Multiple sequence alignment - TraesCS2A01G344000

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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 TraesCS2A01G344000 chr2A 100.000 4197 0 0 1 4197 580846584 580850780 0.000000e+00 7751.0
1 TraesCS2A01G344000 chr2A 90.585 1009 86 8 2198 3201 580721122 580722126 0.000000e+00 1328.0
2 TraesCS2A01G344000 chr2A 86.124 836 98 13 2376 3196 580760279 580761111 0.000000e+00 885.0
3 TraesCS2A01G344000 chr2A 78.357 633 114 16 2569 3191 580253389 580254008 5.090000e-104 388.0
4 TraesCS2A01G344000 chr2B 93.121 1788 71 22 1545 3299 486975793 486977561 0.000000e+00 2573.0
5 TraesCS2A01G344000 chr2B 88.903 1541 110 25 1 1508 486974081 486975593 0.000000e+00 1842.0
6 TraesCS2A01G344000 chr2B 89.940 1004 92 7 2198 3196 486952132 486953131 0.000000e+00 1286.0
7 TraesCS2A01G344000 chr2B 83.366 1034 142 21 2181 3196 486965660 486966681 0.000000e+00 929.0
8 TraesCS2A01G344000 chr2B 89.474 551 47 8 3654 4197 486983405 486983951 0.000000e+00 686.0
9 TraesCS2A01G344000 chr2B 86.190 210 10 5 3403 3602 486982974 486983174 4.250000e-50 209.0
10 TraesCS2A01G344000 chr2B 97.500 80 2 0 3328 3407 486977556 486977635 2.040000e-28 137.0
11 TraesCS2A01G344000 chr2D 92.343 1737 62 29 1950 3643 413773807 413775515 0.000000e+00 2405.0
12 TraesCS2A01G344000 chr2D 90.387 1009 88 8 2198 3201 413690940 413691944 0.000000e+00 1317.0
13 TraesCS2A01G344000 chr2D 86.423 1230 128 19 403 1622 413771138 413772338 0.000000e+00 1310.0
14 TraesCS2A01G344000 chr2D 84.113 1026 126 21 2181 3196 413724557 413725555 0.000000e+00 957.0
15 TraesCS2A01G344000 chr2D 91.619 525 34 6 3676 4197 413775501 413776018 0.000000e+00 717.0
16 TraesCS2A01G344000 chr2D 82.866 321 31 14 1615 1931 413773521 413773821 2.490000e-67 267.0
17 TraesCS2A01G344000 chr2D 90.226 133 13 0 218 350 413771002 413771134 1.550000e-39 174.0
18 TraesCS2A01G344000 chr4A 83.784 74 9 2 218 291 507473742 507473812 2.710000e-07 67.6


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 TraesCS2A01G344000 chr2A 580846584 580850780 4196 False 7751.000000 7751 100.000000 1 4197 1 chr2A.!!$F4 4196
1 TraesCS2A01G344000 chr2A 580721122 580722126 1004 False 1328.000000 1328 90.585000 2198 3201 1 chr2A.!!$F2 1003
2 TraesCS2A01G344000 chr2A 580760279 580761111 832 False 885.000000 885 86.124000 2376 3196 1 chr2A.!!$F3 820
3 TraesCS2A01G344000 chr2A 580253389 580254008 619 False 388.000000 388 78.357000 2569 3191 1 chr2A.!!$F1 622
4 TraesCS2A01G344000 chr2B 486974081 486977635 3554 False 1517.333333 2573 93.174667 1 3407 3 chr2B.!!$F3 3406
5 TraesCS2A01G344000 chr2B 486952132 486953131 999 False 1286.000000 1286 89.940000 2198 3196 1 chr2B.!!$F1 998
6 TraesCS2A01G344000 chr2B 486965660 486966681 1021 False 929.000000 929 83.366000 2181 3196 1 chr2B.!!$F2 1015
7 TraesCS2A01G344000 chr2B 486982974 486983951 977 False 447.500000 686 87.832000 3403 4197 2 chr2B.!!$F4 794
8 TraesCS2A01G344000 chr2D 413690940 413691944 1004 False 1317.000000 1317 90.387000 2198 3201 1 chr2D.!!$F1 1003
9 TraesCS2A01G344000 chr2D 413771002 413776018 5016 False 974.600000 2405 88.695400 218 4197 5 chr2D.!!$F3 3979
10 TraesCS2A01G344000 chr2D 413724557 413725555 998 False 957.000000 957 84.113000 2181 3196 1 chr2D.!!$F2 1015

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
119 120 0.032952 TAGTGCGGTTGTCCTGTGAC 59.967 55.0 0.0 0.0 42.12 3.67 F
