Multiple sequence alignment - TraesCS3D01G512200

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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 TraesCS3D01G512200 chr3D 100.000 2875 0 0 1 2875 596887543 596884669 0.000000e+00 5310.0
1 TraesCS3D01G512200 chr3D 87.593 403 47 1 904 1306 596896314 596896713 5.610000e-127 464.0
2 TraesCS3D01G512200 chr3D 92.982 114 8 0 753 866 596896105 596896218 1.770000e-37 167.0
3 TraesCS3D01G512200 chr3B 90.223 1033 76 13 1 1028 803002081 803003093 0.000000e+00 1325.0
4 TraesCS3D01G512200 chr3B 90.044 683 50 8 676 1345 802902959 802902282 0.000000e+00 869.0
5 TraesCS3D01G512200 chr3B 87.231 697 59 18 2182 2875 801152464 801153133 0.000000e+00 767.0
6 TraesCS3D01G512200 chr3B 90.466 472 36 5 1475 1937 802902282 802901811 5.260000e-172 614.0
7 TraesCS3D01G512200 chr3B 90.476 462 39 2 1475 1931 802921206 802920745 3.170000e-169 604.0
8 TraesCS3D01G512200 chr3B 89.831 413 39 3 933 1345 802921615 802921206 7.060000e-146 527.0
9 TraesCS3D01G512200 chr3B 93.617 329 18 2 1611 1937 803003112 803003439 3.330000e-134 488.0
10 TraesCS3D01G512200 chr3B 94.408 304 16 1 1963 2266 803003431 803003733 1.560000e-127 466.0
11 TraesCS3D01G512200 chr3B 84.696 477 38 6 671 1141 802996801 802996354 7.310000e-121 444.0
12 TraesCS3D01G512200 chr3B 80.727 550 85 10 325 866 802922255 802921719 2.670000e-110 409.0
13 TraesCS3D01G512200 chr3B 88.612 281 25 5 894 1173 802964987 802965261 4.590000e-88 335.0
14 TraesCS3D01G512200 chr3B 88.583 254 22 5 921 1174 802993962 802993716 4.660000e-78 302.0
15 TraesCS3D01G512200 chr3B 84.984 313 23 11 2319 2630 803003733 803004022 2.170000e-76 296.0
16 TraesCS3D01G512200 chr3B 92.195 205 13 1 1736 1937 802993265 802993061 1.300000e-73 287.0
17 TraesCS3D01G512200 chr3B 88.412 233 25 1 1475 1707 802993491 802993261 2.180000e-71 279.0
18 TraesCS3D01G512200 chr3B 90.099 202 16 2 1736 1934 802965266 802965466 2.840000e-65 259.0
19 TraesCS3D01G512200 chr3B 86.404 228 31 0 2640 2867 225815216 225815443 1.710000e-62 250.0
20 TraesCS3D01G512200 chr3B 86.404 228 31 0 2640 2867 225829415 225829642 1.710000e-62 250.0
21 TraesCS3D01G512200 chr3B 92.121 165 7 3 1187 1345 802993655 802993491 8.010000e-56 228.0
22 TraesCS3D01G512200 chr3B 84.348 230 21 7 671 890 802932698 802932922 8.070000e-51 211.0
23 TraesCS3D01G512200 chr3B 80.153 262 49 2 1058 1319 775562777 775562519 2.920000e-45 193.0
24 TraesCS3D01G512200 chr3B 92.982 114 8 0 985 1098 802934192 802934305 1.770000e-37 167.0
25 TraesCS3D01G512200 chr3B 87.805 123 10 3 1354 1472 155822107 155821986 3.860000e-29 139.0
26 TraesCS3D01G512200 chr6D 87.045 247 29 2 2628 2872 13155324 13155569 2.820000e-70 276.0
27 TraesCS3D01G512200 chr6B 87.029 239 30 1 2634 2872 23604842 23604605 4.720000e-68 268.0
28 TraesCS3D01G512200 chr1D 87.225 227 29 0 2640 2866 378551682 378551908 2.840000e-65 259.0
29 TraesCS3D01G512200 chr5D 86.695 233 27 4 2635 2866 2795854 2795625 3.680000e-64 255.0
30 TraesCS3D01G512200 chr2D 86.383 235 31 1 2640 2873 378729391 378729157 3.680000e-64 255.0
31 TraesCS3D01G512200 chr2D 86.017 236 31 1 2633 2866 78385624 78385389 4.760000e-63 252.0
32 TraesCS3D01G512200 chr7B 92.029 138 11 0 2466 2603 744298805 744298668 8.130000e-46 195.0
33 TraesCS3D01G512200 chr7B 87.681 138 16 1 2466 2603 743626106 743626242 2.970000e-35 159.0
34 TraesCS3D01G512200 chr7B 89.815 108 11 0 2496 2603 743628349 743628456 3.860000e-29 139.0
