Multiple sequence alignment - TraesCS4D01G046600

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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 TraesCS4D01G046600 chr4D 100.000 5636 0 0 1 5636 22021016 22026651 0.000000e+00 10408.0
1 TraesCS4D01G046600 chr4D 84.615 156 18 5 2881 3033 428578393 428578545 3.520000e-32 150.0
2 TraesCS4D01G046600 chr4D 100.000 40 0 0 2651 2690 478670926 478670887 2.180000e-09 75.0
3 TraesCS4D01G046600 chr4D 97.368 38 1 0 2653 2690 44439264 44439227 1.310000e-06 65.8
4 TraesCS4D01G046600 chr4A 94.396 2391 93 17 2813 5181 579861855 579859484 0.000000e+00 3635.0
5 TraesCS4D01G046600 chr4A 84.793 1210 120 40 1463 2640 579863131 579861954 0.000000e+00 1157.0
6 TraesCS4D01G046600 chr4A 93.780 627 36 3 803 1429 579863751 579863128 0.000000e+00 939.0
7 TraesCS4D01G046600 chr4A 88.312 462 49 4 5180 5636 579859452 579858991 2.970000e-152 549.0
8 TraesCS4D01G046600 chr4A 77.225 865 107 58 1225 2064 221701022 221701821 1.880000e-114 424.0
9 TraesCS4D01G046600 chr4A 82.933 375 36 8 1370 1743 687394460 687394807 4.240000e-81 313.0
10 TraesCS4D01G046600 chr4A 80.320 437 61 15 1735 2160 687394833 687395255 1.970000e-79 307.0
11 TraesCS4D01G046600 chr4A 95.918 98 3 1 2697 2794 579861941 579861845 2.100000e-34 158.0
12 TraesCS4D01G046600 chr4A 91.837 49 1 3 2653 2700 719728060 719728014 1.310000e-06 65.8
13 TraesCS4D01G046600 chr4B 95.370 2160 78 8 3036 5178 34029552 34031706 0.000000e+00 3415.0
14 TraesCS4D01G046600 chr4B 90.473 1333 61 21 1736 3038 34028133 34029429 0.000000e+00 1698.0
15 TraesCS4D01G046600 chr4B 94.969 795 27 6 957 1744 34027315 34028103 0.000000e+00 1234.0
16 TraesCS4D01G046600 chr4B 88.889 459 40 6 5179 5636 34031738 34032186 6.380000e-154 555.0
17 TraesCS4D01G046600 chr7D 93.983 831 20 4 1 803 597914578 597915406 0.000000e+00 1230.0
18 TraesCS4D01G046600 chr7D 91.807 830 37 16 1 803 602673976 602674801 0.000000e+00 1127.0
19 TraesCS4D01G046600 chr7D 97.297 37 1 0 2654 2690 34378833 34378797 4.710000e-06 63.9
20 TraesCS4D01G046600 chr3D 93.765 834 22 4 1 805 173704306 173703474 0.000000e+00 1225.0
21 TraesCS4D01G046600 chr3D 93.750 832 24 2 1 805 25157128 25156298 0.000000e+00 1223.0
22 TraesCS4D01G046600 chr3D 93.389 832 27 2 1 805 26435818 26434988 0.000000e+00 1206.0
23 TraesCS4D01G046600 chr3D 90.528 834 35 18 1 805 581987378 581988196 0.000000e+00 1062.0
24 TraesCS4D01G046600 chr3D 80.392 153 30 0 2881 3033 206979789 206979637 3.570000e-22 117.0
25 TraesCS4D01G046600 chr3D 100.000 36 0 0 2653 2688 263098160 263098195 3.640000e-07 67.6
26 TraesCS4D01G046600 chr3D 96.970 33 1 0 2692 2724 25970334 25970302 7.890000e-04 56.5
27 TraesCS4D01G046600 chr2A 93.804 807 38 7 1 803 526307682 526306884 0.000000e+00 1203.0
28 TraesCS4D01G046600 chr3A 93.185 807 42 4 1 806 657093005 657092211 0.000000e+00 1173.0
29 TraesCS4D01G046600 chr3A 93.121 785 50 4 22 805 337897874 337897093 0.000000e+00 1147.0
30 TraesCS4D01G046600 chr3A 92.991 642 43 2 1 641 63117014 63116374 0.000000e+00 935.0
31 TraesCS4D01G046600 chr3A 79.232 833 97 43 1 805 719843992 719844776 1.400000e-140 510.0
32 TraesCS4D01G046600 chr3A 82.278 158 24 2 2878 3033 265541487 265541642 3.540000e-27 134.0
33 TraesCS4D01G046600 chr6A 89.702 806 61 15 1 803 516339656 516340442 0.000000e+00 1009.0
34 TraesCS4D01G046600 chr2D 95.230 608 24 5 197 803 33027707 33028310 0.000000e+00 957.0
35 TraesCS4D01G046600 chr2D 84.286 140 21 1 2879 3017 471060231 471060092 9.850000e-28 135.0
