Multiple sequence alignment - TraesCS1B01G383200

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 TraesCS1B01G383200 chr1B 100.000 5279 0 0 1 5279 615114315 615109037 0.000000e+00 9749.0
1 TraesCS1B01G383200 chr1B 79.498 478 73 16 283 749 161987455 161987918 3.070000e-82 316.0
2 TraesCS1B01G383200 chr1D 91.043 4533 273 69 1 4477 449459023 449454568 0.000000e+00 5999.0
3 TraesCS1B01G383200 chr1D 80.549 874 99 35 4469 5276 493226516 493227384 1.630000e-169 606.0
4 TraesCS1B01G383200 chr1D 87.647 510 56 4 4768 5276 281370667 281371170 2.120000e-163 586.0
5 TraesCS1B01G383200 chr1D 87.189 523 37 5 4787 5279 399242571 399242049 7.670000e-158 568.0
6 TraesCS1B01G383200 chr1D 81.921 531 52 14 4771 5279 439064078 439064586 4.920000e-110 409.0
7 TraesCS1B01G383200 chr1D 86.984 315 34 7 4473 4780 269992005 269991691 1.090000e-91 348.0
8 TraesCS1B01G383200 chr1D 76.117 515 93 17 261 772 16392263 16391776 5.280000e-60 243.0
9 TraesCS1B01G383200 chr1A 93.439 3780 180 36 727 4477 544588953 544585213 0.000000e+00 5544.0
10 TraesCS1B01G383200 chr1A 78.082 438 89 3 246 676 16928391 16928828 2.420000e-68 270.0
11 TraesCS1B01G383200 chr2D 91.065 526 27 6 4768 5279 143494730 143495249 0.000000e+00 693.0
12 TraesCS1B01G383200 chr2D 86.214 515 41 5 4795 5279 628950371 628949857 1.010000e-146 531.0
13 TraesCS1B01G383200 chr2D 86.207 319 35 7 4470 4779 143494387 143494705 2.360000e-88 337.0
14 TraesCS1B01G383200 chr2D 76.437 522 93 18 263 772 637975340 637975843 6.780000e-64 255.0
15 TraesCS1B01G383200 chr5D 90.438 502 36 3 4787 5279 432509779 432510277 0.000000e+00 651.0
16 TraesCS1B01G383200 chr5D 87.234 517 42 5 4787 5279 108339738 108340254 7.670000e-158 568.0
17 TraesCS1B01G383200 chr5D 77.513 587 111 16 246 817 344834730 344835310 3.050000e-87 333.0
18 TraesCS1B01G383200 chr5D 85.902 305 32 9 4473 4768 432509421 432509723 1.100000e-81 315.0
19 TraesCS1B01G383200 chr5D 77.333 525 87 21 261 771 397075556 397076062 1.120000e-71 281.0
20 TraesCS1B01G383200 chr6D 90.040 502 31 5 4787 5279 130208503 130208012 2.680000e-177 632.0
21 TraesCS1B01G383200 chr6D 86.822 516 42 11 4789 5279 427340790 427341304 2.150000e-153 553.0
22 TraesCS1B01G383200 chr6D 85.535 318 36 8 4470 4780 463789133 463788819 1.830000e-84 324.0
23 TraesCS1B01G383200 chr6D 80.734 327 46 10 383 698 345358479 345358799 6.830000e-59 239.0
24 TraesCS1B01G383200 chr3D 88.632 519 46 4 4771 5279 304905538 304906053 2.090000e-173 619.0
25 TraesCS1B01G383200 chr3D 80.097 412 54 24 1208 1604 356827861 356827463 1.120000e-71 281.0
26 TraesCS1B01G383200 chr3D 81.667 120 20 2 649 767 416208431 416208549 1.210000e-16 99.0
27 TraesCS1B01G383200 chr3D 81.739 115 19 2 657 769 389914036 389913922 1.570000e-15 95.3
28 TraesCS1B01G383200 chr7D 88.247 519 47 4 4768 5276 83805608 83806122 4.520000e-170 608.0
29 TraesCS1B01G383200 chr7D 87.739 522 51 4 4771 5279 110587873 110587352 9.790000e-167 597.0
30 TraesCS1B01G383200 chr7D 86.898 519 54 5 4771 5279 565209594 565209080 2.130000e-158 569.0
31 TraesCS1B01G383200 chr7D 85.249 522 47 8 4787 5278 99419362 99418841 1.310000e-140 510.0
32 TraesCS1B01G383200 chr7D 87.697 317 31 6 4471 4779 182612921 182612605 3.890000e-96 363.0
33 TraesCS1B01G383200 chr7D 83.715 393 31 18 4471 4832 412230060 412230450 1.820000e-89 340.0
34 TraesCS1B01G383200 chr7D 94.286 140 8 0 5140 5279 33811884 33811745 1.150000e-51 215.0
