Multiple sequence alignment - TraesCS4A01G057500

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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 TraesCS4A01G057500 chr4A 100.000 1852 0 0 761 2612 48275134 48276985 0.000000e+00 3421
1 TraesCS4A01G057500 chr4A 100.000 448 0 0 1 448 48274374 48274821 0.000000e+00 828
2 TraesCS4A01G057500 chr4A 92.800 250 15 3 1 249 444826915 444827162 2.470000e-95 359
3 TraesCS4A01G057500 chr4D 86.214 1857 132 64 792 2612 415584003 415582235 0.000000e+00 1897
4 TraesCS4A01G057500 chr4B 93.251 889 44 10 792 1669 512335517 512334634 0.000000e+00 1295
5 TraesCS4A01G057500 chr4B 87.585 443 52 2 6 448 512336080 512335641 6.450000e-141 510
6 TraesCS4A01G057500 chr4B 84.615 221 14 6 1849 2069 512334546 512334346 4.410000e-48 202
7 TraesCS4A01G057500 chr7B 89.517 725 55 14 798 1507 16135778 16136496 0.000000e+00 898
8 TraesCS4A01G057500 chr7B 85.498 793 85 24 938 1708 13329716 13328932 0.000000e+00 800
9 TraesCS4A01G057500 chr7B 86.951 728 73 19 782 1493 14980484 14981205 0.000000e+00 798
10 TraesCS4A01G057500 chr7A 83.490 957 99 34 798 1718 76954422 76953489 0.000000e+00 837
11 TraesCS4A01G057500 chr7D 85.254 807 71 30 947 1718 70905451 70904658 0.000000e+00 787
12 TraesCS4A01G057500 chr7D 86.771 703 63 20 810 1491 71812297 71812990 0.000000e+00 756
13 TraesCS4A01G057500 chr7D 85.537 726 83 16 782 1490 72128186 72128906 0.000000e+00 739
14 TraesCS4A01G057500 chrUn 85.615 723 82 16 785 1490 273471168 273470451 0.000000e+00 739


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 TraesCS4A01G057500 chr4A 48274374 48276985 2611 False 2124.5 3421 100.000000 1 2612 2 chr4A.!!$F2 2611
1 TraesCS4A01G057500 chr4D 415582235 415584003 1768 True 1897.0 1897 86.214000 792 2612 1 chr4D.!!$R1 1820
2 TraesCS4A01G057500 chr4B 512334346 512336080 1734 True 669.0 1295 88.483667 6 2069 3 chr4B.!!$R1 2063
3 TraesCS4A01G057500 chr7B 16135778 16136496 718 False 898.0 898 89.517000 798 1507 1 chr7B.!!$F2 709
4 TraesCS4A01G057500 chr7B 13328932 13329716 784 True 800.0 800 85.498000 938 1708 1 chr7B.!!$R1 770
5 TraesCS4A01G057500 chr7B 14980484 14981205 721 False 798.0 798 86.951000 782 1493 1 chr7B.!!$F1 711
6 TraesCS4A01G057500 chr7A 76953489 76954422 933 True 837.0 837 83.490000 798 1718 1 chr7A.!!$R1 920
7 TraesCS4A01G057500 chr7D 70904658 70905451 793 True 787.0 787 85.254000 947 1718 1 chr7D.!!$R1 771
8 TraesCS4A01G057500 chr7D 71812297 71812990 693 False 756.0 756 86.771000 810 1491 1 chr7D.!!$F1 681
9 TraesCS4A01G057500 chr7D 72128186 72128906 720 False 739.0 739 85.537000 782 1490 1 chr7D.!!$F2 708
10 TraesCS4A01G057500 chrUn 273470451 273471168 717 True 739.0 739 85.615000 785 1490 1 chrUn.!!$R1 705

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
84 85 0.035056 GTCTTCCACATCACCCCCAG 60.035 60.0 0.0 0.0 0.0 4.45 F
788 789 0.179124 CTGCTCTAGTCCCGCTCAAC 60.179 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1056 1115 0.178891 AGCTTGTTGGAGAGGGGAGA 60.179 55.0 0.0 0.0 0.00 3.71 R
1738 1835 0.182061 ATGCACTCCCAGATCGCAAT 59.818 50.0 0.0 0.0 35.98 3.56 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
18 19 3.706373 TCGACTCTGCCCCCAAGC 61.706 66.667 0.00 0.00 0.00 4.01
30 31 1.593265 CCCAAGCAACCCAAGATGC 59.407 57.895 0.00 0.00 42.87 3.91
37 38 1.673626 GCAACCCAAGATGCAACCATG 60.674 52.381 0.00 0.00 42.12 3.66
38 39 1.066716 CAACCCAAGATGCAACCATGG 60.067 52.381 11.19 11.19 0.00 3.66
75 76 2.579201 CCGCTCCGTCTTCCACAT 59.421 61.111 0.00 0.00 0.00 3.21
