Multiple sequence alignment - TraesCS4D01G123600

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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 TraesCS4D01G123600 chr4D 100.000 2447 0 0 1 2447 108049243 108046797 0.000000e+00 4519.0
1 TraesCS4D01G123600 chr4D 95.312 128 6 0 527 654 108048683 108048556 1.150000e-48 204.0
2 TraesCS4D01G123600 chr4D 95.312 128 6 0 561 688 108048717 108048590 1.150000e-48 204.0
3 TraesCS4D01G123600 chr4D 95.745 94 4 0 527 620 108048649 108048556 4.210000e-33 152.0
4 TraesCS4D01G123600 chr4D 95.745 94 4 0 595 688 108048717 108048624 4.210000e-33 152.0
5 TraesCS4D01G123600 chr4D 93.333 60 4 0 527 586 108048615 108048556 3.350000e-14 89.8
6 TraesCS4D01G123600 chr4B 92.484 1836 104 16 629 2445 168574476 168576296 0.000000e+00 2595.0
7 TraesCS4D01G123600 chr4B 95.400 587 25 2 1 586 168573950 168574535 0.000000e+00 933.0
8 TraesCS4D01G123600 chr4B 76.585 410 72 21 828 1228 623018744 623019138 1.150000e-48 204.0
9 TraesCS4D01G123600 chr4B 95.000 60 3 0 595 654 168574476 168574535 7.200000e-16 95.3
10 TraesCS4D01G123600 chr4A 87.123 1359 134 14 629 1956 468210874 468212222 0.000000e+00 1502.0
11 TraesCS4D01G123600 chr4A 86.755 604 55 9 1 586 468210337 468210933 0.000000e+00 649.0
12 TraesCS4D01G123600 chr4A 87.269 487 51 6 1901 2384 468212211 468212689 1.650000e-151 545.0
13 TraesCS4D01G123600 chr4A 81.864 590 92 9 1 586 518856925 518856347 1.320000e-132 483.0
14 TraesCS4D01G123600 chr4A 93.333 60 4 0 561 620 468210874 468210933 3.350000e-14 89.8
15 TraesCS4D01G123600 chr4A 93.333 60 4 0 595 654 468210874 468210933 3.350000e-14 89.8
16 TraesCS4D01G123600 chr1D 83.747 1329 160 24 636 1939 141897403 141896106 0.000000e+00 1206.0
17 TraesCS4D01G123600 chr1D 86.264 961 109 8 629 1573 338746144 338745191 0.000000e+00 1022.0
18 TraesCS4D01G123600 chr1D 85.448 591 74 7 1 586 141897936 141897353 2.690000e-169 604.0
19 TraesCS4D01G123600 chr1D 75.617 324 69 8 1752 2068 451193856 451194176 4.210000e-33 152.0
20 TraesCS4D01G123600 chr3D 83.320 1271 151 36 832 2081 116080254 116079024 0.000000e+00 1116.0
21 TraesCS4D01G123600 chr3D 87.461 319 27 7 2079 2394 443428500 443428192 2.990000e-94 355.0
22 TraesCS4D01G123600 chr3D 84.691 307 33 9 2079 2381 19719473 19719177 6.620000e-76 294.0
23 TraesCS4D01G123600 chr3D 82.143 308 39 11 2080 2384 11206253 11205959 1.450000e-62 250.0
24 TraesCS4D01G123600 chr3D 76.623 385 71 14 1704 2080 124068972 124069345 6.900000e-46 195.0
25 TraesCS4D01G123600 chr7A 83.730 1051 132 22 663 1695 238870908 238871937 0.000000e+00 957.0
26 TraesCS4D01G123600 chr7A 87.379 309 27 6 2079 2384 408692628 408692927 6.480000e-91 344.0
27 TraesCS4D01G123600 chr7A 75.289 692 127 29 1341 2013 531181972 531182638 8.560000e-75 291.0
28 TraesCS4D01G123600 chr7A 82.201 309 37 14 2079 2381 5009405 5009109 1.450000e-62 250.0
