Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012267.1 Kokia drynarioides strain JFW-HI SEQ_127268, 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: 30363
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1222 original size:27 final size:27
Alignment explanation
Indices: 1184--1248 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
1174 TCTTTTTCAT
1184 TCATTTCCAACGTCACGTGCATATCTC
1 TCATTTCCAACGTCACGTGCATATCTC
1211 TCATTTCCAACGTCACGTGCATATCTC
1 TCATTTCCAACGTCACGTGCATATCTC
*
1238 TCCTTTCCAAC
1 TCATTTCCAAC
1249 TTTTATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.22, C:0.35, G:0.09, T:0.34
Consensus pattern (27 bp):
TCATTTCCAACGTCACGTGCATATCTC
Found at i:2592 original size:23 final size:23
Alignment explanation
Indices: 2554--2651 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 23
2544 CATTAGCGCA
2554 CTTACTG-TTCAGCACTGTGTGTG
1 CTTACTGATTCA-CACTGTGTGTG
* *
2577 CTTACTGATTCACACTATATGTG
1 CTTACTGATTCACACTGTGTGTG
* * **
2600 CTTATTGTTTTGCACTGTGTGTG
1 CTTACTGATTCACACTGTGTGTG
* **
2623 CCTACTGATTTGCACTGTGTGTG
1 CTTACTGATTCACACTGTGTGTG
2646 CTTACT
1 CTTACT
2652 ATTTCCCCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
23 58 0.94
24 4 0.06
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.43
Consensus pattern (23 bp):
CTTACTGATTCACACTGTGTGTG
Found at i:8899 original size:162 final size:162
Alignment explanation
Indices: 8637--9094 Score: 695
Period size: 162 Copynumber: 2.8 Consensus size: 162
8627 CAGGAGTGCT
* * * * * *
8637 GAATTGGATGCAATTGTGGAAGAGAGTAGTGAGGTTGAGAAGGTCAAGTGTGTC-GTTACTTCAC
1 GAATTGGATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATG-CAGCTACTTCAC
* * * *
8701 AACAACAAGCCCCCTCGAGAAGGAGCAGACGCAAGACTGAGGCTCATACCGCTCCAGCTGCTGAT
65 AACAAGAAGCCCCCTCGAGGAGGAGCAGACGCAAGACTGAGGCTCTTACCGCTCCAGCTGCCGAT
*
8766 TTGGCACCGGTTGTG-GGGAAGGGCTCGACTGAA
130 TTGGCACCGATTG-GAGGGAAGGGCTCGACTGAA
* *
8799 GAATTGGATGCAATTGTTGAAGATAGTAGTAAGGTTGAGAGGGCCAAGTATGCAGCTACTTCACA
1 GAATTGGATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACTTCACA
*
8864 ACAAGAAGCCCCCTCGAGGAGGAGCAGACGCAAGACTGGGGCTCTTACCGCTCCAGCTGCCGATT
66 ACAAGAAGCCCCCTCGAGGAGGAGCAGACGCAAGACTGAGGCTCTTACCGCTCCAGCTGCCGATT
* *
8929 TGGCATCGATTGGAGGGAAGGGCTCGGCTGAA
131 TGGCACCGATTGGAGGGAAGGGCTCGACTGAA
*
8961 GAATTGGATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTAGTTCACA
1 GAATTGGATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACTTCACA
* * * *
9026 ACAAGAAGCCCCCTCGAGGAGGGGCAGACGCAAGACTGTGGTTCTTACTGCTCCAGCTGCCGATT
66 ACAAGAAGCCCCCTCGAGGAGGAGCAGACGCAAGACTGAGGCTCTTACCGCTCCAGCTGCCGATT
9091 TGGC
131 TGGC
9095 CAATAAGGAA
Statistics
Matches: 272, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
161 2 0.01
162 270 0.99
ACGTcount: A:0.27, C:0.21, G:0.32, T:0.21
Consensus pattern (162 bp):
GAATTGGATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACTTCACA
ACAAGAAGCCCCCTCGAGGAGGAGCAGACGCAAGACTGAGGCTCTTACCGCTCCAGCTGCCGATT
TGGCACCGATTGGAGGGAAGGGCTCGACTGAA
Found at i:9301 original size:201 final size:202
Alignment explanation
Indices: 8956--9722 Score: 999
Period size: 201 Copynumber: 3.9 Consensus size: 202
8946 AAGGGCTCGG
* *
