Multiple sequence alignment - TraesCS7D01G066900

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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 TraesCS7D01G066900 chr7D 100.000 4442 0 0 1 4442 37669206 37664765 0.000000e+00 8203.0
1 TraesCS7D01G066900 chr7D 79.769 519 72 17 1338 1824 48133208 48132691 3.290000e-91 346.0
2 TraesCS7D01G066900 chr3D 97.417 4259 59 16 1 4216 25517996 25522246 0.000000e+00 7208.0
3 TraesCS7D01G066900 chr4A 89.345 3482 180 65 89 3446 687311305 687314719 0.000000e+00 4198.0
4 TraesCS7D01G066900 chr4A 82.000 250 31 7 3537 3779 687314808 687315050 2.710000e-47 200.0
5 TraesCS7D01G066900 chr2A 93.011 2833 127 20 738 3520 720379342 720382153 0.000000e+00 4069.0
6 TraesCS7D01G066900 chr2A 81.030 369 39 25 2 361 720378219 720378565 9.470000e-67 265.0
7 TraesCS7D01G066900 chr2A 77.933 358 44 20 381 703 720378621 720378978 1.630000e-44 191.0
8 TraesCS7D01G066900 chr3A 82.095 525 65 18 1328 1824 242902391 242901868 5.310000e-114 422.0
9 TraesCS7D01G066900 chr2B 81.621 506 66 15 1338 1817 65242807 65243311 1.160000e-105 394.0
10 TraesCS7D01G066900 chr6A 81.154 520 68 17 1338 1828 120275828 120275310 1.500000e-104 390.0
11 TraesCS7D01G066900 chr6A 80.851 517 69 17 1338 1825 120355144 120355659 3.240000e-101 379.0
12 TraesCS7D01G066900 chr5B 81.496 508 65 18 1338 1817 517822128 517822634 1.500000e-104 390.0
13 TraesCS7D01G066900 chr5B 82.045 401 49 9 1567 1945 35283714 35284113 1.990000e-83 320.0
14 TraesCS7D01G066900 chr5B 95.000 40 2 0 3607 3646 35285786 35285825 3.710000e-06 63.9
15 TraesCS7D01G066900 chr5D 81.818 396 54 11 1567 1945 41292160 41292554 2.580000e-82 316.0
16 TraesCS7D01G066900 chr5A 80.370 270 40 6 1567 1824 639312035 639311767 4.530000e-45 193.0
17 TraesCS7D01G066900 chr1B 81.624 234 40 2 1593 1824 490597894 490598126 1.630000e-44 191.0
18 TraesCS7D01G066900 chr7A 94.286 105 6 0 960 1064 37085018 37084914 1.280000e-35 161.0
19 TraesCS7D01G066900 chr7A 82.796 93 11 5 615 703 37085247 37085156 1.320000e-10 78.7


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 TraesCS7D01G066900 chr7D 37664765 37669206 4441 True 8203.000000 8203 100.000000 1 4442 1 chr7D.!!$R1 4441
1 TraesCS7D01G066900 chr7D 48132691 48133208 517 True 346.000000 346 79.769000 1338 1824 1 chr7D.!!$R2 486
2 TraesCS7D01G066900 chr3D 25517996 25522246 4250 False 7208.000000 7208 97.417000 1 4216 1 chr3D.!!$F1 4215
3 TraesCS7D01G066900 chr4A 687311305 687315050 3745 False 2199.000000 4198 85.672500 89 3779 2 chr4A.!!$F1 3690
4 TraesCS7D01G066900 chr2A 720378219 720382153 3934 False 1508.333333 4069 83.991333 2 3520 3 chr2A.!!$F1 3518
5 TraesCS7D01G066900 chr3A 242901868 242902391 523 True 422.000000 422 82.095000 1328 1824 1 chr3A.!!$R1 496
6 TraesCS7D01G066900 chr2B 65242807 65243311 504 False 394.000000 394 81.621000 1338 1817 1 chr2B.!!$F1 479
7 TraesCS7D01G066900 chr6A 120275310 120275828 518 True 390.000000 390 81.154000 1338 1828 1 chr6A.!!$R1 490
8 TraesCS7D01G066900 chr6A 120355144 120355659 515 False 379.000000 379 80.851000 1338 1825 1 chr6A.!!$F1 487
9 TraesCS7D01G066900 chr5B 517822128 517822634 506 False 390.000000 390 81.496000 1338 1817 1 chr5B.!!$F1 479

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
890 1353 7.093201 TGTCTTTAATCTTCCAGGTTACCGTAT 60.093 37.037 0.0 0.0 0.0 3.06 F
1110 1579 0.178876 TCACCATGAACCCCTCCTCA 60.179 55.000 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3390 3984 1.410517 GGCCATGTCTCGATCTTCTCA 59.589 52.381 0.00 0.0 0.00 3.27 R
