Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012144.1 Kokia drynarioides strain JFW-HI SEQ_127143, 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: 62497
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:528 original size:20 final size:21
Alignment explanation
Indices: 497--537 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
487 GATCAATGTG
497 AGATTGAAATTAACTTTTAAT
1 AGATTGAAATTAACTTTTAAT
*
518 AGATT-AAATTAATTTTTAAT
1 AGATTGAAATTAACTTTTAAT
538 GAAAATAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (21 bp):
AGATTGAAATTAACTTTTAAT
Found at i:1517 original size:67 final size:64
Alignment explanation
Indices: 1409--1538 Score: 181
Period size: 67 Copynumber: 2.0 Consensus size: 64
1399 TATACATAAT
* * * *
1409 ATTTAATTACTTCATATTTTATATATAATATTTGCATATAATATAA-TTCAATGCATATATAAAG
1 ATTTAATTAATTCATATTTTATATATAATATTTACACATAATACAACTT-AATGCATATATAAAG
1473 ATTTAATTAATTCATATTTGTATATATAAAATATTTACACATAATACAACTTAATGCATATATAA
1 ATTTAATTAATTCATATTT-TATATAT--AATATTTACACATAATACAACTTAATGCATATATAA
1538 A
63 A
1539 AAGATTTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
64 18 0.31
65 7 0.12
67 31 0.53
68 2 0.03
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (64 bp):
ATTTAATTAATTCATATTTTATATATAATATTTACACATAATACAACTTAATGCATATATAAAG
Found at i:7895 original size:39 final size:40
Alignment explanation
Indices: 7841--7920 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
7831 TATGCACTCA
7841 ATGGACACCTTTTGAAGAGTCACAACAC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACACTTTTCAAATTGG
* *
7880 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACACTTTTCAAATTGG
7920 A
1 A
7921 CATACCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACACTTTTCAAATTGG
Found at i:7936 original size:39 final size:38
Alignment explanation
Indices: 7845--7937 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 38
7835 CACTCAATGG
* *
7845 ACACCTTTTGAAGAGTCACAACACTTTCAAATTGGATGG
1 ACACCTTTGGAAGAGTCACAACACTTTCAAATTGGA-GC
* * *
7884 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACAC-TTTCAAATTGGAGC
*
7922 ATACCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
7938 ATTTGTCCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 5 0.11
39 31 0.66
40 11 0.23
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACACTTTCAAATTGGAGC
Found at i:12815 original size:39 final size:40
Alignment explanation
Indices: 12761--12840 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
12751 TATGCACTAA
12761 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
* *
12800 ATGGACACCTTTTGAAGAGTCATAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
12840 A
1 A
12841 CATACCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:12856 original size:39 final size:38
Alignment explanation
Indices: 12765--12857 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 38
12755 CACTAAATGG
* *
12765 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGG
1 ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGA-GC
* * *
12804 ACACCTTTTGAAGAGTCATAACCCTTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACCC-TTTCAAATTGGAGC
*
12842 ATACCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
12858 ATTTGTCCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 5 0.11
39 31 0.66
40 11 0.23
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:17771 original size:40 final size:40
Alignment explanation
Indices: 17727--17985 Score: 225
Period size: 40 Copynumber: 6.5 Consensus size: 40
17717 TACAGTACAA
* *
17727 GTAGTGACACTGTAAACACTACGATATTACAACTGAACCG
