Multiple sequence alignment - TraesCS5A01G343800

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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 TraesCS5A01G343800 chr5A 100.000 3683 0 0 1 3683 548430712 548427030 0.000000e+00 6802.0
1 TraesCS5A01G343800 chr5A 82.212 1085 140 29 1683 2734 548415502 548414438 0.000000e+00 885.0
2 TraesCS5A01G343800 chr5A 86.748 815 53 22 760 1558 548411156 548410381 0.000000e+00 856.0
3 TraesCS5A01G343800 chr5A 85.755 702 58 16 760 1456 548437492 548436828 0.000000e+00 704.0
4 TraesCS5A01G343800 chr5A 83.006 712 65 31 760 1443 548418001 548417318 8.810000e-166 593.0
5 TraesCS5A01G343800 chr5A 81.735 219 30 2 3348 3557 548414267 548414050 1.360000e-39 174.0
6 TraesCS5A01G343800 chr5D 90.769 3629 210 48 1 3557 434442792 434439217 0.000000e+00 4730.0
7 TraesCS5A01G343800 chr5D 90.895 659 35 10 760 1412 434434273 434433634 0.000000e+00 861.0
8 TraesCS5A01G343800 chr5D 89.116 147 15 1 3535 3680 565101118 565101264 8.120000e-42 182.0
9 TraesCS5A01G343800 chr5B 91.892 1517 91 13 1052 2547 527196107 527194602 0.000000e+00 2091.0
10 TraesCS5A01G343800 chr5B 91.446 982 68 8 1576 2547 527155376 527154401 0.000000e+00 1334.0
11 TraesCS5A01G343800 chr5B 93.333 825 37 6 760 1577 527156350 527155537 0.000000e+00 1203.0
12 TraesCS5A01G343800 chr5B 89.605 962 58 13 2607 3557 527154405 527153475 0.000000e+00 1184.0
13 TraesCS5A01G343800 chr5B 89.419 964 57 16 2607 3557 527175440 527174509 0.000000e+00 1173.0
14 TraesCS5A01G343800 chr5B 92.443 741 44 7 2829 3557 527194092 527193352 0.000000e+00 1048.0
15 TraesCS5A01G343800 chr5B 82.075 1311 153 43 1527 2780 527183994 527182709 0.000000e+00 1044.0
16 TraesCS5A01G343800 chr5B 91.478 751 52 4 2818 3557 527144422 527143673 0.000000e+00 1022.0
17 TraesCS5A01G343800 chr5B 84.015 1051 106 38 1527 2547 527176454 527175436 0.000000e+00 953.0
18 TraesCS5A01G343800 chr5B 83.673 1029 119 31 1527 2532 527145713 527144711 0.000000e+00 924.0
19 TraesCS5A01G343800 chr5B 85.333 825 56 27 760 1558 527172443 527171658 0.000000e+00 793.0
20 TraesCS5A01G343800 chr5B 84.830 824 62 23 760 1558 527100227 527099442 0.000000e+00 771.0
21 TraesCS5A01G343800 chr5B 85.490 510 37 17 949 1437 527176964 527176471 7.100000e-137 497.0
22 TraesCS5A01G343800 chr5B 84.510 510 42 15 949 1437 527184504 527184011 1.550000e-128 470.0
23 TraesCS5A01G343800 chr5B 87.714 350 23 11 760 1095 527146535 527146192 1.240000e-104 390.0
24 TraesCS5A01G343800 chr5B 88.820 161 9 3 2607 2767 527194606 527194455 4.860000e-44 189.0
25 TraesCS5A01G343800 chr5B 91.111 90 5 2 2618 2704 527144707 527144618 6.460000e-23 119.0
26 TraesCS5A01G343800 chr2D 92.468 770 50 4 1 763 36578902 36579670 0.000000e+00 1094.0
27 TraesCS5A01G343800 chr2D 92.318 768 52 3 1 762 607135812 607135046 0.000000e+00 1085.0
28 TraesCS5A01G343800 chr1D 92.068 769 52 5 1 762 474020822 474020056 0.000000e+00 1074.0
29 TraesCS5A01G343800 chr1D 91.667 768 57 3 1 762 238647983 238647217 0.000000e+00 1057.0
30 TraesCS5A01G343800 chr1D 91.299 770 56 10 1 762 298440677 298439911 0.000000e+00 1040.0
31 TraesCS5A01G343800 chr1D 91.473 129 11 0 3552 3680 326522483 326522611 1.050000e-40 178.0
32 TraesCS5A01G343800 chr1D 88.710 62 7 0 1948 2009 31691296 31691357 3.940000e-10 76.8
33 TraesCS5A01G343800 chr7A 91.797 768 57 2 1 762 53731721 53730954 0.000000e+00 1064.0