35 TraesCS1B01G383200 chr7D 82.123 179 24 4 397 568 99283367 99283544 4.260000e-31 147.0
36 TraesCS1B01G383200 chr4D 92.204 372 25 2 4768 5138 432952742 432953110 1.680000e-144 523.0
37 TraesCS1B01G383200 chr4D 81.439 528 76 11 266 783 469197672 469197157 3.800000e-111 412.0
38 TraesCS1B01G383200 chr4D 86.435 317 34 6 4473 4780 315023182 315022866 6.550000e-89 339.0
39 TraesCS1B01G383200 chr4D 85.220 318 35 9 4473 4780 11877761 11877446 3.070000e-82 316.0
40 TraesCS1B01G383200 chr4A 85.029 521 48 6 4789 5279 609125780 609126300 2.190000e-138 503.0
41 TraesCS1B01G383200 chr5B 80.418 526 94 8 246 762 709830420 709830945 4.960000e-105 392.0
42 TraesCS1B01G383200 chr5B 76.952 538 96 17 263 783 406886518 406885992 1.120000e-71 281.0
43 TraesCS1B01G383200 chr5B 80.583 103 20 0 694 796 38627980 38628082 4.380000e-11 80.5
44 TraesCS1B01G383200 chr4B 78.498 586 102 11 261 826 125451810 125451229 3.890000e-96 363.0
45 TraesCS1B01G383200 chr4B 78.545 536 85 18 263 783 535300545 535301065 5.100000e-85 326.0
46 TraesCS1B01G383200 chr2A 78.571 546 89 18 261 795 745774967 745774439 8.470000e-88 335.0
47 TraesCS1B01G383200 chr6A 78.992 476 91 4 246 714 547288581 547289054 3.070000e-82 316.0
48 TraesCS1B01G383200 chr6A 76.457 429 79 14 248 666 114456932 114456516 4.140000e-51 213.0
49 TraesCS1B01G383200 chr7B 79.493 434 76 10 261 685 385919410 385918981 4.000000e-76 296.0
50 TraesCS1B01G383200 chr3A 80.357 392 53 21 1226 1604 475722319 475721939 5.210000e-70 276.0
51 TraesCS1B01G383200 chr3B 80.102 392 52 23 1226 1604 457970957 457970579 8.710000e-68 268.0
52 TraesCS1B01G383200 chr6B 79.202 351 65 7 454 796 707852709 707853059 2.460000e-58 237.0
53 TraesCS1B01G383200 chr2B 78.814 236 40 9 542 772 705724093 705723863 3.290000e-32 150.0


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 TraesCS1B01G383200 chr1B 615109037 615114315 5278 True 9749 9749 100.000 1 5279 1 chr1B.!!$R1 5278
1 TraesCS1B01G383200 chr1D 449454568 449459023 4455 True 5999 5999 91.043 1 4477 1 chr1D.!!$R4 4476
2 TraesCS1B01G383200 chr1D 493226516 493227384 868 False 606 606 80.549 4469 5276 1 chr1D.!!$F3 807
3 TraesCS1B01G383200 chr1D 281370667 281371170 503 False 586 586 87.647 4768 5276 1 chr1D.!!$F1 508
4 TraesCS1B01G383200 chr1D 399242049 399242571 522 True 568 568 87.189 4787 5279 1 chr1D.!!$R3 492
5 TraesCS1B01G383200 chr1D 439064078 439064586 508 False 409 409 81.921 4771 5279 1 chr1D.!!$F2 508
6 TraesCS1B01G383200 chr1A 544585213 544588953 3740 True 5544 5544 93.439 727 4477 1 chr1A.!!$R1 3750
7 TraesCS1B01G383200 chr2D 628949857 628950371 514 True 531 531 86.214 4795 5279 1 chr2D.!!$R1 484
8 TraesCS1B01G383200 chr2D 143494387 143495249 862 False 515 693 88.636 4470 5279 2 chr2D.!!$F2 809
9 TraesCS1B01G383200 chr2D 637975340 637975843 503 False 255 255 76.437 263 772 1 chr2D.!!$F1 509
10 TraesCS1B01G383200 chr5D 108339738 108340254 516 False 568 568 87.234 4787 5279 1 chr5D.!!$F1 492
11 TraesCS1B01G383200 chr5D 432509421 432510277 856 False 483 651 88.170 4473 5279 2 chr5D.!!$F4 806
12 TraesCS1B01G383200 chr5D 344834730 344835310 580 False 333 333 77.513 246 817 1 chr5D.!!$F2 571
13 TraesCS1B01G383200 chr5D 397075556 397076062 506 False 281 281 77.333 261 771 1 chr5D.!!$F3 510
14 TraesCS1B01G383200 chr6D 427340790 427341304 514 False 553 553 86.822 4789 5279 1 chr6D.!!$F2 490
