Multiple sequence alignment - TraesCS4A01G460800

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 TraesCS4A01G460800 chr4A 100.000 1859 0 0 748 2606 725859902 725861760 0.000000e+00 3434.0
1 TraesCS4A01G460800 chr4A 100.000 387 0 0 1 387 725859155 725859541 0.000000e+00 715.0
2 TraesCS4A01G460800 chr4A 80.423 378 58 13 1324 1691 725842280 725842651 9.190000e-70 274.0
3 TraesCS4A01G460800 chr4A 100.000 40 0 0 2117 2156 725861229 725861268 1.000000e-09 75.0
4 TraesCS4A01G460800 chr4A 100.000 40 0 0 2075 2114 725861271 725861310 1.000000e-09 75.0
5 TraesCS4A01G460800 chr7A 91.916 1002 80 1 751 1752 11582384 11581384 0.000000e+00 1400.0
6 TraesCS4A01G460800 chr7A 88.265 980 110 5 748 1724 11844484 11845461 0.000000e+00 1168.0
7 TraesCS4A01G460800 chr7A 87.602 984 113 8 748 1724 11944076 11945057 0.000000e+00 1133.0
8 TraesCS4A01G460800 chr7A 95.607 387 17 0 1 387 11582838 11582452 2.850000e-174 621.0
9 TraesCS4A01G460800 chr7A 88.722 399 43 2 1328 1724 11891005 11891403 1.080000e-133 486.0
10 TraesCS4A01G460800 chr7A 89.175 388 41 1 1 387 11843770 11844157 1.400000e-132 483.0
11 TraesCS4A01G460800 chr7A 88.918 388 42 1 1 387 11943621 11944008 6.520000e-131 477.0
12 TraesCS4A01G460800 chr7A 84.375 512 43 15 2117 2606 11577021 11576525 3.930000e-128 468.0
13 TraesCS4A01G460800 chr7A 91.901 284 18 2 1836 2114 11577265 11576982 2.430000e-105 392.0
14 TraesCS4A01G460800 chr7D 92.161 944 69 5 751 1692 12188779 12187839 0.000000e+00 1328.0
15 TraesCS4A01G460800 chr7D 83.122 948 152 7 751 1694 12125888 12126831 0.000000e+00 857.0
16 TraesCS4A01G460800 chr7D 95.866 387 16 0 1 387 12189233 12188847 6.120000e-176 627.0
17 TraesCS4A01G460800 chr7D 83.237 519 44 19 2117 2606 12184747 12184243 1.110000e-118 436.0
18 TraesCS4A01G460800 chr7D 92.254 284 21 1 1831 2114 12184990 12184708 4.040000e-108 401.0
19 TraesCS4A01G460800 chr7D 88.462 52 4 2 1761 1810 585556039 585556090 7.790000e-06 62.1
20 TraesCS4A01G460800 chr7B 88.536 977 107 5 751 1724 717029106 717028132 0.000000e+00 1179.0
21 TraesCS4A01G460800 chr7B 88.624 545 60 1 1182 1724 717052470 717051926 0.000000e+00 662.0
22 TraesCS4A01G460800 chr4D 87.660 235 24 5 2375 2606 428987938 428988170 4.270000e-68 268.0
23 TraesCS4A01G460800 chr4D 84.388 237 27 9 2375 2606 51845538 51845307 9.390000e-55 224.0
24 TraesCS4A01G460800 chr6D 86.818 220 24 4 2375 2591 80150844 80150627 9.320000e-60 241.0
25 TraesCS4A01G460800 chr6D 85.169 236 28 6 2375 2606 428261432 428261200 4.340000e-58 235.0
26 TraesCS4A01G460800 chr6B 85.714 217 25 6 2377 2591 389904355 389904567 9.390000e-55 224.0
27 TraesCS4A01G460800 chr5D 84.120 233 36 1 2375 2606 8630384 8630616 9.390000e-55 224.0
28 TraesCS4A01G460800 chr4B 83.761 234 36 2 2373 2604 183522749 183522982 1.210000e-53 220.0
29 TraesCS4A01G460800 chr4B 96.970 33 1 0 1781 1813 601931888 601931856 3.620000e-04 56.5


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 TraesCS4A01G460800 chr4A 725859155 725861760 2605 False 1074.75 3434 100.0000 1 2606 4 chr4A.!!$F2 2605
1 TraesCS4A01G460800 chr7A 11581384 11582838 1454 True 1010.50 1400 93.7615 1 1752 2 chr7A.!!$R2 1751
2 TraesCS4A01G460800 chr7A 11843770 11845461 1691 False 825.50 1168 88.7200 1 1724 2 chr7A.!!$F2 1723
