Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007921.1 Kokia drynarioides strain JFW-HI SEQ_122566, 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: 7576
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:74 original size:42 final size:42
Alignment explanation
Indices: 3--173 Score: 202
Period size: 42 Copynumber: 4.1 Consensus size: 42
1 CT
* *
3 CGTCCACTCCTCACCCTCACCAGTAGACTCACCAACACCACC
1 CGTCCACTCCTCACCCTCACCAATGGACTCACCAACACCACC
* *
45 CGTCGACTCCTCA-CCTCGATCAATGGACTCACCAACACCACC
1 CGTCCACTCCTCACCCTC-ACCAATGGACTCACCAACACCACC
* *
87 CGTCCACTCTTCACCCTCACCAATGGACTCACCACCACCACC
1 CGTCCACTCCTCACCCTCACCAATGGACTCACCAACACCACC
* * * * * *
129 CGTCCACT-CTCCACCTTTACCAGTGCACTCACCACCACTACC
1 CGTCCACTCCT-CACCCTCACCAATGGACTCACCAACACCACC
171 CGT
1 CGT
174 TCATTCACCA
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
41 5 0.04
42 103 0.92
43 4 0.04
ACGTcount: A:0.24, C:0.50, G:0.09, T:0.18
Consensus pattern (42 bp):
CGTCCACTCCTCACCCTCACCAATGGACTCACCAACACCACC
Found at i:137 original size:21 final size:21
Alignment explanation
Indices: 71--185 Score: 70
Period size: 21 Copynumber: 5.5 Consensus size: 21
61 CGATCAATGG
*
71 ACTCACCAACACCACCCGTCC
1 ACTCACCACCACCACCCGTCC
** ** **
92 ACTCTTCACC-CTCACCAATGG
1 ACTCACCACCAC-CACCCGTCC
113 ACTCACCACCACCACCCGTCC
1 ACTCACCACCACCACCCGTCC
* *** * *
134 ACTCTCCACCTTTACCAGTGC
1 ACTCACCACCACCACCCGTCC
* *
155 ACTCACCACCACTACCCGTTC
1 ACTCACCACCACCACCCGTCC
*
176 ATTCACCACC
1 ACTCACCACC
186 TTCACCCATC
Statistics
Matches: 67, Mismatches: 25, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.24, C:0.51, G:0.06, T:0.18
Consensus pattern (21 bp):
ACTCACCACCACCACCCGTCC
Found at i:423 original size:60 final size:60
Alignment explanation
Indices: 242--428 Score: 221
Period size: 60 Copynumber: 3.1 Consensus size: 60
232 GTTTATTCAC
* * * * *
242 CACCTCCACCCATTAAGTCTCTACCACCGCTAGTACAATCCCGACCTCCACCAAGTCTAT
1 CACCTCCACCCGTCAAGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTAT
* * * *
302 CACCTCCACCCGTCAAGTCTTTACCACCACCTGTACAGTCCCAACCTCCACCAACTCTAT
1 CACCTCCACCCGTCAAGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTAT
* * * * * * * *
362 CACCTCCACCCGTCAAGTCTCCACCACTACCAATACAATCTCGACCTTCACCTATTTTAT
1 CACCTCCACCCGTCAAGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTAT
422 CACCTCC
1 CACCTCC
429 TCCTGTTTTG
Statistics
Matches: 106, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 106 1.00
ACGTcount: A:0.26, C:0.45, G:0.06, T:0.23
Consensus pattern (60 bp):
CACCTCCACCCGTCAAGTCTCTACCACCACCAGTACAATCCCGACCTCCACCAACTCTAT
Found at i:1359 original size:20 final size:21
Alignment explanation
Indices: 1336--1389 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 21
