Multiple sequence alignment - TraesCS3A01G220900

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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 TraesCS3A01G220900 chr3A 100.000 4599 0 0 1 4599 410039409 410044007 0.000000e+00 8493
1 TraesCS3A01G220900 chr3A 93.040 4454 290 16 1 4449 312244734 312249172 0.000000e+00 6490
2 TraesCS3A01G220900 chr3A 96.918 1655 46 5 1 1653 410048928 410050579 0.000000e+00 2769
3 TraesCS3A01G220900 chr3A 90.634 1655 139 11 1 1652 312261615 312263256 0.000000e+00 2183
4 TraesCS3A01G220900 chr7A 95.656 4466 178 10 1 4455 647053563 647049103 0.000000e+00 7158
5 TraesCS3A01G220900 chr4A 94.584 4450 226 8 7 4449 548058701 548063142 0.000000e+00 6868
6 TraesCS3A01G220900 chr4A 94.447 4106 211 8 352 4455 327020940 327025030 0.000000e+00 6303
7 TraesCS3A01G220900 chr4A 98.658 149 2 0 4451 4599 109512892 109512744 9.810000e-67 265
8 TraesCS3A01G220900 chr4A 98.658 149 2 0 4451 4599 610968468 610968320 9.810000e-67 265
9 TraesCS3A01G220900 chr6A 94.254 4107 221 7 352 4455 94639815 94635721 0.000000e+00 6263
10 TraesCS3A01G220900 chr6A 98.658 149 2 0 4451 4599 254270353 254270205 9.810000e-67 265
11 TraesCS3A01G220900 chr2A 91.385 4109 312 24 352 4455 396588776 396592847 0.000000e+00 5589
12 TraesCS3A01G220900 chr2A 98.026 152 3 0 4448 4599 396601617 396601768 9.810000e-67 265
13 TraesCS3A01G220900 chr5A 93.869 3507 197 11 953 4455 67822514 67819022 0.000000e+00 5269
14 TraesCS3A01G220900 chr5A 97.987 149 3 0 4451 4599 67810079 67809931 4.560000e-65 259
15 TraesCS3A01G220900 chr3B 91.360 3854 306 17 618 4463 379335650 379331816 0.000000e+00 5247
16 TraesCS3A01G220900 chr6B 91.298 3505 277 18 963 4463 133785484 133788964 0.000000e+00 4758
17 TraesCS3A01G220900 chr5B 88.648 1894 178 28 1 1887 404470423 404468560 0.000000e+00 2272
18 TraesCS3A01G220900 chr1A 88.179 1895 171 36 7 1887 483487847 483485992 0.000000e+00 2209
19 TraesCS3A01G220900 chr1A 88.074 1895 173 36 7 1887 483474619 483472764 0.000000e+00 2198
20 TraesCS3A01G220900 chrUn 98.658 149 2 0 4451 4599 284015666 284015518 9.810000e-67 265
21 TraesCS3A01G220900 chr7B 98.026 152 3 0 4448 4599 258337566 258337717 9.810000e-67 265
22 TraesCS3A01G220900 chr6D 97.368 152 4 0 4448 4599 30039598 30039749 4.560000e-65 259
23 TraesCS3A01G220900 chr6D 97.368 152 4 0 4448 4599 192178154 192178305 4.560000e-65 259


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 TraesCS3A01G220900 chr3A 410039409 410044007 4598 False 8493 8493 100.000 1 4599 1 chr3A.!!$F3 4598
1 TraesCS3A01G220900 chr3A 312244734 312249172 4438 False 6490 6490 93.040 1 4449 1 chr3A.!!$F1 4448
2 TraesCS3A01G220900 chr3A 410048928 410050579 1651 False 2769 2769 96.918 1 1653 1 chr3A.!!$F4 1652
3 TraesCS3A01G220900 chr3A 312261615 312263256 1641 False 2183 2183 90.634 1 1652 1 chr3A.!!$F2 1651
4 TraesCS3A01G220900 chr7A 647049103 647053563 4460 True 7158 7158 95.656 1 4455 1 chr7A.!!$R1 4454
5 TraesCS3A01G220900 chr4A 548058701 548063142 4441 False 6868 6868 94.584 7 4449 1 chr4A.!!$F2 4442
6 TraesCS3A01G220900 chr4A 327020940 327025030 4090 False 6303 6303 94.447 352 4455 1 chr4A.!!$F1 4103
