Multiple sequence alignment - TraesCS4B01G227300

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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 TraesCS4B01G227300 chr4B 100.000 3891 0 0 1 3891 475810026 475813916 0.000000e+00 7186.0
1 TraesCS4B01G227300 chr4B 91.034 145 5 4 514 650 1803562 1803418 5.130000e-44 189.0
2 TraesCS4B01G227300 chr4B 96.923 65 2 0 261 325 1803631 1803567 4.110000e-20 110.0
3 TraesCS4B01G227300 chr4D 88.644 4033 210 98 1 3891 387440566 387444492 0.000000e+00 4682.0
4 TraesCS4B01G227300 chr4A 84.692 3619 241 139 1 3443 68688177 68691658 0.000000e+00 3325.0
5 TraesCS4B01G227300 chr4A 88.732 426 30 9 3472 3891 68697289 68697702 4.490000e-139 505.0
6 TraesCS4B01G227300 chr4A 89.796 147 5 6 514 650 654143949 654143803 3.090000e-41 180.0
7 TraesCS4B01G227300 chr4A 98.462 65 1 0 261 325 654173301 654173237 8.830000e-22 115.0
8 TraesCS4B01G227300 chr6B 92.611 406 16 8 258 650 33444286 33444690 4.360000e-159 571.0
9 TraesCS4B01G227300 chr6B 94.872 195 10 0 261 455 97522429 97522235 4.880000e-79 305.0
10 TraesCS4B01G227300 chr6B 90.449 178 5 5 485 650 97522236 97522059 1.410000e-54 224.0
11 TraesCS4B01G227300 chr6B 84.211 95 15 0 1298 1392 502484242 502484148 4.140000e-15 93.5
12 TraesCS4B01G227300 chr7B 90.617 405 26 5 258 650 618473290 618473694 9.580000e-146 527.0
13 TraesCS4B01G227300 chr7B 91.724 145 4 4 514 650 63521013 63520869 1.100000e-45 195.0
14 TraesCS4B01G227300 chr7B 97.059 68 2 0 258 325 33344968 33345035 8.830000e-22 115.0
15 TraesCS4B01G227300 chr7B 96.923 65 2 0 261 325 63521082 63521018 4.110000e-20 110.0
16 TraesCS4B01G227300 chr3B 91.724 145 4 4 514 650 527366646 527366502 1.100000e-45 195.0
17 TraesCS4B01G227300 chr2B 90.345 145 6 5 514 650 587674846 587674702 2.390000e-42 183.0
18 TraesCS4B01G227300 chr2B 80.556 180 29 5 1215 1391 616934689 616934865 2.440000e-27 134.0
19 TraesCS4B01G227300 chr2D 81.564 179 29 4 1215 1391 523028588 523028764 1.130000e-30 145.0
20 TraesCS4B01G227300 chr2A 81.564 179 29 4 1215 1391 668242841 668243017 1.130000e-30 145.0
21 TraesCS4B01G227300 chr6A 85.263 95 14 0 1298 1392 457686099 457686193 8.900000e-17 99.0
22 TraesCS4B01G227300 chr6D 83.908 87 14 0 1306 1392 320228345 320228431 2.490000e-12 84.2


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 TraesCS4B01G227300 chr4B 475810026 475813916 3890 False 7186 7186 100.000 1 3891 1 chr4B.!!$F1 3890
1 TraesCS4B01G227300 chr4D 387440566 387444492 3926 False 4682 4682 88.644 1 3891 1 chr4D.!!$F1 3890
2 TraesCS4B01G227300 chr4A 68688177 68691658 3481 False 3325 3325 84.692 1 3443 1 chr4A.!!$F1 3442

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
139 145 0.240945 CTTTTCTCGCGGCAAATGGT 59.759 50.0 6.13 0.00 0.00 3.55 F
249 266 0.312416 ATGACGAGCCTGCGTAGATC 59.688 55.0 0.53 0.00 45.72 2.75 F
1922 2068 0.179127 ATGCTCACACCAGACGATCG 60.179 55.0 14.88 14.88 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1126 0.251165 GGCAGTGGTAAAGGCCTGAA 60.251 55.0 5.69 0.0 43.09 3.02 R
1964 2122 0.603975 GATAAGGATGCGGGTCAGGC 60.604 60.0 0.00 0.0 0.00 4.85 R
2899 3108 0.321298 TAAAACTCACTCCCGGCAGC 60.321 55.0 0.00 0.0 0.00 5.25 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
82 83 4.981794 CGAGGAAAAACGGATAAAGCATT 58.018 39.130 0.00 0.00 0.00 3.56
139 145 0.240945 CTTTTCTCGCGGCAAATGGT 59.759 50.000 6.13 0.00 0.00 3.55
148 154 1.607767 GCGGCAAATGGTGAATTGGTT 60.608 47.619 0.00 0.00 0.00 3.67
149 155 2.067766 CGGCAAATGGTGAATTGGTTG 58.932 47.619 0.00 0.00 0.00 3.77
152 158 3.307621 GGCAAATGGTGAATTGGTTGGAT 60.308 43.478 0.00 0.00 0.00 3.41
