Multiple sequence alignment - TraesCS3A01G455600

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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 TraesCS3A01G455600 chr3A 100.000 7138 0 0 1 7138 693174770 693181907 0.000000e+00 13182.0
1 TraesCS3A01G455600 chr3D 95.060 2753 80 19 4350 7060 556167399 556170137 0.000000e+00 4279.0
2 TraesCS3A01G455600 chr3D 97.363 2124 47 5 718 2840 556163545 556165660 0.000000e+00 3603.0
3 TraesCS3A01G455600 chr3D 98.479 1512 23 0 2840 4351 556165744 556167255 0.000000e+00 2665.0
4 TraesCS3A01G455600 chr3D 91.828 722 42 7 3 720 556162426 556163134 0.000000e+00 990.0
5 TraesCS3A01G455600 chr3D 94.444 54 1 1 7069 7122 556170928 556170979 1.650000e-11 82.4
6 TraesCS3A01G455600 chr3B 95.523 2658 85 22 764 3401 739165209 739167852 0.000000e+00 4218.0
7 TraesCS3A01G455600 chr3B 92.294 2232 118 19 4348 6566 739169067 739171257 0.000000e+00 3120.0
8 TraesCS3A01G455600 chr3B 94.963 953 38 2 3402 4351 739167983 739168928 0.000000e+00 1485.0
9 TraesCS3A01G455600 chr3B 89.944 716 55 7 3 714 739163904 739164606 0.000000e+00 907.0
10 TraesCS3A01G455600 chr3B 89.865 296 21 8 1949 2238 739828263 739828555 8.740000e-99 372.0
11 TraesCS3A01G455600 chr3B 92.827 237 17 0 1717 1953 739715662 739715898 1.910000e-90 344.0
12 TraesCS3A01G455600 chr3B 94.022 184 11 0 2240 2423 739828715 739828898 5.450000e-71 279.0
13 TraesCS3A01G455600 chr4A 92.151 637 50 0 954 1590 598223605 598224241 0.000000e+00 900.0
14 TraesCS3A01G455600 chr4A 89.011 637 68 1 954 1590 590152044 590152678 0.000000e+00 787.0
15 TraesCS3A01G455600 chr5A 91.366 637 54 1 954 1590 619179183 619179818 0.000000e+00 870.0
16 TraesCS3A01G455600 chr5A 90.909 638 55 3 954 1590 356477203 356477838 0.000000e+00 854.0
17 TraesCS3A01G455600 chr5A 90.738 637 59 0 954 1590 474913395 474914031 0.000000e+00 850.0
18 TraesCS3A01G455600 chr7A 90.267 637 60 2 954 1590 115498440 115499074 0.000000e+00 832.0
19 TraesCS3A01G455600 chr5B 86.688 616 63 8 1387 2002 692329180 692329776 0.000000e+00 665.0
20 TraesCS3A01G455600 chr5D 88.454 511 33 10 954 1462 217658115 217658601 1.710000e-165 593.0
21 TraesCS3A01G455600 chr5D 95.000 40 2 0 91 130 170579459 170579498 5.980000e-06 63.9
22 TraesCS3A01G455600 chr7D 88.557 402 22 4 1320 1718 34136336 34136716 3.900000e-127 466.0
23 TraesCS3A01G455600 chr7D 95.502 289 12 1 1714 2002 34137336 34137623 1.810000e-125 460.0
24 TraesCS3A01G455600 chr2A 79.703 202 36 3 30 227 384968506 384968706 2.680000e-29 141.0
25 TraesCS3A01G455600 chr2D 95.122 41 1 1 93 132 553104536 553104496 5.980000e-06 63.9
26 TraesCS3A01G455600 chr6D 97.222 36 1 0 97 132 393443921 393443886 2.150000e-05 62.1
27 TraesCS3A01G455600 chr6D 92.857 42 3 0 91 132 440918291 440918332 2.150000e-05 62.1
