Multiple sequence alignment - TraesCS6A01G401700

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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 TraesCS6A01G401700 chr6A 100.000 3323 0 0 1 3323 610124024 610127346 0.000000e+00 6137.0
1 TraesCS6A01G401700 chr6A 84.957 1396 181 20 850 2238 610066715 610068088 0.000000e+00 1387.0
2 TraesCS6A01G401700 chr6A 83.012 1401 198 24 850 2238 610063221 610064593 0.000000e+00 1232.0
3 TraesCS6A01G401700 chr6A 84.585 772 116 3 1468 2238 610087981 610088750 0.000000e+00 763.0
4 TraesCS6A01G401700 chr6A 84.966 745 98 7 1257 1991 610061121 610061861 0.000000e+00 743.0
5 TraesCS6A01G401700 chr6A 81.329 632 79 23 850 1472 610078646 610079247 8.340000e-131 477.0
6 TraesCS6A01G401700 chr6A 80.584 582 86 13 850 1429 610090845 610091401 1.100000e-114 424.0
7 TraesCS6A01G401700 chr6B 94.368 3125 155 10 214 3323 706867860 706870978 0.000000e+00 4776.0
8 TraesCS6A01G401700 chr6B 83.739 1396 202 18 850 2238 706850603 706851980 0.000000e+00 1297.0
9 TraesCS6A01G401700 chr6B 83.491 1054 150 16 850 1900 706855831 706856863 0.000000e+00 961.0
10 TraesCS6A01G401700 chr6B 83.468 248 29 2 1246 1493 706797445 706797680 1.550000e-53 220.0
11 TraesCS6A01G401700 chr5B 80.980 1551 244 31 1033 2546 46747264 46745728 0.000000e+00 1182.0
12 TraesCS6A01G401700 chr5B 80.105 1523 250 38 970 2463 48146329 48147827 0.000000e+00 1085.0
13 TraesCS6A01G401700 chr5B 84.125 674 58 24 2654 3323 60588780 60589408 1.020000e-169 606.0
14 TraesCS6A01G401700 chr5B 81.363 719 110 20 1847 2546 46770902 46770189 6.220000e-157 564.0
15 TraesCS6A01G401700 chr5B 79.740 691 107 21 2652 3313 623109282 623108596 1.400000e-128 470.0
16 TraesCS6A01G401700 chr5B 86.391 169 20 3 2412 2578 48147892 48148059 7.320000e-42 182.0
17 TraesCS6A01G401700 chr6D 86.355 1004 125 4 1246 2238 463531518 463532520 0.000000e+00 1085.0
18 TraesCS6A01G401700 chr5D 79.078 1606 262 41 1012 2579 46128600 46127031 0.000000e+00 1037.0
19 TraesCS6A01G401700 chr5D 88.450 684 66 8 2652 3323 357879695 357880377 0.000000e+00 813.0
20 TraesCS6A01G401700 chr5D 86.604 642 76 4 2684 3322 184101462 184102096 0.000000e+00 701.0
21 TraesCS6A01G401700 chr5D 83.671 692 96 8 1768 2445 46085511 46084823 1.300000e-178 636.0
22 TraesCS6A01G401700 chr5D 76.588 551 75 30 2063 2589 46126744 46126224 1.530000e-63 254.0
23 TraesCS6A01G401700 chr5D 90.278 72 5 2 2412 2482 46274256 46274186 3.530000e-15 93.5
24 TraesCS6A01G401700 chr5D 89.831 59 5 1 2405 2463 46084811 46084754 1.280000e-09 75.0
25 TraesCS6A01G401700 chr2B 78.596 1467 242 37 1006 2439 731710588 731712015 0.000000e+00 904.0
26 TraesCS6A01G401700 chr2B 88.856 682 62 9 2655 3323 29538589 29539269 0.000000e+00 826.0
27 TraesCS6A01G401700 chr7A 86.370 675 80 5 2654 3323 108788805 108788138 0.000000e+00 726.0
28 TraesCS6A01G401700 chr7A 83.792 654 76 19 2680 3323 119303941 119303308 7.940000e-166 593.0
29 TraesCS6A01G401700 chr7A 90.995 211 19 0 214 424 336207458 336207668 5.430000e-73 285.0
30 TraesCS6A01G401700 chr7A 82.812 320 50 5 522 838 336208924 336209241 7.020000e-72 281.0
31 TraesCS6A01G401700 chr7A 94.340 53 3 0 798 850 107872657 107872709 7.640000e-12 82.4
