Multiple sequence alignment - TraesCS2A01G197900

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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 TraesCS2A01G197900 chr2A 100.000 5781 0 0 1 5781 168985931 168980151 0.000000e+00 10676
1 TraesCS2A01G197900 chr2A 89.109 101 10 1 1699 1798 170470397 170470497 2.190000e-24 124
2 TraesCS2A01G197900 chr2A 88.462 104 11 1 1699 1801 559118416 559118519 2.190000e-24 124
3 TraesCS2A01G197900 chr2B 90.065 2476 159 50 76 2500 215599357 215596918 0.000000e+00 3129
4 TraesCS2A01G197900 chr2B 93.130 1936 97 19 3863 5781 215594961 215593045 0.000000e+00 2806
5 TraesCS2A01G197900 chr2B 98.757 1368 13 2 2500 3866 215596485 215595121 0.000000e+00 2429
6 TraesCS2A01G197900 chr2B 90.099 101 9 1 1699 1798 216462814 216462914 4.700000e-26 130
7 TraesCS2A01G197900 chr2D 96.606 1385 26 6 1774 3153 158283316 158281948 0.000000e+00 2278
8 TraesCS2A01G197900 chr2D 92.277 1489 66 19 4324 5781 158275760 158274290 0.000000e+00 2067
9 TraesCS2A01G197900 chr2D 92.038 942 42 10 871 1788 158284345 158283413 0.000000e+00 1293
10 TraesCS2A01G197900 chr2D 98.192 719 9 2 3148 3866 158277216 158276502 0.000000e+00 1253
11 TraesCS2A01G197900 chr2D 96.352 466 10 5 3863 4328 158276338 158275880 0.000000e+00 760
12 TraesCS2A01G197900 chr2D 83.400 747 76 22 1 738 158285277 158284570 0.000000e+00 649
13 TraesCS2A01G197900 chr1B 90.909 99 9 0 1707 1805 160325233 160325331 3.630000e-27 134
14 TraesCS2A01G197900 chr7A 91.579 95 8 0 1704 1798 48103168 48103074 1.310000e-26 132
15 TraesCS2A01G197900 chr5B 90.099 101 9 1 1699 1798 55370944 55371044 4.700000e-26 130
16 TraesCS2A01G197900 chr1D 88.571 105 10 2 1696 1798 128529209 128529105 6.080000e-25 126


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 TraesCS2A01G197900 chr2A 168980151 168985931 5780 True 10676.000000 10676 100.000000 1 5781 1 chr2A.!!$R1 5780
1 TraesCS2A01G197900 chr2B 215593045 215599357 6312 True 2788.000000 3129 93.984000 76 5781 3 chr2B.!!$R1 5705
2 TraesCS2A01G197900 chr2D 158281948 158285277 3329 True 1406.666667 2278 90.681333 1 3153 3 chr2D.!!$R2 3152
3 TraesCS2A01G197900 chr2D 158274290 158277216 2926 True 1360.000000 2067 95.607000 3148 5781 3 chr2D.!!$R1 2633

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
308 311 0.161446 CCATTTTTGCTTGTTCGCGC 59.839 50.000 0.00 0.00 0.00 6.86 F
1131 1273 0.031857 TTCGTTGAAACCCGCGAGTA 59.968 50.000 8.23 0.00 34.78 2.59 F
1482 1638 1.059584 TGTCTTCCCCAGGCTGTTGA 61.060 55.000 14.43 6.43 0.00 3.18 F
1491 1650 3.054361 CCCCAGGCTGTTGAAATACTAGT 60.054 47.826 14.43 0.00 0.00 2.57 F
1788 1953 3.197766 TGAGCATCAACTAATTCCGGACT 59.802 43.478 1.83 0.00 45.97 3.85 F
1789 1954 3.535561 AGCATCAACTAATTCCGGACTG 58.464 45.455 1.83 0.00 0.00 3.51 F
1790 1955 3.197766 AGCATCAACTAATTCCGGACTGA 59.802 43.478 1.83 0.52 0.00 3.41 F
1791 1956 3.557595 GCATCAACTAATTCCGGACTGAG 59.442 47.826 1.83 3.53 0.00 3.35 F
3986 4870 3.558418 ACAACCACGTATGAACTGTTGAC 59.442 43.478 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1170 1312 0.179156 TACAGTGCTTACTACGCCGC 60.179 55.000 0.00 0.00 0.00 6.53 R
2086 2368 1.140312 AGAAACCCACTGCTCCAGAA 58.860 50.000 0.00 0.00 35.18 3.02 R
