Multiple sequence alignment - TraesCS4A01G327600

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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 TraesCS4A01G327600 chr4A 100.000 8386 0 0 1 8386 613854345 613862730 0.000000e+00 15487.0
1 TraesCS4A01G327600 chr4A 78.726 1523 243 54 5133 6615 613810571 613812052 0.000000e+00 942.0
2 TraesCS4A01G327600 chr4A 85.338 607 86 3 6784 7388 613812162 613812767 7.150000e-175 625.0
3 TraesCS4A01G327600 chr4A 76.568 1148 224 35 3066 4188 613700192 613701319 9.380000e-164 588.0
4 TraesCS4A01G327600 chr4A 81.883 563 54 14 799 1336 613803989 613804528 1.670000e-116 431.0
5 TraesCS4A01G327600 chr4A 83.815 173 23 3 953 1124 613697294 613697462 8.710000e-35 159.0
6 TraesCS4A01G327600 chr4A 88.636 44 5 0 30 73 189611939 189611982 4.000000e-03 54.7
7 TraesCS4A01G327600 chr5D 93.895 3833 135 36 4613 8386 554927632 554923840 0.000000e+00 5690.0
8 TraesCS4A01G327600 chr5D 94.848 1650 63 8 2958 4590 554929396 554927752 0.000000e+00 2556.0
9 TraesCS4A01G327600 chr5D 94.982 1136 37 9 1 1120 554930584 554929453 0.000000e+00 1764.0
10 TraesCS4A01G327600 chr5D 81.321 1317 202 30 2958 4252 555024160 555022866 0.000000e+00 1029.0
11 TraesCS4A01G327600 chr5D 82.079 1222 158 39 5429 6622 555020063 555018875 0.000000e+00 987.0
12 TraesCS4A01G327600 chr5D 85.585 881 110 15 5417 6291 554774161 554775030 0.000000e+00 907.0
13 TraesCS4A01G327600 chr5D 85.597 611 84 4 6784 7391 555018772 555018163 9.180000e-179 638.0
14 TraesCS4A01G327600 chr5D 76.592 1021 198 29 3188 4180 560036543 560037550 2.680000e-144 523.0
15 TraesCS4A01G327600 chr5D 84.483 522 79 2 6869 7388 554816783 554817304 1.610000e-141 514.0
16 TraesCS4A01G327600 chr5D 77.115 922 170 31 3076 3969 554604921 554604013 5.850000e-136 496.0
17 TraesCS4A01G327600 chr5D 86.553 409 53 2 125 532 370385960 370386367 4.620000e-122 449.0
18 TraesCS4A01G327600 chr5D 83.610 482 67 10 1341 1814 486817674 486817197 7.730000e-120 442.0
19 TraesCS4A01G327600 chr5D 86.072 359 36 3 799 1157 555027830 555027486 2.860000e-99 374.0
20 TraesCS4A01G327600 chr5D 76.451 603 114 20 5596 6187 554601877 554601292 1.370000e-77 302.0
21 TraesCS4A01G327600 chr5D 73.673 923 180 36 1629 2501 520749311 520750220 4.920000e-77 300.0
22 TraesCS4A01G327600 chr5D 82.993 294 36 4 8095 8386 205576772 205577053 3.890000e-63 254.0
23 TraesCS4A01G327600 chr5D 77.465 284 46 10 7631 7899 95881982 95881702 4.050000e-33 154.0
24 TraesCS4A01G327600 chr5D 80.311 193 30 4 939 1124 560035615 560035806 1.140000e-28 139.0
25 TraesCS4A01G327600 chr5D 89.474 76 8 0 4 79 345668117 345668192 6.930000e-16 97.1
26 TraesCS4A01G327600 chr5D 100.000 30 0 0 4595 4624 554927664 554927635 1.000000e-03 56.5
27 TraesCS4A01G327600 chr5B 94.418 2902 111 12 5485 8359 696091439 696094316 0.000000e+00 4414.0
28 TraesCS4A01G327600 chr5B 95.413 2725 84 13 2707 5398 696088305 696091021 0.000000e+00 4301.0
29 TraesCS4A01G327600 chr5B 95.274 2687 97 17 1 2678 696085648 696088313 0.000000e+00 4231.0
30 TraesCS4A01G327600 chr5B 81.454 1224 168 39 5427 6615 696021175 696022374 0.000000e+00 948.0
31 TraesCS4A01G327600 chr5B 84.628 605 90 3 6784 7386 696022484 696023087 4.330000e-167 599.0