32 TraesCS6A01G401700 chr1A 88.453 433 37 8 2654 3083 45834999 45834577 8.220000e-141 510.0
33 TraesCS6A01G401700 chr1A 84.906 212 25 3 214 422 331791951 331792158 1.210000e-49 207.0
34 TraesCS6A01G401700 chr5A 80.671 626 97 19 1940 2546 36945739 36945119 6.490000e-127 464.0
35 TraesCS6A01G401700 chr5A 85.135 148 19 3 2401 2546 37592686 37592540 7.430000e-32 148.0
36 TraesCS6A01G401700 chr5A 92.857 42 3 0 2654 2695 18940378 18940337 9.950000e-06 62.1
37 TraesCS6A01G401700 chr5A 100.000 28 0 0 2654 2681 538955586 538955613 6.000000e-03 52.8
38 TraesCS6A01G401700 chr4D 85.645 411 51 4 439 849 233196148 233195746 3.060000e-115 425.0
39 TraesCS6A01G401700 chr2A 84.337 332 49 3 517 846 597496408 597496738 4.140000e-84 322.0
40 TraesCS6A01G401700 chr2A 89.573 211 18 2 214 422 2769054 2769262 7.070000e-67 265.0
41 TraesCS6A01G401700 chr2A 89.573 211 18 3 214 424 597494952 597495158 7.070000e-67 265.0
42 TraesCS6A01G401700 chr2A 84.434 212 26 3 214 422 3452557 3452764 5.620000e-48 202.0
43 TraesCS6A01G401700 chr2A 84.186 215 27 4 214 425 424558602 424558392 5.620000e-48 202.0
44 TraesCS6A01G401700 chr2A 84.434 212 26 4 214 422 565490636 565490843 5.620000e-48 202.0
45 TraesCS6A01G401700 chr2A 81.061 264 33 6 587 850 2770520 2770766 9.410000e-46 195.0
46 TraesCS6A01G401700 chr1D 82.796 372 48 11 483 849 396104080 396103720 5.350000e-83 318.0
47 TraesCS6A01G401700 chr1D 86.321 212 27 2 211 422 396112162 396111953 2.580000e-56 230.0
48 TraesCS6A01G401700 chr3D 80.851 188 30 3 2654 2841 579506213 579506032 3.460000e-30 143.0


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 TraesCS6A01G401700 chr6A 610124024 610127346 3322 False 6137.000000 6137 100.000000 1 3323 1 chr6A.!!$F2 3322
1 TraesCS6A01G401700 chr6A 610061121 610068088 6967 False 1120.666667 1387 84.311667 850 2238 3 chr6A.!!$F3 1388
2 TraesCS6A01G401700 chr6A 610087981 610091401 3420 False 593.500000 763 82.584500 850 2238 2 chr6A.!!$F4 1388
3 TraesCS6A01G401700 chr6A 610078646 610079247 601 False 477.000000 477 81.329000 850 1472 1 chr6A.!!$F1 622
4 TraesCS6A01G401700 chr6B 706867860 706870978 3118 False 4776.000000 4776 94.368000 214 3323 1 chr6B.!!$F2 3109
5 TraesCS6A01G401700 chr6B 706850603 706856863 6260 False 1129.000000 1297 83.615000 850 2238 2 chr6B.!!$F3 1388
6 TraesCS6A01G401700 chr5B 46745728 46747264 1536 True 1182.000000 1182 80.980000 1033 2546 1 chr5B.!!$R1 1513
7 TraesCS6A01G401700 chr5B 48146329 48148059 1730 False 633.500000 1085 83.248000 970 2578 2 chr5B.!!$F2 1608
8 TraesCS6A01G401700 chr5B 60588780 60589408 628 False 606.000000 606 84.125000 2654 3323 1 chr5B.!!$F1 669
9 TraesCS6A01G401700 chr5B 46770189 46770902 713 True 564.000000 564 81.363000 1847 2546 1 chr5B.!!$R2 699
10 TraesCS6A01G401700 chr5B 623108596 623109282 686 True 470.000000 470 79.740000 2652 3313 1 chr5B.!!$R3 661
11 TraesCS6A01G401700 chr6D 463531518 463532520 1002 False 1085.000000 1085 86.355000 1246 2238 1 chr6D.!!$F1 992
12 TraesCS6A01G401700 chr5D 357879695 357880377 682 False 813.000000 813 88.450000 2652 3323 1 chr5D.!!$F2 671
