Multiple sequence alignment - TraesCS6B01G090200

Loading Multiple Alignment...

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 TraesCS6B01G090200 chr6B 100.000 3390 0 0 1 3390 65734981 65731592 0.000000e+00 6261
1 TraesCS6B01G090200 chrUn 92.993 1941 97 24 918 2846 100837794 100839707 0.000000e+00 2795
2 TraesCS6B01G090200 chrUn 92.014 864 64 3 1 863 100836835 100837694 0.000000e+00 1208
3 TraesCS6B01G090200 chrUn 89.730 185 18 1 2852 3036 100839800 100839983 5.660000e-58 235
4 TraesCS6B01G090200 chr6A 91.924 1944 122 20 924 2852 35639375 35637452 0.000000e+00 2687
5 TraesCS6B01G090200 chr6A 92.511 454 33 1 411 863 35639940 35639487 0.000000e+00 649
6 TraesCS6B01G090200 chr6A 88.860 386 37 3 1 385 35640315 35639935 1.420000e-128 470
7 TraesCS6B01G090200 chr6A 87.662 308 32 6 2730 3036 35637452 35637150 1.500000e-93 353
8 TraesCS6B01G090200 chr6A 88.614 202 20 2 3191 3390 35637003 35636803 3.380000e-60 243


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 TraesCS6B01G090200 chr6B 65731592 65734981 3389 True 6261.000000 6261 100.0000 1 3390 1 chr6B.!!$R1 3389
1 TraesCS6B01G090200 chrUn 100836835 100839983 3148 False 1412.666667 2795 91.5790 1 3036 3 chrUn.!!$F1 3035
2 TraesCS6B01G090200 chr6A 35636803 35640315 3512 True 880.400000 2687 89.9142 1 3390 5 chr6A.!!$R1 3389

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
636 637 0.179702 CCAAGCAGAGCCAGCTCATA 59.820 55.0 21.06 0.0 44.99 2.15 F
754 755 0.456142 CGACGTCTGCCTCGAAATCA 60.456 55.0 14.70 0.0 31.24 2.57 F
871 872 0.687354 ACATGGAGCTTCGTGTTCCT 59.313 50.0 14.52 0.0 45.05 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2261 2365 0.377554 CTGTCGACTACACGGCCTAG 59.622 60.000 17.92 0.0 37.06 3.02 R
2329 2433 0.742281 GGTCATCGTCATGCTGCAGT 60.742 55.000 16.64 0.0 0.00 4.40 R
2582 2687 2.035704 CAGCAGAGCATAGTCCTACCAG 59.964 54.545 0.00 0.0 0.00 4.00 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
98 99 4.577246 GCGGCGCGGAGAGAGAAT 62.577 66.667 19.09 0.00 0.00 2.40
100 101 1.359117 CGGCGCGGAGAGAGAATAA 59.641 57.895 9.72 0.00 0.00 1.40
128 129 3.003763 GCCGTGGAGAGGAAGGGT 61.004 66.667 0.00 0.00 0.00 4.34
133 134 1.535444 TGGAGAGGAAGGGTGCGAA 60.535 57.895 0.00 0.00 0.00 4.70
203 204 3.844090 GGAGACGAGGCTGGAGGC 61.844 72.222 2.65 0.00 41.43 4.70
303 304 1.227380 ATCGCCGGTGATCAAGAGC 60.227 57.895 24.82 0.00 0.00 4.09
341 342 2.031516 CCAGCAGTCAAGCGAGGTG 61.032 63.158 0.00 0.00 40.15 4.00
342 343 2.358003 AGCAGTCAAGCGAGGTGC 60.358 61.111 0.00 0.00 46.98 5.01
353 354 3.961414 GAGGTGCGGAAACCCCCA 61.961 66.667 0.00 0.00 41.54 4.96
385 386 4.267536 TCCTTCTCTTCAAATGCTCATGG 58.732 43.478 0.00 0.00 0.00 3.66
433 434 3.007831 TCTGATTTGCCCCCAAAATCAAC 59.992 43.478 11.47 0.00 43.58 3.18
473 474 1.337635 ACCTTTCTTCGCTCTGCAGAG 60.338 52.381 34.82 34.82 44.75 3.35
486 487 2.110967 GCAGAGCACCATGTCGCAT 61.111 57.895 6.39 0.00 0.00 4.73
510 511 4.170062 CAATCACGGCGCCTGCAG 62.170 66.667 26.68 11.62 45.35 4.41
613 614 0.747283 CAAGCCATCAGAGGAGCACC 60.747 60.000 0.00 0.00 0.00 5.01
629 630 2.149383 ACCTGTCCAAGCAGAGCCA 61.149 57.895 0.00 0.00 38.70 4.75
636 637 0.179702 CCAAGCAGAGCCAGCTCATA 59.820 55.000 21.06 0.00 44.99 2.15
648 649 2.630580 CCAGCTCATAGACTCCCTAACC 59.369 54.545 0.00 0.00 0.00 2.85
714 715 1.000938 GGATCATGCGCCAATTCCTTC 60.001 52.381 4.18 0.00 0.00 3.46
717 718 2.120909 ATGCGCCAATTCCTTCGGG 61.121 57.895 4.18 0.00 0.00 5.14
738 739 3.547249 TTCCCACAGCGACGTCGAC 62.547 63.158 39.74 28.78 43.02 4.20
