAAATAAT-AAAATTTAATTTAACCAT
*
9600 TTAAAAATTATAAA
1 TTAAAAATAATAAA
9614 GATATAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 6 0.16
30 26 0.68
31 6 0.16
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAAAATAATAAAATTTAATTTAACCAT
Found at i:11079 original size:2 final size:2
Alignment explanation
Indices: 11072--11108 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11062 AATCATATTA
11072 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11109 AACTAGTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16145 original size:20 final size:20
Alignment explanation
Indices: 16123--16173 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
16113 AAGCATTGCT
16123 AAATTCTTAGAAAATTTAATA
1 AAATT-TTAGAAAATTTAATA
**
16144 AAATTTTAGAAAATTTGTTA
1 AAATTTTAGAAAATTTAATA
*
16164 AAACTTTAGA
1 AAATTTTAGA
16174 TATTTTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (20 bp):
AAATTTTAGAAAATTTAATA
Found at i:18735 original size:25 final size:25
Alignment explanation
Indices: 18688--18736 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
18678 ATTTATTCAA
*
18688 AAAATATTTTTTATTCATGTTAAAT
1 AAAATATTTTTTATTCATATTAAAT
*
18713 AAAATA-TTTTTATTATATATTAAA
1 AAAATATTTTTTATT-CATATTAAA
18737 GGATTTACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
AAAATATTTTTTATTCATATTAAAT
Found at i:19142 original size:20 final size:18
Alignment explanation
Indices: 19113--19158 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
19103 TAATTTTAAT
*
19113 AATT-TATAAAATTAAATTA
1 AATTATATAAAA-TAAA-AA
19132 AATTATATAAAATAAAAA
1 AATTATATAAAATAAAAA
19150 AATTATATA
1 AATTATATA
19159 TTAAGTTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 10 0.40
19 8 0.32
20 7 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTATATAAAATAAAAA
Found at i:21274 original size:21 final size:22
Alignment explanation
Indices: 21248--21290 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
21238 CAAAACGACG
* *
21248 TAGTTTTGCCTTTTAA-TTTAA
1 TAGTTTCGACTTTTAACTTTAA
21269 TAGTTTCGACTTTTAACTTTAA
1 TAGTTTCGACTTTTAACTTTAA
21291 AAAAGGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (22 bp):
TAGTTTCGACTTTTAACTTTAA
Found at i:21579 original size:16 final size:15
Alignment explanation
Indices: 21555--21584 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21545 TTATCATATG
21555 TTTTTTTAATATTTA
1 TTTTTTTAATATTTA
21570 TTTTTCTTAATATTT
1 TTTTT-TTAATATTT
21585 TACTATACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTAATATTTA
Found at i:21942 original size:29 final size:29
Alignment explanation
Indices: 21903--21961 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
21893 AACTAAAAAC
21903 TCAAAATCATAAAAATAAATCACGAGATG
1 TCAAAATCATAAAAATAAATCACGAGATG
* *
21932 TCAAAATCATAAAAGTAAATCATGAGATG
1 TCAAAATCATAAAAATAAATCACGAGATG
21961 T
1 T
21962 AGTGTGGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (29 bp):
TCAAAATCATAAAAATAAATCACGAGATG
Found at i:29988 original size:9 final size:9
Alignment explanation
