Multiple sequence alignment - TraesCS4A01G436600

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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 TraesCS4A01G436600 chr4A 100.000 4398 0 0 1 4398 706500477 706496080 0.000000e+00 8122.0
1 TraesCS4A01G436600 chr4A 83.004 2224 278 56 1041 3215 706553118 706555290 0.000000e+00 1921.0
2 TraesCS4A01G436600 chr4A 82.110 654 114 1 1213 1863 711840148 711840801 1.380000e-154 556.0
3 TraesCS4A01G436600 chr4A 81.804 654 116 1 1213 1863 711778922 711779575 2.990000e-151 545.0
4 TraesCS4A01G436600 chr4A 85.294 374 44 8 3227 3595 706555424 706555791 4.150000e-100 375.0
5 TraesCS4A01G436600 chr7A 93.739 2236 111 14 2176 4398 24095780 24097999 0.000000e+00 3326.0
6 TraesCS4A01G436600 chr7A 93.688 2234 114 13 2176 4398 23896125 23898342 0.000000e+00 3319.0
7 TraesCS4A01G436600 chr7A 93.534 2227 117 13 2176 4391 23788096 23790306 0.000000e+00 3290.0
8 TraesCS4A01G436600 chr7A 93.407 1714 90 7 2176 3881 24279502 24281200 0.000000e+00 2518.0
9 TraesCS4A01G436600 chr7A 95.915 1371 48 5 797 2161 23894772 23896140 0.000000e+00 2215.0
10 TraesCS4A01G436600 chr7A 95.842 1371 49 5 797 2161 24278149 24279517 0.000000e+00 2209.0
11 TraesCS4A01G436600 chr7A 95.697 1371 51 5 797 2161 24094427 24095795 0.000000e+00 2198.0
12 TraesCS4A01G436600 chr7A 92.523 1391 74 13 789 2161 23786733 23788111 0.000000e+00 1965.0
13 TraesCS4A01G436600 chr7A 79.051 1012 186 15 2204 3209 22627200 22628191 0.000000e+00 671.0
14 TraesCS4A01G436600 chr7A 89.313 524 25 13 3879 4398 24283074 24283570 2.890000e-176 628.0
15 TraesCS4A01G436600 chr7A 82.722 654 110 1 1213 1863 22666154 22666807 2.950000e-161 579.0
16 TraesCS4A01G436600 chr6A 93.410 698 36 6 1 689 617594273 617593577 0.000000e+00 1026.0
17 TraesCS4A01G436600 chr2A 92.541 724 41 10 1 715 772764595 772765314 0.000000e+00 1026.0
18 TraesCS4A01G436600 chr2A 80.213 470 65 23 83 533 772764573 772765033 1.180000e-85 327.0
19 TraesCS4A01G436600 chr2A 78.571 364 68 8 2221 2579 81066116 81066474 9.510000e-57 231.0
20 TraesCS4A01G436600 chr2D 91.851 724 47 8 1 715 647654644 647653924 0.000000e+00 1000.0
21 TraesCS4A01G436600 chr2D 80.086 467 65 22 83 531 647654665 647654209 5.490000e-84 322.0
22 TraesCS4A01G436600 chr2D 78.177 362 69 7 2221 2579 80658010 80658364 5.730000e-54 222.0
23 TraesCS4A01G436600 chr7D 85.477 964 84 31 1014 1954 23071503 23070573 0.000000e+00 953.0
24 TraesCS4A01G436600 chr7D 82.416 654 112 1 1213 1863 22039095 22039748 6.380000e-158 568.0
25 TraesCS4A01G436600 chr7D 82.110 654 114 1 1213 1863 21939671 21939018 1.380000e-154 556.0
26 TraesCS4A01G436600 chr7D 78.846 208 41 3 3019 3225 22919893 22920098 2.130000e-28 137.0
27 TraesCS4A01G436600 chr1D 86.753 619 51 13 126 715 352562816 352562200 0.000000e+00 660.0
28 TraesCS4A01G436600 chr1D 91.304 115 10 0 3904 4018 385627552 385627438 1.640000e-34 158.0
29 TraesCS4A01G436600 chr4D 83.821 581 77 13 152 721 381393569 381392995 1.800000e-148 536.0
30 TraesCS4A01G436600 chr3B 82.067 658 79 29 83 715 507283926 507284569 3.900000e-145 525.0
31 TraesCS4A01G436600 chr6D 84.348 460 55 12 259 710 63126511 63126061 6.760000e-118 435.0
32 TraesCS4A01G436600 chr1A 87.654 243 23 4 4102 4338 485348608 485348367 4.330000e-70 276.0
33 TraesCS4A01G436600 chr1B 85.657 251 22 8 4102 4338 517912512 517912262 7.300000e-63 252.0
34 TraesCS4A01G436600 chr1B 92.373 118 9 0 3904 4021 517912625 517912508 7.560000e-38 169.0
35 TraesCS4A01G436600 chr2B 79.379 354 67 5 2229 2579 132279119 132279469 1.220000e-60 244.0
