Multiple sequence alignment - TraesCS7A01G045200

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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 TraesCS7A01G045200 chr7A 100.000 4754 0 0 1 4754 20658674 20663427 0.000000e+00 8780.0
1 TraesCS7A01G045200 chr7A 95.426 2842 110 5 1780 4621 20722274 20725095 0.000000e+00 4510.0
2 TraesCS7A01G045200 chr7A 84.437 2930 436 17 804 3725 20482634 20485551 0.000000e+00 2867.0
3 TraesCS7A01G045200 chr7A 86.947 452 24 9 1 432 20720379 20720815 4.300000e-130 475.0
4 TraesCS7A01G045200 chr7D 96.054 4105 143 8 519 4621 20403856 20407943 0.000000e+00 6665.0
5 TraesCS7A01G045200 chr7D 85.437 2884 403 14 886 3760 89533132 89530257 0.000000e+00 2983.0
6 TraesCS7A01G045200 chr7D 83.896 2993 456 14 816 3792 20946977 20949959 0.000000e+00 2833.0
7 TraesCS7A01G045200 chr7D 83.903 2982 452 23 816 3787 20310696 20313659 0.000000e+00 2822.0
8 TraesCS7A01G045200 chr7D 83.255 854 52 35 1 799 20402999 20403816 0.000000e+00 701.0
9 TraesCS7A01G045200 chr2A 85.483 2907 402 18 890 3784 733087691 733090589 0.000000e+00 3013.0
10 TraesCS7A01G045200 chr2D 85.511 2878 404 12 911 3782 598814010 598816880 0.000000e+00 2992.0
11 TraesCS7A01G045200 chr2D 84.058 138 19 2 4318 4453 598889029 598889165 3.860000e-26 130.0
12 TraesCS7A01G045200 chr2B 85.238 2879 408 15 911 3782 727685968 727688836 0.000000e+00 2946.0
13 TraesCS7A01G045200 chr2B 96.226 53 1 1 4314 4366 727710642 727710693 8.480000e-13 86.1
14 TraesCS7A01G045200 chr7B 83.791 3023 460 24 816 3828 601114309 601117311 0.000000e+00 2841.0
15 TraesCS7A01G045200 chr3A 83.114 533 48 17 1 512 714515536 714515025 9.380000e-122 448.0
16 TraesCS7A01G045200 chr3A 86.705 346 31 9 568 903 714515014 714514674 2.090000e-98 370.0
17 TraesCS7A01G045200 chr3A 80.000 385 42 16 431 784 204559099 204559479 7.900000e-63 252.0
18 TraesCS7A01G045200 chr3A 74.107 448 86 23 1 428 204558627 204559064 1.770000e-34 158.0
19 TraesCS7A01G045200 chr5A 76.275 451 72 24 1 428 705546247 705545809 1.730000e-49 207.0
20 TraesCS7A01G045200 chr5A 86.957 92 12 0 431 522 705545774 705545683 2.340000e-18 104.0


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 TraesCS7A01G045200 chr7A 20658674 20663427 4753 False 8780.0 8780 100.0000 1 4754 1 chr7A.!!$F2 4753
1 TraesCS7A01G045200 chr7A 20482634 20485551 2917 False 2867.0 2867 84.4370 804 3725 1 chr7A.!!$F1 2921
2 TraesCS7A01G045200 chr7A 20720379 20725095 4716 False 2492.5 4510 91.1865 1 4621 2 chr7A.!!$F3 4620
3 TraesCS7A01G045200 chr7D 20402999 20407943 4944 False 3683.0 6665 89.6545 1 4621 2 chr7D.!!$F3 4620
4 TraesCS7A01G045200 chr7D 89530257 89533132 2875 True 2983.0 2983 85.4370 886 3760 1 chr7D.!!$R1 2874
5 TraesCS7A01G045200 chr7D 20946977 20949959 2982 False 2833.0 2833 83.8960 816 3792 1 chr7D.!!$F2 2976
6 TraesCS7A01G045200 chr7D 20310696 20313659 2963 False 2822.0 2822 83.9030 816 3787 1 chr7D.!!$F1 2971
7 TraesCS7A01G045200 chr2A 733087691 733090589 2898 False 3013.0 3013 85.4830 890 3784 1 chr2A.!!$F1 2894
8 TraesCS7A01G045200 chr2D 598814010 598816880 2870 False 2992.0 2992 85.5110 911 3782 1 chr2D.!!$F1 2871
9 TraesCS7A01G045200 chr2B 727685968 727688836 2868 False 2946.0 2946 85.2380 911 3782 1 chr2B.!!$F1 2871
10 TraesCS7A01G045200 chr7B 601114309 601117311 3002 False 2841.0 2841 83.7910 816 3828 1 chr7B.!!$F1 3012
11 TraesCS7A01G045200 chr3A 714514674 714515536 862 True 409.0 448 84.9095 1 903 2 chr3A.!!$R1 902
12 TraesCS7A01G045200 chr3A 204558627 204559479 852 False 205.0 252 77.0535 1 784 2 chr3A.!!$F1 783

