Multiple sequence alignment - TraesCS4D01G123500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G123500 chr4D 100.000 2465 0 0 1 2465 108044058 108046522 0.000000e+00 4553.0
1 TraesCS4D01G123500 chr4D 84.010 394 54 7 1808 2198 397155701 397156088 1.080000e-98 370.0
2 TraesCS4D01G123500 chr4D 83.905 379 53 6 1808 2184 95174726 95175098 3.020000e-94 355.0
3 TraesCS4D01G123500 chr4D 87.444 223 22 2 1031 1253 108182889 108183105 4.070000e-63 252.0
4 TraesCS4D01G123500 chr4D 99.200 125 1 0 1 125 367993120 367993244 2.470000e-55 226.0
5 TraesCS4D01G123500 chr4B 92.971 1565 82 16 124 1676 168579082 168577534 0.000000e+00 2255.0
6 TraesCS4D01G123500 chr4B 93.179 777 45 2 1690 2465 168577342 168576573 0.000000e+00 1134.0
7 TraesCS4D01G123500 chr4B 83.453 139 22 1 2327 2465 567645054 567644917 7.160000e-26 128.0
8 TraesCS4D01G123500 chr4B 97.436 39 1 0 1690 1728 168192635 168192597 1.580000e-07 67.6
9 TraesCS4D01G123500 chr4A 92.036 1444 69 21 124 1552 468215557 468214145 0.000000e+00 1988.0
10 TraesCS4D01G123500 chr4A 98.361 122 2 0 1555 1676 468214037 468213916 5.340000e-52 215.0
11 TraesCS4D01G123500 chr4A 88.800 125 6 2 1693 1809 468213661 468213537 1.980000e-31 147.0
12 TraesCS4D01G123500 chr7D 81.226 522 75 18 1948 2465 368813916 368813414 1.370000e-107 399.0
13 TraesCS4D01G123500 chr7D 83.905 379 54 5 1808 2184 54442525 54442898 3.020000e-94 355.0
14 TraesCS4D01G123500 chr7D 82.609 391 57 7 1809 2197 159897954 159897573 3.930000e-88 335.0
15 TraesCS4D01G123500 chr6A 77.293 665 119 25 1808 2465 508855323 508854684 1.800000e-96 363.0
16 TraesCS4D01G123500 chr7B 79.278 526 84 17 1948 2465 313768884 313769392 6.530000e-91 344.0
17 TraesCS4D01G123500 chr1D 76.506 664 132 18 1808 2465 423918740 423918095 8.440000e-90 340.0
18 TraesCS4D01G123500 chr2D 83.146 356 52 6 1808 2161 435208473 435208822 3.960000e-83 318.0
19 TraesCS4D01G123500 chr2D 98.413 126 2 0 1 126 55125963 55126088 3.190000e-54 222.0
20 TraesCS4D01G123500 chr2D 98.413 126 2 0 1 126 315432897 315433022 3.190000e-54 222.0
21 TraesCS4D01G123500 chr2D 92.763 152 8 2 1 149 36106409 36106560 1.480000e-52 217.0
22 TraesCS4D01G123500 chr3B 81.170 393 65 7 1808 2198 733346171 733346556 8.560000e-80 307.0
23 TraesCS4D01G123500 chr3D 99.206 126 1 0 1 126 377985694 377985819 6.860000e-56 228.0
24 TraesCS4D01G123500 chr3D 97.710 131 3 0 1 131 533806495 533806625 2.470000e-55 226.0
25 TraesCS4D01G123500 chr6D 100.000 122 0 0 4 125 325735886 325735765 2.470000e-55 226.0
26 TraesCS4D01G123500 chr5D 100.000 122 0 0 4 125 519846920 519846799 2.470000e-55 226.0
27 TraesCS4D01G123500 chr5D 97.674 129 3 0 1 129 139127849 139127977 3.190000e-54 222.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G123500 chr4D 108044058 108046522 2464 False 4553.000000 4553 100.000000 1 2465 1 chr4D.!!$F2 2464
1 TraesCS4D01G123500 chr4B 168576573 168579082 2509 True 1694.500000 2255 93.075000 124 2465 2 chr4B.!!$R3 2341
2 TraesCS4D01G123500 chr4A 468213537 468215557 2020 True 783.333333 1988 93.065667 124 1809 3 chr4A.!!$R1 1685
3 TraesCS4D01G123500 chr7D 368813414 368813916 502 True 399.000000 399 81.226000 1948 2465 1 chr7D.!!$R2 517