958 995 0.252197 ATCCACTCGGTTTAGTGCCC 59.748 55.0 0.0 0.0 44.56 5.36 F
1087 1124 0.909610 AGCGAGGAAGATGGTTGGGA 60.910 55.0 0.0 0.0 0.00 4.37 F
1131 1168 1.348064 TCTCCGTGAAGGTCACCAAT 58.652 50.0 0.0 0.0 44.20 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1025 1062 0.250727 GGCCACAAGGTACAAGAGCA 60.251 55.000 0.00 0.0 37.19 4.26 R
2177 3589 1.027357 TAGGCCGTATCGTTCTGGTC 58.973 55.000 0.00 0.0 0.00 4.02 R
2585 4015 2.427245 CGTCGCGTACACGTCCAA 60.427 61.111 5.77 0.0 42.22 3.53 R
3206 4642 8.801882 TTTTATTTTCTCGATGGGAATGTACT 57.198 30.769 0.00 0.0 0.00 2.73 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
41 42 3.444703 TGAAATTTTCCGTGTTGGGTG 57.555 42.857 6.68 0.00 38.76 4.61
64 65 3.805108 GCTTCATAGGAGTGGTAGCATGG 60.805 52.174 0.00 0.00 31.73 3.66
78 79 0.324645 GCATGGTCCCCAACATCCTT 60.325 55.000 0.00 0.00 36.95 3.36
88 89 3.206150 CCCAACATCCTTGAATACCTCG 58.794 50.000 0.00 0.00 0.00 4.63
105 106 2.036089 CCTCGACCCCTCTTAATAGTGC 59.964 54.545 0.00 0.00 0.00 4.40
115 116 3.857052 TCTTAATAGTGCGGTTGTCCTG 58.143 45.455 0.00 0.00 0.00 3.86
119 120 0.032952 TAGTGCGGTTGTCCTGTGAC 59.967 55.000 0.00 0.00 42.12 3.67
163 164 5.586243 TCTTTGAGTCTTCAGAAAACTGGTG 59.414 40.000 0.00 0.00 34.15 4.17
165 166 2.550180 GAGTCTTCAGAAAACTGGTGCC 59.450 50.000 0.00 0.00 0.00 5.01
166 167 1.609072 GTCTTCAGAAAACTGGTGCCC 59.391 52.381 0.00 0.00 0.00 5.36
171 172 2.693074 TCAGAAAACTGGTGCCCTTTTC 59.307 45.455 10.74 10.74 35.15 2.29
178 179 1.768275 CTGGTGCCCTTTTCCCTTTTT 59.232 47.619 0.00 0.00 0.00 1.94
193 194 3.769300 CCCTTTTTGAATTAGGGGGTCAG 59.231 47.826 2.61 0.00 44.11 3.51
202 203 4.489771 GGGGGTCAGCCATGTCCG 62.490 72.222 0.00 0.00 35.67 4.79
265 294 5.868801 CCATTGTCATCAACACCAAAATACC 59.131 40.000 0.00 0.00 37.70 2.73
297 326 7.812669 AGGAACAACACACTTTCAAGTTAAAAG 59.187 33.333 0.00 0.00 37.08 2.27
355 384 8.768957 ATGATTTATGATCCATCTTCGTGTAG 57.231 34.615 0.00 0.00 0.00 2.74
382 411 3.064271 GTCTCGACAAGAGCTTCGATACT 59.936 47.826 13.68 0.00 46.44 2.12
395 424 8.001875 AGAGCTTCGATACTATATCCCATATGT 58.998 37.037 1.24 0.00 0.00 2.29
452 481 6.425735 TGTCATCCCATGATGTATGAAGTTT 58.574 36.000 8.67 0.00 46.96 2.66
455 484 3.627123 TCCCATGATGTATGAAGTTTGCG 59.373 43.478 0.00 0.00 39.21 4.85
486 515 5.046591 TGGTACCAAAATTGTTCAACAACCA 60.047 36.000 13.60 3.63 41.40 3.67
488 517 3.938334 ACCAAAATTGTTCAACAACCAGC 59.062 39.130 4.73 0.00 41.40 4.85
739 775 1.006043 CACCTCTCCCTAGTCCACTCA 59.994 57.143 0.00 0.00 0.00 3.41
769 805 2.294479 CGTGTTTACGCTTGAACTGG 57.706 50.000 0.00 0.00 44.11 4.00
770 806 1.862201 CGTGTTTACGCTTGAACTGGA 59.138 47.619 0.00 0.00 44.11 3.86
771 807 2.096909 CGTGTTTACGCTTGAACTGGAG 60.097 50.000 0.00 0.00 44.11 3.86
777 813 1.151668 CGCTTGAACTGGAGTCCTTG 58.848 55.000 11.33 5.98 0.00 3.61
834 870 3.459232 TCTTGGAGCCATTAGTCATCG 57.541 47.619 0.00 0.00 0.00 3.84
891 927 5.107104 CGAGATCTTCTCACTTCCTCGATAG 60.107 48.000 0.00 0.00 43.55 2.08
892 928 4.518970 AGATCTTCTCACTTCCTCGATAGC 59.481 45.833 0.00 0.00 0.00 2.97
917 953 6.017026 CGAGTGCTCCTAGTTGATATAACTGA 60.017 42.308 2.75 0.00 0.00 3.41
941 978 4.280461 CATCCGTTCTACTACGTGTGATC 58.720 47.826 0.00 0.00 39.81 2.92
951 988 3.210857 CGTGTGATCCACTCGGTTT 57.789 52.632 12.06 0.00 44.17 3.27
958 995 0.252197 ATCCACTCGGTTTAGTGCCC 59.748 55.000 0.00 0.00 44.56 5.36
962 999 2.357760 TCGGTTTAGTGCCCGCAC 60.358 61.111 11.91 11.91 43.87 5.34