28 TraesCS3A01G455600 chr1D 93.023 43 1 2 91 132 228527034 228526993 2.150000e-05 62.1
29 TraesCS3A01G455600 chr1D 92.857 42 3 0 91 132 228681917 228681958 2.150000e-05 62.1


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 TraesCS3A01G455600 chr3A 693174770 693181907 7137 False 13182.00 13182 100.0000 1 7138 1 chr3A.!!$F1 7137
1 TraesCS3A01G455600 chr3D 556162426 556170979 8553 False 2323.88 4279 95.4348 3 7122 5 chr3D.!!$F1 7119
2 TraesCS3A01G455600 chr3B 739163904 739171257 7353 False 2432.50 4218 93.1810 3 6566 4 chr3B.!!$F2 6563
3 TraesCS3A01G455600 chr3B 739828263 739828898 635 False 325.50 372 91.9435 1949 2423 2 chr3B.!!$F3 474
4 TraesCS3A01G455600 chr4A 598223605 598224241 636 False 900.00 900 92.1510 954 1590 1 chr4A.!!$F2 636
5 TraesCS3A01G455600 chr4A 590152044 590152678 634 False 787.00 787 89.0110 954 1590 1 chr4A.!!$F1 636
6 TraesCS3A01G455600 chr5A 619179183 619179818 635 False 870.00 870 91.3660 954 1590 1 chr5A.!!$F3 636
7 TraesCS3A01G455600 chr5A 356477203 356477838 635 False 854.00 854 90.9090 954 1590 1 chr5A.!!$F1 636
8 TraesCS3A01G455600 chr5A 474913395 474914031 636 False 850.00 850 90.7380 954 1590 1 chr5A.!!$F2 636
9 TraesCS3A01G455600 chr7A 115498440 115499074 634 False 832.00 832 90.2670 954 1590 1 chr7A.!!$F1 636
10 TraesCS3A01G455600 chr5B 692329180 692329776 596 False 665.00 665 86.6880 1387 2002 1 chr5B.!!$F1 615
11 TraesCS3A01G455600 chr7D 34136336 34137623 1287 False 463.00 466 92.0295 1320 2002 2 chr7D.!!$F1 682

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
544 549 0.249911 GTGGCACTCTTCCGACACTT 60.250 55.000 11.13 0.00 0.00 3.16 F
988 1590 0.252421 TCACTGAGATCCACCCTGCT 60.252 55.000 0.00 0.00 0.00 4.24 F
989 1591 0.617413 CACTGAGATCCACCCTGCTT 59.383 55.000 0.00 0.00 0.00 3.91 F
1980 3207 1.334689 CGTCGCTATGCTGATTACCGA 60.335 52.381 0.00 0.00 0.00 4.69 F
2724 4115 2.084546 ACGGATTTGGCAGTTAAGCTC 58.915 47.619 0.00 0.00 34.17 4.09 F
3556 5173 1.160137 GAGACCCAGCACATGTGTTC 58.840 55.000 26.01 11.26 0.00 3.18 F
4186 5803 4.149598 GGAGCCCTCCTTTGAAACTAAAA 58.850 43.478 7.08 0.00 46.16 1.52 F
5714 7486 1.905637 ACGGGGAAAATGAGGTGAAC 58.094 50.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 3207 1.949257 CGAAAGACGGGCAAGCTTT 59.051 52.632 0.00 0.0 38.46 3.51 R
2696 4087 2.268076 GCCAAATCCGTGCCAGTGT 61.268 57.895 0.00 0.0 0.00 3.55 R
3121 4597 6.718454 AGTGAATGGTTGAGATCATTTTCTGT 59.282 34.615 0.00 0.0 34.18 3.41 R
3375 4859 1.969256 CGTGTTTTGTAACTGCGATGC 59.031 47.619 0.00 0.0 36.33 3.91 R
4186 5803 1.681264 GTTTTGTTGTAGGCAGGCTGT 59.319 47.619 17.16 0.0 0.00 4.40 R
4971 6738 2.192664 TCCGCTTGCAAACATAGGAA 57.807 45.000 0.00 0.0 0.00 3.36 R
5747 7519 2.597305 GAGCCATGTAACGTTAGTGTCG 59.403 50.000 8.60 1.2 0.00 4.35 R
6709 8490 0.109412 CTCGGTCACCACGGTAACTC 60.109 60.000 0.00 0.0 0.00 3.01 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