13 TraesCS6A01G401700 chr5D 184101462 184102096 634 False 701.000000 701 86.604000 2684 3322 1 chr5D.!!$F1 638
14 TraesCS6A01G401700 chr5D 46126224 46128600 2376 True 645.500000 1037 77.833000 1012 2589 2 chr5D.!!$R3 1577
15 TraesCS6A01G401700 chr5D 46084754 46085511 757 True 355.500000 636 86.751000 1768 2463 2 chr5D.!!$R2 695
16 TraesCS6A01G401700 chr2B 731710588 731712015 1427 False 904.000000 904 78.596000 1006 2439 1 chr2B.!!$F2 1433
17 TraesCS6A01G401700 chr2B 29538589 29539269 680 False 826.000000 826 88.856000 2655 3323 1 chr2B.!!$F1 668
18 TraesCS6A01G401700 chr7A 108788138 108788805 667 True 726.000000 726 86.370000 2654 3323 1 chr7A.!!$R1 669
19 TraesCS6A01G401700 chr7A 119303308 119303941 633 True 593.000000 593 83.792000 2680 3323 1 chr7A.!!$R2 643
20 TraesCS6A01G401700 chr7A 336207458 336209241 1783 False 283.000000 285 86.903500 214 838 2 chr7A.!!$F2 624
21 TraesCS6A01G401700 chr5A 36945119 36945739 620 True 464.000000 464 80.671000 1940 2546 1 chr5A.!!$R2 606
22 TraesCS6A01G401700 chr2A 597494952 597496738 1786 False 293.500000 322 86.955000 214 846 2 chr2A.!!$F4 632
23 TraesCS6A01G401700 chr2A 2769054 2770766 1712 False 230.000000 265 85.317000 214 850 2 chr2A.!!$F3 636

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
510 1848 0.035152 TGTCCATGCGAGCCATTCTT 60.035 50.0 0.0 0.0 29.71 2.52 F
1179 2549 0.833949 AATTCCTCTCTTCTCCGCCC 59.166 55.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 3078 2.444766 CTCTTTCTCCCCCATAGCCATT 59.555 50.0 0.00 0.0 0.00 3.16 R
2882 10169 1.705256 TCGTGCCACGACAAGAATAC 58.295 50.0 17.22 0.0 46.73 1.89 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
21 22 3.890128 CGCGAGAGAGATTATTACAGCA 58.110 45.455 0.00 0.00 0.00 4.41
23 24 3.984633 GCGAGAGAGATTATTACAGCACC 59.015 47.826 0.00 0.00 0.00 5.01
24 25 4.499865 GCGAGAGAGATTATTACAGCACCA 60.500 45.833 0.00 0.00 0.00 4.17
25 26 5.592054 CGAGAGAGATTATTACAGCACCAA 58.408 41.667 0.00 0.00 0.00 3.67
27 28 6.019479 CGAGAGAGATTATTACAGCACCAAAC 60.019 42.308 0.00 0.00 0.00 2.93
30 31 5.581085 AGAGATTATTACAGCACCAAACGAC 59.419 40.000 0.00 0.00 0.00 4.34
32 33 1.530323 ATTACAGCACCAAACGACCC 58.470 50.000 0.00 0.00 0.00 4.46
33 34 0.470766 TTACAGCACCAAACGACCCT 59.529 50.000 0.00 0.00 0.00 4.34
34 35 1.340088 TACAGCACCAAACGACCCTA 58.660 50.000 0.00 0.00 0.00 3.53
35 36 0.470766 ACAGCACCAAACGACCCTAA 59.529 50.000 0.00 0.00 0.00 2.69
36 37 1.134037 ACAGCACCAAACGACCCTAAA 60.134 47.619 0.00 0.00 0.00 1.85
37 38 2.159382 CAGCACCAAACGACCCTAAAT 58.841 47.619 0.00 0.00 0.00 1.40
38 39 2.161609 CAGCACCAAACGACCCTAAATC 59.838 50.000 0.00 0.00 0.00 2.17
39 40 1.471287 GCACCAAACGACCCTAAATCC 59.529 52.381 0.00 0.00 0.00 3.01
40 41 2.089201 CACCAAACGACCCTAAATCCC 58.911 52.381 0.00 0.00 0.00 3.85
41 42 1.339342 ACCAAACGACCCTAAATCCCG 60.339 52.381 0.00 0.00 0.00 5.14
43 44 0.393402 AAACGACCCTAAATCCCGGC 60.393 55.000 0.00 0.00 0.00 6.13
44 45 1.555477 AACGACCCTAAATCCCGGCA 61.555 55.000 0.00 0.00 0.00 5.69
45 46 1.222387 CGACCCTAAATCCCGGCAA 59.778 57.895 0.00 0.00 0.00 4.52
46 47 1.093496 CGACCCTAAATCCCGGCAAC 61.093 60.000 0.00 0.00 0.00 4.17
49 50 0.814010 CCCTAAATCCCGGCAACTCG 60.814 60.000 0.00 0.00 0.00 4.18
