Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014784.1 Kokia drynarioides strain JFW-HI SEQ_129826, 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: 87361
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:4766 original size:2 final size:2
Alignment explanation
Indices: 4761--4786 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4751 TACTGTTTGC
4761 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4787 GTAGCTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15785 original size:2 final size:2
Alignment explanation
Indices: 15778--15806 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15768 ATGTGCATTT
15778 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15807 TTGTTATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16047 original size:23 final size:23
Alignment explanation
Indices: 16000--16047 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
15990 AATATTTTAT
* * **
16000 ATTGATGCTTTATTTTTTATTGA
1 ATTGATGCTTTAATTTATAAAGA
16023 ATTGATGCTTTAATTTATAAAGA
1 ATTGATGCTTTAATTTATAAAGA
16046 AT
1 AT
16048 AAAAGAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.52
Consensus pattern (23 bp):
ATTGATGCTTTAATTTATAAAGA
Found at i:18974 original size:112 final size:112
Alignment explanation
Indices: 18713--18937 Score: 450
Period size: 112 Copynumber: 2.0 Consensus size: 112
18703 AAACTTTTTT
18713 TAACAACAATAACAAAATTACAAAAAAAAAAAATATTAAGTGACCAAAATAAAAACACCTTAAAA
1 TAACAACAATAACAAAATTACAAAAAAAAAAAATATTAAGTGACCAAAATAAAAACACCTTAAAA
18778 GTTAGACAATCAACCAAGTAATTACCCTTTAGGATGGTTTCAAGCTA
66 GTTAGACAATCAACCAAGTAATTACCCTTTAGGATGGTTTCAAGCTA
18825 TAACAACAATAACAAAATTACAAAAAAAAAAAATATTAAGTGACCAAAATAAAAACACCTTAAAA
1 TAACAACAATAACAAAATTACAAAAAAAAAAAATATTAAGTGACCAAAATAAAAACACCTTAAAA
18890 GTTAGACAATCAACCAAGTAATTACCCTTTAGGATGGTTTCAAGCTA
66 GTTAGACAATCAACCAAGTAATTACCCTTTAGGATGGTTTCAAGCTA
18937 T
1 T
18938 TATTGGCCAT
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.23
Consensus pattern (112 bp):
TAACAACAATAACAAAATTACAAAAAAAAAAAATATTAAGTGACCAAAATAAAAACACCTTAAAA
GTTAGACAATCAACCAAGTAATTACCCTTTAGGATGGTTTCAAGCTA
Found at i:24722 original size:23 final size:23
Alignment explanation
Indices: 24696--24769 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
24686 AATGTTCACA
*
24696 AACATGTTCATTTAAC-TTAATTG
1 AACATGTTCA-TAAACATTAATTG
*
24719 AACATGTTCACAAACATTAATTG
1 AACATGTTCATAAACATTAATTG
* *
24742 ACCATGTTCATGAACATATAATTG
1 AACATGTTCATAAACAT-TAATTG
24766 AACA
1 AACA
24770 CATTCACGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
22 3 0.07
23 31 0.72
24 9 0.21
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (23 bp):
AACATGTTCATAAACATTAATTG
Found at i:24896 original size:12 final size:12
Alignment explanation
Indices: 24867--24913 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
24857 ATCATTAATA
24867 AATAAACGAGCT
1 AATAAACGAGCT
*
24879 -ATAAACGAGTT
1 AATAAACGAGCT
*
24890 AATAAACGAGCC
1 AATAAACGAGCT
24902 AATAAACGAGCT
1 AATAAACGAGCT
24914 TGTTCGTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (12 bp):
AATAAACGAGCT
Found at i:24897 original size:23 final size:24
Alignment explanation
Indices: 24867--24911 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
24857 ATCATTAATA
*
24867 AATAAACGAG-CTATAAACGAGTT
1 AATAAACGAGCCAATAAACGAGTT
24890 AATAAACGAGCCAATAAACGAG
1 AATAAACGAGCCAATAAACGAG
24912 CTTGTTCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.16
Consensus pattern (24 bp):
AATAAACGAGCCAATAAACGAGTT
Found at i:42482 original size:17 final size:17
Alignment explanation
Indices: 42455--42494 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
42445 AAAATAAAAA
42455 AAGGT-AAATTACATCC
1 AAGGTCAAATTACATCC
42471 AAGGTCAAATTACATCC
1 AAGGTCAAATTACATCC
42488 AAGGTCA
1 AAGGTCA
42495 TTGAACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (17 bp):
AAGGTCAAATTACATCC
Found at i:58032 original size:30 final size:27