4 TraesCS4D01G123500 chr6A 508854684 508855323 639 True 363.000000 363 77.293000 1808 2465 1 chr6A.!!$R1 657
5 TraesCS4D01G123500 chr7B 313768884 313769392 508 False 344.000000 344 79.278000 1948 2465 1 chr7B.!!$F1 517
6 TraesCS4D01G123500 chr1D 423918095 423918740 645 True 340.000000 340 76.506000 1808 2465 1 chr1D.!!$R1 657

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
50 51 0.103937 GATGCACTCCTTCCCTCTCG 59.896 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1818 1.039856 GAGAGGCTGGAGAGATGGTC 58.96 60.0 0.0 0.0 0.0 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.579787 CGTTTCCGCTCGCGATCT 60.580 61.111 10.36 0.00 42.83 2.75
18 19 1.298116 CGTTTCCGCTCGCGATCTA 60.298 57.895 10.36 0.00 42.83 1.98
19 20 1.529883 CGTTTCCGCTCGCGATCTAC 61.530 60.000 10.36 0.00 42.83 2.59
20 21 0.524816 GTTTCCGCTCGCGATCTACA 60.525 55.000 10.36 0.00 42.83 2.74
21 22 0.171679 TTTCCGCTCGCGATCTACAA 59.828 50.000 10.36 0.00 42.83 2.41
22 23 0.248498 TTCCGCTCGCGATCTACAAG 60.248 55.000 10.36 0.00 42.83 3.16
23 24 1.658717 CCGCTCGCGATCTACAAGG 60.659 63.158 10.36 0.00 42.83 3.61
24 25 1.658717 CGCTCGCGATCTACAAGGG 60.659 63.158 10.36 0.00 42.83 3.95
25 26 1.437986 GCTCGCGATCTACAAGGGT 59.562 57.895 10.36 0.00 0.00 4.34
26 27 0.666913 GCTCGCGATCTACAAGGGTA 59.333 55.000 10.36 0.00 0.00 3.69
27 28 1.269998 GCTCGCGATCTACAAGGGTAT 59.730 52.381 10.36 0.00 0.00 2.73
28 29 2.922758 GCTCGCGATCTACAAGGGTATG 60.923 54.545 10.36 0.00 0.00 2.39
29 30 2.293677 CTCGCGATCTACAAGGGTATGT 59.706 50.000 10.36 0.00 37.32 2.29
30 31 3.479489 TCGCGATCTACAAGGGTATGTA 58.521 45.455 3.71 0.00 34.75 2.29
39 40 4.408182 ACAAGGGTATGTAGATGCACTC 57.592 45.455 0.00 0.00 25.83 3.51
40 41 3.134804 ACAAGGGTATGTAGATGCACTCC 59.865 47.826 0.00 0.00 25.83 3.85
41 42 3.336509 AGGGTATGTAGATGCACTCCT 57.663 47.619 0.00 0.00 0.00 3.69
42 43 3.658725 AGGGTATGTAGATGCACTCCTT 58.341 45.455 0.00 0.00 0.00 3.36
43 44 3.643792 AGGGTATGTAGATGCACTCCTTC 59.356 47.826 0.00 0.00 0.00 3.46
44 45 3.244249 GGGTATGTAGATGCACTCCTTCC 60.244 52.174 0.00 0.00 0.00 3.46
45 46 3.244249 GGTATGTAGATGCACTCCTTCCC 60.244 52.174 0.00 0.00 0.00 3.97
46 47 2.254152 TGTAGATGCACTCCTTCCCT 57.746 50.000 0.00 0.00 0.00 4.20
47 48 2.111384 TGTAGATGCACTCCTTCCCTC 58.889 52.381 0.00 0.00 0.00 4.30
48 49 2.292521 TGTAGATGCACTCCTTCCCTCT 60.293 50.000 0.00 0.00 0.00 3.69
49 50 1.494960 AGATGCACTCCTTCCCTCTC 58.505 55.000 0.00 0.00 0.00 3.20
50 51 0.103937 GATGCACTCCTTCCCTCTCG 59.896 60.000 0.00 0.00 0.00 4.04
51 52 0.616111 ATGCACTCCTTCCCTCTCGT 60.616 55.000 0.00 0.00 0.00 4.18
52 53 0.832135 TGCACTCCTTCCCTCTCGTT 60.832 55.000 0.00 0.00 0.00 3.85
53 54 0.390472 GCACTCCTTCCCTCTCGTTG 60.390 60.000 0.00 0.00 0.00 4.10
54 55 0.390472 CACTCCTTCCCTCTCGTTGC 60.390 60.000 0.00 0.00 0.00 4.17
55 56 0.543174 ACTCCTTCCCTCTCGTTGCT 60.543 55.000 0.00 0.00 0.00 3.91
56 57 1.272536 ACTCCTTCCCTCTCGTTGCTA 60.273 52.381 0.00 0.00 0.00 3.49
57 58 1.407258 CTCCTTCCCTCTCGTTGCTAG 59.593 57.143 0.00 0.00 0.00 3.42
58 59 1.187087 CCTTCCCTCTCGTTGCTAGT 58.813 55.000 0.00 0.00 0.00 2.57
59 60 2.025605 TCCTTCCCTCTCGTTGCTAGTA 60.026 50.000 0.00 0.00 0.00 1.82
60 61 2.758979 CCTTCCCTCTCGTTGCTAGTAA 59.241 50.000 0.00 0.00 0.00 2.24
61 62 3.194968 CCTTCCCTCTCGTTGCTAGTAAA 59.805 47.826 0.00 0.00 0.00 2.01