35 TraesCS3D01G512200 chr7D 79.554 269 41 7 1057 1315 46523595 46523859 2.280000e-41 180.0
36 TraesCS3D01G512200 chr3A 78.626 262 53 2 1058 1319 715594803 715594545 1.370000e-38 171.0
37 TraesCS3D01G512200 chr7A 86.713 143 10 5 2469 2603 735848124 735847983 1.780000e-32 150.0
38 TraesCS3D01G512200 chr7A 87.500 128 16 0 2466 2593 736335867 736335740 6.420000e-32 148.0
39 TraesCS3D01G512200 chr7A 87.200 125 11 3 1355 1476 238809999 238809877 1.390000e-28 137.0
40 TraesCS3D01G512200 chr2A 87.500 120 12 1 1355 1471 65156355 65156474 5.000000e-28 135.0
41 TraesCS3D01G512200 chr1A 86.066 122 13 4 1354 1473 23853184 23853065 8.360000e-26 128.0
42 TraesCS3D01G512200 chr4A 83.471 121 20 0 1117 1237 659460305 659460425 2.340000e-21 113.0
43 TraesCS3D01G512200 chr4A 83.471 121 20 0 1117 1237 659527741 659527861 2.340000e-21 113.0
44 TraesCS3D01G512200 chr6A 81.481 108 12 8 1365 1466 523245910 523246015 6.600000e-12 82.4


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 TraesCS3D01G512200 chr3D 596884669 596887543 2874 True 5310.000000 5310 100.000000 1 2875 1 chr3D.!!$R1 2874
1 TraesCS3D01G512200 chr3D 596896105 596896713 608 False 315.500000 464 90.287500 753 1306 2 chr3D.!!$F1 553
2 TraesCS3D01G512200 chr3B 801152464 801153133 669 False 767.000000 767 87.231000 2182 2875 1 chr3B.!!$F3 693
3 TraesCS3D01G512200 chr3B 802901811 802902959 1148 True 741.500000 869 90.255000 676 1937 2 chr3B.!!$R3 1261
4 TraesCS3D01G512200 chr3B 803002081 803004022 1941 False 643.750000 1325 90.808000 1 2630 4 chr3B.!!$F6 2629
5 TraesCS3D01G512200 chr3B 802920745 802922255 1510 True 513.333333 604 87.011333 325 1931 3 chr3B.!!$R4 1606
6 TraesCS3D01G512200 chr3B 802993061 802996801 3740 True 308.000000 444 89.201400 671 1937 5 chr3B.!!$R5 1266

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
306 307 0.179078 TGTCGGGGTAACACACACAC 60.179 55.0 0.0 0.0 44.36 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2261 5009 0.032316 AGATCTCTGCCCTGCTCTGA 60.032 55.0 0.0 0.0 0.0 3.27 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
37 38 2.931969 GCACTTTGCAAGAAAAGCAGTT 59.068 40.909 0.00 0.00 44.26 3.16
56 57 1.323271 TGCTAGAGTCCCTTGCCTCG 61.323 60.000 0.00 0.00 41.87 4.63
60 61 1.056660 AGAGTCCCTTGCCTCGAAAA 58.943 50.000 0.00 0.00 32.88 2.29
79 80 0.537653 AGGAAAAGACGCTAGAGGCC 59.462 55.000 0.00 0.00 37.74 5.19
80 81 0.249398 GGAAAAGACGCTAGAGGCCA 59.751 55.000 5.01 0.00 37.74 5.36
83 84 2.317530 AAAGACGCTAGAGGCCAATC 57.682 50.000 5.01 0.00 37.74 2.67
109 110 4.222145 TCAATAACCGTGAAGCTCCTAGTT 59.778 41.667 0.00 0.00 0.00 2.24
117 118 0.322008 AAGCTCCTAGTTGCCTGTGC 60.322 55.000 0.00 0.00 38.26 4.57
127 128 3.127533 GCCTGTGCGTTGGCCTAG 61.128 66.667 3.32 0.00 43.11 3.02
140 141 2.758130 TGGCCTAGATGTCCACACATA 58.242 47.619 3.32 0.00 43.79 2.29
279 280 3.644966 ATCCTATTTGTCGCCCTTTGA 57.355 42.857 0.00 0.00 0.00 2.69
280 281 2.985896 TCCTATTTGTCGCCCTTTGAG 58.014 47.619 0.00 0.00 0.00 3.02
293 294 3.733337 CCCTTTGAGATAAGATGTCGGG 58.267 50.000 0.00 0.00 0.00 5.14
306 307 0.179078 TGTCGGGGTAACACACACAC 60.179 55.000 0.00 0.00 44.36 3.82
337 338 1.748879 GCTGACCCAAATAGCGCCA 60.749 57.895 2.29 0.00 0.00 5.69
381 382 0.313672 GCATTTCCTGTTTGCACGGA 59.686 50.000 0.00 0.00 36.40 4.69
401 402 2.166907 TTTGGGAAGGCTTTGTGGAA 57.833 45.000 0.00 0.00 0.00 3.53
408 409 0.752658 AGGCTTTGTGGAAGGTTTGC 59.247 50.000 0.00 0.00 35.82 3.68
414 415 0.759959 TGTGGAAGGTTTGCCGAGTA 59.240 50.000 0.00 0.00 40.50 2.59