34 TraesCS5A01G343800 chr7A 93.496 123 8 0 3558 3680 30637620 30637498 2.260000e-42 183.0
35 TraesCS5A01G343800 chr2B 91.656 767 57 3 1 762 88914986 88915750 0.000000e+00 1055.0
36 TraesCS5A01G343800 chr6D 91.180 771 61 3 1 764 343618621 343619391 0.000000e+00 1040.0
37 TraesCS5A01G343800 chr6D 88.356 146 13 3 3538 3680 430460239 430460383 4.890000e-39 172.0
38 TraesCS5A01G343800 chr4A 90.979 776 63 3 1 770 600684105 600683331 0.000000e+00 1038.0
39 TraesCS5A01G343800 chr4D 92.308 130 10 0 3551 3680 44218885 44218756 6.280000e-43 185.0
40 TraesCS5A01G343800 chr7D 93.496 123 8 0 3558 3680 588785803 588785925 2.260000e-42 183.0
41 TraesCS5A01G343800 chr7D 92.800 125 9 0 3557 3681 2829840 2829716 8.120000e-42 182.0
42 TraesCS5A01G343800 chr7D 92.126 127 10 0 3557 3683 63805056 63805182 2.920000e-41 180.0
43 TraesCS5A01G343800 chr3D 92.857 126 9 0 3555 3680 566900116 566899991 2.260000e-42 183.0
44 TraesCS5A01G343800 chr3A 94.737 57 3 0 1950 2006 491182090 491182146 5.070000e-14 89.8
45 TraesCS5A01G343800 chr4B 94.286 35 2 0 1899 1933 664392356 664392322 2.000000e-03 54.7


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 TraesCS5A01G343800 chr5A 548427030 548430712 3682 True 6802.000000 6802 100.000000 1 3683 1 chr5A.!!$R1 3682
1 TraesCS5A01G343800 chr5A 548436828 548437492 664 True 704.000000 704 85.755000 760 1456 1 chr5A.!!$R2 696
2 TraesCS5A01G343800 chr5A 548410381 548418001 7620 True 627.000000 885 83.425250 760 3557 4 chr5A.!!$R3 2797
3 TraesCS5A01G343800 chr5D 434439217 434442792 3575 True 4730.000000 4730 90.769000 1 3557 1 chr5D.!!$R2 3556
4 TraesCS5A01G343800 chr5D 434433634 434434273 639 True 861.000000 861 90.895000 760 1412 1 chr5D.!!$R1 652
5 TraesCS5A01G343800 chr5B 527153475 527156350 2875 True 1240.333333 1334 91.461333 760 3557 3 chr5B.!!$R3 2797
6 TraesCS5A01G343800 chr5B 527193352 527196107 2755 True 1109.333333 2091 91.051667 1052 3557 3 chr5B.!!$R6 2505
7 TraesCS5A01G343800 chr5B 527171658 527176964 5306 True 854.000000 1173 86.064250 760 3557 4 chr5B.!!$R4 2797
8 TraesCS5A01G343800 chr5B 527099442 527100227 785 True 771.000000 771 84.830000 760 1558 1 chr5B.!!$R1 798
9 TraesCS5A01G343800 chr5B 527182709 527184504 1795 True 757.000000 1044 83.292500 949 2780 2 chr5B.!!$R5 1831
10 TraesCS5A01G343800 chr5B 527143673 527146535 2862 True 613.750000 1022 88.494000 760 3557 4 chr5B.!!$R2 2797
11 TraesCS5A01G343800 chr2D 36578902 36579670 768 False 1094.000000 1094 92.468000 1 763 1 chr2D.!!$F1 762
12 TraesCS5A01G343800 chr2D 607135046 607135812 766 True 1085.000000 1085 92.318000 1 762 1 chr2D.!!$R1 761
13 TraesCS5A01G343800 chr1D 474020056 474020822 766 True 1074.000000 1074 92.068000 1 762 1 chr1D.!!$R3 761
14 TraesCS5A01G343800 chr1D 238647217 238647983 766 True 1057.000000 1057 91.667000 1 762 1 chr1D.!!$R1 761
15 TraesCS5A01G343800 chr1D 298439911 298440677 766 True 1040.000000 1040 91.299000 1 762 1 chr1D.!!$R2 761
16 TraesCS5A01G343800 chr7A 53730954 53731721 767 True 1064.000000 1064 91.797000 1 762 1 chr7A.!!$R2 761
17 TraesCS5A01G343800 chr2B 88914986 88915750 764 False 1055.000000 1055 91.656000 1 762 1 chr2B.!!$F1 761
18 TraesCS5A01G343800 chr6D 343618621 343619391 770 False 1040.000000 1040 91.180000 1 764 1 chr6D.!!$F1 763
19 TraesCS5A01G343800 chr4A 600683331 600684105 774 True 1038.000000 1038 90.979000 1 770 1 chr4A.!!$R1 769

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