3666 4282 8.404000 AGAATGCATGCAAATTTTACACAAAAA 58.596 25.926 26.68 0.0 41.21 1.94 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
890 1353 7.093201 TGTCTTTAATCTTCCAGGTTACCGTAT 60.093 37.037 0.00 0.00 0.00 3.06
891 1354 7.767659 GTCTTTAATCTTCCAGGTTACCGTATT 59.232 37.037 0.00 0.00 0.00 1.89
1110 1579 0.178876 TCACCATGAACCCCTCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
1111 1580 0.921896 CACCATGAACCCCTCCTCAT 59.078 55.000 0.00 0.00 32.40 2.90
1112 1581 1.133976 CACCATGAACCCCTCCTCATC 60.134 57.143 0.00 0.00 29.69 2.92
1113 1582 0.475906 CCATGAACCCCTCCTCATCC 59.524 60.000 0.00 0.00 29.69 3.51
1114 1583 1.516110 CATGAACCCCTCCTCATCCT 58.484 55.000 0.00 0.00 29.69 3.24
1115 1584 1.419387 CATGAACCCCTCCTCATCCTC 59.581 57.143 0.00 0.00 29.69 3.71
1336 1814 3.119424 GGGTACTCACTAGTGCTTCTGTC 60.119 52.174 18.45 4.32 38.31 3.51
3276 3870 7.500559 GCAAATCATTTGGGTTCTCTAGACTAT 59.499 37.037 12.14 0.00 40.94 2.12
3366 3960 2.427245 CCTGACGGAGGGCTTCGAT 61.427 63.158 0.00 0.00 38.36 3.59
3390 3984 3.408634 CGTTGTCCCCATCAAGTACTTT 58.591 45.455 5.07 0.00 0.00 2.66
3442 4036 1.001597 CGATACCGTTCCAGAGGTAGC 60.002 57.143 0.32 0.32 45.08 3.58
3478 4072 3.699894 CTGGAGTCCTGCACGGCT 61.700 66.667 11.33 0.00 0.00 5.52
3707 4323 5.769484 TGCATTCTACGGTGGTTTAAAAA 57.231 34.783 0.00 0.00 0.00 1.94
4009 4660 1.678635 CTGCCCCATTTTCGCAGGA 60.679 57.895 0.33 0.00 45.00 3.86
4204 4855 2.158813 TCTCCCAGTTCAAACACTCACC 60.159 50.000 0.00 0.00 0.00 4.02
4244 4895 4.335082 TTTTGCGAATGGAGTTCATACG 57.665 40.909 0.00 0.00 36.60 3.06
4245 4896 1.286501 TGCGAATGGAGTTCATACGC 58.713 50.000 0.00 0.00 43.79 4.42
4246 4897 1.134818 TGCGAATGGAGTTCATACGCT 60.135 47.619 0.00 0.00 43.85 5.07
4247 4898 2.100087 TGCGAATGGAGTTCATACGCTA 59.900 45.455 0.00 0.00 43.85 4.26
4248 4899 3.120792 GCGAATGGAGTTCATACGCTAA 58.879 45.455 0.00 0.00 41.07 3.09
4249 4900 3.060473 GCGAATGGAGTTCATACGCTAAC 60.060 47.826 0.00 0.00 41.07 2.34
4250 4901 4.360563 CGAATGGAGTTCATACGCTAACT 58.639 43.478 0.00 0.00 38.62 2.24
4256 4907 7.201644 AATGGAGTTCATACGCTAACTCAATTG 60.202 37.037 14.14 0.00 46.97 2.32
4258 4909 6.408858 AGTTCATACGCTAACTCAATTGTG 57.591 37.500 5.13 5.59 30.08 3.33
4259 4910 6.163476 AGTTCATACGCTAACTCAATTGTGA 58.837 36.000 14.16 0.00 30.08 3.58
4269 4920 3.967332 CTCAATTGTGAGGCCCAAATT 57.033 42.857 5.13 0.00 46.55 1.82
4270 4921 3.592059 CTCAATTGTGAGGCCCAAATTG 58.408 45.455 17.59 17.59 46.55 2.32
4271 4922 2.302445 TCAATTGTGAGGCCCAAATTGG 59.698 45.455 20.89 4.74 37.25 3.16
4281 4932 2.134789 CCCAAATTGGCTGAGCTACT 57.865 50.000 6.48 0.00 35.79 2.57
4282 4933 2.019984 CCCAAATTGGCTGAGCTACTC 58.980 52.381 6.48 0.00 35.79 2.59
4283 4934 1.667724 CCAAATTGGCTGAGCTACTCG 59.332 52.381 3.72 0.00 32.35 4.18
4284 4935 1.063174 CAAATTGGCTGAGCTACTCGC 59.937 52.381 3.72 0.00 39.57 5.03
4285 4936 0.250234 AATTGGCTGAGCTACTCGCA 59.750 50.000 3.72 0.00 42.61 5.10
4286 4937 0.179089 ATTGGCTGAGCTACTCGCAG 60.179 55.000 3.72 0.00 44.19 5.18
4287 4938 1.250840 TTGGCTGAGCTACTCGCAGA 61.251 55.000 3.72 0.00 44.12 4.26
4288 4939 1.250840 TGGCTGAGCTACTCGCAGAA 61.251 55.000 3.72 0.00 44.12 3.02
4289 4940 0.103937 GGCTGAGCTACTCGCAGAAT 59.896 55.000 3.72 0.00 44.12 2.40
4290 4941 1.338337 GGCTGAGCTACTCGCAGAATA 59.662 52.381 3.72 0.00 44.12 1.75
4291 4942 2.606795 GGCTGAGCTACTCGCAGAATAG 60.607 54.545 3.72 0.00 44.12 1.73
4292 4943 2.292016 GCTGAGCTACTCGCAGAATAGA 59.708 50.000 0.00 0.00 44.12 1.98
4293 4944 3.057596 GCTGAGCTACTCGCAGAATAGAT 60.058 47.826 0.00 0.00 44.12 1.98
4294 4945 4.475028 CTGAGCTACTCGCAGAATAGATG 58.525 47.826 0.00 0.00 44.12 2.90
