Multiple sequence alignment - TraesCS3A01G255800

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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 TraesCS3A01G255800 chr3A 100.000 7116 0 0 1 7116 477591500 477584385 0.000000e+00 13141.0
1 TraesCS3A01G255800 chr3A 78.125 960 94 56 2672 3573 655868927 655868026 2.960000e-138 503.0
2 TraesCS3A01G255800 chr3A 99.107 112 1 0 3667 3778 477587727 477587616 1.210000e-47 202.0
3 TraesCS3A01G255800 chr3A 84.080 201 22 5 3380 3572 722488283 722488481 1.220000e-42 185.0
4 TraesCS3A01G255800 chr1B 99.266 2315 17 0 2672 4986 162184172 162181858 0.000000e+00 4181.0
5 TraesCS3A01G255800 chr1B 97.924 1108 21 2 2672 3778 38607476 38606370 0.000000e+00 1917.0
6 TraesCS3A01G255800 chr1B 97.677 1033 23 1 3774 4806 38606481 38605450 0.000000e+00 1773.0
7 TraesCS3A01G255800 chr1B 88.855 332 32 5 2672 3000 589228664 589228993 3.090000e-108 403.0
8 TraesCS3A01G255800 chr1B 84.767 407 44 13 2671 3070 203655983 203656378 6.690000e-105 392.0
9 TraesCS3A01G255800 chr1B 83.721 258 42 0 1868 2125 468503709 468503966 1.980000e-60 244.0
10 TraesCS3A01G255800 chr1B 78.431 408 57 18 5036 5419 468504602 468505002 3.320000e-58 237.0
11 TraesCS3A01G255800 chr1B 100.000 112 0 0 3774 3885 162183177 162183066 2.600000e-49 207.0
12 TraesCS3A01G255800 chr1B 99.107 112 1 0 3667 3778 162183070 162182959 1.210000e-47 202.0
13 TraesCS3A01G255800 chr1B 98.387 62 1 0 6961 7022 135124290 135124351 7.550000e-20 110.0
14 TraesCS3A01G255800 chr1B 85.366 82 12 0 3696 3777 41423649 41423568 1.270000e-12 86.1
15 TraesCS3A01G255800 chr1B 89.062 64 7 0 3696 3759 359370948 359370885 5.920000e-11 80.5
16 TraesCS3A01G255800 chr3B 98.556 2286 12 6 1 2282 463114340 463112072 0.000000e+00 4019.0
17 TraesCS3A01G255800 chr3B 97.864 2154 15 12 4985 7116 463111562 463109418 0.000000e+00 3694.0
18 TraesCS3A01G255800 chr3B 98.966 387 3 1 2280 2666 463111949 463111564 0.000000e+00 691.0
19 TraesCS3A01G255800 chr3B 95.694 209 9 0 1274 1482 464610213 464610421 3.180000e-88 337.0
20 TraesCS3A01G255800 chr3B 79.944 354 44 21 2656 3000 131059430 131059095 1.190000e-57 235.0
21 TraesCS3A01G255800 chr3B 100.000 43 0 0 7036 7078 463109554 463109512 5.920000e-11 80.5
22 TraesCS3A01G255800 chr2B 97.692 1213 28 0 3774 4986 784716219 784717431 0.000000e+00 2085.0
23 TraesCS3A01G255800 chr2B 97.485 835 20 1 2672 3505 784715286 784716120 0.000000e+00 1424.0
24 TraesCS3A01G255800 chr2B 87.879 1155 109 17 3803 4948 772633653 772634785 0.000000e+00 1328.0
25 TraesCS3A01G255800 chr2B 99.091 220 2 0 3559 3778 784716111 784716330 5.170000e-106 396.0
26 TraesCS3A01G255800 chr2B 93.333 225 13 2 1258 1482 496538375 496538153 1.480000e-86 331.0
27 TraesCS3A01G255800 chr2B 80.893 403 53 17 2667 3062 246110948 246111333 5.400000e-76 296.0
28 TraesCS3A01G255800 chr6A 98.106 1109 19 2 2672 3778 461983678 461982570 0.000000e+00 1930.0
29 TraesCS3A01G255800 chr6A 97.776 1034 21 2 3774 4806 461982681 461981649 0.000000e+00 1781.0
30 TraesCS3A01G255800 chr6A 82.265 733 99 15 1868 2599 23888385 23889087 7.900000e-169 604.0
31 TraesCS3A01G255800 chr6A 81.390 403 48 15 5036 5419 23889242 23889636 3.230000e-78 303.0
32 TraesCS3A01G255800 chr6A 80.178 338 52 15 2672 3000 188254675 188254344 9.230000e-59 239.0