50 51 0.107848 CCTAAATCCCGGCAACTCGT 60.108 55.000 0.00 0.00 0.00 4.18
52 53 1.396996 CTAAATCCCGGCAACTCGTTG 59.603 52.381 0.00 5.45 43.14 4.10
55 56 0.744414 ATCCCGGCAACTCGTTGATG 60.744 55.000 13.57 4.68 42.93 3.07
56 57 1.671054 CCCGGCAACTCGTTGATGT 60.671 57.895 13.57 0.00 42.93 3.06
57 58 1.635663 CCCGGCAACTCGTTGATGTC 61.636 60.000 13.57 0.00 42.93 3.06
58 59 0.948623 CCGGCAACTCGTTGATGTCA 60.949 55.000 13.57 0.00 42.93 3.58
59 60 1.078709 CGGCAACTCGTTGATGTCAT 58.921 50.000 13.57 0.00 42.93 3.06
60 61 2.267426 CGGCAACTCGTTGATGTCATA 58.733 47.619 13.57 0.00 42.93 2.15
63 64 3.307242 GGCAACTCGTTGATGTCATACTC 59.693 47.826 13.57 0.00 42.93 2.59
66 67 4.017380 ACTCGTTGATGTCATACTCGAC 57.983 45.455 0.00 0.00 36.40 4.20
68 69 2.109463 CGTTGATGTCATACTCGACGG 58.891 52.381 6.76 0.00 42.75 4.79
70 71 0.384309 TGATGTCATACTCGACGGGC 59.616 55.000 0.00 0.00 38.84 6.13
72 73 0.669077 ATGTCATACTCGACGGGCTC 59.331 55.000 0.00 0.00 38.84 4.70
75 76 1.299468 CATACTCGACGGGCTCAGC 60.299 63.158 0.00 0.00 0.00 4.26
77 78 3.963687 TACTCGACGGGCTCAGCGA 62.964 63.158 0.00 0.00 0.00 4.93
78 79 3.893763 CTCGACGGGCTCAGCGAT 61.894 66.667 0.00 0.00 31.87 4.58
79 80 2.515290 TCGACGGGCTCAGCGATA 60.515 61.111 0.00 0.00 0.00 2.92
80 81 1.857318 CTCGACGGGCTCAGCGATAT 61.857 60.000 0.00 0.00 31.87 1.63
81 82 1.442857 CGACGGGCTCAGCGATATC 60.443 63.158 0.00 0.00 0.00 1.63
82 83 1.080434 GACGGGCTCAGCGATATCC 60.080 63.158 0.00 0.00 0.00 2.59
83 84 2.126307 CGGGCTCAGCGATATCCG 60.126 66.667 0.00 0.00 42.21 4.18
84 85 2.920645 CGGGCTCAGCGATATCCGT 61.921 63.158 3.31 0.00 41.15 4.69
86 87 1.373497 GGCTCAGCGATATCCGTGG 60.373 63.158 0.00 0.00 41.15 4.94
87 88 2.024319 GCTCAGCGATATCCGTGGC 61.024 63.158 0.00 0.00 41.15 5.01
89 90 0.941463 CTCAGCGATATCCGTGGCAC 60.941 60.000 7.79 7.79 41.15 5.01
104 105 2.359107 CACGGGCAGCAGTGACAT 60.359 61.111 13.28 0.00 40.56 3.06
106 107 2.267006 CGGGCAGCAGTGACATCT 59.733 61.111 0.00 0.00 30.34 2.90
107 108 1.812922 CGGGCAGCAGTGACATCTC 60.813 63.158 0.00 0.00 30.34 2.75
108 109 1.451028 GGGCAGCAGTGACATCTCC 60.451 63.158 0.00 0.00 30.34 3.71
109 110 1.451028 GGCAGCAGTGACATCTCCC 60.451 63.158 0.00 0.00 0.00 4.30
111 112 0.461693 GCAGCAGTGACATCTCCCTC 60.462 60.000 0.00 0.00 0.00 4.30
112 113 1.193323 CAGCAGTGACATCTCCCTCT 58.807 55.000 0.00 0.00 0.00 3.69
113 114 1.554160 CAGCAGTGACATCTCCCTCTT 59.446 52.381 0.00 0.00 0.00 2.85
115 116 2.763448 AGCAGTGACATCTCCCTCTTAC 59.237 50.000 0.00 0.00 0.00 2.34
116 117 2.159028 GCAGTGACATCTCCCTCTTACC 60.159 54.545 0.00 0.00 0.00 2.85
117 118 3.370104 CAGTGACATCTCCCTCTTACCT 58.630 50.000 0.00 0.00 0.00 3.08
118 119 3.383185 CAGTGACATCTCCCTCTTACCTC 59.617 52.174 0.00 0.00 0.00 3.85
120 121 3.634910 GTGACATCTCCCTCTTACCTCTC 59.365 52.174 0.00 0.00 0.00 3.20
121 122 2.882137 GACATCTCCCTCTTACCTCTCG 59.118 54.545 0.00 0.00 0.00 4.04
122 123 1.611491 CATCTCCCTCTTACCTCTCGC 59.389 57.143 0.00 0.00 0.00 5.03
123 124 0.624254 TCTCCCTCTTACCTCTCGCA 59.376 55.000 0.00 0.00 0.00 5.10
124 125 1.005569 TCTCCCTCTTACCTCTCGCAA 59.994 52.381 0.00 0.00 0.00 4.85
125 126 1.825474 CTCCCTCTTACCTCTCGCAAA 59.175 52.381 0.00 0.00 0.00 3.68
126 127 2.233922 CTCCCTCTTACCTCTCGCAAAA 59.766 50.000 0.00 0.00 0.00 2.44