737 745 0.031716 TCCTAGATGCAGAGGCTGGT 60.032 55.0 7.13 0.0 41.91 4.00 F
1330 7621 0.387239 GCGTCCAATGTTTGCAGGTC 60.387 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 9203 0.250513 GAAGATGGACCGGCTGTCTT 59.749 55.0 0.0 6.52 43.89 3.01 R
2698 9300 2.758736 AGCAACACTCCTAGCAAGAG 57.241 50.0 0.0 0.00 37.39 2.85 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
129 131 1.132849 TCTCCTCACTTCACCTTCCCA 60.133 52.381 0.00 0.00 0.00 4.37
135 137 4.030913 CTCACTTCACCTTCCCATAGGTA 58.969 47.826 0.00 0.00 46.80 3.08
217 220 4.947147 AGGCGCCGCTTTGGAACA 62.947 61.111 23.20 0.00 42.00 3.18
250 253 4.217210 CCTTGTGGGTGGTGGGCA 62.217 66.667 0.00 0.00 0.00 5.36
263 266 4.922026 GGGCAACGACGGTGGTGT 62.922 66.667 15.86 0.00 37.60 4.16
333 336 0.904649 TAGGTGGAGGTCGTCGTCTA 59.095 55.000 2.61 0.00 0.00 2.59
392 395 4.125695 GCGTAGGCCGAGGTCGTT 62.126 66.667 7.41 0.00 39.56 3.85
466 469 3.686241 TCAATTTGCTCTGAAGATGGACG 59.314 43.478 0.00 0.00 0.00 4.79
550 553 3.369410 ATGGCTCGGTCGGGGTCTA 62.369 63.158 0.00 0.00 0.00 2.59
639 642 3.763057 TGGATAGAAGTAGCGGCAGATA 58.237 45.455 1.45 0.00 0.00 1.98
643 646 3.393089 AGAAGTAGCGGCAGATATTGG 57.607 47.619 1.45 0.00 0.00 3.16
721 729 2.635787 AATGGCCGCATGCATCTCCT 62.636 55.000 19.57 0.00 43.89 3.69
737 745 0.031716 TCCTAGATGCAGAGGCTGGT 60.032 55.000 7.13 0.00 41.91 4.00
847 6934 1.839354 TGATAGGCTGGTCAGATGCAA 59.161 47.619 0.00 0.00 0.00 4.08
888 6976 4.759693 TCAGGCAAACATTTACTACACCAG 59.240 41.667 0.00 0.00 0.00 4.00
947 7042 2.108566 CAGCCCATCTCCGCTCTG 59.891 66.667 0.00 0.00 31.40 3.35
1008 7117 4.142271 CGAGCAATCTAGTAGATGGATCCC 60.142 50.000 21.81 4.76 37.70 3.85
1184 7455 8.888419 ACATAATCCAGTTCCAGATGAATCTAT 58.112 33.333 0.00 0.00 34.85 1.98
1274 7553 3.824001 TTTCCAGACCCATCCATTTCA 57.176 42.857 0.00 0.00 0.00 2.69
1330 7621 0.387239 GCGTCCAATGTTTGCAGGTC 60.387 55.000 0.00 0.00 0.00 3.85
1680 8151 2.234300 TCCCATTAGCGATTCCGTTC 57.766 50.000 0.00 0.00 38.24 3.95
1769 8243 0.523072 CACCCCATCAAAAGCTCACG 59.477 55.000 0.00 0.00 0.00 4.35
1771 8245 1.247567 CCCCATCAAAAGCTCACGTT 58.752 50.000 0.00 0.00 0.00 3.99
1816 8292 7.273457 TCATTATTTAGTTGGTCCCCACTAA 57.727 36.000 6.03 6.03 30.78 2.24
1817 8293 7.343357 TCATTATTTAGTTGGTCCCCACTAAG 58.657 38.462 9.26 0.75 32.88 2.18
1828 8304 8.683615 GTTGGTCCCCACTAAGATTTATTTTAG 58.316 37.037 0.00 0.03 30.78 1.85
1841 8317 2.109609 ATTTTAGCATGCGCACATCG 57.890 45.000 14.90 2.33 42.27 3.84
1879 8355 2.167075 CCAGCTCATCAAATTTCCACCC 59.833 50.000 0.00 0.00 0.00 4.61
2096 8598 2.722094 AGTGTGGAAAAGTGTTCTGCA 58.278 42.857 0.00 0.00 0.00 4.41
2103 8606 4.278170 TGGAAAAGTGTTCTGCATTGGTAG 59.722 41.667 0.00 0.00 0.00 3.18
2108 8611 3.838317 AGTGTTCTGCATTGGTAGGAGTA 59.162 43.478 0.00 0.00 0.00 2.59
2117 8620 7.290014 TCTGCATTGGTAGGAGTAGATCAATAA 59.710 37.037 0.00 0.00 0.00 1.40
2204 8708 2.201921 TCAGTGTCTAGCTTCCGTCT 57.798 50.000 0.00 0.00 0.00 4.18
2329 8837 8.655970 GTTTATTTGGTTTTGTGCTTGGATATC 58.344 33.333 0.00 0.00 0.00 1.63
2338 8846 4.383173 TGTGCTTGGATATCATAGTGCTG 58.617 43.478 4.83 0.00 0.00 4.41
2368 8876 4.690748 CGCAAGACATGGAAGAAGAAGTTA 59.309 41.667 0.00 0.00 43.02 2.24
2372 8880 8.897752 GCAAGACATGGAAGAAGAAGTTAATAT 58.102 33.333 0.00 0.00 0.00 1.28
2376 8884 8.218338 ACATGGAAGAAGAAGTTAATATGCTG 57.782 34.615 0.00 0.00 0.00 4.41
2512 9023 0.834261 TGCACACCCAGGCTGTACTA 60.834 55.000 14.43 0.00 0.00 1.82