Alignment explanation
Indices: 57981--58039 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
57971 CAGTCAATTA
*
57981 TAAAAAAAAAAAATTATTTTAAGTATT
1 TAAAAAAAAAAAATTATTTTAAATATT
*
58008 TAAAATAAAAAAATTTATAATTTAAATATT
1 TAAAA-AAAAAAAATTAT--TTTAAATATT
58038 TA
1 TA
58040 TATTATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 5 0.19
28 11 0.41
30 11 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAAAAAAAAAATTATTTTAAATATT
Found at i:58289 original size:22 final size:21
Alignment explanation
Indices: 58235--58289 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
58225 TAAAAATACA
58235 TAAATATTTATTATTATATTT
1 TAAATATTTATTATTATATTT
* * *
58256 TAAATTTATTATTATGTTTTTTT
1 TAAATAT-TTATTAT-TATATTT
58279 TAAATATTTAT
1 TAAATATTTAT
58290 GCATTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 6 0.21
22 11 0.39
23 11 0.39
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TAAATATTTATTATTATATTT
Found at i:65245 original size:60 final size:59
Alignment explanation
Indices: 65125--65248 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 59
65115 TACATAAGAG
* * * * * *
65125 TTGAATTTTTTTTTGTCTAAGTTAAGCTTTGAATTTGACAATTGTTCTCGTATTAGGGC
1 TTGAATTTTTTTTTGTCCAAGTTAAGCTCTGAACTTAACAATTGTTCTCATATTAAGGC
*
65184 TTGAATTTTTTTATTGTCCAAGTT-AGTCTCTGAACTTAACAATTGATTC-CATTTTAAGGC
1 TTGAATTTTTTT-TTGTCCAAGTTAAG-CTCTGAACTTAACAATTG-TTCTCATATTAAGGC
65244 TTGAA
1 TTGAA
65249 CTTGACAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
59 14 0.25
60 38 0.69
61 3 0.05
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (59 bp):
TTGAATTTTTTTTTGTCCAAGTTAAGCTCTGAACTTAACAATTGTTCTCATATTAAGGC
Found at i:73833 original size:19 final size:20
Alignment explanation
Indices: 73782--73840 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
73772 CAACAAAATA
73782 AAATAT-ATCATTTAATATTT
1 AAATATAAT-ATTTAATATTT
73802 AAATATAAT-TTTAATATTT
1 AAATATAATATTTAATATTT
* *
73821 -AATTTGATATTTAAATATTT
1 AAATATAATATTT-AATATTT
73841 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.18
19 13 0.38
20 13 0.38
21 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATATAATATTTAATATTT
Found at i:77128 original size:3 final size:3
Alignment explanation
Indices: 77120--77187 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
77110 CTTATAACTA
77120 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
77168 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
77188 ATATAATAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:80312 original size:23 final size:22
Alignment explanation
Indices: 80270--80312 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
80260 TTAAAAATAC
* *
80270 ATTTTTATATTAATATTTATAT
1 ATTTTTATATTAAAAATTATAT
80292 ATTTTTATAATTAAAAATTAT
1 ATTTTTAT-ATTAAAAATTAT
80313 TTACTTCGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTTATATTAAAAATTATAT
Found at i:84002 original size:210 final size:210
Alignment explanation
Indices: 83640--84766 Score: 1852
Period size: 210 Copynumber: 5.4 Consensus size: 210
83630 CCTTGCTTGG
83640 AAGAATTAGAACTAAGAGATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTCT
1 AAGAATTAGAACTAAGAGATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTCT
**
83705 CTTCGAAATCTGAGAATTCTTAACTGCAACAAATTGGAAGTTCTTCCATTGACAGGAGGATGTTC
66 CTTCGAAATCTGAGAATTCTTGCCTGCAACAAATTGGAAGTTCTTCCATTGACAGGAGGATGTTC
*
83770 ATCTCTTGAAAAGCTTCAGATTGACGGTTGCGAAAAATTAAGCAAGATTGGAGACGGATTATCTA
131 ATCTCTTGAAAAGCTTCAGATTGACGGTTGCGCAAAATTAAGCAAGATTGGAGACGGATTATCTA
83835 CCTCCACTTGTCTCA
196 CCTCCACTTGTCTCA
* *
83850 AAGAATTAGAACT-AGAGTTTTGCTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTC
1 AAGAATTAGAACTAAGAG-ATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTC
* *
83914 TCTTCGAAATCTGAGAATTCTTGCCTGCAAAAAATTGGAAGTTCTTCCATTGACAGGAGAATGTT
65 TCTTCGAAATCTGAGAATTCTTGCCTGCAACAAATTGGAAGTTCTTCCATTGACAGGAGGATGTT
** *
83979 CATCTCTTGAAAAGCTTCAGATTGACGGTTGCAAAAAATTAAGCAAGATTGGAGACGAATTATCT
