Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012514.1 Kokia drynarioides strain JFW-HI SEQ_127519, 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: 29607
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:12065 original size:18 final size:18
Alignment explanation
Indices: 12042--12077 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12032 ATGTTATTAA
12042 ATTTTATTTAATAATAAT
1 ATTTTATTTAATAATAAT
12060 ATTTTATTTAATAATAAT
1 ATTTTATTTAATAATAAT
12078 TATGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTATTTAATAATAAT
Found at i:12139 original size:52 final size:53
Alignment explanation
Indices: 11992--12140 Score: 162
Period size: 52 Copynumber: 2.8 Consensus size: 53
11982 ATATATTATG
* *
11992 ATTT-TTATT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTTT
1 ATTTATTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAA-TTT
* * * *
12047 ATTTAATAATAATATTTTATTTAATAATAATTATGTTAAAATATAATTAAA-TT
1 ATTTATTATTAA-ATTATATTTAATAATAATTATATTAAAATATAATTAAATTT
12100 ATTTATTATTAAATTATATTTAATAATAATCT-TATTAAAAT
1 ATTTATTATTAAATTATATTTAATAATAAT-TATATTAAAAT
12141 TTAAAAACAA
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
52 25 0.31
53 13 0.16
55 16 0.20
56 20 0.25
57 3 0.04
58 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (53 bp):
ATTTATTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTT
Found at i:14038 original size:23 final size:23
Alignment explanation
Indices: 13994--14038 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
13984 CGATGAAGGA
* *
13994 TTATTTTACTTTTTAGTGATTAC
1 TTATTTTACTTTTAAGTAATTAC
* *
14017 TTATTTTTCTTTTAATTAATTA
1 TTATTTTACTTTTAAGTAATTA
14039 GAAATGCCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.64
Consensus pattern (23 bp):
TTATTTTACTTTTAAGTAATTAC
Found at i:18102 original size:125 final size:120
Alignment explanation
Indices: 17857--18095 Score: 307
Period size: 125 Copynumber: 1.9 Consensus size: 120
17847 ACCCTTCCGC
* * * * *
17857 TTTTTATTTTCTGAGCAAACTTTCATCTAGGTGATCCAAAATCATTGTAGTAGTGATTTCATCTG
1 TTTTTGTTTTCAGAGCAAACTTTCATCTAGATGATCCAAAATCATTATAGTAGTGACTTCATCTG
* *
17922 TAGCTGCATCTGCCATAGGCCTTGCACAAATAGAAATGCCAAAAATTTGTCAACT
66 TAGCTGCATATGCAATAGGCCTTGCACAAATAGAAATGCCAAAAATTTGTCAACT
17977 TTTTTGTTTTCAGAGCAAACTTTCATCTTGTTTAGATGATCCAAAATCATTATAGTAGTGACTTC
1 TTTTTGTTTTCAGAGCAAACTTTCATC-----TAGATGATCCAAAATCATTATAGTAGTGACTTC
* * * * * *
18042 ATCTTTAGGTGCCTATGCTAATATGCCTTGCACAAATCGAAGTGCCAAAAATTT
61 ATCTGTAGCTGCATATGC-AATAGGCCTTGCACAAATAGAAATGCCAAAAATTT
18096 TTAACTTCTT
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
120 25 0.25
125 44 0.44
126 31 0.31
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (120 bp):
TTTTTGTTTTCAGAGCAAACTTTCATCTAGATGATCCAAAATCATTATAGTAGTGACTTCATCTG
TAGCTGCATATGCAATAGGCCTTGCACAAATAGAAATGCCAAAAATTTGTCAACT
Found at i:19371 original size:27 final size:27
Alignment explanation
Indices: 19340--19391 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
19330 TATTTTAAAG
*
