Multiple sequence alignment - TraesCS5A01G302400

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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 TraesCS5A01G302400 chr5A 100.000 4818 0 0 1 4818 511902711 511907528 0.000000e+00 8898.0
1 TraesCS5A01G302400 chr5D 94.662 4459 163 34 1 4411 406330376 406334807 0.000000e+00 6846.0
2 TraesCS5A01G302400 chr5B 93.261 3710 144 35 788 4461 487220241 487223880 0.000000e+00 5369.0
3 TraesCS5A01G302400 chr5B 91.576 736 46 9 1 724 487219494 487220225 0.000000e+00 1002.0
4 TraesCS5A01G302400 chr1D 94.118 221 11 2 4506 4724 441038825 441039045 7.730000e-88 335.0
5 TraesCS5A01G302400 chr1D 93.013 229 12 4 4499 4724 441038334 441038561 9.990000e-87 331.0
6 TraesCS5A01G302400 chr1D 89.855 207 21 0 3359 3565 471841334 471841540 2.860000e-67 267.0
7 TraesCS5A01G302400 chr1D 93.678 174 9 2 4553 4724 441040921 441041094 4.780000e-65 259.0
8 TraesCS5A01G302400 chr4B 93.396 212 12 2 4499 4708 643525832 643525621 3.620000e-81 313.0
9 TraesCS5A01G302400 chr4B 91.250 80 4 3 4496 4575 483917812 483917736 6.590000e-19 106.0
10 TraesCS5A01G302400 chr4B 100.000 28 0 0 60 87 625960578 625960551 9.000000e-03 52.8
11 TraesCS5A01G302400 chrUn 92.891 211 13 2 4500 4708 60419573 60419783 6.060000e-79 305.0
12 TraesCS5A01G302400 chr1A 90.821 207 19 0 3359 3565 566111186 566111392 1.320000e-70 278.0
13 TraesCS5A01G302400 chr1B 90.338 207 20 0 3359 3565 655849215 655849421 6.140000e-69 272.0
14 TraesCS5A01G302400 chr6B 90.588 85 6 2 4497 4579 477190277 477190361 1.420000e-20 111.0
15 TraesCS5A01G302400 chr6B 88.636 88 7 3 4492 4576 187991246 187991333 2.370000e-18 104.0
16 TraesCS5A01G302400 chr6B 89.157 83 7 2 4499 4579 34162017 34162099 8.530000e-18 102.0
17 TraesCS5A01G302400 chr2B 89.157 83 7 2 4499 4579 776082812 776082730 8.530000e-18 102.0
18 TraesCS5A01G302400 chr2B 100.000 28 0 0 61 88 470520076 470520049 9.000000e-03 52.8
19 TraesCS5A01G302400 chr2B 100.000 28 0 0 61 88 692920069 692920096 9.000000e-03 52.8
20 TraesCS5A01G302400 chr7D 100.000 28 0 0 63 90 93046563 93046590 9.000000e-03 52.8
21 TraesCS5A01G302400 chr3A 100.000 28 0 0 60 87 404715385 404715412 9.000000e-03 52.8


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 TraesCS5A01G302400 chr5A 511902711 511907528 4817 False 8898.000000 8898 100.0000 1 4818 1 chr5A.!!$F1 4817
1 TraesCS5A01G302400 chr5D 406330376 406334807 4431 False 6846.000000 6846 94.6620 1 4411 1 chr5D.!!$F1 4410
2 TraesCS5A01G302400 chr5B 487219494 487223880 4386 False 3185.500000 5369 92.4185 1 4461 2 chr5B.!!$F1 4460
3 TraesCS5A01G302400 chr1D 441038334 441041094 2760 False 308.333333 335 93.6030 4499 4724 3 chr1D.!!$F2 225

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
394 409 0.036858 GGGAGAGAGACAACTGTGGC 60.037 60.000 0.00 0.00 0.00 5.01 F
399 414 0.326264 AGAGACAACTGTGGCCATCC 59.674 55.000 9.72 0.00 30.22 3.51 F
902 925 0.863144 TGAAACAAGTTCTACGCGGC 59.137 50.000 12.47 0.00 37.13 6.53 F
1077 1123 1.032114 TCGAGAAGCTGCGGATCTCA 61.032 55.000 23.12 13.21 39.62 3.27 F