36 TraesCS4D01G046600 chr2D 77.143 140 28 1 2874 3013 5239990 5240125 1.680000e-10 78.7
37 TraesCS4D01G046600 chr2D 100.000 28 0 0 2692 2719 142092311 142092338 1.000000e-02 52.8
38 TraesCS4D01G046600 chr1B 81.043 786 65 37 1 780 39592891 39592184 2.970000e-152 549.0
39 TraesCS4D01G046600 chr1B 77.252 866 103 42 1226 2064 190284596 190285394 6.750000e-114 422.0
40 TraesCS4D01G046600 chr1B 97.368 38 1 0 2653 2690 547029459 547029496 1.310000e-06 65.8
41 TraesCS4D01G046600 chr6D 82.819 454 59 12 1743 2189 66626940 66626499 6.850000e-104 388.0
42 TraesCS4D01G046600 chr6D 82.599 454 59 13 1743 2189 66261944 66261504 3.190000e-102 383.0
43 TraesCS4D01G046600 chr6D 81.690 426 45 10 1319 1743 66627369 66626976 1.960000e-84 324.0
44 TraesCS4D01G046600 chr6D 81.455 426 46 11 1319 1743 66262373 66261980 9.110000e-83 318.0
45 TraesCS4D01G046600 chr6D 97.619 42 0 1 2649 2690 353812349 353812309 2.820000e-08 71.3
46 TraesCS4D01G046600 chr5A 91.367 278 18 6 1 274 524645643 524645918 5.330000e-100 375.0
47 TraesCS4D01G046600 chr1D 81.935 465 61 15 1735 2189 470455740 470456191 6.900000e-99 372.0
48 TraesCS4D01G046600 chr1D 84.118 170 19 5 1575 1743 470455552 470455714 2.100000e-34 158.0
49 TraesCS4D01G046600 chr1D 79.412 136 28 0 2882 3017 417259737 417259602 4.650000e-16 97.1
50 TraesCS4D01G046600 chr1D 93.750 48 3 0 2966 3013 317458022 317458069 7.830000e-09 73.1
51 TraesCS4D01G046600 chr1D 96.774 31 1 0 2692 2722 406665002 406664972 1.000000e-02 52.8
52 TraesCS4D01G046600 chr7A 83.598 378 51 9 1818 2189 63313819 63313447 1.500000e-90 344.0
53 TraesCS4D01G046600 chr7A 83.529 170 20 5 1575 1743 63314085 63313923 9.780000e-33 152.0
54 TraesCS4D01G046600 chr7A 85.714 133 16 2 5395 5527 63110253 63110124 2.740000e-28 137.0
55 TraesCS4D01G046600 chr5B 81.208 447 62 16 1751 2189 649866770 649867202 1.940000e-89 340.0
56 TraesCS4D01G046600 chr5B 81.055 417 46 13 1328 1743 649866343 649866727 9.180000e-78 302.0
57 TraesCS4D01G046600 chr5B 86.638 232 30 1 1958 2189 425669260 425669490 7.250000e-64 255.0
58 TraesCS4D01G046600 chr2B 84.472 161 23 2 2874 3034 369489683 369489841 2.100000e-34 158.0
59 TraesCS4D01G046600 chr3B 81.410 156 29 0 2878 3033 284677627 284677782 1.650000e-25 128.0
60 TraesCS4D01G046600 chr6B 83.333 120 16 3 2911 3028 612060479 612060596 2.150000e-19 108.0
61 TraesCS4D01G046600 chrUn 91.837 49 1 3 2653 2700 471786190 471786144 1.310000e-06 65.8
62 TraesCS4D01G046600 chr5D 97.368 38 1 0 2653 2690 10274425 10274388 1.310000e-06 65.8
63 TraesCS4D01G046600 chr7B 100.000 28 0 0 2692 2719 211792094 211792067 1.000000e-02 52.8


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 TraesCS4D01G046600 chr4D 22021016 22026651 5635 False 10408.0 10408 100.00000 1 5636 1 chr4D.!!$F1 5635
1 TraesCS4D01G046600 chr4A 579858991 579863751 4760 True 1287.6 3635 91.43980 803 5636 5 chr4A.!!$R2 4833
2 TraesCS4D01G046600 chr4A 221701022 221701821 799 False 424.0 424 77.22500 1225 2064 1 chr4A.!!$F1 839
3 TraesCS4D01G046600 chr4A 687394460 687395255 795 False 310.0 313 81.62650 1370 2160 2 chr4A.!!$F2 790
4 TraesCS4D01G046600 chr4B 34027315 34032186 4871 False 1725.5 3415 92.42525 957 5636 4 chr4B.!!$F1 4679
5 TraesCS4D01G046600 chr7D 597914578 597915406 828 False 1230.0 1230 93.98300 1 803 1 chr7D.!!$F1 802
6 TraesCS4D01G046600 chr7D 602673976 602674801 825 False 1127.0 1127 91.80700 1 803 1 chr7D.!!$F2 802
7 TraesCS4D01G046600 chr3D 173703474 173704306 832 True 1225.0 1225 93.76500 1 805 1 chr3D.!!$R4 804