15 TraesCS1B01G383200 chr3D 304905538 304906053 515 False 619 619 88.632 4771 5279 1 chr3D.!!$F1 508
16 TraesCS1B01G383200 chr7D 83805608 83806122 514 False 608 608 88.247 4768 5276 1 chr7D.!!$F1 508
17 TraesCS1B01G383200 chr7D 110587352 110587873 521 True 597 597 87.739 4771 5279 1 chr7D.!!$R3 508
18 TraesCS1B01G383200 chr7D 565209080 565209594 514 True 569 569 86.898 4771 5279 1 chr7D.!!$R5 508
19 TraesCS1B01G383200 chr7D 99418841 99419362 521 True 510 510 85.249 4787 5278 1 chr7D.!!$R2 491
20 TraesCS1B01G383200 chr4D 469197157 469197672 515 True 412 412 81.439 266 783 1 chr4D.!!$R3 517
21 TraesCS1B01G383200 chr4A 609125780 609126300 520 False 503 503 85.029 4789 5279 1 chr4A.!!$F1 490
22 TraesCS1B01G383200 chr5B 709830420 709830945 525 False 392 392 80.418 246 762 1 chr5B.!!$F2 516
23 TraesCS1B01G383200 chr5B 406885992 406886518 526 True 281 281 76.952 263 783 1 chr5B.!!$R1 520
24 TraesCS1B01G383200 chr4B 125451229 125451810 581 True 363 363 78.498 261 826 1 chr4B.!!$R1 565
25 TraesCS1B01G383200 chr4B 535300545 535301065 520 False 326 326 78.545 263 783 1 chr4B.!!$F1 520
26 TraesCS1B01G383200 chr2A 745774439 745774967 528 True 335 335 78.571 261 795 1 chr2A.!!$R1 534

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
785 822 0.317160 TCAGCCTCGACGTTTGATGT 59.683 50.0 0.00 0.0 0.00 3.06 F
1404 1472 0.179092 TCAGATCTGTGCAGCATCGG 60.179 55.0 21.92 0.0 0.00 4.18 F
2002 2071 0.677731 CACCCATGGCAGTGACGAAT 60.678 55.0 14.16 0.0 36.01 3.34 F
2084 2153 0.678048 CCTGCCCCTGTTTACTCTGC 60.678 60.0 0.00 0.0 0.00 4.26 F
3730 3808 0.886490 ACAACTTTCTCTGGCAGCCG 60.886 55.0 10.34 3.3 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 1903 0.474184 CGTCCATAAGCCCCTCCAAT 59.526 55.000 0.00 0.00 0.00 3.16 R
3400 3477 0.453793 AGACCATTGCGTCTCTCTCG 59.546 55.000 2.95 0.00 38.83 4.04 R
3905 3986 1.077068 CCTCGCCTCCTCAGACTCT 60.077 63.158 0.00 0.00 0.00 3.24 R
4052 4138 3.555956 CCGATGGATGTAACTTACAGCAC 59.444 47.826 16.89 8.48 46.29 4.40 R
4785 4932 1.600636 CACGAGGCTTGCCTTTCCA 60.601 57.895 15.92 0.00 0.00 3.53 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
24 25 5.587388 ATTCGTTACCGGATCACTAAAGA 57.413 39.130 9.46 0.27 33.95 2.52
31 32 4.087182 ACCGGATCACTAAAGAGACTCAA 58.913 43.478 9.46 0.00 0.00 3.02
44 45 5.836821 AGAGACTCAACAAACCTTTTTCC 57.163 39.130 5.02 0.00 0.00 3.13
49 50 1.930503 CAACAAACCTTTTTCCGGTGC 59.069 47.619 0.00 0.00 34.33 5.01
97 98 7.171508 TCACTAGTCATTGTGCTAGAGTTTTTG 59.828 37.037 18.00 9.42 38.36 2.44
105 106 5.428253 TGTGCTAGAGTTTTTGTCAGAGTT 58.572 37.500 0.00 0.00 0.00 3.01
154 155 9.093970 GTTCTAGTTTTTATTTTGTGCCAAGTT 57.906 29.630 0.00 0.00 0.00 2.66
217 218 5.105756 CCTTGAAGACTTTGTTGTTCCAAGT 60.106 40.000 0.00 0.00 0.00 3.16
221 222 6.657541 TGAAGACTTTGTTGTTCCAAGTAAGT 59.342 34.615 0.00 0.00 0.00 2.24
222 223 7.825270 TGAAGACTTTGTTGTTCCAAGTAAGTA 59.175 33.333 0.00 0.00 0.00 2.24
224 225 8.209917 AGACTTTGTTGTTCCAAGTAAGTAAG 57.790 34.615 0.00 0.00 0.00 2.34
225 226 6.792326 ACTTTGTTGTTCCAAGTAAGTAAGC 58.208 36.000 0.00 0.00 0.00 3.09
238 239 6.759497 AGTAAGTAAGCCAATTCCACAATC 57.241 37.500 0.00 0.00 0.00 2.67
250 251 7.816995 GCCAATTCCACAATCTAATGTTGTTTA 59.183 33.333 0.00 0.00 37.69 2.01
255 256 6.706716 TCCACAATCTAATGTTGTTTACGTCA 59.293 34.615 0.00 0.00 37.69 4.35