7 TraesCS3A01G220900 chr6A 94635721 94639815 4094 True 6263 6263 94.254 352 4455 1 chr6A.!!$R1 4103
8 TraesCS3A01G220900 chr2A 396588776 396592847 4071 False 5589 5589 91.385 352 4455 1 chr2A.!!$F1 4103
9 TraesCS3A01G220900 chr5A 67819022 67822514 3492 True 5269 5269 93.869 953 4455 1 chr5A.!!$R2 3502
10 TraesCS3A01G220900 chr3B 379331816 379335650 3834 True 5247 5247 91.360 618 4463 1 chr3B.!!$R1 3845
11 TraesCS3A01G220900 chr6B 133785484 133788964 3480 False 4758 4758 91.298 963 4463 1 chr6B.!!$F1 3500
12 TraesCS3A01G220900 chr5B 404468560 404470423 1863 True 2272 2272 88.648 1 1887 1 chr5B.!!$R1 1886
13 TraesCS3A01G220900 chr1A 483485992 483487847 1855 True 2209 2209 88.179 7 1887 1 chr1A.!!$R2 1880
14 TraesCS3A01G220900 chr1A 483472764 483474619 1855 True 2198 2198 88.074 7 1887 1 chr1A.!!$R1 1880

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
273 280 0.037326 TACGAGCAGGGCAAGACTTG 60.037 55.0 11.02 11.02 0.00 3.16 F
1059 1085 0.177141 ATTACGCTACACACGGGCAT 59.823 50.0 0.00 0.00 34.00 4.40 F
2359 2407 0.396974 AACACAAAGGGCTTGCTCCA 60.397 50.0 0.00 0.00 38.75 3.86 F
2934 2982 1.575244 CCATCATGCGGTGTGTAGAG 58.425 55.0 0.00 0.00 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2036 1.971481 TGCTGACTTTGTGAGCACAT 58.029 45.0 7.69 0.0 44.52 3.21 R
2489 2537 0.620556 CTCACCCACTAGGCATGGTT 59.379 55.0 0.00 0.0 40.58 3.67 R
3355 3403 0.473694 TCTGAACCCTTCTGGCTCCA 60.474 55.0 0.00 0.0 37.83 3.86 R
4513 4563 0.036952 ACACGACCATCCTGAGCTTG 60.037 55.0 0.00 0.0 0.00 4.01 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
106 111 9.788960 GGAATGAAATTATGAAGTCACTAAACC 57.211 33.333 0.00 0.00 36.07 3.27
143 148 1.740585 CTTGTTTGGTTGTGTCACGGA 59.259 47.619 0.00 0.00 0.00 4.69
182 187 4.610945 AGTTGCAATACAAACAAGAGCAC 58.389 39.130 0.59 0.00 40.82 4.40
273 280 0.037326 TACGAGCAGGGCAAGACTTG 60.037 55.000 11.02 11.02 0.00 3.16
282 290 5.246883 AGCAGGGCAAGACTTGATTAAAAAT 59.753 36.000 19.51 0.00 0.00 1.82
316 325 6.370442 CGATACACACCTAGAAACCAAATCAA 59.630 38.462 0.00 0.00 0.00 2.57
563 575 4.893424 TCACAAACTCACTTTACTTGGC 57.107 40.909 0.00 0.00 0.00 4.52
616 628 7.967303 GTGACACTATGTGGAGTTAGTACTAAC 59.033 40.741 30.33 30.33 40.52 2.34
756 776 5.094812 CACGCGGTGTTAGTAGTAATACAA 58.905 41.667 12.47 0.00 33.13 2.41
975 1001 3.340034 ACCGTGTGAAGTCAAAGTCAAA 58.660 40.909 0.00 0.00 0.00 2.69
1059 1085 0.177141 ATTACGCTACACACGGGCAT 59.823 50.000 0.00 0.00 34.00 4.40
1935 1983 1.526575 AAACAACAGCTGCATCCCCG 61.527 55.000 15.27 0.00 0.00 5.73
1988 2036 2.637872 CACTGAAGGAGGGGTTTACTCA 59.362 50.000 0.00 0.00 36.70 3.41
2317 2365 5.104900 GGGTTAGGAGAAAGCTCACATAAGA 60.105 44.000 0.00 0.00 43.14 2.10
2328 2376 6.506538 AGCTCACATAAGATTATCCCAAGT 57.493 37.500 0.00 0.00 0.00 3.16
2359 2407 0.396974 AACACAAAGGGCTTGCTCCA 60.397 50.000 0.00 0.00 38.75 3.86
2408 2456 2.158385 AGGACACTGAGTCTTCCTCACT 60.158 50.000 6.48 0.00 45.34 3.41
2572 2620 4.528206 TCACTTCAGATGACTTCCAAGCTA 59.472 41.667 0.00 0.00 0.00 3.32
2872 2920 3.126073 GTTTGCCAAGCTTTGAAGGAAG 58.874 45.455 0.86 0.00 0.00 3.46
2912 2960 4.824479 TCTCTGCTGATAATGTTGGTGA 57.176 40.909 0.00 0.00 0.00 4.02