3 TraesCS4A01G460800 chr7A 11943621 11945057 1436 False 805.00 1133 88.2600 1 1724 2 chr7A.!!$F3 1723
4 TraesCS4A01G460800 chr7A 11576525 11577265 740 True 430.00 468 88.1380 1836 2606 2 chr7A.!!$R1 770
5 TraesCS4A01G460800 chr7D 12125888 12126831 943 False 857.00 857 83.1220 751 1694 1 chr7D.!!$F1 943
6 TraesCS4A01G460800 chr7D 12184243 12189233 4990 True 698.00 1328 90.8795 1 2606 4 chr7D.!!$R1 2605
7 TraesCS4A01G460800 chr7B 717028132 717029106 974 True 1179.00 1179 88.5360 751 1724 1 chr7B.!!$R1 973
8 TraesCS4A01G460800 chr7B 717051926 717052470 544 True 662.00 662 88.6240 1182 1724 1 chr7B.!!$R2 542

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
841 846 0.802494 CCGTGACCAAGTTGCATACC 59.198 55.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 3040 0.033503 CCCTCCGCCCCAAAATAAGT 60.034 55.0 0.0 0.0 0.0 2.24 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
32 33 1.971149 TCATGGACTTGATGAGGGGT 58.029 50.000 0.00 0.00 0.00 4.95
47 48 3.202151 TGAGGGGTAACTTGATCAATCCC 59.798 47.826 20.41 20.41 0.00 3.85
183 184 5.419542 GTGCATTCACTGGACACTAATCTA 58.580 41.667 0.00 0.00 44.95 1.98
240 241 4.391830 TGAAACGATGGAAGTTAGATGTGC 59.608 41.667 0.00 0.00 0.00 4.57
824 829 9.770097 ATTAGACAATAATCATAGGCATATCCG 57.230 33.333 0.00 0.00 40.77 4.18
841 846 0.802494 CCGTGACCAAGTTGCATACC 59.198 55.000 0.00 0.00 0.00 2.73
875 881 7.940137 TGAACCCCACTATACGCATTATAAATT 59.060 33.333 0.00 0.00 0.00 1.82
891 897 8.806146 CATTATAAATTAATCCCAACCTCCCAG 58.194 37.037 0.00 0.00 0.00 4.45
947 953 5.797457 TCCATCTGTATCCATTTATCCCCAT 59.203 40.000 0.00 0.00 0.00 4.00
994 1000 1.001815 GCTTCTAACAAGCCGTGCAAA 60.002 47.619 0.00 0.00 37.30 3.68
1095 1105 3.399181 GCCGGTGGATCTGGTGGA 61.399 66.667 1.90 0.00 44.16 4.02
1138 1148 1.001974 TCATGGTAGAAGCGTGCAAGT 59.998 47.619 0.59 0.00 32.96 3.16
1140 1150 0.679505 TGGTAGAAGCGTGCAAGTCT 59.320 50.000 0.59 0.00 0.00 3.24
1141 1151 1.070134 TGGTAGAAGCGTGCAAGTCTT 59.930 47.619 0.59 5.34 0.00 3.01
1167 1177 4.949856 ACATTCAACAACCCATATGGAGAC 59.050 41.667 24.00 0.00 37.39 3.36
1180 1190 1.781786 TGGAGACCCTGACATAGAGC 58.218 55.000 0.00 0.00 0.00 4.09
1203 1213 3.842007 TTCTGTTTAACGACCCTCCAA 57.158 42.857 0.00 0.00 0.00 3.53
1233 1243 3.031736 TCGAAGCACTAAGGCTAAGGAT 58.968 45.455 0.00 0.00 45.07 3.24
1289 1299 4.446023 CCTTAGGGGTCGAGTCACTACTAT 60.446 50.000 0.00 0.00 35.56 2.12
1292 1302 2.559440 GGGTCGAGTCACTACTATCGT 58.441 52.381 0.00 0.00 35.56 3.73
1295 1305 3.808726 GGTCGAGTCACTACTATCGTCAT 59.191 47.826 0.00 0.00 35.56 3.06
1296 1306 4.272991 GGTCGAGTCACTACTATCGTCATT 59.727 45.833 0.00 0.00 35.56 2.57
1326 1336 8.663911 GTCAAGAAAATGTTGGAAAACATCAAA 58.336 29.630 4.67 0.00 42.13 2.69
1335 1345 3.198635 TGGAAAACATCAAAAAGGGCACA 59.801 39.130 0.00 0.00 0.00 4.57
1431 1441 3.499202 CCATGATCAGGGATTACCAAGGG 60.499 52.174 21.94 0.00 43.89 3.95
1555 1565 2.351738 GGGGCTCTTGTCAATGAAAACG 60.352 50.000 0.00 0.00 0.00 3.60
1582 1592 1.256812 GGGCATGCTGGTTAAACTGT 58.743 50.000 18.92 0.00 0.00 3.55
1623 1639 9.209175 GCACCATAGGTTTCTTGAGTAATATAG 57.791 37.037 0.00 0.00 31.02 1.31
1731 2979 5.181056 TGTGTTGTGGCATCAATTGTACTAG 59.819 40.000 5.13 0.00 0.00 2.57
1742 2990 2.885135 TTGTACTAGTCCCTCCGTCA 57.115 50.000 0.00 0.00 0.00 4.35