36 TraesCS4A01G436600 chr2B 76.712 219 32 13 1 210 153220935 153220727 2.160000e-18 104.0
37 TraesCS4A01G436600 chr5D 73.346 544 129 16 2677 3215 72910706 72910174 2.090000e-43 187.0
38 TraesCS4A01G436600 chr3D 91.489 94 8 0 3900 3993 560106110 560106203 3.570000e-26 130.0
39 TraesCS4A01G436600 chr5B 79.048 210 27 13 8 209 529530789 529530589 1.280000e-25 128.0
40 TraesCS4A01G436600 chr3A 96.226 53 2 0 4108 4160 696239715 696239767 2.180000e-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 TraesCS4A01G436600 chr4A 706496080 706500477 4397 True 8122.0 8122 100.0000 1 4398 1 chr4A.!!$R1 4397
1 TraesCS4A01G436600 chr4A 706553118 706555791 2673 False 1148.0 1921 84.1490 1041 3595 2 chr4A.!!$F3 2554
2 TraesCS4A01G436600 chr4A 711840148 711840801 653 False 556.0 556 82.1100 1213 1863 1 chr4A.!!$F2 650
3 TraesCS4A01G436600 chr4A 711778922 711779575 653 False 545.0 545 81.8040 1213 1863 1 chr4A.!!$F1 650
4 TraesCS4A01G436600 chr7A 23894772 23898342 3570 False 2767.0 3319 94.8015 797 4398 2 chr7A.!!$F4 3601
5 TraesCS4A01G436600 chr7A 24094427 24097999 3572 False 2762.0 3326 94.7180 797 4398 2 chr7A.!!$F5 3601
6 TraesCS4A01G436600 chr7A 23786733 23790306 3573 False 2627.5 3290 93.0285 789 4391 2 chr7A.!!$F3 3602
7 TraesCS4A01G436600 chr7A 24278149 24283570 5421 False 1785.0 2518 92.8540 797 4398 3 chr7A.!!$F6 3601
8 TraesCS4A01G436600 chr7A 22627200 22628191 991 False 671.0 671 79.0510 2204 3209 1 chr7A.!!$F1 1005
9 TraesCS4A01G436600 chr7A 22666154 22666807 653 False 579.0 579 82.7220 1213 1863 1 chr7A.!!$F2 650
10 TraesCS4A01G436600 chr6A 617593577 617594273 696 True 1026.0 1026 93.4100 1 689 1 chr6A.!!$R1 688
11 TraesCS4A01G436600 chr2A 772764573 772765314 741 False 676.5 1026 86.3770 1 715 2 chr2A.!!$F2 714
12 TraesCS4A01G436600 chr2D 647653924 647654665 741 True 661.0 1000 85.9685 1 715 2 chr2D.!!$R1 714
13 TraesCS4A01G436600 chr7D 23070573 23071503 930 True 953.0 953 85.4770 1014 1954 1 chr7D.!!$R2 940
14 TraesCS4A01G436600 chr7D 22039095 22039748 653 False 568.0 568 82.4160 1213 1863 1 chr7D.!!$F1 650
15 TraesCS4A01G436600 chr7D 21939018 21939671 653 True 556.0 556 82.1100 1213 1863 1 chr7D.!!$R1 650
16 TraesCS4A01G436600 chr1D 352562200 352562816 616 True 660.0 660 86.7530 126 715 1 chr1D.!!$R1 589
17 TraesCS4A01G436600 chr4D 381392995 381393569 574 True 536.0 536 83.8210 152 721 1 chr4D.!!$R1 569
18 TraesCS4A01G436600 chr3B 507283926 507284569 643 False 525.0 525 82.0670 83 715 1 chr3B.!!$F1 632

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
716 896 0.172352 CGCTCAAGAGGAGGTCTCAC 59.828 60.0 0.00 0.0 44.81 3.51 F
722 902 0.323908 AGAGGAGGTCTCACCCTTCG 60.324 60.0 0.14 0.0 44.81 3.79 F
1185 1377 0.535102 CCCAGAACAACGACAAGGCT 60.535 55.0 0.00 0.0 0.00 4.58 F
2594 2855 0.693049 AGGTTTGATTCTCCCACGCT 59.307 50.0 0.00 0.0 0.00 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1931 0.319641 GCTCCTCGACGACAACCTTT 60.320 55.0 0.0 0.0 0.00 3.11 R
2594 2855 0.322816 GATGTGCAGGAAGCCAGGAA 60.323 55.0 0.0 0.0 44.83 3.36 R
2596 2857 0.323178 AAGATGTGCAGGAAGCCAGG 60.323 55.0 0.0 0.0 44.83 4.45 R
3976 6246 0.392193 ATGCCAAGCTCTGAAGACCG 60.392 55.0 0.0 0.0 0.00 4.79 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
49 73 8.709386 TTTTCAAATTTCGATGAACCTTTTCA 57.291 26.923 0.00 0.00 45.93 2.69
50 74 8.709386 TTTCAAATTTCGATGAACCTTTTCAA 57.291 26.923 0.00 0.00 45.01 2.69
51 75 7.928908 TCAAATTTCGATGAACCTTTTCAAG 57.071 32.000 0.00 0.00 45.01 3.02