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
90 92 2.277120 CGACGACGAGGTAAGCCG 60.277 66.667 0.0 0.0 42.66 5.52 F
1545 2049 2.045885 AGAAGATCTAGTGGGGGTGGAA 59.954 50.000 0.0 0.0 0.00 3.53 F
3321 3891 0.035343 GACTAGCGGAAGGGGCTTTT 60.035 55.000 0.0 0.0 41.80 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 2193 2.503382 GGAGACGGAGATCCAGGCC 61.503 68.421 0.00 0.00 37.01 5.19 R
3427 3997 3.529634 TTGTAGACGCGTCAAATTTGG 57.470 42.857 37.85 4.32 0.00 3.28 R
4476 5050 0.102844 ATGCATAAACATGCCGTGGC 59.897 50.000 3.30 3.30 46.43 5.01 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
90 92 2.277120 CGACGACGAGGTAAGCCG 60.277 66.667 0.00 0.00 42.66 5.52
103 105 2.404566 TAAGCCGACCTGCAGCCAAA 62.405 55.000 8.66 0.00 0.00 3.28
167 172 7.503230 TCAATTAAGCATTGCCATCTTGAGATA 59.497 33.333 4.70 0.00 42.06 1.98
214 237 7.186570 TGATCTGATGTTTGGATCTACTGAA 57.813 36.000 0.00 0.00 37.38 3.02
215 238 7.799081 TGATCTGATGTTTGGATCTACTGAAT 58.201 34.615 0.00 0.00 37.38 2.57
218 241 9.775854 ATCTGATGTTTGGATCTACTGAATAAG 57.224 33.333 0.00 0.00 0.00 1.73
219 242 7.712639 TCTGATGTTTGGATCTACTGAATAAGC 59.287 37.037 0.00 0.00 0.00 3.09
230 253 3.696898 ACTGAATAAGCGACGAGATGTC 58.303 45.455 0.00 0.00 44.53 3.06
252 286 4.714802 TCAAGTGTGGTACTGCCTATACAT 59.285 41.667 0.00 0.00 40.26 2.29
253 287 5.894964 TCAAGTGTGGTACTGCCTATACATA 59.105 40.000 0.00 0.00 40.26 2.29
254 288 5.786264 AGTGTGGTACTGCCTATACATAC 57.214 43.478 0.00 0.00 38.49 2.39
255 289 5.455872 AGTGTGGTACTGCCTATACATACT 58.544 41.667 0.00 0.00 38.49 2.12
256 290 5.302059 AGTGTGGTACTGCCTATACATACTG 59.698 44.000 0.00 0.00 38.49 2.74
257 291 5.068723 GTGTGGTACTGCCTATACATACTGT 59.931 44.000 0.00 0.00 38.35 3.55
305 339 9.906660 AAATTAGAAGACATTTGCGTGATTTAA 57.093 25.926 0.00 0.00 0.00 1.52
309 343 8.492673 AGAAGACATTTGCGTGATTTAATCTA 57.507 30.769 6.50 0.00 0.00 1.98
373 427 7.775093 GCAGTAATATATTGATATTCCCTGCCA 59.225 37.037 19.44 0.00 45.04 4.92
488 598 4.908601 ACATTCCTGTTGTGTGAGGATA 57.091 40.909 0.00 0.00 38.21 2.59
493 603 9.172712 ACATTCCTGTTGTGTGAGGATATCCTT 62.173 40.741 25.25 9.44 38.43 3.36
543 697 5.965033 ATGTTTCCTGATGACTCCTATGT 57.035 39.130 0.00 0.00 0.00 2.29
617 1090 3.631686 TGCAGCTTAATCAACAACACTGT 59.368 39.130 0.00 0.00 37.39 3.55
630 1105 8.050778 TCAACAACACTGTCTATTTGTTTCTT 57.949 30.769 0.00 0.00 39.56 2.52
656 1131 4.660168 ACATCTGGGATGCAATTAGATCC 58.340 43.478 7.35 6.41 37.94 3.36
657 1132 4.353191 ACATCTGGGATGCAATTAGATCCT 59.647 41.667 12.49 0.00 38.61 3.24
788 1282 5.941948 ACTTAATTGACACAGTTGGCTAC 57.058 39.130 0.00 0.00 0.00 3.58
833 1328 5.654650 ACTTGTACTTTTCCATTGTGGTTGA 59.345 36.000 0.00 0.00 39.03 3.18
840 1335 6.986231 ACTTTTCCATTGTGGTTGAAGATTTC 59.014 34.615 12.21 0.00 39.03 2.17
990 1493 5.593909 CCAATAGTGGGACATTAGCAATTCA 59.406 40.000 0.00 0.00 44.52 2.57
1029 1533 5.700373 GGAGATTGTGATTCTTCTAGCCATC 59.300 44.000 0.00 0.00 0.00 3.51
1094 1598 2.919860 GCGCGCAGTTTGCAAAGTG 61.920 57.895 33.26 33.26 45.36 3.16
1303 1807 8.768501 TCTAGTAGGACAGAAACATGATACAT 57.231 34.615 0.00 0.00 0.00 2.29
1340 1844 4.351192 CTCAAAAGGGTGTTCAGAAAACG 58.649 43.478 0.00 0.00 0.00 3.60
1545 2049 2.045885 AGAAGATCTAGTGGGGGTGGAA 59.954 50.000 0.00 0.00 0.00 3.53
1852 2421 8.084684 AGAGTTTTCTGGAGCAACAAAAATATC 58.915 33.333 0.00 0.00 30.72 1.63
2025 2594 3.557595 CAGCTTTACCAGAAGATAAGGCG 59.442 47.826 0.00 0.00 38.16 5.52
2170 2739 2.425668 GTTGGTAGCCTTTTGTGTGTGT 59.574 45.455 0.00 0.00 0.00 3.72
2742 3312 6.319152 TCACTCTACTTCCTCTGCTATGTAAC 59.681 42.308 0.00 0.00 0.00 2.50