127 128 2.635915 TCCCTCTTACCTCTCGCAAAAA 59.364 45.455 0.00 0.00 0.00 1.94
181 182 9.151471 TCAGAACTAAAGTACTCACATAAATGC 57.849 33.333 0.00 0.00 0.00 3.56
182 183 9.155975 CAGAACTAAAGTACTCACATAAATGCT 57.844 33.333 0.00 0.00 0.00 3.79
183 184 9.726438 AGAACTAAAGTACTCACATAAATGCTT 57.274 29.630 0.00 0.00 0.00 3.91
188 189 8.863872 AAAGTACTCACATAAATGCTTTACCT 57.136 30.769 0.00 0.00 0.00 3.08
189 190 8.863872 AAGTACTCACATAAATGCTTTACCTT 57.136 30.769 0.00 0.00 0.00 3.50
190 191 8.863872 AGTACTCACATAAATGCTTTACCTTT 57.136 30.769 0.00 0.00 0.00 3.11
191 192 9.297037 AGTACTCACATAAATGCTTTACCTTTT 57.703 29.630 0.00 0.00 0.00 2.27
192 193 9.908152 GTACTCACATAAATGCTTTACCTTTTT 57.092 29.630 0.00 0.00 0.00 1.94
194 195 9.908152 ACTCACATAAATGCTTTACCTTTTTAC 57.092 29.630 0.00 0.00 0.00 2.01
195 196 9.906660 CTCACATAAATGCTTTACCTTTTTACA 57.093 29.630 0.00 0.00 0.00 2.41
228 229 6.359804 ACATCACATTAATGTAGATGCCACT 58.640 36.000 32.99 22.75 42.85 4.00
347 348 5.567623 GCTCTTGTCTTCCATCAAGTAGACA 60.568 44.000 0.00 0.00 43.69 3.41
367 368 3.087031 CAGAGCACCACAAATCAGGAAT 58.913 45.455 0.00 0.00 0.00 3.01
383 384 8.545229 AATCAGGAATCTATCTAATTTCTGCG 57.455 34.615 0.19 0.00 38.91 5.18
448 1786 2.668457 CTCATGTTACGTTGGTCAGAGC 59.332 50.000 0.00 0.00 0.00 4.09
484 1822 1.742880 CATGTGGGTCGGACTGCAG 60.743 63.158 13.48 13.48 0.00 4.41
485 1823 2.959484 ATGTGGGTCGGACTGCAGG 61.959 63.158 19.93 0.00 0.00 4.85
510 1848 0.035152 TGTCCATGCGAGCCATTCTT 60.035 50.000 0.00 0.00 29.71 2.52
524 1862 1.033746 ATTCTTCGCCCGACCGTAGA 61.034 55.000 0.00 0.00 33.73 2.59
581 1919 4.326507 AAGAGCTGCGCAGGTGCT 62.327 61.111 43.35 32.96 39.57 4.40
635 1974 2.267426 CGGTCAACGCATCACATCTAA 58.733 47.619 0.00 0.00 34.82 2.10
719 2058 1.517361 CAGCGCTCTGTGGTATCCA 59.483 57.895 7.13 0.00 35.61 3.41
770 2109 2.642254 CCTACGGACAGGAACGCCA 61.642 63.158 0.00 0.00 38.00 5.69
829 2168 3.439857 AAGATGGCTGGAAAAGTGCTA 57.560 42.857 0.00 0.00 0.00 3.49
890 2231 3.946606 TCCAAATCGAAACCCTAACCTC 58.053 45.455 0.00 0.00 0.00 3.85
952 2298 3.775654 CGCCACTCCTCCTCCCAC 61.776 72.222 0.00 0.00 0.00 4.61
961 2312 4.348495 TCCTCCCACACCCTCCCC 62.348 72.222 0.00 0.00 0.00 4.81
1179 2549 0.833949 AATTCCTCTCTTCTCCGCCC 59.166 55.000 0.00 0.00 0.00 6.13
1224 2594 1.147191 TGCATCCTCTACTACCCCGAT 59.853 52.381 0.00 0.00 0.00 4.18
1291 2676 1.674057 CTCCTGACCAAGAACGCCT 59.326 57.895 0.00 0.00 0.00 5.52
1302 2687 3.553095 GAACGCCTTGGTGAGGGCT 62.553 63.158 7.26 0.00 46.40 5.19
1435 2833 2.248248 AGTTCATGAAGACCACCGAGA 58.752 47.619 8.80 0.00 0.00 4.04
1482 2889 1.381327 GATGGAGTGGGAGGTCCGA 60.381 63.158 0.00 0.00 38.76 4.55
1572 2985 1.843206 GAGGGGAAGAAAGGAGCAGAT 59.157 52.381 0.00 0.00 0.00 2.90
1596 3009 3.053245 TGACTTTCAAGGTTCAAGGGGAA 60.053 43.478 0.00 0.00 0.00 3.97
1665 3078 1.077787 CGCCAAGTTCTATGGGCCA 60.078 57.895 9.61 9.61 43.50 5.36
1720 3140 2.103771 ACTATCGATGACATGCAGCCTT 59.896 45.455 8.54 0.00 0.00 4.35
1749 3169 6.409524 TTCAAGGCATTTCTTCACTTCATT 57.590 33.333 0.00 0.00 0.00 2.57
1873 3297 3.281727 TGAAGGTGATATGTGAAGGCC 57.718 47.619 0.00 0.00 0.00 5.19
2037 6956 7.921041 AGGGTATCTACATCTCAAAAGATCA 57.079 36.000 0.00 0.00 40.38 2.92