Indices: 29976--30132 Score: 93
Period size: 9 Copynumber: 16.4 Consensus size: 9
29966 TATGGTTTTT
29976 TTTTTATAA
1 TTTTTATAA
29985 TTTTT-TAA
1 TTTTTATAA
* *
29993 TATGTAATAA
1 T-TTTTATAA
*
30003 ATTTTATAA
1 TTTTTATAA
*
30012 GTTTTTATACC
1 -TTTTTATA-A
*
30023 TTTTTAATGAT
1 TTTTT-AT-AA
30034 TTTTTATAA
1 TTTTTATAA
*
30043 GTTTTTAAGAA
1 -TTTTT-ATAA
30054 TTTTTATAAA
1 TTTTTAT-AA
* *
30064 ATTTTAAATA
1 TTTTTATA-A
*
30074 TGTTTTATTA
1 T-TTTTATAA
30084 TTTTTAT-A
1 TTTTTATAA
30092 TTTTTATAA
1 TTTTTATAA
*
30101 TATTTATAA
1 TTTTTATAA
*
30110 TATTTATAA
1 TTTTTATAA
*
30119 TATTTTATTA
1 T-TTTTATAA
30129 TTTT
1 TTTT
30133 ATTATGAGTT
Statistics
Matches: 116, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
8 12 0.10
9 44 0.38
10 44 0.38
11 15 0.13
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29988 original size:10 final size:10
Alignment explanation
Indices: 29975--30137 Score: 58
Period size: 10 Copynumber: 16.8 Consensus size: 10
29965 TTATGGTTTT
29975 TTTTTTATAA
1 TTTTTTATAA
29985 -TTTTT-TAA
1 TTTTTTATAA
* * *
29993 TATGTAATAA
1 TTTTTTATAA
*
30003 -ATTTTATAA
1 TTTTTTATAA
* *
30012 GTTTTTATACC
1 TTTTTTATA-A
* *
30023 TTTTTAATGA
1 TTTTTTATAA
30033 TTTTTTATAA
1 TTTTTTATAA
*
30043 GTTTTTA-AGA
1 TTTTTTATA-A
*
30053 ATTTTTATAA
1 TTTTTTATAA
**
30063 AATTTTA-AA
1 TTTTTTATAA
*
30072 TATGTTTTATTA
1 T-T-TTTTATAA
30084 -TTTTTAT-A
1 TTTTTTATAA
30092 -TTTTTATAA
1 TTTTTTATAA
*
30101 -TATTTATAA
1 TTTTTTATAA
*
30110 -TATTTATAA
1 TTTTTTATAA
* *
30119 TATTTTATTA
1 TTTTTTATAA
30129 TTTTATTAT
1 TTTT-TTAT
30138 GAGTTTTATA
Statistics
Matches: 117, Mismatches: 24, Indels: 23
0.71 0.15 0.14
Matches are distributed among these distances:
8 11 0.09
9 41 0.35
10 48 0.41
11 16 0.14
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:30062 original size:20 final size:21
Alignment explanation
Indices: 30013--30062 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
30003 ATTTTATAAG
* *
30013 TTTTTATACCTTTTTAATGAT
1 TTTTTATAACTTTTTAATGAA
*
30034 TTTTTATAAGTTTTTAA-GAA
1 TTTTTATAACTTTTTAATGAA
30054 TTTTTATAA
1 TTTTTATAA
30063 AATTTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTTTATAACTTTTTAATGAA
Found at i:30068 original size:21 final size:21
Alignment explanation
Indices: 30013--30070 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
30003 ATTTTATAAG
** *
30013 TTTTTATACCTTTTTAATGAT
1 TTTTTATAAATTTTTAATGAA
*
30034 TTTTTATAAGTTTTTAA-GAA
1 TTTTTATAAATTTTTAATGAA
*
30054 TTTTTATAAAATTTTAA
1 TTTTTATAAATTTTTAA
30071 ATATGTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTTATAAATTTTTAATGAA
Found at i:41538 original size:23 final size:23
Alignment explanation
Indices: 41512--41583 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
41502 AAATAACCTA
41512 AAAATAATAAAAGATAGTTCTTG
1 AAAATAATAAAAGATAGTTCTTG
* ** * * *
41535 AAAATATTTTAA-AT--TACCTA
1 AAAATAATAAAAGATAGTTCTTG
41555 AAAATAATAAAAGATAGTTCTTG
1 AAAATAATAAAAGATAGTTCTTG
*
41578 GAAATA
1 AAAATA
41584 TTTTAAATTA
Statistics