1773 3021 7.986085 AAGTATCACTGATTTAGCACAAACT 57.014 32.000 0.00 0.00 0.00 2.66
1775 3023 9.672673 AAGTATCACTGATTTAGCACAAACTAT 57.327 29.630 0.00 0.00 0.00 2.12
1776 3024 9.102757 AGTATCACTGATTTAGCACAAACTATG 57.897 33.333 0.00 0.00 0.00 2.23
1777 3025 7.928307 ATCACTGATTTAGCACAAACTATGT 57.072 32.000 0.00 0.00 45.34 2.29
1791 3039 7.133891 ACAAACTATGTGCTAAATCAGTGAC 57.866 36.000 0.00 0.00 41.93 3.67
1792 3040 6.710295 ACAAACTATGTGCTAAATCAGTGACA 59.290 34.615 0.00 0.00 41.93 3.58
1793 3041 6.727824 AACTATGTGCTAAATCAGTGACAC 57.272 37.500 0.00 0.00 0.00 3.67
1794 3042 6.042638 ACTATGTGCTAAATCAGTGACACT 57.957 37.500 1.07 1.07 0.00 3.55
1795 3043 6.467677 ACTATGTGCTAAATCAGTGACACTT 58.532 36.000 5.04 7.92 0.00 3.16
1796 3044 7.611770 ACTATGTGCTAAATCAGTGACACTTA 58.388 34.615 5.04 0.00 0.00 2.24
1797 3045 8.260818 ACTATGTGCTAAATCAGTGACACTTAT 58.739 33.333 5.04 0.08 0.00 1.73
1798 3046 7.928307 ATGTGCTAAATCAGTGACACTTATT 57.072 32.000 5.04 7.30 0.00 1.40
1799 3047 7.744087 TGTGCTAAATCAGTGACACTTATTT 57.256 32.000 24.06 24.06 36.39 1.40
1800 3048 8.165239 TGTGCTAAATCAGTGACACTTATTTT 57.835 30.769 25.20 17.54 34.78 1.82
1801 3049 8.075574 TGTGCTAAATCAGTGACACTTATTTTG 58.924 33.333 25.20 23.47 34.78 2.44
1802 3050 7.538678 GTGCTAAATCAGTGACACTTATTTTGG 59.461 37.037 25.20 19.85 34.78 3.28
1803 3051 7.029563 GCTAAATCAGTGACACTTATTTTGGG 58.970 38.462 25.20 18.15 34.78 4.12
1804 3052 5.982890 AATCAGTGACACTTATTTTGGGG 57.017 39.130 5.04 0.00 0.00 4.96
1805 3053 3.153919 TCAGTGACACTTATTTTGGGGC 58.846 45.455 5.04 0.00 0.00 5.80
1806 3054 2.095263 CAGTGACACTTATTTTGGGGCG 60.095 50.000 5.04 0.00 0.00 6.13
1807 3055 1.201414 GTGACACTTATTTTGGGGCGG 59.799 52.381 0.00 0.00 0.00 6.13
1808 3056 1.074084 TGACACTTATTTTGGGGCGGA 59.926 47.619 0.00 0.00 0.00 5.54
1809 3057 1.743394 GACACTTATTTTGGGGCGGAG 59.257 52.381 0.00 0.00 0.00 4.63
1810 3058 1.102978 CACTTATTTTGGGGCGGAGG 58.897 55.000 0.00 0.00 0.00 4.30
1818 3066 3.942439 GGGGCGGAGGGACTATGC 61.942 72.222 0.00 0.00 41.55 3.14
1825 3073 2.280628 CGGAGGGACTATGCTTTTGTC 58.719 52.381 0.00 0.00 41.55 3.18
1873 4657 5.921004 TTGCAACAATTCTACATTTTGCC 57.079 34.783 0.00 0.00 38.84 4.52
1908 4692 3.423179 TTTTTGGGCACGTCCGTC 58.577 55.556 0.00 0.00 34.94 4.79
1909 4693 1.153127 TTTTTGGGCACGTCCGTCT 60.153 52.632 0.00 0.00 34.94 4.18
2106 4896 4.415881 AAACAAATTGGTGGGGAGAAAC 57.584 40.909 0.00 0.00 0.00 2.78
2107 4897 3.039252 ACAAATTGGTGGGGAGAAACA 57.961 42.857 0.00 0.00 0.00 2.83
2108 4898 3.379452 ACAAATTGGTGGGGAGAAACAA 58.621 40.909 0.00 0.00 0.00 2.83
2109 4899 3.973305 ACAAATTGGTGGGGAGAAACAAT 59.027 39.130 0.00 0.00 33.55 2.71
2110 4900 4.411869 ACAAATTGGTGGGGAGAAACAATT 59.588 37.500 0.00 0.00 41.84 2.32
2111 4901 5.604650 ACAAATTGGTGGGGAGAAACAATTA 59.395 36.000 0.00 0.00 39.89 1.40
2112 4902 6.100424 ACAAATTGGTGGGGAGAAACAATTAA 59.900 34.615 0.00 0.00 39.89 1.40
2113 4903 6.755542 AATTGGTGGGGAGAAACAATTAAA 57.244 33.333 0.00 0.00 39.26 1.52
2114 4904 5.538849 TTGGTGGGGAGAAACAATTAAAC 57.461 39.130 0.00 0.00 0.00 2.01
2115 4905 4.810345 TGGTGGGGAGAAACAATTAAACT 58.190 39.130 0.00 0.00 0.00 2.66
2116 4906 4.586841 TGGTGGGGAGAAACAATTAAACTG 59.413 41.667 0.00 0.00 0.00 3.16
2117 4907 4.830600 GGTGGGGAGAAACAATTAAACTGA 59.169 41.667 0.00 0.00 0.00 3.41
