Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010899.1 Kokia drynarioides strain JFW-HI SEQ_125867, 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: 40440
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:82 original size:22 final size:22
Alignment explanation
Indices: 25--103 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
15 GCTGGGGAAA
*
25 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
47 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * * *
70 CAATAGGCGCACATAGGGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
93 CAGTAGGCACA
1 CAGTAGGCACA
104 TAAAGTGCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.31
23 33 0.69
ACGTcount: A:0.38, C:0.27, G:0.23, T:0.13
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:2390 original size:11 final size:11
Alignment explanation
Indices: 2335--2404 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
2325 ATTTAATTGT
2335 TTAATATTAA-A
1 TTAAT-TTAATA
2346 TTAAATTTAATA
1 TT-AATTTAATA
*
2358 CTTATTTTAATA
1 -TTAATTTAATA
*
2370 AT-ATTT--TA
1 TTAATTTAATA
2378 TTAATTTAATA
1 TTAATTTAATA
2389 TTAAATTTAAT-
1 TT-AATTTAATA
2400 TTAAT
1 TTAAT
2405 GTTTATATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 6 0.12
11 13 0.27
12 20 0.42
13 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAATTTAATA
Found at i:8670 original size:22 final size:22
Alignment explanation
Indices: 8613--8691 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
8603 GCTGGGGAAA
*
8613 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
8635 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * * *
8658 CAATAGGCGCACATAGGGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
8681 CAGTAGGCACA
1 CAGTAGGCACA
8692 TAAAGTGCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.31
23 33 0.69
ACGTcount: A:0.38, C:0.27, G:0.23, T:0.13
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:10977 original size:11 final size:11
Alignment explanation
Indices: 10922--10991 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
10912 ATTTAATTGT
10922 TTAATATTAA-A
1 TTAAT-TTAATA
10933 TTAAATTTAATA
1 TT-AATTTAATA
*
10945 CTTATTTTAATA
1 -TTAATTTAATA
*
10957 AT-ATTT--TA
1 TTAATTTAATA
10965 TTAATTTAATA
1 TTAATTTAATA
10976 TTAAATTTAAT-
1 TT-AATTTAATA
10987 TTAAT
1 TTAAT
10992 GTTTATATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 6 0.12
11 13 0.27
12 20 0.42
13 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAATTTAATA
Found at i:26498 original size:2 final size:2
Alignment explanation
Indices: 26491--26526 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
26481 CCTTTGTTTA
26491 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
26527 GCCTTTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28315 original size:39 final size:40
Alignment explanation
Indices: 28262--28339 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 40
28252 CAATGAATAC
* * * *
28262 TTTTTGAAGAGTCACAATCC-TTTCACATTGGATGGACAT
1 TTTTTAAAAAGTCACAACCCTTTTCACATTGGATAGACAT
*
28301 TTTTTAAAAAGTCACAACCCTTTTCATATTGGATAGACA
1 TTTTTAAAAAGTCACAACCCTTTTCACATTGGATAGACA
28340 CCTTTTGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 17 0.52
40 16 0.48
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (40 bp):
TTTTTAAAAAGTCACAACCCTTTTCACATTGGATAGACAT
Found at i:30638 original size:6 final size:6
Alignment explanation
Indices: 30622--30655 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
30612 CAAAGAATTG
*
30622 GAAAGT AAAAGT GAAAGT GAAAGT GAAAGT GAAA
1 GAAAGT GAAAGT GAAAGT GAAAGT GAAAGT GAAA
30656 CTAAACATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (6 bp):
GAAAGT
Found at i:38085 original size:25 final size:25
Alignment explanation
Indices: 38052--38099 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
38042 TTGTAAATAA
38052 GAAAAATATCTTTAGA-AATTTTTT
1 GAAAAATATCTTTAGAGAATTTTTT
* *
38076 GAAATAATATTTTTCGAGAATTTT
1 GAAA-AATATCTTTAGAGAATTTT
38100 CTCTTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 10 0.50
26 6 0.30
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (25 bp):
GAAAAATATCTTTAGAGAATTTTTT
Found at i:38229 original size:20 final size:20
Alignment explanation
Indices: 38161--38229 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
38151 TTCAACTATG
* *
38161 ATTAAACTTAATCACATAAAT
1 ATTAAA-TTAATCACTTTAAT
*
38182 ATTAGATT-AT-A-TTTAAT
1 ATTAAATTAATCACTTTAAT
38199 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAATCACTTTAAT
38219 ATTAAATTAAT
1 ATTAAATTAAT
38230 AAAATACTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
17 9 0.23
18 4 0.10
19 4 0.10
20 17 0.44
21 5 0.13
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTAAATTAATCACTTTAAT
Found at i:38545 original size:3 final size:3
Alignment explanation
Indices: 38537--38574 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
38527 AAAAGTGTGA
38537 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
38575 GCAAGTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39616 original size:23 final size:23
Alignment explanation
Indices: 39585--39711 Score: 164
Period size: 23 Copynumber: 5.4 Consensus size: 23
39575 AGTGTTGGGC
*
39585 AACATAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
39608 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
39631 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
39654 ATCAGAGAGCACACACAGTACTAA
1 AACAGAGAGCACACACAGTGCT-A
39678 TAACAGAGAGCACACACAGTGCTA
1 -AACAGAGAGCACACACAGTGCTA
39702 AACAGAGAGC
1 AACAGAGAGC
39712 GCGCTAGTGT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 69 0.76
24 2 0.02
25 20 0.22
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:39689 original size:48 final size:48
Alignment explanation
Indices: 39585--39711 Score: 195
Period size: 46 Copynumber: 2.7 Consensus size: 48
39575 AGTGTTGGGC
* *
39585 AACATAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * *
39633 --CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTACTAAT
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
39679 AACAGAGAGCACACACAGTGCTAAACAGAGAGC
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGC
39712 GCGCTAGTGT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
46 41 0.59
48 29 0.41
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.12
Consensus pattern (48 bp):
AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Done.