Multiple sequence alignment - TraesCS1A01G237100

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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 TraesCS1A01G237100 chr1A 100.000 4359 0 0 1 4359 420398117 420393759 0.000000e+00 8050.0
1 TraesCS1A01G237100 chr1A 94.366 71 4 0 428 498 420397619 420397549 4.610000e-20 110.0
2 TraesCS1A01G237100 chr1A 94.366 71 4 0 499 569 420397690 420397620 4.610000e-20 110.0
3 TraesCS1A01G237100 chr1D 94.358 3013 87 33 499 3466 324616385 324619359 0.000000e+00 4545.0
4 TraesCS1A01G237100 chr1D 92.016 501 36 4 1 498 324615958 324616457 0.000000e+00 701.0
5 TraesCS1A01G237100 chr1D 86.855 601 50 7 3785 4359 324619405 324620002 0.000000e+00 645.0
6 TraesCS1A01G237100 chr3A 81.912 774 108 22 2631 3382 213132059 213132822 3.700000e-175 625.0
7 TraesCS1A01G237100 chr3A 94.565 184 10 0 1243 1426 213129496 213129679 7.140000e-73 285.0
8 TraesCS1A01G237100 chr3A 86.395 147 15 2 991 1137 213129275 213129416 5.840000e-34 156.0
9 TraesCS1A01G237100 chr3D 81.538 780 114 22 2631 3388 174417584 174418355 2.230000e-172 616.0
10 TraesCS1A01G237100 chr3D 92.748 262 16 3 2 262 122095556 122095297 4.120000e-100 375.0
11 TraesCS1A01G237100 chr3D 93.989 183 11 0 1244 1426 174414962 174415144 1.190000e-70 278.0
12 TraesCS1A01G237100 chr3D 87.755 147 13 2 991 1137 174414740 174414881 2.700000e-37 167.0
13 TraesCS1A01G237100 chr3B 81.026 780 118 20 2631 3388 252932433 252933204 1.040000e-165 593.0
14 TraesCS1A01G237100 chr3B 93.478 184 12 0 1243 1426 252929940 252930123 1.540000e-69 274.0
15 TraesCS1A01G237100 chr3B 85.714 147 16 2 991 1137 252929719 252929860 2.720000e-32 150.0
16 TraesCS1A01G237100 chr2B 93.561 264 14 3 1 263 340719232 340719493 1.470000e-104 390.0
17 TraesCS1A01G237100 chr7B 92.395 263 18 2 1 262 241581817 241582078 1.480000e-99 374.0
18 TraesCS1A01G237100 chr6D 91.822 269 20 2 1 268 299991689 299991956 1.480000e-99 374.0
19 TraesCS1A01G237100 chr6D 92.395 263 17 3 2 263 398747274 398747014 5.320000e-99 372.0
20 TraesCS1A01G237100 chr2D 92.424 264 17 3 1 262 406134852 406134590 1.480000e-99 374.0
21 TraesCS1A01G237100 chr2D 92.424 264 17 3 1 262 406137009 406136747 1.480000e-99 374.0
22 TraesCS1A01G237100 chr2A 92.424 264 16 4 1 262 490613624 490613885 1.480000e-99 374.0
23 TraesCS1A01G237100 chrUn 96.226 212 6 2 3467 3677 171112391 171112601 3.230000e-91 346.0
24 TraesCS1A01G237100 chrUn 95.735 211 8 1 3467 3677 138272143 138271934 5.400000e-89 339.0
25 TraesCS1A01G237100 chrUn 95.735 211 8 1 3467 3677 138484939 138484730 5.400000e-89 339.0
26 TraesCS1A01G237100 chrUn 95.735 211 8 1 3467 3677 172123455 172123664 5.400000e-89 339.0
27 TraesCS1A01G237100 chrUn 95.261 211 8 1 3467 3677 138346160 138345952 2.510000e-87 333.0
28 TraesCS1A01G237100 chr6A 96.209 211 7 1 3467 3677 558457496 558457705 1.160000e-90 344.0
29 TraesCS1A01G237100 chr6A 96.209 211 7 1 3467 3677 558460816 558461025 1.160000e-90 344.0
30 TraesCS1A01G237100 chr6A 95.735 211 8 1 3467 3677 542705073 542704864 5.400000e-89 339.0
31 TraesCS1A01G237100 chr6A 95.735 211 8 1 3467 3677 558552553 558552762 5.400000e-89 339.0
32 TraesCS1A01G237100 chr5A 100.000 29 0 0 948 976 569444603 569444575 2.000000e-03 54.7


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 TraesCS1A01G237100 chr1A 420393759 420398117 4358 True 2756.666667 8050 96.244000 1 4359 3 chr1A.!!$R1 4358
1 TraesCS1A01G237100 chr1D 324615958 324620002 4044 False 1963.666667 4545 91.076333 1 4359 3 chr1D.!!$F1 4358
2 TraesCS1A01G237100 chr3A 213129275 213132822 3547 False 355.333333 625 87.624000 991 3382 3 chr3A.!!$F1 2391