154 160 4.761227 GCAAATGGTGAATTGGTTGGATTT 59.239 37.500 0.00 0.00 0.00 2.17
155 161 5.241285 GCAAATGGTGAATTGGTTGGATTTT 59.759 36.000 0.00 0.00 0.00 1.82
156 162 6.238981 GCAAATGGTGAATTGGTTGGATTTTT 60.239 34.615 0.00 0.00 0.00 1.94
205 218 0.545071 AAGCAAAGAATGGGTGGGGG 60.545 55.000 0.00 0.00 0.00 5.40
206 219 1.078347 GCAAAGAATGGGTGGGGGA 59.922 57.895 0.00 0.00 0.00 4.81
249 266 0.312416 ATGACGAGCCTGCGTAGATC 59.688 55.000 0.53 0.00 45.72 2.75
353 374 4.443857 CCGACGGCATCATCACAT 57.556 55.556 0.00 0.00 0.00 3.21
354 375 2.694065 CCGACGGCATCATCACATT 58.306 52.632 0.00 0.00 0.00 2.71
355 376 0.583438 CCGACGGCATCATCACATTC 59.417 55.000 0.00 0.00 0.00 2.67
356 377 1.289276 CGACGGCATCATCACATTCA 58.711 50.000 0.00 0.00 0.00 2.57
357 378 1.004610 CGACGGCATCATCACATTCAC 60.005 52.381 0.00 0.00 0.00 3.18
359 380 2.011947 ACGGCATCATCACATTCACTG 58.988 47.619 0.00 0.00 0.00 3.66
360 381 1.268386 CGGCATCATCACATTCACTGC 60.268 52.381 0.00 0.00 0.00 4.40
361 382 1.066605 GGCATCATCACATTCACTGCC 59.933 52.381 0.00 0.00 40.68 4.85
372 393 4.157105 CACATTCACTGCCAATTCAGATCA 59.843 41.667 0.00 0.00 37.51 2.92
478 508 3.669251 AAGGCGCTCTTATGGATAGAC 57.331 47.619 7.64 0.00 33.14 2.59
480 510 3.169099 AGGCGCTCTTATGGATAGACAT 58.831 45.455 7.64 0.00 34.90 3.06
482 512 4.772624 AGGCGCTCTTATGGATAGACATTA 59.227 41.667 7.64 0.00 32.39 1.90
483 513 5.105554 AGGCGCTCTTATGGATAGACATTAG 60.106 44.000 7.64 0.00 32.39 1.73
497 527 7.859377 GGATAGACATTAGTGATTAACGACGAA 59.141 37.037 0.00 0.00 0.00 3.85
500 530 7.033791 AGACATTAGTGATTAACGACGAACAT 58.966 34.615 0.00 0.00 0.00 2.71
501 531 7.544566 AGACATTAGTGATTAACGACGAACATT 59.455 33.333 0.00 0.00 0.00 2.71
502 532 8.025243 ACATTAGTGATTAACGACGAACATTT 57.975 30.769 0.00 0.00 0.00 2.32
548 578 6.995091 GCAGACTGTTATCTTGAAGGGATATT 59.005 38.462 3.99 0.00 0.00 1.28
583 617 7.869937 TGTTCAGATATCTATCTAGTGCAAAGC 59.130 37.037 4.54 0.00 40.91 3.51
608 643 9.807649 GCAACAAGAATTCCATATCTGTAAAAT 57.192 29.630 0.65 0.00 0.00 1.82
643 678 9.793259 AATTCTTCTGTATCACAAAAAGTAGGA 57.207 29.630 0.00 0.00 0.00 2.94
644 679 8.833231 TTCTTCTGTATCACAAAAAGTAGGAG 57.167 34.615 0.00 0.00 0.00 3.69
645 680 7.963532 TCTTCTGTATCACAAAAAGTAGGAGT 58.036 34.615 0.00 0.00 0.00 3.85
646 681 9.085645 TCTTCTGTATCACAAAAAGTAGGAGTA 57.914 33.333 0.00 0.00 0.00 2.59
647 682 9.141400 CTTCTGTATCACAAAAAGTAGGAGTAC 57.859 37.037 0.00 0.00 0.00 2.73
648 683 8.418597 TCTGTATCACAAAAAGTAGGAGTACT 57.581 34.615 0.00 0.00 41.61 2.73
649 684 8.521176 TCTGTATCACAAAAAGTAGGAGTACTC 58.479 37.037 14.87 14.87 38.66 2.59
650 685 8.418597 TGTATCACAAAAAGTAGGAGTACTCT 57.581 34.615 21.88 10.81 38.66 3.24
651 686 9.524496 TGTATCACAAAAAGTAGGAGTACTCTA 57.476 33.333 21.88 9.87 38.66 2.43
749 791 3.327404 CCCGTACCCCCAGTTGCT 61.327 66.667 0.00 0.00 0.00 3.91
767 809 2.228822 TGCTTCCTCGCCTTTTCATTTC 59.771 45.455 0.00 0.00 0.00 2.17
773 815 4.515944 TCCTCGCCTTTTCATTTCGTTTTA 59.484 37.500 0.00 0.00 0.00 1.52
775 817 6.372103 TCCTCGCCTTTTCATTTCGTTTTATA 59.628 34.615 0.00 0.00 0.00 0.98
902 955 2.489985 CCAAACCCACACCCATACAAGA 60.490 50.000 0.00 0.00 0.00 3.02
961 1047 0.892755 ACGCAGTTCTTCCACCGATA 59.107 50.000 0.00 0.00 37.78 2.92
962 1048 1.480954 ACGCAGTTCTTCCACCGATAT 59.519 47.619 0.00 0.00 37.78 1.63
969 1059 5.294552 CAGTTCTTCCACCGATATTTCCTTC 59.705 44.000 0.00 0.00 0.00 3.46
975 1065 1.070289 ACCGATATTTCCTTCCCTCGC 59.930 52.381 0.00 0.00 0.00 5.03
977 1067 1.797025 GATATTTCCTTCCCTCGCCG 58.203 55.000 0.00 0.00 0.00 6.46
