Multiple sequence alignment - TraesCS1B01G355600

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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 TraesCS1B01G355600 chr1B 100.000 5098 0 0 902 5999 585068924 585074021 0.000000e+00 9415
1 TraesCS1B01G355600 chr1B 100.000 654 0 0 1 654 585068023 585068676 0.000000e+00 1208
2 TraesCS1B01G355600 chr1A 95.067 3264 100 22 2761 5999 531605518 531608745 0.000000e+00 5079
3 TraesCS1B01G355600 chr1A 93.219 1755 97 8 968 2706 531603633 531605381 0.000000e+00 2562
4 TraesCS1B01G355600 chr1A 86.435 634 47 24 24 654 531602933 531603530 0.000000e+00 658
5 TraesCS1B01G355600 chr1D 93.477 1717 65 14 4294 5999 433212298 433213978 0.000000e+00 2507
6 TraesCS1B01G355600 chr1D 91.703 1844 88 24 902 2706 433208778 433210595 0.000000e+00 2497
7 TraesCS1B01G355600 chr1D 95.623 1051 38 6 2761 3805 433210732 433211780 0.000000e+00 1679
8 TraesCS1B01G355600 chr1D 88.802 643 44 16 30 654 433208125 433208757 0.000000e+00 763
9 TraesCS1B01G355600 chr1D 89.266 354 12 10 3802 4145 433211818 433212155 2.590000e-113 420
10 TraesCS1B01G355600 chr1D 89.394 132 7 1 4181 4312 433212158 433212282 6.220000e-35 159
11 TraesCS1B01G355600 chr3D 76.358 313 59 12 1000 1303 382746778 382747084 2.900000e-33 154
12 TraesCS1B01G355600 chr3A 76.358 313 59 12 1000 1303 505716625 505716931 2.900000e-33 154
13 TraesCS1B01G355600 chr3B 75.641 312 63 13 1000 1303 498360299 498360605 6.270000e-30 143


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 TraesCS1B01G355600 chr1B 585068023 585074021 5998 False 5311.500000 9415 100.000000 1 5999 2 chr1B.!!$F1 5998
1 TraesCS1B01G355600 chr1A 531602933 531608745 5812 False 2766.333333 5079 91.573667 24 5999 3 chr1A.!!$F1 5975
2 TraesCS1B01G355600 chr1D 433208125 433213978 5853 False 1337.500000 2507 91.377500 30 5999 6 chr1D.!!$F1 5969

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
619 641 0.109153 AGGGGCGGTTAAAAAGTCGT 59.891 50.0 0.00 0.0 0.00 4.34 F
1420 1478 0.179018 GGAAAGTGGCCTGCGGATAT 60.179 55.0 3.32 0.0 0.00 1.63 F
2532 2603 0.316841 GGGCTTTTCAATCAACGGCA 59.683 50.0 0.00 0.0 0.00 5.69 F
3233 3401 0.178932 AGTGGACTGGACTACTGCCA 60.179 55.0 0.00 0.0 30.79 4.92 F
4588 4850 0.863144 CGTTGGGGTACGACTGTTTG 59.137 55.0 0.00 0.0 43.99 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1617 0.321298 ACGGTGTTCCTGATTTCGGG 60.321 55.000 0.00 0.00 43.86 5.14 R
3028 3194 0.306533 ACGACCATGTTTGTTCGCAC 59.693 50.000 0.00 0.00 0.00 5.34 R
3970 4189 1.268896 CCGGCAATGATCAATCAGCAC 60.269 52.381 0.00 0.00 40.64 4.40 R
4899 5161 0.321122 CAACCAGCGAAGAAGAGGCT 60.321 55.000 0.00 0.00 37.55 4.58 R
5645 5917 1.077089 GCAAGGGTAGCTTCGACGTC 61.077 60.000 5.18 5.18 0.00 4.34 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
21 22 3.797546 GCTCTGCAGCAAGTCGCC 61.798 66.667 9.47 0.00 46.06 5.54
22 23 3.485431 CTCTGCAGCAAGTCGCCG 61.485 66.667 9.47 0.00 44.04 6.46
79 80 3.499737 CGGTAGTACGTCGGCGGT 61.500 66.667 16.39 1.44 43.45 5.68
126 131 2.462898 GAACGAACGAACGCCGAC 59.537 61.111 14.02 6.34 41.76 4.79
175 192 2.046604 GGTGGCGGTTGACCCTAC 60.047 66.667 0.00 0.00 0.00 3.18
180 197 3.387947 CGGTTGACCCTACGGCCT 61.388 66.667 0.00 0.00 0.00 5.19
181 198 2.053865 CGGTTGACCCTACGGCCTA 61.054 63.158 0.00 0.00 0.00 3.93
182 199 1.519246 GGTTGACCCTACGGCCTAC 59.481 63.158 0.00 0.00 0.00 3.18
183 200 0.974525 GGTTGACCCTACGGCCTACT 60.975 60.000 0.00 0.00 0.00 2.57
184 201 0.175073 GTTGACCCTACGGCCTACTG 59.825 60.000 0.00 0.00 0.00 2.74
