Multiple sequence alignment - TraesCS3B01G532100

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 TraesCS3B01G532100 chr3B 100.000 5083 0 0 1 5083 772727572 772722490 0.000000e+00 9387
1 TraesCS3B01G532100 chr3B 89.241 1199 99 12 2448 3632 772987395 772986213 0.000000e+00 1472
2 TraesCS3B01G532100 chr3B 92.110 545 30 5 1635 2174 773006549 773006013 0.000000e+00 756
3 TraesCS3B01G532100 chr3B 88.163 566 55 9 16 577 682951768 682952325 0.000000e+00 664
4 TraesCS3B01G532100 chr3B 88.468 555 54 4 3628 4181 772959418 772958873 0.000000e+00 662
5 TraesCS3B01G532100 chr3B 87.611 565 57 9 16 577 465670929 465671483 1.190000e-180 643
6 TraesCS3B01G532100 chr3B 92.308 325 25 0 1037 1361 773029052 773028728 3.590000e-126 462
7 TraesCS3B01G532100 chr3B 89.315 365 27 6 577 939 773010921 773010567 1.000000e-121 448
8 TraesCS3B01G532100 chr3B 87.467 375 27 5 1034 1403 773036307 773035948 1.020000e-111 414
9 TraesCS3B01G532100 chr3B 88.923 325 36 0 1037 1361 772662949 772662625 7.930000e-108 401
10 TraesCS3B01G532100 chr3B 79.715 562 93 18 3510 4063 772466135 772465587 2.220000e-103 387
11 TraesCS3B01G532100 chr3B 78.428 598 98 21 3504 4085 773025794 773025212 1.350000e-95 361
12 TraesCS3B01G532100 chr3B 90.038 261 6 4 2200 2447 773005960 773005707 2.280000e-83 320
13 TraesCS3B01G532100 chr3B 80.157 383 74 2 3728 4109 773034880 773034499 8.330000e-73 285
14 TraesCS3B01G532100 chr3B 87.773 229 24 3 1680 1906 773028065 773027839 1.090000e-66 265
15 TraesCS3B01G532100 chr3B 88.372 215 25 0 1681 1895 772466905 772466691 5.050000e-65 259
16 TraesCS3B01G532100 chr3B 89.565 115 12 0 2060 2174 769704324 769704210 4.100000e-31 147
17 TraesCS3B01G532100 chr3A 90.274 1460 120 17 2801 4252 714365844 714364399 0.000000e+00 1890
18 TraesCS3B01G532100 chr3A 92.655 953 50 12 577 1516 714368642 714367697 0.000000e+00 1354
19 TraesCS3B01G532100 chr3A 92.045 440 27 4 4251 4683 726011133 726010695 3.360000e-171 612
20 TraesCS3B01G532100 chr3A 92.837 349 24 1 1034 1382 714423503 714423156 5.870000e-139 505
21 TraesCS3B01G532100 chr3A 92.331 326 25 0 1036 1361 714419953 714419628 9.970000e-127 464
22 TraesCS3B01G532100 chr3A 80.565 566 88 18 3510 4066 714290484 714289932 2.830000e-112 416
23 TraesCS3B01G532100 chr3A 93.050 259 16 1 1681 1939 714367495 714367239 1.340000e-100 377
24 TraesCS3B01G532100 chr3A 89.520 229 23 1 1681 1908 714423008 714422780 6.440000e-74 289
25 TraesCS3B01G532100 chr3A 87.391 230 23 5 1680 1906 714418734 714418508 5.050000e-65 259
26 TraesCS3B01G532100 chr3D 89.411 1426 67 42 577 1939 578772567 578773971 0.000000e+00 1720
27 TraesCS3B01G532100 chr3D 88.727 1375 110 18 2801 4145 578775246 578776605 0.000000e+00 1639
28 TraesCS3B01G532100 chr3D 92.765 857 27 9 4251 5082 141455000 141455846 0.000000e+00 1206
29 TraesCS3B01G532100 chr3D 84.226 672 69 15 3464 4116 578870910 578871563 2.010000e-173 619
30 TraesCS3B01G532100 chr3D 83.259 675 76 14 2761 3435 578870190 578870827 2.040000e-163 586
31 TraesCS3B01G532100 chr3D 92.615 325 24 0 1037 1361 578673892 578674216 7.710000e-128 468
32 TraesCS3B01G532100 chr3D 81.038 559 91 15 3510 4063 578927150 578927698 1.010000e-116 431
33 TraesCS3B01G532100 chr3D 88.081 344 33 6 1022 1361 578921669 578922008 7.930000e-108 401