62 63 3.863142 TCCCTCTCGTTGCTAGTAAAC 57.137 47.619 0.00 0.00 0.00 2.01
63 64 3.428532 TCCCTCTCGTTGCTAGTAAACT 58.571 45.455 0.00 0.00 0.00 2.66
64 65 3.442977 TCCCTCTCGTTGCTAGTAAACTC 59.557 47.826 0.00 0.00 0.00 3.01
65 66 3.429135 CCCTCTCGTTGCTAGTAAACTCC 60.429 52.174 0.00 0.00 0.00 3.85
66 67 3.192844 CCTCTCGTTGCTAGTAAACTCCA 59.807 47.826 0.00 0.00 0.00 3.86
67 68 4.142138 CCTCTCGTTGCTAGTAAACTCCAT 60.142 45.833 0.00 0.00 0.00 3.41
68 69 5.067413 CCTCTCGTTGCTAGTAAACTCCATA 59.933 44.000 0.00 0.00 0.00 2.74
69 70 6.132791 TCTCGTTGCTAGTAAACTCCATAG 57.867 41.667 0.00 0.00 0.00 2.23
70 71 5.884232 TCTCGTTGCTAGTAAACTCCATAGA 59.116 40.000 0.00 0.00 0.00 1.98
71 72 6.546403 TCTCGTTGCTAGTAAACTCCATAGAT 59.454 38.462 0.00 0.00 0.00 1.98
72 73 7.068348 TCTCGTTGCTAGTAAACTCCATAGATT 59.932 37.037 0.00 0.00 0.00 2.40
73 74 6.978659 TCGTTGCTAGTAAACTCCATAGATTG 59.021 38.462 0.00 0.00 0.00 2.67
74 75 6.978659 CGTTGCTAGTAAACTCCATAGATTGA 59.021 38.462 0.00 0.00 0.00 2.57
75 76 7.653713 CGTTGCTAGTAAACTCCATAGATTGAT 59.346 37.037 0.00 0.00 0.00 2.57
76 77 8.983724 GTTGCTAGTAAACTCCATAGATTGATC 58.016 37.037 0.00 0.00 0.00 2.92
77 78 8.484214 TGCTAGTAAACTCCATAGATTGATCT 57.516 34.615 0.00 0.00 40.86 2.75
78 79 8.928448 TGCTAGTAAACTCCATAGATTGATCTT 58.072 33.333 0.00 0.00 38.32 2.40
79 80 9.202273 GCTAGTAAACTCCATAGATTGATCTTG 57.798 37.037 0.00 0.00 38.32 3.02
80 81 9.703892 CTAGTAAACTCCATAGATTGATCTTGG 57.296 37.037 0.00 7.19 38.32 3.61
81 82 8.095452 AGTAAACTCCATAGATTGATCTTGGT 57.905 34.615 15.48 5.78 38.32 3.67
82 83 7.989741 AGTAAACTCCATAGATTGATCTTGGTG 59.010 37.037 15.48 15.28 38.32 4.17
83 84 6.566079 AACTCCATAGATTGATCTTGGTGA 57.434 37.500 19.38 6.63 38.32 4.02
84 85 6.760440 ACTCCATAGATTGATCTTGGTGAT 57.240 37.500 19.38 0.00 38.32 3.06
85 86 6.531923 ACTCCATAGATTGATCTTGGTGATG 58.468 40.000 19.38 10.22 38.32 3.07
86 87 5.311265 TCCATAGATTGATCTTGGTGATGC 58.689 41.667 15.48 0.00 38.32 3.91
87 88 4.153655 CCATAGATTGATCTTGGTGATGCG 59.846 45.833 0.00 0.00 38.32 4.73
88 89 3.272574 AGATTGATCTTGGTGATGCGT 57.727 42.857 0.00 0.00 35.14 5.24
89 90 4.406648 AGATTGATCTTGGTGATGCGTA 57.593 40.909 0.00 0.00 35.14 4.42
90 91 4.375272 AGATTGATCTTGGTGATGCGTAG 58.625 43.478 0.00 0.00 35.14 3.51
91 92 3.885724 TTGATCTTGGTGATGCGTAGA 57.114 42.857 0.00 0.00 35.14 2.59
92 93 3.885724 TGATCTTGGTGATGCGTAGAA 57.114 42.857 0.00 0.00 35.14 2.10
93 94 4.200838 TGATCTTGGTGATGCGTAGAAA 57.799 40.909 0.00 0.00 35.14 2.52
94 95 4.574892 TGATCTTGGTGATGCGTAGAAAA 58.425 39.130 0.00 0.00 35.14 2.29
95 96 5.185454 TGATCTTGGTGATGCGTAGAAAAT 58.815 37.500 0.00 0.00 35.14 1.82
96 97 5.647658 TGATCTTGGTGATGCGTAGAAAATT 59.352 36.000 0.00 0.00 35.14 1.82
97 98 5.957842 TCTTGGTGATGCGTAGAAAATTT 57.042 34.783 0.00 0.00 0.00 1.82
98 99 6.325919 TCTTGGTGATGCGTAGAAAATTTT 57.674 33.333 2.28 2.28 0.00 1.82
99 100 6.148948 TCTTGGTGATGCGTAGAAAATTTTG 58.851 36.000 8.47 0.00 0.00 2.44
100 101 5.697473 TGGTGATGCGTAGAAAATTTTGA 57.303 34.783 8.47 0.00 0.00 2.69
101 102 6.078202 TGGTGATGCGTAGAAAATTTTGAA 57.922 33.333 8.47 0.00 0.00 2.69
102 103 6.686630 TGGTGATGCGTAGAAAATTTTGAAT 58.313 32.000 8.47 0.00 0.00 2.57
103 104 7.151308 TGGTGATGCGTAGAAAATTTTGAATT 58.849 30.769 8.47 0.00 0.00 2.17
