Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011981.1 Kokia drynarioides strain JFW-HI SEQ_126979, 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: 27262
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:3169 original size:2 final size:2
Alignment explanation
Indices: 3164--3205 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3154 CACACAAACT
3164 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3206 TGTAAAGTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4721 original size:206 final size:207
Alignment explanation
Indices: 4361--4782 Score: 595
Period size: 207 Copynumber: 2.0 Consensus size: 207
4351 AAGTTTACCA
* *
4361 AATGTGTGATATATTACTTACACTCTCTCTCATATGTAGGCCCAATATTAGCAATTTAACAATCT
1 AATGTGTGACATATTACTTACACTCTCTCT-ATATGTAGGACCAATATTAGCAATTTAACAATCT
**
4426 TGCATCATTAAAAATAGAGAGTAGCAACAACAAACATAACAAACTAGGCAACAAGCAAACTGGAT
65 TGCATCATTAAAAATAGAGACAAGCAACAACAAACATAACAAACTAGGCAACAAGCAAACTGGAT
* * *
4491 TATGAAATAGTAACAACAACTAGAT-AAAGTGAAAAGAATTAACTTAAATATAAGATACAACAAT
130 TATGAAATAGTAACAACAACTAGATCAAAGTAAAAAGAATTAACTTAAAAATAAGACACAACAAT
*
4555 CCCAAACTTGGCC
195 CCCAAACTTAGCC
4568 AATGTGTGACATATTACTTACA-TGCTCTCT-TATGAATAGGACCAATATTAGCAATTTAAACAA
1 AATGTGTGACATATTACTTACACT-CTCTCTATATG--TAGGACCAATATTAGCAATTT-AACAA
* * **
4631 TCTTGCATCATTAAAAATAGA-ACAAGTAGCAACAAA-ATAACAAACTAGGCAATGAGCAAACTA
62 TCTTGCATCATTAAAAATAGAGACAAGCAACAACAAACATAACAAACTAGGCAACAAGCAAACT-
* * * * *
4694 GGCTT-TGAAATAGTAATAACAACTAGATCTAAGTAAAAAGAATTAAGTTAAAAATAAGACACCA
126 GGATTATGAAATAGTAACAACAACTAGATCAAAGTAAAAAGAATTAACTTAAAAATAAGACACAA
4758 CAATCCCAAACTTAGCC
191 CAATCCCAAACTTAGCC
4775 AATGTGTG
1 AATGTGTG
4783 CAATAGCAAT
Statistics
Matches: 192, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
205 4 0.02
206 47 0.24
207 115 0.60
208 26 0.14
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (207 bp):
AATGTGTGACATATTACTTACACTCTCTCTATATGTAGGACCAATATTAGCAATTTAACAATCTT
GCATCATTAAAAATAGAGACAAGCAACAACAAACATAACAAACTAGGCAACAAGCAAACTGGATT
ATGAAATAGTAACAACAACTAGATCAAAGTAAAAAGAATTAACTTAAAAATAAGACACAACAATC
CCAAACTTAGCC
Found at i:6478 original size:2 final size:2
Alignment explanation
Indices: 6473--6512 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6463 CAAATATATT
6473 GA GA GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
6513 CATATGCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12040 original size:34 final size:34
Alignment explanation
Indices: 12002--12081 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
11992 AGTAAAAATA
*
12002 TAAATTTTAAAAT-TAAATTAAAATTTTATTATTT
1 TAAATTTTAAAATAT-AATTAAAATTTTATTAATT
* **
12036 TAAATATTAAAATATAATTTTAATTTTATTAATT
1 TAAATTTTAAAATATAATTAAAATTTTATTAATT
*
12070 TAAAATTTAAAA
1 TAAATTTTAAAA
12082 CTTTTAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 38 0.97
35 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TAAATTTTAAAATATAATTAAAATTTTATTAATT
Found at i:12054 original size:28 final size:27
Alignment explanation
Indices: 12005--12057 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
11995 AAAAATATAA
*
12005 ATTTTAAAATTAAATTAAAATTTTATT
1 ATTTTAAAATTAAAATAAAATTTTATT
*
12032 ATTTTAAATATTAAAATATAATTTTA
1 ATTTTAAA-ATTAAAATAAAATTTTA
12058 ATTTTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTTAAAATTAAAATAAAATTTTATT
Found at i:17740 original size:23 final size:23
Alignment explanation
Indices: 17688--17740 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
17678 AGAAGGTCTG
*
17688 ATATA-ATATAATACAATTCCAA
1 ATATAGATATAATACAATTACAA
*
17710 ATACAGATATAATACAGA-TACAA
1 ATATAGATATAATACA-ATTACAA
*
17733 TTATAGAT
1 ATATAGAT
17741 GCATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 4 0.16
23 20 0.80
24 1 0.04
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (23 bp):
ATATAGATATAATACAATTACAA
Found at i:17748 original size:29 final size:29
Alignment explanation
Indices: 17688--17804 Score: 101
Period size: 29 Copynumber: 4.1 Consensus size: 29
17678 AGAAGGTCTG
* * * * *
17688 ATATAATATA-ATACAATTCCAAATACAG
1 ATATAATACAGATACAATTACAGATGCAA
* *
17716 ATATAATACAGATACAATTATAGATGCAT
1 ATATAATACAGATACAATTACAGATGCAA
* ** * * *
