Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007506.1 Kokia drynarioides strain JFW-HI SEQ_122130, 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: 72374
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:8482 original size:20 final size:19
Alignment explanation
Indices: 8453--8490 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
8443 TAATTAACAA
*
8453 AATATAATATATCAATTAT
1 AATATAATATAACAATTAT
8472 AATATTAATATAACAATTA
1 AATA-TAATATAACAATTA
8491 AAAATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATAATATAACAATTAT
Found at i:21989 original size:8 final size:8
Alignment explanation
Indices: 21976--22000 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21966 ATTTGCATTC
21976 ACATATAT
1 ACATATAT
21984 ACATATAT
1 ACATATAT
21992 ACATATAT
1 ACATATAT
22000 A
1 A
22001 TATCCGCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (8 bp):
ACATATAT
Found at i:25263 original size:22 final size:22
Alignment explanation
Indices: 25232--25277 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
25222 CAGGTAAAGA
*
25232 AAATTAGTAA-TATTATATATTT
1 AAATTAGTAACGATTATAT-TTT
*
25254 AAATTTGTAACGATTATATTTT
1 AAATTAGTAACGATTATATTTT
25276 AA
1 AA
25278 TAATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (22 bp):
AAATTAGTAACGATTATATTTT
Found at i:25882 original size:46 final size:46
Alignment explanation
Indices: 25818--25912 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
25808 ATATATCCAA
*
25818 TTTTTTTAATATTAATTTCATTATAGATTTTATCATATTTATCTTT
1 TTTTTTTAATATTAATTTCATTATAAATTTTATCATATTTATCTTT
* *
25864 TTTTTTTTATATTAATTTCATTATAAATTTTATCGTATTTATCTTT
1 TTTTTTTAATATTAATTTCATTATAAATTTTATCATATTTATCTTT
25910 TTT
1 TTT
25913 GATATAATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.65
Consensus pattern (46 bp):
TTTTTTTAATATTAATTTCATTATAAATTTTATCATATTTATCTTT
Found at i:27558 original size:3 final size:3
Alignment explanation
Indices: 27550--27592 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
27540 ATCTGCAACA
*
27550 TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
27593 GAAATGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:37059 original size:6 final size:6
Alignment explanation
Indices: 37050--37084 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
37040 TTAATTTGAG
* *
37050 TTCTCT TTCTCT TTCTCT TTCTCT CTCTCT CTCTC
1 TTCTCT TTCTCT TTCTCT TTCTCT TTCTCT TTCTC
37085 CAGTCTCCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (6 bp):
TTCTCT
Found at i:38248 original size:3 final size:3
Alignment explanation
Indices: 38240--38273 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
38230 TGTTTCTGTT
38240 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38274 AGGTATAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:49673 original size:2 final size:2
Alignment explanation
Indices: 49666--49692 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49656 TAAAGTTGTG
49666 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
49693 GATGGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60118 original size:25 final size:25
Alignment explanation
Indices: 60084--60133 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
60074 AATTTATTGG
60084 CTTAAAACTGACAAAACAAAACCGT
1 CTTAAAACTGACAAAACAAAACCGT
60109 CTTAAAACTGACAAAACAAAACCGT
1 CTTAAAACTGACAAAACAAAACCGT
60134 TCCTTTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (25 bp):
CTTAAAACTGACAAAACAAAACCGT
Found at i:62978 original size:24 final size:24
Alignment explanation
Indices: 62936--62983 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
62926 CACACAAATT
*
62936 TTAAAATTAAAAACTAAAAATAAA
1 TTAAAATTAAAAACAAAAAATAAA
* * *
62960 TTAAAATTGAAAAGAAAAAGTAAA
1 TTAAAATTAAAAACAAAAAATAAA
62984 CCATAATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (24 bp):
TTAAAATTAAAAACAAAAAATAAA
Found at i:66302 original size:15 final size:16
Alignment explanation
Indices: 66277--66313 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
66267 TATTCATGGT
66277 TATATTATATTT-TAAA
1 TATA-TATATTTATAAA
66293 TATATATATTTATAAA
1 TATATATATTTATAAA
66309 T-TATA
1 TATATA
66314 AATTAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATATATTTATAAA
Done.