104 105 7.655328 TGGTGATGCGTAGAAAATTTTGAATTT 59.345 29.630 8.47 0.00 0.00 1.82
105 106 8.162245 GGTGATGCGTAGAAAATTTTGAATTTC 58.838 33.333 8.47 0.00 36.11 2.17
106 107 8.915654 GTGATGCGTAGAAAATTTTGAATTTCT 58.084 29.630 8.47 0.48 45.29 2.52
107 108 8.914654 TGATGCGTAGAAAATTTTGAATTTCTG 58.085 29.630 8.47 0.00 43.67 3.02
108 109 7.104326 TGCGTAGAAAATTTTGAATTTCTGC 57.896 32.000 8.47 8.21 43.67 4.26
109 110 6.922957 TGCGTAGAAAATTTTGAATTTCTGCT 59.077 30.769 8.47 0.00 43.67 4.24
110 111 8.079203 TGCGTAGAAAATTTTGAATTTCTGCTA 58.921 29.630 8.47 0.00 43.67 3.49
111 112 8.365938 GCGTAGAAAATTTTGAATTTCTGCTAC 58.634 33.333 8.47 8.90 43.67 3.58
112 113 8.567221 CGTAGAAAATTTTGAATTTCTGCTACG 58.433 33.333 22.91 22.91 43.67 3.51
113 114 9.394477 GTAGAAAATTTTGAATTTCTGCTACGT 57.606 29.630 8.47 0.00 43.67 3.57
114 115 8.871686 AGAAAATTTTGAATTTCTGCTACGTT 57.128 26.923 8.47 0.00 42.62 3.99
115 116 9.959749 AGAAAATTTTGAATTTCTGCTACGTTA 57.040 25.926 8.47 0.00 42.62 3.18
116 117 9.989394 GAAAATTTTGAATTTCTGCTACGTTAC 57.011 29.630 8.47 0.00 33.72 2.50
117 118 8.515473 AAATTTTGAATTTCTGCTACGTTACC 57.485 30.769 0.00 0.00 0.00 2.85
118 119 5.616488 TTTGAATTTCTGCTACGTTACCC 57.384 39.130 0.00 0.00 0.00 3.69
119 120 4.274602 TGAATTTCTGCTACGTTACCCA 57.725 40.909 0.00 0.00 0.00 4.51
120 121 4.643463 TGAATTTCTGCTACGTTACCCAA 58.357 39.130 0.00 0.00 0.00 4.12
121 122 4.453136 TGAATTTCTGCTACGTTACCCAAC 59.547 41.667 0.00 0.00 0.00 3.77
122 123 3.472283 TTTCTGCTACGTTACCCAACA 57.528 42.857 0.00 0.00 34.05 3.33
194 196 1.225376 TGGCAAGTTGCTCGTAACCG 61.225 55.000 26.16 0.00 44.28 4.44
200 209 1.006832 GTTGCTCGTAACCGCATCAT 58.993 50.000 0.00 0.00 35.85 2.45
233 242 0.318762 GTTCAGAAGAGGCACGGTCT 59.681 55.000 0.00 0.00 0.00 3.85
259 268 2.258286 GGAATTGCGTGTGGTGCC 59.742 61.111 0.00 0.00 0.00 5.01
312 322 4.566004 TCAAGTGTATAGTTGCTCGCTTT 58.434 39.130 2.31 0.00 37.20 3.51
314 324 5.805486 TCAAGTGTATAGTTGCTCGCTTTAG 59.195 40.000 2.31 0.00 37.20 1.85
367 378 0.768622 TGGAACCCAAGTGGATTCGT 59.231 50.000 0.00 0.00 37.39 3.85
443 454 2.524204 GGTTTTGGGGGCATTGGCA 61.524 57.895 12.70 0.00 43.71 4.92
447 458 2.760562 TTTGGGGGCATTGGCATGGA 62.761 55.000 12.70 0.00 43.71 3.41
461 472 1.003118 GCATGGACCTTGTGGACTACA 59.997 52.381 9.01 0.00 37.56 2.74
574 586 2.224042 GGCAAAGTCAAAGGACAAAGGG 60.224 50.000 0.00 0.00 46.80 3.95
687 699 1.542030 CCGATATCTTCTGGGAGTCGG 59.458 57.143 0.34 0.00 39.33 4.79
706 718 1.339711 GCAATGTTAGTTGGCTTGCG 58.660 50.000 0.00 0.00 33.67 4.85
708 720 2.415893 GCAATGTTAGTTGGCTTGCGAT 60.416 45.455 0.00 0.00 33.67 4.58
731 743 2.287308 GGCGTTGTGTTGCTGTTATCAA 60.287 45.455 0.00 0.00 0.00 2.57
893 911 2.222027 ACGCCTTTGGTTGAAGAAGAG 58.778 47.619 0.00 0.00 0.00 2.85
1618 1748 7.672983 TTGTTCCAAAACTGCAATTGTTAAA 57.327 28.000 7.40 0.00 36.30 1.52
1676 1806 9.208022 CCCAGTAAGGAATTTCTTTTGAATTTC 57.792 33.333 3.81 0.00 43.00 2.17
1678 1808 9.677567 CAGTAAGGAATTTCTTTTGAATTTCGA 57.322 29.630 3.81 0.00 43.87 3.71
1688 1818 7.627585 TCTTTTGAATTTCGAAAGATTGCAG 57.372 32.000 27.15 10.26 46.48 4.41
1755 2123 3.079578 AGATGGAGCTGAAACACACATG 58.920 45.455 0.00 0.00 0.00 3.21
1792 2168 1.762419 TAACAGACTCACGTTGCGAC 58.238 50.000 0.00 0.00 0.00 5.19
