Multiple sequence alignment - TraesCS2A01G476400

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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 TraesCS2A01G476400 chr2A 100.000 2651 0 0 1 2651 716233492 716236142 0.000000e+00 4896
1 TraesCS2A01G476400 chr2A 79.562 411 68 11 2233 2641 716455155 716455551 2.010000e-71 279
2 TraesCS2A01G476400 chr2B 89.340 1454 77 31 337 1740 695593837 695595262 0.000000e+00 1755
3 TraesCS2A01G476400 chr2B 92.073 492 29 6 2164 2651 695595615 695596100 0.000000e+00 684
4 TraesCS2A01G476400 chr2B 95.484 310 14 0 1756 2065 695595308 695595617 1.830000e-136 496
5 TraesCS2A01G476400 chr2B 90.544 349 22 5 1 339 695593432 695593779 4.020000e-123 451
6 TraesCS2A01G476400 chr2D 87.086 1510 96 49 544 1990 578703183 578704656 0.000000e+00 1616
7 TraesCS2A01G476400 chr2D 91.304 437 32 5 2218 2651 578705196 578705629 2.270000e-165 592
8 TraesCS2A01G476400 chr2D 91.049 324 17 4 1 313 578702527 578702849 6.780000e-116 427
9 TraesCS2A01G476400 chr2D 93.304 224 10 4 337 555 578702942 578703165 2.540000e-85 326
10 TraesCS2A01G476400 chr2D 78.417 417 70 11 2233 2641 578927577 578927981 1.220000e-63 254
11 TraesCS2A01G476400 chr4B 86.792 106 8 5 2060 2165 664775717 664775618 2.160000e-21 113
12 TraesCS2A01G476400 chr4B 85.714 105 9 3 2063 2167 116483338 116483436 3.610000e-19 106
13 TraesCS2A01G476400 chr5D 87.379 103 6 6 2063 2165 50675117 50675212 7.760000e-21 111
14 TraesCS2A01G476400 chr6B 84.615 117 10 7 2055 2171 141106395 141106503 2.790000e-20 110
15 TraesCS2A01G476400 chr1A 86.538 104 8 5 2062 2165 82720016 82720113 2.790000e-20 110
16 TraesCS2A01G476400 chr6A 86.408 103 8 5 2063 2165 15768095 15767999 1.000000e-19 108
17 TraesCS2A01G476400 chr7A 86.408 103 7 4 2063 2165 651673895 651673800 3.610000e-19 106
18 TraesCS2A01G476400 chr6D 83.761 117 11 7 2055 2171 65994309 65994417 1.300000e-18 104
19 TraesCS2A01G476400 chr4D 84.762 105 10 3 2063 2167 82462583 82462681 1.680000e-17 100


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 TraesCS2A01G476400 chr2A 716233492 716236142 2650 False 4896.00 4896 100.00000 1 2651 1 chr2A.!!$F1 2650
1 TraesCS2A01G476400 chr2B 695593432 695596100 2668 False 846.50 1755 91.86025 1 2651 4 chr2B.!!$F1 2650
2 TraesCS2A01G476400 chr2D 578702527 578705629 3102 False 740.25 1616 90.68575 1 2651 4 chr2D.!!$F2 2650

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
334 352 1.078848 GCCAGCCTCGATGAACACT 60.079 57.895 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2095 1.205655 CATCGTGGAGGAGAAGAGCAA 59.794 52.381 0.0 0.0 0.0 3.91 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 1.595357 CTACCCCGCCGAGTTCTTT 59.405 57.895 0.00 0.00 0.00 2.52
