Multiple sequence alignment - TraesCS3A01G116900

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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 TraesCS3A01G116900 chr3A 100.000 5021 0 0 1 5021 86366088 86371108 0.000000e+00 9273.0
1 TraesCS3A01G116900 chr3D 93.758 4438 180 33 644 5021 73387405 73391805 0.000000e+00 6571.0
2 TraesCS3A01G116900 chr3D 94.291 543 18 6 1 536 73386871 73387407 0.000000e+00 819.0
3 TraesCS3A01G116900 chr3D 82.353 238 30 7 303 534 29739378 29739609 3.970000e-46 196.0
4 TraesCS3A01G116900 chr3D 81.405 242 32 9 303 537 200518422 200518187 8.580000e-43 185.0
5 TraesCS3A01G116900 chr3B 91.226 3237 168 28 780 3934 118735948 118739150 0.000000e+00 4298.0
6 TraesCS3A01G116900 chr3B 81.667 720 81 30 3951 4653 118739326 118740011 7.350000e-153 551.0
7 TraesCS3A01G116900 chr3B 86.093 302 26 13 4726 5021 118742483 118742774 1.360000e-80 311.0
8 TraesCS3A01G116900 chr3B 84.039 307 31 10 234 529 118735396 118735695 3.830000e-71 279.0
9 TraesCS3A01G116900 chr3B 81.679 262 27 12 1 243 118735027 118735286 1.100000e-46 198.0
10 TraesCS3A01G116900 chr3B 94.167 120 7 0 2216 2335 118737378 118737497 3.090000e-42 183.0
11 TraesCS3A01G116900 chr3B 96.875 32 1 0 1740 1771 118735920 118735889 3.000000e-03 54.7
12 TraesCS3A01G116900 chr7D 86.610 1053 121 11 811 1855 7305667 7304627 0.000000e+00 1146.0
13 TraesCS3A01G116900 chr7D 79.045 1298 127 67 2307 3491 7304324 7303059 0.000000e+00 756.0
14 TraesCS3A01G116900 chr7D 83.264 239 32 5 303 537 7306356 7306122 3.940000e-51 213.0
15 TraesCS3A01G116900 chr7D 94.872 117 4 2 529 643 11409308 11409192 1.110000e-41 182.0
16 TraesCS3A01G116900 chr4A 85.627 981 124 10 888 1855 732520708 732519732 0.000000e+00 1014.0
17 TraesCS3A01G116900 chr4A 75.875 1285 166 72 2307 3492 732519445 732518206 1.600000e-144 523.0
18 TraesCS3A01G116900 chr4A 96.364 110 2 2 530 638 340694684 340694792 3.990000e-41 180.0
19 TraesCS3A01G116900 chr4A 95.575 113 1 4 534 643 187572346 187572235 1.440000e-40 178.0
20 TraesCS3A01G116900 chr7A 90.890 472 41 2 1387 1856 8265143 8264672 2.550000e-177 632.0
21 TraesCS3A01G116900 chr7A 81.226 767 71 33 2307 3007 8264367 8263608 7.350000e-153 551.0
22 TraesCS3A01G116900 chr7A 81.287 171 24 5 363 530 8265862 8265697 1.130000e-26 132.0
23 TraesCS3A01G116900 chr7B 80.990 384 61 6 2470 2843 296667642 296667261 1.370000e-75 294.0
24 TraesCS3A01G116900 chr7B 83.938 193 30 1 1293 1484 296667909 296667717 3.090000e-42 183.0
25 TraesCS3A01G116900 chr5A 74.507 812 106 55 2752 3489 609689046 609689830 4.990000e-65 259.0
26 TraesCS3A01G116900 chr5A 97.196 107 1 2 533 638 115018636 115018741 3.990000e-41 180.0
27 TraesCS3A01G116900 chr6B 75.623 562 86 29 2960 3489 650677231 650677773 1.090000e-56 231.0
28 TraesCS3A01G116900 chr6B 81.013 237 34 8 303 534 647891552 647891782 1.440000e-40 178.0
29 TraesCS3A01G116900 chr6D 96.330 109 2 2 531 638 287025895 287026002 1.440000e-40 178.0
30 TraesCS3A01G116900 chr5D 95.575 113 1 4 534 643 138565671 138565560 1.440000e-40 178.0
31 TraesCS3A01G116900 chr1D 95.575 113 1 4 534 643 136673597 136673486 1.440000e-40 178.0
32 TraesCS3A01G116900 chr2B 94.118 119 2 5 528 643 441077077 441076961 5.170000e-40 176.0
33 TraesCS3A01G116900 chr1A 92.683 123 6 3 523 643 385891919 385891798 1.860000e-39 174.0


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 TraesCS3A01G116900 chr3A 86366088 86371108 5020 False 9273.000000 9273 100.000000 1 5021 1 chr3A.!!$F1 5020
