Multiple sequence alignment - TraesCS4A01G177300

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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 TraesCS4A01G177300 chr4A 100.000 2906 0 0 1 2906 449118908 449116003 0.000000e+00 5367.0
1 TraesCS4A01G177300 chr4B 95.076 2051 74 14 1 2036 184863731 184865769 0.000000e+00 3203.0
2 TraesCS4A01G177300 chr4B 91.396 523 43 2 2385 2906 122040253 122039732 0.000000e+00 715.0
3 TraesCS4A01G177300 chr4B 87.703 553 67 1 2354 2906 73655755 73655204 0.000000e+00 643.0
4 TraesCS4A01G177300 chr4B 97.222 36 1 0 1533 1568 494692058 494692023 8.700000e-06 62.1
5 TraesCS4A01G177300 chr4D 93.644 1117 45 9 1 1108 121969633 121970732 0.000000e+00 1646.0
6 TraesCS4A01G177300 chr4D 97.056 917 21 4 1140 2050 121970735 121971651 0.000000e+00 1539.0
7 TraesCS4A01G177300 chr4D 87.368 95 11 1 2245 2338 121971842 121971936 1.100000e-19 108.0
8 TraesCS4A01G177300 chr4D 94.286 35 2 0 1533 1567 386831469 386831503 1.000000e-03 54.7
9 TraesCS4A01G177300 chr6D 93.807 549 33 1 2353 2901 401173727 401174274 0.000000e+00 824.0
10 TraesCS4A01G177300 chr7B 91.788 548 45 0 2359 2906 63765363 63764816 0.000000e+00 763.0
11 TraesCS4A01G177300 chr7B 86.800 500 61 5 2394 2892 703794354 703794849 1.180000e-153 553.0
12 TraesCS4A01G177300 chr7B 77.885 208 34 11 1367 1568 590500936 590500735 5.090000e-23 119.0
13 TraesCS4A01G177300 chr5B 91.188 522 46 0 2385 2906 688713446 688712925 0.000000e+00 710.0
14 TraesCS4A01G177300 chr5B 72.727 220 46 11 1355 1567 656925914 656926126 8.700000e-06 62.1
15 TraesCS4A01G177300 chr2D 91.618 513 42 1 2394 2906 617425164 617425675 0.000000e+00 708.0
16 TraesCS4A01G177300 chr1A 89.216 510 54 1 2397 2906 386787587 386787079 1.140000e-178 636.0
17 TraesCS4A01G177300 chr3B 90.269 483 36 2 2353 2835 727001610 727002081 3.180000e-174 621.0
18 TraesCS4A01G177300 chr5A 91.973 299 24 0 2608 2906 214060689 214060987 1.250000e-113 420.0
19 TraesCS4A01G177300 chr5A 94.872 39 2 0 1529 1567 649441752 649441790 8.700000e-06 62.1
20 TraesCS4A01G177300 chr7D 77.404 208 35 11 1367 1568 547458011 547457810 2.370000e-21 113.0
21 TraesCS4A01G177300 chr7A 76.303 211 38 11 1364 1568 631365254 631365458 5.120000e-18 102.0
22 TraesCS4A01G177300 chr2B 76.064 188 28 10 1774 1961 643387358 643387528 6.670000e-12 82.4
23 TraesCS4A01G177300 chr5D 71.893 338 58 29 1529 1840 520910292 520910618 2.420000e-06 63.9