3397 4113 3.815401 GTGCTAACAATCAGTGAAGGTGT 59.185 43.478 0.00 0.00 0.00 4.16 R
3537 4254 4.272504 TGAACAACTACACTTAAGCAGCAC 59.727 41.667 1.29 0.00 0.00 4.40 R
3819 4536 3.898482 AGTAGGGTGGCCAATCATAAAC 58.102 45.455 7.24 0.00 0.00 2.01 R
3986 4870 8.334016 TGTGATTTAACAACTTTCATGAAACG 57.666 30.769 16.91 14.56 0.00 3.60 R
4059 4943 6.512342 TGACTTTTACCAAGTTCGGAAAAA 57.488 33.333 0.00 0.00 0.00 1.94 R
4080 4964 5.866092 CAGAAAAGAACAGAGATCGACATGA 59.134 40.000 0.00 0.00 0.00 3.07 R
5007 6038 0.033796 ACCCAATGAGTGCATCCCAG 60.034 55.000 0.00 0.00 32.35 4.45 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
39 40 5.763204 AGCGAAGGAAGAAACATAGAAAACA 59.237 36.000 0.00 0.00 0.00 2.83
40 41 6.262273 AGCGAAGGAAGAAACATAGAAAACAA 59.738 34.615 0.00 0.00 0.00 2.83
85 87 8.989653 AACTGAAAAGGAAACAAATAAAACGA 57.010 26.923 0.00 0.00 0.00 3.85
131 133 3.628008 ACAGAAGAAAACCCGGAAAACT 58.372 40.909 0.73 0.00 0.00 2.66
147 149 3.401033 AAACTATTGCAAAACAGCCCC 57.599 42.857 1.71 0.00 0.00 5.80
194 196 2.042464 GAGGGGAGCATACATCTCACA 58.958 52.381 0.00 0.00 35.73 3.58
219 221 1.633774 CCAGATATAGCTCCCACCGT 58.366 55.000 0.00 0.00 0.00 4.83
225 227 4.838986 AGATATAGCTCCCACCGTAATTGT 59.161 41.667 0.00 0.00 0.00 2.71
238 240 4.059511 CCGTAATTGTTATGTATCGCCCA 58.940 43.478 0.00 0.00 0.00 5.36
299 302 1.247567 CAGACCGGTCCATTTTTGCT 58.752 50.000 30.82 6.14 0.00 3.91
305 308 2.050691 CGGTCCATTTTTGCTTGTTCG 58.949 47.619 0.00 0.00 0.00 3.95
306 309 1.792367 GGTCCATTTTTGCTTGTTCGC 59.208 47.619 0.00 0.00 0.00 4.70
307 310 1.451651 GTCCATTTTTGCTTGTTCGCG 59.548 47.619 0.00 0.00 0.00 5.87
308 311 0.161446 CCATTTTTGCTTGTTCGCGC 59.839 50.000 0.00 0.00 0.00 6.86
309 312 0.179302 CATTTTTGCTTGTTCGCGCG 60.179 50.000 26.76 26.76 0.00 6.86
310 313 0.593773 ATTTTTGCTTGTTCGCGCGT 60.594 45.000 30.98 1.54 0.00 6.01
311 314 0.798771 TTTTTGCTTGTTCGCGCGTT 60.799 45.000 30.98 0.00 0.00 4.84
312 315 0.798771 TTTTGCTTGTTCGCGCGTTT 60.799 45.000 30.98 0.00 0.00 3.60
313 316 1.467556 TTTGCTTGTTCGCGCGTTTG 61.468 50.000 30.98 16.74 0.00 2.93
314 317 2.351888 GCTTGTTCGCGCGTTTGT 60.352 55.556 30.98 0.00 0.00 2.83
315 318 2.347168 GCTTGTTCGCGCGTTTGTC 61.347 57.895 30.98 16.07 0.00 3.18
316 319 1.721133 CTTGTTCGCGCGTTTGTCC 60.721 57.895 30.98 12.30 0.00 4.02
317 320 3.170810 TTGTTCGCGCGTTTGTCCC 62.171 57.895 30.98 10.90 0.00 4.46
318 321 4.712873 GTTCGCGCGTTTGTCCCG 62.713 66.667 30.98 0.00 0.00 5.14
325 328 3.943034 CGTTTGTCCCGTTGCGCA 61.943 61.111 5.66 5.66 0.00 6.09
326 329 2.353030 GTTTGTCCCGTTGCGCAC 60.353 61.111 11.12 4.51 0.00 5.34
327 330 2.515057 TTTGTCCCGTTGCGCACT 60.515 55.556 11.12 0.00 0.00 4.40
328 331 2.829206 TTTGTCCCGTTGCGCACTG 61.829 57.895 11.12 5.08 0.00 3.66
329 332 4.539083 TGTCCCGTTGCGCACTGT 62.539 61.111 11.12 0.00 0.00 3.55
330 333 3.712881 GTCCCGTTGCGCACTGTC 61.713 66.667 11.12 0.00 0.00 3.51
357 360 2.677003 ATTTGCTTCGCCGGTCGTG 61.677 57.895 16.00 11.83 39.67 4.35
359 362 4.595538 TGCTTCGCCGGTCGTGTT 62.596 61.111 16.00 0.00 39.67 3.32
422 452 6.911250 ATTTGTATCCTCCGGTTTTCTTTT 57.089 33.333 0.00 0.00 0.00 2.27
427 458 8.047413 TGTATCCTCCGGTTTTCTTTTATTTC 57.953 34.615 0.00 0.00 0.00 2.17