Matches: 33, Mismatches: 13, Indels: 6
0.63 0.25 0.12
Matches are distributed among these distances:
20 12 0.36
21 2 0.06
22 2 0.06
23 17 0.52
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.32
Consensus pattern (23 bp):
AAAATAATAAAAGATAGTTCTTG
Found at i:41568 original size:43 final size:43
Alignment explanation
Indices: 41502--41607 Score: 167
Period size: 43 Copynumber: 2.4 Consensus size: 43
41492 TTCTCCAAAA
*
41502 AAATAACCTAAAAATAATAAAAGATAGTTCTTGAAAATATTTT
1 AAATTACCTAAAAATAATAAAAGATAGTTCTTGAAAATATTTT
*
41545 AAATTACCTAAAAATAATAAAAGATAGTTCTTGGAAATATTTT
1 AAATTACCTAAAAATAATAAAAGATAGTTCTTGAAAATATTTT
41588 AAATTAAATCCTAAAAATAA
1 AAATT--A-CCTAAAAATAA
41608 AAGATAATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
43 46 0.79
45 1 0.02
46 11 0.19
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.32
Consensus pattern (43 bp):
AAATTACCTAAAAATAATAAAAGATAGTTCTTGAAAATATTTT
Found at i:44468 original size:23 final size:23
Alignment explanation
Indices: 44414--44468 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
44404 AGTCCATCCT
*
44414 TGCTGACTAAACCTTCTAGAAGC
1 TGCTGACTGAACCTTCTAGAAGC
*
44437 TGTTGACTGAACCTTCTAGAAGC
1 TGCTGACTGAACCTTCTAGAAGC
44460 TGCTGACTG
1 TGCTGACTG
44469 GATGCCACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (23 bp):
TGCTGACTGAACCTTCTAGAAGC
Found at i:45270 original size:29 final size:29
Alignment explanation
Indices: 45238--45372 Score: 121
Period size: 29 Copynumber: 4.7 Consensus size: 29
45228 AAATAATATG
* * *
45238 GATACAGTTACATATATAGTCATGTCATA
1 GATACAGTTACAGATACAGTCATGTCACA
* *
45267 GATACAGTTATAGATACGGTCATGTCACA
1 GATACAGTTACAGATACAGTCATGTCACA
* * * *
45296 AATACAGTTACGGATGCAGACATGAT-ACA
1 GATACAGTTACAGATACAGTCATG-TCACA
* *
45325 GATACAGTTACAGATGCAGACATGAT-ACA
1 GATACAGTTACAGATACAGTCATG-TCACA
* *
45354 GATACAATTACAAATACAG
1 GATACAGTTACAGATACAG
45373 ATATGATACC
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
29 88 0.99
30 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (29 bp):
GATACAGTTACAGATACAGTCATGTCACA
Found at i:45355 original size:17 final size:17
Alignment explanation
Indices: 45308--45356 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
45298 TACAGTTACG
45308 GATGCAGACATGATACA
1 GATGCAGACATGATACA
*
45325 GAT----ACA-GTTACA
1 GATGCAGACATGATACA
45337 GATGCAGACATGATACA
1 GATGCAGACATGATACA
45354 GAT
1 GAT
45357 ACAATTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
12 8 0.32
13 3 0.12
16 3 0.12
17 11 0.44
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (17 bp):
GATGCAGACATGATACA
Found at i:45373 original size:29 final size:29
Alignment explanation
Indices: 45312--45381 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
45302 GTTACGGATG
* * *
45312 CAGACATGATACAGATACAGTTACAGATG
1 CAGACATGATACAGATACAATTACAAATA
45341 CAGACATGATACAGATACAATTACAAATA
1 CAGACATGATACAGATACAATTACAAATA
*
45370 CAGATATGATAC
1 CAGACATGATAC
45382 CCCCATCCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (29 bp):