3063 3633 7.256296 CCCAAAGGTCTTGGAAATCTAACAAAT 60.256 37.037 5.07 0.00 42.06 2.32
3244 3814 1.881973 TGAATGCAAGTGCTGAGAACC 59.118 47.619 4.69 0.00 42.66 3.62
3321 3891 0.035343 GACTAGCGGAAGGGGCTTTT 60.035 55.000 0.00 0.00 41.80 2.27
3330 3900 2.557452 GGAAGGGGCTTTTGAGGAATCA 60.557 50.000 0.00 0.00 0.00 2.57
3346 3916 3.452627 GGAATCACCTCTCTTCCAAGCTA 59.547 47.826 0.00 0.00 38.64 3.32
3427 3997 1.657751 GCCATCCCTTTCTCGGTTGC 61.658 60.000 0.00 0.00 0.00 4.17
3606 4176 5.026790 AGATTAGTCTTAGCCAACCTCAGT 58.973 41.667 0.00 0.00 0.00 3.41
3621 4191 2.103771 CCTCAGTGGTATGATGGAGGTG 59.896 54.545 0.00 0.00 37.68 4.00
3920 4494 2.208619 TAGGTCACCGGCGGAAACA 61.209 57.895 35.78 11.79 0.00 2.83
4166 4740 0.107831 TTGTGGCTAAAGGCGAGTGT 59.892 50.000 0.00 0.00 44.42 3.55
4206 4780 9.908152 AGACTAATTTTTACATTACCTGTTTGC 57.092 29.630 0.00 0.00 39.39 3.68
4240 4814 4.321745 GCTATTTCGTGTGCATTCTTGTTG 59.678 41.667 0.00 0.00 0.00 3.33
4275 4849 8.492673 TCCAGCTGTGTCTGTTAAATAAATAG 57.507 34.615 13.81 0.00 32.32 1.73
4415 4989 5.437289 TTGGACATCTGTGAATGTTGTTC 57.563 39.130 0.00 0.00 39.93 3.18
4420 4994 5.835257 ACATCTGTGAATGTTGTTCCTTTG 58.165 37.500 0.00 0.00 36.47 2.77
4444 5018 5.934935 TGGATTACGTTCCTTGTTTTCTC 57.065 39.130 7.76 0.00 36.68 2.87
4448 5022 2.480845 ACGTTCCTTGTTTTCTCGAGG 58.519 47.619 13.56 0.00 39.65 4.63
4476 5050 4.874966 TGCAGTGAAAATGTTTTGGAAAGG 59.125 37.500 0.00 0.00 32.28 3.11
4492 5066 0.817013 AAGGCCACGGCATGTTTATG 59.183 50.000 10.83 0.00 44.11 1.90
4509 5083 9.188588 CATGTTTATGCATGTCCTTATGATTTC 57.811 33.333 10.16 0.00 40.81 2.17
4515 5089 6.430864 TGCATGTCCTTATGATTTCCCTTTA 58.569 36.000 0.00 0.00 0.00 1.85
4594 5168 6.736561 TTCTACTCCTAGATGATATGGGGA 57.263 41.667 0.00 0.00 0.00 4.81
4621 5195 2.949644 AGTTCAAGCTGTACCAAACCAC 59.050 45.455 0.00 0.00 0.00 4.16
4622 5196 2.949644 GTTCAAGCTGTACCAAACCACT 59.050 45.455 0.00 0.00 0.00 4.00
4623 5197 3.290948 TCAAGCTGTACCAAACCACTT 57.709 42.857 0.00 0.00 0.00 3.16
4624 5198 3.626930 TCAAGCTGTACCAAACCACTTT 58.373 40.909 0.00 0.00 0.00 2.66
4625 5199 3.630312 TCAAGCTGTACCAAACCACTTTC 59.370 43.478 0.00 0.00 0.00 2.62
4626 5200 3.577805 AGCTGTACCAAACCACTTTCT 57.422 42.857 0.00 0.00 0.00 2.52
4627 5201 3.214328 AGCTGTACCAAACCACTTTCTG 58.786 45.455 0.00 0.00 0.00 3.02
4628 5202 2.287608 GCTGTACCAAACCACTTTCTGC 60.288 50.000 0.00 0.00 0.00 4.26
4629 5203 2.293399 CTGTACCAAACCACTTTCTGCC 59.707 50.000 0.00 0.00 0.00 4.85
4630 5204 2.092103 TGTACCAAACCACTTTCTGCCT 60.092 45.455 0.00 0.00 0.00 4.75
4631 5205 1.692411 ACCAAACCACTTTCTGCCTC 58.308 50.000 0.00 0.00 0.00 4.70
4632 5206 1.064017 ACCAAACCACTTTCTGCCTCA 60.064 47.619 0.00 0.00 0.00 3.86
4633 5207 2.242043 CCAAACCACTTTCTGCCTCAT 58.758 47.619 0.00 0.00 0.00 2.90
4634 5208 2.629617 CCAAACCACTTTCTGCCTCATT 59.370 45.455 0.00 0.00 0.00 2.57
4635 5209 3.305608 CCAAACCACTTTCTGCCTCATTC 60.306 47.826 0.00 0.00 0.00 2.67
4636 5210 2.957402 ACCACTTTCTGCCTCATTCA 57.043 45.000 0.00 0.00 0.00 2.57
4637 5211 2.787994 ACCACTTTCTGCCTCATTCAG 58.212 47.619 0.00 0.00 0.00 3.02
4638 5212 1.471684 CCACTTTCTGCCTCATTCAGC 59.528 52.381 0.00 0.00 0.00 4.26
4639 5213 2.156917 CACTTTCTGCCTCATTCAGCA 58.843 47.619 0.00 0.00 37.46 4.41
4643 5217 2.664398 TGCCTCATTCAGCAGCGA 59.336 55.556 0.00 0.00 33.08 4.93
4644 5218 1.222661 TGCCTCATTCAGCAGCGAT 59.777 52.632 0.00 0.00 33.08 4.58
4645 5219 1.093496 TGCCTCATTCAGCAGCGATG 61.093 55.000 0.00 0.00 33.08 3.84
4646 5220 0.812811 GCCTCATTCAGCAGCGATGA 60.813 55.000 4.02 8.32 0.00 2.92