4295 4946 3.254411 TGAGCTACTCGCAGAATAGATGG 59.746 47.826 0.00 0.00 42.61 3.51
4296 4947 3.491342 AGCTACTCGCAGAATAGATGGA 58.509 45.455 0.00 0.00 42.61 3.41
4297 4948 4.085733 AGCTACTCGCAGAATAGATGGAT 58.914 43.478 0.00 0.00 42.61 3.41
4298 4949 4.157656 AGCTACTCGCAGAATAGATGGATC 59.842 45.833 0.00 0.00 42.61 3.36
4299 4950 4.157656 GCTACTCGCAGAATAGATGGATCT 59.842 45.833 0.00 0.00 38.58 2.75
4300 4951 5.355630 GCTACTCGCAGAATAGATGGATCTA 59.644 44.000 0.00 0.00 39.99 1.98
4301 4952 6.039270 GCTACTCGCAGAATAGATGGATCTAT 59.961 42.308 3.67 3.67 43.63 1.98
4302 4953 6.206395 ACTCGCAGAATAGATGGATCTATG 57.794 41.667 9.46 1.74 46.49 2.23
4303 4954 5.003692 TCGCAGAATAGATGGATCTATGC 57.996 43.478 9.46 7.97 46.49 3.14
4304 4955 4.463891 TCGCAGAATAGATGGATCTATGCA 59.536 41.667 14.61 0.00 46.49 3.96
4305 4956 5.047092 TCGCAGAATAGATGGATCTATGCAA 60.047 40.000 14.61 0.00 46.49 4.08
4306 4957 5.640783 CGCAGAATAGATGGATCTATGCAAA 59.359 40.000 14.61 0.00 46.49 3.68
4307 4958 6.315642 CGCAGAATAGATGGATCTATGCAAAT 59.684 38.462 14.61 0.00 46.49 2.32
4308 4959 7.465647 CGCAGAATAGATGGATCTATGCAAATC 60.466 40.741 14.61 7.10 46.49 2.17
4309 4960 7.465647 GCAGAATAGATGGATCTATGCAAATCG 60.466 40.741 14.61 5.64 46.49 3.34
4310 4961 7.763071 CAGAATAGATGGATCTATGCAAATCGA 59.237 37.037 14.61 0.00 46.49 3.59
4311 4962 8.484575 AGAATAGATGGATCTATGCAAATCGAT 58.515 33.333 14.61 0.00 46.49 3.59
4312 4963 8.434733 AATAGATGGATCTATGCAAATCGATG 57.565 34.615 9.46 0.00 46.49 3.84
4313 4964 6.046290 AGATGGATCTATGCAAATCGATGA 57.954 37.500 0.00 0.00 34.85 2.92
4314 4965 6.470278 AGATGGATCTATGCAAATCGATGAA 58.530 36.000 0.00 0.00 34.85 2.57
4315 4966 5.929697 TGGATCTATGCAAATCGATGAAC 57.070 39.130 0.00 0.00 0.00 3.18
4316 4967 5.614308 TGGATCTATGCAAATCGATGAACT 58.386 37.500 0.00 0.00 0.00 3.01
4317 4968 5.698089 TGGATCTATGCAAATCGATGAACTC 59.302 40.000 0.00 0.00 0.00 3.01
4318 4969 5.698089 GGATCTATGCAAATCGATGAACTCA 59.302 40.000 0.00 0.00 0.00 3.41
4319 4970 6.128607 GGATCTATGCAAATCGATGAACTCAG 60.129 42.308 0.00 0.00 0.00 3.35
4320 4971 5.906073 TCTATGCAAATCGATGAACTCAGA 58.094 37.500 0.00 0.00 0.00 3.27
4321 4972 4.871993 ATGCAAATCGATGAACTCAGAC 57.128 40.909 0.00 0.00 0.00 3.51
4322 4973 3.663025 TGCAAATCGATGAACTCAGACA 58.337 40.909 0.00 0.00 0.00 3.41
4323 4974 3.681417 TGCAAATCGATGAACTCAGACAG 59.319 43.478 0.00 0.00 0.00 3.51
4324 4975 3.928992 GCAAATCGATGAACTCAGACAGA 59.071 43.478 0.00 0.00 0.00 3.41
4325 4976 4.389992 GCAAATCGATGAACTCAGACAGAA 59.610 41.667 0.00 0.00 0.00 3.02
4326 4977 5.064452 GCAAATCGATGAACTCAGACAGAAT 59.936 40.000 0.00 0.00 0.00 2.40
4327 4978 6.256539 GCAAATCGATGAACTCAGACAGAATA 59.743 38.462 0.00 0.00 0.00 1.75
4328 4979 7.201556 GCAAATCGATGAACTCAGACAGAATAA 60.202 37.037 0.00 0.00 0.00 1.40
4329 4980 8.659491 CAAATCGATGAACTCAGACAGAATAAA 58.341 33.333 0.00 0.00 0.00 1.40
4330 4981 8.954950 AATCGATGAACTCAGACAGAATAAAT 57.045 30.769 0.00 0.00 0.00 1.40
4332 4983 9.689976 ATCGATGAACTCAGACAGAATAAATAG 57.310 33.333 0.00 0.00 0.00 1.73
4333 4984 8.903820 TCGATGAACTCAGACAGAATAAATAGA 58.096 33.333 0.00 0.00 0.00 1.98
4334 4985 9.521503 CGATGAACTCAGACAGAATAAATAGAA 57.478 33.333 0.00 0.00 0.00 2.10
4340 4991 9.401058 ACTCAGACAGAATAAATAGAATTTGGG 57.599 33.333 0.00 0.00 0.00 4.12
4341 4992 8.752005 TCAGACAGAATAAATAGAATTTGGGG 57.248 34.615 0.00 0.00 0.00 4.96
4342 4993 8.556589 TCAGACAGAATAAATAGAATTTGGGGA 58.443 33.333 0.00 0.00 0.00 4.81
4343 4994 9.359653 CAGACAGAATAAATAGAATTTGGGGAT 57.640 33.333 0.00 0.00 0.00 3.85
4357 5008 9.619842 AGAATTTGGGGATAAATATAAGCCATT 57.380 29.630 0.00 0.00 30.47 3.16
