Multiple sequence alignment - TraesCS5B01G083100

Loading Multiple Alignment...

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 TraesCS5B01G083100 chr5B 100.000 4691 0 0 1 4691 103575204 103579894 0.000000e+00 8663.0
1 TraesCS5B01G083100 chr5B 97.351 4040 69 14 1 4008 105774340 105778373 0.000000e+00 6833.0
2 TraesCS5B01G083100 chr5B 97.619 42 1 0 4464 4505 103579585 103579626 6.510000e-09 73.1
3 TraesCS5B01G083100 chr5B 97.619 42 1 0 4382 4423 103579667 103579708 6.510000e-09 73.1
4 TraesCS5B01G083100 chr5D 94.623 4259 142 30 2 4211 97330114 97334334 0.000000e+00 6516.0
5 TraesCS5B01G083100 chr5D 88.038 209 15 4 4215 4423 97334373 97334571 6.070000e-59 239.0
6 TraesCS5B01G083100 chr5D 90.667 150 12 1 4464 4613 97334530 97334677 1.030000e-46 198.0
7 TraesCS5B01G083100 chr5A 94.223 4068 129 39 14 4022 106732364 106728344 0.000000e+00 6113.0
8 TraesCS5B01G083100 chr5A 90.786 369 14 9 3669 4020 106723227 106722862 4.250000e-130 475.0
9 TraesCS5B01G083100 chr5A 87.383 214 17 5 4218 4423 106722630 106722419 2.180000e-58 237.0
10 TraesCS5B01G083100 chr5A 83.088 136 12 4 4216 4344 106728144 106728013 3.840000e-21 113.0
11 TraesCS5B01G083100 chr5A 100.000 47 0 0 4645 4691 593723960 593723914 2.330000e-13 87.9
12 TraesCS5B01G083100 chr5A 100.000 47 0 0 4645 4691 677458506 677458552 2.330000e-13 87.9
13 TraesCS5B01G083100 chr7A 100.000 47 0 0 4645 4691 97003429 97003475 2.330000e-13 87.9
14 TraesCS5B01G083100 chr6A 100.000 47 0 0 4645 4691 102059343 102059297 2.330000e-13 87.9
15 TraesCS5B01G083100 chr6A 100.000 47 0 0 4645 4691 525299954 525300000 2.330000e-13 87.9
16 TraesCS5B01G083100 chr3A 100.000 47 0 0 4645 4691 375988879 375988925 2.330000e-13 87.9
17 TraesCS5B01G083100 chr2A 100.000 47 0 0 4645 4691 214704708 214704754 2.330000e-13 87.9
18 TraesCS5B01G083100 chr2A 100.000 47 0 0 4645 4691 747850973 747850927 2.330000e-13 87.9
19 TraesCS5B01G083100 chr1A 100.000 47 0 0 4645 4691 487808405 487808359 2.330000e-13 87.9


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 TraesCS5B01G083100 chr5B 103575204 103579894 4690 False 2936.400000 8663 98.412667 1 4691 3 chr5B.!!$F2 4690
1 TraesCS5B01G083100 chr5B 105774340 105778373 4033 False 6833.000000 6833 97.351000 1 4008 1 chr5B.!!$F1 4007
2 TraesCS5B01G083100 chr5D 97330114 97334677 4563 False 2317.666667 6516 91.109333 2 4613 3 chr5D.!!$F1 4611
3 TraesCS5B01G083100 chr5A 106728013 106732364 4351 True 3113.000000 6113 88.655500 14 4344 2 chr5A.!!$R3 4330
4 TraesCS5B01G083100 chr5A 106722419 106723227 808 True 356.000000 475 89.084500 3669 4423 2 chr5A.!!$R2 754

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
318 321 0.468226 TCTCTCGTGTGGTTTGGCTT 59.532 50.0 0.00 0.00 0.0 4.35 F
1203 1256 0.108756 GAAGTACCGGTGCTGAGTCC 60.109 60.0 26.69 9.39 0.0 3.85 F
2583 2638 1.014352 GTTGAACGGCACACTGAAGT 58.986 50.0 0.00 0.00 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1469 0.257905 TAAGAGCACCTCGGCCTCTA 59.742 55.0 0.0 0.0 35.36 2.43 R
2951 3006 0.389817 TGTGCTTGTAGGCTGTAGCG 60.390 55.0 0.0 0.0 43.26 4.26 R
4500 4670 0.033504 TGTGTCTCGTTGGCTTCCTC 59.966 55.0 0.0 0.0 0.00 3.71 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
56 57 4.143333 GGCTGAGGGCGTTCGCTA 62.143 66.667 16.40 1.45 42.94 4.26
64 65 1.158484 GGGCGTTCGCTAGGATTTCC 61.158 60.000 16.40 3.47 0.00 3.13
318 321 0.468226 TCTCTCGTGTGGTTTGGCTT 59.532 50.000 0.00 0.00 0.00 4.35