49 50 1.840635 CCCTCCTTAAGCTACTTGCCT 59.159 52.381 0.00 0.00 44.23 4.75
134 135 2.597510 GCCACCTCAAAGGCGGTT 60.598 61.111 2.21 0.00 39.79 4.44
205 206 1.759299 CATGGCCCTGGTTGATGGG 60.759 63.158 0.00 0.00 46.00 4.00
234 235 1.006758 ACCCTAGTTCTCACGGGATCA 59.993 52.381 0.00 0.00 39.08 2.92
263 267 4.040706 TGGAGGCTTTGAGCAAATTTTCAT 59.959 37.500 2.04 0.00 44.75 2.57
273 277 3.698040 AGCAAATTTTCATCCGAGCTGAT 59.302 39.130 0.00 0.00 0.00 2.90
274 278 4.883585 AGCAAATTTTCATCCGAGCTGATA 59.116 37.500 0.00 0.00 0.00 2.15
305 309 1.601419 CTTCGCGTCCCTCCCACTTA 61.601 60.000 5.77 0.00 0.00 2.24
367 372 5.991328 TGAACAAGAGTGTGAATGAGTTC 57.009 39.130 0.00 0.00 38.27 3.01
390 395 3.941573 TCAACATGCTCAAGACTGCATA 58.058 40.909 0.00 0.00 46.65 3.14
441 446 6.215495 TCATGTGATGATGATGCACAAAAT 57.785 33.333 0.00 0.00 44.62 1.82
447 452 4.443913 TGATGATGCACAAAATGACCAG 57.556 40.909 0.00 0.00 0.00 4.00
459 464 7.488322 CACAAAATGACCAGTTTTAAGAAGGA 58.512 34.615 0.00 0.00 0.00 3.36
502 507 0.736325 CCAAGAGTGCCGGTAAGACG 60.736 60.000 1.90 0.00 0.00 4.18
544 549 0.249911 GTGGCACTCTTCCGACACTT 60.250 55.000 11.13 0.00 0.00 3.16
546 551 1.689813 TGGCACTCTTCCGACACTTAA 59.310 47.619 0.00 0.00 0.00 1.85
555 560 6.766467 ACTCTTCCGACACTTAATGTTTCTTT 59.234 34.615 0.00 0.00 43.56 2.52
557 562 7.414436 TCTTCCGACACTTAATGTTTCTTTTG 58.586 34.615 0.00 0.00 43.56 2.44
571 576 5.010617 TGTTTCTTTTGTAATGAGAAGGGCC 59.989 40.000 0.00 0.00 31.67 5.80
611 616 8.893219 TGCAAGAAATATTCGACAGATAAGAT 57.107 30.769 0.00 0.00 34.02 2.40
714 719 2.490903 GCTCAACAACATCTCTGCCATT 59.509 45.455 0.00 0.00 0.00 3.16
732 1166 6.938507 TGCCATTGCAATCTCTAAAGAAAAT 58.061 32.000 9.53 0.00 46.66 1.82
816 1409 5.048782 TCAAGGATGATGTAAGTGTGCAAAC 60.049 40.000 0.00 0.00 0.00 2.93
817 1410 4.397420 AGGATGATGTAAGTGTGCAAACA 58.603 39.130 10.29 0.00 0.00 2.83
818 1411 4.826733 AGGATGATGTAAGTGTGCAAACAA 59.173 37.500 10.29 0.00 0.00 2.83
819 1412 5.301551 AGGATGATGTAAGTGTGCAAACAAA 59.698 36.000 10.29 0.00 0.00 2.83
820 1413 6.015180 AGGATGATGTAAGTGTGCAAACAAAT 60.015 34.615 10.29 0.00 0.00 2.32
821 1414 7.176515 AGGATGATGTAAGTGTGCAAACAAATA 59.823 33.333 10.29 0.00 0.00 1.40
822 1415 7.485913 GGATGATGTAAGTGTGCAAACAAATAG 59.514 37.037 10.29 0.00 0.00 1.73
904 1497 1.202359 GGCCAAAGCGACACTGAAAAA 60.202 47.619 0.00 0.00 41.24 1.94
988 1590 0.252421 TCACTGAGATCCACCCTGCT 60.252 55.000 0.00 0.00 0.00 4.24
989 1591 0.617413 CACTGAGATCCACCCTGCTT 59.383 55.000 0.00 0.00 0.00 3.91
1980 3207 1.334689 CGTCGCTATGCTGATTACCGA 60.335 52.381 0.00 0.00 0.00 4.69
2049 3276 2.828520 TCTCTCTGTCATGGGTTCTGTC 59.171 50.000 0.00 0.00 0.00 3.51
2050 3277 2.564504 CTCTCTGTCATGGGTTCTGTCA 59.435 50.000 0.00 0.00 0.00 3.58
2238 3629 2.158943 AGCCTTCCGTAATGGTAGCTTC 60.159 50.000 0.00 0.00 35.76 3.86