4360 5011 8.560124 TTTGGGGATAAATATAAGCCATTTGT 57.440 30.769 0.00 0.00 0.00 2.83
4361 5012 7.775053 TGGGGATAAATATAAGCCATTTGTC 57.225 36.000 0.00 0.00 34.54 3.18
4362 5013 7.534852 TGGGGATAAATATAAGCCATTTGTCT 58.465 34.615 0.00 0.00 35.22 3.41
4363 5014 7.451255 TGGGGATAAATATAAGCCATTTGTCTG 59.549 37.037 0.00 0.00 35.22 3.51
4364 5015 7.315890 GGGATAAATATAAGCCATTTGTCTGC 58.684 38.462 0.00 0.00 35.22 4.26
4365 5016 7.039784 GGGATAAATATAAGCCATTTGTCTGCA 60.040 37.037 0.00 0.00 35.22 4.41
4366 5017 7.809806 GGATAAATATAAGCCATTTGTCTGCAC 59.190 37.037 0.00 0.00 35.22 4.57
4367 5018 6.780457 AAATATAAGCCATTTGTCTGCACT 57.220 33.333 0.00 0.00 0.00 4.40
4368 5019 6.780457 AATATAAGCCATTTGTCTGCACTT 57.220 33.333 0.00 0.00 0.00 3.16
4369 5020 7.880160 AATATAAGCCATTTGTCTGCACTTA 57.120 32.000 0.00 0.00 0.00 2.24
4370 5021 8.469309 AATATAAGCCATTTGTCTGCACTTAT 57.531 30.769 5.93 5.93 32.90 1.73
4371 5022 4.708726 AAGCCATTTGTCTGCACTTATC 57.291 40.909 0.00 0.00 0.00 1.75
4372 5023 3.960571 AGCCATTTGTCTGCACTTATCT 58.039 40.909 0.00 0.00 0.00 1.98
4373 5024 4.338879 AGCCATTTGTCTGCACTTATCTT 58.661 39.130 0.00 0.00 0.00 2.40
4374 5025 4.157289 AGCCATTTGTCTGCACTTATCTTG 59.843 41.667 0.00 0.00 0.00 3.02
4375 5026 4.418392 CCATTTGTCTGCACTTATCTTGC 58.582 43.478 0.00 0.00 40.63 4.01
4376 5027 3.811722 TTTGTCTGCACTTATCTTGCG 57.188 42.857 0.00 0.00 43.34 4.85
4377 5028 2.741759 TGTCTGCACTTATCTTGCGA 57.258 45.000 0.00 0.00 43.34 5.10
4378 5029 2.610433 TGTCTGCACTTATCTTGCGAG 58.390 47.619 0.00 0.00 43.34 5.03
4379 5030 1.325943 GTCTGCACTTATCTTGCGAGC 59.674 52.381 0.00 0.00 43.34 5.03
4380 5031 0.299895 CTGCACTTATCTTGCGAGCG 59.700 55.000 0.00 0.00 43.34 5.03
4381 5032 0.389817 TGCACTTATCTTGCGAGCGT 60.390 50.000 0.00 0.00 43.34 5.07
4382 5033 0.299003 GCACTTATCTTGCGAGCGTC 59.701 55.000 0.00 0.00 0.00 5.19
4383 5034 1.629013 CACTTATCTTGCGAGCGTCA 58.371 50.000 0.00 0.00 0.00 4.35
4384 5035 1.585668 CACTTATCTTGCGAGCGTCAG 59.414 52.381 0.00 0.00 0.00 3.51
4385 5036 1.202582 ACTTATCTTGCGAGCGTCAGT 59.797 47.619 0.00 0.00 0.00 3.41
4386 5037 1.849219 CTTATCTTGCGAGCGTCAGTC 59.151 52.381 0.00 0.00 0.00 3.51
4387 5038 1.095600 TATCTTGCGAGCGTCAGTCT 58.904 50.000 0.00 0.00 0.00 3.24
4388 5039 0.179150 ATCTTGCGAGCGTCAGTCTC 60.179 55.000 0.00 0.00 0.00 3.36
4389 5040 1.081175 CTTGCGAGCGTCAGTCTCA 60.081 57.895 0.00 0.00 0.00 3.27
4390 5041 0.664466 CTTGCGAGCGTCAGTCTCAA 60.664 55.000 0.00 0.00 0.00 3.02
4391 5042 0.939577 TTGCGAGCGTCAGTCTCAAC 60.940 55.000 0.00 0.00 0.00 3.18
4392 5043 2.089349 GCGAGCGTCAGTCTCAACC 61.089 63.158 0.00 0.00 0.00 3.77
4393 5044 1.444553 CGAGCGTCAGTCTCAACCC 60.445 63.158 0.00 0.00 0.00 4.11
4394 5045 1.666011 GAGCGTCAGTCTCAACCCA 59.334 57.895 0.00 0.00 0.00 4.51
4395 5046 0.389166 GAGCGTCAGTCTCAACCCAG 60.389 60.000 0.00 0.00 0.00 4.45
4396 5047 2.029844 GCGTCAGTCTCAACCCAGC 61.030 63.158 0.00 0.00 0.00 4.85
4397 5048 1.367471 CGTCAGTCTCAACCCAGCA 59.633 57.895 0.00 0.00 0.00 4.41
4398 5049 0.036952 CGTCAGTCTCAACCCAGCAT 60.037 55.000 0.00 0.00 0.00 3.79
4399 5050 1.204704 CGTCAGTCTCAACCCAGCATA 59.795 52.381 0.00 0.00 0.00 3.14
4400 5051 2.159043 CGTCAGTCTCAACCCAGCATAT 60.159 50.000 0.00 0.00 0.00 1.78
4401 5052 3.679917 CGTCAGTCTCAACCCAGCATATT 60.680 47.826 0.00 0.00 0.00 1.28
4402 5053 4.265073 GTCAGTCTCAACCCAGCATATTT 58.735 43.478 0.00 0.00 0.00 1.40
4403 5054 4.095483 GTCAGTCTCAACCCAGCATATTTG 59.905 45.833 0.00 0.00 0.00 2.32
4404 5055 4.012374 CAGTCTCAACCCAGCATATTTGT 58.988 43.478 0.00 0.00 0.00 2.83