52 76 7.488322 TCAAATTTCGATGAACCTTTTCAAGT 58.512 30.769 0.00 0.00 45.01 3.16
53 77 7.978975 TCAAATTTCGATGAACCTTTTCAAGTT 59.021 29.630 0.00 0.00 45.01 2.66
54 78 7.930513 AATTTCGATGAACCTTTTCAAGTTC 57.069 32.000 0.00 0.00 45.01 3.01
55 79 6.443934 TTTCGATGAACCTTTTCAAGTTCA 57.556 33.333 7.92 7.92 45.01 3.18
56 80 6.443934 TTCGATGAACCTTTTCAAGTTCAA 57.556 33.333 9.38 0.00 45.01 2.69
57 81 5.816919 TCGATGAACCTTTTCAAGTTCAAC 58.183 37.500 9.38 6.41 45.01 3.18
58 82 5.355630 TCGATGAACCTTTTCAAGTTCAACA 59.644 36.000 9.38 0.00 45.01 3.33
59 83 6.033341 CGATGAACCTTTTCAAGTTCAACAA 58.967 36.000 9.38 0.00 45.01 2.83
60 84 6.529829 CGATGAACCTTTTCAAGTTCAACAAA 59.470 34.615 9.38 0.00 45.01 2.83
61 85 7.462724 CGATGAACCTTTTCAAGTTCAACAAAC 60.463 37.037 9.38 0.61 45.01 2.93
62 86 5.631512 TGAACCTTTTCAAGTTCAACAAACG 59.368 36.000 3.24 0.00 38.87 3.60
63 87 5.128992 ACCTTTTCAAGTTCAACAAACGT 57.871 34.783 0.00 0.00 43.02 3.99
64 88 5.534407 ACCTTTTCAAGTTCAACAAACGTT 58.466 33.333 0.00 0.00 43.02 3.99
65 89 5.986741 ACCTTTTCAAGTTCAACAAACGTTT 59.013 32.000 7.96 7.96 43.02 3.60
66 90 6.480651 ACCTTTTCAAGTTCAACAAACGTTTT 59.519 30.769 11.66 0.20 43.02 2.43
67 91 7.011576 ACCTTTTCAAGTTCAACAAACGTTTTT 59.988 29.630 11.66 1.42 43.02 1.94
100 124 9.434420 TGATGAACTTTTTGTTTCAAATTCAGT 57.566 25.926 12.13 6.32 39.30 3.41
101 125 9.693157 GATGAACTTTTTGTTTCAAATTCAGTG 57.307 29.630 12.13 0.00 39.30 3.66
102 126 8.824159 TGAACTTTTTGTTTCAAATTCAGTGA 57.176 26.923 0.00 0.00 39.30 3.41
103 127 9.265901 TGAACTTTTTGTTTCAAATTCAGTGAA 57.734 25.926 8.27 8.27 39.30 3.18
104 128 9.528847 GAACTTTTTGTTTCAAATTCAGTGAAC 57.471 29.630 7.96 0.00 39.30 3.18
105 129 8.831715 ACTTTTTGTTTCAAATTCAGTGAACT 57.168 26.923 7.96 0.00 34.78 3.01
106 130 9.271828 ACTTTTTGTTTCAAATTCAGTGAACTT 57.728 25.926 7.96 0.00 34.78 2.66
130 154 6.654793 TTTTCAAATCCGGTGAACTTTTTG 57.345 33.333 0.00 2.47 34.78 2.44
131 155 3.712187 TCAAATCCGGTGAACTTTTTGC 58.288 40.909 0.00 0.00 0.00 3.68
134 158 3.810310 ATCCGGTGAACTTTTTGCAAA 57.190 38.095 8.05 8.05 0.00 3.68
149 173 7.904461 ACTTTTTGCAAATCGATGAACTTTTTG 59.096 29.630 13.65 0.00 0.00 2.44
152 176 5.182525 GCAAATCGATGAACTTTTTGCTC 57.817 39.130 18.38 0.00 45.29 4.26
154 178 5.175491 GCAAATCGATGAACTTTTTGCTCAA 59.825 36.000 18.38 0.00 45.29 3.02
155 179 6.292274 GCAAATCGATGAACTTTTTGCTCAAA 60.292 34.615 18.38 0.00 45.29 2.69
218 376 2.223923 CCGGTGAACTTTTGGCAAATCA 60.224 45.455 14.29 11.81 0.00 2.57
220 378 3.392882 GGTGAACTTTTGGCAAATCAGG 58.607 45.455 14.29 7.26 0.00 3.86
558 725 9.443323 TCAGATCCATTCGTTTTATCAGTTTTA 57.557 29.630 0.00 0.00 0.00 1.52
605 783 2.496794 CGAAGCAACGAAACGCGG 60.497 61.111 12.47 0.00 46.49 6.46
608 786 2.494504 GAAGCAACGAAACGCGGAGG 62.495 60.000 12.47 0.00 46.49 4.30
715 895 1.599606 GCGCTCAAGAGGAGGTCTCA 61.600 60.000 0.00 0.00 44.81 3.27
716 896 0.172352 CGCTCAAGAGGAGGTCTCAC 59.828 60.000 0.00 0.00 44.81 3.51
721 901 1.552792 CAAGAGGAGGTCTCACCCTTC 59.447 57.143 0.14 0.00 44.81 3.46
722 902 0.323908 AGAGGAGGTCTCACCCTTCG 60.324 60.000 0.14 0.00 44.81 3.79
723 903 1.950973 GAGGAGGTCTCACCCTTCGC 61.951 65.000 0.14 0.00 39.75 4.70
724 904 2.283529 GGAGGTCTCACCCTTCGCA 61.284 63.158 0.14 0.00 39.75 5.10
725 905 1.079750 GAGGTCTCACCCTTCGCAC 60.080 63.158 0.00 0.00 39.75 5.34
726 906 2.047179 GGTCTCACCCTTCGCACC 60.047 66.667 0.00 0.00 30.04 5.01
727 907 2.584391 GGTCTCACCCTTCGCACCT 61.584 63.158 0.00 0.00 30.04 4.00
728 908 1.079750 GTCTCACCCTTCGCACCTC 60.080 63.158 0.00 0.00 0.00 3.85
729 909 1.228894 TCTCACCCTTCGCACCTCT 60.229 57.895 0.00 0.00 0.00 3.69
