Multiple sequence alignment - TraesCS2A01G156900

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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 TraesCS2A01G156900 chr2A 100.000 2584 0 0 1 2584 103363197 103365780 0.000000e+00 4772.0
1 TraesCS2A01G156900 chr2A 94.118 34 2 0 2547 2580 212633658 212633625 5.000000e-03 52.8
2 TraesCS2A01G156900 chr2B 89.493 2170 137 43 485 2584 157313840 157315988 0.000000e+00 2660.0
3 TraesCS2A01G156900 chr2D 92.714 1702 73 22 35 1721 106999526 107001191 0.000000e+00 2409.0
4 TraesCS2A01G156900 chr2D 87.482 703 64 15 1892 2584 107010554 107011242 0.000000e+00 789.0
5 TraesCS2A01G156900 chr2D 92.614 176 9 4 1720 1891 107001217 107001392 1.540000e-62 250.0
6 TraesCS2A01G156900 chr2D 74.713 435 92 14 2037 2468 6967166 6966747 7.350000e-41 178.0
7 TraesCS2A01G156900 chr3B 83.554 681 62 22 779 1429 152878522 152877862 2.210000e-165 592.0
8 TraesCS2A01G156900 chr3D 83.206 655 77 17 871 1514 101861132 101860500 1.040000e-158 569.0
9 TraesCS2A01G156900 chr3A 82.732 637 62 26 821 1429 554017824 554018440 8.190000e-145 523.0
10 TraesCS2A01G156900 chr4A 77.652 443 82 13 2037 2473 613371389 613370958 1.190000e-63 254.0
11 TraesCS2A01G156900 chr1A 91.908 173 14 0 1246 1418 536930769 536930597 2.570000e-60 243.0
12 TraesCS2A01G156900 chr1B 88.083 193 22 1 1238 1429 598925999 598926191 7.190000e-56 228.0
13 TraesCS2A01G156900 chr5D 76.485 404 79 14 2075 2473 52278712 52278320 3.370000e-49 206.0
14 TraesCS2A01G156900 chr5D 75.940 399 79 14 2037 2428 432026785 432027173 3.390000e-44 189.0
15 TraesCS2A01G156900 chr6D 77.285 361 66 13 2037 2391 9788564 9788914 5.640000e-47 198.0
16 TraesCS2A01G156900 chr6D 76.602 359 70 12 2037 2390 9550184 9550533 4.390000e-43 185.0
17 TraesCS2A01G156900 chr6D 74.652 359 76 12 2124 2472 469522674 469522321 7.450000e-31 145.0
18 TraesCS2A01G156900 chr6A 75.231 432 92 12 2037 2461 560695215 560694792 9.440000e-45 191.0
19 TraesCS2A01G156900 chr6B 75.115 434 87 16 2045 2468 144850024 144850446 1.580000e-42 183.0
20 TraesCS2A01G156900 chr6B 83.621 116 16 3 2470 2584 83128901 83128788 3.520000e-19 106.0
21 TraesCS2A01G156900 chr7A 89.189 111 10 1 2363 2473 641583196 641583088 1.250000e-28 137.0
22 TraesCS2A01G156900 chr7A 85.088 114 15 2 2472 2584 200235460 200235572 5.840000e-22 115.0
23 TraesCS2A01G156900 chr5A 79.310 116 23 1 2470 2584 456168211 456168096 2.130000e-11 80.5


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 TraesCS2A01G156900 chr2A 103363197 103365780 2583 False 4772.0 4772 100.000 1 2584 1 chr2A.!!$F1 2583
1 TraesCS2A01G156900 chr2B 157313840 157315988 2148 False 2660.0 2660 89.493 485 2584 1 chr2B.!!$F1 2099
2 TraesCS2A01G156900 chr2D 106999526 107001392 1866 False 1329.5 2409 92.664 35 1891 2 chr2D.!!$F2 1856
3 TraesCS2A01G156900 chr2D 107010554 107011242 688 False 789.0 789 87.482 1892 2584 1 chr2D.!!$F1 692