988 1025 1.270907 AGCCATCGTCTTCTTCCTGT 58.729 50.000 0.00 0.00 0.00 4.00
996 1033 3.258372 TCGTCTTCTTCCTGTGTGCTAAT 59.742 43.478 0.00 0.00 0.00 1.73
1015 1052 5.280727 GCTAATCCAATGGCTAGGGTTCTAT 60.281 44.000 0.00 0.00 29.40 1.98
1025 1062 3.066481 GCTAGGGTTCTATCGTTTCTCGT 59.934 47.826 0.00 0.00 40.80 4.18
1034 1071 3.570926 ATCGTTTCTCGTGCTCTTGTA 57.429 42.857 0.00 0.00 40.80 2.41
1048 1085 2.832129 CTCTTGTACCTTGTGGCCTCTA 59.168 50.000 3.32 0.00 36.63 2.43
1087 1124 0.909610 AGCGAGGAAGATGGTTGGGA 60.910 55.000 0.00 0.00 0.00 4.37
1089 1126 1.416401 GCGAGGAAGATGGTTGGGATA 59.584 52.381 0.00 0.00 0.00 2.59
1131 1168 1.348064 TCTCCGTGAAGGTCACCAAT 58.652 50.000 0.00 0.00 44.20 3.16
1199 1236 4.498894 TGATGAGCAGATGATGTTCCTT 57.501 40.909 0.00 0.00 38.31 3.36
1201 1238 3.986996 TGAGCAGATGATGTTCCTTCA 57.013 42.857 0.00 0.00 38.31 3.02
1210 1247 7.646922 GCAGATGATGTTCCTTCATTTCAATAC 59.353 37.037 0.00 0.00 34.03 1.89
1404 1442 4.516321 TCGATGAGTATTCATGCCAATTGG 59.484 41.667 20.81 20.81 44.01 3.16
1412 1450 7.860584 AGTATTCATGCCAATTGGGTTTTATT 58.139 30.769 25.73 0.00 39.65 1.40
1420 1458 5.423886 CCAATTGGGTTTTATTGGCGTAAT 58.576 37.500 17.36 0.00 42.96 1.89
1492 1530 6.502074 AGAACATAGGGGAGTTAGATTTCC 57.498 41.667 0.00 0.00 0.00 3.13
1598 1799 4.287766 AGGCTCGTGTTAGGAGAAAAAT 57.712 40.909 2.98 0.00 32.18 1.82
1599 1800 5.416271 AGGCTCGTGTTAGGAGAAAAATA 57.584 39.130 2.98 0.00 32.18 1.40
1607 1808 6.961554 CGTGTTAGGAGAAAAATATCTTGCAC 59.038 38.462 0.00 0.00 0.00 4.57
1671 3064 9.691362 AAGTTCGAATGTGCATATTAAAAAGTT 57.309 25.926 8.83 9.46 0.00 2.66
1712 3105 7.093771 GGAAGGGTTGTGTGATAAATCTTTGAT 60.094 37.037 0.00 0.00 0.00 2.57
1722 3115 5.662208 TGATAAATCTTTGATGGCCCACATT 59.338 36.000 0.00 0.00 40.72 2.71
1724 3117 7.510001 TGATAAATCTTTGATGGCCCACATTAT 59.490 33.333 0.00 1.41 40.72 1.28
1726 3119 7.860649 AAATCTTTGATGGCCCACATTATAT 57.139 32.000 0.00 0.00 40.72 0.86
1768 3167 9.248417 CTTTGTAAAGAATTGCATTCCATGCCG 62.248 40.741 6.27 0.00 45.84 5.69
1823 3223 7.283329 AGTTTTGCCCCATACACAAATTAAAA 58.717 30.769 0.00 0.00 33.62 1.52
1852 3252 2.687935 CCTATACACATGTGGGTTTGGC 59.312 50.000 28.64 0.00 31.69 4.52
1927 3328 5.260424 TGCCATGTTTAATAGCTTCCTTCA 58.740 37.500 0.00 0.00 0.00 3.02
1986 3396 2.605030 TGTGAGCTTGTTTTTGTGTGC 58.395 42.857 0.00 0.00 0.00 4.57
2075 3485 5.985530 CCTCGCTGAATATGTTGTAAGATCA 59.014 40.000 0.00 0.00 0.00 2.92
2168 3580 9.840427 TTTCAATTCGTTTCCTCTGAATATTTC 57.160 29.630 0.00 0.00 32.32 2.17
2177 3589 3.812053 CCTCTGAATATTTCCTCTTGCGG 59.188 47.826 0.00 0.00 0.00 5.69
2492 3906 4.148825 CGGGGAGCAAGGTCGGAG 62.149 72.222 0.00 0.00 0.00 4.63
2512 3934 5.111293 GGAGAAACGATACGACCCATTTTA 58.889 41.667 0.00 0.00 0.00 1.52
2513 3935 5.006068 GGAGAAACGATACGACCCATTTTAC 59.994 44.000 0.00 0.00 0.00 2.01
2514 3936 4.872124 AGAAACGATACGACCCATTTTACC 59.128 41.667 0.00 0.00 0.00 2.85
2515 3937 3.891422 ACGATACGACCCATTTTACCA 57.109 42.857 0.00 0.00 0.00 3.25
2518 3940 4.632688 ACGATACGACCCATTTTACCAAAG 59.367 41.667 0.00 0.00 0.00 2.77
2526 3951 6.704050 CGACCCATTTTACCAAAGAAAATGTT 59.296 34.615 15.78 6.18 46.12 2.71
2527 3952 7.307101 CGACCCATTTTACCAAAGAAAATGTTG 60.307 37.037 15.78 10.78 46.12 3.33
2567 3995 7.775397 ATCATGCTTGCAACCAATTATTAAC 57.225 32.000 0.00 0.00 0.00 2.01
2585 4015 1.383248 CCAGGATTCCCCGGAGACT 60.383 63.158 0.73 0.00 40.87 3.24
