Multiple sequence alignment - TraesCS4A01G364900

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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 TraesCS4A01G364900 chr4A 100.000 7278 0 0 1 7278 638212514 638219791 0.000000e+00 13441.0
1 TraesCS4A01G364900 chr4A 84.268 1907 249 27 1408 3276 638170264 638172157 0.000000e+00 1812.0
2 TraesCS4A01G364900 chr4A 84.756 820 72 19 3411 4178 638172433 638173251 0.000000e+00 773.0
3 TraesCS4A01G364900 chr5B 96.854 3783 63 19 2524 6284 673690443 673686695 0.000000e+00 6276.0
4 TraesCS4A01G364900 chr5B 89.631 2247 155 46 311 2543 673692644 673690462 0.000000e+00 2787.0
5 TraesCS4A01G364900 chr5B 84.134 2874 356 48 1408 4189 673938982 673936117 0.000000e+00 2689.0
6 TraesCS4A01G364900 chr5B 87.789 909 107 4 3047 3952 597233416 597234323 0.000000e+00 1061.0
7 TraesCS4A01G364900 chr5B 92.636 679 47 1 4419 5097 673765005 673764330 0.000000e+00 974.0
8 TraesCS4A01G364900 chr5B 89.142 571 42 7 6714 7278 673683189 673682633 0.000000e+00 693.0
9 TraesCS4A01G364900 chr5B 82.735 724 107 12 1118 1833 597232697 597233410 4.790000e-176 628.0
10 TraesCS4A01G364900 chr5B 92.723 426 28 3 6315 6739 673683620 673683197 4.830000e-171 612.0
11 TraesCS4A01G364900 chr5B 92.148 433 30 2 3758 4189 673765531 673765102 6.240000e-170 608.0
12 TraesCS4A01G364900 chr5B 92.615 325 19 3 1 323 673757456 673757135 5.140000e-126 462.0
13 TraesCS4A01G364900 chr5B 87.855 387 26 9 5086 5469 673764290 673763922 1.120000e-117 435.0
14 TraesCS4A01G364900 chr5B 84.574 376 52 4 5827 6202 673763882 673763513 1.150000e-97 368.0
15 TraesCS4A01G364900 chr5B 92.632 95 7 0 5086 5180 347698540 347698634 3.540000e-28 137.0
16 TraesCS4A01G364900 chr5B 93.103 87 6 0 4187 4273 306447511 306447597 2.130000e-25 128.0
17 TraesCS4A01G364900 chr5D 96.554 3569 95 12 2736 6297 533643164 533639617 0.000000e+00 5884.0
18 TraesCS4A01G364900 chr5D 96.927 1855 44 7 888 2738 533645266 533643421 0.000000e+00 3097.0
19 TraesCS4A01G364900 chr5D 88.946 2515 216 39 923 3408 533666528 533664047 0.000000e+00 3048.0
20 TraesCS4A01G364900 chr5D 83.468 2474 314 48 1408 3797 533868309 533865847 0.000000e+00 2215.0
21 TraesCS4A01G364900 chr5D 94.346 902 29 12 1 894 533646190 533645303 0.000000e+00 1363.0
22 TraesCS4A01G364900 chr5D 90.120 830 66 10 4271 5097 533659927 533659111 0.000000e+00 1064.0
23 TraesCS4A01G364900 chr5D 95.526 380 17 0 6311 6690 533637041 533636662 6.240000e-170 608.0
24 TraesCS4A01G364900 chr5D 91.917 433 31 2 3758 4189 533660354 533659925 2.900000e-168 603.0
25 TraesCS4A01G364900 chr5D 94.509 346 18 1 6870 7214 533636298 533635953 3.870000e-147 532.0
26 TraesCS4A01G364900 chr5D 88.372 387 24 9 5086 5469 533659086 533658718 5.180000e-121 446.0
27 TraesCS4A01G364900 chr5D 85.372 376 52 2 5827 6202 533658678 533658306 3.180000e-103 387.0
