Multiple sequence alignment - TraesCS4B01G211200

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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 TraesCS4B01G211200 chr4B 100.000 5175 0 0 1 5175 449640926 449646100 0.000000e+00 9557.0
1 TraesCS4B01G211200 chr4D 94.436 4134 154 28 34 4109 364540135 364544250 0.000000e+00 6290.0
2 TraesCS4B01G211200 chr4D 91.016 935 25 22 4277 5175 364544569 364545480 0.000000e+00 1206.0
3 TraesCS4B01G211200 chr4D 90.798 163 15 0 4111 4273 364544441 364544603 8.720000e-53 219.0
4 TraesCS4B01G211200 chr4A 93.925 3885 167 23 255 4095 100675444 100671585 0.000000e+00 5803.0
5 TraesCS4B01G211200 chr4A 90.149 1005 37 25 4214 5175 100669862 100668877 0.000000e+00 1251.0
6 TraesCS4B01G211200 chr4A 88.000 275 17 6 1 264 100676039 100675770 1.400000e-80 311.0
7 TraesCS4B01G211200 chr4A 96.875 32 1 0 4081 4112 692728154 692728185 3.000000e-03 54.7
8 TraesCS4B01G211200 chr1B 100.000 58 0 0 533 590 430899778 430899721 1.970000e-19 108.0
9 TraesCS4B01G211200 chrUn 97.059 34 0 1 4076 4108 326972496 326972463 7.240000e-04 56.5
10 TraesCS4B01G211200 chrUn 97.059 34 0 1 4076 4108 326975522 326975489 7.240000e-04 56.5
11 TraesCS4B01G211200 chrUn 97.059 34 0 1 4076 4108 345995504 345995471 7.240000e-04 56.5
12 TraesCS4B01G211200 chr7B 100.000 30 0 0 4076 4105 518910629 518910658 7.240000e-04 56.5
13 TraesCS4B01G211200 chr2D 92.105 38 1 1 4074 4109 23305994 23306031 9.000000e-03 52.8
14 TraesCS4B01G211200 chr2A 100.000 28 0 0 4082 4109 25484348 25484321 9.000000e-03 52.8


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 TraesCS4B01G211200 chr4B 449640926 449646100 5174 False 9557.000000 9557 100.000000 1 5175 1 chr4B.!!$F1 5174
1 TraesCS4B01G211200 chr4D 364540135 364545480 5345 False 2571.666667 6290 92.083333 34 5175 3 chr4D.!!$F1 5141
2 TraesCS4B01G211200 chr4A 100668877 100676039 7162 True 2455.000000 5803 90.691333 1 5175 3 chr4A.!!$R1 5174

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
49 50 0.697658 TGGGTGATGCAATCTGTGGA 59.302 50.0 0.00 0.00 45.81 4.02 F
1407 1794 0.247460 TCGCAAGGTGGTCTCATGAG 59.753 55.0 17.07 17.07 38.47 2.90 F
2428 2818 0.380378 TTCTGTTGCGCCAACTCAAC 59.620 50.0 18.81 10.66 43.85 3.18 F
2652 3042 0.031178 CAACAAGGCAAGCGCTTCTT 59.969 50.0 22.21 18.57 38.60 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2289 0.035725 CATTGCTCTGCAGAGGGTCA 60.036 55.0 37.86 26.81 40.61 4.02 R
2633 3023 0.031178 AAGAAGCGCTTGCCTTGTTG 59.969 50.0 30.47 0.00 40.41 3.33 R
4170 6234 0.179108 ATCAAGCGGACCGAGCTAAC 60.179 55.0 20.50 0.00 45.31 2.34 R
4603 6688 0.329931 ACCAACACCACCACAGAACA 59.670 50.0 0.00 0.00 0.00 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.697658 TGGGTGATGCAATCTGTGGA 59.302 50.000 0.00 0.00 45.81 4.02
135 148 9.877178 ATTTCTTGTCTATCTTCGTTATTCAGT 57.123 29.630 0.00 0.00 0.00 3.41
174 194 7.614583 GGATGACCCATCAATCAATCATCTATT 59.385 37.037 10.81 0.00 42.13 1.73
294 649 3.873952 GGCTCACAGGATTATGTCTTGTC 59.126 47.826 0.00 0.00 42.91 3.18