978 1068 0.396811 ATATTTCCTTCCCTCGCCGG 59.603 55.000 0.00 0.00 0.00 6.13
1032 1126 5.456763 GGCTTACAAGATGGTAAGGATCCAT 60.457 44.000 15.82 4.17 46.56 3.41
1033 1127 6.064717 GCTTACAAGATGGTAAGGATCCATT 58.935 40.000 15.82 8.04 46.56 3.16
1034 1128 6.205658 GCTTACAAGATGGTAAGGATCCATTC 59.794 42.308 15.82 0.00 46.56 2.67
1035 1129 5.715439 ACAAGATGGTAAGGATCCATTCA 57.285 39.130 15.82 7.03 44.52 2.57
1412 1506 7.881232 TGGTAATTATTCACTCCTTTCTCGTTT 59.119 33.333 0.00 0.00 0.00 3.60
1417 1511 8.976986 TTATTCACTCCTTTCTCGTTTACTAC 57.023 34.615 0.00 0.00 0.00 2.73
1419 1513 6.645790 TCACTCCTTTCTCGTTTACTACTT 57.354 37.500 0.00 0.00 0.00 2.24
1420 1514 7.750229 TCACTCCTTTCTCGTTTACTACTTA 57.250 36.000 0.00 0.00 0.00 2.24
1515 1650 1.546029 GCTGGATGGTTTCTTGGTTCC 59.454 52.381 0.00 0.00 0.00 3.62
1542 1677 2.965716 AAGCGTTCCTTGCTGGCTGT 62.966 55.000 0.00 0.00 43.14 4.40
1551 1686 2.355108 CCTTGCTGGCTGTACACTGTAT 60.355 50.000 0.00 0.00 0.00 2.29
1552 1687 2.385013 TGCTGGCTGTACACTGTATG 57.615 50.000 0.00 0.00 0.00 2.39
1553 1688 1.623311 TGCTGGCTGTACACTGTATGT 59.377 47.619 0.00 0.00 46.06 2.29
1620 1755 3.565902 GTCTAAGTTTTTGCCTGTCAGCT 59.434 43.478 0.00 0.00 0.00 4.24
1668 1808 3.002348 GTCATTCATAAACTACGGCAGCC 59.998 47.826 0.00 0.00 0.00 4.85
1686 1826 1.523758 CCGCCAACAAGAAACTAGCT 58.476 50.000 0.00 0.00 0.00 3.32
1760 1900 6.592607 CCAAGTTGGTAGTAATTACATGACGT 59.407 38.462 17.65 0.00 33.73 4.34
1835 1980 1.136000 TCGCAATCAAGCAATCACACG 60.136 47.619 0.00 0.00 0.00 4.49
1920 2066 3.132824 TCAATATGCTCACACCAGACGAT 59.867 43.478 0.00 0.00 0.00 3.73
1922 2068 0.179127 ATGCTCACACCAGACGATCG 60.179 55.000 14.88 14.88 0.00 3.69
1964 2122 3.094572 AGGAAATCTGCAGACCAAATGG 58.905 45.455 20.97 0.00 42.17 3.16
1966 2124 1.188863 AATCTGCAGACCAAATGGCC 58.811 50.000 20.97 0.00 39.32 5.36
1967 2125 0.333993 ATCTGCAGACCAAATGGCCT 59.666 50.000 20.97 0.00 39.32 5.19
1968 2126 0.609957 TCTGCAGACCAAATGGCCTG 60.610 55.000 13.74 11.02 46.80 4.85
1984 2150 0.758734 CCTGACCCGCATCCTTATCA 59.241 55.000 0.00 0.00 0.00 2.15
2019 2189 2.719046 CCGAACACGCATCAAACTTTTC 59.281 45.455 0.00 0.00 0.00 2.29
2083 2255 2.111756 CTTGTCAAACTCAAACGCAGC 58.888 47.619 0.00 0.00 0.00 5.25
2084 2256 1.090728 TGTCAAACTCAAACGCAGCA 58.909 45.000 0.00 0.00 0.00 4.41
2085 2257 1.063912 TGTCAAACTCAAACGCAGCAG 59.936 47.619 0.00 0.00 0.00 4.24
2334 2512 6.802608 TGTATATTAGATTTATCGCCCCTCG 58.197 40.000 0.00 0.00 40.15 4.63
2444 2627 3.664551 TCGATCAGTTCCTCCTCCTTA 57.335 47.619 0.00 0.00 0.00 2.69
2486 2674 3.563808 AGCACGATTAAAGCACTTGACAA 59.436 39.130 0.00 0.00 0.00 3.18
2525 2713 8.937634 TTAAGTACTGTTAGGTTAGCAATAGC 57.062 34.615 0.00 0.00 42.56 2.97
2526 2714 6.540438 AGTACTGTTAGGTTAGCAATAGCA 57.460 37.500 0.00 0.00 45.49 3.49
2527 2715 6.942976 AGTACTGTTAGGTTAGCAATAGCAA 58.057 36.000 0.00 0.00 45.49 3.91
2528 2716 7.042335 AGTACTGTTAGGTTAGCAATAGCAAG 58.958 38.462 0.00 0.00 45.49 4.01
2529 2717 4.636206 ACTGTTAGGTTAGCAATAGCAAGC 59.364 41.667 0.00 0.00 45.49 4.01
2530 2718 3.945285 TGTTAGGTTAGCAATAGCAAGCC 59.055 43.478 0.00 0.00 45.49 4.35
2531 2719 4.200092 GTTAGGTTAGCAATAGCAAGCCT 58.800 43.478 0.00 0.00 45.49 4.58
2532 2720 2.648059 AGGTTAGCAATAGCAAGCCTG 58.352 47.619 0.00 0.00 45.49 4.85
2537 2733 0.737219 GCAATAGCAAGCCTGTCCAG 59.263 55.000 0.00 0.00 41.58 3.86
2553 2749 3.170672 AGTGTCCACCAGCAGCCA 61.171 61.111 0.00 0.00 0.00 4.75
2575 2771 3.883489 AGTCTCCTTTTGTTAAAGCGCTT 59.117 39.130 18.98 18.98 39.55 4.68
2630 2826 3.538591 TCGGTCTCACACGAGTACATAT 58.461 45.455 0.00 0.00 40.44 1.78
2642 2838 9.563898 CACACGAGTACATATAAAGTAGTTTCA 57.436 33.333 0.00 0.00 0.00 2.69