430 461 4.770531 CCTCCGGTTTTCTTTTATTTCCCT 59.229 41.667 0.00 0.00 0.00 4.20
474 505 5.126384 TGTTTTCTTTCATCGGTTTTCACCT 59.874 36.000 0.00 0.00 41.64 4.00
833 909 2.291282 ACACGGCCCATAAGAAATTCCA 60.291 45.455 0.00 0.00 0.00 3.53
834 910 2.958355 CACGGCCCATAAGAAATTCCAT 59.042 45.455 0.00 0.00 0.00 3.41
841 917 6.043127 GGCCCATAAGAAATTCCATACCAATT 59.957 38.462 0.00 0.00 0.00 2.32
842 918 7.154656 GCCCATAAGAAATTCCATACCAATTC 58.845 38.462 0.00 0.00 0.00 2.17
844 920 7.370383 CCATAAGAAATTCCATACCAATTCGG 58.630 38.462 0.00 0.00 42.50 4.30
846 922 3.636764 AGAAATTCCATACCAATTCGGCC 59.363 43.478 0.00 0.00 39.03 6.13
847 923 2.746279 ATTCCATACCAATTCGGCCA 57.254 45.000 2.24 0.00 39.03 5.36
848 924 2.051334 TTCCATACCAATTCGGCCAG 57.949 50.000 2.24 0.00 39.03 4.85
850 926 1.455383 CCATACCAATTCGGCCAGCC 61.455 60.000 2.24 0.00 39.03 4.85
915 1047 1.819632 CGGCCATTTCCCTCCTTCG 60.820 63.158 2.24 0.00 0.00 3.79
1131 1273 0.031857 TTCGTTGAAACCCGCGAGTA 59.968 50.000 8.23 0.00 34.78 2.59
1159 1301 6.038271 ACCCGTATTCTGCTTTTATCATTCAC 59.962 38.462 0.00 0.00 0.00 3.18
1161 1303 6.019075 CCGTATTCTGCTTTTATCATTCACGA 60.019 38.462 0.00 0.00 0.00 4.35
1170 1312 5.977171 TTTATCATTCACGATACGGGTTG 57.023 39.130 0.00 0.00 0.00 3.77
1313 1464 3.917988 TGCATCGAGCCAACATATAGAG 58.082 45.455 0.00 0.00 44.83 2.43
1410 1561 2.689553 TCAGCCTGCATTTCACGATA 57.310 45.000 0.00 0.00 0.00 2.92
1431 1582 9.525409 ACGATACTTGTGGAAAATATGTACTAC 57.475 33.333 0.00 0.00 0.00 2.73
1482 1638 1.059584 TGTCTTCCCCAGGCTGTTGA 61.060 55.000 14.43 6.43 0.00 3.18
1490 1649 3.199946 TCCCCAGGCTGTTGAAATACTAG 59.800 47.826 14.43 0.00 0.00 2.57
1491 1650 3.054361 CCCCAGGCTGTTGAAATACTAGT 60.054 47.826 14.43 0.00 0.00 2.57
1492 1651 4.163458 CCCCAGGCTGTTGAAATACTAGTA 59.837 45.833 14.43 4.77 0.00 1.82
1493 1652 5.116882 CCCAGGCTGTTGAAATACTAGTAC 58.883 45.833 14.43 0.00 0.00 2.73
1516 1675 6.977213 ACGTATTTCTTTGCACTTAAATGGT 58.023 32.000 8.76 5.25 0.00 3.55
1608 1768 9.896645 AGCCATTTATAAATCGATGTATCTCAT 57.103 29.630 11.47 0.65 39.77 2.90
1716 1881 4.863548 TCTACTCCCTCGGAATTAGTTGA 58.136 43.478 0.00 0.00 0.00 3.18
1739 1904 5.892568 ACACTCAAACGGATGTATCTAGAC 58.107 41.667 0.00 0.00 0.00 2.59
1744 1909 7.013083 ACTCAAACGGATGTATCTAGACGTATT 59.987 37.037 0.00 0.00 33.85 1.89
1748 1913 7.268199 ACGGATGTATCTAGACGTATTTCAA 57.732 36.000 0.00 0.00 32.30 2.69
1757 1922 8.978564 ATCTAGACGTATTTCAATGCTAGATG 57.021 34.615 13.68 0.00 40.64 2.90
1788 1953 3.197766 TGAGCATCAACTAATTCCGGACT 59.802 43.478 1.83 0.00 45.97 3.85
1789 1954 3.535561 AGCATCAACTAATTCCGGACTG 58.464 45.455 1.83 0.00 0.00 3.51
1790 1955 3.197766 AGCATCAACTAATTCCGGACTGA 59.802 43.478 1.83 0.52 0.00 3.41
1791 1956 3.557595 GCATCAACTAATTCCGGACTGAG 59.442 47.826 1.83 3.53 0.00 3.35
1806 2086 5.127491 CGGACTGAGGAAGTAGATAAGAGT 58.873 45.833 0.00 0.00 40.07 3.24
1814 2094 6.066032 AGGAAGTAGATAAGAGTAGACTGCC 58.934 44.000 0.00 0.00 33.37 4.85
1843 2123 7.649533 TCACATAATTTCATCAGCAAGGAAT 57.350 32.000 0.00 0.00 0.00 3.01
1873 2153 3.755112 AGGCATCATCAGTCATCAGAG 57.245 47.619 0.00 0.00 0.00 3.35
1878 2158 5.179533 GCATCATCAGTCATCAGAGCATAT 58.820 41.667 0.00 0.00 0.00 1.78