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 TraesCS4A01G177300 chr4A 449116003 449118908 2905 True 5367.000000 5367 100.000000 1 2906 1 chr4A.!!$R1 2905
1 TraesCS4A01G177300 chr4B 184863731 184865769 2038 False 3203.000000 3203 95.076000 1 2036 1 chr4B.!!$F1 2035
2 TraesCS4A01G177300 chr4B 122039732 122040253 521 True 715.000000 715 91.396000 2385 2906 1 chr4B.!!$R2 521
3 TraesCS4A01G177300 chr4B 73655204 73655755 551 True 643.000000 643 87.703000 2354 2906 1 chr4B.!!$R1 552
4 TraesCS4A01G177300 chr4D 121969633 121971936 2303 False 1097.666667 1646 92.689333 1 2338 3 chr4D.!!$F2 2337
5 TraesCS4A01G177300 chr6D 401173727 401174274 547 False 824.000000 824 93.807000 2353 2901 1 chr6D.!!$F1 548
6 TraesCS4A01G177300 chr7B 63764816 63765363 547 True 763.000000 763 91.788000 2359 2906 1 chr7B.!!$R1 547
7 TraesCS4A01G177300 chr5B 688712925 688713446 521 True 710.000000 710 91.188000 2385 2906 1 chr5B.!!$R1 521
8 TraesCS4A01G177300 chr2D 617425164 617425675 511 False 708.000000 708 91.618000 2394 2906 1 chr2D.!!$F1 512
9 TraesCS4A01G177300 chr1A 386787079 386787587 508 True 636.000000 636 89.216000 2397 2906 1 chr1A.!!$R1 509

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
179 180 0.449786 AGCGACAGTGAGATCGACTG 59.550 55.0 20.36 20.36 45.39 3.51 F
1023 1042 1.886422 CCTCCCCTAAGCTCTTCCTT 58.114 55.0 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 1177 0.650512 CGGACATTACATCACCGTGC 59.349 55.0 0.0 0.0 38.97 5.34 R
2338 2398 0.037605 GGCGGGGTGTAGGATTATCG 60.038 60.0 0.0 0.0 0.00 2.92 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
118 119 7.167968 CAGTTGTTGTGTTGAACCATAATCTTG 59.832 37.037 0.00 0.00 0.00 3.02
179 180 0.449786 AGCGACAGTGAGATCGACTG 59.550 55.000 20.36 20.36 45.39 3.51
197 198 3.938109 GGAAGAGTCCGCCTTTCTT 57.062 52.632 0.00 0.00 33.05 2.52
202 203 4.333095 GGAAGAGTCCGCCTTTCTTATTTC 59.667 45.833 0.00 0.00 33.05 2.17
208 209 4.153655 GTCCGCCTTTCTTATTTCGAAAGT 59.846 41.667 16.80 7.31 43.54 2.66
213 214 6.237861 CGCCTTTCTTATTTCGAAAGTAGGAG 60.238 42.308 16.80 12.50 43.54 3.69
273 274 7.707464 TGTGATGAATCAAATTGATATGTTGCC 59.293 33.333 9.09 0.00 35.76 4.52
557 561 1.960689 GTCTGCTCTATCTCCCTGACC 59.039 57.143 0.00 0.00 0.00 4.02
615 619 2.027192 GGTAGCCCACTCACTGATGAAA 60.027 50.000 0.00 0.00 33.30 2.69
620 624 4.946157 AGCCCACTCACTGATGAAATTAAG 59.054 41.667 0.00 0.00 33.30 1.85
624 628 6.259608 CCCACTCACTGATGAAATTAAGCTAG 59.740 42.308 0.00 0.00 33.30 3.42