28 TraesCS4A01G364900 chr5D 84.804 408 32 15 3812 4189 533865727 533865320 4.120000e-102 383.0
29 TraesCS4A01G364900 chr5D 78.316 392 64 11 6900 7278 207817786 207818169 4.390000e-57 233.0
30 TraesCS4A01G364900 chr5D 90.526 95 9 0 5086 5180 205118319 205118225 7.670000e-25 126.0
31 TraesCS4A01G364900 chr5D 90.805 87 8 0 4187 4273 270222345 270222431 4.610000e-22 117.0
32 TraesCS4A01G364900 chr5D 97.727 44 1 0 4368 4411 340516179 340516136 7.830000e-10 76.8
33 TraesCS4A01G364900 chr6D 90.327 1406 112 13 4271 5658 352906205 352904806 0.000000e+00 1821.0
34 TraesCS4A01G364900 chr6D 91.515 1261 87 8 2940 4189 352907454 352906203 0.000000e+00 1718.0
35 TraesCS4A01G364900 chr6D 88.926 1192 122 5 1722 2910 352908701 352907517 0.000000e+00 1461.0
36 TraesCS4A01G364900 chr6D 88.162 963 102 6 3231 4189 406560116 406559162 0.000000e+00 1136.0
37 TraesCS4A01G364900 chr6D 88.043 460 47 6 1281 1734 352909670 352909213 8.310000e-149 538.0
38 TraesCS4A01G364900 chr6D 86.978 407 47 5 5812 6215 352904862 352904459 3.100000e-123 453.0
39 TraesCS4A01G364900 chr6D 82.178 404 58 7 6885 7278 354066318 354066717 1.170000e-87 335.0
40 TraesCS4A01G364900 chr6D 100.000 28 0 0 6249 6276 352904432 352904405 1.300000e-02 52.8
41 TraesCS4A01G364900 chr4B 84.621 1450 185 27 1408 2832 14392137 14393573 0.000000e+00 1408.0
42 TraesCS4A01G364900 chr4B 85.319 1410 146 38 2831 4189 14393728 14395127 0.000000e+00 1400.0
43 TraesCS4A01G364900 chr4B 86.747 166 19 3 4462 4626 14395259 14395422 1.610000e-41 182.0
44 TraesCS4A01G364900 chr4B 100.000 42 0 0 4370 4411 564902383 564902342 2.180000e-10 78.7
45 TraesCS4A01G364900 chr6B 87.899 909 106 4 3047 3952 504290535 504291442 0.000000e+00 1066.0
46 TraesCS4A01G364900 chr6B 82.597 724 108 12 1118 1833 504289816 504290529 2.230000e-174 623.0
47 TraesCS4A01G364900 chr6B 84.270 356 36 13 4271 4626 687250701 687251036 5.440000e-86 329.0
48 TraesCS4A01G364900 chr6B 83.861 316 45 5 6956 7267 478750198 478750511 5.520000e-76 296.0
49 TraesCS4A01G364900 chr6B 94.340 53 2 1 4368 4419 20393387 20393439 6.050000e-11 80.5
50 TraesCS4A01G364900 chr3B 87.899 909 106 4 3047 3952 677306442 677305535 0.000000e+00 1066.0
51 TraesCS4A01G364900 chr3B 87.679 909 107 5 3047 3952 144789954 144790860 0.000000e+00 1053.0
52 TraesCS4A01G364900 chr3B 82.735 724 107 12 1118 1833 144789235 144789948 4.790000e-176 628.0
53 TraesCS4A01G364900 chr3B 82.735 724 107 12 1118 1833 677307161 677306448 4.790000e-176 628.0
54 TraesCS4A01G364900 chr3B 82.865 356 42 11 4271 4626 7080576 7080912 1.190000e-77 302.0
55 TraesCS4A01G364900 chr7A 87.740 677 76 5 3518 4189 94704707 94704033 0.000000e+00 784.0
56 TraesCS4A01G364900 chr7A 83.565 359 39 13 4271 4629 82160423 82160085 1.180000e-82 318.0
57 TraesCS4A01G364900 chr7A 81.818 374 49 11 4271 4644 94704035 94703681 5.520000e-76 296.0
