Multiple sequence alignment - TraesCS5A01G348900

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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 TraesCS5A01G348900 chr5A 100.000 2396 0 0 1 2396 552277787 552280182 0.000000e+00 4425.0
1 TraesCS5A01G348900 chr5A 86.076 79 11 0 1001 1079 552298394 552298472 4.240000e-13 86.1
2 TraesCS5A01G348900 chr5B 83.529 2125 268 51 301 2396 531197011 531199082 0.000000e+00 1910.0
3 TraesCS5A01G348900 chr5B 81.018 511 40 25 290 780 531196541 531197014 1.050000e-93 353.0
4 TraesCS5A01G348900 chr5B 72.626 358 71 20 1000 1339 543282509 543282161 2.540000e-15 93.5
5 TraesCS5A01G348900 chr5B 86.076 79 11 0 1001 1079 531204686 531204764 4.240000e-13 86.1
6 TraesCS5A01G348900 chr5D 95.010 521 13 5 1 517 436985405 436985916 0.000000e+00 806.0
7 TraesCS5A01G348900 chr5D 83.986 843 126 5 1560 2396 437009575 437010414 0.000000e+00 800.0
8 TraesCS5A01G348900 chr5D 88.511 470 20 9 610 1054 437009089 437009549 2.710000e-149 538.0
9 TraesCS5A01G348900 chr5D 70.802 524 123 25 1001 1503 437015195 437015709 2.540000e-15 93.5
10 TraesCS5A01G348900 chr5D 74.884 215 46 8 999 1209 553910500 553910710 9.120000e-15 91.6
11 TraesCS5A01G348900 chr4D 72.467 523 114 23 1000 1501 1687317 1687830 8.930000e-30 141.0
12 TraesCS5A01G348900 chr7D 73.300 397 95 10 996 1388 554981133 554980744 4.150000e-28 135.0
13 TraesCS5A01G348900 chr7D 73.165 395 94 11 1000 1388 555158910 555158522 5.370000e-27 132.0
14 TraesCS5A01G348900 chr2B 80.645 124 21 3 996 1118 693708634 693708513 2.540000e-15 93.5
15 TraesCS5A01G348900 chr2B 75.897 195 37 9 1024 1213 794611695 794611506 9.120000e-15 91.6
16 TraesCS5A01G348900 chr2B 85.227 88 11 2 25 111 5690522 5690608 3.280000e-14 89.8
17 TraesCS5A01G348900 chr2A 84.091 88 12 2 28 114 4159958 4159872 1.530000e-12 84.2
18 TraesCS5A01G348900 chr4A 84.932 73 11 0 45 117 678200583 678200655 9.190000e-10 75.0
19 TraesCS5A01G348900 chr7A 89.286 56 4 2 66 119 80731696 80731751 4.270000e-08 69.4
20 TraesCS5A01G348900 chr7A 89.286 56 4 2 66 119 80753926 80753981 4.270000e-08 69.4
21 TraesCS5A01G348900 chr7A 89.286 56 4 2 66 119 80810272 80810327 4.270000e-08 69.4
22 TraesCS5A01G348900 chr7B 92.683 41 3 0 77 117 626603315 626603355 2.570000e-05 60.2


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 TraesCS5A01G348900 chr5A 552277787 552280182 2395 False 4425.0 4425 100.0000 1 2396 1 chr5A.!!$F1 2395
1 TraesCS5A01G348900 chr5B 531196541 531199082 2541 False 1131.5 1910 82.2735 290 2396 2 chr5B.!!$F2 2106
2 TraesCS5A01G348900 chr5D 436985405 436985916 511 False 806.0 806 95.0100 1 517 1 chr5D.!!$F1 516
3 TraesCS5A01G348900 chr5D 437009089 437010414 1325 False 669.0 800 86.2485 610 2396 2 chr5D.!!$F4 1786

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
922 1449 0.170561 CCCGTCGATCGAACTGTCTT 59.829 55.0 21.31 0.0 42.86 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2385 0.036732 TGACCATCCTTGTGGCTCAC 59.963 55.0 0.0 0.0 43.27 3.51 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
233 237 1.902918 GGTTGCATGCTGTGGTGGA 60.903 57.895 20.33 0.00 0.00 4.02