1 TraesCS3A01G116900 chr3D 73386871 73391805 4934 False 3695.000000 6571 94.024500 1 5021 2 chr3D.!!$F2 5020
2 TraesCS3A01G116900 chr3B 118735027 118742774 7747 False 970.000000 4298 86.478500 1 5021 6 chr3B.!!$F1 5020
3 TraesCS3A01G116900 chr7D 7303059 7306356 3297 True 705.000000 1146 82.973000 303 3491 3 chr7D.!!$R2 3188
4 TraesCS3A01G116900 chr4A 732518206 732520708 2502 True 768.500000 1014 80.751000 888 3492 2 chr4A.!!$R2 2604
5 TraesCS3A01G116900 chr7A 8263608 8265862 2254 True 438.333333 632 84.467667 363 3007 3 chr7A.!!$R1 2644
6 TraesCS3A01G116900 chr7B 296667261 296667909 648 True 238.500000 294 82.464000 1293 2843 2 chr7B.!!$R1 1550
7 TraesCS3A01G116900 chr5A 609689046 609689830 784 False 259.000000 259 74.507000 2752 3489 1 chr5A.!!$F2 737
8 TraesCS3A01G116900 chr6B 650677231 650677773 542 False 231.000000 231 75.623000 2960 3489 1 chr6B.!!$F2 529

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
551 706 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.0 44.66 3.13 F
556 711 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.0 44.66 2.24 F
560 715 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.0 42.05 4.02 F
561 716 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.0 37.50 3.85 F
1677 2255 1.291906 CACAAAATGGGGCCGTTCC 59.708 57.895 0.00 0.0 0.00 3.62 F
3470 4281 0.539051 AATCTGCTCGGCTGCTTACT 59.461 50.000 0.00 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2483 0.391130 AAGACACACACACACGCACT 60.391 50.000 0.00 0.00 0.00 4.40 R
2022 2618 5.400066 TTGACATGACGAGACTCCAAATA 57.600 39.130 0.00 0.00 0.00 1.40 R
2660 3318 2.356382 CGGTTGGTTACTTGTTTGCTGA 59.644 45.455 0.00 0.00 0.00 4.26 R
2908 3616 1.080974 CGCTGCAGCAAGAAAAGGG 60.081 57.895 36.03 14.34 42.21 3.95 R
3563 4374 0.451783 GCCATTCACAAGTAAGCCCG 59.548 55.000 0.00 0.00 0.00 6.13 R
4370 5369 0.614697 TTCTCCGTCAGCATCTCCCA 60.615 55.000 0.00 0.00 0.00 4.37 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
46 47 2.125431 TTCCGTTCCCGAATCCGC 60.125 61.111 0.00 0.00 35.63 5.54
89 91 0.527817 CTCTTTATTCGAGCCGCGGT 60.528 55.000 28.70 13.92 41.33 5.68
191 201 4.287067 TCTGGCTTGATTTCTCTGGTACTT 59.713 41.667 0.00 0.00 0.00 2.24
192 202 5.483937 TCTGGCTTGATTTCTCTGGTACTTA 59.516 40.000 0.00 0.00 0.00 2.24
193 203 5.734720 TGGCTTGATTTCTCTGGTACTTAG 58.265 41.667 0.00 0.00 0.00 2.18
194 204 5.119694 GGCTTGATTTCTCTGGTACTTAGG 58.880 45.833 0.00 0.00 0.00 2.69
212 230 3.936203 TGAGCGCGGAAACCCTGT 61.936 61.111 8.83 0.00 0.00 4.00
243 381 0.990374 GATGGGGATGATGAGAGGGG 59.010 60.000 0.00 0.00 0.00 4.79
377 520 1.546323 CCACCTGGGGCTTATGCATAG 60.546 57.143 6.50 2.95 41.91 2.23
538 693 9.503399 CCCTAACTGGAACAAATATTATACTCC 57.497 37.037 0.00 0.00 38.70 3.85
539 694 9.503399 CCTAACTGGAACAAATATTATACTCCC 57.497 37.037 0.00 0.00 38.70 4.30
543 698 6.765403 TGGAACAAATATTATACTCCCTCCG 58.235 40.000 0.00 0.00 31.92 4.63
544 699 6.328148 TGGAACAAATATTATACTCCCTCCGT 59.672 38.462 0.00 0.00 31.92 4.69
545 700 6.872547 GGAACAAATATTATACTCCCTCCGTC 59.127 42.308 0.00 0.00 0.00 4.79
546 701 6.356186 ACAAATATTATACTCCCTCCGTCC 57.644 41.667 0.00 0.00 0.00 4.79
547 702 5.047519 ACAAATATTATACTCCCTCCGTCCG 60.048 44.000 0.00 0.00 0.00 4.79
548 703 1.920610 ATTATACTCCCTCCGTCCGG 58.079 55.000 0.00 0.00 0.00 5.14
549 704 0.846015 TTATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
551 706 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
552 707 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
553 708 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
