Multiple sequence alignment - TraesCS2A01G359700

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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 TraesCS2A01G359700 chr2A 100.000 5124 0 0 1 5124 603556921 603562044 0.000000e+00 9463.0
1 TraesCS2A01G359700 chr2D 92.943 5073 253 46 2 5025 460755807 460760823 0.000000e+00 7287.0
2 TraesCS2A01G359700 chr2D 93.204 103 6 1 5023 5124 460760926 460761028 3.200000e-32 150.0
3 TraesCS2A01G359700 chr2B 94.318 3960 199 21 425 4373 542259405 542263349 0.000000e+00 6043.0
4 TraesCS2A01G359700 chr2B 85.479 365 26 15 49 399 542258519 542258870 6.310000e-94 355.0
5 TraesCS2A01G359700 chr2B 83.626 171 16 7 4537 4700 542263500 542263665 3.200000e-32 150.0
6 TraesCS2A01G359700 chr6D 79.856 139 20 7 3758 3892 291928722 291928856 1.520000e-15 95.3
7 TraesCS2A01G359700 chr3B 95.000 60 3 0 5023 5082 513659106 513659047 1.520000e-15 95.3


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 TraesCS2A01G359700 chr2A 603556921 603562044 5123 False 9463.000000 9463 100.000000 1 5124 1 chr2A.!!$F1 5123
1 TraesCS2A01G359700 chr2D 460755807 460761028 5221 False 3718.500000 7287 93.073500 2 5124 2 chr2D.!!$F1 5122
2 TraesCS2A01G359700 chr2B 542258519 542263665 5146 False 2182.666667 6043 87.807667 49 4700 3 chr2B.!!$F1 4651

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
360 370 0.036765 TCGTCATGGCTACCACCAAC 60.037 55.0 0.00 0.0 44.65 3.77 F
1215 1751 0.034476 TGAAGTGCAGCCTCACAGAG 59.966 55.0 8.41 0.0 39.35 3.35 F
1445 1981 0.538287 AACTGCTCCAACTTGAGGGC 60.538 55.0 0.00 0.0 32.81 5.19 F
3270 3806 0.250124 TGAGAAACATTCGGCACCGT 60.250 50.0 9.23 0.0 40.74 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2531 0.685458 CCAAGAATTCCCAGCCCCAG 60.685 60.0 0.65 0.0 0.00 4.45 R
2844 3380 0.320683 AAAGCCGCCAATTGCCTTTC 60.321 50.0 0.00 0.0 36.24 2.62 R
3314 3850 0.251787 AGCTTTGAAATCCCGGCCTT 60.252 50.0 0.00 0.0 0.00 4.35 R
5091 5785 0.537188 TCGATTCTGGTGGGAGAAGC 59.463 55.0 0.00 0.0 35.44 3.86 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
80 81 3.374012 AACACCGCCGCCGCTATTA 62.374 57.895 0.00 0.00 0.00 0.98
87 88 2.506962 CGCCGCTATTACCCCCAA 59.493 61.111 0.00 0.00 0.00 4.12
88 89 1.597027 CGCCGCTATTACCCCCAAG 60.597 63.158 0.00 0.00 0.00 3.61
89 90 1.228154 GCCGCTATTACCCCCAAGG 60.228 63.158 0.00 0.00 43.78 3.61
90 91 1.228154 CCGCTATTACCCCCAAGGC 60.228 63.158 0.00 0.00 40.58 4.35
91 92 1.228154 CGCTATTACCCCCAAGGCC 60.228 63.158 0.00 0.00 40.58 5.19
92 93 1.153061 GCTATTACCCCCAAGGCCC 59.847 63.158 0.00 0.00 40.58 5.80
93 94 1.851267 CTATTACCCCCAAGGCCCC 59.149 63.158 0.00 0.00 40.58 5.80
94 95 0.996762 CTATTACCCCCAAGGCCCCA 60.997 60.000 0.00 0.00 40.58 4.96
95 96 0.555369 TATTACCCCCAAGGCCCCAA 60.555 55.000 0.00 0.00 40.58 4.12
148 149 1.749334 CTCCCCTATGGCACGTCCTC 61.749 65.000 0.00 0.00 35.26 3.71
150 151 2.808206 CCCTATGGCACGTCCTCCC 61.808 68.421 0.00 0.00 35.26 4.30
151 152 1.762460 CCTATGGCACGTCCTCCCT 60.762 63.158 0.00 0.00 35.26 4.20
153 154 1.749334 CTATGGCACGTCCTCCCTCC 61.749 65.000 0.00 0.00 35.26 4.30
156 157 3.775654 GCACGTCCTCCCTCCCAG 61.776 72.222 0.00 0.00 0.00 4.45
358 368 0.613572 TCTCGTCATGGCTACCACCA 60.614 55.000 0.00 0.00 45.82 4.17
360 370 0.036765 TCGTCATGGCTACCACCAAC 60.037 55.000 0.00 0.00 44.65 3.77
361 371 1.024579 CGTCATGGCTACCACCAACC 61.025 60.000 0.00 0.00 44.65 3.77
362 372 0.037590 GTCATGGCTACCACCAACCA 59.962 55.000 0.00 0.00 44.65 3.67
363 373 0.998928 TCATGGCTACCACCAACCAT 59.001 50.000 0.00 0.00 44.65 3.55
364 374 3.594453 ATGGCTACCACCAACCATG 57.406 52.632 0.00 0.00 44.65 3.66