2537 9048 2.730090 GCTTGCATCACATGAAGAACCG 60.730 50.000 0.00 0.00 0.00 4.44
2556 9154 1.737793 CGCCCTGAACACTTACATTCC 59.262 52.381 0.00 0.00 0.00 3.01
2587 9185 1.473258 AGCTAGCACTCTCAGGTCTG 58.527 55.000 18.83 0.00 0.00 3.51
2605 9203 2.041755 TCTGAAGCTGTAGACTGGGAGA 59.958 50.000 0.00 0.00 0.00 3.71
2698 9300 3.545078 CGCTTAGCTCATTTTGACATTGC 59.455 43.478 1.76 0.00 0.00 3.56
2700 9304 4.797349 GCTTAGCTCATTTTGACATTGCTC 59.203 41.667 0.00 0.00 28.99 4.26
2810 9427 2.381752 CCCCCTTGTTTCTCCTTGTT 57.618 50.000 0.00 0.00 0.00 2.83
2811 9428 2.677914 CCCCCTTGTTTCTCCTTGTTT 58.322 47.619 0.00 0.00 0.00 2.83
2812 9429 2.628178 CCCCCTTGTTTCTCCTTGTTTC 59.372 50.000 0.00 0.00 0.00 2.78
2866 9785 7.388437 AGTACTTCGTAATGGTTCCAACATTA 58.612 34.615 0.00 0.00 39.18 1.90
2950 9873 4.644234 TCATTTGTGTTGTGGTGTCTCATT 59.356 37.500 0.00 0.00 0.00 2.57
3018 9941 4.162320 TCCGCATATTCTTCTTCCTGAACT 59.838 41.667 0.00 0.00 0.00 3.01
3044 9967 3.290710 GCCATGTGGGTCATATTCAACT 58.709 45.455 0.54 0.00 39.65 3.16
3045 9968 4.080072 TGCCATGTGGGTCATATTCAACTA 60.080 41.667 0.54 0.00 39.65 2.24
3052 9975 7.653647 TGTGGGTCATATTCAACTAAACAAAC 58.346 34.615 0.00 0.00 0.00 2.93
3061 9985 9.979578 ATATTCAACTAAACAAACAATGCTTCA 57.020 25.926 0.00 0.00 0.00 3.02
3080 10004 8.065473 TGCTTCATGTCCAATATAACAATGTT 57.935 30.769 3.43 3.43 0.00 2.71
3187 10111 8.457238 AAATCATAGCTATGGAAGAAACTTCC 57.543 34.615 29.02 19.74 39.03 3.46
3199 10123 5.453567 AAGAAACTTCCCAACAAGCATAC 57.546 39.130 0.00 0.00 0.00 2.39
3272 10197 7.766283 TCATAATCATATTGGAAAACGCACAA 58.234 30.769 0.00 0.00 0.00 3.33
3282 10207 4.944317 TGGAAAACGCACAACCATATATGA 59.056 37.500 14.54 0.00 0.00 2.15
3356 10281 3.716601 ACTATTGCTTTGTTGGTTGTGC 58.283 40.909 0.00 0.00 0.00 4.57
3384 10309 5.182190 TGCCGTTGCAAGTATTAGATTCAAA 59.818 36.000 0.00 0.00 46.66 2.69
3408 10333 1.319541 TATTCTCGCCTCCCTCTTCG 58.680 55.000 0.00 0.00 0.00 3.79
3419 10344 1.268899 TCCCTCTTCGAAACGAGTCAC 59.731 52.381 12.02 0.00 37.14 3.67
3440 10365 1.618343 GGGGTTGCAAAGCACTATGTT 59.382 47.619 0.00 0.00 46.08 2.71
3494 10419 2.496871 CCAGCTCAAATAAACATGGCCA 59.503 45.455 8.56 8.56 0.00 5.36
3572 10506 9.653287 TGGATAACATTCACTAGTAGAAAACAG 57.347 33.333 3.59 5.73 0.00 3.16
3573 10507 9.099454 GGATAACATTCACTAGTAGAAAACAGG 57.901 37.037 3.59 3.79 0.00 4.00
3574 10508 9.654663 GATAACATTCACTAGTAGAAAACAGGT 57.345 33.333 3.59 4.86 0.00 4.00
3575 10509 7.964604 AACATTCACTAGTAGAAAACAGGTC 57.035 36.000 3.59 0.00 0.00 3.85
3576 10510 7.304497 ACATTCACTAGTAGAAAACAGGTCT 57.696 36.000 3.59 0.00 0.00 3.85
3577 10511 7.736893 ACATTCACTAGTAGAAAACAGGTCTT 58.263 34.615 3.59 0.00 0.00 3.01
3578 10512 7.873505 ACATTCACTAGTAGAAAACAGGTCTTC 59.126 37.037 3.59 0.00 0.00 2.87
3580 10514 5.766670 TCACTAGTAGAAAACAGGTCTTCGA 59.233 40.000 3.59 0.00 0.00 3.71
3581 10515 6.433404 TCACTAGTAGAAAACAGGTCTTCGAT 59.567 38.462 3.59 0.00 0.00 3.59
3582 10516 6.748198 CACTAGTAGAAAACAGGTCTTCGATC 59.252 42.308 3.59 0.00 0.00 3.69
3583 10517 5.723672 AGTAGAAAACAGGTCTTCGATCA 57.276 39.130 0.00 0.00 0.00 2.92
3584 10518 5.471257 AGTAGAAAACAGGTCTTCGATCAC 58.529 41.667 0.00 0.00 0.00 3.06
3585 10519 4.336889 AGAAAACAGGTCTTCGATCACA 57.663 40.909 0.00 0.00 0.00 3.58
3587 10521 4.511826 AGAAAACAGGTCTTCGATCACAAC 59.488 41.667 0.00 0.00 0.00 3.32
3588 10522 2.065993 ACAGGTCTTCGATCACAACG 57.934 50.000 0.00 0.00 0.00 4.10