3 TraesCS1A01G237100 chr3D 174414740 174418355 3615 False 353.666667 616 87.760667 991 3388 3 chr3D.!!$F1 2397
4 TraesCS1A01G237100 chr3B 252929719 252933204 3485 False 339.000000 593 86.739333 991 3388 3 chr3B.!!$F1 2397
5 TraesCS1A01G237100 chr2D 406134590 406137009 2419 True 374.000000 374 92.424000 1 262 2 chr2D.!!$R1 261
6 TraesCS1A01G237100 chr6A 558457496 558461025 3529 False 344.000000 344 96.209000 3467 3677 2 chr6A.!!$F2 210

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
141 143 1.060729 TTGAAGGGGATTCCACGTCA 58.939 50.000 18.23 18.23 37.08 4.35 F
156 158 1.806542 ACGTCATCTTGTCATTGCCAC 59.193 47.619 0.00 0.00 0.00 5.01 F
1183 1668 1.224592 CTCTCCACCCCCGGATTTG 59.775 63.158 0.73 0.00 33.56 2.32 F
1663 2771 0.107268 TCATGCAGCGCAGGATACAT 59.893 50.000 11.47 0.00 44.36 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1177 1662 0.684153 TAGCCTGGCTTGCCAAATCC 60.684 55.000 28.55 4.44 40.44 3.01 R
1642 2750 1.070275 TATCCTGCGCTGCATGAGG 59.930 57.895 9.73 5.81 36.72 3.86 R
2712 5201 1.410517 AGACGGAATGCATCGATGACT 59.589 47.619 29.20 11.76 0.00 3.41 R
3511 6492 0.796312 CAAATCAAGCCACGTACGCT 59.204 50.000 16.72 0.80 38.53 5.07 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
40 42 6.434340 CCATCCCCTTTAATAGTATTGGCTTC 59.566 42.308 5.61 0.00 0.00 3.86
131 133 3.075283 TGTCCTTAGCATTTTGAAGGGGA 59.925 43.478 0.00 0.00 40.23 4.81
138 140 2.417243 GCATTTTGAAGGGGATTCCACG 60.417 50.000 4.80 0.00 37.08 4.94
141 143 1.060729 TTGAAGGGGATTCCACGTCA 58.939 50.000 18.23 18.23 37.08 4.35
149 151 2.354704 GGGATTCCACGTCATCTTGTCA 60.355 50.000 4.80 0.00 0.00 3.58
156 158 1.806542 ACGTCATCTTGTCATTGCCAC 59.193 47.619 0.00 0.00 0.00 5.01
158 160 1.806542 GTCATCTTGTCATTGCCACGT 59.193 47.619 0.00 0.00 0.00 4.49
177 179 4.150627 CACGTCACTGTTGAACTTATCTGG 59.849 45.833 0.00 0.00 31.90 3.86
244 246 7.671819 TGACATTAATTACCAAAATCACCCAGA 59.328 33.333 0.00 0.00 0.00 3.86
277 710 4.688879 TGCTTTCAGTACACGTGAATTAGG 59.311 41.667 25.01 6.46 33.95 2.69
285 718 6.849305 CAGTACACGTGAATTAGGTTTTTGAC 59.151 38.462 25.01 0.00 0.00 3.18
291 724 6.038825 ACGTGAATTAGGTTTTTGACACATGA 59.961 34.615 0.00 0.00 0.00 3.07
296 729 9.643693 GAATTAGGTTTTTGACACATGATGAAT 57.356 29.630 0.00 0.00 0.00 2.57
342 775 8.696410 ACAATTCTTTTAACGTGTTTGAACAT 57.304 26.923 0.00 0.00 41.59 2.71
344 777 9.618410 CAATTCTTTTAACGTGTTTGAACATTC 57.382 29.630 0.00 0.00 41.59 2.67
428 861 6.945072 AGACATTTTTCTCAACTACGTGAAC 58.055 36.000 0.00 0.00 0.00 3.18
429 862 6.537301 AGACATTTTTCTCAACTACGTGAACA 59.463 34.615 0.00 0.00 0.00 3.18
430 863 7.065324 AGACATTTTTCTCAACTACGTGAACAA 59.935 33.333 0.00 0.00 0.00 2.83
431 864 7.703328 ACATTTTTCTCAACTACGTGAACAAT 58.297 30.769 0.00 0.00 0.00 2.71
432 865 8.188139 ACATTTTTCTCAACTACGTGAACAATT 58.812 29.630 0.00 0.00 0.00 2.32
433 866 9.019764 CATTTTTCTCAACTACGTGAACAATTT 57.980 29.630 0.00 0.00 0.00 1.82
434 867 8.973835 TTTTTCTCAACTACGTGAACAATTTT 57.026 26.923 0.00 0.00 0.00 1.82
435 868 8.973835 TTTTCTCAACTACGTGAACAATTTTT 57.026 26.923 0.00 0.00 0.00 1.94
584 1019 8.677300 GTGAGGATGTTTCTTCAAAATATAGCA 58.323 33.333 0.00 0.00 39.41 3.49
729 1164 8.268738 GTCATGAACATTTTGTTTGAAAGCTAC 58.731 33.333 0.00 0.00 41.28 3.58
774 1209 9.127277 TGTGCTAACCTTTTCTTGTTACTATTT 57.873 29.630 0.00 0.00 0.00 1.40
872 1309 8.822105 AAATAAGAAAGAAATTATCGTGACGC 57.178 30.769 0.00 0.00 0.00 5.19
974 1411 3.989595 GCGAGACATAAGCGCGCC 61.990 66.667 30.33 11.57 46.37 6.53
975 1412 3.330853 CGAGACATAAGCGCGCCC 61.331 66.667 30.33 10.22 0.00 6.13
976 1413 2.107141 GAGACATAAGCGCGCCCT 59.893 61.111 30.33 18.55 0.00 5.19