2694 2898 3.027170 GCAGTGCGTTGGGTCGATG 62.027 63.158 0.00 0.00 0.00 3.84
2910 3119 4.400961 GAGCTTGCTGCCGGGAGT 62.401 66.667 24.99 3.38 44.23 3.85
2911 3120 4.711949 AGCTTGCTGCCGGGAGTG 62.712 66.667 24.99 15.42 44.23 3.51
2912 3121 4.704833 GCTTGCTGCCGGGAGTGA 62.705 66.667 24.99 12.18 35.15 3.41
2913 3122 2.435586 CTTGCTGCCGGGAGTGAG 60.436 66.667 24.99 17.65 0.00 3.51
2917 3126 1.600916 GCTGCCGGGAGTGAGTTTT 60.601 57.895 24.99 0.00 0.00 2.43
2918 3127 0.321298 GCTGCCGGGAGTGAGTTTTA 60.321 55.000 24.99 0.00 0.00 1.52
2920 3129 2.009774 CTGCCGGGAGTGAGTTTTATG 58.990 52.381 16.00 0.00 0.00 1.90
2922 3131 2.007608 GCCGGGAGTGAGTTTTATGTC 58.992 52.381 2.18 0.00 0.00 3.06
2924 3133 3.262420 CCGGGAGTGAGTTTTATGTCTG 58.738 50.000 0.00 0.00 0.00 3.51
2925 3134 2.673368 CGGGAGTGAGTTTTATGTCTGC 59.327 50.000 0.00 0.00 0.00 4.26
2926 3135 3.674997 GGGAGTGAGTTTTATGTCTGCA 58.325 45.455 0.00 0.00 0.00 4.41
2927 3136 3.686726 GGGAGTGAGTTTTATGTCTGCAG 59.313 47.826 7.63 7.63 0.00 4.41
2928 3137 4.319177 GGAGTGAGTTTTATGTCTGCAGT 58.681 43.478 14.67 0.00 0.00 4.40
2929 3138 4.390297 GGAGTGAGTTTTATGTCTGCAGTC 59.610 45.833 14.67 9.06 0.00 3.51
2930 3139 5.220710 AGTGAGTTTTATGTCTGCAGTCT 57.779 39.130 14.67 2.14 0.00 3.24
2931 3140 4.993584 AGTGAGTTTTATGTCTGCAGTCTG 59.006 41.667 14.67 0.00 0.00 3.51
2960 3174 1.198408 TCGCCGCTGTACTATAATCGG 59.802 52.381 0.00 0.00 39.81 4.18
2982 3196 3.628646 GACGCTGATTGGGGCTGGT 62.629 63.158 0.00 0.00 33.29 4.00
2998 3223 3.357079 GTTGGGTGTGCTCTGCCG 61.357 66.667 0.00 0.00 0.00 5.69
3057 3291 9.855021 CTTTGATTTAGAAAAATTATCCGTGGT 57.145 29.630 0.00 0.00 35.41 4.16
3085 3327 1.217882 GTGCCGTGTGATGTATAGGC 58.782 55.000 0.00 0.00 44.38 3.93
3196 3438 3.313803 TCGTTTGCTATTGTGCTTCAACA 59.686 39.130 0.00 0.00 38.97 3.33
3197 3439 3.421888 CGTTTGCTATTGTGCTTCAACAC 59.578 43.478 0.00 0.00 38.97 3.32
3198 3440 4.610945 GTTTGCTATTGTGCTTCAACACT 58.389 39.130 0.00 0.00 41.30 3.55
3201 3443 3.882288 TGCTATTGTGCTTCAACACTTCA 59.118 39.130 0.00 0.00 41.30 3.02
3202 3444 4.337836 TGCTATTGTGCTTCAACACTTCAA 59.662 37.500 0.00 0.00 41.30 2.69
3203 3445 4.676924 GCTATTGTGCTTCAACACTTCAAC 59.323 41.667 0.00 0.00 41.30 3.18
3204 3446 3.502191 TTGTGCTTCAACACTTCAACC 57.498 42.857 0.00 0.00 41.30 3.77
3205 3447 1.400142 TGTGCTTCAACACTTCAACCG 59.600 47.619 0.00 0.00 41.30 4.44
3214 3456 5.361427 TCAACACTTCAACCGTTCAAGATA 58.639 37.500 1.45 0.00 0.00 1.98
3236 3481 5.656213 AGTACTACTACGGTTGATTGCTT 57.344 39.130 0.00 0.00 0.00 3.91
3238 3483 7.161773 AGTACTACTACGGTTGATTGCTTTA 57.838 36.000 0.00 0.00 0.00 1.85
3240 3485 6.276832 ACTACTACGGTTGATTGCTTTAGA 57.723 37.500 0.00 0.00 0.00 2.10
3241 3486 6.098017 ACTACTACGGTTGATTGCTTTAGAC 58.902 40.000 0.00 0.00 0.00 2.59
3244 3489 2.484264 ACGGTTGATTGCTTTAGACTGC 59.516 45.455 0.00 0.00 0.00 4.40
3250 3495 4.005650 TGATTGCTTTAGACTGCCTCTTG 58.994 43.478 0.00 0.00 0.00 3.02
3259 3504 1.002868 CTGCCTCTTGGTCTGGTGG 60.003 63.158 0.00 0.00 35.27 4.61
3326 3572 1.129811 GCGGAATTTGTAAGGACACGG 59.870 52.381 0.00 0.00 34.48 4.94
3330 3576 2.781681 ATTTGTAAGGACACGGGAGG 57.218 50.000 0.00 0.00 34.48 4.30
3349 3595 4.380339 GGAGGCTCTTCTTCAGATTTTTGC 60.380 45.833 15.23 0.00 0.00 3.68
3367 3613 1.279271 TGCAAGGAACTAGAAGGAGCC 59.721 52.381 0.00 0.00 38.49 4.70
3372 3618 3.701604 AACTAGAAGGAGCCGCGCG 62.702 63.158 25.67 25.67 0.00 6.86
3400 3646 0.455464 GTGGCGGCGTGTATTTTTCC 60.455 55.000 9.37 0.00 0.00 3.13
3428 3684 5.111293 CCAAATCTAAAACATGGGCATCAC 58.889 41.667 0.00 0.00 0.00 3.06