8 TraesCS4D01G046600 chr3D 25156298 25157128 830 True 1223.0 1223 93.75000 1 805 1 chr3D.!!$R1 804
9 TraesCS4D01G046600 chr3D 26434988 26435818 830 True 1206.0 1206 93.38900 1 805 1 chr3D.!!$R3 804
10 TraesCS4D01G046600 chr3D 581987378 581988196 818 False 1062.0 1062 90.52800 1 805 1 chr3D.!!$F2 804
11 TraesCS4D01G046600 chr2A 526306884 526307682 798 True 1203.0 1203 93.80400 1 803 1 chr2A.!!$R1 802
12 TraesCS4D01G046600 chr3A 657092211 657093005 794 True 1173.0 1173 93.18500 1 806 1 chr3A.!!$R3 805
13 TraesCS4D01G046600 chr3A 337897093 337897874 781 True 1147.0 1147 93.12100 22 805 1 chr3A.!!$R2 783
14 TraesCS4D01G046600 chr3A 63116374 63117014 640 True 935.0 935 92.99100 1 641 1 chr3A.!!$R1 640
15 TraesCS4D01G046600 chr3A 719843992 719844776 784 False 510.0 510 79.23200 1 805 1 chr3A.!!$F2 804
16 TraesCS4D01G046600 chr6A 516339656 516340442 786 False 1009.0 1009 89.70200 1 803 1 chr6A.!!$F1 802
17 TraesCS4D01G046600 chr2D 33027707 33028310 603 False 957.0 957 95.23000 197 803 1 chr2D.!!$F2 606
18 TraesCS4D01G046600 chr1B 39592184 39592891 707 True 549.0 549 81.04300 1 780 1 chr1B.!!$R1 779
19 TraesCS4D01G046600 chr1B 190284596 190285394 798 False 422.0 422 77.25200 1226 2064 1 chr1B.!!$F1 838
20 TraesCS4D01G046600 chr6D 66626499 66627369 870 True 356.0 388 82.25450 1319 2189 2 chr6D.!!$R3 870
21 TraesCS4D01G046600 chr6D 66261504 66262373 869 True 350.5 383 82.02700 1319 2189 2 chr6D.!!$R2 870
22 TraesCS4D01G046600 chr1D 470455552 470456191 639 False 265.0 372 83.02650 1575 2189 2 chr1D.!!$F2 614
23 TraesCS4D01G046600 chr7A 63313447 63314085 638 True 248.0 344 83.56350 1575 2189 2 chr7A.!!$R2 614
24 TraesCS4D01G046600 chr5B 649866343 649867202 859 False 321.0 340 81.13150 1328 2189 2 chr5B.!!$F2 861

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
907 1088 0.667184 GCTGGGCCAAAAACGATGTG 60.667 55.000 8.04 0.00 0.00 3.21 F
1565 1751 0.250124 CTTCCGTGTTGGGTACTGCA 60.250 55.000 0.00 0.00 38.76 4.41 F
1566 1752 0.250124 TTCCGTGTTGGGTACTGCAG 60.250 55.000 13.48 13.48 38.76 4.41 F
1951 2226 0.381801 CACCACTTGCCACACTGAAC 59.618 55.000 0.00 0.00 0.00 3.18 F
1963 2254 2.027745 CACACTGAACTACCAGGATGCT 60.028 50.000 0.00 0.00 38.44 3.79 F
3034 3374 2.028130 CTCTCGAGGCACCTTACATCT 58.972 52.381 13.56 0.00 0.00 2.90 F
3431 3896 2.676471 CCAAAGGGCCTGGTTCCG 60.676 66.667 6.92 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2226 0.391661 AACGCACAGCATCCTGGTAG 60.392 55.000 0.00 0.00 43.53 3.18 R
2819 3155 1.005512 TGCAGCATGGCAAGCAAAG 60.006 52.632 17.75 7.41 41.65 2.77 R
3045 3510 1.834263 ACCACAGGAGAAGGCATAGTC 59.166 52.381 0.00 0.00 0.00 2.59 R
3774 4249 0.251653 TCAGTACAGGCGAGAGGGTT 60.252 55.000 0.00 0.00 0.00 4.11 R
4088 4570 6.911250 TGAAGTTCAGATAGTTACACCTGA 57.089 37.500 0.08 0.00 34.25 3.86 R
4349 4831 0.304098 GAGCATGCTGTTCTCATCGC 59.696 55.000 28.27 1.91 0.00 4.58 R
5005 5492 0.325671 TTTCAAAGGGTTGGTGGCCA 60.326 50.000 0.00 0.00 35.29 5.36 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
592 739 5.276678 CGGCGAACTTTGTCGAAATATATGT 60.277 40.000 0.00 0.00 43.86 2.29
828 1009 5.987347 ACAAGTTGAAATCAGAAATGCCAAG 59.013 36.000 10.54 0.00 0.00 3.61
831 1012 7.001099 AGTTGAAATCAGAAATGCCAAGATT 57.999 32.000 0.00 0.00 0.00 2.40
907 1088 0.667184 GCTGGGCCAAAAACGATGTG 60.667 55.000 8.04 0.00 0.00 3.21
909 1090 1.545582 CTGGGCCAAAAACGATGTGAT 59.454 47.619 8.04 0.00 0.00 3.06
912 1093 2.479560 GGGCCAAAAACGATGTGATAGC 60.480 50.000 4.39 0.00 0.00 2.97
