Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011330.1 Kokia drynarioides strain JFW-HI SEQ_126310, 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: 97165
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:499 original size:19 final size:18
Alignment explanation
Indices: 475--523 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
465 AATCAGGACT
475 AATTTAA-AACAAATTAGAA
1 AATTTAAGAA-AAATT-GAA
494 AATTTAAGAAAAATTGAA
1 AATTTAAGAAAAATTGAA
*
512 AAGTTTTAGAAA
1 AA-TTTAAGAAA
524 CAGGGGCACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 5 0.19
19 20 0.74
20 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (18 bp):
AATTTAAGAAAAATTGAA
Found at i:2737 original size:15 final size:15
Alignment explanation
Indices: 2717--2772 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
2707 ATAATAGATA
*
2717 CGAGCATGGATAGTG
1 CGAGCATGGATAATG
*
2732 CGAGCATGAATAATG
1 CGAGCATGGATAATG
* * *
2747 CGAGTATGGGTATTG
1 CGAGCATGGATAATG
2762 CGAGCATGGAT
1 CGAGCATGGAT
2773 GAAGGACAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.23
Consensus pattern (15 bp):
CGAGCATGGATAATG
Found at i:4124 original size:22 final size:25
Alignment explanation
Indices: 4099--4156 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
4089 ATTAAAAATT
4099 AAAAAAATAAATTC-AAAA-AAAGAA
1 AAAAAAATAAATTCAAAAAGAAAG-A
*
4123 AAAAAAAGAAATTCAAAAAGAAAGA
1 AAAAAAATAAATTCAAAAAGAAAGA
*
4148 AGAAAAATA
1 AAAAAAATA
4157 TACATCATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.45
25 12 0.41
26 4 0.14
ACGTcount: A:0.78, C:0.03, G:0.09, T:0.10
Consensus pattern (25 bp):
AAAAAAATAAATTCAAAAAGAAAGA
Found at i:8431 original size:52 final size:52
Alignment explanation
Indices: 8292--8432 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 52
8282 ATTTCATTTC
* * *
8292 ATTCATATACTCACGATGACACATACCCATTAGACCTCATAATCTGCAAAGG
1 ATTCATATACTCACGATGACACATAGCCATTGGACCTCATAATCCGCAAAGG
* *
8344 ATTCATATACTCACGATGATACATAGCCATTGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATTGGACCTCATAATCCGCAAAGG
* *
8396 ATTCATATAC-CAACGATGACACATAGTCATCGGACCT
1 ATTCATATACTC-ACGATGACACATAGCCATTGGACCT
8433 TTCTCATTTA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 1 0.01
52 79 0.99
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGCCATTGGACCTCATAATCCGCAAAGG
Found at i:8949 original size:16 final size:17
Alignment explanation
Indices: 8928--8968 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
8918 CCTCAATACC
8928 ATTTCATTTA-AATTTA
1 ATTTCATTTACAATTTA
8944 ATTTCATTTATCAATTTA
1 ATTTCATTTA-CAATTTA
8962 ATATTCA
1 AT-TTCA
8969 CTAAGCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.45
18 8 0.36
19 4 0.18
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTCATTTACAATTTA
Found at i:43071 original size:19 final size:19
Alignment explanation
Indices: 43047--43083 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43037 AATATTTTTT
43047 TATTTTT-TTATTTTTCTCG
1 TATTTTTCTT-TTTTTCTCG
43066 TATTTTTCTTTTTTTCTC
1 TATTTTTCTTTTTTTCTC
43084 AACTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.76
Consensus pattern (19 bp):
TATTTTTCTTTTTTTCTCG
Found at i:54326 original size:76 final size:76
Alignment explanation
Indices: 54200--54351 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
54190 ACACAAACTT
54200 ATTGACTTGGACGAGAACATCTTTTATCTGTCCTTTAGGTTGTGCTAAAAATTTGTCTGCTAATT
1 ATTGACTTGGACGAGAACATCTTTTATCTGTCCTTTAGGTTGTGCTAAAAATTTGTCTGCTAATT
54265 GCAATGTCACC
66 GCAATGTCACC
54276 ATTGACTTGGACGAGAACATCTTTTATCTGTCCTTTAGGTTGTGCTAAAAATTTGTCTGCTAATT
1 ATTGACTTGGACGAGAACATCTTTTATCTGTCCTTTAGGTTGTGCTAAAAATTTGTCTGCTAATT
54341 GCAATGTCACC
66 GCAATGTCACC
54352 GCAGTGGGCT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (76 bp):
ATTGACTTGGACGAGAACATCTTTTATCTGTCCTTTAGGTTGTGCTAAAAATTTGTCTGCTAATT
GCAATGTCACC
Found at i:58856 original size:21 final size:21
Alignment explanation
Indices: 58806--58882 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
58796 TAAAGTGTAC
58806 ACTTCTACCGATACAAGTGAT
1 ACTTCTACCGATACAAGTGAT
*
58827 AGTTCTACCGATACAAGTGACT
1 ACTTCTACCGATACAAGTGA-T
* * * **
