Multiple sequence alignment - TraesCS4D01G173800

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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 TraesCS4D01G173800 chr4D 100.000 4387 0 0 2223 6609 301730391 301734777 0.000000e+00 8102.0
1 TraesCS4D01G173800 chr4D 100.000 1949 0 0 1 1949 301728169 301730117 0.000000e+00 3600.0
2 TraesCS4D01G173800 chr4D 94.982 837 35 6 1 833 408574305 408575138 0.000000e+00 1306.0
3 TraesCS4D01G173800 chr4D 93.309 837 48 6 4 834 485688368 485687534 0.000000e+00 1229.0
4 TraesCS4D01G173800 chr4D 91.358 81 6 1 3256 3335 50156044 50156124 7.010000e-20 110.0
5 TraesCS4D01G173800 chr4B 93.752 3697 130 50 2974 6609 376137772 376141428 0.000000e+00 5454.0
6 TraesCS4D01G173800 chr4B 89.692 1135 43 14 834 1937 376135309 376136400 0.000000e+00 1380.0
7 TraesCS4D01G173800 chr4B 95.376 757 31 4 2231 2985 376136401 376137155 0.000000e+00 1201.0
8 TraesCS4D01G173800 chr4A 96.157 2758 82 15 2247 4993 179145003 179142259 0.000000e+00 4484.0
9 TraesCS4D01G173800 chr4A 94.671 1126 34 8 841 1944 179146122 179145001 0.000000e+00 1724.0
10 TraesCS4D01G173800 chr4A 90.122 1063 55 15 5202 6245 179142262 179141231 0.000000e+00 1336.0
11 TraesCS4D01G173800 chr4A 88.754 907 53 19 5741 6609 179141742 179140847 0.000000e+00 1064.0
12 TraesCS4D01G173800 chrUn 93.810 840 46 5 1 836 46214487 46213650 0.000000e+00 1258.0
13 TraesCS4D01G173800 chr2D 93.787 837 43 8 1 833 275778196 275779027 0.000000e+00 1249.0
14 TraesCS4D01G173800 chr2D 91.866 836 51 10 1 834 562806238 562807058 0.000000e+00 1151.0
15 TraesCS4D01G173800 chr2D 86.022 93 11 2 3252 3342 383812738 383812646 1.520000e-16 99.0
16 TraesCS4D01G173800 chr1D 92.575 835 48 11 1 831 241263252 241264076 0.000000e+00 1186.0
17 TraesCS4D01G173800 chr3D 91.856 835 51 9 1 831 473752816 473753637 0.000000e+00 1149.0
18 TraesCS4D01G173800 chr3D 90.952 840 59 11 1 835 290031769 290032596 0.000000e+00 1114.0
19 TraesCS4D01G173800 chr3D 87.342 79 9 1 2730 2807 469158978 469159056 9.130000e-14 89.8
20 TraesCS4D01G173800 chr6A 90.573 838 65 9 1 833 39455657 39456485 0.000000e+00 1098.0
21 TraesCS4D01G173800 chr5A 89.655 87 8 1 3251 3336 59700797 59700883 7.010000e-20 110.0
22 TraesCS4D01G173800 chr5A 90.476 84 7 1 3252 3334 427829078 427829161 7.010000e-20 110.0
23 TraesCS4D01G173800 chr6B 90.123 81 7 1 3256 3335 40678309 40678229 3.260000e-18 104.0
24 TraesCS4D01G173800 chr2B 87.209 86 10 1 3252 3336 691462324 691462409 5.450000e-16 97.1
25 TraesCS4D01G173800 chr5B 85.263 95 11 3 3249 3341 179505180 179505087 1.960000e-15 95.3
26 TraesCS4D01G173800 chr5B 88.636 44 5 0 2434 2477 531407979 531408022 3.000000e-03 54.7
27 TraesCS4D01G173800 chr3A 88.608 79 8 1 2728 2805 611706263 611706341 1.960000e-15 95.3
28 TraesCS4D01G173800 chr3B 87.654 81 9 1 2728 2807 623154512 623154592 7.060000e-15 93.5
29 TraesCS4D01G173800 chr3B 89.130 46 5 0 2432 2477 448908820 448908775 2.570000e-04 58.4


