Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001624.1 Kokia drynarioides strain JFW-HI SEQ_113260, 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: 19713
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:5467 original size:261 final size:260
Alignment explanation
Indices: 4983--5505 Score: 868
Period size: 261 Copynumber: 2.0 Consensus size: 260
4973 AAGTATTAGG
*
4983 GGTAATTTCGTAATTTTCTTAAAAGGGTCAAATTGTACTAAATGATCTAATTGTGTGTTTAATGT
1 GGTAATTTCGTAATTTTATTAAAAGGGTCAAATTGTACTAAATGATCTAATTGTGTGTTTAATGT
* * *
5048 GGAAATTTGGATGATTTGTTGATTTAGATTGTGAGCGTGACACGGATCGTGAAAAAGGGAAATTA
66 GGAAATTTGGATGATTTGTTGATTTAGATTATGAGCGTCACACGGATCGCGAAAAAGGGAAATTA
* *
5113 GCAAGTAATCCTTGAAGCCTATCTGTAATTGCAATTTAGTTCGATTATTTTGTTGCCTGAAGATC
131 GCAAGTAATCCTTGAAGCCTATCTGTAACTGCAATTTAGTTCGATTATTTTGCTGCCTGAAGATC
*
5178 AGATTGTCTCAAGAAGTCACATTATCGCGGAGCTCGTTTGGTAGTTTTTCATCACTTGGTTATAT
196 AGATTGTCTCAAGAAGTCACACTATCGCGGAGCTCGTTTGGTAGTTTTTCATCACTTGGTTATAT
* *
5243 GGTAATTTCGTAATTTTATTAAAAAGGGTCAACTTGTGCTAAATGATCTAATTGTGTGTTTAATG
1 GGTAATTTCGTAATTTTATT-AAAAGGGTCAAATTGTACTAAATGATCTAATTGTGTGTTTAATG
* *
5308 TGGAAATTTGGATGATTTGTTTATTTAGATTATGAGCGTCACACGGATCGCGGAAAAGGGAAATT
65 TGGAAATTTGGATGATTTGTTGATTTAGATTATGAGCGTCACACGGATCGCGAAAAAGGGAAATT
* * *
5373 AGCAAGTAATCCTTGAAGTCTATCTGTAACTGTAATTTAG-TCTGATTATTTTGCTGCTTGAAGA
130 AGCAAGTAATCCTTGAAGCCTATCTGTAACTGCAATTTAGTTC-GATTATTTTGCTGCCTGAAGA
* * *
5437 TCGGATTGTCTCAAGAAGTTACACTATCGCGGAGCTCGTTTGGTAGTTTTTCATCACTTGGTTTT
194 TCAGATTGTCTCAAGAAGTCACACTATCGCGGAGCTCGTTTGGTAGTTTTTCATCACTTGGTTAT
5502 AT
259 AT
5504 GG
1 GG
5506 CATGTACTAG
Statistics
Matches: 244, Mismatches: 17, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
260 21 0.09
261 223 0.91
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (260 bp):
GGTAATTTCGTAATTTTATTAAAAGGGTCAAATTGTACTAAATGATCTAATTGTGTGTTTAATGT
GGAAATTTGGATGATTTGTTGATTTAGATTATGAGCGTCACACGGATCGCGAAAAAGGGAAATTA
GCAAGTAATCCTTGAAGCCTATCTGTAACTGCAATTTAGTTCGATTATTTTGCTGCCTGAAGATC
AGATTGTCTCAAGAAGTCACACTATCGCGGAGCTCGTTTGGTAGTTTTTCATCACTTGGTTATAT
Found at i:9115 original size:29 final size:28
Alignment explanation
Indices: 9006--9188 Score: 192
Period size: 28 Copynumber: 6.5 Consensus size: 28
8996 GTGTTTCCAA
*
9006 ATTTTT-AGATTTTATAGTTTTGCCCTT
1 ATTTTTCAGATTTTATAATTTTGCCCTT
* * * *
9033 GTTTTTCAGATGTTGTAATTTTGCCCCT
1 ATTTTTCAGATTTTATAATTTTGCCCTT
* *
9061 A-TTTCCAAATTTTATAATTTTGCCCTT
1 ATTTTTCAGATTTTATAATTTTGCCCTT
* *
9088 ATTTTTCAGATTTGATAGTTTTGTCCCTT
1 ATTTTTCAGATTTTATAATTTTG-CCCTT
*
9117 ATTTTTCAAATTTTATAATTTTG-CCTCT
1 ATTTTTCAGATTTTATAATTTTGCCCT-T
* * *
9145 ATTTTTTTAGATTTTATAGTTTTGCCCCT
1 A-TTTTTCAGATTTTATAATTTTGCCCTT
*
9174 ATTTTTTAGATTTTA
1 ATTTTTCAGATTTTA
9189 CATATTTACC
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
27 30 0.23
28 50 0.39
29 46 0.36
30 2 0.02
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.56
Consensus pattern (28 bp):
ATTTTTCAGATTTTATAATTTTGCCCTT