29 TraesCS4D01G123600 chr7A 80.180 333 54 10 1752 2082 238873404 238873726 3.140000e-59 239.0
30 TraesCS4D01G123600 chr5A 79.673 1407 215 40 719 2078 354971350 354969968 0.000000e+00 948.0
31 TraesCS4D01G123600 chr5A 79.205 327 65 2 936 1259 668982794 668983120 8.810000e-55 224.0
32 TraesCS4D01G123600 chr1A 85.558 914 110 9 716 1611 148747061 148747970 0.000000e+00 937.0
33 TraesCS4D01G123600 chr1A 80.665 662 92 14 716 1359 124532667 124533310 4.730000e-132 481.0
34 TraesCS4D01G123600 chr1A 89.091 110 12 0 656 765 148746975 148747084 1.180000e-28 137.0
35 TraesCS4D01G123600 chr7B 80.225 1244 170 35 637 1860 413576753 413575566 0.000000e+00 865.0
36 TraesCS4D01G123600 chr3B 82.425 899 122 19 1197 2082 169657830 169656955 0.000000e+00 752.0
37 TraesCS4D01G123600 chr3B 82.863 496 78 6 1 494 433749164 433749654 2.890000e-119 438.0
38 TraesCS4D01G123600 chr3B 86.084 309 31 8 2079 2384 581132222 581131923 3.040000e-84 322.0
39 TraesCS4D01G123600 chr3B 82.041 245 32 7 2079 2319 2132526 2132290 5.340000e-47 198.0
40 TraesCS4D01G123600 chr1B 89.239 539 57 1 656 1193 196059351 196058813 0.000000e+00 673.0
41 TraesCS4D01G123600 chr1B 82.231 726 105 15 1197 1913 196048735 196048025 2.690000e-169 604.0
42 TraesCS4D01G123600 chr1B 84.890 589 79 6 1 586 196059900 196059319 9.750000e-164 586.0
43 TraesCS4D01G123600 chr3A 76.055 1161 216 43 742 1855 707115841 707116986 4.600000e-152 547.0
44 TraesCS4D01G123600 chr3A 83.662 557 82 8 1 552 51696842 51696290 1.300000e-142 516.0
45 TraesCS4D01G123600 chr5B 87.202 461 48 3 796 1246 439876977 439876518 4.670000e-142 514.0
46 TraesCS4D01G123600 chr5B 80.640 594 92 15 607 1199 230690721 230690150 2.890000e-119 438.0
47 TraesCS4D01G123600 chr5B 81.238 533 89 7 5 530 439877648 439877120 1.050000e-113 420.0
48 TraesCS4D01G123600 chr5B 81.198 484 70 12 1481 1956 302066143 302065673 1.070000e-98 370.0
49 TraesCS4D01G123600 chr5D 85.356 478 60 9 1 473 512390127 512389655 1.020000e-133 486.0
50 TraesCS4D01G123600 chr5D 83.333 426 54 8 1078 1487 391275298 391274874 6.390000e-101 377.0
51 TraesCS4D01G123600 chr2B 87.338 308 28 4 2079 2383 488002081 488002380 2.330000e-90 342.0
52 TraesCS4D01G123600 chr2B 93.478 46 3 0 2073 2118 63172229 63172274 4.370000e-08 69.4
53 TraesCS4D01G123600 chr2D 89.020 255 24 3 2133 2384 327757901 327757648 1.830000e-81 313.0
54 TraesCS4D01G123600 chr2D 84.688 320 36 6 2079 2394 61329513 61329203 8.500000e-80 307.0
55 TraesCS4D01G123600 chr7D 82.196 337 54 4 887 1223 494988559 494988889 3.980000e-73 285.0
56 TraesCS4D01G123600 chr7D 75.393 382 69 19 1704 2074 535833334 535833701 7.000000e-36 161.0
57 TraesCS4D01G123600 chr6A 78.892 379 68 5 884 1250 559138797 559139175 1.880000e-61 246.0


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 TraesCS4D01G123600 chr4D 108046797 108049243 2446 True 886.800000 4519 95.907833 1 2447 6 chr4D.!!$R1 2446