231 248 1.302366 CACCATGGATGACATCACCG 58.698 55.000 21.47 4.31 37.84 4.94
240 257 1.254975 TGACATCACCGTCCCGTCAT 61.255 55.000 0.00 0.00 34.88 3.06
249 266 1.888018 GTCCCGTCATCGAACTCCA 59.112 57.895 0.00 0.00 39.71 3.86
250 267 0.245539 GTCCCGTCATCGAACTCCAA 59.754 55.000 0.00 0.00 39.71 3.53
325 344 2.097629 TCTACGCATCTGACTTTCCTCG 59.902 50.000 0.00 0.00 0.00 4.63
333 352 0.320771 TGACTTTCCTCGCAAGCCTC 60.321 55.000 0.00 0.00 37.18 4.70
334 353 1.003233 ACTTTCCTCGCAAGCCTCC 60.003 57.895 0.00 0.00 37.18 4.30
347 367 2.534272 CCTCCCCCACCCTCCAAA 60.534 66.667 0.00 0.00 0.00 3.28
348 368 2.763902 CTCCCCCACCCTCCAAAC 59.236 66.667 0.00 0.00 0.00 2.93
443 464 6.989155 TGTATATCCAGGTAAATCCGTTCT 57.011 37.500 0.00 0.00 41.99 3.01
471 492 4.293634 TCCAAAAAGGAATACCCAGATCCA 59.706 41.667 0.00 0.00 45.65 3.41
479 500 4.232091 GAATACCCAGATCCACTTCCCTA 58.768 47.826 0.00 0.00 0.00 3.53
481 502 0.753262 CCCAGATCCACTTCCCTACG 59.247 60.000 0.00 0.00 0.00 3.51
617 639 2.511659 AGAAGGGGCGGTTAAAAAGTC 58.488 47.619 0.00 0.00 0.00 3.01
619 641 0.109153 AGGGGCGGTTAAAAAGTCGT 59.891 50.000 0.00 0.00 0.00 4.34
620 642 1.347378 AGGGGCGGTTAAAAAGTCGTA 59.653 47.619 0.00 0.00 0.00 3.43
635 657 3.438360 AGTCGTATAGCGGTTAAAACGG 58.562 45.455 0.00 0.00 41.72 4.44
936 964 3.237741 CCAGCGATCCCTCCTCCC 61.238 72.222 0.00 0.00 0.00 4.30
937 965 3.237741 CAGCGATCCCTCCTCCCC 61.238 72.222 0.00 0.00 0.00 4.81
939 967 4.565850 GCGATCCCTCCTCCCCCT 62.566 72.222 0.00 0.00 0.00 4.79
940 968 2.287251 CGATCCCTCCTCCCCCTT 59.713 66.667 0.00 0.00 0.00 3.95
942 970 1.318380 GATCCCTCCTCCCCCTTCA 59.682 63.158 0.00 0.00 0.00 3.02
943 971 1.004891 ATCCCTCCTCCCCCTTCAC 59.995 63.158 0.00 0.00 0.00 3.18
944 972 1.837533 ATCCCTCCTCCCCCTTCACA 61.838 60.000 0.00 0.00 0.00 3.58
945 973 1.541368 CCCTCCTCCCCCTTCACAA 60.541 63.158 0.00 0.00 0.00 3.33
946 974 1.566298 CCCTCCTCCCCCTTCACAAG 61.566 65.000 0.00 0.00 0.00 3.16
947 975 1.301293 CTCCTCCCCCTTCACAAGC 59.699 63.158 0.00 0.00 0.00 4.01
948 976 2.203549 CTCCTCCCCCTTCACAAGCC 62.204 65.000 0.00 0.00 0.00 4.35
949 977 2.538141 CCTCCCCCTTCACAAGCCA 61.538 63.158 0.00 0.00 0.00 4.75
984 1012 3.148279 GGAGCCGACCGATCCAGT 61.148 66.667 8.19 0.00 33.08 4.00
998 1045 2.103143 CAGTAGTCCAGGCGCGAG 59.897 66.667 12.10 0.00 0.00 5.03
1233 1280 3.586961 CTCGAGATGGAGCGCGGA 61.587 66.667 6.58 0.00 0.00 5.54
1322 1370 1.680989 GGAAACCACCCCCATTCCG 60.681 63.158 0.00 0.00 32.72 4.30
1343 1391 3.537874 CTGACCCGATCCCGTCCC 61.538 72.222 4.77 0.00 0.00 4.46
1356 1404 1.420430 CCGTCCCATCCTTAGCCTTA 58.580 55.000 0.00 0.00 0.00 2.69
1358 1406 2.484947 CCGTCCCATCCTTAGCCTTAAC 60.485 54.545 0.00 0.00 0.00 2.01
1399 1457 2.182791 CGTGATCCGTCTGCTGCT 59.817 61.111 0.00 0.00 0.00 4.24
1408 1466 1.572085 CGTCTGCTGCTGGGAAAGTG 61.572 60.000 6.69 0.00 0.00 3.16
1414 1472 3.376918 GCTGGGAAAGTGGCCTGC 61.377 66.667 3.32 0.00 0.00 4.85
1415 1473 3.058160 CTGGGAAAGTGGCCTGCG 61.058 66.667 3.32 0.00 0.00 5.18
1419 1477 1.223487 GGAAAGTGGCCTGCGGATA 59.777 57.895 3.32 0.00 0.00 2.59
1420 1478 0.179018 GGAAAGTGGCCTGCGGATAT 60.179 55.000 3.32 0.00 0.00 1.63
1437 1495 3.821033 GGATATATTGCGCTTTCCTTGGT 59.179 43.478 9.73 0.00 0.00 3.67
1447 1505 3.919973 TTCCTTGGTCGCGTACGCC 62.920 63.158 32.64 20.17 39.84 5.68
1461 1519 1.259142 TACGCCACGGGAATTCTCCA 61.259 55.000 5.23 0.00 44.51 3.86
1462 1520 1.376683 CGCCACGGGAATTCTCCAA 60.377 57.895 5.23 0.00 44.51 3.53
1467 1525 2.438021 CCACGGGAATTCTCCAATCCTA 59.562 50.000 5.23 0.00 44.51 2.94
