Multiple sequence alignment - TraesCS3D01G249200

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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 TraesCS3D01G249200 chr3D 100.000 2236 0 0 686 2921 348913456 348911221 0.000000e+00 4130.0
1 TraesCS3D01G249200 chr3D 100.000 384 0 0 3286 3669 348910856 348910473 0.000000e+00 710.0
2 TraesCS3D01G249200 chr3D 100.000 304 0 0 1 304 348914141 348913838 2.470000e-156 562.0
3 TraesCS3D01G249200 chr3D 89.286 196 17 4 686 881 585246994 585246803 3.660000e-60 243.0
4 TraesCS3D01G249200 chr3D 94.737 38 2 0 1312 1349 419464186 419464223 3.960000e-05 60.2
5 TraesCS3D01G249200 chr3A 94.680 1654 71 12 884 2521 467404272 467402620 0.000000e+00 2551.0
6 TraesCS3D01G249200 chr3A 89.034 383 37 3 3287 3669 494023697 494024074 1.540000e-128 470.0
7 TraesCS3D01G249200 chr3A 90.492 305 23 4 1 304 468252769 468252470 7.380000e-107 398.0
8 TraesCS3D01G249200 chr3A 92.308 195 10 2 686 880 468252389 468252200 4.670000e-69 272.0
9 TraesCS3D01G249200 chr3B 93.891 1555 75 15 884 2426 448314852 448313306 0.000000e+00 2327.0
10 TraesCS3D01G249200 chr3B 87.696 382 44 3 3286 3667 821157531 821157909 3.360000e-120 442.0
11 TraesCS3D01G249200 chr3B 93.069 101 5 1 2421 2521 448313109 448313011 2.950000e-31 147.0
12 TraesCS3D01G249200 chr5A 89.583 384 37 3 3286 3669 269329031 269329411 5.510000e-133 484.0
13 TraesCS3D01G249200 chr5A 89.836 305 21 7 1 304 442539846 442539551 2.070000e-102 383.0
14 TraesCS3D01G249200 chr5A 84.848 198 19 1 686 883 590352227 590352413 4.840000e-44 189.0
15 TraesCS3D01G249200 chr5A 84.184 196 20 1 687 882 556865557 556865373 2.910000e-41 180.0
16 TraesCS3D01G249200 chr1A 87.961 407 38 5 2520 2920 166260351 166259950 1.540000e-128 470.0
17 TraesCS3D01G249200 chr1A 90.820 305 27 1 1 304 482221889 482222193 1.230000e-109 407.0
18 TraesCS3D01G249200 chr1A 86.601 306 38 3 1 304 504066135 504066439 5.870000e-88 335.0
19 TraesCS3D01G249200 chr1A 92.424 198 13 1 686 883 482222273 482222468 7.760000e-72 281.0
20 TraesCS3D01G249200 chr6A 87.760 384 46 1 3286 3669 218263707 218263325 7.230000e-122 448.0
21 TraesCS3D01G249200 chr6A 83.854 384 49 7 2543 2921 218264325 218263950 1.620000e-93 353.0
22 TraesCS3D01G249200 chr6A 86.224 196 13 9 686 880 583026866 583027048 2.230000e-47 200.0
23 TraesCS3D01G249200 chr1B 91.304 322 27 1 3348 3669 328966304 328966624 4.350000e-119 438.0
24 TraesCS3D01G249200 chr5B 91.475 305 25 1 1 304 659478614 659478918 5.670000e-113 418.0
25 TraesCS3D01G249200 chr5B 88.822 331 35 2 3339 3669 402758542 402758214 4.410000e-109 405.0
26 TraesCS3D01G249200 chr5B 89.216 306 27 6 1 304 331825175 331825476 9.620000e-101 377.0
27 TraesCS3D01G249200 chr6B 87.725 334 39 2 3336 3669 84366717 84367048 4.440000e-104 388.0
28 TraesCS3D01G249200 chr6D 87.463 335 33 6 3336 3669 67505462 67505136 9.620000e-101 377.0
29 TraesCS3D01G249200 chrUn 86.905 336 39 5 3337 3669 383736547 383736880 4.470000e-99 372.0