4405 5056 4.095483 CAGTCTCAACCCAGCATATTTGTC 59.905 45.833 0.00 0.00 0.00 3.18
4406 5057 4.018960 AGTCTCAACCCAGCATATTTGTCT 60.019 41.667 0.00 0.00 0.00 3.41
4407 5058 4.702131 GTCTCAACCCAGCATATTTGTCTT 59.298 41.667 0.00 0.00 0.00 3.01
4408 5059 5.183904 GTCTCAACCCAGCATATTTGTCTTT 59.816 40.000 0.00 0.00 0.00 2.52
4409 5060 5.774690 TCTCAACCCAGCATATTTGTCTTTT 59.225 36.000 0.00 0.00 0.00 2.27
4410 5061 5.782047 TCAACCCAGCATATTTGTCTTTTG 58.218 37.500 0.00 0.00 0.00 2.44
4411 5062 5.304101 TCAACCCAGCATATTTGTCTTTTGT 59.696 36.000 0.00 0.00 0.00 2.83
4412 5063 6.491745 TCAACCCAGCATATTTGTCTTTTGTA 59.508 34.615 0.00 0.00 0.00 2.41
4413 5064 6.909550 ACCCAGCATATTTGTCTTTTGTAA 57.090 33.333 0.00 0.00 0.00 2.41
4414 5065 7.296628 ACCCAGCATATTTGTCTTTTGTAAA 57.703 32.000 0.00 0.00 0.00 2.01
4415 5066 7.378181 ACCCAGCATATTTGTCTTTTGTAAAG 58.622 34.615 0.00 0.00 0.00 1.85
4416 5067 7.015195 ACCCAGCATATTTGTCTTTTGTAAAGT 59.985 33.333 0.00 0.00 0.00 2.66
4417 5068 7.542130 CCCAGCATATTTGTCTTTTGTAAAGTC 59.458 37.037 0.00 0.00 0.00 3.01
4418 5069 8.299570 CCAGCATATTTGTCTTTTGTAAAGTCT 58.700 33.333 0.00 0.00 0.00 3.24
4419 5070 9.683069 CAGCATATTTGTCTTTTGTAAAGTCTT 57.317 29.630 0.00 0.00 0.00 3.01
4420 5071 9.683069 AGCATATTTGTCTTTTGTAAAGTCTTG 57.317 29.630 0.00 0.00 0.00 3.02
4421 5072 9.463443 GCATATTTGTCTTTTGTAAAGTCTTGT 57.537 29.630 0.00 0.00 0.00 3.16
4424 5075 8.911247 ATTTGTCTTTTGTAAAGTCTTGTGTC 57.089 30.769 0.00 0.00 0.00 3.67
4425 5076 7.441890 TTGTCTTTTGTAAAGTCTTGTGTCA 57.558 32.000 0.00 0.00 0.00 3.58
4426 5077 7.072177 TGTCTTTTGTAAAGTCTTGTGTCAG 57.928 36.000 0.00 0.00 0.00 3.51
4427 5078 5.965918 GTCTTTTGTAAAGTCTTGTGTCAGC 59.034 40.000 0.00 0.00 0.00 4.26
4428 5079 4.893424 TTTGTAAAGTCTTGTGTCAGCC 57.107 40.909 0.00 0.00 0.00 4.85
4429 5080 3.838244 TGTAAAGTCTTGTGTCAGCCT 57.162 42.857 0.00 0.00 0.00 4.58
4430 5081 4.948341 TGTAAAGTCTTGTGTCAGCCTA 57.052 40.909 0.00 0.00 0.00 3.93
4431 5082 4.628074 TGTAAAGTCTTGTGTCAGCCTAC 58.372 43.478 0.00 0.00 0.00 3.18
4432 5083 4.344102 TGTAAAGTCTTGTGTCAGCCTACT 59.656 41.667 0.00 0.00 0.00 2.57
4433 5084 3.393089 AAGTCTTGTGTCAGCCTACTG 57.607 47.619 0.00 0.00 45.95 2.74
4434 5085 2.320781 AGTCTTGTGTCAGCCTACTGT 58.679 47.619 0.00 0.00 44.77 3.55
4435 5086 2.700897 AGTCTTGTGTCAGCCTACTGTT 59.299 45.455 0.00 0.00 44.77 3.16
4436 5087 3.134804 AGTCTTGTGTCAGCCTACTGTTT 59.865 43.478 0.00 0.00 44.77 2.83
4437 5088 3.877508 GTCTTGTGTCAGCCTACTGTTTT 59.122 43.478 0.00 0.00 44.77 2.43
4438 5089 4.335594 GTCTTGTGTCAGCCTACTGTTTTT 59.664 41.667 0.00 0.00 44.77 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
890 1353 4.918278 TGCTGCCTGGGCTTGCAA 62.918 61.111 22.23 0.00 43.47 4.08
891 1354 4.918278 TTGCTGCCTGGGCTTGCA 62.918 61.111 21.25 21.25 44.18 4.08
1110 1579 0.189822 GGTAGCCAGAGGAGGAGGAT 59.810 60.000 0.00 0.00 0.00 3.24
1111 1580 1.621377 GGTAGCCAGAGGAGGAGGA 59.379 63.158 0.00 0.00 0.00 3.71
1112 1581 1.830408 CGGTAGCCAGAGGAGGAGG 60.830 68.421 0.00 0.00 0.00 4.30
1113 1582 2.494530 GCGGTAGCCAGAGGAGGAG 61.495 68.421 0.00 0.00 37.42 3.69
1114 1583 2.442272 GCGGTAGCCAGAGGAGGA 60.442 66.667 0.00 0.00 37.42 3.71
1115 1584 2.443016 AGCGGTAGCCAGAGGAGG 60.443 66.667 0.00 0.00 46.67 4.30
1221 1699 0.461870 CATCGATGCGGTTTCCTCCA 60.462 55.000 13.37 0.00 0.00 3.86
1224 1702 3.813596 GCATCGATGCGGTTTCCT 58.186 55.556 32.60 0.00 44.67 3.36
1254 1732 3.331150 CTTTGTGCCGGTGTATTACAGA 58.669 45.455 1.90 0.00 0.00 3.41
1301 1779 1.889829 GAGTACCCAGCTAGCATCGAT 59.110 52.381 18.83 0.00 0.00 3.59
3390 3984 1.410517 GGCCATGTCTCGATCTTCTCA 59.589 52.381 0.00 0.00 0.00 3.27