236 240 0.607217 TTGCATGCTGTGGTGGAGAG 60.607 55.000 20.33 0.00 0.00 3.20
411 427 6.538945 TCATAGATGCCCCCTTTTTAAAAC 57.461 37.500 0.00 0.00 0.00 2.43
464 480 8.122952 AGTTCACTTTTAGAATTTGTCTCAACG 58.877 33.333 0.00 0.00 37.84 4.10
541 1034 5.343307 AAAGTTGAGTGGCAATGTTTCTT 57.657 34.783 0.00 0.00 39.03 2.52
573 1066 5.620654 GCATGCATATATAAGCAAGTGTGGG 60.621 44.000 15.92 2.95 44.88 4.61
574 1067 5.047566 TGCATATATAAGCAAGTGTGGGT 57.952 39.130 10.10 0.00 37.90 4.51
575 1068 4.821260 TGCATATATAAGCAAGTGTGGGTG 59.179 41.667 10.10 0.00 37.90 4.61
576 1069 4.821805 GCATATATAAGCAAGTGTGGGTGT 59.178 41.667 5.10 0.00 0.00 4.16
578 1071 6.728200 CATATATAAGCAAGTGTGGGTGTTG 58.272 40.000 0.00 0.00 0.00 3.33
579 1072 2.428544 TAAGCAAGTGTGGGTGTTGT 57.571 45.000 0.00 0.00 0.00 3.32
580 1073 2.428544 AAGCAAGTGTGGGTGTTGTA 57.571 45.000 0.00 0.00 0.00 2.41
581 1074 2.656947 AGCAAGTGTGGGTGTTGTAT 57.343 45.000 0.00 0.00 0.00 2.29
582 1075 3.780804 AGCAAGTGTGGGTGTTGTATA 57.219 42.857 0.00 0.00 0.00 1.47
583 1076 3.408634 AGCAAGTGTGGGTGTTGTATAC 58.591 45.455 0.00 0.00 0.00 1.47
584 1077 2.158841 GCAAGTGTGGGTGTTGTATACG 59.841 50.000 0.00 0.00 0.00 3.06
585 1078 3.395639 CAAGTGTGGGTGTTGTATACGT 58.604 45.455 0.00 0.00 0.00 3.57
586 1079 4.558178 CAAGTGTGGGTGTTGTATACGTA 58.442 43.478 0.00 0.00 0.00 3.57
587 1080 4.870123 AGTGTGGGTGTTGTATACGTAA 57.130 40.909 0.00 0.00 0.00 3.18
588 1081 5.410355 AGTGTGGGTGTTGTATACGTAAT 57.590 39.130 0.00 0.00 0.00 1.89
589 1082 6.528537 AGTGTGGGTGTTGTATACGTAATA 57.471 37.500 0.00 0.00 0.00 0.98
623 1125 5.966742 AAGAAGTTTGATAAGGTTGAGGC 57.033 39.130 0.00 0.00 0.00 4.70
635 1137 3.035173 TTGAGGCTCCGGATGGCTG 62.035 63.158 26.70 8.76 40.49 4.85
649 1151 1.993391 GGCTGGTACTGGTAGGCCA 60.993 63.158 5.01 0.00 43.73 5.36
685 1187 5.238868 TCATGCGTAGAGGTATTACTGACTC 59.761 44.000 0.00 0.00 0.00 3.36
768 1271 2.803670 CCAGTGGCGTACGTCGTG 60.804 66.667 16.05 14.61 42.13 4.35
922 1449 0.170561 CCCGTCGATCGAACTGTCTT 59.829 55.000 21.31 0.00 42.86 3.01
957 1484 0.173708 CCTTCCTTCTCCCGTTCTCG 59.826 60.000 0.00 0.00 0.00 4.04
965 1492 1.720694 CTCCCGTTCTCGCTCTCCTC 61.721 65.000 0.00 0.00 35.54 3.71
1057 1584 3.456365 AGCTGCGCATCCTCGTCT 61.456 61.111 12.24 0.00 0.00 4.18
1088 1615 5.389520 CCTCTTCATCCAGTACATCCTCTA 58.610 45.833 0.00 0.00 0.00 2.43
1092 1619 6.547880 TCTTCATCCAGTACATCCTCTACTTC 59.452 42.308 0.00 0.00 0.00 3.01
1093 1620 4.822350 TCATCCAGTACATCCTCTACTTCG 59.178 45.833 0.00 0.00 0.00 3.79
1098 1625 1.471119 ACATCCTCTACTTCGCCGAA 58.529 50.000 0.00 0.00 0.00 4.30
1101 1628 3.004524 ACATCCTCTACTTCGCCGAATAC 59.995 47.826 0.00 0.00 0.00 1.89
1103 1630 1.396644 CTCTACTTCGCCGAATACGC 58.603 55.000 0.00 0.00 38.29 4.42
1110 1637 1.153597 TCGCCGAATACGCTCGTAGA 61.154 55.000 8.16 0.00 37.11 2.59
1128 1655 0.458716 GAGTTCCTGTCCTACGCAGC 60.459 60.000 0.00 0.00 32.93 5.25
1131 1658 0.246635 TTCCTGTCCTACGCAGCTTC 59.753 55.000 0.00 0.00 32.93 3.86
1147 1674 1.227943 TTCAGAGTGCTGGTGTGGC 60.228 57.895 0.00 0.00 42.53 5.01
1155 1682 2.809601 CTGGTGTGGCTCGCGTAC 60.810 66.667 5.77 0.00 0.00 3.67