918 1099 3.350219 AAACGATGTGATAGCCCAAGT 57.650 42.857 0.00 0.00 0.00 3.16
1430 1611 3.003480 GGAATCCTGCTTGTGTGTCTAC 58.997 50.000 0.00 0.00 0.00 2.59
1455 1636 0.320421 TTCTTGTACTGGGACTGCGC 60.320 55.000 0.00 0.00 0.00 6.09
1456 1637 1.741770 CTTGTACTGGGACTGCGCC 60.742 63.158 4.18 0.00 0.00 6.53
1457 1638 2.172483 CTTGTACTGGGACTGCGCCT 62.172 60.000 4.18 0.00 0.00 5.52
1458 1639 2.125512 GTACTGGGACTGCGCCTG 60.126 66.667 4.18 0.00 0.00 4.85
1459 1640 4.082523 TACTGGGACTGCGCCTGC 62.083 66.667 4.18 0.00 43.20 4.85
1471 1652 4.819761 GCCTGCGCGTCTGGATGA 62.820 66.667 23.29 0.00 35.98 2.92
1480 1661 2.743195 GTCTGGATGACGCTGTCAC 58.257 57.895 12.43 7.69 45.65 3.67
1482 1663 0.528017 TCTGGATGACGCTGTCACTC 59.472 55.000 12.43 10.94 45.65 3.51
1559 1745 1.826487 GTTGCCTTCCGTGTTGGGT 60.826 57.895 0.00 0.00 38.76 4.51
1565 1751 0.250124 CTTCCGTGTTGGGTACTGCA 60.250 55.000 0.00 0.00 38.76 4.41
1566 1752 0.250124 TTCCGTGTTGGGTACTGCAG 60.250 55.000 13.48 13.48 38.76 4.41
1567 1753 1.070786 CCGTGTTGGGTACTGCAGT 59.929 57.895 25.12 25.12 0.00 4.40
1568 1754 1.227999 CCGTGTTGGGTACTGCAGTG 61.228 60.000 29.57 8.81 0.00 3.66
1569 1755 1.841663 CGTGTTGGGTACTGCAGTGC 61.842 60.000 29.57 27.19 0.00 4.40
1570 1756 0.817634 GTGTTGGGTACTGCAGTGCA 60.818 55.000 31.81 18.58 36.92 4.57
1586 1772 1.980772 GCAGATTGCAGGCTGGGTT 60.981 57.895 17.64 0.00 44.26 4.11
1924 2199 2.426738 GCAGCAGTGTTATTATTGGCCA 59.573 45.455 0.00 0.00 0.00 5.36
1951 2226 0.381801 CACCACTTGCCACACTGAAC 59.618 55.000 0.00 0.00 0.00 3.18
1963 2254 2.027745 CACACTGAACTACCAGGATGCT 60.028 50.000 0.00 0.00 38.44 3.79
2027 2318 3.067833 GGAACTCTTCTGTTGCAGGTAC 58.932 50.000 0.00 0.00 38.02 3.34
2179 2470 3.817084 TGTGTGCAGAGGAATTTCTCTTG 59.183 43.478 14.01 10.51 41.76 3.02
2247 2541 6.491394 TGTACAAATGTTCTGGAGAAAAACG 58.509 36.000 0.00 0.00 35.58 3.60
2277 2571 9.471084 CCAGAAAAACGTTTTCTTAACCAATAT 57.529 29.630 25.37 6.32 36.69 1.28
2498 2794 4.139038 TGAAGTAGTTAACAGTTTGCCCC 58.861 43.478 8.61 0.00 0.00 5.80
2501 2797 2.287977 AGTTAACAGTTTGCCCCCTC 57.712 50.000 8.61 0.00 0.00 4.30
2597 2893 6.488817 TCAACCTAAAAGCTAAAACACGTTC 58.511 36.000 0.00 0.00 0.00 3.95
2661 2957 5.494390 TTTTTCTGGTAACTACTCCCTCC 57.506 43.478 0.00 0.00 37.61 4.30
2662 2958 3.839323 TTCTGGTAACTACTCCCTCCA 57.161 47.619 0.00 0.00 37.61 3.86
2664 2960 5.476950 TTCTGGTAACTACTCCCTCCATA 57.523 43.478 0.00 0.00 37.61 2.74
2665 2961 5.476950 TCTGGTAACTACTCCCTCCATAA 57.523 43.478 0.00 0.00 37.61 1.90
2666 2962 5.845734 TCTGGTAACTACTCCCTCCATAAA 58.154 41.667 0.00 0.00 37.61 1.40
2667 2963 6.449956 TCTGGTAACTACTCCCTCCATAAAT 58.550 40.000 0.00 0.00 37.61 1.40
2668 2964 7.598248 TCTGGTAACTACTCCCTCCATAAATA 58.402 38.462 0.00 0.00 37.61 1.40
2783 3119 4.020928 TCCGTATACCTCTGCAAAAGACAA 60.021 41.667 0.00 0.00 0.00 3.18
2784 3120 4.876107 CCGTATACCTCTGCAAAAGACAAT 59.124 41.667 0.00 0.00 0.00 2.71
2785 3121 5.220662 CCGTATACCTCTGCAAAAGACAATG 60.221 44.000 0.00 0.00 0.00 2.82
2786 3122 5.351465 CGTATACCTCTGCAAAAGACAATGT 59.649 40.000 0.00 0.00 0.00 2.71
2787 3123 6.128282 CGTATACCTCTGCAAAAGACAATGTT 60.128 38.462 0.00 0.00 0.00 2.71
2788 3124 4.574599 ACCTCTGCAAAAGACAATGTTC 57.425 40.909 0.00 0.00 0.00 3.18
2789 3125 3.953612 ACCTCTGCAAAAGACAATGTTCA 59.046 39.130 0.00 0.00 0.00 3.18
2790 3126 4.037208 ACCTCTGCAAAAGACAATGTTCAG 59.963 41.667 0.00 0.00 0.00 3.02
2791 3127 4.037208 CCTCTGCAAAAGACAATGTTCAGT 59.963 41.667 0.00 0.00 0.00 3.41