4647 5221 1.880271 CCTCATTCAGCAGCGATGAT 58.120 50.000 4.02 0.00 0.00 2.45
4648 5222 2.219458 CCTCATTCAGCAGCGATGATT 58.781 47.619 4.02 0.00 0.00 2.57
4649 5223 2.031944 CCTCATTCAGCAGCGATGATTG 60.032 50.000 4.02 1.46 32.79 2.67
4650 5224 1.944709 TCATTCAGCAGCGATGATTGG 59.055 47.619 4.02 0.00 32.52 3.16
4651 5225 1.944709 CATTCAGCAGCGATGATTGGA 59.055 47.619 4.02 0.00 29.45 3.53
4652 5226 1.660167 TTCAGCAGCGATGATTGGAG 58.340 50.000 4.02 0.00 0.00 3.86
4653 5227 0.812811 TCAGCAGCGATGATTGGAGC 60.813 55.000 4.02 0.00 0.00 4.70
4654 5228 0.814410 CAGCAGCGATGATTGGAGCT 60.814 55.000 4.02 0.00 41.07 4.09
4657 5231 3.376218 AGCGATGATTGGAGCTGAC 57.624 52.632 0.00 0.00 38.67 3.51
4658 5232 0.179062 AGCGATGATTGGAGCTGACC 60.179 55.000 0.00 0.00 38.67 4.02
4659 5233 0.462581 GCGATGATTGGAGCTGACCA 60.463 55.000 0.00 0.00 38.24 4.02
4660 5234 1.813092 GCGATGATTGGAGCTGACCAT 60.813 52.381 0.00 0.00 39.82 3.55
4661 5235 2.569059 CGATGATTGGAGCTGACCATT 58.431 47.619 0.00 0.00 39.82 3.16
4662 5236 2.947652 CGATGATTGGAGCTGACCATTT 59.052 45.455 0.00 0.00 39.82 2.32
4663 5237 3.003068 CGATGATTGGAGCTGACCATTTC 59.997 47.826 0.00 0.00 39.82 2.17
4664 5238 2.726821 TGATTGGAGCTGACCATTTCC 58.273 47.619 0.00 0.00 39.82 3.13
4665 5239 2.041485 TGATTGGAGCTGACCATTTCCA 59.959 45.455 0.00 0.00 39.82 3.53
4666 5240 2.905415 TTGGAGCTGACCATTTCCAT 57.095 45.000 0.00 0.00 39.33 3.41
4667 5241 2.133281 TGGAGCTGACCATTTCCATG 57.867 50.000 0.00 0.00 34.90 3.66
4668 5242 1.634973 TGGAGCTGACCATTTCCATGA 59.365 47.619 0.00 0.00 34.90 3.07
4669 5243 2.041485 TGGAGCTGACCATTTCCATGAA 59.959 45.455 0.00 0.00 34.90 2.57
4670 5244 2.686915 GGAGCTGACCATTTCCATGAAG 59.313 50.000 0.00 0.00 31.07 3.02
4671 5245 3.614092 GAGCTGACCATTTCCATGAAGA 58.386 45.455 0.00 0.00 31.07 2.87
4672 5246 4.012374 GAGCTGACCATTTCCATGAAGAA 58.988 43.478 0.00 0.00 31.07 2.52
4673 5247 4.410099 AGCTGACCATTTCCATGAAGAAA 58.590 39.130 0.00 0.00 39.92 2.52
4674 5248 5.021458 AGCTGACCATTTCCATGAAGAAAT 58.979 37.500 0.00 0.00 45.21 2.17
4675 5249 6.189859 AGCTGACCATTTCCATGAAGAAATA 58.810 36.000 8.92 0.00 43.06 1.40
4676 5250 6.837568 AGCTGACCATTTCCATGAAGAAATAT 59.162 34.615 8.92 2.78 43.06 1.28
4677 5251 8.000709 AGCTGACCATTTCCATGAAGAAATATA 58.999 33.333 8.92 0.00 43.06 0.86
4678 5252 8.800332 GCTGACCATTTCCATGAAGAAATATAT 58.200 33.333 8.92 0.60 43.06 0.86
4699 5273 7.872113 ATATTAATCAAGGCATAAGCTAGGC 57.128 36.000 0.00 0.00 41.70 3.93
4700 5274 3.582998 AATCAAGGCATAAGCTAGGCA 57.417 42.857 9.42 0.00 41.70 4.75
4701 5275 2.332063 TCAAGGCATAAGCTAGGCAC 57.668 50.000 9.42 0.00 41.70 5.01
4702 5276 0.940126 CAAGGCATAAGCTAGGCACG 59.060 55.000 9.42 0.00 41.70 5.34
4703 5277 0.830648 AAGGCATAAGCTAGGCACGA 59.169 50.000 9.42 0.00 41.70 4.35
4704 5278 1.051812 AGGCATAAGCTAGGCACGAT 58.948 50.000 9.42 0.00 41.70 3.73
4705 5279 1.417890 AGGCATAAGCTAGGCACGATT 59.582 47.619 9.42 0.00 41.70 3.34
4706 5280 1.801178 GGCATAAGCTAGGCACGATTC 59.199 52.381 6.52 0.00 41.70 2.52
4707 5281 2.483876 GCATAAGCTAGGCACGATTCA 58.516 47.619 0.00 0.00 37.91 2.57
4708 5282 3.070018 GCATAAGCTAGGCACGATTCAT 58.930 45.455 0.00 0.00 37.91 2.57
4709 5283 3.499918 GCATAAGCTAGGCACGATTCATT 59.500 43.478 0.00 0.00 37.91 2.57
4710 5284 4.377841 GCATAAGCTAGGCACGATTCATTC 60.378 45.833 0.00 0.00 37.91 2.67
4711 5285 2.988010 AGCTAGGCACGATTCATTCA 57.012 45.000 0.00 0.00 0.00 2.57
4712 5286 2.831333 AGCTAGGCACGATTCATTCAG 58.169 47.619 0.00 0.00 0.00 3.02
4713 5287 1.262683 GCTAGGCACGATTCATTCAGC 59.737 52.381 0.00 0.00 0.00 4.26
4714 5288 2.554142 CTAGGCACGATTCATTCAGCA 58.446 47.619 0.00 0.00 0.00 4.41