4 TraesCS2A01G156900 chr3B 152877862 152878522 660 True 592.0 592 83.554 779 1429 1 chr3B.!!$R1 650
5 TraesCS2A01G156900 chr3D 101860500 101861132 632 True 569.0 569 83.206 871 1514 1 chr3D.!!$R1 643
6 TraesCS2A01G156900 chr3A 554017824 554018440 616 False 523.0 523 82.732 821 1429 1 chr3A.!!$F1 608

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
719 752 0.249868 AGGTGTCCACATGTCACGTG 60.25 55.0 9.94 9.94 33.51 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2113 0.249489 GATGGACGCTCGCTAACCAT 60.249 55.0 0.0 0.0 42.9 3.55 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
28 29 7.887996 TTTTATCATTGTGATTTGTGAAGCC 57.112 32.000 0.00 0.00 38.26 4.35
29 30 3.940209 TCATTGTGATTTGTGAAGCCC 57.060 42.857 0.00 0.00 0.00 5.19
30 31 3.499338 TCATTGTGATTTGTGAAGCCCT 58.501 40.909 0.00 0.00 0.00 5.19
31 32 3.507233 TCATTGTGATTTGTGAAGCCCTC 59.493 43.478 0.00 0.00 0.00 4.30
32 33 2.957402 TGTGATTTGTGAAGCCCTCT 57.043 45.000 0.00 0.00 0.00 3.69
33 34 2.507484 TGTGATTTGTGAAGCCCTCTG 58.493 47.619 0.00 0.00 0.00 3.35
37 38 0.250901 TTTGTGAAGCCCTCTGCCTC 60.251 55.000 0.00 0.00 42.71 4.70
48 49 1.902508 CCTCTGCCTCTGGAGTTAACA 59.097 52.381 8.61 0.00 0.00 2.41
116 117 0.824759 GTACTGACGGGGATTCTGCT 59.175 55.000 0.00 0.00 0.00 4.24
119 120 1.089920 CTGACGGGGATTCTGCTTTG 58.910 55.000 0.00 0.00 0.00 2.77
121 122 1.626321 TGACGGGGATTCTGCTTTGTA 59.374 47.619 0.00 0.00 0.00 2.41
122 123 2.238646 TGACGGGGATTCTGCTTTGTAT 59.761 45.455 0.00 0.00 0.00 2.29
123 124 3.452990 TGACGGGGATTCTGCTTTGTATA 59.547 43.478 0.00 0.00 0.00 1.47
124 125 4.102524 TGACGGGGATTCTGCTTTGTATAT 59.897 41.667 0.00 0.00 0.00 0.86
125 126 5.305902 TGACGGGGATTCTGCTTTGTATATA 59.694 40.000 0.00 0.00 0.00 0.86
126 127 5.548406 ACGGGGATTCTGCTTTGTATATAC 58.452 41.667 5.89 5.89 0.00 1.47
127 128 5.307196 ACGGGGATTCTGCTTTGTATATACT 59.693 40.000 13.89 0.00 0.00 2.12
129 130 6.534634 GGGGATTCTGCTTTGTATATACTGT 58.465 40.000 13.89 0.00 0.00 3.55
130 131 7.524863 CGGGGATTCTGCTTTGTATATACTGTA 60.525 40.741 13.89 3.77 0.00 2.74
139 147 8.935844 TGCTTTGTATATACTGTATTATGCAGC 58.064 33.333 13.89 7.81 37.47 5.25
180 188 3.764885 GCGTTGGCAAATGAGTAGAAT 57.235 42.857 0.00 0.00 39.62 2.40
182 190 4.485163 GCGTTGGCAAATGAGTAGAATTT 58.515 39.130 0.00 0.00 39.62 1.82
183 191 4.558860 GCGTTGGCAAATGAGTAGAATTTC 59.441 41.667 0.00 0.00 39.62 2.17
184 192 5.095490 CGTTGGCAAATGAGTAGAATTTCC 58.905 41.667 0.00 0.00 0.00 3.13
185 193 4.963276 TGGCAAATGAGTAGAATTTCCG 57.037 40.909 0.00 0.00 0.00 4.30
186 194 4.331968 TGGCAAATGAGTAGAATTTCCGT 58.668 39.130 0.00 0.00 0.00 4.69
187 195 4.764823 TGGCAAATGAGTAGAATTTCCGTT 59.235 37.500 0.00 0.00 0.00 4.44
188 196 5.941058 TGGCAAATGAGTAGAATTTCCGTTA 59.059 36.000 0.00 0.00 0.00 3.18
189 197 6.093495 TGGCAAATGAGTAGAATTTCCGTTAG 59.907 38.462 0.00 0.00 0.00 2.34
190 198 6.315393 GGCAAATGAGTAGAATTTCCGTTAGA 59.685 38.462 0.00 0.00 0.00 2.10
191 199 7.012421 GGCAAATGAGTAGAATTTCCGTTAGAT 59.988 37.037 0.00 0.00 0.00 1.98
