Multiple sequence alignment - TraesCS4B01G254700

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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 TraesCS4B01G254700 chr4B 100.000 3406 0 0 1 3406 519825805 519822400 0.000000e+00 6290.0
1 TraesCS4B01G254700 chr4D 91.828 1958 97 24 1483 3406 423429607 423427679 0.000000e+00 2671.0
2 TraesCS4B01G254700 chr4D 89.974 1137 68 22 336 1439 423430728 423429605 0.000000e+00 1426.0
3 TraesCS4B01G254700 chr4D 96.599 147 5 0 203 349 423430895 423430749 9.440000e-61 244.0
4 TraesCS4B01G254700 chr4D 93.023 129 9 0 1 129 423431043 423430915 4.490000e-44 189.0
5 TraesCS4B01G254700 chr4A 91.598 1940 104 32 1479 3406 40860476 40862368 0.000000e+00 2625.0
6 TraesCS4B01G254700 chr4A 87.967 1205 67 30 285 1439 40859305 40860481 0.000000e+00 1351.0
7 TraesCS4B01G254700 chr5A 84.000 175 24 3 1221 1393 592638837 592638665 7.560000e-37 165.0
8 TraesCS4B01G254700 chr5B 84.211 171 23 3 1221 1389 580366673 580366505 2.720000e-36 163.0
9 TraesCS4B01G254700 chr5D 83.626 171 24 3 1221 1389 473003387 473003219 1.270000e-34 158.0
10 TraesCS4B01G254700 chr1D 87.786 131 13 3 1 129 18713715 18713844 2.120000e-32 150.0
11 TraesCS4B01G254700 chr2B 79.670 182 27 8 1184 1360 675514515 675514691 4.620000e-24 122.0
12 TraesCS4B01G254700 chr2B 100.000 29 0 0 3239 3267 729630668 729630640 2.000000e-03 54.7
13 TraesCS4B01G254700 chr2A 79.121 182 28 9 1184 1360 705068453 705068629 2.150000e-22 117.0
14 TraesCS4B01G254700 chr2D 78.453 181 31 8 1184 1360 564383979 564384155 9.990000e-21 111.0
15 TraesCS4B01G254700 chr3D 91.379 58 5 0 1306 1363 613780056 613780113 2.820000e-11 80.5
16 TraesCS4B01G254700 chr7B 86.301 73 6 3 2804 2875 291577667 291577598 3.640000e-10 76.8
17 TraesCS4B01G254700 chr7A 94.000 50 3 0 2825 2874 206950004 206950053 3.640000e-10 76.8


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 TraesCS4B01G254700 chr4B 519822400 519825805 3405 True 6290.0 6290 100.0000 1 3406 1 chr4B.!!$R1 3405
1 TraesCS4B01G254700 chr4D 423427679 423431043 3364 True 1132.5 2671 92.8560 1 3406 4 chr4D.!!$R1 3405
2 TraesCS4B01G254700 chr4A 40859305 40862368 3063 False 1988.0 2625 89.7825 285 3406 2 chr4A.!!$F1 3121

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
169 170 0.040499 GGGCCCAAAATAGACCCACA 59.960 55.0 19.95 0.0 40.52 4.17 F
464 501 0.171455 CTCAAGGAACGAGGACGAGG 59.829 60.0 0.00 0.0 42.66 4.63 F
1402 1493 0.245539 CATCCAAGGTTTGCCTGCTG 59.754 55.0 0.00 0.0 46.33 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1570 0.316689 GTCAACAAACAAGGTCGCCG 60.317 55.000 0.00 0.0 0.0 6.46 R
1476 1571 1.002792 GAGTCAACAAACAAGGTCGCC 60.003 52.381 0.00 0.0 0.0 5.54 R
2937 3061 0.036671 AGGGAGACGGCGGTTTTTAG 60.037 55.000 13.24 0.0 0.0 1.85 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 2.845019 ATGTCAGTCATGTGTGCGG 58.155 52.632 0.00 0.00 35.19 5.69
49 50 1.527457 AAATGGCATCCCCTAGAGCT 58.473 50.000 0.00 0.00 0.00 4.09
85 86 2.229062 GGCAACTCCTTTAGGCAGTTTC 59.771 50.000 9.48 6.57 35.15 2.78
103 104 5.064198 CAGTTTCAGACACGTGTCCTTTAAA 59.936 40.000 38.00 28.53 45.85 1.52
108 109 1.223187 CACGTGTCCTTTAAAGGCGT 58.777 50.000 26.75 25.28 46.06 5.68
151 152 7.937700 ATATCCCATAGATATACAAGGTGGG 57.062 40.000 1.11 1.11 44.79 4.61
152 153 4.435137 TCCCATAGATATACAAGGTGGGG 58.565 47.826 7.61 0.00 43.89 4.96
153 154 3.054361 CCCATAGATATACAAGGTGGGGC 60.054 52.174 0.00 0.00 40.84 5.80
154 155 3.054361 CCATAGATATACAAGGTGGGGCC 60.054 52.174 0.00 0.00 37.58 5.80