33 TraesCS3A01G255800 chr6A 98.387 62 1 0 6961 7022 84436732 84436671 7.550000e-20 110.0
34 TraesCS3A01G255800 chr6B 90.320 1188 101 8 3803 4983 3581604 3582784 0.000000e+00 1544.0
35 TraesCS3A01G255800 chr6B 92.926 1032 67 3 3955 4986 18395668 18394643 0.000000e+00 1496.0
36 TraesCS3A01G255800 chr6B 90.706 1119 88 12 3803 4911 77795497 77796609 0.000000e+00 1476.0
37 TraesCS3A01G255800 chr6B 92.773 1024 66 6 3955 4977 461680819 461681835 0.000000e+00 1474.0
38 TraesCS3A01G255800 chr6B 90.332 331 27 5 2672 3001 18396851 18396525 5.100000e-116 429.0
39 TraesCS3A01G255800 chr6B 85.266 414 58 2 2187 2599 41992659 41993070 2.370000e-114 424.0
40 TraesCS3A01G255800 chr6B 88.855 332 31 6 2672 3001 461678477 461678804 3.090000e-108 403.0
41 TraesCS3A01G255800 chr6B 94.444 216 12 0 1267 1482 583189240 583189025 4.110000e-87 333.0
42 TraesCS3A01G255800 chr6B 81.188 404 48 17 5036 5419 41993227 41993622 4.170000e-77 300.0
43 TraesCS3A01G255800 chr6B 98.413 63 1 0 6961 7023 596622909 596622847 2.100000e-20 111.0
44 TraesCS3A01G255800 chr6B 88.158 76 9 0 3696 3771 3581604 3581679 2.730000e-14 91.6
45 TraesCS3A01G255800 chr6B 84.211 76 11 1 3715 3789 77795516 77795591 9.900000e-09 73.1
46 TraesCS3A01G255800 chr2D 92.976 1025 64 5 3956 4979 82001283 82002300 0.000000e+00 1487.0
47 TraesCS3A01G255800 chr2D 98.413 63 1 0 6961 7023 461033323 461033261 2.100000e-20 111.0
48 TraesCS3A01G255800 chr7B 91.582 1081 77 8 3905 4977 2671003 2669929 0.000000e+00 1480.0
49 TraesCS3A01G255800 chr7B 83.835 631 52 19 2870 3455 720175862 720176487 8.070000e-154 555.0
50 TraesCS3A01G255800 chr7B 95.694 209 9 0 1274 1482 464539692 464539900 3.180000e-88 337.0
51 TraesCS3A01G255800 chr7B 82.799 343 44 13 2667 3000 484625334 484624998 6.980000e-75 292.0
52 TraesCS3A01G255800 chr7B 89.175 194 14 5 3567 3756 720177421 720177611 1.190000e-57 235.0
53 TraesCS3A01G255800 chr7B 82.812 256 39 2 1868 2123 126777815 126778065 2.580000e-54 224.0
54 TraesCS3A01G255800 chr7B 77.566 419 61 20 5036 5429 126778702 126779112 9.290000e-54 222.0
55 TraesCS3A01G255800 chr7B 91.150 113 10 0 3458 3570 720177280 720177392 3.440000e-33 154.0
56 TraesCS3A01G255800 chr7B 98.413 63 1 0 6961 7023 742919280 742919218 2.100000e-20 111.0
57 TraesCS3A01G255800 chr7B 78.417 139 21 8 4845 4979 23249190 23249057 1.650000e-11 82.4
58 TraesCS3A01G255800 chr6D 82.128 733 100 14 1868 2599 25782114 25782816 3.670000e-167 599.0
59 TraesCS3A01G255800 chr6D 95.694 209 9 0 1274 1482 151317473 151317265 3.180000e-88 337.0
60 TraesCS3A01G255800 chr6D 81.141 403 50 14 5036 5419 25782970 25783365 4.170000e-77 300.0
61 TraesCS3A01G255800 chr6D 96.774 62 2 0 6961 7022 168769369 168769308 3.510000e-18 104.0
62 TraesCS3A01G255800 chr5B 90.060 332 27 5 2672 3000 378907176 378907504 6.600000e-115 425.0
63 TraesCS3A01G255800 chr5A 85.672 335 43 4 2668 3000 618404947 618405278 1.470000e-91 348.0
64 TraesCS3A01G255800 chr5A 83.279 305 36 6 3286 3575 536272078 536271774 4.230000e-67 267.0
65 TraesCS3A01G255800 chr2A 94.037 218 12 1 1265 1482 29592017 29591801 5.320000e-86 329.0
66 TraesCS3A01G255800 chr2A 83.085 201 23 6 3380 3572 573660239 573660436 9.490000e-39 172.0