302 657 7.388776 CACAGGATTATGTCTTGTCTTTTCTCA 59.611 37.037 0.00 0.00 42.91 3.27
311 666 5.760253 GTCTTGTCTTTTCTCATGTTCTCCA 59.240 40.000 0.00 0.00 0.00 3.86
342 701 5.269554 TCAAATGGACAAATAGGTTCCCT 57.730 39.130 0.00 0.00 37.71 4.20
343 702 5.650283 TCAAATGGACAAATAGGTTCCCTT 58.350 37.500 0.00 0.00 34.61 3.95
344 703 6.081356 TCAAATGGACAAATAGGTTCCCTTT 58.919 36.000 0.00 0.00 34.61 3.11
345 704 6.556874 TCAAATGGACAAATAGGTTCCCTTTT 59.443 34.615 0.00 0.00 34.61 2.27
346 705 6.605471 AATGGACAAATAGGTTCCCTTTTC 57.395 37.500 0.00 0.00 34.61 2.29
383 742 1.766496 GGGGAAAGATGGTCCGATGTA 59.234 52.381 0.00 0.00 35.86 2.29
457 816 1.721489 CGTGCGTTGTACTTGTGCATC 60.721 52.381 0.00 0.00 37.93 3.91
460 819 1.531149 GCGTTGTACTTGTGCATCACT 59.469 47.619 0.00 0.00 35.11 3.41
461 820 2.734606 GCGTTGTACTTGTGCATCACTA 59.265 45.455 0.00 0.00 35.11 2.74
462 821 3.423123 GCGTTGTACTTGTGCATCACTAC 60.423 47.826 0.00 0.00 35.11 2.73
463 822 3.987868 CGTTGTACTTGTGCATCACTACT 59.012 43.478 0.00 0.00 35.11 2.57
464 823 5.158494 CGTTGTACTTGTGCATCACTACTA 58.842 41.667 0.00 0.00 35.11 1.82
465 824 5.805486 CGTTGTACTTGTGCATCACTACTAT 59.195 40.000 0.00 0.00 35.11 2.12
466 825 6.970613 CGTTGTACTTGTGCATCACTACTATA 59.029 38.462 0.00 0.00 35.11 1.31
524 886 7.492669 CACTAATATATGAATAGCTTCACCCCG 59.507 40.741 0.00 0.00 43.92 5.73
539 901 1.454539 CCCGACCTCCCAACTTTGT 59.545 57.895 0.00 0.00 0.00 2.83
548 910 3.031013 CTCCCAACTTTGTTGTTCCCTT 58.969 45.455 9.20 0.00 0.00 3.95
556 919 6.121776 ACTTTGTTGTTCCCTTTTCCTTTT 57.878 33.333 0.00 0.00 0.00 2.27
643 1008 4.767255 CCGACCAGCTGAGGGCAC 62.767 72.222 17.39 0.00 44.79 5.01
664 1029 2.800544 CGGGGACACGTCATAAATCATC 59.199 50.000 0.00 0.00 0.00 2.92
666 1031 4.196193 GGGGACACGTCATAAATCATCAA 58.804 43.478 0.00 0.00 0.00 2.57
667 1032 4.035208 GGGGACACGTCATAAATCATCAAC 59.965 45.833 0.00 0.00 0.00 3.18
678 1043 2.219216 ATCATCAACCCAGGATCCCT 57.781 50.000 8.55 0.00 0.00 4.20
763 1129 8.387354 CAACACAATATTAAATCTGTACAGCGA 58.613 33.333 18.45 2.32 0.00 4.93
764 1130 7.906160 ACACAATATTAAATCTGTACAGCGAC 58.094 34.615 18.45 0.00 0.00 5.19
784 1153 3.415212 ACACTGTGTGCTATTGCTGATT 58.585 40.909 13.50 0.00 40.48 2.57
790 1159 6.313905 ACTGTGTGCTATTGCTGATTACTAAC 59.686 38.462 0.00 0.00 40.48 2.34
791 1160 5.290885 TGTGTGCTATTGCTGATTACTAACG 59.709 40.000 0.00 0.00 40.48 3.18
813 1182 3.490249 GCCGGTTAATTTGTATTCTGGCC 60.490 47.826 1.90 0.00 35.47 5.36
824 1193 2.664402 ATTCTGGCCGGCAGAAATAT 57.336 45.000 33.45 19.31 41.34 1.28
830 1199 2.360801 TGGCCGGCAGAAATATAAAAGC 59.639 45.455 30.85 5.62 0.00 3.51
832 1201 3.304726 GGCCGGCAGAAATATAAAAGCTC 60.305 47.826 30.85 0.00 0.00 4.09
834 1203 4.137543 CCGGCAGAAATATAAAAGCTCCT 58.862 43.478 0.00 0.00 0.00 3.69
857 1244 2.614057 GTTTGACTGAATATGAGCCCCG 59.386 50.000 0.00 0.00 0.00 5.73
874 1261 3.214328 CCCCGGGATTTAAGAGATTGTG 58.786 50.000 26.32 0.00 0.00 3.33
919 1306 7.454380 TGTTGAACCTTTCAGGATATTGGATTT 59.546 33.333 0.00 0.00 41.38 2.17