211 219 6.506538 AGATAGGTTTCCAGTATGCTCAAT 57.493 37.500 0.00 0.00 31.97 2.57
231 239 5.893255 TCAATATTGGAGTGGAATTTCTGGG 59.107 40.000 15.36 0.00 0.00 4.45
232 240 1.923356 TTGGAGTGGAATTTCTGGGC 58.077 50.000 0.00 0.00 0.00 5.36
238 246 0.825425 TGGAATTTCTGGGCGTTGCA 60.825 50.000 0.00 0.00 0.00 4.08
258 266 3.128242 GCATGTCTGGAATCCTTGAACTG 59.872 47.826 0.00 2.11 0.00 3.16
261 269 2.485814 GTCTGGAATCCTTGAACTGCAC 59.514 50.000 0.00 0.00 0.00 4.57
276 284 7.275888 TGAACTGCACTTTCAAATTCAGTAT 57.724 32.000 3.90 0.00 34.14 2.12
334 342 4.348656 CTCGTCCGAATTAGATCAAACGA 58.651 43.478 0.00 0.00 35.73 3.85
338 346 2.544267 CCGAATTAGATCAAACGAGCCC 59.456 50.000 0.00 0.00 0.00 5.19
339 347 3.458189 CGAATTAGATCAAACGAGCCCT 58.542 45.455 0.00 0.00 0.00 5.19
350 358 0.979665 ACGAGCCCTGATCCATATGG 59.020 55.000 16.25 16.25 0.00 2.74
387 395 9.214957 TCGGATACATAATACACATGAAATTCC 57.785 33.333 0.00 0.00 0.00 3.01
460 468 7.217200 TCATAGAGTTACATCAGGCATAAACC 58.783 38.462 0.00 0.00 0.00 3.27
461 469 4.781934 AGAGTTACATCAGGCATAAACCC 58.218 43.478 0.00 0.00 0.00 4.11
463 471 2.616842 GTTACATCAGGCATAAACCCGG 59.383 50.000 0.00 0.00 0.00 5.73
465 473 1.005450 ACATCAGGCATAAACCCGGTT 59.995 47.619 0.00 0.00 0.00 4.44
466 474 1.405105 CATCAGGCATAAACCCGGTTG 59.595 52.381 2.79 0.00 0.00 3.77
467 475 0.963355 TCAGGCATAAACCCGGTTGC 60.963 55.000 2.79 3.70 0.00 4.17
512 522 2.003196 CAGCCTCGTCTCTTTCTTCC 57.997 55.000 0.00 0.00 0.00 3.46
521 531 1.000955 TCTCTTTCTTCCACGGCTGTC 59.999 52.381 0.00 0.00 0.00 3.51
719 752 0.249868 AGGTGTCCACATGTCACGTG 60.250 55.000 9.94 9.94 33.51 4.49
768 801 2.838202 TGGGTCTTCCTAGCACCTAAAG 59.162 50.000 0.00 0.00 36.20 1.85
773 806 5.421374 GGTCTTCCTAGCACCTAAAGTTAGA 59.579 44.000 0.00 0.00 32.47 2.10
776 809 5.672421 TCCTAGCACCTAAAGTTAGAACC 57.328 43.478 0.00 0.00 32.47 3.62
886 941 1.463214 TGCTCCCTCTCCAAACCCA 60.463 57.895 0.00 0.00 0.00 4.51
903 958 3.090532 ACTTCCCCCGCATCTCCC 61.091 66.667 0.00 0.00 0.00 4.30
949 1006 4.349342 TCCCTTCAAAGAGAGAAGAAAGCT 59.651 41.667 4.61 0.00 44.00 3.74
983 1040 1.354040 CTAGCTGCAGACCGACAAAG 58.646 55.000 20.43 0.00 0.00 2.77
988 1045 2.668280 GCAGACCGACAAAGCGACC 61.668 63.158 0.00 0.00 0.00 4.79
989 1046 2.049433 AGACCGACAAAGCGACCG 60.049 61.111 0.00 0.00 0.00 4.79
1029 1086 0.895530 CCAGCTACCGGACAGAAGAA 59.104 55.000 9.46 0.00 0.00 2.52
1030 1087 1.134965 CCAGCTACCGGACAGAAGAAG 60.135 57.143 9.46 0.00 0.00 2.85
1031 1088 1.819288 CAGCTACCGGACAGAAGAAGA 59.181 52.381 9.46 0.00 0.00 2.87
1035 1092 0.969894 ACCGGACAGAAGAAGACTGG 59.030 55.000 9.46 0.00 39.38 4.00
1206 1263 2.065906 GACGAGGACGAGGAGATGGC 62.066 65.000 0.00 0.00 42.66 4.40
1208 1265 3.492311 GAGGACGAGGAGATGGCGC 62.492 68.421 0.00 0.00 0.00 6.53
1415 1491 0.099436 GCGCAACATGAACTGATCCC 59.901 55.000 0.30 0.00 0.00 3.85
1444 1520 3.197790 CCTGGTGGATCTTGCGCG 61.198 66.667 0.00 0.00 34.57 6.86
1465 1541 0.527600 GTACGGCAGTGATCGATGCA 60.528 55.000 19.87 0.00 44.37 3.96