17745 ATATATTGTAGATACAGTTACAAATACAA
1 ATATAATACAGATACAATTACAGATGCAA
*
17774 ATATAATACAAATACAATTACAGATGCAA
1 ATATAATACAGATACAATTACAGATGCAA
17803 AT
1 AT
17805 TCCTACCCCT
Statistics
Matches: 67, Mismatches: 21, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
28 9 0.13
29 58 0.87
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.29
Consensus pattern (29 bp):
ATATAATACAGATACAATTACAGATGCAA
Found at i:19537 original size:6 final size:6
Alignment explanation
Indices: 19526--19551 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19516 ATGTTTAATC
19526 ATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT AT
19552 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATAAAT
Found at i:19846 original size:29 final size:29
Alignment explanation
Indices: 19773--19858 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
19763 ATAAAAATCA
*
19773 ATAAAAATTAAAGAAAAATAATTAAAATTT
1 ATAAAAATTAGA-AAAAATAATTAAAATTT
*
19803 ATAAAAATTATAAAAAAT-ATTAAAAGTTT
1 ATAAAAATTAGAAAAAATAATTAAAA-TTT
* * *
19832 ATTAACAA-TAGAAAAAATTATAAAAAT
1 A-TAAAAATTAGAAAAAATAATTAAAAT
19859 CACAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
28 7 0.14
29 20 0.41
30 22 0.45
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (29 bp):
ATAAAAATTAGAAAAAATAATTAAAATTT
Found at i:19925 original size:29 final size:28
Alignment explanation
Indices: 19892--19969 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
19882 AAGGATTTAC
*
19892 TAAAAATTACATTTTTTTATAAAAATCG
1 TAAAAATTACATTTTTTTATAAAAATAG
* *
19920 TAAAAATTTATAATTTGTTTAT-AAAATAG
1 TAAAAA-TTA-CATTTTTTTATAAAAATAG
*
19949 TAAAAATTAC-TATTTTTATAA
1 TAAAAATTACATTTTTTTATAA
19970 TTTCTTTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
26 7 0.17
27 1 0.02
28 9 0.22
29 15 0.37
30 9 0.22
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (28 bp):
TAAAAATTACATTTTTTTATAAAAATAG
Found at i:20914 original size:88 final size:88
Alignment explanation
Indices: 20731--20917 Score: 200
Period size: 89 Copynumber: 2.1 Consensus size: 88
20721 ATTCACTTAG
* * * * * ** * *
20731 GTACTTAAACTTTTAAAATGTATCAAAAAGGTCCTTAAACTTTTTAAAAAAAGTAATTAAGTCCC
1 GTACTTGAACATTCAAAATGCATAAAAAAGCCCCTCAAACTTTTTAAAAAAAGCAATTAAGTCCC
* *
20796 TACTTTTATTTTGCACTTAATTGG
66 TAC-TCTATTTTGCACTTAATTGA
20820 GTACTTGAACATTCAAAATGCATAAAAAAGCCCCTCAAACTTTTTCAAAAAAAGCAATTAAGTCC
1 GTACTTGAACATTCAAAATGCATAAAAAAGCCCCTCAAACTTTTT-AAAAAAAGCAATTAAGTCC
* *
20885 TTGA-TCT-TTTTGC-TTTCAATTGA
65 CT-ACTCTATTTTGCACTT-AATTGA
20908 GTACTTGAAC
1 GTACTTGAAC
20918 TGTCAAATAC
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
87 2 0.02
88 21 0.26
89 39 0.48
90 19 0.23
91 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (88 bp):
GTACTTGAACATTCAAAATGCATAAAAAAGCCCCTCAAACTTTTTAAAAAAAGCAATTAAGTCCC
TACTCTATTTTGCACTTAATTGA
Found at i:20934 original size:88 final size:88
Alignment explanation
Indices: 20767--20936 Score: 197
Period size: 88 Copynumber: 1.9 Consensus size: 88
20757 AAAGGTCCTT
* * *
20767 AAACTTTTTAAAAAAAGTAATTAAGTCCCTACTTTTATTTTGCACTTAATTGGGTACTTGAACAT
1 AAACTTTTTAAAAAAAGCAATTAAGTCCCTAC-TCTATTTTGCACTTAATTGAGTACTTGAACAT
*
20832 TCAAAATGCATAAAAAAGCCCCTC
65 TCAAAATACATAAAAAAGCCCCTC
* *
20856 AAACTTTTTCAAAAAAAGCAATTAAGTCCTTGA-TCT-TTTTGC-TTTCAATTGAGTACTTGAAC
1 AAACTTTTT-AAAAAAAGCAATTAAGTCCCT-ACTCTATTTTGCACTT-AATTGAGTACTTGAAC
*
20918 -TGTC-AAATACATTAAAAAG
63 AT-TCAAAATACATAAAAAAG
20937 GCCTTTTAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
87 16 0.23
88 23 0.33
89 11 0.16
90 19 0.27
91 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (88 bp):
AAACTTTTTAAAAAAAGCAATTAAGTCCCTACTCTATTTTGCACTTAATTGAGTACTTGAACATT
CAAAATACATAAAAAAGCCCCTC
Found at i:22770 original size:25 final size:25
Alignment explanation
Indices: 22742--22830 Score: 160
Period size: 25 Copynumber: 3.6 Consensus size: 25
22732 GACAGAATCA
*
22742 CGCTCTTACGAGCCAAATAGAATAT
1 CGCTCTTACGAGCCAAATAGTATAT
22767 CGCTCTTACGAGCCAAATAGTATAT
1 CGCTCTTACGAGCCAAATAGTATAT
*
22792 CGCTCTTACGAGCCAAATATTATAT
1 CGCTCTTACGAGCCAAATAGTATAT
22817 CGCTCTTACGAGCC
1 CGCTCTTACGAGCC
22831 TGGACAAAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (25 bp):
CGCTCTTACGAGCCAAATAGTATAT
Done.