977 1414 2.202932 AGACATAAGCGCGCCCTG 60.203 61.111 30.33 23.96 0.00 4.45
978 1415 2.511600 GACATAAGCGCGCCCTGT 60.512 61.111 30.33 27.07 0.00 4.00
1113 1583 1.827789 CTCCTCCCTCGCTCTCCTG 60.828 68.421 0.00 0.00 0.00 3.86
1180 1665 4.499116 CCCTCTCCACCCCCGGAT 62.499 72.222 0.73 0.00 33.56 4.18
1183 1668 1.224592 CTCTCCACCCCCGGATTTG 59.775 63.158 0.73 0.00 33.56 2.32
1185 1670 4.055227 TCCACCCCCGGATTTGGC 62.055 66.667 0.73 0.00 0.00 4.52
1187 1672 2.283532 CACCCCCGGATTTGGCAA 60.284 61.111 0.73 0.00 0.00 4.52
1188 1673 2.037208 ACCCCCGGATTTGGCAAG 59.963 61.111 0.73 0.00 0.00 4.01
1189 1674 3.460868 CCCCCGGATTTGGCAAGC 61.461 66.667 0.73 0.00 0.00 4.01
1190 1675 3.460868 CCCCGGATTTGGCAAGCC 61.461 66.667 0.73 3.61 34.82 4.35
1191 1676 2.679642 CCCGGATTTGGCAAGCCA 60.680 61.111 10.24 10.24 45.63 4.75
1240 1725 4.747529 TCACGCGCTGCTGCTGAT 62.748 61.111 5.73 0.00 36.97 2.90
1251 1736 2.611800 TGCTGATGCAGGGAGGGT 60.612 61.111 0.00 0.00 45.31 4.34
1459 2026 6.869695 TGATAAGCGATAGTAACTTGGTTCA 58.130 36.000 0.00 0.00 39.35 3.18
1525 2092 4.654091 ATTGTGGACACCAAAACTTCTG 57.346 40.909 0.00 0.00 33.05 3.02
1526 2093 1.748493 TGTGGACACCAAAACTTCTGC 59.252 47.619 0.00 0.00 34.18 4.26
1528 2095 3.211045 GTGGACACCAAAACTTCTGCTA 58.789 45.455 0.00 0.00 34.18 3.49
1642 2750 7.228706 CAGGTTCCTAAATGTACATAATCACCC 59.771 40.741 9.21 4.68 0.00 4.61
1663 2771 0.107268 TCATGCAGCGCAGGATACAT 59.893 50.000 11.47 0.00 44.36 2.29
1664 2772 1.344114 TCATGCAGCGCAGGATACATA 59.656 47.619 11.47 0.00 44.36 2.29
1676 2784 7.038659 GCGCAGGATACATATCTAGATTTCTT 58.961 38.462 11.25 0.00 41.41 2.52
1723 2831 7.868415 TGTTTTATTAATTATATTGGCCGTGGC 59.132 33.333 1.16 1.16 41.06 5.01
1928 4304 2.646930 CAGGTCTATGCAAATGCCAGA 58.353 47.619 2.46 3.05 41.18 3.86
2047 4423 8.523915 TTTGTAATTCACTAATCCATGCTCAT 57.476 30.769 0.00 0.00 0.00 2.90
2053 4429 8.883954 ATTCACTAATCCATGCTCATATATCG 57.116 34.615 0.00 0.00 0.00 2.92
2112 4488 9.667107 TTCTCCATTTCATCGTAAAAACTATCT 57.333 29.630 0.00 0.00 0.00 1.98
2162 4538 0.465460 TGGTTGTTCTGCAGTCCCAC 60.465 55.000 14.67 7.26 0.00 4.61
2178 4554 2.027561 TCCCACTGTACTGTATGCCAAC 60.028 50.000 4.96 0.00 0.00 3.77
2186 4616 7.119116 CACTGTACTGTATGCCAACTCATAAAA 59.881 37.037 4.96 0.00 31.43 1.52
2188 4618 8.574251 TGTACTGTATGCCAACTCATAAAAAT 57.426 30.769 0.00 0.00 31.43 1.82
2356 4845 4.340950 AGAGGCTAGTCTAATGAGCTTCAC 59.659 45.833 0.00 0.00 42.90 3.18
2359 4848 5.130145 AGGCTAGTCTAATGAGCTTCACATT 59.870 40.000 0.00 4.70 40.40 2.71
2461 4950 2.847327 ATGTCCCATCATAAGAGGCG 57.153 50.000 0.00 0.00 0.00 5.52
2468 4957 3.007940 CCCATCATAAGAGGCGGTGATAA 59.992 47.826 0.00 0.00 30.63 1.75
2477 4966 4.369182 AGAGGCGGTGATAAATAAGTTCG 58.631 43.478 0.00 0.00 0.00 3.95
2480 4969 3.064271 GGCGGTGATAAATAAGTTCGCAA 59.936 43.478 0.00 0.00 43.07 4.85
2484 4973 5.490213 GGTGATAAATAAGTTCGCAACGAG 58.510 41.667 0.00 0.00 37.14 4.18
2509 4998 8.542926 AGCCTCAAAGCCTAATTTATTTCAAAT 58.457 29.630 0.00 0.00 0.00 2.32
2554 5043 8.716646 ATTTTACTCTTGTTTTTCCACAAAGG 57.283 30.769 0.00 0.00 36.22 3.11
2599 5088 8.976986 AAATATTTCTGCTGAATTGACTTGAC 57.023 30.769 6.88 0.00 31.56 3.18
2611 5100 6.148315 TGAATTGACTTGACTATGCTTGTGAG 59.852 38.462 0.00 0.00 0.00 3.51
2635 5124 8.029642 AGATGTAACATCTTAAAACTTGGACG 57.970 34.615 0.00 0.00 0.00 4.79
2712 5201 2.257207 CAGAGTGTCAAGGGGAAGGTA 58.743 52.381 0.00 0.00 0.00 3.08
2846 5335 8.975663 AGTATTAGTGTACTACATAGTGCTGA 57.024 34.615 8.36 0.00 39.30 4.26
3112 5601 0.532573 CCTACCTGCGCTCAGAAGAA 59.467 55.000 9.73 0.00 42.95 2.52
3511 6492 4.408821 GTGCCCATCCGTGCTCCA 62.409 66.667 0.00 0.00 0.00 3.86