2792 3128 5.450965 CCTCTGCAAAAGACAATGTTCAGTT 60.451 40.000 0.00 0.00 0.00 3.16
2793 3129 5.964758 TCTGCAAAAGACAATGTTCAGTTT 58.035 33.333 0.00 0.00 0.00 2.66
2794 3130 6.397272 TCTGCAAAAGACAATGTTCAGTTTT 58.603 32.000 0.00 0.00 0.00 2.43
2795 3131 6.531240 TCTGCAAAAGACAATGTTCAGTTTTC 59.469 34.615 0.00 0.00 0.00 2.29
2796 3132 6.397272 TGCAAAAGACAATGTTCAGTTTTCT 58.603 32.000 0.00 0.00 0.00 2.52
2797 3133 6.873076 TGCAAAAGACAATGTTCAGTTTTCTT 59.127 30.769 0.00 0.00 0.00 2.52
2798 3134 7.387397 TGCAAAAGACAATGTTCAGTTTTCTTT 59.613 29.630 0.00 0.00 34.16 2.52
2799 3135 7.899841 GCAAAAGACAATGTTCAGTTTTCTTTC 59.100 33.333 0.00 0.00 32.10 2.62
2800 3136 8.382875 CAAAAGACAATGTTCAGTTTTCTTTCC 58.617 33.333 0.00 0.00 32.10 3.13
2801 3137 6.773976 AGACAATGTTCAGTTTTCTTTCCA 57.226 33.333 0.00 0.00 0.00 3.53
2802 3138 7.352079 AGACAATGTTCAGTTTTCTTTCCAT 57.648 32.000 0.00 0.00 0.00 3.41
2803 3139 7.205297 AGACAATGTTCAGTTTTCTTTCCATG 58.795 34.615 0.00 0.00 0.00 3.66
2804 3140 5.754890 ACAATGTTCAGTTTTCTTTCCATGC 59.245 36.000 0.00 0.00 0.00 4.06
2805 3141 5.796424 ATGTTCAGTTTTCTTTCCATGCT 57.204 34.783 0.00 0.00 0.00 3.79
2806 3142 5.596836 TGTTCAGTTTTCTTTCCATGCTT 57.403 34.783 0.00 0.00 0.00 3.91
2807 3143 5.591099 TGTTCAGTTTTCTTTCCATGCTTC 58.409 37.500 0.00 0.00 0.00 3.86
2808 3144 5.126869 TGTTCAGTTTTCTTTCCATGCTTCA 59.873 36.000 0.00 0.00 0.00 3.02
2809 3145 5.443185 TCAGTTTTCTTTCCATGCTTCAG 57.557 39.130 0.00 0.00 0.00 3.02
2810 3146 5.132502 TCAGTTTTCTTTCCATGCTTCAGA 58.867 37.500 0.00 0.00 0.00 3.27
2811 3147 5.240183 TCAGTTTTCTTTCCATGCTTCAGAG 59.760 40.000 0.00 0.00 0.00 3.35
2819 3155 3.603532 TCCATGCTTCAGAGATGTTCAC 58.396 45.455 0.00 0.00 0.00 3.18
2898 3237 6.467677 TGCAAAGTGCTTAGAGAAATAGACT 58.532 36.000 1.43 0.00 45.31 3.24
2994 3334 3.957468 CACTGGTGCTGAAGAAAAACTC 58.043 45.455 0.00 0.00 0.00 3.01
3019 3359 6.237755 CGGTTTATTTTACTAAGCACCTCTCG 60.238 42.308 0.00 0.00 0.00 4.04
3034 3374 2.028130 CTCTCGAGGCACCTTACATCT 58.972 52.381 13.56 0.00 0.00 2.90
3045 3510 4.572389 GCACCTTACATCTTACATGGTCTG 59.428 45.833 0.00 0.00 0.00 3.51
3241 3706 5.843019 ATTTAAGGGGAAGTTGTGAGAGA 57.157 39.130 0.00 0.00 0.00 3.10
3348 3813 3.117284 ACTGGTAATGTGGGGAACAAAGT 60.117 43.478 0.00 0.00 43.61 2.66
3431 3896 2.676471 CCAAAGGGCCTGGTTCCG 60.676 66.667 6.92 0.00 0.00 4.30
3520 3985 4.086457 GGAATTGTCCCAAGTATGTTGGT 58.914 43.478 7.65 0.00 38.08 3.67
3774 4249 4.788925 CAGTTTATATTGGACTGGGGGA 57.211 45.455 0.00 0.00 37.67 4.81
4043 4525 5.509272 CGCATTGTTATTTTGCTCTGTACTG 59.491 40.000 0.00 0.00 34.23 2.74
4320 4802 5.046087 TGAAGATTCAGATTTCTGGAGCTCA 60.046 40.000 17.19 5.04 46.72 4.26
4349 4831 2.277120 GGACGATGACGACGACGG 60.277 66.667 12.58 0.00 44.46 4.79
4399 4881 2.165845 AGGGACTACAAATTCCTCGACG 59.834 50.000 0.00 0.00 36.02 5.12
4524 5006 4.446371 AGGCATCAGAAGAAAGTAATCGG 58.554 43.478 0.00 0.00 0.00 4.18
4669 5151 4.170256 GTGTAAATGCCGGTAATTTGTGG 58.830 43.478 20.88 0.00 0.00 4.17
4692 5174 7.696453 GTGGAATTTCACATGTAAAATCTACCG 59.304 37.037 12.24 0.00 37.57 4.02
4708 5190 0.966920 ACCGTTGTCCAGAGGTACAG 59.033 55.000 0.00 0.00 34.83 2.74
4948 5435 6.655062 TCCGATTGAAAATTATCCGAAATCG 58.345 36.000 7.67 7.67 42.61 3.34
4973 5460 4.272489 AGGATTTTCGCAGGAATTGATGA 58.728 39.130 0.00 0.00 30.88 2.92
4980 5467 2.100252 CGCAGGAATTGATGAAATGGCT 59.900 45.455 0.00 0.00 0.00 4.75
4996 5483 3.156288 TGGCTACGAGCATATCTACCT 57.844 47.619 8.71 0.00 44.75 3.08
5005 5492 4.217334 CGAGCATATCTACCTGTCATGACT 59.783 45.833 25.55 9.24 0.00 3.41