556 711 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
557 712 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
558 713 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
559 714 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
560 715 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
561 716 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
562 717 2.428171 CCGTCCGGAAATACTTGTCCTA 59.572 50.000 5.23 0.00 37.50 2.94
563 718 3.490419 CCGTCCGGAAATACTTGTCCTAG 60.490 52.174 5.23 0.00 37.50 3.02
564 719 3.379372 CGTCCGGAAATACTTGTCCTAGA 59.621 47.826 5.23 0.00 0.00 2.43
565 720 4.142315 CGTCCGGAAATACTTGTCCTAGAA 60.142 45.833 5.23 0.00 0.00 2.10
566 721 5.622914 CGTCCGGAAATACTTGTCCTAGAAA 60.623 44.000 5.23 0.00 0.00 2.52
567 722 6.346896 GTCCGGAAATACTTGTCCTAGAAAT 58.653 40.000 5.23 0.00 0.00 2.17
568 723 6.258068 GTCCGGAAATACTTGTCCTAGAAATG 59.742 42.308 5.23 0.00 0.00 2.32
569 724 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
570 725 6.346096 CGGAAATACTTGTCCTAGAAATGGA 58.654 40.000 0.00 0.00 0.00 3.41
571 726 6.992715 CGGAAATACTTGTCCTAGAAATGGAT 59.007 38.462 0.00 0.00 35.87 3.41
572 727 8.148351 CGGAAATACTTGTCCTAGAAATGGATA 58.852 37.037 0.00 0.00 35.87 2.59
573 728 9.847224 GGAAATACTTGTCCTAGAAATGGATAA 57.153 33.333 0.00 0.00 35.87 1.75
578 733 8.525290 ACTTGTCCTAGAAATGGATAAAATGG 57.475 34.615 0.00 0.00 34.98 3.16
579 734 8.336235 ACTTGTCCTAGAAATGGATAAAATGGA 58.664 33.333 0.00 0.00 34.98 3.41
580 735 9.359653 CTTGTCCTAGAAATGGATAAAATGGAT 57.640 33.333 0.00 0.00 34.98 3.41
581 736 8.696043 TGTCCTAGAAATGGATAAAATGGATG 57.304 34.615 0.00 0.00 35.87 3.51
582 737 8.281531 TGTCCTAGAAATGGATAAAATGGATGT 58.718 33.333 0.00 0.00 35.87 3.06
583 738 9.793259 GTCCTAGAAATGGATAAAATGGATGTA 57.207 33.333 0.00 0.00 35.87 2.29
636 791 6.604735 CTTTCATAGGACAAGTATTTCCGG 57.395 41.667 0.00 0.00 36.95 5.14
637 792 5.943349 TTCATAGGACAAGTATTTCCGGA 57.057 39.130 0.00 0.00 36.95 5.14
638 793 5.531122 TCATAGGACAAGTATTTCCGGAG 57.469 43.478 3.34 0.00 36.95 4.63
719 882 9.922305 GAAAGTTTGTGCTCATTCAGTATATAC 57.078 33.333 4.60 4.60 0.00 1.47
1062 1627 1.873486 GCAAAGGTCAAACATGGTGGC 60.873 52.381 0.00 0.00 0.00 5.01
1104 1669 4.536765 AGCCAGGGAAATATACCAACAAG 58.463 43.478 0.00 0.00 0.00 3.16
1189 1754 6.205464 TGAACTTCAGATCAGACAAATCAACC 59.795 38.462 0.00 0.00 0.00 3.77
1242 1810 5.106157 GCAGCTACATTTGGACTGTAACAAT 60.106 40.000 0.00 0.00 0.00 2.71
1677 2255 1.291906 CACAAAATGGGGCCGTTCC 59.708 57.895 0.00 0.00 0.00 3.62
2144 2753 2.615447 TGAGCAACAAAGCAGTGAAGAG 59.385 45.455 0.00 0.00 36.85 2.85
2660 3318 2.519771 TTGCCTCCTTGATTGCTCAT 57.480 45.000 0.00 0.00 0.00 2.90
2993 3708 4.262164 CCAGGCTTGGGCAATAATGATAAC 60.262 45.833 7.05 0.00 41.05 1.89
3007 3725 3.885724 TGATAACGTGAAGCCAGATGA 57.114 42.857 0.00 0.00 0.00 2.92
3125 3877 1.078709 TTCGCTTTCAGCCTGAATCG 58.921 50.000 17.93 17.93 38.18 3.34
3173 3925 2.303022 TGACTCTAGGCTTTTGAGTGGG 59.697 50.000 17.81 0.00 40.63 4.61
3272 4058 6.237969 GCTCAGAAATTTACATCGAAGACCTC 60.238 42.308 0.00 0.00 42.51 3.85
3416 4226 0.803768 TTCTTGCTGATCGCTCGCTC 60.804 55.000 10.16 0.00 40.11 5.03
3470 4281 0.539051 AATCTGCTCGGCTGCTTACT 59.461 50.000 0.00 0.00 0.00 2.24
3478 4289 3.001736 GCTCGGCTGCTTACTATTTTCTG 59.998 47.826 0.00 0.00 0.00 3.02
3508 4319 8.155821 TCCTGTATTTCGTCAAATGTTTTACA 57.844 30.769 0.00 0.00 33.95 2.41
3545 4356 9.971922 CTCTTTGAAACTTTGGACTTGAATATT 57.028 29.630 0.00 0.00 0.00 1.28
3591 4402 6.621596 GCTTACTTGTGAATGGCTTACTGAAG 60.622 42.308 0.00 0.00 35.60 3.02
