Multiple sequence alignment - TraesCS4A01G181400

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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 TraesCS4A01G181400 chr4A 100.000 2767 0 0 1 2767 456292850 456295616 0.000000e+00 5110.0
1 TraesCS4A01G181400 chr4A 84.173 695 86 14 1001 1674 456336196 456336887 0.000000e+00 652.0
2 TraesCS4A01G181400 chr4A 84.579 629 77 10 1001 1612 457568184 457568809 8.480000e-170 606.0
3 TraesCS4A01G181400 chr4A 81.946 709 114 13 11 711 585703793 585703091 3.070000e-164 588.0
4 TraesCS4A01G181400 chr4A 80.481 707 127 11 12 712 737162622 737163323 5.250000e-147 531.0
5 TraesCS4A01G181400 chr4A 79.677 620 102 15 96 712 296326955 296326357 2.550000e-115 425.0
6 TraesCS4A01G181400 chr4A 78.443 167 34 2 2079 2244 644443549 644443384 1.050000e-19 108.0
7 TraesCS4A01G181400 chr4B 90.423 1253 90 16 754 1987 179842942 179841701 0.000000e+00 1622.0
8 TraesCS4A01G181400 chr4B 86.239 763 97 5 2007 2767 179841603 179840847 0.000000e+00 821.0
9 TraesCS4A01G181400 chr4B 84.604 695 76 20 1001 1675 179751033 179751716 0.000000e+00 662.0
10 TraesCS4A01G181400 chr4B 87.949 473 55 2 176 647 179846008 179845537 8.660000e-155 556.0
11 TraesCS4A01G181400 chr4B 97.436 39 1 0 721 759 465146050 465146012 1.780000e-07 67.6
12 TraesCS4A01G181400 chr4D 92.681 1052 50 16 754 1786 117706736 117705693 0.000000e+00 1491.0
13 TraesCS4A01G181400 chr4D 88.220 764 83 7 2007 2767 117704023 117703264 0.000000e+00 905.0
14 TraesCS4A01G181400 chr4D 87.749 653 74 3 1 647 117712448 117711796 0.000000e+00 758.0
15 TraesCS4A01G181400 chr4D 84.317 695 79 19 1001 1675 117663162 117662478 0.000000e+00 652.0
16 TraesCS4A01G181400 chr4D 86.266 233 31 1 1778 2010 117704329 117704098 4.570000e-63 252.0
17 TraesCS4A01G181400 chr3A 85.455 715 100 4 1 712 729395655 729394942 0.000000e+00 741.0
18 TraesCS4A01G181400 chr3A 77.869 488 105 3 2283 2767 741747917 741747430 1.610000e-77 300.0
19 TraesCS4A01G181400 chr7A 83.377 770 111 17 2007 2767 492554933 492554172 0.000000e+00 697.0
20 TraesCS4A01G181400 chr7A 80.804 224 28 6 1743 1966 492555263 492555055 7.930000e-36 161.0
21 TraesCS4A01G181400 chr7A 97.561 41 1 0 721 761 487312659 487312619 1.370000e-08 71.3
22 TraesCS4A01G181400 chr7A 95.238 42 2 0 721 762 619886036 619886077 1.780000e-07 67.6
23 TraesCS4A01G181400 chr7D 81.057 908 102 33 754 1607 611445520 611444629 0.000000e+00 660.0
24 TraesCS4A01G181400 chr7D 79.421 656 128 7 2116 2767 351980282 351979630 9.030000e-125 457.0
25 TraesCS4A01G181400 chr7D 97.436 39 1 0 722 760 491856238 491856276 1.780000e-07 67.6
26 TraesCS4A01G181400 chr7B 80.564 957 103 42 773 1671 700724652 700723721 0.000000e+00 660.0
27 TraesCS4A01G181400 chr7B 81.001 879 93 26 754 1578 700736577 700735719 5.030000e-177 630.0
28 TraesCS4A01G181400 chr7B 83.619 641 78 16 1001 1622 700630487 700629855 6.640000e-161 577.0