58 TraesCS4A01G364900 chr7A 80.617 227 36 5 5958 6183 680390402 680390621 1.260000e-37 169.0
59 TraesCS4A01G364900 chr7A 86.792 106 12 2 4180 4285 720848302 720848405 4.610000e-22 117.0
60 TraesCS4A01G364900 chr7A 95.652 46 2 0 4369 4414 409259570 409259615 2.820000e-09 75.0
61 TraesCS4A01G364900 chr3D 84.012 344 51 3 6938 7278 453768240 453767898 1.960000e-85 327.0
62 TraesCS4A01G364900 chr1B 82.609 391 49 15 6900 7278 610025200 610025583 1.960000e-85 327.0
63 TraesCS4A01G364900 chr1B 91.579 95 7 1 4179 4273 618697571 618697664 5.930000e-26 130.0
64 TraesCS4A01G364900 chr1B 100.000 42 0 0 4370 4411 386519898 386519939 2.180000e-10 78.7
65 TraesCS4A01G364900 chr3A 82.216 388 60 4 6900 7278 595754188 595753801 7.040000e-85 326.0
66 TraesCS4A01G364900 chr7B 83.565 359 39 13 4271 4629 606781811 606781473 1.180000e-82 318.0
67 TraesCS4A01G364900 chr2A 80.905 398 53 12 6903 7278 724363770 724364166 7.140000e-75 292.0
68 TraesCS4A01G364900 chr2A 89.691 97 7 2 4180 4273 574962322 574962226 3.570000e-23 121.0
69 TraesCS4A01G364900 chr6A 80.049 411 62 10 6884 7278 530135087 530135493 3.320000e-73 287.0
70 TraesCS4A01G364900 chr7D 84.477 277 40 2 7005 7278 529038729 529038453 3.350000e-68 270.0
71 TraesCS4A01G364900 chr7D 79.888 358 57 10 4271 4626 603580660 603581004 1.570000e-61 248.0
72 TraesCS4A01G364900 chr7D 79.934 304 59 2 5879 6181 376955369 376955067 9.500000e-54 222.0
73 TraesCS4A01G364900 chr7D 79.412 306 51 8 5881 6183 588790177 588789881 9.570000e-49 206.0
74 TraesCS4A01G364900 chr7D 90.526 95 7 2 4184 4276 121937342 121937436 2.760000e-24 124.0
75 TraesCS4A01G364900 chr5A 92.632 95 7 0 5086 5180 244758073 244757979 3.540000e-28 137.0
76 TraesCS4A01G364900 chr5A 92.632 95 6 1 5086 5180 395056151 395056058 1.270000e-27 135.0
77 TraesCS4A01G364900 chr5A 93.103 87 6 0 4187 4273 359044347 359044433 2.130000e-25 128.0
78 TraesCS4A01G364900 chr2B 91.837 98 5 2 5086 5180 549724366 549724269 4.580000e-27 134.0
79 TraesCS4A01G364900 chr4D 97.778 45 1 0 4371 4415 287544124 287544168 2.180000e-10 78.7
80 TraesCS4A01G364900 chr4D 97.826 46 0 1 4367 4411 486185387 486185342 2.180000e-10 78.7


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 TraesCS4A01G364900 chr4A 638212514 638219791 7277 False 13441.000000 13441 100.000000 1 7278 1 chr4A.!!$F1 7277
1 TraesCS4A01G364900 chr4A 638170264 638173251 2987 False 1292.500000 1812 84.512000 1408 4178 2 chr4A.!!$F2 2770
2 TraesCS4A01G364900 chr5B 673936117 673938982 2865 True 2689.000000 2689 84.134000 1408 4189 1 chr5B.!!$R2 2781
3 TraesCS4A01G364900 chr5B 673682633 673692644 10011 True 2592.000000 6276 92.087500 311 7278 4 chr5B.!!$R3 6967
4 TraesCS4A01G364900 chr5B 597232697 597234323 1626 False 844.500000 1061 85.262000 1118 3952 2 chr5B.!!$F3 2834
5 TraesCS4A01G364900 chr5B 673763513 673765531 2018 True 596.250000 974 89.303250 3758 6202 4 chr5B.!!$R4 2444
