Multiple sequence alignment - TraesCS6D01G335000

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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 TraesCS6D01G335000 chr6D 100.000 4913 0 0 1 4913 436732860 436737772 0.000000e+00 9073.0
1 TraesCS6D01G335000 chr6A 90.624 4757 268 69 1 4715 584942675 584947295 0.000000e+00 6150.0
2 TraesCS6D01G335000 chr6A 88.462 156 18 0 4758 4913 584947302 584947457 6.490000e-44 189.0
3 TraesCS6D01G335000 chr6B 93.014 3049 132 30 1309 4311 660218458 660221471 0.000000e+00 4375.0
4 TraesCS6D01G335000 chr6B 89.976 1227 54 21 69 1264 660217276 660218464 0.000000e+00 1520.0
5 TraesCS6D01G335000 chr6B 89.241 474 30 10 4309 4763 660224333 660224804 1.530000e-159 573.0
6 TraesCS6D01G335000 chr6B 82.769 325 18 13 1 318 660216002 660216295 6.310000e-64 255.0
7 TraesCS6D01G335000 chr6B 90.968 155 13 1 4751 4904 660224830 660224984 1.790000e-49 207.0
8 TraesCS6D01G335000 chr7B 77.213 610 80 30 2961 3528 472335230 472335822 7.990000e-78 302.0
9 TraesCS6D01G335000 chr7B 77.213 610 80 30 2961 3528 472400713 472401305 7.990000e-78 302.0
10 TraesCS6D01G335000 chr3D 81.308 321 50 8 2523 2840 576611480 576611793 8.160000e-63 252.0
11 TraesCS6D01G335000 chr3D 87.692 65 4 2 2983 3043 576611922 576611986 6.820000e-09 73.1
12 TraesCS6D01G335000 chr5D 80.294 340 51 12 2524 2860 3787694 3788020 4.910000e-60 243.0
13 TraesCS6D01G335000 chr1A 79.772 351 58 10 2523 2870 42509347 42509687 4.910000e-60 243.0
14 TraesCS6D01G335000 chr7A 86.585 82 6 4 2957 3037 13464184 13464107 8.760000e-13 86.1
15 TraesCS6D01G335000 chr3B 86.585 82 6 4 2957 3037 356861341 356861264 8.760000e-13 86.1
16 TraesCS6D01G335000 chr4A 90.769 65 3 2 2957 3020 511081475 511081413 3.150000e-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 TraesCS6D01G335000 chr6D 436732860 436737772 4912 False 9073.0 9073 100.0000 1 4913 1 chr6D.!!$F1 4912
1 TraesCS6D01G335000 chr6A 584942675 584947457 4782 False 3169.5 6150 89.5430 1 4913 2 chr6A.!!$F1 4912
2 TraesCS6D01G335000 chr6B 660216002 660224984 8982 False 1386.0 4375 89.1936 1 4904 5 chr6B.!!$F1 4903
3 TraesCS6D01G335000 chr7B 472335230 472335822 592 False 302.0 302 77.2130 2961 3528 1 chr7B.!!$F1 567
4 TraesCS6D01G335000 chr7B 472400713 472401305 592 False 302.0 302 77.2130 2961 3528 1 chr7B.!!$F2 567

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
79 80 0.178944 TCTCCCTCGGTCTTTGGTCA 60.179 55.0 0.00 0.0 0.00 4.02 F
892 2131 0.811281 GTTCTTGCCATCTTTCCCCG 59.189 55.0 0.00 0.0 0.00 5.73 F
1696 2952 0.376152 CTGCTATCCACTTTGCTGCG 59.624 55.0 0.00 0.0 0.00 5.18 F
1787 3043 0.526211 CCAGACGAACCACAGATCGA 59.474 55.0 1.84 0.0 41.43 3.59 F
2018 3274 0.776810 TGGGGGCATCTGTTTCTGAA 59.223 50.0 0.00 0.0 0.00 3.02 F
2316 3586 1.438651 TACACCGTTGAATGCAGCTC 58.561 50.0 0.00 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1307 2557 0.530650 ATCTAGACATGGCGCCAACG 60.531 55.000 36.33 28.91 44.07 4.10 R
2720 3992 0.474184 ATATTGTCCCCGGCCTTCTG 59.526 55.000 0.00 0.00 0.00 3.02 R
3042 4322 1.079503 CTCCCTACAAAGCAACGAGC 58.920 55.000 0.00 0.00 46.19 5.03 R
3045 4325 1.531149 CACACTCCCTACAAAGCAACG 59.469 52.381 0.00 0.00 0.00 4.10 R
3046 4326 1.880027 CCACACTCCCTACAAAGCAAC 59.120 52.381 0.00 0.00 0.00 4.17 R
4206 5545 0.590230 TTCAAACAAAAGCGTCGCCG 60.590 50.000 14.86 2.67 37.07 6.46 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
30 31 9.908747 AAATACGATGAGATATACCTAGCTAGT 57.091 33.333 19.31 10.02 0.00 2.57