2184 7118 5.062809 GGAGAAGAAAATGAAGTCGTGCTAG 59.937 44.000 0.00 0.00 0.00 3.42
2217 7156 2.357050 CCATCATGGGTTGGCTTCTACA 60.357 50.000 0.00 0.00 32.67 2.74
2294 7969 4.065088 TCGGAGATCTTTTGGACAAAGTG 58.935 43.478 0.00 0.00 0.00 3.16
2381 8986 9.504708 GATTCTATGGTAGCTCACTAGTTACTA 57.495 37.037 0.00 0.00 38.91 1.82
2465 9683 5.821995 TGGCGATCACATTTGAGATAATTCA 59.178 36.000 0.00 0.00 34.35 2.57
2546 9767 9.301153 GACAGTTACAAATTGTTTCTTGACATT 57.699 29.630 3.17 0.00 30.93 2.71
2627 9902 5.376854 AATTCTTGTATGCAACTGGTCAC 57.623 39.130 0.00 0.00 0.00 3.67
2646 9921 7.202526 TGGTCACTTTTCTGAATTTTCATCAC 58.797 34.615 0.00 0.00 36.46 3.06
2668 9943 0.187851 AGGGTACTAGCATAGCCCGT 59.812 55.000 5.27 0.00 43.44 5.28
2866 10153 8.725405 AACACGGAAATACATGTTCATACATA 57.275 30.769 2.30 0.00 43.07 2.29
2925 10218 9.116054 CGACTACTACAGTAAGAAGAAAGAAAC 57.884 37.037 0.00 0.00 37.72 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.188327 TGGTGCTGTAATAATCTCTCTCG 57.812 43.478 0.00 0.00 0.00 4.04
4 5 5.812642 CGTTTGGTGCTGTAATAATCTCTCT 59.187 40.000 0.00 0.00 0.00 3.10
6 7 5.581085 GTCGTTTGGTGCTGTAATAATCTCT 59.419 40.000 0.00 0.00 0.00 3.10
7 8 5.220605 GGTCGTTTGGTGCTGTAATAATCTC 60.221 44.000 0.00 0.00 0.00 2.75
8 9 4.634443 GGTCGTTTGGTGCTGTAATAATCT 59.366 41.667 0.00 0.00 0.00 2.40
10 11 3.692593 GGGTCGTTTGGTGCTGTAATAAT 59.307 43.478 0.00 0.00 0.00 1.28
13 14 1.073284 AGGGTCGTTTGGTGCTGTAAT 59.927 47.619 0.00 0.00 0.00 1.89
14 15 0.470766 AGGGTCGTTTGGTGCTGTAA 59.529 50.000 0.00 0.00 0.00 2.41
15 16 1.340088 TAGGGTCGTTTGGTGCTGTA 58.660 50.000 0.00 0.00 0.00 2.74
16 17 0.470766 TTAGGGTCGTTTGGTGCTGT 59.529 50.000 0.00 0.00 0.00 4.40
18 19 2.433436 GATTTAGGGTCGTTTGGTGCT 58.567 47.619 0.00 0.00 0.00 4.40
19 20 1.471287 GGATTTAGGGTCGTTTGGTGC 59.529 52.381 0.00 0.00 0.00 5.01
21 22 1.339342 CGGGATTTAGGGTCGTTTGGT 60.339 52.381 0.00 0.00 0.00 3.67
23 24 1.375551 CCGGGATTTAGGGTCGTTTG 58.624 55.000 0.00 0.00 0.00 2.93
24 25 0.393402 GCCGGGATTTAGGGTCGTTT 60.393 55.000 2.18 0.00 0.00 3.60
25 26 1.222661 GCCGGGATTTAGGGTCGTT 59.777 57.895 2.18 0.00 0.00 3.85
27 28 1.093496 GTTGCCGGGATTTAGGGTCG 61.093 60.000 2.18 0.00 0.00 4.79
30 31 0.814010 CGAGTTGCCGGGATTTAGGG 60.814 60.000 2.18 0.00 0.00 3.53
32 33 1.396996 CAACGAGTTGCCGGGATTTAG 59.603 52.381 2.18 0.00 33.45 1.85
33 34 1.002201 TCAACGAGTTGCCGGGATTTA 59.998 47.619 2.18 0.00 40.24 1.40
34 35 0.250553 TCAACGAGTTGCCGGGATTT 60.251 50.000 2.18 0.00 40.24 2.17
35 36 0.035439 ATCAACGAGTTGCCGGGATT 60.035 50.000 2.18 0.00 40.24 3.01
36 37 0.744414 CATCAACGAGTTGCCGGGAT 60.744 55.000 2.18 0.00 40.24 3.85
37 38 1.375396 CATCAACGAGTTGCCGGGA 60.375 57.895 2.18 0.00 40.24 5.14
38 39 1.635663 GACATCAACGAGTTGCCGGG 61.636 60.000 2.18 0.00 40.24 5.73
39 40 0.948623 TGACATCAACGAGTTGCCGG 60.949 55.000 10.83 0.00 40.24 6.13
40 41 1.078709 ATGACATCAACGAGTTGCCG 58.921 50.000 10.83 6.93 40.24 5.69
41 42 3.262420 AGTATGACATCAACGAGTTGCC 58.738 45.455 10.83 1.97 40.24 4.52
43 44 4.263209 GTCGAGTATGACATCAACGAGTTG 59.737 45.833 9.51 9.51 38.99 3.16
44 45 4.413087 GTCGAGTATGACATCAACGAGTT 58.587 43.478 9.76 0.00 38.75 3.01
