Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014464.1 Kokia drynarioides strain JFW-HI SEQ_129503, 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: 7682
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.31
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:2027 original size:206 final size:206
Alignment explanation
Indices: 1670--2224 Score: 779
Period size: 206 Copynumber: 2.7 Consensus size: 206
1660 ACAAACAGTG
* * * * * *
1670 ATGCGGTCACCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACGAGGCTCAAAGTG
1 ATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATC-A--AACCCACGCTCGATGTG
* * *
1735 AGTAAATCTTCAAACCCCAGCTTCCTAACGAGATACTAAGAGGCAGGTCGAAGCAATAAAACGGT
63 AGCAAATCTTCAAACCCCAGCTTCCTGACGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGGT
*
1800 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCG
128 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCA
* *
1865 GATTGAAACAAGCA
193 AATTGAAACAAACA
1879 ATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
1 ATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
* * * *
1944 AAATCTTCAAATCCTAACTTCCTGACGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAG
66 AAATCTTCAAACCCCAGCTTCCTGACGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGGTTAG
2009 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCAAAT
131 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCAAAT
**
2074 TGAAACAAATG
196 TGAAACAAACA
* * * * *
2085 ACGCAGTCATCTTCCTGATGAGATA-TCGAGAAGAAGACCAAGTCAAGCCCACGCTCGGTGTGAG
1 ATGCGGTCATCTTCCTGATGAGATACT-GAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAG
* * * * * **
2149 CAAACCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCTGGTCGAAATAATAAAACGGATT
65 CAAATCTTCAAACCCCAGCTTCCTGACGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGG-TT
*
2214 AGCATCCTGAT
129 AGCTTCCTGAT
2225 ACGGGGAAGT
Statistics
Matches: 309, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
205 1 0.00
206 252 0.82
207 12 0.04
208 1 0.00
209 43 0.14
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (206 bp):
ATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
AAATCTTCAAACCCCAGCTTCCTGACGAGATACTAAGAAGCAGGTCGAAGCAATAAAACGGTTAG
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCAAAT
TGAAACAAACA
Found at i:2702 original size:6 final size:6
Alignment explanation
Indices: 2693--2775 Score: 82
Period size: 6 Copynumber: 14.2 Consensus size: 6
2683 CAAATTTATT
* **
2693 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTATCT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
** *
2741 TTT-GC TTTAAA TTTAAA TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
2776 GGATTTAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
5 11 0.18
6 46 0.75
7 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:2714 original size:17 final size:17
Alignment explanation
Indices: 2684--2775 Score: 121
Period size: 17 Copynumber: 5.2 Consensus size: 17
2674 AAATTGATTC
2684 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAATTT
2702 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
2719 AAATTTATCTTTTAAATTT
1 AAATTTA--TTTTAAATTT
**
2738 AAATTTGCTTTAAATTT
1 AAATTTATTTTAAATTT
* *
2755 AAATTTAATTAAAATTT
1 AAATTTATTTTAAATTT
2772 AAAT
1 AAAT
2776 GGATTTAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
17 44 0.66
18 7 0.10
19 16 0.24
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:2735 original size:36 final size:35
Alignment explanation
Indices: 2684--2775 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 35
2674 AAATTGATTC
*
2684 AAATTTATTTTTAAATTTAAATTTATTTTAAATTT
1 AAATTTATTTTTAAATTTAAATTTACTTTAAATTT
*
2719 AAATTTATCTTTTAAATTTAAATTTGCTTTAAATTT
1 AAATTTAT-TTTTAAATTTAAATTTACTTTAAATTT
* *
2755 AAATTTA-ATTAAAATTTAAAT
1 AAATTTATTTTTAAATTTAAAT
2776 GGATTTAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 12 0.23
35 8 0.15
36 32 0.62
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (35 bp):
AAATTTATTTTTAAATTTAAATTTACTTTAAATTT
Found at i:2764 original size:11 final size:12
Alignment explanation
Indices: 2693--2775 Score: 82
Period size: 11 Copynumber: 7.1 Consensus size: 12
2683 CAAATTTATT
2693 TTTAAATTTAAA
1 TTTAAATTTAAA
*
2705 TTT-ATTTTAAA
1 TTTAAATTTAAA
**
2716 TTTAAATTTATCT
1 TTTAAATTTA-AA
2729 TTTAAATTTAAA
1 TTTAAATTTAAA
**
2741 TTT-GCTTTAAA
1 TTTAAATTTAAA
2752 TTTAAATTT-AA
1 TTTAAATTTAAA
*
2763 TTAAAATTTAAA
1 TTTAAATTTAAA
2775 T
1 T
2776 GGATTTAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
11 29 0.52
12 17 0.30
13 10 0.18
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:2994 original size:21 final size:20
Alignment explanation
Indices: 2970--3011 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
2960 GCCATGTCAT
*
2970 CGACACGTAATGACGCGACGA
1 CGACACGTAATAACGCG-CGA
2991 CGACACGTAATAACGCGCGA
1 CGACACGTAATAACGCGCGA
3011 C
1 C
3012 CGCGGAAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.33, C:0.31, G:0.26, T:0.10
Consensus pattern (20 bp):
CGACACGTAATAACGCGCGA
Found at i:3746 original size:51 final size:50
Alignment explanation
Indices: 3666--3772 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 50
3656 CCGAAACTGT
* *
3666 CCAAAAATTCCATTTTCACCCCCGTACTTCTAAAAAATTCCATTTTTAACC
1 CCAAAAATTCCATTTTCACCCCCGAACTTC-AAAAAATCCCATTTTTAACC
* * *
3717 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACC
1 CCAAAAATTCCATTTTCACCCCCGAACTTCAAAAAATCCCATTTTTAACC
*
3767 TCAAAA
1 CCAAAA
3773 CTTCTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
50 23 0.46
51 27 0.54
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.32
Consensus pattern (50 bp):
CCAAAAATTCCATTTTCACCCCCGAACTTCAAAAAATCCCATTTTTAACC
Found at i:3759 original size:29 final size:30
Alignment explanation
Indices: 3717--3791 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
3707 ATTTTTAACC
* *
3717 CCAAAAATTCCATTTTTACCCTC-GAACTT
1 CCAAAAATTCCATTTTTAACCTCAAAACTT
*
3746 CCAAAAATCCCATTTTTAACCTCAAAACTT
1 CCAAAAATTCCATTTTTAACCTCAAAACTT
*
3776 CTAAAAATTCCATTTT
1 CCAAAAATTCCATTTT
3792 CGACCTCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 21 0.52
30 19 0.47
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.35
Consensus pattern (30 bp):
CCAAAAATTCCATTTTTAACCTCAAAACTT
Found at i:3798 original size:30 final size:28
Alignment explanation
Indices: 3719--3822 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 28
3709 TTTTAACCCC
* * *
3719 AAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATTCCA-TTTTAACCTCAAACTTCT
*
3748 AAAAATCCCATTTTTAACCTCAAAACTTCT
1 AAAAATTCCA-TTTTAACCTC-AAACTTCT
*
3778 AAAAATTCCATTTTCGACCTCGAAAC-TCT
1 AAAAATTCCATTTT-AACCTC-AAACTTCT
* *
3807 CAAAATTACCCTTTTA
1 AAAAATT-CCATTTTA
3823 CCCTTGAATG
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
29 32 0.52
30 30 0.48
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAAATTCCATTTTAACCTCAAACTTCT
Found at i:6065 original size:2 final size:2
Alignment explanation
Indices: 6060--6088 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6050 TATATATATA
6060 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
6089 AAATTTGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.