8956 CTGAAGAATTGGATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTAGT
1 CTGAAGAATTGGATGCAATTGTAGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACT
** *
9021 TCACAACAAGAAGCCCCCTCGAGGAGGGGCAGACGCAAGACTGTGGTTCTTACTGCTCCAGCTGC
66 TCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGCTGC
* *
9086 CGATTTGGCCAA-TAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGGTTGTAGGGAAA
131 CGATTTGGCCAAGTAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGAAAA
9150 GGCACGA
196 GGCACGA
* * * *
9157 CTGAAGAATTGGACGCAATTCTTGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCAGCTACT
1 CTGAAGAATTGGATGCAATTGTAGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACT
** *
9222 TCACAACAAGAAGCCCCCTCGAGGAGGGGCAGACGCAAGACTGTGGTTCTTACTGCTCCAGCTGC
66 TCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGCTGC
* *
9287 CGATTTGGCCAA-TAAGGAAGATATTGGTAGAACGGAGCAGCTAGAGGCACAGCTTGTAGGAAAA
131 CGATTTGGCCAAGTAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGAAAA
*
9351 GGCAAGA
196 GGCACGA
* * ** *
9358 CTGAAGAATTGCATGCAATTGTGGAAGATAGTAGTGAGGTTGAGAGGGCCAAGGGTGC-CCT--T
1 CTGAAGAATTGGATGCAATTGTAGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACT
*
9420 TCTTC-AC---AAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCT---GCTG
66 TC-ACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGCTG
* * *
9478 CAGATTTGG-CAAGTAAGGAAGATATTGGTAGTACGGAGCAGTT-GAAGGCACCGCTTCTAGGAA
130 CCGATTTGGCCAAGTAAGGAAGATATTGGTAGAACGGAGCAGTTAG-AGGCACCGCTTGTAGGAA
*
9541 AAGGCACAA
194 AAGGCACGA
* * * * *
9550 CTGAAGAATTGGATGCAATTGTACAAGATAGGAGTGAGGTTGGGAGGGCCAAGTCTGCTATC-AC
1 CTGAAGAATTGGATGCAATTGTAGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGC-AGCTAC
** * * * * *
9614 TTCACAACACCAATCCCCCTTGAGGAAGAACAGACACAAGACTGTGATTTTTACTGCTCCAGCTG
65 TTCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGCTG
* * * * *
9679 CCGAGTT-GCCAATTAGGGAAGATATTAGTAGAATGGAGCAGTTA
130 CCGATTTGGCCAAGTAAGGAAGATATTGGTAGAACGGAGCAGTTA
9723 AGATTACCGC
Statistics
Matches: 500, Mismatches: 50, Indels: 31
0.86 0.09 0.05
Matches are distributed among these distances:
191 4 0.01
192 114 0.23
194 2 0.00
195 49 0.10
198 47 0.09
199 1 0.00
200 3 0.01
201 280 0.56
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (202 bp):
CTGAAGAATTGGATGCAATTGTAGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTACT
TCACAACAAGAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCCAGCTGC
CGATTTGGCCAAGTAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTGTAGGAAAA
GGCACGA
Found at i:9701 original size:393 final size:397
Alignment explanation
Indices: 8956--9719 Score: 1033
Period size: 393 Copynumber: 1.9 Consensus size: 397
8946 AAGGGCTCGG
* * *
8956 CTGAAGAATTGGATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGTATGCAGCTAGT
1 CTGAAGAATTGCATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGGATGCACCTA-T
** *
9021 TCACAACAAGAAGCCCCCTCGAGGAGGGGCAGACGCAAGACTGTGGTTCTTACTGCTCCAGCTGC
65 TCACAAC-A-AAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCT-C-GCTGC
* * * *
9086 CGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGGTTGTAGGGAAAG
126 AGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTCTAGGAAAAG
* ** *