453 454 9.463443 CTAGTAAATTCTTGTTTGGGTTTTCAG 57.537 33.333 0.00 0.00 0.00 3.02
457 458 3.855858 TCTTGTTTGGGTTTTCAGTTGC 58.144 40.909 0.00 0.00 0.00 4.17
469 470 6.207614 GGGTTTTCAGTTGCTTTCTCTCTTAT 59.792 38.462 0.00 0.00 0.00 1.73
470 471 7.390718 GGGTTTTCAGTTGCTTTCTCTCTTATA 59.609 37.037 0.00 0.00 0.00 0.98
583 584 8.379902 GTTCACTATTTTCACACAAACTTTTGG 58.620 33.333 6.65 0.00 42.34 3.28
587 588 9.665719 ACTATTTTCACACAAACTTTTGGAAAT 57.334 25.926 6.65 1.26 42.34 2.17
591 592 9.455847 TTTTCACACAAACTTTTGGAAATTTTG 57.544 25.926 12.00 12.00 42.34 2.44
592 593 7.969536 TCACACAAACTTTTGGAAATTTTGA 57.030 28.000 17.47 0.01 42.34 2.69
629 633 5.096443 AGTTTTCAAAATGTTTGGCTCCA 57.904 34.783 1.15 0.00 0.00 3.86
640 644 2.024176 TTGGCTCCAGAGTAACTCCA 57.976 50.000 0.00 0.00 0.00 3.86
647 651 4.177026 CTCCAGAGTAACTCCATTGAACG 58.823 47.826 0.00 0.00 0.00 3.95
686 690 1.891150 GGCTTGATTATCCCATGGCTG 59.109 52.381 6.09 0.00 33.47 4.85
711 715 2.290916 TCATCTCGAGGCGCTTACTTAG 59.709 50.000 13.56 0.00 0.00 2.18
797 807 4.280677 CAGCCAAGAACAAGTTTATTGGGA 59.719 41.667 21.93 0.00 38.79 4.37
900 953 6.287589 TCTCACCTTTCAAGAGAAGATACC 57.712 41.667 0.00 0.00 35.62 2.73
930 1009 3.074538 AGCATCCCCTGACCCATATAAAC 59.925 47.826 0.00 0.00 0.00 2.01
941 1020 4.113085 ACCCATATAAACAGTACCACCCA 58.887 43.478 0.00 0.00 0.00 4.51
1101 3785 1.103803 TACCTTACGAGCTGCTCCTG 58.896 55.000 22.97 12.91 0.00 3.86
1149 3833 2.281070 CTGCTCACGCACAACCCT 60.281 61.111 0.00 0.00 42.25 4.34
1176 3860 2.363795 CTGGTCCCCGTGCTCCTA 60.364 66.667 0.00 0.00 0.00 2.94
1185 3869 2.494918 GTGCTCCTACACGGCGAT 59.505 61.111 16.62 3.31 0.00 4.58
1188 3872 0.384309 TGCTCCTACACGGCGATAAG 59.616 55.000 16.62 7.04 0.00 1.73
1337 4075 5.046950 AGGTACCATCTCTTGTGAACTTCTC 60.047 44.000 15.94 0.00 0.00 2.87
1344 4082 7.388776 CCATCTCTTGTGAACTTCTCAACAATA 59.611 37.037 2.75 0.00 35.22 1.90
1345 4083 7.715265 TCTCTTGTGAACTTCTCAACAATAC 57.285 36.000 2.75 0.00 35.22 1.89
1346 4084 7.500992 TCTCTTGTGAACTTCTCAACAATACT 58.499 34.615 2.75 0.00 35.22 2.12
1347 4085 7.653713 TCTCTTGTGAACTTCTCAACAATACTC 59.346 37.037 2.75 0.00 35.22 2.59
1348 4086 7.272244 TCTTGTGAACTTCTCAACAATACTCA 58.728 34.615 2.75 0.00 35.22 3.41
1349 4087 6.844696 TGTGAACTTCTCAACAATACTCAC 57.155 37.500 0.00 0.00 35.22 3.51
1350 4088 6.345298 TGTGAACTTCTCAACAATACTCACA 58.655 36.000 0.00 0.00 38.56 3.58
1351 4089 6.479990 TGTGAACTTCTCAACAATACTCACAG 59.520 38.462 0.00 0.00 36.61 3.66
1352 4090 6.701841 GTGAACTTCTCAACAATACTCACAGA 59.298 38.462 0.00 0.00 35.22 3.41
1353 4091 7.386299 GTGAACTTCTCAACAATACTCACAGAT 59.614 37.037 0.00 0.00 35.22 2.90
1354 4092 7.386025 TGAACTTCTCAACAATACTCACAGATG 59.614 37.037 0.00 0.00 0.00 2.90
1355 4093 6.997655 ACTTCTCAACAATACTCACAGATGA 58.002 36.000 0.00 0.00 0.00 2.92
1356 4094 7.445121 ACTTCTCAACAATACTCACAGATGAA 58.555 34.615 0.00 0.00 33.30 2.57
1357 4095 8.099537 ACTTCTCAACAATACTCACAGATGAAT 58.900 33.333 0.00 0.00 33.30 2.57
1358 4096 8.484641 TTCTCAACAATACTCACAGATGAATC 57.515 34.615 0.00 0.00 33.30 2.52
1359 4097 7.845037 TCTCAACAATACTCACAGATGAATCT 58.155 34.615 0.00 0.00 37.72 2.40
1360 4098 8.971073 TCTCAACAATACTCACAGATGAATCTA 58.029 33.333 0.00 0.00 34.85 1.98
1361 4099 9.247126 CTCAACAATACTCACAGATGAATCTAG 57.753 37.037 0.00 0.00 34.85 2.43
1362 4100 8.753133 TCAACAATACTCACAGATGAATCTAGT 58.247 33.333 0.00 0.00 34.85 2.57
1464 4202 7.589574 AAAAATAATACGCACATTTGGGAAC 57.410 32.000 2.56 0.00 39.02 3.62
1465 4203 2.911819 AATACGCACATTTGGGAACG 57.088 45.000 2.56 0.00 39.02 3.95