32 TraesCS4A01G327600 chr5B 76.891 952 172 28 3163 4084 710478105 710479038 5.850000e-136 496.0
33 TraesCS4A01G327600 chr5B 76.400 911 158 35 3084 3969 696127665 696128543 9.990000e-119 438.0
34 TraesCS4A01G327600 chr5B 83.156 469 49 14 799 1256 696015364 696015813 1.310000e-107 401.0
35 TraesCS4A01G327600 chr5B 76.378 635 115 28 5569 6187 696129745 696130360 8.180000e-80 309.0
36 TraesCS4A01G327600 chr5B 83.333 276 34 3 8111 8386 206790244 206789981 2.340000e-60 244.0
37 TraesCS4A01G327600 chr5B 83.152 184 24 5 939 1120 696120213 696120391 2.420000e-35 161.0
38 TraesCS4A01G327600 chr5B 76.677 313 52 15 7597 7889 102607167 102606856 4.050000e-33 154.0
39 TraesCS4A01G327600 chr7B 79.226 982 169 28 1377 2342 364212537 364213499 0.000000e+00 651.0
40 TraesCS4A01G327600 chr7B 88.276 290 32 2 8098 8386 15336614 15336902 6.230000e-91 346.0
41 TraesCS4A01G327600 chr7B 72.904 513 109 22 1655 2152 562223031 562222534 5.240000e-32 150.0
42 TraesCS4A01G327600 chr7D 81.000 800 126 21 1377 2159 327401926 327402716 5.560000e-171 612.0
43 TraesCS4A01G327600 chr7D 78.922 835 151 23 1337 2155 37551734 37552559 2.060000e-150 544.0
44 TraesCS4A01G327600 chr7D 72.914 875 167 45 1657 2506 403762065 403761236 1.090000e-58 239.0
45 TraesCS4A01G327600 chr7D 75.793 347 73 11 2165 2505 8903793 8904134 1.870000e-36 165.0
46 TraesCS4A01G327600 chr2D 77.551 882 160 25 1658 2508 543833026 543832152 1.630000e-136 497.0
47 TraesCS4A01G327600 chr2D 83.231 489 68 13 1335 1814 189373986 189373503 3.590000e-118 436.0
48 TraesCS4A01G327600 chr2D 83.128 486 69 11 1337 1814 347796683 347796203 1.670000e-116 431.0
49 TraesCS4A01G327600 chr2D 91.200 125 10 1 8145 8269 555568551 555568428 1.450000e-37 169.0
50 TraesCS4A01G327600 chr2D 88.636 44 5 0 33 76 77550326 77550283 4.000000e-03 54.7
51 TraesCS4A01G327600 chr4B 86.553 409 53 2 125 532 626467491 626467084 4.620000e-122 449.0
52 TraesCS4A01G327600 chr4B 87.234 47 6 0 33 79 190192773 190192727 4.000000e-03 54.7
53 TraesCS4A01G327600 chr1B 86.553 409 53 2 125 532 288040779 288040372 4.620000e-122 449.0
54 TraesCS4A01G327600 chr7A 82.123 537 82 11 1377 1902 327915790 327915257 1.660000e-121 448.0
55 TraesCS4A01G327600 chr7A 83.102 432 63 9 1371 1796 566986345 566985918 1.320000e-102 385.0
56 TraesCS4A01G327600 chr3A 76.403 873 156 37 1645 2481 251370266 251371124 7.780000e-115 425.0
57 TraesCS4A01G327600 chr5A 75.113 884 179 30 1656 2508 568707821 568706948 7.950000e-100 375.0
58 TraesCS4A01G327600 chr5A 90.698 86 5 3 607 691 11113317 11113234 2.470000e-20 111.0
59 TraesCS4A01G327600 chr5A 85.859 99 4 6 615 712 564544811 564544900 6.930000e-16 97.1
60 TraesCS4A01G327600 chr5A 87.059 85 8 3 608 691 564540035 564540117 8.960000e-15 93.5
61 TraesCS4A01G327600 chr3D 75.214 819 144 32 1657 2425 41726166 41726975 4.850000e-87 333.0
62 TraesCS4A01G327600 chr2B 80.583 412 70 5 1655 2058 249523788 249523379 8.180000e-80 309.0
63 TraesCS4A01G327600 chr2B 87.195 164 21 0 8106 8269 662348829 662348666 4.000000e-43 187.0
64 TraesCS4A01G327600 chr2B 76.190 189 43 2 270 457 512584580 512584767 1.930000e-16 99.0
65 TraesCS4A01G327600 chr2B 84.286 70 11 0 10 79 36424798 36424729 1.510000e-07 69.4
