Multiple sequence alignment - TraesCS5D01G305700

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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 TraesCS5D01G305700 chr5D 100.000 8808 0 0 1 8808 400894924 400903731 0.000000e+00 16266.0
1 TraesCS5D01G305700 chr5D 97.574 2927 53 4 5896 8808 401315758 401318680 0.000000e+00 4996.0
2 TraesCS5D01G305700 chr5D 95.071 2658 81 20 5599 8233 401003730 401006360 0.000000e+00 4137.0
3 TraesCS5D01G305700 chr5D 86.553 2588 299 23 2387 4941 550599755 550602326 0.000000e+00 2806.0
4 TraesCS5D01G305700 chr5D 89.157 581 19 13 4854 5432 401001604 401002142 0.000000e+00 684.0
5 TraesCS5D01G305700 chr5D 93.040 273 13 5 8533 8805 401006442 401006708 2.300000e-105 394.0
6 TraesCS5D01G305700 chr5D 87.847 288 13 6 5472 5737 401002921 401003208 1.430000e-82 318.0
7 TraesCS5D01G305700 chr5D 95.758 165 7 0 8231 8395 48983315 48983479 5.240000e-67 267.0
8 TraesCS5D01G305700 chr5D 93.525 139 9 0 6215 6353 29634968 29635106 3.220000e-49 207.0
9 TraesCS5D01G305700 chr5D 84.337 166 16 4 5652 5808 556631451 556631287 4.260000e-33 154.0
10 TraesCS5D01G305700 chr5D 98.387 62 1 0 6108 6169 400900967 400901028 9.350000e-20 110.0
11 TraesCS5D01G305700 chr5D 98.387 62 1 0 6044 6105 400901031 400901092 9.350000e-20 110.0
12 TraesCS5D01G305700 chr5D 96.825 63 1 1 6108 6169 401004156 401004218 4.350000e-18 104.0
13 TraesCS5D01G305700 chr5D 93.548 62 4 0 6044 6105 401315970 401316031 9.420000e-15 93.5
14 TraesCS5D01G305700 chr5D 91.935 62 2 2 6044 6105 401004221 401004279 5.670000e-12 84.2
15 TraesCS5D01G305700 chr5B 96.263 4977 111 18 3302 8233 480754093 480759039 0.000000e+00 8091.0
16 TraesCS5D01G305700 chr5B 86.140 2583 306 26 2387 4937 711407320 711409882 0.000000e+00 2739.0
17 TraesCS5D01G305700 chr5B 93.114 1917 54 24 599 2487 480752235 480754101 0.000000e+00 2737.0
18 TraesCS5D01G305700 chr5B 95.657 1658 52 5 6596 8233 480805205 480806862 0.000000e+00 2645.0
19 TraesCS5D01G305700 chr5B 95.111 1166 35 5 7089 8233 480793074 480794238 0.000000e+00 1818.0
20 TraesCS5D01G305700 chr5B 96.378 497 18 0 6596 7092 480770793 480771289 0.000000e+00 819.0
21 TraesCS5D01G305700 chr5B 94.431 413 11 5 8394 8806 480759037 480759437 7.510000e-175 625.0
22 TraesCS5D01G305700 chr5B 91.355 428 13 10 8394 8806 480794236 480794654 1.660000e-156 564.0
23 TraesCS5D01G305700 chr5B 91.768 413 20 6 8394 8806 480806860 480807258 5.970000e-156 562.0
24 TraesCS5D01G305700 chr5B 87.435 191 15 5 421 602 480750043 480750233 2.490000e-50 211.0
25 TraesCS5D01G305700 chr5B 98.387 62 1 0 6108 6169 480756841 480756902 9.350000e-20 110.0
26 TraesCS5D01G305700 chr5B 95.161 62 3 0 6044 6105 480756905 480756966 2.020000e-16 99.0
27 TraesCS5D01G305700 chr5B 100.000 35 0 0 5425 5459 692817830 692817864 2.050000e-06 65.8
28 TraesCS5D01G305700 chr5A 94.818 3377 101 32 1 3336 506129405 506132748 0.000000e+00 5199.0
29 TraesCS5D01G305700 chr5A 95.751 2165 53 16 6108 8233 506140472 506142636 0.000000e+00 3452.0
30 TraesCS5D01G305700 chr5A 95.143 1709 41 16 3324 5030 506137833 506139501 0.000000e+00 2658.0
31 TraesCS5D01G305700 chr5A 95.856 1110 35 4 5047 6154 506139482 506140582 0.000000e+00 1784.0
32 TraesCS5D01G305700 chr5A 91.990 412 19 7 8394 8805 506142634 506143031 4.620000e-157 566.0
33 TraesCS5D01G305700 chr5A 93.370 181 11 1 8216 8395 668081945 668081765 5.240000e-67 267.0