3136 4572 4.078516 CACCCCGAGTTCCCGTCC 62.079 72.222 0.00 0.00 0.00 4.79
3204 4640 7.600752 CCTCAAGTTCTCCTTCTAACTTTGTAG 59.399 40.741 0.00 0.00 41.89 2.74
3206 4642 9.139734 TCAAGTTCTCCTTCTAACTTTGTAGTA 57.860 33.333 0.00 0.00 41.89 1.82
3208 4644 8.709272 AGTTCTCCTTCTAACTTTGTAGTAGT 57.291 34.615 0.00 0.00 32.00 2.73
3272 4730 2.922503 GTTGGGTTTGGGCCAGGG 60.923 66.667 6.23 0.00 0.00 4.45
3290 4748 2.158755 AGGGCATCGGGTATCTTCTTTG 60.159 50.000 0.00 0.00 0.00 2.77
3299 4788 2.163613 GGTATCTTCTTTGCAAACGGGG 59.836 50.000 8.05 0.00 0.00 5.73
3300 4789 0.603065 ATCTTCTTTGCAAACGGGGC 59.397 50.000 8.05 0.00 0.00 5.80
3301 4790 0.467290 TCTTCTTTGCAAACGGGGCT 60.467 50.000 8.05 0.00 0.00 5.19
3302 4791 0.318955 CTTCTTTGCAAACGGGGCTG 60.319 55.000 8.05 0.00 0.00 4.85
3303 4792 1.743321 TTCTTTGCAAACGGGGCTGG 61.743 55.000 8.05 0.00 0.00 4.85
3304 4793 3.864160 CTTTGCAAACGGGGCTGGC 62.864 63.158 8.05 0.00 0.00 4.85
3305 4794 4.912395 TTGCAAACGGGGCTGGCT 62.912 61.111 0.00 0.00 0.00 4.75
3317 4806 4.181010 CTGGCTGGCCCGTATGCT 62.181 66.667 9.28 0.00 35.87 3.79
3318 4807 4.488136 TGGCTGGCCCGTATGCTG 62.488 66.667 9.28 0.00 35.87 4.41
3321 4810 2.438254 CTGGCCCGTATGCTGCAA 60.438 61.111 6.36 0.00 0.00 4.08
3322 4811 2.749839 TGGCCCGTATGCTGCAAC 60.750 61.111 6.36 5.69 0.00 4.17
3323 4812 3.518068 GGCCCGTATGCTGCAACC 61.518 66.667 6.36 0.00 0.00 3.77
3324 4813 2.749839 GCCCGTATGCTGCAACCA 60.750 61.111 6.36 0.00 0.00 3.67
3325 4814 2.339556 GCCCGTATGCTGCAACCAA 61.340 57.895 6.36 0.00 0.00 3.67
3326 4815 1.506262 CCCGTATGCTGCAACCAAC 59.494 57.895 6.36 2.12 0.00 3.77
3327 4816 1.240641 CCCGTATGCTGCAACCAACA 61.241 55.000 6.36 0.00 0.00 3.33
3328 4817 0.595588 CCGTATGCTGCAACCAACAA 59.404 50.000 6.36 0.00 0.00 2.83
3329 4818 1.665735 CCGTATGCTGCAACCAACAAC 60.666 52.381 6.36 0.00 0.00 3.32
3330 4819 1.685302 GTATGCTGCAACCAACAACG 58.315 50.000 6.36 0.00 0.00 4.10
3331 4820 0.595588 TATGCTGCAACCAACAACGG 59.404 50.000 6.36 0.00 0.00 4.44
3332 4821 2.027460 GCTGCAACCAACAACGGG 59.973 61.111 0.00 0.00 0.00 5.28
3374 4863 0.532573 TTGACTCTGAGGATCACGCC 59.467 55.000 9.85 0.00 42.56 5.68
3419 4908 4.337060 CACCGAGTGCGACGACCA 62.337 66.667 0.00 0.00 40.82 4.02
3494 4984 2.616330 CGAAAGCGCAAGGAAGCCA 61.616 57.895 11.47 0.00 38.28 4.75
3496 4986 0.457337 GAAAGCGCAAGGAAGCCATG 60.457 55.000 11.47 0.00 38.28 3.66
3595 5285 3.365265 GGTCAGGTGGCAAAGGCG 61.365 66.667 0.00 0.00 42.47 5.52
3602 5292 2.197324 TGGCAAAGGCGAAACCCT 59.803 55.556 0.00 0.00 42.47 4.34
3613 5303 0.446222 CGAAACCCTAACACGCATGG 59.554 55.000 0.00 0.00 0.00 3.66
3641 5331 1.678635 CCATGGCCACAACATCGGT 60.679 57.895 8.16 0.00 0.00 4.69
3642 5332 1.250154 CCATGGCCACAACATCGGTT 61.250 55.000 8.16 0.00 37.87 4.44
3643 5333 0.602562 CATGGCCACAACATCGGTTT 59.397 50.000 8.16 0.00 34.21 3.27
3644 5334 1.000731 CATGGCCACAACATCGGTTTT 59.999 47.619 8.16 0.00 34.21 2.43
3645 5335 1.115467 TGGCCACAACATCGGTTTTT 58.885 45.000 0.00 0.00 34.21 1.94
3646 5336 1.067821 TGGCCACAACATCGGTTTTTC 59.932 47.619 0.00 0.00 34.21 2.29
3647 5337 1.339929 GGCCACAACATCGGTTTTTCT 59.660 47.619 0.00 0.00 34.21 2.52
3648 5338 2.223947 GGCCACAACATCGGTTTTTCTT 60.224 45.455 0.00 0.00 34.21 2.52
3649 5339 3.453424 GCCACAACATCGGTTTTTCTTT 58.547 40.909 0.00 0.00 34.21 2.52
3650 5340 3.868661 GCCACAACATCGGTTTTTCTTTT 59.131 39.130 0.00 0.00 34.21 2.27