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 TraesCS4D01G173800 chr4D 301728169 301734777 6608 False 5851.000000 8102 100.000 1 6609 2 chr4D.!!$F3 6608
1 TraesCS4D01G173800 chr4D 408574305 408575138 833 False 1306.000000 1306 94.982 1 833 1 chr4D.!!$F2 832
2 TraesCS4D01G173800 chr4D 485687534 485688368 834 True 1229.000000 1229 93.309 4 834 1 chr4D.!!$R1 830
3 TraesCS4D01G173800 chr4B 376135309 376141428 6119 False 2678.333333 5454 92.940 834 6609 3 chr4B.!!$F1 5775
4 TraesCS4D01G173800 chr4A 179140847 179146122 5275 True 2152.000000 4484 92.426 841 6609 4 chr4A.!!$R1 5768
5 TraesCS4D01G173800 chrUn 46213650 46214487 837 True 1258.000000 1258 93.810 1 836 1 chrUn.!!$R1 835
6 TraesCS4D01G173800 chr2D 275778196 275779027 831 False 1249.000000 1249 93.787 1 833 1 chr2D.!!$F1 832
7 TraesCS4D01G173800 chr2D 562806238 562807058 820 False 1151.000000 1151 91.866 1 834 1 chr2D.!!$F2 833
8 TraesCS4D01G173800 chr1D 241263252 241264076 824 False 1186.000000 1186 92.575 1 831 1 chr1D.!!$F1 830
9 TraesCS4D01G173800 chr3D 473752816 473753637 821 False 1149.000000 1149 91.856 1 831 1 chr3D.!!$F3 830
10 TraesCS4D01G173800 chr3D 290031769 290032596 827 False 1114.000000 1114 90.952 1 835 1 chr3D.!!$F1 834
11 TraesCS4D01G173800 chr6A 39455657 39456485 828 False 1098.000000 1098 90.573 1 833 1 chr6A.!!$F1 832

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
334 339 0.608640 CAGCTAGAGACCCAAACCGT 59.391 55.000 0.00 0.0 0.0 4.83 F
426 431 1.068895 CATTGAGCACCACTGGCAAAA 59.931 47.619 0.00 0.0 0.0 2.44 F
1886 1943 1.335496 GAGTGATAGACAGGGAGACGC 59.665 57.143 0.00 0.0 0.0 5.19 F
2615 2676 0.036765 CCTAAACCAGCCGCACTACA 60.037 55.000 0.00 0.0 0.0 2.74 F
2958 3025 2.017049 CTCCGTTTTCATGCCTAAGGG 58.983 52.381 0.00 0.0 0.0 3.95 F
4115 4810 2.482296 AAGCGCAGTTCATTGCTGGC 62.482 55.000 11.47 0.0 41.9 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1388 2.040412 CCTCTTAGCAACCAAGGGAAGT 59.960 50.000 0.00 0.00 0.00 3.01 R
2362 2419 0.656785 TGTTTCCGTTTCCGTTTCCG 59.343 50.000 0.00 0.00 0.00 4.30 R
3780 4475 1.206849 TCAAGCGGATGCACATCTGTA 59.793 47.619 18.27 2.69 44.17 2.74 R
4115 4810 1.523758 CCTCGAAAAACCTCCCACAG 58.476 55.000 0.00 0.00 0.00 3.66 R
4668 5364 0.168128 GGCGCACACATGGAGTTAAC 59.832 55.000 10.83 0.00 0.00 2.01 R
6086 6812 0.108585 GACAGCTCCAAGGTGACCAA 59.891 55.000 12.67 0.00 45.98 3.67 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
47 48 3.393278 GGTATATACCCTCCTTGGTGCAA 59.607 47.826 19.76 0.00 40.53 4.08
80 82 5.096443 AGCATCAAAGAACCCAAAACAAA 57.904 34.783 0.00 0.00 0.00 2.83
138 141 4.099419 AGCCCGAAAAGACATTGAAAAAGT 59.901 37.500 0.00 0.00 0.00 2.66
308 313 1.082117 CGACAATGTGGGTAGCCGTC 61.082 60.000 6.45 6.20 0.00 4.79
309 314 1.079405 ACAATGTGGGTAGCCGTCG 60.079 57.895 6.45 0.00 0.00 5.12
334 339 0.608640 CAGCTAGAGACCCAAACCGT 59.391 55.000 0.00 0.00 0.00 4.83
385 390 5.336213 GGAGATTGAAAATGCAGACACACAT 60.336 40.000 0.00 0.00 0.00 3.21
418 423 4.094590 CAGAAAGATCTCATTGAGCACCAC 59.905 45.833 8.89 0.00 32.03 4.16
