Multiple sequence alignment - TraesCS2A01G329400

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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 TraesCS2A01G329400 chr2A 100.000 4815 0 0 1 4815 561557647 561552833 0.000000e+00 8892.0
1 TraesCS2A01G329400 chr2A 73.420 459 95 21 1346 1789 761305507 761305953 3.880000e-31 147.0
2 TraesCS2A01G329400 chr2A 97.059 34 1 0 3562 3595 563919128 563919161 1.870000e-04 58.4
3 TraesCS2A01G329400 chr2B 94.288 4202 159 33 1 4153 503769619 503773788 0.000000e+00 6355.0
4 TraesCS2A01G329400 chr2B 91.537 449 27 2 4174 4612 503773883 503774330 4.120000e-170 608.0
5 TraesCS2A01G329400 chr2B 76.681 476 77 21 2722 3175 499561478 499561015 2.900000e-57 233.0
6 TraesCS2A01G329400 chr2B 79.141 163 11 6 3978 4121 503774038 503774196 1.850000e-14 91.6
7 TraesCS2A01G329400 chr2B 89.091 55 5 1 4032 4086 499559768 499559715 3.110000e-07 67.6
8 TraesCS2A01G329400 chr2B 97.222 36 1 0 3560 3595 499560880 499560845 1.450000e-05 62.1
9 TraesCS2A01G329400 chr2D 95.363 3709 120 21 1 3676 426941344 426945033 0.000000e+00 5849.0
10 TraesCS2A01G329400 chr2D 89.072 1153 78 12 3629 4763 426945055 426946177 0.000000e+00 1387.0
11 TraesCS2A01G329400 chr2D 92.000 75 5 1 2702 2776 76629924 76629997 2.370000e-18 104.0
12 TraesCS2A01G329400 chr2D 85.417 96 9 3 4033 4126 426945813 426945905 1.430000e-15 95.3
13 TraesCS2A01G329400 chr2D 90.909 55 4 1 4032 4086 424677645 424677592 6.680000e-09 73.1
14 TraesCS2A01G329400 chr2D 97.222 36 1 0 3560 3595 424678722 424678687 1.450000e-05 62.1
15 TraesCS2A01G329400 chr7B 91.429 875 38 18 2757 3623 738144216 738145061 0.000000e+00 1166.0
16 TraesCS2A01G329400 chr7B 88.664 988 43 21 1686 2656 738143249 738144184 0.000000e+00 1140.0
17 TraesCS2A01G329400 chr7B 75.219 1142 201 55 1490 2599 540248441 540249532 2.620000e-127 466.0
18 TraesCS2A01G329400 chr7B 95.556 45 2 0 2677 2721 738144169 738144213 6.680000e-09 73.1
19 TraesCS2A01G329400 chr7A 75.633 1145 194 60 1490 2599 583871778 583872872 1.560000e-134 490.0
20 TraesCS2A01G329400 chr7D 75.197 1145 193 64 1493 2599 511325038 511326129 1.580000e-124 457.0
21 TraesCS2A01G329400 chr4A 85.227 176 15 3 39 203 602241242 602241417 2.300000e-38 171.0
22 TraesCS2A01G329400 chr4D 80.435 138 11 7 9 132 3284633 3284498 1.850000e-14 91.6
23 TraesCS2A01G329400 chr4B 83.019 106 6 6 39 132 3862685 3862580 8.590000e-13 86.1


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 TraesCS2A01G329400 chr2A 561552833 561557647 4814 True 8892.000000 8892 100.000000 1 4815 1 chr2A.!!$R1 4814
1 TraesCS2A01G329400 chr2B 503769619 503774330 4711 False 2351.533333 6355 88.322000 1 4612 3 chr2B.!!$F1 4611
2 TraesCS2A01G329400 chr2D 426941344 426946177 4833 False 2443.766667 5849 89.950667 1 4763 3 chr2D.!!$F2 4762
3 TraesCS2A01G329400 chr7B 738143249 738145061 1812 False 793.033333 1166 91.883000 1686 3623 3 chr7B.!!$F2 1937
4 TraesCS2A01G329400 chr7B 540248441 540249532 1091 False 466.000000 466 75.219000 1490 2599 1 chr7B.!!$F1 1109
5 TraesCS2A01G329400 chr7A 583871778 583872872 1094 False 490.000000 490 75.633000 1490 2599 1 chr7A.!!$F1 1109