9151 GCACGACTGAAGAATTGGACGCAATTCTTGAAGATAGTAGTGAGGTCGAGAGGGCCAAGTATGCA
191 GCACAACTGAAGAATTGGACGCAATTCTACAAGATAGGAGTGAGGTCGAGAGGGCCAAGTATGCA
* * ** * *
9216 GCTACTTCACAACAAGAAGCCCCCTCGAGGAGGGGCAGACGCAAGACTGTGGTTCTTACTGCTCC
256 GCTACTTCACAACAACAAGCCCCCTCGAGGAAGAACAGACACAAGACTGTGATTCTTACTGCTCC
* *
9281 AGCTGCCGATTTGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGCTAGAGGCACAGCTTGTAG
321 AGCTGCCGAGTTGGCCAATAAGGAAGATATTAGTAGAACGGAGCAGCTAGAGGCACAGCTTGTAG
9346 GAAAAGGCAAGA
386 GAAAAGGCAAGA
* *
9358 CTGAAGAATTGCATGCAATTGTGGAAGATAGTAGTGAGGTTGAGAGGGCCAAGGGTGC-CCT-TT
1 CTGAAGAATTGCATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGGATGCACCTATT
*
9421 CTTC-AC-AAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCT-GCTGCAGAT
66 C-ACAACAAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCGCTGCAGAT
*
9483 TTGG-CAAGTAAGGAAGATATTGGTAGTACGGAGCAGTT-GAAGGCACCGCTTCTAGGAAAAGGC
130 TTGGCCAA-TAAGGAAGATATTGGTAGAACGGAGCAGTTAG-AGGCACCGCTTCTAGGAAAAGGC
* * * * * *
9546 ACAACTGAAGAATTGGATGCAATTGTACAAGATAGGAGTGAGGTTGGGAGGGCCAAGTCTGCTAT
193 ACAACTGAAGAATTGGACGCAATTCTACAAGATAGGAGTGAGGTCGAGAGGGCCAAGTATGC-AG
* * * *
9611 C-ACTTCACAACACCAATCCCCCTTGAGGAAGAACAGACACAAGACTGTGATTTTTACTGCTCCA
257 CTACTTCACAACAACAAGCCCCCTCGAGGAAGAACAGACACAAGACTGTGATTCTTACTGCTCCA
* *
9675 GCTGCCGAGTT-GCCAATTAGGGAAGATATTAGTAGAATGGAGCAG
322 GCTGCCGAGTTGGCCAA-TAAGGAAGATATTAGTAGAACGGAGCAG
9720 TTAAGATTAC
Statistics
Matches: 319, Mismatches: 38, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
392 9 0.03
393 202 0.63
394 2 0.01
396 44 0.14
399 5 0.02
400 1 0.00
401 2 0.01
402 54 0.17
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (397 bp):
CTGAAGAATTGCATGCAATTGTCGAAGATAGTAGTGAGGTTGAGAGGGCCAAGGATGCACCTATT
CACAACAAAGCCCCCTCGAGGAGGAACAGACGCAAGACTGTGATTCTTACTGCTCGCTGCAGATT
TGGCCAATAAGGAAGATATTGGTAGAACGGAGCAGTTAGAGGCACCGCTTCTAGGAAAAGGCACA
ACTGAAGAATTGGACGCAATTCTACAAGATAGGAGTGAGGTCGAGAGGGCCAAGTATGCAGCTAC
TTCACAACAACAAGCCCCCTCGAGGAAGAACAGACACAAGACTGTGATTCTTACTGCTCCAGCTG
CCGAGTTGGCCAATAAGGAAGATATTAGTAGAACGGAGCAGCTAGAGGCACAGCTTGTAGGAAAA
GGCAAGA
Found at i:13170 original size:14 final size:13
Alignment explanation
Indices: 13140--13166 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13130 TCAGTTTAAC
13140 ATTGTTTTTAAAA
1 ATTGTTTTTAAAA
13153 ATTGTTTTTAAAA
1 ATTGTTTTTAAAA
13166 A
1 A
13167 ATTGATGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTGTTTTTAAAA
Found at i:25473 original size:16 final size:15
Alignment explanation
Indices: 25427--25476 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
25417 AAATTATGGA
25427 TTTAA-TCTATATTT
1 TTTAATTCTATATTT
25441 TTTAATT-TGAT-TATT
1 TTTAATTCT-ATAT-TT
25456 TTTAATCTCTATATTT
1 TTTAAT-TCTATATTT
25472 TTTAA
1 TTTAA
25477 ATTGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 7 0.23
15 11 0.37
16 10 0.33
17 2 0.07
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTAATTCTATATTT
Found at i:28049 original size:82 final size:82
Alignment explanation
Indices: 27907--28058 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 82
27897 AAAGCAACAT
* * *
27907 AAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGTGAAAGCGCCGCTAAAGGTCAGAGCAA
