Multiple sequence alignment - TraesCS6D01G273900

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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 TraesCS6D01G273900 chr6D 100.000 3306 0 0 1 3306 382561623 382564928 0.000000e+00 6106.0
1 TraesCS6D01G273900 chr6D 87.910 670 75 6 2471 3137 382577304 382577970 0.000000e+00 784.0
2 TraesCS6D01G273900 chr6D 87.342 237 22 3 2124 2359 382576965 382577194 7.030000e-67 265.0
3 TraesCS6D01G273900 chr6D 100.000 37 0 0 3251 3287 382578309 382578345 5.920000e-08 69.4
4 TraesCS6D01G273900 chr6A 91.749 2036 85 45 1 2001 524362333 524364320 0.000000e+00 2752.0
5 TraesCS6D01G273900 chr6A 86.923 650 76 5 2359 3000 524364950 524365598 0.000000e+00 721.0
6 TraesCS6D01G273900 chr6A 88.767 365 32 6 1999 2359 524364625 524364984 3.920000e-119 438.0
7 TraesCS6D01G273900 chr6B 88.007 2393 140 84 38 2359 572111310 572113626 0.000000e+00 2693.0
8 TraesCS6D01G273900 chr6B 88.189 127 12 2 3165 3288 572182043 572182169 7.390000e-32 148.0
9 TraesCS6D01G273900 chr6B 91.045 67 5 1 2177 2243 164563066 164563001 4.540000e-14 89.8
10 TraesCS6D01G273900 chr4A 77.976 672 125 15 2471 3137 47738319 47738972 1.850000e-107 399.0
11 TraesCS6D01G273900 chr4B 79.215 433 79 8 2471 2900 512787250 512786826 1.160000e-74 291.0
12 TraesCS6D01G273900 chr7D 78.723 188 39 1 2944 3130 442401025 442400838 1.250000e-24 124.0
13 TraesCS6D01G273900 chr7D 92.405 79 6 0 1841 1919 167557174 167557096 2.700000e-21 113.0
14 TraesCS6D01G273900 chr7B 92.405 79 6 0 1841 1919 132109906 132109828 2.700000e-21 113.0
15 TraesCS6D01G273900 chr7B 87.671 73 4 2 2167 2237 554155896 554155965 2.730000e-11 80.5
16 TraesCS6D01G273900 chr4D 89.855 69 6 1 2176 2244 53577267 53577200 1.630000e-13 87.9
17 TraesCS6D01G273900 chr5B 89.706 68 6 1 2176 2243 425562300 425562366 5.880000e-13 86.1
18 TraesCS6D01G273900 chr5A 90.909 66 3 2 2173 2236 559744417 559744353 5.880000e-13 86.1
19 TraesCS6D01G273900 chr3B 89.706 68 5 2 2173 2239 187445567 187445501 5.880000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G273900 chr6D 382561623 382564928 3305 False 6106.000000 6106 100.000000 1 3306 1 chr6D.!!$F1 3305
1 TraesCS6D01G273900 chr6D 382576965 382578345 1380 False 372.800000 784 91.750667 2124 3287 3 chr6D.!!$F2 1163
2 TraesCS6D01G273900 chr6A 524362333 524365598 3265 False 1303.666667 2752 89.146333 1 3000 3 chr6A.!!$F1 2999
3 TraesCS6D01G273900 chr6B 572111310 572113626 2316 False 2693.000000 2693 88.007000 38 2359 1 chr6B.!!$F1 2321
4 TraesCS6D01G273900 chr4A 47738319 47738972 653 False 399.000000 399 77.976000 2471 3137 1 chr4A.!!$F1 666

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
32 33 0.097674 GCGTGCAGAACTAGCATTGG 59.902 55.0 0.0 0.0 44.79 3.16 F
436 461 0.318360 TGTCGCACACAAGGACGTAG 60.318 55.0 0.0 0.0 33.45 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 1217 0.460987 GCTATGCTGACACGCTCCTT 60.461 55.0 0.0 0.0 0.0 3.36 R
2378 2786 0.392998 GCCCCGGCGATGATGATTAT 60.393 55.0 9.3 0.0 0.0 1.28 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
32 33 0.097674 GCGTGCAGAACTAGCATTGG 59.902 55.000 0.00 0.00 44.79 3.16
