Multiple sequence alignment - TraesCS2A01G508100

Loading Multiple Alignment...

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 TraesCS2A01G508100 chr2A 100.000 2516 0 0 1 2516 734798985 734801500 0.000000e+00 4647.0
1 TraesCS2A01G508100 chr2A 97.478 793 19 1 781 1572 734737699 734738491 0.000000e+00 1352.0
2 TraesCS2A01G508100 chr2A 95.082 244 11 1 1600 1842 729186494 729186737 1.410000e-102 383.0
3 TraesCS2A01G508100 chr2A 96.875 128 4 0 385 512 729185458 729185585 5.450000e-52 215.0
4 TraesCS2A01G508100 chr2A 98.214 112 2 0 668 779 729186366 729186477 1.970000e-46 196.0
5 TraesCS2A01G508100 chr2A 97.183 71 2 0 520 590 729185979 729186049 1.220000e-23 121.0
6 TraesCS2A01G508100 chr2A 92.727 55 4 0 2357 2411 659705339 659705285 2.070000e-11 80.5
7 TraesCS2A01G508100 chr2D 90.539 687 41 13 1842 2515 601427823 601428498 0.000000e+00 887.0
8 TraesCS2A01G508100 chr2D 93.657 268 17 0 1 268 601427561 601427828 3.900000e-108 401.0
9 TraesCS2A01G508100 chr2D 89.655 290 28 2 780 1068 62384351 62384063 3.950000e-98 368.0
10 TraesCS2A01G508100 chr2D 87.285 291 31 6 780 1067 548264535 548264822 6.710000e-86 327.0
11 TraesCS2A01G508100 chr2D 86.752 234 28 3 1610 1842 633229025 633228794 8.930000e-65 257.0
12 TraesCS2A01G508100 chr2D 94.828 116 6 0 272 387 572033368 572033253 5.530000e-42 182.0
13 TraesCS2A01G508100 chr2D 93.388 121 7 1 268 387 572032217 572032337 7.150000e-41 178.0
14 TraesCS2A01G508100 chr2B 89.781 685 46 12 1844 2516 731711522 731712194 0.000000e+00 856.0
15 TraesCS2A01G508100 chr2B 94.403 268 15 0 1 268 731711258 731711525 1.800000e-111 412.0
16 TraesCS2A01G508100 chr2B 95.690 116 5 0 272 387 747817801 747817686 1.190000e-43 187.0
17 TraesCS2A01G508100 chr7A 93.673 569 14 3 989 1557 709291208 709290662 0.000000e+00 832.0
18 TraesCS2A01G508100 chr7A 86.792 53 7 0 2358 2410 157173049 157173101 2.700000e-05 60.2
19 TraesCS2A01G508100 chr4B 96.035 454 18 0 783 1236 637350108 637350561 0.000000e+00 739.0
20 TraesCS2A01G508100 chr4B 91.667 276 23 0 1296 1571 637350999 637351274 1.410000e-102 383.0
21 TraesCS2A01G508100 chr4B 95.312 64 3 0 1240 1303 637350976 637351039 4.430000e-18 102.0
22 TraesCS2A01G508100 chr5D 86.000 450 43 8 1842 2276 46274851 46274407 4.900000e-127 464.0
23 TraesCS2A01G508100 chr5D 95.971 273 11 0 1569 1841 530409062 530409334 6.390000e-121 444.0
24 TraesCS2A01G508100 chr5D 95.185 270 13 0 1572 1841 406476028 406475759 6.430000e-116 427.0
25 TraesCS2A01G508100 chr5D 82.027 523 65 19 1842 2349 46085334 46084826 3.870000e-113 418.0
26 TraesCS2A01G508100 chr5D 93.359 256 17 0 16 271 46275098 46274843 1.830000e-101 379.0
27 TraesCS2A01G508100 chr5D 94.186 172 10 0 609 780 406476191 406476020 1.920000e-66 263.0
28 TraesCS2A01G508100 chr5D 95.625 160 7 0 621 780 530408914 530409073 8.930000e-65 257.0
29 TraesCS2A01G508100 chr5D 84.766 256 35 4 1590 1844 443905668 443905920 1.160000e-63 254.0
30 TraesCS2A01G508100 chr5D 94.531 128 7 0 385 512 530408348 530408475 5.490000e-47 198.0
31 TraesCS2A01G508100 chr5D 93.750 128 8 0 385 512 406476757 406476630 2.550000e-45 193.0