77 78 1.215382 CGCTCCGTCTTCCACATCA 59.785 57.895 0.00 0.00 0.00 3.07
78 79 1.078759 CGCTCCGTCTTCCACATCAC 61.079 60.000 0.00 0.00 0.00 3.06
84 85 0.035056 GTCTTCCACATCACCCCCAG 60.035 60.000 0.00 0.00 0.00 4.45
116 117 1.206132 ACCTATCCGACAACGATGCAA 59.794 47.619 0.00 0.00 42.66 4.08
119 120 3.126171 CCTATCCGACAACGATGCAAAAA 59.874 43.478 0.00 0.00 42.66 1.94
147 148 4.041740 TCATGTGCTAGTGTTATCCGAC 57.958 45.455 0.00 0.00 0.00 4.79
167 168 4.339530 CGACAGAAGATGATACCTCCAAGA 59.660 45.833 0.00 0.00 0.00 3.02
176 177 0.324091 TACCTCCAAGACGACTCCCC 60.324 60.000 0.00 0.00 0.00 4.81
192 193 3.197790 CCCAAGGAGCATGCGACG 61.198 66.667 13.01 0.25 0.00 5.12
198 199 1.446099 GGAGCATGCGACGAGAACA 60.446 57.895 13.01 0.00 0.00 3.18
202 203 1.886861 GCATGCGACGAGAACAACGT 61.887 55.000 0.00 0.00 46.58 3.99
203 204 0.506932 CATGCGACGAGAACAACGTT 59.493 50.000 0.00 0.00 43.97 3.99
211 212 1.153329 AGAACAACGTTGACGCCCA 60.153 52.632 33.66 0.00 44.43 5.36
215 216 2.280592 AACGTTGACGCCCACTCC 60.281 61.111 0.00 0.00 44.43 3.85
221 222 3.998672 GACGCCCACTCCGACCAA 61.999 66.667 0.00 0.00 0.00 3.67
234 235 4.351054 ACCAAGGCCGGAGCTTGG 62.351 66.667 17.02 17.02 45.34 3.61
269 270 4.933400 AGCTTCATGATGCAAATTTGAACC 59.067 37.500 29.04 2.29 34.33 3.62
289 290 7.436118 TGAACCAAAAATCAGGAGAAATTCAG 58.564 34.615 0.00 0.00 0.00 3.02
300 301 5.008980 AGGAGAAATTCAGAAAAGGCTCAG 58.991 41.667 0.00 0.00 0.00 3.35
303 304 5.380043 AGAAATTCAGAAAAGGCTCAGACA 58.620 37.500 0.00 0.00 0.00 3.41
311 312 4.225942 AGAAAAGGCTCAGACACATATCCA 59.774 41.667 0.00 0.00 0.00 3.41
334 335 6.403636 CCACATAACAAGGTAAGCAAGATGAC 60.404 42.308 0.00 0.00 0.00 3.06
337 338 2.076100 CAAGGTAAGCAAGATGACGCA 58.924 47.619 0.00 0.00 0.00 5.24
339 340 1.009829 GGTAAGCAAGATGACGCAGG 58.990 55.000 0.00 0.00 0.00 4.85
377 378 6.954944 ACCGTGGTAAAAATTATCGATCATG 58.045 36.000 0.00 0.00 0.00 3.07
393 394 3.840890 TCATGCAACGGTCCATTTAAC 57.159 42.857 0.00 0.00 0.00 2.01
397 398 4.592485 TGCAACGGTCCATTTAACATTT 57.408 36.364 0.00 0.00 0.00 2.32
399 400 6.085555 TGCAACGGTCCATTTAACATTTTA 57.914 33.333 0.00 0.00 0.00 1.52
401 402 6.984474 TGCAACGGTCCATTTAACATTTTAAA 59.016 30.769 0.00 0.00 40.63 1.52
428 429 4.684242 CCTTTTAACAAATTGCTCCGGAAC 59.316 41.667 5.23 0.16 0.00 3.62
435 436 4.258543 CAAATTGCTCCGGAACTAGGTTA 58.741 43.478 5.23 0.00 0.00 2.85
442 443 7.166691 TGCTCCGGAACTAGGTTATATTATC 57.833 40.000 5.23 0.00 0.00 1.75
445 446 7.921745 GCTCCGGAACTAGGTTATATTATCATC 59.078 40.741 5.23 0.00 0.00 2.92
787 788 0.612174 ACTGCTCTAGTCCCGCTCAA 60.612 55.000 0.00 0.00 33.17 3.02
788 789 0.179124 CTGCTCTAGTCCCGCTCAAC 60.179 60.000 0.00 0.00 0.00 3.18
789 790 0.898326 TGCTCTAGTCCCGCTCAACA 60.898 55.000 0.00 0.00 0.00 3.33
790 791 0.179124 GCTCTAGTCCCGCTCAACAG 60.179 60.000 0.00 0.00 0.00 3.16
791 792 0.179124 CTCTAGTCCCGCTCAACAGC 60.179 60.000 0.00 0.00 42.96 4.40
845 860 3.645975 CGTGACGGCCGCAAACTT 61.646 61.111 28.58 3.50 0.00 2.66
852 867 1.861542 CGGCCGCAAACTTGAATCCA 61.862 55.000 14.67 0.00 0.00 3.41
857 872 2.050691 CGCAAACTTGAATCCAAACCG 58.949 47.619 0.00 0.00 0.00 4.44
1016 1054 1.375396 CCACCACCGCGAGAAATCA 60.375 57.895 8.23 0.00 0.00 2.57
1051 1110 3.193614 CCGTAGCAGCAGCAGCAG 61.194 66.667 12.92 0.00 45.49 4.24
1065 1124 1.049855 CAGCAGCATCTCTCCCCTCT 61.050 60.000 0.00 0.00 0.00 3.69
1068 1127 0.398239 CAGCATCTCTCCCCTCTCCA 60.398 60.000 0.00 0.00 0.00 3.86
1069 1128 0.341258 AGCATCTCTCCCCTCTCCAA 59.659 55.000 0.00 0.00 0.00 3.53
1076 1143 0.695347 CTCCCCTCTCCAACAAGCTT 59.305 55.000 0.00 0.00 0.00 3.74