1487 1545 7.473735 TCCTACTCTTGATTAGGCATATGAG 57.526 40.000 6.97 0.00 35.67 2.90
1519 1577 3.309954 GGTGAAATGTGCGGATCTTAGTC 59.690 47.826 0.00 0.00 0.00 2.59
1599 1657 0.537653 GCCTCTTAGGTGACCTCCAC 59.462 60.000 7.77 0.00 44.95 4.02
1602 1660 2.557676 CCTCTTAGGTGACCTCCACTGA 60.558 54.545 7.77 0.00 45.03 3.41
1609 1672 1.819288 GTGACCTCCACTGATTCTCGA 59.181 52.381 0.00 0.00 42.44 4.04
1713 1777 0.384309 TGCTGATCGTATGGTCGTCC 59.616 55.000 0.00 0.00 0.00 4.79
2004 2072 7.094508 TCTGTTATGTGCTTTGTTTCTCAAA 57.905 32.000 0.00 0.00 42.79 2.69
2114 2185 1.838112 TTGGGTGCTATTTCTGCAGG 58.162 50.000 15.13 0.00 41.41 4.85
2180 2251 1.734477 CCGTGTTCTGCGAGTCCAG 60.734 63.158 0.00 3.04 0.00 3.86
2304 2375 1.434188 TTTCAAGCTCCCTGGAGTCA 58.566 50.000 14.45 0.00 43.70 3.41
2310 2381 1.280421 AGCTCCCTGGAGTCACAAATC 59.720 52.381 14.45 0.00 43.70 2.17
2324 2395 7.148255 GGAGTCACAAATCTACATGCATGTTTA 60.148 37.037 35.45 23.79 41.97 2.01
2373 2444 7.318141 ACAGGAACTATTTGATTTCATTGCTG 58.682 34.615 9.44 9.44 36.02 4.41
2424 2495 0.761323 TGACGAGTTCCACCTCCCAA 60.761 55.000 0.00 0.00 0.00 4.12
2480 2551 4.877251 TCCTTTCCGGTAAACCAATTATCG 59.123 41.667 0.00 0.00 45.63 2.92
2532 2603 0.316841 GGGCTTTTCAATCAACGGCA 59.683 50.000 0.00 0.00 0.00 5.69
2586 2657 3.861840 TGAGCAGTTCCTAGCACATTAC 58.138 45.455 0.00 0.00 0.00 1.89
2587 2658 2.860735 GAGCAGTTCCTAGCACATTACG 59.139 50.000 0.00 0.00 0.00 3.18
2598 2669 8.092521 TCCTAGCACATTACGTAGTATAAGTC 57.907 38.462 0.00 0.00 45.21 3.01
2654 2725 2.955660 TGGCAAGTTTCTGGTGGTAAAG 59.044 45.455 0.00 0.00 0.00 1.85
2663 2734 5.452078 TTCTGGTGGTAAAGCTTGATTTG 57.548 39.130 0.00 0.00 0.00 2.32
2664 2735 4.724399 TCTGGTGGTAAAGCTTGATTTGA 58.276 39.130 0.00 0.00 0.00 2.69
2694 2816 8.398665 GTCAATCAGAACTTAAGTGTTGAAGTT 58.601 33.333 20.01 11.81 46.09 2.66
2695 2817 8.956426 TCAATCAGAACTTAAGTGTTGAAGTTT 58.044 29.630 20.01 11.30 44.04 2.66
2703 2825 9.581099 AACTTAAGTGTTGAAGTTTAATTGTGG 57.419 29.630 9.34 0.00 41.93 4.17
2705 2827 9.581099 CTTAAGTGTTGAAGTTTAATTGTGGTT 57.419 29.630 0.00 0.00 0.00 3.67
2707 2829 8.920509 AAGTGTTGAAGTTTAATTGTGGTTAC 57.079 30.769 0.00 0.00 0.00 2.50
2708 2830 8.288689 AGTGTTGAAGTTTAATTGTGGTTACT 57.711 30.769 0.00 0.00 0.00 2.24
2709 2831 8.188139 AGTGTTGAAGTTTAATTGTGGTTACTG 58.812 33.333 0.00 0.00 0.00 2.74
2710 2832 7.434013 GTGTTGAAGTTTAATTGTGGTTACTGG 59.566 37.037 0.00 0.00 0.00 4.00
2712 2834 7.648039 TGAAGTTTAATTGTGGTTACTGGTT 57.352 32.000 0.00 0.00 0.00 3.67
2713 2835 8.749026 TGAAGTTTAATTGTGGTTACTGGTTA 57.251 30.769 0.00 0.00 0.00 2.85
2714 2836 8.842280 TGAAGTTTAATTGTGGTTACTGGTTAG 58.158 33.333 0.00 0.00 0.00 2.34
2715 2837 7.754851 AGTTTAATTGTGGTTACTGGTTAGG 57.245 36.000 0.00 0.00 0.00 2.69
2716 2838 7.519927 AGTTTAATTGTGGTTACTGGTTAGGA 58.480 34.615 0.00 0.00 0.00 2.94
2717 2839 8.000127 AGTTTAATTGTGGTTACTGGTTAGGAA 59.000 33.333 0.00 0.00 0.00 3.36
2718 2840 7.989416 TTAATTGTGGTTACTGGTTAGGAAG 57.011 36.000 0.00 0.00 0.00 3.46
2719 2841 3.412237 TGTGGTTACTGGTTAGGAAGC 57.588 47.619 0.00 0.00 43.95 3.86
2726 2848 6.592870 GGTTACTGGTTAGGAAGCATATTCT 58.407 40.000 0.00 0.00 43.31 2.40
2727 2849 7.054751 GGTTACTGGTTAGGAAGCATATTCTT 58.945 38.462 0.00 0.00 43.31 2.52
2728 2850 7.012421 GGTTACTGGTTAGGAAGCATATTCTTG 59.988 40.741 0.00 0.00 43.31 3.02
2729 2851 6.313519 ACTGGTTAGGAAGCATATTCTTGA 57.686 37.500 0.00 0.00 38.36 3.02
2731 2853 8.034313 ACTGGTTAGGAAGCATATTCTTGATA 57.966 34.615 0.00 0.00 38.36 2.15
2755 2920 9.950680 ATATGCAGTACAAATAGTATGTTTTGC 57.049 29.630 0.00 0.00 38.40 3.68