2301 3692 2.305927 GGAGGAGTTCTTCATGGTGGAA 59.694 50.000 0.00 0.00 0.00 3.53
2619 4010 5.046376 TGTGAGCTCAGAATATGTCCTGAAA 60.046 40.000 18.89 0.00 38.75 2.69
2696 4087 6.485313 CCTTCTACCTGTTTGTGTATGTCAAA 59.515 38.462 0.00 0.00 33.28 2.69
2724 4115 2.084546 ACGGATTTGGCAGTTAAGCTC 58.915 47.619 0.00 0.00 34.17 4.09
2737 4128 6.183360 GGCAGTTAAGCTCTGTACACATTTAG 60.183 42.308 0.00 0.00 35.60 1.85
3107 4583 6.295719 TCACTAACTTCTTATCCTGTTCCC 57.704 41.667 0.00 0.00 0.00 3.97
3388 4872 6.981559 TGTAATAACATAGCATCGCAGTTACA 59.018 34.615 0.00 0.00 30.34 2.41
3414 5028 4.523943 ACACGTTTACTGGTATCCACAGTA 59.476 41.667 1.48 1.48 46.62 2.74
3556 5173 1.160137 GAGACCCAGCACATGTGTTC 58.840 55.000 26.01 11.26 0.00 3.18
3876 5493 7.034685 ACGAAAAAGGTGTAACTATTTGCTT 57.965 32.000 0.00 0.00 36.74 3.91
4186 5803 4.149598 GGAGCCCTCCTTTGAAACTAAAA 58.850 43.478 7.08 0.00 46.16 1.52
4679 6445 6.509358 GCTGAATCTTTTGACGAGCTATCTTC 60.509 42.308 0.00 0.00 0.00 2.87
4767 6533 5.794289 AGGTTTATAGTGTTTTCCCCTAGGT 59.206 40.000 8.29 0.00 0.00 3.08
4873 6639 5.074804 ACTTTAGAACATGTGGTTTACCCC 58.925 41.667 0.00 0.00 40.63 4.95
4897 6664 8.347771 CCCAAATCAATGTGATTACAGAGTATG 58.652 37.037 4.00 0.00 45.57 2.39
4901 6668 5.519927 TCAATGTGATTACAGAGTATGTGCG 59.480 40.000 0.00 0.00 43.80 5.34
4971 6738 6.320494 TGTTTGCAAAATCTTACGTGGTAT 57.680 33.333 14.67 0.00 0.00 2.73
5018 6786 6.704050 TCATCCTTTTATGCATGCAATCAATG 59.296 34.615 26.68 19.53 0.00 2.82
5022 6790 7.390996 TCCTTTTATGCATGCAATCAATGTTTT 59.609 29.630 26.68 6.39 0.00 2.43
5023 6791 7.483375 CCTTTTATGCATGCAATCAATGTTTTG 59.517 33.333 26.68 5.96 0.00 2.44
5041 6809 5.641209 TGTTTTGAAACTTTGACCACCAATG 59.359 36.000 7.97 0.00 39.59 2.82
5150 6918 5.476945 ACATGATTACAGTTTCCCTTCCAAC 59.523 40.000 0.00 0.00 0.00 3.77
5260 7031 8.732746 TTGGTAATAAGAAGAGGAACTAATGC 57.267 34.615 0.00 0.00 41.55 3.56
5288 7059 8.638873 CAAGGTATCTGTTGTACTGTATCCATA 58.361 37.037 0.00 0.00 0.00 2.74
5367 7138 8.177119 TGGAGCAATTAACTCACTTACAAATT 57.823 30.769 9.25 0.00 35.79 1.82
5395 7166 4.154918 GGCTCTTATGTGTTGTTCCTCAAG 59.845 45.833 0.00 0.00 36.66 3.02
5714 7486 1.905637 ACGGGGAAAATGAGGTGAAC 58.094 50.000 0.00 0.00 0.00 3.18
5747 7519 2.075338 CAGAAGCTTCTCCTTGCAGTC 58.925 52.381 26.18 0.00 34.74 3.51
5869 7641 4.290711 TCATGATGCAGAAGAGGTTCAA 57.709 40.909 0.00 0.00 34.82 2.69
5876 7648 2.856222 CAGAAGAGGTTCAACCAGCTT 58.144 47.619 9.90 11.74 41.95 3.74
6139 7911 5.062809 CGATTTCTGCTTTGAGACTCTAACC 59.937 44.000 3.68 0.00 0.00 2.85
6302 8078 4.967575 AGTGAATTTGTCGCGTTAACTTTG 59.032 37.500 5.77 0.00 41.95 2.77
6494 8274 3.929610 GACGAGACCCTTTCTTGATGAAG 59.070 47.826 0.00 0.00 37.93 3.02
6496 8276 4.040461 ACGAGACCCTTTCTTGATGAAGAA 59.960 41.667 2.95 2.95 44.83 2.52
