Multiple sequence alignment - TraesCS1B01G343800

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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 TraesCS1B01G343800 chr1B 100.000 4077 0 0 1 4077 572296575 572292499 0.000000e+00 7529.0
1 TraesCS1B01G343800 chr1D 92.717 3048 163 31 406 3422 423044036 423041017 0.000000e+00 4344.0
2 TraesCS1B01G343800 chr1D 88.406 483 24 9 1 451 423044537 423044055 1.660000e-153 553.0
3 TraesCS1B01G343800 chr1D 87.407 270 29 1 3808 4077 423040542 423040278 5.120000e-79 305.0
4 TraesCS1B01G343800 chr1D 88.816 152 16 1 3536 3686 423040891 423040740 6.960000e-43 185.0
5 TraesCS1B01G343800 chr1D 92.784 97 7 0 3626 3722 141345571 141345667 1.530000e-29 141.0
6 TraesCS1B01G343800 chr1D 92.771 83 5 1 3626 3708 350966113 350966194 7.160000e-23 119.0
7 TraesCS1B01G343800 chr1D 94.545 55 3 0 3765 3819 141345683 141345737 7.260000e-13 86.1
8 TraesCS1B01G343800 chr1D 95.455 44 2 0 3821 3864 350965466 350965509 2.030000e-08 71.3
9 TraesCS1B01G343800 chr1A 93.558 2018 108 17 798 2802 518974487 518972479 0.000000e+00 2987.0
10 TraesCS1B01G343800 chr1A 93.713 509 28 3 2923 3430 518972468 518971963 0.000000e+00 760.0
11 TraesCS1B01G343800 chr1A 87.477 543 61 3 3536 4077 518971852 518971316 1.610000e-173 619.0
12 TraesCS1B01G343800 chr1A 87.026 501 29 14 1 466 518975707 518975208 2.160000e-147 532.0
13 TraesCS1B01G343800 chr1A 83.750 320 23 6 428 738 518975049 518974750 4.010000e-70 276.0
14 TraesCS1B01G343800 chr1A 90.526 95 9 0 403 497 518975145 518975051 4.280000e-25 126.0
15 TraesCS1B01G343800 chr3D 91.083 157 14 0 1162 1318 418727422 418727578 3.190000e-51 213.0
16 TraesCS1B01G343800 chr3D 93.000 100 7 0 3626 3725 202637068 202636969 3.280000e-31 147.0
17 TraesCS1B01G343800 chr3D 85.000 140 18 3 2944 3083 270439056 270439192 5.500000e-29 139.0
18 TraesCS1B01G343800 chr3D 95.455 44 2 0 3821 3864 56126574 56126531 2.030000e-08 71.3
19 TraesCS1B01G343800 chr3B 91.083 157 14 0 1162 1318 545066482 545066638 3.190000e-51 213.0
20 TraesCS1B01G343800 chr3A 91.083 157 14 0 1162 1318 532451182 532451026 3.190000e-51 213.0
21 TraesCS1B01G343800 chr3A 92.414 145 9 2 3873 4015 695635177 695635321 5.340000e-49 206.0
22 TraesCS1B01G343800 chr3A 92.414 145 9 2 3873 4015 695645161 695645305 5.340000e-49 206.0
23 TraesCS1B01G343800 chr4A 92.414 145 9 2 3873 4015 219345640 219345496 5.340000e-49 206.0
24 TraesCS1B01G343800 chr4A 96.875 32 1 0 3873 3904 703743721 703743752 2.000000e-03 54.7
25 TraesCS1B01G343800 chr5D 91.034 145 11 2 3873 4015 432338619 432338475 1.160000e-45 195.0
26 TraesCS1B01G343800 chr5D 92.000 100 8 0 3626 3725 3134225 3134126 1.530000e-29 141.0
27 TraesCS1B01G343800 chr5D 95.455 44 2 0 3821 3864 324471635 324471678 2.030000e-08 71.3
28 TraesCS1B01G343800 chr6B 92.000 100 8 0 3626 3725 626833929 626833830 1.530000e-29 141.0
29 TraesCS1B01G343800 chr4D 92.784 97 7 0 3626 3722 135036661 135036757 1.530000e-29 141.0
30 TraesCS1B01G343800 chr4D 91.566 83 7 0 3626 3708 241236790 241236872 9.260000e-22 115.0
31 TraesCS1B01G343800 chr4D 95.455 44 2 0 3821 3864 135036012 135036055 2.030000e-08 71.3
32 TraesCS1B01G343800 chr4D 95.455 44 2 0 3821 3864 241191751 241191794 2.030000e-08 71.3
33 TraesCS1B01G343800 chr7A 84.507 142 17 4 2944 3083 145768124 145767986 7.110000e-28 135.0
