Multiple sequence alignment - TraesCS4A01G108500

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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 TraesCS4A01G108500 chr4A 100.000 4160 0 0 1524 5683 126414903 126419062 0.000000e+00 7683.0
1 TraesCS4A01G108500 chr4A 100.000 1197 0 0 1 1197 126413380 126414576 0.000000e+00 2211.0
2 TraesCS4A01G108500 chr4A 75.556 495 106 12 5148 5632 596714943 596715432 4.430000e-56 230.0
3 TraesCS4A01G108500 chr4A 80.829 193 21 6 2829 3020 278427840 278427663 2.760000e-28 137.0
4 TraesCS4A01G108500 chr4A 78.866 194 24 10 2828 3020 403966495 403966318 1.290000e-21 115.0
5 TraesCS4A01G108500 chr4D 96.259 2860 94 4 1524 4379 341037851 341035001 0.000000e+00 4676.0
6 TraesCS4A01G108500 chr4D 90.783 575 21 14 4381 4949 341034958 341034410 0.000000e+00 739.0
7 TraesCS4A01G108500 chr4D 95.111 450 13 2 757 1197 341038357 341037908 0.000000e+00 701.0
8 TraesCS4A01G108500 chr4D 94.323 458 23 3 1 456 341039910 341039454 0.000000e+00 699.0
9 TraesCS4A01G108500 chr4D 84.910 444 37 12 4987 5402 341034410 341033969 6.810000e-114 422.0
10 TraesCS4A01G108500 chr4D 90.681 279 21 1 457 730 341039265 341038987 3.240000e-97 366.0
11 TraesCS4A01G108500 chr4D 86.161 224 31 0 5395 5618 341033001 341032778 5.690000e-60 243.0
12 TraesCS4A01G108500 chr4D 76.087 368 65 21 98 451 502528999 502529357 2.720000e-38 171.0
13 TraesCS4A01G108500 chr4B 96.025 2516 80 7 1524 4029 422529695 422527190 0.000000e+00 4074.0
14 TraesCS4A01G108500 chr4B 91.352 821 36 13 4140 4949 422527187 422526391 0.000000e+00 1090.0
15 TraesCS4A01G108500 chr4B 95.946 444 15 3 757 1197 422530211 422529768 0.000000e+00 717.0
16 TraesCS4A01G108500 chr4B 84.085 710 82 18 4987 5669 422526391 422525686 0.000000e+00 656.0
17 TraesCS4A01G108500 chr4B 93.213 442 27 3 1 440 422531396 422530956 0.000000e+00 647.0
18 TraesCS4A01G108500 chr4B 89.825 285 23 2 451 729 422530696 422530412 1.510000e-95 361.0
19 TraesCS4A01G108500 chr3D 79.703 404 64 8 70 456 13853626 13854028 5.610000e-70 276.0
20 TraesCS4A01G108500 chr2A 76.553 499 104 10 5149 5640 449264610 449265102 1.570000e-65 261.0
21 TraesCS4A01G108500 chr6D 78.880 393 75 6 71 456 257954046 257954437 5.650000e-65 259.0
22 TraesCS4A01G108500 chr2D 79.221 385 66 11 80 455 210862071 210861692 7.310000e-64 255.0
23 TraesCS4A01G108500 chr2D 74.115 452 102 12 5196 5640 627362387 627362830 7.570000e-39 172.0
24 TraesCS4A01G108500 chr2D 92.958 71 4 1 2951 3020 221044924 221044994 1.010000e-17 102.0
25 TraesCS4A01G108500 chr2D 82.178 101 15 3 5362 5460 103145641 103145542 3.650000e-12 84.2
26 TraesCS4A01G108500 chr7D 80.812 271 40 7 458 721 595786576 595786841 9.650000e-48 202.0
27 TraesCS4A01G108500 chr1B 77.313 335 69 6 5249 5578 588446466 588446798 2.090000e-44 191.0
28 TraesCS4A01G108500 chr5A 72.983 533 121 15 5148 5667 26478865 26478343 1.270000e-36 165.0
