Multiple sequence alignment - TraesCS4A01G304200

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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 TraesCS4A01G304200 chr4A 100.000 4783 0 0 1 4783 599647362 599642580 0.000000e+00 8833
1 TraesCS4A01G304200 chr4A 73.231 1498 288 64 1275 2756 599628296 599629696 1.580000e-119 440
2 TraesCS4A01G304200 chr4A 79.554 538 98 11 64 592 600279848 600280382 1.630000e-99 374
3 TraesCS4A01G304200 chr4D 93.303 4808 230 30 1 4778 4245830 4250575 0.000000e+00 7011
4 TraesCS4A01G304200 chr4D 86.056 1714 158 31 128 1809 4287940 4286276 0.000000e+00 1766
5 TraesCS4A01G304200 chr4D 88.677 1051 82 20 2930 3965 4285342 4284314 0.000000e+00 1247
6 TraesCS4A01G304200 chr4D 78.182 1265 210 42 2849 4088 4273340 4272117 0.000000e+00 747
7 TraesCS4A01G304200 chr4D 85.804 634 57 16 982 1606 4333066 4332457 4.040000e-180 641
8 TraesCS4A01G304200 chr4D 88.755 498 44 6 1602 2090 4331976 4331482 2.460000e-167 599
9 TraesCS4A01G304200 chr4D 82.167 600 75 21 1950 2537 4286231 4285652 2.000000e-133 486
10 TraesCS4A01G304200 chr4D 90.171 234 21 1 2541 2772 4285620 4285387 2.160000e-78 303
11 TraesCS4A01G304200 chr4D 73.188 869 164 43 1908 2756 4274308 4273489 2.860000e-62 250
12 TraesCS4A01G304200 chr4B 92.074 3722 221 23 5 3710 4334275 4330612 0.000000e+00 5171
13 TraesCS4A01G304200 chr4B 91.967 2577 165 21 1902 4460 4301749 4299197 0.000000e+00 3574
14 TraesCS4A01G304200 chr4B 90.632 918 70 6 4 913 4303224 4302315 0.000000e+00 1205
15 TraesCS4A01G304200 chr4B 89.631 704 63 6 3765 4460 4330585 4329884 0.000000e+00 887
16 TraesCS4A01G304200 chr4B 93.717 573 33 2 1300 1871 4302320 4301750 0.000000e+00 856
17 TraesCS4A01G304200 chr4B 88.450 329 36 2 4455 4783 4287631 4287305 3.470000e-106 396
18 TraesCS4A01G304200 chr4B 80.723 166 25 7 4624 4783 328144491 328144655 6.500000e-24 122
19 TraesCS4A01G304200 chr4B 76.263 198 40 5 2549 2744 7501243 7501435 1.100000e-16 99
20 TraesCS4A01G304200 chr5A 82.609 713 100 9 1077 1784 555596464 555595771 4.090000e-170 608
21 TraesCS4A01G304200 chr5D 81.476 718 110 12 1071 1783 439980435 439979736 6.950000e-158 568
22 TraesCS4A01G304200 chr5D 82.895 228 30 9 4555 4778 228558865 228558643 3.780000e-46 196
23 TraesCS4A01G304200 chr5D 78.776 245 39 11 4541 4778 530777004 530777242 8.290000e-33 152
24 TraesCS4A01G304200 chr5D 77.523 218 38 8 4570 4783 3685493 3685703 2.340000e-23 121
25 TraesCS4A01G304200 chr5B 82.643 628 88 9 1184 1806 534487935 534487324 1.960000e-148 536
26 TraesCS4A01G304200 chr5B 78.408 741 101 21 1071 1806 534589618 534588932 1.230000e-115 427
27 TraesCS4A01G304200 chr5B 79.935 309 47 8 1071 1373 534605452 534605153 3.750000e-51 213
28 TraesCS4A01G304200 chrUn 73.231 1498 288 64 1275 2756 47346710 47348110 1.580000e-119 440
29 TraesCS4A01G304200 chr3D 86.826 167 13 4 872 1030 542140147 542140312 1.370000e-40 178
30 TraesCS4A01G304200 chr3D 86.624 157 13 3 872 1020 542132283 542132439 2.960000e-37 167
31 TraesCS4A01G304200 chr3D 85.030 167 16 4 872 1030 542143788 542143953 1.380000e-35 161
