Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001081.1 Kokia drynarioides strain JFW-HI SEQ_112337, 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: 15537
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:732 original size:17 final size:17
Alignment explanation
Indices: 710--785 Score: 109
Period size: 17 Copynumber: 4.4 Consensus size: 17
700 ACCCATTTTA
710 AAATTTATTTTAAGA-TT
1 AAATTTATTTTAA-ATTT
*
727 AAATTTATTTTGAATTT
1 AAATTTATTTTAAATTT
744 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
761 AAATTTGTTTTAAAATTT
1 AAATTTATTTT-AAATTT
779 AAATTTA
1 AAATTTA
786 AATTTATTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
16 1 0.02
17 40 0.75
18 12 0.23
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:760 original size:24 final size:24
Alignment explanation
Indices: 750--799 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
740 ATTTAAATTT
* *
750 ATTTTAAATTTAAATTTGTTTTAA
1 ATTTTAAATTTAAATTTATTATAA
*
774 AATTTAAATTTAAATTTATTATAA
1 ATTTTAAATTTAAATTTATTATAA
798 AT
1 AT
800 ATTGAAAGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTTAAATTTAAATTTATTATAA
Found at i:779 original size:7 final size:6
Alignment explanation
Indices: 725--791 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
715 TATTTTAAGA
* * * **
725 TTAAAT TT-ATT TTGAAT TTAAAT TT-ATT TTAAAT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
770 TTAAAAT TTAAAT TTAAAT TTA
1 TT-AAAT TTAAAT TTAAAT TTA
792 TTATAAATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
5 11 0.23
6 34 0.71
7 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (6 bp):
TTAAAT
Found at i:1499 original size:3 final size:3
Alignment explanation
Indices: 1493--1613 Score: 107
Period size: 3 Copynumber: 39.0 Consensus size: 3
1483 TAAGTAGTAT
* * * * *
1493 TAA TAA TACT TAA TAAA TAC TAA TGA TAT TAA TAA TAA CAA TAA TTAA
1 TAA TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* * **
1541 TAT TAA TAA TAA TAA TAA CTAT TTT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1587 TAA TAA TAT TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1614 AGGATTTGAA
Statistics
Matches: 94, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
3 84 0.89
4 10 0.11
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2882 original size:29 final size:29
Alignment explanation
Indices: 2710--3117 Score: 179
Period size: 29 Copynumber: 14.0 Consensus size: 29
2700 CCTTAAAGGT
* * *
2710 CCCT-AAACTATCCAAAAATCATATTTTAA
1 CCCTCAAACTTTCCAAAATTC-TATTTTTA
2739 CCCTCAAAC-TTCCAAAAATT-TCATTTTTA
1 CCCTCAAACTTTCC-AAAATTCT-ATTTTTA
*
2768 CCCTCGAAA-TTTCCAAAAATTAC-AATTTTA
1 CCCTC-AAACTTTCC-AAAATT-CTATTTTTA
* *
2798 CCCTCAAACTTTCTAAAATT-TCATTTTAA
1 CCCTCAAACTTTCCAAAATTCT-ATTTTTA
* *
2827 CCC-CAAATTTTCCAAAAAATAC-ATTTTT-
1 CCCTCAAACTTTCC--AAAATTCTATTTTTA
2855 CCCTCAAACTTTCCAAAATTCTATTTTTGA
1 CCCTCAAACTTTCCAAAATTCTATTTTT-A
* * *** * *
2885 ACCTTATTTTTTCAAAAATTATATTTTTA
1 CCCTCAAACTTTCCAAAATTCTATTTTTA
* *
