Multiple sequence alignment - TraesCS3B01G607300

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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 TraesCS3B01G607300 chr3B 100.000 2522 0 0 1 2522 825972126 825969605 0.000000e+00 4658.0
1 TraesCS3B01G607300 chr3B 93.548 589 17 9 1955 2522 54608961 54608373 0.000000e+00 857.0
2 TraesCS3B01G607300 chr3B 93.367 588 17 6 1955 2522 8791258 8790673 0.000000e+00 850.0
3 TraesCS3B01G607300 chr3B 87.387 222 21 3 164 385 825964208 825963994 5.390000e-62 248.0
4 TraesCS3B01G607300 chr3A 95.852 1133 34 6 614 1742 747727355 747728478 0.000000e+00 1820.0
5 TraesCS3B01G607300 chr3A 93.155 599 21 8 1944 2522 474444414 474445012 0.000000e+00 861.0
6 TraesCS3B01G607300 chr3A 93.537 588 18 7 1955 2522 66352250 66351663 0.000000e+00 857.0
7 TraesCS3B01G607300 chr3A 92.982 342 13 3 288 618 747726931 747727272 2.920000e-134 488.0
8 TraesCS3B01G607300 chr3A 87.859 313 25 6 220 519 747754112 747754424 3.090000e-94 355.0
9 TraesCS3B01G607300 chr3A 90.141 142 12 2 1758 1897 747728564 747728705 1.540000e-42 183.0
10 TraesCS3B01G607300 chr3D 95.328 1113 47 3 641 1749 613075692 613076803 0.000000e+00 1762.0
11 TraesCS3B01G607300 chr3D 84.068 590 43 23 1 580 613074553 613075101 2.870000e-144 521.0
12 TraesCS3B01G607300 chr3D 83.784 481 60 13 789 1256 613115384 613115859 8.280000e-120 440.0
13 TraesCS3B01G607300 chr3D 87.037 216 21 3 164 379 613110782 613110990 1.170000e-58 237.0
14 TraesCS3B01G607300 chr3D 95.105 143 6 1 1756 1897 613076971 613077113 9.080000e-55 224.0
15 TraesCS3B01G607300 chr3D 95.833 48 2 0 571 618 613075469 613075516 7.480000e-11 78.7
16 TraesCS3B01G607300 chrUn 93.888 589 16 7 1954 2522 53744972 53744384 0.000000e+00 870.0
17 TraesCS3B01G607300 chr4B 94.027 586 15 6 1955 2522 660132144 660131561 0.000000e+00 870.0
18 TraesCS3B01G607300 chr2A 93.857 586 18 7 1955 2522 762717293 762717878 0.000000e+00 867.0
19 TraesCS3B01G607300 chr7B 93.857 586 16 7 1955 2522 741904457 741903874 0.000000e+00 865.0
20 TraesCS3B01G607300 chr7B 93.412 592 14 12 1955 2522 641138397 641138987 0.000000e+00 854.0
21 TraesCS3B01G607300 chr4A 92.230 592 21 10 1955 2522 152760728 152761318 0.000000e+00 815.0
22 TraesCS3B01G607300 chr4A 90.443 429 21 8 1946 2354 727732914 727733342 4.740000e-152 547.0
23 TraesCS3B01G607300 chr5B 92.000 600 16 11 1955 2522 163987749 163987150 0.000000e+00 813.0
24 TraesCS3B01G607300 chr5B 91.905 420 14 8 1955 2354 641106230 641105811 1.010000e-158 569.0
25 TraesCS3B01G607300 chr5B 81.818 99 14 4 1759 1854 21742108 21742011 2.080000e-11 80.5
26 TraesCS3B01G607300 chr2B 91.611 596 21 10 1955 2522 788004098 788003504 0.000000e+00 797.0
27 TraesCS3B01G607300 chr2B 91.832 453 17 9 1952 2384 750108298 750108750 4.610000e-172 614.0
28 TraesCS3B01G607300 chr6B 91.905 420 14 8 1955 2354 633351383 633350964 1.010000e-158 569.0
29 TraesCS3B01G607300 chr6B 91.429 420 16 8 1955 2354 178267599 178267180 2.190000e-155 558.0


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 TraesCS3B01G607300 chr3B 825969605 825972126 2521 True 4658.000000 4658 100.000000 1 2522 1 chr3B.!!$R4 2521
1 TraesCS3B01G607300 chr3B 54608373 54608961 588 True 857.000000 857 93.548000 1955 2522 1 chr3B.!!$R2 567
2 TraesCS3B01G607300 chr3B 8790673 8791258 585 True 850.000000 850 93.367000 1955 2522 1 chr3B.!!$R1 567
3 TraesCS3B01G607300 chr3A 474444414 474445012 598 False 861.000000 861 93.155000 1944 2522 1 chr3A.!!$F1 578
4 TraesCS3B01G607300 chr3A 66351663 66352250 587 True 857.000000 857 93.537000 1955 2522 1 chr3A.!!$R1 567