426 431 1.068895 CATTGAGCACCACTGGCAAAA 59.931 47.619 0.00 0.00 0.00 2.44
568 577 9.248291 GCGGATGATTATTGTTTTATGTTTGAT 57.752 29.630 0.00 0.00 0.00 2.57
606 616 8.487176 AGTTTGTTTTCGATTGTTGAATTATGC 58.513 29.630 0.00 0.00 0.00 3.14
715 727 6.747659 ATTTCGCGAATATGCATTTTTACC 57.252 33.333 24.05 0.00 34.15 2.85
721 733 5.561919 GCGAATATGCATTTTTACCGATCCA 60.562 40.000 3.54 0.00 34.15 3.41
725 737 9.906660 GAATATGCATTTTTACCGATCCATTTA 57.093 29.630 3.54 0.00 0.00 1.40
753 765 3.005539 ATCTGTGCCAGCCCGAGT 61.006 61.111 0.00 0.00 0.00 4.18
766 778 1.374505 CCGAGTCGGCCCGTAAAAA 60.375 57.895 20.50 0.00 41.17 1.94
776 788 2.541556 GCCCGTAAAAACTGTTTTGCA 58.458 42.857 18.33 7.70 38.75 4.08
925 944 1.369625 GCTCACCAATTGACGGGTAG 58.630 55.000 7.12 0.00 35.09 3.18
1105 1125 4.161565 TGCCTACCTGTACGAATCTTGAAT 59.838 41.667 0.00 0.00 0.00 2.57
1114 1134 6.166279 TGTACGAATCTTGAATCTTGCTTCT 58.834 36.000 0.00 0.00 0.00 2.85
1115 1135 6.650807 TGTACGAATCTTGAATCTTGCTTCTT 59.349 34.615 0.00 0.00 0.00 2.52
1118 1138 7.080724 ACGAATCTTGAATCTTGCTTCTTTTC 58.919 34.615 0.00 0.00 0.00 2.29
1345 1386 5.482908 CAGCCTAGTAATTCATCGGCTTAT 58.517 41.667 8.13 0.00 44.90 1.73
1346 1387 5.934625 CAGCCTAGTAATTCATCGGCTTATT 59.065 40.000 8.13 0.00 44.90 1.40
1347 1388 7.097192 CAGCCTAGTAATTCATCGGCTTATTA 58.903 38.462 8.13 0.00 44.90 0.98
1361 1403 3.130516 GGCTTATTACTTCCCTTGGTTGC 59.869 47.826 0.00 0.00 0.00 4.17
1825 1882 2.894126 TCTCTTTCGCTTCTCCTCAAGT 59.106 45.455 0.00 0.00 0.00 3.16
1886 1943 1.335496 GAGTGATAGACAGGGAGACGC 59.665 57.143 0.00 0.00 0.00 5.19
1941 1998 2.743718 CTCTGTCAACCCCGTGCT 59.256 61.111 0.00 0.00 0.00 4.40
1942 1999 1.669115 CTCTGTCAACCCCGTGCTG 60.669 63.158 0.00 0.00 0.00 4.41
1943 2000 2.111043 CTGTCAACCCCGTGCTGT 59.889 61.111 0.00 0.00 0.00 4.40
1944 2001 1.525995 CTGTCAACCCCGTGCTGTT 60.526 57.895 0.00 0.00 0.00 3.16
1945 2002 1.785041 CTGTCAACCCCGTGCTGTTG 61.785 60.000 0.00 0.00 42.46 3.33
1946 2003 2.904866 TCAACCCCGTGCTGTTGC 60.905 61.111 0.00 0.00 41.21 4.17
1947 2004 2.906897 CAACCCCGTGCTGTTGCT 60.907 61.111 0.00 0.00 40.48 3.91
1948 2005 2.906897 AACCCCGTGCTGTTGCTG 60.907 61.111 0.00 0.00 40.48 4.41
2282 2339 1.917872 TGTAAACATTCTGCCCCCAC 58.082 50.000 0.00 0.00 0.00 4.61
2357 2414 7.026631 CCCCCTGAAAATTCAAAAAGAAAAC 57.973 36.000 0.00 0.00 40.22 2.43
2360 2417 8.518702 CCCCTGAAAATTCAAAAAGAAAACAAA 58.481 29.630 0.00 0.00 40.22 2.83
2361 2418 9.558648 CCCTGAAAATTCAAAAAGAAAACAAAG 57.441 29.630 0.00 0.00 40.22 2.77
2362 2419 9.064804 CCTGAAAATTCAAAAAGAAAACAAAGC 57.935 29.630 0.00 0.00 40.22 3.51
2366 2423 6.976636 ATTCAAAAAGAAAACAAAGCGGAA 57.023 29.167 0.00 0.00 40.22 4.30
2367 2424 6.787085 TTCAAAAAGAAAACAAAGCGGAAA 57.213 29.167 0.00 0.00 32.05 3.13
2478 2538 1.223187 GGTAATGAATACGGTGCGGG 58.777 55.000 0.00 0.00 35.19 6.13
2492 2552 0.179070 TGCGGGCGCTGATACAAATA 60.179 50.000 7.64 0.00 42.51 1.40
2519 2580 1.356527 CGCCGGAACTAAAAGACCCG 61.357 60.000 5.05 0.00 39.85 5.28