66 TraesCS4A01G327600 chr4D 74.359 507 109 18 1834 2329 8004356 8004852 6.640000e-46 196.0
67 TraesCS4A01G327600 chr6A 90.816 98 9 0 3 100 114476722 114476625 1.900000e-26 132.0
68 TraesCS4A01G327600 chr6A 87.234 47 6 0 33 79 168092831 168092785 4.000000e-03 54.7
69 TraesCS4A01G327600 chr3B 81.690 71 11 1 2176 2246 754024745 754024813 3.270000e-04 58.4


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 TraesCS4A01G327600 chr4A 613854345 613862730 8385 False 15487.000000 15487 100.00000 1 8386 1 chr4A.!!$F3 8385
1 TraesCS4A01G327600 chr4A 613810571 613812767 2196 False 783.500000 942 82.03200 5133 7388 2 chr4A.!!$F5 2255
2 TraesCS4A01G327600 chr4A 613803989 613804528 539 False 431.000000 431 81.88300 799 1336 1 chr4A.!!$F2 537
3 TraesCS4A01G327600 chr4A 613697294 613701319 4025 False 373.500000 588 80.19150 953 4188 2 chr4A.!!$F4 3235
4 TraesCS4A01G327600 chr5D 554923840 554930584 6744 True 2516.625000 5690 95.93125 1 8386 4 chr5D.!!$R4 8385
5 TraesCS4A01G327600 chr5D 554774161 554775030 869 False 907.000000 907 85.58500 5417 6291 1 chr5D.!!$F5 874
6 TraesCS4A01G327600 chr5D 555018163 555027830 9667 True 757.000000 1029 83.76725 799 7391 4 chr5D.!!$R5 6592
7 TraesCS4A01G327600 chr5D 554816783 554817304 521 False 514.000000 514 84.48300 6869 7388 1 chr5D.!!$F6 519
8 TraesCS4A01G327600 chr5D 554601292 554604921 3629 True 399.000000 496 76.78300 3076 6187 2 chr5D.!!$R3 3111
9 TraesCS4A01G327600 chr5D 560035615 560037550 1935 False 331.000000 523 78.45150 939 4180 2 chr5D.!!$F7 3241
10 TraesCS4A01G327600 chr5D 520749311 520750220 909 False 300.000000 300 73.67300 1629 2501 1 chr5D.!!$F4 872
11 TraesCS4A01G327600 chr5B 696085648 696094316 8668 False 4315.333333 4414 95.03500 1 8359 3 chr5B.!!$F5 8358
12 TraesCS4A01G327600 chr5B 696021175 696023087 1912 False 773.500000 948 83.04100 5427 7386 2 chr5B.!!$F4 1959
13 TraesCS4A01G327600 chr5B 710478105 710479038 933 False 496.000000 496 76.89100 3163 4084 1 chr5B.!!$F3 921
14 TraesCS4A01G327600 chr5B 696127665 696130360 2695 False 373.500000 438 76.38900 3084 6187 2 chr5B.!!$F6 3103
15 TraesCS4A01G327600 chr7B 364212537 364213499 962 False 651.000000 651 79.22600 1377 2342 1 chr7B.!!$F2 965
16 TraesCS4A01G327600 chr7D 327401926 327402716 790 False 612.000000 612 81.00000 1377 2159 1 chr7D.!!$F3 782
17 TraesCS4A01G327600 chr7D 37551734 37552559 825 False 544.000000 544 78.92200 1337 2155 1 chr7D.!!$F2 818
18 TraesCS4A01G327600 chr7D 403761236 403762065 829 True 239.000000 239 72.91400 1657 2506 1 chr7D.!!$R1 849
19 TraesCS4A01G327600 chr2D 543832152 543833026 874 True 497.000000 497 77.55100 1658 2508 1 chr2D.!!$R4 850
20 TraesCS4A01G327600 chr7A 327915257 327915790 533 True 448.000000 448 82.12300 1377 1902 1 chr7A.!!$R1 525
21 TraesCS4A01G327600 chr3A 251370266 251371124 858 False 425.000000 425 76.40300 1645 2481 1 chr3A.!!$F1 836
22 TraesCS4A01G327600 chr5A 568706948 568707821 873 True 375.000000 375 75.11300 1656 2508 1 chr5A.!!$R2 852
23 TraesCS4A01G327600 chr3D 41726166 41726975 809 False 333.000000 333 75.21400 1657 2425 1 chr3D.!!$F1 768

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
121 138 0.385751 CGATCCCACACACTATCGCT 59.614 55.000 0.00 0.00 35.36 4.93 F