34 TraesCS1B01G343800 chr7A 83.099 142 19 4 2944 3083 119583980 119583842 1.540000e-24 124.0
35 TraesCS1B01G343800 chr6D 91.000 100 9 0 3626 3725 430481053 430480954 7.110000e-28 135.0
36 TraesCS1B01G343800 chr6D 96.364 55 2 0 3765 3819 430480941 430480887 1.560000e-14 91.6
37 TraesCS1B01G343800 chr6D 95.455 44 2 0 3821 3864 430481702 430481659 2.030000e-08 71.3
38 TraesCS1B01G343800 chr2D 91.753 97 8 0 3626 3722 500892907 500893003 7.110000e-28 135.0
39 TraesCS1B01G343800 chr2D 91.566 83 7 0 3626 3708 500891759 500891841 9.260000e-22 115.0
40 TraesCS1B01G343800 chr2D 95.455 44 2 0 3821 3864 634995117 634995074 2.030000e-08 71.3
41 TraesCS1B01G343800 chrUn 92.771 83 6 0 3626 3708 223707638 223707720 1.990000e-23 121.0
42 TraesCS1B01G343800 chrUn 91.566 83 7 0 3626 3708 246709844 246709762 9.260000e-22 115.0
43 TraesCS1B01G343800 chrUn 91.566 83 7 0 3626 3708 266188785 266188867 9.260000e-22 115.0
44 TraesCS1B01G343800 chrUn 90.588 85 7 1 3873 3957 21928654 21928571 1.200000e-20 111.0
45 TraesCS1B01G343800 chr2A 93.750 64 2 2 3954 4015 724271406 724271469 1.210000e-15 95.3
46 TraesCS1B01G343800 chr5A 86.765 68 6 3 3950 4015 598052664 598052730 5.650000e-09 73.1


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 TraesCS1B01G343800 chr1B 572292499 572296575 4076 True 7529.000000 7529 100.000000 1 4077 1 chr1B.!!$R1 4076
1 TraesCS1B01G343800 chr1D 423040278 423044537 4259 True 1346.750000 4344 89.336500 1 4077 4 chr1D.!!$R1 4076
2 TraesCS1B01G343800 chr1A 518971316 518975707 4391 True 883.333333 2987 89.341667 1 4077 6 chr1A.!!$R1 4076

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
585 828 0.031585 TCTCACCGTCACTGAAACCG 59.968 55.0 0.00 0.0 0.0 4.44 F
1576 2029 0.038159 CCTCGAGCCTCTGAAAACGT 60.038 55.0 6.99 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 2037 0.675522 CGTACCCCCAACTCGCAATT 60.676 55.0 0.00 0.00 0.00 2.32 R
3135 3608 0.251653 TACGTTCTGGAGGCCTCAGT 60.252 55.0 33.29 22.16 34.15 3.41 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
22 23 5.643421 ATAGAACCAGCATTCTCCTTCAT 57.357 39.130 1.58 0.00 39.65 2.57
197 202 4.020218 TGGCTGTGCAAGTAGAGTTTCTAT 60.020 41.667 0.00 0.00 30.76 1.98
230 240 0.668535 GTTGCTTCTTGGTGGTGGAC 59.331 55.000 0.00 0.00 0.00 4.02
232 242 1.227853 GCTTCTTGGTGGTGGACGT 60.228 57.895 0.00 0.00 0.00 4.34
239 249 4.636435 GTGGTGGACGTGTGGGGG 62.636 72.222 0.00 0.00 0.00 5.40
240 250 4.882396 TGGTGGACGTGTGGGGGA 62.882 66.667 0.00 0.00 0.00 4.81
241 251 3.327404 GGTGGACGTGTGGGGGAT 61.327 66.667 0.00 0.00 0.00 3.85
242 252 2.267961 GTGGACGTGTGGGGGATC 59.732 66.667 0.00 0.00 0.00 3.36
243 253 2.121832 TGGACGTGTGGGGGATCT 59.878 61.111 0.00 0.00 0.00 2.75
279 305 2.542411 GCAGTGTTGAAGCTCAGTTTGG 60.542 50.000 0.00 0.00 0.00 3.28
286 320 4.207891 TGAAGCTCAGTTTGGTCTATCC 57.792 45.455 0.00 0.00 0.00 2.59
369 417 2.328473 TGCGTCTTCTCTCATTTCGTG 58.672 47.619 0.00 0.00 0.00 4.35
415 463 2.604914 CGTTATGCTCATTCACTTCGCT 59.395 45.455 0.00 0.00 0.00 4.93
418 466 3.808466 ATGCTCATTCACTTCGCTCTA 57.192 42.857 0.00 0.00 0.00 2.43
451 625 5.465390 GGCTTTTGTTCCTGGAAATTTGTAC 59.535 40.000 11.40 0.00 0.00 2.90
452 626 6.045955 GCTTTTGTTCCTGGAAATTTGTACA 58.954 36.000 11.40 0.44 0.00 2.90
509 743 3.940221 AGCAGAGCAAATGACTGAAGATC 59.060 43.478 0.00 0.00 34.07 2.75
550 784 3.244946 ACAGCAGACTACTACTCACAGGA 60.245 47.826 0.00 0.00 0.00 3.86