3538 6519 3.244976 CGTGGCTTGATTTGATTGGAAC 58.755 45.455 0.00 0.00 0.00 3.62
3570 6551 1.691163 CGGCCCCATCCCCTTAAAATT 60.691 52.381 0.00 0.00 0.00 1.82
3572 6553 3.239449 GGCCCCATCCCCTTAAAATTAG 58.761 50.000 0.00 0.00 0.00 1.73
3678 6659 4.473520 CAGGCAAGCCGGATCCGT 62.474 66.667 31.22 12.64 41.95 4.69
3679 6660 3.717294 AGGCAAGCCGGATCCGTT 61.717 61.111 31.22 18.10 41.95 4.44
3680 6661 2.750237 GGCAAGCCGGATCCGTTT 60.750 61.111 31.22 21.81 37.81 3.60
3704 6685 2.113860 TCTGAAATGCAGGCACTACC 57.886 50.000 0.00 0.00 44.98 3.18
3705 6686 1.350684 TCTGAAATGCAGGCACTACCA 59.649 47.619 0.00 0.00 44.98 3.25
3706 6687 2.025981 TCTGAAATGCAGGCACTACCAT 60.026 45.455 0.00 0.00 44.98 3.55
3707 6688 2.756760 CTGAAATGCAGGCACTACCATT 59.243 45.455 0.00 0.00 43.14 3.16
3709 6690 1.477553 AATGCAGGCACTACCATTGG 58.522 50.000 0.00 0.00 43.14 3.16
3713 6694 1.683011 GCAGGCACTACCATTGGATGT 60.683 52.381 10.37 4.65 43.14 3.06
3714 6695 2.726821 CAGGCACTACCATTGGATGTT 58.273 47.619 10.37 0.00 43.14 2.71
3715 6696 3.884895 CAGGCACTACCATTGGATGTTA 58.115 45.455 10.37 0.00 43.14 2.41
3716 6697 4.464008 CAGGCACTACCATTGGATGTTAT 58.536 43.478 10.37 0.00 43.14 1.89
3717 6698 4.516698 CAGGCACTACCATTGGATGTTATC 59.483 45.833 10.37 0.57 43.14 1.75
3718 6699 4.413520 AGGCACTACCATTGGATGTTATCT 59.586 41.667 10.37 2.60 43.14 1.98
3719 6700 4.516698 GGCACTACCATTGGATGTTATCTG 59.483 45.833 10.37 0.00 38.86 2.90
3720 6701 5.126067 GCACTACCATTGGATGTTATCTGT 58.874 41.667 10.37 0.00 0.00 3.41
3722 6703 6.115446 CACTACCATTGGATGTTATCTGTGT 58.885 40.000 10.37 0.00 0.00 3.72
3723 6704 6.599244 CACTACCATTGGATGTTATCTGTGTT 59.401 38.462 10.37 0.00 0.00 3.32
3724 6705 5.902613 ACCATTGGATGTTATCTGTGTTG 57.097 39.130 10.37 0.00 0.00 3.33
3727 6708 4.649267 TTGGATGTTATCTGTGTTGGGA 57.351 40.909 0.00 0.00 0.00 4.37
3728 6709 4.220693 TGGATGTTATCTGTGTTGGGAG 57.779 45.455 0.00 0.00 0.00 4.30
3729 6710 2.945668 GGATGTTATCTGTGTTGGGAGC 59.054 50.000 0.00 0.00 0.00 4.70
3731 6712 1.702401 TGTTATCTGTGTTGGGAGCCA 59.298 47.619 0.00 0.00 0.00 4.75
3732 6713 2.084546 GTTATCTGTGTTGGGAGCCAC 58.915 52.381 0.00 0.00 30.78 5.01
3733 6714 1.656587 TATCTGTGTTGGGAGCCACT 58.343 50.000 0.00 0.00 30.78 4.00
3734 6715 0.037303 ATCTGTGTTGGGAGCCACTG 59.963 55.000 0.00 0.00 30.78 3.66
3735 6716 1.149174 CTGTGTTGGGAGCCACTGT 59.851 57.895 0.00 0.00 30.78 3.55
3736 6717 0.466189 CTGTGTTGGGAGCCACTGTT 60.466 55.000 0.00 0.00 30.78 3.16
3737 6718 0.840617 TGTGTTGGGAGCCACTGTTA 59.159 50.000 0.00 0.00 30.78 2.41
3738 6719 1.213182 TGTGTTGGGAGCCACTGTTAA 59.787 47.619 0.00 0.00 30.78 2.01
3739 6720 2.158534 TGTGTTGGGAGCCACTGTTAAT 60.159 45.455 0.00 0.00 30.78 1.40
3742 6723 2.749621 GTTGGGAGCCACTGTTAATCTG 59.250 50.000 0.00 0.00 30.78 2.90
3743 6724 1.985159 TGGGAGCCACTGTTAATCTGT 59.015 47.619 0.00 0.00 0.00 3.41
3744 6725 2.290260 TGGGAGCCACTGTTAATCTGTG 60.290 50.000 0.00 7.57 42.84 3.66
3745 6726 2.290323 GGGAGCCACTGTTAATCTGTGT 60.290 50.000 11.27 0.00 42.05 3.72
3746 6727 3.412386 GGAGCCACTGTTAATCTGTGTT 58.588 45.455 11.27 3.61 42.05 3.32
3762 9968 3.650950 TTGGGAGGGAGCAGGCAC 61.651 66.667 0.00 0.00 0.00 5.01
3763 9969 4.664267 TGGGAGGGAGCAGGCACT 62.664 66.667 0.00 0.00 43.88 4.40
3782 9988 3.101209 CCATTGGACCATGCGACG 58.899 61.111 0.00 0.00 0.00 5.12
3788 10009 4.865761 GACCATGCGACGCGGCTA 62.866 66.667 11.76 0.00 0.00 3.93
3789 10010 4.221422 ACCATGCGACGCGGCTAT 62.221 61.111 11.76 0.47 0.00 2.97
3803 10024 3.914966 CGCGGCTATCTGTTAATCTACTG 59.085 47.826 0.00 0.00 0.00 2.74
3804 10025 4.556898 CGCGGCTATCTGTTAATCTACTGT 60.557 45.833 0.00 0.00 0.00 3.55