34 TraesCS5D01G305700 chr5A 92.771 83 5 1 1811 1892 562386484 562386566 1.550000e-22 119.0
35 TraesCS5D01G305700 chr5A 80.986 142 22 5 444 581 575260949 575260809 3.360000e-19 108.0
36 TraesCS5D01G305700 chr5A 90.244 82 8 0 1811 1892 693649641 693649560 3.360000e-19 108.0
37 TraesCS5D01G305700 chr5A 81.119 143 16 8 441 572 316508991 316509133 4.350000e-18 104.0
38 TraesCS5D01G305700 chr5A 88.095 84 7 2 1808 1891 669727462 669727542 7.280000e-16 97.1
39 TraesCS5D01G305700 chr4B 86.355 2587 305 23 2390 4944 8933703 8931133 0.000000e+00 2778.0
40 TraesCS5D01G305700 chr4B 85.240 2588 330 23 2390 4944 8018611 8016043 0.000000e+00 2615.0
41 TraesCS5D01G305700 chr4B 91.579 95 7 1 1894 1988 89454941 89455034 7.180000e-26 130.0
42 TraesCS5D01G305700 chr4B 79.487 156 18 9 430 572 94793942 94794096 2.020000e-16 99.0
43 TraesCS5D01G305700 chr4B 78.107 169 21 11 427 581 517443049 517442883 9.420000e-15 93.5
44 TraesCS5D01G305700 chr6D 86.316 2587 306 22 2390 4944 17160760 17158190 0.000000e+00 2772.0
45 TraesCS5D01G305700 chr6D 86.306 2585 310 19 2387 4941 472122050 472124620 0.000000e+00 2772.0
46 TraesCS5D01G305700 chr6D 90.361 83 7 1 1811 1892 148175332 148175250 3.360000e-19 108.0
47 TraesCS5D01G305700 chr6B 85.896 2588 305 28 2387 4937 674953436 674956000 0.000000e+00 2702.0
48 TraesCS5D01G305700 chr6B 86.953 1142 129 14 3810 4937 715065776 715066911 0.000000e+00 1266.0
49 TraesCS5D01G305700 chrUn 95.657 1658 52 4 6596 8233 301894888 301896545 0.000000e+00 2645.0
50 TraesCS5D01G305700 chrUn 95.279 1165 34 5 7089 8233 378853835 378854998 0.000000e+00 1827.0
51 TraesCS5D01G305700 chrUn 91.768 413 20 6 8394 8806 301896543 301896941 5.970000e-156 562.0
52 TraesCS5D01G305700 chrUn 94.762 210 7 1 8597 8806 356980734 356980529 3.070000e-84 324.0
53 TraesCS5D01G305700 chrUn 91.549 142 7 3 8394 8535 378854996 378855132 3.250000e-44 191.0
54 TraesCS5D01G305700 chrUn 86.538 104 11 3 1891 1992 76644719 76644821 2.600000e-20 111.0
55 TraesCS5D01G305700 chr7B 84.982 1405 172 18 2387 3768 578992931 578994319 0.000000e+00 1389.0
56 TraesCS5D01G305700 chr7A 77.618 2301 420 58 2559 4799 39331051 39333316 0.000000e+00 1308.0
57 TraesCS5D01G305700 chr7A 93.514 185 7 5 8231 8413 156115839 156116020 4.050000e-68 270.0
58 TraesCS5D01G305700 chr7A 93.258 178 10 2 8228 8405 643186887 643187062 2.440000e-65 261.0
59 TraesCS5D01G305700 chr7A 90.526 95 5 4 1891 1983 490271095 490271187 1.200000e-23 122.0
60 TraesCS5D01G305700 chr7A 95.833 48 2 0 5348 5395 350572783 350572736 2.640000e-10 78.7
61 TraesCS5D01G305700 chr7D 86.847 1148 137 8 3806 4941 20631964 20633109 0.000000e+00 1271.0
62 TraesCS5D01G305700 chr7D 84.680 594 63 11 2387 2963 20631383 20631965 1.280000e-157 568.0
63 TraesCS5D01G305700 chr7D 96.988 166 5 0 8230 8395 457217441 457217276 6.730000e-71 279.0
64 TraesCS5D01G305700 chr7D 94.245 139 8 0 6215 6353 594653369 594653507 6.930000e-51 213.0
65 TraesCS5D01G305700 chr7D 91.566 83 6 1 1811 1892 428711391 428711473 7.230000e-21 113.0
66 TraesCS5D01G305700 chr7D 81.102 127 19 3 464 585 220208502 220208376 7.280000e-16 97.1
67 TraesCS5D01G305700 chr1A 88.158 456 41 8 2625 3074 6419231 6418783 1.680000e-146 531.0
68 TraesCS5D01G305700 chr1A 94.118 85 3 2 1900 1982 440889656 440889572 2.580000e-25 128.0