5193 5728 3.687698 GCGGAGGTTAAGCAACAATAGAA 59.312 43.478 7.52 0.00 36.29 2.10
5228 5763 3.506067 AGTTATTGAGAAAAACCGGCCAG 59.494 43.478 0.00 0.00 0.00 4.85
5275 5810 4.383118 CGGCTAGCTAATTAGGGCATGTAT 60.383 45.833 15.72 0.00 0.00 2.29
5277 5812 6.463049 CGGCTAGCTAATTAGGGCATGTATAT 60.463 42.308 15.72 0.00 0.00 0.86
5288 5823 9.821240 ATTAGGGCATGTATATTGGTTGATAAA 57.179 29.630 0.00 0.00 0.00 1.40
5290 5825 7.951591 AGGGCATGTATATTGGTTGATAAAAC 58.048 34.615 0.00 0.00 0.00 2.43
5312 5847 4.404073 ACAGTCTAATCTTAGTCCTGCCAG 59.596 45.833 13.99 0.00 35.86 4.85
5313 5848 3.386402 AGTCTAATCTTAGTCCTGCCAGC 59.614 47.826 0.00 0.00 32.61 4.85
5400 5937 9.479549 AGATATTCCTAAAATTGTGAATGTGGT 57.520 29.630 0.00 0.00 0.00 4.16
5487 6026 4.276183 GGTTTCTCTTTTCTCCACCTGAAC 59.724 45.833 0.00 0.00 0.00 3.18
5538 6077 6.791867 AGCATCATTATATACGCCCTTAGA 57.208 37.500 0.00 0.00 0.00 2.10
5548 6087 5.995565 ATACGCCCTTAGATATGTAGCAA 57.004 39.130 0.00 0.00 0.00 3.91
5555 6094 6.934645 GCCCTTAGATATGTAGCAAATACACA 59.065 38.462 0.00 0.00 47.00 3.72
5558 6097 7.387948 CCTTAGATATGTAGCAAATACACACCC 59.612 40.741 0.00 0.00 47.00 4.61
5559 6098 6.247229 AGATATGTAGCAAATACACACCCA 57.753 37.500 0.00 0.00 47.00 4.51
5604 6143 3.199071 ACTGGATATGGGCTTTCGTACAA 59.801 43.478 0.00 0.00 0.00 2.41
5614 6153 5.154222 GGGCTTTCGTACAAATTTTCTCTG 58.846 41.667 0.00 0.00 0.00 3.35
5632 6171 4.081198 TCTCTGAAAAGAATCTCTCAGGGC 60.081 45.833 17.19 0.00 36.52 5.19
5633 6172 3.843027 TCTGAAAAGAATCTCTCAGGGCT 59.157 43.478 17.19 0.00 36.71 5.19
5634 6173 5.026121 TCTGAAAAGAATCTCTCAGGGCTA 58.974 41.667 17.19 1.80 36.71 3.93
5635 6174 5.091261 TGAAAAGAATCTCTCAGGGCTAC 57.909 43.478 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 209 4.201951 GTTGATGACGATGCCGGT 57.798 55.556 1.90 0.00 40.78 5.28
592 739 2.035321 GACAAATTTCGGCCAACTTGGA 59.965 45.455 12.37 0.00 40.96 3.53
866 1047 6.636850 CAGCGAGTGCAGTTTTAGTTTTAATT 59.363 34.615 0.00 0.00 46.23 1.40
867 1048 6.142817 CAGCGAGTGCAGTTTTAGTTTTAAT 58.857 36.000 0.00 0.00 46.23 1.40
868 1049 5.504994 CCAGCGAGTGCAGTTTTAGTTTTAA 60.505 40.000 0.00 0.00 46.23 1.52
887 1068 1.444212 CATCGTTTTTGGCCCAGCG 60.444 57.895 0.00 0.00 0.00 5.18
1113 1294 2.188161 GCGGGAGAGGTCTAGGTCG 61.188 68.421 0.00 0.00 0.00 4.79
1430 1611 0.682852 TCCCAGTACAAGAACCCACG 59.317 55.000 0.00 0.00 0.00 4.94
1455 1636 2.887568 GTCATCCAGACGCGCAGG 60.888 66.667 5.73 5.76 37.53 4.85
1466 1647 0.814457 AGAGAGTGACAGCGTCATCC 59.186 55.000 13.12 8.94 44.63 3.51
1471 1652 2.653702 GCCAGAGAGTGACAGCGT 59.346 61.111 0.00 0.00 0.00 5.07
1474 1655 2.125753 GGCGCCAGAGAGTGACAG 60.126 66.667 24.80 0.00 0.00 3.51
1480 1661 1.667724 CTAAACAATGGCGCCAGAGAG 59.332 52.381 35.36 24.27 0.00 3.20
1482 1663 0.099436 GCTAAACAATGGCGCCAGAG 59.901 55.000 35.36 29.29 0.00 3.35
1568 1754 1.980772 AACCCAGCCTGCAATCTGC 60.981 57.895 8.85 0.01 45.29 4.26
1569 1755 0.896940 ACAACCCAGCCTGCAATCTG 60.897 55.000 7.66 7.66 0.00 2.90
1570 1756 0.178953 AACAACCCAGCCTGCAATCT 60.179 50.000 0.00 0.00 0.00 2.40
1571 1757 0.037975 CAACAACCCAGCCTGCAATC 60.038 55.000 0.00 0.00 0.00 2.67
1573 1759 2.795110 GCAACAACCCAGCCTGCAA 61.795 57.895 0.00 0.00 33.19 4.08
1800 2074 8.793592 ACCCTGTATATTTTTGTTCAGAAGTTC 58.206 33.333 0.00 0.00 0.00 3.01
1879 2154 5.957771 ATACAAGCAGAAATCCTGTCCTA 57.042 39.130 0.00 0.00 44.71 2.94
1924 2199 1.152963 GGCAAGTGGTGACTGGTGT 60.153 57.895 0.00 0.00 30.61 4.16
1951 2226 0.391661 AACGCACAGCATCCTGGTAG 60.392 55.000 0.00 0.00 43.53 3.18
