Multiple sequence alignment - TraesCS1D01G176300

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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 TraesCS1D01G176300 chr1D 100.000 5710 0 0 1 5710 250741408 250747117 0.000000e+00 10545
1 TraesCS1D01G176300 chr1A 91.920 2834 141 31 355 3158 320895324 320898099 0.000000e+00 3884
2 TraesCS1D01G176300 chr1A 96.117 1777 58 10 3142 4912 320898689 320900460 0.000000e+00 2889
3 TraesCS1D01G176300 chr1A 92.222 810 40 8 4904 5710 320900519 320901308 0.000000e+00 1125
4 TraesCS1D01G176300 chr1A 96.978 364 9 2 8 371 320894951 320895312 1.360000e-170 610
5 TraesCS1D01G176300 chr1B 95.137 1748 69 12 3974 5710 363627053 363625311 0.000000e+00 2743
6 TraesCS1D01G176300 chr1B 94.856 1283 63 3 2699 3980 363628364 363627084 0.000000e+00 2001
7 TraesCS1D01G176300 chr1B 89.357 1306 70 27 786 2064 363629663 363628400 0.000000e+00 1578
8 TraesCS1D01G176300 chr1B 91.525 472 18 8 8 468 363630374 363629914 1.040000e-176 630


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 TraesCS1D01G176300 chr1D 250741408 250747117 5709 False 10545 10545 100.00000 1 5710 1 chr1D.!!$F1 5709
1 TraesCS1D01G176300 chr1A 320894951 320901308 6357 False 2127 3884 94.30925 8 5710 4 chr1A.!!$F1 5702
2 TraesCS1D01G176300 chr1B 363625311 363630374 5063 True 1738 2743 92.71875 8 5710 4 chr1B.!!$R1 5702

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
44 45 0.599558 GCAGCTTGAATGCTTGGTCA 59.400 50.0 0.00 0.00 41.98 4.02 F
389 418 0.888619 TGTCGAGACATGTCCCTGTC 59.111 55.0 22.21 12.00 44.78 3.51 F
1454 1568 0.251634 CCCCTCTCTCCTCTTGTTGC 59.748 60.0 0.00 0.00 0.00 4.17 F
1956 2093 0.179073 CTACATTGGCTCCTCACGGG 60.179 60.0 0.00 0.00 0.00 5.28 F
2228 2373 0.251341 CCTGGTTTGAAGGTCCTGGG 60.251 60.0 0.00 0.00 36.92 4.45 F
2453 2601 0.454600 TGAGATCGGCGTAGTCAACC 59.545 55.0 6.85 0.00 0.00 3.77 F
2759 2907 0.865769 CAAAAGAACGTAGTGGCGCT 59.134 50.0 7.64 5.62 45.00 5.92 F
3300 4055 1.540267 TGCCTAAACCACCAATTCGG 58.460 50.0 0.00 0.00 42.50 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 1561 0.385974 GCACTAACCGCAGCAACAAG 60.386 55.000 0.00 0.00 0.00 3.16 R
1898 2033 0.438830 GTTTGCGTCGACTCATCCAC 59.561 55.000 14.70 5.72 0.00 4.02 R
2425 2573 0.249868 CGCCGATCTCATTTAGGGCA 60.250 55.000 5.11 0.00 40.52 5.36 R
3164 3919 0.850100 ACACCCAAACTCCATGACCA 59.150 50.000 0.00 0.00 0.00 4.02 R
4199 4992 2.985896 TGTGCAAGCTATCCCAAGTAC 58.014 47.619 0.00 0.00 0.00 2.73 R
4442 5237 1.075212 TGGTCAACAGCAATGGATCCA 59.925 47.619 18.88 18.88 0.00 3.41 R
4701 5496 3.439857 TTTTTGATGCTGCTACCCTCT 57.560 42.857 0.00 0.00 0.00 3.69 R
4980 5845 1.638589 TGGGAGGGTGAAGGTTTATGG 59.361 52.381 0.00 0.00 0.00 2.74 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
43 44 3.413522 GCAGCTTGAATGCTTGGTC 57.586 52.632 0.00 0.00 41.98 4.02
44 45 0.599558 GCAGCTTGAATGCTTGGTCA 59.400 50.000 0.00 0.00 41.98 4.02
45 46 1.668047 GCAGCTTGAATGCTTGGTCAC 60.668 52.381 0.00 0.00 41.98 3.67
46 47 1.884579 CAGCTTGAATGCTTGGTCACT 59.115 47.619 0.00 0.00 41.98 3.41
302 303 8.729805 TGTACAATGTGCATTATGATGTTCTA 57.270 30.769 0.00 0.00 35.63 2.10
350 351 3.077359 AGAGCTCGTGGAAATTCCTTTG 58.923 45.455 13.78 3.21 37.46 2.77
383 412 5.403897 TGTTCTTTTTGTCGAGACATGTC 57.596 39.130 18.47 18.47 41.52 3.06
389 418 0.888619 TGTCGAGACATGTCCCTGTC 59.111 55.000 22.21 12.00 44.78 3.51
409 449 1.383523 GGATGGCTTGTTGGTAGCTC 58.616 55.000 0.00 0.00 38.67 4.09
588 639 6.521151 ACATTCAGAAAATCCAGACCATTC 57.479 37.500 0.00 0.00 0.00 2.67