106 110 1.093159 GAGGCTGCAGATGTTCAAGG 58.907 55.000 20.43 0.00 0.00 3.61
136 140 3.284323 ACAGCACTGTGAGTTACTACG 57.716 47.619 12.86 0.00 43.11 3.51
161 180 1.939974 GCAGATGGCGAGTGATTACA 58.060 50.000 0.00 0.00 0.00 2.41
162 181 2.487934 GCAGATGGCGAGTGATTACAT 58.512 47.619 0.00 0.00 0.00 2.29
163 182 2.874701 GCAGATGGCGAGTGATTACATT 59.125 45.455 0.00 0.00 0.00 2.71
292 317 4.371417 ACGTGGAGTAGGGCGGGA 62.371 66.667 0.00 0.00 0.00 5.14
384 409 1.139734 CTAGATCTGCACACCGCGT 59.860 57.895 5.18 0.00 46.97 6.01
385 410 0.867753 CTAGATCTGCACACCGCGTC 60.868 60.000 5.18 0.00 46.97 5.19
386 411 1.591504 TAGATCTGCACACCGCGTCA 61.592 55.000 5.18 0.00 46.97 4.35
387 412 2.730672 GATCTGCACACCGCGTCAC 61.731 63.158 4.92 0.00 46.97 3.67
436 461 0.318360 TGTCGCACACAAGGACGTAG 60.318 55.000 0.00 0.00 33.45 3.51
582 633 2.591753 CACGGCCATGGATCCACT 59.408 61.111 18.99 3.52 0.00 4.00
615 680 3.627218 GCCGCGAATGCTACCGTC 61.627 66.667 8.23 0.00 39.65 4.79
849 927 2.515523 CATGGGCCAGCTTCGGAG 60.516 66.667 13.78 0.00 0.00 4.63
925 1003 0.611200 TCCTACGGGACAATGTGGTG 59.389 55.000 0.00 0.00 36.57 4.17
926 1004 0.392461 CCTACGGGACAATGTGGTGG 60.392 60.000 0.00 0.00 33.58 4.61
927 1005 0.323629 CTACGGGACAATGTGGTGGT 59.676 55.000 0.00 0.00 0.00 4.16
938 1016 0.981183 TGTGGTGGTCTGGTATGGAC 59.019 55.000 0.00 0.00 0.00 4.02
1089 1167 5.010749 CGCAAAAGCATCAAATCAAATTCG 58.989 37.500 0.00 0.00 0.00 3.34
1135 1217 1.982395 CCAGGGACGCACAGGACTA 60.982 63.158 0.00 0.00 0.00 2.59
1192 1275 1.303561 GCAGGTGAGAACATGGCCA 60.304 57.895 8.56 8.56 0.00 5.36
1223 1306 4.077184 TACGGCGCTTCTGGGTGG 62.077 66.667 6.90 0.00 0.00 4.61
1303 1386 1.405661 GGCGTAACTTCTCCCCTCTTG 60.406 57.143 0.00 0.00 0.00 3.02
1337 1420 1.862815 GCACGGTACCTATACTGCGTG 60.863 57.143 10.90 11.07 43.79 5.34
1346 1429 3.383505 ACCTATACTGCGTGCTACATTCA 59.616 43.478 0.00 0.00 0.00 2.57
1347 1430 4.039245 ACCTATACTGCGTGCTACATTCAT 59.961 41.667 0.00 0.00 0.00 2.57
1348 1431 4.991056 CCTATACTGCGTGCTACATTCATT 59.009 41.667 0.00 0.00 0.00 2.57
1392 1475 3.861689 ACGTAGACGCCTTAACAATTAGC 59.138 43.478 1.14 0.00 44.43 3.09
1400 1483 4.436852 CGCCTTAACAATTAGCACGATGTT 60.437 41.667 0.00 0.00 39.23 2.71
1412 1495 7.908827 TTAGCACGATGTTTTTAACCAGATA 57.091 32.000 0.00 0.00 0.00 1.98
1531 1614 1.134699 TCAGAACAGGAGGCGCTAATG 60.135 52.381 7.64 4.03 0.00 1.90
1720 1803 1.462238 AACTCCCTGCCTCTGGTGT 60.462 57.895 0.00 0.00 0.00 4.16
1732 1815 2.165641 CCTCTGGTGTGTACGCTCATAA 59.834 50.000 8.10 0.00 0.00 1.90
1733 1816 3.439293 CTCTGGTGTGTACGCTCATAAG 58.561 50.000 8.10 3.82 0.00 1.73
1925 2018 2.383527 CCTCTTCAAGGTGCGCGAC 61.384 63.158 12.10 5.05 40.67 5.19
1987 2080 6.307155 AGAACTAATTCGATTGCAAGAAACG 58.693 36.000 4.94 8.38 40.04 3.60
2021 2421 7.696453 CGTTAACATGATCTTGGACAAAATACC 59.304 37.037 12.76 0.00 0.00 2.73
2038 2438 2.703798 CCATTGCAGGAACGCAGGG 61.704 63.158 0.00 0.00 44.14 4.45
2174 2580 2.749621 CGCTTATCAGAGGGTTTGCTTT 59.250 45.455 0.00 0.00 0.00 3.51
2219 2625 9.558396 AAAGACTTGCCATTTTCATTGATTAAA 57.442 25.926 0.00 0.00 0.00 1.52
2224 2630 9.211485 CTTGCCATTTTCATTGATTAAAGAAGT 57.789 29.630 0.00 0.00 0.00 3.01
2225 2631 8.761575 TGCCATTTTCATTGATTAAAGAAGTC 57.238 30.769 0.00 0.00 0.00 3.01