155 156 1.446016 AGATATACAAGGTGGGGCCC 58.554 55.000 18.17 18.17 38.26 5.80
156 157 1.145571 GATATACAAGGTGGGGCCCA 58.854 55.000 24.76 24.76 38.26 5.36
157 158 1.497286 GATATACAAGGTGGGGCCCAA 59.503 52.381 30.70 10.65 38.26 4.12
158 159 1.383963 TATACAAGGTGGGGCCCAAA 58.616 50.000 30.70 8.53 38.26 3.28
159 160 0.489567 ATACAAGGTGGGGCCCAAAA 59.510 50.000 30.70 9.58 38.26 2.44
160 161 0.489567 TACAAGGTGGGGCCCAAAAT 59.510 50.000 30.70 13.75 38.26 1.82
161 162 0.489567 ACAAGGTGGGGCCCAAAATA 59.510 50.000 30.70 0.00 38.26 1.40
162 163 1.194218 CAAGGTGGGGCCCAAAATAG 58.806 55.000 30.70 12.94 38.26 1.73
163 164 1.089123 AAGGTGGGGCCCAAAATAGA 58.911 50.000 30.70 0.00 38.26 1.98
164 165 0.335019 AGGTGGGGCCCAAAATAGAC 59.665 55.000 30.70 13.21 38.26 2.59
165 166 0.686441 GGTGGGGCCCAAAATAGACC 60.686 60.000 30.70 19.08 34.18 3.85
166 167 0.686441 GTGGGGCCCAAAATAGACCC 60.686 60.000 30.70 7.68 40.05 4.46
167 168 1.149782 TGGGGCCCAAAATAGACCCA 61.150 55.000 26.55 4.81 45.38 4.51
168 169 0.686441 GGGGCCCAAAATAGACCCAC 60.686 60.000 26.86 0.00 42.76 4.61
169 170 0.040499 GGGCCCAAAATAGACCCACA 59.960 55.000 19.95 0.00 40.52 4.17
170 171 1.474330 GGCCCAAAATAGACCCACAG 58.526 55.000 0.00 0.00 0.00 3.66
171 172 1.005450 GGCCCAAAATAGACCCACAGA 59.995 52.381 0.00 0.00 0.00 3.41
172 173 2.369394 GCCCAAAATAGACCCACAGAG 58.631 52.381 0.00 0.00 0.00 3.35
173 174 2.290960 GCCCAAAATAGACCCACAGAGT 60.291 50.000 0.00 0.00 0.00 3.24
174 175 3.054655 GCCCAAAATAGACCCACAGAGTA 60.055 47.826 0.00 0.00 0.00 2.59
175 176 4.770795 CCCAAAATAGACCCACAGAGTAG 58.229 47.826 0.00 0.00 0.00 2.57
176 177 4.225267 CCCAAAATAGACCCACAGAGTAGT 59.775 45.833 0.00 0.00 0.00 2.73
177 178 5.424252 CCCAAAATAGACCCACAGAGTAGTA 59.576 44.000 0.00 0.00 0.00 1.82
178 179 6.099845 CCCAAAATAGACCCACAGAGTAGTAT 59.900 42.308 0.00 0.00 0.00 2.12
179 180 7.289317 CCCAAAATAGACCCACAGAGTAGTATA 59.711 40.741 0.00 0.00 0.00 1.47
180 181 8.871125 CCAAAATAGACCCACAGAGTAGTATAT 58.129 37.037 0.00 0.00 0.00 0.86
181 182 9.915629 CAAAATAGACCCACAGAGTAGTATATC 57.084 37.037 0.00 0.00 0.00 1.63
182 183 8.653036 AAATAGACCCACAGAGTAGTATATCC 57.347 38.462 0.00 0.00 0.00 2.59
183 184 5.000570 AGACCCACAGAGTAGTATATCCC 57.999 47.826 0.00 0.00 0.00 3.85
184 185 4.419200 AGACCCACAGAGTAGTATATCCCA 59.581 45.833 0.00 0.00 0.00 4.37
185 186 5.076598 AGACCCACAGAGTAGTATATCCCAT 59.923 44.000 0.00 0.00 0.00 4.00
186 187 6.277283 AGACCCACAGAGTAGTATATCCCATA 59.723 42.308 0.00 0.00 0.00 2.74
187 188 6.494952 ACCCACAGAGTAGTATATCCCATAG 58.505 44.000 0.00 0.00 0.00 2.23
188 189 6.277283 ACCCACAGAGTAGTATATCCCATAGA 59.723 42.308 0.00 0.00 0.00 1.98
189 190 7.035764 ACCCACAGAGTAGTATATCCCATAGAT 60.036 40.741 0.00 0.00 39.15 1.98
190 191 8.503573 CCCACAGAGTAGTATATCCCATAGATA 58.496 40.741 0.00 0.00 41.73 1.98
380 417 2.413502 CGAGTGAGGAAACAGAGACGAG 60.414 54.545 0.00 0.00 0.00 4.18
419 456 0.319211 GTTGTCACACGTCCGATCCA 60.319 55.000 0.00 0.00 0.00 3.41
434 471 3.068448 CCGATCCAATGGCATTGAAATCA 59.932 43.478 35.39 16.93 42.83 2.57
456 493 5.767665 TCAAATTTCCATTCTCAAGGAACGA 59.232 36.000 0.00 0.00 43.23 3.85
458 495 3.334583 TTCCATTCTCAAGGAACGAGG 57.665 47.619 0.00 0.00 38.91 4.63
463 500 1.166129 TCTCAAGGAACGAGGACGAG 58.834 55.000 0.00 0.00 42.66 4.18
464 501 0.171455 CTCAAGGAACGAGGACGAGG 59.829 60.000 0.00 0.00 42.66 4.63
487 524 2.281761 CTGCCAGACCACACCACC 60.282 66.667 0.00 0.00 0.00 4.61
491 528 1.455383 GCCAGACCACACCACCTTTG 61.455 60.000 0.00 0.00 0.00 2.77