1914 2194 5.116882 GTTGTGGTTCTTTCTCAGTACTGT 58.883 41.667 21.99 0.00 0.00 3.55
1922 2202 7.435305 GTTCTTTCTCAGTACTGTTTCTACCT 58.565 38.462 21.99 0.00 0.00 3.08
1927 2207 9.706691 TTTCTCAGTACTGTTTCTACCTTATTG 57.293 33.333 21.99 0.00 0.00 1.90
1928 2208 8.418597 TCTCAGTACTGTTTCTACCTTATTGT 57.581 34.615 21.99 0.00 0.00 2.71
1929 2209 9.524496 TCTCAGTACTGTTTCTACCTTATTGTA 57.476 33.333 21.99 0.00 0.00 2.41
2166 2448 7.822658 AGGCGAGTAGTTTTGCATTTAAATAA 58.177 30.769 0.00 0.00 0.00 1.40
2357 2640 5.534654 TGCCTTGTAAAGTCTTTTAGCATGT 59.465 36.000 2.51 0.00 44.25 3.21
2495 2778 5.124457 CGACAGGATTGAGGTTTGATGATTT 59.876 40.000 0.00 0.00 0.00 2.17
3237 3953 8.700051 TCTTCCTTGTGTTAAAATTCAATTGGA 58.300 29.630 5.42 0.00 0.00 3.53
3258 3974 8.600449 TTGGAAAATATGACAACAACAAATCC 57.400 30.769 0.00 0.00 0.00 3.01
3397 4113 6.303054 TGAAACTTATGTGATTCCCAAGTGA 58.697 36.000 0.00 0.00 30.20 3.41
3537 4254 4.188462 TGGATTATCTGGTAAGTGTTGCG 58.812 43.478 0.00 0.00 0.00 4.85
3819 4536 6.198029 TCTGTACAACGTTTTCATGCATTTTG 59.802 34.615 0.00 0.00 0.00 2.44
3986 4870 3.558418 ACAACCACGTATGAACTGTTGAC 59.442 43.478 0.00 0.00 0.00 3.18
4174 5058 7.023575 AGATGTTGAGTTGCACGATAATTTTC 58.976 34.615 0.00 0.00 0.00 2.29
4230 5114 9.127560 TGGATCCTAATAAGAATGGGTGATAAT 57.872 33.333 14.23 0.00 0.00 1.28
4362 5373 5.099042 TCTACCTTTGCCCTCAGATTAAC 57.901 43.478 0.00 0.00 0.00 2.01
4367 5378 2.698855 TGCCCTCAGATTAACAGCTC 57.301 50.000 0.00 0.00 0.00 4.09
4508 5519 5.011738 TGGGGACTAAGACTAACTTCTTGTG 59.988 44.000 0.00 0.00 39.72 3.33
4510 5521 5.510861 GGGACTAAGACTAACTTCTTGTGCA 60.511 44.000 0.00 0.00 39.72 4.57
4584 5595 4.439253 AAGCAGAAGGAACAGGTACTTT 57.561 40.909 0.00 0.00 34.60 2.66
4585 5596 5.562298 AAGCAGAAGGAACAGGTACTTTA 57.438 39.130 0.00 0.00 34.60 1.85
4610 5621 5.495926 CCATAAGATGGTCCTGCTTATCT 57.504 43.478 11.56 0.00 45.54 1.98
4643 5654 7.125811 TGCTACTCCTGTCTTAAGATAATTGGT 59.874 37.037 8.75 6.78 0.00 3.67
4662 5673 7.675962 ATTGGTTAATTTGACGCAACTAGTA 57.324 32.000 0.00 0.00 0.00 1.82
4715 5729 8.749841 AGTTACTGTATTATTCATCATCGCTC 57.250 34.615 0.00 0.00 0.00 5.03
4785 5808 2.843113 AGCTGAGCAAGGTTTAGATCCT 59.157 45.455 7.39 0.00 36.81 3.24
4842 5871 2.565834 GTCCTGTGAAGTACCTTGGCTA 59.434 50.000 0.00 0.00 0.00 3.93
4847 5876 5.338056 CCTGTGAAGTACCTTGGCTATGTTA 60.338 44.000 0.00 0.00 0.00 2.41
4954 5983 3.187227 AGCAGCTAACACGTGAATTTCTG 59.813 43.478 25.01 20.39 0.00 3.02
4996 6027 1.109920 CCTCCTCGTCATCGGATGGT 61.110 60.000 17.42 0.00 37.69 3.55
5002 6033 1.705337 CGTCATCGGATGGTTGCCAC 61.705 60.000 17.42 6.65 35.80 5.01
5007 6038 4.120331 GGATGGTTGCCACTGCGC 62.120 66.667 0.00 0.00 41.78 6.09
5020 6051 3.963687 CTGCGCTGGGATGCACTCA 62.964 63.158 9.73 0.00 35.90 3.41
5038 6069 3.117512 ACTCATTGGGTTGTTGGAGTCTT 60.118 43.478 0.00 0.00 30.27 3.01
5044 6075 3.219281 GGGTTGTTGGAGTCTTGCTAAA 58.781 45.455 0.00 0.00 0.00 1.85
5057 6088 3.374988 TCTTGCTAAAACTGATGGATGCG 59.625 43.478 0.00 0.00 0.00 4.73
5062 6094 4.494855 GCTAAAACTGATGGATGCGAGTTC 60.495 45.833 0.00 0.00 0.00 3.01
5071 6103 0.718343 GATGCGAGTTCAGACAGTGC 59.282 55.000 0.00 0.00 0.00 4.40
5072 6104 0.671781 ATGCGAGTTCAGACAGTGCC 60.672 55.000 0.00 0.00 0.00 5.01