1540 1609 0.464036 TTGCCGGTAGCTGTCTATGG 59.536 55.000 1.90 0.00 44.23 2.74
1577 1666 1.210478 CCTCCTTGTATGTCCTGTGGG 59.790 57.143 0.00 0.00 0.00 4.61
1694 1791 4.712476 AGATCTTGTATGCTTGATGGTCC 58.288 43.478 0.00 0.00 0.00 4.46
1738 1835 2.246067 TGCTAAGGCCCCCATTTGATTA 59.754 45.455 0.00 0.00 37.74 1.75
1739 1836 3.116784 TGCTAAGGCCCCCATTTGATTAT 60.117 43.478 0.00 0.00 37.74 1.28
1750 1847 4.321452 CCCATTTGATTATTGCGATCTGGG 60.321 45.833 0.00 0.00 33.10 4.45
1778 1875 0.676466 TGCGGGCTACAGTTTCATGG 60.676 55.000 0.00 0.00 0.00 3.66
1780 1877 1.369625 CGGGCTACAGTTTCATGGTC 58.630 55.000 0.00 0.00 0.00 4.02
1782 1879 2.359900 GGGCTACAGTTTCATGGTCTG 58.640 52.381 0.00 2.19 35.60 3.51
1783 1880 2.290323 GGGCTACAGTTTCATGGTCTGT 60.290 50.000 17.29 17.29 43.46 3.41
1784 1881 3.412386 GGCTACAGTTTCATGGTCTGTT 58.588 45.455 17.97 7.69 41.66 3.16
1785 1882 3.189287 GGCTACAGTTTCATGGTCTGTTG 59.811 47.826 17.97 16.87 41.66 3.33
1786 1883 3.189287 GCTACAGTTTCATGGTCTGTTGG 59.811 47.826 17.97 13.77 41.66 3.77
1787 1884 1.956477 ACAGTTTCATGGTCTGTTGGC 59.044 47.619 10.78 0.00 39.00 4.52
1788 1885 2.233271 CAGTTTCATGGTCTGTTGGCT 58.767 47.619 0.00 0.00 0.00 4.75
1789 1886 2.624838 CAGTTTCATGGTCTGTTGGCTT 59.375 45.455 0.00 0.00 0.00 4.35
1790 1887 3.068590 CAGTTTCATGGTCTGTTGGCTTT 59.931 43.478 0.00 0.00 0.00 3.51
1791 1888 3.706086 AGTTTCATGGTCTGTTGGCTTTT 59.294 39.130 0.00 0.00 0.00 2.27
1792 1889 4.162131 AGTTTCATGGTCTGTTGGCTTTTT 59.838 37.500 0.00 0.00 0.00 1.94
1837 1934 5.689819 CGACTACCAGTTTCTTGGAAATTG 58.310 41.667 8.03 8.03 40.87 2.32
1852 1957 4.883585 TGGAAATTGAGGCTGTGATACATC 59.116 41.667 0.00 0.00 0.00 3.06
1955 2067 0.598065 ATTTGCTGCGGGTTCAGTTC 59.402 50.000 0.00 0.00 36.49 3.01
1958 2070 0.037326 TGCTGCGGGTTCAGTTCTAG 60.037 55.000 0.00 0.00 36.49 2.43
2027 2153 6.039605 TCAATTCTGAAACAGCTCATTTGTGA 59.960 34.615 0.00 0.00 0.00 3.58
2028 2154 4.818534 TCTGAAACAGCTCATTTGTGAC 57.181 40.909 0.00 0.00 0.00 3.67
2063 2198 9.752961 TGCTCATATGGAATGACAAATATTTTG 57.247 29.630 2.13 0.00 0.00 2.44
2067 2202 8.767085 CATATGGAATGACAAATATTTTGGCAC 58.233 33.333 10.51 0.01 40.72 5.01
2070 2205 6.165577 GGAATGACAAATATTTTGGCACACT 58.834 36.000 10.51 0.00 40.72 3.55
2163 2298 8.352201 TGTCTTTCAATGTGTTATTTGAAGAGG 58.648 33.333 0.00 0.00 41.42 3.69
2164 2299 7.809806 GTCTTTCAATGTGTTATTTGAAGAGGG 59.190 37.037 0.00 0.00 41.42 4.30
2166 2301 7.595819 TTCAATGTGTTATTTGAAGAGGGTT 57.404 32.000 0.00 0.00 37.03 4.11
2167 2302 7.595819 TCAATGTGTTATTTGAAGAGGGTTT 57.404 32.000 0.00 0.00 0.00 3.27
2168 2303 8.017418 TCAATGTGTTATTTGAAGAGGGTTTT 57.983 30.769 0.00 0.00 0.00 2.43
2169 2304 8.141268 TCAATGTGTTATTTGAAGAGGGTTTTC 58.859 33.333 0.00 0.00 0.00 2.29
2170 2305 6.399639 TGTGTTATTTGAAGAGGGTTTTCC 57.600 37.500 0.00 0.00 39.75 3.13
2188 2323 6.389906 GTTTTCCCATGTGGAGTATCAAAAG 58.610 40.000 0.00 0.00 46.24 2.27
2193 2328 5.586243 CCCATGTGGAGTATCAAAAGTAGTG 59.414 44.000 0.00 0.00 36.25 2.74
2196 2331 7.492669 CCATGTGGAGTATCAAAAGTAGTGTAG 59.507 40.741 0.00 0.00 36.25 2.74
2211 2346 3.467803 AGTGTAGTTTGTCTGTTCCAGC 58.532 45.455 0.00 0.00 0.00 4.85
2231 2366 2.323959 CTTCAGAGTTGAGCGAGTCAC 58.676 52.381 0.00 0.00 33.71 3.67
2242 2377 2.484651 GAGCGAGTCACTGAGAGTTGTA 59.515 50.000 0.00 0.00 34.11 2.41
2244 2379 2.857618 CGAGTCACTGAGAGTTGTAGC 58.142 52.381 0.00 0.00 0.00 3.58
2245 2380 2.486203 CGAGTCACTGAGAGTTGTAGCT 59.514 50.000 0.00 0.00 0.00 3.32
2246 2381 3.669290 CGAGTCACTGAGAGTTGTAGCTG 60.669 52.174 0.00 0.00 0.00 4.24