67 TraesCS3A01G255800 chr2A 92.857 84 6 0 3607 3690 20528064 20528147 9.690000e-24 122.0
68 TraesCS3A01G255800 chr2A 87.736 106 9 1 3223 3328 20527768 20527869 3.490000e-23 121.0
69 TraesCS3A01G255800 chr1D 94.009 217 11 1 1268 1482 153918993 153918777 1.910000e-85 327.0
70 TraesCS3A01G255800 chr1D 78.133 407 60 18 5036 5419 347397237 347397637 1.540000e-56 231.0
71 TraesCS3A01G255800 chr1D 95.161 62 0 1 6961 7022 351076860 351076918 2.110000e-15 95.3
72 TraesCS3A01G255800 chr4D 92.920 226 11 4 1258 1482 43773890 43773669 2.480000e-84 324.0
73 TraesCS3A01G255800 chr4D 96.825 63 2 0 6961 7023 123426293 123426231 9.760000e-19 106.0
74 TraesCS3A01G255800 chr4B 97.382 191 4 1 2664 2854 23669267 23669456 2.480000e-84 324.0
75 TraesCS3A01G255800 chr7A 83.898 354 38 6 3234 3572 76988488 76988837 3.200000e-83 320.0
76 TraesCS3A01G255800 chr7A 98.413 63 1 0 6961 7023 563585763 563585701 2.100000e-20 111.0
77 TraesCS3A01G255800 chr1A 82.946 258 43 1 1868 2125 448009633 448009889 1.540000e-56 231.0
78 TraesCS3A01G255800 chr1A 84.080 201 22 5 3380 3572 12820494 12820692 1.220000e-42 185.0
79 TraesCS3A01G255800 chr1A 98.387 62 1 0 6961 7022 94785893 94785832 7.550000e-20 110.0
80 TraesCS3A01G255800 chrUn 78.025 405 60 21 5036 5417 16579941 16580339 2.000000e-55 228.0
81 TraesCS3A01G255800 chrUn 82.186 247 44 0 1868 2114 16579048 16579294 5.590000e-51 213.0
82 TraesCS3A01G255800 chrUn 98.413 63 1 0 6961 7023 86507427 86507489 2.100000e-20 111.0
83 TraesCS3A01G255800 chrUn 98.413 63 1 0 6961 7023 282362111 282362173 2.100000e-20 111.0
84 TraesCS3A01G255800 chrUn 98.387 62 1 0 6961 7022 260201153 260201214 7.550000e-20 110.0
85 TraesCS3A01G255800 chrUn 98.387 62 1 0 6961 7022 270906648 270906709 7.550000e-20 110.0
86 TraesCS3A01G255800 chr5D 97.059 68 2 0 6956 7023 324422790 324422723 1.620000e-21 115.0
87 TraesCS3A01G255800 chr4A 98.413 63 1 0 6961 7023 67574097 67574159 2.100000e-20 111.0
88 TraesCS3A01G255800 chr3D 98.413 63 1 0 6961 7023 213412420 213412482 2.100000e-20 111.0
89 TraesCS3A01G255800 chr3D 95.161 62 3 0 6961 7022 154702378 154702439 1.630000e-16 99.0
90 TraesCS3A01G255800 chr3D 87.013 77 10 0 3695 3771 604550775 604550851 3.540000e-13 87.9
91 TraesCS3A01G255800 chr7D 91.379 58 3 2 3721 3776 577938923 577938980 2.130000e-10 78.7
92 TraesCS3A01G255800 chr7D 97.619 42 1 0 3718 3759 69129662 69129703 9.900000e-09 73.1


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 TraesCS3A01G255800 chr3A 477584385 477591500 7115 True 6671.500000 13141 99.553500 1 7116 2 chr3A.!!$R2 7115
1 TraesCS3A01G255800 chr3A 655868026 655868927 901 True 503.000000 503 78.125000 2672 3573 1 chr3A.!!$R1 901
2 TraesCS3A01G255800 chr1B 38605450 38607476 2026 True 1845.000000 1917 97.800500 2672 4806 2 chr1B.!!$R3 2134
3 TraesCS3A01G255800 chr1B 162181858 162184172 2314 True 1530.000000 4181 99.457667 2672 4986 3 chr1B.!!$R4 2314
4 TraesCS3A01G255800 chr1B 468503709 468505002 1293 False 240.500000 244 81.076000 1868 5419 2 chr1B.!!$F4 3551
5 TraesCS3A01G255800 chr3B 463109418 463114340 4922 True 2121.125000 4019 98.846500 1 7116 4 chr3B.!!$R2 7115
6 TraesCS3A01G255800 chr2B 772633653 772634785 1132 False 1328.000000 1328 87.879000 3803 4948 1 chr2B.!!$F2 1145