29 TraesCS4A01G108500 chr7A 89.231 130 12 2 2616 2743 399043480 399043351 1.640000e-35 161.0
30 TraesCS4A01G108500 chr7A 87.302 126 14 2 2620 2743 505565632 505565507 5.940000e-30 143.0
31 TraesCS4A01G108500 chr1D 83.069 189 17 2 2829 3017 421382042 421381869 2.120000e-34 158.0
32 TraesCS4A01G108500 chr1D 87.629 97 6 3 626 721 429918944 429919035 2.170000e-19 108.0
33 TraesCS4A01G108500 chr1D 75.117 213 42 10 248 454 104237866 104238073 7.840000e-14 89.8
34 TraesCS4A01G108500 chr1A 78.571 224 43 2 5417 5640 573229347 573229565 5.940000e-30 143.0
35 TraesCS4A01G108500 chr1A 77.982 109 23 1 5036 5143 493297481 493297589 3.670000e-07 67.6
36 TraesCS4A01G108500 chr6B 76.800 250 51 5 5417 5664 26001323 26001079 3.570000e-27 134.0
37 TraesCS4A01G108500 chr5D 76.549 226 53 0 5353 5578 539853331 539853556 2.150000e-24 124.0
38 TraesCS4A01G108500 chr2B 92.958 71 4 1 2951 3020 503320933 503321003 1.010000e-17 102.0


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 TraesCS4A01G108500 chr4A 126413380 126419062 5682 False 4947.000000 7683 100.000000 1 5683 2 chr4A.!!$F2 5682
1 TraesCS4A01G108500 chr4D 341032778 341039910 7132 True 1120.857143 4676 91.175429 1 5618 7 chr4D.!!$R1 5617
2 TraesCS4A01G108500 chr4B 422525686 422531396 5710 True 1257.500000 4074 91.741000 1 5669 6 chr4B.!!$R1 5668

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
241 244 1.879380 CTGGACCGAATCAAACTGCAA 59.121 47.619 0.0 0.0 0.0 4.08 F
1606 2511 1.294659 CTCTTCAAGGTCGCTGGTGC 61.295 60.000 0.0 0.0 0.0 5.01 F
2038 2950 1.433053 TTGTGTTGTCCGAACGCCAG 61.433 55.000 0.0 0.0 0.0 4.85 F
2485 3397 1.488393 TCAGTCACCACATCAACCACA 59.512 47.619 0.0 0.0 0.0 4.17 F
4076 4992 1.423584 TGTGAGTGGGAAAGAGCTGA 58.576 50.000 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 2565 0.039617 TTCAAAACGCCCAATGCTCG 60.040 50.000 0.00 0.0 38.05 5.03 R
2422 3334 1.003355 CGTGATGGTTGCTGGAGGT 60.003 57.895 0.00 0.0 0.00 3.85 R
3787 4701 2.025037 AGCTCCTGGGTGAATAATTGCA 60.025 45.455 0.00 0.0 0.00 4.08 R
4220 5136 0.314935 CACACCAAACCACTCCATGC 59.685 55.000 0.00 0.0 0.00 4.06 R
5583 7561 0.032130 ATGCATCCGCGTTCGTAGAT 59.968 50.000 4.92 0.0 42.97 1.98 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
68 69 3.744660 CATTAGGAATGTGGGACTAGCC 58.255 50.000 0.00 0.00 34.18 3.93
125 128 7.588512 CAGAAATGATTCTCGTCTTTTTCCTT 58.411 34.615 0.00 0.00 44.11 3.36
131 134 4.950205 TCTCGTCTTTTTCCTTAGGTGT 57.050 40.909 0.00 0.00 0.00 4.16
144 147 4.030913 CCTTAGGTGTCCCTGAGTTATCA 58.969 47.826 0.00 0.00 41.75 2.15
173 176 3.433615 CGAGAGGAAGTGCACTTTTAAGG 59.566 47.826 31.58 16.18 36.11 2.69
235 238 2.803956 GTTTCGACTGGACCGAATCAAA 59.196 45.455 0.00 0.00 44.15 2.69
241 244 1.879380 CTGGACCGAATCAAACTGCAA 59.121 47.619 0.00 0.00 0.00 4.08
343 346 2.271800 GATAGTCGTTTGTGCTCAGGG 58.728 52.381 0.00 0.00 0.00 4.45
384 388 3.438216 TGCAACATCTCAGAAATGGGA 57.562 42.857 0.00 0.00 0.00 4.37