30 TraesCS3D01G249200 chr4D 90.637 267 24 1 1 266 327728284 327728018 1.620000e-93 353.0
31 TraesCS3D01G249200 chr4D 90.256 195 14 1 686 880 201706682 201706871 2.190000e-62 250.0
32 TraesCS3D01G249200 chr4D 100.000 32 0 0 1609 1640 309943995 309944026 3.960000e-05 60.2
33 TraesCS3D01G249200 chr1D 92.149 242 17 2 3 243 482826236 482825996 1.260000e-89 340.0
34 TraesCS3D01G249200 chr1D 85.149 303 43 2 2 304 216720189 216720489 3.560000e-80 309.0
35 TraesCS3D01G249200 chr1D 93.401 197 13 0 686 882 482825416 482825220 3.580000e-75 292.0
36 TraesCS3D01G249200 chr2A 94.737 190 8 1 686 875 149241687 149241500 9.960000e-76 294.0
37 TraesCS3D01G249200 chr2A 87.273 55 5 2 1305 1358 729980044 729980097 1.100000e-05 62.1
38 TraesCS3D01G249200 chr7A 86.447 273 29 3 2522 2789 669245067 669244798 3.580000e-75 292.0
39 TraesCS3D01G249200 chr7A 84.834 211 16 2 686 882 93124707 93124499 8.040000e-47 198.0
40 TraesCS3D01G249200 chr7D 82.051 195 24 5 686 880 163517755 163517938 4.910000e-34 156.0
41 TraesCS3D01G249200 chr7D 75.936 187 38 7 1480 1663 401717246 401717064 5.050000e-14 89.8
42 TraesCS3D01G249200 chr4A 85.000 60 7 2 1609 1667 164687991 164687933 3.960000e-05 60.2
43 TraesCS3D01G249200 chr2D 94.595 37 1 1 1476 1512 643878758 643878793 5.120000e-04 56.5
44 TraesCS3D01G249200 chr2B 94.595 37 1 1 1476 1512 793169494 793169459 5.120000e-04 56.5


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 TraesCS3D01G249200 chr3D 348910473 348914141 3668 True 1800.666667 4130 100.000 1 3669 3 chr3D.!!$R2 3668
1 TraesCS3D01G249200 chr3A 467402620 467404272 1652 True 2551.000000 2551 94.680 884 2521 1 chr3A.!!$R1 1637
2 TraesCS3D01G249200 chr3A 468252200 468252769 569 True 335.000000 398 91.400 1 880 2 chr3A.!!$R2 879
3 TraesCS3D01G249200 chr3B 448313011 448314852 1841 True 1237.000000 2327 93.480 884 2521 2 chr3B.!!$R1 1637
4 TraesCS3D01G249200 chr1A 482221889 482222468 579 False 344.000000 407 91.622 1 883 2 chr1A.!!$F2 882
5 TraesCS3D01G249200 chr6A 218263325 218264325 1000 True 400.500000 448 85.807 2543 3669 2 chr6A.!!$R1 1126
6 TraesCS3D01G249200 chr1D 482825220 482826236 1016 True 316.000000 340 92.775 3 882 2 chr1D.!!$R1 879

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
888 1028 0.563672 GGAGGGGAGGGAGTGTAGAT 59.436 60.0 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2709 3083 0.036388 GTGGAGCGGAAGTGATGGAA 60.036 55.0 0.0 0.0 0.0 3.53 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
26 27 1.445410 CATCGGTCGTCGCCAGAAA 60.445 57.895 6.53 0.00 39.05 2.52
44 45 2.284699 CCGGAGAGGGAGGGTTGT 60.285 66.667 0.00 0.00 35.97 3.32
75 77 4.749310 CTGCCGCCTGAAGACGCT 62.749 66.667 0.00 0.00 0.00 5.07
76 78 4.742201 TGCCGCCTGAAGACGCTC 62.742 66.667 0.00 0.00 0.00 5.03
883 1023 1.690985 GAAGGGAGGGGAGGGAGTG 60.691 68.421 0.00 0.00 0.00 3.51
884 1024 2.478722 GAAGGGAGGGGAGGGAGTGT 62.479 65.000 0.00 0.00 0.00 3.55
885 1025 1.160289 AAGGGAGGGGAGGGAGTGTA 61.160 60.000 0.00 0.00 0.00 2.90