1466 4204 1.091537 ATACGCACATTTGGGAACGG 58.908 50.000 2.56 0.00 39.02 4.44
1467 4205 0.035036 TACGCACATTTGGGAACGGA 59.965 50.000 2.56 0.00 39.02 4.69
1468 4206 1.234615 ACGCACATTTGGGAACGGAG 61.235 55.000 2.56 0.00 39.02 4.63
1469 4207 1.883021 GCACATTTGGGAACGGAGG 59.117 57.895 0.00 0.00 0.00 4.30
1470 4208 1.595093 GCACATTTGGGAACGGAGGG 61.595 60.000 0.00 0.00 0.00 4.30
1471 4209 0.037590 CACATTTGGGAACGGAGGGA 59.962 55.000 0.00 0.00 0.00 4.20
1472 4210 0.328258 ACATTTGGGAACGGAGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
1473 4211 1.032114 CATTTGGGAACGGAGGGAGC 61.032 60.000 0.00 0.00 0.00 4.70
1538 4276 4.089361 TCTGGATGTCGATATGTATGGCT 58.911 43.478 0.00 0.00 0.00 4.75
1563 4304 2.530701 GTGACAAGGAAGAGGAGGAGA 58.469 52.381 0.00 0.00 0.00 3.71
1584 4325 3.864789 ACTTCTTGAAGGAAGCCAAGA 57.135 42.857 13.97 0.00 44.51 3.02
1622 4364 2.361737 GGGCAGCTCAAGGGGAAC 60.362 66.667 0.00 0.00 0.00 3.62
1652 4394 2.044946 GGCGACTCCATTGGCCTT 60.045 61.111 3.32 0.00 42.29 4.35
1667 4409 0.677731 GCCTTGTGGACATAGCTGCA 60.678 55.000 1.02 0.00 34.57 4.41
1688 4430 2.269241 GGGTTAGCTCGCTGGCTT 59.731 61.111 0.85 0.00 42.97 4.35
1715 4457 0.033405 TCGAAGAGATCTCCGGGGTT 60.033 55.000 19.30 6.49 0.00 4.11
1727 4469 3.028850 CTCCGGGGTTAATCTACTCACA 58.971 50.000 0.00 0.00 0.00 3.58
1778 4520 1.148310 CGAAAGAATATGCCGGCGAT 58.852 50.000 23.90 18.31 0.00 4.58
1827 4569 0.036388 GGATGAACTGGTCGCCAAGA 60.036 55.000 0.13 0.00 30.80 3.02
1937 4684 8.724229 CATGAATCAATCGTATGGACATGTTAT 58.276 33.333 0.00 0.51 0.00 1.89
1938 4685 8.675705 TGAATCAATCGTATGGACATGTTATT 57.324 30.769 0.00 0.00 0.00 1.40
1939 4686 9.119418 TGAATCAATCGTATGGACATGTTATTT 57.881 29.630 0.00 0.00 0.00 1.40
1940 4687 9.950680 GAATCAATCGTATGGACATGTTATTTT 57.049 29.630 0.00 0.00 0.00 1.82
1968 4715 3.430473 TTTTTGCGGGGAGACATGT 57.570 47.368 0.00 0.00 0.00 3.21
1969 4716 1.698506 TTTTTGCGGGGAGACATGTT 58.301 45.000 0.00 0.00 0.00 2.71
1970 4717 2.570415 TTTTGCGGGGAGACATGTTA 57.430 45.000 0.00 0.00 0.00 2.41
1995 4742 3.589951 ATGATCATGGTTTCCTGGGAG 57.410 47.619 7.59 0.00 0.00 4.30
2078 4825 3.595173 GGTGTAATTCCCATTTGGTTGC 58.405 45.455 0.00 0.00 34.77 4.17
2104 4851 5.938438 AACTTGTCTTGCTTTCTCAGATC 57.062 39.130 0.00 0.00 0.00 2.75
2127 4874 2.766263 AGAAATCGGTAGAGACATGGCA 59.234 45.455 0.00 0.00 0.00 4.92
2146 4893 7.816031 ACATGGCAGATTGTATTTCTTTTTCAG 59.184 33.333 0.00 0.00 0.00 3.02
2148 4895 8.402798 TGGCAGATTGTATTTCTTTTTCAGTA 57.597 30.769 0.00 0.00 0.00 2.74
2150 4897 8.296713 GGCAGATTGTATTTCTTTTTCAGTACA 58.703 33.333 0.00 0.00 0.00 2.90
2173 4920 1.745115 GCAGCCACCATTACGAGCA 60.745 57.895 0.00 0.00 0.00 4.26
2213 4960 9.787626 GTTAATTTTGATGGTATACGTATCGTG 57.212 33.333 12.24 0.00 41.39 4.35
2261 5009 5.647658 TCCTAATTTTGATGATGACAACGCT 59.352 36.000 0.00 0.00 0.00 5.07
2271 5019 1.739562 GACAACGCTCAGAGCAGGG 60.740 63.158 22.49 12.22 42.58 4.45
2275 5023 3.767806 CGCTCAGAGCAGGGCAGA 61.768 66.667 22.49 0.00 42.58 4.26
2276 5024 2.187424 GCTCAGAGCAGGGCAGAG 59.813 66.667 18.17 0.00 41.89 3.35
2368 5116 8.547967 TGGATAAATCTATTCTTAATCCGTGC 57.452 34.615 0.00 0.00 0.00 5.34
2413 5161 8.596781 AAATTAGACCTATATAGCAGATCCGT 57.403 34.615 4.04 0.00 0.00 4.69
2414 5162 7.575414 ATTAGACCTATATAGCAGATCCGTG 57.425 40.000 4.04 0.00 0.00 4.94
2417 5165 3.027412 CCTATATAGCAGATCCGTGCCT 58.973 50.000 4.04 0.00 45.20 4.75
2418 5166 3.181482 CCTATATAGCAGATCCGTGCCTG 60.181 52.174 4.04 0.00 45.20 4.85