4715 5289 1.376543 AGGCACGATTCATTCAGCAG 58.623 50.000 0.00 0.00 0.00 4.24
4716 5290 0.248377 GGCACGATTCATTCAGCAGC 60.248 55.000 0.00 0.00 0.00 5.25
4717 5291 0.731417 GCACGATTCATTCAGCAGCT 59.269 50.000 0.00 0.00 0.00 4.24
4718 5292 1.131883 GCACGATTCATTCAGCAGCTT 59.868 47.619 0.00 0.00 0.00 3.74
4719 5293 2.782163 CACGATTCATTCAGCAGCTTG 58.218 47.619 0.00 0.00 0.00 4.01
4720 5294 2.417586 CACGATTCATTCAGCAGCTTGA 59.582 45.455 0.00 0.00 0.00 3.02
4721 5295 3.064958 CACGATTCATTCAGCAGCTTGAT 59.935 43.478 0.00 0.00 0.00 2.57
4722 5296 3.064958 ACGATTCATTCAGCAGCTTGATG 59.935 43.478 0.00 0.00 34.61 3.07
4723 5297 3.064958 CGATTCATTCAGCAGCTTGATGT 59.935 43.478 12.40 0.00 34.94 3.06
4724 5298 4.271776 CGATTCATTCAGCAGCTTGATGTA 59.728 41.667 12.40 5.85 34.94 2.29
4725 5299 5.049612 CGATTCATTCAGCAGCTTGATGTAT 60.050 40.000 12.40 9.48 34.94 2.29
4726 5300 5.494632 TTCATTCAGCAGCTTGATGTATG 57.505 39.130 12.40 11.77 41.04 2.39
4727 5301 4.520179 TCATTCAGCAGCTTGATGTATGT 58.480 39.130 15.15 0.00 40.70 2.29
4728 5302 5.673514 TCATTCAGCAGCTTGATGTATGTA 58.326 37.500 15.15 5.65 40.70 2.29
4729 5303 6.114767 TCATTCAGCAGCTTGATGTATGTAA 58.885 36.000 15.15 2.12 40.70 2.41
4730 5304 6.259387 TCATTCAGCAGCTTGATGTATGTAAG 59.741 38.462 15.15 0.00 40.70 2.34
4731 5305 5.343307 TCAGCAGCTTGATGTATGTAAGA 57.657 39.130 0.00 0.00 34.94 2.10
4732 5306 5.922053 TCAGCAGCTTGATGTATGTAAGAT 58.078 37.500 0.00 0.00 34.94 2.40
4733 5307 6.351711 TCAGCAGCTTGATGTATGTAAGATT 58.648 36.000 0.00 0.00 34.94 2.40
4734 5308 6.259387 TCAGCAGCTTGATGTATGTAAGATTG 59.741 38.462 0.00 0.00 34.94 2.67
4735 5309 5.530171 AGCAGCTTGATGTATGTAAGATTGG 59.470 40.000 0.00 0.00 0.00 3.16
4736 5310 5.297776 GCAGCTTGATGTATGTAAGATTGGT 59.702 40.000 0.00 0.00 0.00 3.67
4737 5311 6.512415 GCAGCTTGATGTATGTAAGATTGGTC 60.512 42.308 0.00 0.00 0.00 4.02
4738 5312 6.765036 CAGCTTGATGTATGTAAGATTGGTCT 59.235 38.462 0.00 0.00 35.82 3.85
4739 5313 6.989169 AGCTTGATGTATGTAAGATTGGTCTC 59.011 38.462 0.00 0.00 32.15 3.36
4740 5314 6.763135 GCTTGATGTATGTAAGATTGGTCTCA 59.237 38.462 0.00 0.00 32.15 3.27
4741 5315 7.254590 GCTTGATGTATGTAAGATTGGTCTCAC 60.255 40.741 0.00 0.00 32.15 3.51
4742 5316 7.423844 TGATGTATGTAAGATTGGTCTCACT 57.576 36.000 0.00 0.00 32.15 3.41
4743 5317 8.533569 TGATGTATGTAAGATTGGTCTCACTA 57.466 34.615 0.00 0.00 32.15 2.74
4744 5318 8.977412 TGATGTATGTAAGATTGGTCTCACTAA 58.023 33.333 0.00 0.00 32.15 2.24
4745 5319 9.817809 GATGTATGTAAGATTGGTCTCACTAAA 57.182 33.333 0.00 0.00 32.15 1.85
4750 5324 8.547967 TGTAAGATTGGTCTCACTAAATTGTC 57.452 34.615 0.00 0.00 32.15 3.18
4751 5325 7.606456 TGTAAGATTGGTCTCACTAAATTGTCC 59.394 37.037 0.00 0.00 32.15 4.02
4752 5326 5.501156 AGATTGGTCTCACTAAATTGTCCC 58.499 41.667 0.00 0.00 0.00 4.46
4753 5327 4.993705 TTGGTCTCACTAAATTGTCCCT 57.006 40.909 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 92 3.808728 TCATAGTATTTGGCTGCAGGTC 58.191 45.455 17.12 0.00 0.00 3.85
103 105 7.823665 TGTACGCGGAGAATAAATCATAGTAT 58.176 34.615 12.47 0.00 0.00 2.12
167 172 3.071874 TCAGACGATTTCAAGGCCATT 57.928 42.857 5.01 0.00 0.00 3.16
173 178 7.299787 TCAGATCAAATCAGACGATTTCAAG 57.700 36.000 0.00 0.00 46.69 3.02
230 253 4.465632 TGTATAGGCAGTACCACACTTG 57.534 45.455 0.00 0.00 43.14 3.16
252 286 4.221924 TGCTAGGCACAACAGAATACAGTA 59.778 41.667 0.00 0.00 31.71 2.74
253 287 3.007940 TGCTAGGCACAACAGAATACAGT 59.992 43.478 0.00 0.00 31.71 3.55
254 288 3.599343 TGCTAGGCACAACAGAATACAG 58.401 45.455 0.00 0.00 31.71 2.74
255 289 3.007940 ACTGCTAGGCACAACAGAATACA 59.992 43.478 0.00 0.00 33.79 2.29