1515 1593 1.792949 CCGTGCGAGCATCTAATTACC 59.207 52.381 0.00 0.00 0.00 2.85
1536 1616 5.007682 ACCAATTGTATTTGTAGAACGCCT 58.992 37.500 4.43 0.00 0.00 5.52
1553 1633 1.947678 GCCTGTGCATTGCTACAGACT 60.948 52.381 27.82 0.00 45.46 3.24
1595 1675 7.990917 TGAAGCTGACTGTACAAATTTACAAA 58.009 30.769 0.00 0.00 31.52 2.83
1636 1719 3.194861 TGTCCTTTTTGTCACGAGACTG 58.805 45.455 14.15 0.34 45.20 3.51
1642 1725 3.660501 TTTGTCACGAGACTGCTACAT 57.339 42.857 14.15 0.00 45.20 2.29
1675 1758 8.602472 TTAGCTTCACATTAACCCCAATTATT 57.398 30.769 0.00 0.00 0.00 1.40
1685 1768 9.142014 CATTAACCCCAATTATTGTCCTCAATA 57.858 33.333 4.15 0.00 43.12 1.90
1702 1785 9.267084 GTCCTCAATAAGTTTATCATCTTCCTC 57.733 37.037 0.00 0.00 0.00 3.71
1725 1835 2.774439 AACAATTGCGTGGAGACAAC 57.226 45.000 5.05 0.00 46.06 3.32
1726 1836 1.674359 ACAATTGCGTGGAGACAACA 58.326 45.000 5.05 0.00 46.06 3.33
1748 1858 5.244402 ACAAACATGAGCATTGATGGAAAGA 59.756 36.000 0.00 0.00 0.00 2.52
1752 1862 3.264947 TGAGCATTGATGGAAAGAGACG 58.735 45.455 0.00 0.00 0.00 4.18
1771 1881 2.855963 ACGGTTTAATACGATCACGCTG 59.144 45.455 6.35 0.00 43.96 5.18
1809 1921 0.034186 TCGCTTTCTTCCCATGGCAT 60.034 50.000 6.09 0.00 0.00 4.40
1871 1983 5.732647 CCAACGAATTTAACGACTGCTATTG 59.267 40.000 0.00 0.00 34.70 1.90
1912 2026 7.614192 TGAGTAGTAGTTTCTATGTGTCCATCA 59.386 37.037 0.00 0.00 32.29 3.07
1918 2032 6.475504 AGTTTCTATGTGTCCATCATGTTCA 58.524 36.000 0.00 0.00 32.29 3.18
1924 2038 3.940852 TGTGTCCATCATGTTCATGCTAC 59.059 43.478 7.80 4.53 0.00 3.58
1953 2067 4.942483 TGCATGGCAATTTATTCCTTTTGG 59.058 37.500 0.00 0.00 34.76 3.28
1981 2095 6.861065 TGTCTTCGTATTTGAAAAAGAGCT 57.139 33.333 0.00 0.00 0.00 4.09
1999 2113 6.959639 AGAGCTGAGTTTTATTTTTGGACA 57.040 33.333 0.00 0.00 0.00 4.02
2003 2117 6.041979 AGCTGAGTTTTATTTTTGGACATGGT 59.958 34.615 0.00 0.00 0.00 3.55
2016 2130 1.153647 CATGGTTAGCGAGCGTCCA 60.154 57.895 10.06 10.06 0.00 4.02
2019 2133 1.141019 GGTTAGCGAGCGTCCATCA 59.859 57.895 0.00 0.00 0.00 3.07
2029 2160 3.669290 CGAGCGTCCATCATCTCATACTC 60.669 52.174 0.00 0.00 0.00 2.59
2033 2164 4.492611 CGTCCATCATCTCATACTCCATG 58.507 47.826 0.00 0.00 35.81 3.66
2035 2166 5.477510 GTCCATCATCTCATACTCCATGAC 58.522 45.833 0.00 0.00 38.79 3.06
2041 2172 9.205719 CATCATCTCATACTCCATGACTTTTAG 57.794 37.037 0.00 0.00 38.79 1.85
2043 2174 6.485830 TCTCATACTCCATGACTTTTAGGG 57.514 41.667 0.00 0.00 38.79 3.53
2044 2175 5.036117 TCATACTCCATGACTTTTAGGGC 57.964 43.478 0.00 0.00 38.79 5.19
2061 2192 7.654022 TTTAGGGCCTCACAATTAATTAAGG 57.346 36.000 10.74 14.70 0.00 2.69
2097 2242 7.959718 AAATTGAGTCATTCGATTTTGATCG 57.040 32.000 0.00 2.58 44.13 3.69
2122 2267 7.012327 CGGATCAACAATATTTTAAGGAGCTCA 59.988 37.037 17.19 0.00 0.00 4.26
2176 2321 7.927048 TCTTTACTTTTGGAGCTTTTCTGTAC 58.073 34.615 0.00 0.00 0.00 2.90
2181 2326 4.537135 TTGGAGCTTTTCTGTACGATCT 57.463 40.909 0.00 0.00 0.00 2.75