754 755 0.456142 CGACGTCTGCCTCGAAATCA 60.456 55.000 14.70 0.00 31.24 2.57
783 784 4.828925 GGCAGCGAGGTGGAGCTC 62.829 72.222 4.71 4.71 42.52 4.09
795 796 2.202864 GAGCTCCTTCTGCGGCTC 60.203 66.667 0.87 0.00 43.07 4.70
839 840 0.892755 TTCGACAGCGTGGAGGTAAT 59.107 50.000 0.00 0.00 38.98 1.89
859 860 3.616956 TCAAGCCTTCACTACATGGAG 57.383 47.619 2.41 2.41 32.95 3.86
863 864 2.093235 AGCCTTCACTACATGGAGCTTC 60.093 50.000 4.32 0.00 31.56 3.86
865 866 2.093973 CCTTCACTACATGGAGCTTCGT 60.094 50.000 4.32 0.00 31.56 3.85
866 867 2.654749 TCACTACATGGAGCTTCGTG 57.345 50.000 13.01 13.01 0.00 4.35
867 868 1.893137 TCACTACATGGAGCTTCGTGT 59.107 47.619 23.28 23.28 39.81 4.49
869 870 2.668457 CACTACATGGAGCTTCGTGTTC 59.332 50.000 24.79 0.00 37.90 3.18
870 871 2.271800 CTACATGGAGCTTCGTGTTCC 58.728 52.381 24.79 1.67 45.03 3.62
871 872 0.687354 ACATGGAGCTTCGTGTTCCT 59.313 50.000 14.52 0.00 45.05 3.36
873 874 2.154462 CATGGAGCTTCGTGTTCCTTT 58.846 47.619 6.00 1.96 45.05 3.11
874 875 2.341846 TGGAGCTTCGTGTTCCTTTT 57.658 45.000 12.90 0.00 45.05 2.27
875 876 3.478857 TGGAGCTTCGTGTTCCTTTTA 57.521 42.857 12.90 0.00 45.05 1.52
876 877 3.811083 TGGAGCTTCGTGTTCCTTTTAA 58.189 40.909 12.90 0.00 45.05 1.52
877 878 4.200874 TGGAGCTTCGTGTTCCTTTTAAA 58.799 39.130 12.90 0.00 45.05 1.52
878 879 4.641094 TGGAGCTTCGTGTTCCTTTTAAAA 59.359 37.500 12.90 0.00 45.05 1.52
879 880 5.125739 TGGAGCTTCGTGTTCCTTTTAAAAA 59.874 36.000 1.66 0.00 45.05 1.94
950 1036 2.957402 TGAGGCTGTTGGTTTGATCT 57.043 45.000 0.00 0.00 0.00 2.75
952 1038 3.565307 TGAGGCTGTTGGTTTGATCTTT 58.435 40.909 0.00 0.00 0.00 2.52
962 1048 8.421249 TGTTGGTTTGATCTTTTATCATCCTT 57.579 30.769 0.00 0.00 0.00 3.36
969 1055 3.966979 TCTTTTATCATCCTTGCAGGCA 58.033 40.909 0.00 0.00 34.61 4.75
984 1070 2.292267 CAGGCAATTACCAGTGCTAGG 58.708 52.381 0.00 0.00 43.78 3.02
1050 1136 5.463286 TGTGACATTTGCATCAACAATCTC 58.537 37.500 0.00 0.00 0.00 2.75
1051 1137 5.242171 TGTGACATTTGCATCAACAATCTCT 59.758 36.000 0.00 0.00 0.00 3.10
1101 1187 3.201708 AGGATTATGCCCAGATAGATGGC 59.798 47.826 0.00 0.00 45.56 4.40
1198 1284 1.134995 TCTCCAGCTATGCGTGAGTTG 60.135 52.381 0.00 0.00 34.45 3.16
1271 1357 2.206576 AAGAATGGGGACTCACTTGC 57.793 50.000 0.00 0.00 0.00 4.01
1324 1410 4.248859 GCATCAGTTTCTTACAGCTGAGA 58.751 43.478 23.35 11.21 40.67 3.27
1336 1422 3.684693 GCTGAGAGAGCCCAAGATC 57.315 57.895 0.00 0.00 42.54 2.75
1348 1434 2.025321 GCCCAAGATCCTTCCCTGTTTA 60.025 50.000 0.00 0.00 0.00 2.01
1421 1511 5.237127 TGTGTCAATGCAGAAACTACTGAAG 59.763 40.000 0.00 0.00 39.94 3.02
1423 1513 5.237127 TGTCAATGCAGAAACTACTGAAGTG 59.763 40.000 0.00 0.00 41.24 3.16
1426 1516 1.461127 GCAGAAACTACTGAAGTGCCG 59.539 52.381 0.00 0.00 38.88 5.69
1442 1532 0.947180 GCCGAGTGCACTCCGTAAAA 60.947 55.000 35.07 0.00 39.79 1.52
1448 1538 5.490213 CGAGTGCACTCCGTAAAATTTATC 58.510 41.667 35.07 11.45 39.79 1.75
1561 1654 4.141551 TGCTCTAGTCATCATGGATTTGCT 60.142 41.667 0.00 0.00 0.00 3.91
1788 1890 5.302568 TCTTGTCCATGTTTTCAGCTTCATT 59.697 36.000 0.00 0.00 0.00 2.57
1805 1907 4.764679 TCATTATATGCATCGGTTTGGC 57.235 40.909 0.19 0.00 0.00 4.52
1810 1912 1.394266 ATGCATCGGTTTGGCCCATC 61.394 55.000 0.00 0.00 0.00 3.51
1852 1954 1.181786 TCCGCATTTCCCCACATTTC 58.818 50.000 0.00 0.00 0.00 2.17
1909 2011 4.764679 TGACACTGAATGCGCTTATTTT 57.235 36.364 9.73 0.00 0.00 1.82
2029 2131 6.097554 ACGATTACAGGAAAGATGTCATCTCT 59.902 38.462 15.75 1.48 39.08 3.10
2062 2164 7.974504 TGGGAAAGATAATCAGGTAGGTAATC 58.025 38.462 0.00 0.00 0.00 1.75
