Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000709.1 Kokia drynarioides strain JFW-HI SEQ_111714, 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: 79169
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1510 original size:2 final size:2
Alignment explanation
Indices: 1493--1533 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
1483 ATAATGTGAA
1493 AT AT GAT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1534 AAATCAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 33 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3761 original size:22 final size:22
Alignment explanation
Indices: 3736--3806 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
3726 TGCCATAGCG
3736 TCTTTCAACTATGGACTTCTCC
1 TCTTTCAACTATGGACTTCTCC
* * *
3758 TCTTT-TAC-AT-GATTTCATAGCG
1 TCTTTCAACTATGGACTTC-T--CC
*
3780 TCTTTCAAATATGGACTTCTCC
1 TCTTTCAACTATGGACTTCTCC
3802 TCTTT
1 TCTTT
3807 TACATGATGC
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
19 5 0.14
20 3 0.08
21 2 0.06
22 17 0.47
23 1 0.03
24 3 0.08
25 5 0.14
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (22 bp):
TCTTTCAACTATGGACTTCTCC
Found at i:3777 original size:44 final size:44
Alignment explanation
Indices: 3721--3837 Score: 180
Period size: 44 Copynumber: 2.7 Consensus size: 44
3711 TCATTTCTCT
3721 CATGATGCCATAGCGTCTTTCAACTATGGACTTCTCCTCTTTTA
1 CATGATGCCATAGCGTCTTTCAACTATGGACTTCTCCTCTTTTA
** *
3765 CATGATTTCATAGCGTCTTTCAAATATGGACTTCTCCTCTTTTA
1 CATGATGCCATAGCGTCTTTCAACTATGGACTTCTCCTCTTTTA
* * *
3809 CATGATGCCATAGCATCTTTTAGCTATGG
1 CATGATGCCATAGCGTCTTTCAACTATGG
3838 TTTTACTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 64 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (44 bp):
CATGATGCCATAGCGTCTTTCAACTATGGACTTCTCCTCTTTTA
Found at i:4744 original size:21 final size:21
Alignment explanation
Indices: 4718--4758 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4708 TACTTGGTTG
4718 GTGAGAAAACTAAAGAAAATT
1 GTGAGAAAACTAAAGAAAATT
*
4739 GTGAGAAAACTGAAGAAAAT
1 GTGAGAAAACTAAAGAAAAT
4759 GGATTTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.22, T:0.17
Consensus pattern (21 bp):
GTGAGAAAACTAAAGAAAATT
Found at i:4951 original size:73 final size:73
Alignment explanation
Indices: 4864--5156 Score: 442
Period size: 73 Copynumber: 4.0 Consensus size: 73
4854 GGAGGCATTG
* * *
4864 AGAAAATCTAGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAAAGAGAAACTCTAGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
4929 TTGAGAAA
66 TTGAGAAA
* *
4937 AGAAAATCTGGAAAGAGAGAAAAAATTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
* *
5002 TTAACAAA
66 TTGAGAAA
* * * * *
5010 AGAAAATCTGAAAAGAAAGGAAAAACTAAAGATGTATTTGGAAAGATAGAAAATTTGGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
5075 TTGAGAAA
66 TTGAGAAA
* * * *
5083 AGAAAATCTGGAAAGAGAGAAAAAACTAAAGATGTGTTTGGAAAGAGAGAAAATTTGGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
5148 TTGAGAAA
66 TTGAGAAA
5156 A
1 A
5157 AAATGTTTTA
Statistics
Matches: 199, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 199 1.00
ACGTcount: A:0.53, C:0.04, G:0.25, T:0.19
Consensus pattern (73 bp):
AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
TTGAGAAA
Found at i:5196 original size:10 final size:10
Alignment explanation
Indices: 5181--5206 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5171 GGAAGAGAGA
5181 AAGAAAGAAG
1 AAGAAAGAAG
5191 AAGAAAGAAG
1 AAGAAAGAAG
5201 AAGAAA
1 AAGAAA
5207 AAAATGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAG
Found at i:11354 original size:56 final size:57
Alignment explanation
Indices: 11269--11385 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 57
11259 AGAATTGGTG
* *
11269 AAATGGAGAAATAGGAAACATTTTGAAATGATTAAGGTTTTCTC-AAAATGAAAATGA
