Multiple sequence alignment - TraesCS5A01G443900

Loading Multiple Alignment...

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 TraesCS5A01G443900 chr5A 100.000 2815 0 0 1 2815 623954021 623956835 0.000000e+00 5199
1 TraesCS5A01G443900 chr5A 79.750 1758 232 69 1 1673 623684150 623685868 0.000000e+00 1160
2 TraesCS5A01G443900 chr5A 84.795 1072 146 16 9 1074 624476304 624475244 0.000000e+00 1061
3 TraesCS5A01G443900 chr5A 83.716 479 44 16 1217 1673 624475031 624474565 3.350000e-114 422
4 TraesCS5A01G443900 chr5A 81.590 239 41 3 19 256 623677987 623678223 7.960000e-46 195
5 TraesCS5A01G443900 chr5D 91.504 1942 136 18 1 1928 499652121 499654047 0.000000e+00 2645
6 TraesCS5A01G443900 chr5D 80.204 1768 235 60 1 1689 499446980 499448711 0.000000e+00 1219
7 TraesCS5A01G443900 chr5D 83.542 1118 160 22 9 1116 499957284 499956181 0.000000e+00 1024
8 TraesCS5A01G443900 chr5D 85.050 903 66 36 1930 2805 499654083 499654943 0.000000e+00 856
9 TraesCS5A01G443900 chr5D 82.745 510 54 16 1217 1704 499956013 499955516 9.320000e-115 424
10 TraesCS5A01G443900 chr5B 91.330 1880 133 19 66 1928 620825478 620827344 0.000000e+00 2542
11 TraesCS5A01G443900 chr5B 79.621 1899 230 86 5 1806 620668437 620670275 0.000000e+00 1218
12 TraesCS5A01G443900 chr5B 79.441 1790 248 73 1 1716 620305957 620307700 0.000000e+00 1157
13 TraesCS5A01G443900 chr5B 83.186 1130 160 24 9 1120 621399920 621398803 0.000000e+00 1007
14 TraesCS5A01G443900 chr5B 86.458 576 47 14 2246 2815 620827690 620828240 1.120000e-168 603
15 TraesCS5A01G443900 chr5B 81.732 635 67 25 1081 1673 621398809 621398182 4.220000e-133 484


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 TraesCS5A01G443900 chr5A 623954021 623956835 2814 False 5199.0 5199 100.0000 1 2815 1 chr5A.!!$F3 2814
1 TraesCS5A01G443900 chr5A 623684150 623685868 1718 False 1160.0 1160 79.7500 1 1673 1 chr5A.!!$F2 1672
2 TraesCS5A01G443900 chr5A 624474565 624476304 1739 True 741.5 1061 84.2555 9 1673 2 chr5A.!!$R1 1664
3 TraesCS5A01G443900 chr5D 499652121 499654943 2822 False 1750.5 2645 88.2770 1 2805 2 chr5D.!!$F2 2804
4 TraesCS5A01G443900 chr5D 499446980 499448711 1731 False 1219.0 1219 80.2040 1 1689 1 chr5D.!!$F1 1688
5 TraesCS5A01G443900 chr5D 499955516 499957284 1768 True 724.0 1024 83.1435 9 1704 2 chr5D.!!$R1 1695
6 TraesCS5A01G443900 chr5B 620825478 620828240 2762 False 1572.5 2542 88.8940 66 2815 2 chr5B.!!$F3 2749