3651 5341 4.026062 GCCACAACATCGGTTTTTCTTTTC 60.026 41.667 0.00 0.00 34.21 2.29
3652 5342 5.348164 CCACAACATCGGTTTTTCTTTTCT 58.652 37.500 0.00 0.00 34.21 2.52
3653 5343 5.810074 CCACAACATCGGTTTTTCTTTTCTT 59.190 36.000 0.00 0.00 34.21 2.52
3700 5390 2.280797 ATCGGTTGCGTGCACTGT 60.281 55.556 16.19 0.00 0.00 3.55
3702 5392 1.444119 ATCGGTTGCGTGCACTGTTT 61.444 50.000 16.19 0.00 0.00 2.83
3753 5443 5.597806 ACATATGTGGACATAACGTCGATT 58.402 37.500 7.78 0.00 46.42 3.34
3764 5454 6.075280 ACATAACGTCGATTGCTTTAACAAC 58.925 36.000 0.00 0.00 31.03 3.32
3775 5465 8.798153 CGATTGCTTTAACAACTTATGGATTTC 58.202 33.333 0.00 0.00 31.03 2.17
3817 5507 1.729149 GCACGTTGCTAAGCATGAACC 60.729 52.381 0.00 0.00 40.96 3.62
3819 5509 1.806542 ACGTTGCTAAGCATGAACCTG 59.193 47.619 0.00 0.00 38.76 4.00
3848 5538 1.095228 ACGCAAGAGGGTTGTGTGTG 61.095 55.000 3.26 0.00 41.07 3.82
3865 5559 9.619316 GTTGTGTGTGTTTTGCATTAAGATATA 57.381 29.630 0.00 0.00 0.00 0.86
3866 5560 9.838975 TTGTGTGTGTTTTGCATTAAGATATAG 57.161 29.630 0.00 0.00 0.00 1.31
3867 5561 9.008965 TGTGTGTGTTTTGCATTAAGATATAGT 57.991 29.630 0.00 0.00 0.00 2.12
3920 5614 1.067693 TATGTGCAACGTGAGCGAAG 58.932 50.000 8.48 0.00 42.39 3.79
4015 5714 7.588488 CCAAATGTGAAATCTTCAACAAATTGC 59.412 33.333 0.00 0.00 42.15 3.56
4019 5718 7.495901 TGTGAAATCTTCAACAAATTGCCTAA 58.504 30.769 0.00 0.00 42.15 2.69
4066 5766 1.151777 ATGAATAGACCGCGCCAACG 61.152 55.000 0.00 0.00 44.07 4.10
4120 5821 2.043411 CACGCATTGGAACGAACAAAG 58.957 47.619 0.00 0.00 0.00 2.77
4130 5831 3.304190 GGAACGAACAAAGTAAACGCCAT 60.304 43.478 0.00 0.00 0.00 4.40
4161 5862 2.541588 CGAAATGGATGGTTCATTCGGC 60.542 50.000 0.00 0.00 34.15 5.54
4165 5866 0.746563 GGATGGTTCATTCGGCGGAA 60.747 55.000 7.21 9.32 36.41 4.30
4190 5892 1.288335 ACGGAGGAGGAATACAGGTCT 59.712 52.381 0.00 0.00 0.00 3.85
4192 5894 2.321719 GGAGGAGGAATACAGGTCTCC 58.678 57.143 0.00 0.00 44.46 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.987220 CACCCAACACGGAAAATTTCATC 59.013 43.478 8.09 0.00 36.56 2.92
25 26 0.469144 AGCCACCCAACACGGAAAAT 60.469 50.000 0.00 0.00 36.56 1.82
30 31 0.322098 TATGAAGCCACCCAACACGG 60.322 55.000 0.00 0.00 0.00 4.94
41 42 1.762957 TGCTACCACTCCTATGAAGCC 59.237 52.381 0.00 0.00 31.19 4.35
64 65 3.053619 AGGTATTCAAGGATGTTGGGGAC 60.054 47.826 0.00 0.00 0.00 4.46
78 79 2.544844 AAGAGGGGTCGAGGTATTCA 57.455 50.000 0.00 0.00 0.00 2.57
88 89 2.528041 CCGCACTATTAAGAGGGGTC 57.472 55.000 0.78 0.00 40.23 4.46
105 106 1.948104 TTTGAGTCACAGGACAACCG 58.052 50.000 0.00 0.00 46.80 4.44
163 164 5.245531 CCTAATTCAAAAAGGGAAAAGGGC 58.754 41.667 0.00 0.00 32.22 5.19
178 179 1.215173 CATGGCTGACCCCCTAATTCA 59.785 52.381 0.00 0.00 33.59 2.57
202 203 9.953825 CTAATGTCGTTTTCAATAGTTGTCTAC 57.046 33.333 0.00 0.00 0.00 2.59
212 213 5.995282 TGTGAGGTCTAATGTCGTTTTCAAT 59.005 36.000 0.00 0.00 0.00 2.57
213 214 5.361427 TGTGAGGTCTAATGTCGTTTTCAA 58.639 37.500 0.00 0.00 0.00 2.69
265 294 5.649557 TGAAAGTGTGTTGTTCCTTCAATG 58.350 37.500 0.00 0.00 0.00 2.82
442 471 4.155280 ACCAATACACCGCAAACTTCATAC 59.845 41.667 0.00 0.00 0.00 2.39
452 481 2.563261 TTTGGTACCAATACACCGCA 57.437 45.000 27.57 7.73 37.66 5.69
455 484 6.750148 TGAACAATTTTGGTACCAATACACC 58.250 36.000 27.57 13.76 35.70 4.16
486 515 5.016173 TGCTAGAAAATAATGTGGTTGGCT 58.984 37.500 0.00 0.00 0.00 4.75
488 517 6.924111 ACTTGCTAGAAAATAATGTGGTTGG 58.076 36.000 1.04 0.00 0.00 3.77