2118 4908 5.303333 GGTGGGGAGAAACAATTAAACTGAA 59.697 40.000 0.00 0.00 0.00 3.02
2119 4909 6.183360 GGTGGGGAGAAACAATTAAACTGAAA 60.183 38.462 0.00 0.00 0.00 2.69
2120 4910 7.441836 GTGGGGAGAAACAATTAAACTGAAAT 58.558 34.615 0.00 0.00 0.00 2.17
2121 4911 7.598869 GTGGGGAGAAACAATTAAACTGAAATC 59.401 37.037 0.00 0.00 0.00 2.17
2122 4912 7.288852 TGGGGAGAAACAATTAAACTGAAATCA 59.711 33.333 0.00 0.00 0.00 2.57
2123 4913 8.147704 GGGGAGAAACAATTAAACTGAAATCAA 58.852 33.333 0.00 0.00 0.00 2.57
2124 4914 9.710900 GGGAGAAACAATTAAACTGAAATCAAT 57.289 29.630 0.00 0.00 0.00 2.57
2138 4928 9.612066 AACTGAAATCAATGTAAACAAATTGGT 57.388 25.926 0.00 0.00 35.04 3.67
2139 4929 9.044150 ACTGAAATCAATGTAAACAAATTGGTG 57.956 29.630 0.00 0.00 35.04 4.17
2140 4930 8.375608 TGAAATCAATGTAAACAAATTGGTGG 57.624 30.769 0.00 0.00 35.04 4.61
2141 4931 7.443575 TGAAATCAATGTAAACAAATTGGTGGG 59.556 33.333 0.00 0.00 35.04 4.61
2142 4932 5.220710 TCAATGTAAACAAATTGGTGGGG 57.779 39.130 0.00 0.00 35.04 4.96
2143 4933 4.901849 TCAATGTAAACAAATTGGTGGGGA 59.098 37.500 0.00 0.00 35.04 4.81
2144 4934 5.011533 TCAATGTAAACAAATTGGTGGGGAG 59.988 40.000 0.00 0.00 35.04 4.30
2145 4935 4.186077 TGTAAACAAATTGGTGGGGAGA 57.814 40.909 0.00 0.00 0.00 3.71
2146 4936 4.547671 TGTAAACAAATTGGTGGGGAGAA 58.452 39.130 0.00 0.00 0.00 2.87
2147 4937 4.962995 TGTAAACAAATTGGTGGGGAGAAA 59.037 37.500 0.00 0.00 0.00 2.52
2148 4938 4.415881 AAACAAATTGGTGGGGAGAAAC 57.584 40.909 0.00 0.00 0.00 2.78
2197 4993 1.816074 TCACCGGTTTAGCCAACATC 58.184 50.000 2.97 0.00 37.07 3.06
2198 4994 1.349688 TCACCGGTTTAGCCAACATCT 59.650 47.619 2.97 0.00 37.07 2.90
2207 5003 0.615331 AGCCAACATCTCACGACCAT 59.385 50.000 0.00 0.00 0.00 3.55
2208 5004 1.003580 AGCCAACATCTCACGACCATT 59.996 47.619 0.00 0.00 0.00 3.16
2226 5028 3.131933 CCATTTGGGTGTCAAACTGTCAA 59.868 43.478 0.00 0.00 46.72 3.18
2229 5031 5.508200 TTTGGGTGTCAAACTGTCAATAC 57.492 39.130 0.00 0.00 40.14 1.89
2243 5059 7.964604 ACTGTCAATACTACTTGAAACTTCC 57.035 36.000 0.00 0.00 36.92 3.46
2277 5095 1.900486 AGCTCCGTTTGGTAAGCTAGT 59.100 47.619 0.00 0.00 42.12 2.57
2278 5096 3.094572 AGCTCCGTTTGGTAAGCTAGTA 58.905 45.455 0.00 0.00 42.12 1.82
2279 5097 3.130693 AGCTCCGTTTGGTAAGCTAGTAG 59.869 47.826 0.00 0.00 42.12 2.57
2280 5098 3.445857 CTCCGTTTGGTAAGCTAGTAGC 58.554 50.000 14.62 14.62 37.84 3.58
2281 5099 2.827322 TCCGTTTGGTAAGCTAGTAGCA 59.173 45.455 23.77 1.17 39.24 3.49
2282 5100 3.258872 TCCGTTTGGTAAGCTAGTAGCAA 59.741 43.478 23.77 8.91 39.24 3.91
2283 5101 3.998341 CCGTTTGGTAAGCTAGTAGCAAA 59.002 43.478 23.77 15.44 45.56 3.68
2284 5102 4.453136 CCGTTTGGTAAGCTAGTAGCAAAA 59.547 41.667 23.77 12.36 46.99 2.44
2285 5103 5.049267 CCGTTTGGTAAGCTAGTAGCAAAAA 60.049 40.000 23.77 12.66 46.99 1.94
2286 5104 6.349033 CCGTTTGGTAAGCTAGTAGCAAAAAT 60.349 38.462 23.77 7.19 46.99 1.82
2287 5105 7.081976 CGTTTGGTAAGCTAGTAGCAAAAATT 58.918 34.615 23.77 11.28 46.99 1.82
2288 5106 8.231837 CGTTTGGTAAGCTAGTAGCAAAAATTA 58.768 33.333 23.77 10.31 46.99 1.40
2289 5107 9.338291 GTTTGGTAAGCTAGTAGCAAAAATTAC 57.662 33.333 23.77 19.76 46.99 1.89
2290 5108 7.298507 TGGTAAGCTAGTAGCAAAAATTACG 57.701 36.000 23.77 0.00 45.56 3.18
2294 5112 9.983804 GTAAGCTAGTAGCAAAAATTACGAAAT 57.016 29.630 23.77 0.00 45.56 2.17