5 TraesCS3B01G607300 chr3A 747726931 747728705 1774 False 830.333333 1820 92.991667 288 1897 3 chr3A.!!$F3 1609
6 TraesCS3B01G607300 chr3D 613074553 613077113 2560 False 646.425000 1762 92.583500 1 1897 4 chr3D.!!$F3 1896
7 TraesCS3B01G607300 chrUn 53744384 53744972 588 True 870.000000 870 93.888000 1954 2522 1 chrUn.!!$R1 568
8 TraesCS3B01G607300 chr4B 660131561 660132144 583 True 870.000000 870 94.027000 1955 2522 1 chr4B.!!$R1 567
9 TraesCS3B01G607300 chr2A 762717293 762717878 585 False 867.000000 867 93.857000 1955 2522 1 chr2A.!!$F1 567
10 TraesCS3B01G607300 chr7B 741903874 741904457 583 True 865.000000 865 93.857000 1955 2522 1 chr7B.!!$R1 567
11 TraesCS3B01G607300 chr7B 641138397 641138987 590 False 854.000000 854 93.412000 1955 2522 1 chr7B.!!$F1 567
12 TraesCS3B01G607300 chr4A 152760728 152761318 590 False 815.000000 815 92.230000 1955 2522 1 chr4A.!!$F1 567
13 TraesCS3B01G607300 chr5B 163987150 163987749 599 True 813.000000 813 92.000000 1955 2522 1 chr5B.!!$R2 567
14 TraesCS3B01G607300 chr2B 788003504 788004098 594 True 797.000000 797 91.611000 1955 2522 1 chr2B.!!$R1 567

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
127 136 0.10741 ACAGGACTTGGTCGCAAACA 60.107 50.0 0.0 0.0 32.65 2.83 F
129 138 0.10741 AGGACTTGGTCGCAAACACA 60.107 50.0 0.0 0.0 32.65 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1920 0.322546 AACCCCAGTTTCTCATCGCC 60.323 55.0 0.00 0.00 29.61 5.54 R
1861 2677 0.895559 GAAGTTCAACCTGGGCCTGG 60.896 60.0 26.31 26.31 0.00 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
22 23 1.388768 CGTGCGTGTGTAAGTGGTATG 59.611 52.381 0.00 0.00 0.00 2.39
35 36 2.452600 TGGTATGCCCAAGGAAATCC 57.547 50.000 0.00 0.00 41.50 3.01
60 61 1.144093 AGCTAGATCCTGAGCCTACGT 59.856 52.381 7.96 0.00 39.65 3.57
81 82 1.961277 ACTGCTACGGTTGCTGCAC 60.961 57.895 18.05 0.00 33.58 4.57
103 112 4.471386 ACTAGATACAAGGGCAACTGATGT 59.529 41.667 0.00 0.00 0.00 3.06
105 114 1.533625 TACAAGGGCAACTGATGTGC 58.466 50.000 0.00 0.00 0.00 4.57
111 120 1.089920 GGCAACTGATGTGCCTACAG 58.910 55.000 8.18 0.00 44.72 2.74
112 121 1.089920 GCAACTGATGTGCCTACAGG 58.910 55.000 0.00 0.00 40.79 4.00
113 122 1.339055 GCAACTGATGTGCCTACAGGA 60.339 52.381 0.00 0.00 40.79 3.86
114 123 2.350522 CAACTGATGTGCCTACAGGAC 58.649 52.381 0.00 0.00 40.79 3.85
115 124 1.944177 ACTGATGTGCCTACAGGACT 58.056 50.000 0.00 0.00 40.79 3.85
116 125 2.260822 ACTGATGTGCCTACAGGACTT 58.739 47.619 0.00 0.00 40.79 3.01
117 126 2.027745 ACTGATGTGCCTACAGGACTTG 60.028 50.000 0.00 0.00 40.79 3.16
118 127 1.278985 TGATGTGCCTACAGGACTTGG 59.721 52.381 0.00 0.00 40.79 3.61
119 128 1.279271 GATGTGCCTACAGGACTTGGT 59.721 52.381 0.00 0.00 40.79 3.67
120 129 0.685097 TGTGCCTACAGGACTTGGTC 59.315 55.000 0.00 0.00 37.39 4.02
121 130 0.389948 GTGCCTACAGGACTTGGTCG 60.390 60.000 0.00 0.00 37.39 4.79
122 131 1.448013 GCCTACAGGACTTGGTCGC 60.448 63.158 0.00 0.00 37.39 5.19
123 132 1.972198 CCTACAGGACTTGGTCGCA 59.028 57.895 0.00 0.00 37.39 5.10
124 133 0.320374 CCTACAGGACTTGGTCGCAA 59.680 55.000 0.00 0.00 37.39 4.85
125 134 1.270625 CCTACAGGACTTGGTCGCAAA 60.271 52.381 0.00 0.00 37.39 3.68
126 135 1.798813 CTACAGGACTTGGTCGCAAAC 59.201 52.381 0.00 0.00 32.65 2.93
127 136 0.107410 ACAGGACTTGGTCGCAAACA 60.107 50.000 0.00 0.00 32.65 2.83
128 137 0.307760 CAGGACTTGGTCGCAAACAC 59.692 55.000 0.00 0.00 32.65 3.32
129 138 0.107410 AGGACTTGGTCGCAAACACA 60.107 50.000 0.00 0.00 32.65 3.72
132 141 1.131504 GACTTGGTCGCAAACACAACA 59.868 47.619 0.00 0.00 0.00 3.33
133 142 1.135517 ACTTGGTCGCAAACACAACAC 60.136 47.619 0.00 0.00 0.00 3.32