153 154 1.741770 GGCGGTGGTCAGTGATCAC 60.742 63.158 25.59 25.59 42.37 3.06
216 224 4.674475 TGATGTGTATTACGCGTGTACAT 58.326 39.130 29.31 24.87 31.71 2.29
260 272 6.773080 TCTTCATTTGCATTGTTTGTTTGTG 58.227 32.000 0.00 0.00 0.00 3.33
307 320 3.244976 GTTTGCTTGATTGATTCGGTGG 58.755 45.455 0.00 0.00 0.00 4.61
313 326 5.417266 TGCTTGATTGATTCGGTGGAATAAA 59.583 36.000 0.00 0.00 42.86 1.40
314 327 6.071672 TGCTTGATTGATTCGGTGGAATAAAA 60.072 34.615 0.00 0.00 42.86 1.52
320 338 4.097741 TGATTCGGTGGAATAAAATGCCAG 59.902 41.667 0.00 0.00 42.86 4.85
334 352 1.078848 GCCAGCCTCGATGAACACT 60.079 57.895 0.00 0.00 0.00 3.55
390 472 2.226674 GCAGAAGAGTTTACTTGGTGCC 59.773 50.000 0.00 0.00 33.74 5.01
391 473 3.476552 CAGAAGAGTTTACTTGGTGCCA 58.523 45.455 0.00 0.00 0.00 4.92
450 537 7.934457 AGCTAATGGATTAAGCATAACAACAG 58.066 34.615 0.00 0.00 0.00 3.16
458 545 7.862873 GGATTAAGCATAACAACAGATTAAGCC 59.137 37.037 0.00 0.00 32.21 4.35
515 602 1.867233 TCGTCAACTCTTCAAGCTTGC 59.133 47.619 21.99 3.30 0.00 4.01
608 725 8.616076 CAGTTGAGTTGTGAGTAAAAAGAAGAT 58.384 33.333 0.00 0.00 0.00 2.40
702 828 8.436046 TTTTTGTTTGAGCTGAGCAATATTTT 57.564 26.923 7.39 0.00 0.00 1.82
703 829 8.436046 TTTTGTTTGAGCTGAGCAATATTTTT 57.564 26.923 7.39 0.00 0.00 1.94
745 895 1.532868 CACCTTTCTTTGCTCGTCCAG 59.467 52.381 0.00 0.00 0.00 3.86
746 896 1.141053 ACCTTTCTTTGCTCGTCCAGT 59.859 47.619 0.00 0.00 0.00 4.00
747 897 1.532868 CCTTTCTTTGCTCGTCCAGTG 59.467 52.381 0.00 0.00 0.00 3.66
748 898 2.483876 CTTTCTTTGCTCGTCCAGTGA 58.516 47.619 0.00 0.00 0.00 3.41
749 899 2.839486 TTCTTTGCTCGTCCAGTGAT 57.161 45.000 0.00 0.00 0.00 3.06
750 900 3.953712 TTCTTTGCTCGTCCAGTGATA 57.046 42.857 0.00 0.00 0.00 2.15
751 901 4.471904 TTCTTTGCTCGTCCAGTGATAT 57.528 40.909 0.00 0.00 0.00 1.63
752 902 4.046938 TCTTTGCTCGTCCAGTGATATC 57.953 45.455 0.00 0.00 0.00 1.63
753 903 3.447229 TCTTTGCTCGTCCAGTGATATCA 59.553 43.478 0.00 0.00 0.00 2.15
754 904 2.871182 TGCTCGTCCAGTGATATCAC 57.129 50.000 25.47 25.47 46.77 3.06
777 927 2.294074 CAAGTTCCCAACCGAAAGACA 58.706 47.619 0.00 0.00 0.00 3.41
778 928 2.256117 AGTTCCCAACCGAAAGACAG 57.744 50.000 0.00 0.00 0.00 3.51
779 929 1.489230 AGTTCCCAACCGAAAGACAGT 59.511 47.619 0.00 0.00 0.00 3.55
783 933 1.602377 CCCAACCGAAAGACAGTGAAC 59.398 52.381 0.00 0.00 0.00 3.18
873 1030 1.196354 CGCTTTCTGTTCCTTGCTCTG 59.804 52.381 0.00 0.00 0.00 3.35
894 1051 3.181459 TGTCTTCAAAGAATCACCACGGA 60.181 43.478 0.00 0.00 36.68 4.69
960 1141 1.674322 GCCAATGCACACGTAGGGT 60.674 57.895 0.00 0.00 37.47 4.34
1101 1288 1.880340 CAAGATCGTCTGCTCGGCC 60.880 63.158 0.00 0.00 0.00 6.13
1248 1438 2.668550 GCCGGCGTGGTCTTTTCT 60.669 61.111 12.58 0.00 41.21 2.52