1523 2747 0.180171 CATCCCCGCAACCATAGTGA 59.820 55.000 0.00 0.00 0.00 3.41 F
2355 6653 1.282930 GACCTGAAGCGAACGACCAC 61.283 60.000 0.00 0.00 0.00 4.16 F
2698 6997 0.167470 CAACGCTCAACATGCAGGAG 59.833 55.000 4.84 4.18 0.00 3.69 F
2951 7250 0.179081 GGGTAGAGGCGTGTCCAATC 60.179 60.000 0.00 0.00 37.29 2.67 F
3845 8220 0.038744 CCAGGGCCAATGACTTCAGT 59.961 55.000 6.18 0.00 0.00 3.41 F
4787 12084 1.067516 CATAAAGGGCCGGAATGCAAG 59.932 52.381 5.05 0.00 0.00 4.01 F
5469 13159 0.937304 CTCCGTCTTTGTGTGTGTGG 59.063 55.000 0.00 0.00 0.00 4.17 F
6089 13789 1.003355 CCCGTGATGTGCAGGTTCT 60.003 57.895 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 5837 1.606668 CTTTTGTGTGGTATGTGCCGT 59.393 47.619 0.00 0.0 0.00 5.68 R
2679 6978 0.167470 CTCCTGCATGTTGAGCGTTG 59.833 55.000 0.00 0.0 33.85 4.10 R
3554 7913 0.400213 ATCTTCGTGCCAAACCTCCA 59.600 50.000 0.00 0.0 0.00 3.86 R
3845 8220 4.261572 GCAGTGATCCAAAGCTGTGTTAAA 60.262 41.667 2.51 0.0 0.00 1.52 R
4765 12062 1.111277 GCATTCCGGCCCTTTATGTT 58.889 50.000 0.00 0.0 0.00 2.71 R
5404 12713 0.478507 GAGAGAGAGAGAGGGAGGGG 59.521 65.000 0.00 0.0 0.00 4.79 R
6550 14278 1.078214 AGGATCATGTGGTGGTGCG 60.078 57.895 0.00 0.0 33.94 5.34 R
6875 14606 0.461693 GAGCTGACAGGGATGAGTGC 60.462 60.000 4.26 0.0 0.00 4.40 R
7985 15729 0.819259 GTGCCCAGACACACACACAT 60.819 55.000 0.00 0.0 40.40 3.21 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
101 102 6.877855 CACTAGTAGTAAGATATCCGCCACTA 59.122 42.308 1.57 0.00 0.00 2.74
121 138 0.385751 CGATCCCACACACTATCGCT 59.614 55.000 0.00 0.00 35.36 4.93
170 187 1.466167 GCTTTGTCTCGTCATGCATGT 59.534 47.619 25.43 0.00 0.00 3.21
212 229 1.808411 CTGCTTAAGCGGGTTCTTCA 58.192 50.000 25.93 3.44 45.83 3.02
268 285 2.337749 CTACCGCTCGTCCTCGCATT 62.338 60.000 0.00 0.00 36.96 3.56
282 299 4.284490 TCCTCGCATTATCTCCTTGCTTAT 59.716 41.667 0.00 0.00 34.23 1.73
459 476 2.813042 GCTGAGTCGTGCTGGCTC 60.813 66.667 4.45 4.45 0.00 4.70
460 477 2.969016 CTGAGTCGTGCTGGCTCT 59.031 61.111 11.49 0.00 0.00 4.09
484 501 4.992951 GCCAGTTTTTCATTGAGCTTCATT 59.007 37.500 0.00 0.00 0.00 2.57
486 503 5.987347 CCAGTTTTTCATTGAGCTTCATTGT 59.013 36.000 0.00 0.00 31.68 2.71
503 520 2.203224 TCCTCCTCGCCGAGCTAG 60.203 66.667 9.01 8.10 0.00 3.42
559 576 1.442769 TTGAAGCTCTTCGACCATGC 58.557 50.000 5.30 0.00 42.28 4.06
786 803 8.658619 TCCAAGTTCCTAGTAGTAGTCCTATAG 58.341 40.741 3.91 0.00 0.00 1.31
950 969 1.330655 ATAGCTAGCACAGTGGCGGT 61.331 55.000 18.83 0.00 39.27 5.68
1286 2028 5.798015 TGCGTGTTCTTGTAAGTGTTTAA 57.202 34.783 0.00 0.00 0.00 1.52
1351 2323 7.654287 AATTGGGAATGTAGAAGGGATAGAT 57.346 36.000 0.00 0.00 0.00 1.98
1523 2747 0.180171 CATCCCCGCAACCATAGTGA 59.820 55.000 0.00 0.00 0.00 3.41
1940 5837 3.159472 TCTCACGCTAAGGAAGGTGTTA 58.841 45.455 0.00 0.00 31.81 2.41
2028 5925 3.512516 GAAGGGGTGATGCAGCGC 61.513 66.667 7.05 7.05 43.43 5.92
2288 6586 1.392710 GCCACGCTCTCTAAGGCCTA 61.393 60.000 5.16 0.00 39.42 3.93
2332 6630 4.408821 GGTCGGTGCAGCCATGGA 62.409 66.667 18.40 0.00 36.97 3.41
2355 6653 1.282930 GACCTGAAGCGAACGACCAC 61.283 60.000 0.00 0.00 0.00 4.16
2694 6993 3.748623 AGCAACGCTCAACATGCA 58.251 50.000 0.00 0.00 41.18 3.96
2695 6994 1.577922 AGCAACGCTCAACATGCAG 59.422 52.632 0.00 0.00 41.18 4.41