3589 10523 0.716108 CAGGTCTTCGATCACAACGC 59.284 55.000 0.00 0.00 0.00 4.84
3593 11441 2.927477 GGTCTTCGATCACAACGCAATA 59.073 45.455 0.00 0.00 0.00 1.90
3596 11444 5.332355 GGTCTTCGATCACAACGCAATATAC 60.332 44.000 0.00 0.00 0.00 1.47
3604 11452 8.860128 CGATCACAACGCAATATACATATTAGT 58.140 33.333 0.00 0.00 32.05 2.24
3606 11454 8.528917 TCACAACGCAATATACATATTAGTCC 57.471 34.615 0.00 0.00 32.05 3.85
3607 11455 8.364894 TCACAACGCAATATACATATTAGTCCT 58.635 33.333 0.00 0.00 32.05 3.85
3608 11456 8.435430 CACAACGCAATATACATATTAGTCCTG 58.565 37.037 0.00 0.00 32.05 3.86
3609 11457 7.602644 ACAACGCAATATACATATTAGTCCTGG 59.397 37.037 0.00 0.00 32.05 4.45
3610 11458 7.241042 ACGCAATATACATATTAGTCCTGGT 57.759 36.000 0.00 0.00 32.05 4.00
3612 11460 7.602644 ACGCAATATACATATTAGTCCTGGTTG 59.397 37.037 0.00 0.00 32.05 3.77
3613 11461 7.413000 CGCAATATACATATTAGTCCTGGTTGC 60.413 40.741 0.00 0.00 32.05 4.17
3614 11462 7.390440 GCAATATACATATTAGTCCTGGTTGCA 59.610 37.037 0.00 0.00 36.61 4.08
3615 11463 9.453572 CAATATACATATTAGTCCTGGTTGCAT 57.546 33.333 0.00 0.00 32.05 3.96
3618 11466 8.848474 ATACATATTAGTCCTGGTTGCATTAC 57.152 34.615 0.00 0.00 0.00 1.89
3619 11467 5.758296 ACATATTAGTCCTGGTTGCATTACG 59.242 40.000 0.00 0.00 0.00 3.18
3622 11470 2.423577 AGTCCTGGTTGCATTACGAAC 58.576 47.619 0.00 0.00 0.00 3.95
3623 11471 1.467342 GTCCTGGTTGCATTACGAACC 59.533 52.381 0.00 0.00 41.85 3.62
3624 11472 0.446222 CCTGGTTGCATTACGAACCG 59.554 55.000 0.00 0.00 44.04 4.44
3625 11473 0.446222 CTGGTTGCATTACGAACCGG 59.554 55.000 0.00 0.00 44.04 5.28
3626 11474 0.956410 TGGTTGCATTACGAACCGGG 60.956 55.000 6.32 0.00 44.04 5.73
3627 11475 0.674269 GGTTGCATTACGAACCGGGA 60.674 55.000 6.32 0.00 32.66 5.14
3628 11476 0.445043 GTTGCATTACGAACCGGGAC 59.555 55.000 6.32 0.00 0.00 4.46
3631 11479 1.549620 TGCATTACGAACCGGGACTAA 59.450 47.619 6.32 0.00 0.00 2.24
3633 11481 2.542595 GCATTACGAACCGGGACTAATG 59.457 50.000 6.32 11.95 0.00 1.90
3634 11482 3.788937 CATTACGAACCGGGACTAATGT 58.211 45.455 6.32 0.00 0.00 2.71
3635 11483 2.945447 TACGAACCGGGACTAATGTG 57.055 50.000 6.32 0.00 0.00 3.21
3637 11485 1.203994 ACGAACCGGGACTAATGTGAG 59.796 52.381 6.32 0.00 0.00 3.51
3639 11487 0.981183 AACCGGGACTAATGTGAGCA 59.019 50.000 6.32 0.00 0.00 4.26
3641 11489 1.559682 ACCGGGACTAATGTGAGCATT 59.440 47.619 6.32 0.00 46.14 3.56
3649 11497 2.332063 AATGTGAGCATTAGTCCCGG 57.668 50.000 0.00 0.00 42.96 5.73
3651 11499 0.981183 TGTGAGCATTAGTCCCGGTT 59.019 50.000 0.00 0.00 0.00 4.44
3652 11500 1.066430 TGTGAGCATTAGTCCCGGTTC 60.066 52.381 0.00 0.00 0.00 3.62
3653 11501 0.174845 TGAGCATTAGTCCCGGTTCG 59.825 55.000 0.00 0.00 0.00 3.95
3655 11503 0.460311 AGCATTAGTCCCGGTTCGAG 59.540 55.000 0.00 0.00 0.00 4.04
3656 11504 0.175073 GCATTAGTCCCGGTTCGAGT 59.825 55.000 0.00 0.00 0.00 4.18
3657 11505 1.922570 CATTAGTCCCGGTTCGAGTG 58.077 55.000 0.00 0.00 0.00 3.51
3658 11506 1.475280 CATTAGTCCCGGTTCGAGTGA 59.525 52.381 0.00 0.00 0.00 3.41
3659 11507 0.883833 TTAGTCCCGGTTCGAGTGAC 59.116 55.000 0.00 0.00 0.00 3.67
3660 11508 0.037303 TAGTCCCGGTTCGAGTGACT 59.963 55.000 11.29 11.29 39.47 3.41
3661 11509 0.037303 AGTCCCGGTTCGAGTGACTA 59.963 55.000 0.00 0.00 34.68 2.59
3662 11510 0.883833 GTCCCGGTTCGAGTGACTAA 59.116 55.000 0.00 0.00 0.00 2.24
3664 11512 1.542915 TCCCGGTTCGAGTGACTAAAG 59.457 52.381 0.00 0.00 0.00 1.85
3666 11514 1.347320 CGGTTCGAGTGACTAAAGGC 58.653 55.000 0.00 0.00 0.00 4.35