931 1318 5.765182 GGATATTGGATTTAGTCAGGTGGTG 59.235 44.000 0.00 0.00 0.00 4.17
954 1341 3.334583 TTCTCCTGTTGCTCATACACC 57.665 47.619 0.00 0.00 0.00 4.16
961 1348 4.813161 CCTGTTGCTCATACACCAGATAAG 59.187 45.833 0.00 0.00 32.20 1.73
1068 1455 0.878523 CAAGCCGTGAAGGTCGTCAA 60.879 55.000 0.00 0.00 43.70 3.18
1083 1470 3.187842 GTCGTCAAAGGGGTAATTCACAC 59.812 47.826 0.00 0.00 0.00 3.82
1089 1476 5.014123 TCAAAGGGGTAATTCACACTCAGAT 59.986 40.000 0.00 0.00 0.00 2.90
1107 1494 4.631377 TCAGATCAATTAGTGCAAGTTCCG 59.369 41.667 0.00 0.00 0.00 4.30
1113 1500 1.795768 TAGTGCAAGTTCCGAAGCAG 58.204 50.000 0.00 0.00 37.72 4.24
1311 1698 4.922206 AGCATATGTCCAAAGTTCCTTCA 58.078 39.130 4.29 0.00 0.00 3.02
1407 1794 0.247460 TCGCAAGGTGGTCTCATGAG 59.753 55.000 17.07 17.07 38.47 2.90
1424 1811 1.614903 TGAGCAAAAACATGAGCCCTG 59.385 47.619 0.00 0.00 0.00 4.45
1583 1970 1.458827 GAAGTCTCAGCAAAGCAGTCG 59.541 52.381 0.00 0.00 0.00 4.18
1705 2092 4.475345 TGGTAACAGTGGTGGCTTAAATT 58.525 39.130 0.00 0.00 46.17 1.82
1824 2214 2.550855 GGAGGCTGTTCATCACTGTTCA 60.551 50.000 0.00 0.00 0.00 3.18
1899 2289 3.673902 TGACGATGATTCCATGTGTGTT 58.326 40.909 0.00 0.00 32.09 3.32
1948 2338 2.395654 GTCTAATACCTAGCGCTGTGC 58.604 52.381 22.90 4.76 46.98 4.57
1971 2361 3.243839 TGGAAACAGAAAGAAATGGCAGC 60.244 43.478 0.00 0.00 35.01 5.25
1973 2363 3.375782 AACAGAAAGAAATGGCAGCAC 57.624 42.857 0.00 0.00 0.00 4.40
1983 2373 2.591715 GGCAGCACGTCACCTGTT 60.592 61.111 0.00 0.00 0.00 3.16
2034 2424 6.476378 CCCTGAATTTCCTCGTATTCCATAT 58.524 40.000 0.00 0.00 31.29 1.78
2101 2491 4.824537 CCAGTAGCTCTGCAACTAGAGATA 59.175 45.833 6.95 2.08 45.61 1.98
2110 2500 7.095017 GCTCTGCAACTAGAGATACTTTTGTTT 60.095 37.037 6.95 0.00 45.61 2.83
2126 2516 3.857549 TGTTTGTGCAGCTGTAACAAA 57.142 38.095 29.99 29.99 40.49 2.83
2134 2524 3.445450 TGCAGCTGTAACAAAAGGTGAAA 59.555 39.130 16.64 0.00 43.06 2.69
2226 2616 2.541120 GGATGTGCTGCCTGATCGC 61.541 63.158 0.00 0.00 0.00 4.58
2229 2619 3.503363 GTGCTGCCTGATCGCCAC 61.503 66.667 0.00 0.00 0.00 5.01
2251 2641 2.205022 TGTTTCTGGGCTGAATGGAG 57.795 50.000 0.00 0.00 0.00 3.86
2254 2644 1.361204 TTCTGGGCTGAATGGAGTGA 58.639 50.000 0.00 0.00 0.00 3.41
2255 2645 1.361204 TCTGGGCTGAATGGAGTGAA 58.639 50.000 0.00 0.00 0.00 3.18
2289 2679 1.558756 CTGAAGGAAGCACCATCTCCT 59.441 52.381 6.71 0.00 42.04 3.69
2352 2742 2.544685 CGATCAAACAGCAGAGGTAGG 58.455 52.381 0.00 0.00 0.00 3.18
2391 2781 9.225682 AGGAGGATGTTAGATCCACTATTAAAA 57.774 33.333 11.08 0.00 40.61 1.52
2401 2791 7.816411 AGATCCACTATTAAAACCTAGGCAAT 58.184 34.615 9.30 6.24 0.00 3.56
2418 2808 2.730090 GCAATCATCCACTTCTGTTGCG 60.730 50.000 0.00 0.00 32.42 4.85
2423 2813 1.008538 CCACTTCTGTTGCGCCAAC 60.009 57.895 4.18 10.34 43.78 3.77
2428 2818 0.380378 TTCTGTTGCGCCAACTCAAC 59.620 50.000 18.81 10.66 43.85 3.18
2459 2849 4.335315 TGTTCCAAAGTGTCATCTGTCAAC 59.665 41.667 0.00 0.00 0.00 3.18
2462 2852 3.631686 CCAAAGTGTCATCTGTCAACCAA 59.368 43.478 0.00 0.00 0.00 3.67
2496 2886 4.846168 ATCTCTTAACTTGGAAGGGTCC 57.154 45.455 0.00 0.00 45.21 4.46