1505 1695 1.372997 CGGTGGAGTTCACGGTGAG 60.373 63.158 11.14 0.00 46.96 3.51
1645 1835 2.240500 CGCTGCGCCATAGACTTCC 61.241 63.158 9.88 0.00 0.00 3.46
1647 1837 0.878086 GCTGCGCCATAGACTTCCTC 60.878 60.000 4.18 0.00 0.00 3.71
1654 1844 2.036604 GCCATAGACTTCCTCTAGGTGC 59.963 54.545 0.00 0.00 34.80 5.01
1655 1845 2.294791 CCATAGACTTCCTCTAGGTGCG 59.705 54.545 0.00 0.00 34.80 5.34
1656 1846 2.054232 TAGACTTCCTCTAGGTGCGG 57.946 55.000 0.00 0.00 36.34 5.69
1675 1865 3.264897 CCGCCTGCATGAGTACGC 61.265 66.667 0.00 0.00 0.00 4.42
1679 1869 1.091771 GCCTGCATGAGTACGCACAT 61.092 55.000 0.00 0.00 33.75 3.21
1686 1876 3.785505 GCATGAGTACGCACATAACAAGC 60.786 47.826 0.00 0.00 0.00 4.01
1696 1907 5.556470 CGCACATAACAAGCGTTTAGTAAT 58.444 37.500 0.00 0.00 45.82 1.89
1697 1908 6.698107 CGCACATAACAAGCGTTTAGTAATA 58.302 36.000 0.00 0.00 45.82 0.98
1698 1909 7.174746 CGCACATAACAAGCGTTTAGTAATAA 58.825 34.615 0.00 0.00 45.82 1.40
1740 1958 7.445707 TGCCGGCAAGTAATTAACATCATATAA 59.554 33.333 30.74 0.00 0.00 0.98
1798 2046 1.171308 CCCATCACCTGTTGCTTCTG 58.829 55.000 0.00 0.00 0.00 3.02
1861 2109 0.617935 AAGCCTTGCTCTTCTCCTCC 59.382 55.000 0.00 0.00 38.25 4.30
1862 2110 0.546267 AGCCTTGCTCTTCTCCTCCA 60.546 55.000 0.00 0.00 30.62 3.86
1863 2111 0.392327 GCCTTGCTCTTCTCCTCCAC 60.392 60.000 0.00 0.00 0.00 4.02
1920 2168 3.692406 GTCAACGCCGACTCCCCT 61.692 66.667 0.00 0.00 32.92 4.79
1933 2181 1.657162 ACTCCCCTTCCATCCTTCCTA 59.343 52.381 0.00 0.00 0.00 2.94
2037 2285 4.051922 GCTCATTCCTACAATACGGAGTG 58.948 47.826 0.00 0.00 45.73 3.51
2046 2294 5.300034 CCTACAATACGGAGTGGTACATGTA 59.700 44.000 0.08 0.08 45.73 2.29
2075 2323 9.708092 GTAATTAACATTATACTCCCTCTGTCC 57.292 37.037 0.00 0.00 0.00 4.02
2076 2324 4.939052 AACATTATACTCCCTCTGTCCG 57.061 45.455 0.00 0.00 0.00 4.79
2077 2325 4.180377 ACATTATACTCCCTCTGTCCGA 57.820 45.455 0.00 0.00 0.00 4.55
2078 2326 4.543689 ACATTATACTCCCTCTGTCCGAA 58.456 43.478 0.00 0.00 0.00 4.30
2079 2327 4.960469 ACATTATACTCCCTCTGTCCGAAA 59.040 41.667 0.00 0.00 0.00 3.46
2080 2328 5.424252 ACATTATACTCCCTCTGTCCGAAAA 59.576 40.000 0.00 0.00 0.00 2.29
2081 2329 6.099845 ACATTATACTCCCTCTGTCCGAAAAT 59.900 38.462 0.00 0.00 0.00 1.82
2082 2330 7.289317 ACATTATACTCCCTCTGTCCGAAAATA 59.711 37.037 0.00 0.00 0.00 1.40
2083 2331 7.664552 TTATACTCCCTCTGTCCGAAAATAA 57.335 36.000 0.00 0.00 0.00 1.40
2084 2332 4.903045 ACTCCCTCTGTCCGAAAATAAA 57.097 40.909 0.00 0.00 0.00 1.40
2085 2333 5.437191 ACTCCCTCTGTCCGAAAATAAAT 57.563 39.130 0.00 0.00 0.00 1.40
2086 2334 5.186198 ACTCCCTCTGTCCGAAAATAAATG 58.814 41.667 0.00 0.00 0.00 2.32
2087 2335 5.174037 TCCCTCTGTCCGAAAATAAATGT 57.826 39.130 0.00 0.00 0.00 2.71