365 375 0.684153 ATGGCTACCACCAACCATGC 60.684 55.000 0.00 0.00 44.65 4.06
366 376 2.406616 GGCTACCACCAACCATGCG 61.407 63.158 0.00 0.00 0.00 4.73
367 377 3.051392 GCTACCACCAACCATGCGC 62.051 63.158 0.00 0.00 0.00 6.09
368 378 1.673993 CTACCACCAACCATGCGCA 60.674 57.895 14.96 14.96 0.00 6.09
385 401 2.475187 GCGCATTGTACAAAGCTCTGAG 60.475 50.000 27.47 16.80 33.33 3.35
470 998 2.035449 AGTACTGACGCTGCACTTGTTA 59.965 45.455 0.00 0.00 0.00 2.41
498 1034 8.309656 ACCCTTATTTAGAACTATATACGGCAC 58.690 37.037 8.30 0.00 0.00 5.01
514 1050 1.079197 CACCGCATCAGCCTGTACA 60.079 57.895 0.00 0.00 37.52 2.90
518 1054 2.093181 ACCGCATCAGCCTGTACAATTA 60.093 45.455 0.00 0.00 37.52 1.40
543 1079 6.974965 AGAAGCTTGAATAGTTCCAAACAAG 58.025 36.000 2.10 0.00 38.07 3.16
701 1237 1.530720 TGTGCGCGGCAATTAGATATG 59.469 47.619 8.83 0.00 41.47 1.78
705 1241 3.810386 TGCGCGGCAATTAGATATGTTTA 59.190 39.130 8.83 0.00 34.76 2.01
738 1274 1.801178 GCTAACGCCATCTCTATTGCC 59.199 52.381 0.00 0.00 0.00 4.52
769 1305 3.594134 CTCTCAGAAGGGCAAACTACAG 58.406 50.000 0.00 0.00 0.00 2.74
825 1361 2.697229 TCCTGTCTCCTGTGATATGCTG 59.303 50.000 0.00 0.00 0.00 4.41
862 1398 1.019805 GGTAGGTGCACGCTTCTTCC 61.020 60.000 11.45 5.78 0.00 3.46
863 1399 0.320421 GTAGGTGCACGCTTCTTCCA 60.320 55.000 11.45 0.00 0.00 3.53
877 1413 8.226448 CACGCTTCTTCCATCTATGAATATTTC 58.774 37.037 0.00 0.00 0.00 2.17
879 1415 7.116948 CGCTTCTTCCATCTATGAATATTTCGT 59.883 37.037 0.00 0.00 0.00 3.85
885 1421 7.666623 TCCATCTATGAATATTTCGTGCACTA 58.333 34.615 16.19 0.00 0.00 2.74
886 1422 7.598869 TCCATCTATGAATATTTCGTGCACTAC 59.401 37.037 16.19 0.00 0.00 2.73
887 1423 7.600375 CCATCTATGAATATTTCGTGCACTACT 59.400 37.037 16.19 0.00 0.00 2.57
888 1424 8.982685 CATCTATGAATATTTCGTGCACTACTT 58.017 33.333 16.19 0.00 0.00 2.24
889 1425 8.575565 TCTATGAATATTTCGTGCACTACTTC 57.424 34.615 16.19 9.35 0.00 3.01
943 1479 7.397221 TCAGATCTTTTACATGTGAATCAGGT 58.603 34.615 9.11 0.00 43.61 4.00
947 1483 5.711506 TCTTTTACATGTGAATCAGGTGCAT 59.288 36.000 9.11 0.00 41.30 3.96
957 1493 4.155826 TGAATCAGGTGCATTTAAACTCCG 59.844 41.667 0.00 0.00 0.00 4.63
960 1496 2.556622 CAGGTGCATTTAAACTCCGGTT 59.443 45.455 0.00 0.00 37.24 4.44
969 1505 5.461032 TTTAAACTCCGGTTTTGCATCAT 57.539 34.783 0.00 0.00 42.28 2.45
977 1513 4.704540 TCCGGTTTTGCATCATGAAATAGT 59.295 37.500 0.00 0.00 0.00 2.12
981 1517 6.038356 GGTTTTGCATCATGAAATAGTGAGG 58.962 40.000 0.00 0.00 0.00 3.86
988 1524 3.450817 TCATGAAATAGTGAGGGAGCGAA 59.549 43.478 0.00 0.00 0.00 4.70
1018 1554 0.644331 CATGAAGCTCTTCGTGCTCG 59.356 55.000 16.15 0.81 45.85 5.03
1022 1558 0.456995 AAGCTCTTCGTGCTCGTAGC 60.457 55.000 18.25 18.25 40.22 3.58
1068 1604 1.064654 GGATCTGGAAGCGTCATTTGC 59.935 52.381 1.14 0.00 0.00 3.68
1134 1670 3.047280 AAGCGCGCAATCACCGAA 61.047 55.556 35.10 0.00 0.00 4.30
1156 1692 4.701663 CGAAAGGGCTCTTGAGCA 57.298 55.556 21.97 0.00 36.33 4.26
1210 1746 1.227943 GGTGTGAAGTGCAGCCTCA 60.228 57.895 0.00 0.00 0.00 3.86
1211 1747 1.510480 GGTGTGAAGTGCAGCCTCAC 61.510 60.000 13.37 13.37 37.24 3.51
1215 1751 0.034476 TGAAGTGCAGCCTCACAGAG 59.966 55.000 8.41 0.00 39.35 3.35
1361 1897 4.054825 ACATTTTGGCCGGCTGCG 62.055 61.111 28.56 11.59 42.61 5.18
1445 1981 0.538287 AACTGCTCCAACTTGAGGGC 60.538 55.000 0.00 0.00 32.81 5.19
1500 2036 3.884037 ATTCCCGCAGAAATATCCCTT 57.116 42.857 0.00 0.00 38.21 3.95
1509 2045 4.819088 GCAGAAATATCCCTTCTCTCCAAC 59.181 45.833 0.00 0.00 30.58 3.77
1591 2127 6.988580 TGGCAATATCACTTCTCTAGAACATG 59.011 38.462 0.00 0.00 0.00 3.21
1702 2238 3.689872 AGCTATCAGGTAGAGTCCCAA 57.310 47.619 0.00 0.00 31.71 4.12