2254 2660 4.220163 AGACAAAACCCGTCTAGTAGGAAG 59.780 45.833 7.63 0.00 41.91 3.46
2334 2742 2.247358 CAGAGCCTATCCTCCTCCTTC 58.753 57.143 0.00 0.00 32.17 3.46
2351 2759 6.723515 TCCTCCTTCATCTTCGAGATAATCAT 59.276 38.462 0.00 0.00 32.12 2.45
2357 2765 6.032717 TCATCTTCGAGATAATCATCATCGC 58.967 40.000 0.00 0.00 32.12 4.58
2358 2766 4.738124 TCTTCGAGATAATCATCATCGCC 58.262 43.478 0.00 0.00 34.55 5.54
2359 2767 3.510388 TCGAGATAATCATCATCGCCC 57.490 47.619 0.00 0.00 34.55 6.13
2360 2768 3.092301 TCGAGATAATCATCATCGCCCT 58.908 45.455 0.00 0.00 34.55 5.19
2361 2769 3.129462 TCGAGATAATCATCATCGCCCTC 59.871 47.826 0.00 0.00 34.55 4.30
2362 2770 3.736433 CGAGATAATCATCATCGCCCTCC 60.736 52.174 0.00 0.00 33.21 4.30
2363 2771 3.448934 AGATAATCATCATCGCCCTCCT 58.551 45.455 0.00 0.00 33.21 3.69
2364 2772 3.450457 AGATAATCATCATCGCCCTCCTC 59.550 47.826 0.00 0.00 33.21 3.71
2365 2773 0.689623 AATCATCATCGCCCTCCTCC 59.310 55.000 0.00 0.00 0.00 4.30
2366 2774 0.178909 ATCATCATCGCCCTCCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
2367 2775 0.399091 TCATCATCGCCCTCCTCCTT 60.399 55.000 0.00 0.00 0.00 3.36
2368 2776 0.034616 CATCATCGCCCTCCTCCTTC 59.965 60.000 0.00 0.00 0.00 3.46
2369 2777 0.399091 ATCATCGCCCTCCTCCTTCA 60.399 55.000 0.00 0.00 0.00 3.02
2370 2778 0.399091 TCATCGCCCTCCTCCTTCAT 60.399 55.000 0.00 0.00 0.00 2.57
2371 2779 0.034616 CATCGCCCTCCTCCTTCATC 59.965 60.000 0.00 0.00 0.00 2.92
2372 2780 0.105246 ATCGCCCTCCTCCTTCATCT 60.105 55.000 0.00 0.00 0.00 2.90
2373 2781 0.757188 TCGCCCTCCTCCTTCATCTC 60.757 60.000 0.00 0.00 0.00 2.75
2374 2782 1.753368 CGCCCTCCTCCTTCATCTCC 61.753 65.000 0.00 0.00 0.00 3.71
2375 2783 0.692419 GCCCTCCTCCTTCATCTCCA 60.692 60.000 0.00 0.00 0.00 3.86
2376 2784 1.885049 CCCTCCTCCTTCATCTCCAA 58.115 55.000 0.00 0.00 0.00 3.53
2377 2785 1.767681 CCCTCCTCCTTCATCTCCAAG 59.232 57.143 0.00 0.00 0.00 3.61
2378 2786 2.628021 CCCTCCTCCTTCATCTCCAAGA 60.628 54.545 0.00 0.00 0.00 3.02
2379 2787 3.316501 CCTCCTCCTTCATCTCCAAGAT 58.683 50.000 0.00 0.00 34.74 2.40
2380 2788 4.487804 CCTCCTCCTTCATCTCCAAGATA 58.512 47.826 0.00 0.00 32.12 1.98
2381 2789 4.904251 CCTCCTCCTTCATCTCCAAGATAA 59.096 45.833 0.00 0.00 32.12 1.75
2382 2790 5.547276 CCTCCTCCTTCATCTCCAAGATAAT 59.453 44.000 0.00 0.00 32.12 1.28
2383 2791 6.295802 CCTCCTCCTTCATCTCCAAGATAATC 60.296 46.154 0.00 0.00 32.12 1.75
2384 2792 6.146047 TCCTCCTTCATCTCCAAGATAATCA 58.854 40.000 0.00 0.00 32.12 2.57
2385 2793 6.791466 TCCTCCTTCATCTCCAAGATAATCAT 59.209 38.462 0.00 0.00 32.12 2.45
2386 2794 7.038445 TCCTCCTTCATCTCCAAGATAATCATC 60.038 40.741 0.00 0.00 32.12 2.92
2387 2795 7.256583 CCTCCTTCATCTCCAAGATAATCATCA 60.257 40.741 0.00 0.00 32.12 3.07
2388 2796 8.215954 TCCTTCATCTCCAAGATAATCATCAT 57.784 34.615 0.00 0.00 32.12 2.45
2389 2797 8.319881 TCCTTCATCTCCAAGATAATCATCATC 58.680 37.037 0.00 0.00 32.12 2.92
2390 2798 7.278203 CCTTCATCTCCAAGATAATCATCATCG 59.722 40.741 0.00 0.00 32.12 3.84
2418 2826 3.243336 CACTGAGGTTGCGTAAGACTAC 58.757 50.000 0.00 0.00 43.02 2.73
2569 3009 3.263425 AGTGACCTCCGACCAAATATGTT 59.737 43.478 0.00 0.00 0.00 2.71