2332 5150 7.434897 TCGGAACAGTTGATTTGATTTTTCTTG 59.565 33.333 0.00 0.00 0.00 3.02
2380 5198 2.306219 ACCTTAAGAAAGCCACCTCCTC 59.694 50.000 3.36 0.00 0.00 3.71
2384 5202 2.121506 AAAGCCACCTCCTCCCCA 60.122 61.111 0.00 0.00 0.00 4.96
2386 5206 1.793820 AAAGCCACCTCCTCCCCAAG 61.794 60.000 0.00 0.00 0.00 3.61
2401 5221 2.826128 CCCCAAGAAAAGCTTAGGGTTC 59.174 50.000 0.00 0.00 46.80 3.62
2409 5229 0.252927 AGCTTAGGGTTCCTCTGCCT 60.253 55.000 7.24 0.00 34.24 4.75
2410 5230 0.621082 GCTTAGGGTTCCTCTGCCTT 59.379 55.000 0.00 0.00 34.61 4.35
2415 5235 1.761174 GGTTCCTCTGCCTTCACCA 59.239 57.895 0.00 0.00 0.00 4.17
2441 5261 3.745803 GCCCGTCCGTCTCGTCTT 61.746 66.667 0.00 0.00 0.00 3.01
2487 5307 2.609299 TGGATCCCGGTCCTTGCA 60.609 61.111 9.90 0.00 39.12 4.08
2488 5308 2.000701 TGGATCCCGGTCCTTGCAT 61.001 57.895 9.90 0.00 39.12 3.96
2502 5322 0.548031 TTGCATAAGGGAGGGCTCTG 59.452 55.000 0.00 0.00 0.00 3.35
2533 5353 8.519799 AGATGTTTCTTTGAGTTTTGTTAGGA 57.480 30.769 0.00 0.00 0.00 2.94
2562 5382 2.548904 CCTACTCAGGAATACGAGACCG 59.451 54.545 0.00 0.00 45.91 4.79
2566 5386 1.751927 AGGAATACGAGACCGCGGT 60.752 57.895 34.89 34.89 39.95 5.68
2581 5401 1.153289 CGGTGGCTCCCTGAAGATG 60.153 63.158 0.00 0.00 0.00 2.90
2594 5414 5.104360 TCCCTGAAGATGGAATAAGGTTCTG 60.104 44.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.523558 TCATCAAGTCCATGATTGCACAAA 59.476 37.500 0.00 0.00 37.96 2.83
16 17 2.915869 AGTTACCCCTCATCAAGTCCA 58.084 47.619 0.00 0.00 0.00 4.02
32 33 3.945285 GGCTTTCGGGATTGATCAAGTTA 59.055 43.478 14.54 0.00 0.00 2.24
47 48 7.584123 CGATTTTCTATTTCTACATGGCTTTCG 59.416 37.037 0.00 0.00 0.00 3.46
93 94 5.106594 TGTCAAATCTGGATTGATGTGTTCG 60.107 40.000 0.00 0.00 34.26 3.95
312 313 7.447853 TGCAAGTTTGTCATGGATATGCATATA 59.552 33.333 19.12 5.42 36.46 0.86
767 769 7.173047 GCACAAATATTTGAGGGTTCATTTTGT 59.827 33.333 30.18 5.47 40.55 2.83
776 780 4.406456 TCTGTGCACAAATATTTGAGGGT 58.594 39.130 30.18 8.94 40.55 4.34
824 829 0.168128 GCGGTATGCAACTTGGTCAC 59.832 55.000 0.00 0.00 45.45 3.67
841 846 4.151689 CGTATAGTGGGGTTCATAAATGCG 59.848 45.833 0.00 0.00 0.00 4.73
875 881 2.352561 TGTCTGGGAGGTTGGGATTA 57.647 50.000 0.00 0.00 0.00 1.75
880 886 3.244700 GGATATGATGTCTGGGAGGTTGG 60.245 52.174 0.00 0.00 0.00 3.77
891 897 6.462909 GGGGAAAATTGGTTGGATATGATGTC 60.463 42.308 0.00 0.00 0.00 3.06
947 953 9.616156 CTTGAACTATACTACAACCTAGAGAGA 57.384 37.037 0.00 0.00 0.00 3.10
994 1000 3.892284 TCGGTGTTGGTGCCATATATTT 58.108 40.909 0.00 0.00 0.00 1.40
1138 1148 3.304911 TGGGTTGTTGAATGTGGAAGA 57.695 42.857 0.00 0.00 0.00 2.87
1140 1150 4.465660 CCATATGGGTTGTTGAATGTGGAA 59.534 41.667 14.52 0.00 34.26 3.53
1141 1151 4.022603 CCATATGGGTTGTTGAATGTGGA 58.977 43.478 14.52 0.00 34.26 4.02
1167 1177 4.148128 ACAGAATTGCTCTATGTCAGGG 57.852 45.455 0.00 0.00 31.12 4.45
1180 1190 4.069304 TGGAGGGTCGTTAAACAGAATTG 58.931 43.478 0.00 0.00 0.00 2.32
1203 1213 3.448686 CTTAGTGCTTCGATTGTCCGAT 58.551 45.455 0.00 0.00 38.45 4.18
1233 1243 1.304134 TAGCTGCAGGTCACGGAGA 60.304 57.895 23.94 0.00 0.00 3.71
1289 1299 7.359595 CAACATTTTCTTGACCTTAATGACGA 58.640 34.615 0.00 0.00 32.15 4.20
1292 1302 7.831691 TCCAACATTTTCTTGACCTTAATGA 57.168 32.000 0.00 0.00 32.15 2.57