554 595 1.794151 CTGCCGCATTCCACACAACA 61.794 55.000 0.00 0.00 0.00 3.33
589 630 4.966850 ACGATGACACGACAAAACTAAG 57.033 40.909 0.00 0.00 37.03 2.18
590 631 3.183775 ACGATGACACGACAAAACTAAGC 59.816 43.478 0.00 0.00 37.03 3.09
592 633 1.862201 TGACACGACAAAACTAAGCCG 59.138 47.619 0.00 0.00 0.00 5.52
593 634 1.862827 GACACGACAAAACTAAGCCGT 59.137 47.619 0.00 0.00 0.00 5.68
594 635 2.294479 CACGACAAAACTAAGCCGTG 57.706 50.000 0.00 0.00 40.70 4.94
625 673 4.468510 TGCCCTTTTCCTCGAAAGTCTATA 59.531 41.667 0.00 0.00 35.37 1.31
705 753 1.691219 GTCCCTTTCCCATCAGCCA 59.309 57.895 0.00 0.00 0.00 4.75
709 757 1.496429 CCCTTTCCCATCAGCCATAGT 59.504 52.381 0.00 0.00 0.00 2.12
712 760 3.371917 CCTTTCCCATCAGCCATAGTGAA 60.372 47.826 0.00 0.00 0.00 3.18
713 761 4.467769 CTTTCCCATCAGCCATAGTGAAT 58.532 43.478 0.00 0.00 0.00 2.57
714 762 4.524802 TTCCCATCAGCCATAGTGAATT 57.475 40.909 0.00 0.00 0.00 2.17
715 763 4.090761 TCCCATCAGCCATAGTGAATTC 57.909 45.455 0.00 0.00 0.00 2.17
717 765 3.494924 CCCATCAGCCATAGTGAATTCGA 60.495 47.826 0.04 0.00 0.00 3.71
718 766 3.744942 CCATCAGCCATAGTGAATTCGAG 59.255 47.826 0.04 0.00 0.00 4.04
719 767 4.502087 CCATCAGCCATAGTGAATTCGAGA 60.502 45.833 0.04 0.00 0.00 4.04
720 768 4.944619 TCAGCCATAGTGAATTCGAGAT 57.055 40.909 0.04 0.00 0.00 2.75
721 769 4.625028 TCAGCCATAGTGAATTCGAGATG 58.375 43.478 0.04 3.95 0.00 2.90
722 770 3.186001 CAGCCATAGTGAATTCGAGATGC 59.814 47.826 0.04 0.00 0.00 3.91
723 771 3.133691 GCCATAGTGAATTCGAGATGCA 58.866 45.455 0.04 0.00 0.00 3.96
763 812 9.396964 CCAGATGGAATTGAGCTAGAGCTAGAG 62.397 48.148 3.49 0.00 45.01 2.43
856 912 0.985549 GTGCGTCGTTGAGATGTCTC 59.014 55.000 3.07 3.07 43.15 3.36
894 954 7.655490 CATGAGACTGGAAAAAGAGTTTGAAT 58.345 34.615 0.00 0.00 0.00 2.57
947 1007 1.900498 ACCCCTCGTTTCTCGTCGT 60.900 57.895 0.00 0.00 40.80 4.34
1012 1072 0.828022 CCCGCCTATGAGTACACCAA 59.172 55.000 0.00 0.00 0.00 3.67
1043 1103 1.487452 GAACGCTTGTCACACTCGCA 61.487 55.000 0.00 0.00 0.00 5.10
1045 1105 2.939022 GCTTGTCACACTCGCACC 59.061 61.111 0.00 0.00 0.00 5.01
1053 1113 2.669569 CACTCGCACCCCACAAGG 60.670 66.667 0.00 0.00 0.00 3.61
1063 1123 2.352805 CCACAAGGCACTCCCTCC 59.647 66.667 0.00 0.00 45.62 4.30
1064 1124 2.352805 CACAAGGCACTCCCTCCC 59.647 66.667 0.00 0.00 45.62 4.30
1081 1150 1.377725 CCCCGCAGCTCTTTCACAT 60.378 57.895 0.00 0.00 0.00 3.21
1251 1338 2.402787 GAGTACTCCGTCGCCGTC 59.597 66.667 12.13 0.00 0.00 4.79
1402 1493 0.245539 CATCCAAGGTTTGCCTGCTG 59.754 55.000 0.00 0.00 46.33 4.41
1404 1495 2.205152 CCAAGGTTTGCCTGCTGCT 61.205 57.895 0.00 0.00 46.33 4.24
1439 1534 2.538737 CGTGTTCGTCATGCACAACTTT 60.539 45.455 0.00 0.00 33.70 2.66
1440 1535 3.434637 GTGTTCGTCATGCACAACTTTT 58.565 40.909 0.00 0.00 33.70 2.27
1441 1536 4.593157 GTGTTCGTCATGCACAACTTTTA 58.407 39.130 0.00 0.00 33.70 1.52
1442 1537 4.436523 GTGTTCGTCATGCACAACTTTTAC 59.563 41.667 0.00 0.00 33.70 2.01
1443 1538 4.334203 TGTTCGTCATGCACAACTTTTACT 59.666 37.500 0.00 0.00 0.00 2.24
1444 1539 4.725556 TCGTCATGCACAACTTTTACTC 57.274 40.909 0.00 0.00 0.00 2.59
1445 1540 4.377021 TCGTCATGCACAACTTTTACTCT 58.623 39.130 0.00 0.00 0.00 3.24
1446 1541 5.534407 TCGTCATGCACAACTTTTACTCTA 58.466 37.500 0.00 0.00 0.00 2.43
1447 1542 5.404366 TCGTCATGCACAACTTTTACTCTAC 59.596 40.000 0.00 0.00 0.00 2.59
1448 1543 5.389516 CGTCATGCACAACTTTTACTCTACC 60.390 44.000 0.00 0.00 0.00 3.18
1449 1544 5.468746 GTCATGCACAACTTTTACTCTACCA 59.531 40.000 0.00 0.00 0.00 3.25