2914 CCCTTAAACTTTACAAAATTAC-ATTTTTA
1 CCCTCAAACTTTCCAAAATT-CTATTTTTA
* *
2943 CCC-CTAAACTTTCCAAAAATTCCATTTTGA
1 CCCTC-AAACTTTCC-AAAATTCTATTTTTA
** ** * *
2973 -CCTTGATTTTTCCAAAA-ACTACCATTTTA
1 CCCTCAAACTTTCCAAAATTCTA--TTTTTA
* **
3002 CCCTCAAAC-TCCCAAAAATTCCCTTTTTGA
1 CCCTCAAACTTTCC-AAAATTCTATTTTT-A
*
3032 -CTTCAAA-TTTCCAAAAATTAC-ATTTTTA
1 CCCTCAAACTTTCC-AAAATT-CTATTTTTA
*
3060 CCC-CTGAACTTTCCAAAATTAC-ATTTTTA
1 CCCTC-AAACTTTCCAAAATT-CTATTTTTA
* * * *
3089 CCATCGAACTTTTCAAATATTCCATTTTT
1 CCCTCAAACTTTCCAAA-ATTCTATTTTT
3118 GACTCTGATT
Statistics
Matches: 289, Mismatches: 54, Indels: 71
0.70 0.13 0.17
Matches are distributed among these distances:
27 8 0.03
28 24 0.08
29 155 0.54
30 101 0.35
31 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.39
Consensus pattern (29 bp):
CCCTCAAACTTTCCAAAATTCTATTTTTA
Found at i:2901 original size:146 final size:146
Alignment explanation
Indices: 2742--3177 Score: 420
Period size: 146 Copynumber: 3.0 Consensus size: 146
2732 ATTTTAACCC
* *
2742 TCAAACTTCCAAAAATTTCATTTTTACCCTCGAAATTTCCAAAAATTACAATTTTACCCTCAAAC
1 TCAAATTTCCAAAAATTTCATTTTTACCCTCGAAATTTCC-AAAATTACATTTTTACCCTCAAAC
* * * *
2807 TTT-CTAAAATTTCATTTTAACCCCAAATTTTCCAAAAAATA-CATTTTTCCCTCAAACTTTCC-
65 TTTCCAAAAATTCCATTTTAACCCCAAATTTTCCAAAAAATACCATTTTACCCTCAAAC-TCCCA
*
2869 AAAATTCTATTTTTGAACCT
129 AAAATTCCATTTTTG-A-CT
** * * *
2889 T-ATTTTTTCAAAAATTAT-ATTTTTACCCT-TAAACTTTACAAAATTACATTTTTACCC-CTAA
1 TCAAATTTCCAAAAATT-TCATTTTTACCCTCGAAA-TTTCCAAAATTACATTTTTACCCTC-AA
* *** * *
2950 ACTTTCCAAAAATTCCATTTTGACCTTGATTTTTCCAAAAACTACCATTTTACCCTCAAACTCCC
63 ACTTTCCAAAAATTCCATTTTAACCCCAAATTTTCCAAAAAATACCATTTTACCCTCAAACTCCC
*
3015 AAAAATTCCCTTTTTGACT
128 AAAAATTCCATTTTTGACT
* * * *
3034 TCAAATTTCCAAAAATTACATTTTTACCC-CTGAACTTTCCAAAATTACATTTTTACCATCGAAC
1 TCAAATTTCCAAAAATTTCATTTTTACCCTC-GAAATTTCCAAAATTACATTTTTACCCTCAAAC
* * * * ** * * * *
3098 TTTTCAAATATTCCATTTTTGACTCTGATTTTTCCAAAAACTATCATTTTACCCTCGAACTCCCA
65 TTTCCAAAAATTCCA-TTTTAACCCCAAATTTTCCAAAAAATACCATTTTACCCTCAAACTCCC-
*
3163 AAAAATACCATTTTT
128 AAAAATTCCATTTTT
3178 CCCCTGAGTG
Statistics
Matches: 240, Mismatches: 36, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
144 1 0.00
145 30 0.12
146 119 0.50
147 77 0.32
148 13 0.05
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (146 bp):
TCAAATTTCCAAAAATTTCATTTTTACCCTCGAAATTTCCAAAATTACATTTTTACCCTCAAACT
TTCCAAAAATTCCATTTTAACCCCAAATTTTCCAAAAAATACCATTTTACCCTCAAACTCCCAAA
AATTCCATTTTTGACT
Found at i:3087 original size:58 final size:59
Alignment explanation
Indices: 2710--3117 Score: 295
Period size: 59 Copynumber: 7.0 Consensus size: 59
2700 CCTTAAAGGT
* * * * * *
2710 CCCTAAACTATCCAAAAATCATATTTTAACCCTCAAAC-TTCCAAAAATTTCATTTTTA
1 CCCTAAACTTTCCAAAAATTACATTTTTACCTTCAAACTTTCCAAAAATTACATTTTTA
* * * * *
2768 CCCTCGAAA-TTTCCAAAAATTACAATTTTACCCTCAAACTTT-CTAAAATTTCATTTTAA
1 CCCT--AAACTTTCCAAAAATTACATTTTTACCTTCAAACTTTCCAAAAATTACATTTTTA
* * * *