553 796 3.759618 GCAGACTACTACTCACAGGAACT 59.240 47.826 0.00 0.00 43.88 3.01
578 821 1.616865 TCGGATTTTCTCACCGTCACT 59.383 47.619 0.00 0.00 45.71 3.41
585 828 0.031585 TCTCACCGTCACTGAAACCG 59.968 55.000 0.00 0.00 0.00 4.44
659 902 3.537874 CCTTCTCCCTACCCGCCG 61.538 72.222 0.00 0.00 0.00 6.46
681 924 3.641986 GTTCGTCCAACGCGGCAA 61.642 61.111 12.47 0.00 42.21 4.52
702 945 2.983030 GTTGGCACCATCGCACCA 60.983 61.111 0.00 0.00 0.00 4.17
711 954 1.600636 CATCGCACCAACCACCACT 60.601 57.895 0.00 0.00 0.00 4.00
738 981 4.359706 GTCAAAAACTGCTTACCAACCAG 58.640 43.478 0.00 0.00 0.00 4.00
747 990 2.607187 CTTACCAACCAGTACTCAGCG 58.393 52.381 0.00 0.00 0.00 5.18
749 992 0.317479 ACCAACCAGTACTCAGCGTC 59.683 55.000 0.00 0.00 0.00 5.19
751 994 1.402984 CCAACCAGTACTCAGCGTCTC 60.403 57.143 0.00 0.00 0.00 3.36
753 996 1.169577 ACCAGTACTCAGCGTCTCAG 58.830 55.000 0.00 0.00 0.00 3.35
755 998 0.179150 CAGTACTCAGCGTCTCAGCC 60.179 60.000 0.00 0.00 38.01 4.85
758 1001 0.609406 TACTCAGCGTCTCAGCCTGT 60.609 55.000 0.00 0.00 38.01 4.00
759 1002 1.445754 CTCAGCGTCTCAGCCTGTG 60.446 63.158 0.00 0.00 38.01 3.66
762 1005 1.005630 AGCGTCTCAGCCTGTGTTC 60.006 57.895 0.00 0.00 38.01 3.18
763 1006 1.300931 GCGTCTCAGCCTGTGTTCA 60.301 57.895 0.00 0.00 0.00 3.18
787 1030 0.589223 TTAAAAACACGGCGAGGCTG 59.411 50.000 16.62 3.21 41.29 4.85
788 1031 1.231958 TAAAAACACGGCGAGGCTGG 61.232 55.000 16.62 0.00 39.57 4.85
796 1039 3.741476 GCGAGGCTGGCTTTGGTG 61.741 66.667 14.72 0.00 0.00 4.17
797 1040 3.741476 CGAGGCTGGCTTTGGTGC 61.741 66.667 4.82 0.00 0.00 5.01
798 1041 3.741476 GAGGCTGGCTTTGGTGCG 61.741 66.667 4.82 0.00 0.00 5.34
799 1042 4.269523 AGGCTGGCTTTGGTGCGA 62.270 61.111 0.00 0.00 0.00 5.10
800 1043 4.043200 GGCTGGCTTTGGTGCGAC 62.043 66.667 0.00 0.00 0.00 5.19
841 1287 1.194781 CCATCCTACCCTCCCCATCG 61.195 65.000 0.00 0.00 0.00 3.84
845 1291 4.892291 TACCCTCCCCATCGCCCC 62.892 72.222 0.00 0.00 0.00 5.80
879 1326 1.416401 GATCTCAGGGGCAAATCCGTA 59.584 52.381 0.00 0.00 34.94 4.02
882 1329 0.988832 TCAGGGGCAAATCCGTAACT 59.011 50.000 0.00 0.00 34.94 2.24
892 1339 0.905357 ATCCGTAACTGCCAGAAGCT 59.095 50.000 0.00 0.00 44.23 3.74
898 1345 0.246086 AACTGCCAGAAGCTCTCTCG 59.754 55.000 0.00 0.00 44.23 4.04
1143 1596 1.443872 GTCGTCGTCGTTGGCATCT 60.444 57.895 1.33 0.00 38.33 2.90
1377 1830 4.699522 GTGGCCCGGGTGAGTGTC 62.700 72.222 24.63 2.30 0.00 3.67
1390 1843 3.059884 GTGAGTGTCTTCAGCGATTTGA 58.940 45.455 0.00 0.00 0.00 2.69
1396 1849 4.330894 GTGTCTTCAGCGATTTGATGATGA 59.669 41.667 4.17 4.17 43.68 2.92
1545 1998 0.770557 AGACCAGTAACAAGCCCCCA 60.771 55.000 0.00 0.00 0.00 4.96
1576 2029 0.038159 CCTCGAGCCTCTGAAAACGT 60.038 55.000 6.99 0.00 0.00 3.99
1584 2037 1.428448 CTCTGAAAACGTCCATCGCA 58.572 50.000 0.00 0.00 44.19 5.10
1616 2069 2.483188 GGGGGTACGATCACTGACAATC 60.483 54.545 0.00 0.00 0.00 2.67
1626 2079 1.019673 ACTGACAATCATCGGCATGC 58.980 50.000 9.90 9.90 0.00 4.06
1642 2098 4.024556 CGGCATGCTAAGAACTTAAGATGG 60.025 45.833 18.92 0.00 0.00 3.51
1649 2105 6.595326 TGCTAAGAACTTAAGATGGTGTGATG 59.405 38.462 10.09 0.00 0.00 3.07
1651 2107 7.334421 GCTAAGAACTTAAGATGGTGTGATGAA 59.666 37.037 10.09 0.00 0.00 2.57
1652 2108 9.388506 CTAAGAACTTAAGATGGTGTGATGAAT 57.611 33.333 10.09 0.00 0.00 2.57
1654 2110 9.911788 AAGAACTTAAGATGGTGTGATGAATAT 57.088 29.630 10.09 0.00 0.00 1.28
1783 2239 1.202818 GCTCTCAAGGTTTGTCCCTGT 60.203 52.381 0.00 0.00 34.19 4.00