5118 6150 0.546598 ATTAGGCCTTCCCCGTCTTG 59.453 55.000 12.58 0.00 0.00 3.02
5122 6154 2.747855 CCTTCCCCGTCTTGCTGC 60.748 66.667 0.00 0.00 0.00 5.25
5189 6221 6.551736 TGTGCACTCTAAAAGTTCTTTTCAC 58.448 36.000 19.41 13.17 35.45 3.18
5195 6227 7.162062 CACTCTAAAAGTTCTTTTCACGTTTCG 59.838 37.037 12.82 0.00 35.45 3.46
5209 6241 8.644264 TTTCACGTTTCGTTTGCTAATTATAC 57.356 30.769 0.00 0.00 38.32 1.47
5214 6246 5.721876 TTCGTTTGCTAATTATACACCCG 57.278 39.130 0.00 0.00 0.00 5.28
5242 6274 0.462047 CTCCACTACAATCGGGTGCC 60.462 60.000 0.00 0.00 0.00 5.01
5298 6331 6.228258 AGATTGAAACGAGGCTTTACTGTAA 58.772 36.000 0.00 0.00 0.00 2.41
5303 6336 6.316890 TGAAACGAGGCTTTACTGTAACTTTT 59.683 34.615 0.00 0.00 0.00 2.27
5304 6337 5.668558 ACGAGGCTTTACTGTAACTTTTG 57.331 39.130 0.00 0.00 0.00 2.44
5305 6338 5.362263 ACGAGGCTTTACTGTAACTTTTGA 58.638 37.500 0.00 0.00 0.00 2.69
5306 6339 5.235831 ACGAGGCTTTACTGTAACTTTTGAC 59.764 40.000 0.00 0.00 0.00 3.18
5307 6340 5.235616 CGAGGCTTTACTGTAACTTTTGACA 59.764 40.000 0.00 0.00 0.00 3.58
5308 6341 6.373186 AGGCTTTACTGTAACTTTTGACAC 57.627 37.500 0.00 0.00 0.00 3.67
5309 6342 5.007332 AGGCTTTACTGTAACTTTTGACACG 59.993 40.000 0.00 0.00 0.00 4.49
5310 6343 5.006941 GGCTTTACTGTAACTTTTGACACGA 59.993 40.000 0.00 0.00 0.00 4.35
5311 6344 6.293244 GGCTTTACTGTAACTTTTGACACGAT 60.293 38.462 0.00 0.00 0.00 3.73
5312 6345 7.095523 GGCTTTACTGTAACTTTTGACACGATA 60.096 37.037 0.00 0.00 0.00 2.92
5313 6346 8.440833 GCTTTACTGTAACTTTTGACACGATAT 58.559 33.333 0.00 0.00 0.00 1.63
5314 6347 9.741168 CTTTACTGTAACTTTTGACACGATATG 57.259 33.333 0.00 0.00 0.00 1.78
5347 6380 1.768275 TGTAGCCAGTGTATCATGGGG 59.232 52.381 0.00 0.00 37.05 4.96
5352 6385 0.106708 CAGTGTATCATGGGGTCCCG 59.893 60.000 0.48 0.00 39.42 5.14
5386 6419 2.670635 GCATCAGCGACGATGACTT 58.329 52.632 19.23 0.00 44.67 3.01
5407 6440 4.309950 GGGCGACACGTCCCTTGT 62.310 66.667 3.28 0.00 46.90 3.16
5490 6523 1.079819 CTCGTGTGGCAGTGGTAGG 60.080 63.158 0.00 0.00 0.00 3.18
5491 6524 2.047274 CGTGTGGCAGTGGTAGGG 60.047 66.667 0.00 0.00 0.00 3.53
5492 6525 2.359975 GTGTGGCAGTGGTAGGGC 60.360 66.667 0.00 0.00 0.00 5.19
5544 6578 0.249398 AGTACGTCCCATTCCTGTGC 59.751 55.000 0.00 0.00 0.00 4.57
5558 6592 1.686052 CCTGTGCTCTCCACTAGGATC 59.314 57.143 0.00 0.00 44.70 3.36
5569 6609 3.137728 TCCACTAGGATCGAGTGATGGTA 59.862 47.826 21.88 5.24 46.01 3.25
5637 6677 1.730501 TGAATGCTGTGCTAGTGCTC 58.269 50.000 0.00 0.00 40.48 4.26
5638 6678 0.649475 GAATGCTGTGCTAGTGCTCG 59.351 55.000 0.00 0.00 40.48 5.03
5639 6679 0.247460 AATGCTGTGCTAGTGCTCGA 59.753 50.000 0.00 0.00 40.48 4.04
5641 6681 1.214062 GCTGTGCTAGTGCTCGAGT 59.786 57.895 15.13 0.00 40.48 4.18
5642 6682 0.452184 GCTGTGCTAGTGCTCGAGTA 59.548 55.000 15.13 6.73 40.48 2.59
5643 6683 1.532921 GCTGTGCTAGTGCTCGAGTAG 60.533 57.143 15.13 9.12 40.48 2.57
5648 6688 1.332375 GCTAGTGCTCGAGTAGGAGTG 59.668 57.143 15.13 0.00 36.41 3.51
5649 6689 1.332375 CTAGTGCTCGAGTAGGAGTGC 59.668 57.143 15.13 0.00 36.41 4.40
5694 6742 1.405821 ACCTCAACGATAGGAGAAGCG 59.594 52.381 8.99 0.00 43.77 4.68
5734 6782 2.481104 CCACCATGCAGTTCGTTTTGTT 60.481 45.455 0.00 0.00 0.00 2.83
5742 6790 3.300009 CAGTTCGTTTTGTTCTCATGGC 58.700 45.455 0.00 0.00 0.00 4.40
