Multiple sequence alignment - TraesCS2B01G067700

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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 TraesCS2B01G067700 chr2B 100.000 3106 0 0 1 3106 34433778 34436883 0.000000e+00 5736.0
1 TraesCS2B01G067700 chr2B 93.690 2298 114 13 371 2646 34474838 34477126 0.000000e+00 3411.0
2 TraesCS2B01G067700 chr2B 96.334 2073 70 4 580 2646 34453556 34455628 0.000000e+00 3402.0
3 TraesCS2B01G067700 chr2B 90.535 803 49 8 2291 3068 34542447 34543247 0.000000e+00 1037.0
4 TraesCS2B01G067700 chr2B 94.318 176 7 2 371 543 34453381 34453556 1.840000e-67 267.0
5 TraesCS2B01G067700 chr2B 94.318 176 7 2 371 543 34538908 34539083 1.840000e-67 267.0
6 TraesCS2B01G067700 chrUn 89.046 1908 182 18 523 2424 154084220 154082334 0.000000e+00 2340.0
7 TraesCS2B01G067700 chrUn 89.046 1908 182 18 523 2424 210798586 210800472 0.000000e+00 2340.0
8 TraesCS2B01G067700 chrUn 88.889 1908 185 18 523 2424 146914020 146912134 0.000000e+00 2324.0
9 TraesCS2B01G067700 chrUn 88.790 1909 185 19 523 2424 154097384 154095498 0.000000e+00 2313.0
10 TraesCS2B01G067700 chr2A 88.994 1908 183 18 523 2424 22651280 22653166 0.000000e+00 2335.0
11 TraesCS2B01G067700 chr2A 88.994 1908 182 19 523 2424 22802579 22800694 0.000000e+00 2335.0
12 TraesCS2B01G067700 chr2A 88.994 1908 183 18 523 2424 22939668 22937782 0.000000e+00 2335.0
13 TraesCS2B01G067700 chr2A 88.941 1908 184 18 523 2424 22618898 22620784 0.000000e+00 2329.0
14 TraesCS2B01G067700 chr2A 83.083 266 25 10 69 322 22603516 22603773 1.120000e-54 224.0
15 TraesCS2B01G067700 chr2A 83.083 266 25 10 69 322 22635511 22635768 1.120000e-54 224.0
16 TraesCS2B01G067700 chr2D 93.399 303 16 4 69 370 21067346 21067645 2.200000e-121 446.0
17 TraesCS2B01G067700 chr6D 85.961 406 47 7 2671 3068 98114404 98114807 2.860000e-115 425.0
18 TraesCS2B01G067700 chr5D 83.453 417 47 7 2668 3068 487866169 487865759 4.890000e-98 368.0
19 TraesCS2B01G067700 chr5D 94.286 70 4 0 1 70 363232534 363232465 1.180000e-19 108.0
20 TraesCS2B01G067700 chr5D 89.474 76 7 1 2670 2745 381150736 381150662 9.170000e-16 95.3
21 TraesCS2B01G067700 chr4A 82.443 393 57 8 2687 3071 624353748 624353360 1.790000e-87 333.0
22 TraesCS2B01G067700 chr5B 80.386 311 41 11 2700 2994 537858833 537859139 5.220000e-53 219.0
23 TraesCS2B01G067700 chr5B 85.849 106 15 0 2670 2775 600483899 600483794 2.530000e-21 113.0
24 TraesCS2B01G067700 chr7B 77.692 390 57 17 2670 3029 733023037 733022648 8.730000e-51 211.0
25 TraesCS2B01G067700 chr4B 94.366 71 4 0 1 71 667405559 667405629 3.270000e-20 110.0
26 TraesCS2B01G067700 chr3D 93.333 75 3 1 2996 3068 429807335 429807409 3.270000e-20 110.0