730 910 1.216710 CTCACCCTTCGCACCTCTC 59.783 63.158 0.00 0.00 0.00 3.20
731 911 2.232298 CTCACCCTTCGCACCTCTCC 62.232 65.000 0.00 0.00 0.00 3.71
732 912 2.203788 ACCCTTCGCACCTCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
733 913 1.613630 ACCCTTCGCACCTCTCCAT 60.614 57.895 0.00 0.00 0.00 3.41
734 914 1.153289 CCCTTCGCACCTCTCCATG 60.153 63.158 0.00 0.00 0.00 3.66
735 915 1.153289 CCTTCGCACCTCTCCATGG 60.153 63.158 4.97 4.97 0.00 3.66
736 916 1.817099 CTTCGCACCTCTCCATGGC 60.817 63.158 6.96 0.00 0.00 4.40
760 940 3.404707 CCGAACGTAACCGCGCAA 61.405 61.111 8.75 0.00 37.70 4.85
761 941 2.201959 CGAACGTAACCGCGCAAC 60.202 61.111 8.75 0.00 37.70 4.17
762 942 2.171701 GAACGTAACCGCGCAACC 59.828 61.111 8.75 0.00 37.70 3.77
763 943 3.618644 GAACGTAACCGCGCAACCG 62.619 63.158 8.75 4.19 37.70 4.44
794 974 3.069684 GCCGCCCCTAATCCCCTTT 62.070 63.158 0.00 0.00 0.00 3.11
966 1155 4.353788 ACATATATATGCACCCCACAACCT 59.646 41.667 20.46 0.00 37.19 3.50
1185 1377 0.535102 CCCAGAACAACGACAAGGCT 60.535 55.000 0.00 0.00 0.00 4.58
1209 1401 2.669569 GCCATCACCACGTGCAGT 60.670 61.111 10.91 0.00 32.98 4.40
1251 1443 2.683933 AGGGCTGATCCGGTCGTT 60.684 61.111 0.00 0.00 34.94 3.85
1290 1482 1.298413 CCGCGTCGTCTGTATCCTG 60.298 63.158 4.92 0.00 0.00 3.86
1503 1702 1.825090 TGAAAGACGCCATCAAGCAT 58.175 45.000 0.00 0.00 0.00 3.79
1710 1931 2.668212 CTTGAGCGCCGGTTCCAA 60.668 61.111 2.29 1.94 0.00 3.53
2077 2328 9.732130 AAAGTGGAGAATAATATGATTAGCTCC 57.268 33.333 11.42 11.42 40.73 4.70
2144 2403 6.963242 CGCACAGGTAAATCATAATCATATGC 59.037 38.462 0.00 0.00 39.04 3.14
2157 2416 9.710900 TCATAATCATATGCGTGAATAGTTTCT 57.289 29.630 0.00 0.00 39.04 2.52
2158 2417 9.750882 CATAATCATATGCGTGAATAGTTTCTG 57.249 33.333 0.00 0.00 33.01 3.02
2159 2418 7.792374 AATCATATGCGTGAATAGTTTCTGT 57.208 32.000 0.00 0.00 32.78 3.41
2191 2450 4.010349 GAGGGGGTGAATAGTTTCTGTTG 58.990 47.826 0.00 0.00 32.78 3.33
2195 2454 5.949952 GGGGGTGAATAGTTTCTGTTGTTAT 59.050 40.000 0.00 0.00 32.78 1.89
2198 2457 7.175990 GGGGTGAATAGTTTCTGTTGTTATCAA 59.824 37.037 0.00 0.00 32.78 2.57
2310 2569 3.097614 GGAGAAGTTAGTCCACCTAGCA 58.902 50.000 0.00 0.00 32.55 3.49
2399 2658 2.551032 GTTCTAGGGTTGGTTTTGGTCG 59.449 50.000 0.00 0.00 0.00 4.79
2463 2723 5.393678 GCTTGGTGTTGGAAAAACAGAACTA 60.394 40.000 0.00 0.00 35.09 2.24
2590 2851 2.027192 CCTCGAAGGTTTGATTCTCCCA 60.027 50.000 0.00 0.00 0.00 4.37
2591 2852 3.003480 CTCGAAGGTTTGATTCTCCCAC 58.997 50.000 0.00 0.00 0.00 4.61
2592 2853 1.732259 CGAAGGTTTGATTCTCCCACG 59.268 52.381 0.00 0.00 0.00 4.94
2593 2854 1.468914 GAAGGTTTGATTCTCCCACGC 59.531 52.381 0.00 0.00 0.00 5.34
2594 2855 0.693049 AGGTTTGATTCTCCCACGCT 59.307 50.000 0.00 0.00 0.00 5.07
2595 2856 1.073923 AGGTTTGATTCTCCCACGCTT 59.926 47.619 0.00 0.00 0.00 4.68
2596 2857 1.468914 GGTTTGATTCTCCCACGCTTC 59.531 52.381 0.00 0.00 0.00 3.86
2597 2858 1.468914 GTTTGATTCTCCCACGCTTCC 59.531 52.381 0.00 0.00 0.00 3.46
2598 2859 0.984230 TTGATTCTCCCACGCTTCCT 59.016 50.000 0.00 0.00 0.00 3.36
2599 2860 0.250234 TGATTCTCCCACGCTTCCTG 59.750 55.000 0.00 0.00 0.00 3.86
2613 2874 0.322816 TTCCTGGCTTCCTGCACATC 60.323 55.000 0.00 0.00 45.15 3.06
2617 2878 2.618816 CCTGGCTTCCTGCACATCTTTA 60.619 50.000 0.00 0.00 45.15 1.85
2686 2947 8.553459 TTGACTTTCTAAAGCTATGAAGAAGG 57.447 34.615 2.37 0.00 39.63 3.46
2717 2978 1.270358 ACCGAGAAAGTCAAGAGGTGC 60.270 52.381 0.00 0.00 0.00 5.01
2726 2987 0.253044 TCAAGAGGTGCCCATACAGC 59.747 55.000 0.00 0.00 38.33 4.40
2727 2988 0.035152 CAAGAGGTGCCCATACAGCA 60.035 55.000 0.00 0.00 40.52 4.41