408 412 8.475639 GGAGATGTGTCTAAATTACCTTGACTA 58.524 37.037 0.00 0.00 33.97 2.59
490 766 7.700322 TGCGAATGAGATAAGAGACAATTAC 57.300 36.000 0.00 0.00 0.00 1.89
497 773 9.743057 ATGAGATAAGAGACAATTACGAAGAAG 57.257 33.333 0.00 0.00 0.00 2.85
594 880 2.484742 ACCCATGACTTTACCGAACC 57.515 50.000 0.00 0.00 0.00 3.62
606 892 5.046878 ACTTTACCGAACCACTCACATATGA 60.047 40.000 10.38 0.00 0.00 2.15
656 942 7.864379 ACTGAAAAACACATCATGAAGATTGAC 59.136 33.333 4.68 0.00 33.72 3.18
658 944 9.065798 TGAAAAACACATCATGAAGATTGACTA 57.934 29.630 4.68 0.00 33.72 2.59
705 991 2.876091 CCGGATGCGATACACGATTAT 58.124 47.619 8.71 0.00 45.77 1.28
768 1663 2.030893 TGTACTTGTCCGATTCGTTCGT 60.031 45.455 5.20 0.00 46.65 3.85
793 1688 7.396540 AGTAGAATTCAAATCAAAGGCGAAT 57.603 32.000 8.44 0.00 0.00 3.34
965 1870 4.592192 CGGCCCATCGCATCGTCT 62.592 66.667 0.00 0.00 40.31 4.18
978 1883 4.007644 CGTCTCAGGCAGCCCACA 62.008 66.667 8.22 0.00 0.00 4.17
1014 1919 3.093278 GCGATGGAGTTTCGGCAG 58.907 61.111 0.00 0.00 37.10 4.85
1081 1986 5.014858 AGAAGTTCTCGGTATACCAGAACA 58.985 41.667 36.50 20.30 45.68 3.18
1152 2057 2.664081 CCTCCTCCTCCTTGCGCTT 61.664 63.158 9.73 0.00 0.00 4.68
1188 2093 1.759881 CTCATCCCTCATGGCCCTC 59.240 63.158 0.00 0.00 32.64 4.30
1606 2511 1.294659 CTCTTCAAGGTCGCTGGTGC 61.295 60.000 0.00 0.00 0.00 5.01
1623 2528 2.867855 GCCGCGGGTCTATCCATGA 61.868 63.158 29.38 0.00 38.11 3.07
1639 2544 2.612972 CCATGACTGCTGTCGGTAAGTT 60.613 50.000 17.59 0.00 45.70 2.66
1660 2565 4.757799 TCGCTTGTCTCTATGCTAGATC 57.242 45.455 0.00 0.00 33.66 2.75
1661 2566 3.187432 TCGCTTGTCTCTATGCTAGATCG 59.813 47.826 0.00 0.00 33.66 3.69
1662 2567 3.187432 CGCTTGTCTCTATGCTAGATCGA 59.813 47.826 0.00 0.00 33.66 3.59
1663 2568 4.668941 CGCTTGTCTCTATGCTAGATCGAG 60.669 50.000 0.00 0.00 33.66 4.04
1664 2569 4.722194 CTTGTCTCTATGCTAGATCGAGC 58.278 47.826 19.76 19.76 43.16 5.03
1887 2799 3.316588 TGCCTGCAAAATTTAACTCGTCA 59.683 39.130 0.00 0.00 0.00 4.35
1900 2812 2.953020 ACTCGTCATGCTCTTTCAGTC 58.047 47.619 0.00 0.00 0.00 3.51
1936 2848 3.791586 GAGGCAGCCCTGGGTCTC 61.792 72.222 15.56 12.22 43.12 3.36
2038 2950 1.433053 TTGTGTTGTCCGAACGCCAG 61.433 55.000 0.00 0.00 0.00 4.85
2254 3166 6.942005 AGAGATTGACCACATTACAAATGTCA 59.058 34.615 2.36 0.00 0.00 3.58
2422 3334 4.662468 TTCAGCCAATAAAACTGCAACA 57.338 36.364 0.00 0.00 0.00 3.33
2485 3397 1.488393 TCAGTCACCACATCAACCACA 59.512 47.619 0.00 0.00 0.00 4.17
2641 3553 3.037549 TGCCTTTGAAAATCTGGGTGTT 58.962 40.909 0.00 0.00 0.00 3.32
2848 3760 5.784177 TGTTTCAGGTTAAGCAAACAACAA 58.216 33.333 16.47 0.00 40.08 2.83
3073 3985 5.437060 TGAACTTTCCTGCTTAGTCTTGTT 58.563 37.500 0.00 0.00 0.00 2.83
3134 4046 8.752254 GCTTTTGATGTGGTTAAAGTTAGTTTC 58.248 33.333 0.00 0.00 31.81 2.78
3201 4113 5.514500 TTCTCTATACAGCCCAAACCTTT 57.486 39.130 0.00 0.00 0.00 3.11
3288 4200 1.912043 ACAGAGCACCAGAGGCTTAAT 59.088 47.619 0.00 0.00 42.78 1.40