Found at i:9148 original size:57 final size:56
Alignment explanation
Indices: 9006--9188 Score: 212
Period size: 57 Copynumber: 3.3 Consensus size: 56
8996 GTGTTTCCAA
* * * *
9006 ATTTTT-AGATTTTATAGTTTTGCCCTTGTTTTTCAGATGTTG-TAATTTTGCCCCT
1 ATTTTTCAAATTTTATAATTTTGCCCTTATTTTTCAGAT-TTGATAGTTTTGCCCCT
* *
9061 A-TTTCCAAATTTTATAATTTTGCCCTTATTTTTCAGATTTGATAGTTTTGTCCCTT
1 ATTTTTCAAATTTTATAATTTTGCCCTTATTTTTCAGATTTGATAGTTTTG-CCCCT
* *
9117 ATTTTTCAAATTTTATAATTTTG-CCTCTATTTTTTTAGATTTTATAGTTTTGCCCCT
1 ATTTTTCAAATTTTATAATTTTGCCCT-TA-TTTTTCAGATTTGATAGTTTTGCCCCT
* *
9174 ATTTTTTAGATTTTA
1 ATTTTTCAAATTTTA
9189 CATATTTACC
Statistics
Matches: 110, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
54 6 0.05
55 37 0.34
56 8 0.07
57 39 0.35
58 20 0.18
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.56
Consensus pattern (56 bp):
ATTTTTCAAATTTTATAATTTTGCCCTTATTTTTCAGATTTGATAGTTTTGCCCCT
Found at i:9201 original size:57 final size:58
Alignment explanation
Indices: 9051--9225 Score: 166
Period size: 57 Copynumber: 3.1 Consensus size: 58
9041 GATGTTGTAA
* * * * *
9051 TTTTG-CCCCTA-TTTCCAAATTTTATAATTTTGCC-CT-TATTTTTCAGATTTGATAG
1 TTTTGTCCCCTATTTTTCAAATTTTACAATTTTACCTCTAT-TTTTTTAGATTTTATAG
* * *
9106 TTTTGTCCCTTATTTTTCAAATTTTATAATTTTGCCTCTATTTTTTTAGATTTTATAG
1 TTTTGTCCCCTATTTTTCAAATTTTACAATTTTACCTCTATTTTTTTAGATTTTATAG
* * *
9164 TTTTG-CCCCTATTTTTTAGATTTTAC-ATATTTACCTCTATTATTTTTAAATTTT-TAAG
1 TTTTGTCCCCTATTTTTCAAATTTTACAAT-TTTACCTCTATT-TTTTTAGATTTTAT-AG
9222 TTTT
1 TTTT
9226 AGCCATTTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
55 5 0.05
56 7 0.07
57 51 0.50
58 39 0.38
59 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.07, T:0.57
Consensus pattern (58 bp):
TTTTGTCCCCTATTTTTCAAATTTTACAATTTTACCTCTATTTTTTTAGATTTTATAG
Found at i:9203 original size:28 final size:28
Alignment explanation
Indices: 9116--9249 Score: 82
Period size: 28 Copynumber: 4.8 Consensus size: 28
9106 TTTTGTCCCT
* * * * *
9116 TATTTTTCAAATTTTATAATTTTGCCTC
1 TATTTTTTAGATTTTACAGTTTTACCTC
* * *
9144 TATTTTTTTAGATTTTATAGTTTTGCCCC
1 TA-TTTTTTAGATTTTACAGTTTTACCTC
9173 TATTTTTTAGATTTTACA-TATTTACCTC
1 TATTTTTTAGATTTTACAGT-TTTACCTC
* *
9201 TATTATTTTTAAATTTTTA-AGTTTTAGC-C
1 TA-T-TTTTTAGA-TTTTACAGTTTTACCTC
*
9230 -A--TTTTAGATTTTACAATTTT
1 TATTTTTTAGATTTTACAGTTTT
9250 GCCCAGAATT
Statistics
Matches: 88, Mismatches: 11, Indels: 18
0.75 0.09 0.15
Matches are distributed among these distances:
23 5 0.06
24 11 0.12
27 1 0.01
28 26 0.30
29 26 0.30
30 13 0.15
31 6 0.07
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (28 bp):
TATTTTTTAGATTTTACAGTTTTACCTC
Found at i:17139 original size:14 final size:14
Alignment explanation
Indices: 17120--17153 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17110 AGTGAAATTA
17120 TCTTTACCCGTGAT
1 TCTTTACCCGTGAT
*
17134 TCTTTACTCGTGAT
1 TCTTTACCCGTGAT
*
17148 TTTTTA
1 TCTTTA
17154 TCCTTTTCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.53
Consensus pattern (14 bp):
TCTTTACCCGTGAT
Done.