29 TraesCS4A01G181400 chr7B 82.496 657 107 8 2115 2767 458457784 458457132 1.110000e-158 569.0
30 TraesCS4A01G181400 chr7B 83.133 249 38 3 1762 2010 458458189 458457945 9.970000e-55 224.0
31 TraesCS4A01G181400 chr3D 81.127 710 116 16 11 711 27304108 27304808 1.120000e-153 553.0
32 TraesCS4A01G181400 chr2B 80.864 648 115 8 1 644 532478568 532477926 4.110000e-138 501.0
33 TraesCS4A01G181400 chr2B 81.690 568 97 7 11 573 496175658 496175093 1.500000e-127 466.0
34 TraesCS4A01G181400 chr5D 82.971 552 87 5 23 573 64140139 64139594 2.480000e-135 492.0
35 TraesCS4A01G181400 chr5D 77.381 420 85 10 2312 2725 350801235 350800820 9.900000e-60 241.0
36 TraesCS4A01G181400 chr5D 80.147 272 46 7 1742 2010 442915306 442915040 2.170000e-46 196.0
37 TraesCS4A01G181400 chr5D 77.032 283 51 10 1733 2010 247139632 247139905 1.720000e-32 150.0
38 TraesCS4A01G181400 chr5D 95.238 42 2 0 718 759 282249570 282249611 1.780000e-07 67.6
39 TraesCS4A01G181400 chr6D 73.729 708 171 13 2067 2767 7869711 7870410 2.110000e-66 263.0
40 TraesCS4A01G181400 chr6D 97.436 39 1 0 721 759 312130526 312130488 1.780000e-07 67.6
41 TraesCS4A01G181400 chr6D 86.207 58 5 3 722 779 102243374 102243428 2.980000e-05 60.2
42 TraesCS4A01G181400 chr2A 73.475 705 177 8 2070 2767 121597346 121598047 9.830000e-65 257.0
43 TraesCS4A01G181400 chr6A 80.714 280 41 8 1734 2010 127876294 127876563 3.610000e-49 206.0
44 TraesCS4A01G181400 chr6A 100.000 39 0 0 721 759 467574833 467574871 3.820000e-09 73.1
45 TraesCS4A01G181400 chr6B 80.469 256 37 8 1741 1990 566532838 566532590 1.690000e-42 183.0
46 TraesCS4A01G181400 chrUn 78.439 269 49 8 1742 2006 90724199 90724462 1.700000e-37 167.0
47 TraesCS4A01G181400 chr5B 76.157 281 54 12 1734 2008 545120559 545120286 4.810000e-28 135.0
48 TraesCS4A01G181400 chr5B 77.512 209 37 6 1739 1945 316403855 316404055 1.740000e-22 117.0
49 TraesCS4A01G181400 chr1A 97.436 39 1 0 721 759 453769740 453769778 1.780000e-07 67.6


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 TraesCS4A01G181400 chr4A 456292850 456295616 2766 False 5110.000000 5110 100.000000 1 2767 1 chr4A.!!$F1 2766
1 TraesCS4A01G181400 chr4A 456336196 456336887 691 False 652.000000 652 84.173000 1001 1674 1 chr4A.!!$F2 673
2 TraesCS4A01G181400 chr4A 457568184 457568809 625 False 606.000000 606 84.579000 1001 1612 1 chr4A.!!$F3 611
3 TraesCS4A01G181400 chr4A 585703091 585703793 702 True 588.000000 588 81.946000 11 711 1 chr4A.!!$R2 700
4 TraesCS4A01G181400 chr4A 737162622 737163323 701 False 531.000000 531 80.481000 12 712 1 chr4A.!!$F4 700
5 TraesCS4A01G181400 chr4A 296326357 296326955 598 True 425.000000 425 79.677000 96 712 1 chr4A.!!$R1 616
6 TraesCS4A01G181400 chr4B 179840847 179846008 5161 True 999.666667 1622 88.203667 176 2767 3 chr4B.!!$R2 2591
7 TraesCS4A01G181400 chr4B 179751033 179751716 683 False 662.000000 662 84.604000 1001 1675 1 chr4B.!!$F1 674