3669 11517 3.335579 GGTTCGAGTGACTAAAGGCATT 58.664 45.455 0.00 0.00 0.00 3.56
3670 11518 4.501071 GGTTCGAGTGACTAAAGGCATTA 58.499 43.478 0.00 0.00 0.00 1.90
3679 11527 3.277142 CTAAAGGCATTAGTCCCGGTT 57.723 47.619 0.00 0.00 36.94 4.44
3680 11528 2.597578 AAAGGCATTAGTCCCGGTTT 57.402 45.000 0.00 0.00 0.00 3.27
3681 11529 1.834188 AAGGCATTAGTCCCGGTTTG 58.166 50.000 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 220 4.330960 GGGCCACCCAACCCCAAT 62.331 66.667 4.39 0.00 44.65 3.16
250 253 4.922026 GGCCACACCACCGTCGTT 62.922 66.667 0.00 0.00 38.86 3.85
263 266 2.377810 CCATGCTAGGACAGGGCCA 61.378 63.158 6.18 0.00 34.27 5.36
270 273 3.391049 GGACGTAAATCCATGCTAGGAC 58.609 50.000 0.00 0.00 41.30 3.85
382 385 2.943653 GCCAAACAACGACCTCGG 59.056 61.111 0.00 0.00 44.95 4.63
383 386 1.768112 AACGCCAAACAACGACCTCG 61.768 55.000 0.00 0.00 46.33 4.63
392 395 3.069980 GCCACCACAACGCCAAACA 62.070 57.895 0.00 0.00 0.00 2.83
449 452 1.895798 ACTCGTCCATCTTCAGAGCAA 59.104 47.619 0.00 0.00 32.60 3.91
466 469 2.892425 CGCCGCCATCTTCCACTC 60.892 66.667 0.00 0.00 0.00 3.51
550 553 3.629142 AAGCCTAACATCTAAAGCCGT 57.371 42.857 0.00 0.00 0.00 5.68
639 642 1.035139 GAATCCGCCATCTTGCCAAT 58.965 50.000 0.00 0.00 0.00 3.16
643 646 2.028130 CCTGAATCCGCCATCTTGC 58.972 57.895 0.00 0.00 0.00 4.01
721 729 0.618680 ACCACCAGCCTCTGCATCTA 60.619 55.000 0.00 0.00 41.13 1.98
847 6934 1.533711 AGTTGGCAAGGTGACAGCT 59.466 52.632 0.00 0.07 42.39 4.24
888 6976 6.201044 CGTGGCCTATGCTGTTTATATATAGC 59.799 42.308 3.32 5.21 37.74 2.97
947 7042 3.161866 AGATCCGAGGAGAAAGATAGCC 58.838 50.000 0.00 0.00 0.00 3.93
1008 7117 2.765807 ATGGCAGGGGAGGACGAG 60.766 66.667 0.00 0.00 0.00 4.18
1029 7138 3.920093 GGCTTGCTTGGTAGCCGGT 62.920 63.158 1.90 0.00 46.65 5.28
1184 7455 5.413833 CAGGTGTTTCTACTTACCTCTACGA 59.586 44.000 0.00 0.00 41.42 3.43
1282 7569 7.306213 TGCACGTTAAATTCCAAATCGAAATA 58.694 30.769 0.00 0.00 0.00 1.40
1285 7572 5.109662 TGCACGTTAAATTCCAAATCGAA 57.890 34.783 0.00 0.00 0.00 3.71
1549 7854 7.969536 ATAGTTAAAGCAGACGATTATGCAT 57.030 32.000 3.79 3.79 45.01 3.96
1592 8062 5.482878 AGGGACAGCTCAAAATTCAATGATT 59.517 36.000 0.00 0.00 0.00 2.57
1703 8174 6.879458 AGTAGAAGTTGTGTGGATCAATTACC 59.121 38.462 0.00 0.00 0.00 2.85
1717 8188 9.672673 ATGCATGTTTAGATAAGTAGAAGTTGT 57.327 29.630 0.00 0.00 0.00 3.32
1754 8228 3.185594 TCGTTAACGTGAGCTTTTGATGG 59.814 43.478 25.98 0.00 40.80 3.51
1816 8292 5.247507 TGTGCGCATGCTAAAATAAATCT 57.752 34.783 15.91 0.00 43.34 2.40
1817 8293 5.164254 CGATGTGCGCATGCTAAAATAAATC 60.164 40.000 19.33 6.99 43.34 2.17
1841 8317 2.797087 GCTGGCATGTGTAATGTGATGC 60.797 50.000 0.00 0.00 40.44 3.91
1846 8322 2.495155 TGAGCTGGCATGTGTAATGT 57.505 45.000 0.00 0.00 0.00 2.71
2096 8598 9.315363 CCTACTTATTGATCTACTCCTACCAAT 57.685 37.037 0.00 0.00 0.00 3.16
2103 8606 9.474313 AGATGATCCTACTTATTGATCTACTCC 57.526 37.037 0.00 0.00 36.65 3.85
2159 8662 8.728088 AATTAATTAGCAACTCGTTGTTTCTG 57.272 30.769 11.05 0.00 42.31 3.02
2245 8751 3.123050 CAAACACCAAAGCTAAAGTGCC 58.877 45.455 9.22 0.00 33.46 5.01
2338 8846 1.372582 TCCATGTCTTGCGCTTCATC 58.627 50.000 9.73 0.00 0.00 2.92
2368 8876 3.941483 CCTTCTTCGTTGTCCAGCATATT 59.059 43.478 0.00 0.00 0.00 1.28
2372 8880 0.756294 TCCTTCTTCGTTGTCCAGCA 59.244 50.000 0.00 0.00 0.00 4.41
2376 8884 3.594603 TCATCTCCTTCTTCGTTGTCC 57.405 47.619 0.00 0.00 0.00 4.02