134 143 0.881796 TTGGTCGCAAACACAACACA 59.118 45.000 0.00 0.00 0.00 3.72
136 145 0.169230 GGTCGCAAACACAACACACA 59.831 50.000 0.00 0.00 0.00 3.72
137 146 1.202245 GGTCGCAAACACAACACACAT 60.202 47.619 0.00 0.00 0.00 3.21
139 148 1.064803 TCGCAAACACAACACACATCC 59.935 47.619 0.00 0.00 0.00 3.51
140 149 1.202234 CGCAAACACAACACACATCCA 60.202 47.619 0.00 0.00 0.00 3.41
141 150 2.543445 CGCAAACACAACACACATCCAT 60.543 45.455 0.00 0.00 0.00 3.41
142 151 2.796031 GCAAACACAACACACATCCATG 59.204 45.455 0.00 0.00 0.00 3.66
143 152 3.490590 GCAAACACAACACACATCCATGA 60.491 43.478 0.00 0.00 0.00 3.07
144 153 4.680702 CAAACACAACACACATCCATGAA 58.319 39.130 0.00 0.00 0.00 2.57
145 154 4.998671 AACACAACACACATCCATGAAA 57.001 36.364 0.00 0.00 0.00 2.69
146 155 4.998671 ACACAACACACATCCATGAAAA 57.001 36.364 0.00 0.00 0.00 2.29
147 156 4.681744 ACACAACACACATCCATGAAAAC 58.318 39.130 0.00 0.00 0.00 2.43
148 157 4.402155 ACACAACACACATCCATGAAAACT 59.598 37.500 0.00 0.00 0.00 2.66
149 158 4.977963 CACAACACACATCCATGAAAACTC 59.022 41.667 0.00 0.00 0.00 3.01
150 159 4.644234 ACAACACACATCCATGAAAACTCA 59.356 37.500 0.00 0.00 0.00 3.41
151 160 5.302568 ACAACACACATCCATGAAAACTCAT 59.697 36.000 0.00 0.00 0.00 2.90
152 161 6.489700 ACAACACACATCCATGAAAACTCATA 59.510 34.615 0.00 0.00 0.00 2.15
153 162 6.500684 ACACACATCCATGAAAACTCATAC 57.499 37.500 0.00 0.00 0.00 2.39
154 163 6.003326 ACACACATCCATGAAAACTCATACA 58.997 36.000 0.00 0.00 0.00 2.29
155 164 6.660521 ACACACATCCATGAAAACTCATACAT 59.339 34.615 0.00 0.00 0.00 2.29
156 165 6.970613 CACACATCCATGAAAACTCATACATG 59.029 38.462 0.00 0.00 39.51 3.21
157 166 6.660521 ACACATCCATGAAAACTCATACATGT 59.339 34.615 2.69 2.69 38.56 3.21
158 167 7.148188 ACACATCCATGAAAACTCATACATGTC 60.148 37.037 0.00 0.00 38.56 3.06
159 168 6.885918 ACATCCATGAAAACTCATACATGTCA 59.114 34.615 0.00 0.00 38.56 3.58
160 169 7.394077 ACATCCATGAAAACTCATACATGTCAA 59.606 33.333 0.00 0.00 38.56 3.18
161 170 7.144722 TCCATGAAAACTCATACATGTCAAC 57.855 36.000 0.00 0.00 38.56 3.18
162 171 6.942005 TCCATGAAAACTCATACATGTCAACT 59.058 34.615 0.00 0.00 38.56 3.16
197 206 3.058914 GTCCTGTAAGCACAACACACATC 60.059 47.826 0.00 0.00 33.22 3.06
205 214 1.845568 CACAACACACATCGCAACAAC 59.154 47.619 0.00 0.00 0.00 3.32
206 215 1.470494 ACAACACACATCGCAACAACA 59.530 42.857 0.00 0.00 0.00 3.33
207 216 2.095008 ACAACACACATCGCAACAACAA 60.095 40.909 0.00 0.00 0.00 2.83
208 217 2.187351 ACACACATCGCAACAACAAC 57.813 45.000 0.00 0.00 0.00 3.32
209 218 1.470494 ACACACATCGCAACAACAACA 59.530 42.857 0.00 0.00 0.00 3.33
210 219 2.095008 ACACACATCGCAACAACAACAA 60.095 40.909 0.00 0.00 0.00 2.83
211 220 3.114809 CACACATCGCAACAACAACAAT 58.885 40.909 0.00 0.00 0.00 2.71
212 221 3.061073 CACACATCGCAACAACAACAATG 60.061 43.478 0.00 0.00 0.00 2.82
213 222 2.472115 CACATCGCAACAACAACAATGG 59.528 45.455 0.00 0.00 0.00 3.16
214 223 2.100584 ACATCGCAACAACAACAATGGT 59.899 40.909 0.00 0.00 0.00 3.55
231 240 7.823149 ACAATGGTTAGTAAACTCGTACATC 57.177 36.000 0.00 0.00 35.81 3.06
242 251 7.874016 AGTAAACTCGTACATCAAAACCATACA 59.126 33.333 0.00 0.00 0.00 2.29
252 261 6.885918 ACATCAAAACCATACATGTCAGATCA 59.114 34.615 0.00 0.00 0.00 2.92
326 335 7.370383 TGACGTAACCTAGAATTAACGACTTT 58.630 34.615 0.00 0.00 0.00 2.66
363 372 3.201353 AGAGTAGCGATAGACTGCAGA 57.799 47.619 23.35 0.00 39.76 4.26
452 461 2.811431 TGGCGAGGGAATAATATTTGCG 59.189 45.455 0.00 0.00 0.00 4.85
732 1381 9.822185 ATCCTTTTATTTAATTTGGTGCAGATC 57.178 29.630 0.00 0.00 0.00 2.75
753 1402 1.299541 AATATTTGCGCTCCTCGTGG 58.700 50.000 9.73 0.00 41.07 4.94
914 1567 4.437682 TTCTCCTTTATGTAGGGGCATG 57.562 45.455 0.00 0.00 35.61 4.06