3666 4282 8.404000 AGAATGCATGCAAATTTTACACAAAAA 58.596 25.926 26.68 0.00 41.21 1.94
3884 4535 2.094286 ACTGCTCGACTCTGAATTCTGG 60.094 50.000 11.89 6.02 0.00 3.86
4009 4660 6.784031 AGAAGTCCTGAATGGTGAAAGTTAT 58.216 36.000 0.00 0.00 37.07 1.89
4222 4873 4.717991 CGTATGAACTCCATTCGCAAAAA 58.282 39.130 0.00 0.00 40.56 1.94
4223 4874 4.335082 CGTATGAACTCCATTCGCAAAA 57.665 40.909 0.00 0.00 40.56 2.44
4228 4879 4.360563 AGTTAGCGTATGAACTCCATTCG 58.639 43.478 0.00 0.00 45.16 3.34
4229 4880 5.891810 GAGTTAGCGTATGAACTCCATTC 57.108 43.478 3.85 0.00 43.80 2.67
4235 4886 6.163476 TCACAATTGAGTTAGCGTATGAACT 58.837 36.000 13.59 0.00 38.60 3.01
4236 4887 6.403333 TCACAATTGAGTTAGCGTATGAAC 57.597 37.500 13.59 0.00 0.00 3.18
4237 4888 6.647212 CTCACAATTGAGTTAGCGTATGAA 57.353 37.500 13.59 0.00 43.95 2.57
4245 4896 9.872362 CCAATTTGGGCCTCACAATTGAGTTAG 62.872 44.444 23.77 3.55 39.91 2.34
4246 4897 8.198474 CCAATTTGGGCCTCACAATTGAGTTA 62.198 42.308 23.77 0.00 39.91 2.24
4247 4898 7.488169 CCAATTTGGGCCTCACAATTGAGTT 62.488 44.000 23.77 0.00 39.91 3.01
4248 4899 6.078825 CCAATTTGGGCCTCACAATTGAGT 62.079 45.833 23.77 0.00 39.91 3.41
4249 4900 3.618019 CCAATTTGGGCCTCACAATTGAG 60.618 47.826 23.77 4.14 40.60 3.02
4250 4901 2.302445 CCAATTTGGGCCTCACAATTGA 59.698 45.455 23.77 0.00 36.77 2.57
4251 4902 2.702261 CCAATTTGGGCCTCACAATTG 58.298 47.619 19.99 19.99 35.76 2.32
4262 4913 2.019984 GAGTAGCTCAGCCAATTTGGG 58.980 52.381 17.03 1.62 38.19 4.12
4263 4914 1.667724 CGAGTAGCTCAGCCAATTTGG 59.332 52.381 11.27 11.27 41.55 3.28
4264 4915 1.063174 GCGAGTAGCTCAGCCAATTTG 59.937 52.381 0.00 0.00 44.04 2.32
4265 4916 1.373570 GCGAGTAGCTCAGCCAATTT 58.626 50.000 0.00 0.00 44.04 1.82
4266 4917 3.071580 GCGAGTAGCTCAGCCAATT 57.928 52.632 0.00 0.00 44.04 2.32
4267 4918 4.844420 GCGAGTAGCTCAGCCAAT 57.156 55.556 0.00 0.00 44.04 3.16
4274 4925 7.793398 AGATCCATCTATTCTGCGAGTAGCTC 61.793 46.154 0.00 0.00 40.29 4.09
4275 4926 6.039519 AGATCCATCTATTCTGCGAGTAGCT 61.040 44.000 0.00 0.00 40.29 3.32
4276 4927 4.157656 AGATCCATCTATTCTGCGAGTAGC 59.842 45.833 0.00 0.00 40.14 3.58
4277 4928 5.895636 AGATCCATCTATTCTGCGAGTAG 57.104 43.478 0.00 3.02 34.85 2.57
4278 4929 6.183360 GCATAGATCCATCTATTCTGCGAGTA 60.183 42.308 6.38 0.00 45.32 2.59
4279 4930 5.394005 GCATAGATCCATCTATTCTGCGAGT 60.394 44.000 6.38 0.00 45.32 4.18
4280 4931 5.042593 GCATAGATCCATCTATTCTGCGAG 58.957 45.833 6.38 0.00 45.32 5.03
4281 4932 4.463891 TGCATAGATCCATCTATTCTGCGA 59.536 41.667 6.38 0.00 45.32 5.10
4282 4933 4.752146 TGCATAGATCCATCTATTCTGCG 58.248 43.478 6.38 0.00 45.32 5.18
4283 4934 7.465647 CGATTTGCATAGATCCATCTATTCTGC 60.466 40.741 6.38 9.25 45.32 4.26
4284 4935 7.763071 TCGATTTGCATAGATCCATCTATTCTG 59.237 37.037 6.38 0.09 45.32 3.02
4285 4936 7.845037 TCGATTTGCATAGATCCATCTATTCT 58.155 34.615 6.38 0.00 45.32 2.40
4286 4937 8.549548 CATCGATTTGCATAGATCCATCTATTC 58.450 37.037 6.38 3.37 45.32 1.75
4287 4938 8.262933 TCATCGATTTGCATAGATCCATCTATT 58.737 33.333 6.38 0.00 45.32 1.73
4289 4940 7.174107 TCATCGATTTGCATAGATCCATCTA 57.826 36.000 0.00 0.00 43.00 1.98
4290 4941 6.046290 TCATCGATTTGCATAGATCCATCT 57.954 37.500 0.00 0.00 40.86 2.90
4291 4942 6.370994 AGTTCATCGATTTGCATAGATCCATC 59.629 38.462 0.00 0.00 0.00 3.51
4292 4943 6.236409 AGTTCATCGATTTGCATAGATCCAT 58.764 36.000 0.00 0.00 0.00 3.41
4293 4944 5.614308 AGTTCATCGATTTGCATAGATCCA 58.386 37.500 0.00 0.00 0.00 3.41
4294 4945 5.698089 TGAGTTCATCGATTTGCATAGATCC 59.302 40.000 0.00 0.00 0.00 3.36
4295 4946 6.644181 TCTGAGTTCATCGATTTGCATAGATC 59.356 38.462 0.00 0.00 0.00 2.75