6 TraesCS2A01G329400 chr7D 511325038 511326129 1091 False 457.000000 457 75.197000 1493 2599 1 chr7D.!!$F1 1106

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
132 144 1.069906 GGTAAAGCACGTGCACTCAAG 60.070 52.381 39.21 1.57 45.16 3.02 F
682 696 1.733912 TGCGATCTGTTAGTACGACGT 59.266 47.619 5.52 5.52 0.00 4.34 F
968 996 2.094675 GTTCTGCAAGGCCACATGTAT 58.905 47.619 5.01 0.00 0.00 2.29 F
1072 1100 2.182030 GGGAAGTCGACCGCTGAG 59.818 66.667 13.01 0.00 0.00 3.35 F
3007 3087 2.335712 CGGAGCAAGGCCAACTTCC 61.336 63.158 5.01 5.88 37.29 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1317 2.272146 CAAGACCCATCCACCCGG 59.728 66.667 0.00 0.0 0.00 5.73 R
1834 1871 2.341176 GTACACCTTGGACCGCGT 59.659 61.111 4.92 0.0 0.00 6.01 R
1940 1977 2.479412 GAAGACCTCGACGTGCTGCT 62.479 60.000 0.00 0.0 0.00 4.24 R
3135 3215 1.456705 GGTCGGGAGGATGAGCTCT 60.457 63.158 16.19 0.0 0.00 4.09 R
4785 5076 1.004745 GGGCTGGGAAAGAGTTCATCA 59.995 52.381 0.00 0.0 35.25 3.07 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
26 27 3.118445 TGCTTCGGATTCACATGGTATGA 60.118 43.478 0.00 0.00 0.00 2.15
71 72 3.225104 GGCCTTATGATTTGCTCCATCA 58.775 45.455 0.00 0.00 35.12 3.07
102 114 8.507524 AAGATACTTGGGTTATTTCTTAGCAC 57.492 34.615 0.00 0.00 0.00 4.40
132 144 1.069906 GGTAAAGCACGTGCACTCAAG 60.070 52.381 39.21 1.57 45.16 3.02
155 167 2.544267 GACAACAACGAACAAGAGGAGG 59.456 50.000 0.00 0.00 0.00 4.30
157 169 2.240493 ACAACGAACAAGAGGAGGTG 57.760 50.000 0.00 0.00 0.00 4.00
171 183 4.536090 AGAGGAGGTGTAACAAATGGATCA 59.464 41.667 0.00 0.00 39.98 2.92
316 329 5.411977 CCTAGATTGATGCTAGATTTGCCTG 59.588 44.000 0.00 0.00 38.03 4.85
366 379 2.354103 GCAGTCAGCACCACTCTTCATA 60.354 50.000 0.00 0.00 44.79 2.15
445 458 6.712276 AGTGTAGGAGAATAAAGTTCCAAGG 58.288 40.000 0.00 0.00 33.32 3.61
446 459 6.500751 AGTGTAGGAGAATAAAGTTCCAAGGA 59.499 38.462 0.00 0.00 33.32 3.36
485 498 6.112058 AGAGCTTATCAGGTTAAAGCAGAAG 58.888 40.000 8.78 0.00 46.35 2.85
580 593 2.378038 TGCAATCCCATAAACTCTGCC 58.622 47.619 0.00 0.00 0.00 4.85
583 596 3.278574 CAATCCCATAAACTCTGCCGAA 58.721 45.455 0.00 0.00 0.00 4.30
647 661 7.488187 TTACTTCTATACGCGATGTTAGAGT 57.512 36.000 15.93 10.73 0.00 3.24
678 692 6.089920 TCATTTTTGCGATCTGTTAGTACG 57.910 37.500 0.00 0.00 0.00 3.67
679 693 5.865013 TCATTTTTGCGATCTGTTAGTACGA 59.135 36.000 0.00 0.00 0.00 3.43
680 694 5.505165 TTTTTGCGATCTGTTAGTACGAC 57.495 39.130 0.00 0.00 0.00 4.34
681 695 2.447089 TGCGATCTGTTAGTACGACG 57.553 50.000 0.00 0.00 0.00 5.12
682 696 1.733912 TGCGATCTGTTAGTACGACGT 59.266 47.619 5.52 5.52 0.00 4.34
683 697 2.929398 TGCGATCTGTTAGTACGACGTA 59.071 45.455 2.97 2.97 0.00 3.57
712 730 6.195868 TGACAGTACAAAAGTTTAACGCATG 58.804 36.000 0.00 0.00 0.00 4.06
718 736 5.646606 ACAAAAGTTTAACGCATGACAGTT 58.353 33.333 0.00 1.71 0.00 3.16
760 778 5.156804 CACTACTGTGGAAACTTCACAAC 57.843 43.478 0.00 0.00 43.45 3.32
769 787 3.428862 GGAAACTTCACAACACAGTTGGG 60.429 47.826 13.71 10.03 31.00 4.12
855 881 4.057428 ACCAGCTCGCCGTGACTC 62.057 66.667 0.00 0.00 0.00 3.36