3596 4407 5.316167 TGTGAATGGCTTACTGAAGTTGAT 58.684 37.500 0.00 0.00 34.90 2.57
3665 4482 3.631145 TGTCATGAAAGAAACAGCTGC 57.369 42.857 15.27 0.00 0.00 5.25
3691 4508 4.067896 AGAAGTTCAGTGGTATGTTGCTG 58.932 43.478 5.50 0.00 0.00 4.41
3697 4514 4.847198 TCAGTGGTATGTTGCTGAATGAT 58.153 39.130 0.00 0.00 35.36 2.45
3735 4552 8.902806 TGTGTTATCATTCTGTCCATTATTTCC 58.097 33.333 0.00 0.00 0.00 3.13
3774 4591 9.654663 GTTGTCCTTTACTACAAGATACAAGAT 57.345 33.333 0.00 0.00 36.33 2.40
3781 4598 9.653287 TTTACTACAAGATACAAGATGTTGAGG 57.347 33.333 9.96 0.00 37.10 3.86
3948 4780 7.849496 CTAGAATTCTAGACATGACAACATGC 58.151 38.462 30.83 4.05 46.80 4.06
4016 5007 5.617252 TCCATATGATCTTTTAACCGGGTC 58.383 41.667 6.32 0.00 0.00 4.46
4043 5034 6.413052 AGTGATGCACTTCTATTTCATGTCT 58.587 36.000 0.00 0.00 42.59 3.41
4116 5114 2.860136 GTCACAAAGAAGCAAAGCAACC 59.140 45.455 0.00 0.00 0.00 3.77
4124 5122 0.541296 AGCAAAGCAACCAGGAGCAT 60.541 50.000 10.59 0.00 0.00 3.79
4125 5123 0.319405 GCAAAGCAACCAGGAGCATT 59.681 50.000 10.59 3.00 0.00 3.56
4126 5124 1.545582 GCAAAGCAACCAGGAGCATTA 59.454 47.619 10.59 0.00 0.00 1.90
4140 5138 5.809051 CAGGAGCATTATTTTGCCTTCTTTC 59.191 40.000 0.00 0.00 43.83 2.62
4145 5143 6.875726 AGCATTATTTTGCCTTCTTTCCTTTC 59.124 34.615 0.00 0.00 43.83 2.62
4231 5229 1.947642 GTTCCGCGACGTGTGTTCT 60.948 57.895 8.23 0.00 0.00 3.01
4232 5230 1.947146 TTCCGCGACGTGTGTTCTG 60.947 57.895 8.23 0.00 0.00 3.02
4266 5264 4.753877 TGAGAAGACGGCGTCGCG 62.754 66.667 31.59 0.00 40.63 5.87
4302 5300 1.588824 CGTCACTACGGTACCAGCCA 61.589 60.000 13.54 0.00 45.50 4.75
4311 5309 1.684869 CGGTACCAGCCATTTTCCCAT 60.685 52.381 13.54 0.00 0.00 4.00
4322 5321 3.565482 CCATTTTCCCATCTGGATACGTG 59.435 47.826 0.00 0.00 44.66 4.49
4325 5324 1.423584 TCCCATCTGGATACGTGCAT 58.576 50.000 0.00 0.00 38.61 3.96
4350 5349 8.630054 TTACATATTTATGGATACTGTTGGCC 57.370 34.615 0.00 0.00 38.00 5.36
4370 5369 3.177605 CGTTGCGGATCGTTTTTAACT 57.822 42.857 0.00 0.00 0.00 2.24
4371 5370 2.900046 CGTTGCGGATCGTTTTTAACTG 59.100 45.455 0.00 0.00 0.00 3.16
4378 5383 4.034048 CGGATCGTTTTTAACTGGGAGATG 59.966 45.833 0.00 0.00 0.00 2.90
4403 5408 1.923204 CGGAGAATGCTTCTTCTGACG 59.077 52.381 2.18 3.67 40.87 4.35
4449 5458 0.518636 CCCACTTGTGAAGCACGATG 59.481 55.000 1.89 0.00 37.14 3.84
4454 5463 4.260990 CCACTTGTGAAGCACGATGTTTTA 60.261 41.667 1.89 0.00 37.14 1.52
4455 5464 5.270083 CACTTGTGAAGCACGATGTTTTAA 58.730 37.500 0.00 0.00 37.14 1.52
4456 5465 5.741510 CACTTGTGAAGCACGATGTTTTAAA 59.258 36.000 0.00 0.00 37.14 1.52
4458 5467 4.286910 TGTGAAGCACGATGTTTTAAAGC 58.713 39.130 0.00 0.00 37.14 3.51
4459 5468 4.036262 TGTGAAGCACGATGTTTTAAAGCT 59.964 37.500 3.62 0.00 37.14 3.74
4460 5469 4.613031 GTGAAGCACGATGTTTTAAAGCTC 59.387 41.667 3.62 0.00 0.00 4.09
4461 5470 3.831715 AGCACGATGTTTTAAAGCTCC 57.168 42.857 3.62 0.00 0.00 4.70
4462 5471 2.488153 AGCACGATGTTTTAAAGCTCCC 59.512 45.455 3.62 0.00 0.00 4.30
4506 5522 4.937201 AGTTTGAAGGGATTTCACAACC 57.063 40.909 0.00 0.00 45.22 3.77
4545 5562 1.285280 TGTTTGACCATCGGATCCCT 58.715 50.000 6.06 0.00 0.00 4.20
4551 5568 1.490910 GACCATCGGATCCCTTTTCCT 59.509 52.381 6.06 0.00 0.00 3.36
4625 5643 3.531538 GTCAAATCTGGCGTTCCATCTA 58.468 45.455 0.00 0.00 42.51 1.98
4637 5655 3.060895 CGTTCCATCTAAGCGAAACTGAC 59.939 47.826 0.00 0.00 0.00 3.51
4641 5659 4.461431 TCCATCTAAGCGAAACTGACACTA 59.539 41.667 0.00 0.00 0.00 2.74
4642 5660 4.563184 CCATCTAAGCGAAACTGACACTAC 59.437 45.833 0.00 0.00 0.00 2.73
4663 8097 6.996879 ACTACTGCATACTTATCTCTCCGTTA 59.003 38.462 0.00 0.00 0.00 3.18