32 TraesCS4A01G304200 chr3D 88.462 130 10 3 905 1030 542136543 542136671 8.290000e-33 152
33 TraesCS4A01G304200 chr3D 77.406 239 45 8 4544 4778 191565852 191566085 3.000000e-27 134
34 TraesCS4A01G304200 chr3A 87.421 159 12 3 872 1022 678379032 678379190 4.920000e-40 176
35 TraesCS4A01G304200 chr3A 76.987 239 44 9 4544 4778 267050403 267050634 5.030000e-25 126
36 TraesCS4A01G304200 chr3B 85.629 167 15 4 872 1030 717689044 717689209 2.960000e-37 167
37 TraesCS4A01G304200 chr2D 78.481 237 43 8 4544 4778 472020066 472020296 1.070000e-31 148
38 TraesCS4A01G304200 chr1B 75.962 208 47 1 2549 2756 46226863 46227067 2.350000e-18 104


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 TraesCS4A01G304200 chr4A 599642580 599647362 4782 True 8833.000000 8833 100.000000 1 4783 1 chr4A.!!$R1 4782
1 TraesCS4A01G304200 chr4A 599628296 599629696 1400 False 440.000000 440 73.231000 1275 2756 1 chr4A.!!$F1 1481
2 TraesCS4A01G304200 chr4A 600279848 600280382 534 False 374.000000 374 79.554000 64 592 1 chr4A.!!$F2 528
3 TraesCS4A01G304200 chr4D 4245830 4250575 4745 False 7011.000000 7011 93.303000 1 4778 1 chr4D.!!$F1 4777
4 TraesCS4A01G304200 chr4D 4284314 4287940 3626 True 950.500000 1766 86.767750 128 3965 4 chr4D.!!$R2 3837
5 TraesCS4A01G304200 chr4D 4331482 4333066 1584 True 620.000000 641 87.279500 982 2090 2 chr4D.!!$R3 1108
6 TraesCS4A01G304200 chr4D 4272117 4274308 2191 True 498.500000 747 75.685000 1908 4088 2 chr4D.!!$R1 2180
7 TraesCS4A01G304200 chr4B 4329884 4334275 4391 True 3029.000000 5171 90.852500 5 4460 2 chr4B.!!$R3 4455
8 TraesCS4A01G304200 chr4B 4299197 4303224 4027 True 1878.333333 3574 92.105333 4 4460 3 chr4B.!!$R2 4456
9 TraesCS4A01G304200 chr5A 555595771 555596464 693 True 608.000000 608 82.609000 1077 1784 1 chr5A.!!$R1 707
10 TraesCS4A01G304200 chr5D 439979736 439980435 699 True 568.000000 568 81.476000 1071 1783 1 chr5D.!!$R2 712
11 TraesCS4A01G304200 chr5B 534487324 534487935 611 True 536.000000 536 82.643000 1184 1806 1 chr5B.!!$R1 622
12 TraesCS4A01G304200 chr5B 534588932 534589618 686 True 427.000000 427 78.408000 1071 1806 1 chr5B.!!$R2 735
13 TraesCS4A01G304200 chrUn 47346710 47348110 1400 False 440.000000 440 73.231000 1275 2756 1 chrUn.!!$F1 1481

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
686 757 0.821711 CCCAAGTTCGGCAAGGTTCA 60.822 55.0 0.00 0.0 0.00 3.18 F
1199 1271 0.036022 TCACATCCATGTTCGCCACA 59.964 50.0 0.00 0.0 39.39 4.17 F
1221 1293 0.465097 GAGTCCATCCCCTCGTCGTA 60.465 60.0 0.00 0.0 0.00 3.43 F
1841 2433 0.750249 TTATGGCTTGCCGATCGAGA 59.250 50.0 18.66 0.0 0.00 4.04 F
3692 4438 0.329596 GGTGTCTGGCTTTGGAGGAT 59.670 55.0 0.00 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 2288 0.538118 GGCATGCCCATGACAAACAT 59.462 50.000 27.24 0.0 46.06 2.71 R
2682 3346 1.470098 CTTCTTGGCTCATTGAACCGG 59.530 52.381 0.00 0.0 0.00 5.28 R
3210 3941 7.606349 TCCATGTCCGATCTTTAGAATATGAG 58.394 38.462 0.00 0.0 0.00 2.90 R
3706 4452 0.179111 CCTACGCAAGATTCCTCGCA 60.179 55.000 0.00 0.0 43.62 5.10 R
4514 5279 0.540365 AATGCACCAACTCTGTGGGG 60.540 55.000 0.00 0.0 45.74 4.96 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