256 257 7.389330 TCCACAATCTAATGTTGTTTACGTCAT 59.611 33.333 0.00 0.00 37.69 3.06
379 380 0.661552 AGCGACGACACATATAGCGT 59.338 50.000 0.00 0.00 39.99 5.07
380 381 1.869132 AGCGACGACACATATAGCGTA 59.131 47.619 0.00 0.00 37.07 4.42
398 399 3.242739 GCGTAAGATCCATGCGTCATTTT 60.243 43.478 8.07 0.00 43.02 1.82
588 605 1.188219 TAGATGGCCAGAGATCGCCC 61.188 60.000 13.05 0.00 45.07 6.13
631 649 2.633488 GGAGTGGATTGAAGTGGCTAC 58.367 52.381 0.00 0.00 0.00 3.58
678 699 5.607171 GGAGGAATATATATGGGGTCGGATT 59.393 44.000 0.00 0.00 0.00 3.01
682 703 1.735926 TATATGGGGTCGGATTGGCA 58.264 50.000 0.00 0.00 0.00 4.92
785 822 0.317160 TCAGCCTCGACGTTTGATGT 59.683 50.000 0.00 0.00 0.00 3.06
818 855 4.201822 GCGTTAGTCTGGATCACATTTTCC 60.202 45.833 0.00 0.00 0.00 3.13
822 859 5.447778 AGTCTGGATCACATTTTCCTGAT 57.552 39.130 0.00 0.00 40.63 2.90
826 863 4.676109 TGGATCACATTTTCCTGATTGGT 58.324 39.130 0.00 0.00 37.07 3.67
828 865 4.706476 GGATCACATTTTCCTGATTGGTCA 59.294 41.667 0.00 0.00 37.07 4.02
843 904 2.753043 TCAGAGACCGGGCCGTAC 60.753 66.667 26.32 17.72 0.00 3.67
863 924 4.148128 ACATGCTCTTACCTTGATCCTG 57.852 45.455 0.00 0.00 0.00 3.86
864 925 3.521126 ACATGCTCTTACCTTGATCCTGT 59.479 43.478 0.00 0.00 0.00 4.00
865 926 4.716784 ACATGCTCTTACCTTGATCCTGTA 59.283 41.667 0.00 0.00 0.00 2.74
905 966 6.350103 TCACACATGTGTTACTCCTGTTAAA 58.650 36.000 28.64 0.00 45.76 1.52
1005 1066 1.884235 GATCCGATCCATCCAACCAC 58.116 55.000 0.00 0.00 0.00 4.16
1006 1067 1.417890 GATCCGATCCATCCAACCACT 59.582 52.381 0.00 0.00 0.00 4.00
1404 1472 0.179092 TCAGATCTGTGCAGCATCGG 60.179 55.000 21.92 0.00 0.00 4.18
1685 1754 1.503542 CAACGGGCATTCTGCTCAC 59.496 57.895 0.00 0.00 46.28 3.51
1731 1800 4.141711 TGTTCAAGCACTACTTTGAGGAGT 60.142 41.667 0.00 0.00 36.04 3.85
1834 1903 2.813754 GTTTGAGTTGCTGCCACTGATA 59.186 45.455 11.45 0.00 0.00 2.15
1900 1969 6.054295 GCTACTTGATGAGATGATGGACTTT 58.946 40.000 0.00 0.00 0.00 2.66
1903 1972 3.548770 TGATGAGATGATGGACTTTGGC 58.451 45.455 0.00 0.00 0.00 4.52
1984 2053 2.217038 GGAGGTCACACAGAGGCCA 61.217 63.158 5.01 0.00 0.00 5.36
2002 2071 0.677731 CACCCATGGCAGTGACGAAT 60.678 55.000 14.16 0.00 36.01 3.34
2065 2134 3.527533 TGAAGTGCGATACATTACACCC 58.472 45.455 0.00 0.00 33.46 4.61
2084 2153 0.678048 CCTGCCCCTGTTTACTCTGC 60.678 60.000 0.00 0.00 0.00 4.26
2100 2169 3.567164 ACTCTGCTTCACTTTGATGGTTG 59.433 43.478 0.00 0.00 0.00 3.77
2271 2341 7.392418 CATGATATCATTCCCACAGTCATACT 58.608 38.462 15.74 0.00 33.61 2.12
2272 2342 7.333672 CATGATATCATTCCCACAGTCATACTG 59.666 40.741 15.74 5.53 42.35 2.74
2295 2365 8.834465 ACTGCAAATTCACTCTATGCTTATAAG 58.166 33.333 8.20 8.20 37.86 1.73
2420 2493 5.640189 TTAGGAGTGTGTAGTAGCAGTTC 57.360 43.478 0.00 0.00 0.00 3.01
2486 2559 6.403878 ACATACCCTGTCAACTACAACATAC 58.596 40.000 0.00 0.00 37.74 2.39
2692 2767 6.575244 ATGTTTTCCCTGTATATCCTGTGA 57.425 37.500 0.00 0.00 0.00 3.58
2693 2768 5.989477 TGTTTTCCCTGTATATCCTGTGAG 58.011 41.667 0.00 0.00 0.00 3.51
2694 2769 5.724370 TGTTTTCCCTGTATATCCTGTGAGA 59.276 40.000 0.00 0.00 0.00 3.27
2742 2819 3.848272 ATTTGTAACAGTGGAATGCCG 57.152 42.857 0.00 0.00 36.79 5.69
2972 3049 3.128938 GGACTATATCATTCGTCCCTCCG 59.871 52.174 0.00 0.00 39.96 4.63
3000 3077 6.823689 TGGAGCTTTTGATCTAATGACTTACC 59.176 38.462 6.91 0.00 34.81 2.85
3310 3387 3.963665 TGTTTTTCTCATTTCCAGCACG 58.036 40.909 0.00 0.00 0.00 5.34
3400 3477 1.823470 TTCTGCGGCATATGCACCC 60.823 57.895 28.07 15.64 44.36 4.61