6 TraesCS4A01G364900 chr5D 533635953 533646190 10237 True 2296.800000 5884 95.572400 1 7214 5 chr5D.!!$R3 7213
7 TraesCS4A01G364900 chr5D 533865320 533868309 2989 True 1299.000000 2215 84.136000 1408 4189 2 chr5D.!!$R5 2781
8 TraesCS4A01G364900 chr5D 533658306 533666528 8222 True 1109.600000 3048 88.945400 923 6202 5 chr5D.!!$R4 5279
9 TraesCS4A01G364900 chr6D 406559162 406560116 954 True 1136.000000 1136 88.162000 3231 4189 1 chr6D.!!$R1 958
10 TraesCS4A01G364900 chr6D 352904405 352909670 5265 True 1007.300000 1821 90.964833 1281 6276 6 chr6D.!!$R2 4995
11 TraesCS4A01G364900 chr4B 14392137 14395422 3285 False 996.666667 1408 85.562333 1408 4626 3 chr4B.!!$F1 3218
12 TraesCS4A01G364900 chr6B 504289816 504291442 1626 False 844.500000 1066 85.248000 1118 3952 2 chr6B.!!$F4 2834
13 TraesCS4A01G364900 chr3B 677305535 677307161 1626 True 847.000000 1066 85.317000 1118 3952 2 chr3B.!!$R1 2834
14 TraesCS4A01G364900 chr3B 144789235 144790860 1625 False 840.500000 1053 85.207000 1118 3952 2 chr3B.!!$F2 2834
15 TraesCS4A01G364900 chr7A 94703681 94704707 1026 True 540.000000 784 84.779000 3518 4644 2 chr7A.!!$R2 1126

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
278 280 1.435577 ACGAAAGTACGTGGCCAATC 58.564 50.000 7.24 0.0 46.88 2.67 F
1102 1173 0.537653 GAAGAAGCCCTACGAAGCCT 59.462 55.000 0.00 0.0 0.00 4.58 F
1556 1636 1.067283 ACATGAGCACGAACAGGAGAG 60.067 52.381 0.00 0.0 0.00 3.20 F
1720 1809 1.603802 ACCGCATGTGTTCTTCAAGTG 59.396 47.619 5.38 0.0 0.00 3.16 F
3247 4386 0.178767 TGCCTCACGCTGCATATTCT 59.821 50.000 0.00 0.0 38.78 2.40 F
5466 10350 0.392998 AGTTTTCTCGCCATCGCCAT 60.393 50.000 0.00 0.0 35.26 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1461 1.474077 AGGAATTGCAATTCGTCTGCC 59.526 47.619 34.37 24.68 44.43 4.85 R
2296 2937 3.660865 ACTTCTTTTATGAGGTCGCGTT 58.339 40.909 5.77 0.00 0.00 4.84 R
2769 3712 7.232534 ACATTTCACCAACAAAGGAAAGCTATA 59.767 33.333 0.00 0.00 33.28 1.31 R
3979 8741 6.073167 GGGCTGTTTCTCTTCAAAGTACTTAC 60.073 42.308 8.92 0.47 0.00 2.34 R
5469 10353 0.179137 CGCCTCAAGTATGACGCTGA 60.179 55.000 0.00 0.00 36.01 4.26 R
6754 14822 0.099968 GCTACCGTGTAGCATCGTGA 59.900 55.000 23.03 0.00 40.14 4.35 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
89 91 7.880105 ACTATAGACCTAGTTAAATACCGTGC 58.120 38.462 6.78 0.00 0.00 5.34
236 238 4.422073 TTCAAGTGATTATCCATCGGCT 57.578 40.909 0.00 0.00 34.08 5.52
278 280 1.435577 ACGAAAGTACGTGGCCAATC 58.564 50.000 7.24 0.00 46.88 2.67
290 292 5.189928 ACGTGGCCAATCTCATAAAATACA 58.810 37.500 7.24 0.00 0.00 2.29
291 293 5.296780 ACGTGGCCAATCTCATAAAATACAG 59.703 40.000 7.24 0.00 0.00 2.74
292 294 5.527214 CGTGGCCAATCTCATAAAATACAGA 59.473 40.000 7.24 0.00 0.00 3.41
293 295 6.205464 CGTGGCCAATCTCATAAAATACAGAT 59.795 38.462 7.24 0.00 0.00 2.90
294 296 7.255242 CGTGGCCAATCTCATAAAATACAGATT 60.255 37.037 7.24 0.00 36.26 2.40