2587 2648 8.932791 CCAGTTTATATGACTACAACGTCTTTT 58.067 33.333 0.00 0.00 35.00 2.27
2615 2676 0.036765 CCTAAACCAGCCGCACTACA 60.037 55.000 0.00 0.00 0.00 2.74
2641 2702 2.031012 CCTGGACAGTGCAGCGAA 59.969 61.111 16.46 0.00 34.22 4.70
2701 2762 5.494724 AGTGACACGTATAAGGAGACTACA 58.505 41.667 0.00 0.00 42.68 2.74
2881 2947 6.597832 TTCCGTTTCCATTCCACAATATTT 57.402 33.333 0.00 0.00 0.00 1.40
2887 2953 7.751348 CGTTTCCATTCCACAATATTTCGTTTA 59.249 33.333 0.00 0.00 0.00 2.01
2950 3017 4.537015 GAAGTTTCCACTCCGTTTTCATG 58.463 43.478 0.00 0.00 30.45 3.07
2958 3025 2.017049 CTCCGTTTTCATGCCTAAGGG 58.983 52.381 0.00 0.00 0.00 3.95
3026 3721 8.933807 CGATTCATTAGCAATCATGTAGAGAAT 58.066 33.333 0.00 0.00 31.53 2.40
3141 3836 8.267894 ACTGAATATGCAGTCTAAGTAATTGGT 58.732 33.333 10.87 0.00 45.54 3.67
3153 3848 9.391006 GTCTAAGTAATTGGTGTATTCCATTCA 57.609 33.333 0.00 0.00 37.33 2.57
3242 3937 4.547671 AGCTATCTGGCAGTAGGTAGAAA 58.452 43.478 19.89 0.00 34.03 2.52
3324 4019 8.458573 TGCAAAAACATCTTATATTACGGGAT 57.541 30.769 0.00 0.00 0.00 3.85
3422 4117 8.749354 TCATATGTGCTATAATCGTCAGGTATT 58.251 33.333 1.90 0.00 0.00 1.89
3842 4537 6.017400 AGCACAACTACTTCATGGATTTTG 57.983 37.500 0.00 0.00 0.00 2.44
3936 4631 4.028993 TCTTGATTTGGTGGTCCTTACC 57.971 45.455 0.00 0.00 46.98 2.85
3937 4632 2.891191 TGATTTGGTGGTCCTTACCC 57.109 50.000 0.00 0.00 46.16 3.69
4115 4810 2.482296 AAGCGCAGTTCATTGCTGGC 62.482 55.000 11.47 0.00 41.90 4.85
4519 5215 6.690194 ACATGAATTCTGAATGAGGTTAGC 57.310 37.500 7.05 0.00 0.00 3.09
4667 5363 3.299503 ACATCCTGAAAACACCTTTGCT 58.700 40.909 0.00 0.00 0.00 3.91
4668 5364 3.068590 ACATCCTGAAAACACCTTTGCTG 59.931 43.478 0.00 0.00 0.00 4.41
5021 5717 7.145985 TGATACCATCTTCTGTAATTCGTAGC 58.854 38.462 0.00 0.00 0.00 3.58
5046 5742 6.237490 CGCCAGTTTTAGATAGTAACTTGTCG 60.237 42.308 0.00 0.00 30.08 4.35
5065 5761 5.168569 TGTCGCCTCACAAATAAGAACTAG 58.831 41.667 0.00 0.00 0.00 2.57
5140 5836 6.266323 GTTTCTTTTCTTCCTCACCAGTTTC 58.734 40.000 0.00 0.00 0.00 2.78
5166 5862 5.563671 GCTCATCTGGTCTCTTTGGTTTTTC 60.564 44.000 0.00 0.00 0.00 2.29
5167 5863 4.827284 TCATCTGGTCTCTTTGGTTTTTCC 59.173 41.667 0.00 0.00 0.00 3.13
5177 5873 2.969628 TGGTTTTTCCGTTGCATTGT 57.030 40.000 0.00 0.00 39.52 2.71
5423 6119 4.331108 TGGCTGATGCAGTAATTGTTACA 58.669 39.130 0.00 0.00 41.91 2.41
5481 6187 4.692625 AGAGCTACGTACGTGTTAAGAAGA 59.307 41.667 30.25 6.36 0.00 2.87
5546 6252 5.363939 GAGTCCAGTCTGCTAATATGCTTT 58.636 41.667 0.00 0.00 0.00 3.51
5617 6323 8.279800 GGTATGTTATTTCTTGGCAAAACAAAC 58.720 33.333 15.86 10.44 31.33 2.93
5623 6329 7.865875 ATTTCTTGGCAAAACAAACAAAAAC 57.134 28.000 0.00 0.00 0.00 2.43
5682 6390 3.409026 AGTCTGTGATGGTTGGAACTC 57.591 47.619 0.00 0.00 0.00 3.01
5696 6404 5.393027 GGTTGGAACTCGCATACATTTGATT 60.393 40.000 0.00 0.00 0.00 2.57
5709 6417 5.490139 ACATTTGATTATGAGCAACCTCG 57.510 39.130 0.00 0.00 41.13 4.63
5711 6419 3.627395 TTGATTATGAGCAACCTCGGT 57.373 42.857 0.00 0.00 41.13 4.69