544 575 3.393800 TGTGAGCTTGCTTCAACTACTC 58.606 45.455 0.00 0.00 0.00 2.59
613 649 4.908601 ACCATTGTCCTGATTGACAGTA 57.091 40.909 0.00 0.00 45.37 2.74
616 652 4.468713 TCAAACCATTGTCCTGATTGACA 58.531 39.130 0.00 0.00 43.26 3.58
672 708 6.208007 ACAATGACCCATATGCATGACATTAG 59.792 38.462 10.16 8.12 40.38 1.73
684 720 3.032459 TGCATGCAACAATGACCCATAT 58.968 40.909 20.30 0.00 0.00 1.78
717 753 1.379977 TGGACTAGGGAGAGGTGCG 60.380 63.158 0.00 0.00 0.00 5.34
751 787 2.870411 ACTCCAGTTCAAGCGTAAACAC 59.130 45.455 0.00 0.00 0.00 3.32
764 800 1.202818 GGCAGTTCAAGGACTCCAGTT 60.203 52.381 0.00 0.00 0.00 3.16
765 801 0.398318 GGCAGTTCAAGGACTCCAGT 59.602 55.000 0.00 0.00 0.00 4.00
766 802 0.397941 TGGCAGTTCAAGGACTCCAG 59.602 55.000 0.00 0.00 0.00 3.86
767 803 0.843309 TTGGCAGTTCAAGGACTCCA 59.157 50.000 0.00 0.00 0.00 3.86
768 804 1.239347 GTTGGCAGTTCAAGGACTCC 58.761 55.000 0.00 0.00 0.00 3.85
769 805 1.239347 GGTTGGCAGTTCAAGGACTC 58.761 55.000 0.00 0.00 0.00 3.36
770 806 0.550914 TGGTTGGCAGTTCAAGGACT 59.449 50.000 0.00 0.00 0.00 3.85
771 807 1.067060 GTTGGTTGGCAGTTCAAGGAC 59.933 52.381 0.00 0.00 0.00 3.85
777 813 1.358759 CACGGTTGGTTGGCAGTTC 59.641 57.895 0.00 0.00 0.00 3.01
819 855 2.515926 TGCTCGATGACTAATGGCTC 57.484 50.000 0.00 0.00 0.00 4.70
834 870 5.816777 ACTTTTTCTAGAGATCTGCATGCTC 59.183 40.000 20.33 8.36 0.00 4.26
875 911 2.327200 TCGCTATCGAGGAAGTGAGA 57.673 50.000 4.80 0.00 40.21 3.27
891 927 3.651803 ATATCAACTAGGAGCACTCGC 57.348 47.619 0.00 0.00 38.99 5.03
892 928 6.017026 TCAGTTATATCAACTAGGAGCACTCG 60.017 42.308 0.00 0.00 0.00 4.18
941 978 4.296265 GGGCACTAAACCGAGTGG 57.704 61.111 5.76 0.00 45.85 4.00
951 988 0.535335 CTTAGAAGGTGCGGGCACTA 59.465 55.000 21.71 5.22 45.52 2.74
958 995 0.460284 ACGATGGCTTAGAAGGTGCG 60.460 55.000 0.00 0.00 0.00 5.34
962 999 3.810310 AGAAGACGATGGCTTAGAAGG 57.190 47.619 0.00 0.00 0.00 3.46
988 1025 2.158623 CCCTAGCCATTGGATTAGCACA 60.159 50.000 6.95 0.00 0.00 4.57
996 1033 2.632996 CGATAGAACCCTAGCCATTGGA 59.367 50.000 6.95 0.00 39.76 3.53
1015 1052 2.606308 GGTACAAGAGCACGAGAAACGA 60.606 50.000 0.00 0.00 45.77 3.85
1025 1062 0.250727 GGCCACAAGGTACAAGAGCA 60.251 55.000 0.00 0.00 37.19 4.26
1034 1071 1.913762 AGCGTAGAGGCCACAAGGT 60.914 57.895 5.01 0.00 37.19 3.50
1063 1100 1.142748 CCATCTTCCTCGCTTCGCT 59.857 57.895 0.00 0.00 0.00 4.93
1087 1124 5.912149 TCCCCTTTCTTGAGCATGTATAT 57.088 39.130 0.00 0.00 0.00 0.86
1089 1126 4.803329 ATCCCCTTTCTTGAGCATGTAT 57.197 40.909 0.00 0.00 0.00 2.29
1131 1168 1.152984 CATGATAGTGGCGCCCCAA 60.153 57.895 26.77 9.35 44.33 4.12
1311 1348 4.219507 TGGACATCAACGCCACAAATTTAT 59.780 37.500 0.00 0.00 0.00 1.40
1313 1350 2.363680 TGGACATCAACGCCACAAATTT 59.636 40.909 0.00 0.00 0.00 1.82
1319 1356 1.164411 TTCATGGACATCAACGCCAC 58.836 50.000 0.00 0.00 33.93 5.01
1323 1360 7.854557 ATGGATATATTCATGGACATCAACG 57.145 36.000 5.65 0.00 0.00 4.10
1537 1575 4.983671 ATGCACACTAGAGATCGTGTTA 57.016 40.909 0.00 0.00 42.05 2.41
1598 1799 5.181009 CACATGAAAGAGAGGTGCAAGATA 58.819 41.667 0.00 0.00 0.00 1.98
1599 1800 4.008330 CACATGAAAGAGAGGTGCAAGAT 58.992 43.478 0.00 0.00 0.00 2.40
1607 1808 2.431954 ATGGGCACATGAAAGAGAGG 57.568 50.000 0.00 0.00 35.57 3.69
1671 3064 7.881232 CACAACCCTTCCTTTTGTAAGTAGATA 59.119 37.037 0.00 0.00 32.19 1.98
1712 3105 8.840200 TTAAAACCTTTATATAATGTGGGCCA 57.160 30.769 0.00 0.00 0.00 5.36
1768 3167 8.718734 GGTTGGTAATCCGATTATTTATGAGTC 58.281 37.037 4.15 0.00 36.30 3.36