8 TraesCS4A01G181400 chr4D 117703264 117706736 3472 True 882.666667 1491 89.055667 754 2767 3 chr4D.!!$R3 2013
9 TraesCS4A01G181400 chr4D 117711796 117712448 652 True 758.000000 758 87.749000 1 647 1 chr4D.!!$R2 646
10 TraesCS4A01G181400 chr4D 117662478 117663162 684 True 652.000000 652 84.317000 1001 1675 1 chr4D.!!$R1 674
11 TraesCS4A01G181400 chr3A 729394942 729395655 713 True 741.000000 741 85.455000 1 712 1 chr3A.!!$R1 711
12 TraesCS4A01G181400 chr7A 492554172 492555263 1091 True 429.000000 697 82.090500 1743 2767 2 chr7A.!!$R2 1024
13 TraesCS4A01G181400 chr7D 611444629 611445520 891 True 660.000000 660 81.057000 754 1607 1 chr7D.!!$R2 853
14 TraesCS4A01G181400 chr7D 351979630 351980282 652 True 457.000000 457 79.421000 2116 2767 1 chr7D.!!$R1 651
15 TraesCS4A01G181400 chr7B 700723721 700724652 931 True 660.000000 660 80.564000 773 1671 1 chr7B.!!$R2 898
16 TraesCS4A01G181400 chr7B 700735719 700736577 858 True 630.000000 630 81.001000 754 1578 1 chr7B.!!$R3 824
17 TraesCS4A01G181400 chr7B 700629855 700630487 632 True 577.000000 577 83.619000 1001 1622 1 chr7B.!!$R1 621
18 TraesCS4A01G181400 chr7B 458457132 458458189 1057 True 396.500000 569 82.814500 1762 2767 2 chr7B.!!$R4 1005
19 TraesCS4A01G181400 chr3D 27304108 27304808 700 False 553.000000 553 81.127000 11 711 1 chr3D.!!$F1 700
20 TraesCS4A01G181400 chr2B 532477926 532478568 642 True 501.000000 501 80.864000 1 644 1 chr2B.!!$R2 643
21 TraesCS4A01G181400 chr2B 496175093 496175658 565 True 466.000000 466 81.690000 11 573 1 chr2B.!!$R1 562
22 TraesCS4A01G181400 chr5D 64139594 64140139 545 True 492.000000 492 82.971000 23 573 1 chr5D.!!$R1 550
23 TraesCS4A01G181400 chr6D 7869711 7870410 699 False 263.000000 263 73.729000 2067 2767 1 chr6D.!!$F1 700
24 TraesCS4A01G181400 chr2A 121597346 121598047 701 False 257.000000 257 73.475000 2070 2767 1 chr2A.!!$F1 697

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
339 342 0.178891 ACCACCCTCATGGAGTCACT 60.179 55.0 0.0 0.0 43.02 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 6345 0.039437 CTATTACGCGACCGCATCCT 60.039 55.0 15.93 0.0 42.06 3.24 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
44 46 2.260869 CCTGGCACCAACAAGACCG 61.261 63.158 0.00 0.00 0.00 4.79
47 49 2.485795 GGCACCAACAAGACCGCAA 61.486 57.895 0.00 0.00 0.00 4.85
117 119 1.680651 CACCTCTCCTCGAGCAGGT 60.681 63.158 18.50 18.50 43.95 4.00
134 136 2.981909 TGACTCCGACTTCGCCGT 60.982 61.111 0.00 0.00 38.18 5.68
152 154 2.353406 CCGTTAACGACCCATCAAGACT 60.353 50.000 28.79 0.00 43.02 3.24
157 159 1.272760 ACGACCCATCAAGACTCCTCT 60.273 52.381 0.00 0.00 0.00 3.69
206 209 3.194116 CAGCCATAGCCAAACAATCAACT 59.806 43.478 0.00 0.00 41.25 3.16
208 211 3.056607 GCCATAGCCAAACAATCAACTGT 60.057 43.478 0.00 0.00 0.00 3.55
223 226 1.888215 ACTGTAGACGTCGAGGACAA 58.112 50.000 12.85 0.00 32.09 3.18
230 233 1.373497 CGTCGAGGACAAGCAGCTT 60.373 57.895 0.21 0.21 32.09 3.74