3439 4352 6.499172 TCAGTCTCTTGATGCTATTTAGACG 58.501 40.000 0.00 0.00 37.53 4.18
3465 4378 7.954248 GCGCAGTCATAAAATAGAGTGATTATG 59.046 37.037 0.30 0.00 37.37 1.90
3556 4470 8.621532 TGAAGAATTATGATTACATGGGCTAC 57.378 34.615 0.00 0.00 37.87 3.58
3781 4695 7.341805 AGAAGTATGTTGCTTTGATATCTGGT 58.658 34.615 3.98 0.00 0.00 4.00
3787 4701 4.574674 TGCTTTGATATCTGGTGTTCCT 57.425 40.909 3.98 0.00 34.23 3.36
3815 4729 2.254152 TCACCCAGGAGCTCTTGTAT 57.746 50.000 22.79 8.93 0.00 2.29
3850 4764 1.882623 CAGAGTCCTCCAGTTTTTGCC 59.117 52.381 0.00 0.00 0.00 4.52
3910 4824 6.014840 AGGTGATTCAAGCATTTCTGTTGATT 60.015 34.615 0.00 0.00 30.50 2.57
3991 4907 7.972832 ACATGAATTGTGAAATTGCTGAAAT 57.027 28.000 0.00 0.00 37.11 2.17
3992 4908 8.385898 ACATGAATTGTGAAATTGCTGAAATT 57.614 26.923 0.00 0.00 37.33 1.82
4076 4992 1.423584 TGTGAGTGGGAAAGAGCTGA 58.576 50.000 0.00 0.00 0.00 4.26
4138 5054 7.337480 TGTTCTGATGCAGCAATTATACATT 57.663 32.000 5.96 0.00 0.00 2.71
4170 5086 3.641437 TGTCTTGCTTTATGTTGGTGC 57.359 42.857 0.00 0.00 0.00 5.01
4196 5112 9.748708 CGGAAATGGTGAATTATGATAACAAAT 57.251 29.630 0.00 0.00 0.00 2.32
4287 5203 8.964772 AGCTTCATATCTGCCAAAATATTATCC 58.035 33.333 0.00 0.00 0.00 2.59
4316 5232 6.758416 TGTTCTAGCTTAGCATGACAATAGTG 59.242 38.462 7.07 0.00 0.00 2.74
4374 5292 5.016051 TGTTTTGTGTTTGTATGCATGGT 57.984 34.783 10.16 0.00 0.00 3.55
4479 5443 5.291614 AGTTGCTTGCAAAATGTTGTTACTG 59.708 36.000 9.75 0.00 37.06 2.74
4495 5459 9.352784 TGTTGTTACTGAACTCAAAGAAATTTG 57.647 29.630 0.00 0.00 36.45 2.32
4538 5513 5.359716 TGTACACACGTGTTTTGACTTTT 57.640 34.783 20.79 0.00 41.83 2.27
4694 5669 1.748500 GAGCTGAAGAAGGGCTGCC 60.749 63.158 11.05 11.05 36.37 4.85
4720 5695 2.685100 GTCGGGAGGAAACTGTTGTAG 58.315 52.381 0.00 0.00 44.43 2.74
4721 5696 1.001633 TCGGGAGGAAACTGTTGTAGC 59.998 52.381 0.00 0.00 44.43 3.58
4834 5809 5.357257 ACTTAGTGTTAGAATGCGGTATGG 58.643 41.667 0.00 0.00 0.00 2.74
4867 5842 7.062749 AGCGGACACCTGATATTTATTTCTA 57.937 36.000 0.00 0.00 0.00 2.10
4916 5891 9.290988 TGTTCAAACTCCTTAATGTAATGCTTA 57.709 29.630 0.00 0.00 0.00 3.09
4949 5924 9.434275 TGAATTTCCTACTACATCATCTTCCTA 57.566 33.333 0.00 0.00 0.00 2.94
4952 5927 7.689446 TTCCTACTACATCATCTTCCTATCG 57.311 40.000 0.00 0.00 0.00 2.92
4953 5928 7.017319 TCCTACTACATCATCTTCCTATCGA 57.983 40.000 0.00 0.00 0.00 3.59
4954 5929 7.106890 TCCTACTACATCATCTTCCTATCGAG 58.893 42.308 0.00 0.00 0.00 4.04
4955 5930 7.038231 TCCTACTACATCATCTTCCTATCGAGA 60.038 40.741 0.00 0.00 0.00 4.04
4956 5931 7.279981 CCTACTACATCATCTTCCTATCGAGAG 59.720 44.444 0.00 0.00 0.00 3.20
4957 5932 5.943416 ACTACATCATCTTCCTATCGAGAGG 59.057 44.000 20.33 20.33 38.03 3.69
4958 5933 4.085733 ACATCATCTTCCTATCGAGAGGG 58.914 47.826 25.26 10.93 37.20 4.30
4959 5934 4.202620 ACATCATCTTCCTATCGAGAGGGA 60.203 45.833 25.26 16.92 37.20 4.20