79 80 0.178944 TCTCCCTCGGTCTTTGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
107 108 7.867403 CCTAGCGTTATCGGTACCTTTTATTTA 59.133 37.037 10.90 0.00 46.01 1.40
253 1476 4.600111 ACACAAGTAAACAATAGGGAGGGA 59.400 41.667 0.00 0.00 0.00 4.20
279 1502 2.361757 CCAAATGTGAGCTTTGTCACCA 59.638 45.455 1.77 0.00 45.42 4.17
319 1542 5.049828 CAGGTTGGAAAAGGTAAAGCAAAG 58.950 41.667 0.00 0.00 0.00 2.77
320 1543 3.807622 GGTTGGAAAAGGTAAAGCAAAGC 59.192 43.478 0.00 0.00 0.00 3.51
321 1544 4.438148 GTTGGAAAAGGTAAAGCAAAGCA 58.562 39.130 0.00 0.00 0.00 3.91
322 1545 4.953940 TGGAAAAGGTAAAGCAAAGCAT 57.046 36.364 0.00 0.00 0.00 3.79
323 1546 5.289083 TGGAAAAGGTAAAGCAAAGCATT 57.711 34.783 0.00 0.00 0.00 3.56
324 1547 6.412362 TGGAAAAGGTAAAGCAAAGCATTA 57.588 33.333 0.00 0.00 0.00 1.90
325 1548 6.821388 TGGAAAAGGTAAAGCAAAGCATTAA 58.179 32.000 0.00 0.00 0.00 1.40
326 1549 6.704050 TGGAAAAGGTAAAGCAAAGCATTAAC 59.296 34.615 0.00 0.00 30.78 2.01
327 1550 6.704050 GGAAAAGGTAAAGCAAAGCATTAACA 59.296 34.615 5.06 0.00 32.73 2.41
328 1551 7.307160 GGAAAAGGTAAAGCAAAGCATTAACAC 60.307 37.037 5.06 0.00 32.73 3.32
329 1552 5.134202 AGGTAAAGCAAAGCATTAACACC 57.866 39.130 5.06 0.00 32.73 4.16
330 1553 4.832823 AGGTAAAGCAAAGCATTAACACCT 59.167 37.500 5.06 0.65 32.73 4.00
331 1554 5.048013 AGGTAAAGCAAAGCATTAACACCTC 60.048 40.000 5.06 0.00 32.73 3.85
332 1555 3.942130 AAGCAAAGCATTAACACCTCC 57.058 42.857 0.00 0.00 0.00 4.30
333 1556 2.171003 AGCAAAGCATTAACACCTCCC 58.829 47.619 0.00 0.00 0.00 4.30
334 1557 1.204704 GCAAAGCATTAACACCTCCCC 59.795 52.381 0.00 0.00 0.00 4.81
335 1558 1.824852 CAAAGCATTAACACCTCCCCC 59.175 52.381 0.00 0.00 0.00 5.40
336 1559 1.382914 AAGCATTAACACCTCCCCCT 58.617 50.000 0.00 0.00 0.00 4.79
337 1560 2.280308 AGCATTAACACCTCCCCCTA 57.720 50.000 0.00 0.00 0.00 3.53
378 1601 2.064434 TCAGATCAGAGTCGCCATCT 57.936 50.000 0.00 0.00 0.00 2.90
380 1603 0.950836 AGATCAGAGTCGCCATCTCG 59.049 55.000 0.00 0.00 37.07 4.04
386 1609 2.278857 GTCGCCATCTCGCATCGT 60.279 61.111 0.00 0.00 0.00 3.73
782 2021 0.887933 TGCTTTTCTTGCCGGGATTC 59.112 50.000 2.18 0.00 0.00 2.52
844 2083 3.471244 CTCGATCGGGACCAGCGAC 62.471 68.421 10.16 0.00 0.00 5.19
892 2131 0.811281 GTTCTTGCCATCTTTCCCCG 59.189 55.000 0.00 0.00 0.00 5.73
899 2148 3.387947 ATCTTTCCCCGACGGCGT 61.388 61.111 14.65 14.65 35.23 5.68
910 2159 1.149964 CGACGGCGTCCCCTAATTTC 61.150 60.000 31.86 6.22 0.00 2.17
928 2177 1.227380 CTGAGGAATTCGGGGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
1224 2473 2.260844 TTTGTCTTCCAGACTGGCTG 57.739 50.000 17.33 2.72 45.27 4.85
1238 2487 4.217118 AGACTGGCTGAAATGTTGACATTC 59.783 41.667 9.59 5.04 45.06 2.67
1250 2499 7.915293 AATGTTGACATTCATGCATTCAAAT 57.085 28.000 11.36 3.23 42.45 2.32
1264 2513 6.757237 TGCATTCAAATAAACCTGTTGACAT 58.243 32.000 0.00 0.00 31.21 3.06
1265 2514 6.867816 TGCATTCAAATAAACCTGTTGACATC 59.132 34.615 0.00 0.00 31.21 3.06
1267 2516 7.062605 GCATTCAAATAAACCTGTTGACATCTG 59.937 37.037 0.00 0.00 31.21 2.90
1268 2517 6.012658 TCAAATAAACCTGTTGACATCTGC 57.987 37.500 0.00 0.00 0.00 4.26
1269 2518 4.685169 AATAAACCTGTTGACATCTGCG 57.315 40.909 0.00 0.00 0.00 5.18
1270 2519 1.967319 AAACCTGTTGACATCTGCGT 58.033 45.000 0.00 0.00 0.00 5.24
1276 2526 3.058016 CCTGTTGACATCTGCGTTGATTT 60.058 43.478 0.00 0.00 0.00 2.17
1289 2539 2.403259 GTTGATTTGGCAAAGGAACCG 58.597 47.619 18.61 0.00 0.00 4.44
1301 2551 2.851263 AGGAACCGCACTCACATTTA 57.149 45.000 0.00 0.00 0.00 1.40