1963 2254 4.038282 AGGGATATCGTATTGTAACGCACA 59.962 41.667 0.00 0.00 42.56 4.57
2027 2318 4.103785 ACCTGAATATCCCATCTTGACAGG 59.896 45.833 0.00 0.00 45.07 4.00
2195 2489 6.094881 TGGGTAAGTTCAAAACTGAAGTGAAG 59.905 38.462 0.00 0.00 41.91 3.02
2247 2541 6.254157 GGTTAAGAAAACGTTTTTCTGGTTCC 59.746 38.462 25.86 17.48 38.62 3.62
2412 2708 9.958285 GCTTTTTATAAGCAAGCAGATTAAAAC 57.042 29.630 19.41 0.00 42.18 2.43
2498 2794 4.345257 TGAGTAAGGCAAGGCTAATAGAGG 59.655 45.833 0.00 0.00 0.00 3.69
2501 2797 6.291377 TGATTGAGTAAGGCAAGGCTAATAG 58.709 40.000 0.00 0.00 0.00 1.73
2593 2889 1.795768 TCCTAGTTTGCAGCAGAACG 58.204 50.000 12.11 0.00 0.00 3.95
2597 2893 6.767902 TCCTAATATTTCCTAGTTTGCAGCAG 59.232 38.462 0.00 0.00 0.00 4.24
2644 2940 6.749036 ATTTATGGAGGGAGTAGTTACCAG 57.251 41.667 0.00 0.00 0.00 4.00
2687 2983 9.151177 ACTCCCTCCGTAAATAAATATAACTGA 57.849 33.333 0.00 0.00 0.00 3.41
2698 2994 9.420118 TGTTAAATAGTACTCCCTCCGTAAATA 57.580 33.333 0.00 0.00 0.00 1.40
2699 2995 8.310122 TGTTAAATAGTACTCCCTCCGTAAAT 57.690 34.615 0.00 0.00 0.00 1.40
2783 3119 5.796424 AGCATGGAAAGAAAACTGAACAT 57.204 34.783 0.00 0.00 0.00 2.71
2784 3120 5.126869 TGAAGCATGGAAAGAAAACTGAACA 59.873 36.000 0.00 0.00 0.00 3.18
2785 3121 5.591099 TGAAGCATGGAAAGAAAACTGAAC 58.409 37.500 0.00 0.00 0.00 3.18
2786 3122 5.593909 TCTGAAGCATGGAAAGAAAACTGAA 59.406 36.000 0.00 0.00 0.00 3.02
2787 3123 5.132502 TCTGAAGCATGGAAAGAAAACTGA 58.867 37.500 0.00 0.00 0.00 3.41
2788 3124 5.240183 TCTCTGAAGCATGGAAAGAAAACTG 59.760 40.000 0.00 0.00 0.00 3.16
2789 3125 5.380043 TCTCTGAAGCATGGAAAGAAAACT 58.620 37.500 0.00 0.00 0.00 2.66
2790 3126 5.695851 TCTCTGAAGCATGGAAAGAAAAC 57.304 39.130 0.00 0.00 0.00 2.43
2791 3127 5.771666 ACATCTCTGAAGCATGGAAAGAAAA 59.228 36.000 0.00 0.00 0.00 2.29
2792 3128 5.319453 ACATCTCTGAAGCATGGAAAGAAA 58.681 37.500 0.00 0.00 0.00 2.52
2793 3129 4.914983 ACATCTCTGAAGCATGGAAAGAA 58.085 39.130 0.00 0.00 0.00 2.52
2794 3130 4.564782 ACATCTCTGAAGCATGGAAAGA 57.435 40.909 0.00 0.00 0.00 2.52
2795 3131 4.698780 TGAACATCTCTGAAGCATGGAAAG 59.301 41.667 0.00 0.00 0.00 2.62
2796 3132 4.456911 GTGAACATCTCTGAAGCATGGAAA 59.543 41.667 0.00 0.00 0.00 3.13
2797 3133 4.005650 GTGAACATCTCTGAAGCATGGAA 58.994 43.478 0.00 0.00 0.00 3.53
2798 3134 3.262660 AGTGAACATCTCTGAAGCATGGA 59.737 43.478 0.00 0.00 0.00 3.41
2799 3135 3.607741 AGTGAACATCTCTGAAGCATGG 58.392 45.455 0.00 0.00 0.00 3.66
2800 3136 5.391449 CAAAGTGAACATCTCTGAAGCATG 58.609 41.667 0.00 0.00 0.00 4.06
2801 3137 4.082895 GCAAAGTGAACATCTCTGAAGCAT 60.083 41.667 0.00 0.00 0.00 3.79
2802 3138 3.251729 GCAAAGTGAACATCTCTGAAGCA 59.748 43.478 0.00 0.00 0.00 3.91
2803 3139 3.501445 AGCAAAGTGAACATCTCTGAAGC 59.499 43.478 0.00 0.00 0.00 3.86
2804 3140 5.450171 CAAGCAAAGTGAACATCTCTGAAG 58.550 41.667 0.00 0.00 0.00 3.02
2805 3141 4.261322 GCAAGCAAAGTGAACATCTCTGAA 60.261 41.667 0.00 0.00 0.00 3.02
2806 3142 3.251729 GCAAGCAAAGTGAACATCTCTGA 59.748 43.478 0.00 0.00 0.00 3.27
2807 3143 3.562505 GCAAGCAAAGTGAACATCTCTG 58.437 45.455 0.00 0.00 0.00 3.35
2808 3144 2.555757 GGCAAGCAAAGTGAACATCTCT 59.444 45.455 0.00 0.00 0.00 3.10
2809 3145 2.294233 TGGCAAGCAAAGTGAACATCTC 59.706 45.455 0.00 0.00 0.00 2.75
2810 3146 2.309613 TGGCAAGCAAAGTGAACATCT 58.690 42.857 0.00 0.00 0.00 2.90
2811 3147 2.798976 TGGCAAGCAAAGTGAACATC 57.201 45.000 0.00 0.00 0.00 3.06
2819 3155 1.005512 TGCAGCATGGCAAGCAAAG 60.006 52.632 17.75 7.41 41.65 2.77
2994 3334 6.237755 CGAGAGGTGCTTAGTAAAATAAACCG 60.238 42.308 0.00 0.00 0.00 4.44