CAGACATGATACAGATACAATTACAAATA
Found at i:46053 original size:41 final size:40
Alignment explanation
Indices: 46008--46138 Score: 100
Period size: 41 Copynumber: 3.1 Consensus size: 40
45998 ACACACCCTG
46008 ACACACGCCTATGTGTTAGCACGTGTGTTCTAGAATAGTAT
1 ACACACGCCTATGTGTTAGCACGTGTG-TCTAGAATAGTAT
* * * * * *
46049 ACACACACGCTTATGTGTCAGCCCGTATGTCTCAAAACAGTAT
1 --ACACACGCCTATGTGTTAGCACGTGTGTCT-AGAATAGTAT
* * ** * *
46092 ACACACACCCATGTGTTAGCTTGTGTGCCCCAGAATAGTAT
1 ACACACGCCTATGTGTTAGCACGTGTG-TCTAGAATAGTAT
*
46133 ATACAC
1 ACACAC
46139 ACCTTGACAC
Statistics
Matches: 68, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
41 33 0.49
42 4 0.06
43 31 0.46
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (40 bp):
ACACACGCCTATGTGTTAGCACGTGTGTCTAGAATAGTAT
Found at i:46091 original size:43 final size:43
Alignment explanation
Indices: 46008--46107 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
45998 ACACACCCTG
* * * *
46008 ACACACGCCTATGTGTTAGCACGTGTGTTCTAGAATAGTATAC
1 ACACACGCCTATGTGTCAGCACGTATGTTCTAAAACAGTATAC
* *
46051 ACACACGCTTATGTGTCAGCCCGTATG-TCTCAAAACAGTATAC
1 ACACACGCCTATGTGTCAGCACGTATGTTCT-AAAACAGTATAC
46094 ACACAC-CC-ATGTGT
1 ACACACGCCTATGTGT
46108 TAGCTTGTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
41 6 0.12
42 4 0.08
43 39 0.80
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
ACACACGCCTATGTGTCAGCACGTATGTTCTAAAACAGTATAC
Found at i:46172 original size:53 final size:53
Alignment explanation
Indices: 46114--46214 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 53
46104 GTGTTAGCTT
* * *
46114 GTGTGCC-CCAGAATAGTATATACACACCTTGACACACACTCATGTGCCAGCCC
1 GTGTGCCTCCA-AACAGTATACACACACCTTAACACACACTCATGTGCCAGCCC
* * * *
46167 GTGTGCCTCTAAACAGTATACACGCACCTTAACACACATTTATGTGCC
1 GTGTGCCTCCAAACAGTATACACACACCTTAACACACACTCATGTGCC
46215 TCCAAACAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 38 0.95
54 2 0.05
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.24
Consensus pattern (53 bp):
GTGTGCCTCCAAACAGTATACACACACCTTAACACACACTCATGTGCCAGCCC
Found at i:46280 original size:30 final size:31
Alignment explanation
Indices: 46211--46294 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
46201 CACATTTATG
* *
46211 TGCCTCCAAACAGTATACACAGATGCTTGTG
1 TGCCTCCAAACAGTATACACACATGCTTGTA
*
46242 TGCCTCCAAATAGTATACA-ACATGCCTT-TA
1 TGCCTCCAAACAGTATACACACATG-CTTGTA
* * *
46272 TTCCTCCAAACATTATATACACA
1 TGCCTCCAAACAGTATACACACA
46295 CACACATACC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 20 0.45
31 24 0.55
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (31 bp):
TGCCTCCAAACAGTATACACACATGCTTGTA
Found at i:46390 original size:21 final size:21
Alignment explanation
Indices: 46360--46402 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
46350 CACATGCCCG
46360 TGTGCCTTCGAAAAGCACTAT
1 TGTGCCTTCGAAAAGCACTAT
*
46381 TGTGCTTTCGAAAAGCACTAT
1 TGTGCCTTCGAAAAGCACTAT
46402 T
1 T
46403 TTGACAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTGCCTTCGAAAAGCACTAT
Done.