2247 2382 2.029470 AGTCACTGAGAGTTGTAGCTGC 60.029 50.000 0.00 0.00 0.00 5.25
2248 2383 1.963515 TCACTGAGAGTTGTAGCTGCA 59.036 47.619 0.00 0.00 0.00 4.41
2249 2384 2.029560 TCACTGAGAGTTGTAGCTGCAG 60.030 50.000 10.11 10.11 0.00 4.41
2250 2385 2.029560 CACTGAGAGTTGTAGCTGCAGA 60.030 50.000 20.43 0.00 0.00 4.26
2251 2386 2.830923 ACTGAGAGTTGTAGCTGCAGAT 59.169 45.455 20.43 15.46 0.00 2.90
2252 2387 3.260380 ACTGAGAGTTGTAGCTGCAGATT 59.740 43.478 20.43 7.19 0.00 2.40
2253 2388 4.252073 CTGAGAGTTGTAGCTGCAGATTT 58.748 43.478 20.43 4.34 0.00 2.17
2254 2389 4.645535 TGAGAGTTGTAGCTGCAGATTTT 58.354 39.130 20.43 1.55 0.00 1.82
2255 2390 5.065914 TGAGAGTTGTAGCTGCAGATTTTT 58.934 37.500 20.43 0.00 0.00 1.94
2256 2391 5.180117 TGAGAGTTGTAGCTGCAGATTTTTC 59.820 40.000 20.43 5.76 0.00 2.29
2260 2395 6.809869 AGTTGTAGCTGCAGATTTTTCTTTT 58.190 32.000 20.43 0.00 0.00 2.27
2271 2406 6.155827 CAGATTTTTCTTTTCCCGCATACAA 58.844 36.000 0.00 0.00 0.00 2.41
2275 2410 5.975693 TTTCTTTTCCCGCATACAAATCT 57.024 34.783 0.00 0.00 0.00 2.40
2284 2419 4.024556 CCCGCATACAAATCTTAGCAGAAG 60.025 45.833 0.00 0.00 30.76 2.85
2285 2420 4.521943 CGCATACAAATCTTAGCAGAAGC 58.478 43.478 0.00 0.00 42.56 3.86
2336 2471 5.706916 AGACAACAATCAATTCTGATGCAC 58.293 37.500 0.00 0.00 41.66 4.57
2341 2476 5.232463 ACAATCAATTCTGATGCACAAACC 58.768 37.500 0.00 0.00 41.66 3.27
2394 2530 6.405538 TCAAACTTTCTTGTTTCCATGCTTT 58.594 32.000 0.00 0.00 37.98 3.51
2398 2534 6.172630 ACTTTCTTGTTTCCATGCTTTTGTT 58.827 32.000 0.00 0.00 0.00 2.83
2404 2540 6.175712 TGTTTCCATGCTTTTGTTTTGTTC 57.824 33.333 0.00 0.00 0.00 3.18
2420 2556 4.463050 TTGTTCTGGGGTTAACTGGAAT 57.537 40.909 5.42 0.00 0.00 3.01
2427 2563 2.358195 GGGGTTAACTGGAATGATGCCT 60.358 50.000 5.42 0.00 0.00 4.75
2430 2566 4.141482 GGGTTAACTGGAATGATGCCTCTA 60.141 45.833 5.42 0.00 0.00 2.43
2439 2575 5.066375 TGGAATGATGCCTCTACAATTTTCG 59.934 40.000 0.00 0.00 0.00 3.46
2490 2626 9.546428 CTTTCCTCTTTTGAAAAATACCATTGT 57.454 29.630 0.00 0.00 31.77 2.71
2525 2668 3.869187 CGCATACGTGGTGAAGCA 58.131 55.556 0.00 0.00 33.53 3.91
2526 2669 2.383170 CGCATACGTGGTGAAGCAT 58.617 52.632 0.00 0.00 33.53 3.79
2527 2670 1.566404 CGCATACGTGGTGAAGCATA 58.434 50.000 0.00 0.00 33.53 3.14
2528 2671 2.135139 CGCATACGTGGTGAAGCATAT 58.865 47.619 0.00 0.00 33.53 1.78
2529 2672 2.096762 CGCATACGTGGTGAAGCATATG 60.097 50.000 0.00 0.00 33.53 1.78
2530 2673 2.349817 GCATACGTGGTGAAGCATATGC 60.350 50.000 20.36 20.36 38.46 3.14
2531 2674 1.948104 TACGTGGTGAAGCATATGCC 58.052 50.000 23.96 10.41 43.38 4.40
2532 2675 1.089481 ACGTGGTGAAGCATATGCCG 61.089 55.000 23.96 19.17 43.38 5.69
2533 2676 1.089481 CGTGGTGAAGCATATGCCGT 61.089 55.000 23.96 12.61 43.38 5.68
2534 2677 1.804746 CGTGGTGAAGCATATGCCGTA 60.805 52.381 23.96 7.64 43.38 4.02
2535 2678 2.494059 GTGGTGAAGCATATGCCGTAT 58.506 47.619 23.96 8.28 43.38 3.06
2536 2679 2.878406 GTGGTGAAGCATATGCCGTATT 59.122 45.455 23.96 11.72 43.38 1.89
2537 2680 3.315191 GTGGTGAAGCATATGCCGTATTT 59.685 43.478 23.96 11.33 43.38 1.40
2538 2681 3.563808 TGGTGAAGCATATGCCGTATTTC 59.436 43.478 23.96 19.29 43.38 2.17
2539 2682 3.563808 GGTGAAGCATATGCCGTATTTCA 59.436 43.478 23.96 21.46 43.38 2.69
2540 2683 4.036262 GGTGAAGCATATGCCGTATTTCAA 59.964 41.667 23.23 10.73 43.38 2.69
2541 2684 5.449862 GGTGAAGCATATGCCGTATTTCAAA 60.450 40.000 23.23 6.70 43.38 2.69
2542 2685 5.455525 GTGAAGCATATGCCGTATTTCAAAC 59.544 40.000 23.23 13.06 43.38 2.93
2543 2686 5.356751 TGAAGCATATGCCGTATTTCAAACT 59.643 36.000 23.96 0.00 43.38 2.66
2549 2692 1.732405 GCCGTATTTCAAACTGCAGGC 60.732 52.381 19.93 3.83 35.00 4.85