7 TraesCS3A01G255800 chr2B 784715286 784717431 2145 False 1301.666667 2085 98.089333 2672 4986 3 chr2B.!!$F3 2314
8 TraesCS3A01G255800 chr6A 461981649 461983678 2029 True 1855.500000 1930 97.941000 2672 4806 2 chr6A.!!$R3 2134
9 TraesCS3A01G255800 chr6A 23888385 23889636 1251 False 453.500000 604 81.827500 1868 5419 2 chr6A.!!$F1 3551
10 TraesCS3A01G255800 chr6B 18394643 18396851 2208 True 962.500000 1496 91.629000 2672 4986 2 chr6B.!!$R3 2314
11 TraesCS3A01G255800 chr6B 461678477 461681835 3358 False 938.500000 1474 90.814000 2672 4977 2 chr6B.!!$F4 2305
12 TraesCS3A01G255800 chr6B 3581604 3582784 1180 False 817.800000 1544 89.239000 3696 4983 2 chr6B.!!$F1 1287
13 TraesCS3A01G255800 chr6B 77795497 77796609 1112 False 774.550000 1476 87.458500 3715 4911 2 chr6B.!!$F3 1196
14 TraesCS3A01G255800 chr6B 41992659 41993622 963 False 362.000000 424 83.227000 2187 5419 2 chr6B.!!$F2 3232
15 TraesCS3A01G255800 chr2D 82001283 82002300 1017 False 1487.000000 1487 92.976000 3956 4979 1 chr2D.!!$F1 1023
16 TraesCS3A01G255800 chr7B 2669929 2671003 1074 True 1480.000000 1480 91.582000 3905 4977 1 chr7B.!!$R1 1072
17 TraesCS3A01G255800 chr7B 720175862 720177611 1749 False 314.666667 555 88.053333 2870 3756 3 chr7B.!!$F3 886
18 TraesCS3A01G255800 chr7B 126777815 126779112 1297 False 223.000000 224 80.189000 1868 5429 2 chr7B.!!$F2 3561
19 TraesCS3A01G255800 chr6D 25782114 25783365 1251 False 449.500000 599 81.634500 1868 5419 2 chr6D.!!$F1 3551
20 TraesCS3A01G255800 chrUn 16579048 16580339 1291 False 220.500000 228 80.105500 1868 5417 2 chrUn.!!$F5 3549

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
840 842 0.106569 TAGCAGGATACCGGTCGGAA 60.107 55.000 12.40 0.0 38.96 4.30 F
950 952 1.155424 TGCTTTTGGACGACGGACAC 61.155 55.000 0.00 0.0 0.00 3.67 F
2501 2631 0.764890 CTGGGAGTGGAAGGACACAA 59.235 55.000 0.00 0.0 43.72 3.33 F
3734 6335 0.387878 CGGAGCCGAGCTACATCATC 60.388 60.000 2.00 0.0 39.98 2.92 F
3791 6392 0.541392 ACGGCTTGCCATCTACATCA 59.459 50.000 12.45 0.0 0.00 3.07 F
3792 6393 1.065491 ACGGCTTGCCATCTACATCAA 60.065 47.619 12.45 0.0 0.00 2.57 F
5958 9130 1.203376 TGGTGGTACCTTGGAGGATCA 60.203 52.381 14.36 0.0 39.58 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 2631 3.686227 TGGCTTTTGATGGTATGGGAT 57.314 42.857 0.00 0.00 0.00 3.85 R
2641 2772 9.726232 CATATAACACCTGATCAAGTTTGAATG 57.274 33.333 11.59 9.64 41.13 2.67 R
3794 6395 0.030369 GGCCGGTGTAGATCGTACAG 59.970 60.000 1.90 0.00 0.00 2.74 R
5468 8639 8.401046 CTGAAGTACAGCTGTATCTAAACTTC 57.599 38.462 32.29 32.29 39.86 3.01 R
5959 9131 3.181410 TGAGAAGGGACTGGTTAAGGAGA 60.181 47.826 0.00 0.00 40.86 3.71 R
6107 9279 1.227645 TCGCAGGTGGCTATGATGC 60.228 57.895 0.00 0.00 41.67 3.91 R
6765 9954 0.318699 TGTGCGCTAGACATATCGCC 60.319 55.000 9.73 1.27 43.96 5.54 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
238 239 5.746721 GCTCAAATTTTGGTACGACAAGTTT 59.253 36.000 9.18 0.00 0.00 2.66
336 337 2.629617 CCCAACAGCTCCAGTTCAAAAT 59.370 45.455 0.00 0.00 0.00 1.82
558 560 9.030301 ACACTAGTATTTGCAAAATTTTGACAC 57.970 29.630 30.40 18.85 40.55 3.67
563 565 9.553064 AGTATTTGCAAAATTTTGACACCATTA 57.447 25.926 30.40 12.00 40.55 1.90
745 747 4.438148 CGGTTGAACTGGGTTTTGAATTT 58.562 39.130 0.00 0.00 0.00 1.82