32 TraesCS2A01G508100 chr5D 95.690 116 5 0 272 387 530408193 530408308 1.190000e-43 187.0
33 TraesCS2A01G508100 chr5D 94.828 116 6 0 272 387 406476912 406476797 5.530000e-42 182.0
34 TraesCS2A01G508100 chr5D 94.286 70 2 2 520 587 530408869 530408938 3.420000e-19 106.0
35 TraesCS2A01G508100 chr3D 95.620 274 12 0 1569 1842 92363337 92363610 8.260000e-120 440.0
36 TraesCS2A01G508100 chr3D 97.902 143 2 1 638 780 92363207 92363348 1.930000e-61 246.0
37 TraesCS2A01G508100 chr3D 95.200 125 6 0 385 509 92362415 92362539 5.490000e-47 198.0
38 TraesCS2A01G508100 chr3D 96.522 115 4 0 273 387 92362261 92362375 9.190000e-45 191.0
39 TraesCS2A01G508100 chr7D 94.891 274 12 2 1569 1841 140294000 140294272 6.430000e-116 427.0
40 TraesCS2A01G508100 chr7D 97.647 170 2 2 613 780 140293842 140294011 8.800000e-75 291.0
41 TraesCS2A01G508100 chr7D 96.094 128 5 0 385 512 140293279 140293406 2.540000e-50 209.0
42 TraesCS2A01G508100 chr7D 94.400 125 6 1 270 394 318844324 318844201 9.190000e-45 191.0
43 TraesCS2A01G508100 chr7D 95.726 117 4 1 272 387 140293123 140293239 1.190000e-43 187.0
44 TraesCS2A01G508100 chr7D 96.429 56 2 0 2357 2412 154179924 154179869 2.660000e-15 93.5
45 TraesCS2A01G508100 chr7D 86.792 53 7 0 2358 2410 155311431 155311483 2.700000e-05 60.2
46 TraesCS2A01G508100 chr5A 82.583 511 60 10 1842 2337 37401348 37400852 8.320000e-115 424.0
47 TraesCS2A01G508100 chr5A 92.565 269 20 0 3 271 37401608 37401340 1.090000e-103 387.0
48 TraesCS2A01G508100 chr5A 91.513 271 23 0 1 271 36942314 36942044 8.500000e-100 374.0
49 TraesCS2A01G508100 chr5A 80.273 512 62 25 1846 2347 36825892 36825410 1.430000e-92 350.0
50 TraesCS2A01G508100 chr5A 82.100 419 55 14 1842 2245 37193454 37193041 8.620000e-90 340.0
51 TraesCS2A01G508100 chr5B 82.192 511 62 10 1842 2337 48147297 48147793 1.800000e-111 412.0
52 TraesCS2A01G508100 chr5B 93.462 260 17 0 9 268 48147043 48147302 1.090000e-103 387.0
53 TraesCS2A01G508100 chr5B 89.701 301 23 4 769 1068 475687613 475687320 6.570000e-101 377.0
54 TraesCS2A01G508100 chr5B 91.144 271 24 0 1 271 46746613 46746343 3.950000e-98 368.0
55 TraesCS2A01G508100 chr5B 90.775 271 25 0 1 271 46767760 46767490 1.840000e-96 363.0
56 TraesCS2A01G508100 chr5B 91.635 263 21 1 9 271 47127420 47127159 1.840000e-96 363.0
57 TraesCS2A01G508100 chr5B 79.920 503 66 20 1843 2337 47127166 47126691 1.110000e-88 337.0
58 TraesCS2A01G508100 chr5B 84.706 255 33 5 1590 1842 52310233 52310483 1.490000e-62 250.0
59 TraesCS2A01G508100 chr1D 93.431 274 18 0 1569 1842 46386610 46386883 8.380000e-110 407.0
60 TraesCS2A01G508100 chr1D 84.765 361 42 7 1214 1565 434266809 434267165 1.430000e-92 350.0
61 TraesCS2A01G508100 chr1D 95.028 181 7 1 600 780 46386443 46386621 1.470000e-72 283.0
62 TraesCS2A01G508100 chr1D 95.349 129 6 0 385 513 46385877 46386005 3.280000e-49 206.0
63 TraesCS2A01G508100 chr1D 89.524 105 6 5 520 624 46386397 46386496 7.310000e-26 128.0
64 TraesCS2A01G508100 chr4A 88.514 296 26 8 780 1070 596132558 596132266 3.980000e-93 351.0
65 TraesCS2A01G508100 chr6A 88.136 295 27 8 781 1070 273927060 273927351 6.660000e-91 344.0