34 TraesCS3B01G532100 chr3D 87.773 229 24 3 1680 1906 578675274 578675500 1.090000e-66 265
35 TraesCS3B01G532100 chr3D 88.837 215 24 0 1681 1895 578926389 578926603 1.090000e-66 265
36 TraesCS3B01G532100 chr3D 76.882 372 69 14 2390 2752 578869746 578870109 1.440000e-45 195
37 TraesCS3B01G532100 chr3D 97.115 104 3 0 4149 4252 578871563 578871666 5.230000e-40 176
38 TraesCS3B01G532100 chr5B 98.445 836 12 1 4249 5083 474469325 474470160 0.000000e+00 1471
39 TraesCS3B01G532100 chr5B 97.126 835 22 2 4250 5083 455258506 455259339 0.000000e+00 1408
40 TraesCS3B01G532100 chr5B 95.808 835 33 2 4249 5082 645086101 645086934 0.000000e+00 1347
41 TraesCS3B01G532100 chr5B 97.396 576 12 1 4507 5082 445180712 445181284 0.000000e+00 977
42 TraesCS3B01G532100 chr5B 88.793 116 12 1 2060 2175 640424629 640424743 1.910000e-29 141
43 TraesCS3B01G532100 chr2A 96.274 832 28 2 4251 5082 444666448 444665620 0.000000e+00 1362
44 TraesCS3B01G532100 chr5D 91.034 870 34 16 4251 5082 254357424 254356561 0.000000e+00 1134
45 TraesCS3B01G532100 chr7A 91.047 860 46 6 4247 5082 511445362 511446214 0.000000e+00 1133
46 TraesCS3B01G532100 chr7A 95.856 555 15 4 4528 5082 133639536 133638990 0.000000e+00 891
47 TraesCS3B01G532100 chr7A 87.931 116 14 0 2060 2175 532735280 532735395 2.470000e-28 137
48 TraesCS3B01G532100 chr7B 98.535 546 8 0 4537 5082 85833602 85834147 0.000000e+00 965
49 TraesCS3B01G532100 chr4A 97.996 549 11 0 4534 5082 650382751 650383299 0.000000e+00 953
50 TraesCS3B01G532100 chr6B 86.827 873 47 31 4251 5083 706069122 706069966 0.000000e+00 913
51 TraesCS3B01G532100 chr6B 87.698 569 59 10 16 577 17040431 17040995 0.000000e+00 652
52 TraesCS3B01G532100 chr6B 87.413 572 57 11 16 581 44058246 44058808 1.190000e-180 643
53 TraesCS3B01G532100 chr4B 88.360 567 54 9 16 577 472267464 472266905 0.000000e+00 671
54 TraesCS3B01G532100 chr1A 87.346 569 58 13 16 577 216458100 216457539 1.540000e-179 640
55 TraesCS3B01G532100 chr1B 87.279 566 60 9 16 577 493722540 493723097 2.000000e-178 636
56 TraesCS3B01G532100 chr1B 86.609 575 58 17 16 582 8963774 8964337 7.230000e-173 617
57 TraesCS3B01G532100 chr1B 88.696 115 13 0 2060 2174 427602993 427603107 1.910000e-29 141
58 TraesCS3B01G532100 chr2D 87.148 568 59 14 16 577 80110097 80109538 2.580000e-177 632
59 TraesCS3B01G532100 chr7D 92.601 446 22 6 4246 4683 521631660 521632102 9.290000e-177 630
60 TraesCS3B01G532100 chr7D 89.565 115 12 0 2060 2174 404245444 404245330 4.100000e-31 147
61 TraesCS3B01G532100 chr1D 90.517 116 11 0 2060 2175 494168579 494168464 2.450000e-33 154
62 TraesCS3B01G532100 chr1D 88.696 115 13 0 2060 2174 253222096 253222210 1.910000e-29 141
63 TraesCS3B01G532100 chr1D 88.696 115 13 0 2060 2174 288789714 288789828 1.910000e-29 141


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 TraesCS3B01G532100 chr3B 772722490 772727572 5082 True 9387.000000 9387 100.000000 1 5083 1 chr3B.!!$R3 5082
1 TraesCS3B01G532100 chr3B 772986213 772987395 1182 True 1472.000000 1472 89.241000 2448 3632 1 chr3B.!!$R5 1184
2 TraesCS3B01G532100 chr3B 682951768 682952325 557 False 664.000000 664 88.163000 16 577 1 chr3B.!!$F2 561
3 TraesCS3B01G532100 chr3B 772958873 772959418 545 True 662.000000 662 88.468000 3628 4181 1 chr3B.!!$R4 553
