Multiple sequence alignment - TraesCS5A01G341500

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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 TraesCS5A01G341500 chr5A 100.000 2372 0 0 748 3119 547543252 547545623 0.000000e+00 4381.0
1 TraesCS5A01G341500 chr5A 100.000 457 0 0 1 457 547542505 547542961 0.000000e+00 845.0
2 TraesCS5A01G341500 chr5A 78.073 1131 168 41 998 2064 547508859 547509973 2.620000e-180 641.0
3 TraesCS5A01G341500 chr5A 78.622 711 125 19 998 1694 547590255 547590952 2.210000e-121 446.0
4 TraesCS5A01G341500 chr5A 77.546 432 76 13 1062 1487 547612908 547613324 1.120000e-59 241.0
5 TraesCS5A01G341500 chr5A 82.895 76 11 1 2570 2643 528486553 528486478 2.010000e-07 67.6
6 TraesCS5A01G341500 chr5B 94.105 1357 64 7 752 2100 526517621 526518969 0.000000e+00 2049.0
7 TraesCS5A01G341500 chr5B 92.551 443 27 3 1 439 526446644 526447084 5.680000e-177 630.0
8 TraesCS5A01G341500 chr5B 81.552 683 117 4 998 1680 526429653 526430326 3.510000e-154 555.0
9 TraesCS5A01G341500 chr5B 78.182 825 147 16 875 1683 526248131 526248938 2.160000e-136 496.0
10 TraesCS5A01G341500 chr5B 77.322 829 144 22 875 1683 526269434 526270238 1.710000e-122 449.0
11 TraesCS5A01G341500 chr5B 77.473 546 98 18 1000 1543 526174200 526174722 1.410000e-78 303.0
12 TraesCS5A01G341500 chr5B 79.861 432 70 8 1267 1694 526556217 526556635 1.820000e-77 300.0
13 TraesCS5A01G341500 chr5D 93.919 1365 63 9 750 2100 432995050 432996408 0.000000e+00 2043.0
14 TraesCS5A01G341500 chr5D 77.921 1241 185 50 918 2097 432988128 432989340 0.000000e+00 691.0
15 TraesCS5A01G341500 chr5D 92.511 454 32 1 1 454 432994575 432995026 0.000000e+00 649.0
16 TraesCS5A01G341500 chr5D 77.914 815 144 20 884 1683 432933414 432934207 2.810000e-130 475.0
17 TraesCS5A01G341500 chr5D 82.412 199 20 4 2872 3070 360550771 360550588 3.220000e-35 159.0
18 TraesCS5A01G341500 chr2D 96.654 508 15 1 2612 3119 154950821 154951326 0.000000e+00 843.0
19 TraesCS5A01G341500 chr2D 93.638 503 14 4 2120 2620 154947930 154948416 0.000000e+00 736.0
20 TraesCS5A01G341500 chr3B 84.043 376 38 11 2267 2634 651683732 651683371 2.980000e-90 342.0
21 TraesCS5A01G341500 chr3B 87.111 225 21 5 2872 3095 794784651 794784434 6.680000e-62 248.0
22 TraesCS5A01G341500 chr3B 87.111 225 21 5 2872 3095 794810365 794810148 6.680000e-62 248.0
23 TraesCS5A01G341500 chr6D 89.333 225 18 1 2871 3095 34337667 34337449 8.520000e-71 278.0
24 TraesCS5A01G341500 chr6D 86.607 224 24 1 2872 3095 5660202 5659985 3.110000e-60 243.0