924 951 2.944557 CGCGGTCACACGATCTCG 60.945 66.667 0.00 0.00 46.33 4.04
968 996 2.094675 GTTCTGCAAGGCCACATGTAT 58.905 47.619 5.01 0.00 0.00 2.29
969 997 3.278574 GTTCTGCAAGGCCACATGTATA 58.721 45.455 5.01 0.00 0.00 1.47
1072 1100 2.182030 GGGAAGTCGACCGCTGAG 59.818 66.667 13.01 0.00 0.00 3.35
3007 3087 2.335712 CGGAGCAAGGCCAACTTCC 61.336 63.158 5.01 5.88 37.29 3.46
3087 3167 2.663196 CACTGGAGGAACCCGGTC 59.337 66.667 0.00 0.00 43.67 4.79
3135 3215 1.672030 CACGCTCATGTGCTTCCCA 60.672 57.895 16.99 0.00 32.31 4.37
3147 3227 0.106521 GCTTCCCAGAGCTCATCCTC 59.893 60.000 17.77 0.00 39.57 3.71
3175 3255 1.632920 TGTTCCTGTACATGGCCATGA 59.367 47.619 44.72 28.03 41.20 3.07
3686 3848 1.726791 GCCGTGATGTGTAAGTGTCAG 59.273 52.381 0.00 0.00 0.00 3.51
3687 3849 2.866460 GCCGTGATGTGTAAGTGTCAGT 60.866 50.000 0.00 0.00 0.00 3.41
3688 3850 2.731451 CCGTGATGTGTAAGTGTCAGTG 59.269 50.000 0.00 0.00 0.00 3.66
3689 3851 3.552068 CCGTGATGTGTAAGTGTCAGTGA 60.552 47.826 0.00 0.00 0.00 3.41
3690 3852 3.425525 CGTGATGTGTAAGTGTCAGTGAC 59.574 47.826 16.68 16.68 0.00 3.67
3691 3853 3.425525 GTGATGTGTAAGTGTCAGTGACG 59.574 47.826 18.17 0.00 34.95 4.35
3692 3854 2.502213 TGTGTAAGTGTCAGTGACGG 57.498 50.000 18.17 0.00 34.95 4.79
3693 3855 2.025898 TGTGTAAGTGTCAGTGACGGA 58.974 47.619 18.17 0.00 34.95 4.69
3774 3945 2.222508 CGCTAAATGTCGGTGAACTTCG 60.223 50.000 0.00 0.00 0.00 3.79
3790 3961 1.740025 CTTCGAAGTGAAATGCCTCCC 59.260 52.381 17.24 0.00 35.79 4.30
3841 4013 3.889538 TCGTGCTGCTATTCCTGTATACT 59.110 43.478 4.17 0.00 0.00 2.12
3842 4014 3.983988 CGTGCTGCTATTCCTGTATACTG 59.016 47.826 4.17 3.48 0.00 2.74
3846 4018 4.991687 GCTGCTATTCCTGTATACTGTTCC 59.008 45.833 4.17 0.00 0.00 3.62
3847 4019 5.221541 GCTGCTATTCCTGTATACTGTTCCT 60.222 44.000 4.17 0.00 0.00 3.36
3848 4020 6.161855 TGCTATTCCTGTATACTGTTCCTG 57.838 41.667 4.17 0.00 0.00 3.86
3849 4021 5.661312 TGCTATTCCTGTATACTGTTCCTGT 59.339 40.000 4.17 0.00 0.00 4.00
3851 4023 7.509318 TGCTATTCCTGTATACTGTTCCTGTAT 59.491 37.037 4.17 0.00 34.03 2.29
3852 4024 9.021807 GCTATTCCTGTATACTGTTCCTGTATA 57.978 37.037 4.17 0.00 32.37 1.47
3913 4090 9.252962 ACTTTCACAAAATCTGAATTCATTCAC 57.747 29.630 8.96 0.00 41.51 3.18
3925 4102 6.916440 TGAATTCATTCACCAGACTGAAATG 58.084 36.000 3.38 10.65 43.70 2.32
4101 4299 5.068198 ACGACCACTTGAAAGTACAGAGTAA 59.932 40.000 0.00 0.00 37.08 2.24
4102 4300 5.981315 CGACCACTTGAAAGTACAGAGTAAA 59.019 40.000 0.00 0.00 37.08 2.01
4103 4301 6.645415 CGACCACTTGAAAGTACAGAGTAAAT 59.355 38.462 0.00 0.00 37.08 1.40
4136 4334 6.653020 TCCAGCAACATAAATGTATCTCACT 58.347 36.000 0.00 0.00 40.80 3.41
4164 4444 5.650266 TCAGGCAAGTACTTCTTTTGTTTGA 59.350 36.000 4.77 1.28 33.63 2.69
4167 4447 5.515270 GGCAAGTACTTCTTTTGTTTGACAC 59.485 40.000 4.77 0.00 33.63 3.67
4202 4482 9.656040 CATTTTCCACAAAATCTGAATCCATTA 57.344 29.630 0.00 0.00 39.75 1.90
4260 4540 3.307691 GGAATGACAGATTGACAGGTCCA 60.308 47.826 0.00 0.00 33.59 4.02
4359 4639 4.279169 ACATGTGTTCCAGTTTGATCCTTG 59.721 41.667 0.00 0.00 0.00 3.61
4378 4658 4.335416 CTTGGCATCTTTCCAGAACCTAA 58.665 43.478 0.00 0.00 34.66 2.69
4393 4673 6.647067 CCAGAACCTAAAACAGAGTTACAGAG 59.353 42.308 0.00 0.00 0.00 3.35