4960 5935 4.455070 TCATCTTCCTATCGAGAGGGAA 57.545 45.455 25.26 18.43 37.20 3.97
4961 5936 4.804597 TCATCTTCCTATCGAGAGGGAAA 58.195 43.478 25.26 12.58 38.45 3.13
4962 5937 5.208890 TCATCTTCCTATCGAGAGGGAAAA 58.791 41.667 25.26 11.88 38.45 2.29
4963 5938 5.661312 TCATCTTCCTATCGAGAGGGAAAAA 59.339 40.000 25.26 11.52 38.45 1.94
5047 6022 3.304726 CGCCCTCTCTTTTTGTTTCTTCC 60.305 47.826 0.00 0.00 0.00 3.46
5081 6056 2.327325 AAGCTCCCAACAGTCTAGGA 57.673 50.000 0.00 0.00 0.00 2.94
5100 6075 1.550976 GATTTCTCCACCTCCTGTCGT 59.449 52.381 0.00 0.00 0.00 4.34
5114 6089 1.738099 GTCGTCGCTGCCACTGAAT 60.738 57.895 0.00 0.00 0.00 2.57
5116 6091 1.133253 CGTCGCTGCCACTGAATTG 59.867 57.895 0.00 0.00 0.00 2.32
5134 6110 2.896443 CCTCGTCTTCTGGGCCTC 59.104 66.667 4.53 0.00 0.00 4.70
5147 6123 3.318191 GCCTCAGAGCCATGGAGT 58.682 61.111 18.40 0.01 0.00 3.85
5149 6125 1.440893 CCTCAGAGCCATGGAGTCG 59.559 63.158 18.40 7.82 0.00 4.18
5150 6126 1.326213 CCTCAGAGCCATGGAGTCGT 61.326 60.000 18.40 0.00 0.00 4.34
5151 6127 0.534412 CTCAGAGCCATGGAGTCGTT 59.466 55.000 18.40 0.00 0.00 3.85
5152 6128 0.532573 TCAGAGCCATGGAGTCGTTC 59.467 55.000 18.40 2.41 0.00 3.95
5154 6130 1.066573 CAGAGCCATGGAGTCGTTCTT 60.067 52.381 18.40 0.00 0.00 2.52
5155 6131 2.166459 CAGAGCCATGGAGTCGTTCTTA 59.834 50.000 18.40 0.00 0.00 2.10
5156 6132 2.428890 AGAGCCATGGAGTCGTTCTTAG 59.571 50.000 18.40 0.00 0.00 2.18
5157 6133 1.482593 AGCCATGGAGTCGTTCTTAGG 59.517 52.381 18.40 0.00 0.00 2.69
5158 6134 1.207329 GCCATGGAGTCGTTCTTAGGT 59.793 52.381 18.40 0.00 0.00 3.08
5159 6135 2.893637 CCATGGAGTCGTTCTTAGGTG 58.106 52.381 5.56 0.00 0.00 4.00
5160 6136 2.233922 CCATGGAGTCGTTCTTAGGTGT 59.766 50.000 5.56 0.00 0.00 4.16
5161 6137 3.306780 CCATGGAGTCGTTCTTAGGTGTT 60.307 47.826 5.56 0.00 0.00 3.32
5162 6138 4.315803 CATGGAGTCGTTCTTAGGTGTTT 58.684 43.478 0.00 0.00 0.00 2.83
5163 6139 4.411256 TGGAGTCGTTCTTAGGTGTTTT 57.589 40.909 0.00 0.00 0.00 2.43
5164 6140 4.773013 TGGAGTCGTTCTTAGGTGTTTTT 58.227 39.130 0.00 0.00 0.00 1.94
5210 6207 1.965754 GCTCAGGAAGGTGAGGCGAT 61.966 60.000 3.20 0.00 43.71 4.58
5235 6232 5.988561 AGCGGCTTCTTGAAGATAGAATAAG 59.011 40.000 13.87 0.00 31.66 1.73
5241 6238 9.389755 GCTTCTTGAAGATAGAATAAGGTTCTT 57.610 33.333 13.87 0.00 31.66 2.52
5277 6274 1.004560 CCAGCGGTGTGTCTCACAT 60.005 57.895 14.40 0.00 46.32 3.21
5326 6327 0.657840 GATCTTGCGGGATTTGGTCG 59.342 55.000 0.00 0.00 0.00 4.79
5381 6384 3.108144 CCTTTGTTCTTCTGCGTTTGTG 58.892 45.455 0.00 0.00 0.00 3.33
5402 6405 8.461249 TTGTGTGTCTATAGGTTAGATCCTAC 57.539 38.462 0.00 0.00 42.02 3.18
5467 7445 1.825641 GCTGGTCTTTTGGGGCCTTAA 60.826 52.381 0.84 0.00 0.00 1.85
5476 7454 2.685106 TGGGGCCTTAACATGACAAA 57.315 45.000 0.84 0.00 0.00 2.83
5503 7481 5.475909 TCCTACTGTCTACTACAACAAGGTG 59.524 44.000 0.00 0.00 37.74 4.00
5504 7482 3.991367 ACTGTCTACTACAACAAGGTGC 58.009 45.455 0.00 0.00 37.74 5.01
5535 7513 1.541118 TGAGGGAGGGGCAATGACA 60.541 57.895 0.00 0.00 0.00 3.58