1295 1305 8.314751 TGTTTTCCAACATTTTCTTGACCTTAA 58.685 29.630 0.00 0.00 38.03 1.85
1296 1306 7.841956 TGTTTTCCAACATTTTCTTGACCTTA 58.158 30.769 0.00 0.00 38.03 2.69
1335 1345 3.628646 GAGGACCCGCATTGGCACT 62.629 63.158 0.00 0.00 41.24 4.40
1449 1459 3.132289 TCCAACGGACTAGCTTTATGGAG 59.868 47.826 0.00 0.00 32.29 3.86
1456 1466 1.568504 TCCATCCAACGGACTAGCTT 58.431 50.000 0.00 0.00 32.98 3.74
1555 1565 1.117150 ACCAGCATGCCCAATTCATC 58.883 50.000 15.66 0.00 31.97 2.92
1753 3001 7.928307 ACATAGTTTGTGCTAAATCAGTGAT 57.072 32.000 0.00 0.00 37.11 3.06
1767 3015 6.710295 TGTCACTGATTTAGCACATAGTTTGT 59.290 34.615 0.00 0.00 39.91 2.83
1768 3016 7.017645 GTGTCACTGATTTAGCACATAGTTTG 58.982 38.462 0.00 0.00 0.00 2.93
1769 3017 6.936900 AGTGTCACTGATTTAGCACATAGTTT 59.063 34.615 4.21 0.00 0.00 2.66
1770 3018 6.467677 AGTGTCACTGATTTAGCACATAGTT 58.532 36.000 4.21 0.00 0.00 2.24
1771 3019 6.042638 AGTGTCACTGATTTAGCACATAGT 57.957 37.500 4.21 0.00 0.00 2.12
1772 3020 6.974932 AAGTGTCACTGATTTAGCACATAG 57.025 37.500 6.18 0.00 0.00 2.23
1773 3021 9.448438 AAATAAGTGTCACTGATTTAGCACATA 57.552 29.630 22.17 1.58 37.48 2.29
1774 3022 7.928307 AATAAGTGTCACTGATTTAGCACAT 57.072 32.000 9.52 0.00 24.03 3.21
1775 3023 7.744087 AAATAAGTGTCACTGATTTAGCACA 57.256 32.000 22.17 0.00 37.48 4.57
1776 3024 7.538678 CCAAAATAAGTGTCACTGATTTAGCAC 59.461 37.037 23.29 0.00 38.11 4.40
1777 3025 7.309133 CCCAAAATAAGTGTCACTGATTTAGCA 60.309 37.037 23.29 0.00 38.11 3.49
1778 3026 7.029563 CCCAAAATAAGTGTCACTGATTTAGC 58.970 38.462 23.29 0.00 38.11 3.09
1779 3027 7.538575 CCCCAAAATAAGTGTCACTGATTTAG 58.461 38.462 23.29 18.16 38.11 1.85
1780 3028 6.071616 GCCCCAAAATAAGTGTCACTGATTTA 60.072 38.462 23.29 6.65 38.11 1.40
1781 3029 5.279456 GCCCCAAAATAAGTGTCACTGATTT 60.279 40.000 19.08 19.08 40.21 2.17
1782 3030 4.220602 GCCCCAAAATAAGTGTCACTGATT 59.779 41.667 9.52 9.52 30.51 2.57
1783 3031 3.763897 GCCCCAAAATAAGTGTCACTGAT 59.236 43.478 6.18 0.77 0.00 2.90
1784 3032 3.153919 GCCCCAAAATAAGTGTCACTGA 58.846 45.455 6.18 0.00 0.00 3.41
1785 3033 2.095263 CGCCCCAAAATAAGTGTCACTG 60.095 50.000 6.18 0.00 0.00 3.66
1786 3034 2.159382 CGCCCCAAAATAAGTGTCACT 58.841 47.619 0.00 0.00 0.00 3.41
1787 3035 1.201414 CCGCCCCAAAATAAGTGTCAC 59.799 52.381 0.00 0.00 0.00 3.67
1788 3036 1.074084 TCCGCCCCAAAATAAGTGTCA 59.926 47.619 0.00 0.00 0.00 3.58
1789 3037 1.743394 CTCCGCCCCAAAATAAGTGTC 59.257 52.381 0.00 0.00 0.00 3.67
1790 3038 1.615919 CCTCCGCCCCAAAATAAGTGT 60.616 52.381 0.00 0.00 0.00 3.55
1791 3039 1.102978 CCTCCGCCCCAAAATAAGTG 58.897 55.000 0.00 0.00 0.00 3.16
1792 3040 0.033503 CCCTCCGCCCCAAAATAAGT 60.034 55.000 0.00 0.00 0.00 2.24
1793 3041 0.257616 TCCCTCCGCCCCAAAATAAG 59.742 55.000 0.00 0.00 0.00 1.73
1794 3042 0.033894 GTCCCTCCGCCCCAAAATAA 60.034 55.000 0.00 0.00 0.00 1.40
1795 3043 0.917333 AGTCCCTCCGCCCCAAAATA 60.917 55.000 0.00 0.00 0.00 1.40
1796 3044 0.917333 TAGTCCCTCCGCCCCAAAAT 60.917 55.000 0.00 0.00 0.00 1.82
1797 3045 0.917333 ATAGTCCCTCCGCCCCAAAA 60.917 55.000 0.00 0.00 0.00 2.44
1798 3046 1.307517 ATAGTCCCTCCGCCCCAAA 60.308 57.895 0.00 0.00 0.00 3.28
1799 3047 2.070039 CATAGTCCCTCCGCCCCAA 61.070 63.158 0.00 0.00 0.00 4.12
1800 3048 2.445845 CATAGTCCCTCCGCCCCA 60.446 66.667 0.00 0.00 0.00 4.96
1801 3049 3.942439 GCATAGTCCCTCCGCCCC 61.942 72.222 0.00 0.00 0.00 5.80
