Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004191.1 Kokia drynarioides strain JFW-HI SEQ_117424, 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: 57067
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:11767 original size:32 final size:33
Alignment explanation
Indices: 11726--11795 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
11716 AAACAACAGT
* *
11726 AAAAATAACAGCGAAAA-AGCAATAAAAATAAC
1 AAAAATAACAACAAAAATAGCAATAAAAATAAC
* * *
11758 AAAAATAACAACAAAAATAGCACTCAAAATAAT
1 AAAAATAACAACAAAAATAGCAATAAAAATAAC
11791 AAAAA
1 AAAAA
11796 AGCACCAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.70, C:0.13, G:0.06, T:0.11
Consensus pattern (33 bp):
AAAAATAACAACAAAAATAGCAATAAAAATAAC
Found at i:11772 original size:12 final size:12
Alignment explanation
Indices: 11696--11776 Score: 53
Period size: 12 Copynumber: 7.1 Consensus size: 12
11686 AAAAAATCTA
11696 AACAACAAAAAT
1 AACAACAAAAAT
* * *
11708 AATAACCAAAAC
1 AACAACAAAAAT
**
11720 AACAGTAAAAAT
1 AACAACAAAAAT
* *
11732 AACAGCGAAAA-
1 AACAACAAAAAT
* *
11743 AGCAATAAAAAT
1 AACAACAAAAAT
11755 ---AACAAAAAT
1 AACAACAAAAAT
11764 AACAACAAAAAT
1 AACAACAAAAAT
11776 A
1 A
11777 GCACTCAAAA
Statistics
Matches: 50, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
9 8 0.16
11 7 0.14
12 35 0.70
ACGTcount: A:0.70, C:0.15, G:0.05, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:11799 original size:20 final size:20
Alignment explanation
Indices: 11770--11840 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
11760 AAATAACAAC
*
11770 AAAAATAGCACTCAAAATAAT
1 AAAAACAGCAC-CAAAATAAT
* *
11791 AAAAA-AGCACCAAAACAGT
1 AAAAACAGCACCAAAATAAT
*
11810 AAAAACAACACCAAAATAGCA-
1 AAAAACAGCACCAAAATA--AT
11831 AAAAACAGCA
1 AAAAACAGCA
11841 ATCAAAACAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 12 0.29
20 15 0.37
21 14 0.34
ACGTcount: A:0.65, C:0.20, G:0.07, T:0.08
Consensus pattern (20 bp):
AAAAACAGCACCAAAATAAT
Found at i:11836 original size:21 final size:21
Alignment explanation
Indices: 11798--11870 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
11788 AATAAAAAAG
*
11798 CACCAAAACAG-TAAAAACAA
1 CACCAAAACAGCAAAAAACAA
* *
11818 CACCAAAATAGCAAAAAACAG
1 CACCAAAACAGCAAAAAACAA
* * *
11839 CAATCAAAACAGTAAAAAAAAA
1 C-ACCAAAACAGCAAAAAACAA
11861 CACCAAAACA
1 CACCAAAACA
11871 ACAATATAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
20 10 0.24
21 16 0.38
22 16 0.38
ACGTcount: A:0.66, C:0.23, G:0.05, T:0.05
Consensus pattern (21 bp):
CACCAAAACAGCAAAAAACAA
Found at i:14607 original size:34 final size:34
Alignment explanation
Indices: 14568--14634 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
14558 TGTTTTAATC
14568 TATAATTTAGTATGAATAAAATTTTCTTCATTTT
1 TATAATTTAGTATGAATAAAATTTTCTTCATTTT
14602 TATAATTTAGTATGAATAAAATTTTCTTCATTT
1 TATAATTTAGTATGAATAAAATTTTCTTCATTT
14635 GTAAGTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (34 bp):
TATAATTTAGTATGAATAAAATTTTCTTCATTTT
Found at i:16126 original size:29 final size:29
Alignment explanation
Indices: 16087--16145 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
16077 AAAATTATTT
*
16087 TTCAAATCTATATTATTTCACAAAATCTC
1 TTCAAATCTATATTATTACACAAAATCTC
16116 TTCAAATCTATATTATTACACAAAATCTC
1 TTCAAATCTATATTATTACACAAAATCTC
16145 T
1 T