2827 CCCCAAATTTTCCAAAAAATACATTTTT-CCCTCAAACTTTCC-AAAATT-CTATTTTTGA
1 CCCTAAACTTTCCAAAAATTACATTTTTACCTTCAAACTTTCCAAAAATTAC-ATTTTT-A
* * ** * * *
2885 ACCTTATTTTTTCAAAAATTATATTTTTACCCTT-AAACTTTAC-AAAATTACATTTTTA
1 CCCTAAACTTTCCAAAAATTACATTTTTA-CCTTCAAACTTTCCAAAAATTACATTTTTA
* * * ** *
2943 CCCCTAAACTTTCCAAAAATTCCATTTTGACCTT-GATTTTTCCAAAAACTACCA-TTTTA
1 -CCCTAAACTTTCCAAAAATTACATTTTTACCTTCAAACTTTCCAAAAATTA-CATTTTTA
* * *
3002 CCCTCAAAC-TCCCAAAAATTCCCTTTTTGA-CTTCAAA-TTTCCAAAAATTACATTTTTA
1 CCCT-AAACTTTCCAAAAATTACATTTTT-ACCTTCAAACTTTCCAAAAATTACATTTTTA
* * * * * *
3060 CCCCTGAACTTTCC-AAAATTACATTTTTACCATCGAACTTTTCAAATATTCCATTTTT
1 -CCCTAAACTTTCCAAAAATTACATTTTTACCTTCAAACTTTCCAAAAATTACATTTTT
3118 GACTCTGATT
Statistics
Matches: 281, Mismatches: 48, Indels: 41
0.76 0.13 0.11
Matches are distributed among these distances:
56 1 0.00
57 29 0.10
58 115 0.41
59 125 0.44
60 11 0.04
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.39
Consensus pattern (59 bp):
CCCTAAACTTTCCAAAAATTACATTTTTACCTTCAAACTTTCCAAAAATTACATTTTTA
Found at i:3224 original size:29 final size:29
Alignment explanation
Indices: 3160--3224 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
3150 CCTCGAACTC
* * * *
3160 CCAAAAAATACCATTTTTCCCCTGAGTGT
1 CCAAAAATTACCATTTTCCCCCCGAGTAT
3189 CC-AAAATTACCATTTTACCCCCCG-GTAT
1 CCAAAAATTACCATTTT-CCCCCCGAGTAT
3217 CCAAAAAT
1 CCAAAAAT
3225 CTCATTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.34, C:0.31, G:0.08, T:0.28
Consensus pattern (29 bp):
CCAAAAATTACCATTTTCCCCCCGAGTAT
Found at i:7991 original size:23 final size:22
Alignment explanation
Indices: 7959--8038 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
7949 GATGGGGAAA
*
7959 CAGTAAGCACACATAGTGCAAT
1 CAGTAGGCACACATAGTGCAAT
* * *
7981 CCAGTCGGCACAAACAGTGCAAT
1 -CAGTAGGCACACATAGTGCAAT
* *
8004 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACATAGTGC-AAT
*
8027 CAATAGGCACAC
1 CAGTAGGCACAC
8039 GAGGTGCGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 14 0.31
23 31 0.69
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACATAGTGCAAT
Found at i:8061 original size:21 final size:21
Alignment explanation
Indices: 8036--8103 Score: 91
Period size: 21 Copynumber: 3.1 Consensus size: 21
8026 TCAATAGGCA
*
8036 CACGAGGTGCGAAACAGTAAG
1 CACGAAGTGCGAAACAGTAAG
8057 CACGAAGTGCGAAACAGTAAG
1 CACGAAGTGCGAAACAGTAAG
* *
8078 CACACGAAATACGAAACAGTAAG
1 --CACGAAGTGCGAAACAGTAAG
8101 CAC
1 CAC
8104 ACACAGTGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 23 0.55
23 19 0.45
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.09
Consensus pattern (21 bp):
CACGAAGTGCGAAACAGTAAG
Found at i:8092 original size:23 final size:23
Alignment explanation
Indices: 8045--8105 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
8035 ACACGAGGTG
* *
8045 CGAAACAGTAAG--CACGAAGTG
1 CGAAACAGTAAGCACACGAAATA
8066 CGAAACAGTAAGCACACGAAATA
1 CGAAACAGTAAGCACACGAAATA
8089 CGAAACAGTAAGCACAC
1 CGAAACAGTAAGCACAC