1890 2266 3.950794 CTTTGCAGCCCGCGGTCTA 62.951 63.158 26.12 0.00 46.97 2.59
1942 2318 4.720902 CCACGGTGGATGGCAGCA 62.721 66.667 22.77 0.00 40.96 4.41
1968 2345 0.396417 CACTCTCTCCTCGTGGGGAT 60.396 60.000 6.54 0.00 42.97 3.85
2052 2429 2.048127 GTGGACCTCACGTCAGCC 60.048 66.667 0.00 0.00 43.95 4.85
2077 2454 2.743928 GAGGTTCTGCGTGGCTGG 60.744 66.667 0.00 0.00 0.00 4.85
2111 2488 0.544697 GAGGGATTCGGGCCTTGTTA 59.455 55.000 0.84 0.00 0.00 2.41
2132 2510 0.681733 CCGGATTGATCTCGGATGGT 59.318 55.000 0.00 0.00 40.63 3.55
2134 2512 1.341209 CGGATTGATCTCGGATGGTGA 59.659 52.381 0.00 0.00 0.00 4.02
2139 2517 0.461548 GATCTCGGATGGTGACTGCA 59.538 55.000 0.00 0.00 0.00 4.41
2216 2594 2.203280 TTCAGGTGTTGGGTGGCG 60.203 61.111 0.00 0.00 0.00 5.69
2275 2653 4.338710 GGTGTTGGGTGGCGGCTA 62.339 66.667 11.43 0.00 0.00 3.93
2301 2698 1.080093 GTTCAGATCCGTCGTGGCA 60.080 57.895 0.00 0.00 37.80 4.92
2422 2821 0.242825 CGTTCGGTTCCTGTCAGCTA 59.757 55.000 0.00 0.00 0.00 3.32
2439 2838 2.203451 ACGAGAGTGGGGTGACGT 60.203 61.111 0.00 0.00 46.97 4.34
2445 2844 0.106149 GAGTGGGGTGACGTGACTTT 59.894 55.000 4.85 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.524816 TGTAGATCGCGAGCGGAAAC 60.525 55.000 19.77 15.62 40.25 2.78
2 3 0.171679 TTGTAGATCGCGAGCGGAAA 59.828 50.000 19.77 11.38 40.25 3.13
3 4 0.248498 CTTGTAGATCGCGAGCGGAA 60.248 55.000 19.77 11.67 40.25 4.30
4 5 1.355563 CTTGTAGATCGCGAGCGGA 59.644 57.895 19.77 8.43 40.25 5.54
5 6 1.658717 CCTTGTAGATCGCGAGCGG 60.659 63.158 19.77 9.89 40.25 5.52
6 7 1.658717 CCCTTGTAGATCGCGAGCG 60.659 63.158 19.77 11.64 41.35 5.03
7 8 0.666913 TACCCTTGTAGATCGCGAGC 59.333 55.000 18.21 18.21 0.00 5.03
8 9 2.293677 ACATACCCTTGTAGATCGCGAG 59.706 50.000 16.66 0.00 0.00 5.03
9 10 2.304092 ACATACCCTTGTAGATCGCGA 58.696 47.619 13.09 13.09 0.00 5.87
10 11 2.795175 ACATACCCTTGTAGATCGCG 57.205 50.000 0.00 0.00 0.00 5.87
16 17 5.509840 GGAGTGCATCTACATACCCTTGTAG 60.510 48.000 5.47 5.47 46.85 2.74
17 18 4.344102 GGAGTGCATCTACATACCCTTGTA 59.656 45.833 0.00 0.00 0.00 2.41
18 19 3.134804 GGAGTGCATCTACATACCCTTGT 59.865 47.826 0.00 0.00 0.00 3.16
19 20 3.389329 AGGAGTGCATCTACATACCCTTG 59.611 47.826 0.00 0.00 0.00 3.61
20 21 3.658725 AGGAGTGCATCTACATACCCTT 58.341 45.455 0.00 0.00 0.00 3.95
21 22 3.336509 AGGAGTGCATCTACATACCCT 57.663 47.619 0.00 0.00 0.00 4.34
22 23 3.244249 GGAAGGAGTGCATCTACATACCC 60.244 52.174 0.00 0.00 0.00 3.69
23 24 3.244249 GGGAAGGAGTGCATCTACATACC 60.244 52.174 0.00 0.00 0.00 2.73
24 25 3.643792 AGGGAAGGAGTGCATCTACATAC 59.356 47.826 0.00 0.00 0.00 2.39
25 26 3.898123 GAGGGAAGGAGTGCATCTACATA 59.102 47.826 0.00 0.00 0.00 2.29
26 27 2.703007 GAGGGAAGGAGTGCATCTACAT 59.297 50.000 0.00 0.00 0.00 2.29
27 28 2.111384 GAGGGAAGGAGTGCATCTACA 58.889 52.381 0.00 0.00 0.00 2.74
28 29 2.364002 GAGAGGGAAGGAGTGCATCTAC 59.636 54.545 0.00 0.00 38.99 2.59
29 30 2.672098 GAGAGGGAAGGAGTGCATCTA 58.328 52.381 0.00 0.00 38.99 1.98
30 31 1.494960 GAGAGGGAAGGAGTGCATCT 58.505 55.000 0.00 0.00 41.89 2.90
31 32 0.103937 CGAGAGGGAAGGAGTGCATC 59.896 60.000 0.00 0.00 0.00 3.91
32 33 0.616111 ACGAGAGGGAAGGAGTGCAT 60.616 55.000 0.00 0.00 0.00 3.96
33 34 0.832135 AACGAGAGGGAAGGAGTGCA 60.832 55.000 0.00 0.00 0.00 4.57