2782 3043 9.413734 AGATCCCTCAATATTCAAGGTTTTTAG 57.586 33.333 10.96 0.00 0.00 1.85
2810 3071 3.713248 TCCTTGATGATGGTATGCTGACT 59.287 43.478 0.00 0.00 0.00 3.41
2882 3143 2.098614 TCAACTCTAGGAGCAGAGCAG 58.901 52.381 0.10 0.00 45.03 4.24
3001 3266 0.675633 AATGGATGCCCGCTAATTGC 59.324 50.000 0.00 0.00 38.57 3.56
3157 3422 4.215399 GTCATTGCCACAGTAGCTAACAAA 59.785 41.667 0.00 0.00 0.00 2.83
3318 3705 1.074752 GAAGCTTGTGAAGGCTCGAG 58.925 55.000 2.10 8.45 37.87 4.04
3319 3706 0.321122 AAGCTTGTGAAGGCTCGAGG 60.321 55.000 15.58 0.00 37.87 4.63
3381 3768 2.012673 CCATGTACTGAAGAAGCAGGC 58.987 52.381 0.00 0.00 40.20 4.85
3465 3852 9.599866 CTGACAAAAACAGTGGATGTATATAGA 57.400 33.333 0.00 0.00 43.00 1.98
3466 3853 9.378551 TGACAAAAACAGTGGATGTATATAGAC 57.621 33.333 0.00 0.00 43.00 2.59
3476 3863 9.642343 AGTGGATGTATATAGACTGTTAGTGAA 57.358 33.333 0.00 0.00 0.00 3.18
3612 4001 5.358160 TCAGTCCATGATCTGTGTGTAGTAG 59.642 44.000 13.77 0.00 31.12 2.57
3642 4033 7.605449 ACACAAATTTATCCAGGTTGATCAAG 58.395 34.615 8.80 0.00 0.00 3.02
3714 4105 8.911918 TCTTACTTGCTTATTTAAACTGTCCA 57.088 30.769 0.00 0.00 0.00 4.02
3731 4122 1.964373 CACCTTTCGGGGGTTGTCG 60.964 63.158 0.00 0.00 40.03 4.35
3738 4129 1.301874 CGGGGGTTGTCGTAAGCAA 60.302 57.895 6.68 0.00 37.18 3.91
3779 4173 9.669887 TTTTTAGGACTATTGTATCGGCTTTTA 57.330 29.630 0.00 0.00 0.00 1.52
3780 4174 9.841295 TTTTAGGACTATTGTATCGGCTTTTAT 57.159 29.630 0.00 0.00 0.00 1.40
3781 4175 8.827177 TTAGGACTATTGTATCGGCTTTTATG 57.173 34.615 0.00 0.00 0.00 1.90
3782 4176 6.827727 AGGACTATTGTATCGGCTTTTATGT 58.172 36.000 0.00 0.00 0.00 2.29
3794 4188 4.553742 CGGCTTTTATGTATGCGCACAATA 60.554 41.667 14.90 8.42 30.84 1.90
3802 4196 5.114785 TGTATGCGCACAATAAAGTGTTT 57.885 34.783 14.90 0.00 41.52 2.83
3807 4201 2.651703 CGCACAATAAAGTGTTTCTGCG 59.348 45.455 0.00 0.00 41.52 5.18
3810 4204 3.908382 CACAATAAAGTGTTTCTGCGCTC 59.092 43.478 9.73 0.00 34.83 5.03
3906 6176 3.444742 CCTGCCTGCTGATTGTAATTTCA 59.555 43.478 0.00 0.00 0.00 2.69
3911 6181 5.973565 GCCTGCTGATTGTAATTTCATACAC 59.026 40.000 0.00 0.00 35.60 2.90
3955 6225 8.556194 GCACTGATATTATTGTCGGATAAAACA 58.444 33.333 0.00 0.00 0.00 2.83
3997 6267 1.339438 GGTCTTCAGAGCTTGGCATGA 60.339 52.381 4.32 0.00 39.31 3.07
4017 6287 1.338200 ACTCTTTCGTGCTGTGGGATC 60.338 52.381 0.00 0.00 0.00 3.36
4024 6294 2.060383 TGCTGTGGGATCTCCTCCG 61.060 63.158 0.00 0.00 46.01 4.63
4043 6313 5.986135 CCTCCGTCTCCAAAGAATTGTATAG 59.014 44.000 0.00 0.00 34.60 1.31
4129 6399 3.570975 TGCATCACCATGGAGAATTATGC 59.429 43.478 21.47 21.57 0.00 3.14
4203 6473 2.539547 CCCGAAAGCTATGCATTGTTCG 60.540 50.000 19.55 19.55 38.02 3.95
4211 6481 0.734889 ATGCATTGTTCGCAGTAGCC 59.265 50.000 0.00 0.00 43.88 3.93
4213 6483 0.804989 GCATTGTTCGCAGTAGCCTT 59.195 50.000 0.00 0.00 37.52 4.35
4214 6484 2.006888 GCATTGTTCGCAGTAGCCTTA 58.993 47.619 0.00 0.00 37.52 2.69
4239 6510 8.964476 ATTTTAGCTAGTTAATCTTAGCTGCA 57.036 30.769 20.45 10.37 44.59 4.41
4240 6511 8.964476 TTTTAGCTAGTTAATCTTAGCTGCAT 57.036 30.769 20.45 5.80 44.59 3.96
4241 6512 7.953158 TTAGCTAGTTAATCTTAGCTGCATG 57.047 36.000 20.45 0.00 44.59 4.06
4246 6517 7.641802 GCTAGTTAATCTTAGCTGCATGTTTTC 59.358 37.037 1.02 0.00 33.15 2.29
4258 6529 6.377996 AGCTGCATGTTTTCATAGGTTGATTA 59.622 34.615 1.02 0.00 38.64 1.75
4275 6546 8.950210 AGGTTGATTATTTGTGTGAGATTAGTG 58.050 33.333 0.00 0.00 0.00 2.74
4337 6608 6.264067 GCATTCTCCAGCTTAGATTTACCAAT 59.736 38.462 0.00 0.00 0.00 3.16
4338 6609 7.445402 GCATTCTCCAGCTTAGATTTACCAATA 59.555 37.037 0.00 0.00 0.00 1.90