886 1026 1.075151 GGGAGGGGAGGGAGTGTAG 60.075 68.421 0.00 0.00 0.00 2.74
887 1027 1.591280 GGGAGGGGAGGGAGTGTAGA 61.591 65.000 0.00 0.00 0.00 2.59
888 1028 0.563672 GGAGGGGAGGGAGTGTAGAT 59.436 60.000 0.00 0.00 0.00 1.98
897 1037 3.292460 AGGGAGTGTAGATCTTCTTCCG 58.708 50.000 0.00 0.00 31.35 4.30
909 1049 2.028385 TCTTCTTCCGCTGAACCTAACC 60.028 50.000 0.00 0.00 0.00 2.85
937 1079 5.003160 AGGCCCACAAAGCAAAAATATTTC 58.997 37.500 0.00 0.00 0.00 2.17
958 1100 1.401800 CCCGCGCCGTTTTAAAATTCT 60.402 47.619 0.00 0.00 0.00 2.40
966 1108 4.089493 GCCGTTTTAAAATTCTTCGCCTTC 59.911 41.667 3.52 0.00 0.00 3.46
991 1133 3.412386 CCTTAACTTCCAACACCTCCAG 58.588 50.000 0.00 0.00 0.00 3.86
1018 1163 4.837093 AAATCGAATGTAGAACAGGGGA 57.163 40.909 0.00 0.00 0.00 4.81
1069 1214 2.513026 ATCTGCTTGCTCGCCGTCTT 62.513 55.000 0.00 0.00 0.00 3.01
1199 1356 2.683933 TCCTTCTCCTCCCCGCAC 60.684 66.667 0.00 0.00 0.00 5.34
1201 1358 3.068691 CTTCTCCTCCCCGCACGA 61.069 66.667 0.00 0.00 0.00 4.35
1356 1513 0.386352 CGACTGCTTCGTCCACGTAA 60.386 55.000 0.00 0.00 43.24 3.18
1377 1534 0.667993 TACGAACCGAACTCCGTGTT 59.332 50.000 0.00 0.00 42.38 3.32
1432 1589 3.467119 GCTCACGTACGCACACGG 61.467 66.667 16.72 1.18 46.12 4.94
1465 1622 2.879026 GCTCTGTTTTCTTTTCGTCCCT 59.121 45.455 0.00 0.00 0.00 4.20
1595 1755 2.664568 CGTCGACAAAATTAAGGCGAGA 59.335 45.455 17.16 0.00 0.00 4.04
1638 1798 3.838271 TCTCCTGCGCCGACATCC 61.838 66.667 4.18 0.00 0.00 3.51
1751 1911 3.186047 GACGTGAACATCCCGGCG 61.186 66.667 0.00 0.00 0.00 6.46
1880 2040 3.236047 TCCCTGCAGAACTTACTACACA 58.764 45.455 17.39 0.00 0.00 3.72
1903 2063 6.690194 ACATTTTATGTGATCCAAGCTCTC 57.310 37.500 0.00 0.00 43.01 3.20
2368 2535 2.049156 GGGCTTTTTGTCAGCGCC 60.049 61.111 2.29 0.00 42.84 6.53
2369 2536 2.429069 GGCTTTTTGTCAGCGCCG 60.429 61.111 2.29 0.00 38.24 6.46
2388 2555 1.067212 CGGGGATTCTAACTCGGTCTG 59.933 57.143 0.00 0.00 0.00 3.51
2521 2890 0.469917 CCACACACTTCTGTCAGGGT 59.530 55.000 0.00 0.00 0.00 4.34
2524 2893 2.332063 CACACTTCTGTCAGGGTGTT 57.668 50.000 21.39 10.54 42.46 3.32
2525 2894 1.942657 CACACTTCTGTCAGGGTGTTG 59.057 52.381 21.39 15.67 42.46 3.33
2526 2895 1.837439 ACACTTCTGTCAGGGTGTTGA 59.163 47.619 19.50 0.00 39.47 3.18
2527 2896 2.238646 ACACTTCTGTCAGGGTGTTGAA 59.761 45.455 19.50 0.00 39.47 2.69
2528 2897 2.614057 CACTTCTGTCAGGGTGTTGAAC 59.386 50.000 14.51 0.00 0.00 3.18
2529 2898 1.867233 CTTCTGTCAGGGTGTTGAACG 59.133 52.381 0.00 0.00 0.00 3.95
2530 2899 0.828022 TCTGTCAGGGTGTTGAACGT 59.172 50.000 0.00 0.00 0.00 3.99
2531 2900 0.937304 CTGTCAGGGTGTTGAACGTG 59.063 55.000 0.00 0.00 0.00 4.49
2532 2901 0.537653 TGTCAGGGTGTTGAACGTGA 59.462 50.000 0.00 0.00 0.00 4.35
2533 2902 0.935196 GTCAGGGTGTTGAACGTGAC 59.065 55.000 0.00 0.00 36.69 3.67
2534 2903 0.537653 TCAGGGTGTTGAACGTGACA 59.462 50.000 0.00 0.00 0.00 3.58
2535 2904 1.140052 TCAGGGTGTTGAACGTGACAT 59.860 47.619 0.00 0.00 0.00 3.06
2536 2905 2.365941 TCAGGGTGTTGAACGTGACATA 59.634 45.455 0.00 0.00 0.00 2.29