2696 6995 1.443194 GCAACGCTCAACATGCAGG 60.443 57.895 0.00 0.00 38.63 4.85
2697 6996 1.855213 GCAACGCTCAACATGCAGGA 61.855 55.000 4.84 0.00 38.63 3.86
2698 6997 0.167470 CAACGCTCAACATGCAGGAG 59.833 55.000 4.84 4.18 0.00 3.69
2709 7008 3.138798 GCAGGAGCAGCCACCATG 61.139 66.667 8.66 5.55 41.58 3.66
2710 7009 3.138798 CAGGAGCAGCCACCATGC 61.139 66.667 8.66 0.00 44.18 4.06
2711 7010 3.654143 AGGAGCAGCCACCATGCA 61.654 61.111 8.66 0.00 46.31 3.96
2712 7011 3.446570 GGAGCAGCCACCATGCAC 61.447 66.667 0.00 0.00 46.31 4.57
2713 7012 3.807538 GAGCAGCCACCATGCACG 61.808 66.667 0.00 0.00 46.31 5.34
2714 7013 4.334118 AGCAGCCACCATGCACGA 62.334 61.111 0.00 0.00 46.31 4.35
2813 7112 2.048222 CCGCTCGAAGAAGTGGCA 60.048 61.111 0.00 0.00 34.09 4.92
2855 7154 0.652592 CGAGCGGAGTGGCATTAAAG 59.347 55.000 0.00 0.00 34.64 1.85
2929 7228 2.359107 TGTAGTCGCCGTCGAGGT 60.359 61.111 4.18 0.00 46.46 3.85
2948 7247 2.682494 GGGGTAGAGGCGTGTCCA 60.682 66.667 0.00 0.00 37.29 4.02
2951 7250 0.179081 GGGTAGAGGCGTGTCCAATC 60.179 60.000 0.00 0.00 37.29 2.67
3300 7653 8.848474 ACTATACAGGTAATATTTGGCACATC 57.152 34.615 0.00 0.00 39.30 3.06
3490 7849 4.040706 ACATGGCATCAAAATGGAAAGTGT 59.959 37.500 0.00 0.00 33.19 3.55
3554 7913 1.494721 TCTTGAGGGCCAGTTCAGTTT 59.505 47.619 6.18 0.00 0.00 2.66
3845 8220 0.038744 CCAGGGCCAATGACTTCAGT 59.961 55.000 6.18 0.00 0.00 3.41
4527 11725 5.815581 TGCCACTTACCAATCTTTGATAGT 58.184 37.500 0.00 0.00 0.00 2.12
4533 11731 8.960591 CACTTACCAATCTTTGATAGTGGAAAT 58.039 33.333 5.57 0.00 33.51 2.17
4679 11974 2.872858 GCGGATTAAACTAGGAAGCCAG 59.127 50.000 8.67 3.96 30.23 4.85
4697 11992 7.329471 GGAAGCCAGAATTTGAACTAATGAAAC 59.671 37.037 0.00 0.00 0.00 2.78
4787 12084 1.067516 CATAAAGGGCCGGAATGCAAG 59.932 52.381 5.05 0.00 0.00 4.01
4807 12104 7.147312 TGCAAGTTGGAAAAACTATCAATCAG 58.853 34.615 4.75 0.00 0.00 2.90
4820 12117 9.865321 AAACTATCAATCAGGATGTGAAAATTG 57.135 29.630 0.00 0.00 39.19 2.32
5203 12507 6.374333 GTGTTGAAGGGATAAGATGCAACTAA 59.626 38.462 0.00 0.00 36.17 2.24
5237 12543 8.353423 TGGAATAAAGAATTTGGAGAAAGGAG 57.647 34.615 0.00 0.00 39.63 3.69
5247 12553 7.767250 ATTTGGAGAAAGGAGTAAAAAGAGG 57.233 36.000 0.00 0.00 0.00 3.69
5331 12637 4.895297 GGATAATTGCAATGGAAGGAAGGA 59.105 41.667 13.82 0.00 0.00 3.36
5469 13159 0.937304 CTCCGTCTTTGTGTGTGTGG 59.063 55.000 0.00 0.00 0.00 4.17
5524 13218 8.934023 TCCACCTAATTAATAAATCCCATGTC 57.066 34.615 0.00 0.00 0.00 3.06
5610 13304 5.125417 TGCCTTATCTTTCATTGTGCCTAAC 59.875 40.000 0.00 0.00 0.00 2.34
5671 13365 9.113838 CCAAATCTATATGGTGATAGCAATACC 57.886 37.037 0.00 0.00 35.05 2.73
5867 13566 3.754965 CTCAGGGTTCATCCAAACAAGA 58.245 45.455 0.00 0.00 38.11 3.02
6021 13720 3.119531 TGCGCCTACCAATTCAATCAAAG 60.120 43.478 4.18 0.00 0.00 2.77
6023 13722 4.618227 GCGCCTACCAATTCAATCAAAGTT 60.618 41.667 0.00 0.00 0.00 2.66
6089 13789 1.003355 CCCGTGATGTGCAGGTTCT 60.003 57.895 0.00 0.00 0.00 3.01
6098 13798 1.765904 TGTGCAGGTTCTCTTACACCA 59.234 47.619 0.00 0.00 35.25 4.17
6195 13899 1.229975 TGAGTTGCATGCACCGACAG 61.230 55.000 22.58 0.00 0.00 3.51
6328 14032 6.379988 ACTGTGTTTCCTTATTCTGTTTTGGT 59.620 34.615 0.00 0.00 0.00 3.67
6346 14050 9.083422 TGTTTTGGTTCAATAATGGATTAGACA 57.917 29.630 0.00 0.00 0.00 3.41