2934 2982 1.575244 CCATCATGCGGTGTGTAGAG 58.425 55.000 0.00 0.00 0.00 2.43
3058 3106 5.072741 CCCTGAAACAAAGAGAGATGGAAA 58.927 41.667 0.00 0.00 0.00 3.13
3095 3143 6.053005 CGGGTTATAGCAGAATACAAGGAAA 58.947 40.000 0.00 0.00 0.00 3.13
3124 3172 3.072330 TCCATCAACAAGCCAAGTCAGTA 59.928 43.478 0.00 0.00 0.00 2.74
3135 3183 3.055094 GCCAAGTCAGTAGAGGAAATGGA 60.055 47.826 0.00 0.00 0.00 3.41
3354 3402 4.980805 GGTCCTTGCCGCACGACA 62.981 66.667 17.44 0.00 0.00 4.35
3355 3403 2.742372 GTCCTTGCCGCACGACAT 60.742 61.111 12.80 0.00 0.00 3.06
3645 3694 2.358737 GGTGGCGCAAGTGCTAGT 60.359 61.111 10.83 0.00 39.32 2.57
3697 3746 3.118298 TGAGGCGATCCAAAGAATGATCA 60.118 43.478 0.00 0.00 33.74 2.92
3700 3749 4.101585 AGGCGATCCAAAGAATGATCACTA 59.898 41.667 0.00 0.00 33.74 2.74
3742 3791 3.934457 TGCAAACTCAGTACTCGATGA 57.066 42.857 0.00 0.00 0.00 2.92
4148 4197 0.828022 CATTGCCCACAGCCAATCAT 59.172 50.000 0.00 0.00 42.71 2.45
4381 4430 1.001764 TCTGCACAAGCCATGGAGG 60.002 57.895 18.40 6.02 41.13 4.30
4466 4516 4.329545 GCAGGTGCGGGAGGTTGA 62.330 66.667 0.00 0.00 0.00 3.18
4467 4517 2.671070 CAGGTGCGGGAGGTTGAT 59.329 61.111 0.00 0.00 0.00 2.57
4468 4518 1.904771 CAGGTGCGGGAGGTTGATA 59.095 57.895 0.00 0.00 0.00 2.15
4469 4519 0.251916 CAGGTGCGGGAGGTTGATAA 59.748 55.000 0.00 0.00 0.00 1.75
4470 4520 0.252197 AGGTGCGGGAGGTTGATAAC 59.748 55.000 0.00 0.00 0.00 1.89
4471 4521 0.035820 GGTGCGGGAGGTTGATAACA 60.036 55.000 0.00 0.00 0.00 2.41
4472 4522 1.612199 GGTGCGGGAGGTTGATAACAA 60.612 52.381 0.00 0.00 0.00 2.83
4484 4534 5.591643 GTTGATAACAACGAGCTGAGAAA 57.408 39.130 0.00 0.00 45.06 2.52
4485 4535 5.612865 GTTGATAACAACGAGCTGAGAAAG 58.387 41.667 0.00 0.00 45.06 2.62
4486 4536 5.134202 TGATAACAACGAGCTGAGAAAGA 57.866 39.130 0.00 0.00 0.00 2.52
4487 4537 5.724328 TGATAACAACGAGCTGAGAAAGAT 58.276 37.500 0.00 0.00 0.00 2.40
4488 4538 5.578336 TGATAACAACGAGCTGAGAAAGATG 59.422 40.000 0.00 0.00 0.00 2.90
4489 4539 2.693069 ACAACGAGCTGAGAAAGATGG 58.307 47.619 0.00 0.00 0.00 3.51
4490 4540 1.396301 CAACGAGCTGAGAAAGATGGC 59.604 52.381 0.00 0.00 0.00 4.40
4491 4541 0.107945 ACGAGCTGAGAAAGATGGCC 60.108 55.000 0.00 0.00 0.00 5.36
4492 4542 0.813210 CGAGCTGAGAAAGATGGCCC 60.813 60.000 0.00 0.00 0.00 5.80
4493 4543 0.545646 GAGCTGAGAAAGATGGCCCT 59.454 55.000 0.00 0.00 0.00 5.19
4494 4544 0.255318 AGCTGAGAAAGATGGCCCTG 59.745 55.000 0.00 0.00 0.00 4.45
4495 4545 1.382692 GCTGAGAAAGATGGCCCTGC 61.383 60.000 0.00 0.00 0.00 4.85
4507 4557 4.838152 CCCTGCCGTCCATCCACG 62.838 72.222 0.00 0.00 39.61 4.94
4508 4558 4.082523 CCTGCCGTCCATCCACGT 62.083 66.667 0.00 0.00 38.14 4.49
4509 4559 2.815211 CTGCCGTCCATCCACGTG 60.815 66.667 9.08 9.08 38.14 4.49
4510 4560 4.386951 TGCCGTCCATCCACGTGG 62.387 66.667 29.26 29.26 38.14 4.94
4511 4561 4.388499 GCCGTCCATCCACGTGGT 62.388 66.667 32.74 18.15 40.27 4.16
4512 4562 2.125673 CCGTCCATCCACGTGGTC 60.126 66.667 32.74 17.47 40.27 4.02
4513 4563 2.125673 CGTCCATCCACGTGGTCC 60.126 66.667 32.74 16.03 40.27 4.46
4514 4564 2.938086 CGTCCATCCACGTGGTCCA 61.938 63.158 32.74 15.85 40.27 4.02
4515 4565 1.373435 GTCCATCCACGTGGTCCAA 59.627 57.895 32.74 15.46 40.27 3.53