1226 1753 1.162698 CACAGGCAGACTTGTGATGG 58.837 55.000 2.45 0.00 33.08 3.51
1266 1793 0.253160 TCCTATGGGTGCCTGTCCTT 60.253 55.000 0.00 0.00 0.00 3.36
1269 1796 1.139853 CTATGGGTGCCTGTCCTTCTC 59.860 57.143 0.00 0.00 0.00 2.87
1275 1802 1.211457 GTGCCTGTCCTTCTCATCCAT 59.789 52.381 0.00 0.00 0.00 3.41
1281 1808 2.092753 TGTCCTTCTCATCCATCTTGGC 60.093 50.000 0.00 0.00 37.47 4.52
1287 1814 2.191513 CATCCATCTTGGCGGCCAG 61.192 63.158 22.59 15.90 37.47 4.85
1297 1824 2.124320 GCGGCCAGCCAAGGATAA 60.124 61.111 9.78 0.00 40.81 1.75
1298 1825 2.189499 GCGGCCAGCCAAGGATAAG 61.189 63.158 9.78 0.00 40.81 1.73
1311 1838 3.330126 AGGATAAGTGCCTACAGCCTA 57.670 47.619 0.00 0.00 42.71 3.93
1366 1893 0.673985 CCTTGTGTCTCAGGTCACGA 59.326 55.000 0.00 0.00 37.38 4.35
1371 1898 1.226717 GTCTCAGGTCACGATCGCC 60.227 63.158 16.60 8.70 0.00 5.54
1377 1904 1.112113 AGGTCACGATCGCCTTGTAT 58.888 50.000 16.60 0.00 0.00 2.29
1395 1922 3.515104 TGTATGTCTTCTGCAGATGGTGA 59.485 43.478 24.74 14.92 32.60 4.02
1407 1934 0.598680 GATGGTGATCCGGCGAGAAG 60.599 60.000 9.30 0.00 36.30 2.85
1441 1968 2.223135 GCAGCGGTCTTGCTCTTTATTC 60.223 50.000 0.00 0.00 45.23 1.75
1446 1973 4.253685 CGGTCTTGCTCTTTATTCTTGGA 58.746 43.478 0.00 0.00 0.00 3.53
1449 1976 5.707764 GGTCTTGCTCTTTATTCTTGGAGTT 59.292 40.000 0.00 0.00 0.00 3.01
1452 1979 7.174080 GTCTTGCTCTTTATTCTTGGAGTTCTT 59.826 37.037 0.00 0.00 0.00 2.52
1484 2011 4.232310 GCCATGGGCTCTCAAGAC 57.768 61.111 15.13 0.00 46.69 3.01
1494 2021 1.404851 GCTCTCAAGACCGCTAGCTTT 60.405 52.381 13.93 0.00 0.00 3.51
1511 2038 4.362932 GCTTTAACAGCTTCCAATCCTC 57.637 45.455 0.00 0.00 46.27 3.71
1512 2039 3.129462 GCTTTAACAGCTTCCAATCCTCC 59.871 47.826 0.00 0.00 46.27 4.30
1518 2045 1.034292 GCTTCCAATCCTCCAGCACC 61.034 60.000 0.00 0.00 0.00 5.01
1535 2062 4.415150 CGTGCCCCTGTCAGCCAT 62.415 66.667 0.00 0.00 0.00 4.40
1542 2069 1.214589 CCTGTCAGCCATGCAAAGC 59.785 57.895 3.21 3.21 0.00 3.51
1546 2073 0.455633 GTCAGCCATGCAAAGCGAAG 60.456 55.000 5.75 1.52 0.00 3.79
1548 2075 0.241749 CAGCCATGCAAAGCGAAGAA 59.758 50.000 5.75 0.00 0.00 2.52
1549 2076 0.524862 AGCCATGCAAAGCGAAGAAG 59.475 50.000 5.75 0.00 0.00 2.85
1550 2077 0.523072 GCCATGCAAAGCGAAGAAGA 59.477 50.000 0.00 0.00 0.00 2.87
1551 2078 1.068333 GCCATGCAAAGCGAAGAAGAA 60.068 47.619 0.00 0.00 0.00 2.52
1552 2079 2.416431 GCCATGCAAAGCGAAGAAGAAT 60.416 45.455 0.00 0.00 0.00 2.40
1553 2080 3.181497 GCCATGCAAAGCGAAGAAGAATA 60.181 43.478 0.00 0.00 0.00 1.75
1558 2085 4.204581 GCAAAGCGAAGAAGAATATACGC 58.795 43.478 0.00 0.00 45.03 4.42
1600 2127 1.000955 CAAAGAGGTGCGTACTGGACT 59.999 52.381 3.01 0.00 39.22 3.85
1601 2128 0.603569 AAGAGGTGCGTACTGGACTG 59.396 55.000 3.01 0.00 39.22 3.51
1607 2134 1.000506 GTGCGTACTGGACTGAAAGGA 59.999 52.381 0.00 0.00 39.30 3.36
1609 2136 2.288825 TGCGTACTGGACTGAAAGGAAG 60.289 50.000 0.00 0.00 39.30 3.46
1622 2149 8.207545 GGACTGAAAGGAAGACATTGAGTATAT 58.792 37.037 0.00 0.00 39.30 0.86
1658 2185 7.094634 GGATTGTATGTTTGTTGATCAGTCTGT 60.095 37.037 0.00 0.00 0.00 3.41
1670 2197 3.876274 TCAGTCTGTTCCATACTCTGC 57.124 47.619 0.00 0.00 0.00 4.26