2580 3020 6.018588 CCGACCAAATATGTTGCGTTTATCTA 60.019 38.462 0.00 0.00 0.00 1.98
2615 3055 1.294780 GCACCACAGACTCCTGGAG 59.705 63.158 22.00 22.00 44.60 3.86
2631 3071 3.648067 CCTGGAGATTGCTTACATAGGGA 59.352 47.826 0.00 0.00 0.00 4.20
2655 3095 2.174424 ACAACCCATGGTTTGGCAATTT 59.826 40.909 24.16 1.04 44.33 1.82
2656 3096 3.392616 ACAACCCATGGTTTGGCAATTTA 59.607 39.130 24.16 0.00 44.33 1.40
2668 3109 2.095969 TGGCAATTTACGACGAAGCAAG 60.096 45.455 0.00 0.00 0.00 4.01
2694 3140 0.671251 CGGTCCAGACTCTATCCTGC 59.329 60.000 0.00 0.00 0.00 4.85
2776 3222 1.745489 GAACCATGGTCGTGGAGGC 60.745 63.158 20.07 0.00 42.02 4.70
2843 3289 3.272581 CCCATTGGCAATGAATTTCCAC 58.727 45.455 35.39 0.00 41.46 4.02
2848 3294 4.167554 TGGCAATGAATTTCCACGTAAC 57.832 40.909 0.00 0.00 0.00 2.50
2851 3297 3.120130 GCAATGAATTTCCACGTAACGGA 60.120 43.478 0.00 0.00 0.00 4.69
2868 3314 1.290134 GGAGTCCAGGATTCCTTGGT 58.710 55.000 21.55 0.00 35.86 3.67
2889 3338 4.943705 GGTTGAGGTGAATATGAGCAAGAA 59.056 41.667 0.00 0.00 0.00 2.52
2900 3349 7.396907 TGAATATGAGCAAGAATTTCCCAAAGA 59.603 33.333 0.00 0.00 0.00 2.52
2902 3351 3.828451 TGAGCAAGAATTTCCCAAAGAGG 59.172 43.478 0.00 0.00 37.03 3.69
2911 3360 5.535753 ATTTCCCAAAGAGGAACAAACTG 57.464 39.130 0.00 0.00 45.65 3.16
2927 3376 2.996249 ACTGGTGGATGTGCTCTATG 57.004 50.000 0.00 0.00 0.00 2.23
2930 3379 2.171237 CTGGTGGATGTGCTCTATGGAA 59.829 50.000 0.00 0.00 0.00 3.53
2955 3404 2.602878 CATGCTGAGTGTCAATTTGGC 58.397 47.619 0.00 0.00 0.00 4.52
2974 3423 0.102481 CGGACCCACGAGTTATCCAG 59.898 60.000 0.00 0.00 35.47 3.86
3002 3451 3.367292 CCATGCTAACCGTGCAATTCTTT 60.367 43.478 0.00 0.00 44.01 2.52
3022 3471 1.561643 TTGCTGGAGAGGTCGAAGAT 58.438 50.000 0.00 0.00 40.67 2.40
3023 3472 1.107114 TGCTGGAGAGGTCGAAGATC 58.893 55.000 0.00 0.00 40.67 2.75
3037 3486 1.480954 GAAGATCTTGGGGTAGACGCA 59.519 52.381 14.00 0.00 40.66 5.24
3039 3488 2.119495 AGATCTTGGGGTAGACGCATT 58.881 47.619 0.00 0.00 42.07 3.56
3041 3490 2.871096 TCTTGGGGTAGACGCATTTT 57.129 45.000 0.00 0.00 42.07 1.82
3045 3494 0.679960 GGGGTAGACGCATTTTGGCT 60.680 55.000 0.00 0.00 0.00 4.75
3049 3498 3.427098 GGGTAGACGCATTTTGGCTTAAC 60.427 47.826 0.00 0.00 0.00 2.01
3103 3554 1.200020 CTTGTTTTCATCTCCCACGGC 59.800 52.381 0.00 0.00 0.00 5.68
3115 3567 2.906897 CACGGCAACTTGGTGGCT 60.907 61.111 10.39 0.00 41.74 4.75
3124 3576 1.286880 CTTGGTGGCTTCCGCAAAG 59.713 57.895 0.00 0.00 38.49 2.77
3130 3582 1.298157 TGGCTTCCGCAAAGATGTCG 61.298 55.000 0.17 0.00 37.12 4.35
3150 3666 2.852413 CGCGATCAGTGGTGTTACTTAG 59.148 50.000 0.00 0.00 0.00 2.18
3154 3670 5.466819 CGATCAGTGGTGTTACTTAGAACA 58.533 41.667 0.00 0.00 36.98 3.18
3158 3674 3.326880 AGTGGTGTTACTTAGAACAGGGG 59.673 47.826 0.00 0.00 39.93 4.79
3180 3696 5.776208 GGGGGTTTACTTTGAATTTAGTGGA 59.224 40.000 0.00 0.00 0.00 4.02
3193 3709 4.931661 TTTAGTGGAGATTAGCCCGTAG 57.068 45.455 0.00 0.00 0.00 3.51
3212 3728 2.691927 AGGAAATTGGACCGTACGTTC 58.308 47.619 15.21 9.71 0.00 3.95
3214 3730 3.004862 GGAAATTGGACCGTACGTTCAT 58.995 45.455 15.00 0.00 26.83 2.57
3216 3732 4.269363 GGAAATTGGACCGTACGTTCATAG 59.731 45.833 15.00 0.16 26.83 2.23
3217 3733 4.724074 AATTGGACCGTACGTTCATAGA 57.276 40.909 15.00 0.00 26.83 1.98