960 1613 7.334171 TGAATCATATGGTAGAACACAACACAG 59.666 37.037 2.13 0.00 0.00 3.66
1060 1713 1.443872 CTCGTTGTCGTTCCCTCCG 60.444 63.158 0.00 0.00 38.33 4.63
1145 1798 3.695606 GGTGCTCAGCTCCGACCA 61.696 66.667 1.00 0.00 32.56 4.02
1232 1885 1.603455 CCAGGGAAGGCGCAAAGAA 60.603 57.895 10.83 0.00 0.00 2.52
1267 1920 3.114616 CCAAGCACGAGCACGAGG 61.115 66.667 11.40 3.00 45.49 4.63
1321 1974 1.068610 GCAGCAGCGAATACAACCAAA 60.069 47.619 0.00 0.00 0.00 3.28
1422 2075 3.199880 AGCTTAGCCGCAGATAATTGT 57.800 42.857 0.00 0.00 0.00 2.71
1614 2267 3.818210 TGGAAACATACATGTGTGTGGAC 59.182 43.478 26.34 18.85 41.61 4.02
1646 2299 7.397192 ACCCACTTTATTTGATATTGCTCAAGT 59.603 33.333 0.00 0.00 36.55 3.16
1742 2395 4.536765 ACTTGGTATTATTTGGAGGCCAG 58.463 43.478 5.01 0.00 33.81 4.85
1749 2402 5.582950 ATTATTTGGAGGCCAGTGCTATA 57.417 39.130 5.01 0.00 33.81 1.31
1750 2403 3.498774 ATTTGGAGGCCAGTGCTATAG 57.501 47.619 5.01 0.00 33.81 1.31
1753 2406 2.317040 TGGAGGCCAGTGCTATAGTAC 58.683 52.381 12.62 12.62 37.74 2.73
1878 2694 1.774217 TCCAGGCCCAGGTTGAACT 60.774 57.895 11.36 0.00 0.00 3.01
1897 2713 6.489675 TGAACTTCGTTGATATCGTAGTACC 58.510 40.000 0.00 0.00 37.79 3.34
1898 2714 5.088141 ACTTCGTTGATATCGTAGTACCG 57.912 43.478 0.00 0.00 37.22 4.02
1899 2715 4.811024 ACTTCGTTGATATCGTAGTACCGA 59.189 41.667 0.00 0.00 37.22 4.69
1900 2716 4.715520 TCGTTGATATCGTAGTACCGAC 57.284 45.455 0.00 0.00 40.08 4.79
1901 2717 4.119136 TCGTTGATATCGTAGTACCGACA 58.881 43.478 0.00 0.00 40.08 4.35
1902 2718 4.570369 TCGTTGATATCGTAGTACCGACAA 59.430 41.667 0.00 0.00 40.08 3.18
1903 2719 4.667948 CGTTGATATCGTAGTACCGACAAC 59.332 45.833 12.38 12.38 40.08 3.32
1904 2720 5.572211 GTTGATATCGTAGTACCGACAACA 58.428 41.667 15.24 1.90 39.32 3.33
1905 2721 6.204359 GTTGATATCGTAGTACCGACAACAT 58.796 40.000 15.24 2.66 39.32 2.71
1906 2722 6.381481 TGATATCGTAGTACCGACAACATT 57.619 37.500 0.00 0.00 40.08 2.71
1907 2723 6.432936 TGATATCGTAGTACCGACAACATTC 58.567 40.000 0.00 0.00 40.08 2.67
1908 2724 4.707030 ATCGTAGTACCGACAACATTCA 57.293 40.909 0.00 0.00 40.08 2.57
1909 2725 4.087510 TCGTAGTACCGACAACATTCAG 57.912 45.455 0.00 0.00 30.63 3.02
1910 2726 2.597305 CGTAGTACCGACAACATTCAGC 59.403 50.000 0.00 0.00 0.00 4.26
1911 2727 3.672511 CGTAGTACCGACAACATTCAGCT 60.673 47.826 0.00 0.00 0.00 4.24
1912 2728 3.402628 AGTACCGACAACATTCAGCTT 57.597 42.857 0.00 0.00 0.00 3.74
1913 2729 3.740115 AGTACCGACAACATTCAGCTTT 58.260 40.909 0.00 0.00 0.00 3.51
1914 2730 4.890088 AGTACCGACAACATTCAGCTTTA 58.110 39.130 0.00 0.00 0.00 1.85
1915 2731 4.689345 AGTACCGACAACATTCAGCTTTAC 59.311 41.667 0.00 0.00 0.00 2.01
1916 2732 2.812011 ACCGACAACATTCAGCTTTACC 59.188 45.455 0.00 0.00 0.00 2.85
1917 2733 2.811431 CCGACAACATTCAGCTTTACCA 59.189 45.455 0.00 0.00 0.00 3.25
1918 2734 3.252215 CCGACAACATTCAGCTTTACCAA 59.748 43.478 0.00 0.00 0.00 3.67
1919 2735 4.261405 CCGACAACATTCAGCTTTACCAAA 60.261 41.667 0.00 0.00 0.00 3.28
1920 2736 4.675114 CGACAACATTCAGCTTTACCAAAC 59.325 41.667 0.00 0.00 0.00 2.93
1921 2737 5.505654 CGACAACATTCAGCTTTACCAAACT 60.506 40.000 0.00 0.00 0.00 2.66
1922 2738 6.293190 CGACAACATTCAGCTTTACCAAACTA 60.293 38.462 0.00 0.00 0.00 2.24
1923 2739 6.970484 ACAACATTCAGCTTTACCAAACTAG 58.030 36.000 0.00 0.00 0.00 2.57
1924 2740 5.629079 ACATTCAGCTTTACCAAACTAGC 57.371 39.130 0.00 0.00 0.00 3.42
1925 2741 5.316987 ACATTCAGCTTTACCAAACTAGCT 58.683 37.500 0.00 0.00 44.34 3.32
1926 2742 5.412904 ACATTCAGCTTTACCAAACTAGCTC 59.587 40.000 0.00 0.00 41.76 4.09
1927 2743 4.617253 TCAGCTTTACCAAACTAGCTCA 57.383 40.909 0.00 0.00 41.76 4.26