1678 2205 5.359860 TCTGTTCCATACTCTGCTCGAATTA 59.640 40.000 0.00 0.00 0.00 1.40
1687 2214 2.747446 TCTGCTCGAATTAAAGGGTTGC 59.253 45.455 0.00 0.00 0.00 4.17
1698 2225 3.825908 AAAGGGTTGCCATCTTTCCTA 57.174 42.857 0.00 0.00 0.00 2.94
1736 2263 2.972625 TGCATACAGTAGGTTGCAGAC 58.027 47.619 3.60 0.00 38.05 3.51
1738 2265 2.416836 GCATACAGTAGGTTGCAGACGA 60.417 50.000 0.00 0.00 35.20 4.20
1760 2287 5.123820 CGAGGCTAGGAAAAACATTTGATGA 59.876 40.000 0.00 0.00 0.00 2.92
1764 2291 7.038799 AGGCTAGGAAAAACATTTGATGACATT 60.039 33.333 0.00 0.00 0.00 2.71
1774 2301 7.523293 ACATTTGATGACATTTACACCAGAA 57.477 32.000 0.00 0.00 0.00 3.02
1775 2302 7.950512 ACATTTGATGACATTTACACCAGAAA 58.049 30.769 0.00 0.00 0.00 2.52
1778 2305 7.757941 TTGATGACATTTACACCAGAAATGA 57.242 32.000 13.48 0.00 43.85 2.57
1805 2332 0.478072 TCCACTGGACTTGGCATTGT 59.522 50.000 0.00 0.00 33.71 2.71
1810 2337 1.808945 CTGGACTTGGCATTGTCTCAC 59.191 52.381 16.82 5.49 34.01 3.51
1812 2339 2.079925 GGACTTGGCATTGTCTCACTC 58.920 52.381 16.82 1.64 34.01 3.51
1827 2354 2.618709 CTCACTCCTTTTGCTTCCGTTT 59.381 45.455 0.00 0.00 0.00 3.60
1858 2385 2.476854 GCTTCTATTGTGCTCTTTGCCG 60.477 50.000 0.00 0.00 42.00 5.69
1859 2386 2.472695 TCTATTGTGCTCTTTGCCGT 57.527 45.000 0.00 0.00 42.00 5.68
1882 2409 1.545428 GCCACAAGGATGGTCAGAACA 60.545 52.381 0.00 0.00 42.28 3.18
1884 2411 2.816087 CCACAAGGATGGTCAGAACAAG 59.184 50.000 0.00 0.00 36.89 3.16
1893 2420 4.008074 TGGTCAGAACAAGAAGGACATC 57.992 45.455 0.00 0.00 0.00 3.06
1927 2454 6.569127 ACATCCTATTATGTTGTACCACCA 57.431 37.500 0.00 0.00 36.71 4.17
1938 2465 1.423541 TGTACCACCATGTTGGAGCTT 59.576 47.619 17.31 0.00 40.96 3.74
1942 2469 1.606224 CCACCATGTTGGAGCTTTTGC 60.606 52.381 2.44 0.00 40.96 3.68
1952 2479 4.661461 GCTTTTGCTTCCCTGCAC 57.339 55.556 0.00 0.00 43.20 4.57
1953 2480 1.741525 GCTTTTGCTTCCCTGCACA 59.258 52.632 0.00 0.00 43.20 4.57
1954 2481 0.104671 GCTTTTGCTTCCCTGCACAA 59.895 50.000 0.00 0.00 43.20 3.33
1956 2483 2.807837 GCTTTTGCTTCCCTGCACAATT 60.808 45.455 0.00 0.00 43.20 2.32
1961 2488 2.297033 TGCTTCCCTGCACAATTTTCTC 59.703 45.455 0.00 0.00 38.12 2.87
1962 2489 2.560105 GCTTCCCTGCACAATTTTCTCT 59.440 45.455 0.00 0.00 0.00 3.10
1963 2490 3.613432 GCTTCCCTGCACAATTTTCTCTG 60.613 47.826 0.00 0.00 0.00 3.35
1964 2491 2.517959 TCCCTGCACAATTTTCTCTGG 58.482 47.619 0.00 0.00 0.00 3.86
1965 2492 1.547372 CCCTGCACAATTTTCTCTGGG 59.453 52.381 0.00 0.00 0.00 4.45
2050 2577 1.536940 CCAGCACAACATCATGTCCA 58.463 50.000 0.00 0.00 0.00 4.02
2082 2609 2.206576 AGAACAAGCCCACATTCCTC 57.793 50.000 0.00 0.00 0.00 3.71
2089 2616 0.743097 GCCCACATTCCTCATGAAGC 59.257 55.000 0.00 0.00 36.14 3.86
2093 2620 3.087031 CCACATTCCTCATGAAGCTTGT 58.913 45.455 2.10 0.00 36.14 3.16
2109 2636 4.058817 AGCTTGTTACCTTCGACTTTCTG 58.941 43.478 0.00 0.00 0.00 3.02
2112 2639 5.524971 TTGTTACCTTCGACTTTCTGAGA 57.475 39.130 0.00 0.00 0.00 3.27
2172 2699 0.469331 TAGCCTACCAGATCACGGGG 60.469 60.000 6.19 0.00 35.72 5.73
2174 2701 1.335132 GCCTACCAGATCACGGGGAA 61.335 60.000 6.19 0.00 35.72 3.97
2175 2702 1.200519 CCTACCAGATCACGGGGAAA 58.799 55.000 6.19 0.00 35.72 3.13
