Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013796.1 Kokia drynarioides strain JFW-HI SEQ_128824, 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: 20032
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:4975 original size:35 final size:35
Alignment explanation
Indices: 4920--4989 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
4910 AATGAAGTAG
*
4920 AGATGTATATCTAACAACTATTAGAGTTAAAGGTA
1 AGATCTATATCTAACAACTATTAGAGTTAAAGGTA
* * *
4955 AGATCTATTTCTAATAACTATTAGAGTTCAAGGTA
1 AGATCTATATCTAACAACTATTAGAGTTAAAGGTA
4990 TATCAAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (35 bp):
AGATCTATATCTAACAACTATTAGAGTTAAAGGTA
Found at i:9432 original size:20 final size:20
Alignment explanation
Indices: 9407--9451 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9397 ATAGAAAAAT
*
9407 AAATATATAAAAATTTATTA
1 AAATATATAAAAATTTATAA
* * *
9427 AAATATTTTAAATTTTATAA
1 AAATATATAAAAATTTATAA
9447 AAATA
1 AAATA
9452 AAGAAAACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATATAAAAATTTATAA
Found at i:10160 original size:6 final size:6
Alignment explanation
Indices: 10118--10226 Score: 61
Period size: 6 Copynumber: 19.0 Consensus size: 6
10108 TAAAGTCATT
* * **
10118 TTTAAA TTT--A TTATAAGA TTT-AA TTT-AT TTTACA TTTAAA TTT-GT
1 TTTAAA TTTAAA TT-TAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
10163 TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA TTTACT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
10210 ATT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
10227 AAGTCTCATT
Statistics
Matches: 77, Mismatches: 18, Indels: 16
0.69 0.16 0.14
Matches are distributed among these distances:
4 3 0.04
5 19 0.25
6 51 0.66
7 1 0.01
8 3 0.04
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:10177 original size:23 final size:23
Alignment explanation
Indices: 10146--10226 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
10136 TTTAATTTAT
* *
10146 TTTACATTTAAATT-TGTTTTAAA
1 TTTAAATTTAAATTAAG-TTTAAA
10169 TTTAAATTTAAATTAAGTTTAAA
1 TTTAAATTTAAATTAAGTTTAAA
** ** *
10192 TTTACTTTTAAAATTAAAATT-AT
1 TTTAAATTT-AAATTAAGTTTAAA
10215 TTTAAATTTAAA
1 TTTAAATTTAAA
10227 AAGTCTCATT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
22 3 0.06
23 34 0.72
24 10 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAAATTTAAATTAAGTTTAAA
Found at i:10227 original size:17 final size:17
Alignment explanation
Indices: 10118--10226 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
10108 TAAAGTCATT
*
10118 TTTAAATTTATTATAAGA
1 TTTAAATTTATTTTAA-A
*
10136 TTT-AATTTATTTTACA
1 TTTAAATTTATTTTAAA
*
10152 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
** *
10169 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
10186 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
10204 ATTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
10221 TTTAAA
1 TTTAAA
10227 AAGTCTCATT
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
16 4 0.05
17 56 0.75
18 15 0.20
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:10897 original size:9 final size:9
Alignment explanation
Indices: 10885--10923 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
10875 AAGTTATCAT
10885 TATTATTAA
1 TATTATTAA
10894 TATTATTAA
1 TATTATTAA
10903 TATTAATTTAA
1 TATT-A-TTAA
*
10914 TAATATTAA
1 TATTATTAA
10923 T
1 T
10924 GACCATAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 18 0.67
10 2 0.07
11 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTATTAA
Found at i:12088 original size:29 final size:29
Alignment explanation
Indices: 12047--12332 Score: 283
Period size: 29 Copynumber: 9.8 Consensus size: 29
12037 AAACTGTCTG
* *
12047 AAAATTACATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
* *
12076 AAAA-TCTCATTTTGA-CCTTGAAACTTCCA
1 AAAATTC-CATTTTTACCCTCG-AACTTCCA
* *
12105 AAAATTCCTTTTTTACCCTCGAACTTTCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
* * * *
12134 AAAATCCCATTTTGA-CCTCAAAACTTTCA
1 AAAATTCCATTTTTACCCTC-GAACTTCCA
* *
12163 AAAATTCCATTTTTACACTCGAACTTTCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
* * * * *
12192 AAATTTTCATTTTTAACCTCGAAATTTCTA
1 AAAATTCCATTTTTACCCTCG-AACTTCCA
12222 AAAATTCCATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
* **
12251 AAATTTCCATTTTTGACCCTAAAACTTCCA
1 AAAATTCCATTTTT-ACCCTCGAACTTCCA
* *
12281 AAAATTCCATTTTTACCCCCGAACCTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
*
12310 AAATTTCCATTTTTTACCC-CGAA
1 AAAATTCCA-TTTTTACCCTCGAA
12333 ACTTTCATTT
Statistics
Matches: 211, Mismatches: 37, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
28 8 0.04
29 136 0.64
30 67 0.32
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCGAACTTCCA
Found at i:12229 original size:59 final size:59
Alignment explanation
Indices: 12047--12338 Score: 324
Period size: 59 Copynumber: 5.0 Consensus size: 59
12037 AAACTGTCTG
* * * * *
12047 AAAATTACATTTTTACCCCCGAACTTCCAAAA-ATCTCA-TTTTGACCTTGAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAATTTC-CATTTTTGACCTCGAAATTTCCA
* * * * *
12105 AAAATTCCTTTTTTACCCTCGAACTTTCAAAAATCCCA-TTTTGACCTCAAAACTTT-CA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGACCTCGAAA-TTTCCA
* * * * *
12163 AAAATTCCATTTTTACACTCGAACTTTCAAAATTTTCATTTTTAACCTCGAAATTTCTA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGACCTCGAAATTTCCA
* *
12222 AAAATTCCATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGACC-CTAAAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGACCTC-GAAATTTCCA
* * * *
12281 AAAATTCCATTTTTACCCCCGAACCTCCAAAATTTCCATTTTTTACCCCGAAACTTTC
1 AAAATTCCATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGACCTCGAAA-TTTC
12339 ATTTTGCCCT
Statistics
Matches: 198, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
58 81 0.41
59 113 0.57
60 4 0.02
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAATTCCATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGACCTCGAAATTTCCA
Found at i:14102 original size:13 final size:13
Alignment explanation
Indices: 14084--14109 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14074 TTAACCGGGC
14084 CCAAAAAATAAAA
1 CCAAAAAATAAAA
14097 CCAAAAAATAAAA
1 CCAAAAAATAAAA
14110 ATAAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.15, G:0.00, T:0.08
Consensus pattern (13 bp):
CCAAAAAATAAAA
Done.