2537 9048 2.790433 TGGAATGTAAGTGTTCAGGGC 58.210 47.619 0.00 0.00 0.00 5.19
2587 9185 3.093057 TCTTCTCCCAGTCTACAGCTTC 58.907 50.000 0.00 0.00 0.00 3.86
2598 9196 2.232298 GACCGGCTGTCTTCTCCCAG 62.232 65.000 0.00 0.00 41.03 4.45
2605 9203 0.250513 GAAGATGGACCGGCTGTCTT 59.749 55.000 0.00 6.52 43.89 3.01
2698 9300 2.758736 AGCAACACTCCTAGCAAGAG 57.241 50.000 0.00 0.00 37.39 2.85
2700 9304 3.051081 AGAAGCAACACTCCTAGCAAG 57.949 47.619 0.00 0.00 0.00 4.01
2866 9785 7.823665 TCGTTGTTGTCTGTACTAGTAATGAT 58.176 34.615 3.61 0.00 0.00 2.45
2950 9873 6.208007 TGGAGAGTCGTAAATCTCTGTTTACA 59.792 38.462 9.39 0.00 42.10 2.41
3044 9967 6.154203 TGGACATGAAGCATTGTTTGTTTA 57.846 33.333 0.00 0.00 0.00 2.01
3045 9968 5.021033 TGGACATGAAGCATTGTTTGTTT 57.979 34.783 0.00 0.00 0.00 2.83
3052 9975 8.974408 CATTGTTATATTGGACATGAAGCATTG 58.026 33.333 0.00 0.00 0.00 2.82
3130 10054 7.672240 TGTTATATATTGGCCGAGAACATACA 58.328 34.615 0.00 0.00 0.00 2.29
3176 10100 4.590850 ATGCTTGTTGGGAAGTTTCTTC 57.409 40.909 1.39 1.39 0.00 2.87
3187 10111 5.991328 ACGATCTTATGTATGCTTGTTGG 57.009 39.130 0.00 0.00 0.00 3.77
3199 10123 8.031864 ACTTTCATAGATGGCTACGATCTTATG 58.968 37.037 0.00 1.78 32.32 1.90
3259 10184 4.944317 TCATATATGGTTGTGCGTTTTCCA 59.056 37.500 12.78 0.00 0.00 3.53
3266 10191 4.221342 GCATGTTCATATATGGTTGTGCG 58.779 43.478 12.78 0.00 0.00 5.34
3267 10192 4.037803 TGGCATGTTCATATATGGTTGTGC 59.962 41.667 12.78 15.94 0.00 4.57
3384 10309 4.120946 AGAGGGAGGCGAGAATAATAGT 57.879 45.455 0.00 0.00 0.00 2.12
3408 10333 1.838568 GCAACCCCGTGACTCGTTTC 61.839 60.000 0.00 0.00 37.94 2.78
3419 10344 0.171007 CATAGTGCTTTGCAACCCCG 59.829 55.000 0.00 0.00 41.47 5.73
3440 10365 2.787339 TACTCTATTGGGCTAGGGCA 57.213 50.000 0.00 0.00 40.87 5.36
3557 10491 6.010294 TCGAAGACCTGTTTTCTACTAGTG 57.990 41.667 5.39 0.00 0.00 2.74
3558 10492 6.433404 TGATCGAAGACCTGTTTTCTACTAGT 59.567 38.462 0.00 0.00 42.51 2.57
3559 10493 6.748198 GTGATCGAAGACCTGTTTTCTACTAG 59.252 42.308 0.00 0.00 42.51 2.57
3560 10494 6.208007 TGTGATCGAAGACCTGTTTTCTACTA 59.792 38.462 0.00 0.00 42.51 1.82
3563 10497 5.462530 TGTGATCGAAGACCTGTTTTCTA 57.537 39.130 0.00 0.00 42.51 2.10
3564 10498 4.336889 TGTGATCGAAGACCTGTTTTCT 57.663 40.909 0.00 0.00 42.51 2.52
3565 10499 4.608445 CGTTGTGATCGAAGACCTGTTTTC 60.608 45.833 0.00 0.00 42.51 2.29
3566 10500 3.247648 CGTTGTGATCGAAGACCTGTTTT 59.752 43.478 0.00 0.00 42.51 2.43
3567 10501 2.800544 CGTTGTGATCGAAGACCTGTTT 59.199 45.455 0.00 0.00 42.51 2.83
3568 10502 2.404215 CGTTGTGATCGAAGACCTGTT 58.596 47.619 0.00 0.00 42.51 3.16
3569 10503 1.935300 GCGTTGTGATCGAAGACCTGT 60.935 52.381 0.00 0.00 42.51 4.00
3570 10504 0.716108 GCGTTGTGATCGAAGACCTG 59.284 55.000 0.00 0.00 42.51 4.00
3572 10506 1.144969 TTGCGTTGTGATCGAAGACC 58.855 50.000 0.00 0.00 42.51 3.85
3573 10507 4.778842 ATATTGCGTTGTGATCGAAGAC 57.221 40.909 0.00 0.00 42.51 3.01
3574 10508 5.344884 TGTATATTGCGTTGTGATCGAAGA 58.655 37.500 0.00 0.00 45.75 2.87
3575 10509 5.635549 TGTATATTGCGTTGTGATCGAAG 57.364 39.130 0.00 0.00 0.00 3.79
3576 10510 7.883229 ATATGTATATTGCGTTGTGATCGAA 57.117 32.000 0.00 0.00 0.00 3.71
3577 10511 7.883229 AATATGTATATTGCGTTGTGATCGA 57.117 32.000 0.00 0.00 32.07 3.59
3578 10512 8.860128 ACTAATATGTATATTGCGTTGTGATCG 58.140 33.333 7.25 0.00 34.91 3.69
3580 10514 9.151471 GGACTAATATGTATATTGCGTTGTGAT 57.849 33.333 7.25 0.00 34.91 3.06
3581 10515 8.364894 AGGACTAATATGTATATTGCGTTGTGA 58.635 33.333 7.25 0.00 34.91 3.58