2196 2300 3.586618 AGCAAGAAGGAGAAGAACTGGAT 59.413 43.478 0.00 0.00 0.00 3.41
2261 2365 2.515996 TTTCGAGACCGGCCATGACC 62.516 60.000 0.00 0.00 36.24 4.02
2263 2367 2.125326 CGAGACCGGCCATGACCTA 61.125 63.158 0.00 0.00 0.00 3.08
2270 2374 2.203070 GCCATGACCTAGGCCGTG 60.203 66.667 9.30 9.82 45.18 4.94
2354 2458 1.026182 GCATGACGATGACCCTTGCA 61.026 55.000 0.00 0.00 33.08 4.08
2375 2479 1.074889 TGACCCTTTTTGAGCCCTACC 59.925 52.381 0.00 0.00 0.00 3.18
2386 2490 5.708736 TTGAGCCCTACCATTATGAGAAA 57.291 39.130 0.00 0.00 0.00 2.52
2393 2497 7.721399 AGCCCTACCATTATGAGAAATAAACAG 59.279 37.037 0.00 0.00 0.00 3.16
2408 2512 2.844122 AACAGCGAAAACACCTGAAC 57.156 45.000 0.00 0.00 0.00 3.18
2414 2518 3.569701 AGCGAAAACACCTGAACATTCAT 59.430 39.130 0.00 0.00 36.46 2.57
2415 2519 3.914364 GCGAAAACACCTGAACATTCATC 59.086 43.478 0.00 0.00 36.46 2.92
2416 2520 4.556501 GCGAAAACACCTGAACATTCATCA 60.557 41.667 0.00 0.00 36.46 3.07
2582 2687 2.596452 TCGTCGCAGAGAAAACTGATC 58.404 47.619 0.00 0.00 39.94 2.92
2652 2757 2.031682 GCAATGAGTTCACTGTGACCAC 60.032 50.000 10.56 7.25 0.00 4.16
2736 2841 2.273370 GCAACTGCATGGATTCACAG 57.727 50.000 0.00 0.00 41.59 3.66
2755 2860 6.650120 TCACAGTAGGGAAACTTAATGATCC 58.350 40.000 0.00 0.00 40.00 3.36
2774 2879 6.129179 TGATCCCACTTTCCAGGATATTTTC 58.871 40.000 0.00 0.00 40.54 2.29
2775 2880 4.867086 TCCCACTTTCCAGGATATTTTCC 58.133 43.478 0.00 0.00 45.85 3.13
2891 3115 3.246699 GCGTAACTGCACTTTTACAGTCA 59.753 43.478 0.00 0.00 46.17 3.41
2893 3117 3.944422 AACTGCACTTTTACAGTCACG 57.056 42.857 0.00 0.00 46.17 4.35
2894 3118 2.210116 ACTGCACTTTTACAGTCACGG 58.790 47.619 0.00 0.00 43.55 4.94
2908 3132 1.169661 TCACGGGTGTTGGACAATGC 61.170 55.000 0.00 0.00 0.00 3.56
2915 3139 2.158971 GGTGTTGGACAATGCAACCTTT 60.159 45.455 10.21 0.00 46.28 3.11
2925 3149 1.208614 GCAACCTTTCTCTGCAGCG 59.791 57.895 9.47 2.08 36.09 5.18
2931 3155 2.290323 ACCTTTCTCTGCAGCGGTAAAT 60.290 45.455 9.47 0.00 0.00 1.40
2932 3156 2.749621 CCTTTCTCTGCAGCGGTAAATT 59.250 45.455 9.47 0.00 0.00 1.82
2933 3157 3.426695 CCTTTCTCTGCAGCGGTAAATTG 60.427 47.826 9.47 0.00 0.00 2.32
2946 3170 3.065371 CGGTAAATTGTGAGATGAAGGCC 59.935 47.826 0.00 0.00 0.00 5.19
2966 3190 3.433740 GCCCCTAGGACAAAAGGATACTG 60.434 52.174 11.48 0.00 41.46 2.74
2969 3193 7.662526 CCCCTAGGACAAAAGGATACTGCAG 62.663 52.000 13.48 13.48 41.46 4.41
3019 3243 2.572104 GGACTTTCCTAGCCCTGAAGAA 59.428 50.000 0.00 0.00 32.53 2.52
3022 3246 4.849518 ACTTTCCTAGCCCTGAAGAAATC 58.150 43.478 0.00 0.00 0.00 2.17
3036 3260 2.966050 AGAAATCGAGCAGGTCTTGAC 58.034 47.619 0.00 0.00 38.01 3.18
3037 3261 2.564947 AGAAATCGAGCAGGTCTTGACT 59.435 45.455 0.00 0.00 38.01 3.41
3038 3262 2.663826 AATCGAGCAGGTCTTGACTC 57.336 50.000 0.00 0.00 38.01 3.36
3039 3263 0.453793 ATCGAGCAGGTCTTGACTCG 59.546 55.000 16.88 16.88 45.91 4.18
3040 3264 1.803519 CGAGCAGGTCTTGACTCGC 60.804 63.158 12.98 4.21 42.21 5.03
3041 3265 1.290324 GAGCAGGTCTTGACTCGCA 59.710 57.895 13.96 0.00 0.00 5.10
3042 3266 0.319900 GAGCAGGTCTTGACTCGCAA 60.320 55.000 13.96 0.00 34.73 4.85
3043 3267 0.601311 AGCAGGTCTTGACTCGCAAC 60.601 55.000 13.96 0.00 31.96 4.17
3044 3268 0.880278 GCAGGTCTTGACTCGCAACA 60.880 55.000 0.61 0.00 31.96 3.33
3045 3269 1.800805 CAGGTCTTGACTCGCAACAT 58.199 50.000 0.61 0.00 31.96 2.71
3046 3270 2.930887 GCAGGTCTTGACTCGCAACATA 60.931 50.000 0.61 0.00 31.96 2.29
3047 3271 3.325870 CAGGTCTTGACTCGCAACATAA 58.674 45.455 0.61 0.00 31.96 1.90
3048 3272 3.745975 CAGGTCTTGACTCGCAACATAAA 59.254 43.478 0.61 0.00 31.96 1.40