1 TraesCS4D01G123600 chr4B 168573950 168576296 2346 False 1207.766667 2595 94.294667 1 2445 3 chr4B.!!$F2 2444
2 TraesCS4D01G123600 chr4A 468210337 468212689 2352 False 575.120000 1502 89.562600 1 2384 5 chr4A.!!$F1 2383
3 TraesCS4D01G123600 chr4A 518856347 518856925 578 True 483.000000 483 81.864000 1 586 1 chr4A.!!$R1 585
4 TraesCS4D01G123600 chr1D 338745191 338746144 953 True 1022.000000 1022 86.264000 629 1573 1 chr1D.!!$R1 944
5 TraesCS4D01G123600 chr1D 141896106 141897936 1830 True 905.000000 1206 84.597500 1 1939 2 chr1D.!!$R2 1938
6 TraesCS4D01G123600 chr3D 116079024 116080254 1230 True 1116.000000 1116 83.320000 832 2081 1 chr3D.!!$R3 1249
7 TraesCS4D01G123600 chr7A 238870908 238873726 2818 False 598.000000 957 81.955000 663 2082 2 chr7A.!!$F3 1419
8 TraesCS4D01G123600 chr7A 531181972 531182638 666 False 291.000000 291 75.289000 1341 2013 1 chr7A.!!$F2 672
9 TraesCS4D01G123600 chr5A 354969968 354971350 1382 True 948.000000 948 79.673000 719 2078 1 chr5A.!!$R1 1359
10 TraesCS4D01G123600 chr1A 148746975 148747970 995 False 537.000000 937 87.324500 656 1611 2 chr1A.!!$F2 955
11 TraesCS4D01G123600 chr1A 124532667 124533310 643 False 481.000000 481 80.665000 716 1359 1 chr1A.!!$F1 643
12 TraesCS4D01G123600 chr7B 413575566 413576753 1187 True 865.000000 865 80.225000 637 1860 1 chr7B.!!$R1 1223
13 TraesCS4D01G123600 chr3B 169656955 169657830 875 True 752.000000 752 82.425000 1197 2082 1 chr3B.!!$R2 885
14 TraesCS4D01G123600 chr1B 196058813 196059900 1087 True 629.500000 673 87.064500 1 1193 2 chr1B.!!$R2 1192
15 TraesCS4D01G123600 chr1B 196048025 196048735 710 True 604.000000 604 82.231000 1197 1913 1 chr1B.!!$R1 716
16 TraesCS4D01G123600 chr3A 707115841 707116986 1145 False 547.000000 547 76.055000 742 1855 1 chr3A.!!$F1 1113
17 TraesCS4D01G123600 chr3A 51696290 51696842 552 True 516.000000 516 83.662000 1 552 1 chr3A.!!$R1 551
18 TraesCS4D01G123600 chr5B 439876518 439877648 1130 True 467.000000 514 84.220000 5 1246 2 chr5B.!!$R3 1241
19 TraesCS4D01G123600 chr5B 230690150 230690721 571 True 438.000000 438 80.640000 607 1199 1 chr5B.!!$R1 592

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
299 314 0.179097 GACCCTCCATGAGAAGCGAC 60.179 60.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 3746 0.595095 GGACGTGTTCGGTAGTCTGT 59.405 55.0 0.0 0.0 41.85 3.41 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
134 144 4.154015 CGCACTTGATCACCACTAAAATGA 59.846 41.667 0.00 0.00 0.00 2.57
299 314 0.179097 GACCCTCCATGAGAAGCGAC 60.179 60.000 0.00 0.00 0.00 5.19
436 451 1.210234 CACCCTCATCATGGTAGTGCA 59.790 52.381 0.00 0.00 32.32 4.57
451 466 4.382320 GCACCCGTAGTTCCGGCA 62.382 66.667 0.00 0.00 46.71 5.69
551 574 2.985847 GTGGCACCACCTCCTTGC 60.986 66.667 6.29 0.00 40.79 4.01
552 575 3.497115 TGGCACCACCTCCTTGCA 61.497 61.111 0.00 0.00 40.22 4.08