8106 ACAGTGCTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.33
23 24 0.67
ACGTcount: A:0.48, C:0.23, G:0.21, T:0.08
Consensus pattern (23 bp):
CGAAACAGTAAGCACACGAAATA
Found at i:8225 original size:24 final size:26
Alignment explanation
Indices: 8187--8234 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
8177 TCTACATGGG
8187 CATAATGTCTCATAT-TCATCATTTCT
1 CATAATGTCTCATATATCA-CATTTCT
8213 CATAAT-T-TCATATATCACATTT
1 CATAATGTCTCATATATCACATTT
8235 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.21, G:0.02, T:0.46
Consensus pattern (26 bp):
CATAATGTCTCATATATCACATTTCT
Found at i:10459 original size:31 final size:32
Alignment explanation
Indices: 10424--10496 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 32
10414 ATGACGATTG
*
10424 CATATATG-ACGTGGTCTATTGTAAAACCTTA
1 CATATATGCACGTGGTCTATTATAAAACCTTA
* * *
10455 CATATATGCCATGTGGTGTATTATAAATCCTTA
1 CATATATG-CACGTGGTCTATTATAAAACCTTA
*
10488 CATACATGC
1 CATATATGC
10497 CAAAGACAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 8 0.23
32 1 0.03
33 26 0.74
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (32 bp):
CATATATGCACGTGGTCTATTATAAAACCTTA
Found at i:10487 original size:33 final size:33
Alignment explanation
Indices: 10434--10498 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
10424 CATATATGAC
* *
10434 GTGGTCTATTGTAAAACCTTACATATATGCCAT
1 GTGGTCTATTATAAAACCTTACATACATGCCAT
* *
10467 GTGGTGTATTATAAATCCTTACATACATGCCA
1 GTGGTCTATTATAAAACCTTACATACATGCCA
10499 AAGACAATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (33 bp):
GTGGTCTATTATAAAACCTTACATACATGCCAT
Found at i:10930 original size:58 final size:58
Alignment explanation
Indices: 10840--10959 Score: 197
Period size: 58 Copynumber: 2.1 Consensus size: 58
10830 ACCCATCAAC
* *
10840 AAACTAAACCCAAATATTTTTAAACCTAAATATAATTTCATTCTTCAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCTAAATATAATTTCATTCCTAAAAAACACTCAT
*
10898 AAACTAAACCCAAATATTTTTAAA-CTCAAATATAATTTTATTCCTAAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCT-AAATATAATTTCATTCCTAAAAAACACTCAT
10956 AAAC
1 AAAC
10960 AACTCTTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 2 0.03
58 56 0.97
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCTAAATATAATTTCATTCCTAAAAAACACTCAT
Found at i:14968 original size:21 final size:21
Alignment explanation
Indices: 14942--14987 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
14932 GAACCCCGAA
14942 AAGCAATTACCAAAATGCTCC
1 AAGCAATTACCAAAATGCTCC
*
14963 AAGCAATTACCAAAATGCTTC
1 AAGCAATTACCAAAATGCTCC
14984 AAGC
1 AAGC
14988 TCAAAGCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (21 bp):
AAGCAATTACCAAAATGCTCC
Found at i:15457 original size:2 final size:2
Alignment explanation
Indices: 15450--15497 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
15440 TAGTATATGC
15450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15492 AT AT AT
1 AT AT AT
15498 TTACAACCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.