2384 2437 1.260544 ATGGCTTGGAGAAACTTGCC 58.739 50.000 0.00 0.00 40.62 4.52 F
2948 3008 2.622436 GACGGCAGCTTTAGTTCTGAT 58.378 47.619 0.00 0.00 32.26 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 1324 0.400381 TCCCTCCCATATCAGCTGCA 60.400 55.000 9.47 0.00 0.00 4.41 R
2384 2437 1.610038 TGCTTGCACAATTCCTCAGTG 59.390 47.619 0.00 0.00 36.39 3.66 R
2846 2906 9.616156 TCATGCAAAATTTATTCCATGCTAATT 57.384 25.926 10.65 0.00 34.97 1.40 R
3072 3132 2.998279 GCTTGCTGGGCCATCACAC 61.998 63.158 10.08 1.11 0.00 3.82 R
3205 3265 1.395954 CTCATCAGGAACACATGTGCG 59.604 52.381 25.68 9.31 0.00 5.34 R
4778 7375 0.245813 GCGACCCGGAAAAGTAGAGT 59.754 55.000 0.73 0.00 0.00 3.24 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
38 39 0.461961 AGCAGCTTAGCCTAACTCCG 59.538 55.000 0.00 0.00 34.23 4.63
47 48 1.062206 CCTAACTCCGAGCGACGAC 59.938 63.158 0.00 0.00 45.77 4.34
59 60 2.105128 GACGACCCGATCCAGCTG 59.895 66.667 6.78 6.78 0.00 4.24
138 152 1.836802 AGCCTGACCCTCATCTCTTTC 59.163 52.381 0.00 0.00 0.00 2.62
153 167 3.191186 TTTCCCTCCCCGGTACCCA 62.191 63.158 6.25 0.00 0.00 4.51
224 238 1.003118 TCCCTCCATCAGTTTTCGGTG 59.997 52.381 0.00 0.00 0.00 4.94
250 264 1.227205 CTCCGAGCTCATCCACTGC 60.227 63.158 15.40 0.00 0.00 4.40
373 388 0.905357 CAGATCGAGGGGTTGACCTT 59.095 55.000 0.00 0.00 42.10 3.50
387 402 1.203013 TGACCTTCGGGAGAGAGACAA 60.203 52.381 0.00 0.00 41.75 3.18
388 403 1.202817 GACCTTCGGGAGAGAGACAAC 59.797 57.143 0.00 0.00 41.75 3.32
389 404 1.203075 ACCTTCGGGAGAGAGACAACT 60.203 52.381 0.00 0.00 41.75 3.16
390 405 1.203523 CCTTCGGGAGAGAGACAACTG 59.796 57.143 0.00 0.00 41.75 3.16
391 406 1.889829 CTTCGGGAGAGAGACAACTGT 59.110 52.381 0.00 0.00 41.75 3.55
392 407 1.248486 TCGGGAGAGAGACAACTGTG 58.752 55.000 0.00 0.00 0.00 3.66
394 409 0.036858 GGGAGAGAGACAACTGTGGC 60.037 60.000 0.00 0.00 0.00 5.01
397 412 1.277557 GAGAGAGACAACTGTGGCCAT 59.722 52.381 9.72 0.00 30.22 4.40
398 413 1.277557 AGAGAGACAACTGTGGCCATC 59.722 52.381 9.72 0.00 30.22 3.51
399 414 0.326264 AGAGACAACTGTGGCCATCC 59.674 55.000 9.72 0.00 30.22 3.51
618 638 4.835056 CCTTCTTGGAAGAAAGGAAACCAT 59.165 41.667 8.64 0.00 43.84 3.55
643 664 5.944007 ACAAGGGTCTATTATTGCTTTCGTT 59.056 36.000 0.00 0.00 0.00 3.85
747 768 2.941064 AGTGATGGATGCTCATTTGACG 59.059 45.455 0.00 0.00 0.00 4.35
778 799 2.125912 CCCGGCTTCGTCAGTCAG 60.126 66.667 0.00 0.00 0.00 3.51
781 802 1.797933 CGGCTTCGTCAGTCAGTCG 60.798 63.158 0.00 0.00 0.00 4.18
900 923 3.277481 GTGTTGAAACAAGTTCTACGCG 58.723 45.455 3.53 3.53 42.73 6.01
901 924 2.285756 TGTTGAAACAAGTTCTACGCGG 59.714 45.455 12.47 0.00 42.73 6.46
902 925 0.863144 TGAAACAAGTTCTACGCGGC 59.137 50.000 12.47 0.00 37.13 6.53
903 926 1.145803 GAAACAAGTTCTACGCGGCT 58.854 50.000 12.47 0.00 33.03 5.52
904 927 1.529865 GAAACAAGTTCTACGCGGCTT 59.470 47.619 12.47 3.68 33.03 4.35
937 982 5.992729 TGTTATTGTTTGCCGTAAGAAGTC 58.007 37.500 0.00 0.00 43.02 3.01
948 993 4.212213 CGTAAGAAGTCGGAGTCCTATG 57.788 50.000 7.77 0.00 43.02 2.23
949 994 3.875727 CGTAAGAAGTCGGAGTCCTATGA 59.124 47.826 7.77 0.00 43.02 2.15