66 TraesCS2A01G508100 chr3A 87.755 294 29 7 781 1070 740333857 740334147 1.110000e-88 337.0
67 TraesCS2A01G508100 chr1B 87.500 296 28 8 777 1067 190770876 190771167 1.440000e-87 333.0
68 TraesCS2A01G508100 chr4D 95.690 116 5 0 272 387 504891646 504891531 1.190000e-43 187.0
69 TraesCS2A01G508100 chr3B 91.150 113 7 3 669 779 8037795 8037684 1.560000e-32 150.0
70 TraesCS2A01G508100 chr7B 96.429 56 2 0 2357 2412 116376450 116376395 2.660000e-15 93.5


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 TraesCS2A01G508100 chr2A 734798985 734801500 2515 False 4647.00 4647 100.00000 1 2516 1 chr2A.!!$F2 2515
1 TraesCS2A01G508100 chr2A 734737699 734738491 792 False 1352.00 1352 97.47800 781 1572 1 chr2A.!!$F1 791
2 TraesCS2A01G508100 chr2A 729185458 729186737 1279 False 228.75 383 96.83850 385 1842 4 chr2A.!!$F3 1457
3 TraesCS2A01G508100 chr2D 601427561 601428498 937 False 644.00 887 92.09800 1 2515 2 chr2D.!!$F3 2514
4 TraesCS2A01G508100 chr2B 731711258 731712194 936 False 634.00 856 92.09200 1 2516 2 chr2B.!!$F1 2515
5 TraesCS2A01G508100 chr7A 709290662 709291208 546 True 832.00 832 93.67300 989 1557 1 chr7A.!!$R1 568
6 TraesCS2A01G508100 chr4B 637350108 637351274 1166 False 408.00 739 94.33800 783 1571 3 chr4B.!!$F1 788
7 TraesCS2A01G508100 chr5D 46274407 46275098 691 True 421.50 464 89.67950 16 2276 2 chr5D.!!$R2 2260
8 TraesCS2A01G508100 chr5D 46084826 46085334 508 True 418.00 418 82.02700 1842 2349 1 chr5D.!!$R1 507
9 TraesCS2A01G508100 chr5D 406475759 406476912 1153 True 266.25 427 94.48725 272 1841 4 chr5D.!!$R3 1569
10 TraesCS2A01G508100 chr5D 530408193 530409334 1141 False 238.40 444 95.22060 272 1841 5 chr5D.!!$F2 1569
11 TraesCS2A01G508100 chr3D 92362261 92363610 1349 False 268.75 440 96.31100 273 1842 4 chr3D.!!$F1 1569
12 TraesCS2A01G508100 chr7D 140293123 140294272 1149 False 278.50 427 96.08950 272 1841 4 chr7D.!!$F2 1569
13 TraesCS2A01G508100 chr5A 37400852 37401608 756 True 405.50 424 87.57400 3 2337 2 chr5A.!!$R4 2334
14 TraesCS2A01G508100 chr5B 48147043 48147793 750 False 399.50 412 87.82700 9 2337 2 chr5B.!!$F2 2328
15 TraesCS2A01G508100 chr5B 47126691 47127420 729 True 350.00 363 85.77750 9 2337 2 chr5B.!!$R4 2328
16 TraesCS2A01G508100 chr1D 46385877 46386883 1006 False 256.00 407 93.33300 385 1842 4 chr1D.!!$F2 1457

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
602 1075 0.105709 GGGAGAGGGAGAAGGAGAGG 60.106 65.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 2966 1.270094 TGCAGAAACCACACCTCTACG 60.27 52.381 0.0 0.0 0.0 3.51 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
103 104 2.831333 CCTTCCATGGACGATCTTGAG 58.169 52.381 19.45 9.14 0.00 3.02
125 126 6.944290 TGAGGATGATGACAAAAGAGAAATGT 59.056 34.615 0.00 0.00 0.00 2.71
140 141 8.677148 AAGAGAAATGTTTAAGCACTTACTCA 57.323 30.769 14.59 0.00 0.00 3.41
151 152 2.005451 CACTTACTCATGGCTGCAGAC 58.995 52.381 20.43 17.52 0.00 3.51
165 166 1.421410 GCAGACAAGTATGCGACGGG 61.421 60.000 3.91 0.00 38.08 5.28
169 170 0.892755 ACAAGTATGCGACGGGAAGA 59.107 50.000 0.00 0.00 0.00 2.87
