Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008231.1 Kokia drynarioides strain JFW-HI SEQ_122895, 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: 45912
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:5575 original size:41 final size:41
Alignment explanation
Indices: 5518--5613 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 41
5508 TTGTTCGTAG
*
5518 AGAATTCTTGTCAAGGTGGAGATTGTTAAAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAAAATTGGGTGACT
* * *
5559 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTTGGTGAGT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAAAATTGGGTGACT
5600 AGAACTT-TTGTTAA
1 AGAA-TTCTTGTTAA
5614 AATAAAATTC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 48 0.96
42 2 0.04
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAAAATTGGGTGACT
Found at i:18843 original size:39 final size:38
Alignment explanation
Indices: 18796--18872 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 38
18786 TAAAATCATA
18796 TAATATTTT-TATATTTCAAAAAAATAA-TATAATAATTT
1 TAATATTTTGTAT-TTT-AAAAAAATAAGTATAATAATTT
*
18834 TAATAATTTTGTATTTTAAAAAAATAAGTTTAATAATTT
1 TAAT-ATTTTGTATTTTAAAAAAATAAGTATAATAATTT
18873 AAAAATCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
38 14 0.40
39 18 0.51
40 3 0.09
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (38 bp):
TAATATTTTGTATTTTAAAAAAATAAGTATAATAATTT
Found at i:18849 original size:38 final size:39
Alignment explanation
Indices: 18796--18872 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
18786 TAAAATCATA
*
18796 TAATATTTTTATATTTCAAAAAAATAA-TATAATAATTT
1 TAATAATTTTATATTTCAAAAAAATAAGTATAATAATTT
* * *
18834 TAATAATTTTGTATTTTAAAAAAATAAGTTTAATAATTT
1 TAATAATTTTATATTTCAAAAAAATAAGTATAATAATTT
18873 AAAAATCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 24 0.71
39 10 0.29
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (39 bp):
TAATAATTTTATATTTCAAAAAAATAAGTATAATAATTT
Found at i:26772 original size:6 final size:6
Alignment explanation
Indices: 26761--26797 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
26751 ATAATTCATA
* *
26761 TATTCC TATTCC CATACC TATTCC TATTCC TATTCC T
1 TATTCC TATTCC TATTCC TATTCC TATTCC TATTCC T
26798 GTATTTTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (6 bp):
TATTCC
Found at i:32493 original size:31 final size:31
Alignment explanation
Indices: 32450--32511 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
32440 TCATAGATGC
*
32450 TTTTTGCATAATATCTTCCTTGACATTAATG
1 TTTTTGCATAATATCTTCCTTGAAATTAATG
* *
32481 TTTTTGCCTAATATCTTCTTTGAAATTAATG
1 TTTTTGCATAATATCTTCCTTGAAATTAATG
32512 CATCTATGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.50
Consensus pattern (31 bp):
TTTTTGCATAATATCTTCCTTGAAATTAATG
Found at i:36556 original size:3 final size:3
Alignment explanation
Indices: 36548--36595 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
36538 ACTTGGGTTC
36548 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36595 T
1 T
36596 GTTTTCTTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:37398 original size:31 final size:28
Alignment explanation
Indices: 37341--37403 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 28
37331 ACAAATTTGG
*
37341 AATTTAGTCTTTATCTTTTTATTTTCATA
1 AATTTAGTCTTTATCTTTTTAATTTCA-A
37370 AATTTAGTTTCTTTAT-TTTTTAAATTTCAA
1 AATTTAG--TCTTTATCTTTTT-AATTTCAA
37400 AATT
1 AATT
37404 CAGGTCCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 7 0.23
30 10 0.33
31 13 0.43
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (28 bp):
AATTTAGTCTTTATCTTTTTAATTTCAA
Found at i:42703 original size:21 final size:21
Alignment explanation
Indices: 42679--42718 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42669 AAATATAATT
*
42679 AAAATACAAAATCACACAACA
1 AAAATACAAAACCACACAACA
*
42700 AAAATATAAAACCACACAA
1 AAAATACAAAACCACACAA
42719 ATACAAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.23, G:0.00, T:0.10
Consensus pattern (21 bp):
AAAATACAAAACCACACAACA
Done.