1 GTAGTGACACTGTAAACACTGCGATATTACAACTGAACTG
* *
17767 GTAGTGACACTGTAAACACTGCGATATTACAA-TTAAATGG
1 GTAGTGACACTGTAAACACTGCGATATTACAACTGAACT-G
* *
17807 GTAGTGACACTGTAAATACTGCGATATTACAACTGAACTA
1 GTAGTGACACTGTAAACACTGCGATATTACAACTGAACTG
** * * * * * * *
17847 CCATTGATACTGTAAACACTACAATACTACCACTGAATTG
1 GTAGTGACACTGTAAACACTGCGATATTACAACTGAACTG
* * * * * * *
17887 GCAGTGACACTGTAGATACCGCGATATCATAATTGAACTG
1 GTAGTGACACTGTAAACACTGCGATATTACAACTGAACTG
* * * * ** * *
17927 GCAGTGATATTGTAAACACTGCAATGCTACAA-TGAGCTA
1 GTAGTGACACTGTAAACACTGCGATATTACAACTGAACTG
17966 GTAGTGACACTGTAAACACT
1 GTAGTGACACTGTAAACACT
17986 ACTAGGTTAC
Statistics
Matches: 169, Mismatches: 48, Indels: 5
0.76 0.22 0.02
Matches are distributed among these distances:
39 25 0.15
40 140 0.83
41 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (40 bp):
GTAGTGACACTGTAAACACTGCGATATTACAACTGAACTG
Found at i:17833 original size:80 final size:80
Alignment explanation
Indices: 17727--17958 Score: 257
Period size: 80 Copynumber: 2.9 Consensus size: 80
17717 TACAGTACAA
* * * * * *
17727 GTAGTGACACTGTAAACACTACGATATTACAACTGAACCGGTAGTGACACTGTAAACACTGCGAT
1 GTAGTGACACTGTAAATACTGCGATATTACAACTGAACTGGCAGTGATACTGTAAACACTGCAAT
* *
17792 ATTACAATTAAATGG
66 ACTACAACTAAATGG
** * *
17807 GTAGTGACACTGTAAATACTGCGATATTACAACTGAACTACCATTGATACTGTAAACACTACAAT
1 GTAGTGACACTGTAAATACTGCGATATTACAACTGAACTGGCAGTGATACTGTAAACACTGCAAT
* * *
17872 ACTACCACTGAATTG
66 ACTACAACTAAATGG
* * * * * * *
17887 GCAGTGACACTGTAGATACCGCGATATCATAATTGAACTGGCAGTGATATTGTAAACACTGCAAT
1 GTAGTGACACTGTAAATACTGCGATATTACAACTGAACTGGCAGTGATACTGTAAACACTGCAAT
*
17952 GCTACAA
66 ACTACAA
17959 TGAGCTAGTA
Statistics
Matches: 124, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
80 124 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (80 bp):
GTAGTGACACTGTAAATACTGCGATATTACAACTGAACTGGCAGTGATACTGTAAACACTGCAAT
ACTACAACTAAATGG
Found at i:17958 original size:120 final size:119
Alignment explanation
Indices: 17729--17987 Score: 277
Period size: 120 Copynumber: 2.2 Consensus size: 119
17719 CAGTACAAGT
* * * *
17729 AGTGACACTGTAAACACTACGATATTACAACTGAACCGGTAGTGACACTGTAAACACTGCGATAT
1 AGTGACACTGTAAACACTACAATACTACAACTGAACCGGCAGTGACACTGTAAACACCGCGATAT
* * * * *
17794 TACAATTAAATGGGTAGTGACACTGTAAATACTGCGATATTACAACTGAACTACC
66 CACAATTAAATGGGCAGTGACACTGTAAACACTGCAATACTACAA-TGAACTACC
* * * ** * *
17849 ATTGATACTGTAAACACTACAATACTACCACTGAATTGGCAGTGACACTGTAGATACCGCGATAT
1 AGTGACACTGTAAACACTACAATACTACAACTGAACCGGCAGTGACACTGTAAACACCGCGATAT
* * * * * * **
17914 CATAATTGAACT-GGCAGTGATATTGTAAACACTGCAATGCTACAATGAGCTAGT
66 CACAATT-AAATGGGCAGTGACACTGTAAACACTGCAATACTACAATGAACTACC
17968 AGTGACACTGTAAACACTAC
1 AGTGACACTGTAAACACTAC
17988 TAGGTTACTA
Statistics
Matches: 112, Mismatches: 26, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
119 24 0.21
120 85 0.76
121 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (119 bp):
AGTGACACTGTAAACACTACAATACTACAACTGAACCGGCAGTGACACTGTAAACACCGCGATAT
CACAATTAAATGGGCAGTGACACTGTAAACACTGCAATACTACAATGAACTACC
Found at i:24420 original size:31 final size:31
Alignment explanation
Indices: 24382--24442 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
24372 TAAACATTGT
* *
24382 GATATTACAACTGAA-TGGGCAGTGACACTGC
1 GATATTACAACTAAACT-AGCAGTGACACTGC
24413 GATATTACAACTAAACTAGCAGTGACACTG
1 GATATTACAACTAAACTAGCAGTGACACTG
24443 TAAACACTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (31 bp):
GATATTACAACTAAACTAGCAGTGACACTGC
Found at i:24450 original size:40 final size:39