339 342 0.178891 ACCACCCTCATGGAGTCACT 60.179 55.000 0.00 0.00 43.02 3.41
343 346 2.567169 CACCCTCATGGAGTCACTGTTA 59.433 50.000 0.00 0.00 38.00 2.41
344 347 3.007940 CACCCTCATGGAGTCACTGTTAA 59.992 47.826 0.00 0.00 38.00 2.01
386 390 1.546476 GGTCCGACTTCTCTGTCACAT 59.454 52.381 0.00 0.00 36.82 3.21
387 391 2.600731 GTCCGACTTCTCTGTCACATG 58.399 52.381 0.00 0.00 36.82 3.21
542 554 3.697166 GGAACCTACCAACCATGATGTT 58.303 45.455 0.00 0.00 0.00 2.71
544 556 4.331968 GAACCTACCAACCATGATGTTGA 58.668 43.478 14.29 0.00 46.77 3.18
576 588 1.148310 CAAGAAAAGCGCGGAGAAGA 58.852 50.000 8.83 0.00 0.00 2.87
599 611 1.597027 CCGGTCTCCAAAGCAACGT 60.597 57.895 0.00 0.00 0.00 3.99
663 2411 2.761208 CCAGATGGGTCTAGACTTTCGT 59.239 50.000 21.88 12.92 32.09 3.85
678 2426 3.244112 ACTTTCGTCCGAAGAACCAGATT 60.244 43.478 2.12 0.00 35.38 2.40
696 2444 2.839486 TTCAGGAATGAAGCGTGTCT 57.161 45.000 0.00 0.00 0.00 3.41
702 2452 4.328440 CAGGAATGAAGCGTGTCTAAGAAG 59.672 45.833 0.00 0.00 0.00 2.85
707 2457 1.257743 AGCGTGTCTAAGAAGCTCCA 58.742 50.000 0.00 0.00 31.94 3.86
727 2477 2.003672 GGCAACGCGTACATAGTGG 58.996 57.895 14.46 0.00 0.00 4.00
729 2479 1.426041 GCAACGCGTACATAGTGGGG 61.426 60.000 14.46 0.00 0.00 4.96
731 2481 0.458669 AACGCGTACATAGTGGGGAG 59.541 55.000 14.46 0.00 0.00 4.30
734 2484 1.677576 CGCGTACATAGTGGGGAGTAA 59.322 52.381 0.00 0.00 0.00 2.24
735 2485 2.542411 CGCGTACATAGTGGGGAGTAAC 60.542 54.545 0.00 0.00 0.00 2.50
736 2486 2.692041 GCGTACATAGTGGGGAGTAACT 59.308 50.000 0.00 0.00 0.00 2.24
737 2487 3.131755 GCGTACATAGTGGGGAGTAACTT 59.868 47.826 0.00 0.00 0.00 2.66
738 2488 4.339247 GCGTACATAGTGGGGAGTAACTTA 59.661 45.833 0.00 0.00 0.00 2.24
739 2489 5.010415 GCGTACATAGTGGGGAGTAACTTAT 59.990 44.000 0.00 0.00 0.00 1.73
740 2490 6.207417 GCGTACATAGTGGGGAGTAACTTATA 59.793 42.308 0.00 0.00 0.00 0.98
741 2491 7.588512 CGTACATAGTGGGGAGTAACTTATAC 58.411 42.308 0.00 0.00 0.00 1.47
742 2492 7.446625 CGTACATAGTGGGGAGTAACTTATACT 59.553 40.741 0.00 0.00 0.00 2.12
743 2493 9.799106 GTACATAGTGGGGAGTAACTTATACTA 57.201 37.037 0.00 0.00 0.00 1.82
744 2494 8.937207 ACATAGTGGGGAGTAACTTATACTAG 57.063 38.462 0.00 0.00 0.00 2.57
745 2495 8.509441 ACATAGTGGGGAGTAACTTATACTAGT 58.491 37.037 0.00 0.00 0.00 2.57
746 2496 8.794553 CATAGTGGGGAGTAACTTATACTAGTG 58.205 40.741 5.39 0.00 0.00 2.74
747 2497 6.739664 AGTGGGGAGTAACTTATACTAGTGT 58.260 40.000 5.39 0.39 0.00 3.55
748 2498 6.832900 AGTGGGGAGTAACTTATACTAGTGTC 59.167 42.308 5.39 0.00 0.00 3.67
749 2499 6.604795 GTGGGGAGTAACTTATACTAGTGTCA 59.395 42.308 5.39 0.00 0.00 3.58
750 2500 7.287235 GTGGGGAGTAACTTATACTAGTGTCAT 59.713 40.741 5.39 0.00 0.00 3.06
751 2501 7.287005 TGGGGAGTAACTTATACTAGTGTCATG 59.713 40.741 5.39 0.00 0.00 3.07
752 2502 7.287235 GGGGAGTAACTTATACTAGTGTCATGT 59.713 40.741 5.39 0.00 0.00 3.21
817 3323 1.131771 CGACGCATGCACCATACTAG 58.868 55.000 19.57 0.00 0.00 2.57
818 3324 0.861837 GACGCATGCACCATACTAGC 59.138 55.000 19.57 0.00 0.00 3.42
