Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012793.1 Kokia drynarioides strain JFW-HI SEQ_127806, 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: 4541
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:98 original size:28 final size:28
Alignment explanation
Indices: 58--111 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
48 TTCTAGTGGA
*
58 GAAAGTTAACTTTCTCTATGTGGAAAGC
1 GAAAGTTAACTTTCTCTATGGGGAAAGC
86 GAAAGTTAACTTTCTCTATGGGGAAA
1 GAAAGTTAACTTTCTCTATGGGGAAA
112 ATCAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (28 bp):
GAAAGTTAACTTTCTCTATGGGGAAAGC
Found at i:2875 original size:57 final size:57
Alignment explanation
Indices: 2814--2948 Score: 173
Period size: 57 Copynumber: 2.4 Consensus size: 57
2804 AATGGAGCCT
* *
2814 TTTGTGGCTGATTTTGTTAAAGAAAACCTTTGTGATTGAA-TCTATTAAAGTCAAACC
1 TTTGTGGCTGATTTTGTTAAAGAAAACCTATGTGACT-AATTCTATTAAAGTCAAACC
* * * * * * *
2871 TTTGTGACTGATTCTGTTAAAGAGAGCCTATGTGGCTAATTCTATTAAAGTGAAGCC
1 TTTGTGGCTGATTTTGTTAAAGAAAACCTATGTGACTAATTCTATTAAAGTCAAACC
2928 TTTGTGGCTGATTTTGTTAAA
1 TTTGTGGCTGATTTTGTTAAA
2949 ATGACCCTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
56 2 0.03
57 64 0.97
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (57 bp):
TTTGTGGCTGATTTTGTTAAAGAAAACCTATGTGACTAATTCTATTAAAGTCAAACC
Found at i:2947 original size:29 final size:29
Alignment explanation
Indices: 2775--2948 Score: 158
Period size: 29 Copynumber: 6.1 Consensus size: 29
2765 GTTTCTCGAA
*
2775 AAAGTG-AGCCTTTGTGGCTGATTCTATT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
* *
2803 AAA-TGGAGCCTTTTGTGGCTGATTTTGTT
1 AAAGTGAAGCC-TTTGTGGCTGATTCTGTT
* * ** * *
2832 AAAG-AAAACCTTTGTGATTGAATCTATT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
* * *
2860 AAAGTCAAACCTTTGTGACTGATTCTGTT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
* * * *
2889 AAAGAG-AGCCTATGTGGCTAATTCTATT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
*
2917 AAAGTGAAGCCTTTGTGGCTGATTTTGTT
1 AAAGTGAAGCCTTTGTGGCTGATTCTGTT
2946 AAA
1 AAA
2949 ATGACCCTCA
Statistics
Matches: 115, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
27 2 0.02
28 46 0.40
29 67 0.58
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (29 bp):
AAAGTGAAGCCTTTGTGGCTGATTCTGTT
Found at i:2989 original size:27 final size:28
Alignment explanation
Indices: 2774--2990 Score: 77
Period size: 29 Copynumber: 7.6 Consensus size: 28
2764 AGTTTCTCGA
* * *
2774 AAAAGTGAGCCTTTGTGGCTGATTCTATT
1 AAAAG-GACCCTTTGTGGCTGATTTTGTT
* *
2803 AAATGGAGCCTTTTGTGGCTGATTTTGTT
1 AAAAGGA-CCCTTTGTGGCTGATTTTGTT
* * ** * * *
2832 -AAAGAAAACCTTTGTGATTGAATCTATT
1 AAAAG-GACCCTTTGTGGCTGATTTTGTT
* * * *
2860 -AAAGTCAAACCTTTGTGACTGATTCTGTT
1 AAAAG--GACCCTTTGTGGCTGATTTTGTT
* * * * *
2889 -AAAGAGAGCCTATGTGGCTAATTCTATT
1 AAAAG-GACCCTTTGTGGCTGATTTTGTT
*
2917 -AAAGTGAAGCCTTTGTGGCTGATTTTGTT
1 AAAAG-G-ACCCTTTGTGGCTGATTTTGTT
* ** *
2946 AAAATGACCCTCAGTGGTTGATTTTG-T
1 AAAAGGACCCTTTGTGGCTGATTTTGTT
2973 -AAAGGACACCTTTGTGGC
1 AAAAGGAC-CCTTTGTGGC
2991 ATTGTTAATG
Statistics
Matches: 143, Mismatches: 39, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
26 6 0.04
27 8 0.06
28 61 0.43
29 65 0.45
30 3 0.02
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (28 bp):
AAAAGGACCCTTTGTGGCTGATTTTGTT