4516 4566 0.673644 GTCCATCCACGTGGTCCAAG 60.674 60.000 32.74 18.16 40.27 3.61
4517 4567 2.040544 CCATCCACGTGGTCCAAGC 61.041 63.158 32.74 0.00 34.46 4.01
4518 4568 1.003355 CATCCACGTGGTCCAAGCT 60.003 57.895 32.74 8.43 36.34 3.74
4519 4569 1.021390 CATCCACGTGGTCCAAGCTC 61.021 60.000 32.74 0.00 36.34 4.09
4520 4570 1.480212 ATCCACGTGGTCCAAGCTCA 61.480 55.000 32.74 11.90 36.34 4.26
4521 4571 1.669115 CCACGTGGTCCAAGCTCAG 60.669 63.158 26.95 0.00 0.00 3.35
4522 4572 1.669115 CACGTGGTCCAAGCTCAGG 60.669 63.158 7.95 0.00 0.00 3.86
4523 4573 1.837051 ACGTGGTCCAAGCTCAGGA 60.837 57.895 4.52 3.84 0.00 3.86
4524 4574 1.194781 ACGTGGTCCAAGCTCAGGAT 61.195 55.000 10.70 0.00 37.52 3.24
4525 4575 0.742281 CGTGGTCCAAGCTCAGGATG 60.742 60.000 10.70 0.00 37.52 3.51
4526 4576 0.393537 GTGGTCCAAGCTCAGGATGG 60.394 60.000 10.70 3.12 37.52 3.51
4527 4577 0.842030 TGGTCCAAGCTCAGGATGGT 60.842 55.000 10.70 0.00 37.52 3.55
4528 4578 0.107459 GGTCCAAGCTCAGGATGGTC 60.107 60.000 10.70 1.07 37.52 4.02
4529 4579 0.460987 GTCCAAGCTCAGGATGGTCG 60.461 60.000 10.70 0.00 37.52 4.79
4530 4580 0.904865 TCCAAGCTCAGGATGGTCGT 60.905 55.000 3.84 0.00 36.16 4.34
4531 4581 0.742281 CCAAGCTCAGGATGGTCGTG 60.742 60.000 0.00 0.00 36.16 4.35
4532 4582 0.036952 CAAGCTCAGGATGGTCGTGT 60.037 55.000 0.00 0.00 36.16 4.49
4533 4583 0.036952 AAGCTCAGGATGGTCGTGTG 60.037 55.000 0.00 0.00 36.16 3.82
4534 4584 1.448540 GCTCAGGATGGTCGTGTGG 60.449 63.158 0.36 0.00 36.16 4.17
4535 4585 1.975327 CTCAGGATGGTCGTGTGGT 59.025 57.895 0.36 0.00 36.16 4.16
4536 4586 1.182667 CTCAGGATGGTCGTGTGGTA 58.817 55.000 0.36 0.00 36.16 3.25
4537 4587 0.892755 TCAGGATGGTCGTGTGGTAC 59.107 55.000 0.36 0.00 36.16 3.34
4538 4588 2.820656 TCAGGATGGTCGTGTGGTACG 61.821 57.143 0.00 0.00 45.92 3.67
4546 4596 3.502237 CGTGTGGTACGCCTAACTT 57.498 52.632 0.00 0.00 46.92 2.66
4547 4597 1.343506 CGTGTGGTACGCCTAACTTC 58.656 55.000 0.00 0.00 46.92 3.01
4548 4598 1.343506 GTGTGGTACGCCTAACTTCG 58.656 55.000 0.00 0.00 38.60 3.79
4549 4599 0.961019 TGTGGTACGCCTAACTTCGT 59.039 50.000 0.00 0.00 42.09 3.85
4550 4600 2.095263 GTGTGGTACGCCTAACTTCGTA 60.095 50.000 0.00 0.00 39.79 3.43
4551 4601 2.556189 TGTGGTACGCCTAACTTCGTAA 59.444 45.455 0.00 0.00 41.92 3.18
4552 4602 3.193267 TGTGGTACGCCTAACTTCGTAAT 59.807 43.478 0.00 0.00 41.92 1.89
4553 4603 3.793492 GTGGTACGCCTAACTTCGTAATC 59.207 47.826 0.00 0.00 41.92 1.75
4554 4604 3.443329 TGGTACGCCTAACTTCGTAATCA 59.557 43.478 0.00 0.00 41.92 2.57
4555 4605 3.793492 GGTACGCCTAACTTCGTAATCAC 59.207 47.826 0.00 0.00 41.92 3.06
4556 4606 3.863142 ACGCCTAACTTCGTAATCACT 57.137 42.857 0.00 0.00 37.14 3.41
4557 4607 3.508762 ACGCCTAACTTCGTAATCACTG 58.491 45.455 0.00 0.00 37.14 3.66
4558 4608 2.858344 CGCCTAACTTCGTAATCACTGG 59.142 50.000 0.00 0.00 0.00 4.00
4559 4609 3.428452 CGCCTAACTTCGTAATCACTGGA 60.428 47.826 0.00 0.00 0.00 3.86
4560 4610 4.694339 GCCTAACTTCGTAATCACTGGAT 58.306 43.478 0.00 0.00 34.43 3.41
4561 4611 5.116882 GCCTAACTTCGTAATCACTGGATT 58.883 41.667 0.00 0.00 45.50 3.01
4562 4612 5.006746 GCCTAACTTCGTAATCACTGGATTG 59.993 44.000 0.41 0.00 43.47 2.67
4563 4613 5.523916 CCTAACTTCGTAATCACTGGATTGG 59.476 44.000 0.41 0.00 43.47 3.16