950 995 4.515944 CGTAAGAAGTCGGAGTCCTATGAT 59.484 45.833 7.77 0.00 43.02 2.45
951 996 5.008811 CGTAAGAAGTCGGAGTCCTATGATT 59.991 44.000 7.77 0.00 43.02 2.57
1077 1123 1.032114 TCGAGAAGCTGCGGATCTCA 61.032 55.000 23.12 13.21 39.62 3.27
1344 1390 5.610398 TCTGTCATCATGTACAACAACACT 58.390 37.500 0.00 0.00 30.75 3.55
1372 1418 3.691118 CAGCTTTAACATGCTTGAGGCTA 59.309 43.478 6.60 0.00 42.39 3.93
1515 1561 5.996669 TTTTCGACAAAGGTTTAGGTCTC 57.003 39.130 0.00 0.00 0.00 3.36
1635 1686 6.942005 ACATCTTTGTTCAGTTCATGGATACA 59.058 34.615 0.00 0.00 42.90 2.29
1725 1776 7.269316 TCATAGTTATGTTTGCTGACGGATAA 58.731 34.615 0.00 0.00 35.26 1.75
1727 1778 5.242434 AGTTATGTTTGCTGACGGATAACA 58.758 37.500 0.00 4.68 31.54 2.41
1795 1846 4.165950 TGCAAGGTGATGGGTTGATATAGT 59.834 41.667 0.00 0.00 0.00 2.12
1866 1917 4.153371 AGACCATCTTATCTGCCCCTAT 57.847 45.455 0.00 0.00 0.00 2.57
1877 1928 7.734865 TCTTATCTGCCCCTATCTTTTATCTCA 59.265 37.037 0.00 0.00 0.00 3.27
1979 2032 5.388654 ACTGATCCTTGAAAACATTGTCCT 58.611 37.500 0.00 0.00 0.00 3.85
2062 2115 7.328249 CAGAAAGTTGCAGTTTTGTTTAGTCAA 59.672 33.333 2.66 0.00 0.00 3.18
2104 2157 9.631639 GAAAACATATTACAACAGCAAAACAAC 57.368 29.630 0.00 0.00 0.00 3.32
2258 2311 2.338785 GCTTGGCCTGCAGAGGTTC 61.339 63.158 17.39 0.02 42.15 3.62
2274 2327 4.222810 AGAGGTTCCAAAACTTTTGCACTT 59.777 37.500 8.53 4.48 35.61 3.16
2384 2437 1.260544 ATGGCTTGGAGAAACTTGCC 58.739 50.000 0.00 0.00 40.62 4.52
2494 2547 7.129660 TGGGACATGGAAGGGTAAGATTTTATA 59.870 37.037 0.00 0.00 0.00 0.98
2536 2589 5.912892 AGGTGTTTTTCTTAATGTGTTGGG 58.087 37.500 0.00 0.00 0.00 4.12
2813 2873 3.188159 TCAAATCCGGTACTGGTATGC 57.812 47.619 20.40 0.00 0.00 3.14
2856 2916 7.330208 GCTGAAATATGCCTTAAATTAGCATGG 59.670 37.037 9.20 0.70 46.30 3.66
2931 2991 4.571984 TGCTGAGATGACAATTAATGGACG 59.428 41.667 0.00 0.00 0.00 4.79
2948 3008 2.622436 GACGGCAGCTTTAGTTCTGAT 58.378 47.619 0.00 0.00 32.26 2.90
3017 3077 9.417561 AGTTTCATATGAGATGTTGATTTCCAT 57.582 29.630 5.39 0.00 0.00 3.41
3130 3190 5.726980 ATTCCAAAAGCTGCAGTGATTTA 57.273 34.783 16.64 0.74 0.00 1.40
3141 3201 9.846248 AAGCTGCAGTGATTTAATTTACTTTAG 57.154 29.630 16.64 0.00 0.00 1.85
3142 3202 8.462016 AGCTGCAGTGATTTAATTTACTTTAGG 58.538 33.333 16.64 0.00 0.00 2.69
3143 3203 8.458843 GCTGCAGTGATTTAATTTACTTTAGGA 58.541 33.333 16.64 0.00 0.00 2.94
3220 3280 1.737838 ATACCGCACATGTGTTCCTG 58.262 50.000 26.01 12.79 0.00 3.86
3264 3324 7.601508 TCATTGAATCATCATTCTCATCCTACG 59.398 37.037 0.00 0.00 39.49 3.51
3310 3370 4.758674 TCTCTCCTTTGTTGAAGAGCAATG 59.241 41.667 0.00 0.00 39.03 2.82
3312 3372 4.889409 TCTCCTTTGTTGAAGAGCAATGTT 59.111 37.500 0.00 0.00 39.03 2.71
3318 3378 8.490355 CCTTTGTTGAAGAGCAATGTTATTTTC 58.510 33.333 0.00 0.00 39.03 2.29
3326 3386 5.410355 AGCAATGTTATTTTCATGGCTGT 57.590 34.783 6.94 0.00 46.73 4.40
3821 3881 1.808945 CAGATGGCAAGGAGTGAACAC 59.191 52.381 0.00 0.00 0.00 3.32
3822 3882 1.701847 AGATGGCAAGGAGTGAACACT 59.298 47.619 7.20 7.20 45.84 3.55
3909 3970 8.565896 AACTTTCACATACTGCATGAGATTTA 57.434 30.769 0.00 0.00 38.10 1.40