3807 10028 6.362820 GCGGCTATCTGTTAATCTACTGTTAC 59.637 42.308 0.00 0.00 0.00 2.50
3808 10029 6.862090 CGGCTATCTGTTAATCTACTGTTACC 59.138 42.308 0.00 0.00 0.00 2.85
3820 10041 0.911769 CTGTTACCATCTCCCCTGCA 59.088 55.000 0.00 0.00 0.00 4.41
3908 10143 9.922305 GTTGCTCATTCTTGTTCTAATATACAC 57.078 33.333 0.00 0.00 0.00 2.90
3913 10148 7.979537 TCATTCTTGTTCTAATATACACGCTGT 59.020 33.333 0.00 0.00 0.00 4.40
3939 10174 6.092748 GGTTTGATGCACTGTGGTAATAAAG 58.907 40.000 10.21 0.00 0.00 1.85
3977 10212 8.721019 ACCAAAATATTATGGCATGAACAAAG 57.279 30.769 10.98 0.00 40.51 2.77
3989 10224 8.640063 TGGCATGAACAAAGCATATAGATAAT 57.360 30.769 0.00 0.00 0.00 1.28
4015 10250 3.552604 TGTTAGAATTCAGCGCAAACC 57.447 42.857 11.47 0.00 0.00 3.27
4050 10285 4.334837 GAGCATCTACAGCCTCGC 57.665 61.111 0.00 0.00 0.00 5.03
4086 10328 4.176752 GGAGGATGCCCGGGTCAC 62.177 72.222 24.63 13.17 37.58 3.67
4116 10363 1.460497 AAAAACCAACCCGGCCCAT 60.460 52.632 0.00 0.00 39.03 4.00
4130 10377 3.515286 CCATGCAGCGGCCTCAAG 61.515 66.667 6.32 0.00 40.13 3.02
4132 10379 2.437359 ATGCAGCGGCCTCAAGTC 60.437 61.111 6.32 0.00 40.13 3.01
4154 10401 1.153568 CTCGAATGCTCGGGCTGAA 60.154 57.895 9.62 0.00 45.49 3.02
4155 10402 0.531532 CTCGAATGCTCGGGCTGAAT 60.532 55.000 9.62 0.00 45.49 2.57
4158 10405 2.068277 GAATGCTCGGGCTGAATGGC 62.068 60.000 9.62 0.00 39.59 4.40
4181 10428 4.637534 CGCCCCTCATATCCAATCTAAATG 59.362 45.833 0.00 0.00 0.00 2.32
4191 10438 3.139077 CCAATCTAAATGTAGGGCGGAC 58.861 50.000 0.00 0.00 0.00 4.79
4195 10442 3.035363 TCTAAATGTAGGGCGGACATGA 58.965 45.455 0.00 0.00 37.59 3.07
4234 10481 1.901591 CCACATTGGAACTGACAGCT 58.098 50.000 1.25 0.00 40.96 4.24
4235 10482 2.233271 CCACATTGGAACTGACAGCTT 58.767 47.619 1.25 0.00 40.96 3.74
4238 10485 2.880890 ACATTGGAACTGACAGCTTGAC 59.119 45.455 1.25 0.00 0.00 3.18
4259 10506 1.134670 CCCCGCAAAAAGTGAACCAAA 60.135 47.619 0.00 0.00 0.00 3.28
4268 10515 1.760405 AGTGAACCAAATCCCCCTCT 58.240 50.000 0.00 0.00 0.00 3.69
4269 10516 2.929301 AGTGAACCAAATCCCCCTCTA 58.071 47.619 0.00 0.00 0.00 2.43
4275 10522 4.035967 ACCAAATCCCCCTCTAACCTAT 57.964 45.455 0.00 0.00 0.00 2.57
4298 10545 1.227999 TTTTCACTTGCTCCTCCGCG 61.228 55.000 0.00 0.00 0.00 6.46
4301 10548 4.421479 ACTTGCTCCTCCGCGTCG 62.421 66.667 4.92 0.00 0.00 5.12
4325 10572 4.129737 TGCTAGCTCCGTCGCCAC 62.130 66.667 17.23 0.00 0.00 5.01
4327 10574 3.449227 CTAGCTCCGTCGCCACCA 61.449 66.667 0.00 0.00 0.00 4.17
4352 10599 2.281761 CGACTGCACCTTGCCCTT 60.282 61.111 0.00 0.00 44.23 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.246163 CCAATACTATTAAAGGGGATGGGAC 58.754 44.000 0.00 0.00 0.00 4.46
13 14 5.222254 GCCAATACTATTAAAGGGGATGGGA 60.222 44.000 0.00 0.00 0.00 4.37
15 16 5.892348 AGCCAATACTATTAAAGGGGATGG 58.108 41.667 0.00 0.00 0.00 3.51
40 42 4.970860 AGATCACATTGAGTCCATAGGG 57.029 45.455 0.00 0.00 0.00 3.53
131 133 3.127548 GCAATGACAAGATGACGTGGAAT 59.872 43.478 0.00 0.00 0.00 3.01
138 140 1.806542 ACGTGGCAATGACAAGATGAC 59.193 47.619 9.41 0.00 0.00 3.06
141 143 1.806542 GTGACGTGGCAATGACAAGAT 59.193 47.619 9.41 0.00 0.00 2.40
149 151 1.333619 GTTCAACAGTGACGTGGCAAT 59.666 47.619 0.00 0.00 31.90 3.56
156 158 4.556233 TCCAGATAAGTTCAACAGTGACG 58.444 43.478 0.00 0.00 31.90 4.35
158 160 9.817809 GTATATTCCAGATAAGTTCAACAGTGA 57.182 33.333 0.00 0.00 0.00 3.41
342 775 9.974980 GAAAAGGTTGACCATGTATTAAAAGAA 57.025 29.630 2.56 0.00 38.89 2.52
344 777 9.981114 AAGAAAAGGTTGACCATGTATTAAAAG 57.019 29.630 2.56 0.00 38.89 2.27
405 838 6.711579 TGTTCACGTAGTTGAGAAAAATGTC 58.288 36.000 0.00 0.00 41.61 3.06
408 841 9.581099 AAAATTGTTCACGTAGTTGAGAAAAAT 57.419 25.926 0.00 0.00 41.61 1.82