2249 2394 9.250624 CAACAATTTTTGAAATCAATTGGCAAT 57.749 25.926 6.96 6.96 40.68 3.56
2275 2420 6.252995 ACTGGCCCATAAAAAGAGTGAATTA 58.747 36.000 0.00 0.00 0.00 1.40
2327 2474 3.312146 CGCCAACATGTGATATTGTAGCA 59.688 43.478 0.00 0.00 0.00 3.49
2336 2483 7.555914 ACATGTGATATTGTAGCACCAACATAA 59.444 33.333 0.00 0.00 44.02 1.90
2343 2490 7.880160 ATTGTAGCACCAACATAATACATGT 57.120 32.000 2.69 2.69 0.00 3.21
2392 2539 7.291416 TCCACATAAGTATGGGTAGATTAGCAA 59.709 37.037 3.48 0.00 35.33 3.91
2431 2578 3.118445 CCACAAAAGACCCACCAAAACAT 60.118 43.478 0.00 0.00 0.00 2.71
2465 2612 6.279513 ACAAAAAGAAAACACACTCCATCA 57.720 33.333 0.00 0.00 0.00 3.07
2468 2615 6.713762 AAAAGAAAACACACTCCATCATCA 57.286 33.333 0.00 0.00 0.00 3.07
2540 2687 2.099263 GAGTCATCTGATTTCGACCGGA 59.901 50.000 9.46 0.00 0.00 5.14
2545 2692 1.076332 CTGATTTCGACCGGACCAAC 58.924 55.000 9.46 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.387397 GGGCTTCACAAATCACAATGATAAAAA 59.613 33.333 0.00 0.00 35.76 1.94
4 5 6.873076 GGGCTTCACAAATCACAATGATAAAA 59.127 34.615 0.00 0.00 35.76 1.52
6 7 5.716228 AGGGCTTCACAAATCACAATGATAA 59.284 36.000 0.00 0.00 35.76 1.75
7 8 5.263599 AGGGCTTCACAAATCACAATGATA 58.736 37.500 0.00 0.00 35.76 2.15
8 9 4.091549 AGGGCTTCACAAATCACAATGAT 58.908 39.130 0.00 0.00 39.09 2.45
9 10 3.499338 AGGGCTTCACAAATCACAATGA 58.501 40.909 0.00 0.00 0.00 2.57
10 11 3.508793 AGAGGGCTTCACAAATCACAATG 59.491 43.478 0.00 0.00 0.00 2.82
11 12 3.508793 CAGAGGGCTTCACAAATCACAAT 59.491 43.478 0.00 0.00 0.00 2.71
12 13 2.886523 CAGAGGGCTTCACAAATCACAA 59.113 45.455 0.00 0.00 0.00 3.33
13 14 2.507484 CAGAGGGCTTCACAAATCACA 58.493 47.619 0.00 0.00 0.00 3.58
14 15 1.200948 GCAGAGGGCTTCACAAATCAC 59.799 52.381 0.00 0.00 40.25 3.06
15 16 1.538047 GCAGAGGGCTTCACAAATCA 58.462 50.000 0.00 0.00 40.25 2.57
16 17 0.813821 GGCAGAGGGCTTCACAAATC 59.186 55.000 0.00 0.00 44.01 2.17
17 18 2.967270 GGCAGAGGGCTTCACAAAT 58.033 52.632 0.00 0.00 44.01 2.32
18 19 4.500265 GGCAGAGGGCTTCACAAA 57.500 55.556 0.00 0.00 44.01 2.83
26 27 0.978146 TAACTCCAGAGGCAGAGGGC 60.978 60.000 0.00 0.00 43.74 5.19
27 28 1.208293 GTTAACTCCAGAGGCAGAGGG 59.792 57.143 0.00 0.00 34.27 4.30
28 29 1.902508 TGTTAACTCCAGAGGCAGAGG 59.097 52.381 7.22 0.00 34.27 3.69
29 30 2.093764 CCTGTTAACTCCAGAGGCAGAG 60.094 54.545 7.22 0.00 36.16 3.35
30 31 1.902508 CCTGTTAACTCCAGAGGCAGA 59.097 52.381 7.22 0.00 31.38 4.26
31 32 1.625818 ACCTGTTAACTCCAGAGGCAG 59.374 52.381 7.22 2.56 31.38 4.85
32 33 1.623811 GACCTGTTAACTCCAGAGGCA 59.376 52.381 7.22 0.00 31.38 4.75
33 34 1.066071 GGACCTGTTAACTCCAGAGGC 60.066 57.143 7.22 1.87 31.38 4.70
37 38 3.403038 CAGTTGGACCTGTTAACTCCAG 58.597 50.000 13.12 0.75 35.47 3.86
48 49 2.779430 TCATCATATGCCAGTTGGACCT 59.221 45.455 1.45 0.00 37.39 3.85
96 97 0.535335 GCAGAATCCCCGTCAGTACA 59.465 55.000 0.00 0.00 0.00 2.90
97 98 0.824759 AGCAGAATCCCCGTCAGTAC 59.175 55.000 0.00 0.00 0.00 2.73
121 122 9.159364 CAGACAATGCTGCATAATACAGTATAT 57.841 33.333 16.58 0.00 39.21 0.86