69 TraesCS5D01G305700 chr1A 85.841 113 9 6 1891 2002 402235518 402235624 7.230000e-21 113.0
70 TraesCS5D01G305700 chr1A 93.023 43 3 0 5417 5459 361351035 361351077 7.380000e-06 63.9
71 TraesCS5D01G305700 chr2B 93.785 177 10 1 8222 8397 781778554 781778730 1.890000e-66 265.0
72 TraesCS5D01G305700 chr2B 94.245 139 8 0 6215 6353 306847270 306847132 6.930000e-51 213.0
73 TraesCS5D01G305700 chr2B 91.463 82 6 1 1811 1891 245996252 245996333 2.600000e-20 111.0
74 TraesCS5D01G305700 chr3A 92.432 185 13 1 8212 8395 529671316 529671132 6.780000e-66 263.0
75 TraesCS5D01G305700 chr3A 80.769 156 19 5 427 572 597183370 597183524 2.600000e-20 111.0
76 TraesCS5D01G305700 chr3A 100.000 35 0 0 5425 5459 650111794 650111760 2.050000e-06 65.8
77 TraesCS5D01G305700 chr2D 91.979 187 14 1 8216 8401 445190006 445189820 2.440000e-65 261.0
78 TraesCS5D01G305700 chr2D 94.203 138 8 0 6216 6353 147703994 147704131 2.490000e-50 211.0
79 TraesCS5D01G305700 chr2D 81.356 118 18 2 465 581 87804846 87804732 9.420000e-15 93.5
80 TraesCS5D01G305700 chr2D 79.487 117 22 2 464 578 2489399 2489515 2.040000e-11 82.4
81 TraesCS5D01G305700 chr2D 86.486 74 10 0 508 581 187967681 187967608 2.040000e-11 82.4
82 TraesCS5D01G305700 chr3B 94.245 139 8 0 6215 6353 350051748 350051886 6.930000e-51 213.0
83 TraesCS5D01G305700 chr1B 90.099 101 7 3 1894 1994 169001952 169001855 2.580000e-25 128.0
84 TraesCS5D01G305700 chr1B 80.473 169 17 11 427 581 668070751 668070585 2.010000e-21 115.0
85 TraesCS5D01G305700 chr1B 79.747 158 18 9 428 572 618195594 618195750 1.560000e-17 102.0
86 TraesCS5D01G305700 chr6A 90.526 95 7 2 1894 1987 169514912 169515005 3.340000e-24 124.0
87 TraesCS5D01G305700 chr3D 91.358 81 7 0 1811 1891 418784756 418784836 2.600000e-20 111.0
88 TraesCS5D01G305700 chr3D 80.508 118 18 3 465 581 30436319 30436206 1.580000e-12 86.1
89 TraesCS5D01G305700 chr1D 81.250 96 18 0 490 585 410264397 410264302 2.640000e-10 78.7


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 TraesCS5D01G305700 chr5D 400894924 400903731 8807 False 5495.333333 16266 98.924667 1 8808 3 chr5D.!!$F4 8807
1 TraesCS5D01G305700 chr5D 550599755 550602326 2571 False 2806.000000 2806 86.553000 2387 4941 1 chr5D.!!$F3 2554
2 TraesCS5D01G305700 chr5D 401315758 401318680 2922 False 2544.750000 4996 95.561000 5896 8808 2 chr5D.!!$F6 2912
3 TraesCS5D01G305700 chr5D 401001604 401006708 5104 False 953.533333 4137 92.312500 4854 8805 6 chr5D.!!$F5 3951
4 TraesCS5D01G305700 chr5B 711407320 711409882 2562 False 2739.000000 2739 86.140000 2387 4937 1 chr5B.!!$F3 2550
5 TraesCS5D01G305700 chr5B 480750043 480759437 9394 False 1978.833333 8091 94.131833 421 8806 6 chr5B.!!$F4 8385
6 TraesCS5D01G305700 chr5B 480805205 480807258 2053 False 1603.500000 2645 93.712500 6596 8806 2 chr5B.!!$F6 2210
7 TraesCS5D01G305700 chr5B 480793074 480794654 1580 False 1191.000000 1818 93.233000 7089 8806 2 chr5B.!!$F5 1717
8 TraesCS5D01G305700 chr5A 506129405 506132748 3343 False 5199.000000 5199 94.818000 1 3336 1 chr5A.!!$F2 3335
9 TraesCS5D01G305700 chr5A 506137833 506143031 5198 False 2115.000000 3452 94.685000 3324 8805 4 chr5A.!!$F5 5481
10 TraesCS5D01G305700 chr4B 8931133 8933703 2570 True 2778.000000 2778 86.355000 2390 4944 1 chr4B.!!$R2 2554
11 TraesCS5D01G305700 chr4B 8016043 8018611 2568 True 2615.000000 2615 85.240000 2390 4944 1 chr4B.!!$R1 2554