553 576 2.036256 GGCACCACCTCCTTGCAT 59.964 61.111 0.00 0.00 38.04 3.96
554 577 2.345760 GGCACCACCTCCTTGCATG 61.346 63.158 0.00 0.00 38.04 4.06
555 578 2.998279 GCACCACCTCCTTGCATGC 61.998 63.158 11.82 11.82 36.22 4.06
556 579 2.036256 ACCACCTCCTTGCATGCC 59.964 61.111 16.68 0.00 0.00 4.40
557 580 2.757099 CCACCTCCTTGCATGCCC 60.757 66.667 16.68 0.00 0.00 5.36
558 581 2.357836 CACCTCCTTGCATGCCCT 59.642 61.111 16.68 0.00 0.00 5.19
559 582 1.304713 CACCTCCTTGCATGCCCTT 60.305 57.895 16.68 0.00 0.00 3.95
560 583 1.000396 ACCTCCTTGCATGCCCTTC 60.000 57.895 16.68 0.00 0.00 3.46
561 584 1.305623 CCTCCTTGCATGCCCTTCT 59.694 57.895 16.68 0.00 0.00 2.85
562 585 0.750911 CCTCCTTGCATGCCCTTCTC 60.751 60.000 16.68 0.00 0.00 2.87
563 586 0.750911 CTCCTTGCATGCCCTTCTCC 60.751 60.000 16.68 0.00 0.00 3.71
564 587 1.000521 CCTTGCATGCCCTTCTCCA 60.001 57.895 16.68 0.00 0.00 3.86
565 588 0.396695 CCTTGCATGCCCTTCTCCAT 60.397 55.000 16.68 0.00 0.00 3.41
566 589 1.133699 CCTTGCATGCCCTTCTCCATA 60.134 52.381 16.68 0.00 0.00 2.74
567 590 2.228059 CTTGCATGCCCTTCTCCATAG 58.772 52.381 16.68 0.00 0.00 2.23
568 591 0.475475 TGCATGCCCTTCTCCATAGG 59.525 55.000 16.68 0.00 0.00 2.57
569 592 0.892814 GCATGCCCTTCTCCATAGGC 60.893 60.000 6.36 0.00 45.96 3.93
571 594 2.427753 GCCCTTCTCCATAGGCGG 59.572 66.667 0.00 0.00 35.30 6.13
572 595 2.427753 CCCTTCTCCATAGGCGGC 59.572 66.667 0.00 0.00 0.00 6.53
573 596 2.443394 CCCTTCTCCATAGGCGGCA 61.443 63.158 13.08 0.00 0.00 5.69
574 597 1.227674 CCTTCTCCATAGGCGGCAC 60.228 63.158 13.08 0.00 0.00 5.01
575 598 1.227674 CTTCTCCATAGGCGGCACC 60.228 63.158 13.08 0.00 39.61 5.01
576 599 1.971505 CTTCTCCATAGGCGGCACCA 61.972 60.000 13.08 0.00 43.14 4.17
577 600 2.203070 CTCCATAGGCGGCACCAC 60.203 66.667 13.08 0.00 43.14 4.16
578 601 3.757248 CTCCATAGGCGGCACCACC 62.757 68.421 13.08 0.00 43.14 4.61
579 602 3.797353 CCATAGGCGGCACCACCT 61.797 66.667 13.08 1.15 43.14 4.00
580 603 2.203070 CATAGGCGGCACCACCTC 60.203 66.667 13.08 0.00 43.14 3.85
581 604 3.480133 ATAGGCGGCACCACCTCC 61.480 66.667 13.08 0.00 44.51 4.30
586 609 4.641645 CGGCACCACCTCCTTGCA 62.642 66.667 0.00 0.00 38.04 4.08
587 610 2.036256 GGCACCACCTCCTTGCAT 59.964 61.111 0.00 0.00 38.04 3.96
588 611 2.345760 GGCACCACCTCCTTGCATG 61.346 63.158 0.00 0.00 38.04 4.06
589 612 2.998279 GCACCACCTCCTTGCATGC 61.998 63.158 11.82 11.82 36.22 4.06
590 613 2.036256 ACCACCTCCTTGCATGCC 59.964 61.111 16.68 0.00 0.00 4.40
591 614 2.757099 CCACCTCCTTGCATGCCC 60.757 66.667 16.68 0.00 0.00 5.36
592 615 2.357836 CACCTCCTTGCATGCCCT 59.642 61.111 16.68 0.00 0.00 5.19
593 616 1.304713 CACCTCCTTGCATGCCCTT 60.305 57.895 16.68 0.00 0.00 3.95
594 617 1.000396 ACCTCCTTGCATGCCCTTC 60.000 57.895 16.68 0.00 0.00 3.46
595 618 1.305623 CCTCCTTGCATGCCCTTCT 59.694 57.895 16.68 0.00 0.00 2.85
596 619 0.750911 CCTCCTTGCATGCCCTTCTC 60.751 60.000 16.68 0.00 0.00 2.87