857 3365 0.538287 AACTTCTGCAAGGGACCTGC 60.538 55.000 0.00 0.00 33.37 4.85
956 3494 1.372087 CTTCTCCATCGCTGCCAACC 61.372 60.000 0.00 0.00 0.00 3.77
974 3512 1.299541 CCTGTTGTCTTGTGTTCGCT 58.700 50.000 0.00 0.00 0.00 4.93
995 3533 5.861725 GCTCGCCGCGTATATATATATACA 58.138 41.667 29.53 15.89 43.23 2.29
998 3536 5.122239 TCGCCGCGTATATATATATACACCC 59.878 44.000 29.53 20.20 43.23 4.61
999 3537 5.106594 CGCCGCGTATATATATATACACCCA 60.107 44.000 29.53 5.43 43.23 4.51
1017 3564 4.455533 CACCCACCATATTATCCATCAACG 59.544 45.833 0.00 0.00 0.00 4.10
1024 3571 5.065602 CCATATTATCCATCAACGGCATCAG 59.934 44.000 0.00 0.00 0.00 2.90
1065 3622 0.461693 GCTCCCAGCTCAGCTAGTTG 60.462 60.000 0.00 0.00 36.40 3.16
1066 3623 1.189752 CTCCCAGCTCAGCTAGTTGA 58.810 55.000 9.11 9.11 38.64 3.18
1067 3624 0.898320 TCCCAGCTCAGCTAGTTGAC 59.102 55.000 0.00 3.48 38.64 3.18
1086 3649 3.568007 TGACTACCTGCAAATTTGGTGAC 59.432 43.478 19.47 3.64 35.48 3.67
1100 3663 1.202758 TGGTGACAAGGTTGCTAGGTG 60.203 52.381 0.00 0.00 37.44 4.00
1107 3670 2.749621 CAAGGTTGCTAGGTGGATGAAC 59.250 50.000 0.00 0.00 0.00 3.18
1118 3684 2.329379 GTGGATGAACAGTCACTCGAC 58.671 52.381 0.00 0.00 42.95 4.20
1165 3741 3.562779 TTCGACAAGGACGGCGACC 62.563 63.158 20.56 20.56 31.91 4.79
1401 4013 1.658114 CTCCACGGAAGACACGACA 59.342 57.895 0.00 0.00 34.93 4.35
1419 4031 1.273688 CAACGACGATGATTACGCCA 58.726 50.000 0.00 0.00 0.00 5.69
1637 4271 9.927668 ATTCATCGATCACATATGTATGTACAA 57.072 29.630 8.32 0.18 44.57 2.41
1709 4343 8.393671 AGTATGTTATAGTAGTAGCTGTCCAC 57.606 38.462 0.00 0.00 0.00 4.02
1720 4354 6.299805 AGTAGCTGTCCACATGAAAAGATA 57.700 37.500 0.00 0.00 0.00 1.98
1795 5801 4.559300 GCAACTGTTCATACAACCAGCATT 60.559 41.667 0.00 0.00 32.92 3.56
1797 5803 3.436704 ACTGTTCATACAACCAGCATTCG 59.563 43.478 0.00 0.00 32.92 3.34
1822 5828 3.954258 TCTCTGATCAAGAATGACGGCTA 59.046 43.478 0.00 0.00 38.69 3.93
1834 5840 0.676782 GACGGCTAGGGCAACAACAT 60.677 55.000 0.00 0.00 40.87 2.71
1841 5847 5.070001 GGCTAGGGCAACAACATAATCATA 58.930 41.667 0.00 0.00 40.87 2.15
1959 5965 0.535780 GCATCCATCATGAGGCCGAA 60.536 55.000 0.73 0.00 36.10 4.30
1990 5996 2.490903 GTTACGCTACCTCAAGAGTGGA 59.509 50.000 0.00 0.00 31.57 4.02
1995 6001 0.824109 TACCTCAAGAGTGGATGCCG 59.176 55.000 0.00 0.00 32.71 5.69
1999 6005 0.904649 TCAAGAGTGGATGCCGATGT 59.095 50.000 0.00 0.00 0.00 3.06
2015 6102 3.689161 CCGATGTTGCAGAAAAGTCCATA 59.311 43.478 0.00 0.00 0.00 2.74
2025 6112 2.396590 AAAGTCCATAACATCGCCGT 57.603 45.000 0.00 0.00 0.00 5.68
2035 6122 5.924254 CCATAACATCGCCGTAAAGATAAGA 59.076 40.000 0.00 0.00 0.00 2.10
2042 6129 5.657474 TCGCCGTAAAGATAAGACAGAATT 58.343 37.500 0.00 0.00 0.00 2.17
2047 6134 7.705325 GCCGTAAAGATAAGACAGAATTAGTGA 59.295 37.037 0.00 0.00 0.00 3.41
2048 6135 9.239002 CCGTAAAGATAAGACAGAATTAGTGAG 57.761 37.037 0.00 0.00 0.00 3.51
2072 6159 6.267928 AGAATATCTCGTATAGTTTGTGGCCT 59.732 38.462 3.32 0.00 0.00 5.19