4 TraesCS3B01G532100 chr3B 465670929 465671483 554 False 643.000000 643 87.611000 16 577 1 chr3B.!!$F1 561
5 TraesCS3B01G532100 chr3B 773005707 773006549 842 True 538.000000 756 91.074000 1635 2447 2 chr3B.!!$R8 812
6 TraesCS3B01G532100 chr3B 773025212 773029052 3840 True 362.666667 462 86.169667 1037 4085 3 chr3B.!!$R9 3048
7 TraesCS3B01G532100 chr3B 773034499 773036307 1808 True 349.500000 414 83.812000 1034 4109 2 chr3B.!!$R10 3075
8 TraesCS3B01G532100 chr3B 772465587 772466905 1318 True 323.000000 387 84.043500 1681 4063 2 chr3B.!!$R7 2382
9 TraesCS3B01G532100 chr3A 714364399 714368642 4243 True 1207.000000 1890 91.993000 577 4252 3 chr3A.!!$R3 3675
10 TraesCS3B01G532100 chr3A 714289932 714290484 552 True 416.000000 416 80.565000 3510 4066 1 chr3A.!!$R1 556
11 TraesCS3B01G532100 chr3A 714418508 714423503 4995 True 379.250000 505 90.519750 1034 1908 4 chr3A.!!$R4 874
12 TraesCS3B01G532100 chr3D 578772567 578776605 4038 False 1679.500000 1720 89.069000 577 4145 2 chr3D.!!$F4 3568
13 TraesCS3B01G532100 chr3D 141455000 141455846 846 False 1206.000000 1206 92.765000 4251 5082 1 chr3D.!!$F1 831
14 TraesCS3B01G532100 chr3D 578869746 578871666 1920 False 394.000000 619 85.370500 2390 4252 4 chr3D.!!$F5 1862
15 TraesCS3B01G532100 chr3D 578673892 578675500 1608 False 366.500000 468 90.194000 1037 1906 2 chr3D.!!$F3 869
16 TraesCS3B01G532100 chr3D 578926389 578927698 1309 False 348.000000 431 84.937500 1681 4063 2 chr3D.!!$F6 2382
17 TraesCS3B01G532100 chr5B 474469325 474470160 835 False 1471.000000 1471 98.445000 4249 5083 1 chr5B.!!$F3 834
18 TraesCS3B01G532100 chr5B 455258506 455259339 833 False 1408.000000 1408 97.126000 4250 5083 1 chr5B.!!$F2 833
19 TraesCS3B01G532100 chr5B 645086101 645086934 833 False 1347.000000 1347 95.808000 4249 5082 1 chr5B.!!$F5 833
20 TraesCS3B01G532100 chr5B 445180712 445181284 572 False 977.000000 977 97.396000 4507 5082 1 chr5B.!!$F1 575
21 TraesCS3B01G532100 chr2A 444665620 444666448 828 True 1362.000000 1362 96.274000 4251 5082 1 chr2A.!!$R1 831
22 TraesCS3B01G532100 chr5D 254356561 254357424 863 True 1134.000000 1134 91.034000 4251 5082 1 chr5D.!!$R1 831
23 TraesCS3B01G532100 chr7A 511445362 511446214 852 False 1133.000000 1133 91.047000 4247 5082 1 chr7A.!!$F1 835
24 TraesCS3B01G532100 chr7A 133638990 133639536 546 True 891.000000 891 95.856000 4528 5082 1 chr7A.!!$R1 554
25 TraesCS3B01G532100 chr7B 85833602 85834147 545 False 965.000000 965 98.535000 4537 5082 1 chr7B.!!$F1 545
26 TraesCS3B01G532100 chr4A 650382751 650383299 548 False 953.000000 953 97.996000 4534 5082 1 chr4A.!!$F1 548
27 TraesCS3B01G532100 chr6B 706069122 706069966 844 False 913.000000 913 86.827000 4251 5083 1 chr6B.!!$F3 832
28 TraesCS3B01G532100 chr6B 17040431 17040995 564 False 652.000000 652 87.698000 16 577 1 chr6B.!!$F1 561
29 TraesCS3B01G532100 chr6B 44058246 44058808 562 False 643.000000 643 87.413000 16 581 1 chr6B.!!$F2 565
30 TraesCS3B01G532100 chr4B 472266905 472267464 559 True 671.000000 671 88.360000 16 577 1 chr4B.!!$R1 561
31 TraesCS3B01G532100 chr1A 216457539 216458100 561 True 640.000000 640 87.346000 16 577 1 chr1A.!!$R1 561
32 TraesCS3B01G532100 chr1B 493722540 493723097 557 False 636.000000 636 87.279000 16 577 1 chr1B.!!$F3 561