597 620 0.750911 CTCCTTGCATGCCCTTCTCC 60.751 60.000 16.68 0.00 0.00 3.71
598 621 1.000521 CCTTGCATGCCCTTCTCCA 60.001 57.895 16.68 0.00 0.00 3.86
599 622 0.396695 CCTTGCATGCCCTTCTCCAT 60.397 55.000 16.68 0.00 0.00 3.41
600 623 1.133699 CCTTGCATGCCCTTCTCCATA 60.134 52.381 16.68 0.00 0.00 2.74
601 624 2.228059 CTTGCATGCCCTTCTCCATAG 58.772 52.381 16.68 0.00 0.00 2.23
602 625 0.475475 TGCATGCCCTTCTCCATAGG 59.525 55.000 16.68 0.00 0.00 2.57
603 626 0.475906 GCATGCCCTTCTCCATAGGT 59.524 55.000 6.36 0.00 0.00 3.08
604 627 1.816961 GCATGCCCTTCTCCATAGGTG 60.817 57.143 6.36 0.00 0.00 4.00
606 629 1.149401 GCCCTTCTCCATAGGTGGC 59.851 63.158 0.00 0.00 45.63 5.01
607 630 1.635817 GCCCTTCTCCATAGGTGGCA 61.636 60.000 0.00 0.00 45.63 4.92
608 631 0.181350 CCCTTCTCCATAGGTGGCAC 59.819 60.000 9.70 9.70 45.63 5.01
609 632 0.181350 CCTTCTCCATAGGTGGCACC 59.819 60.000 29.32 29.32 45.63 5.01
610 633 0.911769 CTTCTCCATAGGTGGCACCA 59.088 55.000 36.28 22.90 45.63 4.17
611 634 0.618458 TTCTCCATAGGTGGCACCAC 59.382 55.000 36.28 12.66 45.63 4.16
619 642 2.985847 GTGGCACCACCTCCTTGC 60.986 66.667 6.29 0.00 40.79 4.01
620 643 3.497115 TGGCACCACCTCCTTGCA 61.497 61.111 0.00 0.00 40.22 4.08
621 644 2.036256 GGCACCACCTCCTTGCAT 59.964 61.111 0.00 0.00 38.04 3.96
622 645 2.345760 GGCACCACCTCCTTGCATG 61.346 63.158 0.00 0.00 38.04 4.06
623 646 2.998279 GCACCACCTCCTTGCATGC 61.998 63.158 11.82 11.82 36.22 4.06
624 647 2.036256 ACCACCTCCTTGCATGCC 59.964 61.111 16.68 0.00 0.00 4.40
625 648 2.757099 CCACCTCCTTGCATGCCC 60.757 66.667 16.68 0.00 0.00 5.36
626 649 2.357836 CACCTCCTTGCATGCCCT 59.642 61.111 16.68 0.00 0.00 5.19
627 650 1.304713 CACCTCCTTGCATGCCCTT 60.305 57.895 16.68 0.00 0.00 3.95
633 656 0.396695 CCTTGCATGCCCTTCTCCAT 60.397 55.000 16.68 0.00 0.00 3.41
634 657 1.133699 CCTTGCATGCCCTTCTCCATA 60.134 52.381 16.68 0.00 0.00 2.74
701 750 2.629617 CTCCTTGCCCTTGTCATTGTTT 59.370 45.455 0.00 0.00 0.00 2.83
947 1091 1.342275 CCCTTGAGGCATTGGATGGAA 60.342 52.381 0.00 0.00 0.00 3.53
1102 1248 3.330267 GAGTTGAAGTCGCTGATTCCTT 58.670 45.455 0.00 0.00 0.00 3.36
1259 1422 0.110486 AGTACTTTGGTGGCACTGGG 59.890 55.000 18.45 8.07 0.00 4.45
1297 1472 0.684805 GGAGGAGGAGGAAGAAGCGA 60.685 60.000 0.00 0.00 0.00 4.93
1319 1494 1.277557 GGAGATGGTTGTCAGAGCACT 59.722 52.381 0.00 0.00 0.00 4.40
1351 1526 5.353123 GGCCACTTTACTTTGACAATCGATA 59.647 40.000 0.00 0.00 0.00 2.92
1479 1667 8.788325 AACTATTGTGTAAGATTTACCCTGAC 57.212 34.615 0.00 0.00 0.00 3.51
1699 1898 0.247814 GCAGGTGATGTTGCGAATCG 60.248 55.000 0.00 0.00 0.00 3.34
1700 1899 1.358877 CAGGTGATGTTGCGAATCGA 58.641 50.000 6.91 0.00 0.00 3.59
1701 1900 1.731709 CAGGTGATGTTGCGAATCGAA 59.268 47.619 6.91 0.00 0.00 3.71
1702 1901 2.352651 CAGGTGATGTTGCGAATCGAAT 59.647 45.455 6.91 0.00 0.00 3.34
1703 1902 2.352651 AGGTGATGTTGCGAATCGAATG 59.647 45.455 6.91 0.00 0.00 2.67