1307 2557 3.262420 ACCGCACTCACATTTATCTGTC 58.738 45.455 0.00 0.00 0.00 3.51
1309 2559 2.923655 CGCACTCACATTTATCTGTCGT 59.076 45.455 0.00 0.00 0.00 4.34
1312 2562 4.436050 GCACTCACATTTATCTGTCGTTGG 60.436 45.833 0.00 0.00 0.00 3.77
1313 2563 3.684788 ACTCACATTTATCTGTCGTTGGC 59.315 43.478 0.00 0.00 0.00 4.52
1314 2564 2.670905 TCACATTTATCTGTCGTTGGCG 59.329 45.455 0.00 0.00 39.92 5.69
1438 2692 6.480524 TGTAATTTTCAGTTCGACATCAGG 57.519 37.500 0.00 0.00 0.00 3.86
1460 2714 2.198827 TGAAGTCGGTCGGTAACCTA 57.801 50.000 0.00 0.00 46.87 3.08
1462 2716 2.424601 TGAAGTCGGTCGGTAACCTATG 59.575 50.000 0.00 0.00 46.87 2.23
1476 2730 5.011738 GGTAACCTATGCTGAAGCCTGTATA 59.988 44.000 0.00 0.00 41.18 1.47
1511 2765 0.614294 AGACTGCTCTGATGCAAGCT 59.386 50.000 9.40 0.00 42.83 3.74
1547 2801 2.632996 CTGGGAGGTTGTTCAGACACTA 59.367 50.000 0.00 0.00 34.98 2.74
1591 2845 4.061570 GCATTTTGCTTGCTGTTCATTC 57.938 40.909 0.00 0.00 40.96 2.67
1592 2846 3.744426 GCATTTTGCTTGCTGTTCATTCT 59.256 39.130 0.00 0.00 40.96 2.40
1594 2848 4.652421 TTTTGCTTGCTGTTCATTCTGA 57.348 36.364 0.00 0.00 0.00 3.27
1595 2849 4.859304 TTTGCTTGCTGTTCATTCTGAT 57.141 36.364 0.00 0.00 0.00 2.90
1596 2850 4.430137 TTGCTTGCTGTTCATTCTGATC 57.570 40.909 0.00 0.00 0.00 2.92
1597 2851 2.751259 TGCTTGCTGTTCATTCTGATCC 59.249 45.455 0.00 0.00 0.00 3.36
1614 2870 5.649395 TCTGATCCTTTTTACTGCTTGGATG 59.351 40.000 0.00 0.00 34.82 3.51
1687 2943 2.044806 ATGGCGGGACTGCTATCCAC 62.045 60.000 8.79 1.04 40.96 4.02
1696 2952 0.376152 CTGCTATCCACTTTGCTGCG 59.624 55.000 0.00 0.00 0.00 5.18
1726 2982 4.699522 GCCCGGTGCCTTCGTCTT 62.700 66.667 0.00 0.00 0.00 3.01
1787 3043 0.526211 CCAGACGAACCACAGATCGA 59.474 55.000 1.84 0.00 41.43 3.59
1831 3087 7.201758 GCTGATTTTGATGATGAGTATGTTGGA 60.202 37.037 0.00 0.00 0.00 3.53
1845 3101 3.663995 TGTTGGATCCATTGCTTGTTG 57.336 42.857 17.06 0.00 0.00 3.33
1849 3105 2.097825 GGATCCATTGCTTGTTGCTCT 58.902 47.619 6.95 0.00 43.37 4.09
1854 3110 4.870363 TCCATTGCTTGTTGCTCTTTTAC 58.130 39.130 0.00 0.00 43.37 2.01
1855 3111 3.670055 CCATTGCTTGTTGCTCTTTTACG 59.330 43.478 0.00 0.00 43.37 3.18
2003 3259 2.225017 ACAGTTGTTATTGGACCTGGGG 60.225 50.000 0.00 0.00 0.00 4.96
2018 3274 0.776810 TGGGGGCATCTGTTTCTGAA 59.223 50.000 0.00 0.00 0.00 3.02
2098 3368 5.656480 TCCTGTTGCTTTTTAGGTGTTTTC 58.344 37.500 0.00 0.00 0.00 2.29
2102 3372 5.186021 TGTTGCTTTTTAGGTGTTTTCCAGA 59.814 36.000 0.00 0.00 0.00 3.86
2116 3386 8.674607 GGTGTTTTCCAGATTTATACTTCGATT 58.325 33.333 0.00 0.00 0.00 3.34
2233 3503 8.560355 AATGCTGTATGTTGTCAAGTATGTTA 57.440 30.769 0.00 0.00 0.00 2.41
2256 3526 5.726980 TGCTAATCTGAAGGCAATTTTGT 57.273 34.783 0.00 0.00 0.00 2.83
2302 3572 4.513442 TCAACATCAGCTAACCATACACC 58.487 43.478 0.00 0.00 0.00 4.16
2316 3586 1.438651 TACACCGTTGAATGCAGCTC 58.561 50.000 0.00 0.00 0.00 4.09
2376 3646 7.333528 TGCTAGTGGGTATGATTTTGAATTC 57.666 36.000 0.00 0.00 0.00 2.17
2380 3650 5.658190 AGTGGGTATGATTTTGAATTCCTGG 59.342 40.000 2.27 0.00 0.00 4.45
2410 3681 6.686630 ACAAAGAACTGTCATTGTTTTGTCA 58.313 32.000 0.00 0.00 41.66 3.58
2416 3687 8.199449 AGAACTGTCATTGTTTTGTCATCATTT 58.801 29.630 0.00 0.00 0.00 2.32
2418 3689 9.814899 AACTGTCATTGTTTTGTCATCATTTTA 57.185 25.926 0.00 0.00 0.00 1.52
2537 3808 3.197116 AGGGGGTCAAATACGTACTCTTG 59.803 47.826 0.00 2.48 0.00 3.02
2645 3917 1.962144 CTTTCCAGTTGGCCTGCTG 59.038 57.895 16.79 16.79 40.06 4.41
2720 3992 2.007608 GGCTGTCCGTATCTTTGGTTC 58.992 52.381 0.00 0.00 0.00 3.62