2447 5195 1.272480 TGCCTACAGAGTCCTAGCACA 60.272 52.381 0.00 0.00 0.00 4.57
2491 5239 8.106247 AGCTTAATTTTTGGTTTCGATGAGTA 57.894 30.769 0.00 0.00 0.00 2.59
2605 5355 4.837093 TTACCTACTTGCAATGCCTACT 57.163 40.909 1.53 0.00 0.00 2.57
2607 5357 4.837093 ACCTACTTGCAATGCCTACTTA 57.163 40.909 1.53 0.00 0.00 2.24
2645 5396 7.835634 TTTGAAACGCGCATCCATATATATA 57.164 32.000 5.73 0.00 0.00 0.86
2646 5397 8.432110 TTTGAAACGCGCATCCATATATATAT 57.568 30.769 5.73 0.00 0.00 0.86
2647 5398 9.535878 TTTGAAACGCGCATCCATATATATATA 57.464 29.630 5.73 4.92 0.00 0.86
2648 5399 9.535878 TTGAAACGCGCATCCATATATATATAA 57.464 29.630 5.73 0.00 0.00 0.98
2651 5402 6.100004 ACGCGCATCCATATATATATAAGGC 58.900 40.000 16.14 8.66 29.47 4.35
2667 5418 7.875327 ATATAAGGCCTAATGTGTTTTTCGT 57.125 32.000 5.16 0.00 0.00 3.85
2671 5422 4.082787 AGGCCTAATGTGTTTTTCGTGATG 60.083 41.667 1.29 0.00 0.00 3.07
2694 5445 7.572523 TGGCCTTTGACTATTGATAAGATTG 57.427 36.000 3.32 0.00 0.00 2.67
2741 5492 9.748708 TGTGAAAATTATATTATTGCAAGCTCC 57.251 29.630 4.94 0.00 0.00 4.70
2751 5502 6.892658 TTATTGCAAGCTCCTTTCTTGTAA 57.107 33.333 4.94 8.27 45.33 2.41
2760 5511 8.302438 CAAGCTCCTTTCTTGTAAGAATTTGAT 58.698 33.333 7.80 0.00 43.92 2.57
2769 5520 9.679661 TTCTTGTAAGAATTTGATGGTATGCTA 57.320 29.630 3.05 0.00 39.95 3.49
2785 5536 6.149308 TGGTATGCTATATGTAACTTGCATGC 59.851 38.462 11.82 11.82 40.65 4.06
2820 5571 7.561021 TGCTCTAACATGTGTTCAAAGTTTA 57.439 32.000 0.00 0.00 39.31 2.01
2822 5573 6.856426 GCTCTAACATGTGTTCAAAGTTTACC 59.144 38.462 0.00 0.00 39.31 2.85
2831 5582 7.540299 TGTGTTCAAAGTTTACCTCGAAAAAT 58.460 30.769 0.00 0.00 0.00 1.82
2832 5583 7.698970 TGTGTTCAAAGTTTACCTCGAAAAATC 59.301 33.333 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.596776 GAGGCAAGGGACTCTAGCA 58.403 57.895 0.00 0.00 46.33 3.49
43 44 0.036875 CCTTTTCGAGGCAAGGGACT 59.963 55.000 10.80 0.00 38.93 3.85
56 57 3.125487 GCCTCTAGCGTCTTTTCCTTTTC 59.875 47.826 0.00 0.00 0.00 2.29
60 61 0.537653 GGCCTCTAGCGTCTTTTCCT 59.462 55.000 0.00 0.00 45.17 3.36
62 63 2.094762 TTGGCCTCTAGCGTCTTTTC 57.905 50.000 3.32 0.00 45.17 2.29
79 80 3.485216 GCTTCACGGTTATTGACGGATTG 60.485 47.826 0.00 0.00 33.21 2.67
80 81 2.676342 GCTTCACGGTTATTGACGGATT 59.324 45.455 0.00 0.00 33.21 3.01
83 84 1.659098 GAGCTTCACGGTTATTGACGG 59.341 52.381 0.00 0.00 34.94 4.79
127 128 6.801539 TCTTCAAGTTTATGTGTGGACATC 57.198 37.500 0.00 0.00 42.14 3.06
140 141 8.800332 AGCATAATGAACATCTTCTTCAAGTTT 58.200 29.630 0.00 0.00 31.48 2.66
223 224 6.404074 CCAATGCAGCAAAAACTAAAAACCAA 60.404 34.615 0.00 0.00 0.00 3.67
239 240 2.798976 TCACTGTTTTCCAATGCAGC 57.201 45.000 0.00 0.00 32.65 5.25
279 280 4.028131 TGTGTTACCCCGACATCTTATCT 58.972 43.478 0.00 0.00 0.00 1.98
280 281 4.117685 GTGTGTTACCCCGACATCTTATC 58.882 47.826 0.00 0.00 0.00 1.75
293 294 2.634600 TCACTTGGTGTGTGTGTTACC 58.365 47.619 0.00 0.00 46.27 2.85
306 307 0.954452 GGTCAGCCAACTTCACTTGG 59.046 55.000 0.00 0.00 43.36 3.61
318 319 2.481471 GGCGCTATTTGGGTCAGCC 61.481 63.158 7.64 0.00 36.08 4.85
323 324 0.618458 TCTCTTGGCGCTATTTGGGT 59.382 50.000 7.64 0.00 0.00 4.51
337 338 1.075659 GGCCAGCCCAACTTCTCTT 59.924 57.895 0.00 0.00 0.00 2.85
381 382 2.397044 TCCACAAAGCCTTCCCAAAT 57.603 45.000 0.00 0.00 0.00 2.32
401 402 5.014202 ACCATTTTAATACTCGGCAAACCT 58.986 37.500 0.00 0.00 0.00 3.50
470 471 9.990360 AAAACGGATGAATTAAACCTGTAAAAT 57.010 25.926 0.00 0.00 0.00 1.82
552 553 9.301153 AGTTTGTGTGAAAATAGTGAACATTTC 57.699 29.630 0.00 0.00 33.48 2.17
605 606 4.511454 GGAGCCAAACATTTTGAAAACTCC 59.489 41.667 5.75 5.75 33.81 3.85