1450 1545 6.149474 GTCATGCACAACTTTTACTCTACCAT 59.851 38.462 0.00 0.00 0.00 3.55
1451 1546 6.714810 TCATGCACAACTTTTACTCTACCATT 59.285 34.615 0.00 0.00 0.00 3.16
1452 1547 7.880713 TCATGCACAACTTTTACTCTACCATTA 59.119 33.333 0.00 0.00 0.00 1.90
1453 1548 8.677300 CATGCACAACTTTTACTCTACCATTAT 58.323 33.333 0.00 0.00 0.00 1.28
1454 1549 8.630054 TGCACAACTTTTACTCTACCATTATT 57.370 30.769 0.00 0.00 0.00 1.40
1455 1550 8.511321 TGCACAACTTTTACTCTACCATTATTG 58.489 33.333 0.00 0.00 0.00 1.90
1456 1551 8.512138 GCACAACTTTTACTCTACCATTATTGT 58.488 33.333 0.00 0.00 0.00 2.71
1478 1573 7.576750 TGTAGTAATAATCAAATCGATCGGC 57.423 36.000 16.41 0.00 31.11 5.54
1479 1574 5.763444 AGTAATAATCAAATCGATCGGCG 57.237 39.130 16.41 0.00 42.69 6.46
1501 1596 2.285083 CCTTGTTTGTTGACTCGTGGA 58.715 47.619 0.00 0.00 0.00 4.02
1511 1609 1.336517 TGACTCGTGGATTCGTTGGTC 60.337 52.381 0.00 0.00 0.00 4.02
2275 2373 2.337361 TCGTGCTCTTCCTCGACAA 58.663 52.632 0.00 0.00 0.00 3.18
2444 2542 4.034258 TCGGTCAGCGACGTGGAC 62.034 66.667 0.11 11.12 32.65 4.02
2473 2571 0.318614 ACGTGGTACCGTAAACGTGG 60.319 55.000 22.89 0.75 46.58 4.94
2522 2620 2.427453 GCTCTCTGGAACGGAAGATACA 59.573 50.000 0.00 0.00 46.55 2.29
2611 2713 0.931005 GTAGATAAGCAGTGCCGTGC 59.069 55.000 12.58 0.00 44.35 5.34
2635 2738 5.008217 CCGTGTTGGTGTGAAGAGAATTAAA 59.992 40.000 0.00 0.00 0.00 1.52
2658 2761 3.263261 GGTACTCTGTGCTTAAGCTTCC 58.737 50.000 26.90 15.40 42.66 3.46
2672 2775 6.127786 GCTTAAGCTTCCTCTGTGATCAATTT 60.128 38.462 20.38 0.00 38.21 1.82
2698 2801 0.904394 TGCTTTGCCCCCTCCAATTC 60.904 55.000 0.00 0.00 0.00 2.17
2711 2814 4.006319 CCTCCAATTCCTTGTCTGTTCTC 58.994 47.826 0.00 0.00 0.00 2.87
2784 2907 3.086282 TGTTTTCGGGGAAATCTTAGCC 58.914 45.455 0.00 0.00 31.34 3.93
2794 2917 0.457035 AATCTTAGCCGGCGAACGTA 59.543 50.000 23.20 8.71 42.24 3.57
2862 2985 2.442236 ATCCGATGGATGGCAGTTTT 57.558 45.000 0.00 0.00 41.43 2.43
2863 2986 1.750193 TCCGATGGATGGCAGTTTTC 58.250 50.000 0.00 0.00 0.00 2.29
2864 2987 1.004161 TCCGATGGATGGCAGTTTTCA 59.996 47.619 0.00 0.00 0.00 2.69
2865 2988 2.026641 CCGATGGATGGCAGTTTTCAT 58.973 47.619 0.00 0.00 0.00 2.57
2866 2989 2.223641 CCGATGGATGGCAGTTTTCATG 60.224 50.000 0.00 0.00 0.00 3.07
2869 2992 4.380761 CGATGGATGGCAGTTTTCATGAAA 60.381 41.667 16.91 16.91 0.00 2.69
2920 3043 3.148412 GTTTCTAAAAACCGCCACCCTA 58.852 45.455 0.00 0.00 39.10 3.53
2937 3061 1.445871 CTACCACCCCTTAAACGCAC 58.554 55.000 0.00 0.00 0.00 5.34
2956 3080 0.036671 CTAAAAACCGCCGTCTCCCT 60.037 55.000 0.00 0.00 0.00 4.20
2962 3086 3.744719 CGCCGTCTCCCTCGTTCA 61.745 66.667 0.00 0.00 0.00 3.18
2964 3088 1.218316 GCCGTCTCCCTCGTTCATT 59.782 57.895 0.00 0.00 0.00 2.57
2965 3089 0.391263 GCCGTCTCCCTCGTTCATTT 60.391 55.000 0.00 0.00 0.00 2.32
2966 3090 1.359848 CCGTCTCCCTCGTTCATTTG 58.640 55.000 0.00 0.00 0.00 2.32
2967 3091 0.721718 CGTCTCCCTCGTTCATTTGC 59.278 55.000 0.00 0.00 0.00 3.68
2968 3092 1.087501 GTCTCCCTCGTTCATTTGCC 58.912 55.000 0.00 0.00 0.00 4.52
2969 3093 0.690192 TCTCCCTCGTTCATTTGCCA 59.310 50.000 0.00 0.00 0.00 4.92
2970 3094 1.281867 TCTCCCTCGTTCATTTGCCAT 59.718 47.619 0.00 0.00 0.00 4.40
2971 3095 1.402968 CTCCCTCGTTCATTTGCCATG 59.597 52.381 0.00 0.00 0.00 3.66
2972 3096 0.179129 CCCTCGTTCATTTGCCATGC 60.179 55.000 0.00 0.00 0.00 4.06
2973 3097 0.527113 CCTCGTTCATTTGCCATGCA 59.473 50.000 0.00 0.00 36.47 3.96
2974 3098 1.468565 CCTCGTTCATTTGCCATGCAG 60.469 52.381 0.00 0.00 40.61 4.41
2975 3099 0.527113 TCGTTCATTTGCCATGCAGG 59.473 50.000 0.00 0.00 40.61 4.85