3218 3734 4.724074 ATTGGACCGTACGTTCATAGAA 57.276 40.909 15.00 2.24 26.83 2.10
3228 3746 6.345803 CCGTACGTTCATAGAATGCTATTGTG 60.346 42.308 15.21 0.00 35.13 3.33
3247 3765 5.305139 TGTGAATTTGAGATGATGCACTG 57.695 39.130 0.00 0.00 33.72 3.66
3249 3767 3.129813 TGAATTTGAGATGATGCACTGCC 59.870 43.478 0.00 0.00 0.00 4.85
3287 3964 2.329379 GTTTGGTCTGCTCGTAGACTG 58.671 52.381 13.49 0.10 45.03 3.51
3288 3965 0.888619 TTGGTCTGCTCGTAGACTGG 59.111 55.000 13.49 0.00 45.03 4.00
3289 3966 0.037734 TGGTCTGCTCGTAGACTGGA 59.962 55.000 13.49 0.00 45.03 3.86
3290 3967 0.452585 GGTCTGCTCGTAGACTGGAC 59.547 60.000 13.49 0.00 45.03 4.02
3291 3968 1.455248 GTCTGCTCGTAGACTGGACT 58.545 55.000 7.74 0.00 42.93 3.85
3292 3969 1.131504 GTCTGCTCGTAGACTGGACTG 59.868 57.143 7.74 0.00 42.93 3.51
3293 3970 0.179150 CTGCTCGTAGACTGGACTGC 60.179 60.000 0.00 0.00 0.00 4.40
3294 3971 0.893727 TGCTCGTAGACTGGACTGCA 60.894 55.000 0.00 0.00 0.00 4.41
3295 3972 0.456995 GCTCGTAGACTGGACTGCAC 60.457 60.000 0.00 0.00 0.00 4.57
3296 3973 0.881796 CTCGTAGACTGGACTGCACA 59.118 55.000 0.00 0.00 0.00 4.57
3297 3974 1.474478 CTCGTAGACTGGACTGCACAT 59.526 52.381 0.00 0.00 0.00 3.21
3298 3975 1.893137 TCGTAGACTGGACTGCACATT 59.107 47.619 0.00 0.00 0.00 2.71
3299 3976 2.094700 TCGTAGACTGGACTGCACATTC 60.095 50.000 0.00 0.00 0.00 2.67
3300 3977 2.352715 CGTAGACTGGACTGCACATTCA 60.353 50.000 0.00 0.00 0.00 2.57
3301 3978 2.469274 AGACTGGACTGCACATTCAG 57.531 50.000 0.61 0.61 39.86 3.02
3302 3979 1.002888 AGACTGGACTGCACATTCAGG 59.997 52.381 6.49 0.00 38.36 3.86
3303 3980 0.607489 ACTGGACTGCACATTCAGGC 60.607 55.000 6.49 0.00 41.37 4.85
3304 3981 0.322277 CTGGACTGCACATTCAGGCT 60.322 55.000 0.00 0.00 41.79 4.58
3305 3982 0.607217 TGGACTGCACATTCAGGCTG 60.607 55.000 8.58 8.58 41.79 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.506438 GCCTGGTACGTCGTCAGC 60.506 66.667 0.00 0.00 0.00 4.26
106 110 1.242076 ACAGTGCTGTGCCATCTTTC 58.758 50.000 3.80 0.00 43.11 2.62
133 137 1.871676 CTCGCCATCTGCTAGTACGTA 59.128 52.381 0.00 0.00 38.05 3.57
134 138 0.663688 CTCGCCATCTGCTAGTACGT 59.336 55.000 0.00 0.00 38.05 3.57
135 139 0.663688 ACTCGCCATCTGCTAGTACG 59.336 55.000 0.00 0.00 43.58 3.67
136 140 1.676529 TCACTCGCCATCTGCTAGTAC 59.323 52.381 0.00 0.00 43.57 2.73
157 176 0.246910 TCGCACCGCCAGTAATGTAA 59.753 50.000 0.00 0.00 0.00 2.41
158 177 0.179121 CTCGCACCGCCAGTAATGTA 60.179 55.000 0.00 0.00 0.00 2.29
159 178 1.447838 CTCGCACCGCCAGTAATGT 60.448 57.895 0.00 0.00 0.00 2.71
160 179 1.447838 ACTCGCACCGCCAGTAATG 60.448 57.895 0.00 0.00 0.00 1.90
161 180 1.447838 CACTCGCACCGCCAGTAAT 60.448 57.895 0.00 0.00 0.00 1.89
162 181 1.525718 TACACTCGCACCGCCAGTAA 61.526 55.000 0.00 0.00 0.00 2.24
163 182 1.929806 CTACACTCGCACCGCCAGTA 61.930 60.000 0.00 0.00 0.00 2.74
387 412 1.001048 TGGTCTGGTTAACGACGTGAG 60.001 52.381 0.00 0.00 0.00 3.51
436 461 4.759096 ACGCACCGCCGTACGTAC 62.759 66.667 15.90 15.90 40.19 3.67
582 633 2.838225 GCCGGGGAGCTAGCAGTA 60.838 66.667 18.83 0.00 0.00 2.74
601 652 2.202703 ACCGACGGTAGCATTCGC 60.203 61.111 20.23 0.00 32.11 4.70
614 679 2.190841 TGCACACACTCGAGACCGA 61.191 57.895 21.68 0.00 43.35 4.69