2537 2906 3.007506 TCAGGGTGTTGAACGTGACATAT 59.992 43.478 0.00 0.00 0.00 1.78
2538 2907 3.125146 CAGGGTGTTGAACGTGACATATG 59.875 47.826 0.00 0.00 0.00 1.78
2539 2908 3.071479 GGGTGTTGAACGTGACATATGT 58.929 45.455 8.43 8.43 0.00 2.29
2540 2909 3.120338 GGGTGTTGAACGTGACATATGTG 60.120 47.826 14.43 1.19 0.00 3.21
2541 2910 3.496884 GGTGTTGAACGTGACATATGTGT 59.503 43.478 14.43 1.91 42.49 3.72
2577 2951 8.152246 TCTATAGTCTCTAGCCTAGTTGACTTC 58.848 40.741 23.82 5.88 39.41 3.01
2582 2956 6.824704 GTCTCTAGCCTAGTTGACTTCTAGAA 59.175 42.308 4.81 4.81 37.62 2.10
2586 2960 9.122779 TCTAGCCTAGTTGACTTCTAGAAATAC 57.877 37.037 6.63 2.76 37.62 1.89
2588 2962 6.602406 AGCCTAGTTGACTTCTAGAAATACGA 59.398 38.462 6.63 0.00 37.62 3.43
2613 2987 1.225855 TTAGTTGGCTTGTCACGCAG 58.774 50.000 3.49 0.00 0.00 5.18
2614 2988 0.391228 TAGTTGGCTTGTCACGCAGA 59.609 50.000 3.49 0.00 0.00 4.26
2645 3019 8.851960 TCGTGTATATATTGTGAACAACTCTC 57.148 34.615 0.00 0.00 38.86 3.20
2668 3042 6.182627 TCAGGAATACAATTGAGTTGCATCT 58.817 36.000 13.59 0.00 41.69 2.90
2674 3048 9.823098 GAATACAATTGAGTTGCATCTCATATC 57.177 33.333 24.37 12.82 42.84 1.63
2683 3057 8.481314 TGAGTTGCATCTCATATCTTTTCTACT 58.519 33.333 20.98 0.00 39.20 2.57
2684 3058 9.973450 GAGTTGCATCTCATATCTTTTCTACTA 57.027 33.333 18.01 0.00 34.88 1.82
2685 3059 9.757227 AGTTGCATCTCATATCTTTTCTACTAC 57.243 33.333 0.00 0.00 0.00 2.73
2686 3060 9.534565 GTTGCATCTCATATCTTTTCTACTACA 57.465 33.333 0.00 0.00 0.00 2.74
2689 3063 9.149225 GCATCTCATATCTTTTCTACTACATGG 57.851 37.037 0.00 0.00 0.00 3.66
2705 3079 7.478520 ACTACATGGTATAAGTTTTCATCGC 57.521 36.000 0.00 0.00 0.00 4.58
2709 3083 6.260050 ACATGGTATAAGTTTTCATCGCGATT 59.740 34.615 21.14 6.47 0.00 3.34
2713 3087 5.811399 ATAAGTTTTCATCGCGATTTCCA 57.189 34.783 21.14 0.81 0.00 3.53
2714 3088 4.701956 AAGTTTTCATCGCGATTTCCAT 57.298 36.364 21.14 0.95 0.00 3.41
2716 3090 3.689161 AGTTTTCATCGCGATTTCCATCA 59.311 39.130 21.14 0.00 0.00 3.07
2723 3097 0.028110 GCGATTTCCATCACTTCCGC 59.972 55.000 0.00 0.00 34.71 5.54
2724 3098 1.656652 CGATTTCCATCACTTCCGCT 58.343 50.000 0.00 0.00 0.00 5.52
2758 3132 4.162690 CCTCCCTGTAGCCGCCAC 62.163 72.222 0.00 0.00 0.00 5.01
2776 3150 3.264845 TGCCCCTCCTCCCAAACC 61.265 66.667 0.00 0.00 0.00 3.27
2782 3156 0.252197 CCTCCTCCCAAACCCTAACG 59.748 60.000 0.00 0.00 0.00 3.18
2788 3162 3.795342 CAAACCCTAACGCCGCCG 61.795 66.667 0.00 0.00 41.14 6.46
2803 3177 1.525535 GCCGTCGCTACTCCCTCTA 60.526 63.158 0.00 0.00 0.00 2.43
2809 3183 1.088306 CGCTACTCCCTCTATAGCCG 58.912 60.000 0.00 0.00 38.48 5.52
2812 3186 0.322277 TACTCCCTCTATAGCCGCCG 60.322 60.000 0.00 0.00 0.00 6.46
2834 3208 1.301954 CCTTCCCCCAAACCCTACG 59.698 63.158 0.00 0.00 0.00 3.51
2836 3210 1.848886 CTTCCCCCAAACCCTACGCT 61.849 60.000 0.00 0.00 0.00 5.07
2837 3211 2.045340 CCCCCAAACCCTACGCTG 60.045 66.667 0.00 0.00 0.00 5.18
2886 3260 1.614226 TCCTCCCCCAAACCCTACG 60.614 63.158 0.00 0.00 0.00 3.51
2889 3263 4.789123 CCCCCAAACCCTACGCCG 62.789 72.222 0.00 0.00 0.00 6.46