5563 7541 2.771763 CTTTCGGCTCGCTCCAGTGT 62.772 60.000 0.00 0.00 0.00 3.55
5566 7544 1.080093 CGGCTCGCTCCAGTGTTTA 60.080 57.895 0.00 0.00 0.00 2.01
5579 7557 4.395854 TCCAGTGTTTATAGTCGTCGCTTA 59.604 41.667 0.00 0.00 0.00 3.09
5580 7558 5.066893 TCCAGTGTTTATAGTCGTCGCTTAT 59.933 40.000 0.00 0.00 0.00 1.73
5583 7561 6.471198 CAGTGTTTATAGTCGTCGCTTATTGA 59.529 38.462 0.00 0.00 0.00 2.57
5593 7571 3.115897 CGTCGCTTATTGATCTACGAACG 59.884 47.826 0.00 0.00 0.00 3.95
5594 7572 3.040795 TCGCTTATTGATCTACGAACGC 58.959 45.455 0.00 0.00 0.00 4.84
5600 7578 0.594028 TGATCTACGAACGCGGATGC 60.594 55.000 12.47 0.00 43.17 3.91
5659 7637 9.049523 CCATGATATTTGGTGAATATATCGGAG 57.950 37.037 0.00 0.00 40.26 4.63
5660 7638 9.605275 CATGATATTTGGTGAATATATCGGAGT 57.395 33.333 0.00 0.00 40.26 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.590451 CATTCCTAATGTCATTGCTTAAAATGT 57.410 29.630 8.39 0.00 38.46 2.71
68 69 4.929808 CCGGATTACTAAAGGGAATCATCG 59.070 45.833 0.00 0.00 32.30 3.84
125 128 4.841813 TGTTTGATAACTCAGGGACACCTA 59.158 41.667 0.00 0.00 39.02 3.08
131 134 3.322541 TCGTGTGTTTGATAACTCAGGGA 59.677 43.478 10.77 3.05 40.90 4.20
144 147 1.134521 TGCACTTCCTCTCGTGTGTTT 60.135 47.619 0.00 0.00 33.78 2.83
173 176 3.650070 AAGCTTGCTAGAAACCTTTGC 57.350 42.857 0.00 0.00 0.00 3.68
375 378 7.775561 GGTAATTTAGACACATCTCCCATTTCT 59.224 37.037 0.00 0.00 36.29 2.52
384 388 7.982354 GCTAGTCAAGGTAATTTAGACACATCT 59.018 37.037 0.00 0.00 39.15 2.90
408 412 1.904852 CTTGATGCAAGACGCGTGCT 61.905 55.000 20.70 11.30 46.97 4.40
546 822 3.692101 CCTGCAACCCGATGTATTTGTTA 59.308 43.478 0.00 0.00 0.00 2.41
584 870 5.172934 GTCATATGTGAGTGGTTCGGTAAA 58.827 41.667 1.90 0.00 34.36 2.01
670 956 4.870426 CGCATCCGGCAACTATTATAAGAT 59.130 41.667 0.00 0.00 45.17 2.40
676 962 2.831685 ATCGCATCCGGCAACTATTA 57.168 45.000 0.00 0.00 45.17 0.98
686 972 5.571741 ACTTTATAATCGTGTATCGCATCCG 59.428 40.000 0.00 0.00 39.67 4.18
768 1663 7.915293 TTCGCCTTTGATTTGAATTCTACTA 57.085 32.000 7.05 0.00 0.00 1.82
793 1688 2.363306 AAACCTGCACAGATTCACCA 57.637 45.000 0.00 0.00 0.00 4.17
930 1834 3.121030 CGGAGGCTGAGGTTTGCG 61.121 66.667 0.00 0.00 0.00 4.85
1056 1961 5.113446 TCTGGTATACCGAGAACTTCTCT 57.887 43.478 17.13 2.23 41.26 3.10
1129 2034 1.000486 CAAGGAGGAGGAGGACGGA 60.000 63.158 0.00 0.00 0.00 4.69
1152 2057 2.192979 GCAGATGCGATGGGGGAA 59.807 61.111 0.00 0.00 0.00 3.97
1606 2511 1.006102 GTCATGGATAGACCCGCGG 60.006 63.158 21.04 21.04 38.00 6.46
1623 2528 0.666577 GCGAACTTACCGACAGCAGT 60.667 55.000 0.00 0.00 0.00 4.40
1660 2565 0.039617 TTCAAAACGCCCAATGCTCG 60.040 50.000 0.00 0.00 38.05 5.03
1661 2566 1.418373 GTTCAAAACGCCCAATGCTC 58.582 50.000 0.00 0.00 38.05 4.26
1662 2567 3.586430 GTTCAAAACGCCCAATGCT 57.414 47.368 0.00 0.00 38.05 3.79
1680 2585 2.046023 TGCTGCTCCACCCATTCG 60.046 61.111 0.00 0.00 0.00 3.34