7 TraesCS5A01G443900 chr5B 620668437 620670275 1838 False 1218.0 1218 79.6210 5 1806 1 chr5B.!!$F2 1801
8 TraesCS5A01G443900 chr5B 620305957 620307700 1743 False 1157.0 1157 79.4410 1 1716 1 chr5B.!!$F1 1715
9 TraesCS5A01G443900 chr5B 621398182 621399920 1738 True 745.5 1007 82.4590 9 1673 2 chr5B.!!$R1 1664

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
976 1054 0.463654 AAAACACACCAGAGCTCGCA 60.464 50.0 8.37 0.0 0.0 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2679 0.032678 CCGTGCTCTGTCTGTGTCTT 59.967 55.0 0.0 0.0 0.0 3.01 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
154 165 2.303175 GGTGCAAATTAATCCGGGCTA 58.697 47.619 0.00 0.00 0.00 3.93
158 169 3.181480 TGCAAATTAATCCGGGCTAAAGC 60.181 43.478 0.00 6.76 41.14 3.51
188 199 0.541296 AAATGCAGCAGCTGGGAAGT 60.541 50.000 24.13 0.00 42.74 3.01
337 349 1.503818 AACTTGCGTCGCGTTCCATT 61.504 50.000 13.38 0.00 0.00 3.16
434 446 3.666253 CACGCCGGAAAACCCCAC 61.666 66.667 5.05 0.00 0.00 4.61
512 524 1.990060 ACCATCCTGACCAGTCCCG 60.990 63.158 0.00 0.00 0.00 5.14
513 525 1.685765 CCATCCTGACCAGTCCCGA 60.686 63.158 0.00 0.00 0.00 5.14
514 526 1.050988 CCATCCTGACCAGTCCCGAT 61.051 60.000 0.00 0.00 0.00 4.18
520 532 0.834261 TGACCAGTCCCGATTCACCA 60.834 55.000 0.00 0.00 0.00 4.17
525 537 3.390521 TCCCGATTCACCAGCGCT 61.391 61.111 2.64 2.64 0.00 5.92
534 546 2.358737 ACCAGCGCTTTTCTCCCG 60.359 61.111 7.50 0.00 0.00 5.14
543 555 1.664151 GCTTTTCTCCCGGAATACACG 59.336 52.381 0.73 0.00 33.53 4.49
563 575 0.593128 ACCAAATCACACAAGCTCGC 59.407 50.000 0.00 0.00 0.00 5.03
566 578 1.135859 CAAATCACACAAGCTCGCTCC 60.136 52.381 0.00 0.00 0.00 4.70
602 614 3.838244 ATCCGTACCTACACAATGCAT 57.162 42.857 0.00 0.00 0.00 3.96
603 615 3.620427 TCCGTACCTACACAATGCATT 57.380 42.857 5.99 5.99 0.00 3.56
604 616 3.945346 TCCGTACCTACACAATGCATTT 58.055 40.909 9.83 0.00 0.00 2.32
605 617 4.328536 TCCGTACCTACACAATGCATTTT 58.671 39.130 9.83 0.00 0.00 1.82
786 799 1.707239 GAGACAGATCGGACGTCGCT 61.707 60.000 9.92 1.23 39.05 4.93
974 1052 1.070577 CGAAAAACACACCAGAGCTCG 60.071 52.381 8.37 3.24 0.00 5.03
976 1054 0.463654 AAAACACACCAGAGCTCGCA 60.464 50.000 8.37 0.00 0.00 5.10
987 1065 3.219928 GCTCGCATCTCCCCTCGA 61.220 66.667 0.00 0.00 0.00 4.04
993 1071 1.633774 GCATCTCCCCTCGATTCCTA 58.366 55.000 0.00 0.00 0.00 2.94
1017 1098 1.800805 CAATGTCGACTGAAGTGGCT 58.199 50.000 17.92 0.00 0.00 4.75
1018 1099 1.462283 CAATGTCGACTGAAGTGGCTG 59.538 52.381 17.92 0.00 0.00 4.85
1019 1100 0.671781 ATGTCGACTGAAGTGGCTGC 60.672 55.000 17.92 0.00 0.00 5.25