3326 3700 4.817909 CGCCCCTCCCCTACCCTT 62.818 72.222 0.00 0.00 0.00 3.95
3327 3701 3.097162 GCCCCTCCCCTACCCTTG 61.097 72.222 0.00 0.00 0.00 3.61
3329 3703 2.459710 CCCTCCCCTACCCTTGGT 59.540 66.667 0.00 0.00 40.16 3.67
3330 3704 1.230182 CCCTCCCCTACCCTTGGTT 60.230 63.158 0.00 0.00 37.09 3.67
3331 3705 1.571773 CCCTCCCCTACCCTTGGTTG 61.572 65.000 0.00 0.00 37.09 3.77
3337 3711 0.395724 CCTACCCTTGGTTGCCATCC 60.396 60.000 0.00 0.00 37.09 3.51
3346 3720 0.761802 GGTTGCCATCCTCTCCCTAG 59.238 60.000 0.00 0.00 0.00 3.02
3350 3724 0.839853 GCCATCCTCTCCCTAGCCAT 60.840 60.000 0.00 0.00 0.00 4.40
3355 3729 0.105246 CCTCTCCCTAGCCATCACCT 60.105 60.000 0.00 0.00 0.00 4.00
3365 3739 4.165372 CCTAGCCATCACCTAAACCCTAAA 59.835 45.833 0.00 0.00 0.00 1.85
3370 3744 3.405823 TCACCTAAACCCTAAACACCG 57.594 47.619 0.00 0.00 0.00 4.94
3372 3746 1.271543 ACCTAAACCCTAAACACCGCC 60.272 52.381 0.00 0.00 0.00 6.13
3375 3749 4.710167 ACCCTAAACACCGCCGCC 62.710 66.667 0.00 0.00 0.00 6.13
3394 3768 4.354943 CCCCACCTCCCTCCCACT 62.355 72.222 0.00 0.00 0.00 4.00
3408 3782 2.747460 CACTGCCACCATGTCCCG 60.747 66.667 0.00 0.00 0.00 5.14
3414 3788 2.350895 CACCATGTCCCGCTCCAA 59.649 61.111 0.00 0.00 0.00 3.53
3417 3791 2.825836 CATGTCCCGCTCCAAGGC 60.826 66.667 0.00 0.00 0.00 4.35
3430 3804 1.519455 CAAGGCCGATCTGTCCGAC 60.519 63.158 0.00 0.00 0.00 4.79
3449 3823 4.785453 CCGGCTCCTTCACTGGCC 62.785 72.222 0.00 0.00 41.02 5.36
3451 3825 3.650950 GGCTCCTTCACTGGCCCA 61.651 66.667 0.00 0.00 38.77 5.36
3466 3840 1.341383 GGCCCAATGTTCACCTCTGAT 60.341 52.381 0.00 0.00 0.00 2.90
3481 3855 4.005032 GATCGCCTCAACGAGCTC 57.995 61.111 2.73 2.73 46.69 4.09
3482 3856 1.590259 GATCGCCTCAACGAGCTCC 60.590 63.158 8.47 0.00 46.69 4.70
3503 3877 1.271325 ACATCAAAGATCACGTGCCCA 60.271 47.619 11.67 0.00 0.00 5.36
3505 3879 1.737838 TCAAAGATCACGTGCCCATC 58.262 50.000 11.67 9.17 0.00 3.51
3511 3885 2.298158 ATCACGTGCCCATCGTCCTC 62.298 60.000 11.67 0.00 39.55 3.71
3542 3916 2.024918 CCATCCTACAACGCATGGC 58.975 57.895 0.00 0.00 29.71 4.40
3566 3940 2.288886 ACCTACTTCACGCTCTTGTTCC 60.289 50.000 0.00 0.00 0.00 3.62
3601 3975 2.456119 CGAGCATGTTGACGGGAGC 61.456 63.158 0.00 0.00 0.00 4.70
3604 3978 2.325082 GCATGTTGACGGGAGCGTT 61.325 57.895 0.00 0.00 0.00 4.84
3621 3995 0.716108 GTTGACTTCCGCGACATGAG 59.284 55.000 8.23 0.00 0.00 2.90
3625 3999 1.519455 CTTCCGCGACATGAGGGAC 60.519 63.158 8.23 0.00 38.24 4.46
3631 4005 1.226323 CGACATGAGGGACGACGAC 60.226 63.158 0.00 0.00 0.00 4.34
3632 4006 1.880894 GACATGAGGGACGACGACA 59.119 57.895 0.00 0.00 0.00 4.35
3641 4015 1.557443 GGACGACGACAAGTGGCTTG 61.557 60.000 0.00 7.27 45.85 4.01
3649 4023 1.941812 CAAGTGGCTTGTCGTGGAC 59.058 57.895 1.06 0.00 36.79 4.02
3654 4028 2.668280 GGCTTGTCGTGGACGCTTC 61.668 63.158 0.00 0.00 39.60 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.498520 CTGGCGACGACCGATGCT 62.499 66.667 0.00 0.00 41.76 3.79
26 27 2.284699 CAACCCTCCCTCTCCGGT 60.285 66.667 0.00 0.00 0.00 5.28