27 TraesCS2B01G067700 chr5A 94.203 69 4 0 1 69 683596860 683596928 4.240000e-19 106.0
28 TraesCS2B01G067700 chr5A 92.754 69 5 0 1 69 473057218 473057286 1.970000e-17 100.0
29 TraesCS2B01G067700 chr6A 91.892 74 6 0 1 74 504353187 504353260 1.520000e-18 104.0
30 TraesCS2B01G067700 chr1A 92.958 71 5 0 1 71 435856693 435856763 1.520000e-18 104.0
31 TraesCS2B01G067700 chr7D 92.857 70 5 0 1 70 20724062 20724131 5.480000e-18 102.0
32 TraesCS2B01G067700 chr7D 90.541 74 7 0 1 74 254982878 254982951 7.090000e-17 99.0
33 TraesCS2B01G067700 chr3A 90.541 74 6 1 1 73 264430141 264430214 2.550000e-16 97.1


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 TraesCS2B01G067700 chr2B 34433778 34436883 3105 False 5736.0 5736 100.0000 1 3106 1 chr2B.!!$F1 3105
1 TraesCS2B01G067700 chr2B 34474838 34477126 2288 False 3411.0 3411 93.6900 371 2646 1 chr2B.!!$F2 2275
2 TraesCS2B01G067700 chr2B 34453381 34455628 2247 False 1834.5 3402 95.3260 371 2646 2 chr2B.!!$F3 2275
3 TraesCS2B01G067700 chr2B 34538908 34543247 4339 False 652.0 1037 92.4265 371 3068 2 chr2B.!!$F4 2697
4 TraesCS2B01G067700 chrUn 154082334 154084220 1886 True 2340.0 2340 89.0460 523 2424 1 chrUn.!!$R2 1901
5 TraesCS2B01G067700 chrUn 210798586 210800472 1886 False 2340.0 2340 89.0460 523 2424 1 chrUn.!!$F1 1901
6 TraesCS2B01G067700 chrUn 146912134 146914020 1886 True 2324.0 2324 88.8890 523 2424 1 chrUn.!!$R1 1901
7 TraesCS2B01G067700 chrUn 154095498 154097384 1886 True 2313.0 2313 88.7900 523 2424 1 chrUn.!!$R3 1901
8 TraesCS2B01G067700 chr2A 22651280 22653166 1886 False 2335.0 2335 88.9940 523 2424 1 chr2A.!!$F4 1901
9 TraesCS2B01G067700 chr2A 22800694 22802579 1885 True 2335.0 2335 88.9940 523 2424 1 chr2A.!!$R1 1901
10 TraesCS2B01G067700 chr2A 22937782 22939668 1886 True 2335.0 2335 88.9940 523 2424 1 chr2A.!!$R2 1901
11 TraesCS2B01G067700 chr2A 22618898 22620784 1886 False 2329.0 2329 88.9410 523 2424 1 chr2A.!!$F2 1901

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
63 64 0.110373 GTAACGCACGGGCTCTTTTG 60.110 55.0 8.62 0.0 38.1 2.44 F
1243 1259 0.901827 TCATAAGTTCTGGCTCGGCA 59.098 50.0 0.00 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 3790 2.030540 CACACATGCCCTTCTTGTCTTG 60.031 50.0 0.0 0.0 31.52 3.02 R
3086 4882 0.034059 AGTCGGTGAGCTTCTTGGTG 59.966 55.0 0.0 0.0 0.00 4.17 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
20 21 1.600023 TGGTTGTTGGGTTAAGAGCG 58.400 50.000 0.00 0.00 0.00 5.03
21 22 1.134037 TGGTTGTTGGGTTAAGAGCGT 60.134 47.619 0.00 0.00 0.00 5.07
22 23 1.265905 GGTTGTTGGGTTAAGAGCGTG 59.734 52.381 0.00 0.00 0.00 5.34
23 24 0.948678 TTGTTGGGTTAAGAGCGTGC 59.051 50.000 0.00 0.00 0.00 5.34