6360 14064 7.437713 TGGATTAGACATTAGACATTGTCCT 57.562 36.000 13.14 4.93 42.56 3.85
6446 14171 8.598202 TTACCCAGTTAGTGTTGAGACATATA 57.402 34.615 0.00 0.00 38.23 0.86
6550 14278 6.773976 TCTTGTGAATTTTATGGGATGTCC 57.226 37.500 0.00 0.00 0.00 4.02
6580 14308 3.006859 CACATGATCCTCGGGTAGCATAA 59.993 47.826 0.00 0.00 0.00 1.90
6593 14321 3.558829 GGTAGCATAAAAGGGCGTACTTC 59.441 47.826 0.00 0.00 34.54 3.01
6714 14445 4.837860 AGATGGTTGAGTCTGTCTCTTTCT 59.162 41.667 3.71 0.00 43.13 2.52
6780 14511 4.074970 ACCTTGCTTTAGTCTCATGGTTG 58.925 43.478 0.00 0.00 35.53 3.77
7266 15003 1.614317 CCAACTGTCTCAATCCCCCAC 60.614 57.143 0.00 0.00 0.00 4.61
7328 15065 1.613437 GTGCAAAGTGGCAACTATGGT 59.387 47.619 0.00 0.00 46.93 3.55
7358 15095 5.221661 GGGAACTTACATCTACTATGGTGGG 60.222 48.000 0.00 0.00 0.00 4.61
7392 15129 2.365617 CCTAACTGCCCATGACGAGTAT 59.634 50.000 0.00 0.00 0.00 2.12
7436 15173 8.884124 TTAAAGAGAGGATGATTTCATGGTTT 57.116 30.769 0.00 0.00 36.57 3.27
7460 15197 5.852282 TCATCCGTCATCTCTTTACATCA 57.148 39.130 0.00 0.00 0.00 3.07
7592 15335 4.440839 AAGAAATGATCCGTTTTCAGCC 57.559 40.909 12.60 0.00 34.91 4.85
7593 15336 3.690460 AGAAATGATCCGTTTTCAGCCT 58.310 40.909 12.60 0.00 34.91 4.58
7985 15729 0.396435 GTCCATGGAGTGTGTGGTCA 59.604 55.000 16.81 0.00 34.61 4.02
8056 15802 3.177228 ACTTGTCTATGGCCTCTGAGTT 58.823 45.455 3.32 0.00 0.00 3.01
8343 16090 1.537638 CATAGTGTATCTCGAGCGGCT 59.462 52.381 7.81 0.00 0.00 5.52
8371 16118 7.361286 GCGTGTCCTTGAGAAATAAGATTCTTT 60.361 37.037 3.86 0.00 39.70 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 0.102481 GCGATAGTGTGTGGGATCGT 59.898 55.000 5.18 0.00 42.41 3.73
121 138 2.499693 TGGCATACGAAAGATCAGGACA 59.500 45.455 0.00 0.00 0.00 4.02
212 229 1.004918 GTGGTGCCACGAAGCTAGT 60.005 57.895 5.53 0.00 37.19 2.57
268 285 5.336770 CGGCATCACTATAAGCAAGGAGATA 60.337 44.000 0.00 0.00 0.00 1.98
282 299 1.816537 GGCTCAGTCGGCATCACTA 59.183 57.895 0.00 0.00 0.00 2.74
459 476 3.655276 AGCTCAATGAAAAACTGGCAG 57.345 42.857 14.16 14.16 0.00 4.85
460 477 3.384146 TGAAGCTCAATGAAAAACTGGCA 59.616 39.130 0.00 0.00 0.00 4.92
469 486 4.012374 GGAGGACAATGAAGCTCAATGAA 58.988 43.478 7.83 0.00 31.94 2.57
484 501 3.339738 TAGCTCGGCGAGGAGGACA 62.340 63.158 35.03 8.82 34.56 4.02
486 503 2.203224 CTAGCTCGGCGAGGAGGA 60.203 66.667 35.03 0.65 34.56 3.71
503 520 6.818644 ACTCACATTATCACAGTACACAATCC 59.181 38.462 0.00 0.00 0.00 3.01
559 576 2.097728 GCGGCCGTTAAAGCTTCG 59.902 61.111 28.70 0.00 0.00 3.79
609 626 7.968956 CCTGAATGAATCATCTCTTGTTTCTTG 59.031 37.037 0.00 0.00 37.44 3.02
786 803 1.092348 GTCGGCCTTGTTGGAATACC 58.908 55.000 0.00 0.00 38.35 2.73
1026 1054 2.044123 AATTCCCGGCTGACATCTTC 57.956 50.000 0.00 0.00 0.00 2.87
1027 1055 2.094675 CAAATTCCCGGCTGACATCTT 58.905 47.619 0.00 0.00 0.00 2.40
1028 1056 1.683011 CCAAATTCCCGGCTGACATCT 60.683 52.381 0.00 0.00 0.00 2.90
1286 2028 2.391879 GTTTGTAAGACTGAGCGACGT 58.608 47.619 0.00 0.00 0.00 4.34
1330 2116 6.730977 CCTTATCTATCCCTTCTACATTCCCA 59.269 42.308 0.00 0.00 0.00 4.37
1351 2323 4.328536 ACATTGTGTTACGCCAATCCTTA 58.671 39.130 0.00 0.00 0.00 2.69
1927 5737 1.693062 TGTGCCGTAACACCTTCCTTA 59.307 47.619 0.00 0.00 39.93 2.69