25 TraesCS5A01G341500 chr6D 76.642 274 59 4 1084 1356 88891975 88891706 2.510000e-31 147.0
26 TraesCS5A01G341500 chr1A 88.261 230 21 1 2866 3095 542712806 542712583 1.430000e-68 270.0
27 TraesCS5A01G341500 chr2B 84.783 230 29 4 2866 3095 181353944 181353721 3.130000e-55 226.0
28 TraesCS5A01G341500 chr7A 83.544 237 26 2 2866 3095 571709076 571708846 3.150000e-50 209.0
29 TraesCS5A01G341500 chr2A 84.000 225 27 6 2870 3094 711860842 711861057 1.130000e-49 207.0


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 TraesCS5A01G341500 chr5A 547542505 547545623 3118 False 2613.0 4381 100.000 1 3119 2 chr5A.!!$F4 3118
1 TraesCS5A01G341500 chr5A 547508859 547509973 1114 False 641.0 641 78.073 998 2064 1 chr5A.!!$F1 1066
2 TraesCS5A01G341500 chr5A 547590255 547590952 697 False 446.0 446 78.622 998 1694 1 chr5A.!!$F2 696
3 TraesCS5A01G341500 chr5B 526517621 526518969 1348 False 2049.0 2049 94.105 752 2100 1 chr5B.!!$F6 1348
4 TraesCS5A01G341500 chr5B 526429653 526430326 673 False 555.0 555 81.552 998 1680 1 chr5B.!!$F4 682
5 TraesCS5A01G341500 chr5B 526248131 526248938 807 False 496.0 496 78.182 875 1683 1 chr5B.!!$F2 808
6 TraesCS5A01G341500 chr5B 526269434 526270238 804 False 449.0 449 77.322 875 1683 1 chr5B.!!$F3 808
7 TraesCS5A01G341500 chr5B 526174200 526174722 522 False 303.0 303 77.473 1000 1543 1 chr5B.!!$F1 543
8 TraesCS5A01G341500 chr5D 432994575 432996408 1833 False 1346.0 2043 93.215 1 2100 2 chr5D.!!$F3 2099
9 TraesCS5A01G341500 chr5D 432988128 432989340 1212 False 691.0 691 77.921 918 2097 1 chr5D.!!$F2 1179
10 TraesCS5A01G341500 chr5D 432933414 432934207 793 False 475.0 475 77.914 884 1683 1 chr5D.!!$F1 799
11 TraesCS5A01G341500 chr2D 154947930 154951326 3396 False 789.5 843 95.146 2120 3119 2 chr2D.!!$F1 999

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
288 289 0.109597 GGCGACCGTCGAGAAACTAA 60.11 55.0 24.78 0.0 43.74 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2233 0.036388 ATGATTCGAGTTGTGCGGGT 60.036 50.0 0.0 0.0 0.0 5.28 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
27 28 3.879912 CGTTTCACGGGAGTAGTGT 57.120 52.632 0.00 0.00 44.67 3.55
32 33 1.694844 TCACGGGAGTAGTGTTGTCA 58.305 50.000 0.00 0.00 44.67 3.58
70 71 1.067416 TACATCGCCGACATGGAGC 59.933 57.895 0.00 0.00 42.00 4.70
81 82 0.541392 ACATGGAGCGGCAATAGACA 59.459 50.000 1.45 0.00 0.00 3.41
110 111 1.280142 CATCGAGGAGTCGTAGGCG 59.720 63.158 0.00 0.00 46.85 5.52
129 130 1.202533 CGACATACACCCATGACCTCC 60.203 57.143 0.00 0.00 0.00 4.30
130 131 0.830648 ACATACACCCATGACCTCCG 59.169 55.000 0.00 0.00 0.00 4.63