2180 2707 1.003118 CCAGATCACGGGGAAAGTTCA 59.997 52.381 0.00 0.00 0.00 3.18
2196 2723 0.321564 TTCACCGGCACATGGAAGAG 60.322 55.000 0.00 0.00 0.00 2.85
2199 2726 2.124570 CGGCACATGGAAGAGGGG 60.125 66.667 0.00 0.00 0.00 4.79
2206 2733 1.289160 CATGGAAGAGGGGTGGAAGA 58.711 55.000 0.00 0.00 0.00 2.87
2221 2748 4.430007 GTGGAAGAAGTACATATGCGACA 58.570 43.478 1.58 0.00 0.00 4.35
2223 2750 4.081917 TGGAAGAAGTACATATGCGACACA 60.082 41.667 1.58 0.00 0.00 3.72
2224 2751 4.868171 GGAAGAAGTACATATGCGACACAA 59.132 41.667 1.58 0.00 0.00 3.33
2244 2771 2.772287 ACAAGTTACAGGAGCTTCAGC 58.228 47.619 0.00 0.00 42.49 4.26
2256 2783 1.587613 CTTCAGCGAGCTACGAGGC 60.588 63.158 9.32 0.00 45.77 4.70
2288 2818 0.763652 AGGATGCACCATCAGCTAGG 59.236 55.000 7.43 0.00 42.13 3.02
2289 2819 0.761187 GGATGCACCATCAGCTAGGA 59.239 55.000 6.08 0.00 42.13 2.94
2305 2835 3.806507 GCTAGGATGGAGCTTGAAGATGG 60.807 52.174 0.00 0.00 36.96 3.51
2310 2840 2.880443 TGGAGCTTGAAGATGGCTTTT 58.120 42.857 0.00 0.00 36.37 2.27
2320 2850 3.361281 AGATGGCTTTTGATGAGAGCA 57.639 42.857 0.00 0.00 38.14 4.26
2334 2864 0.469070 AGAGCATCCTCATCTGGCAC 59.531 55.000 0.00 0.00 40.68 5.01
2337 2867 0.745845 GCATCCTCATCTGGCACGTT 60.746 55.000 0.00 0.00 0.00 3.99
2378 2908 2.272146 CCCCAACACATCCCCTCG 59.728 66.667 0.00 0.00 0.00 4.63
2380 2910 1.078426 CCCAACACATCCCCTCGAC 60.078 63.158 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
381 390 5.669798 AAGGGGGCATCTATGAAACTATT 57.330 39.130 0.00 0.00 0.00 1.73
411 427 4.431471 CGGATAAAAATATTTGCATGCGCG 60.431 41.667 14.09 0.00 42.97 6.86
464 480 8.554528 CACTTGTTCATCCATGTCAGATAATAC 58.445 37.037 0.00 0.00 0.00 1.89
521 1014 4.311816 CAAGAAACATTGCCACTCAACT 57.688 40.909 0.00 0.00 37.53 3.16
544 1037 7.663081 ACACTTGCTTATATATGCATGCTACTT 59.337 33.333 24.63 11.04 39.07 2.24
547 1040 6.372381 CCACACTTGCTTATATATGCATGCTA 59.628 38.462 24.63 9.18 39.07 3.49
551 1044 5.474532 CACCCACACTTGCTTATATATGCAT 59.525 40.000 20.38 3.79 39.07 3.96
552 1045 4.821260 CACCCACACTTGCTTATATATGCA 59.179 41.667 16.95 16.95 37.42 3.96
553 1046 4.821805 ACACCCACACTTGCTTATATATGC 59.178 41.667 12.51 12.51 0.00 3.14
554 1047 6.318648 ACAACACCCACACTTGCTTATATATG 59.681 38.462 0.00 0.00 0.00 1.78
555 1048 6.423182 ACAACACCCACACTTGCTTATATAT 58.577 36.000 0.00 0.00 0.00 0.86
559 1052 2.944129 ACAACACCCACACTTGCTTAT 58.056 42.857 0.00 0.00 0.00 1.73
599 1092 6.551227 AGCCTCAACCTTATCAAACTTCTTTT 59.449 34.615 0.00 0.00 0.00 2.27
608 1101 1.209504 CCGGAGCCTCAACCTTATCAA 59.790 52.381 0.00 0.00 0.00 2.57
614 1116 2.370445 CCATCCGGAGCCTCAACCT 61.370 63.158 11.34 0.00 0.00 3.50
623 1125 1.443407 CAGTACCAGCCATCCGGAG 59.557 63.158 11.34 0.00 0.00 4.63
649 1151 1.226688 CGCATGACACCGATCGACT 60.227 57.895 18.66 0.00 0.00 4.18
651 1153 0.028902 CTACGCATGACACCGATCGA 59.971 55.000 18.66 0.00 0.00 3.59
652 1154 0.028902 TCTACGCATGACACCGATCG 59.971 55.000 8.51 8.51 0.00 3.69
653 1155 1.600663 CCTCTACGCATGACACCGATC 60.601 57.143 0.00 0.00 0.00 3.69
654 1156 0.385751 CCTCTACGCATGACACCGAT 59.614 55.000 0.00 0.00 0.00 4.18
732 1235 2.039405 GCTCTCAAGTGCCAGCCAG 61.039 63.158 0.00 0.00 0.00 4.85