1717 2253 5.187772 AGAGTCCCAAAGGCCATTTTTAATC 59.812 40.000 5.01 0.00 0.00 1.75
1740 2276 3.374988 TGTCTCTGCTAAATCAAATGGCG 59.625 43.478 0.00 0.00 0.00 5.69
1848 2384 2.270434 TGCTGGAAGGTCTTATCCCT 57.730 50.000 0.00 0.00 34.68 4.20
1995 2531 3.004106 ACAGTCTTGAAGCAAATGACAGC 59.996 43.478 0.00 0.00 0.00 4.40
2373 2909 2.826674 ATCAATTCCACGGTCCCATT 57.173 45.000 0.00 0.00 0.00 3.16
2385 2921 2.423538 CGGTCCCATTCCATCAAGTTTC 59.576 50.000 0.00 0.00 0.00 2.78
2488 3024 1.374505 ACAATTGCCCAATGTGCGC 60.375 52.632 5.05 0.00 0.00 6.09
2577 3113 6.240894 AGATCTTTCATCCAACAAGCTTACA 58.759 36.000 0.00 0.00 0.00 2.41
2615 3151 2.581409 GCGCACATGCCAGCAATC 60.581 61.111 0.30 0.00 37.91 2.67
2629 3165 1.479323 AGCAATCGCAAGCCATCAAAT 59.521 42.857 0.00 0.00 42.27 2.32
2673 3209 3.303351 AGCATTCCCATGTTTCTAGGG 57.697 47.619 0.00 0.00 44.22 3.53
2844 3380 4.806640 AAATACAACAGCCATTTCCCTG 57.193 40.909 0.00 0.00 35.26 4.45
2874 3410 2.908073 GCGGCTTTGTGGAGGTGTG 61.908 63.158 0.00 0.00 0.00 3.82
2932 3468 8.433249 TTCTCATAGAAGATCTAGATGGCAAT 57.567 34.615 10.74 0.00 31.67 3.56
2943 3479 8.099537 AGATCTAGATGGCAATACTATTTGGTG 58.900 37.037 10.74 0.00 0.00 4.17
3113 3649 6.095580 CAGGCTACTGAGAACTTCACAGTATA 59.904 42.308 22.02 9.44 45.03 1.47
3270 3806 0.250124 TGAGAAACATTCGGCACCGT 60.250 50.000 9.23 0.00 40.74 4.83
3312 3848 5.404946 ACTGCATGCTCAACAATTGATAAC 58.595 37.500 20.33 0.00 39.30 1.89
3314 3850 4.220163 TGCATGCTCAACAATTGATAACCA 59.780 37.500 20.33 4.04 39.30 3.67
3357 3893 2.084546 GTCTACCAGTTCATGCCCAAC 58.915 52.381 0.00 0.00 0.00 3.77
3385 3921 4.954970 ACACTTGGCTGCACCCGG 62.955 66.667 0.50 0.00 37.83 5.73
3408 3944 1.827344 GGAGATGGAAAAGCCCCAAAG 59.173 52.381 0.00 0.00 37.22 2.77
3488 4024 7.657354 GCAATATATACACCATGACTGTGAGAA 59.343 37.037 7.48 0.00 37.18 2.87
3489 4025 9.716531 CAATATATACACCATGACTGTGAGAAT 57.283 33.333 7.48 2.01 37.18 2.40
3507 4043 6.820656 GTGAGAATCCTATTGTTCACTGTGAT 59.179 38.462 11.86 0.00 33.86 3.06
3522 4058 2.232941 CTGTGATTTGAAGCCCAGCAAT 59.767 45.455 0.00 0.00 0.00 3.56
3579 4115 0.314935 ACTTTGGCATCGCAAGGTTG 59.685 50.000 2.08 0.00 38.47 3.77
3594 4130 5.537188 GCAAGGTTGTACATCAAATCCAAA 58.463 37.500 0.00 0.00 37.81 3.28
3641 4177 7.106239 AGTTCAATGGGTACAATAACTCTGAG 58.894 38.462 2.45 2.45 0.00 3.35
3660 4196 3.587061 TGAGGGGCACGATTGGATATATT 59.413 43.478 0.00 0.00 0.00 1.28
3702 4238 6.760298 TGTTTCTTGCTGTAAATTTGAATGCA 59.240 30.769 0.00 3.67 0.00 3.96
3769 4305 2.621338 ACATGGTGTTCAGAGTATGCG 58.379 47.619 0.00 0.00 0.00 4.73
3775 4311 0.824759 GTTCAGAGTATGCGGGAGGT 59.175 55.000 0.00 0.00 0.00 3.85
3776 4312 0.824109 TTCAGAGTATGCGGGAGGTG 59.176 55.000 0.00 0.00 0.00 4.00
3820 4356 2.347452 CGCGTACAGTTTTGGGATAGTG 59.653 50.000 0.00 0.00 0.00 2.74
3923 4459 4.811557 GGAACTTTCCGGATCAGATACTTG 59.188 45.833 16.32 0.00 37.65 3.16
3946 4482 0.608308 TCCTTGACGCTTCTCTCCGA 60.608 55.000 0.00 0.00 0.00 4.55
4042 4578 1.383456 AAGTGGCACTTTCTTGCGCA 61.383 50.000 26.54 5.66 44.00 6.09
4091 4627 4.161942 ACATGAGAGAAGCAGCTACTGAAT 59.838 41.667 0.00 0.00 32.44 2.57
4108 4644 1.288419 AATTGCACGCGATCGACACA 61.288 50.000 21.57 7.89 39.41 3.72
4110 4646 1.288419 TTGCACGCGATCGACACATT 61.288 50.000 21.57 0.00 39.41 2.71
4172 4710 8.253113 TGTATCATACATACATACCAGCTGATG 58.747 37.037 17.39 14.50 32.89 3.07
4173 4711 6.670695 TCATACATACATACCAGCTGATGT 57.329 37.500 20.92 20.92 39.57 3.06
4198 4736 3.002451 AGCGTGTAACTAGAGCTGTATCG 59.998 47.826 0.00 0.00 36.73 2.92
4202 4740 5.430462 GTGTAACTAGAGCTGTATCGTACG 58.570 45.833 9.53 9.53 0.00 3.67
