Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013806.1 Kokia drynarioides strain JFW-HI SEQ_128834, 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: 50003
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:7839 original size:23 final size:24
Alignment explanation
Indices: 7808--7859 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
7798 AAATTTGATT
7808 ATTAATTTTTTAA-AAACAA-TCAA
1 ATTAATTTTTTAACAAA-AATTCAA
*
7831 ATTATTTTTTTAACAAAAATTCAA
1 ATTAATTTTTTAACAAAAATTCAA
7855 ATTAA
1 ATTAA
7860 AATATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTAATTTTTTAACAAAAATTCAA
Found at i:8137 original size:31 final size:31
Alignment explanation
Indices: 8102--8170 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
8092 TTAAAAAAAT
*
8102 AATTTAACTCTTTTTAAAAGATCAATAGTCA
1 AATTTAACTCTTTTTAAAAGATCAAGAGTCA
* * * **
8133 AATTTGATTCTTTTTAAAAGTTTGAGAGTCA
1 AATTTAACTCTTTTTAAAAGATCAAGAGTCA
8164 AATTTAA
1 AATTTAA
8171 TTAAAAAACA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (31 bp):
AATTTAACTCTTTTTAAAAGATCAAGAGTCA
Found at i:19429 original size:35 final size:36
Alignment explanation
Indices: 19390--19462 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
19380 GGAAAAAAGG
19390 ATTATTTCTTC-TATTTCTTTTCTCTTAAGTATTTA
1 ATTATTTCTTCATATTTCTTTTCTCTTAAGTATTTA
* *
19425 ATTATTTCTTCATTTTTCTTTTCTCTTAAGTGTTTA
1 ATTATTTCTTCATATTTCTTTTCTCTTAAGTATTTA
19461 AT
1 AT
19463 AAGAAGCTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 11 0.31
36 24 0.69
ACGTcount: A:0.19, C:0.14, G:0.04, T:0.63
Consensus pattern (36 bp):
ATTATTTCTTCATATTTCTTTTCTCTTAAGTATTTA
Found at i:24721 original size:17 final size:17
Alignment explanation
Indices: 24701--24734 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24691 TTTTCTGTCT
*
24701 TTTTCTTTTTGTTTTTG
1 TTTTCTTTTTATTTTTG
24718 TTTTCTTTTTATTTTTG
1 TTTTCTTTTTATTTTTG
24735 GATTTTGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.06, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTTATTTTTG
Found at i:28499 original size:31 final size:30
Alignment explanation
Indices: 28432--28512 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
28422 AATTATCTAT
*
28432 ATTTTTATAATTTTTAAAAGATTAAATCAA
1 ATTTTTATAATTTTTAAAAGATCAAATCAA
* *
28462 ATTTTTATCATTTTTAAAAGGATCAAAGT-GA
1 ATTTTTATAATTTTTAAAA-GATCAAA-TCAA
* *
28493 ATTTTTATAAATTATAAAAG
1 ATTTTTATAATTTTTAAAAG
28513 GGTTAAATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
30 19 0.44
31 23 0.53
32 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAGATCAAATCAA
Found at i:32974 original size:25 final size:25
Alignment explanation
Indices: 32940--32990 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
32930 TAAAAGTATA
32940 TCAGTTTAGGATTAAGAAATAAGAC
1 TCAGTTTAGGATTAAGAAATAAGAC
32965 TCAGTTTAGGATTAAGAAATAAGAC
1 TCAGTTTAGGATTAAGAAATAAGAC
32990 T
1 T
32991 ACAAGTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (25 bp):
TCAGTTTAGGATTAAGAAATAAGAC
Found at i:35605 original size:23 final size:23
Alignment explanation
Indices: 35575--35619 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
35565 GACAATGAGA
35575 TCAAACCAAGGGGAACGAAATTC
1 TCAAACCAAGGGGAACGAAATTC
35598 TCAAACCAAGGGGAACGAAATT
1 TCAAACCAAGGGGAACGAAATT
35620 ACTAGACAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (23 bp):
TCAAACCAAGGGGAACGAAATTC
Found at i:37127 original size:2 final size:2
Alignment explanation
Indices: 37120--37144 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37110 ATTATGCTAA
37120 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
37145 CACATTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37639 original size:27 final size:30
Alignment explanation
Indices: 37578--37636 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
37568 AATAAAATAA
*
37578 TAATCACTCAACTATTTAATTCATTCTATTT
1 TAATCACTCAACTATTTAATT-ATTCGATTT
*
37609 TAATCACTCAATTA-TTAATT-TTCGATTT
1 TAATCACTCAACTATTTAATTATTCGATTT
37637 AATTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.27
30 6 0.23
31 13 0.50
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (30 bp):
TAATCACTCAACTATTTAATTATTCGATTT
Found at i:46094 original size:20 final size:19
Alignment explanation
Indices: 46066--46107 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
46056 TTTTTTCTGA
*
46066 TTTTTTGCCTTTATTATCTC
1 TTTTATGCCTTTATTATC-C
*
46086 TTTTATGCCTTTCTTATCC
1 TTTTATGCCTTTATTATCC
46105 TTT
1 TTT
46108 GCATGCCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.10, C:0.21, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTATGCCTTTATTATCC
Found at i:46113 original size:20 final size:20
Alignment explanation
Indices: 46071--46114 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
46061 TCTGATTTTT
*
46071 TGCCTTTATTATCTCTTTTA
1 TGCCTTTATTATCTCTTTCA
*
46091 TGCCTTTCTTATC-CTTTGCA
1 TGCCTTTATTATCTCTTT-CA
46111 TGCC
1 TGCC
46115 AATCTTGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.11, C:0.27, G:0.09, T:0.52
Consensus pattern (20 bp):
TGCCTTTATTATCTCTTTCA
Done.