4670 8104 8.913656 GCATACTTATCTCTCCGTTATTGTTAC 58.086 37.037 0.00 0.00 0.00 2.50
4673 8107 8.064336 ACTTATCTCTCCGTTATTGTTACTGT 57.936 34.615 0.00 0.00 0.00 3.55
4674 8108 8.529476 ACTTATCTCTCCGTTATTGTTACTGTT 58.471 33.333 0.00 0.00 0.00 3.16
4676 8110 6.092955 TCTCTCCGTTATTGTTACTGTTGT 57.907 37.500 0.00 0.00 0.00 3.32
4704 8138 0.250684 TGCCCATCAAAACTCGCTCA 60.251 50.000 0.00 0.00 0.00 4.26
4717 8151 1.001406 CTCGCTCATTCCATACCCTCC 59.999 57.143 0.00 0.00 0.00 4.30
4775 8220 2.863137 GAGAGATTGATCTTCCACACGC 59.137 50.000 0.00 0.00 37.25 5.34
4810 8255 0.170339 GGGAAACATGTAACTGCCGC 59.830 55.000 0.00 0.00 0.00 6.53
4832 8277 3.399330 GTCAACTGCTAAAGTGCCACTA 58.601 45.455 0.00 0.00 39.81 2.74
4833 8278 3.186613 GTCAACTGCTAAAGTGCCACTAC 59.813 47.826 0.00 0.00 39.81 2.73
4834 8279 3.138304 CAACTGCTAAAGTGCCACTACA 58.862 45.455 0.00 0.00 39.81 2.74
4835 8280 3.703001 ACTGCTAAAGTGCCACTACAT 57.297 42.857 0.00 0.00 37.88 2.29
4836 8281 3.338249 ACTGCTAAAGTGCCACTACATG 58.662 45.455 0.00 0.00 37.88 3.21
4837 8282 3.244561 ACTGCTAAAGTGCCACTACATGT 60.245 43.478 2.69 2.69 37.88 3.21
4877 8322 6.553524 GTCAGTAGACCTGTCACTACATTAC 58.446 44.000 0.00 0.00 42.19 1.89
4905 8350 5.405571 ACTTGCACACTACTCGTTTCATAAG 59.594 40.000 0.00 0.00 0.00 1.73
4918 8363 8.552034 ACTCGTTTCATAAGAAGAAAAGAACAG 58.448 33.333 0.00 0.00 40.88 3.16
4919 8364 7.861630 TCGTTTCATAAGAAGAAAAGAACAGG 58.138 34.615 0.00 0.00 39.38 4.00
4920 8365 7.713507 TCGTTTCATAAGAAGAAAAGAACAGGA 59.286 33.333 0.00 0.00 39.38 3.86
4928 8373 7.117285 AGAAGAAAAGAACAGGAAAAATGCT 57.883 32.000 0.00 0.00 0.00 3.79
4981 8430 8.824159 ACACAATATTGTATCAGTATCAGAGC 57.176 34.615 20.39 0.00 39.91 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.136305 TCGAATAAAGAGTCAGGGGCG 59.864 52.381 0.00 0.00 0.00 6.13
62 63 2.827652 CTCGAATAAAGAGTCAGGGGC 58.172 52.381 0.00 0.00 0.00 5.80
67 68 1.797713 CGCGGCTCGAATAAAGAGTCA 60.798 52.381 0.00 0.00 40.12 3.41
68 69 0.847035 CGCGGCTCGAATAAAGAGTC 59.153 55.000 0.00 0.00 41.67 3.36
69 70 0.527817 CCGCGGCTCGAATAAAGAGT 60.528 55.000 14.67 0.00 41.67 3.24
191 201 2.263540 GGTTTCCGCGCTCACCTA 59.736 61.111 5.56 0.00 0.00 3.08
192 202 4.699522 GGGTTTCCGCGCTCACCT 62.700 66.667 5.56 0.00 0.00 4.00
193 203 4.699522 AGGGTTTCCGCGCTCACC 62.700 66.667 5.56 5.33 38.33 4.02
194 204 3.423154 CAGGGTTTCCGCGCTCAC 61.423 66.667 5.56 0.00 38.33 3.51
212 230 5.985175 TCATCCCCATCCATTAGTTAACA 57.015 39.130 8.61 0.00 0.00 2.41
243 381 8.870075 AAGGATACCTATCAAAGCATAAATCC 57.130 34.615 0.00 0.00 34.40 3.01
341 480 0.605319 GTGGCGGTGGATCTCAACAA 60.605 55.000 0.00 0.00 30.96 2.83
342 481 1.003839 GTGGCGGTGGATCTCAACA 60.004 57.895 0.00 0.00 30.96 3.33
346 485 2.187946 CAGGTGGCGGTGGATCTC 59.812 66.667 0.00 0.00 0.00 2.75
377 520 3.486841 CACACAGTTATGCAACAACAAGC 59.513 43.478 14.77 0.00 37.10 4.01
493 648 4.944048 AGGGTTCAAAAAGAAATGTTCCG 58.056 39.130 0.00 0.00 38.13 4.30
534 689 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
537 692 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
538 693 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
539 694 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
540 695 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
541 696 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
543 698 4.996788 TCTAGGACAAGTATTTCCGGAC 57.003 45.455 1.83 0.00 36.95 4.79
544 699 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
545 700 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