615 680 2.016704 GTGCACACACTCGAGACCG 61.017 63.158 21.68 9.53 43.85 4.79
701 771 3.439540 CATCACAAACGGCCCCGG 61.440 66.667 11.83 0.00 44.69 5.73
702 772 2.359354 TCATCACAAACGGCCCCG 60.359 61.111 4.96 4.96 46.03 5.73
703 773 2.686816 CGTCATCACAAACGGCCCC 61.687 63.158 0.00 0.00 35.32 5.80
704 774 2.867472 CGTCATCACAAACGGCCC 59.133 61.111 0.00 0.00 35.32 5.80
925 1003 1.955080 CTCCGTAGTCCATACCAGACC 59.045 57.143 0.00 0.00 34.67 3.85
926 1004 1.337387 GCTCCGTAGTCCATACCAGAC 59.663 57.143 0.00 0.00 34.31 3.51
927 1005 1.214673 AGCTCCGTAGTCCATACCAGA 59.785 52.381 0.00 0.00 0.00 3.86
1089 1167 4.410400 CTCCTTGTGTCCCGGGCC 62.410 72.222 18.49 4.39 0.00 5.80
1135 1217 0.460987 GCTATGCTGACACGCTCCTT 60.461 55.000 0.00 0.00 0.00 3.36
1192 1275 2.430244 CGTAGAGCACGCCGTTGT 60.430 61.111 0.00 0.00 45.03 3.32
1265 1348 2.979649 GTGGGAGGAGAACGGACC 59.020 66.667 0.00 0.00 0.00 4.46
1266 1349 2.572284 CGTGGGAGGAGAACGGAC 59.428 66.667 0.00 0.00 33.77 4.79
1275 1358 1.447314 GAAGTTACGCCGTGGGAGG 60.447 63.158 0.00 0.00 0.00 4.30
1337 1420 2.859806 GCCATTGCGGAATGAATGTAGC 60.860 50.000 28.69 18.49 41.49 3.58
1392 1475 6.311723 GGTGTATCTGGTTAAAAACATCGTG 58.688 40.000 0.00 0.00 0.00 4.35
1400 1483 2.348660 CCGCGGTGTATCTGGTTAAAA 58.651 47.619 19.50 0.00 0.00 1.52
1412 1495 3.753434 CAGAGAGAGCCGCGGTGT 61.753 66.667 28.70 15.17 0.00 4.16
1510 1593 0.973632 TTAGCGCCTCCTGTTCTGAA 59.026 50.000 2.29 0.00 0.00 3.02
1531 1614 0.944386 TACGTACTCCCCGAATACGC 59.056 55.000 2.89 0.00 44.26 4.42
1538 1621 1.723870 CCGTTCTACGTACTCCCCG 59.276 63.158 0.00 0.00 40.58 5.73
1586 1669 0.565679 CGACAAAGCAAACAACACGC 59.434 50.000 0.00 0.00 0.00 5.34
1811 1904 6.814644 AGAAATTATTCAACGTGTCATCGGTA 59.185 34.615 0.00 0.00 38.06 4.02
1925 2018 0.527817 CTAAGCGAGCCCGTAACTGG 60.528 60.000 0.00 0.00 38.24 4.00
1945 2038 5.202004 AGTTCTACCACCAGATACTACCAG 58.798 45.833 0.00 0.00 0.00 4.00
1987 2080 7.903431 GTCCAAGATCATGTTAACGAATTACAC 59.097 37.037 0.26 0.00 0.00 2.90
2021 2421 1.243342 TTCCCTGCGTTCCTGCAATG 61.243 55.000 0.00 0.00 45.74 2.82
2038 2438 2.507324 GTCGTCGGCCAGCTCTTC 60.507 66.667 2.24 0.00 0.00 2.87
2141 2547 5.123186 CCTCTGATAAGCGTTCTCGAGATAT 59.877 44.000 17.44 10.52 39.71 1.63
2145 2551 2.287308 CCCTCTGATAAGCGTTCTCGAG 60.287 54.545 5.93 5.93 39.71 4.04
2146 2552 1.676529 CCCTCTGATAAGCGTTCTCGA 59.323 52.381 0.00 0.00 39.71 4.04
2147 2553 1.405821 ACCCTCTGATAAGCGTTCTCG 59.594 52.381 0.00 0.00 40.37 4.04
2219 2625 4.132336 GGGTTTTGTCTAAACGGACTTCT 58.868 43.478 4.21 0.00 45.75 2.85
2224 2630 2.102925 AGACGGGTTTTGTCTAAACGGA 59.897 45.455 4.21 0.00 45.75 4.69
2225 2631 2.486918 AGACGGGTTTTGTCTAAACGG 58.513 47.619 4.21 2.17 45.75 4.44
2274 2680 7.148407 GCTGCACACTTGAGTATTGTAAATACT 60.148 37.037 11.47 11.47 37.53 2.12
2276 2682 6.093495 GGCTGCACACTTGAGTATTGTAAATA 59.907 38.462 0.50 0.00 0.00 1.40
2308 2716 1.627864 GAGGATAGGCTCTGTCCCTC 58.372 60.000 12.33 7.17 41.76 4.30
2334 2742 5.231779 GGCGATGATGATTATCTCGAAGATG 59.768 44.000 17.32 0.00 35.37 2.90
2351 2759 0.399091 ATGAAGGAGGAGGGCGATGA 60.399 55.000 0.00 0.00 0.00 2.92
2357 2765 1.767681 CTTGGAGATGAAGGAGGAGGG 59.232 57.143 0.00 0.00 0.00 4.30