746 748 4.269844 CGGTTGAACTGGGTTTTGAATTTG 59.730 41.667 0.00 0.00 0.00 2.32
747 749 5.423886 GGTTGAACTGGGTTTTGAATTTGA 58.576 37.500 0.00 0.00 0.00 2.69
748 750 6.054941 GGTTGAACTGGGTTTTGAATTTGAT 58.945 36.000 0.00 0.00 0.00 2.57
749 751 6.542005 GGTTGAACTGGGTTTTGAATTTGATT 59.458 34.615 0.00 0.00 0.00 2.57
750 752 7.066887 GGTTGAACTGGGTTTTGAATTTGATTT 59.933 33.333 0.00 0.00 0.00 2.17
751 753 8.458052 GTTGAACTGGGTTTTGAATTTGATTTT 58.542 29.630 0.00 0.00 0.00 1.82
752 754 8.572855 TGAACTGGGTTTTGAATTTGATTTTT 57.427 26.923 0.00 0.00 0.00 1.94
839 841 0.820891 GTAGCAGGATACCGGTCGGA 60.821 60.000 12.40 0.00 38.96 4.55
840 842 0.106569 TAGCAGGATACCGGTCGGAA 60.107 55.000 12.40 0.00 38.96 4.30
871 873 2.879646 CCTGGGTGTTGCGTACTTTTTA 59.120 45.455 0.00 0.00 0.00 1.52
950 952 1.155424 TGCTTTTGGACGACGGACAC 61.155 55.000 0.00 0.00 0.00 3.67
1119 1122 3.469970 TGGATGAGCCACGGCGAT 61.470 61.111 16.62 0.00 43.33 4.58
1299 1302 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
1449 1452 8.880244 TGCATTTGGTATTCTAGATGTACCTAT 58.120 33.333 24.31 17.95 38.89 2.57
2501 2631 0.764890 CTGGGAGTGGAAGGACACAA 59.235 55.000 0.00 0.00 43.72 3.33
2666 2797 8.906867 CCATTCAAACTTGATCAGGTGTTATAT 58.093 33.333 11.70 0.00 37.00 0.86
2667 2798 9.726232 CATTCAAACTTGATCAGGTGTTATATG 57.274 33.333 11.70 8.21 37.00 1.78
2668 2799 9.685276 ATTCAAACTTGATCAGGTGTTATATGA 57.315 29.630 11.70 8.57 37.00 2.15
2669 2800 9.685276 TTCAAACTTGATCAGGTGTTATATGAT 57.315 29.630 11.70 0.00 37.00 2.45
2670 2801 9.112725 TCAAACTTGATCAGGTGTTATATGATG 57.887 33.333 11.70 5.48 33.90 3.07
3711 6312 3.161450 ATCTACACCGGCCGCCAT 61.161 61.111 22.85 9.25 0.00 4.40
3712 6313 3.460672 ATCTACACCGGCCGCCATG 62.461 63.158 22.85 19.65 0.00 3.66
3713 6314 4.467084 CTACACCGGCCGCCATGT 62.467 66.667 22.85 24.26 0.00 3.21
3714 6315 4.460683 TACACCGGCCGCCATGTC 62.461 66.667 25.32 0.00 0.00 3.06
3724 6325 4.899239 GCCATGTCCGGAGCCGAG 62.899 72.222 3.06 0.73 42.83 4.63
3725 6326 4.899239 CCATGTCCGGAGCCGAGC 62.899 72.222 3.06 3.25 42.83 5.03
3726 6327 3.842923 CATGTCCGGAGCCGAGCT 61.843 66.667 3.06 0.00 43.88 4.09
3727 6328 2.123854 ATGTCCGGAGCCGAGCTA 60.124 61.111 3.06 0.00 39.88 3.32
3728 6329 2.491022 ATGTCCGGAGCCGAGCTAC 61.491 63.158 3.06 3.92 39.88 3.58
3729 6330 3.138798 GTCCGGAGCCGAGCTACA 61.139 66.667 3.06 0.00 39.98 2.74
3730 6331 2.123854 TCCGGAGCCGAGCTACAT 60.124 61.111 11.05 0.00 39.98 2.29
3731 6332 2.194212 TCCGGAGCCGAGCTACATC 61.194 63.158 11.05 0.00 39.98 3.06
3732 6333 2.490148 CCGGAGCCGAGCTACATCA 61.490 63.158 11.05 0.00 39.98 3.07
3733 6334 1.662608 CGGAGCCGAGCTACATCAT 59.337 57.895 2.00 0.00 39.98 2.45
3734 6335 0.387878 CGGAGCCGAGCTACATCATC 60.388 60.000 2.00 0.00 39.98 2.92
3735 6336 0.965439 GGAGCCGAGCTACATCATCT 59.035 55.000 3.51 0.00 39.71 2.90
3736 6337 1.342819 GGAGCCGAGCTACATCATCTT 59.657 52.381 3.51 0.00 39.71 2.40
3737 6338 2.609244 GGAGCCGAGCTACATCATCTTC 60.609 54.545 3.51 0.00 39.71 2.87
3738 6339 2.295909 GAGCCGAGCTACATCATCTTCT 59.704 50.000 0.00 0.00 39.88 2.85
3739 6340 2.035704 AGCCGAGCTACATCATCTTCTG 59.964 50.000 0.00 0.00 36.99 3.02
3740 6341 2.402305 CCGAGCTACATCATCTTCTGC 58.598 52.381 0.00 0.00 0.00 4.26
3741 6342 2.223900 CCGAGCTACATCATCTTCTGCA 60.224 50.000 0.00 0.00 0.00 4.41