608 659 6.541641 CCATTCTCGATCTGGAGATTCTTTTT 59.458 38.462 1.70 0.00 42.33 1.94
621 672 7.235193 TGGAGATTCTTTTTCAAATCCAATGGA 59.765 33.333 3.67 3.67 32.84 3.41
624 675 9.276590 AGATTCTTTTTCAAATCCAATGGAAAC 57.723 29.630 5.89 0.00 34.34 2.78
636 687 8.980481 AATCCAATGGAAACTATCGAAATAGT 57.020 30.769 5.89 0.00 40.80 2.12
643 694 9.838339 ATGGAAACTATCGAAATAGTCTTTCAT 57.162 29.630 10.55 9.19 45.92 2.57
646 697 8.664211 AAACTATCGAAATAGTCTTTCATCCC 57.336 34.615 0.00 0.00 45.92 3.85
693 744 3.934068 TCCAACGGGAATCTAACAGTTC 58.066 45.455 0.00 0.00 41.32 3.01
694 745 3.007635 CCAACGGGAATCTAACAGTTCC 58.992 50.000 0.00 0.00 42.51 3.62
695 746 2.667473 ACGGGAATCTAACAGTTCCG 57.333 50.000 7.19 7.19 43.84 4.30
696 747 2.173519 ACGGGAATCTAACAGTTCCGA 58.826 47.619 14.09 2.37 43.84 4.55
697 748 2.764572 ACGGGAATCTAACAGTTCCGAT 59.235 45.455 14.09 4.45 43.84 4.18
779 830 6.116711 TGTATGGCAACCTAGAACTGTTAA 57.883 37.500 0.00 0.00 0.00 2.01
828 927 5.597806 TGAGTGTAGTGTTCTCGTTTGAAT 58.402 37.500 0.00 0.00 0.00 2.57
883 990 1.216710 CCGAGCCAGGAGTTCTGAC 59.783 63.158 0.00 0.00 46.18 3.51
909 1016 1.253100 CTTATCTCCTCCCTCTCGCC 58.747 60.000 0.00 0.00 0.00 5.54
933 1040 2.559840 CTCTGCAGTTGCGGCTTG 59.440 61.111 14.67 0.00 46.62 4.01
940 1048 3.286751 GTTGCGGCTTGGCAGTCA 61.287 61.111 0.00 0.00 44.94 3.41
944 1052 3.357079 CGGCTTGGCAGTCACCAC 61.357 66.667 0.00 0.00 40.19 4.16
945 1053 2.985847 GGCTTGGCAGTCACCACC 60.986 66.667 0.00 0.00 40.19 4.61
946 1054 2.985847 GCTTGGCAGTCACCACCC 60.986 66.667 0.00 0.00 40.19 4.61
947 1055 2.669569 CTTGGCAGTCACCACCCG 60.670 66.667 0.00 0.00 40.19 5.28
971 1079 1.789523 CTTATCCCCTCCCGAGTTCA 58.210 55.000 0.00 0.00 0.00 3.18
1011 1119 1.282248 CGAACACCATGACGAGCGTT 61.282 55.000 0.00 0.00 0.00 4.84
1071 1179 4.753662 TCCTCCCACCTCCGGTCG 62.754 72.222 0.00 0.00 31.02 4.79
1447 1561 1.760480 GTGCCTCCCCTCTCTCCTC 60.760 68.421 0.00 0.00 0.00 3.71
1450 1564 1.048160 GCCTCCCCTCTCTCCTCTTG 61.048 65.000 0.00 0.00 0.00 3.02
1451 1565 0.338120 CCTCCCCTCTCTCCTCTTGT 59.662 60.000 0.00 0.00 0.00 3.16
1452 1566 1.273552 CCTCCCCTCTCTCCTCTTGTT 60.274 57.143 0.00 0.00 0.00 2.83
1453 1567 1.830477 CTCCCCTCTCTCCTCTTGTTG 59.170 57.143 0.00 0.00 0.00 3.33
1454 1568 0.251634 CCCCTCTCTCCTCTTGTTGC 59.748 60.000 0.00 0.00 0.00 4.17
1455 1569 1.274712 CCCTCTCTCCTCTTGTTGCT 58.725 55.000 0.00 0.00 0.00 3.91
1456 1570 1.066286 CCCTCTCTCCTCTTGTTGCTG 60.066 57.143 0.00 0.00 0.00 4.41
1459 1573 1.004560 TCTCCTCTTGTTGCTGCGG 60.005 57.895 0.00 0.00 0.00 5.69
1466 1580 0.385974 CTTGTTGCTGCGGTTAGTGC 60.386 55.000 0.00 0.00 0.00 4.40
1486 1600 1.470098 CTGCCTGCTAGAAAATTGCGT 59.530 47.619 0.00 0.00 31.64 5.24
1487 1601 2.677836 CTGCCTGCTAGAAAATTGCGTA 59.322 45.455 0.00 0.00 31.64 4.42
1489 1603 3.065233 TGCCTGCTAGAAAATTGCGTATG 59.935 43.478 0.00 0.00 31.64 2.39
1490 1604 3.312421 GCCTGCTAGAAAATTGCGTATGA 59.688 43.478 0.00 0.00 31.64 2.15
1491 1605 4.023707 GCCTGCTAGAAAATTGCGTATGAT 60.024 41.667 0.00 0.00 31.64 2.45
1492 1606 5.506317 GCCTGCTAGAAAATTGCGTATGATT 60.506 40.000 0.00 0.00 31.64 2.57
1493 1607 6.498304 CCTGCTAGAAAATTGCGTATGATTT 58.502 36.000 0.00 0.00 31.64 2.17
1494 1608 6.634436 CCTGCTAGAAAATTGCGTATGATTTC 59.366 38.462 0.00 0.00 31.64 2.17
1495 1609 7.082700 TGCTAGAAAATTGCGTATGATTTCA 57.917 32.000 0.00 0.00 33.53 2.69
1496 1610 7.188834 TGCTAGAAAATTGCGTATGATTTCAG 58.811 34.615 0.00 5.70 33.53 3.02
1497 1611 7.148255 TGCTAGAAAATTGCGTATGATTTCAGT 60.148 33.333 0.00 0.00 33.53 3.41
1515 1629 9.922305 GATTTCAGTTATATGTCAAGCAACTAC 57.078 33.333 0.00 0.00 0.00 2.73