5762 6810 2.032054 GCTGTTTTCCTTTTTGCAAGGC 59.968 45.455 0.00 0.00 37.34 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.963428 TTCTTCCTTCGCTTTCTAGCT 57.037 42.857 0.00 0.00 45.51 3.32
111 113 5.959618 ATAGTTTTCCGGGTTTTCTTCTG 57.040 39.130 0.00 0.00 0.00 3.02
131 133 2.224402 GGTTTGGGGCTGTTTTGCAATA 60.224 45.455 0.00 0.00 34.04 1.90
147 149 2.006888 CCAGTACCGTAGCATGGTTTG 58.993 52.381 1.12 0.00 38.67 2.93
194 196 3.048600 TGGGAGCTATATCTGGCTTGTT 58.951 45.455 0.00 0.00 39.63 2.83
219 221 7.672240 TCAGTATGGGCGATACATAACAATTA 58.328 34.615 19.75 0.00 39.71 1.40
238 240 7.469537 GGCGAGCCCTATTATATATCAGTAT 57.530 40.000 1.97 0.00 0.00 2.12
299 302 2.325166 GGACAAACGCGCGAACAA 59.675 55.556 39.36 0.00 0.00 2.83
308 311 3.943034 TGCGCAACGGGACAAACG 61.943 61.111 8.16 0.00 37.36 3.60
309 312 2.353030 GTGCGCAACGGGACAAAC 60.353 61.111 14.00 0.00 0.00 2.93
310 313 2.515057 AGTGCGCAACGGGACAAA 60.515 55.556 14.00 0.00 0.00 2.83
311 314 3.276091 CAGTGCGCAACGGGACAA 61.276 61.111 14.00 0.00 0.00 3.18
312 315 4.539083 ACAGTGCGCAACGGGACA 62.539 61.111 14.00 0.00 0.00 4.02
313 316 3.712881 GACAGTGCGCAACGGGAC 61.713 66.667 14.00 0.00 0.00 4.46
324 327 2.616330 AAATGTGCCCGCGACAGTG 61.616 57.895 8.23 0.00 0.00 3.66
325 328 2.281484 AAATGTGCCCGCGACAGT 60.281 55.556 8.23 0.00 0.00 3.55
326 329 2.176546 CAAATGTGCCCGCGACAG 59.823 61.111 8.23 0.00 0.00 3.51
327 330 4.036804 GCAAATGTGCCCGCGACA 62.037 61.111 8.23 4.15 45.68 4.35
539 574 6.509418 ACGCATAGGAAAAATGTACAATGT 57.491 33.333 0.00 0.00 0.00 2.71
796 860 5.124936 GGGCCGTGTATAAAACTTGAGATTT 59.875 40.000 0.00 0.00 0.00 2.17
797 861 4.638865 GGGCCGTGTATAAAACTTGAGATT 59.361 41.667 0.00 0.00 0.00 2.40
811 887 3.054287 TGGAATTTCTTATGGGCCGTGTA 60.054 43.478 8.97 0.00 0.00 2.90
812 888 2.291282 TGGAATTTCTTATGGGCCGTGT 60.291 45.455 8.97 0.00 0.00 4.49
833 909 4.579127 GGCTGGCCGAATTGGTAT 57.421 55.556 0.00 0.00 41.21 2.73
866 970 2.100916 GTGAGCTCTCGTGGGCTAATAA 59.899 50.000 12.63 0.00 39.05 1.40
867 971 1.681793 GTGAGCTCTCGTGGGCTAATA 59.318 52.381 12.63 0.00 39.05 0.98
915 1047 1.578897 AAGGAGAGGAAGAAGGAGGC 58.421 55.000 0.00 0.00 0.00 4.70
1131 1273 5.680619 TGATAAAAGCAGAATACGGGTGAT 58.319 37.500 0.00 0.00 0.00 3.06
1159 1301 3.754740 TACGCCGCAACCCGTATCG 62.755 63.158 0.00 0.00 38.75 2.92
1161 1303 1.383456 TACTACGCCGCAACCCGTAT 61.383 55.000 0.00 0.00 38.97 3.06
1170 1312 0.179156 TACAGTGCTTACTACGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
1313 1464 6.594159 TCCAAATCCGATTCAGTCTTAGTTTC 59.406 38.462 0.00 0.00 0.00 2.78
1434 1585 8.565416 AGCTCAAAACCACAAGTAAAGTAATAC 58.435 33.333 0.00 0.00 0.00 1.89
1435 1586 8.685838 AGCTCAAAACCACAAGTAAAGTAATA 57.314 30.769 0.00 0.00 0.00 0.98
1436 1587 7.582667 AGCTCAAAACCACAAGTAAAGTAAT 57.417 32.000 0.00 0.00 0.00 1.89
1437 1588 8.508883 TTAGCTCAAAACCACAAGTAAAGTAA 57.491 30.769 0.00 0.00 0.00 2.24
1438 1589 8.564574 CATTAGCTCAAAACCACAAGTAAAGTA 58.435 33.333 0.00 0.00 0.00 2.24
1439 1590 7.068226 ACATTAGCTCAAAACCACAAGTAAAGT 59.932 33.333 0.00 0.00 0.00 2.66
1440 1591 7.425606 ACATTAGCTCAAAACCACAAGTAAAG 58.574 34.615 0.00 0.00 0.00 1.85
1441 1592 7.284489 AGACATTAGCTCAAAACCACAAGTAAA 59.716 33.333 0.00 0.00 0.00 2.01