45 46 3.485381 CGTCGAGTATGACATCAACGAGT 60.485 47.826 9.76 0.00 38.84 4.18
46 47 3.029757 CGTCGAGTATGACATCAACGAG 58.970 50.000 9.76 3.71 38.84 4.18
49 50 2.460918 CCCGTCGAGTATGACATCAAC 58.539 52.381 0.00 0.00 38.84 3.18
50 51 1.202371 GCCCGTCGAGTATGACATCAA 60.202 52.381 0.00 0.00 38.84 2.57
52 53 0.669077 AGCCCGTCGAGTATGACATC 59.331 55.000 0.00 0.00 38.84 3.06
55 56 0.029567 CTGAGCCCGTCGAGTATGAC 59.970 60.000 0.00 0.00 35.49 3.06
56 57 1.725557 GCTGAGCCCGTCGAGTATGA 61.726 60.000 0.00 0.00 0.00 2.15
57 58 1.299468 GCTGAGCCCGTCGAGTATG 60.299 63.158 0.00 0.00 0.00 2.39
58 59 2.835705 CGCTGAGCCCGTCGAGTAT 61.836 63.158 0.00 0.00 0.00 2.12
59 60 3.506096 CGCTGAGCCCGTCGAGTA 61.506 66.667 0.00 0.00 0.00 2.59
63 64 1.442857 GATATCGCTGAGCCCGTCG 60.443 63.158 0.00 0.00 0.00 5.12
66 67 2.126307 CGGATATCGCTGAGCCCG 60.126 66.667 4.78 4.78 0.00 6.13
68 69 1.373497 CCACGGATATCGCTGAGCC 60.373 63.158 0.00 0.00 43.89 4.70
70 71 0.941463 GTGCCACGGATATCGCTGAG 60.941 60.000 0.00 0.00 43.89 3.35
72 73 2.302952 CGTGCCACGGATATCGCTG 61.303 63.158 9.90 0.00 43.89 5.18
87 88 2.359107 ATGTCACTGCTGCCCGTG 60.359 61.111 11.51 11.51 0.00 4.94
89 90 1.812922 GAGATGTCACTGCTGCCCG 60.813 63.158 0.00 0.00 0.00 6.13
92 93 0.461693 GAGGGAGATGTCACTGCTGC 60.462 60.000 0.00 0.00 36.15 5.25
93 94 1.193323 AGAGGGAGATGTCACTGCTG 58.807 55.000 0.00 0.00 36.15 4.41
94 95 1.949799 AAGAGGGAGATGTCACTGCT 58.050 50.000 0.00 0.00 36.15 4.24
95 96 2.159028 GGTAAGAGGGAGATGTCACTGC 60.159 54.545 0.00 0.00 36.15 4.40
96 97 3.370104 AGGTAAGAGGGAGATGTCACTG 58.630 50.000 0.00 0.00 36.15 3.66
97 98 3.270960 AGAGGTAAGAGGGAGATGTCACT 59.729 47.826 0.00 0.00 40.13 3.41
98 99 3.634910 GAGAGGTAAGAGGGAGATGTCAC 59.365 52.174 0.00 0.00 0.00 3.67
99 100 3.685835 CGAGAGGTAAGAGGGAGATGTCA 60.686 52.174 0.00 0.00 0.00 3.58
100 101 2.882137 CGAGAGGTAAGAGGGAGATGTC 59.118 54.545 0.00 0.00 0.00 3.06
101 102 2.938838 CGAGAGGTAAGAGGGAGATGT 58.061 52.381 0.00 0.00 0.00 3.06
102 103 1.611491 GCGAGAGGTAAGAGGGAGATG 59.389 57.143 0.00 0.00 0.00 2.90
104 105 0.624254 TGCGAGAGGTAAGAGGGAGA 59.376 55.000 0.00 0.00 0.00 3.71
106 107 1.933021 TTTGCGAGAGGTAAGAGGGA 58.067 50.000 0.00 0.00 0.00 4.20
107 108 2.762535 TTTTGCGAGAGGTAAGAGGG 57.237 50.000 0.00 0.00 0.00 4.30
155 156 9.151471 GCATTTATGTGAGTACTTTAGTTCTGA 57.849 33.333 0.00 0.00 0.00 3.27
156 157 9.155975 AGCATTTATGTGAGTACTTTAGTTCTG 57.844 33.333 0.00 0.00 0.00 3.02
157 158 9.726438 AAGCATTTATGTGAGTACTTTAGTTCT 57.274 29.630 0.00 0.00 0.00 3.01
162 163 9.953565 AGGTAAAGCATTTATGTGAGTACTTTA 57.046 29.630 0.00 0.00 43.30 1.85
165 166 8.863872 AAAGGTAAAGCATTTATGTGAGTACT 57.136 30.769 0.00 0.00 43.30 2.73
166 167 9.908152 AAAAAGGTAAAGCATTTATGTGAGTAC 57.092 29.630 0.00 0.00 43.30 2.73
168 169 9.908152 GTAAAAAGGTAAAGCATTTATGTGAGT 57.092 29.630 0.00 0.00 43.30 3.41
169 170 9.906660 TGTAAAAAGGTAAAGCATTTATGTGAG 57.093 29.630 0.00 0.00 43.30 3.51
185 186 9.349713 TGTGATGTAGAGAAAATGTAAAAAGGT 57.650 29.630 0.00 0.00 0.00 3.50
204 205 6.359804 AGTGGCATCTACATTAATGTGATGT 58.640 36.000 32.86 22.90 42.09 3.06
205 206 6.872628 AGTGGCATCTACATTAATGTGATG 57.127 37.500 31.23 31.23 42.47 3.07
206 207 7.508687 TGTAGTGGCATCTACATTAATGTGAT 58.491 34.615 27.62 22.78 43.26 3.06