2756 2921 6.310960 TGCAGTACAAATAGTATGTTTTGCG 58.689 36.000 0.00 0.00 39.62 4.85
2757 2922 5.737290 GCAGTACAAATAGTATGTTTTGCGG 59.263 40.000 0.00 0.00 36.51 5.69
2758 2923 6.622028 GCAGTACAAATAGTATGTTTTGCGGT 60.622 38.462 0.00 0.00 36.51 5.68
2759 2924 7.302524 CAGTACAAATAGTATGTTTTGCGGTT 58.697 34.615 0.00 0.00 36.51 4.44
2792 2957 3.937706 CTGAGCCAATTGTCGATCTTTCT 59.062 43.478 4.43 0.00 0.00 2.52
2830 2996 6.202516 TCCTTGATTTTGACGTGTTCTTTT 57.797 33.333 0.00 0.00 0.00 2.27
2831 2997 6.626302 TCCTTGATTTTGACGTGTTCTTTTT 58.374 32.000 0.00 0.00 0.00 1.94
2914 3080 3.435026 GCAGGGGCTGGATATGAAAGTTA 60.435 47.826 0.00 0.00 36.96 2.24
2987 3153 7.649306 ACAATGCTAATTTCTGTGTTTTCTGAC 59.351 33.333 0.00 0.00 0.00 3.51
2996 3162 4.051922 CTGTGTTTTCTGACGCTACTTCT 58.948 43.478 0.00 0.00 0.00 2.85
2997 3163 5.009310 TCTGTGTTTTCTGACGCTACTTCTA 59.991 40.000 0.00 0.00 0.00 2.10
3044 3210 0.951558 GGAGTGCGAACAAACATGGT 59.048 50.000 0.00 0.00 0.00 3.55
3058 3224 1.673920 ACATGGTCGTGTGTCCAAAAC 59.326 47.619 0.00 0.00 36.86 2.43
3059 3225 1.673400 CATGGTCGTGTGTCCAAAACA 59.327 47.619 0.00 0.00 36.86 2.83
3061 3227 3.195471 TGGTCGTGTGTCCAAAACATA 57.805 42.857 0.00 0.00 40.80 2.29
3155 3323 2.954318 GGATAATGATGTGGTTGCTGCT 59.046 45.455 0.00 0.00 0.00 4.24
3156 3324 3.243301 GGATAATGATGTGGTTGCTGCTG 60.243 47.826 0.00 0.00 0.00 4.41
3233 3401 0.178932 AGTGGACTGGACTACTGCCA 60.179 55.000 0.00 0.00 30.79 4.92
3275 3443 8.915654 GTTAGTGTTTGAAATTCCTTATGCTTG 58.084 33.333 0.00 0.00 0.00 4.01
3280 3448 8.855110 TGTTTGAAATTCCTTATGCTTGAAGTA 58.145 29.630 0.00 0.00 0.00 2.24
3304 3472 4.535526 AAAGCCCCATGAAACATTGTAC 57.464 40.909 0.00 0.00 0.00 2.90
3452 3620 5.473504 AGAATACGACAAAGCATTGGACTTT 59.526 36.000 6.62 0.00 41.01 2.66
3492 3663 5.048846 AGAACAGGTGTTTATCTTGGTGT 57.951 39.130 0.00 0.00 38.56 4.16
3501 3672 7.926018 AGGTGTTTATCTTGGTGTTTTCAATTC 59.074 33.333 0.00 0.00 0.00 2.17
3524 3695 2.553079 TCACGTTTTTGTGCTGAACC 57.447 45.000 0.00 0.00 39.73 3.62
3733 3904 1.250328 TGCTTGCTTCTTGACATGGG 58.750 50.000 0.00 0.00 0.00 4.00
3907 4126 1.452145 TTTGGGAAGTTGCGTGCCTC 61.452 55.000 0.00 0.00 0.00 4.70
3922 4141 4.122776 CGTGCCTCTTGAAGCTATACATT 58.877 43.478 0.00 0.00 0.00 2.71
3948 4167 6.045318 ACTTCATTCGAGTAATCCATGTGAG 58.955 40.000 0.00 0.00 0.00 3.51
4061 4281 9.853921 CTTTGTTCAATTCAAAGCTTTGTATTC 57.146 29.630 30.10 22.46 42.93 1.75
4062 4282 9.598517 TTTGTTCAATTCAAAGCTTTGTATTCT 57.401 25.926 30.10 15.89 36.45 2.40
4063 4283 9.598517 TTGTTCAATTCAAAGCTTTGTATTCTT 57.401 25.926 30.10 15.87 36.45 2.52
4064 4284 9.598517 TGTTCAATTCAAAGCTTTGTATTCTTT 57.401 25.926 30.10 15.58 36.45 2.52
4071 4291 9.520204 TTCAAAGCTTTGTATTCTTTTTCTCTG 57.480 29.630 32.46 7.66 39.18 3.35
4135 4358 9.063739 GTCTAGTTAGATAGAGTTTGTTTCGTG 57.936 37.037 0.00 0.00 32.49 4.35
4156 4379 8.812147 TCGTGCACACCTTAATATTATAAGAG 57.188 34.615 18.64 0.00 35.35 2.85
4242 4465 4.551671 AGTCTGAGTAGTGGCCTAATGAT 58.448 43.478 3.32 0.00 0.00 2.45
4269 4492 8.712228 AATTTTCACCTTCTCCTTGTTAGAAT 57.288 30.769 0.00 0.00 32.72 2.40
4270 4493 9.807921 AATTTTCACCTTCTCCTTGTTAGAATA 57.192 29.630 0.00 0.00 32.72 1.75
4292 4516 9.976511 GAATAAATAAAGTATTTACTTGGGGGC 57.023 33.333 3.84 0.00 44.35 5.80
4312 4536 8.845793 TGGGGGCAAATAGATTATATAAGTCAT 58.154 33.333 1.02 0.00 0.00 3.06
4354 4612 6.554982 TGAGTAGCATACCATTCTTGATACCT 59.445 38.462 0.00 0.00 44.47 3.08
4371 4630 2.731572 ACCTGATGAAGCTTCCATTGG 58.268 47.619 23.42 20.26 0.00 3.16