2633 3023 4.937201 ACCAAGAAAGGGATTCAACAAC 57.063 40.909 0.00 0.00 40.72 3.32
2652 3042 0.031178 CAACAAGGCAAGCGCTTCTT 59.969 50.000 22.21 18.57 38.60 2.52
2772 3162 4.712476 AGGATGATCTGGAAAGTGCATAC 58.288 43.478 0.00 0.00 0.00 2.39
2850 3240 7.965107 GCAGGTAATAAGAACAAGAAACATCAG 59.035 37.037 0.00 0.00 0.00 2.90
2851 3241 9.003658 CAGGTAATAAGAACAAGAAACATCAGT 57.996 33.333 0.00 0.00 0.00 3.41
3041 3431 0.179045 AGCGCAGTTCCTCAAACAGT 60.179 50.000 11.47 0.00 40.56 3.55
3047 3437 4.084328 CGCAGTTCCTCAAACAGTAGAAAG 60.084 45.833 0.00 0.00 40.56 2.62
3083 3473 4.017126 TCTTCACAGAATTCTAGCCGAGA 58.983 43.478 7.86 5.75 0.00 4.04
3369 3759 2.180017 CAAACGCAGGATGGCAGC 59.820 61.111 0.00 0.00 35.86 5.25
3473 3867 4.314961 TGACATAGCAAATCAACTGACGT 58.685 39.130 0.00 0.00 0.00 4.34
3487 3881 6.282167 TCAACTGACGTTTGATGTAACCTTA 58.718 36.000 0.00 0.00 0.00 2.69
3564 3958 8.866970 TGGTTTCGTTTAAAGAAGGGTTATAT 57.133 30.769 0.00 0.00 0.00 0.86
3592 3986 5.008415 GTCGAATTCAGATCATCCATTGCTT 59.992 40.000 6.22 0.00 0.00 3.91
3609 4003 1.946283 GCTTTACTTCAGGCCTTCGCT 60.946 52.381 0.00 0.00 34.44 4.93
3630 4024 5.866092 CGCTATGTGTATAGTGATGCTTCAT 59.134 40.000 5.49 0.00 45.86 2.57
3817 4215 3.551551 ACAAGCTTGTCGCGATAAAAAC 58.448 40.909 26.36 11.43 45.59 2.43
3871 4269 3.677648 CAGTGCTGCTGGGCCAAC 61.678 66.667 8.04 3.02 41.42 3.77
4074 4478 7.094805 CCATGCAGTAACGGTATGCTTATTTAT 60.095 37.037 13.53 0.00 40.62 1.40
4157 6221 8.777413 CATTCTTATTCAGAGAAGTGTTGTTCA 58.223 33.333 0.00 0.00 36.64 3.18
4168 6232 2.797491 GTGTTGTTCACTGCAGTTTCC 58.203 47.619 18.94 8.05 43.13 3.13
4170 6234 2.423185 TGTTGTTCACTGCAGTTTCCTG 59.577 45.455 18.94 5.69 41.91 3.86
4174 6238 3.876914 TGTTCACTGCAGTTTCCTGTTAG 59.123 43.478 18.94 2.28 41.02 2.34
4186 6250 1.215647 CTGTTAGCTCGGTCCGCTT 59.784 57.895 6.34 0.00 38.86 4.68
4205 6269 2.787473 TGATTGCCCACACTTCCTAG 57.213 50.000 0.00 0.00 0.00 3.02
4247 6311 0.036765 GTCCCTGTGGCGTCATACAA 60.037 55.000 0.00 0.00 0.00 2.41
4259 6323 5.122239 TGGCGTCATACAATTTCTTCAGAAG 59.878 40.000 3.45 3.45 35.21 2.85
4272 6336 3.898529 CTTCAGAAGAAGGCAAGCTTTG 58.101 45.455 3.82 0.00 46.01 2.77
4280 6344 0.603975 AGGCAAGCTTTGTCTCGTCC 60.604 55.000 0.00 0.00 43.25 4.79
4296 6360 6.157211 GTCTCGTCCTACATTTTCTTCAGAA 58.843 40.000 0.00 0.00 0.00 3.02
4310 6374 3.701040 TCTTCAGAAAAGGCAAGCTTTGT 59.299 39.130 0.00 0.00 0.00 2.83
4322 6386 5.770162 AGGCAAGCTTTGTAAGACAAGTTAT 59.230 36.000 0.00 0.00 39.53 1.89
4323 6387 6.265422 AGGCAAGCTTTGTAAGACAAGTTATT 59.735 34.615 0.00 0.00 39.53 1.40
4324 6388 6.923508 GGCAAGCTTTGTAAGACAAGTTATTT 59.076 34.615 0.00 0.00 39.53 1.40
4459 6524 6.256539 CCGAATTACTCACTACTACTGTACGA 59.743 42.308 0.00 0.00 0.00 3.43
4505 6570 4.016444 GGCTTTATCCACACCTCATCAAA 58.984 43.478 0.00 0.00 0.00 2.69
4506 6571 4.462483 GGCTTTATCCACACCTCATCAAAA 59.538 41.667 0.00 0.00 0.00 2.44
4508 6573 6.095377 GCTTTATCCACACCTCATCAAAAAG 58.905 40.000 0.00 0.00 0.00 2.27