3742 6343 3.554544 CCGAGCTACATCATCTTCTGCAT 60.555 47.826 0.00 0.00 0.00 3.96
3743 6344 3.429207 CGAGCTACATCATCTTCTGCATG 59.571 47.826 0.00 0.00 0.00 4.06
3744 6345 3.741249 AGCTACATCATCTTCTGCATGG 58.259 45.455 0.00 0.00 0.00 3.66
3745 6346 2.225963 GCTACATCATCTTCTGCATGGC 59.774 50.000 0.00 0.00 0.00 4.40
3746 6347 2.730934 ACATCATCTTCTGCATGGCT 57.269 45.000 0.00 0.00 0.00 4.75
3747 6348 2.298610 ACATCATCTTCTGCATGGCTG 58.701 47.619 0.00 0.00 0.00 4.85
3757 6358 3.945434 CATGGCTGCATCGACCGC 61.945 66.667 0.50 1.72 0.00 5.68
3762 6363 3.190849 CTGCATCGACCGCCACAG 61.191 66.667 6.22 0.00 0.00 3.66
3763 6364 3.939837 CTGCATCGACCGCCACAGT 62.940 63.158 6.22 0.00 0.00 3.55
3764 6365 3.188786 GCATCGACCGCCACAGTC 61.189 66.667 0.00 0.00 0.00 3.51
3769 6370 2.885861 GACCGCCACAGTCGATCT 59.114 61.111 0.00 0.00 0.00 2.75
3777 6378 2.182791 CAGTCGATCTGCACGGCT 59.817 61.111 0.00 0.00 46.50 5.52
3778 6379 1.446792 CAGTCGATCTGCACGGCTT 60.447 57.895 0.00 0.00 43.07 4.35
3779 6380 1.446792 AGTCGATCTGCACGGCTTG 60.447 57.895 0.00 0.00 43.07 4.01
3787 6388 3.102097 GCACGGCTTGCCATCTAC 58.898 61.111 12.45 0.00 46.63 2.59
3788 6389 1.745115 GCACGGCTTGCCATCTACA 60.745 57.895 12.45 0.00 46.63 2.74
3789 6390 1.097547 GCACGGCTTGCCATCTACAT 61.098 55.000 12.45 0.00 46.63 2.29
3790 6391 0.940126 CACGGCTTGCCATCTACATC 59.060 55.000 12.45 0.00 0.00 3.06
3791 6392 0.541392 ACGGCTTGCCATCTACATCA 59.459 50.000 12.45 0.00 0.00 3.07
3792 6393 1.065491 ACGGCTTGCCATCTACATCAA 60.065 47.619 12.45 0.00 0.00 2.57
3793 6394 1.600957 CGGCTTGCCATCTACATCAAG 59.399 52.381 12.45 0.00 39.00 3.02
3796 6397 3.965292 CTTGCCATCTACATCAAGCTG 57.035 47.619 0.00 0.00 31.02 4.24
3797 6398 3.276857 CTTGCCATCTACATCAAGCTGT 58.723 45.455 0.00 0.00 31.02 4.40
3798 6399 4.445453 CTTGCCATCTACATCAAGCTGTA 58.555 43.478 0.00 0.00 31.02 2.74
3799 6400 3.797039 TGCCATCTACATCAAGCTGTAC 58.203 45.455 0.00 0.00 0.00 2.90
5957 9129 1.580059 TGGTGGTACCTTGGAGGATC 58.420 55.000 14.36 0.00 39.58 3.36
5958 9130 1.203376 TGGTGGTACCTTGGAGGATCA 60.203 52.381 14.36 0.00 39.58 2.92
5959 9131 2.127708 GGTGGTACCTTGGAGGATCAT 58.872 52.381 14.36 0.00 37.67 2.45
6107 9279 1.497278 CGTGTTTGCCAGGACATCG 59.503 57.895 0.00 0.00 0.00 3.84
6485 9667 4.350346 CACCATGTTACGGCACATATTTG 58.650 43.478 1.75 0.00 35.51 2.32
6765 9954 1.804151 TCCCGAGAAAAATTGAGCACG 59.196 47.619 0.00 0.00 0.00 5.34
6982 10171 1.211212 TCATCATCTGGCTGGGTCTTG 59.789 52.381 0.00 0.00 0.00 3.02
6988 10177 3.712907 GGCTGGGTCTTGCCGGTA 61.713 66.667 1.90 0.00 39.71 4.02
6989 10178 2.590092 GCTGGGTCTTGCCGGTAT 59.410 61.111 1.90 0.00 38.44 2.73
6990 10179 1.523938 GCTGGGTCTTGCCGGTATC 60.524 63.158 1.90 0.00 38.44 2.24
6991 10180 1.904771 CTGGGTCTTGCCGGTATCA 59.095 57.895 1.90 0.00 38.44 2.15
6992 10181 0.251916 CTGGGTCTTGCCGGTATCAA 59.748 55.000 1.90 0.00 38.44 2.57
6996 10185 1.467342 GGTCTTGCCGGTATCAACAAC 59.533 52.381 1.90 0.00 0.00 3.32
6997 10186 1.127951 GTCTTGCCGGTATCAACAACG 59.872 52.381 1.90 0.00 0.00 4.10
6998 10187 1.001068 TCTTGCCGGTATCAACAACGA 59.999 47.619 1.90 0.00 0.00 3.85
6999 10188 1.393539 CTTGCCGGTATCAACAACGAG 59.606 52.381 1.90 0.00 0.00 4.18
7000 10189 0.604073 TGCCGGTATCAACAACGAGA 59.396 50.000 1.90 0.00 0.00 4.04