2554 2697 1.180907 TTTCAAACTGCAGGCACACA 58.819 45.000 19.93 0.00 0.00 3.72
2558 2701 1.466025 AAACTGCAGGCACACATGGG 61.466 55.000 19.93 0.00 0.00 4.00
2585 2728 3.548014 CGGTTTGTCCACATGACTCAAAC 60.548 47.826 20.35 20.35 44.75 2.93
2588 2731 2.221169 TGTCCACATGACTCAAACTGC 58.779 47.619 0.00 0.00 44.75 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.266055 CTTGGGGGCAGAGTCGAC 59.734 66.667 7.70 7.70 0.00 4.20
1 2 3.706373 GCTTGGGGGCAGAGTCGA 61.706 66.667 0.00 0.00 0.00 4.20
2 3 3.551496 TTGCTTGGGGGCAGAGTCG 62.551 63.158 0.00 0.00 43.39 4.18
3 4 1.973812 GTTGCTTGGGGGCAGAGTC 60.974 63.158 0.00 0.00 43.39 3.36
4 5 2.116125 GTTGCTTGGGGGCAGAGT 59.884 61.111 0.00 0.00 43.39 3.24
18 19 1.066716 CCATGGTTGCATCTTGGGTTG 60.067 52.381 2.57 0.00 0.00 3.77
30 31 1.826385 GAGTTCACCCTCCATGGTTG 58.174 55.000 12.58 6.09 36.12 3.77
37 38 3.020237 GCTCCGGAGTTCACCCTCC 62.020 68.421 31.43 8.71 46.37 4.30
38 39 2.579738 GCTCCGGAGTTCACCCTC 59.420 66.667 31.43 9.46 0.00 4.30
78 79 4.447342 GGGTGCATGACCTGGGGG 62.447 72.222 12.27 0.00 45.33 5.40
84 85 0.179018 GGATAGGTGGGTGCATGACC 60.179 60.000 0.00 0.90 45.28 4.02
95 96 1.209128 GCATCGTTGTCGGATAGGTG 58.791 55.000 0.00 0.00 37.69 4.00
96 97 0.821517 TGCATCGTTGTCGGATAGGT 59.178 50.000 0.00 0.00 37.69 3.08
119 120 6.151144 GGATAACACTAGCACATGAGGTTTTT 59.849 38.462 0.00 0.00 0.00 1.94
120 121 5.648092 GGATAACACTAGCACATGAGGTTTT 59.352 40.000 0.00 0.00 0.00 2.43
121 122 5.186198 GGATAACACTAGCACATGAGGTTT 58.814 41.667 0.00 0.00 0.00 3.27
122 123 4.680708 CGGATAACACTAGCACATGAGGTT 60.681 45.833 0.00 0.00 0.00 3.50
133 134 6.378710 TCATCTTCTGTCGGATAACACTAG 57.621 41.667 0.00 0.00 0.00 2.57
147 148 4.339530 TCGTCTTGGAGGTATCATCTTCTG 59.660 45.833 0.00 0.00 0.00 3.02
176 177 2.125552 TCGTCGCATGCTCCTTGG 60.126 61.111 17.13 0.00 0.00 3.61
184 185 0.506932 AACGTTGTTCTCGTCGCATG 59.493 50.000 0.00 0.00 40.69 4.06
186 187 0.525882 TCAACGTTGTTCTCGTCGCA 60.526 50.000 26.47 1.47 40.69 5.10
188 189 0.156035 CGTCAACGTTGTTCTCGTCG 59.844 55.000 26.47 15.89 40.69 5.12
192 193 1.155424 TGGGCGTCAACGTTGTTCTC 61.155 55.000 26.47 16.69 42.22 2.87
198 199 2.280592 GGAGTGGGCGTCAACGTT 60.281 61.111 0.00 0.00 42.22 3.99
202 203 3.998672 GGTCGGAGTGGGCGTCAA 61.999 66.667 0.00 0.00 0.00 3.18
215 216 4.394712 AAGCTCCGGCCTTGGTCG 62.395 66.667 6.69 6.69 39.73 4.79
221 222 2.656698 AAAAACCCAAGCTCCGGCCT 62.657 55.000 0.00 0.00 39.73 5.19
261 262 9.276590 GAATTTCTCCTGATTTTTGGTTCAAAT 57.723 29.630 0.00 0.00 33.19 2.32
269 270 8.985805 CCTTTTCTGAATTTCTCCTGATTTTTG 58.014 33.333 0.00 0.00 0.00 2.44
289 290 4.333926 GTGGATATGTGTCTGAGCCTTTTC 59.666 45.833 0.00 0.00 0.00 2.29
300 301 7.254795 GCTTACCTTGTTATGTGGATATGTGTC 60.255 40.741 0.00 0.00 0.00 3.67
303 304 6.658849 TGCTTACCTTGTTATGTGGATATGT 58.341 36.000 0.00 0.00 0.00 2.29
311 312 5.351465 CGTCATCTTGCTTACCTTGTTATGT 59.649 40.000 0.00 0.00 0.00 2.29
334 335 3.126831 GGTCTAATTCACATCTCCTGCG 58.873 50.000 0.00 0.00 0.00 5.18
337 338 3.133003 CCACGGTCTAATTCACATCTCCT 59.867 47.826 0.00 0.00 0.00 3.69
339 340 4.124851 ACCACGGTCTAATTCACATCTC 57.875 45.455 0.00 0.00 0.00 2.75
377 378 7.042658 TGTTTAAAATGTTAAATGGACCGTTGC 60.043 33.333 4.14 0.00 40.43 4.17
397 398 9.267084 GGAGCAATTTGTTAAAAGGATGTTTAA 57.733 29.630 0.00 0.00 31.97 1.52
399 400 6.423604 CGGAGCAATTTGTTAAAAGGATGTTT 59.576 34.615 0.00 0.00 0.00 2.83
401 402 5.469479 CGGAGCAATTTGTTAAAAGGATGT 58.531 37.500 0.00 0.00 0.00 3.06
409 410 4.698304 CCTAGTTCCGGAGCAATTTGTTAA 59.302 41.667 21.22 0.00 0.00 2.01