2754 4026 7.602517 GGGACAATATCTCCATTATCGAAAG 57.397 40.000 0.00 0.00 0.00 2.62
2841 4113 7.650504 TGTAATAGAGAACCGAACATTATTCCG 59.349 37.037 0.00 0.00 0.00 4.30
2842 4114 3.195661 AGAGAACCGAACATTATTCCGC 58.804 45.455 0.00 0.00 0.00 5.54
2861 4133 3.436704 CCGCATAAGTTGTCATCTGTTGT 59.563 43.478 0.00 0.00 0.00 3.32
2903 4175 6.942532 TGACTTGCATAATTATTGGTCTCC 57.057 37.500 0.00 0.00 0.00 3.71
3025 4298 8.581578 CCAGTGTTTATTTTGGTTAGTGGTAAT 58.418 33.333 0.00 0.00 0.00 1.89
3037 4317 7.867921 TGGTTAGTGGTAATATCTGATGGTTT 58.132 34.615 0.00 0.00 0.00 3.27
3042 4322 5.299279 GTGGTAATATCTGATGGTTTGGTGG 59.701 44.000 0.00 0.00 0.00 4.61
3045 4325 2.134789 ATCTGATGGTTTGGTGGCTC 57.865 50.000 0.00 0.00 0.00 4.70
3046 4326 0.321564 TCTGATGGTTTGGTGGCTCG 60.322 55.000 0.00 0.00 0.00 5.03
3212 4497 8.237267 GCTATTGTACTTTAAGCAAACTGTCAT 58.763 33.333 0.00 0.00 33.38 3.06
3224 4522 6.373779 AGCAAACTGTCATTTTACTCGATTG 58.626 36.000 0.00 0.00 0.00 2.67
3230 4528 7.968246 ACTGTCATTTTACTCGATTGATCTTG 58.032 34.615 0.00 0.00 0.00 3.02
3242 4540 4.320421 CGATTGATCTTGCACAAAAGGACA 60.320 41.667 0.00 0.00 0.00 4.02
3243 4541 5.620654 CGATTGATCTTGCACAAAAGGACAT 60.621 40.000 0.00 0.00 0.00 3.06
3244 4542 4.508461 TGATCTTGCACAAAAGGACATG 57.492 40.909 0.00 0.00 0.00 3.21
3245 4543 4.143543 TGATCTTGCACAAAAGGACATGA 58.856 39.130 0.00 0.00 0.00 3.07
3246 4544 4.583907 TGATCTTGCACAAAAGGACATGAA 59.416 37.500 0.00 0.00 0.00 2.57
3247 4545 4.998671 TCTTGCACAAAAGGACATGAAA 57.001 36.364 0.00 0.00 0.00 2.69
3248 4546 4.681744 TCTTGCACAAAAGGACATGAAAC 58.318 39.130 0.00 0.00 0.00 2.78
3249 4547 4.402155 TCTTGCACAAAAGGACATGAAACT 59.598 37.500 0.00 0.00 0.00 2.66
3274 4580 6.096673 TCAAAGTACTTGTAGCATGAGTGA 57.903 37.500 9.34 2.08 36.34 3.41
3285 4591 6.276091 TGTAGCATGAGTGACATATGAAGTC 58.724 40.000 10.38 9.91 37.46 3.01
3366 4674 1.270465 GGGAGCACAAAAAGCAAGCAT 60.270 47.619 0.00 0.00 0.00 3.79
3370 4679 2.610374 AGCACAAAAAGCAAGCATGTTG 59.390 40.909 0.00 0.00 0.00 3.33
3762 5086 1.413767 CGATGAAGCTGAACCCGTCG 61.414 60.000 0.00 0.00 0.00 5.12
3916 5243 2.113433 GCCACCAGCAGCTGATGAG 61.113 63.158 32.59 23.22 42.97 2.90
3995 5326 0.242017 CTGTTAGTTTGGCTGGCTGC 59.758 55.000 7.96 7.96 41.94 5.25
4046 5377 2.585247 GCGGTCGAAATCCCTCCG 60.585 66.667 4.17 4.17 43.37 4.63
4081 5414 8.093659 TCTATCTATCATATCATGAGTAGCGC 57.906 38.462 0.00 0.00 43.53 5.92
4095 5428 3.384668 AGTAGCGCTGTAGCAACATATG 58.615 45.455 22.90 0.00 42.21 1.78
4125 5458 5.963092 GGAACTATTCCTACCTACCTACCT 58.037 45.833 0.10 0.00 46.57 3.08
4126 5459 7.096402 GGAACTATTCCTACCTACCTACCTA 57.904 44.000 0.10 0.00 46.57 3.08
4127 5460 6.945435 GGAACTATTCCTACCTACCTACCTAC 59.055 46.154 0.10 0.00 46.57 3.18
4128 5461 6.461577 ACTATTCCTACCTACCTACCTACC 57.538 45.833 0.00 0.00 0.00 3.18
4129 5462 6.164086 ACTATTCCTACCTACCTACCTACCT 58.836 44.000 0.00 0.00 0.00 3.08
4130 5463 7.324672 ACTATTCCTACCTACCTACCTACCTA 58.675 42.308 0.00 0.00 0.00 3.08
4131 5464 5.913946 TTCCTACCTACCTACCTACCTAC 57.086 47.826 0.00 0.00 0.00 3.18
4132 5465 4.243643 TCCTACCTACCTACCTACCTACC 58.756 52.174 0.00 0.00 0.00 3.18
4175 5514 0.891449 TTTTTGGGCGAGCGATTGGA 60.891 50.000 0.00 0.00 0.00 3.53
4209 5548 2.413765 TTTTTGAACGGTGGCGGC 59.586 55.556 0.00 0.00 0.00 6.53
4210 5549 3.471244 TTTTTGAACGGTGGCGGCG 62.471 57.895 0.51 0.51 0.00 6.46
4299 5642 3.307906 TCGCCGTTGGTACAGCCT 61.308 61.111 0.00 0.00 42.39 4.58
4336 8543 4.404654 CGCTTTTGGTGGCTCCGC 62.405 66.667 0.53 0.00 39.52 5.54