3496 3573 5.304101 TGAACACTTTGGCTTCCATGTTATT 59.696 36.000 4.00 0.00 35.30 1.40
3499 3576 5.539955 ACACTTTGGCTTCCATGTTATTCTT 59.460 36.000 0.00 0.00 31.53 2.52
3500 3577 6.041979 ACACTTTGGCTTCCATGTTATTCTTT 59.958 34.615 0.00 0.00 31.53 2.52
3504 3581 4.158394 TGGCTTCCATGTTATTCTTTGCTC 59.842 41.667 0.00 0.00 0.00 4.26
3505 3582 4.400567 GGCTTCCATGTTATTCTTTGCTCT 59.599 41.667 0.00 0.00 0.00 4.09
3516 3593 8.883731 TGTTATTCTTTGCTCTATTGCTCTAAC 58.116 33.333 0.00 0.00 0.00 2.34
3528 3605 1.203313 TGCTCTAACTCCCTGGACCTT 60.203 52.381 0.00 0.00 0.00 3.50
3532 3609 4.019591 GCTCTAACTCCCTGGACCTTTTAA 60.020 45.833 0.00 0.00 0.00 1.52
3612 3689 0.969149 CAACCCCTGAAAAGAAGGCC 59.031 55.000 0.00 0.00 33.07 5.19
3666 3743 2.233271 ACTGTTTCAGGCATTCAGGTG 58.767 47.619 1.90 0.00 35.51 4.00
3696 3773 8.506437 CATCAGCTTTTGTTGTAGATCTGTTAA 58.494 33.333 5.18 0.00 32.23 2.01
3728 3806 1.534595 CTCACAACTTTCTCTGGCAGC 59.465 52.381 10.34 0.00 0.00 5.25
3730 3808 0.886490 ACAACTTTCTCTGGCAGCCG 60.886 55.000 10.34 3.30 0.00 5.52
3733 3811 1.302033 CTTTCTCTGGCAGCCGTGT 60.302 57.895 10.34 0.00 0.00 4.49
3784 3865 3.745975 TGCAGGTTCGTTATCTGAAAGTG 59.254 43.478 5.02 0.00 33.76 3.16
3832 3913 2.419574 CCCTTGGGTTAGGTACATCACG 60.420 54.545 0.00 0.00 33.17 4.35
3905 3986 3.188460 GGAGCAATCGAGCAGTTTGTTAA 59.812 43.478 0.00 0.00 36.85 2.01
4052 4138 6.001460 TCTCTTAGTGGTTTTTACCCATGTG 58.999 40.000 0.00 0.00 33.76 3.21
4192 4279 1.478105 CTTGGGCCCTGTTTCTAATGC 59.522 52.381 25.70 0.00 0.00 3.56
4251 4341 8.114743 GGTGTATTACCCTCTGATACCTAGTAT 58.885 40.741 0.00 0.00 44.15 2.12
4285 4375 3.894427 ACAATTTGTTGGGTGCATGTCTA 59.106 39.130 0.00 0.00 0.00 2.59
4310 4400 3.643320 CTGTATTCCCTGTGGAGCATCTA 59.357 47.826 0.00 0.00 43.07 1.98
4345 4436 5.542635 ACCTCTCTTACCAGTGTGAATGTAA 59.457 40.000 0.00 0.00 0.00 2.41
4346 4437 6.213600 ACCTCTCTTACCAGTGTGAATGTAAT 59.786 38.462 0.00 0.00 0.00 1.89
4347 4438 6.536582 CCTCTCTTACCAGTGTGAATGTAATG 59.463 42.308 0.00 0.00 0.00 1.90
4348 4439 7.004555 TCTCTTACCAGTGTGAATGTAATGT 57.995 36.000 0.00 0.00 0.00 2.71
4349 4440 8.129496 TCTCTTACCAGTGTGAATGTAATGTA 57.871 34.615 0.00 0.00 0.00 2.29
4392 4483 6.449698 ACACCAGCAAATCTACAAAGAAATG 58.550 36.000 0.00 0.00 34.73 2.32
4395 4486 6.925165 ACCAGCAAATCTACAAAGAAATGTTG 59.075 34.615 0.00 0.00 34.73 3.33
4461 4557 2.032550 CGGTTGCCATCATGATTCTCAC 59.967 50.000 5.16 1.08 0.00 3.51
4465 4561 2.093021 TGCCATCATGATTCTCACGGAA 60.093 45.455 5.16 0.00 38.41 4.30
4493 4589 1.754234 GCAACTCCAATGGGGCGAT 60.754 57.895 0.00 0.00 36.21 4.58
4518 4615 1.005867 GTCCGCTGGTGTCCGTTTA 60.006 57.895 0.00 0.00 0.00 2.01
4527 4624 2.259511 GTCCGTTTAGGTCGGCGT 59.740 61.111 6.85 0.00 46.49 5.68
4550 4647 2.122167 ACAAAAAGCGGCCCAACGA 61.122 52.632 0.00 0.00 35.47 3.85
4571 4668 3.053291 GACCCAAATGGACGCGCA 61.053 61.111 5.73 0.00 37.39 6.09
4576 4673 2.435938 AAATGGACGCGCATCCGT 60.436 55.556 18.86 15.74 42.24 4.69
4613 4712 1.521616 CCATTCCCGGCCCATTTTG 59.478 57.895 0.00 0.00 0.00 2.44
4614 4713 0.975040 CCATTCCCGGCCCATTTTGA 60.975 55.000 0.00 0.00 0.00 2.69
4615 4714 0.461135 CATTCCCGGCCCATTTTGAG 59.539 55.000 0.00 0.00 0.00 3.02
4619 4720 3.825611 CGGCCCATTTTGAGCGGG 61.826 66.667 0.00 0.00 43.42 6.13
4625 4726 0.033228 CCATTTTGAGCGGGTTTGCA 59.967 50.000 0.00 0.00 37.31 4.08
4671 4777 2.363925 GCACCTACTCTCCCCGGT 60.364 66.667 0.00 0.00 0.00 5.28