4461 4742 2.223572 CCAGCAGACAACCACTTCAAAC 60.224 50.000 0.00 0.00 0.00 2.93
4499 4780 4.336993 AGTTCCAGCAACATCAAAACGTAA 59.663 37.500 0.00 0.00 37.48 3.18
4507 4788 6.928492 AGCAACATCAAAACGTAATCCAATTT 59.072 30.769 0.00 0.00 0.00 1.82
4516 4797 7.985634 AAACGTAATCCAATTTATGATGCAC 57.014 32.000 0.00 0.00 0.00 4.57
4537 4818 8.429493 TGCACAACTCTTTCATATTCATCTAG 57.571 34.615 0.00 0.00 0.00 2.43
4564 4855 2.341176 GCAAAGCTGCCCTTGTGG 59.659 61.111 12.10 0.00 43.26 4.17
4574 4865 1.004679 CCCTTGTGGCCATGCAAAC 60.005 57.895 9.72 0.00 0.00 2.93
4575 4866 1.747145 CCTTGTGGCCATGCAAACA 59.253 52.632 9.72 0.00 0.00 2.83
4576 4867 0.106335 CCTTGTGGCCATGCAAACAA 59.894 50.000 9.72 6.35 36.05 2.83
4591 4882 4.795795 TGCAAACAATTGAAGTACACAACG 59.204 37.500 13.59 5.52 38.94 4.10
4595 4886 1.873698 ATTGAAGTACACAACGGCGT 58.126 45.000 6.77 6.77 0.00 5.68
4612 4903 3.678662 GGCGTAGTCGTAACTGAACTAG 58.321 50.000 0.00 0.00 36.92 2.57
4613 4904 3.126000 GGCGTAGTCGTAACTGAACTAGT 59.874 47.826 0.00 0.00 39.36 2.57
4614 4905 4.330074 GGCGTAGTCGTAACTGAACTAGTA 59.670 45.833 0.00 0.00 37.80 1.82
4615 4906 5.251832 GCGTAGTCGTAACTGAACTAGTAC 58.748 45.833 0.00 0.00 37.80 2.73
4616 4907 5.062809 GCGTAGTCGTAACTGAACTAGTACT 59.937 44.000 0.00 0.00 37.80 2.73
4617 4908 6.253727 GCGTAGTCGTAACTGAACTAGTACTA 59.746 42.308 1.89 1.89 37.80 1.82
4624 4915 9.435688 TCGTAACTGAACTAGTACTACATGTTA 57.564 33.333 2.30 4.81 39.18 2.41
4676 4967 6.645700 TGCAACAAGATTTTTGTTCAACTC 57.354 33.333 2.53 0.00 40.30 3.01
4681 4972 9.532697 CAACAAGATTTTTGTTCAACTCAAAAG 57.467 29.630 2.53 0.00 42.80 2.27
4684 4975 9.143631 CAAGATTTTTGTTCAACTCAAAAGACT 57.856 29.630 0.00 0.00 42.80 3.24
4695 4986 6.708949 TCAACTCAAAAGACTACAATACCCAC 59.291 38.462 0.00 0.00 0.00 4.61
4714 5005 3.004106 CCACAATGCTAGCAAATCTAGGC 59.996 47.826 23.54 0.00 43.95 3.93
4715 5006 3.628942 CACAATGCTAGCAAATCTAGGCA 59.371 43.478 23.54 0.00 43.95 4.75
4723 5014 7.428020 TGCTAGCAAATCTAGGCAAAATAATG 58.572 34.615 16.84 0.00 43.95 1.90
4738 5029 7.959109 GGCAAAATAATGTGAAGAAATTGAAGC 59.041 33.333 0.00 0.00 0.00 3.86
4746 5037 3.253188 TGAAGAAATTGAAGCCTTGGACG 59.747 43.478 0.00 0.00 0.00 4.79
4763 5054 3.133901 TGGACGAATTGAGGCAATAGCTA 59.866 43.478 0.00 0.00 41.70 3.32
4764 5055 3.743396 GGACGAATTGAGGCAATAGCTAG 59.257 47.826 0.00 0.00 41.70 3.42
4765 5056 3.134458 ACGAATTGAGGCAATAGCTAGC 58.866 45.455 6.62 6.62 41.70 3.42
4766 5057 3.181461 ACGAATTGAGGCAATAGCTAGCT 60.181 43.478 23.12 23.12 41.70 3.32
4767 5058 3.186001 CGAATTGAGGCAATAGCTAGCTG 59.814 47.826 27.68 12.77 41.70 4.24
4768 5059 3.853355 ATTGAGGCAATAGCTAGCTGT 57.147 42.857 27.68 18.59 41.70 4.40
4769 5060 2.609427 TGAGGCAATAGCTAGCTGTG 57.391 50.000 27.68 23.44 41.70 3.66
4770 5061 1.224965 GAGGCAATAGCTAGCTGTGC 58.775 55.000 31.97 31.97 41.70 4.57
4771 5062 0.543277 AGGCAATAGCTAGCTGTGCA 59.457 50.000 36.23 19.04 38.99 4.57
4772 5063 0.659957 GGCAATAGCTAGCTGTGCAC 59.340 55.000 36.23 27.32 38.99 4.57
4773 5064 1.372582 GCAATAGCTAGCTGTGCACA 58.627 50.000 33.48 20.37 37.92 4.57
