Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003378.1 Kokia drynarioides strain JFW-HI SEQ_116106, 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: 40146
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:2845 original size:15 final size:15
Alignment explanation
Indices: 2825--2863 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
2815 GTTGCTGACT
2825 TCATGGTTTTACCAC
1 TCATGGTTTTACCAC
2840 TCATGGTTTTACCAC
1 TCATGGTTTTACCAC
*
2855 TCAAGGTTT
1 TCATGGTTT
2864 GTGATGTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (15 bp):
TCATGGTTTTACCAC
Found at i:3862 original size:21 final size:22
Alignment explanation
Indices: 3831--3902 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
3821 AACTATAATA
*
3831 TTTTATATTTTTACCCAAAATC
1 TTTTATATTTTTACCCAAAAAC
**
3853 TTTT-TATTTTTTTCCAAAAAC
1 TTTTATATTTTTACCCAAAAAC
*
3874 TTTTACTCACTTTTT-CCCCAAAAC
1 TTTTA-T-A-TTTTTACCCAAAAAC
3898 TTTTA
1 TTTTA
3903 CCCCCTTCCC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 18 0.44
22 4 0.10
23 1 0.02
24 13 0.32
25 5 0.12
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTATATTTTTACCCAAAAAC
Found at i:3863 original size:22 final size:22
Alignment explanation
Indices: 3831--3901 Score: 65
Period size: 24 Copynumber: 3.1 Consensus size: 22
3821 AACTATAATA
*
3831 TTTTATATTTTTACCCAAAATCT
1 TTTTATATTTTT-CCCAAAAACT
*
3854 TTTTAT-TTTTTTCCAAAAAC-
1 TTTTATATTTTTCCCAAAAACT
*
3874 TTTTACTCACTTTTTCCCCAAAACT
1 TTTTA-T-A-TTTTTCCCAAAAACT
3899 TTT
1 TTT
3902 ACCCCCTTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 5 0.13
21 8 0.21
22 5 0.13
23 6 0.15
24 12 0.31
25 3 0.08
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTATATTTTTCCCAAAAACT
Found at i:4056 original size:19 final size:20
Alignment explanation
Indices: 4012--4056 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
4002 TCCCCAAAAA
* *
4012 CCCTCAAAACTTTTTATTTT
1 CCCTCAAAACTTTTTACTCT
4032 CCCTCAAAAC-TTTTACTCT
1 CCCTCAAAACTTTTTACTCT
*
4051 CTCTCA
1 CCCTCA
4057 CTTTCCCCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.42
Consensus pattern (20 bp):
CCCTCAAAACTTTTTACTCT
Found at i:18065 original size:27 final size:27
Alignment explanation
Indices: 18029--18091 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
18019 TTGCTGCTGC
18029 TGCTGTTGTGGAAACTGCAACTGTGGT
1 TGCTGTTGTGGAAACTGCAACTGTGGT
18056 TGCTGTTGTGGAAACTGCAACTGTGGT
1 TGCTGTTGTGGAAACTGCAACTGTGGT
18083 TGCTGTTGT
1 TGCTGTTGT
18092 TGTAGTTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.16, C:0.14, G:0.33, T:0.37
Consensus pattern (27 bp):
TGCTGTTGTGGAAACTGCAACTGTGGT
Found at i:18451 original size:29 final size:28
Alignment explanation
Indices: 18419--18481 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
18409 TTTTATCATT
*
18419 CAACTATCATATATTTAAATTTGATCACC
1 CAACTATCA-ATATTTAAATTTAATCACC
* * * *
18448 CAACTATTAATTTTTCAATTTAATCTCC
1 CAACTATCAATATTTAAATTTAATCACC
18476 CAACTA
1 CAACTA
18482 ATAGTTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.40
Consensus pattern (28 bp):
CAACTATCAATATTTAAATTTAATCACC
Found at i:21120 original size:20 final size:20
Alignment explanation
Indices: 21087--21135 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
21077 TTTTTAAATT
* *
21087 AAAAAGTTTAAAAATTATAAA
1 AAAAAATTTAAAAATT-GAAA
21108 AAAAAATTTAAAAATTGAAA
1 AAAAAATTTAAAAATTGAAA
21128 AAAAAATT
1 AAAAAATT
21136 CAAATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAAAATTTAAAAATTGAAA
Found at i:21324 original size:28 final size:29
Alignment explanation
Indices: 21274--21335 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
21264 TTATTCAAAT
21274 ATTTTAAATAATTTTTAACATATATTATG
1 ATTTTAAATAATTTTTAACATATATTATG
*
21303 CTTTTAAAT-ATTTTTAACATATATTATG
1 ATTTTAAATAATTTTTAACATATATTATG
21331 ATTTT
1 ATTTT
21336 TTTATAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 23 0.74
29 8 0.26
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTAAATAATTTTTAACATATATTATG
Found at i:24424 original size:28 final size:28
Alignment explanation
Indices: 24392--24447 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
24382 CTATTTTACT
*
24392 CTTTTTAACTCTATTTGTAGAGTCTAAA
1 CTTTTTAACTCTATCTGTAGAGTCTAAA
24420 CTTTTTAACTCTATCTGTAGAGTCTAAA
1 CTTTTTAACTCTATCTGTAGAGTCTAAA
24448 TTATTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (28 bp):
CTTTTTAACTCTATCTGTAGAGTCTAAA
Found at i:27649 original size:17 final size:17
Alignment explanation
Indices: 27627--27661 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27617 ATTACAAAAC
*
27627 CAAATCTTATCAGATTA
1 CAAATCTTATAAGATTA
*
27644 CAAATCTTTTAAGATTA
1 CAAATCTTATAAGATTA
27661 C
1 C
27662 TTTCCCTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:30755 original size:23 final size:23
Alignment explanation
Indices: 30714--30757 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
30704 AATCTCCAAG
*
30714 ATTACAAAATCAAATATTATTAT
1 ATTACAAAATCAAAGATTATTAT
* *
30737 ATTACAAATTCTAAGATTATT
1 ATTACAAAATCAAAGATTATT
30758 TTCTCTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (23 bp):
ATTACAAAATCAAAGATTATTAT
Done.