3049 3273 4.213270 CAGGTCTTGACTCGCAACATAAAA 59.787 41.667 0.61 0.00 31.96 1.52
3050 3274 4.819630 AGGTCTTGACTCGCAACATAAAAA 59.180 37.500 0.61 0.00 31.96 1.94
3080 3304 4.297299 TCGAGTACGTCTTGAACTTTGT 57.703 40.909 0.00 0.00 40.69 2.83
3088 3312 6.687081 ACGTCTTGAACTTTGTTTCCAATA 57.313 33.333 0.00 0.00 0.00 1.90
3103 3327 6.321945 TGTTTCCAATATTATCATGTGCAGCT 59.678 34.615 0.00 0.00 0.00 4.24
3104 3328 6.564709 TTCCAATATTATCATGTGCAGCTC 57.435 37.500 0.00 0.00 0.00 4.09
3105 3329 5.005740 TCCAATATTATCATGTGCAGCTCC 58.994 41.667 0.00 0.00 0.00 4.70
3123 3380 4.555262 GCTCCTGCTCTAATCATAGACAC 58.445 47.826 0.00 0.00 34.45 3.67
3139 3396 7.330262 TCATAGACACTGCTGAATGATGTTTA 58.670 34.615 0.00 0.00 0.00 2.01
3140 3397 5.869753 AGACACTGCTGAATGATGTTTAC 57.130 39.130 0.00 0.00 0.00 2.01
3141 3398 4.389992 AGACACTGCTGAATGATGTTTACG 59.610 41.667 0.00 0.00 0.00 3.18
3143 3400 3.684305 CACTGCTGAATGATGTTTACGGA 59.316 43.478 0.00 0.00 0.00 4.69
3144 3401 4.154015 CACTGCTGAATGATGTTTACGGAA 59.846 41.667 0.00 0.00 0.00 4.30
3145 3402 4.943705 ACTGCTGAATGATGTTTACGGAAT 59.056 37.500 0.00 0.00 0.00 3.01
3152 3409 6.925718 TGAATGATGTTTACGGAATTGCAAAA 59.074 30.769 1.71 0.00 0.00 2.44
3153 3410 6.704512 ATGATGTTTACGGAATTGCAAAAC 57.295 33.333 1.71 14.31 0.00 2.43
3154 3411 5.592054 TGATGTTTACGGAATTGCAAAACA 58.408 33.333 21.64 21.64 42.35 2.83
3156 3413 5.896922 TGTTTACGGAATTGCAAAACATG 57.103 34.783 17.90 0.00 35.69 3.21
3167 3424 2.288961 CAAAACATGCATGCCCTCTC 57.711 50.000 26.53 0.00 0.00 3.20
3168 3425 1.822990 CAAAACATGCATGCCCTCTCT 59.177 47.619 26.53 1.90 0.00 3.10
3169 3426 1.760192 AAACATGCATGCCCTCTCTC 58.240 50.000 26.53 0.00 0.00 3.20
3170 3427 0.622136 AACATGCATGCCCTCTCTCA 59.378 50.000 26.53 0.00 0.00 3.27
3171 3428 0.622136 ACATGCATGCCCTCTCTCAA 59.378 50.000 26.53 0.00 0.00 3.02
3174 3431 1.300963 GCATGCCCTCTCTCAACCA 59.699 57.895 6.36 0.00 0.00 3.67
3175 3432 0.747283 GCATGCCCTCTCTCAACCAG 60.747 60.000 6.36 0.00 0.00 4.00
3176 3433 0.617413 CATGCCCTCTCTCAACCAGT 59.383 55.000 0.00 0.00 0.00 4.00
3177 3434 0.617413 ATGCCCTCTCTCAACCAGTG 59.383 55.000 0.00 0.00 0.00 3.66
3178 3435 0.471780 TGCCCTCTCTCAACCAGTGA 60.472 55.000 0.00 0.00 34.17 3.41
3180 3437 2.111384 GCCCTCTCTCAACCAGTGATA 58.889 52.381 0.00 0.00 35.07 2.15
3181 3438 2.159028 GCCCTCTCTCAACCAGTGATAC 60.159 54.545 0.00 0.00 35.07 2.24
3183 3440 3.708631 CCCTCTCTCAACCAGTGATACAT 59.291 47.826 0.00 0.00 35.07 2.29
3185 3442 4.202202 CCTCTCTCAACCAGTGATACATCC 60.202 50.000 0.00 0.00 35.07 3.51
3186 3443 4.614475 TCTCTCAACCAGTGATACATCCT 58.386 43.478 0.00 0.00 35.07 3.24
3187 3444 4.646945 TCTCTCAACCAGTGATACATCCTC 59.353 45.833 0.00 0.00 35.07 3.71
3189 3446 5.026121 TCTCAACCAGTGATACATCCTCTT 58.974 41.667 0.00 0.00 35.07 2.85
3190 3447 6.194967 TCTCAACCAGTGATACATCCTCTTA 58.805 40.000 0.00 0.00 35.07 2.10
3191 3448 6.841229 TCTCAACCAGTGATACATCCTCTTAT 59.159 38.462 0.00 0.00 35.07 1.73
3192 3449 6.820335 TCAACCAGTGATACATCCTCTTATG 58.180 40.000 0.00 0.00 0.00 1.90
3193 3450 6.384015 TCAACCAGTGATACATCCTCTTATGT 59.616 38.462 0.00 0.00 42.62 2.29
3194 3451 6.814954 ACCAGTGATACATCCTCTTATGTT 57.185 37.500 0.00 0.00 40.52 2.71
3209 3466 5.376625 TCTTATGTTGCCTTCACTTTGACT 58.623 37.500 0.00 0.00 0.00 3.41
3233 3490 3.568538 CTCAGGCTGGTTGAAATTTTCG 58.431 45.455 15.73 0.00 0.00 3.46
3236 3493 4.580995 TCAGGCTGGTTGAAATTTTCGTTA 59.419 37.500 15.73 0.00 0.00 3.18
3271 3528 2.920524 TGGAGAAACAAGCCGTTGTAA 58.079 42.857 0.00 0.00 46.68 2.41
3293 3550 0.600255 CGCTTCCAAACCGACTCTGT 60.600 55.000 0.00 0.00 0.00 3.41