122 123 8.538409 CAGACAATGCTGCATAATACAGTATA 57.462 34.615 16.58 0.00 39.21 1.47
123 124 7.430992 CAGACAATGCTGCATAATACAGTAT 57.569 36.000 16.58 3.05 41.48 2.12
124 125 6.849588 CAGACAATGCTGCATAATACAGTA 57.150 37.500 16.58 0.00 37.47 2.74
125 126 5.746307 CAGACAATGCTGCATAATACAGT 57.254 39.130 16.58 7.85 37.47 3.55
139 147 3.550233 GCAGAGCCAATATGCAGACAATG 60.550 47.826 0.00 0.00 45.71 2.82
173 181 8.202811 GGAAACCTATCTAACGGAAATTCTACT 58.797 37.037 0.00 0.00 0.00 2.57
174 182 7.983484 TGGAAACCTATCTAACGGAAATTCTAC 59.017 37.037 0.00 0.00 0.00 2.59
175 183 8.081517 TGGAAACCTATCTAACGGAAATTCTA 57.918 34.615 0.00 0.00 0.00 2.10
176 184 6.954232 TGGAAACCTATCTAACGGAAATTCT 58.046 36.000 0.00 0.00 0.00 2.40
177 185 6.822170 ACTGGAAACCTATCTAACGGAAATTC 59.178 38.462 0.00 0.00 0.00 2.17
178 186 6.718294 ACTGGAAACCTATCTAACGGAAATT 58.282 36.000 0.00 0.00 0.00 1.82
180 188 5.750352 ACTGGAAACCTATCTAACGGAAA 57.250 39.130 0.00 0.00 0.00 3.13
182 190 5.221382 GCATACTGGAAACCTATCTAACGGA 60.221 44.000 0.00 0.00 0.00 4.69
183 191 4.989168 GCATACTGGAAACCTATCTAACGG 59.011 45.833 0.00 0.00 0.00 4.44
184 192 5.844004 AGCATACTGGAAACCTATCTAACG 58.156 41.667 0.00 0.00 0.00 3.18
185 193 6.817184 TGAGCATACTGGAAACCTATCTAAC 58.183 40.000 0.00 0.00 0.00 2.34
186 194 7.432148 TTGAGCATACTGGAAACCTATCTAA 57.568 36.000 0.00 0.00 0.00 2.10
187 195 7.618019 ATTGAGCATACTGGAAACCTATCTA 57.382 36.000 0.00 0.00 0.00 1.98
188 196 5.957771 TTGAGCATACTGGAAACCTATCT 57.042 39.130 0.00 0.00 0.00 1.98
189 197 8.725148 CAATATTGAGCATACTGGAAACCTATC 58.275 37.037 10.04 0.00 0.00 2.08
190 198 7.667219 CCAATATTGAGCATACTGGAAACCTAT 59.333 37.037 17.23 0.00 36.94 2.57
191 199 6.998074 CCAATATTGAGCATACTGGAAACCTA 59.002 38.462 17.23 0.00 36.94 3.08
211 219 3.631250 GCCCAGAAATTCCACTCCAATA 58.369 45.455 0.00 0.00 0.00 1.90
231 239 0.099436 GGATTCCAGACATGCAACGC 59.901 55.000 0.00 0.00 0.00 4.84
232 240 1.742761 AGGATTCCAGACATGCAACG 58.257 50.000 5.29 0.00 0.00 4.10
238 246 3.245016 TGCAGTTCAAGGATTCCAGACAT 60.245 43.478 5.29 0.00 0.00 3.06
258 266 8.810652 TTTACCAATACTGAATTTGAAAGTGC 57.189 30.769 0.00 0.00 0.00 4.40
276 284 3.153919 GGCCAGACACAGAATTTACCAA 58.846 45.455 0.00 0.00 0.00 3.67
334 342 4.754411 AATTTCCATATGGATCAGGGCT 57.246 40.909 25.07 3.57 44.98 5.19
338 346 8.292448 CCGAAGTTTAATTTCCATATGGATCAG 58.708 37.037 25.07 11.52 44.98 2.90
339 347 7.996066 TCCGAAGTTTAATTTCCATATGGATCA 59.004 33.333 25.07 15.10 44.98 2.92
362 370 8.450964 GGGAATTTCATGTGTATTATGTATCCG 58.549 37.037 0.00 0.00 0.00 4.18
367 375 7.125391 ACCTGGGAATTTCATGTGTATTATGT 58.875 34.615 0.00 0.00 0.00 2.29
381 389 3.915346 ACTTGGGTTACCTGGGAATTT 57.085 42.857 0.00 0.00 37.76 1.82
387 395 2.827921 AGTACGTACTTGGGTTACCTGG 59.172 50.000 22.45 0.00 37.76 4.45
460 468 4.093952 CTGCTTCTGCGCAACCGG 62.094 66.667 13.05 0.00 43.34 5.28
461 469 3.020026 CTCTGCTTCTGCGCAACCG 62.020 63.158 13.05 0.00 43.34 4.44