177 178 1.207089 TGCGACGGGAAGAATGAAGAT 59.793 47.619 0.00 0.00 0.00 2.40
329 330 2.812011 GTTGCAGAAACCACGGTTCTAT 59.188 45.455 1.05 0.00 37.35 1.98
413 499 2.094182 GGATAGAGTGACGTGGCAAAGA 60.094 50.000 0.00 0.00 0.00 2.52
418 504 3.632145 AGAGTGACGTGGCAAAGAAAAAT 59.368 39.130 0.00 0.00 0.00 1.82
579 1052 2.979814 TCGTGGAGAGAGAGAGAGAG 57.020 55.000 0.00 0.00 0.00 3.20
580 1053 2.462723 TCGTGGAGAGAGAGAGAGAGA 58.537 52.381 0.00 0.00 0.00 3.10
581 1054 2.430694 TCGTGGAGAGAGAGAGAGAGAG 59.569 54.545 0.00 0.00 0.00 3.20
582 1055 2.430694 CGTGGAGAGAGAGAGAGAGAGA 59.569 54.545 0.00 0.00 0.00 3.10
583 1056 3.491619 CGTGGAGAGAGAGAGAGAGAGAG 60.492 56.522 0.00 0.00 0.00 3.20
584 1057 3.041211 TGGAGAGAGAGAGAGAGAGAGG 58.959 54.545 0.00 0.00 0.00 3.69
585 1058 2.370189 GGAGAGAGAGAGAGAGAGAGGG 59.630 59.091 0.00 0.00 0.00 4.30
586 1059 3.309296 GAGAGAGAGAGAGAGAGAGGGA 58.691 54.545 0.00 0.00 0.00 4.20
587 1060 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.00 0.00 0.00 4.30
588 1061 3.051803 AGAGAGAGAGAGAGAGAGGGAGA 60.052 52.174 0.00 0.00 0.00 3.71
589 1062 3.312890 AGAGAGAGAGAGAGAGGGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
590 1063 2.370189 GAGAGAGAGAGAGAGGGAGAGG 59.630 59.091 0.00 0.00 0.00 3.69
591 1064 1.421646 GAGAGAGAGAGAGGGAGAGGG 59.578 61.905 0.00 0.00 0.00 4.30
592 1065 1.010793 AGAGAGAGAGAGGGAGAGGGA 59.989 57.143 0.00 0.00 0.00 4.20
593 1066 1.421646 GAGAGAGAGAGGGAGAGGGAG 59.578 61.905 0.00 0.00 0.00 4.30
594 1067 1.010793 AGAGAGAGAGGGAGAGGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
595 1068 1.850345 GAGAGAGAGGGAGAGGGAGAA 59.150 57.143 0.00 0.00 0.00 2.87
596 1069 1.852965 AGAGAGAGGGAGAGGGAGAAG 59.147 57.143 0.00 0.00 0.00 2.85
597 1070 0.933700 AGAGAGGGAGAGGGAGAAGG 59.066 60.000 0.00 0.00 0.00 3.46
598 1071 0.930726 GAGAGGGAGAGGGAGAAGGA 59.069 60.000 0.00 0.00 0.00 3.36
599 1072 0.933700 AGAGGGAGAGGGAGAAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
600 1073 0.930726 GAGGGAGAGGGAGAAGGAGA 59.069 60.000 0.00 0.00 0.00 3.71
601 1074 0.933700 AGGGAGAGGGAGAAGGAGAG 59.066 60.000 0.00 0.00 0.00 3.20
602 1075 0.105709 GGGAGAGGGAGAAGGAGAGG 60.106 65.000 0.00 0.00 0.00 3.69
603 1076 0.105709 GGAGAGGGAGAAGGAGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
604 1077 0.930726 GAGAGGGAGAAGGAGAGGGA 59.069 60.000 0.00 0.00 0.00 4.20
605 1078 0.933700 AGAGGGAGAAGGAGAGGGAG 59.066 60.000 0.00 0.00 0.00 4.30
606 1079 0.930726 GAGGGAGAAGGAGAGGGAGA 59.069 60.000 0.00 0.00 0.00 3.71
607 1080 0.933700 AGGGAGAAGGAGAGGGAGAG 59.066 60.000 0.00 0.00 0.00 3.20
608 1081 0.105709 GGGAGAAGGAGAGGGAGAGG 60.106 65.000 0.00 0.00 0.00 3.69
609 1082 0.105709 GGAGAAGGAGAGGGAGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
610 1083 0.930726 GAGAAGGAGAGGGAGAGGGA 59.069 60.000 0.00 0.00 0.00 4.20
611 1084 0.933700 AGAAGGAGAGGGAGAGGGAG 59.066 60.000 0.00 0.00 0.00 4.30
612 1085 0.930726 GAAGGAGAGGGAGAGGGAGA 59.069 60.000 0.00 0.00 0.00 3.71
613 1086 1.503347 GAAGGAGAGGGAGAGGGAGAT 59.497 57.143 0.00 0.00 0.00 2.75
614 1087 0.859760 AGGAGAGGGAGAGGGAGATG 59.140 60.000 0.00 0.00 0.00 2.90