34 35 0.390472 CAACGAGAGGGAAGGAGTGC 60.390 60.000 0.00 0.00 0.00 4.40
35 36 0.390472 GCAACGAGAGGGAAGGAGTG 60.390 60.000 0.00 0.00 0.00 3.51
36 37 0.543174 AGCAACGAGAGGGAAGGAGT 60.543 55.000 0.00 0.00 0.00 3.85
37 38 1.407258 CTAGCAACGAGAGGGAAGGAG 59.593 57.143 0.00 0.00 0.00 3.69
38 39 1.272536 ACTAGCAACGAGAGGGAAGGA 60.273 52.381 0.00 0.00 0.00 3.36
39 40 1.187087 ACTAGCAACGAGAGGGAAGG 58.813 55.000 0.00 0.00 0.00 3.46
40 41 4.082136 AGTTTACTAGCAACGAGAGGGAAG 60.082 45.833 0.00 0.00 0.00 3.46
41 42 3.830755 AGTTTACTAGCAACGAGAGGGAA 59.169 43.478 0.00 0.00 0.00 3.97
42 43 3.428532 AGTTTACTAGCAACGAGAGGGA 58.571 45.455 0.00 0.00 0.00 4.20
43 44 3.429135 GGAGTTTACTAGCAACGAGAGGG 60.429 52.174 0.00 0.00 0.00 4.30
44 45 3.192844 TGGAGTTTACTAGCAACGAGAGG 59.807 47.826 0.00 0.00 0.00 3.69
45 46 4.436242 TGGAGTTTACTAGCAACGAGAG 57.564 45.455 0.00 0.00 0.00 3.20
46 47 5.884232 TCTATGGAGTTTACTAGCAACGAGA 59.116 40.000 0.00 0.00 0.00 4.04
47 48 6.132791 TCTATGGAGTTTACTAGCAACGAG 57.867 41.667 0.00 0.00 0.00 4.18
48 49 6.710597 ATCTATGGAGTTTACTAGCAACGA 57.289 37.500 0.00 0.00 0.00 3.85
49 50 6.978659 TCAATCTATGGAGTTTACTAGCAACG 59.021 38.462 0.00 0.00 0.00 4.10
50 51 8.894768 ATCAATCTATGGAGTTTACTAGCAAC 57.105 34.615 0.00 0.00 0.00 4.17
51 52 8.928448 AGATCAATCTATGGAGTTTACTAGCAA 58.072 33.333 0.00 0.00 34.85 3.91
52 53 8.484214 AGATCAATCTATGGAGTTTACTAGCA 57.516 34.615 0.00 0.00 34.85 3.49
53 54 9.202273 CAAGATCAATCTATGGAGTTTACTAGC 57.798 37.037 0.00 0.00 35.76 3.42
54 55 9.703892 CCAAGATCAATCTATGGAGTTTACTAG 57.296 37.037 12.26 0.00 37.31 2.57
55 56 9.213777 ACCAAGATCAATCTATGGAGTTTACTA 57.786 33.333 19.34 0.00 37.92 1.82
56 57 7.989741 CACCAAGATCAATCTATGGAGTTTACT 59.010 37.037 19.34 0.00 37.92 2.24
57 58 7.987458 TCACCAAGATCAATCTATGGAGTTTAC 59.013 37.037 19.34 0.00 37.92 2.01
58 59 8.089625 TCACCAAGATCAATCTATGGAGTTTA 57.910 34.615 19.34 3.42 37.92 2.01
59 60 6.962182 TCACCAAGATCAATCTATGGAGTTT 58.038 36.000 19.34 3.87 37.92 2.66
60 61 6.566079 TCACCAAGATCAATCTATGGAGTT 57.434 37.500 19.34 4.10 37.92 3.01
61 62 6.531923 CATCACCAAGATCAATCTATGGAGT 58.468 40.000 19.34 8.56 37.92 3.85
62 63 5.411977 GCATCACCAAGATCAATCTATGGAG 59.588 44.000 19.34 14.57 37.92 3.86
63 64 5.311265 GCATCACCAAGATCAATCTATGGA 58.689 41.667 19.34 6.96 37.92 3.41
64 65 4.153655 CGCATCACCAAGATCAATCTATGG 59.846 45.833 14.46 14.46 39.18 2.74
65 66 4.753610 ACGCATCACCAAGATCAATCTATG 59.246 41.667 0.00 0.00 35.76 2.23
66 67 4.965814 ACGCATCACCAAGATCAATCTAT 58.034 39.130 0.00 0.00 35.76 1.98
67 68 4.406648 ACGCATCACCAAGATCAATCTA 57.593 40.909 0.00 0.00 35.76 1.98
68 69 3.272574 ACGCATCACCAAGATCAATCT 57.727 42.857 0.00 0.00 39.22 2.40
69 70 4.371786 TCTACGCATCACCAAGATCAATC 58.628 43.478 0.00 0.00 33.72 2.67
70 71 4.406648 TCTACGCATCACCAAGATCAAT 57.593 40.909 0.00 0.00 33.72 2.57
71 72 3.885724 TCTACGCATCACCAAGATCAA 57.114 42.857 0.00 0.00 33.72 2.57
72 73 3.885724 TTCTACGCATCACCAAGATCA 57.114 42.857 0.00 0.00 33.72 2.92
73 74 5.741388 ATTTTCTACGCATCACCAAGATC 57.259 39.130 0.00 0.00 33.72 2.75
74 75 6.515272 AAATTTTCTACGCATCACCAAGAT 57.485 33.333 0.00 0.00 37.48 2.40
75 76 5.957842 AAATTTTCTACGCATCACCAAGA 57.042 34.783 0.00 0.00 0.00 3.02
76 77 6.148948 TCAAAATTTTCTACGCATCACCAAG 58.851 36.000 0.00 0.00 0.00 3.61