207 208 6.883744 TGTAGTGGCATCTACATTAATGTGA 58.116 36.000 27.62 21.80 43.26 3.58
228 229 7.118680 GCAGTAACTTTGTACTTTGGCTATGTA 59.881 37.037 0.00 0.00 31.78 2.29
347 348 2.957402 TTCCTGATTTGTGGTGCTCT 57.043 45.000 0.00 0.00 0.00 4.09
367 368 8.780846 TTGTTTAACCGCAGAAATTAGATAGA 57.219 30.769 0.00 0.00 0.00 1.98
383 384 7.146648 TGGTGAATTTACGGATTTGTTTAACC 58.853 34.615 0.00 0.00 0.00 2.85
448 1786 5.506483 CCACATGAGTTATACGAGTCTCTGG 60.506 48.000 0.00 0.00 0.00 3.86
485 1823 3.490759 CTCGCATGGACACCACGC 61.491 66.667 0.00 0.00 39.53 5.34
510 1848 2.821366 GAGTCTACGGTCGGGCGA 60.821 66.667 0.00 0.00 0.00 5.54
550 1888 3.551496 CTCTTGCCTGCCGGTGGAA 62.551 63.158 17.84 6.04 0.00 3.53
554 1892 4.711949 CAGCTCTTGCCTGCCGGT 62.712 66.667 1.90 0.00 40.80 5.28
576 1914 2.513026 ATCGTCTGCACAGGAGCACC 62.513 60.000 0.00 0.00 40.11 5.01
581 1919 0.392706 AACACATCGTCTGCACAGGA 59.607 50.000 0.00 0.00 0.00 3.86
635 1974 1.153168 CGATTTGGCCCAGATCGGT 60.153 57.895 24.72 0.00 42.23 4.69
719 2058 0.465460 TCTCGCTTGGGCTTTGTTGT 60.465 50.000 0.00 0.00 36.09 3.32
770 2109 1.227999 CCGTCGGATGCACTGTTGTT 61.228 55.000 4.91 0.00 0.00 2.83
944 2290 4.348495 GGGGAGGGTGTGGGAGGA 62.348 72.222 0.00 0.00 0.00 3.71
961 2312 1.669115 CCTCGGCGATGCTATTGGG 60.669 63.158 11.27 0.76 0.00 4.12
1179 2549 1.134367 TCGTAACCGCTGATGGAGAAG 59.866 52.381 0.00 0.00 0.00 2.85
1224 2594 2.678934 CTCTCGTCCCCGGAACCA 60.679 66.667 0.73 0.00 33.95 3.67
1291 2676 1.351017 CCTGTAGAAAGCCCTCACCAA 59.649 52.381 0.00 0.00 0.00 3.67
1302 2687 3.788227 AGATGCCACAACCTGTAGAAA 57.212 42.857 0.00 0.00 0.00 2.52
1341 2726 3.202906 GCTGAACACCGGCTTAATCATA 58.797 45.455 0.00 0.00 43.80 2.15
1413 2798 2.996621 CTCGGTGGTCTTCATGAACTTC 59.003 50.000 3.38 0.00 32.49 3.01
1435 2833 2.595124 TCATTCCGCACATACGTCAT 57.405 45.000 0.00 0.00 0.00 3.06
1482 2889 8.772250 TGGATCTCTAGTGTTTCCTTGATAATT 58.228 33.333 13.74 0.00 0.00 1.40
1572 2985 3.287222 CCCTTGAACCTTGAAAGTCACA 58.713 45.455 0.00 0.00 0.00 3.58
1665 3078 2.444766 CTCTTTCTCCCCCATAGCCATT 59.555 50.000 0.00 0.00 0.00 3.16
1720 3140 7.765695 AGTGAAGAAATGCCTTGAAAATAGA 57.234 32.000 0.00 0.00 0.00 1.98
1749 3169 3.013921 GGAAGGCAATGAATCCGTGTAA 58.986 45.455 0.00 0.00 0.00 2.41
1873 3297 4.190001 ACATCAAGACTCTTGCATAGCAG 58.810 43.478 13.24 2.04 40.61 4.24
2037 6956 7.673180 ACAAATCAACAATGATGTCAGGAAAT 58.327 30.769 0.00 0.00 45.60 2.17
2217 7156 8.639761 AGGTCGCTATGTATCAAAAGTAACTAT 58.360 33.333 0.00 0.00 0.00 2.12
2294 7969 7.924412 TGGAGACATACATTTATAGAACGAACC 59.076 37.037 0.00 0.00 33.40 3.62
2381 8986 8.416329 CCAGCAATTAAGGTAAGCAGATAAAAT 58.584 33.333 0.00 0.00 0.00 1.82
2546 9767 2.997980 TCTTTGCTTGGTCTGACAACA 58.002 42.857 10.38 0.00 0.00 3.33
2627 9902 7.088905 CCCTCTGTGATGAAAATTCAGAAAAG 58.911 38.462 1.98 0.00 41.08 2.27
2646 9921 1.896465 GGGCTATGCTAGTACCCTCTG 59.104 57.143 0.00 0.00 37.59 3.35
2681 9956 3.533105 ATGGTATCGACGGGCGCA 61.533 61.111 10.83 0.00 40.61 6.09
2882 10169 1.705256 TCGTGCCACGACAAGAATAC 58.295 50.000 17.22 0.00 46.73 1.89
3142 11095 1.756024 CTAACCACCCACCGGAACA 59.244 57.895 9.46 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.