419 420 7.166691 TGATAATATAACCTAGTTCCGGAGC 57.833 40.000 10.83 10.83 0.00 4.70
760 761 3.444388 CGGGACTAGAGCAGTAGACTTTT 59.556 47.826 0.00 0.00 37.72 2.27
761 762 3.018149 CGGGACTAGAGCAGTAGACTTT 58.982 50.000 0.00 0.00 37.72 2.66
762 763 2.645802 CGGGACTAGAGCAGTAGACTT 58.354 52.381 0.00 0.00 37.72 3.01
763 764 1.747898 GCGGGACTAGAGCAGTAGACT 60.748 57.143 0.00 0.00 37.72 3.24
764 765 0.664224 GCGGGACTAGAGCAGTAGAC 59.336 60.000 0.00 0.00 37.72 2.59
765 766 0.547075 AGCGGGACTAGAGCAGTAGA 59.453 55.000 0.00 0.00 37.72 2.59
766 767 0.948678 GAGCGGGACTAGAGCAGTAG 59.051 60.000 0.00 0.00 37.72 2.57
767 768 0.255033 TGAGCGGGACTAGAGCAGTA 59.745 55.000 0.00 0.00 37.72 2.74
768 769 0.612174 TTGAGCGGGACTAGAGCAGT 60.612 55.000 0.00 0.00 41.47 4.40
769 770 0.179124 GTTGAGCGGGACTAGAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
770 771 0.898326 TGTTGAGCGGGACTAGAGCA 60.898 55.000 0.00 0.00 0.00 4.26
771 772 0.179124 CTGTTGAGCGGGACTAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
845 860 2.617788 CCAGATGGACGGTTTGGATTCA 60.618 50.000 0.00 0.00 37.39 2.57
852 867 0.673644 CGCTTCCAGATGGACGGTTT 60.674 55.000 0.00 0.00 45.39 3.27
857 872 3.297391 GGATCGCTTCCAGATGGAC 57.703 57.895 0.00 0.00 45.39 4.02
955 988 6.458784 GGGGGTATAAATAGGATCTGGGATA 58.541 44.000 0.00 0.00 0.00 2.59
1016 1054 4.021102 ACGGTTTGGAGATTGAGATTGT 57.979 40.909 0.00 0.00 0.00 2.71
1051 1110 0.467804 GTTGGAGAGGGGAGAGATGC 59.532 60.000 0.00 0.00 0.00 3.91
1052 1111 1.871418 TGTTGGAGAGGGGAGAGATG 58.129 55.000 0.00 0.00 0.00 2.90
1053 1112 2.476199 CTTGTTGGAGAGGGGAGAGAT 58.524 52.381 0.00 0.00 0.00 2.75
1056 1115 0.178891 AGCTTGTTGGAGAGGGGAGA 60.179 55.000 0.00 0.00 0.00 3.71
1065 1124 0.960364 GGCCATCGAAGCTTGTTGGA 60.960 55.000 20.81 8.61 0.00 3.53
1068 1127 2.040544 CGGGCCATCGAAGCTTGTT 61.041 57.895 2.10 0.00 0.00 2.83
1069 1128 2.436646 CGGGCCATCGAAGCTTGT 60.437 61.111 2.10 0.00 0.00 3.16
1076 1143 4.812476 CTTCGTGCGGGCCATCGA 62.812 66.667 4.39 7.50 0.00 3.59
1513 1582 3.124921 CTACCGGCAACCAAGCGG 61.125 66.667 0.00 0.00 38.77 5.52
1540 1609 2.552743 GGAGGGCAAACAACTACAGAAC 59.447 50.000 0.00 0.00 0.00 3.01
1577 1666 4.095483 AGAGATTTGAACAATCGATGGCAC 59.905 41.667 0.00 0.00 0.00 5.01
1694 1791 5.175859 ACTTACAGTGAACCCACATAATCG 58.824 41.667 0.00 0.00 45.54 3.34
1718 1815 1.793414 AATCAAATGGGGGCCTTAGC 58.207 50.000 0.84 0.00 38.76 3.09
1719 1816 4.262592 GCAATAATCAAATGGGGGCCTTAG 60.263 45.833 0.84 0.00 0.00 2.18
1720 1817 3.645687 GCAATAATCAAATGGGGGCCTTA 59.354 43.478 0.84 0.00 0.00 2.69
1722 1819 2.049372 GCAATAATCAAATGGGGGCCT 58.951 47.619 0.84 0.00 0.00 5.19
1723 1820 1.270252 CGCAATAATCAAATGGGGGCC 60.270 52.381 0.00 0.00 0.00 5.80
1724 1821 1.686052 TCGCAATAATCAAATGGGGGC 59.314 47.619 0.00 0.00 0.00 5.80
1725 1822 3.828451 AGATCGCAATAATCAAATGGGGG 59.172 43.478 0.00 0.00 0.00 5.40
1726 1823 4.321452 CCAGATCGCAATAATCAAATGGGG 60.321 45.833 0.00 0.00 0.00 4.96
1738 1835 0.182061 ATGCACTCCCAGATCGCAAT 59.818 50.000 0.00 0.00 35.98 3.56
1739 1836 0.462581 GATGCACTCCCAGATCGCAA 60.463 55.000 0.00 0.00 35.98 4.85
1750 1847 1.884926 GTAGCCCGCAGATGCACTC 60.885 63.158 5.55 0.00 42.21 3.51
1807 1904 3.547746 AGAAACTGGTAGTCGCCAAAAA 58.452 40.909 0.00 0.00 38.18 1.94
1815 1912 6.072452 CCTCAATTTCCAAGAAACTGGTAGTC 60.072 42.308 0.00 0.00 37.74 2.59
1821 1918 4.038402 ACAGCCTCAATTTCCAAGAAACTG 59.962 41.667 0.00 0.00 0.00 3.16
1837 1934 3.891977 TCACCTAGATGTATCACAGCCTC 59.108 47.826 0.00 0.00 34.53 4.70
