Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012869.1 Kokia drynarioides strain JFW-HI SEQ_127883, 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: 30245
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:291 original size:24 final size:24
Alignment explanation
Indices: 264--325 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
254 AAAAAAATAT
*
264 ATATTTAA-TATTCAAAAGTATGTC
1 ATATTTAAGCATT-AAAAGTATGTC
288 ATATTTAAGCATTAAAAGTATGTC
1 ATATTTAAGCATTAAAAGTATGTC
312 ATATTTAAGCATTA
1 ATATTTAAGCATTA
326 TCATTGTCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 33 0.92
25 3 0.08
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (24 bp):
ATATTTAAGCATTAAAAGTATGTC
Found at i:5806 original size:7 final size:7
Alignment explanation
Indices: 5796--5838 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
5786 AAATGAAGAC
5796 TGAAAAG
1 TGAAAAG
5803 TGAAAAG
1 TGAAAAG
5810 TGAAAAG
1 TGAAAAG
5817 TGAAAAG
1 TGAAAAG
5824 TGAAAAG
1 TGAAAAG
5831 TGAAAAG
1 TGAAAAG
5838 T
1 T
5839 TTAATTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (7 bp):
TGAAAAG
Found at i:5808 original size:21 final size:21
Alignment explanation
Indices: 5784--5836 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5774 AAATAAAAAT
* *
5784 AAAAATGAAGACTGAAAAGTG
1 AAAAGTGAAAACTGAAAAGTG
*
5805 AAAAGTGAAAAGTGAAAAGTG
1 AAAAGTGAAAACTGAAAAGTG
5826 AAAAGTGAAAA
1 AAAAGTGAAAA
5837 GTTTAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.60, C:0.02, G:0.25, T:0.13
Consensus pattern (21 bp):
AAAAGTGAAAACTGAAAAGTG
Found at i:14680 original size:30 final size:29
Alignment explanation
Indices: 14638--14707 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
14628 CTCCAATTGT
* * *
14638 AAATTTGGAGGGTTTTAGTTGAA-TCACAA
1 AAATTAGGAGGGTTCTAATT-AAGTCACAA
*
14667 AAATTAGGAAGGGTTCTAATTAAGTCATAA
1 AAATTAGG-AGGGTTCTAATTAAGTCACAA
14697 AAATTA-GAGGG
1 AAATTAGGAGGG
14708 AATGTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.11
29 10 0.29
30 21 0.60
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.30
Consensus pattern (29 bp):
AAATTAGGAGGGTTCTAATTAAGTCACAA
Found at i:18743 original size:24 final size:23
Alignment explanation
Indices: 18705--18758 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
18695 GGAAAAGGAG
18705 AAGAGAATAAAAAGA-GAAAGAAA
1 AAGA-AATAAAAAGACGAAAGAAA
*
18728 AATGAAATAAATAAGACTAAAGAAA
1 AA-GAAATAAA-AAGACGAAAGAAA
18753 AAGAAA
1 AAGAAA
18759 AGAAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 8 0.30
24 10 0.37
25 9 0.33
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (23 bp):
AAGAAATAAAAAGACGAAAGAAA
Found at i:22039 original size:24 final size:24
Alignment explanation
Indices: 22011--22057 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
22001 AGAATTTGAC
22011 TGAAACAAATAAACAAAGTTTAAT
1 TGAAACAAATAAACAAAGTTTAAT
* * *
22035 TGAAACAAGTAAATAGAGTTTAA
1 TGAAACAAATAAACAAAGTTTAA
22058 CTAGAAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (24 bp):
TGAAACAAATAAACAAAGTTTAAT
Found at i:22515 original size:18 final size:18
Alignment explanation
Indices: 22488--22530 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
22478 CGCATAAAAA
* *
22488 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
22506 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
22524 GAAAGAA
1 GAAAGAA
22531 GGGTAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:26423 original size:12 final size:11
Alignment explanation
Indices: 26396--26422 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
26386 TTTTTTTCAG
26396 AAAAATACGAC
1 AAAAATACGAC
26407 AAAAATACGAC
1 AAAAATACGAC
26418 AAAAA
1 AAAAA
26423 AACACCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAATACGAC
Found at i:26674 original size:4 final size:4
Alignment explanation
Indices: 26665--26730 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
26655 AAATAAACGG
* * *
26665 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* *
26715 G-AA GAAG GAGA GAAA G
1 GAAA GAAA GAAA GAAA G
26731 GTAATGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 40 0.78
5 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:26687 original size:17 final size:17
Alignment explanation
Indices: 26665--26697 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
26655 AAATAAACGG
26665 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
26682 GAAAGAAAGAAAGGAA
1 GAAAGAAAGAAAGGAA
26698 GAAGGAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:26710 original size:17 final size:16
Alignment explanation
Indices: 26672--26731 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 16
26662 CGGGAAAGAA
* *
26672 AGAAAGGAAAGAAAGAA
1 AGAAAGG-AAGAAGGAG
26689 AGAAAGGAAGAAGGAG
1 AGAAAGGAAGAAGGAG
26705 AGGAAAGAAAGAAGAAGGAG
1 A-GAAAG---GAAGAAGGAG
26725 AGAAAGG
1 AGAAAGG
26732 TAATGTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 9 0.24
17 12 0.32
19 5 0.14
20 11 0.30
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AGAAAGGAAGAAGGAG
Found at i:26731 original size:29 final size:30
Alignment explanation
Indices: 26667--26731 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
26657 ATAAACGGGA
26667 AAGAAA-GAAAGGAAAGAAAGAAAGAAAGG
1 AAGAAAGGAAAGGAAAGAAAGAAAGAAAGG
*
26696 AAG-AAGGAGAGGAAAGAAAG-AAG-AAGG
1 AAGAAAGGAAAGGAAAGAAAGAAAGAAAGG
26723 AGAGAAAGG
1 A-AGAAAGG
26732 TAATGTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 5 0.16
28 7 0.22
29 20 0.62
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (30 bp):
AAGAAAGGAAAGGAAAGAAAGAAAGAAAGG
Found at i:30074 original size:21 final size:21
Alignment explanation
Indices: 30050--30092 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30040 TAAGGTCTAT
* *
30050 TTGCCCTGGAGGAGTAAAGTA
1 TTGCCCGGGAGGAATAAAGTA
*
30071 TTGCCCGGGAGGAATAGAGTA
1 TTGCCCGGGAGGAATAAAGTA
30092 T
1 T
30093 CGCGATGGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (21 bp):
TTGCCCGGGAGGAATAAAGTA
Found at i:30217 original size:45 final size:45
Alignment explanation
Indices: 30087--30223 Score: 184
Period size: 45 Copynumber: 3.0 Consensus size: 45
30077 GGGAGGAATA
* * * * * * **
30087 GAGTATCGCGATGGCTCGTCAAACTCAGCCTAATATCCTTCCCTT
1 GAGTATTGCGGTGGCTAGTCAAACTGAGGCTGATATCCTTGGCTT
*
30132 GAGTATTGCGGTGGCTAGTCAAATTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTAGTCAAACTGAGGCTGATATCCTTGGCTT
*
30177 GAGTATTGCGGTGGCTTGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTAGTCAAACTGAGGCTGATATCCTTGGCTT
30222 GA
1 GA
30224 TGAGCTATGC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTAGTCAAACTGAGGCTGATATCCTTGGCTT
Done.