55 64 3.118454 CGCAAACTCGACCGGCAT 61.118 61.111 0.00 0.00 0.00 4.40
78 87 3.806667 GGAGGCTGGCAGCTCCAT 61.807 66.667 33.82 22.58 45.50 3.41
126 137 2.781158 GCAGGCACAAAACCACGGT 61.781 57.895 0.00 0.00 0.00 4.83
237 250 2.819595 GATCACGCACCATGCCGT 60.820 61.111 0.00 0.00 41.12 5.68
246 259 2.224159 ACCATGCCGTGAAGGAGGT 61.224 57.895 0.00 0.00 45.00 3.85
292 305 2.357034 GAACACTTCGAGGCGGCA 60.357 61.111 13.08 0.00 0.00 5.69
384 418 1.302033 CTGCTGCCGTTCCTCAGTT 60.302 57.895 0.00 0.00 33.09 3.16
417 454 7.789273 TTTTAATTTTAGTCTGTCCGTGTGA 57.211 32.000 0.00 0.00 0.00 3.58
454 500 4.760715 GCGAGGTCTGGACTATCTATGTAA 59.239 45.833 0.67 0.00 0.00 2.41
557 603 4.494484 GCAAAATTGTCTTAGGGCGAAAT 58.506 39.130 0.00 0.00 0.00 2.17
600 647 4.982295 AGAAAATTTAACAGACTTTGCGGC 59.018 37.500 0.00 0.00 0.00 6.53
634 681 2.029470 AGAGATGCTCTTATAGTGCGGC 60.029 50.000 0.00 0.00 37.60 6.53
683 754 2.597510 GCCCAAGTTCGGCAAGGT 60.598 61.111 6.63 0.00 46.27 3.50
685 756 1.956802 CCCAAGTTCGGCAAGGTTC 59.043 57.895 0.00 0.00 0.00 3.62
686 757 0.821711 CCCAAGTTCGGCAAGGTTCA 60.822 55.000 0.00 0.00 0.00 3.18
720 791 1.227118 CCCAACAAAACCCACGCAC 60.227 57.895 0.00 0.00 0.00 5.34
803 874 5.351465 AGACAGTTCACACACACAAAAGTAG 59.649 40.000 0.00 0.00 0.00 2.57
818 889 5.345202 ACAAAAGTAGAACAAGAGTATCGCG 59.655 40.000 0.00 0.00 42.67 5.87
988 1060 4.421948 CAAGCAAGTAGAGGTAACGTAGG 58.578 47.826 0.00 0.00 46.39 3.18
1068 1140 0.343372 TCCCCTGGCTACTCCTTCAT 59.657 55.000 0.00 0.00 35.26 2.57
1069 1141 1.216990 CCCCTGGCTACTCCTTCATT 58.783 55.000 0.00 0.00 35.26 2.57
1136 1208 1.153489 CCACTCCAGCACCTCATCG 60.153 63.158 0.00 0.00 0.00 3.84
1199 1271 0.036022 TCACATCCATGTTCGCCACA 59.964 50.000 0.00 0.00 39.39 4.17
1221 1293 0.465097 GAGTCCATCCCCTCGTCGTA 60.465 60.000 0.00 0.00 0.00 3.43
1434 1522 3.369892 CCAAGAGGATCCTCAACGACATT 60.370 47.826 37.28 21.27 44.99 2.71
1678 2262 9.655769 CTGTATATATGATTGTTTCTGTGTTGC 57.344 33.333 0.00 0.00 0.00 4.17
1703 2288 5.291971 CATCCATATCGTGTGATTCAGACA 58.708 41.667 13.66 2.45 35.99 3.41
1791 2383 7.078228 CGAATTTAGCTGTGCTTCTTTTAACT 58.922 34.615 0.00 0.00 40.44 2.24
1841 2433 0.750249 TTATGGCTTGCCGATCGAGA 59.250 50.000 18.66 0.00 0.00 4.04
1868 2460 4.510340 ACTTTGTCGCGTTGTAAAGATTCT 59.490 37.500 23.01 7.59 34.94 2.40
2061 2656 4.392047 CCATGGCAATGTTATAGCTCTGA 58.608 43.478 0.00 0.00 31.27 3.27
2208 2819 8.583810 TTGCTATATTCTACGTAACACCAATC 57.416 34.615 0.00 0.00 0.00 2.67
2247 2858 4.280174 TGTCCAGTCGCTACTAGAAAAACT 59.720 41.667 0.00 0.00 33.48 2.66
2262 2873 8.235905 ACTAGAAAAACTGAGTACTGTATCGAC 58.764 37.037 0.00 0.00 0.00 4.20
2275 2886 6.354039 ACTGTATCGACGTTGTTTCTTTTT 57.646 33.333 1.96 0.00 0.00 1.94
2323 2942 2.672996 GGGCATGTGGCTCGTGTT 60.673 61.111 10.18 0.00 44.01 3.32
2370 2989 9.920946 ATAATTAGAAGAGCCCAATTTACTTGA 57.079 29.630 0.00 0.00 36.97 3.02
2451 3072 5.585047 ACTTTGCCGTATTGTAGAAATCTCC 59.415 40.000 0.00 0.00 0.00 3.71
2632 3296 6.103330 GTCCTGATCTTCCTCTTCTTTGTAC 58.897 44.000 0.00 0.00 0.00 2.90
2682 3346 0.953727 TATCCTGCATGCAATTCCGC 59.046 50.000 22.88 0.00 0.00 5.54