1802 3050 1.984288 AAAGCATAGTCCCTCCGCCC 61.984 60.000 0.00 0.00 0.00 6.13
1803 3051 0.107165 AAAAGCATAGTCCCTCCGCC 60.107 55.000 0.00 0.00 0.00 6.13
1804 3052 1.017387 CAAAAGCATAGTCCCTCCGC 58.983 55.000 0.00 0.00 0.00 5.54
1805 3053 2.093447 AGACAAAAGCATAGTCCCTCCG 60.093 50.000 0.00 0.00 32.82 4.63
1806 3054 3.636153 AGACAAAAGCATAGTCCCTCC 57.364 47.619 0.00 0.00 32.82 4.30
1807 3055 5.473504 TCAAAAGACAAAAGCATAGTCCCTC 59.526 40.000 0.00 0.00 32.82 4.30
1808 3056 5.385198 TCAAAAGACAAAAGCATAGTCCCT 58.615 37.500 0.00 0.00 32.82 4.20
1809 3057 5.705609 TCAAAAGACAAAAGCATAGTCCC 57.294 39.130 0.00 0.00 32.82 4.46
1825 3073 9.701098 AAACCATGCATGCTAATATATCAAAAG 57.299 29.630 21.69 4.16 0.00 2.27
1864 4648 5.979993 TCTGCAATTATCATGGCAAAATGT 58.020 33.333 0.00 0.00 35.59 2.71
1895 4679 1.153127 AAAAAGACGGACGTGCCCA 60.153 52.632 0.53 0.00 0.00 5.36
1929 4715 5.784750 ACGAGTGACACATGACATTATTG 57.215 39.130 8.59 0.00 0.00 1.90
1978 4764 4.648762 ACACACTGACAATGGGATTTCAAA 59.351 37.500 0.00 0.00 0.00 2.69
2024 4814 5.065346 CGCATAGACGTCACTGGAGATATAT 59.935 44.000 19.50 0.00 0.00 0.86
2028 4818 1.335182 CGCATAGACGTCACTGGAGAT 59.665 52.381 19.50 0.00 0.00 2.75
2037 4827 2.546195 AAGACTCACGCATAGACGTC 57.454 50.000 7.70 7.70 46.34 4.34
2112 4902 9.612066 ACCAATTTGTTTACATTGATTTCAGTT 57.388 25.926 0.00 0.00 32.91 3.16
2113 4903 9.044150 CACCAATTTGTTTACATTGATTTCAGT 57.956 29.630 0.00 0.00 32.91 3.41
2114 4904 8.497554 CCACCAATTTGTTTACATTGATTTCAG 58.502 33.333 0.00 0.00 32.91 3.02
2115 4905 7.443575 CCCACCAATTTGTTTACATTGATTTCA 59.556 33.333 0.00 0.00 32.91 2.69
2116 4906 7.094848 CCCCACCAATTTGTTTACATTGATTTC 60.095 37.037 0.00 0.00 32.91 2.17
2117 4907 6.714356 CCCCACCAATTTGTTTACATTGATTT 59.286 34.615 0.00 0.00 32.91 2.17
2118 4908 6.043706 TCCCCACCAATTTGTTTACATTGATT 59.956 34.615 0.00 0.00 32.91 2.57
2119 4909 5.545723 TCCCCACCAATTTGTTTACATTGAT 59.454 36.000 0.00 0.00 32.91 2.57
2120 4910 4.901849 TCCCCACCAATTTGTTTACATTGA 59.098 37.500 0.00 0.00 32.91 2.57
2121 4911 5.011533 TCTCCCCACCAATTTGTTTACATTG 59.988 40.000 0.00 0.00 0.00 2.82
2122 4912 5.151454 TCTCCCCACCAATTTGTTTACATT 58.849 37.500 0.00 0.00 0.00 2.71
2123 4913 4.746466 TCTCCCCACCAATTTGTTTACAT 58.254 39.130 0.00 0.00 0.00 2.29
2124 4914 4.186077 TCTCCCCACCAATTTGTTTACA 57.814 40.909 0.00 0.00 0.00 2.41
2125 4915 5.163395 TGTTTCTCCCCACCAATTTGTTTAC 60.163 40.000 0.00 0.00 0.00 2.01
2126 4916 4.962995 TGTTTCTCCCCACCAATTTGTTTA 59.037 37.500 0.00 0.00 0.00 2.01
2127 4917 3.777522 TGTTTCTCCCCACCAATTTGTTT 59.222 39.130 0.00 0.00 0.00 2.83
2128 4918 3.379452 TGTTTCTCCCCACCAATTTGTT 58.621 40.909 0.00 0.00 0.00 2.83
2129 4919 3.039252 TGTTTCTCCCCACCAATTTGT 57.961 42.857 0.00 0.00 0.00 2.83
2130 4920 4.622260 ATTGTTTCTCCCCACCAATTTG 57.378 40.909 0.00 0.00 0.00 2.32
2131 4921 6.755542 TTAATTGTTTCTCCCCACCAATTT 57.244 33.333 0.00 0.00 37.09 1.82
2132 4922 6.755542 TTTAATTGTTTCTCCCCACCAATT 57.244 33.333 0.00 0.00 38.74 2.32
2133 4923 6.350949 CGATTTAATTGTTTCTCCCCACCAAT 60.351 38.462 0.00 0.00 0.00 3.16
2134 4924 5.047660 CGATTTAATTGTTTCTCCCCACCAA 60.048 40.000 0.00 0.00 0.00 3.67
2135 4925 4.461081 CGATTTAATTGTTTCTCCCCACCA 59.539 41.667 0.00 0.00 0.00 4.17