24 25 0.179043 TGTTGGGTTAAGAGCGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
25 26 1.165270 GTTGGGTTAAGAGCGTGCAT 58.835 50.000 0.00 0.00 0.00 3.96
26 27 1.539827 GTTGGGTTAAGAGCGTGCATT 59.460 47.619 0.00 0.00 0.00 3.56
27 28 2.745281 GTTGGGTTAAGAGCGTGCATTA 59.255 45.455 0.00 0.00 0.00 1.90
28 29 3.275617 TGGGTTAAGAGCGTGCATTAT 57.724 42.857 0.00 0.00 0.00 1.28
29 30 2.942376 TGGGTTAAGAGCGTGCATTATG 59.058 45.455 0.00 0.00 0.00 1.90
30 31 2.943033 GGGTTAAGAGCGTGCATTATGT 59.057 45.455 0.00 0.00 0.00 2.29
31 32 3.377172 GGGTTAAGAGCGTGCATTATGTT 59.623 43.478 0.00 0.00 0.00 2.71
32 33 4.142469 GGGTTAAGAGCGTGCATTATGTTT 60.142 41.667 0.00 0.00 0.00 2.83
33 34 5.399013 GGTTAAGAGCGTGCATTATGTTTT 58.601 37.500 0.00 0.00 0.00 2.43
34 35 5.861787 GGTTAAGAGCGTGCATTATGTTTTT 59.138 36.000 0.00 0.00 0.00 1.94
57 58 3.039588 CGTTGTAACGCACGGGCT 61.040 61.111 8.62 0.00 46.06 5.19
58 59 2.858158 GTTGTAACGCACGGGCTC 59.142 61.111 8.62 0.00 38.10 4.70
59 60 1.666872 GTTGTAACGCACGGGCTCT 60.667 57.895 8.62 0.00 38.10 4.09
60 61 1.070105 TTGTAACGCACGGGCTCTT 59.930 52.632 8.62 0.60 38.10 2.85
61 62 0.533308 TTGTAACGCACGGGCTCTTT 60.533 50.000 8.62 0.00 38.10 2.52
62 63 0.533308 TGTAACGCACGGGCTCTTTT 60.533 50.000 8.62 0.00 38.10 2.27
63 64 0.110373 GTAACGCACGGGCTCTTTTG 60.110 55.000 8.62 0.00 38.10 2.44
64 65 1.847890 TAACGCACGGGCTCTTTTGC 61.848 55.000 8.62 0.00 38.10 3.68
65 66 3.357079 CGCACGGGCTCTTTTGCT 61.357 61.111 8.62 0.00 38.10 3.91
66 67 2.032634 CGCACGGGCTCTTTTGCTA 61.033 57.895 8.62 0.00 38.10 3.49
67 68 1.796796 GCACGGGCTCTTTTGCTAG 59.203 57.895 0.00 0.00 36.96 3.42
68 69 0.955919 GCACGGGCTCTTTTGCTAGT 60.956 55.000 0.00 0.00 36.96 2.57
69 70 1.674817 GCACGGGCTCTTTTGCTAGTA 60.675 52.381 0.00 0.00 36.96 1.82
70 71 2.906354 CACGGGCTCTTTTGCTAGTAT 58.094 47.619 0.00 0.00 0.00 2.12
71 72 2.609459 CACGGGCTCTTTTGCTAGTATG 59.391 50.000 0.00 0.00 0.00 2.39
72 73 2.236395 ACGGGCTCTTTTGCTAGTATGT 59.764 45.455 0.00 0.00 0.00 2.29
73 74 3.449737 ACGGGCTCTTTTGCTAGTATGTA 59.550 43.478 0.00 0.00 0.00 2.29
74 75 3.802685 CGGGCTCTTTTGCTAGTATGTAC 59.197 47.826 0.00 0.00 0.00 2.90
75 76 4.679639 CGGGCTCTTTTGCTAGTATGTACA 60.680 45.833 0.00 0.00 0.00 2.90
76 77 5.183228 GGGCTCTTTTGCTAGTATGTACAA 58.817 41.667 0.00 0.00 0.00 2.41
77 78 5.646360 GGGCTCTTTTGCTAGTATGTACAAA 59.354 40.000 0.00 0.00 0.00 2.83
78 79 6.150474 GGGCTCTTTTGCTAGTATGTACAAAA 59.850 38.462 0.00 0.00 39.09 2.44
79 80 7.021790 GGCTCTTTTGCTAGTATGTACAAAAC 58.978 38.462 0.00 1.21 37.15 2.43
80 81 7.308348 GGCTCTTTTGCTAGTATGTACAAAACA 60.308 37.037 0.00 0.00 43.86 2.83