4719 4826 1.304936 TTCCCCCAAAAACCCTCCCA 61.305 55.000 0.00 0.00 0.00 4.37
4753 4863 4.343323 CCACACCCGCCATGGACA 62.343 66.667 18.40 0.00 42.00 4.02
4756 4866 2.282110 CACCCGCCATGGACAACA 60.282 61.111 18.40 0.00 42.00 3.33
4785 4932 4.117661 GACGCCGTCGCCTCTCTT 62.118 66.667 0.00 0.00 39.84 2.85
5026 5220 2.031163 GCACAGCCTCCTCAACGT 59.969 61.111 0.00 0.00 0.00 3.99
5146 5363 0.818445 GTCTACCCGCATCTCTCCGA 60.818 60.000 0.00 0.00 0.00 4.55
5155 5372 1.110442 CATCTCTCCGAGGAGTGCTT 58.890 55.000 17.75 5.17 42.49 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.125097 TGAGTCTCTTTAGTGATCCGGTAAC 59.875 44.000 0.00 0.00 0.00 2.50
18 19 7.915923 GGAAAAAGGTTTGTTGAGTCTCTTTAG 59.084 37.037 0.65 0.00 0.00 1.85
24 25 3.380320 CCGGAAAAAGGTTTGTTGAGTCT 59.620 43.478 0.00 0.00 0.00 3.24
31 32 0.462375 GGCACCGGAAAAAGGTTTGT 59.538 50.000 9.46 0.00 40.59 2.83
59 60 7.225538 CACAATGACTAGTGACATAATTCCTCC 59.774 40.741 0.00 0.00 37.97 4.30
60 61 7.254590 GCACAATGACTAGTGACATAATTCCTC 60.255 40.741 0.00 0.00 37.97 3.71
68 69 5.420421 ACTCTAGCACAATGACTAGTGACAT 59.580 40.000 0.00 0.00 37.97 3.06
125 126 8.641499 TGGCACAAAATAAAAACTAGAACAAG 57.359 30.769 0.00 0.00 31.92 3.16
139 140 9.383519 TTGAATAACAAAACTTGGCACAAAATA 57.616 25.926 0.00 0.00 38.59 1.40
140 141 8.273780 TTGAATAACAAAACTTGGCACAAAAT 57.726 26.923 0.00 0.00 38.59 1.82
188 189 4.850680 ACAACAAAGTCTTCAAGGGTACA 58.149 39.130 0.00 0.00 0.00 2.90
192 193 3.699038 TGGAACAACAAAGTCTTCAAGGG 59.301 43.478 0.00 0.00 31.92 3.95
217 218 8.902806 CATTAGATTGTGGAATTGGCTTACTTA 58.097 33.333 0.00 0.00 0.00 2.24
221 222 7.178274 ACAACATTAGATTGTGGAATTGGCTTA 59.822 33.333 0.00 0.00 38.84 3.09
222 223 6.014327 ACAACATTAGATTGTGGAATTGGCTT 60.014 34.615 0.00 0.00 38.84 4.35
224 225 5.723295 ACAACATTAGATTGTGGAATTGGC 58.277 37.500 0.00 0.00 38.84 4.52
225 226 9.139174 GTAAACAACATTAGATTGTGGAATTGG 57.861 33.333 0.00 0.00 40.16 3.16
250 251 0.248012 TCATGGGCGTTGTATGACGT 59.752 50.000 0.00 0.00 44.50 4.34
352 353 1.170442 TGTGTCGTCGCTTCCTCATA 58.830 50.000 0.00 0.00 0.00 2.15
379 380 4.096231 CACCAAAATGACGCATGGATCTTA 59.904 41.667 0.00 0.00 36.75 2.10
380 381 3.091545 ACCAAAATGACGCATGGATCTT 58.908 40.909 0.00 0.00 36.75 2.40
398 399 0.679640 GGAATCCATTGCGTCCACCA 60.680 55.000 0.00 0.00 0.00 4.17
484 491 2.203082 CCGATGAGGAGATGGCCGA 61.203 63.158 0.00 0.00 45.00 5.54
588 605 1.436336 CGTACCCAAGCTCCCGTAG 59.564 63.158 0.00 0.00 0.00 3.51
631 649 0.448990 TCCACTCGTCGAACCATACG 59.551 55.000 0.00 0.00 40.40 3.06
749 786 4.371417 ACCGGCACCCCTCGTCTA 62.371 66.667 0.00 0.00 0.00 2.59
773 810 4.698276 CCTTAAACAGACATCAAACGTCG 58.302 43.478 0.00 0.00 38.46 5.12
785 822 3.575256 TCCAGACTAACGCCTTAAACAGA 59.425 43.478 0.00 0.00 0.00 3.41
826 863 2.753043 GTACGGCCCGGTCTCTGA 60.753 66.667 8.57 0.00 0.00 3.27
828 865 2.043248 ATGTACGGCCCGGTCTCT 60.043 61.111 8.57 0.00 0.00 3.10
830 867 4.157120 GCATGTACGGCCCGGTCT 62.157 66.667 8.57 0.00 0.00 3.85
831 868 4.157120 AGCATGTACGGCCCGGTC 62.157 66.667 8.57 0.00 0.00 4.79
832 869 4.157120 GAGCATGTACGGCCCGGT 62.157 66.667 8.57 0.00 0.00 5.28
833 870 2.023414 TAAGAGCATGTACGGCCCGG 62.023 60.000 8.57 0.00 0.00 5.73
835 872 0.532196 GGTAAGAGCATGTACGGCCC 60.532 60.000 0.00 0.00 0.00 5.80
839 900 4.051922 GGATCAAGGTAAGAGCATGTACG 58.948 47.826 0.00 0.00 0.00 3.67