615 1088 0.178935 GGAGAGGGAGAGGGAGATGG 60.179 65.000 0.00 0.00 0.00 3.51
616 1089 0.856982 GAGAGGGAGAGGGAGATGGA 59.143 60.000 0.00 0.00 0.00 3.41
617 1090 0.859760 AGAGGGAGAGGGAGATGGAG 59.140 60.000 0.00 0.00 0.00 3.86
618 1091 0.856982 GAGGGAGAGGGAGATGGAGA 59.143 60.000 0.00 0.00 0.00 3.71
619 1092 0.859760 AGGGAGAGGGAGATGGAGAG 59.140 60.000 0.00 0.00 0.00 3.20
772 1540 3.060866 GGCACGACCTTGTCCTCT 58.939 61.111 0.00 0.00 34.51 3.69
773 1541 1.371558 GGCACGACCTTGTCCTCTT 59.628 57.895 0.00 0.00 34.51 2.85
774 1542 0.250338 GGCACGACCTTGTCCTCTTT 60.250 55.000 0.00 0.00 34.51 2.52
775 1543 1.594331 GCACGACCTTGTCCTCTTTT 58.406 50.000 0.00 0.00 0.00 2.27
776 1544 1.947456 GCACGACCTTGTCCTCTTTTT 59.053 47.619 0.00 0.00 0.00 1.94
831 1599 5.306678 TCTTTGGACTTTGGTAATTTGCCAT 59.693 36.000 7.07 0.00 35.71 4.40
841 1609 6.524101 TGGTAATTTGCCATCCTTTACTTC 57.476 37.500 1.64 0.00 0.00 3.01
1024 1793 1.871126 CTCGTGCTGCACTCTCTCCA 61.871 60.000 28.04 4.71 31.34 3.86
1029 1798 1.670015 CTGCACTCTCTCCAGCACA 59.330 57.895 0.00 0.00 32.87 4.57
1455 2635 3.698040 ACATTTGTTGCAGGATCCATCTC 59.302 43.478 15.82 0.00 0.00 2.75
1607 2791 5.570844 GCACCAACCTTATCCTCTTAGTTCA 60.571 44.000 0.00 0.00 0.00 3.18
1648 2832 7.546316 TCCATGCAATTTTGTCTATTTGTGATG 59.454 33.333 0.00 0.00 0.00 3.07
1687 2871 0.036306 CACCTTGTTAAGCGGGACCT 59.964 55.000 0.00 0.00 0.00 3.85
1816 3001 1.168714 CTGCAACCCTAGCCTTCAAC 58.831 55.000 0.00 0.00 0.00 3.18
1946 3131 5.772169 CCTCAAAAGATCTTTTCCTGGTCTT 59.228 40.000 26.87 4.13 40.45 3.01
2077 3263 0.918983 TATGTTGGGCTGGAGAAGGG 59.081 55.000 0.00 0.00 0.00 3.95
2083 3269 2.283834 TGGGCTGGAGAAGGGAATTAA 58.716 47.619 0.00 0.00 0.00 1.40
2089 3275 5.104485 GGCTGGAGAAGGGAATTAAGTCTTA 60.104 44.000 2.56 0.00 0.00 2.10
2246 3450 1.691976 TGGTTGGCCGGTCTGATATAG 59.308 52.381 7.97 0.00 37.67 1.31
2252 3456 4.275810 TGGCCGGTCTGATATAGGTATAC 58.724 47.826 7.97 0.00 0.00 1.47
2254 3458 4.338682 GGCCGGTCTGATATAGGTATACAG 59.661 50.000 1.90 0.00 0.00 2.74
2290 3494 2.289547 TCACTAGCAGTTGCCGTTTTTC 59.710 45.455 0.00 0.00 43.38 2.29
2296 3500 2.349912 GCAGTTGCCGTTTTTCTCTCTC 60.350 50.000 0.00 0.00 34.31 3.20
2297 3501 3.134458 CAGTTGCCGTTTTTCTCTCTCT 58.866 45.455 0.00 0.00 0.00 3.10
2298 3502 3.561725 CAGTTGCCGTTTTTCTCTCTCTT 59.438 43.478 0.00 0.00 0.00 2.85
2299 3503 4.750098 CAGTTGCCGTTTTTCTCTCTCTTA 59.250 41.667 0.00 0.00 0.00 2.10
2300 3504 5.409826 CAGTTGCCGTTTTTCTCTCTCTTAT 59.590 40.000 0.00 0.00 0.00 1.73
2301 3505 6.590292 CAGTTGCCGTTTTTCTCTCTCTTATA 59.410 38.462 0.00 0.00 0.00 0.98
2329 3533 3.589951 ATGCCTGGCTTATGTGAAGAT 57.410 42.857 21.03 0.00 0.00 2.40
2339 3544 8.213518 TGGCTTATGTGAAGATTGATAAACTC 57.786 34.615 0.00 0.00 0.00 3.01
2410 3615 9.681692 TCATTCAAAATGAAACTGATAACACAG 57.318 29.630 0.00 0.00 40.12 3.66
2424 3631 6.052360 TGATAACACAGTGAGTTTTGTGCTA 58.948 36.000 11.28 0.00 46.59 3.49
2428 3635 4.273480 ACACAGTGAGTTTTGTGCTATCAC 59.727 41.667 7.81 0.00 46.59 3.06
2462 3670 9.574516 AGATCTGTTTTACCTGTATGAAAAACT 57.425 29.630 0.00 0.00 40.67 2.66