1928 2744 4.968259 TCAGCTTTACCAAACTAGCTCAA 58.032 39.130 0.00 0.00 41.76 3.02
1929 2745 4.755123 TCAGCTTTACCAAACTAGCTCAAC 59.245 41.667 0.00 0.00 41.76 3.18
1930 2746 4.757149 CAGCTTTACCAAACTAGCTCAACT 59.243 41.667 0.00 0.00 41.76 3.16
1931 2747 5.932303 CAGCTTTACCAAACTAGCTCAACTA 59.068 40.000 0.00 0.00 41.76 2.24
1932 2748 6.426937 CAGCTTTACCAAACTAGCTCAACTAA 59.573 38.462 0.00 0.00 41.76 2.24
1933 2749 6.427242 AGCTTTACCAAACTAGCTCAACTAAC 59.573 38.462 0.00 0.00 39.67 2.34
1934 2750 6.617953 GCTTTACCAAACTAGCTCAACTAACG 60.618 42.308 0.00 0.00 0.00 3.18
1935 2751 3.064931 ACCAAACTAGCTCAACTAACGC 58.935 45.455 0.00 0.00 0.00 4.84
1936 2752 3.064207 CCAAACTAGCTCAACTAACGCA 58.936 45.455 0.00 0.00 0.00 5.24
1937 2753 3.120649 CCAAACTAGCTCAACTAACGCAC 60.121 47.826 0.00 0.00 0.00 5.34
1938 2754 3.662247 AACTAGCTCAACTAACGCACT 57.338 42.857 0.00 0.00 0.00 4.40
1939 2755 4.778534 AACTAGCTCAACTAACGCACTA 57.221 40.909 0.00 0.00 0.00 2.74
1940 2756 4.358494 ACTAGCTCAACTAACGCACTAG 57.642 45.455 0.00 0.00 33.50 2.57
1941 2757 1.997669 AGCTCAACTAACGCACTAGC 58.002 50.000 0.00 0.00 37.42 3.42
1942 2758 1.546476 AGCTCAACTAACGCACTAGCT 59.454 47.619 0.00 0.00 39.10 3.32
1943 2759 1.921230 GCTCAACTAACGCACTAGCTC 59.079 52.381 0.00 0.00 39.10 4.09
1944 2760 2.671351 GCTCAACTAACGCACTAGCTCA 60.671 50.000 0.00 0.00 39.10 4.26
1945 2761 3.575630 CTCAACTAACGCACTAGCTCAA 58.424 45.455 0.00 0.00 39.10 3.02
1946 2762 3.314553 TCAACTAACGCACTAGCTCAAC 58.685 45.455 0.00 0.00 39.10 3.18
1947 2763 3.005472 TCAACTAACGCACTAGCTCAACT 59.995 43.478 0.00 0.00 39.10 3.16
1948 2764 4.216902 TCAACTAACGCACTAGCTCAACTA 59.783 41.667 0.00 0.00 39.10 2.24
1949 2765 4.094090 ACTAACGCACTAGCTCAACTAC 57.906 45.455 0.00 0.00 39.10 2.73
1950 2766 2.365408 AACGCACTAGCTCAACTACC 57.635 50.000 0.00 0.00 39.10 3.18
1951 2767 1.254026 ACGCACTAGCTCAACTACCA 58.746 50.000 0.00 0.00 39.10 3.25
1952 2768 1.067776 ACGCACTAGCTCAACTACCAC 60.068 52.381 0.00 0.00 39.10 4.16
2076 2892 1.538075 ACATTGGCGACCTTTTTACCG 59.462 47.619 0.00 0.00 0.00 4.02
2164 2999 7.342581 TCTCTCTCTCTAACACACACATATCT 58.657 38.462 0.00 0.00 0.00 1.98
2197 3032 1.684983 ACGGGACCATAATCCAGTACG 59.315 52.381 0.00 0.00 44.27 3.67
2198 3033 1.000506 CGGGACCATAATCCAGTACGG 59.999 57.143 0.00 0.00 40.96 4.02
2199 3034 1.346722 GGGACCATAATCCAGTACGGG 59.653 57.143 5.57 5.57 40.96 5.28
2200 3035 2.322658 GGACCATAATCCAGTACGGGA 58.677 52.381 17.46 17.46 42.21 5.14
2201 3036 2.036862 GGACCATAATCCAGTACGGGAC 59.963 54.545 17.49 2.57 40.44 4.46
2303 3156 7.229306 TGCACTGAAGACAAGATAAACAATTCT 59.771 33.333 0.00 0.00 0.00 2.40
2337 3190 5.047092 TCAGAGCATCACAGAACATTACTGA 60.047 40.000 0.00 0.00 37.82 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.379527 CTACACGGATTTCCTTGGGC 58.620 55.000 7.86 0.00 39.36 5.36
34 35 1.268352 GCTCAGGATCTAGCTACACGG 59.732 57.143 7.67 0.00 35.80 4.94
35 36 1.268352 GGCTCAGGATCTAGCTACACG 59.732 57.143 12.72 0.00 38.80 4.49
60 61 1.960763 CAGCAACCGTAGCAGTGCA 60.961 57.895 19.20 0.00 0.00 4.57
81 82 4.813161 CACATCAGTTGCCCTTGTATCTAG 59.187 45.833 0.00 0.00 0.00 2.43
95 104 2.260822 AGTCCTGTAGGCACATCAGTT 58.739 47.619 0.00 0.00 33.14 3.16
103 112 1.972198 CGACCAAGTCCTGTAGGCA 59.028 57.895 0.00 0.00 34.44 4.75
105 114 0.320374 TTGCGACCAAGTCCTGTAGG 59.680 55.000 0.00 0.00 0.00 3.18
107 116 1.139256 TGTTTGCGACCAAGTCCTGTA 59.861 47.619 0.00 0.00 31.52 2.74
109 118 0.307760 GTGTTTGCGACCAAGTCCTG 59.692 55.000 0.00 0.00 31.52 3.86
111 120 0.736053 TTGTGTTTGCGACCAAGTCC 59.264 50.000 0.00 0.00 31.52 3.85
112 121 1.131504 TGTTGTGTTTGCGACCAAGTC 59.868 47.619 0.00 0.00 31.52 3.01