4564 4614 3.270877 ACTTCGTAATCACTGGATTGGC 58.729 45.455 0.41 0.00 43.47 4.52
4565 4615 3.055094 ACTTCGTAATCACTGGATTGGCT 60.055 43.478 0.41 0.00 43.47 4.75
4566 4616 4.161565 ACTTCGTAATCACTGGATTGGCTA 59.838 41.667 0.41 0.00 43.47 3.93
4567 4617 4.746535 TCGTAATCACTGGATTGGCTAA 57.253 40.909 0.41 0.00 43.47 3.09
4568 4618 4.439057 TCGTAATCACTGGATTGGCTAAC 58.561 43.478 0.41 0.00 43.47 2.34
4569 4619 4.161565 TCGTAATCACTGGATTGGCTAACT 59.838 41.667 0.41 0.00 43.47 2.24
4570 4620 4.508124 CGTAATCACTGGATTGGCTAACTC 59.492 45.833 0.41 0.00 43.47 3.01
4571 4621 4.574674 AATCACTGGATTGGCTAACTCA 57.425 40.909 0.00 0.00 42.10 3.41
4572 4622 3.334583 TCACTGGATTGGCTAACTCAC 57.665 47.619 0.00 0.00 0.00 3.51
4573 4623 2.906389 TCACTGGATTGGCTAACTCACT 59.094 45.455 0.00 0.00 0.00 3.41
4574 4624 4.093743 TCACTGGATTGGCTAACTCACTA 58.906 43.478 0.00 0.00 0.00 2.74
4575 4625 4.160439 TCACTGGATTGGCTAACTCACTAG 59.840 45.833 0.00 0.00 0.00 2.57
4576 4626 4.081420 CACTGGATTGGCTAACTCACTAGT 60.081 45.833 0.00 0.00 37.65 2.57
4577 4627 5.127194 CACTGGATTGGCTAACTCACTAGTA 59.873 44.000 0.00 0.00 33.75 1.82
4578 4628 5.900123 ACTGGATTGGCTAACTCACTAGTAT 59.100 40.000 0.00 0.00 33.75 2.12
4579 4629 6.041069 ACTGGATTGGCTAACTCACTAGTATC 59.959 42.308 0.00 0.00 33.75 2.24
4580 4630 5.897250 TGGATTGGCTAACTCACTAGTATCA 59.103 40.000 0.00 0.00 33.75 2.15
4581 4631 6.040955 TGGATTGGCTAACTCACTAGTATCAG 59.959 42.308 0.00 0.00 33.75 2.90
4582 4632 5.854010 TTGGCTAACTCACTAGTATCAGG 57.146 43.478 0.00 0.00 33.75 3.86
4583 4633 4.868268 TGGCTAACTCACTAGTATCAGGT 58.132 43.478 0.00 0.00 33.75 4.00
4584 4634 5.269991 TGGCTAACTCACTAGTATCAGGTT 58.730 41.667 0.00 0.00 33.75 3.50
4585 4635 5.360144 TGGCTAACTCACTAGTATCAGGTTC 59.640 44.000 0.00 0.00 33.75 3.62
4586 4636 5.360144 GGCTAACTCACTAGTATCAGGTTCA 59.640 44.000 0.00 0.00 33.75 3.18
4587 4637 6.127423 GGCTAACTCACTAGTATCAGGTTCAA 60.127 42.308 0.00 0.00 33.75 2.69
4588 4638 7.321153 GCTAACTCACTAGTATCAGGTTCAAA 58.679 38.462 0.00 0.00 33.75 2.69
4589 4639 7.982354 GCTAACTCACTAGTATCAGGTTCAAAT 59.018 37.037 0.00 0.00 33.75 2.32
4592 4642 8.012957 ACTCACTAGTATCAGGTTCAAATAGG 57.987 38.462 0.00 0.00 32.84 2.57
4593 4643 7.620094 ACTCACTAGTATCAGGTTCAAATAGGT 59.380 37.037 0.00 0.00 32.84 3.08
4594 4644 7.782049 TCACTAGTATCAGGTTCAAATAGGTG 58.218 38.462 0.00 0.00 0.00 4.00
4595 4645 7.399191 TCACTAGTATCAGGTTCAAATAGGTGT 59.601 37.037 0.00 0.00 0.00 4.16
4596 4646 8.041323 CACTAGTATCAGGTTCAAATAGGTGTT 58.959 37.037 0.00 0.00 0.00 3.32
4597 4647 8.603304 ACTAGTATCAGGTTCAAATAGGTGTTT 58.397 33.333 0.00 0.00 0.00 2.83
4598 4648 9.449719 CTAGTATCAGGTTCAAATAGGTGTTTT 57.550 33.333 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.259876 AGGTTTTCGCACCTATGACACTA 59.740 43.478 0.00 0.00 46.14 2.74
92 97 2.960384 TGAGTCCGGTTTAGTGACTTCA 59.040 45.455 0.00 0.00 39.36 3.02
97 102 5.925506 TTATCATGAGTCCGGTTTAGTGA 57.074 39.130 0.00 2.58 0.00 3.41
106 111 6.018425 CCAAACAAGAGATTATCATGAGTCCG 60.018 42.308 0.09 0.00 31.02 4.79
316 325 7.277098 GCAACATGTTTTATCATTCATCTTGCT 59.723 33.333 8.77 0.00 38.32 3.91
563 575 4.268767 TGACGCTCGTGTGTAGTATAAG 57.731 45.455 3.31 0.00 37.00 1.73