134 135 0.545787 ACACCCATGACCTCCGGTAA 60.546 55.000 0.00 0.00 35.25 2.85
183 184 0.983378 AAGGATAAGGAGGCAGCGGT 60.983 55.000 0.00 0.00 0.00 5.68
204 205 3.112263 TGACATAAGAGGAATTCCCGGT 58.888 45.455 21.22 10.00 40.87 5.28
230 231 2.738846 GCCATGATGATGCCTAACTACG 59.261 50.000 0.00 0.00 0.00 3.51
257 258 2.854777 GTCATCTCATTTGACTCCGACG 59.145 50.000 0.00 0.00 40.26 5.12
288 289 0.109597 GGCGACCGTCGAGAAACTAA 60.110 55.000 24.78 0.00 43.74 2.24
290 291 1.400759 GCGACCGTCGAGAAACTAAGT 60.401 52.381 24.78 0.00 43.74 2.24
385 386 1.608025 CGCAACTCTAGAACCCAAGCA 60.608 52.381 0.00 0.00 0.00 3.91
399 400 1.352352 CCAAGCATATGTAGGGAGGGG 59.648 57.143 4.29 0.00 0.00 4.79
419 420 1.203001 GGGAATTTGGGTGTCCAGACA 60.203 52.381 0.00 0.00 45.04 3.41
442 443 3.316821 CGACAGCTCATCATGGCG 58.683 61.111 0.00 0.00 42.30 5.69
447 448 2.068821 AGCTCATCATGGCGGACCT 61.069 57.895 0.00 0.00 36.63 3.85
786 787 6.790232 ATCCCGGACAATTTGAAAACATAT 57.210 33.333 0.73 0.00 0.00 1.78
848 849 3.997681 GTCCACCTAGCTGAAAGAAGTTC 59.002 47.826 0.00 0.00 34.07 3.01
863 864 9.950680 TGAAAGAAGTTCAGTTTGTAATCAATC 57.049 29.630 5.50 0.00 41.47 2.67
864 865 9.950680 GAAAGAAGTTCAGTTTGTAATCAATCA 57.049 29.630 5.50 0.00 36.15 2.57
866 867 9.956720 AAGAAGTTCAGTTTGTAATCAATCAAG 57.043 29.630 5.50 0.00 33.32 3.02
867 868 9.125026 AGAAGTTCAGTTTGTAATCAATCAAGT 57.875 29.630 5.50 0.00 33.32 3.16
868 869 9.736023 GAAGTTCAGTTTGTAATCAATCAAGTT 57.264 29.630 0.00 0.00 33.32 2.66
869 870 9.736023 AAGTTCAGTTTGTAATCAATCAAGTTC 57.264 29.630 0.00 0.00 33.32 3.01
870 871 8.902806 AGTTCAGTTTGTAATCAATCAAGTTCA 58.097 29.630 0.00 0.00 33.32 3.18
934 944 5.374071 GGTGATCCCGTACAAATATTTCCT 58.626 41.667 0.00 0.00 0.00 3.36
954 964 0.675083 TTCCGCTGTCGTTTACCTCA 59.325 50.000 0.00 0.00 0.00 3.86
965 980 7.201487 GCTGTCGTTTACCTCAAAACAAAAATT 60.201 33.333 0.00 0.00 38.93 1.82
1114 1161 4.335584 GCGAGATCCTCCTCCGCG 62.336 72.222 0.00 0.00 0.00 6.46
1200 1247 0.542232 CCTCCCCCGACTTCCGATAT 60.542 60.000 0.00 0.00 41.76 1.63
1260 1307 0.241213 TCGAAGACTCGTTCTGGCAG 59.759 55.000 8.58 8.58 45.62 4.85
1663 1723 4.025858 GCAGGGAGTGGCAGAGCA 62.026 66.667 0.00 0.00 0.00 4.26
1715 1790 4.980805 GTCTTGCCCCGACACGCA 62.981 66.667 0.00 0.00 0.00 5.24
2037 2145 2.663852 CAGGTTTCGGCGGTCGTT 60.664 61.111 7.21 0.00 40.32 3.85
2083 2191 9.574458 CTGTTAAGAATGATATGTATACCGAGG 57.426 37.037 0.00 0.00 0.00 4.63
2100 2208 1.072965 GAGGGCATCCTATCCTTGTGG 59.927 57.143 0.00 0.00 45.05 4.17
2101 2209 0.111253 GGGCATCCTATCCTTGTGGG 59.889 60.000 0.00 0.00 0.00 4.61