4390 4649 2.680841 TGGCATTAACACCACTAATCGC 59.319 45.455 0.00 0.00 0.00 4.58
4391 4650 2.943033 GGCATTAACACCACTAATCGCT 59.057 45.455 0.00 0.00 0.00 4.93
4392 4651 4.124238 GGCATTAACACCACTAATCGCTA 58.876 43.478 0.00 0.00 0.00 4.26
4393 4652 4.573201 GGCATTAACACCACTAATCGCTAA 59.427 41.667 0.00 0.00 0.00 3.09
4394 4653 5.238650 GGCATTAACACCACTAATCGCTAAT 59.761 40.000 0.00 0.00 0.00 1.73
4395 4654 6.363473 GCATTAACACCACTAATCGCTAATC 58.637 40.000 0.00 0.00 0.00 1.75
4396 4655 6.581370 CATTAACACCACTAATCGCTAATCG 58.419 40.000 0.00 0.00 40.15 3.34
4411 4670 4.386049 CGCTAATCGGTGATAATTCCTGAC 59.614 45.833 0.00 0.00 33.78 3.51
4425 4684 9.449719 GATAATTCCTGACGAATATTTACCCAT 57.550 33.333 0.00 0.00 40.47 4.00
4554 4816 5.185828 ACATGACCTTAAAATTCTGGGAAGC 59.814 40.000 0.00 0.00 0.00 3.86
4588 4850 0.863144 CGTTGGGGTACGACTGTTTG 59.137 55.000 0.00 0.00 43.99 2.93
4635 4897 6.489700 TGTTCAGTGACCATTGATTAACATGT 59.510 34.615 0.00 0.00 0.00 3.21
4818 5080 2.485795 GCAAAGGACCGTGGTTGCA 61.486 57.895 15.84 0.00 44.53 4.08
4830 5092 1.901464 GGTTGCATTGGACGGTGGT 60.901 57.895 0.00 0.00 0.00 4.16
5519 5785 0.982704 ACTGCTCATCTGAAGGCTGT 59.017 50.000 0.00 0.00 33.35 4.40
5777 6049 0.598158 CGTCGAGGTTTTTCCGGTGA 60.598 55.000 0.00 0.00 41.99 4.02
5822 6094 1.237285 GCAGCACGTCCTTCATGGTT 61.237 55.000 0.00 0.00 37.07 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.599047 GACTTGCTGCAGAGCCCTA 59.401 57.895 20.43 0.00 45.57 3.53
1 2 2.350514 GACTTGCTGCAGAGCCCT 59.649 61.111 20.43 0.00 45.57 5.19
2 3 3.123620 CGACTTGCTGCAGAGCCC 61.124 66.667 20.43 0.00 45.57 5.19
3 4 3.797546 GCGACTTGCTGCAGAGCC 61.798 66.667 20.43 0.00 45.57 4.70
4 5 3.797546 GGCGACTTGCTGCAGAGC 61.798 66.667 20.43 11.58 46.44 4.09
5 6 3.485431 CGGCGACTTGCTGCAGAG 61.485 66.667 20.43 9.64 44.47 3.35
11 12 1.153429 GGATTACCGGCGACTTGCT 60.153 57.895 9.30 0.00 45.43 3.91
12 13 1.152383 GAGGATTACCGGCGACTTGC 61.152 60.000 9.30 0.00 45.38 4.01
13 14 0.870307 CGAGGATTACCGGCGACTTG 60.870 60.000 9.30 0.00 41.83 3.16
14 15 1.436336 CGAGGATTACCGGCGACTT 59.564 57.895 9.30 0.00 41.83 3.01
15 16 3.117372 CGAGGATTACCGGCGACT 58.883 61.111 9.30 0.00 41.83 4.18
16 17 2.657620 GCGAGGATTACCGGCGAC 60.658 66.667 9.30 0.00 41.83 5.19
19 20 2.657620 GACGCGAGGATTACCGGC 60.658 66.667 15.93 0.00 41.83 6.13
20 21 2.353145 CGACGCGAGGATTACCGG 60.353 66.667 15.93 0.00 41.83 5.28
21 22 3.022914 GCGACGCGAGGATTACCG 61.023 66.667 15.93 3.93 41.83 4.02
53 54 1.870901 CGTACTACCGGCGACTTGC 60.871 63.158 9.30 0.00 45.38 4.01
190 207 4.447342 CATGTGGGGGAGGGGTGC 62.447 72.222 0.00 0.00 0.00 5.01
231 248 0.245539 TTGGAGTTCGATGACGGGAC 59.754 55.000 0.00 0.00 40.21 4.46
240 257 2.747686 GGCCCACTTGGAGTTCGA 59.252 61.111 0.00 0.00 37.39 3.71
283 301 5.101529 AGAGAGAGGGTAAAAAGGATTGGA 58.898 41.667 0.00 0.00 0.00 3.53
333 352 2.117423 GTGTTTGGAGGGTGGGGG 59.883 66.667 0.00 0.00 0.00 5.40
334 353 1.228552 CTGTGTTTGGAGGGTGGGG 60.229 63.158 0.00 0.00 0.00 4.96
347 367 3.475494 TGTCGGTGGGTGCTGTGT 61.475 61.111 0.00 0.00 0.00 3.72
348 368 2.972505 GTGTCGGTGGGTGCTGTG 60.973 66.667 0.00 0.00 0.00 3.66
373 393 3.074281 CCGTTGACTTAGGGCCCA 58.926 61.111 27.56 7.27 0.00 5.36
379 399 1.673033 CCTGTCAGGCCGTTGACTTAG 60.673 57.143 21.87 13.62 46.00 2.18
380 400 0.320374 CCTGTCAGGCCGTTGACTTA 59.680 55.000 21.87 5.98 46.00 2.24
411 432 1.404181 CCTGGATATACATCGCGGTGG 60.404 57.143 25.34 7.70 31.33 4.61
443 464 6.795590 TCTGGGTATTCCTTTTTGGATTACA 58.204 36.000 14.60 0.75 46.05 2.41