1704 1903 2.104144 GTGATGTTGCGAATCGAATGC 58.896 47.619 6.91 0.00 0.00 3.56
1751 3379 1.078759 CTGTTGTCCGATCCGCTGAC 61.079 60.000 0.00 0.00 0.00 3.51
1781 3424 0.543174 GGTGAGAGTGGGAGAGTGGT 60.543 60.000 0.00 0.00 0.00 4.16
1805 3449 3.069318 GAAGGGGAGCGACGAGGT 61.069 66.667 0.00 0.00 0.00 3.85
1967 3658 1.077212 CCTGGCTGGGAGGTGATTG 60.077 63.158 1.84 0.00 0.00 2.67
2027 3720 6.004574 GGAACCAAACAACCTATTCTCTTCT 58.995 40.000 0.00 0.00 0.00 2.85
2052 3746 3.496337 CGTGGGTCTGACTAGCCTCTATA 60.496 52.174 7.85 0.00 37.91 1.31
2056 3750 4.202482 GGGTCTGACTAGCCTCTATACAGA 60.202 50.000 7.85 0.00 34.08 3.41
2062 3756 4.897140 ACTAGCCTCTATACAGACTACCG 58.103 47.826 0.00 0.00 0.00 4.02
2118 3814 2.801631 CCCCCGGTCTCTGCATCTC 61.802 68.421 0.00 0.00 0.00 2.75
2123 3819 1.142748 GGTCTCTGCATCTCGGTGG 59.857 63.158 0.00 0.00 0.00 4.61
2128 3824 2.046988 TGCATCTCGGTGGTGCAG 60.047 61.111 13.50 0.00 43.30 4.41
2129 3825 2.046892 GCATCTCGGTGGTGCAGT 60.047 61.111 10.22 0.00 38.68 4.40
2130 3826 2.393768 GCATCTCGGTGGTGCAGTG 61.394 63.158 10.22 0.00 38.68 3.66
2131 3827 1.742880 CATCTCGGTGGTGCAGTGG 60.743 63.158 0.00 0.00 0.00 4.00
2132 3828 2.217038 ATCTCGGTGGTGCAGTGGT 61.217 57.895 0.00 0.00 0.00 4.16
2133 3829 2.454832 ATCTCGGTGGTGCAGTGGTG 62.455 60.000 0.00 0.00 0.00 4.17
2288 3985 1.403679 CAAACAGACCTCGCACCAAAA 59.596 47.619 0.00 0.00 0.00 2.44
2331 4028 1.039068 CCAACCAAGCCACATTGTCA 58.961 50.000 0.00 0.00 0.00 3.58
2413 4110 2.725644 GTCACCACGACGTGAGATG 58.274 57.895 28.83 21.44 43.26 2.90
2438 4135 1.789464 CATCCTTCTGCGCGATTCTAC 59.211 52.381 12.10 0.00 0.00 2.59
2445 4142 1.343821 GCGCGATTCTACCAACACG 59.656 57.895 12.10 0.00 0.00 4.49
2446 4143 1.343821 CGCGATTCTACCAACACGC 59.656 57.895 0.00 0.00 42.07 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 120 3.394674 TTTAGTGGTGATCAAGTGCGA 57.605 42.857 0.00 0.00 0.00 5.10
451 466 2.430367 GAGACCCCAACGGCAAGT 59.570 61.111 0.00 0.00 33.26 3.16
544 567 0.750911 GGAGAAGGGCATGCAAGGAG 60.751 60.000 21.36 0.00 0.00 3.69
545 568 1.304282 GGAGAAGGGCATGCAAGGA 59.696 57.895 21.36 0.00 0.00 3.36
546 569 0.396695 ATGGAGAAGGGCATGCAAGG 60.397 55.000 21.36 0.00 0.00 3.61
547 570 2.228059 CTATGGAGAAGGGCATGCAAG 58.772 52.381 21.36 0.00 0.00 4.01
548 571 1.133699 CCTATGGAGAAGGGCATGCAA 60.134 52.381 21.36 0.00 0.00 4.08
549 572 0.475475 CCTATGGAGAAGGGCATGCA 59.525 55.000 21.36 0.00 0.00 3.96
550 573 0.892814 GCCTATGGAGAAGGGCATGC 60.893 60.000 9.90 9.90 43.59 4.06
551 574 0.604780 CGCCTATGGAGAAGGGCATG 60.605 60.000 0.00 0.00 44.27 4.06
552 575 1.757306 CGCCTATGGAGAAGGGCAT 59.243 57.895 0.00 0.00 44.27 4.40
553 576 2.443394 CCGCCTATGGAGAAGGGCA 61.443 63.158 0.00 0.00 44.27 5.36
554 577 2.427753 CCGCCTATGGAGAAGGGC 59.572 66.667 0.00 0.00 41.02 5.19
555 578 2.427753 GCCGCCTATGGAGAAGGG 59.572 66.667 0.00 0.00 34.46 3.95
556 579 1.227674 GTGCCGCCTATGGAGAAGG 60.228 63.158 0.00 0.00 37.17 3.46