843 904 4.148128 ACAGGATCAAGGTAAGAGCATG 57.852 45.455 0.00 0.00 38.90 4.06
905 966 3.826729 GCCAGGATTAGTTGTTGGTCTTT 59.173 43.478 0.00 0.00 0.00 2.52
963 1024 1.738099 CGGTTCTCTTGCTGTCCCG 60.738 63.158 0.00 0.00 0.00 5.14
997 1058 0.465460 GGTTGTGCTGAGTGGTTGGA 60.465 55.000 0.00 0.00 0.00 3.53
1001 1062 1.451936 GGAGGTTGTGCTGAGTGGT 59.548 57.895 0.00 0.00 0.00 4.16
1002 1063 1.302832 GGGAGGTTGTGCTGAGTGG 60.303 63.158 0.00 0.00 0.00 4.00
1004 1065 2.883828 CGGGGAGGTTGTGCTGAGT 61.884 63.158 0.00 0.00 0.00 3.41
1005 1066 2.046892 CGGGGAGGTTGTGCTGAG 60.047 66.667 0.00 0.00 0.00 3.35
1006 1067 4.329545 GCGGGGAGGTTGTGCTGA 62.330 66.667 0.00 0.00 0.00 4.26
1192 1254 0.531532 GATCTGGATCTGCCGGTGTG 60.532 60.000 1.90 0.00 44.00 3.82
1377 1445 2.759535 CTGCACAGATCTGAGAGGAGAA 59.240 50.000 29.27 5.34 0.00 2.87
1404 1472 1.427592 GCAGAGCTCAGACCGCAATC 61.428 60.000 17.77 0.00 0.00 2.67
1638 1707 2.274437 TGCTCGCAATGCTAAAGAGAG 58.726 47.619 11.15 6.62 33.19 3.20
1685 1754 3.490759 GCCCACGCACAGATCACG 61.491 66.667 0.00 0.00 34.03 4.35
1731 1800 2.628021 CCCTCAGAGATTCCTCCTCCAA 60.628 54.545 0.00 0.00 40.30 3.53
1834 1903 0.474184 CGTCCATAAGCCCCTCCAAT 59.526 55.000 0.00 0.00 0.00 3.16
1877 1946 6.482641 CCAAAGTCCATCATCTCATCAAGTAG 59.517 42.308 0.00 0.00 0.00 2.57
1903 1972 2.408050 GCCTCTGTGTATTGCGGATAG 58.592 52.381 0.00 0.00 0.00 2.08
1984 2053 0.677731 CATTCGTCACTGCCATGGGT 60.678 55.000 15.13 0.00 0.00 4.51
2065 2134 0.678048 GCAGAGTAAACAGGGGCAGG 60.678 60.000 0.00 0.00 0.00 4.85
2084 2153 4.898829 TCACACAACCATCAAAGTGAAG 57.101 40.909 0.00 0.00 33.55 3.02
2100 2169 5.200368 AGTCAACAATTTTCCCATCACAC 57.800 39.130 0.00 0.00 0.00 3.82
2191 2260 2.223900 GCCGATGATGTCAGATCTCACA 60.224 50.000 0.50 0.50 0.00 3.58
2230 2299 8.267620 TGATATCATGGAGTTACCTCAGAAAT 57.732 34.615 0.00 0.00 39.64 2.17
2245 2314 4.976864 TGACTGTGGGAATGATATCATGG 58.023 43.478 18.85 6.39 36.56 3.66
2271 2341 8.737168 ACTTATAAGCATAGAGTGAATTTGCA 57.263 30.769 12.54 0.00 35.79 4.08
2272 2342 8.830580 TGACTTATAAGCATAGAGTGAATTTGC 58.169 33.333 12.54 0.00 0.00 3.68
2282 2352 5.798125 AGCAGCTGACTTATAAGCATAGA 57.202 39.130 20.43 0.00 42.06 1.98
2323 2395 4.510711 CAGAGCTACATGGATGTGATTCAC 59.489 45.833 9.93 9.93 41.89 3.18
2420 2493 8.870160 TTTATTCCTCACTGTCAATTTGTTTG 57.130 30.769 0.00 0.00 36.61 2.93
2472 2545 6.647481 ACTTGCAATACGTATGTTGTAGTTGA 59.353 34.615 9.24 0.00 29.99 3.18
2598 2673 2.614057 CAGCTGGTTCGAGTCAAAGTTT 59.386 45.455 5.57 0.00 0.00 2.66
2692 2767 8.437575 TGCATATCAGCCATGATGAATATATCT 58.562 33.333 0.00 0.00 45.89 1.98
2693 2768 8.617290 TGCATATCAGCCATGATGAATATATC 57.383 34.615 0.00 0.00 45.89 1.63
2694 2769 9.014297 CATGCATATCAGCCATGATGAATATAT 57.986 33.333 0.00 0.00 45.89 0.86
2742 2819 4.825085 TCATTCAACCCAAGTTTACACTCC 59.175 41.667 0.00 0.00 32.45 3.85
2972 3049 6.060788 AGTCATTAGATCAAAAGCTCCATCC 58.939 40.000 0.00 0.00 0.00 3.51
3310 3387 8.027189 GGTACTTCAATTTCTACATTTGTTCCC 58.973 37.037 0.00 0.00 0.00 3.97
3400 3477 0.453793 AGACCATTGCGTCTCTCTCG 59.546 55.000 2.95 0.00 38.83 4.04
3482 3559 4.400567 AGAGCAAAGAATAACATGGAAGCC 59.599 41.667 0.00 0.00 0.00 4.35
3496 3573 5.395768 GGGAGTTAGAGCAATAGAGCAAAGA 60.396 44.000 0.00 0.00 36.85 2.52
3499 3576 4.033709 AGGGAGTTAGAGCAATAGAGCAA 58.966 43.478 0.00 0.00 36.85 3.91
3500 3577 3.386078 CAGGGAGTTAGAGCAATAGAGCA 59.614 47.826 0.00 0.00 36.85 4.26