606 643 6.509523 TTCTGGGTTTTCTTTAGAGGAAGA 57.490 37.500 0.00 0.00 34.00 2.87
780 827 6.544197 GGAGGGATTTTGCCTTTGTTTAAAAA 59.456 34.615 0.00 0.00 38.79 1.94
786 833 5.803020 TTGCCTTTGTTTAAAAATTGCGT 57.197 30.435 0.00 0.00 0.00 5.24
894 947 0.740149 TCGTTGCCCATCATTCATGC 59.260 50.000 0.00 0.00 0.00 4.06
901 954 3.389656 TGCCCATCATTCATGCATGATTT 59.610 39.130 29.13 17.19 41.20 2.17
903 956 4.502431 GCCCATCATTCATGCATGATTTCA 60.502 41.667 29.13 15.38 41.20 2.69
921 974 5.359194 TTTCACAGGTTGGAGATCCTATC 57.641 43.478 0.00 0.00 36.82 2.08
976 1029 2.233922 GCCTTGTGCTGAGGAACTAGTA 59.766 50.000 0.00 0.00 35.99 1.82
1203 1256 0.108756 GAAGTACCGGTGCTGAGTCC 60.109 60.000 26.69 9.39 0.00 3.85
1296 1349 2.414481 CAGCACGAAGAACAATGAGGAG 59.586 50.000 0.00 0.00 0.00 3.69
1317 1370 1.513858 TGGTGGTTCCAAGTGGTAGT 58.486 50.000 0.00 0.00 44.12 2.73
1416 1469 1.774217 TCTTGGTTCTGGGCCTGGT 60.774 57.895 10.79 0.00 0.00 4.00
1449 1502 1.757682 CTCTTAGGAGCAGACGACCT 58.242 55.000 0.00 0.00 37.76 3.85
2008 2061 2.936498 AGTAGAAATTTCGCCGTCATGG 59.064 45.455 12.42 0.00 42.50 3.66
2153 2207 4.015084 CTCCCAGAATTTGCTCAATCTGT 58.985 43.478 10.53 0.00 0.00 3.41
2583 2638 1.014352 GTTGAACGGCACACTGAAGT 58.986 50.000 0.00 0.00 0.00 3.01
2652 2707 3.072622 AGAGGGGTTAACTGTGAAGGAAC 59.927 47.826 5.42 0.00 0.00 3.62
3014 3069 6.064717 TCTAGATCGATCAGGAGTTCATTGA 58.935 40.000 26.47 6.84 0.00 2.57
3775 3844 8.936864 GTTGCAGGACTATATTGTATACCATTC 58.063 37.037 0.00 0.00 0.00 2.67
3848 3918 8.409358 AGAAGCAAAGTATTAGTTTGGTGATT 57.591 30.769 22.69 11.94 45.30 2.57
4008 4100 4.523083 GACTATTGTGCAGACCCCAAATA 58.477 43.478 0.00 0.00 0.00 1.40
4026 4118 6.484977 CCCAAATATACTTCTCTTTGCCTCTC 59.515 42.308 0.00 0.00 0.00 3.20
4027 4119 7.278875 CCAAATATACTTCTCTTTGCCTCTCT 58.721 38.462 0.00 0.00 0.00 3.10
4028 4120 7.440856 CCAAATATACTTCTCTTTGCCTCTCTC 59.559 40.741 0.00 0.00 0.00 3.20
4033 4125 5.440610 ACTTCTCTTTGCCTCTCTCAAAAA 58.559 37.500 0.00 0.00 33.60 1.94
4073 4165 5.405571 TCTCTTTGCGACATCTTTGTTACTC 59.594 40.000 0.00 0.00 35.79 2.59
4132 4224 7.673180 AGGTTTCATTTTCATTGATGTGTGAT 58.327 30.769 0.00 0.00 0.00 3.06
4133 4225 7.601130 AGGTTTCATTTTCATTGATGTGTGATG 59.399 33.333 0.00 0.00 0.00 3.07
4185 4310 9.917118 TTATACTATATAAAACCCCCTCCTTCA 57.083 33.333 0.00 0.00 0.00 3.02
4187 4312 7.723109 ACTATATAAAACCCCCTCCTTCATT 57.277 36.000 0.00 0.00 0.00 2.57
4196 4321 3.205282 CCCCCTCCTTCATTAGTGGATTT 59.795 47.826 0.00 0.00 0.00 2.17
4298 4461 0.752658 AGCAAGAAAAACAGTGCCCC 59.247 50.000 0.00 0.00 37.73 5.80
4299 4462 0.463620 GCAAGAAAAACAGTGCCCCA 59.536 50.000 0.00 0.00 0.00 4.96
4309 4479 1.688197 ACAGTGCCCCAATGTTTCTTG 59.312 47.619 0.00 0.00 39.70 3.02
4328 4498 6.877611 TCTTGGTTACTCCTTGAATTGTTC 57.122 37.500 0.00 0.00 37.07 3.18
4355 4525 1.071542 TGTTTCTGACCCTTGCGATGA 59.928 47.619 0.00 0.00 0.00 2.92
4418 4588 1.078848 CTGTCTCTTCCCGGCCAAG 60.079 63.158 2.24 0.00 0.00 3.61
4419 4589 1.535444 TGTCTCTTCCCGGCCAAGA 60.535 57.895 2.24 12.25 0.00 3.02
4420 4590 1.219393 GTCTCTTCCCGGCCAAGAG 59.781 63.158 25.34 25.34 45.77 2.85
4421 4591 1.990060 TCTCTTCCCGGCCAAGAGG 60.990 63.158 28.26 11.95 44.87 3.69
4422 4592 1.990060 CTCTTCCCGGCCAAGAGGA 60.990 63.158 24.28 12.14 42.22 3.71
4423 4593 1.306997 TCTTCCCGGCCAAGAGGAT 60.307 57.895 2.24 0.00 36.89 3.24
4424 4594 0.914417 TCTTCCCGGCCAAGAGGATT 60.914 55.000 2.24 0.00 36.89 3.01