2102 2210 4.674254 AGGGCATCCTATCCTTGTGGGA 62.674 54.545 0.00 0.00 42.75 4.37
2109 2217 3.000819 TCCTTGTGGGACGCGGAT 61.001 61.111 12.47 0.00 45.01 4.18
2110 2218 2.046314 CCTTGTGGGACGCGGATT 60.046 61.111 12.47 0.00 45.01 3.01
2111 2219 1.674322 CCTTGTGGGACGCGGATTT 60.674 57.895 12.47 0.00 45.01 2.17
2112 2220 0.391927 CCTTGTGGGACGCGGATTTA 60.392 55.000 12.47 0.00 45.01 1.40
2113 2221 1.663695 CTTGTGGGACGCGGATTTAT 58.336 50.000 12.47 0.00 45.01 1.40
2114 2222 1.597663 CTTGTGGGACGCGGATTTATC 59.402 52.381 12.47 0.00 45.01 1.75
2115 2223 0.179067 TGTGGGACGCGGATTTATCC 60.179 55.000 12.47 6.88 45.01 2.59
2116 2224 0.106149 GTGGGACGCGGATTTATCCT 59.894 55.000 12.47 0.00 44.93 3.24
2117 2225 1.342174 GTGGGACGCGGATTTATCCTA 59.658 52.381 12.47 1.37 44.93 2.94
2118 2226 2.040939 TGGGACGCGGATTTATCCTAA 58.959 47.619 12.47 0.00 44.93 2.69
2119 2227 2.224113 TGGGACGCGGATTTATCCTAAC 60.224 50.000 12.47 0.00 44.93 2.34
2120 2228 2.410939 GGACGCGGATTTATCCTAACC 58.589 52.381 12.47 2.40 44.93 2.85
2121 2229 2.224113 GGACGCGGATTTATCCTAACCA 60.224 50.000 12.47 0.00 44.93 3.67
2122 2230 3.057734 GACGCGGATTTATCCTAACCAG 58.942 50.000 12.47 0.00 44.93 4.00
2123 2231 2.433239 ACGCGGATTTATCCTAACCAGT 59.567 45.455 12.47 0.00 44.93 4.00
2124 2232 3.118519 ACGCGGATTTATCCTAACCAGTT 60.119 43.478 12.47 0.00 44.93 3.16
2125 2233 4.099881 ACGCGGATTTATCCTAACCAGTTA 59.900 41.667 12.47 0.00 44.93 2.24
2126 2234 4.446719 CGCGGATTTATCCTAACCAGTTAC 59.553 45.833 0.00 0.00 44.93 2.50
2127 2235 4.753610 GCGGATTTATCCTAACCAGTTACC 59.246 45.833 7.16 0.00 44.93 2.85
2210 2318 3.529533 GTCTCAGCATGCAGTGTATTCT 58.470 45.455 21.98 0.00 34.76 2.40
2231 2339 2.509131 TGGGGCATGTGATATTCTGACA 59.491 45.455 0.00 0.00 0.00 3.58
2238 2346 7.040201 GGGCATGTGATATTCTGACATTTGTAT 60.040 37.037 0.00 0.00 0.00 2.29
2293 2401 2.877168 GCCTAGTGATTCTTCTGCCATG 59.123 50.000 0.00 0.00 0.00 3.66
2294 2402 3.683847 GCCTAGTGATTCTTCTGCCATGT 60.684 47.826 0.00 0.00 0.00 3.21
2295 2403 4.443457 GCCTAGTGATTCTTCTGCCATGTA 60.443 45.833 0.00 0.00 0.00 2.29
2317 2425 2.320681 AGTACTGTTAGGCCAGGTCA 57.679 50.000 5.01 0.00 36.75 4.02
2360 2468 2.486951 GATGTGCAGCATCCAACATC 57.513 50.000 14.64 2.53 46.26 3.06
2361 2469 1.066605 GATGTGCAGCATCCAACATCC 59.933 52.381 14.64 0.00 46.26 3.51
2362 2470 0.251253 TGTGCAGCATCCAACATCCA 60.251 50.000 0.00 0.00 0.00 3.41
2499 2609 8.449251 TTTTTGGAGGTTACGTTATAAAGTGT 57.551 30.769 13.48 3.40 0.00 3.55
2511 2621 8.080083 ACGTTATAAAGTGTTGTCGAAAAGAT 57.920 30.769 3.08 0.00 0.00 2.40