33 TraesCS3B01G532100 chr1B 8963774 8964337 563 False 617.000000 617 86.609000 16 582 1 chr1B.!!$F1 566
34 TraesCS3B01G532100 chr2D 80109538 80110097 559 True 632.000000 632 87.148000 16 577 1 chr2D.!!$R1 561

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
622 647 0.171903 GCTGCGTCCAAAGCATGAAT 59.828 50.0 0.0 0.0 44.26 2.57 F
736 762 0.231279 GTTGAACCACGCTACACACG 59.769 55.0 0.0 0.0 0.00 4.49 F
988 1019 0.892063 AGGAACTCGGCAGAAGAGAC 59.108 55.0 0.0 0.0 38.97 3.36 F
2710 7382 0.258774 ATCGGGGAATTGGTCCTTGG 59.741 55.0 0.0 0.0 46.92 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 5941 0.321564 ACATGCGTCTGGCTGCTAAA 60.322 50.0 0.00 0.0 44.05 1.85 R
2557 7228 0.609131 AGCAAAATGACCACGAGGGG 60.609 55.0 3.29 0.0 42.91 4.79 R
2977 8747 0.251341 GGCTCATCAACAACCCCACT 60.251 55.0 0.00 0.0 0.00 4.00 R
4158 11309 0.601576 ACGATAACACTGCCGCACAA 60.602 50.0 0.00 0.0 0.00 3.33 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 0.706433 TTCCCTAGTAGTGTCCCCGT 59.294 55.000 0.00 0.00 0.00 5.28
26 27 0.324091 CCCTAGTAGTGTCCCCGTGT 60.324 60.000 0.00 0.00 0.00 4.49
40 41 2.203294 GTGTCTGGCAAACCCGGT 60.203 61.111 0.00 0.00 41.11 5.28
42 43 2.203294 GTCTGGCAAACCCGGTGT 60.203 61.111 0.00 0.00 41.11 4.16
48 49 2.590575 CAAACCCGGTGTGACGCT 60.591 61.111 0.75 0.00 0.00 5.07
50 51 1.452470 AAACCCGGTGTGACGCTTT 60.452 52.632 0.00 0.00 0.00 3.51
72 73 2.043992 TCAACACCTTCTTCTTCCCGA 58.956 47.619 0.00 0.00 0.00 5.14
105 107 1.073025 GACACCACTGCACCCATGA 59.927 57.895 0.00 0.00 0.00 3.07
106 108 1.228245 ACACCACTGCACCCATGAC 60.228 57.895 0.00 0.00 0.00 3.06
107 109 1.073722 CACCACTGCACCCATGACT 59.926 57.895 0.00 0.00 0.00 3.41
123 125 1.946475 GACTACTCGGCGCCTCCTTT 61.946 60.000 26.68 6.50 0.00 3.11
201 204 1.242076 GGCATTCTTCGCATGGCTAT 58.758 50.000 0.00 0.00 42.53 2.97
367 380 1.143183 GATCCGTCGGCTTGCCTTA 59.857 57.895 6.34 0.00 0.00 2.69
373 386 1.202486 CGTCGGCTTGCCTTAGGATTA 60.202 52.381 0.69 0.00 0.00 1.75
378 391 4.137543 CGGCTTGCCTTAGGATTATTCTT 58.862 43.478 0.69 0.00 0.00 2.52
433 448 3.307379 GGGGGATGTTGAGTATCGC 57.693 57.895 0.00 0.00 38.61 4.58
448 464 6.978338 TGAGTATCGCGATTATTAGGAAAGT 58.022 36.000 28.81 8.41 38.61 2.66
452 468 8.790718 AGTATCGCGATTATTAGGAAAGTTAGA 58.209 33.333 28.81 0.00 0.00 2.10
505 522 7.770801 TTGTACTCCAAGATGATCATTTACG 57.229 36.000 10.14 0.00 0.00 3.18
521 540 6.765403 TCATTTACGCCTATATATATGCCCC 58.235 40.000 12.67 0.00 0.00 5.80
537 556 2.117156 CCCCGAGGCTCAAGCAATG 61.117 63.158 15.95 0.00 44.36 2.82
622 647 0.171903 GCTGCGTCCAAAGCATGAAT 59.828 50.000 0.00 0.00 44.26 2.57
736 762 0.231279 GTTGAACCACGCTACACACG 59.769 55.000 0.00 0.00 0.00 4.49
751 777 5.176958 GCTACACACGAAACATCACTTTAGT 59.823 40.000 0.00 0.00 0.00 2.24
799 826 1.115930 AATCAGAGGATCGGACGGGG 61.116 60.000 0.00 0.00 43.42 5.73
804 831 1.807495 GAGGATCGGACGGGGACATC 61.807 65.000 0.00 0.00 0.00 3.06
808 835 4.570663 CGGACGGGGACATCGAGC 62.571 72.222 0.00 0.00 0.00 5.03
819 846 3.802685 GGGACATCGAGCAGTATAACAAC 59.197 47.826 0.00 0.00 0.00 3.32
988 1019 0.892063 AGGAACTCGGCAGAAGAGAC 59.108 55.000 0.00 0.00 38.97 3.36
1450 5782 1.642952 GCAGCTGCTTCTAGTGCCAC 61.643 60.000 31.33 0.00 38.21 5.01
1535 5940 6.830873 TTCTAGTGGTAGTCAACTTACTCC 57.169 41.667 0.00 0.00 31.21 3.85