4425 4595 0.749454 CTTCCCGGCCAAGAGGATTG 60.749 60.000 2.24 0.00 36.89 2.67
4426 4596 1.204786 TTCCCGGCCAAGAGGATTGA 61.205 55.000 2.24 0.00 36.89 2.57
4427 4597 1.204786 TCCCGGCCAAGAGGATTGAA 61.205 55.000 2.24 0.00 36.89 2.69
4428 4598 0.106519 CCCGGCCAAGAGGATTGAAT 60.107 55.000 2.24 0.00 36.89 2.57
4429 4599 1.686115 CCCGGCCAAGAGGATTGAATT 60.686 52.381 2.24 0.00 36.89 2.17
4430 4600 1.406539 CCGGCCAAGAGGATTGAATTG 59.593 52.381 2.24 0.00 36.89 2.32
4431 4601 2.094675 CGGCCAAGAGGATTGAATTGT 58.905 47.619 2.24 0.00 36.89 2.71
4432 4602 2.493278 CGGCCAAGAGGATTGAATTGTT 59.507 45.455 2.24 0.00 36.89 2.83
4433 4603 3.674138 CGGCCAAGAGGATTGAATTGTTG 60.674 47.826 2.24 0.00 36.89 3.33
4434 4604 3.256558 GCCAAGAGGATTGAATTGTTGC 58.743 45.455 0.00 0.00 36.89 4.17
4435 4605 3.504863 CCAAGAGGATTGAATTGTTGCG 58.495 45.455 0.00 0.00 36.89 4.85
4436 4606 3.504863 CAAGAGGATTGAATTGTTGCGG 58.495 45.455 0.00 0.00 0.00 5.69
4437 4607 2.795329 AGAGGATTGAATTGTTGCGGT 58.205 42.857 0.00 0.00 0.00 5.68
4438 4608 2.749621 AGAGGATTGAATTGTTGCGGTC 59.250 45.455 0.00 0.00 0.00 4.79
4439 4609 2.487762 GAGGATTGAATTGTTGCGGTCA 59.512 45.455 0.00 0.00 0.00 4.02
4440 4610 2.890311 AGGATTGAATTGTTGCGGTCAA 59.110 40.909 0.00 0.00 34.68 3.18
4441 4611 3.511146 AGGATTGAATTGTTGCGGTCAAT 59.489 39.130 0.00 0.00 42.05 2.57
4442 4612 3.613737 GGATTGAATTGTTGCGGTCAATG 59.386 43.478 2.66 0.00 40.03 2.82
4443 4613 3.724508 TTGAATTGTTGCGGTCAATGT 57.275 38.095 2.50 0.00 35.95 2.71
4444 4614 3.010624 TGAATTGTTGCGGTCAATGTG 57.989 42.857 2.50 0.00 35.95 3.21
4445 4615 1.720852 GAATTGTTGCGGTCAATGTGC 59.279 47.619 2.50 0.00 35.95 4.57
4446 4616 0.672889 ATTGTTGCGGTCAATGTGCA 59.327 45.000 0.00 0.00 34.74 4.57
4447 4617 0.672889 TTGTTGCGGTCAATGTGCAT 59.327 45.000 0.00 0.00 38.60 3.96
4448 4618 0.672889 TGTTGCGGTCAATGTGCATT 59.327 45.000 0.00 0.00 38.60 3.56
4449 4619 1.335780 TGTTGCGGTCAATGTGCATTC 60.336 47.619 0.00 0.00 38.60 2.67
4450 4620 0.109827 TTGCGGTCAATGTGCATTCG 60.110 50.000 0.00 0.00 38.60 3.34
4451 4621 1.869132 GCGGTCAATGTGCATTCGC 60.869 57.895 11.63 11.63 35.49 4.70
4452 4622 1.796151 CGGTCAATGTGCATTCGCT 59.204 52.632 0.00 0.00 39.64 4.93
4453 4623 0.168788 CGGTCAATGTGCATTCGCTT 59.831 50.000 0.00 0.00 39.64 4.68
4454 4624 1.621107 GGTCAATGTGCATTCGCTTG 58.379 50.000 0.00 0.00 39.64 4.01
4455 4625 0.986992 GTCAATGTGCATTCGCTTGC 59.013 50.000 0.00 2.82 43.07 4.01
4461 4631 3.391355 GCATTCGCTTGCAATGGC 58.609 55.556 0.00 0.00 42.31 4.40
4477 4647 6.724694 GCAATGGCATTGTGAAAAAGATAA 57.275 33.333 33.64 0.00 42.20 1.75
4478 4648 7.311364 GCAATGGCATTGTGAAAAAGATAAT 57.689 32.000 33.64 0.00 42.20 1.28
4479 4649 8.422973 GCAATGGCATTGTGAAAAAGATAATA 57.577 30.769 33.64 0.00 42.20 0.98
4480 4650 8.330302 GCAATGGCATTGTGAAAAAGATAATAC 58.670 33.333 33.64 13.10 42.20 1.89
4481 4651 9.590451 CAATGGCATTGTGAAAAAGATAATACT 57.410 29.630 27.93 0.00 35.57 2.12
4482 4652 9.807649 AATGGCATTGTGAAAAAGATAATACTC 57.192 29.630 12.82 0.00 0.00 2.59
4483 4653 8.579850 TGGCATTGTGAAAAAGATAATACTCT 57.420 30.769 0.00 0.00 0.00 3.24
4484 4654 8.461222 TGGCATTGTGAAAAAGATAATACTCTG 58.539 33.333 0.00 0.00 0.00 3.35
4485 4655 8.462016 GGCATTGTGAAAAAGATAATACTCTGT 58.538 33.333 0.00 0.00 0.00 3.41
4486 4656 9.495754 GCATTGTGAAAAAGATAATACTCTGTC 57.504 33.333 0.00 0.00 0.00 3.51
4492 4662 9.877178 TGAAAAAGATAATACTCTGTCTCTTCC 57.123 33.333 0.00 0.00 0.00 3.46