12 TraesCS5D01G305700 chr6D 17158190 17160760 2570 True 2772.000000 2772 86.316000 2390 4944 1 chr6D.!!$R1 2554
13 TraesCS5D01G305700 chr6D 472122050 472124620 2570 False 2772.000000 2772 86.306000 2387 4941 1 chr6D.!!$F1 2554
14 TraesCS5D01G305700 chr6B 674953436 674956000 2564 False 2702.000000 2702 85.896000 2387 4937 1 chr6B.!!$F1 2550
15 TraesCS5D01G305700 chr6B 715065776 715066911 1135 False 1266.000000 1266 86.953000 3810 4937 1 chr6B.!!$F2 1127
16 TraesCS5D01G305700 chrUn 301894888 301896941 2053 False 1603.500000 2645 93.712500 6596 8806 2 chrUn.!!$F2 2210
17 TraesCS5D01G305700 chrUn 378853835 378855132 1297 False 1009.000000 1827 93.414000 7089 8535 2 chrUn.!!$F3 1446
18 TraesCS5D01G305700 chr7B 578992931 578994319 1388 False 1389.000000 1389 84.982000 2387 3768 1 chr7B.!!$F1 1381
19 TraesCS5D01G305700 chr7A 39331051 39333316 2265 False 1308.000000 1308 77.618000 2559 4799 1 chr7A.!!$F1 2240
20 TraesCS5D01G305700 chr7D 20631383 20633109 1726 False 919.500000 1271 85.763500 2387 4941 2 chr7D.!!$F3 2554

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
67 68 0.030908 GCTCGTTCGATACTCCCTGG 59.969 60.000 0.00 0.00 0.00 4.45 F
892 2912 0.460284 GGATTCGCTGTGACGTCCAT 60.460 55.000 14.12 0.00 33.67 3.41 F
1391 3416 1.736681 GAGGCTTCAGATCAGTGCAAC 59.263 52.381 0.00 0.00 0.00 4.17 F
2515 4567 1.202475 GGAGAGAACGGATGCTCTTCC 60.202 57.143 0.00 0.00 41.33 3.46 F
2552 4604 1.522569 GTGCAGTAGGCCCCAGTAG 59.477 63.158 0.00 0.00 43.89 2.57 F
2553 4605 1.689233 TGCAGTAGGCCCCAGTAGG 60.689 63.158 0.00 0.00 43.89 3.18 F
3578 5678 2.095567 CAGCAATGTCAACTCCTTTCCG 60.096 50.000 0.00 0.00 0.00 4.30 F
4644 6761 1.373059 GCCTCCAATCCCTCGATCC 59.627 63.158 0.00 0.00 0.00 3.36 F
5620 9182 0.397254 CCTAAGGAAGAGGAGCCCGA 60.397 60.000 0.00 0.00 35.99 5.14 F
5796 9365 1.191535 AGGGTTCGATTCGATCCACA 58.808 50.000 28.30 5.99 44.59 4.17 F
6009 9586 1.227147 GCCACTACAGCGCCGATAA 60.227 57.895 2.29 0.00 0.00 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 3862 0.539438 TCAGGGCGGAATTGCTTTGT 60.539 50.000 0.00 0.00 34.52 2.83 R
2299 4348 2.033448 TGTTGCTTCGGCGGGAAT 59.967 55.556 7.21 0.00 45.37 3.01 R
3163 5254 1.003696 TGGAATGGACATTGCCGTACA 59.996 47.619 12.92 0.00 38.21 2.90 R
3578 5678 2.091541 TGGTGCAATCGGAATCCTTTC 58.908 47.619 0.00 0.00 0.00 2.62 R
4249 6365 2.914536 TGGATGGGCCTAGTGCATATA 58.085 47.619 4.53 0.00 43.89 0.86 R
4462 6579 5.292101 CCTAGCATCGAAGAAAGTGTTAAGG 59.708 44.000 0.00 0.00 43.58 2.69 R
4826 6943 1.212616 GCGCTCTTGTAGATGCGAAT 58.787 50.000 18.03 0.00 41.18 3.34 R
6200 9778 0.390209 TACCTCTAAACAACGCCGCC 60.390 55.000 0.00 0.00 0.00 6.13 R
6628 10208 0.671472 TCATGCAGAACTCCACAGCG 60.671 55.000 0.00 0.00 0.00 5.18 R
6943 10523 3.840831 TGCTTAGTACAGCAGCCAG 57.159 52.632 3.87 0.00 45.14 4.85 R
8331 11936 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51 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
20 21 1.369839 GCAAAACCTCCCGCTAGAGC 61.370 60.000 0.00 0.00 37.78 4.09
35 36 0.913205 AGAGCGGACACCTAGAGAGA 59.087 55.000 0.00 0.00 0.00 3.10
65 66 1.471119 TTGCTCGTTCGATACTCCCT 58.529 50.000 0.00 0.00 0.00 4.20
66 67 0.738975 TGCTCGTTCGATACTCCCTG 59.261 55.000 0.00 0.00 0.00 4.45
67 68 0.030908 GCTCGTTCGATACTCCCTGG 59.969 60.000 0.00 0.00 0.00 4.45
91 92 0.983378 ACACATAGGCTCCAGGGACC 60.983 60.000 0.00 0.00 0.00 4.46