1940 5837 1.606668 CTTTTGTGTGGTATGTGCCGT 59.393 47.619 0.00 0.00 0.00 5.68
2288 6586 3.434319 CCGCTGCGTTGCCTCATT 61.434 61.111 21.59 0.00 0.00 2.57
2312 6610 2.045926 ATGGCTGCACCGACCTTC 60.046 61.111 0.50 0.00 43.94 3.46
2332 6630 1.081376 CGTTCGCTTCAGGTCGTCT 60.081 57.895 0.00 0.00 0.00 4.18
2355 6653 2.178521 CGGTCCACCTTCGTCTCG 59.821 66.667 0.00 0.00 0.00 4.04
2422 6720 3.563808 GGTATTTCCTACGCATGCATTGA 59.436 43.478 19.57 5.29 0.00 2.57
2463 6761 1.153823 CTGTGTCGTCCCATCGGTC 60.154 63.158 0.00 0.00 0.00 4.79
2678 6977 1.443194 CCTGCATGTTGAGCGTTGC 60.443 57.895 0.00 0.00 33.85 4.17
2679 6978 0.167470 CTCCTGCATGTTGAGCGTTG 59.833 55.000 0.00 0.00 33.85 4.10
2680 6979 1.580845 GCTCCTGCATGTTGAGCGTT 61.581 55.000 14.49 0.00 41.74 4.84
2681 6980 2.037136 GCTCCTGCATGTTGAGCGT 61.037 57.895 14.49 0.00 41.74 5.07
2682 6981 2.789917 GCTCCTGCATGTTGAGCG 59.210 61.111 14.49 0.00 41.74 5.03
2692 6991 3.138798 CATGGTGGCTGCTCCTGC 61.139 66.667 13.37 0.00 40.20 4.85
2693 6992 3.138798 GCATGGTGGCTGCTCCTG 61.139 66.667 13.37 10.52 36.68 3.86
2694 6993 3.654143 TGCATGGTGGCTGCTCCT 61.654 61.111 13.37 0.56 40.34 3.69
2695 6994 3.446570 GTGCATGGTGGCTGCTCC 61.447 66.667 0.00 3.54 40.34 4.70
2696 6995 3.807538 CGTGCATGGTGGCTGCTC 61.808 66.667 0.00 0.00 40.34 4.26
2697 6996 3.848301 TTCGTGCATGGTGGCTGCT 62.848 57.895 5.98 0.00 40.34 4.24
2698 6997 3.364441 TTCGTGCATGGTGGCTGC 61.364 61.111 5.98 0.00 40.10 5.25
2699 6998 2.191354 CTGTTCGTGCATGGTGGCTG 62.191 60.000 5.98 0.00 34.04 4.85
2700 6999 1.968017 CTGTTCGTGCATGGTGGCT 60.968 57.895 5.98 0.00 34.04 4.75
2701 7000 2.562912 CTGTTCGTGCATGGTGGC 59.437 61.111 5.98 0.00 0.00 5.01
2702 7001 2.562912 GCTGTTCGTGCATGGTGG 59.437 61.111 5.98 0.00 0.00 4.61
2703 7002 2.174107 CGCTGTTCGTGCATGGTG 59.826 61.111 5.98 0.00 0.00 4.17
2768 7067 1.475280 CCTACGGCTACACACTAAGCA 59.525 52.381 0.00 0.00 40.61 3.91
2929 7228 2.753043 GACACGCCTCTACCCCGA 60.753 66.667 0.00 0.00 0.00 5.14
3490 7849 4.342951 CGTATTGGTATGGTGTCCTTAGGA 59.657 45.833 0.00 0.00 0.00 2.94
3554 7913 0.400213 ATCTTCGTGCCAAACCTCCA 59.600 50.000 0.00 0.00 0.00 3.86
3845 8220 4.261572 GCAGTGATCCAAAGCTGTGTTAAA 60.262 41.667 2.51 0.00 0.00 1.52
4501 11698 8.052748 ACTATCAAAGATTGGTAAGTGGCATAA 58.947 33.333 0.00 0.00 0.00 1.90
4516 11714 9.965902 AGAAGTTGTATTTCCACTATCAAAGAT 57.034 29.630 0.00 0.00 0.00 2.40
4527 11725 5.240121 GGTAACGGAGAAGTTGTATTTCCA 58.760 41.667 0.00 0.00 35.70 3.53
4679 11974 9.090692 CCATCATGGTTTCATTAGTTCAAATTC 57.909 33.333 0.00 0.00 31.35 2.17
4765 12062 1.111277 GCATTCCGGCCCTTTATGTT 58.889 50.000 0.00 0.00 0.00 2.71
4787 12084 7.756722 CACATCCTGATTGATAGTTTTTCCAAC 59.243 37.037 0.00 0.00 0.00 3.77
4807 12104 9.921637 TTCTATTACAAACCAATTTTCACATCC 57.078 29.630 0.00 0.00 0.00 3.51
4886 12183 9.300681 CCATGGCTAATCAAATTTCTTATCCTA 57.699 33.333 0.00 1.43 0.00 2.94
5096 12395 9.301153 TGTTCACGCTATACATGCTTATATATG 57.699 33.333 0.00 0.00 0.00 1.78
5203 12507 6.096846 CCAAATTCTTTATTCCAATCCCTCGT 59.903 38.462 0.00 0.00 0.00 4.18
5237 12543 4.889995 CCCATGGAATCTCCCTCTTTTTAC 59.110 45.833 15.22 0.00 35.03 2.01
5247 12553 2.889678 GAGAAATGCCCATGGAATCTCC 59.110 50.000 15.22 0.00 36.96 3.71
5403 12712 0.998945 AGAGAGAGAGAGGGAGGGGG 60.999 65.000 0.00 0.00 0.00 5.40