4009 4070 5.763204 ACATGTAAAATCTGGTCAGTTCGTT 59.237 36.000 0.00 0.00 0.00 3.85
4010 4071 5.917541 TGTAAAATCTGGTCAGTTCGTTC 57.082 39.130 0.00 0.00 0.00 3.95
4011 4072 5.361427 TGTAAAATCTGGTCAGTTCGTTCA 58.639 37.500 0.00 0.00 0.00 3.18
4191 4252 9.793259 TTTAGGAGTATTTTTCTGTCTTGACAT 57.207 29.630 3.79 0.00 0.00 3.06
4265 4326 4.780815 AGAATAGATGCCCAAATCGAACA 58.219 39.130 0.00 0.00 0.00 3.18
4294 4355 3.239254 CGTCTTTATTTGGTTTTCGGCC 58.761 45.455 0.00 0.00 0.00 6.13
4299 4360 0.315886 ATTTGGTTTTCGGCCGGTTC 59.684 50.000 27.83 13.25 0.00 3.62
4332 4393 8.771920 TCTTTTTCTTTGTTTCTTCCTTTTCC 57.228 30.769 0.00 0.00 0.00 3.13
4550 5096 9.262358 CCTACTACCTTATTTCTCTAAACATGC 57.738 37.037 0.00 0.00 0.00 4.06
4566 5112 2.097036 CATGCAAGGTGTCCACATCAT 58.903 47.619 0.00 0.00 0.00 2.45
4571 5117 3.613030 CAAGGTGTCCACATCATCATCA 58.387 45.455 0.00 0.00 0.00 3.07
4572 5118 3.555527 AGGTGTCCACATCATCATCAG 57.444 47.619 0.00 0.00 0.00 2.90
4573 5119 1.945394 GGTGTCCACATCATCATCAGC 59.055 52.381 0.00 0.00 0.00 4.26
4575 5121 1.560611 TGTCCACATCATCATCAGCCA 59.439 47.619 0.00 0.00 0.00 4.75
4576 5122 1.945394 GTCCACATCATCATCAGCCAC 59.055 52.381 0.00 0.00 0.00 5.01
4577 5123 1.560611 TCCACATCATCATCAGCCACA 59.439 47.619 0.00 0.00 0.00 4.17
4578 5124 2.173996 TCCACATCATCATCAGCCACAT 59.826 45.455 0.00 0.00 0.00 3.21
4579 5125 3.391955 TCCACATCATCATCAGCCACATA 59.608 43.478 0.00 0.00 0.00 2.29
4580 5126 4.042435 TCCACATCATCATCAGCCACATAT 59.958 41.667 0.00 0.00 0.00 1.78
4636 5184 1.133790 GTGAGACATGCATCCTTTGGC 59.866 52.381 0.00 0.00 0.00 4.52
4682 7279 5.649782 ATGCAAAAGAAATCGATTCCAGT 57.350 34.783 11.83 0.00 38.94 4.00
4724 7321 0.861837 GCCCAATCGTCTCATTAGCG 59.138 55.000 0.00 0.00 0.00 4.26
4725 7322 1.502231 CCCAATCGTCTCATTAGCGG 58.498 55.000 0.00 0.00 0.00 5.52
4726 7323 1.502231 CCAATCGTCTCATTAGCGGG 58.498 55.000 0.00 0.00 0.00 6.13
4727 7324 1.068588 CCAATCGTCTCATTAGCGGGA 59.931 52.381 0.00 0.00 0.00 5.14
4728 7325 2.398498 CAATCGTCTCATTAGCGGGAG 58.602 52.381 0.00 0.00 0.00 4.30
4745 7342 5.873179 CGGGAGCAACTAGTTAATTGAAA 57.127 39.130 8.04 0.00 0.00 2.69
4746 7343 5.628134 CGGGAGCAACTAGTTAATTGAAAC 58.372 41.667 8.04 0.00 0.00 2.78
4747 7344 5.391629 CGGGAGCAACTAGTTAATTGAAACC 60.392 44.000 8.04 3.98 0.00 3.27
4748 7345 5.475564 GGGAGCAACTAGTTAATTGAAACCA 59.524 40.000 8.04 0.00 0.00 3.67
4749 7346 6.379386 GGAGCAACTAGTTAATTGAAACCAC 58.621 40.000 8.04 0.00 0.00 4.16
4750 7347 6.206829 GGAGCAACTAGTTAATTGAAACCACT 59.793 38.462 8.04 0.00 0.00 4.00
4751 7348 7.389607 GGAGCAACTAGTTAATTGAAACCACTA 59.610 37.037 8.04 0.00 0.00 2.74
4752 7349 8.685838 AGCAACTAGTTAATTGAAACCACTAA 57.314 30.769 8.04 0.00 0.00 2.24
4753 7350 9.297037 AGCAACTAGTTAATTGAAACCACTAAT 57.703 29.630 8.04 0.00 0.00 1.73
4754 7351 9.908152 GCAACTAGTTAATTGAAACCACTAATT 57.092 29.630 8.04 0.00 0.00 1.40
4764 7361 9.588096 AATTGAAACCACTAATTAAGGAGTTCT 57.412 29.630 9.89 0.00 0.00 3.01
4765 7362 8.617290 TTGAAACCACTAATTAAGGAGTTCTC 57.383 34.615 9.89 0.00 0.00 2.87
4766 7363 6.872020 TGAAACCACTAATTAAGGAGTTCTCG 59.128 38.462 9.89 0.00 0.00 4.04