1865 2321 3.380637 TCAGGAGTTGAAGCCTACGATAC 59.619 47.826 0.00 0.00 32.03 2.24
2017 2473 3.665190 CCGAGCAGGGTAATAAGATTCC 58.335 50.000 0.00 0.00 35.97 3.01
2094 2550 3.547746 ACTAGGAGAGTCCTCTAAAGCG 58.452 50.000 0.00 0.00 45.66 4.68
2108 2564 7.009999 GTCCTCTAAAGCGCTATATCATCAATG 59.990 40.741 12.05 0.00 0.00 2.82
2212 2668 9.932699 CATCTTCACTGATAATTTTAGAAGCAG 57.067 33.333 0.00 0.00 33.06 4.24
2232 2688 4.154918 GCAGTTACAGAAGGGAAATCACTG 59.845 45.833 0.00 0.00 33.69 3.66
2345 2804 2.330440 CAAAGGCTTGCAAAAAGGGT 57.670 45.000 0.00 0.00 0.00 4.34
2354 2813 4.481463 CTTGCAAAAAGGGTATGGTAACG 58.519 43.478 0.00 0.00 42.51 3.18
2402 2861 4.158025 GGTGAGACAGACGAGGAGATAAAA 59.842 45.833 0.00 0.00 0.00 1.52
2517 2977 7.868415 AGGAGAATATTTATCGACTTACAGTGC 59.132 37.037 0.00 0.00 0.00 4.40
2524 2984 2.750948 TCGACTTACAGTGCACCTTTC 58.249 47.619 14.63 0.89 0.00 2.62
2539 3004 6.376018 GTGCACCTTTCAGTTTATATTACCCA 59.624 38.462 5.22 0.00 0.00 4.51
2564 3029 5.521906 TGCCTTTGTAAATGCTGTAACAA 57.478 34.783 6.26 0.00 31.87 2.83
2667 3132 5.994250 TGGAAGGAGTATGGAGAATCTTTG 58.006 41.667 0.00 0.00 33.73 2.77
2707 3172 3.450904 AGTGGACCTCTGGTAAGCATTA 58.549 45.455 0.00 0.00 35.25 1.90
2724 3189 6.992063 AGCATTACATATAGCTGGTTATGC 57.008 37.500 17.88 17.88 35.72 3.14
2768 3233 5.648092 AGACAAGGAATGCCAGTGTTTATAC 59.352 40.000 0.76 0.00 35.53 1.47
2853 3318 4.487714 TCCTCGATAAAACATGCCTCTT 57.512 40.909 0.00 0.00 0.00 2.85
2895 3360 4.159506 ACCACACAAAAGAAAAAGCTAGCA 59.840 37.500 18.83 0.00 0.00 3.49
2920 3385 6.831868 ACTTGTCTTGTTAGTTATTGGTGGTT 59.168 34.615 0.00 0.00 0.00 3.67
2921 3386 7.994334 ACTTGTCTTGTTAGTTATTGGTGGTTA 59.006 33.333 0.00 0.00 0.00 2.85
3059 3532 2.108250 AGACAGAAAAAGGCCCAGCTTA 59.892 45.455 0.00 0.00 0.00 3.09
3135 3608 8.358148 CAGAGTTTTACACAGGAAGAGTTAGTA 58.642 37.037 0.00 0.00 0.00 1.82
3150 3623 3.097614 GTTAGTACTGAGGCCTCCAGAA 58.902 50.000 29.95 10.44 35.69 3.02
3228 3701 9.547753 GCTTACACCTGATATTCAATTTCTCTA 57.452 33.333 0.00 0.00 0.00 2.43
3276 3749 8.816640 ATTTTTGTTTGTATCACTTGCTTAGG 57.183 30.769 0.00 0.00 0.00 2.69
3297 3770 3.334691 GCAGATAGTTGTGTGCCTGTAA 58.665 45.455 0.00 0.00 32.68 2.41
3317 3790 3.208747 AGGAAATCCGTCAGTTGTTGT 57.791 42.857 0.00 0.00 42.08 3.32
3379 3852 3.187227 CGGTGTCCTGATTGTTTCTGAAG 59.813 47.826 0.00 0.00 0.00 3.02
3385 3858 3.562505 CTGATTGTTTCTGAAGCACAGC 58.437 45.455 6.43 2.86 45.38 4.40
3403 3876 0.030638 GCGTGTTTTGGCATGTCTGT 59.969 50.000 0.00 0.00 0.00 3.41
3422 3895 5.467063 GTCTGTTGGAGTTCCTTTAGAGTTG 59.533 44.000 0.00 0.00 36.82 3.16
3423 3896 4.134563 TGTTGGAGTTCCTTTAGAGTTGC 58.865 43.478 0.00 0.00 36.82 4.17
3424 3897 3.418684 TGGAGTTCCTTTAGAGTTGCC 57.581 47.619 0.00 0.00 36.82 4.52
3426 3899 3.330701 TGGAGTTCCTTTAGAGTTGCCAT 59.669 43.478 0.00 0.00 36.82 4.40
3519 4032 3.708563 GCGGGTGCAAATGTAATATGT 57.291 42.857 0.00 0.00 42.15 2.29
3520 4033 4.040445 GCGGGTGCAAATGTAATATGTT 57.960 40.909 0.00 0.00 42.15 2.71
3521 4034 4.041723 GCGGGTGCAAATGTAATATGTTC 58.958 43.478 0.00 0.00 42.15 3.18
3522 4035 4.202010 GCGGGTGCAAATGTAATATGTTCT 60.202 41.667 0.00 0.00 42.15 3.01
3523 4036 5.008217 GCGGGTGCAAATGTAATATGTTCTA 59.992 40.000 0.00 0.00 42.15 2.10
3524 4037 6.658831 CGGGTGCAAATGTAATATGTTCTAG 58.341 40.000 0.00 0.00 0.00 2.43
3525 4038 6.260050 CGGGTGCAAATGTAATATGTTCTAGT 59.740 38.462 0.00 0.00 0.00 2.57