1681 2586 1.001641 AGTGCTGCTCCACCCATTC 60.002 57.895 0.00 0.00 36.38 2.67
1682 2587 1.303888 CAGTGCTGCTCCACCCATT 60.304 57.895 0.00 0.00 36.38 3.16
1822 2734 7.380065 GCATCTTTATAAGACCTAAGAGTGTCG 59.620 40.741 0.00 0.00 41.01 4.35
1887 2799 1.808945 CGGCAAAGACTGAAAGAGCAT 59.191 47.619 0.00 0.00 37.43 3.79
1900 2812 1.654220 CACCAACCTGACGGCAAAG 59.346 57.895 0.00 0.00 0.00 2.77
1936 2848 0.654472 GCAGTGTCAAAAGTGCGACG 60.654 55.000 0.00 0.00 36.80 5.12
2038 2950 0.251608 TTAACCCAAGAAGCCCCAGC 60.252 55.000 0.00 0.00 40.32 4.85
2254 3166 2.696526 TCTGTAGTGGAGTGGAAGGT 57.303 50.000 0.00 0.00 0.00 3.50
2397 3309 3.831333 TGCAGTTTTATTGGCTGAATCCA 59.169 39.130 0.00 0.00 32.39 3.41
2422 3334 1.003355 CGTGATGGTTGCTGGAGGT 60.003 57.895 0.00 0.00 0.00 3.85
2641 3553 2.625314 CCACTGCTCGATCTCAGGATAA 59.375 50.000 12.20 0.00 34.76 1.75
2848 3760 7.852263 ACATTAACTGAAGCTCCAATACTAGT 58.148 34.615 0.00 0.00 0.00 2.57
2964 3876 8.493607 TGATTAAGAATACCATCCTCATCAACA 58.506 33.333 0.00 0.00 0.00 3.33
3004 3916 3.623060 GGAGCATTACGAGATTGCAGAAA 59.377 43.478 0.00 0.00 36.97 2.52
3073 3985 6.434596 CAAGTTGATGGAAACGTATGAACAA 58.565 36.000 0.00 0.00 35.13 2.83
3134 4046 5.649782 AGTTCATGCCAAACTTAATGAGG 57.350 39.130 0.00 0.00 33.19 3.86
3201 4113 2.434331 GGCTGTTGTGGGCTACCA 59.566 61.111 0.00 0.00 46.94 3.25
3439 4352 5.914085 ATCACTCTATTTTATGACTGCGC 57.086 39.130 0.00 0.00 0.00 6.09
3556 4470 6.014755 TCTCTGATTTACCATAGCCATCTCTG 60.015 42.308 0.00 0.00 0.00 3.35
3781 4695 3.763360 CTGGGTGAATAATTGCAGGAACA 59.237 43.478 0.00 0.00 0.00 3.18
3787 4701 2.025037 AGCTCCTGGGTGAATAATTGCA 60.025 45.455 0.00 0.00 0.00 4.08
3815 4729 2.913578 CTGCTTGCCCACAGCCAA 60.914 61.111 0.00 0.00 42.71 4.52
3850 4764 3.742640 GCAGCTTCTTGTCCCAGTATAGG 60.743 52.174 0.00 0.00 0.00 2.57
3991 4907 7.473366 TGTTGCGTGTTTTATTAAACTCTCAA 58.527 30.769 8.63 9.10 43.25 3.02
3992 4908 7.017498 TGTTGCGTGTTTTATTAAACTCTCA 57.983 32.000 8.63 3.92 43.25 3.27
4006 4922 5.518487 CCTTTAACTTTCAATGTTGCGTGTT 59.482 36.000 0.00 0.00 0.00 3.32
4076 4992 8.879759 CCACTTGTTATAACACGAAACATATCT 58.120 33.333 24.27 0.75 38.92 1.98
4155 5071 1.610363 TTCCGCACCAACATAAAGCA 58.390 45.000 0.00 0.00 0.00 3.91
4159 5075 2.230025 CACCATTTCCGCACCAACATAA 59.770 45.455 0.00 0.00 0.00 1.90
4170 5086 9.748708 ATTTGTTATCATAATTCACCATTTCCG 57.251 29.630 0.00 0.00 0.00 4.30
4220 5136 0.314935 CACACCAAACCACTCCATGC 59.685 55.000 0.00 0.00 0.00 4.06
4286 5202 5.412594 TGTCATGCTAAGCTAGAACAAAAGG 59.587 40.000 0.00 0.00 0.00 3.11
4287 5203 6.486253 TGTCATGCTAAGCTAGAACAAAAG 57.514 37.500 0.00 0.00 0.00 2.27
4316 5232 5.047021 TCTGCTTGATGTATACCTCTATGCC 60.047 44.000 9.23 0.00 0.00 4.40
4374 5292 6.398234 TGTCAGCAACAATAAAAAGCCTTA 57.602 33.333 0.00 0.00 34.03 2.69
4538 5513 1.131638 ACAGTGCTGTTCTTCCCTGA 58.868 50.000 0.00 0.00 41.83 3.86
4694 5669 1.446272 GTTTCCTCCCGACGAGCAG 60.446 63.158 0.00 0.00 37.27 4.24