2497 3713 5.880332 TGCCAACTGCTAGATTTTAGTTAGG 59.120 40.000 0.00 0.00 42.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 9.912634 TTAAACATTTCTCTTTTGTCATCATCC 57.087 29.630 0.00 0.00 0.00 3.51
125 126 3.440173 GCAGCCATGAGTAAGTGCTTAAA 59.560 43.478 0.00 0.00 0.00 1.52
140 141 1.386533 GCATACTTGTCTGCAGCCAT 58.613 50.000 9.47 0.00 38.28 4.40
151 152 2.004583 TTCTTCCCGTCGCATACTTG 57.995 50.000 0.00 0.00 0.00 3.16
162 163 6.226052 TCACATATCATCTTCATTCTTCCCG 58.774 40.000 0.00 0.00 0.00 5.14
165 166 7.935755 TCCCTTCACATATCATCTTCATTCTTC 59.064 37.037 0.00 0.00 0.00 2.87
169 170 6.433404 GCATCCCTTCACATATCATCTTCATT 59.567 38.462 0.00 0.00 0.00 2.57
177 178 4.041938 TGCATAGCATCCCTTCACATATCA 59.958 41.667 0.00 0.00 31.71 2.15
262 263 3.817084 TCTGCAATTCACTCTTCAGGTTG 59.183 43.478 0.00 0.00 0.00 3.77
263 264 4.090761 TCTGCAATTCACTCTTCAGGTT 57.909 40.909 0.00 0.00 0.00 3.50
264 265 3.777106 TCTGCAATTCACTCTTCAGGT 57.223 42.857 0.00 0.00 0.00 4.00
265 266 5.218139 GTTTTCTGCAATTCACTCTTCAGG 58.782 41.667 0.00 0.00 0.00 3.86
266 267 5.824429 TGTTTTCTGCAATTCACTCTTCAG 58.176 37.500 0.00 0.00 0.00 3.02
267 268 5.833406 TGTTTTCTGCAATTCACTCTTCA 57.167 34.783 0.00 0.00 0.00 3.02
268 269 5.566774 CGATGTTTTCTGCAATTCACTCTTC 59.433 40.000 0.00 0.00 0.00 2.87
269 270 5.239306 TCGATGTTTTCTGCAATTCACTCTT 59.761 36.000 0.00 0.00 0.00 2.85
270 271 4.756642 TCGATGTTTTCTGCAATTCACTCT 59.243 37.500 0.00 0.00 0.00 3.24
413 499 7.675062 TGTATCAGGGTGTAATTTGCATTTTT 58.325 30.769 0.00 0.00 0.00 1.94
418 504 4.917385 ACTGTATCAGGGTGTAATTTGCA 58.083 39.130 1.90 0.00 35.51 4.08
513 599 3.426568 GCCAACTCCACGAGCAGC 61.427 66.667 0.00 0.00 32.04 5.25
514 600 2.743928 GGCCAACTCCACGAGCAG 60.744 66.667 0.00 0.00 32.04 4.24
515 601 4.680237 CGGCCAACTCCACGAGCA 62.680 66.667 2.24 0.00 32.04 4.26
516 602 4.681978 ACGGCCAACTCCACGAGC 62.682 66.667 2.24 0.00 32.04 5.03
517 603 2.738521 CACGGCCAACTCCACGAG 60.739 66.667 2.24 0.00 35.52 4.18
518 604 3.220999 CTCACGGCCAACTCCACGA 62.221 63.158 2.24 0.00 0.00 4.35
521 994 4.680237 CGCTCACGGCCAACTCCA 62.680 66.667 2.24 0.00 37.74 3.86
564 1037 2.370189 CCCTCTCTCTCTCTCTCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
565 1038 3.309296 TCCCTCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
566 1039 3.051803 TCTCCCTCTCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
567 1040 3.309296 TCTCCCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
568 1041 3.312890 CTCTCCCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
569 1042 2.370189 CCTCTCCCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
570 1043 2.412591 CCTCTCCCTCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
571 1044 1.421646 CCCTCTCCCTCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
572 1045 1.010793 TCCCTCTCCCTCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
573 1046 1.421646 CTCCCTCTCCCTCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
574 1047 1.010793 TCTCCCTCTCCCTCTCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
575 1048 1.518367 TCTCCCTCTCCCTCTCTCTC 58.482 60.000 0.00 0.00 0.00 3.20
576 1049 1.852965 CTTCTCCCTCTCCCTCTCTCT 59.147 57.143 0.00 0.00 0.00 3.10