113 122 1.135517 GTGTTGTGTTTGCGACCAAGT 60.136 47.619 0.00 0.00 31.52 3.16
114 123 1.135546 TGTGTTGTGTTTGCGACCAAG 60.136 47.619 0.00 0.00 31.52 3.61
115 124 0.881796 TGTGTTGTGTTTGCGACCAA 59.118 45.000 0.00 0.00 0.00 3.67
116 125 0.169230 GTGTGTTGTGTTTGCGACCA 59.831 50.000 0.00 0.00 0.00 4.02
117 126 0.169230 TGTGTGTTGTGTTTGCGACC 59.831 50.000 0.00 0.00 0.00 4.79
118 127 2.108700 GATGTGTGTTGTGTTTGCGAC 58.891 47.619 0.00 0.00 0.00 5.19
119 128 1.064803 GGATGTGTGTTGTGTTTGCGA 59.935 47.619 0.00 0.00 0.00 5.10
120 129 1.202234 TGGATGTGTGTTGTGTTTGCG 60.202 47.619 0.00 0.00 0.00 4.85
121 130 2.575694 TGGATGTGTGTTGTGTTTGC 57.424 45.000 0.00 0.00 0.00 3.68
122 131 4.304537 TCATGGATGTGTGTTGTGTTTG 57.695 40.909 0.00 0.00 0.00 2.93
123 132 4.998671 TTCATGGATGTGTGTTGTGTTT 57.001 36.364 0.00 0.00 0.00 2.83
124 133 4.998671 TTTCATGGATGTGTGTTGTGTT 57.001 36.364 0.00 0.00 0.00 3.32
125 134 4.402155 AGTTTTCATGGATGTGTGTTGTGT 59.598 37.500 0.00 0.00 0.00 3.72
126 135 4.935702 AGTTTTCATGGATGTGTGTTGTG 58.064 39.130 0.00 0.00 0.00 3.33
127 136 4.644234 TGAGTTTTCATGGATGTGTGTTGT 59.356 37.500 0.00 0.00 0.00 3.32
128 137 5.185668 TGAGTTTTCATGGATGTGTGTTG 57.814 39.130 0.00 0.00 0.00 3.33
129 138 6.489700 TGTATGAGTTTTCATGGATGTGTGTT 59.510 34.615 0.00 0.00 43.76 3.32
132 141 6.660521 ACATGTATGAGTTTTCATGGATGTGT 59.339 34.615 0.00 4.19 43.76 3.72
133 142 7.092137 ACATGTATGAGTTTTCATGGATGTG 57.908 36.000 0.00 3.77 43.76 3.21
134 143 6.885918 TGACATGTATGAGTTTTCATGGATGT 59.114 34.615 0.00 12.33 43.76 3.06
136 145 7.613022 AGTTGACATGTATGAGTTTTCATGGAT 59.387 33.333 0.00 0.00 43.76 3.41
137 146 6.942005 AGTTGACATGTATGAGTTTTCATGGA 59.058 34.615 0.00 0.00 43.76 3.41
139 148 7.120285 AGGAGTTGACATGTATGAGTTTTCATG 59.880 37.037 0.00 0.00 43.76 3.07
140 149 7.170965 AGGAGTTGACATGTATGAGTTTTCAT 58.829 34.615 0.00 0.00 45.77 2.57
141 150 6.533730 AGGAGTTGACATGTATGAGTTTTCA 58.466 36.000 0.00 0.00 37.81 2.69
142 151 7.440523 AAGGAGTTGACATGTATGAGTTTTC 57.559 36.000 0.00 0.00 0.00 2.29
143 152 6.147821 CGAAGGAGTTGACATGTATGAGTTTT 59.852 38.462 0.00 0.00 0.00 2.43
144 153 5.639506 CGAAGGAGTTGACATGTATGAGTTT 59.360 40.000 0.00 0.00 0.00 2.66
145 154 5.171476 CGAAGGAGTTGACATGTATGAGTT 58.829 41.667 0.00 0.00 0.00 3.01
146 155 4.748892 CGAAGGAGTTGACATGTATGAGT 58.251 43.478 0.00 0.00 0.00 3.41
197 206 3.701241 ACTAACCATTGTTGTTGTTGCG 58.299 40.909 0.00 0.00 35.87 4.85
205 214 7.410800 TGTACGAGTTTACTAACCATTGTTG 57.589 36.000 0.00 0.00 35.87 3.33
206 215 7.874016 TGATGTACGAGTTTACTAACCATTGTT 59.126 33.333 0.00 0.00 38.52 2.83
207 216 7.380536 TGATGTACGAGTTTACTAACCATTGT 58.619 34.615 0.00 0.00 34.71 2.71
208 217 7.821595 TGATGTACGAGTTTACTAACCATTG 57.178 36.000 0.00 0.00 34.71 2.82
209 218 8.836268 TTTGATGTACGAGTTTACTAACCATT 57.164 30.769 0.00 0.00 34.71 3.16
210 219 8.715088 GTTTTGATGTACGAGTTTACTAACCAT 58.285 33.333 0.00 0.00 34.71 3.55
211 220 7.171337 GGTTTTGATGTACGAGTTTACTAACCA 59.829 37.037 0.00 0.00 34.71 3.67
212 221 7.171337 TGGTTTTGATGTACGAGTTTACTAACC 59.829 37.037 0.00 0.00 34.71 2.85
213 222 8.075593 TGGTTTTGATGTACGAGTTTACTAAC 57.924 34.615 0.00 0.00 34.36 2.34
214 223 8.836268 ATGGTTTTGATGTACGAGTTTACTAA 57.164 30.769 0.00 0.00 0.00 2.24
231 240 7.149569 ACTTGATCTGACATGTATGGTTTTG 57.850 36.000 0.00 0.00 0.00 2.44
242 251 4.011966 TGTGCTGAACTTGATCTGACAT 57.988 40.909 0.00 0.00 0.00 3.06
252 261 7.594351 TGATCTCTATAGATGTGCTGAACTT 57.406 36.000 2.11 0.00 42.73 2.66
326 335 8.943002 TCGCTACTCTATAATATGAACGATTCA 58.057 33.333 0.00 0.00 45.01 2.57
342 351 4.338379 TCTGCAGTCTATCGCTACTCTA 57.662 45.455 14.67 0.00 0.00 2.43