546 701 6.346096 TCCATTTCTAGGACAAGTATTTCCG 58.654 40.000 0.00 0.00 36.95 4.30
547 702 9.847224 TTATCCATTTCTAGGACAAGTATTTCC 57.153 33.333 0.00 0.00 38.13 3.13
552 707 9.627123 CCATTTTATCCATTTCTAGGACAAGTA 57.373 33.333 0.00 0.00 38.13 2.24
553 708 8.336235 TCCATTTTATCCATTTCTAGGACAAGT 58.664 33.333 0.00 0.00 38.13 3.16
556 711 8.281531 ACATCCATTTTATCCATTTCTAGGACA 58.718 33.333 0.00 0.00 38.13 4.02
557 712 8.697507 ACATCCATTTTATCCATTTCTAGGAC 57.302 34.615 0.00 0.00 38.13 3.85
597 752 9.931698 TCCTATGAAAGGTTGTATCTAGACTTA 57.068 33.333 0.00 0.00 46.62 2.24
598 753 8.697292 GTCCTATGAAAGGTTGTATCTAGACTT 58.303 37.037 0.00 0.00 46.62 3.01
599 754 7.839705 TGTCCTATGAAAGGTTGTATCTAGACT 59.160 37.037 0.00 0.00 46.62 3.24
600 755 8.008513 TGTCCTATGAAAGGTTGTATCTAGAC 57.991 38.462 0.00 0.00 46.62 2.59
601 756 8.603898 TTGTCCTATGAAAGGTTGTATCTAGA 57.396 34.615 0.00 0.00 46.62 2.43
602 757 8.478877 ACTTGTCCTATGAAAGGTTGTATCTAG 58.521 37.037 0.00 0.00 46.62 2.43
603 758 8.375493 ACTTGTCCTATGAAAGGTTGTATCTA 57.625 34.615 0.00 0.00 46.62 1.98
604 759 7.259088 ACTTGTCCTATGAAAGGTTGTATCT 57.741 36.000 0.00 0.00 46.62 1.98
605 760 9.614792 AATACTTGTCCTATGAAAGGTTGTATC 57.385 33.333 0.00 0.00 46.62 2.24
606 761 9.975218 AAATACTTGTCCTATGAAAGGTTGTAT 57.025 29.630 0.00 0.00 46.62 2.29
607 762 9.444600 GAAATACTTGTCCTATGAAAGGTTGTA 57.555 33.333 0.00 0.00 46.62 2.41
608 763 7.393515 GGAAATACTTGTCCTATGAAAGGTTGT 59.606 37.037 0.00 0.00 46.62 3.32
609 764 7.414098 CGGAAATACTTGTCCTATGAAAGGTTG 60.414 40.741 0.00 0.00 46.62 3.77
610 765 6.598064 CGGAAATACTTGTCCTATGAAAGGTT 59.402 38.462 0.00 0.00 46.62 3.50
611 766 6.113411 CGGAAATACTTGTCCTATGAAAGGT 58.887 40.000 0.00 0.00 46.62 3.50
613 768 6.346096 TCCGGAAATACTTGTCCTATGAAAG 58.654 40.000 0.00 0.00 0.00 2.62
614 769 6.302535 TCCGGAAATACTTGTCCTATGAAA 57.697 37.500 0.00 0.00 0.00 2.69
615 770 5.163343 CCTCCGGAAATACTTGTCCTATGAA 60.163 44.000 5.23 0.00 0.00 2.57
616 771 4.344102 CCTCCGGAAATACTTGTCCTATGA 59.656 45.833 5.23 0.00 0.00 2.15
617 772 4.503296 CCCTCCGGAAATACTTGTCCTATG 60.503 50.000 5.23 0.00 0.00 2.23
618 773 3.646637 CCCTCCGGAAATACTTGTCCTAT 59.353 47.826 5.23 0.00 0.00 2.57
619 774 3.036091 CCCTCCGGAAATACTTGTCCTA 58.964 50.000 5.23 0.00 0.00 2.94
620 775 1.838077 CCCTCCGGAAATACTTGTCCT 59.162 52.381 5.23 0.00 0.00 3.85
621 776 1.134189 CCCCTCCGGAAATACTTGTCC 60.134 57.143 5.23 0.00 0.00 4.02
622 777 1.134189 CCCCCTCCGGAAATACTTGTC 60.134 57.143 5.23 0.00 0.00 3.18
623 778 0.916809 CCCCCTCCGGAAATACTTGT 59.083 55.000 5.23 0.00 0.00 3.16
624 779 0.916809 ACCCCCTCCGGAAATACTTG 59.083 55.000 5.23 0.00 0.00 3.16
625 780 2.121948 GTACCCCCTCCGGAAATACTT 58.878 52.381 5.23 0.00 0.00 2.24
626 781 1.693726 GGTACCCCCTCCGGAAATACT 60.694 57.143 5.23 0.00 0.00 2.12
627 782 0.761187 GGTACCCCCTCCGGAAATAC 59.239 60.000 5.23 3.77 0.00 1.89
628 783 0.643822 AGGTACCCCCTCCGGAAATA 59.356 55.000 8.74 0.00 40.71 1.40
629 784 0.253488 AAGGTACCCCCTCCGGAAAT 60.253 55.000 8.74 0.00 45.47 2.17
630 785 0.476219 AAAGGTACCCCCTCCGGAAA 60.476 55.000 8.74 0.00 45.47 3.13
631 786 1.161598 AAAGGTACCCCCTCCGGAA 59.838 57.895 8.74 0.00 45.47 4.30
632 787 1.614226 CAAAGGTACCCCCTCCGGA 60.614 63.158 8.74 2.93 45.47 5.14
633 788 1.494716 AACAAAGGTACCCCCTCCGG 61.495 60.000 8.74 0.00 45.47 5.14
634 789 0.322187 CAACAAAGGTACCCCCTCCG 60.322 60.000 8.74 0.00 45.47 4.63
635 790 0.039180 CCAACAAAGGTACCCCCTCC 59.961 60.000 8.74 0.00 45.47 4.30
636 791 0.775542 ACCAACAAAGGTACCCCCTC 59.224 55.000 8.74 0.00 45.47 4.30