2512 2622 9.195411 ACGTTATAAAGTGTTGTCGAAAAGATA 57.805 29.630 3.08 0.00 0.00 1.98
2551 2661 2.932614 CAGCCATAAAGTTCTCTGGTCG 59.067 50.000 0.00 0.00 0.00 4.79
2557 2667 1.120530 AAGTTCTCTGGTCGGTGTGT 58.879 50.000 0.00 0.00 0.00 3.72
2559 2669 1.069090 TTCTCTGGTCGGTGTGTGC 59.931 57.895 0.00 0.00 0.00 4.57
2607 2717 2.775911 ACAGTCTATGTGCATGCACT 57.224 45.000 41.43 30.70 46.30 4.40
2689 5212 0.727398 GTGTTAACGCAGGAGATGGC 59.273 55.000 14.22 0.00 0.00 4.40
2690 5213 0.392461 TGTTAACGCAGGAGATGGCC 60.392 55.000 0.00 0.00 0.00 5.36
2771 5294 9.138062 CATGAAATCACGAAAACCATGATAAAA 57.862 29.630 0.00 0.00 32.74 1.52
2772 5295 9.703892 ATGAAATCACGAAAACCATGATAAAAA 57.296 25.926 0.00 0.00 32.74 1.94
2802 5325 4.288105 AGAGGAGACATGTCCAGAAACATT 59.712 41.667 22.21 0.00 37.78 2.71
2804 5327 5.388654 AGGAGACATGTCCAGAAACATTTT 58.611 37.500 22.21 0.00 37.78 1.82
2815 5338 9.447157 TGTCCAGAAACATTTTCAAGAAAAATT 57.553 25.926 11.53 7.07 43.51 1.82
2914 5437 2.499520 CATTGTCGTTGTGGCGCG 60.500 61.111 0.00 0.00 0.00 6.86
3007 5530 1.336755 GCAAAACACCGGAACTGTCAT 59.663 47.619 9.46 0.00 0.00 3.06
3023 5546 0.948623 TCATCCACAAGCGTCCAACG 60.949 55.000 0.00 0.00 45.88 4.10
3029 5552 0.375803 ACAAGCGTCCAACGTTGTTC 59.624 50.000 25.63 16.56 44.73 3.18
3083 5606 0.741326 CCACACGAGATGAGATCCGT 59.259 55.000 0.00 0.00 36.90 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.535335 GGTACCGGAGCTCATGACAA 59.465 55.000 17.19 0.00 0.00 3.18
32 33 3.900892 CGCGGTACCGGAGCTCAT 61.901 66.667 33.98 2.63 40.19 2.90
52 53 1.067416 GCTCCATGTCGGCGATGTA 59.933 57.895 14.79 3.05 33.14 2.29
60 61 0.249447 TCTATTGCCGCTCCATGTCG 60.249 55.000 0.00 0.00 0.00 4.35
70 71 0.447801 GCACCACTTGTCTATTGCCG 59.552 55.000 0.00 0.00 0.00 5.69
73 74 2.503331 TGGTGCACCACTTGTCTATTG 58.497 47.619 34.74 0.00 42.01 1.90
110 111 1.202533 CGGAGGTCATGGGTGTATGTC 60.203 57.143 0.00 0.00 0.00 3.06
129 130 3.132289 ACTCATAGGTGGTCATGTTACCG 59.868 47.826 9.13 0.00 42.91 4.02
130 131 4.161565 TGACTCATAGGTGGTCATGTTACC 59.838 45.833 7.42 7.42 40.19 2.85
134 135 4.225942 ACAATGACTCATAGGTGGTCATGT 59.774 41.667 15.15 12.88 41.35 3.21
183 184 3.112263 ACCGGGAATTCCTCTTATGTCA 58.888 45.455 23.63 0.00 35.95 3.58
399 400 1.203001 TGTCTGGACACCCAAATTCCC 60.203 52.381 0.00 0.00 42.98 3.97
401 402 3.157087 ACATGTCTGGACACCCAAATTC 58.843 45.455 5.52 0.00 45.05 2.17
407 408 1.741770 GCGACATGTCTGGACACCC 60.742 63.158 22.95 0.00 45.05 4.61
419 420 0.103755 ATGATGAGCTGTCGCGACAT 59.896 50.000 39.09 27.36 41.01 3.06
747 748 3.181438 CCGGGATAAAGAGAGGAGAGAGA 60.181 52.174 0.00 0.00 0.00 3.10