1516 1630 9.672673 ATTTCAGTTATATGTCAAGCAACTACT 57.327 29.630 0.00 0.00 0.00 2.57
1532 1649 7.232794 AGCAACTACTAGCATGCTACTAATGC 61.233 42.308 23.52 24.72 46.61 3.56
1559 1676 3.304829 CCGGGAAATGGGGATTAATGTT 58.695 45.455 0.00 0.00 0.00 2.71
1585 1706 6.793505 AGACTCATAATAGGGTTTCGTTCT 57.206 37.500 0.00 0.00 0.00 3.01
1637 1758 7.308589 CCTTAGTCCAGTTCATAACCTTGTTTG 60.309 40.741 0.00 0.00 0.00 2.93
1638 1759 5.690865 AGTCCAGTTCATAACCTTGTTTGA 58.309 37.500 0.00 0.00 0.00 2.69
1644 1779 7.596248 CCAGTTCATAACCTTGTTTGAATTGAG 59.404 37.037 17.83 10.78 37.76 3.02
1681 1816 3.126858 TGCCTTCGCTTTATGTTCATGTC 59.873 43.478 0.00 0.00 35.36 3.06
1709 1844 7.452880 TTTCACAAGGAAATGTATGAAGAGG 57.547 36.000 0.00 0.00 40.51 3.69
1738 1873 5.123979 GCGATCATTAAAACCAACTCCTCTT 59.876 40.000 0.00 0.00 0.00 2.85
1765 1900 3.952967 GGATAGTTCTCGTACCACCTCTT 59.047 47.826 0.00 0.00 0.00 2.85
1771 1906 4.252971 TCTCGTACCACCTCTTTTTGAG 57.747 45.455 0.00 0.00 42.30 3.02
1806 1941 1.567357 TGAGGGAACGACATCATGGA 58.433 50.000 0.00 0.00 0.00 3.41
1897 2032 3.129502 CCACACATCTGGCGCCTG 61.130 66.667 29.70 27.77 0.00 4.85
1898 2033 3.129502 CACACATCTGGCGCCTGG 61.130 66.667 30.13 21.23 0.00 4.45
1899 2034 3.640407 ACACATCTGGCGCCTGGT 61.640 61.111 30.13 23.15 0.00 4.00
1956 2093 0.179073 CTACATTGGCTCCTCACGGG 60.179 60.000 0.00 0.00 0.00 5.28
1974 2111 1.135721 GGGCAATGCTCAAAGATGACC 59.864 52.381 4.82 0.00 30.76 4.02
2013 2150 7.496346 AAGGAGATCAATACAGTCCTTGTAA 57.504 36.000 8.86 0.00 44.33 2.41
2020 2157 9.277783 GATCAATACAGTCCTTGTAAATAGCAT 57.722 33.333 0.00 0.00 45.00 3.79
2073 2218 7.129457 TCATATCAGCTAGAACCAATGAGTT 57.871 36.000 0.00 0.00 0.00 3.01
2093 2238 7.097192 TGAGTTCATAAAACGAAGTCAGCTAT 58.903 34.615 6.37 0.00 45.00 2.97
2115 2260 7.989741 GCTATAACCATCTATGTTCCTATGCAT 59.010 37.037 3.79 3.79 0.00 3.96
2116 2261 9.539825 CTATAACCATCTATGTTCCTATGCATC 57.460 37.037 0.19 0.00 0.00 3.91
2121 2266 5.233083 TCTATGTTCCTATGCATCCCTTG 57.767 43.478 0.19 0.00 0.00 3.61
2169 2314 1.304713 AGCACCTTTGGCCAGATGG 60.305 57.895 5.11 12.29 38.53 3.51
2194 2339 0.322997 TCTAATTGTTGGGGTGGCCG 60.323 55.000 0.00 0.00 0.00 6.13
2206 2351 3.656280 TGGCCGGGCATTCCAGAA 61.656 61.111 29.27 0.25 34.36 3.02
2228 2373 0.251341 CCTGGTTTGAAGGTCCTGGG 60.251 60.000 0.00 0.00 36.92 4.45
2234 2379 2.190578 GAAGGTCCTGGGGCGATG 59.809 66.667 0.00 0.00 0.00 3.84
2247 2392 1.971167 GCGATGCCCAGTTGTTCCA 60.971 57.895 0.00 0.00 0.00 3.53
2271 2416 3.195698 GCATGGACTTCGGACGGC 61.196 66.667 0.00 0.00 0.00 5.68
2287 2432 1.667154 CGGCCGATGAAGAGGTGAGA 61.667 60.000 24.07 0.00 0.00 3.27
2313 2458 2.741486 TTTGGAGTAGTGGCCGCACC 62.741 60.000 20.59 15.75 39.84 5.01
2315 2460 4.065281 GAGTAGTGGCCGCACCGT 62.065 66.667 20.59 0.00 43.94 4.83
2316 2461 4.373116 AGTAGTGGCCGCACCGTG 62.373 66.667 20.59 0.00 43.94 4.94
2387 2535 3.056107 TGTTTAGACAGCCGCAGAATAGT 60.056 43.478 0.00 0.00 0.00 2.12
2425 2573 1.771255 CACCTTATTAGGAGCCCTGCT 59.229 52.381 4.40 0.00 45.05 4.24
2453 2601 0.454600 TGAGATCGGCGTAGTCAACC 59.545 55.000 6.85 0.00 0.00 3.77
2456 2604 0.454600 GATCGGCGTAGTCAACCTCA 59.545 55.000 6.85 0.00 0.00 3.86
2472 2620 1.277273 CCTCACTGTCCTCATGCAAGA 59.723 52.381 0.00 0.00 0.00 3.02
2509 2657 2.194326 GGAGGAGAAGCCATGGCC 59.806 66.667 33.14 18.87 43.17 5.36
2510 2658 2.683465 GGAGGAGAAGCCATGGCCA 61.683 63.158 33.14 8.56 43.17 5.36
2597 2745 1.000506 TCTAGCTCGTTTGACACCACC 59.999 52.381 0.00 0.00 0.00 4.61
2656 2804 2.996621 GTTTCAAGATCACGGAGACCAG 59.003 50.000 0.00 0.00 0.00 4.00