1020 1101 1.005630 GTCGACTGAAGTGGCTGCT 60.006 57.895 8.70 0.00 0.00 4.24
1210 1373 2.506438 CTTCGCCGTCGTTCCTCC 60.506 66.667 0.00 0.00 36.96 4.30
1248 1412 3.815401 CGTGTTTCCCTGATCTGACTTTT 59.185 43.478 0.38 0.00 0.00 2.27
1249 1413 4.994852 CGTGTTTCCCTGATCTGACTTTTA 59.005 41.667 0.38 0.00 0.00 1.52
1397 1568 0.107945 ACTTCCGCAAGATCCTGCTC 60.108 55.000 14.20 0.00 40.33 4.26
1424 1595 4.057428 AAGAAGCTCGTCGCCGCT 62.057 61.111 3.45 3.45 40.39 5.52
1550 1772 2.359230 GCGCCAGCCAAGAAGACT 60.359 61.111 0.00 0.00 37.42 3.24
1827 2097 0.530870 GAAGTAGAGCCCGGCATGAC 60.531 60.000 13.15 5.84 0.00 3.06
1840 2110 0.034059 GCATGACCGGACCTAGATGG 59.966 60.000 9.46 0.00 42.93 3.51
1847 2117 2.423446 GACCTAGATGGCCTGGCG 59.577 66.667 13.40 0.00 40.22 5.69
1857 2127 1.070957 GGCCTGGCGGGTAGTATTC 59.929 63.158 15.16 0.00 37.43 1.75
1881 2151 3.528597 AGCCTAATTCTCTGTTCGGTC 57.471 47.619 0.00 0.00 0.00 4.79
1921 2191 4.308458 CCGTGTCTTGGGCGGTGA 62.308 66.667 0.00 0.00 40.53 4.02
1928 2198 4.424711 TTGGGCGGTGATGGGCTC 62.425 66.667 0.00 0.00 0.00 4.70
1946 2250 2.488545 GCTCTTGTGTCGAGGAAGAGTA 59.511 50.000 20.82 0.00 43.12 2.59
1958 2262 4.081420 CGAGGAAGAGTAATATCCATGGGG 60.081 50.000 13.02 0.00 35.62 4.96
1971 2275 3.189606 TCCATGGGGATCAGTTGTACTT 58.810 45.455 13.02 0.00 38.64 2.24
1972 2276 3.199946 TCCATGGGGATCAGTTGTACTTC 59.800 47.826 13.02 0.00 38.64 3.01
1973 2277 3.200825 CCATGGGGATCAGTTGTACTTCT 59.799 47.826 2.85 0.00 35.59 2.85
1988 2292 7.450944 AGTTGTACTTCTAGTAGCAGTAACCTT 59.549 37.037 10.72 0.00 30.12 3.50
1997 2301 9.431887 TCTAGTAGCAGTAACCTTTGTAATTTG 57.568 33.333 0.00 0.00 0.00 2.32
2028 2332 8.789825 TTTTTATTGTTGCAGCAATATCCATT 57.210 26.923 29.21 11.64 39.95 3.16
2029 2333 7.773864 TTTATTGTTGCAGCAATATCCATTG 57.226 32.000 29.21 0.00 43.79 2.82
2031 2335 3.363627 TGTTGCAGCAATATCCATTGGA 58.636 40.909 11.96 8.08 41.64 3.53
2033 2337 4.202172 TGTTGCAGCAATATCCATTGGATG 60.202 41.667 25.47 13.46 43.06 3.51
2044 2348 8.658609 CAATATCCATTGGATGTTTGTCAAAAC 58.341 33.333 25.47 0.00 39.87 2.43
2070 2374 3.429543 CGTGTTTCATTTGCCAAATCTGG 59.570 43.478 0.00 0.00 46.65 3.86
2077 2381 1.126488 TTGCCAAATCTGGTGCCAAA 58.874 45.000 0.00 0.00 45.53 3.28
2078 2382 0.680618 TGCCAAATCTGGTGCCAAAG 59.319 50.000 0.00 0.00 45.53 2.77
2079 2383 0.968405 GCCAAATCTGGTGCCAAAGA 59.032 50.000 0.00 0.00 45.53 2.52
2081 2385 2.027837 GCCAAATCTGGTGCCAAAGATT 60.028 45.455 0.00 0.00 45.53 2.40