1 AAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGGGAAAGCACCGCTAAAGATCAGAGCAA
27972 TAGCGACGCTTATGGGG
66 TAGCGACGCTTATGGGG
* * * * * *
27989 AAGCGCCGCTAAAGGTTAGAGTATTAGCGGCGCTTATGGGCAAGCACCGTTAAAGATCAGAGCAT
1 AAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGGGAAAGCACCGCTAAAGATCAGAGCAA
28054 TAGCG
66 TAGCG
28059 GCGTTTTCCC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 61 1.00
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.18
Consensus pattern (82 bp):
AAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGGGAAAGCACCGCTAAAGATCAGAGCAA
TAGCGACGCTTATGGGG
Found at i:28061 original size:41 final size:41
Alignment explanation
Indices: 27907--28058 Score: 196
Period size: 41 Copynumber: 3.7 Consensus size: 41
27897 AAAGCAACAT
* *
27907 AAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGTGA
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGA
*
27948 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGG
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGA
* * * * *
27989 AAGCGCCGCTAAAGGTTAGAGTATTAGCGGCGCTTATGGGC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGA
* * * *
28030 AAGCACCGTTAAAGATCAGAGCATTAGCG
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCG
28059 GCGTTTTCCC
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 98 1.00
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.18
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGGA
Found at i:28080 original size:82 final size:82
Alignment explanation
Indices: 27904--28082 Score: 198
Period size: 82 Copynumber: 2.2 Consensus size: 82
27894 GACAAAGCAA
* * *
27904 CATAAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGTGAAAGCGCCGCTAAAGGTCAGAG
1 CATAAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGGGAAAGCACCGCTAAAGATCAGAG
*
27969 CAATAGCGACGCTTATG
66 CAATAGCGACGCTTATC
*** * * * * *
27986 GGGAAGCGCCGCTAAAGGTTAGAGTATTAGCGGCGCTTATGGGCAAGCACCGTTAAAGATCAGAG
1 CATAAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGGGAAAGCACCGCTAAAGATCAGAG
* * *
28051 CATTAGCGGCG-TTTTCC
66 CAATAGCGACGCTTAT-C
*
28068 CATAAGCACCGCTAA
1 CATAAGCGCCGCTAA
28083 TTTATTTAAA
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
81 3 0.04
82 74 0.96
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (82 bp):
CATAAGCGCCGCTAAAGGTTAGAGCAATAGCGACGCTTATGGGAAAGCACCGCTAAAGATCAGAG
CAATAGCGACGCTTATC
Found at i:29609 original size:23 final size:23
Alignment explanation
Indices: 29575--29722 Score: 165
Period size: 23 Copynumber: 6.3 Consensus size: 23
29565 TGCTGGGCAA
29575 CAGAGAGCACACAAAGTGCTAAAT
1 CAGAGAGCACACAAAGTGCT-AAT
* * * *
29599 -AGAGAGTACACCAAGTACTAGT
1 CAGAGAGCACACAAAGTGCTAAT
29621 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
29644 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* * *
29667 AACAGAGAGCACGA-GACGTGCTAAA
1 --CAGAGAGCAC-ACAAAGTGCTAAT
*
29692 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
29715 CAGAGAGC
1 CAGAGAGC
29723 GCGCTAGTGT
Statistics
Matches: 102, Mismatches: 17, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
22 3 0.03
23 81 0.79
25 17 0.17
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Done.