2875 3601 4.992319 CACTTCATTTGCAACCATGTGATT 59.008 37.500 0.00 0.00 0.00 2.57
2891 3617 6.238103 CCATGTGATTGTATTACTCGGTTCAC 60.238 42.308 0.00 0.00 34.33 3.18
3210 3941 7.095565 GCTTTGACTTCCAACTTCTTACTAGTC 60.096 40.741 0.00 0.00 33.85 2.59
3363 4102 8.726650 TTAATTTTTGTCATCACGATTCAGTG 57.273 30.769 0.00 3.29 43.11 3.66
3391 4130 4.371855 TGAGGTAGTTCGAAGCAGTATG 57.628 45.455 0.00 0.00 40.87 2.39
3465 4204 2.870175 TCAACCACCTTGTAACATGGG 58.130 47.619 0.00 0.00 36.47 4.00
3478 4217 6.662865 TGTAACATGGGTGATTTGTGAAAT 57.337 33.333 0.00 0.00 0.00 2.17
3515 4259 3.885297 ACCAATATGCACCTTAGACATGC 59.115 43.478 0.00 0.00 39.88 4.06
3621 4365 6.402658 GGAAAAAGAGCATAGCTACAAGTGAC 60.403 42.308 0.00 0.00 39.88 3.67
3691 4437 0.768221 AGGTGTCTGGCTTTGGAGGA 60.768 55.000 0.00 0.00 0.00 3.71
3692 4438 0.329596 GGTGTCTGGCTTTGGAGGAT 59.670 55.000 0.00 0.00 0.00 3.24
3730 4476 3.738281 CGAGGAATCTTGCGTAGGAACAT 60.738 47.826 0.00 0.00 31.87 2.71
3731 4477 3.535561 AGGAATCTTGCGTAGGAACATG 58.464 45.455 0.00 0.00 31.87 3.21
3733 4479 3.938963 GGAATCTTGCGTAGGAACATGAA 59.061 43.478 0.00 0.00 31.87 2.57
3734 4480 4.034510 GGAATCTTGCGTAGGAACATGAAG 59.965 45.833 0.00 0.00 31.87 3.02
3735 4481 3.953712 TCTTGCGTAGGAACATGAAGA 57.046 42.857 0.00 0.00 31.87 2.87
3736 4482 3.849911 TCTTGCGTAGGAACATGAAGAG 58.150 45.455 0.00 0.00 31.87 2.85
3738 4484 1.899814 TGCGTAGGAACATGAAGAGGT 59.100 47.619 0.00 0.00 0.00 3.85
3739 4485 2.271800 GCGTAGGAACATGAAGAGGTG 58.728 52.381 0.00 0.00 0.00 4.00
3740 4486 2.893637 CGTAGGAACATGAAGAGGTGG 58.106 52.381 0.00 0.00 0.00 4.61
3741 4487 2.418746 CGTAGGAACATGAAGAGGTGGG 60.419 54.545 0.00 0.00 0.00 4.61
3742 4488 0.329596 AGGAACATGAAGAGGTGGGC 59.670 55.000 0.00 0.00 0.00 5.36
3743 4489 0.038166 GGAACATGAAGAGGTGGGCA 59.962 55.000 0.00 0.00 0.00 5.36
3744 4490 1.547675 GGAACATGAAGAGGTGGGCAA 60.548 52.381 0.00 0.00 0.00 4.52
3746 4492 2.134789 ACATGAAGAGGTGGGCAATC 57.865 50.000 0.00 0.00 0.00 2.67
3747 4493 1.637553 ACATGAAGAGGTGGGCAATCT 59.362 47.619 0.00 0.00 0.00 2.40
3748 4494 2.042162 ACATGAAGAGGTGGGCAATCTT 59.958 45.455 0.00 0.00 36.02 2.40
3749 4495 2.978156 TGAAGAGGTGGGCAATCTTT 57.022 45.000 0.00 0.00 33.53 2.52
3750 4496 4.263905 ACATGAAGAGGTGGGCAATCTTTA 60.264 41.667 0.00 0.00 33.53 1.85
3751 4497 4.380843 TGAAGAGGTGGGCAATCTTTAA 57.619 40.909 0.00 0.00 33.53 1.52
3752 4498 4.735369 TGAAGAGGTGGGCAATCTTTAAA 58.265 39.130 0.00 0.00 33.53 1.52
3753 4499 5.332743 TGAAGAGGTGGGCAATCTTTAAAT 58.667 37.500 0.00 0.00 33.53 1.40
3754 4500 5.779771 TGAAGAGGTGGGCAATCTTTAAATT 59.220 36.000 0.00 0.00 33.53 1.82
3755 4501 6.951198 TGAAGAGGTGGGCAATCTTTAAATTA 59.049 34.615 0.00 0.00 33.53 1.40
3756 4502 6.775594 AGAGGTGGGCAATCTTTAAATTAC 57.224 37.500 0.00 0.00 0.00 1.89
3757 4503 5.656859 AGAGGTGGGCAATCTTTAAATTACC 59.343 40.000 0.00 0.00 0.00 2.85
3758 4504 5.589831 AGGTGGGCAATCTTTAAATTACCT 58.410 37.500 0.00 0.00 0.00 3.08
3759 4505 5.422012 AGGTGGGCAATCTTTAAATTACCTG 59.578 40.000 0.00 0.00 33.85 4.00
3760 4506 5.395214 GGTGGGCAATCTTTAAATTACCTGG 60.395 44.000 0.00 0.00 0.00 4.45