4389 8603 2.646143 TGCGCTGCACGTAGTACA 59.354 55.556 9.73 0.00 41.61 2.90
4390 8604 1.007154 TGCGCTGCACGTAGTACAA 60.007 52.632 9.73 0.00 41.61 2.41
4490 8721 5.090139 TCCAGAACCAGAAGAGATCTTTCT 58.910 41.667 11.90 11.90 36.22 2.52
4492 8723 6.043706 TCCAGAACCAGAAGAGATCTTTCTTT 59.956 38.462 13.97 9.35 34.45 2.52
4497 8729 6.413892 ACCAGAAGAGATCTTTCTTTCCATC 58.586 40.000 13.97 0.00 37.53 3.51
4517 8749 8.913487 TCCATCGTGATTAGAATAGTACACTA 57.087 34.615 0.00 0.00 0.00 2.74
4600 8832 1.077501 AGGTGGTTCGCATGATGGG 60.078 57.895 2.72 2.72 0.00 4.00
4602 8834 1.097547 GGTGGTTCGCATGATGGGAG 61.098 60.000 12.04 0.00 40.47 4.30
4620 8852 2.633509 GCCTGGCTGCAGGAACTTG 61.634 63.158 17.12 0.00 45.00 3.16
4623 8855 0.250640 CTGGCTGCAGGAACTTGTCT 60.251 55.000 17.12 0.00 34.60 3.41
4686 8918 3.702555 GCGTGCACGTCCAGACAC 61.703 66.667 36.80 16.46 42.22 3.67
4697 8929 2.357034 CAGACACAACGGTCGGGG 60.357 66.667 0.00 0.00 42.62 5.73
4794 9064 2.224549 GCAACACTACACGGCATTGTTA 59.775 45.455 0.00 0.00 0.00 2.41
4802 9072 0.450184 ACGGCATTGTTATTGTCCGC 59.550 50.000 0.00 0.00 37.31 5.54
4874 9145 1.142748 CATCCTCTGGTCAGCCGAC 59.857 63.158 0.00 0.00 41.80 4.79
4909 9180 0.963962 AAACCTAGCTCGAACACGGA 59.036 50.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.740123 TTGCTACTAGCTAGGTATATCTCATC 57.260 38.462 24.35 1.70 42.97 2.92
27 28 7.086376 GTCGGACCGATTATTATTTGCTACTA 58.914 38.462 21.53 0.00 38.42 1.82
28 29 5.924825 GTCGGACCGATTATTATTTGCTACT 59.075 40.000 21.53 0.00 38.42 2.57
29 30 5.164119 CGTCGGACCGATTATTATTTGCTAC 60.164 44.000 21.53 1.00 38.42 3.58
30 31 4.919168 CGTCGGACCGATTATTATTTGCTA 59.081 41.667 21.53 0.00 38.42 3.49
79 80 1.133668 AGGTACCGATAACGCTAGGGT 60.134 52.381 6.62 6.62 38.29 4.34
107 108 0.532862 CCTCCCGCGCTATTGATTGT 60.533 55.000 5.56 0.00 0.00 2.71
134 139 4.503007 CCTTGTGATTTATAGACGTGGTCG 59.497 45.833 0.00 0.00 37.67 4.79
186 1405 8.474025 TGCTTTTCTTTGGTTTTTGAGATAGAA 58.526 29.630 0.00 0.00 0.00 2.10
279 1502 5.882557 CCAACCTGCAAGATAGATAGTTGTT 59.117 40.000 0.00 0.00 34.07 2.83
319 1542 1.477014 GCTAGGGGGAGGTGTTAATGC 60.477 57.143 0.00 0.00 0.00 3.56
320 1543 1.143073 GGCTAGGGGGAGGTGTTAATG 59.857 57.143 0.00 0.00 0.00 1.90
321 1544 1.274767 TGGCTAGGGGGAGGTGTTAAT 60.275 52.381 0.00 0.00 0.00 1.40
322 1545 0.119561 TGGCTAGGGGGAGGTGTTAA 59.880 55.000 0.00 0.00 0.00 2.01
323 1546 0.345502 ATGGCTAGGGGGAGGTGTTA 59.654 55.000 0.00 0.00 0.00 2.41
324 1547 1.084842 ATGGCTAGGGGGAGGTGTT 59.915 57.895 0.00 0.00 0.00 3.32
325 1548 1.694169 CATGGCTAGGGGGAGGTGT 60.694 63.158 0.00 0.00 0.00 4.16
326 1549 1.694169 ACATGGCTAGGGGGAGGTG 60.694 63.158 0.00 0.00 0.00 4.00
327 1550 1.384643 GACATGGCTAGGGGGAGGT 60.385 63.158 0.00 0.00 0.00 3.85
328 1551 0.695803 AAGACATGGCTAGGGGGAGG 60.696 60.000 0.00 0.00 0.00 4.30
329 1552 2.103153 TAAGACATGGCTAGGGGGAG 57.897 55.000 0.00 0.00 0.00 4.30
330 1553 2.182312 AGATAAGACATGGCTAGGGGGA 59.818 50.000 0.00 0.00 0.00 4.81
331 1554 2.625639 AGATAAGACATGGCTAGGGGG 58.374 52.381 0.00 0.00 0.00 5.40
332 1555 4.713792 AAAGATAAGACATGGCTAGGGG 57.286 45.455 0.00 0.00 0.00 4.79
360 1583 1.334870 CGAGATGGCGACTCTGATCTG 60.335 57.143 0.00 0.00 32.87 2.90
378 1601 0.452585 TAATCACCACGACGATGCGA 59.547 50.000 0.00 0.00 34.83 5.10
380 1603 3.733024 TTTTAATCACCACGACGATGC 57.267 42.857 0.00 0.00 0.00 3.91
386 1609 9.632807 CTTGGATTTAAATTTTAATCACCACGA 57.367 29.630 23.89 10.80 33.43 4.35