4774 5065 1.329906 GCAATAGCTAGCTGTGCACAG 59.670 52.381 37.09 37.09 41.42 3.66
4775 5066 2.625737 CAATAGCTAGCTGTGCACAGT 58.374 47.619 39.30 29.30 45.45 3.55
4776 5067 3.785486 CAATAGCTAGCTGTGCACAGTA 58.215 45.455 39.30 28.93 45.45 2.74
4777 5068 2.941453 TAGCTAGCTGTGCACAGTAC 57.059 50.000 39.30 27.22 45.45 2.73
4778 5069 0.969149 AGCTAGCTGTGCACAGTACA 59.031 50.000 39.30 26.00 45.45 2.90
4779 5070 1.344438 AGCTAGCTGTGCACAGTACAA 59.656 47.619 39.30 24.15 45.45 2.41
4780 5071 2.143122 GCTAGCTGTGCACAGTACAAA 58.857 47.619 39.30 22.67 45.45 2.83
4781 5072 2.096218 GCTAGCTGTGCACAGTACAAAC 60.096 50.000 39.30 25.28 45.45 2.93
4782 5073 2.332063 AGCTGTGCACAGTACAAACT 57.668 45.000 39.30 26.85 45.45 2.66
4795 5086 6.851222 CAGTACAAACTGTTGATGAACTCT 57.149 37.500 0.00 0.00 46.76 3.24
4796 5087 7.251704 CAGTACAAACTGTTGATGAACTCTT 57.748 36.000 0.00 0.00 46.76 2.85
4797 5088 7.697691 CAGTACAAACTGTTGATGAACTCTTT 58.302 34.615 0.00 0.00 46.76 2.52
4798 5089 7.852945 CAGTACAAACTGTTGATGAACTCTTTC 59.147 37.037 0.00 0.00 46.76 2.62
4799 5090 6.136541 ACAAACTGTTGATGAACTCTTTCC 57.863 37.500 0.00 0.00 38.20 3.13
4800 5091 5.067805 ACAAACTGTTGATGAACTCTTTCCC 59.932 40.000 0.00 0.00 38.20 3.97
4801 5092 4.437682 ACTGTTGATGAACTCTTTCCCA 57.562 40.909 0.00 0.00 32.79 4.37
4802 5093 4.392940 ACTGTTGATGAACTCTTTCCCAG 58.607 43.478 0.00 0.00 32.79 4.45
4803 5094 3.149196 TGTTGATGAACTCTTTCCCAGC 58.851 45.455 0.00 0.00 32.79 4.85
4804 5095 2.489722 GTTGATGAACTCTTTCCCAGCC 59.510 50.000 0.00 0.00 0.00 4.85
4805 5096 1.004745 TGATGAACTCTTTCCCAGCCC 59.995 52.381 0.00 0.00 0.00 5.19
4806 5097 1.283321 GATGAACTCTTTCCCAGCCCT 59.717 52.381 0.00 0.00 0.00 5.19
4807 5098 2.038863 TGAACTCTTTCCCAGCCCTA 57.961 50.000 0.00 0.00 0.00 3.53
4808 5099 2.344592 TGAACTCTTTCCCAGCCCTAA 58.655 47.619 0.00 0.00 0.00 2.69
4809 5100 2.039879 TGAACTCTTTCCCAGCCCTAAC 59.960 50.000 0.00 0.00 0.00 2.34
4810 5101 1.742308 ACTCTTTCCCAGCCCTAACA 58.258 50.000 0.00 0.00 0.00 2.41
4811 5102 1.351350 ACTCTTTCCCAGCCCTAACAC 59.649 52.381 0.00 0.00 0.00 3.32
4812 5103 1.630878 CTCTTTCCCAGCCCTAACACT 59.369 52.381 0.00 0.00 0.00 3.55
4813 5104 1.351017 TCTTTCCCAGCCCTAACACTG 59.649 52.381 0.00 0.00 0.00 3.66
4814 5105 1.351017 CTTTCCCAGCCCTAACACTGA 59.649 52.381 0.00 0.00 35.90 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.264832 CAACATGTTATTATCAACGGCATGT 58.735 36.000 11.53 0.00 44.64 3.21
31 32 4.338118 AGGCCAACATGTTATTATCAACGG 59.662 41.667 11.53 6.12 0.00 4.44
94 96 6.206048 GCTTTACCAAAGGTTAAGTGCTAAGA 59.794 38.462 14.22 0.00 42.26 2.10
102 114 4.533222 CACGTGCTTTACCAAAGGTTAAG 58.467 43.478 0.82 9.84 42.89 1.85
132 144 2.933906 TCCTCTTGTTCGTTGTTGTCAC 59.066 45.455 0.00 0.00 0.00 3.67
138 150 1.485066 ACACCTCCTCTTGTTCGTTGT 59.515 47.619 0.00 0.00 0.00 3.32
155 167 9.139174 CTTGGTTTATTGATCCATTTGTTACAC 57.861 33.333 0.00 0.00 0.00 2.90
157 169 7.277760 GCCTTGGTTTATTGATCCATTTGTTAC 59.722 37.037 0.00 0.00 0.00 2.50
171 183 2.279935 TGTCGGTGCCTTGGTTTATT 57.720 45.000 0.00 0.00 0.00 1.40
316 329 9.020813 GGTCTTTCAAAAGAAACAACTTACATC 57.979 33.333 6.76 0.00 45.77 3.06