3761 4507 5.186992 GTGGGCAATCTTTAAATTACCTGGT 59.813 40.000 4.05 4.05 0.00 4.00
3762 4508 5.782845 TGGGCAATCTTTAAATTACCTGGTT 59.217 36.000 3.84 0.00 0.00 3.67
3763 4509 6.106003 GGGCAATCTTTAAATTACCTGGTTG 58.894 40.000 3.84 0.00 0.00 3.77
3880 4636 1.827969 TGGTTGGTTTTTCACTGGTGG 59.172 47.619 0.70 0.00 0.00 4.61
3923 4679 2.119495 GGCTCTCCCATCTCTTTACCA 58.881 52.381 0.00 0.00 0.00 3.25
3982 4746 6.014584 GGGGAAAGTTCTGTTGGTTATCAAAT 60.015 38.462 0.00 0.00 37.08 2.32
4017 4781 3.943381 TGAGTGCATGGCTTGATCTTTAG 59.057 43.478 4.32 0.00 0.00 1.85
4096 4860 1.906574 ACCTCCAGAAAACCATCGCTA 59.093 47.619 0.00 0.00 0.00 4.26
4152 4916 2.874447 ACTAGGAGGAGGAGGTAAGGA 58.126 52.381 0.00 0.00 0.00 3.36
4190 4954 5.003160 TGAAATGGTGTCTGGTAGAACATG 58.997 41.667 0.00 0.00 0.00 3.21
4204 4968 0.036010 AACATGAAGAGGGCCACGAG 60.036 55.000 6.18 0.00 0.00 4.18
4217 4981 2.101582 GGCCACGAGTCAAGTGATCTAT 59.898 50.000 0.00 0.00 41.83 1.98
4316 5080 0.611340 GGGACTCGGTCACCTACACT 60.611 60.000 0.00 0.00 33.68 3.55
4317 5081 1.254954 GGACTCGGTCACCTACACTT 58.745 55.000 0.00 0.00 33.68 3.16
4329 5093 1.490693 CTACACTTAGCATGCCGGCG 61.491 60.000 23.90 9.82 39.27 6.46
4385 5150 2.598565 TCAAGTAGAGAGCACCAGTGT 58.401 47.619 0.00 0.00 0.00 3.55
4409 5174 1.596477 CCCTCTATGGCTTCTGCGC 60.596 63.158 0.00 0.00 40.82 6.09
4426 5191 2.092968 TGCGCCTAGATCACCAAATTCT 60.093 45.455 4.18 0.00 0.00 2.40
4440 5205 2.945668 CAAATTCTTGACCCCCTCGATC 59.054 50.000 0.00 0.00 34.14 3.69
4500 5265 2.528813 TCTCCCCCTCCCAGAAATATCT 59.471 50.000 0.00 0.00 35.88 1.98
4501 5266 2.909662 CTCCCCCTCCCAGAAATATCTC 59.090 54.545 0.00 0.00 32.03 2.75
4508 5273 3.231818 TCCCAGAAATATCTCGTCCTCC 58.768 50.000 0.00 0.00 32.03 4.30
4514 5279 0.410270 ATATCTCGTCCTCCCCTCCC 59.590 60.000 0.00 0.00 0.00 4.30
4534 5299 0.599558 CCCACAGAGTTGGTGCATTG 59.400 55.000 0.00 0.00 34.44 2.82
4538 5303 1.603802 ACAGAGTTGGTGCATTGTTCG 59.396 47.619 0.00 0.00 0.00 3.95
4580 5345 4.101448 ATCCCACGGCCTCTGCAC 62.101 66.667 0.00 0.00 40.13 4.57
4586 5351 2.743928 CGGCCTCTGCACCAGAAC 60.744 66.667 0.00 0.00 40.18 3.01
4587 5352 2.431683 GGCCTCTGCACCAGAACA 59.568 61.111 0.00 0.00 40.18 3.18
4591 5356 1.171308 CCTCTGCACCAGAACAATGG 58.829 55.000 0.00 0.00 46.47 3.16
4599 5364 1.272313 ACCAGAACAATGGATGCAGCT 60.272 47.619 0.22 0.00 43.57 4.24
4602 5367 3.635373 CCAGAACAATGGATGCAGCTATT 59.365 43.478 7.83 7.83 43.57 1.73
4632 5397 4.384940 ACAGTGCCAAAACAAAACAAAGT 58.615 34.783 0.00 0.00 0.00 2.66
4634 5399 3.677596 AGTGCCAAAACAAAACAAAGTCG 59.322 39.130 0.00 0.00 0.00 4.18
4653 5418 4.122776 GTCGGCAATTCAGTACATCTCAT 58.877 43.478 0.00 0.00 0.00 2.90
4663 5428 2.363680 AGTACATCTCATGGAAGGAGCG 59.636 50.000 0.00 0.00 46.01 5.03
4668 5433 3.973206 TCTCATGGAAGGAGCGTAAAA 57.027 42.857 0.00 0.00 46.01 1.52
4706 5471 3.297830 AGGCCACAAATAGCGAAAAAC 57.702 42.857 5.01 0.00 0.00 2.43
4709 5474 2.986479 GCCACAAATAGCGAAAAACAGG 59.014 45.455 0.00 0.00 0.00 4.00
4726 5491 6.575162 AAACAGGACAAGATGATAAACACC 57.425 37.500 0.00 0.00 0.00 4.16
4766 5531 3.444388 GCCATCCAAACCGGTTGTAAATA 59.556 43.478 23.08 4.03 35.23 1.40