1852 1957 5.879223 AGATCTGCATTTTCACTTCACCTAG 59.121 40.000 0.00 0.00 0.00 3.02
1919 2031 9.419297 CGCAGCAAATAGTTACCTATATAAAGA 57.581 33.333 0.00 0.00 32.57 2.52
1920 2032 8.656849 CCGCAGCAAATAGTTACCTATATAAAG 58.343 37.037 0.00 0.00 32.57 1.85
1921 2033 7.604927 CCCGCAGCAAATAGTTACCTATATAAA 59.395 37.037 0.00 0.00 32.57 1.40
1922 2034 7.101054 CCCGCAGCAAATAGTTACCTATATAA 58.899 38.462 0.00 0.00 32.57 0.98
1923 2035 6.211986 ACCCGCAGCAAATAGTTACCTATATA 59.788 38.462 0.00 0.00 32.57 0.86
1924 2036 5.012768 ACCCGCAGCAAATAGTTACCTATAT 59.987 40.000 0.00 0.00 32.57 0.86
1925 2037 4.345837 ACCCGCAGCAAATAGTTACCTATA 59.654 41.667 0.00 0.00 32.57 1.31
1926 2038 3.135895 ACCCGCAGCAAATAGTTACCTAT 59.864 43.478 0.00 0.00 35.33 2.57
1927 2039 2.502538 ACCCGCAGCAAATAGTTACCTA 59.497 45.455 0.00 0.00 0.00 3.08
1928 2040 1.280998 ACCCGCAGCAAATAGTTACCT 59.719 47.619 0.00 0.00 0.00 3.08
1929 2041 1.746470 ACCCGCAGCAAATAGTTACC 58.254 50.000 0.00 0.00 0.00 2.85
1930 2042 2.745281 TGAACCCGCAGCAAATAGTTAC 59.255 45.455 0.00 0.00 0.00 2.50
1931 2043 3.006940 CTGAACCCGCAGCAAATAGTTA 58.993 45.455 0.00 0.00 0.00 2.24
1932 2044 1.812571 CTGAACCCGCAGCAAATAGTT 59.187 47.619 0.00 0.00 0.00 2.24
1933 2045 1.271379 ACTGAACCCGCAGCAAATAGT 60.271 47.619 0.00 0.00 39.51 2.12
1942 2054 2.895404 ACTTACTAGAACTGAACCCGCA 59.105 45.455 0.00 0.00 0.00 5.69
2027 2153 1.069823 CCATATGAGCAAGCCTCTCGT 59.930 52.381 3.65 0.00 41.35 4.18
2028 2154 1.342496 TCCATATGAGCAAGCCTCTCG 59.658 52.381 3.65 0.00 41.35 4.04
2063 2198 3.889196 TCACGATAAAACAAGTGTGCC 57.111 42.857 0.00 0.00 36.16 5.01
2067 2202 5.536554 AGAGCATCACGATAAAACAAGTG 57.463 39.130 0.00 0.00 37.82 3.16
2070 2205 8.282592 GCATAATAGAGCATCACGATAAAACAA 58.717 33.333 0.00 0.00 37.82 2.83
2168 2303 4.927267 ACTTTTGATACTCCACATGGGA 57.073 40.909 0.00 0.00 45.89 4.37
2169 2304 5.586243 CACTACTTTTGATACTCCACATGGG 59.414 44.000 0.00 0.00 35.41 4.00
2170 2305 6.173339 ACACTACTTTTGATACTCCACATGG 58.827 40.000 0.00 0.00 0.00 3.66
2171 2306 8.035394 ACTACACTACTTTTGATACTCCACATG 58.965 37.037 0.00 0.00 0.00 3.21
2172 2307 8.135382 ACTACACTACTTTTGATACTCCACAT 57.865 34.615 0.00 0.00 0.00 3.21
2173 2308 7.534723 ACTACACTACTTTTGATACTCCACA 57.465 36.000 0.00 0.00 0.00 4.17
2174 2309 8.709646 CAAACTACACTACTTTTGATACTCCAC 58.290 37.037 0.00 0.00 31.79 4.02
2175 2310 8.426489 ACAAACTACACTACTTTTGATACTCCA 58.574 33.333 0.00 0.00 33.90 3.86
2176 2311 8.828688 ACAAACTACACTACTTTTGATACTCC 57.171 34.615 0.00 0.00 33.90 3.85
2177 2312 9.694137 AGACAAACTACACTACTTTTGATACTC 57.306 33.333 0.00 0.00 33.90 2.59
2178 2313 9.477484 CAGACAAACTACACTACTTTTGATACT 57.523 33.333 0.00 0.00 33.90 2.12
2179 2314 9.257651 ACAGACAAACTACACTACTTTTGATAC 57.742 33.333 0.00 0.00 33.90 2.24
2211 2346 2.030363 AGTGACTCGCTCAACTCTGAAG 60.030 50.000 0.00 0.00 0.00 3.02
2231 2366 3.523606 ATCTGCAGCTACAACTCTCAG 57.476 47.619 9.47 0.00 0.00 3.35
2242 2377 3.305608 CGGGAAAAGAAAAATCTGCAGCT 60.306 43.478 9.47 0.00 0.00 4.24
2244 2379 2.989166 GCGGGAAAAGAAAAATCTGCAG 59.011 45.455 7.63 7.63 0.00 4.41
2245 2380 2.363680 TGCGGGAAAAGAAAAATCTGCA 59.636 40.909 0.00 0.00 0.00 4.41
2246 2381 3.025287 TGCGGGAAAAGAAAAATCTGC 57.975 42.857 0.00 0.00 0.00 4.26
2247 2382 5.708948 TGTATGCGGGAAAAGAAAAATCTG 58.291 37.500 0.00 0.00 0.00 2.90
2248 2383 5.975693 TGTATGCGGGAAAAGAAAAATCT 57.024 34.783 0.00 0.00 0.00 2.40
2249 2384 7.545615 AGATTTGTATGCGGGAAAAGAAAAATC 59.454 33.333 0.00 0.00 32.90 2.17
2250 2385 7.386059 AGATTTGTATGCGGGAAAAGAAAAAT 58.614 30.769 0.00 0.00 0.00 1.82
