Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000675.1 Kokia drynarioides strain JFW-HI SEQ_111669, 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: 65547
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:987 original size:23 final size:22
Alignment explanation
Indices: 957--1129 Score: 123
Period size: 23 Copynumber: 7.5 Consensus size: 22
947 ACGCAAGCGC
957 GCTTACTGTTTTGCACTTCGTGT
1 GCTTACTGTTTTGCACTT-GTGT
*
980 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTTGCAC-TTGTGT
*
1003 GCTTATTGTTTTGCACCTTGTGT
1 GCTTACTGTTTTGCA-CTTGTGT
* * ** *
1026 GCCTACTGATTTGGGCTATGTGC
1 GCTTACTGTTTTGCACT-TGTGT
* *
1049 GCCTACTG-ATTGCACTGTGTGT
1 GCTTACTGTTTTGCACT-TGTGT
* * **
1071 GCCTATTGGATTGCACTGTGTGT
1 GCTTACTGTTTTGCACT-TGTGT
*
1094 GCTTACTGTTTTTCCAACACTTGTGT
1 GCTTACTG-TTTT---GCACTTGTGT
1120 GCTTACTGTT
1 GCTTACTGTT
1130 AAGTACTTCG
Statistics
Matches: 122, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
22 18 0.15
23 80 0.66
24 5 0.04
25 2 0.02
26 13 0.11
27 4 0.03
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.44
Consensus pattern (22 bp):
GCTTACTGTTTTGCACTTGTGT
Found at i:3120 original size:17 final size:17
Alignment explanation
Indices: 3085--3125 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3075 GGAAAAAGTA
*
3085 GTTACAAGAATATGAAAT
1 GTTA-AAGAAGATGAAAT
*
3103 GTTAAAGAAGATGGAAT
1 GTTAAAGAAGATGAAAT
3120 GTTAAA
1 GTTAAA
3126 AGTCAAGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAT
Found at i:5847 original size:24 final size:23
Alignment explanation
Indices: 5795--5839 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
5785 ATGCCTAGCA
5795 AGCTTCGTACCGGTGTATTTAAC
1 AGCTTCGTACCGGTGTATTTAAC
**
5818 AGGCTTCGTGTCGGTGTATTTA
1 A-GCTTCGTACCGGTGTATTTA
5840 TCGAGCTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (23 bp):
AGCTTCGTACCGGTGTATTTAAC
Found at i:5862 original size:40 final size:40
Alignment explanation
Indices: 5817--5920 Score: 104
Period size: 41 Copynumber: 2.5 Consensus size: 40
5807 GTGTATTTAA
*
5817 CAGGCTTCGTGTCGGTGTATTTATC-GAGCTTAGTGCCTAG
1 CAGGCTTCGTGTCGGTGTATTTATCAG-GCTTAGAGCCTAG
* * *
5857 TAGGCTTCGTG-CTGGTGTATACTATCAGGCTTTGAGCCTAG
1 CAGGCTTCGTGTC-GGTGTAT-TTATCAGGCTTAGAGCCTAG
* *
5898 CAGGTTTCGTGTCGATGCTATTT
1 CAGGCTTCGTGTCGGTG-TATTT
5921 TCTTAAGTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
39 1 0.02
40 17 0.33
41 28 0.55
42 5 0.10
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.37
Consensus pattern (40 bp):
CAGGCTTCGTGTCGGTGTATTTATCAGGCTTAGAGCCTAG
Found at i:6116 original size:16 final size:16
Alignment explanation
Indices: 6095--6126 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6085 CTATTTATTA
6095 CCCTAAGATTTCAATG
1 CCCTAAGATTTCAATG
6111 CCCTAAGATTTCAATG
1 CCCTAAGATTTCAATG
6127 AGTAAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (16 bp):
CCCTAAGATTTCAATG
Found at i:8540 original size:15 final size:15
Alignment explanation
Indices: 8516--8570 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
8506 CCAAAAATTT
*
8516 TTTAAATTAAATTCA
1 TTTAAATTAAATTAA
*
8531 TTT-AATTTAA-TAA
1 TTTAAATTAAATTAA
*
8544 TTTTAAATTAAATTTA
1 -TTTAAATTAAATTAA
*
8560 TTTAATTTAAA
1 TTTAAATTAAA
8571 AAAGTAGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 2 0.06
14 9 0.28
15 19 0.59
16 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAATTAAATTAA
Found at i:10178 original size:30 final size:30
Alignment explanation
Indices: 10138--10628 Score: 403
Period size: 30 Copynumber: 16.6 Consensus size: 30
10128 GGTCCCAAAA
* * *
10138 TTTTTCAAAATTATAGTTTGACCCCTAAAC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
* *
10168 TTTTCTAAAATTACATTTTGACCCC-AAAT