463 471 0.110464 GAACTCTGCTTCTGCGCAAC 60.110 55.000 13.05 1.54 43.34 4.17
465 473 0.321034 ATGAACTCTGCTTCTGCGCA 60.321 50.000 10.98 10.98 43.34 6.09
466 474 1.645034 TATGAACTCTGCTTCTGCGC 58.355 50.000 0.00 0.00 43.34 6.09
467 475 3.451526 TGATATGAACTCTGCTTCTGCG 58.548 45.455 0.00 0.00 43.34 5.18
512 522 1.143305 CAACTGAAGAGACAGCCGTG 58.857 55.000 0.00 0.00 41.06 4.94
668 701 2.697761 TTTCGAGCGTCCTCTCCCG 61.698 63.158 0.00 0.00 35.90 5.14
719 752 0.037232 GGTGTCCACTGACCACTAGC 60.037 60.000 0.00 0.00 41.01 3.42
768 801 2.497107 TACGCGCCATAGGTTCTAAC 57.503 50.000 5.73 0.00 0.00 2.34
773 806 1.608025 CCATCATACGCGCCATAGGTT 60.608 52.381 5.73 0.00 0.00 3.50
776 809 1.795768 AACCATCATACGCGCCATAG 58.204 50.000 5.73 0.00 0.00 2.23
886 941 3.090532 GGGAGATGCGGGGGAAGT 61.091 66.667 0.00 0.00 0.00 3.01
949 1006 0.105453 GCTAGGGTGGATCTCTCCCA 60.105 60.000 18.06 7.92 43.31 4.37
983 1040 3.774702 GGTTTGAGTCGCGGTCGC 61.775 66.667 6.13 5.16 35.26 5.19
1029 1086 2.362120 GCCTTGCCATGCCAGTCT 60.362 61.111 0.00 0.00 0.00 3.24
1030 1087 2.362120 AGCCTTGCCATGCCAGTC 60.362 61.111 0.00 0.00 0.00 3.51
1031 1088 2.362120 GAGCCTTGCCATGCCAGT 60.362 61.111 0.00 0.00 0.00 4.00
1166 1223 4.241555 GCCGCACTCCCCGATGAT 62.242 66.667 0.00 0.00 0.00 2.45
1415 1491 2.754658 ACCAGGCCTACGGACGAG 60.755 66.667 15.94 0.00 34.63 4.18
1444 1520 1.299165 ATCGATCACTGCCGTACGC 60.299 57.895 10.49 6.24 38.31 4.42
1515 1593 5.794945 CACAGGCGTTCTACAAATACAATTG 59.205 40.000 3.24 3.24 36.37 2.32
1536 1616 4.831107 TCATTAGTCTGTAGCAATGCACA 58.169 39.130 8.35 9.01 0.00 4.57
1595 1675 6.891908 AGGACAAGCCATGAAACATAAGTAAT 59.108 34.615 0.00 0.00 40.02 1.89
1606 1686 3.703556 TGACAAAAAGGACAAGCCATGAA 59.296 39.130 0.00 0.00 40.02 2.57
1636 1719 5.179368 TGTGAAGCTAAGTGTTTGATGTAGC 59.821 40.000 0.00 0.00 37.94 3.58
1642 1725 6.016610 GGGTTAATGTGAAGCTAAGTGTTTGA 60.017 38.462 0.00 0.00 0.00 2.69
1675 1758 8.772250 AGGAAGATGATAAACTTATTGAGGACA 58.228 33.333 0.00 0.00 0.00 4.02
1685 1768 9.838339 ATTGTTATCGAGGAAGATGATAAACTT 57.162 29.630 0.00 0.00 36.61 2.66
1702 1785 2.670905 TGTCTCCACGCAATTGTTATCG 59.329 45.455 7.40 4.50 0.00 2.92
1725 1835 5.716094 TCTTTCCATCAATGCTCATGTTTG 58.284 37.500 0.00 0.00 0.00 2.93
1726 1836 5.713389 TCTCTTTCCATCAATGCTCATGTTT 59.287 36.000 0.00 0.00 0.00 2.83
1748 1858 3.111098 GCGTGATCGTATTAAACCGTCT 58.889 45.455 0.00 0.00 39.49 4.18
1752 1862 4.085210 GCTACAGCGTGATCGTATTAAACC 60.085 45.833 0.00 0.00 39.49 3.27
1809 1921 4.671508 GCAGCACAAACGCATACAATTAGA 60.672 41.667 0.00 0.00 0.00 2.10
1888 2002 7.956328 TGATGGACACATAGAAACTACTACT 57.044 36.000 0.00 0.00 37.47 2.57
1889 2003 8.198109 ACATGATGGACACATAGAAACTACTAC 58.802 37.037 0.00 0.00 37.47 2.73
1890 2004 8.306313 ACATGATGGACACATAGAAACTACTA 57.694 34.615 0.00 0.00 37.47 1.82
1896 2010 6.183360 GCATGAACATGATGGACACATAGAAA 60.183 38.462 17.40 0.00 41.20 2.52
1912 2026 1.679680 GCATGGCAGTAGCATGAACAT 59.320 47.619 0.00 0.00 44.61 2.71