557 580 1.227674 GGTGCCGCCTATGGAGAAG 60.228 63.158 0.00 0.00 0.00 2.85
558 581 1.992834 TGGTGCCGCCTATGGAGAA 60.993 57.895 0.00 0.00 38.35 2.87
559 582 2.364973 TGGTGCCGCCTATGGAGA 60.365 61.111 0.00 0.00 38.35 3.71
560 583 2.203070 GTGGTGCCGCCTATGGAG 60.203 66.667 0.00 0.00 38.35 3.86
561 584 3.792736 GGTGGTGCCGCCTATGGA 61.793 66.667 13.23 0.00 42.89 3.41
569 592 3.925630 ATGCAAGGAGGTGGTGCCG 62.926 63.158 0.00 0.00 43.70 5.69
570 593 2.036256 ATGCAAGGAGGTGGTGCC 59.964 61.111 0.00 0.00 37.48 5.01
571 594 2.998279 GCATGCAAGGAGGTGGTGC 61.998 63.158 14.21 0.00 38.78 5.01
572 595 2.345760 GGCATGCAAGGAGGTGGTG 61.346 63.158 21.36 0.00 0.00 4.17
573 596 2.036256 GGCATGCAAGGAGGTGGT 59.964 61.111 21.36 0.00 0.00 4.16
574 597 2.757099 GGGCATGCAAGGAGGTGG 60.757 66.667 21.36 0.00 0.00 4.61
575 598 1.304713 AAGGGCATGCAAGGAGGTG 60.305 57.895 21.36 0.00 0.00 4.00
576 599 1.000396 GAAGGGCATGCAAGGAGGT 60.000 57.895 21.36 0.00 0.00 3.85
577 600 0.750911 GAGAAGGGCATGCAAGGAGG 60.751 60.000 21.36 0.00 0.00 4.30
578 601 0.750911 GGAGAAGGGCATGCAAGGAG 60.751 60.000 21.36 0.00 0.00 3.69
579 602 1.304282 GGAGAAGGGCATGCAAGGA 59.696 57.895 21.36 0.00 0.00 3.36
580 603 0.396695 ATGGAGAAGGGCATGCAAGG 60.397 55.000 21.36 0.00 0.00 3.61
581 604 2.228059 CTATGGAGAAGGGCATGCAAG 58.772 52.381 21.36 0.00 0.00 4.01
582 605 1.133699 CCTATGGAGAAGGGCATGCAA 60.134 52.381 21.36 0.00 0.00 4.08
583 606 0.475475 CCTATGGAGAAGGGCATGCA 59.525 55.000 21.36 0.00 0.00 3.96
584 607 0.475906 ACCTATGGAGAAGGGCATGC 59.524 55.000 9.90 9.90 38.54 4.06
585 608 2.267174 CACCTATGGAGAAGGGCATG 57.733 55.000 0.00 0.00 38.54 4.06
602 625 2.985847 GCAAGGAGGTGGTGCCAC 60.986 66.667 12.66 12.66 45.49 5.01
603 626 2.844195 ATGCAAGGAGGTGGTGCCA 61.844 57.895 0.00 0.00 40.61 4.92
604 627 2.036256 ATGCAAGGAGGTGGTGCC 59.964 61.111 0.00 0.00 37.48 5.01
605 628 2.998279 GCATGCAAGGAGGTGGTGC 61.998 63.158 14.21 0.00 38.78 5.01
606 629 2.345760 GGCATGCAAGGAGGTGGTG 61.346 63.158 21.36 0.00 0.00 4.17
607 630 2.036256 GGCATGCAAGGAGGTGGT 59.964 61.111 21.36 0.00 0.00 4.16
608 631 2.757099 GGGCATGCAAGGAGGTGG 60.757 66.667 21.36 0.00 0.00 4.61
609 632 1.304713 AAGGGCATGCAAGGAGGTG 60.305 57.895 21.36 0.00 0.00 4.00
610 633 1.000396 GAAGGGCATGCAAGGAGGT 60.000 57.895 21.36 0.00 0.00 3.85
611 634 0.750911 GAGAAGGGCATGCAAGGAGG 60.751 60.000 21.36 0.00 0.00 4.30
612 635 0.750911 GGAGAAGGGCATGCAAGGAG 60.751 60.000 21.36 0.00 0.00 3.69
613 636 1.304282 GGAGAAGGGCATGCAAGGA 59.696 57.895 21.36 0.00 0.00 3.36
614 637 0.396695 ATGGAGAAGGGCATGCAAGG 60.397 55.000 21.36 0.00 0.00 3.61
615 638 2.228059 CTATGGAGAAGGGCATGCAAG 58.772 52.381 21.36 0.00 0.00 4.01
616 639 1.133699 CCTATGGAGAAGGGCATGCAA 60.134 52.381 21.36 0.00 0.00 4.08
617 640 0.475475 CCTATGGAGAAGGGCATGCA 59.525 55.000 21.36 0.00 0.00 3.96