748 749 3.153919 CCGGGATAAAGAGAGGAGAGAG 58.846 54.545 0.00 0.00 0.00 3.20
934 944 1.068895 TGAGGTAAACGACAGCGGAAA 59.931 47.619 0.00 0.00 43.17 3.13
954 964 0.855995 CGGCGGCGAATTTTTGTTTT 59.144 45.000 29.19 0.00 0.00 2.43
1114 1161 3.412408 GCTTGGGAGGGAGGGGAC 61.412 72.222 0.00 0.00 0.00 4.46
1176 1223 0.111832 GGAAGTCGGGGGAGGTTTTT 59.888 55.000 0.00 0.00 0.00 1.94
1178 1225 2.590114 CGGAAGTCGGGGGAGGTTT 61.590 63.158 0.00 0.00 34.75 3.27
1200 1247 3.700970 TGGAGCGCCATGAACCGA 61.701 61.111 4.49 0.00 39.92 4.69
1228 1275 1.546961 TCTTCGAAGACTCCCAGGAC 58.453 55.000 23.74 0.00 34.32 3.85
1663 1723 3.508048 GGTGTCCACCCAAGGGAT 58.492 61.111 13.15 0.00 45.68 3.85
1715 1790 3.897657 AGGCAAATCCATCCATCATCT 57.102 42.857 0.00 0.00 37.29 2.90
1847 1934 0.968901 ATCGTCGGTCTGGCCAAGTA 60.969 55.000 7.01 0.00 36.97 2.24
2037 2145 4.405680 ACAGACAGGAATACGAATCCATCA 59.594 41.667 8.23 0.00 39.55 3.07
2083 2191 1.140312 TCCCACAAGGATAGGATGCC 58.860 55.000 0.00 0.00 40.93 4.40
2105 2213 6.023615 CGGGTAACTGGTTAGGATAAATCCG 61.024 48.000 3.36 0.00 45.47 4.18
2106 2214 5.303165 CGGGTAACTGGTTAGGATAAATCC 58.697 45.833 0.35 0.35 42.94 3.01
2107 2215 4.753610 GCGGGTAACTGGTTAGGATAAATC 59.246 45.833 0.00 0.00 45.89 2.17
2108 2216 4.164604 TGCGGGTAACTGGTTAGGATAAAT 59.835 41.667 0.00 0.00 45.89 1.40
2109 2217 3.518705 TGCGGGTAACTGGTTAGGATAAA 59.481 43.478 0.00 0.00 45.89 1.40
2110 2218 3.106054 TGCGGGTAACTGGTTAGGATAA 58.894 45.455 0.00 0.00 45.89 1.75
2111 2219 2.431782 GTGCGGGTAACTGGTTAGGATA 59.568 50.000 0.00 0.00 45.89 2.59
2112 2220 1.208776 GTGCGGGTAACTGGTTAGGAT 59.791 52.381 0.00 0.00 45.89 3.24
2113 2221 0.609662 GTGCGGGTAACTGGTTAGGA 59.390 55.000 0.00 0.00 45.89 2.94
2114 2222 0.322322 TGTGCGGGTAACTGGTTAGG 59.678 55.000 0.00 0.00 45.89 2.69
2115 2223 1.802365 GTTGTGCGGGTAACTGGTTAG 59.198 52.381 0.00 0.00 45.89 2.34
2116 2224 1.417145 AGTTGTGCGGGTAACTGGTTA 59.583 47.619 0.00 0.00 45.89 2.85
2117 2225 0.181824 AGTTGTGCGGGTAACTGGTT 59.818 50.000 0.00 0.00 45.89 3.67
2118 2226 0.250166 GAGTTGTGCGGGTAACTGGT 60.250 55.000 0.00 0.00 45.89 4.00
2119 2227 1.289109 CGAGTTGTGCGGGTAACTGG 61.289 60.000 0.00 0.00 45.89 4.00
2121 2229 0.390124 TTCGAGTTGTGCGGGTAACT 59.610 50.000 0.00 0.00 39.67 2.24
2122 2230 1.392510 GATTCGAGTTGTGCGGGTAAC 59.607 52.381 0.00 0.00 0.00 2.50
2123 2231 1.001068 TGATTCGAGTTGTGCGGGTAA 59.999 47.619 0.00 0.00 0.00 2.85
2124 2232 0.604073 TGATTCGAGTTGTGCGGGTA 59.396 50.000 0.00 0.00 0.00 3.69
2125 2233 0.036388 ATGATTCGAGTTGTGCGGGT 60.036 50.000 0.00 0.00 0.00 5.28