4493 4663 9.320352 GAAAAAGATAATACTCTGTCTCTTCCC 57.680 37.037 0.00 0.00 0.00 3.97
4494 4664 6.642707 AAGATAATACTCTGTCTCTTCCCG 57.357 41.667 0.00 0.00 0.00 5.14
4495 4665 5.074115 AGATAATACTCTGTCTCTTCCCGG 58.926 45.833 0.00 0.00 0.00 5.73
4496 4666 1.404843 ATACTCTGTCTCTTCCCGGC 58.595 55.000 0.00 0.00 0.00 6.13
4497 4667 0.683504 TACTCTGTCTCTTCCCGGCC 60.684 60.000 0.00 0.00 0.00 6.13
4498 4668 1.984570 CTCTGTCTCTTCCCGGCCA 60.985 63.158 2.24 0.00 0.00 5.36
4499 4669 1.535444 TCTGTCTCTTCCCGGCCAA 60.535 57.895 2.24 0.00 0.00 4.52
4500 4670 1.078848 CTGTCTCTTCCCGGCCAAG 60.079 63.158 2.24 0.00 0.00 3.61
4518 4688 0.318762 AGAGGAAGCCAACGAGACAC 59.681 55.000 0.00 0.00 0.00 3.67
4519 4689 0.033504 GAGGAAGCCAACGAGACACA 59.966 55.000 0.00 0.00 0.00 3.72
4520 4690 0.034059 AGGAAGCCAACGAGACACAG 59.966 55.000 0.00 0.00 0.00 3.66
4521 4691 0.249911 GGAAGCCAACGAGACACAGT 60.250 55.000 0.00 0.00 0.00 3.55
4523 4693 0.464036 AAGCCAACGAGACACAGTCA 59.536 50.000 0.00 0.00 34.60 3.41
4524 4694 0.249489 AGCCAACGAGACACAGTCAC 60.249 55.000 0.00 0.00 34.60 3.67
4525 4695 1.222115 GCCAACGAGACACAGTCACC 61.222 60.000 0.00 0.00 34.60 4.02
4526 4696 0.389391 CCAACGAGACACAGTCACCT 59.611 55.000 0.00 0.00 34.60 4.00
4534 4704 2.146342 GACACAGTCACCTGGTTCATG 58.854 52.381 0.00 0.00 43.36 3.07
4549 4719 0.392060 TCATGTCATGCGCTGAAGCT 60.392 50.000 9.73 0.00 39.32 3.74
4550 4720 0.027716 CATGTCATGCGCTGAAGCTC 59.972 55.000 9.73 0.00 39.32 4.09
4556 4726 3.843240 GCGCTGAAGCTCGGTTCG 61.843 66.667 0.00 1.64 39.32 3.95
4567 4737 2.358125 CGGTTCGGCCATGTGTCA 60.358 61.111 2.24 0.00 36.97 3.58
4571 4741 1.135402 GGTTCGGCCATGTGTCAAATC 60.135 52.381 2.24 0.00 37.17 2.17
4573 4743 3.006940 GTTCGGCCATGTGTCAAATCTA 58.993 45.455 2.24 0.00 0.00 1.98
4577 4747 3.181507 CGGCCATGTGTCAAATCTAGTTG 60.182 47.826 2.24 0.00 0.00 3.16
4613 4783 3.247648 ACGAACAAGAAGAAATGTCACCG 59.752 43.478 0.00 0.00 0.00 4.94
4614 4784 3.555518 GAACAAGAAGAAATGTCACCGC 58.444 45.455 0.00 0.00 0.00 5.68
4615 4785 2.851195 ACAAGAAGAAATGTCACCGCT 58.149 42.857 0.00 0.00 0.00 5.52
4616 4786 3.214328 ACAAGAAGAAATGTCACCGCTT 58.786 40.909 0.00 0.00 0.00 4.68
4617 4787 3.632145 ACAAGAAGAAATGTCACCGCTTT 59.368 39.130 0.00 0.00 0.00 3.51
4618 4788 3.904136 AGAAGAAATGTCACCGCTTTG 57.096 42.857 0.00 0.00 0.00 2.77
4619 4789 3.214328 AGAAGAAATGTCACCGCTTTGT 58.786 40.909 0.00 0.00 0.00 2.83
4620 4790 3.632145 AGAAGAAATGTCACCGCTTTGTT 59.368 39.130 0.00 0.00 0.00 2.83
4621 4791 4.097892 AGAAGAAATGTCACCGCTTTGTTT 59.902 37.500 0.00 0.00 0.00 2.83
4622 4792 3.705604 AGAAATGTCACCGCTTTGTTTG 58.294 40.909 0.00 0.00 0.00 2.93
4623 4793 2.507339 AATGTCACCGCTTTGTTTGG 57.493 45.000 0.00 0.00 0.00 3.28
4624 4794 1.398692 ATGTCACCGCTTTGTTTGGT 58.601 45.000 0.00 0.00 36.10 3.67
4625 4795 1.178276 TGTCACCGCTTTGTTTGGTT 58.822 45.000 0.00 0.00 32.48 3.67
4626 4796 1.546476 TGTCACCGCTTTGTTTGGTTT 59.454 42.857 0.00 0.00 32.48 3.27
4627 4797 2.190161 GTCACCGCTTTGTTTGGTTTC 58.810 47.619 0.00 0.00 32.48 2.78
4628 4798 1.135333 TCACCGCTTTGTTTGGTTTCC 59.865 47.619 0.00 0.00 32.48 3.13
4629 4799 0.462375 ACCGCTTTGTTTGGTTTCCC 59.538 50.000 0.00 0.00 29.87 3.97
4630 4800 0.750249 CCGCTTTGTTTGGTTTCCCT 59.250 50.000 0.00 0.00 0.00 4.20
4631 4801 1.269569 CCGCTTTGTTTGGTTTCCCTC 60.270 52.381 0.00 0.00 0.00 4.30
4632 4802 1.269569 CGCTTTGTTTGGTTTCCCTCC 60.270 52.381 0.00 0.00 0.00 4.30