2659 2807 3.099905 TCAAGATCACGGAGACCAGAAT 58.900 45.455 0.00 0.00 0.00 2.40
2681 2829 3.319972 TGTCAGTGCGTAAGTAAGGAGTT 59.680 43.478 0.00 0.00 41.68 3.01
2706 2854 3.264964 TGTATAGGTTCGGGAAGGCTTTT 59.735 43.478 0.00 0.00 0.00 2.27
2748 2896 2.288395 CCAGGTGTCATGCCAAAAGAAC 60.288 50.000 0.00 0.00 0.00 3.01
2756 2904 3.767287 GCCAAAAGAACGTAGTGGC 57.233 52.632 10.78 10.78 45.00 5.01
2759 2907 0.865769 CAAAAGAACGTAGTGGCGCT 59.134 50.000 7.64 5.62 45.00 5.92
2771 2919 2.050985 GGCGCTGCAGTTTGTGAC 60.051 61.111 16.64 0.00 0.00 3.67
2851 2999 3.289834 CCTGCTGCGGTTGCTTGT 61.290 61.111 7.82 0.00 43.34 3.16
2879 3027 1.881973 CTGTGGATGTCAAGTTGTGGG 59.118 52.381 2.11 0.00 0.00 4.61
2994 3142 3.415087 CCCCTGCCTTCCTCTGGG 61.415 72.222 0.00 0.00 40.99 4.45
3076 3224 2.086610 AAATGTTCAGGTGGGCTTGT 57.913 45.000 0.00 0.00 0.00 3.16
3084 3232 2.597510 GTGGGCTTGTGGTGACCC 60.598 66.667 0.00 0.00 43.14 4.46
3164 3919 2.798445 GAAGGTTTTGCCCGGGGGAT 62.798 60.000 25.28 0.00 38.26 3.85
3247 4002 7.359181 CGGAAAGGATTTTGAAGGAAAAATTCG 60.359 37.037 0.00 0.00 39.27 3.34
3300 4055 1.540267 TGCCTAAACCACCAATTCGG 58.460 50.000 0.00 0.00 42.50 4.30
3437 4192 4.811557 CCCGGAGAGAGAAAATCAACATAC 59.188 45.833 0.73 0.00 0.00 2.39
3438 4193 4.504461 CCGGAGAGAGAAAATCAACATACG 59.496 45.833 0.00 0.00 0.00 3.06
3624 4379 2.552315 TGTGGGAAAGAAGAAACATCGC 59.448 45.455 0.00 0.00 0.00 4.58
3844 4600 3.221771 TGGACTGGGTGAATTTGTGAAG 58.778 45.455 0.00 0.00 0.00 3.02
4100 4893 4.933400 TGTTTGTCCTCGAAGTAATTAGCC 59.067 41.667 0.00 0.00 0.00 3.93
4122 4915 6.946009 AGCCTACTTTGGATATCTCTAGAGTC 59.054 42.308 19.21 9.69 31.14 3.36
4199 4992 3.945921 TGTGTCCTTGTATCCGAGTCTAG 59.054 47.826 0.00 0.00 0.00 2.43
4237 5030 6.899393 TGCACAAAAATGTTCCTTCTATCT 57.101 33.333 0.00 0.00 0.00 1.98
4246 5041 9.449719 AAAATGTTCCTTCTATCTATTTCGTGT 57.550 29.630 0.00 0.00 0.00 4.49
4294 5089 5.948758 TGTATGGTTTGGTGCATCTTAATCA 59.051 36.000 0.00 0.00 0.00 2.57
4391 5186 7.048629 TCAACAACAGCTAAAAATTCATGGA 57.951 32.000 0.00 0.00 0.00 3.41
4442 5237 2.431057 ACGACAACTTGAGGAGTCAACT 59.569 45.455 0.00 0.00 37.79 3.16
4526 5321 6.569418 GCAAGATGAAAAAGAGGGAAGAAGTC 60.569 42.308 0.00 0.00 0.00 3.01
4538 5333 3.056749 GGGAAGAAGTCGCTAGAAACAGA 60.057 47.826 0.00 0.00 36.28 3.41
4562 5357 5.352569 AGAAGAGTATGCAAGAAACAATCCG 59.647 40.000 0.00 0.00 0.00 4.18
4701 5496 0.249120 CAAGGGGTCGTCATACAGCA 59.751 55.000 0.00 0.00 0.00 4.41
4717 5512 0.979709 AGCAGAGGGTAGCAGCATCA 60.980 55.000 0.00 0.00 0.00 3.07
4732 5527 9.956720 GTAGCAGCATCAAAAATAATAGATTGT 57.043 29.630 0.00 0.00 0.00 2.71
4766 5562 9.645128 ATTGTATGGAGGAATCATGTAAATTGA 57.355 29.630 0.00 0.00 0.00 2.57
4767 5563 8.681486 TGTATGGAGGAATCATGTAAATTGAG 57.319 34.615 0.00 0.00 0.00 3.02
4768 5564 8.493607 TGTATGGAGGAATCATGTAAATTGAGA 58.506 33.333 0.00 0.00 0.00 3.27
4769 5565 7.814264 ATGGAGGAATCATGTAAATTGAGAC 57.186 36.000 0.00 0.00 0.00 3.36
4823 5621 5.137551 AGTTTGTGCTAGTAACCATGGTTT 58.862 37.500 34.04 20.17 39.31 3.27
4903 5701 6.401796 CCTTTTATTCGGTTGGAAGTTCGTAG 60.402 42.308 0.00 0.00 38.24 3.51
4921 5785 8.192110 AGTTCGTAGGATCTACTTGAGAATTTC 58.808 37.037 0.00 0.00 37.85 2.17
4950 5815 2.742053 AGACAACCAATGATGTGCGTAC 59.258 45.455 0.00 0.00 0.00 3.67
4955 5820 2.092968 ACCAATGATGTGCGTACCTCAT 60.093 45.455 16.41 16.41 41.87 2.90
4972 5837 4.946157 ACCTCATCTATTCCAGCAAGTTTG 59.054 41.667 0.00 0.00 0.00 2.93
4973 5838 4.946157 CCTCATCTATTCCAGCAAGTTTGT 59.054 41.667 0.00 0.00 0.00 2.83
4974 5839 5.163683 CCTCATCTATTCCAGCAAGTTTGTG 60.164 44.000 0.00 0.00 0.00 3.33