782 2021 4.241555 CCCTCCGAATCAGCCCCG 62.242 72.222 0.00 0.00 0.00 5.73
819 2058 3.524606 TCCCGATCGAGGCGAACC 61.525 66.667 18.66 0.00 39.99 3.62
821 2060 3.524606 GGTCCCGATCGAGGCGAA 61.525 66.667 18.66 0.00 39.99 4.70
892 2131 0.177373 AGAAATTAGGGGACGCCGTC 59.823 55.000 9.15 9.15 0.00 4.79
899 2148 4.141482 CCGAATTCCTCAGAAATTAGGGGA 60.141 45.833 0.00 0.00 35.09 4.81
905 2154 3.891049 CTCCCCGAATTCCTCAGAAATT 58.109 45.455 0.00 0.00 35.09 1.82
910 2159 1.227380 CGCTCCCCGAATTCCTCAG 60.227 63.158 0.00 0.00 40.02 3.35
928 2177 1.270147 CGGGGATCCCTCGTATCAAAC 60.270 57.143 30.08 8.46 42.67 2.93
941 2190 4.899239 CTCTGGCGCACGGGGATC 62.899 72.222 10.83 0.00 0.00 3.36
956 2205 1.377856 GGCCAGAGCACCTTTCCTC 60.378 63.158 0.00 0.00 42.56 3.71
1224 2473 6.954616 TGAATGCATGAATGTCAACATTTC 57.045 33.333 9.59 2.96 45.72 2.17
1238 2487 6.645827 TGTCAACAGGTTTATTTGAATGCATG 59.354 34.615 0.00 0.00 31.21 4.06
1250 2499 3.120321 ACGCAGATGTCAACAGGTTTA 57.880 42.857 0.00 0.00 0.00 2.01
1264 2513 1.000385 CCTTTGCCAAATCAACGCAGA 60.000 47.619 0.00 0.00 33.30 4.26
1265 2514 1.000385 TCCTTTGCCAAATCAACGCAG 60.000 47.619 0.00 0.00 33.30 5.18
1267 2516 1.792367 GTTCCTTTGCCAAATCAACGC 59.208 47.619 0.00 0.00 0.00 4.84
1268 2517 2.403259 GGTTCCTTTGCCAAATCAACG 58.597 47.619 0.00 0.00 0.00 4.10
1269 2518 2.403259 CGGTTCCTTTGCCAAATCAAC 58.597 47.619 0.00 0.00 0.00 3.18
1270 2519 1.270041 GCGGTTCCTTTGCCAAATCAA 60.270 47.619 0.00 0.00 0.00 2.57
1276 2526 1.896660 GAGTGCGGTTCCTTTGCCA 60.897 57.895 0.00 0.00 0.00 4.92
1289 2539 4.436050 CCAACGACAGATAAATGTGAGTGC 60.436 45.833 0.00 0.00 32.25 4.40
1307 2557 0.530650 ATCTAGACATGGCGCCAACG 60.531 55.000 36.33 28.91 44.07 4.10
1309 2559 1.065491 ACAATCTAGACATGGCGCCAA 60.065 47.619 36.33 16.31 0.00 4.52
1312 2562 2.939103 AGAAACAATCTAGACATGGCGC 59.061 45.455 0.00 0.00 36.32 6.53
1313 2563 4.269603 CAGAGAAACAATCTAGACATGGCG 59.730 45.833 11.05 0.00 38.96 5.69
1314 2564 5.181748 ACAGAGAAACAATCTAGACATGGC 58.818 41.667 11.05 0.00 38.96 4.40
1438 2692 1.470458 GGTTACCGACCGACTTCATCC 60.470 57.143 0.00 0.00 39.00 3.51
1460 2714 5.933617 TCAGAAATATACAGGCTTCAGCAT 58.066 37.500 0.30 0.00 44.36 3.79
1462 2716 6.874288 AATCAGAAATATACAGGCTTCAGC 57.126 37.500 0.00 0.00 41.14 4.26
1476 2730 7.710044 CAGAGCAGTCTACACATAATCAGAAAT 59.290 37.037 0.00 0.00 0.00 2.17
1547 2801 5.142061 TCACATTTGCATTGAAGAGCATT 57.858 34.783 4.32 0.00 40.94 3.56
1587 2841 6.151648 TCCAAGCAGTAAAAAGGATCAGAATG 59.848 38.462 0.00 0.00 37.54 2.67
1588 2842 6.248433 TCCAAGCAGTAAAAAGGATCAGAAT 58.752 36.000 0.00 0.00 0.00 2.40
1589 2843 5.630121 TCCAAGCAGTAAAAAGGATCAGAA 58.370 37.500 0.00 0.00 0.00 3.02
1590 2844 5.241403 TCCAAGCAGTAAAAAGGATCAGA 57.759 39.130 0.00 0.00 0.00 3.27
1591 2845 5.416952 ACATCCAAGCAGTAAAAAGGATCAG 59.583 40.000 0.00 0.00 33.81 2.90
1592 2846 5.183713 CACATCCAAGCAGTAAAAAGGATCA 59.816 40.000 0.00 0.00 33.81 2.92
1594 2848 5.079643 ACACATCCAAGCAGTAAAAAGGAT 58.920 37.500 0.00 0.00 36.35 3.24
1595 2849 4.469657 ACACATCCAAGCAGTAAAAAGGA 58.530 39.130 0.00 0.00 0.00 3.36
1596 2850 4.853924 ACACATCCAAGCAGTAAAAAGG 57.146 40.909 0.00 0.00 0.00 3.11
1597 2851 6.348540 GGACTACACATCCAAGCAGTAAAAAG 60.349 42.308 0.00 0.00 36.15 2.27
1614 2870 2.184579 GCCGCCTCAGGACTACAC 59.815 66.667 0.00 0.00 0.00 2.90
1726 2982 1.473677 GGCACATAATCTGCAAGCACA 59.526 47.619 0.00 0.00 36.27 4.57
1787 3043 4.965814 TCAGCATCTGAAACTTCTTCAGT 58.034 39.130 12.81 0.70 44.58 3.41