4296 4947 6.423302 GTCTGAGTTCATCGATTTGCATAGAT 59.577 38.462 0.00 0.00 0.00 1.98
4297 4948 5.750547 GTCTGAGTTCATCGATTTGCATAGA 59.249 40.000 0.00 0.00 0.00 1.98
4298 4949 5.521372 TGTCTGAGTTCATCGATTTGCATAG 59.479 40.000 0.00 0.00 0.00 2.23
4299 4950 5.418676 TGTCTGAGTTCATCGATTTGCATA 58.581 37.500 0.00 0.00 0.00 3.14
4300 4951 4.256110 TGTCTGAGTTCATCGATTTGCAT 58.744 39.130 0.00 0.00 0.00 3.96
4301 4952 3.663025 TGTCTGAGTTCATCGATTTGCA 58.337 40.909 0.00 0.00 0.00 4.08
4302 4953 3.928992 TCTGTCTGAGTTCATCGATTTGC 59.071 43.478 0.00 0.00 0.00 3.68
4303 4954 6.659361 ATTCTGTCTGAGTTCATCGATTTG 57.341 37.500 0.00 0.00 0.00 2.32
4304 4955 8.777865 TTTATTCTGTCTGAGTTCATCGATTT 57.222 30.769 0.00 0.00 0.00 2.17
4305 4956 8.954950 ATTTATTCTGTCTGAGTTCATCGATT 57.045 30.769 0.00 0.00 0.00 3.34
4306 4957 9.689976 CTATTTATTCTGTCTGAGTTCATCGAT 57.310 33.333 0.00 0.00 0.00 3.59
4307 4958 8.903820 TCTATTTATTCTGTCTGAGTTCATCGA 58.096 33.333 0.00 0.00 0.00 3.59
4308 4959 9.521503 TTCTATTTATTCTGTCTGAGTTCATCG 57.478 33.333 0.00 0.00 0.00 3.84
4314 4965 9.401058 CCCAAATTCTATTTATTCTGTCTGAGT 57.599 33.333 0.00 0.00 0.00 3.41
4315 4966 8.844244 CCCCAAATTCTATTTATTCTGTCTGAG 58.156 37.037 0.00 0.00 0.00 3.35
4316 4967 8.556589 TCCCCAAATTCTATTTATTCTGTCTGA 58.443 33.333 0.00 0.00 0.00 3.27
4317 4968 8.752005 TCCCCAAATTCTATTTATTCTGTCTG 57.248 34.615 0.00 0.00 0.00 3.51
4331 4982 9.619842 AATGGCTTATATTTATCCCCAAATTCT 57.380 29.630 0.00 0.00 30.84 2.40
4334 4985 9.169721 ACAAATGGCTTATATTTATCCCCAAAT 57.830 29.630 0.00 0.00 32.91 2.32
4335 4986 8.560124 ACAAATGGCTTATATTTATCCCCAAA 57.440 30.769 0.00 0.00 0.00 3.28
4336 4987 8.010105 AGACAAATGGCTTATATTTATCCCCAA 58.990 33.333 0.00 0.00 0.00 4.12
4337 4988 7.451255 CAGACAAATGGCTTATATTTATCCCCA 59.549 37.037 0.00 0.00 0.00 4.96
4338 4989 7.577616 GCAGACAAATGGCTTATATTTATCCCC 60.578 40.741 0.00 0.00 0.00 4.81
4339 4990 7.039784 TGCAGACAAATGGCTTATATTTATCCC 60.040 37.037 0.00 0.00 0.00 3.85
4340 4991 7.809806 GTGCAGACAAATGGCTTATATTTATCC 59.190 37.037 0.00 0.00 0.00 2.59
4341 4992 8.571336 AGTGCAGACAAATGGCTTATATTTATC 58.429 33.333 0.00 0.00 0.00 1.75
4342 4993 8.469309 AGTGCAGACAAATGGCTTATATTTAT 57.531 30.769 0.00 0.00 0.00 1.40
4343 4994 7.880160 AGTGCAGACAAATGGCTTATATTTA 57.120 32.000 0.00 0.00 0.00 1.40
4344 4995 6.780457 AGTGCAGACAAATGGCTTATATTT 57.220 33.333 0.00 0.00 0.00 1.40
4345 4996 6.780457 AAGTGCAGACAAATGGCTTATATT 57.220 33.333 0.00 0.00 0.00 1.28
4346 4997 7.941238 AGATAAGTGCAGACAAATGGCTTATAT 59.059 33.333 0.00 0.00 30.69 0.86
4347 4998 7.282585 AGATAAGTGCAGACAAATGGCTTATA 58.717 34.615 0.00 0.00 30.69 0.98
4348 4999 6.125029 AGATAAGTGCAGACAAATGGCTTAT 58.875 36.000 0.00 0.00 32.46 1.73
4349 5000 5.500234 AGATAAGTGCAGACAAATGGCTTA 58.500 37.500 0.00 0.00 0.00 3.09
4350 5001 4.338879 AGATAAGTGCAGACAAATGGCTT 58.661 39.130 0.00 0.00 0.00 4.35
4351 5002 3.960571 AGATAAGTGCAGACAAATGGCT 58.039 40.909 0.00 0.00 0.00 4.75
4352 5003 4.418392 CAAGATAAGTGCAGACAAATGGC 58.582 43.478 0.00 0.00 0.00 4.40
4353 5004 4.418392 GCAAGATAAGTGCAGACAAATGG 58.582 43.478 0.00 0.00 41.80 3.16
4354 5005 4.093514 CGCAAGATAAGTGCAGACAAATG 58.906 43.478 0.00 0.00 42.33 2.32
4355 5006 4.002982 TCGCAAGATAAGTGCAGACAAAT 58.997 39.130 0.00 0.00 45.01 2.32
4356 5007 3.398406 TCGCAAGATAAGTGCAGACAAA 58.602 40.909 0.00 0.00 45.01 2.83
4357 5008 3.038788 TCGCAAGATAAGTGCAGACAA 57.961 42.857 0.00 0.00 45.01 3.18
4358 5009 2.741759 TCGCAAGATAAGTGCAGACA 57.258 45.000 0.00 0.00 45.01 3.41
4371 5022 0.664466 TTGAGACTGACGCTCGCAAG 60.664 55.000 0.00 0.00 35.15 4.01