Alignment explanation
Indices: 24426--24571 Score: 177
Period size: 40 Copynumber: 3.7 Consensus size: 39
24416 ATTACAACTA
24426 AACTAGCAGTGACACTGTAAACACTACAATACTATCACTG
1 AACTAGCAGTGACACTGTAAACACTACAATACTA-CACTG
* *
24466 AACTGGCAGTGACACTGTAAACACTACGATATCATA-ACTG
1 AACTAGCAGTGACACTGTAAACACTACAATA-C-TACACTG
* * * * *
24506 AACTGGCAGTGACAATGTAAACACTGCAATGCTACATTG
1 AACTAGCAGTGACACTGTAAACACTACAATACTACACTG
* *
24545 AGCTAGTAGTGACACTGTAAACACTAC
1 AACTAGCAGTGACACTGTAAACACTAC
24572 TAGGCTACTA
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
38 2 0.02
39 26 0.29
40 60 0.66
41 1 0.01
42 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (39 bp):
AACTAGCAGTGACACTGTAAACACTACAATACTACACTG
Found at i:24589 original size:79 final size:80
Alignment explanation
Indices: 24406--24571 Score: 217
Period size: 80 Copynumber: 2.1 Consensus size: 80
24396 ATGGGCAGTG
* * * * * * *
24406 ACACTGCGATATTACAACTAAACTAGCAGTGACACTGTAAACACTACAATACTATCACTGAACTG
1 ACACTACGATATCATAACTGAACTGGCAGTGACAATGTAAACACTACAATACTATCACTGAACTA
24471 GCAGTGACACTGTAA
66 GCAGTGACACTGTAA
* * * *
24486 ACACTACGATATCATAACTGAACTGGCAGTGACAATGTAAACACTGCAATGCTA-CATTGAGCTA
1 ACACTACGATATCATAACTGAACTGGCAGTGACAATGTAAACACTACAATACTATCACTGAACTA
*
24550 GTAGTGACACTGTAA
66 GCAGTGACACTGTAA
24565 ACACTAC
1 ACACTAC
24572 TAGGCTACTA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 28 0.38
80 46 0.62
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (80 bp):
ACACTACGATATCATAACTGAACTGGCAGTGACAATGTAAACACTACAATACTATCACTGAACTA
GCAGTGACACTGTAA
Found at i:36217 original size:15 final size:15
Alignment explanation
Indices: 36178--36224 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
36168 CGCGATGACT
*
36178 TAAGTGACTAAAATA
1 TAAGTGATTAAAATA
*
36193 TAA-T-ATTTAAAAAA
1 TAAGTGA-TTAAAATA
36207 TAAGTGATTAAAATA
1 TAAGTGATTAAAATA
36222 TAA
1 TAA
36225 ACTGAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
13 1 0.04
14 10 0.38
15 14 0.54
16 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (15 bp):
TAAGTGATTAAAATA
Found at i:54722 original size:24 final size:24
Alignment explanation
Indices: 54693--54742 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
54683 ATGACTATGA
54693 GTGGCCCCTTAGTGGTGGTCCAGT
1 GTGGCCCCTTAGTGGTGGTCCAGT
54717 GTGGCCCCTTAGTGGTGGTCCAGT
1 GTGGCCCCTTAGTGGTGGTCCAGT
54741 GT
1 GT
54743 CAAATCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.08, C:0.24, G:0.38, T:0.30
Consensus pattern (24 bp):
GTGGCCCCTTAGTGGTGGTCCAGT
Found at i:60255 original size:18 final size:18
Alignment explanation
Indices: 60232--60266 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
60222 GGAAGAAATG
60232 TAAGTTTAATTAATTTTT
1 TAAGTTTAATTAATTTTT
*
60250 TAAGTTTGATTAATTTT
1 TAAGTTTAATTAATTTT
60267 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (18 bp):
TAAGTTTAATTAATTTTT
Found at i:61357 original size:17 final size:18
Alignment explanation
Indices: 61326--61359 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
61316 TTTACAAATA
*
61326 ATTTTTGTTATATTAACT
1 ATTTTTGTTAAATTAACT
61344 ATTTTTG-TAAATTAAC
1 ATTTTTGTTAAATTAAC
61360 AGTAAAAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTTTTGTTAAATTAACT
Found at i:62351 original size:43 final size:43
Alignment explanation
Indices: 62269--62353 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
62259 ATTAACATGT
* *
62269 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
62312 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
62354 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Done.