59 60 4.742201 GAGCGTCTTCAGGCGGCA 62.742 66.667 13.08 0.00 38.51 5.69
164 166 2.117423 GGTGTTTGGTGGGAGGGG 59.883 66.667 0.00 0.00 0.00 4.79
168 170 2.193517 CCGTGGTGTTTGGTGGGA 59.806 61.111 0.00 0.00 0.00 4.37
171 173 2.892334 CTCGCCGTGGTGTTTGGTG 61.892 63.158 0.00 0.00 34.58 4.17
176 178 4.003788 CCCTCTCGCCGTGGTGTT 62.004 66.667 0.00 0.00 0.00 3.32
866 1006 1.160289 TACACTCCCTCCCCTCCCTT 61.160 60.000 0.00 0.00 0.00 3.95
883 1023 3.131400 AGGTTCAGCGGAAGAAGATCTAC 59.869 47.826 0.00 0.00 32.62 2.59
884 1024 3.366396 AGGTTCAGCGGAAGAAGATCTA 58.634 45.455 0.00 0.00 32.62 1.98
885 1025 2.183679 AGGTTCAGCGGAAGAAGATCT 58.816 47.619 0.00 0.00 32.62 2.75
886 1026 2.682155 AGGTTCAGCGGAAGAAGATC 57.318 50.000 0.00 0.00 32.62 2.75
887 1027 3.369576 GGTTAGGTTCAGCGGAAGAAGAT 60.370 47.826 0.00 0.00 32.62 2.40
888 1028 2.028385 GGTTAGGTTCAGCGGAAGAAGA 60.028 50.000 0.00 0.00 32.62 2.87
897 1037 0.323451 CCTTGGGGGTTAGGTTCAGC 60.323 60.000 0.00 0.00 0.00 4.26
909 1049 3.313524 GCTTTGTGGGCCTTGGGG 61.314 66.667 4.53 0.00 0.00 4.96
937 1079 0.388778 AATTTTAAAACGGCGCGGGG 60.389 50.000 19.75 5.01 0.00 5.73
966 1108 1.265905 GGTGTTGGAAGTTAAGGCGTG 59.734 52.381 0.00 0.00 0.00 5.34
991 1133 6.024049 CCTGTTCTACATTCGATTTTTGAGC 58.976 40.000 0.00 0.00 0.00 4.26
1069 1214 2.111669 CTGTGCACAGGACCAGCA 59.888 61.111 34.65 3.23 40.20 4.41
1164 1321 1.919956 GAGAAAGACGACGAGCCGGA 61.920 60.000 5.05 0.00 0.00 5.14
1165 1322 1.514443 GAGAAAGACGACGAGCCGG 60.514 63.158 0.00 0.00 0.00 6.13
1178 1335 1.265454 GCGGGGAGGAGAAGGAGAAA 61.265 60.000 0.00 0.00 0.00 2.52
1199 1356 4.099170 AGTTCGTCCGGCGTCTCG 62.099 66.667 16.00 7.70 42.13 4.04
1201 1358 4.052229 CCAGTTCGTCCGGCGTCT 62.052 66.667 16.00 12.90 42.13 4.18
1322 1479 0.038159 AGTCGTGAAAGAAGAGGCGG 60.038 55.000 0.00 0.00 0.00 6.13
1356 1513 0.239347 CACGGAGTTCGGTTCGTACT 59.761 55.000 0.00 0.00 41.61 2.73
1377 1534 6.517027 GCAGAAGAGATATCTTGATCTGCAGA 60.517 42.308 34.68 20.79 45.27 4.26
1379 1536 5.511031 GGCAGAAGAGATATCTTGATCTGCA 60.511 44.000 36.85 0.00 46.34 4.41
1432 1589 1.502163 AACAGAGCACAGCGTCTTGC 61.502 55.000 0.00 0.00 46.98 4.01
1595 1755 2.753029 GGGCACTGCTTCTCCAGT 59.247 61.111 0.00 0.00 46.47 4.00
1880 2040 5.295292 CGAGAGCTTGGATCACATAAAATGT 59.705 40.000 0.00 0.00 46.22 2.71
1892 2052 0.394488 TCGAGTCCGAGAGCTTGGAT 60.394 55.000 9.61 0.10 44.51 3.41
1894 2054 1.137825 GTCGAGTCCGAGAGCTTGG 59.862 63.158 0.00 0.00 46.52 3.61
1895 2055 1.137825 GGTCGAGTCCGAGAGCTTG 59.862 63.158 0.00 0.00 46.52 4.01
1896 2056 2.047443 GGGTCGAGTCCGAGAGCTT 61.047 63.158 0.00 0.00 46.52 3.74
1897 2057 2.438795 GGGTCGAGTCCGAGAGCT 60.439 66.667 0.00 0.00 46.52 4.09
2315 2482 1.739562 CGGACTTGGAGCAGCTGAC 60.740 63.158 20.43 10.42 0.00 3.51
2368 2535 1.067212 CAGACCGAGTTAGAATCCCCG 59.933 57.143 0.00 0.00 0.00 5.73
2369 2536 2.362717 CTCAGACCGAGTTAGAATCCCC 59.637 54.545 0.00 0.00 36.94 4.81
2388 2555 6.851222 ACAATTCGTATGTGATCCAATCTC 57.149 37.500 0.00 0.00 0.00 2.75