4372 5023 0.939577 GTTGAGACTGACGCTCGCAA 60.940 55.000 0.00 0.00 35.15 4.85
4373 5024 1.371758 GTTGAGACTGACGCTCGCA 60.372 57.895 0.00 0.00 35.15 5.10
4374 5025 2.089349 GGTTGAGACTGACGCTCGC 61.089 63.158 0.00 0.00 35.15 5.03
4375 5026 1.444553 GGGTTGAGACTGACGCTCG 60.445 63.158 0.00 0.00 35.15 5.03
4376 5027 0.389166 CTGGGTTGAGACTGACGCTC 60.389 60.000 0.00 0.00 0.00 5.03
4377 5028 1.668294 CTGGGTTGAGACTGACGCT 59.332 57.895 4.83 0.00 0.00 5.07
4378 5029 2.029844 GCTGGGTTGAGACTGACGC 61.030 63.158 0.00 0.00 0.00 5.19
4379 5030 0.036952 ATGCTGGGTTGAGACTGACG 60.037 55.000 0.00 0.00 0.00 4.35
4380 5031 3.550437 ATATGCTGGGTTGAGACTGAC 57.450 47.619 0.00 0.00 0.00 3.51
4381 5032 4.263462 ACAAATATGCTGGGTTGAGACTGA 60.263 41.667 0.00 0.00 0.00 3.41
4382 5033 4.012374 ACAAATATGCTGGGTTGAGACTG 58.988 43.478 0.00 0.00 0.00 3.51
4383 5034 4.018960 AGACAAATATGCTGGGTTGAGACT 60.019 41.667 0.00 0.00 0.00 3.24
4384 5035 4.265073 AGACAAATATGCTGGGTTGAGAC 58.735 43.478 0.00 0.00 0.00 3.36
4385 5036 4.574674 AGACAAATATGCTGGGTTGAGA 57.425 40.909 0.00 0.00 0.00 3.27
4386 5037 5.649782 AAAGACAAATATGCTGGGTTGAG 57.350 39.130 0.00 0.00 0.00 3.02
4387 5038 5.304101 ACAAAAGACAAATATGCTGGGTTGA 59.696 36.000 0.00 0.00 0.00 3.18
4388 5039 5.540911 ACAAAAGACAAATATGCTGGGTTG 58.459 37.500 0.00 0.00 0.00 3.77
4389 5040 5.806654 ACAAAAGACAAATATGCTGGGTT 57.193 34.783 0.00 0.00 0.00 4.11
4390 5041 6.909550 TTACAAAAGACAAATATGCTGGGT 57.090 33.333 0.00 0.00 0.00 4.51
4391 5042 7.378181 ACTTTACAAAAGACAAATATGCTGGG 58.622 34.615 6.41 0.00 0.00 4.45
4392 5043 8.299570 AGACTTTACAAAAGACAAATATGCTGG 58.700 33.333 6.41 0.00 0.00 4.85
4393 5044 9.683069 AAGACTTTACAAAAGACAAATATGCTG 57.317 29.630 6.41 0.00 0.00 4.41
4394 5045 9.683069 CAAGACTTTACAAAAGACAAATATGCT 57.317 29.630 6.41 0.00 0.00 3.79
4395 5046 9.463443 ACAAGACTTTACAAAAGACAAATATGC 57.537 29.630 6.41 0.00 0.00 3.14
4398 5049 9.997482 GACACAAGACTTTACAAAAGACAAATA 57.003 29.630 6.41 0.00 0.00 1.40
4399 5050 8.519526 TGACACAAGACTTTACAAAAGACAAAT 58.480 29.630 6.41 0.00 0.00 2.32
4400 5051 7.877003 TGACACAAGACTTTACAAAAGACAAA 58.123 30.769 6.41 0.00 0.00 2.83
4401 5052 7.441890 TGACACAAGACTTTACAAAAGACAA 57.558 32.000 6.41 0.00 0.00 3.18
4402 5053 6.403200 GCTGACACAAGACTTTACAAAAGACA 60.403 38.462 6.41 0.00 0.00 3.41
4403 5054 5.965918 GCTGACACAAGACTTTACAAAAGAC 59.034 40.000 6.41 0.57 0.00 3.01
4404 5055 5.065988 GGCTGACACAAGACTTTACAAAAGA 59.934 40.000 6.41 0.00 0.00 2.52
4405 5056 5.066505 AGGCTGACACAAGACTTTACAAAAG 59.933 40.000 0.00 0.00 27.87 2.27
4406 5057 4.947388 AGGCTGACACAAGACTTTACAAAA 59.053 37.500 0.00 0.00 27.87 2.44
4407 5058 4.523083 AGGCTGACACAAGACTTTACAAA 58.477 39.130 0.00 0.00 27.87 2.83
4408 5059 4.150897 AGGCTGACACAAGACTTTACAA 57.849 40.909 0.00 0.00 27.87 2.41
4409 5060 3.838244 AGGCTGACACAAGACTTTACA 57.162 42.857 0.00 0.00 27.87 2.41
4410 5061 4.686554 CAGTAGGCTGACACAAGACTTTAC 59.313 45.833 0.00 0.00 45.28 2.01
4411 5062 4.344102 ACAGTAGGCTGACACAAGACTTTA 59.656 41.667 0.00 0.00 45.28 1.85
4412 5063 3.134804 ACAGTAGGCTGACACAAGACTTT 59.865 43.478 0.00 0.00 45.28 2.66
4413 5064 2.700897 ACAGTAGGCTGACACAAGACTT 59.299 45.455 0.00 0.00 45.28 3.01
4414 5065 2.320781 ACAGTAGGCTGACACAAGACT 58.679 47.619 0.00 0.00 45.28 3.24
4415 5066 2.821991 ACAGTAGGCTGACACAAGAC 57.178 50.000 0.00 0.00 45.28 3.01
4416 5067 3.838244 AAACAGTAGGCTGACACAAGA 57.162 42.857 0.00 0.00 45.28 3.02
4417 5068 4.900635 AAAAACAGTAGGCTGACACAAG 57.099 40.909 0.00 0.00 45.28 3.16


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

AutoCloner maintained by Alex Coulton.