4380 6652 2.088950 TGCGCCTGTAGGTTTTCTAC 57.911 50.000 4.18 0.00 46.49 2.59
4392 6666 3.610911 GGTTTTCTACCATCTCCACTGG 58.389 50.000 0.00 0.00 46.92 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 98 9.434420 ACTGAATTTGAAACAAAAAGTTCATCA 57.566 25.926 10.17 0.00 40.26 3.07
75 99 9.693157 CACTGAATTTGAAACAAAAAGTTCATC 57.307 29.630 10.17 0.00 40.26 2.92
76 100 9.434420 TCACTGAATTTGAAACAAAAAGTTCAT 57.566 25.926 10.17 2.80 40.26 2.57
77 101 8.824159 TCACTGAATTTGAAACAAAAAGTTCA 57.176 26.923 0.00 0.00 40.26 3.18
78 102 9.528847 GTTCACTGAATTTGAAACAAAAAGTTC 57.471 29.630 0.00 0.00 40.26 3.01
79 103 9.271828 AGTTCACTGAATTTGAAACAAAAAGTT 57.728 25.926 0.00 0.00 43.89 2.66
80 104 8.831715 AGTTCACTGAATTTGAAACAAAAAGT 57.168 26.923 0.00 0.00 34.78 2.66
106 130 6.402658 GCAAAAAGTTCACCGGATTTGAAAAA 60.403 34.615 9.46 0.00 34.78 1.94
107 131 5.064071 GCAAAAAGTTCACCGGATTTGAAAA 59.936 36.000 9.46 0.00 34.78 2.29
108 132 4.568760 GCAAAAAGTTCACCGGATTTGAAA 59.431 37.500 9.46 0.00 34.78 2.69
109 133 4.116238 GCAAAAAGTTCACCGGATTTGAA 58.884 39.130 9.46 4.89 31.23 2.69
110 134 3.131223 TGCAAAAAGTTCACCGGATTTGA 59.869 39.130 9.46 0.00 31.23 2.69
111 135 3.452474 TGCAAAAAGTTCACCGGATTTG 58.548 40.909 9.46 8.67 0.00 2.32
112 136 3.810310 TGCAAAAAGTTCACCGGATTT 57.190 38.095 9.46 0.00 0.00 2.17
113 137 3.810310 TTGCAAAAAGTTCACCGGATT 57.190 38.095 9.46 0.00 0.00 3.01
114 138 3.810310 TTTGCAAAAAGTTCACCGGAT 57.190 38.095 9.46 0.00 0.00 4.18
115 139 3.712187 GATTTGCAAAAAGTTCACCGGA 58.288 40.909 17.19 0.00 0.00 5.14
116 140 2.470999 CGATTTGCAAAAAGTTCACCGG 59.529 45.455 17.19 0.00 0.00 5.28
117 141 3.367607 TCGATTTGCAAAAAGTTCACCG 58.632 40.909 17.19 9.45 0.00 4.94
118 142 4.981674 TCATCGATTTGCAAAAAGTTCACC 59.018 37.500 17.19 0.00 0.00 4.02
119 143 6.198966 AGTTCATCGATTTGCAAAAAGTTCAC 59.801 34.615 17.19 8.06 0.00 3.18
120 144 6.272318 AGTTCATCGATTTGCAAAAAGTTCA 58.728 32.000 17.19 1.18 0.00 3.18
121 145 6.753897 AGTTCATCGATTTGCAAAAAGTTC 57.246 33.333 17.19 8.18 0.00 3.01
122 146 7.538303 AAAGTTCATCGATTTGCAAAAAGTT 57.462 28.000 17.19 10.65 0.00 2.66
123 147 7.538303 AAAAGTTCATCGATTTGCAAAAAGT 57.462 28.000 17.19 4.79 0.00 2.66
124 148 8.248547 CAAAAAGTTCATCGATTTGCAAAAAG 57.751 30.769 17.19 12.97 0.00 2.27
131 155 6.752335 TTGAGCAAAAAGTTCATCGATTTG 57.248 33.333 0.00 0.00 37.31 2.32
134 158 6.095377 GGATTTGAGCAAAAAGTTCATCGAT 58.905 36.000 0.00 0.00 37.31 3.59
149 173 3.643159 AAAAGTTCACCGGATTTGAGC 57.357 42.857 9.46 3.44 0.00 4.26
549 716 6.472887 TCGTTCCTTCCTTCATAAAACTGAT 58.527 36.000 0.00 0.00 0.00 2.90
558 725 1.439679 GCGTTCGTTCCTTCCTTCAT 58.560 50.000 0.00 0.00 0.00 2.57
593 771 2.549282 CACCTCCGCGTTTCGTTG 59.451 61.111 4.92 0.00 36.19 4.10
605 783 1.014564 CCTTTCCTCGTTCGCACCTC 61.015 60.000 0.00 0.00 0.00 3.85
608 786 1.627550 GCTCCTTTCCTCGTTCGCAC 61.628 60.000 0.00 0.00 0.00 5.34
715 895 1.613630 ATGGAGAGGTGCGAAGGGT 60.614 57.895 0.00 0.00 0.00 4.34
716 896 1.153289 CATGGAGAGGTGCGAAGGG 60.153 63.158 0.00 0.00 0.00 3.95
743 923 3.404707 TTGCGCGGTTACGTTCGG 61.405 61.111 8.83 0.00 43.45 4.30
744 924 2.201959 GTTGCGCGGTTACGTTCG 60.202 61.111 8.83 0.00 43.45 3.95
745 925 2.171701 GGTTGCGCGGTTACGTTC 59.828 61.111 8.83 0.00 43.45 3.95
746 926 3.704609 CGGTTGCGCGGTTACGTT 61.705 61.111 8.83 0.00 43.45 3.99
776 956 2.978298 GAAAGGGGATTAGGGGCGGC 62.978 65.000 0.00 0.00 0.00 6.53
777 957 1.150764 GAAAGGGGATTAGGGGCGG 59.849 63.158 0.00 0.00 0.00 6.13
778 958 0.108774 GAGAAAGGGGATTAGGGGCG 59.891 60.000 0.00 0.00 0.00 6.13