4206 4744 2.733820 AGAGCTGTATCGTACGTTCG 57.266 50.000 16.05 8.41 0.00 3.95
4212 4750 4.747108 AGCTGTATCGTACGTTCGTACTAT 59.253 41.667 25.46 22.70 38.90 2.12
4239 4777 3.120782 GCCGTGTAGAACTTTTGTACTCG 59.879 47.826 9.46 9.46 42.37 4.18
4241 4779 4.977963 CCGTGTAGAACTTTTGTACTCGAA 59.022 41.667 15.20 0.00 44.15 3.71
4245 4784 8.060090 CGTGTAGAACTTTTGTACTCGAAAAAT 58.940 33.333 10.44 0.00 44.15 1.82
4263 4802 6.565623 CGAAAAATTTATTTGTTGGGCTGTGG 60.566 38.462 0.00 0.00 0.00 4.17
4304 4844 6.050432 TGAAATGCTCATCTTTTTGCAAAGT 58.950 32.000 12.41 0.00 40.47 2.66
4324 4864 3.746492 AGTACGAATCAGCCTTTGTGTTC 59.254 43.478 0.00 0.00 0.00 3.18
4335 4875 8.177119 TCAGCCTTTGTGTTCTTTATAATTGT 57.823 30.769 0.00 0.00 0.00 2.71
4337 4877 9.906660 CAGCCTTTGTGTTCTTTATAATTGTAA 57.093 29.630 0.00 0.00 0.00 2.41
4382 4924 3.947612 AGATTGCCCTGACATCATCTT 57.052 42.857 0.00 0.00 0.00 2.40
4386 4928 5.826737 AGATTGCCCTGACATCATCTTAAAG 59.173 40.000 0.00 0.00 0.00 1.85
4407 4955 9.748708 TTAAAGAAAAGATTGTCCTGACATTTG 57.251 29.630 0.03 0.00 41.52 2.32
4429 4979 4.725790 GCTTTTTGCCTGATAAGGTGAT 57.274 40.909 0.00 0.00 35.15 3.06
4440 4990 5.183713 CCTGATAAGGTGATTGCAGAAAACA 59.816 40.000 0.00 0.00 30.43 2.83
4448 4998 7.765307 AGGTGATTGCAGAAAACAGTATATTG 58.235 34.615 0.00 0.00 0.00 1.90
4452 5002 7.541783 TGATTGCAGAAAACAGTATATTGTTGC 59.458 33.333 13.68 13.36 40.24 4.17
4455 5005 6.155827 GCAGAAAACAGTATATTGTTGCCAA 58.844 36.000 13.68 0.00 40.24 4.52
4456 5006 6.644592 GCAGAAAACAGTATATTGTTGCCAAA 59.355 34.615 13.68 0.00 40.24 3.28
4457 5007 7.170658 GCAGAAAACAGTATATTGTTGCCAAAA 59.829 33.333 13.68 0.00 40.24 2.44
4458 5008 9.039870 CAGAAAACAGTATATTGTTGCCAAAAA 57.960 29.630 13.68 0.00 40.24 1.94
4478 5028 5.813513 AAAAGAAAGATTGCCCTGACATT 57.186 34.783 0.00 0.00 0.00 2.71
4479 5029 5.813513 AAAGAAAGATTGCCCTGACATTT 57.186 34.783 0.00 0.00 0.00 2.32
4480 5030 4.796038 AGAAAGATTGCCCTGACATTTG 57.204 40.909 0.00 0.00 0.00 2.32
4482 5032 1.188863 AGATTGCCCTGACATTTGGC 58.811 50.000 4.31 4.31 45.56 4.52
4483 5033 1.188863 GATTGCCCTGACATTTGGCT 58.811 50.000 10.91 0.00 45.56 4.75
4484 5034 1.551883 GATTGCCCTGACATTTGGCTT 59.448 47.619 10.91 1.25 45.56 4.35
4485 5035 1.422531 TTGCCCTGACATTTGGCTTT 58.577 45.000 10.91 0.00 45.56 3.51
4486 5036 1.422531 TGCCCTGACATTTGGCTTTT 58.577 45.000 10.91 0.00 45.56 2.27
4511 5062 2.547299 AACATTTGCACATGTTGGGG 57.453 45.000 26.17 0.00 44.19 4.96
4714 5290 1.731433 CTGGGCGCTTCCATTCCATG 61.731 60.000 7.64 0.00 36.05 3.66
4785 5361 2.588620 GGATGGATCCTGACGACTACT 58.411 52.381 14.23 0.00 43.73 2.57
4786 5362 2.294791 GGATGGATCCTGACGACTACTG 59.705 54.545 14.23 0.00 43.73 2.74
4787 5363 2.509166 TGGATCCTGACGACTACTGT 57.491 50.000 14.23 0.00 0.00 3.55
4807 5383 4.436332 TGTAGAGTAGAAGCATCGTACGA 58.564 43.478 21.93 21.93 0.00 3.43
4880 5466 1.351430 GCGCGTGTTGCTGATCTACA 61.351 55.000 8.43 0.00 43.27 2.74
4883 5469 2.544685 GCGTGTTGCTGATCTACATCT 58.455 47.619 0.00 0.00 41.73 2.90
4935 5521 0.314302 AACTGAGACGTGGAAGGACG 59.686 55.000 0.00 0.00 45.09 4.79
4945 5531 1.607148 GTGGAAGGACGGAAAACTTGG 59.393 52.381 0.00 0.00 0.00 3.61
4984 5572 5.008217 CACGTGTGGAAAACCTTAGAATCAA 59.992 40.000 7.58 0.00 0.00 2.57
4989 5577 5.944007 GTGGAAAACCTTAGAATCAAGCCTA 59.056 40.000 0.00 0.00 0.00 3.93
5000 5588 9.436957 CTTAGAATCAAGCCTAAAACAAGACTA 57.563 33.333 0.00 0.00 0.00 2.59
5001 5589 7.913674 AGAATCAAGCCTAAAACAAGACTAG 57.086 36.000 0.00 0.00 0.00 2.57
5053 5746 2.248248 AGATGTCCCAAGAACAGACGA 58.752 47.619 0.00 0.00 33.09 4.20