2088 2336 5.183228 TCCCTCTGTCCGAAAATAAATGTC 58.817 41.667 0.00 0.00 0.00 3.06
2089 2337 5.045869 TCCCTCTGTCCGAAAATAAATGTCT 60.046 40.000 0.00 0.00 0.00 3.41
2090 2338 5.648092 CCCTCTGTCCGAAAATAAATGTCTT 59.352 40.000 0.00 0.00 0.00 3.01
2091 2339 6.821665 CCCTCTGTCCGAAAATAAATGTCTTA 59.178 38.462 0.00 0.00 0.00 2.10
2092 2340 7.335924 CCCTCTGTCCGAAAATAAATGTCTTAA 59.664 37.037 0.00 0.00 0.00 1.85
2093 2341 8.893727 CCTCTGTCCGAAAATAAATGTCTTAAT 58.106 33.333 0.00 0.00 0.00 1.40
2155 2403 8.926710 AGTTGAGACACTTATTATTTTGAGACG 58.073 33.333 0.00 0.00 0.00 4.18
2156 2404 7.827819 TGAGACACTTATTATTTTGAGACGG 57.172 36.000 0.00 0.00 0.00 4.79
2157 2405 7.608153 TGAGACACTTATTATTTTGAGACGGA 58.392 34.615 0.00 0.00 0.00 4.69
2158 2406 7.759886 TGAGACACTTATTATTTTGAGACGGAG 59.240 37.037 0.00 0.00 0.00 4.63
2159 2407 7.042335 AGACACTTATTATTTTGAGACGGAGG 58.958 38.462 0.00 0.00 0.00 4.30
2160 2408 6.113411 ACACTTATTATTTTGAGACGGAGGG 58.887 40.000 0.00 0.00 0.00 4.30
2161 2409 6.070424 ACACTTATTATTTTGAGACGGAGGGA 60.070 38.462 0.00 0.00 0.00 4.20
2162 2410 6.480320 CACTTATTATTTTGAGACGGAGGGAG 59.520 42.308 0.00 0.00 0.00 4.30
2163 2411 6.156429 ACTTATTATTTTGAGACGGAGGGAGT 59.844 38.462 0.00 0.00 0.00 3.85
2191 2439 9.265938 CATTCATACTCTTACAAAACAACATCG 57.734 33.333 0.00 0.00 0.00 3.84
2197 2445 8.073355 ACTCTTACAAAACAACATCGTCTAAG 57.927 34.615 0.00 0.00 0.00 2.18
2226 2474 7.171848 ACACGAAGTAAATACTTGCATACACAA 59.828 33.333 10.41 0.00 45.84 3.33
2244 2931 4.984161 ACACAAACACTTTAAGATGCATGC 59.016 37.500 11.82 11.82 0.00 4.06
2253 2940 6.034577 CACTTTAAGATGCATGCATGAACAAG 59.965 38.462 36.73 29.02 36.70 3.16
2358 3049 7.054491 TGAATATTTGGATCATCTCAGACGA 57.946 36.000 0.00 0.00 0.00 4.20
2364 3055 0.749649 ATCATCTCAGACGAGTGCCC 59.250 55.000 0.00 0.00 40.44 5.36
2386 3077 2.622942 CGCAATAACATGCCCAACCTAT 59.377 45.455 0.00 0.00 43.47 2.57
2390 3081 6.318648 CGCAATAACATGCCCAACCTATATAT 59.681 38.462 0.00 0.00 43.47 0.86
2391 3082 7.483307 GCAATAACATGCCCAACCTATATATG 58.517 38.462 0.00 0.00 40.49 1.78
2455 3146 5.784578 AACAACCTCAGTAATCCAAAACC 57.215 39.130 0.00 0.00 0.00 3.27
2469 3160 4.628074 TCCAAAACCAACGAACAAACAAA 58.372 34.783 0.00 0.00 0.00 2.83
2472 3163 5.370000 CAAAACCAACGAACAAACAAACAG 58.630 37.500 0.00 0.00 0.00 3.16
2497 3188 0.174617 TGTACCTCATGCGCGATGAA 59.825 50.000 12.10 0.00 40.73 2.57
2500 3191 1.227350 CCTCATGCGCGATGAAGGA 60.227 57.895 12.10 0.00 40.73 3.36
2544 3235 3.604875 AACGATCAAGTAATCCCGTGT 57.395 42.857 0.00 0.00 0.00 4.49
2551 3242 5.824904 TCAAGTAATCCCGTGTAGACTAC 57.175 43.478 5.62 5.62 0.00 2.73
2563 3254 5.125097 CCGTGTAGACTACAATCTTACCACT 59.875 44.000 16.84 0.00 40.93 4.00