178 179 8.806146 AGGAAATGAACATTTATACATATGGCC 58.194 33.333 11.89 0.00 40.77 5.36
179 180 8.806146 GGAAATGAACATTTATACATATGGCCT 58.194 33.333 3.32 0.00 40.77 5.19
228 229 5.389859 TTTTCCTGGCATTCACTGTAATG 57.610 39.130 0.00 0.00 39.41 1.90
229 230 3.719268 TCCTGGCATTCACTGTAATGT 57.281 42.857 0.00 0.00 38.78 2.71
230 231 3.346315 TCCTGGCATTCACTGTAATGTG 58.654 45.455 0.00 0.00 38.78 3.21
231 232 3.084039 CCTGGCATTCACTGTAATGTGT 58.916 45.455 0.00 0.00 38.78 3.72
232 233 3.507233 CCTGGCATTCACTGTAATGTGTT 59.493 43.478 0.00 0.00 38.78 3.32
233 234 4.699735 CCTGGCATTCACTGTAATGTGTTA 59.300 41.667 0.00 0.00 38.78 2.41
234 235 5.182950 CCTGGCATTCACTGTAATGTGTTAA 59.817 40.000 0.00 0.00 38.78 2.01
235 236 6.252967 TGGCATTCACTGTAATGTGTTAAG 57.747 37.500 0.00 0.00 38.78 1.85
236 237 6.000840 TGGCATTCACTGTAATGTGTTAAGA 58.999 36.000 0.00 0.00 38.78 2.10
237 238 6.488344 TGGCATTCACTGTAATGTGTTAAGAA 59.512 34.615 0.00 0.00 38.78 2.52
238 239 7.013750 TGGCATTCACTGTAATGTGTTAAGAAA 59.986 33.333 0.00 0.00 38.78 2.52
239 240 7.865385 GGCATTCACTGTAATGTGTTAAGAAAA 59.135 33.333 0.00 0.00 38.78 2.29
240 241 8.690840 GCATTCACTGTAATGTGTTAAGAAAAC 58.309 33.333 0.00 0.00 38.78 2.43
241 242 9.950680 CATTCACTGTAATGTGTTAAGAAAACT 57.049 29.630 0.00 0.00 38.90 2.66
242 243 9.950680 ATTCACTGTAATGTGTTAAGAAAACTG 57.049 29.630 0.00 0.00 38.90 3.16
243 244 8.500753 TCACTGTAATGTGTTAAGAAAACTGT 57.499 30.769 0.00 0.00 38.90 3.55
244 245 8.952278 TCACTGTAATGTGTTAAGAAAACTGTT 58.048 29.630 0.00 0.00 38.90 3.16
245 246 9.567848 CACTGTAATGTGTTAAGAAAACTGTTT 57.432 29.630 0.00 0.00 33.61 2.83
353 354 3.432186 GGACATATTGGCCGTGGC 58.568 61.111 1.16 1.16 34.69 5.01
396 397 4.217836 TCTTTCCTGCTAGACTACGAGA 57.782 45.455 0.00 0.00 0.00 4.04
401 402 5.312120 TCCTGCTAGACTACGAGAAAAAG 57.688 43.478 0.00 0.00 0.00 2.27
502 506 6.662865 TTTTTAATCAGGCAGGACATTCAA 57.337 33.333 0.00 0.00 0.00 2.69
506 510 1.980765 TCAGGCAGGACATTCAAGTCT 59.019 47.619 0.00 0.00 38.57 3.24
725 733 5.097529 CGTACTTCTTTGTTCTGCCGTATA 58.902 41.667 0.00 0.00 0.00 1.47
727 735 5.857822 ACTTCTTTGTTCTGCCGTATAAC 57.142 39.130 0.00 0.00 0.00 1.89
1243 1259 0.901827 TCATAAGTTCTGGCTCGGCA 59.098 50.000 0.00 0.00 0.00 5.69
1712 3453 1.621072 GGAGGTCTGACCATGGAGTCT 60.621 57.143 27.48 8.55 41.95 3.24
2488 4263 9.524496 TTTGTACCACTAGAGAATACTACAAGA 57.476 33.333 0.00 0.00 0.00 3.02
2527 4303 6.044046 TCAATCCATTGCAACAAGATTATGC 58.956 36.000 15.99 0.00 40.45 3.14
2533 4309 6.036300 CCATTGCAACAAGATTATGCGAAAAT 59.964 34.615 0.00 0.00 42.91 1.82
2594 4370 7.746243 ATGATAAGGTGATAGGCTATGACAT 57.254 36.000 22.68 15.01 0.00 3.06
2665 4441 9.003112 CATTAGAGTAAAATGCAAAGAATCACG 57.997 33.333 0.00 0.00 0.00 4.35