2245 6333 2.354303 CGGCCATGTCACTTAAGTACCA 60.354 50.000 8.04 8.24 0.00 3.25
2251 6339 5.279506 CCATGTCACTTAAGTACCACAGTCT 60.280 44.000 8.04 0.00 0.00 3.24
2253 6341 5.138276 TGTCACTTAAGTACCACAGTCTCT 58.862 41.667 8.04 0.00 0.00 3.10
2257 6345 6.322969 TCACTTAAGTACCACAGTCTCTGAAA 59.677 38.462 8.04 0.00 35.18 2.69
2281 6369 1.299165 CGGTCGCGTAATAGCTGCT 60.299 57.895 7.57 7.57 34.40 4.24
2515 6606 3.699067 AGTACGACGGAACCGAATATTG 58.301 45.455 20.14 3.99 42.83 1.90
2518 6609 1.864711 CGACGGAACCGAATATTGCAT 59.135 47.619 20.14 0.00 42.83 3.96
2523 6614 3.312421 CGGAACCGAATATTGCATTGTCT 59.688 43.478 7.53 0.00 42.83 3.41
2537 6628 3.217626 CATTGTCTAGAATGGAAGGCCC 58.782 50.000 0.00 0.00 30.82 5.80
2544 6635 0.259938 GAATGGAAGGCCCTGGACAT 59.740 55.000 0.00 0.00 35.38 3.06
2583 6674 3.803555 CACAAATCGAGAACAAGTCAGC 58.196 45.455 0.00 0.00 0.00 4.26
2587 6678 2.502213 TCGAGAACAAGTCAGCGAAA 57.498 45.000 0.00 0.00 33.94 3.46
2594 6685 2.906354 ACAAGTCAGCGAAACTCACTT 58.094 42.857 0.00 0.00 0.00 3.16
2624 6716 2.092646 TCATTATCCAACCAGGGGTTCG 60.093 50.000 0.00 0.00 43.05 3.95
2638 6730 1.202710 GGGTTCGGCAAAAATTGGGTT 60.203 47.619 0.00 0.00 0.00 4.11
2661 6753 3.373438 CCATCCCCATTTCTTGTGGAGAT 60.373 47.826 0.00 0.00 35.15 2.75
2725 6818 1.127567 CCAGAACTGTGACCCTCCCA 61.128 60.000 1.18 0.00 0.00 4.37
2759 6852 1.909302 CTTGAGAGGCTCACCCCTAAA 59.091 52.381 18.26 0.00 40.46 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 1.903404 GGTCTTGTTGGTGCCAGGG 60.903 63.158 0.00 0.00 0.00 4.45
44 46 1.600413 CCTCTTTTCAGCGGTGTTTGC 60.600 52.381 15.22 0.00 0.00 3.68
47 49 1.134220 TGTCCTCTTTTCAGCGGTGTT 60.134 47.619 15.22 0.00 0.00 3.32
134 136 3.170717 AGGAGTCTTGATGGGTCGTTAA 58.829 45.455 0.00 0.00 0.00 2.01
152 154 1.026584 TGTGTCGTTCGTTCAGAGGA 58.973 50.000 0.00 0.00 0.00 3.71
157 159 0.593008 CCTCGTGTGTCGTTCGTTCA 60.593 55.000 0.00 0.00 40.80 3.18
206 209 0.520404 GCTTGTCCTCGACGTCTACA 59.480 55.000 14.70 9.58 34.95 2.74
208 211 0.803117 CTGCTTGTCCTCGACGTCTA 59.197 55.000 14.70 0.95 34.95 2.59
230 233 0.804364 AAGCGCATCAGCAAAATCGA 59.196 45.000 11.47 0.00 42.27 3.59
291 294 2.261671 GCGCTCTTCGGAGGTTGA 59.738 61.111 0.00 0.00 42.06 3.18
339 342 1.816259 GCGGGCCTATGCGTTAACA 60.816 57.895 0.84 0.00 38.85 2.41
367 371 2.600731 CATGTGACAGAGAAGTCGGAC 58.399 52.381 0.00 0.00 41.41 4.79
386 390 3.568007 GTGTGCCTATGTTTGTTTCTCCA 59.432 43.478 0.00 0.00 0.00 3.86
387 391 3.057526 GGTGTGCCTATGTTTGTTTCTCC 60.058 47.826 0.00 0.00 0.00 3.71
576 588 0.400213 TGCTTTGGAGACCGGTGATT 59.600 50.000 14.63 0.00 0.00 2.57
656 2404 5.091828 GAATCTGGTTCTTCGGACGAAAGT 61.092 45.833 8.59 0.00 39.66 2.66
663 2411 2.536066 TCCTGAATCTGGTTCTTCGGA 58.464 47.619 6.07 3.03 37.72 4.55
678 2426 3.509967 TCTTAGACACGCTTCATTCCTGA 59.490 43.478 0.00 0.00 0.00 3.86
696 2444 0.669318 CGTTGCCGTGGAGCTTCTTA 60.669 55.000 0.00 0.00 0.00 2.10
707 2457 1.074319 CACTATGTACGCGTTGCCGT 61.074 55.000 20.78 10.14 44.62 5.68
