Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014107.1 Kokia drynarioides strain JFW-HI SEQ_129138, 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: 49822
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:16075 original size:26 final size:26
Alignment explanation
Indices: 16014--16077 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
16004 GAAGAAAGCT
16014 TTTTTTTTTAAACCATGAAGAAATTA
1 TTTTTTTTTAAACCATGAAGAAATTA
** *
16040 TTAATGTTTAAACCATGAAGAAATTA
1 TTTTTTTTTAAACCATGAAGAAATTA
16066 TTTTTTTTTAAA
1 TTTTTTTTTAAA
16078 AAAAGGTGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (26 bp):
TTTTTTTTTAAACCATGAAGAAATTA
Found at i:19353 original size:52 final size:51
Alignment explanation
Indices: 19268--19665 Score: 467
Period size: 52 Copynumber: 7.7 Consensus size: 51
19258 TTTCACTTCG
* * * * * *
19268 TTCATATACTCACGGTAACACATAGCCACCGGACCTTATAATCCATAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTT-TAATCCGTAAAGGA
*
19320 TTCATATACTCAAGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCT-TTAATCCGTAAAGGA
* * *
19372 TTCATATACTCACAATGACACTTAGTCATCGAACCTTTTAATCCGTAAAGAA
1 TTCATATACTCACGATGACACTTAGTCATCGGACC-TTTAATCCGTAAAGGA
**
19424 TTCATATACTCACGATGACACTTAGTTGTCGGACCTCTTAATCCGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCT-TTAATCCGTAAAGGA
* * * * * * * *
19476 TTGATATACTCATGATGACAGTTAGTCATTGAACCTCTTAAACCGTCAAGAA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCT-TTAATCCGTAAAGGA
* * * * *
19528 TTTATACACTCACGATGACACTTAGTCATTGGACCACTTAATTCGTAAA-GA
1 TTCATATACTCACGATGACACTTAGTCATCGGACC-TTTAATCCGTAAAGGA
* * *
19579 TTCATATACTCACGATGACACTTAATCATTGGACCTTTTAATTCGTAAA-GA
1 TTCATATACTCACGATGACACTTAGTCATCGGACC-TTTAATCCGTAAAGGA
19630 TTCATATACTCACGATGACACTTAGTCATCGGACCT
1 TTCATATACTCACGATGACACTTAGTCATCGGACCT
19666 CTTTATTTAT
Statistics
Matches: 299, Mismatches: 43, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
50 1 0.00
51 81 0.27
52 215 0.72
53 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (51 bp):
TTCATATACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGA
Found at i:19448 original size:104 final size:104
Alignment explanation
Indices: 19268--19668 Score: 527
Period size: 104 Copynumber: 3.9 Consensus size: 104
19258 TTTCACTTCG
* * * * * * * * * *
19268 TTCATATACTCACGGTAACACATAGCCACCGGACCTTATAATCCATAAAGGATTCATATACTCAA
1 TTCATATACTCACGATGACACTTAGTCATCGAACCTTTTAATCCGTAAAGAATTCATATACTCAC
19333 GATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
66 GATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
*
19372 TTCATATACTCACAATGACACTTAGTCATCGAACCTTTTAATCCGTAAAGAATTCATATACTCAC
1 TTCATATACTCACGATGACACTTAGTCATCGAACCTTTTAATCCGTAAAGAATTCATATACTCAC
**
19437 GATGACACTTAGTTGTCGGACCTCTTAATCCGTAAAGGA
66 GATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* * * * * * * * *
19476 TTGATATACTCATGATGACAGTTAGTCATTGAACCTCTTAAACCGTCAAGAATTTATACACTCAC
1 TTCATATACTCACGATGACACTTAGTCATCGAACCTTTTAATCCGTAAAGAATTCATATACTCAC
* * *
19541 GATGACACTTAGTCATTGGACCACTTAATTCGTAAA-GA
66 GATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* * * *
19579 TTCATATACTCACGATGACACTTAATCATTGGACCTTTTAATTCGTAAAG-ATTCATATACTCAC
1 TTCATATACTCACGATGACACTTAGTCATCGAACCTTTTAATCCGTAAAGAATTCATATACTCAC
19643 GATGACACTTAGTCATCGGACCTCTT
66 GATGACACTTAGTCATCGGACCTCTT
19669 TATTTATGGC
Statistics
Matches: 256, Mismatches: 41, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
102 36 0.14
103 43 0.17
104 177 0.69
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (104 bp):
TTCATATACTCACGATGACACTTAGTCATCGAACCTTTTAATCCGTAAAGAATTCATATACTCAC
GATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
Found at i:38142 original size:21 final size:23
Alignment explanation
Indices: 38093--38150 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 23
38083 CAAGTATGCA
38093 AACTATCGATACATCTAAAAATAC
1 AACTATCGATACATC-AAAAATAC
* *
38117 AACTATCGATAC-TC-ACAATTC
1 AACTATCGATACATCAAAAATAC
38138 AACTATCGATACA
1 AACTATCGATACA
38151 ACTTAAGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 17 0.55
23 2 0.06
24 12 0.39
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (23 bp):
AACTATCGATACATCAAAAATAC
Found at i:38814 original size:52 final size:52
Alignment explanation
Indices: 38729--38975 Score: 343
Period size: 52 Copynumber: 4.8 Consensus size: 52
38719 TTTCACTTCG
* * * * ** *
38729 TTCATATACTCACGGTGACACATAGCCACCGGACCT-TATAATCCACAAGGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCT-TAATCCGTAAAGGA
*
38781 TTCATATACTTACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* * *
38833 TTCGTATACTCACGATGACACTTAGTCATCGAACCTCTTAATCTGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* *
38885 TTCATATACTCATGATGACACTTAGTCATCGGACCTCTTAATCTGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* *
38937 TTTAGATACTCACGATGACACTTAGTCATCGGACCTCTT
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTT
38976 CGTTTATGGC
Statistics
Matches: 176, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 175 0.99
53 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (52 bp):
TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
Done.