4771 5536 4.017808 CCAAACCGGTTGTAAATATCCCA 58.982 43.478 23.08 0.00 35.23 4.37
4778 5543 5.305585 CGGTTGTAAATATCCCATGCTACT 58.694 41.667 0.00 0.00 0.00 2.57
4779 5544 6.460781 CGGTTGTAAATATCCCATGCTACTA 58.539 40.000 0.00 0.00 0.00 1.82
4780 5545 7.103641 CGGTTGTAAATATCCCATGCTACTAT 58.896 38.462 0.00 0.00 0.00 2.12
4781 5546 7.277981 CGGTTGTAAATATCCCATGCTACTATC 59.722 40.741 0.00 0.00 0.00 2.08
4782 5547 8.322091 GGTTGTAAATATCCCATGCTACTATCT 58.678 37.037 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 177 0.179062 GTGGCTCGGAGCTCATTGAT 60.179 55.000 27.47 0.00 41.99 2.57
237 250 3.160585 CCACCAGCACCTCCTTCA 58.839 61.111 0.00 0.00 0.00 3.02
279 292 2.358737 CCTTTGCCGCCTCGAAGT 60.359 61.111 0.00 0.00 0.00 3.01
292 305 3.591254 GAGCTCGTGGTCCGCCTTT 62.591 63.158 0.00 0.00 34.87 3.11
370 391 3.410631 TTAATCAACTGAGGAACGGCA 57.589 42.857 0.00 0.00 0.00 5.69
406 441 2.061773 GTTCATCACTCACACGGACAG 58.938 52.381 0.00 0.00 0.00 3.51
417 454 1.513158 CTCGCCGGAGTTCATCACT 59.487 57.895 5.05 0.00 39.07 3.41
600 647 4.300803 GAGCATCTCTAGCAGAACAGATG 58.699 47.826 10.91 10.91 33.62 2.90
634 681 1.888018 CTTGGCCTGGCTCACAATG 59.112 57.895 19.68 5.20 0.00 2.82
683 754 8.642935 TGTTGGGTTTAAGATTATGTCATGAA 57.357 30.769 0.00 0.00 0.00 2.57
685 756 9.703892 TTTTGTTGGGTTTAAGATTATGTCATG 57.296 29.630 0.00 0.00 0.00 3.07
686 757 9.705290 GTTTTGTTGGGTTTAAGATTATGTCAT 57.295 29.630 0.00 0.00 0.00 3.06
803 874 1.189403 CGTCCGCGATACTCTTGTTC 58.811 55.000 8.23 0.00 41.33 3.18
818 889 1.074872 GATGGTTCCGTCGTTCGTCC 61.075 60.000 0.00 0.00 37.94 4.79
1068 1140 3.640029 GGGATCCGAAGATGTAGTGGTAA 59.360 47.826 5.45 0.00 30.90 2.85
1069 1141 3.117246 AGGGATCCGAAGATGTAGTGGTA 60.117 47.826 5.45 0.00 30.90 3.25
1104 1176 2.187946 GTGGATCTGGTGGCGGAG 59.812 66.667 0.00 0.00 0.00 4.63
1199 1271 0.684805 GACGAGGGGATGGACTCACT 60.685 60.000 0.00 0.00 33.36 3.41
1221 1293 2.987125 GGCCGAGGTGTACATGGT 59.013 61.111 0.00 0.00 0.00 3.55
1379 1467 1.134580 AGAGGTTGATCATGTCGGCAG 60.135 52.381 0.00 0.00 0.00 4.85
1677 2261 1.432514 ATCACACGATATGGATGCGC 58.567 50.000 0.00 0.00 0.00 6.09
1678 2262 3.059166 TGAATCACACGATATGGATGCG 58.941 45.455 0.00 0.00 0.00 4.73
1703 2288 0.538118 GGCATGCCCATGACAAACAT 59.462 50.000 27.24 0.00 46.06 2.71
1751 2339 8.012241 CAGCTAAATTCGGCAATTCTACTTATC 58.988 37.037 0.00 0.00 30.37 1.75
1791 2383 4.769345 TGGCATGAATACTGGTACATCA 57.231 40.909 0.00 2.17 38.20 3.07
1841 2433 6.289745 TCTTTACAACGCGACAAAGTATTT 57.710 33.333 15.93 0.00 40.26 1.40
1899 2491 4.226761 CAGAAAAACTACCATTGGCGTTC 58.773 43.478 1.54 0.00 0.00 3.95
2061 2656 4.359706 GCAAGACGACAAATTGTTCCTTT 58.640 39.130 0.00 0.00 0.00 3.11
2208 2819 4.300189 TGGACAAACCAGAAAAATGACG 57.700 40.909 0.00 0.00 44.64 4.35
2247 2858 4.754372 AACAACGTCGATACAGTACTCA 57.246 40.909 0.00 0.00 0.00 3.41
2262 2873 5.275695 CCAACACATCGAAAAAGAAACAACG 60.276 40.000 0.00 0.00 0.00 4.10
2323 2942 3.848272 TGATATATGACAGCGCGATCA 57.152 42.857 12.10 17.26 0.00 2.92
2443 3064 8.685838 AGTAGATCAGTAGTACTGGAGATTTC 57.314 38.462 26.30 14.75 45.94 2.17
2527 3150 8.186163 CCATACTAGCGATAATAATCACGGTTA 58.814 37.037 0.00 0.00 37.61 2.85
