Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001633.1 Kokia drynarioides strain JFW-HI SEQ_113271, 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: 33792
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3176 original size:155 final size:155
Alignment explanation
Indices: 2894--3186 Score: 559
Period size: 155 Copynumber: 1.9 Consensus size: 155
2884 AGTGGGGGAC
* *
2894 GAGTATGGATGGAAAATGAGTGAACATTGAGGCTTGAACCTTGGACCTCTAGGATAATTAGTTAA
1 GAGTATGGATGGAAAAGGAGTGAACATTGAGGCTTGAACCTTGGACCTCTAAGATAATTAGTTAA
2959 CCACTAAGCCACTTAATCATTTATTCCCTTGTGTCAATACTTGCGAACTTAATTTAAAACATAGG
66 CCACTAAGCCACTTAATCATTTATTCCCTTGTGTCAATACTTGCGAACTTAATTTAAAACATAGG
3024 AGTGGGTAGTTTAGTAGAGGACAGA
131 AGTGGGTAGTTTAGTAGAGGACAGA
*
3049 GAGTATGGATGGAAAAGGAGTGAACATTGAGGCTTGAACCTTGGACCTCTAAGATAGTTAGTTAA
1 GAGTATGGATGGAAAAGGAGTGAACATTGAGGCTTGAACCTTGGACCTCTAAGATAATTAGTTAA
3114 CCACTAAGCCACTTAATCATTTATTCCCTTGTGTCAATACTTGCGAACTTAATTTAAAACATAGG
66 CCACTAAGCCACTTAATCATTTATTCCCTTGTGTCAATACTTGCGAACTTAATTTAAAACATAGG
3179 AGTGGGTA
131 AGTGGGTA
3187 CTTTCACTAT
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
155 135 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (155 bp):
GAGTATGGATGGAAAAGGAGTGAACATTGAGGCTTGAACCTTGGACCTCTAAGATAATTAGTTAA
CCACTAAGCCACTTAATCATTTATTCCCTTGTGTCAATACTTGCGAACTTAATTTAAAACATAGG
AGTGGGTAGTTTAGTAGAGGACAGA
Found at i:4831 original size:20 final size:20
Alignment explanation
Indices: 4808--4867 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
4798 AATCAAGTTG
4808 AAATGATTTTAGACAAGTCA
1 AAATGATTTTAGACAAGTCA
*
4828 AAATCATTTTAG-CATA-TCA
1 AAATGATTTTAGACA-AGTCA
* *
4847 AAATGTTTTTCAAACAAGTCA
1 AAATGATTTT-AGACAAGTCA
4868 GAATAGCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 13 0.41
20 14 0.44
21 5 0.16
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (20 bp):
AAATGATTTTAGACAAGTCA
Found at i:11080 original size:20 final size:20
Alignment explanation
Indices: 11057--11105 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
11047 GACTTAACAT
11057 TATCGATACTTATATAAAAA
1 TATCGATACTTATATAAAAA
* * *
11077 TATCGATACTTGTGTAAAAT
1 TATCGATACTTATATAAAAA
11097 TATCGATAC
1 TATCGATAC
11106 CATGGGGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (20 bp):
TATCGATACTTATATAAAAA
Found at i:24110 original size:37 final size:37
Alignment explanation
Indices: 24069--24143 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
24059 ATTTTGGTTA
24069 AACTTGATTGCTTTATTGGTATTTTTAGATACAATTG
1 AACTTGATTGCTTTATTGGTATTTTTAGATACAATTG
*
24106 AACTTGATTGCTTTATTGGTATTTTTTGATACAATTG
1 AACTTGATTGCTTTATTGGTATTTTTAGATACAATTG
24143 A
1 A
24144 TGTTTTTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (37 bp):
AACTTGATTGCTTTATTGGTATTTTTAGATACAATTG
Found at i:24572 original size:14 final size:14
Alignment explanation
Indices: 24555--24582 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24545 ATAATTTCTC
24555 AATTTAAATTTTAA
1 AATTTAAATTTTAA
24569 AATTTAAATTTTAA
1 AATTTAAATTTTAA
24583 GAGATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAAATTTTAA
Found at i:27990 original size:10 final size:9
Alignment explanation
Indices: 27966--27995 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
27956 TTTCATTTTT
27966 TCTCTCAAA
1 TCTCTCAAA
27975 TCTCTCAAA
1 TCTCTCAAA
27984 CTCTCTCAAA
1 -TCTCTCAAA
27994 TC
1 TC
27996 CTCTAAAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (9 bp):
TCTCTCAAA
Found at i:28198 original size:15 final size:15
Alignment explanation
Indices: 28180--28224 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
28170 ATTTAAATTG
28180 TGTTAATTTGAATAT
1 TGTTAATTTGAATAT
*
28195 TGTTAAATTT-AATTT
1 TGTT-AATTTGAATAT
*
28210 TATTAATTTGAATAT
1 TGTTAATTTGAATAT
28225 ATATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 5 0.20
15 15 0.60
16 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (15 bp):
TGTTAATTTGAATAT
Found at i:33765 original size:6 final size:6
Alignment explanation
Indices: 33757--33792 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
33747 GTAGACAACA
*
33757 CACACA CACACC CACACC CACACC CACACC CACACC
1 CACACC CACACC CACACC CACACC CACACC CACACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (6 bp):
CACACC
Done.