577 1050 1.133482 CCTTCTCCCTCTCCCTCTCTC 60.133 61.905 0.00 0.00 0.00 3.20
578 1051 0.933700 CCTTCTCCCTCTCCCTCTCT 59.066 60.000 0.00 0.00 0.00 3.10
579 1052 0.930726 TCCTTCTCCCTCTCCCTCTC 59.069 60.000 0.00 0.00 0.00 3.20
580 1053 0.933700 CTCCTTCTCCCTCTCCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
581 1054 0.930726 TCTCCTTCTCCCTCTCCCTC 59.069 60.000 0.00 0.00 0.00 4.30
582 1055 0.933700 CTCTCCTTCTCCCTCTCCCT 59.066 60.000 0.00 0.00 0.00 4.20
583 1056 0.105709 CCTCTCCTTCTCCCTCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
584 1057 0.105709 CCCTCTCCTTCTCCCTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
585 1058 0.930726 TCCCTCTCCTTCTCCCTCTC 59.069 60.000 0.00 0.00 0.00 3.20
586 1059 0.933700 CTCCCTCTCCTTCTCCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
587 1060 0.930726 TCTCCCTCTCCTTCTCCCTC 59.069 60.000 0.00 0.00 0.00 4.30
588 1061 0.933700 CTCTCCCTCTCCTTCTCCCT 59.066 60.000 0.00 0.00 0.00 4.20
589 1062 0.105709 CCTCTCCCTCTCCTTCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
590 1063 0.105709 CCCTCTCCCTCTCCTTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
591 1064 0.930726 TCCCTCTCCCTCTCCTTCTC 59.069 60.000 0.00 0.00 0.00 2.87
592 1065 0.933700 CTCCCTCTCCCTCTCCTTCT 59.066 60.000 0.00 0.00 0.00 2.85
593 1066 0.930726 TCTCCCTCTCCCTCTCCTTC 59.069 60.000 0.00 0.00 0.00 3.46
594 1067 1.220236 CATCTCCCTCTCCCTCTCCTT 59.780 57.143 0.00 0.00 0.00 3.36
595 1068 0.859760 CATCTCCCTCTCCCTCTCCT 59.140 60.000 0.00 0.00 0.00 3.69
596 1069 0.178935 CCATCTCCCTCTCCCTCTCC 60.179 65.000 0.00 0.00 0.00 3.71
597 1070 0.856982 TCCATCTCCCTCTCCCTCTC 59.143 60.000 0.00 0.00 0.00 3.20
598 1071 0.859760 CTCCATCTCCCTCTCCCTCT 59.140 60.000 0.00 0.00 0.00 3.69
599 1072 0.856982 TCTCCATCTCCCTCTCCCTC 59.143 60.000 0.00 0.00 0.00 4.30
600 1073 0.859760 CTCTCCATCTCCCTCTCCCT 59.140 60.000 0.00 0.00 0.00 4.20
601 1074 0.178935 CCTCTCCATCTCCCTCTCCC 60.179 65.000 0.00 0.00 0.00 4.30
602 1075 0.178935 CCCTCTCCATCTCCCTCTCC 60.179 65.000 0.00 0.00 0.00 3.71
603 1076 0.856982 TCCCTCTCCATCTCCCTCTC 59.143 60.000 0.00 0.00 0.00 3.20
604 1077 0.859760 CTCCCTCTCCATCTCCCTCT 59.140 60.000 0.00 0.00 0.00 3.69
605 1078 0.856982 TCTCCCTCTCCATCTCCCTC 59.143 60.000 0.00 0.00 0.00 4.30
606 1079 0.859760 CTCTCCCTCTCCATCTCCCT 59.140 60.000 0.00 0.00 0.00 4.20
607 1080 0.856982 TCTCTCCCTCTCCATCTCCC 59.143 60.000 0.00 0.00 0.00 4.30
608 1081 1.780309 TCTCTCTCCCTCTCCATCTCC 59.220 57.143 0.00 0.00 0.00 3.71
609 1082 2.711009 TCTCTCTCTCCCTCTCCATCTC 59.289 54.545 0.00 0.00 0.00 2.75
610 1083 2.713167 CTCTCTCTCTCCCTCTCCATCT 59.287 54.545 0.00 0.00 0.00 2.90
611 1084 2.711009 TCTCTCTCTCTCCCTCTCCATC 59.289 54.545 0.00 0.00 0.00 3.51
612 1085 2.713167 CTCTCTCTCTCTCCCTCTCCAT 59.287 54.545 0.00 0.00 0.00 3.41
613 1086 2.126882 CTCTCTCTCTCTCCCTCTCCA 58.873 57.143 0.00 0.00 0.00 3.86
614 1087 2.370189 CTCTCTCTCTCTCTCCCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
615 1088 2.370189 CCTCTCTCTCTCTCTCCCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