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
**
10197 TTTTCCAAAATTACATTTTGA-CAATAAAC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
* *
10226 TTTTTCCAAAATGACATTTTAACCCC-AAAC
1 -TTTTCCAAAATTACATTTTGACCCCTAAAC
** *
10256 TTTTCCAAAATTGTATTTTGACCCCTAAAT
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
* * *
10286 TTTTCCAAAATTTCATTTTGACTCTTAAAC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
* *
10316 TTTTCCAAAATGACATTTTGA-CCCTCGAAC
1 TTTTCCAAAATTACATTTTGACCCCT-AAAC
*** *
10346 TTTAAAAAAATTACATTTTGACCCTTAAAC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
* **
10376 TTTTCTAAAATTGTATTTTGACCCCTAAAC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
**
10406 TTTTTTAAAATTACATTTT-ACCCC-AAAC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
* ** *
10434 TTTTCCAAAAGTATGTTTTTA-CCCTAAAC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
** * *
10463 TTTTCCAAAATTATGTTTTAACCCC-ATAC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
* * * ** *
10492 TTTTCGAAAATCACATTTTTA-CTATAATC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
** * *
10521 TTTTCCAAAATTATGTTTTTACCCCCAAAC
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
** * * *
10551 TTCCCCAAAATCACATTTTTTAACCCTAAAC
1 TTTTCCAAAATTACA-TTTTGACCCCTAAAC
*
10582 TTTTCCAAAATTACATTTTGACACC-AAA-
1 TTTTCCAAAATTACATTTTGACCCCTAAAC
*
10610 TTCTCCAAAACTT-CATTTT
1 TTTTCCAAAA-TTACATTTT
10629 TTGACCCTTT
Statistics
Matches: 366, Mismatches: 82, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
28 38 0.10
29 121 0.33
30 178 0.49
31 29 0.08
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (30 bp):
TTTTCCAAAATTACATTTTGACCCCTAAAC
Found at i:10206 original size:59 final size:58
Alignment explanation
Indices: 10131--10628 Score: 426
Period size: 59 Copynumber: 8.4 Consensus size: 58
10121 CTCGAGAGGT
* * * * *
10131 CCCAAAATTTTTCAAAATTATAGTTTGACCCCTAAACTTTTCTAAAATTACATTTTGAC
1 CCCAAACTTTTCCAAAATTACATTTTGA-CCCTAAACTTTTCCAAAATTACATTTTGAC
* ** * *
10190 CCCAAATTTTTCCAAAATTACATTTTGACAATAAACTTTTTCCAAAATGACATTTTAAC
1 CCCAAACTTTTCCAAAATTACATTTTGACCCTAAAC-TTTTCCAAAATTACATTTTGAC
** * *
10249 CCCAAACTTTTCCAAAATTGTATTTTGACCCCTAAATTTTTCCAAAATTTCATTTTGAC
1 CCCAAACTTTTCCAAAATTACATTTTGA-CCCTAAACTTTTCCAAAATTACATTTTGAC
** * * ***
10308 TCTTAAACTTTTCCAAAATGACATTTTGACCCTCGAACTTTAAAAAAATTACATTTTGAC
1 -CCCAAACTTTTCCAAAATTACATTTTGACCCT-AAACTTTTCCAAAATTACATTTTGAC
* * ** **
10368 CCTTAAACTTTTCTAAAATTGTATTTTGACCCCTAAACTTTTTTAAAATTACATTTT-AC
1 CC-CAAACTTTTCCAAAATTACATTTTGA-CCCTAAACTTTTCCAAAATTACATTTTGAC
* ** * ** *
10427 CCCAAACTTTTCCAAAAGTATGTTTTTACCCTAAACTTTTCCAAAATTATGTTTTAAC
1 CCCAAACTTTTCCAAAATTACATTTTGACCCTAAACTTTTCCAAAATTACATTTTGAC
* * * * ** * ** *
10485 CCCATACTTTTCGAAAATCACATTTTTACTATAATCTTTTCCAAAATTATGTTTTTACC
1 CCCAAACTTTTCCAAAATTACATTTTGACCCTAAACTTTTCCAAAATTACATTTTGA-C
** * *
10544 CCCAAACTTCCCCAAAATCACATTTTTTAACCCTAAACTTTTCCAAAATTACATTTTGAC
1 CCCAAACTTTTCCAAAATTACA--TTTTGACCCTAAACTTTTCCAAAATTACATTTTGAC
* *
10604 ACCAAA-TTCTCCAAAACTT-CATTTT
1 CCCAAACTTTTCCAAAA-TTACATTTT
10629 TTGACCCTTT
Statistics
Matches: 356, Mismatches: 72, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
57 27 0.08
58 75 0.21
59 126 0.35
60 96 0.27
61 32 0.09
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.39
Consensus pattern (58 bp):
CCCAAACTTTTCCAAAATTACATTTTGACCCTAAACTTTTCCAAAATTACATTTTGAC
Found at i:10582 original size:31 final size:31
Alignment explanation
Indices: 10536--10600 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
10526 CAAAATTATG
*
10536 TTTTTACCCCCAAACTTCCCCAAAATCACAT
1 TTTTTAACCCCAAACTTCCCCAAAATCACAT
* ** *
10567 TTTTTAACCCTAAACTTTTCCAAAATTACAT
1 TTTTTAACCCCAAACTTCCCCAAAATCACAT
10598 TTT
1 TTT