16146 CATTTGATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (29 bp):
TTCAAATCTATATTATTACACAAAATCTC
Found at i:22428 original size:12 final size:12
Alignment explanation
Indices: 22411--22435 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22401 TATGGGGTAG
22411 ATTACTAATTTT
1 ATTACTAATTTT
22423 ATTACTAATTTT
1 ATTACTAATTTT
22435 A
1 A
22436 AGGAATGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTACTAATTTT
Found at i:32288 original size:24 final size:25
Alignment explanation
Indices: 32234--32295 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 25
32224 TTTTTTTGTT
*
32234 TTATTTTTATT-CA-AATTATTTAA
1 TTATTTTTATTAAATAATTATTTAA
32257 TTATTTTTA-TAAATAATTA-TTAA
1 TTATTTTTATTAAATAATTATTTAA
32280 TTATTTTTTATTAAAT
1 TTA-TTTTTATTAAAT
32296 CATAATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 1 0.03
23 17 0.50
24 11 0.32
25 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATTTTTATTAAATAATTATTTAA
Found at i:33440 original size:271 final size:271
Alignment explanation
Indices: 32957--33497 Score: 967
Period size: 271 Copynumber: 2.0 Consensus size: 271
32947 CTGCGACGAC
*
32957 GATTGCCTATATATCGTCGGTTGACTTGGAGTCATCGGGATATTCAATGCACCGGGCCACATATT
1 GATTGCCTATATATCGTCGGTTGACTTGGAGTCATCGAGATATTCAATGCACCGGGCCACATATT
*
33022 CCAACTTGGCATAGGCATAGAACTAGAAAGTGGAAACATATAAGGGTTAGGATATGCACCCGGCA
66 CCAACTTGGCATAGGCATAGAACGAGAAAGTGGAAACATATAAGGGTTAGGATATGCACCCGGCA
*
33087 TAAACTGAAGGGGATGTGGTGACACAATCGTAACTTGCTGCATTGGGGCTAGTGCTTACGTGAGC
131 TAAACTGAAGGGGATGTGGTGACACAATCGTAACTTGCTGCATTGGGGCCAGTGCTTACGTGAGC
*
33152 AGTGCTTACATGGGCGGTGCTTG-AGTGGCTGGTGATGATGGGCTCGCCTCACCACCTCTTCTCC
196 AGTGCTTACATGGGCGGTGCTTGCA-TGGCTGGTGATGATGGGCCCGCCTCACCACCTCTTCTCC
33216 TTGGATTTAAAT
260 TTGGATTTAAAT
*
33228 GATTGCCTATATATCGTCGGTTGACTTGGAGTCATCGAGATATTCAATGCATCGGGCCACATATT
1 GATTGCCTATATATCGTCGGTTGACTTGGAGTCATCGAGATATTCAATGCACCGGGCCACATATT
**
33293 CCAACTTGGCATAGGCATAGAACGAGAAAGTGGAAACATATAAGGGTTAGGATATGCACTTGGCA
66 CCAACTTGGCATAGGCATAGAACGAGAAAGTGGAAACATATAAGGGTTAGGATATGCACCCGGCA
* *
33358 TAACCTGAAGGGGATGTGGTGACACAATCGTAACTTGCTGCATTGGGGCCAGTGCTTGCGTGAGC
131 TAAACTGAAGGGGATGTGGTGACACAATCGTAACTTGCTGCATTGGGGCCAGTGCTTACGTGAGC
**
33423 AGTGCTTGTATGGGCGGTGCTTGCATGGCTGGTGATGATGGGCCCGCCTCACCACCTCTTCTCCT
196 AGTGCTTACATGGGCGGTGCTTGCATGGCTGGTGATGATGGGCCCGCCTCACCACCTCTTCTCCT
33488 TGGATTTAAA
261 TGGATTTAAA
33498 GGGCCCCGTC
Statistics
Matches: 258, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
271 257 1.00
272 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (271 bp):
GATTGCCTATATATCGTCGGTTGACTTGGAGTCATCGAGATATTCAATGCACCGGGCCACATATT
CCAACTTGGCATAGGCATAGAACGAGAAAGTGGAAACATATAAGGGTTAGGATATGCACCCGGCA
TAAACTGAAGGGGATGTGGTGACACAATCGTAACTTGCTGCATTGGGGCCAGTGCTTACGTGAGC
AGTGCTTACATGGGCGGTGCTTGCATGGCTGGTGATGATGGGCCCGCCTCACCACCTCTTCTCCT
TGGATTTAAAT
Found at i:34953 original size:14 final size:14
Alignment explanation
Indices: 34933--34986 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
34923 ATTAAATTAT
34933 AAAAATTATATAAA
1 AAAAATTATATAAA
*
34947 AATAATTAAATTATAAA
1 AAAAATT--A-TATAAA
*
34964 AACAAAATATATAAA
1 AA-AAATTATATAAA
34979 AAAAATTA
1 AAAAATTA
34987 AAATTAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 11 0.34
15 8 0.25
16 2 0.06
17 8 0.25