2564 3255 6.028368 CGTGTAGACTACAATCTTACCACTG 58.972 44.000 16.84 0.00 40.93 3.66
2568 3259 1.933853 CTACAATCTTACCACTGCCGC 59.066 52.381 0.00 0.00 0.00 6.53
2580 3271 1.444895 CTGCCGCCAAAGCAATGTC 60.445 57.895 0.00 0.00 40.35 3.06
2594 3285 3.311966 GCAATGTCCTTTCTTGCTGTTC 58.688 45.455 0.00 0.00 41.52 3.18
2646 3337 1.135112 CGTCGATCCAATCCAGACACA 60.135 52.381 0.00 0.00 32.57 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.435008 CGAAGTCCGCAAAGAACTCG 59.565 55.000 0.00 0.00 0.00 4.18
134 135 2.213513 TGATCACTGACCACCGCCA 61.214 57.895 0.00 0.00 0.00 5.69
145 146 1.546589 TTTACGGGCCGGTGATCACT 61.547 55.000 31.78 8.94 0.00 3.41
153 154 1.868469 TTCGATAATTTACGGGCCGG 58.132 50.000 31.78 12.53 0.00 6.13
216 224 5.518848 AGAAAGACAATGATGCACACAAA 57.481 34.783 0.00 0.00 0.00 2.83
303 316 2.101415 GAGGCTGGCATTTTATTCCACC 59.899 50.000 3.38 0.00 0.00 4.61
307 320 3.565482 TCATCGAGGCTGGCATTTTATTC 59.435 43.478 3.38 0.00 0.00 1.75
313 326 0.035152 TGTTCATCGAGGCTGGCATT 60.035 50.000 3.38 0.00 0.00 3.56
314 327 0.745845 GTGTTCATCGAGGCTGGCAT 60.746 55.000 3.38 0.00 0.00 4.40
320 338 2.480416 CCTGTAGAGTGTTCATCGAGGC 60.480 54.545 0.00 0.00 0.00 4.70
334 352 2.303022 CCAGCCTCAAGTTTCCTGTAGA 59.697 50.000 0.00 0.00 0.00 2.59
390 472 5.817816 GGCCTACGGAAATAGAATATCCATG 59.182 44.000 0.00 0.00 32.58 3.66
391 473 5.395324 CGGCCTACGGAAATAGAATATCCAT 60.395 44.000 0.00 0.00 39.42 3.41
450 537 1.952296 CCATGTGGAGCTGGCTTAATC 59.048 52.381 0.00 0.00 37.39 1.75
453 540 2.695561 TCCATGTGGAGCTGGCTTA 58.304 52.632 0.00 0.00 39.78 3.09
515 602 3.555168 GGAAGTGTACAAGGAGTGTGAGG 60.555 52.174 0.00 0.00 41.89 3.86
620 738 9.379770 TCATAAACCTGGTCTCATGAGATTATA 57.620 33.333 27.51 14.01 39.97 0.98
626 744 8.915057 AATTATCATAAACCTGGTCTCATGAG 57.085 34.615 17.07 17.07 0.00 2.90
628 746 9.123902 TGAAATTATCATAAACCTGGTCTCATG 57.876 33.333 0.00 4.44 31.50 3.07
630 748 8.548025 TCTGAAATTATCATAAACCTGGTCTCA 58.452 33.333 0.00 0.00 37.44 3.27
701 827 9.853555 GTGGTGTATACAAATGATGATCAAAAA 57.146 29.630 7.25 0.00 0.00 1.94
702 828 8.465999 GGTGGTGTATACAAATGATGATCAAAA 58.534 33.333 7.25 0.00 0.00 2.44
703 829 7.833682 AGGTGGTGTATACAAATGATGATCAAA 59.166 33.333 7.25 0.00 0.00 2.69
704 830 7.345691 AGGTGGTGTATACAAATGATGATCAA 58.654 34.615 7.25 0.00 0.00 2.57
705 831 6.899089 AGGTGGTGTATACAAATGATGATCA 58.101 36.000 7.25 0.00 0.00 2.92
706 832 7.807977 AAGGTGGTGTATACAAATGATGATC 57.192 36.000 7.25 0.00 0.00 2.92
707 833 8.055181 AGAAAGGTGGTGTATACAAATGATGAT 58.945 33.333 7.25 0.00 0.00 2.45
708 834 7.402054 AGAAAGGTGGTGTATACAAATGATGA 58.598 34.615 7.25 0.00 0.00 2.92
709 835 7.630242 AGAAAGGTGGTGTATACAAATGATG 57.370 36.000 7.25 0.00 0.00 3.07