638 793 0.186630 ACACCAACAAAGGTACCCCC 59.813 55.000 8.74 0.00 40.77 5.40
639 794 2.955342 TACACCAACAAAGGTACCCC 57.045 50.000 8.74 0.00 40.77 4.95
640 795 3.824133 ACTTACACCAACAAAGGTACCC 58.176 45.455 8.74 0.00 40.77 3.69
641 796 5.367302 TGTACTTACACCAACAAAGGTACC 58.633 41.667 2.73 2.73 40.77 3.34
642 797 8.606040 TTATGTACTTACACCAACAAAGGTAC 57.394 34.615 0.00 0.00 40.77 3.34
682 845 3.124976 GCACAAACTTTCAAGCAAAAGCA 59.875 39.130 6.26 0.00 39.39 3.91
806 1360 9.577110 GATATGTTTCAGATCAGAAAATTTGCA 57.423 29.630 14.13 8.62 39.05 4.08
935 1497 4.984146 ATTGATCTAGCCCTAGGAAACC 57.016 45.455 11.48 0.00 34.06 3.27
1062 1627 3.688272 CTTCAGGCAATGCAACTTATCG 58.312 45.455 7.79 0.00 0.00 2.92
1089 1654 7.552687 TCACCTGATGACTTGTTGGTATATTTC 59.447 37.037 0.00 0.00 29.99 2.17
1189 1754 4.217118 AGCACCTACTTTTCTGCTTCAATG 59.783 41.667 0.00 0.00 36.57 2.82
1242 1810 4.974645 AGAACTTAACAGGGACATGTGA 57.025 40.909 1.15 0.00 32.52 3.58
1532 2106 9.899226 ATAAGACAAGAAACATGAACTTAAAGC 57.101 29.630 0.00 0.00 30.91 3.51
1677 2255 1.081641 CTCGCCTTTTGCACAGCTG 60.082 57.895 13.48 13.48 41.33 4.24
1905 2483 0.391130 AAGACACACACACACGCACT 60.391 50.000 0.00 0.00 0.00 4.40
2022 2618 5.400066 TTGACATGACGAGACTCCAAATA 57.600 39.130 0.00 0.00 0.00 1.40
2660 3318 2.356382 CGGTTGGTTACTTGTTTGCTGA 59.644 45.455 0.00 0.00 0.00 4.26
2908 3616 1.080974 CGCTGCAGCAAGAAAAGGG 60.081 57.895 36.03 14.34 42.21 3.95
2993 3708 0.674581 TTGGCTCATCTGGCTTCACG 60.675 55.000 0.00 0.00 0.00 4.35
3007 3725 3.500343 GCCCTAAATGATACCATTGGCT 58.500 45.455 1.54 0.00 41.97 4.75
3173 3925 3.509740 GCTTAGACCTAAACTGTCGGTC 58.490 50.000 13.03 13.03 45.88 4.79
3272 4058 9.482627 GGTGATCTTTACAGGATCTATAACTTG 57.517 37.037 0.00 0.00 39.95 3.16
3416 4226 7.496529 TTGAAAATACAGAGTTCTCACAAGG 57.503 36.000 2.64 0.00 0.00 3.61
3470 4281 6.597672 ACGAAATACAGGATGCACAGAAAATA 59.402 34.615 0.00 0.00 42.53 1.40
3478 4289 4.678509 TTTGACGAAATACAGGATGCAC 57.321 40.909 0.00 0.00 42.53 4.57
3508 4319 9.971922 CCAAAGTTTCAAAGAGAATATCTGTTT 57.028 29.630 0.00 0.00 40.10 2.83
3545 4356 3.191791 GCCCGCTCAGGTTTTACATAAAA 59.808 43.478 0.00 0.00 38.74 1.52
3547 4358 2.026636 AGCCCGCTCAGGTTTTACATAA 60.027 45.455 0.00 0.00 38.74 1.90
3563 4374 0.451783 GCCATTCACAAGTAAGCCCG 59.548 55.000 0.00 0.00 0.00 6.13
3591 4402 9.003112 CAATGTAACGATGAAGAATTGATCAAC 57.997 33.333 11.07 0.00 38.72 3.18
3596 4407 6.741992 AGCAATGTAACGATGAAGAATTGA 57.258 33.333 0.00 0.00 0.00 2.57
3665 4482 5.334414 GCAACATACCACTGAACTTCTCAAG 60.334 44.000 0.00 0.00 32.17 3.02
3735 4552 1.417890 AGGACAACAGGTGAGTTCCAG 59.582 52.381 0.00 0.00 0.00 3.86
3774 4591 2.766263 ACGATATGCCTCTTCCTCAACA 59.234 45.455 0.00 0.00 0.00 3.33
3781 4598 2.072298 GCCATCACGATATGCCTCTTC 58.928 52.381 0.00 0.00 0.00 2.87
3969 4960 5.316987 ACTGGTCCCTGTAAATGAAAGAAG 58.683 41.667 0.00 0.00 0.00 2.85
4016 5007 8.151141 ACATGAAATAGAAGTGCATCACTATG 57.849 34.615 0.00 1.23 44.62 2.23
4099 5090 2.101249 TCCTGGTTGCTTTGCTTCTTTG 59.899 45.455 0.00 0.00 0.00 2.77
4116 5114 4.996788 AGAAGGCAAAATAATGCTCCTG 57.003 40.909 0.00 0.00 45.68 3.86
4294 5292 2.358090 CCAGATGGGAAAATGGCTGGTA 60.358 50.000 0.00 0.00 40.01 3.25
4311 5309 9.150348 CATAAATATGTAATGCACGTATCCAGA 57.850 33.333 0.00 0.00 38.21 3.86
4325 5324 7.389330 CGGCCAACAGTATCCATAAATATGTAA 59.611 37.037 2.24 0.00 31.82 2.41
4350 5349 2.900046 CAGTTAAAAACGATCCGCAACG 59.100 45.455 0.00 0.00 36.23 4.10
4357 5356 4.636206 AGCATCTCCCAGTTAAAAACGATC 59.364 41.667 0.00 0.00 36.23 3.69
4367 5366 0.904865 TCCGTCAGCATCTCCCAGTT 60.905 55.000 0.00 0.00 0.00 3.16