3504 3581 3.070302 GGTCCAGGGAGTTAGAGCAATAG 59.930 52.174 0.00 0.00 0.00 1.73
3505 3582 3.039011 GGTCCAGGGAGTTAGAGCAATA 58.961 50.000 0.00 0.00 0.00 1.90
3516 3593 6.465035 CCTGATAGATTAAAAGGTCCAGGGAG 60.465 46.154 0.00 0.00 36.07 4.30
3532 3609 9.706529 TGCTCTACACATATATTCCTGATAGAT 57.293 33.333 0.00 0.00 0.00 1.98
3612 3689 5.621197 TCTCAAATTTCACACGTATTGGG 57.379 39.130 0.00 0.00 0.00 4.12
3678 3755 8.770828 GCTAACTGTTAACAGATCTACAACAAA 58.229 33.333 36.14 10.14 46.59 2.83
3696 3773 1.417890 AGTTGTGAGGCAGCTAACTGT 59.582 47.619 0.00 0.00 46.30 3.55
3728 3806 3.509967 TGGTATATGAGCAGGATACACGG 59.490 47.826 0.00 0.00 41.41 4.94
3730 3808 6.042638 ACATGGTATATGAGCAGGATACAC 57.957 41.667 0.00 0.00 39.70 2.90
3733 3811 8.924303 GGTATAACATGGTATATGAGCAGGATA 58.076 37.037 13.52 0.00 39.70 2.59
3784 3865 4.372656 CCTGGTATCCACTTTTCTCGATC 58.627 47.826 0.00 0.00 0.00 3.69
3832 3913 2.812591 CAGCTCATATTCACCAGCCATC 59.187 50.000 0.00 0.00 31.81 3.51
3905 3986 1.077068 CCTCGCCTCCTCAGACTCT 60.077 63.158 0.00 0.00 0.00 3.24
4052 4138 3.555956 CCGATGGATGTAACTTACAGCAC 59.444 47.826 16.89 8.48 46.29 4.40
4151 4238 5.411831 AGCTTGTGAGTGACATCAATAGA 57.588 39.130 0.00 0.00 33.40 1.98
4251 4341 7.923344 CACCCAACAAATTGTTTTACTCATGTA 59.077 33.333 8.85 0.00 38.77 2.29
4264 4354 3.389925 AGACATGCACCCAACAAATTG 57.610 42.857 0.00 0.00 35.40 2.32
4268 4358 2.371841 AGAGTAGACATGCACCCAACAA 59.628 45.455 0.00 0.00 0.00 2.83
4285 4375 1.834263 GCTCCACAGGGAATACAGAGT 59.166 52.381 0.00 0.00 44.38 3.24
4310 4400 5.580998 TGGTAAGAGAGGTCAATACAGTCT 58.419 41.667 0.00 0.00 0.00 3.24
4345 4436 2.239402 TGCACCACAGGTCATCATACAT 59.761 45.455 0.00 0.00 31.02 2.29
4346 4437 1.627834 TGCACCACAGGTCATCATACA 59.372 47.619 0.00 0.00 31.02 2.29
4347 4438 2.283298 CTGCACCACAGGTCATCATAC 58.717 52.381 0.00 0.00 43.19 2.39
4348 4439 2.696989 CTGCACCACAGGTCATCATA 57.303 50.000 0.00 0.00 43.19 2.15
4349 4440 3.564262 CTGCACCACAGGTCATCAT 57.436 52.632 0.00 0.00 43.19 2.45
4378 4469 7.229306 TGCTCAGTTCAACATTTCTTTGTAGAT 59.771 33.333 0.00 0.00 0.00 1.98
4392 4483 5.173774 TGTTTCAGATTGCTCAGTTCAAC 57.826 39.130 0.00 0.00 0.00 3.18
4395 4486 5.855395 GTGATTGTTTCAGATTGCTCAGTTC 59.145 40.000 0.00 0.00 34.17 3.01
4461 4557 4.253685 TGGAGTTGCTCTAAGAAATTCCG 58.746 43.478 5.13 0.00 41.30 4.30
4465 4561 4.952335 CCCATTGGAGTTGCTCTAAGAAAT 59.048 41.667 3.62 0.00 34.66 2.17
4493 4589 0.669318 GACACCAGCGGACGAAATGA 60.669 55.000 0.00 0.00 0.00 2.57
4518 4615 2.596553 TTTTGTGTCCACGCCGACCT 62.597 55.000 0.00 0.00 31.35 3.85
4527 4624 2.494530 GGGCCGCTTTTTGTGTCCA 61.495 57.895 0.00 0.00 0.00 4.02
4550 4647 2.046314 CGTCCATTTGGGTCGGCT 60.046 61.111 0.00 0.00 43.28 5.52
4613 4712 4.179579 GCCGATGCAAACCCGCTC 62.180 66.667 0.00 0.00 37.47 5.03
4619 4720 2.869702 GTTCGCGCCGATGCAAAC 60.870 61.111 0.00 0.00 35.23 2.93
4625 4726 4.111016 TCTCGTGTTCGCGCCGAT 62.111 61.111 0.00 0.00 35.23 4.18
4634 4735 2.729862 GCGCGTCTGTCTCGTGTT 60.730 61.111 8.43 0.00 40.28 3.32
4656 4757 2.688538 GGACCGGGGAGAGTAGGT 59.311 66.667 6.32 0.00 40.11 3.08
4769 4915 4.421479 CAAGAGAGGCGACGGCGT 62.421 66.667 14.65 14.65 41.24 5.68
4785 4932 1.600636 CACGAGGCTTGCCTTTCCA 60.601 57.895 15.92 0.00 0.00 3.53
5048 5245 3.202706 GGAAACGCCGATGAGCCC 61.203 66.667 0.00 0.00 0.00 5.19
5146 5363 4.379243 CGTCGGGCAAGCACTCCT 62.379 66.667 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.