4767 7364 5.997384 ACCACTAATTAAGGAGTTCTCGT 57.003 39.130 9.89 0.00 0.00 4.18
4768 7365 6.356186 ACCACTAATTAAGGAGTTCTCGTT 57.644 37.500 9.89 11.50 0.00 3.85
4769 7366 6.164176 ACCACTAATTAAGGAGTTCTCGTTG 58.836 40.000 15.14 3.95 0.00 4.10
4770 7367 5.063564 CCACTAATTAAGGAGTTCTCGTTGC 59.936 44.000 15.14 0.00 0.00 4.17
4771 7368 5.637810 CACTAATTAAGGAGTTCTCGTTGCA 59.362 40.000 15.14 0.00 0.00 4.08
4772 7369 6.147164 CACTAATTAAGGAGTTCTCGTTGCAA 59.853 38.462 15.14 0.00 0.00 4.08
4773 7370 6.708949 ACTAATTAAGGAGTTCTCGTTGCAAA 59.291 34.615 15.14 5.21 0.00 3.68
4774 7371 6.385649 AATTAAGGAGTTCTCGTTGCAAAA 57.614 33.333 15.14 0.00 0.00 2.44
4775 7372 5.821516 TTAAGGAGTTCTCGTTGCAAAAA 57.178 34.783 15.14 0.00 0.00 1.94
4794 7391 3.851458 AAACACTCTACTTTTCCGGGT 57.149 42.857 0.00 0.00 0.00 5.28
4795 7392 3.397849 AACACTCTACTTTTCCGGGTC 57.602 47.619 0.00 0.00 0.00 4.46
4796 7393 1.271656 ACACTCTACTTTTCCGGGTCG 59.728 52.381 0.00 0.00 0.00 4.79
4797 7394 0.245813 ACTCTACTTTTCCGGGTCGC 59.754 55.000 0.00 0.00 0.00 5.19
4798 7395 0.801067 CTCTACTTTTCCGGGTCGCG 60.801 60.000 0.00 0.00 0.00 5.87
4799 7396 1.213537 CTACTTTTCCGGGTCGCGA 59.786 57.895 3.71 3.71 0.00 5.87
4800 7397 1.074872 CTACTTTTCCGGGTCGCGAC 61.075 60.000 30.67 30.67 0.00 5.19
4801 7398 1.804396 TACTTTTCCGGGTCGCGACA 61.804 55.000 37.26 17.11 0.00 4.35
4802 7399 1.957186 CTTTTCCGGGTCGCGACAA 60.957 57.895 37.26 21.93 0.00 3.18
4803 7400 1.500512 CTTTTCCGGGTCGCGACAAA 61.501 55.000 37.26 25.98 0.00 2.83
4804 7401 0.885596 TTTTCCGGGTCGCGACAAAT 60.886 50.000 37.26 0.00 0.00 2.32
4805 7402 1.570347 TTTCCGGGTCGCGACAAATG 61.570 55.000 37.26 23.16 0.00 2.32
4806 7403 3.496131 CCGGGTCGCGACAAATGG 61.496 66.667 37.26 27.32 0.00 3.16
4807 7404 4.160635 CGGGTCGCGACAAATGGC 62.161 66.667 37.26 20.32 0.00 4.40
4814 7411 4.060658 CGACAAATGGCGCACATG 57.939 55.556 10.83 4.84 40.91 3.21
4815 7412 2.153945 CGACAAATGGCGCACATGC 61.154 57.895 10.83 0.00 40.91 4.06
4816 7413 1.080637 GACAAATGGCGCACATGCA 60.081 52.632 10.83 0.00 40.44 3.96
4817 7414 1.074319 GACAAATGGCGCACATGCAG 61.074 55.000 10.83 6.79 40.44 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.537135 GCTCGGAGTTAGGCTAAGCTG 60.537 57.143 7.33 8.22 0.00 4.24
38 39 3.471244 CTGGATCGGGTCGTCGCTC 62.471 68.421 0.00 0.00 0.00 5.03
47 48 2.203126 GGCTTCAGCTGGATCGGG 60.203 66.667 15.13 0.00 41.70 5.14
104 110 1.303888 AGGCTGACGACCTCGGTTA 60.304 57.895 0.00 0.00 44.95 2.85
105 111 2.600769 AGGCTGACGACCTCGGTT 60.601 61.111 0.00 0.00 44.95 4.44
153 167 4.018779 TCCGTTTTGTCCCCAGAATATTCT 60.019 41.667 12.37 12.37 38.25 2.40
168 182 3.129638 TGGAGACTGGTTTTTCCGTTTTG 59.870 43.478 0.00 0.00 39.52 2.44
232 246 1.227205 GCAGTGGATGAGCTCGGAG 60.227 63.158 9.64 0.00 0.00 4.63
373 388 1.248486 CACAGTTGTCTCTCTCCCGA 58.752 55.000 0.00 0.00 0.00 5.14
399 414 3.986006 GCATCGCCATGGCCCATG 61.986 66.667 30.79 29.21 41.10 3.66
618 638 6.646267 ACGAAAGCAATAATAGACCCTTGTA 58.354 36.000 0.00 0.00 0.00 2.41
652 673 8.461249 AAGCAATAATGAATGAATGACTAGCT 57.539 30.769 0.00 0.00 0.00 3.32