477 910 6.438259 TGTAACATCCTCACGTTTCAAAAA 57.562 33.333 0.00 0.00 0.00 1.94
478 911 6.627395 ATGTAACATCCTCACGTTTCAAAA 57.373 33.333 0.00 0.00 0.00 2.44
479 912 6.627395 AATGTAACATCCTCACGTTTCAAA 57.373 33.333 0.00 0.00 0.00 2.69
480 913 6.627395 AAATGTAACATCCTCACGTTTCAA 57.373 33.333 0.00 0.00 27.77 2.69
481 914 6.627395 AAAATGTAACATCCTCACGTTTCA 57.373 33.333 0.00 0.00 31.83 2.69
548 983 8.256605 TGAAGAAACATCCTCACATTTCAAAAA 58.743 29.630 0.00 0.00 34.22 1.94
557 992 8.677300 GCTATATTTTGAAGAAACATCCTCACA 58.323 33.333 0.00 0.00 0.00 3.58
747 1182 8.685838 ATAGTAACAAGAAAAGGTTAGCACAA 57.314 30.769 0.00 0.00 30.70 3.33
846 1282 9.274065 GCGTCACGATAATTTCTTTCTTATTTT 57.726 29.630 0.00 0.00 0.00 1.82
855 1291 2.351726 GCTGGCGTCACGATAATTTCTT 59.648 45.455 0.00 0.00 0.00 2.52
857 1293 1.663643 TGCTGGCGTCACGATAATTTC 59.336 47.619 0.00 0.00 0.00 2.17
860 1296 2.677971 GTGCTGGCGTCACGATAAT 58.322 52.632 0.00 0.00 0.00 1.28
872 1309 2.433145 ACGCTGACATCGTGCTGG 60.433 61.111 3.11 0.00 38.88 4.85
960 1397 2.202932 CAGGGCGCGCTTATGTCT 60.203 61.111 32.29 15.24 0.00 3.41
962 1399 2.819595 CACAGGGCGCGCTTATGT 60.820 61.111 32.29 27.20 0.00 2.29
975 1412 4.724697 CTCGCCGCGTTTGCACAG 62.725 66.667 13.39 0.00 42.97 3.66
977 1414 3.911155 CTTCTCGCCGCGTTTGCAC 62.911 63.158 13.39 0.00 42.97 4.57
978 1415 3.711842 CTTCTCGCCGCGTTTGCA 61.712 61.111 13.39 0.00 42.97 4.08
983 1420 2.325082 ATTTTGCTTCTCGCCGCGT 61.325 52.632 13.39 0.00 38.05 6.01
1176 1661 2.887360 CCTGGCTTGCCAAATCCG 59.113 61.111 15.63 3.51 0.00 4.18
1177 1662 0.684153 TAGCCTGGCTTGCCAAATCC 60.684 55.000 28.55 4.44 40.44 3.01
1180 1665 4.421365 CTAGCCTGGCTTGCCAAA 57.579 55.556 28.55 6.45 40.44 3.28
1194 1679 4.856801 AACCATGGCGGGCGCTAG 62.857 66.667 13.04 2.28 40.22 3.42
1195 1680 4.849310 GAACCATGGCGGGCGCTA 62.849 66.667 13.04 0.00 40.22 4.26
1459 2026 7.540183 AGGAATACTACAATCAGGAGAGGTAT 58.460 38.462 0.00 0.00 0.00 2.73
1525 2092 8.812329 CATGACTAACTGAATTCTAACACTAGC 58.188 37.037 7.05 0.00 0.00 3.42
1526 2093 9.307121 CCATGACTAACTGAATTCTAACACTAG 57.693 37.037 7.05 0.00 0.00 2.57
1528 2095 6.595716 GCCATGACTAACTGAATTCTAACACT 59.404 38.462 7.05 0.00 0.00 3.55
1642 2750 1.070275 TATCCTGCGCTGCATGAGG 59.930 57.895 9.73 5.81 36.72 3.86
1983 4359 6.482973 ACTGTGGCAAAAATAAAATCAGTTGG 59.517 34.615 0.00 0.00 31.02 3.77
1984 4360 7.481275 ACTGTGGCAAAAATAAAATCAGTTG 57.519 32.000 0.00 0.00 31.02 3.16
1988 4364 6.586344 TGGAACTGTGGCAAAAATAAAATCA 58.414 32.000 0.00 0.00 0.00 2.57
1989 4365 7.671495 ATGGAACTGTGGCAAAAATAAAATC 57.329 32.000 0.00 0.00 0.00 2.17
2123 4499 2.287373 CAGCGCATCTTTTTGCCAAAAA 59.713 40.909 11.47 14.19 39.52 1.94
2162 4538 7.609760 TTTTATGAGTTGGCATACAGTACAG 57.390 36.000 0.00 0.00 30.89 2.74
2356 4845 3.221771 TGGACTTGGGAAGACACAAATG 58.778 45.455 0.00 0.00 39.04 2.32
2359 4848 3.020984 GTTTGGACTTGGGAAGACACAA 58.979 45.455 0.00 0.00 37.05 3.33
2419 4908 9.768215 ACATTTTCCCTTTTCCTATTCTATTCA 57.232 29.630 0.00 0.00 0.00 2.57
2461 4950 5.459110 TCGTTGCGAACTTATTTATCACC 57.541 39.130 0.00 0.00 31.06 4.02
2468 4957 2.000447 GAGGCTCGTTGCGAACTTATT 59.000 47.619 0.00 0.00 44.05 1.40
2477 4966 2.563427 GGCTTTGAGGCTCGTTGC 59.437 61.111 10.42 12.72 37.85 4.17
2484 4973 8.722480 ATTTGAAATAAATTAGGCTTTGAGGC 57.278 30.769 0.00 0.00 41.73 4.70
2516 5005 8.000780 ACAAGAGTAAAATCAGAGCAGTTTTT 57.999 30.769 0.00 0.00 0.00 1.94
2599 5088 7.783090 AAGATGTTACATCTCACAAGCATAG 57.217 36.000 25.61 0.00 0.00 2.23
2611 5100 7.744715 CACGTCCAAGTTTTAAGATGTTACATC 59.255 37.037 16.80 16.80 0.00 3.06