647 651 4.706035 CAGCTAGCCTGAAGAATTGATCT 58.294 43.478 12.13 0.00 44.64 2.75
679 683 7.011482 GTCTAATTCTTAATCTCCATTGCACGT 59.989 37.037 0.00 0.00 0.00 4.49
699 709 3.402681 GCAGGGGAGTAGCCAGCA 61.403 66.667 0.00 0.00 38.95 4.41
730 740 7.659652 AGTTTCAGTTCAGATAACTAACTGC 57.340 36.000 9.08 0.00 46.18 4.40
736 752 8.409371 TCAGTTCAGATAACTAACTGCATAGAG 58.591 37.037 9.08 0.00 46.18 2.43
771 787 4.202010 TGCACTGGAGCTTAAACTTTTGTC 60.202 41.667 0.00 0.00 34.99 3.18
875 894 9.965824 CTTATTAAGTGGTTCAACTGTCAAATT 57.034 29.630 0.00 0.00 0.00 1.82
1009 1028 4.864334 CAGACGCCATGGCCTCCC 62.864 72.222 30.79 16.43 37.98 4.30
1023 1042 1.886422 CCTCCCCTAAGCTCTTCCTT 58.114 55.000 0.00 0.00 0.00 3.36
1037 1056 3.768757 CTCTTCCTTCTCCTCATCAGTGT 59.231 47.826 0.00 0.00 0.00 3.55
1153 1177 4.726021 GCGAACTTCAATGCAGAGTATGTG 60.726 45.833 0.00 0.00 0.00 3.21
1201 1225 6.400568 CCTAATGCATTTGTCTGATGGTTTT 58.599 36.000 18.75 0.00 0.00 2.43
1359 1383 3.509137 GACCACCTTCGACGTGCCA 62.509 63.158 0.00 0.00 0.00 4.92
1518 1542 2.284625 ATGACGCTGGGGACTCCA 60.285 61.111 0.00 0.00 44.79 3.86
1906 1930 1.892329 GCCCACCACAACCTGAATGAT 60.892 52.381 0.00 0.00 0.00 2.45
1930 1954 4.143030 GCATCGCTATCAATCACCATGTAC 60.143 45.833 0.00 0.00 0.00 2.90
1989 2013 9.179909 GTGTAGCTACATGGAGTATATGATACT 57.820 37.037 28.37 0.00 38.63 2.12
2023 2053 8.409358 AGGGTGTTATTTTGGCTTATGATATC 57.591 34.615 0.00 0.00 0.00 1.63
2048 2089 9.430623 TCAAAGAGACACGTATTATCATGAAAA 57.569 29.630 0.00 0.00 0.00 2.29
2077 2118 9.529325 AGTGAAAAGACCAAATAAAAGCTTAAC 57.471 29.630 0.00 0.00 0.00 2.01
2078 2119 8.761497 GTGAAAAGACCAAATAAAAGCTTAACC 58.239 33.333 0.00 0.00 0.00 2.85
2079 2120 8.478877 TGAAAAGACCAAATAAAAGCTTAACCA 58.521 29.630 0.00 0.00 0.00 3.67
2080 2121 9.320352 GAAAAGACCAAATAAAAGCTTAACCAA 57.680 29.630 0.00 0.00 0.00 3.67
2081 2122 9.674068 AAAAGACCAAATAAAAGCTTAACCAAA 57.326 25.926 0.00 0.00 0.00 3.28
2083 2124 7.787028 AGACCAAATAAAAGCTTAACCAAACA 58.213 30.769 0.00 0.00 0.00 2.83
2085 2126 7.561251 ACCAAATAAAAGCTTAACCAAACACT 58.439 30.769 0.00 0.00 0.00 3.55
2086 2127 7.494298 ACCAAATAAAAGCTTAACCAAACACTG 59.506 33.333 0.00 0.00 0.00 3.66
2092 2150 3.564225 AGCTTAACCAAACACTGTACAGC 59.436 43.478 22.90 4.81 0.00 4.40
2112 2170 2.885554 GCCTGATCCCAAACCAGTCAAT 60.886 50.000 0.00 0.00 0.00 2.57
2113 2171 3.434309 CCTGATCCCAAACCAGTCAATT 58.566 45.455 0.00 0.00 0.00 2.32