2455 2824 3.244422 CGTGAGAGACCTAGCTAGGAGAT 60.244 52.174 40.40 26.24 46.63 2.75
2521 2890 8.535690 TTAATACACATATGTCACGTTCAACA 57.464 30.769 5.07 0.00 40.48 3.33
2522 2891 9.632969 GATTAATACACATATGTCACGTTCAAC 57.367 33.333 5.07 0.00 40.48 3.18
2523 2892 9.594478 AGATTAATACACATATGTCACGTTCAA 57.406 29.630 5.07 0.00 40.48 2.69
2524 2893 9.594478 AAGATTAATACACATATGTCACGTTCA 57.406 29.630 5.07 0.00 40.48 3.18
2527 2896 9.817809 AGAAAGATTAATACACATATGTCACGT 57.182 29.630 5.07 3.93 40.48 4.49
2556 2925 5.187621 AGAAGTCAACTAGGCTAGAGACT 57.812 43.478 30.40 30.40 42.15 3.24
2557 2926 6.350906 TCTAGAAGTCAACTAGGCTAGAGAC 58.649 44.000 27.59 27.96 38.19 3.36
2562 2931 7.772292 TCGTATTTCTAGAAGTCAACTAGGCTA 59.228 37.037 3.43 0.00 38.19 3.93
2577 2951 9.915629 AGCCAACTAATTCTATCGTATTTCTAG 57.084 33.333 0.00 0.00 0.00 2.43
2582 2956 7.985184 TGACAAGCCAACTAATTCTATCGTATT 59.015 33.333 0.00 0.00 0.00 1.89
2586 2960 5.276395 CGTGACAAGCCAACTAATTCTATCG 60.276 44.000 0.00 0.00 0.00 2.92
2588 2962 4.332819 GCGTGACAAGCCAACTAATTCTAT 59.667 41.667 1.44 0.00 0.00 1.98
2592 2966 2.226330 TGCGTGACAAGCCAACTAATT 58.774 42.857 10.95 0.00 0.00 1.40
2637 3011 6.773638 ACTCAATTGTATTCCTGAGAGTTGT 58.226 36.000 5.13 0.00 38.91 3.32
2644 3018 6.182627 AGATGCAACTCAATTGTATTCCTGA 58.817 36.000 5.13 0.00 42.98 3.86
2645 3019 6.094464 TGAGATGCAACTCAATTGTATTCCTG 59.906 38.462 22.87 0.00 42.98 3.86
2683 3057 6.274579 TCGCGATGAAAACTTATACCATGTA 58.725 36.000 3.71 0.00 0.00 2.29
2684 3058 5.113383 TCGCGATGAAAACTTATACCATGT 58.887 37.500 3.71 0.00 0.00 3.21
2685 3059 5.651172 TCGCGATGAAAACTTATACCATG 57.349 39.130 3.71 0.00 0.00 3.66
2686 3060 6.861065 AATCGCGATGAAAACTTATACCAT 57.139 33.333 24.47 0.00 0.00 3.55
2689 3063 6.711579 TGGAAATCGCGATGAAAACTTATAC 58.288 36.000 24.47 6.60 0.00 1.47
2690 3064 6.912203 TGGAAATCGCGATGAAAACTTATA 57.088 33.333 24.47 1.75 0.00 0.98
2691 3065 5.811399 TGGAAATCGCGATGAAAACTTAT 57.189 34.783 24.47 0.00 0.00 1.73
2692 3066 5.352846 TGATGGAAATCGCGATGAAAACTTA 59.647 36.000 24.47 3.51 0.00 2.24
2693 3067 4.155826 TGATGGAAATCGCGATGAAAACTT 59.844 37.500 24.47 12.01 0.00 2.66
2694 3068 3.689161 TGATGGAAATCGCGATGAAAACT 59.311 39.130 24.47 1.93 0.00 2.66
2703 3077 0.301687 CGGAAGTGATGGAAATCGCG 59.698 55.000 0.00 0.00 36.27 5.87
2705 3079 1.594862 GAGCGGAAGTGATGGAAATCG 59.405 52.381 0.00 0.00 0.00 3.34
2709 3083 0.036388 GTGGAGCGGAAGTGATGGAA 60.036 55.000 0.00 0.00 0.00 3.53
2713 3087 2.125512 GCGTGGAGCGGAAGTGAT 60.126 61.111 0.00 0.00 41.69 3.06
2757 3131 2.121506 TTTGGGAGGAGGGGCAGT 60.122 61.111 0.00 0.00 0.00 4.40
2758 3132 2.356667 GTTTGGGAGGAGGGGCAG 59.643 66.667 0.00 0.00 0.00 4.85
2765 3139 1.681076 GCGTTAGGGTTTGGGAGGA 59.319 57.895 0.00 0.00 0.00 3.71
2766 3140 1.378119 GGCGTTAGGGTTTGGGAGG 60.378 63.158 0.00 0.00 0.00 4.30
2788 3162 2.086094 GGCTATAGAGGGAGTAGCGAC 58.914 57.143 3.21 0.00 41.26 5.19
2789 3163 1.338864 CGGCTATAGAGGGAGTAGCGA 60.339 57.143 3.21 0.00 41.26 4.93
2812 3186 2.997315 GGTTTGGGGGAAGGCAGC 60.997 66.667 0.00 0.00 0.00 5.25