5404 12713 0.478507 GAGAGAGAGAGAGGGAGGGG 59.521 65.000 0.00 0.00 0.00 4.79
5405 12714 1.421646 GAGAGAGAGAGAGAGGGAGGG 59.578 61.905 0.00 0.00 0.00 4.30
5406 12715 2.370189 GAGAGAGAGAGAGAGAGGGAGG 59.630 59.091 0.00 0.00 0.00 4.30
5407 12716 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.00 0.00 0.00 4.30
5408 12717 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
5409 12718 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
5524 13218 9.227490 GTATAATAGCTATGTCTAAGCATGACG 57.773 37.037 7.09 0.00 42.62 4.35
5610 13304 2.890808 TTGTAGAGAGCATAAGGCCG 57.109 50.000 0.00 0.00 46.50 6.13
5671 13365 3.066064 CGGTCCAGTAGATGAAGAGTCTG 59.934 52.174 0.00 0.00 0.00 3.51
5867 13566 3.002102 GCCGCCAATTGTGATTTGATTT 58.998 40.909 4.43 0.00 0.00 2.17
6021 13720 5.123979 CACTTTTCCCCTATAGCTTCACAAC 59.876 44.000 0.00 0.00 0.00 3.32
6023 13722 4.324254 CCACTTTTCCCCTATAGCTTCACA 60.324 45.833 0.00 0.00 0.00 3.58
6074 13774 3.433615 GTGTAAGAGAACCTGCACATCAC 59.566 47.826 0.00 0.00 34.10 3.06
6089 13789 8.698973 TCCTATTTGAACATTTTGGTGTAAGA 57.301 30.769 0.00 0.00 0.00 2.10
6195 13899 4.364860 ACATACGGTTTTTGGCTTGAAAC 58.635 39.130 0.00 0.00 35.54 2.78
6340 14044 7.710907 GTGCATAGGACAATGTCTAATGTCTAA 59.289 37.037 20.79 9.08 44.20 2.10
6346 14050 7.886629 AAATGTGCATAGGACAATGTCTAAT 57.113 32.000 13.53 4.44 32.47 1.73
6347 14051 8.800370 TTAAATGTGCATAGGACAATGTCTAA 57.200 30.769 13.53 2.11 32.47 2.10
6348 14052 8.978874 ATTAAATGTGCATAGGACAATGTCTA 57.021 30.769 13.53 4.41 32.47 2.59
6349 14053 7.886629 ATTAAATGTGCATAGGACAATGTCT 57.113 32.000 13.53 2.24 32.47 3.41
6446 14171 7.208080 CCTAGTTAAGTATGTGGCTCGTATTT 58.792 38.462 2.77 2.77 0.00 1.40
6550 14278 1.078214 AGGATCATGTGGTGGTGCG 60.078 57.895 0.00 0.00 33.94 5.34
6580 14308 1.948391 AGGGTAGAAGTACGCCCTTT 58.052 50.000 8.50 0.00 42.78 3.11
6714 14445 1.546923 TCGAGTCCGCCAATCAAACTA 59.453 47.619 0.00 0.00 35.37 2.24
6780 14511 8.987890 ACTTGCATTGTAAAAATATGTTCCAAC 58.012 29.630 0.00 0.00 0.00 3.77
6875 14606 0.461693 GAGCTGACAGGGATGAGTGC 60.462 60.000 4.26 0.00 0.00 4.40
7266 15003 2.352651 CAGTTATCAAGCCCACATCACG 59.647 50.000 0.00 0.00 0.00 4.35
7328 15065 4.684724 AGTAGATGTAAGTTCCCCAGTCA 58.315 43.478 0.00 0.00 0.00 3.41
7417 15154 7.729124 ATGAAAAACCATGAAATCATCCTCT 57.271 32.000 0.00 0.00 33.61 3.69
7436 15173 6.639563 TGATGTAAAGAGATGACGGATGAAA 58.360 36.000 0.00 0.00 0.00 2.69
7573 15316 3.485877 CGAGGCTGAAAACGGATCATTTC 60.486 47.826 0.00 9.63 36.35 2.17
7627 15370 4.069232 CAGCAGCCCCGACGAAGA 62.069 66.667 0.00 0.00 0.00 2.87
7696 15439 3.688272 CAGTGCGAAAATGGATGATGAC 58.312 45.455 0.00 0.00 0.00 3.06
7837 15580 0.885879 CAGTGACATGCATGCCTGTT 59.114 50.000 26.30 10.92 0.00 3.16
7985 15729 0.819259 GTGCCCAGACACACACACAT 60.819 55.000 0.00 0.00 40.40 3.21
8014 15760 3.004106 GTCGGACTACGCCAGTACAATAT 59.996 47.826 0.00 0.00 38.09 1.28
8015 15761 2.355756 GTCGGACTACGCCAGTACAATA 59.644 50.000 0.00 0.00 38.09 1.90
8056 15802 3.870422 CGCCACACACGCACACAA 61.870 61.111 0.00 0.00 0.00 3.33
8281 16028 2.579878 CCTACACGAGGGCAGAGAA 58.420 57.895 0.00 0.00 42.39 2.87
8343 16090 4.637276 TCTTATTTCTCAAGGACACGCAA 58.363 39.130 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.