2114 2172 3.834231 CCTGATCCCAAACCAGTCAATTT 59.166 43.478 0.00 0.00 0.00 1.82
2115 2173 4.284234 CCTGATCCCAAACCAGTCAATTTT 59.716 41.667 0.00 0.00 0.00 1.82
2116 2174 5.221702 CCTGATCCCAAACCAGTCAATTTTT 60.222 40.000 0.00 0.00 0.00 1.94
2147 2205 3.946308 GGCAGCTTAACCGATAAGTTC 57.054 47.619 8.94 1.34 42.58 3.01
2149 2207 4.690122 GGCAGCTTAACCGATAAGTTCTA 58.310 43.478 8.94 0.00 42.58 2.10
2184 2243 2.542597 ACGACGTGTAGCAAGTTCAAA 58.457 42.857 0.00 0.00 0.00 2.69
2187 2246 2.870411 GACGTGTAGCAAGTTCAAAGGT 59.130 45.455 0.00 0.00 0.00 3.50
2217 2276 5.488262 AAAAAGGCATAGTTCAAAGGCAT 57.512 34.783 0.00 0.00 0.00 4.40
2220 2279 5.582689 AAGGCATAGTTCAAAGGCATAAC 57.417 39.130 0.00 0.00 0.00 1.89
2221 2280 4.599041 AGGCATAGTTCAAAGGCATAACA 58.401 39.130 0.00 0.00 0.00 2.41
2222 2281 4.399303 AGGCATAGTTCAAAGGCATAACAC 59.601 41.667 0.00 0.00 0.00 3.32
2223 2282 4.342772 GCATAGTTCAAAGGCATAACACG 58.657 43.478 0.00 0.00 0.00 4.49
2224 2283 2.989422 AGTTCAAAGGCATAACACGC 57.011 45.000 0.00 0.00 0.00 5.34
2239 2298 4.838152 CGCCAGACGGGGGTGATG 62.838 72.222 0.24 0.00 44.34 3.07
2240 2299 4.489771 GCCAGACGGGGGTGATGG 62.490 72.222 0.00 0.00 37.04 3.51
2241 2300 4.489771 CCAGACGGGGGTGATGGC 62.490 72.222 0.00 0.00 0.00 4.40
2242 2301 4.838152 CAGACGGGGGTGATGGCG 62.838 72.222 0.00 0.00 0.00 5.69
2247 2306 4.176752 GGGGGTGATGGCGGAGAC 62.177 72.222 0.00 0.00 0.00 3.36
2267 2326 7.148423 CGGAGACACAAATCTTAAACATCATCA 60.148 37.037 0.00 0.00 0.00 3.07
2270 2329 6.317088 ACACAAATCTTAAACATCATCAGCG 58.683 36.000 0.00 0.00 0.00 5.18
2294 2353 4.717629 CGTCGGCGTTCCAGCTCA 62.718 66.667 6.85 0.00 37.29 4.26
2295 2354 2.357034 GTCGGCGTTCCAGCTCAA 60.357 61.111 6.85 0.00 37.29 3.02
2296 2355 2.048222 TCGGCGTTCCAGCTCAAG 60.048 61.111 6.85 0.00 37.29 3.02
2346 2406 7.472543 GGCAACCATTATGAATACGATAATCC 58.527 38.462 0.00 0.00 0.00 3.01
2347 2407 7.336931 GGCAACCATTATGAATACGATAATCCT 59.663 37.037 0.00 0.00 0.00 3.24
2348 2408 9.378551 GCAACCATTATGAATACGATAATCCTA 57.621 33.333 0.00 0.00 0.00 2.94
2351 2411 9.871238 ACCATTATGAATACGATAATCCTACAC 57.129 33.333 0.00 0.00 0.00 2.90
2481 2542 3.581770 CCTCCTTCAGATCCATGCTCATA 59.418 47.826 0.00 0.00 0.00 2.15
2602 2663 1.822186 GGTTTGTGCCCGTGTCAGT 60.822 57.895 0.00 0.00 0.00 3.41
2632 2693 0.618680 ATGGAGGACTGCTGCCACTA 60.619 55.000 0.00 0.18 32.42 2.74
2659 2720 1.278413 GTTCCCTCTAACCTTCGGCTT 59.722 52.381 0.00 0.00 0.00 4.35
2753 2814 0.392193 CATCTTCTTGGAGGCGCTGT 60.392 55.000 7.64 0.00 0.00 4.40