2666 4442 5.393962 AGAGTAAAATGCAAAGAATCACGC 58.606 37.500 0.00 0.00 0.00 5.34
2679 4472 0.523072 ATCACGCATGTGGCACTTTC 59.477 50.000 19.83 6.13 46.42 2.62
2688 4481 0.453390 GTGGCACTTTCCATAGCAGC 59.547 55.000 11.13 0.00 38.57 5.25
2743 4536 2.589798 TTCTGAGACCGTTTTGACGT 57.410 45.000 0.00 0.00 0.00 4.34
2747 4540 0.878961 GAGACCGTTTTGACGTGGCT 60.879 55.000 0.00 0.00 0.00 4.75
2748 4541 1.157870 AGACCGTTTTGACGTGGCTG 61.158 55.000 0.00 0.00 0.00 4.85
2756 4549 0.388520 TTGACGTGGCTGATCACTCG 60.389 55.000 0.00 0.00 35.63 4.18
2757 4550 1.213013 GACGTGGCTGATCACTCGT 59.787 57.895 11.70 11.70 35.63 4.18
2758 4551 0.388649 GACGTGGCTGATCACTCGTT 60.389 55.000 12.73 0.86 35.63 3.85
2767 4560 0.669318 GATCACTCGTTGGCCGACAA 60.669 55.000 23.21 3.26 41.60 3.18
2805 4601 2.477880 CCGTTAATGGCAGTGTCCC 58.522 57.895 0.00 0.00 0.00 4.46
2860 4656 2.812011 GCCGTCTATCTCTCTTCTCTCC 59.188 54.545 0.00 0.00 0.00 3.71
2862 4658 3.072476 CCGTCTATCTCTCTTCTCTCCCT 59.928 52.174 0.00 0.00 0.00 4.20
2866 4662 0.621082 TCTCTCTTCTCTCCCTCGCA 59.379 55.000 0.00 0.00 0.00 5.10
2869 4665 2.015227 CTCTTCTCTCCCTCGCAGGC 62.015 65.000 0.00 0.00 32.73 4.85
2915 4711 1.002134 AATTGGCGAGGGAGTGGTG 60.002 57.895 0.00 0.00 0.00 4.17
2943 4739 4.158394 GCAAGGTGTGGTGAACATATTCAT 59.842 41.667 0.00 0.00 46.43 2.57
3031 4827 8.110860 TCTTGGAGGAAAATTTGTTGATCTAC 57.889 34.615 0.00 0.00 0.00 2.59
3033 4829 9.231297 CTTGGAGGAAAATTTGTTGATCTACTA 57.769 33.333 8.74 0.00 0.00 1.82
3050 4846 5.858381 TCTACTATCAAATGATGCTGGTCC 58.142 41.667 6.17 0.00 36.05 4.46
3098 4894 3.435186 GCGGCCACCAAGAAGCTC 61.435 66.667 2.24 0.00 0.00 4.09
3099 4895 2.032528 CGGCCACCAAGAAGCTCA 59.967 61.111 2.24 0.00 0.00 4.26
3100 4896 2.328099 CGGCCACCAAGAAGCTCAC 61.328 63.158 2.24 0.00 0.00 3.51
3101 4897 1.973812 GGCCACCAAGAAGCTCACC 60.974 63.158 0.00 0.00 0.00 4.02
3102 4898 2.328099 GCCACCAAGAAGCTCACCG 61.328 63.158 0.00 0.00 0.00 4.94
3103 4899 1.371183 CCACCAAGAAGCTCACCGA 59.629 57.895 0.00 0.00 0.00 4.69
3104 4900 0.951040 CCACCAAGAAGCTCACCGAC 60.951 60.000 0.00 0.00 0.00 4.79
3105 4901 0.034059 CACCAAGAAGCTCACCGACT 59.966 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.159382 CGCTCTTAACCCAACAACCAT 58.841 47.619 0.00 0.00 0.00 3.55
1 2 1.134037 ACGCTCTTAACCCAACAACCA 60.134 47.619 0.00 0.00 0.00 3.67
2 3 1.265905 CACGCTCTTAACCCAACAACC 59.734 52.381 0.00 0.00 0.00 3.77
3 4 1.334689 GCACGCTCTTAACCCAACAAC 60.335 52.381 0.00 0.00 0.00 3.32
4 5 0.948678 GCACGCTCTTAACCCAACAA 59.051 50.000 0.00 0.00 0.00 2.83
5 6 0.179043 TGCACGCTCTTAACCCAACA 60.179 50.000 0.00 0.00 0.00 3.33
6 7 1.165270 ATGCACGCTCTTAACCCAAC 58.835 50.000 0.00 0.00 0.00 3.77