2635 5124 5.232202 GGTTTAAAGCTTCAAAACTCTGCAC 59.768 40.000 24.93 11.99 34.34 4.57
2712 5201 1.410517 AGACGGAATGCATCGATGACT 59.589 47.619 29.20 11.76 0.00 3.41
2840 5329 2.266554 CGAGTTCAGAAGGATCAGCAC 58.733 52.381 0.00 0.00 0.00 4.40
2846 5335 9.892130 AAATTATAAAGACGAGTTCAGAAGGAT 57.108 29.630 0.00 0.00 0.00 3.24
3112 5601 4.339247 ACATTGCAGCTTCAACTAAACTGT 59.661 37.500 0.00 0.00 0.00 3.55
3511 6492 0.796312 CAAATCAAGCCACGTACGCT 59.204 50.000 16.72 0.80 38.53 5.07
3626 6607 1.002134 CCATCCGTGCTCCCACTTT 60.002 57.895 0.00 0.00 39.86 2.66
3679 6660 3.132646 AGTGCCTGCATTTCAGACAAAAA 59.867 39.130 0.00 0.00 45.72 1.94
3680 6661 2.694628 AGTGCCTGCATTTCAGACAAAA 59.305 40.909 0.00 0.00 45.72 2.44
3683 6664 2.426522 GTAGTGCCTGCATTTCAGACA 58.573 47.619 0.00 0.00 45.72 3.41
3684 6665 1.740025 GGTAGTGCCTGCATTTCAGAC 59.260 52.381 0.00 0.00 45.72 3.51
3685 6666 1.350684 TGGTAGTGCCTGCATTTCAGA 59.649 47.619 0.00 0.00 45.72 3.27
3686 6667 1.825090 TGGTAGTGCCTGCATTTCAG 58.175 50.000 0.00 0.00 42.49 3.02
3687 6668 2.492881 CAATGGTAGTGCCTGCATTTCA 59.507 45.455 0.00 0.00 38.35 2.69
3688 6669 2.159198 CCAATGGTAGTGCCTGCATTTC 60.159 50.000 0.00 0.00 38.35 2.17
3689 6670 1.826720 CCAATGGTAGTGCCTGCATTT 59.173 47.619 0.00 0.00 38.35 2.32
3691 6672 0.625316 TCCAATGGTAGTGCCTGCAT 59.375 50.000 0.00 0.00 38.35 3.96
3692 6673 0.625316 ATCCAATGGTAGTGCCTGCA 59.375 50.000 0.00 0.00 38.35 4.41
3693 6674 1.027357 CATCCAATGGTAGTGCCTGC 58.973 55.000 0.00 0.00 38.35 4.85
3695 6676 4.413520 AGATAACATCCAATGGTAGTGCCT 59.586 41.667 0.00 0.00 35.61 4.75
3697 6678 5.008019 CACAGATAACATCCAATGGTAGTGC 59.992 44.000 0.00 0.00 35.61 4.40
3698 6679 6.115446 ACACAGATAACATCCAATGGTAGTG 58.885 40.000 0.00 0.00 35.61 2.74
3699 6680 6.313519 ACACAGATAACATCCAATGGTAGT 57.686 37.500 0.00 0.00 35.61 2.73
3700 6681 6.038603 CCAACACAGATAACATCCAATGGTAG 59.961 42.308 0.00 0.00 35.61 3.18
3701 6682 5.885352 CCAACACAGATAACATCCAATGGTA 59.115 40.000 0.00 0.00 36.78 3.25
3702 6683 4.706476 CCAACACAGATAACATCCAATGGT 59.294 41.667 0.00 0.00 33.60 3.55
3703 6684 4.098349 CCCAACACAGATAACATCCAATGG 59.902 45.833 0.00 0.00 33.60 3.16
3704 6685 4.949238 TCCCAACACAGATAACATCCAATG 59.051 41.667 0.00 0.00 0.00 2.82
3705 6686 5.191727 TCCCAACACAGATAACATCCAAT 57.808 39.130 0.00 0.00 0.00 3.16
3706 6687 4.588899 CTCCCAACACAGATAACATCCAA 58.411 43.478 0.00 0.00 0.00 3.53
3707 6688 3.622206 GCTCCCAACACAGATAACATCCA 60.622 47.826 0.00 0.00 0.00 3.41
3709 6690 2.945668 GGCTCCCAACACAGATAACATC 59.054 50.000 0.00 0.00 0.00 3.06
3713 6694 1.985159 AGTGGCTCCCAACACAGATAA 59.015 47.619 0.00 0.00 39.99 1.75
3714 6695 1.278985 CAGTGGCTCCCAACACAGATA 59.721 52.381 0.00 0.00 39.99 1.98
3715 6696 0.037303 CAGTGGCTCCCAACACAGAT 59.963 55.000 0.00 0.00 39.99 2.90
3716 6697 1.344953 ACAGTGGCTCCCAACACAGA 61.345 55.000 0.00 0.00 39.99 3.41
3717 6698 0.466189 AACAGTGGCTCCCAACACAG 60.466 55.000 0.00 0.00 39.99 3.66
3718 6699 0.840617 TAACAGTGGCTCCCAACACA 59.159 50.000 0.00 0.00 39.99 3.72
3719 6700 1.975660 TTAACAGTGGCTCCCAACAC 58.024 50.000 0.00 0.00 34.18 3.32
3720 6701 2.375174 AGATTAACAGTGGCTCCCAACA 59.625 45.455 0.00 0.00 34.18 3.33
3722 6703 2.375174 ACAGATTAACAGTGGCTCCCAA 59.625 45.455 0.00 0.00 34.18 4.12
3723 6704 1.985159 ACAGATTAACAGTGGCTCCCA 59.015 47.619 0.00 0.00 0.00 4.37
3724 6705 2.290323 ACACAGATTAACAGTGGCTCCC 60.290 50.000 0.00 0.00 39.73 4.30
3727 6708 3.149196 CCAACACAGATTAACAGTGGCT 58.851 45.455 0.00 0.00 39.73 4.75
3728 6709 2.228822 CCCAACACAGATTAACAGTGGC 59.771 50.000 0.00 0.00 39.73 5.01
3729 6710 3.750371 TCCCAACACAGATTAACAGTGG 58.250 45.455 0.00 0.00 39.73 4.00