4976 5841 4.098914 TCTATTCCAGCAAGTTTGTGGT 57.901 40.909 10.90 0.00 33.75 4.16
4978 5843 3.733443 ATTCCAGCAAGTTTGTGGTTC 57.267 42.857 10.90 0.00 33.75 3.62
4979 5844 2.136298 TCCAGCAAGTTTGTGGTTCA 57.864 45.000 10.90 0.00 33.75 3.18
4980 5845 1.748493 TCCAGCAAGTTTGTGGTTCAC 59.252 47.619 10.90 0.00 33.75 3.18
4982 5847 1.476085 CAGCAAGTTTGTGGTTCACCA 59.524 47.619 0.00 0.00 45.30 4.17
4996 5865 3.499745 GGTTCACCATAAACCTTCACCCT 60.500 47.826 0.00 0.00 42.42 4.34
5020 5889 7.421853 CCTCCCATCTCTTTATTATGGTCCTTT 60.422 40.741 0.00 0.00 38.83 3.11
5137 6006 5.171476 TGCTTCTATGTCTGTTAGCACTTC 58.829 41.667 0.00 0.00 34.05 3.01
5174 6043 0.710567 CGTCTGCAACTTCTGTAGCG 59.289 55.000 0.00 0.00 37.65 4.26
5303 6173 3.425625 GCGCATTTGGAACGAGATAAACA 60.426 43.478 0.30 0.00 0.00 2.83
5320 6190 0.474184 ACAACTACTGGGCAGTGCTT 59.526 50.000 16.11 0.00 42.52 3.91
5345 6215 4.602340 TCCTAGTTTCACAGTTGAGACC 57.398 45.455 0.00 0.00 37.53 3.85
5353 6223 0.036952 ACAGTTGAGACCGAGGCATG 60.037 55.000 0.00 0.00 0.00 4.06
5454 6324 3.149196 GCCCATTTCTTCTTGACTGACA 58.851 45.455 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.034939 CAGCAAAGTGACCAAGCATTCA 59.965 45.455 0.00 0.00 0.00 2.57
41 42 6.142958 GCACTAAGAAAATTCAGCAAAGTGAC 59.857 38.462 0.00 0.00 35.05 3.67
42 43 6.208644 GCACTAAGAAAATTCAGCAAAGTGA 58.791 36.000 0.00 0.00 35.05 3.41
43 44 5.403466 GGCACTAAGAAAATTCAGCAAAGTG 59.597 40.000 0.00 0.00 35.94 3.16
44 45 5.302823 AGGCACTAAGAAAATTCAGCAAAGT 59.697 36.000 0.00 0.00 36.02 2.66
45 46 5.776744 AGGCACTAAGAAAATTCAGCAAAG 58.223 37.500 0.00 0.00 36.02 2.77
46 47 5.562696 CGAGGCACTAAGAAAATTCAGCAAA 60.563 40.000 0.00 0.00 41.55 3.68
374 403 2.579878 TCCGACAGGGACATGTCTC 58.420 57.895 24.50 21.73 46.04 3.36
383 412 1.002134 AACAAGCCATCCGACAGGG 60.002 57.895 0.00 0.00 38.33 4.45
389 418 0.392998 AGCTACCAACAAGCCATCCG 60.393 55.000 0.00 0.00 41.02 4.18
409 449 3.313249 TGAAGATGAACAACAGTGCACAG 59.687 43.478 21.04 14.44 0.00 3.66
482 533 0.542805 TATACTTTGGGTCCCCGCAC 59.457 55.000 5.13 0.00 39.42 5.34
568 619 4.937620 CGAGAATGGTCTGGATTTTCTGAA 59.062 41.667 0.00 0.00 32.80 3.02
588 639 6.974932 TTGAAAAAGAATCTCCAGATCGAG 57.025 37.500 0.00 0.00 32.75 4.04
608 659 7.695480 TTTCGATAGTTTCCATTGGATTTGA 57.305 32.000 6.15 0.00 37.40 2.69
621 672 7.438459 CGGGATGAAAGACTATTTCGATAGTTT 59.562 37.037 0.44 0.00 37.48 2.66
624 675 5.346281 GCGGGATGAAAGACTATTTCGATAG 59.654 44.000 0.00 0.00 0.00 2.08
655 706 6.183360 CCCGTTGGATTCAGTTATTTGTCTAC 60.183 42.308 0.00 0.00 0.00 2.59
660 711 5.637006 TTCCCGTTGGATTCAGTTATTTG 57.363 39.130 0.00 0.00 41.40 2.32
684 735 5.805994 GGAACTGTTAGATCGGAACTGTTAG 59.194 44.000 24.83 13.57 44.21 2.34
685 736 5.620654 CGGAACTGTTAGATCGGAACTGTTA 60.621 44.000 24.83 5.50 44.21 2.41
686 737 4.566987 GGAACTGTTAGATCGGAACTGTT 58.433 43.478 24.95 24.95 45.76 3.16
687 738 3.367087 CGGAACTGTTAGATCGGAACTGT 60.367 47.826 15.51 15.51 39.70 3.55
688 739 3.179830 CGGAACTGTTAGATCGGAACTG 58.820 50.000 14.58 14.58 33.39 3.16
689 740 2.824341 ACGGAACTGTTAGATCGGAACT 59.176 45.455 12.82 0.00 0.00 3.01
690 741 3.227810 ACGGAACTGTTAGATCGGAAC 57.772 47.619 6.60 6.60 0.00 3.62
691 742 4.641541 TCATACGGAACTGTTAGATCGGAA 59.358 41.667 0.00 0.00 0.00 4.30
692 743 4.201657 TCATACGGAACTGTTAGATCGGA 58.798 43.478 0.00 0.00 0.00 4.55
693 744 4.563337 TCATACGGAACTGTTAGATCGG 57.437 45.455 0.00 0.00 0.00 4.18
694 745 7.435488 AGAATTTCATACGGAACTGTTAGATCG 59.565 37.037 0.00 0.00 34.56 3.69
695 746 8.649973 AGAATTTCATACGGAACTGTTAGATC 57.350 34.615 0.00 0.00 34.56 2.75