779 959 0.478942 GGAGAAAGGGGATTAGGGGC 59.521 60.000 0.00 0.00 0.00 5.80
780 960 0.765510 CGGAGAAAGGGGATTAGGGG 59.234 60.000 0.00 0.00 0.00 4.79
781 961 0.108774 GCGGAGAAAGGGGATTAGGG 59.891 60.000 0.00 0.00 0.00 3.53
782 962 0.108774 GGCGGAGAAAGGGGATTAGG 59.891 60.000 0.00 0.00 0.00 2.69
783 963 0.249911 CGGCGGAGAAAGGGGATTAG 60.250 60.000 0.00 0.00 0.00 1.73
784 964 1.827394 CGGCGGAGAAAGGGGATTA 59.173 57.895 0.00 0.00 0.00 1.75
785 965 2.590092 CGGCGGAGAAAGGGGATT 59.410 61.111 0.00 0.00 0.00 3.01
786 966 4.176752 GCGGCGGAGAAAGGGGAT 62.177 66.667 9.78 0.00 0.00 3.85
1185 1377 4.408821 GTGGTGATGGCCCGCTCA 62.409 66.667 0.00 0.00 0.00 4.26
1203 1395 3.418068 GCGCTGAGGACACTGCAC 61.418 66.667 0.00 0.00 35.10 4.57
1209 1401 2.922503 TCCAAGGCGCTGAGGACA 60.923 61.111 7.64 0.00 0.00 4.02
1329 1521 3.384532 GTCTTACCGACCCCCGCA 61.385 66.667 0.00 0.00 36.62 5.69
1710 1931 0.319641 GCTCCTCGACGACAACCTTT 60.320 55.000 0.00 0.00 0.00 3.11
1895 2131 7.852971 AGTTGCAACTAACACAGTAGTAAAA 57.147 32.000 30.25 0.00 37.52 1.52
1945 2195 5.125100 ACACACAAAATCAATCAATCGCT 57.875 34.783 0.00 0.00 0.00 4.93
2077 2328 5.123186 TGTTAACTCCTTCGGTGCAAATATG 59.877 40.000 7.22 0.00 0.00 1.78
2101 2352 1.271054 GCGATATGATCTGGGCCAACT 60.271 52.381 8.04 0.00 0.00 3.16
2164 2423 5.538433 CAGAAACTATTCACCCCCTCAAAAA 59.462 40.000 0.00 0.00 38.06 1.94
2165 2424 5.076873 CAGAAACTATTCACCCCCTCAAAA 58.923 41.667 0.00 0.00 38.06 2.44
2169 2428 4.010349 CAACAGAAACTATTCACCCCCTC 58.990 47.826 0.00 0.00 38.06 4.30
2171 2430 3.763057 ACAACAGAAACTATTCACCCCC 58.237 45.455 0.00 0.00 38.06 5.40
2172 2431 6.657541 TGATAACAACAGAAACTATTCACCCC 59.342 38.462 0.00 0.00 38.06 4.95
2173 2432 7.681939 TGATAACAACAGAAACTATTCACCC 57.318 36.000 0.00 0.00 38.06 4.61
2310 2569 3.425359 CGACTCGCTCATGCAATTTTTCT 60.425 43.478 0.00 0.00 39.64 2.52
2399 2658 1.823797 ACCTATCGGTCGGCTAGATC 58.176 55.000 0.00 0.00 40.27 2.75
2590 2851 2.348998 CAGGAAGCCAGGAAGCGT 59.651 61.111 0.00 0.00 38.01 5.07
2591 2852 3.130160 GCAGGAAGCCAGGAAGCG 61.130 66.667 0.00 0.00 38.01 4.68
2592 2853 2.034687 TGCAGGAAGCCAGGAAGC 59.965 61.111 0.00 0.00 44.83 3.86
2593 2854 0.323178 ATGTGCAGGAAGCCAGGAAG 60.323 55.000 0.00 0.00 44.83 3.46
2594 2855 0.322816 GATGTGCAGGAAGCCAGGAA 60.323 55.000 0.00 0.00 44.83 3.36
2595 2856 1.203441 AGATGTGCAGGAAGCCAGGA 61.203 55.000 0.00 0.00 44.83 3.86
2596 2857 0.323178 AAGATGTGCAGGAAGCCAGG 60.323 55.000 0.00 0.00 44.83 4.45
2597 2858 1.542492 AAAGATGTGCAGGAAGCCAG 58.458 50.000 0.00 0.00 44.83 4.85
2598 2859 2.877097 TAAAGATGTGCAGGAAGCCA 57.123 45.000 0.00 0.00 44.83 4.75
2599 2860 4.440663 GGAATTAAAGATGTGCAGGAAGCC 60.441 45.833 0.00 0.00 44.83 4.35
2613 2874 7.736447 AGAGTGTGACAAGAAGGAATTAAAG 57.264 36.000 0.00 0.00 0.00 1.85
2617 2878 7.391833 GGAAATAGAGTGTGACAAGAAGGAATT 59.608 37.037 0.00 0.00 0.00 2.17
2686 2947 3.725490 ACTTTCTCGGTAAGTTGTCCAC 58.275 45.455 0.00 0.00 32.06 4.02
2717 2978 3.181497 CGAAAAGGACAATGCTGTATGGG 60.181 47.826 0.00 0.00 35.30 4.00
2726 2987 2.226437 CACCTGGTCGAAAAGGACAATG 59.774 50.000 18.99 5.41 38.70 2.82
2727 2988 2.504367 CACCTGGTCGAAAAGGACAAT 58.496 47.619 18.99 0.00 38.70 2.71
2782 3043 2.134789 ACCATCATCAAGGAGTTGGC 57.865 50.000 0.00 0.00 34.09 4.52
2810 3071 0.948623 CGACGTGTCCTTTGCCATCA 60.949 55.000 0.00 0.00 0.00 3.07
2882 3143 3.874392 ATGCCCATTCTTGTTGTTAGC 57.126 42.857 0.00 0.00 0.00 3.09
3010 3275 4.674101 CGTTTCTGAACCTGCAAGAACAAA 60.674 41.667 0.00 0.00 34.07 2.83
3157 3422 8.364142 GCATCAGTTATAAATAGAGAGACACCT 58.636 37.037 0.00 0.00 0.00 4.00