4633 4803 1.760029 GCTTTGTTTGGTTTCCCTCCA 59.240 47.619 0.00 0.00 0.00 3.86
4634 4804 2.169561 GCTTTGTTTGGTTTCCCTCCAA 59.830 45.455 0.00 0.00 42.29 3.53
4635 4805 3.181455 GCTTTGTTTGGTTTCCCTCCAAT 60.181 43.478 0.00 0.00 43.25 3.16
4636 4806 4.039852 GCTTTGTTTGGTTTCCCTCCAATA 59.960 41.667 0.00 0.00 43.25 1.90
4637 4807 5.279960 GCTTTGTTTGGTTTCCCTCCAATAT 60.280 40.000 0.00 0.00 43.25 1.28
4638 4808 5.993748 TTGTTTGGTTTCCCTCCAATATC 57.006 39.130 0.00 0.00 43.25 1.63
4639 4809 4.349365 TGTTTGGTTTCCCTCCAATATCC 58.651 43.478 0.00 0.00 43.25 2.59
4640 4810 3.680777 TTGGTTTCCCTCCAATATCCC 57.319 47.619 0.00 0.00 39.62 3.85
4641 4811 2.579100 TGGTTTCCCTCCAATATCCCA 58.421 47.619 0.00 0.00 31.50 4.37
4642 4812 2.513738 TGGTTTCCCTCCAATATCCCAG 59.486 50.000 0.00 0.00 31.50 4.45
4643 4813 2.783510 GGTTTCCCTCCAATATCCCAGA 59.216 50.000 0.00 0.00 0.00 3.86
4644 4814 3.181439 GGTTTCCCTCCAATATCCCAGAG 60.181 52.174 0.00 0.00 0.00 3.35
4645 4815 3.438131 TTCCCTCCAATATCCCAGAGT 57.562 47.619 0.00 0.00 0.00 3.24
4646 4816 2.694397 TCCCTCCAATATCCCAGAGTG 58.306 52.381 0.00 0.00 0.00 3.51
4647 4817 2.250008 TCCCTCCAATATCCCAGAGTGA 59.750 50.000 0.00 0.00 0.00 3.41
4648 4818 2.636893 CCCTCCAATATCCCAGAGTGAG 59.363 54.545 0.00 0.00 0.00 3.51
4649 4819 2.038295 CCTCCAATATCCCAGAGTGAGC 59.962 54.545 0.00 0.00 0.00 4.26
4650 4820 2.971330 CTCCAATATCCCAGAGTGAGCT 59.029 50.000 0.00 0.00 0.00 4.09
4651 4821 2.702478 TCCAATATCCCAGAGTGAGCTG 59.298 50.000 0.00 0.00 35.66 4.24
4652 4822 2.492012 CAATATCCCAGAGTGAGCTGC 58.508 52.381 0.00 0.00 34.56 5.25
4653 4823 2.100128 ATATCCCAGAGTGAGCTGCT 57.900 50.000 0.00 0.00 34.56 4.24
4654 4824 1.407936 TATCCCAGAGTGAGCTGCTC 58.592 55.000 22.38 22.38 34.56 4.26
4655 4825 1.674764 ATCCCAGAGTGAGCTGCTCG 61.675 60.000 23.35 9.53 37.99 5.03
4656 4826 2.508887 CCAGAGTGAGCTGCTCGC 60.509 66.667 30.40 30.40 40.84 5.03
4666 4836 3.791539 CTGCTCGCTACCAGCAAG 58.208 61.111 0.00 0.00 46.22 4.01
4669 4839 4.606071 CTCGCTACCAGCAAGCTT 57.394 55.556 0.00 0.00 42.58 3.74
4670 4840 2.846371 CTCGCTACCAGCAAGCTTT 58.154 52.632 0.00 0.00 42.58 3.51
4671 4841 0.445436 CTCGCTACCAGCAAGCTTTG 59.555 55.000 0.00 0.00 42.58 2.77
4680 4850 2.202349 CAAGCTTTGCGCCGCTAC 60.202 61.111 11.67 0.00 40.39 3.58
4681 4851 3.431725 AAGCTTTGCGCCGCTACC 61.432 61.111 11.67 0.00 40.39 3.18
4682 4852 4.697756 AGCTTTGCGCCGCTACCA 62.698 61.111 11.67 0.00 40.39 3.25
4683 4853 3.508840 GCTTTGCGCCGCTACCAT 61.509 61.111 11.67 0.00 0.00 3.55
4684 4854 2.177580 GCTTTGCGCCGCTACCATA 61.178 57.895 11.67 0.00 0.00 2.74
4685 4855 1.934463 CTTTGCGCCGCTACCATAG 59.066 57.895 11.67 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
318 321 2.376518 AGGCAAGAAGAACATCCCAAGA 59.623 45.455 0.00 0.00 0.00 3.02
780 827 1.366111 CCCAATTCGTCCGACGCAAT 61.366 55.000 16.24 12.95 42.21 3.56
786 833 0.746563 GCAATCCCCAATTCGTCCGA 60.747 55.000 0.00 0.00 0.00 4.55
894 947 4.337555 GGATCTCCAACCTGTGAAATCATG 59.662 45.833 0.00 0.00 35.64 3.07
901 954 2.959030 CGATAGGATCTCCAACCTGTGA 59.041 50.000 0.00 0.00 38.89 3.58
903 956 3.226777 CTCGATAGGATCTCCAACCTGT 58.773 50.000 0.00 0.00 38.89 4.00
921 974 0.953727 CTCCTCATCTCCAGAGCTCG 59.046 60.000 8.37 3.24 0.00 5.03
976 1029 3.177884 TCCTGCCTGCAACCTGGT 61.178 61.111 0.00 0.00 32.98 4.00
1203 1256 2.786495 ATACTCGCCTGGGCTGACG 61.786 63.158 10.04 5.95 39.32 4.35
1317 1370 2.615986 TGCCTCTACCAACTGACCTA 57.384 50.000 0.00 0.00 0.00 3.08