715 2465 2.692041 AGTTACTCCCCACTATGTACGC 59.308 50.000 0.00 0.00 0.00 4.42
716 2466 4.996788 AAGTTACTCCCCACTATGTACG 57.003 45.455 0.00 0.00 0.00 3.67
717 2467 8.703378 AGTATAAGTTACTCCCCACTATGTAC 57.297 38.462 0.00 0.00 0.00 2.90
719 2469 8.509441 ACTAGTATAAGTTACTCCCCACTATGT 58.491 37.037 0.00 0.00 0.00 2.29
722 2472 7.876371 ACACTAGTATAAGTTACTCCCCACTA 58.124 38.462 0.00 0.00 0.00 2.74
724 2474 6.604795 TGACACTAGTATAAGTTACTCCCCAC 59.395 42.308 0.00 0.00 0.00 4.61
725 2475 6.734532 TGACACTAGTATAAGTTACTCCCCA 58.265 40.000 0.00 0.00 0.00 4.96
727 2477 8.235359 ACATGACACTAGTATAAGTTACTCCC 57.765 38.462 0.00 0.00 0.00 4.30
748 2498 4.309933 AGCACCACGATATCATGTACATG 58.690 43.478 26.83 26.83 40.09 3.21
749 2499 4.607293 AGCACCACGATATCATGTACAT 57.393 40.909 1.41 1.41 0.00 2.29
750 2500 4.400529 AAGCACCACGATATCATGTACA 57.599 40.909 0.00 0.00 0.00 2.90
751 2501 7.421530 AATTAAGCACCACGATATCATGTAC 57.578 36.000 3.12 0.00 0.00 2.90
752 2502 9.719355 ATTAATTAAGCACCACGATATCATGTA 57.281 29.630 3.94 0.00 0.00 2.29
817 3323 2.469274 ATCATCGATCATGGAGGTGC 57.531 50.000 0.00 0.00 32.64 5.01
818 3324 5.545588 AGTTTATCATCGATCATGGAGGTG 58.454 41.667 0.00 0.00 32.64 4.00
956 3494 1.071239 CGAGCGAACACAAGACAACAG 60.071 52.381 0.00 0.00 0.00 3.16
995 3533 4.506625 CCGTTGATGGATAATATGGTGGGT 60.507 45.833 0.00 0.00 0.00 4.51
998 3536 4.071423 TGCCGTTGATGGATAATATGGTG 58.929 43.478 0.00 0.00 0.00 4.17
999 3537 4.365514 TGCCGTTGATGGATAATATGGT 57.634 40.909 0.00 0.00 0.00 3.55
1009 3555 2.484062 GCCCTGATGCCGTTGATGG 61.484 63.158 0.00 0.00 0.00 3.51
1017 3564 0.174162 GATTTGTGTGCCCTGATGCC 59.826 55.000 0.00 0.00 0.00 4.40
1024 3571 0.244721 GGAGCTTGATTTGTGTGCCC 59.755 55.000 0.00 0.00 0.00 5.36
1065 3622 3.568007 TGTCACCAAATTTGCAGGTAGTC 59.432 43.478 12.92 1.34 33.49 2.59
1066 3623 3.561143 TGTCACCAAATTTGCAGGTAGT 58.439 40.909 12.92 1.31 33.49 2.73
1067 3624 4.549458 CTTGTCACCAAATTTGCAGGTAG 58.451 43.478 12.92 0.66 33.49 3.18
1086 3649 2.749621 GTTCATCCACCTAGCAACCTTG 59.250 50.000 0.00 0.00 0.00 3.61
1092 3655 2.028112 GTGACTGTTCATCCACCTAGCA 60.028 50.000 0.00 0.00 33.11 3.49
1100 3663 1.272490 TGGTCGAGTGACTGTTCATCC 59.728 52.381 0.00 0.00 44.83 3.51
1107 3670 0.390340 CCACCATGGTCGAGTGACTG 60.390 60.000 16.53 0.00 44.83 3.51
1118 3684 2.185867 CCGACGGTACCACCATGG 59.814 66.667 11.19 11.19 45.02 3.66
1165 3741 3.041940 GGACACGGACACCTTGCG 61.042 66.667 0.00 0.00 46.25 4.85
1401 4013 1.556564 CTGGCGTAATCATCGTCGTT 58.443 50.000 0.00 0.00 35.59 3.85
1637 4271 9.496873 AAAACAATGAATGAATGAACACATGAT 57.503 25.926 0.00 0.00 0.00 2.45
1727 4361 4.801164 AGCCTATTTCAAGGAGATTGCAT 58.199 39.130 0.00 0.00 39.15 3.96
1795 5801 5.277047 CGTCATTCTTGATCAGAGATTCGA 58.723 41.667 0.00 0.00 33.56 3.71
1797 5803 4.210955 GCCGTCATTCTTGATCAGAGATTC 59.789 45.833 0.00 0.00 33.56 2.52
1822 5828 4.215109 GGGTATGATTATGTTGTTGCCCT 58.785 43.478 0.00 0.00 0.00 5.19