2082 2386 3.195396 GCCAAATCTGGTGCCAAAGATTA 59.805 43.478 4.75 0.00 45.53 1.75
2084 2388 5.627503 GCCAAATCTGGTGCCAAAGATTATT 60.628 40.000 4.75 0.00 45.53 1.40
2085 2389 6.044682 CCAAATCTGGTGCCAAAGATTATTC 58.955 40.000 4.75 0.00 41.24 1.75
2086 2390 6.351202 CCAAATCTGGTGCCAAAGATTATTCA 60.351 38.462 4.75 0.00 41.24 2.57
2093 2418 5.241728 GGTGCCAAAGATTATTCAGGGATAC 59.758 44.000 0.00 0.00 0.00 2.24
2094 2419 5.827797 GTGCCAAAGATTATTCAGGGATACA 59.172 40.000 0.00 0.00 39.74 2.29
2102 2427 6.500049 AGATTATTCAGGGATACAGAAGGAGG 59.500 42.308 0.00 0.00 35.92 4.30
2103 2428 3.491766 TTCAGGGATACAGAAGGAGGT 57.508 47.619 0.00 0.00 39.74 3.85
2122 2447 6.013032 AGGAGGTTTGAGATCTGAAATTGAGA 60.013 38.462 10.64 0.00 0.00 3.27
2136 2461 9.481340 TCTGAAATTGAGATTCGTATCTTATGG 57.519 33.333 5.98 0.00 41.23 2.74
2137 2462 8.087982 TGAAATTGAGATTCGTATCTTATGGC 57.912 34.615 5.98 0.00 41.23 4.40
2138 2463 7.714813 TGAAATTGAGATTCGTATCTTATGGCA 59.285 33.333 5.98 0.00 41.23 4.92
2139 2464 8.450578 AAATTGAGATTCGTATCTTATGGCAA 57.549 30.769 5.98 5.90 41.23 4.52
2140 2465 8.627208 AATTGAGATTCGTATCTTATGGCAAT 57.373 30.769 5.98 7.78 41.23 3.56
2141 2466 7.425577 TTGAGATTCGTATCTTATGGCAATG 57.574 36.000 5.98 0.00 41.23 2.82
2148 2483 5.863935 TCGTATCTTATGGCAATGAATCTCG 59.136 40.000 0.00 0.00 0.00 4.04
2154 2489 8.122472 TCTTATGGCAATGAATCTCGTAGATA 57.878 34.615 0.00 0.00 32.89 1.98
2156 2491 8.932945 TTATGGCAATGAATCTCGTAGATATC 57.067 34.615 0.00 0.00 32.89 1.63
2158 2493 7.703058 TGGCAATGAATCTCGTAGATATCTA 57.297 36.000 8.44 8.44 32.89 1.98
2159 2494 7.539436 TGGCAATGAATCTCGTAGATATCTAC 58.461 38.462 26.64 26.64 44.00 2.59
2160 2495 7.176690 TGGCAATGAATCTCGTAGATATCTACA 59.823 37.037 32.22 21.65 46.92 2.74
2161 2496 8.029522 GGCAATGAATCTCGTAGATATCTACAA 58.970 37.037 32.22 20.08 46.92 2.41
2162 2497 9.411801 GCAATGAATCTCGTAGATATCTACAAA 57.588 33.333 32.22 22.12 46.92 2.83
2206 2562 9.640963 TCTGACTTACTATAAGAAAGCAAGAAC 57.359 33.333 2.65 0.00 0.00 3.01
2209 2565 7.384477 ACTTACTATAAGAAAGCAAGAACGGT 58.616 34.615 2.65 0.00 0.00 4.83
2212 2568 1.318576 AAGAAAGCAAGAACGGTGGG 58.681 50.000 0.00 0.00 0.00 4.61
2215 2571 0.755327 AAAGCAAGAACGGTGGGCTT 60.755 50.000 0.00 0.00 45.92 4.35
2232 2588 3.147629 GGCTTGAAGAGATGGATGATGG 58.852 50.000 0.00 0.00 0.00 3.51
2235 2591 4.685302 GCTTGAAGAGATGGATGATGGTCA 60.685 45.833 0.00 0.00 0.00 4.02
2244 2600 1.162698 GATGATGGTCATCGGCATGG 58.837 55.000 4.37 0.00 43.11 3.66