1326 TGATGACTAA
1336 AATAAAATAAATACATG-TA-T
1 AATAAAATAAATA-ATGATACT
1356 AATAAAATAAAATAATGATACT
1 AATAAAAT-AAATAATGATACT
1378 AATAATAATAAA
1 AATAA-AATAAA
1390 ATTAGCAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 11 0.37
21 7 0.23
22 9 0.30
23 3 0.10
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (21 bp):
AATAAAATAAATAATGATACT
Found at i:1657 original size:22 final size:22
Alignment explanation
Indices: 1636--1678 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1626 TTATACAAAG
*
1636 GCAAAATAAA-AGAAAAATAAA
1 GCAAAAGAAATAGAAAAATAAA
*
1657 GCAAAAGAAATAGAAAGATAAA
1 GCAAAAGAAATAGAAAAATAAA
1679 ATAAATAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.72, C:0.05, G:0.14, T:0.09
Consensus pattern (22 bp):
GCAAAAGAAATAGAAAAATAAA
Found at i:3911 original size:101 final size:101
Alignment explanation
Indices: 3791--4095 Score: 574
Period size: 102 Copynumber: 3.0 Consensus size: 101
3781 GAACAAAAAA
3791 GCCAACAAAAAAAAAAACAAAATGTATTTAATTTCAGCTATAAAAGCCACAACCATTTTTTGTAA
1 GCCAAC-AAAAAAAAAACAAAATGTATTTAATTTCAGCTATAAAAGCCACAACCATTTTTTGTAA
3856 TTTTTGGACACAATCAATACAAAAAAGCAAAAAAATT
65 TTTTTGGACACAATCAATACAAAAAAGCAAAAAAATT
*
3893 GCCAACAAAAAAAAAACAAAATGTATTTAATTTCAGCTATAAAAACCACAACCATTTTTTTGTAA
1 GCCAACAAAAAAAAAACAAAATGTATTTAATTTCAGCTATAAAAGCCACAACCA-TTTTTTGTAA
3958 TTTTTGGACACAATCAATACAAAAAAGCAAAAAAATT
65 TTTTTGGACACAATCAATACAAAAAAGCAAAAAAATT
*
3995 GCCAACAAAAAAAAAACAAAATGTATTTAATTTCAACTATAAAAGCCACAACCATTTTTTGTAAT
1 GCCAACAAAAAAAAAACAAAATGTATTTAATTTCAGCTATAAAAGCCACAACCATTTTTTGTAAT
4060 TTTTGGACACAATCAATACAAAAAAGCAAAAAAATT
66 TTTTGGACACAATCAATACAAAAAAGCAAAAAAATT
4096 CAAAGGTAGC
Statistics
Matches: 199, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
101 94 0.47
102 105 0.53
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (101 bp):
GCCAACAAAAAAAAAACAAAATGTATTTAATTTCAGCTATAAAAGCCACAACCATTTTTTGTAAT
TTTTGGACACAATCAATACAAAAAAGCAAAAAAATT
Found at i:5879 original size:77 final size:77
Alignment explanation
Indices: 5793--5948 Score: 278
Period size: 77 Copynumber: 2.0 Consensus size: 77
5783 TAAAAACTAA
*
5793 ATCATGAATTTTAGATATAGTATAAGGACCAAAATATAATTTAAAC-TATTGCAAACTAAAGATA
1 ATCATGAATTTTAGATATAGTATAAGGACAAAAATATAATTT-AACTTATTGCAAACTAAAGATA
5857 GAAAATACAAGTT
65 GAAAATACAAGTT
*
5870 ATCATGAATTTTAGATATAGTATAAGGACAAAAATATAATTTAACTTATTGTAAACTAAAGATAG
1 ATCATGAATTTTAGATATAGTATAAGGACAAAAATATAATTTAACTTATTGCAAACTAAAGATAG
5935 AAAATACAAGTT
66 AAAATACAAGTT
5947 AT
1 AT
5949 ATTTGGTAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
76 3 0.04
77 73 0.96
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (77 bp):
ATCATGAATTTTAGATATAGTATAAGGACAAAAATATAATTTAACTTATTGCAAACTAAAGATAG
AAAATACAAGTT
Done.