Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008250.1 Kokia drynarioides strain JFW-HI SEQ_122915, 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: 28857
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:7270 original size:17 final size:19
Alignment explanation
Indices: 7241--7289 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
7231 AAGTAATGAT
* *
7241 ATTAATCTATAAATTAAA-
1 ATTAATTTATAAAGTAAAC
7259 ATT-ATTTATAAAGTAAATC
1 ATTAATTTATAAAGTAAA-C
7278 ATTAATTTATAA
1 ATTAATTTATAA
7290 CATCTATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 12 0.46
18 3 0.12
19 3 0.12
20 8 0.31
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTAATTTATAAAGTAAAC
Found at i:10270 original size:3 final size:3
Alignment explanation
Indices: 10262--10291 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
10252 AGCCCTTTGT
10262 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
10292 GTGGTTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:17462 original size:12 final size:11
Alignment explanation
Indices: 17440--17480 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
17430 AATTTCCTTG
17440 AGCTTCTTTTC
1 AGCTTCTTTTC
17451 AGCTTCCTTTTC
1 AGCTT-CTTTTC
17463 AGC-TCTTTT-
1 AGCTTCTTTTC
*
17472 AGCTGCTTT
1 AGCTTCTTT
17481 GGCTGCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 3 0.11
10 9 0.33
11 6 0.22
12 9 0.33
ACGTcount: A:0.10, C:0.27, G:0.12, T:0.51
Consensus pattern (11 bp):
AGCTTCTTTTC
Found at i:26406 original size:20 final size:20
Alignment explanation
Indices: 26368--26405 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
26358 TAATAAATTA
26368 TTAAAAATTATAATAAAAAT
1 TTAAAAATTATAATAAAAAT
*
26388 TTAAAAA-TATATTAAAAA
1 TTAAAAATTATAATAAAAA
26406 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAAAAATTATAATAAAAAT
Found at i:26417 original size:31 final size:31
Alignment explanation
Indices: 26354--26417 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
26344 TGTTAGATTT
** * *
26354 AATTTAATAAATTATTAAAAATTATAATAAA
1 AATTTAATAAATTATTAAAAAAAAAAAAAAA
26385 AATTTAA-AAATATATTAAAAAAAAAAAAAAA
1 AATTTAATAAAT-TATTAAAAAAAAAAAAAAA
26416 AA
1 AA
26418 AAATTCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (31 bp):
AATTTAATAAATTATTAAAAAAAAAAAAAAA
Found at i:27063 original size:18 final size:19
Alignment explanation
Indices: 27040--27082 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
27030 TTTTTTTGAA
*
27040 AATTTTATAAAT-ACTTTG
1 AATTTTAAAAATCACTTTG
*
27058 AATTTTAAAAATCATTTTG
1 AATTTTAAAAATCACTTTG
27077 AATTTT
1 AATTTT
27083 TGAAAGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
AATTTTAAAAATCACTTTG
Found at i:27078 original size:19 final size:18
Alignment explanation
Indices: 27040--27102 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 18
27030 TTTTTTTGAA
* *
27040 AATTTTATAAATACTTTG
1 AATTTTAAAAATATTTTG
27058 AATTTTAAAAATCATTTTG
1 AATTTTAAAAAT-ATTTTG
**
27077 AATTTTTGAAAGTTATTTTG
1 AA-TTTT-AAAAATATTTTG
27097 AATTTT
1 AATTTT
27103 TAATCAAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 11 0.29
19 11 0.29
20 12 0.32
21 4 0.11
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (18 bp):
AATTTTAAAAATATTTTG
Done.