696 717 1.917495 CCACAGGATGGCAGATGGA 59.083 57.895 0.00 0.00 43.24 3.41
747 768 1.021968 GCCGGGTTCAATCATACCAC 58.978 55.000 2.18 0.00 36.10 4.16
778 799 2.411031 CCACATTAGCAAACGTGACGAC 60.411 50.000 13.70 0.00 0.00 4.34
781 802 1.401018 GGCCACATTAGCAAACGTGAC 60.401 52.381 0.00 0.00 0.00 3.67
900 923 9.665264 GCAAACAATAACATCTTATACTAAGCC 57.335 33.333 0.00 0.00 0.00 4.35
901 924 9.665264 GGCAAACAATAACATCTTATACTAAGC 57.335 33.333 0.00 0.00 0.00 3.09
902 925 9.864034 CGGCAAACAATAACATCTTATACTAAG 57.136 33.333 0.00 0.00 0.00 2.18
903 926 9.386010 ACGGCAAACAATAACATCTTATACTAA 57.614 29.630 0.00 0.00 0.00 2.24
904 927 8.951787 ACGGCAAACAATAACATCTTATACTA 57.048 30.769 0.00 0.00 0.00 1.82
937 982 9.658799 ACAAAATATCATAATCATAGGACTCCG 57.341 33.333 0.00 0.00 0.00 4.63
1077 1123 1.136329 ACCCACCAGCTCCAGTGATT 61.136 55.000 9.16 0.00 36.01 2.57
1275 1321 1.544982 CCTCCCATATCAGCTGCAAGG 60.545 57.143 9.47 8.04 0.00 3.61
1278 1324 0.400381 TCCCTCCCATATCAGCTGCA 60.400 55.000 9.47 0.00 0.00 4.41
1344 1390 6.261603 CCTCAAGCATGTTAAAGCTGATCATA 59.738 38.462 0.00 0.00 41.70 2.15
1372 1418 5.249393 ACCTCTTGACACCATTGATTCTACT 59.751 40.000 0.00 0.00 0.00 2.57
1445 1491 5.512232 GCAGTTAGCATCTTATAGCTTCCCT 60.512 44.000 0.00 0.00 44.79 4.20
1725 1776 4.419282 CCTATATGGGCCCATTTGAATGT 58.581 43.478 41.49 19.24 37.82 2.71
1795 1846 3.472652 ACGCCAATGTAACAAAGAGTCA 58.527 40.909 0.00 0.00 0.00 3.41
1979 2032 9.730705 ATATTCTTCTTTCTTGTGATGAGTTCA 57.269 29.630 0.00 0.00 0.00 3.18
2062 2115 3.181429 TGTTTTCCTTCCTTCCATCTGCT 60.181 43.478 0.00 0.00 0.00 4.24
2104 2157 4.576463 AGTTTCAGTCAGCTGTTAAGGTTG 59.424 41.667 14.67 3.45 43.05 3.77
2144 2197 4.657814 AGAACCTGCAGGAAGGAAATTA 57.342 40.909 39.19 0.00 40.02 1.40
2323 2376 7.938140 AGATAAGGCATTGCAAAAGTTAGTA 57.062 32.000 11.39 0.00 0.00 1.82
2332 2385 4.280819 AGGCTAAAGATAAGGCATTGCAA 58.719 39.130 11.39 0.00 41.75 4.08
2384 2437 1.610038 TGCTTGCACAATTCCTCAGTG 59.390 47.619 0.00 0.00 36.39 3.66
2494 2547 9.933240 AAACACCTAGATACTACTAACTACCAT 57.067 33.333 0.00 0.00 0.00 3.55
2846 2906 9.616156 TCATGCAAAATTTATTCCATGCTAATT 57.384 25.926 10.65 0.00 34.97 1.40
2931 2991 3.758554 TGGAAATCAGAACTAAAGCTGCC 59.241 43.478 0.00 0.00 32.27 4.85
2948 3008 4.464008 ACAACTGATGCTTCTCTTGGAAA 58.536 39.130 0.88 0.00 33.07 3.13
3017 3077 5.687770 TCTCAAATTGCAATTCTGTCGAA 57.312 34.783 24.28 8.55 0.00 3.71
3072 3132 2.998279 GCTTGCTGGGCCATCACAC 61.998 63.158 10.08 1.11 0.00 3.82
3140 3200 9.454859 CAATAGAACTTTTGAGTTTCCTATCCT 57.545 33.333 0.00 0.00 31.35 3.24
3141 3201 8.184848 GCAATAGAACTTTTGAGTTTCCTATCC 58.815 37.037 8.66 0.00 31.35 2.59
3142 3202 8.730680 TGCAATAGAACTTTTGAGTTTCCTATC 58.269 33.333 8.66 0.00 31.35 2.08
3143 3203 8.635765 TGCAATAGAACTTTTGAGTTTCCTAT 57.364 30.769 8.66 0.00 31.35 2.57
3155 3215 8.362639 ACATCACAGAATTTGCAATAGAACTTT 58.637 29.630 0.00 0.00 0.00 2.66
3195 3255 4.541779 GAACACATGTGCGGTATTTTGAA 58.458 39.130 25.68 0.00 0.00 2.69
3205 3265 1.395954 CTCATCAGGAACACATGTGCG 59.604 52.381 25.68 9.31 0.00 5.34
3238 3298 7.601508 CGTAGGATGAGAATGATGATTCAATGA 59.398 37.037 7.67 0.00 40.59 2.57