6547 8327 7.338800 GGATCATCAATGATACAGGTGTTTT 57.661 36.000 9.84 0.00 46.84 2.43
6577 8358 4.352595 TGGAAAGGGTTGGAAGTGAGATAA 59.647 41.667 0.00 0.00 0.00 1.75
6600 8381 0.688487 TTTACAGCTAGCCAACCCGT 59.312 50.000 12.13 2.06 0.00 5.28
6602 8383 1.189524 TACAGCTAGCCAACCCGTGT 61.190 55.000 12.13 9.88 0.00 4.49
6671 8452 2.961741 TGTGTTCATTTGCTTGCCCTAA 59.038 40.909 0.00 0.00 0.00 2.69
6678 8459 2.584835 TTGCTTGCCCTAAGATGTGT 57.415 45.000 0.00 0.00 38.76 3.72
6689 8470 4.568359 CCCTAAGATGTGTGACTTGATTCG 59.432 45.833 0.00 0.00 0.00 3.34
6708 8489 7.036220 TGATTCGAACTCTCCAACTCTTTATC 58.964 38.462 0.00 0.00 0.00 1.75
6709 8490 4.982999 TCGAACTCTCCAACTCTTTATCG 58.017 43.478 0.00 0.00 0.00 2.92
6746 8527 2.367202 GGGAAGGAGATGGTGGCGA 61.367 63.158 0.00 0.00 0.00 5.54
6747 8528 1.602237 GGAAGGAGATGGTGGCGAA 59.398 57.895 0.00 0.00 0.00 4.70
6748 8529 0.462759 GGAAGGAGATGGTGGCGAAG 60.463 60.000 0.00 0.00 0.00 3.79
6750 8531 0.909610 AAGGAGATGGTGGCGAAGGA 60.910 55.000 0.00 0.00 0.00 3.36
6752 8533 0.181350 GGAGATGGTGGCGAAGGAAT 59.819 55.000 0.00 0.00 0.00 3.01
6754 8535 2.158813 GGAGATGGTGGCGAAGGAATTA 60.159 50.000 0.00 0.00 0.00 1.40
6755 8536 3.134458 GAGATGGTGGCGAAGGAATTAG 58.866 50.000 0.00 0.00 0.00 1.73
6757 8538 1.281419 TGGTGGCGAAGGAATTAGGA 58.719 50.000 0.00 0.00 0.00 2.94
6879 8668 6.378564 CACTCTTACTTTCCTAGATCCTCACA 59.621 42.308 0.00 0.00 0.00 3.58
6896 8685 6.610830 TCCTCACAGATACATCCTACATACA 58.389 40.000 0.00 0.00 0.00 2.29
6919 8708 7.331791 ACAGGAGACATGAATAAAAGGTACTC 58.668 38.462 0.00 0.00 38.49 2.59
6923 8712 8.475639 GGAGACATGAATAAAAGGTACTCTGTA 58.524 37.037 0.00 0.00 38.49 2.74
6924 8713 9.522804 GAGACATGAATAAAAGGTACTCTGTAG 57.477 37.037 0.00 0.00 38.49 2.74
7060 8872 6.708502 TGCATTAACTACAACACATACACACT 59.291 34.615 0.00 0.00 0.00 3.55
7061 8873 7.095397 TGCATTAACTACAACACATACACACTC 60.095 37.037 0.00 0.00 0.00 3.51
7062 8874 7.623506 GCATTAACTACAACACATACACACTCC 60.624 40.741 0.00 0.00 0.00 3.85
7066 8878 2.438021 ACAACACATACACACTCCACCT 59.562 45.455 0.00 0.00 0.00 4.00
7067 8879 3.118038 ACAACACATACACACTCCACCTT 60.118 43.478 0.00 0.00 0.00 3.50
7070 9664 5.298989 ACACATACACACTCCACCTTTTA 57.701 39.130 0.00 0.00 0.00 1.52
7086 9680 4.167307 ACCTTTTATTCCCCGTGGTCATAT 59.833 41.667 0.00 0.00 0.00 1.78
7087 9681 5.137551 CCTTTTATTCCCCGTGGTCATATT 58.862 41.667 0.00 0.00 0.00 1.28
7122 9716 2.557490 GTCTTCCAGTCTCCAACGTACT 59.443 50.000 0.00 0.00 0.00 2.73
7123 9717 2.818432 TCTTCCAGTCTCCAACGTACTC 59.182 50.000 0.00 0.00 0.00 2.59
7124 9718 1.542492 TCCAGTCTCCAACGTACTCC 58.458 55.000 0.00 0.00 0.00 3.85
7125 9719 0.531200 CCAGTCTCCAACGTACTCCC 59.469 60.000 0.00 0.00 0.00 4.30
7126 9720 1.546961 CAGTCTCCAACGTACTCCCT 58.453 55.000 0.00 0.00 0.00 4.20
7127 9721 1.473278 CAGTCTCCAACGTACTCCCTC 59.527 57.143 0.00 0.00 0.00 4.30