7001 10190 1.001068 TGCCGGTATCAACAACGAGAA 59.999 47.619 1.90 0.00 0.00 2.87
7003 10192 2.481185 GCCGGTATCAACAACGAGAAAA 59.519 45.455 1.90 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
238 239 4.022416 GCACATCTGTTTTATGGGTGTCAA 60.022 41.667 0.00 0.00 30.08 3.18
558 560 7.482654 TTTCAAGATGCGTAGAATCTAATGG 57.517 36.000 0.00 0.00 33.17 3.16
749 751 7.304919 GGTTAAAACCGGTCAAATTCAAAAA 57.695 32.000 8.04 0.00 39.66 1.94
750 752 6.905544 GGTTAAAACCGGTCAAATTCAAAA 57.094 33.333 8.04 0.00 39.66 2.44
849 851 0.536460 AAAGTACGCAACACCCAGGG 60.536 55.000 2.85 2.85 0.00 4.45
871 873 3.444792 AAATTAGTTACGGGCCCAGTT 57.555 42.857 24.92 7.80 0.00 3.16
950 952 3.731652 TTTTTCTGTGTGCATTCCCTG 57.268 42.857 0.00 0.00 0.00 4.45
994 996 6.699575 ACCTGTATCTGCATACATTTTTCC 57.300 37.500 0.76 0.00 43.29 3.13
1119 1122 2.583441 CGGGAGCTTGACCACCTCA 61.583 63.158 0.00 0.00 0.00 3.86
1299 1302 9.442047 AGTTTGACTTTCACAGAAATCTATAGG 57.558 33.333 0.00 0.00 0.00 2.57
2501 2631 3.686227 TGGCTTTTGATGGTATGGGAT 57.314 42.857 0.00 0.00 0.00 3.85
2641 2772 9.726232 CATATAACACCTGATCAAGTTTGAATG 57.274 33.333 11.59 9.64 41.13 2.67
3711 6312 3.138798 GTAGCTCGGCTCCGGACA 61.139 66.667 0.00 0.00 40.44 4.02
3712 6313 2.409241 GATGTAGCTCGGCTCCGGAC 62.409 65.000 0.00 0.00 40.44 4.79
3713 6314 2.123854 ATGTAGCTCGGCTCCGGA 60.124 61.111 2.93 2.93 40.44 5.14
3714 6315 1.810606 ATGATGTAGCTCGGCTCCGG 61.811 60.000 8.59 0.00 40.44 5.14
3715 6316 0.387878 GATGATGTAGCTCGGCTCCG 60.388 60.000 1.14 1.14 40.44 4.63
3716 6317 0.965439 AGATGATGTAGCTCGGCTCC 59.035 55.000 1.46 0.00 40.44 4.70
3717 6318 2.295909 AGAAGATGATGTAGCTCGGCTC 59.704 50.000 1.46 0.00 40.44 4.70
3718 6319 2.035704 CAGAAGATGATGTAGCTCGGCT 59.964 50.000 0.00 3.87 43.41 5.52
3719 6320 2.402305 CAGAAGATGATGTAGCTCGGC 58.598 52.381 0.00 0.00 0.00 5.54
3720 6321 2.223900 TGCAGAAGATGATGTAGCTCGG 60.224 50.000 0.00 0.00 0.00 4.63
3721 6322 3.089573 TGCAGAAGATGATGTAGCTCG 57.910 47.619 0.00 0.00 0.00 5.03
3722 6323 3.747010 CCATGCAGAAGATGATGTAGCTC 59.253 47.826 0.00 0.00 0.00 4.09
3723 6324 3.741249 CCATGCAGAAGATGATGTAGCT 58.259 45.455 0.00 0.00 0.00 3.32
3724 6325 2.225963 GCCATGCAGAAGATGATGTAGC 59.774 50.000 0.00 0.00 0.00 3.58
3725 6326 3.498777 CAGCCATGCAGAAGATGATGTAG 59.501 47.826 0.00 0.00 0.00 2.74
3726 6327 3.473625 CAGCCATGCAGAAGATGATGTA 58.526 45.455 0.00 0.00 0.00 2.29
3727 6328 2.298610 CAGCCATGCAGAAGATGATGT 58.701 47.619 0.00 0.00 0.00 3.06
3740 6341 3.945434 GCGGTCGATGCAGCCATG 61.945 66.667 7.63 0.00 0.00 3.66
3745 6346 3.190849 CTGTGGCGGTCGATGCAG 61.191 66.667 13.60 0.59 0.00 4.41
3746 6347 3.932580 GACTGTGGCGGTCGATGCA 62.933 63.158 13.60 0.00 29.77 3.96
3747 6348 3.188786 GACTGTGGCGGTCGATGC 61.189 66.667 4.18 4.18 29.77 3.91
3752 6353 1.517257 CAGATCGACTGTGGCGGTC 60.517 63.158 0.00 0.00 41.30 4.79
3753 6354 2.573869 CAGATCGACTGTGGCGGT 59.426 61.111 0.00 0.00 41.30 5.68
3761 6362 1.446792 CAAGCCGTGCAGATCGACT 60.447 57.895 0.00 0.00 0.00 4.18
3762 6363 3.084579 CAAGCCGTGCAGATCGAC 58.915 61.111 0.00 0.00 0.00 4.20
3771 6372 0.940126 GATGTAGATGGCAAGCCGTG 59.060 55.000 11.14 0.00 39.42 4.94
3772 6373 0.541392 TGATGTAGATGGCAAGCCGT 59.459 50.000 5.30 5.30 39.42 5.68
3773 6374 1.600957 CTTGATGTAGATGGCAAGCCG 59.399 52.381 6.60 0.00 39.42 5.52