2136 4926 4.676986 GCGATTTAATTGTTTCTCCCCACC 60.677 45.833 0.00 0.00 0.00 4.61
2137 4927 4.157840 AGCGATTTAATTGTTTCTCCCCAC 59.842 41.667 0.00 0.00 0.00 4.61
2138 4928 4.340617 AGCGATTTAATTGTTTCTCCCCA 58.659 39.130 0.00 0.00 0.00 4.96
2139 4929 4.495844 CGAGCGATTTAATTGTTTCTCCCC 60.496 45.833 0.00 0.00 0.00 4.81
2140 4930 4.331717 TCGAGCGATTTAATTGTTTCTCCC 59.668 41.667 0.00 0.00 0.00 4.30
2141 4931 5.464965 TCGAGCGATTTAATTGTTTCTCC 57.535 39.130 0.00 0.00 0.00 3.71
2142 4932 6.938542 AGATCGAGCGATTTAATTGTTTCTC 58.061 36.000 6.84 0.00 34.60 2.87
2143 4933 6.291849 CGAGATCGAGCGATTTAATTGTTTCT 60.292 38.462 6.84 0.00 43.02 2.52
2144 4934 5.836170 CGAGATCGAGCGATTTAATTGTTTC 59.164 40.000 6.84 0.00 43.02 2.78
2145 4935 5.518847 TCGAGATCGAGCGATTTAATTGTTT 59.481 36.000 6.84 0.00 44.22 2.83
2146 4936 5.041287 TCGAGATCGAGCGATTTAATTGTT 58.959 37.500 6.84 0.00 44.22 2.83
2147 4937 4.607955 TCGAGATCGAGCGATTTAATTGT 58.392 39.130 6.84 0.00 44.22 2.71
2175 4965 3.420300 TGTTGGCTAAACCGGTGATTA 57.580 42.857 8.52 2.66 43.94 1.75
2207 5003 5.197451 AGTATTGACAGTTTGACACCCAAA 58.803 37.500 0.00 0.00 42.07 3.28
2208 5004 4.787551 AGTATTGACAGTTTGACACCCAA 58.212 39.130 0.00 0.00 0.00 4.12
2226 5028 6.756221 ACTGTTCGGAAGTTTCAAGTAGTAT 58.244 36.000 0.00 0.00 0.00 2.12
2229 5031 5.522460 TCAACTGTTCGGAAGTTTCAAGTAG 59.478 40.000 0.00 0.00 35.70 2.57
2243 5059 0.868406 GGAGCTTGGTCAACTGTTCG 59.132 55.000 2.24 0.00 0.00 3.95
2283 5101 9.337091 CCGAAGTTGATTGTAATTTCGTAATTT 57.663 29.630 5.29 0.00 43.68 1.82
2284 5102 8.723311 TCCGAAGTTGATTGTAATTTCGTAATT 58.277 29.630 12.69 5.32 43.68 1.40
2285 5103 8.259049 TCCGAAGTTGATTGTAATTTCGTAAT 57.741 30.769 12.69 0.00 43.68 1.89
2286 5104 7.655236 TCCGAAGTTGATTGTAATTTCGTAA 57.345 32.000 12.69 1.87 43.68 3.18
2287 5105 7.171167 TGTTCCGAAGTTGATTGTAATTTCGTA 59.829 33.333 12.69 0.00 43.68 3.43
2288 5106 6.017770 TGTTCCGAAGTTGATTGTAATTTCGT 60.018 34.615 12.69 0.00 43.68 3.85
2289 5107 6.367421 TGTTCCGAAGTTGATTGTAATTTCG 58.633 36.000 8.53 8.53 44.33 3.46
2290 5108 7.360361 ACTGTTCCGAAGTTGATTGTAATTTC 58.640 34.615 0.00 0.00 0.00 2.17
2332 5150 5.628134 CCTAGAAAATTGTTGCTACGGTTC 58.372 41.667 0.00 0.00 0.00 3.62
2373 5191 0.405973 GCTTTTCTTGGGGAGGAGGT 59.594 55.000 0.00 0.00 0.00 3.85
2384 5202 4.657013 CAGAGGAACCCTAAGCTTTTCTT 58.343 43.478 3.20 0.00 38.79 2.52
2386 5206 2.750166 GCAGAGGAACCCTAAGCTTTTC 59.250 50.000 3.20 1.68 31.76 2.29
2401 5221 2.435586 CGCTGGTGAAGGCAGAGG 60.436 66.667 0.00 0.00 0.00 3.69
2432 5252 2.126031 GGCCACCGAAGACGAGAC 60.126 66.667 0.00 0.00 42.66 3.36
2433 5253 0.609957 TAAGGCCACCGAAGACGAGA 60.610 55.000 5.01 0.00 42.66 4.04
2437 5257 1.221021 CCCTAAGGCCACCGAAGAC 59.779 63.158 5.01 0.00 0.00 3.01
2463 5283 1.146263 GACCGGGATCCACCATGTC 59.854 63.158 15.23 8.19 41.20 3.06
2467 5287 2.124085 AAGGACCGGGATCCACCA 59.876 61.111 15.23 0.00 41.73 4.17
2487 5307 4.788617 TCTAAAAACAGAGCCCTCCCTTAT 59.211 41.667 0.00 0.00 0.00 1.73
2488 5308 4.172807 TCTAAAAACAGAGCCCTCCCTTA 58.827 43.478 0.00 0.00 0.00 2.69
2562 5382 3.036429 ATCTTCAGGGAGCCACCGC 62.036 63.158 0.00 0.00 40.11 5.68
2566 5386 1.600058 ATTCCATCTTCAGGGAGCCA 58.400 50.000 0.00 0.00 34.02 4.75
2581 5401 3.636153 AGGCAGACAGAACCTTATTCC 57.364 47.619 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.