5081 5774 8.898983 AATACAATGCATTTGCTTATTTTTGC 57.101 26.923 9.83 0.00 42.66 3.68
5083 5776 5.241064 ACAATGCATTTGCTTATTTTTGCCA 59.759 32.000 9.83 0.00 42.66 4.92
5084 5777 4.745837 TGCATTTGCTTATTTTTGCCAC 57.254 36.364 3.94 0.00 42.66 5.01
5088 5782 5.975939 GCATTTGCTTATTTTTGCCACAAAA 59.024 32.000 1.50 1.50 38.21 2.44
5091 5785 7.982371 TTTGCTTATTTTTGCCACAAAAATG 57.018 28.000 28.37 19.01 39.40 2.32
5095 5789 6.360414 GCTTATTTTTGCCACAAAAATGCTTC 59.640 34.615 28.37 16.70 39.40 3.86
5114 5808 2.376109 TCTCCCACCAGAATCGAGTAC 58.624 52.381 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 0.539438 TGTTGCTAGGGTTTGGCTGG 60.539 55.000 0.00 0.00 0.00 4.85
52 53 1.602605 GGCGGTGTTGCTAGGGTTT 60.603 57.895 0.00 0.00 34.52 3.27
153 154 3.672295 GAAGACAGCCGAGGCCTGG 62.672 68.421 12.00 9.69 43.17 4.45
154 155 2.125350 GAAGACAGCCGAGGCCTG 60.125 66.667 12.00 10.69 43.17 4.85
155 156 2.284258 AGAAGACAGCCGAGGCCT 60.284 61.111 3.86 3.86 43.17 5.19
156 157 2.185608 GAGAAGACAGCCGAGGCC 59.814 66.667 10.95 0.00 43.17 5.19
162 163 2.182030 CCGACGGAGAAGACAGCC 59.818 66.667 8.64 0.00 0.00 4.85
358 368 2.926159 GCTTTGTACAATGCGCATGGTT 60.926 45.455 33.95 18.47 32.96 3.67
360 370 1.135315 AGCTTTGTACAATGCGCATGG 60.135 47.619 29.82 24.64 43.59 3.66
361 371 2.159476 AGAGCTTTGTACAATGCGCATG 60.159 45.455 34.69 19.60 43.59 4.06
362 372 2.086869 AGAGCTTTGTACAATGCGCAT 58.913 42.857 34.69 19.28 43.59 4.73
363 373 1.197492 CAGAGCTTTGTACAATGCGCA 59.803 47.619 34.69 14.96 43.59 6.09
364 374 1.464608 TCAGAGCTTTGTACAATGCGC 59.535 47.619 30.09 30.09 43.59 6.09
365 375 2.475187 GCTCAGAGCTTTGTACAATGCG 60.475 50.000 29.82 20.51 43.59 4.73
366 376 3.128465 GCTCAGAGCTTTGTACAATGC 57.872 47.619 29.52 29.52 38.45 3.56
385 401 9.935241 TCATATAATATTGACCTCTTGAAGAGC 57.065 33.333 16.57 4.88 40.98 4.09
420 436 5.618561 CATCTGAAGTACCGTGTTTTTAGC 58.381 41.667 0.00 0.00 0.00 3.09
470 998 9.716531 GCCGTATATAGTTCTAAATAAGGGTTT 57.283 33.333 0.00 0.00 0.00 3.27
491 1027 4.830765 GGCTGATGCGGTGCCGTA 62.831 66.667 12.46 8.25 42.09 4.02
498 1034 1.382522 AATTGTACAGGCTGATGCGG 58.617 50.000 23.66 0.00 40.82 5.69
514 1050 9.914131 GTTTGGAACTATTCAAGCTTCTTAATT 57.086 29.630 0.00 0.00 0.00 1.40
518 1054 6.959639 TGTTTGGAACTATTCAAGCTTCTT 57.040 33.333 0.00 0.00 0.00 2.52
543 1079 3.285745 CGTTCTTTGTCGCTTTTACACC 58.714 45.455 0.00 0.00 0.00 4.16
663 1199 1.066430 ACACGTTGACACTTGACACCT 60.066 47.619 0.00 0.00 0.00 4.00
665 1201 1.529010 GCACACGTTGACACTTGACAC 60.529 52.381 0.00 0.00 0.00 3.67
727 1263 5.848921 AGAGGGATTAAGTGGCAATAGAGAT 59.151 40.000 0.00 0.00 0.00 2.75
769 1305 2.027192 TGGTTTAGGTGGAGATGAGTGC 60.027 50.000 0.00 0.00 0.00 4.40
825 1361 4.097286 CCTACCTCTAGTCTTCAGAAGCAC 59.903 50.000 5.15 5.16 0.00 4.40
862 1398 8.526218 AGTAGTGCACGAAATATTCATAGATG 57.474 34.615 12.01 0.00 0.00 2.90
863 1399 9.197694 GAAGTAGTGCACGAAATATTCATAGAT 57.802 33.333 12.01 0.00 0.00 1.98
877 1413 4.242475 TGTATGAAAGGAAGTAGTGCACG 58.758 43.478 12.01 0.00 0.00 5.34
879 1415 5.109210 CGATGTATGAAAGGAAGTAGTGCA 58.891 41.667 0.00 0.00 0.00 4.57
885 1421 7.063074 CGAAAAGTACGATGTATGAAAGGAAGT 59.937 37.037 0.00 0.00 0.00 3.01
886 1422 7.391786 CGAAAAGTACGATGTATGAAAGGAAG 58.608 38.462 0.00 0.00 0.00 3.46
887 1423 6.183360 GCGAAAAGTACGATGTATGAAAGGAA 60.183 38.462 0.00 0.00 0.00 3.36
888 1424 5.290158 GCGAAAAGTACGATGTATGAAAGGA 59.710 40.000 0.00 0.00 0.00 3.36
889 1425 5.291128 AGCGAAAAGTACGATGTATGAAAGG 59.709 40.000 0.00 0.00 0.00 3.11
943 1479 3.181475 TGCAAAACCGGAGTTTAAATGCA 60.181 39.130 9.46 9.78 46.90 3.96