3526 4039 7.417612 GGGTGCAAATGTAATATGTTCTAGTG 58.582 38.462 0.00 0.00 0.00 2.74
3527 4040 6.912591 GGTGCAAATGTAATATGTTCTAGTGC 59.087 38.462 0.00 0.00 0.00 4.40
3528 4041 7.415095 GGTGCAAATGTAATATGTTCTAGTGCA 60.415 37.037 0.00 0.00 0.00 4.57
3529 4042 7.967854 GTGCAAATGTAATATGTTCTAGTGCAA 59.032 33.333 0.00 0.00 0.00 4.08
3530 4043 7.967854 TGCAAATGTAATATGTTCTAGTGCAAC 59.032 33.333 0.00 0.00 0.00 4.17
3563 4076 6.866010 TCTGAATTGGATGCATATACACAC 57.134 37.500 0.00 0.00 0.00 3.82
3570 4083 6.352682 TGGATGCATATACACACGTTTTAC 57.647 37.500 0.00 0.00 0.00 2.01
3592 4106 4.949856 ACTGTGTTTGTTCCTCATTTCAGT 59.050 37.500 0.00 0.00 0.00 3.41
3598 4112 6.483307 TGTTTGTTCCTCATTTCAGTCTGTAG 59.517 38.462 0.00 0.00 0.00 2.74
3608 4122 5.661056 TTTCAGTCTGTAGGTAGTCCATG 57.339 43.478 0.00 0.00 35.89 3.66
3612 4126 4.646945 CAGTCTGTAGGTAGTCCATGATGT 59.353 45.833 0.00 0.00 35.89 3.06
3622 4136 7.680730 AGGTAGTCCATGATGTAATATCCAAC 58.319 38.462 0.00 0.00 35.89 3.77
3624 4138 8.103305 GGTAGTCCATGATGTAATATCCAACAT 58.897 37.037 0.00 0.00 39.00 2.71
3632 4146 8.291191 TGATGTAATATCCAACATGAGCAAAA 57.709 30.769 0.00 0.00 36.48 2.44
3673 4187 6.353602 GGGACCTTTGGATACCAAGATTTCTA 60.354 42.308 3.49 0.00 44.84 2.10
3686 4200 8.850007 ACCAAGATTTCTAACCTCTTACTTTC 57.150 34.615 0.00 0.00 0.00 2.62
3687 4201 7.883833 ACCAAGATTTCTAACCTCTTACTTTCC 59.116 37.037 0.00 0.00 0.00 3.13
3796 4474 2.188062 TTGGTATCGGTTTGGGTCAC 57.812 50.000 0.00 0.00 0.00 3.67
3811 4489 1.349067 GTCACTACCCAGAACCCTGT 58.651 55.000 0.00 0.00 38.74 4.00
3814 4492 1.697432 CACTACCCAGAACCCTGTCAA 59.303 52.381 0.00 0.00 38.74 3.18
3819 4497 0.111253 CCAGAACCCTGTCAAAGCCT 59.889 55.000 0.00 0.00 38.74 4.58
3821 4499 0.846693 AGAACCCTGTCAAAGCCTGT 59.153 50.000 0.00 0.00 0.00 4.00
3828 4506 3.826157 CCCTGTCAAAGCCTGTCAATTTA 59.174 43.478 0.00 0.00 0.00 1.40
3846 4524 7.008628 GTCAATTTATCAAGTTGAGGCATTTCG 59.991 37.037 11.91 0.00 32.98 3.46
3851 4529 5.452078 TCAAGTTGAGGCATTTCGATTTT 57.548 34.783 0.08 0.00 0.00 1.82
3852 4530 5.841810 TCAAGTTGAGGCATTTCGATTTTT 58.158 33.333 0.08 0.00 0.00 1.94
3894 4572 2.849880 GCAAAATAGCTCGATGCCAA 57.150 45.000 0.00 0.00 44.23 4.52
3898 4576 4.026310 GCAAAATAGCTCGATGCCAAAATG 60.026 41.667 0.00 1.15 44.23 2.32
3948 4626 8.451687 TGACTTCTTCATTATTTTGAAATGCG 57.548 30.769 0.00 0.00 35.31 4.73
3964 4642 5.868801 TGAAATGCGAAAAAGATCCAAATCC 59.131 36.000 0.00 0.00 31.78 3.01
3979 4657 4.820716 TCCAAATCCAAAATGCAAAGGTTG 59.179 37.500 0.00 0.00 0.00 3.77
4006 4684 8.514594 TCTTATTCAAAACCTCAATCATCACAC 58.485 33.333 0.00 0.00 0.00 3.82
4007 4685 5.452078 TTCAAAACCTCAATCATCACACC 57.548 39.130 0.00 0.00 0.00 4.16
4010 4688 1.673767 ACCTCAATCATCACACCCCT 58.326 50.000 0.00 0.00 0.00 4.79
4024 4702 4.043310 TCACACCCCTTCTCTTGATTTGAT 59.957 41.667 0.00 0.00 0.00 2.57
4032 4710 4.128925 TCTCTTGATTTGATCGACCCTG 57.871 45.455 0.00 0.00 0.00 4.45
4033 4711 2.611292 CTCTTGATTTGATCGACCCTGC 59.389 50.000 0.00 0.00 0.00 4.85
4034 4712 2.237143 TCTTGATTTGATCGACCCTGCT 59.763 45.455 0.00 0.00 0.00 4.24
4035 4713 2.315925 TGATTTGATCGACCCTGCTC 57.684 50.000 0.00 0.00 0.00 4.26
4036 4714 1.134401 TGATTTGATCGACCCTGCTCC 60.134 52.381 0.00 0.00 0.00 4.70
4050 4728 1.734117 GCTCCGCCACAACATTTGC 60.734 57.895 0.00 0.00 0.00 3.68
4057 4735 3.055591 CGCCACAACATTTGCACATTTA 58.944 40.909 0.00 0.00 0.00 1.40