733 1236 2.033141 GCTCTCAAGTGCCAGCCA 59.967 61.111 0.00 0.00 0.00 4.75
768 1271 1.201647 TCGTCTTCCTCATGTTCGTCC 59.798 52.381 0.00 0.00 0.00 4.79
922 1449 2.563179 GGAAGGTGCTCAAGTGAGAGTA 59.437 50.000 12.54 0.00 44.74 2.59
957 1484 3.528597 ACTCAATTTACCGAGGAGAGC 57.471 47.619 0.00 0.00 33.36 4.09
965 1492 2.936498 CTGCCACCTACTCAATTTACCG 59.064 50.000 0.00 0.00 0.00 4.02
1057 1584 2.842496 ACTGGATGAAGAGGCTGATGAA 59.158 45.455 0.00 0.00 0.00 2.57
1088 1615 1.585521 CGAGCGTATTCGGCGAAGT 60.586 57.895 27.35 17.09 36.95 3.01
1092 1619 0.721811 CTCTACGAGCGTATTCGGCG 60.722 60.000 0.00 0.00 44.57 6.46
1093 1620 0.307146 ACTCTACGAGCGTATTCGGC 59.693 55.000 2.97 0.00 44.57 5.54
1098 1625 2.613133 GACAGGAACTCTACGAGCGTAT 59.387 50.000 2.97 0.00 34.60 3.06
1101 1628 0.099082 GGACAGGAACTCTACGAGCG 59.901 60.000 0.00 0.00 34.60 5.03
1110 1637 0.900647 AGCTGCGTAGGACAGGAACT 60.901 55.000 1.76 0.00 43.88 3.01
1128 1655 1.233285 GCCACACCAGCACTCTGAAG 61.233 60.000 0.00 0.00 42.95 3.02
1131 1658 1.670406 GAGCCACACCAGCACTCTG 60.670 63.158 0.00 0.00 40.02 3.35
1147 1674 2.556677 CGCTGCTTACGTACGCGAG 61.557 63.158 15.93 14.27 45.99 5.03
1188 1715 2.742372 CGGTTGAAGAGGGTGGCG 60.742 66.667 0.00 0.00 0.00 5.69
1215 1742 1.077429 GCCCTCCCCATCACAAGTC 60.077 63.158 0.00 0.00 0.00 3.01
1226 1753 4.748144 CCAGGTTGCTGCCCTCCC 62.748 72.222 0.00 0.00 0.00 4.30
1251 1778 0.842030 TGAGAAGGACAGGCACCCAT 60.842 55.000 0.00 0.00 0.00 4.00
1266 1793 1.146930 GCCGCCAAGATGGATGAGA 59.853 57.895 0.00 0.00 40.96 3.27
1269 1796 2.124193 TGGCCGCCAAGATGGATG 60.124 61.111 10.50 0.00 40.96 3.51
1281 1808 1.097547 CACTTATCCTTGGCTGGCCG 61.098 60.000 7.14 0.00 39.42 6.13
1287 1814 2.565841 CTGTAGGCACTTATCCTTGGC 58.434 52.381 0.00 0.00 41.75 4.52
1288 1815 2.565841 GCTGTAGGCACTTATCCTTGG 58.434 52.381 0.00 0.00 41.75 3.61
1292 1819 3.231818 TCTAGGCTGTAGGCACTTATCC 58.768 50.000 8.22 0.00 44.01 2.59
1297 1824 2.104170 GTCTTCTAGGCTGTAGGCACT 58.896 52.381 8.22 0.00 44.01 4.40
1298 1825 1.825474 TGTCTTCTAGGCTGTAGGCAC 59.175 52.381 8.22 0.00 44.01 5.01
1311 1838 4.246458 GTTTCCATAGCTCGTTGTCTTCT 58.754 43.478 0.00 0.00 0.00 2.85
1366 1893 2.093500 TGCAGAAGACATACAAGGCGAT 60.093 45.455 0.00 0.00 0.00 4.58
1371 1898 4.331992 CACCATCTGCAGAAGACATACAAG 59.668 45.833 22.50 3.29 37.88 3.16
1377 1904 2.093288 GGATCACCATCTGCAGAAGACA 60.093 50.000 22.50 4.31 37.88 3.41
1424 1951 4.253685 TCCAAGAATAAAGAGCAAGACCG 58.746 43.478 0.00 0.00 0.00 4.79
1429 1956 8.375506 TCTAAGAACTCCAAGAATAAAGAGCAA 58.624 33.333 0.00 0.00 0.00 3.91
1441 1968 6.169094 TCTGAGCAAATCTAAGAACTCCAAG 58.831 40.000 0.00 0.00 29.04 3.61
1476 2003 3.257375 TGTTAAAGCTAGCGGTCTTGAGA 59.743 43.478 9.55 0.00 0.00 3.27
1479 2006 3.999229 CTGTTAAAGCTAGCGGTCTTG 57.001 47.619 9.55 0.00 0.00 3.02
1494 2021 2.356125 GCTGGAGGATTGGAAGCTGTTA 60.356 50.000 0.00 0.00 0.00 2.41
1501 2028 1.299648 CGGTGCTGGAGGATTGGAA 59.700 57.895 0.00 0.00 0.00 3.53
1506 2033 4.101448 GGCACGGTGCTGGAGGAT 62.101 66.667 29.92 0.00 44.28 3.24
1518 2045 4.415150 ATGGCTGACAGGGGCACG 62.415 66.667 4.26 0.00 41.82 5.34