613 614 5.010012 AGTTACTCTGGAGCCAAACATTTTG 59.990 40.000 5.03 0.00 0.00 2.44
629 633 4.822026 CTTCCGTTCAATGGAGTTACTCT 58.178 43.478 12.41 0.00 34.21 3.24
640 644 9.965824 CCATTTTATATAAAGCTTCCGTTCAAT 57.034 29.630 0.00 0.00 0.00 2.57
647 651 7.951591 TCAAGCCCATTTTATATAAAGCTTCC 58.048 34.615 20.89 8.40 33.49 3.46
686 690 2.985512 AAGCGCCTCGAGATGATGCC 62.986 60.000 15.71 2.80 35.05 4.40
797 807 9.178758 GTGTAAAGAAACCTATTTGATCCTCAT 57.821 33.333 0.00 0.00 0.00 2.90
900 953 1.213537 CAGGGGATGCTTTGTTGCG 59.786 57.895 0.00 0.00 35.36 4.85
930 1009 4.067896 GCTGATATGAATGGGTGGTACTG 58.932 47.826 0.00 0.00 0.00 2.74
941 1020 3.474600 GTGACTGCTGGCTGATATGAAT 58.525 45.455 6.47 0.00 0.00 2.57
1101 3785 0.467290 TGTTGTTGGGCAGGTCTTCC 60.467 55.000 0.00 0.00 0.00 3.46
1176 3860 1.112113 AGATGGACTTATCGCCGTGT 58.888 50.000 0.00 0.00 32.33 4.49
1337 4075 8.939201 ACTAGATTCATCTGTGAGTATTGTTG 57.061 34.615 0.00 0.00 37.76 3.33
1440 4178 6.309251 CGTTCCCAAATGTGCGTATTATTTTT 59.691 34.615 0.00 0.00 0.00 1.94
1441 4179 5.802956 CGTTCCCAAATGTGCGTATTATTTT 59.197 36.000 0.00 0.00 0.00 1.82
1442 4180 5.336744 CGTTCCCAAATGTGCGTATTATTT 58.663 37.500 0.00 0.00 0.00 1.40
1443 4181 4.201970 CCGTTCCCAAATGTGCGTATTATT 60.202 41.667 0.00 0.00 0.00 1.40
1444 4182 3.314080 CCGTTCCCAAATGTGCGTATTAT 59.686 43.478 0.00 0.00 0.00 1.28
1445 4183 2.678836 CCGTTCCCAAATGTGCGTATTA 59.321 45.455 0.00 0.00 0.00 0.98
1446 4184 1.470890 CCGTTCCCAAATGTGCGTATT 59.529 47.619 0.00 0.00 0.00 1.89
1447 4185 1.091537 CCGTTCCCAAATGTGCGTAT 58.908 50.000 0.00 0.00 0.00 3.06
1448 4186 0.035036 TCCGTTCCCAAATGTGCGTA 59.965 50.000 0.00 0.00 0.00 4.42
1449 4187 1.228003 TCCGTTCCCAAATGTGCGT 60.228 52.632 0.00 0.00 0.00 5.24
1450 4188 1.501741 CTCCGTTCCCAAATGTGCG 59.498 57.895 0.00 0.00 0.00 5.34
1451 4189 1.595093 CCCTCCGTTCCCAAATGTGC 61.595 60.000 0.00 0.00 0.00 4.57
1452 4190 0.037590 TCCCTCCGTTCCCAAATGTG 59.962 55.000 0.00 0.00 0.00 3.21
1453 4191 0.328258 CTCCCTCCGTTCCCAAATGT 59.672 55.000 0.00 0.00 0.00 2.71
1454 4192 1.032114 GCTCCCTCCGTTCCCAAATG 61.032 60.000 0.00 0.00 0.00 2.32
1455 4193 1.303282 GCTCCCTCCGTTCCCAAAT 59.697 57.895 0.00 0.00 0.00 2.32
1456 4194 1.497309 ATGCTCCCTCCGTTCCCAAA 61.497 55.000 0.00 0.00 0.00 3.28
1457 4195 1.923395 ATGCTCCCTCCGTTCCCAA 60.923 57.895 0.00 0.00 0.00 4.12
1458 4196 2.285368 ATGCTCCCTCCGTTCCCA 60.285 61.111 0.00 0.00 0.00 4.37
1459 4197 2.190578 CATGCTCCCTCCGTTCCC 59.809 66.667 0.00 0.00 0.00 3.97
1460 4198 0.322546 AAACATGCTCCCTCCGTTCC 60.323 55.000 0.00 0.00 0.00 3.62
1461 4199 1.087501 GAAACATGCTCCCTCCGTTC 58.912 55.000 0.00 0.00 0.00 3.95
1462 4200 0.693049 AGAAACATGCTCCCTCCGTT 59.307 50.000 0.00 0.00 0.00 4.44
1463 4201 0.036010 CAGAAACATGCTCCCTCCGT 60.036 55.000 0.00 0.00 0.00 4.69
1464 4202 0.036010 ACAGAAACATGCTCCCTCCG 60.036 55.000 0.00 0.00 0.00 4.63
1465 4203 1.680249 GGACAGAAACATGCTCCCTCC 60.680 57.143 0.00 0.00 0.00 4.30
1466 4204 1.280421 AGGACAGAAACATGCTCCCTC 59.720 52.381 0.00 0.00 0.00 4.30
1467 4205 1.004044 CAGGACAGAAACATGCTCCCT 59.996 52.381 0.00 0.00 0.00 4.20
1468 4206 1.003580 TCAGGACAGAAACATGCTCCC 59.996 52.381 0.00 0.00 0.00 4.30
1469 4207 2.479566 TCAGGACAGAAACATGCTCC 57.520 50.000 0.00 0.00 0.00 4.70
1470 4208 2.158449 CGTTCAGGACAGAAACATGCTC 59.842 50.000 0.00 0.00 0.00 4.26
1471 4209 2.146342 CGTTCAGGACAGAAACATGCT 58.854 47.619 0.00 0.00 0.00 3.79
1472 4210 1.400242 GCGTTCAGGACAGAAACATGC 60.400 52.381 0.00 0.00 0.00 4.06