18 3 0.09
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATTATATAAA
Found at i:35169 original size:32 final size:31
Alignment explanation
Indices: 35110--35175 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
35100 AACACGACCT
* *
35110 AAAGCGCGTCCACGTAGGCGCTCTTTTGGGCA
1 AAAGCGCGTCCACGTAGGCACTATTTT-GGCA
* * *
35142 AAAGCGCTTCCATGTGGGCACTATTTTGGCA
1 AAAGCGCGTCCACGTAGGCACTATTTTGGCA
35173 AAA
1 AAA
35176 ACGTACCTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (31 bp):
AAAGCGCGTCCACGTAGGCACTATTTTGGCA
Found at i:37111 original size:4 final size:4
Alignment explanation
Indices: 37102--37127 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
37092 ATGGACAACA
37102 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
37128 CCATTACCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:40244 original size:7 final size:7
Alignment explanation
Indices: 40232--40265 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
40222 AACAACACTC
40232 CTTTACT
1 CTTTACT
40239 CTTTACT
1 CTTTACT
40246 CTTTACT
1 CTTTACT
*
40253 CTGTACT
1 CTTTACT
40260 CTTTAC
1 CTTTAC
40266 ACTGCTCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.15, C:0.29, G:0.03, T:0.53
Consensus pattern (7 bp):
CTTTACT
Found at i:41719 original size:29 final size:29
Alignment explanation
Indices: 41669--41752 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 29
41659 AAAAGCTCAA
*
41669 AATATATATTTAATTA-TATAATAAATTATT
1 AATATA-ATTT-ATTATTTTAATAAATTATT
*
41699 AATATAATTTATTATTTTAATAAATTTTT
1 AATATAATTTATTATTTTAATAAATTATT
41728 AATACTGCAA-TT-TTATTTTAATAAA
1 AATA-T--AATTTATTATTTTAATAAA
41753 ATGATAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.08
29 20 0.42
30 20 0.42
31 2 0.04
32 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (29 bp):
AATATAATTTATTATTTTAATAAATTATT
Found at i:43634 original size:6 final size:6
Alignment explanation
Indices: 43623--43679 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
43613 GCAACTTGCT
43623 AATTCC AATTCC AATTCC AATTCC AATTCC AATTCC AATTCC AATTCC
1 AATTCC AATTCC AATTCC AATTCC AATTCC AATTCC AATTCC AATTCC
43671 AATTCC AAT
1 AATTCC AAT
43680 GTCAAATGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTCC
Found at i:55088 original size:12 final size:12
Alignment explanation
Indices: 55071--55143 Score: 60
Period size: 12 Copynumber: 6.1 Consensus size: 12
55061 ATAACATCCG
*
55071 AACAATAAAAAC
1 AACAACAAAAAC
55083 AACAATC-AAAAC
1 AACAA-CAAAAAC
** *
55095 AGA-AGGAAAAAT
1 A-ACAACAAAAAC
55107 AACAACAAAAAC
1 AACAACAAAAAC
* *
55119 AATAACAAAAAT
1 AACAACAAAAAC
55131 AACAACAAAAAC
1 AACAACAAAAAC
55143 A
1 A
55144 TAACCAAAAC
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
11 1 0.02
12 44 0.96
13 1 0.02
ACGTcount: A:0.73, C:0.16, G:0.04, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:55117 original size:24 final size:24
Alignment explanation
Indices: 55101--55152 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
55091 AAACAGAAGG
55101 AAAAATAACAACAAAAACAATAAC
1 AAAAATAACAACAAAAACAATAAC
55125 AAAAATAACAACAAAAAC-ATAAC
1 AAAAATAACAACAAAAACAATAAC
*
55148 CAAAA
1 AAAAA
55153 CAGTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.75, C:0.17, G:0.00, T:0.08
Consensus pattern (24 bp):
AAAAATAACAACAAAAACAATAAC
Done.