1416 1469 0.257905 TAAGAGCACCTCGGCCTCTA 59.742 55.000 0.00 0.00 35.36 2.43
1449 1502 7.615365 ACAAGTGGATTAATAAAATGCCTCTGA 59.385 33.333 0.00 0.00 0.00 3.27
1727 1780 3.989056 TGGGATCCCCTTTTGGATTTAC 58.011 45.455 28.58 0.00 45.25 2.01
2087 2141 6.616774 TTTCAGGAATGGCAATTGTTTTTC 57.383 33.333 7.40 7.43 0.00 2.29
2583 2638 3.394274 TCCTGAACCAAGTTCTCCATTCA 59.606 43.478 8.77 0.00 42.39 2.57
2652 2707 1.478510 ACCAGACGTCTCATTAGGCAG 59.521 52.381 16.96 0.49 0.00 4.85
2663 2718 2.492484 ACCATCTAGTTCACCAGACGTC 59.508 50.000 7.70 7.70 0.00 4.34
2951 3006 0.389817 TGTGCTTGTAGGCTGTAGCG 60.390 55.000 0.00 0.00 43.26 4.26
4008 4100 6.365970 TTTGAGAGAGGCAAAGAGAAGTAT 57.634 37.500 0.00 0.00 32.04 2.12
4037 4129 6.791303 TGTCGCAAAGAGAAGTACAATTTTT 58.209 32.000 0.00 0.00 0.00 1.94
4038 4130 6.371809 TGTCGCAAAGAGAAGTACAATTTT 57.628 33.333 0.00 0.00 0.00 1.82
4039 4131 6.428159 AGATGTCGCAAAGAGAAGTACAATTT 59.572 34.615 0.00 0.00 0.00 1.82
4040 4132 5.934625 AGATGTCGCAAAGAGAAGTACAATT 59.065 36.000 0.00 0.00 0.00 2.32
4041 4133 5.482908 AGATGTCGCAAAGAGAAGTACAAT 58.517 37.500 0.00 0.00 0.00 2.71
4042 4134 4.883083 AGATGTCGCAAAGAGAAGTACAA 58.117 39.130 0.00 0.00 0.00 2.41
4043 4135 4.521130 AGATGTCGCAAAGAGAAGTACA 57.479 40.909 0.00 0.00 0.00 2.90
4044 4136 5.177696 ACAAAGATGTCGCAAAGAGAAGTAC 59.822 40.000 0.00 0.00 33.41 2.73
4045 4137 5.297547 ACAAAGATGTCGCAAAGAGAAGTA 58.702 37.500 0.00 0.00 33.41 2.24
4046 4138 4.130118 ACAAAGATGTCGCAAAGAGAAGT 58.870 39.130 0.00 0.00 33.41 3.01
4047 4139 4.739046 ACAAAGATGTCGCAAAGAGAAG 57.261 40.909 0.00 0.00 33.41 2.85
4048 4140 5.758296 AGTAACAAAGATGTCGCAAAGAGAA 59.242 36.000 0.00 0.00 39.40 2.87
4073 4165 8.368126 GCAAATATGTCGAAATGAACTTCAAAG 58.632 33.333 0.00 0.00 0.00 2.77
4151 4247 7.335171 GGGGTTTTATATAGTATAAAGGCACGG 59.665 40.741 0.00 0.00 0.00 4.94
4174 4299 1.893315 TCCACTAATGAAGGAGGGGG 58.107 55.000 0.00 0.00 36.83 5.40
4196 4321 8.300286 TGCCTTTTCGATTATTCATTTTGTACA 58.700 29.630 0.00 0.00 0.00 2.90
4211 4336 8.137437 CCATAGTTCATAATTTGCCTTTTCGAT 58.863 33.333 0.00 0.00 0.00 3.59
4213 4338 7.479980 TCCATAGTTCATAATTTGCCTTTTCG 58.520 34.615 0.00 0.00 0.00 3.46
4234 4397 3.972638 ACATCTGCTCTCCAGTATTCCAT 59.027 43.478 0.00 0.00 42.38 3.41
4298 4461 6.633500 TCAAGGAGTAACCAAGAAACATTG 57.367 37.500 0.00 0.00 42.04 2.82
4299 4462 7.839680 ATTCAAGGAGTAACCAAGAAACATT 57.160 32.000 0.00 0.00 42.04 2.71
4309 4479 6.655003 TGATCAGAACAATTCAAGGAGTAACC 59.345 38.462 0.00 0.00 39.35 2.85
4328 4498 3.128242 GCAAGGGTCAGAAACATGATCAG 59.872 47.826 0.00 0.00 31.55 2.90
4418 4588 2.487762 TGACCGCAACAATTCAATCCTC 59.512 45.455 0.00 0.00 0.00 3.71
4419 4589 2.513753 TGACCGCAACAATTCAATCCT 58.486 42.857 0.00 0.00 0.00 3.24
4420 4590 3.296322 TTGACCGCAACAATTCAATCC 57.704 42.857 0.00 0.00 0.00 3.01
4421 4591 4.090354 CACATTGACCGCAACAATTCAATC 59.910 41.667 0.00 0.00 36.72 2.67
4422 4592 3.989167 CACATTGACCGCAACAATTCAAT 59.011 39.130 0.00 0.00 38.87 2.57
4423 4593 3.379240 CACATTGACCGCAACAATTCAA 58.621 40.909 0.00 0.00 36.72 2.69
4424 4594 2.861750 GCACATTGACCGCAACAATTCA 60.862 45.455 0.00 0.00 36.72 2.57
4425 4595 1.720852 GCACATTGACCGCAACAATTC 59.279 47.619 0.00 0.00 36.72 2.17
4426 4596 1.068281 TGCACATTGACCGCAACAATT 59.932 42.857 0.00 0.00 36.72 2.32
4427 4597 0.672889 TGCACATTGACCGCAACAAT 59.327 45.000 0.00 0.00 36.72 2.71
4428 4598 0.672889 ATGCACATTGACCGCAACAA 59.327 45.000 0.00 0.00 39.48 2.83