389 392 4.017499 AGAACCACAATAATAGGTTGCCCT 60.017 41.667 0.15 0.00 45.15 5.19
456 459 3.148412 TGGTCATCCAACATGAACACAG 58.852 45.455 0.00 0.00 40.46 3.66
656 663 8.421249 TCATGAACACTTTTAAGAAATCCCAT 57.579 30.769 0.00 0.00 0.00 4.00
1067 1135 3.003763 GGCGAGGAGGTCCAAGGT 61.004 66.667 0.00 0.00 38.89 3.50
1102 1173 0.537653 GAAGAAGCCCTACGAAGCCT 59.462 55.000 0.00 0.00 0.00 4.58
1275 1352 1.204467 GTCTTGACTCTCTGGCAGGAG 59.796 57.143 23.16 23.16 40.67 3.69
1379 1458 7.175467 TCCTGTATGTGATGCCATAATTTGATC 59.825 37.037 0.00 0.00 0.00 2.92
1382 1461 3.569277 TGTGATGCCATAATTTGATCCCG 59.431 43.478 0.00 0.00 0.00 5.14
1472 1552 4.911514 TTTGGGCAACTCTAAGTTTGAC 57.088 40.909 0.00 0.00 36.03 3.18
1556 1636 1.067283 ACATGAGCACGAACAGGAGAG 60.067 52.381 0.00 0.00 0.00 3.20
1720 1809 1.603802 ACCGCATGTGTTCTTCAAGTG 59.396 47.619 5.38 0.00 0.00 3.16
1776 2389 9.124807 GTTGCTTATGGTGTTTTGTTACTTATC 57.875 33.333 0.00 0.00 0.00 1.75
2302 2943 1.646540 CTTTTGTCAGGCAACGCGA 59.353 52.632 15.93 0.00 46.39 5.87
2308 2949 2.434884 CAGGCAACGCGACCTCAT 60.435 61.111 15.93 0.00 46.39 2.90
2445 3086 4.282496 TGCTTTGAAGTTTCCCCTTAACA 58.718 39.130 0.00 0.00 0.00 2.41
2645 3329 3.558829 CCTGCAGCATATGACTACTGTTG 59.441 47.826 8.66 2.11 32.65 3.33
3154 4290 3.266772 TGCCCACTCATCTGTTTTATCCT 59.733 43.478 0.00 0.00 0.00 3.24
3247 4386 0.178767 TGCCTCACGCTGCATATTCT 59.821 50.000 0.00 0.00 38.78 2.40
3979 8741 8.142551 AGGCAAGTTACCTATTCTATTAACTCG 58.857 37.037 0.00 0.00 34.41 4.18
4157 8955 3.119137 GGCAAGAACTGTTGGTGAAAAGT 60.119 43.478 0.00 0.00 0.00 2.66
4253 9051 4.661993 TGTACTAAAGCTGCGACAATTG 57.338 40.909 3.24 3.24 0.00 2.32
4326 9124 5.489792 TTCTCTTGGAGCATGTACTTCTT 57.510 39.130 0.00 0.00 0.00 2.52
4773 9599 5.306678 TCTGTATTGCCATTTTCCAAGGTTT 59.693 36.000 0.00 0.00 0.00 3.27
4874 9701 2.105128 CGCCCGAGGACAGATGAC 59.895 66.667 0.00 0.00 0.00 3.06
5099 9977 4.339439 GCAAATGCAACAACAACAAAGT 57.661 36.364 0.00 0.00 41.59 2.66
5281 10162 5.514274 TGAAGGACAAACAAAGGAATCAC 57.486 39.130 0.00 0.00 0.00 3.06
5466 10350 0.392998 AGTTTTCTCGCCATCGCCAT 60.393 50.000 0.00 0.00 35.26 4.40
5469 10353 2.572095 TTTCTCGCCATCGCCATCGT 62.572 55.000 0.00 0.00 36.96 3.73
5537 10421 7.535489 AGCCGAAATATAGTTAACACACTTC 57.465 36.000 8.61 3.38 0.00 3.01
5591 10475 0.899720 CCGGCTTAAGGTGAGGTACA 59.100 55.000 4.29 0.00 0.00 2.90
5600 10484 2.047274 TGAGGTACAAGCGCCTGC 60.047 61.111 5.77 0.00 43.24 4.85
5669 10555 6.208204 AGCAAAGAACTTACGAGTAGGTTAGA 59.792 38.462 10.12 0.00 35.82 2.10
5729 10615 6.110707 GTGCAAGGTGCCTATTTAAGTAGTA 58.889 40.000 4.51 0.00 44.23 1.82
5730 10616 6.258068 GTGCAAGGTGCCTATTTAAGTAGTAG 59.742 42.308 4.51 0.00 44.23 2.57
5731 10617 6.070424 TGCAAGGTGCCTATTTAAGTAGTAGT 60.070 38.462 4.51 0.00 44.23 2.73
5768 10654 8.940397 TCTGATGAAAAAGGAGGTTATTCTTT 57.060 30.769 0.00 0.00 32.77 2.52
