Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010669.1 Kokia drynarioides strain JFW-HI SEQ_125614, 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: 6253
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Found at i:142 original size:33 final size:32
Alignment explanation
Indices: 80--281 Score: 110
Period size: 33 Copynumber: 6.3 Consensus size: 32
70 CCATGCCCAC
* * ** *
80 CACCCTTGCCATTCCTACCACCATATTCACCA
1 CACCCTTGCCATGCCCACCTTCATCTTCACCA
112 TCACCCTTGCCATGCCCACCTTCATCTTCA-C-
1 -CACCCTTGCCATGCCCACCTTCATCTTCACCA
* * * *
143 CACCCTTTCCATGCCCACCTTTAGCTCCACCA
1 CACCCTTGCCATGCCCACCTTCATCTTCACCA
* * * * ** *
175 CCACCCTTGCCATTCCTA-CTACCATATAGATCA
1 -CACCCTTGCCATGCCCACCT-TCATCTTCACCA
* * *
208 TCACCCTTTCCATGACCACCTTCATCTTC-TC-
1 -CACCCTTGCCATGCCCACCTTCATCTTCACCA
* * *
239 CACCCTTTCCATGCCCACC-TCTAGCTCCACCA
1 CACCCTTGCCATGCCCACCTTC-ATCTTCACCA
271 CCACCCTTGCC
1 -CACCCTTGCC
282 GTTCCTACTA
Statistics
Matches: 127, Mismatches: 33, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
29 2 0.02
30 47 0.37
31 2 0.02
32 5 0.04
33 69 0.54
34 2 0.02
ACGTcount: A:0.20, C:0.48, G:0.05, T:0.27
Consensus pattern (32 bp):
CACCCTTGCCATGCCCACCTTCATCTTCACCA
Found at i:162 original size:30 final size:31
Alignment explanation
Indices: 113--353 Score: 118
Period size: 30 Copynumber: 7.6 Consensus size: 31
103 TATTCACCAT
* *
113 CACCCTTGCCATGCCCACCTTCAT-CTTCAC
1 CACCCTTTCCATGCCCACCTTCATACATCAC
* * *
143 CACCCTTTCCATGCCCACCTTTAGCTCCACCAC
1 CACCCTTTCCATGCCCACCTTCA--TACATCAC
* * * * *
176 CACCCTTGCCATTCCTACTACCAT-ATAGATCAT
1 CACCCTTTCCATGCC--C-ACCTTCATACATCAC
* * *
209 CACCCTTTCCATGACCACCTTCAT-CTTCTC
1 CACCCTTTCCATGCCCACCTTCATACATCAC
* *
239 CACCCTTTCCATGCCCACC-TCTAGCTCCACCAC
1 CACCCTTTCCATGCCCACCTTC-A--TACATCAC
* * * * * *
272 CACCCTTGCCGTTCCTACTACCAT-ATAGATCAT
1 CACCCTTTCCATGCC--C-ACCTTCATACATCAC
* *
305 CACCCTTTCCAT-CACCACCTTCAT-CTTCTC
1 CACCCTTTCCATGC-CCACCTTCATACATCAC
335 CACCCTTTCCATGCCCACC
1 CACCCTTTCCATGCCCACC
354 ACAGAAACTA
Statistics
Matches: 156, Mismatches: 37, Indels: 36
0.68 0.16 0.16
Matches are distributed among these distances:
29 2 0.01
30 69 0.44
31 7 0.04
32 3 0.02
33 63 0.40
35 4 0.03
36 7 0.04
37 1 0.01
ACGTcount: A:0.20, C:0.47, G:0.05, T:0.28
Consensus pattern (31 bp):
CACCCTTTCCATGCCCACCTTCATACATCAC
Found at i:210 original size:96 final size:96
Alignment explanation
Indices: 76--353 Score: 459
Period size: 96 Copynumber: 2.9 Consensus size: 96
66 ACCCCCATGC
* ** * *
76 CCACCACCCTTGCCATTCCTACCACCATATTCACCATCACCCTTGCCATGCCCACCTTCATCTTC
1 CCACCACCCTTGCCATTCCTACTACCATATAGATCATCACCCTTTCCATGCCCACCTTCATCTTC
* *
141 ACCACCCTTTCCATGCCCACCTTTAGCTCCA
66 TCCACCCTTTCCATGCCCACCTCTAGCTCCA
*
172 CCACCACCCTTGCCATTCCTACTACCATATAGATCATCACCCTTTCCATGACCACCTTCATCTTC
1 CCACCACCCTTGCCATTCCTACTACCATATAGATCATCACCCTTTCCATGCCCACCTTCATCTTC
237 TCCACCCTTTCCATGCCCACCTCTAGCTCCA
66 TCCACCCTTTCCATGCCCACCTCTAGCTCCA
*
268 CCACCACCCTTGCCGTTCCTACTACCATATAGATCATCACCCTTTCCAT-CACCACCTTCATCTT
1 CCACCACCCTTGCCATTCCTACTACCATATAGATCATCACCCTTTCCATGC-CCACCTTCATCTT
332 CTCCACCCTTTCCATGCCCACC
65 CTCCACCCTTTCCATGCCCACC
354 ACAGAAACTA
Statistics
Matches: 171, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
96 171 1.00
ACGTcount: A:0.20, C:0.47, G:0.05, T:0.27
Consensus pattern (96 bp):
CCACCACCCTTGCCATTCCTACTACCATATAGATCATCACCCTTTCCATGCCCACCTTCATCTTC
TCCACCCTTTCCATGCCCACCTCTAGCTCCA
Found at i:1627 original size:29 final size:29
Alignment explanation
Indices: 1584--1639 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1574 TTTTATTCCT
* *
1584 TTTAATAGTAAAGAGATTAAATTGATCAA
1 TTTAATAATAAAGAGACTAAATTGATCAA
* *
1613 TTTAATAATAGAGAGACTAATTTGATC
1 TTTAATAATAAAGAGACTAAATTGATC
1640 TAGTCCTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (29 bp):
TTTAATAATAAAGAGACTAAATTGATCAA
Done.