3193 3458 3.247648 GGTATGATTCCGACCAAATGACG 59.752 47.826 0.00 0.00 33.16 4.35
3318 3705 0.034476 TGCAGCATCGATGGAGATCC 59.966 55.000 26.00 8.80 0.00 3.36
3319 3706 1.000618 TCTGCAGCATCGATGGAGATC 59.999 52.381 26.00 9.51 41.07 2.75
3381 3768 1.009829 GCTTTATGGGTCTGTGCTCG 58.990 55.000 0.00 0.00 0.00 5.03
3612 4001 8.050778 TCAACCTGGATAAATTTGTGTATGTC 57.949 34.615 0.00 0.00 0.00 3.06
3618 4009 7.037438 CCTTGATCAACCTGGATAAATTTGTG 58.963 38.462 3.38 0.00 0.00 3.33
3625 4016 4.721776 AGTAGCCTTGATCAACCTGGATAA 59.278 41.667 14.70 0.00 0.00 1.75
3642 4033 4.188247 TGTGACAATGTACTGAGTAGCC 57.812 45.455 0.00 0.00 0.00 3.93
3731 4122 2.426842 ATCCTCTTGGCCTTGCTTAC 57.573 50.000 3.32 0.00 0.00 2.34
3776 4170 6.847400 ACACTTTATTGTGCGCATACATAAA 58.153 32.000 15.91 19.51 41.30 1.40
3779 4173 4.963276 ACACTTTATTGTGCGCATACAT 57.037 36.364 15.91 8.84 41.30 2.29
3780 4174 4.757799 AACACTTTATTGTGCGCATACA 57.242 36.364 15.91 4.58 41.30 2.29
3781 4175 5.283717 CAGAAACACTTTATTGTGCGCATAC 59.716 40.000 15.91 1.03 41.30 2.39
3782 4176 5.389778 CAGAAACACTTTATTGTGCGCATA 58.610 37.500 15.91 8.59 41.30 3.14
3794 4188 1.279840 GCGAGCGCAGAAACACTTT 59.720 52.632 11.47 0.00 41.49 2.66
3807 4201 1.859080 CGGTCCTAAAATAGTGCGAGC 59.141 52.381 0.00 0.00 0.00 5.03
3810 4204 1.647346 TGCGGTCCTAAAATAGTGCG 58.353 50.000 0.00 0.00 0.00 5.34
3863 4257 5.810587 CAGGTACCATAGATTACACACACAC 59.189 44.000 15.94 0.00 0.00 3.82
3867 4261 4.101119 AGGCAGGTACCATAGATTACACAC 59.899 45.833 15.94 0.00 0.00 3.82
3873 4267 2.105477 CAGCAGGCAGGTACCATAGATT 59.895 50.000 15.94 0.00 0.00 2.40
3906 6176 2.371841 TGCTTCACTCCTGTTGGTGTAT 59.628 45.455 0.00 0.00 37.92 2.29
3911 6181 0.595095 GCTTGCTTCACTCCTGTTGG 59.405 55.000 0.00 0.00 0.00 3.77
3976 6246 0.392193 ATGCCAAGCTCTGAAGACCG 60.392 55.000 0.00 0.00 0.00 4.79
3982 6252 1.273759 AGAGTCATGCCAAGCTCTGA 58.726 50.000 0.00 0.00 37.00 3.27
3997 6267 0.687354 ATCCCACAGCACGAAAGAGT 59.313 50.000 0.00 0.00 0.00 3.24
4017 6287 3.265791 CAATTCTTTGGAGACGGAGGAG 58.734 50.000 0.00 0.00 0.00 3.69
4024 6294 6.818644 TGTCAGCTATACAATTCTTTGGAGAC 59.181 38.462 0.00 0.00 37.15 3.36
4129 6399 4.813161 CCTGAAGTAGGCATTGATGTACAG 59.187 45.833 0.33 0.00 40.38 2.74
4203 6473 8.658499 TTAACTAGCTAAAATAAGGCTACTGC 57.342 34.615 0.00 0.00 37.50 4.40
4214 6484 8.964476 TGCAGCTAAGATTAACTAGCTAAAAT 57.036 30.769 12.75 0.00 43.27 1.82
4230 6501 5.824904 ACCTATGAAAACATGCAGCTAAG 57.175 39.130 0.00 0.00 0.00 2.18
4231 6502 5.709631 TCAACCTATGAAAACATGCAGCTAA 59.290 36.000 0.00 0.00 34.30 3.09
4232 6503 5.252547 TCAACCTATGAAAACATGCAGCTA 58.747 37.500 0.00 0.00 34.30 3.32
4233 6504 4.081406 TCAACCTATGAAAACATGCAGCT 58.919 39.130 0.00 0.00 34.30 4.24
4236 6507 9.368674 CAAATAATCAACCTATGAAAACATGCA 57.631 29.630 0.00 0.00 42.54 3.96
4237 6508 9.369904 ACAAATAATCAACCTATGAAAACATGC 57.630 29.630 0.00 0.00 42.54 4.06
4240 6511 9.689976 CACACAAATAATCAACCTATGAAAACA 57.310 29.630 0.00 0.00 42.54 2.83
4241 6512 9.906660 TCACACAAATAATCAACCTATGAAAAC 57.093 29.630 0.00 0.00 42.54 2.43
4282 6553 8.034313 TCCTGTACAAGATTAGCCTTCATAAT 57.966 34.615 0.00 0.00 0.00 1.28
4291 6562 5.178797 TGCTTCTTCCTGTACAAGATTAGC 58.821 41.667 10.74 10.74 35.56 3.09
4294 6565 6.479884 AGAATGCTTCTTCCTGTACAAGATT 58.520 36.000 0.00 0.00 36.36 2.40
4361 6633 2.088950 GTAGAAAACCTACAGGCGCA 57.911 50.000 10.83 0.00 45.51 6.09
4380 6652 3.628989 TACCGCCAGTGGAGATGG 58.371 61.111 15.20 10.89 41.04 3.51


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

AutoCloner maintained by Alex Coulton.