696 747 8.478877 AGAGAATTTCATACGGAACTGTTAGAT 58.521 33.333 0.00 0.00 34.56 1.98
697 748 7.837863 AGAGAATTTCATACGGAACTGTTAGA 58.162 34.615 0.00 0.00 34.56 2.10
779 830 1.132262 CGCTGTTTGTTGTCAACAGGT 59.868 47.619 17.49 0.00 43.27 4.00
828 927 2.094182 GTCTGATAGAAGTTCGGTGCCA 60.094 50.000 0.00 0.00 0.00 4.92
883 990 3.323403 AGAGGGAGGAGATAAGCAATTCG 59.677 47.826 0.00 0.00 0.00 3.34
931 1038 4.947147 GCGGGTGGTGACTGCCAA 62.947 66.667 0.00 0.00 40.68 4.52
940 1048 2.590092 GATAAGCAGGCGGGTGGT 59.410 61.111 0.00 0.00 0.00 4.16
942 1050 2.203209 GGGATAAGCAGGCGGGTG 60.203 66.667 0.00 0.00 0.00 4.61
943 1051 3.489513 GGGGATAAGCAGGCGGGT 61.490 66.667 0.00 0.00 0.00 5.28
944 1052 3.171388 AGGGGATAAGCAGGCGGG 61.171 66.667 0.00 0.00 0.00 6.13
945 1053 2.427753 GAGGGGATAAGCAGGCGG 59.572 66.667 0.00 0.00 0.00 6.13
946 1054 2.427753 GGAGGGGATAAGCAGGCG 59.572 66.667 0.00 0.00 0.00 5.52
947 1055 2.839836 GGGAGGGGATAAGCAGGC 59.160 66.667 0.00 0.00 0.00 4.85
1049 1157 2.781406 GGAGGTGGGAGGAGAGGT 59.219 66.667 0.00 0.00 0.00 3.85
1190 1304 4.207281 CCTCTTCATCCGCCGCGA 62.207 66.667 15.93 0.32 0.00 5.87
1447 1561 0.385974 GCACTAACCGCAGCAACAAG 60.386 55.000 0.00 0.00 0.00 3.16
1450 1564 1.207593 CAGCACTAACCGCAGCAAC 59.792 57.895 0.00 0.00 0.00 4.17
1451 1565 2.616330 GCAGCACTAACCGCAGCAA 61.616 57.895 0.00 0.00 41.13 3.91
1452 1566 3.049674 GCAGCACTAACCGCAGCA 61.050 61.111 0.00 0.00 41.13 4.41
1453 1567 3.804193 GGCAGCACTAACCGCAGC 61.804 66.667 0.00 0.00 40.79 5.25
1454 1568 2.046892 AGGCAGCACTAACCGCAG 60.047 61.111 0.00 0.00 0.00 5.18
1455 1569 2.358615 CAGGCAGCACTAACCGCA 60.359 61.111 0.00 0.00 0.00 5.69
1456 1570 3.804193 GCAGGCAGCACTAACCGC 61.804 66.667 0.00 0.00 44.79 5.68
1466 1580 1.470098 ACGCAATTTTCTAGCAGGCAG 59.530 47.619 0.00 0.00 0.00 4.85
1487 1601 9.182214 AGTTGCTTGACATATAACTGAAATCAT 57.818 29.630 0.00 0.00 31.00 2.45
1489 1603 9.922305 GTAGTTGCTTGACATATAACTGAAATC 57.078 33.333 0.00 0.00 33.93 2.17
1490 1604 9.672673 AGTAGTTGCTTGACATATAACTGAAAT 57.327 29.630 0.00 0.00 33.93 2.17
1492 1606 9.803315 CTAGTAGTTGCTTGACATATAACTGAA 57.197 33.333 0.00 0.00 33.93 3.02
1493 1607 7.921214 GCTAGTAGTTGCTTGACATATAACTGA 59.079 37.037 0.00 0.00 33.93 3.41
1494 1608 7.706607 TGCTAGTAGTTGCTTGACATATAACTG 59.293 37.037 5.59 0.00 33.93 3.16
1495 1609 7.782049 TGCTAGTAGTTGCTTGACATATAACT 58.218 34.615 5.59 0.00 35.86 2.24
1496 1610 8.491152 CATGCTAGTAGTTGCTTGACATATAAC 58.509 37.037 12.48 0.00 36.75 1.89
1497 1611 7.171508 GCATGCTAGTAGTTGCTTGACATATAA 59.828 37.037 19.23 0.00 36.75 0.98
1532 1649 2.489275 CCCCATTTCCCGGCGAATG 61.489 63.158 9.30 16.74 33.97 2.67
1559 1676 9.584008 AGAACGAAACCCTATTATGAGTCTATA 57.416 33.333 0.00 0.00 0.00 1.31
1585 1706 3.961849 TGGTTGCTATGCACCTGATAAA 58.038 40.909 0.00 0.00 38.71 1.40
1637 1758 1.795768 TCTCGGCACACACTCAATTC 58.204 50.000 0.00 0.00 0.00 2.17
1638 1759 1.873591 GTTCTCGGCACACACTCAATT 59.126 47.619 0.00 0.00 0.00 2.32
1644 1779 2.607892 GGCAGTTCTCGGCACACAC 61.608 63.158 0.00 0.00 36.53 3.82
1709 1844 4.098416 GTTGGTTTTAATGATCGCTGCTC 58.902 43.478 0.00 0.00 0.00 4.26
1738 1873 5.895534 AGGTGGTACGAGAACTATCCAATAA 59.104 40.000 0.00 0.00 0.00 1.40
1765 1900 4.751767 AAAAACATGCAGGTCCTCAAAA 57.248 36.364 3.65 0.00 0.00 2.44
1830 1965 6.016777 GTGCCTTTCCTCATGGATAATGTAAG 60.017 42.308 0.00 0.00 42.81 2.34
1893 2028 1.153549 GTCGACTCATCCACCAGGC 60.154 63.158 8.70 0.00 33.74 4.85
1894 2029 1.139734 CGTCGACTCATCCACCAGG 59.860 63.158 14.70 0.00 0.00 4.45