343 352 3.201353 TCTGCAGTCTATCGCTACTCT 57.799 47.619 14.67 0.00 0.00 3.24
452 461 8.503196 TGACCATATGTAAACATTTCATATCGC 58.497 33.333 0.12 0.00 37.76 4.58
468 488 2.642311 TGGTTGTGACCTGACCATATGT 59.358 45.455 1.24 0.00 46.66 2.29
524 545 1.698506 CAAGGTGCACTAACCCCAAA 58.301 50.000 17.98 0.00 41.54 3.28
720 1369 5.733091 GCGCAAATATTAGATCTGCACCAAA 60.733 40.000 5.18 0.00 33.19 3.28
723 1372 3.499918 AGCGCAAATATTAGATCTGCACC 59.500 43.478 11.47 1.01 33.19 5.01
731 1380 3.381045 CACGAGGAGCGCAAATATTAGA 58.619 45.455 11.47 0.00 46.04 2.10
732 1381 2.476619 CCACGAGGAGCGCAAATATTAG 59.523 50.000 11.47 0.00 46.04 1.73
819 1468 8.291740 CGCAGTCATAAATGGATTTGATCAATA 58.708 33.333 9.40 0.91 0.00 1.90
820 1469 7.143340 CGCAGTCATAAATGGATTTGATCAAT 58.857 34.615 9.40 0.00 0.00 2.57
821 1470 6.095300 ACGCAGTCATAAATGGATTTGATCAA 59.905 34.615 3.38 3.38 29.74 2.57
823 1472 6.064846 ACGCAGTCATAAATGGATTTGATC 57.935 37.500 0.00 0.00 29.74 2.92
824 1473 7.663081 AGATACGCAGTCATAAATGGATTTGAT 59.337 33.333 0.00 0.00 43.93 2.57
960 1613 5.175673 GGTTTGCTCTTATTTTGTGCTTGAC 59.824 40.000 0.00 0.00 0.00 3.18
990 1643 4.829492 GCTAACAGGGCCATTTCTATTGAT 59.171 41.667 6.18 0.00 0.00 2.57
1145 1798 2.048597 TCGCATTCACGCTCCGTT 60.049 55.556 0.00 0.00 38.32 4.44
1226 1879 3.032017 TCTCTTCCTCGCAGTTCTTTG 57.968 47.619 0.00 0.00 0.00 2.77
1232 1885 1.594310 GCCTTCTCTTCCTCGCAGT 59.406 57.895 0.00 0.00 0.00 4.40
1267 1920 0.322546 AACCCCAGTTTCTCATCGCC 60.323 55.000 0.00 0.00 29.61 5.54
1422 2075 5.123227 CCCTGATTATAAAACGCCTTCTCA 58.877 41.667 0.00 0.00 0.00 3.27
1614 2267 7.436118 CAATATCAAATAAAGTGGGTCCATGG 58.564 38.462 4.97 4.97 0.00 3.66
1646 2299 8.876275 ACGCTTTATATCTTTGTTTATCCGTA 57.124 30.769 0.00 0.00 0.00 4.02
1682 2335 7.230108 ACAGGATCCATATATGCAAGAACAAAG 59.770 37.037 15.82 0.00 0.00 2.77
1717 2370 4.709886 GGCCTCCAAATAATACCAAGTTGT 59.290 41.667 0.00 0.00 0.00 3.32
1732 2385 1.879575 ACTATAGCACTGGCCTCCAA 58.120 50.000 3.32 0.00 42.56 3.53
1734 2387 2.317040 TGTACTATAGCACTGGCCTCC 58.683 52.381 3.32 0.00 42.56 4.30
1768 2582 6.842807 CCTATAAGGGGGTTTTCTACTAGTGA 59.157 42.308 5.39 0.00 0.00 3.41
1819 2635 1.519408 ATAGTTGCCGCGTTCAGTTT 58.481 45.000 4.92 0.00 0.00 2.66
1858 2674 2.081787 TTCAACCTGGGCCTGGACA 61.082 57.895 33.41 14.76 0.00 4.02
1861 2677 0.895559 GAAGTTCAACCTGGGCCTGG 60.896 60.000 26.31 26.31 0.00 4.45
1878 2694 4.570369 TGTCGGTACTACGATATCAACGAA 59.430 41.667 3.12 0.00 45.47 3.85
1897 2713 4.481930 TTGGTAAAGCTGAATGTTGTCG 57.518 40.909 0.00 0.00 0.00 4.35
1898 2714 5.831997 AGTTTGGTAAAGCTGAATGTTGTC 58.168 37.500 0.00 0.00 0.00 3.18
1899 2715 5.852282 AGTTTGGTAAAGCTGAATGTTGT 57.148 34.783 0.00 0.00 0.00 3.32
1900 2716 5.858581 GCTAGTTTGGTAAAGCTGAATGTTG 59.141 40.000 0.00 0.00 32.18 3.33
1901 2717 5.770162 AGCTAGTTTGGTAAAGCTGAATGTT 59.230 36.000 0.00 0.00 43.46 2.71
1902 2718 5.316987 AGCTAGTTTGGTAAAGCTGAATGT 58.683 37.500 0.00 0.00 43.46 2.71
1903 2719 5.412594 TGAGCTAGTTTGGTAAAGCTGAATG 59.587 40.000 0.00 0.00 45.04 2.67
1904 2720 5.560724 TGAGCTAGTTTGGTAAAGCTGAAT 58.439 37.500 0.00 0.00 45.04 2.57
1905 2721 4.968259 TGAGCTAGTTTGGTAAAGCTGAA 58.032 39.130 0.00 0.00 45.04 3.02
1906 2722 4.617253 TGAGCTAGTTTGGTAAAGCTGA 57.383 40.909 0.00 0.00 45.04 4.26
1907 2723 4.757149 AGTTGAGCTAGTTTGGTAAAGCTG 59.243 41.667 0.00 0.00 45.04 4.24
1909 2725 6.600350 GTTAGTTGAGCTAGTTTGGTAAAGC 58.400 40.000 0.00 0.00 35.16 3.51
1910 2726 6.617953 GCGTTAGTTGAGCTAGTTTGGTAAAG 60.618 42.308 0.00 0.00 0.00 1.85
1911 2727 5.178067 GCGTTAGTTGAGCTAGTTTGGTAAA 59.822 40.000 0.00 0.00 0.00 2.01