3429 3685 4.637483 AATCTAAAACATGGGCATCACG 57.363 40.909 0.00 0.00 0.00 4.35
3432 3688 1.176527 AAAACATGGGCATCACGGAG 58.823 50.000 0.00 0.00 0.00 4.63
3443 3699 3.627577 GGCATCACGGAGACAACATAATT 59.372 43.478 0.00 0.00 0.00 1.40
3452 3708 7.118390 CACGGAGACAACATAATTTTCTCTCTT 59.882 37.037 3.57 0.00 34.36 2.85
3453 3709 8.311836 ACGGAGACAACATAATTTTCTCTCTTA 58.688 33.333 3.57 0.00 34.36 2.10
3523 3779 5.183904 AGGACAAAAGCATACACCAATCTTC 59.816 40.000 0.00 0.00 0.00 2.87
3533 3789 6.700081 GCATACACCAATCTTCGTATACTCAA 59.300 38.462 0.56 0.00 0.00 3.02
3614 3870 6.147821 AGGTAGATCAACTTGAACACATTTCG 59.852 38.462 0.00 0.00 0.00 3.46
3615 3871 6.073222 GGTAGATCAACTTGAACACATTTCGT 60.073 38.462 0.00 0.00 0.00 3.85
3616 3872 6.377327 AGATCAACTTGAACACATTTCGTT 57.623 33.333 0.00 0.00 0.00 3.85
3629 3885 4.035091 CACATTTCGTTTGGTGTGAAGAGA 59.965 41.667 0.00 0.00 43.41 3.10
3635 3891 4.698304 TCGTTTGGTGTGAAGAGAAAGTTT 59.302 37.500 0.00 0.00 0.00 2.66
3664 3920 9.252635 ACATTCATCATATCTACTCTAGCATCA 57.747 33.333 0.00 0.00 0.00 3.07
3708 3964 2.805099 GCTGCAACTCTAGCATACCATC 59.195 50.000 0.00 0.00 41.82 3.51
3712 3968 5.500234 TGCAACTCTAGCATACCATCTTTT 58.500 37.500 0.00 0.00 37.02 2.27
3743 3999 5.571784 TTATTTGAAAGATCCAGCAGCTG 57.428 39.130 16.23 16.23 0.00 4.24
3806 4062 9.844257 AAATACAAAAGGTGGATTTTGATCAAA 57.156 25.926 16.91 16.91 46.92 2.69
3837 4094 6.434340 AGGAGAAAAATAGAAAACTTCGCCAT 59.566 34.615 5.82 0.00 38.13 4.40
3843 4100 1.153353 GAAAACTTCGCCATCGGTGA 58.847 50.000 0.00 0.00 40.77 4.02
3874 4131 2.088423 TGTTTTGTCAGGCAAACGACT 58.912 42.857 0.00 0.00 45.70 4.18
3884 4141 2.158871 AGGCAAACGACTGAAACACCTA 60.159 45.455 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 0.258774 GGGGGCTCCTCAATGCTTTA 59.741 55.000 0.52 0.00 0.00 1.85
100 106 2.048127 GAGAAAGCGGTGGCGACT 60.048 61.111 0.00 0.00 46.35 4.18
157 163 4.587262 GGAAGAAGGGAGCAAAGGTAAAAA 59.413 41.667 0.00 0.00 0.00 1.94
345 366 4.080687 TGAATTGGCAGTGAATGTGATGA 58.919 39.130 0.00 0.00 0.00 2.92
351 372 4.439700 GGTGATCTGAATTGGCAGTGAATG 60.440 45.833 0.00 0.00 37.20 2.67
352 373 3.698040 GGTGATCTGAATTGGCAGTGAAT 59.302 43.478 0.00 0.00 37.20 2.57
353 374 3.084039 GGTGATCTGAATTGGCAGTGAA 58.916 45.455 0.00 0.00 37.20 3.18
354 375 2.040145 TGGTGATCTGAATTGGCAGTGA 59.960 45.455 0.00 0.00 37.20 3.41
355 376 2.439409 TGGTGATCTGAATTGGCAGTG 58.561 47.619 0.00 0.00 37.20 3.66
356 377 2.885135 TGGTGATCTGAATTGGCAGT 57.115 45.000 0.00 0.00 37.20 4.40
357 378 3.066342 GTCATGGTGATCTGAATTGGCAG 59.934 47.826 0.00 0.00 37.24 4.85
359 380 2.032550 CGTCATGGTGATCTGAATTGGC 59.967 50.000 0.00 0.00 0.00 4.52
360 381 3.534554 TCGTCATGGTGATCTGAATTGG 58.465 45.455 0.00 0.00 0.00 3.16
361 382 4.812626 TCATCGTCATGGTGATCTGAATTG 59.187 41.667 0.00 0.00 0.00 2.32
372 393 1.009078 CGTGCAATCATCGTCATGGT 58.991 50.000 0.00 0.00 0.00 3.55
427 448 5.693104 TCACCCGTTAATATAACGAAGATGC 59.307 40.000 20.62 0.00 45.64 3.91
478 508 8.516571 GAAATGTTCGTCGTTAATCACTAATG 57.483 34.615 0.00 0.00 0.00 1.90
497 527 2.496899 AGATTGCTCCACCGAAATGT 57.503 45.000 0.00 0.00 0.00 2.71
500 530 1.406887 GCCTAGATTGCTCCACCGAAA 60.407 52.381 0.00 0.00 0.00 3.46
501 531 0.178068 GCCTAGATTGCTCCACCGAA 59.822 55.000 0.00 0.00 0.00 4.30
502 532 0.975556 TGCCTAGATTGCTCCACCGA 60.976 55.000 0.00 0.00 0.00 4.69
640 675 6.954352 AAAAACAGGGAATAGAGTACTCCT 57.046 37.500 19.38 5.99 0.00 3.69
670 706 7.592051 CCTCTCCATTTCTCTTGAAAGAAAAG 58.408 38.462 3.45 0.00 45.62 2.27
672 708 5.474876 GCCTCTCCATTTCTCTTGAAAGAAA 59.525 40.000 1.91 1.91 46.31 2.52