1895 2030 1.517257 GCGTCGACTCATCCACCAG 60.517 63.158 14.70 0.00 0.00 4.00
1896 2031 1.811645 TTGCGTCGACTCATCCACCA 61.812 55.000 14.70 0.00 0.00 4.17
1897 2032 0.669318 TTTGCGTCGACTCATCCACC 60.669 55.000 14.70 0.00 0.00 4.61
1898 2033 0.438830 GTTTGCGTCGACTCATCCAC 59.561 55.000 14.70 5.72 0.00 4.02
1899 2034 0.669318 GGTTTGCGTCGACTCATCCA 60.669 55.000 14.70 0.00 0.00 3.41
1974 2111 3.766545 TCTCCTTGGTGATTTTGGGAAG 58.233 45.455 0.00 0.00 0.00 3.46
2073 2218 7.324935 TGGTTATAGCTGACTTCGTTTTATGA 58.675 34.615 0.00 0.00 0.00 2.15
2081 2226 6.682746 ACATAGATGGTTATAGCTGACTTCG 58.317 40.000 0.00 0.00 0.00 3.79
2082 2227 7.600752 GGAACATAGATGGTTATAGCTGACTTC 59.399 40.741 0.00 0.00 0.00 3.01
2093 2238 6.296432 GGGATGCATAGGAACATAGATGGTTA 60.296 42.308 0.00 0.00 0.00 2.85
2115 2260 2.308866 GGAAGATTTGGGACTCAAGGGA 59.691 50.000 0.00 0.00 36.62 4.20
2116 2261 2.041620 TGGAAGATTTGGGACTCAAGGG 59.958 50.000 0.00 0.00 36.62 3.95
2121 2266 6.874288 CATTCTATGGAAGATTTGGGACTC 57.126 41.667 0.00 0.00 34.70 3.36
2169 2314 2.689983 CACCCCAACAATTAGATGGCTC 59.310 50.000 0.00 0.00 38.77 4.70
2178 2323 2.603171 CCGGCCACCCCAACAATT 60.603 61.111 2.24 0.00 0.00 2.32
2179 2324 4.694987 CCCGGCCACCCCAACAAT 62.695 66.667 2.24 0.00 0.00 2.71
2194 2339 3.181526 CAGGACTTCTGGAATGCCC 57.818 57.895 0.00 0.00 39.76 5.36
2206 2351 1.421646 CAGGACCTTCAAACCAGGACT 59.578 52.381 0.00 0.00 35.14 3.85
2247 2392 2.749621 GTCCGAAGTCCATGCAGATTTT 59.250 45.455 0.00 0.00 0.00 1.82
2271 2416 1.680735 CTCCTCTCACCTCTTCATCGG 59.319 57.143 0.00 0.00 0.00 4.18
2287 2432 1.903183 GCCACTACTCCAAAGACTCCT 59.097 52.381 0.00 0.00 0.00 3.69
2387 2535 3.199946 AGGTGAAAATCTTCGGATGGCTA 59.800 43.478 0.00 0.00 34.49 3.93
2425 2573 0.249868 CGCCGATCTCATTTAGGGCA 60.250 55.000 5.11 0.00 40.52 5.36
2428 2576 3.004419 TGACTACGCCGATCTCATTTAGG 59.996 47.826 0.00 0.00 0.00 2.69
2453 2601 2.756840 TCTTGCATGAGGACAGTGAG 57.243 50.000 0.00 0.00 0.00 3.51
2456 2604 3.521126 ACCTAATCTTGCATGAGGACAGT 59.479 43.478 11.85 2.50 0.00 3.55
2472 2620 7.988937 TCCTCCAATAATGCATAAGACCTAAT 58.011 34.615 0.00 0.00 0.00 1.73
2509 2657 5.335426 CCAGATCAACACTTTCTCAACCATG 60.335 44.000 0.00 0.00 0.00 3.66
2510 2658 4.763793 CCAGATCAACACTTTCTCAACCAT 59.236 41.667 0.00 0.00 0.00 3.55
2520 2668 2.037772 ACGAAGAGCCAGATCAACACTT 59.962 45.455 0.00 0.00 0.00 3.16
2597 2745 2.009774 CTGCGGAATCACCTTACCTTG 58.990 52.381 0.00 0.00 36.31 3.61
2656 2804 4.491676 TCCTTACTTACGCACTGACATTC 58.508 43.478 0.00 0.00 0.00 2.67
2659 2807 2.889045 ACTCCTTACTTACGCACTGACA 59.111 45.455 0.00 0.00 0.00 3.58
2681 2829 2.112998 CCTTCCCGAACCTATACACCA 58.887 52.381 0.00 0.00 0.00 4.17
2706 2854 3.592059 GCTACTACACCAACCAATCGAA 58.408 45.455 0.00 0.00 0.00 3.71
2748 2896 2.317609 AAACTGCAGCGCCACTACG 61.318 57.895 15.27 0.00 0.00 3.51
2756 2904 1.083401 GTCGTCACAAACTGCAGCG 60.083 57.895 15.27 7.51 0.00 5.18
2759 2907 1.400142 CCTTTGTCGTCACAAACTGCA 59.600 47.619 0.00 0.00 45.73 4.41
2771 2919 3.664107 TCCAGAACAATCTCCTTTGTCG 58.336 45.455 0.00 0.00 38.85 4.35
2879 3027 4.521062 ACGCGAGCATCTCCAGCC 62.521 66.667 15.93 0.00 0.00 4.85
3137 3286 0.881796 GGCAAAACCTTCCTTCCTCG 59.118 55.000 0.00 0.00 34.51 4.63
3164 3919 0.850100 ACACCCAAACTCCATGACCA 59.150 50.000 0.00 0.00 0.00 4.02
3279 4034 3.283751 CCGAATTGGTGGTTTAGGCATA 58.716 45.455 0.00 0.00 0.00 3.14
3437 4192 5.289675 CACTTGACTCTCTTGCTATTTACCG 59.710 44.000 0.00 0.00 0.00 4.02
3438 4193 5.064071 GCACTTGACTCTCTTGCTATTTACC 59.936 44.000 0.00 0.00 0.00 2.85
3812 4568 4.394729 TCACCCAGTCCAATCAACTAAAC 58.605 43.478 0.00 0.00 0.00 2.01