366 379 9.698309 CTCGTTAAGTATATTGACCAATCTCAT 57.302 33.333 0.00 0.00 32.50 2.90
438 451 3.835478 TTCCTCTCTCTCTCCTTGGAA 57.165 47.619 0.00 0.00 0.00 3.53
445 458 5.405935 AAGCTCTTTTTCCTCTCTCTCTC 57.594 43.478 0.00 0.00 0.00 3.20
446 459 6.667414 TGATAAGCTCTTTTTCCTCTCTCTCT 59.333 38.462 0.00 0.00 0.00 3.10
485 498 0.533951 CTTTGATCTTTGGGGCCTGC 59.466 55.000 0.84 0.00 0.00 4.85
533 546 2.039084 AGGGAGCAAAGTGTCTACTTGG 59.961 50.000 0.00 0.00 46.14 3.61
540 553 3.366374 GCAATACAAGGGAGCAAAGTGTC 60.366 47.826 0.00 0.00 0.00 3.67
618 632 6.807708 ACATCGCGTATAGAAGTAAACAAG 57.192 37.500 5.77 0.00 0.00 3.16
647 661 7.615582 ACAGATCGCAAAAATGATTCTTCTA 57.384 32.000 0.00 0.00 0.00 2.10
662 676 1.733912 ACGTCGTACTAACAGATCGCA 59.266 47.619 0.00 0.00 0.00 5.10
678 692 6.940714 ACTTTTGTACTGTCAATTGTACGTC 58.059 36.000 5.13 0.00 41.16 4.34
679 693 6.913873 ACTTTTGTACTGTCAATTGTACGT 57.086 33.333 5.13 0.00 41.16 3.57
680 694 9.705471 TTAAACTTTTGTACTGTCAATTGTACG 57.295 29.630 5.13 0.00 41.16 3.67
682 696 9.705471 CGTTAAACTTTTGTACTGTCAATTGTA 57.295 29.630 5.13 0.00 0.00 2.41
683 697 7.219344 GCGTTAAACTTTTGTACTGTCAATTGT 59.781 33.333 5.13 0.00 0.00 2.71
712 730 3.511934 ACCAGGTAGACATCTGAACTGTC 59.488 47.826 0.00 3.72 42.68 3.51
718 736 5.084519 AGTGTAAACCAGGTAGACATCTGA 58.915 41.667 9.24 0.00 33.11 3.27
760 778 0.813610 TGCGTCTGTTCCCAACTGTG 60.814 55.000 0.00 0.00 0.00 3.66
769 787 0.235926 GAAACTGCCTGCGTCTGTTC 59.764 55.000 0.00 0.00 0.00 3.18
855 881 1.780806 AAGATGAGCGAGATCATGCG 58.219 50.000 8.67 0.00 40.02 4.73
918 945 0.107703 TTGTGGTGGATGGCGAGATC 60.108 55.000 0.00 0.00 0.00 2.75
924 951 0.609662 AAGCATTTGTGGTGGATGGC 59.390 50.000 0.00 0.00 0.00 4.40
989 1017 2.095461 CAGTCAGCTCAGCTAGTACCA 58.905 52.381 0.00 0.00 36.40 3.25
990 1018 2.370349 TCAGTCAGCTCAGCTAGTACC 58.630 52.381 0.00 0.00 36.40 3.34
1050 1078 4.125695 CGGTCGACTTCCCCGGAC 62.126 72.222 16.46 0.00 38.09 4.79
1289 1317 2.272146 CAAGACCCATCCACCCGG 59.728 66.667 0.00 0.00 0.00 5.73
1476 1507 2.360801 CTCTGGATTCGACTTCCTCTCC 59.639 54.545 13.32 0.41 34.17 3.71
1705 1742 4.803426 GACCTCGGTCGGCAGCAG 62.803 72.222 0.00 0.00 35.30 4.24
1834 1871 2.341176 GTACACCTTGGACCGCGT 59.659 61.111 4.92 0.00 0.00 6.01
1939 1976 2.755542 AAGACCTCGACGTGCTGCTG 62.756 60.000 0.00 0.00 0.00 4.41
1940 1977 2.479412 GAAGACCTCGACGTGCTGCT 62.479 60.000 0.00 0.00 0.00 4.24
3135 3215 1.456705 GGTCGGGAGGATGAGCTCT 60.457 63.158 16.19 0.00 0.00 4.09
3147 3227 1.080298 GTACAGGAACACGGTCGGG 60.080 63.158 0.00 0.00 0.00 5.14
3175 3255 1.988406 GGTAGTTCCAGAGGCCGGT 60.988 63.158 1.90 0.00 35.97 5.28
3214 3294 4.193334 CCTCGCGTCCATGCTCGA 62.193 66.667 5.77 4.78 0.00 4.04
3258 3338 1.429927 GCTCCTCGTCGATCTCGTCA 61.430 60.000 0.00 0.00 40.80 4.35
3686 3848 3.986006 TGGCCGTCACTCCGTCAC 61.986 66.667 0.00 0.00 0.00 3.67
3687 3849 3.986006 GTGGCCGTCACTCCGTCA 61.986 66.667 0.00 0.00 42.86 4.35
3688 3850 3.296709 ATGTGGCCGTCACTCCGTC 62.297 63.158 4.47 0.00 46.20 4.79
3689 3851 3.296709 GATGTGGCCGTCACTCCGT 62.297 63.158 4.47 0.00 46.20 4.69
3690 3852 2.509336 GATGTGGCCGTCACTCCG 60.509 66.667 4.47 0.00 46.20 4.63