5712 6420 2.905075 TGATTATGAGCAACCTCGGTG 58.095 47.619 0.00 0.00 41.13 4.94
5713 6421 1.599542 GATTATGAGCAACCTCGGTGC 59.400 52.381 0.00 0.00 41.13 5.01
5714 6422 0.613260 TTATGAGCAACCTCGGTGCT 59.387 50.000 3.33 3.33 41.13 4.40
5715 6423 1.480789 TATGAGCAACCTCGGTGCTA 58.519 50.000 3.76 0.00 41.13 3.49
5716 6424 0.176680 ATGAGCAACCTCGGTGCTAG 59.823 55.000 3.76 0.00 41.13 3.42
5717 6425 1.185618 TGAGCAACCTCGGTGCTAGT 61.186 55.000 3.76 0.00 41.13 2.57
5718 6426 0.037232 GAGCAACCTCGGTGCTAGTT 60.037 55.000 3.76 0.00 39.21 2.24
5719 6427 0.320771 AGCAACCTCGGTGCTAGTTG 60.321 55.000 1.49 0.00 41.94 3.16
5720 6428 2.162716 CAACCTCGGTGCTAGTTGC 58.837 57.895 0.00 0.00 43.25 4.17
5815 6527 5.552870 AATACTATCATTTCCCGCTGACT 57.447 39.130 0.00 0.00 0.00 3.41
5836 6548 3.627395 TTGAGCGATACAATGGGAGTT 57.373 42.857 0.00 0.00 0.00 3.01
5908 6628 4.398044 GTCCTTCATTCTCGTCTCTTCTCT 59.602 45.833 0.00 0.00 0.00 3.10
5929 6649 3.165875 TCCAGGAGATTTCGACTTCACT 58.834 45.455 0.00 0.00 0.00 3.41
5930 6650 3.056536 TCCAGGAGATTTCGACTTCACTG 60.057 47.826 0.00 0.00 0.00 3.66
5944 6664 3.872603 ACTGTGAACGGCTGGGCA 61.873 61.111 0.00 0.00 0.00 5.36
5951 6671 3.259633 AACGGCTGGGCAGAAGAGG 62.260 63.158 0.00 0.00 0.00 3.69
6019 6742 0.953471 CGAATGGTCCGAAAGTGGCA 60.953 55.000 0.00 0.00 0.00 4.92
6022 6745 3.423154 GGTCCGAAAGTGGCAGCG 61.423 66.667 0.00 0.00 0.00 5.18
6060 6783 2.816958 CTGCGGCGCTTCTGTGAT 60.817 61.111 33.26 0.00 0.00 3.06
6076 6802 0.605319 TGATGGTGACCTTTGCGTCC 60.605 55.000 2.11 0.00 31.35 4.79
6078 6804 0.110486 ATGGTGACCTTTGCGTCCTT 59.890 50.000 2.11 0.00 31.35 3.36
6082 6808 1.896660 GACCTTTGCGTCCTTGGCA 60.897 57.895 0.00 0.00 38.93 4.92
6086 6812 1.799258 CTTTGCGTCCTTGGCAGCTT 61.799 55.000 0.00 0.00 42.12 3.74
6111 6837 0.178921 ACCTTGGAGCTGTCCTCAGA 60.179 55.000 0.00 0.00 44.30 3.27
6172 6898 3.589881 GGCGTGCCCATCAGCATC 61.590 66.667 0.00 0.00 46.24 3.91
6197 6923 3.343788 CTGAGCAGGTCGTCCGTCC 62.344 68.421 0.00 0.00 39.05 4.79
6304 7057 1.706443 CGAAACCGTTCCAGTAGGAC 58.294 55.000 0.00 0.00 45.73 3.85
6462 7215 2.758736 TGTTGCTGCACCAAAACTTT 57.241 40.000 0.00 0.00 0.00 2.66
6472 7225 3.684305 GCACCAAAACTTTGCTTCAGTTT 59.316 39.130 3.50 3.50 44.67 2.66
6477 7230 3.420839 AACTTTGCTTCAGTTTCCACG 57.579 42.857 0.00 0.00 29.75 4.94
6478 7231 1.065551 ACTTTGCTTCAGTTTCCACGC 59.934 47.619 0.00 0.00 0.00 5.34
6479 7232 1.065401 CTTTGCTTCAGTTTCCACGCA 59.935 47.619 0.00 0.00 0.00 5.24
6480 7233 0.380378 TTGCTTCAGTTTCCACGCAC 59.620 50.000 0.00 0.00 0.00 5.34
6481 7234 0.746204 TGCTTCAGTTTCCACGCACA 60.746 50.000 0.00 0.00 0.00 4.57
6482 7235 0.317020 GCTTCAGTTTCCACGCACAC 60.317 55.000 0.00 0.00 0.00 3.82
6484 7237 2.042520 TTCAGTTTCCACGCACACGC 62.043 55.000 0.00 0.00 45.53 5.34
6485 7238 2.512745 AGTTTCCACGCACACGCA 60.513 55.556 0.00 0.00 45.53 5.24
6486 7239 1.891919 AGTTTCCACGCACACGCAT 60.892 52.632 0.00 0.00 45.53 4.73
6511 7264 7.389232 TGCATCCATGATTGTTACTCCTATAG 58.611 38.462 0.00 0.00 0.00 1.31