4071 4749 4.142026 TGCACATTTAGATGCTACTACCGT 60.142 41.667 0.00 0.00 42.55 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 202 6.206634 CCAAGAAGCAACCACAAGATAGTTTA 59.793 38.462 0.00 0.00 0.00 2.01
211 216 0.668535 GTCCACCACCAAGAAGCAAC 59.331 55.000 0.00 0.00 0.00 4.17
230 240 0.250727 ACACAAAGATCCCCCACACG 60.251 55.000 0.00 0.00 0.00 4.49
232 242 1.073763 CTCACACAAAGATCCCCCACA 59.926 52.381 0.00 0.00 0.00 4.17
239 249 1.537202 GCCACCACTCACACAAAGATC 59.463 52.381 0.00 0.00 0.00 2.75
240 250 1.133823 TGCCACCACTCACACAAAGAT 60.134 47.619 0.00 0.00 0.00 2.40
241 251 0.254462 TGCCACCACTCACACAAAGA 59.746 50.000 0.00 0.00 0.00 2.52
242 252 0.664761 CTGCCACCACTCACACAAAG 59.335 55.000 0.00 0.00 0.00 2.77
243 253 0.034574 ACTGCCACCACTCACACAAA 60.035 50.000 0.00 0.00 0.00 2.83
279 305 5.798132 TCTCACCAATGCATATGGATAGAC 58.202 41.667 25.31 0.00 40.56 2.59
286 320 7.553044 ACATCTCATATCTCACCAATGCATATG 59.447 37.037 0.00 0.00 33.81 1.78
408 456 2.618053 CCCGATTTTGTAGAGCGAAGT 58.382 47.619 0.00 0.00 0.00 3.01
412 460 1.369625 AAGCCCGATTTTGTAGAGCG 58.630 50.000 0.00 0.00 0.00 5.03
451 625 2.731968 GCGTGCCAAATTCACCTGTATG 60.732 50.000 0.00 0.00 0.00 2.39
452 626 1.472480 GCGTGCCAAATTCACCTGTAT 59.528 47.619 0.00 0.00 0.00 2.29
509 743 2.046313 GTTGCTGTCAAAGTTCATGCG 58.954 47.619 0.00 0.00 33.37 4.73
550 784 2.808543 GTGAGAAAATCCGACTGCAGTT 59.191 45.455 22.65 2.03 0.00 3.16
553 796 1.808411 GGTGAGAAAATCCGACTGCA 58.192 50.000 0.00 0.00 0.00 4.41
578 821 1.343465 GACTGGAGGAAGACGGTTTCA 59.657 52.381 3.99 0.00 0.00 2.69
585 828 2.579738 GCCGGACTGGAGGAAGAC 59.420 66.667 5.05 0.00 42.00 3.01
665 908 3.342627 CTTGCCGCGTTGGACGAA 61.343 61.111 4.92 0.00 46.05 3.85
702 945 2.818751 TTTGACCTTGAGTGGTGGTT 57.181 45.000 0.00 0.00 41.00 3.67
711 954 4.274147 TGGTAAGCAGTTTTTGACCTTGA 58.726 39.130 0.00 0.00 0.00 3.02
738 981 0.179150 CAGGCTGAGACGCTGAGTAC 60.179 60.000 9.42 0.00 0.00 2.73
747 990 2.289320 ACTGATGAACACAGGCTGAGAC 60.289 50.000 23.66 13.25 39.38 3.36
749 992 2.469274 ACTGATGAACACAGGCTGAG 57.531 50.000 23.66 16.77 39.38 3.35
751 994 5.437289 TTTTAACTGATGAACACAGGCTG 57.563 39.130 14.16 14.16 39.38 4.85
753 996 5.458779 GTGTTTTTAACTGATGAACACAGGC 59.541 40.000 11.48 0.00 45.62 4.85
755 998 5.681105 CCGTGTTTTTAACTGATGAACACAG 59.319 40.000 15.28 0.00 46.26 3.66
758 1001 4.602995 GCCGTGTTTTTAACTGATGAACA 58.397 39.130 0.00 0.00 0.00 3.18
759 1002 3.662186 CGCCGTGTTTTTAACTGATGAAC 59.338 43.478 0.00 0.00 0.00 3.18
762 1005 3.479006 CTCGCCGTGTTTTTAACTGATG 58.521 45.455 0.00 0.00 0.00 3.07
763 1006 2.482721 CCTCGCCGTGTTTTTAACTGAT 59.517 45.455 0.00 0.00 0.00 2.90
845 1291 0.459237 GAGATCTGGTGGACTGCACG 60.459 60.000 0.00 0.00 0.00 5.34
879 1326 0.246086 CGAGAGAGCTTCTGGCAGTT 59.754 55.000 15.27 0.00 44.79 3.16
1136 1586 3.824425 GGGCCCATCCAGATGCCA 61.824 66.667 19.95 0.00 45.83 4.92
1373 1826 4.330894 TCATCATCAAATCGCTGAAGACAC 59.669 41.667 0.00 0.00 0.00 3.67
1376 1829 6.492254 CAAATCATCATCAAATCGCTGAAGA 58.508 36.000 0.00 0.00 0.00 2.87
1377 1830 5.173312 GCAAATCATCATCAAATCGCTGAAG 59.827 40.000 0.00 0.00 0.00 3.02
1470 1923 1.890979 GCCGAGGAGCATGATGGTG 60.891 63.158 0.12 0.00 0.00 4.17
1584 2037 0.675522 CGTACCCCCAACTCGCAATT 60.676 55.000 0.00 0.00 0.00 2.32
1616 2069 4.811024 TCTTAAGTTCTTAGCATGCCGATG 59.189 41.667 15.66 5.42 0.00 3.84
1626 2079 8.777865 TTCATCACACCATCTTAAGTTCTTAG 57.222 34.615 1.63 0.00 0.00 2.18