4509 6574 6.588719 TTTATCCACACCTCATCAAAAAGG 57.411 37.500 0.00 0.00 38.70 3.11
4510 6575 3.593442 TCCACACCTCATCAAAAAGGT 57.407 42.857 0.00 0.00 46.94 3.50
4512 6577 5.055265 TCCACACCTCATCAAAAAGGTAA 57.945 39.130 0.00 0.00 44.13 2.85
4515 6581 6.040391 TCCACACCTCATCAAAAAGGTAAAAG 59.960 38.462 0.00 0.00 44.13 2.27
4544 6610 3.194005 AGAAAAGTCTCGCCTGAAACA 57.806 42.857 0.00 0.00 0.00 2.83
4556 6622 6.701841 TCTCGCCTGAAACATATTTACAGATC 59.298 38.462 0.00 0.00 30.63 2.75
4575 6648 5.117745 CAGATCTTGTAGATATTTGCGACGG 59.882 44.000 0.00 0.00 34.53 4.79
4576 6649 4.380841 TCTTGTAGATATTTGCGACGGT 57.619 40.909 0.00 0.00 0.00 4.83
4580 6665 4.353737 TGTAGATATTTGCGACGGTACAC 58.646 43.478 0.00 0.00 0.00 2.90
4592 6677 3.179830 GACGGTACACACAGCTCTATTG 58.820 50.000 0.00 0.00 0.00 1.90
4601 6686 7.883391 ACACACAGCTCTATTGTACTACTAT 57.117 36.000 0.00 0.00 0.00 2.12
4602 6687 7.708051 ACACACAGCTCTATTGTACTACTATG 58.292 38.462 0.00 0.00 0.00 2.23
4603 6688 7.339721 ACACACAGCTCTATTGTACTACTATGT 59.660 37.037 0.00 0.00 0.00 2.29
4604 6689 7.645735 CACACAGCTCTATTGTACTACTATGTG 59.354 40.741 0.00 0.00 39.15 3.21
4605 6690 7.339721 ACACAGCTCTATTGTACTACTATGTGT 59.660 37.037 0.00 0.00 40.91 3.72
4607 6692 8.407064 ACAGCTCTATTGTACTACTATGTGTTC 58.593 37.037 0.00 0.00 0.00 3.18
4609 6694 8.625651 AGCTCTATTGTACTACTATGTGTTCTG 58.374 37.037 0.00 0.00 0.00 3.02
4610 6695 8.407064 GCTCTATTGTACTACTATGTGTTCTGT 58.593 37.037 0.00 0.00 0.00 3.41
4611 6696 9.723447 CTCTATTGTACTACTATGTGTTCTGTG 57.277 37.037 0.00 0.00 0.00 3.66
4761 6857 4.415332 TTGACGACGGCGAGCTCC 62.415 66.667 22.49 0.64 41.64 4.70
4763 6859 4.539881 GACGACGGCGAGCTCCTC 62.540 72.222 22.49 0.00 41.64 3.71
4766 6862 4.200283 GACGGCGAGCTCCTCCTG 62.200 72.222 16.62 8.64 0.00 3.86
4769 6865 4.527583 GGCGAGCTCCTCCTGCTG 62.528 72.222 8.47 0.00 41.30 4.41
4789 6891 2.101770 GCTGCTGCGATTCCTTGC 59.898 61.111 0.00 0.00 0.00 4.01
4790 6892 2.796651 CTGCTGCGATTCCTTGCC 59.203 61.111 0.00 0.00 0.00 4.52
4791 6893 3.104602 CTGCTGCGATTCCTTGCCG 62.105 63.158 0.00 0.00 0.00 5.69
5127 7244 1.592669 GGTGTGGCGGATGATCTCG 60.593 63.158 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.332686 CAGATTGCATCACCCACGATG 59.667 52.381 0.00 0.00 44.69 3.84
49 50 0.106918 TTCCTTGTTTGCGGACCAGT 60.107 50.000 0.00 0.00 0.00 4.00
198 218 8.900781 ACAACTGTACTCGTACATATACAAGAT 58.099 33.333 10.06 0.00 44.15 2.40
200 220 9.430838 GTACAACTGTACTCGTACATATACAAG 57.569 37.037 11.89 0.71 45.47 3.16
294 649 5.772825 TTTGGTGGAGAACATGAGAAAAG 57.227 39.130 0.00 0.00 0.00 2.27
342 701 4.098807 CCCGTTTCCCTCAAGAAAAGAAAA 59.901 41.667 2.22 0.00 37.40 2.29
343 702 3.634910 CCCGTTTCCCTCAAGAAAAGAAA 59.365 43.478 2.22 0.00 37.40 2.52
344 703 3.219281 CCCGTTTCCCTCAAGAAAAGAA 58.781 45.455 2.22 0.00 37.40 2.52
345 704 2.488347 CCCCGTTTCCCTCAAGAAAAGA 60.488 50.000 2.22 0.00 37.40 2.52
346 705 1.886542 CCCCGTTTCCCTCAAGAAAAG 59.113 52.381 0.00 0.00 37.49 2.27
383 742 9.710818 TCAAGGTACTAGTCCAGTATTAAATCT 57.289 33.333 0.00 0.00 41.77 2.40