6513 7266 7.880195 GCATCCATGATTGTTACTCCTATAGTT 59.120 37.037 0.00 0.00 39.80 2.24
6517 7270 8.642432 CCATGATTGTTACTCCTATAGTTGAGA 58.358 37.037 11.63 0.00 39.80 3.27
6518 7271 9.689976 CATGATTGTTACTCCTATAGTTGAGAG 57.310 37.037 11.63 7.40 39.80 3.20
6519 7272 8.239038 TGATTGTTACTCCTATAGTTGAGAGG 57.761 38.462 11.63 0.00 39.80 3.69
6522 7275 6.195700 TGTTACTCCTATAGTTGAGAGGCTT 58.804 40.000 11.63 0.00 39.80 4.35
6523 7276 6.668283 TGTTACTCCTATAGTTGAGAGGCTTT 59.332 38.462 11.63 0.00 39.80 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 6.218746 GGTTCTTTGATGCTCTTGACAAATT 58.781 36.000 0.00 0.00 33.01 1.82
138 141 5.250200 ACCTAGATTGCAAAACACCGAATA 58.750 37.500 1.71 0.00 0.00 1.75
166 169 0.535335 GAGCAGGACCACGGACAATA 59.465 55.000 0.00 0.00 0.00 1.90
283 288 3.502979 GGCTACCCACATTGTCGTAAAAA 59.497 43.478 0.00 0.00 0.00 1.94
308 313 0.741221 GGGTCTCTAGCTGGTTTGCG 60.741 60.000 0.00 0.00 38.13 4.85
309 314 0.324943 TGGGTCTCTAGCTGGTTTGC 59.675 55.000 0.00 0.00 0.00 3.68
385 390 9.123902 TCAATGAGATCTTTCTGAAGTTGAAAA 57.876 29.630 0.00 0.00 33.70 2.29
418 423 0.825010 ACTGTCCAGCCTTTTGCCAG 60.825 55.000 0.00 0.00 42.71 4.85
426 431 4.373156 AAAATTAGTCACTGTCCAGCCT 57.627 40.909 0.00 0.00 0.00 4.58
606 616 2.001872 GCCCGCAAAAATCAAATCCAG 58.998 47.619 0.00 0.00 0.00 3.86
707 719 5.144832 CCCCCTAAATGGATCGGTAAAAAT 58.855 41.667 0.00 0.00 38.35 1.82
715 727 1.543429 GCAGACCCCCTAAATGGATCG 60.543 57.143 0.00 0.00 38.35 3.69
721 733 2.092212 CACAGATGCAGACCCCCTAAAT 60.092 50.000 0.00 0.00 0.00 1.40
725 737 3.408229 CACAGATGCAGACCCCCT 58.592 61.111 0.00 0.00 0.00 4.79
753 765 1.677942 AAACAGTTTTTACGGGCCGA 58.322 45.000 35.78 13.93 0.00 5.54
776 788 0.865639 GCAAAACGCTTGCAGTTCGT 60.866 50.000 15.79 4.50 44.34 3.85
907 925 2.496070 TCTCTACCCGTCAATTGGTGAG 59.504 50.000 5.42 5.88 36.74 3.51
1105 1125 4.823989 AGCTAAGCAAGAAAAGAAGCAAGA 59.176 37.500 0.00 0.00 0.00 3.02
1345 1386 4.263331 CCTCTTAGCAACCAAGGGAAGTAA 60.263 45.833 0.00 0.00 0.00 2.24
1346 1387 3.263425 CCTCTTAGCAACCAAGGGAAGTA 59.737 47.826 0.00 0.00 0.00 2.24
1347 1388 2.040412 CCTCTTAGCAACCAAGGGAAGT 59.960 50.000 0.00 0.00 0.00 3.01
1361 1403 5.202004 TCTAGAAAGTAGTGGCCCTCTTAG 58.798 45.833 0.00 0.00 0.00 2.18
1503 1549 8.306761 GCTTTATCTTTCCTTTTCCATTTCTCA 58.693 33.333 0.00 0.00 0.00 3.27
1705 1751 3.663815 ATGGCCGGAGAGACGTCCT 62.664 63.158 13.01 9.18 34.00 3.85
1886 1943 2.278206 CGATCAGCCACGAGTCGG 60.278 66.667 18.30 5.77 0.00 4.79
2228 2285 4.723309 AGACAACAGGCAGAGAGATTTTT 58.277 39.130 0.00 0.00 0.00 1.94
2229 2286 4.041444 AGAGACAACAGGCAGAGAGATTTT 59.959 41.667 0.00 0.00 0.00 1.82
2352 2409 2.478547 TCCGTTTCCGCTTTGTTTTC 57.521 45.000 0.00 0.00 0.00 2.29
2357 2414 0.659123 CCGTTTCCGTTTCCGCTTTG 60.659 55.000 0.00 0.00 0.00 2.77
2360 2417 0.814812 TTTCCGTTTCCGTTTCCGCT 60.815 50.000 0.00 0.00 0.00 5.52
2361 2418 0.658244 GTTTCCGTTTCCGTTTCCGC 60.658 55.000 0.00 0.00 0.00 5.54