2757 2818 0.394938 TTCTTGGAGGCGCTGTTGTA 59.605 50.000 7.64 0.00 0.00 2.41
2766 2827 0.440371 GCGCTGTTGTAGAGTTCAGC 59.560 55.000 0.00 6.02 46.38 4.26
2805 2866 0.254178 AAAGTCCTGCGATGATGGCT 59.746 50.000 0.29 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 180 3.545366 ATAAGAAAGGCGGACTCTTCC 57.455 47.619 0.00 0.00 38.77 3.46
197 198 8.114331 TGTTGAGTACTCCTACTTTCGAAATA 57.886 34.615 20.11 5.60 32.96 1.40
202 203 7.310664 TGTAATGTTGAGTACTCCTACTTTCG 58.689 38.462 20.11 0.00 32.96 3.46
273 274 3.554692 GGAAGTGCGTGCGATCCG 61.555 66.667 0.00 0.00 0.00 4.18
557 561 5.292765 ACATATCTTGTAGCCGACAATCAG 58.707 41.667 2.48 0.00 46.95 2.90
624 628 2.636830 TCAATTCTTCAGGCTAGCTGC 58.363 47.619 15.72 0.00 41.94 5.25
649 653 8.772705 GCAATGGAGATTAAGAATTAGACTCTG 58.227 37.037 0.00 0.00 36.01 3.35
655 659 7.251704 ACGTGCAATGGAGATTAAGAATTAG 57.748 36.000 0.00 0.00 0.00 1.73
679 683 1.685224 CTGGCTACTCCCCTGCAAA 59.315 57.895 0.00 0.00 0.00 3.68
730 740 2.681344 TGCATTCAAGCTGCACTCTATG 59.319 45.455 1.02 0.19 44.30 2.23
771 787 5.144692 TCTCTCTTCCATGTCTGAAACAG 57.855 43.478 0.00 0.00 42.37 3.16
918 937 7.175641 GTGTGGTGGTCTTACTCTTAAGTAGTA 59.824 40.741 1.63 6.54 39.14 1.82
919 938 6.015603 GTGTGGTGGTCTTACTCTTAAGTAGT 60.016 42.308 1.63 7.46 39.14 2.73
920 939 6.388278 GTGTGGTGGTCTTACTCTTAAGTAG 58.612 44.000 1.63 1.70 39.14 2.57
921 940 5.244626 GGTGTGGTGGTCTTACTCTTAAGTA 59.755 44.000 1.63 0.00 36.75 2.24
922 941 4.040095 GGTGTGGTGGTCTTACTCTTAAGT 59.960 45.833 1.63 0.00 36.75 2.24
1009 1028 3.370104 TGAGGAGAAGGAAGAGCTTAGG 58.630 50.000 0.00 0.00 0.00 2.69
1023 1042 4.544683 AGATGATGACACTGATGAGGAGA 58.455 43.478 0.00 0.00 0.00 3.71
1037 1056 3.137728 AGTGATTGCCATGGAGATGATGA 59.862 43.478 18.40 0.00 0.00 2.92
1123 1147 1.453148 GCATTGAAGTTCGCTGCAAAC 59.547 47.619 19.17 0.00 45.28 2.93
1153 1177 0.650512 CGGACATTACATCACCGTGC 59.349 55.000 0.00 0.00 38.97 5.34
1518 1542 1.738099 GAAGTGCATCGGCGACTGT 60.738 57.895 13.76 0.00 45.35 3.55
1575 1599 4.444838 CCGACCGGCGTCATGGAA 62.445 66.667 15.38 0.00 39.11 3.53
1906 1930 2.618442 TGGTGATTGATAGCGATGCA 57.382 45.000 0.00 0.00 0.00 3.96
1989 2013 8.041143 AGCCAAAATAACACCCTCATACTATA 57.959 34.615 0.00 0.00 0.00 1.31
1990 2014 6.911308 AGCCAAAATAACACCCTCATACTAT 58.089 36.000 0.00 0.00 0.00 2.12
1993 2017 5.914898 AAGCCAAAATAACACCCTCATAC 57.085 39.130 0.00 0.00 0.00 2.39
1994 2018 7.350382 TCATAAGCCAAAATAACACCCTCATA 58.650 34.615 0.00 0.00 0.00 2.15