2358 2766 2.756907 TCTTGGAGATGAAGGAGGAGG 58.243 52.381 0.00 0.00 0.00 4.30
2359 2767 6.269538 TGATTATCTTGGAGATGAAGGAGGAG 59.730 42.308 0.82 0.00 35.37 3.69
2360 2768 6.146047 TGATTATCTTGGAGATGAAGGAGGA 58.854 40.000 0.82 0.00 35.37 3.71
2361 2769 6.430962 TGATTATCTTGGAGATGAAGGAGG 57.569 41.667 0.82 0.00 35.37 4.30
2362 2770 7.677892 TGATGATTATCTTGGAGATGAAGGAG 58.322 38.462 0.00 0.00 35.37 3.69
2363 2771 7.622502 TGATGATTATCTTGGAGATGAAGGA 57.377 36.000 0.00 0.00 35.37 3.36
2364 2772 7.278203 CGATGATGATTATCTTGGAGATGAAGG 59.722 40.741 0.00 0.00 35.37 3.46
2365 2773 7.201539 GCGATGATGATTATCTTGGAGATGAAG 60.202 40.741 0.00 0.00 35.37 3.02
2366 2774 6.592994 GCGATGATGATTATCTTGGAGATGAA 59.407 38.462 0.00 0.00 35.37 2.57
2367 2775 6.104665 GCGATGATGATTATCTTGGAGATGA 58.895 40.000 0.00 0.00 35.37 2.92
2368 2776 5.293814 GGCGATGATGATTATCTTGGAGATG 59.706 44.000 0.00 0.00 35.37 2.90
2369 2777 5.426504 GGCGATGATGATTATCTTGGAGAT 58.573 41.667 0.00 0.00 38.70 2.75
2370 2778 4.619160 CGGCGATGATGATTATCTTGGAGA 60.619 45.833 0.00 0.00 34.31 3.71
2371 2779 3.615937 CGGCGATGATGATTATCTTGGAG 59.384 47.826 0.00 0.00 34.31 3.86
2372 2780 3.588955 CGGCGATGATGATTATCTTGGA 58.411 45.455 0.00 0.00 34.31 3.53
2373 2781 2.674852 CCGGCGATGATGATTATCTTGG 59.325 50.000 9.30 0.00 34.31 3.61
2374 2782 2.674852 CCCGGCGATGATGATTATCTTG 59.325 50.000 9.30 0.00 34.31 3.02
2375 2783 2.355108 CCCCGGCGATGATGATTATCTT 60.355 50.000 9.30 0.00 34.31 2.40
2376 2784 1.208052 CCCCGGCGATGATGATTATCT 59.792 52.381 9.30 0.00 34.31 1.98
2377 2785 1.656652 CCCCGGCGATGATGATTATC 58.343 55.000 9.30 0.00 0.00 1.75
2378 2786 0.392998 GCCCCGGCGATGATGATTAT 60.393 55.000 9.30 0.00 0.00 1.28
2379 2787 1.003839 GCCCCGGCGATGATGATTA 60.004 57.895 9.30 0.00 0.00 1.75
2380 2788 2.281761 GCCCCGGCGATGATGATT 60.282 61.111 9.30 0.00 0.00 2.57
2381 2789 3.559263 TGCCCCGGCGATGATGAT 61.559 61.111 9.30 0.00 45.51 2.45
2382 2790 4.545706 GTGCCCCGGCGATGATGA 62.546 66.667 9.30 0.00 45.51 2.92
2383 2791 4.552365 AGTGCCCCGGCGATGATG 62.552 66.667 9.30 0.00 45.51 3.07
2384 2792 4.552365 CAGTGCCCCGGCGATGAT 62.552 66.667 9.30 0.00 45.51 2.45
2418 2826 4.278419 AGAAGTTTGGAAAGAACGGAATGG 59.722 41.667 0.00 0.00 32.38 3.16
2569 3009 7.438160 CCTCATTTGTCACTATAGATAAACGCA 59.562 37.037 6.78 0.00 32.61 5.24
2580 3020 3.244875 TGGTGCACCTCATTTGTCACTAT 60.245 43.478 34.75 0.00 36.82 2.12
2615 3055 3.808728 TGTGCTCCCTATGTAAGCAATC 58.191 45.455 0.00 0.00 46.73 2.67
2631 3071 2.439837 CCAAACCATGGGTTGTGCT 58.560 52.632 34.82 3.09 46.20 4.40
2655 3095 2.264813 GCCAATACTTGCTTCGTCGTA 58.735 47.619 0.00 0.00 0.00 3.43
2656 3096 1.076332 GCCAATACTTGCTTCGTCGT 58.924 50.000 0.00 0.00 0.00 4.34
2668 3109 0.824759 AGAGTCTGGACCGCCAATAC 59.175 55.000 0.00 0.00 45.41 1.89
2676 3118 1.781786 TGCAGGATAGAGTCTGGACC 58.218 55.000 1.86 3.56 0.00 4.46
2694 3140 6.698766 GCAATTTCTTTACCTGGCTTATCATG 59.301 38.462 0.00 0.00 0.00 3.07
2776 3222 0.319469 GGTGCAATTTGTTGGGTCGG 60.319 55.000 0.00 0.00 0.00 4.79
2778 3224 2.158971 ACAAGGTGCAATTTGTTGGGTC 60.159 45.455 10.41 0.00 34.00 4.46
2779 3225 1.836802 ACAAGGTGCAATTTGTTGGGT 59.163 42.857 10.41 0.00 34.00 4.51