77 78 6.078202 TCAAAATTTTCTACGCATCACCAA 57.922 33.333 0.00 0.00 0.00 3.67
78 79 5.697473 TCAAAATTTTCTACGCATCACCA 57.303 34.783 0.00 0.00 0.00 4.17
79 80 7.581011 AATTCAAAATTTTCTACGCATCACC 57.419 32.000 0.00 0.00 0.00 4.02
80 81 8.915654 AGAAATTCAAAATTTTCTACGCATCAC 58.084 29.630 0.00 0.00 39.70 3.06
81 82 8.914654 CAGAAATTCAAAATTTTCTACGCATCA 58.085 29.630 0.00 0.00 39.53 3.07
82 83 7.894753 GCAGAAATTCAAAATTTTCTACGCATC 59.105 33.333 0.00 0.00 39.53 3.91
83 84 7.599998 AGCAGAAATTCAAAATTTTCTACGCAT 59.400 29.630 0.00 0.00 39.53 4.73
84 85 6.922957 AGCAGAAATTCAAAATTTTCTACGCA 59.077 30.769 0.00 0.00 39.53 5.24
85 86 7.338440 AGCAGAAATTCAAAATTTTCTACGC 57.662 32.000 0.00 0.00 39.53 4.42
86 87 8.567221 CGTAGCAGAAATTCAAAATTTTCTACG 58.433 33.333 19.51 19.51 39.53 3.51
87 88 9.394477 ACGTAGCAGAAATTCAAAATTTTCTAC 57.606 29.630 0.00 5.68 39.53 2.59
88 89 9.959749 AACGTAGCAGAAATTCAAAATTTTCTA 57.040 25.926 0.00 0.00 39.53 2.10
89 90 8.871686 AACGTAGCAGAAATTCAAAATTTTCT 57.128 26.923 0.00 0.00 41.61 2.52
90 91 9.989394 GTAACGTAGCAGAAATTCAAAATTTTC 57.011 29.630 0.00 0.00 33.08 2.29
91 92 8.974408 GGTAACGTAGCAGAAATTCAAAATTTT 58.026 29.630 0.00 0.00 0.00 1.82
92 93 7.597369 GGGTAACGTAGCAGAAATTCAAAATTT 59.403 33.333 0.00 0.00 37.60 1.82
93 94 7.088272 GGGTAACGTAGCAGAAATTCAAAATT 58.912 34.615 0.00 0.00 37.60 1.82
94 95 6.207810 TGGGTAACGTAGCAGAAATTCAAAAT 59.792 34.615 0.00 0.00 37.60 1.82
95 96 5.531659 TGGGTAACGTAGCAGAAATTCAAAA 59.468 36.000 0.00 0.00 37.60 2.44
96 97 5.064558 TGGGTAACGTAGCAGAAATTCAAA 58.935 37.500 0.00 0.00 37.60 2.69
97 98 4.643463 TGGGTAACGTAGCAGAAATTCAA 58.357 39.130 0.00 0.00 37.60 2.69
98 99 4.274602 TGGGTAACGTAGCAGAAATTCA 57.725 40.909 0.00 0.00 37.60 2.57
99 100 4.453136 TGTTGGGTAACGTAGCAGAAATTC 59.547 41.667 0.00 0.00 39.71 2.17
100 101 4.391155 TGTTGGGTAACGTAGCAGAAATT 58.609 39.130 0.00 0.00 39.71 1.82
101 102 4.010667 TGTTGGGTAACGTAGCAGAAAT 57.989 40.909 0.00 0.00 39.71 2.17
102 103 3.472283 TGTTGGGTAACGTAGCAGAAA 57.528 42.857 0.00 0.00 39.71 2.52
103 104 3.472283 TTGTTGGGTAACGTAGCAGAA 57.528 42.857 0.00 0.00 39.71 3.02
104 105 3.688694 ATTGTTGGGTAACGTAGCAGA 57.311 42.857 0.00 0.00 39.71 4.26
105 106 4.214545 TCAAATTGTTGGGTAACGTAGCAG 59.785 41.667 0.00 0.00 39.71 4.24
106 107 4.135306 TCAAATTGTTGGGTAACGTAGCA 58.865 39.130 0.00 0.00 39.71 3.49
107 108 4.719040 CTCAAATTGTTGGGTAACGTAGC 58.281 43.478 0.00 0.00 39.71 3.58
108 109 4.668177 CGCTCAAATTGTTGGGTAACGTAG 60.668 45.833 0.00 0.00 37.56 3.51
109 110 3.186817 CGCTCAAATTGTTGGGTAACGTA 59.813 43.478 0.00 0.00 37.56 3.57
110 111 2.031508 CGCTCAAATTGTTGGGTAACGT 60.032 45.455 0.00 0.00 37.56 3.99
111 112 2.580589 CGCTCAAATTGTTGGGTAACG 58.419 47.619 0.00 0.00 37.56 3.18
112 113 2.352323 CCCGCTCAAATTGTTGGGTAAC 60.352 50.000 10.31 0.00 37.56 2.50
113 114 1.889829 CCCGCTCAAATTGTTGGGTAA 59.110 47.619 10.31 0.00 37.56 2.85
114 115 1.074084 TCCCGCTCAAATTGTTGGGTA 59.926 47.619 15.49 4.82 37.56 3.69
115 116 0.178975 TCCCGCTCAAATTGTTGGGT 60.179 50.000 15.49 0.00 37.56 4.51
116 117 1.185315 ATCCCGCTCAAATTGTTGGG 58.815 50.000 11.69 11.69 38.37 4.12
117 118 2.995258 CAAATCCCGCTCAAATTGTTGG 59.005 45.455 0.00 0.00 35.29 3.77