1642 2098 9.424319 ACCGTTTATCAGATATATTCATCACAC 57.576 33.333 0.00 0.00 0.00 3.82
1652 2108 8.609176 GCAAAGAAACACCGTTTATCAGATATA 58.391 33.333 0.00 0.00 0.00 0.86
1653 2109 7.120579 TGCAAAGAAACACCGTTTATCAGATAT 59.879 33.333 0.00 0.00 0.00 1.63
1654 2110 6.428465 TGCAAAGAAACACCGTTTATCAGATA 59.572 34.615 0.00 0.00 0.00 1.98
1656 2112 4.576873 TGCAAAGAAACACCGTTTATCAGA 59.423 37.500 0.00 0.00 0.00 3.27
1657 2113 4.854399 TGCAAAGAAACACCGTTTATCAG 58.146 39.130 0.00 0.00 0.00 2.90
1658 2114 4.576873 TCTGCAAAGAAACACCGTTTATCA 59.423 37.500 0.00 0.00 0.00 2.15
1659 2115 5.103290 TCTGCAAAGAAACACCGTTTATC 57.897 39.130 0.00 0.00 0.00 1.75
1783 2239 2.979814 TAATCAGCAAGCTAAGGCGA 57.020 45.000 0.00 0.00 44.37 5.54
1865 2321 3.574396 TCTGAAGTTAGACACTCCACCAG 59.426 47.826 0.00 0.00 32.94 4.00
1933 2389 2.223537 TGTGCGCATACACATCTAGG 57.776 50.000 15.91 0.00 45.36 3.02
2017 2473 5.239306 TGAGCAACATACAAAAGAAGTCAGG 59.761 40.000 0.00 0.00 0.00 3.86
2094 2550 4.163839 AGAGGAGGGCATTGATGATATAGC 59.836 45.833 0.00 0.00 0.00 2.97
2108 2564 1.251527 TGACGAACTCAGAGGAGGGC 61.252 60.000 1.53 0.00 45.81 5.19
2168 2624 7.437862 GTGAAGATGCAGGTTTTGAAATTACAA 59.562 33.333 0.00 0.00 0.00 2.41
2212 2668 5.940470 ACATCAGTGATTTCCCTTCTGTAAC 59.060 40.000 1.86 0.00 0.00 2.50
2232 2688 3.499537 TCGCCAGATGCAAATATGACATC 59.500 43.478 0.00 5.23 41.33 3.06
2354 2813 2.208431 CCAAGCATGATCGAGGACTTC 58.792 52.381 0.00 0.00 0.00 3.01
2402 2861 2.233271 CTCAAGTCAGCCATGGTTTGT 58.767 47.619 14.67 0.00 0.00 2.83
2517 2977 6.828785 AGCTGGGTAATATAAACTGAAAGGTG 59.171 38.462 0.00 0.00 39.30 4.00
2524 2984 4.718961 AGGCAGCTGGGTAATATAAACTG 58.281 43.478 17.12 0.00 0.00 3.16
2564 3029 6.501805 TGGCTGTATAATCAAGGAGATATGGT 59.498 38.462 0.00 0.00 35.39 3.55
2667 3132 4.096382 CCACTAGCAACATACACAAATCCC 59.904 45.833 0.00 0.00 0.00 3.85
2740 3205 1.338200 ACTGGCATTCCTTGTCTCGAC 60.338 52.381 0.00 0.00 0.00 4.20
2742 3207 1.081892 CACTGGCATTCCTTGTCTCG 58.918 55.000 0.00 0.00 0.00 4.04
2768 3233 8.116136 GCATTGGTAAAAGTTTTGTCTTCTTTG 58.884 33.333 11.18 0.86 32.74 2.77
2853 3318 5.816821 GTGGTTTCACAAGCTGGATAGCAA 61.817 45.833 0.00 0.00 46.28 3.91
2895 3360 6.362248 ACCACCAATAACTAACAAGACAAGT 58.638 36.000 0.00 0.00 0.00 3.16
2920 3385 3.367992 CAGCAACCACAAAACTGCATA 57.632 42.857 0.00 0.00 37.26 3.14
2921 3386 2.228138 CAGCAACCACAAAACTGCAT 57.772 45.000 0.00 0.00 37.26 3.96
3010 3483 7.237471 ACAAAATTTTGGACAAATATCTCCCCT 59.763 33.333 29.37 4.72 42.34 4.79
3059 3532 4.414677 TCAGACTAGGATGCAGCAGATAT 58.585 43.478 3.51 0.00 0.00 1.63
3135 3608 0.251653 TACGTTCTGGAGGCCTCAGT 60.252 55.000 33.29 22.16 34.15 3.41
3150 3623 1.559682 AGGATCAACATTGCCCTACGT 59.440 47.619 0.00 0.00 32.06 3.57
3196 3669 7.558161 TTGAATATCAGGTGTAAGCAATCAG 57.442 36.000 0.00 0.00 36.26 2.90
3242 3715 7.754924 AGTGATACAAACAAAAATATTCGGCAG 59.245 33.333 0.00 0.00 0.00 4.85
3276 3749 1.813513 ACAGGCACACAACTATCTGC 58.186 50.000 0.00 0.00 0.00 4.26
3297 3770 3.208747 ACAACAACTGACGGATTTCCT 57.791 42.857 0.00 0.00 0.00 3.36
3307 3780 3.407424 AGCAGCAGATACAACAACTGA 57.593 42.857 0.00 0.00 34.07 3.41
3311 3784 4.136796 AGACAAAGCAGCAGATACAACAA 58.863 39.130 0.00 0.00 0.00 2.83
3357 3830 2.766313 TCAGAAACAATCAGGACACCG 58.234 47.619 0.00 0.00 0.00 4.94
3379 3852 1.300080 ATGCCAAAACACGCTGTGC 60.300 52.632 8.31 0.52 36.98 4.57