2632 3296 3.845178 TCTTAGCACCAACACTGATACG 58.155 45.455 0.00 0.00 0.00 3.06
2682 3346 1.470098 CTTCTTGGCTCATTGAACCGG 59.530 52.381 0.00 0.00 0.00 5.28
3210 3941 7.606349 TCCATGTCCGATCTTTAGAATATGAG 58.394 38.462 0.00 0.00 0.00 2.90
3363 4102 4.022242 TGCTTCGAACTACCTCATATAGCC 60.022 45.833 0.00 0.00 0.00 3.93
3391 4130 8.507470 AATTTACGCTGAGAAACAAAGAAATC 57.493 30.769 0.00 0.00 0.00 2.17
3478 4217 0.257328 TTGGTGGCCAAGTCACAAGA 59.743 50.000 7.24 0.00 40.26 3.02
3691 4437 9.458727 AGATTCCTCGCATTATTTCATAATCAT 57.541 29.630 0.00 0.00 33.34 2.45
3692 4438 8.853077 AGATTCCTCGCATTATTTCATAATCA 57.147 30.769 0.00 0.00 33.34 2.57
3706 4452 0.179111 CCTACGCAAGATTCCTCGCA 60.179 55.000 0.00 0.00 43.62 5.10
3730 4476 2.978156 AAAGATTGCCCACCTCTTCA 57.022 45.000 0.00 0.00 0.00 3.02
3731 4477 5.921962 ATTTAAAGATTGCCCACCTCTTC 57.078 39.130 0.00 0.00 0.00 2.87
3733 4479 5.656859 GGTAATTTAAAGATTGCCCACCTCT 59.343 40.000 0.00 0.00 36.22 3.69
3734 4480 5.656859 AGGTAATTTAAAGATTGCCCACCTC 59.343 40.000 5.38 0.00 41.17 3.85
3735 4481 5.422012 CAGGTAATTTAAAGATTGCCCACCT 59.578 40.000 5.38 0.00 41.17 4.00
3736 4482 5.395214 CCAGGTAATTTAAAGATTGCCCACC 60.395 44.000 5.38 0.00 41.17 4.61
3738 4484 5.337788 ACCAGGTAATTTAAAGATTGCCCA 58.662 37.500 0.00 0.00 41.17 5.36
3739 4485 5.932619 ACCAGGTAATTTAAAGATTGCCC 57.067 39.130 0.00 0.00 41.17 5.36
3740 4486 6.697395 ACAACCAGGTAATTTAAAGATTGCC 58.303 36.000 0.00 1.58 40.74 4.52
3741 4487 7.375053 TGACAACCAGGTAATTTAAAGATTGC 58.625 34.615 0.00 0.00 0.00 3.56
3742 4488 9.757227 TTTGACAACCAGGTAATTTAAAGATTG 57.243 29.630 0.00 0.00 0.00 2.67
3743 4489 9.758651 GTTTGACAACCAGGTAATTTAAAGATT 57.241 29.630 0.00 0.00 0.00 2.40
3744 4490 8.919145 TGTTTGACAACCAGGTAATTTAAAGAT 58.081 29.630 0.00 0.00 31.02 2.40
3746 4492 8.934507 TTGTTTGACAACCAGGTAATTTAAAG 57.065 30.769 0.00 0.00 32.34 1.85
3747 4493 9.720769 TTTTGTTTGACAACCAGGTAATTTAAA 57.279 25.926 0.00 0.00 37.90 1.52
3748 4494 9.152595 GTTTTGTTTGACAACCAGGTAATTTAA 57.847 29.630 0.00 0.00 37.90 1.52
3749 4495 8.311836 TGTTTTGTTTGACAACCAGGTAATTTA 58.688 29.630 0.00 0.00 37.90 1.40
3750 4496 7.162082 TGTTTTGTTTGACAACCAGGTAATTT 58.838 30.769 0.00 0.00 37.90 1.82
3751 4497 6.702329 TGTTTTGTTTGACAACCAGGTAATT 58.298 32.000 0.00 0.00 37.90 1.40
3752 4498 6.287589 TGTTTTGTTTGACAACCAGGTAAT 57.712 33.333 0.00 0.00 37.90 1.89
3753 4499 5.723672 TGTTTTGTTTGACAACCAGGTAA 57.276 34.783 0.00 0.00 37.90 2.85
3754 4500 5.186021 ACATGTTTTGTTTGACAACCAGGTA 59.814 36.000 0.00 0.00 37.90 3.08
3755 4501 4.020662 ACATGTTTTGTTTGACAACCAGGT 60.021 37.500 0.00 0.00 37.90 4.00
3756 4502 4.502962 ACATGTTTTGTTTGACAACCAGG 58.497 39.130 0.00 0.00 37.90 4.45
3757 4503 5.407995 ACAACATGTTTTGTTTGACAACCAG 59.592 36.000 8.77 0.00 46.51 4.00
3758 4504 5.300752 ACAACATGTTTTGTTTGACAACCA 58.699 33.333 8.77 0.00 46.51 3.67
3759 4505 5.854431 ACAACATGTTTTGTTTGACAACC 57.146 34.783 8.77 0.00 46.51 3.77
3760 4506 8.439286 ACATAACAACATGTTTTGTTTGACAAC 58.561 29.630 18.42 0.00 45.57 3.32
3761 4507 8.438513 CACATAACAACATGTTTTGTTTGACAA 58.561 29.630 18.42 3.85 45.57 3.18