2843 3289 1.202382 GGAATCCTGGACTCCGTTACG 60.202 57.143 8.65 0.00 0.00 3.18
2848 3294 0.179000 CCAAGGAATCCTGGACTCCG 59.821 60.000 17.81 5.42 32.72 4.63
2851 3297 2.307098 CTCAACCAAGGAATCCTGGACT 59.693 50.000 19.81 0.00 32.13 3.85
2868 3314 7.148018 GGAAATTCTTGCTCATATTCACCTCAA 60.148 37.037 0.00 0.00 0.00 3.02
2889 3338 4.344968 CCAGTTTGTTCCTCTTTGGGAAAT 59.655 41.667 0.00 0.00 45.55 2.17
2900 3349 2.586425 CACATCCACCAGTTTGTTCCT 58.414 47.619 0.00 0.00 0.00 3.36
2902 3351 1.956477 AGCACATCCACCAGTTTGTTC 59.044 47.619 0.00 0.00 0.00 3.18
2911 3360 3.281727 TTTCCATAGAGCACATCCACC 57.718 47.619 0.00 0.00 0.00 4.61
2927 3376 1.200948 GACACTCAGCATGGCTTTTCC 59.799 52.381 0.00 0.00 36.40 3.13
2930 3379 1.985473 TTGACACTCAGCATGGCTTT 58.015 45.000 0.00 0.00 36.40 3.51
2937 3386 0.592637 CGCCAAATTGACACTCAGCA 59.407 50.000 0.00 0.00 0.00 4.41
2939 3388 1.197721 GTCCGCCAAATTGACACTCAG 59.802 52.381 0.00 0.00 0.00 3.35
2955 3404 0.102481 CTGGATAACTCGTGGGTCCG 59.898 60.000 0.00 0.00 0.00 4.79
3002 3451 1.338107 TCTTCGACCTCTCCAGCAAA 58.662 50.000 0.00 0.00 0.00 3.68
3007 3456 2.103373 CCAAGATCTTCGACCTCTCCA 58.897 52.381 4.57 0.00 0.00 3.86
3022 3471 2.432444 CAAAATGCGTCTACCCCAAGA 58.568 47.619 0.00 0.00 0.00 3.02
3023 3472 1.472480 CCAAAATGCGTCTACCCCAAG 59.528 52.381 0.00 0.00 0.00 3.61
3030 3479 2.159626 GCGTTAAGCCAAAATGCGTCTA 60.160 45.455 0.00 0.00 40.81 2.59
3045 3494 0.035820 CCTTGGCTACAGGGCGTTAA 60.036 55.000 0.00 0.00 44.11 2.01
3049 3498 1.899437 TTCTCCTTGGCTACAGGGCG 61.899 60.000 0.00 0.00 43.20 6.13
3053 3502 1.839994 TGGGATTCTCCTTGGCTACAG 59.160 52.381 0.00 0.00 36.57 2.74
3080 3529 2.238521 GTGGGAGATGAAAACAAGGCA 58.761 47.619 0.00 0.00 0.00 4.75
3124 3576 0.458543 ACACCACTGATCGCGACATC 60.459 55.000 12.93 6.91 0.00 3.06
3130 3582 4.106029 TCTAAGTAACACCACTGATCGC 57.894 45.455 0.00 0.00 0.00 4.58
3158 3674 7.754851 TCTCCACTAAATTCAAAGTAAACCC 57.245 36.000 0.00 0.00 0.00 4.11
3171 3687 4.283722 CCTACGGGCTAATCTCCACTAAAT 59.716 45.833 0.00 0.00 0.00 1.40
3180 3696 3.714798 TCCAATTTCCTACGGGCTAATCT 59.285 43.478 0.00 0.00 0.00 2.40
3193 3709 2.415776 TGAACGTACGGTCCAATTTCC 58.584 47.619 29.19 4.07 0.00 3.13
3200 3716 2.793232 GCATTCTATGAACGTACGGTCC 59.207 50.000 29.19 12.74 0.00 4.46
3201 3717 3.703420 AGCATTCTATGAACGTACGGTC 58.297 45.455 26.15 26.15 0.00 4.79
3202 3718 3.795623 AGCATTCTATGAACGTACGGT 57.204 42.857 21.06 14.45 0.00 4.83
3203 3719 5.690409 ACAATAGCATTCTATGAACGTACGG 59.310 40.000 21.06 0.00 35.75 4.02
3214 3730 9.617523 TCATCTCAAATTCACAATAGCATTCTA 57.382 29.630 0.00 0.00 0.00 2.10
3216 3732 9.181805 CATCATCTCAAATTCACAATAGCATTC 57.818 33.333 0.00 0.00 0.00 2.67
3217 3733 7.652105 GCATCATCTCAAATTCACAATAGCATT 59.348 33.333 0.00 0.00 0.00 3.56
3218 3734 7.145985 GCATCATCTCAAATTCACAATAGCAT 58.854 34.615 0.00 0.00 0.00 3.79
3228 3746 3.129813 TGGCAGTGCATCATCTCAAATTC 59.870 43.478 18.61 0.00 0.00 2.17
3249 3767 0.393944 ACCAGCATGCCTCACATCTG 60.394 55.000 15.66 2.94 36.64 2.90
3287 3964 2.177950 CAGCCTGAATGTGCAGTCC 58.822 57.895 0.00 0.00 34.06 3.85


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

AutoCloner maintained by Alex Coulton.