3691 3853 2.125106 GGATGTGGCCGTCACTCC 60.125 66.667 4.47 5.40 46.20 3.85
3692 3854 1.448540 CAGGATGTGGCCGTCACTC 60.449 63.158 4.47 0.00 46.20 3.51
3693 3855 2.665000 CAGGATGTGGCCGTCACT 59.335 61.111 4.47 0.00 46.20 3.41
3774 3945 1.200020 CGTTGGGAGGCATTTCACTTC 59.800 52.381 0.00 0.00 0.00 3.01
3790 3961 5.621197 TGTGAAAAATATCAGTCCCGTTG 57.379 39.130 0.00 0.00 0.00 4.10
3841 4013 9.661954 AAAGAGGAAGAGATATATACAGGAACA 57.338 33.333 0.00 0.00 0.00 3.18
3842 4014 9.921637 CAAAGAGGAAGAGATATATACAGGAAC 57.078 37.037 0.00 0.00 0.00 3.62
3847 4019 9.547753 GCAAACAAAGAGGAAGAGATATATACA 57.452 33.333 0.00 0.00 0.00 2.29
3848 4020 8.994170 GGCAAACAAAGAGGAAGAGATATATAC 58.006 37.037 0.00 0.00 0.00 1.47
3849 4021 8.713971 TGGCAAACAAAGAGGAAGAGATATATA 58.286 33.333 0.00 0.00 0.00 0.86
3851 4023 6.957631 TGGCAAACAAAGAGGAAGAGATATA 58.042 36.000 0.00 0.00 0.00 0.86
3852 4024 5.819991 TGGCAAACAAAGAGGAAGAGATAT 58.180 37.500 0.00 0.00 0.00 1.63
3853 4025 5.241403 TGGCAAACAAAGAGGAAGAGATA 57.759 39.130 0.00 0.00 0.00 1.98
3856 4028 5.884792 AGATATGGCAAACAAAGAGGAAGAG 59.115 40.000 0.00 0.00 0.00 2.85
3857 4029 5.649395 CAGATATGGCAAACAAAGAGGAAGA 59.351 40.000 0.00 0.00 0.00 2.87
3913 4090 1.681166 CCCTCCAGCATTTCAGTCTGG 60.681 57.143 0.00 1.29 46.60 3.86
3925 4102 1.324740 TGAAATGCATGCCCTCCAGC 61.325 55.000 16.68 0.00 0.00 4.85
4079 4264 7.964604 ATTTACTCTGTACTTTCAAGTGGTC 57.035 36.000 2.26 0.00 40.07 4.02
4136 4334 7.817418 ACAAAAGAAGTACTTGCCTGATTTA 57.183 32.000 14.14 0.00 38.98 1.40
4164 4444 6.653526 TTGTGGAAAATGATTCAGATGTGT 57.346 33.333 0.00 0.00 0.00 3.72
4167 4447 8.869897 CAGATTTTGTGGAAAATGATTCAGATG 58.130 33.333 0.00 0.00 36.00 2.90
4202 4482 9.838339 CATTCCCTCTAGTATTTCAGTATGTTT 57.162 33.333 0.00 0.00 37.40 2.83
4260 4540 6.737720 TGTTCCATTAGCATCTCATCTACT 57.262 37.500 0.00 0.00 0.00 2.57
4294 4574 2.979240 TGGTACAAATGCGCTGATACA 58.021 42.857 9.73 0.00 31.92 2.29
4336 4616 4.104383 AGGATCAAACTGGAACACATGT 57.896 40.909 0.00 0.00 0.00 3.21
4359 4639 4.522789 TGTTTTAGGTTCTGGAAAGATGCC 59.477 41.667 0.00 0.00 0.00 4.40
4393 4673 2.300437 ACCCTGCAGAAGTCAGAAGTAC 59.700 50.000 17.39 0.00 33.54 2.73
4461 4742 4.683832 CTGGAACTACATTTACTCGGGAG 58.316 47.826 0.00 0.00 0.00 4.30
4499 4780 7.414222 AAGAGTTGTGCATCATAAATTGGAT 57.586 32.000 0.00 0.00 0.00 3.41
4507 4788 8.735692 TGAATATGAAAGAGTTGTGCATCATA 57.264 30.769 5.18 5.18 35.11 2.15
4511 4792 7.876936 AGATGAATATGAAAGAGTTGTGCAT 57.123 32.000 0.00 0.00 0.00 3.96
4559 4850 2.158856 TCAATTGTTTGCATGGCCACAA 60.159 40.909 8.16 6.03 35.95 3.33
4564 4855 4.150451 GTGTACTTCAATTGTTTGCATGGC 59.850 41.667 5.13 0.00 32.61 4.40
4574 4865 2.032377 ACGCCGTTGTGTACTTCAATTG 60.032 45.455 0.00 0.00 32.21 2.32
4575 4866 2.215196 ACGCCGTTGTGTACTTCAATT 58.785 42.857 7.17 0.00 32.21 2.32
4576 4867 1.873698 ACGCCGTTGTGTACTTCAAT 58.126 45.000 7.17 0.00 32.21 2.57
4591 4882 2.626088 AGTTCAGTTACGACTACGCC 57.374 50.000 0.00 0.00 43.96 5.68
4595 4886 9.091784 CATGTAGTACTAGTTCAGTTACGACTA 57.908 37.037 1.87 0.00 38.80 2.59
4653 4944 6.162079 TGAGTTGAACAAAAATCTTGTTGCA 58.838 32.000 7.55 3.78 42.11 4.08