3299 3556 2.901192 TCCAAACCGACTCTGTAATGGA 59.099 45.455 4.75 4.75 32.52 3.41
3302 3559 4.083484 CCAAACCGACTCTGTAATGGAAAC 60.083 45.833 0.00 0.00 0.00 2.78
3318 3575 5.514274 TGGAAACATTGTTCAAAGAGACC 57.486 39.130 1.83 0.00 33.40 3.85
3354 3611 6.925610 TCGTAAGATGCTGCATTTCTAAAT 57.074 33.333 17.36 0.00 45.01 1.40
3356 3613 7.851508 TCGTAAGATGCTGCATTTCTAAATAC 58.148 34.615 17.36 8.86 45.01 1.89
3358 3615 8.122330 CGTAAGATGCTGCATTTCTAAATACAA 58.878 33.333 17.36 0.00 43.02 2.41
3359 3616 9.956720 GTAAGATGCTGCATTTCTAAATACAAT 57.043 29.630 17.36 0.00 0.00 2.71
3360 3617 8.867112 AAGATGCTGCATTTCTAAATACAATG 57.133 30.769 17.36 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 0.661780 CTTATTCTCTCTCCGCGCCG 60.662 60.000 0.00 0.00 0.00 6.46
83 84 0.319125 CCTTATTCTCTCTCCGCGCC 60.319 60.000 0.00 0.00 0.00 6.53
84 85 0.386113 ACCTTATTCTCTCTCCGCGC 59.614 55.000 0.00 0.00 0.00 6.86
92 93 2.290960 GGCAACCCACACCTTATTCTCT 60.291 50.000 0.00 0.00 0.00 3.10
98 99 1.228003 CACGGCAACCCACACCTTA 60.228 57.895 0.00 0.00 0.00 2.69
100 101 4.579384 CCACGGCAACCCACACCT 62.579 66.667 0.00 0.00 0.00 4.00
128 129 4.751093 TCGCTTCCGCCATTCGCA 62.751 61.111 0.00 0.00 37.30 5.10
133 134 2.436646 CCAAGTCGCTTCCGCCAT 60.437 61.111 0.00 0.00 0.00 4.40
140 141 1.006102 CTGGTCGTCCAAGTCGCTT 60.006 57.895 2.32 0.00 43.81 4.68
176 177 3.456431 CTCGTCTCCGCCTGCGTAG 62.456 68.421 10.94 4.12 37.81 3.51
197 198 2.586245 CCTTCGATGCTGCCTCCA 59.414 61.111 0.00 0.00 0.00 3.86
200 201 2.262774 CTTCCCCTTCGATGCTGCCT 62.263 60.000 0.00 0.00 0.00 4.75
203 204 0.813210 GCTCTTCCCCTTCGATGCTG 60.813 60.000 0.00 0.00 0.00 4.41
207 208 0.980231 AGCTGCTCTTCCCCTTCGAT 60.980 55.000 0.00 0.00 0.00 3.59
367 368 5.065602 CGAATTCCATGAGCATTTGAAGAGA 59.934 40.000 0.00 0.00 0.00 3.10
379 380 3.376234 AGTGTGCAATCGAATTCCATGAG 59.624 43.478 0.00 0.00 0.00 2.90
385 386 4.032789 GATGGCAGTGTGCAATCGAATTC 61.033 47.826 0.54 0.00 43.18 2.17
473 474 3.485110 TCGAATGCGACATGGTGC 58.515 55.556 0.00 0.37 42.51 5.01
486 487 2.673114 GCGCCGTGATTGGTTCGAA 61.673 57.895 0.00 0.00 0.00 3.71
510 511 2.146342 CACCCTGTGTGTGTTCTGATC 58.854 52.381 0.00 0.00 40.26 2.92
613 614 2.039405 GCTGGCTCTGCTTGGACAG 61.039 63.158 0.00 0.00 39.12 3.51
629 630 3.689872 TGGTTAGGGAGTCTATGAGCT 57.310 47.619 0.00 0.00 0.00 4.09
636 637 2.900546 CACTGACTTGGTTAGGGAGTCT 59.099 50.000 4.61 0.00 40.28 3.24
648 649 3.611057 GCCATTCTTTGCTCACTGACTTG 60.611 47.826 0.00 0.00 0.00 3.16
717 718 1.733399 GACGTCGCTGTGGGAAGTC 60.733 63.158 0.00 12.68 43.32 3.01
738 739 1.996292 TCTTGATTTCGAGGCAGACG 58.004 50.000 0.00 0.00 0.00 4.18
805 806 1.437089 CGAAATTATCGCCGCGCAG 60.437 57.895 8.75 0.00 45.89 5.18
839 840 2.355108 GCTCCATGTAGTGAAGGCTTGA 60.355 50.000 3.46 0.00 0.00 3.02
962 1048 0.251297 AGCACTGGTAATTGCCTGCA 60.251 50.000 22.78 0.98 39.75 4.41
969 1055 1.064685 GGCACCCTAGCACTGGTAATT 60.065 52.381 0.00 0.00 35.83 1.40
1101 1187 0.680280 AGGCCAGCTGAAGCAATCTG 60.680 55.000 17.39 0.00 45.16 2.90
1245 1331 4.104738 AGTGAGTCCCCATTCTTTTGAGAA 59.895 41.667 0.00 0.00 0.00 2.87
1246 1332 3.652869 AGTGAGTCCCCATTCTTTTGAGA 59.347 43.478 0.00 0.00 0.00 3.27
1249 1335 3.305608 GCAAGTGAGTCCCCATTCTTTTG 60.306 47.826 0.00 0.00 0.00 2.44
1271 1357 9.740239 AAGCACATATCTGCAATTTTACATAAG 57.260 29.630 5.72 0.00 39.86 1.73
1324 1410 0.045469 AGGGAAGGATCTTGGGCTCT 59.955 55.000 0.00 0.00 0.00 4.09
1396 1486 5.122519 TCAGTAGTTTCTGCATTGACACAA 58.877 37.500 0.00 0.00 35.63 3.33