58849 -CTTTTACCAAAACAAGTCCT
1 ACTTCTACCGATACAAGTGAT
*
58869 ACTTCTATCGATAC
1 ACTTCTACCGATAC
58883 TAAAAAATCT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAT
Found at i:66871 original size:21 final size:22
Alignment explanation
Indices: 66845--66890 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
66835 ATAAATATAA
*
66845 TTCTTTT-TCTTTTCTTTTCTT
1 TTCTTTTCTCTTCTCTTTTCTT
*
66866 TTCTTTTCGTCTTCTCTTTTTTT
1 TTCTTTTC-TCTTCTCTTTTCTT
66889 TT
1 TT
66891 ATATGTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
23 14 0.67
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (22 bp):
TTCTTTTCTCTTCTCTTTTCTT
Found at i:66883 original size:5 final size:5
Alignment explanation
Indices: 66849--66873 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
66839 ATATAATTCT
66849 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
66874 GTCTTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:67934 original size:27 final size:27
Alignment explanation
Indices: 67904--67961 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
67894 GACAGTAGGT
67904 TCTTCCT-TTCTTTCTTCTTTCCCTTCC
1 TCTTCCTGTTCTTT-TTCTTTCCCTTCC
* * *
67931 TCTTCTTGTTCTTTTTCTTTTCCTTCT
1 TCTTCCTGTTCTTTTTCTTTCCCTTCC
67958 TCTT
1 TCTT
67962 TCTCCTCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.66
Consensus pattern (27 bp):
TCTTCCTGTTCTTTTTCTTTCCCTTCC
Found at i:74055 original size:15 final size:17
Alignment explanation
Indices: 74030--74071 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
74020 ATTGTTGATT
*
74030 ATAATTCCCTTG-TCGA
1 ATAATTTCCTTGCTCGA
74046 A-AATTTCCTTGCCTCGA
1 ATAATTTCCTTG-CTCGA
74063 ATAATTTCC
1 ATAATTTCC
74072 ATATCTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 1 0.05
17 5 0.23
18 7 0.32
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (17 bp):
ATAATTTCCTTGCTCGA
Found at i:77747 original size:21 final size:21
Alignment explanation
Indices: 77683--77747 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
77673 AATCTCAAGA
77683 ATCATGCAAAAACACAAGTTT
1 ATCATGCAAAAACACAAGTTT
* * * * *
77704 ATCGA-CCCAAATCTCAAG--A
1 ATC-ATGCAAAAACACAAGTTT
77723 ATCATGCAAAAACACAAGTTT
1 ATCATGCAAAAACACAAGTTT
77744 ATCA
1 ATCA
77748 ACCTAAAACA
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
18 1 0.03
19 12 0.40
21 16 0.53
22 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.22
Consensus pattern (21 bp):
ATCATGCAAAAACACAAGTTT
Found at i:82889 original size:24 final size:25
Alignment explanation
Indices: 82857--82909 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
82847 TGTATGGGTA
* *
82857 TCTTCTTGTTTTTCA-TTTTCTTTT
1 TCTTCTTGTTATTCATTTTTCATTT
82881 TCTTCTTGTTATTCATTTTTCATTT
1 TCTTCTTGTTATTCATTTTTCATTT
82906 TCTT
1 TCTT
82910 TTTCCTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.72
Consensus pattern (25 bp):
TCTTCTTGTTATTCATTTTTCATTT
Found at i:84549 original size:20 final size:20
Alignment explanation
Indices: 84524--84567 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
84514 ATATTTGTTA
84524 TTTTCTTATTTTTCACGTAT
1 TTTTCTTATTTTTCACGTAT
* * *
84544 TTTTCTTTTTTTTCTCGTCT
1 TTTTCTTATTTTTCACGTAT
84564 TTTT
1 TTTT
84568 TATCACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.16, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTCTTATTTTTCACGTAT
Found at i:88072 original size:11 final size:10
Alignment explanation
Indices: 88046--88082 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
88036 GAATATTGTT
88046 TTTATTTTT-
1 TTTATTTTTC
88055 TTTATTTTTC
1 TTTATTTTTC
88065 TATTATTTTTC
1 T-TTATTTTTC
88076 TTT-TTTT
1 TTTATTTT
88083 CTCGACTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 13 0.50
10 3 0.12
11 10 0.38
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:88072 original size:20 final size:19
Alignment explanation
Indices: 88047--88084 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
88037 AATATTGTTT
*
88047 TTATTTTTTTTATTTTTCTA
1 TTATTTTTCTT-TTTTTCTA
88067 TTATTTTTCTTTTTTTCT
1 TTATTTTTCTTTTTTTCT
88085 CGACTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.82
Consensus pattern (19 bp):
TTATTTTTCTTTTTTTCTA
Done.