19340 ATAAAGTATAACATTTACA-AATTTCGA
1 ATAAAGTAGAACATTTA-AGAATTTCGA
19367 ATAAAGTAGAACATTTAAGAATTTC
1 ATAAAGTAGAACATTTAAGAATTTC
19392 TTAATTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (27 bp):
ATAAAGTAGAACATTTAAGAATTTCGA
Found at i:20205 original size:15 final size:15
Alignment explanation
Indices: 20185--20273 Score: 65
Period size: 15 Copynumber: 5.8 Consensus size: 15
20175 TAAATTATAG
20185 TATATAAAAATTAAA
1 TATATAAAAATTAAA
* *
20200 TATAT-AATATTACTA
1 TATATAAAAATTA-AA
*
20215 TAATATAAATATTAAA
1 T-ATATAAAAATTAAA
* * *
20231 AATATTAAAA-TAAT
1 TATATAAAAATTAAA
20245 TATATATAAAATTATAA
1 TATATA-AAAATTA-AA
*
20262 TAAATAAAAATT
1 TATATAAAAATT
20274 TAAAAAACTT
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
14 13 0.23
15 18 0.32
16 13 0.23
17 13 0.23
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (15 bp):
TATATAAAAATTAAA
Found at i:20252 original size:31 final size:29
Alignment explanation
Indices: 20185--20258 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 29
20175 TAAATTATAG
* * *
20185 TATATA-AAAATTAAATATATAATATTAC
1 TATATATAAAATTAAAAATATAAAATAAC
*
20213 TATAATATAAATATTAAAAATATTAAAATAAT
1 TAT-ATATAAA-ATTAAAAATA-TAAAATAAC
20245 TATATATAAAATTA
1 TATATATAAAATTA
20259 TAATAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 3 0.08
29 3 0.08
30 7 0.18
31 16 0.42
32 9 0.24
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (29 bp):
TATATATAAAATTAAAAATATAAAATAAC
Found at i:20253 original size:47 final size:46
Alignment explanation
Indices: 20190--20296 Score: 114
Period size: 47 Copynumber: 2.3 Consensus size: 46
20180 TATAGTATAT
* *
20190 AAAAATTAAATATATAATATTACT-AT-AATATAAATATTAAAAATA-TTA
1 AAAAATT--ATATATAAAATTA-TAATAAATAAAAAT-TTAAAAA-ACTTA
20238 AAATAATTATATATAAAATTATAATAAATAAAAATTTAAAAAACTTA
1 AAA-AATTATATATAAAATTATAATAAATAAAAATTTAAAAAACTTA
20285 AAAAATTA-ATAT
1 AAAAATTATATAT
20297 CATACCTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
45 4 0.08
46 7 0.13
47 27 0.51
48 11 0.21
49 4 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (46 bp):
AAAAATTATATATAAAATTATAATAAATAAAAATTTAAAAAACTTA
Found at i:21649 original size:33 final size:33
Alignment explanation
Indices: 21612--21678 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
21602 TTCCCTACAC
*
21612 TCCTAGTAAGGATGAGTTTCAATTGGAGGTTCA
1 TCCTAGTAAGGATGAGTTTAAATTGGAGGTTCA
21645 TCCTAGTAAGGATGAGTTTAAATTGGAGGTTCA
1 TCCTAGTAAGGATGAGTTTAAATTGGAGGTTCA
21678 T
1 T
21679 TCTTTCTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.34
Consensus pattern (33 bp):
TCCTAGTAAGGATGAGTTTAAATTGGAGGTTCA
Found at i:25360 original size:66 final size:66
Alignment explanation
Indices: 25254--25384 Score: 262
Period size: 66 Copynumber: 2.0 Consensus size: 66
25244 ATATCTCAAG
25254 CCGATGAGAGAGTCAAACTTCAACATGTATGCATTGTAAGATAAAAATGGTAAAAGTATCATGGA
1 CCGATGAGAGAGTCAAACTTCAACATGTATGCATTGTAAGATAAAAATGGTAAAAGTATCATGGA
25319 A
66 A
25320 CCGATGAGAGAGTCAAACTTCAACATGTATGCATTGTAAGATAAAAATGGTAAAAGTATCATGGA