1959 5965 1.468054 GGTAGCGTAACCGTGATCGTT 60.468 52.381 0.00 0.00 36.15 3.85
1977 5983 0.904865 TCGGCATCCACTCTTGAGGT 60.905 55.000 2.55 0.00 0.00 3.85
1990 5996 1.888512 ACTTTTCTGCAACATCGGCAT 59.111 42.857 0.00 0.00 41.06 4.40
1995 6001 6.012658 TGTTATGGACTTTTCTGCAACATC 57.987 37.500 0.00 0.00 0.00 3.06
1999 6005 4.379394 GCGATGTTATGGACTTTTCTGCAA 60.379 41.667 0.00 0.00 0.00 4.08
2015 6102 4.751060 TGTCTTATCTTTACGGCGATGTT 58.249 39.130 16.62 0.00 0.00 2.71
2047 6134 6.267928 AGGCCACAAACTATACGAGATATTCT 59.732 38.462 5.01 0.00 0.00 2.40
2048 6135 6.456501 AGGCCACAAACTATACGAGATATTC 58.543 40.000 5.01 0.00 0.00 1.75
2049 6136 6.420913 AGGCCACAAACTATACGAGATATT 57.579 37.500 5.01 0.00 0.00 1.28
2052 6139 4.161565 TCAAGGCCACAAACTATACGAGAT 59.838 41.667 5.01 0.00 0.00 2.75
2061 6148 1.425066 TCCAGATCAAGGCCACAAACT 59.575 47.619 5.01 0.00 0.00 2.66
2107 6194 4.740822 GGCACTGGGGCCGATTGT 62.741 66.667 7.67 0.00 45.40 2.71
2149 6237 1.520600 TTCTCCTGTACAGCGACGCA 61.521 55.000 23.70 0.00 0.00 5.24
2153 6241 3.292492 TCCTATTCTCCTGTACAGCGA 57.708 47.619 17.86 14.34 0.00 4.93
2224 6312 2.277084 GGTACTTAAGTGACATGGCCG 58.723 52.381 18.56 0.00 0.00 6.13
2245 6333 1.066573 CCGCATCCTTTCAGAGACTGT 60.067 52.381 0.00 0.00 32.61 3.55
2251 6339 1.447838 GCGACCGCATCCTTTCAGA 60.448 57.895 9.73 0.00 41.49 3.27
2253 6341 2.215465 TACGCGACCGCATCCTTTCA 62.215 55.000 15.93 0.00 42.06 2.69
2257 6345 0.039437 CTATTACGCGACCGCATCCT 60.039 55.000 15.93 0.00 42.06 3.24
2305 6393 0.829182 CTGTGGAAAGGCCCTTTGCT 60.829 55.000 25.46 0.00 41.30 3.91
2348 6437 2.372264 ACCATGCTTTATGCCAGTCAG 58.628 47.619 0.00 0.00 42.00 3.51
2458 6549 6.756074 CAGAGAGTGACAATTGGACTAGATTC 59.244 42.308 10.83 7.44 0.00 2.52
2515 6606 2.620585 GGCCTTCCATTCTAGACAATGC 59.379 50.000 0.00 0.00 33.08 3.56
2518 6609 2.239654 CAGGGCCTTCCATTCTAGACAA 59.760 50.000 1.32 0.00 38.24 3.18
2523 6614 1.213296 GTCCAGGGCCTTCCATTCTA 58.787 55.000 1.32 0.00 38.24 2.10
2537 6628 4.935808 GGACCCGCTATTAATTATGTCCAG 59.064 45.833 13.21 0.00 40.52 3.86
2594 6685 3.010027 TGGTTGGATAATGAGCCACTCAA 59.990 43.478 0.74 0.00 42.14 3.02
2605 6696 1.214424 CCGAACCCCTGGTTGGATAAT 59.786 52.381 9.27 0.00 46.95 1.28
2609 6700 3.961414 GCCGAACCCCTGGTTGGA 61.961 66.667 9.27 0.00 46.95 3.53
2622 6714 1.414158 TGGAACCCAATTTTTGCCGA 58.586 45.000 0.00 0.00 0.00 5.54
2624 6716 2.710377 GGATGGAACCCAATTTTTGCC 58.290 47.619 0.00 0.00 36.95 4.52
2652 6744 4.007581 TCTAGGGATTCCATCTCCACAA 57.992 45.455 4.80 0.00 34.24 3.33
2661 6753 3.116199 AGGACATCCATCTAGGGATTCCA 60.116 47.826 18.50 0.00 45.42 3.53
2705 6798 0.836400 GGGAGGGTCACAGTTCTGGA 60.836 60.000 4.82 0.00 0.00 3.86
2725 6818 2.281761 CAAGGTGTGCTCCCGCTT 60.282 61.111 0.00 0.00 36.97 4.68
2740 6833 1.909302 CTTTAGGGGTGAGCCTCTCAA 59.091 52.381 0.00 0.00 43.71 3.02


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

AutoCloner maintained by Alex Coulton.