616 1089 2.022035 TCCTCTCTCTCTCTCTCCCTCT 60.022 54.545 0.00 0.00 0.00 3.69
617 1090 2.370189 CTCCTCTCTCTCTCTCTCCCTC 59.630 59.091 0.00 0.00 0.00 4.30
618 1091 2.022035 TCTCCTCTCTCTCTCTCTCCCT 60.022 54.545 0.00 0.00 0.00 4.20
619 1092 2.408565 TCTCCTCTCTCTCTCTCTCCC 58.591 57.143 0.00 0.00 0.00 4.30
774 1542 5.877564 GCAAATAATCAAATCCCCCGAAAAA 59.122 36.000 0.00 0.00 0.00 1.94
775 1543 5.423886 GCAAATAATCAAATCCCCCGAAAA 58.576 37.500 0.00 0.00 0.00 2.29
776 1544 4.141824 GGCAAATAATCAAATCCCCCGAAA 60.142 41.667 0.00 0.00 0.00 3.46
777 1545 3.386402 GGCAAATAATCAAATCCCCCGAA 59.614 43.478 0.00 0.00 0.00 4.30
778 1546 2.962421 GGCAAATAATCAAATCCCCCGA 59.038 45.455 0.00 0.00 0.00 5.14
779 1547 2.697751 TGGCAAATAATCAAATCCCCCG 59.302 45.455 0.00 0.00 0.00 5.73
1455 2635 3.256631 ACTTTGCTATTTTGCCCTCTGTG 59.743 43.478 0.00 0.00 0.00 3.66
1607 2791 5.543507 TGCATGGACCAAACTGTAAAAAT 57.456 34.783 0.00 0.00 0.00 1.82
1648 2832 1.856597 GGCGGTGACACGATATAACAC 59.143 52.381 0.00 0.00 35.47 3.32
1687 2871 8.407832 TCGTTTTAAGTCCGATTATGACAGATA 58.592 33.333 0.00 0.00 35.15 1.98
1781 2966 1.270094 TGCAGAAACCACACCTCTACG 60.270 52.381 0.00 0.00 0.00 3.51
1816 3001 3.599514 GTGAATTGCAGAAAACATCGACG 59.400 43.478 0.00 0.00 0.00 5.12
1885 3070 3.243301 GCTTGCGATCACATCATCCATTT 60.243 43.478 0.00 0.00 0.00 2.32
1946 3131 7.987458 ACACTTCTCTCAAACATCTCTACAAAA 59.013 33.333 0.00 0.00 0.00 2.44
2067 3252 7.189079 ACTAAGACTTAATTCCCTTCTCCAG 57.811 40.000 0.00 0.00 0.00 3.86
2083 3269 7.868415 GGATAGACATGCGAAATTACTAAGACT 59.132 37.037 0.00 0.00 0.00 3.24
2089 3275 5.163301 ACCAGGATAGACATGCGAAATTACT 60.163 40.000 0.00 0.00 0.00 2.24
2246 3450 4.532521 AGCTACCATGGATTCCTGTATACC 59.467 45.833 21.47 0.00 0.00 2.73
2252 3456 2.437281 AGTGAGCTACCATGGATTCCTG 59.563 50.000 21.47 2.55 0.00 3.86
2254 3458 3.556004 GCTAGTGAGCTACCATGGATTCC 60.556 52.174 21.47 3.48 45.98 3.01
2276 3480 3.134458 AGAGAGAGAAAAACGGCAACTG 58.866 45.455 0.00 0.00 0.00 3.16
2277 3481 3.477210 AGAGAGAGAAAAACGGCAACT 57.523 42.857 0.00 0.00 0.00 3.16
2278 3482 5.864628 ATAAGAGAGAGAAAAACGGCAAC 57.135 39.130 0.00 0.00 0.00 4.17
2290 3494 9.868277 CCAGGCATTAAAGTATATAAGAGAGAG 57.132 37.037 0.00 0.00 0.00 3.20
2298 3502 9.448438 CACATAAGCCAGGCATTAAAGTATATA 57.552 33.333 15.80 0.00 0.00 0.86
2299 3503 8.163408 TCACATAAGCCAGGCATTAAAGTATAT 58.837 33.333 15.80 0.00 0.00 0.86
2300 3504 7.513856 TCACATAAGCCAGGCATTAAAGTATA 58.486 34.615 15.80 3.17 0.00 1.47
2301 3505 6.364701 TCACATAAGCCAGGCATTAAAGTAT 58.635 36.000 15.80 0.00 0.00 2.12
2312 3516 7.284034 AGTTTATCAATCTTCACATAAGCCAGG 59.716 37.037 0.00 0.00 0.00 4.45
2396 3601 7.250569 CACAAAACTCACTGTGTTATCAGTTT 58.749 34.615 14.96 14.96 44.92 2.66
2419 3626 6.105333 ACAGATCTCTCAAAAGTGATAGCAC 58.895 40.000 2.01 2.01 45.49 4.40
2424 3631 8.160106 AGGTAAAACAGATCTCTCAAAAGTGAT 58.840 33.333 0.00 0.00 38.20 3.06
2428 3635 7.736447 ACAGGTAAAACAGATCTCTCAAAAG 57.264 36.000 0.00 0.00 0.00 2.27
2477 3693 7.038231 ACTGTCCCTAACTAAAATCTAGCAGTT 60.038 37.037 0.00 0.00 35.50 3.16


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

AutoCloner maintained by Alex Coulton.