1996 2020 5.575157 TCATAAGCCAAAATAACACCCTCA 58.425 37.500 0.00 0.00 0.00 3.86
1998 2022 8.004215 TGATATCATAAGCCAAAATAACACCCT 58.996 33.333 0.00 0.00 0.00 4.34
2048 2089 9.448438 AAGCTTTTATTTGGTCTTTTCACTTTT 57.552 25.926 0.00 0.00 0.00 2.27
2052 2093 8.761497 GGTTAAGCTTTTATTTGGTCTTTTCAC 58.239 33.333 3.20 0.00 0.00 3.18
2054 2095 8.880878 TGGTTAAGCTTTTATTTGGTCTTTTC 57.119 30.769 3.20 0.00 0.00 2.29
2055 2096 9.674068 TTTGGTTAAGCTTTTATTTGGTCTTTT 57.326 25.926 3.20 0.00 0.00 2.27
2059 2100 7.709182 AGTGTTTGGTTAAGCTTTTATTTGGTC 59.291 33.333 3.20 0.00 0.00 4.02
2064 2105 8.688151 TGTACAGTGTTTGGTTAAGCTTTTATT 58.312 29.630 3.20 0.00 0.00 1.40
2068 2109 5.449999 GCTGTACAGTGTTTGGTTAAGCTTT 60.450 40.000 23.44 0.00 0.00 3.51
2069 2110 4.036380 GCTGTACAGTGTTTGGTTAAGCTT 59.964 41.667 23.44 3.48 0.00 3.74
2070 2111 3.564225 GCTGTACAGTGTTTGGTTAAGCT 59.436 43.478 23.44 0.00 0.00 3.74
2071 2112 3.304458 GGCTGTACAGTGTTTGGTTAAGC 60.304 47.826 23.44 5.60 0.00 3.09
2072 2113 4.024048 CAGGCTGTACAGTGTTTGGTTAAG 60.024 45.833 23.44 0.00 0.00 1.85
2075 2116 2.092646 TCAGGCTGTACAGTGTTTGGTT 60.093 45.455 23.44 0.00 0.00 3.67
2076 2117 1.488812 TCAGGCTGTACAGTGTTTGGT 59.511 47.619 23.44 0.00 0.00 3.67
2077 2118 2.254546 TCAGGCTGTACAGTGTTTGG 57.745 50.000 23.44 8.40 0.00 3.28
2078 2119 2.744202 GGATCAGGCTGTACAGTGTTTG 59.256 50.000 23.44 15.66 0.00 2.93
2079 2120 2.290323 GGGATCAGGCTGTACAGTGTTT 60.290 50.000 23.44 7.81 0.00 2.83
2080 2121 1.279271 GGGATCAGGCTGTACAGTGTT 59.721 52.381 23.44 10.25 0.00 3.32
2081 2122 0.905357 GGGATCAGGCTGTACAGTGT 59.095 55.000 23.44 8.87 0.00 3.55
2083 2124 1.656587 TTGGGATCAGGCTGTACAGT 58.343 50.000 23.44 3.56 0.00 3.55
2085 2126 1.004277 GGTTTGGGATCAGGCTGTACA 59.996 52.381 15.27 6.73 0.00 2.90
2086 2127 1.004277 TGGTTTGGGATCAGGCTGTAC 59.996 52.381 15.27 9.53 0.00 2.90
2092 2150 2.584835 TTGACTGGTTTGGGATCAGG 57.415 50.000 0.00 0.00 33.19 3.86
2115 2173 4.261280 GGTTAAGCTGCCGACTTGTAAAAA 60.261 41.667 0.00 0.00 0.00 1.94
2116 2174 3.251487 GGTTAAGCTGCCGACTTGTAAAA 59.749 43.478 0.00 0.00 0.00 1.52
2117 2175 2.809696 GGTTAAGCTGCCGACTTGTAAA 59.190 45.455 0.00 0.00 0.00 2.01
2127 2185 3.532542 AGAACTTATCGGTTAAGCTGCC 58.467 45.455 2.76 0.00 40.94 4.85
2129 2187 6.421202 GTGGATAGAACTTATCGGTTAAGCTG 59.579 42.308 2.76 0.00 40.94 4.24
2131 2189 6.278363 TGTGGATAGAACTTATCGGTTAAGC 58.722 40.000 5.88 0.00 40.94 3.09