1771 3170 7.663905 CAGGGTTGGTAATCCGATTATTTATGA 59.336 37.037 4.15 0.00 36.30 2.15
1823 3223 1.553248 ACATGTGTATAGGTGCGGTGT 59.447 47.619 0.00 0.00 0.00 4.16
1852 3252 6.739331 AGGAATACTCAGGAGTTTGGATAG 57.261 41.667 7.33 0.00 42.54 2.08
1927 3328 9.443323 AGCTACCCGCAAAATAAAAATAAAAAT 57.557 25.926 0.00 0.00 42.61 1.82
1933 3334 5.186992 AGGAAGCTACCCGCAAAATAAAAAT 59.813 36.000 0.00 0.00 42.61 1.82
1934 3335 4.525100 AGGAAGCTACCCGCAAAATAAAAA 59.475 37.500 0.00 0.00 42.61 1.94
1939 3340 2.092323 GAAGGAAGCTACCCGCAAAAT 58.908 47.619 0.00 0.00 42.61 1.82
2075 3485 5.365021 AGTTGGAGAAGATGGAATTCGAT 57.635 39.130 2.18 2.18 0.00 3.59
2150 3562 6.457528 GCAAGAGGAAATATTCAGAGGAAACG 60.458 42.308 0.00 0.00 36.43 3.60
2168 3580 1.738099 CGTTCTGGTCCGCAAGAGG 60.738 63.158 0.00 0.00 43.02 3.69
2177 3589 1.027357 TAGGCCGTATCGTTCTGGTC 58.973 55.000 0.00 0.00 0.00 4.02
2492 3906 4.630940 TGGTAAAATGGGTCGTATCGTTTC 59.369 41.667 0.00 0.00 0.00 2.78
2512 3934 6.991531 ACATTACATGCAACATTTTCTTTGGT 59.008 30.769 0.00 0.00 0.00 3.67
2513 3935 7.171167 TCACATTACATGCAACATTTTCTTTGG 59.829 33.333 0.00 0.00 0.00 3.28
2514 3936 8.074474 TCACATTACATGCAACATTTTCTTTG 57.926 30.769 0.00 0.00 0.00 2.77
2515 3937 8.836268 ATCACATTACATGCAACATTTTCTTT 57.164 26.923 0.00 0.00 0.00 2.52
2518 3940 7.815398 TGATCACATTACATGCAACATTTTC 57.185 32.000 0.00 0.00 0.00 2.29
2526 3951 5.300792 AGCATGATTGATCACATTACATGCA 59.699 36.000 30.20 12.18 46.10 3.96
2527 3952 5.769367 AGCATGATTGATCACATTACATGC 58.231 37.500 26.19 26.19 45.29 4.06
2585 4015 2.427245 CGTCGCGTACACGTCCAA 60.427 61.111 5.77 0.00 42.22 3.53
3204 4640 8.882415 TTATTTTCTCGATGGGAATGTACTAC 57.118 34.615 0.00 0.00 0.00 2.73
3206 4642 8.801882 TTTTATTTTCTCGATGGGAATGTACT 57.198 30.769 0.00 0.00 0.00 2.73
3272 4730 2.288666 TGCAAAGAAGATACCCGATGC 58.711 47.619 0.00 0.00 0.00 3.91
3300 4789 4.181010 AGCATACGGGCCAGCCAG 62.181 66.667 11.50 9.35 37.98 4.85
3301 4790 4.488136 CAGCATACGGGCCAGCCA 62.488 66.667 11.50 0.00 37.98 4.75
3304 4793 2.438254 TTGCAGCATACGGGCCAG 60.438 61.111 4.39 1.85 0.00 4.85
3305 4794 2.749839 GTTGCAGCATACGGGCCA 60.750 61.111 4.39 0.00 0.00 5.36
3306 4795 3.518068 GGTTGCAGCATACGGGCC 61.518 66.667 2.05 0.00 0.00 5.80
3307 4796 2.339556 TTGGTTGCAGCATACGGGC 61.340 57.895 2.05 0.00 0.00 6.13
3308 4797 1.240641 TGTTGGTTGCAGCATACGGG 61.241 55.000 2.05 0.00 0.00 5.28
3309 4798 0.595588 TTGTTGGTTGCAGCATACGG 59.404 50.000 2.05 0.00 0.00 4.02
3310 4799 1.685302 GTTGTTGGTTGCAGCATACG 58.315 50.000 2.05 0.00 0.00 3.06
3311 4800 1.665735 CCGTTGTTGGTTGCAGCATAC 60.666 52.381 2.05 0.02 0.00 2.39
3312 4801 0.595588 CCGTTGTTGGTTGCAGCATA 59.404 50.000 2.05 0.00 0.00 3.14
3313 4802 1.363443 CCGTTGTTGGTTGCAGCAT 59.637 52.632 2.05 0.00 0.00 3.79
3314 4803 2.780094 CCCGTTGTTGGTTGCAGCA 61.780 57.895 2.05 0.00 0.00 4.41
3315 4804 2.027460 CCCGTTGTTGGTTGCAGC 59.973 61.111 0.00 0.00 0.00 5.25
3316 4805 2.027460 GCCCGTTGTTGGTTGCAG 59.973 61.111 0.00 0.00 0.00 4.41
3317 4806 3.532155 GGCCCGTTGTTGGTTGCA 61.532 61.111 0.00 0.00 0.00 4.08
3318 4807 4.293648 GGGCCCGTTGTTGGTTGC 62.294 66.667 5.69 0.00 0.00 4.17
3319 4808 2.427245 TTGGGCCCGTTGTTGGTTG 61.427 57.895 19.37 0.00 0.00 3.77
3320 4809 2.042843 TTGGGCCCGTTGTTGGTT 60.043 55.556 19.37 0.00 0.00 3.67
3321 4810 2.835895 GTTGGGCCCGTTGTTGGT 60.836 61.111 19.37 0.00 0.00 3.67