4429 4599 0.672889 AATGCACATTGACCGCAACA 59.327 45.000 0.00 0.00 39.48 3.33
4430 4600 1.339711 GAATGCACATTGACCGCAAC 58.660 50.000 0.00 0.77 39.48 4.17
4431 4601 0.109827 CGAATGCACATTGACCGCAA 60.110 50.000 0.00 0.00 39.48 4.85
4432 4602 1.501292 CGAATGCACATTGACCGCA 59.499 52.632 0.00 0.00 40.50 5.69
4433 4603 1.869132 GCGAATGCACATTGACCGC 60.869 57.895 10.76 10.76 42.15 5.68
4434 4604 0.168788 AAGCGAATGCACATTGACCG 59.831 50.000 0.00 0.00 46.23 4.79
4435 4605 1.621107 CAAGCGAATGCACATTGACC 58.379 50.000 0.00 0.00 46.23 4.02
4436 4606 0.986992 GCAAGCGAATGCACATTGAC 59.013 50.000 0.00 0.00 45.70 3.18
4437 4607 3.404978 GCAAGCGAATGCACATTGA 57.595 47.368 0.00 0.00 45.70 2.57
4444 4614 1.446445 TGCCATTGCAAGCGAATGC 60.446 52.632 4.94 5.97 46.66 3.56
4445 4615 4.893709 TGCCATTGCAAGCGAATG 57.106 50.000 4.94 0.00 46.66 2.67
4454 4624 6.724694 TTATCTTTTTCACAATGCCATTGC 57.275 33.333 17.14 0.00 43.98 3.56
4455 4625 9.590451 AGTATTATCTTTTTCACAATGCCATTG 57.410 29.630 15.71 15.71 45.59 2.82
4456 4626 9.807649 GAGTATTATCTTTTTCACAATGCCATT 57.192 29.630 0.00 0.00 0.00 3.16
4457 4627 9.193806 AGAGTATTATCTTTTTCACAATGCCAT 57.806 29.630 0.00 0.00 0.00 4.40
4458 4628 8.461222 CAGAGTATTATCTTTTTCACAATGCCA 58.539 33.333 0.00 0.00 0.00 4.92
4459 4629 8.462016 ACAGAGTATTATCTTTTTCACAATGCC 58.538 33.333 0.00 0.00 0.00 4.40
4460 4630 9.495754 GACAGAGTATTATCTTTTTCACAATGC 57.504 33.333 0.00 0.00 0.00 3.56
4466 4636 9.877178 GGAAGAGACAGAGTATTATCTTTTTCA 57.123 33.333 0.00 0.00 0.00 2.69
4467 4637 9.320352 GGGAAGAGACAGAGTATTATCTTTTTC 57.680 37.037 0.00 0.00 0.00 2.29
4468 4638 7.982354 CGGGAAGAGACAGAGTATTATCTTTTT 59.018 37.037 0.00 0.00 0.00 1.94
4469 4639 7.418025 CCGGGAAGAGACAGAGTATTATCTTTT 60.418 40.741 0.00 0.00 0.00 2.27
4470 4640 6.041069 CCGGGAAGAGACAGAGTATTATCTTT 59.959 42.308 0.00 0.00 0.00 2.52
4471 4641 5.536916 CCGGGAAGAGACAGAGTATTATCTT 59.463 44.000 0.00 0.00 0.00 2.40
4472 4642 5.074115 CCGGGAAGAGACAGAGTATTATCT 58.926 45.833 0.00 0.00 0.00 1.98
4473 4643 4.321378 GCCGGGAAGAGACAGAGTATTATC 60.321 50.000 2.18 0.00 0.00 1.75
4474 4644 3.574826 GCCGGGAAGAGACAGAGTATTAT 59.425 47.826 2.18 0.00 0.00 1.28
4475 4645 2.957006 GCCGGGAAGAGACAGAGTATTA 59.043 50.000 2.18 0.00 0.00 0.98
4476 4646 1.757699 GCCGGGAAGAGACAGAGTATT 59.242 52.381 2.18 0.00 0.00 1.89
4477 4647 1.404843 GCCGGGAAGAGACAGAGTAT 58.595 55.000 2.18 0.00 0.00 2.12
4478 4648 0.683504 GGCCGGGAAGAGACAGAGTA 60.684 60.000 2.18 0.00 0.00 2.59
4479 4649 1.985116 GGCCGGGAAGAGACAGAGT 60.985 63.158 2.18 0.00 0.00 3.24
4480 4650 1.544825 TTGGCCGGGAAGAGACAGAG 61.545 60.000 2.18 0.00 0.00 3.35
4481 4651 1.535444 TTGGCCGGGAAGAGACAGA 60.535 57.895 2.18 0.00 0.00 3.41
4482 4652 1.078848 CTTGGCCGGGAAGAGACAG 60.079 63.158 2.18 0.00 0.00 3.51
4483 4653 1.535444 TCTTGGCCGGGAAGAGACA 60.535 57.895 2.18 0.00 0.00 3.41
4484 4654 1.219393 CTCTTGGCCGGGAAGAGAC 59.781 63.158 21.38 0.00 46.44 3.36
4485 4655 1.990060 CCTCTTGGCCGGGAAGAGA 60.990 63.158 25.60 9.78 46.44 3.10
4486 4656 1.553690 TTCCTCTTGGCCGGGAAGAG 61.554 60.000 19.74 19.74 44.16 2.85
4487 4657 1.537889 TTCCTCTTGGCCGGGAAGA 60.538 57.895 2.18 8.99 34.64 2.87
4488 4658 1.078143 CTTCCTCTTGGCCGGGAAG 60.078 63.158 22.85 22.85 46.36 3.46
4489 4659 3.077907 CTTCCTCTTGGCCGGGAA 58.922 61.111 2.18 15.27 37.53 3.97
4490 4660 3.717294 GCTTCCTCTTGGCCGGGA 61.717 66.667 2.18 0.00 0.00 5.14