1536 5941 6.137104 TCTAGTGGTAGTCAACTTACTCCT 57.863 41.667 0.00 0.00 31.21 3.69
1541 5946 5.868258 GTGGTAGTCAACTTACTCCTTTAGC 59.132 44.000 0.00 0.00 0.00 3.09
1543 5948 6.100668 GGTAGTCAACTTACTCCTTTAGCAG 58.899 44.000 0.00 0.00 0.00 4.24
1544 5949 4.570930 AGTCAACTTACTCCTTTAGCAGC 58.429 43.478 0.00 0.00 0.00 5.25
1548 5953 3.173965 ACTTACTCCTTTAGCAGCCAGA 58.826 45.455 0.00 0.00 0.00 3.86
1562 5972 1.448540 CCAGACGCATGTGGAGTCC 60.449 63.158 11.65 0.73 46.25 3.85
1567 6111 1.293179 CGCATGTGGAGTCCTGACA 59.707 57.895 11.33 7.81 0.00 3.58
1792 6400 1.736645 CCTGGCGTCCAAGTACGTG 60.737 63.158 0.00 1.33 44.64 4.49
1879 6487 1.302832 CTCCTGGTTCGGCAAGCTT 60.303 57.895 0.00 0.00 0.00 3.74
1972 6594 7.056006 TGACATCGTTAACTCTACCCATACTA 58.944 38.462 3.71 0.00 0.00 1.82
1973 6595 7.012704 TGACATCGTTAACTCTACCCATACTAC 59.987 40.741 3.71 0.00 0.00 2.73
1974 6596 7.059156 ACATCGTTAACTCTACCCATACTACT 58.941 38.462 3.71 0.00 0.00 2.57
2070 6692 4.813161 TCTACCTCCGTTCTACATACGAAG 59.187 45.833 0.00 0.00 41.33 3.79
2174 6796 8.804204 ACTTATATTTAGGAACGGATGGAGTAG 58.196 37.037 0.00 0.00 0.00 2.57
2175 6797 8.945195 TTATATTTAGGAACGGATGGAGTAGA 57.055 34.615 0.00 0.00 0.00 2.59
2177 6799 5.593679 TTTAGGAACGGATGGAGTAGAAG 57.406 43.478 0.00 0.00 0.00 2.85
2179 6801 3.025262 AGGAACGGATGGAGTAGAAGTC 58.975 50.000 0.00 0.00 0.00 3.01
2180 6802 2.758979 GGAACGGATGGAGTAGAAGTCA 59.241 50.000 0.00 0.00 0.00 3.41
2182 6804 4.425520 GAACGGATGGAGTAGAAGTCAAG 58.574 47.826 0.00 0.00 0.00 3.02
2183 6805 2.166664 ACGGATGGAGTAGAAGTCAAGC 59.833 50.000 0.00 0.00 0.00 4.01
2184 6806 2.166459 CGGATGGAGTAGAAGTCAAGCA 59.834 50.000 0.00 0.00 0.00 3.91
2185 6807 3.181471 CGGATGGAGTAGAAGTCAAGCAT 60.181 47.826 0.00 0.00 0.00 3.79
2186 6808 4.125703 GGATGGAGTAGAAGTCAAGCATG 58.874 47.826 0.00 0.00 0.00 4.06
2187 6809 4.383552 GGATGGAGTAGAAGTCAAGCATGT 60.384 45.833 0.00 0.00 0.00 3.21
2188 6810 4.193826 TGGAGTAGAAGTCAAGCATGTC 57.806 45.455 0.00 0.00 0.00 3.06
2189 6811 3.834813 TGGAGTAGAAGTCAAGCATGTCT 59.165 43.478 0.00 0.00 0.00 3.41
2190 6812 5.016831 TGGAGTAGAAGTCAAGCATGTCTA 58.983 41.667 0.00 0.00 0.00 2.59
2192 6814 6.833933 TGGAGTAGAAGTCAAGCATGTCTATA 59.166 38.462 0.00 0.00 0.00 1.31
2193 6815 7.507277 TGGAGTAGAAGTCAAGCATGTCTATAT 59.493 37.037 0.00 0.00 0.00 0.86
2194 6816 8.364142 GGAGTAGAAGTCAAGCATGTCTATATT 58.636 37.037 0.00 0.00 0.00 1.28
2195 6817 9.757227 GAGTAGAAGTCAAGCATGTCTATATTT 57.243 33.333 0.00 0.00 0.00 1.40
2196 6818 9.539825 AGTAGAAGTCAAGCATGTCTATATTTG 57.460 33.333 0.00 0.00 0.00 2.32
2523 7188 5.675827 GCACCAAACTTTTGAAAATTGGGTG 60.676 40.000 20.81 21.40 43.77 4.61
2710 7382 0.258774 ATCGGGGAATTGGTCCTTGG 59.741 55.000 0.00 0.00 46.92 3.61
2788 8492 5.748152 ACAAAACGATTCCATCAACTTTGTG 59.252 36.000 0.00 0.00 35.47 3.33
2846 8577 8.860780 AGAAATTGACTAAGCTCTTGAGAAAT 57.139 30.769 1.30 0.00 0.00 2.17
2977 8747 3.636300 ACAACAAGGCTTACATTCTTGCA 59.364 39.130 0.00 0.00 40.90 4.08
3081 8870 8.918116 ACTCTGCTGATCACTTAATTATCTACA 58.082 33.333 0.00 0.00 0.00 2.74
3082 8871 9.926158 CTCTGCTGATCACTTAATTATCTACAT 57.074 33.333 0.00 0.00 0.00 2.29
3136 9030 2.605338 GCTTGCACTTGTACACATGTGG 60.605 50.000 28.64 13.47 46.12 4.17
3237 9131 0.105142 GGATCTACCTGGTGGCCCTA 60.105 60.000 10.23 0.00 36.63 3.53