256 290 3.600388 ACTGCTAGGCACAACAGAATAC 58.400 45.455 0.00 0.00 33.79 1.89
257 291 3.981071 ACTGCTAGGCACAACAGAATA 57.019 42.857 0.00 0.00 33.79 1.75
373 427 8.814931 TCCAGATATTTTGTGAAAACAATGGAT 58.185 29.630 5.62 0.00 32.11 3.41
375 429 8.830201 TTCCAGATATTTTGTGAAAACAATGG 57.170 30.769 0.00 0.00 32.37 3.16
412 466 6.115448 AGAGCAAGATTACCAACAACTACT 57.885 37.500 0.00 0.00 0.00 2.57
488 598 3.525199 AGGCTTCATGTTCACCTAAGGAT 59.475 43.478 0.00 0.00 0.00 3.24
493 603 4.640771 AAGAAGGCTTCATGTTCACCTA 57.359 40.909 27.70 0.00 0.00 3.08
495 605 4.590850 AAAAGAAGGCTTCATGTTCACC 57.409 40.909 27.70 0.00 31.82 4.02
506 616 8.650143 TCAGGAAACATAATTAAAAGAAGGCT 57.350 30.769 0.00 0.00 0.00 4.58
574 1047 6.589135 TGCAAGAAGATGTATCTGTGATCAT 58.411 36.000 0.00 0.00 37.19 2.45
580 1053 4.484537 AGCTGCAAGAAGATGTATCTGT 57.515 40.909 1.02 0.00 37.19 3.41
582 1055 7.278135 TGATTAAGCTGCAAGAAGATGTATCT 58.722 34.615 1.02 0.00 39.22 1.98
617 1090 8.548025 TCCCAGATGTATGAAGAAACAAATAGA 58.452 33.333 0.00 0.00 0.00 1.98
630 1105 6.438186 TCTAATTGCATCCCAGATGTATGA 57.562 37.500 6.46 0.00 0.00 2.15
656 1131 9.671279 AAAATGCCCTAAATTTTCCTAAATGAG 57.329 29.630 0.00 0.00 33.03 2.90
705 1192 1.119684 ACATACATACTCCGCTGCCA 58.880 50.000 0.00 0.00 0.00 4.92
765 1259 6.526526 TGTAGCCAACTGTGTCAATTAAGTA 58.473 36.000 0.00 0.00 0.00 2.24
788 1282 2.554142 TCAGAACACTTGTGACTGCTG 58.446 47.619 18.78 14.00 35.12 4.41
833 1328 9.014297 CACCTACCAAAATACTTGAGAAATCTT 57.986 33.333 0.00 0.00 0.00 2.40
840 1335 6.879458 AGTAAGCACCTACCAAAATACTTGAG 59.121 38.462 0.00 0.00 0.00 3.02
903 1406 5.798125 TGACCACTGCAAAATGGAATAAA 57.202 34.783 16.22 0.00 39.46 1.40
948 1451 1.557832 TGGATGGTGGCCTAGTTGTAC 59.442 52.381 3.32 0.00 0.00 2.90
990 1493 0.976641 TCTCCGCCATCACTTTCTGT 59.023 50.000 0.00 0.00 0.00 3.41
1029 1533 3.928375 CCAAGGCAATTCCGATCTTTTTG 59.072 43.478 0.00 0.00 40.77 2.44
1303 1807 5.514274 CTTTTGAGGTAAAAGCAAGACCA 57.486 39.130 0.00 0.00 46.12 4.02
1340 1844 5.934625 TGGTTCATAGAAAGCAGAGAACTTC 59.065 40.000 0.00 0.00 36.52 3.01
1689 2193 2.503382 GGAGACGGAGATCCAGGCC 61.503 68.421 0.00 0.00 37.01 5.19
1852 2421 7.447545 AGTCCAAACATCATCCAATATGATCAG 59.552 37.037 0.09 0.00 36.69 2.90
2059 2628 6.060136 CCACAGGACATTCATGATCAGTATT 58.940 40.000 0.09 0.00 31.79 1.89
2170 2739 2.613026 TCTTCCACAGTTTTCTCGCA 57.387 45.000 0.00 0.00 0.00 5.10
2742 3312 9.702494 TCTAGCACTGTCATATATCTTGATTTG 57.298 33.333 0.00 0.00 0.00 2.32
3063 3633 6.048732 TCCAATGCTTGTAATGTCTGTAGA 57.951 37.500 0.00 0.00 0.00 2.59
3244 3814 4.320057 GCAGACATTCAACAAGAGAACCTG 60.320 45.833 0.00 0.00 0.00 4.00
3427 3997 3.529634 TTGTAGACGCGTCAAATTTGG 57.470 42.857 37.85 4.32 0.00 3.28
3606 4176 3.019816 TGGCACCTCCATCATACCA 57.980 52.632 0.00 0.00 40.72 3.25
3948 4522 7.418025 CGGATACTCCTTTTTCCTTGATCTACT 60.418 40.741 0.00 0.00 33.30 2.57
4191 4765 7.547722 CAGTATACAGTGCAAACAGGTAATGTA 59.452 37.037 5.50 0.00 43.00 2.29
4206 4780 5.276395 GCACACGAAATAGCAGTATACAGTG 60.276 44.000 5.50 0.00 0.00 3.66
4240 4814 4.093998 CAGACACAGCTGGAATATGTTCAC 59.906 45.833 19.93 1.38 36.01 3.18
4275 4849 7.583860 ACTAAGAATCGCAAACTAAGTCTTC 57.416 36.000 0.00 0.00 0.00 2.87
4317 4891 7.144661 TGCAACAACCATAGTGACAATAAAAG 58.855 34.615 0.00 0.00 0.00 2.27
4415 4989 4.277423 ACAAGGAACGTAATCCAACAAAGG 59.723 41.667 8.93 0.00 42.27 3.11
4420 4994 6.068473 AGAAAACAAGGAACGTAATCCAAC 57.932 37.500 8.93 0.00 42.27 3.77
4444 5018 5.490139 ACATTTTCACTGCATATTCCTCG 57.510 39.130 0.00 0.00 0.00 4.63
4448 5022 7.887996 TCCAAAACATTTTCACTGCATATTC 57.112 32.000 0.00 0.00 0.00 1.75