673 709 5.006386 GCCTCTCCATTTCTCTTGAAAGAA 58.994 41.667 0.00 0.00 44.25 2.52
674 710 4.042062 TGCCTCTCCATTTCTCTTGAAAGA 59.958 41.667 0.00 0.00 44.25 2.52
675 711 4.330250 TGCCTCTCCATTTCTCTTGAAAG 58.670 43.478 0.00 0.00 44.25 2.62
677 713 4.074970 GTTGCCTCTCCATTTCTCTTGAA 58.925 43.478 0.00 0.00 0.00 2.69
678 714 3.679389 GTTGCCTCTCCATTTCTCTTGA 58.321 45.455 0.00 0.00 0.00 3.02
679 715 2.417933 CGTTGCCTCTCCATTTCTCTTG 59.582 50.000 0.00 0.00 0.00 3.02
680 716 2.704572 CGTTGCCTCTCCATTTCTCTT 58.295 47.619 0.00 0.00 0.00 2.85
681 717 1.677217 GCGTTGCCTCTCCATTTCTCT 60.677 52.381 0.00 0.00 0.00 3.10
692 728 2.253452 CTTGTGCTGCGTTGCCTC 59.747 61.111 0.00 0.00 0.00 4.70
749 791 2.500229 ACGAAATGAAAAGGCGAGGAA 58.500 42.857 0.00 0.00 0.00 3.36
848 894 5.407407 GTCTCTTGACAATTAGGTGAGGA 57.593 43.478 0.00 0.00 42.48 3.71
872 918 1.352622 TGTGGGTTTGGCAGTCCTCT 61.353 55.000 9.28 0.00 0.00 3.69
961 1047 2.590092 CCGGCGAGGGAAGGAAAT 59.410 61.111 9.30 0.00 35.97 2.17
962 1048 4.404098 GCCGGCGAGGGAAGGAAA 62.404 66.667 12.58 0.00 41.48 3.13
984 1074 2.107750 ATGGCTGCAGATCGTCGG 59.892 61.111 20.43 0.00 0.00 4.79
991 1081 2.055633 CCATTGCCATGGCTGCAGA 61.056 57.895 35.53 14.23 43.95 4.26
1032 1126 0.251165 GGCAGTGGTAAAGGCCTGAA 60.251 55.000 5.69 0.00 43.09 3.02
1033 1127 1.378762 GGCAGTGGTAAAGGCCTGA 59.621 57.895 5.69 0.00 43.09 3.86
1034 1128 2.040544 CGGCAGTGGTAAAGGCCTG 61.041 63.158 5.69 0.00 44.23 4.85
1035 1129 2.351276 CGGCAGTGGTAAAGGCCT 59.649 61.111 0.00 0.00 44.23 5.19
1078 1172 5.083533 TCATAAAACATGGTCAATTGCCC 57.916 39.130 13.99 7.45 0.00 5.36
1093 1187 3.129462 TCCGCCGCAAAATCATCATAAAA 59.871 39.130 0.00 0.00 0.00 1.52
1420 1514 8.289618 CCATGATTTAATCGATTTGACGGTAAT 58.710 33.333 17.19 5.34 0.00 1.89
1515 1650 4.814294 AGGAACGCTTAGCCGCCG 62.814 66.667 0.00 0.00 0.00 6.46
1527 1662 0.875059 GTGTACAGCCAGCAAGGAAC 59.125 55.000 0.00 0.00 41.22 3.62
1620 1755 4.637534 GCATATCTTCCAAAGAGCAGTTGA 59.362 41.667 0.00 0.00 41.61 3.18
1668 1808 3.994392 TCTTAGCTAGTTTCTTGTTGGCG 59.006 43.478 0.00 0.00 0.00 5.69
1673 1813 9.384764 GATTTGGTATCTTAGCTAGTTTCTTGT 57.615 33.333 0.00 0.00 0.00 3.16
1760 1900 9.486497 TCAATTGCTTGATTTAATTTGCACTTA 57.514 25.926 0.00 0.00 36.46 2.24
1773 1913 5.513233 AGGACTATGGTCAATTGCTTGATT 58.487 37.500 11.67 0.00 43.08 2.57
1774 1914 5.121380 AGGACTATGGTCAATTGCTTGAT 57.879 39.130 11.67 0.00 43.08 2.57
1775 1915 4.574674 AGGACTATGGTCAATTGCTTGA 57.425 40.909 11.67 0.00 43.77 3.02
1776 1916 4.576463 GGTAGGACTATGGTCAATTGCTTG 59.424 45.833 11.67 0.00 43.77 4.01
1777 1917 4.227300 TGGTAGGACTATGGTCAATTGCTT 59.773 41.667 11.67 0.00 43.77 3.91
1779 1919 4.150897 TGGTAGGACTATGGTCAATTGC 57.849 45.455 11.67 0.04 43.77 3.56
1920 2066 2.094234 TCAATTTCTCGATGCACCTCGA 60.094 45.455 11.61 11.61 44.85 4.04
1922 2068 3.002791 TGTCAATTTCTCGATGCACCTC 58.997 45.455 0.00 0.00 0.00 3.85
1964 2122 0.603975 GATAAGGATGCGGGTCAGGC 60.604 60.000 0.00 0.00 0.00 4.85
1966 2124 1.138859 TGTGATAAGGATGCGGGTCAG 59.861 52.381 0.00 0.00 0.00 3.51
1967 2125 1.199615 TGTGATAAGGATGCGGGTCA 58.800 50.000 0.00 0.00 0.00 4.02
1968 2126 2.325583 TTGTGATAAGGATGCGGGTC 57.674 50.000 0.00 0.00 0.00 4.46
1969 2127 2.643551 CTTTGTGATAAGGATGCGGGT 58.356 47.619 0.00 0.00 0.00 5.28
1984 2150 1.210967 TGTTCGGTGTTCCTCCTTTGT 59.789 47.619 0.00 0.00 0.00 2.83
2019 2189 2.965147 ACCAACTCTTGTGGAAAATGGG 59.035 45.455 0.00 0.00 0.00 4.00
2083 2255 2.027385 TCATGATCTCGACCAGACCTG 58.973 52.381 0.00 0.00 32.26 4.00
2084 2256 2.028130 GTCATGATCTCGACCAGACCT 58.972 52.381 0.00 0.00 32.26 3.85