947 1483 4.920640 TGATGCAAAACCGGAGTTTAAA 57.079 36.364 9.46 0.18 45.54 1.52
957 1493 6.038356 CCTCACTATTTCATGATGCAAAACC 58.962 40.000 0.00 0.00 0.00 3.27
960 1496 5.508567 TCCCTCACTATTTCATGATGCAAA 58.491 37.500 0.00 0.00 0.00 3.68
969 1505 3.973206 TTTCGCTCCCTCACTATTTCA 57.027 42.857 0.00 0.00 0.00 2.69
977 1513 2.027192 ACATAGCTTTTTCGCTCCCTCA 60.027 45.455 0.00 0.00 41.30 3.86
981 1517 3.623060 TCATGACATAGCTTTTTCGCTCC 59.377 43.478 0.00 0.00 41.30 4.70
988 1524 5.064452 CGAAGAGCTTCATGACATAGCTTTT 59.936 40.000 18.94 18.73 44.78 2.27
1018 1554 1.247567 AACAACAGTGCCCATGCTAC 58.752 50.000 0.00 0.00 38.71 3.58
1022 1558 3.507233 AGACAATAACAACAGTGCCCATG 59.493 43.478 0.00 0.00 0.00 3.66
1068 1604 3.781307 TTCCCATGGAGGACGGCG 61.781 66.667 15.22 4.80 41.22 6.46
1071 1607 1.037493 TATCGTTCCCATGGAGGACG 58.963 55.000 21.59 21.59 41.22 4.79
1156 1692 2.291209 TGAATGCTGGTGTTCCATGT 57.709 45.000 0.00 0.00 43.43 3.21
1210 1746 1.572085 GCAACACGCTCATGCTCTGT 61.572 55.000 0.00 0.00 37.12 3.41
1211 1747 1.134075 GCAACACGCTCATGCTCTG 59.866 57.895 0.00 0.00 37.12 3.35
1215 1751 1.134075 CTCTGCAACACGCTCATGC 59.866 57.895 0.00 0.00 43.06 4.06
1361 1897 2.301583 AGGTCAAGAAACTCCAGCTCTC 59.698 50.000 0.00 0.00 0.00 3.20
1445 1981 7.063544 CCAATAAGTTTCTTGAGAGGTCTAACG 59.936 40.741 0.71 0.00 0.00 3.18
1500 2036 0.827925 AGCGTGTCAGGTTGGAGAGA 60.828 55.000 0.00 0.00 0.00 3.10
1591 2127 9.408069 CTCTAACCGGTTATACATCAGAATAAC 57.592 37.037 26.70 0.00 37.68 1.89
1653 2189 5.305585 TCACCAAGGAGTAAGTTTGACATC 58.694 41.667 0.00 0.00 0.00 3.06
1702 2238 5.105595 GCAGAGACAGATTAAAAATGGCCTT 60.106 40.000 3.32 0.00 0.00 4.35
1717 2253 4.495349 CGCCATTTGATTTAGCAGAGACAG 60.495 45.833 0.00 0.00 0.00 3.51
1740 2276 4.274459 CCAACTAGCATATTCAACTCCAGC 59.726 45.833 0.00 0.00 0.00 4.85
1848 2384 3.216800 GGATGCATTGCCTAATGAGTCA 58.783 45.455 6.12 0.00 45.21 3.41
1995 2531 0.685458 CCAAGAATTCCCAGCCCCAG 60.685 60.000 0.65 0.00 0.00 4.45
2373 2909 4.884744 TGAAGGTTTTCGAAACTTGATGGA 59.115 37.500 15.99 0.00 36.04 3.41
2385 2921 3.065371 ACAAGAGTTGCTGAAGGTTTTCG 59.935 43.478 0.00 0.00 36.04 3.46
2488 3024 4.442192 GCCTTCTAGACTGTTGTGGGATAG 60.442 50.000 0.00 0.00 0.00 2.08
2577 3113 3.817931 GCAAAGTAGGTGGAATTTCCCCT 60.818 47.826 21.80 21.80 39.50 4.79
2615 3151 1.632422 GTCCAATTTGATGGCTTGCG 58.368 50.000 0.00 0.00 40.46 4.85
2629 3165 0.974383 GAGAGGAAGTTCCGGTCCAA 59.026 55.000 16.31 0.00 42.75 3.53
2664 3200 3.259625 AGCTGTTCAGACTCCCTAGAAAC 59.740 47.826 3.84 0.00 0.00 2.78
2673 3209 3.178267 CTCGATCAAGCTGTTCAGACTC 58.822 50.000 3.84 0.00 0.00 3.36
2844 3380 0.320683 AAAGCCGCCAATTGCCTTTC 60.321 50.000 0.00 0.00 36.24 2.62
2874 3410 2.104792 TGAAGGCATATGTAGGTCCAGC 59.895 50.000 4.29 0.00 0.00 4.85
2932 3468 6.099269 GGGACCAATACTCTCACCAAATAGTA 59.901 42.308 0.00 0.00 0.00 1.82
2943 3479 6.668283 TGCCTAATATAGGGACCAATACTCTC 59.332 42.308 5.62 0.00 46.32 3.20
2998 3534 2.503356 GCATCCTCTTTCTGAGAAGGGA 59.497 50.000 13.16 13.16 45.39 4.20
3085 3621 2.300152 TGAAGTTCTCAGTAGCCTGTGG 59.700 50.000 4.17 0.00 39.82 4.17
3113 3649 4.476479 AGCTTCCTCTCCCAATCAAGTTAT 59.524 41.667 0.00 0.00 0.00 1.89
3216 3752 4.566759 TCTGAGATGAAACTTTTATCCGCG 59.433 41.667 0.00 0.00 0.00 6.46
3270 3806 6.475504 TGCAGTCAGAATTGGAAGAAGATTA 58.524 36.000 0.00 0.00 0.00 1.75
3312 3848 0.532115 CTTTGAAATCCCGGCCTTGG 59.468 55.000 0.00 0.50 0.00 3.61
3314 3850 0.251787 AGCTTTGAAATCCCGGCCTT 60.252 50.000 0.00 0.00 0.00 4.35
3357 3893 2.260869 CCAAGTGTCCAGGTTGCCG 61.261 63.158 0.00 0.00 0.00 5.69
3364 3900 2.263741 GGTGCAGCCAAGTGTCCAG 61.264 63.158 4.03 0.00 37.17 3.86