4368 5367 1.305297 TCCGTCAGCATCTCCCAGT 60.305 57.895 0.00 0.00 0.00 4.00
4370 5369 0.614697 TTCTCCGTCAGCATCTCCCA 60.615 55.000 0.00 0.00 0.00 4.37
4371 5370 0.755686 ATTCTCCGTCAGCATCTCCC 59.244 55.000 0.00 0.00 0.00 4.30
4403 5408 1.140816 GCGTCTGTTCAGACTTGTCC 58.859 55.000 24.21 8.95 36.71 4.02
4449 5458 5.483685 AAATTCCCTGGGAGCTTTAAAAC 57.516 39.130 16.38 0.00 31.21 2.43
4454 5463 3.586429 TGAAAAATTCCCTGGGAGCTTT 58.414 40.909 16.38 16.00 31.21 3.51
4455 5464 3.258722 TGAAAAATTCCCTGGGAGCTT 57.741 42.857 16.38 10.88 31.21 3.74
4456 5465 2.999185 TGAAAAATTCCCTGGGAGCT 57.001 45.000 16.38 4.74 31.21 4.09
4458 5467 4.151883 TGACTTGAAAAATTCCCTGGGAG 58.848 43.478 16.38 3.37 31.21 4.30
4459 5468 4.191804 TGACTTGAAAAATTCCCTGGGA 57.808 40.909 12.53 12.53 0.00 4.37
4460 5469 4.953940 TTGACTTGAAAAATTCCCTGGG 57.046 40.909 6.33 6.33 0.00 4.45
4461 5470 5.669477 TGTTTGACTTGAAAAATTCCCTGG 58.331 37.500 0.00 0.00 0.00 4.45
4462 5471 6.818142 ACTTGTTTGACTTGAAAAATTCCCTG 59.182 34.615 0.00 0.00 0.00 4.45
4493 5509 2.985896 TCAGATCGGTTGTGAAATCCC 58.014 47.619 0.00 0.00 0.00 3.85
4501 5517 1.573108 ACCAGGATCAGATCGGTTGT 58.427 50.000 4.23 0.00 0.00 3.32
4506 5522 2.322355 AAGCAACCAGGATCAGATCG 57.678 50.000 4.23 0.00 0.00 3.69
4545 5562 2.031120 CAGGCAAGTTGGTGAGGAAAA 58.969 47.619 4.75 0.00 0.00 2.29
4551 5568 1.003580 GATCTCCAGGCAAGTTGGTGA 59.996 52.381 4.75 0.00 41.06 4.02
4625 5643 2.135933 GCAGTAGTGTCAGTTTCGCTT 58.864 47.619 0.00 0.00 0.00 4.68
4637 5655 5.239744 ACGGAGAGATAAGTATGCAGTAGTG 59.760 44.000 0.00 0.00 0.00 2.74
4641 5659 6.902771 ATAACGGAGAGATAAGTATGCAGT 57.097 37.500 0.00 0.00 0.00 4.40
4642 5660 7.148641 ACAATAACGGAGAGATAAGTATGCAG 58.851 38.462 0.00 0.00 0.00 4.41
4663 8097 3.381272 ACAGCAGCAACAACAGTAACAAT 59.619 39.130 0.00 0.00 0.00 2.71
4670 8104 1.299620 GGCACAGCAGCAACAACAG 60.300 57.895 0.00 0.00 35.83 3.16
4673 8107 1.808531 GATGGGCACAGCAGCAACAA 61.809 55.000 0.00 0.00 35.83 2.83
4674 8108 2.203523 ATGGGCACAGCAGCAACA 60.204 55.556 0.00 0.00 35.83 3.33
4676 8110 1.114119 TTTGATGGGCACAGCAGCAA 61.114 50.000 7.12 0.00 44.77 3.91
4775 8220 4.638421 TGTTTCCCTTCTAACACACACAAG 59.362 41.667 0.00 0.00 29.82 3.16
4810 8255 1.069906 GTGGCACTTTAGCAGTTGACG 60.070 52.381 11.13 0.00 30.92 4.35
4832 8277 1.213537 CGACGTCCGGGTTACATGT 59.786 57.895 10.58 2.69 33.91 3.21
4833 8278 0.799534 GTCGACGTCCGGGTTACATG 60.800 60.000 10.58 0.00 39.14 3.21
4834 8279 1.508088 GTCGACGTCCGGGTTACAT 59.492 57.895 10.58 0.00 39.14 2.29
4835 8280 2.953821 GTCGACGTCCGGGTTACA 59.046 61.111 10.58 0.00 39.14 2.41
4836 8281 2.202349 CGTCGACGTCCGGGTTAC 60.202 66.667 29.08 0.00 39.14 2.50
4877 8322 3.833545 ACGAGTAGTGTGCAAGTAGAG 57.166 47.619 0.00 0.00 0.00 2.43
4905 8350 8.871686 TTAGCATTTTTCCTGTTCTTTTCTTC 57.128 30.769 0.00 0.00 0.00 2.87
4916 8361 7.229306 TCAGCCATATACTTAGCATTTTTCCTG 59.771 37.037 0.00 0.00 0.00 3.86
4918 8363 7.510549 TCAGCCATATACTTAGCATTTTTCC 57.489 36.000 0.00 0.00 0.00 3.13
4919 8364 7.540055 GCATCAGCCATATACTTAGCATTTTTC 59.460 37.037 0.00 0.00 33.58 2.29
4920 8365 7.014518 TGCATCAGCCATATACTTAGCATTTTT 59.985 33.333 0.00 0.00 41.13 1.94
4926 8371 4.756642 TGTTGCATCAGCCATATACTTAGC 59.243 41.667 0.00 0.00 41.13 3.09
4928 8373 6.118852 TGTTGTTGCATCAGCCATATACTTA 58.881 36.000 8.86 0.00 41.13 2.24
4981 8430 5.523916 CGTTACTTGGGGAAATCAGTCTATG 59.476 44.000 0.00 0.00 0.00 2.23
4987 8436 4.069304 TGTTCGTTACTTGGGGAAATCAG 58.931 43.478 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.