1401 1491 4.214119 GCACTTCAGTAGTTTCTGCATTGA 59.786 41.667 0.00 0.00 33.85 2.57
1403 1493 3.503748 GGCACTTCAGTAGTTTCTGCATT 59.496 43.478 0.00 0.00 33.85 3.56
1423 1513 0.947180 TTTTACGGAGTGCACTCGGC 60.947 55.000 39.18 26.63 45.73 5.54
1426 1516 6.417191 TGATAAATTTTACGGAGTGCACTC 57.583 37.500 34.25 34.25 45.73 3.51
1532 1625 5.847304 TCCATGATGACTAGAGCACATAAC 58.153 41.667 0.00 0.00 0.00 1.89
1561 1654 0.604073 CATGCACAGTGCCAAATGGA 59.396 50.000 23.06 2.24 44.23 3.41
1569 1662 4.412207 CATATCATATGCATGCACAGTGC 58.588 43.478 25.37 19.37 45.29 4.40
1669 1770 7.254353 GCAAAATAACCTACTACATCGGAGAAC 60.254 40.741 0.00 0.00 43.58 3.01
1672 1773 5.465724 GGCAAAATAACCTACTACATCGGAG 59.534 44.000 0.00 0.00 0.00 4.63
1673 1774 5.104859 TGGCAAAATAACCTACTACATCGGA 60.105 40.000 0.00 0.00 0.00 4.55
1735 1836 2.038557 TGTTCCTTCTGACTTACCTGGC 59.961 50.000 0.00 0.00 0.00 4.85
1788 1890 1.143889 TGGGCCAAACCGATGCATATA 59.856 47.619 2.13 0.00 40.62 0.86
1833 1935 1.181786 GAAATGTGGGGAAATGCGGA 58.818 50.000 0.00 0.00 0.00 5.54
1836 1938 1.207811 CCTGGAAATGTGGGGAAATGC 59.792 52.381 0.00 0.00 0.00 3.56
2029 2131 6.729100 ACCTGATTATCTTTCCCATACGGATA 59.271 38.462 0.00 0.00 41.63 2.59
2062 2164 2.751806 GGAAGAAGAATGCTGGTCCTTG 59.248 50.000 0.00 0.00 0.00 3.61
2167 2271 5.489792 TCTTCTCCTTCTTGCTACATGTT 57.510 39.130 2.30 0.00 0.00 2.71
2196 2300 0.731514 GTCGTTTCCGATGCGAGTCA 60.732 55.000 0.00 0.00 46.30 3.41
2261 2365 0.377554 CTGTCGACTACACGGCCTAG 59.622 60.000 17.92 0.00 37.06 3.02
2263 2367 2.341101 CCTGTCGACTACACGGCCT 61.341 63.158 17.92 0.00 37.06 5.19
2269 2373 1.324383 TTGTCTGCCTGTCGACTACA 58.676 50.000 17.92 10.93 36.42 2.74
2270 2374 2.094700 TGATTGTCTGCCTGTCGACTAC 60.095 50.000 17.92 6.60 0.00 2.73
2327 2431 1.590238 GTCATCGTCATGCTGCAGTAC 59.410 52.381 16.64 7.74 0.00 2.73
2329 2433 0.742281 GGTCATCGTCATGCTGCAGT 60.742 55.000 16.64 0.00 0.00 4.40
2354 2458 2.291605 GGTAGGGCTCAAAAAGGGTCAT 60.292 50.000 0.00 0.00 0.00 3.06
2375 2479 9.340695 TGTTTTCGCTGTTTATTTCTCATAATG 57.659 29.630 0.00 0.00 0.00 1.90
2386 2490 4.336993 TGTTCAGGTGTTTTCGCTGTTTAT 59.663 37.500 0.00 0.00 0.00 1.40
2393 2497 3.347958 TGAATGTTCAGGTGTTTTCGC 57.652 42.857 0.00 0.00 32.50 4.70
2408 2512 4.868171 CCTGGCAGAAATGTTTGATGAATG 59.132 41.667 17.94 0.00 0.00 2.67
2414 2518 2.892852 CCTTCCTGGCAGAAATGTTTGA 59.107 45.455 17.94 0.00 0.00 2.69
2415 2519 2.629617 ACCTTCCTGGCAGAAATGTTTG 59.370 45.455 17.94 0.00 40.22 2.93
2416 2520 2.629617 CACCTTCCTGGCAGAAATGTTT 59.370 45.455 17.94 0.00 40.22 2.83
2522 2627 4.819783 GTGAATGCACCTGACCCA 57.180 55.556 0.00 0.00 39.14 4.51
2582 2687 2.035704 CAGCAGAGCATAGTCCTACCAG 59.964 54.545 0.00 0.00 0.00 4.00
2652 2757 4.082300 AGAGCACAGAACATGAGAGTGTAG 60.082 45.833 0.00 0.00 32.99 2.74
2736 2841 6.002653 AGTGGGATCATTAAGTTTCCCTAC 57.997 41.667 16.29 13.14 46.73 3.18
2774 2879 7.997107 CAACATGAAAGAATATGGATGTTGG 57.003 36.000 12.67 0.00 43.38 3.77
2846 2951 6.570789 CGCAAGCATGTAAAGAATTTTTGTTG 59.429 34.615 0.00 0.00 40.09 3.33
2847 2952 6.257630 ACGCAAGCATGTAAAGAATTTTTGTT 59.742 30.769 0.00 0.00 39.87 2.83
2891 3115 0.753479 TTGCATTGTCCAACACCCGT 60.753 50.000 0.00 0.00 0.00 5.28
2893 3117 0.033366 GGTTGCATTGTCCAACACCC 59.967 55.000 6.60 0.00 43.24 4.61
2894 3118 1.039856 AGGTTGCATTGTCCAACACC 58.960 50.000 6.60 0.00 43.24 4.16
2908 3132 0.886490 ACCGCTGCAGAGAAAGGTTG 60.886 55.000 20.43 1.64 0.00 3.77
2915 3139 2.076100 CACAATTTACCGCTGCAGAGA 58.924 47.619 20.43 0.00 0.00 3.10
2925 3149 3.381590 GGGCCTTCATCTCACAATTTACC 59.618 47.826 0.84 0.00 0.00 2.85