2268 2679 3.244215 GCAGGGAGATGAATGGAATCGTA 60.244 47.826 0.00 0.00 0.00 3.43
2286 2704 2.320367 GTAAGACACAGACAGAGCACG 58.680 52.381 0.00 0.00 0.00 5.34
2290 2708 0.598562 ACACAGACAGAGCACGGTAG 59.401 55.000 0.00 0.00 0.00 3.18
2378 2796 2.168313 TGCTTTCAGCGAGATGTATGGA 59.832 45.455 0.00 0.00 46.26 3.41
2379 2797 2.799412 GCTTTCAGCGAGATGTATGGAG 59.201 50.000 0.00 0.00 0.00 3.86
2380 2798 3.388308 CTTTCAGCGAGATGTATGGAGG 58.612 50.000 0.00 0.00 0.00 4.30
2381 2799 1.332195 TCAGCGAGATGTATGGAGGG 58.668 55.000 0.00 0.00 0.00 4.30
2382 2800 0.320247 CAGCGAGATGTATGGAGGGC 60.320 60.000 0.00 0.00 0.00 5.19
2383 2801 0.470833 AGCGAGATGTATGGAGGGCT 60.471 55.000 0.00 0.00 0.00 5.19
2384 2802 0.320247 GCGAGATGTATGGAGGGCTG 60.320 60.000 0.00 0.00 0.00 4.85
2385 2803 0.319728 CGAGATGTATGGAGGGCTGG 59.680 60.000 0.00 0.00 0.00 4.85
2386 2804 1.722034 GAGATGTATGGAGGGCTGGA 58.278 55.000 0.00 0.00 0.00 3.86
2523 2941 3.050275 GTCCCGCCTGCAGTGTTC 61.050 66.667 13.81 0.00 0.00 3.18
2551 2969 1.518572 CGCGTCCGAAACCTATGCT 60.519 57.895 0.00 0.00 36.29 3.79
2581 3001 2.741878 GCAAGCGTGTGGATGTAGGTAT 60.742 50.000 0.59 0.00 0.00 2.73
2656 3076 2.935849 CCACACTTTCCTTTTGCCAAAC 59.064 45.455 0.00 0.00 0.00 2.93
2705 3125 4.378046 CGAGTAAATTGTTAGCCACGCTTT 60.378 41.667 0.00 0.00 40.44 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.631377 ACTTCGAATGATTTCTCGATGCAA 59.369 37.500 0.00 0.00 43.14 4.08
51 53 6.516527 GCTTTGTTCTACATGTGGGATCAAAA 60.517 38.462 23.83 13.61 32.21 2.44
158 169 1.129879 GCTGCATTTGCGATGTCACG 61.130 55.000 0.00 0.00 45.83 4.35
188 199 0.904865 AGGCGTGGACATGAGGAAGA 60.905 55.000 0.00 0.00 0.00 2.87
261 272 1.674322 GTTCAGCCCGGCTTTGCTA 60.674 57.895 9.99 0.00 36.40 3.49
337 349 1.066605 GTTTCGATAGGCTACGAGGCA 59.933 52.381 15.22 3.54 44.19 4.75
512 524 1.131315 GGAGAAAAGCGCTGGTGAATC 59.869 52.381 12.58 4.79 0.00 2.52
513 525 1.168714 GGAGAAAAGCGCTGGTGAAT 58.831 50.000 12.58 0.00 0.00 2.57
514 526 0.889186 GGGAGAAAAGCGCTGGTGAA 60.889 55.000 12.58 0.00 0.00 3.18
520 532 0.539986 TATTCCGGGAGAAAAGCGCT 59.460 50.000 2.64 2.64 38.21 5.92
525 537 2.354003 GGTCGTGTATTCCGGGAGAAAA 60.354 50.000 0.00 0.00 38.21 2.29
534 546 3.749088 TGTGTGATTTGGTCGTGTATTCC 59.251 43.478 0.00 0.00 0.00 3.01
543 555 1.400242 GCGAGCTTGTGTGATTTGGTC 60.400 52.381 2.14 0.00 0.00 4.02
563 575 4.506654 CGGATAATGTCTTTGTAACGGGAG 59.493 45.833 0.00 0.00 0.00 4.30
566 578 5.232838 GGTACGGATAATGTCTTTGTAACGG 59.767 44.000 0.00 0.00 0.00 4.44