95 96 0.760945 ATAGGCTCCAGGGACCTTCG 60.761 60.000 12.60 0.00 34.92 3.79
108 109 3.369381 CCTTCGTGAGGGCACATAG 57.631 57.895 0.00 0.00 45.41 2.23
153 154 1.154225 GATGCAACAACGAAGCGGG 60.154 57.895 0.00 0.00 0.00 6.13
163 164 2.042843 GAAGCGGGGAGGAGGAGA 60.043 66.667 0.00 0.00 0.00 3.71
202 203 1.184431 TTTCGGTGGCGGTATCACTA 58.816 50.000 0.00 0.00 35.61 2.74
209 210 4.700700 GGTGGCGGTATCACTATAACTTT 58.299 43.478 0.00 0.00 35.61 2.66
210 211 4.510340 GGTGGCGGTATCACTATAACTTTG 59.490 45.833 0.00 0.00 35.61 2.77
215 216 6.040878 GCGGTATCACTATAACTTTGTCTGT 58.959 40.000 0.00 0.00 0.00 3.41
222 223 8.378172 TCACTATAACTTTGTCTGTTTGGAAG 57.622 34.615 0.00 0.00 0.00 3.46
276 277 1.611977 GTTTTGGCCCCACAGAACTAC 59.388 52.381 0.00 0.00 33.93 2.73
384 385 1.751924 GTGGCGATAGAGTCAACTCCT 59.248 52.381 6.54 0.00 43.88 3.69
415 417 8.822855 TGGCTGTTATATTTGTCGTTATTACAG 58.177 33.333 0.00 0.00 37.99 2.74
445 447 0.460722 TGTGGGTGACGAAAACGAGA 59.539 50.000 0.00 0.00 0.00 4.04
505 519 2.802724 CCACGTGTGGGTCTCACCA 61.803 63.158 15.65 0.00 46.81 4.17
514 528 5.250200 GTGTGGGTCTCACCATTAATAACA 58.750 41.667 0.00 0.00 45.48 2.41
558 572 1.244019 GGAGTTGACTTTGCCGCCAT 61.244 55.000 0.00 0.00 0.00 4.40
605 2624 8.713271 CCTACAACTCAAAGAGACACTAAAATC 58.287 37.037 0.31 0.00 33.32 2.17
690 2709 2.685017 TGATCAGTGGGGCGCTCT 60.685 61.111 7.48 1.00 0.00 4.09
692 2711 3.781770 GATCAGTGGGGCGCTCTCG 62.782 68.421 7.48 0.00 39.07 4.04
853 2873 1.667154 CCGAAGAGCATCCGACTCCA 61.667 60.000 0.00 0.00 34.56 3.86
892 2912 0.460284 GGATTCGCTGTGACGTCCAT 60.460 55.000 14.12 0.00 33.67 3.41
897 2917 2.027073 GCTGTGACGTCCATCGCAA 61.027 57.895 14.12 0.00 44.19 4.85
1033 3058 4.179599 GGGAGGAGGGGGAGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1139 3164 4.124351 CTACCGCGGCGACTTCCA 62.124 66.667 28.58 0.00 0.00 3.53
1391 3416 1.736681 GAGGCTTCAGATCAGTGCAAC 59.263 52.381 0.00 0.00 0.00 4.17
1599 3626 2.427506 GACTGGAACCATGGAACTGTC 58.572 52.381 21.47 20.41 0.00 3.51
1815 3862 2.561209 TAGGACCCTGATAAGTGCCA 57.439 50.000 0.00 0.00 0.00 4.92
1984 4032 3.509575 GTGTGGCACTTATCATTTGGGAA 59.490 43.478 19.83 0.00 0.00 3.97
1985 4033 4.021544 GTGTGGCACTTATCATTTGGGAAA 60.022 41.667 19.83 0.00 0.00 3.13
2165 4214 5.091431 GCAAAGCAAAGAACAGCTACATAG 58.909 41.667 0.00 0.00 40.90 2.23
2299 4348 7.768120 ACATAACAAATCAAAGCAAAGTTTGGA 59.232 29.630 17.11 6.27 37.89 3.53
2503 4555 6.682746 TCATCGATGCTATTAAGGAGAGAAC 58.317 40.000 20.81 0.00 0.00 3.01
2515 4567 1.202475 GGAGAGAACGGATGCTCTTCC 60.202 57.143 0.00 0.00 41.33 3.46
2549 4601 4.115199 GGGTGCAGTAGGCCCCAG 62.115 72.222 0.00 0.00 46.52 4.45
2550 4602 3.330720 GGTGCAGTAGGCCCCAGT 61.331 66.667 0.00 0.00 40.21 4.00
2551 4603 1.993391 GGTGCAGTAGGCCCCAGTA 60.993 63.158 0.00 0.00 40.21 2.74
2552 4604 1.522569 GTGCAGTAGGCCCCAGTAG 59.477 63.158 0.00 0.00 43.89 2.57
2553 4605 1.689233 TGCAGTAGGCCCCAGTAGG 60.689 63.158 0.00 0.00 43.89 3.18
2685 4737 6.373774 GTGATGAACTCATTGTCTTCATCCTT 59.626 38.462 22.44 4.40 44.29 3.36
2704 4756 3.753272 CCTTGAGAACATCCACGATTGTT 59.247 43.478 0.00 0.00 0.00 2.83
3035 5118 4.789012 ATTCAACCACCATTTAGCTGTG 57.211 40.909 0.00 0.00 0.00 3.66
3189 5280 2.167075 GGCAATGTCCATTCCAAAGGAG 59.833 50.000 0.00 0.00 33.85 3.69
3267 5361 9.442047 TTTTGATGTTGAACCAACTTTGTAATT 57.558 25.926 10.63 0.00 43.85 1.40