1490 1649 8.019094 ACCATTTAAGTGCAAAGAAATACGTAC 58.981 33.333 0.00 0.00 0.00 3.67
1491 1650 8.101654 ACCATTTAAGTGCAAAGAAATACGTA 57.898 30.769 0.00 0.00 0.00 3.57
1492 1651 6.977213 ACCATTTAAGTGCAAAGAAATACGT 58.023 32.000 0.00 0.00 0.00 3.57
1493 1652 7.867445 AACCATTTAAGTGCAAAGAAATACG 57.133 32.000 0.00 0.00 0.00 3.06
1516 1675 6.767902 GCTGTCAATGGTTTCCTGATATCTAA 59.232 38.462 3.98 0.00 0.00 2.10
1629 1789 2.088423 AGTTTTCCACGACAAACAGCA 58.912 42.857 0.00 0.00 35.66 4.41
1631 1791 2.422127 ACCAGTTTTCCACGACAAACAG 59.578 45.455 0.00 0.00 35.66 3.16
1716 1881 5.448768 CGTCTAGATACATCCGTTTGAGTGT 60.449 44.000 0.00 0.00 0.00 3.55
1757 1922 3.844577 AGTTGATGCTCAAACAGATGC 57.155 42.857 0.96 0.00 38.22 3.91
1788 1953 6.768861 GCAGTCTACTCTTATCTACTTCCTCA 59.231 42.308 0.00 0.00 0.00 3.86
1789 1954 6.206048 GGCAGTCTACTCTTATCTACTTCCTC 59.794 46.154 0.00 0.00 0.00 3.71
1790 1955 6.066032 GGCAGTCTACTCTTATCTACTTCCT 58.934 44.000 0.00 0.00 0.00 3.36
1791 1956 5.049267 CGGCAGTCTACTCTTATCTACTTCC 60.049 48.000 0.00 0.00 0.00 3.46
1806 2086 7.269316 TGAAATTATGTGAATACGGCAGTCTA 58.731 34.615 0.00 0.00 0.00 2.59
1814 2094 7.588854 CCTTGCTGATGAAATTATGTGAATACG 59.411 37.037 0.00 0.00 0.00 3.06
1843 2123 4.847198 ACTGATGATGCCTTGTCACATTA 58.153 39.130 0.00 0.00 0.00 1.90
1878 2158 3.815856 ACCACAACATGTTGAATGCAA 57.184 38.095 38.30 0.00 42.93 4.08
1927 2207 8.663025 GTTGCTTGGTAAACTAGTAGGAATTAC 58.337 37.037 0.00 0.66 0.00 1.89
1928 2208 7.825761 GGTTGCTTGGTAAACTAGTAGGAATTA 59.174 37.037 0.00 0.00 0.00 1.40
1929 2209 6.657966 GGTTGCTTGGTAAACTAGTAGGAATT 59.342 38.462 0.00 0.00 0.00 2.17
1939 2221 3.577805 ACTCTGGTTGCTTGGTAAACT 57.422 42.857 0.00 0.00 0.00 2.66
2086 2368 1.140312 AGAAACCCACTGCTCCAGAA 58.860 50.000 0.00 0.00 35.18 3.02
2590 3306 5.298777 ACACGTAGCCTAGTTATGGAGTAAG 59.701 44.000 0.00 0.00 0.00 2.34
3258 3974 6.603237 TTCGAGAAATGGTGTGCATATTAG 57.397 37.500 0.00 0.00 0.00 1.73
3397 4113 3.815401 GTGCTAACAATCAGTGAAGGTGT 59.185 43.478 0.00 0.00 0.00 4.16
3537 4254 4.272504 TGAACAACTACACTTAAGCAGCAC 59.727 41.667 1.29 0.00 0.00 4.40
3819 4536 3.898482 AGTAGGGTGGCCAATCATAAAC 58.102 45.455 7.24 0.00 0.00 2.01
3986 4870 8.334016 TGTGATTTAACAACTTTCATGAAACG 57.666 30.769 16.91 14.56 0.00 3.60
4059 4943 6.512342 TGACTTTTACCAAGTTCGGAAAAA 57.488 33.333 0.00 0.00 0.00 1.94
4080 4964 5.866092 CAGAAAAGAACAGAGATCGACATGA 59.134 40.000 0.00 0.00 0.00 3.07
4174 5058 8.910944 AGGAGAAGGAAATCACAATATTTCATG 58.089 33.333 10.50 0.00 44.28 3.07
4243 5127 7.334421 GTCTTATGTTTCTGATAGCAACCTGAA 59.666 37.037 0.00 0.00 0.00 3.02
4367 5378 4.743151 TCTTTTCCTATGTATACAAGCGCG 59.257 41.667 10.14 0.00 0.00 6.86
4473 5484 3.452990 TCTTAGTCCCCAATGCATCGTTA 59.547 43.478 0.00 0.00 0.00 3.18
4508 5519 6.521133 CGTCTGTGATTTTCTGTAGAATTTGC 59.479 38.462 0.00 0.00 33.54 3.68
4510 5521 7.657761 ACTCGTCTGTGATTTTCTGTAGAATTT 59.342 33.333 0.00 0.00 33.54 1.82
4610 5621 6.437477 TCTTAAGACAGGAGTAGCATTGAAGA 59.563 38.462 0.00 0.00 0.00 2.87
4715 5729 7.938563 TTTGTTTATTTTTCCATGGTTCTCG 57.061 32.000 12.58 0.00 0.00 4.04
4747 5761 2.421424 CAGCTCCTGAAAAGGGAAATCG 59.579 50.000 0.00 0.00 32.44 3.34