3821 4577 3.843422 TCACAAATTCACCCAGTCCAAT 58.157 40.909 0.00 0.00 0.00 3.16
3844 4600 7.606456 TCAGTCAAACAGAATATAGGTTGGTTC 59.394 37.037 0.00 0.00 0.00 3.62
3985 4778 5.897377 AAGATAGGCTTGCGTTACAATTT 57.103 34.783 0.00 0.00 37.72 1.82
3988 4781 4.320023 TGAAAGATAGGCTTGCGTTACAA 58.680 39.130 0.00 0.00 34.60 2.41
3990 4783 3.309954 CCTGAAAGATAGGCTTGCGTTAC 59.690 47.826 0.00 0.00 34.60 2.50
4100 4893 7.942341 ACAGGACTCTAGAGATATCCAAAGTAG 59.058 40.741 26.57 11.16 33.76 2.57
4122 4915 5.615925 ACTTGGCTAGGTTAGAATACAGG 57.384 43.478 0.20 0.00 0.00 4.00
4199 4992 2.985896 TGTGCAAGCTATCCCAAGTAC 58.014 47.619 0.00 0.00 0.00 2.73
4237 5030 2.546368 GCTGTTCCACACACACGAAATA 59.454 45.455 0.00 0.00 0.00 1.40
4246 5041 1.596603 CACTGATGCTGTTCCACACA 58.403 50.000 0.00 0.00 0.00 3.72
4263 5058 2.030274 GCACCAAACCATACAGTTCCAC 60.030 50.000 0.00 0.00 0.00 4.02
4294 5089 6.599356 AAGGGACACTAAAACACAAAAAGT 57.401 33.333 0.00 0.00 0.00 2.66
4391 5186 1.351350 GGTAGTTCTCCAGGGCAGTTT 59.649 52.381 0.00 0.00 0.00 2.66
4442 5237 1.075212 TGGTCAACAGCAATGGATCCA 59.925 47.619 18.88 18.88 0.00 3.41
4526 5321 4.737765 GCATACTCTTCTCTGTTTCTAGCG 59.262 45.833 0.00 0.00 0.00 4.26
4538 5333 5.352569 CGGATTGTTTCTTGCATACTCTTCT 59.647 40.000 0.00 0.00 0.00 2.85
4562 5357 5.990996 TGCATTTTCAGATTTTCCAAACCTC 59.009 36.000 0.00 0.00 0.00 3.85
4701 5496 3.439857 TTTTTGATGCTGCTACCCTCT 57.560 42.857 0.00 0.00 0.00 3.69
4765 5561 6.097839 TGTCCATTATACAACTAGTGGGTCTC 59.902 42.308 1.45 0.00 31.29 3.36
4766 5562 5.962031 TGTCCATTATACAACTAGTGGGTCT 59.038 40.000 1.45 0.00 31.29 3.85
4767 5563 6.229936 TGTCCATTATACAACTAGTGGGTC 57.770 41.667 1.45 0.00 31.29 4.46
4768 5564 6.824958 ATGTCCATTATACAACTAGTGGGT 57.175 37.500 1.45 4.00 31.29 4.51
4769 5565 8.429641 ACTAATGTCCATTATACAACTAGTGGG 58.570 37.037 1.45 0.00 32.56 4.61
4823 5621 4.816385 GTCTTTGTGGTTGATGAGACTTGA 59.184 41.667 0.00 0.00 32.79 3.02
4903 5701 7.495934 TCGGATTTGAAATTCTCAAGTAGATCC 59.504 37.037 14.28 14.28 44.84 3.36
4921 5785 4.156556 ACATCATTGGTTGTCTCGGATTTG 59.843 41.667 0.00 0.00 0.00 2.32
4950 5815 4.946157 ACAAACTTGCTGGAATAGATGAGG 59.054 41.667 0.00 0.00 0.00 3.86
4955 5820 4.098914 ACCACAAACTTGCTGGAATAGA 57.901 40.909 14.20 0.00 35.09 1.98
4974 5839 2.823747 GGGTGAAGGTTTATGGTGAACC 59.176 50.000 0.00 0.00 45.49 3.62
4976 5841 3.245122 GGAGGGTGAAGGTTTATGGTGAA 60.245 47.826 0.00 0.00 0.00 3.18
4978 5843 2.620627 GGGAGGGTGAAGGTTTATGGTG 60.621 54.545 0.00 0.00 0.00 4.17
4979 5844 1.639108 GGGAGGGTGAAGGTTTATGGT 59.361 52.381 0.00 0.00 0.00 3.55
4980 5845 1.638589 TGGGAGGGTGAAGGTTTATGG 59.361 52.381 0.00 0.00 0.00 2.74
4982 5847 3.459969 GAGATGGGAGGGTGAAGGTTTAT 59.540 47.826 0.00 0.00 0.00 1.40
4983 5848 2.844348 GAGATGGGAGGGTGAAGGTTTA 59.156 50.000 0.00 0.00 0.00 2.01
4996 5865 7.465900 AAAGGACCATAATAAAGAGATGGGA 57.534 36.000 5.21 0.00 43.81 4.37
5073 5942 4.215908 ACCTGACAGTGAGAGTAAAGTGA 58.784 43.478 0.00 0.00 0.00 3.41
5137 6006 3.043419 CCCGGACCTGATAGAGCG 58.957 66.667 0.73 0.00 0.00 5.03
5174 6043 9.009327 CCACGATAACATGAAACAAATAACATC 57.991 33.333 0.00 0.00 0.00 3.06
5303 6173 3.721087 AATAAGCACTGCCCAGTAGTT 57.279 42.857 0.00 0.89 40.20 2.24
5320 6190 7.159372 GGTCTCAACTGTGAAACTAGGAAATA 58.841 38.462 0.00 0.00 38.04 1.40
5345 6215 3.176708 CAAGAAAATTCAGCATGCCTCG 58.823 45.455 15.66 3.24 34.76 4.63
5454 6324 0.614979 TTCCTTCTGCGGTAGGCTCT 60.615 55.000 13.21 0.00 44.05 4.09


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

AutoCloner maintained by Alex Coulton.