2991 3115 1.068474 CAGGCTTTAGTGAACGGACG 58.932 55.000 0.00 0.00 0.00 4.79
2993 3117 1.632948 GGCTTTAGTGAACGGACGCC 61.633 60.000 0.00 0.00 0.00 5.68
2999 3123 0.606604 AGTGAACGGACGCCAGTTAT 59.393 50.000 0.00 0.00 0.00 1.89
3009 3133 1.227147 GCCAGTTATGCGCGTCCTA 60.227 57.895 4.79 0.00 0.00 2.94
3018 3142 5.583457 AGTTATGCGCGTCCTATTTTTAAGT 59.417 36.000 4.79 0.00 0.00 2.24
3026 3150 5.121768 GCGTCCTATTTTTAAGTCAAGAGCA 59.878 40.000 0.00 0.00 0.00 4.26
3028 3152 6.590292 CGTCCTATTTTTAAGTCAAGAGCAGA 59.410 38.462 0.00 0.00 0.00 4.26
3033 3157 9.617975 CTATTTTTAAGTCAAGAGCAGAAAAGG 57.382 33.333 0.00 0.00 0.00 3.11
3061 3185 3.072915 TCAACGGACGGAGGGATATAGTA 59.927 47.826 0.00 0.00 0.00 1.82
3072 3196 8.583296 ACGGAGGGATATAGTATAAAGAAACAC 58.417 37.037 0.00 0.00 0.00 3.32
3091 3215 8.491134 AGAAACACATATACTATTTACCAGGCA 58.509 33.333 0.00 0.00 0.00 4.75
3119 3243 4.776795 ATTTTCCCAAGCGTAAAACGAT 57.223 36.364 3.22 0.00 44.59 3.73
3133 3257 6.839796 GCGTAAAACGATTTAGAATGAGTAGC 59.160 38.462 3.22 0.00 46.05 3.58
3136 3260 9.303537 GTAAAACGATTTAGAATGAGTAGCTCT 57.696 33.333 0.00 0.00 31.81 4.09
3190 3314 1.597461 GAGGACGGGAAGGAGGTTG 59.403 63.158 0.00 0.00 0.00 3.77
3250 3374 2.134933 GGAGGACGGGGCTTAGAGG 61.135 68.421 0.00 0.00 0.00 3.69
3267 3391 4.241555 GGATGATCGGGGCAGCGT 62.242 66.667 0.00 0.00 0.00 5.07
3273 3397 1.712018 GATCGGGGCAGCGTTAAACC 61.712 60.000 0.00 0.00 0.00 3.27
3280 3404 1.431496 GCAGCGTTAAACCGGTAGAA 58.569 50.000 8.00 1.36 36.69 2.10
3288 3412 0.589708 AAACCGGTAGAAAACAGCGC 59.410 50.000 8.00 0.00 35.66 5.92
3312 3442 2.691771 GCGTGCGTGAGAGAGAGGA 61.692 63.158 0.00 0.00 0.00 3.71
3315 3445 2.049185 TGCGTGAGAGAGAGGAGGC 61.049 63.158 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.792047 CCGCCGCACACATGACTG 61.792 66.667 0.00 0.00 0.00 3.51
7 8 2.593148 AAACCGCCGCACACATGA 60.593 55.556 0.00 0.00 0.00 3.07
18 19 1.226575 GCCATTTAGCCGAAACCGC 60.227 57.895 0.00 0.00 0.00 5.68
32 33 1.776975 GCAGCTCTAGGGGATGCCAT 61.777 60.000 5.30 0.00 0.00 4.40
49 50 1.804151 GTTGCCACGTGAAGATAAGCA 59.196 47.619 19.30 13.29 0.00 3.91
131 132 3.054361 GCCCCACCTTGTATATCTATGGG 60.054 52.174 0.00 0.00 44.22 4.00
132 133 3.054361 GGCCCCACCTTGTATATCTATGG 60.054 52.174 0.00 0.00 34.51 2.74
133 134 3.054361 GGGCCCCACCTTGTATATCTATG 60.054 52.174 12.23 0.00 39.10 2.23
134 135 3.190439 GGGCCCCACCTTGTATATCTAT 58.810 50.000 12.23 0.00 39.10 1.98
136 137 1.346046 TGGGCCCCACCTTGTATATCT 60.346 52.381 22.27 0.00 39.10 1.98
137 138 1.145571 TGGGCCCCACCTTGTATATC 58.854 55.000 22.27 0.00 39.10 1.63
138 139 1.614449 TTGGGCCCCACCTTGTATAT 58.386 50.000 22.27 0.00 39.10 0.86
139 140 1.383963 TTTGGGCCCCACCTTGTATA 58.616 50.000 22.27 0.00 39.10 1.47
140 141 0.489567 TTTTGGGCCCCACCTTGTAT 59.510 50.000 22.27 0.00 39.10 2.29
141 142 0.489567 ATTTTGGGCCCCACCTTGTA 59.510 50.000 22.27 0.00 39.10 2.41
142 143 0.489567 TATTTTGGGCCCCACCTTGT 59.510 50.000 22.27 0.96 39.10 3.16
144 145 1.089123 TCTATTTTGGGCCCCACCTT 58.911 50.000 22.27 2.60 39.10 3.50
145 146 0.335019 GTCTATTTTGGGCCCCACCT 59.665 55.000 22.27 4.05 39.10 4.00
147 148 0.686441 GGGTCTATTTTGGGCCCCAC 60.686 60.000 22.27 0.00 30.78 4.61
148 149 1.149782 TGGGTCTATTTTGGGCCCCA 61.150 55.000 22.27 4.90 39.77 4.96
149 150 0.686441 GTGGGTCTATTTTGGGCCCC 60.686 60.000 22.27 0.85 38.57 5.80
150 151 0.040499 TGTGGGTCTATTTTGGGCCC 59.960 55.000 17.59 17.59 39.73 5.80
151 152 1.005450 TCTGTGGGTCTATTTTGGGCC 59.995 52.381 0.00 0.00 0.00 5.80