1528 2055 0.606130 TCTTCGCTTTGCATGGCTGA 60.606 50.000 9.22 6.06 0.00 4.26
1529 2056 0.241749 TTCTTCGCTTTGCATGGCTG 59.758 50.000 9.22 4.21 0.00 4.85
1531 2058 0.523072 TCTTCTTCGCTTTGCATGGC 59.477 50.000 0.00 0.00 0.00 4.40
1532 2059 2.995466 TTCTTCTTCGCTTTGCATGG 57.005 45.000 0.00 0.00 0.00 3.66
1533 2060 5.842843 CGTATATTCTTCTTCGCTTTGCATG 59.157 40.000 0.00 0.00 0.00 4.06
1534 2061 5.559035 GCGTATATTCTTCTTCGCTTTGCAT 60.559 40.000 0.00 0.00 40.39 3.96
1535 2062 4.260212 GCGTATATTCTTCTTCGCTTTGCA 60.260 41.667 0.00 0.00 40.39 4.08
1542 2069 4.968181 TCTTCACGCGTATATTCTTCTTCG 59.032 41.667 13.44 0.00 0.00 3.79
1546 2073 8.228921 ACATATTCTTCACGCGTATATTCTTC 57.771 34.615 13.44 0.00 0.00 2.87
1548 2075 8.294577 TGTACATATTCTTCACGCGTATATTCT 58.705 33.333 13.44 1.70 0.00 2.40
1549 2076 8.443898 TGTACATATTCTTCACGCGTATATTC 57.556 34.615 13.44 5.27 0.00 1.75
1550 2077 8.806177 TTGTACATATTCTTCACGCGTATATT 57.194 30.769 13.44 5.38 0.00 1.28
1551 2078 7.061905 GCTTGTACATATTCTTCACGCGTATAT 59.938 37.037 13.44 8.66 0.00 0.86
1552 2079 6.361481 GCTTGTACATATTCTTCACGCGTATA 59.639 38.462 13.44 6.24 0.00 1.47
1553 2080 5.175126 GCTTGTACATATTCTTCACGCGTAT 59.825 40.000 13.44 3.59 0.00 3.06
1558 2085 4.329801 TGCTGCTTGTACATATTCTTCACG 59.670 41.667 0.00 0.00 0.00 4.35
1600 2127 9.817809 GTACATATACTCAATGTCTTCCTTTCA 57.182 33.333 0.00 0.00 38.49 2.69
1601 2128 8.969267 CGTACATATACTCAATGTCTTCCTTTC 58.031 37.037 0.00 0.00 38.49 2.62
1622 2149 8.608317 CAACAAACATACAATCCATATCGTACA 58.392 33.333 0.00 0.00 0.00 2.90
1658 2185 6.049149 CCTTTAATTCGAGCAGAGTATGGAA 58.951 40.000 0.00 0.00 0.00 3.53
1670 2197 3.947834 AGATGGCAACCCTTTAATTCGAG 59.052 43.478 0.00 0.00 0.00 4.04
1678 2205 2.702270 AGGAAAGATGGCAACCCTTT 57.298 45.000 11.07 11.07 39.95 3.11
1726 2253 1.608717 CCTAGCCTCGTCTGCAACCT 61.609 60.000 0.00 0.00 0.00 3.50
1727 2254 1.153549 CCTAGCCTCGTCTGCAACC 60.154 63.158 0.00 0.00 0.00 3.77
1736 2263 5.123820 TCATCAAATGTTTTTCCTAGCCTCG 59.876 40.000 0.00 0.00 0.00 4.63
1738 2265 5.774690 TGTCATCAAATGTTTTTCCTAGCCT 59.225 36.000 0.00 0.00 0.00 4.58
1764 2291 8.087750 GTGGAAATTGATTCATTTCTGGTGTAA 58.912 33.333 15.12 0.00 39.98 2.41
1774 2301 6.295462 CCAAGTCCAGTGGAAATTGATTCATT 60.295 38.462 28.16 6.37 39.98 2.57
1775 2302 5.186409 CCAAGTCCAGTGGAAATTGATTCAT 59.814 40.000 28.16 2.76 39.98 2.57
1778 2305 3.259123 GCCAAGTCCAGTGGAAATTGATT 59.741 43.478 28.16 10.91 38.54 2.57
1786 2313 0.478072 ACAATGCCAAGTCCAGTGGA 59.522 50.000 8.12 8.12 38.54 4.02
1787 2314 0.883833 GACAATGCCAAGTCCAGTGG 59.116 55.000 1.40 1.40 39.33 4.00
1805 2332 1.416401 ACGGAAGCAAAAGGAGTGAGA 59.584 47.619 0.00 0.00 0.00 3.27
1810 2337 3.120165 GCTAGAAACGGAAGCAAAAGGAG 60.120 47.826 0.00 0.00 36.26 3.69
1812 2339 2.095212 GGCTAGAAACGGAAGCAAAAGG 60.095 50.000 0.00 0.00 38.01 3.11
1858 2385 0.036732 TGACCATCCTTGTGGCTCAC 59.963 55.000 0.00 0.00 43.27 3.51
1859 2386 0.325933 CTGACCATCCTTGTGGCTCA 59.674 55.000 0.00 0.00 43.27 4.26
1882 2409 2.338809 TGTCACCCTGATGTCCTTCTT 58.661 47.619 0.00 0.00 0.00 2.52
1884 2411 3.197766 TGTATGTCACCCTGATGTCCTTC 59.802 47.826 0.00 0.00 0.00 3.46