10601 GACACCAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTTTAACCCCAAACTTCCCCAAAATCACAT
Found at i:15121 original size:15 final size:15
Alignment explanation
Indices: 15101--15131 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15091 AGTAGTATTT
15101 ATATTAACTTTAAAG
1 ATATTAACTTTAAAG
*
15116 ATATTATCTTTAAAG
1 ATATTAACTTTAAAG
15131 A
1 A
15132 AAACGAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
ATATTAACTTTAAAG
Found at i:17963 original size:2 final size:2
Alignment explanation
Indices: 17956--18001 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
17946 ATTCTATTAC
* *
17956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17998 AT AT
1 AT AT
18002 CCAAGAAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20948 original size:6 final size:6
Alignment explanation
Indices: 20937--20974 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
20927 CACTATTCAT
20937 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CA
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CA
20975 ACAAAACTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (6 bp):
CATCAC
Found at i:22231 original size:7 final size:7
Alignment explanation
Indices: 22219--22267 Score: 98
Period size: 7 Copynumber: 7.0 Consensus size: 7
22209 CACATAATGT
22219 ATTGGAA
1 ATTGGAA
22226 ATTGGAA
1 ATTGGAA
22233 ATTGGAA
1 ATTGGAA
22240 ATTGGAA
1 ATTGGAA
22247 ATTGGAA
1 ATTGGAA
22254 ATTGGAA
1 ATTGGAA
22261 ATTGGAA
1 ATTGGAA
22268 TGTAATGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
ATTGGAA
Found at i:24840 original size:109 final size:108
Alignment explanation
Indices: 24682--24894 Score: 277
Period size: 109 Copynumber: 2.0 Consensus size: 108
24672 TCTATATGTG
* * *
24682 AACCATGCTTTATGAATAGAACAAAGTCAAATATTCAACATAAATTAAAATATATTTAGAAAATA
1 AACCATGCTTTAGGAATAGAACAAAGTCAAATATTCAACATAAACTAAAATACATTTAGAAAATA
*
24747 TACGTTT-GTTT-AAGTATGGAAATATTTTCAATGAATCACTGTC
66 -A-GTTTCGTTTCAAGTAAGGAAATATTTTCAATGAATCACTGTC
* * * *
24790 AACCATGTTTTACGGAATAGGACAACGTTAAATATTCAACATAAACTAAAATACATTTAGAAAAT
1 AACCATGCTTTA-GGAATAGAACAAAGTCAAATATTCAACATAAACTAAAATACATTTAGAAAAT
* * *
24855 AATTTTCCTTTTCAAGTAAGGAAATATTTTCAATTAATCA
65 AAGTTT-CGTTTCAAGTAAGGAAATATTTTCAATGAATCA
24895 ATCTGGAGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
107 3 0.03
108 12 0.13
109 50 0.56
110 25 0.28
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (108 bp):
AACCATGCTTTAGGAATAGAACAAAGTCAAATATTCAACATAAACTAAAATACATTTAGAAAATA
AGTTTCGTTTCAAGTAAGGAAATATTTTCAATGAATCACTGTC
Found at i:25647 original size:54 final size:54
Alignment explanation
Indices: 25563--25667 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
25553 CCTGTTGAGA
* *
25563 ATTCAGATCACTGTGTTCACCCTGCCGAGTTTCAGTGTGAATAGTAGTACCCTC
1 ATTCAGATCACTGTATTCACCCTGCCGAGTTTCAGTGTGAACAGTAGTACCCTC
* **
25617 ATTCAGATCACTGTATTCACCCTGCTGAGTTTTGGTGTGAACAGTAGTACC
1 ATTCAGATCACTGTATTCACCCTGCCGAGTTTCAGTGTGAACAGTAGTACC
25668 AACAGATTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (54 bp):
ATTCAGATCACTGTATTCACCCTGCCGAGTTTCAGTGTGAACAGTAGTACCCTC
Found at i:32225 original size:2 final size:2
Alignment explanation
Indices: 32218--32242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32208 AGGGGATTGA
32218 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
32243 ACGATACTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54111 original size:12 final size:13
Alignment explanation
Indices: 54084--54116 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
54074 CAATAATAAC
54084 AAAATTTAACATT
1 AAAATTTAACATT
54097 AAAATTTAA-ATT
1 AAAATTTAACATT
54109 AAAATTTA
1 AAAATTTA
54117 TGTAGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATTTAACATT
Done.