2085 2257 1.268794 CGTCATGATCTCGACCAGACC 60.269 57.143 0.00 0.00 32.26 3.85
2137 2309 4.208666 GCAAAGCAAGCAAGAAAAGAGAAG 59.791 41.667 0.00 0.00 0.00 2.85
2139 2311 3.382546 AGCAAAGCAAGCAAGAAAAGAGA 59.617 39.130 0.00 0.00 0.00 3.10
2334 2512 4.090057 GCGGTGCCTGCTTTCGAC 62.090 66.667 0.00 0.00 0.00 4.20
2426 2609 7.673926 AGATAATCTAAGGAGGAGGAACTGATC 59.326 40.741 0.00 0.00 41.55 2.92
2444 2627 7.280876 TCGTGCTTGCTTTTGATAAGATAATCT 59.719 33.333 0.00 0.00 0.00 2.40
2486 2674 7.312415 ACAGTACTTAAATACCCAGTTCTGT 57.688 36.000 0.00 5.32 41.61 3.41
2522 2710 0.321671 GACACTGGACAGGCTTGCTA 59.678 55.000 4.14 0.00 0.00 3.49
2523 2711 1.072159 GACACTGGACAGGCTTGCT 59.928 57.895 4.14 0.00 0.00 3.91
2524 2712 1.968540 GGACACTGGACAGGCTTGC 60.969 63.158 4.14 0.00 0.00 4.01
2525 2713 0.886490 GTGGACACTGGACAGGCTTG 60.886 60.000 4.14 0.00 0.00 4.01
2526 2714 1.451936 GTGGACACTGGACAGGCTT 59.548 57.895 4.14 0.00 0.00 4.35
2527 2715 2.520536 GGTGGACACTGGACAGGCT 61.521 63.158 4.14 0.00 0.00 4.58
2528 2716 2.032681 GGTGGACACTGGACAGGC 59.967 66.667 4.14 0.00 0.00 4.85
2529 2717 1.372683 CTGGTGGACACTGGACAGG 59.627 63.158 4.14 0.00 0.00 4.00
2530 2718 1.302033 GCTGGTGGACACTGGACAG 60.302 63.158 2.13 0.00 0.00 3.51
2531 2719 2.043604 CTGCTGGTGGACACTGGACA 62.044 60.000 2.13 0.00 0.00 4.02
2532 2720 1.302033 CTGCTGGTGGACACTGGAC 60.302 63.158 2.13 0.00 0.00 4.02
2537 2733 2.670934 CTGGCTGCTGGTGGACAC 60.671 66.667 0.00 0.00 0.00 3.67
2575 2771 1.035923 TTGCCATCGAACAAAGCCAA 58.964 45.000 0.00 0.00 0.00 4.52
2613 2809 8.728337 ACTACTTTATATGTACTCGTGTGAGA 57.272 34.615 0.00 0.00 45.57 3.27
2642 2838 6.888632 GCATCCTAATCCCACTGAATTATGAT 59.111 38.462 0.00 0.00 0.00 2.45
2682 2878 0.392461 ATCAACCCATCGACCCAACG 60.392 55.000 0.00 0.00 0.00 4.10
2694 2898 5.292589 GCAACAAATCATCAATCATCAACCC 59.707 40.000 0.00 0.00 0.00 4.11
2897 3106 2.337879 AAACTCACTCCCGGCAGCAA 62.338 55.000 0.00 0.00 0.00 3.91
2898 3107 2.337879 AAAACTCACTCCCGGCAGCA 62.338 55.000 0.00 0.00 0.00 4.41
2899 3108 0.321298 TAAAACTCACTCCCGGCAGC 60.321 55.000 0.00 0.00 0.00 5.25
2901 3110 1.349688 ACATAAAACTCACTCCCGGCA 59.650 47.619 0.00 0.00 0.00 5.69
2902 3111 2.007608 GACATAAAACTCACTCCCGGC 58.992 52.381 0.00 0.00 0.00 6.13
2905 3114 3.674997 TGCAGACATAAAACTCACTCCC 58.325 45.455 0.00 0.00 0.00 4.30
2907 3116 5.119898 CAGACTGCAGACATAAAACTCACTC 59.880 44.000 23.35 1.55 0.00 3.51
2908 3117 4.993584 CAGACTGCAGACATAAAACTCACT 59.006 41.667 23.35 0.00 0.00 3.41
2909 3118 4.377841 GCAGACTGCAGACATAAAACTCAC 60.378 45.833 23.35 0.00 44.26 3.51
2910 3119 3.748048 GCAGACTGCAGACATAAAACTCA 59.252 43.478 23.35 0.00 44.26 3.41
2911 3120 3.181526 CGCAGACTGCAGACATAAAACTC 60.182 47.826 26.32 3.67 45.36 3.01
2912 3121 2.738846 CGCAGACTGCAGACATAAAACT 59.261 45.455 26.32 0.00 45.36 2.66
2913 3122 2.726066 GCGCAGACTGCAGACATAAAAC 60.726 50.000 26.32 0.00 45.36 2.43
2917 3126 1.517039 CGCGCAGACTGCAGACATA 60.517 57.895 26.32 0.00 45.36 2.29
2918 3127 2.812609 CGCGCAGACTGCAGACAT 60.813 61.111 26.32 0.00 45.36 3.06
2920 3129 3.474034 GTCGCGCAGACTGCAGAC 61.474 66.667 26.68 26.68 45.36 3.51
2946 3160 3.666374 GCGTCCGTCCGATTATAGTACAG 60.666 52.174 0.00 0.00 0.00 2.74
2960 3174 2.511600 CCCCAATCAGCGTCCGTC 60.512 66.667 0.00 0.00 0.00 4.79
2982 3196 4.641645 CCGGCAGAGCACACCCAA 62.642 66.667 0.00 0.00 0.00 4.12
2998 3223 3.512516 GGTTGCATCGAGGCTGCC 61.513 66.667 23.78 19.74 38.89 4.85
3008 3233 1.761174 AACCCTCGTCAGGTTGCAT 59.239 52.632 5.85 0.00 45.93 3.96
3013 3238 3.157680 CCCAAACCCTCGTCAGGT 58.842 61.111 0.00 0.00 38.30 4.00