4476 5050 0.102844 ATGCATAAACATGCCGTGGC 59.897 50.000 3.30 3.30 46.43 5.01
4492 5066 5.859205 AAAGGGAAATCATAAGGACATGC 57.141 39.130 0.00 0.00 0.00 4.06
4503 5077 9.015367 TGTTCACGATTTTATAAAGGGAAATCA 57.985 29.630 3.04 0.00 38.87 2.57
4509 5083 5.025826 GCGTGTTCACGATTTTATAAAGGG 58.974 41.667 25.87 0.00 34.64 3.95
4515 5089 2.339418 TCCGCGTGTTCACGATTTTAT 58.661 42.857 25.87 0.00 34.64 1.40
4566 5140 9.184523 CCCATATCATCTAGGAGTAGAAAGTAG 57.815 40.741 0.00 0.00 38.82 2.57
4594 5168 2.222027 GGTACAGCTTGAACTGCAACT 58.778 47.619 0.00 0.00 41.60 3.16
4626 5200 1.093496 CATCGCTGCTGAATGAGGCA 61.093 55.000 0.00 0.00 36.94 4.75
4627 5201 0.812811 TCATCGCTGCTGAATGAGGC 60.813 55.000 0.00 0.00 0.00 4.70
4628 5202 1.880271 ATCATCGCTGCTGAATGAGG 58.120 50.000 12.52 0.00 0.00 3.86
4629 5203 2.031944 CCAATCATCGCTGCTGAATGAG 60.032 50.000 8.13 0.85 0.00 2.90
4630 5204 1.944709 CCAATCATCGCTGCTGAATGA 59.055 47.619 8.13 9.27 0.00 2.57
4631 5205 1.944709 TCCAATCATCGCTGCTGAATG 59.055 47.619 0.00 0.00 0.00 2.67
4632 5206 2.219458 CTCCAATCATCGCTGCTGAAT 58.781 47.619 0.00 0.00 0.00 2.57
4633 5207 1.660167 CTCCAATCATCGCTGCTGAA 58.340 50.000 0.00 0.00 0.00 3.02
4634 5208 0.812811 GCTCCAATCATCGCTGCTGA 60.813 55.000 0.00 0.00 0.00 4.26
4635 5209 0.814410 AGCTCCAATCATCGCTGCTG 60.814 55.000 0.00 0.00 0.00 4.41
4636 5210 0.814410 CAGCTCCAATCATCGCTGCT 60.814 55.000 0.00 0.00 42.66 4.24
4637 5211 0.812811 TCAGCTCCAATCATCGCTGC 60.813 55.000 5.31 0.00 46.95 5.25
4639 5213 0.179062 GGTCAGCTCCAATCATCGCT 60.179 55.000 0.00 0.00 0.00 4.93
4640 5214 0.462581 TGGTCAGCTCCAATCATCGC 60.463 55.000 0.00 0.00 34.24 4.58
4641 5215 2.251409 ATGGTCAGCTCCAATCATCG 57.749 50.000 0.00 0.00 41.09 3.84
4642 5216 3.317430 GGAAATGGTCAGCTCCAATCATC 59.683 47.826 0.00 0.00 41.09 2.92
4643 5217 3.294214 GGAAATGGTCAGCTCCAATCAT 58.706 45.455 0.00 0.00 41.09 2.45
4644 5218 2.041485 TGGAAATGGTCAGCTCCAATCA 59.959 45.455 0.00 0.00 41.09 2.57
4645 5219 2.726821 TGGAAATGGTCAGCTCCAATC 58.273 47.619 0.00 0.91 41.09 2.67
4646 5220 2.905415 TGGAAATGGTCAGCTCCAAT 57.095 45.000 0.00 0.00 41.09 3.16
4647 5221 2.041485 TCATGGAAATGGTCAGCTCCAA 59.959 45.455 0.00 0.00 41.20 3.53
4648 5222 1.634973 TCATGGAAATGGTCAGCTCCA 59.365 47.619 0.00 0.00 42.04 3.86
4649 5223 2.425143 TCATGGAAATGGTCAGCTCC 57.575 50.000 0.00 0.00 0.00 4.70
4650 5224 3.614092 TCTTCATGGAAATGGTCAGCTC 58.386 45.455 0.00 0.00 0.00 4.09
4651 5225 3.726557 TCTTCATGGAAATGGTCAGCT 57.273 42.857 0.00 0.00 0.00 4.24
4652 5226 4.789012 TTTCTTCATGGAAATGGTCAGC 57.211 40.909 0.00 0.00 31.29 4.26
4673 5247 9.566432 GCCTAGCTTATGCCTTGATTAATATAT 57.434 33.333 0.00 0.00 40.80 0.86
4674 5248 8.548025 TGCCTAGCTTATGCCTTGATTAATATA 58.452 33.333 0.00 0.00 40.80 0.86
4675 5249 7.337942 GTGCCTAGCTTATGCCTTGATTAATAT 59.662 37.037 0.00 0.00 40.80 1.28
4676 5250 6.655003 GTGCCTAGCTTATGCCTTGATTAATA 59.345 38.462 0.00 0.00 40.80 0.98
4677 5251 5.474876 GTGCCTAGCTTATGCCTTGATTAAT 59.525 40.000 0.00 0.00 40.80 1.40
4678 5252 4.821805 GTGCCTAGCTTATGCCTTGATTAA 59.178 41.667 0.00 0.00 40.80 1.40
4679 5253 4.389374 GTGCCTAGCTTATGCCTTGATTA 58.611 43.478 0.00 0.00 40.80 1.75
4680 5254 3.217626 GTGCCTAGCTTATGCCTTGATT 58.782 45.455 0.00 0.00 40.80 2.57
4681 5255 2.808202 CGTGCCTAGCTTATGCCTTGAT 60.808 50.000 0.00 0.00 40.80 2.57
4682 5256 1.473257 CGTGCCTAGCTTATGCCTTGA 60.473 52.381 0.00 0.00 40.80 3.02
4683 5257 0.940126 CGTGCCTAGCTTATGCCTTG 59.060 55.000 0.00 0.00 40.80 3.61
4684 5258 0.830648 TCGTGCCTAGCTTATGCCTT 59.169 50.000 0.00 0.00 40.80 4.35