152 153 2.290960 ACTCTGTGGGTCTATTTTGGGC 60.291 50.000 0.00 0.00 0.00 5.36
153 154 3.721087 ACTCTGTGGGTCTATTTTGGG 57.279 47.619 0.00 0.00 0.00 4.12
154 155 5.422214 ACTACTCTGTGGGTCTATTTTGG 57.578 43.478 0.00 0.00 0.00 3.28
155 156 9.915629 GATATACTACTCTGTGGGTCTATTTTG 57.084 37.037 0.00 0.00 0.00 2.44
156 157 9.091220 GGATATACTACTCTGTGGGTCTATTTT 57.909 37.037 0.00 0.00 0.00 1.82
157 158 7.674772 GGGATATACTACTCTGTGGGTCTATTT 59.325 40.741 0.00 0.00 0.00 1.40
158 159 7.183460 GGGATATACTACTCTGTGGGTCTATT 58.817 42.308 0.00 0.00 0.00 1.73
159 160 6.277283 TGGGATATACTACTCTGTGGGTCTAT 59.723 42.308 0.00 0.00 0.00 1.98
160 161 5.613973 TGGGATATACTACTCTGTGGGTCTA 59.386 44.000 0.00 0.00 0.00 2.59
161 162 4.419200 TGGGATATACTACTCTGTGGGTCT 59.581 45.833 0.00 0.00 0.00 3.85
162 163 4.737578 TGGGATATACTACTCTGTGGGTC 58.262 47.826 0.00 0.00 0.00 4.46
163 164 4.827036 TGGGATATACTACTCTGTGGGT 57.173 45.455 0.00 0.00 0.00 4.51
164 165 6.732487 TCTATGGGATATACTACTCTGTGGG 58.268 44.000 0.00 0.00 0.00 4.61
176 177 9.500701 TGCCACTTTGTATATCTATGGGATATA 57.499 33.333 0.00 0.00 43.54 0.86
177 178 8.392631 TGCCACTTTGTATATCTATGGGATAT 57.607 34.615 0.00 0.00 46.11 1.63
178 179 7.806680 TGCCACTTTGTATATCTATGGGATA 57.193 36.000 0.00 0.00 40.69 2.59
179 180 6.702449 TGCCACTTTGTATATCTATGGGAT 57.298 37.500 0.00 0.00 38.38 3.85
180 181 6.702449 ATGCCACTTTGTATATCTATGGGA 57.298 37.500 0.00 0.00 0.00 4.37
181 182 8.489489 AGATATGCCACTTTGTATATCTATGGG 58.511 37.037 9.08 0.00 39.70 4.00
210 211 4.507342 AGGCCCACAGAAGATTATATCCT 58.493 43.478 0.00 0.00 0.00 3.24
295 296 3.550820 TCACTTTGCCGGTATATGCAAT 58.449 40.909 1.90 0.00 45.96 3.56
314 317 2.432456 GTGATGACACGGCGCTCA 60.432 61.111 6.90 8.77 37.28 4.26
380 417 5.237344 ACAACACTTGTAATCTTGTCTCTGC 59.763 40.000 0.00 0.00 43.27 4.26
404 441 0.108377 CCATTGGATCGGACGTGTGA 60.108 55.000 0.00 0.00 0.00 3.58
434 471 5.183904 CCTCGTTCCTTGAGAATGGAAATTT 59.816 40.000 0.00 0.00 43.06 1.82
481 518 1.202806 TCCTTGCTCTCAAAGGTGGTG 60.203 52.381 2.35 0.00 0.00 4.17
487 524 8.366401 TCTCAAGATATATCCTTGCTCTCAAAG 58.634 37.037 9.18 5.57 40.45 2.77
491 528 9.723601 AATTTCTCAAGATATATCCTTGCTCTC 57.276 33.333 9.18 0.00 40.45 3.20
554 595 3.945921 TGTCATCGTTTACTCCGAGAGAT 59.054 43.478 1.33 0.00 37.81 2.75
625 673 2.900546 GGGAGGATCGGTCACATATCTT 59.099 50.000 0.00 0.00 34.37 2.40
659 707 1.072666 GCTAAATGCTGTTGCCACGC 61.073 55.000 0.00 0.00 38.71 5.34
667 715 1.262417 CGCATGATCGCTAAATGCTGT 59.738 47.619 11.77 0.00 43.59 4.40
679 727 0.107214 TGGGAAAGGGACGCATGATC 60.107 55.000 0.00 0.00 0.00 2.92
705 753 7.381323 TGATATGTGCATCTCGAATTCACTAT 58.619 34.615 6.22 0.00 0.00 2.12
709 757 7.500720 AATTGATATGTGCATCTCGAATTCA 57.499 32.000 6.22 0.00 0.00 2.57
712 760 7.094890 GGAGAAATTGATATGTGCATCTCGAAT 60.095 37.037 0.00 0.00 34.35 3.34
713 761 6.203530 GGAGAAATTGATATGTGCATCTCGAA 59.796 38.462 0.00 0.00 34.35 3.71
714 762 5.698089 GGAGAAATTGATATGTGCATCTCGA 59.302 40.000 0.00 0.00 34.35 4.04
715 763 5.467735 TGGAGAAATTGATATGTGCATCTCG 59.532 40.000 0.00 0.00 34.35 4.04
717 765 6.598503 TCTGGAGAAATTGATATGTGCATCT 58.401 36.000 0.00 0.00 0.00 2.90
718 766 6.872628 TCTGGAGAAATTGATATGTGCATC 57.127 37.500 0.00 0.00 0.00 3.91
719 767 6.208797 CCATCTGGAGAAATTGATATGTGCAT 59.791 38.462 0.00 0.00 37.39 3.96
720 768 5.533528 CCATCTGGAGAAATTGATATGTGCA 59.466 40.000 0.00 0.00 37.39 4.57
721 769 5.766670 TCCATCTGGAGAAATTGATATGTGC 59.233 40.000 0.00 0.00 39.78 4.57
722 770 7.812690 TTCCATCTGGAGAAATTGATATGTG 57.187 36.000 0.00 0.00 46.36 3.21