3385 3921 1.039785 GGGGCTTTTCCATCTCCTGC 61.040 60.000 0.00 0.00 36.21 4.85
3408 3944 2.037772 TCTTTGAGAGAGGTCCAGTTGC 59.962 50.000 0.00 0.00 0.00 4.17
3488 4024 7.362401 GCTTCAAATCACAGTGAACAATAGGAT 60.362 37.037 7.50 0.00 30.73 3.24
3489 4025 6.072508 GCTTCAAATCACAGTGAACAATAGGA 60.073 38.462 7.50 0.00 30.73 2.94
3507 4043 3.290710 GAGGATATTGCTGGGCTTCAAA 58.709 45.455 0.00 0.00 0.00 2.69
3522 4058 9.360901 GCTGTCATATCATAATCTAGGAGGATA 57.639 37.037 0.00 0.00 0.00 2.59
3579 4115 4.601019 CCGCTGATTTGGATTTGATGTAC 58.399 43.478 0.00 0.00 0.00 2.90
3609 4145 2.635915 TGTACCCATTGAACTCGAACCT 59.364 45.455 0.00 0.00 0.00 3.50
3641 4177 2.423538 GCAATATATCCAATCGTGCCCC 59.576 50.000 0.00 0.00 0.00 5.80
3660 4196 5.815581 AGAAACATATTGTTACCTGGAGCA 58.184 37.500 0.00 0.00 40.14 4.26
3702 4238 0.383949 AAACAACCGCTTCGTTGCAT 59.616 45.000 7.78 0.00 45.75 3.96
3740 4276 5.355910 ACTCTGAACACCATGTAAAACGTTT 59.644 36.000 7.96 7.96 0.00 3.60
3751 4287 1.134401 CCCGCATACTCTGAACACCAT 60.134 52.381 0.00 0.00 0.00 3.55
3756 4292 0.824759 ACCTCCCGCATACTCTGAAC 59.175 55.000 0.00 0.00 0.00 3.18
3775 4311 1.306148 CAGACGTCGATAGGTAGCCA 58.694 55.000 10.46 0.00 0.00 4.75
3776 4312 0.592148 CCAGACGTCGATAGGTAGCC 59.408 60.000 10.46 0.00 0.00 3.93
3790 4326 0.240411 AACTGTACGCGTCTCCAGAC 59.760 55.000 28.99 17.66 41.47 3.51
3801 4337 3.370978 CAGCACTATCCCAAAACTGTACG 59.629 47.826 0.00 0.00 0.00 3.67
3820 4356 1.078637 TGTCAGCATCTCCAGCAGC 60.079 57.895 0.00 0.00 0.00 5.25
3923 4459 3.610585 CGGAGAGAAGCGTCAAGGATATC 60.611 52.174 1.61 0.00 0.00 1.63
3946 4482 6.166984 TGAGAACAGTCTTGACATTCTTCT 57.833 37.500 16.18 9.99 32.80 2.85
3955 4491 6.127225 CCAGATTATCCTGAGAACAGTCTTGA 60.127 42.308 0.00 0.00 42.05 3.02
4042 4578 1.134788 CGTTCGTTAGGATCCTGGCTT 60.135 52.381 25.28 0.00 0.00 4.35
4091 4627 1.288419 AATGTGTCGATCGCGTGCAA 61.288 50.000 11.09 0.00 38.98 4.08
4108 4644 3.937814 TCCGCTTCAAGACACATACAAT 58.062 40.909 0.00 0.00 0.00 2.71
4110 4646 3.261580 CATCCGCTTCAAGACACATACA 58.738 45.455 0.00 0.00 0.00 2.29
4138 4674 8.132362 GGTATGTATGTATGATACAGCTCTAGC 58.868 40.741 11.32 6.49 42.77 3.42
4172 4710 2.917971 CAGCTCTAGTTACACGCTTCAC 59.082 50.000 0.00 0.00 0.00 3.18
4173 4711 2.557056 ACAGCTCTAGTTACACGCTTCA 59.443 45.455 0.00 0.00 0.00 3.02
4202 4740 2.098117 ACACGGCCACTATAGTACGAAC 59.902 50.000 22.60 6.17 0.00 3.95
4206 4744 4.578105 AGTTCTACACGGCCACTATAGTAC 59.422 45.833 4.74 0.68 0.00 2.73
4212 4750 3.181463 ACAAAAGTTCTACACGGCCACTA 60.181 43.478 2.24 0.00 0.00 2.74
4239 4777 6.667370 CCACAGCCCAACAAATAAATTTTTC 58.333 36.000 0.00 0.00 0.00 2.29
4241 4779 4.518590 GCCACAGCCCAACAAATAAATTTT 59.481 37.500 0.00 0.00 0.00 1.82
4245 4784 2.324541 AGCCACAGCCCAACAAATAAA 58.675 42.857 0.00 0.00 41.25 1.40
4263 4802 4.584327 TTTCAAAGGCTAGGAACAAAGC 57.416 40.909 0.73 0.00 38.61 3.51
4304 4844 4.002906 AGAACACAAAGGCTGATTCGTA 57.997 40.909 0.00 0.00 32.35 3.43
4335 4875 5.250200 AGGAACATGCGTACCATCTTTTTA 58.750 37.500 0.00 0.00 29.71 1.52
4337 4877 3.686016 AGGAACATGCGTACCATCTTTT 58.314 40.909 0.00 0.00 29.71 2.27
4348 4890 2.523015 GCAATCTTGAAGGAACATGCG 58.477 47.619 0.00 0.00 0.00 4.73
4382 4924 8.359642 CCAAATGTCAGGACAATCTTTTCTTTA 58.640 33.333 6.17 0.00 45.41 1.85
4386 4928 4.925646 GCCAAATGTCAGGACAATCTTTTC 59.074 41.667 6.17 0.00 45.41 2.29
4396 4944 3.110447 GCAAAAAGCCAAATGTCAGGA 57.890 42.857 0.00 0.00 37.23 3.86
4429 4979 6.155827 GGCAACAATATACTGTTTTCTGCAA 58.844 36.000 10.00 0.00 37.43 4.08
4455 5005 5.813513 ATGTCAGGGCAATCTTTCTTTTT 57.186 34.783 0.00 0.00 0.00 1.94