3322 4811 2.131067 AAGTTGGGCCCGTTGTTGG 61.131 57.895 19.37 0.00 0.00 3.77
3323 4812 1.067250 CAAGTTGGGCCCGTTGTTG 59.933 57.895 19.37 14.08 0.00 3.33
3324 4813 1.380650 ACAAGTTGGGCCCGTTGTT 60.381 52.632 24.46 11.07 28.62 2.83
3325 4814 2.124693 CACAAGTTGGGCCCGTTGT 61.125 57.895 24.46 24.46 33.37 3.32
3326 4815 0.820074 TACACAAGTTGGGCCCGTTG 60.820 55.000 23.37 23.37 0.00 4.10
3327 4816 0.106619 TTACACAAGTTGGGCCCGTT 60.107 50.000 19.37 7.76 0.00 4.44
3328 4817 0.536460 CTTACACAAGTTGGGCCCGT 60.536 55.000 19.37 9.55 0.00 5.28
3329 4818 1.862602 GCTTACACAAGTTGGGCCCG 61.863 60.000 19.37 4.36 34.00 6.13
3330 4819 0.825840 TGCTTACACAAGTTGGGCCC 60.826 55.000 17.59 17.59 34.00 5.80
3331 4820 1.036707 TTGCTTACACAAGTTGGGCC 58.963 50.000 4.63 0.00 34.00 5.80
3332 4821 2.880963 TTTGCTTACACAAGTTGGGC 57.119 45.000 4.63 2.91 34.00 5.36
3408 4897 2.476051 CAATGCTGGTCGTCGCAC 59.524 61.111 0.00 0.00 39.21 5.34
3419 4908 2.289195 CCAAACTTGTGATGGCAATGCT 60.289 45.455 4.82 0.00 0.00 3.79
3466 4955 2.561373 CGCTTTCGGTTCTTGGCC 59.439 61.111 0.00 0.00 0.00 5.36
3595 5285 0.170339 GCCATGCGTGTTAGGGTTTC 59.830 55.000 4.96 0.00 0.00 2.78
3628 5318 2.793278 AGAAAAACCGATGTTGTGGC 57.207 45.000 0.00 0.00 34.13 5.01
3629 5319 5.348164 AGAAAAGAAAAACCGATGTTGTGG 58.652 37.500 0.00 0.00 34.13 4.17
3630 5320 6.885735 AAGAAAAGAAAAACCGATGTTGTG 57.114 33.333 0.00 0.00 34.13 3.33
3662 5352 4.545823 TGTTGTAGCCGTTCTCAAAAAG 57.454 40.909 0.00 0.00 0.00 2.27
3670 5360 1.127951 CAACCGATGTTGTAGCCGTTC 59.872 52.381 0.00 0.00 45.51 3.95
3736 5426 2.268298 AGCAATCGACGTTATGTCCAC 58.732 47.619 0.00 0.00 45.23 4.02
3753 5443 8.637986 ACAAGAAATCCATAAGTTGTTAAAGCA 58.362 29.630 0.00 0.00 0.00 3.91
3764 5454 8.438676 ACCGAGATTAACAAGAAATCCATAAG 57.561 34.615 0.00 0.00 34.50 1.73
3775 5465 3.679980 CACTGGTGACCGAGATTAACAAG 59.320 47.826 7.84 0.00 0.00 3.16
3817 5507 1.194098 CTCTTGCGTGTTCTTGCTCAG 59.806 52.381 0.00 0.00 0.00 3.35
3819 5509 0.514691 CCTCTTGCGTGTTCTTGCTC 59.485 55.000 0.00 0.00 0.00 4.26
3865 5559 4.944930 GCACCATCTCCGATATCTACTACT 59.055 45.833 0.34 0.00 0.00 2.57
3866 5560 4.944930 AGCACCATCTCCGATATCTACTAC 59.055 45.833 0.34 0.00 0.00 2.73
3867 5561 4.944317 CAGCACCATCTCCGATATCTACTA 59.056 45.833 0.34 0.00 0.00 1.82
3868 5562 3.761218 CAGCACCATCTCCGATATCTACT 59.239 47.826 0.34 0.00 0.00 2.57
3869 5563 3.674682 GCAGCACCATCTCCGATATCTAC 60.675 52.174 0.34 0.00 0.00 2.59
3870 5564 2.493675 GCAGCACCATCTCCGATATCTA 59.506 50.000 0.34 0.00 0.00 1.98
3893 5587 4.457810 CTCACGTTGCACATAACTGAAAG 58.542 43.478 0.00 0.00 42.29 2.62
3920 5614 7.394872 CAAAGAACTAGAAATCACGATAGCAC 58.605 38.462 0.00 0.00 42.67 4.40
4015 5714 7.857885 GCCTGAATATTTCACGAGAAAATTAGG 59.142 37.037 12.02 15.32 46.06 2.69
4019 5718 6.757897 TGCCTGAATATTTCACGAGAAAAT 57.242 33.333 12.02 5.99 46.06 1.82
4036 5735 3.552890 CGGTCTATTCATCGAATGCCTGA 60.553 47.826 0.00 0.00 33.95 3.86
4066 5766 2.299993 TGCATCTCTCATGTTCCGAC 57.700 50.000 0.00 0.00 0.00 4.79
4097 5798 0.450482 GTTCGTTCCAATGCGTGTCG 60.450 55.000 0.00 0.00 0.00 4.35
4120 5821 5.146482 TCGTTTAATGCTATGGCGTTTAC 57.854 39.130 14.14 11.31 44.28 2.01
4130 5831 6.375736 TGAACCATCCATTTCGTTTAATGCTA 59.624 34.615 0.00 0.00 34.81 3.49
4161 5862 1.141881 CCTCCTCCGTGATGTTCCG 59.858 63.158 0.00 0.00 0.00 4.30
4165 5866 2.695666 CTGTATTCCTCCTCCGTGATGT 59.304 50.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.