118 119 2.995258 CCAAATCCCGCTCAAATTGTTG 59.005 45.455 0.00 0.00 35.95 3.33
119 120 2.896685 TCCAAATCCCGCTCAAATTGTT 59.103 40.909 0.00 0.00 0.00 2.83
120 121 2.524306 TCCAAATCCCGCTCAAATTGT 58.476 42.857 0.00 0.00 0.00 2.71
121 122 3.514645 CTTCCAAATCCCGCTCAAATTG 58.485 45.455 0.00 0.00 0.00 2.32
122 123 2.497273 CCTTCCAAATCCCGCTCAAATT 59.503 45.455 0.00 0.00 0.00 1.82
154 155 6.127479 TGCCACAGAAATATTTAATTTCGGCT 60.127 34.615 19.42 2.98 40.01 5.52
194 196 1.869767 CTTGGTCTCCGCTAATGATGC 59.130 52.381 0.00 0.00 0.00 3.91
200 209 2.244695 TCTGAACTTGGTCTCCGCTAA 58.755 47.619 0.00 0.00 0.00 3.09
233 242 1.991167 ACGCAATTCCCGTCCCCTA 60.991 57.895 0.00 0.00 32.83 3.53
367 378 5.342017 CCTGAACCATCCTATATAGGTCCA 58.658 45.833 25.06 9.57 44.02 4.02
443 454 1.275291 CGTGTAGTCCACAAGGTCCAT 59.725 52.381 0.00 0.00 44.78 3.41
447 458 0.466543 TTGCGTGTAGTCCACAAGGT 59.533 50.000 0.00 0.00 44.78 3.50
501 512 7.568349 ACCATTTTGTATAGAAGATCAGCTGA 58.432 34.615 20.79 20.79 0.00 4.26
551 562 3.491447 CCTTTGTCCTTTGACTTTGCCTG 60.491 47.826 0.00 0.00 42.28 4.85
552 563 2.695147 CCTTTGTCCTTTGACTTTGCCT 59.305 45.455 0.00 0.00 42.28 4.75
574 586 4.427661 ACGAGCTGCTCCACGCTC 62.428 66.667 22.97 0.00 46.91 5.03
652 664 3.411517 CGGGAAGGATGGCACCCT 61.412 66.667 0.00 0.00 40.12 4.34
687 699 1.068610 TCGCAAGCCAACTAACATTGC 60.069 47.619 0.00 0.00 42.12 3.56
702 714 2.248135 AACACAACGCCGATCGCAA 61.248 52.632 10.32 0.00 43.23 4.85
705 717 2.202171 GCAACACAACGCCGATCG 60.202 61.111 8.51 8.51 45.38 3.69
706 718 1.154413 CAGCAACACAACGCCGATC 60.154 57.895 0.00 0.00 0.00 3.69
708 720 0.810426 TAACAGCAACACAACGCCGA 60.810 50.000 0.00 0.00 0.00 5.54
714 726 2.946329 ACGGTTGATAACAGCAACACAA 59.054 40.909 9.25 0.00 45.58 3.33
717 729 3.303461 CGAAACGGTTGATAACAGCAACA 60.303 43.478 9.25 0.00 45.58 3.33
874 892 2.494059 TCTCTTCTTCAACCAAAGGCG 58.506 47.619 0.00 0.00 0.00 5.52
893 911 5.717251 CGTGAAAGTTGCAACTGATTTTTC 58.283 37.500 31.73 27.38 39.66 2.29
1618 1748 3.159472 TGCAATCTTTCCATCTGTTGCT 58.841 40.909 8.99 0.00 41.67 3.91
1676 1806 3.529533 AGAGATGGTCTGCAATCTTTCG 58.470 45.455 0.31 0.00 35.59 3.46
1678 1808 3.883669 GGAGAGATGGTCTGCAATCTTT 58.116 45.455 0.31 0.00 43.11 2.52
1679 1809 3.557228 GGAGAGATGGTCTGCAATCTT 57.443 47.619 0.31 0.00 43.11 2.40
1685 1815 1.145819 GGCTGGAGAGATGGTCTGC 59.854 63.158 0.00 0.00 43.89 4.26
1688 1818 1.039856 GAGAGGCTGGAGAGATGGTC 58.960 60.000 0.00 0.00 0.00 4.02
1792 2168 2.859032 GCGAGCGACAGGTTCCTAATAG 60.859 54.545 0.00 0.00 0.00 1.73
1942 2318 1.685421 GAGGAGAGAGTGCCCTGCT 60.685 63.158 0.00 0.00 33.69 4.24
2052 2429 4.821589 GCAGAACCTCCTCGCCGG 62.822 72.222 0.00 0.00 0.00 6.13
2111 2488 0.681733 CATCCGAGATCAATCCGGGT 59.318 55.000 0.00 0.00 39.49 5.28
2160 2538 4.988598 CACGCCAAGGTCGCCACT 62.989 66.667 3.47 0.00 0.00 4.00
2216 2594 4.176752 CCCACTAGCCCCTTCCGC 62.177 72.222 0.00 0.00 0.00 5.54
2323 2720 4.289101 TCACCGGTCCCTCCACGA 62.289 66.667 2.59 0.00 35.57 4.35
2422 2821 2.203451 ACGTCACCCCACTCTCGT 60.203 61.111 0.00 0.00 0.00 4.18
2439 2838 2.856720 GCGCAATTTTCACCGAAAGTCA 60.857 45.455 0.30 0.00 32.93 3.41
2445 2844 2.558821 CGGCGCAATTTTCACCGA 59.441 55.556 10.83 0.00 46.71 4.69


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.