2362 2419 0.656785 TGTTTCCGTTTCCGTTTCCG 59.343 50.000 0.00 0.00 0.00 4.30
2366 2423 1.937899 CTGTCTGTTTCCGTTTCCGTT 59.062 47.619 0.00 0.00 0.00 4.44
2367 2424 1.137479 TCTGTCTGTTTCCGTTTCCGT 59.863 47.619 0.00 0.00 0.00 4.69
2478 2538 5.599715 CGAACATAGTATTTGTATCAGCGC 58.400 41.667 0.00 0.00 0.00 5.92
2519 2580 5.918387 TGTGTTTTTCGAAATCGTTCAAC 57.082 34.783 12.12 12.03 40.80 3.18
2587 2648 2.103094 CGGCTGGTTTAGGAGATCATCA 59.897 50.000 0.00 0.00 0.00 3.07
2615 2676 3.790437 CTGTCCAGGCGCCTCCAT 61.790 66.667 30.29 1.77 37.29 3.41
2641 2702 0.692419 CTACACCCTCCTGCCCATCT 60.692 60.000 0.00 0.00 0.00 2.90
2701 2762 6.859112 ACATCCAGATCGCTAATACCTAAT 57.141 37.500 0.00 0.00 0.00 1.73
2881 2947 6.529125 GTGATGGAGAAGAAATACGTAAACGA 59.471 38.462 9.86 0.00 43.02 3.85
2887 2953 3.194968 ACGGTGATGGAGAAGAAATACGT 59.805 43.478 0.00 0.00 0.00 3.57
2950 3017 6.189036 ACTAATATTCTGTTCCCCTTAGGC 57.811 41.667 0.00 0.00 34.51 3.93
3141 3836 6.710295 GCCACATGTAGTATGAATGGAATACA 59.290 38.462 0.00 0.00 33.70 2.29
3153 3848 7.494211 TGTATTAGAAACGCCACATGTAGTAT 58.506 34.615 0.00 0.00 0.00 2.12
3242 3937 3.963374 GGACGAAGGGGGTACTACTTATT 59.037 47.826 0.00 0.00 0.00 1.40
3319 4014 2.350057 TGAGTACTCTCTCCATCCCG 57.650 55.000 23.01 0.00 40.98 5.14
3324 4019 5.204292 AGCACATATTGAGTACTCTCTCCA 58.796 41.667 23.01 0.51 40.98 3.86
3373 4068 6.767902 TGAAGTAAATCATCATTACCAGCTCC 59.232 38.462 0.00 0.00 34.50 4.70
3422 4117 3.437741 CAGCTCACTACATGATTGCAACA 59.562 43.478 0.00 2.38 36.48 3.33
3606 4301 2.223947 TGGCGTATGTAGGCACAGTATG 60.224 50.000 6.99 0.00 38.30 2.39
3780 4475 1.206849 TCAAGCGGATGCACATCTGTA 59.793 47.619 18.27 2.69 44.17 2.74
3842 4537 8.438676 ACACCATTCAAATCAGTAATACTAGC 57.561 34.615 0.00 0.00 0.00 3.42
4115 4810 1.523758 CCTCGAAAAACCTCCCACAG 58.476 55.000 0.00 0.00 0.00 3.66
4325 5020 3.754323 AGAAACACACAGAACCGAACAAA 59.246 39.130 0.00 0.00 0.00 2.83
4667 5363 0.871722 GCGCACACATGGAGTTAACA 59.128 50.000 8.61 0.00 0.00 2.41
4668 5364 0.168128 GGCGCACACATGGAGTTAAC 59.832 55.000 10.83 0.00 0.00 2.01
4913 5609 4.393062 ACGCATGAAGGTGTTTATCTCAAG 59.607 41.667 0.00 0.00 0.00 3.02
5021 5717 6.237490 CGACAAGTTACTATCTAAAACTGGCG 60.237 42.308 0.00 0.00 33.85 5.69
5046 5742 4.695455 TGTGCTAGTTCTTATTTGTGAGGC 59.305 41.667 0.00 0.00 0.00 4.70
5065 5761 5.877012 TGAAATTAAGAGACTCCTGATGTGC 59.123 40.000 0.00 0.00 0.00 4.57
5140 5836 2.027377 ACCAAAGAGACCAGATGAGCAG 60.027 50.000 0.00 0.00 0.00 4.24
5166 5862 1.464023 CGCAAGAGTACAATGCAACGG 60.464 52.381 15.02 0.00 40.04 4.44
5167 5863 1.869503 CGCAAGAGTACAATGCAACG 58.130 50.000 15.02 0.00 40.04 4.10
5177 5873 1.135139 GTCTGAGATGGCGCAAGAGTA 59.865 52.381 10.83 0.00 43.02 2.59
5423 6119 1.607251 GCTGTAAACGCCACCTACACT 60.607 52.381 0.00 0.00 0.00 3.55
5466 6172 8.583810 TGGCATATTATCTTCTTAACACGTAC 57.416 34.615 0.00 0.00 0.00 3.67
5481 6187 9.474313 TTCTTAAAGGAAACACTGGCATATTAT 57.526 29.630 0.00 0.00 0.00 1.28
5546 6252 7.882791 ACAACAGTTGTATTCTGATTGATACCA 59.117 33.333 17.74 0.00 43.27 3.25