5769 10655 9.014297 TCTGATGAAAAAGGAGGTTATTCTTTC 57.986 33.333 0.00 0.00 31.25 2.62
5770 10656 8.704849 TGATGAAAAAGGAGGTTATTCTTTCA 57.295 30.769 0.00 0.00 36.19 2.69
5774 10660 9.762933 TGAAAAAGGAGGTTATTCTTTCATTTG 57.237 29.630 0.00 0.00 31.25 2.32
5775 10661 9.764363 GAAAAAGGAGGTTATTCTTTCATTTGT 57.236 29.630 0.00 0.00 31.25 2.83
5905 10796 0.462759 GGTCTGCCATGGAGTGTAGC 60.463 60.000 18.40 0.00 34.09 3.58
5989 10883 2.163211 GGATTTGAAGTCTGGCAAGCTC 59.837 50.000 0.00 0.00 0.00 4.09
6075 10975 0.914551 CGTTACCGTGAGCTGATTCG 59.085 55.000 0.00 0.00 0.00 3.34
6297 11199 4.733542 TGCCGCCTACCTTTGCCC 62.734 66.667 0.00 0.00 0.00 5.36
6299 11201 4.815108 CCGCCTACCTTTGCCCCC 62.815 72.222 0.00 0.00 0.00 5.40
6300 11202 4.041762 CGCCTACCTTTGCCCCCA 62.042 66.667 0.00 0.00 0.00 4.96
6301 11203 2.362503 GCCTACCTTTGCCCCCAC 60.363 66.667 0.00 0.00 0.00 4.61
6302 11204 2.919096 GCCTACCTTTGCCCCCACT 61.919 63.158 0.00 0.00 0.00 4.00
6303 11205 1.568118 GCCTACCTTTGCCCCCACTA 61.568 60.000 0.00 0.00 0.00 2.74
6304 11206 0.255033 CCTACCTTTGCCCCCACTAC 59.745 60.000 0.00 0.00 0.00 2.73
6305 11207 1.286248 CTACCTTTGCCCCCACTACT 58.714 55.000 0.00 0.00 0.00 2.57
6306 11208 2.474112 CTACCTTTGCCCCCACTACTA 58.526 52.381 0.00 0.00 0.00 1.82
6307 11209 0.989602 ACCTTTGCCCCCACTACTAC 59.010 55.000 0.00 0.00 0.00 2.73
6308 11210 1.286248 CCTTTGCCCCCACTACTACT 58.714 55.000 0.00 0.00 0.00 2.57
6309 11211 1.209747 CCTTTGCCCCCACTACTACTC 59.790 57.143 0.00 0.00 0.00 2.59
6402 14437 7.727331 TCTTTTACAAAGCCATTTCCATTTG 57.273 32.000 0.00 0.00 38.35 2.32
6455 14490 2.791383 TTGGCACATGCAAGTAACAC 57.209 45.000 6.15 0.00 44.36 3.32
6506 14541 1.473258 TCGCTGCCAATTATTGCCTT 58.527 45.000 0.00 0.00 0.00 4.35
6530 14565 6.959639 ACAATATATGGCCAAACTACCTTG 57.040 37.500 10.96 10.09 0.00 3.61
6664 14699 2.657237 GTGGAGTCGTGGGACCAG 59.343 66.667 0.00 0.00 44.54 4.00
6684 14719 4.441913 CCAGCACAATGTGGAAGAAAAACT 60.442 41.667 15.78 0.00 35.67 2.66
6693 14728 4.127907 GTGGAAGAAAAACTCCGAGAAGT 58.872 43.478 1.33 0.00 0.00 3.01
6707 14742 1.414550 GAGAAGTAGGCATGACTCCCC 59.585 57.143 2.95 0.00 0.00 4.81
6708 14743 1.204146 GAAGTAGGCATGACTCCCCA 58.796 55.000 2.95 0.00 0.00 4.96
6710 14745 0.339859 AGTAGGCATGACTCCCCAGA 59.660 55.000 2.95 0.00 0.00 3.86
6711 14746 0.755686 GTAGGCATGACTCCCCAGAG 59.244 60.000 2.95 0.00 46.36 3.35
6741 14809 5.788450 AGTGAGTTCAAGTCATAGAACCAG 58.212 41.667 0.00 0.00 43.89 4.00
6787 14855 7.849515 GCTACACGGTAGCATTAAAATAGTTTC 59.150 37.037 23.03 0.00 40.14 2.78
6789 14857 7.748847 ACACGGTAGCATTAAAATAGTTTCTG 58.251 34.615 0.00 0.00 0.00 3.02
6805 14873 6.566197 AGTTTCTGTTCAAAATAGGAGCAG 57.434 37.500 0.00 0.00 42.72 4.24
6958 15183 6.596497 GTCTCTATATTTTTCGTCCAAACCCA 59.404 38.462 0.00 0.00 0.00 4.51
6964 15189 1.065647 TTCGTCCAAACCCATACCCA 58.934 50.000 0.00 0.00 0.00 4.51