1473 4211 2.146342 AGCGTTCAGGACAGAAACATG 58.854 47.619 0.00 0.00 0.00 3.21
1538 4276 2.568956 CTCCTCTTCCTTGTCACCATCA 59.431 50.000 0.00 0.00 0.00 3.07
1553 4291 3.837731 CCTTCAAGAAGTTCTCCTCCTCT 59.162 47.826 5.70 0.00 36.72 3.69
1563 4304 4.170468 TCTTGGCTTCCTTCAAGAAGTT 57.830 40.909 8.83 0.00 44.14 2.66
1622 4364 0.035458 AGTCGCCTCCAAAGAACCTG 59.965 55.000 0.00 0.00 0.00 4.00
1652 4394 1.611410 CCACTTGCAGCTATGTCCACA 60.611 52.381 0.00 0.00 0.00 4.17
1667 4409 1.296715 CCAGCGAGCTAACCCACTT 59.703 57.895 0.00 0.00 0.00 3.16
1688 4430 2.028130 GAGATCTCTTCGAAGGCTCCA 58.972 52.381 24.37 4.34 0.00 3.86
1715 4457 7.363880 GGGAACTGTTCATCTGTGAGTAGATTA 60.364 40.741 21.01 0.00 35.28 1.75
1778 4520 1.079819 GCACTCCTTAGCACGCTCA 60.080 57.895 0.00 0.00 0.00 4.26
1950 4697 1.698506 AACATGTCTCCCCGCAAAAA 58.301 45.000 0.00 0.00 0.00 1.94
1951 4698 2.570415 TAACATGTCTCCCCGCAAAA 57.430 45.000 0.00 0.00 0.00 2.44
1952 4699 2.570415 TTAACATGTCTCCCCGCAAA 57.430 45.000 0.00 0.00 0.00 3.68
1953 4700 2.799126 ATTAACATGTCTCCCCGCAA 57.201 45.000 0.00 0.00 0.00 4.85
1954 4701 2.799126 AATTAACATGTCTCCCCGCA 57.201 45.000 0.00 0.00 0.00 5.69
1955 4702 4.819630 TCATTAATTAACATGTCTCCCCGC 59.180 41.667 0.00 0.00 0.00 6.13
1956 4703 6.710295 TGATCATTAATTAACATGTCTCCCCG 59.290 38.462 0.00 0.00 0.00 5.73
1957 4704 8.517878 CATGATCATTAATTAACATGTCTCCCC 58.482 37.037 5.16 0.00 33.08 4.81
1958 4705 8.517878 CCATGATCATTAATTAACATGTCTCCC 58.482 37.037 18.11 0.00 35.04 4.30
1959 4706 9.071276 ACCATGATCATTAATTAACATGTCTCC 57.929 33.333 18.11 2.92 35.04 3.71
1966 4713 8.694540 CCAGGAAACCATGATCATTAATTAACA 58.305 33.333 5.16 0.00 0.00 2.41
1967 4714 8.143835 CCCAGGAAACCATGATCATTAATTAAC 58.856 37.037 5.16 0.00 0.00 2.01
1968 4715 8.064389 TCCCAGGAAACCATGATCATTAATTAA 58.936 33.333 5.16 0.00 0.00 1.40
1969 4716 7.590907 TCCCAGGAAACCATGATCATTAATTA 58.409 34.615 5.16 0.00 0.00 1.40
1970 4717 6.442961 TCCCAGGAAACCATGATCATTAATT 58.557 36.000 5.16 0.82 0.00 1.40
1991 4738 2.567615 TCAGTAGCTTGTTCCTTCTCCC 59.432 50.000 0.00 0.00 0.00 4.30
1995 4742 4.212214 CACACTTCAGTAGCTTGTTCCTTC 59.788 45.833 0.00 0.00 0.00 3.46
2078 4825 5.755375 TCTGAGAAAGCAAGACAAGTTACTG 59.245 40.000 0.00 0.00 0.00 2.74
2104 4851 3.722147 CCATGTCTCTACCGATTTCTGG 58.278 50.000 0.00 0.00 0.00 3.86
2127 4874 9.014297 CCCTGTACTGAAAAAGAAATACAATCT 57.986 33.333 0.60 0.00 0.00 2.40
2146 4893 2.359975 GGTGGCTGCACCCTGTAC 60.360 66.667 0.50 0.00 39.27 2.90
2148 4895 1.788518 TAATGGTGGCTGCACCCTGT 61.789 55.000 15.42 6.35 44.38 4.00
2150 4897 1.000896 GTAATGGTGGCTGCACCCT 60.001 57.895 15.42 6.15 44.38 4.34
2207 4954 1.844497 TCCAGACCCTCTCTCACGATA 59.156 52.381 0.00 0.00 0.00 2.92
2208 4955 0.626382 TCCAGACCCTCTCTCACGAT 59.374 55.000 0.00 0.00 0.00 3.73
2209 4956 0.404426 TTCCAGACCCTCTCTCACGA 59.596 55.000 0.00 0.00 0.00 4.35
2210 4957 1.479709 ATTCCAGACCCTCTCTCACG 58.520 55.000 0.00 0.00 0.00 4.35
2211 4958 5.622346 AATAATTCCAGACCCTCTCTCAC 57.378 43.478 0.00 0.00 0.00 3.51
2213 4960 6.418946 ACAAAATAATTCCAGACCCTCTCTC 58.581 40.000 0.00 0.00 0.00 3.20
2261 5009 0.032316 AGATCTCTGCCCTGCTCTGA 60.032 55.000 0.00 0.00 0.00 3.27
2271 5019 4.886489 AGGAAGGCAATTTTAGATCTCTGC 59.114 41.667 0.00 1.86 0.00 4.26
2275 5023 4.400567 GTGCAGGAAGGCAATTTTAGATCT 59.599 41.667 0.00 0.00 46.93 2.75
2276 5024 4.440663 GGTGCAGGAAGGCAATTTTAGATC 60.441 45.833 0.00 0.00 46.93 2.75
2391 5139 5.357314 GCACGGATCTGCTATATAGGTCTAA 59.643 44.000 11.72 0.00 34.06 2.10