4720 5695 5.047943 TCCTTCAGTTCAGAGTACTACAAGC 60.048 44.000 0.00 0.00 0.00 4.01
4721 5696 6.431543 TCTCCTTCAGTTCAGAGTACTACAAG 59.568 42.308 0.00 0.00 0.00 3.16
4768 5743 1.346395 TGATAACAAGGTCGCACCAGT 59.654 47.619 7.86 3.68 41.95 4.00
4776 5751 3.146066 TGCTGGTGTTGATAACAAGGTC 58.854 45.455 0.00 0.00 44.16 3.85
4834 5809 2.102553 GTGTCCGCTCGACTAGGC 59.897 66.667 0.00 0.00 42.49 3.93
4867 5842 6.874134 ACAGTCAGCGATTTAAGATACAACTT 59.126 34.615 0.00 0.00 0.00 2.66
4916 5891 7.112122 TGATGTAGTAGGAAATTCAAGCACAT 58.888 34.615 0.00 0.00 0.00 3.21
5047 6022 5.316987 TGGGAGCTTTTCTTTCTTTCTAGG 58.683 41.667 0.00 0.00 0.00 3.02
5081 6056 1.550976 GACGACAGGAGGTGGAGAAAT 59.449 52.381 0.00 0.00 0.00 2.17
5100 6075 2.334946 GGCAATTCAGTGGCAGCGA 61.335 57.895 0.00 0.00 43.33 4.93
5114 6089 2.347490 GCCCAGAAGACGAGGCAA 59.653 61.111 0.00 0.00 45.07 4.52
5116 6091 3.378399 GAGGCCCAGAAGACGAGGC 62.378 68.421 0.00 0.00 44.99 4.70
5134 6110 0.534412 AGAACGACTCCATGGCTCTG 59.466 55.000 6.96 0.00 0.00 3.35
5137 6113 1.482593 CCTAAGAACGACTCCATGGCT 59.517 52.381 6.96 0.00 0.00 4.75
5190 6187 2.125350 GCCTCACCTTCCTGAGCG 60.125 66.667 0.00 0.00 37.01 5.03
5210 6207 5.537300 ATTCTATCTTCAAGAAGCCGCTA 57.463 39.130 4.95 0.00 36.46 4.26
5235 6232 2.101082 CGAGGGCTAAGTAGGAAGAACC 59.899 54.545 0.00 0.00 39.35 3.62
5241 6238 0.106318 GGGACGAGGGCTAAGTAGGA 60.106 60.000 0.00 0.00 0.00 2.94
5247 6244 3.458163 CGCTGGGACGAGGGCTAA 61.458 66.667 0.00 0.00 34.06 3.09
5268 6265 1.001974 CCCTCCGACAAATGTGAGACA 59.998 52.381 0.00 0.00 0.00 3.41
5277 6274 2.280524 CACACGCCCTCCGACAAA 60.281 61.111 0.00 0.00 41.02 2.83
5326 6327 1.007387 CCCAACAAAGACAAGCGCC 60.007 57.895 2.29 0.00 0.00 6.53
5381 6384 6.471146 TCGGTAGGATCTAACCTATAGACAC 58.529 44.000 0.00 0.00 43.25 3.67
5402 6405 6.032775 CGTTGATGAAGAAAAACATTGATCGG 59.967 38.462 0.00 0.00 0.00 4.18
5410 7388 3.623960 ACCGTCGTTGATGAAGAAAAACA 59.376 39.130 0.00 0.00 0.00 2.83
5411 7389 4.205323 ACCGTCGTTGATGAAGAAAAAC 57.795 40.909 0.00 0.00 0.00 2.43
5440 7418 1.732917 CAAAAGACCAGCGCACCAA 59.267 52.632 11.47 0.00 0.00 3.67
5467 7445 7.680730 AGTAGACAGTAGGAAATTTGTCATGT 58.319 34.615 0.00 0.00 41.74 3.21
5476 7454 7.234988 ACCTTGTTGTAGTAGACAGTAGGAAAT 59.765 37.037 9.67 0.00 39.88 2.17
5515 7493 2.276740 CATTGCCCCTCCCTCACC 59.723 66.667 0.00 0.00 0.00 4.02
5544 7522 2.097038 CACTGGAGCGAGCCGAAAG 61.097 63.158 0.00 0.00 0.00 2.62
5563 7541 7.743400 CGTAGATCAATAAGCGACGACTATAAA 59.257 37.037 0.00 0.00 0.00 1.40
5566 7544 5.407691 TCGTAGATCAATAAGCGACGACTAT 59.592 40.000 0.00 0.00 33.33 2.12
5579 7557 2.394708 CATCCGCGTTCGTAGATCAAT 58.605 47.619 4.92 0.00 35.04 2.57
5580 7558 1.835121 CATCCGCGTTCGTAGATCAA 58.165 50.000 4.92 0.00 35.04 2.57
5583 7561 0.032130 ATGCATCCGCGTTCGTAGAT 59.968 50.000 4.92 0.00 42.97 1.98


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

AutoCloner maintained by Alex Coulton.