4785 5808 2.680841 CAGTTTTTGTTCAGTCGGGTCA 59.319 45.455 0.00 0.00 0.00 4.02
4899 5928 0.796927 GACTGCCGTTTTAGGAGCAC 59.203 55.000 0.00 0.00 0.00 4.40
4954 5983 3.671702 GCTTCAGAAAACATGTAGCCTGC 60.672 47.826 0.00 0.00 35.68 4.85
4996 6027 4.349503 ATCCCAGCGCAGTGGCAA 62.350 61.111 11.47 0.49 41.24 4.52
5007 6038 0.033796 ACCCAATGAGTGCATCCCAG 60.034 55.000 0.00 0.00 32.35 4.45
5012 6043 1.619827 CCAACAACCCAATGAGTGCAT 59.380 47.619 0.00 0.00 35.92 3.96
5020 6051 1.963515 GCAAGACTCCAACAACCCAAT 59.036 47.619 0.00 0.00 0.00 3.16
5038 6069 2.938451 CTCGCATCCATCAGTTTTAGCA 59.062 45.455 0.00 0.00 0.00 3.49
5044 6075 2.234661 TCTGAACTCGCATCCATCAGTT 59.765 45.455 0.00 0.00 38.83 3.16
5057 6088 1.005630 AGCGGCACTGTCTGAACTC 60.006 57.895 1.45 0.00 0.00 3.01
5071 6103 3.083600 GAAACGATGGACGCAGCGG 62.084 63.158 21.15 1.91 46.94 5.52
5072 6104 2.395690 GAAACGATGGACGCAGCG 59.604 61.111 14.82 14.82 46.94 5.18
5122 6154 2.036958 TATTGACAATGGCAGTCGGG 57.963 50.000 11.05 0.00 38.83 5.14
5189 6221 5.961263 GGGTGTATAATTAGCAAACGAAACG 59.039 40.000 0.00 0.00 0.00 3.60
5195 6227 3.566742 CCCCGGGTGTATAATTAGCAAAC 59.433 47.826 21.85 0.00 0.00 2.93
5230 6262 1.000731 CAATTTGTGGCACCCGATTGT 59.999 47.619 16.26 0.00 0.00 2.71
5242 6274 3.809279 GGAAAGAACTTGCCCAATTTGTG 59.191 43.478 0.22 0.00 31.77 3.33
5298 6331 2.006888 CCGGCATATCGTGTCAAAAGT 58.993 47.619 0.00 0.00 30.99 2.66
5303 6336 2.108157 GGCCGGCATATCGTGTCA 59.892 61.111 30.85 0.00 30.99 3.58
5304 6337 2.108157 TGGCCGGCATATCGTGTC 59.892 61.111 30.85 7.78 0.00 3.67
5305 6338 2.203015 GTGGCCGGCATATCGTGT 60.203 61.111 30.85 0.00 0.00 4.49
5306 6339 2.972505 GGTGGCCGGCATATCGTG 60.973 66.667 30.85 0.00 0.00 4.35
5307 6340 4.602259 CGGTGGCCGGCATATCGT 62.602 66.667 30.85 0.00 44.15 3.73
5347 6380 1.329599 GTGGATATTTTCACGCGGGAC 59.670 52.381 12.52 0.00 0.00 4.46
5368 6401 0.299895 CAAGTCATCGTCGCTGATGC 59.700 55.000 1.62 7.19 44.32 3.91
5407 6440 2.338620 CAGCCTGGTCGTTGTCGA 59.661 61.111 0.00 0.00 44.12 4.20
5521 6554 2.494870 ACAGGAATGGGACGTACTGTAC 59.505 50.000 7.90 7.90 37.41 2.90
5544 6578 3.201353 TCACTCGATCCTAGTGGAGAG 57.799 52.381 18.15 5.91 46.91 3.20
5558 6592 0.815734 ACCGGAGTTACCATCACTCG 59.184 55.000 9.46 0.00 41.54 4.18
5569 6609 3.262405 TGAATACTTTGCCTACCGGAGTT 59.738 43.478 9.46 0.00 0.00 3.01
5632 6672 1.064357 GTAGCACTCCTACTCGAGCAC 59.936 57.143 13.61 0.00 42.58 4.40
5641 6681 3.447586 GGACACATGAAGTAGCACTCCTA 59.552 47.826 0.00 0.00 0.00 2.94
5642 6682 2.234908 GGACACATGAAGTAGCACTCCT 59.765 50.000 0.00 0.00 0.00 3.69
5643 6683 2.622436 GGACACATGAAGTAGCACTCC 58.378 52.381 0.00 0.00 0.00 3.85
5648 6688 2.094700 TCTGACGGACACATGAAGTAGC 60.095 50.000 0.00 0.00 0.00 3.58
5649 6689 3.850122 TCTGACGGACACATGAAGTAG 57.150 47.619 0.00 0.00 0.00 2.57
5694 6742 6.578023 TGGTGGTAATAATTTGCTAATTGCC 58.422 36.000 15.16 11.81 42.00 4.52
5714 6762 2.490328 ACAAAACGAACTGCATGGTG 57.510 45.000 0.00 0.00 0.00 4.17
5734 6782 4.740334 GCAAAAAGGAAAACAGCCATGAGA 60.740 41.667 0.00 0.00 0.00 3.27
5742 6790 3.534554 AGCCTTGCAAAAAGGAAAACAG 58.465 40.909 7.13 0.00 39.81 3.16


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

AutoCloner maintained by Alex Coulton.