2819 3193 2.204029 AGCGTAGGGTTTGGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
2821 3195 2.750237 GCAGCGTAGGGTTTGGGG 60.750 66.667 0.00 0.00 0.00 4.96
2865 3239 1.466062 TAGGGTTTGGGGGAGGAGGA 61.466 60.000 0.00 0.00 0.00 3.71
2867 3241 1.623542 CGTAGGGTTTGGGGGAGGAG 61.624 65.000 0.00 0.00 0.00 3.69
2868 3242 1.614226 CGTAGGGTTTGGGGGAGGA 60.614 63.158 0.00 0.00 0.00 3.71
2894 3268 3.747266 CTACGGGAGGGAGTAGCG 58.253 66.667 0.00 0.00 34.68 4.26
3309 3683 4.817909 AAGGGTAGGGGAGGGGCG 62.818 72.222 0.00 0.00 0.00 6.13
3310 3684 3.097162 CAAGGGTAGGGGAGGGGC 61.097 72.222 0.00 0.00 0.00 5.80
3326 3700 0.044092 TAGGGAGAGGATGGCAACCA 59.956 55.000 16.72 0.00 38.19 3.67
3327 3701 0.761802 CTAGGGAGAGGATGGCAACC 59.238 60.000 5.52 5.52 0.00 3.77
3329 3703 1.056700 GGCTAGGGAGAGGATGGCAA 61.057 60.000 0.00 0.00 0.00 4.52
3330 3704 1.460305 GGCTAGGGAGAGGATGGCA 60.460 63.158 0.00 0.00 0.00 4.92
3331 3705 0.839853 ATGGCTAGGGAGAGGATGGC 60.840 60.000 0.00 0.00 0.00 4.40
3337 3711 2.685106 TAGGTGATGGCTAGGGAGAG 57.315 55.000 0.00 0.00 0.00 3.20
3346 3720 3.442625 GTGTTTAGGGTTTAGGTGATGGC 59.557 47.826 0.00 0.00 0.00 4.40
3350 3724 2.550639 GCGGTGTTTAGGGTTTAGGTGA 60.551 50.000 0.00 0.00 0.00 4.02
3355 3729 0.954938 GCGGCGGTGTTTAGGGTTTA 60.955 55.000 9.78 0.00 0.00 2.01
3375 3749 4.675303 TGGGAGGGAGGTGGGGTG 62.675 72.222 0.00 0.00 0.00 4.61
3390 3764 2.361610 GGGACATGGTGGCAGTGG 60.362 66.667 0.00 0.00 0.00 4.00
3394 3768 4.408821 GAGCGGGACATGGTGGCA 62.409 66.667 0.00 0.00 0.00 4.92
3408 3782 1.522580 GACAGATCGGCCTTGGAGC 60.523 63.158 0.00 0.00 0.00 4.70
3414 3788 3.518998 CGTCGGACAGATCGGCCT 61.519 66.667 9.10 0.00 0.00 5.19
3417 3791 4.907034 CGGCGTCGGACAGATCGG 62.907 72.222 0.00 0.00 0.00 4.18
3443 3817 0.251341 GAGGTGAACATTGGGCCAGT 60.251 55.000 6.23 0.00 0.00 4.00
3449 3823 1.667724 GCGATCAGAGGTGAACATTGG 59.332 52.381 0.00 0.00 35.88 3.16
3451 3825 1.556911 AGGCGATCAGAGGTGAACATT 59.443 47.619 0.00 0.00 35.88 2.71
3466 3840 2.989253 TGGAGCTCGTTGAGGCGA 60.989 61.111 7.83 0.00 39.22 5.54
3481 3855 1.131126 GGCACGTGATCTTTGATGTGG 59.869 52.381 22.23 0.00 30.98 4.17
3482 3856 1.131126 GGGCACGTGATCTTTGATGTG 59.869 52.381 22.23 0.00 33.06 3.21
3511 3885 2.024871 GATGGCGAGTCGAGGTCG 59.975 66.667 18.61 11.83 40.50 4.79
3542 3916 0.388649 AAGAGCGTGAAGTAGGTGCG 60.389 55.000 0.00 0.00 0.00 5.34
3566 3940 1.158484 TCGATGAGACGGTAGGAGCG 61.158 60.000 0.00 0.00 45.69 5.03
3601 3975 1.006825 TCATGTCGCGGAAGTCAACG 61.007 55.000 6.13 0.00 0.00 4.10
3604 3978 1.215382 CCTCATGTCGCGGAAGTCA 59.785 57.895 6.13 0.00 0.00 3.41
3614 3988 0.242825 TTGTCGTCGTCCCTCATGTC 59.757 55.000 0.00 0.00 0.00 3.06
3621 3995 2.710724 AAGCCACTTGTCGTCGTCCC 62.711 60.000 0.00 0.00 0.00 4.46
3631 4005 1.831389 CGTCCACGACAAGCCACTTG 61.831 60.000 5.80 5.80 45.85 3.16
3632 4006 1.594293 CGTCCACGACAAGCCACTT 60.594 57.895 0.00 0.00 43.02 3.16


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

AutoCloner maintained by Alex Coulton.