524 886 2.361119 GGAACAACAAAGTTGGGAGGTC 59.639 50.000 13.71 3.92 0.00 3.85
643 1008 2.303163 TGATTTATGACGTGTCCCCG 57.697 50.000 0.00 0.00 0.00 5.73
652 1017 5.474876 GGATCCTGGGTTGATGATTTATGAC 59.525 44.000 3.84 0.00 0.00 3.06
678 1043 4.920999 TGATCACATCATTTTGTCTCCCA 58.079 39.130 0.00 0.00 33.59 4.37
763 1129 2.549064 TCAGCAATAGCACACAGTGT 57.451 45.000 0.00 0.00 45.49 3.55
764 1130 4.633126 AGTAATCAGCAATAGCACACAGTG 59.367 41.667 0.00 0.00 45.49 3.66
769 1135 4.270084 GCGTTAGTAATCAGCAATAGCACA 59.730 41.667 0.00 0.00 45.49 4.57
784 1153 7.010367 CAGAATACAAATTAACCGGCGTTAGTA 59.990 37.037 6.01 0.00 35.88 1.82
790 1159 3.790789 GCCAGAATACAAATTAACCGGCG 60.791 47.826 0.00 0.00 0.00 6.46
791 1160 3.490249 GGCCAGAATACAAATTAACCGGC 60.490 47.826 0.00 0.00 35.05 6.13
813 1182 5.066505 ACAAGGAGCTTTTATATTTCTGCCG 59.933 40.000 0.00 0.00 0.00 5.69
824 1193 6.959639 ATTCAGTCAAACAAGGAGCTTTTA 57.040 33.333 0.00 0.00 0.00 1.52
830 1199 5.065731 GGCTCATATTCAGTCAAACAAGGAG 59.934 44.000 0.00 0.00 0.00 3.69
832 1201 4.096984 GGGCTCATATTCAGTCAAACAAGG 59.903 45.833 0.00 0.00 0.00 3.61
834 1203 4.016444 GGGGCTCATATTCAGTCAAACAA 58.984 43.478 0.00 0.00 0.00 2.83
857 1244 5.952347 AGGAAACCACAATCTCTTAAATCCC 59.048 40.000 0.00 0.00 0.00 3.85
874 1261 6.805713 TCAACAGAAAAAGATTCAGGAAACC 58.194 36.000 0.00 0.00 0.00 3.27
919 1306 3.791320 AGGAGAAATCACCACCTGACTA 58.209 45.455 0.00 0.00 0.00 2.59
931 1318 4.333926 GGTGTATGAGCAACAGGAGAAATC 59.666 45.833 0.00 0.00 0.00 2.17
954 1341 5.437289 TGCACACCTTTTCAACTTATCTG 57.563 39.130 0.00 0.00 0.00 2.90
961 1348 5.288804 ACATAACATGCACACCTTTTCAAC 58.711 37.500 0.00 0.00 0.00 3.18
1068 1455 4.536090 TGATCTGAGTGTGAATTACCCCTT 59.464 41.667 0.00 0.00 0.00 3.95
1083 1470 5.220548 CGGAACTTGCACTAATTGATCTGAG 60.221 44.000 0.00 0.00 0.00 3.35
1089 1476 3.188460 GCTTCGGAACTTGCACTAATTGA 59.812 43.478 0.00 0.00 0.00 2.57
1107 1494 0.739112 CTGCCGAGTCCTTCTGCTTC 60.739 60.000 0.00 0.00 37.00 3.86
1113 1500 2.125350 CTGGCTGCCGAGTCCTTC 60.125 66.667 14.98 0.00 0.00 3.46
1311 1698 3.555956 CCGTCTCTTTGCGCTGTAAATAT 59.444 43.478 9.73 0.00 0.00 1.28
1407 1794 2.672195 GCTACAGGGCTCATGTTTTTGC 60.672 50.000 0.00 0.00 32.02 3.68
1583 1970 2.571212 TCTCATGGTGTTTGTCCACAC 58.429 47.619 0.00 0.00 45.54 3.82
1694 2081 3.831715 ACTCGCTGAAATTTAAGCCAC 57.168 42.857 19.94 0.00 35.98 5.01
1705 2092 0.036306 GGGGGAGAAAACTCGCTGAA 59.964 55.000 12.48 0.00 36.66 3.02
1824 2214 2.778299 TCATCTGTAAAAAGCCTGCGT 58.222 42.857 0.00 0.00 0.00 5.24
1899 2289 0.035725 CATTGCTCTGCAGAGGGTCA 60.036 55.000 37.86 26.81 40.61 4.02
1941 2331 0.662619 TTTCTGTTTCCAGCACAGCG 59.337 50.000 0.00 0.00 41.37 5.18
1948 2338 4.553323 CTGCCATTTCTTTCTGTTTCCAG 58.447 43.478 0.00 0.00 40.25 3.86
1971 2361 1.663695 AGAAACCAACAGGTGACGTG 58.336 50.000 3.43 3.43 35.32 4.49
1973 2363 1.333619 CCAAGAAACCAACAGGTGACG 59.666 52.381 0.00 0.00 35.32 4.35
1983 2373 3.627237 GGCCAATATCCTCCAAGAAACCA 60.627 47.826 0.00 0.00 0.00 3.67
2034 2424 1.667595 TGATGGGGAGTGGACATGAA 58.332 50.000 0.00 0.00 0.00 2.57