616 628 6.551736 GCTTATGTTTGTACCTTACATGGTG 58.448 40.000 12.31 6.01 41.05 4.17
975 1001 8.809066 AGTGCATATGATATGTGCCATATTTTT 58.191 29.630 13.48 2.17 45.45 1.94
1059 1085 2.804931 CGCGCGACACTGACATGA 60.805 61.111 28.94 0.00 0.00 3.07
1530 1562 7.593273 TCAAACATTGCAGGTACTTTATTTTCG 59.407 33.333 0.00 0.00 34.60 3.46
1630 1675 2.336400 GATGACGGGAAAATGGCGGC 62.336 60.000 0.00 0.00 0.00 6.53
1814 1862 2.983192 TGTTGGACTTGTCCCTCCATAA 59.017 45.455 16.23 1.24 36.42 1.90
1966 2014 2.638363 GAGTAAACCCCTCCTTCAGTGT 59.362 50.000 0.00 0.00 0.00 3.55
1988 2036 1.971481 TGCTGACTTTGTGAGCACAT 58.029 45.000 7.69 0.00 44.52 3.21
2137 2185 2.725723 GTGTCATGCGAACAACATTTGG 59.274 45.455 0.00 0.00 34.12 3.28
2317 2365 3.072038 GCCCCTACGTTACTTGGGATAAT 59.928 47.826 10.58 0.00 42.11 1.28
2328 2376 2.496111 CTTTGTGTTGCCCCTACGTTA 58.504 47.619 0.00 0.00 0.00 3.18
2359 2407 2.430248 ACACCTTTTCCTTTGTCCGT 57.570 45.000 0.00 0.00 0.00 4.69
2408 2456 1.254975 TGGACGAGCCGATCCTTCAA 61.255 55.000 1.50 0.00 40.66 2.69
2489 2537 0.620556 CTCACCCACTAGGCATGGTT 59.379 55.000 0.00 0.00 40.58 3.67
2572 2620 1.632409 AGCAGTTGGATCCACATGACT 59.368 47.619 23.60 17.63 0.00 3.41
2649 2697 3.346315 ACGACATGCTGGATCAATTGAA 58.654 40.909 13.09 0.00 0.00 2.69
2653 2701 1.134699 ACGACGACATGCTGGATCAAT 60.135 47.619 0.00 0.00 0.00 2.57
2682 2730 4.008933 GCACGGTGAGCCCTCTGT 62.009 66.667 13.29 0.00 0.00 3.41
2872 2920 5.048083 CAGAGATAGAGCATCCTGGAAGTAC 60.048 48.000 0.00 0.00 33.75 2.73
3058 3106 1.321474 TAACCCGAATCGGCTCGTAT 58.679 50.000 17.50 3.39 46.86 3.06
3095 3143 4.038271 TGGCTTGTTGATGGAGAATCTT 57.962 40.909 0.00 0.00 36.15 2.40
3124 3172 5.046807 CCATTTCTTTTGCTCCATTTCCTCT 60.047 40.000 0.00 0.00 0.00 3.69
3135 3183 4.584325 TCTGTACTTGCCATTTCTTTTGCT 59.416 37.500 0.00 0.00 0.00 3.91
3354 3402 0.622665 CTGAACCCTTCTGGCTCCAT 59.377 55.000 0.00 0.00 37.83 3.41
3355 3403 0.473694 TCTGAACCCTTCTGGCTCCA 60.474 55.000 0.00 0.00 37.83 3.86
3645 3694 0.543277 CTGCTCCTCCATGTTGGCTA 59.457 55.000 0.00 0.00 37.47 3.93
3697 3746 3.775261 TTGCGACTTTACCCCTTTAGT 57.225 42.857 0.00 0.00 0.00 2.24
3700 3749 5.623596 GCATTAATTGCGACTTTACCCCTTT 60.624 40.000 0.00 0.00 42.54 3.11
3742 3791 0.551396 GGCTTAACATACCCTGGCCT 59.449 55.000 3.32 0.00 35.73 5.19
4119 4168 3.869912 GCTGTGGGCAATGAAGACTTAGA 60.870 47.826 0.00 0.00 41.35 2.10
4148 4197 1.962822 CGCACTGCTTCTGGCTCAA 60.963 57.895 0.00 0.00 42.39 3.02
4289 4338 5.154932 TGTTGAACGTTGTTTTTGTTCGAT 58.845 33.333 5.00 0.00 43.74 3.59
4381 4430 1.193874 CTGAGGTTTTACCGTCGTTGC 59.806 52.381 0.00 0.00 44.90 4.17
4449 4499 2.252072 TATCAACCTCCCGCACCTGC 62.252 60.000 0.00 0.00 37.78 4.85
4463 4513 5.538118 TCTTTCTCAGCTCGTTGTTATCAA 58.462 37.500 0.00 0.00 0.00 2.57
4464 4514 5.134202 TCTTTCTCAGCTCGTTGTTATCA 57.866 39.130 0.00 0.00 0.00 2.15
4465 4515 5.006165 CCATCTTTCTCAGCTCGTTGTTATC 59.994 44.000 0.00 0.00 0.00 1.75
4466 4516 4.872691 CCATCTTTCTCAGCTCGTTGTTAT 59.127 41.667 0.00 0.00 0.00 1.89
4467 4517 4.245660 CCATCTTTCTCAGCTCGTTGTTA 58.754 43.478 0.00 0.00 0.00 2.41
4468 4518 3.070018 CCATCTTTCTCAGCTCGTTGTT 58.930 45.455 0.00 0.00 0.00 2.83
