Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011660.1 Kokia drynarioides strain JFW-HI SEQ_126652, 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: 24663
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:591 original size:25 final size:25
Alignment explanation
Indices: 555--604 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
545 TATATGTTAC
*
555 ATATACAAAT-AATTATATGTATTTA
1 ATATACAAATAAATTA-ATGCATTTA
580 ATATA-AAGATAAATTAATGCATTTA
1 ATATACAA-ATAAATTAATGCATTTA
605 TTTCTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 2 0.09
25 15 0.68
26 5 0.23
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (25 bp):
ATATACAAATAAATTAATGCATTTA
Found at i:881 original size:33 final size:28
Alignment explanation
Indices: 820--884 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 28
810 CCAAGGCTAA
820 AAGGGGCCAAAATATTTTTTCAGATTTT
1 AAGGGGCCAAAATATTTTTTCAGATTTT
*
848 AAGGGGCTCAAAAATTATTTTTTTCAGCTTTTT
1 AAGGGGC-C-AAAA-TA-TTTTTTCAG-ATTTT
881 AAGG
1 AAGG
885 ATCCAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 7 0.23
29 1 0.03
30 4 0.13
31 2 0.06
32 9 0.29
33 8 0.26
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (28 bp):
AAGGGGCCAAAATATTTTTTCAGATTTT
Found at i:2461 original size:16 final size:16
Alignment explanation
Indices: 2440--2472 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2430 AGACTAACCG
2440 CGCCACTACTCCTATT
1 CGCCACTACTCCTATT
2456 CGCCACTACTCCTATT
1 CGCCACTACTCCTATT
2472 C
1 C
2473 TCTCTGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.45, G:0.06, T:0.30
Consensus pattern (16 bp):
CGCCACTACTCCTATT
Found at i:12550 original size:18 final size:17
Alignment explanation
Indices: 12503--12551 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
12493 GAACTTTTAA
*
12503 TTTTAAA-TTTTAAAAC
1 TTTTAAATTTTTATAAC
*
12519 TTTGAATATTTTTATAAC
1 TTTTAA-ATTTTTATAAC
12537 TTTTAAATTATTTAT
1 TTTTAAATT-TTTAT
12552 TGACATGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.19
17 4 0.15
18 18 0.67
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTTAAATTTTTATAAC
Found at i:15569 original size:23 final size:23
Alignment explanation
Indices: 15495--15708 Score: 169
Period size: 23 Copynumber: 9.5 Consensus size: 23
15485 TAAACGGAAC
* * *
15495 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
15517 AAACAGAGAGCACA-AAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
15539 AGGCAACAGAGAGTACACAAAGTGCT
1 A---AACAGAGAGCACACAAAGTGCT
*
15565 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
15585 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
15604 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
15627 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
15652 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*** *
15675 AGTTAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
15698 AAACAGAGAGC
1 AAACAGAGAGC
15709 GCACTAATGT
Statistics
Matches: 156, Mismatches: 20, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
16 10 0.06
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 20 0.13
23 77 0.49
24 2 0.01
25 30 0.19
26 10 0.06
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:15659 original size:48 final size:46
Alignment explanation
Indices: 15588--15708 Score: 147
Period size: 48 Copynumber: 2.6 Consensus size: 46
15578 ACAAAGTACT
* *
15588 GAGCACACAAAGTGCTAATCAGAGAGCACACGA-AGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAACAGAGAGCACAC-ACAGTGCTAAT--CAGA
* * *
15636 GAGCACGAGAC-GTGCTAAACAGAGAGCACACACAGTGCTAGTTAGA
1 GAGCAC-ACACAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
15682 GAGCACACACAGTGCTAAACAGAGAGC
1 GAGCACACACAGTGCTAAACAGAGAGC
15709 GCACTAATGT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
45 3 0.05
46 25 0.39
47 1 0.02
48 33 0.52
49 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
Found at i:15809 original size:24 final size:26
Alignment explanation
Indices: 15771--15818 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
15761 TCTACATGGG
15771 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
15797 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
15819 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:18120 original size:17 final size:18
Alignment explanation
Indices: 18093--18126 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
18083 GCTTCAAGGA
18093 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
18111 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
18127 TAATTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Done.