723 771 8.857098 CAATTCCATCTGGAGAAATTGATATGT 58.143 33.333 13.39 0.00 46.36 2.29
763 812 2.220761 CTCGCGCAGGAATTCTAGC 58.779 57.895 8.75 8.79 0.00 3.42
835 891 1.352156 GACATCTCAACGACGCACCC 61.352 60.000 0.00 0.00 0.00 4.61
894 954 1.456544 CGCGTTCGTTAAGTTTGGCTA 59.543 47.619 0.00 0.00 0.00 3.93
964 1024 2.592861 GGATGGCAGCGGTGGATC 60.593 66.667 17.54 0.00 0.00 3.36
1025 1085 1.520564 TGCGAGTGTGACAAGCGTT 60.521 52.632 9.50 0.00 0.00 4.84
1026 1086 2.106131 TGCGAGTGTGACAAGCGT 59.894 55.556 9.50 0.00 0.00 5.07
1043 1103 3.580319 GGGAGTGCCTTGTGGGGT 61.580 66.667 0.00 0.00 35.12 4.95
1045 1105 2.352805 GAGGGAGTGCCTTGTGGG 59.647 66.667 4.00 0.00 38.36 4.61
1063 1123 1.372087 GATGTGAAAGAGCTGCGGGG 61.372 60.000 0.00 0.00 0.00 5.73
1064 1124 0.674581 TGATGTGAAAGAGCTGCGGG 60.675 55.000 0.00 0.00 0.00 6.13
1402 1493 4.470050 CGCGCGTTGAACGAGAGC 62.470 66.667 24.69 20.93 46.05 4.09
1404 1495 3.391631 CACGCGCGTTGAACGAGA 61.392 61.111 35.90 0.00 46.05 4.04
1452 1547 8.656849 GCCGATCGATTTGATTATTACTACAAT 58.343 33.333 18.66 0.00 37.47 2.71
1453 1548 7.148869 CGCCGATCGATTTGATTATTACTACAA 60.149 37.037 18.66 0.00 41.67 2.41
1454 1549 6.307077 CGCCGATCGATTTGATTATTACTACA 59.693 38.462 18.66 0.00 41.67 2.74
1455 1550 6.525628 TCGCCGATCGATTTGATTATTACTAC 59.474 38.462 18.66 0.00 43.16 2.73
1456 1551 6.614160 TCGCCGATCGATTTGATTATTACTA 58.386 36.000 18.66 0.00 43.16 1.82
1457 1552 5.466819 TCGCCGATCGATTTGATTATTACT 58.533 37.500 18.66 0.00 43.16 2.24
1458 1553 5.756950 TCGCCGATCGATTTGATTATTAC 57.243 39.130 18.66 0.00 43.16 1.89
1470 1565 1.011968 CAAACAAGGTCGCCGATCGA 61.012 55.000 18.66 0.00 46.29 3.59
1471 1566 1.289109 ACAAACAAGGTCGCCGATCG 61.289 55.000 8.51 8.51 40.15 3.69
1472 1567 0.872388 AACAAACAAGGTCGCCGATC 59.128 50.000 0.00 0.00 0.00 3.69
1473 1568 0.591170 CAACAAACAAGGTCGCCGAT 59.409 50.000 0.00 0.00 0.00 4.18
1474 1569 0.462225 TCAACAAACAAGGTCGCCGA 60.462 50.000 0.00 0.00 0.00 5.54
1475 1570 0.316689 GTCAACAAACAAGGTCGCCG 60.317 55.000 0.00 0.00 0.00 6.46
1476 1571 1.002792 GAGTCAACAAACAAGGTCGCC 60.003 52.381 0.00 0.00 0.00 5.54
1477 1572 1.332904 CGAGTCAACAAACAAGGTCGC 60.333 52.381 0.00 0.00 0.00 5.19
1478 1573 1.931172 ACGAGTCAACAAACAAGGTCG 59.069 47.619 0.00 0.00 0.00 4.79
1479 1574 2.031683 CCACGAGTCAACAAACAAGGTC 59.968 50.000 0.00 0.00 0.00 3.85
1480 1575 2.014128 CCACGAGTCAACAAACAAGGT 58.986 47.619 0.00 0.00 0.00 3.50
1481 1576 2.285083 TCCACGAGTCAACAAACAAGG 58.715 47.619 0.00 0.00 0.00 3.61
1482 1577 4.527564 GAATCCACGAGTCAACAAACAAG 58.472 43.478 0.00 0.00 0.00 3.16
1483 1578 3.001838 CGAATCCACGAGTCAACAAACAA 59.998 43.478 0.00 0.00 35.09 2.83
1484 1579 2.542178 CGAATCCACGAGTCAACAAACA 59.458 45.455 0.00 0.00 35.09 2.83
1501 1596 1.429463 GAACTCTGCGACCAACGAAT 58.571 50.000 0.00 0.00 45.77 3.34
1539 1637 2.279120 GATCACCTGCGCCGAGAG 60.279 66.667 4.18 0.00 0.00 3.20
1919 2017 3.766691 TCGGGCCGCTTCAGGTAC 61.767 66.667 23.83 0.00 0.00 3.34
2174 2272 4.158025 TCGTACTTGATGTCCTTCTTCCTC 59.842 45.833 0.00 0.00 0.00 3.71
2473 2571 1.853253 GCCGAAAATTAACGCCGCTAC 60.853 52.381 0.00 0.00 0.00 3.58
2522 2620 0.607489 AGCAAAGAACGCATGCTCCT 60.607 50.000 17.13 6.82 46.98 3.69
2611 2713 1.948104 TTCTCTTCACACCAACACGG 58.052 50.000 0.00 0.00 42.50 4.94
2635 2738 4.508662 GAAGCTTAAGCACAGAGTACCAT 58.491 43.478 28.39 0.79 45.16 3.55
2658 2761 5.879223 AGCAACCTCTAAATTGATCACAGAG 59.121 40.000 12.64 12.64 33.93 3.35
2672 2775 1.140134 AGGGGGCAAAGCAACCTCTA 61.140 55.000 0.00 0.00 32.26 2.43