2134 2192 6.753279 CGTTTGTGGATAGAACTTATCGGTTA 59.247 38.462 0.00 0.00 0.00 2.85
2145 2203 4.209703 GTCGTTGTTCGTTTGTGGATAGAA 59.790 41.667 0.00 0.00 40.80 2.10
2147 2205 3.421312 CGTCGTTGTTCGTTTGTGGATAG 60.421 47.826 0.00 0.00 40.80 2.08
2149 2207 1.259507 CGTCGTTGTTCGTTTGTGGAT 59.740 47.619 0.00 0.00 40.80 3.41
2166 2224 2.870411 ACCTTTGAACTTGCTACACGTC 59.130 45.455 0.00 0.00 0.00 4.34
2198 2257 5.016173 TGTTATGCCTTTGAACTATGCCTT 58.984 37.500 0.00 0.00 0.00 4.35
2199 2258 4.399303 GTGTTATGCCTTTGAACTATGCCT 59.601 41.667 0.00 0.00 0.00 4.75
2202 2261 4.342772 GCGTGTTATGCCTTTGAACTATG 58.657 43.478 0.00 0.00 0.00 2.23
2217 2276 3.697747 CCCCCGTCTGGCGTGTTA 61.698 66.667 0.00 0.00 39.32 2.41
2222 2281 4.838152 CATCACCCCCGTCTGGCG 62.838 72.222 0.00 0.00 40.95 5.69
2223 2282 4.489771 CCATCACCCCCGTCTGGC 62.490 72.222 0.00 0.00 0.00 4.85
2224 2283 4.489771 GCCATCACCCCCGTCTGG 62.490 72.222 0.00 0.00 0.00 3.86
2225 2284 4.838152 CGCCATCACCCCCGTCTG 62.838 72.222 0.00 0.00 0.00 3.51
2230 2289 4.176752 GTCTCCGCCATCACCCCC 62.177 72.222 0.00 0.00 0.00 5.40
2231 2290 3.399181 TGTCTCCGCCATCACCCC 61.399 66.667 0.00 0.00 0.00 4.95
2232 2291 2.125106 GTGTCTCCGCCATCACCC 60.125 66.667 0.00 0.00 0.00 4.61
2233 2292 0.605319 TTTGTGTCTCCGCCATCACC 60.605 55.000 0.00 0.00 0.00 4.02
2234 2293 1.398390 GATTTGTGTCTCCGCCATCAC 59.602 52.381 0.00 0.00 0.00 3.06
2235 2294 1.278985 AGATTTGTGTCTCCGCCATCA 59.721 47.619 0.00 0.00 0.00 3.07
2236 2295 2.029838 AGATTTGTGTCTCCGCCATC 57.970 50.000 0.00 0.00 0.00 3.51
2237 2296 2.496899 AAGATTTGTGTCTCCGCCAT 57.503 45.000 0.00 0.00 0.00 4.40
2238 2297 3.410631 TTAAGATTTGTGTCTCCGCCA 57.589 42.857 0.00 0.00 0.00 5.69
2239 2298 3.500680 TGTTTAAGATTTGTGTCTCCGCC 59.499 43.478 0.00 0.00 0.00 6.13
2240 2299 4.742438 TGTTTAAGATTTGTGTCTCCGC 57.258 40.909 0.00 0.00 0.00 5.54
2241 2300 6.480524 TGATGTTTAAGATTTGTGTCTCCG 57.519 37.500 0.00 0.00 0.00 4.63
2242 2301 8.044060 TGATGATGTTTAAGATTTGTGTCTCC 57.956 34.615 0.00 0.00 0.00 3.71
2243 2302 7.695618 GCTGATGATGTTTAAGATTTGTGTCTC 59.304 37.037 0.00 0.00 0.00 3.36
2244 2303 7.533426 GCTGATGATGTTTAAGATTTGTGTCT 58.467 34.615 0.00 0.00 0.00 3.41
2245 2304 6.467047 CGCTGATGATGTTTAAGATTTGTGTC 59.533 38.462 0.00 0.00 0.00 3.67
2246 2305 6.149308 TCGCTGATGATGTTTAAGATTTGTGT 59.851 34.615 0.00 0.00 0.00 3.72
2247 2306 6.545508 TCGCTGATGATGTTTAAGATTTGTG 58.454 36.000 0.00 0.00 0.00 3.33