2931 3155 1.839994 CTAGGGGCCTTCATCTCACAA 59.160 52.381 0.84 0.00 0.00 3.33
2932 3156 1.500474 CTAGGGGCCTTCATCTCACA 58.500 55.000 0.84 0.00 0.00 3.58
2933 3157 0.761802 CCTAGGGGCCTTCATCTCAC 59.238 60.000 0.84 0.00 0.00 3.51
2946 3170 3.199946 TGCAGTATCCTTTTGTCCTAGGG 59.800 47.826 9.46 0.00 32.20 3.53
2959 3183 4.100808 AGAATTCAGTCTCCTGCAGTATCC 59.899 45.833 13.81 0.00 38.66 2.59
2966 3190 2.769095 AGGGTAGAATTCAGTCTCCTGC 59.231 50.000 8.44 0.00 38.66 4.85
2969 3193 4.279922 GCTCTAGGGTAGAATTCAGTCTCC 59.720 50.000 8.44 2.10 33.75 3.71
2975 3199 5.397899 CCATTTGGCTCTAGGGTAGAATTCA 60.398 44.000 8.44 0.00 33.75 2.57
3019 3243 1.135257 CGAGTCAAGACCTGCTCGATT 60.135 52.381 6.95 0.00 46.04 3.34
3022 3246 1.803519 GCGAGTCAAGACCTGCTCG 60.804 63.158 8.23 8.23 45.97 5.03
3054 3278 6.839820 AAGTTCAAGACGTACTCGATTTTT 57.160 33.333 0.00 0.00 40.62 1.94
3055 3279 6.257193 ACAAAGTTCAAGACGTACTCGATTTT 59.743 34.615 0.00 0.00 40.62 1.82
3056 3280 5.751990 ACAAAGTTCAAGACGTACTCGATTT 59.248 36.000 0.00 0.00 40.62 2.17
3057 3281 5.287226 ACAAAGTTCAAGACGTACTCGATT 58.713 37.500 0.00 0.00 40.62 3.34
3058 3282 4.868067 ACAAAGTTCAAGACGTACTCGAT 58.132 39.130 0.00 0.00 40.62 3.59
3059 3283 4.297299 ACAAAGTTCAAGACGTACTCGA 57.703 40.909 0.00 0.00 40.62 4.04
3060 3284 5.385396 AAACAAAGTTCAAGACGTACTCG 57.615 39.130 0.00 0.00 43.34 4.18
3061 3285 5.292589 TGGAAACAAAGTTCAAGACGTACTC 59.707 40.000 0.00 0.00 37.44 2.59
3062 3286 5.180271 TGGAAACAAAGTTCAAGACGTACT 58.820 37.500 0.00 0.00 37.44 2.73
3063 3287 5.473796 TGGAAACAAAGTTCAAGACGTAC 57.526 39.130 0.00 0.00 37.44 3.67
3080 3304 6.016024 GGAGCTGCACATGATAATATTGGAAA 60.016 38.462 0.00 0.00 0.00 3.13
3103 3327 4.038522 GCAGTGTCTATGATTAGAGCAGGA 59.961 45.833 0.00 0.00 35.12 3.86
3104 3328 4.039004 AGCAGTGTCTATGATTAGAGCAGG 59.961 45.833 0.00 0.00 35.12 4.85
3105 3329 4.983538 CAGCAGTGTCTATGATTAGAGCAG 59.016 45.833 0.00 0.00 35.12 4.24
3108 3332 7.432059 TCATTCAGCAGTGTCTATGATTAGAG 58.568 38.462 0.00 0.00 35.12 2.43
3109 3333 7.352079 TCATTCAGCAGTGTCTATGATTAGA 57.648 36.000 0.00 0.00 31.89 2.10
3110 3334 7.656542 ACATCATTCAGCAGTGTCTATGATTAG 59.343 37.037 8.74 4.59 31.48 1.73
3112 3336 6.354938 ACATCATTCAGCAGTGTCTATGATT 58.645 36.000 8.74 0.00 31.48 2.57
3113 3337 5.926663 ACATCATTCAGCAGTGTCTATGAT 58.073 37.500 0.00 0.00 32.76 2.45
3114 3338 5.349061 ACATCATTCAGCAGTGTCTATGA 57.651 39.130 0.00 0.00 0.00 2.15
3115 3339 6.432607 AAACATCATTCAGCAGTGTCTATG 57.567 37.500 0.00 0.00 0.00 2.23
3116 3340 6.256539 CGTAAACATCATTCAGCAGTGTCTAT 59.743 38.462 0.00 0.00 0.00 1.98
3117 3341 5.576774 CGTAAACATCATTCAGCAGTGTCTA 59.423 40.000 0.00 0.00 0.00 2.59
3123 3380 4.944962 TTCCGTAAACATCATTCAGCAG 57.055 40.909 0.00 0.00 0.00 4.24
3152 3409 0.622136 TTGAGAGAGGGCATGCATGT 59.378 50.000 26.79 8.33 0.00 3.21
3153 3410 1.022735 GTTGAGAGAGGGCATGCATG 58.977 55.000 22.70 22.70 0.00 4.06
3154 3411 0.106819 GGTTGAGAGAGGGCATGCAT 60.107 55.000 21.36 7.26 0.00 3.96
3155 3412 1.300963 GGTTGAGAGAGGGCATGCA 59.699 57.895 21.36 0.00 0.00 3.96
3156 3413 0.747283 CTGGTTGAGAGAGGGCATGC 60.747 60.000 9.90 9.90 0.00 4.06
3157 3414 0.617413 ACTGGTTGAGAGAGGGCATG 59.383 55.000 0.00 0.00 0.00 4.06
3158 3415 0.617413 CACTGGTTGAGAGAGGGCAT 59.383 55.000 0.00 0.00 0.00 4.40
3159 3416 0.471780 TCACTGGTTGAGAGAGGGCA 60.472 55.000 0.00 0.00 0.00 5.36
3160 3417 0.908198 ATCACTGGTTGAGAGAGGGC 59.092 55.000 0.00 0.00 37.77 5.19
3161 3418 3.099905 TGTATCACTGGTTGAGAGAGGG 58.900 50.000 0.00 0.00 37.77 4.30