541 562 3.618594 CGGCATTTATGATCCACCTATCG 59.381 47.826 0.00 0.00 0.00 2.92
592 613 1.482748 TTAACCGCCCCTTCTTCCGT 61.483 55.000 0.00 0.00 0.00 4.69
593 614 0.321830 TTTAACCGCCCCTTCTTCCG 60.322 55.000 0.00 0.00 0.00 4.30
594 615 1.913778 TTTTAACCGCCCCTTCTTCC 58.086 50.000 0.00 0.00 0.00 3.46
617 639 1.258720 GGCCGTTTTAACCGCTATACG 59.741 52.381 0.00 0.00 43.15 3.06
619 641 1.569708 CGGCCGTTTTAACCGCTATA 58.430 50.000 19.50 0.00 40.55 1.31
620 642 1.091197 CCGGCCGTTTTAACCGCTAT 61.091 55.000 26.12 0.00 45.58 2.97
936 964 2.677875 GGGCTGGCTTGTGAAGGG 60.678 66.667 0.00 0.00 0.00 3.95
937 965 2.677875 GGGGCTGGCTTGTGAAGG 60.678 66.667 0.00 0.00 0.00 3.46
939 967 4.659172 CGGGGGCTGGCTTGTGAA 62.659 66.667 0.00 0.00 0.00 3.18
943 971 4.883354 GATCCGGGGGCTGGCTTG 62.883 72.222 0.00 0.00 0.00 4.01
948 976 3.554342 CTCTGGATCCGGGGGCTG 61.554 72.222 20.82 2.84 0.00 4.85
971 999 0.750546 TGGACTACTGGATCGGTCGG 60.751 60.000 0.00 0.00 0.00 4.79
974 1002 1.043673 GCCTGGACTACTGGATCGGT 61.044 60.000 0.00 0.00 40.42 4.69
975 1003 1.742768 GCCTGGACTACTGGATCGG 59.257 63.158 0.00 0.00 40.42 4.18
976 1004 1.360551 CGCCTGGACTACTGGATCG 59.639 63.158 0.00 0.00 40.42 3.69
977 1005 1.068250 GCGCCTGGACTACTGGATC 59.932 63.158 0.00 0.00 40.42 3.36
978 1006 2.786495 CGCGCCTGGACTACTGGAT 61.786 63.158 0.00 0.00 40.42 3.41
979 1007 3.449227 CGCGCCTGGACTACTGGA 61.449 66.667 0.00 0.00 40.42 3.86
980 1008 3.417275 CTCGCGCCTGGACTACTGG 62.417 68.421 0.00 0.00 40.89 4.00
981 1009 2.103143 CTCGCGCCTGGACTACTG 59.897 66.667 0.00 0.00 0.00 2.74
983 1011 2.491022 ATCCTCGCGCCTGGACTAC 61.491 63.158 16.76 0.00 34.90 2.73
984 1012 2.123854 ATCCTCGCGCCTGGACTA 60.124 61.111 16.76 0.00 34.90 2.59
1248 1295 1.375098 GCATCTTGAGCTGGGAGTGC 61.375 60.000 0.00 0.00 0.00 4.40
1311 1358 1.004230 TCAGATCCGGAATGGGGGT 59.996 57.895 9.01 0.00 38.76 4.95
1343 1391 3.871594 CCGACAAGTTAAGGCTAAGGATG 59.128 47.826 0.00 0.00 0.00 3.51
1399 1457 4.659172 CCGCAGGCCACTTTCCCA 62.659 66.667 5.01 0.00 46.14 4.37
1414 1472 3.120199 CCAAGGAAAGCGCAATATATCCG 60.120 47.826 11.47 2.37 32.22 4.18
1415 1473 3.821033 ACCAAGGAAAGCGCAATATATCC 59.179 43.478 11.47 7.59 0.00 2.59
1419 1477 1.670811 CGACCAAGGAAAGCGCAATAT 59.329 47.619 11.47 0.00 0.00 1.28
1420 1478 1.083489 CGACCAAGGAAAGCGCAATA 58.917 50.000 11.47 0.00 0.00 1.90
1447 1505 2.717639 AGGATTGGAGAATTCCCGTG 57.282 50.000 0.65 0.00 43.33 4.94
1467 1525 5.744300 GCCACTCATATGCCTAATCAAGAGT 60.744 44.000 0.00 0.00 35.66 3.24
1487 1545 0.952010 ACATTTCACCGTACGGCCAC 60.952 55.000 33.62 0.00 39.32 5.01
1519 1577 3.730061 GCGATCTTGGCACAGAAATTCAG 60.730 47.826 0.00 0.00 42.39 3.02
1559 1617 0.321298 ACGGTGTTCCTGATTTCGGG 60.321 55.000 0.00 0.00 43.86 5.14
1609 1672 5.241728 CACATCCTTGCTCATGATGATTCAT 59.758 40.000 0.00 0.00 43.51 2.57
2180 2251 1.827681 GTTTCTCCCTTCCTCCAAGC 58.172 55.000 0.00 0.00 0.00 4.01
2252 2323 2.370849 GGTACTCACCAAGGAAGTTCCA 59.629 50.000 23.87 0.83 45.04 3.53
2282 2353 1.202940 ACTCCAGGGAGCTTGAAAACC 60.203 52.381 15.18 0.00 45.54 3.27
2373 2444 4.314121 TCAACAAATTTGGCCAATACAGC 58.686 39.130 21.26 0.00 0.00 4.40
2424 2495 1.765657 GCTCTCTCTGCCTCCCCAT 60.766 63.158 0.00 0.00 0.00 4.00
2480 2551 7.215789 ACTTGATGAGTGTTCCTGATGATATC 58.784 38.462 0.00 0.00 37.17 1.63
2532 2603 7.168469 GCTGTGTAATGTTTTGAATTTTACCGT 59.832 33.333 0.00 0.00 0.00 4.83
2550 2621 3.631686 ACTGCTCAACAAATGCTGTGTAA 59.368 39.130 0.00 0.00 38.67 2.41
2624 2695 3.193479 CCAGAAACTTGCCAAGGTAATCC 59.807 47.826 9.64 0.00 0.00 3.01