3385 3858 2.118683 CAACAGACATGCCAAAACACG 58.881 47.619 0.00 0.00 0.00 4.49
3403 3876 3.137544 TGGCAACTCTAAAGGAACTCCAA 59.862 43.478 0.00 0.00 34.70 3.53
3422 3895 0.893270 TGGCACACACCAGTAATGGC 60.893 55.000 9.63 0.00 38.39 4.40
3423 3896 3.337834 TGGCACACACCAGTAATGG 57.662 52.632 7.88 7.88 33.75 3.16
3501 4014 7.417612 CACTAGAACATATTACATTTGCACCC 58.582 38.462 0.00 0.00 0.00 4.61
3505 4018 8.184192 AGTTGCACTAGAACATATTACATTTGC 58.816 33.333 0.00 0.00 0.00 3.68
3547 4060 6.036626 CAGTAAAACGTGTGTATATGCATCCA 59.963 38.462 0.19 0.00 0.00 3.41
3559 4072 4.555747 GGAACAAACACAGTAAAACGTGTG 59.444 41.667 0.00 0.98 45.37 3.82
3563 4076 5.224562 TGAGGAACAAACACAGTAAAACG 57.775 39.130 0.00 0.00 0.00 3.60
3570 4083 5.297776 AGACTGAAATGAGGAACAAACACAG 59.702 40.000 0.00 0.00 0.00 3.66
3592 4106 9.244292 GATATTACATCATGGACTACCTACAGA 57.756 37.037 0.00 0.00 37.04 3.41
3598 4112 7.450074 TGTTGGATATTACATCATGGACTACC 58.550 38.462 0.00 0.00 0.00 3.18
3641 4155 3.784202 GGTATCCAAAGGTCCCTAAAGGA 59.216 47.826 0.00 4.43 44.91 3.36
3743 4421 6.603599 AGGGAAGGCTTACTTATTGATTTCAC 59.396 38.462 9.79 0.00 40.21 3.18
3749 4427 5.163195 GGATGAGGGAAGGCTTACTTATTGA 60.163 44.000 9.79 0.00 40.21 2.57
3750 4428 5.066593 GGATGAGGGAAGGCTTACTTATTG 58.933 45.833 9.79 0.00 40.21 1.90
3796 4474 2.876079 GCTTTGACAGGGTTCTGGGTAG 60.876 54.545 0.00 0.00 44.99 3.18
3801 4479 1.242076 CAGGCTTTGACAGGGTTCTG 58.758 55.000 0.00 0.00 46.10 3.02
3811 4489 6.899393 ACTTGATAAATTGACAGGCTTTGA 57.101 33.333 0.00 0.00 0.00 2.69
3814 4492 6.071728 CCTCAACTTGATAAATTGACAGGCTT 60.072 38.462 0.00 0.00 0.00 4.35
3819 4497 6.839124 ATGCCTCAACTTGATAAATTGACA 57.161 33.333 0.00 0.00 0.00 3.58
3821 4499 7.028962 CGAAATGCCTCAACTTGATAAATTGA 58.971 34.615 0.00 0.00 0.00 2.57
3828 4506 5.649782 AAATCGAAATGCCTCAACTTGAT 57.350 34.783 0.00 0.00 0.00 2.57
3851 4529 6.626302 CCGCTCAGGGTTTTATTTGAAATAA 58.374 36.000 6.28 6.28 35.97 1.40
3852 4530 5.393678 GCCGCTCAGGGTTTTATTTGAAATA 60.394 40.000 0.00 0.00 41.48 1.40
3906 4584 9.274206 GAAGAAGTCAAATAAGAGGTGTTAAGT 57.726 33.333 0.00 0.00 0.00 2.24
3907 4585 9.273016 TGAAGAAGTCAAATAAGAGGTGTTAAG 57.727 33.333 0.00 0.00 31.51 1.85
3909 4587 9.793259 AATGAAGAAGTCAAATAAGAGGTGTTA 57.207 29.630 0.00 0.00 40.50 2.41
3948 4626 7.437793 TGCATTTTGGATTTGGATCTTTTTC 57.562 32.000 0.00 0.00 32.66 2.29
3956 4634 4.703379 ACCTTTGCATTTTGGATTTGGA 57.297 36.364 0.00 0.00 0.00 3.53
3964 4642 7.712264 TGAATAAGACAACCTTTGCATTTTG 57.288 32.000 0.00 0.00 36.34 2.44
3979 4657 8.514594 TGTGATGATTGAGGTTTTGAATAAGAC 58.485 33.333 0.00 0.00 0.00 3.01
3994 4672 3.184628 AGAGAAGGGGTGTGATGATTGA 58.815 45.455 0.00 0.00 0.00 2.57
4006 4684 3.873952 GTCGATCAAATCAAGAGAAGGGG 59.126 47.826 0.00 0.00 0.00 4.79
4007 4685 3.873952 GGTCGATCAAATCAAGAGAAGGG 59.126 47.826 0.00 0.00 0.00 3.95
4010 4688 4.507710 CAGGGTCGATCAAATCAAGAGAA 58.492 43.478 0.00 0.00 0.00 2.87
4033 4711 0.664166 GTGCAAATGTTGTGGCGGAG 60.664 55.000 0.00 0.00 0.00 4.63
4034 4712 1.361993 GTGCAAATGTTGTGGCGGA 59.638 52.632 0.00 0.00 0.00 5.54
4035 4713 0.319727 ATGTGCAAATGTTGTGGCGG 60.320 50.000 0.00 0.00 0.00 6.13
4036 4714 1.500108 AATGTGCAAATGTTGTGGCG 58.500 45.000 0.00 0.00 0.00 5.69
4050 4728 6.736123 AGTACGGTAGTAGCATCTAAATGTG 58.264 40.000 0.00 0.00 35.18 3.21


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

AutoCloner maintained by Alex Coulton.