3162 3419 4.202202 GGATGTATCACTGGTTGAGAGAGG 60.202 50.000 0.00 0.00 37.77 3.69
3163 3420 4.648762 AGGATGTATCACTGGTTGAGAGAG 59.351 45.833 0.00 0.00 37.77 3.20
3165 3422 4.648762 AGAGGATGTATCACTGGTTGAGAG 59.351 45.833 0.00 0.00 37.77 3.20
3167 3424 5.350504 AAGAGGATGTATCACTGGTTGAG 57.649 43.478 0.00 0.00 37.77 3.02
3168 3425 6.384015 ACATAAGAGGATGTATCACTGGTTGA 59.616 38.462 0.00 0.00 38.29 3.18
3169 3426 6.586344 ACATAAGAGGATGTATCACTGGTTG 58.414 40.000 0.00 0.00 38.29 3.77
3170 3427 6.814954 ACATAAGAGGATGTATCACTGGTT 57.185 37.500 0.00 0.00 38.29 3.67
3171 3428 6.586344 CAACATAAGAGGATGTATCACTGGT 58.414 40.000 0.00 0.00 39.16 4.00
3174 3431 5.367937 AGGCAACATAAGAGGATGTATCACT 59.632 40.000 0.00 0.00 39.16 3.41
3175 3432 5.615289 AGGCAACATAAGAGGATGTATCAC 58.385 41.667 0.00 0.00 39.16 3.06
3176 3433 5.894298 AGGCAACATAAGAGGATGTATCA 57.106 39.130 0.00 0.00 39.16 2.15
3177 3434 6.203723 GTGAAGGCAACATAAGAGGATGTATC 59.796 42.308 0.00 0.00 39.16 2.24
3178 3435 6.058183 GTGAAGGCAACATAAGAGGATGTAT 58.942 40.000 0.00 0.00 39.16 2.29
3180 3437 4.018960 AGTGAAGGCAACATAAGAGGATGT 60.019 41.667 0.00 0.00 41.92 3.06
3181 3438 4.521146 AGTGAAGGCAACATAAGAGGATG 58.479 43.478 0.00 0.00 41.41 3.51
3183 3440 4.640771 AAGTGAAGGCAACATAAGAGGA 57.359 40.909 0.00 0.00 41.41 3.71
3185 3442 5.471456 AGTCAAAGTGAAGGCAACATAAGAG 59.529 40.000 0.00 0.00 41.41 2.85
3186 3443 5.376625 AGTCAAAGTGAAGGCAACATAAGA 58.623 37.500 0.00 0.00 41.41 2.10
3187 3444 5.695851 AGTCAAAGTGAAGGCAACATAAG 57.304 39.130 0.00 0.00 41.41 1.73
3189 3446 4.261572 GCAAGTCAAAGTGAAGGCAACATA 60.262 41.667 0.00 0.00 41.41 2.29
3190 3447 3.491447 GCAAGTCAAAGTGAAGGCAACAT 60.491 43.478 0.00 0.00 41.41 2.71
3191 3448 2.159254 GCAAGTCAAAGTGAAGGCAACA 60.159 45.455 0.00 0.00 41.41 3.33
3192 3449 2.099756 AGCAAGTCAAAGTGAAGGCAAC 59.900 45.455 0.00 0.00 0.00 4.17
3193 3450 2.358898 GAGCAAGTCAAAGTGAAGGCAA 59.641 45.455 0.00 0.00 0.00 4.52
3194 3451 1.949525 GAGCAAGTCAAAGTGAAGGCA 59.050 47.619 0.00 0.00 0.00 4.75
3209 3466 1.999648 ATTTCAACCAGCCTGAGCAA 58.000 45.000 0.00 0.00 43.56 3.91
3233 3490 3.011119 TCCAACGGGCATGTTGTATAAC 58.989 45.455 17.13 0.00 46.08 1.89
3236 3493 1.280710 TCTCCAACGGGCATGTTGTAT 59.719 47.619 17.13 0.00 46.08 2.29
3293 3550 7.286546 TGGTCTCTTTGAACAATGTTTCCATTA 59.713 33.333 0.00 0.00 39.83 1.90
3306 3563 4.767409 AGCCCTAATTTGGTCTCTTTGAAC 59.233 41.667 5.19 0.00 0.00 3.18
3318 3575 5.934625 AGCATCTTACGATAGCCCTAATTTG 59.065 40.000 0.00 0.00 42.67 2.32
3333 3590 9.956720 ATTGTATTTAGAAATGCAGCATCTTAC 57.043 29.630 8.77 4.18 41.01 2.34
3353 3610 9.926158 TGTTCATTTCTACAAAATGCATTGTAT 57.074 25.926 13.82 0.00 42.96 2.29
3354 3611 9.926158 ATGTTCATTTCTACAAAATGCATTGTA 57.074 25.926 13.82 12.37 43.09 2.41
3355 3612 8.836268 ATGTTCATTTCTACAAAATGCATTGT 57.164 26.923 13.82 11.83 45.14 2.71
3358 3615 7.981225 GGGTATGTTCATTTCTACAAAATGCAT 59.019 33.333 0.00 0.00 37.50 3.96
3359 3616 7.039434 TGGGTATGTTCATTTCTACAAAATGCA 60.039 33.333 5.78 0.00 37.50 3.96
3360 3617 7.275560 GTGGGTATGTTCATTTCTACAAAATGC 59.724 37.037 5.78 0.00 37.50 3.56
3361 3618 8.522830 AGTGGGTATGTTCATTTCTACAAAATG 58.477 33.333 4.50 4.50 38.60 2.32
3362 3619 8.522830 CAGTGGGTATGTTCATTTCTACAAAAT 58.477 33.333 0.00 0.00 0.00 1.82
3363 3620 7.040062 CCAGTGGGTATGTTCATTTCTACAAAA 60.040 37.037 0.00 0.00 0.00 2.44
3364 3621 6.432783 CCAGTGGGTATGTTCATTTCTACAAA 59.567 38.462 0.00 0.00 0.00 2.83
3366 3623 5.496556 CCAGTGGGTATGTTCATTTCTACA 58.503 41.667 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.