7 8 1.904287 AATGCACGCTCTTAACCCAA 58.096 45.000 0.00 0.00 0.00 4.12
8 9 2.772077 TAATGCACGCTCTTAACCCA 57.228 45.000 0.00 0.00 0.00 4.51
9 10 2.943033 ACATAATGCACGCTCTTAACCC 59.057 45.455 0.00 0.00 0.00 4.11
10 11 4.616181 AACATAATGCACGCTCTTAACC 57.384 40.909 0.00 0.00 0.00 2.85
11 12 6.927933 AAAAACATAATGCACGCTCTTAAC 57.072 33.333 0.00 0.00 0.00 2.01
41 42 1.226030 AAGAGCCCGTGCGTTACAAC 61.226 55.000 0.00 0.00 44.33 3.32
42 43 0.533308 AAAGAGCCCGTGCGTTACAA 60.533 50.000 0.00 0.00 44.33 2.41
43 44 0.533308 AAAAGAGCCCGTGCGTTACA 60.533 50.000 0.00 0.00 44.33 2.41
44 45 0.110373 CAAAAGAGCCCGTGCGTTAC 60.110 55.000 0.00 0.00 44.33 2.50
45 46 1.847890 GCAAAAGAGCCCGTGCGTTA 61.848 55.000 0.00 0.00 44.33 3.18
46 47 3.030652 CAAAAGAGCCCGTGCGTT 58.969 55.556 0.00 0.00 44.33 4.84
47 48 2.725203 TAGCAAAAGAGCCCGTGCGT 62.725 55.000 0.00 0.00 44.33 5.24
48 49 1.970917 CTAGCAAAAGAGCCCGTGCG 61.971 60.000 0.00 0.00 44.33 5.34
49 50 0.955919 ACTAGCAAAAGAGCCCGTGC 60.956 55.000 0.00 0.00 37.26 5.34
50 51 2.380084 TACTAGCAAAAGAGCCCGTG 57.620 50.000 0.00 0.00 34.23 4.94
51 52 2.236395 ACATACTAGCAAAAGAGCCCGT 59.764 45.455 0.00 0.00 34.23 5.28
52 53 2.906354 ACATACTAGCAAAAGAGCCCG 58.094 47.619 0.00 0.00 34.23 6.13
53 54 4.766375 TGTACATACTAGCAAAAGAGCCC 58.234 43.478 0.00 0.00 34.23 5.19
54 55 6.737254 TTTGTACATACTAGCAAAAGAGCC 57.263 37.500 0.00 0.00 34.23 4.70
55 56 7.581476 TGTTTTGTACATACTAGCAAAAGAGC 58.419 34.615 0.00 0.00 40.16 4.09
152 153 8.806146 GGCCATATGTATAAATGTTCATTTCCT 58.194 33.333 13.03 6.35 0.00 3.36
153 154 8.806146 AGGCCATATGTATAAATGTTCATTTCC 58.194 33.333 5.01 5.87 0.00 3.13
205 206 5.304101 ACATTACAGTGAATGCCAGGAAAAA 59.696 36.000 0.00 0.00 39.94 1.94
206 207 4.832266 ACATTACAGTGAATGCCAGGAAAA 59.168 37.500 0.00 0.00 39.94 2.29
207 208 4.218200 CACATTACAGTGAATGCCAGGAAA 59.782 41.667 0.00 0.00 42.05 3.13
208 209 3.758023 CACATTACAGTGAATGCCAGGAA 59.242 43.478 0.00 0.00 42.05 3.36
209 210 3.244875 ACACATTACAGTGAATGCCAGGA 60.245 43.478 0.00 0.00 42.05 3.86
210 211 3.084039 ACACATTACAGTGAATGCCAGG 58.916 45.455 0.00 0.00 42.05 4.45
211 212 4.771590 AACACATTACAGTGAATGCCAG 57.228 40.909 0.00 0.47 42.05 4.85
212 213 6.000840 TCTTAACACATTACAGTGAATGCCA 58.999 36.000 0.00 0.00 42.05 4.92
213 214 6.494893 TCTTAACACATTACAGTGAATGCC 57.505 37.500 0.00 0.00 42.05 4.40
214 215 8.690840 GTTTTCTTAACACATTACAGTGAATGC 58.309 33.333 0.00 0.00 42.05 3.56
215 216 9.950680 AGTTTTCTTAACACATTACAGTGAATG 57.049 29.630 0.00 5.51 42.05 2.67
216 217 9.950680 CAGTTTTCTTAACACATTACAGTGAAT 57.049 29.630 0.00 0.00 42.05 2.57
217 218 8.952278 ACAGTTTTCTTAACACATTACAGTGAA 58.048 29.630 0.00 0.00 42.05 3.18