4456 5006 5.813513 AATGTCAGGGCAATCTTTCTTTT 57.186 34.783 0.00 0.00 0.00 2.27
4457 5007 5.511888 CCAAATGTCAGGGCAATCTTTCTTT 60.512 40.000 0.00 0.00 0.00 2.52
4458 5008 4.020839 CCAAATGTCAGGGCAATCTTTCTT 60.021 41.667 0.00 0.00 0.00 2.52
4460 5010 3.853475 CCAAATGTCAGGGCAATCTTTC 58.147 45.455 0.00 0.00 0.00 2.62
4461 5011 2.027837 GCCAAATGTCAGGGCAATCTTT 60.028 45.455 7.81 0.00 46.92 2.52
4462 5012 1.551883 GCCAAATGTCAGGGCAATCTT 59.448 47.619 7.81 0.00 46.92 2.40
4463 5013 1.188863 GCCAAATGTCAGGGCAATCT 58.811 50.000 7.81 0.00 46.92 2.40
4464 5014 3.746900 GCCAAATGTCAGGGCAATC 57.253 52.632 7.81 0.00 46.92 2.67
4469 5019 2.145536 GCAAAAAGCCAAATGTCAGGG 58.854 47.619 0.00 0.00 37.23 4.45
4470 5020 2.545106 GTGCAAAAAGCCAAATGTCAGG 59.455 45.455 0.00 0.00 44.83 3.86
4471 5021 3.196463 TGTGCAAAAAGCCAAATGTCAG 58.804 40.909 0.00 0.00 44.83 3.51
4472 5022 3.257469 TGTGCAAAAAGCCAAATGTCA 57.743 38.095 0.00 0.00 44.83 3.58
4473 5023 3.373439 TGTTGTGCAAAAAGCCAAATGTC 59.627 39.130 0.00 0.00 44.83 3.06
4474 5024 3.341823 TGTTGTGCAAAAAGCCAAATGT 58.658 36.364 0.00 0.00 44.83 2.71
4476 5026 5.341617 CAAATGTTGTGCAAAAAGCCAAAT 58.658 33.333 0.00 0.00 44.83 2.32
4478 5028 3.427233 GCAAATGTTGTGCAAAAAGCCAA 60.427 39.130 0.00 0.00 44.83 4.52
4479 5029 2.097142 GCAAATGTTGTGCAAAAAGCCA 59.903 40.909 0.00 0.00 44.83 4.75
4480 5030 2.718663 GCAAATGTTGTGCAAAAAGCC 58.281 42.857 0.00 0.00 44.83 4.35
4511 5062 9.712305 ATATACTACTATCAACTTGACAATGGC 57.288 33.333 0.00 0.00 0.00 4.40
4621 5197 3.517901 TCGATGCTCTCCCCTAAGAAAAA 59.482 43.478 0.00 0.00 0.00 1.94
4622 5198 3.104512 TCGATGCTCTCCCCTAAGAAAA 58.895 45.455 0.00 0.00 0.00 2.29
4714 5290 3.800628 GGCTTTCATTCACACAGCC 57.199 52.632 0.00 0.00 43.26 4.85
4783 5359 4.270566 CGTACGATGCTTCTACTCTACAGT 59.729 45.833 10.44 0.00 36.55 3.55
4784 5360 4.507021 TCGTACGATGCTTCTACTCTACAG 59.493 45.833 15.28 0.00 0.00 2.74
4785 5361 4.436332 TCGTACGATGCTTCTACTCTACA 58.564 43.478 15.28 0.00 0.00 2.74
4786 5362 5.401033 TTCGTACGATGCTTCTACTCTAC 57.599 43.478 20.27 0.00 0.00 2.59
4787 5363 5.756833 TGATTCGTACGATGCTTCTACTCTA 59.243 40.000 20.27 0.00 0.00 2.43
4802 5378 8.068977 AGAAGATAACGACACTATGATTCGTAC 58.931 37.037 0.00 0.00 44.93 3.67
4807 5383 8.687242 TGAAGAGAAGATAACGACACTATGATT 58.313 33.333 0.00 0.00 0.00 2.57
4865 5441 8.572185 TCTTATCTAGATGTAGATCAGCAACAC 58.428 37.037 15.24 0.00 41.47 3.32
4897 5483 8.655901 TCTCAGTTACATGTGGGCATATATAAA 58.344 33.333 9.11 0.00 33.30 1.40
4902 5488 4.708177 GTCTCAGTTACATGTGGGCATAT 58.292 43.478 9.11 0.00 33.30 1.78
4906 5492 1.337823 ACGTCTCAGTTACATGTGGGC 60.338 52.381 9.11 0.00 0.00 5.36
4935 5521 1.618837 GAAGAAGGCCCCAAGTTTTCC 59.381 52.381 0.00 0.00 0.00 3.13
4945 5531 1.377333 CGTGGAAGGAAGAAGGCCC 60.377 63.158 0.00 0.00 0.00 5.80
4984 5572 6.003950 TCAAATGCTAGTCTTGTTTTAGGCT 58.996 36.000 0.00 0.00 33.88 4.58
4989 5577 6.507023 CAAGGTCAAATGCTAGTCTTGTTTT 58.493 36.000 0.00 0.00 0.00 2.43
5080 5773 1.344114 TGGGAGAAGCATTTTTGTGGC 59.656 47.619 0.00 0.00 0.00 5.01
5081 5774 2.289010 GGTGGGAGAAGCATTTTTGTGG 60.289 50.000 0.00 0.00 0.00 4.17
5083 5776 2.629617 CTGGTGGGAGAAGCATTTTTGT 59.370 45.455 0.00 0.00 0.00 2.83
5084 5777 2.892852 TCTGGTGGGAGAAGCATTTTTG 59.107 45.455 0.00 0.00 0.00 2.44
5088 5782 2.681976 CGATTCTGGTGGGAGAAGCATT 60.682 50.000 0.00 0.00 38.10 3.56
5091 5785 0.537188 TCGATTCTGGTGGGAGAAGC 59.463 55.000 0.00 0.00 35.44 3.86
5095 5789 1.065701 CGTACTCGATTCTGGTGGGAG 59.934 57.143 0.00 0.00 39.71 4.30


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

AutoCloner maintained by Alex Coulton.