1 CCGATGAGAGAGTCAAACTTCAACATGTATGCATTGTAAGATAAAAATGGTAAAAGTATCATGGA
25385 GGCTCTTGTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (66 bp):
CCGATGAGAGAGTCAAACTTCAACATGTATGCATTGTAAGATAAAAATGGTAAAAGTATCATGGA
A
Found at i:26695 original size:11 final size:11
Alignment explanation
Indices: 26679--26744 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 11
26669 TAAATTTGTT
26679 TATAATATTTA
1 TATAATATTTA
26690 TATAATATTT-
1 TATAATATTTA
* *
26700 TCAAAAT-TTTT
1 T-ATAATATTTA
*
26711 TATAACA-TTA
1 TATAATATTTA
26721 TATAATATTTA
1 TATAATATTTA
*
26732 -AGAATATATTA
1 TATAATAT-TTA
26743 TA
1 TA
26745 GTATCCTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
10 21 0.49
11 21 0.49
12 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (11 bp):
TATAATATTTA
Found at i:26724 original size:31 final size:33
Alignment explanation
Indices: 26665--26730 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 33
26655 AAATCTATAA
* *
26665 TTTCTAAATTTGTTTATAATATTTATATAATAT
1 TTTCAAAATTTGTTTATAACATTTATATAATAT
26698 TTTCAAAATTT-TTTATAACA-TTATATAATAT
1 TTTCAAAATTTGTTTATAACATTTATATAATAT
26729 TT
1 TT
26731 AAGAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 13 0.42
32 8 0.26
33 10 0.32
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (33 bp):
TTTCAAAATTTGTTTATAACATTTATATAATAT
Found at i:26921 original size:14 final size:13
Alignment explanation
Indices: 26889--26913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26879 AAGTATGATA
26889 AAATATTAAAAAT
1 AAATATTAAAAAT
26902 AAATATTAAAAA
1 AAATATTAAAAA
26914 ATACATATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATTAAAAAT
Found at i:27205 original size:38 final size:39
Alignment explanation
Indices: 27163--27237 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
27153 GAATCATCAA
27163 ACCTTAAAAAGGTAAATAT-ATATTT-ATTTAAAGTATAC
1 ACCTTAAAAAGGTAAAT-TGATATTTCATTTAAAGTATAC
* * *
27201 ACCTTATAAAGGTAAGTTGATATTTCTTTTAAAGTAT
1 ACCTTAAAAAGGTAAATTGATATTTCATTTAAAGTAT
27238 TATTTTTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 1 0.03
38 21 0.66
39 10 0.31
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (39 bp):
ACCTTAAAAAGGTAAATTGATATTTCATTTAAAGTATAC
Found at i:27894 original size:9 final size:9
Alignment explanation
Indices: 27878--27908 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27868 GGAAAACACT
27878 TATTTAATG
1 TATTTAATG
*
27887 TTTTTAATG
1 TATTTAATG
27896 TATTTAATG
1 TATTTAATG
27905 TATT
1 TATT
27909 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (9 bp):
TATTTAATG
Found at i:28553 original size:27 final size:27
Alignment explanation
Indices: 28517--28571 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
28507 TACCTGACAC
28517 CCAATGGAGGAACA-CAAAGTGGCGGCA
1 CCAATGGAGGAACATC-AAGTGGCGGCA
**
28544 CCAATGGAGGATTATCAAGTGGCGGCA
1 CCAATGGAGGAACATCAAGTGGCGGCA
28571 C
1 C
28572 TCTGGGGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.22, G:0.33, T:0.13
Consensus pattern (27 bp):
CCAATGGAGGAACATCAAGTGGCGGCA
Done.