5561 6267 6.398234 AATTAACATGCCACAACAGTTGTA 57.602 33.333 18.74 4.19 43.23 2.41
5617 6323 3.652274 CCACAGGCCAACATAGTTTTTG 58.348 45.455 5.01 0.00 0.00 2.44
5682 6390 5.626543 GGTTGCTCATAATCAAATGTATGCG 59.373 40.000 0.00 0.00 0.00 4.73
5696 6404 1.409064 CTAGCACCGAGGTTGCTCATA 59.591 52.381 17.80 5.48 39.79 2.15
5815 6527 3.627395 ACTCCCATTGTATCGCTCAAA 57.373 42.857 0.00 0.00 0.00 2.69
5826 6538 1.001974 TCGTGTCCTCAACTCCCATTG 59.998 52.381 0.00 0.00 0.00 2.82
5836 6548 2.912771 ACATTTTGTGTCGTGTCCTCA 58.087 42.857 0.00 0.00 35.77 3.86
5856 6576 1.272490 CTCCAGCAAGTTCACTCCGTA 59.728 52.381 0.00 0.00 0.00 4.02
5908 6628 3.056536 CAGTGAAGTCGAAATCTCCTGGA 60.057 47.826 0.00 0.00 0.00 3.86
5917 6637 2.198406 CCGTTCACAGTGAAGTCGAAA 58.802 47.619 21.81 0.00 37.00 3.46
5929 6649 3.113514 TTCTGCCCAGCCGTTCACA 62.114 57.895 0.00 0.00 0.00 3.58
5930 6650 2.281484 TTCTGCCCAGCCGTTCAC 60.281 61.111 0.00 0.00 0.00 3.18
5944 6664 2.262915 CAGTTCGCCGCCTCTTCT 59.737 61.111 0.00 0.00 0.00 2.85
5951 6671 3.793144 CTTCAGCCAGTTCGCCGC 61.793 66.667 0.00 0.00 0.00 6.53
6004 6724 2.281484 GCTGCCACTTTCGGACCA 60.281 61.111 0.00 0.00 0.00 4.02
6025 6748 2.658707 GACAAGTGACGCAGGCGAC 61.659 63.158 21.62 15.00 42.83 5.19
6034 6757 4.077188 GCGCCGCAGACAAGTGAC 62.077 66.667 3.15 0.00 0.00 3.67
6060 6783 0.817634 CAAGGACGCAAAGGTCACCA 60.818 55.000 0.00 0.00 38.70 4.17
6076 6802 0.825010 AGGTGACCAAAGCTGCCAAG 60.825 55.000 3.63 0.00 0.00 3.61
6078 6804 1.108727 CAAGGTGACCAAAGCTGCCA 61.109 55.000 3.63 0.00 0.00 4.92
6082 6808 0.538287 GCTCCAAGGTGACCAAAGCT 60.538 55.000 3.63 0.00 0.00 3.74
6086 6812 0.108585 GACAGCTCCAAGGTGACCAA 59.891 55.000 12.67 0.00 45.98 3.67
6111 6837 1.243902 CATGTTTGGTTACACGGCCT 58.756 50.000 0.00 0.00 0.00 5.19
6172 6898 2.125753 GACCTGCTCAGCCTCGTG 60.126 66.667 0.00 0.00 0.00 4.35
6200 6926 0.108662 CCTTTTCCGGATTGCAAGCC 60.109 55.000 23.94 23.94 0.00 4.35
6440 7193 2.034124 AGTTTTGGTGCAGCAACATCT 58.966 42.857 29.69 22.55 28.36 2.90
6462 7215 0.746204 TGTGCGTGGAAACTGAAGCA 60.746 50.000 0.00 0.00 0.00 3.91
6477 7230 1.587876 CATGGATGCATGCGTGTGC 60.588 57.895 27.07 9.60 45.25 4.57
6478 7231 0.666374 ATCATGGATGCATGCGTGTG 59.334 50.000 31.65 21.08 36.63 3.82
6479 7232 1.066454 CAATCATGGATGCATGCGTGT 59.934 47.619 31.65 20.06 36.63 4.49
6480 7233 1.066454 ACAATCATGGATGCATGCGTG 59.934 47.619 28.86 28.86 36.59 5.34
6481 7234 1.395635 ACAATCATGGATGCATGCGT 58.604 45.000 21.37 13.43 32.87 5.24
6482 7235 2.502213 AACAATCATGGATGCATGCG 57.498 45.000 21.37 14.24 32.87 4.73
6483 7236 4.543692 GAGTAACAATCATGGATGCATGC 58.456 43.478 21.37 11.82 32.87 4.06
6484 7237 4.825634 AGGAGTAACAATCATGGATGCATG 59.174 41.667 20.28 20.28 0.00 4.06
6485 7238 5.057843 AGGAGTAACAATCATGGATGCAT 57.942 39.130 0.00 0.00 0.00 3.96
6486 7239 4.508551 AGGAGTAACAATCATGGATGCA 57.491 40.909 0.00 0.00 0.00 3.96
6542 7323 0.107654 GAGATGGGCAAGCTACCGTT 60.108 55.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.