3285 9179 2.579201 CTGAGCCCCGACAACGAT 59.421 61.111 0.00 0.00 42.66 3.73
3330 9224 1.834263 GCTCTCTACACCACCTTCCAT 59.166 52.381 0.00 0.00 0.00 3.41
3438 9332 4.116961 CCAGCAATTCGAGGTAATTCGTA 58.883 43.478 0.00 0.00 41.22 3.43
3502 10551 1.476891 GGTGACGCCTCTCAACTATCA 59.523 52.381 0.00 0.00 0.00 2.15
3507 10556 1.506493 GCCTCTCAACTATCATGGCG 58.494 55.000 0.00 0.00 0.00 5.69
3601 10650 1.172180 AGGTGCCGTTGAACATGGTG 61.172 55.000 0.00 0.00 33.34 4.17
3699 10832 6.931281 TCATCTCTAAACATACATAGCTTGGC 59.069 38.462 0.00 0.00 0.00 4.52
3725 10859 8.227119 CGACTCATATTTTTGACATGTGTGTAA 58.773 33.333 1.15 0.00 39.09 2.41
3815 10949 1.815421 CTACGCGCTGCCCATCTTT 60.815 57.895 5.73 0.00 0.00 2.52
3882 11016 3.195591 CTCGGCCAGTACGGGATCG 62.196 68.421 16.97 17.14 43.02 3.69
3883 11017 4.944372 CGGCCAGTACGGGATCGC 62.944 72.222 16.97 0.00 40.63 4.58
3885 11019 4.944372 GCCAGTACGGGATCGCCG 62.944 72.222 16.97 17.75 40.63 6.46
3890 11024 4.854924 TACGGGATCGCCGTCGGA 62.855 66.667 25.30 10.82 43.06 4.55
3894 11028 3.602677 GGATCGCCGTCGGATGGA 61.603 66.667 20.37 9.05 36.13 3.41
3896 11030 3.843117 GATCGCCGTCGGATGGACC 62.843 68.421 20.37 2.21 42.99 4.46
4125 11275 5.627499 TGGTTGCACATGAAAAGATAGAC 57.373 39.130 0.00 0.00 0.00 2.59
4158 11309 4.929146 AAGGTGCACTAATAGGTTCCTT 57.071 40.909 17.98 4.38 0.00 3.36
4245 11396 9.174166 GATAACCCACTTATATGACACTTTTGT 57.826 33.333 0.00 0.00 39.32 2.83
4684 11885 2.185350 CTCCCTCGCGCTCAACAT 59.815 61.111 5.56 0.00 0.00 2.71
5066 12284 1.060729 TACAAGCCACTAGCCACCAA 58.939 50.000 0.00 0.00 45.47 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.838813 GGGACACTACTAGGGAAAAGCT 59.161 50.000 0.00 0.00 0.00 3.74
1 2 2.093075 GGGGACACTACTAGGGAAAAGC 60.093 54.545 0.00 0.00 0.00 3.51
2 3 2.167900 CGGGGACACTACTAGGGAAAAG 59.832 54.545 0.00 0.00 0.00 2.27
3 4 2.181975 CGGGGACACTACTAGGGAAAA 58.818 52.381 0.00 0.00 0.00 2.29
5 6 0.706433 ACGGGGACACTACTAGGGAA 59.294 55.000 0.00 0.00 0.00 3.97
6 7 0.033796 CACGGGGACACTACTAGGGA 60.034 60.000 0.00 0.00 0.00 4.20
7 8 0.324091 ACACGGGGACACTACTAGGG 60.324 60.000 0.00 0.00 0.00 3.53
8 9 1.101331 GACACGGGGACACTACTAGG 58.899 60.000 0.00 0.00 0.00 3.02
9 10 1.743958 CAGACACGGGGACACTACTAG 59.256 57.143 0.00 0.00 0.00 2.57
10 11 1.615116 CCAGACACGGGGACACTACTA 60.615 57.143 0.00 0.00 0.00 1.82
11 12 0.898789 CCAGACACGGGGACACTACT 60.899 60.000 0.00 0.00 0.00 2.57
12 13 1.590147 CCAGACACGGGGACACTAC 59.410 63.158 0.00 0.00 0.00 2.73
13 14 2.280552 GCCAGACACGGGGACACTA 61.281 63.158 0.00 0.00 0.00 2.74
14 15 3.626924 GCCAGACACGGGGACACT 61.627 66.667 0.00 0.00 0.00 3.55
24 25 2.203280 CACCGGGTTTGCCAGACA 60.203 61.111 6.32 0.00 36.17 3.41
26 27 2.203280 CACACCGGGTTTGCCAGA 60.203 61.111 6.32 0.00 36.17 3.86
48 49 3.951680 GGGAAGAAGAAGGTGTTGACAAA 59.048 43.478 0.00 0.00 0.00 2.83
50 51 2.484770 CGGGAAGAAGAAGGTGTTGACA 60.485 50.000 0.00 0.00 0.00 3.58
58 59 1.608283 GGTGTGTCGGGAAGAAGAAGG 60.608 57.143 0.00 0.00 0.00 3.46
60 61 1.124780 TGGTGTGTCGGGAAGAAGAA 58.875 50.000 0.00 0.00 0.00 2.52
72 73 1.068127 GGTGTCGAAGTAGTGGTGTGT 59.932 52.381 0.00 0.00 0.00 3.72
105 107 1.946475 GAAAGGAGGCGCCGAGTAGT 61.946 60.000 23.20 0.68 43.43 2.73
106 108 1.227002 GAAAGGAGGCGCCGAGTAG 60.227 63.158 23.20 0.00 43.43 2.57