4655 4946 9.532697 CTTTTGAGTTGAACAAAAATCTTGTTG 57.467 29.630 7.55 0.00 43.39 3.33
4670 4961 6.708949 GTGGGTATTGTAGTCTTTTGAGTTGA 59.291 38.462 0.00 0.00 33.49 3.18
4676 4967 6.071952 AGCATTGTGGGTATTGTAGTCTTTTG 60.072 38.462 0.00 0.00 0.00 2.44
4681 4972 4.511826 GCTAGCATTGTGGGTATTGTAGTC 59.488 45.833 10.63 0.00 0.00 2.59
4684 4975 4.495690 TGCTAGCATTGTGGGTATTGTA 57.504 40.909 14.93 0.00 0.00 2.41
4695 4986 4.906065 TTGCCTAGATTTGCTAGCATTG 57.094 40.909 20.13 4.34 44.35 2.82
4714 5005 9.211485 AGGCTTCAATTTCTTCACATTATTTTG 57.789 29.630 0.00 0.00 0.00 2.44
4715 5006 9.783081 AAGGCTTCAATTTCTTCACATTATTTT 57.217 25.926 0.00 0.00 0.00 1.82
4723 5014 4.550422 GTCCAAGGCTTCAATTTCTTCAC 58.450 43.478 0.00 0.00 0.00 3.18
4732 5023 2.813754 CTCAATTCGTCCAAGGCTTCAA 59.186 45.455 0.00 0.00 0.00 2.69
4738 5029 1.533625 TTGCCTCAATTCGTCCAAGG 58.466 50.000 0.00 0.00 0.00 3.61
4746 5037 4.024218 CACAGCTAGCTATTGCCTCAATTC 60.024 45.833 18.86 0.00 40.80 2.17
4772 5063 7.852945 GAAAGAGTTCATCAACAGTTTGTACTG 59.147 37.037 3.87 3.87 43.84 2.74
4773 5064 7.012421 GGAAAGAGTTCATCAACAGTTTGTACT 59.988 37.037 0.00 0.00 35.25 2.73
4774 5065 7.132863 GGAAAGAGTTCATCAACAGTTTGTAC 58.867 38.462 0.00 0.00 35.25 2.90
4775 5066 6.262273 GGGAAAGAGTTCATCAACAGTTTGTA 59.738 38.462 0.00 0.00 35.25 2.41
4776 5067 5.067805 GGGAAAGAGTTCATCAACAGTTTGT 59.932 40.000 0.00 0.00 35.25 2.83
4777 5068 5.067674 TGGGAAAGAGTTCATCAACAGTTTG 59.932 40.000 0.00 0.00 35.25 2.93
4778 5069 5.200483 TGGGAAAGAGTTCATCAACAGTTT 58.800 37.500 0.00 0.00 35.25 2.66
4779 5070 4.792068 TGGGAAAGAGTTCATCAACAGTT 58.208 39.130 0.00 0.00 35.25 3.16
4780 5071 4.392940 CTGGGAAAGAGTTCATCAACAGT 58.607 43.478 0.00 0.00 35.25 3.55
4781 5072 3.190118 GCTGGGAAAGAGTTCATCAACAG 59.810 47.826 0.00 0.00 35.25 3.16
4782 5073 3.149196 GCTGGGAAAGAGTTCATCAACA 58.851 45.455 0.00 0.00 35.25 3.33
4783 5074 2.489722 GGCTGGGAAAGAGTTCATCAAC 59.510 50.000 0.00 0.00 35.25 3.18
4784 5075 2.555227 GGGCTGGGAAAGAGTTCATCAA 60.555 50.000 0.00 0.00 35.25 2.57
4785 5076 1.004745 GGGCTGGGAAAGAGTTCATCA 59.995 52.381 0.00 0.00 35.25 3.07
4786 5077 1.283321 AGGGCTGGGAAAGAGTTCATC 59.717 52.381 0.00 0.00 35.25 2.92
4787 5078 1.376649 AGGGCTGGGAAAGAGTTCAT 58.623 50.000 0.00 0.00 35.25 2.57
4788 5079 2.038863 TAGGGCTGGGAAAGAGTTCA 57.961 50.000 0.00 0.00 35.25 3.18
4789 5080 2.039879 TGTTAGGGCTGGGAAAGAGTTC 59.960 50.000 0.00 0.00 0.00 3.01
4790 5081 2.062636 TGTTAGGGCTGGGAAAGAGTT 58.937 47.619 0.00 0.00 0.00 3.01
4791 5082 1.351350 GTGTTAGGGCTGGGAAAGAGT 59.649 52.381 0.00 0.00 0.00 3.24
4792 5083 1.630878 AGTGTTAGGGCTGGGAAAGAG 59.369 52.381 0.00 0.00 0.00 2.85
4793 5084 1.351017 CAGTGTTAGGGCTGGGAAAGA 59.649 52.381 0.00 0.00 0.00 2.52
4794 5085 1.351017 TCAGTGTTAGGGCTGGGAAAG 59.649 52.381 0.00 0.00 33.81 2.62
4795 5086 1.440618 TCAGTGTTAGGGCTGGGAAA 58.559 50.000 0.00 0.00 33.81 3.13
4796 5087 3.173852 TCAGTGTTAGGGCTGGGAA 57.826 52.632 0.00 0.00 33.81 3.97
4797 5088 4.989458 TCAGTGTTAGGGCTGGGA 57.011 55.556 0.00 0.00 33.81 4.37


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

AutoCloner maintained by Alex Coulton.