1792 3048 6.889301 TCAAAATCAGCATCTGAAACTTCT 57.111 33.333 0.27 0.00 44.04 2.85
1854 3110 4.862574 TCACTCCATGATTCGTTTAAGACG 59.137 41.667 0.00 4.47 42.19 4.18
1855 3111 5.637810 TGTCACTCCATGATTCGTTTAAGAC 59.362 40.000 0.00 0.00 40.28 3.01
2003 3259 2.485814 GGTGACTTCAGAAACAGATGCC 59.514 50.000 0.00 0.00 0.00 4.40
2018 3274 4.371624 TGTTCCATCTTCAATGGTGACT 57.628 40.909 4.10 0.00 40.06 3.41
2080 3337 5.923733 TCTGGAAAACACCTAAAAAGCAA 57.076 34.783 0.00 0.00 0.00 3.91
2093 3363 9.922305 CTGAATCGAAGTATAAATCTGGAAAAC 57.078 33.333 0.00 0.00 0.00 2.43
2102 3372 9.574458 CCGTCATATCTGAATCGAAGTATAAAT 57.426 33.333 0.00 0.00 31.85 1.40
2147 3417 6.240894 TGATCCTGTAAGATGAAAGCAAAGT 58.759 36.000 0.00 0.00 34.07 2.66
2162 3432 1.691482 GGGGTGCTACCTGATCCTGTA 60.691 57.143 5.48 0.00 38.64 2.74
2233 3503 6.290294 ACAAAATTGCCTTCAGATTAGCAT 57.710 33.333 0.00 0.00 34.72 3.79
2288 3558 3.688694 TTCAACGGTGTATGGTTAGCT 57.311 42.857 0.00 0.00 0.00 3.32
2302 3572 3.688272 CAATAAGGAGCTGCATTCAACG 58.312 45.455 8.35 0.00 0.00 4.10
2376 3646 5.547465 TGACAGTTCTTTGTATGTACCAGG 58.453 41.667 0.00 0.00 0.00 4.45
2380 3650 9.730420 AAAACAATGACAGTTCTTTGTATGTAC 57.270 29.630 6.40 0.00 45.01 2.90
2410 3681 9.896263 GCAAATGAACAACCAAATTAAAATGAT 57.104 25.926 0.00 0.00 0.00 2.45
2416 3687 8.997323 CATAAGGCAAATGAACAACCAAATTAA 58.003 29.630 0.00 0.00 0.00 1.40
2418 3689 6.072563 GCATAAGGCAAATGAACAACCAAATT 60.073 34.615 3.55 0.00 43.97 1.82
2537 3808 2.620585 GGAGGCACAAATATGGAGAAGC 59.379 50.000 0.00 0.00 0.00 3.86
2690 3962 2.922740 ACGGACAGCCTCAAAAACTA 57.077 45.000 0.00 0.00 0.00 2.24
2720 3992 0.474184 ATATTGTCCCCGGCCTTCTG 59.526 55.000 0.00 0.00 0.00 3.02
2754 4026 3.904136 TTTAGCAGCAGACTTTCTTGC 57.096 42.857 0.00 0.00 32.02 4.01
2828 4100 5.806286 ACAACTTATGCGGAATAATGTTCG 58.194 37.500 0.00 0.00 30.26 3.95
2839 4111 3.436704 ACAACAGATGACAACTTATGCGG 59.563 43.478 0.00 0.00 0.00 5.69
2841 4113 8.236586 TGAATAACAACAGATGACAACTTATGC 58.763 33.333 0.00 0.00 0.00 3.14
3025 4298 2.419990 CGAGCCACCAAACCATCAGATA 60.420 50.000 0.00 0.00 0.00 1.98
3042 4322 1.079503 CTCCCTACAAAGCAACGAGC 58.920 55.000 0.00 0.00 46.19 5.03
3045 4325 1.531149 CACACTCCCTACAAAGCAACG 59.469 52.381 0.00 0.00 0.00 4.10
3046 4326 1.880027 CCACACTCCCTACAAAGCAAC 59.120 52.381 0.00 0.00 0.00 4.17
3212 4497 6.552859 TTGTGCAAGATCAATCGAGTAAAA 57.447 33.333 0.00 0.00 0.00 1.52
3219 4511 4.161333 GTCCTTTTGTGCAAGATCAATCG 58.839 43.478 0.00 0.00 0.00 3.34
3224 4522 4.771590 TCATGTCCTTTTGTGCAAGATC 57.228 40.909 0.00 0.00 0.00 2.75
3230 4528 6.012658 TGATAGTTTCATGTCCTTTTGTGC 57.987 37.500 0.00 0.00 0.00 4.57
3242 4540 9.672673 ATGCTACAAGTACTTTGATAGTTTCAT 57.327 29.630 5.07 5.02 39.21 2.57
3243 4541 8.935844 CATGCTACAAGTACTTTGATAGTTTCA 58.064 33.333 5.07 3.03 39.21 2.69
3244 4542 9.151471 TCATGCTACAAGTACTTTGATAGTTTC 57.849 33.333 5.07 0.00 39.21 2.78
3245 4543 9.155975 CTCATGCTACAAGTACTTTGATAGTTT 57.844 33.333 5.07 0.00 39.21 2.66
3246 4544 8.314751 ACTCATGCTACAAGTACTTTGATAGTT 58.685 33.333 5.07 0.00 39.21 2.24
3247 4545 7.761704 CACTCATGCTACAAGTACTTTGATAGT 59.238 37.037 5.07 3.04 39.21 2.12
3248 4546 7.976175 TCACTCATGCTACAAGTACTTTGATAG 59.024 37.037 5.07 9.28 39.21 2.08
3249 4547 7.759886 GTCACTCATGCTACAAGTACTTTGATA 59.240 37.037 5.07 0.00 39.21 2.15
3274 4580 5.938279 AGCTGATTGATGGACTTCATATGT 58.062 37.500 1.90 0.00 35.97 2.29
3285 4591 5.356190 ACATAAAGTGTGAGCTGATTGATGG 59.644 40.000 0.00 0.00 40.28 3.51