2629 2700 1.402787 CACCAGAAACTTGCCAAGGT 58.597 50.000 9.64 0.00 0.00 3.50
2663 2734 9.979270 CAACACTTAAGTTCTGATTGACATATC 57.021 33.333 5.07 0.00 0.00 1.63
2664 2735 9.725019 TCAACACTTAAGTTCTGATTGACATAT 57.275 29.630 5.07 0.00 0.00 1.78
2694 2816 6.431852 GCTTCCTAACCAGTAACCACAATTAA 59.568 38.462 0.00 0.00 0.00 1.40
2695 2817 5.941647 GCTTCCTAACCAGTAACCACAATTA 59.058 40.000 0.00 0.00 0.00 1.40
2698 2820 3.136809 TGCTTCCTAACCAGTAACCACAA 59.863 43.478 0.00 0.00 0.00 3.33
2700 2822 3.412237 TGCTTCCTAACCAGTAACCAC 57.588 47.619 0.00 0.00 0.00 4.16
2701 2823 5.968676 ATATGCTTCCTAACCAGTAACCA 57.031 39.130 0.00 0.00 0.00 3.67
2702 2824 6.592870 AGAATATGCTTCCTAACCAGTAACC 58.407 40.000 0.00 0.00 0.00 2.85
2703 2825 7.769044 TCAAGAATATGCTTCCTAACCAGTAAC 59.231 37.037 0.00 0.00 0.00 2.50
2705 2827 7.432148 TCAAGAATATGCTTCCTAACCAGTA 57.568 36.000 0.00 0.00 0.00 2.74
2706 2828 6.313519 TCAAGAATATGCTTCCTAACCAGT 57.686 37.500 0.00 0.00 0.00 4.00
2707 2829 8.944029 CATATCAAGAATATGCTTCCTAACCAG 58.056 37.037 0.00 0.00 40.53 4.00
2708 2830 8.853077 CATATCAAGAATATGCTTCCTAACCA 57.147 34.615 0.00 0.00 40.53 3.67
2729 2851 9.950680 GCAAAACATACTATTTGTACTGCATAT 57.049 29.630 0.00 0.00 38.48 1.78
2731 2853 6.966632 CGCAAAACATACTATTTGTACTGCAT 59.033 34.615 0.00 0.00 38.48 3.96
2734 2899 6.837992 ACCGCAAAACATACTATTTGTACTG 58.162 36.000 0.00 0.00 38.48 2.74
2746 2911 8.779303 CAGATACCATATAAACCGCAAAACATA 58.221 33.333 0.00 0.00 0.00 2.29
2747 2912 7.500892 TCAGATACCATATAAACCGCAAAACAT 59.499 33.333 0.00 0.00 0.00 2.71
2748 2913 6.824196 TCAGATACCATATAAACCGCAAAACA 59.176 34.615 0.00 0.00 0.00 2.83
2749 2914 7.254227 TCAGATACCATATAAACCGCAAAAC 57.746 36.000 0.00 0.00 0.00 2.43
2750 2915 6.017440 GCTCAGATACCATATAAACCGCAAAA 60.017 38.462 0.00 0.00 0.00 2.44
2751 2916 5.468746 GCTCAGATACCATATAAACCGCAAA 59.531 40.000 0.00 0.00 0.00 3.68
2752 2917 4.994852 GCTCAGATACCATATAAACCGCAA 59.005 41.667 0.00 0.00 0.00 4.85
2753 2918 4.562757 GGCTCAGATACCATATAAACCGCA 60.563 45.833 0.00 0.00 0.00 5.69
2754 2919 3.933332 GGCTCAGATACCATATAAACCGC 59.067 47.826 0.00 0.00 0.00 5.68
2755 2920 5.147330 TGGCTCAGATACCATATAAACCG 57.853 43.478 0.00 0.00 0.00 4.44
2756 2921 7.448469 ACAATTGGCTCAGATACCATATAAACC 59.552 37.037 10.83 0.00 35.42 3.27
2757 2922 8.396272 ACAATTGGCTCAGATACCATATAAAC 57.604 34.615 10.83 0.00 35.42 2.01
2758 2923 7.387673 CGACAATTGGCTCAGATACCATATAAA 59.612 37.037 10.18 0.00 35.42 1.40
2759 2924 6.873605 CGACAATTGGCTCAGATACCATATAA 59.126 38.462 10.18 0.00 35.42 0.98
2802 2967 8.110860 AGAACACGTCAAAATCAAGGAATTAT 57.889 30.769 0.00 0.00 0.00 1.28
2803 2968 7.504924 AGAACACGTCAAAATCAAGGAATTA 57.495 32.000 0.00 0.00 0.00 1.40
2820 2986 8.339714 TGATTAAGGAGTAACAAAAAGAACACG 58.660 33.333 0.00 0.00 0.00 4.49
2980 3146 8.997621 ACAAATAATAGAAGTAGCGTCAGAAA 57.002 30.769 0.00 0.00 0.00 2.52
3010 3176 7.064609 TGTTCGCACTCCATTAATAGAGAAAAG 59.935 37.037 16.51 6.14 34.13 2.27
3019 3185 5.401550 CATGTTTGTTCGCACTCCATTAAT 58.598 37.500 0.00 0.00 0.00 1.40
3028 3194 0.306533 ACGACCATGTTTGTTCGCAC 59.693 50.000 0.00 0.00 0.00 5.34
3044 3210 7.100409 TGAGAATATATGTTTTGGACACACGA 58.900 34.615 0.00 0.00 42.04 4.35
3155 3323 4.846168 TGTACCAGTGCCCAATATTACA 57.154 40.909 0.00 0.00 0.00 2.41
3156 3324 5.448089 CGTTTGTACCAGTGCCCAATATTAC 60.448 44.000 0.00 0.00 0.00 1.89
3233 3401 7.712204 AACACTAACCATATTTCCGGATTTT 57.288 32.000 4.15 0.00 0.00 1.82
3366 3534 5.913514 CCGTGTTGATTACCTAGAGAATACG 59.086 44.000 0.00 0.00 0.00 3.06