6986 15211 6.220201 CCATACATCGGGTTTCAAACTTTTT 58.780 36.000 0.00 0.00 0.00 1.94
6988 15213 4.356289 ACATCGGGTTTCAAACTTTTTCG 58.644 39.130 0.00 0.00 0.00 3.46
6989 15214 3.423996 TCGGGTTTCAAACTTTTTCGG 57.576 42.857 0.00 0.00 0.00 4.30
7089 15314 7.599998 ACTTCACCATGTATTTTTCAGCATTTC 59.400 33.333 0.00 0.00 0.00 2.17
7184 15409 8.009974 GTCAGCACATATATTTCACGATTTACC 58.990 37.037 0.00 0.00 0.00 2.85
7232 15457 9.063615 GGTATTATTTCGGAAGTGGATAACAAT 57.936 33.333 0.00 0.00 0.00 2.71
7257 15482 4.878397 AGCATGAACTAGATGGCACTAAAC 59.122 41.667 0.00 0.00 0.00 2.01
7259 15484 5.123820 GCATGAACTAGATGGCACTAAACAA 59.876 40.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 4.334481 GCAATGCACGGTATTTAACTAGGT 59.666 41.667 0.00 0.00 0.00 3.08
236 238 6.309494 CGTACTATCGTTGAAGTCAATGGAAA 59.691 38.462 12.21 0.00 41.80 3.13
278 280 7.375280 CGAGCAAAGCAATCTGTATTTTATGAG 59.625 37.037 0.00 0.00 0.00 2.90
389 392 5.279006 GGATGACCATGAGCTTATTAGTCGA 60.279 44.000 11.60 0.00 35.97 4.20
1155 1226 4.201679 CGCTCGTCCATGGCGGTA 62.202 66.667 22.59 8.60 44.32 4.02
1237 1308 1.801178 GACTCCGGTTTCAGCTCAAAG 59.199 52.381 0.00 0.00 0.00 2.77
1275 1352 2.026522 CTCCCTCGACTCGGACATC 58.973 63.158 0.00 0.00 0.00 3.06
1379 1458 1.656818 ATTGCAATTCGTCTGCCGGG 61.657 55.000 5.99 0.00 39.13 5.73
1382 1461 1.474077 AGGAATTGCAATTCGTCTGCC 59.526 47.619 34.37 24.68 44.43 4.85
1556 1636 3.887621 TGATAGTGACACTTACCTGCC 57.112 47.619 14.50 0.00 0.00 4.85
2296 2937 3.660865 ACTTCTTTTATGAGGTCGCGTT 58.339 40.909 5.77 0.00 0.00 4.84
2302 2943 7.123547 TCCAACAACAAACTTCTTTTATGAGGT 59.876 33.333 0.00 0.00 0.00 3.85
2769 3712 7.232534 ACATTTCACCAACAAAGGAAAGCTATA 59.767 33.333 0.00 0.00 33.28 1.31
3979 8741 6.073167 GGGCTGTTTCTCTTCAAAGTACTTAC 60.073 42.308 8.92 0.47 0.00 2.34
4253 9051 8.214364 AGTTAAATACTCCCTCAGATCCAAATC 58.786 37.037 0.00 0.00 28.23 2.17
4326 9124 7.791766 AGAATAAATGTAGATCTCTTGAGGGGA 59.208 37.037 0.00 0.00 0.00 4.81
4874 9701 2.034879 AAAGGCGTGCTCATCACCG 61.035 57.895 0.00 0.00 42.69 4.94
5099 9977 4.445735 CCCTACTTGTTTGGGACTGAAAGA 60.446 45.833 5.88 0.00 42.76 2.52
5281 10162 7.801547 ACAAATTCAAAAGAATATCAGCGTG 57.198 32.000 0.00 0.00 0.00 5.34
5466 10350 1.132453 CCTCAAGTATGACGCTGACGA 59.868 52.381 0.00 0.00 43.93 4.20
5469 10353 0.179137 CGCCTCAAGTATGACGCTGA 60.179 55.000 0.00 0.00 36.01 4.26
5729 10615 9.688592 CTTTTTCATCAGAGAAAGCAATAAACT 57.311 29.630 0.00 0.00 38.58 2.66
5730 10616 8.919661 CCTTTTTCATCAGAGAAAGCAATAAAC 58.080 33.333 3.71 0.00 41.92 2.01
5731 10617 8.859090 TCCTTTTTCATCAGAGAAAGCAATAAA 58.141 29.630 3.71 0.00 41.92 1.40
5989 10883 4.025401 GTGCCAAACCTCGCCACG 62.025 66.667 0.00 0.00 0.00 4.94
6075 10975 0.960364 ACCCACGACAATGACATGCC 60.960 55.000 0.00 0.00 0.00 4.40
6285 11187 0.255033 GTAGTGGGGGCAAAGGTAGG 59.745 60.000 0.00 0.00 0.00 3.18
6297 11199 1.264557 CAGATCGCGAGTAGTAGTGGG 59.735 57.143 16.66 0.00 0.00 4.61