7128 9722 0.816373 GTCTCCAACGTACTCCCTCC 59.184 60.000 0.00 0.00 0.00 4.30
7129 9723 0.679002 TCTCCAACGTACTCCCTCCG 60.679 60.000 0.00 0.00 0.00 4.63
7130 9724 1.664321 CTCCAACGTACTCCCTCCGG 61.664 65.000 0.00 0.00 0.00 5.14
7131 9725 1.980772 CCAACGTACTCCCTCCGGT 60.981 63.158 0.00 0.00 0.00 5.28
7132 9726 1.509923 CAACGTACTCCCTCCGGTC 59.490 63.158 0.00 0.00 0.00 4.79
7133 9727 1.680314 AACGTACTCCCTCCGGTCC 60.680 63.158 0.00 0.00 0.00 4.46
7134 9728 2.147433 AACGTACTCCCTCCGGTCCT 62.147 60.000 0.00 0.00 0.00 3.85
7135 9729 1.379576 CGTACTCCCTCCGGTCCTT 60.380 63.158 0.00 0.00 0.00 3.36
7136 9730 0.969409 CGTACTCCCTCCGGTCCTTT 60.969 60.000 0.00 0.00 0.00 3.11
7137 9731 1.273759 GTACTCCCTCCGGTCCTTTT 58.726 55.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.049888 TGCTGACAACAACATCCACA 57.950 45.000 0.00 0.00 0.00 4.17
1 2 2.287788 CCTTGCTGACAACAACATCCAC 60.288 50.000 0.00 0.00 0.00 4.02
28 29 1.838077 GGCAAGTAGCTTAAGGAGGGA 59.162 52.381 4.29 0.00 44.79 4.20
36 37 2.167281 CTCTCTGCAGGCAAGTAGCTTA 59.833 50.000 15.13 0.00 44.79 3.09
49 50 1.181741 ACAAGCGTCTCCTCTCTGCA 61.182 55.000 0.00 0.00 0.00 4.41
134 135 1.276989 CTCCCGGTAACACAAGGCTAA 59.723 52.381 0.00 0.00 0.00 3.09
167 168 0.185901 ACAGTCCCACTTGGCACATT 59.814 50.000 0.00 0.00 39.30 2.71
205 206 2.497675 TGAGAACTAGGGTCTCACATGC 59.502 50.000 19.25 0.50 35.81 4.06
234 235 2.318908 TGCTCAAAGCCTCCAAATGTT 58.681 42.857 0.00 0.00 41.51 2.71
263 267 3.701542 ACAAGATCAACTATCAGCTCGGA 59.298 43.478 0.00 0.00 37.03 4.55
273 277 3.499048 GACGCGAAGACAAGATCAACTA 58.501 45.455 15.93 0.00 0.00 2.24
274 278 2.329379 GACGCGAAGACAAGATCAACT 58.671 47.619 15.93 0.00 0.00 3.16
331 336 7.963361 ACACTCTTGTTCATCCAATTCATGGTA 60.963 37.037 0.00 0.00 41.06 3.25
332 337 7.198589 ACACTCTTGTTCATCCAATTCATGGT 61.199 38.462 0.00 0.00 41.06 3.55
333 338 5.184479 ACACTCTTGTTCATCCAATTCATGG 59.816 40.000 0.00 0.00 41.46 3.66
334 339 6.072342 TCACACTCTTGTTCATCCAATTCATG 60.072 38.462 0.00 0.00 31.66 3.07
335 340 6.005823 TCACACTCTTGTTCATCCAATTCAT 58.994 36.000 0.00 0.00 31.66 2.57
336 341 5.375773 TCACACTCTTGTTCATCCAATTCA 58.624 37.500 0.00 0.00 31.66 2.57
337 342 5.947228 TCACACTCTTGTTCATCCAATTC 57.053 39.130 0.00 0.00 31.66 2.17
338 343 6.491062 TCATTCACACTCTTGTTCATCCAATT 59.509 34.615 0.00 0.00 31.66 2.32
339 344 6.005823 TCATTCACACTCTTGTTCATCCAAT 58.994 36.000 0.00 0.00 31.66 3.16
340 345 5.375773 TCATTCACACTCTTGTTCATCCAA 58.624 37.500 0.00 0.00 31.66 3.53
341 346 4.971939 TCATTCACACTCTTGTTCATCCA 58.028 39.130 0.00 0.00 31.66 3.41
367 372 2.551032 TGCAGTCTTGAGCATGTTGAAG 59.449 45.455 2.34 2.34 35.51 3.02
390 395 8.208224 TGACGTCCTTATGTATTCCACATATTT 58.792 33.333 14.12 0.00 46.92 1.40
431 436 6.815089 TCTTAAAACTGGTCATTTTGTGCAT 58.185 32.000 0.00 0.00 31.79 3.96