Found at i:3527 original size:29 final size:28
Alignment explanation
Indices: 3485--3649 Score: 147
Period size: 28 Copynumber: 5.8 Consensus size: 28
3475 GTTTCTCGAA
*
3485 AAAGTGAGCCTTTGTGGCTGATTCTATT
1 AAAGAGAGCCTTTGTGGCTGATTCTATT
* * *
3513 AAATG-GAGCCTTTTGTGGTTG-TTTTGTT
1 AAA-GAGAGCC-TTTGTGGCTGATTCTATT
* ** *
3541 AAAGAAAGCCTTTGTGATTGAATCTATT
1 AAAGAGAGCCTTTGTGGCTGATTCTATT
* *
3569 AAAGTTAGA-CCTTTGTGACTGATTCTGTT
1 AAAG--AGAGCCTTTGTGGCTGATTCTATT
* *
3598 AAAGAGAGCCTATGTGGCTAATTCTATT
1 AAAGAGAGCCTTTGTGGCTGATTCTATT
*
3626 AAAGTGAAGCCTTTGTGGCTGATT
1 AAAGAG-AGCCTTTGTGGCTGATT
3650 TTGTTAAAAT
Statistics
Matches: 110, Mismatches: 19, Indels: 15
0.76 0.13 0.10
Matches are distributed among these distances:
27 13 0.12
28 49 0.45
29 46 0.42
30 2 0.02
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (28 bp):
AAAGAGAGCCTTTGTGGCTGATTCTATT
Found at i:3624 original size:57 final size:58
Alignment explanation
Indices: 3485--3657 Score: 187
Period size: 57 Copynumber: 3.1 Consensus size: 58
3475 GTTTCTCGAA
* * * *
3485 AAAGTGAGCCTTTGTGGCTGATTCTATTAAA--TGGAGCCTTTTGTGGTTG-TTTTGTT
1 AAAGAGAGCCTTTGTGGCTAATTCTATTAAAGTTAGAGCC-TTTGTGGCTGATTTTGTT
* ** * *
3541 AAAGAAAGCCTTTGTGATTGAA-TCTATTAAAGTTAGA-CCTTTGTGACTGATTCTGTT
1 AAAGAGAGCCTTTGTGGCT-AATTCTATTAAAGTTAGAGCCTTTGTGGCTGATTTTGTT
* *
3598 AAAGAGAGCCTATGTGGCTAATTCTATTAAAGTGA-AGCCTTTGTGGCTGATTTTGTT
1 AAAGAGAGCCTTTGTGGCTAATTCTATTAAAGTTAGAGCCTTTGTGGCTGATTTTGTT
3655 AAA
1 AAA
3658 ATGACCCTCA
Statistics
Matches: 95, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
56 35 0.37
57 57 0.60
58 3 0.03
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (58 bp):
AAAGAGAGCCTTTGTGGCTAATTCTATTAAAGTTAGAGCCTTTGTGGCTGATTTTGTT
Found at i:3656 original size:29 final size:28
Alignment explanation
Indices: 3485--3657 Score: 152
Period size: 29 Copynumber: 6.1 Consensus size: 28
3475 GTTTCTCGAA
*
3485 AAAGTGAGCCTTTGTGGCTGATTCTATT
1 AAAGTGAGCCTTTGTGGCTGATTCTGTT
* *
3513 AAA-TGGAGCCTTTTGTGGTTG-TTTTGTT
1 AAAGT-GAGCC-TTTGTGGCTGATTCTGTT
** ** * *
3541 AAAGAAAGCCTTTGTGATTGAATCTATT
1 AAAGTGAGCCTTTGTGGCTGATTCTGTT
* *
3569 AAAGTTAGACCTTTGTGACTGATTCTGTT
1 AAAGTGAG-CCTTTGTGGCTGATTCTGTT
* * * *
3598 AAAGAGAGCCTATGTGGCTAATTCTATT
1 AAAGTGAGCCTTTGTGGCTGATTCTGTT
*
3626 AAAGTGAAGCCTTTGTGGCTGATTTTGTT
1 AAAGTG-AGCCTTTGTGGCTGATTCTGTT
3655 AAA
1 AAA
3658 ATGACCCTCA
Statistics
Matches: 114, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
27 10 0.09
28 51 0.45
29 53 0.46
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (28 bp):
AAAGTGAGCCTTTGTGGCTGATTCTGTT
Found at i:3698 original size:27 final size:28
Alignment explanation
Indices: 3578--3699 Score: 72
Period size: 28 Copynumber: 4.4 Consensus size: 28
3568 TAAAGTTAGA
* * *
3578 CCTTTGTGACTGATTCTGTT-AAAGAGAG
1 CCTTTGTGGCTGATTTTGTTAAAAG-GAC
* * * * *
3606 CCTATGTGGCTAATTCTATT-AAAGTGAAG
1 CCTTTGTGGCTGATTTTGTTAAAAG-G-AC
*
3635 CCTTTGTGGCTGATTTTGTTAAAATGAC
1 CCTTTGTGGCTGATTTTGTTAAAAGGAC
** *
3663 CCTCAGTGGTTGATTTTG-T-AAAGGAC
1 CCTTTGTGGCTGATTTTGTTAAAAGGAC
3689 ACCTTTGTGGC
1 -CCTTTGTGGC
3700 ATAGTTAATG
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
26 6 0.08
27 8 0.11
28 37 0.51
29 19 0.26
30 3 0.04
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (28 bp):
CCTTTGTGGCTGATTTTGTTAAAAGGAC
Done.