3269 5363 8.006298 TGATGTTGAACCAACTTTGTAATTCT 57.994 30.769 10.63 0.00 43.85 2.40
3578 5678 2.095567 CAGCAATGTCAACTCCTTTCCG 60.096 50.000 0.00 0.00 0.00 4.30
3821 5925 8.936864 GTGAGCATATAAGAACACAGTTACTTT 58.063 33.333 0.00 0.00 0.00 2.66
3829 5933 4.816925 AGAACACAGTTACTTTCCTTGCTC 59.183 41.667 0.00 0.00 0.00 4.26
4019 6132 7.067129 CCCCTATATCTTCAATGCAATCATCAG 59.933 40.741 0.00 0.00 31.27 2.90
4249 6365 3.245016 TGCAAGAATGGTCCACTCATCTT 60.245 43.478 2.64 4.44 0.00 2.40
4644 6761 1.373059 GCCTCCAATCCCTCGATCC 59.627 63.158 0.00 0.00 0.00 3.36
4815 6932 4.277921 TGTCACAATAATTGCACTTCAGCA 59.722 37.500 0.00 0.00 43.99 4.41
4878 6998 2.560542 GCAGGATCATCCGAGTCTACAT 59.439 50.000 0.00 0.00 42.75 2.29
5058 7197 9.537848 GTTCAATTACAAAGTTACAATAGACCG 57.462 33.333 0.00 0.00 0.00 4.79
5133 7272 8.860780 AAGAATTTAAGACAGAGAGCTTTGAT 57.139 30.769 0.00 0.00 0.00 2.57
5137 7276 8.804912 ATTTAAGACAGAGAGCTTTGATCAAT 57.195 30.769 9.40 0.00 0.00 2.57
5235 7374 5.701750 TGCAAAACGATAAACTAGGCTTACA 59.298 36.000 0.00 0.00 0.00 2.41
5276 7415 3.625649 TGACACATGGCTGCACTAATA 57.374 42.857 0.50 0.00 0.00 0.98
5277 7416 3.949132 TGACACATGGCTGCACTAATAA 58.051 40.909 0.50 0.00 0.00 1.40
5278 7417 4.525996 TGACACATGGCTGCACTAATAAT 58.474 39.130 0.50 0.00 0.00 1.28
5279 7418 5.679601 TGACACATGGCTGCACTAATAATA 58.320 37.500 0.50 0.00 0.00 0.98
5390 7529 1.722034 AGGCTGACTGAAAGGAGACA 58.278 50.000 0.00 0.00 39.30 3.41
5409 7548 1.067846 CAGTGTAACAGCGCCTAGTGA 60.068 52.381 2.29 0.00 41.43 3.41
5541 8421 2.677524 GTTGATGCAGCAGGGCCA 60.678 61.111 4.20 0.00 0.00 5.36
5620 9182 0.397254 CCTAAGGAAGAGGAGCCCGA 60.397 60.000 0.00 0.00 35.99 5.14
5640 9202 1.619669 GACTTGGGGGAGGGGATGT 60.620 63.158 0.00 0.00 0.00 3.06
5796 9365 1.191535 AGGGTTCGATTCGATCCACA 58.808 50.000 28.30 5.99 44.59 4.17
6009 9586 1.227147 GCCACTACAGCGCCGATAA 60.227 57.895 2.29 0.00 0.00 1.75
6024 9601 2.585845 CGATAATGCGTGCTATCTCGT 58.414 47.619 0.00 0.00 0.00 4.18
6200 9778 1.446792 CCAGCTATGCTATCGGCGG 60.447 63.158 7.21 0.00 45.43 6.13
6432 10011 4.765339 GGCTATTCTTGTTAACTTGGTGGT 59.235 41.667 7.22 0.00 0.00 4.16
6434 10013 6.431852 GGCTATTCTTGTTAACTTGGTGGTTA 59.568 38.462 7.22 0.00 0.00 2.85
6586 10166 5.893255 TGAGTCCCATGCAATAAGCTTAATT 59.107 36.000 10.85 3.03 45.94 1.40
6628 10208 6.603599 ACAAGAAACTAATCTCCTATTTGGCC 59.396 38.462 0.00 0.00 35.26 5.36
6710 10290 4.813697 ACTCACTCTTTTCTTTCTCTGTGC 59.186 41.667 0.00 0.00 0.00 4.57
6726 10306 6.240894 TCTCTGTGCTGAAATTCCAACTAAT 58.759 36.000 0.00 0.00 0.00 1.73
6943 10523 4.142881 CCTTTAAGCTTGTTACTTCTCGCC 60.143 45.833 9.86 0.00 0.00 5.54
6979 10559 4.213564 AGCAATTGTAGGACCAAGAGAG 57.786 45.455 7.40 0.00 0.00 3.20
7244 10839 3.949754 CAGCCTTGCAATCTCCATTCTTA 59.050 43.478 0.00 0.00 0.00 2.10
8475 12080 7.344612 ACAATACCCAATCAGTGTCAGTAGATA 59.655 37.037 0.00 0.00 0.00 1.98
8525 12130 6.934056 TGGTATTGCAAGTGCTGATATTTTT 58.066 32.000 4.94 0.00 42.66 1.94
8528 12133 7.761249 GGTATTGCAAGTGCTGATATTTTTCTT 59.239 33.333 4.94 0.00 42.66 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.913205 TCTCTCTAGGTGTCCGCTCT 59.087 55.000 0.00 0.00 0.00 4.09
20 21 2.438411 ACAGTTCTCTCTAGGTGTCCG 58.562 52.381 0.00 0.00 0.00 4.79
26 27 6.815089 AGCAATCAATACAGTTCTCTCTAGG 58.185 40.000 0.00 0.00 0.00 3.02
35 36 4.242475 TCGAACGAGCAATCAATACAGTT 58.758 39.130 0.00 0.00 0.00 3.16