4469 4519 2.693069 CCATCTTTCTCAGCTCGTTGT 58.307 47.619 0.00 0.00 0.00 3.32
4470 4520 1.396301 GCCATCTTTCTCAGCTCGTTG 59.604 52.381 0.00 0.00 0.00 4.10
4471 4521 1.677217 GGCCATCTTTCTCAGCTCGTT 60.677 52.381 0.00 0.00 0.00 3.85
4472 4522 0.107945 GGCCATCTTTCTCAGCTCGT 60.108 55.000 0.00 0.00 0.00 4.18
4473 4523 0.813210 GGGCCATCTTTCTCAGCTCG 60.813 60.000 4.39 0.00 0.00 5.03
4474 4524 0.545646 AGGGCCATCTTTCTCAGCTC 59.454 55.000 6.18 0.00 0.00 4.09
4475 4525 0.255318 CAGGGCCATCTTTCTCAGCT 59.745 55.000 6.18 0.00 0.00 4.24
4476 4526 1.382692 GCAGGGCCATCTTTCTCAGC 61.383 60.000 6.18 0.00 0.00 4.26
4477 4527 2.791170 GCAGGGCCATCTTTCTCAG 58.209 57.895 6.18 0.00 0.00 3.35
4490 4540 4.838152 CGTGGATGGACGGCAGGG 62.838 72.222 0.00 0.00 35.65 4.45
4491 4541 4.082523 ACGTGGATGGACGGCAGG 62.083 66.667 0.00 0.00 43.84 4.85
4492 4542 2.815211 CACGTGGATGGACGGCAG 60.815 66.667 7.95 0.00 43.84 4.85
4493 4543 4.386951 CCACGTGGATGGACGGCA 62.387 66.667 31.31 0.00 43.02 5.69
4494 4544 4.388499 ACCACGTGGATGGACGGC 62.388 66.667 40.21 0.00 43.02 5.68
4495 4545 2.125673 GACCACGTGGATGGACGG 60.126 66.667 40.21 12.45 43.02 4.79
4496 4546 2.125673 GGACCACGTGGATGGACG 60.126 66.667 40.21 12.94 43.02 4.79
4497 4547 0.673644 CTTGGACCACGTGGATGGAC 60.674 60.000 40.21 22.91 43.02 4.02
4498 4548 1.676968 CTTGGACCACGTGGATGGA 59.323 57.895 40.21 20.84 43.02 3.41
4499 4549 2.040544 GCTTGGACCACGTGGATGG 61.041 63.158 40.21 23.17 46.10 3.51
4500 4550 1.003355 AGCTTGGACCACGTGGATG 60.003 57.895 40.21 22.95 38.94 3.51
4501 4551 1.296715 GAGCTTGGACCACGTGGAT 59.703 57.895 40.21 24.06 38.94 3.41
4502 4552 2.099652 CTGAGCTTGGACCACGTGGA 62.100 60.000 40.21 16.59 38.94 4.02
4503 4553 1.669115 CTGAGCTTGGACCACGTGG 60.669 63.158 32.83 32.83 42.17 4.94
4504 4554 1.669115 CCTGAGCTTGGACCACGTG 60.669 63.158 9.08 9.08 0.00 4.49
4505 4555 1.194781 ATCCTGAGCTTGGACCACGT 61.195 55.000 10.96 0.00 36.30 4.49
4506 4556 0.742281 CATCCTGAGCTTGGACCACG 60.742 60.000 10.96 0.00 36.30 4.94
4507 4557 0.393537 CCATCCTGAGCTTGGACCAC 60.394 60.000 10.96 0.00 36.30 4.16
4508 4558 0.842030 ACCATCCTGAGCTTGGACCA 60.842 55.000 8.39 0.00 36.30 4.02
4509 4559 0.107459 GACCATCCTGAGCTTGGACC 60.107 60.000 8.39 0.00 36.30 4.46
4510 4560 0.460987 CGACCATCCTGAGCTTGGAC 60.461 60.000 8.39 1.31 36.30 4.02
4511 4561 0.904865 ACGACCATCCTGAGCTTGGA 60.905 55.000 8.39 9.86 38.06 3.53
4512 4562 0.742281 CACGACCATCCTGAGCTTGG 60.742 60.000 0.00 0.00 36.56 3.61
4513 4563 0.036952 ACACGACCATCCTGAGCTTG 60.037 55.000 0.00 0.00 0.00 4.01
4514 4564 0.036952 CACACGACCATCCTGAGCTT 60.037 55.000 0.00 0.00 0.00 3.74
4515 4565 1.593787 CACACGACCATCCTGAGCT 59.406 57.895 0.00 0.00 0.00 4.09
4516 4566 1.448540 CCACACGACCATCCTGAGC 60.449 63.158 0.00 0.00 0.00 4.26
4517 4567 1.135083 GTACCACACGACCATCCTGAG 60.135 57.143 0.00 0.00 0.00 3.35
4518 4568 0.892755 GTACCACACGACCATCCTGA 59.107 55.000 0.00 0.00 0.00 3.86
4519 4569 3.436001 GTACCACACGACCATCCTG 57.564 57.895 0.00 0.00 0.00 3.86
4529 4579 1.336240 ACGAAGTTAGGCGTACCACAC 60.336 52.381 0.00 0.00 37.78 3.82
4530 4580 0.961019 ACGAAGTTAGGCGTACCACA 59.039 50.000 0.00 0.00 37.78 4.17