2248 2307 6.595326 TCTCGCTGATGATGTTTAAGATTTGT 59.405 34.615 0.00 0.00 0.00 2.83
2249 2308 7.008440 TCTCGCTGATGATGTTTAAGATTTG 57.992 36.000 0.00 0.00 0.00 2.32
2250 2309 7.798596 ATCTCGCTGATGATGTTTAAGATTT 57.201 32.000 0.00 0.00 33.43 2.17
2270 2329 3.255379 GAACGCCGACGCCATCTC 61.255 66.667 0.00 0.00 45.53 2.75
2295 2354 2.636830 ACATCAATAAGCTTGCTCGCT 58.363 42.857 9.86 0.00 43.31 4.93
2296 2355 3.804325 TCTACATCAATAAGCTTGCTCGC 59.196 43.478 9.86 0.00 0.00 5.03
2302 2361 5.116084 TGCCCTTCTACATCAATAAGCTT 57.884 39.130 3.48 3.48 0.00 3.74
2303 2362 4.778213 TGCCCTTCTACATCAATAAGCT 57.222 40.909 0.00 0.00 0.00 3.74
2304 2363 4.036852 GGTTGCCCTTCTACATCAATAAGC 59.963 45.833 0.00 0.00 0.00 3.09
2338 2398 0.037605 GGCGGGGTGTAGGATTATCG 60.038 60.000 0.00 0.00 0.00 2.92
2339 2399 1.002087 CAGGCGGGGTGTAGGATTATC 59.998 57.143 0.00 0.00 0.00 1.75
2340 2400 1.056660 CAGGCGGGGTGTAGGATTAT 58.943 55.000 0.00 0.00 0.00 1.28
2341 2401 0.325860 ACAGGCGGGGTGTAGGATTA 60.326 55.000 0.00 0.00 0.00 1.75
2342 2402 1.615424 ACAGGCGGGGTGTAGGATT 60.615 57.895 0.00 0.00 0.00 3.01
2343 2403 2.040606 ACAGGCGGGGTGTAGGAT 59.959 61.111 0.00 0.00 0.00 3.24
2344 2404 2.682494 GACAGGCGGGGTGTAGGA 60.682 66.667 0.00 0.00 0.00 2.94
2345 2405 4.143333 CGACAGGCGGGGTGTAGG 62.143 72.222 0.00 0.00 36.03 3.18
2346 2406 3.379445 ACGACAGGCGGGGTGTAG 61.379 66.667 0.00 0.00 46.49 2.74
2347 2407 3.687102 CACGACAGGCGGGGTGTA 61.687 66.667 0.00 0.00 46.49 2.90
2451 2511 0.119155 ATCTGAAGGAGGGGTGGTGA 59.881 55.000 0.00 0.00 0.00 4.02
2464 2525 3.495629 GCACCTATGAGCATGGATCTGAA 60.496 47.826 0.00 0.00 0.00 3.02
2481 2542 1.380302 GACAATCCACCCAGCACCT 59.620 57.895 0.00 0.00 0.00 4.00
2555 2616 1.816259 GTAATGCCTGGCCGCGTAA 60.816 57.895 17.53 0.00 0.00 3.18
2565 2626 0.742281 CAGACGCAGCTGTAATGCCT 60.742 55.000 16.64 1.72 40.67 4.75
2602 2663 0.459585 GTCCTCCATGCTAAACGCGA 60.460 55.000 15.93 0.00 43.27 5.87
2632 2693 1.597461 GTTAGAGGGAACTGCGGCT 59.403 57.895 0.00 0.00 44.43 5.52
2659 2720 1.831736 GGATTTCTCCCGGAGACAGAA 59.168 52.381 17.25 9.43 38.51 3.02
2753 2814 0.318441 AGCTGCGCTGAACTCTACAA 59.682 50.000 19.32 0.00 37.57 2.41
2757 2818 0.179089 CCATAGCTGCGCTGAACTCT 60.179 55.000 19.32 7.86 40.10 3.24
2766 2827 0.096976 CGTCCAAAACCATAGCTGCG 59.903 55.000 0.00 0.00 0.00 5.18
2805 2866 0.535335 GTAGAATGACGCCCACAGGA 59.465 55.000 0.00 0.00 33.47 3.86


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

AutoCloner maintained by Alex Coulton.