3452 3620 3.943671 TCTCCAGGGTTCAAACTTTCA 57.056 42.857 0.00 0.00 0.00 2.69
3492 3663 7.459486 CACAAAAACGTGAATGGAATTGAAAA 58.541 30.769 0.00 0.00 36.07 2.29
3501 3672 3.077229 TCAGCACAAAAACGTGAATGG 57.923 42.857 0.00 0.00 39.34 3.16
3551 3722 5.309323 TGCCGGAAATCAACTTTTCATAG 57.691 39.130 5.05 0.00 37.34 2.23
3907 4126 9.855361 CGAATGAAGTAAATGTATAGCTTCAAG 57.145 33.333 8.95 2.06 45.41 3.02
3922 4141 7.552459 TCACATGGATTACTCGAATGAAGTAA 58.448 34.615 0.00 0.00 33.35 2.24
3948 4167 8.947115 AGCACTAAGTTTAGAATATTTGTCACC 58.053 33.333 5.93 0.00 34.84 4.02
3970 4189 1.268896 CCGGCAATGATCAATCAGCAC 60.269 52.381 0.00 0.00 40.64 4.40
4037 4257 9.598517 AAGAATACAAAGCTTTGAATTGAACAA 57.401 25.926 38.78 15.88 40.55 2.83
4085 4307 1.284491 TGCACAGGCCATCCATCTTAA 59.716 47.619 5.01 0.00 40.13 1.85
4156 4379 4.368315 AGTTTGGCTTTGGTTTCGAATTC 58.632 39.130 0.00 0.00 0.00 2.17
4197 4420 9.959749 GACTTTATGATAGGTTTGACAAAAACA 57.040 29.630 1.27 0.07 35.27 2.83
4242 4465 9.635404 TTCTAACAAGGAGAAGGTGAAAATTAA 57.365 29.630 0.00 0.00 0.00 1.40
4269 4492 8.896722 TTGCCCCCAAGTAAATACTTTATTTA 57.103 30.769 3.12 0.00 43.57 1.40
4270 4493 7.800300 TTGCCCCCAAGTAAATACTTTATTT 57.200 32.000 3.12 0.00 43.57 1.40
4307 4531 7.071069 TCAGTGCATCCATCTATTAATGACT 57.929 36.000 0.00 0.00 0.00 3.41
4312 4536 6.041979 TGCTACTCAGTGCATCCATCTATTAA 59.958 38.462 0.00 0.00 33.94 1.40
4354 4612 2.219080 TGCCAATGGAAGCTTCATCA 57.781 45.000 27.02 17.12 0.00 3.07
4371 4630 5.728351 TTAGCGATTAGTGGTGTTAATGC 57.272 39.130 0.00 0.00 0.00 3.56
4390 4649 5.769367 TCGTCAGGAATTATCACCGATTAG 58.231 41.667 0.00 0.00 0.00 1.73
4391 4650 5.777850 TCGTCAGGAATTATCACCGATTA 57.222 39.130 0.00 0.00 0.00 1.75
4392 4651 4.665833 TCGTCAGGAATTATCACCGATT 57.334 40.909 0.00 0.00 0.00 3.34
4393 4652 4.665833 TTCGTCAGGAATTATCACCGAT 57.334 40.909 0.00 0.00 0.00 4.18
4394 4653 4.665833 ATTCGTCAGGAATTATCACCGA 57.334 40.909 0.00 0.00 42.77 4.69
4395 4654 7.421530 AAATATTCGTCAGGAATTATCACCG 57.578 36.000 0.00 0.00 42.77 4.94
4396 4655 8.718734 GGTAAATATTCGTCAGGAATTATCACC 58.281 37.037 0.00 0.00 42.77 4.02
4509 4771 4.541482 GCATCGTGGTGCATGGCG 62.541 66.667 0.00 0.00 44.43 5.69
4554 4816 3.815401 CCCCAACGATATCCTTTAGCTTG 59.185 47.826 0.00 0.00 0.00 4.01
4588 4850 7.506328 ACAACTTTTGTATCCACTTAGGTTC 57.494 36.000 0.00 0.00 43.27 3.62
4635 4897 3.689161 CCGCAACCTAAACATGAGATCAA 59.311 43.478 0.00 0.00 0.00 2.57
4802 5064 0.673437 CAATGCAACCACGGTCCTTT 59.327 50.000 0.00 0.00 0.00 3.11
4818 5080 2.695666 CTCATAGAGACCACCGTCCAAT 59.304 50.000 0.00 0.00 40.12 3.16
4830 5092 6.434340 TGAACTTCTTGTAGTGCTCATAGAGA 59.566 38.462 0.00 0.00 0.00 3.10
4899 5161 0.321122 CAACCAGCGAAGAAGAGGCT 60.321 55.000 0.00 0.00 37.55 4.58
5070 5334 4.023107 GGAAGGTTCGAAGGGAAAAGAAAG 60.023 45.833 0.00 0.00 36.14 2.62
5221 5485 1.945394 CTCCATATGTTGCTGCCACTC 59.055 52.381 5.42 0.00 0.00 3.51
5351 5617 3.714280 TGTCGATCCCCATCTTTATTGGA 59.286 43.478 0.00 0.00 36.26 3.53
5426 5692 7.871463 CAGAGATGAGCATTCAGACATACATAA 59.129 37.037 0.00 0.00 36.61 1.90
5511 5777 2.135933 GTACACAGTGTGACAGCCTTC 58.864 52.381 29.58 0.27 36.96 3.46
5519 5785 3.874543 GTGGAATGTTGTACACAGTGTGA 59.125 43.478 29.58 10.54 39.40 3.58
5645 5917 1.077089 GCAAGGGTAGCTTCGACGTC 61.077 60.000 5.18 5.18 0.00 4.34
5646 5918 1.080025 GCAAGGGTAGCTTCGACGT 60.080 57.895 0.00 0.00 0.00 4.34
5748 6020 1.584380 AACCTCGACGAGAAGACGGG 61.584 60.000 26.11 10.81 38.20 5.28


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

AutoCloner maintained by Alex Coulton.