Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008224.1 Kokia drynarioides strain JFW-HI SEQ_122888, 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: 8424
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:137 original size:55 final size:56
Alignment explanation
Indices: 54--164 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 56
44 TATGAATAAA
54 AAAAAATAATTTTTGGATGTTTGCCACCCAATGACTTACACCACTTTTATCAAATT
1 AAAAAATAATTTTTGGATGTTTGCCACCCAATGACTTACACCACTTTTATCAAATT
* * * * *
110 AAAAAAT-TTTTTTGGGTGTTTGCCACCCAATGACTTGCACCATTTTTTTCAAATT
1 AAAAAATAATTTTTGGATGTTTGCCACCCAATGACTTACACCACTTTTATCAAATT
165 TAATTTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 43 0.86
56 7 0.14
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (56 bp):
AAAAAATAATTTTTGGATGTTTGCCACCCAATGACTTACACCACTTTTATCAAATT
Found at i:420 original size:57 final size:55
Alignment explanation
Indices: 237--485 Score: 198
Period size: 57 Copynumber: 4.5 Consensus size: 55
227 AATTGAGTGT
* * * * *
237 TTGCC-ACTCAATGATCTACATCACCTTTTCCAAATTTAAAAATATTTTTTTGGTGT
1 TTGCCAAC-CAATGACCTACACCATCTTTTCCAGATTTAAAAATATTTTTTT-GTGA
* ** *** * ** *
293 TTGGCAAGTAATGGTGTACACCATCTTTCCCAGA-TT-AATTTTTTTTTTTGTGA
1 TTGCCAACCAATGACCTACACCATCTTTTCCAGATTTAAAAATATTTTTTTGTGA
* * * *
346 TTGCCATCCAATGACCTACACTATCTTTTTCAGATTTAAAAATATTTTTTTTGATGT
1 TTGCCAACCAATGACCTACACCATCTTTTCCAGATTTAAAAATA-TTTTTTTG-TGA
* ** * **
403 TTGGCAAGTAATGACCTACGCCATCTTTTTTAGATTTAAAAATATTTTTTTGTGA
1 TTGCCAACCAATGACCTACACCATCTTTTCCAGATTTAAAAATATTTTTTTGTGA
* *
458 TTGCCATCCAATGACCTACACTATCTTT
1 TTGCCAACCAATGACCTACACCATCTTT
486 ATTTTTCCCT
Statistics
Matches: 147, Mismatches: 41, Indels: 11
0.74 0.21 0.06
Matches are distributed among these distances:
53 27 0.18
54 12 0.08
55 29 0.20
56 39 0.27
57 40 0.27
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (55 bp):
TTGCCAACCAATGACCTACACCATCTTTTCCAGATTTAAAAATATTTTTTTGTGA
Found at i:438 original size:110 final size:111
Alignment explanation
Indices: 261--485 Score: 310
Period size: 112 Copynumber: 2.0 Consensus size: 111
251 TCTACATCAC
* ***
261 CTTTTCCAAATTTAAAAATATTTTTTTGGTGTTTGGCAAGTAATGGTGTACACCATCTTTCCCAG
1 CTTTTCCAAATTTAAAAATATTTTTTTGATGTTTGGCAAGTAATGACCTACACCATCTTTCCCAG
** *
326 A-TT-AATTTTTTTTTTTGTGATTGCCATCCAATGACCTACACTAT
66 ATTTAAAAATATTTTTTTGTGATTGCCATCCAATGACCTACACTAT
* * * ***
370 CTTTTTCAGATTTAAAAATATTTTTTTTGATGTTTGGCAAGTAATGACCTACGCCATCTTTTTTA
1 CTTTTCCAAATTTAAAAATA-TTTTTTTGATGTTTGGCAAGTAATGACCTACACCATCTTTCCCA
435 GATTTAAAAATATTTTTTTGTGATTGCCATCCAATGACCTACACTAT
65 GATTTAAAAATATTTTTTTGTGATTGCCATCCAATGACCTACACTAT
482 CTTT
1 CTTT
486 ATTTTTCCCT
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
109 18 0.18
110 38 0.38
111 2 0.02
112 42 0.42
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (111 bp):
CTTTTCCAAATTTAAAAATATTTTTTTGATGTTTGGCAAGTAATGACCTACACCATCTTTCCCAG
ATTTAAAAATATTTTTTTGTGATTGCCATCCAATGACCTACACTAT
Found at i:484 original size:55 final size:56
Alignment explanation
Indices: 334--485 Score: 216
Period size: 57 Copynumber: 2.7 Consensus size: 56
324 AGATTAATTT
334 TTTTTTTTGTGATTGCCATCCAATGACCTACACTATCTTTTTCAGATTTAAAAATA
1 TTTTTTTTGTGATTGCCATCCAATGACCTACACTATCTTTTTCAGATTTAAAAATA
* * *** * * *
390 TTTTTTTTGATGTTTGGCAAGTAATGACCTACGCCATCTTTTTTAGATTTAAAAATA
1 TTTTTTTTG-TGATTGCCATCCAATGACCTACACTATCTTTTTCAGATTTAAAAATA
447 -TTTTTTTGTGATTGCCATCCAATGACCTACACTATCTTT
1 TTTTTTTTGTGATTGCCATCCAATGACCTACACTATCTTT
486 ATTTTTCCCT
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
55 24 0.30
56 17 0.21
57 39 0.49
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45
Consensus pattern (56 bp):
TTTTTTTTGTGATTGCCATCCAATGACCTACACTATCTTTTTCAGATTTAAAAATA
Found at i:3631 original size:3 final size:3
Alignment explanation
Indices: 3623--3677 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
3613 AGCGCCTGTC
*
3623 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
3671 AGG AGA A
1 AGA AGA A
3678 TTTAGTTTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4186 original size:9 final size:9
Alignment explanation
Indices: 4152--4207 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 9
4142 AAAAATCTTT
4152 AAATTAT-A
1 AAATTATAA
4160 AAA-TAT-A
1 AAATTATAA
4167 AAATTACTAA
1 AAATTA-TAA
4177 AAATTATAAA
1 AAATTAT-AA
4187 AAAGTTATTAA
1 AAA-TTA-TAA
4198 AAATTATAA
1 AAATTATAA
4207 A
1 A
4208 TAACGGTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.17
8 5 0.12
9 6 0.14
10 15 0.36
11 8 0.19
12 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:4200 original size:21 final size:20
Alignment explanation
Indices: 4166--4207 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
4156 TATAAAATAT
4166 AAAATTACTAAAAATTATAA
1 AAAATTACTAAAAATTATAA
*
4186 AAAAGTTATTAAAAATTATAA
1 AAAA-TTACTAAAAATTATAA
4207 A
1 A
4208 TAACGGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATTACTAAAAATTATAA
Done.