1 AAATGGAGAAATA-GAAACATTTTGAAATGAATAAGGTTTTCTCTAAAATGAAAATAA
**
11326 AAATGGAGAAAT-GAAATCA-TTTGAAAATGAATGTGGTTTTCTCTAAAATGAAAATAA
1 AAATGGAGAAATAGAAA-CATTTTG-AAATGAATAAGGTTTTCTCTAAAATGAAAATAA
11383 AAA
1 AAA
11386 ATGACCTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
55 8 0.15
56 18 0.34
57 27 0.51
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (57 bp):
AAATGGAGAAATAGAAACATTTTGAAATGAATAAGGTTTTCTCTAAAATGAAAATAA
Found at i:17950 original size:70 final size:70
Alignment explanation
Indices: 17875--18009 Score: 189
Period size: 70 Copynumber: 1.9 Consensus size: 70
17865 TTTGTTACGA
* *
17875 CGTAGCTCCCCCTATGTCACAACAAACCTATCAGTTTTGAAATTTTAACAATTTGACCCCTTTGT
1 CGTAGCTCCCCCTATGTCACAACAAACCTATCAATTTTGAAATTTCAACAATTTGACCCCTTTGT
17940 TGCCT
66 TGCCT
* * * * * * *
17945 CGTAGCTCCCCCTGTGTCGCGACAAATCTATTAATTTTGAAATTTCAATAGTTTGACCCCTTTGT
1 CGTAGCTCCCCCTATGTCACAACAAACCTATCAATTTTGAAATTTCAACAATTTGACCCCTTTGT
18010 CGCAACATAC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (70 bp):
CGTAGCTCCCCCTATGTCACAACAAACCTATCAATTTTGAAATTTCAACAATTTGACCCCTTTGT
TGCCT
Found at i:42400 original size:18 final size:17
Alignment explanation
Indices: 42369--42402 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42359 AAAAATAAGA
*
42369 AAAAATTAGTAACAAAT
1 AAAAATTAGAAACAAAT
42386 AAAAATTAGGAAACAAA
1 AAAAATTA-GAAACAAA
42403 GAATAACTGC
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:0.68, C:0.06, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAAATTAGAAACAAAT
Found at i:42742 original size:28 final size:28
Alignment explanation
Indices: 42702--42757 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
42692 GTAAAATTGT
42702 AATACAATATGTCAGAGCAATTTAATAA
1 AATACAATATGTCAGAGCAATTTAATAA
42730 AATACAATATGTCAGAGCAATTTAATAA
1 AATACAATATGTCAGAGCAATTTAATAA
42758 GGAAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (28 bp):
AATACAATATGTCAGAGCAATTTAATAA
Found at i:45282 original size:26 final size:26
Alignment explanation
Indices: 45237--45326 Score: 74
Period size: 26 Copynumber: 3.5 Consensus size: 26
45227 CTGCATGAGT
* * *
45237 ATGTCCAAAATTATCGCTGCAGAAAC
1 ATGTCCAGAATTGTCACTGCAGAAAC
* **
45263 ATGTCCAGAGTTGTCACTGCATG-GGC
1 ATGTCCAGAATTGTCACTGCA-GAAAC
* *
45289 ATGTCTAGAATTGTCATTGCAGAAAC
1 ATGTCCAGAATTGTCACTGCAGAAAC
* *
45315 TTGACCAGAATT
1 ATGTCCAGAATT
45327 ATCGTTACAT
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
25 1 0.02
26 46 0.96
27 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (26 bp):
ATGTCCAGAATTGTCACTGCAGAAAC
Found at i:49370 original size:21 final size:21
Alignment explanation
Indices: 49344--49390 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
49334 CTTCTTCATT
* * *
49344 GCAACATTGCATGTTTATGTC
1 GCAACATAGCATGTCTACGTC
49365 GCAACATAGCATGTCTACGTC
1 GCAACATAGCATGTCTACGTC
49386 GCAAC
1 GCAAC
49391 CAACCCTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
GCAACATAGCATGTCTACGTC
Found at i:74569 original size:29 final size:29
Alignment explanation
Indices: 74537--74594 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
74527 TAGAAATACA
74537 AGTGTTGGTTAGGAGCATGTATAATAGGT
1 AGTGTTGGTTAGGAGCATGTATAATAGGT
74566 AGTGTTGGTTAGGAGCATGTATAATAGGT
1 AGTGTTGGTTAGGAGCATGTATAATAGGT
74595 TGATTGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.34, T:0.34
Consensus pattern (29 bp):
AGTGTTGGTTAGGAGCATGTATAATAGGT
Found at i:75152 original size:25 final size:26
Alignment explanation
Indices: 75124--75172 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
75114 GTGAAAATCG
75124 AAAGAAAAAAAAATGAGT-AGAAACA
1 AAAGAAAAAAAAATGAGTAAGAAACA
* **
75149 AAAGAAGAAATCATGAGTAAGAAA
1 AAAGAAAAAAAAATGAGTAAGAAA
75173 ACATATGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.67, C:0.04, G:0.18, T:0.10
Consensus pattern (26 bp):
AAAGAAAAAAAAATGAGTAAGAAACA
Done.