2251 2386 6.754193 AGATTTGTATGCGGGAAAAGAAAAA 58.246 32.000 0.00 0.00 0.00 1.94
2252 2387 6.339587 AGATTTGTATGCGGGAAAAGAAAA 57.660 33.333 0.00 0.00 0.00 2.29
2253 2388 5.975693 AGATTTGTATGCGGGAAAAGAAA 57.024 34.783 0.00 0.00 0.00 2.52
2254 2389 5.975693 AAGATTTGTATGCGGGAAAAGAA 57.024 34.783 0.00 0.00 0.00 2.52
2255 2390 5.065988 GCTAAGATTTGTATGCGGGAAAAGA 59.934 40.000 0.00 0.00 0.00 2.52
2256 2391 5.163663 TGCTAAGATTTGTATGCGGGAAAAG 60.164 40.000 0.00 0.00 0.00 2.27
2260 2395 3.133901 TCTGCTAAGATTTGTATGCGGGA 59.866 43.478 0.00 0.00 0.00 5.14
2271 2406 3.334583 TGGAACGCTTCTGCTAAGATT 57.665 42.857 3.87 0.00 36.97 2.40
2275 2410 2.472695 ACATGGAACGCTTCTGCTAA 57.527 45.000 0.00 0.00 36.97 3.09
2306 2441 5.688621 CAGAATTGATTGTTGTCTTGTGTGG 59.311 40.000 0.00 0.00 0.00 4.17
2307 2442 6.497437 TCAGAATTGATTGTTGTCTTGTGTG 58.503 36.000 0.00 0.00 0.00 3.82
2313 2448 5.242171 TGTGCATCAGAATTGATTGTTGTCT 59.758 36.000 0.00 0.00 42.12 3.41
2336 2471 3.354948 TGATCCTCATGTCCTGGTTTG 57.645 47.619 0.00 0.00 0.00 2.93
2341 2476 5.873712 GTGCTATTATGATCCTCATGTCCTG 59.126 44.000 0.00 0.00 37.70 3.86
2394 2530 4.160626 CCAGTTAACCCCAGAACAAAACAA 59.839 41.667 0.88 0.00 0.00 2.83
2398 2534 3.955524 TCCAGTTAACCCCAGAACAAA 57.044 42.857 0.88 0.00 0.00 2.83
2404 2540 2.689983 GCATCATTCCAGTTAACCCCAG 59.310 50.000 0.88 0.00 0.00 4.45
2420 2556 2.682856 GGCGAAAATTGTAGAGGCATCA 59.317 45.455 0.00 0.00 0.00 3.07
2427 2563 7.429633 TCTTTCAAATTGGCGAAAATTGTAGA 58.570 30.769 9.18 9.91 31.10 2.59
2430 2566 6.566376 GCATCTTTCAAATTGGCGAAAATTGT 60.566 34.615 9.18 0.00 31.10 2.71
2439 2575 3.181504 GCATTGGCATCTTTCAAATTGGC 60.182 43.478 0.00 1.08 40.72 4.52
2508 2651 1.566404 TATGCTTCACCACGTATGCG 58.434 50.000 0.19 0.19 44.93 4.73
2523 2666 3.730715 GCAGTTTGAAATACGGCATATGC 59.269 43.478 19.79 19.79 36.82 3.14
2525 2668 4.036734 CCTGCAGTTTGAAATACGGCATAT 59.963 41.667 13.81 0.00 43.74 1.78
2526 2669 3.376859 CCTGCAGTTTGAAATACGGCATA 59.623 43.478 13.81 0.00 43.74 3.14
2527 2670 2.164219 CCTGCAGTTTGAAATACGGCAT 59.836 45.455 13.81 0.00 43.74 4.40
2528 2671 1.539388 CCTGCAGTTTGAAATACGGCA 59.461 47.619 13.81 0.00 42.83 5.69
2529 2672 1.732405 GCCTGCAGTTTGAAATACGGC 60.732 52.381 13.81 0.67 37.25 5.68
2530 2673 1.539388 TGCCTGCAGTTTGAAATACGG 59.461 47.619 13.81 0.00 0.00 4.02
2531 2674 2.031245 TGTGCCTGCAGTTTGAAATACG 60.031 45.455 13.81 0.00 0.00 3.06
2532 2675 3.243367 TGTGTGCCTGCAGTTTGAAATAC 60.243 43.478 13.81 1.59 0.00 1.89
2533 2676 2.954989 TGTGTGCCTGCAGTTTGAAATA 59.045 40.909 13.81 0.00 0.00 1.40
2534 2677 1.755959 TGTGTGCCTGCAGTTTGAAAT 59.244 42.857 13.81 0.00 0.00 2.17
2535 2678 1.180907 TGTGTGCCTGCAGTTTGAAA 58.819 45.000 13.81 0.00 0.00 2.69
2536 2679 1.067364 CATGTGTGCCTGCAGTTTGAA 59.933 47.619 13.81 0.00 0.00 2.69
2537 2680 0.669619 CATGTGTGCCTGCAGTTTGA 59.330 50.000 13.81 0.00 0.00 2.69
2538 2681 0.319211 CCATGTGTGCCTGCAGTTTG 60.319 55.000 13.81 0.00 0.00 2.93
2539 2682 1.466025 CCCATGTGTGCCTGCAGTTT 61.466 55.000 13.81 0.00 0.00 2.66
2540 2683 1.904865 CCCATGTGTGCCTGCAGTT 60.905 57.895 13.81 0.00 0.00 3.16
2541 2684 2.282674 CCCATGTGTGCCTGCAGT 60.283 61.111 13.81 0.00 0.00 4.40
2542 2685 3.755628 GCCCATGTGTGCCTGCAG 61.756 66.667 6.78 6.78 0.00 4.41
2549 2692 4.697756 ACCGACCGCCCATGTGTG 62.698 66.667 0.00 0.00 0.00 3.82
2554 2697 2.359478 GACAAACCGACCGCCCAT 60.359 61.111 0.00 0.00 0.00 4.00
2558 2701 1.964373 ATGTGGACAAACCGACCGC 60.964 57.895 0.00 0.00 42.61 5.68
2585 2728 5.466393 CCCTTTGTTTTTAATTCAGTGGCAG 59.534 40.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.