3731 6712 3.244911 CCCTCCCAACACAGATTAACAGT 60.245 47.826 0.00 0.00 0.00 3.55
3732 6713 3.009033 TCCCTCCCAACACAGATTAACAG 59.991 47.826 0.00 0.00 0.00 3.16
3733 6714 2.983192 TCCCTCCCAACACAGATTAACA 59.017 45.455 0.00 0.00 0.00 2.41
3734 6715 3.610911 CTCCCTCCCAACACAGATTAAC 58.389 50.000 0.00 0.00 0.00 2.01
3735 6716 2.026262 GCTCCCTCCCAACACAGATTAA 60.026 50.000 0.00 0.00 0.00 1.40
3736 6717 1.559682 GCTCCCTCCCAACACAGATTA 59.440 52.381 0.00 0.00 0.00 1.75
3737 6718 0.329596 GCTCCCTCCCAACACAGATT 59.670 55.000 0.00 0.00 0.00 2.40
3738 6719 0.842030 TGCTCCCTCCCAACACAGAT 60.842 55.000 0.00 0.00 0.00 2.90
3739 6720 1.461268 TGCTCCCTCCCAACACAGA 60.461 57.895 0.00 0.00 0.00 3.41
3742 6723 2.352805 CCTGCTCCCTCCCAACAC 59.647 66.667 0.00 0.00 0.00 3.32
3743 6724 3.650950 GCCTGCTCCCTCCCAACA 61.651 66.667 0.00 0.00 0.00 3.33
3744 6725 3.650950 TGCCTGCTCCCTCCCAAC 61.651 66.667 0.00 0.00 0.00 3.77
3745 6726 3.650950 GTGCCTGCTCCCTCCCAA 61.651 66.667 0.00 0.00 0.00 4.12
3746 6727 4.664267 AGTGCCTGCTCCCTCCCA 62.664 66.667 0.00 0.00 0.00 4.37
3762 9968 1.750018 TCGCATGGTCCAATGGCAG 60.750 57.895 12.36 6.67 0.00 4.85
3763 9969 2.045708 GTCGCATGGTCCAATGGCA 61.046 57.895 12.36 0.00 0.00 4.92
3764 9970 2.800736 GTCGCATGGTCCAATGGC 59.199 61.111 0.00 0.00 0.00 4.40
3766 9972 2.404789 GCGTCGCATGGTCCAATG 59.595 61.111 13.44 0.00 0.00 2.82
3767 9973 3.195002 CGCGTCGCATGGTCCAAT 61.195 61.111 18.75 0.00 0.00 3.16
3771 9977 4.865761 TAGCCGCGTCGCATGGTC 62.866 66.667 18.75 7.60 0.00 4.02
3782 9988 4.872664 ACAGTAGATTAACAGATAGCCGC 58.127 43.478 0.00 0.00 0.00 6.53
3803 10024 2.507407 TTTGCAGGGGAGATGGTAAC 57.493 50.000 0.00 0.00 0.00 2.50
3804 10025 3.534357 TTTTTGCAGGGGAGATGGTAA 57.466 42.857 0.00 0.00 0.00 2.85
3840 10061 3.354948 ACATGCATAGCCTGAACAAGA 57.645 42.857 0.00 0.00 0.00 3.02
3908 10143 1.154413 GTGCATCAAACCGACAGCG 60.154 57.895 0.00 0.00 32.11 5.18
3913 10148 0.179032 ACCACAGTGCATCAAACCGA 60.179 50.000 0.00 0.00 0.00 4.69
3939 10174 1.923356 TTTTGGTCAGGCAGATTCCC 58.077 50.000 0.00 0.00 0.00 3.97
4015 10250 2.749621 GCTCTAACCCCACAAAGTGATG 59.250 50.000 0.00 0.00 35.23 3.07
4050 10285 2.269241 GGAGGGGAGTTTGAGGCG 59.731 66.667 0.00 0.00 0.00 5.52
4121 10368 2.182030 GAGACCGACTTGAGGCCG 59.818 66.667 0.00 0.00 0.00 6.13
4154 10401 1.426251 TTGGATATGAGGGGCGCCAT 61.426 55.000 30.85 17.07 0.00 4.40
4155 10402 1.426251 ATTGGATATGAGGGGCGCCA 61.426 55.000 30.85 7.96 0.00 5.69
4158 10405 3.981071 TTAGATTGGATATGAGGGGCG 57.019 47.619 0.00 0.00 0.00 6.13
4163 10410 6.536582 CGCCCTACATTTAGATTGGATATGAG 59.463 42.308 0.00 0.00 0.00 2.90
4181 10428 2.109181 GCCTCATGTCCGCCCTAC 59.891 66.667 0.00 0.00 0.00 3.18
4209 10456 1.142667 TCAGTTCCAATGTGGCAGACA 59.857 47.619 0.00 0.00 37.47 3.41
4213 10460 1.608055 CTGTCAGTTCCAATGTGGCA 58.392 50.000 0.00 0.00 37.47 4.92
4234 10481 0.395862 TCACTTTTTGCGGGGGTCAA 60.396 50.000 0.00 0.00 0.00 3.18
4235 10482 0.395862 TTCACTTTTTGCGGGGGTCA 60.396 50.000 0.00 0.00 0.00 4.02
4238 10485 1.365999 GGTTCACTTTTTGCGGGGG 59.634 57.895 0.00 0.00 0.00 5.40
4259 10506 2.465769 AGGGATAGGTTAGAGGGGGAT 58.534 52.381 0.00 0.00 0.00 3.85
4268 10515 5.497474 GAGCAAGTGAAAAGGGATAGGTTA 58.503 41.667 0.00 0.00 0.00 2.85
4269 10516 4.336280 GAGCAAGTGAAAAGGGATAGGTT 58.664 43.478 0.00 0.00 0.00 3.50
4275 10522 1.073923 GGAGGAGCAAGTGAAAAGGGA 59.926 52.381 0.00 0.00 0.00 4.20
4304 10551 2.473760 GCGACGGAGCTAGCAGAGA 61.474 63.158 18.83 0.00 0.00 3.10
4307 10554 3.826754 TGGCGACGGAGCTAGCAG 61.827 66.667 18.83 10.33 37.29 4.24


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

AutoCloner maintained by Alex Coulton.