218 219 8.500753 ACAGTTTTCTTAACACATTACAGTGA 57.499 30.769 0.00 0.00 42.05 3.41
219 220 9.567848 AAACAGTTTTCTTAACACATTACAGTG 57.432 29.630 0.00 0.00 44.93 3.66
327 328 3.056179 CGGCCAATATGTCCTTGGTTTTT 60.056 43.478 2.24 0.00 44.17 1.94
328 329 2.495669 CGGCCAATATGTCCTTGGTTTT 59.504 45.455 2.24 0.00 44.17 2.43
329 330 2.099405 CGGCCAATATGTCCTTGGTTT 58.901 47.619 2.24 0.00 44.17 3.27
330 331 1.005450 ACGGCCAATATGTCCTTGGTT 59.995 47.619 2.24 0.00 44.17 3.67
331 332 0.623723 ACGGCCAATATGTCCTTGGT 59.376 50.000 2.24 0.00 44.17 3.67
332 333 1.024271 CACGGCCAATATGTCCTTGG 58.976 55.000 2.24 0.00 44.94 3.61
333 334 1.024271 CCACGGCCAATATGTCCTTG 58.976 55.000 2.24 0.00 0.00 3.61
334 335 0.751643 GCCACGGCCAATATGTCCTT 60.752 55.000 2.24 0.00 34.56 3.36
335 336 1.152963 GCCACGGCCAATATGTCCT 60.153 57.895 2.24 0.00 34.56 3.85
336 337 3.432186 GCCACGGCCAATATGTCC 58.568 61.111 2.24 0.00 34.56 4.02
351 352 2.536997 ATAACACCTCACGGCAGGCC 62.537 60.000 0.00 0.00 36.98 5.19
352 353 0.676782 AATAACACCTCACGGCAGGC 60.677 55.000 1.88 0.00 36.98 4.85
353 354 1.369625 GAATAACACCTCACGGCAGG 58.630 55.000 0.43 0.43 39.80 4.85
354 355 1.066143 AGGAATAACACCTCACGGCAG 60.066 52.381 0.00 0.00 31.43 4.85
355 356 0.981183 AGGAATAACACCTCACGGCA 59.019 50.000 0.00 0.00 31.43 5.69
356 357 2.007608 GAAGGAATAACACCTCACGGC 58.992 52.381 0.00 0.00 36.67 5.68
357 358 3.611766 AGAAGGAATAACACCTCACGG 57.388 47.619 0.00 0.00 36.67 4.94
358 359 4.392138 GGAAAGAAGGAATAACACCTCACG 59.608 45.833 0.00 0.00 36.67 4.35
359 360 5.412904 CAGGAAAGAAGGAATAACACCTCAC 59.587 44.000 0.00 0.00 36.67 3.51
360 361 5.560724 CAGGAAAGAAGGAATAACACCTCA 58.439 41.667 0.00 0.00 36.67 3.86
361 362 4.396478 GCAGGAAAGAAGGAATAACACCTC 59.604 45.833 0.00 0.00 36.67 3.85
362 363 4.043435 AGCAGGAAAGAAGGAATAACACCT 59.957 41.667 0.00 0.00 39.69 4.00
363 364 4.336280 AGCAGGAAAGAAGGAATAACACC 58.664 43.478 0.00 0.00 0.00 4.16
364 365 6.314152 GTCTAGCAGGAAAGAAGGAATAACAC 59.686 42.308 0.00 0.00 0.00 3.32
365 366 6.213600 AGTCTAGCAGGAAAGAAGGAATAACA 59.786 38.462 0.00 0.00 0.00 2.41
366 367 6.645306 AGTCTAGCAGGAAAGAAGGAATAAC 58.355 40.000 0.00 0.00 0.00 1.89
367 368 6.875972 AGTCTAGCAGGAAAGAAGGAATAA 57.124 37.500 0.00 0.00 0.00 1.40
368 369 6.039493 CGTAGTCTAGCAGGAAAGAAGGAATA 59.961 42.308 0.00 0.00 0.00 1.75
369 370 5.163499 CGTAGTCTAGCAGGAAAGAAGGAAT 60.163 44.000 0.00 0.00 0.00 3.01
396 397 0.537371 CACGTCCCAGGCTCCTTTTT 60.537 55.000 0.00 0.00 0.00 1.94
401 402 1.827399 TTTCTCACGTCCCAGGCTCC 61.827 60.000 0.00 0.00 0.00 4.70
484 488 3.009916 AGACTTGAATGTCCTGCCTGATT 59.990 43.478 0.00 0.00 37.66 2.57
502 506 2.588620 AGGCGCTTGCTAGTATAGACT 58.411 47.619 7.64 0.00 42.77 3.24