3300 3360 6.255020 CAGCCATGAAAATAACATTGCTCTTC 59.745 38.462 0.00 0.00 42.16 2.87
3310 3370 9.860898 AATTCTTTAGACAGCCATGAAAATAAC 57.139 29.630 0.00 0.00 0.00 1.89
3312 3372 9.023962 ACAATTCTTTAGACAGCCATGAAAATA 57.976 29.630 0.00 0.00 0.00 1.40
3318 3378 7.951530 AAAAACAATTCTTTAGACAGCCATG 57.048 32.000 0.00 0.00 0.00 3.66
3603 3663 6.225981 TGAGCATCTGTATATGTGTGACTT 57.774 37.500 0.00 0.00 34.92 3.01
3655 3715 2.516460 CTGAGCCCATCCTGCAGC 60.516 66.667 8.66 0.00 0.00 5.25
3821 3881 1.774110 TCTCCTTGCCTAGAGCTGAG 58.226 55.000 0.00 2.23 44.23 3.35
3822 3882 2.315176 GATCTCCTTGCCTAGAGCTGA 58.685 52.381 0.00 0.00 44.23 4.26
3909 3970 5.528870 GTTTACAACAGCACAAAAGGCTAT 58.471 37.500 0.00 0.00 40.23 2.97
4037 4098 7.985184 TGGCTCGTAAATATCTCACAAAGTAAT 59.015 33.333 0.00 0.00 0.00 1.89
4214 4275 4.505191 TCGAGAAATTAATAGGAAACGCCG 59.495 41.667 0.00 0.00 43.43 6.46
4265 4326 2.039879 ACCAAATAAAGACGGTCAGCCT 59.960 45.455 11.27 0.00 0.00 4.58
4294 4355 5.500645 AAGAAAAAGAGAACAAGGAACCG 57.499 39.130 0.00 0.00 0.00 4.44
4299 4360 8.763049 AAGAAACAAAGAAAAAGAGAACAAGG 57.237 30.769 0.00 0.00 0.00 3.61
4372 4434 2.791383 AAAAGCTGCGCACATGTTTA 57.209 40.000 5.66 0.00 0.00 2.01
4383 4445 3.317150 AGCCACGAATTTTAAAAGCTGC 58.683 40.909 6.79 0.00 0.00 5.25
4509 4571 8.493787 AAGGTAGTAGGGATGAACTATTTAGG 57.506 38.462 0.00 0.00 0.00 2.69
4550 5096 3.613030 TGATGATGATGTGGACACCTTG 58.387 45.455 0.00 0.00 0.00 3.61
4566 5112 7.365028 GGTGGAGAATATATATGTGGCTGATGA 60.365 40.741 0.00 0.00 0.00 2.92
4571 5117 6.702449 TTGGTGGAGAATATATATGTGGCT 57.298 37.500 0.00 0.00 0.00 4.75
4572 5118 5.355350 GCTTGGTGGAGAATATATATGTGGC 59.645 44.000 0.00 0.00 0.00 5.01
4573 5119 6.475504 TGCTTGGTGGAGAATATATATGTGG 58.524 40.000 0.00 0.00 0.00 4.17
4575 5121 7.121759 GCATTGCTTGGTGGAGAATATATATGT 59.878 37.037 0.16 0.00 0.00 2.29
4576 5122 7.478322 GCATTGCTTGGTGGAGAATATATATG 58.522 38.462 0.16 0.00 0.00 1.78
4577 5123 6.317140 CGCATTGCTTGGTGGAGAATATATAT 59.683 38.462 7.12 0.00 0.00 0.86
4578 5124 5.643348 CGCATTGCTTGGTGGAGAATATATA 59.357 40.000 7.12 0.00 0.00 0.86
4579 5125 4.456911 CGCATTGCTTGGTGGAGAATATAT 59.543 41.667 7.12 0.00 0.00 0.86
4580 5126 3.814842 CGCATTGCTTGGTGGAGAATATA 59.185 43.478 7.12 0.00 0.00 0.86
4636 5184 1.694844 TGCATGGCAGTTATGATGGG 58.305 50.000 0.00 0.00 33.32 4.00
4673 7270 5.924254 TGCGGTATAAATAAGACTGGAATCG 59.076 40.000 0.00 0.00 0.00 3.34
4682 7279 5.005971 GCTTCGTTGTGCGGTATAAATAAGA 59.994 40.000 0.00 0.00 41.72 2.10
4694 7291 1.154225 GATTGGGCTTCGTTGTGCG 60.154 57.895 0.00 0.00 43.01 5.34
4724 7321 5.475564 TGGTTTCAATTAACTAGTTGCTCCC 59.524 40.000 18.56 7.50 0.00 4.30
4725 7322 6.206829 AGTGGTTTCAATTAACTAGTTGCTCC 59.793 38.462 18.56 9.18 0.00 4.70
4726 7323 7.203255 AGTGGTTTCAATTAACTAGTTGCTC 57.797 36.000 18.56 0.70 0.00 4.26
4727 7324 8.685838 TTAGTGGTTTCAATTAACTAGTTGCT 57.314 30.769 18.56 2.19 0.00 3.91
4728 7325 9.908152 AATTAGTGGTTTCAATTAACTAGTTGC 57.092 29.630 18.56 0.00 0.00 4.17
4738 7335 9.588096 AGAACTCCTTAATTAGTGGTTTCAATT 57.412 29.630 16.32 0.00 0.00 2.32