4531 4581 2.919666 TACGAAGTTAGGCGTACCAC 57.080 50.000 0.00 0.00 37.78 4.16
4532 4582 3.443329 TGATTACGAAGTTAGGCGTACCA 59.557 43.478 0.00 0.00 37.78 3.25
4533 4583 3.793492 GTGATTACGAAGTTAGGCGTACC 59.207 47.826 0.00 0.00 37.78 3.34
4534 4584 4.498323 CAGTGATTACGAAGTTAGGCGTAC 59.502 45.833 0.00 0.00 37.78 3.67
4535 4585 4.439153 CCAGTGATTACGAAGTTAGGCGTA 60.439 45.833 0.00 0.00 37.78 4.42
4536 4586 3.508762 CAGTGATTACGAAGTTAGGCGT 58.491 45.455 0.00 0.00 37.78 5.68
4537 4587 2.858344 CCAGTGATTACGAAGTTAGGCG 59.142 50.000 0.00 0.00 37.78 5.52
4538 4588 4.119442 TCCAGTGATTACGAAGTTAGGC 57.881 45.455 0.00 0.00 37.78 3.93
4539 4589 5.523916 CCAATCCAGTGATTACGAAGTTAGG 59.476 44.000 0.00 0.00 45.11 2.69
4540 4590 5.006746 GCCAATCCAGTGATTACGAAGTTAG 59.993 44.000 0.00 0.00 45.11 2.34
4541 4591 4.873827 GCCAATCCAGTGATTACGAAGTTA 59.126 41.667 0.00 0.00 45.11 2.24
4542 4592 3.689649 GCCAATCCAGTGATTACGAAGTT 59.310 43.478 0.00 0.00 45.11 2.66
4544 4594 3.535561 AGCCAATCCAGTGATTACGAAG 58.464 45.455 0.00 0.00 39.20 3.79
4545 4595 3.627395 AGCCAATCCAGTGATTACGAA 57.373 42.857 0.00 0.00 39.20 3.85
4546 4596 4.161565 AGTTAGCCAATCCAGTGATTACGA 59.838 41.667 0.00 0.00 39.20 3.43
4547 4597 4.442706 AGTTAGCCAATCCAGTGATTACG 58.557 43.478 0.00 0.00 39.20 3.18
4548 4598 5.294552 GTGAGTTAGCCAATCCAGTGATTAC 59.705 44.000 0.00 0.00 39.20 1.89
4549 4599 5.189736 AGTGAGTTAGCCAATCCAGTGATTA 59.810 40.000 0.00 0.00 39.20 1.75
4550 4600 4.018960 AGTGAGTTAGCCAATCCAGTGATT 60.019 41.667 0.00 0.00 41.96 2.57
4551 4601 3.521126 AGTGAGTTAGCCAATCCAGTGAT 59.479 43.478 0.00 0.00 0.00 3.06
4552 4602 2.906389 AGTGAGTTAGCCAATCCAGTGA 59.094 45.455 0.00 0.00 0.00 3.41
4553 4603 3.340814 AGTGAGTTAGCCAATCCAGTG 57.659 47.619 0.00 0.00 0.00 3.66
4554 4604 4.097418 ACTAGTGAGTTAGCCAATCCAGT 58.903 43.478 0.00 0.00 28.61 4.00
4555 4605 4.744795 ACTAGTGAGTTAGCCAATCCAG 57.255 45.455 0.00 0.00 28.61 3.86
4556 4606 5.897250 TGATACTAGTGAGTTAGCCAATCCA 59.103 40.000 5.39 0.00 37.10 3.41
4557 4607 6.406692 TGATACTAGTGAGTTAGCCAATCC 57.593 41.667 5.39 0.00 37.10 3.01
4558 4608 6.041069 ACCTGATACTAGTGAGTTAGCCAATC 59.959 42.308 5.39 0.00 37.10 2.67
4559 4609 5.900123 ACCTGATACTAGTGAGTTAGCCAAT 59.100 40.000 5.39 0.00 37.10 3.16
4560 4610 5.269991 ACCTGATACTAGTGAGTTAGCCAA 58.730 41.667 5.39 0.00 37.10 4.52
4561 4611 4.868268 ACCTGATACTAGTGAGTTAGCCA 58.132 43.478 5.39 0.00 37.10 4.75
4562 4612 5.360144 TGAACCTGATACTAGTGAGTTAGCC 59.640 44.000 5.39 0.00 37.10 3.93
4563 4613 6.452494 TGAACCTGATACTAGTGAGTTAGC 57.548 41.667 5.39 0.00 37.10 3.09
4566 4616 8.478877 CCTATTTGAACCTGATACTAGTGAGTT 58.521 37.037 5.39 1.78 37.10 3.01
4567 4617 7.620094 ACCTATTTGAACCTGATACTAGTGAGT 59.380 37.037 5.39 0.00 39.92 3.41
4568 4618 7.923344 CACCTATTTGAACCTGATACTAGTGAG 59.077 40.741 5.39 0.00 0.00 3.51
4569 4619 7.399191 ACACCTATTTGAACCTGATACTAGTGA 59.601 37.037 5.39 0.00 0.00 3.41
4570 4620 7.556844 ACACCTATTTGAACCTGATACTAGTG 58.443 38.462 5.39 0.00 0.00 2.74
4571 4621 7.735326 ACACCTATTTGAACCTGATACTAGT 57.265 36.000 0.00 0.00 0.00 2.57
4572 4622 9.449719 AAAACACCTATTTGAACCTGATACTAG 57.550 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.