506 510 3.887110 TCAAGTAGGCGCTTGCTAGTATA 59.113 43.478 11.11 0.00 43.92 1.47
601 605 9.428097 GCTTGGAAGATTTGTTAATGAAAGAAT 57.572 29.630 0.00 0.00 0.00 2.40
614 618 2.036217 TGCTTGGTGCTTGGAAGATTTG 59.964 45.455 0.00 0.00 43.37 2.32
638 642 9.862149 TTTAGGAGTGTACATCTGATAGTGATA 57.138 33.333 0.00 0.00 0.00 2.15
725 733 3.380320 GCCGGCCAGATTGTATAAAAGTT 59.620 43.478 18.11 0.00 0.00 2.66
727 735 2.293399 GGCCGGCCAGATTGTATAAAAG 59.707 50.000 40.73 0.00 35.81 2.27
1243 1259 5.057149 GGTGATATCAGCGAACTGGTTAAT 58.943 41.667 18.44 0.00 44.59 1.40
1559 1591 5.769484 TGCCGGTTTTCAGTTTTACAATA 57.231 34.783 1.90 0.00 0.00 1.90
1712 3453 2.832129 GGCTGCAGTATATGGGTAGCTA 59.168 50.000 16.64 0.00 39.72 3.32
2049 3790 2.030540 CACACATGCCCTTCTTGTCTTG 60.031 50.000 0.00 0.00 31.52 3.02
2050 3791 2.233271 CACACATGCCCTTCTTGTCTT 58.767 47.619 0.00 0.00 31.52 3.01
2527 4303 5.179182 CCATTTTGGGAAGTTGGAATTTTCG 59.821 40.000 0.00 0.00 32.67 3.46
2533 4309 1.696884 GGCCATTTTGGGAAGTTGGAA 59.303 47.619 0.00 0.00 38.19 3.53
2643 4419 5.048782 TGCGTGATTCTTTGCATTTTACTCT 60.049 36.000 0.00 0.00 31.31 3.24
2656 4432 0.523072 GTGCCACATGCGTGATTCTT 59.477 50.000 14.17 0.00 46.80 2.52
2665 4441 1.202336 GCTATGGAAAGTGCCACATGC 60.202 52.381 0.00 0.00 41.56 4.06
2666 4442 2.093890 TGCTATGGAAAGTGCCACATG 58.906 47.619 0.00 0.00 41.56 3.21
2679 4472 1.143305 CCGATTCTTCGCTGCTATGG 58.857 55.000 0.00 0.00 44.12 2.74
2688 4481 1.298157 TTGCCACTGCCGATTCTTCG 61.298 55.000 0.00 0.00 45.08 3.79
2743 4536 1.375908 GCCAACGAGTGATCAGCCA 60.376 57.895 0.00 0.00 0.00 4.75
2778 4571 1.639534 CCATTAACGGCCGTTAGCG 59.360 57.895 39.96 33.72 45.17 4.26
2798 4594 3.250847 CCAACCACTGGGGACACT 58.749 61.111 1.10 0.00 42.17 3.55
2823 4619 1.467678 CGGCTAGGGATGGGAGTGAG 61.468 65.000 0.00 0.00 0.00 3.51
2886 4682 0.811219 TCGCCAATTGATCCGAGCTG 60.811 55.000 7.12 0.00 0.00 4.24
2887 4683 0.531532 CTCGCCAATTGATCCGAGCT 60.532 55.000 21.35 0.00 40.35 4.09
2915 4711 2.282462 CACCACACCTTGCTCCCC 60.282 66.667 0.00 0.00 0.00 4.81
2943 4739 4.659172 CCGGCCAGCCAAGGTGAA 62.659 66.667 9.78 0.00 35.37 3.18
3081 4877 3.435186 GAGCTTCTTGGTGGCCGC 61.435 66.667 8.12 8.12 0.00 6.53
3082 4878 2.032528 TGAGCTTCTTGGTGGCCG 59.967 61.111 0.00 0.00 0.00 6.13
3083 4879 1.973812 GGTGAGCTTCTTGGTGGCC 60.974 63.158 0.00 0.00 0.00 5.36
3084 4880 2.328099 CGGTGAGCTTCTTGGTGGC 61.328 63.158 0.00 0.00 0.00 5.01
3085 4881 0.951040 GTCGGTGAGCTTCTTGGTGG 60.951 60.000 0.00 0.00 0.00 4.61
3086 4882 0.034059 AGTCGGTGAGCTTCTTGGTG 59.966 55.000 0.00 0.00 0.00 4.17
3087 4883 2.442056 AGTCGGTGAGCTTCTTGGT 58.558 52.632 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.