3582 10516 8.435430 CAGGACTAATATGTATATTGCGTTGTG 58.565 37.037 7.25 3.79 34.91 3.33
3583 10517 7.602644 CCAGGACTAATATGTATATTGCGTTGT 59.397 37.037 7.25 0.49 34.91 3.32
3584 10518 7.602644 ACCAGGACTAATATGTATATTGCGTTG 59.397 37.037 7.25 2.52 34.91 4.10
3585 10519 7.676947 ACCAGGACTAATATGTATATTGCGTT 58.323 34.615 7.25 0.00 34.91 4.84
3587 10521 7.413000 GCAACCAGGACTAATATGTATATTGCG 60.413 40.741 7.25 2.26 34.91 4.85
3588 10522 7.390440 TGCAACCAGGACTAATATGTATATTGC 59.610 37.037 7.25 0.00 34.91 3.56
3589 10523 8.846943 TGCAACCAGGACTAATATGTATATTG 57.153 34.615 7.25 1.68 34.91 1.90
3593 11441 7.602644 CGTAATGCAACCAGGACTAATATGTAT 59.397 37.037 0.00 0.00 0.00 2.29
3596 11444 5.989168 TCGTAATGCAACCAGGACTAATATG 59.011 40.000 0.00 0.00 0.00 1.78
3604 11452 1.816074 GGTTCGTAATGCAACCAGGA 58.184 50.000 0.00 0.00 41.65 3.86
3605 11453 0.446222 CGGTTCGTAATGCAACCAGG 59.554 55.000 4.00 0.00 42.07 4.45
3606 11454 0.446222 CCGGTTCGTAATGCAACCAG 59.554 55.000 4.00 0.00 42.07 4.00
3607 11455 0.956410 CCCGGTTCGTAATGCAACCA 60.956 55.000 0.00 0.00 42.07 3.67
3608 11456 0.674269 TCCCGGTTCGTAATGCAACC 60.674 55.000 0.00 0.00 39.04 3.77
3609 11457 0.445043 GTCCCGGTTCGTAATGCAAC 59.555 55.000 0.00 0.00 0.00 4.17
3610 11458 0.322322 AGTCCCGGTTCGTAATGCAA 59.678 50.000 0.00 0.00 0.00 4.08
3612 11460 2.298411 TTAGTCCCGGTTCGTAATGC 57.702 50.000 0.00 0.00 0.00 3.56
3613 11461 3.554324 CACATTAGTCCCGGTTCGTAATG 59.446 47.826 15.97 15.97 37.20 1.90
3614 11462 3.448301 TCACATTAGTCCCGGTTCGTAAT 59.552 43.478 0.00 0.00 0.00 1.89
3615 11463 2.824936 TCACATTAGTCCCGGTTCGTAA 59.175 45.455 0.00 0.00 0.00 3.18
3617 11465 1.203994 CTCACATTAGTCCCGGTTCGT 59.796 52.381 0.00 0.00 0.00 3.85
3618 11466 1.922570 CTCACATTAGTCCCGGTTCG 58.077 55.000 0.00 0.00 0.00 3.95
3619 11467 1.066430 TGCTCACATTAGTCCCGGTTC 60.066 52.381 0.00 0.00 0.00 3.62
3622 11470 2.332063 AATGCTCACATTAGTCCCGG 57.668 50.000 0.00 0.00 44.78 5.73
3631 11479 1.204146 ACCGGGACTAATGCTCACAT 58.796 50.000 6.32 0.00 38.49 3.21
3633 11481 1.653151 GAACCGGGACTAATGCTCAC 58.347 55.000 6.32 0.00 0.00 3.51
3634 11482 0.174845 CGAACCGGGACTAATGCTCA 59.825 55.000 6.32 0.00 0.00 4.26
3635 11483 0.458669 TCGAACCGGGACTAATGCTC 59.541 55.000 6.32 0.00 0.00 4.26
3637 11485 0.175073 ACTCGAACCGGGACTAATGC 59.825 55.000 6.32 0.00 0.00 3.56
3639 11487 1.475682 GTCACTCGAACCGGGACTAAT 59.524 52.381 6.32 0.00 0.00 1.73
3641 11489 0.037303 AGTCACTCGAACCGGGACTA 59.963 55.000 6.32 0.00 37.08 2.59
3643 11491 0.883833 TTAGTCACTCGAACCGGGAC 59.116 55.000 6.32 0.83 0.00 4.46
3644 11492 1.542915 CTTTAGTCACTCGAACCGGGA 59.457 52.381 6.32 0.00 0.00 5.14
3645 11493 1.403780 CCTTTAGTCACTCGAACCGGG 60.404 57.143 6.32 0.00 0.00 5.73
3647 11495 1.336517 TGCCTTTAGTCACTCGAACCG 60.337 52.381 0.00 0.00 0.00 4.44
3648 11496 2.450609 TGCCTTTAGTCACTCGAACC 57.549 50.000 0.00 0.00 0.00 3.62
3649 11497 5.169295 ACTAATGCCTTTAGTCACTCGAAC 58.831 41.667 3.91 0.00 46.04 3.95
3659 11507 3.277142 AACCGGGACTAATGCCTTTAG 57.723 47.619 6.32 2.80 42.62 1.85
3660 11508 3.009253 TCAAACCGGGACTAATGCCTTTA 59.991 43.478 6.32 0.00 33.05 1.85
3661 11509 2.167662 CAAACCGGGACTAATGCCTTT 58.832 47.619 6.32 0.00 33.05 3.11
3662 11510 1.353022 TCAAACCGGGACTAATGCCTT 59.647 47.619 6.32 0.00 33.05 4.35
3664 11512 3.562397 TCAAACCGGGACTAATGCC 57.438 52.632 6.32 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.