107 109 2.890371 GAAAGGAGGCGCCGAGTA 59.110 61.111 23.20 0.00 43.43 2.59
169 172 0.739462 GAATGCCGTGGTCGATGTCA 60.739 55.000 0.00 0.00 39.71 3.58
201 204 2.338015 GGTGTAGCCGTGGTCGAGA 61.338 63.158 0.00 0.00 39.71 4.04
294 301 2.266055 GGAAGTCGTGGCTGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
350 363 1.144057 CTAAGGCAAGCCGACGGAT 59.856 57.895 20.50 9.11 41.95 4.18
433 448 9.408069 ACGCTATTCTAACTTTCCTAATAATCG 57.592 33.333 0.00 0.00 0.00 3.34
501 518 3.575256 CGGGGGCATATATATAGGCGTAA 59.425 47.826 19.91 0.00 40.66 3.18
505 522 2.567615 CCTCGGGGGCATATATATAGGC 59.432 54.545 18.81 18.81 39.17 3.93
521 540 1.332997 GATTCATTGCTTGAGCCTCGG 59.667 52.381 0.00 0.00 41.18 4.63
537 556 4.467438 AGGGATTGGTGGAATTGTTGATTC 59.533 41.667 0.00 0.00 42.84 2.52
622 647 0.733566 GGTCGTCGTGCGTGGAATTA 60.734 55.000 0.00 0.00 42.13 1.40
703 729 6.674066 CGTGGTTCAACATACTACCATTTTT 58.326 36.000 0.00 0.00 42.21 1.94
716 742 1.292061 GTGTGTAGCGTGGTTCAACA 58.708 50.000 0.00 0.00 0.00 3.33
736 762 6.650427 AGGGGAAAACTAAAGTGATGTTTC 57.350 37.500 0.00 0.00 33.45 2.78
751 777 2.166664 CGTGTTTGACCAAAGGGGAAAA 59.833 45.455 0.00 0.00 41.15 2.29
799 826 5.874892 GAGTTGTTATACTGCTCGATGTC 57.125 43.478 0.00 0.00 0.00 3.06
808 835 5.973651 ATCATGCACGAGTTGTTATACTG 57.026 39.130 0.00 0.00 0.00 2.74
872 899 2.063378 GGGAGGGAGTGGAGCAGAG 61.063 68.421 0.00 0.00 0.00 3.35
873 900 2.039624 GGGAGGGAGTGGAGCAGA 59.960 66.667 0.00 0.00 0.00 4.26
874 901 1.614824 AAGGGAGGGAGTGGAGCAG 60.615 63.158 0.00 0.00 0.00 4.24
875 902 1.920325 CAAGGGAGGGAGTGGAGCA 60.920 63.158 0.00 0.00 0.00 4.26
876 903 1.613630 TCAAGGGAGGGAGTGGAGC 60.614 63.158 0.00 0.00 0.00 4.70
1284 4879 1.756950 CCAGTAGTAGAGCCCGCCA 60.757 63.158 0.00 0.00 0.00 5.69
1519 5851 6.034161 TGCTAAAGGAGTAAGTTGACTACC 57.966 41.667 0.00 0.00 29.52 3.18
1535 5940 0.376152 CATGCGTCTGGCTGCTAAAG 59.624 55.000 0.00 0.00 44.05 1.85
1536 5941 0.321564 ACATGCGTCTGGCTGCTAAA 60.322 50.000 0.00 0.00 44.05 1.85
1541 5946 2.046988 TCCACATGCGTCTGGCTG 60.047 61.111 0.00 0.00 44.05 4.85
1543 5948 2.046892 ACTCCACATGCGTCTGGC 60.047 61.111 0.00 0.00 43.96 4.85
1544 5949 1.448540 GGACTCCACATGCGTCTGG 60.449 63.158 0.00 0.00 0.00 3.86
1548 5953 1.293498 GTCAGGACTCCACATGCGT 59.707 57.895 0.00 0.00 0.00 5.24
1629 6195 6.437928 ACGTTGCGGATAGTTTATATTACGA 58.562 36.000 0.00 0.00 0.00 3.43
1631 6197 6.788930 GCAACGTTGCGGATAGTTTATATTAC 59.211 38.462 34.84 5.86 45.11 1.89
1632 6198 6.879962 GCAACGTTGCGGATAGTTTATATTA 58.120 36.000 34.84 0.00 45.11 0.98
1633 6199 5.744490 GCAACGTTGCGGATAGTTTATATT 58.256 37.500 34.84 0.00 45.11 1.28
1792 6400 2.203070 CCGTAGATGGCCAGCACC 60.203 66.667 25.38 11.90 0.00 5.01
1879 6487 2.031919 ACGTTCCAGAATGCGCCA 59.968 55.556 4.18 0.00 31.97 5.69
1972 6594 6.381420 CGGGGGAATTAGATCATACTATCAGT 59.619 42.308 0.00 0.00 0.00 3.41
1973 6595 6.381420 ACGGGGGAATTAGATCATACTATCAG 59.619 42.308 0.00 0.00 0.00 2.90
1974 6596 6.261435 ACGGGGGAATTAGATCATACTATCA 58.739 40.000 0.00 0.00 0.00 2.15
1994 6616 4.759516 ATGCACTACACTTTAAAACGGG 57.240 40.909 0.00 0.00 0.00 5.28
2109 6731 8.812147 TCAAATGAACTATCACATACGGATAC 57.188 34.615 0.00 0.00 38.69 2.24
2110 6732 9.825109 TTTCAAATGAACTATCACATACGGATA 57.175 29.630 0.00 0.00 38.69 2.59
2159 6781 2.758979 TGACTTCTACTCCATCCGTTCC 59.241 50.000 0.00 0.00 0.00 3.62