434 439 7.435192 GTCCTTCTTAAAACTGGTCATTTTGTG 59.565 37.037 0.00 0.00 31.79 3.33
441 446 5.130350 CCTTGTCCTTCTTAAAACTGGTCA 58.870 41.667 0.00 0.00 0.00 4.02
447 452 6.877611 TCATGACCTTGTCCTTCTTAAAAC 57.122 37.500 0.00 0.00 0.00 2.43
459 464 1.133199 TGCCCCTTTTCATGACCTTGT 60.133 47.619 0.00 0.00 0.00 3.16
502 507 1.519408 TAGGCTTTTCACTTGCGTCC 58.481 50.000 0.00 0.00 0.00 4.79
544 549 8.303876 GCCCTTCTCATTACAAAAGAAACATTA 58.696 33.333 0.00 0.00 0.00 1.90
546 551 6.295292 GGCCCTTCTCATTACAAAAGAAACAT 60.295 38.462 0.00 0.00 0.00 2.71
555 560 3.011144 TCCAATGGCCCTTCTCATTACAA 59.989 43.478 0.00 0.00 32.92 2.41
557 562 3.297134 TCCAATGGCCCTTCTCATTAC 57.703 47.619 0.00 0.00 32.92 1.89
571 576 5.443185 TTCTTGCAGTTTCTCTTCCAATG 57.557 39.130 0.00 0.00 0.00 2.82
611 616 5.588958 CTCATATCTGAGTTGGACTGTCA 57.411 43.478 10.38 0.00 43.35 3.58
747 1181 9.802039 ACAACAAAGTATTAAATACTCCTTCCA 57.198 29.630 0.00 0.00 44.94 3.53
904 1497 3.192633 GCGTGGGAGAAATTGGTGTTTAT 59.807 43.478 0.00 0.00 0.00 1.40
1305 1907 2.766229 GAGGACTCCCTGAGGGCC 60.766 72.222 14.20 8.80 44.53 5.80
1502 2105 2.803155 GATGGCCAGGAACTCGTGCA 62.803 60.000 13.05 0.00 34.60 4.57
1980 3207 1.949257 CGAAAGACGGGCAAGCTTT 59.051 52.632 0.00 0.00 38.46 3.51
2025 3252 3.513119 CAGAACCCATGACAGAGAGAAGA 59.487 47.826 0.00 0.00 0.00 2.87
2050 3277 2.819984 CTACCACCTGCGGCATTGGT 62.820 60.000 28.95 28.95 44.69 3.67
2238 3629 7.977853 CCAGTCAAATCCTTCTCCATTTTATTG 59.022 37.037 0.00 0.00 0.00 1.90
2301 3692 3.269381 TCTGGATGGCCTTCCTTATGTTT 59.731 43.478 31.68 0.00 36.68 2.83
2619 4010 2.362503 TCGACCTCATGGCGGAGT 60.363 61.111 8.67 0.00 36.63 3.85
2696 4087 2.268076 GCCAAATCCGTGCCAGTGT 61.268 57.895 0.00 0.00 0.00 3.55
3121 4597 6.718454 AGTGAATGGTTGAGATCATTTTCTGT 59.282 34.615 0.00 0.00 34.18 3.41
3375 4859 1.969256 CGTGTTTTGTAACTGCGATGC 59.031 47.619 0.00 0.00 36.33 3.91
3388 4872 5.124645 TGTGGATACCAGTAAACGTGTTTT 58.875 37.500 2.97 0.00 32.34 2.43
3414 5028 8.537728 TCCTTTGCAAGAATGAATATAATGGT 57.462 30.769 0.00 0.00 0.00 3.55
4012 5629 2.714250 ACCCCTGACACAACATTAGGAA 59.286 45.455 0.00 0.00 0.00 3.36
4013 5630 2.344592 ACCCCTGACACAACATTAGGA 58.655 47.619 0.00 0.00 0.00 2.94
4174 5791 3.704061 AGGCAGGCTGTTTTAGTTTCAAA 59.296 39.130 17.16 0.00 0.00 2.69
4186 5803 1.681264 GTTTTGTTGTAGGCAGGCTGT 59.319 47.619 17.16 0.00 0.00 4.40
4258 5875 6.617879 TCTGACAAATGCAAAGATGATTCAG 58.382 36.000 0.00 0.00 0.00 3.02
4587 6353 2.270858 TGTGCTTTACTGGGGTATCCA 58.729 47.619 0.00 0.00 44.79 3.41
4767 6533 5.813672 GCTAACACCCAAATATAAGACGTCA 59.186 40.000 19.50 0.00 0.00 4.35
4838 6604 8.586273 CACATGTTCTAAAGTTGTTGTTTGAAG 58.414 33.333 0.00 0.00 0.00 3.02
4873 6639 9.712359 CACATACTCTGTAATCACATTGATTTG 57.288 33.333 6.71 0.32 45.50 2.32
4897 6664 5.031578 TGTGAACAGATTTTAAACACGCAC 58.968 37.500 0.00 0.00 0.00 5.34