4491 4661 4.803908 GGCTTCCTCTTGGCCGGG 62.804 72.222 2.18 0.00 36.37 5.73
4494 4664 2.335712 CGTTGGCTTCCTCTTGGCC 61.336 63.158 0.00 0.00 45.45 5.36
4495 4665 1.301677 CTCGTTGGCTTCCTCTTGGC 61.302 60.000 0.00 0.00 0.00 4.52
4496 4666 0.321671 TCTCGTTGGCTTCCTCTTGG 59.678 55.000 0.00 0.00 0.00 3.61
4497 4667 1.270305 TGTCTCGTTGGCTTCCTCTTG 60.270 52.381 0.00 0.00 0.00 3.02
4498 4668 1.048601 TGTCTCGTTGGCTTCCTCTT 58.951 50.000 0.00 0.00 0.00 2.85
4499 4669 0.318762 GTGTCTCGTTGGCTTCCTCT 59.681 55.000 0.00 0.00 0.00 3.69
4500 4670 0.033504 TGTGTCTCGTTGGCTTCCTC 59.966 55.000 0.00 0.00 0.00 3.71
4519 4689 2.877300 GCATGACATGAACCAGGTGACT 60.877 50.000 19.76 0.00 46.44 3.41
4520 4690 1.470098 GCATGACATGAACCAGGTGAC 59.530 52.381 19.76 0.00 0.00 3.67
4521 4691 1.825090 GCATGACATGAACCAGGTGA 58.175 50.000 19.76 0.00 0.00 4.02
4523 4693 1.308069 GCGCATGACATGAACCAGGT 61.308 55.000 19.76 0.00 0.00 4.00
4524 4694 1.028330 AGCGCATGACATGAACCAGG 61.028 55.000 19.76 0.00 0.00 4.45
4525 4695 0.098200 CAGCGCATGACATGAACCAG 59.902 55.000 19.76 5.46 0.00 4.00
4526 4696 0.321475 TCAGCGCATGACATGAACCA 60.321 50.000 19.76 0.00 31.12 3.67
4549 4719 2.047655 GACACATGGCCGAACCGA 60.048 61.111 0.00 0.00 43.94 4.69
4550 4720 1.511318 TTTGACACATGGCCGAACCG 61.511 55.000 0.00 0.00 43.94 4.44
4556 4726 3.129287 CCAACTAGATTTGACACATGGCC 59.871 47.826 0.00 0.00 0.00 5.36
4567 4737 6.599638 GTGCTAATCAAGGACCAACTAGATTT 59.400 38.462 0.00 0.00 40.51 2.17
4571 4741 3.865745 CGTGCTAATCAAGGACCAACTAG 59.134 47.826 0.00 0.00 43.29 2.57
4573 4743 2.301870 TCGTGCTAATCAAGGACCAACT 59.698 45.455 0.00 0.00 43.29 3.16
4577 4747 2.695359 TGTTCGTGCTAATCAAGGACC 58.305 47.619 0.00 0.00 43.29 4.46
4623 4793 3.459969 ACTCTGGGATATTGGAGGGAAAC 59.540 47.826 0.00 0.00 0.00 2.78
4624 4794 3.459598 CACTCTGGGATATTGGAGGGAAA 59.540 47.826 0.00 0.00 31.52 3.13
4625 4795 3.048600 CACTCTGGGATATTGGAGGGAA 58.951 50.000 0.00 0.00 31.52 3.97
4626 4796 2.250008 TCACTCTGGGATATTGGAGGGA 59.750 50.000 0.00 0.00 36.11 4.20
4627 4797 2.636893 CTCACTCTGGGATATTGGAGGG 59.363 54.545 0.00 0.00 0.00 4.30
4628 4798 2.038295 GCTCACTCTGGGATATTGGAGG 59.962 54.545 0.00 0.00 0.00 4.30
4629 4799 2.971330 AGCTCACTCTGGGATATTGGAG 59.029 50.000 0.00 0.00 0.00 3.86
4630 4800 2.702478 CAGCTCACTCTGGGATATTGGA 59.298 50.000 0.00 0.00 0.00 3.53
4631 4801 2.809665 GCAGCTCACTCTGGGATATTGG 60.810 54.545 0.00 0.00 34.74 3.16
4632 4802 2.104451 AGCAGCTCACTCTGGGATATTG 59.896 50.000 0.00 0.00 34.74 1.90
4633 4803 2.368221 GAGCAGCTCACTCTGGGATATT 59.632 50.000 18.17 0.00 34.74 1.28
4634 4804 1.969923 GAGCAGCTCACTCTGGGATAT 59.030 52.381 18.17 0.00 34.74 1.63
4635 4805 1.407936 GAGCAGCTCACTCTGGGATA 58.592 55.000 18.17 0.00 34.74 2.59
4636 4806 1.674764 CGAGCAGCTCACTCTGGGAT 61.675 60.000 22.49 0.00 34.74 3.85
4637 4807 2.346541 CGAGCAGCTCACTCTGGGA 61.347 63.158 22.49 0.00 34.74 4.37
4638 4808 2.183811 CGAGCAGCTCACTCTGGG 59.816 66.667 22.49 0.00 34.74 4.45
4639 4809 2.508887 GCGAGCAGCTCACTCTGG 60.509 66.667 22.49 5.82 44.04 3.86
4653 4823 2.543578 CAAAGCTTGCTGGTAGCGA 58.456 52.632 0.00 0.00 46.26 4.93
4667 4837 1.934463 CTATGGTAGCGGCGCAAAG 59.066 57.895 35.02 16.49 0.00 2.77
4668 4838 2.177580 GCTATGGTAGCGGCGCAAA 61.178 57.895 35.02 19.15 42.62 3.68
4669 4839 2.587753 GCTATGGTAGCGGCGCAA 60.588 61.111 35.02 16.67 42.62 4.85


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

AutoCloner maintained by Alex Coulton.