605 617 3.114668 TCCACCGATTCGAGTGAAAAA 57.885 42.857 21.52 7.87 37.71 1.94
649 661 2.165437 GTGTGCTTCTCCTCTCGATTCT 59.835 50.000 0.00 0.00 0.00 2.40
650 662 2.165437 AGTGTGCTTCTCCTCTCGATTC 59.835 50.000 0.00 0.00 0.00 2.52
753 766 1.139095 GTCTCCATCCGACGGTCAC 59.861 63.158 14.79 0.00 0.00 3.67
838 852 2.881266 GAATGCCGCGCGCTGATTA 61.881 57.895 30.48 12.96 38.78 1.75
974 1052 1.548269 CTAGGAATCGAGGGGAGATGC 59.452 57.143 0.00 0.00 0.00 3.91
976 1054 1.431243 AGCTAGGAATCGAGGGGAGAT 59.569 52.381 0.00 0.00 0.00 2.75
987 1065 2.169352 AGTCGACATTGCAGCTAGGAAT 59.831 45.455 19.50 0.00 39.02 3.01
993 1071 1.270518 ACTTCAGTCGACATTGCAGCT 60.271 47.619 19.50 0.00 0.00 4.24
1017 1098 3.321648 ACCGGGATGTCAGCAGCA 61.322 61.111 6.32 0.00 31.62 4.41
1018 1099 2.821366 CACCGGGATGTCAGCAGC 60.821 66.667 6.32 0.00 0.00 5.25
1019 1100 2.821366 GCACCGGGATGTCAGCAG 60.821 66.667 6.32 0.00 0.00 4.24
1020 1101 4.408821 GGCACCGGGATGTCAGCA 62.409 66.667 6.32 0.00 0.00 4.41
1210 1373 1.269102 ACACGGACGAACAGACAGAAG 60.269 52.381 0.00 0.00 0.00 2.85
1248 1412 0.854062 CGCACGAACGAACCAAACTA 59.146 50.000 0.14 0.00 34.06 2.24
1249 1413 1.085501 ACGCACGAACGAACCAAACT 61.086 50.000 8.71 0.00 36.70 2.66
1397 1568 1.066573 ACGAGCTTCTTGATCTGGGTG 60.067 52.381 0.00 0.00 0.00 4.61
1424 1595 1.228245 GACCTTGGTCAGCTTGCCA 60.228 57.895 14.34 2.06 0.00 4.92
1827 2097 2.511452 CCAGGCCATCTAGGTCCGG 61.511 68.421 5.01 0.00 45.84 5.14
1840 2110 0.249911 CTGAATACTACCCGCCAGGC 60.250 60.000 0.00 0.00 40.58 4.85
1847 2117 7.452189 AGAGAATTAGGCTACTGAATACTACCC 59.548 40.741 0.00 0.00 0.00 3.69
1857 2127 4.142138 ACCGAACAGAGAATTAGGCTACTG 60.142 45.833 7.36 7.36 0.00 2.74
1905 2175 2.047274 ATCACCGCCCAAGACACG 60.047 61.111 0.00 0.00 0.00 4.49
1919 2189 0.247460 CTCGACACAAGAGCCCATCA 59.753 55.000 0.00 0.00 0.00 3.07
1921 2191 0.904865 TCCTCGACACAAGAGCCCAT 60.905 55.000 0.00 0.00 34.56 4.00
1928 2198 6.183360 TGGATATTACTCTTCCTCGACACAAG 60.183 42.308 0.00 0.00 0.00 3.16
1958 2262 7.090953 ACTGCTACTAGAAGTACAACTGATC 57.909 40.000 0.00 0.00 30.54 2.92
1971 2275 9.431887 CAAATTACAAAGGTTACTGCTACTAGA 57.568 33.333 0.00 0.00 0.00 2.43
1972 2276 9.431887 TCAAATTACAAAGGTTACTGCTACTAG 57.568 33.333 0.00 0.00 0.00 2.57
1973 2277 9.431887 CTCAAATTACAAAGGTTACTGCTACTA 57.568 33.333 0.00 0.00 0.00 1.82
2011 2315 4.202182 ACATCCAATGGATATTGCTGCAAC 60.202 41.667 18.51 5.47 40.98 4.17
2028 2332 4.035792 CACGGTAGTTTTGACAAACATCCA 59.964 41.667 0.00 0.00 44.32 3.41