2101 2491 4.173256 GTTACAGCTGCACAAACAAAAGT 58.827 39.130 15.27 0.00 0.00 2.66
2110 2500 2.098934 CACCTTTTGTTACAGCTGCACA 59.901 45.455 15.27 14.50 0.00 4.57
2126 2516 3.624410 GTGTCTGTTACCGTTTTCACCTT 59.376 43.478 0.00 0.00 0.00 3.50
2134 2524 4.062991 GGAGATTTGTGTCTGTTACCGTT 58.937 43.478 0.00 0.00 0.00 4.44
2178 2568 5.879223 AGTGAACTTTGAGCTAATCATGAGG 59.121 40.000 0.09 0.00 37.89 3.86
2182 2572 9.053840 CATATCAGTGAACTTTGAGCTAATCAT 57.946 33.333 0.00 0.00 37.89 2.45
2226 2616 0.178992 TCAGCCCAGAAACAAGGTGG 60.179 55.000 0.00 0.00 0.00 4.61
2229 2619 1.547372 CCATTCAGCCCAGAAACAAGG 59.453 52.381 0.00 0.00 0.00 3.61
2254 2644 4.138183 TCCTTCAGGCTAGAGCATCTGTT 61.138 47.826 3.54 0.00 44.36 3.16
2255 2645 2.625352 TCCTTCAGGCTAGAGCATCTGT 60.625 50.000 3.54 0.00 44.36 3.41
2289 2679 3.371063 GAGGTGTCAGGCCGTCGA 61.371 66.667 0.00 0.00 0.00 4.20
2352 2742 2.189499 CCTCCTTAATGGGCTGCGC 61.189 63.158 10.06 10.06 36.20 6.09
2364 2754 8.798975 TTAATAGTGGATCTAACATCCTCCTT 57.201 34.615 2.39 0.00 38.95 3.36
2391 2781 3.118112 CAGAAGTGGATGATTGCCTAGGT 60.118 47.826 11.31 0.00 0.00 3.08
2401 2791 0.955428 GGCGCAACAGAAGTGGATGA 60.955 55.000 10.83 0.00 0.00 2.92
2418 2808 3.733443 ACAAATGAAGGTTGAGTTGGC 57.267 42.857 0.00 0.00 0.00 4.52
2478 2868 1.626825 CCGGACCCTTCCAAGTTAAGA 59.373 52.381 0.00 0.00 43.00 2.10
2479 2869 1.339727 CCCGGACCCTTCCAAGTTAAG 60.340 57.143 0.73 0.00 43.00 1.85
2633 3023 0.031178 AAGAAGCGCTTGCCTTGTTG 59.969 50.000 30.47 0.00 40.41 3.33
2652 3042 2.083774 CCGTTTTTCCATGCTAGCTGA 58.916 47.619 17.23 7.17 0.00 4.26
2772 3162 5.335191 GGGCTCTTCAACAGTGAATAAAGTG 60.335 44.000 0.00 0.00 42.85 3.16
2850 3240 3.951680 CCCCAACAATACTGGATACCAAC 59.048 47.826 0.00 0.00 35.85 3.77
2851 3241 3.853181 TCCCCAACAATACTGGATACCAA 59.147 43.478 0.00 0.00 35.85 3.67
3003 3393 3.737972 CGCTGATAAAAGCCCCAATTTCC 60.738 47.826 0.00 0.00 40.23 3.13
3041 3431 7.984050 GTGAAGATGATTGATGAGGACTTTCTA 59.016 37.037 0.00 0.00 0.00 2.10
3047 3437 5.668471 TCTGTGAAGATGATTGATGAGGAC 58.332 41.667 0.00 0.00 0.00 3.85
3083 3473 3.091633 AGCCAATTGGTGCTGAACTAT 57.908 42.857 25.19 0.00 36.23 2.12
3369 3759 2.123342 GAGAGCAAGTCGAATCGATGG 58.877 52.381 9.10 2.72 38.42 3.51
3447 3841 4.096833 TCAGTTGATTTGCTATGTCATGGC 59.903 41.667 13.89 13.89 37.27 4.40
3458 3852 4.290155 ACATCAAACGTCAGTTGATTTGC 58.710 39.130 10.52 0.00 41.05 3.68
3487 3881 3.945285 CGACCCTGCAAATAAATACAGGT 59.055 43.478 7.10 0.00 46.80 4.00
3564 3958 3.118665 TGGATGATCTGAATTCGACTGCA 60.119 43.478 0.04 0.00 0.00 4.41
3592 3986 2.500098 ACATAGCGAAGGCCTGAAGTAA 59.500 45.455 5.69 0.00 41.24 2.24
3609 4003 6.269769 TCCCATGAAGCATCACTATACACATA 59.730 38.462 0.00 0.00 38.69 2.29
3817 4215 8.566008 AGAGAAAAATGAAAAGAAACACATCG 57.434 30.769 0.00 0.00 0.00 3.84
3871 4269 5.702670 AGAATCGCACAAGGACCATTATATG 59.297 40.000 0.00 0.00 0.00 1.78
4168 6232 1.078759 CAAGCGGACCGAGCTAACAG 61.079 60.000 20.50 0.00 45.31 3.16
4170 6234 0.179108 ATCAAGCGGACCGAGCTAAC 60.179 55.000 20.50 0.00 45.31 2.34