3762 4508 7.600375 ACACATAACAACATGTTTTGTTTGACA 59.400 29.630 18.42 4.17 45.57 3.58
3763 4509 7.958674 ACACATAACAACATGTTTTGTTTGAC 58.041 30.769 18.42 0.00 45.57 3.18
3872 4627 3.817709 AACAAAACCAATCCACCAGTG 57.182 42.857 0.00 0.00 0.00 3.66
3880 4636 8.466798 AGCCTACAACATATAACAAAACCAATC 58.533 33.333 0.00 0.00 0.00 2.67
3923 4679 1.737793 GACGTCGGCATTCCAAAAGAT 59.262 47.619 0.00 0.00 0.00 2.40
4017 4781 8.707839 CACAATGTACCAACCAACAAAATAATC 58.292 33.333 0.00 0.00 0.00 1.75
4096 4860 3.970640 CCCCCAGAGCTAGTTTATTCTCT 59.029 47.826 0.00 0.00 36.43 3.10
4115 4879 3.005578 CCTAGTAGTATCTTGTTCGCCCC 59.994 52.174 0.00 0.00 0.00 5.80
4152 4916 3.691118 CCATTTCACACATCGTCCTTCAT 59.309 43.478 0.00 0.00 0.00 2.57
4190 4954 0.390472 CTTGACTCGTGGCCCTCTTC 60.390 60.000 0.00 0.00 0.00 2.87
4204 4968 4.125703 CTCCAGCCAATAGATCACTTGAC 58.874 47.826 8.41 0.00 0.00 3.18
4246 5010 2.997897 GCACCCAGAGACTCCGGT 60.998 66.667 0.00 5.11 0.00 5.28
4263 5027 1.912371 GCCGAGAAACGCCTTGAAGG 61.912 60.000 6.92 6.92 41.07 3.46
4273 5037 0.586802 GGACAACACTGCCGAGAAAC 59.413 55.000 0.00 0.00 0.00 2.78
4277 5041 3.414700 GCGGACAACACTGCCGAG 61.415 66.667 0.00 0.00 41.74 4.63
4282 5046 2.669569 CCCTGGCGGACAACACTG 60.670 66.667 0.00 0.00 0.00 3.66
4316 5080 1.237954 TTTTGTCGCCGGCATGCTAA 61.238 50.000 28.98 15.10 0.00 3.09
4317 5081 1.672682 TTTTGTCGCCGGCATGCTA 60.673 52.632 28.98 9.58 0.00 3.49
4329 5093 6.693978 GGCATATTGGTATTAACGGTTTTGTC 59.306 38.462 0.00 0.00 0.00 3.18
4405 5170 2.092968 AGAATTTGGTGATCTAGGCGCA 60.093 45.455 10.83 0.00 0.00 6.09
4409 5174 4.884164 GGGTCAAGAATTTGGTGATCTAGG 59.116 45.833 0.00 0.00 34.97 3.02
4426 5191 2.385803 GTAGAAGATCGAGGGGGTCAA 58.614 52.381 0.00 0.00 0.00 3.18
4440 5205 6.017192 TGTGTCAAATGTTGTCATGGTAGAAG 60.017 38.462 0.00 0.00 34.19 2.85
4514 5279 0.540365 AATGCACCAACTCTGTGGGG 60.540 55.000 0.00 0.00 45.74 4.96
4518 5283 1.603802 CGAACAATGCACCAACTCTGT 59.396 47.619 0.00 0.00 0.00 3.41
4551 5316 1.688311 CCGTGGGATGTCCTCCTTCTA 60.688 57.143 0.00 0.00 44.28 2.10
4580 5345 1.471119 AGCTGCATCCATTGTTCTGG 58.529 50.000 1.02 0.00 37.66 3.86
4586 5351 9.531942 TGTTTAATAAAATAGCTGCATCCATTG 57.468 29.630 1.02 0.00 0.00 2.82
4587 5352 9.754382 CTGTTTAATAAAATAGCTGCATCCATT 57.246 29.630 1.02 0.00 28.70 3.16
4591 5356 7.168135 GGCACTGTTTAATAAAATAGCTGCATC 59.832 37.037 1.02 0.00 39.56 3.91
4602 5367 8.999431 TGTTTTGTTTTGGCACTGTTTAATAAA 58.001 25.926 0.00 0.00 0.00 1.40
4632 5397 3.885724 TGAGATGTACTGAATTGCCGA 57.114 42.857 0.00 0.00 0.00 5.54
4634 5399 4.454678 TCCATGAGATGTACTGAATTGCC 58.545 43.478 0.00 0.00 0.00 4.52
4684 5449 3.569250 TTTTCGCTATTTGTGGCCTTC 57.431 42.857 3.32 0.00 0.00 3.46
4696 5461 4.637276 TCATCTTGTCCTGTTTTTCGCTA 58.363 39.130 0.00 0.00 0.00 4.26
4697 5462 3.476552 TCATCTTGTCCTGTTTTTCGCT 58.523 40.909 0.00 0.00 0.00 4.93
4706 5471 6.708054 GGATAGGTGTTTATCATCTTGTCCTG 59.292 42.308 0.00 0.00 38.58 3.86
4726 5491 4.819105 TGGCGGTCCAATAATAGGATAG 57.181 45.455 0.00 0.00 39.99 2.08


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

AutoCloner maintained by Alex Coulton.