2029 2333 4.035909 ACACGGTAGTTTTGACAAACATCC 59.964 41.667 0.00 1.06 44.32 3.51
2031 2335 5.570234 AACACGGTAGTTTTGACAAACAT 57.430 34.783 0.00 0.00 44.32 2.71
2033 2337 5.392286 TGAAACACGGTAGTTTTGACAAAC 58.608 37.500 0.00 0.00 41.48 2.93
2044 2348 3.634568 TTGGCAAATGAAACACGGTAG 57.365 42.857 0.00 0.00 0.00 3.18
2070 2374 5.827797 TGTATCCCTGAATAATCTTTGGCAC 59.172 40.000 0.00 0.00 0.00 5.01
2077 2381 6.500049 CCTCCTTCTGTATCCCTGAATAATCT 59.500 42.308 0.00 0.00 31.53 2.40
2078 2382 6.271159 ACCTCCTTCTGTATCCCTGAATAATC 59.729 42.308 0.00 0.00 31.53 1.75
2079 2383 6.153924 ACCTCCTTCTGTATCCCTGAATAAT 58.846 40.000 0.00 0.00 31.53 1.28
2081 2385 5.157770 ACCTCCTTCTGTATCCCTGAATA 57.842 43.478 0.00 0.00 31.53 1.75
2082 2386 4.014273 ACCTCCTTCTGTATCCCTGAAT 57.986 45.455 0.00 0.00 31.53 2.57
2084 2388 3.491766 AACCTCCTTCTGTATCCCTGA 57.508 47.619 0.00 0.00 0.00 3.86
2085 2389 3.519510 TCAAACCTCCTTCTGTATCCCTG 59.480 47.826 0.00 0.00 0.00 4.45
2086 2390 3.777522 CTCAAACCTCCTTCTGTATCCCT 59.222 47.826 0.00 0.00 0.00 4.20
2093 2418 4.815533 TCAGATCTCAAACCTCCTTCTG 57.184 45.455 0.00 0.00 0.00 3.02
2094 2419 5.832539 TTTCAGATCTCAAACCTCCTTCT 57.167 39.130 0.00 0.00 0.00 2.85
2102 2427 7.746929 ACGAATCTCAATTTCAGATCTCAAAC 58.253 34.615 0.00 0.00 29.82 2.93
2103 2428 7.912056 ACGAATCTCAATTTCAGATCTCAAA 57.088 32.000 0.00 0.00 29.82 2.69
2122 2447 7.063898 CGAGATTCATTGCCATAAGATACGAAT 59.936 37.037 0.00 0.00 0.00 3.34
2133 2458 7.180322 AGATATCTACGAGATTCATTGCCAT 57.820 36.000 2.53 0.00 36.20 4.40
2164 2499 9.688091 AGTAAGTCAGAAATCTCACATACTAGA 57.312 33.333 1.29 0.00 0.00 2.43
2181 2516 8.587950 CGTTCTTGCTTTCTTATAGTAAGTCAG 58.412 37.037 0.00 0.00 36.88 3.51
2183 2518 7.544915 ACCGTTCTTGCTTTCTTATAGTAAGTC 59.455 37.037 0.00 0.00 36.88 3.01
2184 2519 7.331193 CACCGTTCTTGCTTTCTTATAGTAAGT 59.669 37.037 0.00 0.00 36.88 2.24
2185 2520 7.201530 CCACCGTTCTTGCTTTCTTATAGTAAG 60.202 40.741 0.00 0.00 36.88 2.34
2187 2522 6.103997 CCACCGTTCTTGCTTTCTTATAGTA 58.896 40.000 0.00 0.00 0.00 1.82
2195 2530 1.172812 AGCCCACCGTTCTTGCTTTC 61.173 55.000 0.00 0.00 0.00 2.62
2196 2531 0.755327 AAGCCCACCGTTCTTGCTTT 60.755 50.000 0.00 0.00 39.07 3.51
2199 2534 1.452145 TTCAAGCCCACCGTTCTTGC 61.452 55.000 0.00 0.00 37.64 4.01
2200 2535 0.593128 CTTCAAGCCCACCGTTCTTG 59.407 55.000 0.00 0.00 38.73 3.02
2203 2559 0.034896 TCTCTTCAAGCCCACCGTTC 59.965 55.000 0.00 0.00 0.00 3.95
2206 2562 0.745845 CCATCTCTTCAAGCCCACCG 60.746 60.000 0.00 0.00 0.00 4.94