3351 4659 2.976729 GCAACATGCTTGCTTTTTGTG 58.023 42.857 19.37 0.00 40.96 3.33
3366 4674 3.316588 TCATTAACCGAAAGCAAGCAACA 59.683 39.130 0.00 0.00 0.00 3.33
3370 4679 3.492313 CAGTCATTAACCGAAAGCAAGC 58.508 45.455 0.00 0.00 0.00 4.01
3762 5086 3.142838 ATGGCGCCCATGCAGAAC 61.143 61.111 26.77 0.00 43.39 3.01
3916 5243 3.202706 GGCGAAACCGGATGAGGC 61.203 66.667 9.46 5.42 33.69 4.70
3919 5246 2.435938 GCAGGCGAAACCGGATGA 60.436 61.111 9.46 0.00 46.52 2.92
4081 5414 5.132502 TCCATTTCCCATATGTTGCTACAG 58.867 41.667 7.16 0.00 37.77 2.74
4121 5454 3.565617 ACAAACCCAGGTAGGTAGGTA 57.434 47.619 0.00 0.00 40.05 3.08
4122 5455 2.428181 ACAAACCCAGGTAGGTAGGT 57.572 50.000 0.00 0.00 40.05 3.08
4123 5456 4.914177 TTTACAAACCCAGGTAGGTAGG 57.086 45.455 0.00 0.00 40.05 3.18
4124 5457 6.825213 GGTTATTTACAAACCCAGGTAGGTAG 59.175 42.308 0.00 0.00 40.05 3.18
4125 5458 6.504989 AGGTTATTTACAAACCCAGGTAGGTA 59.495 38.462 1.47 0.00 46.33 3.08
4126 5459 5.314039 AGGTTATTTACAAACCCAGGTAGGT 59.686 40.000 1.47 0.00 46.33 3.08
4127 5460 5.823312 AGGTTATTTACAAACCCAGGTAGG 58.177 41.667 1.47 0.00 46.33 3.18
4128 5461 6.717997 ACAAGGTTATTTACAAACCCAGGTAG 59.282 38.462 1.47 0.00 46.33 3.18
4129 5462 6.490721 CACAAGGTTATTTACAAACCCAGGTA 59.509 38.462 1.47 0.00 46.33 3.08
4130 5463 5.303333 CACAAGGTTATTTACAAACCCAGGT 59.697 40.000 1.47 0.00 46.33 4.00
4131 5464 5.303333 ACACAAGGTTATTTACAAACCCAGG 59.697 40.000 1.47 0.00 46.33 4.45
4132 5465 6.399639 ACACAAGGTTATTTACAAACCCAG 57.600 37.500 1.47 0.00 46.33 4.45
4206 5545 0.590230 TTCAAACAAAAGCGTCGCCG 60.590 50.000 14.86 2.67 37.07 6.46
4207 5546 0.843872 GTTCAAACAAAAGCGTCGCC 59.156 50.000 14.86 0.00 0.00 5.54
4208 5547 0.843872 GGTTCAAACAAAAGCGTCGC 59.156 50.000 9.80 9.80 0.00 5.19
4209 5548 1.109296 CGGTTCAAACAAAAGCGTCG 58.891 50.000 0.00 0.00 41.34 5.12
4210 5549 1.202211 ACCGGTTCAAACAAAAGCGTC 60.202 47.619 0.00 0.00 43.88 5.19
4299 5642 2.674954 GCAGCAACATACAACATGCAA 58.325 42.857 0.00 0.00 41.18 4.08
4336 8543 1.397692 GAGAGGACGACGGACAGTTAG 59.602 57.143 0.00 0.00 0.00 2.34
4385 8599 7.436673 TGCCAACAATCATAAACAAGTTTGTAC 59.563 33.333 8.37 0.00 41.31 2.90
4387 8601 6.344500 TGCCAACAATCATAAACAAGTTTGT 58.656 32.000 8.37 0.00 44.72 2.83
4389 8603 6.073112 GCATGCCAACAATCATAAACAAGTTT 60.073 34.615 6.36 3.47 36.63 2.66
4390 8604 5.409214 GCATGCCAACAATCATAAACAAGTT 59.591 36.000 6.36 0.00 0.00 2.66
4409 8634 1.012486 GCAGCAACAGGAAAGCATGC 61.012 55.000 10.51 10.51 37.28 4.06
4490 8721 8.692710 AGTGTACTATTCTAATCACGATGGAAA 58.307 33.333 0.00 0.00 0.00 3.13
4492 8723 7.818997 AGTGTACTATTCTAATCACGATGGA 57.181 36.000 0.00 0.00 0.00 3.41
4497 8729 7.928103 ACCAGTAGTGTACTATTCTAATCACG 58.072 38.462 0.00 0.00 37.23 4.35
4517 8749 1.825474 CTGTAATGTCGGAGGACCAGT 59.175 52.381 0.00 0.00 42.73 4.00
4565 8797 1.089920 CCTCGGCCAAATCAGTTCAG 58.910 55.000 2.24 0.00 0.00 3.02
4623 8855 9.905713 AGTGCCTTGAGAAATATAAAATCTGTA 57.094 29.630 0.00 0.00 0.00 2.74
4697 8929 1.130613 GTCATTCACAGCGTCGCAC 59.869 57.895 21.09 1.85 0.00 5.34
4741 8973 1.212935 TCTCCCTTGCTAAATGGGCTC 59.787 52.381 0.00 0.00 40.69 4.70
4743 8975 2.234143 GATCTCCCTTGCTAAATGGGC 58.766 52.381 0.00 0.00 40.69 5.36
4802 9072 2.060326 TCAAAGACGAGTACGCCAAG 57.940 50.000 0.00 0.00 43.96 3.61
4815 9085 2.289631 TGGCGCTGAAGAAGATCAAAGA 60.290 45.455 7.64 0.00 0.00 2.52
4874 9145 1.375140 TTTGCTCTGCTCCAGCGAG 60.375 57.895 13.00 13.00 45.83 5.03


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

AutoCloner maintained by Alex Coulton.