710 836 8.522830 CAAAGAAAGGTGGTGTATACAAATGAT 58.477 33.333 7.25 0.00 0.00 2.45
711 837 7.523052 GCAAAGAAAGGTGGTGTATACAAATGA 60.523 37.037 7.25 0.00 0.00 2.57
712 838 6.586082 GCAAAGAAAGGTGGTGTATACAAATG 59.414 38.462 7.25 0.00 0.00 2.32
713 839 6.493458 AGCAAAGAAAGGTGGTGTATACAAAT 59.507 34.615 7.25 0.00 0.00 2.32
745 895 2.241176 TGGGAACTTGGGGTGATATCAC 59.759 50.000 24.95 24.95 45.72 3.06
746 896 2.567862 TGGGAACTTGGGGTGATATCA 58.432 47.619 0.00 0.00 0.00 2.15
747 897 3.288092 GTTGGGAACTTGGGGTGATATC 58.712 50.000 0.00 0.00 0.00 1.63
748 898 2.024369 GGTTGGGAACTTGGGGTGATAT 60.024 50.000 0.00 0.00 0.00 1.63
749 899 1.356398 GGTTGGGAACTTGGGGTGATA 59.644 52.381 0.00 0.00 0.00 2.15
750 900 0.114364 GGTTGGGAACTTGGGGTGAT 59.886 55.000 0.00 0.00 0.00 3.06
751 901 1.539665 GGTTGGGAACTTGGGGTGA 59.460 57.895 0.00 0.00 0.00 4.02
752 902 1.901464 CGGTTGGGAACTTGGGGTG 60.901 63.158 0.00 0.00 0.00 4.61
753 903 1.647334 TTCGGTTGGGAACTTGGGGT 61.647 55.000 0.00 0.00 0.00 4.95
754 904 0.468400 TTTCGGTTGGGAACTTGGGG 60.468 55.000 0.00 0.00 0.00 4.96
755 905 0.958822 CTTTCGGTTGGGAACTTGGG 59.041 55.000 0.00 0.00 0.00 4.12
756 906 1.607148 GTCTTTCGGTTGGGAACTTGG 59.393 52.381 0.00 0.00 0.00 3.61
757 907 2.290641 CTGTCTTTCGGTTGGGAACTTG 59.709 50.000 0.00 0.00 0.00 3.16
758 908 2.092592 ACTGTCTTTCGGTTGGGAACTT 60.093 45.455 0.00 0.00 30.45 2.66
873 1030 3.186613 GTCCGTGGTGATTCTTTGAAGAC 59.813 47.826 0.00 0.00 34.13 3.01
894 1051 4.067192 GTTGTTTCGGGTGTTATACTGGT 58.933 43.478 0.00 0.00 0.00 4.00
960 1141 1.185618 CCTTGTCCGGTCTCTGGTCA 61.186 60.000 0.00 0.00 0.00 4.02
1101 1288 1.904032 GAGGAGCAGGGTGAGGAAG 59.096 63.158 0.00 0.00 0.00 3.46
1248 1438 3.473647 CGGATGGAGAGCTGCCCA 61.474 66.667 6.17 6.17 36.79 5.36
1505 1695 3.225061 GGATCCTCGACCGGACCC 61.225 72.222 9.46 0.00 35.52 4.46
1634 1824 2.294791 CGCACCTAGAGGAAGTCTATGG 59.705 54.545 1.60 0.00 37.14 2.74
1654 1844 3.076258 TACTCATGCAGGCGGACCG 62.076 63.158 10.29 10.29 42.76 4.79
1655 1845 1.521681 GTACTCATGCAGGCGGACC 60.522 63.158 0.00 0.00 0.00 4.46
1656 1846 1.878522 CGTACTCATGCAGGCGGAC 60.879 63.158 0.00 0.00 0.00 4.79
1675 1865 9.982291 ATGTTATTACTAAACGCTTGTTATGTG 57.018 29.630 0.00 0.00 33.81 3.21
1679 1869 9.217278 TGGAATGTTATTACTAAACGCTTGTTA 57.783 29.630 0.00 0.00 33.81 2.41
1696 1907 4.578516 CCGGCAGATTACATTGGAATGTTA 59.421 41.667 10.18 2.20 46.95 2.41
1697 1908 3.381272 CCGGCAGATTACATTGGAATGTT 59.619 43.478 10.18 0.00 46.95 2.71
1740 1958 5.379706 TTGGTTTGGGTTTGATTTGGAAT 57.620 34.783 0.00 0.00 0.00 3.01
1742 1960 4.844349 TTTGGTTTGGGTTTGATTTGGA 57.156 36.364 0.00 0.00 0.00 3.53
1743 1961 4.518590 GGATTTGGTTTGGGTTTGATTTGG 59.481 41.667 0.00 0.00 0.00 3.28