4685 5259 1.051812 ATCGTGCCTAGCTTATGCCT 58.948 50.000 0.00 0.00 40.80 4.75
4686 5260 1.801178 GAATCGTGCCTAGCTTATGCC 59.199 52.381 0.00 0.00 40.80 4.40
4687 5261 2.483876 TGAATCGTGCCTAGCTTATGC 58.516 47.619 0.00 0.00 40.05 3.14
4688 5262 4.751600 TGAATGAATCGTGCCTAGCTTATG 59.248 41.667 0.00 0.00 0.00 1.90
4689 5263 4.960938 TGAATGAATCGTGCCTAGCTTAT 58.039 39.130 0.00 0.00 0.00 1.73
4690 5264 4.371786 CTGAATGAATCGTGCCTAGCTTA 58.628 43.478 0.00 0.00 0.00 3.09
4691 5265 3.201290 CTGAATGAATCGTGCCTAGCTT 58.799 45.455 0.00 0.00 0.00 3.74
4692 5266 2.831333 CTGAATGAATCGTGCCTAGCT 58.169 47.619 0.00 0.00 0.00 3.32
4693 5267 1.262683 GCTGAATGAATCGTGCCTAGC 59.737 52.381 0.00 0.00 0.00 3.42
4694 5268 2.543012 CTGCTGAATGAATCGTGCCTAG 59.457 50.000 0.00 0.00 31.62 3.02
4695 5269 2.554142 CTGCTGAATGAATCGTGCCTA 58.446 47.619 0.00 0.00 31.62 3.93
4696 5270 1.376543 CTGCTGAATGAATCGTGCCT 58.623 50.000 0.00 0.00 31.62 4.75
4697 5271 0.248377 GCTGCTGAATGAATCGTGCC 60.248 55.000 0.00 0.00 31.62 5.01
4698 5272 0.731417 AGCTGCTGAATGAATCGTGC 59.269 50.000 0.00 0.00 0.00 5.34
4699 5273 2.417586 TCAAGCTGCTGAATGAATCGTG 59.582 45.455 1.35 0.00 0.00 4.35
4700 5274 2.703416 TCAAGCTGCTGAATGAATCGT 58.297 42.857 1.35 0.00 0.00 3.73
4701 5275 3.064958 ACATCAAGCTGCTGAATGAATCG 59.935 43.478 23.48 11.39 0.00 3.34
4702 5276 4.634184 ACATCAAGCTGCTGAATGAATC 57.366 40.909 23.48 0.00 0.00 2.52
4703 5277 5.593095 ACATACATCAAGCTGCTGAATGAAT 59.407 36.000 23.48 11.32 0.00 2.57
4704 5278 4.945543 ACATACATCAAGCTGCTGAATGAA 59.054 37.500 23.48 4.02 0.00 2.57
4705 5279 4.520179 ACATACATCAAGCTGCTGAATGA 58.480 39.130 23.48 15.71 0.00 2.57
4706 5280 4.895224 ACATACATCAAGCTGCTGAATG 57.105 40.909 17.94 17.94 0.00 2.67
4707 5281 6.351711 TCTTACATACATCAAGCTGCTGAAT 58.648 36.000 1.35 0.00 0.00 2.57
4708 5282 5.733676 TCTTACATACATCAAGCTGCTGAA 58.266 37.500 1.35 0.00 0.00 3.02
4709 5283 5.343307 TCTTACATACATCAAGCTGCTGA 57.657 39.130 1.35 3.46 0.00 4.26
4710 5284 6.427974 CAATCTTACATACATCAAGCTGCTG 58.572 40.000 1.35 0.00 0.00 4.41
4711 5285 5.530171 CCAATCTTACATACATCAAGCTGCT 59.470 40.000 0.00 0.00 0.00 4.24
4712 5286 5.297776 ACCAATCTTACATACATCAAGCTGC 59.702 40.000 0.00 0.00 0.00 5.25
4713 5287 6.765036 AGACCAATCTTACATACATCAAGCTG 59.235 38.462 0.00 0.00 0.00 4.24
4714 5288 6.893583 AGACCAATCTTACATACATCAAGCT 58.106 36.000 0.00 0.00 0.00 3.74
4715 5289 6.763135 TGAGACCAATCTTACATACATCAAGC 59.237 38.462 0.00 0.00 34.34 4.01
4716 5290 7.984050 AGTGAGACCAATCTTACATACATCAAG 59.016 37.037 2.56 0.00 42.56 3.02
4717 5291 7.851228 AGTGAGACCAATCTTACATACATCAA 58.149 34.615 2.56 0.00 42.56 2.57
4718 5292 7.423844 AGTGAGACCAATCTTACATACATCA 57.576 36.000 2.56 0.00 42.56 3.07
4719 5293 9.817809 TTTAGTGAGACCAATCTTACATACATC 57.182 33.333 2.56 0.00 42.56 3.06
4724 5298 9.167311 GACAATTTAGTGAGACCAATCTTACAT 57.833 33.333 2.56 0.00 42.56 2.29
4725 5299 7.606456 GGACAATTTAGTGAGACCAATCTTACA 59.394 37.037 2.56 0.00 42.56 2.41
4726 5300 7.065923 GGGACAATTTAGTGAGACCAATCTTAC 59.934 40.741 0.00 0.00 40.86 2.34
4727 5301 7.037586 AGGGACAATTTAGTGAGACCAATCTTA 60.038 37.037 0.00 0.00 34.34 2.10
4728 5302 5.946377 GGGACAATTTAGTGAGACCAATCTT 59.054 40.000 0.00 0.00 34.34 2.40
4729 5303 5.251700 AGGGACAATTTAGTGAGACCAATCT 59.748 40.000 0.00 0.00 38.15 2.40
4730 5304 5.501156 AGGGACAATTTAGTGAGACCAATC 58.499 41.667 0.00 0.00 0.00 2.67
4731 5305 5.520748 AGGGACAATTTAGTGAGACCAAT 57.479 39.130 0.00 0.00 0.00 3.16
4732 5306 4.993705 AGGGACAATTTAGTGAGACCAA 57.006 40.909 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.