3776 6377 3.276857 ACAGCTTGATGTAGATGGCAAG 58.723 45.455 0.00 0.00 40.40 4.01
3777 6378 3.354948 ACAGCTTGATGTAGATGGCAA 57.645 42.857 0.00 0.00 35.90 4.52
3778 6379 3.737972 CGTACAGCTTGATGTAGATGGCA 60.738 47.826 0.00 0.00 36.36 4.92
3779 6380 2.797156 CGTACAGCTTGATGTAGATGGC 59.203 50.000 0.00 0.00 36.36 4.40
3780 6381 4.307443 TCGTACAGCTTGATGTAGATGG 57.693 45.455 0.00 0.00 36.36 3.51
3781 6382 5.767269 AGATCGTACAGCTTGATGTAGATG 58.233 41.667 12.17 0.00 36.36 2.90
3782 6383 6.486993 TGTAGATCGTACAGCTTGATGTAGAT 59.513 38.462 0.00 5.22 36.36 1.98
3783 6384 5.820947 TGTAGATCGTACAGCTTGATGTAGA 59.179 40.000 0.00 1.00 36.36 2.59
3784 6385 5.910166 GTGTAGATCGTACAGCTTGATGTAG 59.090 44.000 0.00 0.00 36.36 2.74
3785 6386 5.220989 GGTGTAGATCGTACAGCTTGATGTA 60.221 44.000 18.91 0.00 41.26 2.29
3786 6387 4.440250 GGTGTAGATCGTACAGCTTGATGT 60.440 45.833 18.91 0.00 41.26 3.06
3787 6388 4.045104 GGTGTAGATCGTACAGCTTGATG 58.955 47.826 18.91 0.00 41.26 3.07
3788 6389 3.243101 CGGTGTAGATCGTACAGCTTGAT 60.243 47.826 21.40 0.00 42.01 2.57
3789 6390 2.096980 CGGTGTAGATCGTACAGCTTGA 59.903 50.000 21.40 0.00 42.01 3.02
3790 6391 2.451132 CGGTGTAGATCGTACAGCTTG 58.549 52.381 21.40 10.93 42.01 4.01
3791 6392 1.404391 CCGGTGTAGATCGTACAGCTT 59.596 52.381 21.40 0.00 42.01 3.74
3792 6393 1.022735 CCGGTGTAGATCGTACAGCT 58.977 55.000 21.40 0.00 42.01 4.24
3793 6394 0.594284 GCCGGTGTAGATCGTACAGC 60.594 60.000 17.40 17.40 41.11 4.40
3794 6395 0.030369 GGCCGGTGTAGATCGTACAG 59.970 60.000 1.90 0.00 0.00 2.74
3795 6396 1.717791 CGGCCGGTGTAGATCGTACA 61.718 60.000 20.10 2.15 0.00 2.90
3796 6397 1.009222 CGGCCGGTGTAGATCGTAC 60.009 63.158 20.10 0.00 0.00 3.67
3797 6398 2.837883 GCGGCCGGTGTAGATCGTA 61.838 63.158 29.38 0.00 0.00 3.43
3798 6399 4.203076 GCGGCCGGTGTAGATCGT 62.203 66.667 29.38 0.00 0.00 3.73
3799 6400 4.944372 GGCGGCCGGTGTAGATCG 62.944 72.222 29.38 0.00 0.00 3.69
5468 8639 8.401046 CTGAAGTACAGCTGTATCTAAACTTC 57.599 38.462 32.29 32.29 39.86 3.01
5957 9129 3.777522 AGAAGGGACTGGTTAAGGAGATG 59.222 47.826 0.00 0.00 40.86 2.90
5958 9130 4.034410 GAGAAGGGACTGGTTAAGGAGAT 58.966 47.826 0.00 0.00 40.86 2.75
5959 9131 3.181410 TGAGAAGGGACTGGTTAAGGAGA 60.181 47.826 0.00 0.00 40.86 3.71
6107 9279 1.227645 TCGCAGGTGGCTATGATGC 60.228 57.895 0.00 0.00 41.67 3.91
6765 9954 0.318699 TGTGCGCTAGACATATCGCC 60.319 55.000 9.73 1.27 43.96 5.54
6982 10171 1.717194 TTCTCGTTGTTGATACCGGC 58.283 50.000 0.00 0.00 0.00 6.13
7001 10190 6.070251 ACCTCTGTTTCCATTTGGTTCTTTTT 60.070 34.615 0.00 0.00 36.34 1.94
7003 10192 4.962362 ACCTCTGTTTCCATTTGGTTCTTT 59.038 37.500 0.00 0.00 36.34 2.52
7006 10195 3.058224 CGACCTCTGTTTCCATTTGGTTC 60.058 47.826 0.00 0.00 36.34 3.62
7007 10196 2.884639 CGACCTCTGTTTCCATTTGGTT 59.115 45.455 0.00 0.00 36.34 3.67
7008 10197 2.158667 ACGACCTCTGTTTCCATTTGGT 60.159 45.455 0.00 0.00 36.34 3.67
7010 10199 3.058224 GGAACGACCTCTGTTTCCATTTG 60.058 47.826 0.00 0.00 35.41 2.32
7011 10200 3.146847 GGAACGACCTCTGTTTCCATTT 58.853 45.455 0.00 0.00 35.41 2.32
7012 10201 2.779506 GGAACGACCTCTGTTTCCATT 58.220 47.619 0.00 0.00 35.41 3.16
7013 10202 2.474410 GGAACGACCTCTGTTTCCAT 57.526 50.000 0.00 0.00 35.41 3.41


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

AutoCloner maintained by Alex Coulton.