1744 1962 5.375773 AGGATTTGGTTTGGGTTTGATTTG 58.624 37.500 0.00 0.00 0.00 2.32
1745 1963 5.645056 AGGATTTGGTTTGGGTTTGATTT 57.355 34.783 0.00 0.00 0.00 2.17
1748 1966 4.033709 TCAAGGATTTGGTTTGGGTTTGA 58.966 39.130 0.00 0.00 34.97 2.69
1749 1967 4.414337 TCAAGGATTTGGTTTGGGTTTG 57.586 40.909 0.00 0.00 34.97 2.93
1751 1969 4.411869 ACAATCAAGGATTTGGTTTGGGTT 59.588 37.500 0.00 0.00 35.47 4.11
1753 1971 4.317488 CACAATCAAGGATTTGGTTTGGG 58.683 43.478 0.00 2.42 35.47 4.12
1798 2046 4.762251 GGAGGAGGCAATGGAATTATACAC 59.238 45.833 0.00 0.00 32.46 2.90
1847 2095 1.205655 CATCGTGGAGGAGAAGAGCAA 59.794 52.381 0.00 0.00 0.00 3.91
1861 2109 4.439153 CCCATTCAAAACTCATCCATCGTG 60.439 45.833 0.00 0.00 0.00 4.35
1862 2110 3.696051 CCCATTCAAAACTCATCCATCGT 59.304 43.478 0.00 0.00 0.00 3.73
1863 2111 3.947196 TCCCATTCAAAACTCATCCATCG 59.053 43.478 0.00 0.00 0.00 3.84
1876 2124 4.371624 TGCTCTCTTTCTTCCCATTCAA 57.628 40.909 0.00 0.00 0.00 2.69
1920 2168 1.564348 GGCAAGGTAGGAAGGATGGAA 59.436 52.381 0.00 0.00 0.00 3.53
1933 2181 1.762370 CCCTTTGTTCTTTGGCAAGGT 59.238 47.619 9.31 0.00 0.00 3.50
2060 2308 7.664552 TTTATTTTCGGACAGAGGGAGTATA 57.335 36.000 0.00 0.00 0.00 1.47
2063 2311 4.903045 TTTATTTTCGGACAGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
2064 2312 5.186198 ACATTTATTTTCGGACAGAGGGAG 58.814 41.667 0.00 0.00 0.00 4.30
2065 2313 5.045869 AGACATTTATTTTCGGACAGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
2066 2314 5.186198 AGACATTTATTTTCGGACAGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
2067 2315 6.743575 AAGACATTTATTTTCGGACAGAGG 57.256 37.500 0.00 0.00 0.00 3.69
2129 2377 8.926710 CGTCTCAAAATAATAAGTGTCTCAACT 58.073 33.333 0.00 0.00 0.00 3.16
2130 2378 8.169268 CCGTCTCAAAATAATAAGTGTCTCAAC 58.831 37.037 0.00 0.00 0.00 3.18
2131 2379 8.092068 TCCGTCTCAAAATAATAAGTGTCTCAA 58.908 33.333 0.00 0.00 0.00 3.02
2132 2380 7.608153 TCCGTCTCAAAATAATAAGTGTCTCA 58.392 34.615 0.00 0.00 0.00 3.27
2133 2381 7.222999 CCTCCGTCTCAAAATAATAAGTGTCTC 59.777 40.741 0.00 0.00 0.00 3.36
2134 2382 7.042335 CCTCCGTCTCAAAATAATAAGTGTCT 58.958 38.462 0.00 0.00 0.00 3.41
2135 2383 6.258068 CCCTCCGTCTCAAAATAATAAGTGTC 59.742 42.308 0.00 0.00 0.00 3.67
2136 2384 6.070424 TCCCTCCGTCTCAAAATAATAAGTGT 60.070 38.462 0.00 0.00 0.00 3.55
2137 2385 6.346096 TCCCTCCGTCTCAAAATAATAAGTG 58.654 40.000 0.00 0.00 0.00 3.16
2138 2386 6.156429 ACTCCCTCCGTCTCAAAATAATAAGT 59.844 38.462 0.00 0.00 0.00 2.24
2139 2387 6.583562 ACTCCCTCCGTCTCAAAATAATAAG 58.416 40.000 0.00 0.00 0.00 1.73
2140 2388 6.555463 ACTCCCTCCGTCTCAAAATAATAA 57.445 37.500 0.00 0.00 0.00 1.40
2141 2389 6.608405 TGTACTCCCTCCGTCTCAAAATAATA 59.392 38.462 0.00 0.00 0.00 0.98