3019 3359 4.130118 CCATGTAAGATGTAAGGTGCCTC 58.870 47.826 0.00 0.00 0.00 4.70
3034 3374 4.716784 AGAAGGCATAGTCAGACCATGTAA 59.283 41.667 10.27 0.00 0.00 2.41
3045 3510 1.834263 ACCACAGGAGAAGGCATAGTC 59.166 52.381 0.00 0.00 0.00 2.59
3102 3567 3.760738 TCCAAATTGTCACATGTAGGCA 58.239 40.909 0.00 0.00 0.00 4.75
3179 3644 4.086457 TGTCACTCTGTCAGCATAAGGTA 58.914 43.478 0.00 0.00 0.00 3.08
3241 3706 4.344102 TCTTTACGAGCCCTTACATATGCT 59.656 41.667 1.58 0.00 36.62 3.79
3418 3883 4.660938 GTTGCGGAACCAGGCCCT 62.661 66.667 8.86 0.00 0.00 5.19
3774 4249 0.251653 TCAGTACAGGCGAGAGGGTT 60.252 55.000 0.00 0.00 0.00 4.11
4088 4570 6.911250 TGAAGTTCAGATAGTTACACCTGA 57.089 37.500 0.08 0.00 34.25 3.86
4227 4709 1.466856 GCTGGATGCCATCTTGAACA 58.533 50.000 4.41 0.00 35.15 3.18
4320 4802 3.015332 ATCGTCCCCTGCCTCCTCT 62.015 63.158 0.00 0.00 0.00 3.69
4349 4831 0.304098 GAGCATGCTGTTCTCATCGC 59.696 55.000 28.27 1.91 0.00 4.58
4351 4833 1.307097 GGGAGCATGCTGTTCTCATC 58.693 55.000 28.27 7.94 27.72 2.92
4524 5006 2.657066 GGGAACACGAGGGGAGGAC 61.657 68.421 0.00 0.00 0.00 3.85
4566 5048 0.458370 TATCGTCGTCGTCGTCCTCA 60.458 55.000 11.41 0.00 38.33 3.86
4639 5121 4.329462 ACCGGCATTTACACAAATTTGT 57.671 36.364 18.13 18.13 43.36 2.83
4669 5151 9.061610 CAACGGTAGATTTTACATGTGAAATTC 57.938 33.333 24.42 18.05 30.34 2.17
4692 5174 4.894784 TGAATTCTGTACCTCTGGACAAC 58.105 43.478 7.05 0.00 0.00 3.32
4769 5252 6.774656 CCATAAATTTCTGCTCCTTGGATAGT 59.225 38.462 0.00 0.00 0.00 2.12
4770 5253 6.294397 GCCATAAATTTCTGCTCCTTGGATAG 60.294 42.308 0.00 0.00 0.00 2.08
4771 5254 5.536161 GCCATAAATTTCTGCTCCTTGGATA 59.464 40.000 0.00 0.00 0.00 2.59
4948 5435 3.440173 TCAATTCCTGCGAAAATCCTCAC 59.560 43.478 0.00 0.00 0.00 3.51
4973 5460 4.528596 AGGTAGATATGCTCGTAGCCATTT 59.471 41.667 4.73 0.00 41.51 2.32
4980 5467 5.181433 GTCATGACAGGTAGATATGCTCGTA 59.819 44.000 21.07 0.00 0.00 3.43
4996 5483 0.537143 GTTGGTGGCCAGTCATGACA 60.537 55.000 27.02 3.61 33.81 3.58
5005 5492 0.325671 TTTCAAAGGGTTGGTGGCCA 60.326 50.000 0.00 0.00 35.29 5.36
5095 5595 3.020984 ACAAACAAGGGCTCGAGAAAAA 58.979 40.909 18.75 0.00 0.00 1.94
5096 5596 2.650322 ACAAACAAGGGCTCGAGAAAA 58.350 42.857 18.75 0.00 0.00 2.29
5198 5733 9.730420 CCGGTTTTTCTCAATAACTAATAATGG 57.270 33.333 0.00 0.00 0.00 3.16
5223 5758 3.190874 CTCGTCTTATCAGTTTCTGGCC 58.809 50.000 0.00 0.00 31.51 5.36
5228 5763 5.120363 GGGTTGAACTCGTCTTATCAGTTTC 59.880 44.000 0.00 0.00 30.32 2.78
5288 5823 4.777896 TGGCAGGACTAAGATTAGACTGTT 59.222 41.667 19.81 0.00 39.30 3.16
5290 5825 4.739137 GCTGGCAGGACTAAGATTAGACTG 60.739 50.000 17.64 17.06 39.68 3.51
5388 5925 5.132502 ACAAATCTCTCACCACATTCACAA 58.867 37.500 0.00 0.00 0.00 3.33
5454 5993 7.396055 TGGAGAAAAGAGAAACCAGAAGAAAAA 59.604 33.333 0.00 0.00 0.00 1.94
5458 5997 5.368989 GTGGAGAAAAGAGAAACCAGAAGA 58.631 41.667 0.00 0.00 0.00 2.87
5459 5998 4.517075 GGTGGAGAAAAGAGAAACCAGAAG 59.483 45.833 0.00 0.00 0.00 2.85
5487 6026 7.928167 TCTTAGCAGTGTCACATAGGATAAATG 59.072 37.037 5.62 0.00 0.00 2.32
5524 6063 7.655521 TTGCTACATATCTAAGGGCGTATAT 57.344 36.000 0.00 0.00 0.00 0.86
5529 6068 6.090898 GTGTATTTGCTACATATCTAAGGGCG 59.909 42.308 0.00 0.00 42.21 6.13
5538 6077 5.750524 TGTGGGTGTGTATTTGCTACATAT 58.249 37.500 0.00 0.00 42.21 1.78
5548 6087 5.381757 AGTGTAATGTTGTGGGTGTGTATT 58.618 37.500 0.00 0.00 0.00 1.89
5604 6143 9.012161 CCTGAGAGATTCTTTTCAGAGAAAATT 57.988 33.333 21.47 0.00 39.46 1.82


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

AutoCloner maintained by Alex Coulton.