2209 2565 2.199208 TCATCCATCTCTTCAAGCCCA 58.801 47.619 0.00 0.00 0.00 5.36
2212 2568 3.814283 GACCATCATCCATCTCTTCAAGC 59.186 47.826 0.00 0.00 0.00 4.01
2215 2571 5.224821 GATGACCATCATCCATCTCTTCA 57.775 43.478 7.46 0.00 45.66 3.02
2232 2588 2.475466 CCTGCACCATGCCGATGAC 61.475 63.158 0.00 0.00 44.23 3.06
2235 2591 3.410628 TCCCTGCACCATGCCGAT 61.411 61.111 0.00 0.00 44.23 4.18
2240 2596 1.954382 CATTCATCTCCCTGCACCATG 59.046 52.381 0.00 0.00 0.00 3.66
2241 2597 1.133575 CCATTCATCTCCCTGCACCAT 60.134 52.381 0.00 0.00 0.00 3.55
2244 2600 2.425143 TTCCATTCATCTCCCTGCAC 57.575 50.000 0.00 0.00 0.00 4.57
2255 2666 5.168569 GTCTGTGTCTTACGATTCCATTCA 58.831 41.667 0.00 0.00 0.00 2.57
2268 2679 0.032678 CCGTGCTCTGTCTGTGTCTT 59.967 55.000 0.00 0.00 0.00 3.01
2272 2690 0.109086 CCTACCGTGCTCTGTCTGTG 60.109 60.000 0.00 0.00 0.00 3.66
2299 2717 1.871408 GCATCACCATGGACGAGCTAG 60.871 57.143 21.47 7.29 0.00 3.42
2300 2718 0.104855 GCATCACCATGGACGAGCTA 59.895 55.000 21.47 0.00 0.00 3.32
2301 2719 1.153289 GCATCACCATGGACGAGCT 60.153 57.895 21.47 0.00 0.00 4.09
2302 2720 2.182842 GGCATCACCATGGACGAGC 61.183 63.158 21.47 16.24 38.86 5.03
2303 2721 1.884464 CGGCATCACCATGGACGAG 60.884 63.158 21.47 6.70 39.03 4.18
2304 2722 2.186644 CGGCATCACCATGGACGA 59.813 61.111 21.47 14.93 39.03 4.20
2444 2862 2.342279 CCCGAAACGTCTCTGCCA 59.658 61.111 0.00 0.00 0.00 4.92
2445 2863 2.027625 CACCCGAAACGTCTCTGCC 61.028 63.158 0.00 0.00 0.00 4.85
2446 2864 2.027625 CCACCCGAAACGTCTCTGC 61.028 63.158 0.00 0.00 0.00 4.26
2447 2865 1.374252 CCCACCCGAAACGTCTCTG 60.374 63.158 0.00 0.00 0.00 3.35
2448 2866 2.580601 CCCCACCCGAAACGTCTCT 61.581 63.158 0.00 0.00 0.00 3.10
2449 2867 2.047560 CCCCACCCGAAACGTCTC 60.048 66.667 0.00 0.00 0.00 3.36
2536 2954 2.483188 CCCACTAGCATAGGTTTCGGAC 60.483 54.545 0.00 0.00 44.97 4.79
2551 2969 2.358615 CACGCTTGCTGCCCACTA 60.359 61.111 0.00 0.00 38.78 2.74
2581 3001 3.305813 CGTTTAGCCACTCCTGTAGAACA 60.306 47.826 0.00 0.00 0.00 3.18
2644 3064 2.970576 CCACACGTTTGGCAAAAGG 58.029 52.632 25.60 17.78 37.23 3.11
2705 3125 4.527509 TTTTGTTGTCAAGTCTTGCCAA 57.472 36.364 4.96 4.96 34.88 4.52
2711 3131 4.522789 ACACAGGTTTTTGTTGTCAAGTCT 59.477 37.500 0.00 0.00 34.88 3.24
2764 3185 1.164411 CTCGTTTATGGCTTGCCACA 58.836 50.000 17.22 1.61 0.00 4.17
2765 3186 0.451783 CCTCGTTTATGGCTTGCCAC 59.548 55.000 17.22 3.23 0.00 5.01
2777 3198 2.165437 TGCTTGTTTCTTTGCCTCGTTT 59.835 40.909 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.