1953 2067 9.159470 CTCTTTTTCAAATACGAAGACAAGTTC 57.841 33.333 0.00 0.00 0.00 3.01
1981 2095 7.870445 GCTAACCATGTCCAAAAATAAAACTCA 59.130 33.333 0.00 0.00 0.00 3.41
1999 2113 0.249489 GATGGACGCTCGCTAACCAT 60.249 55.000 0.00 0.00 42.90 3.55
2003 2117 1.001268 GAGATGATGGACGCTCGCTAA 60.001 52.381 0.00 0.00 0.00 3.09
2016 2130 8.373981 CCTAAAAGTCATGGAGTATGAGATGAT 58.626 37.037 0.00 0.00 46.09 2.45
2019 2133 6.465035 GCCCTAAAAGTCATGGAGTATGAGAT 60.465 42.308 0.00 0.00 46.09 2.75
2029 2160 2.290896 TGTGAGGCCCTAAAAGTCATGG 60.291 50.000 0.00 0.00 0.00 3.66
2033 2164 6.775594 ATTAATTGTGAGGCCCTAAAAGTC 57.224 37.500 0.00 0.00 0.00 3.01
2035 2166 8.197439 CCTTAATTAATTGTGAGGCCCTAAAAG 58.803 37.037 11.05 1.96 0.00 2.27
2041 2172 7.286775 TGAATACCTTAATTAATTGTGAGGCCC 59.713 37.037 19.10 0.00 0.00 5.80
2091 2236 9.402320 TCCTTAAAATATTGTTGATCCGATCAA 57.598 29.630 18.10 18.10 46.30 2.57
2092 2237 8.972458 TCCTTAAAATATTGTTGATCCGATCA 57.028 30.769 7.00 7.00 37.55 2.92
2093 2238 8.017946 GCTCCTTAAAATATTGTTGATCCGATC 58.982 37.037 1.01 1.01 0.00 3.69
2094 2239 7.721399 AGCTCCTTAAAATATTGTTGATCCGAT 59.279 33.333 0.00 0.00 0.00 4.18
2095 2240 7.054124 AGCTCCTTAAAATATTGTTGATCCGA 58.946 34.615 0.00 0.00 0.00 4.55
2096 2241 7.012327 TGAGCTCCTTAAAATATTGTTGATCCG 59.988 37.037 12.15 0.00 0.00 4.18
2097 2242 8.131731 GTGAGCTCCTTAAAATATTGTTGATCC 58.868 37.037 12.15 0.00 0.00 3.36
2110 2255 9.520515 AAGAATTAAATGAGTGAGCTCCTTAAA 57.479 29.630 12.15 0.00 40.95 1.52
2153 2298 6.539464 TCGTACAGAAAAGCTCCAAAAGTAAA 59.461 34.615 0.00 0.00 0.00 2.01
2157 2302 5.409826 AGATCGTACAGAAAAGCTCCAAAAG 59.590 40.000 0.00 0.00 0.00 2.27
2249 2394 5.249780 TCACTCTTTTTATGGGCCAGTTA 57.750 39.130 13.78 0.00 0.00 2.24
2253 2398 6.406849 GCATAATTCACTCTTTTTATGGGCCA 60.407 38.462 9.61 9.61 34.25 5.36
2258 2403 7.775120 AGGGTGCATAATTCACTCTTTTTATG 58.225 34.615 0.00 0.00 42.21 1.90
2275 2420 2.263895 TAGGTGGTTAGAGGGTGCAT 57.736 50.000 0.00 0.00 0.00 3.96
2327 2474 7.225931 GTCGGTGATAACATGTATTATGTTGGT 59.774 37.037 13.79 4.48 41.73 3.67
2336 2483 9.778741 AAAATCTATGTCGGTGATAACATGTAT 57.221 29.630 0.00 0.00 36.78 2.29
2392 2539 9.173021 TCTTTTGTGGTGTGATTCGATATTATT 57.827 29.630 0.00 0.00 0.00 1.40
2399 2546 2.875933 GGTCTTTTGTGGTGTGATTCGA 59.124 45.455 0.00 0.00 0.00 3.71
2465 2612 8.336235 TGTGAGGTCTTAAAAATTAGGGATGAT 58.664 33.333 0.00 0.00 0.00 2.45
2468 2615 7.699878 ACTGTGAGGTCTTAAAAATTAGGGAT 58.300 34.615 0.00 0.00 0.00 3.85
2504 2651 8.160521 TCAGATGACTCGGTTTTAAATTGAAA 57.839 30.769 0.00 0.00 0.00 2.69
2517 2664 2.464865 GGTCGAAATCAGATGACTCGG 58.535 52.381 13.28 0.00 35.00 4.63
2525 2672 0.970640 TTGGTCCGGTCGAAATCAGA 59.029 50.000 0.00 0.00 0.00 3.27
2540 2687 7.290813 AGAGAACTCCTTAAGAAATTGTTGGT 58.709 34.615 3.36 0.00 0.00 3.67
2545 2692 9.224267 TGAATGAGAGAACTCCTTAAGAAATTG 57.776 33.333 3.36 0.00 41.99 2.32


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

AutoCloner maintained by Alex Coulton.