4901 6668 7.462109 TGCAATGTGAACAGATTTTAAACAC 57.538 32.000 0.00 0.00 0.00 3.32
4971 6738 2.192664 TCCGCTTGCAAACATAGGAA 57.807 45.000 0.00 0.00 0.00 3.36
5018 6786 5.641636 ACATTGGTGGTCAAAGTTTCAAAAC 59.358 36.000 0.00 0.00 39.05 2.43
5022 6790 4.950475 TGTACATTGGTGGTCAAAGTTTCA 59.050 37.500 0.00 0.00 38.17 2.69
5023 6791 5.508200 TGTACATTGGTGGTCAAAGTTTC 57.492 39.130 0.00 0.00 38.17 2.78
5260 7031 7.147897 TGGATACAGTACAACAGATACCTTGAG 60.148 40.741 0.00 0.00 46.17 3.02
5288 7059 7.175641 CCAATCTCTTTACTTGTCACTTTGGAT 59.824 37.037 0.00 0.00 32.42 3.41
5367 7138 4.941263 GGAACAACACATAAGAGCCATACA 59.059 41.667 0.00 0.00 0.00 2.29
5395 7166 4.268884 GCTGTTTCACATAAGATCGAGGAC 59.731 45.833 0.00 0.00 0.00 3.85
5747 7519 2.597305 GAGCCATGTAACGTTAGTGTCG 59.403 50.000 8.60 1.20 0.00 4.35
6139 7911 7.647318 TGACAAGTGTGTATTTTAAATGCACAG 59.353 33.333 31.18 24.02 43.32 3.66
6302 8078 7.047891 TCTACAAATTCATACACACATCTCCC 58.952 38.462 0.00 0.00 0.00 4.30
6350 8129 2.106684 TGTTACACCCAGCATTACCACA 59.893 45.455 0.00 0.00 0.00 4.17
6494 8274 2.223805 CCAGGCGGCCAAAATTATCTTC 60.224 50.000 23.09 0.00 0.00 2.87
6496 8276 1.064017 TCCAGGCGGCCAAAATTATCT 60.064 47.619 23.09 0.00 0.00 1.98
6545 8325 3.200825 TCCAACCCTTTCCATTTTGCAAA 59.799 39.130 8.05 8.05 0.00 3.68
6547 8327 2.402564 TCCAACCCTTTCCATTTTGCA 58.597 42.857 0.00 0.00 0.00 4.08
6577 8358 3.192633 CGGGTTGGCTAGCTGTAAAAATT 59.807 43.478 15.72 0.00 0.00 1.82
6618 8399 6.823689 AGAAATCTGATAATACGCACAAAGGT 59.176 34.615 0.00 0.00 0.00 3.50
6671 8452 4.887748 AGTTCGAATCAAGTCACACATCT 58.112 39.130 0.00 0.00 0.00 2.90
6678 8459 4.039245 AGTTGGAGAGTTCGAATCAAGTCA 59.961 41.667 0.00 0.00 0.00 3.41
6708 8489 1.443194 CGGTCACCACGGTAACTCG 60.443 63.158 0.00 0.00 0.00 4.18
6709 8490 0.109412 CTCGGTCACCACGGTAACTC 60.109 60.000 0.00 0.00 0.00 3.01
6804 8585 3.725740 GCGTCAATTATTTTGGATCGCAG 59.274 43.478 0.00 0.00 40.63 5.18
6879 8668 6.853490 TGTCTCCTGTATGTAGGATGTATCT 58.147 40.000 0.00 0.00 45.44 1.98
6896 8685 7.181125 ACAGAGTACCTTTTATTCATGTCTCCT 59.819 37.037 0.00 0.00 0.00 3.69
6951 8763 4.923281 AGTTTTGCATCCTACGAAATTTGC 59.077 37.500 0.00 0.00 0.00 3.68
7016 8828 9.734620 TTAATGCATATTAAAGCACTGACAATC 57.265 29.630 0.00 0.00 44.49 2.67
7019 8831 8.279970 AGTTAATGCATATTAAAGCACTGACA 57.720 30.769 0.00 0.00 44.49 3.58
7060 8872 1.004979 CCACGGGGAATAAAAGGTGGA 59.995 52.381 0.00 0.00 45.96 4.02
7061 8873 1.470051 CCACGGGGAATAAAAGGTGG 58.530 55.000 0.00 0.00 38.97 4.61
7062 8874 2.089201 GACCACGGGGAATAAAAGGTG 58.911 52.381 12.96 0.00 38.05 4.00
7066 8878 7.483580 AAAAATATGACCACGGGGAATAAAA 57.516 32.000 12.96 0.00 38.05 1.52
7087 9681 5.701224 ACTGGAAGACCAAGGATACAAAAA 58.299 37.500 0.00 0.00 46.32 1.94


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

AutoCloner maintained by Alex Coulton.