67 68 1.692749 TGGAGCCTATGTGTCCCCC 60.693 63.158 0.00 0.00 0.00 5.40
84 85 2.982130 CCCTCACGAAGGTCCCTG 59.018 66.667 7.64 0.00 44.56 4.45
91 92 0.811616 GCCTATGTGCCCTCACGAAG 60.812 60.000 0.00 0.00 46.01 3.79
95 96 1.147153 GGAGCCTATGTGCCCTCAC 59.853 63.158 0.00 0.00 43.40 3.51
125 126 3.119884 TCGTTGTTGCATCATCATGTTCC 60.120 43.478 0.00 0.00 31.86 3.62
153 154 0.689080 TGCCACATCTCTCCTCCTCC 60.689 60.000 0.00 0.00 0.00 4.30
163 164 2.730934 AGATGAGCATTGCCACATCT 57.269 45.000 27.83 27.83 42.93 2.90
202 203 7.839680 AATCCTTCCAAACAGACAAAGTTAT 57.160 32.000 0.00 0.00 0.00 1.89
209 210 8.877864 ACAAATATAATCCTTCCAAACAGACA 57.122 30.769 0.00 0.00 0.00 3.41
243 244 3.398406 GGCCAAAACCTAAAATGTGGTG 58.602 45.455 0.00 0.00 36.57 4.17
276 277 5.830900 TTTTGTTGTCGTTTTGAAAGTGG 57.169 34.783 0.00 0.00 0.00 4.00
339 340 3.327404 CTACCAAGTGGGCCCCGT 61.327 66.667 22.27 10.02 42.05 5.28
359 360 0.733150 TGACTCTATCGCCACGTCAG 59.267 55.000 0.00 0.00 31.62 3.51
390 391 8.280497 CCTGTAATAACGACAAATATAACAGCC 58.720 37.037 0.00 0.00 31.52 4.85
445 447 5.245531 TCTCTTAGGCATTTCAACGAACAT 58.754 37.500 0.00 0.00 0.00 2.71
605 2624 4.209538 TCTCTATGTGGGCAAATTCATGG 58.790 43.478 0.00 0.00 0.00 3.66
690 2709 3.487536 CAAGCAAAACATATTCGTGCGA 58.512 40.909 0.00 0.00 40.17 5.10
692 2711 2.923020 CCCAAGCAAAACATATTCGTGC 59.077 45.455 0.00 0.00 35.41 5.34
694 2713 4.038642 ACAACCCAAGCAAAACATATTCGT 59.961 37.500 0.00 0.00 0.00 3.85
695 2714 4.385447 CACAACCCAAGCAAAACATATTCG 59.615 41.667 0.00 0.00 0.00 3.34
696 2715 4.152223 GCACAACCCAAGCAAAACATATTC 59.848 41.667 0.00 0.00 0.00 1.75
697 2716 4.064388 GCACAACCCAAGCAAAACATATT 58.936 39.130 0.00 0.00 0.00 1.28
698 2717 3.663025 GCACAACCCAAGCAAAACATAT 58.337 40.909 0.00 0.00 0.00 1.78
699 2718 2.544694 CGCACAACCCAAGCAAAACATA 60.545 45.455 0.00 0.00 0.00 2.29
853 2873 1.381165 AAAGTTTTCCGTGCGTGCCT 61.381 50.000 0.00 0.00 0.00 4.75
892 2912 1.302192 GGGGCTGTGTACTTTGCGA 60.302 57.895 0.00 0.00 0.00 5.10
897 2917 1.412453 TTCGTGGGGGCTGTGTACTT 61.412 55.000 0.00 0.00 0.00 2.24
929 2949 5.501156 GTTTTCTCCTCTCTCTCTCTCTCT 58.499 45.833 0.00 0.00 0.00 3.10
930 2950 4.640647 GGTTTTCTCCTCTCTCTCTCTCTC 59.359 50.000 0.00 0.00 0.00 3.20
931 2951 4.292306 AGGTTTTCTCCTCTCTCTCTCTCT 59.708 45.833 0.00 0.00 31.32 3.10
932 2952 4.600062 AGGTTTTCTCCTCTCTCTCTCTC 58.400 47.826 0.00 0.00 31.32 3.20
933 2953 4.675063 AGGTTTTCTCCTCTCTCTCTCT 57.325 45.455 0.00 0.00 31.32 3.10
934 2954 5.751586 TCTAGGTTTTCTCCTCTCTCTCTC 58.248 45.833 0.00 0.00 38.86 3.20
986 3011 1.597302 CCCATGGATGCTCTGCTCG 60.597 63.158 15.22 0.00 0.00 5.03
1139 3164 2.100989 GGAAGTAGTCCATGACCTCGT 58.899 52.381 0.00 0.00 46.97 4.18
1350 3375 3.199946 TCCTCTACTAAAAGCCATGGGTG 59.800 47.826 19.09 7.37 0.00 4.61
1391 3416 2.104331 CGCCACTACCTACTGCCG 59.896 66.667 0.00 0.00 0.00 5.69
1599 3626 2.621055 TGAACAATTGAAACTCCACGGG 59.379 45.455 13.59 0.00 0.00 5.28
1752 3779 2.711542 ACGCTAAATGGGGCATATAGC 58.288 47.619 0.00 0.00 44.65 2.97
1753 3780 4.759693 TGAAACGCTAAATGGGGCATATAG 59.240 41.667 0.00 0.00 0.00 1.31
1754 3781 4.720046 TGAAACGCTAAATGGGGCATATA 58.280 39.130 0.00 0.00 0.00 0.86
1815 3862 0.539438 TCAGGGCGGAATTGCTTTGT 60.539 50.000 0.00 0.00 34.52 2.83
2299 4348 2.033448 TGTTGCTTCGGCGGGAAT 59.967 55.556 7.21 0.00 45.37 3.01
2515 4567 3.874193 GCACCCCCTAAAAAGAAGAGGAG 60.874 52.174 0.00 0.00 31.45 3.69