130 CATCTCTTGAAAAGCTTCAGATTGACGGTTGCGCAAAATTAAGCAAGATTGGAGACGGATTATCT
84044 ACCTCCACTTGTCTCA
195 ACCTCCACTTGTCTCA
84060 AAGAATTAGAACTAAGAGATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTCT
1 AAGAATTAGAACTAAGAGATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTCT
*
84125 CTTCGAAATCTGAGAATTATTGCCTGCAACAAATTGGAAGTTCTTCCATTGACAGGAGGATGTTC
66 CTTCGAAATCTGAGAATTCTTGCCTGCAACAAATTGGAAGTTCTTCCATTGACAGGAGGATGTTC
**
84190 ATCTCTTGAAAAGCTTCAGATTGACTATTGCGCAAAATTAAGCAAGATTGGAGACGGATTATCTA
131 ATCTCTTGAAAAGCTTCAGATTGACGGTTGCGCAAAATTAAGCAAGATTGGAGACGGATTATCTA
84255 CCTCCACTTGTCTCA
196 CCTCCACTTGTCTCA
* *
84270 AAGAATTAGACCTAAAAGATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTCT
1 AAGAATTAGAACTAAGAGATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTCT
*
84335 CTTCGAAATCTGAGAATTGTTGCCTGCAACAAATTGGAAGTTCTTCCATTGACAGGAGGATGTTC
66 CTTCGAAATCTGAGAATTCTTGCCTGCAACAAATTGGAAGTTCTTCCATTGACAGGAGGATGTTC
* ** *
84400 ATCTCTTGAAAAG-TTTAGCATTTTCGGATGCGCAAAATTAAGCAAGATTGGAGACGGATTATCT
131 ATCTCTTGAAAAGCTTCAG-ATTGACGGTTGCGCAAAATTAAGCAAGATTGGAGACGGATTATCT
84464 ACCTCCACTTGTCTCA
195 ACCTCCACTTGTCTCA
* *
84480 AAGAATTAGAACTAATATG-TTGTTCTAGTTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTC
1 AAGAATTAGAACTAAGA-GATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTC
** * * *
84544 TCTTCGAAATCTGATTATT-TCTGGCTGCAACGAATTGGAAGTTCTTCCATTGACAGGAAGATGT
65 TCTTCGAAATCTGAGAATTCT-TGCCTGCAACAAATTGGAAGTTCTTCCATTGACAGGAGGATGT
* ** * *
84608 TCATCTCTTGAAATGCTTGTGATTGACGGTTGTGCAAAATTAATCAAGATTGGAGACGGATTATC
129 TCATCTCTTGAAAAGCTTCAGATTGACGGTTGCGCAAAATTAAGCAAGATTGGAGACGGATTATC
*
84673 TACCTCGACTTGTCTCA
194 TACCTCCACTTGTCTCA
*
84690 AAGAATT-GAAACT-AGTGCATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCT
1 AAGAATTAG-AACTAAGAG-ATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCT
84753 CTCTTCGAAATCTG
64 CTCTTCGAAATCTG
84767 GTAATTGGTG
Statistics
Matches: 861, Mismatches: 47, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
208 1 0.00
209 11 0.01
210 841 0.98
211 8 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (210 bp):
AAGAATTAGAACTAAGAGATTGTTCTAATTTAACTTCCATTCCAGATTTGAAAGGATTTTCCTCT
CTTCGAAATCTGAGAATTCTTGCCTGCAACAAATTGGAAGTTCTTCCATTGACAGGAGGATGTTC
ATCTCTTGAAAAGCTTCAGATTGACGGTTGCGCAAAATTAAGCAAGATTGGAGACGGATTATCTA
CCTCCACTTGTCTCA
Found at i:85335 original size:144 final size:144
Alignment explanation
Indices: 85159--85428 Score: 348
Period size: 144 Copynumber: 1.9 Consensus size: 144
85149 TTGGTTGGGA
* *** * *
85159 AAAGCTAAAGAGTCTTCCCCACCAGCTTCAACTCCTTTCTACCCTTGAA-GATTTGAGGA-T-AG
1 AAAGCTAAAGAGTCTTCCCCACCAACTTCAACTCCCCACTACCCTTGAACG-GTTGA-CATTCAG
* * * *
85221 AAGAGTTTCAAGGAATAGAAGCCTTTCCAGAGTGGTTGGGGAATCTCTCTTCTCTAAAGTATCTA
64 -AGAGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTGGGGAATCTCTCTTCTCTAAAGTATCTA
85286 CGTTTGAGTGGTTTTAG
128 CGTTTGAGTGGTTTTAG
* * * *
85303 AAAGCTAAAGAGTCTTCCTCACCAACTTCAACTCCCCACTGCCCTTGAACGGTTGACATTCTGTG
1 AAAGCTAAAGAGTCTTCCCCACCAACTTCAACTCCCCACTACCCTTGAACGGTTGACATTCAGAG
* *
85368 AGTTTGATGAAATAGAAGCCTTGCCAGACTCGTTGGGGAATCTCTCTTCTCTAAAGTATCT
66 AGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTGGGGAATCTCTCTTCTCTAAAGTATCT
85429 GCGTATTTGT
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
143 1 0.01
144 104 0.97
145 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (144 bp):
AAAGCTAAAGAGTCTTCCCCACCAACTTCAACTCCCCACTACCCTTGAACGGTTGACATTCAGAG
AGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTGGGGAATCTCTCTTCTCTAAAGTATCTACGT
TTGAGTGGTTTTAG
Found at i:86823 original size:15 final size:15
Alignment explanation
Indices: 86803--86831 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
86793 GGATTTTTAA
86803 TAACCCATACCAAAG
1 TAACCCATACCAAAG
86818 TAACCCATACCAAA
1 TAACCCATACCAAA
86832 AAAGGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.34, G:0.03, T:0.14
Consensus pattern (15 bp):
TAACCCATACCAAAG
Done.