6298 11200 1.264557 CCAGATCGCGAGTAGTAGTGG 59.735 57.143 16.66 9.14 0.00 4.00
6299 11201 2.210961 TCCAGATCGCGAGTAGTAGTG 58.789 52.381 16.66 3.68 0.00 2.74
6300 11202 2.616634 TCCAGATCGCGAGTAGTAGT 57.383 50.000 16.66 0.00 0.00 2.73
6301 11203 3.965292 TTTCCAGATCGCGAGTAGTAG 57.035 47.619 16.66 0.82 0.00 2.57
6302 11204 3.181493 GGTTTTCCAGATCGCGAGTAGTA 60.181 47.826 16.66 0.00 40.31 1.82
6303 11205 2.416972 GGTTTTCCAGATCGCGAGTAGT 60.417 50.000 16.66 0.00 40.31 2.73
6304 11206 2.194271 GGTTTTCCAGATCGCGAGTAG 58.806 52.381 16.66 6.20 40.31 2.57
6305 11207 1.546923 TGGTTTTCCAGATCGCGAGTA 59.453 47.619 16.66 0.00 46.22 2.59
6306 11208 0.320374 TGGTTTTCCAGATCGCGAGT 59.680 50.000 16.66 0.37 46.22 4.18
6307 11209 3.137484 TGGTTTTCCAGATCGCGAG 57.863 52.632 16.66 0.00 46.22 5.03
6455 14490 5.551233 TCTTGTGAGTGATTTTGAGGTAGG 58.449 41.667 0.00 0.00 0.00 3.18
6506 14541 7.579105 ACAAGGTAGTTTGGCCATATATTGTA 58.421 34.615 6.09 0.00 32.32 2.41
6664 14699 4.051237 GGAGTTTTTCTTCCACATTGTGC 58.949 43.478 11.41 0.00 31.34 4.57
6684 14719 2.025155 GAGTCATGCCTACTTCTCGGA 58.975 52.381 0.00 0.00 0.00 4.55
6693 14728 0.636647 TCTCTGGGGAGTCATGCCTA 59.363 55.000 0.00 0.00 40.29 3.93
6707 14742 5.841810 ACTTGAACTCACTCTTCTTCTCTG 58.158 41.667 0.00 0.00 0.00 3.35
6708 14743 5.596361 TGACTTGAACTCACTCTTCTTCTCT 59.404 40.000 0.00 0.00 0.00 3.10
6710 14745 5.860941 TGACTTGAACTCACTCTTCTTCT 57.139 39.130 0.00 0.00 0.00 2.85
6711 14746 7.598278 TCTATGACTTGAACTCACTCTTCTTC 58.402 38.462 0.00 0.00 0.00 2.87
6741 14809 2.223340 GCATCGTGACATGGAAACCATC 60.223 50.000 0.00 0.00 43.15 3.51
6754 14822 0.099968 GCTACCGTGTAGCATCGTGA 59.900 55.000 23.03 0.00 40.14 4.35
6781 14849 6.149474 GCTGCTCCTATTTTGAACAGAAACTA 59.851 38.462 0.00 0.00 29.42 2.24
6787 14855 2.424956 GGGCTGCTCCTATTTTGAACAG 59.575 50.000 0.00 0.00 34.39 3.16
6789 14857 2.446435 TGGGCTGCTCCTATTTTGAAC 58.554 47.619 0.00 0.00 34.39 3.18
6828 14896 2.438614 CTCGGCCCTCTCACTCGA 60.439 66.667 0.00 0.00 0.00 4.04
6830 14898 2.419739 GGTCTCGGCCCTCTCACTC 61.420 68.421 0.00 0.00 0.00 3.51
6861 14929 2.746277 CACTAGTGCGGGGGTTGC 60.746 66.667 10.54 0.00 0.00 4.17
6922 15147 6.402456 AAAATATAGAGACGGGTACAGGTC 57.598 41.667 7.29 7.29 34.26 3.85
6964 15189 6.146898 CGAAAAAGTTTGAAACCCGATGTAT 58.853 36.000 4.14 0.00 0.00 2.29
7089 15314 9.891828 ATGTTAAAATGTTGTGCATATATACGG 57.108 29.630 0.00 0.00 36.67 4.02
7099 15324 9.619316 TGAAGTATACATGTTAAAATGTTGTGC 57.381 29.630 16.38 9.50 41.09 4.57
7184 15409 5.200454 CCATTCTTCTTATTCAATCGCACG 58.800 41.667 0.00 0.00 0.00 5.34
7216 15441 5.527214 TCATGCTTATTGTTATCCACTTCCG 59.473 40.000 0.00 0.00 0.00 4.30
7217 15442 6.942532 TCATGCTTATTGTTATCCACTTCC 57.057 37.500 0.00 0.00 0.00 3.46
7232 15457 4.760530 AGTGCCATCTAGTTCATGCTTA 57.239 40.909 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.