2549 4601 2.901338 AAAAAGAAGAGGGGGCCTAC 57.099 50.000 0.84 0.00 31.76 3.18
2685 4737 5.063204 AGAAAACAATCGTGGATGTTCTCA 58.937 37.500 0.00 0.00 0.00 3.27
2704 4756 6.096987 ACAAGCGTAGAGATCCAATAGAGAAA 59.903 38.462 0.00 0.00 0.00 2.52
2844 4912 8.271458 ACATTGATACCATGTGTTCCATACTTA 58.729 33.333 0.00 0.00 30.71 2.24
3163 5254 1.003696 TGGAATGGACATTGCCGTACA 59.996 47.619 12.92 0.00 38.21 2.90
3189 5280 3.519913 ACAAATACCAAGAGGAGGAGGAC 59.480 47.826 0.00 0.00 38.69 3.85
3198 5289 5.869344 TGATGAACTCGACAAATACCAAGAG 59.131 40.000 0.00 0.00 0.00 2.85
3248 5342 8.573035 TCCATAGAATTACAAAGTTGGTTCAAC 58.427 33.333 2.85 2.85 43.83 3.18
3267 5361 2.937519 AGAGCAGTCGTGATCCATAGA 58.062 47.619 0.00 0.00 40.17 1.98
3269 5363 5.301805 TCATTTAGAGCAGTCGTGATCCATA 59.698 40.000 0.00 0.00 40.17 2.74
3578 5678 2.091541 TGGTGCAATCGGAATCCTTTC 58.908 47.619 0.00 0.00 0.00 2.62
3829 5933 2.920490 CGGTTGACAAAATAATTGCCCG 59.080 45.455 0.00 0.00 0.00 6.13
4019 6132 4.754114 TGGCAAATACATTTTTGACCTTGC 59.246 37.500 0.65 0.00 42.80 4.01
4210 6326 7.630242 TTCTTGCAGAAAAGAAAGAAGAAGA 57.370 32.000 0.00 0.00 41.92 2.87
4249 6365 2.914536 TGGATGGGCCTAGTGCATATA 58.085 47.619 4.53 0.00 43.89 0.86
4462 6579 5.292101 CCTAGCATCGAAGAAAGTGTTAAGG 59.708 44.000 0.00 0.00 43.58 2.69
4826 6943 1.212616 GCGCTCTTGTAGATGCGAAT 58.787 50.000 18.03 0.00 41.18 3.34
4878 6998 2.203788 ACCTCCACCCGCTCAAGA 60.204 61.111 0.00 0.00 0.00 3.02
4911 7031 3.872603 TGTGGGTGGCTCAAGCGT 61.873 61.111 0.00 0.00 43.26 5.07
4980 7100 5.031066 ACTAGTGGTTAAGTGTTGCTTCA 57.969 39.130 0.00 0.00 38.57 3.02
5058 7197 5.419542 TGAATTGTACTACTGTCATGGAGC 58.580 41.667 0.00 0.00 0.00 4.70
5133 7272 7.148086 CCATTGTAGCAAGGCTAGTTTAATTGA 60.148 37.037 0.00 0.00 42.11 2.57
5137 7276 5.566469 ACCATTGTAGCAAGGCTAGTTTAA 58.434 37.500 0.00 0.00 42.11 1.52
5276 7415 7.961351 TGGTTTGTTTCAGGTCATTGAATATT 58.039 30.769 0.00 0.00 36.97 1.28
5277 7416 7.537596 TGGTTTGTTTCAGGTCATTGAATAT 57.462 32.000 0.00 0.00 36.97 1.28
5278 7417 6.968263 TGGTTTGTTTCAGGTCATTGAATA 57.032 33.333 0.00 0.00 36.97 1.75
5279 7418 5.867903 TGGTTTGTTTCAGGTCATTGAAT 57.132 34.783 0.00 0.00 36.97 2.57
5390 7529 1.254026 TCACTAGGCGCTGTTACACT 58.746 50.000 7.64 0.00 0.00 3.55
5620 9182 3.268647 ATCCCCTCCCCCAAGTCGT 62.269 63.158 0.00 0.00 0.00 4.34
5796 9365 1.236282 CCGATAACCCCCTCCTCCT 59.764 63.158 0.00 0.00 0.00 3.69
5946 9523 3.921767 CTGCTCGAGTGCCTTCGCA 62.922 63.158 15.13 2.74 44.78 5.10
6009 9586 0.668535 TAGCACGAGATAGCACGCAT 59.331 50.000 0.00 0.00 0.00 4.73
6200 9778 0.390209 TACCTCTAAACAACGCCGCC 60.390 55.000 0.00 0.00 0.00 6.13
6273 9851 6.039270 CACTAAACTGGAAACCACAGAAATCA 59.961 38.462 0.00 0.00 39.24 2.57
6432 10011 6.542370 GCCATACCTATCAAGCAGAAAAGTAA 59.458 38.462 0.00 0.00 0.00 2.24
6434 10013 4.884164 GCCATACCTATCAAGCAGAAAAGT 59.116 41.667 0.00 0.00 0.00 2.66
6586 10166 5.743026 TCTTGTCAAACGCTTGATGTAAA 57.257 34.783 4.30 0.00 43.39 2.01
6628 10208 0.671472 TCATGCAGAACTCCACAGCG 60.671 55.000 0.00 0.00 0.00 5.18
6710 10290 5.591877 CCTGGAGGATTAGTTGGAATTTCAG 59.408 44.000 0.00 0.00 37.39 3.02
6943 10523 3.840831 TGCTTAGTACAGCAGCCAG 57.159 52.632 3.87 0.00 45.14 4.85
8331 11936 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51


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

AutoCloner maintained by Alex Coulton.