2142 2390 5.424252 TGTACTCCCTCCGTCTCAAAATAAT 59.576 40.000 0.00 0.00 0.00 1.28
2143 2391 4.773674 TGTACTCCCTCCGTCTCAAAATAA 59.226 41.667 0.00 0.00 0.00 1.40
2144 2392 4.346730 TGTACTCCCTCCGTCTCAAAATA 58.653 43.478 0.00 0.00 0.00 1.40
2145 2393 3.170717 TGTACTCCCTCCGTCTCAAAAT 58.829 45.455 0.00 0.00 0.00 1.82
2146 2394 2.600790 TGTACTCCCTCCGTCTCAAAA 58.399 47.619 0.00 0.00 0.00 2.44
2147 2395 2.297698 TGTACTCCCTCCGTCTCAAA 57.702 50.000 0.00 0.00 0.00 2.69
2148 2396 2.526888 ATGTACTCCCTCCGTCTCAA 57.473 50.000 0.00 0.00 0.00 3.02
2149 2397 2.291346 TGAATGTACTCCCTCCGTCTCA 60.291 50.000 0.00 0.00 0.00 3.27
2150 2398 2.376109 TGAATGTACTCCCTCCGTCTC 58.624 52.381 0.00 0.00 0.00 3.36
2151 2399 2.526888 TGAATGTACTCCCTCCGTCT 57.473 50.000 0.00 0.00 0.00 4.18
2152 2400 3.890147 AGTATGAATGTACTCCCTCCGTC 59.110 47.826 0.00 0.00 28.99 4.79
2153 2401 3.890147 GAGTATGAATGTACTCCCTCCGT 59.110 47.826 3.31 0.00 42.99 4.69
2154 2402 4.506886 GAGTATGAATGTACTCCCTCCG 57.493 50.000 3.31 0.00 42.99 4.63
2197 2445 8.649841 TGTATGCAAGTATTTACTTCGTGTTAC 58.350 33.333 0.00 1.32 44.19 2.50
2226 2474 5.648178 TCATGCATGCATCTTAAAGTGTT 57.352 34.783 30.07 2.89 33.90 3.32
2244 2931 2.595750 TAACCCCACCCTTGTTCATG 57.404 50.000 0.00 0.00 0.00 3.07
2253 2940 3.232720 TCACTTCTTTTAACCCCACCC 57.767 47.619 0.00 0.00 0.00 4.61
2358 3049 1.666209 GCATGTTATTGCGGGGCACT 61.666 55.000 0.00 0.00 38.71 4.40
2364 3055 0.179113 GGTTGGGCATGTTATTGCGG 60.179 55.000 0.00 0.00 43.71 5.69
2418 3109 4.627058 AGGTTGTTAATTTTCAAAGCCGG 58.373 39.130 0.00 0.00 0.00 6.13
2455 3146 6.690957 ACATACATCTGTTTGTTTGTTCGTTG 59.309 34.615 1.24 0.00 38.20 4.10
2469 3160 3.800261 GCGCATGAGGTACATACATCTGT 60.800 47.826 0.30 0.00 37.82 3.41
2472 3163 1.721389 CGCGCATGAGGTACATACATC 59.279 52.381 8.75 0.00 37.46 3.06
2497 3188 0.473326 GGATGCTGAGATTGCCTCCT 59.527 55.000 0.00 0.00 40.49 3.69
2500 3191 0.463295 CACGGATGCTGAGATTGCCT 60.463 55.000 0.00 0.00 0.00 4.75
2526 3217 4.036498 AGTCTACACGGGATTACTTGATCG 59.964 45.833 0.00 0.00 0.00 3.69
2544 3235 4.097437 CGGCAGTGGTAAGATTGTAGTCTA 59.903 45.833 0.00 0.00 0.00 2.59
2551 3242 0.676466 TGGCGGCAGTGGTAAGATTG 60.676 55.000 7.97 0.00 0.00 2.67
2563 3254 2.650196 GACATTGCTTTGGCGGCA 59.350 55.556 7.97 7.97 42.25 5.69
2564 3255 2.125952 GGACATTGCTTTGGCGGC 60.126 61.111 0.00 0.00 42.25 6.53
2568 3259 3.062042 GCAAGAAAGGACATTGCTTTGG 58.938 45.455 0.00 0.00 44.57 3.28
2580 3271 2.031682 CCGAACAGAACAGCAAGAAAGG 60.032 50.000 0.00 0.00 0.00 3.11
2594 3285 2.271800 GAGGTGATAGTTGCCGAACAG 58.728 52.381 0.00 0.00 34.17 3.16


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

AutoCloner maintained by Alex Coulton.