618 641 0.892814 GCCTATGGAGAAGGGCATGC 60.893 60.000 9.90 9.90 43.59 4.06
619 642 0.604780 CGCCTATGGAGAAGGGCATG 60.605 60.000 0.00 0.00 44.27 4.06
620 643 1.757306 CGCCTATGGAGAAGGGCAT 59.243 57.895 0.00 0.00 44.27 4.40
621 644 2.443394 CCGCCTATGGAGAAGGGCA 61.443 63.158 0.00 0.00 44.27 5.36
622 645 2.427753 CCGCCTATGGAGAAGGGC 59.572 66.667 0.00 0.00 41.02 5.19
623 646 2.427753 GCCGCCTATGGAGAAGGG 59.572 66.667 0.00 0.00 34.46 3.95
624 647 1.227674 GTGCCGCCTATGGAGAAGG 60.228 63.158 0.00 0.00 37.17 3.46
625 648 1.227674 GGTGCCGCCTATGGAGAAG 60.228 63.158 0.00 0.00 0.00 2.85
626 649 1.992834 TGGTGCCGCCTATGGAGAA 60.993 57.895 0.00 0.00 38.35 2.87
627 650 2.364973 TGGTGCCGCCTATGGAGA 60.365 61.111 0.00 0.00 38.35 3.71
701 750 5.022282 TCATAATGCAGATCAAGTCGGAA 57.978 39.130 0.00 0.00 0.00 4.30
947 1091 2.531942 ACCCGGGGAAGAAAGCCT 60.532 61.111 27.92 0.00 0.00 4.58
1259 1422 1.595093 CGGCTCCAAACCAATGACCC 61.595 60.000 0.00 0.00 0.00 4.46
1297 1472 1.911357 TGCTCTGACAACCATCTCCAT 59.089 47.619 0.00 0.00 0.00 3.41
1319 1494 1.952621 AGTAAAGTGGCCTGGCTCTA 58.047 50.000 19.68 2.54 0.00 2.43
1351 1526 3.148279 GTCCTCGCCCGAGTCCAT 61.148 66.667 15.59 0.00 40.44 3.41
1479 1667 2.764269 TGAGTAGAAGGAGAATGGGGG 58.236 52.381 0.00 0.00 0.00 5.40
1661 1854 0.865111 CAACACTTCGACAATGGCGA 59.135 50.000 7.28 7.28 35.76 5.54
1699 1898 1.728490 GGCCTTCATCACCGGCATTC 61.728 60.000 0.00 0.00 45.53 2.67
1700 1899 1.754234 GGCCTTCATCACCGGCATT 60.754 57.895 0.00 0.00 45.53 3.56
1701 1900 2.124151 GGCCTTCATCACCGGCAT 60.124 61.111 0.00 0.00 45.53 4.40
1702 1901 4.776322 CGGCCTTCATCACCGGCA 62.776 66.667 0.00 0.00 45.53 5.69
1781 3424 2.364317 CGCTCCCCTTCCCTCTCA 60.364 66.667 0.00 0.00 0.00 3.27
1805 3449 5.766174 GCCGGTAATAATTTCCATCACCTTA 59.234 40.000 1.90 0.00 0.00 2.69
1967 3658 1.890979 CTGCATCGCATGGACCTCC 60.891 63.158 0.00 0.00 38.13 4.30
2021 3714 1.153939 CAGACCCACGCGAGAAGAG 60.154 63.158 15.93 0.00 0.00 2.85
2027 3720 2.697761 GCTAGTCAGACCCACGCGA 61.698 63.158 15.93 0.00 0.00 5.87
2052 3746 0.595095 GGACGTGTTCGGTAGTCTGT 59.405 55.000 0.00 0.00 41.85 3.41
2056 3750 2.163010 CACATAGGACGTGTTCGGTAGT 59.837 50.000 0.00 0.00 41.85 2.73
2128 3824 4.701956 ATAAAGTAGTTGCATGCACCAC 57.298 40.909 22.58 17.39 0.00 4.16
2129 3825 6.825944 TTAATAAAGTAGTTGCATGCACCA 57.174 33.333 22.58 3.29 0.00 4.17
2130 3826 9.965824 ATAATTAATAAAGTAGTTGCATGCACC 57.034 29.630 22.58 14.82 0.00 5.01
2288 3985 3.681874 GCCTCCGCTTTTAGATGTTAGGT 60.682 47.826 0.00 0.00 0.00 3.08
2407 4104 1.137675 CAGAAGGATGGCGTCATCTCA 59.862 52.381 27.71 0.00 46.70 3.27
2408 4105 1.863267 CAGAAGGATGGCGTCATCTC 58.137 55.000 27.71 18.74 46.70 2.75
2411 4108 1.522355 CGCAGAAGGATGGCGTCAT 60.522 57.895 0.00 0.00 45.27 3.06
2424 4121 0.245266 TGTTGGTAGAATCGCGCAGA 59.755 50.000 8.75 6.27 0.00 4.26


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

AutoCloner maintained by Alex Coulton.