4174 6238 3.093278 CAATCAAGCGGACCGAGC 58.907 61.111 20.50 0.00 0.00 5.03
4186 6250 1.985159 ACTAGGAAGTGTGGGCAATCA 59.015 47.619 0.00 0.00 33.57 2.57
4207 6271 1.078567 CTTCCTGGGAGCAGAGTGC 60.079 63.158 0.00 0.00 45.46 4.40
4209 6273 2.297129 GGCTTCCTGGGAGCAGAGT 61.297 63.158 27.65 0.00 0.00 3.24
4210 6274 2.588989 GGCTTCCTGGGAGCAGAG 59.411 66.667 27.65 2.70 0.00 3.35
4259 6323 1.195674 GACGAGACAAAGCTTGCCTTC 59.804 52.381 0.00 0.00 31.99 3.46
4266 6330 3.963428 AATGTAGGACGAGACAAAGCT 57.037 42.857 0.00 0.00 0.00 3.74
4272 6336 5.710984 TCTGAAGAAAATGTAGGACGAGAC 58.289 41.667 0.00 0.00 0.00 3.36
4296 6360 4.402474 ACTTGTCTTACAAAGCTTGCCTTT 59.598 37.500 0.00 0.00 44.45 3.11
4322 6386 5.069318 TGCTTGGTCACATGATAGACAAAA 58.931 37.500 0.00 2.98 36.50 2.44
4323 6387 4.650734 TGCTTGGTCACATGATAGACAAA 58.349 39.130 0.00 3.69 36.50 2.83
4324 6388 4.020307 TCTGCTTGGTCACATGATAGACAA 60.020 41.667 0.00 0.00 36.50 3.18
4332 6396 1.538512 CCAGTTCTGCTTGGTCACATG 59.461 52.381 0.00 0.00 0.00 3.21
4433 6498 6.256539 CGTACAGTAGTAGTGAGTAATTCGGA 59.743 42.308 12.05 0.00 0.00 4.55
4459 6524 2.843113 AGCTAGAATTGGGAGTGAGCTT 59.157 45.455 0.00 0.00 35.30 3.74
4510 6575 9.285770 GCGAGACTTTTCTTTTCTTTTCTTTTA 57.714 29.630 0.00 0.00 29.47 1.52
4512 6577 6.752351 GGCGAGACTTTTCTTTTCTTTTCTTT 59.248 34.615 0.00 0.00 29.47 2.52
4515 6581 5.683302 CAGGCGAGACTTTTCTTTTCTTTTC 59.317 40.000 0.00 0.00 29.47 2.29
4535 6601 7.989826 ACAAGATCTGTAAATATGTTTCAGGC 58.010 34.615 0.00 7.01 36.10 4.85
4556 6622 5.038683 TGTACCGTCGCAAATATCTACAAG 58.961 41.667 0.00 0.00 0.00 3.16
4575 6648 7.086230 AGTAGTACAATAGAGCTGTGTGTAC 57.914 40.000 22.11 22.11 43.07 2.90
4576 6649 8.837389 CATAGTAGTACAATAGAGCTGTGTGTA 58.163 37.037 2.52 0.00 0.00 2.90
4580 6665 7.708051 ACACATAGTAGTACAATAGAGCTGTG 58.292 38.462 2.52 6.56 36.19 3.66
4592 6677 5.047519 ACCACCACAGAACACATAGTAGTAC 60.048 44.000 0.00 0.00 0.00 2.73
4601 6686 1.458398 CAACACCACCACAGAACACA 58.542 50.000 0.00 0.00 0.00 3.72
4602 6687 0.738389 CCAACACCACCACAGAACAC 59.262 55.000 0.00 0.00 0.00 3.32
4603 6688 0.329931 ACCAACACCACCACAGAACA 59.670 50.000 0.00 0.00 0.00 3.18
4604 6689 2.335316 TACCAACACCACCACAGAAC 57.665 50.000 0.00 0.00 0.00 3.01
4605 6690 2.857483 CATACCAACACCACCACAGAA 58.143 47.619 0.00 0.00 0.00 3.02
4607 6692 0.881118 GCATACCAACACCACCACAG 59.119 55.000 0.00 0.00 0.00 3.66
4609 6694 0.538516 TGGCATACCAACACCACCAC 60.539 55.000 0.00 0.00 45.37 4.16
4610 6695 1.846973 TGGCATACCAACACCACCA 59.153 52.632 0.00 0.00 45.37 4.17
4611 6696 4.832741 TGGCATACCAACACCACC 57.167 55.556 0.00 0.00 45.37 4.61
4761 6857 3.128188 CAGCAGCAGCAGCAGGAG 61.128 66.667 12.92 0.00 45.49 3.69
4767 6863 2.403987 GAATCGCAGCAGCAGCAG 59.596 61.111 10.77 0.00 45.49 4.24
4768 6864 3.129502 GGAATCGCAGCAGCAGCA 61.130 61.111 10.77 0.00 45.49 4.41
4769 6865 2.404995 AAGGAATCGCAGCAGCAGC 61.405 57.895 0.82 0.00 42.27 5.25
4903 7005 3.691342 CTTCGGGGACACGCAGGA 61.691 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.