4739 7336 9.232473 GAGAACTCCTTAATTAGTGGTTTCAAT 57.768 33.333 16.32 0.00 0.00 2.57
4740 7337 7.386848 CGAGAACTCCTTAATTAGTGGTTTCAA 59.613 37.037 16.32 0.00 0.00 2.69
4741 7338 6.872020 CGAGAACTCCTTAATTAGTGGTTTCA 59.128 38.462 16.32 0.00 0.00 2.69
4742 7339 6.872547 ACGAGAACTCCTTAATTAGTGGTTTC 59.127 38.462 0.00 9.34 0.00 2.78
4743 7340 6.766429 ACGAGAACTCCTTAATTAGTGGTTT 58.234 36.000 0.00 2.91 0.00 3.27
4744 7341 6.356186 ACGAGAACTCCTTAATTAGTGGTT 57.644 37.500 0.00 2.23 0.00 3.67
4745 7342 5.997384 ACGAGAACTCCTTAATTAGTGGT 57.003 39.130 0.00 0.00 0.00 4.16
4746 7343 5.063564 GCAACGAGAACTCCTTAATTAGTGG 59.936 44.000 0.00 1.45 0.00 4.00
4747 7344 5.637810 TGCAACGAGAACTCCTTAATTAGTG 59.362 40.000 0.00 0.00 0.00 2.74
4748 7345 5.790593 TGCAACGAGAACTCCTTAATTAGT 58.209 37.500 0.00 0.00 0.00 2.24
4749 7346 6.721571 TTGCAACGAGAACTCCTTAATTAG 57.278 37.500 0.00 0.00 0.00 1.73
4750 7347 7.499321 TTTTGCAACGAGAACTCCTTAATTA 57.501 32.000 0.00 0.00 0.00 1.40
4751 7348 6.385649 TTTTGCAACGAGAACTCCTTAATT 57.614 33.333 0.00 0.00 0.00 1.40
4752 7349 6.385649 TTTTTGCAACGAGAACTCCTTAAT 57.614 33.333 0.00 0.00 0.00 1.40
4753 7350 5.821516 TTTTTGCAACGAGAACTCCTTAA 57.178 34.783 0.00 0.00 0.00 1.85
4772 7369 4.529897 ACCCGGAAAAGTAGAGTGTTTTT 58.470 39.130 0.73 0.00 0.00 1.94
4773 7370 4.132336 GACCCGGAAAAGTAGAGTGTTTT 58.868 43.478 0.73 0.00 0.00 2.43
4774 7371 3.736720 GACCCGGAAAAGTAGAGTGTTT 58.263 45.455 0.73 0.00 0.00 2.83
4775 7372 2.288640 CGACCCGGAAAAGTAGAGTGTT 60.289 50.000 0.73 0.00 0.00 3.32
4776 7373 1.271656 CGACCCGGAAAAGTAGAGTGT 59.728 52.381 0.73 0.00 0.00 3.55
4777 7374 1.992170 CGACCCGGAAAAGTAGAGTG 58.008 55.000 0.73 0.00 0.00 3.51
4778 7375 0.245813 GCGACCCGGAAAAGTAGAGT 59.754 55.000 0.73 0.00 0.00 3.24
4779 7376 0.801067 CGCGACCCGGAAAAGTAGAG 60.801 60.000 0.73 0.00 0.00 2.43
4780 7377 1.213537 CGCGACCCGGAAAAGTAGA 59.786 57.895 0.73 0.00 0.00 2.59
4781 7378 1.074872 GTCGCGACCCGGAAAAGTAG 61.075 60.000 28.61 0.00 37.59 2.57
4782 7379 1.080569 GTCGCGACCCGGAAAAGTA 60.081 57.895 28.61 0.00 37.59 2.24
4783 7380 2.356673 GTCGCGACCCGGAAAAGT 60.357 61.111 28.61 0.00 37.59 2.66
4784 7381 1.500512 TTTGTCGCGACCCGGAAAAG 61.501 55.000 34.34 0.00 37.59 2.27
4785 7382 0.885596 ATTTGTCGCGACCCGGAAAA 60.886 50.000 34.34 26.27 37.59 2.29
4786 7383 1.301874 ATTTGTCGCGACCCGGAAA 60.302 52.632 34.34 26.61 37.59 3.13
4787 7384 2.030401 CATTTGTCGCGACCCGGAA 61.030 57.895 34.34 22.89 37.59 4.30
4788 7385 2.433491 CATTTGTCGCGACCCGGA 60.433 61.111 34.34 18.36 37.59 5.14
4789 7386 3.496131 CCATTTGTCGCGACCCGG 61.496 66.667 34.34 24.10 37.59 5.73
4790 7387 4.160635 GCCATTTGTCGCGACCCG 62.161 66.667 34.34 19.68 38.61 5.28
4797 7394 2.153945 GCATGTGCGCCATTTGTCG 61.154 57.895 4.18 0.00 0.00 4.35
4798 7395 1.074319 CTGCATGTGCGCCATTTGTC 61.074 55.000 4.18 0.00 45.83 3.18
4799 7396 1.080366 CTGCATGTGCGCCATTTGT 60.080 52.632 4.18 0.00 45.83 2.83
4800 7397 3.775314 CTGCATGTGCGCCATTTG 58.225 55.556 4.18 0.00 45.83 2.32


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

AutoCloner maintained by Alex Coulton.