2698 2801 4.749099 CAGAACAGAAGAGAACAGACAAGG 59.251 45.833 0.00 0.00 0.00 3.61
2711 2814 3.976942 CACGAAAATTGGCAGAACAGAAG 59.023 43.478 0.00 0.00 0.00 2.85
2769 2892 1.892391 GCCGGCTAAGATTTCCCCG 60.892 63.158 22.15 0.00 38.71 5.73
2770 2893 1.892391 CGCCGGCTAAGATTTCCCC 60.892 63.158 26.68 0.00 0.00 4.81
2794 2917 1.034838 TGGCAAAACGTCTGTGGCTT 61.035 50.000 16.84 0.00 38.56 4.35
2801 2924 1.647084 GTTCGCTGGCAAAACGTCT 59.353 52.632 0.00 0.00 0.00 4.18
2873 2996 3.243359 TGGCAGTTCCTTCCTTTCATT 57.757 42.857 0.00 0.00 35.26 2.57
2920 3043 1.058284 TAGTGCGTTTAAGGGGTGGT 58.942 50.000 0.00 0.00 0.00 4.16
2937 3061 0.036671 AGGGAGACGGCGGTTTTTAG 60.037 55.000 13.24 0.00 0.00 1.85
2956 3080 0.527113 CCTGCATGGCAAATGAACGA 59.473 50.000 0.00 0.00 38.41 3.85
2967 3091 1.131126 CGTTCACTAAAGCCTGCATGG 59.869 52.381 0.00 0.00 39.35 3.66
2968 3092 1.131126 CCGTTCACTAAAGCCTGCATG 59.869 52.381 0.00 0.00 0.00 4.06
2969 3093 1.003118 TCCGTTCACTAAAGCCTGCAT 59.997 47.619 0.00 0.00 0.00 3.96
2970 3094 0.394938 TCCGTTCACTAAAGCCTGCA 59.605 50.000 0.00 0.00 0.00 4.41
2971 3095 0.796927 GTCCGTTCACTAAAGCCTGC 59.203 55.000 0.00 0.00 0.00 4.85
2972 3096 1.068474 CGTCCGTTCACTAAAGCCTG 58.932 55.000 0.00 0.00 0.00 4.85
2973 3097 0.669625 GCGTCCGTTCACTAAAGCCT 60.670 55.000 0.00 0.00 0.00 4.58
2974 3098 1.632948 GGCGTCCGTTCACTAAAGCC 61.633 60.000 0.00 0.00 36.32 4.35
2975 3099 0.947180 TGGCGTCCGTTCACTAAAGC 60.947 55.000 0.00 0.00 0.00 3.51
2976 3100 1.068474 CTGGCGTCCGTTCACTAAAG 58.932 55.000 0.00 0.00 0.00 1.85
2977 3101 0.390124 ACTGGCGTCCGTTCACTAAA 59.610 50.000 0.00 0.00 0.00 1.85
2978 3102 0.390124 AACTGGCGTCCGTTCACTAA 59.610 50.000 0.00 0.00 0.00 2.24
2979 3103 1.246649 TAACTGGCGTCCGTTCACTA 58.753 50.000 0.00 0.00 0.00 2.74
2980 3104 0.606604 ATAACTGGCGTCCGTTCACT 59.393 50.000 0.00 0.00 0.00 3.41
2991 3115 0.600255 ATAGGACGCGCATAACTGGC 60.600 55.000 5.73 0.00 0.00 4.85
2993 3117 3.944422 AAAATAGGACGCGCATAACTG 57.056 42.857 5.73 0.00 0.00 3.16
2999 3123 3.327626 TGACTTAAAAATAGGACGCGCA 58.672 40.909 5.73 0.00 0.00 6.09
3002 3126 5.121768 TGCTCTTGACTTAAAAATAGGACGC 59.878 40.000 0.00 0.00 0.00 5.19
3009 3133 8.237811 TCCTTTTCTGCTCTTGACTTAAAAAT 57.762 30.769 0.00 0.00 0.00 1.82
3018 3142 4.130118 GACAACTCCTTTTCTGCTCTTGA 58.870 43.478 0.00 0.00 0.00 3.02
3026 3150 3.203716 GTCCGTTGACAACTCCTTTTCT 58.796 45.455 16.02 0.00 41.37 2.52
3028 3152 1.937899 CGTCCGTTGACAACTCCTTTT 59.062 47.619 16.02 0.00 41.85 2.27
3033 3157 0.666577 CCTCCGTCCGTTGACAACTC 60.667 60.000 16.02 5.99 41.85 3.01
3096 3220 4.538917 TCGTTTTACGCTTGGGAAAATTC 58.461 39.130 0.00 0.00 42.21 2.17
3103 3227 4.932268 TCTAAATCGTTTTACGCTTGGG 57.068 40.909 0.00 0.00 42.21 4.12
3111 3235 9.302345 CAGAGCTACTCATTCTAAATCGTTTTA 57.698 33.333 0.00 0.00 32.06 1.52
3112 3236 8.035394 TCAGAGCTACTCATTCTAAATCGTTTT 58.965 33.333 0.00 0.00 32.06 2.43
3136 3260 1.032657 GCCTCACCGTCTCTAGCTCA 61.033 60.000 0.00 0.00 0.00 4.26
3208 3332 4.867599 GTCATCGACCGGCCGTCC 62.868 72.222 26.12 14.20 38.36 4.79
3215 3339 1.158484 TCCTCTAGCGTCATCGACCG 61.158 60.000 0.00 0.00 39.71 4.79
3250 3374 2.377628 TAACGCTGCCCCGATCATCC 62.378 60.000 0.00 0.00 0.00 3.51
3267 3391 2.223845 GCGCTGTTTTCTACCGGTTTAA 59.776 45.455 15.04 4.52 0.00 1.52
3273 3397 2.736682 CCCGCGCTGTTTTCTACCG 61.737 63.158 5.56 0.00 0.00 4.02
3378 3513 7.725844 AGTTGATTTTTCTAACCACTGGATTCT 59.274 33.333 0.71 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.