1912 2728 4.687483 GCGTTAGTTGAGCTAGTTTGGTAA 59.313 41.667 0.00 0.00 0.00 2.85
1913 2729 4.240096 GCGTTAGTTGAGCTAGTTTGGTA 58.760 43.478 0.00 0.00 0.00 3.25
1914 2730 3.064931 GCGTTAGTTGAGCTAGTTTGGT 58.935 45.455 0.00 0.00 0.00 3.67
1915 2731 3.064207 TGCGTTAGTTGAGCTAGTTTGG 58.936 45.455 0.00 0.00 0.00 3.28
1916 2732 3.741344 AGTGCGTTAGTTGAGCTAGTTTG 59.259 43.478 0.00 0.00 0.00 2.93
1917 2733 3.991367 AGTGCGTTAGTTGAGCTAGTTT 58.009 40.909 0.00 0.00 0.00 2.66
1918 2734 3.662247 AGTGCGTTAGTTGAGCTAGTT 57.338 42.857 0.00 0.00 0.00 2.24
1919 2735 3.427773 GCTAGTGCGTTAGTTGAGCTAGT 60.428 47.826 0.00 0.00 0.00 2.57
1920 2736 3.109619 GCTAGTGCGTTAGTTGAGCTAG 58.890 50.000 0.00 0.00 0.00 3.42
1921 2737 2.753452 AGCTAGTGCGTTAGTTGAGCTA 59.247 45.455 0.00 0.00 45.42 3.32
1922 2738 1.546476 AGCTAGTGCGTTAGTTGAGCT 59.454 47.619 0.00 0.00 45.42 4.09
1923 2739 1.921230 GAGCTAGTGCGTTAGTTGAGC 59.079 52.381 0.00 0.00 45.42 4.26
1924 2740 3.217599 TGAGCTAGTGCGTTAGTTGAG 57.782 47.619 0.00 0.00 45.42 3.02
1925 2741 3.005472 AGTTGAGCTAGTGCGTTAGTTGA 59.995 43.478 0.00 0.00 45.42 3.18
1926 2742 3.318017 AGTTGAGCTAGTGCGTTAGTTG 58.682 45.455 0.00 0.00 45.42 3.16
1927 2743 3.662247 AGTTGAGCTAGTGCGTTAGTT 57.338 42.857 0.00 0.00 45.42 2.24
1928 2744 3.119566 GGTAGTTGAGCTAGTGCGTTAGT 60.120 47.826 0.00 0.00 45.42 2.24
1929 2745 3.119602 TGGTAGTTGAGCTAGTGCGTTAG 60.120 47.826 0.00 0.00 45.42 2.34
1930 2746 2.821378 TGGTAGTTGAGCTAGTGCGTTA 59.179 45.455 0.00 0.00 45.42 3.18
1931 2747 1.616865 TGGTAGTTGAGCTAGTGCGTT 59.383 47.619 0.00 0.00 45.42 4.84
1932 2748 1.067776 GTGGTAGTTGAGCTAGTGCGT 60.068 52.381 0.00 0.00 45.42 5.24
1933 2749 1.630148 GTGGTAGTTGAGCTAGTGCG 58.370 55.000 0.00 0.00 45.42 5.34
1934 2750 1.275291 TGGTGGTAGTTGAGCTAGTGC 59.725 52.381 0.00 0.00 40.05 4.40
1935 2751 2.563179 AGTGGTGGTAGTTGAGCTAGTG 59.437 50.000 0.00 0.00 0.00 2.74
1936 2752 2.890814 AGTGGTGGTAGTTGAGCTAGT 58.109 47.619 0.00 0.00 0.00 2.57
1937 2753 4.270834 TCTAGTGGTGGTAGTTGAGCTAG 58.729 47.826 0.00 0.00 0.00 3.42
1938 2754 4.311520 TCTAGTGGTGGTAGTTGAGCTA 57.688 45.455 0.00 0.00 0.00 3.32
1939 2755 3.170991 TCTAGTGGTGGTAGTTGAGCT 57.829 47.619 0.00 0.00 0.00 4.09
1940 2756 3.510360 TCTTCTAGTGGTGGTAGTTGAGC 59.490 47.826 0.00 0.00 0.00 4.26
1941 2757 5.010719 TGTTCTTCTAGTGGTGGTAGTTGAG 59.989 44.000 0.00 0.00 0.00 3.02
1942 2758 4.897076 TGTTCTTCTAGTGGTGGTAGTTGA 59.103 41.667 0.00 0.00 0.00 3.18
1943 2759 4.989168 GTGTTCTTCTAGTGGTGGTAGTTG 59.011 45.833 0.00 0.00 0.00 3.16
1944 2760 4.040095 GGTGTTCTTCTAGTGGTGGTAGTT 59.960 45.833 0.00 0.00 0.00 2.24
1945 2761 3.577415 GGTGTTCTTCTAGTGGTGGTAGT 59.423 47.826 0.00 0.00 0.00 2.73
1946 2762 3.056035 GGGTGTTCTTCTAGTGGTGGTAG 60.056 52.174 0.00 0.00 0.00 3.18
1947 2763 2.901839 GGGTGTTCTTCTAGTGGTGGTA 59.098 50.000 0.00 0.00 0.00 3.25
1948 2764 1.697982 GGGTGTTCTTCTAGTGGTGGT 59.302 52.381 0.00 0.00 0.00 4.16
1949 2765 1.337823 CGGGTGTTCTTCTAGTGGTGG 60.338 57.143 0.00 0.00 0.00 4.61
1950 2766 1.343465 ACGGGTGTTCTTCTAGTGGTG 59.657 52.381 0.00 0.00 0.00 4.17
1951 2767 1.343465 CACGGGTGTTCTTCTAGTGGT 59.657 52.381 0.00 0.00 0.00 4.16
1952 2768 1.939838 GCACGGGTGTTCTTCTAGTGG 60.940 57.143 0.25 0.00 0.00 4.00
2044 2860 3.871006 GTCGCCAATGTCACTTGATATGA 59.129 43.478 0.00 0.00 0.00 2.15
2076 2892 5.053145 AGAGAGTGTGTGTGAGAATTTGAC 58.947 41.667 0.00 0.00 0.00 3.18
2303 3156 2.745821 GTGATGCTCTGATGCACTTTGA 59.254 45.455 0.00 0.00 46.33 2.69
2337 3190 5.981315 CCGGTACATCGTGTATTTATCTTGT 59.019 40.000 0.00 0.00 35.05 3.16
2348 3201 0.389426 GCAGTTCCGGTACATCGTGT 60.389 55.000 14.14 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.