1893 2420 7.009179 ACATAATAGGATGTATGTCACCCTG 57.991 40.000 0.00 0.00 38.29 4.45
1927 2454 1.620323 GGGAAGCAAAAGCTCCAACAT 59.380 47.619 0.00 0.00 0.00 2.71
1942 2469 3.057033 CCAGAGAAAATTGTGCAGGGAAG 60.057 47.826 0.00 0.00 0.00 3.46
1949 2476 3.084786 AGTAGCCCAGAGAAAATTGTGC 58.915 45.455 0.00 0.00 0.00 4.57
1952 2479 5.586643 GGAACTAGTAGCCCAGAGAAAATTG 59.413 44.000 0.00 0.00 0.00 2.32
1953 2480 5.250774 TGGAACTAGTAGCCCAGAGAAAATT 59.749 40.000 11.11 0.00 0.00 1.82
1954 2481 4.783227 TGGAACTAGTAGCCCAGAGAAAAT 59.217 41.667 11.11 0.00 0.00 1.82
1956 2483 3.786553 TGGAACTAGTAGCCCAGAGAAA 58.213 45.455 11.11 0.00 0.00 2.52
1961 2488 4.835615 AGATACATGGAACTAGTAGCCCAG 59.164 45.833 14.78 10.43 31.48 4.45
1962 2489 4.816126 AGATACATGGAACTAGTAGCCCA 58.184 43.478 12.62 12.62 0.00 5.36
1963 2490 5.810080 AAGATACATGGAACTAGTAGCCC 57.190 43.478 11.11 6.99 0.00 5.19
1964 2491 9.780186 AATTAAAGATACATGGAACTAGTAGCC 57.220 33.333 0.00 1.34 0.00 3.93
2005 2532 0.038166 ATGTCGTGCCACCCTTCAAT 59.962 50.000 0.00 0.00 0.00 2.57
2010 2537 2.351924 AAACCATGTCGTGCCACCCT 62.352 55.000 0.00 0.00 0.00 4.34
2067 2594 2.133281 TCATGAGGAATGTGGGCTTG 57.867 50.000 0.00 0.00 37.56 4.01
2082 2609 3.997021 AGTCGAAGGTAACAAGCTTCATG 59.003 43.478 15.27 0.00 41.41 3.07
2089 2616 5.529791 TCTCAGAAAGTCGAAGGTAACAAG 58.470 41.667 0.00 0.00 41.41 3.16
2093 2620 4.082679 GCTCTCTCAGAAAGTCGAAGGTAA 60.083 45.833 0.00 0.00 0.00 2.85
2109 2636 5.123027 CCAATGTTGGTTAAGAAGCTCTCTC 59.877 44.000 3.58 0.00 43.43 3.20
2142 2669 5.658198 TCTGGTAGGCTATAGGTACTTGA 57.342 43.478 0.00 0.00 41.75 3.02
2172 2699 0.240945 CCATGTGCCGGTGAACTTTC 59.759 55.000 1.90 0.00 0.00 2.62
2174 2701 0.179004 TTCCATGTGCCGGTGAACTT 60.179 50.000 1.90 0.00 0.00 2.66
2175 2702 0.606401 CTTCCATGTGCCGGTGAACT 60.606 55.000 1.90 0.00 0.00 3.01
2180 2707 2.671070 CCTCTTCCATGTGCCGGT 59.329 61.111 1.90 0.00 0.00 5.28
2196 2723 3.477530 GCATATGTACTTCTTCCACCCC 58.522 50.000 4.29 0.00 0.00 4.95
2199 2726 4.267928 GTGTCGCATATGTACTTCTTCCAC 59.732 45.833 4.29 0.00 0.00 4.02
2206 2733 4.994852 ACTTGTTGTGTCGCATATGTACTT 59.005 37.500 4.29 0.00 0.00 2.24
2221 2748 4.130118 CTGAAGCTCCTGTAACTTGTTGT 58.870 43.478 0.00 0.00 0.00 3.32
2223 2750 3.142174 GCTGAAGCTCCTGTAACTTGTT 58.858 45.455 0.00 0.00 38.21 2.83
2224 2751 2.772287 GCTGAAGCTCCTGTAACTTGT 58.228 47.619 0.00 0.00 38.21 3.16
2244 2771 1.517257 CAACTGGCCTCGTAGCTCG 60.517 63.158 3.32 0.00 41.41 5.03
2246 2773 2.982130 CCAACTGGCCTCGTAGCT 59.018 61.111 3.32 0.00 0.00 3.32
2256 2783 1.065199 TGCATCCTTAGAGCCAACTGG 60.065 52.381 0.00 0.00 38.53 4.00
2288 2818 2.345124 AGCCATCTTCAAGCTCCATC 57.655 50.000 0.00 0.00 28.40 3.51
2289 2819 2.822707 AAGCCATCTTCAAGCTCCAT 57.177 45.000 0.00 0.00 35.30 3.41
2320 2850 0.745845 GCAACGTGCCAGATGAGGAT 60.746 55.000 0.00 0.00 37.42 3.24
2334 2864 2.675056 GCAGAGCTCTGTGGCAACG 61.675 63.158 37.25 15.98 45.45 4.10
2337 2867 0.179009 AAAAGCAGAGCTCTGTGGCA 60.179 50.000 37.25 0.00 45.45 4.92
2346 2876 2.128771 TGGGGTGATAAAAGCAGAGC 57.871 50.000 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.