2164 6786 3.895232 TGCTTGACTTCTACTCCATCC 57.105 47.619 0.00 0.00 0.00 3.51
2167 6789 3.834813 AGACATGCTTGACTTCTACTCCA 59.165 43.478 6.60 0.00 0.00 3.86
2194 6816 8.879759 GGACGTTGACTTAGATCAATTTATCAA 58.120 33.333 2.60 0.00 40.60 2.57
2195 6817 8.038351 TGGACGTTGACTTAGATCAATTTATCA 58.962 33.333 2.60 0.00 40.60 2.15
2196 6818 8.328864 GTGGACGTTGACTTAGATCAATTTATC 58.671 37.037 0.00 0.00 40.60 1.75
2198 6820 7.156000 TGTGGACGTTGACTTAGATCAATTTA 58.844 34.615 0.00 0.00 40.60 1.40
2211 6860 4.657075 ATTTCGTATTGTGGACGTTGAC 57.343 40.909 0.00 0.00 41.11 3.18
2212 6861 5.927689 ACTAATTTCGTATTGTGGACGTTGA 59.072 36.000 0.00 0.00 41.11 3.18
2213 6862 6.160664 ACTAATTTCGTATTGTGGACGTTG 57.839 37.500 0.00 0.00 41.11 4.10
2349 7011 8.063200 TGATGTACTAGCGCATATTATTAGGT 57.937 34.615 11.47 0.00 0.00 3.08
2350 7012 8.972349 CATGATGTACTAGCGCATATTATTAGG 58.028 37.037 11.47 0.00 0.00 2.69
2351 7013 8.972349 CCATGATGTACTAGCGCATATTATTAG 58.028 37.037 11.47 2.73 0.00 1.73
2352 7014 8.691797 TCCATGATGTACTAGCGCATATTATTA 58.308 33.333 11.47 0.00 0.00 0.98
2364 7026 6.951198 ACTCCCTCTATTCCATGATGTACTAG 59.049 42.308 0.00 0.00 0.00 2.57
2551 7222 1.129058 ATGACCACGAGGGGAATACC 58.871 55.000 3.29 0.00 42.91 2.73
2557 7228 0.609131 AGCAAAATGACCACGAGGGG 60.609 55.000 3.29 0.00 42.91 4.79
2619 7290 4.637977 CCTCATGCTCTACCTTTTTCTTCC 59.362 45.833 0.00 0.00 0.00 3.46
2658 7329 8.881109 AAGTTATTTCCCCCTACCTTTCTATA 57.119 34.615 0.00 0.00 0.00 1.31
2660 7331 7.018851 ACAAAGTTATTTCCCCCTACCTTTCTA 59.981 37.037 0.00 0.00 0.00 2.10
2662 7333 6.014647 ACAAAGTTATTTCCCCCTACCTTTC 58.985 40.000 0.00 0.00 0.00 2.62
2668 7339 7.717875 CGATATCAACAAAGTTATTTCCCCCTA 59.282 37.037 3.12 0.00 0.00 3.53
2674 7345 7.562454 TCCCCGATATCAACAAAGTTATTTC 57.438 36.000 3.12 0.00 0.00 2.17
2788 8492 3.330267 CTCCCAAGTTAAGAGACAGCAC 58.670 50.000 0.00 0.00 0.00 4.40
2846 8577 5.067273 CACCAACACCAAGATACCTACAAA 58.933 41.667 0.00 0.00 0.00 2.83
2977 8747 0.251341 GGCTCATCAACAACCCCACT 60.251 55.000 0.00 0.00 0.00 4.00
3081 8870 5.233083 CCATCAGGTCACCATATGTGTAT 57.767 43.478 0.00 0.00 45.61 2.29
3082 8871 4.687901 CCATCAGGTCACCATATGTGTA 57.312 45.455 0.00 0.00 45.61 2.90
3136 9030 1.809684 CCCTTGGTTTCTTCGGTCTC 58.190 55.000 0.00 0.00 0.00 3.36
3460 10447 7.996644 TCACCATCTTAAGAAACTAAACCAACT 59.003 33.333 9.71 0.00 0.00 3.16
3461 10448 8.074370 GTCACCATCTTAAGAAACTAAACCAAC 58.926 37.037 9.71 0.00 0.00 3.77
3483 10493 2.941453 TGATAGTTGAGAGGCGTCAC 57.059 50.000 9.41 2.75 0.00 3.67
3502 10551 1.152963 GTAACCCATCCTGCGCCAT 60.153 57.895 4.18 0.00 0.00 4.40
3507 10556 1.077716 AAGGCGTAACCCATCCTGC 60.078 57.895 0.00 0.00 40.58 4.85
3699 10832 6.602179 ACACACATGTCAAAAATATGAGTCG 58.398 36.000 0.00 0.00 31.55 4.18
3725 10859 1.001641 GCTCCCCAATGACTGCACT 60.002 57.895 0.00 0.00 0.00 4.40
3890 11024 3.055719 CAAAGCACGGCGGTCCAT 61.056 61.111 13.24 0.00 0.00 3.41
4122 11272 5.594317 AGTGCACCTTTTTAATCAACAGTCT 59.406 36.000 14.63 0.00 0.00 3.24
4125 11275 9.559958 CTATTAGTGCACCTTTTTAATCAACAG 57.440 33.333 14.63 1.69 0.00 3.16
4158 11309 0.601576 ACGATAACACTGCCGCACAA 60.602 50.000 0.00 0.00 0.00 3.33
4684 11885 1.874345 GACGGCGTGGGAGAAGAGAA 61.874 60.000 21.19 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.