2126 2234 1.086696 AATGATTCGAGTTGTGCGGG 58.913 50.000 0.00 0.00 0.00 6.13
2127 2235 1.791555 GCAATGATTCGAGTTGTGCGG 60.792 52.381 0.00 0.00 0.00 5.69
2210 2318 2.509131 TGTCAGAATATCACATGCCCCA 59.491 45.455 0.00 0.00 0.00 4.96
2231 2339 3.671928 GCGATACGGCTCGTTATACAAAT 59.328 43.478 5.57 0.00 41.54 2.32
2238 2346 1.483316 CAATGCGATACGGCTCGTTA 58.517 50.000 5.57 1.84 41.54 3.18
2293 2401 4.276642 ACCTGGCCTAACAGTACTACTAC 58.723 47.826 3.32 0.00 36.75 2.73
2294 2402 4.018141 TGACCTGGCCTAACAGTACTACTA 60.018 45.833 3.32 0.00 36.75 1.82
2295 2403 3.245514 TGACCTGGCCTAACAGTACTACT 60.246 47.826 3.32 0.00 36.75 2.57
2317 2425 3.770933 CTGTCCACATGGGGAATCAAAAT 59.229 43.478 21.01 0.00 39.05 1.82
2356 2464 2.704725 GTGTTTTCACGCATGGATGT 57.295 45.000 0.00 0.00 41.13 3.06
2403 2511 6.673106 TGCGTGTGATTAATTAAAAAGCAGA 58.327 32.000 1.21 0.00 0.00 4.26
2423 2531 0.324943 ACCAGGCTAAACATCTGCGT 59.675 50.000 0.00 0.00 0.00 5.24
2435 2543 4.322499 CGATATAATTAACCCGACCAGGCT 60.322 45.833 0.00 0.00 39.21 4.58
2511 2621 7.131907 TGGCTGCCTCTATGTAACTTTAATA 57.868 36.000 21.03 0.00 0.00 0.98
2512 2622 6.001449 TGGCTGCCTCTATGTAACTTTAAT 57.999 37.500 21.03 0.00 0.00 1.40
2513 2623 5.429681 TGGCTGCCTCTATGTAACTTTAA 57.570 39.130 21.03 0.00 0.00 1.52
2514 2624 5.630415 ATGGCTGCCTCTATGTAACTTTA 57.370 39.130 21.03 0.00 0.00 1.85
2515 2625 4.510167 ATGGCTGCCTCTATGTAACTTT 57.490 40.909 21.03 0.00 0.00 2.66
2516 2626 5.630415 TTATGGCTGCCTCTATGTAACTT 57.370 39.130 21.03 0.00 0.00 2.66
2551 2661 4.107051 GATGGCAGCGCACACACC 62.107 66.667 11.47 3.45 0.00 4.16
2599 2709 4.746309 TGGAGCCCCAGTGCATGC 62.746 66.667 11.82 11.82 37.58 4.06
2678 5201 4.925861 GCCTCGGCCATCTCCTGC 62.926 72.222 2.24 0.00 34.56 4.85
2713 5236 6.146601 TGACATCCGTTTATTGGTATACGA 57.853 37.500 0.00 0.00 37.42 3.43
2771 5294 4.594920 TGGACATGTCTCCTCTCTCTTTTT 59.405 41.667 24.50 0.00 0.00 1.94
2772 5295 4.163427 TGGACATGTCTCCTCTCTCTTTT 58.837 43.478 24.50 0.00 0.00 2.27
2815 5338 8.296713 GGTTGTTGCAGTAATCTTCTTCAATAA 58.703 33.333 0.00 0.00 0.00 1.40
2889 5412 1.106351 ACAACGACAATGGCCTTGCA 61.106 50.000 3.32 0.00 38.50 4.08
2914 5437 2.735237 GGATGATCCCCGGTCGAC 59.265 66.667 7.13 7.13 0.00 4.20
3023 5546 4.695928 GGAAGATGTAGGTCCAAGAACAAC 59.304 45.833 0.00 0.00 0.00 3.32
3029 5552 1.490910 GGGGGAAGATGTAGGTCCAAG 59.509 57.143 0.00 0.00 32.70 3.61
3083 5606 3.609853 GCCACAACCATTGTCTCTATGA 58.390 45.455 0.00 0.00 43.23 2.15


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

AutoCloner maintained by Alex Coulton.