3014 3239 2.359975 GCCCAAACCCTCGTCAGG 60.360 66.667 0.00 0.00 39.98 3.86
3057 3291 1.960417 TCACACGGCACAATCTCAAA 58.040 45.000 0.00 0.00 0.00 2.69
3085 3327 2.282147 CTGCCACTCTCTCAGCTCCG 62.282 65.000 0.00 0.00 0.00 4.63
3196 3438 6.342338 AGTACTATCTTGAACGGTTGAAGT 57.658 37.500 17.52 9.30 0.00 3.01
3197 3439 7.536855 AGTAGTACTATCTTGAACGGTTGAAG 58.463 38.462 13.02 13.02 0.00 3.02
3198 3440 7.458409 AGTAGTACTATCTTGAACGGTTGAA 57.542 36.000 5.75 0.00 0.00 2.69
3201 3443 6.037610 CCGTAGTAGTACTATCTTGAACGGTT 59.962 42.308 22.13 0.00 32.65 4.44
3202 3444 5.525378 CCGTAGTAGTACTATCTTGAACGGT 59.475 44.000 22.13 0.00 32.65 4.83
3203 3445 5.525378 ACCGTAGTAGTACTATCTTGAACGG 59.475 44.000 26.02 26.02 36.82 4.44
3204 3446 6.595772 ACCGTAGTAGTACTATCTTGAACG 57.404 41.667 13.09 11.90 32.65 3.95
3205 3447 7.978982 TCAACCGTAGTAGTACTATCTTGAAC 58.021 38.462 13.09 0.61 32.65 3.18
3214 3456 5.656213 AAGCAATCAACCGTAGTAGTACT 57.344 39.130 8.14 8.14 0.00 2.73
3236 3481 1.902508 CCAGACCAAGAGGCAGTCTAA 59.097 52.381 0.00 0.00 38.80 2.10
3238 3483 0.472734 ACCAGACCAAGAGGCAGTCT 60.473 55.000 0.00 0.00 41.49 3.24
3240 3485 1.757306 CACCAGACCAAGAGGCAGT 59.243 57.895 0.00 0.00 39.06 4.40
3241 3486 1.002868 CCACCAGACCAAGAGGCAG 60.003 63.158 0.00 0.00 39.06 4.85
3244 3489 2.887151 AATTCCACCAGACCAAGAGG 57.113 50.000 0.00 0.00 42.21 3.69
3250 3495 4.983671 GGAACAATAATTCCACCAGACC 57.016 45.455 0.00 0.00 46.49 3.85
3259 3504 6.314784 CGAAGAACACCTGGAACAATAATTC 58.685 40.000 0.00 0.00 38.70 2.17
3275 3520 1.933500 GCGTAACAGAGGCGAAGAACA 60.934 52.381 0.00 0.00 0.00 3.18
3308 3554 3.007635 CTCCCGTGTCCTTACAAATTCC 58.992 50.000 0.00 0.00 37.36 3.01
3326 3572 4.380339 GCAAAAATCTGAAGAAGAGCCTCC 60.380 45.833 0.00 0.00 38.67 4.30
3330 3576 4.922103 CCTTGCAAAAATCTGAAGAAGAGC 59.078 41.667 0.00 0.00 38.67 4.09
3349 3595 1.740718 GCGGCTCCTTCTAGTTCCTTG 60.741 57.143 0.00 0.00 0.00 3.61
3381 3627 0.455464 GGAAAAATACACGCCGCCAC 60.455 55.000 0.00 0.00 0.00 5.01
3386 3632 0.796870 GCGCAGGAAAAATACACGCC 60.797 55.000 0.30 0.00 39.01 5.68
3393 3639 4.799564 TTAGATTTGGCGCAGGAAAAAT 57.200 36.364 10.83 6.83 0.00 1.82
3400 3646 3.181397 CCATGTTTTAGATTTGGCGCAG 58.819 45.455 10.83 0.00 0.00 5.18
3428 3684 7.602517 AAGAGAGAAAATTATGTTGTCTCCG 57.397 36.000 15.87 0.00 43.16 4.63
3474 3730 5.183904 AGGAATGCGCTTTAATTGTTTCTCT 59.816 36.000 9.73 0.00 0.00 3.10
3481 3737 4.335315 TGTCCTAGGAATGCGCTTTAATTG 59.665 41.667 14.65 2.00 0.00 2.32
3487 3743 2.489938 TTTGTCCTAGGAATGCGCTT 57.510 45.000 14.65 0.00 0.00 4.68
3584 3840 7.782049 TGTGTTCAAGTTGATCTACCTATAGG 58.218 38.462 17.73 17.73 42.17 2.57
3585 3841 9.823647 AATGTGTTCAAGTTGATCTACCTATAG 57.176 33.333 6.36 0.00 0.00 1.31
3614 3870 6.308041 GTCAAAACTTTCTCTTCACACCAAAC 59.692 38.462 0.00 0.00 0.00 2.93
3615 3871 6.015856 TGTCAAAACTTTCTCTTCACACCAAA 60.016 34.615 0.00 0.00 0.00 3.28
3616 3872 5.475220 TGTCAAAACTTTCTCTTCACACCAA 59.525 36.000 0.00 0.00 0.00 3.67
3635 3891 9.082313 TGCTAGAGTAGATATGATGAATGTCAA 57.918 33.333 0.00 0.00 0.00 3.18
3651 3907 6.475076 CAGTAAGTTGCTTGATGCTAGAGTAG 59.525 42.308 0.00 0.00 43.37 2.57
3677 3933 4.277174 GCTAGAGTTGCAGCTACTGAGATA 59.723 45.833 14.67 1.79 34.86 1.98
3721 3977 5.571784 CAGCTGCTGGATCTTTCAAATAA 57.428 39.130 21.71 0.00 0.00 1.40
3743 3999 3.190118 GCTATGATCAATACAAGCCAGCC 59.810 47.826 0.00 0.00 0.00 4.85
3824 4081 1.136057 GTCACCGATGGCGAAGTTTTC 60.136 52.381 0.00 0.00 40.82 2.29
3832 4089 1.911293 CTTGTTGGTCACCGATGGCG 61.911 60.000 0.00 0.00 37.24 5.69


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

AutoCloner maintained by Alex Coulton.