2419 5167 3.376935 CTCTGTAGGCAGGCACGGG 62.377 68.421 0.00 0.00 42.78 5.28
2420 5168 2.185350 CTCTGTAGGCAGGCACGG 59.815 66.667 0.00 0.00 42.78 4.94
2421 5169 1.153745 GACTCTGTAGGCAGGCACG 60.154 63.158 0.00 0.00 42.78 5.34
2422 5170 1.219393 GGACTCTGTAGGCAGGCAC 59.781 63.158 0.00 0.00 42.78 5.01
2423 5171 0.335019 TAGGACTCTGTAGGCAGGCA 59.665 55.000 0.00 0.00 42.78 4.75
2424 5172 1.036707 CTAGGACTCTGTAGGCAGGC 58.963 60.000 0.00 0.00 42.78 4.85
2425 5173 1.036707 GCTAGGACTCTGTAGGCAGG 58.963 60.000 0.00 0.00 42.78 4.85
2426 5174 1.407258 GTGCTAGGACTCTGTAGGCAG 59.593 57.143 7.20 0.00 43.87 4.85
2427 5175 1.272480 TGTGCTAGGACTCTGTAGGCA 60.272 52.381 15.92 0.00 29.10 4.75
2428 5176 1.135333 GTGTGCTAGGACTCTGTAGGC 59.865 57.143 15.92 0.00 0.00 3.93
2429 5177 2.425312 CAGTGTGCTAGGACTCTGTAGG 59.575 54.545 28.29 11.22 34.28 3.18
2430 5178 2.159310 GCAGTGTGCTAGGACTCTGTAG 60.159 54.545 33.00 18.06 40.96 2.74
2431 5179 1.819288 GCAGTGTGCTAGGACTCTGTA 59.181 52.381 33.00 7.63 40.96 2.74
2432 5180 0.605589 GCAGTGTGCTAGGACTCTGT 59.394 55.000 33.00 9.58 40.96 3.41
2433 5181 0.605083 TGCAGTGTGCTAGGACTCTG 59.395 55.000 30.76 30.76 45.31 3.35
2434 5182 1.480137 GATGCAGTGTGCTAGGACTCT 59.520 52.381 15.92 14.18 45.31 3.24
2435 5183 1.480137 AGATGCAGTGTGCTAGGACTC 59.520 52.381 15.92 11.99 45.31 3.36
2436 5184 1.206610 CAGATGCAGTGTGCTAGGACT 59.793 52.381 15.92 0.00 45.31 3.85
2437 5185 1.066573 ACAGATGCAGTGTGCTAGGAC 60.067 52.381 7.56 7.56 45.31 3.85
2438 5186 1.066645 CACAGATGCAGTGTGCTAGGA 60.067 52.381 16.62 0.00 45.31 2.94
2439 5187 1.066645 TCACAGATGCAGTGTGCTAGG 60.067 52.381 21.72 4.16 45.31 3.02
2440 5188 1.998315 GTCACAGATGCAGTGTGCTAG 59.002 52.381 21.72 4.47 45.31 3.42
2441 5189 1.338105 GGTCACAGATGCAGTGTGCTA 60.338 52.381 21.72 7.84 45.31 3.49
2447 5195 2.613977 GCTAGTTGGTCACAGATGCAGT 60.614 50.000 0.00 0.00 0.00 4.40
2458 5206 7.114388 CGAAACCAAAAATTAAGCTAGTTGGTC 59.886 37.037 9.75 0.47 46.07 4.02
2491 5239 8.105829 ACTGAATCACATTATTCTTCAACTCCT 58.894 33.333 0.00 0.00 36.90 3.69
2524 5272 8.772250 TCCAACCAGAACTAAGATAATCATTCT 58.228 33.333 0.00 0.00 0.00 2.40
2605 5355 7.270365 CGCGTTTCAAATTCTTAAGCTTCATAA 59.730 33.333 0.00 0.00 0.00 1.90
2607 5357 5.569059 CGCGTTTCAAATTCTTAAGCTTCAT 59.431 36.000 0.00 0.00 0.00 2.57
2645 5396 5.708230 TCACGAAAAACACATTAGGCCTTAT 59.292 36.000 12.58 3.72 0.00 1.73
2646 5397 5.064558 TCACGAAAAACACATTAGGCCTTA 58.935 37.500 12.58 0.11 0.00 2.69
2647 5398 3.886505 TCACGAAAAACACATTAGGCCTT 59.113 39.130 12.58 0.00 0.00 4.35
2648 5399 3.482436 TCACGAAAAACACATTAGGCCT 58.518 40.909 11.78 11.78 0.00 5.19
2651 5402 4.165779 GCCATCACGAAAAACACATTAGG 58.834 43.478 0.00 0.00 0.00 2.69
2659 5410 3.049912 GTCAAAGGCCATCACGAAAAAC 58.950 45.455 5.01 0.00 0.00 2.43
2667 5418 6.899089 TCTTATCAATAGTCAAAGGCCATCA 58.101 36.000 5.01 0.00 0.00 3.07
2671 5422 7.807977 TCAATCTTATCAATAGTCAAAGGCC 57.192 36.000 0.00 0.00 0.00 5.19
2729 5480 6.237901 TCTTACAAGAAAGGAGCTTGCAATA 58.762 36.000 0.00 0.00 45.00 1.90
2760 5511 6.149308 GCATGCAAGTTACATATAGCATACCA 59.851 38.462 14.21 0.00 40.38 3.25
2777 5528 7.096884 AGAGCAATAATATATGGCATGCAAG 57.903 36.000 21.36 0.00 34.89 4.01
2797 5548 6.856426 GGTAAACTTTGAACACATGTTAGAGC 59.144 38.462 0.00 0.00 38.56 4.09
2820 5571 3.288092 GGCCTAATGGATTTTTCGAGGT 58.712 45.455 0.00 0.00 34.57 3.85
2822 5573 3.555966 AGGGCCTAATGGATTTTTCGAG 58.444 45.455 2.82 0.00 34.57 4.04


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

AutoCloner maintained by Alex Coulton.